Multiple sequence alignment - TraesCS3A01G516800

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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 TraesCS3A01G516800 chr3A 100.000 3779 0 0 1 3779 734011261 734015039 0.000000e+00 6979
1 TraesCS3A01G516800 chrUn 91.506 1248 77 15 2050 3287 42181491 42180263 0.000000e+00 1690
2 TraesCS3A01G516800 chrUn 92.667 600 33 5 1433 2025 42182082 42181487 0.000000e+00 854
3 TraesCS3A01G516800 chrUn 79.275 883 79 39 584 1415 42183301 42182472 4.330000e-144 521
4 TraesCS3A01G516800 chrUn 80.108 553 55 27 4 517 42183861 42183325 9.980000e-96 361
5 TraesCS3A01G516800 chr3D 92.790 1165 69 9 2517 3670 604373457 604374617 0.000000e+00 1672
6 TraesCS3A01G516800 chr3D 94.450 1045 45 8 1433 2475 604372420 604373453 0.000000e+00 1596
7 TraesCS3A01G516800 chr3D 83.864 440 44 14 983 1415 604371585 604372004 9.840000e-106 394
8 TraesCS3A01G516800 chr3D 83.067 313 14 17 249 542 604370907 604371199 8.110000e-62 248
9 TraesCS3A01G516800 chr3D 99.029 103 1 0 585 687 604371212 604371314 6.450000e-43 185
10 TraesCS3A01G516800 chr3D 83.951 162 11 7 811 959 604371442 604371601 1.420000e-29 141
11 TraesCS3A01G516800 chr7B 88.542 384 30 5 1462 1835 644740000 644739621 1.600000e-123 453
12 TraesCS3A01G516800 chr2A 79.627 643 59 31 79 686 635259628 635260233 2.740000e-106 396


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 TraesCS3A01G516800 chr3A 734011261 734015039 3778 False 6979.0 6979 100.000000 1 3779 1 chr3A.!!$F1 3778
1 TraesCS3A01G516800 chrUn 42180263 42183861 3598 True 856.5 1690 85.889000 4 3287 4 chrUn.!!$R1 3283
2 TraesCS3A01G516800 chr3D 604370907 604374617 3710 False 706.0 1672 89.525167 249 3670 6 chr3D.!!$F1 3421
3 TraesCS3A01G516800 chr2A 635259628 635260233 605 False 396.0 396 79.627000 79 686 1 chr2A.!!$F1 607

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
755 820 0.033920 CCAAGCAAGCAAACCCCTTC 59.966 55.0 0.00 0.0 0.00 3.46 F
1681 2234 0.030504 TGCATTTGACAAGTGTGCCG 59.969 50.0 11.77 0.0 35.03 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 2252 0.247736 AAGTCCAGCGAGCCTGTAAG 59.752 55.0 0.0 0.0 40.06 2.34 R
3670 4242 0.252239 TAGCTTCCAGAGTCCCAGCA 60.252 55.0 0.0 0.0 32.58 4.41 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
30 31 6.966490 TAGTGTTTAACAGTCCCATGGAACAG 60.966 42.308 15.22 1.49 35.62 3.16
57 58 6.256053 TGACCAGCTATCACCTATCATCATA 58.744 40.000 0.00 0.00 0.00 2.15
58 59 6.899631 TGACCAGCTATCACCTATCATCATAT 59.100 38.462 0.00 0.00 0.00 1.78
74 75 5.769662 TCATCATATTCCATAAGCCACAACC 59.230 40.000 0.00 0.00 0.00 3.77
76 77 4.887071 TCATATTCCATAAGCCACAACCAC 59.113 41.667 0.00 0.00 0.00 4.16
80 81 2.017049 CCATAAGCCACAACCACTAGC 58.983 52.381 0.00 0.00 0.00 3.42
87 88 3.264450 AGCCACAACCACTAGCTAAATCT 59.736 43.478 0.00 0.00 30.46 2.40
116 117 2.064762 GCGCATCATCGAATTAGCTCT 58.935 47.619 0.30 0.00 0.00 4.09
135 136 6.047870 AGCTCTCTGTAGCATCATTTTACAG 58.952 40.000 4.87 4.87 45.30 2.74
151 152 0.764890 ACAGCTACAGTTGCTTCCCA 59.235 50.000 6.78 0.00 38.92 4.37
192 193 2.601314 CGCGACAATAAATTCAGACGGA 59.399 45.455 0.00 0.00 0.00 4.69
238 242 3.258372 TCTTCCGACAGCAACTAGAACAT 59.742 43.478 0.00 0.00 0.00 2.71
239 243 4.461431 TCTTCCGACAGCAACTAGAACATA 59.539 41.667 0.00 0.00 0.00 2.29
241 245 4.682787 TCCGACAGCAACTAGAACATATG 58.317 43.478 0.00 0.00 0.00 1.78
242 246 4.401202 TCCGACAGCAACTAGAACATATGA 59.599 41.667 10.38 0.00 0.00 2.15
243 247 4.504461 CCGACAGCAACTAGAACATATGAC 59.496 45.833 10.38 3.20 0.00 3.06
244 248 5.344066 CGACAGCAACTAGAACATATGACT 58.656 41.667 10.38 10.57 0.00 3.41
245 249 5.807520 CGACAGCAACTAGAACATATGACTT 59.192 40.000 10.38 0.00 0.00 3.01
246 250 6.311445 CGACAGCAACTAGAACATATGACTTT 59.689 38.462 10.38 0.00 0.00 2.66
278 300 2.905736 CCAATCCAAAGGGGTGAAATGT 59.094 45.455 0.00 0.00 38.11 2.71
282 304 0.243636 CAAAGGGGTGAAATGTCGGC 59.756 55.000 0.00 0.00 0.00 5.54
333 360 1.180029 GCAATCACATCAAGGGCAGT 58.820 50.000 0.00 0.00 0.00 4.40
336 363 3.614092 CAATCACATCAAGGGCAGTAGT 58.386 45.455 0.00 0.00 0.00 2.73
338 368 5.185454 CAATCACATCAAGGGCAGTAGTAA 58.815 41.667 0.00 0.00 0.00 2.24
341 371 5.428253 TCACATCAAGGGCAGTAGTAAATC 58.572 41.667 0.00 0.00 0.00 2.17
345 375 7.552687 CACATCAAGGGCAGTAGTAAATCTTTA 59.447 37.037 0.00 0.00 0.00 1.85
349 383 5.919755 AGGGCAGTAGTAAATCTTTAGAGC 58.080 41.667 0.00 0.00 0.00 4.09
368 402 0.447406 CGCGTGGCATTTGAGATTGA 59.553 50.000 0.00 0.00 0.00 2.57
378 412 3.401033 TTTGAGATTGAGCGTGAGGAA 57.599 42.857 0.00 0.00 0.00 3.36
380 414 1.205655 TGAGATTGAGCGTGAGGAAGG 59.794 52.381 0.00 0.00 0.00 3.46
381 415 1.478510 GAGATTGAGCGTGAGGAAGGA 59.521 52.381 0.00 0.00 0.00 3.36
382 416 2.102252 GAGATTGAGCGTGAGGAAGGAT 59.898 50.000 0.00 0.00 0.00 3.24
466 521 2.106332 GGCACGACACCTATCCGG 59.894 66.667 0.00 0.00 39.35 5.14
467 522 2.585247 GCACGACACCTATCCGGC 60.585 66.667 0.00 0.00 35.61 6.13
471 526 2.109181 GACACCTATCCGGCAGCC 59.891 66.667 0.00 0.00 35.61 4.85
472 527 2.687200 ACACCTATCCGGCAGCCA 60.687 61.111 13.30 0.00 35.61 4.75
473 528 2.203070 CACCTATCCGGCAGCCAC 60.203 66.667 13.30 0.00 35.61 5.01
