Multiple sequence alignment - TraesCS2B01G050000

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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 TraesCS2B01G050000 chr2B 100.000 3248 0 0 1 3248 24851525 24854772 0.000000e+00 5999
1 TraesCS2B01G050000 chr2B 82.592 787 106 15 1723 2495 24861089 24861858 0.000000e+00 665
2 TraesCS2B01G050000 chr2B 84.509 581 82 8 2657 3231 244870194 244869616 4.700000e-158 568
3 TraesCS2B01G050000 chr2B 83.193 595 94 6 2658 3248 157678594 157679186 1.030000e-149 540
4 TraesCS2B01G050000 chr2B 76.161 646 120 28 883 1523 24860303 24860919 3.150000e-80 309
5 TraesCS2B01G050000 chr2D 92.089 1757 97 12 758 2498 13624122 13625852 0.000000e+00 2436
6 TraesCS2B01G050000 chr2D 82.122 688 99 15 1 684 592001065 592000398 4.700000e-158 568
7 TraesCS2B01G050000 chr6B 89.150 765 66 11 1 757 142222635 142223390 0.000000e+00 937
8 TraesCS2B01G050000 chr1B 88.843 726 49 14 1 712 17348680 17349387 0.000000e+00 863
9 TraesCS2B01G050000 chr1B 88.828 725 49 16 1 712 16847094 16847799 0.000000e+00 861
10 TraesCS2B01G050000 chr4B 87.320 765 71 21 1 757 473865724 473866470 0.000000e+00 852
11 TraesCS2B01G050000 chr4D 85.209 764 95 12 4 759 44186749 44185996 0.000000e+00 769
12 TraesCS2B01G050000 chr3D 83.901 764 101 15 1 757 63347291 63346543 0.000000e+00 710
13 TraesCS2B01G050000 chr2A 83.154 742 108 11 1 735 4177766 4178497 0.000000e+00 662
14 TraesCS2B01G050000 chr7B 87.161 553 58 7 1 544 687820516 687821064 1.660000e-172 616
15 TraesCS2B01G050000 chr7B 85.260 597 82 6 2657 3248 604800390 604800985 7.700000e-171 610
16 TraesCS2B01G050000 chr5D 85.092 597 80 7 2657 3248 497810500 497809908 4.640000e-168 601
17 TraesCS2B01G050000 chr5A 83.417 597 92 7 2657 3248 621838811 621838217 6.130000e-152 547
18 TraesCS2B01G050000 chr5A 84.278 547 75 11 2657 3198 115703684 115704224 1.030000e-144 523
19 TraesCS2B01G050000 chr4A 83.472 599 88 10 2657 3248 437496107 437496701 6.130000e-152 547
20 TraesCS2B01G050000 chr4A 82.818 582 90 10 2658 3232 645106952 645106374 2.230000e-141 512
21 TraesCS2B01G050000 chr7A 82.972 599 89 10 2657 3248 246620731 246620139 2.220000e-146 529
22 TraesCS2B01G050000 chr3B 86.228 334 36 7 434 763 707255155 707255482 1.430000e-93 353
23 TraesCS2B01G050000 chr3A 88.372 86 8 2 2500 2583 127422118 127422033 5.730000e-18 102


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 TraesCS2B01G050000 chr2B 24851525 24854772 3247 False 5999 5999 100.0000 1 3248 1 chr2B.!!$F1 3247
1 TraesCS2B01G050000 chr2B 244869616 244870194 578 True 568 568 84.5090 2657 3231 1 chr2B.!!$R1 574
2 TraesCS2B01G050000 chr2B 157678594 157679186 592 False 540 540 83.1930 2658 3248 1 chr2B.!!$F2 590
3 TraesCS2B01G050000 chr2B 24860303 24861858 1555 False 487 665 79.3765 883 2495 2 chr2B.!!$F3 1612
4 TraesCS2B01G050000 chr2D 13624122 13625852 1730 False 2436 2436 92.0890 758 2498 1 chr2D.!!$F1 1740
5 TraesCS2B01G050000 chr2D 592000398 592001065 667 True 568 568 82.1220 1 684 1 chr2D.!!$R1 683
6 TraesCS2B01G050000 chr6B 142222635 142223390 755 False 937 937 89.1500 1 757 1 chr6B.!!$F1 756
7 TraesCS2B01G050000 chr1B 17348680 17349387 707 False 863 863 88.8430 1 712 1 chr1B.!!$F2 711
8 TraesCS2B01G050000 chr1B 16847094 16847799 705 False 861 861 88.8280 1 712 1 chr1B.!!$F1 711
9 TraesCS2B01G050000 chr4B 473865724 473866470 746 False 852 852 87.3200 1 757 1 chr4B.!!$F1 756
10 TraesCS2B01G050000 chr4D 44185996 44186749 753 True 769 769 85.2090 4 759 1 chr4D.!!$R1 755
11 TraesCS2B01G050000 chr3D 63346543 63347291 748 True 710 710 83.9010 1 757 1 chr3D.!!$R1 756
12 TraesCS2B01G050000 chr2A 4177766 4178497 731 False 662 662 83.1540 1 735 1 chr2A.!!$F1 734
13 TraesCS2B01G050000 chr7B 687820516 687821064 548 False 616 616 87.1610 1 544 1 chr7B.!!$F2 543
14 TraesCS2B01G050000 chr7B 604800390 604800985 595 False 610 610 85.2600 2657 3248 1 chr7B.!!$F1 591
15 TraesCS2B01G050000 chr5D 497809908 497810500 592 True 601 601 85.0920 2657 3248 1 chr5D.!!$R1 591
16 TraesCS2B01G050000 chr5A 621838217 621838811 594 True 547 547 83.4170 2657 3248 1 chr5A.!!$R1 591
17 TraesCS2B01G050000 chr5A 115703684 115704224 540 False 523 523 84.2780 2657 3198 1 chr5A.!!$F1 541
18 TraesCS2B01G050000 chr4A 437496107 437496701 594 False 547 547 83.4720 2657 3248 1 chr4A.!!$F1 591
19 TraesCS2B01G050000 chr4A 645106374 645106952 578 True 512 512 82.8180 2658 3232 1 chr4A.!!$R1 574
20 TraesCS2B01G050000 chr7A 246620139 246620731 592 True 529 529 82.9720 2657 3248 1 chr7A.!!$R1 591

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
155 156 0.101399 CTCATCGTTGAGGAGGACGG 59.899 60.0 14.54 0.0 44.78 4.79 F
