Multiple sequence alignment - TraesCS6A01G324500

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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 TraesCS6A01G324500 chr6A 100.000 4393 0 0 461 4853 558789340 558784948 0.000000e+00 8113.0
1 TraesCS6A01G324500 chr6A 100.000 81 0 0 1 81 558789800 558789720 3.030000e-32 150.0
2 TraesCS6A01G324500 chr6D 92.903 4072 165 65 461 4498 413273059 413269078 0.000000e+00 5805.0
3 TraesCS6A01G324500 chr6D 92.857 56 3 1 4 59 413273177 413273123 4.030000e-11 80.5
4 TraesCS6A01G324500 chr6B 92.247 3031 135 40 476 3477 623084779 623081820 0.000000e+00 4204.0
5 TraesCS6A01G324500 chr6B 92.747 1034 29 25 3474 4489 623081780 623080775 0.000000e+00 1452.0
6 TraesCS6A01G324500 chr6B 93.617 47 3 0 11 57 623084912 623084866 2.420000e-08 71.3
7 TraesCS6A01G324500 chr2B 96.944 360 9 1 4496 4853 47183165 47182806 1.930000e-168 603.0
8 TraesCS6A01G324500 chr2B 86.538 104 12 1 4676 4777 47182925 47182822 3.970000e-21 113.0
9 TraesCS6A01G324500 chr2A 96.667 360 10 1 4496 4853 765841474 765841115 8.990000e-167 597.0
10 TraesCS6A01G324500 chr2A 87.097 62 7 1 1042 1103 715341510 715341450 8.720000e-08 69.4
11 TraesCS6A01G324500 chr5D 96.399 361 11 1 4495 4853 547235332 547234972 1.160000e-165 593.0
12 TraesCS6A01G324500 chr3A 96.389 360 11 1 4496 4853 685357663 685357304 4.180000e-165 592.0
13 TraesCS6A01G324500 chr7B 96.111 360 12 1 4496 4853 711888122 711887763 1.950000e-163 586.0
14 TraesCS6A01G324500 chr7B 86.972 284 34 2 4496 4776 663654787 663654504 2.820000e-82 316.0
15 TraesCS6A01G324500 chr7B 84.932 219 33 0 2562 2780 80661154 80660936 6.320000e-54 222.0
16 TraesCS6A01G324500 chr7B 81.429 140 26 0 2882 3021 80660833 80660694 1.100000e-21 115.0
17 TraesCS6A01G324500 chr7B 92.208 77 6 0 4775 4851 663633656 663633580 5.140000e-20 110.0
18 TraesCS6A01G324500 chr5A 95.833 360 13 1 4496 4853 357164199 357163840 9.050000e-162 580.0
19 TraesCS6A01G324500 chr4A 97.345 339 6 2 4518 4853 616626374 616626712 1.520000e-159 573.0
20 TraesCS6A01G324500 chr2D 90.785 293 16 4 4496 4777 31476329 31476037 9.860000e-102 381.0
21 TraesCS6A01G324500 chr2D 87.302 63 7 1 1042 1104 577156988 577156927 2.420000e-08 71.3
22 TraesCS6A01G324500 chr7A 78.151 476 87 16 2562 3029 124069304 124068838 2.210000e-73 287.0
23 TraesCS6A01G324500 chr7A 96.104 77 3 0 4776 4852 2659227 2659303 5.100000e-25 126.0
24 TraesCS6A01G324500 chr7D 77.684 475 89 16 2562 3028 119567531 119567066 1.720000e-69 274.0
25 TraesCS6A01G324500 chr7D 87.234 188 17 6 1499 1684 119568516 119568334 1.770000e-49 207.0
26 TraesCS6A01G324500 chr1B 89.431 123 13 0 1195 1317 377969155 377969033 6.500000e-34 156.0
27 TraesCS6A01G324500 chr1A 88.889 126 14 0 1195 1320 350400269 350400144 6.500000e-34 156.0
28 TraesCS6A01G324500 chr1D 88.618 123 14 0 1195 1317 278109820 278109698 3.030000e-32 150.0


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 TraesCS6A01G324500 chr6A 558784948 558789800 4852 True 4131.50 8113 100.000000 1 4853 2 chr6A.!!$R1 4852
1 TraesCS6A01G324500 chr6D 413269078 413273177 4099 True 2942.75 5805 92.880000 4 4498 2 chr6D.!!$R1 4494
2 TraesCS6A01G324500 chr6B 623080775 623084912 4137 True 1909.10 4204 92.870333 11 4489 3 chr6B.!!$R1 4478
3 TraesCS6A01G324500 chr7D 119567066 119568516 1450 True 240.50 274 82.459000 1499 3028 2 chr7D.!!$R1 1529

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
569 619 0.326143 GGGGAAAGCTCTCCTCTCCT 60.326 60.0 5.94 0.0 39.45 3.69 F
1189 1269 0.235665 GTCATTCTGTGTGTGCGTGG 59.764 55.0 0.00 0.0 0.00 4.94 F
1390 1484 0.389391 TTCGGAGCGAGATGATTCCC 59.611 55.0 0.00 0.0 37.14 3.97 F
2940 3119 0.107456 CCGCCATCAACCAGCTCTAT 59.893 55.0 0.00 0.0 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 1875 0.396060 CCCAACCAAAACCACCATGG 59.604 55.000 11.19 11.19 45.02 3.66 R
2343 2521 0.827925 ACTCCGTCCACTTGCTCTGA 60.828 55.000 0.00 0.00 0.00 3.27 R
3057 3236 1.227823 CTTGCCCTCCAACGTCACA 60.228 57.895 0.00 0.00 0.00 3.58 R
4737 4986 0.031449 TTCGTCACATCACTCGTGCA 59.969 50.000 0.00 0.00 34.27 4.57 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 4.599036 GAGAGAGAGGGAGGGAGC 57.401 66.667 0.00 0.00 0.00 4.70
19 20 1.990160 GAGAGAGAGGGAGGGAGCGA 61.990 65.000 0.00 0.00 0.00 4.93
60 76 0.946221 CAACGAGGCCATAGATCGCC 60.946 60.000 5.01 1.37 46.09 5.54
562 612 4.491409 GGGGCGGGGAAAGCTCTC 62.491 72.222 0.00 0.00 34.99 3.20
563 613 4.491409 GGGCGGGGAAAGCTCTCC 62.491 72.222 0.00 0.00 39.11 3.71
564 614 3.403558 GGCGGGGAAAGCTCTCCT 61.404 66.667 5.94 0.00 40.57 3.69
565 615 2.188207 GCGGGGAAAGCTCTCCTC 59.812 66.667 5.94 0.00 40.57 3.71
566 616 2.363172 GCGGGGAAAGCTCTCCTCT 61.363 63.158 3.98 0.00 40.57 3.69
567 617 1.819905 CGGGGAAAGCTCTCCTCTC 59.180 63.158 3.98 0.00 40.57 3.20
568 618 1.681486 CGGGGAAAGCTCTCCTCTCC 61.681 65.000 3.98 0.00 40.57 3.71
569 619 0.326143 GGGGAAAGCTCTCCTCTCCT 60.326 60.000 5.94 0.00 39.45 3.69
570 620 1.119684 GGGAAAGCTCTCCTCTCCTC 58.880 60.000 5.94 0.00 35.63 3.71
571 621 1.342975 GGGAAAGCTCTCCTCTCCTCT 60.343 57.143 5.94 0.00 35.63 3.69
592 642 6.352565 CCTCTCTCTCTCTTCTCTTCTCTTCT 60.353 46.154 0.00 0.00 0.00 2.85
593 643 7.020827 TCTCTCTCTCTTCTCTTCTCTTCTT 57.979 40.000 0.00 0.00 0.00 2.52
594 644 7.106239 TCTCTCTCTCTTCTCTTCTCTTCTTC 58.894 42.308 0.00 0.00 0.00 2.87
