Multiple sequence alignment - TraesCS3A01G177700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G177700 chr3A 100.000 7774 0 0 1 7774 201499056 201506829 0 14356
1 TraesCS3A01G177700 chr3D 96.205 7827 198 35 1 7774 167772504 167764724 0 12717
2 TraesCS3A01G177700 chr3B 96.105 5135 144 22 2681 7774 242874314 242869195 0 8323
3 TraesCS3A01G177700 chr3B 95.492 2285 68 12 1 2270 242878624 242876360 0 3616
4 TraesCS3A01G177700 chr3B 96.495 428 15 0 2267 2694 242876276 242875849 0 708


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G177700 chr3A 201499056 201506829 7773 False 14356.000000 14356 100.000000 1 7774 1 chr3A.!!$F1 7773
1 TraesCS3A01G177700 chr3D 167764724 167772504 7780 True 12717.000000 12717 96.205000 1 7774 1 chr3D.!!$R1 7773
2 TraesCS3A01G177700 chr3B 242869195 242878624 9429 True 4215.666667 8323 96.030667 1 7774 3 chr3B.!!$R1 7773

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
707 717 1.606668 TCTTCGCGGCATTCTTTTTGT 59.393 42.857 6.13 0.0 0.00 2.83 F
1898 1914 1.131303 TTCCCTCCCTCTTTCCGCAA 61.131 55.000 0.00 0.0 0.00 4.85 F
2661 2764 0.405198 TGCTTTCCAGATCAAGCCCA 59.595 50.000 11.70 0.0 44.15 5.36 F
4157 5812 3.030291 TGGGTTTTGCAACAAGAGTGAT 58.970 40.909 0.00 0.0 34.15 3.06 F
4566 6221 2.745515 AAGGAGTTAGAACAGACGGC 57.254 50.000 0.00 0.0 0.00 5.68 F
5400 7055 3.126858 GCAGTTAATCATTTCGCCACAGA 59.873 43.478 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2331 2434 1.227497 GGATTCAGGAGCTGGCTCG 60.227 63.158 15.15 4.2 43.59 5.03 R
2812 4463 4.568072 TGGCTCTGTTACACCATTATGT 57.432 40.909 0.00 0.0 36.56 2.29 R
4347 6002 3.181457 TGGCAGATCTAAATGAGCCTCAG 60.181 47.826 17.58 0.0 42.46 3.35 R
4968 6623 0.099436 GCTCGGTGTCCAATTCATGC 59.901 55.000 0.00 0.0 0.00 4.06 R
5432 7087 1.771073 TTTGTCTCGTTGGTGCTGCG 61.771 55.000 0.00 0.0 0.00 5.18 R
6828 8533 1.398390 CGGCAGTACATTTCCTGAAGC 59.602 52.381 0.00 0.0 0.00 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 117 4.509122 GCCCCATGGTTATGTTATCTCCAT 60.509 45.833 11.73 0.00 39.14 3.41
235 236 6.179756 ACAACCAGAACATACTTGCATATGA 58.820 36.000 13.09 0.00 36.27 2.15
252 253 6.028368 GCATATGATGATGTAGAATTGCAGC 58.972 40.000 6.97 0.00 0.00 5.25
297 298 4.021456 TGTCATCTTTGATAGTGACACGGT 60.021 41.667 0.00 0.00 44.14 4.83
414 421 7.011763 TCACTCTGCAAGAATAAGCAATGTATC 59.988 37.037 3.37 0.00 46.34 2.24
