Output for screening the Marshfield Set 12 (408 primers pairs)

http://research.marshfieldclinic.org/genetics/sets/combo.html

Note: results are best viewed in a Courier type font

Number of Hits = 1224

Number of Sequences = 816

Na+ = 0.085 Ct = 1.0

CATC015-F TAACCACCCATTCATCAACC versus GATA30E06-F TCTGTCTTAGATGGATGAATGG

Matches = 11

Score = 9

CCATTCATCNANC

est. tm = 11.5 oC

DeltaG @37 degrees = -3.74 kcal/mole

3'-GGTAAGTAGGTAGATTCTGTCT-5'

|||||||||x|x|

5'-TAACCACCCATTCATCAACC-3'

CATC015-F TAACCACCCATTCATCAACC versus GATA22F09N-F GTTCAAGCATGGGTGGATAG

Matches = 15

Score = 11

GTTNANGNATGGGTGGNTA

est. tm = 19.6 oC

DeltaG @37 degrees = -4.85 kcal/mole

5'-GTTCAAGCATGGGTGGATAG-3'

|||x|x|x||||||||x||

3'-CCAACTACTTACCCACCAAT-5'

CATC015-F TAACCACCCATTCATCAACC versus GATA178G09-F ATGGGTGGATGTACAAATGG

Matches = 9

Score = 7

ATGGGTGGNTN

est. tm = 19.8 oC

DeltaG @37 degrees = -6.21 kcal/mole

5'-ATGGGTGGATGTACAAATGG-3'

||||||||x|x

3'-CCAACTACTTACCCACCAAT-5'

CATC015-F TAACCACCCATTCATCAACC versus GATA118G10-F ACATACGGATGAATGGATGG

Matches = 12

Score = 7

CCANCCATTCATCNNNN

est. tm = 24.5 oC

DeltaG @37 degrees = -6.07 kcal/mole

3'-GGTAGGTAAGTAGGCATACA-5'

|||x|||||||||xxxx

5'-TAACCACCCATTCATCAACC-3'

CATC015-F TAACCACCCATTCATCAACC versus GATA43H01-R ACGTGGTACAGGTAGATAAATGG

Matches = 11

Score = 9

CCATTNATCNACC

est. tm = 13.5 oC

DeltaG @37 degrees = -4.25 kcal/mole

3'-GGTAAATAGATGGACATGGTGCA-5'

|||||x|||x|||

5'-TAACCACCCATTCATCAACC-3'

GATA185H04N-R ATATTTCAATATTGTAACCAGTCC versus GATA27E01-F TTTATTGAGATATATTTGACATGCA

Matches = 10

Score = 7

NNTATTGANATAT

est. tm = 0.3 oC

DeltaG @37 degrees = -1.71 kcal/mole

5'-TTTATTGAGATATATTTGACATGCA-3'

xx||||||x||||

3'-CCTGACCAATGTTATAACTTTATA-5'

ATA47D07-F TCGAGGCTGCAGTGAACTAT versus AATA036-R ACTGACTGCAGCCTTGACCT

Matches = 13

Score = 9

NNTNACTGCAGCCTNGA

est. tm = 33.4 oC

DeltaG @37 degrees = -8.43 kcal/mole

5'-ACTGACTGCAGCCTTGACCT-3'

xx|x||||||||||x||

3'-TATCAAGTGACGTCGGAGCT-5'

GATA129H04-F AGAGAACGGAACCAACAGAA versus GATA43C11-F TTCAAGTGGTTGGGTTCACT

Matches = 14

Score = 8

TTCNNNTGGTTNNGTTCNCT

est. tm = 12.7 oC

DeltaG @37 degrees = -3.07 kcal/mole

5'-TTCAAGTGGTTGGGTTCACT-3'

|||xxx|||||xx||||x||

3'-AAGACAACCAAGGCAAGAGA-5'

GATA129H04-F AGAGAACGGAACCAACAGAA versus GATA43C11-F TTCAAGTGGTTGGGTTCACT

Matches = 14

Score = 8

AGNGAACNNAACCANNNGAA

est. tm = 12.7 oC

DeltaG @37 degrees = -3.07 kcal/mole

3'-TCACTTGGGTTGGTGAACTT-5'

||x||||xx|||||xxx|||

5'-AGAGAACGGAACCAACAGAA-3'

GATA26G09N-F CTCCAGAGAAGCAGAACCAG versus PAH-F GCCAGAACAACTGCTGGTTC

Matches = 7

Score = 7

GAACCAG

est. tm = 8.5 oC

DeltaG @37 degrees = -4.45 kcal/mole

3'-CTTGGTCGTCAACAAGACCG-5'

|||||||

5'-CTCCAGAGAAGCAGAACCAG-3'