595 645 6.180472 TCTCTCTCTTCTCTTCTCTTCTTCC 58.820 44.000 0.00 0.00 0.00 3.46
596 646 5.886609 TCTCTCTTCTCTTCTCTTCTTCCA 58.113 41.667 0.00 0.00 0.00 3.53
597 647 6.310941 TCTCTCTTCTCTTCTCTTCTTCCAA 58.689 40.000 0.00 0.00 0.00 3.53
598 648 6.208599 TCTCTCTTCTCTTCTCTTCTTCCAAC 59.791 42.308 0.00 0.00 0.00 3.77
625 675 0.692756 CTCCCTCTCCTTCCCTTCCC 60.693 65.000 0.00 0.00 0.00 3.97
626 676 1.162951 TCCCTCTCCTTCCCTTCCCT 61.163 60.000 0.00 0.00 0.00 4.20
627 677 0.985490 CCCTCTCCTTCCCTTCCCTG 60.985 65.000 0.00 0.00 0.00 4.45
628 678 0.985490 CCTCTCCTTCCCTTCCCTGG 60.985 65.000 0.00 0.00 0.00 4.45
629 679 1.616628 TCTCCTTCCCTTCCCTGGC 60.617 63.158 0.00 0.00 0.00 4.85
630 680 1.617839 CTCCTTCCCTTCCCTGGCT 60.618 63.158 0.00 0.00 0.00 4.75
631 681 1.616628 TCCTTCCCTTCCCTGGCTC 60.617 63.158 0.00 0.00 0.00 4.70
632 682 2.684499 CCTTCCCTTCCCTGGCTCC 61.684 68.421 0.00 0.00 0.00 4.70
633 683 1.617839 CTTCCCTTCCCTGGCTCCT 60.618 63.158 0.00 0.00 0.00 3.69
634 684 1.919600 CTTCCCTTCCCTGGCTCCTG 61.920 65.000 0.00 0.00 0.00 3.86
635 685 2.285668 CCCTTCCCTGGCTCCTGA 60.286 66.667 0.00 0.00 0.00 3.86
636 686 2.373707 CCCTTCCCTGGCTCCTGAG 61.374 68.421 0.00 0.00 0.00 3.35
685 735 2.581354 CTTCGCCAGGACCAGAGG 59.419 66.667 0.00 0.00 0.00 3.69
727 777 3.785859 CGCTGGCTGGCTTCCCTA 61.786 66.667 2.00 0.00 0.00 3.53
732 782 1.056700 TGGCTGGCTTCCCTATCTCC 61.057 60.000 2.00 0.00 0.00 3.71
763 813 3.130160 CCCTGCTGCCGCTTCTTC 61.130 66.667 0.70 0.00 36.97 2.87
764 814 2.046507 CCTGCTGCCGCTTCTTCT 60.047 61.111 0.70 0.00 36.97 2.85
779 829 2.245714 CTTCTTTCCTCTTGCGCGCC 62.246 60.000 30.77 11.42 0.00 6.53
856 906 2.812542 TATATAGCGCGCGCCTGGTG 62.813 60.000 46.98 12.50 43.17 4.17
954 1020 3.573489 GAAGCAAACGACGTGCCGG 62.573 63.158 0.00 0.00 43.27 6.13
973 1039 2.025898 GGGAAGAGACCGAAGACTAGG 58.974 57.143 0.00 0.00 0.00 3.02
974 1040 2.356947 GGGAAGAGACCGAAGACTAGGA 60.357 54.545 4.11 0.00 0.00 2.94
1115 1181 1.868251 CGTACGCTCGCTTCCACTC 60.868 63.158 0.52 0.00 0.00 3.51
1129 1209 4.456911 GCTTCCACTCATGAATTCAACTGA 59.543 41.667 13.09 11.58 0.00 3.41
1132 1212 7.528996 TTCCACTCATGAATTCAACTGATTT 57.471 32.000 13.09 0.44 0.00 2.17
1133 1213 7.149569 TCCACTCATGAATTCAACTGATTTC 57.850 36.000 13.09 7.19 35.88 2.17
1134 1214 6.944290 TCCACTCATGAATTCAACTGATTTCT 59.056 34.615 13.09 0.00 36.15 2.52
1135 1215 7.120285 TCCACTCATGAATTCAACTGATTTCTC 59.880 37.037 13.09 0.00 36.15 2.87
1165 1245 4.944317 TCTTCGTCTCTTGCTCATCTTCTA 59.056 41.667 0.00 0.00 0.00 2.10
1167 1247 5.843673 TCGTCTCTTGCTCATCTTCTATT 57.156 39.130 0.00 0.00 0.00 1.73
1168 1248 5.826586 TCGTCTCTTGCTCATCTTCTATTC 58.173 41.667 0.00 0.00 0.00 1.75
1169 1249 5.592282 TCGTCTCTTGCTCATCTTCTATTCT 59.408 40.000 0.00 0.00 0.00 2.40
1170 1250 5.686841 CGTCTCTTGCTCATCTTCTATTCTG 59.313 44.000 0.00 0.00 0.00 3.02
1171 1251 6.572519 GTCTCTTGCTCATCTTCTATTCTGT 58.427 40.000 0.00 0.00 0.00 3.41
1172 1252 6.697019 GTCTCTTGCTCATCTTCTATTCTGTC 59.303 42.308 0.00 0.00 0.00 3.51
1173 1253 6.379417 TCTCTTGCTCATCTTCTATTCTGTCA 59.621 38.462 0.00 0.00 0.00 3.58
1174 1254 7.069702 TCTCTTGCTCATCTTCTATTCTGTCAT 59.930 37.037 0.00 0.00 0.00 3.06
1175 1255 7.563020 TCTTGCTCATCTTCTATTCTGTCATT 58.437 34.615 0.00 0.00 0.00 2.57
1189 1269 0.235665 GTCATTCTGTGTGTGCGTGG 59.764 55.000 0.00 0.00 0.00 4.94
1191 1271 1.148273 ATTCTGTGTGTGCGTGGGT 59.852 52.632 0.00 0.00 0.00 4.51
1343 1437 1.709115 CCCATCCCATCATCCATGTCT 59.291 52.381 0.00 0.00 0.00 3.41
1377 1471 1.267121 TCACCCTCCTTCTTTCGGAG 58.733 55.000 0.00 0.00 46.11 4.63
1390 1484 0.389391 TTCGGAGCGAGATGATTCCC 59.611 55.000 0.00 0.00 37.14 3.97
1408 1502 1.641577 CCGATCCCTCTTCGTGTTTC 58.358 55.000 0.00 0.00 34.85 2.78
1715 1817 3.151958 ATAGCACGCCGCCTACCTG 62.152 63.158 0.00 0.00 44.04 4.00
1773 1875 3.545481 CGCTGACACCACGATCGC 61.545 66.667 16.60 0.00 0.00 4.58
2238 2414 3.060000 ATCGCCCTCGTCGACACA 61.060 61.111 17.16 0.00 38.88 3.72
2314 2490 1.157257 TTTGCGTGACGTGCACTGAT 61.157 50.000 16.19 0.00 45.49 2.90
2315 2491 1.830368 TTGCGTGACGTGCACTGATG 61.830 55.000 16.19 1.10 45.49 3.07
2316 2492 2.021584 GCGTGACGTGCACTGATGA 61.022 57.895 16.19 0.00 45.49 2.92
2318 2494 1.617755 CGTGACGTGCACTGATGACC 61.618 60.000 16.19 0.00 45.49 4.02
2319 2495 0.599991 GTGACGTGCACTGATGACCA 60.600 55.000 16.19 0.89 44.27 4.02
2321 2497 1.270785 TGACGTGCACTGATGACCAAT 60.271 47.619 16.19 0.00 0.00 3.16
2322 2498 1.806542 GACGTGCACTGATGACCAATT 59.193 47.619 16.19 0.00 0.00 2.32
2323 2499 1.536766 ACGTGCACTGATGACCAATTG 59.463 47.619 16.19 0.00 0.00 2.32
2324 2500 1.805943 CGTGCACTGATGACCAATTGA 59.194 47.619 16.19 0.00 0.00 2.57
2334 2510 3.383620 TGACCAATTGACCATTGTTGC 57.616 42.857 7.12 0.00 40.87 4.17
2337 2513 2.887783 ACCAATTGACCATTGTTGCGTA 59.112 40.909 7.12 0.00 40.87 4.42
2343 2521 3.407698 TGACCATTGTTGCGTATGTCTT 58.592 40.909 0.00 0.00 0.00 3.01
2439 2617 2.890371 GGCCGGAGCGAGTCTTTA 59.110 61.111 5.05 0.00 41.24 1.85
2533 2711 2.173382 GCGCACATGGACGAACAC 59.827 61.111 13.08 0.00 0.00 3.32
2859 3038 2.112380 TGTGCCATGATTCATGACGT 57.888 45.000 24.93 0.00 43.81 4.34
2871 3050 2.844946 TCATGACGTGTGTGGAATTGT 58.155 42.857 0.00 0.00 0.00 2.71
2940 3119 0.107456 CCGCCATCAACCAGCTCTAT 59.893 55.000 0.00 0.00 0.00 1.98
3057 3236 4.082523 CACAGGGACATCGCCGGT 62.083 66.667 1.90 0.00 0.00 5.28
3096 3275 0.179702 GGAGCATGATGAGGCTGTCA 59.820 55.000 0.00 0.00 39.98 3.58
