Multiple sequence alignment - TraesCS6A01G080400

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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 TraesCS6A01G080400 chr6A 100.000 2765 0 0 1 2765 49132957 49130193 0.000000e+00 5107.0
1 TraesCS6A01G080400 chr6A 94.107 543 16 13 1 530 328424099 328424638 0.000000e+00 811.0
2 TraesCS6A01G080400 chr6A 86.000 100 9 5 2584 2680 469146195 469146292 4.870000e-18 102.0
3 TraesCS6A01G080400 chr6A 85.714 98 12 2 2584 2680 522351404 522351500 4.870000e-18 102.0
4 TraesCS6A01G080400 chr6B 92.292 1453 79 8 836 2267 88498658 88497218 0.000000e+00 2032.0
5 TraesCS6A01G080400 chr6B 92.713 1043 58 5 826 1860 88573000 88571968 0.000000e+00 1489.0
6 TraesCS6A01G080400 chr6B 95.817 502 13 6 1 499 448026635 448027131 0.000000e+00 804.0
7 TraesCS6A01G080400 chr6B 86.437 435 32 9 2339 2765 88497218 88496803 4.200000e-123 451.0
8 TraesCS6A01G080400 chr6D 90.594 1212 75 12 667 1869 37881498 37880317 0.000000e+00 1570.0
9 TraesCS6A01G080400 chr6D 92.322 1055 64 7 826 1868 37736015 37734966 0.000000e+00 1483.0
10 TraesCS6A01G080400 chr6D 91.732 1028 60 6 858 1869 37839233 37838215 0.000000e+00 1404.0
11 TraesCS6A01G080400 chr6D 90.045 442 22 8 2339 2765 37715314 37714880 1.120000e-153 553.0
12 TraesCS6A01G080400 chr6D 88.128 219 3 7 2070 2267 37715530 37715314 3.560000e-59 239.0
13 TraesCS6A01G080400 chr4B 94.485 544 14 13 1 531 155671778 155672318 0.000000e+00 824.0
14 TraesCS6A01G080400 chr4B 94.475 543 14 13 1 530 155663261 155663800 0.000000e+00 822.0
15 TraesCS6A01G080400 chr4B 94.340 53 3 0 479 531 254171829 254171881 6.350000e-12 82.4
16 TraesCS6A01G080400 chr3A 96.047 506 12 8 1 499 206843228 206842724 0.000000e+00 817.0
17 TraesCS6A01G080400 chr3A 95.850 506 13 8 1 499 206855526 206855022 0.000000e+00 811.0
18 TraesCS6A01G080400 chr3A 86.538 52 5 1 531 580 501726299 501726248 3.850000e-04 56.5
19 TraesCS6A01G080400 chr5B 95.842 505 13 6 4 505 127112928 127112429 0.000000e+00 809.0
20 TraesCS6A01G080400 chr5B 80.860 465 53 28 87 530 81854700 81855149 1.590000e-87 333.0
21 TraesCS6A01G080400 chr5B 91.489 47 3 1 485 530 168024855 168024809 2.300000e-06 63.9
22 TraesCS6A01G080400 chr5B 100.000 30 0 0 531 560 696466650 696466621 3.850000e-04 56.5
23 TraesCS6A01G080400 chr1A 96.008 501 14 6 1 499 318202629 318202133 0.000000e+00 809.0
24 TraesCS6A01G080400 chr4A 95.833 504 14 7 1 499 637570313 637569812 0.000000e+00 808.0
25 TraesCS6A01G080400 chr4A 84.211 95 13 2 2587 2680 49202930 49202837 1.050000e-14 91.6
26 TraesCS6A01G080400 chrUn 100.000 70 0 0 2268 2337 298935724 298935655 2.230000e-26 130.0
27 TraesCS6A01G080400 chrUn 100.000 70 0 0 2268 2337 359774815 359774884 2.230000e-26 130.0
28 TraesCS6A01G080400 chr7D 100.000 70 0 0 2268 2337 231586842 231586773 2.230000e-26 130.0
29 TraesCS6A01G080400 chr7D 93.750 48 3 0 484 531 471767778 471767825 3.820000e-09 73.1
30 TraesCS6A01G080400 chr7D 96.875 32 1 0 531 562 529757365 529757396 1.000000e-03 54.7
31 TraesCS6A01G080400 chr7B 100.000 70 0 0 2268 2337 662746829 662746760 2.230000e-26 130.0
32 TraesCS6A01G080400 chr7B 82.540 126 15 6 2561 2680 436785504 436785380 1.350000e-18 104.0
33 TraesCS6A01G080400 chr7B 95.745 47 2 0 477 523 563867547 563867593 2.950000e-10 76.8
34 TraesCS6A01G080400 chr7B 92.105 38 1 2 531 568 85844047 85844012 5.000000e-03 52.8
35 TraesCS6A01G080400 chr5D 100.000 70 0 0 2268 2337 6245033 6244964 2.230000e-26 130.0
36 TraesCS6A01G080400 chr5D 100.000 70 0 0 2268 2337 268565437 268565368 2.230000e-26 130.0
37 TraesCS6A01G080400 chr5D 100.000 70 0 0 2268 2337 432325819 432325750 2.230000e-26 130.0
38 TraesCS6A01G080400 chr5D 100.000 70 0 0 2268 2337 503321736 503321805 2.230000e-26 130.0
39 TraesCS6A01G080400 chr5D 78.295 129 16 9 2561 2680 356971586 356971711 3.820000e-09 73.1
40 TraesCS6A01G080400 chr3D 100.000 70 0 0 2268 2337 170684587 170684518 2.230000e-26 130.0
41 TraesCS6A01G080400 chr2D 85.859 99 11 3 2584 2680 614840916 614841013 4.870000e-18 102.0
42 TraesCS6A01G080400 chr2D 97.297 37 0 1 531 567 533206935 533206900 8.270000e-06 62.1
43 TraesCS6A01G080400 chr2B 94.545 55 3 0 479 533 206784559 206784505 4.910000e-13 86.1
44 TraesCS6A01G080400 chr2B 94.231 52 3 0 479 530 206792308 206792257 2.280000e-11 80.5
45 TraesCS6A01G080400 chr7A 81.818 99 15 3 2584 2680 652532268 652532171 2.280000e-11 80.5
46 TraesCS6A01G080400 chr7A 94.872 39 1 1 531 569 620404396 620404433 2.970000e-05 60.2
47 TraesCS6A01G080400 chr3B 95.652 46 2 0 485 530 424885720 424885765 1.060000e-09 75.0
48 TraesCS6A01G080400 chr2A 94.595 37 0 1 531 567 516416741 516416775 3.850000e-04 56.5
49 TraesCS6A01G080400 chr5A 96.875 32 1 0 531 562 400505909 400505878 1.000000e-03 54.7
50 TraesCS6A01G080400 chr5A 92.308 39 1 2 531 569 601067964 601067928 1.000000e-03 54.7


