Multiple sequence alignment - TraesCS3D01G096600

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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 TraesCS3D01G096600 chr3D 100.000 2735 0 0 1 2735 48853122 48850388 0.000000e+00 5051
1 TraesCS3D01G096600 chr3D 96.831 284 6 2 2454 2735 350159833 350160115 3.190000e-129 472
2 TraesCS3D01G096600 chr3A 92.906 1452 76 13 1 1433 61320680 61319237 0.000000e+00 2085
3 TraesCS3D01G096600 chr3A 91.912 1051 51 11 1430 2454 61319198 61318156 0.000000e+00 1439
4 TraesCS3D01G096600 chr3A 90.110 91 6 2 2046 2134 518640178 518640267 6.190000e-22 115
5 TraesCS3D01G096600 chr3B 92.521 1404 82 13 1 1385 78233652 78232253 0.000000e+00 1989
6 TraesCS3D01G096600 chr3B 89.130 644 43 11 1432 2061 78232179 78231549 0.000000e+00 776
7 TraesCS3D01G096600 chrUn 92.936 1359 75 11 92 1433 39579924 39578570 0.000000e+00 1958
8 TraesCS3D01G096600 chrUn 93.173 1040 48 11 1430 2454 39578531 39577500 0.000000e+00 1506
9 TraesCS3D01G096600 chr4D 96.491 285 7 2 2453 2735 26070378 26070095 4.120000e-128 468
10 TraesCS3D01G096600 chr4D 96.466 283 9 1 2453 2735 480799642 480799361 1.480000e-127 466
11 TraesCS3D01G096600 chr4D 96.167 287 6 2 2453 2735 463714847 463714562 5.330000e-127 464
12 TraesCS3D01G096600 chr2D 96.491 285 7 2 2453 2735 556104693 556104410 4.120000e-128 468
13 TraesCS3D01G096600 chr1D 96.167 287 8 2 2451 2735 492016845 492016560 1.480000e-127 466
14 TraesCS3D01G096600 chr1D 93.023 86 6 0 2045 2130 311756220 311756135 2.860000e-25 126
15 TraesCS3D01G096600 chr1D 91.111 90 8 0 2045 2134 320589942 320590031 3.700000e-24 122
16 TraesCS3D01G096600 chr7D 96.454 282 9 1 2453 2734 426342343 426342063 5.330000e-127 464
17 TraesCS3D01G096600 chr5D 96.140 285 8 2 2453 2735 288164027 288164310 1.920000e-126 462
18 TraesCS3D01G096600 chr5D 96.127 284 10 1 2452 2735 520123470 520123188 1.920000e-126 462
19 TraesCS3D01G096600 chr6B 81.221 213 35 5 6 215 153401833 153402043 1.680000e-37 167
20 TraesCS3D01G096600 chr6B 95.402 87 4 0 2048 2134 512188590 512188504 3.670000e-29 139
21 TraesCS3D01G096600 chr6A 95.455 88 4 0 2047 2134 64260791 64260704 1.020000e-29 141
22 TraesCS3D01G096600 chr2B 91.765 85 7 0 2050 2134 754008534 754008450 4.780000e-23 119
23 TraesCS3D01G096600 chr1A 89.130 92 8 2 2045 2134 287311436 287311527 2.230000e-21 113
24 TraesCS3D01G096600 chr5B 82.927 123 14 2 101 221 304601709 304601592 1.340000e-18 104


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 TraesCS3D01G096600 chr3D 48850388 48853122 2734 True 5051.0 5051 100.0000 1 2735 1 chr3D.!!$R1 2734
1 TraesCS3D01G096600 chr3A 61318156 61320680 2524 True 1762.0 2085 92.4090 1 2454 2 chr3A.!!$R1 2453
2 TraesCS3D01G096600 chr3B 78231549 78233652 2103 True 1382.5 1989 90.8255 1 2061 2 chr3B.!!$R1 2060
3 TraesCS3D01G096600 chrUn 39577500 39579924 2424 True 1732.0 1958 93.0545 92 2454 2 chrUn.!!$R1 2362

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
741 761 2.037367 CTCTCACCCTGGACCCGA 59.963 66.667 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2702 2815 0.118346 TCTACTTCCCCCTTGCTGGA 59.882 55.0 0.0 0.0 38.35 3.86 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
127 132 9.404348 ACAAATTTTGAAACCACAAACATTTTC 57.596 25.926 15.81 0.00 39.08 2.29
341 349 3.750828 GCTAGAGTGTTCAGCCTCC 57.249 57.895 0.00 0.00 0.00 4.30
366 376 4.521146 CATTCTCAGTCCCAAGCTACAAT 58.479 43.478 0.00 0.00 0.00 2.71
372 382 2.582636 AGTCCCAAGCTACAATCCCAAT 59.417 45.455 0.00 0.00 0.00 3.16
510 521 2.961526 TCGAGCTCACCATTTCCTAC 57.038 50.000 15.40 0.00 0.00 3.18
519 530 6.058183 GCTCACCATTTCCTACTCACATTAT 58.942 40.000 0.00 0.00 0.00 1.28
732 752 4.803426 CGTGGCGCTCTCTCACCC 62.803 72.222 7.64 0.00 0.00 4.61
741 761 2.037367 CTCTCACCCTGGACCCGA 59.963 66.667 0.00 0.00 0.00 5.14
892 912 3.775654 CCCCGACCTGAGAGTGCC 61.776 72.222 0.00 0.00 0.00 5.01
962 982 2.113986 GTGCCTGTCACCCTGCTT 59.886 61.111 0.00 0.00 39.79 3.91
1011 1039 1.945394 CACAGCTCCATGAAGTATGCC 59.055 52.381 0.00 0.00 35.37 4.40
1044 1072 4.521146 AGACAAGAAAGGCATACATGGAG 58.479 43.478 0.00 0.00 0.00 3.86
1134 1162 2.103042 GGTTAGTCCGCAGCAGCTG 61.103 63.158 18.93 18.93 39.10 4.24
1197 1225 2.671682 GCAAGACCAGGACCTCCC 59.328 66.667 0.00 0.00 36.42 4.30
1311 1345 0.478072 TGACCATCAAACCAGCCAGT 59.522 50.000 0.00 0.00 0.00 4.00
1330 1364 4.445453 CAGTATAGCTGCATTCAACCTGA 58.555 43.478 1.02 0.00 38.52 3.86
1367 1401 2.591715 GCCGATTGATGGTCCGGG 60.592 66.667 0.00 0.00 42.02 5.73
1428 1462 2.683933 TTCGAGGACCCCAGAGCC 60.684 66.667 0.00 0.00 0.00 4.70
1608 1684 3.823873 TCTTTGTGATGCAATTAACGGGT 59.176 39.130 0.00 0.00 36.89 5.28
1717 1793 2.222227 TCTGCTGAGTCAAGAGGCTA 57.778 50.000 0.00 0.00 0.00 3.93
1718 1794 1.821753 TCTGCTGAGTCAAGAGGCTAC 59.178 52.381 0.00 0.00 0.00 3.58
