Multiple sequence alignment - TraesCS3D01G118000

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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 TraesCS3D01G118000 chr3D 100.000 2603 0 0 1 2603 71528454 71531056 0.000000e+00 4807.0
1 TraesCS3D01G118000 chr3A 94.317 1355 50 14 754 2096 83774050 83775389 0.000000e+00 2050.0
2 TraesCS3D01G118000 chr3A 80.736 462 47 19 2149 2603 83775385 83775811 3.230000e-84 322.0
3 TraesCS3D01G118000 chr3A 93.706 143 7 2 1 141 83771710 83771852 2.030000e-51 213.0
4 TraesCS3D01G118000 chr3A 86.826 167 16 4 181 342 83771849 83772014 5.720000e-42 182.0
5 TraesCS3D01G118000 chr3A 92.523 107 4 2 501 603 83773952 83774058 1.610000e-32 150.0
6 TraesCS3D01G118000 chr3B 94.924 1182 35 9 754 1924 117600269 117601436 0.000000e+00 1827.0
7 TraesCS3D01G118000 chr3B 85.366 492 40 13 121 603 117599809 117600277 5.040000e-132 481.0
8 TraesCS3D01G118000 chr3B 85.915 355 26 8 2032 2385 117601565 117601896 8.860000e-95 357.0
9 TraesCS3D01G118000 chr3B 91.892 148 12 0 604 751 67911980 67912127 9.440000e-50 207.0
10 TraesCS3D01G118000 chr7D 96.667 150 5 0 602 751 395936316 395936465 1.550000e-62 250.0
11 TraesCS3D01G118000 chr7D 96.053 152 6 0 598 749 578779272 578779423 5.560000e-62 248.0
12 TraesCS3D01G118000 chr4D 96.622 148 5 0 604 751 381102322 381102469 2.000000e-61 246.0
13 TraesCS3D01G118000 chr6D 84.979 233 19 10 2387 2603 27788544 27788776 3.370000e-54 222.0
14 TraesCS3D01G118000 chr6D 97.143 35 1 0 1537 1571 458887699 458887733 2.800000e-05 60.2
15 TraesCS3D01G118000 chr5D 84.322 236 23 3 2380 2601 322989784 322989549 4.360000e-53 219.0
16 TraesCS3D01G118000 chr7A 83.898 236 22 3 2383 2602 478160281 478160046 7.300000e-51 211.0
17 TraesCS3D01G118000 chr7A 83.200 125 19 2 2380 2504 661163881 661164003 2.120000e-21 113.0
18 TraesCS3D01G118000 chr2B 91.503 153 11 2 2453 2603 527886059 527885907 2.620000e-50 209.0
19 TraesCS3D01G118000 chr5A 91.216 148 12 1 2456 2602 502063714 502063567 1.580000e-47 200.0
20 TraesCS3D01G118000 chr2D 90.260 154 12 2 2453 2603 448140659 448140506 5.680000e-47 198.0
21 TraesCS3D01G118000 chr2A 89.542 153 14 2 2453 2603 592782299 592782147 2.640000e-45 193.0
22 TraesCS3D01G118000 chr1A 81.250 224 39 3 2382 2603 14058059 14057837 7.400000e-41 178.0
23 TraesCS3D01G118000 chr7B 83.200 125 19 2 2380 2504 628464107 628464229 2.120000e-21 113.0
24 TraesCS3D01G118000 chr6B 97.368 38 1 0 1534 1571 697950172 697950209 6.010000e-07 65.8
25 TraesCS3D01G118000 chr6B 97.368 38 1 0 1534 1571 698035781 698035818 6.010000e-07 65.8


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 TraesCS3D01G118000 chr3D 71528454 71531056 2602 False 4807.000000 4807 100.0000 1 2603 1 chr3D.!!$F1 2602
1 TraesCS3D01G118000 chr3A 83771710 83775811 4101 False 583.400000 2050 89.6216 1 2603 5 chr3A.!!$F1 2602
2 TraesCS3D01G118000 chr3B 117599809 117601896 2087 False 888.333333 1827 88.7350 121 2385 3 chr3B.!!$F2 2264

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
58 59 0.034089 AATAGCACTTGGCCCTCACC 60.034 55.0 0.00 0.0 46.50 4.02 F
760 2554 0.109272 GTAGCACTGCAGCACGAGTA 60.109 55.0 15.27 0.0 36.85 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 3299 0.325933 TCTCCCAGTTGCTCATGGTG 59.674 55.0 0.0 0.0 34.58 4.17 R
2511 4475 0.664466 GGTGCTTTTTGCTTCGGCTC 60.664 55.0 0.0 0.0 43.37 4.70 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 5.924475 AGTTGACGTATATTGGCAATAGC 57.076 39.130 23.01 16.96 41.10 2.97
58 59 0.034089 AATAGCACTTGGCCCTCACC 60.034 55.000 0.00 0.00 46.50 4.02
137 139 8.740369 CAAAAATGATTTGCGCAAAACAAATTA 58.260 25.926 37.97 21.76 45.33 1.40
157 159 6.920569 ATTAAAATGGTGGTAGTCGTCATC 57.079 37.500 0.00 0.00 0.00 2.92
162 164 3.395639 TGGTGGTAGTCGTCATCAAAAC 58.604 45.455 0.00 0.00 0.00 2.43
350 1790 7.361127 TGCCACAAAAATAAAAATCATTGCAG 58.639 30.769 0.00 0.00 0.00 4.41
395 1835 4.385447 CAGGATTTGTGGCAATAAACAACG 59.615 41.667 0.00 0.00 36.08 4.10
438 1880 3.959943 AGCGACAACAAACATACAAACC 58.040 40.909 0.00 0.00 0.00 3.27
457 1899 6.974048 ACAAACCGTGGTTGTAAAAGATAAAC 59.026 34.615 4.79 0.00 38.47 2.01
462 1909 7.041576 ACCGTGGTTGTAAAAGATAAACTCTTC 60.042 37.037 0.00 0.00 43.60 2.87
517 2307 6.211587 TCGGAGTATATCGTTTTCTTTCCA 57.788 37.500 0.00 0.00 0.00 3.53
561 2351 3.432326 GGTAGAAATCCTAGGGTGCACTG 60.432 52.174 17.98 4.86 0.00 3.66
563 2357 0.392998 AAATCCTAGGGTGCACTGCG 60.393 55.000 17.98 3.02 0.00 5.18
603 2397 1.263217 CAGCCAAACCACACGAGTAAC 59.737 52.381 0.00 0.00 0.00 2.50
605 2399 1.855513 CCAAACCACACGAGTAACGA 58.144 50.000 0.00 0.00 45.77 3.85
606 2400 2.203401 CCAAACCACACGAGTAACGAA 58.797 47.619 0.00 0.00 45.77 3.85
607 2401 2.608546 CCAAACCACACGAGTAACGAAA 59.391 45.455 0.00 0.00 45.77 3.46
608 2402 3.249080 CCAAACCACACGAGTAACGAAAT 59.751 43.478 0.00 0.00 45.77 2.17
609 2403 4.260866 CCAAACCACACGAGTAACGAAATT 60.261 41.667 0.00 0.00 45.77 1.82
610 2404 4.461992 AACCACACGAGTAACGAAATTG 57.538 40.909 0.00 0.00 45.77 2.32
611 2405 2.222445 ACCACACGAGTAACGAAATTGC 59.778 45.455 0.00 0.00 45.77 3.56
612 2406 2.478894 CCACACGAGTAACGAAATTGCT 59.521 45.455 0.00 0.00 45.77 3.91
613 2407 3.059188 CCACACGAGTAACGAAATTGCTT 60.059 43.478 0.00 0.00 45.77 3.91
614 2408 4.523813 CACACGAGTAACGAAATTGCTTT 58.476 39.130 0.00 0.00 45.77 3.51
615 2409 4.375698 CACACGAGTAACGAAATTGCTTTG 59.624 41.667 0.00 0.00 45.77 2.77