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 TraesCS6A01G080400 chr6A 49130193 49132957 2764 True 5107.0 5107 100.0000 1 2765 1 chr6A.!!$R1 2764
1 TraesCS6A01G080400 chr6A 328424099 328424638 539 False 811.0 811 94.1070 1 530 1 chr6A.!!$F1 529
2 TraesCS6A01G080400 chr6B 88571968 88573000 1032 True 1489.0 1489 92.7130 826 1860 1 chr6B.!!$R1 1034
3 TraesCS6A01G080400 chr6B 88496803 88498658 1855 True 1241.5 2032 89.3645 836 2765 2 chr6B.!!$R2 1929
4 TraesCS6A01G080400 chr6D 37880317 37881498 1181 True 1570.0 1570 90.5940 667 1869 1 chr6D.!!$R3 1202
5 TraesCS6A01G080400 chr6D 37734966 37736015 1049 True 1483.0 1483 92.3220 826 1868 1 chr6D.!!$R1 1042
6 TraesCS6A01G080400 chr6D 37838215 37839233 1018 True 1404.0 1404 91.7320 858 1869 1 chr6D.!!$R2 1011
7 TraesCS6A01G080400 chr6D 37714880 37715530 650 True 396.0 553 89.0865 2070 2765 2 chr6D.!!$R4 695
8 TraesCS6A01G080400 chr4B 155671778 155672318 540 False 824.0 824 94.4850 1 531 1 chr4B.!!$F2 530
9 TraesCS6A01G080400 chr4B 155663261 155663800 539 False 822.0 822 94.4750 1 530 1 chr4B.!!$F1 529
10 TraesCS6A01G080400 chr3A 206842724 206843228 504 True 817.0 817 96.0470 1 499 1 chr3A.!!$R1 498
11 TraesCS6A01G080400 chr3A 206855022 206855526 504 True 811.0 811 95.8500 1 499 1 chr3A.!!$R2 498
12 TraesCS6A01G080400 chr4A 637569812 637570313 501 True 808.0 808 95.8330 1 499 1 chr4A.!!$R2 498

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
653 671 0.104855 CGGATGTCCATGGATCACGT 59.895 55.0 19.62 7.14 35.14 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2320 2397 0.104725 TTCCCCAAATTGGCCTGGTT 60.105 50.0 6.48 0.0 35.79 3.67 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
86 91 4.944317 GGTAGGCTTTCTGCTCTGTTTTAT 59.056 41.667 0.00 0.00 42.39 1.40
228 234 6.173427 AGCACATAAAAATGTTTCAGGGTT 57.827 33.333 0.00 0.00 31.37 4.11
499 507 8.296799 TCAGAATTTAAACATGATGCAAACAC 57.703 30.769 0.00 0.00 0.00 3.32
500 508 7.384660 TCAGAATTTAAACATGATGCAAACACC 59.615 33.333 0.00 0.00 0.00 4.16
503 511 3.389925 AAACATGATGCAAACACCAGG 57.610 42.857 0.00 0.00 0.00 4.45
504 512 0.604578 ACATGATGCAAACACCAGGC 59.395 50.000 0.00 0.00 0.00 4.85
506 514 0.892755 ATGATGCAAACACCAGGCAG 59.107 50.000 0.00 0.00 41.40 4.85
526 544 1.762957 GCACCAGAAGCTAGGGATGTA 59.237 52.381 5.33 0.00 0.00 2.29
531 549 3.452627 CCAGAAGCTAGGGATGTAACAGT 59.547 47.826 0.00 0.00 0.00 3.55
532 550 4.437239 CAGAAGCTAGGGATGTAACAGTG 58.563 47.826 0.00 0.00 0.00 3.66
533 551 2.990066 AGCTAGGGATGTAACAGTGC 57.010 50.000 0.00 0.00 0.00 4.40
534 552 1.137086 AGCTAGGGATGTAACAGTGCG 59.863 52.381 0.00 0.00 0.00 5.34
535 553 1.134788 GCTAGGGATGTAACAGTGCGT 60.135 52.381 0.00 0.00 0.00 5.24
536 554 2.677037 GCTAGGGATGTAACAGTGCGTT 60.677 50.000 0.00 0.00 41.91 4.84
537 555 1.808411 AGGGATGTAACAGTGCGTTG 58.192 50.000 0.00 0.00 38.63 4.10
538 556 0.168128 GGGATGTAACAGTGCGTTGC 59.832 55.000 0.00 0.00 38.63 4.17
556 574 1.359848 GCACGTGCATGCTTACTAGT 58.640 50.000 34.52 0.00 42.62 2.57
557 575 1.061131 GCACGTGCATGCTTACTAGTG 59.939 52.381 34.52 18.13 42.62 2.74
558 576 2.606108 CACGTGCATGCTTACTAGTGA 58.394 47.619 20.33 0.00 0.00 3.41
559 577 2.600420 CACGTGCATGCTTACTAGTGAG 59.400 50.000 20.33 10.24 0.00 3.51
560 578 2.231478 ACGTGCATGCTTACTAGTGAGT 59.769 45.455 20.33 0.00 39.92 3.41
561 579 3.442625 ACGTGCATGCTTACTAGTGAGTA 59.557 43.478 20.33 11.81 37.10 2.59
562 580 4.098044 ACGTGCATGCTTACTAGTGAGTAT 59.902 41.667 20.33 13.54 37.99 2.12
563 581 5.298527 ACGTGCATGCTTACTAGTGAGTATA 59.701 40.000 20.33 1.75 37.99 1.47
564 582 5.625721 CGTGCATGCTTACTAGTGAGTATAC 59.374 44.000 20.33 12.14 37.99 1.47
565 583 6.504398 GTGCATGCTTACTAGTGAGTATACA 58.496 40.000 20.33 14.31 37.99 2.29
566 584 6.978659 GTGCATGCTTACTAGTGAGTATACAA 59.021 38.462 20.33 5.54 37.99 2.41
567 585 7.491372 GTGCATGCTTACTAGTGAGTATACAAA 59.509 37.037 20.33 3.59 37.99 2.83
568 586 8.038351 TGCATGCTTACTAGTGAGTATACAAAA 58.962 33.333 20.33 1.05 37.99 2.44
569 587 9.046296 GCATGCTTACTAGTGAGTATACAAAAT 57.954 33.333 16.10 0.00 37.99 1.82
585 603 9.329913 GTATACAAAATAAAATGGATAGCAGCG 57.670 33.333 0.00 0.00 0.00 5.18
586 604 6.207691 ACAAAATAAAATGGATAGCAGCGT 57.792 33.333 0.00 0.00 0.00 5.07
587 605 6.035843 ACAAAATAAAATGGATAGCAGCGTG 58.964 36.000 0.00 0.00 0.00 5.34
588 606 5.835113 AAATAAAATGGATAGCAGCGTGT 57.165 34.783 0.00 0.00 0.00 4.49
589 607 5.424121 AATAAAATGGATAGCAGCGTGTC 57.576 39.130 0.00 0.00 0.00 3.67
590 608 1.668419 AAATGGATAGCAGCGTGTCC 58.332 50.000 6.77 6.77 0.00 4.02
591 609 0.530650 AATGGATAGCAGCGTGTCCG 60.531 55.000 8.60 0.00 33.39 4.79
592 610 1.391933 ATGGATAGCAGCGTGTCCGA 61.392 55.000 8.60 1.00 35.63 4.55
593 611 1.364171 GGATAGCAGCGTGTCCGAT 59.636 57.895 0.00 0.00 35.63 4.18
594 612 0.249489 GGATAGCAGCGTGTCCGATT 60.249 55.000 0.00 0.00 35.63 3.34
