Multiple sequence alignment - TraesCS2A01G477500

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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 TraesCS2A01G477500 chr2A 100.000 3933 0 0 1 3933 716498190 716502122 0.000000e+00 7263
1 TraesCS2A01G477500 chr2B 89.719 2743 195 32 1174 3846 695888989 695891714 0.000000e+00 3422
2 TraesCS2A01G477500 chr2B 86.149 657 82 7 3 656 695865903 695866553 0.000000e+00 701
3 TraesCS2A01G477500 chr2B 82.075 318 32 11 748 1065 695886773 695887065 8.440000e-62 248
4 TraesCS2A01G477500 chr2D 91.176 2482 155 22 1124 3603 578962884 578965303 0.000000e+00 3312
5 TraesCS2A01G477500 chr2D 82.389 653 88 9 3 654 578944195 578944821 9.610000e-151 544
6 TraesCS2A01G477500 chr2D 92.749 331 19 2 3604 3933 578965333 578965659 1.280000e-129 473
7 TraesCS2A01G477500 chr2D 87.376 404 39 9 671 1065 578962087 578962487 1.670000e-123 453
8 TraesCS2A01G477500 chr3A 80.727 1925 331 24 1348 3249 589792452 589794359 0.000000e+00 1463
9 TraesCS2A01G477500 chr3A 76.574 683 150 7 1348 2028 589606326 589607000 2.230000e-97 366
10 TraesCS2A01G477500 chr3D 80.899 1890 321 26 1383 3249 448427986 448429858 0.000000e+00 1454
11 TraesCS2A01G477500 chr3B 80.897 1895 312 32 1383 3249 588471030 588472902 0.000000e+00 1448
12 TraesCS2A01G477500 chr3B 78.996 1395 254 24 1862 3231 588420650 588422030 0.000000e+00 917
13 TraesCS2A01G477500 chr3B 82.151 465 69 11 1383 1843 588420210 588420664 1.710000e-103 387


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 TraesCS2A01G477500 chr2A 716498190 716502122 3932 False 7263.000000 7263 100.000000 1 3933 1 chr2A.!!$F1 3932
1 TraesCS2A01G477500 chr2B 695886773 695891714 4941 False 1835.000000 3422 85.897000 748 3846 2 chr2B.!!$F2 3098
2 TraesCS2A01G477500 chr2B 695865903 695866553 650 False 701.000000 701 86.149000 3 656 1 chr2B.!!$F1 653
3 TraesCS2A01G477500 chr2D 578962087 578965659 3572 False 1412.666667 3312 90.433667 671 3933 3 chr2D.!!$F2 3262
4 TraesCS2A01G477500 chr2D 578944195 578944821 626 False 544.000000 544 82.389000 3 654 1 chr2D.!!$F1 651
5 TraesCS2A01G477500 chr3A 589792452 589794359 1907 False 1463.000000 1463 80.727000 1348 3249 1 chr3A.!!$F2 1901
6 TraesCS2A01G477500 chr3A 589606326 589607000 674 False 366.000000 366 76.574000 1348 2028 1 chr3A.!!$F1 680
7 TraesCS2A01G477500 chr3D 448427986 448429858 1872 False 1454.000000 1454 80.899000 1383 3249 1 chr3D.!!$F1 1866
8 TraesCS2A01G477500 chr3B 588471030 588472902 1872 False 1448.000000 1448 80.897000 1383 3249 1 chr3B.!!$F1 1866
9 TraesCS2A01G477500 chr3B 588420210 588422030 1820 False 652.000000 917 80.573500 1383 3231 2 chr3B.!!$F2 1848

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
58 59 0.105039 CTGATAAGTGGACGGGCTCC 59.895 60.0 0.00 0.0 39.97 4.70 F
128 129 0.107848 CGGGTCGATTAAAGCACCCT 60.108 55.0 14.21 0.0 45.79 4.34 F
224 225 0.179032 ACAACACCAAGTCGGCATCA 60.179 50.0 0.00 0.0 39.03 3.07 F
235 236 0.250684 TCGGCATCAAAGTTCCAGCA 60.251 50.0 0.00 0.0 0.00 4.41 F
479 484 0.256464 ACCGTTGTGGGGAGTGAAAA 59.744 50.0 0.00 0.0 44.64 2.29 F
1082 1096 0.608035 TGGGCATCGAAACACCCTTC 60.608 55.0 14.28 0.0 43.25 3.46 F
2521 4373 0.036952 GAGAGCACCTACAAGCTGCA 60.037 55.0 1.02 0.0 42.04 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1297 3133 0.833287 CGGAGGTGGAAGATGGTCAT 59.167 55.000 0.00 0.0 0.00 3.06 R
1959 3802 0.890996 AAAACCTGCCGAGCAAGAGG 60.891 55.000 2.11 0.0 38.41 3.69 R
2036 3879 0.950555 TGAGACCATTCTGTGCGTGC 60.951 55.000 0.00 0.0 29.47 5.34 R
2202 4054 1.781153 TTTCCACGAAACCCCGGGAT 61.781 55.000 26.32 0.0 34.30 3.85 R
2409 4261 1.137282 TGCGACATTATCTGGCCGTAA 59.863 47.619 0.00 0.0 0.00 3.18 R
2801 4653 1.022735 GCCCAAGCTCTGTCATCATG 58.977 55.000 0.00 0.0 35.50 3.07 R
3858 5806 0.037590 TGTATCAACAGCCCACACCC 59.962 55.000 0.00 0.0 0.00 4.61 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
33 34 0.530870 TCGTGCGAACATGTGTTGGA 60.531 50.000 11.35 0.00 38.56 3.53
43 44 2.573462 ACATGTGTTGGACTAGGCTGAT 59.427 45.455 0.00 0.00 0.00 2.90
51 52 3.031736 TGGACTAGGCTGATAAGTGGAC 58.968 50.000 0.00 0.00 0.00 4.02
57 58 0.530870 GCTGATAAGTGGACGGGCTC 60.531 60.000 0.00 0.00 0.00 4.70
58 59 0.105039 CTGATAAGTGGACGGGCTCC 59.895 60.000 0.00 0.00 39.97 4.70
82 83 7.068348 TCCGCATTGAGACTAGTAGTAGAAAAT 59.932 37.037 11.68 0.00 0.00 1.82
105 106 2.956799 TTTGCAGCGCTGGAGTGGAA 62.957 55.000 36.47 22.87 31.08 3.53