616 2410 3.357823 CACGAGTAACGAAATTGCTTTGC 59.642 43.478 0.00 0.00 45.77 3.68
617 2411 2.583801 CGAGTAACGAAATTGCTTTGCG 59.416 45.455 0.00 0.00 45.77 4.85
618 2412 3.551551 GAGTAACGAAATTGCTTTGCGT 58.448 40.909 0.76 0.76 32.69 5.24
619 2413 4.664640 CGAGTAACGAAATTGCTTTGCGTA 60.665 41.667 6.44 0.00 45.77 4.42
620 2414 4.460505 AGTAACGAAATTGCTTTGCGTAC 58.539 39.130 6.44 5.98 32.07 3.67
621 2415 1.945207 ACGAAATTGCTTTGCGTACG 58.055 45.000 11.84 11.84 31.23 3.67
622 2416 1.527736 ACGAAATTGCTTTGCGTACGA 59.472 42.857 21.65 0.80 31.23 3.43
623 2417 1.896193 CGAAATTGCTTTGCGTACGAC 59.104 47.619 21.65 11.11 0.00 4.34
624 2418 2.411031 CGAAATTGCTTTGCGTACGACT 60.411 45.455 21.65 0.00 0.00 4.18
625 2419 2.594529 AATTGCTTTGCGTACGACTG 57.405 45.000 21.65 6.54 0.00 3.51
626 2420 1.790755 ATTGCTTTGCGTACGACTGA 58.209 45.000 21.65 0.00 0.00 3.41
627 2421 1.790755 TTGCTTTGCGTACGACTGAT 58.209 45.000 21.65 0.00 0.00 2.90
628 2422 1.790755 TGCTTTGCGTACGACTGATT 58.209 45.000 21.65 0.00 0.00 2.57
629 2423 2.949142 TGCTTTGCGTACGACTGATTA 58.051 42.857 21.65 0.00 0.00 1.75
630 2424 2.664568 TGCTTTGCGTACGACTGATTAC 59.335 45.455 21.65 0.00 0.00 1.89
631 2425 2.664568 GCTTTGCGTACGACTGATTACA 59.335 45.455 21.65 1.12 0.00 2.41
632 2426 3.306166 GCTTTGCGTACGACTGATTACAT 59.694 43.478 21.65 0.00 0.00 2.29
633 2427 4.548346 GCTTTGCGTACGACTGATTACATC 60.548 45.833 21.65 0.00 0.00 3.06
634 2428 3.074504 TGCGTACGACTGATTACATCC 57.925 47.619 21.65 0.00 0.00 3.51
635 2429 2.041966 GCGTACGACTGATTACATCCG 58.958 52.381 21.65 0.00 0.00 4.18
636 2430 2.286595 GCGTACGACTGATTACATCCGA 60.287 50.000 21.65 0.00 0.00 4.55
637 2431 3.608707 GCGTACGACTGATTACATCCGAT 60.609 47.826 21.65 0.00 0.00 4.18
638 2432 4.534168 CGTACGACTGATTACATCCGATT 58.466 43.478 10.44 0.00 0.00 3.34
639 2433 4.974275 CGTACGACTGATTACATCCGATTT 59.026 41.667 10.44 0.00 0.00 2.17
640 2434 5.108368 CGTACGACTGATTACATCCGATTTG 60.108 44.000 10.44 0.00 0.00 2.32
641 2435 3.555956 ACGACTGATTACATCCGATTTGC 59.444 43.478 0.00 0.00 0.00 3.68
642 2436 3.555547 CGACTGATTACATCCGATTTGCA 59.444 43.478 0.00 0.00 0.00 4.08
643 2437 4.212004 CGACTGATTACATCCGATTTGCAT 59.788 41.667 0.00 0.00 0.00 3.96
644 2438 5.405269 CGACTGATTACATCCGATTTGCATA 59.595 40.000 0.00 0.00 0.00 3.14
645 2439 6.545504 ACTGATTACATCCGATTTGCATAC 57.454 37.500 0.00 0.00 0.00 2.39
646 2440 6.054941 ACTGATTACATCCGATTTGCATACA 58.945 36.000 0.00 0.00 0.00 2.29
647 2441 6.203530 ACTGATTACATCCGATTTGCATACAG 59.796 38.462 0.00 0.00 0.00 2.74
648 2442 6.054941 TGATTACATCCGATTTGCATACAGT 58.945 36.000 0.00 0.00 0.00 3.55
649 2443 7.213678 TGATTACATCCGATTTGCATACAGTA 58.786 34.615 0.00 0.00 0.00 2.74
650 2444 7.877612 TGATTACATCCGATTTGCATACAGTAT 59.122 33.333 0.00 0.00 0.00 2.12
651 2445 5.929697 ACATCCGATTTGCATACAGTATG 57.070 39.130 15.39 15.39 46.00 2.39
652 2446 4.756642 ACATCCGATTTGCATACAGTATGG 59.243 41.667 20.16 3.97 43.62 2.74
653 2447 4.415881 TCCGATTTGCATACAGTATGGT 57.584 40.909 20.16 0.00 43.62 3.55
654 2448 4.126437 TCCGATTTGCATACAGTATGGTG 58.874 43.478 20.16 0.00 43.62 4.17
655 2449 4.126437 CCGATTTGCATACAGTATGGTGA 58.874 43.478 20.16 0.00 43.62 4.02
656 2450 4.756642 CCGATTTGCATACAGTATGGTGAT 59.243 41.667 20.16 0.81 43.62 3.06
657 2451 5.106948 CCGATTTGCATACAGTATGGTGATC 60.107 44.000 20.16 5.62 43.62 2.92
658 2452 5.106948 CGATTTGCATACAGTATGGTGATCC 60.107 44.000 20.16 4.99 43.62 3.36
659 2453 5.372343 TTTGCATACAGTATGGTGATCCT 57.628 39.130 20.16 0.00 43.62 3.24
660 2454 6.493189 TTTGCATACAGTATGGTGATCCTA 57.507 37.500 20.16 0.00 43.62 2.94
661 2455 5.468540 TGCATACAGTATGGTGATCCTAC 57.531 43.478 20.16 3.09 43.62 3.18
662 2456 4.283467 TGCATACAGTATGGTGATCCTACC 59.717 45.833 20.16 2.45 43.62 3.18
663 2457 4.528596 GCATACAGTATGGTGATCCTACCT 59.471 45.833 20.16 0.00 43.62 3.08
664 2458 5.336849 GCATACAGTATGGTGATCCTACCTC 60.337 48.000 20.16 0.00 43.62 3.85
665 2459 4.544564 ACAGTATGGTGATCCTACCTCT 57.455 45.455 4.04 0.00 43.62 3.69
666 2460 4.219115 ACAGTATGGTGATCCTACCTCTG 58.781 47.826 14.54 14.54 43.62 3.35
667 2461 4.219115 CAGTATGGTGATCCTACCTCTGT 58.781 47.826 4.04 0.00 41.43 3.41
668 2462 4.651503 CAGTATGGTGATCCTACCTCTGTT 59.348 45.833 4.04 0.00 41.43 3.16
669 2463 4.896482 AGTATGGTGATCCTACCTCTGTTC 59.104 45.833 4.04 0.00 41.43 3.18
670 2464 3.474798 TGGTGATCCTACCTCTGTTCT 57.525 47.619 4.04 0.00 41.43 3.01
671 2465 3.791320 TGGTGATCCTACCTCTGTTCTT 58.209 45.455 4.04 0.00 41.43 2.52
672 2466 4.942944 TGGTGATCCTACCTCTGTTCTTA 58.057 43.478 4.04 0.00 41.43 2.10
673 2467 5.338632 TGGTGATCCTACCTCTGTTCTTAA 58.661 41.667 4.04 0.00 41.43 1.85
674 2468 5.783360 TGGTGATCCTACCTCTGTTCTTAAA 59.217 40.000 4.04 0.00 41.43 1.52
675 2469 6.070767 TGGTGATCCTACCTCTGTTCTTAAAG 60.071 42.308 4.04 0.00 41.43 1.85
676 2470 6.342111 GTGATCCTACCTCTGTTCTTAAAGG 58.658 44.000 0.00 0.00 34.94 3.11
677 2471 6.154706 GTGATCCTACCTCTGTTCTTAAAGGA 59.845 42.308 0.00 0.00 36.39 3.36
678 2472 6.381420 TGATCCTACCTCTGTTCTTAAAGGAG 59.619 42.308 0.00 0.00 35.47 3.69
679 2473 5.652324 TCCTACCTCTGTTCTTAAAGGAGT 58.348 41.667 0.00 0.00 32.99 3.85
680 2474 5.480772 TCCTACCTCTGTTCTTAAAGGAGTG 59.519 44.000 0.00 0.00 32.99 3.51
681 2475 5.480772 CCTACCTCTGTTCTTAAAGGAGTGA 59.519 44.000 0.00 0.00 32.99 3.41
682 2476 5.216614 ACCTCTGTTCTTAAAGGAGTGAC 57.783 43.478 0.00 0.00 32.99 3.67
683 2477 4.902448 ACCTCTGTTCTTAAAGGAGTGACT 59.098 41.667 0.00 0.00 32.99 3.41