595 613 1.571919 GATAGCAGCGTGTCCGATTT 58.428 50.000 0.00 0.00 35.63 2.17
596 614 1.258982 GATAGCAGCGTGTCCGATTTG 59.741 52.381 0.00 0.00 35.63 2.32
597 615 0.245266 TAGCAGCGTGTCCGATTTGA 59.755 50.000 0.00 0.00 35.63 2.69
598 616 1.016130 AGCAGCGTGTCCGATTTGAG 61.016 55.000 0.00 0.00 35.63 3.02
599 617 1.014044 GCAGCGTGTCCGATTTGAGA 61.014 55.000 0.00 0.00 35.63 3.27
600 618 0.994995 CAGCGTGTCCGATTTGAGAG 59.005 55.000 0.00 0.00 35.63 3.20
601 619 0.888619 AGCGTGTCCGATTTGAGAGA 59.111 50.000 0.00 0.00 35.63 3.10
602 620 0.992802 GCGTGTCCGATTTGAGAGAC 59.007 55.000 0.00 0.00 35.63 3.36
603 621 1.668919 GCGTGTCCGATTTGAGAGACA 60.669 52.381 0.00 0.00 36.92 3.41
604 622 2.881074 CGTGTCCGATTTGAGAGACAT 58.119 47.619 0.00 0.00 41.01 3.06
605 623 2.600420 CGTGTCCGATTTGAGAGACATG 59.400 50.000 0.00 0.00 41.01 3.21
606 624 2.932614 GTGTCCGATTTGAGAGACATGG 59.067 50.000 0.00 0.00 41.01 3.66
607 625 2.567169 TGTCCGATTTGAGAGACATGGT 59.433 45.455 0.00 0.00 34.44 3.55
608 626 3.007940 TGTCCGATTTGAGAGACATGGTT 59.992 43.478 0.00 0.00 34.44 3.67
609 627 3.372206 GTCCGATTTGAGAGACATGGTTG 59.628 47.826 0.00 0.00 0.00 3.77
610 628 2.679837 CCGATTTGAGAGACATGGTTGG 59.320 50.000 0.00 0.00 0.00 3.77
611 629 3.599343 CGATTTGAGAGACATGGTTGGA 58.401 45.455 0.00 0.00 0.00 3.53
612 630 4.194640 CGATTTGAGAGACATGGTTGGAT 58.805 43.478 0.00 0.00 0.00 3.41
613 631 4.034858 CGATTTGAGAGACATGGTTGGATG 59.965 45.833 0.00 0.00 0.00 3.51
614 632 4.639078 TTTGAGAGACATGGTTGGATGA 57.361 40.909 0.00 0.00 0.00 2.92
615 633 3.616956 TGAGAGACATGGTTGGATGAC 57.383 47.619 0.00 0.00 0.00 3.06
616 634 2.237143 TGAGAGACATGGTTGGATGACC 59.763 50.000 0.00 0.00 40.23 4.02
641 659 4.664677 CGGGCCCGATCGGATGTC 62.665 72.222 41.82 20.53 42.83 3.06
642 660 4.315941 GGGCCCGATCGGATGTCC 62.316 72.222 35.42 25.48 37.50 4.02
643 661 3.546543 GGCCCGATCGGATGTCCA 61.547 66.667 35.42 0.00 37.50 4.02
644 662 2.743718 GCCCGATCGGATGTCCAT 59.256 61.111 35.42 0.00 37.50 3.41
645 663 1.669115 GCCCGATCGGATGTCCATG 60.669 63.158 35.42 16.51 37.50 3.66
646 664 1.004560 CCCGATCGGATGTCCATGG 60.005 63.158 35.42 11.30 37.50 3.66
647 665 1.471829 CCCGATCGGATGTCCATGGA 61.472 60.000 35.42 11.44 37.50 3.41
648 666 0.610174 CCGATCGGATGTCCATGGAT 59.390 55.000 30.62 1.68 37.50 3.41
649 667 1.404717 CCGATCGGATGTCCATGGATC 60.405 57.143 30.62 12.44 37.50 3.36
650 668 1.273327 CGATCGGATGTCCATGGATCA 59.727 52.381 19.62 17.54 34.58 2.92
651 669 2.693069 GATCGGATGTCCATGGATCAC 58.307 52.381 19.62 11.65 34.94 3.06
652 670 0.389025 TCGGATGTCCATGGATCACG 59.611 55.000 19.62 19.16 35.14 4.35
653 671 0.104855 CGGATGTCCATGGATCACGT 59.895 55.000 19.62 7.14 35.14 4.49
654 672 1.869754 CGGATGTCCATGGATCACGTC 60.870 57.143 19.62 15.88 35.14 4.34
655 673 1.414181 GGATGTCCATGGATCACGTCT 59.586 52.381 19.62 3.01 35.64 4.18
656 674 2.628178 GGATGTCCATGGATCACGTCTA 59.372 50.000 19.62 0.00 35.64 2.59
657 675 3.259374 GGATGTCCATGGATCACGTCTAT 59.741 47.826 19.62 1.94 35.64 1.98
658 676 4.262635 GGATGTCCATGGATCACGTCTATT 60.263 45.833 19.62 1.24 35.64 1.73
659 677 4.058721 TGTCCATGGATCACGTCTATTG 57.941 45.455 19.62 0.00 0.00 1.90
660 678 3.704061 TGTCCATGGATCACGTCTATTGA 59.296 43.478 19.62 0.00 0.00 2.57
661 679 4.344968 TGTCCATGGATCACGTCTATTGAT 59.655 41.667 19.62 0.00 36.37 2.57
662 680 4.687948 GTCCATGGATCACGTCTATTGATG 59.312 45.833 19.62 0.00 33.70 3.07
663 681 4.344968 TCCATGGATCACGTCTATTGATGT 59.655 41.667 11.44 0.00 42.66 3.06
664 682 5.059161 CCATGGATCACGTCTATTGATGTT 58.941 41.667 5.56 0.00 40.17 2.71
665 683 5.528690 CCATGGATCACGTCTATTGATGTTT 59.471 40.000 5.56 0.00 40.17 2.83
688 706 1.278637 GCGTCCGTTTGGTGAAGTG 59.721 57.895 0.00 0.00 36.30 3.16
714 732 5.450550 GCTGCTGTTACTGAAAAGGAAAAGT 60.451 40.000 0.00 0.00 0.00 2.66
783 802 0.665068 CGTGCACGTACAGGTAAGCA 60.665 55.000 30.50 0.00 34.11 3.91
847 871 1.717194 GGCACGATCTTTGGTTCGTA 58.283 50.000 0.00 0.00 43.31 3.43
871 895 2.399611 CGAGATCAAAACGCGCCC 59.600 61.111 5.73 0.00 0.00 6.13
954 982 2.665185 CGGGCCATAAGTAGCGGC 60.665 66.667 4.39 0.00 45.47 6.53
1181 1217 4.903010 CCGCCACGTATTCCCGGG 62.903 72.222 16.85 16.85 35.54 5.73
1318 1354 1.153823 GTGGTGGACGACGATGAGG 60.154 63.158 0.00 0.00 0.00 3.86
1766 1810 2.345760 GCCCCGACGTGTTCTAGGA 61.346 63.158 0.00 0.00 0.00 2.94
1772 1816 1.196354 CGACGTGTTCTAGGACTCGTT 59.804 52.381 27.03 14.28 45.98 3.85
1787 1831 2.719798 CTCGTTTGAGTGCTGTTTTGG 58.280 47.619 0.00 0.00 37.46 3.28
1788 1832 2.354510 CTCGTTTGAGTGCTGTTTTGGA 59.645 45.455 0.00 0.00 37.46 3.53
1795 1839 2.887152 GAGTGCTGTTTTGGATCCAAGT 59.113 45.455 25.69 7.32 37.24 3.16
1813 1865 9.099454 GATCCAAGTTCGATTTAGATACAACTT 57.901 33.333 0.00 0.00 35.04 2.66
1843 1897 9.405587 CTTGTAAAACGATTGTAAATCCATGTT 57.594 29.630 0.00 0.00 0.00 2.71
1847 1901 5.229921 ACGATTGTAAATCCATGTTTCGG 57.770 39.130 0.00 0.00 0.00 4.30
1876 1930 6.698008 TTCAATGCAATAGTTCGATTCCAT 57.302 33.333 0.00 0.00 0.00 3.41