109 110 1.004440 AGCGCTGGAGTGGAAGTTC 60.004 57.895 10.39 0.00 0.00 3.01
111 112 1.738099 CGCTGGAGTGGAAGTTCGG 60.738 63.158 0.00 0.00 0.00 4.30
113 114 2.058675 CTGGAGTGGAAGTTCGGGT 58.941 57.895 0.00 0.00 0.00 5.28
115 116 1.080025 GGAGTGGAAGTTCGGGTCG 60.080 63.158 0.00 0.00 0.00 4.79
124 125 2.754946 AGTTCGGGTCGATTAAAGCA 57.245 45.000 0.00 0.00 35.23 3.91
128 129 0.107848 CGGGTCGATTAAAGCACCCT 60.108 55.000 14.21 0.00 45.79 4.34
134 135 4.004982 GTCGATTAAAGCACCCTTGGTAA 58.995 43.478 0.00 0.00 32.11 2.85
143 144 2.099405 CACCCTTGGTAAATTCGCCAT 58.901 47.619 2.32 0.00 32.11 4.40
158 159 1.202222 CGCCATTGATCTCAACCAAGC 60.202 52.381 0.00 0.00 38.86 4.01
162 163 2.254546 TTGATCTCAACCAAGCACGT 57.745 45.000 0.00 0.00 0.00 4.49
169 170 2.805671 CTCAACCAAGCACGTATTGTCA 59.194 45.455 10.70 0.00 0.00 3.58
175 176 2.543777 AGCACGTATTGTCAACCTGT 57.456 45.000 0.00 0.00 0.00 4.00
177 178 4.202245 AGCACGTATTGTCAACCTGTAT 57.798 40.909 0.00 0.00 0.00 2.29
182 183 6.479001 GCACGTATTGTCAACCTGTATAAGAT 59.521 38.462 0.00 0.00 0.00 2.40
185 186 8.038944 ACGTATTGTCAACCTGTATAAGATGTT 58.961 33.333 0.00 0.00 0.00 2.71
210 211 2.571212 GTTGGACATGGAGTGACAACA 58.429 47.619 0.00 0.00 42.77 3.33
224 225 0.179032 ACAACACCAAGTCGGCATCA 60.179 50.000 0.00 0.00 39.03 3.07
235 236 0.250684 TCGGCATCAAAGTTCCAGCA 60.251 50.000 0.00 0.00 0.00 4.41
239 240 0.890683 CATCAAAGTTCCAGCACCCC 59.109 55.000 0.00 0.00 0.00 4.95
242 243 0.758685 CAAAGTTCCAGCACCCCCAA 60.759 55.000 0.00 0.00 0.00 4.12
270 271 2.041115 GCTCTCGCCAAGTTTCCCC 61.041 63.158 0.00 0.00 0.00 4.81
274 275 2.983592 CGCCAAGTTTCCCCGCTT 60.984 61.111 0.00 0.00 0.00 4.68
281 282 1.192428 AGTTTCCCCGCTTCTCGTAT 58.808 50.000 0.00 0.00 36.19 3.06
309 310 1.403687 CCCCTCTTCCCTTCTAGCCG 61.404 65.000 0.00 0.00 0.00 5.52
317 318 1.224592 CCTTCTAGCCGCCCACAAT 59.775 57.895 0.00 0.00 0.00 2.71
330 331 1.283029 CCCACAATCTCCACCATCACT 59.717 52.381 0.00 0.00 0.00 3.41
334 335 2.274437 CAATCTCCACCATCACTGTCG 58.726 52.381 0.00 0.00 0.00 4.35
338 339 0.891904 TCCACCATCACTGTCGACGA 60.892 55.000 11.62 2.29 0.00 4.20
355 358 1.931172 ACGAACTTGGTGTTGTTCTCG 59.069 47.619 0.00 0.00 40.04 4.04
372 375 4.515028 TCTCGAAGGAGGATAACCACTA 57.485 45.455 0.00 0.00 40.85 2.74
402 405 1.377690 TACCAGCCATTTGGGGAGAA 58.622 50.000 0.00 0.00 42.76 2.87
413 416 6.372931 CCATTTGGGGAGAAACATAAGGATA 58.627 40.000 0.00 0.00 0.00 2.59
436 439 1.864711 CGCAAGGATTACCGTATGTGG 59.135 52.381 0.00 0.00 41.83 4.17
438 441 2.745152 GCAAGGATTACCGTATGTGGCT 60.745 50.000 0.00 0.00 41.83 4.75
455 458 2.298729 TGGCTCCAAATGGTTAGCAAAC 59.701 45.455 13.31 0.19 36.93 2.93
467 472 4.338682 TGGTTAGCAAACATTTACCGTTGT 59.661 37.500 0.00 0.00 37.34 3.32
479 484 0.256464 ACCGTTGTGGGGAGTGAAAA 59.744 50.000 0.00 0.00 44.64 2.29
499 504 1.586564 GATCTCGTCGTCGCCCTTG 60.587 63.158 0.00 0.00 36.96 3.61
503 508 3.110178 CGTCGTCGCCCTTGGAAC 61.110 66.667 0.00 0.00 0.00 3.62
505 510 2.027625 GTCGTCGCCCTTGGAACTG 61.028 63.158 0.00 0.00 0.00 3.16
509 514 0.670854 GTCGCCCTTGGAACTGAGTC 60.671 60.000 0.00 0.00 0.00 3.36
510 515 1.738099 CGCCCTTGGAACTGAGTCG 60.738 63.158 0.00 0.00 0.00 4.18
514 519 0.951040 CCTTGGAACTGAGTCGCCAC 60.951 60.000 6.64 0.00 0.00 5.01
522 527 1.880027 ACTGAGTCGCCACCAAAATTC 59.120 47.619 0.00 0.00 0.00 2.17
537 542 0.687354 AATTCAGTCACCCTCGCTGT 59.313 50.000 0.00 0.00 0.00 4.40
544 549 1.197721 GTCACCCTCGCTGTCAAAATG 59.802 52.381 0.00 0.00 0.00 2.32
547 552 1.004745 ACCCTCGCTGTCAAAATGGAT 59.995 47.619 0.00 0.00 0.00 3.41
599 604 0.956633 GTGGGACATCCGCGTAGATA 59.043 55.000 4.92 0.00 44.52 1.98
644 650 2.115427 TCGAGCATGACCTTGGGAATA 58.885 47.619 0.00 0.00 0.00 1.75
656 662 3.371917 CCTTGGGAATAGAGTTGCCATCA 60.372 47.826 1.84 0.00 39.66 3.07
657 663 4.272489 CTTGGGAATAGAGTTGCCATCAA 58.728 43.478 1.84 0.00 39.66 2.57
658 664 4.314522 TGGGAATAGAGTTGCCATCAAA 57.685 40.909 0.00 0.00 34.89 2.69
659 665 4.016444 TGGGAATAGAGTTGCCATCAAAC 58.984 43.478 0.00 0.00 34.89 2.93
660 666 4.016444 GGGAATAGAGTTGCCATCAAACA 58.984 43.478 0.00 0.00 33.37 2.83
661 667 4.646492 GGGAATAGAGTTGCCATCAAACAT 59.354 41.667 0.00 0.00 33.37 2.71
662 668 5.127682 GGGAATAGAGTTGCCATCAAACATT 59.872 40.000 0.00 0.00 33.37 2.71
663 669 6.321181 GGGAATAGAGTTGCCATCAAACATTA 59.679 38.462 0.00 0.00 33.37 1.90
664 670 7.014615 GGGAATAGAGTTGCCATCAAACATTAT 59.985 37.037 0.00 0.00 33.37 1.28
665 671 7.864379 GGAATAGAGTTGCCATCAAACATTATG 59.136 37.037 0.00 0.00 33.37 1.90