684 2478 5.367060 ACCTCTGTTCTTAAAGGAGTGACTT 59.633 40.000 0.00 0.00 32.99 3.01
685 2479 5.698545 CCTCTGTTCTTAAAGGAGTGACTTG 59.301 44.000 0.00 0.00 0.00 3.16
686 2480 6.463049 CCTCTGTTCTTAAAGGAGTGACTTGA 60.463 42.308 0.00 0.00 0.00 3.02
687 2481 7.067496 TCTGTTCTTAAAGGAGTGACTTGAT 57.933 36.000 0.00 0.00 0.00 2.57
688 2482 7.155328 TCTGTTCTTAAAGGAGTGACTTGATC 58.845 38.462 0.00 0.00 0.00 2.92
689 2483 6.231211 TGTTCTTAAAGGAGTGACTTGATCC 58.769 40.000 0.00 0.00 0.00 3.36
690 2484 6.043243 TGTTCTTAAAGGAGTGACTTGATCCT 59.957 38.462 0.00 0.00 45.50 3.24
691 2485 7.234782 TGTTCTTAAAGGAGTGACTTGATCCTA 59.765 37.037 0.00 0.00 42.72 2.94
692 2486 7.411486 TCTTAAAGGAGTGACTTGATCCTAG 57.589 40.000 0.00 0.00 42.72 3.02
693 2487 6.381420 TCTTAAAGGAGTGACTTGATCCTAGG 59.619 42.308 0.82 0.82 42.72 3.02
694 2488 3.039252 AGGAGTGACTTGATCCTAGGG 57.961 52.381 9.46 0.00 41.72 3.53
695 2489 2.316372 AGGAGTGACTTGATCCTAGGGT 59.684 50.000 9.46 0.00 41.72 4.34
696 2490 2.432510 GGAGTGACTTGATCCTAGGGTG 59.567 54.545 9.46 0.00 0.00 4.61
697 2491 3.366396 GAGTGACTTGATCCTAGGGTGA 58.634 50.000 9.46 0.00 0.00 4.02
698 2492 3.100671 AGTGACTTGATCCTAGGGTGAC 58.899 50.000 9.46 2.69 0.00 3.67
699 2493 3.100671 GTGACTTGATCCTAGGGTGACT 58.899 50.000 9.46 0.00 0.00 3.41
700 2494 3.099905 TGACTTGATCCTAGGGTGACTG 58.900 50.000 9.46 0.00 0.00 3.51
701 2495 3.245622 TGACTTGATCCTAGGGTGACTGA 60.246 47.826 9.46 0.00 0.00 3.41
702 2496 3.100671 ACTTGATCCTAGGGTGACTGAC 58.899 50.000 9.46 0.00 0.00 3.51
703 2497 3.245803 ACTTGATCCTAGGGTGACTGACT 60.246 47.826 9.46 0.00 0.00 3.41
704 2498 4.017407 ACTTGATCCTAGGGTGACTGACTA 60.017 45.833 9.46 0.00 0.00 2.59
705 2499 4.603094 TGATCCTAGGGTGACTGACTAA 57.397 45.455 9.46 0.00 0.00 2.24
706 2500 5.144159 TGATCCTAGGGTGACTGACTAAT 57.856 43.478 9.46 0.00 0.00 1.73
707 2501 4.895889 TGATCCTAGGGTGACTGACTAATG 59.104 45.833 9.46 0.00 0.00 1.90
708 2502 4.332683 TCCTAGGGTGACTGACTAATGT 57.667 45.455 9.46 0.00 0.00 2.71
709 2503 4.279145 TCCTAGGGTGACTGACTAATGTC 58.721 47.826 9.46 0.00 43.20 3.06
710 2504 3.066900 CCTAGGGTGACTGACTAATGTCG 59.933 52.174 0.00 0.00 45.70 4.35
711 2505 2.526432 AGGGTGACTGACTAATGTCGT 58.474 47.619 0.00 0.00 45.70 4.34
712 2506 3.693807 AGGGTGACTGACTAATGTCGTA 58.306 45.455 0.00 0.00 45.70 3.43
713 2507 3.442977 AGGGTGACTGACTAATGTCGTAC 59.557 47.826 0.00 0.00 45.70 3.67
714 2508 3.192001 GGGTGACTGACTAATGTCGTACA 59.808 47.826 0.00 0.00 45.70 2.90
715 2509 4.142227 GGGTGACTGACTAATGTCGTACAT 60.142 45.833 0.00 0.00 45.70 2.29
716 2510 5.035443 GGTGACTGACTAATGTCGTACATC 58.965 45.833 0.00 0.00 45.70 3.06
717 2511 5.392703 GGTGACTGACTAATGTCGTACATCA 60.393 44.000 0.00 0.00 45.70 3.07
718 2512 6.266323 GTGACTGACTAATGTCGTACATCAT 58.734 40.000 0.00 0.00 45.70 2.45
719 2513 6.415280 GTGACTGACTAATGTCGTACATCATC 59.585 42.308 0.00 2.03 45.70 2.92
720 2514 5.511571 ACTGACTAATGTCGTACATCATCG 58.488 41.667 0.00 0.00 45.70 3.84
721 2515 4.855531 TGACTAATGTCGTACATCATCGG 58.144 43.478 0.00 0.00 45.70 4.18
722 2516 4.577283 TGACTAATGTCGTACATCATCGGA 59.423 41.667 0.00 0.00 45.70 4.55
723 2517 5.240844 TGACTAATGTCGTACATCATCGGAT 59.759 40.000 0.00 0.00 45.70 4.18
724 2518 5.569441 GACTAATGTCGTACATCATCGGATG 59.431 44.000 11.79 11.79 43.48 3.51
725 2519 6.567891 GACTAATGTCGTACATCATCGGATGA 60.568 42.308 21.92 21.92 42.10 2.92
726 2520 7.995611 GACTAATGTCGTACATCATCGGATGAA 60.996 40.741 23.29 5.80 42.10 2.57
738 2532 7.639162 ATCATCGGATGAAAAGTTATCGTAC 57.361 36.000 23.29 0.00 43.50 3.67
739 2533 5.684184 TCATCGGATGAAAAGTTATCGTACG 59.316 40.000 17.94 9.53 40.68 3.67
740 2534 4.985413 TCGGATGAAAAGTTATCGTACGT 58.015 39.130 16.05 5.39 40.30 3.57
741 2535 4.794762 TCGGATGAAAAGTTATCGTACGTG 59.205 41.667 16.05 0.00 40.30 4.49
742 2536 4.560035 CGGATGAAAAGTTATCGTACGTGT 59.440 41.667 16.05 8.10 35.81 4.49
743 2537 5.738693 CGGATGAAAAGTTATCGTACGTGTA 59.261 40.000 16.05 7.08 35.81 2.90
744 2538 6.075728 CGGATGAAAAGTTATCGTACGTGTAG 60.076 42.308 16.05 0.00 35.81 2.74
745 2539 5.997732 TGAAAAGTTATCGTACGTGTAGC 57.002 39.130 16.05 11.36 0.00 3.58
746 2540 5.459768 TGAAAAGTTATCGTACGTGTAGCA 58.540 37.500 16.05 0.00 0.00 3.49
747 2541 5.343058 TGAAAAGTTATCGTACGTGTAGCAC 59.657 40.000 16.05 6.23 0.00 4.40
748 2542 4.691860 AAGTTATCGTACGTGTAGCACT 57.308 40.909 16.05 8.21 31.34 4.40
749 2543 4.012319 AGTTATCGTACGTGTAGCACTG 57.988 45.455 16.05 0.00 31.34 3.66
750 2544 2.463553 TATCGTACGTGTAGCACTGC 57.536 50.000 16.05 0.00 31.34 4.40
751 2545 0.524414 ATCGTACGTGTAGCACTGCA 59.476 50.000 16.05 0.00 31.34 4.41
752 2546 0.109919 TCGTACGTGTAGCACTGCAG 60.110 55.000 16.05 13.48 31.34 4.41
753 2547 1.674611 CGTACGTGTAGCACTGCAGC 61.675 60.000 15.27 0.57 31.34 5.25
754 2548 0.666274 GTACGTGTAGCACTGCAGCA 60.666 55.000 15.27 0.00 36.85 4.41
755 2549 0.666274 TACGTGTAGCACTGCAGCAC 60.666 55.000 15.27 12.30 36.85 4.40
756 2550 2.856032 GTGTAGCACTGCAGCACG 59.144 61.111 15.27 3.56 36.85 5.34
757 2551 1.664649 GTGTAGCACTGCAGCACGA 60.665 57.895 15.27 0.00 36.85 4.35
758 2552 1.373371 TGTAGCACTGCAGCACGAG 60.373 57.895 15.27 0.00 36.85 4.18
759 2553 1.373497 GTAGCACTGCAGCACGAGT 60.373 57.895 15.27 0.00 36.85 4.18
760 2554 0.109272 GTAGCACTGCAGCACGAGTA 60.109 55.000 15.27 0.00 36.85 2.59
761 2555 0.601057 TAGCACTGCAGCACGAGTAA 59.399 50.000 15.27 0.00 36.85 2.24
792 2587 4.402474 ACGATTCCCCCAAAAGATGAATTC 59.598 41.667 0.00 0.00 0.00 2.17