1882 1936 4.621991 CAATAGTTCGATTCCATCCGAGT 58.378 43.478 0.00 0.00 36.11 4.18
1901 1955 5.427082 CGAGTAGATTTGATGTTTGATCGC 58.573 41.667 0.00 0.00 0.00 4.58
1909 1963 6.757897 TTTGATGTTTGATCGCTTTCCTAT 57.242 33.333 0.00 0.00 0.00 2.57
1912 1966 7.156876 TGATGTTTGATCGCTTTCCTATTTT 57.843 32.000 0.00 0.00 0.00 1.82
2006 2060 3.370527 GGAAAAGAGGTTGGATCGGATGA 60.371 47.826 0.00 0.00 0.00 2.92
2007 2061 4.455606 GAAAAGAGGTTGGATCGGATGAT 58.544 43.478 0.00 0.00 37.60 2.45
2029 2083 7.776107 TGATTGAACCTTTGTAAACACATGAA 58.224 30.769 0.00 0.00 0.00 2.57
2093 2149 7.994911 TGATTTAGGTTGATGCAATGACTCTAT 59.005 33.333 0.00 0.00 0.00 1.98
2094 2150 9.494271 GATTTAGGTTGATGCAATGACTCTATA 57.506 33.333 0.00 0.00 0.00 1.31
2095 2151 9.851686 ATTTAGGTTGATGCAATGACTCTATAA 57.148 29.630 0.00 0.00 0.00 0.98
2097 2153 6.893583 AGGTTGATGCAATGACTCTATAAGT 58.106 36.000 0.00 0.00 42.42 2.24
2225 2302 5.981315 CCTACCAGATAAAGCATGCAATTTG 59.019 40.000 21.98 14.42 0.00 2.32
2266 2343 3.634397 AGGATCCTTCGAGCATTCAAA 57.366 42.857 9.02 0.00 0.00 2.69
2267 2344 3.274288 AGGATCCTTCGAGCATTCAAAC 58.726 45.455 9.02 0.00 0.00 2.93
2268 2345 3.009723 GGATCCTTCGAGCATTCAAACA 58.990 45.455 3.84 0.00 0.00 2.83
2269 2346 3.440173 GGATCCTTCGAGCATTCAAACAA 59.560 43.478 3.84 0.00 0.00 2.83
2270 2347 4.437930 GGATCCTTCGAGCATTCAAACAAG 60.438 45.833 3.84 0.00 0.00 3.16
2271 2348 3.476552 TCCTTCGAGCATTCAAACAAGT 58.523 40.909 0.00 0.00 0.00 3.16
2272 2349 3.498397 TCCTTCGAGCATTCAAACAAGTC 59.502 43.478 0.00 0.00 0.00 3.01
2273 2350 3.365364 CCTTCGAGCATTCAAACAAGTCC 60.365 47.826 0.00 0.00 0.00 3.85
2274 2351 3.126001 TCGAGCATTCAAACAAGTCCT 57.874 42.857 0.00 0.00 0.00 3.85
2275 2352 4.265904 TCGAGCATTCAAACAAGTCCTA 57.734 40.909 0.00 0.00 0.00 2.94
2276 2353 4.637276 TCGAGCATTCAAACAAGTCCTAA 58.363 39.130 0.00 0.00 0.00 2.69
2277 2354 5.245531 TCGAGCATTCAAACAAGTCCTAAT 58.754 37.500 0.00 0.00 0.00 1.73
2278 2355 6.403049 TCGAGCATTCAAACAAGTCCTAATA 58.597 36.000 0.00 0.00 0.00 0.98
2279 2356 6.876789 TCGAGCATTCAAACAAGTCCTAATAA 59.123 34.615 0.00 0.00 0.00 1.40
2280 2357 7.552687 TCGAGCATTCAAACAAGTCCTAATAAT 59.447 33.333 0.00 0.00 0.00 1.28
2281 2358 7.852945 CGAGCATTCAAACAAGTCCTAATAATC 59.147 37.037 0.00 0.00 0.00 1.75
2282 2359 8.000780 AGCATTCAAACAAGTCCTAATAATCC 57.999 34.615 0.00 0.00 0.00 3.01
2283 2360 7.068716 AGCATTCAAACAAGTCCTAATAATCCC 59.931 37.037 0.00 0.00 0.00 3.85
2284 2361 6.995511 TTCAAACAAGTCCTAATAATCCCG 57.004 37.500 0.00 0.00 0.00 5.14
2285 2362 4.879545 TCAAACAAGTCCTAATAATCCCGC 59.120 41.667 0.00 0.00 0.00 6.13
2286 2363 4.772886 AACAAGTCCTAATAATCCCGCT 57.227 40.909 0.00 0.00 0.00 5.52
2287 2364 5.881923 AACAAGTCCTAATAATCCCGCTA 57.118 39.130 0.00 0.00 0.00 4.26
2288 2365 5.881923 ACAAGTCCTAATAATCCCGCTAA 57.118 39.130 0.00 0.00 0.00 3.09
2289 2366 5.855045 ACAAGTCCTAATAATCCCGCTAAG 58.145 41.667 0.00 0.00 0.00 2.18
2290 2367 5.365895 ACAAGTCCTAATAATCCCGCTAAGT 59.634 40.000 0.00 0.00 0.00 2.24
2291 2368 5.470047 AGTCCTAATAATCCCGCTAAGTG 57.530 43.478 0.00 0.00 0.00 3.16
2292 2369 4.283722 AGTCCTAATAATCCCGCTAAGTGG 59.716 45.833 0.00 0.00 0.00 4.00
2293 2370 4.040095 GTCCTAATAATCCCGCTAAGTGGT 59.960 45.833 0.00 0.00 0.00 4.16
2294 2371 4.039973 TCCTAATAATCCCGCTAAGTGGTG 59.960 45.833 0.00 0.00 0.00 4.17
2295 2372 4.039973 CCTAATAATCCCGCTAAGTGGTGA 59.960 45.833 0.00 0.00 0.00 4.02
2296 2373 4.706842 AATAATCCCGCTAAGTGGTGAT 57.293 40.909 0.00 0.00 0.00 3.06
2297 2374 4.706842 ATAATCCCGCTAAGTGGTGATT 57.293 40.909 0.00 0.00 37.14 2.57
2298 2375 2.622064 ATCCCGCTAAGTGGTGATTC 57.378 50.000 0.00 0.00 0.00 2.52
2299 2376 1.271856 TCCCGCTAAGTGGTGATTCA 58.728 50.000 0.00 0.00 0.00 2.57
2300 2377 1.626321 TCCCGCTAAGTGGTGATTCAA 59.374 47.619 0.00 0.00 0.00 2.69
2301 2378 1.737793 CCCGCTAAGTGGTGATTCAAC 59.262 52.381 0.00 0.00 0.00 3.18
2302 2379 2.422597 CCGCTAAGTGGTGATTCAACA 58.577 47.619 0.00 0.00 0.00 3.33
2303 2380 3.009723 CCGCTAAGTGGTGATTCAACAT 58.990 45.455 7.82 0.00 32.11 2.71
2304 2381 3.181507 CCGCTAAGTGGTGATTCAACATG 60.182 47.826 7.82 0.00 32.11 3.21
2305 2382 3.181507 CGCTAAGTGGTGATTCAACATGG 60.182 47.826 7.82 0.00 32.11 3.66
2306 2383 4.009675 GCTAAGTGGTGATTCAACATGGA 58.990 43.478 7.82 0.00 32.11 3.41
2307 2384 4.641989 GCTAAGTGGTGATTCAACATGGAT 59.358 41.667 7.82 0.00 32.11 3.41
2308 2385 5.126061 GCTAAGTGGTGATTCAACATGGATT 59.874 40.000 7.82 4.06 32.11 3.01
2309 2386 5.649782 AAGTGGTGATTCAACATGGATTC 57.350 39.130 7.82 0.00 32.11 2.52
2310 2387 4.927049 AGTGGTGATTCAACATGGATTCT 58.073 39.130 7.82 0.00 32.11 2.40
2311 2388 6.065976 AGTGGTGATTCAACATGGATTCTA 57.934 37.500 7.82 0.00 32.11 2.10
2312 2389 5.882557 AGTGGTGATTCAACATGGATTCTAC 59.117 40.000 7.82 0.00 32.11 2.59
2313 2390 5.647658 GTGGTGATTCAACATGGATTCTACA 59.352 40.000 7.82 0.00 32.11 2.74
