Multiple sequence alignment - TraesCS2B01G583500

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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 TraesCS2B01G583500 chr2B 100.000 4553 0 0 1551 6103 770756967 770761519 0.000000e+00 8408.0
1 TraesCS2B01G583500 chr2B 100.000 1274 0 0 1 1274 770755417 770756690 0.000000e+00 2353.0
2 TraesCS2B01G583500 chr2B 94.728 607 24 4 1 604 74730023 74730624 0.000000e+00 937.0
3 TraesCS2B01G583500 chr2B 86.151 621 70 7 1 618 416524731 416525338 0.000000e+00 656.0
4 TraesCS2B01G583500 chr2A 92.841 3450 156 31 2316 5685 758418517 758421955 0.000000e+00 4918.0
5 TraesCS2B01G583500 chr2A 85.839 572 51 19 715 1274 758417137 758417690 1.140000e-161 580.0
6 TraesCS2B01G583500 chr2A 85.261 536 42 20 1776 2290 758417921 758418440 9.070000e-143 518.0
7 TraesCS2B01G583500 chr2A 90.076 131 8 2 1574 1703 758417763 758417889 1.360000e-36 165.0
8 TraesCS2B01G583500 chr2A 100.000 30 0 0 5100 5129 758422091 758422120 8.550000e-04 56.5
9 TraesCS2B01G583500 chr2A 96.875 32 1 0 673 704 29596081 29596050 3.000000e-03 54.7
10 TraesCS2B01G583500 chr2D 93.928 2668 101 15 2890 5523 627961950 627964590 0.000000e+00 3973.0
11 TraesCS2B01G583500 chr2D 85.691 601 53 12 688 1274 627959752 627960333 2.430000e-168 603.0
12 TraesCS2B01G583500 chr2D 92.593 378 19 5 2316 2687 627961210 627961584 9.000000e-148 534.0
13 TraesCS2B01G583500 chr2D 83.333 462 36 21 1860 2290 627960683 627961134 7.420000e-104 388.0
14 TraesCS2B01G583500 chr2D 82.276 457 37 23 5685 6103 627964942 627965392 7.520000e-94 355.0
15 TraesCS2B01G583500 chr2D 93.798 129 6 2 5557 5685 627964592 627964718 6.240000e-45 193.0
16 TraesCS2B01G583500 chr2D 85.443 158 12 4 1551 1708 627960384 627960530 2.950000e-33 154.0
17 TraesCS2B01G583500 chr1B 88.045 619 15 13 1711 2290 65683315 65683913 0.000000e+00 678.0
18 TraesCS2B01G583500 chr1B 96.552 116 4 0 1159 1274 65682933 65683048 6.240000e-45 193.0
19 TraesCS2B01G583500 chr1B 91.935 124 8 1 1582 1705 65683054 65683175 8.130000e-39 172.0
20 TraesCS2B01G583500 chr1B 92.453 53 3 1 5375 5427 350726909 350726858 2.360000e-09 75.0
21 TraesCS2B01G583500 chr4B 92.346 405 14 3 1 403 621977898 621978287 1.490000e-155 560.0
22 TraesCS2B01G583500 chr6A 73.834 1158 269 27 3934 5076 59786239 59787377 4.370000e-116 429.0
23 TraesCS2B01G583500 chr6A 75.044 565 128 10 3934 4493 59810365 59810921 3.650000e-62 250.0
24 TraesCS2B01G583500 chr7D 79.097 598 117 7 5 596 616575242 616574647 7.370000e-109 405.0
25 TraesCS2B01G583500 chr1A 95.337 193 9 0 46 238 590934726 590934918 2.140000e-79 307.0
26 TraesCS2B01G583500 chr1A 100.000 50 0 0 1 50 590923777 590923826 6.510000e-15 93.5
27 TraesCS2B01G583500 chr1A 100.000 44 0 0 233 276 590962419 590962462 1.410000e-11 82.4
28 TraesCS2B01G583500 chr6B 75.880 568 118 15 3934 4493 114026316 114026872 7.790000e-69 272.0
29 TraesCS2B01G583500 chr6B 70.753 571 139 27 49 604 559331011 559330454 3.010000e-18 104.0
30 TraesCS2B01G583500 chr6D 75.532 564 127 8 3934 4493 45480238 45480794 3.630000e-67 267.0
31 TraesCS2B01G583500 chr7A 92.453 53 3 1 5373 5425 685505149 685505200 2.360000e-09 75.0
32 TraesCS2B01G583500 chr7A 92.453 53 3 1 5373 5425 685542726 685542777 2.360000e-09 75.0
33 TraesCS2B01G583500 chr7A 88.333 60 7 0 5368 5427 516148416 516148357 8.490000e-09 73.1
34 TraesCS2B01G583500 chr1D 91.071 56 4 1 5372 5427 36360227 36360281 2.360000e-09 75.0
35 TraesCS2B01G583500 chr1D 88.136 59 7 0 5382 5440 479208728 479208786 3.050000e-08 71.3
36 TraesCS2B01G583500 chr3D 89.474 57 6 0 5379 5435 582927864 582927920 8.490000e-09 73.1
37 TraesCS2B01G583500 chr3A 100.000 30 0 0 673 702 674078176 674078205 8.550000e-04 56.5
38 TraesCS2B01G583500 chr7B 96.774 31 1 0 674 704 79393424 79393394 1.100000e-02 52.8


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 TraesCS2B01G583500 chr2B 770755417 770761519 6102 False 5380.500000 8408 100.000000 1 6103 2 chr2B.!!$F3 6102
1 TraesCS2B01G583500 chr2B 74730023 74730624 601 False 937.000000 937 94.728000 1 604 1 chr2B.!!$F1 603
2 TraesCS2B01G583500 chr2B 416524731 416525338 607 False 656.000000 656 86.151000 1 618 1 chr2B.!!$F2 617
3 TraesCS2B01G583500 chr2A 758417137 758422120 4983 False 1247.500000 4918 90.803400 715 5685 5 chr2A.!!$F1 4970
4 TraesCS2B01G583500 chr2D 627959752 627965392 5640 False 885.714286 3973 88.151714 688 6103 7 chr2D.!!$F1 5415
5 TraesCS2B01G583500 chr1B 65682933 65683913 980 False 347.666667 678 92.177333 1159 2290 3 chr1B.!!$F1 1131
6 TraesCS2B01G583500 chr6A 59786239 59787377 1138 False 429.000000 429 73.834000 3934 5076 1 chr6A.!!$F1 1142
7 TraesCS2B01G583500 chr6A 59810365 59810921 556 False 250.000000 250 75.044000 3934 4493 1 chr6A.!!$F2 559
8 TraesCS2B01G583500 chr7D 616574647 616575242 595 True 405.000000 405 79.097000 5 596 1 chr7D.!!$R1 591
9 TraesCS2B01G583500 chr6B 114026316 114026872 556 False 272.000000 272 75.880000 3934 4493 1 chr6B.!!$F1 559
10 TraesCS2B01G583500 chr6D 45480238 45480794 556 False 267.000000 267 75.532000 3934 4493 1 chr6D.!!$F1 559

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
978 989 0.179012 TTTCCGAACACAACTCCCCC 60.179 55.0 0.00 0.0 0.0 5.40 F
2201 2421 0.529378 CTCCATGCTGCTTTTGGGAC 59.471 55.0 14.01 0.0 0.0 4.46 F
2628 2904 0.107214 GGGATTTGGGCGACATCAGA 60.107 55.0 0.00 0.0 0.0 3.27 F
