Multiple sequence alignment - TraesCS2B01G616400

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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 TraesCS2B01G616400 chr2B 100.000 3257 0 0 1 3257 793648274 793645018 0.000000e+00 6015.0
1 TraesCS2B01G616400 chr2D 91.554 2522 109 33 1 2491 635652297 635649849 0.000000e+00 3382.0
2 TraesCS2B01G616400 chr2D 83.976 337 36 9 1 322 577750762 577751095 1.140000e-79 307.0
3 TraesCS2B01G616400 chr2D 92.308 39 2 1 2497 2535 495104698 495104661 2.000000e-03 54.7
4 TraesCS2B01G616400 chrUn 95.204 1397 37 5 996 2363 124906081 124907476 0.000000e+00 2182.0
5 TraesCS2B01G616400 chrUn 91.854 356 26 3 2904 3257 124956526 124956880 8.120000e-136 494.0
6 TraesCS2B01G616400 chrUn 95.455 132 6 0 2634 2765 124907932 124908063 9.160000e-51 211.0
7 TraesCS2B01G616400 chrUn 85.549 173 15 7 332 497 124905479 124905648 4.320000e-39 172.0
8 TraesCS2B01G616400 chrUn 100.000 67 0 0 2752 2818 124956459 124956525 1.230000e-24 124.0
9 TraesCS2B01G616400 chrUn 95.122 41 2 0 534 574 124905675 124905715 7.540000e-07 65.8
10 TraesCS2B01G616400 chr5D 84.884 344 34 10 1 329 64139922 64140262 6.740000e-87 331.0
11 TraesCS2B01G616400 chr5D 90.833 120 9 2 2497 2615 420620105 420620223 3.360000e-35 159.0
12 TraesCS2B01G616400 chr3B 84.348 345 38 8 1 330 52700874 52700531 1.130000e-84 324.0
13 TraesCS2B01G616400 chr3B 76.374 182 37 5 1370 1548 23945291 23945113 3.460000e-15 93.5
14 TraesCS2B01G616400 chr1B 83.944 355 40 9 1 340 673451587 673451939 1.130000e-84 324.0
15 TraesCS2B01G616400 chr1B 88.889 126 11 3 2497 2622 495142753 495142631 5.630000e-33 152.0
16 TraesCS2B01G616400 chr1B 89.167 120 12 1 2496 2615 576228515 576228633 7.280000e-32 148.0
17 TraesCS2B01G616400 chr5A 87.636 275 32 2 2818 3091 653858764 653858491 5.240000e-83 318.0
18 TraesCS2B01G616400 chr5A 87.647 170 17 2 3088 3257 653857442 653857277 9.220000e-46 195.0
19 TraesCS2B01G616400 chr6D 84.000 350 35 12 1 334 346462828 346463172 1.890000e-82 316.0
20 TraesCS2B01G616400 chr7B 83.714 350 39 10 1 335 688135612 688135266 6.780000e-82 315.0
21 TraesCS2B01G616400 chr7B 86.667 285 32 5 2824 3107 450579795 450580074 8.780000e-81 311.0
22 TraesCS2B01G616400 chr7B 86.738 279 31 5 2823 3100 448733232 448732959 4.080000e-79 305.0
23 TraesCS2B01G616400 chr1D 84.058 345 36 9 1 330 259684674 259685014 6.780000e-82 315.0
24 TraesCS2B01G616400 chr4A 82.319 345 46 8 1 330 2539312 2539656 5.320000e-73 285.0
25 TraesCS2B01G616400 chr2A 87.879 198 22 2 2823 3019 703182704 703182900 7.030000e-57 231.0
26 TraesCS2B01G616400 chr6B 79.261 352 47 15 1 331 542661239 542661585 4.230000e-54 222.0
27 TraesCS2B01G616400 chr7A 84.615 208 22 5 3055 3257 682989837 682990039 7.130000e-47 198.0
28 TraesCS2B01G616400 chr7A 90.435 115 8 3 2497 2609 34422161 34422048 7.280000e-32 148.0
29 TraesCS2B01G616400 chr3D 88.430 121 10 4 2497 2616 410320116 410319999 3.390000e-30 143.0
30 TraesCS2B01G616400 chr5B 87.097 124 10 3 2496 2615 429636877 429636756 5.670000e-28 135.0
31 TraesCS2B01G616400 chr7D 86.992 123 8 7 2497 2614 584772217 584772336 7.330000e-27 132.0
32 TraesCS2B01G616400 chr3A 77.901 181 32 8 1372 1548 20098362 20098538 4.440000e-19 106.0


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 TraesCS2B01G616400 chr2B 793645018 793648274 3256 True 6015.0 6015 100.0000 1 3257 1 chr2B.!!$R1 3256
1 TraesCS2B01G616400 chr2D 635649849 635652297 2448 True 3382.0 3382 91.5540 1 2491 1 chr2D.!!$R2 2490
2 TraesCS2B01G616400 chrUn 124905479 124908063 2584 False 657.7 2182 92.8325 332 2765 4 chrUn.!!$F1 2433
3 TraesCS2B01G616400 chr5A 653857277 653858764 1487 True 256.5 318 87.6415 2818 3257 2 chr5A.!!$R1 439

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
531 562 0.100146 GGGAAGCTCACGTACGTAGG 59.9 60.0 22.34 16.89 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2493 2640 0.392998 TCCATGAAGCTCGGCCTTTC 60.393 55.0 0.0 0.03 0.0 2.62 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
44 45 3.255379 GACGTCTCGGCCGATTGC 61.255 66.667 31.19 19.78 40.16 3.56
49 50 2.125147 CTCGGCCGATTGCTTGGA 60.125 61.111 31.19 2.04 40.92 3.53
105 119 1.139095 GGGGTCAGTAGCGAAGTCG 59.861 63.158 0.00 0.00 43.27 4.18
107 121 1.139095 GGTCAGTAGCGAAGTCGGG 59.861 63.158 2.47 0.00 40.23 5.14