448 455 3.204306 TGCTTCATGATGATGGTCTCC 57.796 47.619 12.54 0.00 0.00 3.71
563 570 5.957774 ACAAGGATTTAAGCAATGTATGGGT 59.042 36.000 0.00 0.00 0.00 4.51
614 624 5.005740 TCTTGCACACTCTAAGCATTTGAT 58.994 37.500 0.00 0.00 38.19 2.57
638 648 3.733337 GGTATGGAAGTGCAGGTATGAG 58.267 50.000 0.00 0.00 0.00 2.90
661 671 6.349300 AGCTACCAATTTCTCGTTCATATGT 58.651 36.000 1.90 0.00 0.00 2.29
681 691 9.416794 CATATGTTCTATAGATGTGGTGTCTTC 57.583 37.037 2.58 0.00 0.00 2.87
690 700 6.966534 AGATGTGGTGTCTTCAAATTTCTT 57.033 33.333 0.00 0.00 0.00 2.52
694 704 3.226347 GGTGTCTTCAAATTTCTTCGCG 58.774 45.455 0.00 0.00 0.00 5.87
695 705 3.226347 GTGTCTTCAAATTTCTTCGCGG 58.774 45.455 6.13 0.00 0.00 6.46
705 715 3.363341 TTTCTTCGCGGCATTCTTTTT 57.637 38.095 6.13 0.00 0.00 1.94
707 717 1.606668 TCTTCGCGGCATTCTTTTTGT 59.393 42.857 6.13 0.00 0.00 2.83
717 727 5.619757 CGGCATTCTTTTTGTATGCTTCTCA 60.620 40.000 0.00 0.00 45.13 3.27
749 762 6.980397 ACTGCAAAATACTTGGTCAGAAAAAG 59.020 34.615 0.00 0.00 0.00 2.27
751 764 6.097554 TGCAAAATACTTGGTCAGAAAAAGGA 59.902 34.615 0.00 0.00 0.00 3.36
752 765 7.154656 GCAAAATACTTGGTCAGAAAAAGGAT 58.845 34.615 0.00 0.00 0.00 3.24
753 766 7.657354 GCAAAATACTTGGTCAGAAAAAGGATT 59.343 33.333 0.00 0.00 36.27 3.01
791 804 1.821753 CGAGAGGTCTTGGATGTCAGT 59.178 52.381 0.00 0.00 0.00 3.41
792 805 2.159310 CGAGAGGTCTTGGATGTCAGTC 60.159 54.545 0.00 0.00 0.00 3.51
793 806 2.828520 GAGAGGTCTTGGATGTCAGTCA 59.171 50.000 0.00 0.00 0.00 3.41
794 807 3.242867 AGAGGTCTTGGATGTCAGTCAA 58.757 45.455 0.00 0.00 0.00 3.18
842 855 4.819630 TGAAACCGTCTAGTTTGAATTGCT 59.180 37.500 0.00 0.00 40.01 3.91
994 1007 3.931907 TGGTGATAACTTGCTAGGCAT 57.068 42.857 0.00 0.00 38.76 4.40
1005 1018 4.141413 ACTTGCTAGGCATCATACATGGAA 60.141 41.667 0.00 0.00 38.76 3.53
1084 1097 2.120312 TCAACAAGTACCTCACACCCA 58.880 47.619 0.00 0.00 0.00 4.51
1158 1171 5.181748 CCACAGAAAGTAATGGAAGAGGAG 58.818 45.833 0.00 0.00 33.80 3.69
1209 1222 8.165239 ACACAGAATTAGACATTAAAGTTGCA 57.835 30.769 0.00 0.00 0.00 4.08
1233 1246 9.162764 GCAAAGATTCAAGGTATGTACTTCTAA 57.837 33.333 0.00 0.00 0.00 2.10
1400 1416 8.463607 TGAAAGGTAGAACTTTTGTCGAATTTT 58.536 29.630 0.00 0.00 40.55 1.82
1422 1438 7.404671 TTTCTACTCCCAGGAATTTAATTGC 57.595 36.000 0.81 0.81 0.00 3.56
1462 1478 5.122519 TCAAGAAAGAAAAATGGGTTTGCC 58.877 37.500 0.00 0.00 0.00 4.52