3990 4476 0.179045 GCTTACTGGGGATCATGCGT 60.179 55.0 0.00 0.0 0.0 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2402 2676 0.328926 TGGCAGCATCACAGGAATCA 59.671 50.000 0.00 0.0 0.00 2.57 R
3990 4476 1.164411 CATACAAGGTCAAGCCGCAA 58.836 50.000 0.00 0.0 43.70 4.85 R
4014 4500 1.478288 GGCAGCTTCTAGCCCATTCAT 60.478 52.381 1.27 0.0 43.77 2.57 R
5167 5667 1.001520 ACGCCAAACAATTAAAGGGCC 59.998 47.619 0.00 0.0 38.16 5.80 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
111 112 7.681939 ATGTCCTCGCTTAAAAGTTTGAATA 57.318 32.000 0.00 0.00 0.00 1.75
308 309 0.849417 AAGCCCATCCCTCCATCTTC 59.151 55.000 0.00 0.00 0.00 2.87
312 314 2.443255 GCCCATCCCTCCATCTTCTTTA 59.557 50.000 0.00 0.00 0.00 1.85
389 393 3.626222 CCCCCACCAAAATCTTCCGATTA 60.626 47.826 0.00 0.00 38.89 1.75
502 507 9.838339 GAATCTCTTTTCCTTCTATGGATAACA 57.162 33.333 0.00 0.00 35.83 2.41
604 609 4.003584 AGAGCTGGTAACCCAAGGTATA 57.996 45.455 0.00 0.00 41.27 1.47
605 610 4.368067 AGAGCTGGTAACCCAAGGTATAA 58.632 43.478 0.00 0.00 41.27 0.98
606 611 4.409247 AGAGCTGGTAACCCAAGGTATAAG 59.591 45.833 0.00 0.00 41.27 1.73
607 612 4.109320 AGCTGGTAACCCAAGGTATAAGT 58.891 43.478 0.00 0.00 41.27 2.24
608 613 5.282946 AGCTGGTAACCCAAGGTATAAGTA 58.717 41.667 0.00 0.00 41.27 2.24
609 614 5.909417 AGCTGGTAACCCAAGGTATAAGTAT 59.091 40.000 0.00 0.00 41.27 2.12
610 615 6.388983 AGCTGGTAACCCAAGGTATAAGTATT 59.611 38.462 0.00 0.00 41.27 1.89
611 616 7.058525 GCTGGTAACCCAAGGTATAAGTATTT 58.941 38.462 0.00 0.00 41.27 1.40
612 617 8.212995 GCTGGTAACCCAAGGTATAAGTATTTA 58.787 37.037 0.00 0.00 41.27 1.40
619 624 9.220906 ACCCAAGGTATAAGTATTTATCTGACA 57.779 33.333 0.00 0.00 32.11 3.58
620 625 9.712305 CCCAAGGTATAAGTATTTATCTGACAG 57.288 37.037 0.00 0.00 31.97 3.51
621 626 9.712305 CCAAGGTATAAGTATTTATCTGACAGG 57.288 37.037 1.81 0.00 31.97 4.00
622 627 9.712305 CAAGGTATAAGTATTTATCTGACAGGG 57.288 37.037 1.81 0.00 31.97 4.45
623 628 8.437274 AGGTATAAGTATTTATCTGACAGGGG 57.563 38.462 1.81 0.00 31.97 4.79
624 629 8.017251 AGGTATAAGTATTTATCTGACAGGGGT 58.983 37.037 1.81 0.00 31.97 4.95
625 630 8.657712 GGTATAAGTATTTATCTGACAGGGGTT 58.342 37.037 1.81 0.00 31.97 4.11
626 631 9.490379 GTATAAGTATTTATCTGACAGGGGTTG 57.510 37.037 1.81 0.00 31.97 3.77
627 632 6.636454 AAGTATTTATCTGACAGGGGTTGA 57.364 37.500 1.81 0.00 0.00 3.18
628 633 5.990668 AGTATTTATCTGACAGGGGTTGAC 58.009 41.667 1.81 0.00 0.00 3.18
629 634 3.713826 TTTATCTGACAGGGGTTGACC 57.286 47.619 1.81 0.00 39.11 4.02
630 635 1.191535 TATCTGACAGGGGTTGACCG 58.808 55.000 1.81 0.00 41.60 4.79
631 636 0.836400 ATCTGACAGGGGTTGACCGT 60.836 55.000 1.81 0.00 41.60 4.83
632 637 1.004918 CTGACAGGGGTTGACCGTC 60.005 63.158 0.00 0.00 41.60 4.79
633 638 1.754380 CTGACAGGGGTTGACCGTCA 61.754 60.000 0.00 0.00 41.60 4.35
634 639 1.125093 TGACAGGGGTTGACCGTCAT 61.125 55.000 1.09 0.00 41.60 3.06
635 640 0.899720 GACAGGGGTTGACCGTCATA 59.100 55.000 1.09 0.00 41.60 2.15
636 641 0.611714 ACAGGGGTTGACCGTCATAC 59.388 55.000 1.09 4.00 41.60 2.39
637 642 0.902531 CAGGGGTTGACCGTCATACT 59.097 55.000 1.09 0.00 41.60 2.12
638 643 1.278127 CAGGGGTTGACCGTCATACTT 59.722 52.381 1.09 0.00 41.60 2.24
639 644 1.278127 AGGGGTTGACCGTCATACTTG 59.722 52.381 1.09 0.00 41.60 3.16
640 645 1.677820 GGGGTTGACCGTCATACTTGG 60.678 57.143 1.09 0.00 41.60 3.61
641 646 1.002773 GGGTTGACCGTCATACTTGGT 59.997 52.381 1.09 0.00 39.12 3.67
642 647 2.551504 GGGTTGACCGTCATACTTGGTT 60.552 50.000 1.09 0.00 35.75 3.67
643 648 3.306919 GGGTTGACCGTCATACTTGGTTA 60.307 47.826 1.09 0.00 35.75 2.85
644 649 3.930848 GGTTGACCGTCATACTTGGTTAG 59.069 47.826 1.09 0.00 35.75 2.34
645 650 3.880047 TGACCGTCATACTTGGTTAGG 57.120 47.619 0.00 0.00 35.75 2.69
646 651 2.093869 TGACCGTCATACTTGGTTAGGC 60.094 50.000 0.00 0.00 35.75 3.93
647 652 1.134907 ACCGTCATACTTGGTTAGGCG 60.135 52.381 0.00 0.00 29.87 5.52
648 653 1.567504 CGTCATACTTGGTTAGGCGG 58.432 55.000 0.00 0.00 0.00 6.13
649 654 1.134907 CGTCATACTTGGTTAGGCGGT 60.135 52.381 0.00 0.00 0.00 5.68
650 655 2.547826 GTCATACTTGGTTAGGCGGTC 58.452 52.381 0.00 0.00 0.00 4.79
651 656 2.093869 GTCATACTTGGTTAGGCGGTCA 60.094 50.000 0.00 0.00 0.00 4.02
652 657 2.769663 TCATACTTGGTTAGGCGGTCAT 59.230 45.455 0.00 0.00 0.00 3.06
653 658 3.962063 TCATACTTGGTTAGGCGGTCATA 59.038 43.478 0.00 0.00 0.00 2.15
654 659 4.591498 TCATACTTGGTTAGGCGGTCATAT 59.409 41.667 0.00 0.00 0.00 1.78
655 660 5.776208 TCATACTTGGTTAGGCGGTCATATA 59.224 40.000 0.00 0.00 0.00 0.86
656 661 6.268158 TCATACTTGGTTAGGCGGTCATATAA 59.732 38.462 0.00 0.00 0.00 0.98
657 662 5.562298 ACTTGGTTAGGCGGTCATATAAT 57.438 39.130 0.00 0.00 0.00 1.28
658 663 5.548406 ACTTGGTTAGGCGGTCATATAATC 58.452 41.667 0.00 0.00 0.00 1.75
659 664 5.307196 ACTTGGTTAGGCGGTCATATAATCT 59.693 40.000 0.00 0.00 0.00 2.40
660 665 5.818678 TGGTTAGGCGGTCATATAATCTT 57.181 39.130 0.00 0.00 0.00 2.40
661 666 6.182507 TGGTTAGGCGGTCATATAATCTTT 57.817 37.500 0.00 0.00 0.00 2.52
662 667 6.597562 TGGTTAGGCGGTCATATAATCTTTT 58.402 36.000 0.00 0.00 0.00 2.27
663 668 6.485313 TGGTTAGGCGGTCATATAATCTTTTG 59.515 38.462 0.00 0.00 0.00 2.44
664 669 6.485648 GGTTAGGCGGTCATATAATCTTTTGT 59.514 38.462 0.00 0.00 0.00 2.83
665 670 7.012989 GGTTAGGCGGTCATATAATCTTTTGTT 59.987 37.037 0.00 0.00 0.00 2.83
666 671 8.403236 GTTAGGCGGTCATATAATCTTTTGTTT 58.597 33.333 0.00 0.00 0.00 2.83
667 672 6.795399 AGGCGGTCATATAATCTTTTGTTTG 58.205 36.000 0.00 0.00 0.00 2.93
668 673 6.377146 AGGCGGTCATATAATCTTTTGTTTGT 59.623 34.615 0.00 0.00 0.00 2.83
669 674 6.472163 GGCGGTCATATAATCTTTTGTTTGTG 59.528 38.462 0.00 0.00 0.00 3.33
