Multiple sequence alignment - TraesCS2B01G528100

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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 TraesCS2B01G528100 chr2B 100.000 5509 0 0 1 5509 722616021 722621529 0.000000e+00 10174.0
1 TraesCS2B01G528100 chr2B 81.061 132 22 3 494 622 722513437 722513568 9.760000e-18 102.0
2 TraesCS2B01G528100 chr2D 92.604 3894 203 31 1650 5509 595146513 595150355 0.000000e+00 5517.0
3 TraesCS2B01G528100 chr2D 84.402 1154 61 40 561 1650 595145188 595146286 0.000000e+00 1024.0
4 TraesCS2B01G528100 chr2D 89.251 521 42 9 1 508 549981745 549982264 1.670000e-179 640.0
5 TraesCS2B01G528100 chr2D 82.979 423 37 25 4525 4929 595153993 595154398 3.160000e-92 350.0
6 TraesCS2B01G528100 chr2D 93.458 107 7 0 4421 4527 595152095 595152201 5.710000e-35 159.0
7 TraesCS2B01G528100 chr2D 79.762 252 25 13 4980 5215 595154400 595154641 5.710000e-35 159.0
8 TraesCS2B01G528100 chr2D 85.135 148 11 4 5258 5405 595154645 595154781 2.070000e-29 141.0
9 TraesCS2B01G528100 chr2A 95.457 1673 71 3 1644 3314 729283997 729285666 0.000000e+00 2663.0
10 TraesCS2B01G528100 chr2A 95.073 1238 44 7 3368 4598 729285677 729286904 0.000000e+00 1932.0
11 TraesCS2B01G528100 chr2A 86.097 971 85 26 4580 5508 729286919 729287881 0.000000e+00 1000.0
12 TraesCS2B01G528100 chr2A 83.159 1146 84 38 554 1650 729282675 729283760 0.000000e+00 946.0
13 TraesCS2B01G528100 chr3D 88.224 518 45 4 1 502 402495149 402494632 6.100000e-169 604.0
14 TraesCS2B01G528100 chr3D 87.692 130 12 3 1954 2082 423991212 423991086 1.240000e-31 148.0
15 TraesCS2B01G528100 chr5A 88.063 511 52 4 1 505 645417338 645417845 1.020000e-166 597.0
16 TraesCS2B01G528100 chr4B 87.695 512 54 7 1 505 172325589 172325080 6.150000e-164 588.0
17 TraesCS2B01G528100 chr4B 83.429 525 60 19 1 504 652824374 652824892 3.890000e-126 462.0
18 TraesCS2B01G528100 chr4B 86.923 130 13 3 1954 2082 536489041 536489167 5.750000e-30 143.0
19 TraesCS2B01G528100 chr3A 87.500 512 59 2 1 507 28386091 28385580 2.210000e-163 586.0
20 TraesCS2B01G528100 chr1D 87.476 519 50 3 1 504 236079879 236080397 7.950000e-163 584.0
21 TraesCS2B01G528100 chr7D 88.565 481 42 6 4 475 554899819 554899343 6.190000e-159 571.0
22 TraesCS2B01G528100 chr7B 85.910 511 68 4 1 507 522603769 522603259 4.850000e-150 542.0
23 TraesCS2B01G528100 chr7B 83.190 232 24 4 293 509 554786331 554786562 1.210000e-46 198.0
24 TraesCS2B01G528100 chr3B 86.078 510 62 6 1 503 168120965 168121472 1.750000e-149 540.0
25 TraesCS2B01G528100 chr3B 88.571 105 11 1 1954 2058 409966735 409966838 5.790000e-25 126.0
26 TraesCS2B01G528100 chr5B 82.667 525 66 13 4 508 580089303 580088784 5.060000e-120 442.0
27 TraesCS2B01G528100 chr1B 87.692 130 12 3 1954 2082 346283438 346283564 1.240000e-31 148.0
28 TraesCS2B01G528100 chr1B 91.176 68 5 1 1954 2021 174380719 174380653 2.110000e-14 91.6
29 TraesCS2B01G528100 chr6A 85.385 130 15 3 1954 2082 382781927 382781801 1.250000e-26 132.0
30 TraesCS2B01G528100 chr4D 85.484 124 14 3 1960 2082 214971162 214971042 5.790000e-25 126.0


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 TraesCS2B01G528100 chr2B 722616021 722621529 5508 False 10174.00 10174 100.0000 1 5509 1 chr2B.!!$F2 5508
1 TraesCS2B01G528100 chr2D 595145188 595154781 9593 False 1225.00 5517 86.3900 561 5509 6 chr2D.!!$F2 4948
2 TraesCS2B01G528100 chr2D 549981745 549982264 519 False 640.00 640 89.2510 1 508 1 chr2D.!!$F1 507
3 TraesCS2B01G528100 chr2A 729282675 729287881 5206 False 1635.25 2663 89.9465 554 5508 4 chr2A.!!$F1 4954
4 TraesCS2B01G528100 chr3D 402494632 402495149 517 True 604.00 604 88.2240 1 502 1 chr3D.!!$R1 501
5 TraesCS2B01G528100 chr5A 645417338 645417845 507 False 597.00 597 88.0630 1 505 1 chr5A.!!$F1 504
6 TraesCS2B01G528100 chr4B 172325080 172325589 509 True 588.00 588 87.6950 1 505 1 chr4B.!!$R1 504
7 TraesCS2B01G528100 chr4B 652824374 652824892 518 False 462.00 462 83.4290 1 504 1 chr4B.!!$F2 503
8 TraesCS2B01G528100 chr3A 28385580 28386091 511 True 586.00 586 87.5000 1 507 1 chr3A.!!$R1 506
9 TraesCS2B01G528100 chr1D 236079879 236080397 518 False 584.00 584 87.4760 1 504 1 chr1D.!!$F1 503
10 TraesCS2B01G528100 chr7B 522603259 522603769 510 True 542.00 542 85.9100 1 507 1 chr7B.!!$R1 506
11 TraesCS2B01G528100 chr3B 168120965 168121472 507 False 540.00 540 86.0780 1 503 1 chr3B.!!$F1 502
12 TraesCS2B01G528100 chr5B 580088784 580089303 519 True 442.00 442 82.6670 4 508 1 chr5B.!!$R1 504

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
518 560 0.108567 TGCTCTAATGCAACCGCGTA 60.109 50.0 4.92 0.0 42.97 4.42 F
539 581 0.398381 ACCCCAAAAAGAGGCTGCAA 60.398 50.0 0.50 0.0 0.00 4.08 F
552 594 0.668401 GCTGCAAATGCCAGTGTTCC 60.668 55.0 2.46 0.0 41.18 3.62 F
1164 1267 0.928229 GTCGTCAATTCGATTCGGGG 59.072 55.0 6.18 0.0 41.78 5.73 F
1911 2285 0.323816 TTGGTGGTTGACTGTTGCCA 60.324 50.0 0.00 0.0 0.00 4.92 F
2907 3284 0.968901 ACTAATCCGCTCGACCACCA 60.969 55.0 0.00 0.0 0.00 4.17 F
3360 3737 1.105457 AGTGTGCTGCAAATGTGTGT 58.895 45.0 2.77 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1357 1463 1.134491 AGCAGGTGGCCTAACGATTAC 60.134 52.381 3.32 0.00 46.50 1.89 R
1821 2195 1.266696 CGCGAGCCAAAACGTACATAC 60.267 52.381 0.00 0.00 0.00 2.39 R
1890 2264 1.412343 GGCAACAGTCAACCACCAAAT 59.588 47.619 0.00 0.00 0.00 2.32 R