2314 2391 6.319658 GTGGTGATTCAACATGGATTCTACAT 59.680 38.462 7.82 0.00 32.11 2.29
2315 2392 6.543465 TGGTGATTCAACATGGATTCTACATC 59.457 38.462 0.00 0.00 0.00 3.06
2316 2393 6.769822 GGTGATTCAACATGGATTCTACATCT 59.230 38.462 0.00 0.00 0.00 2.90
2317 2394 7.284034 GGTGATTCAACATGGATTCTACATCTT 59.716 37.037 0.00 0.00 0.00 2.40
2318 2395 8.127327 GTGATTCAACATGGATTCTACATCTTG 58.873 37.037 0.00 0.00 0.00 3.02
2319 2396 7.283807 TGATTCAACATGGATTCTACATCTTGG 59.716 37.037 0.00 0.00 29.01 3.61
2320 2397 6.312141 TCAACATGGATTCTACATCTTGGA 57.688 37.500 0.00 0.00 29.01 3.53
2321 2398 6.720309 TCAACATGGATTCTACATCTTGGAA 58.280 36.000 0.00 0.00 29.01 3.53
2322 2399 6.599244 TCAACATGGATTCTACATCTTGGAAC 59.401 38.462 0.00 0.00 29.01 3.62
2323 2400 5.440610 ACATGGATTCTACATCTTGGAACC 58.559 41.667 0.00 0.00 0.00 3.62
2324 2401 5.044919 ACATGGATTCTACATCTTGGAACCA 60.045 40.000 0.00 0.00 0.00 3.67
2325 2402 5.102953 TGGATTCTACATCTTGGAACCAG 57.897 43.478 0.00 0.00 0.00 4.00
2326 2403 4.080356 TGGATTCTACATCTTGGAACCAGG 60.080 45.833 0.00 0.00 0.00 4.45
2327 2404 3.350219 TTCTACATCTTGGAACCAGGC 57.650 47.619 0.00 0.00 0.00 4.85
2328 2405 1.559682 TCTACATCTTGGAACCAGGCC 59.440 52.381 0.00 0.00 0.00 5.19
2329 2406 1.281867 CTACATCTTGGAACCAGGCCA 59.718 52.381 5.01 0.00 0.00 5.36
2330 2407 0.482446 ACATCTTGGAACCAGGCCAA 59.518 50.000 5.01 0.00 42.81 4.52
2331 2408 1.077663 ACATCTTGGAACCAGGCCAAT 59.922 47.619 5.01 0.00 43.90 3.16
2332 2409 2.181975 CATCTTGGAACCAGGCCAATT 58.818 47.619 5.01 0.00 43.90 2.32
2333 2410 2.397044 TCTTGGAACCAGGCCAATTT 57.603 45.000 5.01 0.00 43.90 1.82
2334 2411 1.969923 TCTTGGAACCAGGCCAATTTG 59.030 47.619 5.01 0.00 43.90 2.32
2335 2412 1.002315 CTTGGAACCAGGCCAATTTGG 59.998 52.381 11.27 11.27 43.90 3.28
2336 2413 0.835543 TGGAACCAGGCCAATTTGGG 60.836 55.000 17.03 2.95 38.19 4.12
2337 2414 1.552799 GGAACCAGGCCAATTTGGGG 61.553 60.000 17.03 11.83 38.19 4.96
2356 2433 3.877508 GGGGAATTCGTGTTATCTTCAGG 59.122 47.826 0.00 0.00 0.00 3.86
2393 2477 4.536090 TGGATAAGACAACTTGATGGGTCT 59.464 41.667 0.00 0.00 42.08 3.85
2470 2555 4.444536 GGCATGAATTGGTTGCAATATGT 58.555 39.130 0.59 0.00 38.12 2.29
2483 2568 8.916062 TGGTTGCAATATGTTCTCATGATATTT 58.084 29.630 0.59 0.00 35.70 1.40
2609 2694 4.651778 TGTTGAGGTGGATCTTTTCGATT 58.348 39.130 0.00 0.00 30.84 3.34
2650 2735 2.913777 CATGTGTGCATGTTGAGAGG 57.086 50.000 0.00 0.00 45.48 3.69
2668 2753 4.561752 AGAGGAATATGTTAGTGAGGGCT 58.438 43.478 0.00 0.00 0.00 5.19
2687 2777 7.038941 TGAGGGCTAGCTATTTAGAAAGATACC 60.039 40.741 15.72 0.89 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
385 392 8.129840 TGGAAAATGCATTCAATGTTTTCAAAG 58.870 29.630 19.94 0.00 37.16 2.77
495 503 2.203394 CTGGTGCTGCCTGGTGTT 60.203 61.111 0.00 0.00 38.35 3.32
499 507 2.189191 TAGCTTCTGGTGCTGCCTGG 62.189 60.000 0.00 0.00 41.32 4.45
500 508 0.743701 CTAGCTTCTGGTGCTGCCTG 60.744 60.000 0.00 0.00 41.32 4.85
503 511 1.451028 CCCTAGCTTCTGGTGCTGC 60.451 63.158 0.00 0.00 41.32 5.25
504 512 0.835941 ATCCCTAGCTTCTGGTGCTG 59.164 55.000 0.00 0.00 41.32 4.41
506 514 0.543749 ACATCCCTAGCTTCTGGTGC 59.456 55.000 0.00 0.00 0.00 5.01
537 555 1.061131 CACTAGTAAGCATGCACGTGC 59.939 52.381 33.11 33.11 45.38 5.34
538 556 2.600420 CTCACTAGTAAGCATGCACGTG 59.400 50.000 21.98 12.28 0.00 4.49
539 557 2.231478 ACTCACTAGTAAGCATGCACGT 59.769 45.455 21.98 7.14 32.84 4.49
540 558 2.881074 ACTCACTAGTAAGCATGCACG 58.119 47.619 21.98 3.52 32.84 5.34
541 559 6.504398 TGTATACTCACTAGTAAGCATGCAC 58.496 40.000 21.98 10.48 41.49 4.57
542 560 6.709018 TGTATACTCACTAGTAAGCATGCA 57.291 37.500 21.98 0.00 41.49 3.96
543 561 8.420374 TTTTGTATACTCACTAGTAAGCATGC 57.580 34.615 10.51 10.51 41.49 4.06
559 577 9.329913 CGCTGCTATCCATTTTATTTTGTATAC 57.670 33.333 0.00 0.00 0.00 1.47
560 578 9.062524 ACGCTGCTATCCATTTTATTTTGTATA 57.937 29.630 0.00 0.00 0.00 1.47
561 579 7.862372 CACGCTGCTATCCATTTTATTTTGTAT 59.138 33.333 0.00 0.00 0.00 2.29
562 580 7.148154 ACACGCTGCTATCCATTTTATTTTGTA 60.148 33.333 0.00 0.00 0.00 2.41
563 581 6.035843 CACGCTGCTATCCATTTTATTTTGT 58.964 36.000 0.00 0.00 0.00 2.83
564 582 6.035843 ACACGCTGCTATCCATTTTATTTTG 58.964 36.000 0.00 0.00 0.00 2.44
565 583 6.207691 ACACGCTGCTATCCATTTTATTTT 57.792 33.333 0.00 0.00 0.00 1.82
566 584 5.221048 GGACACGCTGCTATCCATTTTATTT 60.221 40.000 8.34 0.00 0.00 1.40
567 585 4.275936 GGACACGCTGCTATCCATTTTATT 59.724 41.667 8.34 0.00 0.00 1.40
568 586 3.815401 GGACACGCTGCTATCCATTTTAT 59.185 43.478 8.34 0.00 0.00 1.40
569 587 3.202906 GGACACGCTGCTATCCATTTTA 58.797 45.455 8.34 0.00 0.00 1.52
570 588 2.017049 GGACACGCTGCTATCCATTTT 58.983 47.619 8.34 0.00 0.00 1.82
571 589 1.668419 GGACACGCTGCTATCCATTT 58.332 50.000 8.34 0.00 0.00 2.32
572 590 0.530650 CGGACACGCTGCTATCCATT 60.531 55.000 12.33 0.00 0.00 3.16
573 591 1.068083 CGGACACGCTGCTATCCAT 59.932 57.895 12.33 0.00 0.00 3.41