GATA109-F TAGGCAAATAATAAAATTCTAACCA versus ATA25E07-F TAATTTTAATTTTCTCCAAATCTCC

Matches = 13

Score = 7

NAATTTTANTNTTNNCCNA

est. tm = less than 0 oC

DeltaG @37 degrees = > 0 kcal/mole

5'-TAATTTTAATTTTCTCCAAATCTCC-3'

x|||||||x|x||xx||x|

3'-ACCAATCTTAAAATAATAAACGGAT-5'

GATA7C06-R TAGGATTTTACTATATTCCCCAGG versus GATA109-F TAGGCAAATAATAAAATTCTAACCA

Matches = 15

Score = 9

NNGGNANATANTAAAATNCTA

est. tm = 2.0 oC

DeltaG @37 degrees = -0.35 kcal/mole

5'-TAGGCAAATAATAAAATTCTAACCA-3'

xx||x|x|||x||||||x|||

3'-GGACCCCTTATATCATTTTAGGAT-5'

GATA61E03-R GGTATTTTTTGCCCACATGA versus GATA109-F TAGGCAAATAATAAAATTCTAACCA

Matches = 11

Score = 7

TNGGCAAANAATANN

est. tm = 10.1 oC

DeltaG @37 degrees = -3.58 kcal/mole

5'-TAGGCAAATAATAAAATTCTAACCA-3'

|x||||||x||||xx

3'-AGTACACCCGTTTTTTATGG-5'

GATA109-F TAGGCAAATAATAAAATTCTAACCA versus GATA121A08N-F GTTAACAGACTATTACCTGCCTACC

Matches = 16

Score = 9

GTTANNANNNTATTANNTGCCTA

est. tm = 14.1 oC

DeltaG @37 degrees = -2.27 kcal/mole

5'-GTTAACAGACTATTACCTGCCTACC-3'

||||xx|xxx|||||xx||||||

3'-ACCAATCTTAAAATAATAAACGGAT-5'

GATA169E06-R TGGAATTCAGTTATTTGTTAATGC versus GATA109-F TAGGCAAATAATAAAATTCTAACCA

Matches = 14

Score = 7

TNNNCAAATAANNNAATTCNA

est. tm = less than 0 oC

DeltaG @37 degrees = > 0 kcal/mole

5'-TAGGCAAATAATAAAATTCTAACCA-3'

|xxx|||||||xxx|||||x|

3'-CGTAATTGTTTATTGACTTAAGGT-5'

GATA124C08N-F TTCTAACAAGCTCCCAGGTG versus GATA5D08-R TATGACAGGCATCTGGGAGT

Matches = 9

Score = 7

NCTCCCAGNTG

est. tm = 17.4 oC

DeltaG @37 degrees = -5.60 kcal/mole

3'-TGAGGGTCTACGGACAGTAT-5'

x|||||||x||

5'-TTCTAACAAGCTCCCAGGTG-3'

GATA124C08N-F TTCTAACAAGCTCCCAGGTG versus GATA193A07-R AGCCTGTGGCATCTTGTTAG

Matches = 13

Score = 8

CTAACAAGNTNCCANNNG

est. tm = 8.8 oC

DeltaG @37 degrees = -2.40 kcal/mole

3'-GATTGTTCTACGGTGTCCGA-5'

||||||||x|x|||xxx|

5'-TTCTAACAAGCTCCCAGGTG-3'

GATA124C08N-F TTCTAACAAGCTCCCAGGTG versus GATA176C01-F TCTCACTACACCACCTGGGT

Matches = 8

Score = 7

NCCCAGGTG

est. tm = 25.8 oC

DeltaG @37 degrees = -7.24 kcal/mole

3'-TGGGTCCACCACATCACTCT-5'

x||||||||

5'-TTCTAACAAGCTCCCAGGTG-3'

GATA124C08N-F TTCTAACAAGCTCCCAGGTG versus ATA7D07-R ACGGGAGCTTTTGAGAAGTT

Matches = 13

Score = 9

NNGGGAGCTTNTNAGAA

est. tm = 27.8 oC

DeltaG @37 degrees = -7.00 kcal/mole

5'-ACGGGAGCTTTTGAGAAGTT-3'

xx||||||||x|x||||

3'-GTGGACCCTCGAACAATCTT-5'