158 172 1.452651 CATTGCAGGCCACCTCGAT 60.453 57.895 5.01 0.00 0.00 3.59
159 173 1.452651 ATTGCAGGCCACCTCGATG 60.453 57.895 5.01 0.00 0.00 3.84
172 186 1.479709 CTCGATGGTGTCCTCTCCTT 58.520 55.000 0.00 0.00 0.00 3.36
205 219 1.152777 TCTTGTGGGTGCCAGGTTG 60.153 57.895 0.00 0.00 32.34 3.77
226 240 1.621814 GCCGGAGTGCCCTATTATGTA 59.378 52.381 5.05 0.00 0.00 2.29
256 270 3.289062 CGGTTTTCGCCCGGGTTT 61.289 61.111 24.63 0.00 41.78 3.27
258 272 2.194889 GGTTTTCGCCCGGGTTTCA 61.195 57.895 24.63 0.65 0.00 2.69
266 281 3.618351 TCGCCCGGGTTTCATTAATAAA 58.382 40.909 24.63 0.00 0.00 1.40
324 343 6.370433 GCAAATCTTTTGCCTTGGTTTAAA 57.630 33.333 12.74 0.00 39.38 1.52
325 344 6.790282 GCAAATCTTTTGCCTTGGTTTAAAA 58.210 32.000 12.74 0.00 39.38 1.52
326 345 7.254137 GCAAATCTTTTGCCTTGGTTTAAAAA 58.746 30.769 12.74 0.00 39.38 1.94
384 405 0.180171 TGGAACAGTGGAGGTGTGTG 59.820 55.000 0.00 0.00 0.00 3.82
388 409 2.146724 CAGTGGAGGTGTGTGGGGA 61.147 63.158 0.00 0.00 0.00 4.81
497 520 1.341187 TGCATCATGGTCTTGCATGGA 60.341 47.619 8.72 0.00 41.18 3.41
500 523 1.288188 TCATGGTCTTGCATGGAGGA 58.712 50.000 0.00 0.00 0.00 3.71
501 524 1.634973 TCATGGTCTTGCATGGAGGAA 59.365 47.619 0.00 0.00 0.00 3.36
504 527 0.620556 GGTCTTGCATGGAGGAAGGA 59.379 55.000 0.00 0.00 44.91 3.36
505 528 1.004745 GGTCTTGCATGGAGGAAGGAA 59.995 52.381 0.00 0.00 44.91 3.36
527 558 0.458025 GGAAGGGAAGCTCACGTACG 60.458 60.000 15.01 15.01 0.00 3.67
528 559 0.243095 GAAGGGAAGCTCACGTACGT 59.757 55.000 16.72 16.72 0.00 3.57
529 560 1.470098 GAAGGGAAGCTCACGTACGTA 59.530 52.381 22.34 8.85 0.00 3.57
530 561 1.093159 AGGGAAGCTCACGTACGTAG 58.907 55.000 22.34 18.31 0.00 3.51
531 562 0.100146 GGGAAGCTCACGTACGTAGG 59.900 60.000 22.34 16.89 0.00 3.18
532 563 1.089920 GGAAGCTCACGTACGTAGGA 58.910 55.000 22.34 14.21 0.00 2.94
561 592 0.742505 CGTGCATGCCATCCATTCTT 59.257 50.000 16.68 0.00 29.71 2.52
562 593 1.268896 CGTGCATGCCATCCATTCTTC 60.269 52.381 16.68 0.00 29.71 2.87
583 614 2.679837 CCACTCGGTTTGATGATCCTTG 59.320 50.000 0.00 0.00 0.00 3.61
633 677 3.244215 CGACCATCTAGCTCTCTCTCTCT 60.244 52.174 0.00 0.00 0.00 3.10
634 678 4.319177 GACCATCTAGCTCTCTCTCTCTC 58.681 52.174 0.00 0.00 0.00 3.20
637 681 4.285517 CCATCTAGCTCTCTCTCTCTCTCT 59.714 50.000 0.00 0.00 0.00 3.10
638 682 5.477510 CATCTAGCTCTCTCTCTCTCTCTC 58.522 50.000 0.00 0.00 0.00 3.20
641 685 3.652055 AGCTCTCTCTCTCTCTCTCTCT 58.348 50.000 0.00 0.00 0.00 3.10
644 688 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
645 689 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
646 690 3.963374 CTCTCTCTCTCTCTCTCTCTCCA 59.037 52.174 0.00 0.00 0.00 3.86
647 691 4.560739 TCTCTCTCTCTCTCTCTCTCCAT 58.439 47.826 0.00 0.00 0.00 3.41
651 695 1.202758 TCTCTCTCTCTCTCCATCGGC 60.203 57.143 0.00 0.00 0.00 5.54
674 718 4.459089 GCGGCCTCACCTCACCTC 62.459 72.222 0.00 0.00 35.61 3.85
675 719 3.775654 CGGCCTCACCTCACCTCC 61.776 72.222 0.00 0.00 35.61 4.30
676 720 3.775654 GGCCTCACCTCACCTCCG 61.776 72.222 0.00 0.00 34.51 4.63
677 721 3.775654 GCCTCACCTCACCTCCGG 61.776 72.222 0.00 0.00 0.00 5.14
737 784 2.171940 GCGAGCAAACAGTCTGCG 59.828 61.111 0.00 0.00 44.75 5.18
834 905 2.510382 AGGGAGAGATCCGACTTGTCTA 59.490 50.000 0.00 0.00 0.00 2.59
835 906 3.053544 AGGGAGAGATCCGACTTGTCTAA 60.054 47.826 0.00 0.00 0.00 2.10
836 907 3.892588 GGGAGAGATCCGACTTGTCTAAT 59.107 47.826 0.00 0.00 0.00 1.73
837 908 4.342665 GGGAGAGATCCGACTTGTCTAATT 59.657 45.833 0.00 0.00 0.00 1.40
838 909 5.285651 GGAGAGATCCGACTTGTCTAATTG 58.714 45.833 0.00 0.00 0.00 2.32
857 928 1.473278 TGAATTGATTGCTGCATGCGA 59.527 42.857 14.09 1.21 46.63 5.10
860 931 2.352001 GATTGCTGCATGCGAGCG 60.352 61.111 26.18 12.62 46.63 5.03
861 932 3.104602 GATTGCTGCATGCGAGCGT 62.105 57.895 26.18 20.44 46.63 5.07
862 933 3.391160 ATTGCTGCATGCGAGCGTG 62.391 57.895 26.18 12.54 46.63 5.34
924 995 1.019278 GCATACGTGTGGTGTGGGAG 61.019 60.000 14.49 0.00 38.13 4.30
1161 1296 4.131088 GTCCTCCTCACGGGCGTC 62.131 72.222 0.00 0.00 34.39 5.19
1212 1347 2.799412 CTCCCGCTACTACTACTACACG 59.201 54.545 0.00 0.00 0.00 4.49
1326 1464 2.360726 CAGCACATCAGCCAGCCA 60.361 61.111 0.00 0.00 34.23 4.75
1512 1650 3.311110 TGGGAGCGCTTCTTCCGT 61.311 61.111 16.97 0.00 44.03 4.69
1686 1824 3.760035 AACGCGCTCCTCGACCAT 61.760 61.111 5.73 0.00 41.67 3.55