666 672 8.523915 AATAGAGTTGCCATCAAACATTATGA 57.476 30.769 0.00 0.00 33.37 2.15
667 673 6.199937 AGAGTTGCCATCAAACATTATGAC 57.800 37.500 0.00 0.00 33.37 3.06
668 674 5.711506 AGAGTTGCCATCAAACATTATGACA 59.288 36.000 0.00 0.00 33.37 3.58
669 675 6.209192 AGAGTTGCCATCAAACATTATGACAA 59.791 34.615 0.00 0.00 33.37 3.18
670 676 6.938507 AGTTGCCATCAAACATTATGACAAT 58.061 32.000 0.00 0.00 29.97 2.71
671 677 7.388437 AGTTGCCATCAAACATTATGACAATT 58.612 30.769 0.00 0.00 29.97 2.32
672 678 7.546667 AGTTGCCATCAAACATTATGACAATTC 59.453 33.333 0.00 0.00 29.97 2.17
673 679 6.035217 TGCCATCAAACATTATGACAATTCG 58.965 36.000 0.00 0.00 0.00 3.34
674 680 5.459762 GCCATCAAACATTATGACAATTCGG 59.540 40.000 0.00 0.00 0.00 4.30
675 681 6.680131 GCCATCAAACATTATGACAATTCGGA 60.680 38.462 0.00 0.00 0.00 4.55
676 682 7.257003 CCATCAAACATTATGACAATTCGGAA 58.743 34.615 0.00 0.00 0.00 4.30
677 683 7.433131 CCATCAAACATTATGACAATTCGGAAG 59.567 37.037 0.00 0.00 0.00 3.46
678 684 6.321717 TCAAACATTATGACAATTCGGAAGC 58.678 36.000 0.00 0.00 0.00 3.86
679 685 4.900635 ACATTATGACAATTCGGAAGCC 57.099 40.909 0.00 0.00 0.00 4.35
680 686 4.526970 ACATTATGACAATTCGGAAGCCT 58.473 39.130 0.00 0.00 0.00 4.58
681 687 4.576463 ACATTATGACAATTCGGAAGCCTC 59.424 41.667 0.00 0.00 0.00 4.70
682 688 4.487714 TTATGACAATTCGGAAGCCTCT 57.512 40.909 0.00 0.00 0.00 3.69
683 689 2.099141 TGACAATTCGGAAGCCTCTG 57.901 50.000 0.00 0.00 0.00 3.35
688 694 3.134458 CAATTCGGAAGCCTCTGTATCC 58.866 50.000 0.00 0.00 0.00 2.59
698 704 3.056250 AGCCTCTGTATCCATATGAAGCG 60.056 47.826 3.65 0.00 0.00 4.68
724 730 6.292919 CGCTCCATATGCATTATGATCATCAG 60.293 42.308 12.53 4.58 40.22 2.90
726 732 6.419791 TCCATATGCATTATGATCATCAGCA 58.580 36.000 23.37 23.37 40.22 4.41
734 740 8.392612 TGCATTATGATCATCAGCAATATAACG 58.607 33.333 20.64 0.41 0.00 3.18
755 762 3.362237 CGAGTCGTTGAAGTTGCTCTAAG 59.638 47.826 3.82 0.00 0.00 2.18
761 768 5.047590 TCGTTGAAGTTGCTCTAAGATGGTA 60.048 40.000 0.00 0.00 0.00 3.25
762 769 5.812642 CGTTGAAGTTGCTCTAAGATGGTAT 59.187 40.000 0.00 0.00 0.00 2.73
800 807 6.409704 TCTTGATCCCTACAAAACTCATCTG 58.590 40.000 0.00 0.00 0.00 2.90
840 847 9.444600 TCTAGAAACAACTTGTGAGTAAAAAGT 57.555 29.630 0.00 0.00 34.21 2.66
905 912 2.865551 GCATTGGTTGAGTGTGTTTTGG 59.134 45.455 0.00 0.00 0.00 3.28
906 913 3.430098 GCATTGGTTGAGTGTGTTTTGGA 60.430 43.478 0.00 0.00 0.00 3.53
907 914 4.740334 GCATTGGTTGAGTGTGTTTTGGAT 60.740 41.667 0.00 0.00 0.00 3.41
963 976 8.691661 ACTCAAATGTTGTAAGGTTTGACTAT 57.308 30.769 0.00 0.00 36.11 2.12
964 977 9.787435 ACTCAAATGTTGTAAGGTTTGACTATA 57.213 29.630 0.00 0.00 36.11 1.31
971 984 9.787435 TGTTGTAAGGTTTGACTATAAGTTCAT 57.213 29.630 0.00 0.00 0.00 2.57
1020 1033 4.718276 AGCAAATTAAGGGCATCTCCAAAT 59.282 37.500 0.00 0.00 36.21 2.32
1026 1039 7.919385 ATTAAGGGCATCTCCAAATTTGTAT 57.081 32.000 16.73 4.99 36.21 2.29
1037 1050 7.461749 TCTCCAAATTTGTATCTCAAACCTCT 58.538 34.615 16.73 0.00 46.77 3.69
1045 1058 1.497991 TCTCAAACCTCTCGCAAACG 58.502 50.000 0.00 0.00 42.01 3.60
1048 1061 1.595794 TCAAACCTCTCGCAAACGTTC 59.404 47.619 0.00 0.00 41.18 3.95
1065 1079 3.070159 ACGTTCAGATCATATGGTCCTGG 59.930 47.826 12.50 3.21 0.00 4.45
1066 1080 3.555795 CGTTCAGATCATATGGTCCTGGG 60.556 52.174 12.50 0.77 0.00 4.45
1067 1081 1.980765 TCAGATCATATGGTCCTGGGC 59.019 52.381 12.50 0.00 0.00 5.36
1068 1082 1.701292 CAGATCATATGGTCCTGGGCA 59.299 52.381 12.50 0.00 0.00 5.36
1069 1083 2.307980 CAGATCATATGGTCCTGGGCAT 59.692 50.000 12.50 0.00 0.00 4.40
1070 1084 2.575279 AGATCATATGGTCCTGGGCATC 59.425 50.000 12.50 0.19 0.00 3.91
1072 1086 0.686789 CATATGGTCCTGGGCATCGA 59.313 55.000 0.00 0.00 0.00 3.59
1073 1087 1.072173 CATATGGTCCTGGGCATCGAA 59.928 52.381 0.00 0.00 0.00 3.71
1074 1088 1.208706 TATGGTCCTGGGCATCGAAA 58.791 50.000 0.00 0.00 0.00 3.46
1076 1090 1.002624 GGTCCTGGGCATCGAAACA 60.003 57.895 0.00 0.00 0.00 2.83
1077 1091 1.305930 GGTCCTGGGCATCGAAACAC 61.306 60.000 0.00 0.00 0.00 3.32
1078 1092 1.002624 TCCTGGGCATCGAAACACC 60.003 57.895 0.00 0.00 0.00 4.16
1081 1095 0.609131 CTGGGCATCGAAACACCCTT 60.609 55.000 14.28 0.00 43.25 3.95
1082 1096 0.608035 TGGGCATCGAAACACCCTTC 60.608 55.000 14.28 0.00 43.25 3.46
1084 1098 1.087501 GGCATCGAAACACCCTTCTC 58.912 55.000 0.00 0.00 0.00 2.87
1090 1464 4.137116 TCGAAACACCCTTCTCCATATG 57.863 45.455 0.00 0.00 0.00 1.78
1102 1478 9.796242 ACCCTTCTCCATATGATATCTCTATTT 57.204 33.333 3.65 0.00 0.00 1.40