670 675 6.020678 GCGGTCATATAATCTTTTGTTTGTGC 60.021 38.462 0.00 0.00 0.00 4.57
671 676 6.472163 CGGTCATATAATCTTTTGTTTGTGCC 59.528 38.462 0.00 0.00 0.00 5.01
672 677 6.756542 GGTCATATAATCTTTTGTTTGTGCCC 59.243 38.462 0.00 0.00 0.00 5.36
673 678 6.756542 GTCATATAATCTTTTGTTTGTGCCCC 59.243 38.462 0.00 0.00 0.00 5.80
674 679 6.667414 TCATATAATCTTTTGTTTGTGCCCCT 59.333 34.615 0.00 0.00 0.00 4.79
675 680 3.473923 AATCTTTTGTTTGTGCCCCTG 57.526 42.857 0.00 0.00 0.00 4.45
676 681 1.859302 TCTTTTGTTTGTGCCCCTGT 58.141 45.000 0.00 0.00 0.00 4.00
677 682 3.019799 TCTTTTGTTTGTGCCCCTGTA 57.980 42.857 0.00 0.00 0.00 2.74
678 683 3.366396 TCTTTTGTTTGTGCCCCTGTAA 58.634 40.909 0.00 0.00 0.00 2.41
679 684 3.769844 TCTTTTGTTTGTGCCCCTGTAAA 59.230 39.130 0.00 0.00 0.00 2.01
680 685 3.528597 TTTGTTTGTGCCCCTGTAAAC 57.471 42.857 0.00 0.00 34.51 2.01
681 686 2.145397 TGTTTGTGCCCCTGTAAACA 57.855 45.000 0.00 0.00 39.79 2.83
682 687 2.672098 TGTTTGTGCCCCTGTAAACAT 58.328 42.857 0.00 0.00 37.90 2.71
683 688 3.034635 TGTTTGTGCCCCTGTAAACATT 58.965 40.909 0.00 0.00 37.90 2.71
684 689 3.181471 TGTTTGTGCCCCTGTAAACATTG 60.181 43.478 0.00 0.00 37.90 2.82
685 690 2.373335 TGTGCCCCTGTAAACATTGT 57.627 45.000 0.00 0.00 0.00 2.71
686 691 1.959985 TGTGCCCCTGTAAACATTGTG 59.040 47.619 0.00 0.00 0.00 3.33
704 709 5.616488 TTGTGACGGGTTAAATAAAGCTC 57.384 39.130 0.00 0.00 35.83 4.09
705 710 3.680937 TGTGACGGGTTAAATAAAGCTCG 59.319 43.478 0.00 0.00 35.83 5.03
706 711 3.681417 GTGACGGGTTAAATAAAGCTCGT 59.319 43.478 0.00 0.00 41.71 4.18
707 712 4.152938 GTGACGGGTTAAATAAAGCTCGTT 59.847 41.667 0.00 0.00 40.26 3.85
708 713 4.756135 TGACGGGTTAAATAAAGCTCGTTT 59.244 37.500 0.00 0.00 40.26 3.60
709 714 5.038247 ACGGGTTAAATAAAGCTCGTTTG 57.962 39.130 0.00 0.00 38.46 2.93
710 715 4.756135 ACGGGTTAAATAAAGCTCGTTTGA 59.244 37.500 0.00 0.00 38.46 2.69
711 716 5.239087 ACGGGTTAAATAAAGCTCGTTTGAA 59.761 36.000 0.00 0.00 38.46 2.69
712 717 6.144175 CGGGTTAAATAAAGCTCGTTTGAAA 58.856 36.000 0.00 0.00 35.83 2.69
713 718 6.637658 CGGGTTAAATAAAGCTCGTTTGAAAA 59.362 34.615 0.00 0.00 35.83 2.29
840 848 3.787001 CCGCACTCCTCCCTTCCC 61.787 72.222 0.00 0.00 0.00 3.97
846 854 4.089757 TCCTCCCTTCCCTCCCGG 62.090 72.222 0.00 0.00 0.00 5.73
978 989 0.179012 TTTCCGAACACAACTCCCCC 60.179 55.000 0.00 0.00 0.00 5.40
1081 1092 3.853330 CAGGATTCGTGCACGCGG 61.853 66.667 33.63 16.51 39.60 6.46
1134 1145 1.681327 GCTCCCCCTGTACAGACGA 60.681 63.158 24.68 14.04 0.00 4.20
1574 1594 7.727331 CTCCATTTGATTCTTGGATCTAGTC 57.273 40.000 0.00 0.00 38.79 2.59
1575 1595 7.443302 TCCATTTGATTCTTGGATCTAGTCT 57.557 36.000 0.00 0.00 34.65 3.24
1576 1596 8.553085 TCCATTTGATTCTTGGATCTAGTCTA 57.447 34.615 0.00 0.00 34.65 2.59
1577 1597 8.646004 TCCATTTGATTCTTGGATCTAGTCTAG 58.354 37.037 0.00 0.00 34.65 2.43
1621 1641 4.221262 ACAGGTGGATTGGTGATTGAAATG 59.779 41.667 0.00 0.00 0.00 2.32
1622 1642 3.196254 AGGTGGATTGGTGATTGAAATGC 59.804 43.478 0.00 0.00 0.00 3.56
1623 1643 3.055963 GGTGGATTGGTGATTGAAATGCA 60.056 43.478 0.00 0.00 30.41 3.96
1624 1644 4.563168 GGTGGATTGGTGATTGAAATGCAA 60.563 41.667 0.00 0.00 41.53 4.08
1634 1658 2.818130 TGAAATGCAAGCAAGGGTTC 57.182 45.000 0.00 2.02 0.00 3.62
1639 1663 0.823356 TGCAAGCAAGGGTTCTGACC 60.823 55.000 0.00 0.00 45.75 4.02
1654 1678 5.106673 GGTTCTGACCAACTACAAATGTAGC 60.107 44.000 18.14 4.78 46.43 3.58
1702 1781 8.947115 ACCTGAAACTTTATTCTGTTATACTGC 58.053 33.333 0.00 0.00 0.00 4.40
1794 1966 9.323985 AGCAAATAAGTAGATTCTGAAGATGAC 57.676 33.333 0.00 0.00 0.00 3.06
1808 1980 6.975197 TCTGAAGATGACAGTCTAAATTAGCG 59.025 38.462 1.31 0.00 36.81 4.26
1852 2025 1.133668 GCTGATGCCTGGGGATAGTTT 60.134 52.381 0.00 0.00 0.00 2.66
1853 2026 2.106511 GCTGATGCCTGGGGATAGTTTA 59.893 50.000 0.00 0.00 0.00 2.01
1854 2027 3.808618 GCTGATGCCTGGGGATAGTTTAG 60.809 52.174 0.00 0.00 0.00 1.85
1855 2028 3.392616 CTGATGCCTGGGGATAGTTTAGT 59.607 47.826 0.00 0.00 0.00 2.24
1856 2029 3.785887 TGATGCCTGGGGATAGTTTAGTT 59.214 43.478 0.00 0.00 0.00 2.24
1911 2096 3.760580 AATTTAGGGCAGAGAGGATCG 57.239 47.619 0.00 0.00 42.67 3.69
1945 2130 2.637382 TGTCTGTCTTCACCATTAGCCA 59.363 45.455 0.00 0.00 0.00 4.75
1997 2186 6.715264 CCCTACCCTGTAATTTATTCATCCAC 59.285 42.308 0.00 0.00 0.00 4.02
2016 2205 6.780457 TCCACTTACCAGTATACCAGTAAC 57.220 41.667 9.99 0.00 0.00 2.50
2018 2207 6.604795 TCCACTTACCAGTATACCAGTAACTC 59.395 42.308 9.99 0.00 0.00 3.01
2020 2209 7.069578 CCACTTACCAGTATACCAGTAACTCAT 59.930 40.741 9.99 0.00 0.00 2.90
2187 2407 1.642762 AGGCAAAGATTCACCCTCCAT 59.357 47.619 0.00 0.00 0.00 3.41
2201 2421 0.529378 CTCCATGCTGCTTTTGGGAC 59.471 55.000 14.01 0.00 0.00 4.46
2306 2554 6.884836 ACTTGAATTAATGGTAGGAACTGACC 59.115 38.462 0.00 0.00 41.52 4.02
2312 2560 2.176889 TGGTAGGAACTGACCAGCTAC 58.823 52.381 0.00 1.70 41.52 3.58
2313 2561 1.481363 GGTAGGAACTGACCAGCTACC 59.519 57.143 13.01 13.01 41.52 3.18
2402 2676 1.079543 CACGCCTGCTGCTACTTCT 60.080 57.895 0.00 0.00 38.05 2.85
2403 2677 1.079543 ACGCCTGCTGCTACTTCTG 60.080 57.895 0.00 0.00 38.05 3.02
2408 2682 2.559440 CCTGCTGCTACTTCTGATTCC 58.441 52.381 0.00 0.00 0.00 3.01
2430 2704 2.439701 ATGCTGCCAGCGCTGATT 60.440 55.556 38.06 12.81 46.26 2.57
2470 2744 0.854218 TGGTAGGACTTGCCCCAAAA 59.146 50.000 0.00 0.00 37.37 2.44
2515 2789 5.152623 TCGTTCTGAATCAACTCATCCTT 57.847 39.130 0.00 0.00 0.00 3.36
2576 2852 0.250597 GTTCCCACGGCACCTTTACT 60.251 55.000 0.00 0.00 0.00 2.24