1872 2010 1.376466 GGAGCAGCAGTGGAGGAAA 59.624 57.895 0.00 0.00 0.00 3.13
2061 2199 1.079127 CACATGGGTCGACTGGTCC 60.079 63.158 16.46 8.60 0.00 4.46
2349 2496 8.949177 TGATTGATTGATTGATTATATGGACCG 58.051 33.333 0.00 0.00 0.00 4.79
2425 2572 7.571080 TGTACGTATGGATGTATACAGACAA 57.429 36.000 11.91 2.31 32.45 3.18
2432 2579 6.353404 TGGATGTATACAGACAACTTGTGA 57.647 37.500 11.91 0.00 31.83 3.58
2468 2615 7.137490 TCATGAATGAATGACAGACAACTTC 57.863 36.000 0.00 0.00 31.58 3.01
2491 2638 9.350357 CTTCATTGTGAATCACTTCAAATTAGG 57.650 33.333 14.97 0.00 42.85 2.69
2492 2639 8.634335 TCATTGTGAATCACTTCAAATTAGGA 57.366 30.769 14.97 0.00 42.85 2.94
2493 2640 8.733458 TCATTGTGAATCACTTCAAATTAGGAG 58.267 33.333 14.97 0.00 42.85 3.69
2494 2641 8.733458 CATTGTGAATCACTTCAAATTAGGAGA 58.267 33.333 14.97 0.00 42.85 3.71
2495 2642 8.690203 TTGTGAATCACTTCAAATTAGGAGAA 57.310 30.769 14.97 0.00 42.85 2.87
2496 2643 8.690203 TGTGAATCACTTCAAATTAGGAGAAA 57.310 30.769 14.97 0.00 42.85 2.52
2497 2644 8.786898 TGTGAATCACTTCAAATTAGGAGAAAG 58.213 33.333 14.97 0.00 42.85 2.62
2498 2645 8.239998 GTGAATCACTTCAAATTAGGAGAAAGG 58.760 37.037 6.07 0.00 42.85 3.11
2499 2646 6.765915 ATCACTTCAAATTAGGAGAAAGGC 57.234 37.500 0.00 0.00 0.00 4.35
2500 2647 5.010282 TCACTTCAAATTAGGAGAAAGGCC 58.990 41.667 0.00 0.00 0.00 5.19
2501 2648 4.010349 ACTTCAAATTAGGAGAAAGGCCG 58.990 43.478 0.00 0.00 0.00 6.13
2502 2649 3.992943 TCAAATTAGGAGAAAGGCCGA 57.007 42.857 0.00 0.00 0.00 5.54
2503 2650 3.873910 TCAAATTAGGAGAAAGGCCGAG 58.126 45.455 0.00 0.00 0.00 4.63
2504 2651 2.333688 AATTAGGAGAAAGGCCGAGC 57.666 50.000 0.00 0.00 0.00 5.03
2505 2652 1.501582 ATTAGGAGAAAGGCCGAGCT 58.498 50.000 0.00 0.00 0.00 4.09
2506 2653 1.276622 TTAGGAGAAAGGCCGAGCTT 58.723 50.000 0.00 0.00 0.00 3.74
2507 2654 0.824759 TAGGAGAAAGGCCGAGCTTC 59.175 55.000 0.00 0.00 0.00 3.86
2508 2655 1.194781 AGGAGAAAGGCCGAGCTTCA 61.195 55.000 0.00 0.00 0.00 3.02
2509 2656 0.107459 GGAGAAAGGCCGAGCTTCAT 60.107 55.000 0.00 0.00 0.00 2.57
2510 2657 1.012841 GAGAAAGGCCGAGCTTCATG 58.987 55.000 0.00 0.00 0.00 3.07
2511 2658 0.393537 AGAAAGGCCGAGCTTCATGG 60.394 55.000 0.00 0.00 0.00 3.66
2512 2659 0.392998 GAAAGGCCGAGCTTCATGGA 60.393 55.000 0.00 0.00 0.00 3.41
2513 2660 0.393537 AAAGGCCGAGCTTCATGGAG 60.394 55.000 0.00 0.00 0.00 3.86
2514 2661 2.203126 GGCCGAGCTTCATGGAGG 60.203 66.667 2.40 0.00 0.00 4.30
2515 2662 2.899339 GCCGAGCTTCATGGAGGC 60.899 66.667 2.40 0.00 37.61 4.70
2516 2663 2.203126 CCGAGCTTCATGGAGGCC 60.203 66.667 2.40 0.00 35.17 5.19
2517 2664 2.739996 CCGAGCTTCATGGAGGCCT 61.740 63.158 3.86 3.86 35.17 5.19
2518 2665 1.222936 CGAGCTTCATGGAGGCCTT 59.777 57.895 6.77 0.00 35.17 4.35
2519 2666 0.393537 CGAGCTTCATGGAGGCCTTT 60.394 55.000 6.77 0.00 35.17 3.11
2520 2667 1.134401 CGAGCTTCATGGAGGCCTTTA 60.134 52.381 6.77 0.00 35.17 1.85
2521 2668 2.486191 CGAGCTTCATGGAGGCCTTTAT 60.486 50.000 6.77 0.95 35.17 1.40
2522 2669 3.560105 GAGCTTCATGGAGGCCTTTATT 58.440 45.455 6.77 0.00 35.17 1.40
2523 2670 3.956848 GAGCTTCATGGAGGCCTTTATTT 59.043 43.478 6.77 0.00 35.17 1.40
2524 2671 4.356436 AGCTTCATGGAGGCCTTTATTTT 58.644 39.130 6.77 0.00 35.17 1.82
2525 2672 4.779489 AGCTTCATGGAGGCCTTTATTTTT 59.221 37.500 6.77 0.00 35.17 1.94
2526 2673 4.872124 GCTTCATGGAGGCCTTTATTTTTG 59.128 41.667 6.77 0.00 0.00 2.44
2527 2674 5.337491 GCTTCATGGAGGCCTTTATTTTTGA 60.337 40.000 6.77 0.90 0.00 2.69
2528 2675 6.678568 TTCATGGAGGCCTTTATTTTTGAA 57.321 33.333 6.77 7.36 0.00 2.69
2529 2676 6.678568 TCATGGAGGCCTTTATTTTTGAAA 57.321 33.333 6.77 0.00 0.00 2.69
2530 2677 7.072263 TCATGGAGGCCTTTATTTTTGAAAA 57.928 32.000 6.77 0.00 0.00 2.29
2531 2678 7.512992 TCATGGAGGCCTTTATTTTTGAAAAA 58.487 30.769 6.77 5.47 0.00 1.94
2532 2679 7.443879 TCATGGAGGCCTTTATTTTTGAAAAAC 59.556 33.333 6.77 0.00 0.00 2.43
2533 2680 6.894682 TGGAGGCCTTTATTTTTGAAAAACT 58.105 32.000 6.77 0.00 0.00 2.66
2534 2681 6.989759 TGGAGGCCTTTATTTTTGAAAAACTC 59.010 34.615 6.77 5.92 0.00 3.01
2535 2682 6.989759 GGAGGCCTTTATTTTTGAAAAACTCA 59.010 34.615 6.77 0.00 0.00 3.41
2536 2683 7.497579 GGAGGCCTTTATTTTTGAAAAACTCAA 59.502 33.333 6.77 0.00 42.48 3.02
2556 2703 9.936759 AACTCAAATTCAAACTTTTAAGGTTCA 57.063 25.926 0.00 0.00 32.57 3.18
