Multiple sequence alignment - TraesCS1A01G239700

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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 TraesCS1A01G239700 chr1A 100.000 3585 0 0 1 3585 426885996 426889580 0.000000e+00 6621
1 TraesCS1A01G239700 chr1B 90.967 1417 66 25 1238 2627 444687185 444688566 0.000000e+00 1851
2 TraesCS1A01G239700 chr1B 90.160 437 31 9 2653 3084 444688548 444688977 3.130000e-155 558
3 TraesCS1A01G239700 chr1B 91.268 355 17 7 854 1208 444686681 444687021 4.190000e-129 472
4 TraesCS1A01G239700 chr1B 82.469 405 33 11 9 383 444686089 444686485 1.610000e-83 320
5 TraesCS1A01G239700 chr1B 82.482 274 20 8 3150 3396 444688994 444689266 7.800000e-52 215
6 TraesCS1A01G239700 chr1D 93.097 1101 50 9 1576 2654 329730787 329731883 0.000000e+00 1589
7 TraesCS1A01G239700 chr1D 90.031 642 36 18 577 1208 329729704 329730327 0.000000e+00 806
8 TraesCS1A01G239700 chr1D 91.367 417 15 8 2676 3084 329731867 329732270 5.230000e-153 551
9 TraesCS1A01G239700 chr1D 96.346 301 10 1 3285 3585 329732522 329732821 8.940000e-136 494
10 TraesCS1A01G239700 chr1D 85.426 446 27 16 1 427 329728880 329729306 2.560000e-116 429
11 TraesCS1A01G239700 chr1D 92.562 242 13 3 1238 1476 329730494 329730733 3.430000e-90 342
12 TraesCS1A01G239700 chr1D 92.593 81 5 1 3150 3230 329732287 329732366 8.130000e-22 115
13 TraesCS1A01G239700 chr4B 98.701 77 1 0 233 309 488694120 488694044 1.740000e-28 137
14 TraesCS1A01G239700 chr4B 95.181 83 3 1 228 310 14343322 14343241 2.900000e-26 130
15 TraesCS1A01G239700 chr4A 98.701 77 1 0 233 309 78250216 78250140 1.740000e-28 137
16 TraesCS1A01G239700 chr4A 95.238 84 2 2 229 311 595374082 595374164 8.080000e-27 132
17 TraesCS1A01G239700 chr5D 97.436 78 2 0 233 310 465039004 465039081 2.250000e-27 134
18 TraesCS1A01G239700 chr5B 97.436 78 2 0 233 310 572394763 572394840 2.250000e-27 134
19 TraesCS1A01G239700 chr5A 97.436 78 2 0 233 310 585434564 585434641 2.250000e-27 134


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 TraesCS1A01G239700 chr1A 426885996 426889580 3584 False 6621.0 6621 100.000000 1 3585 1 chr1A.!!$F1 3584
1 TraesCS1A01G239700 chr1B 444686089 444689266 3177 False 683.2 1851 87.469200 9 3396 5 chr1B.!!$F1 3387
2 TraesCS1A01G239700 chr1D 329728880 329732821 3941 False 618.0 1589 91.631714 1 3585 7 chr1D.!!$F1 3584

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
181 209 0.321122 GTGAGTGGGAGGAACAGCTG 60.321 60.0 13.48 13.48 0.00 4.24 F
817 1174 0.327576 AGCCAGGCTACTTACCCCAT 60.328 55.0 14.18 0.00 36.99 4.00 F
1478 1991 0.105039 CATACACCTTCGCCTCCTCC 59.895 60.0 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1459 1972 0.105039 GGAGGAGGCGAAGGTGTATG 59.895 60.0 0.0 0.0 0.0 2.39 R
2251 2787 0.179215 CAGTTTTCAGCATCGCCGAC 60.179 55.0 0.0 0.0 0.0 4.79 R
2841 3388 0.618458 ACCATGCCACCGTGTAATCT 59.382 50.0 0.0 0.0 0.0 2.40 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
24 25 6.081872 AGATTTGTTTGGAGCTCTCTTTTG 57.918 37.500 14.64 0.00 0.00 2.44
62 63 3.253230 GTTAAGCAATGCCCATGTGTTC 58.747 45.455 0.00 0.00 0.00 3.18
73 74 3.434309 CCCATGTGTTCCCAAGATTCTT 58.566 45.455 0.00 0.00 0.00 2.52
82 83 2.012673 CCCAAGATTCTTCTTCCAGCG 58.987 52.381 0.00 0.00 40.28 5.18
95 96 0.969149 TCCAGCGTGAGAATGTCTGT 59.031 50.000 0.00 0.00 0.00 3.41
124 145 3.503363 TCATTGTTGCTGCTAAACTCCTG 59.497 43.478 0.00 0.00 0.00 3.86
141 169 1.483316 CTGTGTTGTTGCACATGCTG 58.517 50.000 5.31 0.00 46.65 4.41
181 209 0.321122 GTGAGTGGGAGGAACAGCTG 60.321 60.000 13.48 13.48 0.00 4.24
189 217 1.882623 GGAGGAACAGCTGGTTTGAAG 59.117 52.381 19.93 0.00 40.63 3.02
206 235 4.134379 TGAAGCTGCAGAAGGAATAGAG 57.866 45.455 20.43 0.00 0.00 2.43
231 260 7.992033 AGAGTGGAGAGGAGAAATAAATTCATG 59.008 37.037 0.00 0.00 40.72 3.07
310 339 4.832608 CCCCTACCTGGCGCGTTC 62.833 72.222 8.43 0.58 0.00 3.95
322 351 1.857364 CGCGTTCGCCTACTGTTTT 59.143 52.632 11.51 0.00 0.00 2.43
371 400 2.292103 TGGTGCACTGTTTTTGAAGC 57.708 45.000 17.98 0.00 0.00 3.86
403 434 6.704056 TTTATTTCCCAAGAAGAGGAGAGT 57.296 37.500 0.00 0.00 32.57 3.24
407 438 4.676799 TCCCAAGAAGAGGAGAGTAGAA 57.323 45.455 0.00 0.00 0.00 2.10
412 443 6.129179 CCAAGAAGAGGAGAGTAGAAGAGAT 58.871 44.000 0.00 0.00 0.00 2.75
414 445 5.694995 AGAAGAGGAGAGTAGAAGAGATGG 58.305 45.833 0.00 0.00 0.00 3.51
421 452 6.775629 AGGAGAGTAGAAGAGATGGTATGAAC 59.224 42.308 0.00 0.00 0.00 3.18
469 757 6.255287 TGGTGTGTAAATGGTACTCCTACTA 58.745 40.000 0.00 0.00 34.23 1.82
482 795 9.643693 TGGTACTCCTACTAATTTTCTTTAACG 57.356 33.333 0.00 0.00 34.23 3.18
483 796 8.598924 GGTACTCCTACTAATTTTCTTTAACGC 58.401 37.037 0.00 0.00 0.00 4.84
484 797 9.363763 GTACTCCTACTAATTTTCTTTAACGCT 57.636 33.333 0.00 0.00 0.00 5.07
486 799 8.092687 ACTCCTACTAATTTTCTTTAACGCTCA 58.907 33.333 0.00 0.00 0.00 4.26
487 800 8.475331 TCCTACTAATTTTCTTTAACGCTCAG 57.525 34.615 0.00 0.00 0.00 3.35
488 801 7.548075 TCCTACTAATTTTCTTTAACGCTCAGG 59.452 37.037 0.00 0.00 0.00 3.86
489 802 7.333672 CCTACTAATTTTCTTTAACGCTCAGGT 59.666 37.037 0.00 0.00 0.00 4.00
490 803 7.506328 ACTAATTTTCTTTAACGCTCAGGTT 57.494 32.000 0.00 0.00 0.00 3.50
491 804 7.582352 ACTAATTTTCTTTAACGCTCAGGTTC 58.418 34.615 0.00 0.00 0.00 3.62
492 805 4.823790 TTTTCTTTAACGCTCAGGTTCC 57.176 40.909 0.00 0.00 0.00 3.62