474 529 3.849951 ACCTATCCGGCAGCCACG 61.850 66.667 13.30 0.00 35.61 4.94
476 531 4.529219 CTATCCGGCAGCCACGCA 62.529 66.667 13.30 0.00 0.00 5.24
494 549 0.449786 CACAGCGACGACAGAGAGAT 59.550 55.000 0.00 0.00 0.00 2.75
542 597 0.886490 AAACTGACTGAAGCAGCCGG 60.886 55.000 0.00 0.00 36.86 6.13
543 598 2.435586 CTGACTGAAGCAGCCGGG 60.436 66.667 2.18 0.00 34.37 5.73
544 599 2.922503 TGACTGAAGCAGCCGGGA 60.923 61.111 2.18 0.00 34.37 5.14
545 600 2.435059 GACTGAAGCAGCCGGGAC 60.435 66.667 2.18 0.00 34.37 4.46
546 601 3.959991 GACTGAAGCAGCCGGGACC 62.960 68.421 2.18 0.00 34.37 4.46
575 630 3.554342 CGGGAGGCAGGGAGGATG 61.554 72.222 0.00 0.00 0.00 3.51
576 631 2.040464 GGGAGGCAGGGAGGATGA 60.040 66.667 0.00 0.00 0.00 2.92
577 632 2.146061 GGGAGGCAGGGAGGATGAG 61.146 68.421 0.00 0.00 0.00 2.90
578 633 2.146061 GGAGGCAGGGAGGATGAGG 61.146 68.421 0.00 0.00 0.00 3.86
579 634 2.040043 AGGCAGGGAGGATGAGGG 60.040 66.667 0.00 0.00 0.00 4.30
580 635 3.883549 GGCAGGGAGGATGAGGGC 61.884 72.222 0.00 0.00 0.00 5.19
581 636 3.883549 GCAGGGAGGATGAGGGCC 61.884 72.222 0.00 0.00 0.00 5.80
582 637 3.174265 CAGGGAGGATGAGGGCCC 61.174 72.222 16.46 16.46 41.00 5.80
699 754 4.201122 CATGGCTGGCCTCCCTCC 62.201 72.222 13.05 0.00 36.94 4.30
700 755 4.444957 ATGGCTGGCCTCCCTCCT 62.445 66.667 13.05 0.00 36.94 3.69
702 757 4.814041 GGCTGGCCTCCCTCCTCT 62.814 72.222 3.32 0.00 0.00 3.69
705 760 2.364317 TGGCCTCCCTCCTCTTCG 60.364 66.667 3.32 0.00 0.00 3.79
708 763 2.042435 CCTCCCTCCTCTTCGCCT 60.042 66.667 0.00 0.00 0.00 5.52
710 765 1.076339 CTCCCTCCTCTTCGCCTCT 60.076 63.158 0.00 0.00 0.00 3.69
740 805 0.318955 CGCTGTTCCAAAAGCCCAAG 60.319 55.000 0.00 0.00 35.98 3.61
744 809 1.138661 TGTTCCAAAAGCCCAAGCAAG 59.861 47.619 0.00 0.00 43.56 4.01
749 814 1.331447 CAAAAGCCCAAGCAAGCAAAC 59.669 47.619 0.00 0.00 43.56 2.93
750 815 0.179048 AAAGCCCAAGCAAGCAAACC 60.179 50.000 0.00 0.00 43.56 3.27
751 816 2.031012 GCCCAAGCAAGCAAACCC 59.969 61.111 0.00 0.00 39.53 4.11
752 817 2.743060 CCCAAGCAAGCAAACCCC 59.257 61.111 0.00 0.00 0.00 4.95
753 818 1.838396 CCCAAGCAAGCAAACCCCT 60.838 57.895 0.00 0.00 0.00 4.79
754 819 1.410050 CCCAAGCAAGCAAACCCCTT 61.410 55.000 0.00 0.00 0.00 3.95
755 820 0.033920 CCAAGCAAGCAAACCCCTTC 59.966 55.000 0.00 0.00 0.00 3.46
756 821 0.752054 CAAGCAAGCAAACCCCTTCA 59.248 50.000 0.00 0.00 0.00 3.02
757 822 1.043022 AAGCAAGCAAACCCCTTCAG 58.957 50.000 0.00 0.00 0.00 3.02
769 835 1.745264 CCTTCAGCCCCGAGATCTC 59.255 63.158 13.05 13.05 0.00 2.75
783 849 2.723586 GATCTCTTGCCCTAGCGCCC 62.724 65.000 2.29 0.00 44.31 6.13
834 937 2.437716 CCGTCCCACCAAATCCGG 60.438 66.667 0.00 0.00 0.00 5.14
866 969 3.834350 CAGCGCGAGATGGTATCG 58.166 61.111 12.10 0.00 45.32 2.92
867 970 1.730902 CAGCGCGAGATGGTATCGG 60.731 63.158 12.10 0.00 45.32 4.18
868 971 3.106407 GCGCGAGATGGTATCGGC 61.106 66.667 12.10 0.00 40.50 5.54
869 972 2.335011 CGCGAGATGGTATCGGCA 59.665 61.111 0.00 0.00 40.50 5.69
875 998 1.664965 GATGGTATCGGCAGGTCGC 60.665 63.158 0.00 0.00 41.28 5.19
936 1060 4.154347 GCAGGAGGAGGCGACAGG 62.154 72.222 0.00 0.00 0.00 4.00
937 1061 2.681778 CAGGAGGAGGCGACAGGT 60.682 66.667 0.00 0.00 0.00 4.00
938 1062 2.681778 AGGAGGAGGCGACAGGTG 60.682 66.667 0.00 0.00 0.00 4.00
939 1063 4.459089 GGAGGAGGCGACAGGTGC 62.459 72.222 0.00 0.00 0.00 5.01
940 1064 3.386237 GAGGAGGCGACAGGTGCT 61.386 66.667 0.00 0.00 0.00 4.40
941 1065 3.363844 GAGGAGGCGACAGGTGCTC 62.364 68.421 0.00 0.00 0.00 4.26
971 1095 4.516195 GCCGGGAAGACTCGCTCC 62.516 72.222 2.18 0.00 38.86 4.70
972 1096 4.194720 CCGGGAAGACTCGCTCCG 62.195 72.222 0.00 0.00 38.86 4.63
973 1097 4.856607 CGGGAAGACTCGCTCCGC 62.857 72.222 0.00 0.00 34.17 5.54
974 1098 4.516195 GGGAAGACTCGCTCCGCC 62.516 72.222 0.00 0.00 0.00 6.13
975 1099 4.856607 GGAAGACTCGCTCCGCCG 62.857 72.222 0.00 0.00 0.00 6.46
1021 1145 1.514087 GCGATGACCGTGGAAGGTA 59.486 57.895 0.00 0.00 46.09 3.08
1029 1153 1.273666 ACCGTGGAAGGTAAGGGATCT 60.274 52.381 0.00 0.00 43.89 2.75
1036 1160 3.644265 GGAAGGTAAGGGATCTCTCTTCC 59.356 52.174 20.26 20.26 0.00 3.46
1038 1162 3.922375 AGGTAAGGGATCTCTCTTCCTG 58.078 50.000 10.98 0.00 33.53 3.86
1056 1180 4.475444 CCCCCGACCCAGCTCCTA 62.475 72.222 0.00 0.00 0.00 2.94
1059 1183 1.749033 CCCGACCCAGCTCCTATTC 59.251 63.158 0.00 0.00 0.00 1.75
1062 1186 1.759459 CGACCCAGCTCCTATTCCCC 61.759 65.000 0.00 0.00 0.00 4.81
1065 1189 2.520536 CCAGCTCCTATTCCCCGGG 61.521 68.421 15.80 15.80 0.00 5.73
1128 1254 2.824489 GGCGGCTAGGGTTCTTGC 60.824 66.667 0.00 0.00 40.23 4.01
1152 1279 2.112198 GCATGGGGTCGCGAATTGA 61.112 57.895 12.06 0.00 0.00 2.57
1272 1400 2.494530 GCTGGCACGGGGACAAAAA 61.495 57.895 0.00 0.00 30.64 1.94
1273 1401 1.815817 GCTGGCACGGGGACAAAAAT 61.816 55.000 0.00 0.00 30.64 1.82
1274 1402 0.243636 CTGGCACGGGGACAAAAATC 59.756 55.000 0.00 0.00 30.64 2.17
1276 1404 0.243636 GGCACGGGGACAAAAATCAG 59.756 55.000 0.00 0.00 0.00 2.90
1277 1405 0.958822 GCACGGGGACAAAAATCAGT 59.041 50.000 0.00 0.00 0.00 3.41
1279 1407 0.958822 ACGGGGACAAAAATCAGTGC 59.041 50.000 0.00 0.00 0.00 4.40
1280 1408 0.958091 CGGGGACAAAAATCAGTGCA 59.042 50.000 0.00 0.00 0.00 4.57