2628 2904 0.107214 GGGATTTGGGCGACATCAGA 60.107 55.000 0.00 0.00 0.00 3.27
2629 2905 1.303309 GGATTTGGGCGACATCAGAG 58.697 55.000 0.00 0.00 0.00 3.35
2653 2930 2.343758 GTGCCGCTGGTGAAGAGA 59.656 61.111 0.00 0.00 0.00 3.10
2675 2952 1.611965 AGGGGATCCTGAGCTTTGC 59.388 57.895 12.58 0.00 42.98 3.68
2692 2969 0.669318 TGCTCGGCGTCTTTACCTTG 60.669 55.000 6.85 0.00 0.00 3.61
2719 2996 3.290948 TGGTACCTTGCTTTGTTCTGT 57.709 42.857 14.36 0.00 0.00 3.41
2721 2998 3.211045 GGTACCTTGCTTTGTTCTGTCA 58.789 45.455 4.06 0.00 0.00 3.58
2818 3127 1.078567 GCTGGAGGCTTGGTCTCTG 60.079 63.158 0.00 0.00 34.33 3.35
2854 3163 7.502226 TCTGGATCTTGTTGTGTTATCAGTTTT 59.498 33.333 0.00 0.00 0.00 2.43
2921 3361 2.125350 CTCCGCTGAACCAGGAGC 60.125 66.667 0.00 0.00 44.09 4.70
2922 3362 2.604686 TCCGCTGAACCAGGAGCT 60.605 61.111 0.00 0.00 32.70 4.09
2978 3418 1.065854 CCTTGTCTGGGTAGGAAGCAG 60.066 57.143 0.00 0.00 0.00 4.24
3022 3462 1.185315 GGGCACAACCACATTAGCAT 58.815 50.000 0.00 0.00 42.05 3.79
3137 3577 7.443879 TCAGTTCATTCCAAAATTTTAAAGGGC 59.556 33.333 2.44 1.65 0.00 5.19
3351 3813 6.206829 AGTTATCTTTGCCTTGTCTGGTTTAC 59.793 38.462 0.00 0.00 0.00 2.01
3369 3831 7.609056 TGGTTTACAGAATAAGAGTAGGTGAC 58.391 38.462 0.00 0.00 0.00 3.67
3419 3881 1.739067 AGTTAGGCAGCGAAATCACC 58.261 50.000 0.00 0.00 0.00 4.02
3421 3883 2.500098 AGTTAGGCAGCGAAATCACCTA 59.500 45.455 0.00 0.00 31.79 3.08
3613 4099 7.767745 TTTTTATGGTCGGGTTGTTAAAAAC 57.232 32.000 0.00 0.00 0.00 2.43
3637 4123 4.396166 GCCAGTAGTGCATCAGTTTTACAT 59.604 41.667 0.00 0.00 0.00 2.29
3644 4130 5.922544 AGTGCATCAGTTTTACATTCTTTGC 59.077 36.000 0.00 0.00 0.00 3.68
3681 4167 2.548057 GCTGCAAATCGGATTCGGAATA 59.452 45.455 2.65 0.00 36.95 1.75
3718 4204 8.547967 AAAATACACATGTCTTCAACTATCGT 57.452 30.769 0.00 0.00 0.00 3.73
3780 4266 2.093306 ACGTCATCAGAAATCGCCAA 57.907 45.000 0.00 0.00 0.00 4.52
3843 4329 7.698163 ATAGTTCCATATGGACCTTTTCTCT 57.302 36.000 25.08 14.09 45.39 3.10
3932 4418 5.698832 ACGATTGACCATGTTGTATGTTTG 58.301 37.500 0.00 0.00 0.00 2.93
3967 4453 2.825836 GGAAGCTCGTGGGGCATG 60.826 66.667 0.00 0.00 0.00 4.06
3990 4476 0.179045 GCTTACTGGGGATCATGCGT 60.179 55.000 0.00 0.00 0.00 5.24
4014 4500 2.030363 CGGCTTGACCTTGTATGCAAAA 60.030 45.455 0.00 0.00 35.61 2.44
4174 4663 2.010145 ACCATGAACATCGTTCCGAG 57.990 50.000 0.00 0.00 39.91 4.63
4240 4729 1.066286 CCAGCCAGAGAAAGTCCTCAG 60.066 57.143 0.00 0.00 35.68 3.35
4308 4797 4.134379 ACATACTGCATCCTGACAGAAG 57.866 45.455 3.32 0.00 37.35 2.85
4320 4809 3.755378 CCTGACAGAAGGCCATATTATGC 59.245 47.826 5.01 0.00 0.00 3.14
4361 4850 3.935828 CCGAGAAGTTCCTGGAAGATTTC 59.064 47.826 9.92 13.42 34.07 2.17
4376 4865 5.220491 GGAAGATTTCGAGAAGTCAATTCCG 60.220 44.000 10.26 0.00 38.84 4.30
4389 4878 0.768622 AATTCCGGTTCACTGGTCCA 59.231 50.000 0.00 0.00 43.01 4.02
4448 4937 2.227865 GCAGTTTGACAAGGCGGAATTA 59.772 45.455 0.00 0.00 0.00 1.40
4573 5062 3.589288 AGGCTTTGGGTATCTCTGAAGTT 59.411 43.478 0.00 0.00 0.00 2.66
4582 5071 5.988561 GGGTATCTCTGAAGTTAGCATTGAG 59.011 44.000 0.00 0.00 30.24 3.02
4666 5155 2.110967 CCATGCAGCAGGTCTTCCG 61.111 63.158 6.27 0.00 39.05 4.30
4677 5166 1.295746 GTCTTCCGGGAGTGGGAAC 59.704 63.158 10.32 0.00 38.60 3.62
4697 5186 4.348863 ACTCACTCAACAGAGCTTTGAT 57.651 40.909 11.85 0.00 35.28 2.57
4989 5478 1.901085 GGGATGGAGTCGTTCTGCT 59.099 57.895 4.16 0.00 35.48 4.24
5030 5519 2.653448 CTCGACGCAGATGCTCGG 60.653 66.667 19.25 10.97 39.93 4.63
5079 5568 1.209504 CCGGCAGAACAAATCCCTCTA 59.790 52.381 0.00 0.00 0.00 2.43
5080 5569 2.158755 CCGGCAGAACAAATCCCTCTAT 60.159 50.000 0.00 0.00 0.00 1.98
5081 5570 3.134458 CGGCAGAACAAATCCCTCTATC 58.866 50.000 0.00 0.00 0.00 2.08
5129 5629 0.322816 CCTGGCTAGAAGCAAAGGCA 60.323 55.000 0.00 0.00 44.75 4.75
5340 5840 7.792374 ACAAGCTGGTTATATACATGTTGAG 57.208 36.000 2.30 0.00 0.00 3.02
5386 5887 9.113838 CATGTTGAAGCTACTAACTATTCCATT 57.886 33.333 8.52 0.00 0.00 3.16
5390 5891 7.553334 TGAAGCTACTAACTATTCCATTCGTT 58.447 34.615 0.00 0.00 0.00 3.85
5391 5892 8.038944 TGAAGCTACTAACTATTCCATTCGTTT 58.961 33.333 0.00 0.00 0.00 3.60
5425 5926 9.530633 AGTGTCTCAACTTTGTACTAACTTTAG 57.469 33.333 0.00 0.00 36.82 1.85
5432 5933 5.995897 ACTTTGTACTAACTTTAGTGGGCAG 59.004 40.000 11.24 5.64 43.44 4.85
5434 5935 5.556006 TGTACTAACTTTAGTGGGCAGTT 57.444 39.130 11.24 0.00 43.44 3.16
5448 5949 3.243839 TGGGCAGTTTGAGAATTTTCTGC 60.244 43.478 6.44 6.44 44.74 4.26
5464 5965 5.794687 TTTCTGCGGACTACATGTTTATG 57.205 39.130 2.30 0.00 40.24 1.90
5466 5967 4.682787 TCTGCGGACTACATGTTTATGAG 58.317 43.478 2.30 0.00 37.73 2.90
5496 5999 1.519455 CACTAGTAGCAGTGCCCGC 60.519 63.158 12.58 2.01 39.54 6.13
5504 6007 1.009675 GCAGTGCCCGCGAAATATG 60.010 57.895 8.23 1.44 0.00 1.78
5541 6044 7.606456 TCTCTTGTTTAGTGCCATACTTAAAGG 59.394 37.037 0.00 0.00 40.89 3.11
5542 6045 7.455058 TCTTGTTTAGTGCCATACTTAAAGGA 58.545 34.615 0.00 0.00 40.89 3.36
5543 6046 7.606456 TCTTGTTTAGTGCCATACTTAAAGGAG 59.394 37.037 0.00 0.00 40.89 3.69
5545 6048 3.933861 AGTGCCATACTTAAAGGAGGG 57.066 47.619 0.00 0.00 35.67 4.30
5546 6049 2.509964 AGTGCCATACTTAAAGGAGGGG 59.490 50.000 0.00 0.00 35.67 4.79
5562 6065 7.431936 AAGGAGGGGGTATATCTCTAAAGTA 57.568 40.000 0.00 0.00 0.00 2.24
5563 6066 7.046891 AGGAGGGGGTATATCTCTAAAGTAG 57.953 44.000 0.00 0.00 0.00 2.57
5567 6072 5.957168 GGGGGTATATCTCTAAAGTAGTCCC 59.043 48.000 0.00 0.00 0.00 4.46
5688 6428 8.579850 TGGAAAGATCTGTATTGCAAATAGTT 57.420 30.769 1.71 0.00 0.00 2.24