2557 2704 9.936759 ACTCAAATTCAAACTTTTAAGGTTCAA 57.063 25.926 0.00 0.00 32.57 2.69
2596 2743 9.801873 AAAAATGCATGTATGTAAGGATGTAAC 57.198 29.630 0.00 0.00 0.00 2.50
2597 2744 8.518430 AAATGCATGTATGTAAGGATGTAACA 57.482 30.769 0.00 0.00 0.00 2.41
2598 2745 6.918892 TGCATGTATGTAAGGATGTAACAC 57.081 37.500 0.00 0.00 0.00 3.32
2599 2746 6.410540 TGCATGTATGTAAGGATGTAACACA 58.589 36.000 0.00 0.00 0.00 3.72
2600 2747 6.315144 TGCATGTATGTAAGGATGTAACACAC 59.685 38.462 0.00 0.00 0.00 3.82
2601 2748 6.315144 GCATGTATGTAAGGATGTAACACACA 59.685 38.462 0.00 0.00 42.69 3.72
2602 2749 7.676338 GCATGTATGTAAGGATGTAACACACAC 60.676 40.741 0.00 0.00 40.86 3.82
2603 2750 6.760291 TGTATGTAAGGATGTAACACACACA 58.240 36.000 0.00 0.00 40.86 3.72
2604 2751 6.647481 TGTATGTAAGGATGTAACACACACAC 59.353 38.462 0.00 0.00 40.86 3.82
2605 2752 4.052608 TGTAAGGATGTAACACACACACG 58.947 43.478 0.00 0.00 40.86 4.49
2606 2753 2.902705 AGGATGTAACACACACACGT 57.097 45.000 0.00 0.00 40.86 4.49
2637 2969 2.766828 ACCTGAGAGATTAAGGGGAACG 59.233 50.000 0.00 0.00 35.24 3.95
2657 2989 0.322098 TGGGAACACATTACAGCCCG 60.322 55.000 0.00 0.00 38.42 6.13
2664 2996 3.417101 ACACATTACAGCCCGAATTCAA 58.583 40.909 6.22 0.00 0.00 2.69
2765 3097 2.549754 CCCGTTGAGCTTATATTGGCTG 59.450 50.000 6.81 0.00 39.05 4.85
2766 3098 2.031682 CCGTTGAGCTTATATTGGCTGC 60.032 50.000 6.81 0.00 39.05 5.25
2767 3099 2.874701 CGTTGAGCTTATATTGGCTGCT 59.125 45.455 0.00 0.00 39.05 4.24
2768 3100 4.058124 CGTTGAGCTTATATTGGCTGCTA 58.942 43.478 0.00 0.00 39.05 3.49
2769 3101 4.692625 CGTTGAGCTTATATTGGCTGCTAT 59.307 41.667 0.00 0.00 39.05 2.97
2770 3102 5.390251 CGTTGAGCTTATATTGGCTGCTATG 60.390 44.000 0.00 0.00 39.05 2.23
2771 3103 4.582869 TGAGCTTATATTGGCTGCTATGG 58.417 43.478 0.00 0.00 39.05 2.74
2772 3104 3.350833 AGCTTATATTGGCTGCTATGGC 58.649 45.455 0.00 0.00 37.41 4.40
2782 3114 3.281332 TGCTATGGCAAAAGGGGAC 57.719 52.632 0.00 0.00 46.36 4.46
2783 3115 2.504920 GCTATGGCAAAAGGGGACC 58.495 57.895 0.00 0.00 44.33 4.46
2784 3116 0.324275 GCTATGGCAAAAGGGGACCA 60.324 55.000 0.00 0.00 45.78 4.02
2785 3117 1.689258 GCTATGGCAAAAGGGGACCAT 60.689 52.381 0.00 0.00 45.78 3.55
2786 3118 2.424234 GCTATGGCAAAAGGGGACCATA 60.424 50.000 0.00 0.00 45.78 2.74
2806 3138 4.924368 CCCCCACCTACCCTACAA 57.076 61.111 0.00 0.00 0.00 2.41
2807 3139 3.108047 CCCCCACCTACCCTACAAA 57.892 57.895 0.00 0.00 0.00 2.83
2808 3140 1.603634 CCCCCACCTACCCTACAAAT 58.396 55.000 0.00 0.00 0.00 2.32
2809 3141 1.493446 CCCCCACCTACCCTACAAATC 59.507 57.143 0.00 0.00 0.00 2.17
2810 3142 1.493446 CCCCACCTACCCTACAAATCC 59.507 57.143 0.00 0.00 0.00 3.01
2811 3143 2.201830 CCCACCTACCCTACAAATCCA 58.798 52.381 0.00 0.00 0.00 3.41
2812 3144 2.783510 CCCACCTACCCTACAAATCCAT 59.216 50.000 0.00 0.00 0.00 3.41
2813 3145 3.204382 CCCACCTACCCTACAAATCCATT 59.796 47.826 0.00 0.00 0.00 3.16
2814 3146 4.414182 CCCACCTACCCTACAAATCCATTA 59.586 45.833 0.00 0.00 0.00 1.90
2815 3147 5.074515 CCCACCTACCCTACAAATCCATTAT 59.925 44.000 0.00 0.00 0.00 1.28
2816 3148 6.273730 CCCACCTACCCTACAAATCCATTATA 59.726 42.308 0.00 0.00 0.00 0.98
2879 3211 3.292460 TCAGTTCGGTTTTTCCATTGGT 58.708 40.909 1.86 0.00 35.57 3.67
2888 3220 4.637977 GGTTTTTCCATTGGTTTGCTTTGA 59.362 37.500 1.86 0.00 35.97 2.69
2890 3222 2.818130 TCCATTGGTTTGCTTTGAGC 57.182 45.000 1.86 0.00 42.82 4.26
2912 3244 1.334869 GGATTAAATGGGCTGAGCACG 59.665 52.381 6.82 0.00 32.76 5.34
2920 3252 1.301401 GGCTGAGCACGTGTGGTAA 60.301 57.895 18.38 0.00 41.93 2.85
2934 3266 5.010922 ACGTGTGGTAATTTGGTCTAGTGTA 59.989 40.000 0.00 0.00 0.00 2.90
2940 3272 6.441284 TGGTAATTTGGTCTAGTGTAGGCTTA 59.559 38.462 0.00 0.00 0.00 3.09
2941 3273 6.985059 GGTAATTTGGTCTAGTGTAGGCTTAG 59.015 42.308 0.00 0.00 0.00 2.18
2943 3275 3.028094 TGGTCTAGTGTAGGCTTAGGG 57.972 52.381 0.00 0.00 0.00 3.53
2944 3276 2.313945 TGGTCTAGTGTAGGCTTAGGGT 59.686 50.000 0.00 0.00 0.00 4.34
2945 3277 3.245875 TGGTCTAGTGTAGGCTTAGGGTT 60.246 47.826 0.00 0.00 0.00 4.11
2947 3279 4.958581 GGTCTAGTGTAGGCTTAGGGTTTA 59.041 45.833 0.00 0.00 0.00 2.01
2948 3280 5.601729 GGTCTAGTGTAGGCTTAGGGTTTAT 59.398 44.000 0.00 0.00 0.00 1.40
2964 3296 5.828328 AGGGTTTATTACTAGATTGGCTTGC 59.172 40.000 0.00 0.00 0.00 4.01
2974 3306 0.319405 ATTGGCTTGCTTTGGTCTGC 59.681 50.000 0.00 0.00 0.00 4.26