1719 1795 1.547820 CTGCTGAGTCAAGAGGCTACA 59.452 52.381 0.00 0.00 0.00 2.74
1775 1852 2.306847 GCACATATTTACCAGGGGTGG 58.693 52.381 0.00 0.00 36.19 4.61
1793 1876 4.159693 GGGTGGGACCATAAAAATGAGTTC 59.840 45.833 0.00 0.00 41.02 3.01
1804 1887 4.843220 AAAATGAGTTCAGCCAGTTCTG 57.157 40.909 0.00 0.00 35.46 3.02
1829 1920 4.335315 GCGTCATTCTCAATACCCAATCAA 59.665 41.667 0.00 0.00 0.00 2.57
1830 1921 5.163663 GCGTCATTCTCAATACCCAATCAAA 60.164 40.000 0.00 0.00 0.00 2.69
1917 2009 7.801104 TCCCAGCTGATGATATAACAACTAAA 58.199 34.615 17.39 0.00 0.00 1.85
2136 2238 0.253044 TTGGTGCAGAGGGAGTATGC 59.747 55.000 0.00 0.00 44.20 3.14
2192 2294 7.173907 CCAGATTAATGTAAACTATGAGGGCTG 59.826 40.741 0.00 0.00 0.00 4.85
2195 2297 7.859325 TTAATGTAAACTATGAGGGCTGTTC 57.141 36.000 0.00 0.00 0.00 3.18
2217 2319 9.077885 TGTTCTGTTATTTTGATTCTTAAGGCT 57.922 29.630 1.85 0.00 0.00 4.58
2225 2327 8.722480 ATTTTGATTCTTAAGGCTTATTTGGC 57.278 30.769 7.96 0.00 0.00 4.52
2322 2435 2.231478 GGATCTTCTCACGAACTCCACA 59.769 50.000 0.00 0.00 31.05 4.17
2454 2567 6.264518 AGTGTGGGTTTTGGTAGTATTTTCTG 59.735 38.462 0.00 0.00 0.00 3.02
2455 2568 6.040054 GTGTGGGTTTTGGTAGTATTTTCTGT 59.960 38.462 0.00 0.00 0.00 3.41
2456 2569 6.608002 TGTGGGTTTTGGTAGTATTTTCTGTT 59.392 34.615 0.00 0.00 0.00 3.16
2457 2570 6.921307 GTGGGTTTTGGTAGTATTTTCTGTTG 59.079 38.462 0.00 0.00 0.00 3.33
2458 2571 6.041069 TGGGTTTTGGTAGTATTTTCTGTTGG 59.959 38.462 0.00 0.00 0.00 3.77
2459 2572 6.452242 GGTTTTGGTAGTATTTTCTGTTGGG 58.548 40.000 0.00 0.00 0.00 4.12
2460 2573 6.452242 GTTTTGGTAGTATTTTCTGTTGGGG 58.548 40.000 0.00 0.00 0.00 4.96
2461 2574 5.586155 TTGGTAGTATTTTCTGTTGGGGA 57.414 39.130 0.00 0.00 0.00 4.81
2462 2575 5.789574 TGGTAGTATTTTCTGTTGGGGAT 57.210 39.130 0.00 0.00 0.00 3.85
2463 2576 5.751586 TGGTAGTATTTTCTGTTGGGGATC 58.248 41.667 0.00 0.00 0.00 3.36
2464 2577 4.814771 GGTAGTATTTTCTGTTGGGGATCG 59.185 45.833 0.00 0.00 0.00 3.69
2465 2578 4.569719 AGTATTTTCTGTTGGGGATCGT 57.430 40.909 0.00 0.00 0.00 3.73
2466 2579 5.687166 AGTATTTTCTGTTGGGGATCGTA 57.313 39.130 0.00 0.00 0.00 3.43
2467 2580 6.057321 AGTATTTTCTGTTGGGGATCGTAA 57.943 37.500 0.00 0.00 0.00 3.18
2468 2581 5.878669 AGTATTTTCTGTTGGGGATCGTAAC 59.121 40.000 0.00 0.00 0.00 2.50
2469 2582 3.773418 TTTCTGTTGGGGATCGTAACA 57.227 42.857 7.52 7.52 33.67 2.41
2473 2586 3.773418 TGTTGGGGATCGTAACAGAAA 57.227 42.857 4.54 0.00 31.34 2.52
2474 2587 4.295141 TGTTGGGGATCGTAACAGAAAT 57.705 40.909 4.54 0.00 31.34 2.17
2475 2588 4.658063 TGTTGGGGATCGTAACAGAAATT 58.342 39.130 4.54 0.00 31.34 1.82
2476 2589 5.074115 TGTTGGGGATCGTAACAGAAATTT 58.926 37.500 0.00 0.00 31.34 1.82
2477 2590 6.239396 TGTTGGGGATCGTAACAGAAATTTA 58.761 36.000 0.00 0.00 31.34 1.40
2478 2591 6.715718 TGTTGGGGATCGTAACAGAAATTTAA 59.284 34.615 0.00 0.00 31.34 1.52
2479 2592 7.230913 TGTTGGGGATCGTAACAGAAATTTAAA 59.769 33.333 0.00 0.00 31.34 1.52
2480 2593 7.762588 TGGGGATCGTAACAGAAATTTAAAA 57.237 32.000 0.00 0.00 0.00 1.52
2481 2594 8.356000 TGGGGATCGTAACAGAAATTTAAAAT 57.644 30.769 0.00 0.00 0.00 1.82
2482 2595 8.808092 TGGGGATCGTAACAGAAATTTAAAATT 58.192 29.630 0.00 0.00 0.00 1.82
2483 2596 9.647797 GGGGATCGTAACAGAAATTTAAAATTT 57.352 29.630 0.00 0.00 0.00 1.82
2505 2618 5.697473 TTTTTACGCATCACCAAGATCAA 57.303 34.783 0.00 0.00 33.72 2.57
2506 2619 5.895636 TTTTACGCATCACCAAGATCAAT 57.104 34.783 0.00 0.00 33.72 2.57
2507 2620 5.484173 TTTACGCATCACCAAGATCAATC 57.516 39.130 0.00 0.00 33.72 2.67
2508 2621 3.272574 ACGCATCACCAAGATCAATCT 57.727 42.857 0.00 0.00 39.22 2.40
2509 2622 4.406648 ACGCATCACCAAGATCAATCTA 57.593 40.909 0.00 0.00 35.76 1.98
2510 2623 4.965814 ACGCATCACCAAGATCAATCTAT 58.034 39.130 0.00 0.00 35.76 1.98
2511 2624 4.753610 ACGCATCACCAAGATCAATCTATG 59.246 41.667 0.00 0.00 35.76 2.23
2512 2625 4.153655 CGCATCACCAAGATCAATCTATGG 59.846 45.833 14.46 14.46 39.18 2.74
2513 2626 5.311265 GCATCACCAAGATCAATCTATGGA 58.689 41.667 19.34 6.96 37.92 3.41
2514 2627 5.411977 GCATCACCAAGATCAATCTATGGAG 59.588 44.000 19.34 14.57 37.92 3.86
2515 2628 6.531923 CATCACCAAGATCAATCTATGGAGT 58.468 40.000 19.34 8.56 37.92 3.85
2516 2629 6.166984 TCACCAAGATCAATCTATGGAGTC 57.833 41.667 19.34 0.00 37.92 3.36
2517 2630 5.662657 TCACCAAGATCAATCTATGGAGTCA 59.337 40.000 19.34 3.88 37.92 3.41
2518 2631 6.328410 TCACCAAGATCAATCTATGGAGTCAT 59.672 38.462 19.34 0.00 37.92 3.06
2519 2632 6.649973 CACCAAGATCAATCTATGGAGTCATC 59.350 42.308 19.34 0.00 37.92 2.92
2520 2633 6.558014 ACCAAGATCAATCTATGGAGTCATCT 59.442 38.462 19.34 0.00 37.92 2.90
2521 2634 7.732140 ACCAAGATCAATCTATGGAGTCATCTA 59.268 37.037 19.34 0.00 37.92 1.98
2522 2635 8.252417 CCAAGATCAATCTATGGAGTCATCTAG 58.748 40.741 0.00 0.00 37.31 2.43
2523 2636 7.408756 AGATCAATCTATGGAGTCATCTAGC 57.591 40.000 0.00 0.00 34.85 3.42
2524 2637 6.952938 AGATCAATCTATGGAGTCATCTAGCA 59.047 38.462 0.00 0.00 34.85 3.49