493 806 3.478857 TTCTTTAACGCTCAGGTTCCA 57.521 42.857 0.00 0.00 0.00 3.53
494 807 3.040147 TCTTTAACGCTCAGGTTCCAG 57.960 47.619 0.00 0.00 0.00 3.86
495 808 2.367567 TCTTTAACGCTCAGGTTCCAGT 59.632 45.455 0.00 0.00 0.00 4.00
496 809 3.575256 TCTTTAACGCTCAGGTTCCAGTA 59.425 43.478 0.00 0.00 0.00 2.74
497 810 4.039488 TCTTTAACGCTCAGGTTCCAGTAA 59.961 41.667 0.00 0.00 0.00 2.24
498 811 2.457366 AACGCTCAGGTTCCAGTAAG 57.543 50.000 0.00 0.00 0.00 2.34
499 812 1.629043 ACGCTCAGGTTCCAGTAAGA 58.371 50.000 0.00 0.00 0.00 2.10
500 813 1.968493 ACGCTCAGGTTCCAGTAAGAA 59.032 47.619 0.00 0.00 0.00 2.52
501 814 2.288886 ACGCTCAGGTTCCAGTAAGAAC 60.289 50.000 0.00 0.00 44.45 3.01
502 815 2.288825 CGCTCAGGTTCCAGTAAGAACA 60.289 50.000 6.73 0.00 46.52 3.18
503 816 3.067833 GCTCAGGTTCCAGTAAGAACAC 58.932 50.000 6.73 0.00 46.52 3.32
504 817 3.244249 GCTCAGGTTCCAGTAAGAACACT 60.244 47.826 6.73 0.00 46.52 3.55
505 818 4.561105 CTCAGGTTCCAGTAAGAACACTC 58.439 47.826 6.73 0.00 46.52 3.51
506 819 3.005472 TCAGGTTCCAGTAAGAACACTCG 59.995 47.826 6.73 0.00 46.52 4.18
507 820 2.067013 GGTTCCAGTAAGAACACTCGC 58.933 52.381 6.73 0.00 46.52 5.03
508 821 2.547218 GGTTCCAGTAAGAACACTCGCA 60.547 50.000 6.73 0.00 46.52 5.10
509 822 3.128349 GTTCCAGTAAGAACACTCGCAA 58.872 45.455 0.00 0.00 44.55 4.85
510 823 3.462483 TCCAGTAAGAACACTCGCAAA 57.538 42.857 0.00 0.00 0.00 3.68
511 824 3.799366 TCCAGTAAGAACACTCGCAAAA 58.201 40.909 0.00 0.00 0.00 2.44
512 825 4.193090 TCCAGTAAGAACACTCGCAAAAA 58.807 39.130 0.00 0.00 0.00 1.94
546 859 3.769844 TCCAGTAAGAAGATGGTGAGGAC 59.230 47.826 0.00 0.00 35.51 3.85
558 871 3.541632 TGGTGAGGACAAGTCTGAAAAC 58.458 45.455 0.00 0.00 0.00 2.43
571 884 3.503748 GTCTGAAAACACCCCAAGATCTG 59.496 47.826 0.00 0.00 0.00 2.90
583 896 7.789831 ACACCCCAAGATCTGAATAAGATACTA 59.210 37.037 0.00 0.00 46.12 1.82
584 897 8.310382 CACCCCAAGATCTGAATAAGATACTAG 58.690 40.741 0.00 0.00 46.12 2.57
618 967 5.353400 CAGCATGAGCAAGTCTGAAAATAGA 59.647 40.000 0.00 0.00 45.49 1.98
629 978 4.036144 GTCTGAAAATAGATGAGGCAAGCC 59.964 45.833 2.02 2.02 0.00 4.35
657 1006 8.944212 AACTTAAGAATTATTACAACGTGTGC 57.056 30.769 10.09 0.00 0.00 4.57
664 1013 9.042008 AGAATTATTACAACGTGTGCTATAAGG 57.958 33.333 0.00 0.00 0.00 2.69
670 1019 1.066716 ACGTGTGCTATAAGGCGGAAA 60.067 47.619 0.00 0.00 34.52 3.13
672 1021 2.030457 CGTGTGCTATAAGGCGGAAAAG 59.970 50.000 0.00 0.00 34.52 2.27
677 1026 2.617308 GCTATAAGGCGGAAAAGGGAAC 59.383 50.000 0.00 0.00 0.00 3.62
684 1033 2.233676 GGCGGAAAAGGGAACAATTCAT 59.766 45.455 0.00 0.00 0.00 2.57
687 1036 5.474825 GCGGAAAAGGGAACAATTCATTAA 58.525 37.500 0.00 0.00 0.00 1.40
688 1037 5.576774 GCGGAAAAGGGAACAATTCATTAAG 59.423 40.000 0.00 0.00 0.00 1.85
722 1076 6.126911 ACCCTTTTCCAGCAAACAAATCTAAA 60.127 34.615 0.00 0.00 0.00 1.85
730 1084 7.336931 TCCAGCAAACAAATCTAAATACCTCTC 59.663 37.037 0.00 0.00 0.00 3.20
744 1098 7.814264 AAATACCTCTCCAATGCTGATTAAG 57.186 36.000 0.00 0.00 0.00 1.85
790 1144 1.613317 CCCCTCGCATGACCTGTACA 61.613 60.000 0.00 0.00 0.00 2.90
810 1167 1.352352 ACAACATCAGCCAGGCTACTT 59.648 47.619 15.64 0.00 36.40 2.24
811 1168 2.571653 ACAACATCAGCCAGGCTACTTA 59.428 45.455 15.64 0.00 36.40 2.24
813 1170 1.486726 ACATCAGCCAGGCTACTTACC 59.513 52.381 15.64 0.00 36.40 2.85
814 1171 1.132500 ATCAGCCAGGCTACTTACCC 58.868 55.000 15.64 0.00 36.40 3.69
815 1172 0.981277 TCAGCCAGGCTACTTACCCC 60.981 60.000 15.64 0.00 36.40 4.95
816 1173 1.082206 AGCCAGGCTACTTACCCCA 59.918 57.895 14.18 0.00 36.99 4.96
817 1174 0.327576 AGCCAGGCTACTTACCCCAT 60.328 55.000 14.18 0.00 36.99 4.00
818 1175 0.551396 GCCAGGCTACTTACCCCATT 59.449 55.000 3.29 0.00 0.00 3.16
819 1176 1.772453 GCCAGGCTACTTACCCCATTA 59.228 52.381 3.29 0.00 0.00 1.90
820 1177 2.486727 GCCAGGCTACTTACCCCATTAC 60.487 54.545 3.29 0.00 0.00 1.89
838 1195 6.545666 CCCATTACATTACAAGCTGGATAACA 59.454 38.462 0.00 0.00 0.00 2.41
904 1261 7.127686 CCAAGAAAAACACAATCAAAAGATGC 58.872 34.615 0.00 0.00 0.00 3.91
905 1262 7.201626 CCAAGAAAAACACAATCAAAAGATGCA 60.202 33.333 0.00 0.00 0.00 3.96
982 1339 2.595463 CCCTGGTGGTGTGCTGTG 60.595 66.667 0.00 0.00 0.00 3.66
983 1340 2.595463 CCTGGTGGTGTGCTGTGG 60.595 66.667 0.00 0.00 0.00 4.17
984 1341 2.192979 CTGGTGGTGTGCTGTGGT 59.807 61.111 0.00 0.00 0.00 4.16
985 1342 2.124362 TGGTGGTGTGCTGTGGTG 60.124 61.111 0.00 0.00 0.00 4.17
986 1343 2.124320 GGTGGTGTGCTGTGGTGT 60.124 61.111 0.00 0.00 0.00 4.16
987 1344 2.186826 GGTGGTGTGCTGTGGTGTC 61.187 63.158 0.00 0.00 0.00 3.67
997 1354 0.392706 CTGTGGTGTCTGTGTGGCTA 59.607 55.000 0.00 0.00 0.00 3.93
1015 1372 3.740397 CCATGTGTGGCTGGTGCG 61.740 66.667 0.00 0.00 39.01 5.34
1081 1438 1.515020 CTCCACTTCTCCTCGGCTG 59.485 63.158 0.00 0.00 0.00 4.85
1119 1476 1.406970 GAGAAGAAGGAGCGCGAACG 61.407 60.000 12.10 0.00 44.07 3.95
1208 1565 3.550820 TCAGAAAAGCAGTGCAAGGTAA 58.449 40.909 19.20 0.00 0.00 2.85
1209 1566 3.565482 TCAGAAAAGCAGTGCAAGGTAAG 59.435 43.478 19.20 1.46 0.00 2.34
1210 1567 3.316308 CAGAAAAGCAGTGCAAGGTAAGT 59.684 43.478 19.20 0.00 0.00 2.24
1211 1568 4.515191 CAGAAAAGCAGTGCAAGGTAAGTA 59.485 41.667 19.20 0.00 0.00 2.24
1212 1569 4.515567 AGAAAAGCAGTGCAAGGTAAGTAC 59.484 41.667 19.20 0.00 0.00 2.73