2988 3320 0.032130 GTCTGCACAGAGACCGAACA 59.968 55.000 0.00 0.00 38.27 3.18
2992 3324 0.032130 GCACAGAGACCGAACAGTCA 59.968 55.000 0.00 0.00 39.34 3.41
2995 3327 1.338337 ACAGAGACCGAACAGTCACAG 59.662 52.381 0.00 0.00 39.34 3.66
2999 3331 2.377628 GACCGAACAGTCACAGCCCA 62.378 60.000 0.00 0.00 36.73 5.36
3012 3344 4.402155 GTCACAGCCCATTTCAATCCATAA 59.598 41.667 0.00 0.00 0.00 1.90
3019 3351 6.654582 AGCCCATTTCAATCCATAAACAAAAC 59.345 34.615 0.00 0.00 0.00 2.43
3023 3355 7.877097 CCATTTCAATCCATAAACAAAACCTGA 59.123 33.333 0.00 0.00 0.00 3.86
3040 3372 2.604914 CCTGAATCGAGTGACCAATTCG 59.395 50.000 0.00 0.00 32.09 3.34
3053 3385 4.020573 TGACCAATTCGATTGTACCTCTGT 60.021 41.667 0.00 0.00 38.59 3.41
3074 3406 2.755650 ACGATAACAGCGATTCCATCC 58.244 47.619 0.00 0.00 0.00 3.51
3082 3414 2.513666 GATTCCATCCGCCACGCA 60.514 61.111 0.00 0.00 0.00 5.24
3135 4518 1.961277 CTGACGCCAAGCCTTTCGT 60.961 57.895 1.68 1.68 37.92 3.85
3145 4528 2.594303 CCTTTCGTGGCTGGTGCA 60.594 61.111 0.00 0.00 41.91 4.57
3172 4555 1.600023 CCTCTCGCCTCTGTAGGTAG 58.400 60.000 0.00 0.00 45.64 3.18
3173 4556 1.600023 CTCTCGCCTCTGTAGGTAGG 58.400 60.000 0.00 0.00 45.64 3.18
3174 4557 0.917533 TCTCGCCTCTGTAGGTAGGT 59.082 55.000 0.00 0.00 45.64 3.08
3177 4560 1.214673 TCGCCTCTGTAGGTAGGTGAT 59.785 52.381 0.60 0.00 45.23 3.06
3192 4575 5.243954 GGTAGGTGATATGCTGATGACTACA 59.756 44.000 0.00 0.00 32.21 2.74
3196 4579 6.540189 AGGTGATATGCTGATGACTACAAAAC 59.460 38.462 0.00 0.00 0.00 2.43
3205 4588 1.946768 TGACTACAAAACTGTGCAGGC 59.053 47.619 4.11 0.00 0.00 4.85
3210 4593 0.877213 CAAAACTGTGCAGGCTTGGC 60.877 55.000 0.00 0.00 0.00 4.52
3212 4595 1.044790 AAACTGTGCAGGCTTGGCTT 61.045 50.000 0.00 0.00 0.00 4.35
3214 4597 1.900016 CTGTGCAGGCTTGGCTTGA 60.900 57.895 5.84 0.00 37.87 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.070552 GTCGAGGACCGGCAGCTT 62.071 66.667 0.00 0.00 43.50 3.74
30 31 2.464459 CCAAGCAATCGGCCGAGAC 61.464 63.158 33.87 23.58 46.50 3.36
39 40 1.031571 TCGGCCACATCCAAGCAATC 61.032 55.000 2.24 0.00 0.00 2.67
44 45 1.811266 CTCGTCGGCCACATCCAAG 60.811 63.158 2.24 0.00 0.00 3.61
49 50 3.771160 GGACCTCGTCGGCCACAT 61.771 66.667 2.24 0.00 35.61 3.21
93 94 1.590147 CAACCCCGACTTCGCTACT 59.410 57.895 0.00 0.00 38.18 2.57
107 121 4.785453 CTCCCCGAGCAGCCAACC 62.785 72.222 0.00 0.00 0.00 3.77
158 172 1.185618 CCGTCAAGGAGAGGACACCA 61.186 60.000 0.00 0.00 45.00 4.17
159 173 1.592223 CCGTCAAGGAGAGGACACC 59.408 63.158 0.00 0.00 45.00 4.16
172 186 3.083848 AAGACCACACACGCCGTCA 62.084 57.895 0.00 0.00 0.00 4.35
226 240 1.331447 GAAAACCGTTACAACACGCCT 59.669 47.619 0.00 0.00 38.93 5.52
266 281 7.936584 TGATTAAGAAAAAGACAATTGTCCGT 58.063 30.769 30.34 18.54 45.85 4.69
325 344 7.984617 TGCTCCACTTGCTTTAGTTTTATTTTT 59.015 29.630 0.00 0.00 0.00 1.94
326 345 7.496747 TGCTCCACTTGCTTTAGTTTTATTTT 58.503 30.769 0.00 0.00 0.00 1.82
327 346 7.049799 TGCTCCACTTGCTTTAGTTTTATTT 57.950 32.000 0.00 0.00 0.00 1.40
328 347 6.648879 TGCTCCACTTGCTTTAGTTTTATT 57.351 33.333 0.00 0.00 0.00 1.40
329 348 6.624423 CATGCTCCACTTGCTTTAGTTTTAT 58.376 36.000 0.00 0.00 0.00 1.40
330 349 5.564651 GCATGCTCCACTTGCTTTAGTTTTA 60.565 40.000 11.37 0.00 44.08 1.52
384 405 4.752594 TACCCTGCCCCTGTCCCC 62.753 72.222 0.00 0.00 0.00 4.81
388 409 4.760220 CCCCTACCCTGCCCCTGT 62.760 72.222 0.00 0.00 0.00 4.00
485 508 0.620556 TCCTTCCTCCATGCAAGACC 59.379 55.000 0.00 0.00 0.00 3.85
493 516 2.486716 CCTTCCTCTTCCTTCCTCCAT 58.513 52.381 0.00 0.00 0.00 3.41
497 520 2.556766 CTTCCCTTCCTCTTCCTTCCT 58.443 52.381 0.00 0.00 0.00 3.36
500 523 1.912731 GAGCTTCCCTTCCTCTTCCTT 59.087 52.381 0.00 0.00 0.00 3.36
501 524 1.203364 TGAGCTTCCCTTCCTCTTCCT 60.203 52.381 0.00 0.00 0.00 3.36
504 527 0.610687 CGTGAGCTTCCCTTCCTCTT 59.389 55.000 0.00 0.00 0.00 2.85
505 528 0.543174 ACGTGAGCTTCCCTTCCTCT 60.543 55.000 0.00 0.00 0.00 3.69
527 558 4.724303 CATGCACGCTATACTACTCCTAC 58.276 47.826 0.00 0.00 0.00 3.18
528 559 3.190744 GCATGCACGCTATACTACTCCTA 59.809 47.826 14.21 0.00 0.00 2.94
529 560 2.029828 GCATGCACGCTATACTACTCCT 60.030 50.000 14.21 0.00 0.00 3.69
530 561 2.329379 GCATGCACGCTATACTACTCC 58.671 52.381 14.21 0.00 0.00 3.85
531 562 2.288213 TGGCATGCACGCTATACTACTC 60.288 50.000 21.36 0.00 0.00 2.59
532 563 1.686587 TGGCATGCACGCTATACTACT 59.313 47.619 21.36 0.00 0.00 2.57
