Multiple sequence alignment - TraesCS2B01G457100

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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 TraesCS2B01G457100 chr2B 100.000 5751 0 0 1 5751 651919967 651925717 0.000000e+00 10621
1 TraesCS2B01G457100 chr2B 94.545 165 8 1 1 164 180046995 180047159 2.660000e-63 254
2 TraesCS2B01G457100 chr2D 91.305 4129 172 68 748 4785 545028958 545032990 0.000000e+00 5463
3 TraesCS2B01G457100 chr2D 89.157 913 37 31 4867 5751 545033108 545033986 0.000000e+00 1081
4 TraesCS2B01G457100 chr2D 86.314 738 61 14 1 721 545028284 545028998 0.000000e+00 767
5 TraesCS2B01G457100 chr2A 92.364 3130 133 53 818 3900 688244799 688241729 0.000000e+00 4359
6 TraesCS2B01G457100 chr2A 87.245 980 61 26 4815 5751 688240668 688239710 0.000000e+00 1059
7 TraesCS2B01G457100 chr2A 88.649 881 58 22 3888 4743 688241709 688240846 0.000000e+00 1035
8 TraesCS2B01G457100 chr7A 94.118 170 10 0 1 170 323460661 323460830 5.720000e-65 259
9 TraesCS2B01G457100 chr7D 93.529 170 11 0 1 170 285242115 285242284 2.660000e-63 254
10 TraesCS2B01G457100 chr1B 93.976 166 10 0 1 166 253010621 253010786 9.570000e-63 252
11 TraesCS2B01G457100 chr5D 93.939 165 10 0 1 165 141436578 141436414 3.440000e-62 250
12 TraesCS2B01G457100 chr4B 93.491 169 9 2 1 167 242736606 242736438 3.440000e-62 250
13 TraesCS2B01G457100 chr4B 93.976 166 9 1 1 165 242746865 242746700 3.440000e-62 250
14 TraesCS2B01G457100 chr1D 93.939 165 10 0 1 165 46313468 46313632 3.440000e-62 250


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 TraesCS2B01G457100 chr2B 651919967 651925717 5750 False 10621 10621 100.000000 1 5751 1 chr2B.!!$F2 5750
1 TraesCS2B01G457100 chr2D 545028284 545033986 5702 False 2437 5463 88.925333 1 5751 3 chr2D.!!$F1 5750
2 TraesCS2B01G457100 chr2A 688239710 688244799 5089 True 2151 4359 89.419333 818 5751 3 chr2A.!!$R1 4933

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
153 155 0.179089 CTGCTCCTCCACATCCTTCG 60.179 60.000 0.00 0.00 0.00 3.79 F
1688 1740 0.037697 TACGGCGAGCATTGTCTGTT 60.038 50.000 16.62 0.00 0.00 3.16 F
2134 2186 0.305617 GTCAACGTTTGTTCCCGTCC 59.694 55.000 0.00 0.00 35.72 4.79 F
2190 2242 0.318445 CTTTGGCTGTTGCTGCTGTC 60.318 55.000 0.00 0.00 39.59 3.51 F
3623 3717 1.127582 GCTTAGCGAAACTCACTGCAG 59.872 52.381 13.48 13.48 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 1860 0.320683 CAAGCTGGACGATGACCACA 60.321 55.000 0.00 0.00 33.57 4.17 R
3607 3682 1.069204 TCTTCTGCAGTGAGTTTCGCT 59.931 47.619 14.67 0.00 37.80 4.93 R
3608 3683 1.458827 CTCTTCTGCAGTGAGTTTCGC 59.541 52.381 22.28 0.00 0.00 4.70 R
4083 4263 2.096614 TGTCGTCGCGAAGAAAAATTCC 60.097 45.455 25.87 12.31 37.72 3.01 R
5147 5497 0.029700 CCCCGCTTTTCGTTTCGTTT 59.970 50.000 0.00 0.00 36.19 3.60 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
17 18 4.943822 GTGCCCTAGGAGTTCTGC 57.056 61.111 11.48 4.21 0.00 4.26
72 73 3.275143 GCCTCTAGAGCGATATCTAGCA 58.725 50.000 14.73 4.47 45.65 3.49
83 84 4.102649 CGATATCTAGCACAACACGTTGA 58.897 43.478 16.48 0.00 42.93 3.18
96 97 3.340034 ACACGTTGAAGTTGTTCCTTCA 58.660 40.909 0.00 0.00 46.81 3.02
103 104 5.309323 TGAAGTTGTTCCTTCAACACTTG 57.691 39.130 11.22 0.00 45.82 3.16
104 105 4.764823 TGAAGTTGTTCCTTCAACACTTGT 59.235 37.500 11.22 0.00 45.82 3.16
105 106 4.701956 AGTTGTTCCTTCAACACTTGTG 57.298 40.909 11.22 0.00 45.12 3.33
106 107 4.331968 AGTTGTTCCTTCAACACTTGTGA 58.668 39.130 7.83 0.00 45.12 3.58
125 127 2.002586 GATGTACACATTGTCGCAGCT 58.997 47.619 0.00 0.00 36.57 4.24
128 130 1.927174 GTACACATTGTCGCAGCTAGG 59.073 52.381 0.00 0.00 0.00 3.02
134 136 2.202810 GTCGCAGCTAGGTGGAGC 60.203 66.667 22.69 8.28 43.19 4.70
152 154 0.463474 GCTGCTCCTCCACATCCTTC 60.463 60.000 0.00 0.00 0.00 3.46
153 155 0.179089 CTGCTCCTCCACATCCTTCG 60.179 60.000 0.00 0.00 0.00 3.79
193 195 3.431626 CCGATGGTGCAATGTAGGAGTTA 60.432 47.826 0.00 0.00 0.00 2.24
214 216 7.206687 AGTTACTCAACTCTCTCTTTGTCTTG 58.793 38.462 0.00 0.00 41.25 3.02
215 217 4.376146 ACTCAACTCTCTCTTTGTCTTGC 58.624 43.478 0.00 0.00 0.00 4.01
234 236 2.034053 TGCTGGTTTTCGGTGATCAAAC 59.966 45.455 0.00 0.00 0.00 2.93
239 241 3.314080 GGTTTTCGGTGATCAAACTCACA 59.686 43.478 0.00 0.00 45.95 3.58
242 244 5.766150 TTTCGGTGATCAAACTCACAAAT 57.234 34.783 0.00 0.00 45.95 2.32
249 251 7.169645 CGGTGATCAAACTCACAAATGATTTTT 59.830 33.333 0.00 0.00 45.95 1.94
276 278 1.700955 TACCCTTAGTCCCGATGCTC 58.299 55.000 0.00 0.00 0.00 4.26
294 301 2.787994 CTCCACATCTCCAAAGCACTT 58.212 47.619 0.00 0.00 0.00 3.16
299 306 4.154918 CCACATCTCCAAAGCACTTCTAAC 59.845 45.833 0.00 0.00 0.00 2.34
322 330 0.613853 CTCAAGGTCCGGGGTGTAGA 60.614 60.000 0.00 0.00 0.00 2.59
324 332 1.156803 AAGGTCCGGGGTGTAGACA 59.843 57.895 0.00 0.00 31.99 3.41
344 352 1.129809 GACGAACAACGCCACATCG 59.870 57.895 0.00 0.00 46.94 3.84
347 355 1.495951 GAACAACGCCACATCGTCC 59.504 57.895 0.00 0.00 42.46 4.79
351 359 3.509137 AACGCCACATCGTCCGTGT 62.509 57.895 0.00 0.00 42.46 4.49
360 368 4.385748 CCACATCGTCCGTGTATATTGATG 59.614 45.833 0.00 0.00 38.12 3.07
362 370 3.021269 TCGTCCGTGTATATTGATGGC 57.979 47.619 0.00 0.00 0.00 4.40
364 372 2.547007 CGTCCGTGTATATTGATGGCCA 60.547 50.000 8.56 8.56 0.00 5.36