574 592 1.391933 ATCGGACACGCTGCTATCCA 61.392 55.000 12.33 2.93 40.69 3.41
575 593 0.249489 AATCGGACACGCTGCTATCC 60.249 55.000 0.00 0.84 40.69 2.59
576 594 1.258982 CAAATCGGACACGCTGCTATC 59.741 52.381 0.00 0.00 40.69 2.08
577 595 1.134818 TCAAATCGGACACGCTGCTAT 60.135 47.619 0.00 0.00 40.69 2.97
578 596 0.245266 TCAAATCGGACACGCTGCTA 59.755 50.000 0.00 0.00 40.69 3.49
579 597 1.005037 TCAAATCGGACACGCTGCT 60.005 52.632 0.00 0.00 40.69 4.24
580 598 1.014044 TCTCAAATCGGACACGCTGC 61.014 55.000 0.00 0.00 40.69 5.25
581 599 0.994995 CTCTCAAATCGGACACGCTG 59.005 55.000 0.00 0.00 40.69 5.18
582 600 0.888619 TCTCTCAAATCGGACACGCT 59.111 50.000 0.00 0.00 40.69 5.07
583 601 0.992802 GTCTCTCAAATCGGACACGC 59.007 55.000 0.00 0.00 40.69 5.34
584 602 2.347697 TGTCTCTCAAATCGGACACG 57.652 50.000 0.00 0.00 42.74 4.49
585 603 2.932614 CCATGTCTCTCAAATCGGACAC 59.067 50.000 0.00 0.00 40.71 3.67
586 604 2.567169 ACCATGTCTCTCAAATCGGACA 59.433 45.455 0.00 0.00 41.84 4.02
587 605 3.252974 ACCATGTCTCTCAAATCGGAC 57.747 47.619 0.00 0.00 0.00 4.79
588 606 3.599343 CAACCATGTCTCTCAAATCGGA 58.401 45.455 0.00 0.00 0.00 4.55
589 607 2.679837 CCAACCATGTCTCTCAAATCGG 59.320 50.000 0.00 0.00 0.00 4.18
590 608 3.599343 TCCAACCATGTCTCTCAAATCG 58.401 45.455 0.00 0.00 0.00 3.34
591 609 5.065731 GTCATCCAACCATGTCTCTCAAATC 59.934 44.000 0.00 0.00 0.00 2.17
592 610 4.946157 GTCATCCAACCATGTCTCTCAAAT 59.054 41.667 0.00 0.00 0.00 2.32
593 611 4.326826 GTCATCCAACCATGTCTCTCAAA 58.673 43.478 0.00 0.00 0.00 2.69
594 612 3.307691 GGTCATCCAACCATGTCTCTCAA 60.308 47.826 0.00 0.00 39.27 3.02
595 613 2.237143 GGTCATCCAACCATGTCTCTCA 59.763 50.000 0.00 0.00 39.27 3.27
596 614 2.237143 TGGTCATCCAACCATGTCTCTC 59.763 50.000 0.00 0.00 44.40 3.20
597 615 2.269023 TGGTCATCCAACCATGTCTCT 58.731 47.619 0.00 0.00 44.40 3.10
598 616 2.787473 TGGTCATCCAACCATGTCTC 57.213 50.000 0.00 0.00 44.40 3.36
605 623 2.438434 CGGCCTGGTCATCCAACC 60.438 66.667 0.00 0.00 43.81 3.77
606 624 2.438434 CCGGCCTGGTCATCCAAC 60.438 66.667 0.00 0.00 43.81 3.77
607 625 4.424711 GCCGGCCTGGTCATCCAA 62.425 66.667 18.11 0.00 43.81 3.53
624 642 4.664677 GACATCCGATCGGGCCCG 62.665 72.222 39.13 39.13 41.35 6.13
625 643 4.315941 GGACATCCGATCGGGCCC 62.316 72.222 32.79 22.78 34.94 5.80
626 644 2.883828 ATGGACATCCGATCGGGCC 61.884 63.158 32.79 26.09 39.43 5.80
627 645 1.669115 CATGGACATCCGATCGGGC 60.669 63.158 32.79 19.07 39.43 6.13
628 646 1.004560 CCATGGACATCCGATCGGG 60.005 63.158 32.79 20.49 39.43 5.14
629 647 0.610174 ATCCATGGACATCCGATCGG 59.390 55.000 28.62 28.62 39.43 4.18
630 648 1.273327 TGATCCATGGACATCCGATCG 59.727 52.381 18.99 8.51 39.43 3.69
631 649 2.693069 GTGATCCATGGACATCCGATC 58.307 52.381 18.99 9.54 39.43 3.69
632 650 1.001293 CGTGATCCATGGACATCCGAT 59.999 52.381 18.99 0.00 39.43 4.18
633 651 0.389025 CGTGATCCATGGACATCCGA 59.611 55.000 18.99 0.00 39.43 4.55
634 652 0.104855 ACGTGATCCATGGACATCCG 59.895 55.000 18.99 18.46 39.43 4.18
635 653 1.414181 AGACGTGATCCATGGACATCC 59.586 52.381 18.99 7.44 0.00 3.51
636 654 2.898729 AGACGTGATCCATGGACATC 57.101 50.000 18.99 12.75 0.00 3.06
637 655 4.344968 TCAATAGACGTGATCCATGGACAT 59.655 41.667 18.99 0.80 0.00 3.06
638 656 3.704061 TCAATAGACGTGATCCATGGACA 59.296 43.478 18.99 14.43 0.00 4.02
639 657 4.322080 TCAATAGACGTGATCCATGGAC 57.678 45.455 18.99 11.83 0.00 4.02
640 658 4.344968 ACATCAATAGACGTGATCCATGGA 59.655 41.667 18.88 18.88 33.37 3.41
641 659 4.635223 ACATCAATAGACGTGATCCATGG 58.365 43.478 4.97 4.97 33.37 3.66
642 660 6.609237 AAACATCAATAGACGTGATCCATG 57.391 37.500 0.00 0.00 33.37 3.66
643 661 6.823182 TCAAAACATCAATAGACGTGATCCAT 59.177 34.615 0.00 0.00 33.37 3.41
644 662 6.092122 GTCAAAACATCAATAGACGTGATCCA 59.908 38.462 0.00 0.00 33.37 3.41
645 663 6.478588 GTCAAAACATCAATAGACGTGATCC 58.521 40.000 0.00 0.00 33.37 3.36
646 664 6.178507 CGTCAAAACATCAATAGACGTGATC 58.821 40.000 0.00 0.00 42.55 2.92
647 665 6.094739 CGTCAAAACATCAATAGACGTGAT 57.905 37.500 0.00 0.00 42.55 3.06
648 666 5.509605 CGTCAAAACATCAATAGACGTGA 57.490 39.130 0.00 0.00 42.55 4.35
652 670 4.322101 ACGCGTCAAAACATCAATAGAC 57.678 40.909 5.58 0.00 0.00 2.59
653 671 3.369756 GGACGCGTCAAAACATCAATAGA 59.630 43.478 37.26 0.00 0.00 1.98
654 672 3.670203 GGACGCGTCAAAACATCAATAG 58.330 45.455 37.26 0.00 0.00 1.73
655 673 2.092995 CGGACGCGTCAAAACATCAATA 59.907 45.455 37.26 0.00 0.00 1.90
656 674 1.136085 CGGACGCGTCAAAACATCAAT 60.136 47.619 37.26 0.00 0.00 2.57
657 675 0.233590 CGGACGCGTCAAAACATCAA 59.766 50.000 37.26 0.00 0.00 2.57
658 676 0.876777 ACGGACGCGTCAAAACATCA 60.877 50.000 37.26 0.00 0.00 3.07
659 677 0.233848 AACGGACGCGTCAAAACATC 59.766 50.000 37.26 18.88 0.00 3.06
660 678 0.658897 AAACGGACGCGTCAAAACAT 59.341 45.000 37.26 17.09 0.00 2.71
661 679 0.247735 CAAACGGACGCGTCAAAACA 60.248 50.000 37.26 0.00 0.00 2.83
662 680 0.926628 CCAAACGGACGCGTCAAAAC 60.927 55.000 37.26 20.66 0.00 2.43