3348 3527 3.596066 CTCCCAGTGGGACGTGCTG 62.596 68.421 28.04 12.69 46.17 4.41
3378 3557 4.742201 CCGGTGCAGGAGGTGTCG 62.742 72.222 0.00 0.00 0.00 4.35
3399 3578 3.797353 ATCCCCAACGGCTCGCAT 61.797 61.111 0.00 0.00 0.00 4.73
3411 3590 4.812476 TCGCATCCGGGCAACTCG 62.812 66.667 0.00 0.00 34.56 4.18
3438 3617 0.526310 TGCTCAGAGTAAGCATCGCG 60.526 55.000 0.00 0.00 44.51 5.87
3439 3618 0.526524 GCTCAGAGTAAGCATCGCGT 60.527 55.000 5.77 0.00 39.61 6.01
3440 3619 1.268589 GCTCAGAGTAAGCATCGCGTA 60.269 52.381 5.77 0.00 39.61 4.42
3441 3620 2.645163 CTCAGAGTAAGCATCGCGTAG 58.355 52.381 5.77 0.25 0.00 3.51
3495 3716 4.812626 AGGTGTTAACTTAACGAGGTGTTG 59.187 41.667 7.22 0.00 42.01 3.33
3779 4000 2.338984 GAACGCGGAGTCAGTGGT 59.661 61.111 12.47 0.84 0.00 4.16
3860 4081 1.831286 GCAGCCATTGATGAGGGGG 60.831 63.158 0.00 0.00 0.00 5.40
3970 4191 2.044946 GAGCCTTGAATGCCCCGT 60.045 61.111 0.00 0.00 0.00 5.28
4014 4235 3.867783 CCGTGGTGGTGGTGGTGA 61.868 66.667 0.00 0.00 0.00 4.02
4254 4490 1.999648 AGTTGGAGGCTTTGCATGAA 58.000 45.000 0.00 0.00 0.00 2.57
4320 4556 1.533469 GCGGCCCCGTACTATCATCT 61.533 60.000 8.66 0.00 42.09 2.90
4325 4561 3.071167 GGCCCCGTACTATCATCTTCTTT 59.929 47.826 0.00 0.00 0.00 2.52
4326 4562 4.308265 GCCCCGTACTATCATCTTCTTTC 58.692 47.826 0.00 0.00 0.00 2.62
4327 4563 4.039366 GCCCCGTACTATCATCTTCTTTCT 59.961 45.833 0.00 0.00 0.00 2.52
4341 4577 9.722056 TCATCTTCTTTCTTTCTTTCTTTTTCG 57.278 29.630 0.00 0.00 0.00 3.46
4342 4578 7.971004 TCTTCTTTCTTTCTTTCTTTTTCGC 57.029 32.000 0.00 0.00 0.00 4.70
4360 4596 9.670719 CTTTTTCGCTATTTTCTTCTTCTTCTT 57.329 29.630 0.00 0.00 0.00 2.52
4361 4597 9.665264 TTTTTCGCTATTTTCTTCTTCTTCTTC 57.335 29.630 0.00 0.00 0.00 2.87
4362 4598 8.608844 TTTCGCTATTTTCTTCTTCTTCTTCT 57.391 30.769 0.00 0.00 0.00 2.85
4363 4599 7.820044 TCGCTATTTTCTTCTTCTTCTTCTC 57.180 36.000 0.00 0.00 0.00 2.87
4375 4611 5.549619 TCTTCTTCTTCTCCCCTTTTGATCT 59.450 40.000 0.00 0.00 0.00 2.75
4376 4612 5.428184 TCTTCTTCTCCCCTTTTGATCTC 57.572 43.478 0.00 0.00 0.00 2.75
4377 4613 4.846367 TCTTCTTCTCCCCTTTTGATCTCA 59.154 41.667 0.00 0.00 0.00 3.27
4378 4614 5.490357 TCTTCTTCTCCCCTTTTGATCTCAT 59.510 40.000 0.00 0.00 0.00 2.90
4379 4615 5.365021 TCTTCTCCCCTTTTGATCTCATC 57.635 43.478 0.00 0.00 0.00 2.92
4381 4617 3.463825 TCTCCCCTTTTGATCTCATCCA 58.536 45.455 0.00 0.00 0.00 3.41
4382 4618 4.050037 TCTCCCCTTTTGATCTCATCCAT 58.950 43.478 0.00 0.00 0.00 3.41
4383 4619 4.141321 TCTCCCCTTTTGATCTCATCCATG 60.141 45.833 0.00 0.00 0.00 3.66
4495 4744 5.912149 TTCCTTTGCCCATGATAGTATCT 57.088 39.130 11.40 0.00 0.00 1.98
4498 4747 5.012458 TCCTTTGCCCATGATAGTATCTCAG 59.988 44.000 11.40 1.73 0.00 3.35
4499 4748 4.897509 TTGCCCATGATAGTATCTCAGG 57.102 45.455 11.40 9.43 0.00 3.86
4500 4749 3.176411 TGCCCATGATAGTATCTCAGGG 58.824 50.000 21.31 21.31 42.73 4.45
4501 4750 3.177228 GCCCATGATAGTATCTCAGGGT 58.823 50.000 23.93 2.03 41.79 4.34
4502 4751 3.055530 GCCCATGATAGTATCTCAGGGTG 60.056 52.174 23.93 10.49 41.79 4.61
4503 4752 3.517100 CCCATGATAGTATCTCAGGGTGG 59.483 52.174 19.06 13.23 41.79 4.61
4504 4753 4.420206 CCATGATAGTATCTCAGGGTGGA 58.580 47.826 11.40 0.00 39.22 4.02
4505 4754 4.221703 CCATGATAGTATCTCAGGGTGGAC 59.778 50.000 11.40 0.00 39.22 4.02
4506 4755 4.536295 TGATAGTATCTCAGGGTGGACA 57.464 45.455 11.40 0.00 0.00 4.02
4507 4756 4.215908 TGATAGTATCTCAGGGTGGACAC 58.784 47.826 11.40 0.00 0.00 3.67
4508 4757 1.475403 AGTATCTCAGGGTGGACACG 58.525 55.000 0.00 0.00 0.00 4.49
4509 4758 0.460311 GTATCTCAGGGTGGACACGG 59.540 60.000 0.00 0.00 0.00 4.94
4510 4759 0.686441 TATCTCAGGGTGGACACGGG 60.686 60.000 0.00 0.00 0.00 5.28
4511 4760 4.394712 CTCAGGGTGGACACGGGC 62.395 72.222 0.00 0.00 0.00 6.13
4545 4794 2.125673 CGGTCCGAGCCGTCATTT 60.126 61.111 4.91 0.00 46.11 2.32
4546 4795 2.452813 CGGTCCGAGCCGTCATTTG 61.453 63.158 4.91 0.00 46.11 2.32
4547 4796 2.106683 GGTCCGAGCCGTCATTTGG 61.107 63.158 0.00 0.00 0.00 3.28
4548 4797 1.079405 GTCCGAGCCGTCATTTGGA 60.079 57.895 0.00 0.00 0.00 3.53
4549 4798 1.079405 TCCGAGCCGTCATTTGGAC 60.079 57.895 0.00 0.00 43.36 4.02
4550 4799 2.106683 CCGAGCCGTCATTTGGACC 61.107 63.158 0.00 0.00 43.95 4.46
4551 4800 2.452813 CGAGCCGTCATTTGGACCG 61.453 63.158 0.00 0.00 43.95 4.79
4552 4801 2.046314 AGCCGTCATTTGGACCGG 60.046 61.111 0.00 0.00 43.95 5.28
4554 4803 3.131478 CCGTCATTTGGACCGGCC 61.131 66.667 0.00 4.32 43.95 6.13
4555 4804 3.496131 CGTCATTTGGACCGGCCG 61.496 66.667 21.04 21.04 43.95 6.13
4556 4805 3.810896 GTCATTTGGACCGGCCGC 61.811 66.667 22.85 6.98 40.83 6.53
4587 4836 2.432628 CGGACCGGACTGAGCAAC 60.433 66.667 9.46 0.00 0.00 4.17
4588 4837 2.741092 GGACCGGACTGAGCAACA 59.259 61.111 9.46 0.00 0.00 3.33
4589 4838 1.296715 GGACCGGACTGAGCAACAT 59.703 57.895 9.46 0.00 0.00 2.71
4590 4839 1.021390 GGACCGGACTGAGCAACATG 61.021 60.000 9.46 0.00 0.00 3.21
4591 4840 0.037326 GACCGGACTGAGCAACATGA 60.037 55.000 9.46 0.00 0.00 3.07
4592 4841 0.320771 ACCGGACTGAGCAACATGAC 60.321 55.000 9.46 0.00 0.00 3.06
4593 4842 1.354337 CCGGACTGAGCAACATGACG 61.354 60.000 0.00 0.00 0.00 4.35
4594 4843 1.354337 CGGACTGAGCAACATGACGG 61.354 60.000 0.00 0.00 0.00 4.79
4595 4844 0.320771 GGACTGAGCAACATGACGGT 60.321 55.000 0.00 0.00 0.00 4.83
4596 4845 1.071605 GACTGAGCAACATGACGGTC 58.928 55.000 0.00 0.00 0.00 4.79
4597 4846 0.320771 ACTGAGCAACATGACGGTCC 60.321 55.000 5.55 0.00 0.00 4.46