2270 2644 2.235402 CCATTCTGGCTGGCAGAAAAAT 59.765 45.455 38.79 25.63 41.34 1.82 R
3883 4260 0.586319 CAGCAAGTACACCACCAACG 59.414 55.000 0.00 0.00 0.00 4.10 R
4318 4702 0.108585 GAGAGGGCAGGTCAAACACA 59.891 55.000 0.00 0.00 0.00 3.72 R
5351 5804 0.529378 CATGCAGGTTTCTTCTGGCC 59.471 55.000 0.00 0.00 33.16 5.36 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
91 92 0.677731 TTTGAGAAGATGCAGGCCGG 60.678 55.000 0.00 0.00 0.00 6.13
101 102 3.063704 CAGGCCGGCATGCTCAAA 61.064 61.111 29.89 0.00 0.00 2.69
109 111 1.064505 CGGCATGCTCAAATTGACGAT 59.935 47.619 18.92 0.00 44.56 3.73
174 179 2.048597 GTGCCGACATGACCACGA 60.049 61.111 0.00 0.00 0.00 4.35
186 191 4.193334 CCACGAGAGCCGCGATGA 62.193 66.667 8.23 0.00 43.32 2.92
206 212 0.314302 CGTGGTCGAACTCAAGTCCT 59.686 55.000 0.33 0.00 39.71 3.85
210 216 3.005578 GTGGTCGAACTCAAGTCCTACTT 59.994 47.826 0.33 0.00 39.39 2.24
324 332 3.451004 GCATGGTGCGGGCATGAA 61.451 61.111 0.00 0.00 31.71 2.57
349 361 2.496942 CCACTGGCATGATTGTCCC 58.503 57.895 0.00 0.00 0.00 4.46
352 364 1.077501 CTGGCATGATTGTCCCCGT 60.078 57.895 0.00 0.00 0.00 5.28
392 412 3.289407 TGCGGATATGAAATGGGTCAA 57.711 42.857 0.00 0.00 0.00 3.18
399 419 1.880271 TGAAATGGGTCAACGCGTTA 58.120 45.000 26.11 9.29 37.09 3.18
474 516 2.182614 AAAGCGGACAAATGCGTCGG 62.183 55.000 0.00 0.00 42.52 4.79
494 536 1.888638 CGTTTGGGTCGGACCGTTT 60.889 57.895 20.35 0.00 39.83 3.60
508 550 3.125316 GGACCGTTTGAGTTGCTCTAATG 59.875 47.826 5.85 5.85 34.02 1.90
509 551 2.484264 ACCGTTTGAGTTGCTCTAATGC 59.516 45.455 6.91 0.00 33.32 3.56
510 552 2.483877 CCGTTTGAGTTGCTCTAATGCA 59.516 45.455 0.00 0.00 41.65 3.96
516 558 1.793581 TTGCTCTAATGCAACCGCG 59.206 52.632 0.00 0.00 46.43 6.46
517 559 0.953471 TTGCTCTAATGCAACCGCGT 60.953 50.000 4.92 0.00 46.43 6.01
518 560 0.108567 TGCTCTAATGCAACCGCGTA 60.109 50.000 4.92 0.00 42.97 4.42
519 561 1.217882 GCTCTAATGCAACCGCGTAT 58.782 50.000 4.92 0.00 42.97 3.06
520 562 2.223852 TGCTCTAATGCAACCGCGTATA 60.224 45.455 4.92 0.00 42.97 1.47
521 563 2.155155 GCTCTAATGCAACCGCGTATAC 59.845 50.000 4.92 0.00 42.97 1.47
522 564 2.729882 CTCTAATGCAACCGCGTATACC 59.270 50.000 4.92 0.00 42.97 2.73
523 565 1.796459 CTAATGCAACCGCGTATACCC 59.204 52.381 4.92 0.00 42.97 3.69
524 566 0.816421 AATGCAACCGCGTATACCCC 60.816 55.000 4.92 0.00 42.97 4.95
525 567 1.973816 ATGCAACCGCGTATACCCCA 61.974 55.000 4.92 0.00 42.97 4.96
526 568 1.449956 GCAACCGCGTATACCCCAA 60.450 57.895 4.92 0.00 0.00 4.12
527 569 1.025647 GCAACCGCGTATACCCCAAA 61.026 55.000 4.92 0.00 0.00 3.28
528 570 1.451067 CAACCGCGTATACCCCAAAA 58.549 50.000 4.92 0.00 0.00 2.44
529 571 1.811359 CAACCGCGTATACCCCAAAAA 59.189 47.619 4.92 0.00 0.00 1.94
530 572 1.741528 ACCGCGTATACCCCAAAAAG 58.258 50.000 4.92 0.00 0.00 2.27
531 573 1.278699 ACCGCGTATACCCCAAAAAGA 59.721 47.619 4.92 0.00 0.00 2.52
532 574 1.937899 CCGCGTATACCCCAAAAAGAG 59.062 52.381 4.92 0.00 0.00 2.85
533 575 1.937899 CGCGTATACCCCAAAAAGAGG 59.062 52.381 0.00 0.00 0.00 3.69
534 576 1.674441 GCGTATACCCCAAAAAGAGGC 59.326 52.381 0.00 0.00 0.00 4.70
535 577 2.682858 GCGTATACCCCAAAAAGAGGCT 60.683 50.000 0.00 0.00 0.00 4.58
536 578 2.943033 CGTATACCCCAAAAAGAGGCTG 59.057 50.000 0.00 0.00 0.00 4.85
537 579 1.852633 ATACCCCAAAAAGAGGCTGC 58.147 50.000 0.00 0.00 0.00 5.25
538 580 0.480690 TACCCCAAAAAGAGGCTGCA 59.519 50.000 0.50 0.00 0.00 4.41
539 581 0.398381 ACCCCAAAAAGAGGCTGCAA 60.398 50.000 0.50 0.00 0.00 4.08
540 582 0.758123 CCCCAAAAAGAGGCTGCAAA 59.242 50.000 0.50 0.00 0.00 3.68
541 583 1.348696 CCCCAAAAAGAGGCTGCAAAT 59.651 47.619 0.50 0.00 0.00 2.32
542 584 2.419667 CCCAAAAAGAGGCTGCAAATG 58.580 47.619 0.50 0.00 0.00 2.32
543 585 1.802365 CCAAAAAGAGGCTGCAAATGC 59.198 47.619 0.50 0.00 42.50 3.56
551 593 2.818350 GCTGCAAATGCCAGTGTTC 58.182 52.632 2.46 0.00 41.18 3.18
552 594 0.668401 GCTGCAAATGCCAGTGTTCC 60.668 55.000 2.46 0.00 41.18 3.62
559 601 2.531522 ATGCCAGTGTTCCAAAAAGC 57.468 45.000 0.00 0.00 0.00 3.51
658 710 2.513897 GAAGAATCCCCACCGCCG 60.514 66.667 0.00 0.00 0.00 6.46
780 843 3.058160 CCGACAGCAAGGCAAGGG 61.058 66.667 0.00 0.00 0.00 3.95
817 880 2.728007 GAGGGCCTAAGTGCAAGAAAT 58.272 47.619 5.73 0.00 0.00 2.17
864 935 3.397906 GGAGCAGCTTCCTCCACT 58.602 61.111 20.36 0.00 46.51 4.00
865 936 2.596776 GGAGCAGCTTCCTCCACTA 58.403 57.895 20.36 0.00 46.51 2.74
866 937 1.127343 GGAGCAGCTTCCTCCACTAT 58.873 55.000 20.36 0.00 46.51 2.12
867 938 2.320781 GGAGCAGCTTCCTCCACTATA 58.679 52.381 20.36 0.00 46.51 1.31
868 939 2.298729 GGAGCAGCTTCCTCCACTATAG 59.701 54.545 20.36 0.00 46.51 1.31
869 940 3.226777 GAGCAGCTTCCTCCACTATAGA 58.773 50.000 6.78 0.00 0.00 1.98
871 942 3.640967 AGCAGCTTCCTCCACTATAGAAG 59.359 47.826 6.78 0.00 38.98 2.85
872 943 3.244044 GCAGCTTCCTCCACTATAGAAGG 60.244 52.174 6.78 10.04 36.94 3.46
873 944 4.219115 CAGCTTCCTCCACTATAGAAGGA 58.781 47.826 6.78 12.11 36.94 3.36
874 945 4.651503 CAGCTTCCTCCACTATAGAAGGAA 59.348 45.833 22.82 22.82 36.94 3.36
875 946 5.129485 CAGCTTCCTCCACTATAGAAGGAAA 59.871 44.000 23.64 14.58 36.94 3.13
876 947 5.365314 AGCTTCCTCCACTATAGAAGGAAAG 59.635 44.000 23.64 20.35 36.94 2.62
877 948 5.454045 GCTTCCTCCACTATAGAAGGAAAGG 60.454 48.000 23.64 18.69 36.94 3.11
878 949 5.483174 TCCTCCACTATAGAAGGAAAGGA 57.517 43.478 6.78 13.08 0.00 3.36
879 950 5.850278 TCCTCCACTATAGAAGGAAAGGAA 58.150 41.667 16.94 7.62 0.00 3.36