1281 1409 1.335872 CGGGGACAAAAATCAGTGCAC 60.336 52.381 9.40 9.40 0.00 4.57
1282 1410 1.335872 GGGGACAAAAATCAGTGCACG 60.336 52.381 12.01 6.78 0.00 5.34
1285 1413 0.031994 ACAAAAATCAGTGCACGGCC 59.968 50.000 12.54 0.00 0.00 6.13
1295 1423 2.125952 GCACGGCCTGATTTTGCC 60.126 61.111 0.00 0.00 44.41 4.52
1335 1466 1.202769 CCTTAGGGGAAACGGGGTCA 61.203 60.000 0.00 0.00 37.23 4.02
1357 1488 2.688666 TGCTGCCAGGGACCTAGG 60.689 66.667 7.41 7.41 0.00 3.02
1407 1542 3.555547 TCCACATCGTTTGCATCTTATCG 59.444 43.478 0.00 0.00 0.00 2.92
1496 2046 7.924947 CACTCTGAGCAGTTCTTGATAATATCA 59.075 37.037 4.19 0.00 37.55 2.15
1536 2086 4.548726 GCAAATTGCTTCAAGTGTTTGACG 60.549 41.667 11.19 0.00 40.96 4.35
1537 2087 4.630894 AATTGCTTCAAGTGTTTGACGA 57.369 36.364 0.00 0.00 42.79 4.20
1538 2088 3.398954 TTGCTTCAAGTGTTTGACGAC 57.601 42.857 0.00 0.00 42.79 4.34
1588 2141 2.758089 CGTCCTTGCTGCTGGATGC 61.758 63.158 16.85 7.00 43.25 3.91
1590 2143 1.378119 TCCTTGCTGCTGGATGCTG 60.378 57.895 10.08 0.00 43.37 4.41
1619 2172 2.433868 TACTCTTGGCGTGTGTCTTC 57.566 50.000 0.00 0.00 0.00 2.87
1642 2195 7.364522 TCACAGTGTAAGTTCATTATTCTGC 57.635 36.000 0.00 0.00 33.82 4.26
1644 2197 7.661437 TCACAGTGTAAGTTCATTATTCTGCTT 59.339 33.333 0.00 0.00 33.82 3.91
1679 2232 3.370366 TGTTTTGCATTTGACAAGTGTGC 59.630 39.130 11.77 12.24 36.39 4.57
1681 2234 0.030504 TGCATTTGACAAGTGTGCCG 59.969 50.000 11.77 0.00 35.03 5.69
1699 2252 8.021396 AGTGTGCCGTCTTATTAAAAATTTCTC 58.979 33.333 0.00 0.00 0.00 2.87
1773 2328 6.263168 GCAAATCCTGGTAAGCTATGTACATT 59.737 38.462 14.77 0.00 0.00 2.71
1849 2404 7.044052 GCAATTGTTTTACTCACTGTCAGTTTC 60.044 37.037 1.67 0.00 0.00 2.78
1880 2435 2.867109 AGGACAACCTGACAGATTGG 57.133 50.000 14.22 0.00 45.92 3.16
1906 2461 9.952341 GTTTCAAGTTTTGTTTCTACAATTCAC 57.048 29.630 0.00 0.00 43.43 3.18
1908 2463 9.921637 TTCAAGTTTTGTTTCTACAATTCACTT 57.078 25.926 0.00 0.00 43.43 3.16
1959 2514 0.962356 AAGAGGCAAGGAATGTGCGG 60.962 55.000 0.00 0.00 43.18 5.69
2050 2605 7.500227 CCCACATGCTAGAAAAATCATCTTAGA 59.500 37.037 0.00 0.00 0.00 2.10
2051 2606 8.557864 CCACATGCTAGAAAAATCATCTTAGAG 58.442 37.037 0.00 0.00 0.00 2.43
2052 2607 9.107177 CACATGCTAGAAAAATCATCTTAGAGT 57.893 33.333 0.00 0.00 0.00 3.24
2093 2649 3.865164 GTCTGATTGTATCGACATGCACA 59.135 43.478 0.00 0.00 34.86 4.57
2094 2650 4.329801 GTCTGATTGTATCGACATGCACAA 59.670 41.667 0.00 0.00 34.86 3.33
2154 2710 3.748083 GCATCAGATTGCTATCCCTTCA 58.252 45.455 4.43 0.00 39.57 3.02
2178 2734 8.573035 TCATTATTTGACCAAGTTGTTACTTCC 58.427 33.333 1.45 0.00 42.67 3.46
2185 2741 5.127491 ACCAAGTTGTTACTTCCGAATTCA 58.873 37.500 6.22 0.00 42.67 2.57
2186 2742 5.591067 ACCAAGTTGTTACTTCCGAATTCAA 59.409 36.000 6.22 0.00 42.67 2.69
2192 2748 7.876068 AGTTGTTACTTCCGAATTCAATGACTA 59.124 33.333 6.22 0.00 0.00 2.59
2283 2839 6.380079 AGTTTGTTATCCTCCTCAATCACT 57.620 37.500 0.00 0.00 0.00 3.41
2294 2850 3.144506 CCTCAATCACTGTGAGCAAGTT 58.855 45.455 16.46 2.27 41.04 2.66
2325 2881 0.176910 TCCACTGACGTTCTTGTGCA 59.823 50.000 0.00 0.00 0.00 4.57
2475 3031 8.258850 TCTCTTTCCTTTGGAGAAGTAGTAAA 57.741 34.615 0.00 0.00 33.82 2.01
2476 3032 8.148999 TCTCTTTCCTTTGGAGAAGTAGTAAAC 58.851 37.037 0.00 0.00 33.82 2.01
2498 3054 4.813161 ACTGAACATGTATATCAGCACAGC 59.187 41.667 20.88 0.00 43.41 4.40
2499 3055 4.768583 TGAACATGTATATCAGCACAGCA 58.231 39.130 0.00 0.00 0.00 4.41
2500 3056 4.812626 TGAACATGTATATCAGCACAGCAG 59.187 41.667 0.00 0.00 0.00 4.24
2513 3069 2.847441 CACAGCAGACATGATAGGCAT 58.153 47.619 0.00 0.00 37.85 4.40
2562 3118 4.657013 TCCACACATTTGCTACCATAACA 58.343 39.130 0.00 0.00 0.00 2.41
2563 3119 4.699735 TCCACACATTTGCTACCATAACAG 59.300 41.667 0.00 0.00 0.00 3.16
2566 3122 6.150307 CCACACATTTGCTACCATAACAGTTA 59.850 38.462 0.00 0.00 0.00 2.24
2583 3139 5.615289 ACAGTTATAATCAGACAGGGCATC 58.385 41.667 0.00 0.00 0.00 3.91
2586 3142 5.604231 AGTTATAATCAGACAGGGCATCTCA 59.396 40.000 0.00 0.00 0.00 3.27
2595 3151 2.494870 ACAGGGCATCTCATTTTTCAGC 59.505 45.455 0.00 0.00 0.00 4.26
2607 3163 3.665745 TTTTTCAGCTGGATGAAAGCC 57.334 42.857 15.13 0.00 46.70 4.35
2617 3173 1.541588 GGATGAAAGCCGCAAAGTTCT 59.458 47.619 0.00 0.00 24.31 3.01
2727 3283 3.262915 AGTTCACCTCCTTCTTCATCCTG 59.737 47.826 0.00 0.00 0.00 3.86
2739 3295 1.600636 CATCCTGGTGTGCACGGTT 60.601 57.895 13.13 0.00 0.00 4.44
2792 3348 2.750888 GGTAAAGGCTCGCGCAAGG 61.751 63.158 8.75 0.00 38.10 3.61
2917 3475 6.338146 TCAAGCGCTTGACTACTGTATTTAT 58.662 36.000 41.19 4.47 43.90 1.40
2977 3535 2.279851 TGCTGAACCGGTCGTGTG 60.280 61.111 8.04 0.00 0.00 3.82
2998 3556 2.385013 AGCATATATGATTCGGCGCA 57.615 45.000 17.10 0.00 0.00 6.09
3005 3563 1.382522 ATGATTCGGCGCAGTTGATT 58.617 45.000 10.83 0.00 0.00 2.57
3030 3588 3.181516 CGCAAAGCAGTCTTTCTATGGTC 60.182 47.826 0.00 0.00 40.35 4.02
3037 3595 4.566004 CAGTCTTTCTATGGTCGGTTTGA 58.434 43.478 0.00 0.00 0.00 2.69
3049 3607 2.020720 TCGGTTTGACACTTGTGCATT 58.979 42.857 0.10 0.00 0.00 3.56
3065 3623 2.094906 TGCATTCAGAATCTGCACTTGC 60.095 45.455 5.18 11.44 40.75 4.01
3103 3661 7.121382 ACTATTGGATGGAATGAAGTGACAAT 58.879 34.615 0.00 0.00 0.00 2.71