1663 1679 3.091545 CCCATGCTCAACACAAGGTATT 58.908 45.455 0.00 0.00 0.00 1.89
1664 1680 4.263727 ACCCATGCTCAACACAAGGTATTA 60.264 41.667 0.00 0.00 0.00 0.98
1665 1681 4.336433 CCCATGCTCAACACAAGGTATTAG 59.664 45.833 0.00 0.00 0.00 1.73
1666 1682 4.336433 CCATGCTCAACACAAGGTATTAGG 59.664 45.833 0.00 0.00 0.00 2.69
1667 1683 4.634012 TGCTCAACACAAGGTATTAGGT 57.366 40.909 0.00 0.00 0.00 3.08
1668 1684 5.748670 TGCTCAACACAAGGTATTAGGTA 57.251 39.130 0.00 0.00 0.00 3.08
1669 1685 6.308015 TGCTCAACACAAGGTATTAGGTAT 57.692 37.500 0.00 0.00 0.00 2.73
1726 1742 9.119418 TCTTGATTGTTTGAATTCAAGTCTACA 57.881 29.630 19.64 17.62 37.15 2.74
1764 1780 5.982356 TCTCCAGGTGATGTATTTTCTGAG 58.018 41.667 0.00 0.00 0.00 3.35
1898 1914 1.131303 TTCCCTCCCTCTTTCCGCAA 61.131 55.000 0.00 0.00 0.00 4.85
2174 2190 8.301720 GGTTAAAGAATGTTCCGAGGTAATTTT 58.698 33.333 0.00 0.00 0.00 1.82
2417 2520 2.623416 GGGTGCCTGTTGCCTAATTATC 59.377 50.000 0.00 0.00 40.16 1.75
2427 2530 8.352942 CCTGTTGCCTAATTATCTTAAATCCAC 58.647 37.037 0.00 0.00 0.00 4.02
2657 2760 3.314635 GGCACTATGCTTTCCAGATCAAG 59.685 47.826 0.13 0.00 44.28 3.02
2661 2764 0.405198 TGCTTTCCAGATCAAGCCCA 59.595 50.000 11.70 0.00 44.15 5.36
2691 2794 5.001232 TGTGTAGGTTCTTGGCTCAAATAC 58.999 41.667 0.00 0.00 0.00 1.89
2812 4463 6.502863 ACTTGTTTTGTTCCTATCCTACCCTA 59.497 38.462 0.00 0.00 0.00 3.53
3451 5105 3.384532 CCATGGTTGCACCTGGCC 61.385 66.667 2.57 0.00 43.89 5.36
3480 5134 3.368948 GGTCCTGAATCAGAAGTGGAGAC 60.369 52.174 12.53 8.25 32.44 3.36
3500 5154 4.288626 AGACCAAATGCTCACTAAACCCTA 59.711 41.667 0.00 0.00 0.00 3.53
3518 5172 6.368779 ACCCTACTATGCTTGTGTAAAGAA 57.631 37.500 0.00 0.00 0.00 2.52
3984 5639 3.498774 ACAGAGCCTCACTGAATGTTT 57.501 42.857 0.00 0.00 38.55 2.83
4157 5812 3.030291 TGGGTTTTGCAACAAGAGTGAT 58.970 40.909 0.00 0.00 34.15 3.06
4264 5919 6.161855 TGGTATTCATCATTTCTACGAGCT 57.838 37.500 0.00 0.00 0.00 4.09
4298 5953 3.529634 TTGCGTGGTTTAGTCAATTCG 57.470 42.857 0.00 0.00 0.00 3.34
4302 5957 3.185797 GCGTGGTTTAGTCAATTCGAAGT 59.814 43.478 3.35 0.00 0.00 3.01
4347 6002 5.294306 TGATAAAATGACAACTCAGCCGATC 59.706 40.000 0.00 0.00 0.00 3.69
4494 6149 8.932945 TTGATAACACTCTTGCTACAAGATAG 57.067 34.615 10.25 8.54 0.00 2.08
4566 6221 2.745515 AAGGAGTTAGAACAGACGGC 57.254 50.000 0.00 0.00 0.00 5.68
4819 6474 5.418840 CCAGCACAGGATAGGTTTAAACAAT 59.581 40.000 19.57 12.06 0.00 2.71