880 951 6.269194 TCCTCCACTATAGAAGGAAAGGAAA 58.731 40.000 16.94 4.44 0.00 3.13
881 952 6.384305 TCCTCCACTATAGAAGGAAAGGAAAG 59.616 42.308 16.94 7.67 0.00 2.62
882 953 6.384305 CCTCCACTATAGAAGGAAAGGAAAGA 59.616 42.308 6.78 0.00 0.00 2.52
883 954 7.092846 CCTCCACTATAGAAGGAAAGGAAAGAA 60.093 40.741 6.78 0.00 0.00 2.52
884 955 8.214721 TCCACTATAGAAGGAAAGGAAAGAAA 57.785 34.615 6.78 0.00 0.00 2.52
885 956 8.836735 TCCACTATAGAAGGAAAGGAAAGAAAT 58.163 33.333 6.78 0.00 0.00 2.17
886 957 8.897752 CCACTATAGAAGGAAAGGAAAGAAATG 58.102 37.037 6.78 0.00 0.00 2.32
887 958 8.897752 CACTATAGAAGGAAAGGAAAGAAATGG 58.102 37.037 6.78 0.00 0.00 3.16
888 959 8.836735 ACTATAGAAGGAAAGGAAAGAAATGGA 58.163 33.333 6.78 0.00 0.00 3.41
889 960 7.946381 ATAGAAGGAAAGGAAAGAAATGGAC 57.054 36.000 0.00 0.00 0.00 4.02
890 961 5.080337 AGAAGGAAAGGAAAGAAATGGACC 58.920 41.667 0.00 0.00 0.00 4.46
899 970 3.388552 AAGAAATGGACCAATCCCTCC 57.611 47.619 0.00 0.00 45.59 4.30
952 1023 3.540367 TTGACCCGTTTCTCCGCCC 62.540 63.158 0.00 0.00 0.00 6.13
953 1024 4.772687 GACCCGTTTCTCCGCCCC 62.773 72.222 0.00 0.00 0.00 5.80
1035 1117 4.796495 GTCATCGGCCACCCCACC 62.796 72.222 2.24 0.00 0.00 4.61
1094 1179 2.494530 CCACCCCCGTGTGTTTTGG 61.495 63.158 0.00 0.00 38.41 3.28
1119 1217 1.206610 TGTCTCTGCTTGATCTGCTCC 59.793 52.381 11.38 0.00 0.00 4.70
1164 1267 0.928229 GTCGTCAATTCGATTCGGGG 59.072 55.000 6.18 0.00 41.78 5.73
1169 1272 2.469516 AATTCGATTCGGGGCGCAC 61.470 57.895 10.83 4.83 0.00 5.34
1226 1329 1.813786 GGCGGTGGTAAATGCAGTAAA 59.186 47.619 0.00 0.00 0.00 2.01
1296 1399 2.162208 CCTGGAACATCACACGGATTTG 59.838 50.000 0.00 0.00 38.20 2.32
1297 1400 3.073678 CTGGAACATCACACGGATTTGA 58.926 45.455 0.00 0.00 38.20 2.69
1299 1402 3.074412 GGAACATCACACGGATTTGACT 58.926 45.455 0.00 0.00 32.57 3.41
1300 1403 4.250464 GGAACATCACACGGATTTGACTA 58.750 43.478 0.00 0.00 32.57 2.59
1301 1404 4.330074 GGAACATCACACGGATTTGACTAG 59.670 45.833 0.00 0.00 32.57 2.57
1303 1406 4.894784 ACATCACACGGATTTGACTAGTT 58.105 39.130 0.00 0.00 32.57 2.24
1305 1408 4.330944 TCACACGGATTTGACTAGTTGT 57.669 40.909 0.00 0.00 0.00 3.32
1307 1410 4.055360 CACACGGATTTGACTAGTTGTGA 58.945 43.478 12.61 0.00 0.00 3.58
1308 1411 4.690748 CACACGGATTTGACTAGTTGTGAT 59.309 41.667 12.61 0.00 0.00 3.06
1311 1414 6.262273 ACACGGATTTGACTAGTTGTGATTTT 59.738 34.615 0.00 0.00 0.00 1.82
1314 1417 7.138736 CGGATTTGACTAGTTGTGATTTTGTT 58.861 34.615 0.00 0.00 0.00 2.83
1315 1418 7.113404 CGGATTTGACTAGTTGTGATTTTGTTG 59.887 37.037 0.00 0.00 0.00 3.33
1316 1419 7.096065 GGATTTGACTAGTTGTGATTTTGTTGC 60.096 37.037 0.00 0.00 0.00 4.17
1317 1420 6.449635 TTGACTAGTTGTGATTTTGTTGCT 57.550 33.333 0.00 0.00 0.00 3.91
1318 1421 7.561021 TTGACTAGTTGTGATTTTGTTGCTA 57.439 32.000 0.00 0.00 0.00 3.49
1319 1422 7.744087 TGACTAGTTGTGATTTTGTTGCTAT 57.256 32.000 0.00 0.00 0.00 2.97
1320 1423 8.840833 TGACTAGTTGTGATTTTGTTGCTATA 57.159 30.769 0.00 0.00 0.00 1.31
1321 1424 8.935844 TGACTAGTTGTGATTTTGTTGCTATAG 58.064 33.333 0.00 0.00 0.00 1.31
1357 1463 2.231478 TGTTTCCCTTCTCTGTAGCTCG 59.769 50.000 0.00 0.00 0.00 5.03
1427 1538 7.114953 GGTCATCCAAAGAAAAGAAAATTCGTC 59.885 37.037 0.00 0.00 32.04 4.20
1433 1544 7.275560 CCAAAGAAAAGAAAATTCGTCTTGTGT 59.724 33.333 5.38 0.00 35.50 3.72
1458 1569 2.802247 GGAACTGACAAATTTTGGCTGC 59.198 45.455 18.62 6.41 40.90 5.25
1459 1570 3.493176 GGAACTGACAAATTTTGGCTGCT 60.493 43.478 18.62 9.19 40.90 4.24
1471 1589 1.631405 TGGCTGCTGTTATGCCTTTT 58.369 45.000 0.00 0.00 46.23 2.27
1472 1590 1.969923 TGGCTGCTGTTATGCCTTTTT 59.030 42.857 0.00 0.00 46.23 1.94
1574 1699 6.096695 GCTAGTGAGCTAAGCATATAACTCC 58.903 44.000 5.28 0.00 45.98 3.85
1607 1732 6.570692 TGTCTTGAGTAAATCGAGGGTTATC 58.429 40.000 0.00 0.00 39.62 1.75
1711 2085 4.457257 GCAGCTCCTTTAGACAACATTTCT 59.543 41.667 0.00 0.00 0.00 2.52
1718 2092 7.636326 TCCTTTAGACAACATTTCTTCGTTTC 58.364 34.615 0.00 0.00 0.00 2.78
1721 2095 4.848757 AGACAACATTTCTTCGTTTCTGC 58.151 39.130 0.00 0.00 0.00 4.26
1738 2112 1.869767 CTGCCTCCGCAAGCTAATAAG 59.130 52.381 0.00 0.00 46.66 1.73
1785 2159 2.364632 CTTGGTGCGTTTCATATCCCA 58.635 47.619 0.00 0.00 0.00 4.37
1821 2195 1.020333 GCTCTGCTCTGCTTGTCTGG 61.020 60.000 0.00 0.00 0.00 3.86
1890 2264 6.480763 TCAATTCATTAACTAGGCAGGTTGA 58.519 36.000 0.00 0.00 0.00 3.18
1911 2285 0.323816 TTGGTGGTTGACTGTTGCCA 60.324 50.000 0.00 0.00 0.00 4.92
1965 2339 1.827969 ACCAGCCTCTGATCAGTACAC 59.172 52.381 21.92 10.47 32.44 2.90
1973 2347 3.154710 TCTGATCAGTACACGTTGGAGT 58.845 45.455 21.92 0.00 0.00 3.85
2073 2447 2.288273 GCTTCCTGTAGTGAACTGTCGT 60.288 50.000 0.00 0.00 0.00 4.34
2136 2510 5.237344 GCAGTGATATGTTTGTATCCACTCC 59.763 44.000 0.00 0.00 31.47 3.85
2137 2511 6.348498 CAGTGATATGTTTGTATCCACTCCA 58.652 40.000 0.00 0.00 31.47 3.86
2166 2540 8.830915 ATGGTACTATGGGATCTCTAGTAATG 57.169 38.462 11.31 0.00 31.63 1.90
2193 2567 6.491394 GCAACTCCATATTTGCATTACGTTA 58.509 36.000 0.00 0.00 46.13 3.18
2270 2644 6.330004 TGTTTGCTCAGCATTTCTCATTTA 57.670 33.333 0.00 0.00 38.76 1.40
2439 2813 7.473366 TGTATCATCTCTCTTCACGTAGTTTC 58.527 38.462 0.00 0.00 41.61 2.78
2486 2860 4.957327 AGCTTAGAACTTCGATAAGAGGGT 59.043 41.667 6.87 0.00 36.50 4.34
2508 2882 5.500825 GTGTTTTTCACATTTGGCACAATC 58.499 37.500 0.00 0.00 45.11 2.67
2645 3020 4.141251 AGCAACCATTAATCGAGGGGTTAT 60.141 41.667 6.79 0.00 39.71 1.89