3136 3694 0.681175 GGTTGCACCTGAAGCCAAAT 59.319 50.000 0.00 0.00 34.73 2.32
3174 3732 4.875536 GTGCCTCAATTCTTTGGTTGTTTT 59.124 37.500 0.00 0.00 33.44 2.43
3281 3852 1.564818 TGGTTGTTTGTGGGTGGTCTA 59.435 47.619 0.00 0.00 0.00 2.59
3311 3882 4.021016 ACTTGATAGAAGCAACGGTCTCTT 60.021 41.667 0.00 0.00 0.00 2.85
3376 3947 4.974591 ACTGCTAAAATAAGAAGCGCAAG 58.025 39.130 11.47 0.00 39.14 4.01
3410 3981 1.821753 AGGTCTCTCGTTGTCCATCAG 59.178 52.381 0.00 0.00 0.00 2.90
3423 3994 2.093973 GTCCATCAGTCCATCTGTTCGT 60.094 50.000 0.00 0.00 43.97 3.85
3453 4024 3.359033 TCATCATTTGGAAAGCTCCCTG 58.641 45.455 6.66 0.00 41.64 4.45
3456 4027 2.108075 TCATTTGGAAAGCTCCCTGACA 59.892 45.455 6.66 0.00 41.64 3.58
3474 4045 4.133820 TGACACCAGGAAATTGTGTACTG 58.866 43.478 0.00 0.00 42.89 2.74
3477 4048 3.189287 CACCAGGAAATTGTGTACTGCTC 59.811 47.826 0.00 0.00 0.00 4.26
3479 4050 2.749621 CAGGAAATTGTGTACTGCTCCC 59.250 50.000 0.00 0.00 0.00 4.30
3491 4062 0.674895 CTGCTCCCTCCGTCCAAAAG 60.675 60.000 0.00 0.00 0.00 2.27
3492 4063 1.375326 GCTCCCTCCGTCCAAAAGT 59.625 57.895 0.00 0.00 0.00 2.66
3528 4100 5.126061 CACTTATTTTGGAATGGAGGGAGTG 59.874 44.000 0.00 0.00 0.00 3.51
3531 4103 0.329261 TTGGAATGGAGGGAGTGCTG 59.671 55.000 0.00 0.00 0.00 4.41
3534 4106 0.106819 GAATGGAGGGAGTGCTGCAT 60.107 55.000 5.27 0.00 33.09 3.96
3536 4108 1.442773 ATGGAGGGAGTGCTGCATAT 58.557 50.000 5.27 0.00 29.97 1.78
3582 4154 7.621428 CAGATTCTCTGCCTTCATTAAGAAA 57.379 36.000 0.00 0.00 37.72 2.52
3608 4180 7.735326 AAAGAGGGAGTACTACACATACATT 57.265 36.000 7.57 0.00 0.00 2.71
3610 4182 9.435570 AAAGAGGGAGTACTACACATACATTAT 57.564 33.333 7.57 0.00 0.00 1.28
3657 4229 4.789807 AGCATATGAATCATGGATAGGCC 58.210 43.478 6.97 0.00 31.32 5.19
3670 4242 8.727100 TCATGGATAGGCCGAAATATCTATAT 57.273 34.615 7.88 0.00 40.66 0.86
3671 4243 8.588472 TCATGGATAGGCCGAAATATCTATATG 58.412 37.037 7.88 10.01 40.66 1.78
3672 4244 6.759272 TGGATAGGCCGAAATATCTATATGC 58.241 40.000 9.03 0.00 40.66 3.14
3673 4245 6.554982 TGGATAGGCCGAAATATCTATATGCT 59.445 38.462 9.03 0.00 40.66 3.79
3674 4246 6.870965 GGATAGGCCGAAATATCTATATGCTG 59.129 42.308 9.03 0.00 0.00 4.41
3675 4247 5.028549 AGGCCGAAATATCTATATGCTGG 57.971 43.478 0.00 0.00 0.00 4.85
3676 4248 4.130118 GGCCGAAATATCTATATGCTGGG 58.870 47.826 0.00 0.00 0.00 4.45
3677 4249 4.141711 GGCCGAAATATCTATATGCTGGGA 60.142 45.833 0.00 0.00 0.00 4.37
3678 4250 4.811557 GCCGAAATATCTATATGCTGGGAC 59.188 45.833 0.00 0.00 0.00 4.46
3679 4251 5.395768 GCCGAAATATCTATATGCTGGGACT 60.396 44.000 0.00 0.00 0.00 3.85
3680 4252 6.276847 CCGAAATATCTATATGCTGGGACTC 58.723 44.000 0.00 0.00 0.00 3.36
3681 4253 6.097554 CCGAAATATCTATATGCTGGGACTCT 59.902 42.308 0.00 0.00 0.00 3.24
3682 4254 6.977502 CGAAATATCTATATGCTGGGACTCTG 59.022 42.308 0.00 0.00 0.00 3.35
3683 4255 6.805016 AATATCTATATGCTGGGACTCTGG 57.195 41.667 0.00 0.00 0.00 3.86
3684 4256 3.903530 TCTATATGCTGGGACTCTGGA 57.096 47.619 0.00 0.00 0.00 3.86
3685 4257 4.199002 TCTATATGCTGGGACTCTGGAA 57.801 45.455 0.00 0.00 0.00 3.53
3686 4258 4.155709 TCTATATGCTGGGACTCTGGAAG 58.844 47.826 0.00 0.00 0.00 3.46
3687 4259 0.833287 TATGCTGGGACTCTGGAAGC 59.167 55.000 0.00 0.00 0.00 3.86
3688 4260 0.913451 ATGCTGGGACTCTGGAAGCT 60.913 55.000 0.00 0.00 34.92 3.74
3689 4261 0.252239 TGCTGGGACTCTGGAAGCTA 60.252 55.000 0.00 0.00 34.92 3.32
3690 4262 0.905357 GCTGGGACTCTGGAAGCTAA 59.095 55.000 0.00 0.00 0.00 3.09
3691 4263 1.134551 GCTGGGACTCTGGAAGCTAAG 60.135 57.143 0.00 0.00 0.00 2.18
3692 4264 2.461695 CTGGGACTCTGGAAGCTAAGA 58.538 52.381 0.00 0.00 0.00 2.10
3693 4265 2.167487 CTGGGACTCTGGAAGCTAAGAC 59.833 54.545 0.00 0.00 0.00 3.01
3694 4266 2.225394 TGGGACTCTGGAAGCTAAGACT 60.225 50.000 0.00 0.00 0.00 3.24
3695 4267 2.167487 GGGACTCTGGAAGCTAAGACTG 59.833 54.545 0.00 0.00 0.00 3.51
3696 4268 2.167487 GGACTCTGGAAGCTAAGACTGG 59.833 54.545 0.00 0.00 0.00 4.00
3697 4269 2.829120 GACTCTGGAAGCTAAGACTGGT 59.171 50.000 0.00 0.00 0.00 4.00
3698 4270 3.243724 ACTCTGGAAGCTAAGACTGGTT 58.756 45.455 0.00 0.00 0.00 3.67
3699 4271 3.648545 ACTCTGGAAGCTAAGACTGGTTT 59.351 43.478 0.00 0.00 0.00 3.27
3700 4272 4.103311 ACTCTGGAAGCTAAGACTGGTTTT 59.897 41.667 0.00 0.00 0.00 2.43
3701 4273 5.048846 TCTGGAAGCTAAGACTGGTTTTT 57.951 39.130 0.00 0.00 0.00 1.94
3702 4274 5.063880 TCTGGAAGCTAAGACTGGTTTTTC 58.936 41.667 0.00 0.00 0.00 2.29
3703 4275 4.787551 TGGAAGCTAAGACTGGTTTTTCA 58.212 39.130 0.00 0.00 0.00 2.69
3704 4276 4.578928 TGGAAGCTAAGACTGGTTTTTCAC 59.421 41.667 0.00 0.00 0.00 3.18
3706 4278 3.487372 AGCTAAGACTGGTTTTTCACCC 58.513 45.455 0.00 0.00 46.68 4.61
3707 4279 2.225727 GCTAAGACTGGTTTTTCACCCG 59.774 50.000 0.00 0.00 46.68 5.28
3708 4280 1.687563 AAGACTGGTTTTTCACCCGG 58.312 50.000 0.00 0.00 46.68 5.73
3709 4281 0.841289 AGACTGGTTTTTCACCCGGA 59.159 50.000 0.73 0.00 46.68 5.14
3710 4282 1.213430 AGACTGGTTTTTCACCCGGAA 59.787 47.619 0.73 0.00 46.68 4.30
3711 4283 2.025898 GACTGGTTTTTCACCCGGAAA 58.974 47.619 0.73 0.00 46.68 3.13
3721 4293 5.883503 TTTCACCCGGAAAATGTGTATAC 57.116 39.130 0.73 0.00 42.37 1.47
3722 4294 3.523547 TCACCCGGAAAATGTGTATACG 58.476 45.455 0.73 0.00 0.00 3.06