901 2696 1.532868 GTGGTTGAAGCAGCACTACAG 59.467 52.381 0.00 0.00 41.18 2.74
902 2697 1.140852 TGGTTGAAGCAGCACTACAGT 59.859 47.619 0.00 0.00 0.00 3.55
904 2699 2.031682 GGTTGAAGCAGCACTACAGTTG 60.032 50.000 0.00 0.00 0.00 3.16
905 2700 2.614057 GTTGAAGCAGCACTACAGTTGT 59.386 45.455 0.00 0.00 0.00 3.32
906 2701 3.744238 TGAAGCAGCACTACAGTTGTA 57.256 42.857 0.00 0.00 0.00 2.41
907 2702 3.390135 TGAAGCAGCACTACAGTTGTAC 58.610 45.455 0.00 0.00 0.00 2.90
908 2703 3.069586 TGAAGCAGCACTACAGTTGTACT 59.930 43.478 0.00 0.00 0.00 2.73
909 2704 4.279922 TGAAGCAGCACTACAGTTGTACTA 59.720 41.667 0.00 0.00 0.00 1.82
910 2705 4.175787 AGCAGCACTACAGTTGTACTAC 57.824 45.455 0.00 0.00 0.00 2.73
912 2707 5.008331 AGCAGCACTACAGTTGTACTACTA 58.992 41.667 9.68 0.00 0.00 1.82
913 2708 5.652891 AGCAGCACTACAGTTGTACTACTAT 59.347 40.000 9.68 1.33 0.00 2.12
914 2709 6.827251 AGCAGCACTACAGTTGTACTACTATA 59.173 38.462 9.68 2.54 0.00 1.31
915 2710 7.502895 AGCAGCACTACAGTTGTACTACTATAT 59.497 37.037 9.68 2.14 0.00 0.86
916 2711 8.781196 GCAGCACTACAGTTGTACTACTATATA 58.219 37.037 9.68 3.12 0.00 0.86
947 2742 0.176680 AGACCTAGCCATGAACAGCG 59.823 55.000 0.00 0.00 0.00 5.18
1069 2871 4.293648 CGGTCACCAGCGACACCA 62.294 66.667 0.00 0.00 46.86 4.17
1233 3035 3.699894 ACCAGCTGCCTCGTCCTG 61.700 66.667 8.66 0.00 0.00 3.86
1527 3332 2.511145 GAGAGGCGCCAGCTTGAG 60.511 66.667 31.54 0.00 44.37 3.02
1648 3456 4.036498 GCTTGTCACTCGGAGCTACTATTA 59.964 45.833 4.58 0.00 32.54 0.98
1736 3545 2.784356 GCCAGTGTGGTGCTGCAAA 61.784 57.895 2.77 0.00 40.46 3.68
1772 3581 6.566942 GCATGTTCTATTGTGTTGGTCGTTTA 60.567 38.462 0.00 0.00 0.00 2.01
1783 3592 6.201425 TGTGTTGGTCGTTTACTTGTATTCTC 59.799 38.462 0.00 0.00 0.00 2.87
1791 3600 6.580041 TCGTTTACTTGTATTCTCGACAGTTC 59.420 38.462 0.00 0.00 0.00 3.01
1923 3735 4.401202 TGCATGTCGTCTGGTATTAGAAGA 59.599 41.667 0.00 0.00 33.73 2.87
1924 3736 5.105513 TGCATGTCGTCTGGTATTAGAAGAA 60.106 40.000 0.00 0.00 37.04 2.52
1925 3737 5.232414 GCATGTCGTCTGGTATTAGAAGAAC 59.768 44.000 0.00 0.00 37.04 3.01
1937 3749 2.910688 AGAAGAACGCCAAGAAGACA 57.089 45.000 0.00 0.00 0.00 3.41
1941 3753 1.202486 AGAACGCCAAGAAGACACGAA 60.202 47.619 0.00 0.00 0.00 3.85
1942 3754 1.595794 GAACGCCAAGAAGACACGAAA 59.404 47.619 0.00 0.00 0.00 3.46
1943 3755 1.878953 ACGCCAAGAAGACACGAAAT 58.121 45.000 0.00 0.00 0.00 2.17
1944 3756 1.798813 ACGCCAAGAAGACACGAAATC 59.201 47.619 0.00 0.00 0.00 2.17
1946 3758 2.416547 CGCCAAGAAGACACGAAATCAT 59.583 45.455 0.00 0.00 0.00 2.45
1947 3759 3.616821 CGCCAAGAAGACACGAAATCATA 59.383 43.478 0.00 0.00 0.00 2.15
1948 3760 4.271049 CGCCAAGAAGACACGAAATCATAT 59.729 41.667 0.00 0.00 0.00 1.78
1950 3762 6.562270 CGCCAAGAAGACACGAAATCATATAC 60.562 42.308 0.00 0.00 0.00 1.47
1959 3774 8.234546 AGACACGAAATCATATACAAAACCAAC 58.765 33.333 0.00 0.00 0.00 3.77
1976 3791 8.391106 CAAAACCAACGGAAACAAATGAAAATA 58.609 29.630 0.00 0.00 0.00 1.40
1990 3805 9.180678 ACAAATGAAAATACAAAACGCTAAGAG 57.819 29.630 0.00 0.00 0.00 2.85
2012 3827 3.753797 GACCCAAAACCAAAACAAGCAAA 59.246 39.130 0.00 0.00 0.00 3.68
2016 3831 3.738286 AAACCAAAACAAGCAAAAGCG 57.262 38.095 0.00 0.00 0.00 4.68
2073 4008 1.143813 CTAGTGATCAGGGGGCCAAT 58.856 55.000 4.39 0.00 0.00 3.16
2116 4051 2.602878 CATGGACTGATGCTGCAAAAC 58.397 47.619 6.36 2.07 0.00 2.43
2127 4062 4.488126 TGCTGCAAAACTATTCAGTGTC 57.512 40.909 0.00 0.00 34.36 3.67
2143 4078 5.551233 TCAGTGTCAGCATAATATTAGGCC 58.449 41.667 24.36 12.62 41.02 5.19
2185 4120 2.736670 AGTTGGCAAGTTCTCTGGTT 57.263 45.000 0.00 0.00 0.00 3.67
2186 4121 2.301346 AGTTGGCAAGTTCTCTGGTTG 58.699 47.619 0.00 0.00 0.00 3.77
2192 4127 3.191371 GGCAAGTTCTCTGGTTGGTTATG 59.809 47.826 0.00 0.00 0.00 1.90
2193 4128 4.072131 GCAAGTTCTCTGGTTGGTTATGA 58.928 43.478 0.00 0.00 0.00 2.15
2194 4129 4.518970 GCAAGTTCTCTGGTTGGTTATGAA 59.481 41.667 0.00 0.00 0.00 2.57
2195 4130 5.562890 GCAAGTTCTCTGGTTGGTTATGAAC 60.563 44.000 0.00 0.00 34.39 3.18
2196 4131 5.304686 AGTTCTCTGGTTGGTTATGAACA 57.695 39.130 0.00 0.00 35.98 3.18
2197 4132 5.690865 AGTTCTCTGGTTGGTTATGAACAA 58.309 37.500 0.00 0.00 35.98 2.83
2198 4133 6.126409 AGTTCTCTGGTTGGTTATGAACAAA 58.874 36.000 0.00 0.00 35.98 2.83
2199 4134 6.605594 AGTTCTCTGGTTGGTTATGAACAAAA 59.394 34.615 0.00 0.00 35.98 2.44
2342 4291 7.209528 AGGATAAGACCTTATGCCTATGAGCA 61.210 42.308 14.83 0.00 42.52 4.26
2343 4292 8.628659 AGGATAAGACCTTATGCCTATGAGCAA 61.629 40.741 14.83 0.00 42.52 3.91
2385 4334 7.389053 ACACATTTTTCTCTAAGCTGACTAAGG 59.611 37.037 0.00 0.00 0.00 2.69
2386 4335 6.372937 ACATTTTTCTCTAAGCTGACTAAGGC 59.627 38.462 0.00 0.00 0.00 4.35
2387 4336 4.473477 TTTCTCTAAGCTGACTAAGGCC 57.527 45.455 0.00 0.00 0.00 5.19
2388 4337 2.389715 TCTCTAAGCTGACTAAGGCCC 58.610 52.381 0.00 0.00 0.00 5.80
2389 4338 2.023888 TCTCTAAGCTGACTAAGGCCCT 60.024 50.000 0.00 0.00 0.00 5.19
2390 4339 2.102252 CTCTAAGCTGACTAAGGCCCTG 59.898 54.545 0.00 0.00 0.00 4.45
2391 4340 1.834263 CTAAGCTGACTAAGGCCCTGT 59.166 52.381 0.00 0.00 0.00 4.00
2392 4341 1.068121 AAGCTGACTAAGGCCCTGTT 58.932 50.000 0.00 0.00 0.00 3.16
2393 4342 1.068121 AGCTGACTAAGGCCCTGTTT 58.932 50.000 0.00 0.00 0.00 2.83
2394 4343 1.168714 GCTGACTAAGGCCCTGTTTG 58.831 55.000 0.00 0.00 0.00 2.93
2395 4344 1.545651 GCTGACTAAGGCCCTGTTTGT 60.546 52.381 0.00 0.00 0.00 2.83
2396 4345 2.863809 CTGACTAAGGCCCTGTTTGTT 58.136 47.619 0.00 0.00 0.00 2.83
2397 4346 3.222603 CTGACTAAGGCCCTGTTTGTTT 58.777 45.455 0.00 0.00 0.00 2.83