2907 3284 0.968901 ACTAATCCGCTCGACCACCA 60.969 55.000 0.00 0.00 0.00 4.17
3181 3558 5.122239 TCTGAGACCATGCATTTTCGTTTAG 59.878 40.000 0.00 0.00 0.00 1.85
3218 3595 9.851686 ATGAATATAGCAGAATGGACAAACTTA 57.148 29.630 0.00 0.00 35.86 2.24
3238 3615 8.946797 AACTTAGTCTACTTCCAACCTACTAA 57.053 34.615 0.00 0.00 0.00 2.24
3341 3718 9.573166 CATTCTATAAGGGATGTATTGGAAACA 57.427 33.333 0.00 0.00 39.83 2.83
3360 3737 1.105457 AGTGTGCTGCAAATGTGTGT 58.895 45.000 2.77 0.00 0.00 3.72
3361 3738 1.477700 AGTGTGCTGCAAATGTGTGTT 59.522 42.857 2.77 0.00 0.00 3.32
3362 3739 2.687425 AGTGTGCTGCAAATGTGTGTTA 59.313 40.909 2.77 0.00 0.00 2.41
3363 3740 3.318839 AGTGTGCTGCAAATGTGTGTTAT 59.681 39.130 2.77 0.00 0.00 1.89
3364 3741 3.426191 GTGTGCTGCAAATGTGTGTTATG 59.574 43.478 2.77 0.00 0.00 1.90
3365 3742 3.317430 TGTGCTGCAAATGTGTGTTATGA 59.683 39.130 2.77 0.00 0.00 2.15
3366 3743 3.670055 GTGCTGCAAATGTGTGTTATGAC 59.330 43.478 2.77 0.00 0.00 3.06
3443 3820 7.307694 TCATGCATGCTTGTAAAAGTTAAGAG 58.692 34.615 27.12 3.12 0.00 2.85
3545 3922 3.568007 TGCTTGCCTCGTTTTATGAAAGT 59.432 39.130 0.00 0.00 0.00 2.66
3604 3981 6.631016 TCACACTAAACTAGTCAATAGGCTG 58.369 40.000 0.00 0.00 36.76 4.85
3632 4009 7.147976 AGACTCAAGTTATTTTGATGGCAAAC 58.852 34.615 0.00 0.00 43.27 2.93
3798 4175 3.767131 GGTTTTGTTATGTGGGCAGGTAT 59.233 43.478 0.00 0.00 0.00 2.73
3883 4260 3.094386 TTCCATAGGAACATGGCGC 57.906 52.632 0.00 0.00 44.47 6.53
4058 4435 5.035443 GCATTCATCTTCATGACTCTTTGC 58.965 41.667 0.00 0.00 38.86 3.68
4291 4675 9.889128 AATTCAAGAAAACAGAAGGATTTCAAA 57.111 25.926 0.00 0.00 35.91 2.69
4297 4681 4.590850 ACAGAAGGATTTCAAAACCTGC 57.409 40.909 0.00 0.00 35.70 4.85
4298 4682 3.960102 ACAGAAGGATTTCAAAACCTGCA 59.040 39.130 7.18 0.00 35.70 4.41
4299 4683 4.590222 ACAGAAGGATTTCAAAACCTGCAT 59.410 37.500 7.18 0.00 35.70 3.96
4300 4684 5.070847 ACAGAAGGATTTCAAAACCTGCATT 59.929 36.000 7.18 0.00 35.70 3.56
4301 4685 6.267471 ACAGAAGGATTTCAAAACCTGCATTA 59.733 34.615 7.18 0.00 35.70 1.90
4302 4686 7.038799 ACAGAAGGATTTCAAAACCTGCATTAT 60.039 33.333 7.18 0.00 35.70 1.28
4303 4687 7.490402 CAGAAGGATTTCAAAACCTGCATTATC 59.510 37.037 7.18 0.00 35.70 1.75
4304 4688 6.225981 AGGATTTCAAAACCTGCATTATCC 57.774 37.500 0.00 0.00 32.39 2.59
4305 4689 5.960202 AGGATTTCAAAACCTGCATTATCCT 59.040 36.000 0.00 0.00 35.67 3.24
4308 4692 7.706607 GGATTTCAAAACCTGCATTATCCTTAC 59.293 37.037 0.00 0.00 0.00 2.34
4316 4700 7.335127 ACCTGCATTATCCTTACCATATTCT 57.665 36.000 0.00 0.00 0.00 2.40
4318 4702 7.170965 CCTGCATTATCCTTACCATATTCTGT 58.829 38.462 0.00 0.00 0.00 3.41
4323 4707 9.342308 CATTATCCTTACCATATTCTGTGTGTT 57.658 33.333 0.00 0.00 0.00 3.32
4327 4711 6.653320 TCCTTACCATATTCTGTGTGTTTGAC 59.347 38.462 0.00 0.00 0.00 3.18
4335 4719 0.465460 TGTGTGTTTGACCTGCCCTC 60.465 55.000 0.00 0.00 0.00 4.30
4345 4729 1.834263 GACCTGCCCTCTCTACACAAT 59.166 52.381 0.00 0.00 0.00 2.71
4350 4734 4.323485 CCTGCCCTCTCTACACAATGTTTA 60.323 45.833 0.00 0.00 0.00 2.01
4353 4737 7.136822 TGCCCTCTCTACACAATGTTTATAT 57.863 36.000 0.00 0.00 0.00 0.86
4370 4754 0.175760 TATTGCAGGAGGCTGTCGAC 59.824 55.000 9.11 9.11 45.15 4.20
4382 4766 2.183555 GTCGACATGACCCGGTCC 59.816 66.667 15.24 0.00 42.04 4.46
4406 4790 1.130054 AAGACCCAGAGGAAGCTGCA 61.130 55.000 1.02 0.00 36.73 4.41
4416 4800 1.311651 GGAAGCTGCAAAGAGGCTCC 61.312 60.000 11.71 0.00 35.06 4.70
4466 4850 1.796459 GACAACATAACCTGCGTCGTT 59.204 47.619 0.00 0.00 0.00 3.85
4481 4865 1.069906 GTCGTTGTGCGCTTCTTTCAT 60.070 47.619 9.73 0.00 41.07 2.57
4484 4868 1.001378 GTTGTGCGCTTCTTTCATGGT 60.001 47.619 9.73 0.00 0.00 3.55
4493 4877 2.496899 TCTTTCATGGTCAAGGGAGC 57.503 50.000 0.00 0.00 41.89 4.70
4546 4930 3.118905 ACTCTCAACTTCTCAAGTGGC 57.881 47.619 0.00 0.00 41.91 5.01
4638 5055 7.975058 GGAAGTAGGAAAAGTGTACTCTGATAC 59.025 40.741 0.00 0.00 0.00 2.24
4745 5164 1.084289 GGTTTAGTCGTGGATGGTGC 58.916 55.000 0.00 0.00 0.00 5.01
4773 5192 5.349817 GTCTGATGAGTGTGTTGTATCTTGG 59.650 44.000 0.00 0.00 0.00 3.61
4823 5242 8.589338 AGTGTGATGTAATATCCATAACTCTCC 58.411 37.037 5.05 0.00 26.47 3.71
4833 5252 4.695606 TCCATAACTCTCCCAAGGTAAGT 58.304 43.478 0.00 0.00 0.00 2.24
4852 5271 9.436957 AGGTAAGTGATTATTGTTGTACTGAAG 57.563 33.333 0.00 0.00 0.00 3.02
4892 5331 8.798402 TGGGTCTTAATTTCGATGTTTTATTGT 58.202 29.630 0.00 0.00 0.00 2.71
4893 5332 9.072294 GGGTCTTAATTTCGATGTTTTATTGTG 57.928 33.333 0.00 0.00 0.00 3.33
4898 5337 9.737427 TTAATTTCGATGTTTTATTGTGTGTGT 57.263 25.926 0.00 0.00 0.00 3.72
4899 5338 7.621832 ATTTCGATGTTTTATTGTGTGTGTG 57.378 32.000 0.00 0.00 0.00 3.82
4900 5339 5.743026 TCGATGTTTTATTGTGTGTGTGT 57.257 34.783 0.00 0.00 0.00 3.72
4901 5340 5.506181 TCGATGTTTTATTGTGTGTGTGTG 58.494 37.500 0.00 0.00 0.00 3.82
4902 5341 5.065346 TCGATGTTTTATTGTGTGTGTGTGT 59.935 36.000 0.00 0.00 0.00 3.72
4903 5342 5.171159 CGATGTTTTATTGTGTGTGTGTGTG 59.829 40.000 0.00 0.00 0.00 3.82
4904 5343 5.378292 TGTTTTATTGTGTGTGTGTGTGT 57.622 34.783 0.00 0.00 0.00 3.72
4905 5344 5.157067 TGTTTTATTGTGTGTGTGTGTGTG 58.843 37.500 0.00 0.00 0.00 3.82
4944 5383 2.103263 GTGTGTGGACTCTGGAGACTTT 59.897 50.000 4.49 0.00 0.00 2.66
4945 5384 2.103094 TGTGTGGACTCTGGAGACTTTG 59.897 50.000 4.49 0.00 0.00 2.77
4953 5392 5.011227 GGACTCTGGAGACTTTGTTCTACTT 59.989 44.000 4.49 0.00 0.00 2.24
5002 5441 2.371841 TGATGAGTGGCCTTGTACAGTT 59.628 45.455 3.32 0.00 0.00 3.16