1213 1570 3.771577 AAGCAGTGCAAGGTAAGTACT 57.228 42.857 19.20 0.00 31.92 2.73
1214 1571 3.771577 AGCAGTGCAAGGTAAGTACTT 57.228 42.857 19.20 13.68 29.15 2.24
1215 1572 4.884668 AGCAGTGCAAGGTAAGTACTTA 57.115 40.909 19.20 11.38 29.15 2.24
1216 1573 4.566987 AGCAGTGCAAGGTAAGTACTTAC 58.433 43.478 29.86 29.86 43.40 2.34
1217 1574 3.367025 GCAGTGCAAGGTAAGTACTTACG 59.633 47.826 30.15 21.14 44.67 3.18
1218 1575 4.801891 CAGTGCAAGGTAAGTACTTACGA 58.198 43.478 30.15 14.53 44.67 3.43
1219 1576 5.224888 CAGTGCAAGGTAAGTACTTACGAA 58.775 41.667 30.15 15.11 44.67 3.85
1239 1597 7.365840 ACGAAGATTCAATCAAGTTTACTCC 57.634 36.000 0.00 0.00 0.00 3.85
1240 1598 6.934645 ACGAAGATTCAATCAAGTTTACTCCA 59.065 34.615 0.00 0.00 0.00 3.86
1243 1601 9.565213 GAAGATTCAATCAAGTTTACTCCATTG 57.435 33.333 0.00 7.14 0.00 2.82
1266 1777 6.339730 TGATTGATGTTGTTGTTTTTGCTCT 58.660 32.000 0.00 0.00 0.00 4.09
1268 1779 7.434897 TGATTGATGTTGTTGTTTTTGCTCTAC 59.565 33.333 0.00 0.00 0.00 2.59
1272 1783 2.017782 TGTTGTTTTTGCTCTACCGCA 58.982 42.857 0.00 0.00 38.31 5.69
1280 1791 2.080286 TGCTCTACCGCAAGAAGAAC 57.920 50.000 0.00 0.00 36.89 3.01
1285 1796 2.069273 CTACCGCAAGAAGAACCTGTG 58.931 52.381 0.00 0.00 43.02 3.66
1290 1801 1.534595 GCAAGAAGAACCTGTGCTGAG 59.465 52.381 0.00 0.00 32.43 3.35
1294 1805 2.094286 AGAAGAACCTGTGCTGAGATCG 60.094 50.000 0.00 0.00 0.00 3.69
1295 1806 1.261480 AGAACCTGTGCTGAGATCGT 58.739 50.000 0.00 0.00 0.00 3.73
1459 1972 2.038557 TCTCCAGCCACTTCAAGGTAAC 59.961 50.000 0.00 0.00 0.00 2.50
1476 1989 1.276622 AACATACACCTTCGCCTCCT 58.723 50.000 0.00 0.00 0.00 3.69
1477 1990 0.824759 ACATACACCTTCGCCTCCTC 59.175 55.000 0.00 0.00 0.00 3.71
1478 1991 0.105039 CATACACCTTCGCCTCCTCC 59.895 60.000 0.00 0.00 0.00 4.30
1484 1997 3.764160 CTTCGCCTCCTCCATGGCC 62.764 68.421 6.96 0.00 45.90 5.36
1502 2015 4.243008 GGCGGGCTCCTAGGCTTC 62.243 72.222 2.96 0.00 41.09 3.86
1505 2018 1.443828 CGGGCTCCTAGGCTTCTTC 59.556 63.158 2.96 0.00 41.09 2.87
1506 2019 1.833606 GGGCTCCTAGGCTTCTTCC 59.166 63.158 2.96 0.00 41.09 3.46
1507 2020 0.692756 GGGCTCCTAGGCTTCTTCCT 60.693 60.000 2.96 0.00 41.09 3.36
1508 2021 1.208706 GGCTCCTAGGCTTCTTCCTT 58.791 55.000 2.96 0.00 37.85 3.36
1509 2022 1.140052 GGCTCCTAGGCTTCTTCCTTC 59.860 57.143 2.96 0.00 37.85 3.46
1510 2023 1.202475 GCTCCTAGGCTTCTTCCTTCG 60.202 57.143 2.96 0.00 37.66 3.79
1511 2024 2.104170 CTCCTAGGCTTCTTCCTTCGT 58.896 52.381 2.96 0.00 37.66 3.85
1512 2025 2.100087 CTCCTAGGCTTCTTCCTTCGTC 59.900 54.545 2.96 0.00 37.66 4.20
1513 2026 1.137282 CCTAGGCTTCTTCCTTCGTCC 59.863 57.143 0.00 0.00 37.66 4.79
1514 2027 1.137282 CTAGGCTTCTTCCTTCGTCCC 59.863 57.143 0.00 0.00 37.66 4.46
1515 2028 1.078356 GGCTTCTTCCTTCGTCCCC 60.078 63.158 0.00 0.00 0.00 4.81
1516 2029 1.448013 GCTTCTTCCTTCGTCCCCG 60.448 63.158 0.00 0.00 0.00 5.73
1517 2030 1.218316 CTTCTTCCTTCGTCCCCGG 59.782 63.158 0.00 0.00 33.95 5.73
1548 2061 3.430218 CGTCCGAAATCTAATCTCCATGC 59.570 47.826 0.00 0.00 0.00 4.06
1567 2080 4.980805 TGCGCGTTGGTCTGGTCC 62.981 66.667 8.43 0.00 0.00 4.46
1573 2086 2.446994 TTGGTCTGGTCCGGTGGT 60.447 61.111 0.00 0.00 0.00 4.16
1574 2087 2.513259 TTGGTCTGGTCCGGTGGTC 61.513 63.158 0.00 0.00 0.00 4.02
1845 2360 3.356529 TCCTGGCATTCTCCTTCTTTC 57.643 47.619 0.00 0.00 0.00 2.62
1895 2410 3.725819 CGTTGCCGGTCAGTTGAA 58.274 55.556 1.90 0.00 0.00 2.69
1910 2425 1.215014 TTGAACTGAGCGCTCGTGTG 61.215 55.000 30.75 21.81 0.00 3.82
1956 2471 3.701604 CTGGTGAGCTCGTACCGCC 62.702 68.421 16.22 6.84 39.87 6.13
2150 2665 1.268640 GCCATCGACGAGGTCTACTTC 60.269 57.143 8.86 0.00 0.00 3.01
2151 2666 2.014857 CCATCGACGAGGTCTACTTCA 58.985 52.381 8.86 0.00 0.00 3.02
2156 2678 3.560481 TCGACGAGGTCTACTTCATCATC 59.440 47.826 0.00 0.00 0.00 2.92
2167 2689 8.543774 GGTCTACTTCATCATCATTTTTCTACG 58.456 37.037 0.00 0.00 0.00 3.51
2198 2721 3.290710 ACCTGAGCACACAAAATGAACT 58.709 40.909 0.00 0.00 0.00 3.01
2199 2722 4.460263 ACCTGAGCACACAAAATGAACTA 58.540 39.130 0.00 0.00 0.00 2.24
2251 2787 1.061799 GCAATCGCAACGACAAGCTG 61.062 55.000 0.00 0.00 39.18 4.24
2349 2889 3.040965 CCTTTTCCAGGCTGCTTCA 57.959 52.632 9.56 0.00 35.13 3.02
2354 2894 0.250901 TTCCAGGCTGCTTCAGTTCC 60.251 55.000 9.56 0.00 33.43 3.62
2359 2899 1.427020 GCTGCTTCAGTTCCGATGC 59.573 57.895 0.00 0.00 36.78 3.91
2443 2983 1.139853 GAATCCCTGACCAGAGCGATT 59.860 52.381 0.00 3.28 0.00 3.34
2530 3070 0.896479 TGACCAAGGATGTCGTCGGA 60.896 55.000 0.00 0.00 35.46 4.55
2609 3149 0.182061 GGCAGGATCATCCAAGCTCA 59.818 55.000 17.73 0.00 39.61 4.26
2627 3167 3.003482 GCTCAGAGGATGATGTTCAATGC 59.997 47.826 0.00 0.00 37.28 3.56
2629 3169 3.054213 TCAGAGGATGATGTTCAATGCCA 60.054 43.478 0.00 0.00 31.12 4.92
2637 3177 6.987992 GGATGATGTTCAATGCCATATTGTTT 59.012 34.615 0.00 0.00 0.00 2.83
2638 3178 7.042321 GGATGATGTTCAATGCCATATTGTTTG 60.042 37.037 0.00 0.00 0.00 2.93
2639 3179 6.107343 TGATGTTCAATGCCATATTGTTTGG 58.893 36.000 0.00 0.00 37.31 3.28
2640 3180 5.480642 TGTTCAATGCCATATTGTTTGGT 57.519 34.783 0.00 0.00 36.57 3.67
2641 3181 6.596309 TGTTCAATGCCATATTGTTTGGTA 57.404 33.333 0.00 0.00 36.57 3.25
2642 3182 6.393990 TGTTCAATGCCATATTGTTTGGTAC 58.606 36.000 0.00 0.00 36.57 3.34
2643 3183 6.210385 TGTTCAATGCCATATTGTTTGGTACT 59.790 34.615 0.00 0.00 36.57 2.73