372 380 3.650281 ATATTGATGGCCACTGTGTCA 57.350 42.857 8.16 4.26 0.00 3.58
373 381 2.519771 ATTGATGGCCACTGTGTCAT 57.480 45.000 8.16 9.88 0.00 3.06
380 388 1.565305 GCCACTGTGTCATCGAGATC 58.435 55.000 7.08 0.00 0.00 2.75
411 419 1.168407 GCTCAACACTCCAGCTTGCA 61.168 55.000 0.00 0.00 0.00 4.08
460 478 5.394224 GGACCTTCATAGAGATGACGAACAA 60.394 44.000 0.00 0.00 41.92 2.83
468 486 3.639094 AGAGATGACGAACAATAGAGGGG 59.361 47.826 0.00 0.00 0.00 4.79
472 490 2.758979 TGACGAACAATAGAGGGGAGAC 59.241 50.000 0.00 0.00 0.00 3.36
473 491 3.025262 GACGAACAATAGAGGGGAGACT 58.975 50.000 0.00 0.00 0.00 3.24
474 492 2.761208 ACGAACAATAGAGGGGAGACTG 59.239 50.000 0.00 0.00 0.00 3.51
475 493 2.101582 CGAACAATAGAGGGGAGACTGG 59.898 54.545 0.00 0.00 0.00 4.00
476 494 3.375699 GAACAATAGAGGGGAGACTGGA 58.624 50.000 0.00 0.00 0.00 3.86
477 495 3.715648 ACAATAGAGGGGAGACTGGAT 57.284 47.619 0.00 0.00 0.00 3.41
478 496 3.582164 ACAATAGAGGGGAGACTGGATC 58.418 50.000 0.00 0.00 0.00 3.36
479 497 2.903135 CAATAGAGGGGAGACTGGATCC 59.097 54.545 4.20 4.20 35.99 3.36
491 509 0.463833 CTGGATCCCCTTGGCGTAAC 60.464 60.000 9.90 0.00 0.00 2.50
497 515 0.963856 CCCCTTGGCGTAACCCTTTC 60.964 60.000 0.00 0.00 37.83 2.62
516 534 1.745087 TCGCATGCCAAATTCTCCTTC 59.255 47.619 13.15 0.00 0.00 3.46
517 535 1.747355 CGCATGCCAAATTCTCCTTCT 59.253 47.619 13.15 0.00 0.00 2.85
532 550 1.765314 CCTTCTCGGGACTCCATTGAT 59.235 52.381 0.00 0.00 0.00 2.57
569 587 2.351350 CGAGGTTTGTAACAATGTGGCC 60.351 50.000 0.00 0.00 0.00 5.36
597 615 3.868757 TGAGAAGTGGGTCAATCGTAG 57.131 47.619 0.00 0.00 0.00 3.51
598 616 3.427573 TGAGAAGTGGGTCAATCGTAGA 58.572 45.455 0.00 0.00 45.75 2.59
599 617 3.192844 TGAGAAGTGGGTCAATCGTAGAC 59.807 47.826 0.00 0.00 42.51 2.59
607 625 3.329929 GTCAATCGTAGACCCCTGTTT 57.670 47.619 0.00 0.00 42.51 2.83
608 626 3.259902 GTCAATCGTAGACCCCTGTTTC 58.740 50.000 0.00 0.00 42.51 2.78
609 627 2.901192 TCAATCGTAGACCCCTGTTTCA 59.099 45.455 0.00 0.00 42.51 2.69
610 628 3.517901 TCAATCGTAGACCCCTGTTTCAT 59.482 43.478 0.00 0.00 42.51 2.57
611 629 3.821421 ATCGTAGACCCCTGTTTCATC 57.179 47.619 0.00 0.00 42.51 2.92
640 658 1.529883 CCGAGCGCGAGAATTACGAC 61.530 60.000 12.10 0.00 40.82 4.34
646 664 1.630148 GCGAGAATTACGACTGCAGT 58.370 50.000 21.88 21.88 0.00 4.40
657 675 1.517242 GACTGCAGTGAAGACCCAAG 58.483 55.000 27.27 0.00 0.00 3.61
659 677 2.037251 GACTGCAGTGAAGACCCAAGTA 59.963 50.000 27.27 0.00 0.00 2.24
694 712 9.413734 AGAAGATCTTCAAGAAAAGAAAAAGGA 57.586 29.630 31.79 0.00 41.84 3.36
695 713 9.676195 GAAGATCTTCAAGAAAAGAAAAAGGAG 57.324 33.333 27.08 0.00 38.69 3.69
696 714 8.986929 AGATCTTCAAGAAAAGAAAAAGGAGA 57.013 30.769 0.00 0.00 38.69 3.71
697 715 9.065798 AGATCTTCAAGAAAAGAAAAAGGAGAG 57.934 33.333 0.00 0.00 38.69 3.20
698 716 7.032377 TCTTCAAGAAAAGAAAAAGGAGAGC 57.968 36.000 0.00 0.00 32.42 4.09
699 717 6.603201 TCTTCAAGAAAAGAAAAAGGAGAGCA 59.397 34.615 0.00 0.00 32.42 4.26
700 718 6.382869 TCAAGAAAAGAAAAAGGAGAGCAG 57.617 37.500 0.00 0.00 0.00 4.24
701 719 5.888161 TCAAGAAAAGAAAAAGGAGAGCAGT 59.112 36.000 0.00 0.00 0.00 4.40
702 720 7.054124 TCAAGAAAAGAAAAAGGAGAGCAGTA 58.946 34.615 0.00 0.00 0.00 2.74
703 721 7.721399 TCAAGAAAAGAAAAAGGAGAGCAGTAT 59.279 33.333 0.00 0.00 0.00 2.12
704 722 8.355913 CAAGAAAAGAAAAAGGAGAGCAGTATT 58.644 33.333 0.00 0.00 0.00 1.89
705 723 8.470657 AGAAAAGAAAAAGGAGAGCAGTATTT 57.529 30.769 0.00 0.00 0.00 1.40
706 724 8.572185 AGAAAAGAAAAAGGAGAGCAGTATTTC 58.428 33.333 0.00 0.00 0.00 2.17
707 725 8.470657 AAAAGAAAAAGGAGAGCAGTATTTCT 57.529 30.769 0.00 0.00 37.27 2.52
708 726 7.680442 AAGAAAAAGGAGAGCAGTATTTCTC 57.320 36.000 0.00 0.00 39.25 2.87
709 727 6.773638 AGAAAAAGGAGAGCAGTATTTCTCA 58.226 36.000 4.16 0.00 41.24 3.27
710 728 7.227156 AGAAAAAGGAGAGCAGTATTTCTCAA 58.773 34.615 4.16 0.00 41.24 3.02
711 729 7.721399 AGAAAAAGGAGAGCAGTATTTCTCAAA 59.279 33.333 4.16 0.00 41.24 2.69
712 730 7.823745 AAAAGGAGAGCAGTATTTCTCAAAA 57.176 32.000 4.16 0.00 41.24 2.44
713 731 7.823745 AAAGGAGAGCAGTATTTCTCAAAAA 57.176 32.000 4.16 0.00 41.24 1.94
735 753 5.506686 AAGAAAAAGGAGAGCAGTGTTTC 57.493 39.130 0.00 0.00 0.00 2.78
771 789 5.921962 AAAAAGAAAAAGGAGAGCAGTGT 57.078 34.783 0.00 0.00 0.00 3.55
772 790 5.921962 AAAAGAAAAAGGAGAGCAGTGTT 57.078 34.783 0.00 0.00 0.00 3.32
773 791 5.921962 AAAGAAAAAGGAGAGCAGTGTTT 57.078 34.783 0.00 0.00 0.00 2.83
774 792 5.506686 AAGAAAAAGGAGAGCAGTGTTTC 57.493 39.130 0.00 0.00 0.00 2.78
775 793 4.786425 AGAAAAAGGAGAGCAGTGTTTCT 58.214 39.130 0.00 0.00 0.00 2.52
776 794 4.819088 AGAAAAAGGAGAGCAGTGTTTCTC 59.181 41.667 14.73 14.73 39.25 2.87
777 795 3.845781 AAAGGAGAGCAGTGTTTCTCA 57.154 42.857 20.92 0.00 41.24 3.27
778 796 3.845781 AAGGAGAGCAGTGTTTCTCAA 57.154 42.857 20.92 0.00 41.24 3.02
779 797 3.845781 AGGAGAGCAGTGTTTCTCAAA 57.154 42.857 20.92 0.00 41.24 2.69
780 798 4.156455 AGGAGAGCAGTGTTTCTCAAAA 57.844 40.909 20.92 0.00 41.24 2.44
781 799 4.526970 AGGAGAGCAGTGTTTCTCAAAAA 58.473 39.130 20.92 0.00 41.24 1.94
1232 1263 2.294078 CCCTCAAGCCCCTCGTCTT 61.294 63.158 0.00 0.00 0.00 3.01
1427 1472 3.865929 CTGCCTGACGACGCTTGGT 62.866 63.158 0.00 0.00 0.00 3.67