2398 4347 2.955660 TGACTAAGGCCCTGTTTGTTTG 59.044 45.455 0.00 0.00 0.00 2.93
2399 4348 2.296190 GACTAAGGCCCTGTTTGTTTGG 59.704 50.000 0.00 0.00 0.00 3.28
2400 4349 1.618343 CTAAGGCCCTGTTTGTTTGGG 59.382 52.381 0.00 0.00 43.62 4.12
2401 4350 0.326143 AAGGCCCTGTTTGTTTGGGT 60.326 50.000 0.00 0.00 42.77 4.51
2402 4351 0.326143 AGGCCCTGTTTGTTTGGGTT 60.326 50.000 0.00 0.00 42.77 4.11
2403 4352 0.544223 GGCCCTGTTTGTTTGGGTTT 59.456 50.000 0.00 0.00 42.77 3.27
2404 4353 1.065053 GGCCCTGTTTGTTTGGGTTTT 60.065 47.619 0.00 0.00 42.77 2.43
2405 4354 2.619332 GGCCCTGTTTGTTTGGGTTTTT 60.619 45.455 0.00 0.00 42.77 1.94
2434 4383 5.641777 GCTTTTACAGCTTTTCCACTTTG 57.358 39.130 0.00 0.00 46.27 2.77
2526 4490 1.932156 GCCAAGAGCCGAAGCAAAAAG 60.932 52.381 0.00 0.00 43.56 2.27
2527 4491 1.412387 CAAGAGCCGAAGCAAAAAGC 58.588 50.000 0.00 0.00 43.56 3.51
2548 4513 6.590234 AGCACCTATTTAGGAACTTTTTGG 57.410 37.500 10.61 0.00 46.63 3.28
2592 4558 4.471157 TTGCAAAAGCATAAGCAAAAGC 57.529 36.364 0.00 0.00 43.24 3.51
2594 4560 2.160219 GCAAAAGCATAAGCAAAAGCCC 59.840 45.455 0.00 0.00 45.49 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.314321 GCTATTGCCAATATACGTCAACTATAT 57.686 33.333 0.00 0.00 0.00 0.86
103 104 9.539139 TTTGCGCAAATCATTTTTGTTATAATG 57.461 25.926 30.63 0.00 33.96 1.90
106 107 8.551205 TGTTTTGCGCAAATCATTTTTGTTATA 58.449 25.926 32.25 14.50 0.00 0.98
119 121 7.167136 CACCATTTTAATTTGTTTTGCGCAAAT 59.833 29.630 33.94 21.01 45.21 2.32
137 139 4.280436 TGATGACGACTACCACCATTTT 57.720 40.909 0.00 0.00 0.00 1.82
172 174 9.755804 TGTTGCAATAGTATGTTTTCATTCAAA 57.244 25.926 0.59 0.00 41.25 2.69
269 272 1.885887 GTACCCATGACTTTTGCTGCA 59.114 47.619 0.00 0.00 0.00 4.41
300 303 3.016736 CCTATTTGTTGCTACCCTGTGG 58.983 50.000 0.00 0.00 37.80 4.17
301 304 3.686016 ACCTATTTGTTGCTACCCTGTG 58.314 45.455 0.00 0.00 0.00 3.66
350 1790 4.334203 TGGTTTCGTGGTAATATGATGTGC 59.666 41.667 0.00 0.00 0.00 4.57
407 1847 4.797868 TGTTTGTTGTCGCTCTCATTTTTG 59.202 37.500 0.00 0.00 0.00 2.44
410 1850 4.836125 ATGTTTGTTGTCGCTCTCATTT 57.164 36.364 0.00 0.00 0.00 2.32
413 1853 3.723260 TGTATGTTTGTTGTCGCTCTCA 58.277 40.909 0.00 0.00 0.00 3.27
414 1854 4.725556 TTGTATGTTTGTTGTCGCTCTC 57.274 40.909 0.00 0.00 0.00 3.20
419 1861 3.721798 CACGGTTTGTATGTTTGTTGTCG 59.278 43.478 0.00 0.00 0.00 4.35
483 1933 6.334989 ACGATATACTCCGATTTTGTTGTGA 58.665 36.000 0.00 0.00 0.00 3.58
561 2351 3.363871 GGCAAATTTGACCAAAATCACGC 60.364 43.478 22.31 1.15 37.51 5.34
563 2357 4.319694 GCTGGCAAATTTGACCAAAATCAC 60.320 41.667 21.29 9.10 37.51 3.06
603 2397 1.896193 GTCGTACGCAAAGCAATTTCG 59.104 47.619 11.24 0.00 0.00 3.46
604 2398 2.902484 CAGTCGTACGCAAAGCAATTTC 59.098 45.455 11.24 0.00 0.00 2.17
605 2399 2.546368 TCAGTCGTACGCAAAGCAATTT 59.454 40.909 11.24 0.00 0.00 1.82
606 2400 2.139917 TCAGTCGTACGCAAAGCAATT 58.860 42.857 11.24 0.00 0.00 2.32
607 2401 1.790755 TCAGTCGTACGCAAAGCAAT 58.209 45.000 11.24 0.00 0.00 3.56
608 2402 1.790755 ATCAGTCGTACGCAAAGCAA 58.209 45.000 11.24 0.00 0.00 3.91
609 2403 1.790755 AATCAGTCGTACGCAAAGCA 58.209 45.000 11.24 0.00 0.00 3.91
610 2404 2.664568 TGTAATCAGTCGTACGCAAAGC 59.335 45.455 11.24 0.00 0.00 3.51
611 2405 5.054780 GATGTAATCAGTCGTACGCAAAG 57.945 43.478 11.24 0.30 44.70 2.77
625 2419 6.545504 ACTGTATGCAAATCGGATGTAATC 57.454 37.500 0.00 0.00 44.55 1.75
626 2420 7.119699 CCATACTGTATGCAAATCGGATGTAAT 59.880 37.037 19.90 0.00 34.85 1.89
627 2421 6.426633 CCATACTGTATGCAAATCGGATGTAA 59.573 38.462 19.90 0.00 34.85 2.41
628 2422 5.931724 CCATACTGTATGCAAATCGGATGTA 59.068 40.000 19.90 0.00 34.85 2.29
629 2423 4.756642 CCATACTGTATGCAAATCGGATGT 59.243 41.667 19.90 0.00 34.85 3.06
630 2424 4.756642 ACCATACTGTATGCAAATCGGATG 59.243 41.667 19.90 6.96 34.85 3.51
631 2425 4.756642 CACCATACTGTATGCAAATCGGAT 59.243 41.667 19.90 0.00 34.85 4.18
632 2426 4.126437 CACCATACTGTATGCAAATCGGA 58.874 43.478 19.90 0.00 34.85 4.55
633 2427 4.126437 TCACCATACTGTATGCAAATCGG 58.874 43.478 19.90 8.93 34.85 4.18
634 2428 5.106948 GGATCACCATACTGTATGCAAATCG 60.107 44.000 19.90 9.42 34.85 3.34
635 2429 6.000219 AGGATCACCATACTGTATGCAAATC 59.000 40.000 19.90 18.33 38.94 2.17
636 2430 5.945310 AGGATCACCATACTGTATGCAAAT 58.055 37.500 19.90 12.55 38.94 2.32
637 2431 5.372343 AGGATCACCATACTGTATGCAAA 57.628 39.130 19.90 8.89 38.94 3.68
638 2432 5.221641 GGTAGGATCACCATACTGTATGCAA 60.222 44.000 19.90 9.19 38.55 4.08
639 2433 4.283467 GGTAGGATCACCATACTGTATGCA 59.717 45.833 19.90 8.17 38.55 3.96
640 2434 4.528596 AGGTAGGATCACCATACTGTATGC 59.471 45.833 19.90 7.79 41.40 3.14
641 2435 6.013379 AGAGGTAGGATCACCATACTGTATG 58.987 44.000 18.67 18.67 41.40 2.39
642 2436 6.013379 CAGAGGTAGGATCACCATACTGTAT 58.987 44.000 5.11 0.00 41.40 2.29
643 2437 5.103643 ACAGAGGTAGGATCACCATACTGTA 60.104 44.000 18.57 0.00 42.30 2.74
644 2438 4.219115 CAGAGGTAGGATCACCATACTGT 58.781 47.826 5.11 0.00 41.40 3.55
645 2439 4.219115 ACAGAGGTAGGATCACCATACTG 58.781 47.826 15.54 15.54 41.40 2.74
646 2440 4.544564 ACAGAGGTAGGATCACCATACT 57.455 45.455 5.11 0.00 41.40 2.12
647 2441 4.896482 AGAACAGAGGTAGGATCACCATAC 59.104 45.833 5.11 0.00 41.40 2.39
648 2442 5.144159 AGAACAGAGGTAGGATCACCATA 57.856 43.478 5.11 0.00 41.40 2.74
649 2443 4.000928 AGAACAGAGGTAGGATCACCAT 57.999 45.455 5.11 0.00 41.40 3.55
650 2444 3.474798 AGAACAGAGGTAGGATCACCA 57.525 47.619 5.11 0.00 41.40 4.17
