Multiple sequence alignment - TraesCS5B01G334500

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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 TraesCS5B01G334500 chr5B 100.000 3555 0 0 1 3555 517851428 517854982 0.000000e+00 6565
1 TraesCS5B01G334500 chr5B 84.778 1038 138 13 1540 2563 467371103 467370072 0.000000e+00 1024
2 TraesCS5B01G334500 chr5B 87.556 450 44 4 1028 1477 467372995 467372558 8.800000e-141 510
3 TraesCS5B01G334500 chr5B 75.000 316 67 12 1058 1366 638304528 638304218 6.190000e-28 135
4 TraesCS5B01G334500 chr5D 95.010 2024 68 14 744 2754 428699656 428701659 0.000000e+00 3147
5 TraesCS5B01G334500 chr5D 84.884 1032 136 16 1540 2557 388872660 388871635 0.000000e+00 1024
6 TraesCS5B01G334500 chr5D 87.395 833 58 15 2746 3555 428704287 428705095 0.000000e+00 913
7 TraesCS5B01G334500 chr5D 95.050 505 23 2 1 503 418285203 418285707 0.000000e+00 793
8 TraesCS5B01G334500 chr5D 88.128 438 40 4 1040 1477 388873172 388872747 8.800000e-141 510
9 TraesCS5B01G334500 chr5D 76.627 415 79 16 2132 2540 507617463 507617061 2.780000e-51 213
10 TraesCS5B01G334500 chr5D 76.266 316 64 11 1058 1366 507769046 507768735 1.320000e-34 158
11 TraesCS5B01G334500 chr5A 94.111 1902 60 16 691 2557 544533507 544535391 0.000000e+00 2844
12 TraesCS5B01G334500 chr5A 94.872 507 23 3 1 505 548719151 548719656 0.000000e+00 789
13 TraesCS5B01G334500 chr5A 94.675 507 21 4 1 502 573953877 573953372 0.000000e+00 782
14 TraesCS5B01G334500 chr5A 84.808 520 40 19 3024 3507 544535549 544536065 1.480000e-133 486
15 TraesCS5B01G334500 chr7D 83.508 1528 179 39 1049 2550 634920415 634918935 0.000000e+00 1358
16 TraesCS5B01G334500 chr7D 95.059 506 20 3 1 502 8076432 8075928 0.000000e+00 791
17 TraesCS5B01G334500 chr7A 81.438 1530 188 46 1049 2545 730723134 730721668 0.000000e+00 1164
18 TraesCS5B01G334500 chr7A 95.030 503 19 5 1 498 692300734 692300233 0.000000e+00 785
19 TraesCS5B01G334500 chr7B 83.797 1006 131 26 1537 2524 741226991 741227982 0.000000e+00 926
20 TraesCS5B01G334500 chr7B 82.982 758 106 18 1771 2518 741261807 741261063 0.000000e+00 664
21 TraesCS5B01G334500 chr7B 86.986 146 11 5 3415 3553 559140441 559140585 1.320000e-34 158
22 TraesCS5B01G334500 chr6D 95.040 504 20 5 1 501 454650448 454649947 0.000000e+00 787
23 TraesCS5B01G334500 chr6D 88.194 144 10 5 3415 3553 168246662 168246803 7.900000e-37 165
24 TraesCS5B01G334500 chr4B 94.685 508 20 6 1 502 67496434 67495928 0.000000e+00 782
25 TraesCS5B01G334500 chr1B 94.510 510 21 6 1 504 615023754 615024262 0.000000e+00 780