5731 6471 9.775854 AGACATCTTATCTTTGTGAATGGATAG 57.224 33.333 0.00 0.00 0.00 2.08
5746 6486 7.222999 GTGAATGGATAGAGTAGTTAGCAACAC 59.777 40.741 0.00 0.00 0.00 3.32
5747 6487 5.593679 TGGATAGAGTAGTTAGCAACACC 57.406 43.478 0.00 0.00 0.00 4.16
5749 6489 5.661312 TGGATAGAGTAGTTAGCAACACCAT 59.339 40.000 0.00 0.00 0.00 3.55
5751 6491 6.183360 GGATAGAGTAGTTAGCAACACCATCA 60.183 42.308 0.00 0.00 0.00 3.07
5752 6492 5.078411 AGAGTAGTTAGCAACACCATCAG 57.922 43.478 0.00 0.00 0.00 2.90
5858 6604 5.355350 GCATGGCTAAATCTAACTTGTCTGT 59.645 40.000 0.00 0.00 0.00 3.41
5862 6608 6.174049 GGCTAAATCTAACTTGTCTGTCCTT 58.826 40.000 0.00 0.00 0.00 3.36
5863 6609 6.655425 GGCTAAATCTAACTTGTCTGTCCTTT 59.345 38.462 0.00 0.00 0.00 3.11
5864 6610 7.822822 GGCTAAATCTAACTTGTCTGTCCTTTA 59.177 37.037 0.00 0.00 0.00 1.85
5865 6611 9.216117 GCTAAATCTAACTTGTCTGTCCTTTAA 57.784 33.333 0.00 0.00 0.00 1.52
5870 6616 7.663827 TCTAACTTGTCTGTCCTTTAATTCGA 58.336 34.615 0.00 0.00 0.00 3.71
5885 6662 9.116067 CCTTTAATTCGATCATGGTAAAACCTA 57.884 33.333 0.00 0.00 39.58 3.08
5996 6773 2.500509 TTGACGGCATTTTCAACCAC 57.499 45.000 0.00 0.00 0.00 4.16
6003 6780 4.021544 ACGGCATTTTCAACCACAATGTAT 60.022 37.500 0.00 0.00 31.60 2.29
6017 6794 5.010012 CCACAATGTATAAATTGGCTCCTCC 59.990 44.000 18.01 0.00 41.06 4.30
6026 6803 3.512516 GGCTCCTCCAATGTGCGC 61.513 66.667 0.00 0.00 34.01 6.09
6045 6823 2.740714 GGCGCGTCTGGTCAATGTC 61.741 63.158 8.43 0.00 0.00 3.06
6048 6826 2.100631 GCGTCTGGTCAATGTCCGG 61.101 63.158 0.00 0.00 0.00 5.14
6050 6828 1.745489 GTCTGGTCAATGTCCGGGC 60.745 63.158 0.00 0.00 32.62 6.13
6051 6829 2.220586 TCTGGTCAATGTCCGGGCA 61.221 57.895 13.22 13.22 32.62 5.36
6072 6850 3.695830 TGTCCGCTTTGAATCCTTACT 57.304 42.857 0.00 0.00 0.00 2.24
6077 6855 6.487331 TGTCCGCTTTGAATCCTTACTTTTTA 59.513 34.615 0.00 0.00 0.00 1.52
6094 6872 4.640789 TTTTATGACACACAACCACACC 57.359 40.909 0.00 0.00 0.00 4.16
6096 6874 0.550914 ATGACACACAACCACACCCT 59.449 50.000 0.00 0.00 0.00 4.34
6098 6876 1.021968 GACACACAACCACACCCTTC 58.978 55.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
383 387 6.585702 TGCAAAGAAATCACAAATGTAATCGG 59.414 34.615 0.00 0.00 0.00 4.18
389 393 4.810491 GGTGTGCAAAGAAATCACAAATGT 59.190 37.500 0.00 0.00 41.66 2.71
502 507 3.053842 ACATGTGGATGGAATGAGAAGCT 60.054 43.478 0.00 0.00 33.39 3.74
604 609 6.415573 GTCAACCCCTGTCAGATAAATACTT 58.584 40.000 0.00 0.00 0.00 2.24
605 610 5.104485 GGTCAACCCCTGTCAGATAAATACT 60.104 44.000 0.00 0.00 0.00 2.12
606 611 5.123936 GGTCAACCCCTGTCAGATAAATAC 58.876 45.833 0.00 0.00 0.00 1.89
607 612 4.141801 CGGTCAACCCCTGTCAGATAAATA 60.142 45.833 0.00 0.00 0.00 1.40
608 613 3.370527 CGGTCAACCCCTGTCAGATAAAT 60.371 47.826 0.00 0.00 0.00 1.40
609 614 2.027561 CGGTCAACCCCTGTCAGATAAA 60.028 50.000 0.00 0.00 0.00 1.40
610 615 1.553248 CGGTCAACCCCTGTCAGATAA 59.447 52.381 0.00 0.00 0.00 1.75
611 616 1.191535 CGGTCAACCCCTGTCAGATA 58.808 55.000 0.00 0.00 0.00 1.98
612 617 0.836400 ACGGTCAACCCCTGTCAGAT 60.836 55.000 0.00 0.00 0.00 2.90
613 618 1.458777 ACGGTCAACCCCTGTCAGA 60.459 57.895 0.00 0.00 0.00 3.27
614 619 1.004918 GACGGTCAACCCCTGTCAG 60.005 63.158 2.62 0.00 32.16 3.51
615 620 1.125093 ATGACGGTCAACCCCTGTCA 61.125 55.000 15.72 9.77 40.05 3.58
616 621 0.899720 TATGACGGTCAACCCCTGTC 59.100 55.000 15.72 0.00 0.00 3.51
617 622 0.611714 GTATGACGGTCAACCCCTGT 59.388 55.000 15.72 0.00 0.00 4.00
618 623 0.902531 AGTATGACGGTCAACCCCTG 59.097 55.000 15.72 0.00 0.00 4.45
619 624 1.278127 CAAGTATGACGGTCAACCCCT 59.722 52.381 15.72 5.75 0.00 4.79
620 625 1.677820 CCAAGTATGACGGTCAACCCC 60.678 57.143 15.72 3.52 0.00 4.95
621 626 1.002773 ACCAAGTATGACGGTCAACCC 59.997 52.381 15.72 5.98 0.00 4.11
622 627 2.467566 ACCAAGTATGACGGTCAACC 57.532 50.000 15.72 8.49 0.00 3.77
623 628 3.930848 CCTAACCAAGTATGACGGTCAAC 59.069 47.826 15.72 13.74 30.91 3.18
624 629 3.618019 GCCTAACCAAGTATGACGGTCAA 60.618 47.826 15.72 2.04 30.91 3.18
625 630 2.093869 GCCTAACCAAGTATGACGGTCA 60.094 50.000 14.01 14.01 30.91 4.02
626 631 2.547826 GCCTAACCAAGTATGACGGTC 58.452 52.381 0.00 0.00 30.91 4.79
627 632 1.134907 CGCCTAACCAAGTATGACGGT 60.135 52.381 0.00 0.00 33.32 4.83
628 633 1.567504 CGCCTAACCAAGTATGACGG 58.432 55.000 0.00 0.00 0.00 4.79
629 634 1.134907 ACCGCCTAACCAAGTATGACG 60.135 52.381 0.00 0.00 0.00 4.35
630 635 2.093869 TGACCGCCTAACCAAGTATGAC 60.094 50.000 0.00 0.00 0.00 3.06
631 636 2.181125 TGACCGCCTAACCAAGTATGA 58.819 47.619 0.00 0.00 0.00 2.15
632 637 2.684001 TGACCGCCTAACCAAGTATG 57.316 50.000 0.00 0.00 0.00 2.39
633 638 6.675413 TTATATGACCGCCTAACCAAGTAT 57.325 37.500 0.00 0.00 0.00 2.12
634 639 6.495872 AGATTATATGACCGCCTAACCAAGTA 59.504 38.462 0.00 0.00 0.00 2.24
635 640 5.307196 AGATTATATGACCGCCTAACCAAGT 59.693 40.000 0.00 0.00 0.00 3.16
636 641 5.794894 AGATTATATGACCGCCTAACCAAG 58.205 41.667 0.00 0.00 0.00 3.61
637 642 5.818678 AGATTATATGACCGCCTAACCAA 57.181 39.130 0.00 0.00 0.00 3.67
638 643 5.818678 AAGATTATATGACCGCCTAACCA 57.181 39.130 0.00 0.00 0.00 3.67
639 644 6.485648 ACAAAAGATTATATGACCGCCTAACC 59.514 38.462 0.00 0.00 0.00 2.85
640 645 7.492352 ACAAAAGATTATATGACCGCCTAAC 57.508 36.000 0.00 0.00 0.00 2.34
641 646 8.402472 CAAACAAAAGATTATATGACCGCCTAA 58.598 33.333 0.00 0.00 0.00 2.69
642 647 7.554835 ACAAACAAAAGATTATATGACCGCCTA 59.445 33.333 0.00 0.00 0.00 3.93
643 648 6.377146 ACAAACAAAAGATTATATGACCGCCT 59.623 34.615 0.00 0.00 0.00 5.52
644 649 6.472163 CACAAACAAAAGATTATATGACCGCC 59.528 38.462 0.00 0.00 0.00 6.13