1107 1483 8.481314 TCTCCATATGATATCTCTATTTGGTGC 58.519 37.037 3.65 0.00 0.00 5.01
1116 1492 9.092876 GATATCTCTATTTGGTGCTATACTTGC 57.907 37.037 0.00 0.00 0.00 4.01
1118 1494 6.516718 TCTCTATTTGGTGCTATACTTGCTC 58.483 40.000 0.00 0.00 0.00 4.26
1119 1495 5.611374 TCTATTTGGTGCTATACTTGCTCC 58.389 41.667 0.00 0.00 42.44 4.70
1121 1497 2.988010 TGGTGCTATACTTGCTCCTG 57.012 50.000 8.04 0.00 42.54 3.86
1129 1518 5.175859 GCTATACTTGCTCCTGTAAACACA 58.824 41.667 0.00 0.00 0.00 3.72
1154 1543 9.767684 CAATTAAAGTATGCATCGTTTGACTTA 57.232 29.630 0.19 0.00 0.00 2.24
1182 1571 8.110860 AGAAAATCAATAGGCTTTCTTTTCGA 57.889 30.769 0.00 0.00 35.15 3.71
1217 3052 4.955925 TCTGAAACTTTTTGCAGACGAA 57.044 36.364 0.00 0.00 41.86 3.85
1218 3053 4.658071 TCTGAAACTTTTTGCAGACGAAC 58.342 39.130 0.00 0.00 41.86 3.95
1219 3054 4.155099 TCTGAAACTTTTTGCAGACGAACA 59.845 37.500 0.00 0.00 41.86 3.18
1220 3055 4.162812 TGAAACTTTTTGCAGACGAACAC 58.837 39.130 0.00 0.00 0.00 3.32
1221 3056 4.083003 TGAAACTTTTTGCAGACGAACACT 60.083 37.500 0.00 0.00 0.00 3.55
1279 3115 2.115266 CAAACCGGCCCCAGTTCT 59.885 61.111 0.00 0.00 0.00 3.01
1301 3144 0.870393 CGATGGGCTACATGCATGAC 59.130 55.000 32.75 19.78 45.15 3.06
1710 3553 2.681778 CTCCAGCCACCGTCCTCT 60.682 66.667 0.00 0.00 0.00 3.69
1943 3786 4.744867 GCCAACTGCCTCATATCTGTGTAT 60.745 45.833 0.00 0.00 0.00 2.29
1982 3825 0.667993 TTGCTCGGCAGGTTTTTGAG 59.332 50.000 0.00 0.00 40.61 3.02
2055 3898 0.950555 GCACGCACAGAATGGTCTCA 60.951 55.000 0.00 0.00 43.62 3.27
2072 3915 3.374402 ACTGTGGACGCCCTCGAG 61.374 66.667 5.13 5.13 39.41 4.04
2155 4007 2.031012 CTCCTGCGCACACCTTGA 59.969 61.111 5.66 0.00 0.00 3.02
2164 4016 4.884257 ACACCTTGACGCGCGTGT 62.884 61.111 42.90 28.60 34.69 4.49
2175 4027 4.980903 CGCGTGTTGTTGGCCTGC 62.981 66.667 3.32 0.00 0.00 4.85
2189 4041 1.068083 CCTGCACGTGGATCGCTAT 59.932 57.895 18.88 0.00 44.19 2.97
2218 4070 1.747745 GAATCCCGGGGTTTCGTGG 60.748 63.158 22.88 0.00 0.00 4.94
2219 4071 2.187896 GAATCCCGGGGTTTCGTGGA 62.188 60.000 22.88 0.00 35.29 4.02
2397 4249 5.508657 GCCATTAATCTCTTCCAAAGGATGC 60.509 44.000 0.00 0.00 0.00 3.91
2409 4261 0.990374 AAGGATGCTGTCAGAAGGCT 59.010 50.000 3.32 0.00 0.00 4.58
2521 4373 0.036952 GAGAGCACCTACAAGCTGCA 60.037 55.000 1.02 0.00 42.04 4.41
2809 4661 2.764314 GGGTGCGTGCCATGATGAC 61.764 63.158 0.00 0.00 0.00 3.06
2810 4662 2.039974 GGTGCGTGCCATGATGACA 61.040 57.895 0.00 0.00 0.00 3.58
2815 4667 0.461516 CGTGCCATGATGACAGAGCT 60.462 55.000 0.00 0.00 0.00 4.09
2848 4701 0.466922 GAGCCCGGTGTAGCTACCTA 60.467 60.000 21.01 0.11 40.11 3.08
2849 4702 0.032813 AGCCCGGTGTAGCTACCTAA 60.033 55.000 21.01 0.00 37.64 2.69
2888 4741 1.614903 ACCTGTTAATGGACGACGACA 59.385 47.619 0.00 0.00 0.00 4.35
2919 4772 2.993899 CACAGGCGAAGAGAATTTACGT 59.006 45.455 0.00 0.00 0.00 3.57
2949 4802 5.532032 TGATTGAACTTGAGCAGATTGTCAA 59.468 36.000 0.00 0.00 0.00 3.18
2967 4823 3.626670 GTCAAGGAGAAGATGAATGGCAG 59.373 47.826 0.00 0.00 0.00 4.85
2987 4843 0.786435 AGCAGGAATGGGGGAAAACT 59.214 50.000 0.00 0.00 0.00 2.66
3066 4931 3.306364 GCCGTACCATTCTCTATGCTGAT 60.306 47.826 0.00 0.00 32.60 2.90
3067 4932 4.800914 GCCGTACCATTCTCTATGCTGATT 60.801 45.833 0.00 0.00 32.60 2.57
3068 4933 4.687948 CCGTACCATTCTCTATGCTGATTG 59.312 45.833 0.00 0.00 32.60 2.67
3069 4934 4.151335 CGTACCATTCTCTATGCTGATTGC 59.849 45.833 0.00 0.00 43.25 3.56
3070 4935 4.434545 ACCATTCTCTATGCTGATTGCT 57.565 40.909 0.00 0.00 43.37 3.91
3071 4936 4.135306 ACCATTCTCTATGCTGATTGCTG 58.865 43.478 0.00 0.00 43.37 4.41
3072 4937 4.141551 ACCATTCTCTATGCTGATTGCTGA 60.142 41.667 0.00 0.00 43.37 4.26
3076 4941 4.439968 TCTCTATGCTGATTGCTGAACAG 58.560 43.478 0.00 0.00 43.37 3.16
3113 4978 2.038952 TGTGGTGATGAAGAACCTGAGG 59.961 50.000 0.00 0.00 37.36 3.86
3114 4979 1.630369 TGGTGATGAAGAACCTGAGGG 59.370 52.381 2.38 0.00 37.36 4.30
3115 4980 1.680249 GGTGATGAAGAACCTGAGGGC 60.680 57.143 2.38 0.00 35.63 5.19
3166 5036 0.961019 GTCTCTGCAATTGCCAACCA 59.039 50.000 26.94 7.59 41.18 3.67
3176 5046 1.859302 TTGCCAACCAGGTGTTTCTT 58.141 45.000 0.00 0.00 40.61 2.52
3187 5057 3.891366 CAGGTGTTTCTTGTCAGGGATTT 59.109 43.478 0.00 0.00 0.00 2.17
3213 5083 1.470979 GCTTTCATCGCTTCGAGGGTA 60.471 52.381 0.00 0.00 39.91 3.69
3259 5129 9.699410 TTACTGATGAATAATTGGATTTGGTCT 57.301 29.630 0.00 0.00 0.00 3.85
3291 5170 0.111253 AAGGCTTAGCTGGTTGCACT 59.889 50.000 3.59 0.00 45.94 4.40