26 TraesCS5B01G334500 chr1B 89.706 136 8 4 3423 3553 127255520 127255386 6.100000e-38 169
27 TraesCS5B01G334500 chr1D 94.477 507 23 3 1 503 4576791 4577296 0.000000e+00 776
28 TraesCS5B01G334500 chr1D 87.075 147 10 5 3415 3553 144238166 144238311 1.320000e-34 158
29 TraesCS5B01G334500 chr1D 88.235 136 10 4 3423 3553 254521200 254521334 1.320000e-34 158
30 TraesCS5B01G334500 chr1A 88.194 144 11 4 3415 3553 168443164 168443022 2.200000e-37 167
31 TraesCS5B01G334500 chr1A 87.075 147 10 5 3415 3553 584778572 584778717 1.320000e-34 158
32 TraesCS5B01G334500 chr3B 89.051 137 8 5 3423 3553 201522147 201522282 2.840000e-36 163


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 TraesCS5B01G334500 chr5B 517851428 517854982 3554 False 6565 6565 100.0000 1 3555 1 chr5B.!!$F1 3554
1 TraesCS5B01G334500 chr5B 467370072 467372995 2923 True 767 1024 86.1670 1028 2563 2 chr5B.!!$R2 1535
2 TraesCS5B01G334500 chr5D 428699656 428705095 5439 False 2030 3147 91.2025 744 3555 2 chr5D.!!$F2 2811
3 TraesCS5B01G334500 chr5D 418285203 418285707 504 False 793 793 95.0500 1 503 1 chr5D.!!$F1 502
4 TraesCS5B01G334500 chr5D 388871635 388873172 1537 True 767 1024 86.5060 1040 2557 2 chr5D.!!$R3 1517
5 TraesCS5B01G334500 chr5A 544533507 544536065 2558 False 1665 2844 89.4595 691 3507 2 chr5A.!!$F2 2816
6 TraesCS5B01G334500 chr5A 548719151 548719656 505 False 789 789 94.8720 1 505 1 chr5A.!!$F1 504
7 TraesCS5B01G334500 chr5A 573953372 573953877 505 True 782 782 94.6750 1 502 1 chr5A.!!$R1 501
8 TraesCS5B01G334500 chr7D 634918935 634920415 1480 True 1358 1358 83.5080 1049 2550 1 chr7D.!!$R2 1501
9 TraesCS5B01G334500 chr7D 8075928 8076432 504 True 791 791 95.0590 1 502 1 chr7D.!!$R1 501
10 TraesCS5B01G334500 chr7A 730721668 730723134 1466 True 1164 1164 81.4380 1049 2545 1 chr7A.!!$R2 1496
11 TraesCS5B01G334500 chr7A 692300233 692300734 501 True 785 785 95.0300 1 498 1 chr7A.!!$R1 497
12 TraesCS5B01G334500 chr7B 741226991 741227982 991 False 926 926 83.7970 1537 2524 1 chr7B.!!$F2 987
13 TraesCS5B01G334500 chr7B 741261063 741261807 744 True 664 664 82.9820 1771 2518 1 chr7B.!!$R1 747
14 TraesCS5B01G334500 chr6D 454649947 454650448 501 True 787 787 95.0400 1 501 1 chr6D.!!$R1 500
15 TraesCS5B01G334500 chr4B 67495928 67496434 506 True 782 782 94.6850 1 502 1 chr4B.!!$R1 501
16 TraesCS5B01G334500 chr1B 615023754 615024262 508 False 780 780 94.5100 1 504 1 chr1B.!!$F1 503
17 TraesCS5B01G334500 chr1D 4576791 4577296 505 False 776 776 94.4770 1 503 1 chr1D.!!$F1 502