3723 4295 3.055963 TCACCCGGAAAATGTGTATACGT 60.056 43.478 0.73 0.00 0.00 3.57
3724 4296 4.159321 TCACCCGGAAAATGTGTATACGTA 59.841 41.667 0.73 0.00 0.00 3.57
3725 4297 4.869297 CACCCGGAAAATGTGTATACGTAA 59.131 41.667 0.73 0.00 0.00 3.18
3726 4298 4.869861 ACCCGGAAAATGTGTATACGTAAC 59.130 41.667 0.73 0.11 0.00 2.50
3727 4299 5.111293 CCCGGAAAATGTGTATACGTAACT 58.889 41.667 0.73 0.00 0.00 2.24
3728 4300 5.232838 CCCGGAAAATGTGTATACGTAACTC 59.767 44.000 0.73 1.67 0.00 3.01
3729 4301 6.038356 CCGGAAAATGTGTATACGTAACTCT 58.962 40.000 0.00 0.00 0.00 3.24
3730 4302 7.195646 CCGGAAAATGTGTATACGTAACTCTA 58.804 38.462 0.00 0.00 0.00 2.43
3731 4303 7.166473 CCGGAAAATGTGTATACGTAACTCTAC 59.834 40.741 0.00 0.00 0.00 2.59
3744 4316 2.150397 ACTCTACGAGTTGTGGTTGC 57.850 50.000 0.00 0.00 40.28 4.17
3745 4317 1.270147 ACTCTACGAGTTGTGGTTGCC 60.270 52.381 0.00 0.00 40.28 4.52
3746 4318 0.753867 TCTACGAGTTGTGGTTGCCA 59.246 50.000 0.00 0.00 0.00 4.92
3747 4319 1.139256 TCTACGAGTTGTGGTTGCCAA 59.861 47.619 0.00 0.00 34.18 4.52
3748 4320 1.263217 CTACGAGTTGTGGTTGCCAAC 59.737 52.381 0.00 0.00 41.94 3.77
3749 4321 0.678366 ACGAGTTGTGGTTGCCAACA 60.678 50.000 10.18 0.00 43.61 3.33
3750 4322 0.453793 CGAGTTGTGGTTGCCAACAA 59.546 50.000 10.18 0.00 43.61 2.83
3751 4323 1.066908 CGAGTTGTGGTTGCCAACAAT 59.933 47.619 10.18 0.00 43.61 2.71
3752 4324 2.292016 CGAGTTGTGGTTGCCAACAATA 59.708 45.455 10.18 0.00 43.61 1.90
3753 4325 3.057596 CGAGTTGTGGTTGCCAACAATAT 60.058 43.478 10.18 0.00 43.61 1.28
3754 4326 4.155099 CGAGTTGTGGTTGCCAACAATATA 59.845 41.667 10.18 0.00 43.61 0.86
3755 4327 5.163663 CGAGTTGTGGTTGCCAACAATATAT 60.164 40.000 10.18 0.00 43.61 0.86
3756 4328 6.603940 AGTTGTGGTTGCCAACAATATATT 57.396 33.333 10.18 0.00 43.61 1.28
3757 4329 7.003402 AGTTGTGGTTGCCAACAATATATTT 57.997 32.000 10.18 0.00 43.61 1.40
3758 4330 6.873076 AGTTGTGGTTGCCAACAATATATTTG 59.127 34.615 10.18 0.00 43.61 2.32
3759 4331 5.174395 TGTGGTTGCCAACAATATATTTGC 58.826 37.500 10.18 0.00 38.27 3.68
3760 4332 5.046735 TGTGGTTGCCAACAATATATTTGCT 60.047 36.000 10.18 0.00 38.27 3.91
3761 4333 6.153510 TGTGGTTGCCAACAATATATTTGCTA 59.846 34.615 10.18 0.00 38.27 3.49
3762 4334 7.038659 GTGGTTGCCAACAATATATTTGCTAA 58.961 34.615 10.18 0.00 38.27 3.09
3763 4335 7.710475 GTGGTTGCCAACAATATATTTGCTAAT 59.290 33.333 10.18 0.00 38.27 1.73
3764 4336 8.918116 TGGTTGCCAACAATATATTTGCTAATA 58.082 29.630 10.18 3.06 38.27 0.98
3765 4337 9.191995 GGTTGCCAACAATATATTTGCTAATAC 57.808 33.333 10.18 0.00 38.27 1.89
3766 4338 9.743057 GTTGCCAACAATATATTTGCTAATACA 57.257 29.630 1.91 0.00 38.27 2.29
3767 4339 9.964303 TTGCCAACAATATATTTGCTAATACAG 57.036 29.630 2.62 0.00 0.00 2.74
3768 4340 9.348476 TGCCAACAATATATTTGCTAATACAGA 57.652 29.630 2.62 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.143376 TGGGACTGTTAAACACTACTAGC 57.857 43.478 0.00 0.00 0.00 3.42
1 2 6.070995 TCCATGGGACTGTTAAACACTACTAG 60.071 42.308 13.02 0.00 0.00 2.57
5 6 5.163184 TGTTCCATGGGACTGTTAAACACTA 60.163 40.000 24.02 0.00 0.00 2.74
6 7 4.142038 GTTCCATGGGACTGTTAAACACT 58.858 43.478 16.69 0.00 0.00 3.55
7 8 3.886505 TGTTCCATGGGACTGTTAAACAC 59.113 43.478 24.02 0.00 0.00 3.32
8 9 4.141287 CTGTTCCATGGGACTGTTAAACA 58.859 43.478 24.02 16.18 0.00 2.83
9 10 3.506067 CCTGTTCCATGGGACTGTTAAAC 59.494 47.826 24.02 12.52 0.00 2.01
10 11 3.761897 CCTGTTCCATGGGACTGTTAAA 58.238 45.455 24.02 1.41 0.00 1.52
13 14 0.251341 GCCTGTTCCATGGGACTGTT 60.251 55.000 24.02 0.00 0.00 3.16
33 34 4.482990 TGATGATAGGTGATAGCTGGTCA 58.517 43.478 0.00 0.00 0.00 4.02
36 37 7.147602 TGGAATATGATGATAGGTGATAGCTGG 60.148 40.741 0.00 0.00 0.00 4.85
57 58 3.456380 AGTGGTTGTGGCTTATGGAAT 57.544 42.857 0.00 0.00 0.00 3.01
58 59 2.969821 AGTGGTTGTGGCTTATGGAA 57.030 45.000 0.00 0.00 0.00 3.53
87 88 2.278854 TCGATGATGCGCTCAAATTGA 58.721 42.857 9.73 3.94 37.44 2.57
135 136 1.897560 AACTGGGAAGCAACTGTAGC 58.102 50.000 0.00 0.00 0.00 3.58
176 177 6.035843 CCACCATTTCCGTCTGAATTTATTG 58.964 40.000 0.00 0.00 31.67 1.90
192 193 1.304381 ATCCGTGCTGCCACCATTT 60.304 52.632 0.00 0.00 38.79 2.32
226 227 6.481984 GCAGAAAGTCATATGTTCTAGTTGC 58.518 40.000 1.90 9.05 30.50 4.17
238 242 7.097192 GGATTGGATATACGCAGAAAGTCATA 58.903 38.462 0.00 0.00 0.00 2.15
239 243 5.934625 GGATTGGATATACGCAGAAAGTCAT 59.065 40.000 0.00 0.00 0.00 3.06
241 245 5.297547 TGGATTGGATATACGCAGAAAGTC 58.702 41.667 0.00 0.00 0.00 3.01
242 246 5.290493 TGGATTGGATATACGCAGAAAGT 57.710 39.130 0.00 0.00 0.00 2.66
243 247 6.293626 CCTTTGGATTGGATATACGCAGAAAG 60.294 42.308 0.00 0.00 0.00 2.62
244 248 5.530915 CCTTTGGATTGGATATACGCAGAAA 59.469 40.000 0.00 0.00 0.00 2.52
245 249 5.063204 CCTTTGGATTGGATATACGCAGAA 58.937 41.667 0.00 0.00 0.00 3.02
246 250 4.504864 CCCTTTGGATTGGATATACGCAGA 60.505 45.833 0.00 0.00 0.00 4.26
278 300 9.634021 ACAGATAGATAGATATATTCTTGCCGA 57.366 33.333 0.00 0.00 35.79 5.54
312 338 1.404391 CTGCCCTTGATGTGATTGCTC 59.596 52.381 0.00 0.00 0.00 4.26
333 360 4.357142 CCACGCGCTCTAAAGATTTACTA 58.643 43.478 5.73 0.00 0.00 1.82
336 363 1.931172 GCCACGCGCTCTAAAGATTTA 59.069 47.619 5.73 0.00 0.00 1.40