561 592 2.187958 AGGATCATCAAACCGAGTGGA 58.812 47.619 0.00 0.00 39.21 4.02
562 593 2.679837 CAAGGATCATCAAACCGAGTGG 59.320 50.000 0.00 0.00 42.84 4.00
583 614 2.044946 GGTGTGGCTGTGGGATCC 60.045 66.667 1.92 1.92 0.00 3.36
633 677 0.533978 CGCCGATGGAGAGAGAGAGA 60.534 60.000 0.00 0.00 0.00 3.10
634 678 1.948508 CGCCGATGGAGAGAGAGAG 59.051 63.158 0.00 0.00 0.00 3.20
637 681 3.586961 CGCGCCGATGGAGAGAGA 61.587 66.667 0.00 0.00 0.00 3.10
638 682 4.637489 CCGCGCCGATGGAGAGAG 62.637 72.222 0.00 0.00 0.00 3.20
752 799 1.370437 CGGCCTGGATGAGGATGAG 59.630 63.158 0.00 0.00 46.33 2.90
753 800 2.142761 CCGGCCTGGATGAGGATGA 61.143 63.158 7.77 0.00 46.33 2.92
754 801 2.429058 CCGGCCTGGATGAGGATG 59.571 66.667 7.77 0.00 46.33 3.51
755 802 3.564218 GCCGGCCTGGATGAGGAT 61.564 66.667 18.11 0.00 46.33 3.24
834 905 3.308595 CGCATGCAGCAATCAATTCAATT 59.691 39.130 19.57 0.00 46.13 2.32
835 906 2.863740 CGCATGCAGCAATCAATTCAAT 59.136 40.909 19.57 0.00 46.13 2.57
836 907 2.094649 TCGCATGCAGCAATCAATTCAA 60.095 40.909 19.57 0.00 46.13 2.69
837 908 1.473278 TCGCATGCAGCAATCAATTCA 59.527 42.857 19.57 0.00 46.13 2.57
838 909 2.117137 CTCGCATGCAGCAATCAATTC 58.883 47.619 19.57 0.00 46.13 2.17
857 928 1.815421 GATGGATCAACGCCACGCT 60.815 57.895 0.00 0.00 38.44 5.07
860 931 1.667236 TGATGATGGATCAACGCCAC 58.333 50.000 0.00 0.00 38.19 5.01
861 932 2.416680 TTGATGATGGATCAACGCCA 57.583 45.000 0.00 0.00 44.65 5.69
924 995 1.133945 GCCTTCAATTCCTCCTCCTCC 60.134 57.143 0.00 0.00 0.00 4.30
988 1059 2.930023 GCTGCTTCATGGATCGATCGAT 60.930 50.000 29.76 29.76 37.59 3.59
989 1060 1.603931 GCTGCTTCATGGATCGATCGA 60.604 52.381 21.86 21.86 0.00 3.59
1212 1347 3.023591 GCTCGTGCCCGTTAGCAAC 62.024 63.158 0.00 0.00 46.19 4.17
1326 1464 0.796312 GGTGCACGAACGACATGAAT 59.204 50.000 11.45 0.00 0.00 2.57
1410 1548 2.762875 GGGTACTCCTCCACCCGG 60.763 72.222 0.00 0.00 44.87 5.73
1512 1650 4.392166 TAGAGCCCCTCGTGCCCA 62.392 66.667 0.00 0.00 35.36 5.36
1704 1842 2.640302 GCAGCTCTCCGACACCAGA 61.640 63.158 0.00 0.00 0.00 3.86
1872 2010 1.977544 CTCGAACCACTCCGACCCT 60.978 63.158 0.00 0.00 0.00 4.34
2282 2420 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
2283 2421 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
2284 2422 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
2285 2423 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
2286 2424 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
2287 2425 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
2405 2552 6.978659 ACAAGTTGTCTGTATACATCCATACG 59.021 38.462 5.91 0.00 34.67 3.06
2406 2553 7.979537 TCACAAGTTGTCTGTATACATCCATAC 59.020 37.037 5.27 7.33 32.91 2.39
2408 2555 6.946340 TCACAAGTTGTCTGTATACATCCAT 58.054 36.000 5.27 0.00 0.00 3.41
2409 2556 6.353404 TCACAAGTTGTCTGTATACATCCA 57.647 37.500 5.27 3.35 0.00 3.41
2410 2557 7.849804 AATCACAAGTTGTCTGTATACATCC 57.150 36.000 5.27 0.58 0.00 3.51
2437 2584 9.398538 TGTCTGTCATTCATTCATGATTCATTA 57.601 29.630 0.00 0.00 35.60 1.90
2445 2592 6.905578 TGAAGTTGTCTGTCATTCATTCATG 58.094 36.000 0.00 0.00 0.00 3.07
2447 2594 7.364970 CAATGAAGTTGTCTGTCATTCATTCA 58.635 34.615 11.09 0.00 40.63 2.57
2448 2595 7.792383 CAATGAAGTTGTCTGTCATTCATTC 57.208 36.000 11.09 0.00 40.63 2.67
2468 2615 8.733458 TCTCCTAATTTGAAGTGATTCACAATG 58.267 33.333 18.57 0.28 36.74 2.82
2475 2622 6.153510 GGCCTTTCTCCTAATTTGAAGTGATT 59.846 38.462 0.00 0.00 0.00 2.57
2491 2638 1.012841 CATGAAGCTCGGCCTTTCTC 58.987 55.000 0.00 0.00 0.00 2.87
2492 2639 0.393537 CCATGAAGCTCGGCCTTTCT 60.394 55.000 0.00 0.00 0.00 2.52
2493 2640 0.392998 TCCATGAAGCTCGGCCTTTC 60.393 55.000 0.00 0.03 0.00 2.62
2494 2641 0.393537 CTCCATGAAGCTCGGCCTTT 60.394 55.000 0.00 0.00 0.00 3.11
2495 2642 1.222936 CTCCATGAAGCTCGGCCTT 59.777 57.895 0.00 0.00 0.00 4.35
2496 2643 2.739996 CCTCCATGAAGCTCGGCCT 61.740 63.158 0.00 0.00 0.00 5.19
2497 2644 2.203126 CCTCCATGAAGCTCGGCC 60.203 66.667 0.00 0.00 0.00 6.13
2498 2645 2.899339 GCCTCCATGAAGCTCGGC 60.899 66.667 0.00 0.00 0.00 5.54
2499 2646 2.203126 GGCCTCCATGAAGCTCGG 60.203 66.667 0.00 0.00 0.00 4.63
2500 2647 0.393537 AAAGGCCTCCATGAAGCTCG 60.394 55.000 5.23 0.00 0.00 5.03
2501 2648 2.717639 TAAAGGCCTCCATGAAGCTC 57.282 50.000 5.23 0.00 0.00 4.09