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
526 534 0.099791 ACGGAAAAACTGCCACGTTG 59.900 50.0 0.00 0.00 0.00 4.10 F
531 539 0.179140 AAAACTGCCACGTTGTGCAG 60.179 50.0 22.95 22.95 40.60 4.41 F
571 579 0.249489 CAGGATCCGGCGGTCTTAAG 60.249 60.0 27.32 9.14 0.00 1.85 F
649 657 0.251209 AGAAAAGGAAGGTTCGCCCC 60.251 55.0 0.00 0.00 38.27 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1493 1797 0.579156 CGGACGTACTACCTACTCGC 59.421 60.000 0.0 0.0 0.00 5.03 R
1521 2133 1.589716 GCATGGAGTGTTGGAGCCAC 61.590 60.000 0.0 0.0 32.42 5.01 R
2502 3999 1.748122 TCGACGTACTCCTCCTGCC 60.748 63.158 0.0 0.0 0.00 4.85 R
2574 4074 0.532573 TTTCACCTAGAGGCTGCGAG 59.467 55.000 0.0 0.0 39.32 5.03 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
19 20 2.110213 GGTGCCGTGGTGAGACAA 59.890 61.111 0.00 0.00 0.00 3.18
129 131 2.165998 GAAATCTCTGTTGGCTTGGCT 58.834 47.619 0.00 0.00 0.00 4.75
132 134 0.694771 TCTCTGTTGGCTTGGCTGAT 59.305 50.000 0.00 0.00 0.00 2.90
247 249 2.810887 GCAGCAGCGTCGTCATCA 60.811 61.111 0.00 0.00 0.00 3.07
391 395 6.976636 TCGGCATTTGTTTCTTTTCTTTTT 57.023 29.167 0.00 0.00 0.00 1.94
432 437 1.727467 GTGTTTGTGCTGCTTCCGT 59.273 52.632 0.00 0.00 0.00 4.69
467 472 1.343789 TCGGTTGTATCGGTTGGTTGA 59.656 47.619 0.00 0.00 0.00 3.18
469 474 2.095213 CGGTTGTATCGGTTGGTTGATG 59.905 50.000 0.00 0.00 0.00 3.07
506 514 5.201713 GGGAACCCTTTTTCTCAAAAGAG 57.798 43.478 8.68 0.00 45.20 2.85
507 515 4.893524 GGGAACCCTTTTTCTCAAAAGAGA 59.106 41.667 8.68 0.00 45.20 3.10
508 516 5.221263 GGGAACCCTTTTTCTCAAAAGAGAC 60.221 44.000 8.68 0.00 45.20 3.36
509 517 8.386125 GGGAACCCTTTTTCTCAAAAGAGACG 62.386 46.154 8.68 0.00 45.20 4.18
516 524 7.806149 TTTTTCTCAAAAGAGACGGAAAAAC 57.194 32.000 0.00 0.00 37.57 2.43
517 525 6.753107 TTTCTCAAAAGAGACGGAAAAACT 57.247 33.333 0.00 0.00 31.75 2.66
518 526 5.734855 TCTCAAAAGAGACGGAAAAACTG 57.265 39.130 0.00 0.00 0.00 3.16
519 527 4.035208 TCTCAAAAGAGACGGAAAAACTGC 59.965 41.667 0.00 0.00 0.00 4.40
520 528 3.066203 TCAAAAGAGACGGAAAAACTGCC 59.934 43.478 0.00 0.00 0.00 4.85
521 529 2.341846 AAGAGACGGAAAAACTGCCA 57.658 45.000 0.00 0.00 0.00 4.92
522 530 1.594331 AGAGACGGAAAAACTGCCAC 58.406 50.000 0.00 0.00 0.00 5.01
523 531 0.234884 GAGACGGAAAAACTGCCACG 59.765 55.000 0.00 0.00 0.00 4.94
524 532 0.463116 AGACGGAAAAACTGCCACGT 60.463 50.000 0.00 0.00 37.26 4.49
525 533 0.379316 GACGGAAAAACTGCCACGTT 59.621 50.000 0.00 0.00 34.43 3.99
526 534 0.099791 ACGGAAAAACTGCCACGTTG 59.900 50.000 0.00 0.00 0.00 4.10
527 535 0.099791 CGGAAAAACTGCCACGTTGT 59.900 50.000 0.00 0.00 0.00 3.32