2525 2638 6.983906 TCAATCTATGGAGTCATCTAGCAA 57.016 37.500 0.00 0.00 34.96 3.91
2526 2639 6.753180 TCAATCTATGGAGTCATCTAGCAAC 58.247 40.000 0.00 0.00 34.96 4.17
2527 2640 4.837896 TCTATGGAGTCATCTAGCAACG 57.162 45.455 0.00 0.00 34.96 4.10
2528 2641 4.461198 TCTATGGAGTCATCTAGCAACGA 58.539 43.478 0.00 0.00 34.96 3.85
2529 2642 3.724508 ATGGAGTCATCTAGCAACGAG 57.275 47.619 0.00 0.00 0.00 4.18
2530 2643 2.723273 TGGAGTCATCTAGCAACGAGA 58.277 47.619 0.00 0.00 0.00 4.04
2531 2644 2.685388 TGGAGTCATCTAGCAACGAGAG 59.315 50.000 0.00 0.00 0.00 3.20
2532 2645 2.946329 GGAGTCATCTAGCAACGAGAGA 59.054 50.000 0.00 0.00 0.00 3.10
2533 2646 3.568007 GGAGTCATCTAGCAACGAGAGAT 59.432 47.826 0.00 0.00 0.00 2.75
2534 2647 4.757657 GGAGTCATCTAGCAACGAGAGATA 59.242 45.833 0.00 0.00 0.00 1.98
2535 2648 5.106712 GGAGTCATCTAGCAACGAGAGATAG 60.107 48.000 0.00 0.00 0.00 2.08
2536 2649 4.759693 AGTCATCTAGCAACGAGAGATAGG 59.240 45.833 0.00 0.00 0.00 2.57
2537 2650 4.757657 GTCATCTAGCAACGAGAGATAGGA 59.242 45.833 0.00 0.00 0.00 2.94
2538 2651 5.000591 TCATCTAGCAACGAGAGATAGGAG 58.999 45.833 0.00 0.00 0.00 3.69
2539 2652 4.425180 TCTAGCAACGAGAGATAGGAGT 57.575 45.455 0.00 0.00 0.00 3.85
2540 2653 4.130857 TCTAGCAACGAGAGATAGGAGTG 58.869 47.826 0.00 0.00 0.00 3.51
2541 2654 1.407258 AGCAACGAGAGATAGGAGTGC 59.593 52.381 0.00 0.00 0.00 4.40
2542 2655 1.135139 GCAACGAGAGATAGGAGTGCA 59.865 52.381 0.00 0.00 0.00 4.57
2543 2656 2.223923 GCAACGAGAGATAGGAGTGCAT 60.224 50.000 0.00 0.00 0.00 3.96
2544 2657 3.637432 CAACGAGAGATAGGAGTGCATC 58.363 50.000 0.00 0.00 0.00 3.91
2545 2658 3.222173 ACGAGAGATAGGAGTGCATCT 57.778 47.619 0.00 0.00 34.19 2.90
2546 2659 4.359434 ACGAGAGATAGGAGTGCATCTA 57.641 45.455 0.00 0.00 31.63 1.98
2547 2660 4.069304 ACGAGAGATAGGAGTGCATCTAC 58.931 47.826 0.00 0.00 31.63 2.59
2548 2661 4.068599 CGAGAGATAGGAGTGCATCTACA 58.931 47.826 0.00 0.00 31.63 2.74
2549 2662 4.699735 CGAGAGATAGGAGTGCATCTACAT 59.300 45.833 0.00 0.00 31.63 2.29
2550 2663 5.877564 CGAGAGATAGGAGTGCATCTACATA 59.122 44.000 0.00 0.00 31.63 2.29
2551 2664 6.183360 CGAGAGATAGGAGTGCATCTACATAC 60.183 46.154 0.00 0.00 31.63 2.39
2552 2665 5.949354 AGAGATAGGAGTGCATCTACATACC 59.051 44.000 0.00 0.00 31.63 2.73
2553 2666 5.020132 AGATAGGAGTGCATCTACATACCC 58.980 45.833 0.00 0.00 29.66 3.69
2554 2667 3.336509 AGGAGTGCATCTACATACCCT 57.663 47.619 0.00 0.00 0.00 4.34
2555 2668 3.658725 AGGAGTGCATCTACATACCCTT 58.341 45.455 0.00 0.00 0.00 3.95
2556 2669 3.389329 AGGAGTGCATCTACATACCCTTG 59.611 47.826 0.00 0.00 0.00 3.61
2557 2670 3.134804 GGAGTGCATCTACATACCCTTGT 59.865 47.826 0.00 0.00 0.00 3.16
2558 2671 4.344102 GGAGTGCATCTACATACCCTTGTA 59.656 45.833 0.00 0.00 0.00 2.41
2559 2672 5.509840 GGAGTGCATCTACATACCCTTGTAG 60.510 48.000 5.47 5.47 46.85 2.74
2565 2678 2.795175 ACATACCCTTGTAGATCGCG 57.205 50.000 0.00 0.00 0.00 5.87
2566 2679 2.304092 ACATACCCTTGTAGATCGCGA 58.696 47.619 13.09 13.09 0.00 5.87
2567 2680 2.293677 ACATACCCTTGTAGATCGCGAG 59.706 50.000 16.66 0.00 0.00 5.03
2568 2681 0.666913 TACCCTTGTAGATCGCGAGC 59.333 55.000 18.21 18.21 0.00 5.03
2569 2682 1.658717 CCCTTGTAGATCGCGAGCG 60.659 63.158 19.77 11.64 41.35 5.03
2570 2683 1.658717 CCTTGTAGATCGCGAGCGG 60.659 63.158 19.77 9.89 40.25 5.52
2571 2684 1.355563 CTTGTAGATCGCGAGCGGA 59.644 57.895 19.77 8.43 40.25 5.54
2572 2685 0.248498 CTTGTAGATCGCGAGCGGAA 60.248 55.000 19.77 11.67 40.25 4.30
2573 2686 0.248498 TTGTAGATCGCGAGCGGAAG 60.248 55.000 19.77 0.00 40.25 3.46
2596 2709 3.638484 GTTCAAAAGAACGGGGTTGATG 58.362 45.455 0.00 0.00 30.51 3.07
2597 2710 2.235016 TCAAAAGAACGGGGTTGATGG 58.765 47.619 0.00 0.00 0.00 3.51
2598 2711 2.158593 TCAAAAGAACGGGGTTGATGGA 60.159 45.455 0.00 0.00 0.00 3.41
2599 2712 2.200373 AAAGAACGGGGTTGATGGAG 57.800 50.000 0.00 0.00 0.00 3.86
2600 2713 1.064825 AAGAACGGGGTTGATGGAGT 58.935 50.000 0.00 0.00 0.00 3.85
2601 2714 0.613777 AGAACGGGGTTGATGGAGTC 59.386 55.000 0.00 0.00 0.00 3.36
2602 2715 0.739813 GAACGGGGTTGATGGAGTCG 60.740 60.000 0.00 0.00 0.00 4.18
2603 2716 1.477685 AACGGGGTTGATGGAGTCGT 61.478 55.000 0.00 0.00 0.00 4.34
2604 2717 0.612732 ACGGGGTTGATGGAGTCGTA 60.613 55.000 0.00 0.00 0.00 3.43
2605 2718 0.179119 CGGGGTTGATGGAGTCGTAC 60.179 60.000 0.00 0.00 0.00 3.67
2606 2719 1.192428 GGGGTTGATGGAGTCGTACT 58.808 55.000 0.00 0.00 0.00 2.73
2607 2720 1.136500 GGGGTTGATGGAGTCGTACTC 59.864 57.143 6.50 6.50 44.32 2.59
2608 2721 1.202268 GGGTTGATGGAGTCGTACTCG 60.202 57.143 8.33 0.00 45.96 4.18
2609 2722 1.471684 GGTTGATGGAGTCGTACTCGT 59.528 52.381 8.33 1.85 45.96 4.18
2610 2723 2.477525 GGTTGATGGAGTCGTACTCGTC 60.478 54.545 8.33 9.13 45.96 4.20
2611 2724 1.004595 TGATGGAGTCGTACTCGTCG 58.995 55.000 8.33 0.00 45.96 5.12
2612 2725 1.005340 GATGGAGTCGTACTCGTCGT 58.995 55.000 8.33 0.00 45.96 4.34
2613 2726 0.725686 ATGGAGTCGTACTCGTCGTG 59.274 55.000 8.33 0.00 45.96 4.35