1530 1575 3.393970 CTCCTCCAGCTCCCGCAA 61.394 66.667 0.00 0.00 39.10 4.85
1571 1616 1.337817 CTCGTCGACGGCAACAAGAG 61.338 60.000 35.05 19.64 40.29 2.85
1611 1657 1.737816 GCTCGTACGCCCCTAATCA 59.262 57.895 11.24 0.00 0.00 2.57
1617 1663 0.838987 TACGCCCCTAATCATCCCCC 60.839 60.000 0.00 0.00 0.00 5.40
1688 1740 0.037697 TACGGCGAGCATTGTCTGTT 60.038 50.000 16.62 0.00 0.00 3.16
1692 1744 0.593128 GCGAGCATTGTCTGTTTGGT 59.407 50.000 0.00 0.00 0.00 3.67
1808 1860 1.971357 CTGGGCGTTATCTCCACCTAT 59.029 52.381 0.00 0.00 0.00 2.57
1904 1956 0.323629 CCGGGCTTGTCCTCAACTTA 59.676 55.000 0.00 0.00 34.39 2.24
2007 2059 3.815401 CCCTCAGGTGACACTTACTTTTG 59.185 47.826 5.39 0.00 0.00 2.44
2039 2091 1.153025 TGCAGATCCAGCTGATGCC 60.153 57.895 17.39 1.07 40.80 4.40
2050 2102 1.530771 CTGATGCCCCTGCTAGCTT 59.469 57.895 17.23 0.00 38.71 3.74
2134 2186 0.305617 GTCAACGTTTGTTCCCGTCC 59.694 55.000 0.00 0.00 35.72 4.79
2190 2242 0.318445 CTTTGGCTGTTGCTGCTGTC 60.318 55.000 0.00 0.00 39.59 3.51
2193 2245 3.653009 GCTGTTGCTGCTGTCGCA 61.653 61.111 0.00 0.00 45.60 5.10
2203 2255 1.368641 TGCTGTCGCAATGGTATGAC 58.631 50.000 0.00 0.00 44.62 3.06
2223 2275 3.944015 GACACATCCTCTTGCATAAAGCT 59.056 43.478 0.00 0.00 45.94 3.74
2232 2284 4.300803 TCTTGCATAAAGCTGTTTTGCTG 58.699 39.130 17.61 13.03 43.24 4.41
2321 2383 9.886132 AAGTTATACTGTACAAAGAGGTAATGG 57.114 33.333 0.00 0.00 0.00 3.16
2322 2384 9.043548 AGTTATACTGTACAAAGAGGTAATGGT 57.956 33.333 0.00 0.00 0.00 3.55
2338 2400 8.383374 AGGTAATGGTAATTGTAGACAACCTA 57.617 34.615 0.00 0.00 38.86 3.08
2365 2427 6.593978 GTCACTTGCATGACTTTAGTTAGTG 58.406 40.000 12.27 6.78 44.71 2.74
2433 2498 8.340618 AGAAGCTTGAGTGCAGAATAATTAAA 57.659 30.769 2.10 0.00 34.99 1.52
2446 2511 7.330946 GCAGAATAATTAAACCCAGTTCCAAAC 59.669 37.037 0.00 0.00 0.00 2.93
2447 2512 8.585018 CAGAATAATTAAACCCAGTTCCAAACT 58.415 33.333 0.00 0.00 44.06 2.66
2448 2513 9.816787 AGAATAATTAAACCCAGTTCCAAACTA 57.183 29.630 0.00 0.00 40.46 2.24
2459 2524 6.106673 CCAGTTCCAAACTAGTACGAATCAT 58.893 40.000 0.00 0.00 40.46 2.45
2543 2608 8.565896 TTTTAGCACAGTACAAATCTGATCAT 57.434 30.769 0.00 0.00 36.81 2.45
2780 2854 9.469807 GACTAATGACACAATATCCACTTCTAG 57.530 37.037 0.00 0.00 0.00 2.43
2955 3029 7.773690 ACAGATGGTACTCAAACTTTTACACTT 59.226 33.333 0.00 0.00 0.00 3.16
3174 3249 9.920946 ATGTGGTATGTTCTATTTCAACCTATT 57.079 29.630 0.00 0.00 0.00 1.73
3218 3293 6.886459 ACAACTGCATGAGAATATACAAAGGT 59.114 34.615 0.00 0.00 0.00 3.50
3222 3297 5.822519 TGCATGAGAATATACAAAGGTGGAC 59.177 40.000 0.00 0.00 0.00 4.02
3227 3302 2.747396 TATACAAAGGTGGACGCGTT 57.253 45.000 15.53 0.00 0.00 4.84
3271 3346 5.728471 TGATTCTCATCTGAAGAGTCAACC 58.272 41.667 9.47 0.00 34.73 3.77
3333 3408 8.047310 AGTCAATATCTTCCTAATCACCGTTTT 58.953 33.333 0.00 0.00 0.00 2.43
3341 3416 7.601508 TCTTCCTAATCACCGTTTTAAGAGTTC 59.398 37.037 0.00 0.00 0.00 3.01
3456 3531 8.311836 TCTTGGACCAATTACTAGTTGAGTTAG 58.688 37.037 7.54 0.00 39.81 2.34
3534 3609 3.006247 GGCAAACAGAGAAGATGAGGTC 58.994 50.000 0.00 0.00 0.00 3.85
3548 3623 9.606631 AGAAGATGAGGTCATGTTAAAGTTATC 57.393 33.333 2.53 0.00 39.54 1.75
3556 3631 9.798994 AGGTCATGTTAAAGTTATCGTTACTAG 57.201 33.333 0.00 0.00 0.00 2.57
3577 3652 2.093447 GCCGGAGAGGAAAGAGATTCAA 60.093 50.000 5.05 0.00 45.00 2.69
3596 3671 6.567687 TTCAAATTATGAAGTTTCCGAGCA 57.432 33.333 0.00 0.00 43.08 4.26
3597 3672 6.182039 TCAAATTATGAAGTTTCCGAGCAG 57.818 37.500 0.00 0.00 34.30 4.24
3598 3673 5.705441 TCAAATTATGAAGTTTCCGAGCAGT 59.295 36.000 0.00 0.00 34.30 4.40
3599 3674 6.876789 TCAAATTATGAAGTTTCCGAGCAGTA 59.123 34.615 0.00 0.00 34.30 2.74
3600 3675 6.910536 AATTATGAAGTTTCCGAGCAGTAG 57.089 37.500 0.00 0.00 0.00 2.57
3601 3676 2.743636 TGAAGTTTCCGAGCAGTAGG 57.256 50.000 0.00 0.00 0.00 3.18
3602 3677 1.968493 TGAAGTTTCCGAGCAGTAGGT 59.032 47.619 0.00 0.00 0.00 3.08
3603 3678 2.288825 TGAAGTTTCCGAGCAGTAGGTG 60.289 50.000 0.00 0.00 0.00 4.00
3623 3717 1.127582 GCTTAGCGAAACTCACTGCAG 59.872 52.381 13.48 13.48 0.00 4.41
3679 3773 2.403252 ATGGAACTCTACCAAAGCCG 57.597 50.000 0.00 0.00 40.93 5.52
3722 3817 4.073293 ACATCCTCGGTAATTCCATGAC 57.927 45.455 0.00 0.00 35.57 3.06
3757 3857 6.297694 TGGTTGCTTATTTTGTGAAATTGC 57.702 33.333 0.00 0.00 36.82 3.56
3772 3893 4.512944 TGAAATTGCGATTGAGATAGAGGC 59.487 41.667 0.00 0.00 0.00 4.70
3774 3895 1.413118 TGCGATTGAGATAGAGGCCA 58.587 50.000 5.01 0.00 0.00 5.36
3839 3960 6.375174 TGATGTTTCCCAATACAGTCAATCAG 59.625 38.462 0.00 0.00 0.00 2.90
3847 3968 5.301045 CCAATACAGTCAATCAGATGCCATT 59.699 40.000 0.00 0.00 0.00 3.16
3848 3969 6.183360 CCAATACAGTCAATCAGATGCCATTT 60.183 38.462 0.00 0.00 0.00 2.32
3898 4073 3.259374 TGACCACTCACTCTTGATTCTCC 59.741 47.826 0.00 0.00 0.00 3.71
3994 4169 4.257731 TGGTATGTTTTCGCAGCTATGAA 58.742 39.130 0.00 0.00 0.00 2.57
3995 4170 4.881273 TGGTATGTTTTCGCAGCTATGAAT 59.119 37.500 1.09 0.00 0.00 2.57
3996 4171 5.207768 GGTATGTTTTCGCAGCTATGAATG 58.792 41.667 1.09 0.00 0.00 2.67
3997 4172 5.007626 GGTATGTTTTCGCAGCTATGAATGA 59.992 40.000 1.09 0.00 0.00 2.57
3998 4173 5.762825 ATGTTTTCGCAGCTATGAATGAT 57.237 34.783 1.09 0.00 0.00 2.45
4029 4207 9.494479 CTGATTTACATATACAGCAAGTGTTTG 57.506 33.333 0.00 0.00 40.94 2.93