528 536 1.555477 GGAAAAACTGCCACGTTGTG 58.445 50.000 0.00 0.00 0.00 3.33
529 537 0.920664 GAAAAACTGCCACGTTGTGC 59.079 50.000 0.00 0.00 31.34 4.57
530 538 0.244994 AAAAACTGCCACGTTGTGCA 59.755 45.000 4.34 4.34 31.34 4.57
531 539 0.179140 AAAACTGCCACGTTGTGCAG 60.179 50.000 22.95 22.95 40.60 4.41
532 540 1.029408 AAACTGCCACGTTGTGCAGA 61.029 50.000 28.43 0.00 38.75 4.26
533 541 1.439353 AACTGCCACGTTGTGCAGAG 61.439 55.000 28.43 11.90 38.75 3.35
534 542 1.595109 CTGCCACGTTGTGCAGAGA 60.595 57.895 21.07 0.00 38.75 3.10
535 543 1.153269 TGCCACGTTGTGCAGAGAA 60.153 52.632 0.33 0.00 31.34 2.87
536 544 1.279840 GCCACGTTGTGCAGAGAAC 59.720 57.895 0.00 0.00 31.34 3.01
537 545 1.160329 GCCACGTTGTGCAGAGAACT 61.160 55.000 0.00 0.00 31.34 3.01
538 546 0.583438 CCACGTTGTGCAGAGAACTG 59.417 55.000 0.00 0.00 45.91 3.16
546 554 2.356313 CAGAGAACTGCCGTGCGT 60.356 61.111 0.00 0.00 37.33 5.24
547 555 1.956170 CAGAGAACTGCCGTGCGTT 60.956 57.895 0.00 6.07 37.33 4.84
548 556 1.664965 AGAGAACTGCCGTGCGTTC 60.665 57.895 17.08 17.08 39.93 3.95
549 557 3.000080 GAGAACTGCCGTGCGTTCG 62.000 63.158 17.89 0.00 42.22 3.95
550 558 3.033764 GAACTGCCGTGCGTTCGA 61.034 61.111 13.14 0.00 34.60 3.71
551 559 2.357034 AACTGCCGTGCGTTCGAT 60.357 55.556 0.00 0.00 0.00 3.59
552 560 2.279937 GAACTGCCGTGCGTTCGATC 62.280 60.000 13.14 0.00 34.60 3.69
553 561 2.809174 CTGCCGTGCGTTCGATCA 60.809 61.111 0.00 1.22 0.00 2.92
554 562 2.792290 CTGCCGTGCGTTCGATCAG 61.792 63.158 0.00 6.23 0.00 2.90
555 563 3.554692 GCCGTGCGTTCGATCAGG 61.555 66.667 0.00 0.00 0.00 3.86
556 564 2.180769 CCGTGCGTTCGATCAGGA 59.819 61.111 0.00 0.00 0.00 3.86
557 565 1.226974 CCGTGCGTTCGATCAGGAT 60.227 57.895 0.00 0.00 0.00 3.24
558 566 1.209275 CCGTGCGTTCGATCAGGATC 61.209 60.000 0.00 0.00 34.56 3.36
559 567 1.209275 CGTGCGTTCGATCAGGATCC 61.209 60.000 2.48 2.48 34.40 3.36
560 568 1.065764 TGCGTTCGATCAGGATCCG 59.934 57.895 5.98 1.36 34.40 4.18
561 569 1.661821 GCGTTCGATCAGGATCCGG 60.662 63.158 5.98 5.68 34.40 5.14
562 570 1.661821 CGTTCGATCAGGATCCGGC 60.662 63.158 7.07 0.00 34.40 6.13
563 571 1.661821 GTTCGATCAGGATCCGGCG 60.662 63.158 7.07 9.34 34.40 6.46
564 572 2.856628 TTCGATCAGGATCCGGCGG 61.857 63.158 22.51 22.51 34.40 6.13
565 573 3.606662 CGATCAGGATCCGGCGGT 61.607 66.667 27.32 13.58 34.40 5.68
566 574 2.340443 GATCAGGATCCGGCGGTC 59.660 66.667 27.32 21.13 31.76 4.79
567 575 2.123251 ATCAGGATCCGGCGGTCT 60.123 61.111 27.32 18.36 0.00 3.85
568 576 1.749334 GATCAGGATCCGGCGGTCTT 61.749 60.000 27.32 15.84 31.76 3.01