ATA25E07-F TAATTTTAATTTTCTCCAAATCTCC versus ATA50C05-F TTTGGAAAGAATCTGTATTATCTTT

Matches = 14

Score = 8

TTTGGANANAATNNNNATTA

est. tm = 4.0 oC

DeltaG @37 degrees = -0.92 kcal/mole

5'-TTTGGAAAGAATCTGTATTATCTTT-3'

||||||x|x|||xxxx||||

3'-CCTCTAAACCTCTTTTAATTTTAAT-5'

ATA21F01-R ATGACCAAAATGAAAATCACTG versus ATA25E07-F TAATTTTAATTTTCTCCAAATCTCC

Matches = 13

Score = 7

TNATTTTNATTTTNNNCAN

est. tm = 1.8 oC

DeltaG @37 degrees = -0.92 kcal/mole

5'-TAATTTTAATTTTCTCCAAATCTCC-3'

|x|||||x|||||xxx||x

3'-GTCACTAAAAGTAAAACCAGTA-5'

GATA64G07-R AGACTTGGACTGAATTACACTGC versus ATA25E07-F TAATTTTAATTTTCTCCAAATCTCC

Matches = 15

Score = 7

NNANTNTAATTNNNTCCAANTCT

est. tm = 5.3 oC

DeltaG @37 degrees = -1.02 kcal/mole

5'-TAATTTTAATTTTCTCCAAATCTCC-3'

xx|x|x|||||xxx|||||x|||

3'-CGTCACATTAAGTCAGGTTCAGA-5'

AAAAC001-R CCTTTGGAGAAAACTGAACTCG versus ATA25E07-F TAATTTTAATTTTCTCCAAATCTCC

Matches = 15

Score = 8

NNANTTNANTTTTCTCCAAANN

est. tm = 21.0 oC

DeltaG @37 degrees = -4.70 kcal/mole

5'-TAATTTTAATTTTCTCCAAATCTCC-3'

xx|x||x|x|||||||||||xx

3'-GCTCAAGTCAAAAGAGGTTTCC-5'

ATA7D07-R ACGGGAGCTTTTGAGAAGTT versus ATA25E07-F TAATTTTAATTTTCTCCAAATCTCC

Matches = 13

Score = 9

GGAGNTTTNGAGAANNT

est. tm = 10.4 oC

DeltaG @37 degrees = -3.01 kcal/mole

3'-CCTCTAAACCTCTTTTAATTTTAAT-5'

||||x|||x|||||xx|

5'-ACGGGAGCTTTTGAGAAGTT-3'

ATA25E07-F TAATTTTAATTTTCTCCAAATCTCC versus GATA165B12-R TTAAAATCATTTTCACTGTGTATGC

Matches = 8

Score = 7

TTAAAATNA

est. tm = less than 0 oC

DeltaG @37 degrees = -0.54 kcal/mole

5'-TTAAAATCATTTTCACTGTGTATGC-3'

|||||||x|

3'-CCTCTAAACCTCTTTTAATTTTAAT-5'

GATA12A07N-F AGCACATAGCAGGCACTAGC versus ATA26B08-F ACTGGTATGTCCTAACCCCC

Matches = 10

Score = 7

NCTGNTATGTNCT

est. tm = 0.9 oC

DeltaG @37 degrees = -2.53 kcal/mole

5'-ACTGGTATGTCCTAACCCCC-3'

x|||x|||||x||

3'-CGATCACGGACGATACACGA-5'

GATA71C09-F GAGTTGCGTTACTTGATTTCTT versus GGAA5F09-F GCCATCAAGAAAACTAGTACTGC

Matches = 13

Score = 9

GCNNTACTNGNTTTCTT

est. tm = 10.1 oC

DeltaG @37 degrees = -2.83 kcal/mole

3'-CGTCATGATCAAAAGAACTACCG-5'

||xx||||x|x||||||

5'-GAGTTGCGTTACTTGATTTCTT-3'

TATC028-F CTGCATGACCTTGGGAAAAT versus ATT001-F GCCATGCAGGAAGGAGTAGA

Matches = 8

Score = 7

GNCATGCAG

est. tm = 6.3 oC

DeltaG @37 degrees = -3.90 kcal/mole

5'-GCCATGCAGGAAGGAGTAGA-3'

|x|||||||

3'-TAAAAGGGTTCCAGTACGTC-5'

TATC028-F CTGCATGACCTTGGGAAAAT versus GATA7C06-R TAGGATTTTACTATATTCCCCAGG

Matches = 10

Score = 8

CCTNGGGAANAT

est. tm = 6.9 oC

DeltaG @37 degrees = -3.80 kcal/mole

3'-GGACCCCTTATATCATTTTAGGAT-5'

|||x|||||x||

5'-CTGCATGACCTTGGGAAAAT-3'