651 2445 5.934402 TTAAGAACAGAGGTAGGATCACC 57.066 43.478 0.00 0.00 39.02 4.02
652 2446 6.154706 TCCTTTAAGAACAGAGGTAGGATCAC 59.845 42.308 0.00 0.00 0.00 3.06
653 2447 6.261435 TCCTTTAAGAACAGAGGTAGGATCA 58.739 40.000 0.00 0.00 0.00 2.92
654 2448 6.381707 ACTCCTTTAAGAACAGAGGTAGGATC 59.618 42.308 0.00 0.00 30.73 3.36
655 2449 6.155393 CACTCCTTTAAGAACAGAGGTAGGAT 59.845 42.308 0.00 0.00 30.73 3.24
656 2450 5.480772 CACTCCTTTAAGAACAGAGGTAGGA 59.519 44.000 0.00 0.00 0.00 2.94
657 2451 5.480772 TCACTCCTTTAAGAACAGAGGTAGG 59.519 44.000 0.00 0.00 0.00 3.18
658 2452 6.209788 AGTCACTCCTTTAAGAACAGAGGTAG 59.790 42.308 0.00 0.00 0.00 3.18
659 2453 6.075984 AGTCACTCCTTTAAGAACAGAGGTA 58.924 40.000 0.00 0.00 0.00 3.08
660 2454 4.902448 AGTCACTCCTTTAAGAACAGAGGT 59.098 41.667 0.00 0.00 0.00 3.85
661 2455 5.476091 AGTCACTCCTTTAAGAACAGAGG 57.524 43.478 0.00 0.00 0.00 3.69
662 2456 6.516718 TCAAGTCACTCCTTTAAGAACAGAG 58.483 40.000 0.00 0.00 0.00 3.35
663 2457 6.479972 TCAAGTCACTCCTTTAAGAACAGA 57.520 37.500 0.00 0.00 0.00 3.41
664 2458 6.370166 GGATCAAGTCACTCCTTTAAGAACAG 59.630 42.308 0.00 0.00 0.00 3.16
665 2459 6.043243 AGGATCAAGTCACTCCTTTAAGAACA 59.957 38.462 0.00 0.00 35.90 3.18
666 2460 6.468543 AGGATCAAGTCACTCCTTTAAGAAC 58.531 40.000 0.00 0.00 35.90 3.01
667 2461 6.688073 AGGATCAAGTCACTCCTTTAAGAA 57.312 37.500 0.00 0.00 35.90 2.52
668 2462 6.381420 CCTAGGATCAAGTCACTCCTTTAAGA 59.619 42.308 1.05 0.00 39.99 2.10
669 2463 6.407525 CCCTAGGATCAAGTCACTCCTTTAAG 60.408 46.154 11.48 0.00 39.99 1.85
670 2464 5.425539 CCCTAGGATCAAGTCACTCCTTTAA 59.574 44.000 11.48 0.00 39.99 1.52
671 2465 4.962995 CCCTAGGATCAAGTCACTCCTTTA 59.037 45.833 11.48 0.00 39.99 1.85
672 2466 3.777522 CCCTAGGATCAAGTCACTCCTTT 59.222 47.826 11.48 0.00 39.99 3.11
673 2467 3.246167 ACCCTAGGATCAAGTCACTCCTT 60.246 47.826 11.48 0.00 39.99 3.36
674 2468 2.316372 ACCCTAGGATCAAGTCACTCCT 59.684 50.000 11.48 0.00 42.11 3.69
675 2469 2.432510 CACCCTAGGATCAAGTCACTCC 59.567 54.545 11.48 0.00 0.00 3.85
676 2470 3.131400 GTCACCCTAGGATCAAGTCACTC 59.869 52.174 11.48 0.00 0.00 3.51
677 2471 3.100671 GTCACCCTAGGATCAAGTCACT 58.899 50.000 11.48 0.00 0.00 3.41
678 2472 3.100671 AGTCACCCTAGGATCAAGTCAC 58.899 50.000 11.48 0.00 0.00 3.67
679 2473 3.099905 CAGTCACCCTAGGATCAAGTCA 58.900 50.000 11.48 0.00 0.00 3.41
680 2474 3.131400 GTCAGTCACCCTAGGATCAAGTC 59.869 52.174 11.48 0.00 0.00 3.01
681 2475 3.100671 GTCAGTCACCCTAGGATCAAGT 58.899 50.000 11.48 0.00 0.00 3.16
682 2476 3.370104 AGTCAGTCACCCTAGGATCAAG 58.630 50.000 11.48 0.00 0.00 3.02
683 2477 3.474798 AGTCAGTCACCCTAGGATCAA 57.525 47.619 11.48 0.00 0.00 2.57
684 2478 4.603094 TTAGTCAGTCACCCTAGGATCA 57.397 45.455 11.48 0.00 0.00 2.92
685 2479 4.896482 ACATTAGTCAGTCACCCTAGGATC 59.104 45.833 11.48 0.00 0.00 3.36
686 2480 4.884961 ACATTAGTCAGTCACCCTAGGAT 58.115 43.478 11.48 0.00 0.00 3.24
687 2481 4.279145 GACATTAGTCAGTCACCCTAGGA 58.721 47.826 11.48 0.00 44.34 2.94
688 2482 3.066900 CGACATTAGTCAGTCACCCTAGG 59.933 52.174 0.06 0.06 45.23 3.02
689 2483 3.695060 ACGACATTAGTCAGTCACCCTAG 59.305 47.826 0.00 0.00 45.23 3.02
690 2484 3.693807 ACGACATTAGTCAGTCACCCTA 58.306 45.455 0.00 0.00 45.23 3.53
691 2485 2.526432 ACGACATTAGTCAGTCACCCT 58.474 47.619 0.00 0.00 45.23 4.34
692 2486 3.192001 TGTACGACATTAGTCAGTCACCC 59.808 47.826 0.00 0.00 45.23 4.61
693 2487 4.430137 TGTACGACATTAGTCAGTCACC 57.570 45.455 0.00 0.00 45.23 4.02
694 2488 5.637809 TGATGTACGACATTAGTCAGTCAC 58.362 41.667 0.00 0.00 45.23 3.67
695 2489 5.890424 TGATGTACGACATTAGTCAGTCA 57.110 39.130 0.00 0.00 45.23 3.41
696 2490 5.621634 CGATGATGTACGACATTAGTCAGTC 59.378 44.000 6.16 0.00 45.23 3.51
697 2491 5.505819 CCGATGATGTACGACATTAGTCAGT 60.506 44.000 6.16 0.00 45.23 3.41
698 2492 4.912187 CCGATGATGTACGACATTAGTCAG 59.088 45.833 6.16 0.00 45.23 3.51
699 2493 4.577283 TCCGATGATGTACGACATTAGTCA 59.423 41.667 6.16 0.00 45.23 3.41
700 2494 5.104562 TCCGATGATGTACGACATTAGTC 57.895 43.478 6.16 0.00 39.27 2.59
701 2495 5.240844 TCATCCGATGATGTACGACATTAGT 59.759 40.000 7.00 0.00 46.96 2.24
702 2496 5.699839 TCATCCGATGATGTACGACATTAG 58.300 41.667 7.00 4.65 46.96 1.73
703 2497 5.699097 TCATCCGATGATGTACGACATTA 57.301 39.130 7.00 0.00 46.96 1.90
704 2498 4.584327 TCATCCGATGATGTACGACATT 57.416 40.909 7.00 0.00 46.96 2.71
705 2499 4.584327 TTCATCCGATGATGTACGACAT 57.416 40.909 11.90 4.63 46.96 3.06
706 2500 4.379339 TTTCATCCGATGATGTACGACA 57.621 40.909 11.90 0.00 46.96 4.35
707 2501 4.804139 ACTTTTCATCCGATGATGTACGAC 59.196 41.667 11.90 0.00 46.96 4.34
708 2502 5.006153 ACTTTTCATCCGATGATGTACGA 57.994 39.130 11.90 0.00 46.96 3.43
709 2503 5.718649 AACTTTTCATCCGATGATGTACG 57.281 39.130 11.90 2.86 46.96 3.67
710 2504 7.169308 ACGATAACTTTTCATCCGATGATGTAC 59.831 37.037 11.90 6.63 46.96 2.90
711 2505 7.207383 ACGATAACTTTTCATCCGATGATGTA 58.793 34.615 11.90 0.00 46.96 2.29
712 2506 6.049149 ACGATAACTTTTCATCCGATGATGT 58.951 36.000 11.90 8.66 46.96 3.06
714 2508 6.362551 CGTACGATAACTTTTCATCCGATGAT 59.637 38.462 10.44 0.00 39.39 2.45
715 2509 5.684184 CGTACGATAACTTTTCATCCGATGA 59.316 40.000 10.44 7.00 37.55 2.92
716 2510 5.457799 ACGTACGATAACTTTTCATCCGATG 59.542 40.000 24.41 1.55 0.00 3.84
717 2511 5.457799 CACGTACGATAACTTTTCATCCGAT 59.542 40.000 24.41 0.00 0.00 4.18
718 2512 4.794762 CACGTACGATAACTTTTCATCCGA 59.205 41.667 24.41 0.00 0.00 4.55
719 2513 4.560035 ACACGTACGATAACTTTTCATCCG 59.440 41.667 24.41 0.00 0.00 4.18