569 577 0.469331 ATCAGGATCCGGCGGTCTTA 60.469 55.000 27.32 13.50 0.00 2.10
570 578 0.685131 TCAGGATCCGGCGGTCTTAA 60.685 55.000 27.32 6.22 0.00 1.85
571 579 0.249489 CAGGATCCGGCGGTCTTAAG 60.249 60.000 27.32 9.14 0.00 1.85
572 580 1.069258 GGATCCGGCGGTCTTAAGG 59.931 63.158 27.32 0.00 0.00 2.69
573 581 1.069258 GATCCGGCGGTCTTAAGGG 59.931 63.158 27.32 0.00 0.00 3.95
574 582 1.683418 GATCCGGCGGTCTTAAGGGT 61.683 60.000 27.32 0.00 0.00 4.34
575 583 1.968050 ATCCGGCGGTCTTAAGGGTG 61.968 60.000 27.32 0.00 0.00 4.61
576 584 2.660802 CGGCGGTCTTAAGGGTGT 59.339 61.111 0.00 0.00 0.00 4.16
577 585 1.004200 CGGCGGTCTTAAGGGTGTT 60.004 57.895 0.00 0.00 0.00 3.32
578 586 1.017701 CGGCGGTCTTAAGGGTGTTC 61.018 60.000 0.00 0.00 0.00 3.18
579 587 1.017701 GGCGGTCTTAAGGGTGTTCG 61.018 60.000 1.85 0.06 0.00 3.95
580 588 0.320160 GCGGTCTTAAGGGTGTTCGT 60.320 55.000 1.85 0.00 0.00 3.85
581 589 1.875157 GCGGTCTTAAGGGTGTTCGTT 60.875 52.381 1.85 0.00 0.00 3.85
582 590 1.796459 CGGTCTTAAGGGTGTTCGTTG 59.204 52.381 1.85 0.00 0.00 4.10
583 591 2.148768 GGTCTTAAGGGTGTTCGTTGG 58.851 52.381 1.85 0.00 0.00 3.77
584 592 2.148768 GTCTTAAGGGTGTTCGTTGGG 58.851 52.381 1.85 0.00 0.00 4.12
585 593 2.048601 TCTTAAGGGTGTTCGTTGGGA 58.951 47.619 1.85 0.00 0.00 4.37
586 594 2.640826 TCTTAAGGGTGTTCGTTGGGAT 59.359 45.455 1.85 0.00 0.00 3.85
587 595 3.073356 TCTTAAGGGTGTTCGTTGGGATT 59.927 43.478 1.85 0.00 0.00 3.01
588 596 1.616159 AAGGGTGTTCGTTGGGATTG 58.384 50.000 0.00 0.00 0.00 2.67
589 597 0.893727 AGGGTGTTCGTTGGGATTGC 60.894 55.000 0.00 0.00 0.00 3.56
590 598 0.893727 GGGTGTTCGTTGGGATTGCT 60.894 55.000 0.00 0.00 0.00 3.91
591 599 0.958822 GGTGTTCGTTGGGATTGCTT 59.041 50.000 0.00 0.00 0.00 3.91
592 600 2.156098 GGTGTTCGTTGGGATTGCTTA 58.844 47.619 0.00 0.00 0.00 3.09
593 601 2.554893 GGTGTTCGTTGGGATTGCTTAA 59.445 45.455 0.00 0.00 0.00 1.85
594 602 3.004944 GGTGTTCGTTGGGATTGCTTAAA 59.995 43.478 0.00 0.00 0.00 1.52
595 603 4.500035 GGTGTTCGTTGGGATTGCTTAAAA 60.500 41.667 0.00 0.00 0.00 1.52
596 604 5.044558 GTGTTCGTTGGGATTGCTTAAAAA 58.955 37.500 0.00 0.00 0.00 1.94
597 605 5.044558 TGTTCGTTGGGATTGCTTAAAAAC 58.955 37.500 0.00 0.00 0.00 2.43
598 606 5.163499 TGTTCGTTGGGATTGCTTAAAAACT 60.163 36.000 0.00 0.00 0.00 2.66
599 607 4.865776 TCGTTGGGATTGCTTAAAAACTG 58.134 39.130 0.00 0.00 0.00 3.16
600 608 3.987220 CGTTGGGATTGCTTAAAAACTGG 59.013 43.478 0.00 0.00 0.00 4.00
601 609 3.676291 TGGGATTGCTTAAAAACTGGC 57.324 42.857 0.00 0.00 0.00 4.85
602 610 2.029470 TGGGATTGCTTAAAAACTGGCG 60.029 45.455 0.00 0.00 0.00 5.69
603 611 2.029380 GGGATTGCTTAAAAACTGGCGT 60.029 45.455 0.00 0.00 0.00 5.68