2614 2727 0.319813 TGGAGTCGTACTCGTCGTGA 60.320 55.000 0.56 0.00 45.96 4.35
2615 2728 1.005340 GGAGTCGTACTCGTCGTGAT 58.995 55.000 0.56 0.00 45.96 3.06
2616 2729 1.005137 GGAGTCGTACTCGTCGTGATC 60.005 57.143 0.56 0.00 45.96 2.92
2617 2730 1.005137 GAGTCGTACTCGTCGTGATCC 60.005 57.143 0.56 0.00 35.28 3.36
2618 2731 0.723414 GTCGTACTCGTCGTGATCCA 59.277 55.000 0.56 0.00 38.33 3.41
2619 2732 1.129251 GTCGTACTCGTCGTGATCCAA 59.871 52.381 0.56 0.00 38.33 3.53
2620 2733 1.805943 TCGTACTCGTCGTGATCCAAA 59.194 47.619 0.56 0.00 38.33 3.28
2621 2734 2.421073 TCGTACTCGTCGTGATCCAAAT 59.579 45.455 0.56 0.00 38.33 2.32
2622 2735 2.782192 CGTACTCGTCGTGATCCAAATC 59.218 50.000 0.56 0.00 0.00 2.17
2623 2736 3.729762 CGTACTCGTCGTGATCCAAATCA 60.730 47.826 0.56 0.00 39.63 2.57
2624 2737 7.861595 TCGTACTCGTCGTGATCCAAATCAC 62.862 48.000 8.20 8.20 45.52 3.06
2633 2746 3.743521 TGATCCAAATCACCGATGATCC 58.256 45.455 0.00 0.00 45.26 3.36
2634 2747 3.392285 TGATCCAAATCACCGATGATCCT 59.608 43.478 0.00 0.00 45.26 3.24
2635 2748 4.592778 TGATCCAAATCACCGATGATCCTA 59.407 41.667 0.00 0.00 45.26 2.94
2636 2749 4.607293 TCCAAATCACCGATGATCCTAG 57.393 45.455 0.00 0.00 45.26 3.02
2637 2750 3.070018 CCAAATCACCGATGATCCTAGC 58.930 50.000 0.00 0.00 45.26 3.42
2638 2751 2.732412 AATCACCGATGATCCTAGCG 57.268 50.000 0.00 0.00 45.26 4.26
2639 2752 0.244994 ATCACCGATGATCCTAGCGC 59.755 55.000 0.00 0.00 42.15 5.92
2640 2753 1.373497 CACCGATGATCCTAGCGCC 60.373 63.158 2.29 0.00 0.00 6.53
2641 2754 2.126307 CCGATGATCCTAGCGCCG 60.126 66.667 2.29 0.00 0.00 6.46
2642 2755 2.626780 CCGATGATCCTAGCGCCGA 61.627 63.158 2.29 0.00 0.00 5.54
2643 2756 1.285950 CGATGATCCTAGCGCCGAA 59.714 57.895 2.29 0.00 0.00 4.30
2644 2757 1.004277 CGATGATCCTAGCGCCGAAC 61.004 60.000 2.29 0.00 0.00 3.95
2646 2759 2.354773 GATCCTAGCGCCGAACGG 60.355 66.667 2.29 9.00 43.93 4.44
2647 2760 2.831742 ATCCTAGCGCCGAACGGA 60.832 61.111 17.63 3.21 43.93 4.69
2648 2761 3.135056 ATCCTAGCGCCGAACGGAC 62.135 63.158 17.63 7.92 43.93 4.79
2658 2771 3.998672 GAACGGACGGCACCTCCA 61.999 66.667 0.00 0.00 34.01 3.86
2659 2772 4.309950 AACGGACGGCACCTCCAC 62.310 66.667 0.00 0.00 34.01 4.02
2662 2775 4.309950 GGACGGCACCTCCACGTT 62.310 66.667 0.00 0.00 41.40 3.99
2663 2776 2.737376 GACGGCACCTCCACGTTC 60.737 66.667 0.00 0.00 41.40 3.95
2664 2777 3.509137 GACGGCACCTCCACGTTCA 62.509 63.158 0.00 0.00 41.40 3.18
2665 2778 2.280524 CGGCACCTCCACGTTCAA 60.281 61.111 0.00 0.00 34.01 2.69
2666 2779 2.604174 CGGCACCTCCACGTTCAAC 61.604 63.158 0.00 0.00 34.01 3.18
2667 2780 1.525077 GGCACCTCCACGTTCAACA 60.525 57.895 0.00 0.00 34.01 3.33
2668 2781 1.647084 GCACCTCCACGTTCAACAC 59.353 57.895 0.00 0.00 0.00 3.32
2669 2782 1.092921 GCACCTCCACGTTCAACACA 61.093 55.000 0.00 0.00 0.00 3.72
2670 2783 0.655733 CACCTCCACGTTCAACACAC 59.344 55.000 0.00 0.00 0.00 3.82
2671 2784 0.808453 ACCTCCACGTTCAACACACG 60.808 55.000 0.00 0.00 43.52 4.49
2677 2790 2.870690 CGTTCAACACACGTACGGA 58.129 52.632 21.06 2.65 32.80 4.69
2678 2791 0.774098 CGTTCAACACACGTACGGAG 59.226 55.000 21.06 14.04 32.80 4.63
2679 2792 0.505655 GTTCAACACACGTACGGAGC 59.494 55.000 21.06 4.18 0.00 4.70
2680 2793 0.935831 TTCAACACACGTACGGAGCG 60.936 55.000 21.06 8.27 0.00 5.03
2681 2794 2.049802 AACACACGTACGGAGCGG 60.050 61.111 21.06 9.93 0.00 5.52
2682 2795 2.554636 AACACACGTACGGAGCGGA 61.555 57.895 21.06 0.00 0.00 5.54
2683 2796 2.202440 CACACGTACGGAGCGGAG 60.202 66.667 21.06 2.79 0.00 4.63
2684 2797 2.359107 ACACGTACGGAGCGGAGA 60.359 61.111 21.06 0.00 0.00 3.71
2685 2798 2.099831 CACGTACGGAGCGGAGAC 59.900 66.667 21.06 0.00 0.00 3.36
2700 2813 2.931512 GAGACGTCTCCTCCTTCTTG 57.068 55.000 31.24 0.00 37.02 3.02
2701 2814 2.438411 GAGACGTCTCCTCCTTCTTGA 58.562 52.381 31.24 0.00 37.02 3.02
2702 2815 3.020984 GAGACGTCTCCTCCTTCTTGAT 58.979 50.000 31.24 0.00 37.02 2.57
2703 2816 3.020984 AGACGTCTCCTCCTTCTTGATC 58.979 50.000 13.58 0.00 0.00 2.92
2704 2817 2.100087 GACGTCTCCTCCTTCTTGATCC 59.900 54.545 8.70 0.00 0.00 3.36
2705 2818 2.103373 CGTCTCCTCCTTCTTGATCCA 58.897 52.381 0.00 0.00 0.00 3.41
2706 2819 2.100584 CGTCTCCTCCTTCTTGATCCAG 59.899 54.545 0.00 0.00 0.00 3.86
2707 2820 2.114616 TCTCCTCCTTCTTGATCCAGC 58.885 52.381 0.00 0.00 0.00 4.85
2708 2821 1.836166 CTCCTCCTTCTTGATCCAGCA 59.164 52.381 0.00 0.00 0.00 4.41
2709 2822 2.238144 CTCCTCCTTCTTGATCCAGCAA 59.762 50.000 0.00 0.00 0.00 3.91
2710 2823 2.238144 TCCTCCTTCTTGATCCAGCAAG 59.762 50.000 0.00 0.00 45.10 4.01
2711 2824 2.641305 CTCCTTCTTGATCCAGCAAGG 58.359 52.381 14.03 14.03 44.14 3.61
2712 2825 1.283029 TCCTTCTTGATCCAGCAAGGG 59.717 52.381 17.39 0.00 44.14 3.95
2713 2826 1.684248 CCTTCTTGATCCAGCAAGGGG 60.684 57.143 4.79 4.42 44.14 4.79
2714 2827 0.332632 TTCTTGATCCAGCAAGGGGG 59.667 55.000 4.79 0.00 44.14 5.40