720 2514 6.291479 GCTACACGTACGATAACTTTTCATCC 60.291 42.308 24.41 0.00 0.00 3.51
721 2515 6.252015 TGCTACACGTACGATAACTTTTCATC 59.748 38.462 24.41 0.00 0.00 2.92
722 2516 6.034256 GTGCTACACGTACGATAACTTTTCAT 59.966 38.462 24.41 0.00 0.00 2.57
723 2517 5.343058 GTGCTACACGTACGATAACTTTTCA 59.657 40.000 24.41 4.90 0.00 2.69
724 2518 5.570589 AGTGCTACACGTACGATAACTTTTC 59.429 40.000 24.41 4.58 39.64 2.29
725 2519 5.344128 CAGTGCTACACGTACGATAACTTTT 59.656 40.000 24.41 0.00 39.64 2.27
726 2520 4.855388 CAGTGCTACACGTACGATAACTTT 59.145 41.667 24.41 0.00 39.64 2.66
727 2521 4.409570 CAGTGCTACACGTACGATAACTT 58.590 43.478 24.41 0.00 39.64 2.66
728 2522 3.730061 GCAGTGCTACACGTACGATAACT 60.730 47.826 24.41 12.69 39.64 2.24
729 2523 2.529090 GCAGTGCTACACGTACGATAAC 59.471 50.000 24.41 9.70 39.64 1.89
730 2524 2.162008 TGCAGTGCTACACGTACGATAA 59.838 45.455 24.41 5.15 39.64 1.75
731 2525 1.738908 TGCAGTGCTACACGTACGATA 59.261 47.619 24.41 12.62 39.64 2.92
732 2526 0.524414 TGCAGTGCTACACGTACGAT 59.476 50.000 24.41 12.10 39.64 3.73
733 2527 0.109919 CTGCAGTGCTACACGTACGA 60.110 55.000 24.41 0.00 39.64 3.43
734 2528 1.674611 GCTGCAGTGCTACACGTACG 61.675 60.000 17.60 15.01 39.64 3.67
735 2529 0.666274 TGCTGCAGTGCTACACGTAC 60.666 55.000 17.60 0.00 39.64 3.67
736 2530 0.666274 GTGCTGCAGTGCTACACGTA 60.666 55.000 20.26 0.00 39.64 3.57
737 2531 1.956170 GTGCTGCAGTGCTACACGT 60.956 57.895 20.26 0.00 39.64 4.49
738 2532 2.856032 GTGCTGCAGTGCTACACG 59.144 61.111 20.26 5.31 39.64 4.49
739 2533 1.621301 CTCGTGCTGCAGTGCTACAC 61.621 60.000 23.18 23.18 33.89 2.90
740 2534 1.373371 CTCGTGCTGCAGTGCTACA 60.373 57.895 17.60 11.53 0.00 2.74
741 2535 0.109272 TACTCGTGCTGCAGTGCTAC 60.109 55.000 17.60 11.58 0.00 3.58
742 2536 0.601057 TTACTCGTGCTGCAGTGCTA 59.399 50.000 17.60 1.74 0.00 3.49
743 2537 0.249868 TTTACTCGTGCTGCAGTGCT 60.250 50.000 17.60 0.00 0.00 4.40
744 2538 0.164647 CTTTACTCGTGCTGCAGTGC 59.835 55.000 16.64 8.58 0.00 4.40
745 2539 0.792640 CCTTTACTCGTGCTGCAGTG 59.207 55.000 16.64 5.99 0.00 3.66
746 2540 0.951040 GCCTTTACTCGTGCTGCAGT 60.951 55.000 16.64 0.00 0.00 4.40
747 2541 0.950555 TGCCTTTACTCGTGCTGCAG 60.951 55.000 10.11 10.11 0.00 4.41
748 2542 0.950555 CTGCCTTTACTCGTGCTGCA 60.951 55.000 0.00 0.00 0.00 4.41
749 2543 1.790387 CTGCCTTTACTCGTGCTGC 59.210 57.895 0.00 0.00 0.00 5.25
750 2544 0.950555 TGCTGCCTTTACTCGTGCTG 60.951 55.000 0.00 0.00 0.00 4.41
751 2545 0.951040 GTGCTGCCTTTACTCGTGCT 60.951 55.000 0.00 0.00 0.00 4.40
752 2546 1.497722 GTGCTGCCTTTACTCGTGC 59.502 57.895 0.00 0.00 0.00 5.34
753 2547 0.666274 TCGTGCTGCCTTTACTCGTG 60.666 55.000 0.00 0.00 0.00 4.35
754 2548 0.246635 ATCGTGCTGCCTTTACTCGT 59.753 50.000 0.00 0.00 0.00 4.18
755 2549 1.324736 GAATCGTGCTGCCTTTACTCG 59.675 52.381 0.00 0.00 0.00 4.18
756 2550 1.666189 GGAATCGTGCTGCCTTTACTC 59.334 52.381 0.00 0.00 0.00 2.59
757 2551 1.679032 GGGAATCGTGCTGCCTTTACT 60.679 52.381 0.00 0.00 0.00 2.24
758 2552 0.733150 GGGAATCGTGCTGCCTTTAC 59.267 55.000 0.00 0.00 0.00 2.01
759 2553 0.393808 GGGGAATCGTGCTGCCTTTA 60.394 55.000 0.00 0.00 0.00 1.85
760 2554 1.678970 GGGGAATCGTGCTGCCTTT 60.679 57.895 0.00 0.00 0.00 3.11
761 2555 2.044946 GGGGAATCGTGCTGCCTT 60.045 61.111 0.00 0.00 0.00 4.35
792 2587 3.503748 CCTGTTAGCTTTCCAAGTGAAGG 59.496 47.826 0.00 0.00 33.63 3.46
910 2705 9.724839 GCTAGGTCTCGCTTTATCTTTATATAG 57.275 37.037 0.00 0.00 0.00 1.31
912 2707 7.178628 TGGCTAGGTCTCGCTTTATCTTTATAT 59.821 37.037 0.00 0.00 0.00 0.86
913 2708 6.492429 TGGCTAGGTCTCGCTTTATCTTTATA 59.508 38.462 0.00 0.00 0.00 0.98
914 2709 5.304614 TGGCTAGGTCTCGCTTTATCTTTAT 59.695 40.000 0.00 0.00 0.00 1.40
915 2710 4.647853 TGGCTAGGTCTCGCTTTATCTTTA 59.352 41.667 0.00 0.00 0.00 1.85
916 2711 3.451178 TGGCTAGGTCTCGCTTTATCTTT 59.549 43.478 0.00 0.00 0.00 2.52
917 2712 3.031736 TGGCTAGGTCTCGCTTTATCTT 58.968 45.455 0.00 0.00 0.00 2.40
918 2713 2.667470 TGGCTAGGTCTCGCTTTATCT 58.333 47.619 0.00 0.00 0.00 1.98
919 2714 3.005897 TCATGGCTAGGTCTCGCTTTATC 59.994 47.826 0.00 0.00 0.00 1.75
947 2742 1.192793 GAGCTTGCGTCGTAGTGATC 58.807 55.000 0.00 0.00 0.00 2.92
1185 2987 1.092345 GCTGGAGAATGGCGACCTTC 61.092 60.000 0.00 0.00 0.00 3.46
1233 3035 0.727398 GGTTGGCGTAGAACATCTGC 59.273 55.000 0.00 0.00 0.00 4.26
1468 3273 1.153086 GCGGCTTCTCCATGGTCAT 60.153 57.895 12.58 0.00 34.01 3.06
1494 3299 0.325933 TCTCCCAGTTGCTCATGGTG 59.674 55.000 0.00 0.00 34.58 4.17
1527 3332 3.755628 TACTGGACCTGCGCGACC 61.756 66.667 12.10 4.97 0.00 4.79
1648 3456 7.307751 CCGAATACGATTAAGCACCACATAATT 60.308 37.037 0.00 0.00 42.66 1.40
1736 3545 6.372659 CACAATAGAACATGCTTACTCCAAGT 59.627 38.462 0.00 0.00 36.55 3.16
1772 3581 4.627467 GCATGAACTGTCGAGAATACAAGT 59.373 41.667 0.00 0.00 0.00 3.16
1783 3592 1.730121 GCCACATTGCATGAACTGTCG 60.730 52.381 0.00 0.00 0.00 4.35
1791 3600 4.517815 GCCCGGCCACATTGCATG 62.518 66.667 2.24 0.00 0.00 4.06
1905 3717 3.790288 GCGTTCTTCTAATACCAGACGAC 59.210 47.826 0.00 0.00 0.00 4.34
1910 3722 4.755411 TCTTGGCGTTCTTCTAATACCAG 58.245 43.478 0.00 0.00 0.00 4.00
1923 3735 1.658994 TTTCGTGTCTTCTTGGCGTT 58.341 45.000 0.00 0.00 0.00 4.84
1924 3736 1.798813 GATTTCGTGTCTTCTTGGCGT 59.201 47.619 0.00 0.00 0.00 5.68
1925 3737 1.798223 TGATTTCGTGTCTTCTTGGCG 59.202 47.619 0.00 0.00 0.00 5.69
1937 3749 6.372103 TCCGTTGGTTTTGTATATGATTTCGT 59.628 34.615 0.00 0.00 0.00 3.85