604 612 3.554129 GGGATTGCTTAAAAACTGGCGTT 60.554 43.478 0.00 0.00 34.03 4.84
605 613 3.673338 GGATTGCTTAAAAACTGGCGTTC 59.327 43.478 0.00 0.00 31.66 3.95
606 614 2.392933 TGCTTAAAAACTGGCGTTCG 57.607 45.000 0.00 0.00 31.66 3.95
607 615 1.050009 GCTTAAAAACTGGCGTTCGC 58.950 50.000 8.75 8.75 31.66 4.70
608 616 1.334689 GCTTAAAAACTGGCGTTCGCT 60.335 47.619 16.40 0.00 31.66 4.93
609 617 2.307049 CTTAAAAACTGGCGTTCGCTG 58.693 47.619 16.40 11.90 31.66 5.18
610 618 0.589223 TAAAAACTGGCGTTCGCTGG 59.411 50.000 16.40 11.54 31.66 4.85
611 619 1.381165 AAAAACTGGCGTTCGCTGGT 61.381 50.000 16.40 12.11 31.66 4.00
612 620 1.381165 AAAACTGGCGTTCGCTGGTT 61.381 50.000 16.40 16.45 31.66 3.67
613 621 0.533308 AAACTGGCGTTCGCTGGTTA 60.533 50.000 16.40 0.00 31.66 2.85
614 622 0.533308 AACTGGCGTTCGCTGGTTAA 60.533 50.000 16.40 0.00 0.00 2.01
615 623 1.226030 ACTGGCGTTCGCTGGTTAAC 61.226 55.000 16.40 0.00 0.00 2.01
616 624 0.949105 CTGGCGTTCGCTGGTTAACT 60.949 55.000 16.40 0.00 0.00 2.24
617 625 1.225376 TGGCGTTCGCTGGTTAACTG 61.225 55.000 16.40 0.36 0.00 3.16
618 626 1.495951 GCGTTCGCTGGTTAACTGG 59.504 57.895 9.99 0.03 0.00 4.00
619 627 1.226030 GCGTTCGCTGGTTAACTGGT 61.226 55.000 9.99 0.00 0.00 4.00
620 628 1.223187 CGTTCGCTGGTTAACTGGTT 58.777 50.000 5.42 0.00 0.00 3.67
621 629 2.406130 CGTTCGCTGGTTAACTGGTTA 58.594 47.619 5.42 0.00 0.00 2.85
622 630 2.410730 CGTTCGCTGGTTAACTGGTTAG 59.589 50.000 5.42 0.00 0.00 2.34
623 631 3.396560 GTTCGCTGGTTAACTGGTTAGT 58.603 45.455 5.42 0.00 39.32 2.24
624 632 3.034721 TCGCTGGTTAACTGGTTAGTG 57.965 47.619 5.42 4.11 37.19 2.74
625 633 2.629137 TCGCTGGTTAACTGGTTAGTGA 59.371 45.455 5.42 6.15 37.19 3.41
626 634 2.735134 CGCTGGTTAACTGGTTAGTGAC 59.265 50.000 5.42 0.00 37.19 3.67
627 635 2.735134 GCTGGTTAACTGGTTAGTGACG 59.265 50.000 5.42 0.00 37.19 4.35
628 636 3.801293 GCTGGTTAACTGGTTAGTGACGT 60.801 47.826 5.42 0.00 37.19 4.34
629 637 4.374399 CTGGTTAACTGGTTAGTGACGTT 58.626 43.478 5.42 0.00 37.19 3.99
630 638 5.528043 TGGTTAACTGGTTAGTGACGTTA 57.472 39.130 5.42 0.00 37.19 3.18
631 639 5.531634 TGGTTAACTGGTTAGTGACGTTAG 58.468 41.667 5.42 0.00 37.19 2.34
632 640 5.301551 TGGTTAACTGGTTAGTGACGTTAGA 59.698 40.000 5.42 0.00 37.19 2.10
633 641 6.183360 TGGTTAACTGGTTAGTGACGTTAGAA 60.183 38.462 5.42 0.00 37.19 2.10
634 642 6.701400 GGTTAACTGGTTAGTGACGTTAGAAA 59.299 38.462 5.42 0.00 37.19 2.52
635 643 7.224557 GGTTAACTGGTTAGTGACGTTAGAAAA 59.775 37.037 5.42 0.00 37.19 2.29
636 644 6.839820 AACTGGTTAGTGACGTTAGAAAAG 57.160 37.500 0.00 0.00 37.19 2.27