4968 6623 3.201290 GCAGTATCTCCATGACAAGTGG 58.799 50.000 0.00 0.00 38.11 4.00
5288 6943 3.686016 TCACCAATTAAGACTGAAGGGC 58.314 45.455 0.00 0.00 0.00 5.19
5356 7011 3.402681 CCCCCACCACTCGATGCT 61.403 66.667 0.00 0.00 0.00 3.79
5400 7055 3.126858 GCAGTTAATCATTTCGCCACAGA 59.873 43.478 0.00 0.00 0.00 3.41
5432 7087 4.440880 CAGTCCTCCATCAAGAGAACATC 58.559 47.826 0.00 0.00 35.82 3.06
5568 7223 7.099764 TCTGATCTCAATACAAGTCCTGAAAC 58.900 38.462 0.00 0.00 0.00 2.78
5671 7352 9.499479 GTGATATCTGGATCAGTTGATGTTATT 57.501 33.333 3.98 0.00 36.51 1.40
5748 7429 9.862371 AATTAGAGTATGCATATACAGCAGTAC 57.138 33.333 10.16 9.27 46.36 2.73
5795 7476 6.146673 GGCAAAAAGATCAAAATTCCAGTCAG 59.853 38.462 0.00 0.00 0.00 3.51
5846 7527 5.451908 ACAAACTTTGCTGTATTCACATCG 58.548 37.500 1.14 0.00 33.14 3.84
5882 7563 4.202111 ACAAACACCTGCAGATGGTTTAAC 60.202 41.667 9.23 0.00 35.28 2.01
5917 7598 3.006537 TGGTCTAGAACTGTTTTCTCCCG 59.993 47.826 9.68 0.00 0.00 5.14
5984 7665 0.035317 ACAGCGAAACCTGCAGATGA 59.965 50.000 17.39 0.00 36.29 2.92
5987 7668 2.543012 CAGCGAAACCTGCAGATGATAG 59.457 50.000 17.39 0.00 33.85 2.08
6106 7800 5.656859 ACTCATAGACCATGTGTAACTGCTA 59.343 40.000 0.00 0.00 39.10 3.49
6158 7862 3.045688 GCAAAGTTGTAAGCTTCACTGC 58.954 45.455 0.00 2.30 0.00 4.40
6168 7872 1.415659 AGCTTCACTGCTCACTGTTCT 59.584 47.619 0.00 0.00 39.34 3.01
6186 7890 9.155975 CACTGTTCTAACAAATAACTGAGCTAT 57.844 33.333 0.00 0.00 38.66 2.97
6356 8060 8.031277 GTGAATTCAGCAAAATCAAGTCCTAAT 58.969 33.333 8.80 0.00 0.00 1.73
6398 8102 6.183360 CGTTCCATGGAGGGAGTAGTTTATAA 60.183 42.308 15.53 0.00 38.42 0.98
6428 8132 6.057321 ACTAAGGAAACAACGATGGGATAA 57.943 37.500 0.00 0.00 0.00 1.75
6479 8183 3.690139 TGTTGTTGTCGCCTTAACAGAAA 59.310 39.130 0.00 0.00 37.98 2.52
6576 8280 9.999009 GTACTGTTTATTAATTTTAGTGGCCTC 57.001 33.333 3.32 0.00 0.00 4.70
6639 8344 6.267928 TCCCTCAGAGGCTATATGTTTACTTC 59.732 42.308 11.57 0.00 32.73 3.01
6686 8391 6.357367 ACTGAAAAGGTTCTTTCAAGCTCTA 58.643 36.000 0.00 0.00 43.03 2.43
6689 8394 6.260936 TGAAAAGGTTCTTTCAAGCTCTACAG 59.739 38.462 0.00 0.00 41.25 2.74
6768 8473 6.302615 CACGAGTTCTTTCAAAGCTTGATAG 58.697 40.000 0.00 5.03 39.84 2.08
6926 8631 3.953612 GGTTTGATGCCAGATGGATTGTA 59.046 43.478 2.18 0.00 37.39 2.41
7121 8827 5.235850 TGTCATAAGGCCAGAACAGTAAA 57.764 39.130 5.01 0.00 0.00 2.01