3309 5189 4.955450 TGCACTGGATACCAAAAGCATTAT 59.045 37.500 0.00 0.00 32.49 1.28
3313 5193 8.143835 GCACTGGATACCAAAAGCATTATTTAT 58.856 33.333 0.00 0.00 30.80 1.40
3361 5242 7.387673 TCAAATCTTCTGTACGACATGAAACAT 59.612 33.333 0.00 0.00 0.00 2.71
3396 5277 9.210426 GCTGAAAATTACAACACTAATATCACG 57.790 33.333 0.00 0.00 0.00 4.35
3405 5286 7.478322 ACAACACTAATATCACGTAGTACTGG 58.522 38.462 5.39 0.00 41.61 4.00
3409 5318 6.485984 CACTAATATCACGTAGTACTGGAGGT 59.514 42.308 5.39 0.00 41.61 3.85
3410 5319 7.658982 CACTAATATCACGTAGTACTGGAGGTA 59.341 40.741 5.39 0.00 41.61 3.08
3411 5320 8.381636 ACTAATATCACGTAGTACTGGAGGTAT 58.618 37.037 5.39 0.00 41.61 2.73
3412 5321 7.450124 AATATCACGTAGTACTGGAGGTATG 57.550 40.000 5.39 0.00 41.61 2.39
3413 5322 3.548770 TCACGTAGTACTGGAGGTATGG 58.451 50.000 5.39 0.00 41.61 2.74
3414 5323 2.621998 CACGTAGTACTGGAGGTATGGG 59.378 54.545 5.39 0.00 41.61 4.00
3415 5324 2.236766 CGTAGTACTGGAGGTATGGGG 58.763 57.143 5.39 0.00 32.56 4.96
3416 5325 2.158564 CGTAGTACTGGAGGTATGGGGA 60.159 54.545 5.39 0.00 32.56 4.81
3417 5326 2.473576 AGTACTGGAGGTATGGGGAC 57.526 55.000 0.00 0.00 32.56 4.46
3440 5349 4.447138 TTAGGGACTGGACAAACAACAT 57.553 40.909 0.00 0.00 41.52 2.71
3449 5358 3.876914 TGGACAAACAACATCAGAGACAC 59.123 43.478 0.00 0.00 0.00 3.67
3459 5368 0.485543 TCAGAGACACCCAGTACCCA 59.514 55.000 0.00 0.00 0.00 4.51
3517 5426 3.321111 ACGATGTGTTGAGTAGAACCTGT 59.679 43.478 0.00 0.00 0.00 4.00
3555 5464 1.354031 TCTTGTCCTAATGCTGGCCAA 59.646 47.619 7.01 0.00 0.00 4.52
3629 5568 7.831690 TGGTTCAATGGCTGATAACTAATTGTA 59.168 33.333 0.00 0.00 32.78 2.41
3632 5571 9.679661 TTCAATGGCTGATAACTAATTGTAGAA 57.320 29.630 0.00 0.00 32.78 2.10
3735 5683 5.883661 CAATAGATTGGCATCGTTCAGTTT 58.116 37.500 0.00 0.00 34.17 2.66
3746 5694 5.808540 GCATCGTTCAGTTTAGTGGTGTATA 59.191 40.000 0.00 0.00 0.00 1.47
3753 5701 7.160547 TCAGTTTAGTGGTGTATATCAACGA 57.839 36.000 0.00 0.00 36.36 3.85
3754 5702 7.604549 TCAGTTTAGTGGTGTATATCAACGAA 58.395 34.615 0.00 0.00 36.36 3.85
3756 5704 8.540492 CAGTTTAGTGGTGTATATCAACGAATC 58.460 37.037 0.00 0.00 36.36 2.52
3805 5753 7.524912 GCAATTGCATACAGATGTTATAGAGG 58.475 38.462 25.36 0.00 41.59 3.69
3838 5786 7.367285 CGGAAAGTTTCACTGAAATATGGAAA 58.633 34.615 17.16 0.00 33.97 3.13
3858 5806 6.964370 TGGAAATAAATGTTTTCATACTCGCG 59.036 34.615 0.00 0.00 39.94 5.87
3877 5825 0.037590 GGGTGTGGGCTGTTGATACA 59.962 55.000 0.00 0.00 0.00 2.29
3881 5829 0.811281 GTGGGCTGTTGATACAAGCC 59.189 55.000 4.31 4.31 42.71 4.35
3922 5870 5.458452 CGTGCTGCAAACAAGAAGATAAAAA 59.542 36.000 2.77 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.032620 CCGTCCACTTATCAGCCTAGT 58.967 52.381 0.00 0.00 0.00 2.57
57 58 5.752892 TTCTACTACTAGTCTCAATGCGG 57.247 43.478 0.00 0.00 0.00 5.69
58 59 9.731819 TTATTTTCTACTACTAGTCTCAATGCG 57.268 33.333 0.00 0.00 0.00 4.73
82 83 0.250295 ACTCCAGCGCTGCAAAGTTA 60.250 50.000 31.96 9.03 0.00 2.24
85 86 2.559840 CACTCCAGCGCTGCAAAG 59.440 61.111 31.96 26.66 0.00 2.77
105 106 2.344025 GTGCTTTAATCGACCCGAACT 58.656 47.619 0.00 0.00 39.99 3.01
109 110 2.390427 GGGTGCTTTAATCGACCCG 58.610 57.895 0.00 0.00 38.86 5.28
111 112 1.743394 CCAAGGGTGCTTTAATCGACC 59.257 52.381 0.00 0.00 0.00 4.79
113 114 2.871096 ACCAAGGGTGCTTTAATCGA 57.129 45.000 0.00 0.00 32.98 3.59
115 116 6.033966 CGAATTTACCAAGGGTGCTTTAATC 58.966 40.000 0.00 0.00 36.19 1.75
124 125 2.495669 CAATGGCGAATTTACCAAGGGT 59.504 45.455 4.66 0.00 39.96 4.34
128 129 4.946772 TGAGATCAATGGCGAATTTACCAA 59.053 37.500 4.66 0.00 39.96 3.67
134 135 3.355378 TGGTTGAGATCAATGGCGAATT 58.645 40.909 0.00 0.00 38.24 2.17
143 144 2.254546 ACGTGCTTGGTTGAGATCAA 57.745 45.000 0.00 0.00 0.00 2.57
158 159 7.491372 ACATCTTATACAGGTTGACAATACGTG 59.509 37.037 0.00 0.00 37.40 4.49
162 163 9.952030 TTCAACATCTTATACAGGTTGACAATA 57.048 29.630 9.54 0.00 45.13 1.90
169 170 6.148811 CCAACGTTCAACATCTTATACAGGTT 59.851 38.462 0.00 0.00 0.00 3.50
175 176 6.315144 CCATGTCCAACGTTCAACATCTTATA 59.685 38.462 17.80 0.00 30.16 0.98
177 178 4.454161 CCATGTCCAACGTTCAACATCTTA 59.546 41.667 17.80 0.00 30.16 2.10
182 183 2.217750 CTCCATGTCCAACGTTCAACA 58.782 47.619 13.06 13.06 0.00 3.33
185 186 1.414550 TCACTCCATGTCCAACGTTCA 59.585 47.619 0.00 0.00 0.00 3.18
210 211 1.880027 GAACTTTGATGCCGACTTGGT 59.120 47.619 0.00 0.00 41.21 3.67
224 225 0.759060 GTTGGGGGTGCTGGAACTTT 60.759 55.000 0.00 0.00 0.00 2.66
274 275 3.074687 AGAGGGGCTTCATAGATACGAGA 59.925 47.826 0.00 0.00 0.00 4.04