4598 4847 0.036952 CTGAGCAACATGACGGTCCT 60.037 55.000 5.55 0.00 0.00 3.85
4599 4848 0.320683 TGAGCAACATGACGGTCCTG 60.321 55.000 11.23 11.23 0.00 3.86
4600 4849 0.037326 GAGCAACATGACGGTCCTGA 60.037 55.000 18.40 0.00 0.00 3.86
4601 4850 0.615331 AGCAACATGACGGTCCTGAT 59.385 50.000 18.40 5.49 0.00 2.90
4602 4851 1.009829 GCAACATGACGGTCCTGATC 58.990 55.000 18.40 4.98 0.00 2.92
4603 4852 1.406069 GCAACATGACGGTCCTGATCT 60.406 52.381 18.40 2.04 0.00 2.75
4604 4853 2.544685 CAACATGACGGTCCTGATCTC 58.455 52.381 18.40 0.00 0.00 2.75
4605 4854 1.852633 ACATGACGGTCCTGATCTCA 58.147 50.000 18.40 0.00 0.00 3.27
4606 4855 1.753649 ACATGACGGTCCTGATCTCAG 59.246 52.381 18.40 0.00 43.40 3.35
4614 4863 4.686695 CTGATCTCAGGGACCGGA 57.313 61.111 9.46 0.00 40.20 5.14
4615 4864 2.119886 CTGATCTCAGGGACCGGAC 58.880 63.158 9.46 0.00 40.20 4.79
4616 4865 1.381327 TGATCTCAGGGACCGGACC 60.381 63.158 15.20 15.20 0.00 4.46
4617 4866 2.442272 ATCTCAGGGACCGGACCG 60.442 66.667 16.91 6.99 0.00 4.79
4650 4899 2.124695 GGGCCAGACCGAATGGAC 60.125 66.667 4.39 1.62 45.98 4.02
4651 4900 2.124695 GGCCAGACCGAATGGACC 60.125 66.667 0.00 2.59 40.27 4.46
4652 4901 2.511600 GCCAGACCGAATGGACCG 60.512 66.667 4.89 0.00 40.51 4.79
4653 4902 3.014085 GCCAGACCGAATGGACCGA 62.014 63.158 4.89 0.00 40.51 4.69
4654 4903 1.594833 CCAGACCGAATGGACCGAA 59.405 57.895 0.00 0.00 40.51 4.30
4655 4904 0.036765 CCAGACCGAATGGACCGAAA 60.037 55.000 0.00 0.00 40.51 3.46
4656 4905 1.359848 CAGACCGAATGGACCGAAAG 58.640 55.000 0.00 0.00 39.21 2.62
4678 4927 1.967319 CCGAATGGGTAGGGTTGATG 58.033 55.000 0.00 0.00 0.00 3.07
4679 4928 1.211949 CCGAATGGGTAGGGTTGATGT 59.788 52.381 0.00 0.00 0.00 3.06
4680 4929 2.288666 CGAATGGGTAGGGTTGATGTG 58.711 52.381 0.00 0.00 0.00 3.21
4681 4930 2.355716 CGAATGGGTAGGGTTGATGTGT 60.356 50.000 0.00 0.00 0.00 3.72
4682 4931 2.806945 ATGGGTAGGGTTGATGTGTG 57.193 50.000 0.00 0.00 0.00 3.82
4683 4932 0.037590 TGGGTAGGGTTGATGTGTGC 59.962 55.000 0.00 0.00 0.00 4.57
4684 4933 1.024579 GGGTAGGGTTGATGTGTGCG 61.025 60.000 0.00 0.00 0.00 5.34
4685 4934 1.024579 GGTAGGGTTGATGTGTGCGG 61.025 60.000 0.00 0.00 0.00 5.69
4686 4935 1.024579 GTAGGGTTGATGTGTGCGGG 61.025 60.000 0.00 0.00 0.00 6.13
4687 4936 1.485294 TAGGGTTGATGTGTGCGGGT 61.485 55.000 0.00 0.00 0.00 5.28
4688 4937 2.625823 GGGTTGATGTGTGCGGGTG 61.626 63.158 0.00 0.00 0.00 4.61
4689 4938 2.255252 GTTGATGTGTGCGGGTGC 59.745 61.111 0.00 0.00 43.20 5.01
4728 4977 2.736236 CGAGTGCAGCAGCGAGTT 60.736 61.111 11.25 0.00 46.23 3.01
4729 4978 2.858868 GAGTGCAGCAGCGAGTTG 59.141 61.111 0.00 0.00 46.23 3.16
4730 4979 2.667536 AGTGCAGCAGCGAGTTGG 60.668 61.111 0.00 0.00 46.23 3.77
4731 4980 3.730761 GTGCAGCAGCGAGTTGGG 61.731 66.667 0.00 0.00 46.23 4.12
4735 4984 4.087892 AGCAGCGAGTTGGGCGAT 62.088 61.111 0.00 0.00 35.00 4.58
4736 4985 3.869272 GCAGCGAGTTGGGCGATG 61.869 66.667 0.00 0.00 46.69 3.84
4737 4986 2.434884 CAGCGAGTTGGGCGATGT 60.435 61.111 0.00 0.00 39.97 3.06
4738 4987 2.434884 AGCGAGTTGGGCGATGTG 60.435 61.111 0.00 0.00 35.00 3.21
4739 4988 4.166011 GCGAGTTGGGCGATGTGC 62.166 66.667 0.00 0.00 45.38 4.57
4748 4997 3.786101 GCGATGTGCACGAGTGAT 58.214 55.556 13.13 0.00 45.45 3.06
4749 4998 1.346197 GCGATGTGCACGAGTGATG 59.654 57.895 13.13 0.00 45.45 3.07
4750 4999 1.354337 GCGATGTGCACGAGTGATGT 61.354 55.000 13.13 0.00 45.45 3.06
4751 5000 0.367887 CGATGTGCACGAGTGATGTG 59.632 55.000 13.13 0.00 40.32 3.21
4752 5001 1.713597 GATGTGCACGAGTGATGTGA 58.286 50.000 13.13 0.00 39.73 3.58
4753 5002 1.391485 GATGTGCACGAGTGATGTGAC 59.609 52.381 13.13 0.00 39.73 3.67
4754 5003 0.939106 TGTGCACGAGTGATGTGACG 60.939 55.000 13.13 0.00 39.73 4.35
4755 5004 0.663269 GTGCACGAGTGATGTGACGA 60.663 55.000 0.00 0.00 39.73 4.20
4756 5005 0.031449 TGCACGAGTGATGTGACGAA 59.969 50.000 7.50 0.00 39.73 3.85
4757 5006 0.435008 GCACGAGTGATGTGACGAAC 59.565 55.000 7.50 0.00 39.73 3.95
4758 5007 1.930817 GCACGAGTGATGTGACGAACT 60.931 52.381 7.50 0.00 39.73 3.01
4759 5008 1.716050 CACGAGTGATGTGACGAACTG 59.284 52.381 0.00 0.00 39.73 3.16
4760 5009 1.335964 ACGAGTGATGTGACGAACTGG 60.336 52.381 0.00 0.00 0.00 4.00
4761 5010 1.068541 CGAGTGATGTGACGAACTGGA 60.069 52.381 0.00 0.00 0.00 3.86
4762 5011 2.329379 GAGTGATGTGACGAACTGGAC 58.671 52.381 0.00 0.00 0.00 4.02
4763 5012 1.060713 GTGATGTGACGAACTGGACG 58.939 55.000 0.00 0.00 0.00 4.79
4764 5013 0.955905 TGATGTGACGAACTGGACGA 59.044 50.000 0.00 0.00 34.70 4.20
4765 5014 1.335597 TGATGTGACGAACTGGACGAC 60.336 52.381 0.00 0.00 34.70 4.34
4766 5015 0.386858 ATGTGACGAACTGGACGACG 60.387 55.000 0.00 0.00 34.70 5.12
4767 5016 1.009222 GTGACGAACTGGACGACGT 60.009 57.895 0.00 0.00 41.57 4.34
4768 5017 1.009335 TGACGAACTGGACGACGTG 60.009 57.895 4.58 0.00 39.04 4.49
4769 5018 2.354305 ACGAACTGGACGACGTGC 60.354 61.111 13.06 13.06 37.58 5.34
4771 5020 3.764049 GAACTGGACGACGTGCGC 61.764 66.667 14.94 0.00 46.04 6.09
4789 5038 3.782244 GAGTGCAGCGGCGAGTTG 61.782 66.667 12.98 6.60 45.35 3.16
4809 5058 3.598562 CGACGTGCGCGAGTGATC 61.599 66.667 28.73 12.00 42.00 2.92
4810 5059 2.202492 GACGTGCGCGAGTGATCT 60.202 61.111 28.73 0.41 42.00 2.75
4811 5060 2.500442 GACGTGCGCGAGTGATCTG 61.500 63.158 28.73 0.00 42.00 2.90
4812 5061 2.202479 CGTGCGCGAGTGATCTGA 60.202 61.111 16.08 0.00 41.33 3.27
4813 5062 2.500442 CGTGCGCGAGTGATCTGAC 61.500 63.158 16.08 0.00 41.33 3.51