1406 1465 0.256464 TCGGTTGTTGGGACAGGTTT 59.744 50.0 0.00 0.0 42.39 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1412 1471 0.036388 CGAGCACCTTAAGGCTGGAA 60.036 55.0 21.92 0.0 41.22 3.53 R
2829 2915 0.175760 GGATCCTAGAGTGTGCGCAA 59.824 55.0 14.00 0.0 0.00 4.85 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
104 105 3.474798 TCTGATTACAGACCAGGACCT 57.525 47.619 0.00 0.00 46.55 3.85
144 145 4.514577 CGCCGCCTCCTCATCGTT 62.515 66.667 0.00 0.00 0.00 3.85
155 156 0.101399 CTCATCGTTGAGGAGGACGG 59.899 60.000 14.54 0.00 44.78 4.79
359 362 2.374839 TGACCATTGGGAAGACATGTGA 59.625 45.455 1.15 0.00 38.05 3.58
377 380 2.358267 GTGACTCGATACCTCGGACAAT 59.642 50.000 0.00 0.00 45.10 2.71
572 604 6.682746 TGAACAAAATATGTATGCACCGTTT 58.317 32.000 0.00 0.00 42.99 3.60
633 668 4.801624 CGCTGCTGGAGCTACGCA 62.802 66.667 19.01 13.57 46.64 5.24
698 733 1.866237 GCGCAAAACCAGACGATGA 59.134 52.632 0.30 0.00 0.00 2.92
768 804 3.898123 GGAGATGCTCTTACTATGGACCA 59.102 47.826 0.00 0.00 0.00 4.02
772 808 6.294473 AGATGCTCTTACTATGGACCAAATG 58.706 40.000 0.00 0.00 0.00 2.32
793 830 7.807977 AATGGGTGATATTTGCTAACTACTG 57.192 36.000 0.00 0.00 0.00 2.74
814 863 9.819267 CTACTGGGGACTAAGAAAAATAACTAG 57.181 37.037 0.00 0.00 0.00 2.57
862 911 8.049655 TGCAATAATGAATTGTAAGTACTGCA 57.950 30.769 0.00 0.00 45.78 4.41
916 965 2.933928 GCTCCCGGCCTATAAATTACCG 60.934 54.545 0.00 0.00 43.44 4.02
920 969 3.518590 CCGGCCTATAAATTACCGCTAG 58.481 50.000 0.00 0.00 42.49 3.42
926 975 5.779922 CCTATAAATTACCGCTAGCACTCA 58.220 41.667 16.45 0.00 0.00 3.41
927 976 5.634020 CCTATAAATTACCGCTAGCACTCAC 59.366 44.000 16.45 0.00 0.00 3.51
1062 1111 4.674623 GCATTGAAGCACAAGGAGATTCTG 60.675 45.833 11.30 0.71 41.97 3.02
1137 1186 9.668497 AACCAGAAAACTATAGTGAATCCTAAC 57.332 33.333 6.06 0.00 0.00 2.34
1397 1456 3.266636 TGTATATGCACTCGGTTGTTGG 58.733 45.455 0.00 0.00 0.00 3.77
1406 1465 0.256464 TCGGTTGTTGGGACAGGTTT 59.744 50.000 0.00 0.00 42.39 3.27
1407 1466 0.383949 CGGTTGTTGGGACAGGTTTG 59.616 55.000 0.00 0.00 42.39 2.93
1412 1471 3.063197 TTGGGACAGGTTTGCGGGT 62.063 57.895 0.00 0.00 42.39 5.28
1415 1474 2.265904 GGACAGGTTTGCGGGTTCC 61.266 63.158 0.00 0.00 0.00 3.62
1524 1583 3.692791 GTGTGGTCACCTTCAAGAAAC 57.307 47.619 0.00 0.00 38.51 2.78
1533 1601 2.777692 ACCTTCAAGAAACTCCAGGACA 59.222 45.455 0.00 0.00 0.00 4.02
1650 1721 3.315544 TAGGCACACCCTAGCATGA 57.684 52.632 0.00 0.00 44.08 3.07
1669 1740 7.966812 AGCATGAACTCCATATTACATAGTGA 58.033 34.615 0.00 0.00 33.31 3.41
1821 1892 1.003116 CAAAGTGTGACACTCAGCAGC 60.003 52.381 19.71 0.00 44.62 5.25
1890 1964 2.514505 GAAAGAGGCGCAACGAAGGC 62.515 60.000 10.83 0.00 0.00 4.35
2006 2080 9.003658 ACAGTTAATGTGGTTTCTTATCTTCTG 57.996 33.333 0.00 0.00 41.91 3.02
2073 2147 7.722949 AATATCAGGGACAATTGACAATGTT 57.277 32.000 13.59 6.46 0.00 2.71
2114 2188 7.022055 TCACGACAAACATCAAAAAGTATGT 57.978 32.000 0.00 0.00 37.94 2.29
2139 2213 0.899717 TTGGGCATGAGAAGGGCAAC 60.900 55.000 0.00 0.00 0.00 4.17
2229 2303 4.880899 GCCATTGGCGTTTACCAC 57.119 55.556 12.82 0.00 40.19 4.16
2249 2323 2.081462 CGGACCCATAGTGGTTTGAAC 58.919 52.381 0.00 0.00 39.24 3.18
2256 2330 4.772100 CCCATAGTGGTTTGAACTGGATTT 59.228 41.667 1.86 0.00 35.17 2.17
2258 2332 6.435904 CCCATAGTGGTTTGAACTGGATTTAA 59.564 38.462 1.86 0.00 35.17 1.52
2261 2335 5.783111 AGTGGTTTGAACTGGATTTAATGC 58.217 37.500 0.00 0.00 0.00 3.56
2264 2338 4.627035 GGTTTGAACTGGATTTAATGCTGC 59.373 41.667 3.54 0.00 0.00 5.25
2303 2377 4.418392 GCAATCTCATGCGAGTTCATTTT 58.582 39.130 0.00 0.00 40.44 1.82
2306 2380 6.195983 GCAATCTCATGCGAGTTCATTTTAAG 59.804 38.462 0.00 0.00 40.44 1.85
2308 2382 4.635765 TCTCATGCGAGTTCATTTTAAGGG 59.364 41.667 0.00 0.00 40.44 3.95
2319 2393 7.847096 AGTTCATTTTAAGGGAAAGTGTGTTT 58.153 30.769 0.00 0.00 36.43 2.83
2327 2401 2.494073 GGGAAAGTGTGTTTGTTCCACA 59.506 45.455 3.87 0.00 41.17 4.17
2339 2414 5.641209 TGTTTGTTCCACATTTGTTTTCCAG 59.359 36.000 0.00 0.00 0.00 3.86
2352 2427 3.323115 TGTTTTCCAGCAATAACATGGCA 59.677 39.130 0.00 0.00 33.92 4.92
2369 2444 0.727398 GCAAGGGTCATGCTTACGTC 59.273 55.000 0.00 0.00 40.64 4.34
2371 2446 2.002586 CAAGGGTCATGCTTACGTCTG 58.997 52.381 0.00 0.00 0.00 3.51
2383 2466 3.429547 GCTTACGTCTGTGATCCATGTCT 60.430 47.826 0.00 0.00 0.00 3.41
2404 2487 6.072397 TGTCTCTCTAGTGCAAGAGTACTTTC 60.072 42.308 13.78 3.44 43.02 2.62
2409 2492 8.516234 TCTCTAGTGCAAGAGTACTTTCTTTAG 58.484 37.037 13.78 0.00 43.02 1.85
2417 2500 8.064814 GCAAGAGTACTTTCTTTAGTTTGTCAG 58.935 37.037 0.00 0.00 35.28 3.51
2420 2503 7.439655 AGAGTACTTTCTTTAGTTTGTCAGCTG 59.560 37.037 7.63 7.63 0.00 4.24
2431 2514 9.534565 TTTAGTTTGTCAGCTGCTATATTCTAG 57.465 33.333 9.47 0.00 0.00 2.43