637 645 5.295152 ACTGGTTAGTGACGTTAGAAAAGG 58.705 41.667 0.00 0.00 35.34 3.11
638 646 5.069516 ACTGGTTAGTGACGTTAGAAAAGGA 59.930 40.000 0.00 0.00 35.34 3.36
639 647 5.916318 TGGTTAGTGACGTTAGAAAAGGAA 58.084 37.500 0.00 0.00 0.00 3.36
640 648 5.987347 TGGTTAGTGACGTTAGAAAAGGAAG 59.013 40.000 0.00 0.00 0.00 3.46
641 649 5.407691 GGTTAGTGACGTTAGAAAAGGAAGG 59.592 44.000 0.00 0.00 0.00 3.46
642 650 4.684484 AGTGACGTTAGAAAAGGAAGGT 57.316 40.909 0.00 0.00 0.00 3.50
643 651 5.032327 AGTGACGTTAGAAAAGGAAGGTT 57.968 39.130 0.00 0.00 0.00 3.50
644 652 5.055144 AGTGACGTTAGAAAAGGAAGGTTC 58.945 41.667 0.00 0.00 0.00 3.62
645 653 4.053295 TGACGTTAGAAAAGGAAGGTTCG 58.947 43.478 0.00 0.00 0.00 3.95
646 654 2.804527 ACGTTAGAAAAGGAAGGTTCGC 59.195 45.455 0.00 0.00 0.00 4.70
647 655 2.159037 CGTTAGAAAAGGAAGGTTCGCC 59.841 50.000 0.00 0.00 37.60 5.54
648 656 2.484742 TAGAAAAGGAAGGTTCGCCC 57.515 50.000 0.00 0.00 38.27 6.13
649 657 0.251209 AGAAAAGGAAGGTTCGCCCC 60.251 55.000 0.00 0.00 38.27 5.80
650 658 1.228769 AAAAGGAAGGTTCGCCCCC 60.229 57.895 0.00 0.00 38.27 5.40
665 673 2.489040 CCCCCAAAGATAACGGCAC 58.511 57.895 0.00 0.00 0.00 5.01
684 692 6.785488 GGCACGATCATACTTTTCATATCA 57.215 37.500 0.00 0.00 0.00 2.15
685 693 6.593978 GGCACGATCATACTTTTCATATCAC 58.406 40.000 0.00 0.00 0.00 3.06
686 694 6.292129 GCACGATCATACTTTTCATATCACG 58.708 40.000 0.00 0.00 0.00 4.35
687 695 6.074302 GCACGATCATACTTTTCATATCACGT 60.074 38.462 0.00 0.00 0.00 4.49
688 696 7.276495 CACGATCATACTTTTCATATCACGTG 58.724 38.462 9.94 9.94 38.63 4.49
689 697 6.978659 ACGATCATACTTTTCATATCACGTGT 59.021 34.615 16.51 5.66 0.00 4.49
853 894 2.231721 GAGCAGGACTACCGACTTTCTT 59.768 50.000 0.00 0.00 41.83 2.52
854 895 3.428532 AGCAGGACTACCGACTTTCTTA 58.571 45.455 0.00 0.00 41.83 2.10
855 896 3.444388 AGCAGGACTACCGACTTTCTTAG 59.556 47.826 0.00 0.00 41.83 2.18
856 897 3.193056 GCAGGACTACCGACTTTCTTAGT 59.807 47.826 0.00 0.00 41.83 2.24
917 958 0.307760 CTGTTTTCCGTCTGTGCACC 59.692 55.000 15.69 0.00 0.00 5.01
939 980 1.648467 GGATTCACTCCACGCTTGCC 61.648 60.000 0.00 0.00 44.26 4.52
1488 1792 1.144057 GGTACGTCTCTGCCATGGG 59.856 63.158 15.13 0.00 0.00 4.00
1521 2133 1.717791 TAGTACGTCCGGTCATGGCG 61.718 60.000 0.00 0.58 35.56 5.69
1532 2163 2.672651 CATGGCGTGGCTCCAACA 60.673 61.111 0.00 0.00 37.13 3.33
1544 2987 1.303561 TCCAACACTCCATGCTGCC 60.304 57.895 0.00 0.00 0.00 4.85
1690 3133 2.764967 CCGTTCCCGACCCCCATA 60.765 66.667 0.00 0.00 35.63 2.74
2452 3949 2.683933 GACGAGGAAGGGAGGGCA 60.684 66.667 0.00 0.00 0.00 5.36