4083 4263 3.676216 TGCAACAGCATCAGCAGG 58.324 55.556 0.00 0.00 45.49 4.85
4152 4332 2.557676 CCTCCCCGCTCCATCTCTAATA 60.558 54.545 0.00 0.00 0.00 0.98
4189 4369 4.832248 TCTTTATGATGAACCGCAACTCT 58.168 39.130 0.00 0.00 0.00 3.24
4301 4481 1.836166 TGGATTCTCTGAAGGAGCTGG 59.164 52.381 0.00 0.00 41.60 4.85
4320 4500 1.275291 GGTCTTCGGGAAGTGATGACA 59.725 52.381 8.19 0.00 40.42 3.58
4321 4501 2.338500 GTCTTCGGGAAGTGATGACAC 58.662 52.381 8.19 0.00 46.24 3.67
4340 4520 1.816835 ACCATCATCAGCAAGCAGTTG 59.183 47.619 0.00 0.00 36.67 3.16
4349 4529 0.031721 GCAAGCAGTTGAAAGCAGCT 59.968 50.000 0.00 0.00 35.46 4.24
4364 4544 1.229082 AGCTGACTGTTCCGGGGTA 60.229 57.895 0.00 0.00 0.00 3.69
4366 4546 1.542187 GCTGACTGTTCCGGGGTAGT 61.542 60.000 0.00 3.02 0.00 2.73
4367 4547 1.843368 CTGACTGTTCCGGGGTAGTA 58.157 55.000 0.00 0.00 0.00 1.82
4368 4548 1.749634 CTGACTGTTCCGGGGTAGTAG 59.250 57.143 0.00 0.00 0.00 2.57
4369 4549 1.109609 GACTGTTCCGGGGTAGTAGG 58.890 60.000 0.00 0.00 0.00 3.18
4370 4550 0.706433 ACTGTTCCGGGGTAGTAGGA 59.294 55.000 0.00 0.00 0.00 2.94
4371 4551 1.077663 ACTGTTCCGGGGTAGTAGGAA 59.922 52.381 0.00 0.00 41.28 3.36
4373 4553 3.305181 TTCCGGGGTAGTAGGAACC 57.695 57.895 0.00 0.00 38.94 3.62
4386 4567 0.178961 AGGAACCAACCAGGAAAGCC 60.179 55.000 0.00 0.00 41.22 4.35
4444 4625 0.961857 GAACCGGGCCGTGGTAAAAT 60.962 55.000 26.32 3.23 39.29 1.82
4484 4672 6.603599 GCATAGAGGTGAAAATTAAGAAGGGT 59.396 38.462 0.00 0.00 0.00 4.34
4614 4807 4.920112 CGTGACCACCACCGGCAA 62.920 66.667 0.00 0.00 42.76 4.52
4667 4868 1.645710 AAGGGTACAGTGGAGGAGTG 58.354 55.000 0.00 0.00 0.00 3.51
4744 4949 9.793259 TCTTCTCACCTTGAATAAAGTTTACAT 57.207 29.630 0.00 0.00 33.66 2.29
4773 5037 9.662947 CTTCTCACTCATGCAAATATATATGGA 57.337 33.333 0.00 0.00 0.00 3.41
4775 5039 9.440773 TCTCACTCATGCAAATATATATGGAAC 57.559 33.333 0.00 0.00 0.00 3.62
4814 5139 8.226448 TGAAATATATTTTTGCTTGTTTTGGCG 58.774 29.630 11.92 0.00 0.00 5.69
4852 5181 6.402981 ACAGTAAAAGGGTGGGAATATCTT 57.597 37.500 0.00 0.00 0.00 2.40
4854 5183 7.246027 ACAGTAAAAGGGTGGGAATATCTTTT 58.754 34.615 0.00 0.00 39.80 2.27
4895 5224 1.758440 GCCAGTGGGTCAGTGAGTGA 61.758 60.000 12.15 0.00 36.99 3.41
4898 5227 1.043816 AGTGGGTCAGTGAGTGAGTG 58.956 55.000 0.00 0.00 35.13 3.51
4899 5228 0.034059 GTGGGTCAGTGAGTGAGTGG 59.966 60.000 0.00 0.00 35.13 4.00
4900 5229 1.121407 TGGGTCAGTGAGTGAGTGGG 61.121 60.000 0.00 0.00 35.13 4.61
4941 5274 1.342074 CAGGTCCAGTCCAGTCAAGA 58.658 55.000 0.00 0.00 0.00 3.02
4953 5286 3.451178 TCCAGTCAAGACCAGCCTAATAC 59.549 47.826 0.00 0.00 0.00 1.89
4966 5301 3.632145 AGCCTAATACAAAAATCAGCCCG 59.368 43.478 0.00 0.00 0.00 6.13
4990 5325 5.123661 GGTAAAACGATGATTAAAACCGGGA 59.876 40.000 6.32 0.00 0.00 5.14
4992 5327 5.708877 AAACGATGATTAAAACCGGGAAA 57.291 34.783 6.32 0.00 0.00 3.13
4993 5328 4.690184 ACGATGATTAAAACCGGGAAAC 57.310 40.909 6.32 0.00 0.00 2.78
5050 5400 3.800863 GTCGTCTCCGCGCAGAGA 61.801 66.667 19.24 19.24 40.62 3.10
5051 5401 3.500642 TCGTCTCCGCGCAGAGAG 61.501 66.667 23.29 17.04 43.47 3.20
5052 5402 3.500642 CGTCTCCGCGCAGAGAGA 61.501 66.667 23.29 19.03 43.47 3.10
5053 5403 2.407210 GTCTCCGCGCAGAGAGAG 59.593 66.667 23.29 12.12 43.47 3.20
5054 5404 2.109739 GTCTCCGCGCAGAGAGAGA 61.110 63.158 23.29 14.16 43.47 3.10
5055 5405 1.817520 TCTCCGCGCAGAGAGAGAG 60.818 63.158 19.24 6.80 37.98 3.20
5056 5406 2.826287 TCCGCGCAGAGAGAGAGG 60.826 66.667 8.75 0.00 38.31 3.69
5057 5407 3.898509 CCGCGCAGAGAGAGAGGG 61.899 72.222 8.75 0.00 33.48 4.30
5135 5485 3.822192 CATCCACCGGCGAGACGA 61.822 66.667 9.30 0.00 35.47 4.20
5136 5486 3.518998 ATCCACCGGCGAGACGAG 61.519 66.667 9.30 0.00 35.47 4.18
5137 5487 3.989838 ATCCACCGGCGAGACGAGA 62.990 63.158 9.30 0.00 35.47 4.04
5138 5488 4.180946 CCACCGGCGAGACGAGAG 62.181 72.222 9.30 0.00 35.47 3.20
5139 5489 4.838486 CACCGGCGAGACGAGAGC 62.838 72.222 9.30 0.00 35.47 4.09
5142 5492 4.583254 CGGCGAGACGAGAGCGAG 62.583 72.222 0.00 0.00 41.64 5.03
5143 5493 3.196394 GGCGAGACGAGAGCGAGA 61.196 66.667 0.00 0.00 41.64 4.04
5144 5494 2.751913 GGCGAGACGAGAGCGAGAA 61.752 63.158 0.00 0.00 41.64 2.87
5145 5495 1.297304 GCGAGACGAGAGCGAGAAG 60.297 63.158 0.00 0.00 41.64 2.85
5146 5496 1.697772 GCGAGACGAGAGCGAGAAGA 61.698 60.000 0.00 0.00 41.64 2.87
5147 5497 0.722282 CGAGACGAGAGCGAGAAGAA 59.278 55.000 0.00 0.00 41.64 2.52
5148 5498 1.128878 CGAGACGAGAGCGAGAAGAAA 59.871 52.381 0.00 0.00 41.64 2.52
5149 5499 2.412977 CGAGACGAGAGCGAGAAGAAAA 60.413 50.000 0.00 0.00 41.64 2.29
5150 5500 2.912345 GAGACGAGAGCGAGAAGAAAAC 59.088 50.000 0.00 0.00 41.64 2.43
5151 5501 1.644780 GACGAGAGCGAGAAGAAAACG 59.355 52.381 0.00 0.00 41.64 3.60
5247 5602 3.130160 CAGGCCAGAAAGCGAGCC 61.130 66.667 5.01 0.00 46.13 4.70
5445 5833 2.604686 AAGACGCTCTGGGAGGCA 60.605 61.111 0.00 0.00 0.00 4.75
5540 5928 4.790140 CGTCAACAGATACAAGGTACGTAC 59.210 45.833 17.56 17.56 0.00 3.67
5541 5929 5.098211 GTCAACAGATACAAGGTACGTACC 58.902 45.833 33.16 33.16 46.82 3.34
5554 5942 3.629398 GGTACGTACCTGTGTGCTATACT 59.371 47.826 32.93 0.00 43.10 2.12
5557 5945 3.377485 ACGTACCTGTGTGCTATACTCTG 59.623 47.826 0.00 0.00 0.00 3.35