2435 2518 7.473735 TTGTCAGCTGCTATATTCTAGCTAT 57.526 36.000 9.47 0.00 44.11 2.97
2436 2519 6.861144 TGTCAGCTGCTATATTCTAGCTATG 58.139 40.000 9.47 2.85 44.11 2.23
2439 2522 8.196771 GTCAGCTGCTATATTCTAGCTATGATT 58.803 37.037 9.47 0.00 44.11 2.57
2440 2523 8.756927 TCAGCTGCTATATTCTAGCTATGATTT 58.243 33.333 9.47 0.00 44.11 2.17
2473 2557 5.243426 TGCAAGGTTGTTTTCTAGTGAAC 57.757 39.130 0.00 0.00 31.02 3.18
2476 2560 6.770785 TGCAAGGTTGTTTTCTAGTGAACTAT 59.229 34.615 10.69 0.00 31.02 2.12
2479 2563 8.621286 CAAGGTTGTTTTCTAGTGAACTATTGT 58.379 33.333 10.69 0.00 31.02 2.71
2498 2582 5.984233 TTGTAATTGATATGCTCACGGAC 57.016 39.130 0.00 0.00 32.17 4.79
2499 2583 4.377021 TGTAATTGATATGCTCACGGACC 58.623 43.478 0.00 0.00 32.17 4.46
2500 2584 3.845781 AATTGATATGCTCACGGACCT 57.154 42.857 0.00 0.00 32.17 3.85
2501 2585 3.845781 ATTGATATGCTCACGGACCTT 57.154 42.857 0.00 0.00 32.17 3.50
2502 2586 3.627395 TTGATATGCTCACGGACCTTT 57.373 42.857 0.00 0.00 32.17 3.11
2503 2587 3.627395 TGATATGCTCACGGACCTTTT 57.373 42.857 0.00 0.00 0.00 2.27
2504 2588 3.950397 TGATATGCTCACGGACCTTTTT 58.050 40.909 0.00 0.00 0.00 1.94
2535 2619 3.750501 TCCAAAAAGGAGGATTACCCC 57.249 47.619 0.00 0.00 43.07 4.95
2536 2620 2.025699 TCCAAAAAGGAGGATTACCCCG 60.026 50.000 0.00 0.00 43.07 5.73
2537 2621 2.375146 CAAAAAGGAGGATTACCCCGG 58.625 52.381 0.00 0.00 36.73 5.73
2538 2622 0.257905 AAAAGGAGGATTACCCCGGC 59.742 55.000 0.00 0.00 36.73 6.13
2539 2623 1.642513 AAAGGAGGATTACCCCGGCC 61.643 60.000 0.00 0.00 36.73 6.13
2540 2624 2.447959 GGAGGATTACCCCGGCCT 60.448 66.667 0.00 0.00 36.73 5.19
2541 2625 2.517798 GGAGGATTACCCCGGCCTC 61.518 68.421 13.52 13.52 44.84 4.70
2542 2626 1.459730 GAGGATTACCCCGGCCTCT 60.460 63.158 14.36 0.00 42.81 3.69
2543 2627 1.459730 AGGATTACCCCGGCCTCTC 60.460 63.158 0.00 0.00 36.73 3.20
2544 2628 2.517798 GGATTACCCCGGCCTCTCC 61.518 68.421 0.00 0.00 0.00 3.71
2545 2629 1.764854 GATTACCCCGGCCTCTCCA 60.765 63.158 0.00 0.00 34.01 3.86
2546 2630 1.073706 ATTACCCCGGCCTCTCCAT 60.074 57.895 0.00 0.00 34.01 3.41
2547 2631 1.128188 ATTACCCCGGCCTCTCCATC 61.128 60.000 0.00 0.00 34.01 3.51
2548 2632 2.539277 TTACCCCGGCCTCTCCATCA 62.539 60.000 0.00 0.00 34.01 3.07
2549 2633 2.539277 TACCCCGGCCTCTCCATCAA 62.539 60.000 0.00 0.00 34.01 2.57
2550 2634 2.190578 CCCGGCCTCTCCATCAAC 59.809 66.667 0.00 0.00 34.01 3.18
2551 2635 2.669133 CCCGGCCTCTCCATCAACA 61.669 63.158 0.00 0.00 34.01 3.33
2552 2636 1.528824 CCGGCCTCTCCATCAACAT 59.471 57.895 0.00 0.00 34.01 2.71
2553 2637 0.816825 CCGGCCTCTCCATCAACATG 60.817 60.000 0.00 0.00 34.01 3.21
2554 2638 0.178767 CGGCCTCTCCATCAACATGA 59.821 55.000 0.00 0.00 34.01 3.07
2555 2639 1.202734 CGGCCTCTCCATCAACATGAT 60.203 52.381 0.00 0.00 37.65 2.45
2565 2649 3.247442 CATCAACATGATGCACACAACC 58.753 45.455 0.00 0.00 46.37 3.77
2566 2650 2.305009 TCAACATGATGCACACAACCA 58.695 42.857 0.00 0.00 0.00 3.67
2567 2651 2.892215 TCAACATGATGCACACAACCAT 59.108 40.909 0.00 0.00 0.00 3.55
2568 2652 3.057386 TCAACATGATGCACACAACCATC 60.057 43.478 0.00 0.00 38.60 3.51
2569 2653 2.799017 ACATGATGCACACAACCATCT 58.201 42.857 0.00 0.00 38.84 2.90
2570 2654 3.159472 ACATGATGCACACAACCATCTT 58.841 40.909 0.00 0.00 38.84 2.40
2571 2655 3.575256 ACATGATGCACACAACCATCTTT 59.425 39.130 0.00 0.00 38.84 2.52
2572 2656 4.766373 ACATGATGCACACAACCATCTTTA 59.234 37.500 0.00 0.00 38.84 1.85
2573 2657 5.419788 ACATGATGCACACAACCATCTTTAT 59.580 36.000 0.00 0.00 38.84 1.40
2574 2658 5.981088 TGATGCACACAACCATCTTTATT 57.019 34.783 0.00 0.00 38.84 1.40
2575 2659 7.122501 ACATGATGCACACAACCATCTTTATTA 59.877 33.333 0.00 0.00 38.84 0.98
2576 2660 7.087409 TGATGCACACAACCATCTTTATTAG 57.913 36.000 0.00 0.00 38.84 1.73
2577 2661 6.658816 TGATGCACACAACCATCTTTATTAGT 59.341 34.615 0.00 0.00 38.84 2.24
2578 2662 6.892658 TGCACACAACCATCTTTATTAGTT 57.107 33.333 0.00 0.00 0.00 2.24
2579 2663 7.987750 TGCACACAACCATCTTTATTAGTTA 57.012 32.000 0.00 0.00 0.00 2.24
2580 2664 7.812648 TGCACACAACCATCTTTATTAGTTAC 58.187 34.615 0.00 0.00 0.00 2.50
2581 2665 7.663905 TGCACACAACCATCTTTATTAGTTACT 59.336 33.333 0.00 0.00 0.00 2.24
2582 2666 8.175716 GCACACAACCATCTTTATTAGTTACTC 58.824 37.037 0.00 0.00 0.00 2.59
2583 2667 8.665685 CACACAACCATCTTTATTAGTTACTCC 58.334 37.037 0.00 0.00 0.00 3.85
2584 2668 7.827729 ACACAACCATCTTTATTAGTTACTCCC 59.172 37.037 0.00 0.00 0.00 4.30
2585 2669 8.047310 CACAACCATCTTTATTAGTTACTCCCT 58.953 37.037 0.00 0.00 0.00 4.20
2586 2670 8.265764 ACAACCATCTTTATTAGTTACTCCCTC 58.734 37.037 0.00 0.00 0.00 4.30
2587 2671 8.487028 CAACCATCTTTATTAGTTACTCCCTCT 58.513 37.037 0.00 0.00 0.00 3.69
2588 2672 8.024145 ACCATCTTTATTAGTTACTCCCTCTG 57.976 38.462 0.00 0.00 0.00 3.35