2715 2828 0.549902 TCTTGATCCAGCAAGGGGGA 60.550 55.000 4.79 0.00 44.14 4.81
2716 2829 0.332632 CTTGATCCAGCAAGGGGGAA 59.667 55.000 0.00 0.00 41.15 3.97
2717 2830 0.332632 TTGATCCAGCAAGGGGGAAG 59.667 55.000 0.00 0.00 36.62 3.46
2718 2831 0.846427 TGATCCAGCAAGGGGGAAGT 60.846 55.000 0.00 0.00 36.62 3.01
2719 2832 1.213296 GATCCAGCAAGGGGGAAGTA 58.787 55.000 0.00 0.00 36.62 2.24
2720 2833 1.141858 GATCCAGCAAGGGGGAAGTAG 59.858 57.143 0.00 0.00 36.62 2.57
2721 2834 0.118346 TCCAGCAAGGGGGAAGTAGA 59.882 55.000 0.00 0.00 38.24 2.59
2722 2835 0.991920 CCAGCAAGGGGGAAGTAGAA 59.008 55.000 0.00 0.00 0.00 2.10
2723 2836 1.065126 CCAGCAAGGGGGAAGTAGAAG 60.065 57.143 0.00 0.00 0.00 2.85
2724 2837 1.630878 CAGCAAGGGGGAAGTAGAAGT 59.369 52.381 0.00 0.00 0.00 3.01
2725 2838 2.040412 CAGCAAGGGGGAAGTAGAAGTT 59.960 50.000 0.00 0.00 0.00 2.66
2726 2839 2.040412 AGCAAGGGGGAAGTAGAAGTTG 59.960 50.000 0.00 0.00 0.00 3.16
2727 2840 2.039879 GCAAGGGGGAAGTAGAAGTTGA 59.960 50.000 0.00 0.00 0.00 3.18
2728 2841 3.308473 GCAAGGGGGAAGTAGAAGTTGAT 60.308 47.826 0.00 0.00 0.00 2.57
2729 2842 4.811063 GCAAGGGGGAAGTAGAAGTTGATT 60.811 45.833 0.00 0.00 0.00 2.57
2730 2843 4.576330 AGGGGGAAGTAGAAGTTGATTG 57.424 45.455 0.00 0.00 0.00 2.67
2731 2844 4.175962 AGGGGGAAGTAGAAGTTGATTGA 58.824 43.478 0.00 0.00 0.00 2.57
2732 2845 4.226168 AGGGGGAAGTAGAAGTTGATTGAG 59.774 45.833 0.00 0.00 0.00 3.02
2733 2846 4.225267 GGGGGAAGTAGAAGTTGATTGAGA 59.775 45.833 0.00 0.00 0.00 3.27
2734 2847 5.104318 GGGGGAAGTAGAAGTTGATTGAGAT 60.104 44.000 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 107 9.007901 TCAGAAAATGTTTGTGGTTTCAAAATT 57.992 25.926 0.00 0.00 38.71 1.82
341 349 0.394899 GCTTGGGACTGAGAATGGGG 60.395 60.000 0.00 0.00 0.00 4.96
366 376 1.920351 GTAGGGGTTTGGAGATTGGGA 59.080 52.381 0.00 0.00 0.00 4.37
372 382 1.554822 CCAGAGGTAGGGGTTTGGAGA 60.555 57.143 0.00 0.00 0.00 3.71
485 496 4.101585 AGGAAATGGTGAGCTCGAATGATA 59.898 41.667 9.64 0.00 0.00 2.15
486 497 3.118112 AGGAAATGGTGAGCTCGAATGAT 60.118 43.478 9.64 0.00 0.00 2.45
510 521 8.750416 CACGAGAACTTATCTGAATAATGTGAG 58.250 37.037 0.00 0.00 38.96 3.51
519 530 3.258372 AGCACCACGAGAACTTATCTGAA 59.742 43.478 0.00 0.00 38.96 3.02
529 540 2.021722 GCAAACAGCACCACGAGAA 58.978 52.632 0.00 0.00 44.79 2.87
732 752 0.530744 TTGACGAAGATCGGGTCCAG 59.469 55.000 4.66 0.00 45.59 3.86
741 761 1.079127 CGTGGGCCTTGACGAAGAT 60.079 57.895 14.82 0.00 37.81 2.40
874 894 4.459089 GCACTCTCAGGTCGGGGC 62.459 72.222 0.00 0.00 0.00 5.80
992 1012 1.473965 CGGCATACTTCATGGAGCTGT 60.474 52.381 0.00 0.00 34.97 4.40
993 1013 1.224075 CGGCATACTTCATGGAGCTG 58.776 55.000 0.00 0.03 34.97 4.24
994 1014 0.107456 CCGGCATACTTCATGGAGCT 59.893 55.000 0.00 0.00 34.97 4.09
1011 1039 3.548818 CCTTTCTTGTCTTCAGCAAACCG 60.549 47.826 0.00 0.00 0.00 4.44
1044 1072 3.049912 GACTTTCCCAAAAACGCATGAC 58.950 45.455 0.00 0.00 0.00 3.06
1134 1162 0.528017 TGAGAGTCATGACCTCGCAC 59.472 55.000 25.94 17.63 33.91 5.34
1197 1225 1.693083 GATCGGAAAAGACACGGCCG 61.693 60.000 26.86 26.86 43.11 6.13
1311 1345 5.118990 GTCTTCAGGTTGAATGCAGCTATA 58.881 41.667 0.00 0.00 35.59 1.31
1330 1364 2.636830 CGGCATCCATTCTTCTGTCTT 58.363 47.619 0.00 0.00 0.00 3.01
1367 1401 4.208047 CGTCATATAAGCTGCTGACTTGTC 59.792 45.833 1.35 0.00 36.67 3.18
1428 1462 0.809636 TATGATGAACCTGCGCCACG 60.810 55.000 4.18 0.00 0.00 4.94
1608 1684 5.692115 TTGGATCATAAACCTGTAGCAGA 57.308 39.130 0.00 0.00 32.44 4.26
1691 1767 4.161189 CCTCTTGACTCAGCAGATTTCCTA 59.839 45.833 0.00 0.00 0.00 2.94
1717 1793 1.212935 ACCTCAGCAGTGAAAACCTGT 59.787 47.619 0.00 0.00 30.14 4.00
1718 1794 1.605710 CACCTCAGCAGTGAAAACCTG 59.394 52.381 0.00 0.00 37.42 4.00
1719 1795 1.490490 TCACCTCAGCAGTGAAAACCT 59.510 47.619 0.00 0.00 41.17 3.50
1775 1852 4.462483 TGGCTGAACTCATTTTTATGGTCC 59.538 41.667 0.00 0.00 0.00 4.46
1793 1876 0.390866 ATGACGCTCAGAACTGGCTG 60.391 55.000 1.93 0.00 37.24 4.85
1804 1887 3.179443 TGGGTATTGAGAATGACGCTC 57.821 47.619 0.00 0.00 0.00 5.03
1842 1933 5.278071 CGGCATTACCAAGTCAAGTTTAACA 60.278 40.000 0.00 0.00 39.03 2.41
1917 2009 7.765695 ACCAACATTCAACTAGATGTCATTT 57.234 32.000 0.00 0.00 0.00 2.32
2167 2269 7.716998 ACAGCCCTCATAGTTTACATTAATCTG 59.283 37.037 0.00 0.00 0.00 2.90
2182 2284 6.480763 TCAAAATAACAGAACAGCCCTCATA 58.519 36.000 0.00 0.00 0.00 2.15
2183 2285 5.324409 TCAAAATAACAGAACAGCCCTCAT 58.676 37.500 0.00 0.00 0.00 2.90
2185 2287 5.904362 ATCAAAATAACAGAACAGCCCTC 57.096 39.130 0.00 0.00 0.00 4.30
2192 2294 9.914131 AAGCCTTAAGAATCAAAATAACAGAAC 57.086 29.630 3.36 0.00 0.00 3.01
2380 2493 5.106157 GCATGCCTTGTTGTTGTTAGACTAT 60.106 40.000 6.36 0.00 0.00 2.12
2381 2494 4.215399 GCATGCCTTGTTGTTGTTAGACTA 59.785 41.667 6.36 0.00 0.00 2.59
2382 2495 3.004734 GCATGCCTTGTTGTTGTTAGACT 59.995 43.478 6.36 0.00 0.00 3.24
2383 2496 3.243367 TGCATGCCTTGTTGTTGTTAGAC 60.243 43.478 16.68 0.00 0.00 2.59