645 650 6.020678 GCACAAACAAAAGATTATATGACCGC 60.021 38.462 0.00 0.00 0.00 5.68
646 651 6.472163 GGCACAAACAAAAGATTATATGACCG 59.528 38.462 0.00 0.00 0.00 4.79
647 652 6.756542 GGGCACAAACAAAAGATTATATGACC 59.243 38.462 0.00 0.00 0.00 4.02
648 653 6.756542 GGGGCACAAACAAAAGATTATATGAC 59.243 38.462 0.00 0.00 0.00 3.06
649 654 6.667414 AGGGGCACAAACAAAAGATTATATGA 59.333 34.615 0.00 0.00 0.00 2.15
650 655 6.757947 CAGGGGCACAAACAAAAGATTATATG 59.242 38.462 0.00 0.00 0.00 1.78
651 656 6.440328 ACAGGGGCACAAACAAAAGATTATAT 59.560 34.615 0.00 0.00 0.00 0.86
652 657 5.777732 ACAGGGGCACAAACAAAAGATTATA 59.222 36.000 0.00 0.00 0.00 0.98
653 658 4.592778 ACAGGGGCACAAACAAAAGATTAT 59.407 37.500 0.00 0.00 0.00 1.28
654 659 3.964031 ACAGGGGCACAAACAAAAGATTA 59.036 39.130 0.00 0.00 0.00 1.75
655 660 2.771372 ACAGGGGCACAAACAAAAGATT 59.229 40.909 0.00 0.00 0.00 2.40
656 661 2.397597 ACAGGGGCACAAACAAAAGAT 58.602 42.857 0.00 0.00 0.00 2.40
657 662 1.859302 ACAGGGGCACAAACAAAAGA 58.141 45.000 0.00 0.00 0.00 2.52
658 663 3.810310 TTACAGGGGCACAAACAAAAG 57.190 42.857 0.00 0.00 0.00 2.27
659 664 3.260884 TGTTTACAGGGGCACAAACAAAA 59.739 39.130 1.77 0.00 37.80 2.44
660 665 2.832129 TGTTTACAGGGGCACAAACAAA 59.168 40.909 1.77 0.00 37.80 2.83
661 666 2.457598 TGTTTACAGGGGCACAAACAA 58.542 42.857 1.77 0.00 37.80 2.83
662 667 2.145397 TGTTTACAGGGGCACAAACA 57.855 45.000 0.20 0.20 38.26 2.83
663 668 3.181470 ACAATGTTTACAGGGGCACAAAC 60.181 43.478 0.00 0.00 0.00 2.93
664 669 3.034635 ACAATGTTTACAGGGGCACAAA 58.965 40.909 0.00 0.00 0.00 2.83
665 670 2.363680 CACAATGTTTACAGGGGCACAA 59.636 45.455 0.00 0.00 0.00 3.33
666 671 1.959985 CACAATGTTTACAGGGGCACA 59.040 47.619 0.00 0.00 0.00 4.57
667 672 2.030274 GTCACAATGTTTACAGGGGCAC 60.030 50.000 0.00 0.00 0.00 5.01
668 673 2.235016 GTCACAATGTTTACAGGGGCA 58.765 47.619 0.00 0.00 0.00 5.36
669 674 1.199097 CGTCACAATGTTTACAGGGGC 59.801 52.381 0.00 0.00 0.00 5.80
670 675 1.810151 CCGTCACAATGTTTACAGGGG 59.190 52.381 0.00 0.00 0.00 4.79
671 676 1.810151 CCCGTCACAATGTTTACAGGG 59.190 52.381 9.43 9.43 0.00 4.45
672 677 2.500229 ACCCGTCACAATGTTTACAGG 58.500 47.619 0.00 0.00 0.00 4.00
673 678 5.676532 TTAACCCGTCACAATGTTTACAG 57.323 39.130 0.00 0.00 0.00 2.74
674 679 6.636562 ATTTAACCCGTCACAATGTTTACA 57.363 33.333 0.00 0.00 0.00 2.41
675 680 9.120422 CTTTATTTAACCCGTCACAATGTTTAC 57.880 33.333 0.00 0.00 0.00 2.01
676 681 7.808856 GCTTTATTTAACCCGTCACAATGTTTA 59.191 33.333 0.00 0.00 0.00 2.01
677 682 6.643360 GCTTTATTTAACCCGTCACAATGTTT 59.357 34.615 0.00 0.00 0.00 2.83
678 683 6.015772 AGCTTTATTTAACCCGTCACAATGTT 60.016 34.615 0.00 0.00 0.00 2.71
679 684 5.475564 AGCTTTATTTAACCCGTCACAATGT 59.524 36.000 0.00 0.00 0.00 2.71
680 685 5.949735 AGCTTTATTTAACCCGTCACAATG 58.050 37.500 0.00 0.00 0.00 2.82
681 686 5.163794 CGAGCTTTATTTAACCCGTCACAAT 60.164 40.000 0.00 0.00 0.00 2.71
682 687 4.152759 CGAGCTTTATTTAACCCGTCACAA 59.847 41.667 0.00 0.00 0.00 3.33
683 688 3.680937 CGAGCTTTATTTAACCCGTCACA 59.319 43.478 0.00 0.00 0.00 3.58
684 689 3.681417 ACGAGCTTTATTTAACCCGTCAC 59.319 43.478 0.00 0.00 0.00 3.67
685 690 3.929094 ACGAGCTTTATTTAACCCGTCA 58.071 40.909 0.00 0.00 0.00 4.35
686 691 4.934075 AACGAGCTTTATTTAACCCGTC 57.066 40.909 0.00 0.00 0.00 4.79
722 727 1.531423 GGGATATGTCTCGCCTCGTA 58.469 55.000 0.00 0.00 0.00 3.43
724 729 1.587054 GGGGATATGTCTCGCCTCG 59.413 63.158 0.35 0.00 43.16 4.63
727 732 1.545706 GGGAGGGGATATGTCTCGCC 61.546 65.000 0.00 0.00 45.97 5.54
766 774 1.445716 AACCTAGCGACCTCGGATCG 61.446 60.000 0.00 0.00 42.55 3.69
767 775 0.745468 AAACCTAGCGACCTCGGATC 59.255 55.000 0.00 0.00 40.23 3.36
768 776 1.136500 GAAAACCTAGCGACCTCGGAT 59.864 52.381 0.00 0.00 40.23 4.18
769 777 0.529378 GAAAACCTAGCGACCTCGGA 59.471 55.000 0.00 0.00 40.23 4.55
770 778 0.459759 GGAAAACCTAGCGACCTCGG 60.460 60.000 0.00 0.00 40.23 4.63
771 779 0.801067 CGGAAAACCTAGCGACCTCG 60.801 60.000 0.00 0.00 43.27 4.63
821 829 4.821589 GAAGGGAGGAGTGCGGCG 62.822 72.222 0.51 0.51 0.00 6.46
855 863 1.823899 GCGAGGAAAATGGGCGGAT 60.824 57.895 0.00 0.00 0.00 4.18
978 989 0.392595 GCGGTTCTTGGAGGTTAGGG 60.393 60.000 0.00 0.00 0.00 3.53
979 990 0.392595 GGCGGTTCTTGGAGGTTAGG 60.393 60.000 0.00 0.00 0.00 2.69
980 991 0.739813 CGGCGGTTCTTGGAGGTTAG 60.740 60.000 0.00 0.00 0.00 2.34
982 993 1.838073 ATCGGCGGTTCTTGGAGGTT 61.838 55.000 7.21 0.00 0.00 3.50
983 994 2.291043 ATCGGCGGTTCTTGGAGGT 61.291 57.895 7.21 0.00 0.00 3.85
984 995 1.815421 CATCGGCGGTTCTTGGAGG 60.815 63.158 7.21 0.00 0.00 4.30
986 997 2.435938 GCATCGGCGGTTCTTGGA 60.436 61.111 7.21 0.00 0.00 3.53
1052 1063 3.976701 AATCCTGCCGGAACCTGCG 62.977 63.158 5.05 0.00 44.02 5.18
1053 1064 2.044946 AATCCTGCCGGAACCTGC 60.045 61.111 5.05 0.42 44.02 4.85
1054 1065 1.815421 CGAATCCTGCCGGAACCTG 60.815 63.158 5.05 0.00 44.02 4.00
1055 1066 2.291043 ACGAATCCTGCCGGAACCT 61.291 57.895 5.05 0.00 44.02 3.50
1056 1067 2.106683 CACGAATCCTGCCGGAACC 61.107 63.158 5.05 0.00 44.02 3.62
1057 1068 2.750888 GCACGAATCCTGCCGGAAC 61.751 63.158 5.05 0.00 44.02 3.62
1058 1069 2.435938 GCACGAATCCTGCCGGAA 60.436 61.111 5.05 0.00 44.02 4.30
1059 1070 3.700970 TGCACGAATCCTGCCGGA 61.701 61.111 5.05 0.00 45.16 5.14
1085 1096 4.603946 GTATCGGGCCCTGGCGAC 62.604 72.222 22.43 6.82 43.06 5.19
1134 1145 4.021925 GGGGGCAGCTTCGACAGT 62.022 66.667 0.00 0.00 0.00 3.55
1556 1576 7.126061 TGTCCTAGACTAGATCCAAGAATCAA 58.874 38.462 11.27 0.00 33.15 2.57