2589 2673 7.844779 ACCATCTTTATTAGTTACTCCCTCTGA 59.155 37.037 0.00 0.00 0.00 3.27
2590 2674 8.705594 CCATCTTTATTAGTTACTCCCTCTGAA 58.294 37.037 0.00 0.00 0.00 3.02
2591 2675 9.535878 CATCTTTATTAGTTACTCCCTCTGAAC 57.464 37.037 0.00 0.00 0.00 3.18
2592 2676 8.075761 TCTTTATTAGTTACTCCCTCTGAACC 57.924 38.462 0.00 0.00 0.00 3.62
2593 2677 7.676893 TCTTTATTAGTTACTCCCTCTGAACCA 59.323 37.037 0.00 0.00 0.00 3.67
2594 2678 7.801893 TTATTAGTTACTCCCTCTGAACCAA 57.198 36.000 0.00 0.00 0.00 3.67
2595 2679 6.697641 ATTAGTTACTCCCTCTGAACCAAA 57.302 37.500 0.00 0.00 0.00 3.28
2596 2680 6.503560 TTAGTTACTCCCTCTGAACCAAAA 57.496 37.500 0.00 0.00 0.00 2.44
2597 2681 5.584551 AGTTACTCCCTCTGAACCAAAAT 57.415 39.130 0.00 0.00 0.00 1.82
2598 2682 6.697641 AGTTACTCCCTCTGAACCAAAATA 57.302 37.500 0.00 0.00 0.00 1.40
2599 2683 6.473758 AGTTACTCCCTCTGAACCAAAATAC 58.526 40.000 0.00 0.00 0.00 1.89
2600 2684 6.272558 AGTTACTCCCTCTGAACCAAAATACT 59.727 38.462 0.00 0.00 0.00 2.12
2601 2685 5.584551 ACTCCCTCTGAACCAAAATACTT 57.415 39.130 0.00 0.00 0.00 2.24
2602 2686 5.316987 ACTCCCTCTGAACCAAAATACTTG 58.683 41.667 0.00 0.00 0.00 3.16
2603 2687 5.163088 ACTCCCTCTGAACCAAAATACTTGT 60.163 40.000 0.00 0.00 0.00 3.16
2604 2688 6.043938 ACTCCCTCTGAACCAAAATACTTGTA 59.956 38.462 0.00 0.00 0.00 2.41
2605 2689 6.472887 TCCCTCTGAACCAAAATACTTGTAG 58.527 40.000 0.00 0.00 0.00 2.74
2606 2690 6.043938 TCCCTCTGAACCAAAATACTTGTAGT 59.956 38.462 0.00 0.00 0.00 2.73
2607 2691 6.715264 CCCTCTGAACCAAAATACTTGTAGTT 59.285 38.462 0.00 0.00 0.00 2.24
2608 2692 7.308589 CCCTCTGAACCAAAATACTTGTAGTTG 60.309 40.741 0.00 0.00 0.00 3.16
2609 2693 6.966021 TCTGAACCAAAATACTTGTAGTTGC 58.034 36.000 0.00 0.00 0.00 4.17
2610 2694 5.753744 TGAACCAAAATACTTGTAGTTGCG 58.246 37.500 0.00 0.00 0.00 4.85
2611 2695 4.759516 ACCAAAATACTTGTAGTTGCGG 57.240 40.909 7.62 7.62 0.00 5.69
2612 2696 3.057806 ACCAAAATACTTGTAGTTGCGGC 60.058 43.478 0.00 0.00 0.00 6.53
2613 2697 3.057876 CCAAAATACTTGTAGTTGCGGCA 60.058 43.478 0.00 0.00 0.00 5.69
2614 2698 4.541779 CAAAATACTTGTAGTTGCGGCAA 58.458 39.130 12.11 12.11 0.00 4.52
2615 2699 3.824414 AATACTTGTAGTTGCGGCAAC 57.176 42.857 32.68 32.68 43.83 4.17
2624 2708 2.875080 GTTGCGGCAACTTGTACTAG 57.125 50.000 32.48 2.56 40.73 2.57
2625 2709 2.140717 GTTGCGGCAACTTGTACTAGT 58.859 47.619 32.48 3.98 40.73 2.57
2626 2710 2.536761 TGCGGCAACTTGTACTAGTT 57.463 45.000 15.68 15.68 38.87 2.24
2627 2711 2.409975 TGCGGCAACTTGTACTAGTTC 58.590 47.619 18.09 13.06 36.24 3.01
2628 2712 2.036733 TGCGGCAACTTGTACTAGTTCT 59.963 45.455 18.09 0.00 36.24 3.01
2629 2713 2.666994 GCGGCAACTTGTACTAGTTCTC 59.333 50.000 18.09 13.00 36.24 2.87
2630 2714 3.251571 CGGCAACTTGTACTAGTTCTCC 58.748 50.000 18.09 18.76 36.24 3.71
2631 2715 3.597255 GGCAACTTGTACTAGTTCTCCC 58.403 50.000 18.09 14.60 36.24 4.30
2632 2716 3.597255 GCAACTTGTACTAGTTCTCCCC 58.403 50.000 18.09 3.56 36.24 4.81
2633 2717 3.007614 GCAACTTGTACTAGTTCTCCCCA 59.992 47.826 18.09 0.00 36.24 4.96
2634 2718 4.822026 CAACTTGTACTAGTTCTCCCCAG 58.178 47.826 18.09 3.91 36.24 4.45
2635 2719 2.832733 ACTTGTACTAGTTCTCCCCAGC 59.167 50.000 0.00 0.00 0.00 4.85
2636 2720 2.921834 TGTACTAGTTCTCCCCAGCT 57.078 50.000 0.00 0.00 0.00 4.24
2637 2721 3.185880 TGTACTAGTTCTCCCCAGCTT 57.814 47.619 0.00 0.00 0.00 3.74
2638 2722 3.517612 TGTACTAGTTCTCCCCAGCTTT 58.482 45.455 0.00 0.00 0.00 3.51
2639 2723 3.260884 TGTACTAGTTCTCCCCAGCTTTG 59.739 47.826 0.00 0.00 0.00 2.77
2640 2724 2.339769 ACTAGTTCTCCCCAGCTTTGT 58.660 47.619 0.00 0.00 0.00 2.83
2641 2725 3.517612 ACTAGTTCTCCCCAGCTTTGTA 58.482 45.455 0.00 0.00 0.00 2.41
2642 2726 4.104831 ACTAGTTCTCCCCAGCTTTGTAT 58.895 43.478 0.00 0.00 0.00 2.29
2643 2727 4.536489 ACTAGTTCTCCCCAGCTTTGTATT 59.464 41.667 0.00 0.00 0.00 1.89
2644 2728 4.388577 AGTTCTCCCCAGCTTTGTATTT 57.611 40.909 0.00 0.00 0.00 1.40
2645 2729 4.336280 AGTTCTCCCCAGCTTTGTATTTC 58.664 43.478 0.00 0.00 0.00 2.17
2646 2730 2.985896 TCTCCCCAGCTTTGTATTTCG 58.014 47.619 0.00 0.00 0.00 3.46
2647 2731 2.017049 CTCCCCAGCTTTGTATTTCGG 58.983 52.381 0.00 0.00 0.00 4.30
2648 2732 1.353022 TCCCCAGCTTTGTATTTCGGT 59.647 47.619 0.00 0.00 0.00 4.69
2649 2733 2.572556 TCCCCAGCTTTGTATTTCGGTA 59.427 45.455 0.00 0.00 0.00 4.02
2650 2734 2.681344 CCCCAGCTTTGTATTTCGGTAC 59.319 50.000 0.00 0.00 0.00 3.34
2651 2735 3.340034 CCCAGCTTTGTATTTCGGTACA 58.660 45.455 0.00 0.00 32.99 2.90
2652 2736 3.374058 CCCAGCTTTGTATTTCGGTACAG 59.626 47.826 0.00 0.00 36.08 2.74
2653 2737 4.250464 CCAGCTTTGTATTTCGGTACAGA 58.750 43.478 0.00 0.00 36.08 3.41
2654 2738 4.330074 CCAGCTTTGTATTTCGGTACAGAG 59.670 45.833 0.00 8.61 38.89 3.35