7182 8888 4.927049 AGACATGGGAAACAACTGATCAT 58.073 39.130 0.00 0.00 0.00 2.45
7388 9107 5.652994 ACTCTTCGAAGAATGCTCTTACT 57.347 39.130 26.87 0.00 45.90 2.24
7389 9108 6.031751 ACTCTTCGAAGAATGCTCTTACTT 57.968 37.500 26.87 0.00 45.90 2.24
7390 9109 7.159322 ACTCTTCGAAGAATGCTCTTACTTA 57.841 36.000 26.87 1.57 45.90 2.24
7391 9110 7.603651 ACTCTTCGAAGAATGCTCTTACTTAA 58.396 34.615 26.87 0.93 45.90 1.85
7392 9111 8.254508 ACTCTTCGAAGAATGCTCTTACTTAAT 58.745 33.333 26.87 0.00 45.90 1.40
7393 9112 8.412608 TCTTCGAAGAATGCTCTTACTTAATG 57.587 34.615 25.19 0.00 45.90 1.90
7394 9113 6.589830 TCGAAGAATGCTCTTACTTAATGC 57.410 37.500 0.00 0.00 42.19 3.56
7395 9114 6.341316 TCGAAGAATGCTCTTACTTAATGCT 58.659 36.000 0.00 0.00 42.19 3.79
7396 9115 6.477033 TCGAAGAATGCTCTTACTTAATGCTC 59.523 38.462 0.00 0.00 42.19 4.26
7397 9116 6.478344 CGAAGAATGCTCTTACTTAATGCTCT 59.522 38.462 0.00 0.00 42.19 4.09
7398 9117 7.010923 CGAAGAATGCTCTTACTTAATGCTCTT 59.989 37.037 0.00 0.00 42.19 2.85
7399 9118 9.319143 GAAGAATGCTCTTACTTAATGCTCTTA 57.681 33.333 0.00 0.00 42.19 2.10
7400 9119 8.655651 AGAATGCTCTTACTTAATGCTCTTAC 57.344 34.615 0.00 0.00 0.00 2.34
7522 9241 7.327275 CGTATCTTATGTAAGCAAGGATGAGAC 59.673 40.741 0.00 0.00 33.40 3.36
7627 9346 2.264005 TTGCCTTCCGAAGTTTGCTA 57.736 45.000 7.37 0.00 0.00 3.49
7714 9433 4.080695 TGAGGCTCAAGCTCAATTAGATGT 60.081 41.667 16.28 0.00 41.70 3.06
7750 9469 1.680860 CCAAGCTCAGCATCACCATGA 60.681 52.381 0.00 0.00 30.57 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.057245 GGAGCTCAAATCCAGTCAAAACC 60.057 47.826 17.19 0.00 36.79 3.27
116 117 3.267908 GTCAAGAGGACTCGGAGGA 57.732 57.895 10.23 0.00 43.46 3.71
235 236 3.630769 CAGTGGCTGCAATTCTACATCAT 59.369 43.478 0.50 0.00 0.00 2.45
252 253 0.958822 GCCCAACTACAAACCAGTGG 59.041 55.000 7.91 7.91 0.00 4.00
297 298 1.561542 GCTCTTTCCCTCCAAGGATCA 59.438 52.381 0.00 0.00 37.67 2.92
414 421 3.457610 TGAAGCAAGGCAAAAGAAAGG 57.542 42.857 0.00 0.00 0.00 3.11
448 455 7.980099 ACTACATTTCCTAGGTTAGATGAAACG 59.020 37.037 9.08 0.00 0.00 3.60
476 483 0.532573 TCTACTTCAGAGCCGCCAAG 59.467 55.000 0.00 0.00 0.00 3.61
614 624 1.078497 CCTGCACTTCCATACCGCA 60.078 57.895 0.00 0.00 0.00 5.69
638 648 6.604735 ACATATGAACGAGAAATTGGTAGC 57.395 37.500 10.38 0.00 0.00 3.58
647 657 9.899226 CACATCTATAGAACATATGAACGAGAA 57.101 33.333 10.38 0.00 0.00 2.87
661 671 9.739276 AAATTTGAAGACACCACATCTATAGAA 57.261 29.630 6.52 0.00 0.00 2.10