5566 5954 1.005630 CTATACTCTGCCTGCCGCC 60.006 63.158 0.00 0.00 36.24 6.13
5567 5955 1.748329 CTATACTCTGCCTGCCGCCA 61.748 60.000 0.00 0.00 36.24 5.69
5568 5956 1.121407 TATACTCTGCCTGCCGCCAT 61.121 55.000 0.00 0.00 36.24 4.40
5579 5967 3.451894 CCGCCATTCCCTTGCACC 61.452 66.667 0.00 0.00 0.00 5.01
5580 5968 2.361610 CGCCATTCCCTTGCACCT 60.362 61.111 0.00 0.00 0.00 4.00
5583 5971 1.318158 GCCATTCCCTTGCACCTCTG 61.318 60.000 0.00 0.00 0.00 3.35
5585 5973 1.000396 ATTCCCTTGCACCTCTGCC 60.000 57.895 0.00 0.00 43.51 4.85
5586 5974 1.504275 ATTCCCTTGCACCTCTGCCT 61.504 55.000 0.00 0.00 43.51 4.75
5588 5976 2.045536 CCTTGCACCTCTGCCTCC 60.046 66.667 0.00 0.00 43.51 4.30
5591 5979 1.229496 TTGCACCTCTGCCTCCCTA 60.229 57.895 0.00 0.00 43.51 3.53
5592 5980 0.840288 TTGCACCTCTGCCTCCCTAA 60.840 55.000 0.00 0.00 43.51 2.69
5606 5994 5.014123 TGCCTCCCTAATAATGGAGTAATGG 59.986 44.000 4.96 0.00 45.56 3.16
5608 5996 6.467339 GCCTCCCTAATAATGGAGTAATGGTT 60.467 42.308 4.96 0.00 45.56 3.67
5609 5997 7.256908 GCCTCCCTAATAATGGAGTAATGGTTA 60.257 40.741 4.96 0.00 45.56 2.85
5610 5998 8.836735 CCTCCCTAATAATGGAGTAATGGTTAT 58.163 37.037 4.96 0.00 45.56 1.89
5613 6004 9.614792 CCCTAATAATGGAGTAATGGTTATAGC 57.385 37.037 0.00 0.00 0.00 2.97
5617 6008 9.726438 AATAATGGAGTAATGGTTATAGCTGTC 57.274 33.333 0.00 0.00 0.00 3.51
5619 6010 6.161855 TGGAGTAATGGTTATAGCTGTCTG 57.838 41.667 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.542492 AGGGCAGCAAGAGTTCAATG 58.458 50.000 0.00 0.00 0.00 2.82
67 68 3.607439 CAACTTCAACGTGTTGTGCTAG 58.393 45.455 12.10 8.37 41.16 3.42
83 84 4.764823 TCACAAGTGTTGAAGGAACAACTT 59.235 37.500 11.73 0.00 46.30 2.66
103 104 2.474526 GCTGCGACAATGTGTACATCAC 60.475 50.000 0.00 0.00 46.31 3.06
104 105 1.731709 GCTGCGACAATGTGTACATCA 59.268 47.619 0.00 0.00 35.10 3.07
105 106 2.002586 AGCTGCGACAATGTGTACATC 58.997 47.619 0.00 0.00 35.10 3.06
106 107 2.099141 AGCTGCGACAATGTGTACAT 57.901 45.000 0.00 0.00 38.41 2.29
134 136 0.179089 CGAAGGATGTGGAGGAGCAG 60.179 60.000 0.00 0.00 0.00 4.24
142 144 0.957395 AAGCAGCACGAAGGATGTGG 60.957 55.000 0.00 0.00 37.80 4.17
147 149 0.392706 TTCTGAAGCAGCACGAAGGA 59.607 50.000 0.00 0.00 0.00 3.36
152 154 0.519999 GCGATTTCTGAAGCAGCACG 60.520 55.000 0.00 0.00 0.00 5.34
153 155 0.179179 GGCGATTTCTGAAGCAGCAC 60.179 55.000 12.55 0.00 0.00 4.40
193 195 4.100808 AGCAAGACAAAGAGAGAGTTGAGT 59.899 41.667 0.00 0.00 0.00 3.41
214 216 2.293399 AGTTTGATCACCGAAAACCAGC 59.707 45.455 0.00 0.00 34.96 4.85
215 217 3.563808 TGAGTTTGATCACCGAAAACCAG 59.436 43.478 0.00 0.00 34.96 4.00
249 251 4.415596 TCGGGACTAAGGGTAAACTACAA 58.584 43.478 0.00 0.00 0.00 2.41
263 265 1.040646 GATGTGGAGCATCGGGACTA 58.959 55.000 0.00 0.00 43.75 2.59
276 278 2.787994 AGAAGTGCTTTGGAGATGTGG 58.212 47.619 0.00 0.00 0.00 4.17
285 292 5.403897 TTGAGTTCGTTAGAAGTGCTTTG 57.596 39.130 0.00 0.00 39.94 2.77
294 301 1.542915 CCGGACCTTGAGTTCGTTAGA 59.457 52.381 0.00 0.00 46.85 2.10
336 344 2.433868 ATATACACGGACGATGTGGC 57.566 50.000 0.00 0.00 41.64 5.01
344 352 2.806244 GTGGCCATCAATATACACGGAC 59.194 50.000 9.72 0.00 0.00 4.79
347 355 3.248363 CACAGTGGCCATCAATATACACG 59.752 47.826 9.72 0.00 34.28 4.49
351 359 4.769345 TGACACAGTGGCCATCAATATA 57.231 40.909 9.72 0.00 0.00 0.86
360 368 0.176680 ATCTCGATGACACAGTGGCC 59.823 55.000 3.17 0.00 0.00 5.36
362 370 1.478105 TGGATCTCGATGACACAGTGG 59.522 52.381 5.31 0.00 0.00 4.00
364 372 2.762887 ACATGGATCTCGATGACACAGT 59.237 45.455 8.88 0.00 35.90 3.55
372 380 3.323115 AGCACATACACATGGATCTCGAT 59.677 43.478 0.00 0.00 36.39 3.59
373 381 2.695147 AGCACATACACATGGATCTCGA 59.305 45.455 0.00 0.00 36.39 4.04
380 388 3.476295 GTGTTGAGCACATACACATGG 57.524 47.619 17.67 0.00 46.91 3.66
406 414 5.107453 GCTATTGTAACTACGGCTATGCAAG 60.107 44.000 0.00 0.00 0.00 4.01
411 419 3.571401 ACGGCTATTGTAACTACGGCTAT 59.429 43.478 0.00 0.00 0.00 2.97
416 424 3.065786 TCCTCACGGCTATTGTAACTACG 59.934 47.826 0.00 0.00 0.00 3.51
417 425 4.357996 GTCCTCACGGCTATTGTAACTAC 58.642 47.826 0.00 0.00 0.00 2.73
439 457 7.652727 TCTATTGTTCGTCATCTCTATGAAGG 58.347 38.462 0.00 0.00 43.69 3.46
442 460 6.207614 CCCTCTATTGTTCGTCATCTCTATGA 59.792 42.308 0.00 0.00 39.87 2.15
446 464 3.639094 CCCCTCTATTGTTCGTCATCTCT 59.361 47.826 0.00 0.00 0.00 3.10
448 466 3.639094 CTCCCCTCTATTGTTCGTCATCT 59.361 47.826 0.00 0.00 0.00 2.90
451 469 2.758979 GTCTCCCCTCTATTGTTCGTCA 59.241 50.000 0.00 0.00 0.00 4.35
460 478 1.435168 GGGATCCAGTCTCCCCTCTAT 59.565 57.143 15.23 0.00 45.80 1.98
468 486 1.529309 GCCAAGGGGATCCAGTCTC 59.471 63.158 15.23 0.00 35.59 3.36
472 490 0.463833 GTTACGCCAAGGGGATCCAG 60.464 60.000 15.23 0.00 35.59 3.86
473 491 1.605453 GTTACGCCAAGGGGATCCA 59.395 57.895 15.23 0.00 35.59 3.41
474 492 1.153025 GGTTACGCCAAGGGGATCC 60.153 63.158 10.39 1.92 37.17 3.36
475 493 1.153025 GGGTTACGCCAAGGGGATC 60.153 63.158 10.39 0.00 39.65 3.36
476 494 1.212250 AAGGGTTACGCCAAGGGGAT 61.212 55.000 10.39 0.00 39.65 3.85
477 495 1.428718 AAAGGGTTACGCCAAGGGGA 61.429 55.000 10.39 0.00 39.65 4.81
478 496 0.963856 GAAAGGGTTACGCCAAGGGG 60.964 60.000 1.12 1.12 39.65 4.79
479 497 1.303091 CGAAAGGGTTACGCCAAGGG 61.303 60.000 0.00 0.00 39.65 3.95