2655 2739 4.330074 CAGCTTTGTATTTCGGTACAGAGG 59.670 45.833 12.43 3.94 37.31 3.69
2656 2740 4.020485 AGCTTTGTATTTCGGTACAGAGGT 60.020 41.667 10.58 10.58 40.50 3.85
2670 2754 7.040617 TCGGTACAGAGGTAATATTCATCAGAC 60.041 40.741 0.00 0.00 0.00 3.51
2734 2819 2.034179 GGCAAACAAAGTCACTACACCC 59.966 50.000 0.00 0.00 0.00 4.61
2752 2837 6.808321 ACACCCACAAGTATATAGATGTGT 57.192 37.500 19.15 8.62 41.14 3.72
2753 2838 7.195374 ACACCCACAAGTATATAGATGTGTT 57.805 36.000 19.15 8.89 41.14 3.32
2754 2839 7.047891 ACACCCACAAGTATATAGATGTGTTG 58.952 38.462 19.15 17.53 41.14 3.33
2762 2847 6.504398 AGTATATAGATGTGTTGTGTCCGTG 58.496 40.000 0.00 0.00 0.00 4.94
2769 2854 1.595794 GTGTTGTGTCCGTGTAACAGG 59.404 52.381 0.00 0.00 35.74 4.00
2791 2876 3.065925 GCACAATCTAATTCAGTGGCCTC 59.934 47.826 3.32 0.00 0.00 4.70
2829 2915 0.036388 CGTCCCATAACTGCACCACT 60.036 55.000 0.00 0.00 0.00 4.00
2848 2937 0.175760 TTGCGCACACTCTAGGATCC 59.824 55.000 11.12 2.48 0.00 3.36
2855 2947 2.912542 CTCTAGGATCCGCCGCCA 60.913 66.667 5.98 0.00 43.43 5.69
2863 2955 3.860930 ATCCGCCGCCACCAACTTT 62.861 57.895 0.00 0.00 0.00 2.66
2984 3077 3.189287 GTCAATCAATCTGCGTCCAACTT 59.811 43.478 0.00 0.00 0.00 2.66
3058 3154 1.978455 AACACCGCTCCACCTGTTGA 61.978 55.000 0.00 0.00 0.00 3.18
3122 3218 2.223971 GGAGAACGACACCAAAGTCTCA 60.224 50.000 0.00 0.00 36.38 3.27
3176 3273 2.002018 TTTTCCCCCGGAACAGCTGT 62.002 55.000 15.25 15.25 41.87 4.40
3200 3297 2.266055 GAGGAAGAGGGGCACACG 59.734 66.667 0.00 0.00 0.00 4.49
3220 3317 3.648982 CTGCAACTGCCGACGCAA 61.649 61.111 0.00 0.00 46.66 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 3.998672 GCCGACGGTGGTCCTCAA 61.999 66.667 16.73 0.00 40.17 3.02
143 144 3.068691 CTCGCCCGTCCTCCTCAA 61.069 66.667 0.00 0.00 0.00 3.02
155 156 4.479993 ACTCTGCCATGGCTCGCC 62.480 66.667 35.53 8.88 42.51 5.54
377 380 2.957474 TCATCATCATCCTCGGTGGTA 58.043 47.619 0.00 0.00 37.07 3.25
451 471 3.821421 AGATAAAGAACTACGGGGCAG 57.179 47.619 0.00 0.00 0.00 4.85
455 475 8.057536 AGCATAGATAGATAAAGAACTACGGG 57.942 38.462 0.00 0.00 0.00 5.28
638 673 2.484662 CCGCGCTAAAATGCAGCA 59.515 55.556 5.56 0.00 39.04 4.41
684 719 0.511221 CGCGTTCATCGTCTGGTTTT 59.489 50.000 0.00 0.00 42.13 2.43
698 733 2.785713 AAATTAGTTTGTGGCGCGTT 57.214 40.000 8.43 0.00 0.00 4.84
738 773 4.232310 GAGCATCTCCAACAGCCC 57.768 61.111 0.00 0.00 0.00 5.19
768 804 7.285401 CCAGTAGTTAGCAAATATCACCCATTT 59.715 37.037 0.00 0.00 0.00 2.32
772 808 5.063880 CCCAGTAGTTAGCAAATATCACCC 58.936 45.833 0.00 0.00 0.00 4.61
793 830 7.336176 CACCACTAGTTATTTTTCTTAGTCCCC 59.664 40.741 0.00 0.00 0.00 4.81
810 859 0.469917 ACACAAGCTGCACCACTAGT 59.530 50.000 1.02 0.00 0.00 2.57
814 863 2.026590 GCACACAAGCTGCACCAC 59.973 61.111 1.02 0.00 34.56 4.16
850 899 5.642063 GCTGGTAAAATCTGCAGTACTTACA 59.358 40.000 23.34 13.31 0.00 2.41
858 907 3.871485 AGAGAGCTGGTAAAATCTGCAG 58.129 45.455 7.63 7.63 0.00 4.41
862 911 9.030452 CATATACCTAGAGAGCTGGTAAAATCT 57.970 37.037 4.16 0.00 39.42 2.40
916 965 2.906691 AGATGGATGTGAGTGCTAGC 57.093 50.000 8.10 8.10 0.00 3.42
920 969 2.935201 GTGAGAAGATGGATGTGAGTGC 59.065 50.000 0.00 0.00 0.00 4.40
926 975 4.141390 GGTATTGGGTGAGAAGATGGATGT 60.141 45.833 0.00 0.00 0.00 3.06
927 976 4.392940 GGTATTGGGTGAGAAGATGGATG 58.607 47.826 0.00 0.00 0.00 3.51
1062 1111 1.644786 GCATGTACAGGCCGTCCAAC 61.645 60.000 21.48 0.00 33.74 3.77
1137 1186 1.676967 GCCAAACTGCAGAGGGAGG 60.677 63.158 23.35 14.92 36.68 4.30
1397 1456 2.265904 GGAACCCGCAAACCTGTCC 61.266 63.158 0.00 0.00 0.00 4.02
1406 1465 1.002624 CTTAAGGCTGGAACCCGCA 60.003 57.895 9.23 0.00 0.00 5.69
1407 1466 1.749258 CCTTAAGGCTGGAACCCGC 60.749 63.158 9.00 0.00 0.00 6.13
1412 1471 0.036388 CGAGCACCTTAAGGCTGGAA 60.036 55.000 21.92 0.00 41.22 3.53
1415 1474 0.741221 GTCCGAGCACCTTAAGGCTG 60.741 60.000 21.92 18.19 41.22 4.85
1475 1534 1.376037 GGCAAACTCTCCTGTCCCG 60.376 63.158 0.00 0.00 0.00 5.14
1511 1570 3.142174 GTCCTGGAGTTTCTTGAAGGTG 58.858 50.000 0.00 0.00 0.00 4.00
1524 1583 1.480137 CCTAGTGCTTCTGTCCTGGAG 59.520 57.143 0.00 0.00 0.00 3.86
1533 1601 2.175202 CTGTCTGACCCTAGTGCTTCT 58.825 52.381 5.17 0.00 0.00 2.85
1705 1776 7.539710 CGTAGGCTGCATAAGTTATTCGTATTA 59.460 37.037 2.89 0.00 0.00 0.98
1710 1781 4.295870 TCGTAGGCTGCATAAGTTATTCG 58.704 43.478 7.10 0.26 0.00 3.34
1821 1892 0.175302 AGACAATCCAGCTGCTCTCG 59.825 55.000 8.66 0.00 0.00 4.04
1872 1946 2.617274 GCCTTCGTTGCGCCTCTTT 61.617 57.895 4.18 0.00 0.00 2.52
2006 2080 3.126514 TCCGAACTCGATCTGTAGTCAAC 59.873 47.826 0.00 0.00 43.02 3.18
2073 2147 7.018635 TGTCGTGATAACAAGTGACGATATA 57.981 36.000 0.00 0.00 31.84 0.86
2114 2188 1.339631 CCTTCTCATGCCCAAACGGTA 60.340 52.381 0.00 0.00 0.00 4.02