338 368 0.391130 TGCCACGCGCTCTAAAGATT 60.391 50.000 5.73 0.00 38.78 2.40
341 371 0.447801 AAATGCCACGCGCTCTAAAG 59.552 50.000 5.73 0.00 38.78 1.85
345 375 2.358615 TCAAATGCCACGCGCTCT 60.359 55.556 5.73 0.00 38.78 4.09
349 383 0.447406 TCAATCTCAAATGCCACGCG 59.553 50.000 3.53 3.53 0.00 6.01
368 402 0.824759 GGTACATCCTTCCTCACGCT 59.175 55.000 0.00 0.00 0.00 5.07
380 414 0.589229 CGTCACGCTCGAGGTACATC 60.589 60.000 15.58 0.00 0.00 3.06
381 415 1.022982 TCGTCACGCTCGAGGTACAT 61.023 55.000 15.58 0.00 33.38 2.29
382 416 1.668793 TCGTCACGCTCGAGGTACA 60.669 57.895 15.58 0.00 33.38 2.90
474 529 1.799519 CTCTCTGTCGTCGCTGTGC 60.800 63.158 0.00 0.00 0.00 4.57
475 530 0.449786 ATCTCTCTGTCGTCGCTGTG 59.550 55.000 0.00 0.00 0.00 3.66
476 531 1.937223 CTATCTCTCTGTCGTCGCTGT 59.063 52.381 0.00 0.00 0.00 4.40
479 534 2.803386 TCATCTATCTCTCTGTCGTCGC 59.197 50.000 0.00 0.00 0.00 5.19
484 539 4.984161 GCTTTGCTCATCTATCTCTCTGTC 59.016 45.833 0.00 0.00 0.00 3.51
485 540 4.202243 GGCTTTGCTCATCTATCTCTCTGT 60.202 45.833 0.00 0.00 0.00 3.41
486 541 4.309099 GGCTTTGCTCATCTATCTCTCTG 58.691 47.826 0.00 0.00 0.00 3.35
487 542 3.005684 CGGCTTTGCTCATCTATCTCTCT 59.994 47.826 0.00 0.00 0.00 3.10
488 543 3.316283 CGGCTTTGCTCATCTATCTCTC 58.684 50.000 0.00 0.00 0.00 3.20
494 549 1.521457 CGCCGGCTTTGCTCATCTA 60.521 57.895 26.68 0.00 0.00 1.98
560 615 2.146061 CCTCATCCTCCCTGCCTCC 61.146 68.421 0.00 0.00 0.00 4.30
565 620 3.174265 GGGCCCTCATCCTCCCTG 61.174 72.222 17.04 0.00 35.87 4.45
570 625 1.338136 CGTAAGTGGGCCCTCATCCT 61.338 60.000 25.70 8.00 0.00 3.24
571 626 1.146263 CGTAAGTGGGCCCTCATCC 59.854 63.158 25.70 9.80 0.00 3.51
572 627 4.857251 CGTAAGTGGGCCCTCATC 57.143 61.111 25.70 12.48 0.00 2.92
690 745 3.855853 GGCGAAGAGGAGGGAGGC 61.856 72.222 0.00 0.00 0.00 4.70
691 746 2.042435 AGGCGAAGAGGAGGGAGG 60.042 66.667 0.00 0.00 0.00 4.30
692 747 1.076339 AGAGGCGAAGAGGAGGGAG 60.076 63.158 0.00 0.00 0.00 4.30
693 748 1.076632 GAGAGGCGAAGAGGAGGGA 60.077 63.158 0.00 0.00 0.00 4.20
696 751 3.115556 CGGAGAGGCGAAGAGGAG 58.884 66.667 0.00 0.00 0.00 3.69
697 752 3.141488 GCGGAGAGGCGAAGAGGA 61.141 66.667 0.00 0.00 0.00 3.71
721 786 0.318955 CTTGGGCTTTTGGAACAGCG 60.319 55.000 0.00 0.00 42.39 5.18
722 787 0.601046 GCTTGGGCTTTTGGAACAGC 60.601 55.000 0.00 0.00 35.74 4.40
725 790 1.869774 CTTGCTTGGGCTTTTGGAAC 58.130 50.000 0.00 0.00 39.59 3.62
726 791 0.106521 GCTTGCTTGGGCTTTTGGAA 59.893 50.000 0.00 0.00 39.59 3.53
740 805 1.005748 GCTGAAGGGGTTTGCTTGC 60.006 57.895 0.00 0.00 0.00 4.01
744 809 2.997315 GGGGCTGAAGGGGTTTGC 60.997 66.667 0.00 0.00 0.00 3.68
749 814 2.770048 ATCTCGGGGCTGAAGGGG 60.770 66.667 0.00 0.00 0.00 4.79
750 815 1.753368 GAGATCTCGGGGCTGAAGGG 61.753 65.000 7.04 0.00 0.00 3.95
751 816 0.758685 AGAGATCTCGGGGCTGAAGG 60.759 60.000 16.97 0.00 34.09 3.46
752 817 1.118838 AAGAGATCTCGGGGCTGAAG 58.881 55.000 16.97 0.00 34.09 3.02
753 818 0.826715 CAAGAGATCTCGGGGCTGAA 59.173 55.000 16.97 0.00 34.09 3.02
754 819 1.680522 GCAAGAGATCTCGGGGCTGA 61.681 60.000 21.45 0.00 34.09 4.26
755 820 1.227497 GCAAGAGATCTCGGGGCTG 60.227 63.158 21.45 14.39 34.09 4.85
756 821 2.439104 GGCAAGAGATCTCGGGGCT 61.439 63.158 25.50 5.92 33.05 5.19
757 822 2.110006 GGCAAGAGATCTCGGGGC 59.890 66.667 21.23 21.23 34.09 5.80
769 835 4.424711 TTGGGGCGCTAGGGCAAG 62.425 66.667 30.16 0.00 44.56 4.01
783 849 1.747774 CTTGGTGGGCTTTGGTTGG 59.252 57.895 0.00 0.00 0.00 3.77
820 923 4.418328 CGGCCGGATTTGGTGGGA 62.418 66.667 20.10 0.00 0.00 4.37
868 971 4.477975 GACCGACCGAGCGACCTG 62.478 72.222 0.00 0.00 0.00 4.00
875 998 0.961358 AACTCCTCTGACCGACCGAG 60.961 60.000 0.00 0.00 0.00 4.63
949 1073 4.452733 GAGTCTTCCCGGCGGTGG 62.453 72.222 26.32 10.85 0.00 4.61
950 1074 4.796231 CGAGTCTTCCCGGCGGTG 62.796 72.222 26.32 16.42 0.00 4.94
1021 1145 1.506025 GGCAGGAAGAGAGATCCCTT 58.494 55.000 0.00 0.00 37.71 3.95
1029 1153 2.683933 GTCGGGGGCAGGAAGAGA 60.684 66.667 0.00 0.00 0.00 3.10
1050 1174 1.128188 ATCACCCGGGGAATAGGAGC 61.128 60.000 27.92 0.00 0.00 4.70
1065 1189 4.933064 CGAGCTCGGCCCGATCAC 62.933 72.222 28.40 0.00 34.61 3.06
1136 1263 1.813753 CGTCAATTCGCGACCCCAT 60.814 57.895 9.15 0.00 0.00 4.00
1170 1297 1.714899 CGCACCAACCAATCGGATCC 61.715 60.000 0.00 0.00 35.59 3.36
1223 1351 0.816825 TACCTACCTACGCAGAGCCG 60.817 60.000 0.00 0.00 0.00 5.52
1231 1359 2.028130 CCCACGCTACCTACCTACG 58.972 63.158 0.00 0.00 0.00 3.51
1232 1360 1.738432 GCCCACGCTACCTACCTAC 59.262 63.158 0.00 0.00 0.00 3.18
1235 1363 3.135056 CTCGCCCACGCTACCTACC 62.135 68.421 0.00 0.00 39.84 3.18
1258 1386 0.958822 ACTGATTTTTGTCCCCGTGC 59.041 50.000 0.00 0.00 0.00 5.34
1260 1388 0.958822 GCACTGATTTTTGTCCCCGT 59.041 50.000 0.00 0.00 0.00 5.28
1261 1389 0.958091 TGCACTGATTTTTGTCCCCG 59.042 50.000 0.00 0.00 0.00 5.73
1262 1390 1.335872 CGTGCACTGATTTTTGTCCCC 60.336 52.381 16.19 0.00 0.00 4.81
1264 1392 1.930371 GCCGTGCACTGATTTTTGTCC 60.930 52.381 16.19 0.00 0.00 4.02
1265 1393 1.408422 GCCGTGCACTGATTTTTGTC 58.592 50.000 16.19 0.00 0.00 3.18
1266 1394 0.031994 GGCCGTGCACTGATTTTTGT 59.968 50.000 16.19 0.00 0.00 2.83
1267 1395 0.314935 AGGCCGTGCACTGATTTTTG 59.685 50.000 16.19 0.00 0.00 2.44