480 498 1.918868 GCGAAAGGGTTACGCCAAGG 61.919 60.000 0.00 0.00 45.35 3.61
491 509 1.205417 AGAATTTGGCATGCGAAAGGG 59.795 47.619 27.92 0.00 0.00 3.95
497 515 1.747355 AGAAGGAGAATTTGGCATGCG 59.253 47.619 12.44 0.00 0.00 4.73
516 534 1.759445 AGTGATCAATGGAGTCCCGAG 59.241 52.381 6.74 0.00 34.29 4.63
517 535 1.866015 AGTGATCAATGGAGTCCCGA 58.134 50.000 6.74 0.74 34.29 5.14
532 550 2.922779 TCGAGCACGAGTGTAGTGA 58.077 52.632 0.88 0.00 43.81 3.41
588 606 2.901192 TGAAACAGGGGTCTACGATTGA 59.099 45.455 0.00 0.00 0.00 2.57
597 615 1.680249 GGCTCTGATGAAACAGGGGTC 60.680 57.143 0.00 0.00 38.65 4.46
598 616 0.329596 GGCTCTGATGAAACAGGGGT 59.670 55.000 0.00 0.00 38.65 4.95
599 617 0.394899 GGGCTCTGATGAAACAGGGG 60.395 60.000 0.00 0.00 38.65 4.79
600 618 0.329261 TGGGCTCTGATGAAACAGGG 59.671 55.000 0.00 0.00 40.91 4.45
601 619 1.457346 GTGGGCTCTGATGAAACAGG 58.543 55.000 0.00 0.00 38.31 4.00
602 620 1.457346 GGTGGGCTCTGATGAAACAG 58.543 55.000 0.00 0.00 39.02 3.16
603 621 0.038166 GGGTGGGCTCTGATGAAACA 59.962 55.000 0.00 0.00 0.00 2.83
604 622 1.026718 CGGGTGGGCTCTGATGAAAC 61.027 60.000 0.00 0.00 0.00 2.78
605 623 1.198094 TCGGGTGGGCTCTGATGAAA 61.198 55.000 0.00 0.00 0.00 2.69
606 624 1.612146 TCGGGTGGGCTCTGATGAA 60.612 57.895 0.00 0.00 0.00 2.57
607 625 2.038813 TCGGGTGGGCTCTGATGA 59.961 61.111 0.00 0.00 0.00 2.92
608 626 2.503061 CTCGGGTGGGCTCTGATG 59.497 66.667 0.00 0.00 0.00 3.07
609 627 3.474570 GCTCGGGTGGGCTCTGAT 61.475 66.667 0.00 0.00 0.00 2.90
640 658 2.839486 TACTTGGGTCTTCACTGCAG 57.161 50.000 13.48 13.48 0.00 4.41
686 704 7.440523 TTGAGAAATACTGCTCTCCTTTTTC 57.559 36.000 0.00 0.00 37.82 2.29
687 705 7.823745 TTTGAGAAATACTGCTCTCCTTTTT 57.176 32.000 0.00 0.00 37.82 1.94
688 706 7.823745 TTTTGAGAAATACTGCTCTCCTTTT 57.176 32.000 0.00 0.00 37.82 2.27
689 707 7.823745 TTTTTGAGAAATACTGCTCTCCTTT 57.176 32.000 0.00 0.00 37.82 3.11
710 728 5.921962 ACACTGCTCTCCTTTTTCTTTTT 57.078 34.783 0.00 0.00 0.00 1.94
711 729 5.921962 AACACTGCTCTCCTTTTTCTTTT 57.078 34.783 0.00 0.00 0.00 2.27
712 730 5.654209 AGAAACACTGCTCTCCTTTTTCTTT 59.346 36.000 0.00 0.00 29.61 2.52
713 731 5.196695 AGAAACACTGCTCTCCTTTTTCTT 58.803 37.500 0.00 0.00 29.61 2.52
714 732 4.786425 AGAAACACTGCTCTCCTTTTTCT 58.214 39.130 0.00 0.00 0.00 2.52
715 733 4.576463 TGAGAAACACTGCTCTCCTTTTTC 59.424 41.667 6.37 0.00 37.82 2.29
751 769 5.654209 AGAAACACTGCTCTCCTTTTTCTTT 59.346 36.000 0.00 0.00 29.61 2.52
752 770 5.196695 AGAAACACTGCTCTCCTTTTTCTT 58.803 37.500 0.00 0.00 29.61 2.52
753 771 4.786425 AGAAACACTGCTCTCCTTTTTCT 58.214 39.130 0.00 0.00 0.00 2.52
754 772 4.576463 TGAGAAACACTGCTCTCCTTTTTC 59.424 41.667 6.37 0.00 37.82 2.29
755 773 4.526970 TGAGAAACACTGCTCTCCTTTTT 58.473 39.130 6.37 0.00 37.82 1.94
756 774 4.156455 TGAGAAACACTGCTCTCCTTTT 57.844 40.909 6.37 0.00 37.82 2.27
757 775 3.845781 TGAGAAACACTGCTCTCCTTT 57.154 42.857 6.37 0.00 37.82 3.11
758 776 3.845781 TTGAGAAACACTGCTCTCCTT 57.154 42.857 6.37 0.00 37.82 3.36
759 777 3.845781 TTTGAGAAACACTGCTCTCCT 57.154 42.857 6.37 0.00 37.82 3.69
760 778 4.900635 TTTTTGAGAAACACTGCTCTCC 57.099 40.909 6.37 0.00 37.82 3.71
780 798 9.155975 GCTCTCCTTTTTCTTTTCTTTTTCTTT 57.844 29.630 0.00 0.00 0.00 2.52
781 799 8.314021 TGCTCTCCTTTTTCTTTTCTTTTTCTT 58.686 29.630 0.00 0.00 0.00 2.52
782 800 7.840931 TGCTCTCCTTTTTCTTTTCTTTTTCT 58.159 30.769 0.00 0.00 0.00 2.52
783 801 7.761704 ACTGCTCTCCTTTTTCTTTTCTTTTTC 59.238 33.333 0.00 0.00 0.00 2.29
784 802 7.547019 CACTGCTCTCCTTTTTCTTTTCTTTTT 59.453 33.333 0.00 0.00 0.00 1.94
785 803 7.038048 CACTGCTCTCCTTTTTCTTTTCTTTT 58.962 34.615 0.00 0.00 0.00 2.27
786 804 6.378280 TCACTGCTCTCCTTTTTCTTTTCTTT 59.622 34.615 0.00 0.00 0.00 2.52
787 805 5.888161 TCACTGCTCTCCTTTTTCTTTTCTT 59.112 36.000 0.00 0.00 0.00 2.52
788 806 5.440610 TCACTGCTCTCCTTTTTCTTTTCT 58.559 37.500 0.00 0.00 0.00 2.52
789 807 5.757850 TCACTGCTCTCCTTTTTCTTTTC 57.242 39.130 0.00 0.00 0.00 2.29
790 808 5.888161 TCTTCACTGCTCTCCTTTTTCTTTT 59.112 36.000 0.00 0.00 0.00 2.27
791 809 5.440610 TCTTCACTGCTCTCCTTTTTCTTT 58.559 37.500 0.00 0.00 0.00 2.52
792 810 5.041191 TCTTCACTGCTCTCCTTTTTCTT 57.959 39.130 0.00 0.00 0.00 2.52
793 811 4.696479 TCTTCACTGCTCTCCTTTTTCT 57.304 40.909 0.00 0.00 0.00 2.52
794 812 5.956068 AATCTTCACTGCTCTCCTTTTTC 57.044 39.130 0.00 0.00 0.00 2.29
795 813 5.409826 CGTAATCTTCACTGCTCTCCTTTTT 59.590 40.000 0.00 0.00 0.00 1.94
1031 1062 4.537433 ATTCAGGCGAGGCGAGGC 62.537 66.667 0.00 0.92 0.00 4.70
1039 1070 1.687146 AGGAGCTGGATTCAGGCGA 60.687 57.895 2.40 0.00 41.19 5.54
1210 1241 3.483869 GAGGGGCTTGAGGGCGAT 61.484 66.667 0.00 0.00 41.87 4.58
1290 1321 2.962253 GTCTCGGGCAGCGCATAC 60.962 66.667 11.47 0.00 0.00 2.39
1530 1575 3.270877 GTTGCGGTAGTTGAGGATGATT 58.729 45.455 0.00 0.00 0.00 2.57
1617 1663 6.090358 TGAGAAACTAAGAAAGCGAAATACGG 59.910 38.462 0.00 0.00 42.83 4.02
1620 1666 7.334421 AGCATGAGAAACTAAGAAAGCGAAATA 59.666 33.333 0.00 0.00 0.00 1.40
1692 1744 3.157252 GAGCATCCCCTGGAGCGA 61.157 66.667 0.00 0.00 34.05 4.93
1808 1860 0.320683 CAAGCTGGACGATGACCACA 60.321 55.000 0.00 0.00 33.57 4.17
2007 2059 2.354109 TCTGCACGATGACAGAGAAC 57.646 50.000 0.00 0.00 37.99 3.01
2039 2091 1.612726 GGATGGCATAAGCTAGCAGGG 60.613 57.143 18.83 4.40 39.63 4.45