1559 1579 6.074648 CCTGTCCTAGACTAGATCCAAGAAT 58.925 44.000 11.27 0.00 33.15 2.40
1573 1593 3.506096 CGCGTCGCCTGTCCTAGA 61.506 66.667 12.44 0.00 0.00 2.43
1574 1594 4.554363 CCGCGTCGCCTGTCCTAG 62.554 72.222 12.44 0.00 0.00 3.02
1593 1613 3.912496 TCACCAATCCACCTGTAGATG 57.088 47.619 0.00 0.00 0.00 2.90
1621 1641 0.823356 TGGTCAGAACCCTTGCTTGC 60.823 55.000 0.00 0.00 45.83 4.01
1622 1642 1.338020 GTTGGTCAGAACCCTTGCTTG 59.662 52.381 0.00 0.00 45.83 4.01
1623 1643 1.215423 AGTTGGTCAGAACCCTTGCTT 59.785 47.619 0.00 0.00 45.83 3.91
1624 1644 0.846693 AGTTGGTCAGAACCCTTGCT 59.153 50.000 0.00 0.00 45.83 3.91
1648 1672 4.941263 TGTCGCCAAAATCTAAAGCTACAT 59.059 37.500 0.00 0.00 0.00 2.29
1654 1678 5.629435 GGTTTTCTGTCGCCAAAATCTAAAG 59.371 40.000 0.00 0.00 0.00 1.85
1794 1966 4.363999 CTGGAGACCGCTAATTTAGACTG 58.636 47.826 7.63 0.00 0.00 3.51
1808 1980 1.486211 TAAGGTAGCAGCTGGAGACC 58.514 55.000 17.12 4.34 0.00 3.85
1852 2025 7.795482 TTAAACAGCACTTGAGCTAAAACTA 57.205 32.000 0.00 0.00 44.54 2.24
1853 2026 6.693315 TTAAACAGCACTTGAGCTAAAACT 57.307 33.333 0.00 0.00 44.54 2.66
1854 2027 9.458374 TTTATTAAACAGCACTTGAGCTAAAAC 57.542 29.630 0.00 0.00 44.54 2.43
1855 2028 9.458374 GTTTATTAAACAGCACTTGAGCTAAAA 57.542 29.630 13.23 0.00 44.54 1.52
1856 2029 8.625651 TGTTTATTAAACAGCACTTGAGCTAAA 58.374 29.630 16.17 0.00 45.79 1.85
1891 2076 2.224402 GCGATCCTCTCTGCCCTAAATT 60.224 50.000 0.00 0.00 0.00 1.82
1898 2083 0.883814 CCATTGCGATCCTCTCTGCC 60.884 60.000 0.00 0.00 0.00 4.85
1911 2096 5.874810 TGAAGACAGACACTATAACCATTGC 59.125 40.000 0.00 0.00 0.00 3.56
1997 2186 7.438459 GCAATGAGTTACTGGTATACTGGTAAG 59.562 40.741 15.87 8.69 0.00 2.34
2016 2205 4.099266 TGAATTTTTATCGGGGGCAATGAG 59.901 41.667 0.00 0.00 0.00 2.90
2018 2207 4.141959 ACTGAATTTTTATCGGGGGCAATG 60.142 41.667 0.00 0.00 0.00 2.82
2020 2209 3.436243 ACTGAATTTTTATCGGGGGCAA 58.564 40.909 0.00 0.00 0.00 4.52
2187 2407 1.032014 GACAAGTCCCAAAAGCAGCA 58.968 50.000 0.00 0.00 0.00 4.41
2201 2421 3.024547 TCCTAGATTCAGTCGGGACAAG 58.975 50.000 1.17 0.00 31.84 3.16
2210 2430 3.678965 TCAGAGCCTCCTAGATTCAGT 57.321 47.619 0.00 0.00 0.00 3.41
2292 2540 2.176889 GTAGCTGGTCAGTTCCTACCA 58.823 52.381 0.00 0.00 43.47 3.25
2306 2554 6.036517 GTCTGACATATTGACTTTGGTAGCTG 59.963 42.308 2.24 0.00 0.00 4.24
2312 2560 5.181811 TGCAAGTCTGACATATTGACTTTGG 59.818 40.000 10.88 0.00 45.32 3.28
2313 2561 6.245115 TGCAAGTCTGACATATTGACTTTG 57.755 37.500 10.88 3.71 45.32 2.77
2360 2634 5.531122 AGCCATGTTAATTAGAGAGCGTA 57.469 39.130 0.00 0.00 0.00 4.42
2396 2670 4.763073 CAGCATCACAGGAATCAGAAGTA 58.237 43.478 0.00 0.00 0.00 2.24
2402 2676 0.328926 TGGCAGCATCACAGGAATCA 59.671 50.000 0.00 0.00 0.00 2.57
2403 2677 1.022735 CTGGCAGCATCACAGGAATC 58.977 55.000 0.00 0.00 0.00 2.52
2408 2682 4.175489 GCGCTGGCAGCATCACAG 62.175 66.667 35.94 20.89 42.58 3.66
2430 2704 3.865011 GAGTCAGACTCATCAGCAAGA 57.135 47.619 23.62 0.00 44.45 3.02
2483 2757 2.833631 TTCAGAACGAGGGGAGAAAC 57.166 50.000 0.00 0.00 0.00 2.78
2487 2761 2.234908 AGTTGATTCAGAACGAGGGGAG 59.765 50.000 0.00 0.00 0.00 4.30
2515 2789 4.160439 GTCAGTATCCAGACATCCAACTCA 59.840 45.833 0.00 0.00 34.93 3.41
2527 2801 7.824289 TGGAAGAACTTTAATGTCAGTATCCAG 59.176 37.037 0.00 0.00 31.65 3.86
2528 2802 7.685481 TGGAAGAACTTTAATGTCAGTATCCA 58.315 34.615 0.00 3.34 32.30 3.41
2529 2803 7.201652 GCTGGAAGAACTTTAATGTCAGTATCC 60.202 40.741 8.16 6.79 34.07 2.59
2576 2852 3.950397 AGCTGGGTATCGAATCAACAAA 58.050 40.909 0.00 0.00 0.00 2.83
2675 2952 1.792006 AACAAGGTAAAGACGCCGAG 58.208 50.000 0.00 0.00 0.00 4.63
2692 2969 5.006153 ACAAAGCAAGGTACCAAAGAAAC 57.994 39.130 15.94 0.00 0.00 2.78
2750 3027 5.296035 ACTTAAAAGTTCGTCTCCCAACTTG 59.704 40.000 0.00 0.00 41.09 3.16
2751 3028 5.434408 ACTTAAAAGTTCGTCTCCCAACTT 58.566 37.500 0.00 0.00 43.28 2.66
2753 3030 5.507974 CAACTTAAAAGTTCGTCTCCCAAC 58.492 41.667 5.13 0.00 45.65 3.77
2784 3063 3.976169 TCCAGCTTGAAACCAAAAATCG 58.024 40.909 0.00 0.00 0.00 3.34
2786 3065 3.494924 GCCTCCAGCTTGAAACCAAAAAT 60.495 43.478 0.00 0.00 38.99 1.82
2854 3163 4.579869 GCTCCCAAACTCATTTCTCACTA 58.420 43.478 0.00 0.00 0.00 2.74
2902 3342 1.216710 CTCCTGGTTCAGCGGAGAC 59.783 63.158 9.81 0.00 45.67 3.36
2908 3348 0.390998 GTGAGAGCTCCTGGTTCAGC 60.391 60.000 10.93 0.00 35.73 4.26
2921 3361 2.674852 CGAACCATGGACAATGTGAGAG 59.325 50.000 21.47 0.00 34.11 3.20
2922 3362 2.301583 TCGAACCATGGACAATGTGAGA 59.698 45.455 21.47 1.56 34.11 3.27
2978 3418 1.863454 CAGACATTCTGCATAGGCGAC 59.137 52.381 0.00 0.00 45.35 5.19
3015 3455 5.012561 GGAGTATCAAGGAGACCATGCTAAT 59.987 44.000 0.00 0.00 36.25 1.73
3022 3462 4.026744 CTCAAGGAGTATCAAGGAGACCA 58.973 47.826 0.00 0.00 36.25 4.02
3118 3558 5.590976 TGGGCCCTTTAAAATTTTGGAAT 57.409 34.783 25.70 0.00 0.00 3.01
3137 3577 2.749621 GAGACAGTGCAACCTTTATGGG 59.250 50.000 0.00 0.00 41.11 4.00
3167 3608 2.068213 GTGGGGGCTACCGTACCAT 61.068 63.158 0.00 0.00 41.60 3.55
3303 3744 4.409901 TGCTGTTCATAATCAGATGAGGGA 59.590 41.667 0.00 0.00 37.16 4.20
3363 3825 3.668447 CATTGTGCTAAGTGAGTCACCT 58.332 45.455 19.71 9.75 34.49 4.00
3419 3881 5.409643 CACAGTTGGACAGTCAAACTTAG 57.590 43.478 19.42 12.43 0.00 2.18
3466 3951 5.073554 TCATTCCATATGGCTGGTATCAAGT 59.926 40.000 17.58 0.00 37.57 3.16
3613 4099 1.442769 AAACTGATGCACTACTGGCG 58.557 50.000 0.00 0.00 0.00 5.69
3652 4138 2.646930 TCCGATTTGCAGCATGATTCT 58.353 42.857 0.00 0.00 39.69 2.40
3762 4248 3.181507 ACAATTGGCGATTTCTGATGACG 60.182 43.478 10.83 0.00 0.00 4.35