1268 1396 0.314935 CAGGCCGTGCACTGATTTTT 59.685 50.000 16.19 0.00 36.86 1.94
1269 1397 0.537143 TCAGGCCGTGCACTGATTTT 60.537 50.000 16.19 0.00 38.71 1.82
1272 1400 2.993008 ATCAGGCCGTGCACTGAT 59.007 55.556 16.19 13.91 46.31 2.90
1273 1401 0.537143 AAAATCAGGCCGTGCACTGA 60.537 50.000 16.19 12.09 46.62 3.41
1274 1402 0.387622 CAAAATCAGGCCGTGCACTG 60.388 55.000 16.19 9.93 36.07 3.66
1276 1404 1.734117 GCAAAATCAGGCCGTGCAC 60.734 57.895 6.82 6.82 35.28 4.57
1277 1405 2.650196 GCAAAATCAGGCCGTGCA 59.350 55.556 0.00 0.00 35.28 4.57
1285 1413 3.349927 TGATCTGACTGGGCAAAATCAG 58.650 45.455 0.00 0.00 39.99 2.90
1295 1423 0.390866 AAGCGCACTGATCTGACTGG 60.391 55.000 11.47 0.00 0.00 4.00
1335 1466 4.341783 GTCCCTGGCAGCACAGCT 62.342 66.667 9.56 0.00 40.77 4.24
1351 1482 0.470766 TGTTCCACGCAAACCTAGGT 59.529 50.000 9.21 9.21 0.00 3.08
1357 1488 3.039134 CCCCTGTTCCACGCAAAC 58.961 61.111 0.00 0.00 0.00 2.93
1407 1542 4.914983 TCATGAGAATGGATAAGCCCATC 58.085 43.478 0.00 0.00 45.69 3.51
1511 2061 4.934001 TCAAACACTTGAAGCAATTTGCAA 59.066 33.333 22.55 8.11 40.29 4.08
1536 2086 3.714391 ACGAGGAACACACAAGTTAGTC 58.286 45.455 0.00 0.00 0.00 2.59
1537 2087 3.383825 AGACGAGGAACACACAAGTTAGT 59.616 43.478 0.00 0.00 0.00 2.24
1538 2088 3.736252 CAGACGAGGAACACACAAGTTAG 59.264 47.826 0.00 0.00 0.00 2.34
1588 2141 2.481952 GCCAAGAGTAAGTTGACAGCAG 59.518 50.000 0.00 0.00 0.00 4.24
1590 2143 1.461127 CGCCAAGAGTAAGTTGACAGC 59.539 52.381 0.00 0.00 0.00 4.40
1619 2172 7.369803 AGCAGAATAATGAACTTACACTGTG 57.630 36.000 6.19 6.19 32.79 3.66
1642 2195 7.951530 ATGCAAAACAATGGTTAAGAGAAAG 57.048 32.000 0.00 0.00 35.82 2.62
1644 2197 7.984050 TCAAATGCAAAACAATGGTTAAGAGAA 59.016 29.630 0.00 0.00 35.82 2.87
1699 2252 0.247736 AAGTCCAGCGAGCCTGTAAG 59.752 55.000 0.00 0.00 40.06 2.34
1773 2328 3.701205 TTCAGTGAGCTTTAGGCATGA 57.299 42.857 0.00 0.00 44.79 3.07
1849 2404 3.815401 CAGGTTGTCCTCAAAGTTACTGG 59.185 47.826 0.00 0.00 43.07 4.00
1906 2461 6.992123 TCACACAATAGAATACTGGGCATAAG 59.008 38.462 0.00 0.00 0.00 1.73
1908 2463 6.493189 TCACACAATAGAATACTGGGCATA 57.507 37.500 0.00 0.00 0.00 3.14
1956 2511 6.924060 ACTATGTCACAATATTACTCTTCCGC 59.076 38.462 0.00 0.00 0.00 5.54
1959 2514 9.319143 AGCAACTATGTCACAATATTACTCTTC 57.681 33.333 0.00 0.00 0.00 2.87
2050 2605 3.638160 ACCAATCTTTGTGTGCATCAACT 59.362 39.130 6.76 0.00 0.00 3.16
2051 2606 3.981211 ACCAATCTTTGTGTGCATCAAC 58.019 40.909 6.76 0.00 0.00 3.18
2052 2607 3.890756 AGACCAATCTTTGTGTGCATCAA 59.109 39.130 0.00 0.00 0.00 2.57
2145 2701 7.893302 ACAACTTGGTCAAATAATGAAGGGATA 59.107 33.333 0.00 0.00 40.50 2.59
2153 2709 7.537306 CGGAAGTAACAACTTGGTCAAATAATG 59.463 37.037 0.00 0.00 0.00 1.90
2154 2710 7.446013 TCGGAAGTAACAACTTGGTCAAATAAT 59.554 33.333 0.00 0.00 0.00 1.28
2185 2741 8.253113 CCTGCACCAAGAAAATAAATAGTCATT 58.747 33.333 0.00 0.00 0.00 2.57
2186 2742 7.631377 GCCTGCACCAAGAAAATAAATAGTCAT 60.631 37.037 0.00 0.00 0.00 3.06
2192 2748 4.888326 TGCCTGCACCAAGAAAATAAAT 57.112 36.364 0.00 0.00 0.00 1.40
2283 2839 0.819259 GCCACAGGAACTTGCTCACA 60.819 55.000 0.00 0.00 34.60 3.58
2441 2997 7.408543 TCTCCAAAGGAAAGAGAATCATCAAT 58.591 34.615 0.00 0.00 37.82 2.57
2475 3031 4.813161 GCTGTGCTGATATACATGTTCAGT 59.187 41.667 21.40 3.67 39.24 3.41
2476 3032 4.812626 TGCTGTGCTGATATACATGTTCAG 59.187 41.667 17.95 17.95 39.87 3.02
2491 3047 1.474677 GCCTATCATGTCTGCTGTGCT 60.475 52.381 0.00 0.00 0.00 4.40
2498 3054 4.011966 TGCCTAATGCCTATCATGTCTG 57.988 45.455 0.00 0.00 40.16 3.51
2499 3055 4.712051 TTGCCTAATGCCTATCATGTCT 57.288 40.909 0.00 0.00 40.16 3.41
2500 3056 5.005740 TGATTGCCTAATGCCTATCATGTC 58.994 41.667 0.00 0.00 40.16 3.06
2513 3069 4.640201 GCATCCTAAGTTGTGATTGCCTAA 59.360 41.667 0.00 0.00 0.00 2.69
2562 3118 5.604231 TGAGATGCCCTGTCTGATTATAACT 59.396 40.000 0.00 0.00 0.00 2.24
2563 3119 5.858381 TGAGATGCCCTGTCTGATTATAAC 58.142 41.667 0.00 0.00 0.00 1.89
2566 3122 5.579753 AATGAGATGCCCTGTCTGATTAT 57.420 39.130 0.00 0.00 29.58 1.28
2583 3139 4.863131 GCTTTCATCCAGCTGAAAAATGAG 59.137 41.667 17.39 8.73 42.78 2.90
2586 3142 3.367703 CGGCTTTCATCCAGCTGAAAAAT 60.368 43.478 17.39 0.00 45.27 1.82
2595 3151 0.883833 ACTTTGCGGCTTTCATCCAG 59.116 50.000 0.00 0.00 0.00 3.86
2607 3163 1.082104 GCCGGTCAAGAACTTTGCG 60.082 57.895 1.90 0.00 0.00 4.85
2610 3166 1.880027 GACATGCCGGTCAAGAACTTT 59.120 47.619 1.90 0.00 37.73 2.66
2649 3205 2.341543 CTCAGGATCGCCGGGATG 59.658 66.667 2.18 0.00 39.96 3.51
2727 3283 3.022287 CACAGAACCGTGCACACC 58.978 61.111 18.64 2.13 0.00 4.16
2917 3475 1.882912 ATCTCGGGTACGCGTATACA 58.117 50.000 28.41 10.86 40.69 2.29
2958 3516 2.279851 CACGACCGGTTCAGCACA 60.280 61.111 9.42 0.00 0.00 4.57
2977 3535 2.672874 TGCGCCGAATCATATATGCTTC 59.327 45.455 16.10 16.10 31.51 3.86
2998 3556 1.949525 ACTGCTTTGCGTCAATCAACT 59.050 42.857 0.00 0.00 0.00 3.16
3005 3563 1.953559 AGAAAGACTGCTTTGCGTCA 58.046 45.000 13.49 0.00 44.10 4.35
3011 3569 3.008049 ACCGACCATAGAAAGACTGCTTT 59.992 43.478 0.00 0.00 46.62 3.51
3030 3588 2.223456 TGAATGCACAAGTGTCAAACCG 60.223 45.455 1.79 0.00 0.00 4.44