4814 5063 2.202479 TGCGCGAGTGATCTGACG 60.202 61.111 12.10 0.00 0.00 4.35
4815 5064 2.100410 GCGCGAGTGATCTGACGA 59.900 61.111 12.10 0.00 0.00 4.20
4816 5065 1.514228 GCGCGAGTGATCTGACGAA 60.514 57.895 12.10 0.00 0.00 3.85
4817 5066 1.734359 GCGCGAGTGATCTGACGAAC 61.734 60.000 12.10 0.00 0.00 3.95
4818 5067 0.179187 CGCGAGTGATCTGACGAACT 60.179 55.000 0.00 0.00 0.00 3.01
4819 5068 1.263776 GCGAGTGATCTGACGAACTG 58.736 55.000 9.34 0.00 0.00 3.16
4820 5069 1.901538 CGAGTGATCTGACGAACTGG 58.098 55.000 0.00 0.00 0.00 4.00
4821 5070 1.468914 CGAGTGATCTGACGAACTGGA 59.531 52.381 0.00 0.00 0.00 3.86
4822 5071 2.729467 CGAGTGATCTGACGAACTGGAC 60.729 54.545 0.00 0.00 0.00 4.02
4823 5072 1.200252 AGTGATCTGACGAACTGGACG 59.800 52.381 0.00 0.00 0.00 4.79
4824 5073 1.199327 GTGATCTGACGAACTGGACGA 59.801 52.381 0.00 0.00 34.70 4.20
4825 5074 1.199327 TGATCTGACGAACTGGACGAC 59.801 52.381 0.00 0.00 34.70 4.34
4826 5075 0.168348 ATCTGACGAACTGGACGACG 59.832 55.000 0.00 0.00 34.70 5.12
4827 5076 1.162181 TCTGACGAACTGGACGACGT 61.162 55.000 0.00 0.00 41.57 4.34
4828 5077 0.997226 CTGACGAACTGGACGACGTG 60.997 60.000 4.58 0.00 39.04 4.49
4829 5078 2.354305 ACGAACTGGACGACGTGC 60.354 61.111 13.06 13.06 37.58 5.34
4831 5080 3.764049 GAACTGGACGACGTGCGC 61.764 66.667 14.94 0.00 46.04 6.09
4838 5087 4.617486 ACGACGTGCGCGAGTGAA 62.617 61.111 28.73 0.00 46.04 3.18
4839 5088 3.391631 CGACGTGCGCGAGTGAAA 61.392 61.111 28.73 0.00 42.00 2.69
4840 5089 2.167918 GACGTGCGCGAGTGAAAC 59.832 61.111 28.73 4.62 42.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.522193 CTACCCCTCGCTCCCTCC 60.522 72.222 0.00 0.00 0.00 4.30
13 14 0.749454 TTACGTCTACCCCTCGCTCC 60.749 60.000 0.00 0.00 0.00 4.70
17 18 1.063166 GCGTTACGTCTACCCCTCG 59.937 63.158 6.63 0.00 0.00 4.63
19 20 0.960364 TTCGCGTTACGTCTACCCCT 60.960 55.000 5.77 0.00 44.19 4.79
474 519 1.223763 CCCGCCTTCCTTAACTCCC 59.776 63.158 0.00 0.00 0.00 4.30
561 611 3.711704 GAGAAGAGAGAGAGAGGAGAGGA 59.288 52.174 0.00 0.00 0.00 3.71
562 612 3.713764 AGAGAAGAGAGAGAGAGGAGAGG 59.286 52.174 0.00 0.00 0.00 3.69
563 613 5.130145 AGAAGAGAAGAGAGAGAGAGGAGAG 59.870 48.000 0.00 0.00 0.00 3.20
564 614 5.032846 AGAAGAGAAGAGAGAGAGAGGAGA 58.967 45.833 0.00 0.00 0.00 3.71
565 615 5.130145 AGAGAAGAGAAGAGAGAGAGAGGAG 59.870 48.000 0.00 0.00 0.00 3.69
566 616 5.032846 AGAGAAGAGAAGAGAGAGAGAGGA 58.967 45.833 0.00 0.00 0.00 3.71
567 617 5.365021 AGAGAAGAGAAGAGAGAGAGAGG 57.635 47.826 0.00 0.00 0.00 3.69
568 618 6.648192 AGAAGAGAAGAGAAGAGAGAGAGAG 58.352 44.000 0.00 0.00 0.00 3.20
569 619 6.627087 AGAAGAGAAGAGAAGAGAGAGAGA 57.373 41.667 0.00 0.00 0.00 3.10
570 620 6.317391 GGAAGAAGAGAAGAGAAGAGAGAGAG 59.683 46.154 0.00 0.00 0.00 3.20
571 621 6.180472 GGAAGAAGAGAAGAGAAGAGAGAGA 58.820 44.000 0.00 0.00 0.00 3.10
592 642 2.023888 AGAGGGAGCTAGCTAGTTGGAA 60.024 50.000 19.38 0.00 0.00 3.53
593 643 1.571457 AGAGGGAGCTAGCTAGTTGGA 59.429 52.381 19.38 0.00 0.00 3.53
594 644 1.960689 GAGAGGGAGCTAGCTAGTTGG 59.039 57.143 19.38 0.00 0.00 3.77
595 645 1.960689 GGAGAGGGAGCTAGCTAGTTG 59.039 57.143 19.38 0.00 0.00 3.16
596 646 1.856920 AGGAGAGGGAGCTAGCTAGTT 59.143 52.381 19.38 16.41 0.00 2.24
597 647 1.529744 AGGAGAGGGAGCTAGCTAGT 58.470 55.000 19.38 4.78 0.00 2.57
598 648 2.514803 GAAGGAGAGGGAGCTAGCTAG 58.485 57.143 19.38 16.84 0.00 3.42
648 698 2.227388 AGCAGAAGCAGTAAACATGCAC 59.773 45.455 0.00 0.00 46.31 4.57
718 768 0.037447 GGCATGGAGATAGGGAAGCC 59.963 60.000 0.00 0.00 0.00 4.35
722 772 1.130054 GCAGGGCATGGAGATAGGGA 61.130 60.000 0.00 0.00 0.00 4.20
724 774 1.377994 GGCAGGGCATGGAGATAGG 59.622 63.158 0.00 0.00 0.00 2.57
725 775 1.132554 AGGGCAGGGCATGGAGATAG 61.133 60.000 0.00 0.00 0.00 2.08
726 776 1.073474 AGGGCAGGGCATGGAGATA 60.073 57.895 0.00 0.00 0.00 1.98
727 777 2.369291 AGGGCAGGGCATGGAGAT 60.369 61.111 0.00 0.00 0.00 2.75
763 813 2.743928 AGGCGCGCAAGAGGAAAG 60.744 61.111 34.42 0.00 43.02 2.62
764 814 1.884075 TAGAGGCGCGCAAGAGGAAA 61.884 55.000 34.42 6.26 43.02 3.13
779 829 1.140589 CTCTGCGGTGCCACTAGAG 59.859 63.158 0.00 8.93 0.00 2.43
856 906 0.030101 CGAGGTCTAGTGCTAGCAGC 59.970 60.000 20.03 13.17 42.82 5.25
954 1020 2.946990 CTCCTAGTCTTCGGTCTCTTCC 59.053 54.545 0.00 0.00 0.00 3.46
966 1032 3.151022 GCGCCTGCCTCCTAGTCT 61.151 66.667 0.00 0.00 33.98 3.24
1103 1169 3.264947 TGAATTCATGAGTGGAAGCGAG 58.735 45.455 3.38 0.00 0.00 5.03
1115 1181 7.336176 TGGAGAGAGAAATCAGTTGAATTCATG 59.664 37.037 9.40 5.83 36.64 3.07
1129 1209 5.200483 AGAGACGAAGATGGAGAGAGAAAT 58.800 41.667 0.00 0.00 0.00 2.17
1132 1212 3.924114 AGAGACGAAGATGGAGAGAGA 57.076 47.619 0.00 0.00 0.00 3.10
1133 1213 3.489059 GCAAGAGACGAAGATGGAGAGAG 60.489 52.174 0.00 0.00 0.00 3.20
1134 1214 2.425312 GCAAGAGACGAAGATGGAGAGA 59.575 50.000 0.00 0.00 0.00 3.10
1135 1215 2.426738 AGCAAGAGACGAAGATGGAGAG 59.573 50.000 0.00 0.00 0.00 3.20
1165 1245 2.481568 CGCACACACAGAATGACAGAAT 59.518 45.455 0.00 0.00 39.69 2.40
1167 1247 1.202521 ACGCACACACAGAATGACAGA 60.203 47.619 0.00 0.00 39.69 3.41
1168 1248 1.070376 CACGCACACACAGAATGACAG 60.070 52.381 0.00 0.00 39.69 3.51
1169 1249 0.936600 CACGCACACACAGAATGACA 59.063 50.000 0.00 0.00 39.69 3.58
1170 1250 0.235665 CCACGCACACACAGAATGAC 59.764 55.000 0.00 0.00 39.69 3.06
1171 1251 0.884259 CCCACGCACACACAGAATGA 60.884 55.000 0.00 0.00 39.69 2.57