2644 3184 6.849085 TCAATGCCATATTGTTTGGTACTT 57.151 33.333 0.00 0.00 36.57 2.24
2645 3185 7.946381 TCAATGCCATATTGTTTGGTACTTA 57.054 32.000 0.00 0.00 36.57 2.24
2646 3186 7.995289 TCAATGCCATATTGTTTGGTACTTAG 58.005 34.615 0.00 0.00 36.57 2.18
2647 3187 7.831690 TCAATGCCATATTGTTTGGTACTTAGA 59.168 33.333 0.00 0.00 36.57 2.10
2648 3188 6.995511 TGCCATATTGTTTGGTACTTAGAC 57.004 37.500 0.00 0.00 36.57 2.59
2649 3189 5.883673 TGCCATATTGTTTGGTACTTAGACC 59.116 40.000 0.00 0.00 40.21 3.85
2650 3190 5.007332 GCCATATTGTTTGGTACTTAGACCG 59.993 44.000 0.00 0.00 42.99 4.79
2651 3191 6.110707 CCATATTGTTTGGTACTTAGACCGT 58.889 40.000 0.00 0.00 42.99 4.83
2652 3192 6.596497 CCATATTGTTTGGTACTTAGACCGTT 59.404 38.462 0.00 0.00 42.99 4.44
2653 3193 7.201582 CCATATTGTTTGGTACTTAGACCGTTC 60.202 40.741 0.00 0.00 42.99 3.95
2654 3194 4.669206 TGTTTGGTACTTAGACCGTTCA 57.331 40.909 0.00 0.00 42.99 3.18
2655 3195 4.624015 TGTTTGGTACTTAGACCGTTCAG 58.376 43.478 0.00 0.00 42.99 3.02
2656 3196 4.341806 TGTTTGGTACTTAGACCGTTCAGA 59.658 41.667 0.00 0.00 42.99 3.27
2657 3197 4.778534 TTGGTACTTAGACCGTTCAGAG 57.221 45.455 0.00 0.00 42.99 3.35
2658 3198 3.087031 TGGTACTTAGACCGTTCAGAGG 58.913 50.000 0.00 0.00 42.99 3.69
2659 3199 3.245016 TGGTACTTAGACCGTTCAGAGGA 60.245 47.826 0.00 0.00 42.99 3.71
2660 3200 3.952967 GGTACTTAGACCGTTCAGAGGAT 59.047 47.826 0.00 0.00 0.00 3.24
2661 3201 4.202030 GGTACTTAGACCGTTCAGAGGATG 60.202 50.000 0.00 0.00 0.00 3.51
2662 3202 3.698289 ACTTAGACCGTTCAGAGGATGA 58.302 45.455 0.00 0.00 35.62 2.92
2663 3203 4.282496 ACTTAGACCGTTCAGAGGATGAT 58.718 43.478 0.00 0.00 37.89 2.45
2664 3204 4.098654 ACTTAGACCGTTCAGAGGATGATG 59.901 45.833 0.00 0.00 37.89 3.07
2665 3205 2.461695 AGACCGTTCAGAGGATGATGT 58.538 47.619 0.00 0.00 37.89 3.06
2666 3206 2.834549 AGACCGTTCAGAGGATGATGTT 59.165 45.455 0.00 0.00 37.89 2.71
2667 3207 3.118956 AGACCGTTCAGAGGATGATGTTC 60.119 47.826 0.00 0.00 37.89 3.18
2668 3208 2.567169 ACCGTTCAGAGGATGATGTTCA 59.433 45.455 0.00 0.00 37.89 3.18
2669 3209 3.007940 ACCGTTCAGAGGATGATGTTCAA 59.992 43.478 0.00 0.00 37.89 2.69
2670 3210 4.194640 CCGTTCAGAGGATGATGTTCAAT 58.805 43.478 0.00 0.00 37.89 2.57
2671 3211 4.034858 CCGTTCAGAGGATGATGTTCAATG 59.965 45.833 0.00 0.00 37.89 2.82
2672 3212 4.034858 CGTTCAGAGGATGATGTTCAATGG 59.965 45.833 0.00 0.00 37.89 3.16
2673 3213 3.548770 TCAGAGGATGATGTTCAATGGC 58.451 45.455 0.00 0.00 31.12 4.40
2674 3214 3.054213 TCAGAGGATGATGTTCAATGGCA 60.054 43.478 0.00 0.00 31.12 4.92
2677 3217 2.963101 AGGATGATGTTCAATGGCATGG 59.037 45.455 0.00 0.00 0.00 3.66
2764 3311 4.913784 GGTGTTGTGAAATAAGACCCCTA 58.086 43.478 0.00 0.00 44.10 3.53
2766 3313 5.949952 GGTGTTGTGAAATAAGACCCCTAAT 59.050 40.000 0.00 0.00 44.10 1.73
2809 3356 1.956477 GCACTGGTTTGAGACAATGGT 59.044 47.619 0.00 0.00 0.00 3.55
2810 3357 3.146066 GCACTGGTTTGAGACAATGGTA 58.854 45.455 0.00 0.00 0.00 3.25
2811 3358 3.058224 GCACTGGTTTGAGACAATGGTAC 60.058 47.826 0.00 0.00 0.00 3.34
2841 3388 6.540551 TCCATCACGATTTGATTTATCCGAAA 59.459 34.615 0.00 0.00 42.87 3.46
2842 3389 6.852853 CCATCACGATTTGATTTATCCGAAAG 59.147 38.462 0.00 0.00 42.87 2.62
2843 3390 7.254761 CCATCACGATTTGATTTATCCGAAAGA 60.255 37.037 0.00 0.00 42.87 2.52
2844 3391 7.786178 TCACGATTTGATTTATCCGAAAGAT 57.214 32.000 0.00 0.00 39.15 2.40
2854 3401 2.373540 TCCGAAAGATTACACGGTGG 57.626 50.000 13.48 0.00 44.72 4.61
2904 3452 2.092291 GTTGCGGCGATTCGACTCA 61.092 57.895 12.98 5.15 29.68 3.41
2906 3454 1.351430 TTGCGGCGATTCGACTCAAG 61.351 55.000 13.01 0.00 34.61 3.02
2907 3455 1.805945 GCGGCGATTCGACTCAAGT 60.806 57.895 12.98 0.00 29.68 3.16
2918 3469 4.642445 TCGACTCAAGTAACACAGAACA 57.358 40.909 0.00 0.00 0.00 3.18
2931 3482 3.117794 CACAGAACAAACGGTAGAACGA 58.882 45.455 0.00 0.00 37.61 3.85
3069 3620 1.536940 CCAATCACACCATCTGCACA 58.463 50.000 0.00 0.00 0.00 4.57
3078 3629 0.037303 CCATCTGCACAGAACAGGGT 59.963 55.000 4.14 0.00 41.36 4.34
3084 3635 3.072330 TCTGCACAGAACAGGGTTATCAA 59.928 43.478 0.00 0.00 35.78 2.57
3085 3636 3.411446 TGCACAGAACAGGGTTATCAAG 58.589 45.455 0.00 0.00 0.00 3.02
3086 3637 2.162408 GCACAGAACAGGGTTATCAAGC 59.838 50.000 0.00 0.00 0.00 4.01
3087 3638 3.411446 CACAGAACAGGGTTATCAAGCA 58.589 45.455 0.00 0.00 0.00 3.91
3088 3639 3.820467 CACAGAACAGGGTTATCAAGCAA 59.180 43.478 0.00 0.00 0.00 3.91
3090 3641 5.647658 CACAGAACAGGGTTATCAAGCAATA 59.352 40.000 0.00 0.00 0.00 1.90
3091 3642 6.150976 CACAGAACAGGGTTATCAAGCAATAA 59.849 38.462 0.00 0.00 0.00 1.40
3092 3643 6.375455 ACAGAACAGGGTTATCAAGCAATAAG 59.625 38.462 0.00 0.00 0.00 1.73
3093 3644 6.375455 CAGAACAGGGTTATCAAGCAATAAGT 59.625 38.462 0.00 0.00 0.00 2.24
3094 3645 6.375455 AGAACAGGGTTATCAAGCAATAAGTG 59.625 38.462 0.00 0.00 0.00 3.16
3108 3659 5.940603 CAATAAGTGCACACGTTTTTCAA 57.059 34.783 21.04 0.00 36.20 2.69
3109 3660 6.324522 CAATAAGTGCACACGTTTTTCAAA 57.675 33.333 21.04 0.00 36.20 2.69
3110 3661 6.756176 CAATAAGTGCACACGTTTTTCAAAA 58.244 32.000 21.04 0.00 36.20 2.44
3111 3662 7.397970 CAATAAGTGCACACGTTTTTCAAAAT 58.602 30.769 21.04 0.00 36.20 1.82
3112 3663 5.448926 AAGTGCACACGTTTTTCAAAATC 57.551 34.783 21.04 0.00 36.20 2.17
3113 3664 4.489810 AGTGCACACGTTTTTCAAAATCA 58.510 34.783 21.04 0.00 36.20 2.57
3114 3665 4.926238 AGTGCACACGTTTTTCAAAATCAA 59.074 33.333 21.04 0.00 36.20 2.57