5078 5530 0.249398 GCAGGTCCTTGATACACGGT 59.751 55.000 0.00 0.00 0.00 4.83
5087 5539 2.612746 ATACACGGTGGCCCCCTT 60.613 61.111 13.48 0.00 0.00 3.95
5122 5574 1.442769 ACTCTGCACGGCTGTAATTG 58.557 50.000 0.00 0.00 0.00 2.32
5154 5606 6.556495 TGATCTGCTATCCTATTTTGACCTCT 59.444 38.462 0.00 0.00 0.00 3.69
5166 5618 8.515414 CCTATTTTGACCTCTTTCTAAACAAGG 58.485 37.037 0.00 0.00 0.00 3.61
5210 5662 0.324943 TGTTCAGGCCTTAGACCAGC 59.675 55.000 0.00 0.00 0.00 4.85
5230 5682 4.853007 AGCAGAAGATGGCTGAATTTAGT 58.147 39.130 0.00 0.00 39.30 2.24
5231 5683 4.639310 AGCAGAAGATGGCTGAATTTAGTG 59.361 41.667 0.00 0.00 39.30 2.74
5232 5684 4.397417 GCAGAAGATGGCTGAATTTAGTGT 59.603 41.667 0.00 0.00 35.39 3.55
5233 5685 5.675575 GCAGAAGATGGCTGAATTTAGTGTG 60.676 44.000 0.00 0.00 35.39 3.82
5235 5687 3.960571 AGATGGCTGAATTTAGTGTGCT 58.039 40.909 0.00 0.00 0.00 4.40
5236 5688 4.338879 AGATGGCTGAATTTAGTGTGCTT 58.661 39.130 0.00 0.00 0.00 3.91
5238 5690 3.754965 TGGCTGAATTTAGTGTGCTTCT 58.245 40.909 0.00 0.00 0.00 2.85
5239 5691 3.753272 TGGCTGAATTTAGTGTGCTTCTC 59.247 43.478 0.00 0.00 0.00 2.87
5240 5692 3.181516 GGCTGAATTTAGTGTGCTTCTCG 60.182 47.826 0.00 0.00 0.00 4.04
5241 5693 3.726190 GCTGAATTTAGTGTGCTTCTCGC 60.726 47.826 0.00 0.00 39.77 5.03
5243 5695 2.770164 ATTTAGTGTGCTTCTCGCCT 57.230 45.000 0.00 0.00 38.05 5.52
5244 5696 1.795768 TTTAGTGTGCTTCTCGCCTG 58.204 50.000 0.00 0.00 38.05 4.85
5245 5697 0.679505 TTAGTGTGCTTCTCGCCTGT 59.320 50.000 0.00 0.00 38.05 4.00
5246 5698 1.541379 TAGTGTGCTTCTCGCCTGTA 58.459 50.000 0.00 0.00 38.05 2.74
5247 5699 0.244994 AGTGTGCTTCTCGCCTGTAG 59.755 55.000 0.00 0.00 38.05 2.74
5248 5700 0.737715 GTGTGCTTCTCGCCTGTAGG 60.738 60.000 0.00 0.00 38.05 3.18
5289 5742 3.758755 TGTAGCATGCCTATCTCCTTG 57.241 47.619 15.66 0.00 0.00 3.61
5299 5752 3.017442 CCTATCTCCTTGAGACGTGTCA 58.983 50.000 11.94 11.94 41.76 3.58
5329 5782 3.570212 AGCGTTGCTCCCTTGGGT 61.570 61.111 5.51 0.00 30.62 4.51
5349 5802 6.177610 TGGGTGTCATGGTTTTTATCTAGAC 58.822 40.000 0.00 0.00 0.00 2.59
5350 5803 5.589050 GGGTGTCATGGTTTTTATCTAGACC 59.411 44.000 0.00 0.00 0.00 3.85
5351 5804 5.293569 GGTGTCATGGTTTTTATCTAGACCG 59.706 44.000 0.00 0.00 34.90 4.79
5352 5805 5.293569 GTGTCATGGTTTTTATCTAGACCGG 59.706 44.000 0.00 0.00 34.90 5.28
5453 5925 1.004610 CCACATCGACATGAATCGCAC 60.005 52.381 0.00 0.00 41.97 5.34
5470 5942 1.081892 CACGGATCTGTTCAAGCAGG 58.918 55.000 3.84 0.00 37.12 4.85
5482 5956 7.147312 TCTGTTCAAGCAGGTTTATTTTCATG 58.853 34.615 0.00 0.00 37.12 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 3.181503 ACTCATCGTCAATTTGAGCATGC 60.182 43.478 10.51 10.51 40.40 4.06
101 102 4.564041 GCCATAGATCACTCATCGTCAAT 58.436 43.478 0.00 0.00 36.50 2.57
109 111 1.106944 TCGCCGCCATAGATCACTCA 61.107 55.000 0.00 0.00 0.00 3.41
174 179 4.498520 CCACGTCATCGCGGCTCT 62.499 66.667 6.13 0.00 41.18 4.09
186 191 0.031721 GGACTTGAGTTCGACCACGT 59.968 55.000 0.00 0.00 40.69 4.49
216 222 2.646719 CACACATGCCAGCACACC 59.353 61.111 0.00 0.00 0.00 4.16
264 270 4.155826 CGGCTTCAGAAAATATCACCACAA 59.844 41.667 0.00 0.00 0.00 3.33
316 324 1.218854 GTGGCCATGTTTCATGCCC 59.781 57.895 9.72 10.28 43.35 5.36
333 341 1.077501 CGGGGACAATCATGCCAGT 60.078 57.895 0.00 0.00 0.00 4.00
378 396 2.102070 ACGCGTTGACCCATTTCATA 57.898 45.000 5.58 0.00 0.00 2.15
411 431 3.319689 CCGTCCTGTTTTGTATTTGGGTT 59.680 43.478 0.00 0.00 0.00 4.11
508 550 1.025647 TTTGGGGTATACGCGGTTGC 61.026 55.000 12.47 0.00 37.91 4.17
509 551 1.451067 TTTTGGGGTATACGCGGTTG 58.549 50.000 12.47 0.00 34.15 3.77
510 552 2.086094 CTTTTTGGGGTATACGCGGTT 58.914 47.619 12.47 0.00 34.15 4.44
511 553 1.278699 TCTTTTTGGGGTATACGCGGT 59.721 47.619 12.47 0.22 34.15 5.68
512 554 1.937899 CTCTTTTTGGGGTATACGCGG 59.062 52.381 12.47 0.00 34.15 6.46
513 555 1.937899 CCTCTTTTTGGGGTATACGCG 59.062 52.381 3.53 3.53 34.15 6.01
514 556 1.674441 GCCTCTTTTTGGGGTATACGC 59.326 52.381 11.34 11.34 0.00 4.42
515 557 2.943033 CAGCCTCTTTTTGGGGTATACG 59.057 50.000 0.00 0.00 0.00 3.06
516 558 2.688446 GCAGCCTCTTTTTGGGGTATAC 59.312 50.000 0.00 0.00 0.00 1.47
517 559 2.310349 TGCAGCCTCTTTTTGGGGTATA 59.690 45.455 0.00 0.00 0.00 1.47
518 560 1.077005 TGCAGCCTCTTTTTGGGGTAT 59.923 47.619 0.00 0.00 0.00 2.73
519 561 0.480690 TGCAGCCTCTTTTTGGGGTA 59.519 50.000 0.00 0.00 0.00 3.69
520 562 0.398381 TTGCAGCCTCTTTTTGGGGT 60.398 50.000 0.00 0.00 0.00 4.95
521 563 0.758123 TTTGCAGCCTCTTTTTGGGG 59.242 50.000 0.00 0.00 0.00 4.96
522 564 2.419667 CATTTGCAGCCTCTTTTTGGG 58.580 47.619 0.00 0.00 0.00 4.12
523 565 1.802365 GCATTTGCAGCCTCTTTTTGG 59.198 47.619 0.00 0.00 41.59 3.28
533 575 0.668401 GGAACACTGGCATTTGCAGC 60.668 55.000 4.74 0.00 44.36 5.25
534 576 0.675083 TGGAACACTGGCATTTGCAG 59.325 50.000 4.74 3.11 44.36 4.41
535 577 1.117994 TTGGAACACTGGCATTTGCA 58.882 45.000 4.74 0.00 40.45 4.08
536 578 2.237393 TTTGGAACACTGGCATTTGC 57.763 45.000 0.00 0.00 39.29 3.68
537 579 3.002553 GCTTTTTGGAACACTGGCATTTG 59.997 43.478 0.00 0.00 39.29 2.32
538 580 3.205338 GCTTTTTGGAACACTGGCATTT 58.795 40.909 0.00 0.00 39.29 2.32
539 581 2.170187 TGCTTTTTGGAACACTGGCATT 59.830 40.909 0.00 0.00 39.29 3.56
540 582 1.761784 TGCTTTTTGGAACACTGGCAT 59.238 42.857 0.00 0.00 39.29 4.40
541 583 1.189752 TGCTTTTTGGAACACTGGCA 58.810 45.000 0.00 0.00 39.29 4.92