2502 2649 3.677156 AATAAAGGCCTCCATGAAGCT 57.323 42.857 5.23 0.00 0.00 3.74
2503 2650 4.743057 AAAATAAAGGCCTCCATGAAGC 57.257 40.909 5.23 0.00 0.00 3.86
2504 2651 6.284891 TCAAAAATAAAGGCCTCCATGAAG 57.715 37.500 5.23 0.00 0.00 3.02
2505 2652 6.678568 TTCAAAAATAAAGGCCTCCATGAA 57.321 33.333 5.23 7.78 0.00 2.57
2506 2653 6.678568 TTTCAAAAATAAAGGCCTCCATGA 57.321 33.333 5.23 1.25 0.00 3.07
2507 2654 7.445096 AGTTTTTCAAAAATAAAGGCCTCCATG 59.555 33.333 5.23 0.00 0.00 3.66
2508 2655 7.517320 AGTTTTTCAAAAATAAAGGCCTCCAT 58.483 30.769 5.23 0.00 0.00 3.41
2509 2656 6.894682 AGTTTTTCAAAAATAAAGGCCTCCA 58.105 32.000 5.23 0.00 0.00 3.86
2510 2657 6.989759 TGAGTTTTTCAAAAATAAAGGCCTCC 59.010 34.615 5.23 0.00 31.34 4.30
2511 2658 8.432110 TTGAGTTTTTCAAAAATAAAGGCCTC 57.568 30.769 5.23 0.03 42.69 4.70
2530 2677 9.936759 TGAACCTTAAAAGTTTGAATTTGAGTT 57.063 25.926 0.00 0.00 0.00 3.01
2531 2678 9.936759 TTGAACCTTAAAAGTTTGAATTTGAGT 57.063 25.926 0.00 0.00 0.00 3.41
2570 2717 9.801873 GTTACATCCTTACATACATGCATTTTT 57.198 29.630 0.00 0.00 0.00 1.94
2571 2718 8.965819 TGTTACATCCTTACATACATGCATTTT 58.034 29.630 0.00 0.00 0.00 1.82
2572 2719 8.405531 GTGTTACATCCTTACATACATGCATTT 58.594 33.333 0.00 0.00 0.00 2.32
2573 2720 7.555914 TGTGTTACATCCTTACATACATGCATT 59.444 33.333 0.00 0.00 0.00 3.56
2574 2721 7.012327 GTGTGTTACATCCTTACATACATGCAT 59.988 37.037 0.00 0.00 35.02 3.96
2575 2722 6.315144 GTGTGTTACATCCTTACATACATGCA 59.685 38.462 0.00 0.00 35.02 3.96
2576 2723 6.315144 TGTGTGTTACATCCTTACATACATGC 59.685 38.462 0.00 0.00 38.44 4.06
2577 2724 7.333174 TGTGTGTGTTACATCCTTACATACATG 59.667 37.037 0.00 0.00 42.86 3.21
2578 2725 7.333423 GTGTGTGTGTTACATCCTTACATACAT 59.667 37.037 0.00 0.00 42.86 2.29
2579 2726 6.647481 GTGTGTGTGTTACATCCTTACATACA 59.353 38.462 0.00 0.00 42.24 2.29
2580 2727 6.183360 CGTGTGTGTGTTACATCCTTACATAC 60.183 42.308 0.00 0.00 42.24 2.39
2581 2728 5.865013 CGTGTGTGTGTTACATCCTTACATA 59.135 40.000 0.00 0.00 42.24 2.29
2582 2729 4.688879 CGTGTGTGTGTTACATCCTTACAT 59.311 41.667 0.00 0.00 42.24 2.29
2583 2730 4.052608 CGTGTGTGTGTTACATCCTTACA 58.947 43.478 0.00 0.00 42.24 2.41
2584 2731 4.053295 ACGTGTGTGTGTTACATCCTTAC 58.947 43.478 0.00 0.00 42.24 2.34
2585 2732 4.052608 CACGTGTGTGTGTTACATCCTTA 58.947 43.478 7.58 0.00 42.24 2.69
2586 2733 2.869801 CACGTGTGTGTGTTACATCCTT 59.130 45.455 7.58 0.00 42.24 3.36
2587 2734 2.479837 CACGTGTGTGTGTTACATCCT 58.520 47.619 7.58 0.00 42.24 3.24
2588 2735 2.941891 CACGTGTGTGTGTTACATCC 57.058 50.000 7.58 0.00 42.24 3.51
2612 2759 5.860648 TCCCCTTAATCTCTCAGGTTTTT 57.139 39.130 0.00 0.00 0.00 1.94
2613 2760 5.571285 GTTCCCCTTAATCTCTCAGGTTTT 58.429 41.667 0.00 0.00 0.00 2.43
2614 2761 4.323562 CGTTCCCCTTAATCTCTCAGGTTT 60.324 45.833 0.00 0.00 0.00 3.27
2615 2762 3.197983 CGTTCCCCTTAATCTCTCAGGTT 59.802 47.826 0.00 0.00 0.00 3.50
2616 2763 2.766828 CGTTCCCCTTAATCTCTCAGGT 59.233 50.000 0.00 0.00 0.00 4.00
2617 2764 2.766828 ACGTTCCCCTTAATCTCTCAGG 59.233 50.000 0.00 0.00 0.00 3.86
2618 2765 3.430929 CCACGTTCCCCTTAATCTCTCAG 60.431 52.174 0.00 0.00 0.00 3.35
2619 2766 2.500098 CCACGTTCCCCTTAATCTCTCA 59.500 50.000 0.00 0.00 0.00 3.27
2620 2767 2.158943 CCCACGTTCCCCTTAATCTCTC 60.159 54.545 0.00 0.00 0.00 3.20
2621 2768 1.838077 CCCACGTTCCCCTTAATCTCT 59.162 52.381 0.00 0.00 0.00 3.10
2622 2769 1.835531 TCCCACGTTCCCCTTAATCTC 59.164 52.381 0.00 0.00 0.00 2.75
2623 2770 1.961133 TCCCACGTTCCCCTTAATCT 58.039 50.000 0.00 0.00 0.00 2.40
2624 2771 2.290450 TGTTCCCACGTTCCCCTTAATC 60.290 50.000 0.00 0.00 0.00 1.75
2625 2772 1.706305 TGTTCCCACGTTCCCCTTAAT 59.294 47.619 0.00 0.00 0.00 1.40
2626 2773 1.138568 TGTTCCCACGTTCCCCTTAA 58.861 50.000 0.00 0.00 0.00 1.85
2627 2774 0.397564 GTGTTCCCACGTTCCCCTTA 59.602 55.000 0.00 0.00 0.00 2.69
2628 2775 1.149854 GTGTTCCCACGTTCCCCTT 59.850 57.895 0.00 0.00 0.00 3.95
2629 2776 1.423794 ATGTGTTCCCACGTTCCCCT 61.424 55.000 0.00 0.00 44.92 4.79
2630 2777 0.538746 AATGTGTTCCCACGTTCCCC 60.539 55.000 0.00 0.00 45.50 4.81
2631 2778 1.808343 GTAATGTGTTCCCACGTTCCC 59.192 52.381 3.74 0.00 45.50 3.97
2632 2779 2.482721 CTGTAATGTGTTCCCACGTTCC 59.517 50.000 3.74 0.00 45.50 3.62
2637 2969 1.173913 GGGCTGTAATGTGTTCCCAC 58.826 55.000 0.00 0.00 42.19 4.61
2742 3074 3.073062 AGCCAATATAAGCTCAACGGGAT 59.927 43.478 0.00 0.00 32.71 3.85