3115 3666 5.062058 AGTGCACACGTTTTTCAAAATCAAG 59.938 36.000 21.04 0.00 36.20 3.02
3116 3667 4.926238 TGCACACGTTTTTCAAAATCAAGT 59.074 33.333 0.00 0.00 0.00 3.16
3117 3668 6.034044 GTGCACACGTTTTTCAAAATCAAGTA 59.966 34.615 13.17 0.00 0.00 2.24
3118 3669 6.586463 TGCACACGTTTTTCAAAATCAAGTAA 59.414 30.769 0.00 0.00 0.00 2.24
3119 3670 7.276658 TGCACACGTTTTTCAAAATCAAGTAAT 59.723 29.630 0.00 0.00 0.00 1.89
3120 3671 8.113675 GCACACGTTTTTCAAAATCAAGTAATT 58.886 29.630 0.00 0.00 0.00 1.40
3121 3672 9.965748 CACACGTTTTTCAAAATCAAGTAATTT 57.034 25.926 0.00 0.00 0.00 1.82
3132 3683 9.927668 CAAAATCAAGTAATTTATGAACAGGGT 57.072 29.630 0.00 0.00 0.00 4.34
3137 3688 9.967451 TCAAGTAATTTATGAACAGGGTTATCA 57.033 29.630 0.00 0.00 0.00 2.15
3139 3690 9.975218 AAGTAATTTATGAACAGGGTTATCAGT 57.025 29.630 0.00 0.00 0.00 3.41
3188 3739 9.691362 TTTTGAAAACTCAGCATAAATTACTCC 57.309 29.630 0.00 0.00 0.00 3.85
3193 3744 6.739331 ACTCAGCATAAATTACTCCTAGCT 57.261 37.500 0.00 0.00 0.00 3.32
3194 3745 7.130681 ACTCAGCATAAATTACTCCTAGCTT 57.869 36.000 0.00 0.00 0.00 3.74
3195 3746 6.989169 ACTCAGCATAAATTACTCCTAGCTTG 59.011 38.462 0.00 0.00 0.00 4.01
3248 3914 5.493735 GCATAGTTTTCTACTGTGAATCGC 58.506 41.667 5.94 0.00 45.82 4.58
3269 3935 5.870433 TCGCAGAAAAGTATGGTCGATTAAA 59.130 36.000 0.00 0.00 0.00 1.52
3270 3936 5.957796 CGCAGAAAAGTATGGTCGATTAAAC 59.042 40.000 0.00 0.00 0.00 2.01
3271 3937 6.183360 CGCAGAAAAGTATGGTCGATTAAACT 60.183 38.462 0.00 0.00 0.00 2.66
3272 3938 7.527457 GCAGAAAAGTATGGTCGATTAAACTT 58.473 34.615 0.00 0.00 0.00 2.66
3273 3939 8.662141 GCAGAAAAGTATGGTCGATTAAACTTA 58.338 33.333 6.61 0.00 0.00 2.24
3360 4026 5.945784 CCTCCAATCTGGTTGAATCTACAAA 59.054 40.000 1.35 0.00 40.37 2.83
3385 4051 8.491045 AAAAGGGGACAAGATCAATTAAAAGA 57.509 30.769 0.00 0.00 0.00 2.52
3439 4105 6.320494 ACGGTTGAAAAACATATGCACTTA 57.680 33.333 1.58 0.00 27.66 2.24
3506 4172 7.494211 ACCCCTTAAACAGTTGAAAAACATAC 58.506 34.615 0.00 0.00 0.00 2.39
3528 4194 8.662141 CATACGCACTTATATTACCCCATAAAC 58.338 37.037 0.00 0.00 0.00 2.01
3573 4239 9.104965 CTCTGAATTTTAATTGTATCCCACGTA 57.895 33.333 0.00 0.00 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 2.012673 CGCTGGAAGAAGAATCTTGGG 58.987 52.381 0.00 0.00 45.91 4.12
73 74 1.895798 AGACATTCTCACGCTGGAAGA 59.104 47.619 0.00 0.00 34.07 2.87
110 131 2.222027 ACAACACAGGAGTTTAGCAGC 58.778 47.619 0.00 0.00 0.00 5.25
181 209 1.609208 TCCTTCTGCAGCTTCAAACC 58.391 50.000 9.47 0.00 0.00 3.27
189 217 3.456280 CACTCTCTATTCCTTCTGCAGC 58.544 50.000 9.47 0.00 0.00 5.25
206 235 7.989741 TCATGAATTTATTTCTCCTCTCCACTC 59.010 37.037 0.00 0.00 35.23 3.51
326 355 7.826690 ACTAAGCACAAAAGAAAAGAGACAAA 58.173 30.769 0.00 0.00 0.00 2.83
330 359 6.377146 ACCAACTAAGCACAAAAGAAAAGAGA 59.623 34.615 0.00 0.00 0.00 3.10
331 360 6.473455 CACCAACTAAGCACAAAAGAAAAGAG 59.527 38.462 0.00 0.00 0.00 2.85
332 361 6.329496 CACCAACTAAGCACAAAAGAAAAGA 58.671 36.000 0.00 0.00 0.00 2.52
333 362 5.005682 GCACCAACTAAGCACAAAAGAAAAG 59.994 40.000 0.00 0.00 0.00 2.27
383 414 5.594777 TCTACTCTCCTCTTCTTGGGAAAT 58.405 41.667 0.00 0.00 0.00 2.17
384 415 5.011982 TCTACTCTCCTCTTCTTGGGAAA 57.988 43.478 0.00 0.00 0.00 3.13
386 417 4.292571 TCTTCTACTCTCCTCTTCTTGGGA 59.707 45.833 0.00 0.00 0.00 4.37
387 418 4.605183 TCTTCTACTCTCCTCTTCTTGGG 58.395 47.826 0.00 0.00 0.00 4.12
388 419 5.505780 TCTCTTCTACTCTCCTCTTCTTGG 58.494 45.833 0.00 0.00 0.00 3.61
389 420 6.039717 CCATCTCTTCTACTCTCCTCTTCTTG 59.960 46.154 0.00 0.00 0.00 3.02
390 421 6.129179 CCATCTCTTCTACTCTCCTCTTCTT 58.871 44.000 0.00 0.00 0.00 2.52
391 422 5.193728 ACCATCTCTTCTACTCTCCTCTTCT 59.806 44.000 0.00 0.00 0.00 2.85
392 423 5.445964 ACCATCTCTTCTACTCTCCTCTTC 58.554 45.833 0.00 0.00 0.00 2.87
393 424 5.466127 ACCATCTCTTCTACTCTCCTCTT 57.534 43.478 0.00 0.00 0.00 2.85
394 425 6.331572 TCATACCATCTCTTCTACTCTCCTCT 59.668 42.308 0.00 0.00 0.00 3.69
395 426 6.539173 TCATACCATCTCTTCTACTCTCCTC 58.461 44.000 0.00 0.00 0.00 3.71
396 427 6.523035 TCATACCATCTCTTCTACTCTCCT 57.477 41.667 0.00 0.00 0.00 3.69
397 428 6.547880 TGTTCATACCATCTCTTCTACTCTCC 59.452 42.308 0.00 0.00 0.00 3.71
398 429 7.575414 TGTTCATACCATCTCTTCTACTCTC 57.425 40.000 0.00 0.00 0.00 3.20
399 430 7.617723 ACTTGTTCATACCATCTCTTCTACTCT 59.382 37.037 0.00 0.00 0.00 3.24
400 431 7.777095 ACTTGTTCATACCATCTCTTCTACTC 58.223 38.462 0.00 0.00 0.00 2.59
401 432 7.726033 ACTTGTTCATACCATCTCTTCTACT 57.274 36.000 0.00 0.00 0.00 2.57
402 433 9.469807 CATACTTGTTCATACCATCTCTTCTAC 57.530 37.037 0.00 0.00 0.00 2.59
403 434 9.421399 TCATACTTGTTCATACCATCTCTTCTA 57.579 33.333 0.00 0.00 0.00 2.10
407 438 8.321353 TGTTTCATACTTGTTCATACCATCTCT 58.679 33.333 0.00 0.00 0.00 3.10
412 443 7.994425 ACATGTTTCATACTTGTTCATACCA 57.006 32.000 0.00 0.00 40.98 3.25
443 731 5.514500 AGGAGTACCATTTACACACCATT 57.486 39.130 0.00 0.00 38.94 3.16
444 732 5.724854 AGTAGGAGTACCATTTACACACCAT 59.275 40.000 0.00 0.00 38.94 3.55
445 733 5.088730 AGTAGGAGTACCATTTACACACCA 58.911 41.667 0.00 0.00 38.94 4.17
446 734 5.672421 AGTAGGAGTACCATTTACACACC 57.328 43.478 0.00 0.00 38.94 4.16
458 746 9.363763 AGCGTTAAAGAAAATTAGTAGGAGTAC 57.636 33.333 0.00 0.00 0.00 2.73
469 757 5.300792 TGGAACCTGAGCGTTAAAGAAAATT 59.699 36.000 0.00 0.00 0.00 1.82