542 584 2.531522 ATGCTTTTTGGAACACTGGC 57.468 45.000 0.00 0.00 39.29 4.85
543 585 3.392882 GGAATGCTTTTTGGAACACTGG 58.607 45.455 0.00 0.00 39.29 4.00
544 586 3.052036 CGGAATGCTTTTTGGAACACTG 58.948 45.455 0.00 0.00 39.29 3.66
545 587 2.693074 ACGGAATGCTTTTTGGAACACT 59.307 40.909 0.00 0.00 39.29 3.55
546 588 3.092334 ACGGAATGCTTTTTGGAACAC 57.908 42.857 0.00 0.00 39.29 3.32
547 589 3.810310 AACGGAATGCTTTTTGGAACA 57.190 38.095 0.00 0.00 0.00 3.18
548 590 4.149922 GCTTAACGGAATGCTTTTTGGAAC 59.850 41.667 0.00 0.00 0.00 3.62
549 591 4.303282 GCTTAACGGAATGCTTTTTGGAA 58.697 39.130 0.00 0.00 0.00 3.53
550 592 3.610585 CGCTTAACGGAATGCTTTTTGGA 60.611 43.478 0.00 0.00 38.44 3.53
551 593 2.661195 CGCTTAACGGAATGCTTTTTGG 59.339 45.455 0.00 0.00 38.44 3.28
552 594 2.090503 GCGCTTAACGGAATGCTTTTTG 59.909 45.455 0.00 0.00 43.93 2.44
658 710 2.671963 GCCAACGTGGGAAGGGTC 60.672 66.667 15.02 0.00 38.19 4.46
697 749 2.948134 GCGACGACCGAACCGATC 60.948 66.667 0.00 0.00 41.76 3.69
698 750 4.824166 CGCGACGACCGAACCGAT 62.824 66.667 0.00 0.00 41.76 4.18
773 836 2.112815 AGCGCGTAATTCCCTTGCC 61.113 57.895 8.43 0.00 0.00 4.52
780 843 1.812214 CTCGGAGCAGCGCGTAATTC 61.812 60.000 8.43 0.84 0.00 2.17
836 907 4.154347 CTGCTCCTCCGGCACTCC 62.154 72.222 0.00 0.00 35.71 3.85
837 908 4.828925 GCTGCTCCTCCGGCACTC 62.829 72.222 0.00 0.00 37.08 3.51
839 910 4.400961 AAGCTGCTCCTCCGGCAC 62.401 66.667 1.00 0.00 39.58 5.01
840 911 4.087892 GAAGCTGCTCCTCCGGCA 62.088 66.667 1.00 0.00 39.58 5.69
841 912 4.847444 GGAAGCTGCTCCTCCGGC 62.847 72.222 1.00 0.00 37.37 6.13
842 913 3.080121 AGGAAGCTGCTCCTCCGG 61.080 66.667 13.28 0.00 42.53 5.14
857 928 6.384305 TCTTTCCTTTCCTTCTATAGTGGAGG 59.616 42.308 13.84 12.49 0.00 4.30
859 930 7.808279 TTCTTTCCTTTCCTTCTATAGTGGA 57.192 36.000 11.38 11.38 0.00 4.02
862 933 8.836735 TCCATTTCTTTCCTTTCCTTCTATAGT 58.163 33.333 0.00 0.00 0.00 2.12
863 934 9.114952 GTCCATTTCTTTCCTTTCCTTCTATAG 57.885 37.037 0.00 0.00 0.00 1.31
864 935 8.053355 GGTCCATTTCTTTCCTTTCCTTCTATA 58.947 37.037 0.00 0.00 0.00 1.31
865 936 6.892456 GGTCCATTTCTTTCCTTTCCTTCTAT 59.108 38.462 0.00 0.00 0.00 1.98
866 937 6.183361 TGGTCCATTTCTTTCCTTTCCTTCTA 60.183 38.462 0.00 0.00 0.00 2.10
867 938 5.080337 GGTCCATTTCTTTCCTTTCCTTCT 58.920 41.667 0.00 0.00 0.00 2.85
868 939 4.832823 TGGTCCATTTCTTTCCTTTCCTTC 59.167 41.667 0.00 0.00 0.00 3.46
869 940 4.814967 TGGTCCATTTCTTTCCTTTCCTT 58.185 39.130 0.00 0.00 0.00 3.36
871 942 5.337571 GGATTGGTCCATTTCTTTCCTTTCC 60.338 44.000 0.00 0.00 44.42 3.13
872 943 5.724328 GGATTGGTCCATTTCTTTCCTTTC 58.276 41.667 0.00 0.00 44.42 2.62
873 944 5.745312 GGATTGGTCCATTTCTTTCCTTT 57.255 39.130 0.00 0.00 44.42 3.11
886 957 2.044620 AGGGGGAGGGATTGGTCC 59.955 66.667 0.00 0.00 44.29 4.46
887 958 2.079288 GGAGGGGGAGGGATTGGTC 61.079 68.421 0.00 0.00 0.00 4.02
888 959 2.044620 GGAGGGGGAGGGATTGGT 59.955 66.667 0.00 0.00 0.00 3.67
889 960 3.171388 CGGAGGGGGAGGGATTGG 61.171 72.222 0.00 0.00 0.00 3.16
890 961 2.366972 ACGGAGGGGGAGGGATTG 60.367 66.667 0.00 0.00 0.00 2.67
915 986 2.889521 AATTCGGGGGATTTGGGGGC 62.890 60.000 0.00 0.00 0.00 5.80
952 1023 2.586792 CCGAGCAGAAAGGAGGGG 59.413 66.667 0.00 0.00 0.00 4.79
953 1024 2.245438 GACCCGAGCAGAAAGGAGGG 62.245 65.000 0.00 0.00 44.17 4.30
954 1025 1.219393 GACCCGAGCAGAAAGGAGG 59.781 63.158 0.00 0.00 0.00 4.30
955 1026 1.153745 CGACCCGAGCAGAAAGGAG 60.154 63.158 0.00 0.00 0.00 3.69
956 1027 2.646175 CCGACCCGAGCAGAAAGGA 61.646 63.158 0.00 0.00 0.00 3.36
1085 1167 1.064017 AGAGACAAGGGCCAAAACACA 60.064 47.619 6.18 0.00 0.00 3.72
1086 1168 1.338020 CAGAGACAAGGGCCAAAACAC 59.662 52.381 6.18 0.00 0.00 3.32
1087 1169 1.691196 CAGAGACAAGGGCCAAAACA 58.309 50.000 6.18 0.00 0.00 2.83
1088 1170 0.315251 GCAGAGACAAGGGCCAAAAC 59.685 55.000 6.18 0.00 0.00 2.43
1094 1179 1.065564 AGATCAAGCAGAGACAAGGGC 60.066 52.381 0.00 0.00 0.00 5.19
1119 1217 2.012673 GGACTGCCACTAGAGCAATTG 58.987 52.381 12.18 0.00 40.35 2.32
1203 1306 3.514362 GCATTTACCACCGCCCCG 61.514 66.667 0.00 0.00 0.00 5.73
1204 1307 2.361865 TGCATTTACCACCGCCCC 60.362 61.111 0.00 0.00 0.00 5.80
1205 1308 0.393267 TACTGCATTTACCACCGCCC 60.393 55.000 0.00 0.00 0.00 6.13
1206 1309 1.455248 TTACTGCATTTACCACCGCC 58.545 50.000 0.00 0.00 0.00 6.13
1207 1310 2.414957 GGTTTACTGCATTTACCACCGC 60.415 50.000 0.00 0.00 0.00 5.68
1208 1311 3.078837 AGGTTTACTGCATTTACCACCG 58.921 45.455 9.64 0.00 0.00 4.94
1209 1312 3.126343 CGAGGTTTACTGCATTTACCACC 59.874 47.826 9.64 2.44 0.00 4.61
1210 1313 3.749609 ACGAGGTTTACTGCATTTACCAC 59.250 43.478 9.64 4.08 0.00 4.16
1211 1314 3.998341 GACGAGGTTTACTGCATTTACCA 59.002 43.478 9.64 0.00 0.00 3.25
1212 1315 3.061697 CGACGAGGTTTACTGCATTTACC 59.938 47.826 0.00 0.00 0.00 2.85
1266 1369 3.301222 ATGTTCCAGGCCGCCCATT 62.301 57.895 5.55 0.00 0.00 3.16
1296 1399 8.936864 ACTATAGCAACAAAATCACAACTAGTC 58.063 33.333 0.00 0.00 0.00 2.59
1297 1400 8.848474 ACTATAGCAACAAAATCACAACTAGT 57.152 30.769 0.00 0.00 0.00 2.57
1299 1402 8.865978 CGTACTATAGCAACAAAATCACAACTA 58.134 33.333 0.00 0.00 0.00 2.24
1300 1403 7.601130 TCGTACTATAGCAACAAAATCACAACT 59.399 33.333 0.00 0.00 0.00 3.16
1301 1404 7.735500 TCGTACTATAGCAACAAAATCACAAC 58.264 34.615 0.00 0.00 0.00 3.32
1303 1406 6.035650 GCTCGTACTATAGCAACAAAATCACA 59.964 38.462 0.00 0.00 38.63 3.58
1305 1408 5.231357 CGCTCGTACTATAGCAACAAAATCA 59.769 40.000 0.00 0.00 38.70 2.57