2190 2242 2.545526 GAGGATGTGTCATACCATTGCG 59.454 50.000 0.00 0.00 0.00 4.85
2193 2245 4.202441 GCAAGAGGATGTGTCATACCATT 58.798 43.478 0.00 0.00 0.00 3.16
2203 2255 3.693085 ACAGCTTTATGCAAGAGGATGTG 59.307 43.478 5.18 0.00 45.94 3.21
2223 2275 4.554526 CGCACATCTAACTTCAGCAAAACA 60.555 41.667 0.00 0.00 0.00 2.83
2232 2284 4.734917 AGAGTACACGCACATCTAACTTC 58.265 43.478 0.00 0.00 0.00 3.01
2365 2427 6.233905 ACAACCTCAAATTTATTATGGGGC 57.766 37.500 0.00 0.00 38.32 5.80
2433 2498 3.233507 TCGTACTAGTTTGGAACTGGGT 58.766 45.455 0.00 7.48 43.50 4.51
2477 2542 9.052759 TCACACTTAAAGAATCTAAAACACCTC 57.947 33.333 0.00 0.00 0.00 3.85
2576 2648 6.069905 TGGGCCTAAGTACAGATCAAAACATA 60.070 38.462 4.53 0.00 0.00 2.29
3174 3249 4.844998 TGTGCTCGGATTTGAAAAATGA 57.155 36.364 0.00 0.00 0.00 2.57
3271 3346 3.744660 AGTAGAAAAGCAGGTTGTGGAG 58.255 45.455 0.00 0.00 0.00 3.86
3421 3496 1.270907 TTGGTCCAAGAGAGCTCCTC 58.729 55.000 10.93 7.57 43.71 3.71
3456 3531 6.484977 GGTGGATGTTTCTAGGAGATTGAATC 59.515 42.308 0.00 0.00 0.00 2.52
3534 3609 7.306399 CCGGCTAGTAACGATAACTTTAACATG 60.306 40.741 0.00 0.00 0.00 3.21
3548 3623 1.386533 TTCCTCTCCGGCTAGTAACG 58.613 55.000 0.00 0.00 0.00 3.18
3556 3631 1.482593 TGAATCTCTTTCCTCTCCGGC 59.517 52.381 0.00 0.00 33.04 6.13
3577 3652 5.817816 CCTACTGCTCGGAAACTTCATAATT 59.182 40.000 0.00 0.00 0.00 1.40
3595 3670 2.924290 GAGTTTCGCTAAGCACCTACTG 59.076 50.000 0.00 0.00 0.00 2.74
3596 3671 2.561419 TGAGTTTCGCTAAGCACCTACT 59.439 45.455 0.00 0.00 0.00 2.57
3597 3672 2.666994 GTGAGTTTCGCTAAGCACCTAC 59.333 50.000 0.00 0.00 0.00 3.18
3598 3673 2.561419 AGTGAGTTTCGCTAAGCACCTA 59.439 45.455 0.00 0.00 35.10 3.08
3599 3674 1.344763 AGTGAGTTTCGCTAAGCACCT 59.655 47.619 0.00 0.00 35.10 4.00
3600 3675 1.461127 CAGTGAGTTTCGCTAAGCACC 59.539 52.381 0.00 0.00 34.53 5.01
3601 3676 1.136224 GCAGTGAGTTTCGCTAAGCAC 60.136 52.381 0.00 0.00 34.53 4.40
3602 3677 1.148310 GCAGTGAGTTTCGCTAAGCA 58.852 50.000 0.00 0.00 34.53 3.91
3603 3678 1.127582 CTGCAGTGAGTTTCGCTAAGC 59.872 52.381 5.25 0.00 34.53 3.09
3604 3679 2.677199 TCTGCAGTGAGTTTCGCTAAG 58.323 47.619 14.67 0.00 34.53 2.18
3605 3680 2.812358 TCTGCAGTGAGTTTCGCTAA 57.188 45.000 14.67 0.00 34.53 3.09
3606 3681 2.296190 TCTTCTGCAGTGAGTTTCGCTA 59.704 45.455 14.67 0.00 34.53 4.26
3607 3682 1.069204 TCTTCTGCAGTGAGTTTCGCT 59.931 47.619 14.67 0.00 37.80 4.93
3608 3683 1.458827 CTCTTCTGCAGTGAGTTTCGC 59.541 52.381 22.28 0.00 0.00 4.70
3623 3717 7.046652 GGTTAGGTTAGTCATTTACCCTCTTC 58.953 42.308 0.00 0.00 32.20 2.87
3747 3847 5.525012 CCTCTATCTCAATCGCAATTTCACA 59.475 40.000 0.00 0.00 0.00 3.58
3757 3857 4.384056 ACATTTGGCCTCTATCTCAATCG 58.616 43.478 3.32 0.00 0.00 3.34
3898 4073 4.777463 ACCGGTGAACCTAAATGGATTAG 58.223 43.478 6.12 0.00 40.67 1.73
3994 4169 7.989741 GCTGTATATGTAAATCAGGGCTATCAT 59.010 37.037 0.00 0.00 0.00 2.45
3995 4170 7.038373 TGCTGTATATGTAAATCAGGGCTATCA 60.038 37.037 0.00 0.00 0.00 2.15
3996 4171 7.331026 TGCTGTATATGTAAATCAGGGCTATC 58.669 38.462 0.00 0.00 0.00 2.08
3997 4172 7.257790 TGCTGTATATGTAAATCAGGGCTAT 57.742 36.000 0.00 0.00 0.00 2.97
3998 4173 6.680148 TGCTGTATATGTAAATCAGGGCTA 57.320 37.500 0.00 0.00 0.00 3.93
4011 4186 7.957484 GTCTTGTACAAACACTTGCTGTATATG 59.043 37.037 10.03 0.00 35.84 1.78
4029 4207 4.246458 CAGCTCAGGGTTAAGTCTTGTAC 58.754 47.826 0.00 0.00 0.00 2.90
4083 4263 2.096614 TGTCGTCGCGAAGAAAAATTCC 60.097 45.455 25.87 12.31 37.72 3.01
4189 4369 3.622166 GGTTAGGAGACCGATTCCAAA 57.378 47.619 3.26 0.00 37.18 3.28
4276 4456 1.492176 TCCTTCAGAGAATCCATGGGC 59.508 52.381 13.02 1.74 33.66 5.36
4301 4481 2.338500 GTGTCATCACTTCCCGAAGAC 58.662 52.381 11.35 0.00 40.79 3.01
4320 4500 1.816835 CAACTGCTTGCTGATGATGGT 59.183 47.619 6.50 0.00 0.00 3.55
4321 4501 2.089201 TCAACTGCTTGCTGATGATGG 58.911 47.619 7.99 0.00 0.00 3.51
4340 4520 0.514691 CGGAACAGTCAGCTGCTTTC 59.485 55.000 9.47 13.98 46.30 2.62
4349 4529 1.617804 CCTACTACCCCGGAACAGTCA 60.618 57.143 0.73 0.00 0.00 3.41
4364 4544 2.224793 GCTTTCCTGGTTGGTTCCTACT 60.225 50.000 0.00 0.00 37.07 2.57
4366 4546 1.074889 GGCTTTCCTGGTTGGTTCCTA 59.925 52.381 0.00 0.00 37.07 2.94
4367 4547 0.178961 GGCTTTCCTGGTTGGTTCCT 60.179 55.000 0.00 0.00 37.07 3.36
4368 4548 1.185618 GGGCTTTCCTGGTTGGTTCC 61.186 60.000 0.00 0.00 37.07 3.62
4369 4549 0.178961 AGGGCTTTCCTGGTTGGTTC 60.179 55.000 0.00 0.00 46.07 3.62
4370 4550 1.938327 AGGGCTTTCCTGGTTGGTT 59.062 52.632 0.00 0.00 46.07 3.67
4371 4551 3.688032 AGGGCTTTCCTGGTTGGT 58.312 55.556 0.00 0.00 46.07 3.67
4386 4567 6.318900 GGTCACCAGAAAATTATTGTAGGAGG 59.681 42.308 0.00 0.00 0.00 4.30
4444 4625 4.284490 CCTCTATGCTATGCCTACCAAGAA 59.716 45.833 0.00 0.00 0.00 2.52
4566 4759 1.153269 TTCTGCTGCCACGTGAACA 60.153 52.632 19.30 13.93 0.00 3.18
4667 4868 6.033341 CGAATAGAATAGATCTGCTGCTACC 58.967 44.000 5.18 0.00 39.30 3.18
4746 4951 9.662947 CCATATATATTTGCATGAGTGAGAAGA 57.337 33.333 0.00 0.00 0.00 2.87
4747 4952 9.662947 TCCATATATATTTGCATGAGTGAGAAG 57.337 33.333 0.00 0.00 0.00 2.85
4749 4954 9.440773 GTTCCATATATATTTGCATGAGTGAGA 57.559 33.333 0.00 0.00 0.00 3.27
4750 4955 9.223099 TGTTCCATATATATTTGCATGAGTGAG 57.777 33.333 0.00 0.00 0.00 3.51