475 763 2.767505 ACTGGAACCTGAGCGTTAAAG 58.232 47.619 4.82 0.00 0.00 1.85
479 792 1.968493 TCTTACTGGAACCTGAGCGTT 59.032 47.619 4.82 0.00 0.00 4.84
481 794 2.288825 TGTTCTTACTGGAACCTGAGCG 60.289 50.000 4.82 0.00 43.31 5.03
482 795 3.067833 GTGTTCTTACTGGAACCTGAGC 58.932 50.000 4.82 0.00 43.31 4.26
483 796 4.561105 GAGTGTTCTTACTGGAACCTGAG 58.439 47.826 4.82 0.00 43.31 3.35
484 797 3.005472 CGAGTGTTCTTACTGGAACCTGA 59.995 47.826 4.82 0.00 43.31 3.86
486 799 2.288886 GCGAGTGTTCTTACTGGAACCT 60.289 50.000 5.15 2.64 43.31 3.50
487 800 2.067013 GCGAGTGTTCTTACTGGAACC 58.933 52.381 5.15 0.00 43.31 3.62
488 801 2.750948 TGCGAGTGTTCTTACTGGAAC 58.249 47.619 0.00 0.00 43.97 3.62
489 802 3.462483 TTGCGAGTGTTCTTACTGGAA 57.538 42.857 0.00 0.00 0.00 3.53
490 803 3.462483 TTTGCGAGTGTTCTTACTGGA 57.538 42.857 0.00 0.00 0.00 3.86
491 804 4.545823 TTTTTGCGAGTGTTCTTACTGG 57.454 40.909 0.00 0.00 0.00 4.00
516 829 6.265422 CACCATCTTCTTACTGGAACCTTTTT 59.735 38.462 0.00 0.00 34.08 1.94
517 830 5.770162 CACCATCTTCTTACTGGAACCTTTT 59.230 40.000 0.00 0.00 34.08 2.27
518 831 5.073144 TCACCATCTTCTTACTGGAACCTTT 59.927 40.000 0.00 0.00 34.08 3.11
519 832 4.597507 TCACCATCTTCTTACTGGAACCTT 59.402 41.667 0.00 0.00 34.08 3.50
528 841 5.046950 AGACTTGTCCTCACCATCTTCTTAC 60.047 44.000 0.00 0.00 0.00 2.34
546 859 3.287222 TCTTGGGGTGTTTTCAGACTTG 58.713 45.455 0.00 0.00 0.00 3.16
558 871 7.072263 AGTATCTTATTCAGATCTTGGGGTG 57.928 40.000 0.00 0.00 41.80 4.61
583 896 4.743057 TGCTCATGCTGTACTGTAATCT 57.257 40.909 1.46 0.00 40.48 2.40
584 897 4.872691 ACTTGCTCATGCTGTACTGTAATC 59.127 41.667 1.46 0.00 40.48 1.75
593 941 2.556144 TTCAGACTTGCTCATGCTGT 57.444 45.000 0.00 0.00 40.48 4.40
595 943 5.494724 TCTATTTTCAGACTTGCTCATGCT 58.505 37.500 0.00 0.00 40.48 3.79
618 967 5.179452 TCTTAAGTTAAGGCTTGCCTCAT 57.821 39.130 20.04 2.79 36.45 2.90
650 999 0.533491 TTCCGCCTTATAGCACACGT 59.467 50.000 0.00 0.00 0.00 4.49
657 1006 3.881220 TGTTCCCTTTTCCGCCTTATAG 58.119 45.455 0.00 0.00 0.00 1.31
664 1013 3.592898 ATGAATTGTTCCCTTTTCCGC 57.407 42.857 0.00 0.00 0.00 5.54
684 1033 6.882678 GCTGGAAAAGGGTGAGTAATACTTAA 59.117 38.462 0.00 0.00 0.00 1.85
687 1036 4.288626 TGCTGGAAAAGGGTGAGTAATACT 59.711 41.667 0.00 0.00 0.00 2.12
688 1037 4.585879 TGCTGGAAAAGGGTGAGTAATAC 58.414 43.478 0.00 0.00 0.00 1.89
695 1049 2.151502 TGTTTGCTGGAAAAGGGTGA 57.848 45.000 0.00 0.00 0.00 4.02
700 1054 8.925700 GGTATTTAGATTTGTTTGCTGGAAAAG 58.074 33.333 0.00 0.00 0.00 2.27
722 1076 6.506538 ACTTAATCAGCATTGGAGAGGTAT 57.493 37.500 0.00 0.00 0.00 2.73
730 1084 4.454678 TGCTCCTACTTAATCAGCATTGG 58.545 43.478 0.00 0.00 35.17 3.16
744 1098 4.150897 TGGGTATGTTCATTGCTCCTAC 57.849 45.455 0.00 0.00 0.00 3.18
790 1144 0.987294 AGTAGCCTGGCTGATGTTGT 59.013 50.000 30.83 4.64 40.10 3.32
810 1167 4.475381 TCCAGCTTGTAATGTAATGGGGTA 59.525 41.667 0.00 0.00 0.00 3.69
811 1168 3.268334 TCCAGCTTGTAATGTAATGGGGT 59.732 43.478 0.00 0.00 0.00 4.95
813 1170 6.545666 TGTTATCCAGCTTGTAATGTAATGGG 59.454 38.462 0.00 0.00 0.00 4.00
814 1171 7.283127 ACTGTTATCCAGCTTGTAATGTAATGG 59.717 37.037 0.00 0.00 45.68 3.16
815 1172 8.124823 CACTGTTATCCAGCTTGTAATGTAATG 58.875 37.037 0.00 0.00 45.68 1.90
816 1173 7.283127 CCACTGTTATCCAGCTTGTAATGTAAT 59.717 37.037 0.00 0.00 45.68 1.89
817 1174 6.597672 CCACTGTTATCCAGCTTGTAATGTAA 59.402 38.462 0.00 0.00 45.68 2.41
818 1175 6.112734 CCACTGTTATCCAGCTTGTAATGTA 58.887 40.000 0.00 0.00 45.68 2.29
819 1176 4.943705 CCACTGTTATCCAGCTTGTAATGT 59.056 41.667 0.00 0.00 45.68 2.71
820 1177 4.201950 GCCACTGTTATCCAGCTTGTAATG 60.202 45.833 0.00 0.00 45.68 1.90
838 1195 4.218417 GTCATGAGTTTTAATGGTGCCACT 59.782 41.667 0.00 0.00 0.00 4.00
978 1335 0.392706 TAGCCACACAGACACCACAG 59.607 55.000 0.00 0.00 0.00 3.66
979 1336 0.105964 GTAGCCACACAGACACCACA 59.894 55.000 0.00 0.00 0.00 4.17
980 1337 0.602905 GGTAGCCACACAGACACCAC 60.603 60.000 0.00 0.00 0.00 4.16
981 1338 1.051556 TGGTAGCCACACAGACACCA 61.052 55.000 0.00 0.00 33.78 4.17
982 1339 0.324943 ATGGTAGCCACACAGACACC 59.675 55.000 0.00 0.00 35.80 4.16
983 1340 1.270839 ACATGGTAGCCACACAGACAC 60.271 52.381 0.00 0.00 35.80 3.67
984 1341 1.055849 ACATGGTAGCCACACAGACA 58.944 50.000 0.00 0.00 35.80 3.41
985 1342 1.270839 ACACATGGTAGCCACACAGAC 60.271 52.381 0.00 0.00 35.80 3.51
986 1343 1.055849 ACACATGGTAGCCACACAGA 58.944 50.000 0.00 0.00 35.80 3.41
987 1344 1.159285 CACACATGGTAGCCACACAG 58.841 55.000 0.00 0.00 35.80 3.66
1015 1372 2.894387 GATGCACTCGAGGCAGCC 60.894 66.667 24.57 17.90 45.68 4.85
1081 1438 4.452733 CTCCCTTCCCGTCCGTGC 62.453 72.222 0.00 0.00 0.00 5.34
1167 1524 1.067250 GCTCTCTGCATCCTCGGTC 59.933 63.158 0.00 0.00 42.31 4.79
1188 1545 3.316308 ACTTACCTTGCACTGCTTTTCTG 59.684 43.478 1.98 0.00 0.00 3.02
1208 1565 9.490379 AAACTTGATTGAATCTTCGTAAGTACT 57.510 29.630 6.73 0.00 39.48 2.73
1211 1568 9.490379 AGTAAACTTGATTGAATCTTCGTAAGT 57.510 29.630 6.73 4.60 39.48 2.24
1212 1569 9.959775 GAGTAAACTTGATTGAATCTTCGTAAG 57.040 33.333 6.73 4.00 0.00 2.34
1213 1570 8.932791 GGAGTAAACTTGATTGAATCTTCGTAA 58.067 33.333 6.73 0.00 0.00 3.18
1214 1571 8.092068 TGGAGTAAACTTGATTGAATCTTCGTA 58.908 33.333 6.73 0.00 0.00 3.43
1215 1572 6.934645 TGGAGTAAACTTGATTGAATCTTCGT 59.065 34.615 6.73 0.00 0.00 3.85