1307 1410 5.345702 TCGCTCGTACTATAGCAACAAAAT 58.654 37.500 0.00 0.00 38.70 1.82
1308 1411 4.735985 TCGCTCGTACTATAGCAACAAAA 58.264 39.130 0.00 0.00 38.70 2.44
1311 1414 2.289820 CCTCGCTCGTACTATAGCAACA 59.710 50.000 0.00 0.00 38.70 3.33
1314 1417 2.414806 CTCCTCGCTCGTACTATAGCA 58.585 52.381 0.00 0.00 38.70 3.49
1315 1418 1.129064 GCTCCTCGCTCGTACTATAGC 59.871 57.143 0.00 0.00 35.14 2.97
1335 1441 3.674682 CGAGCTACAGAGAAGGGAAACAG 60.675 52.174 0.00 0.00 0.00 3.16
1357 1463 1.134491 AGCAGGTGGCCTAACGATTAC 60.134 52.381 3.32 0.00 46.50 1.89
1417 1528 6.530181 AGTTCCAAAACACAAGACGAATTTTC 59.470 34.615 0.00 0.00 37.88 2.29
1419 1530 5.804979 CAGTTCCAAAACACAAGACGAATTT 59.195 36.000 0.00 0.00 37.88 1.82
1420 1531 5.124776 TCAGTTCCAAAACACAAGACGAATT 59.875 36.000 0.00 0.00 37.88 2.17
1421 1532 4.638421 TCAGTTCCAAAACACAAGACGAAT 59.362 37.500 0.00 0.00 37.88 3.34
1427 1538 6.966435 AATTTGTCAGTTCCAAAACACAAG 57.034 33.333 0.00 0.00 34.60 3.16
1433 1544 5.353678 CAGCCAAAATTTGTCAGTTCCAAAA 59.646 36.000 4.92 0.00 35.60 2.44
1498 1623 1.735571 TCTTGGCGAACGAAATTAGGC 59.264 47.619 0.00 0.00 38.73 3.93
1564 1689 8.258007 TCAAGACAACAAGGTAGGAGTTATATG 58.742 37.037 0.00 0.00 0.00 1.78
1568 1693 5.601313 ACTCAAGACAACAAGGTAGGAGTTA 59.399 40.000 0.00 0.00 29.46 2.24
1569 1694 4.409247 ACTCAAGACAACAAGGTAGGAGTT 59.591 41.667 0.00 0.00 29.46 3.01
1570 1695 3.967987 ACTCAAGACAACAAGGTAGGAGT 59.032 43.478 0.00 0.00 0.00 3.85
1571 1696 4.608948 ACTCAAGACAACAAGGTAGGAG 57.391 45.455 0.00 0.00 0.00 3.69
1572 1697 6.488769 TTTACTCAAGACAACAAGGTAGGA 57.511 37.500 0.00 0.00 0.00 2.94
1573 1698 6.090898 CGATTTACTCAAGACAACAAGGTAGG 59.909 42.308 0.00 0.00 0.00 3.18
1574 1699 6.866770 TCGATTTACTCAAGACAACAAGGTAG 59.133 38.462 0.00 0.00 0.00 3.18
1607 1732 1.934589 TCATTTGATCTACGTGCCGG 58.065 50.000 0.00 0.00 0.00 6.13
1662 2036 3.928992 AGCATGATGAAACTACACACGAG 59.071 43.478 0.00 0.00 0.00 4.18
1711 2085 2.423874 TGCGGAGGCAGAAACGAA 59.576 55.556 0.00 0.00 46.21 3.85
1721 2095 3.179443 TGTCTTATTAGCTTGCGGAGG 57.821 47.619 0.00 0.00 0.00 4.30
1738 2112 2.171448 AGGACAGAACCTATGCCATGTC 59.829 50.000 0.00 0.00 38.65 3.06
1785 2159 3.036429 GCAGGGCAGACTCGGGAAT 62.036 63.158 0.00 0.00 0.00 3.01
1821 2195 1.266696 CGCGAGCCAAAACGTACATAC 60.267 52.381 0.00 0.00 0.00 2.39
1890 2264 1.412343 GGCAACAGTCAACCACCAAAT 59.588 47.619 0.00 0.00 0.00 2.32
1911 2285 7.039504 AGGACAAATAATTGAGCAGTTTCATGT 60.040 33.333 0.00 0.00 38.94 3.21
1965 2339 5.411361 TGATTCCAGAAATGTTACTCCAACG 59.589 40.000 0.00 0.00 40.26 4.10
2073 2447 8.795513 TGCGCCACTACAATAGTTATATACTAA 58.204 33.333 4.18 0.00 42.45 2.24
2136 2510 6.617782 AGAGATCCCATAGTACCATTCATG 57.382 41.667 0.00 0.00 0.00 3.07
2137 2511 7.483018 ACTAGAGATCCCATAGTACCATTCAT 58.517 38.462 0.00 0.00 0.00 2.57
2184 2558 8.219105 GGTCTTTTAGCCGATAATAACGTAATG 58.781 37.037 0.00 0.00 0.00 1.90
2214 2588 5.488341 ACTACACAGTAACAGCCCTAATTG 58.512 41.667 0.00 0.00 31.45 2.32
2270 2644 2.235402 CCATTCTGGCTGGCAGAAAAAT 59.765 45.455 38.79 25.63 41.34 1.82
2439 2813 7.223387 GCTTAAATAAGAATTGGCCATGAACAG 59.777 37.037 6.09 0.00 35.33 3.16
2486 2860 5.293814 CAGATTGTGCCAAATGTGAAAAACA 59.706 36.000 0.72 0.00 44.79 2.83
2508 2882 8.680903 AGAAATATAAGTGTGATCTTTTGGCAG 58.319 33.333 0.00 0.00 0.00 4.85
2837 3214 4.151258 CACTTTTGTGTCGCTCATGAAT 57.849 40.909 0.00 0.00 44.94 2.57
3181 3558 7.792374 TCTGCTATATTCATTGAACAAGTCC 57.208 36.000 0.15 0.00 0.00 3.85
3218 3595 8.260099 ACTTTTTAGTAGGTTGGAAGTAGACT 57.740 34.615 0.00 0.00 0.00 3.24
3328 3705 3.057315 GCAGCACACTGTTTCCAATACAT 60.057 43.478 0.00 0.00 46.30 2.29
3341 3718 1.105457 ACACACATTTGCAGCACACT 58.895 45.000 0.00 0.00 0.00 3.55
3360 3737 6.070824 TGTGCTCTCAACCTCATAAGTCATAA 60.071 38.462 0.00 0.00 0.00 1.90
3361 3738 5.422012 TGTGCTCTCAACCTCATAAGTCATA 59.578 40.000 0.00 0.00 0.00 2.15
3362 3739 4.223700 TGTGCTCTCAACCTCATAAGTCAT 59.776 41.667 0.00 0.00 0.00 3.06
3363 3740 3.578282 TGTGCTCTCAACCTCATAAGTCA 59.422 43.478 0.00 0.00 0.00 3.41
3364 3741 4.193826 TGTGCTCTCAACCTCATAAGTC 57.806 45.455 0.00 0.00 0.00 3.01
3365 3742 4.223700 TGATGTGCTCTCAACCTCATAAGT 59.776 41.667 0.00 0.00 0.00 2.24
3366 3743 4.763073 TGATGTGCTCTCAACCTCATAAG 58.237 43.478 0.00 0.00 0.00 1.73
3545 3922 2.030007 GCATCTACAGGCAAAAACAGCA 60.030 45.455 0.00 0.00 0.00 4.41
3604 3981 8.213518 TGCCATCAAAATAACTTGAGTCTATC 57.786 34.615 0.00 0.00 38.66 2.08
3632 4009 3.016736 ACTTTACTTCCCATCGCATTGG 58.983 45.455 0.00 0.00 36.46 3.16
3798 4175 1.134431 TGAAGAGACTGCAGTGCACAA 60.134 47.619 27.27 2.07 33.79 3.33
3810 4187 6.595682 TCCCATCCAGATAATTTGAAGAGAC 58.404 40.000 0.00 0.00 0.00 3.36
3883 4260 0.586319 CAGCAAGTACACCACCAACG 59.414 55.000 0.00 0.00 0.00 4.10
4058 4435 6.645415 AGTTCTTTTATTGGTACAGTGACTCG 59.355 38.462 0.00 0.00 42.39 4.18
4168 4552 1.952296 CCTATGACCCAGCAAAGCATC 59.048 52.381 0.00 0.00 0.00 3.91
4241 4625 2.747177 TCGTTAGAGACCACATCCCAT 58.253 47.619 0.00 0.00 0.00 4.00
4291 4675 7.667219 CAGAATATGGTAAGGATAATGCAGGTT 59.333 37.037 0.00 0.00 0.00 3.50
4297 4681 8.908786 ACACACAGAATATGGTAAGGATAATG 57.091 34.615 0.00 0.00 0.00 1.90
4298 4682 9.920946 AAACACACAGAATATGGTAAGGATAAT 57.079 29.630 0.00 0.00 0.00 1.28
4299 4683 9.173021 CAAACACACAGAATATGGTAAGGATAA 57.827 33.333 0.00 0.00 0.00 1.75
4300 4684 8.544622 TCAAACACACAGAATATGGTAAGGATA 58.455 33.333 0.00 0.00 0.00 2.59