2384 2497 2.954989 TGCATGCCTTGTTGTTGTTAGA 59.045 40.909 16.68 0.00 0.00 2.10
2385 2498 3.367992 TGCATGCCTTGTTGTTGTTAG 57.632 42.857 16.68 0.00 0.00 2.34
2386 2499 4.764308 TCTATGCATGCCTTGTTGTTGTTA 59.236 37.500 16.68 0.00 0.00 2.41
2387 2500 2.914695 ATGCATGCCTTGTTGTTGTT 57.085 40.000 16.68 0.00 0.00 2.83
2388 2501 3.156293 TCTATGCATGCCTTGTTGTTGT 58.844 40.909 16.68 0.00 0.00 3.32
2389 2502 3.853831 TCTATGCATGCCTTGTTGTTG 57.146 42.857 16.68 0.00 0.00 3.33
2454 2567 5.638596 AAATTTCTGTTACGATCCCCAAC 57.361 39.130 0.00 0.00 0.00 3.77
2455 2568 7.762588 TTTAAATTTCTGTTACGATCCCCAA 57.237 32.000 0.00 0.00 0.00 4.12
2456 2569 7.762588 TTTTAAATTTCTGTTACGATCCCCA 57.237 32.000 0.00 0.00 0.00 4.96
2457 2570 9.647797 AAATTTTAAATTTCTGTTACGATCCCC 57.352 29.630 9.58 0.00 0.00 4.81
2483 2596 5.697473 TTGATCTTGGTGATGCGTAAAAA 57.303 34.783 0.00 0.00 35.14 1.94
2484 2597 5.647658 AGATTGATCTTGGTGATGCGTAAAA 59.352 36.000 0.00 0.00 35.14 1.52
2485 2598 5.185454 AGATTGATCTTGGTGATGCGTAAA 58.815 37.500 0.00 0.00 35.14 2.01
2486 2599 4.769688 AGATTGATCTTGGTGATGCGTAA 58.230 39.130 0.00 0.00 35.14 3.18
2487 2600 4.406648 AGATTGATCTTGGTGATGCGTA 57.593 40.909 0.00 0.00 35.14 4.42
2488 2601 3.272574 AGATTGATCTTGGTGATGCGT 57.727 42.857 0.00 0.00 35.14 5.24
2489 2602 4.153655 CCATAGATTGATCTTGGTGATGCG 59.846 45.833 0.00 0.00 38.32 4.73
2490 2603 5.311265 TCCATAGATTGATCTTGGTGATGC 58.689 41.667 15.48 0.00 38.32 3.91
2491 2604 6.531923 ACTCCATAGATTGATCTTGGTGATG 58.468 40.000 19.38 10.22 38.32 3.07
2492 2605 6.328410 TGACTCCATAGATTGATCTTGGTGAT 59.672 38.462 19.38 10.95 38.32 3.06
2493 2606 5.662657 TGACTCCATAGATTGATCTTGGTGA 59.337 40.000 19.38 6.63 38.32 4.02
2494 2607 5.922053 TGACTCCATAGATTGATCTTGGTG 58.078 41.667 15.48 15.28 38.32 4.17
2495 2608 6.558014 AGATGACTCCATAGATTGATCTTGGT 59.442 38.462 15.48 4.75 38.32 3.67
2496 2609 7.006865 AGATGACTCCATAGATTGATCTTGG 57.993 40.000 0.00 7.19 38.32 3.61
2497 2610 7.760794 GCTAGATGACTCCATAGATTGATCTTG 59.239 40.741 0.00 0.00 38.32 3.02
2498 2611 7.454066 TGCTAGATGACTCCATAGATTGATCTT 59.546 37.037 0.00 0.00 38.32 2.40
2499 2612 6.952938 TGCTAGATGACTCCATAGATTGATCT 59.047 38.462 0.00 0.00 40.86 2.75
2500 2613 7.167924 TGCTAGATGACTCCATAGATTGATC 57.832 40.000 0.00 0.00 32.09 2.92
2501 2614 7.385267 GTTGCTAGATGACTCCATAGATTGAT 58.615 38.462 0.00 0.00 32.09 2.57
2502 2615 6.515696 CGTTGCTAGATGACTCCATAGATTGA 60.516 42.308 0.00 0.00 32.09 2.57
2503 2616 5.632764 CGTTGCTAGATGACTCCATAGATTG 59.367 44.000 0.00 0.00 32.09 2.67
2504 2617 5.536538 TCGTTGCTAGATGACTCCATAGATT 59.463 40.000 0.00 0.00 32.09 2.40
2505 2618 5.073428 TCGTTGCTAGATGACTCCATAGAT 58.927 41.667 0.00 0.00 32.09 1.98
2506 2619 4.461198 TCGTTGCTAGATGACTCCATAGA 58.539 43.478 0.00 0.00 32.09 1.98
2507 2620 4.517075 TCTCGTTGCTAGATGACTCCATAG 59.483 45.833 0.00 0.00 32.09 2.23
2508 2621 4.461198 TCTCGTTGCTAGATGACTCCATA 58.539 43.478 0.00 0.00 32.09 2.74
2509 2622 3.291584 TCTCGTTGCTAGATGACTCCAT 58.708 45.455 0.00 0.00 35.29 3.41
2510 2623 2.685388 CTCTCGTTGCTAGATGACTCCA 59.315 50.000 0.00 0.00 0.00 3.86
2511 2624 2.946329 TCTCTCGTTGCTAGATGACTCC 59.054 50.000 0.00 0.00 0.00 3.85
2512 2625 4.829064 ATCTCTCGTTGCTAGATGACTC 57.171 45.455 0.00 0.00 0.00 3.36
2513 2626 4.759693 CCTATCTCTCGTTGCTAGATGACT 59.240 45.833 0.00 0.00 32.39 3.41
2514 2627 4.757657 TCCTATCTCTCGTTGCTAGATGAC 59.242 45.833 0.00 0.00 32.39 3.06
2515 2628 4.974399 TCCTATCTCTCGTTGCTAGATGA 58.026 43.478 0.00 0.00 32.39 2.92
2516 2629 4.759693 ACTCCTATCTCTCGTTGCTAGATG 59.240 45.833 0.00 0.00 32.39 2.90
2517 2630 4.759693 CACTCCTATCTCTCGTTGCTAGAT 59.240 45.833 0.00 0.00 34.44 1.98
2518 2631 4.130857 CACTCCTATCTCTCGTTGCTAGA 58.869 47.826 0.00 0.00 0.00 2.43
2519 2632 3.304391 GCACTCCTATCTCTCGTTGCTAG 60.304 52.174 0.00 0.00 0.00 3.42
2520 2633 2.619177 GCACTCCTATCTCTCGTTGCTA 59.381 50.000 0.00 0.00 0.00 3.49
2521 2634 1.407258 GCACTCCTATCTCTCGTTGCT 59.593 52.381 0.00 0.00 0.00 3.91
2522 2635 1.135139 TGCACTCCTATCTCTCGTTGC 59.865 52.381 0.00 0.00 0.00 4.17
2523 2636 3.317711 AGATGCACTCCTATCTCTCGTTG 59.682 47.826 0.00 0.00 0.00 4.10
2524 2637 3.561143 AGATGCACTCCTATCTCTCGTT 58.439 45.455 0.00 0.00 0.00 3.85
2525 2638 3.222173 AGATGCACTCCTATCTCTCGT 57.778 47.619 0.00 0.00 0.00 4.18
2526 2639 4.068599 TGTAGATGCACTCCTATCTCTCG 58.931 47.826 0.00 0.00 35.42 4.04
2527 2640 6.094881 GGTATGTAGATGCACTCCTATCTCTC 59.905 46.154 0.00 0.00 35.42 3.20
2528 2641 5.949354 GGTATGTAGATGCACTCCTATCTCT 59.051 44.000 0.00 0.00 35.42 3.10
2529 2642 5.126384 GGGTATGTAGATGCACTCCTATCTC 59.874 48.000 0.00 0.00 35.42 2.75
2530 2643 5.020132 GGGTATGTAGATGCACTCCTATCT 58.980 45.833 0.00 0.00 37.42 1.98
2531 2644 5.020132 AGGGTATGTAGATGCACTCCTATC 58.980 45.833 0.00 0.00 0.00 2.08
2532 2645 5.017093 AGGGTATGTAGATGCACTCCTAT 57.983 43.478 0.00 0.00 0.00 2.57