GATA7C01-F TGCAGATCTTGGGACTTCTC versus GATA124F08-R GAGAAAGAAGCCCCAAGAAC

Matches = 13

Score = 10

GNTCTTGGGNCTTCTN

est. tm = 29.3 oC

DeltaG @37 degrees = -7.36 kcal/mole

3'-CAAGAACCCCGAAGAAAGAG-5'

|x|||||||x|||||x

5'-TGCAGATCTTGGGACTTCTC-3'

GATA7C01-F TGCAGATCTTGGGACTTCTC versus ATA26B08-R GATCTGCAGTTGGATTCTGG

Matches = 8

Score = 8

GATCTGCA

est. tm = 17.8 oC

DeltaG @37 degrees = -5.69 kcal/mole

5'-GATCTGCAGTTGGATTCTGG-3'

||||||||

3'-CTCTTCAGGGTTCTAGACGT-5'

GATA7C01-F TGCAGATCTTGGGACTTCTC versus GATA14E09-R GTCATAATATCTGCCAATGATTG

Matches = 11

Score = 7

GTCNNAANATCTGCN

est. tm = 15.5 oC

DeltaG @37 degrees = -4.56 kcal/mole

5'-GTCATAATATCTGCCAATGATTG-3'

|||xx||x||||||x

3'-CTCTTCAGGGTTCTAGACGT-5'

GATA124F08-F TATCTAGCTGGCTGGCTAGC versus GGAA22G10N-F AGTCAGCTTGATTGATCCAG

Matches = 10

Score = 7

AGNCAGCTNGATN

est. tm = 10.2 oC

DeltaG @37 degrees = -4.25 kcal/mole

5'-AGTCAGCTTGATTGATCCAG-3'

||x|||||x|||x

3'-CGATCGGTCGGTCGATCTAT-5'

GATA124F08-F TATCTAGCTGGCTGGCTAGC versus GATA27C08N-F GGCAGGCAGGTAGATAGACA

Matches = 13

Score = 10

GNCAGNCAGNTAGATA

est. tm = 7.8 oC

DeltaG @37 degrees = -2.46 kcal/mole

5'-GGCAGGCAGGTAGATAGACA-3'

|x|||x|||x||||||

3'-CGATCGGTCGGTCGATCTAT-5'

GATA11E02N-F TTGCCTTGTTAACATGTACAGG versus ATA29C07-F TTTCTCACCTTTAAATGTCATCA

Matches = 12

Score = 8

TGNTNACATNTANAGG

est. tm = less than zero

DeltaG @37 degrees = -0.85 kcal/mole

3'-ACTACTGTAAATTTCCACTCTTT-5'

||x|x||||x||x|||

5'-TTGCCTTGTTAACATGTACAGG-3'

GATA32F05-R AAGGTCAGAATCCCTCATCC versus ATA29C07-F TTTCTCACCTTTAAATGTCATCA

Matches = 9

Score = 7

NTTCTNACCTT

est. tm = 9.8 oC

DeltaG @37 degrees = -4.28 kcal/mole

5'-TTTCTCACCTTTAAATGTCATCA-3'

x||||x|||||

3'-CCTACTCCCTAAGACTGGAA-5'

GATA22D12-F TGCTATCAAATGACAAAGTTAGC versus GATA187D09N-F CTTAGTCTTTTCTTACCAAAACAGC

Matches = 13

Score = 8

CTTNGTCNTTTNNTANCA

est. tm = less than 0 oC

DeltaG @37 degrees = -0.09 kcal/mole

5'-CTTAGTCTTTTCTTACCAAAACAGC-3'

|||x|||x|||xx||x||

3'-CGATTGAAACAGTAAACTATCGT-5'

GATA72G09N-R TTGGTGATTTAATTCCAGGC versus GATA22D12-F TGCTATCAAATGACAAAGTTAGC

Matches = 12

Score = 7

TGNNATNAAATNACNAA

est. tm = less than 0 oC

DeltaG @37 degrees = > 0 kcal/mole

5'-TGCTATCAAATGACAAAGTTAGC-3'

||xx||x||||x||x||

3'-CGGACCTTAATTTAGTGGTT-5'

AAT243-F AATCGCTTGAACCCAGGAG versus TTTA049-F TCCATGCGATTTATCCAAGA

Matches = 9

Score = 7

TNCANGCGATT

est. tm = 0.4 oC

DeltaG @37 degrees = -3.11 kcal/mole

5'-TCCATGCGATTTATCCAAGA-3'

|x||x||||||

3'-GAGGACCCAAGTTCGCTAA-5'