1172 1252 1.165907 ACCCACGCACACACAGAATG 61.166 55.000 0.00 0.00 46.00 2.67
1173 1253 1.148273 ACCCACGCACACACAGAAT 59.852 52.632 0.00 0.00 0.00 2.40
1174 1254 1.817520 CACCCACGCACACACAGAA 60.818 57.895 0.00 0.00 0.00 3.02
1175 1255 2.203001 CACCCACGCACACACAGA 60.203 61.111 0.00 0.00 0.00 3.41
1189 1269 1.503542 CTTGAACATCCTGCGCACC 59.496 57.895 5.66 0.00 0.00 5.01
1191 1271 0.674581 CTCCTTGAACATCCTGCGCA 60.675 55.000 10.98 10.98 0.00 6.09
1343 1437 1.691434 GGGTGAAAAAGATGGGTTGCA 59.309 47.619 0.00 0.00 0.00 4.08
1390 1484 1.269166 CGAAACACGAAGAGGGATCG 58.731 55.000 0.00 0.00 45.77 3.69
1447 1541 1.800805 AGAAGCGACACACATGGAAG 58.199 50.000 0.00 0.00 0.00 3.46
1698 1798 3.833645 CAGGTAGGCGGCGTGCTA 61.834 66.667 9.37 0.00 45.43 3.49
1773 1875 0.396060 CCCAACCAAAACCACCATGG 59.604 55.000 11.19 11.19 45.02 3.66
1848 1955 4.147449 TGCATCGACGGGAGCTGG 62.147 66.667 0.00 0.00 0.00 4.85
2238 2414 4.446371 GAAATCTCACCGAGTCCATGAAT 58.554 43.478 0.00 0.00 0.00 2.57
2314 2490 2.288091 CGCAACAATGGTCAATTGGTCA 60.288 45.455 5.42 4.92 42.88 4.02
2315 2491 2.288152 ACGCAACAATGGTCAATTGGTC 60.288 45.455 5.42 0.00 42.88 4.02
2319 2495 4.458989 AGACATACGCAACAATGGTCAATT 59.541 37.500 0.00 0.00 0.00 2.32
2321 2497 3.407698 AGACATACGCAACAATGGTCAA 58.592 40.909 0.00 0.00 0.00 3.18
2322 2498 3.052455 AGACATACGCAACAATGGTCA 57.948 42.857 0.00 0.00 0.00 4.02
2323 2499 3.435327 TGAAGACATACGCAACAATGGTC 59.565 43.478 0.00 0.00 0.00 4.02
2324 2500 3.407698 TGAAGACATACGCAACAATGGT 58.592 40.909 0.00 0.00 0.00 3.55
2334 2510 2.926200 CCACTTGCTCTGAAGACATACG 59.074 50.000 0.00 0.00 0.00 3.06
2337 2513 2.611473 CGTCCACTTGCTCTGAAGACAT 60.611 50.000 0.00 0.00 0.00 3.06
2343 2521 0.827925 ACTCCGTCCACTTGCTCTGA 60.828 55.000 0.00 0.00 0.00 3.27
2460 2638 2.804931 GCAAAATGGACACGGCGC 60.805 61.111 6.90 0.00 0.00 6.53
2466 2644 1.459455 CCACCCGTGCAAAATGGACA 61.459 55.000 2.99 0.00 38.73 4.02
2839 3018 2.162008 CACGTCATGAATCATGGCACAA 59.838 45.455 25.03 3.24 45.55 3.33
2859 3038 4.082733 TGACAAAACGAACAATTCCACACA 60.083 37.500 0.00 0.00 0.00 3.72
2871 3050 2.702592 AGGTCACCTGACAAAACGAA 57.297 45.000 0.00 0.00 46.47 3.85
2923 3102 1.506493 CGATAGAGCTGGTTGATGGC 58.494 55.000 0.00 0.00 39.76 4.40
2940 3119 3.125573 CTCAGGACGAGGTCGCGA 61.126 66.667 3.71 3.71 44.43 5.87
3057 3236 1.227823 CTTGCCCTCCAACGTCACA 60.228 57.895 0.00 0.00 0.00 3.58
3096 3275 4.415150 CTGCCCACCATCCGCTGT 62.415 66.667 0.00 0.00 0.00 4.40
3295 3474 2.030562 CACGAAGGCGAACACCCT 59.969 61.111 0.00 0.00 41.64 4.34
3399 3578 2.423898 GGAGATCGAGTTGCCCGGA 61.424 63.158 0.73 0.00 0.00 5.14
3411 3590 3.131933 TGCTTACTCTGAGCAAGGAGATC 59.868 47.826 17.12 3.34 46.35 2.75
3495 3716 4.115199 AGGCCCTGCATTCCGTCC 62.115 66.667 0.00 0.00 0.00 4.79
3779 4000 0.037326 GATGAGGCTGTTGACCGTGA 60.037 55.000 0.00 0.00 0.00 4.35
3970 4191 1.153107 CTCCGCCTCCATGAATGCA 60.153 57.895 0.00 0.00 0.00 3.96
4014 4235 4.457496 CCAGCCGAGCGACACCAT 62.457 66.667 0.00 0.00 0.00 3.55
4067 4291 3.781307 CCCATCCAGCGACCGGAA 61.781 66.667 9.46 0.00 35.77 4.30
4101 4325 2.506438 GGAAGAAGGCGACGACGG 60.506 66.667 9.67 0.00 40.15 4.79
4254 4490 0.317479 CGTTCTTGACTCCTTCGGGT 59.683 55.000 0.00 0.00 36.28 5.28
4307 4543 8.934507 AAGAAAGAAAGAAGATGATAGTACGG 57.065 34.615 0.00 0.00 0.00 4.02
4341 4577 6.317642 GGGGAGAAGAAGAAGAAGAAAATAGC 59.682 42.308 0.00 0.00 0.00 2.97
4342 4578 7.629157 AGGGGAGAAGAAGAAGAAGAAAATAG 58.371 38.462 0.00 0.00 0.00 1.73
4357 4593 4.164988 GGATGAGATCAAAAGGGGAGAAGA 59.835 45.833 0.00 0.00 0.00 2.87
4360 4596 3.463825 TGGATGAGATCAAAAGGGGAGA 58.536 45.455 0.00 0.00 0.00 3.71
4361 4597 3.939740 TGGATGAGATCAAAAGGGGAG 57.060 47.619 0.00 0.00 0.00 4.30
4362 4598 3.117398 CCATGGATGAGATCAAAAGGGGA 60.117 47.826 5.56 0.00 0.00 4.81
4363 4599 3.228453 CCATGGATGAGATCAAAAGGGG 58.772 50.000 5.56 0.00 0.00 4.79
4375 4611 1.146041 GCGGCTACACCATGGATGA 59.854 57.895 21.47 1.02 39.03 2.92
4376 4612 1.153188 TGCGGCTACACCATGGATG 60.153 57.895 21.47 15.31 39.03 3.51
4377 4613 1.146930 CTGCGGCTACACCATGGAT 59.853 57.895 21.47 8.74 39.03 3.41
4378 4614 2.584064 CTGCGGCTACACCATGGA 59.416 61.111 21.47 0.00 39.03 3.41
4379 4615 3.204827 GCTGCGGCTACACCATGG 61.205 66.667 11.19 11.19 39.03 3.66
4381 4617 2.124983 CTGCTGCGGCTACACCAT 60.125 61.111 20.27 0.00 39.03 3.55
4382 4618 3.300934 CTCTGCTGCGGCTACACCA 62.301 63.158 20.27 0.00 39.03 4.17
4383 4619 2.510238 CTCTGCTGCGGCTACACC 60.510 66.667 20.27 0.00 39.59 4.16
4485 4734 4.215908 GTGTCCACCCTGAGATACTATCA 58.784 47.826 0.00 0.00 0.00 2.15
4529 4778 2.106683 CCAAATGACGGCTCGGACC 61.107 63.158 0.00 0.00 0.00 4.46
4530 4779 1.079405 TCCAAATGACGGCTCGGAC 60.079 57.895 0.00 0.00 0.00 4.79
4531 4780 1.079405 GTCCAAATGACGGCTCGGA 60.079 57.895 0.00 0.00 33.49 4.55
4532 4781 2.106683 GGTCCAAATGACGGCTCGG 61.107 63.158 0.00 0.00 45.46 4.63
4533 4782 2.452813 CGGTCCAAATGACGGCTCG 61.453 63.158 0.00 0.00 45.46 5.03
4534 4783 2.106683 CCGGTCCAAATGACGGCTC 61.107 63.158 0.00 0.00 45.46 4.70
4535 4784 2.046314 CCGGTCCAAATGACGGCT 60.046 61.111 0.00 0.00 45.46 5.52
4537 4786 3.131478 GGCCGGTCCAAATGACGG 61.131 66.667 1.90 0.00 45.46 4.79
4538 4787 3.496131 CGGCCGGTCCAAATGACG 61.496 66.667 20.10 0.00 45.46 4.35
4539 4788 3.810896 GCGGCCGGTCCAAATGAC 61.811 66.667 29.38 1.03 43.67 3.06
4570 4819 2.432628 GTTGCTCAGTCCGGTCCG 60.433 66.667 3.60 3.60 0.00 4.79