3780 4266 4.949856 ACACAACTCCAAGAGAAACACAAT 59.050 37.500 0.00 0.00 33.32 2.71
3897 4383 9.607988 AACATGGTCAATCGTAATATAGTGAAA 57.392 29.630 0.00 0.00 0.00 2.69
3904 4390 8.902540 ACATACAACATGGTCAATCGTAATAT 57.097 30.769 0.00 0.00 0.00 1.28
3932 4418 1.690893 TCCATCCAGTCTATCAGCTGC 59.309 52.381 9.47 0.00 0.00 5.25
3967 4453 1.952296 CATGATCCCCAGTAAGCAAGC 59.048 52.381 0.00 0.00 0.00 4.01
3975 4461 1.750399 GCAACGCATGATCCCCAGT 60.750 57.895 0.00 0.00 0.00 4.00
3990 4476 1.164411 CATACAAGGTCAAGCCGCAA 58.836 50.000 0.00 0.00 43.70 4.85
4014 4500 1.478288 GGCAGCTTCTAGCCCATTCAT 60.478 52.381 1.27 0.00 43.77 2.57
4049 4535 6.533730 TGATTTATGCATATCCGGAAGACTT 58.466 36.000 9.01 0.00 0.00 3.01
4188 4677 5.939883 TCAGGTACAAGGACATCAAATTCTG 59.060 40.000 0.00 0.00 0.00 3.02
4308 4797 4.391405 GGCCATTAAGCATAATATGGCC 57.609 45.455 22.83 22.83 45.81 5.36
4320 4809 2.310538 GGTGGATTCTGGGCCATTAAG 58.689 52.381 6.72 0.00 36.41 1.85
4330 4819 2.234908 AGGAACTTCTCGGTGGATTCTG 59.765 50.000 0.00 0.00 27.25 3.02
4361 4850 2.412089 GTGAACCGGAATTGACTTCTCG 59.588 50.000 9.46 0.00 34.08 4.04
4376 4865 2.038557 AGTGTACATGGACCAGTGAACC 59.961 50.000 5.38 0.00 0.00 3.62
4389 4878 2.038426 TGTTAGCCAGCACAGTGTACAT 59.962 45.455 0.00 0.00 0.00 2.29
4448 4937 2.269940 TCCTCAGCTTTCTTTAGGGCT 58.730 47.619 0.00 0.00 35.23 5.19
4573 5062 7.337938 TCTGTTTGAACATATCCTCAATGCTA 58.662 34.615 0.00 0.00 38.41 3.49
4677 5166 6.104665 TCATATCAAAGCTCTGTTGAGTGAG 58.895 40.000 5.61 0.00 42.13 3.51
4697 5186 5.862678 TCATCACGTTTGGTATCCTCATA 57.137 39.130 0.00 0.00 0.00 2.15
4853 5342 4.079850 CAGACCTGGAGCGCTGCT 62.080 66.667 29.46 9.95 43.88 4.24
4989 5478 1.004560 CCAGCTTCTCAAGGCACGA 60.005 57.895 0.00 0.00 0.00 4.35
5079 5568 1.978580 ACCTGGTCTTCTTCCGTTGAT 59.021 47.619 0.00 0.00 0.00 2.57
5080 5569 1.420430 ACCTGGTCTTCTTCCGTTGA 58.580 50.000 0.00 0.00 0.00 3.18
5081 5570 1.873591 CAACCTGGTCTTCTTCCGTTG 59.126 52.381 0.00 0.00 0.00 4.10
5167 5667 1.001520 ACGCCAAACAATTAAAGGGCC 59.998 47.619 0.00 0.00 38.16 5.80
5212 5712 5.702209 CAGCATGAAACTAAAGGGCAAAATT 59.298 36.000 0.00 0.00 39.69 1.82
5340 5840 5.069516 ACATGAATAATTCTGGTTGCCATCC 59.930 40.000 0.00 0.00 30.82 3.51
5381 5882 7.227711 TGAGACACTTATTTTGAAACGAATGGA 59.772 33.333 0.00 0.00 0.00 3.41
5386 5887 7.548196 AGTTGAGACACTTATTTTGAAACGA 57.452 32.000 0.00 0.00 0.00 3.85
5390 5891 9.997482 GTACAAAGTTGAGACACTTATTTTGAA 57.003 29.630 0.00 0.00 35.87 2.69
5391 5892 9.391006 AGTACAAAGTTGAGACACTTATTTTGA 57.609 29.630 0.00 0.00 35.87 2.69
5425 5926 4.301628 CAGAAAATTCTCAAACTGCCCAC 58.698 43.478 0.00 0.00 34.74 4.61
5432 5933 4.489679 AGTCCGCAGAAAATTCTCAAAC 57.510 40.909 0.00 0.00 34.74 2.93
5434 5935 4.637276 TGTAGTCCGCAGAAAATTCTCAA 58.363 39.130 0.00 0.00 34.74 3.02
5448 5949 4.682787 TCTGCTCATAAACATGTAGTCCG 58.317 43.478 0.00 0.00 0.00 4.79
5464 5965 1.896465 ACTAGTGTTGACCCTCTGCTC 59.104 52.381 0.00 0.00 0.00 4.26
5466 5967 2.417515 GCTACTAGTGTTGACCCTCTGC 60.418 54.545 5.39 0.00 0.00 4.26
5504 6007 7.803659 GGCACTAAACAAGAGAATTTCAACTAC 59.196 37.037 0.00 0.00 0.00 2.73
5541 6044 6.891361 GGACTACTTTAGAGATATACCCCCTC 59.109 46.154 0.00 0.00 0.00 4.30
5542 6045 6.240822 GGGACTACTTTAGAGATATACCCCCT 60.241 46.154 0.00 0.00 0.00 4.79
5543 6046 5.957168 GGGACTACTTTAGAGATATACCCCC 59.043 48.000 0.00 0.00 0.00 5.40
5545 6048 7.240167 AGTGGGACTACTTTAGAGATATACCC 58.760 42.308 0.00 0.00 0.00 3.69
5546 6049 9.804977 TTAGTGGGACTACTTTAGAGATATACC 57.195 37.037 0.00 0.00 28.93 2.73
5562 6065 7.402054 TGTGTTGATGAATATTTAGTGGGACT 58.598 34.615 0.00 0.00 0.00 3.85
5563 6066 7.624360 TGTGTTGATGAATATTTAGTGGGAC 57.376 36.000 0.00 0.00 0.00 4.46
5730 6470 4.081420 CCTGATGGTGTTGCTAACTACTCT 60.081 45.833 0.00 0.00 0.00 3.24
5731 6471 4.184629 CCTGATGGTGTTGCTAACTACTC 58.815 47.826 0.00 0.00 0.00 2.59
5746 6486 2.100584 GAGAGCAGTAGACACCTGATGG 59.899 54.545 0.00 0.00 39.83 3.51
5747 6487 3.023119 AGAGAGCAGTAGACACCTGATG 58.977 50.000 0.00 0.00 31.38 3.07
5749 6489 2.224892 ACAGAGAGCAGTAGACACCTGA 60.225 50.000 0.00 0.00 31.38 3.86
5751 6491 2.595750 ACAGAGAGCAGTAGACACCT 57.404 50.000 0.00 0.00 0.00 4.00
5752 6492 2.094442 GGAACAGAGAGCAGTAGACACC 60.094 54.545 0.00 0.00 0.00 4.16
5858 6604 7.832187 AGGTTTTACCATGATCGAATTAAAGGA 59.168 33.333 0.00 0.00 41.95 3.36
5977 6754 1.751351 TGTGGTTGAAAATGCCGTCAA 59.249 42.857 0.00 0.00 0.00 3.18
5979 6756 2.500509 TTGTGGTTGAAAATGCCGTC 57.499 45.000 0.00 0.00 0.00 4.79
5989 6766 6.127479 GGAGCCAATTTATACATTGTGGTTGA 60.127 38.462 10.04 0.00 32.95 3.18
6010 6787 3.869272 CGCGCACATTGGAGGAGC 61.869 66.667 8.75 0.00 0.00 4.70
6026 6803 3.853330 CATTGACCAGACGCGCCG 61.853 66.667 5.73 0.00 0.00 6.46
6029 6806 2.444624 CGGACATTGACCAGACGCG 61.445 63.158 3.53 3.53 0.00 6.01
6030 6807 2.100631 CCGGACATTGACCAGACGC 61.101 63.158 0.00 0.00 0.00 5.19
6031 6808 1.447838 CCCGGACATTGACCAGACG 60.448 63.158 0.73 0.00 0.00 4.18
6034 6812 1.077501 ATGCCCGGACATTGACCAG 60.078 57.895 0.73 0.00 0.00 4.00
6048 6826 0.101219 GGATTCAAAGCGGACATGCC 59.899 55.000 0.00 0.00 34.65 4.40
6050 6828 3.941483 AGTAAGGATTCAAAGCGGACATG 59.059 43.478 0.00 0.00 0.00 3.21
6051 6829 4.222124 AGTAAGGATTCAAAGCGGACAT 57.778 40.909 0.00 0.00 0.00 3.06
6072 6850 4.142138 GGGTGTGGTTGTGTGTCATAAAAA 60.142 41.667 0.00 0.00 0.00 1.94
6077 6855 0.550914 AGGGTGTGGTTGTGTGTCAT 59.449 50.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.