2229 2303 2.081462 GTTCAAACCACTATGGGTCCG 58.919 52.381 0.00 0.00 35.52 4.79
2232 2306 2.714250 TCCAGTTCAAACCACTATGGGT 59.286 45.455 0.00 0.00 40.89 4.51
2238 2312 5.539955 AGCATTAAATCCAGTTCAAACCACT 59.460 36.000 0.00 0.00 0.00 4.00
2249 2323 4.119442 AGCAAAGCAGCATTAAATCCAG 57.881 40.909 0.00 0.00 36.85 3.86
2256 2330 7.035004 CCATAAACTAAAGCAAAGCAGCATTA 58.965 34.615 0.00 0.00 36.85 1.90
2258 2332 5.413499 CCATAAACTAAAGCAAAGCAGCAT 58.587 37.500 0.00 0.00 36.85 3.79
2261 2335 4.808558 TGCCATAAACTAAAGCAAAGCAG 58.191 39.130 0.00 0.00 0.00 4.24
2264 2338 7.315142 TGAGATTGCCATAAACTAAAGCAAAG 58.685 34.615 0.00 0.00 45.61 2.77
2293 2367 7.039313 ACACACTTTCCCTTAAAATGAACTC 57.961 36.000 0.00 0.00 0.00 3.01
2298 2372 7.011016 GGAACAAACACACTTTCCCTTAAAATG 59.989 37.037 0.00 0.00 32.75 2.32
2303 2377 4.399934 GTGGAACAAACACACTTTCCCTTA 59.600 41.667 0.00 0.00 44.16 2.69
2306 2380 3.159353 GTGGAACAAACACACTTTCCC 57.841 47.619 0.00 0.00 44.16 3.97
2327 2401 5.412286 GCCATGTTATTGCTGGAAAACAAAT 59.588 36.000 11.30 0.00 35.63 2.32
2339 2414 1.824230 TGACCCTTGCCATGTTATTGC 59.176 47.619 0.00 0.00 0.00 3.56
2352 2427 1.623811 ACAGACGTAAGCATGACCCTT 59.376 47.619 0.00 0.00 45.62 3.95
2361 2436 2.860735 GACATGGATCACAGACGTAAGC 59.139 50.000 0.00 0.00 45.62 3.09
2369 2444 4.499526 GCACTAGAGAGACATGGATCACAG 60.500 50.000 0.00 0.00 0.00 3.66
2371 2446 3.382865 TGCACTAGAGAGACATGGATCAC 59.617 47.826 0.00 0.00 0.00 3.06
2383 2466 6.902771 AAGAAAGTACTCTTGCACTAGAGA 57.097 37.500 19.91 4.13 43.54 3.10
2404 2487 8.430801 AGAATATAGCAGCTGACAAACTAAAG 57.569 34.615 20.43 0.00 0.00 1.85
2409 2492 5.988561 AGCTAGAATATAGCAGCTGACAAAC 59.011 40.000 20.43 0.00 42.60 2.93
2431 2514 9.403110 CCTTGCATCACTTTATTAAATCATAGC 57.597 33.333 0.00 0.00 0.00 2.97
2435 2518 8.584157 ACAACCTTGCATCACTTTATTAAATCA 58.416 29.630 0.00 0.00 0.00 2.57
2436 2519 8.986477 ACAACCTTGCATCACTTTATTAAATC 57.014 30.769 0.00 0.00 0.00 2.17
2439 2522 9.255304 GAAAACAACCTTGCATCACTTTATTAA 57.745 29.630 0.00 0.00 0.00 1.40
2440 2523 8.637986 AGAAAACAACCTTGCATCACTTTATTA 58.362 29.630 0.00 0.00 0.00 0.98
2473 2557 7.148573 GGTCCGTGAGCATATCAATTACAATAG 60.149 40.741 0.00 0.00 40.43 1.73
2476 2560 4.814234 GGTCCGTGAGCATATCAATTACAA 59.186 41.667 0.00 0.00 40.43 2.41
2479 2563 4.955811 AGGTCCGTGAGCATATCAATTA 57.044 40.909 6.00 0.00 40.43 1.40
2482 2566 3.627395 AAAGGTCCGTGAGCATATCAA 57.373 42.857 6.00 0.00 40.43 2.57
2511 2595 5.308497 GGGGTAATCCTCCTTTTTGGAAAAA 59.692 40.000 0.00 0.00 45.63 1.94
2512 2596 4.841813 GGGGTAATCCTCCTTTTTGGAAAA 59.158 41.667 0.00 0.00 45.63 2.29
2513 2597 4.422057 GGGGTAATCCTCCTTTTTGGAAA 58.578 43.478 0.00 0.00 45.63 3.13
2514 2598 3.562609 CGGGGTAATCCTCCTTTTTGGAA 60.563 47.826 0.00 0.00 45.63 3.53
2515 2599 2.025699 CGGGGTAATCCTCCTTTTTGGA 60.026 50.000 0.00 0.00 43.86 3.53
2516 2600 2.375146 CGGGGTAATCCTCCTTTTTGG 58.625 52.381 0.00 0.00 35.33 3.28
2517 2601 2.375146 CCGGGGTAATCCTCCTTTTTG 58.625 52.381 0.00 0.00 35.33 2.44
2518 2602 1.341679 GCCGGGGTAATCCTCCTTTTT 60.342 52.381 2.18 0.00 35.33 1.94
2519 2603 0.257905 GCCGGGGTAATCCTCCTTTT 59.742 55.000 2.18 0.00 35.33 2.27
2520 2604 1.642513 GGCCGGGGTAATCCTCCTTT 61.643 60.000 2.18 0.00 35.33 3.11
2521 2605 2.076803 GGCCGGGGTAATCCTCCTT 61.077 63.158 2.18 0.00 35.33 3.36
2522 2606 2.447959 GGCCGGGGTAATCCTCCT 60.448 66.667 2.18 0.00 35.33 3.69
2523 2607 2.447959 AGGCCGGGGTAATCCTCC 60.448 66.667 2.18 0.00 35.33 4.30
2524 2608 1.459730 AGAGGCCGGGGTAATCCTC 60.460 63.158 13.92 13.92 44.09 3.71
2525 2609 1.459730 GAGAGGCCGGGGTAATCCT 60.460 63.158 2.18 0.00 35.33 3.24
2526 2610 2.517798 GGAGAGGCCGGGGTAATCC 61.518 68.421 2.18 0.00 0.00 3.01
2527 2611 1.128188 ATGGAGAGGCCGGGGTAATC 61.128 60.000 2.18 0.00 40.66 1.75
2528 2612 1.073706 ATGGAGAGGCCGGGGTAAT 60.074 57.895 2.18 0.00 40.66 1.89
2529 2613 1.764854 GATGGAGAGGCCGGGGTAA 60.765 63.158 2.18 0.00 40.66 2.85
2530 2614 2.122989 GATGGAGAGGCCGGGGTA 60.123 66.667 2.18 0.00 40.66 3.69
2531 2615 3.943137 TTGATGGAGAGGCCGGGGT 62.943 63.158 2.18 0.00 40.66 4.95
2532 2616 3.089874 TTGATGGAGAGGCCGGGG 61.090 66.667 2.18 0.00 40.66 5.73
2533 2617 1.987807 ATGTTGATGGAGAGGCCGGG 61.988 60.000 2.18 0.00 40.66 5.73
2534 2618 0.816825 CATGTTGATGGAGAGGCCGG 60.817 60.000 0.00 0.00 40.66 6.13
2535 2619 0.178767 TCATGTTGATGGAGAGGCCG 59.821 55.000 0.00 0.00 40.66 6.13
2536 2620 2.653234 ATCATGTTGATGGAGAGGCC 57.347 50.000 0.00 0.00 35.43 5.19
2545 2629 2.892215 TGGTTGTGTGCATCATGTTGAT 59.108 40.909 7.98 0.00 37.65 2.57
2546 2630 2.305009 TGGTTGTGTGCATCATGTTGA 58.695 42.857 7.98 0.00 0.00 3.18
2547 2631 2.797074 TGGTTGTGTGCATCATGTTG 57.203 45.000 0.00 0.00 0.00 3.33