4751 4956 9.571816 TTGTTCCATATATATTTGCATGAGTGA 57.428 29.630 0.00 0.00 0.00 3.41
4787 5051 9.328721 GCCAAAACAAGCAAAAATATATTTCAC 57.671 29.630 11.08 4.45 0.00 3.18
4789 5053 7.691877 CCGCCAAAACAAGCAAAAATATATTTC 59.308 33.333 11.08 0.00 0.00 2.17
4791 5055 6.876257 TCCGCCAAAACAAGCAAAAATATATT 59.124 30.769 0.00 0.00 0.00 1.28
4792 5056 6.402222 TCCGCCAAAACAAGCAAAAATATAT 58.598 32.000 0.00 0.00 0.00 0.86
4793 5057 5.784177 TCCGCCAAAACAAGCAAAAATATA 58.216 33.333 0.00 0.00 0.00 0.86
4794 5058 4.636249 TCCGCCAAAACAAGCAAAAATAT 58.364 34.783 0.00 0.00 0.00 1.28
4803 5128 5.801947 CAGATTATTCTTCCGCCAAAACAAG 59.198 40.000 0.00 0.00 0.00 3.16
4810 5135 4.161565 ACTGTACAGATTATTCTTCCGCCA 59.838 41.667 29.30 0.00 0.00 5.69
4814 5139 9.110502 CCCTTTTACTGTACAGATTATTCTTCC 57.889 37.037 29.30 0.00 0.00 3.46
4852 5181 2.703007 CCCATCCCCAAGAACAAACAAA 59.297 45.455 0.00 0.00 0.00 2.83
4854 5183 1.501170 TCCCATCCCCAAGAACAAACA 59.499 47.619 0.00 0.00 0.00 2.83
4941 5274 4.402474 GGCTGATTTTTGTATTAGGCTGGT 59.598 41.667 0.00 0.00 34.92 4.00
4953 5286 2.983803 CGTTTTACCGGGCTGATTTTTG 59.016 45.455 6.32 0.00 0.00 2.44
4966 5301 5.123661 TCCCGGTTTTAATCATCGTTTTACC 59.876 40.000 0.00 0.00 0.00 2.85
4990 5325 1.443872 CTAGCTGTCGTCCGCGTTT 60.444 57.895 4.92 0.00 39.49 3.60
4992 5327 3.054503 ACTAGCTGTCGTCCGCGT 61.055 61.111 4.92 0.00 39.49 6.01
4993 5328 2.577112 CACTAGCTGTCGTCCGCG 60.577 66.667 0.00 0.00 39.92 6.46
5050 5400 1.680651 CACACGCCTCTCCCTCTCT 60.681 63.158 0.00 0.00 0.00 3.10
5051 5401 1.251527 TTCACACGCCTCTCCCTCTC 61.252 60.000 0.00 0.00 0.00 3.20
5052 5402 0.616111 ATTCACACGCCTCTCCCTCT 60.616 55.000 0.00 0.00 0.00 3.69
5053 5403 0.460987 CATTCACACGCCTCTCCCTC 60.461 60.000 0.00 0.00 0.00 4.30
5054 5404 1.599047 CATTCACACGCCTCTCCCT 59.401 57.895 0.00 0.00 0.00 4.20
5055 5405 1.450312 CCATTCACACGCCTCTCCC 60.450 63.158 0.00 0.00 0.00 4.30
5056 5406 1.450312 CCCATTCACACGCCTCTCC 60.450 63.158 0.00 0.00 0.00 3.71
5057 5407 2.109126 GCCCATTCACACGCCTCTC 61.109 63.158 0.00 0.00 0.00 3.20
5133 5483 1.965083 TCGTTTTCTTCTCGCTCTCG 58.035 50.000 0.00 0.00 0.00 4.04
5134 5484 3.420672 CGTTTCGTTTTCTTCTCGCTCTC 60.421 47.826 0.00 0.00 0.00 3.20
5135 5485 2.471743 CGTTTCGTTTTCTTCTCGCTCT 59.528 45.455 0.00 0.00 0.00 4.09
5136 5486 2.470257 TCGTTTCGTTTTCTTCTCGCTC 59.530 45.455 0.00 0.00 0.00 5.03
5137 5487 2.466846 TCGTTTCGTTTTCTTCTCGCT 58.533 42.857 0.00 0.00 0.00 4.93
5138 5488 2.916735 TCGTTTCGTTTTCTTCTCGC 57.083 45.000 0.00 0.00 0.00 5.03
5139 5489 4.142532 GCTTTTCGTTTCGTTTTCTTCTCG 59.857 41.667 0.00 0.00 0.00 4.04
5142 5492 3.177061 CCGCTTTTCGTTTCGTTTTCTTC 59.823 43.478 0.00 0.00 36.19 2.87
5143 5493 3.103007 CCGCTTTTCGTTTCGTTTTCTT 58.897 40.909 0.00 0.00 36.19 2.52
5144 5494 2.540157 CCCGCTTTTCGTTTCGTTTTCT 60.540 45.455 0.00 0.00 36.19 2.52
5145 5495 1.776897 CCCGCTTTTCGTTTCGTTTTC 59.223 47.619 0.00 0.00 36.19 2.29
5146 5496 1.534385 CCCCGCTTTTCGTTTCGTTTT 60.534 47.619 0.00 0.00 36.19 2.43
5147 5497 0.029700 CCCCGCTTTTCGTTTCGTTT 59.970 50.000 0.00 0.00 36.19 3.60
5148 5498 1.650363 CCCCGCTTTTCGTTTCGTT 59.350 52.632 0.00 0.00 36.19 3.85
5149 5499 2.900167 GCCCCGCTTTTCGTTTCGT 61.900 57.895 0.00 0.00 36.19 3.85
5150 5500 2.127003 GCCCCGCTTTTCGTTTCG 60.127 61.111 0.00 0.00 36.19 3.46
5151 5501 2.127003 CGCCCCGCTTTTCGTTTC 60.127 61.111 0.00 0.00 36.19 2.78
5313 5692 3.083997 CTGAACCCTCCTCCCCCG 61.084 72.222 0.00 0.00 0.00 5.73
5540 5928 1.759445 AGGCAGAGTATAGCACACAGG 59.241 52.381 0.00 0.00 0.00 4.00
5541 5929 2.819115 CAGGCAGAGTATAGCACACAG 58.181 52.381 0.00 0.00 0.00 3.66
5542 5930 1.134699 GCAGGCAGAGTATAGCACACA 60.135 52.381 0.00 0.00 0.00 3.72
5543 5931 1.576356 GCAGGCAGAGTATAGCACAC 58.424 55.000 0.00 0.00 0.00 3.82
5544 5932 0.465705 GGCAGGCAGAGTATAGCACA 59.534 55.000 0.00 0.00 0.00 4.57
5545 5933 0.598680 CGGCAGGCAGAGTATAGCAC 60.599 60.000 0.00 0.00 0.00 4.40
5546 5934 1.742146 CGGCAGGCAGAGTATAGCA 59.258 57.895 0.00 0.00 0.00 3.49
5547 5935 1.666234 GCGGCAGGCAGAGTATAGC 60.666 63.158 0.00 0.00 42.87 2.97
5548 5936 1.005630 GGCGGCAGGCAGAGTATAG 60.006 63.158 3.07 0.00 46.16 1.31
5549 5937 3.138625 GGCGGCAGGCAGAGTATA 58.861 61.111 3.07 0.00 46.16 1.47
5579 5967 4.550076 CTCCATTATTAGGGAGGCAGAG 57.450 50.000 4.50 0.00 46.28 3.35
5591 5979 9.726438 GACAGCTATAACCATTACTCCATTATT 57.274 33.333 0.00 0.00 0.00 1.40
5592 5980 9.105844 AGACAGCTATAACCATTACTCCATTAT 57.894 33.333 0.00 0.00 0.00 1.28
5606 5994 3.195825 ACACCAGACCAGACAGCTATAAC 59.804 47.826 0.00 0.00 0.00 1.89
5608 5996 3.024547 GACACCAGACCAGACAGCTATA 58.975 50.000 0.00 0.00 0.00 1.31
5609 5997 1.827969 GACACCAGACCAGACAGCTAT 59.172 52.381 0.00 0.00 0.00 2.97
5610 5998 1.203063 AGACACCAGACCAGACAGCTA 60.203 52.381 0.00 0.00 0.00 3.32
5611 6002 0.470833 AGACACCAGACCAGACAGCT 60.471 55.000 0.00 0.00 0.00 4.24
5613 6004 0.605589 GGAGACACCAGACCAGACAG 59.394 60.000 0.00 0.00 38.79 3.51
5614 6005 0.105709 TGGAGACACCAGACCAGACA 60.106 55.000 0.00 0.00 44.64 3.41
5615 6006 2.746697 TGGAGACACCAGACCAGAC 58.253 57.895 0.00 0.00 44.64 3.51


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

AutoCloner maintained by Alex Coulton.