681 691 2.867429 AGAATGCCGCGAAGAAATTTG 58.133 42.857 8.23 0.00 0.00 2.32
690 700 2.730715 GCATACAAAAAGAATGCCGCGA 60.731 45.455 8.23 0.00 40.06 5.87
694 704 5.713025 TGAGAAGCATACAAAAAGAATGCC 58.287 37.500 3.08 0.00 45.66 4.40
695 705 6.865205 ACTTGAGAAGCATACAAAAAGAATGC 59.135 34.615 0.00 0.00 45.02 3.56
705 715 5.171476 GCAGTTAGACTTGAGAAGCATACA 58.829 41.667 0.00 0.00 0.00 2.29
707 717 5.405935 TGCAGTTAGACTTGAGAAGCATA 57.594 39.130 0.00 0.00 0.00 3.14
717 727 6.770785 TGACCAAGTATTTTGCAGTTAGACTT 59.229 34.615 0.00 0.00 0.00 3.01
772 785 2.828520 TGACTGACATCCAAGACCTCTC 59.171 50.000 0.00 0.00 0.00 3.20
778 791 5.012046 ACATGTAGTTGACTGACATCCAAGA 59.988 40.000 0.00 0.00 31.44 3.02
791 804 3.442625 CCGAGTCTACCACATGTAGTTGA 59.557 47.826 1.28 3.19 45.99 3.18
792 805 3.770666 CCGAGTCTACCACATGTAGTTG 58.229 50.000 1.28 0.46 45.99 3.16
793 806 2.165845 GCCGAGTCTACCACATGTAGTT 59.834 50.000 1.28 0.00 45.99 2.24
794 807 1.749634 GCCGAGTCTACCACATGTAGT 59.250 52.381 0.00 0.00 45.99 2.73
842 855 2.309528 ACGCTGTGTCAAAGTCAGAA 57.690 45.000 0.00 0.00 0.00 3.02
994 1007 2.171237 CTGACTGCCCTTCCATGTATGA 59.829 50.000 0.00 0.00 0.00 2.15
1005 1018 1.360393 TGGTTTTCCCTGACTGCCCT 61.360 55.000 0.00 0.00 39.73 5.19
1084 1097 3.074390 TGGGACACTGATTCAATCCAACT 59.926 43.478 11.43 0.00 0.00 3.16
1233 1246 4.401925 CTGGAGGTTTTGAGGTCAAGAAT 58.598 43.478 0.00 0.00 37.15 2.40
1400 1416 5.123227 CGCAATTAAATTCCTGGGAGTAGA 58.877 41.667 0.00 0.00 0.00 2.59
1422 1438 9.199982 TCTTTCTTGAAGTATACTAACCAAACG 57.800 33.333 5.65 1.77 36.70 3.60
1668 1684 9.425248 TGGCTCCTATTAAAAATCTGATGAAAT 57.575 29.630 0.00 0.00 0.00 2.17
1669 1685 8.821686 TGGCTCCTATTAAAAATCTGATGAAA 57.178 30.769 0.00 0.00 0.00 2.69
1764 1780 4.201822 GCTGATTTTATCACTGGTTCGACC 60.202 45.833 0.00 0.00 35.41 4.79
2023 2039 4.935205 CGATCAAACAGTACTTGAATCCCA 59.065 41.667 0.00 0.00 36.43 4.37
2174 2190 8.478877 GTCCATTCTCCTTCTATCAAGTTTAGA 58.521 37.037 0.00 0.00 0.00 2.10
2331 2434 1.227497 GGATTCAGGAGCTGGCTCG 60.227 63.158 15.15 4.20 43.59 5.03
2657 2760 2.192605 CCTACACAGGCATTTGGGC 58.807 57.895 0.00 0.00 43.80 5.36
2691 2794 9.739276 TCATATATTTACATGAGGCCCTTTTAG 57.261 33.333 0.00 0.00 0.00 1.85
2731 4382 7.707624 AACAATACCACATTGACATGAGATT 57.292 32.000 0.00 0.00 34.11 2.40
2812 4463 4.568072 TGGCTCTGTTACACCATTATGT 57.432 40.909 0.00 0.00 36.56 2.29