2533 2646 4.471078 AGGGTATGTAGATGCACTCCTA 57.529 45.455 0.00 0.00 0.00 2.94
2534 2647 3.336509 AGGGTATGTAGATGCACTCCT 57.663 47.619 0.00 0.00 0.00 3.69
2535 2648 3.134804 ACAAGGGTATGTAGATGCACTCC 59.865 47.826 0.00 0.00 25.83 3.85
2536 2649 4.408182 ACAAGGGTATGTAGATGCACTC 57.592 45.455 0.00 0.00 25.83 3.51
2545 2658 3.479489 TCGCGATCTACAAGGGTATGTA 58.521 45.455 3.71 0.00 34.75 2.29
2546 2659 2.293677 CTCGCGATCTACAAGGGTATGT 59.706 50.000 10.36 0.00 37.32 2.29
2547 2660 2.922758 GCTCGCGATCTACAAGGGTATG 60.923 54.545 10.36 0.00 0.00 2.39
2548 2661 1.269998 GCTCGCGATCTACAAGGGTAT 59.730 52.381 10.36 0.00 0.00 2.73
2549 2662 0.666913 GCTCGCGATCTACAAGGGTA 59.333 55.000 10.36 0.00 0.00 3.69
2550 2663 1.437986 GCTCGCGATCTACAAGGGT 59.562 57.895 10.36 0.00 0.00 4.34
2551 2664 1.658717 CGCTCGCGATCTACAAGGG 60.659 63.158 10.36 0.00 42.83 3.95
2552 2665 1.658717 CCGCTCGCGATCTACAAGG 60.659 63.158 10.36 0.00 42.83 3.61
2553 2666 0.248498 TTCCGCTCGCGATCTACAAG 60.248 55.000 10.36 0.00 42.83 3.16
2554 2667 0.248498 CTTCCGCTCGCGATCTACAA 60.248 55.000 10.36 0.00 42.83 2.41
2555 2668 1.355563 CTTCCGCTCGCGATCTACA 59.644 57.895 10.36 0.00 42.83 2.74
2556 2669 2.011881 GCTTCCGCTCGCGATCTAC 61.012 63.158 10.36 0.00 42.83 2.59
2557 2670 2.331805 GCTTCCGCTCGCGATCTA 59.668 61.111 10.36 0.00 42.83 1.98
2563 2676 2.438385 TTTTGAACGCTTCCGCTCGC 62.438 55.000 0.00 0.00 38.22 5.03
2564 2677 0.451135 CTTTTGAACGCTTCCGCTCG 60.451 55.000 0.00 0.00 38.22 5.03
2565 2678 0.865769 TCTTTTGAACGCTTCCGCTC 59.134 50.000 0.00 0.00 38.22 5.03
2566 2679 1.305201 TTCTTTTGAACGCTTCCGCT 58.695 45.000 0.00 0.00 38.22 5.52
2567 2680 3.837669 TTCTTTTGAACGCTTCCGC 57.162 47.368 0.00 0.00 38.22 5.54
2576 2689 2.625790 CCATCAACCCCGTTCTTTTGAA 59.374 45.455 0.00 0.00 31.96 2.69
2577 2690 2.158593 TCCATCAACCCCGTTCTTTTGA 60.159 45.455 0.00 0.00 32.71 2.69
2578 2691 2.228822 CTCCATCAACCCCGTTCTTTTG 59.771 50.000 0.00 0.00 0.00 2.44
2579 2692 2.158519 ACTCCATCAACCCCGTTCTTTT 60.159 45.455 0.00 0.00 0.00 2.27
2580 2693 1.423921 ACTCCATCAACCCCGTTCTTT 59.576 47.619 0.00 0.00 0.00 2.52
2581 2694 1.003233 GACTCCATCAACCCCGTTCTT 59.997 52.381 0.00 0.00 0.00 2.52
2582 2695 0.613777 GACTCCATCAACCCCGTTCT 59.386 55.000 0.00 0.00 0.00 3.01
2583 2696 0.739813 CGACTCCATCAACCCCGTTC 60.740 60.000 0.00 0.00 0.00 3.95
2584 2697 1.295423 CGACTCCATCAACCCCGTT 59.705 57.895 0.00 0.00 0.00 4.44
2585 2698 0.612732 TACGACTCCATCAACCCCGT 60.613 55.000 0.00 0.00 0.00 5.28
2586 2699 0.179119 GTACGACTCCATCAACCCCG 60.179 60.000 0.00 0.00 0.00 5.73
2587 2700 1.136500 GAGTACGACTCCATCAACCCC 59.864 57.143 0.00 0.00 39.28 4.95
2588 2701 1.202268 CGAGTACGACTCCATCAACCC 60.202 57.143 8.73 0.00 42.12 4.11
2589 2702 1.471684 ACGAGTACGACTCCATCAACC 59.528 52.381 8.73 0.00 42.12 3.77
2590 2703 2.783333 GACGAGTACGACTCCATCAAC 58.217 52.381 8.73 0.00 42.12 3.18
2591 2704 1.395954 CGACGAGTACGACTCCATCAA 59.604 52.381 8.73 0.00 42.12 2.57
2592 2705 1.004595 CGACGAGTACGACTCCATCA 58.995 55.000 8.73 0.00 42.12 3.07
2593 2706 1.005340 ACGACGAGTACGACTCCATC 58.995 55.000 0.00 6.63 42.12 3.51
2594 2707 0.725686 CACGACGAGTACGACTCCAT 59.274 55.000 0.00 0.00 42.12 3.41
2595 2708 0.319813 TCACGACGAGTACGACTCCA 60.320 55.000 0.00 0.00 42.12 3.86
2596 2709 1.005137 GATCACGACGAGTACGACTCC 60.005 57.143 0.00 0.00 42.12 3.85
2597 2710 1.005137 GGATCACGACGAGTACGACTC 60.005 57.143 0.00 0.00 41.71 3.36
2598 2711 1.005340 GGATCACGACGAGTACGACT 58.995 55.000 0.00 0.00 42.66 4.18
2599 2712 0.723414 TGGATCACGACGAGTACGAC 59.277 55.000 0.00 0.00 42.66 4.34
2600 2713 1.441738 TTGGATCACGACGAGTACGA 58.558 50.000 0.00 0.00 42.66 3.43
2601 2714 2.251869 TTTGGATCACGACGAGTACG 57.748 50.000 0.00 0.00 45.75 3.67
2602 2715 3.766151 TGATTTGGATCACGACGAGTAC 58.234 45.455 0.00 0.00 37.37 2.73
2612 2725 3.392285 AGGATCATCGGTGATTTGGATCA 59.608 43.478 13.46 0.00 44.96 2.92
2613 2726 4.013267 AGGATCATCGGTGATTTGGATC 57.987 45.455 13.46 0.00 44.96 3.36
2614 2727 4.564406 GCTAGGATCATCGGTGATTTGGAT 60.564 45.833 13.46 0.35 44.96 3.41
2615 2728 3.244215 GCTAGGATCATCGGTGATTTGGA 60.244 47.826 13.46 0.00 44.96 3.53
2616 2729 3.070018 GCTAGGATCATCGGTGATTTGG 58.930 50.000 13.46 7.76 44.96 3.28
2617 2730 2.733552 CGCTAGGATCATCGGTGATTTG 59.266 50.000 13.46 4.89 44.96 2.32
2618 2731 2.868044 GCGCTAGGATCATCGGTGATTT 60.868 50.000 13.46 7.21 44.96 2.17
2619 2732 1.337260 GCGCTAGGATCATCGGTGATT 60.337 52.381 13.46 0.00 44.96 2.57
2621 2734 1.660355 GCGCTAGGATCATCGGTGA 59.340 57.895 0.00 0.00 39.04 4.02
2622 2735 1.373497 GGCGCTAGGATCATCGGTG 60.373 63.158 7.64 0.00 0.00 4.94
2623 2736 2.920645 CGGCGCTAGGATCATCGGT 61.921 63.158 7.64 0.00 0.00 4.69
2624 2737 2.126307 CGGCGCTAGGATCATCGG 60.126 66.667 7.64 0.00 0.00 4.18
2625 2738 1.004277 GTTCGGCGCTAGGATCATCG 61.004 60.000 7.64 0.00 0.00 3.84