4571 4820 1.021390 CATGTTGCTCAGTCCGGTCC 61.021 60.000 0.00 0.00 0.00 4.46
4572 4821 0.037326 TCATGTTGCTCAGTCCGGTC 60.037 55.000 0.00 0.00 0.00 4.79
4573 4822 0.320771 GTCATGTTGCTCAGTCCGGT 60.321 55.000 0.00 0.00 0.00 5.28
4574 4823 1.354337 CGTCATGTTGCTCAGTCCGG 61.354 60.000 0.00 0.00 0.00 5.14
4575 4824 1.354337 CCGTCATGTTGCTCAGTCCG 61.354 60.000 0.00 0.00 0.00 4.79
4576 4825 0.320771 ACCGTCATGTTGCTCAGTCC 60.321 55.000 0.00 0.00 0.00 3.85
4577 4826 1.071605 GACCGTCATGTTGCTCAGTC 58.928 55.000 0.00 0.00 0.00 3.51
4578 4827 0.320771 GGACCGTCATGTTGCTCAGT 60.321 55.000 0.00 0.00 0.00 3.41
4579 4828 0.036952 AGGACCGTCATGTTGCTCAG 60.037 55.000 0.00 0.00 0.00 3.35
4580 4829 0.320683 CAGGACCGTCATGTTGCTCA 60.321 55.000 4.99 0.00 0.00 4.26
4581 4830 0.037326 TCAGGACCGTCATGTTGCTC 60.037 55.000 12.62 0.00 29.15 4.26
4582 4831 0.615331 ATCAGGACCGTCATGTTGCT 59.385 50.000 12.62 0.00 29.15 3.91
4583 4832 1.009829 GATCAGGACCGTCATGTTGC 58.990 55.000 12.62 0.98 29.15 4.17
4584 4833 2.094026 TGAGATCAGGACCGTCATGTTG 60.094 50.000 12.62 0.10 29.15 3.33
4585 4834 2.167281 CTGAGATCAGGACCGTCATGTT 59.833 50.000 12.62 4.83 40.20 2.71
4586 4835 1.753649 CTGAGATCAGGACCGTCATGT 59.246 52.381 12.62 1.10 40.20 3.21
4587 4836 2.505628 CTGAGATCAGGACCGTCATG 57.494 55.000 6.86 6.86 40.20 3.07
4597 4846 1.395826 GGTCCGGTCCCTGAGATCAG 61.396 65.000 6.44 2.72 43.40 2.90
4598 4847 1.381327 GGTCCGGTCCCTGAGATCA 60.381 63.158 6.44 0.00 0.00 2.92
4599 4848 2.491022 CGGTCCGGTCCCTGAGATC 61.491 68.421 12.41 0.00 0.00 2.75
4600 4849 2.442272 CGGTCCGGTCCCTGAGAT 60.442 66.667 12.41 0.00 0.00 2.75
4601 4850 4.753662 CCGGTCCGGTCCCTGAGA 62.754 72.222 23.02 0.00 42.73 3.27
4633 4882 2.124695 GTCCATTCGGTCTGGCCC 60.125 66.667 0.00 0.00 33.56 5.80
4634 4883 2.124695 GGTCCATTCGGTCTGGCC 60.125 66.667 0.00 0.00 33.56 5.36
4635 4884 2.511600 CGGTCCATTCGGTCTGGC 60.512 66.667 0.00 0.00 33.56 4.85
4636 4885 0.036765 TTTCGGTCCATTCGGTCTGG 60.037 55.000 0.00 0.00 34.93 3.86
4637 4886 1.359848 CTTTCGGTCCATTCGGTCTG 58.640 55.000 0.00 0.00 0.00 3.51
4638 4887 0.249398 CCTTTCGGTCCATTCGGTCT 59.751 55.000 0.00 0.00 0.00 3.85
4639 4888 0.248289 TCCTTTCGGTCCATTCGGTC 59.752 55.000 0.00 0.00 0.00 4.79
4640 4889 0.036671 GTCCTTTCGGTCCATTCGGT 60.037 55.000 0.00 0.00 0.00 4.69
4641 4890 0.743345 GGTCCTTTCGGTCCATTCGG 60.743 60.000 0.00 0.00 38.26 4.30
4642 4891 1.082117 CGGTCCTTTCGGTCCATTCG 61.082 60.000 0.00 0.00 38.28 3.34
4643 4892 0.248289 TCGGTCCTTTCGGTCCATTC 59.752 55.000 0.00 0.00 38.28 2.67
4644 4893 0.688487 TTCGGTCCTTTCGGTCCATT 59.312 50.000 0.00 0.00 38.28 3.16
4645 4894 0.909623 ATTCGGTCCTTTCGGTCCAT 59.090 50.000 0.00 0.00 38.28 3.41
4646 4895 0.036765 CATTCGGTCCTTTCGGTCCA 60.037 55.000 0.00 0.00 38.28 4.02
4647 4896 0.743345 CCATTCGGTCCTTTCGGTCC 60.743 60.000 0.00 0.00 35.43 4.46
4648 4897 0.743345 CCCATTCGGTCCTTTCGGTC 60.743 60.000 0.00 0.00 0.00 4.79
4649 4898 1.298667 CCCATTCGGTCCTTTCGGT 59.701 57.895 0.00 0.00 0.00 4.69
4650 4899 0.538118 TACCCATTCGGTCCTTTCGG 59.462 55.000 0.00 0.00 43.58 4.30
4651 4900 1.472728 CCTACCCATTCGGTCCTTTCG 60.473 57.143 0.00 0.00 43.58 3.46
4652 4901 1.134189 CCCTACCCATTCGGTCCTTTC 60.134 57.143 0.00 0.00 43.58 2.62
4653 4902 0.916809 CCCTACCCATTCGGTCCTTT 59.083 55.000 0.00 0.00 43.58 3.11
4654 4903 0.253020 ACCCTACCCATTCGGTCCTT 60.253 55.000 0.00 0.00 43.58 3.36
4655 4904 0.253020 AACCCTACCCATTCGGTCCT 60.253 55.000 0.00 0.00 43.58 3.85
4656 4905 0.107361 CAACCCTACCCATTCGGTCC 60.107 60.000 0.00 0.00 43.58 4.46
4657 4906 0.906775 TCAACCCTACCCATTCGGTC 59.093 55.000 0.00 0.00 43.58 4.79
4659 4908 1.211949 ACATCAACCCTACCCATTCGG 59.788 52.381 0.00 0.00 37.81 4.30
4660 4909 2.288666 CACATCAACCCTACCCATTCG 58.711 52.381 0.00 0.00 0.00 3.34
4661 4910 3.016736 CACACATCAACCCTACCCATTC 58.983 50.000 0.00 0.00 0.00 2.67
4662 4911 2.883888 GCACACATCAACCCTACCCATT 60.884 50.000 0.00 0.00 0.00 3.16
4663 4912 1.340991 GCACACATCAACCCTACCCAT 60.341 52.381 0.00 0.00 0.00 4.00
4664 4913 0.037590 GCACACATCAACCCTACCCA 59.962 55.000 0.00 0.00 0.00 4.51
4665 4914 1.024579 CGCACACATCAACCCTACCC 61.025 60.000 0.00 0.00 0.00 3.69
4666 4915 1.024579 CCGCACACATCAACCCTACC 61.025 60.000 0.00 0.00 0.00 3.18
4667 4916 1.024579 CCCGCACACATCAACCCTAC 61.025 60.000 0.00 0.00 0.00 3.18
4668 4917 1.298340 CCCGCACACATCAACCCTA 59.702 57.895 0.00 0.00 0.00 3.53
4669 4918 2.034066 CCCGCACACATCAACCCT 59.966 61.111 0.00 0.00 0.00 4.34
4670 4919 2.282180 ACCCGCACACATCAACCC 60.282 61.111 0.00 0.00 0.00 4.11
4671 4920 2.953821 CACCCGCACACATCAACC 59.046 61.111 0.00 0.00 0.00 3.77
4672 4921 2.255252 GCACCCGCACACATCAAC 59.745 61.111 0.00 0.00 38.36 3.18
4673 4922 2.203266 TGCACCCGCACACATCAA 60.203 55.556 0.00 0.00 45.36 2.57
4674 4923 2.669229 CTGCACCCGCACACATCA 60.669 61.111 0.00 0.00 45.36 3.07
4675 4924 4.107051 GCTGCACCCGCACACATC 62.107 66.667 0.00 0.00 45.36 3.06
4711 4960 2.736236 AACTCGCTGCTGCACTCG 60.736 61.111 16.29 11.80 39.64 4.18
4712 4961 2.675056 CCAACTCGCTGCTGCACTC 61.675 63.158 16.29 0.00 39.64 3.51
4713 4962 2.667536 CCAACTCGCTGCTGCACT 60.668 61.111 16.29 0.00 39.64 4.40
4714 4963 3.730761 CCCAACTCGCTGCTGCAC 61.731 66.667 16.29 0.00 39.64 4.57
4718 4967 4.087892 ATCGCCCAACTCGCTGCT 62.088 61.111 0.00 0.00 0.00 4.24
4719 4968 3.869272 CATCGCCCAACTCGCTGC 61.869 66.667 0.00 0.00 0.00 5.25