3007 4660 9.686683 TCTCTTTCTCTTCCCTAAATAAAATGG 57.313 33.333 0.00 0.00 0.00 3.16
3451 5105 5.180868 CACTTCTGATTCAGGACCTCTTTTG 59.819 44.000 13.59 0.00 31.51 2.44
3480 5134 4.589908 AGTAGGGTTTAGTGAGCATTTGG 58.410 43.478 0.00 0.00 0.00 3.28
3500 5154 8.850156 AGTCATTTTTCTTTACACAAGCATAGT 58.150 29.630 0.00 0.00 0.00 2.12
4065 5720 4.341806 ACAAGCATCAATGTTTTGGACTCA 59.658 37.500 11.41 0.00 33.44 3.41
4157 5812 8.571461 TTCTTCACTTTCTAGACGGATACTTA 57.429 34.615 0.00 0.00 0.00 2.24
4259 5914 4.611355 CGCAATATTTGACCCATAAGCTCG 60.611 45.833 0.00 0.00 0.00 5.03
4264 5919 4.274147 ACCACGCAATATTTGACCCATAA 58.726 39.130 0.00 0.00 0.00 1.90
4298 5953 7.581011 ATCGAAATGTTTTGGCATTAACTTC 57.419 32.000 12.38 8.68 38.03 3.01
4302 5957 9.645059 TTATCAATCGAAATGTTTTGGCATTAA 57.355 25.926 0.00 0.00 38.03 1.40
4347 6002 3.181457 TGGCAGATCTAAATGAGCCTCAG 60.181 47.826 17.58 0.00 42.46 3.35
4566 6221 6.863126 GTCACATTCTTGTTCCAAATTACTGG 59.137 38.462 0.00 0.00 33.85 4.00
4819 6474 8.096621 TCATCCTGTTAATACTGGGAACATTA 57.903 34.615 0.00 0.00 42.09 1.90
4968 6623 0.099436 GCTCGGTGTCCAATTCATGC 59.901 55.000 0.00 0.00 0.00 4.06
5280 6935 2.586648 ACAACCTTTAGGCCCTTCAG 57.413 50.000 0.00 0.00 39.32 3.02
5288 6943 3.568007 TGTGCTTGCTTACAACCTTTAGG 59.432 43.478 0.00 0.00 42.17 2.69
5356 7011 4.504340 GCCTTGGGTCGCTTTATATCCTTA 60.504 45.833 0.00 0.00 0.00 2.69
5400 7055 5.378230 TGATGGAGGACTGCATAATTCTT 57.622 39.130 6.30 0.00 41.80 2.52
5432 7087 1.771073 TTTGTCTCGTTGGTGCTGCG 61.771 55.000 0.00 0.00 0.00 5.18
5577 7232 2.420687 CCTATGCTGTGTTCCTCTTCCC 60.421 54.545 0.00 0.00 0.00 3.97
5611 7266 2.613691 CCAAAGCACATTCTCCAATGC 58.386 47.619 0.00 0.00 43.03 3.56
5748 7429 8.600449 TGCCCACTTTTGTTTTCTAAATAATG 57.400 30.769 0.00 0.00 0.00 1.90
5846 7527 5.858581 GCAGGTGTTTGTAATCACTTGAATC 59.141 40.000 17.02 2.21 41.81 2.52
5882 7563 9.436957 ACAGTTCTAGACCACACATAATTTAAG 57.563 33.333 0.00 0.00 0.00 1.85
5917 7598 4.022849 GCTAAATGAAGATGGTGGGTATGC 60.023 45.833 0.00 0.00 0.00 3.14
6023 7704 2.014064 TTTTGCCTTTGCTGCGCTCA 62.014 50.000 9.73 3.52 38.71 4.26
6158 7862 7.386299 AGCTCAGTTATTTGTTAGAACAGTGAG 59.614 37.037 0.00 8.89 40.50 3.51
6186 7890 2.311841 TCACTCTGGGATGGTGACTCTA 59.688 50.000 0.00 0.00 35.44 2.43
6254 7958 7.548196 AAGTCTCGTGTTAGTTTGAATTTCA 57.452 32.000 0.00 0.00 0.00 2.69