309 310 0.034186 TGATGGTGGAGATTGTGGGC 60.034 55.000 0.00 0.00 0.00 5.36
317 318 0.888619 GTCGACAGTGATGGTGGAGA 59.111 55.000 11.55 0.00 0.00 3.71
330 331 1.282817 CAACACCAAGTTCGTCGACA 58.717 50.000 17.16 0.00 38.74 4.35
334 335 2.034001 CGAGAACAACACCAAGTTCGTC 60.034 50.000 0.00 0.00 46.54 4.20
338 339 2.943033 CCTTCGAGAACAACACCAAGTT 59.057 45.455 0.00 0.00 42.42 2.66
355 358 9.682465 AATTTTTACTAGTGGTTATCCTCCTTC 57.318 33.333 5.39 0.00 34.23 3.46
372 375 7.147567 CCCCAAATGGCTGGTATAATTTTTACT 60.148 37.037 0.00 0.00 34.33 2.24
388 391 3.132824 CCTTATGTTTCTCCCCAAATGGC 59.867 47.826 0.00 0.00 0.00 4.40
402 405 4.974645 TCCTTGCGGATATCCTTATGTT 57.025 40.909 19.61 0.00 33.30 2.71
436 439 3.658757 TGTTTGCTAACCATTTGGAGC 57.341 42.857 8.56 3.52 38.94 4.70
438 441 6.459923 GGTAAATGTTTGCTAACCATTTGGA 58.540 36.000 20.24 8.29 38.94 3.53
455 458 1.810151 CACTCCCCACAACGGTAAATG 59.190 52.381 0.00 0.00 0.00 2.32
467 472 1.067142 CGAGATCGTTTTCACTCCCCA 60.067 52.381 0.00 0.00 34.11 4.96
488 493 2.154798 CTCAGTTCCAAGGGCGACGA 62.155 60.000 0.00 0.00 0.00 4.20
499 504 0.534203 TTTGGTGGCGACTCAGTTCC 60.534 55.000 0.00 0.00 0.00 3.62
503 508 1.879380 TGAATTTTGGTGGCGACTCAG 59.121 47.619 0.00 0.00 0.00 3.35
505 510 1.880027 ACTGAATTTTGGTGGCGACTC 59.120 47.619 0.00 0.00 0.00 3.36
509 514 1.335872 GGTGACTGAATTTTGGTGGCG 60.336 52.381 0.00 0.00 0.00 5.69
510 515 1.000843 GGGTGACTGAATTTTGGTGGC 59.999 52.381 0.00 0.00 0.00 5.01
514 519 1.200020 GCGAGGGTGACTGAATTTTGG 59.800 52.381 0.00 0.00 0.00 3.28
522 527 0.249868 TTTGACAGCGAGGGTGACTG 60.250 55.000 1.38 0.00 37.45 3.51
537 542 5.506686 TTGAACAACGACATCCATTTTGA 57.493 34.783 0.00 0.00 0.00 2.69
544 549 9.781834 TTATCATAATTTTGAACAACGACATCC 57.218 29.630 2.59 0.00 0.00 3.51
547 552 8.293157 TGCTTATCATAATTTTGAACAACGACA 58.707 29.630 2.59 0.00 0.00 4.35
577 582 0.671796 CTACGCGGATGTCCCACATA 59.328 55.000 12.47 0.00 39.27 2.29
578 583 1.040893 TCTACGCGGATGTCCCACAT 61.041 55.000 12.47 0.00 42.43 3.21
595 600 6.370186 TGATAAGCATTCAGGCAGATATCT 57.630 37.500 0.00 0.00 35.83 1.98
599 604 8.418597 AAATTATGATAAGCATTCAGGCAGAT 57.581 30.769 0.00 0.00 38.44 2.90
644 650 5.711506 TGTCATAATGTTTGATGGCAACTCT 59.288 36.000 0.00 0.00 34.83 3.24
656 662 5.418840 AGGCTTCCGAATTGTCATAATGTTT 59.581 36.000 0.00 0.00 0.00 2.83
657 663 4.949856 AGGCTTCCGAATTGTCATAATGTT 59.050 37.500 0.00 0.00 0.00 2.71
658 664 4.526970 AGGCTTCCGAATTGTCATAATGT 58.473 39.130 0.00 0.00 0.00 2.71
659 665 4.818546 AGAGGCTTCCGAATTGTCATAATG 59.181 41.667 0.00 0.00 0.00 1.90
660 666 4.818546 CAGAGGCTTCCGAATTGTCATAAT 59.181 41.667 0.00 0.00 0.00 1.28
661 667 4.191544 CAGAGGCTTCCGAATTGTCATAA 58.808 43.478 0.00 0.00 0.00 1.90
662 668 3.197766 ACAGAGGCTTCCGAATTGTCATA 59.802 43.478 0.00 0.00 0.00 2.15
663 669 2.026822 ACAGAGGCTTCCGAATTGTCAT 60.027 45.455 0.00 0.00 0.00 3.06
664 670 1.347707 ACAGAGGCTTCCGAATTGTCA 59.652 47.619 0.00 0.00 0.00 3.58
665 671 2.100605 ACAGAGGCTTCCGAATTGTC 57.899 50.000 0.00 0.00 0.00 3.18
666 672 3.432326 GGATACAGAGGCTTCCGAATTGT 60.432 47.826 0.00 0.00 0.00 2.71
667 673 3.134458 GGATACAGAGGCTTCCGAATTG 58.866 50.000 0.00 0.00 0.00 2.32
668 674 2.771943 TGGATACAGAGGCTTCCGAATT 59.228 45.455 0.00 0.00 46.17 2.17
669 675 2.398588 TGGATACAGAGGCTTCCGAAT 58.601 47.619 0.00 0.00 46.17 3.34
670 676 1.860641 TGGATACAGAGGCTTCCGAA 58.139 50.000 0.00 0.00 46.17 4.30
671 677 3.607871 TGGATACAGAGGCTTCCGA 57.392 52.632 0.00 0.00 46.17 4.55
683 689 1.656095 GAGCGCGCTTCATATGGATAC 59.344 52.381 36.87 13.94 0.00 2.24
688 694 1.713597 TATGGAGCGCGCTTCATATG 58.286 50.000 43.79 1.28 40.28 1.78
698 704 3.624410 TGATCATAATGCATATGGAGCGC 59.376 43.478 0.00 0.00 41.53 5.92
734 740 4.547532 TCTTAGAGCAACTTCAACGACTC 58.452 43.478 0.00 0.00 0.00 3.36
736 742 4.092091 CCATCTTAGAGCAACTTCAACGAC 59.908 45.833 0.00 0.00 0.00 4.34
742 749 7.149307 GGTCTATACCATCTTAGAGCAACTTC 58.851 42.308 4.72 0.00 45.98 3.01
761 768 5.163258 GGGATCAAGAGTTGTCATGGTCTAT 60.163 44.000 0.00 0.00 32.95 1.98
762 769 4.162320 GGGATCAAGAGTTGTCATGGTCTA 59.838 45.833 0.00 0.00 32.95 2.59
769 776 5.560722 TTTGTAGGGATCAAGAGTTGTCA 57.439 39.130 0.00 0.00 0.00 3.58
840 847 9.348476 TGTGCAAGGCATATAAATTATAGTTGA 57.652 29.630 0.00 0.00 41.91 3.18
905 912 8.593492 AAAATGCCTTCTGACAAAGTTTTATC 57.407 30.769 0.00 0.00 0.00 1.75
906 913 8.962884 AAAAATGCCTTCTGACAAAGTTTTAT 57.037 26.923 0.00 0.00 0.00 1.40