2548 2632 3.159472 AGATGGTTGTGTGCATCATGTT 58.841 40.909 0.00 0.00 0.00 2.71
2549 2633 2.799017 AGATGGTTGTGTGCATCATGT 58.201 42.857 0.00 0.00 0.00 3.21
2550 2634 3.861276 AAGATGGTTGTGTGCATCATG 57.139 42.857 0.00 0.00 0.00 3.07
2551 2635 6.534475 AATAAAGATGGTTGTGTGCATCAT 57.466 33.333 0.00 0.00 0.00 2.45
2552 2636 5.981088 AATAAAGATGGTTGTGTGCATCA 57.019 34.783 0.00 0.00 0.00 3.07
2553 2637 7.088589 ACTAATAAAGATGGTTGTGTGCATC 57.911 36.000 0.00 0.00 0.00 3.91
2554 2638 7.466746 AACTAATAAAGATGGTTGTGTGCAT 57.533 32.000 0.00 0.00 0.00 3.96
2555 2639 6.892658 AACTAATAAAGATGGTTGTGTGCA 57.107 33.333 0.00 0.00 0.00 4.57
2556 2640 8.040716 AGTAACTAATAAAGATGGTTGTGTGC 57.959 34.615 0.00 0.00 0.00 4.57
2557 2641 8.665685 GGAGTAACTAATAAAGATGGTTGTGTG 58.334 37.037 0.00 0.00 0.00 3.82
2558 2642 7.827729 GGGAGTAACTAATAAAGATGGTTGTGT 59.172 37.037 0.00 0.00 0.00 3.72
2559 2643 8.047310 AGGGAGTAACTAATAAAGATGGTTGTG 58.953 37.037 0.00 0.00 0.00 3.33
2560 2644 8.159229 AGGGAGTAACTAATAAAGATGGTTGT 57.841 34.615 0.00 0.00 0.00 3.32
2561 2645 8.487028 AGAGGGAGTAACTAATAAAGATGGTTG 58.513 37.037 0.00 0.00 0.00 3.77
2562 2646 8.487028 CAGAGGGAGTAACTAATAAAGATGGTT 58.513 37.037 0.00 0.00 0.00 3.67
2563 2647 7.844779 TCAGAGGGAGTAACTAATAAAGATGGT 59.155 37.037 0.00 0.00 0.00 3.55
2564 2648 8.251383 TCAGAGGGAGTAACTAATAAAGATGG 57.749 38.462 0.00 0.00 0.00 3.51
2565 2649 9.535878 GTTCAGAGGGAGTAACTAATAAAGATG 57.464 37.037 0.00 0.00 0.00 2.90
2566 2650 8.706521 GGTTCAGAGGGAGTAACTAATAAAGAT 58.293 37.037 0.00 0.00 0.00 2.40
2567 2651 7.676893 TGGTTCAGAGGGAGTAACTAATAAAGA 59.323 37.037 0.00 0.00 0.00 2.52
2568 2652 7.848128 TGGTTCAGAGGGAGTAACTAATAAAG 58.152 38.462 0.00 0.00 0.00 1.85
2569 2653 7.801893 TGGTTCAGAGGGAGTAACTAATAAA 57.198 36.000 0.00 0.00 0.00 1.40
2570 2654 7.801893 TTGGTTCAGAGGGAGTAACTAATAA 57.198 36.000 0.00 0.00 0.00 1.40
2571 2655 7.801893 TTTGGTTCAGAGGGAGTAACTAATA 57.198 36.000 0.00 0.00 0.00 0.98
2572 2656 6.697641 TTTGGTTCAGAGGGAGTAACTAAT 57.302 37.500 0.00 0.00 0.00 1.73
2573 2657 6.503560 TTTTGGTTCAGAGGGAGTAACTAA 57.496 37.500 0.00 0.00 0.00 2.24
2574 2658 6.697641 ATTTTGGTTCAGAGGGAGTAACTA 57.302 37.500 0.00 0.00 0.00 2.24
2575 2659 5.584551 ATTTTGGTTCAGAGGGAGTAACT 57.415 39.130 0.00 0.00 0.00 2.24
2576 2660 6.473758 AGTATTTTGGTTCAGAGGGAGTAAC 58.526 40.000 0.00 0.00 0.00 2.50
2577 2661 6.697641 AGTATTTTGGTTCAGAGGGAGTAA 57.302 37.500 0.00 0.00 0.00 2.24
2578 2662 6.043938 ACAAGTATTTTGGTTCAGAGGGAGTA 59.956 38.462 0.00 0.00 0.00 2.59
2579 2663 5.163088 ACAAGTATTTTGGTTCAGAGGGAGT 60.163 40.000 0.00 0.00 0.00 3.85
2580 2664 5.316987 ACAAGTATTTTGGTTCAGAGGGAG 58.683 41.667 0.00 0.00 0.00 4.30
2581 2665 5.319043 ACAAGTATTTTGGTTCAGAGGGA 57.681 39.130 0.00 0.00 0.00 4.20
2582 2666 6.238648 ACTACAAGTATTTTGGTTCAGAGGG 58.761 40.000 0.00 0.00 0.00 4.30
2583 2667 7.584987 CAACTACAAGTATTTTGGTTCAGAGG 58.415 38.462 0.00 0.00 0.00 3.69
2584 2668 7.078228 GCAACTACAAGTATTTTGGTTCAGAG 58.922 38.462 0.00 0.00 0.00 3.35
2585 2669 6.293190 CGCAACTACAAGTATTTTGGTTCAGA 60.293 38.462 0.00 0.00 0.00 3.27
2586 2670 5.851177 CGCAACTACAAGTATTTTGGTTCAG 59.149 40.000 0.00 0.00 0.00 3.02
2587 2671 5.278071 CCGCAACTACAAGTATTTTGGTTCA 60.278 40.000 0.00 0.00 0.00 3.18
2588 2672 5.151389 CCGCAACTACAAGTATTTTGGTTC 58.849 41.667 0.00 0.00 0.00 3.62
2589 2673 4.557895 GCCGCAACTACAAGTATTTTGGTT 60.558 41.667 0.00 0.00 0.00 3.67
2590 2674 3.057806 GCCGCAACTACAAGTATTTTGGT 60.058 43.478 0.00 0.00 0.00 3.67
2591 2675 3.057876 TGCCGCAACTACAAGTATTTTGG 60.058 43.478 0.00 0.00 0.00 3.28
2592 2676 4.153958 TGCCGCAACTACAAGTATTTTG 57.846 40.909 0.00 0.00 0.00 2.44
2593 2677 4.542735 GTTGCCGCAACTACAAGTATTTT 58.457 39.130 25.78 0.00 40.73 1.82
2594 2678 4.155310 GTTGCCGCAACTACAAGTATTT 57.845 40.909 25.78 0.00 40.73 1.40
2595 2679 3.824414 GTTGCCGCAACTACAAGTATT 57.176 42.857 25.78 0.00 40.73 1.89
2605 2689 2.140717 ACTAGTACAAGTTGCCGCAAC 58.859 47.619 25.74 25.74 43.83 4.17
2606 2690 2.536761 ACTAGTACAAGTTGCCGCAA 57.463 45.000 0.38 0.38 0.00 4.85
2607 2691 2.036733 AGAACTAGTACAAGTTGCCGCA 59.963 45.455 1.81 0.00 39.78 5.69
2608 2692 2.666994 GAGAACTAGTACAAGTTGCCGC 59.333 50.000 1.81 0.00 39.78 6.53
2609 2693 3.251571 GGAGAACTAGTACAAGTTGCCG 58.748 50.000 1.81 0.00 39.78 5.69
2610 2694 3.597255 GGGAGAACTAGTACAAGTTGCC 58.403 50.000 1.81 0.00 39.78 4.52
2611 2695 3.007614 TGGGGAGAACTAGTACAAGTTGC 59.992 47.826 1.81 0.00 39.78 4.17
2612 2696 4.822026 CTGGGGAGAACTAGTACAAGTTG 58.178 47.826 0.00 0.00 39.78 3.16
2613 2697 3.261137 GCTGGGGAGAACTAGTACAAGTT 59.739 47.826 0.00 0.00 42.36 2.66
2614 2698 2.832733 GCTGGGGAGAACTAGTACAAGT 59.167 50.000 0.00 0.00 0.00 3.16
2615 2699 3.100671 AGCTGGGGAGAACTAGTACAAG 58.899 50.000 0.00 0.00 0.00 3.16