663 681 1.352404 CCAAACGGACGCGTCAAAA 59.648 52.632 37.26 0.00 0.00 2.44
664 682 1.814586 ACCAAACGGACGCGTCAAA 60.815 52.632 37.26 0.00 0.00 2.69
665 683 2.202905 ACCAAACGGACGCGTCAA 60.203 55.556 37.26 0.00 0.00 3.18
682 700 0.764890 AGTAACAGCAGCCCACTTCA 59.235 50.000 0.00 0.00 0.00 3.02
683 701 1.160137 CAGTAACAGCAGCCCACTTC 58.840 55.000 0.00 0.00 0.00 3.01
688 706 1.541588 CCTTTTCAGTAACAGCAGCCC 59.458 52.381 0.00 0.00 0.00 5.19
741 759 9.869844 CACGTGAATATCTAATCCAAGATTTTC 57.130 33.333 10.90 8.97 40.99 2.29
774 793 5.119694 GGAAAGAACTAGGATGCTTACCTG 58.880 45.833 0.00 0.00 38.31 4.00
783 802 1.906574 TGCCGTGGAAAGAACTAGGAT 59.093 47.619 0.00 0.00 0.00 3.24
814 838 0.871722 CGTGCCGTGATCCTCAAAAA 59.128 50.000 0.00 0.00 0.00 1.94
815 839 0.034198 TCGTGCCGTGATCCTCAAAA 59.966 50.000 0.00 0.00 0.00 2.44
816 840 0.249120 ATCGTGCCGTGATCCTCAAA 59.751 50.000 0.00 0.00 0.00 2.69
817 841 0.179111 GATCGTGCCGTGATCCTCAA 60.179 55.000 0.00 0.00 36.97 3.02
818 842 1.037579 AGATCGTGCCGTGATCCTCA 61.038 55.000 6.37 0.00 42.57 3.86
819 843 0.103208 AAGATCGTGCCGTGATCCTC 59.897 55.000 6.37 0.00 42.57 3.71
820 844 0.537188 AAAGATCGTGCCGTGATCCT 59.463 50.000 6.37 0.00 42.57 3.24
821 845 0.652592 CAAAGATCGTGCCGTGATCC 59.347 55.000 6.37 0.00 42.57 3.36
822 846 0.652592 CCAAAGATCGTGCCGTGATC 59.347 55.000 2.62 2.62 42.04 2.92
823 847 0.036388 ACCAAAGATCGTGCCGTGAT 60.036 50.000 0.00 0.00 0.00 3.06
824 848 0.250124 AACCAAAGATCGTGCCGTGA 60.250 50.000 0.00 0.00 0.00 4.35
847 871 1.415374 CGTTTTGATCTCGGACACGT 58.585 50.000 0.00 0.00 41.85 4.49
871 895 0.160182 GCGTCAAGTTTACGTCGGTG 59.840 55.000 10.98 0.00 42.26 4.94
1766 1810 2.097466 CCAAAACAGCACTCAAACGAGT 59.903 45.455 0.00 0.00 44.80 4.18
1772 1816 2.942804 TGGATCCAAAACAGCACTCAA 58.057 42.857 13.46 0.00 0.00 3.02
1787 1831 8.649973 AGTTGTATCTAAATCGAACTTGGATC 57.350 34.615 11.23 6.28 0.00 3.36
1788 1832 9.449719 AAAGTTGTATCTAAATCGAACTTGGAT 57.550 29.630 12.17 12.17 34.66 3.41
1795 1839 9.706691 ACAAGAGAAAGTTGTATCTAAATCGAA 57.293 29.630 0.00 0.00 36.35 3.71
1813 1865 9.058174 TGGATTTACAATCGTTTTACAAGAGAA 57.942 29.630 0.00 0.00 0.00 2.87
1843 1897 4.704540 ACTATTGCATTGAATTCCACCGAA 59.295 37.500 2.27 0.00 0.00 4.30
1847 1901 5.879237 TCGAACTATTGCATTGAATTCCAC 58.121 37.500 2.27 0.00 0.00 4.02
1876 1930 5.748630 CGATCAAACATCAAATCTACTCGGA 59.251 40.000 0.00 0.00 0.00 4.55
1882 1936 6.599244 AGGAAAGCGATCAAACATCAAATCTA 59.401 34.615 0.00 0.00 0.00 1.98
1912 1966 6.128391 CGTTCAAATCCATCTTAGAACCGAAA 60.128 38.462 0.00 0.00 33.65 3.46
2006 2060 9.044150 CAATTCATGTGTTTACAAAGGTTCAAT 57.956 29.630 0.00 0.00 40.84 2.57
2007 2061 8.037758 ACAATTCATGTGTTTACAAAGGTTCAA 58.962 29.630 0.00 0.00 41.93 2.69
2029 2083 8.908786 TCTCACAACTCTTTTATTCTCACAAT 57.091 30.769 0.00 0.00 0.00 2.71
2093 2149 4.431416 TGGTTTTCTGCCAGAAGACTTA 57.569 40.909 22.73 12.60 38.80 2.24
2094 2150 3.297134 TGGTTTTCTGCCAGAAGACTT 57.703 42.857 22.73 0.00 38.80 3.01
2095 2151 3.515602 ATGGTTTTCTGCCAGAAGACT 57.484 42.857 22.73 6.16 38.80 3.24
2097 2153 5.185635 CCAAATATGGTTTTCTGCCAGAAGA 59.814 40.000 7.29 0.00 42.18 2.87
2098 2154 5.413499 CCAAATATGGTTTTCTGCCAGAAG 58.587 41.667 7.29 0.00 42.18 2.85
2225 2302 4.457257 CCTTTCCACAAGAAGGTTGAGATC 59.543 45.833 0.00 0.00 35.40 2.75
2256 2333 8.131731 GGATTATTAGGACTTGTTTGAATGCTC 58.868 37.037 0.00 0.00 0.00 4.26
2266 2343 5.365895 ACTTAGCGGGATTATTAGGACTTGT 59.634 40.000 0.00 0.00 0.00 3.16
2267 2344 5.696724 CACTTAGCGGGATTATTAGGACTTG 59.303 44.000 0.00 0.00 0.00 3.16
2268 2345 5.221661 CCACTTAGCGGGATTATTAGGACTT 60.222 44.000 0.00 0.00 0.00 3.01
2269 2346 4.283722 CCACTTAGCGGGATTATTAGGACT 59.716 45.833 0.00 0.00 0.00 3.85
2270 2347 4.040095 ACCACTTAGCGGGATTATTAGGAC 59.960 45.833 0.00 0.00 0.00 3.85
2271 2348 4.039973 CACCACTTAGCGGGATTATTAGGA 59.960 45.833 0.00 0.00 0.00 2.94
2272 2349 4.039973 TCACCACTTAGCGGGATTATTAGG 59.960 45.833 0.00 0.00 0.00 2.69
2273 2350 5.209818 TCACCACTTAGCGGGATTATTAG 57.790 43.478 0.00 0.00 0.00 1.73
2274 2351 5.818678 ATCACCACTTAGCGGGATTATTA 57.181 39.130 0.00 0.00 0.00 0.98
2275 2352 4.706842 ATCACCACTTAGCGGGATTATT 57.293 40.909 0.00 0.00 0.00 1.40
2276 2353 4.102524 TGAATCACCACTTAGCGGGATTAT 59.897 41.667 0.00 0.00 0.00 1.28
2277 2354 3.452990 TGAATCACCACTTAGCGGGATTA 59.547 43.478 0.00 0.00 0.00 1.75
2278 2355 2.238646 TGAATCACCACTTAGCGGGATT 59.761 45.455 0.00 0.00 0.00 3.01
2279 2356 1.837439 TGAATCACCACTTAGCGGGAT 59.163 47.619 0.00 0.00 0.00 3.85
2280 2357 1.271856 TGAATCACCACTTAGCGGGA 58.728 50.000 0.00 0.00 0.00 5.14
2281 2358 1.737793 GTTGAATCACCACTTAGCGGG 59.262 52.381 0.00 0.00 0.00 6.13
2282 2359 2.422597 TGTTGAATCACCACTTAGCGG 58.577 47.619 0.00 0.00 0.00 5.52
2283 2360 3.181507 CCATGTTGAATCACCACTTAGCG 60.182 47.826 0.00 0.00 0.00 4.26
2284 2361 4.009675 TCCATGTTGAATCACCACTTAGC 58.990 43.478 0.00 0.00 0.00 3.09