993 1006 6.609876 TGGAGATGCCCTTAATTTGCTATTA 58.390 36.000 0.00 0.00 34.97 0.98
998 1011 4.470334 TTTGGAGATGCCCTTAATTTGC 57.530 40.909 0.00 0.00 34.97 3.68
1020 1033 4.265904 TGCGAGAGGTTTGAGATACAAA 57.734 40.909 0.00 0.00 44.79 2.83
1026 1039 1.202486 ACGTTTGCGAGAGGTTTGAGA 60.202 47.619 0.00 0.00 42.00 3.27
1037 1050 3.555547 CCATATGATCTGAACGTTTGCGA 59.444 43.478 0.46 0.00 42.00 5.10
1045 1058 3.808618 GCCCAGGACCATATGATCTGAAC 60.809 52.174 3.65 1.53 0.00 3.18
1048 1061 1.701292 TGCCCAGGACCATATGATCTG 59.299 52.381 3.65 8.35 0.00 2.90
1065 1079 1.087501 GAGAAGGGTGTTTCGATGCC 58.912 55.000 0.00 0.00 32.33 4.40
1066 1080 1.087501 GGAGAAGGGTGTTTCGATGC 58.912 55.000 0.00 0.00 32.33 3.91
1067 1081 2.472695 TGGAGAAGGGTGTTTCGATG 57.527 50.000 0.00 0.00 32.33 3.84
1068 1082 4.408921 TCATATGGAGAAGGGTGTTTCGAT 59.591 41.667 2.13 0.00 32.33 3.59
1069 1083 3.772572 TCATATGGAGAAGGGTGTTTCGA 59.227 43.478 2.13 0.00 32.33 3.71
1070 1084 4.137116 TCATATGGAGAAGGGTGTTTCG 57.863 45.455 2.13 0.00 32.33 3.46
1072 1086 7.515514 AGAGATATCATATGGAGAAGGGTGTTT 59.484 37.037 5.32 0.00 0.00 2.83
1073 1087 7.021873 AGAGATATCATATGGAGAAGGGTGTT 58.978 38.462 5.32 0.00 0.00 3.32
1074 1088 6.569737 AGAGATATCATATGGAGAAGGGTGT 58.430 40.000 5.32 0.00 0.00 4.16
1076 1090 9.796242 AAATAGAGATATCATATGGAGAAGGGT 57.204 33.333 5.32 0.00 0.00 4.34
1081 1095 8.481314 GCACCAAATAGAGATATCATATGGAGA 58.519 37.037 5.32 0.00 0.00 3.71
1082 1096 8.484575 AGCACCAAATAGAGATATCATATGGAG 58.515 37.037 5.32 4.70 0.00 3.86
1090 1464 9.092876 GCAAGTATAGCACCAAATAGAGATATC 57.907 37.037 0.00 0.00 0.00 1.63
1102 1478 2.187958 ACAGGAGCAAGTATAGCACCA 58.812 47.619 4.57 0.00 43.95 4.17
1107 1483 7.849804 ATTGTGTTTACAGGAGCAAGTATAG 57.150 36.000 0.00 0.00 38.23 1.31
1112 1488 7.425606 ACTTTAATTGTGTTTACAGGAGCAAG 58.574 34.615 0.00 0.00 38.23 4.01
1116 1492 8.511321 TGCATACTTTAATTGTGTTTACAGGAG 58.489 33.333 0.00 0.00 38.23 3.69
1118 1494 9.289303 GATGCATACTTTAATTGTGTTTACAGG 57.711 33.333 0.00 0.00 38.23 4.00
1119 1495 8.998989 CGATGCATACTTTAATTGTGTTTACAG 58.001 33.333 0.00 0.00 38.23 2.74
1121 1497 8.889849 ACGATGCATACTTTAATTGTGTTTAC 57.110 30.769 0.00 0.00 0.00 2.01
1154 1543 9.920133 GAAAAGAAAGCCTATTGATTTTCTCTT 57.080 29.630 0.00 0.00 38.54 2.85
1182 1571 7.404671 AAAGTTTCAGAAAATGGTGTGTACT 57.595 32.000 0.00 0.00 0.00 2.73
1217 3052 3.611057 CGTTCTTTCGGCTAGTGTAGTGT 60.611 47.826 0.00 0.00 0.00 3.55
1218 3053 2.915463 CGTTCTTTCGGCTAGTGTAGTG 59.085 50.000 0.00 0.00 0.00 2.74
1219 3054 2.670509 GCGTTCTTTCGGCTAGTGTAGT 60.671 50.000 0.00 0.00 0.00 2.73
1220 3055 1.918609 GCGTTCTTTCGGCTAGTGTAG 59.081 52.381 0.00 0.00 0.00 2.74
1221 3056 1.270274 TGCGTTCTTTCGGCTAGTGTA 59.730 47.619 0.00 0.00 0.00 2.90
1297 3133 0.833287 CGGAGGTGGAAGATGGTCAT 59.167 55.000 0.00 0.00 0.00 3.06
1301 3144 1.450312 GTGCGGAGGTGGAAGATGG 60.450 63.158 0.00 0.00 0.00 3.51
1660 3503 2.401195 GCATTTCGTCGAGCAGCC 59.599 61.111 0.00 0.00 0.00 4.85
1703 3546 1.446272 GTTGAAGGCGGAGAGGACG 60.446 63.158 0.00 0.00 0.00 4.79
1710 3553 0.909610 ATGAGGGAGTTGAAGGCGGA 60.910 55.000 0.00 0.00 0.00 5.54
1959 3802 0.890996 AAAACCTGCCGAGCAAGAGG 60.891 55.000 2.11 0.00 38.41 3.69
2036 3879 0.950555 TGAGACCATTCTGTGCGTGC 60.951 55.000 0.00 0.00 29.47 5.34
2055 3898 3.374402 CTCGAGGGCGTCCACAGT 61.374 66.667 9.71 0.00 38.98 3.55
2164 4016 2.974692 ATCCACGTGCAGGCCAACAA 62.975 55.000 10.91 0.00 0.00 2.83
2175 4027 1.927210 GCACATAGCGATCCACGTG 59.073 57.895 9.08 9.08 44.60 4.49
2202 4054 1.781153 TTTCCACGAAACCCCGGGAT 61.781 55.000 26.32 0.00 34.30 3.85
2345 4197 2.176045 CCATGTCCATGCATGCCATAT 58.824 47.619 21.69 10.29 43.46 1.78
2397 4249 2.755929 GCCGTAAGCCTTCTGACAG 58.244 57.895 0.00 0.00 34.35 3.51
2409 4261 1.137282 TGCGACATTATCTGGCCGTAA 59.863 47.619 0.00 0.00 0.00 3.18
2438 4290 3.782244 CTGCACGCCGACAAGAGC 61.782 66.667 0.00 0.00 0.00 4.09
2521 4373 1.187087 GTAGTGCTCCAGTGTAGGCT 58.813 55.000 0.00 0.00 0.00 4.58
2720 4572 1.278127 ACGTAGTAGCCCACATTGCTT 59.722 47.619 0.00 0.00 41.94 3.91
2801 4653 1.022735 GCCCAAGCTCTGTCATCATG 58.977 55.000 0.00 0.00 35.50 3.07
2848 4701 3.288092 GTGAACTCTCCCCTTGTGTTTT 58.712 45.455 0.00 0.00 0.00 2.43
2849 4702 2.422945 GGTGAACTCTCCCCTTGTGTTT 60.423 50.000 0.00 0.00 0.00 2.83
2919 4772 2.950975 TGCTCAAGTTCAATCACAAGCA 59.049 40.909 0.00 0.00 36.26 3.91
2949 4802 2.158784 GCTCTGCCATTCATCTTCTCCT 60.159 50.000 0.00 0.00 0.00 3.69