2616 2700 3.185880 AGCTGGGGAGAACTAGTACAA 57.814 47.619 0.00 0.00 0.00 2.41
2617 2701 2.921834 AGCTGGGGAGAACTAGTACA 57.078 50.000 0.00 0.00 0.00 2.90
2618 2702 3.261137 ACAAAGCTGGGGAGAACTAGTAC 59.739 47.826 0.00 0.00 0.00 2.73
2619 2703 3.517612 ACAAAGCTGGGGAGAACTAGTA 58.482 45.455 0.00 0.00 0.00 1.82
2620 2704 2.339769 ACAAAGCTGGGGAGAACTAGT 58.660 47.619 0.00 0.00 0.00 2.57
2621 2705 4.762289 ATACAAAGCTGGGGAGAACTAG 57.238 45.455 0.00 0.00 0.00 2.57
2622 2706 5.497474 GAAATACAAAGCTGGGGAGAACTA 58.503 41.667 0.00 0.00 0.00 2.24
2623 2707 4.336280 GAAATACAAAGCTGGGGAGAACT 58.664 43.478 0.00 0.00 0.00 3.01
2624 2708 3.127030 CGAAATACAAAGCTGGGGAGAAC 59.873 47.826 0.00 0.00 0.00 3.01
2625 2709 3.343617 CGAAATACAAAGCTGGGGAGAA 58.656 45.455 0.00 0.00 0.00 2.87
2626 2710 2.355716 CCGAAATACAAAGCTGGGGAGA 60.356 50.000 0.00 0.00 0.00 3.71
2627 2711 2.017049 CCGAAATACAAAGCTGGGGAG 58.983 52.381 0.00 0.00 0.00 4.30
2628 2712 1.353022 ACCGAAATACAAAGCTGGGGA 59.647 47.619 0.00 0.00 0.00 4.81
2629 2713 1.834188 ACCGAAATACAAAGCTGGGG 58.166 50.000 0.00 0.00 0.00 4.96
2630 2714 3.340034 TGTACCGAAATACAAAGCTGGG 58.660 45.455 0.00 0.00 32.07 4.45
2631 2715 4.250464 TCTGTACCGAAATACAAAGCTGG 58.750 43.478 0.00 0.00 34.68 4.85
2632 2716 4.330074 CCTCTGTACCGAAATACAAAGCTG 59.670 45.833 0.00 0.00 34.68 4.24
2633 2717 4.020485 ACCTCTGTACCGAAATACAAAGCT 60.020 41.667 0.00 0.00 34.68 3.74
2634 2718 4.251268 ACCTCTGTACCGAAATACAAAGC 58.749 43.478 0.00 0.00 34.68 3.51
2635 2719 9.760077 ATATTACCTCTGTACCGAAATACAAAG 57.240 33.333 0.00 0.00 34.68 2.77
2637 2721 9.754382 GAATATTACCTCTGTACCGAAATACAA 57.246 33.333 0.00 0.00 34.68 2.41
2638 2722 8.916062 TGAATATTACCTCTGTACCGAAATACA 58.084 33.333 0.00 0.00 33.96 2.29
2639 2723 9.924650 ATGAATATTACCTCTGTACCGAAATAC 57.075 33.333 0.00 0.00 0.00 1.89
2641 2725 8.647796 TGATGAATATTACCTCTGTACCGAAAT 58.352 33.333 0.00 0.00 0.00 2.17
2642 2726 8.014070 TGATGAATATTACCTCTGTACCGAAA 57.986 34.615 0.00 0.00 0.00 3.46
2643 2727 7.504574 TCTGATGAATATTACCTCTGTACCGAA 59.495 37.037 0.00 0.00 0.00 4.30
2644 2728 7.002276 TCTGATGAATATTACCTCTGTACCGA 58.998 38.462 0.00 0.00 0.00 4.69
2645 2729 7.040340 AGTCTGATGAATATTACCTCTGTACCG 60.040 40.741 0.00 0.00 0.00 4.02
2646 2730 8.184304 AGTCTGATGAATATTACCTCTGTACC 57.816 38.462 0.00 0.00 0.00 3.34
2647 2731 9.073475 AGAGTCTGATGAATATTACCTCTGTAC 57.927 37.037 0.00 0.00 0.00 2.90
2648 2732 9.072375 CAGAGTCTGATGAATATTACCTCTGTA 57.928 37.037 15.46 0.00 32.44 2.74
2649 2733 7.782168 TCAGAGTCTGATGAATATTACCTCTGT 59.218 37.037 19.10 0.00 35.39 3.41
2650 2734 8.081633 GTCAGAGTCTGATGAATATTACCTCTG 58.918 40.741 25.17 3.46 42.73 3.35
2651 2735 7.782168 TGTCAGAGTCTGATGAATATTACCTCT 59.218 37.037 25.17 0.00 42.73 3.69
2652 2736 7.946207 TGTCAGAGTCTGATGAATATTACCTC 58.054 38.462 25.17 8.59 42.73 3.85
2653 2737 7.904558 TGTCAGAGTCTGATGAATATTACCT 57.095 36.000 25.17 0.00 42.73 3.08
2654 2738 8.948631 TTTGTCAGAGTCTGATGAATATTACC 57.051 34.615 25.17 9.27 42.73 2.85
2716 2801 3.958018 TGTGGGTGTAGTGACTTTGTTT 58.042 40.909 0.00 0.00 0.00 2.83
2734 2819 7.043391 CGGACACAACACATCTATATACTTGTG 60.043 40.741 14.52 14.52 43.88 3.33
2752 2837 0.178301 TGCCTGTTACACGGACACAA 59.822 50.000 5.30 0.00 0.00 3.33
2753 2838 0.531090 GTGCCTGTTACACGGACACA 60.531 55.000 15.48 0.00 31.83 3.72
2754 2839 0.531090 TGTGCCTGTTACACGGACAC 60.531 55.000 4.83 10.86 41.03 3.67
2762 2847 6.403636 CCACTGAATTAGATTGTGCCTGTTAC 60.404 42.308 0.00 0.00 0.00 2.50
2769 2854 3.019564 AGGCCACTGAATTAGATTGTGC 58.980 45.455 5.01 0.00 0.00 4.57
2829 2915 0.175760 GGATCCTAGAGTGTGCGCAA 59.824 55.000 14.00 0.00 0.00 4.85
2848 2937 4.383602 CGAAAGTTGGTGGCGGCG 62.384 66.667 0.51 0.51 0.00 6.46
2855 2947 1.674322 CGGGATGGCGAAAGTTGGT 60.674 57.895 0.00 0.00 0.00 3.67
2859 2951 0.391263 GAAGACGGGATGGCGAAAGT 60.391 55.000 0.00 0.00 0.00 2.66
2863 2955 2.721167 CCTGAAGACGGGATGGCGA 61.721 63.158 0.00 0.00 44.87 5.54
2954 3047 1.225991 GATTGATTGACGCGCGCAA 60.226 52.632 30.88 30.88 0.00 4.85
2965 3058 3.820467 TCAAAGTTGGACGCAGATTGATT 59.180 39.130 0.00 0.00 0.00 2.57
2984 3077 1.536073 CGGGAGCAGTGGAGTCTCAA 61.536 60.000 1.47 0.00 0.00 3.02
3027 3123 2.805277 CGGTGTTATATCGACCGCC 58.195 57.895 0.00 0.00 45.55 6.13
3058 3154 3.560226 AGTGGTTCACTGGAGAGGT 57.440 52.632 0.00 0.00 43.63 3.85
3122 3218 2.158400 TCTCCCAGATCGGATGATGACT 60.158 50.000 0.00 0.00 36.56 3.41
3176 3273 1.081092 CCCCTCTTCCTCCAGGTGA 59.919 63.158 0.00 0.00 36.34 4.02
3200 3297 3.084579 CGTCGGCAGTTGCAGATC 58.915 61.111 10.00 4.13 46.08 2.75


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

AutoCloner maintained by Alex Coulton.