1216 1573 7.364522 TGGAGTAAACTTGATTGAATCTTCG 57.635 36.000 6.73 0.00 0.00 3.79
1217 1574 9.565213 CAATGGAGTAAACTTGATTGAATCTTC 57.435 33.333 6.73 0.00 31.66 2.87
1218 1575 9.300681 TCAATGGAGTAAACTTGATTGAATCTT 57.699 29.630 6.73 0.00 34.11 2.40
1219 1576 8.868522 TCAATGGAGTAAACTTGATTGAATCT 57.131 30.769 6.73 0.00 34.11 2.40
1239 1597 7.411274 AGCAAAAACAACAACATCAATCAATG 58.589 30.769 0.00 0.00 0.00 2.82
1240 1598 7.496591 AGAGCAAAAACAACAACATCAATCAAT 59.503 29.630 0.00 0.00 0.00 2.57
1243 1601 6.833342 AGAGCAAAAACAACAACATCAATC 57.167 33.333 0.00 0.00 0.00 2.67
1266 1777 1.876416 GCACAGGTTCTTCTTGCGGTA 60.876 52.381 0.00 0.00 0.00 4.02
1268 1779 0.886490 AGCACAGGTTCTTCTTGCGG 60.886 55.000 0.00 0.00 38.26 5.69
1272 1783 3.616076 CGATCTCAGCACAGGTTCTTCTT 60.616 47.826 0.00 0.00 0.00 2.52
1280 1791 0.813821 TCTCACGATCTCAGCACAGG 59.186 55.000 0.00 0.00 0.00 4.00
1285 1796 2.208431 CCCATTTCTCACGATCTCAGC 58.792 52.381 0.00 0.00 0.00 4.26
1290 1801 1.303309 CCTGCCCATTTCTCACGATC 58.697 55.000 0.00 0.00 0.00 3.69
1294 1805 0.967380 CCACCCTGCCCATTTCTCAC 60.967 60.000 0.00 0.00 0.00 3.51
1295 1806 1.383799 CCACCCTGCCCATTTCTCA 59.616 57.895 0.00 0.00 0.00 3.27
1459 1972 0.105039 GGAGGAGGCGAAGGTGTATG 59.895 60.000 0.00 0.00 0.00 2.39
1489 2002 1.140052 GAAGGAAGAAGCCTAGGAGCC 59.860 57.143 14.75 3.46 37.26 4.70
1490 2003 1.202475 CGAAGGAAGAAGCCTAGGAGC 60.202 57.143 14.75 0.00 37.26 4.70
1498 2011 4.619852 GGGGACGAAGGAAGAAGC 57.380 61.111 0.00 0.00 0.00 3.86
1531 2044 3.188048 CGCAGGCATGGAGATTAGATTTC 59.812 47.826 0.00 0.00 0.00 2.17
1533 2046 2.775890 CGCAGGCATGGAGATTAGATT 58.224 47.619 0.00 0.00 0.00 2.40
1534 2047 1.610102 GCGCAGGCATGGAGATTAGAT 60.610 52.381 0.30 0.00 39.62 1.98
1535 2048 0.250038 GCGCAGGCATGGAGATTAGA 60.250 55.000 0.30 0.00 39.62 2.10
1536 2049 1.563435 CGCGCAGGCATGGAGATTAG 61.563 60.000 8.75 0.00 39.92 1.73
1537 2050 1.595109 CGCGCAGGCATGGAGATTA 60.595 57.895 8.75 0.00 39.92 1.75
1548 2061 4.988598 ACCAGACCAACGCGCAGG 62.989 66.667 15.09 15.09 0.00 4.85
1559 2072 1.878656 CTGAGACCACCGGACCAGAC 61.879 65.000 9.46 0.00 0.00 3.51
1573 2086 4.193334 CGTCATCGCGCCCTGAGA 62.193 66.667 0.00 0.00 0.00 3.27
1861 2376 0.883833 ACGGCAAGAGCAAGAAATGG 59.116 50.000 0.00 0.00 44.61 3.16
1862 2377 2.322161 CAACGGCAAGAGCAAGAAATG 58.678 47.619 0.00 0.00 44.61 2.32
1903 2418 4.339809 CACGCACACGCACACGAG 62.340 66.667 0.00 0.00 45.53 4.18
1910 2425 4.236416 AACTGCACACGCACACGC 62.236 61.111 0.00 0.00 45.36 5.34
1911 2426 2.035617 AAGAACTGCACACGCACACG 62.036 55.000 0.00 0.00 45.36 4.49
1912 2427 0.589729 CAAGAACTGCACACGCACAC 60.590 55.000 0.00 0.00 45.36 3.82
1913 2428 1.713937 CCAAGAACTGCACACGCACA 61.714 55.000 0.00 0.00 45.36 4.57
1914 2429 1.009675 CCAAGAACTGCACACGCAC 60.010 57.895 0.00 0.00 45.36 5.34
2194 2717 7.095229 TGTGGCGCATCAAAATAGATATAGTTC 60.095 37.037 10.83 0.00 0.00 3.01
2198 2721 5.643348 CCTGTGGCGCATCAAAATAGATATA 59.357 40.000 10.83 0.00 0.00 0.86
2199 2722 4.456911 CCTGTGGCGCATCAAAATAGATAT 59.543 41.667 10.83 0.00 0.00 1.63
2210 2738 2.456119 CGAGAACCTGTGGCGCATC 61.456 63.158 10.83 1.19 0.00 3.91
2251 2787 0.179215 CAGTTTTCAGCATCGCCGAC 60.179 55.000 0.00 0.00 0.00 4.79
2349 2889 1.745141 GCCATGAAGAGCATCGGAACT 60.745 52.381 0.00 0.00 42.67 3.01
2354 2894 1.218763 CAGAGCCATGAAGAGCATCG 58.781 55.000 0.00 0.00 42.67 3.84
2476 3016 3.519913 ACCTCACCTTGTATTCCTCCTTC 59.480 47.826 0.00 0.00 0.00 3.46
2536 3076 2.132352 GCCCTGGTAGTACCCGGAG 61.132 68.421 26.80 18.42 44.49 4.63
2591 3131 1.140452 TCTGAGCTTGGATGATCCTGC 59.860 52.381 13.44 15.97 37.46 4.85
2609 3149 3.657398 TGGCATTGAACATCATCCTCT 57.343 42.857 0.00 0.00 0.00 3.69
2617 3157 6.052405 ACCAAACAATATGGCATTGAACAT 57.948 33.333 4.78 0.00 41.89 2.71
2618 3158 5.480642 ACCAAACAATATGGCATTGAACA 57.519 34.783 4.78 0.00 41.89 3.18
2627 3167 6.110707 ACGGTCTAAGTACCAAACAATATGG 58.889 40.000 0.00 0.00 43.84 2.74
2629 3169 7.388437 TGAACGGTCTAAGTACCAAACAATAT 58.612 34.615 0.33 0.00 39.71 1.28
2637 3177 3.087031 CCTCTGAACGGTCTAAGTACCA 58.913 50.000 0.33 0.00 39.71 3.25
2638 3178 3.350833 TCCTCTGAACGGTCTAAGTACC 58.649 50.000 0.33 0.00 36.08 3.34
2639 3179 4.639310 TCATCCTCTGAACGGTCTAAGTAC 59.361 45.833 0.33 0.00 0.00 2.73
2640 3180 4.851843 TCATCCTCTGAACGGTCTAAGTA 58.148 43.478 0.33 0.00 0.00 2.24
2641 3181 3.698289 TCATCCTCTGAACGGTCTAAGT 58.302 45.455 0.33 0.00 0.00 2.24
2642 3182 4.098654 ACATCATCCTCTGAACGGTCTAAG 59.901 45.833 0.33 0.00 37.44 2.18
2643 3183 4.023980 ACATCATCCTCTGAACGGTCTAA 58.976 43.478 0.33 0.00 37.44 2.10
2644 3184 3.632333 ACATCATCCTCTGAACGGTCTA 58.368 45.455 0.33 0.00 37.44 2.59
2645 3185 2.461695 ACATCATCCTCTGAACGGTCT 58.538 47.619 0.33 0.00 37.44 3.85
2646 3186 2.969628 ACATCATCCTCTGAACGGTC 57.030 50.000 0.00 0.00 37.44 4.79
2647 3187 2.567169 TGAACATCATCCTCTGAACGGT 59.433 45.455 0.00 0.00 37.44 4.83
2648 3188 3.251479 TGAACATCATCCTCTGAACGG 57.749 47.619 0.00 0.00 37.44 4.44
2649 3189 4.034858 CCATTGAACATCATCCTCTGAACG 59.965 45.833 0.00 0.00 37.44 3.95
2650 3190 4.201990 GCCATTGAACATCATCCTCTGAAC 60.202 45.833 0.00 0.00 37.44 3.18
2651 3191 3.949754 GCCATTGAACATCATCCTCTGAA 59.050 43.478 0.00 0.00 37.44 3.02
2652 3192 3.054213 TGCCATTGAACATCATCCTCTGA 60.054 43.478 0.00 0.00 38.53 3.27