3037 3595 3.057736 GCAGATTCTGAATGCACAAGTGT 60.058 43.478 17.87 0.00 39.75 3.55
3065 3623 7.279615 TCCATCCAATAGTTTGTACCATACTG 58.720 38.462 0.00 0.00 29.38 2.74
3068 3626 8.498575 TCATTCCATCCAATAGTTTGTACCATA 58.501 33.333 0.00 0.00 0.00 2.74
3118 3676 2.531522 AATTTGGCTTCAGGTGCAAC 57.468 45.000 0.00 0.00 0.00 4.17
3136 3694 2.813754 GAGGCACACATAACTGAGCAAA 59.186 45.455 0.00 0.00 0.00 3.68
3174 3732 7.572523 AAAATGTTCTCTGAAGATCACACAA 57.427 32.000 0.00 0.00 34.79 3.33
3281 3852 6.127310 ACCGTTGCTTCTATCAAGTTCTCTAT 60.127 38.462 0.00 0.00 0.00 1.98
3311 3882 1.002624 GGAGTTGGCAACGGATCCA 60.003 57.895 24.41 0.00 42.51 3.41
3351 3922 5.416083 TGCGCTTCTTATTTTAGCAGTAGA 58.584 37.500 9.73 0.00 34.62 2.59
3376 3947 6.744112 ACGAGAGACCTCTGAATAATTGATC 58.256 40.000 3.99 0.00 40.61 2.92
3410 3981 5.123502 TGAGAGTAACTACGAACAGATGGAC 59.876 44.000 0.00 0.00 0.00 4.02
3423 3994 7.624549 AGCTTTCCAAATGATGAGAGTAACTA 58.375 34.615 0.00 0.00 0.00 2.24
3453 4024 3.058224 GCAGTACACAATTTCCTGGTGTC 60.058 47.826 2.10 0.00 44.06 3.67
3456 4027 3.412386 GAGCAGTACACAATTTCCTGGT 58.588 45.455 0.00 0.00 36.65 4.00
3474 4045 0.611714 TACTTTTGGACGGAGGGAGC 59.388 55.000 0.00 0.00 0.00 4.70
3477 4048 2.224450 ACACTTACTTTTGGACGGAGGG 60.224 50.000 0.00 0.00 0.00 4.30
3479 4050 3.250040 CCAACACTTACTTTTGGACGGAG 59.750 47.826 0.00 0.00 42.17 4.63
3516 4088 1.216064 TATGCAGCACTCCCTCCATT 58.784 50.000 0.00 0.00 0.00 3.16
3518 4090 1.216064 AATATGCAGCACTCCCTCCA 58.784 50.000 0.00 0.00 0.00 3.86
3582 4154 7.549147 TGTATGTGTAGTACTCCCTCTTTTT 57.451 36.000 0.00 0.00 0.00 1.94
3587 4159 8.298140 GTGATAATGTATGTGTAGTACTCCCTC 58.702 40.741 0.00 0.00 0.00 4.30
3588 4160 8.005388 AGTGATAATGTATGTGTAGTACTCCCT 58.995 37.037 0.00 0.00 0.00 4.20
3608 4180 5.584253 GGCAACTTCTCAGAGTAGTGATA 57.416 43.478 10.28 0.00 0.00 2.15
3610 4182 3.944055 GGCAACTTCTCAGAGTAGTGA 57.056 47.619 10.28 0.00 0.00 3.41
3657 4229 6.977502 CAGAGTCCCAGCATATAGATATTTCG 59.022 42.308 0.00 0.00 0.00 3.46
3670 4242 0.252239 TAGCTTCCAGAGTCCCAGCA 60.252 55.000 0.00 0.00 32.58 4.41
3671 4243 0.905357 TTAGCTTCCAGAGTCCCAGC 59.095 55.000 0.00 0.00 0.00 4.85
3672 4244 2.167487 GTCTTAGCTTCCAGAGTCCCAG 59.833 54.545 0.00 0.00 0.00 4.45
3673 4245 2.180276 GTCTTAGCTTCCAGAGTCCCA 58.820 52.381 0.00 0.00 0.00 4.37
3674 4246 2.167487 CAGTCTTAGCTTCCAGAGTCCC 59.833 54.545 0.00 0.00 0.00 4.46
3675 4247 2.167487 CCAGTCTTAGCTTCCAGAGTCC 59.833 54.545 0.00 0.00 0.00 3.85
3676 4248 2.829120 ACCAGTCTTAGCTTCCAGAGTC 59.171 50.000 0.00 0.00 0.00 3.36
3677 4249 2.896039 ACCAGTCTTAGCTTCCAGAGT 58.104 47.619 0.00 0.00 0.00 3.24
3678 4250 3.971245 AACCAGTCTTAGCTTCCAGAG 57.029 47.619 0.00 0.00 0.00 3.35
3679 4251 4.706842 AAAACCAGTCTTAGCTTCCAGA 57.293 40.909 0.00 0.00 0.00 3.86
3680 4252 4.821805 TGAAAAACCAGTCTTAGCTTCCAG 59.178 41.667 0.00 0.00 0.00 3.86
3681 4253 4.578928 GTGAAAAACCAGTCTTAGCTTCCA 59.421 41.667 0.00 0.00 0.00 3.53
3682 4254 5.109662 GTGAAAAACCAGTCTTAGCTTCC 57.890 43.478 0.00 0.00 0.00 3.46
3699 4271 4.392445 CGTATACACATTTTCCGGGTGAAA 59.608 41.667 13.81 7.72 41.18 2.69
3700 4272 3.933955 CGTATACACATTTTCCGGGTGAA 59.066 43.478 13.81 1.53 36.42 3.18
3701 4273 3.055963 ACGTATACACATTTTCCGGGTGA 60.056 43.478 13.81 0.00 36.42 4.02
3702 4274 3.264104 ACGTATACACATTTTCCGGGTG 58.736 45.455 0.00 3.56 38.47 4.61
3703 4275 3.615224 ACGTATACACATTTTCCGGGT 57.385 42.857 0.00 0.00 0.00 5.28
3704 4276 5.111293 AGTTACGTATACACATTTTCCGGG 58.889 41.667 0.00 0.00 0.00 5.73
3705 4277 6.038356 AGAGTTACGTATACACATTTTCCGG 58.962 40.000 3.32 0.00 0.00 5.14
3706 4278 7.097289 CGTAGAGTTACGTATACACATTTTCCG 60.097 40.741 3.32 0.00 45.79 4.30
3707 4279 8.043570 CGTAGAGTTACGTATACACATTTTCC 57.956 38.462 3.32 0.00 45.79 3.13
3727 4299 0.753867 TGGCAACCACAACTCGTAGA 59.246 50.000 0.00 0.00 0.00 2.59
3728 4300 1.263217 GTTGGCAACCACAACTCGTAG 59.737 52.381 19.57 0.00 43.59 3.51
3729 4301 1.301423 GTTGGCAACCACAACTCGTA 58.699 50.000 19.57 0.00 43.59 3.43
3730 4302 0.678366 TGTTGGCAACCACAACTCGT 60.678 50.000 26.31 0.00 46.28 4.18
3731 4303 0.453793 TTGTTGGCAACCACAACTCG 59.546 50.000 26.31 0.00 46.28 4.18
3732 4304 2.888834 ATTGTTGGCAACCACAACTC 57.111 45.000 26.31 0.45 46.28 3.01
3733 4305 6.603940 AATATATTGTTGGCAACCACAACT 57.396 33.333 26.31 9.62 46.28 3.16
3734 4306 6.402011 GCAAATATATTGTTGGCAACCACAAC 60.402 38.462 26.31 2.63 46.30 3.32
3735 4307 5.641209 GCAAATATATTGTTGGCAACCACAA 59.359 36.000 26.31 16.05 37.44 3.33
3736 4308 5.046735 AGCAAATATATTGTTGGCAACCACA 60.047 36.000 26.31 6.38 37.44 4.17
3737 4309 5.418676 AGCAAATATATTGTTGGCAACCAC 58.581 37.500 26.31 4.24 37.44 4.16
3738 4310 5.674052 AGCAAATATATTGTTGGCAACCA 57.326 34.783 26.31 17.12 37.44 3.67
3739 4311 9.191995 GTATTAGCAAATATATTGTTGGCAACC 57.808 33.333 26.31 10.03 32.28 3.77
3740 4312 9.743057 TGTATTAGCAAATATATTGTTGGCAAC 57.257 29.630 23.12 23.12 32.28 4.17
3741 4313 9.964303 CTGTATTAGCAAATATATTGTTGGCAA 57.036 29.630 0.00 0.00 33.17 4.52
3742 4314 9.348476 TCTGTATTAGCAAATATATTGTTGGCA 57.652 29.630 0.00 0.00 30.42 4.92


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

AutoCloner maintained by Alex Coulton.