2626 2739 1.004277 CGTTCGGCGCTAGGATCATC 61.004 60.000 7.64 0.00 0.00 2.92
2627 2740 1.007271 CGTTCGGCGCTAGGATCAT 60.007 57.895 7.64 0.00 0.00 2.45
2628 2741 2.411701 CGTTCGGCGCTAGGATCA 59.588 61.111 7.64 0.00 0.00 2.92
2629 2742 2.354773 CCGTTCGGCGCTAGGATC 60.355 66.667 7.64 1.16 39.71 3.36
2630 2743 2.831742 TCCGTTCGGCGCTAGGAT 60.832 61.111 7.64 0.00 39.71 3.24
2631 2744 3.818787 GTCCGTTCGGCGCTAGGA 61.819 66.667 7.64 7.54 39.71 2.94
2641 2754 3.998672 TGGAGGTGCCGTCCGTTC 61.999 66.667 8.70 0.00 40.66 3.95
2642 2755 4.309950 GTGGAGGTGCCGTCCGTT 62.310 66.667 8.70 0.00 40.66 4.44
2645 2758 4.309950 AACGTGGAGGTGCCGTCC 62.310 66.667 0.00 6.90 40.66 4.79
2646 2759 2.737376 GAACGTGGAGGTGCCGTC 60.737 66.667 0.00 0.00 40.66 4.79
2647 2760 3.096633 TTGAACGTGGAGGTGCCGT 62.097 57.895 0.00 0.00 40.66 5.68
2648 2761 2.280524 TTGAACGTGGAGGTGCCG 60.281 61.111 0.00 0.00 40.66 5.69
2649 2762 1.525077 TGTTGAACGTGGAGGTGCC 60.525 57.895 0.00 0.00 37.10 5.01
2650 2763 1.092921 TGTGTTGAACGTGGAGGTGC 61.093 55.000 0.00 0.00 0.00 5.01
2651 2764 0.655733 GTGTGTTGAACGTGGAGGTG 59.344 55.000 0.00 0.00 0.00 4.00
2652 2765 0.808453 CGTGTGTTGAACGTGGAGGT 60.808 55.000 0.00 0.00 36.31 3.85
2653 2766 1.931551 CGTGTGTTGAACGTGGAGG 59.068 57.895 0.00 0.00 36.31 4.30
2659 2772 0.774098 CTCCGTACGTGTGTTGAACG 59.226 55.000 15.21 0.00 46.32 3.95
2660 2773 0.505655 GCTCCGTACGTGTGTTGAAC 59.494 55.000 15.21 0.00 0.00 3.18
2661 2774 0.935831 CGCTCCGTACGTGTGTTGAA 60.936 55.000 15.21 0.00 0.00 2.69
2662 2775 1.370778 CGCTCCGTACGTGTGTTGA 60.371 57.895 15.21 1.92 0.00 3.18
2663 2776 2.369629 CCGCTCCGTACGTGTGTTG 61.370 63.158 15.21 0.00 0.00 3.33
2664 2777 2.049802 CCGCTCCGTACGTGTGTT 60.050 61.111 15.21 0.00 0.00 3.32
2665 2778 2.974489 CTCCGCTCCGTACGTGTGT 61.974 63.158 15.21 0.00 0.00 3.72
2666 2779 2.202440 CTCCGCTCCGTACGTGTG 60.202 66.667 15.21 12.57 0.00 3.82
2667 2780 2.359107 TCTCCGCTCCGTACGTGT 60.359 61.111 15.21 0.00 0.00 4.49
2668 2781 2.099831 GTCTCCGCTCCGTACGTG 59.900 66.667 15.21 7.80 0.00 4.49
2669 2782 3.494336 CGTCTCCGCTCCGTACGT 61.494 66.667 15.21 0.00 0.00 3.57
2670 2783 3.431683 GACGTCTCCGCTCCGTACG 62.432 68.421 8.69 8.69 39.37 3.67
2671 2784 2.034472 GAGACGTCTCCGCTCCGTAC 62.034 65.000 31.24 6.08 37.02 3.67
2672 2785 1.812922 GAGACGTCTCCGCTCCGTA 60.813 63.158 31.24 0.00 37.02 4.02
2673 2786 3.126225 GAGACGTCTCCGCTCCGT 61.126 66.667 31.24 0.55 37.02 4.69
2681 2794 2.438411 TCAAGAAGGAGGAGACGTCTC 58.562 52.381 32.96 32.96 42.14 3.36
2682 2795 2.588464 TCAAGAAGGAGGAGACGTCT 57.412 50.000 20.18 20.18 0.00 4.18
2683 2796 2.100087 GGATCAAGAAGGAGGAGACGTC 59.900 54.545 7.70 7.70 0.00 4.34
2684 2797 2.104170 GGATCAAGAAGGAGGAGACGT 58.896 52.381 0.00 0.00 0.00 4.34
2685 2798 2.100584 CTGGATCAAGAAGGAGGAGACG 59.899 54.545 0.00 0.00 0.00 4.18
2686 2799 2.158971 GCTGGATCAAGAAGGAGGAGAC 60.159 54.545 0.00 0.00 0.00 3.36
2687 2800 2.114616 GCTGGATCAAGAAGGAGGAGA 58.885 52.381 0.00 0.00 0.00 3.71
2688 2801 1.836166 TGCTGGATCAAGAAGGAGGAG 59.164 52.381 0.00 0.00 0.00 3.69
2689 2802 1.956869 TGCTGGATCAAGAAGGAGGA 58.043 50.000 0.00 0.00 0.00 3.71
2690 2803 2.641305 CTTGCTGGATCAAGAAGGAGG 58.359 52.381 0.00 0.00 44.61 4.30
2691 2804 2.641305 CCTTGCTGGATCAAGAAGGAG 58.359 52.381 17.24 0.00 44.61 3.69
2692 2805 1.283029 CCCTTGCTGGATCAAGAAGGA 59.717 52.381 21.16 3.00 44.61 3.36
2693 2806 1.684248 CCCCTTGCTGGATCAAGAAGG 60.684 57.143 16.02 16.02 44.61 3.46
2694 2807 1.684248 CCCCCTTGCTGGATCAAGAAG 60.684 57.143 0.00 2.15 44.61 2.85
2695 2808 0.332632 CCCCCTTGCTGGATCAAGAA 59.667 55.000 0.00 0.00 44.61 2.52
2696 2809 0.549902 TCCCCCTTGCTGGATCAAGA 60.550 55.000 0.00 0.00 44.61 3.02
2697 2810 0.332632 TTCCCCCTTGCTGGATCAAG 59.667 55.000 0.00 0.00 42.23 3.02
2698 2811 0.332632 CTTCCCCCTTGCTGGATCAA 59.667 55.000 0.00 0.00 38.35 2.57
2699 2812 0.846427 ACTTCCCCCTTGCTGGATCA 60.846 55.000 0.00 0.00 38.35 2.92
2700 2813 1.141858 CTACTTCCCCCTTGCTGGATC 59.858 57.143 0.00 0.00 38.35 3.36
2701 2814 1.216990 CTACTTCCCCCTTGCTGGAT 58.783 55.000 0.00 0.00 38.35 3.41
2702 2815 0.118346 TCTACTTCCCCCTTGCTGGA 59.882 55.000 0.00 0.00 38.35 3.86
2703 2816 0.991920 TTCTACTTCCCCCTTGCTGG 59.008 55.000 0.00 0.00 0.00 4.85
2704 2817 1.630878 ACTTCTACTTCCCCCTTGCTG 59.369 52.381 0.00 0.00 0.00 4.41
2705 2818 2.040412 CAACTTCTACTTCCCCCTTGCT 59.960 50.000 0.00 0.00 0.00 3.91
2706 2819 2.039879 TCAACTTCTACTTCCCCCTTGC 59.960 50.000 0.00 0.00 0.00 4.01
2707 2820 4.576330 ATCAACTTCTACTTCCCCCTTG 57.424 45.455 0.00 0.00 0.00 3.61
2708 2821 4.601857 TCAATCAACTTCTACTTCCCCCTT 59.398 41.667 0.00 0.00 0.00 3.95
2709 2822 4.175962 TCAATCAACTTCTACTTCCCCCT 58.824 43.478 0.00 0.00 0.00 4.79
2710 2823 4.225267 TCTCAATCAACTTCTACTTCCCCC 59.775 45.833 0.00 0.00 0.00 5.40
2711 2824 5.422214 TCTCAATCAACTTCTACTTCCCC 57.578 43.478 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.