6356 8060 4.106825 TGGAACGGAGGGAGTATTATCCTA 59.893 45.833 0.00 0.00 39.50 2.94
6398 8102 8.899771 CCCATCGTTGTTTCCTTAGTTATTATT 58.100 33.333 0.00 0.00 0.00 1.40
6576 8280 4.843220 AGAAGTGCAGAAGTGGAAATTG 57.157 40.909 0.00 0.00 0.00 2.32
6639 8344 7.904461 CAGTTTTCCTGTGCAAAACAATAAAAG 59.096 33.333 12.22 0.00 43.40 2.27
6670 8375 4.632153 TGTCTGTAGAGCTTGAAAGAACC 58.368 43.478 0.00 0.00 0.00 3.62
6768 8473 7.169035 TGACGACATTACAGTTACTTCAAAC 57.831 36.000 0.00 0.00 0.00 2.93
6828 8533 1.398390 CGGCAGTACATTTCCTGAAGC 59.602 52.381 0.00 0.00 0.00 3.86
6953 8659 8.902540 TCATAGTTTGTTCACTCATACACTTT 57.097 30.769 0.00 0.00 0.00 2.66
7097 8803 6.553953 TTACTGTTCTGGCCTTATGACATA 57.446 37.500 3.32 0.00 0.00 2.29
7162 8868 7.537596 TTAAATGATCAGTTGTTTCCCATGT 57.462 32.000 18.22 0.00 0.00 3.21
7182 8888 3.137728 GGAGCCCCTTACCTGCTATTAAA 59.862 47.826 0.00 0.00 34.99 1.52
7388 9107 4.713321 AGGGTAAGACCGTAAGAGCATTAA 59.287 41.667 0.00 0.00 39.83 1.40
7389 9108 4.284178 AGGGTAAGACCGTAAGAGCATTA 58.716 43.478 0.00 0.00 39.83 1.90
7390 9109 3.105283 AGGGTAAGACCGTAAGAGCATT 58.895 45.455 0.00 0.00 39.83 3.56
7391 9110 2.748388 AGGGTAAGACCGTAAGAGCAT 58.252 47.619 0.00 0.00 39.83 3.79
7392 9111 2.226962 AGGGTAAGACCGTAAGAGCA 57.773 50.000 0.00 0.00 39.83 4.26
7393 9112 2.759535 AGAAGGGTAAGACCGTAAGAGC 59.240 50.000 0.00 0.00 39.83 4.09
7394 9113 4.461781 TGAAGAAGGGTAAGACCGTAAGAG 59.538 45.833 0.00 0.00 39.83 2.85
7395 9114 4.410099 TGAAGAAGGGTAAGACCGTAAGA 58.590 43.478 0.00 0.00 39.83 2.10
7396 9115 4.796038 TGAAGAAGGGTAAGACCGTAAG 57.204 45.455 0.00 0.00 39.83 2.34
7397 9116 5.750352 ATTGAAGAAGGGTAAGACCGTAA 57.250 39.130 0.00 0.00 39.83 3.18
7398 9117 6.608405 TGATATTGAAGAAGGGTAAGACCGTA 59.392 38.462 0.00 0.00 39.83 4.02
7399 9118 5.424252 TGATATTGAAGAAGGGTAAGACCGT 59.576 40.000 0.00 0.00 39.83 4.83
7400 9119 5.914033 TGATATTGAAGAAGGGTAAGACCG 58.086 41.667 0.00 0.00 39.83 4.79
7442 9161 1.745232 TCCATTGGTTATGTCGCCAC 58.255 50.000 1.86 0.00 34.02 5.01
7443 9162 2.727123 ATCCATTGGTTATGTCGCCA 57.273 45.000 1.86 0.00 31.99 5.69
7522 9241 2.568956 TGAGTTCACTTCCAGAGATGGG 59.431 50.000 0.00 0.00 0.00 4.00
7627 9346 1.912043 CAGGAGAGGTGGGATGAAGTT 59.088 52.381 0.00 0.00 0.00 2.66
7750 9469 2.047465 CTTGCTGCTGCTCGGACT 60.047 61.111 17.00 0.00 40.48 3.85


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.