2950 4803 2.220313 GCTCTGCCATTCATCTTCTCC 58.780 52.381 0.00 0.00 0.00 3.71
2951 4804 2.873472 CTGCTCTGCCATTCATCTTCTC 59.127 50.000 0.00 0.00 0.00 2.87
2967 4823 1.186200 GTTTTCCCCCATTCCTGCTC 58.814 55.000 0.00 0.00 0.00 4.26
2987 4843 3.803715 GCTACCTTCTTGTCAAGCACTCA 60.804 47.826 7.78 0.00 0.00 3.41
3041 4906 2.545113 GCATAGAGAATGGTACGGCGAA 60.545 50.000 16.62 0.00 35.99 4.70
3066 4931 2.880268 CAACATCCACTCTGTTCAGCAA 59.120 45.455 0.00 0.00 34.69 3.91
3067 4932 2.104622 TCAACATCCACTCTGTTCAGCA 59.895 45.455 0.00 0.00 34.69 4.41
3068 4933 2.740981 CTCAACATCCACTCTGTTCAGC 59.259 50.000 0.00 0.00 34.69 4.26
3069 4934 4.263018 TCTCAACATCCACTCTGTTCAG 57.737 45.455 0.00 0.00 34.69 3.02
3070 4935 4.897509 ATCTCAACATCCACTCTGTTCA 57.102 40.909 0.00 0.00 34.69 3.18
3071 4936 4.999950 ACAATCTCAACATCCACTCTGTTC 59.000 41.667 0.00 0.00 34.69 3.18
3072 4937 4.758674 CACAATCTCAACATCCACTCTGTT 59.241 41.667 0.00 0.00 37.31 3.16
3076 4941 3.438087 CACCACAATCTCAACATCCACTC 59.562 47.826 0.00 0.00 0.00 3.51
3166 5036 3.884037 AATCCCTGACAAGAAACACCT 57.116 42.857 0.00 0.00 0.00 4.00
3176 5046 0.694771 AGCAGCTCAAATCCCTGACA 59.305 50.000 0.00 0.00 0.00 3.58
3187 5057 1.081892 GAAGCGATGAAAGCAGCTCA 58.918 50.000 0.00 0.00 39.25 4.26
3259 5129 3.807209 GCTAAGCCTTCCTTCACAGTGAA 60.807 47.826 15.39 15.39 34.95 3.18
3309 5189 7.548075 AGCAAAAGCTAGCTTACGAACTATAAA 59.452 33.333 29.52 0.00 38.01 1.40
3313 5193 4.817517 AGCAAAAGCTAGCTTACGAACTA 58.182 39.130 29.52 0.00 38.01 2.24
3316 5196 3.659786 TGAGCAAAAGCTAGCTTACGAA 58.340 40.909 29.52 11.25 42.04 3.85
3318 5198 4.404507 TTTGAGCAAAAGCTAGCTTACG 57.595 40.909 29.52 22.75 42.04 3.18
3361 5242 6.200665 GTGTTGTAATTTTCAGCAATCAAGCA 59.799 34.615 0.00 0.00 36.85 3.91
3396 5277 3.229293 GTCCCCATACCTCCAGTACTAC 58.771 54.545 0.00 0.00 32.46 2.73
3405 5286 2.638363 GTCCCTAATGTCCCCATACCTC 59.362 54.545 0.00 0.00 0.00 3.85
3409 5318 2.251605 TCCAGTCCCTAATGTCCCCATA 59.748 50.000 0.00 0.00 0.00 2.74
3410 5319 1.010793 TCCAGTCCCTAATGTCCCCAT 59.989 52.381 0.00 0.00 0.00 4.00
3411 5320 0.419865 TCCAGTCCCTAATGTCCCCA 59.580 55.000 0.00 0.00 0.00 4.96
3412 5321 0.837940 GTCCAGTCCCTAATGTCCCC 59.162 60.000 0.00 0.00 0.00 4.81
3413 5322 1.580059 TGTCCAGTCCCTAATGTCCC 58.420 55.000 0.00 0.00 0.00 4.46
3414 5323 3.244770 TGTTTGTCCAGTCCCTAATGTCC 60.245 47.826 0.00 0.00 0.00 4.02
3415 5324 4.015872 TGTTTGTCCAGTCCCTAATGTC 57.984 45.455 0.00 0.00 0.00 3.06
3416 5325 4.142038 GTTGTTTGTCCAGTCCCTAATGT 58.858 43.478 0.00 0.00 0.00 2.71
3417 5326 4.141287 TGTTGTTTGTCCAGTCCCTAATG 58.859 43.478 0.00 0.00 0.00 1.90
3418 5327 4.447138 TGTTGTTTGTCCAGTCCCTAAT 57.553 40.909 0.00 0.00 0.00 1.73
3419 5328 3.935818 TGTTGTTTGTCCAGTCCCTAA 57.064 42.857 0.00 0.00 0.00 2.69
3420 5329 3.392947 TGATGTTGTTTGTCCAGTCCCTA 59.607 43.478 0.00 0.00 0.00 3.53
3421 5330 2.174639 TGATGTTGTTTGTCCAGTCCCT 59.825 45.455 0.00 0.00 0.00 4.20
3422 5331 2.554032 CTGATGTTGTTTGTCCAGTCCC 59.446 50.000 0.00 0.00 0.00 4.46
3423 5332 3.476552 TCTGATGTTGTTTGTCCAGTCC 58.523 45.455 0.00 0.00 0.00 3.85
3424 5333 4.212214 GTCTCTGATGTTGTTTGTCCAGTC 59.788 45.833 0.00 0.00 0.00 3.51
3425 5334 4.130118 GTCTCTGATGTTGTTTGTCCAGT 58.870 43.478 0.00 0.00 0.00 4.00
3440 5349 0.485543 TGGGTACTGGGTGTCTCTGA 59.514 55.000 0.00 0.00 0.00 3.27
3517 5426 2.808919 AGAGTCTTCGGATCTGAACCA 58.191 47.619 13.13 0.11 0.00 3.67
3572 5482 0.323629 CCAGCCTGTCGGGAAACTTA 59.676 55.000 0.31 0.00 37.23 2.24
3582 5492 1.066787 GGAGTACAAGACCAGCCTGTC 60.067 57.143 0.00 0.00 35.43 3.51
3629 5568 6.385176 TCACACCTCTGAAATCAGGATATTCT 59.615 38.462 10.37 0.00 43.91 2.40
3632 5571 5.426509 TGTCACACCTCTGAAATCAGGATAT 59.573 40.000 10.37 0.00 43.91 1.63
3735 5683 8.255206 ACAAAGATTCGTTGATATACACCACTA 58.745 33.333 17.47 0.00 0.00 2.74
3756 5704 8.077991 TGCAGTTTATCATCTTCTTCAACAAAG 58.922 33.333 0.00 0.00 36.22 2.77
3802 5750 2.125766 AACTTTCCGCCACCTCCCTC 62.126 60.000 0.00 0.00 0.00 4.30
3803 5751 1.716028 AAACTTTCCGCCACCTCCCT 61.716 55.000 0.00 0.00 0.00 4.20
3804 5752 1.228459 AAACTTTCCGCCACCTCCC 60.228 57.895 0.00 0.00 0.00 4.30
3805 5753 0.536460 TGAAACTTTCCGCCACCTCC 60.536 55.000 0.00 0.00 0.00 4.30
3838 5786 4.879545 ACCCGCGAGTATGAAAACATTTAT 59.120 37.500 8.23 0.00 0.00 1.40
3858 5806 0.037590 TGTATCAACAGCCCACACCC 59.962 55.000 0.00 0.00 0.00 4.61
3870 5818 3.394674 TTCACTGTCGGCTTGTATCAA 57.605 42.857 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.