2285 2362 6.600822 AGAATCCATGTTGAATCACCACTTAG 59.399 38.462 0.00 0.00 0.00 2.18
2286 2363 6.484288 AGAATCCATGTTGAATCACCACTTA 58.516 36.000 0.00 0.00 0.00 2.24
2287 2364 5.327732 AGAATCCATGTTGAATCACCACTT 58.672 37.500 0.00 0.00 0.00 3.16
2288 2365 4.927049 AGAATCCATGTTGAATCACCACT 58.073 39.130 0.00 0.00 0.00 4.00
2289 2366 5.647658 TGTAGAATCCATGTTGAATCACCAC 59.352 40.000 0.00 0.00 0.00 4.16
2290 2367 5.814481 TGTAGAATCCATGTTGAATCACCA 58.186 37.500 0.00 0.00 0.00 4.17
2291 2368 6.769822 AGATGTAGAATCCATGTTGAATCACC 59.230 38.462 0.00 0.00 0.00 4.02
2292 2369 7.798596 AGATGTAGAATCCATGTTGAATCAC 57.201 36.000 0.00 0.00 0.00 3.06
2293 2370 7.283807 CCAAGATGTAGAATCCATGTTGAATCA 59.716 37.037 10.68 0.00 42.85 2.57
2294 2371 7.500227 TCCAAGATGTAGAATCCATGTTGAATC 59.500 37.037 10.68 0.00 42.85 2.52
2295 2372 7.348815 TCCAAGATGTAGAATCCATGTTGAAT 58.651 34.615 10.68 0.00 42.85 2.57
2296 2373 6.720309 TCCAAGATGTAGAATCCATGTTGAA 58.280 36.000 10.68 0.00 42.85 2.69
2297 2374 6.312141 TCCAAGATGTAGAATCCATGTTGA 57.688 37.500 10.68 0.00 42.85 3.18
2298 2375 6.183360 GGTTCCAAGATGTAGAATCCATGTTG 60.183 42.308 0.00 0.00 41.02 3.33
2299 2376 5.888161 GGTTCCAAGATGTAGAATCCATGTT 59.112 40.000 0.00 0.00 0.00 2.71
2300 2377 5.044919 TGGTTCCAAGATGTAGAATCCATGT 60.045 40.000 0.00 0.00 0.00 3.21
2301 2378 5.439721 TGGTTCCAAGATGTAGAATCCATG 58.560 41.667 0.00 0.00 0.00 3.66
2302 2379 5.398353 CCTGGTTCCAAGATGTAGAATCCAT 60.398 44.000 0.00 0.00 0.00 3.41
2303 2380 4.080356 CCTGGTTCCAAGATGTAGAATCCA 60.080 45.833 0.00 0.00 0.00 3.41
2304 2381 4.455606 CCTGGTTCCAAGATGTAGAATCC 58.544 47.826 0.00 0.00 0.00 3.01
2305 2382 3.879892 GCCTGGTTCCAAGATGTAGAATC 59.120 47.826 0.00 0.00 0.00 2.52
2306 2383 3.372025 GGCCTGGTTCCAAGATGTAGAAT 60.372 47.826 0.00 0.00 0.00 2.40
2307 2384 2.026262 GGCCTGGTTCCAAGATGTAGAA 60.026 50.000 0.00 0.00 0.00 2.10
2308 2385 1.559682 GGCCTGGTTCCAAGATGTAGA 59.440 52.381 0.00 0.00 0.00 2.59
2309 2386 1.281867 TGGCCTGGTTCCAAGATGTAG 59.718 52.381 3.32 0.00 0.00 2.74
2310 2387 1.367346 TGGCCTGGTTCCAAGATGTA 58.633 50.000 3.32 0.00 0.00 2.29
2311 2388 0.482446 TTGGCCTGGTTCCAAGATGT 59.518 50.000 3.32 0.00 38.57 3.06
2312 2389 1.856629 ATTGGCCTGGTTCCAAGATG 58.143 50.000 3.32 0.00 45.69 2.90
2313 2390 2.568509 CAAATTGGCCTGGTTCCAAGAT 59.431 45.455 3.32 1.54 45.69 2.40
2314 2391 1.969923 CAAATTGGCCTGGTTCCAAGA 59.030 47.619 3.32 0.00 45.69 3.02
2315 2392 1.002315 CCAAATTGGCCTGGTTCCAAG 59.998 52.381 3.32 0.00 45.69 3.61
2316 2393 1.055040 CCAAATTGGCCTGGTTCCAA 58.945 50.000 3.32 8.04 46.44 3.53
2317 2394 0.835543 CCCAAATTGGCCTGGTTCCA 60.836 55.000 6.48 0.00 35.79 3.53
2318 2395 1.552799 CCCCAAATTGGCCTGGTTCC 61.553 60.000 6.48 0.00 35.79 3.62
2319 2396 0.544120 TCCCCAAATTGGCCTGGTTC 60.544 55.000 6.48 0.00 35.79 3.62
2320 2397 0.104725 TTCCCCAAATTGGCCTGGTT 60.105 50.000 6.48 0.00 35.79 3.67
2321 2398 0.118952 ATTCCCCAAATTGGCCTGGT 59.881 50.000 6.48 0.00 35.79 4.00
2322 2399 1.210234 GAATTCCCCAAATTGGCCTGG 59.790 52.381 6.48 2.34 37.70 4.45
2323 2400 1.134729 CGAATTCCCCAAATTGGCCTG 60.135 52.381 6.48 0.00 37.70 4.85
2324 2401 1.194218 CGAATTCCCCAAATTGGCCT 58.806 50.000 6.48 0.00 37.70 5.19
2325 2402 0.901827 ACGAATTCCCCAAATTGGCC 59.098 50.000 6.48 0.00 37.70 5.36
2326 2403 1.275010 ACACGAATTCCCCAAATTGGC 59.725 47.619 6.48 0.00 37.70 4.52
2327 2404 3.676291 AACACGAATTCCCCAAATTGG 57.324 42.857 4.74 4.74 37.70 3.16
2328 2405 6.207691 AGATAACACGAATTCCCCAAATTG 57.792 37.500 0.00 0.00 37.70 2.32
2329 2406 6.435904 TGAAGATAACACGAATTCCCCAAATT 59.564 34.615 0.00 0.00 40.34 1.82
2330 2407 5.949354 TGAAGATAACACGAATTCCCCAAAT 59.051 36.000 0.00 0.00 0.00 2.32
2331 2408 5.317808 TGAAGATAACACGAATTCCCCAAA 58.682 37.500 0.00 0.00 0.00 3.28
2332 2409 4.912586 TGAAGATAACACGAATTCCCCAA 58.087 39.130 0.00 0.00 0.00 4.12
2333 2410 4.513442 CTGAAGATAACACGAATTCCCCA 58.487 43.478 0.00 0.00 0.00 4.96
2334 2411 3.877508 CCTGAAGATAACACGAATTCCCC 59.122 47.826 0.00 0.00 0.00 4.81
2335 2412 4.514401 ACCTGAAGATAACACGAATTCCC 58.486 43.478 0.00 0.00 0.00 3.97
2336 2413 5.420409 AGACCTGAAGATAACACGAATTCC 58.580 41.667 0.00 0.00 0.00 3.01
2337 2414 6.036191 GGAAGACCTGAAGATAACACGAATTC 59.964 42.308 0.00 0.00 0.00 2.17
2419 2503 8.424918 CGAGGGGCATCATCTAGTTTATATATT 58.575 37.037 0.00 0.00 0.00 1.28
2443 2528 1.677300 AACCAATTCATGCCCGCGA 60.677 52.632 8.23 0.00 0.00 5.87
2451 2536 7.172868 TGAGAACATATTGCAACCAATTCAT 57.827 32.000 0.00 0.00 41.68 2.57
2452 2537 6.587206 TGAGAACATATTGCAACCAATTCA 57.413 33.333 0.00 0.00 41.68 2.57
2609 2694 7.557358 ACATGCTACCTCATCATTAAAACATGA 59.443 33.333 0.00 0.00 37.58 3.07
2644 2729 4.345257 GCCCTCACTAACATATTCCTCTCA 59.655 45.833 0.00 0.00 0.00 3.27
2650 2735 5.476091 AGCTAGCCCTCACTAACATATTC 57.524 43.478 12.13 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.