1941 3753 7.887381 TGTTTCCGTTGGTTTTGTATATGATT 58.113 30.769 0.00 0.00 0.00 2.57
1942 3754 7.455641 TGTTTCCGTTGGTTTTGTATATGAT 57.544 32.000 0.00 0.00 0.00 2.45
1943 3755 6.879276 TGTTTCCGTTGGTTTTGTATATGA 57.121 33.333 0.00 0.00 0.00 2.15
1944 3756 7.932120 TTTGTTTCCGTTGGTTTTGTATATG 57.068 32.000 0.00 0.00 0.00 1.78
1946 3758 7.713750 TCATTTGTTTCCGTTGGTTTTGTATA 58.286 30.769 0.00 0.00 0.00 1.47
1947 3759 6.574350 TCATTTGTTTCCGTTGGTTTTGTAT 58.426 32.000 0.00 0.00 0.00 2.29
1948 3760 5.962433 TCATTTGTTTCCGTTGGTTTTGTA 58.038 33.333 0.00 0.00 0.00 2.41
1950 3762 5.786401 TTCATTTGTTTCCGTTGGTTTTG 57.214 34.783 0.00 0.00 0.00 2.44
1959 3774 6.568238 GCGTTTTGTATTTTCATTTGTTTCCG 59.432 34.615 0.00 0.00 0.00 4.30
1976 3791 2.922740 TGGGTCTCTTAGCGTTTTGT 57.077 45.000 0.00 0.00 0.00 2.83
1990 3805 2.979240 TGCTTGTTTTGGTTTTGGGTC 58.021 42.857 0.00 0.00 0.00 4.46
2012 3827 6.987404 GGTTTATATCCTCTCTTCTTTCGCTT 59.013 38.462 0.00 0.00 0.00 4.68
2016 3831 6.517605 AGCGGTTTATATCCTCTCTTCTTTC 58.482 40.000 0.00 0.00 0.00 2.62
2096 4031 2.230508 AGTTTTGCAGCATCAGTCCATG 59.769 45.455 0.00 0.00 0.00 3.66
2097 4032 2.522185 AGTTTTGCAGCATCAGTCCAT 58.478 42.857 0.00 0.00 0.00 3.41
2098 4033 1.985473 AGTTTTGCAGCATCAGTCCA 58.015 45.000 0.00 0.00 0.00 4.02
2099 4034 4.156556 TGAATAGTTTTGCAGCATCAGTCC 59.843 41.667 0.00 0.00 0.00 3.85
2100 4035 5.106396 ACTGAATAGTTTTGCAGCATCAGTC 60.106 40.000 16.50 2.42 41.62 3.51
2101 4036 4.763793 ACTGAATAGTTTTGCAGCATCAGT 59.236 37.500 16.50 16.50 40.87 3.41
2102 4037 5.093457 CACTGAATAGTTTTGCAGCATCAG 58.907 41.667 15.41 15.41 39.09 2.90
2103 4038 4.520111 ACACTGAATAGTTTTGCAGCATCA 59.480 37.500 0.00 0.00 34.07 3.07
2104 4039 5.051891 ACACTGAATAGTTTTGCAGCATC 57.948 39.130 0.00 0.00 34.07 3.91
2105 4040 4.520111 TGACACTGAATAGTTTTGCAGCAT 59.480 37.500 0.00 0.00 34.07 3.79
2106 4041 3.882288 TGACACTGAATAGTTTTGCAGCA 59.118 39.130 0.00 0.00 34.07 4.41
2107 4042 4.470462 CTGACACTGAATAGTTTTGCAGC 58.530 43.478 0.00 0.00 34.07 5.25
2116 4051 8.877779 GCCTAATATTATGCTGACACTGAATAG 58.122 37.037 13.63 0.00 0.00 1.73
2127 4062 6.183360 CGATGTTCAGGCCTAATATTATGCTG 60.183 42.308 18.47 14.84 0.00 4.41
2143 4078 8.023050 ACTAGAAAAATGAGTTCGATGTTCAG 57.977 34.615 0.00 0.00 0.00 3.02
2240 4175 7.598118 TCAAGCGCAATCAAAAGATTAAATTCA 59.402 29.630 11.47 0.00 0.00 2.57
2241 4176 7.952339 TCAAGCGCAATCAAAAGATTAAATTC 58.048 30.769 11.47 0.00 0.00 2.17
2242 4177 7.814107 TCTCAAGCGCAATCAAAAGATTAAATT 59.186 29.630 11.47 0.00 0.00 1.82
2243 4178 7.315142 TCTCAAGCGCAATCAAAAGATTAAAT 58.685 30.769 11.47 0.00 0.00 1.40
2244 4179 6.676950 TCTCAAGCGCAATCAAAAGATTAAA 58.323 32.000 11.47 0.00 0.00 1.52
2245 4180 6.252967 TCTCAAGCGCAATCAAAAGATTAA 57.747 33.333 11.47 0.00 0.00 1.40
2246 4181 5.878332 TCTCAAGCGCAATCAAAAGATTA 57.122 34.783 11.47 0.00 0.00 1.75
2247 4182 4.771590 TCTCAAGCGCAATCAAAAGATT 57.228 36.364 11.47 0.00 0.00 2.40
2248 4183 4.771590 TTCTCAAGCGCAATCAAAAGAT 57.228 36.364 11.47 0.00 0.00 2.40
2249 4184 4.566545 TTTCTCAAGCGCAATCAAAAGA 57.433 36.364 11.47 0.00 0.00 2.52
2250 4185 6.583806 AGTTATTTCTCAAGCGCAATCAAAAG 59.416 34.615 11.47 0.00 0.00 2.27
2251 4186 6.446318 AGTTATTTCTCAAGCGCAATCAAAA 58.554 32.000 11.47 4.89 0.00 2.44
2252 4187 6.012658 AGTTATTTCTCAAGCGCAATCAAA 57.987 33.333 11.47 1.81 0.00 2.69
2253 4188 5.627499 AGTTATTTCTCAAGCGCAATCAA 57.373 34.783 11.47 0.00 0.00 2.57
2258 4207 3.064207 ACGAAGTTATTTCTCAAGCGCA 58.936 40.909 11.47 0.00 37.78 6.09
2360 4309 7.625185 GCCTTAGTCAGCTTAGAGAAAAATGTG 60.625 40.741 0.00 0.00 0.00 3.21
2385 4334 2.411628 AAAACCCAAACAAACAGGGC 57.588 45.000 0.00 0.00 46.88 5.19
2387 4336 3.342719 AGCAAAAACCCAAACAAACAGG 58.657 40.909 0.00 0.00 0.00 4.00
2388 4337 5.369685 AAAGCAAAAACCCAAACAAACAG 57.630 34.783 0.00 0.00 0.00 3.16
2389 4338 5.523369 CAAAAGCAAAAACCCAAACAAACA 58.477 33.333 0.00 0.00 0.00 2.83
2390 4339 4.384247 GCAAAAGCAAAAACCCAAACAAAC 59.616 37.500 0.00 0.00 0.00 2.93
2391 4340 4.279420 AGCAAAAGCAAAAACCCAAACAAA 59.721 33.333 0.00 0.00 0.00 2.83
2392 4341 3.823304 AGCAAAAGCAAAAACCCAAACAA 59.177 34.783 0.00 0.00 0.00 2.83
2393 4342 3.416156 AGCAAAAGCAAAAACCCAAACA 58.584 36.364 0.00 0.00 0.00 2.83
2394 4343 4.433186 AAGCAAAAGCAAAAACCCAAAC 57.567 36.364 0.00 0.00 0.00 2.93
2395 4344 5.459536 AAAAGCAAAAGCAAAAACCCAAA 57.540 30.435 0.00 0.00 0.00 3.28
2396 4345 5.473504 TGTAAAAGCAAAAGCAAAAACCCAA 59.526 32.000 0.00 0.00 0.00 4.12
2397 4346 5.003804 TGTAAAAGCAAAAGCAAAAACCCA 58.996 33.333 0.00 0.00 0.00 4.51
2398 4347 5.553290 TGTAAAAGCAAAAGCAAAAACCC 57.447 34.783 0.00 0.00 0.00 4.11
2418 4367 1.484038 TGCCAAAGTGGAAAAGCTGT 58.516 45.000 0.00 0.00 40.96 4.40
2448 4397 2.715749 AGCCAAAGCAAAAGCCTTTT 57.284 40.000 0.00 0.00 43.56 2.27
2452 4401 1.334556 CCAAAAGCCAAAGCAAAAGCC 59.665 47.619 0.00 0.00 43.56 4.35
2463 4427 9.381033 CAATATTGATTCATAAACCAAAAGCCA 57.619 29.630 10.04 0.00 0.00 4.75
2511 4475 0.664466 GGTGCTTTTTGCTTCGGCTC 60.664 55.000 0.00 0.00 43.37 4.70
2526 4490 5.047306 AGCCAAAAAGTTCCTAAATAGGTGC 60.047 40.000 6.39 1.62 44.02 5.01
2527 4491 6.590234 AGCCAAAAAGTTCCTAAATAGGTG 57.410 37.500 6.39 0.00 44.02 4.00
2528 4492 7.612065 AAAGCCAAAAAGTTCCTAAATAGGT 57.388 32.000 6.39 0.00 44.02 3.08
2529 4493 8.902540 AAAAAGCCAAAAAGTTCCTAAATAGG 57.097 30.769 0.00 0.00 45.02 2.57


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

AutoCloner maintained by Alex Coulton.