4301 4685 7.336931 GTCAAACACACAGAATATGGTAAGGAT 59.663 37.037 0.00 0.00 0.00 3.24
4302 4686 6.653320 GTCAAACACACAGAATATGGTAAGGA 59.347 38.462 0.00 0.00 0.00 3.36
4303 4687 6.128007 GGTCAAACACACAGAATATGGTAAGG 60.128 42.308 0.00 0.00 0.00 2.69
4304 4688 6.655003 AGGTCAAACACACAGAATATGGTAAG 59.345 38.462 0.00 0.00 0.00 2.34
4305 4689 6.429692 CAGGTCAAACACACAGAATATGGTAA 59.570 38.462 0.00 0.00 0.00 2.85
4308 4692 4.379813 GCAGGTCAAACACACAGAATATGG 60.380 45.833 0.00 0.00 0.00 2.74
4316 4700 0.465460 GAGGGCAGGTCAAACACACA 60.465 55.000 0.00 0.00 0.00 3.72
4318 4702 0.108585 GAGAGGGCAGGTCAAACACA 59.891 55.000 0.00 0.00 0.00 3.72
4323 4707 1.267121 GTGTAGAGAGGGCAGGTCAA 58.733 55.000 0.00 0.00 0.00 3.18
4327 4711 1.556911 ACATTGTGTAGAGAGGGCAGG 59.443 52.381 0.00 0.00 0.00 4.85
4335 4719 8.437360 TCCTGCAATATAAACATTGTGTAGAG 57.563 34.615 0.00 0.00 38.04 2.43
4345 4729 4.199310 GACAGCCTCCTGCAATATAAACA 58.801 43.478 0.00 0.00 43.02 2.83
4350 4734 1.123077 TCGACAGCCTCCTGCAATAT 58.877 50.000 0.00 0.00 43.02 1.28
4353 4737 1.830587 ATGTCGACAGCCTCCTGCAA 61.831 55.000 24.41 0.00 43.02 4.08
4370 4754 1.484653 TCTTGTATGGACCGGGTCATG 59.515 52.381 27.32 10.30 33.68 3.07
4382 4766 2.503356 AGCTTCCTCTGGGTCTTGTATG 59.497 50.000 0.00 0.00 0.00 2.39
4406 4790 4.239991 TCCTGCAGGAGCCTCTTT 57.760 55.556 32.00 0.00 39.78 2.52
4427 4811 1.144936 GCTGCTCTCCCGCTTGTAT 59.855 57.895 0.00 0.00 0.00 2.29
4466 4850 0.874390 GACCATGAAAGAAGCGCACA 59.126 50.000 11.47 0.00 0.00 4.57
4481 4865 4.020617 CCGCTGCTCCCTTGACCA 62.021 66.667 0.00 0.00 0.00 4.02
4493 4877 3.056313 GCTTTAAGCAGGCCCGCTG 62.056 63.158 15.87 2.56 42.89 5.18
4638 5055 5.646467 TCGTTCCTAAACTTTTGTTCTCG 57.354 39.130 0.00 0.00 42.67 4.04
4680 5097 9.202273 TCATCACCAGCAAATTTATTGTTAAAC 57.798 29.630 0.00 0.00 30.33 2.01
4745 5164 2.224378 ACAACACACTCATCAGACCCAG 60.224 50.000 0.00 0.00 0.00 4.45
4773 5192 1.344114 ACATGGTTTGGCAATCCACAC 59.656 47.619 27.56 10.90 43.33 3.82
4823 5242 8.450964 CAGTACAACAATAATCACTTACCTTGG 58.549 37.037 0.00 0.00 0.00 3.61
4833 5252 8.902540 ACTCAACTTCAGTACAACAATAATCA 57.097 30.769 0.00 0.00 0.00 2.57
4852 5271 7.923414 ATTAAGACCCATCTAACAACTCAAC 57.077 36.000 0.00 0.00 33.57 3.18
4892 5331 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4893 5332 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4895 5334 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4896 5335 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4897 5336 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4898 5337 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4899 5338 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4900 5339 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4901 5340 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4902 5341 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4903 5342 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4904 5343 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4905 5344 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4944 5383 6.819146 TGTACACAACACAATCAAGTAGAACA 59.181 34.615 0.00 0.00 31.43 3.18
4945 5384 7.241663 TGTACACAACACAATCAAGTAGAAC 57.758 36.000 0.00 0.00 31.43 3.01
4953 5392 8.462811 AGTTTTTGTATGTACACAACACAATCA 58.537 29.630 11.42 2.63 42.09 2.57
5009 5451 5.975693 TGGAATAAAATCATTATCCCCGC 57.024 39.130 0.00 0.00 0.00 6.13
5010 5452 7.701539 TCATGGAATAAAATCATTATCCCCG 57.298 36.000 0.00 0.00 0.00 5.73
5078 5530 3.481163 ATGGTTGCAAAGGGGGCCA 62.481 57.895 4.39 3.27 0.00 5.36
5113 5565 3.019564 AGATCAGTTGGCCAATTACAGC 58.980 45.455 23.66 10.23 0.00 4.40
5122 5574 1.419387 AGGATAGCAGATCAGTTGGCC 59.581 52.381 0.00 0.00 0.00 5.36
5128 5580 6.767456 AGGTCAAAATAGGATAGCAGATCAG 58.233 40.000 0.00 0.00 0.00 2.90
5166 5618 3.304659 CCATTCTGTGTGTGGTTTAGCAC 60.305 47.826 5.17 5.17 36.26 4.40
5200 5652 2.170187 AGCCATCTTCTGCTGGTCTAAG 59.830 50.000 0.00 0.00 36.23 2.18
5202 5654 1.871418 AGCCATCTTCTGCTGGTCTA 58.129 50.000 0.00 0.00 36.23 2.59
5210 5662 5.675575 GCACACTAAATTCAGCCATCTTCTG 60.676 44.000 0.00 0.00 0.00 3.02
5241 5693 4.162690 GGACTGCCCGCCTACAGG 62.163 72.222 0.00 0.00 38.25 4.00
5243 5695 3.075005 GAGGACTGCCCGCCTACA 61.075 66.667 0.00 0.00 40.87 2.74
5269 5722 3.308401 TCAAGGAGATAGGCATGCTACA 58.692 45.455 18.92 3.11 0.00 2.74
5289 5742 6.633634 GCTGAAACTATATAGTGACACGTCTC 59.366 42.308 16.11 4.50 36.50 3.36
5299 5752 5.290386 GGAGCAACGCTGAAACTATATAGT 58.710 41.667 9.71 9.71 39.88 2.12
5329 5782 5.424757 CCGGTCTAGATAAAAACCATGACA 58.575 41.667 0.00 0.00 0.00 3.58
5349 5802 2.335712 GCAGGTTTCTTCTGGCCGG 61.336 63.158 4.71 4.71 33.16 6.13
5350 5803 0.962356 ATGCAGGTTTCTTCTGGCCG 60.962 55.000 0.00 0.00 33.16 6.13
5351 5804 0.529378 CATGCAGGTTTCTTCTGGCC 59.471 55.000 0.00 0.00 33.16 5.36
5352 5805 0.529378 CCATGCAGGTTTCTTCTGGC 59.471 55.000 0.00 0.00 33.16 4.85
5435 5907 0.923403 CGTGCGATTCATGTCGATGT 59.077 50.000 9.68 0.00 44.06 3.06
5441 5913 1.134699 ACAGATCCGTGCGATTCATGT 60.135 47.619 0.00 0.00 0.00 3.21
5453 5925 1.813513 AACCTGCTTGAACAGATCCG 58.186 50.000 0.00 0.00 40.25 4.18
5470 5942 9.726034 CGCATACTTTTGTTCATGAAAATAAAC 57.274 29.630 10.35 0.00 0.00 2.01
5482 5956 6.034577 GGCTTTTATTCCGCATACTTTTGTTC 59.965 38.462 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.