2653 3193 3.284617 TGCCATTGAACATCATCCTCTG 58.715 45.455 0.00 0.00 0.00 3.35
2654 3194 3.657398 TGCCATTGAACATCATCCTCT 57.343 42.857 0.00 0.00 0.00 3.69
2655 3195 3.005472 CCATGCCATTGAACATCATCCTC 59.995 47.826 0.00 0.00 0.00 3.71
2656 3196 2.963101 CCATGCCATTGAACATCATCCT 59.037 45.455 0.00 0.00 0.00 3.24
2657 3197 2.696707 ACCATGCCATTGAACATCATCC 59.303 45.455 0.00 0.00 0.00 3.51
2658 3198 4.581824 AGTACCATGCCATTGAACATCATC 59.418 41.667 0.00 0.00 0.00 2.92
2659 3199 4.539726 AGTACCATGCCATTGAACATCAT 58.460 39.130 0.00 0.00 0.00 2.45
2660 3200 3.966979 AGTACCATGCCATTGAACATCA 58.033 40.909 0.00 0.00 0.00 3.07
2661 3201 4.989279 AAGTACCATGCCATTGAACATC 57.011 40.909 0.00 0.00 0.00 3.06
2662 3202 5.590259 GTCTAAGTACCATGCCATTGAACAT 59.410 40.000 0.00 0.00 0.00 2.71
2663 3203 4.941263 GTCTAAGTACCATGCCATTGAACA 59.059 41.667 0.00 0.00 0.00 3.18
2664 3204 4.335594 GGTCTAAGTACCATGCCATTGAAC 59.664 45.833 0.00 0.00 39.50 3.18
2665 3205 4.523083 GGTCTAAGTACCATGCCATTGAA 58.477 43.478 0.00 0.00 39.50 2.69
2666 3206 3.431626 CGGTCTAAGTACCATGCCATTGA 60.432 47.826 0.00 0.00 39.71 2.57
2667 3207 2.872245 CGGTCTAAGTACCATGCCATTG 59.128 50.000 0.00 0.00 39.71 2.82
2668 3208 2.504175 ACGGTCTAAGTACCATGCCATT 59.496 45.455 0.00 0.00 39.71 3.16
2669 3209 2.116238 ACGGTCTAAGTACCATGCCAT 58.884 47.619 0.00 0.00 39.71 4.40
2670 3210 1.563924 ACGGTCTAAGTACCATGCCA 58.436 50.000 0.00 0.00 39.71 4.92
2671 3211 2.547826 GAACGGTCTAAGTACCATGCC 58.452 52.381 0.00 0.00 39.71 4.40
2672 3212 2.159338 TCGAACGGTCTAAGTACCATGC 60.159 50.000 0.00 0.00 39.71 4.06
2673 3213 3.770263 TCGAACGGTCTAAGTACCATG 57.230 47.619 0.00 0.00 39.71 3.66
2674 3214 3.003068 CGATCGAACGGTCTAAGTACCAT 59.997 47.826 10.26 0.00 39.71 3.55
2677 3217 3.933155 TCGATCGAACGGTCTAAGTAC 57.067 47.619 16.99 0.00 0.00 2.73
2766 3313 8.673711 GTGCTGAATACACCAATAAATGAACTA 58.326 33.333 0.00 0.00 31.67 2.24
2794 3341 5.642491 GGAAGTAGTACCATTGTCTCAAACC 59.358 44.000 0.00 0.00 0.00 3.27
2810 3357 8.964476 ATAAATCAAATCGTGATGGAAGTAGT 57.036 30.769 0.00 0.00 46.80 2.73
2811 3358 8.499162 GGATAAATCAAATCGTGATGGAAGTAG 58.501 37.037 0.00 0.00 46.80 2.57
2841 3388 0.618458 ACCATGCCACCGTGTAATCT 59.382 50.000 0.00 0.00 0.00 2.40
2842 3389 2.319136 TACCATGCCACCGTGTAATC 57.681 50.000 0.00 0.00 0.00 1.75
2843 3390 2.171659 TGATACCATGCCACCGTGTAAT 59.828 45.455 0.00 0.00 0.00 1.89
2844 3391 1.555533 TGATACCATGCCACCGTGTAA 59.444 47.619 0.00 0.00 0.00 2.41
2904 3452 5.663456 TCTACCGTTTGTTCTGTGTTACTT 58.337 37.500 0.00 0.00 0.00 2.24
2906 3454 5.555069 CGTTCTACCGTTTGTTCTGTGTTAC 60.555 44.000 0.00 0.00 0.00 2.50
2907 3455 4.503734 CGTTCTACCGTTTGTTCTGTGTTA 59.496 41.667 0.00 0.00 0.00 2.41
2918 3469 4.789012 TGGTTCTATCGTTCTACCGTTT 57.211 40.909 0.00 0.00 0.00 3.60
2931 3482 7.888021 TGAAATAGGATGTGTGTTTGGTTCTAT 59.112 33.333 0.00 0.00 0.00 1.98
3069 3620 6.375455 CACTTATTGCTTGATAACCCTGTTCT 59.625 38.462 0.00 0.00 0.00 3.01
3086 3637 5.940603 TTGAAAAACGTGTGCACTTATTG 57.059 34.783 19.41 5.66 0.00 1.90
3087 3638 6.952935 TTTTGAAAAACGTGTGCACTTATT 57.047 29.167 19.41 6.31 0.00 1.40
3088 3639 6.754209 TGATTTTGAAAAACGTGTGCACTTAT 59.246 30.769 19.41 0.00 0.00 1.73
3090 3641 4.926238 TGATTTTGAAAAACGTGTGCACTT 59.074 33.333 19.41 1.94 0.00 3.16
3091 3642 4.489810 TGATTTTGAAAAACGTGTGCACT 58.510 34.783 19.41 0.00 0.00 4.40
3092 3643 4.831741 TGATTTTGAAAAACGTGTGCAC 57.168 36.364 10.75 10.75 0.00 4.57
3093 3644 4.926238 ACTTGATTTTGAAAAACGTGTGCA 59.074 33.333 0.00 0.00 0.00 4.57
3094 3645 5.448926 ACTTGATTTTGAAAAACGTGTGC 57.551 34.783 0.00 0.00 0.00 4.57
3106 3657 9.927668 ACCCTGTTCATAAATTACTTGATTTTG 57.072 29.630 0.00 0.00 31.96 2.44
3111 3662 9.967451 TGATAACCCTGTTCATAAATTACTTGA 57.033 29.630 0.00 0.00 0.00 3.02
3113 3664 9.975218 ACTGATAACCCTGTTCATAAATTACTT 57.025 29.630 0.00 0.00 0.00 2.24
3135 3686 9.719355 TCAAGCAACTGTAAAAATAGATACTGA 57.281 29.630 0.00 0.00 0.00 3.41
3145 3696 9.818796 GTTTTCAAAATCAAGCAACTGTAAAAA 57.181 25.926 0.00 0.00 0.00 1.94
3146 3697 9.213799 AGTTTTCAAAATCAAGCAACTGTAAAA 57.786 25.926 0.00 0.00 0.00 1.52
3147 3698 8.770438 AGTTTTCAAAATCAAGCAACTGTAAA 57.230 26.923 0.00 0.00 0.00 2.01
3148 3699 8.031864 TGAGTTTTCAAAATCAAGCAACTGTAA 58.968 29.630 0.05 0.00 39.68 2.41
3149 3700 7.542890 TGAGTTTTCAAAATCAAGCAACTGTA 58.457 30.769 0.05 0.00 39.68 2.74
3150 3701 6.397272 TGAGTTTTCAAAATCAAGCAACTGT 58.603 32.000 0.05 0.00 39.68 3.55
3151 3702 6.509039 GCTGAGTTTTCAAAATCAAGCAACTG 60.509 38.462 14.03 1.37 41.68 3.16
3152 3703 5.521372 GCTGAGTTTTCAAAATCAAGCAACT 59.479 36.000 14.03 0.00 41.68 3.16
3153 3704 5.291614 TGCTGAGTTTTCAAAATCAAGCAAC 59.708 36.000 16.96 3.62 41.68 4.17
3188 3739 3.133691 TGAAGTGACAACAGCAAGCTAG 58.866 45.455 0.00 0.00 0.00 3.42
3225 3776 5.063438 TGCGATTCACAGTAGAAAACTATGC 59.937 40.000 0.00 0.00 35.76 3.14
3360 4026 8.491045 TCTTTTAATTGATCTTGTCCCCTTTT 57.509 30.769 0.00 0.00 0.00 2.27
3385 4051 3.306472 TGCCGCCTTTATAAATTCCCT 57.694 42.857 0.00 0.00 0.00 4.20
3506 4172 7.739498 AAGTTTATGGGGTAATATAAGTGCG 57.261 36.000 0.00 0.00 0.00 5.34
3547 4213 7.985476 ACGTGGGATACAATTAAAATTCAGAG 58.015 34.615 0.00 0.00 39.74 3.35


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

AutoCloner maintained by Alex Coulton.