GGAA20G10-F TGGAATCGTTTTACCTCTGC versus GATA168F06-F ACAATTCCAGAAACTTCCCC

Matches = 8

Score = 7

ACNATTCCA

est. tm = less than 0 oC

DeltaG @37 degrees = -2.95 kcal/mole

5'-ACAATTCCAGAAACTTCCCC-3'

||x||||||

3'-CGTCTCCATTTTGCTAAGGT-5'

GGAA20G10-F TGGAATCGTTTTACCTCTGC versus UT7136-F AGGAGGCAGAGGTTACAGTA

Matches = 11

Score = 7

TNNTNTNACCTCTGC

est. tm = 4.8 oC

DeltaG @37 degrees = -3.04 kcal/mole

3'-ATGACATTGGAGACGGAGGA-5'

|xx|x|x||||||||

5'-TGGAATCGTTTTACCTCTGC-3'

GATA8F07-F CAGAAGCGTGGCAGTTTATT versus GATA89A11-F GCTTCTGAAAGCTTCTAGTTTACC

Matches = 7

Score = 7

GCTTCTG

est. tm = 10.4 oC

DeltaG @37 degrees = -4.69 kcal/mole

5'-GCTTCTGAAAGCTTCTAGTTTACC-3'

|||||||

3'-TTATTTGACGGTGCGAAGAC-5'

ATA47C04N-F TCTCTCACACAAAAAAACCC versus GATA164B08N-R TGGGGTATCCTGTGTCAGAGC

Matches = 14

Score = 8

NCTCTNACACANNANANCCC

est. tm = 16.6 oC

DeltaG @37 degrees = -4.37 kcal/mole

3'-CGAGACTGTGTCCTATGGGGT-5'

x||||x|||||xx|x|x|||

5'-TCTCTCACACAAAAAAACCC-3'

ATA47C04N-F TCTCTCACACAAAAAAACCC versus AGAT113Z-R CGCTACCACGGGTGTTTTTA

Matches = 9

Score = 7

NAAAAANACCC

est. tm = 10.9 oC

DeltaG @37 degrees = -4.30 kcal/mole

3'-ATTTTTGTGGGCACCATCGC-5'

x|||||x||||

5'-TCTCTCACACAAAAAAACCC-3'

GATA66D01-F TAATTCAAATCTTTCCTGTCAGG versus GATA66D01-F TAATTCAAATCTTTCCTGTCAGG

Matches = 8

Score = 7

CCTGNCAGG

est. tm = 7.3 oC

DeltaG @37 degrees = -4.28 kcal/mole

3'-GGACTGTCCTTTCTAAACTTAAT-5'

||||x||||

5'-TAATTCAAATCTTTCCTGTCAGG-3'

ATT001-F GCCATGCAGGAAGGAGTAGA versus GATA66D01-F TAATTCAAATCTTTCCTGTCAGG

Matches = 13

Score = 7

CCNNNCAGGAANGANTNGA

est. tm = 1.5 oC

DeltaG @37 degrees = -1.62 kcal/mole

3'-GGACTGTCCTTTCTAAACTTAAT-5'

||xxx||||||x||x|x||

5'-GCCATGCAGGAAGGAGTAGA-3'

GATA66D01-F TAATTCAAATCTTTCCTGTCAGG versus GATA66D01-R TAATTCAAATCTTTCCTGTCAGG

Matches = 8

Score = 7

CCTGNCAGG

est. tm = 7.3 oC

DeltaG @37 degrees = -4.28 kcal/mole

3'-GGACTGTCCTTTCTAAACTTAAT-5'

||||x||||

5'-TAATTCAAATCTTTCCTGTCAGG-3'

GATA88G05-F ACATGTCGATCTCAGCGTTC versus ATGT006Z-F AAGGCTGAGGTAGGCTTATTTTT

Matches = 13

Score = 7

AANGCTGAGNTNGNCNTNT

est. tm = less than 0 oC

DeltaG @37 degrees = > 0 kcal/mole

5'-AAGGCTGAGGTAGGCTTATTTTT-3'

||x||||||x|x|x|x|x|

3'-CTTGCGACTCTAGCTGTACA-5'

GATA4E11-F TGAGCGGAATGAAAAGAGAG versus GATA31F01-F TTGGTACTTAATAAACCCTCTTTT

Matches = 8

Score = 7

AAAAGAGNG

est. tm = less than zero

DeltaG