4720 4969 2.434884 ACATCGCCCAACTCGCTG 60.435 61.111 0.00 0.00 0.00 5.18
4721 4970 2.434884 CACATCGCCCAACTCGCT 60.435 61.111 0.00 0.00 0.00 4.93
4722 4971 4.166011 GCACATCGCCCAACTCGC 62.166 66.667 0.00 0.00 32.94 5.03
4723 4972 2.741985 TGCACATCGCCCAACTCG 60.742 61.111 0.00 0.00 41.33 4.18
4724 4973 2.870372 GTGCACATCGCCCAACTC 59.130 61.111 13.17 0.00 41.33 3.01
4725 4974 3.049674 CGTGCACATCGCCCAACT 61.050 61.111 18.64 0.00 41.33 3.16
4726 4975 3.027170 CTCGTGCACATCGCCCAAC 62.027 63.158 18.64 0.00 41.33 3.77
4727 4976 2.741985 CTCGTGCACATCGCCCAA 60.742 61.111 18.64 0.00 41.33 4.12
4728 4977 4.002506 ACTCGTGCACATCGCCCA 62.003 61.111 18.64 0.00 41.33 5.36
4729 4978 3.490759 CACTCGTGCACATCGCCC 61.491 66.667 18.64 0.00 41.33 6.13
4730 4979 1.811266 ATCACTCGTGCACATCGCC 60.811 57.895 18.64 0.00 41.33 5.54
4731 4980 1.346197 CATCACTCGTGCACATCGC 59.654 57.895 18.64 0.00 42.89 4.58
4732 4981 0.367887 CACATCACTCGTGCACATCG 59.632 55.000 18.64 2.80 0.00 3.84
4733 4982 1.391485 GTCACATCACTCGTGCACATC 59.609 52.381 18.64 0.00 34.27 3.06
4734 4983 1.432514 GTCACATCACTCGTGCACAT 58.567 50.000 18.64 0.00 34.27 3.21
4735 4984 0.939106 CGTCACATCACTCGTGCACA 60.939 55.000 18.64 3.15 34.27 4.57
4736 4985 0.663269 TCGTCACATCACTCGTGCAC 60.663 55.000 6.82 6.82 34.27 4.57
4737 4986 0.031449 TTCGTCACATCACTCGTGCA 59.969 50.000 0.00 0.00 34.27 4.57
4738 4987 0.435008 GTTCGTCACATCACTCGTGC 59.565 55.000 0.00 0.00 34.27 5.34
4739 4988 1.716050 CAGTTCGTCACATCACTCGTG 59.284 52.381 0.00 0.00 35.63 4.35
4740 4989 1.335964 CCAGTTCGTCACATCACTCGT 60.336 52.381 0.00 0.00 0.00 4.18
4741 4990 1.068541 TCCAGTTCGTCACATCACTCG 60.069 52.381 0.00 0.00 0.00 4.18
4742 4991 2.329379 GTCCAGTTCGTCACATCACTC 58.671 52.381 0.00 0.00 0.00 3.51
4743 4992 1.335964 CGTCCAGTTCGTCACATCACT 60.336 52.381 0.00 0.00 0.00 3.41
4744 4993 1.060713 CGTCCAGTTCGTCACATCAC 58.939 55.000 0.00 0.00 0.00 3.06
4745 4994 0.955905 TCGTCCAGTTCGTCACATCA 59.044 50.000 0.00 0.00 0.00 3.07
4746 4995 1.337821 GTCGTCCAGTTCGTCACATC 58.662 55.000 0.00 0.00 0.00 3.06
4747 4996 0.386858 CGTCGTCCAGTTCGTCACAT 60.387 55.000 0.00 0.00 0.00 3.21
4748 4997 1.009335 CGTCGTCCAGTTCGTCACA 60.009 57.895 0.00 0.00 0.00 3.58
4749 4998 1.009222 ACGTCGTCCAGTTCGTCAC 60.009 57.895 0.00 0.00 30.71 3.67
4750 4999 1.009335 CACGTCGTCCAGTTCGTCA 60.009 57.895 0.00 0.00 34.30 4.35
4751 5000 2.362800 GCACGTCGTCCAGTTCGTC 61.363 63.158 0.00 0.00 34.30 4.20
4752 5001 2.354305 GCACGTCGTCCAGTTCGT 60.354 61.111 0.00 0.00 36.99 3.85
4753 5002 3.458579 CGCACGTCGTCCAGTTCG 61.459 66.667 0.00 0.00 0.00 3.95
4754 5003 3.764049 GCGCACGTCGTCCAGTTC 61.764 66.667 0.30 0.00 41.07 3.01
4772 5021 3.782244 CAACTCGCCGCTGCACTC 61.782 66.667 0.00 0.00 37.32 3.51
4792 5041 3.598562 GATCACTCGCGCACGTCG 61.599 66.667 8.75 3.50 41.18 5.12
4793 5042 2.202492 AGATCACTCGCGCACGTC 60.202 61.111 8.75 0.00 41.18 4.34
4794 5043 2.504899 CAGATCACTCGCGCACGT 60.505 61.111 8.75 0.00 41.18 4.49
4795 5044 2.202479 TCAGATCACTCGCGCACG 60.202 61.111 8.75 0.00 42.01 5.34
4796 5045 2.500442 CGTCAGATCACTCGCGCAC 61.500 63.158 8.75 0.00 0.00 5.34
4797 5046 2.195123 TTCGTCAGATCACTCGCGCA 62.195 55.000 8.75 0.00 0.00 6.09
4798 5047 1.514228 TTCGTCAGATCACTCGCGC 60.514 57.895 0.00 0.00 0.00 6.86
4799 5048 0.179187 AGTTCGTCAGATCACTCGCG 60.179 55.000 0.00 0.00 0.00 5.87
4800 5049 1.263776 CAGTTCGTCAGATCACTCGC 58.736 55.000 0.00 0.00 0.00 5.03
4801 5050 1.468914 TCCAGTTCGTCAGATCACTCG 59.531 52.381 0.00 0.00 0.00 4.18
4802 5051 2.729467 CGTCCAGTTCGTCAGATCACTC 60.729 54.545 0.00 0.00 0.00 3.51
4803 5052 1.200252 CGTCCAGTTCGTCAGATCACT 59.800 52.381 0.00 0.00 0.00 3.41
4804 5053 1.199327 TCGTCCAGTTCGTCAGATCAC 59.801 52.381 0.00 0.00 0.00 3.06
4805 5054 1.199327 GTCGTCCAGTTCGTCAGATCA 59.801 52.381 0.00 0.00 0.00 2.92
4806 5055 1.790838 CGTCGTCCAGTTCGTCAGATC 60.791 57.143 0.00 0.00 0.00 2.75
4807 5056 0.168348 CGTCGTCCAGTTCGTCAGAT 59.832 55.000 0.00 0.00 0.00 2.90
4808 5057 1.162181 ACGTCGTCCAGTTCGTCAGA 61.162 55.000 0.00 0.00 30.71 3.27
4809 5058 0.997226 CACGTCGTCCAGTTCGTCAG 60.997 60.000 0.00 0.00 34.30 3.51
4810 5059 1.009335 CACGTCGTCCAGTTCGTCA 60.009 57.895 0.00 0.00 34.30 4.35
4811 5060 2.362800 GCACGTCGTCCAGTTCGTC 61.363 63.158 0.00 0.00 34.30 4.20
4812 5061 2.354305 GCACGTCGTCCAGTTCGT 60.354 61.111 0.00 0.00 36.99 3.85
4813 5062 3.458579 CGCACGTCGTCCAGTTCG 61.459 66.667 0.00 0.00 0.00 3.95
4814 5063 3.764049 GCGCACGTCGTCCAGTTC 61.764 66.667 0.30 0.00 41.07 3.01
4821 5070 4.617486 TTCACTCGCGCACGTCGT 62.617 61.111 8.75 0.00 41.18 4.34
4822 5071 3.391631 TTTCACTCGCGCACGTCG 61.392 61.111 8.75 3.50 41.18 5.12
4823 5072 2.167918 GTTTCACTCGCGCACGTC 59.832 61.111 8.75 0.00 41.18 4.34
4824 5073 2.279252 AGTTTCACTCGCGCACGT 60.279 55.556 8.75 0.00 41.18 4.49
4825 5074 2.168621 CAGTTTCACTCGCGCACG 59.831 61.111 8.75 0.00 42.01 5.34
4826 5075 1.201825 GTCAGTTTCACTCGCGCAC 59.798 57.895 8.75 0.00 0.00 5.34
4827 5076 2.300066 CGTCAGTTTCACTCGCGCA 61.300 57.895 8.75 0.00 0.00 6.09
4828 5077 1.545614 TTCGTCAGTTTCACTCGCGC 61.546 55.000 0.00 0.00 0.00 6.86
4829 5078 0.158928 GTTCGTCAGTTTCACTCGCG 59.841 55.000 0.00 0.00 0.00 5.87
4830 5079 1.190323 CAGTTCGTCAGTTTCACTCGC 59.810 52.381 0.00 0.00 0.00 5.03
4831 5080 2.727777 TCAGTTCGTCAGTTTCACTCG 58.272 47.619 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.