2746 3078 2.874701 AGCAGCCAATATAAGCTCAACG 59.125 45.455 0.00 0.00 37.18 4.10
2765 3097 0.324275 TGGTCCCCTTTTGCCATAGC 60.324 55.000 0.00 0.00 40.48 2.97
2766 3098 2.459555 ATGGTCCCCTTTTGCCATAG 57.540 50.000 0.00 0.00 39.67 2.23
2767 3099 2.424234 GCTATGGTCCCCTTTTGCCATA 60.424 50.000 0.00 0.00 41.45 2.74
2768 3100 1.689258 GCTATGGTCCCCTTTTGCCAT 60.689 52.381 0.00 0.00 43.38 4.40
2769 3101 0.324275 GCTATGGTCCCCTTTTGCCA 60.324 55.000 0.00 0.00 35.28 4.92
2770 3102 1.043116 GGCTATGGTCCCCTTTTGCC 61.043 60.000 0.00 0.00 0.00 4.52
2771 3103 1.043116 GGGCTATGGTCCCCTTTTGC 61.043 60.000 0.00 0.00 38.30 3.68
2772 3104 3.207452 GGGCTATGGTCCCCTTTTG 57.793 57.895 0.00 0.00 38.30 2.44
2789 3121 1.493446 GATTTGTAGGGTAGGTGGGGG 59.507 57.143 0.00 0.00 0.00 5.40
2790 3122 1.493446 GGATTTGTAGGGTAGGTGGGG 59.507 57.143 0.00 0.00 0.00 4.96
2791 3123 2.201830 TGGATTTGTAGGGTAGGTGGG 58.798 52.381 0.00 0.00 0.00 4.61
2792 3124 4.519906 AATGGATTTGTAGGGTAGGTGG 57.480 45.455 0.00 0.00 0.00 4.61
2871 3203 2.036217 CAGCTCAAAGCAAACCAATGGA 59.964 45.455 6.16 0.00 45.56 3.41
2879 3211 5.481105 CCATTTAATCCAGCTCAAAGCAAA 58.519 37.500 1.29 0.00 45.56 3.68
2888 3220 2.941480 CTCAGCCCATTTAATCCAGCT 58.059 47.619 0.00 0.00 0.00 4.24
2890 3222 2.360165 GTGCTCAGCCCATTTAATCCAG 59.640 50.000 0.00 0.00 0.00 3.86
2912 3244 5.873164 CCTACACTAGACCAAATTACCACAC 59.127 44.000 0.00 0.00 0.00 3.82
2920 3252 4.409247 CCCTAAGCCTACACTAGACCAAAT 59.591 45.833 0.00 0.00 0.00 2.32
2934 3266 7.692040 GCCAATCTAGTAATAAACCCTAAGCCT 60.692 40.741 0.00 0.00 0.00 4.58
2940 3272 5.828328 GCAAGCCAATCTAGTAATAAACCCT 59.172 40.000 0.00 0.00 0.00 4.34
2941 3273 5.828328 AGCAAGCCAATCTAGTAATAAACCC 59.172 40.000 0.00 0.00 0.00 4.11
2943 3275 7.702348 CCAAAGCAAGCCAATCTAGTAATAAAC 59.298 37.037 0.00 0.00 0.00 2.01
2944 3276 7.396055 ACCAAAGCAAGCCAATCTAGTAATAAA 59.604 33.333 0.00 0.00 0.00 1.40
2945 3277 6.889722 ACCAAAGCAAGCCAATCTAGTAATAA 59.110 34.615 0.00 0.00 0.00 1.40
2947 3279 5.264395 ACCAAAGCAAGCCAATCTAGTAAT 58.736 37.500 0.00 0.00 0.00 1.89
2948 3280 4.662278 ACCAAAGCAAGCCAATCTAGTAA 58.338 39.130 0.00 0.00 0.00 2.24
2974 3306 1.067060 TGTGACTGTTCGGTCTCTGTG 59.933 52.381 12.14 0.00 37.16 3.66
2983 3315 1.197721 GAAATGGGCTGTGACTGTTCG 59.802 52.381 0.00 0.00 0.00 3.95
2988 3320 2.225091 TGGATTGAAATGGGCTGTGACT 60.225 45.455 0.00 0.00 0.00 3.41
2992 3324 4.776837 TGTTTATGGATTGAAATGGGCTGT 59.223 37.500 0.00 0.00 0.00 4.40
2995 3327 6.128035 GGTTTTGTTTATGGATTGAAATGGGC 60.128 38.462 0.00 0.00 0.00 5.36
3012 3344 3.564225 GGTCACTCGATTCAGGTTTTGTT 59.436 43.478 0.00 0.00 0.00 2.83
3019 3351 2.604914 CGAATTGGTCACTCGATTCAGG 59.395 50.000 0.00 0.00 37.38 3.86
3053 3385 3.610821 CGGATGGAATCGCTGTTATCGTA 60.611 47.826 0.00 0.00 46.86 3.43
3058 3390 0.531974 GGCGGATGGAATCGCTGTTA 60.532 55.000 7.60 0.00 46.86 2.41
3060 3392 2.203070 GGCGGATGGAATCGCTGT 60.203 61.111 7.60 0.00 46.86 4.40
3078 3410 2.341176 GACACCTAACCCGTGCGT 59.659 61.111 0.00 0.00 34.45 5.24
3082 3414 1.301165 GCAACGACACCTAACCCGT 60.301 57.895 0.00 0.00 36.77 5.28
3084 3416 3.976758 GGCAACGACACCTAACCC 58.023 61.111 0.00 0.00 0.00 4.11
3119 4502 2.556287 CACGAAAGGCTTGGCGTC 59.444 61.111 20.87 6.09 34.37 5.19
3144 4527 4.864334 GGCGAGAGGGGGCACATG 62.864 72.222 0.00 0.00 0.00 3.21
3172 4555 6.540189 AGTTTTGTAGTCATCAGCATATCACC 59.460 38.462 0.00 0.00 0.00 4.02
3173 4556 7.065085 ACAGTTTTGTAGTCATCAGCATATCAC 59.935 37.037 0.00 0.00 35.25 3.06
3174 4557 7.064966 CACAGTTTTGTAGTCATCAGCATATCA 59.935 37.037 0.00 0.00 35.25 2.15
3177 4560 5.122239 GCACAGTTTTGTAGTCATCAGCATA 59.878 40.000 0.00 0.00 35.25 3.14
3192 4575 1.044790 AGCCAAGCCTGCACAGTTTT 61.045 50.000 0.00 0.00 0.00 2.43
3196 4579 1.248785 ATCAAGCCAAGCCTGCACAG 61.249 55.000 0.00 0.00 0.00 3.66
3205 4588 1.134610 GGGCAATCCAATCAAGCCAAG 60.135 52.381 0.00 0.00 46.96 3.61
3210 4593 4.891756 AGTAATCTGGGCAATCCAATCAAG 59.108 41.667 0.00 0.00 46.51 3.02
3212 4595 4.524802 AGTAATCTGGGCAATCCAATCA 57.475 40.909 0.00 0.00 46.51 2.57
3214 4597 4.870636 TGAAGTAATCTGGGCAATCCAAT 58.129 39.130 0.00 0.00 46.51 3.16
3227 4610 9.060347 TCAGGCATAATGATTTCTGAAGTAATC 57.940 33.333 3.46 3.46 33.95 1.75


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

AutoCloner maintained by Alex Coulton.