2563 4063 1.280457 GACTGCCATAGGGATAGGGG 58.720 60.000 0.00 0.00 35.59 4.79
2574 4074 0.464554 GGATAGGGGTGCAGTTCTGC 60.465 60.000 16.65 16.65 0.00 4.26
2576 4076 0.543749 ATAGGGGTGCAGTTCTGCTC 59.456 55.000 22.44 18.93 35.49 4.26
2577 4077 1.888436 TAGGGGTGCAGTTCTGCTCG 61.888 60.000 22.44 0.00 35.49 5.03
2631 4131 3.806625 ACCATGGAATAAATGCACTGC 57.193 42.857 21.47 0.00 29.34 4.40
2633 4133 2.431419 CCATGGAATAAATGCACTGCCA 59.569 45.455 5.56 0.00 29.34 4.92
2767 6932 5.594725 TGATGTAAAAACACTACCTTGCCAA 59.405 36.000 0.00 0.00 0.00 4.52
2864 7029 1.679977 GCATGCCACCACATCCACT 60.680 57.895 6.36 0.00 0.00 4.00
2866 7031 0.322726 CATGCCACCACATCCACTCA 60.323 55.000 0.00 0.00 0.00 3.41
2869 7034 1.203038 TGCCACCACATCCACTCAATT 60.203 47.619 0.00 0.00 0.00 2.32
2871 7036 2.517959 CCACCACATCCACTCAATTGT 58.482 47.619 5.13 0.00 0.00 2.71
2872 7037 2.489329 CCACCACATCCACTCAATTGTC 59.511 50.000 5.13 0.00 0.00 3.18
2877 7042 5.059161 CCACATCCACTCAATTGTCGATAT 58.941 41.667 5.13 0.00 0.00 1.63
2885 7050 1.282248 AATTGTCGATATCCGCGCCG 61.282 55.000 0.00 0.00 38.37 6.46
2890 7055 3.545481 GATATCCGCGCCGCATCG 61.545 66.667 10.75 0.00 0.00 3.84
2918 7083 3.055719 CCTGCAACAACCGCCGAT 61.056 61.111 0.00 0.00 0.00 4.18
2959 7124 4.227134 CCCCATCGCCCTCAGTCG 62.227 72.222 0.00 0.00 0.00 4.18
2962 7127 2.278206 CATCGCCCTCAGTCGTCG 60.278 66.667 0.00 0.00 0.00 5.12
2967 7132 1.227002 GCCCTCAGTCGTCGAATCC 60.227 63.158 0.00 0.00 0.00 3.01
2973 7138 2.884207 GTCGTCGAATCCACGCCC 60.884 66.667 0.00 0.00 37.18 6.13
3133 7300 1.335964 CCATTACGCCGTCGAGATCAT 60.336 52.381 0.00 0.00 39.41 2.45
3153 7343 2.184322 GCGAGGGCGAGACATCAA 59.816 61.111 0.00 0.00 40.82 2.57
3167 7357 1.005037 ATCAAAGCTCACCGCGTGA 60.005 52.632 4.92 8.28 45.59 4.35
3243 7434 0.834612 CAACCCCCTAGCCGATGTAA 59.165 55.000 0.00 0.00 0.00 2.41
3254 7445 0.732571 CCGATGTAAAATGCACCGCT 59.267 50.000 0.00 0.00 0.00 5.52
3260 7451 1.312371 TAAAATGCACCGCTGAGGCC 61.312 55.000 0.00 0.00 46.52 5.19
3266 7457 3.249189 ACCGCTGAGGCCAGGAAA 61.249 61.111 5.01 0.00 46.52 3.13
3301 7492 0.678048 AAGCTCACCGAGGCCAATTC 60.678 55.000 5.01 0.00 0.00 2.17
3302 7493 1.377202 GCTCACCGAGGCCAATTCA 60.377 57.895 5.01 0.00 0.00 2.57
3394 7585 5.072329 TCAAGAGGAAGACAAGAATCACCTT 59.928 40.000 0.00 0.00 31.05 3.50
3409 7600 2.528743 CCTTGCAGTATCAGCGCCG 61.529 63.158 2.29 0.00 33.85 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.300697 GGACACGAAGCTTCCACGT 60.301 57.895 20.62 13.10 40.87 4.49
160 162 1.627297 GCCCTCCAAGAAGGTCCGAT 61.627 60.000 0.00 0.00 39.02 4.18
187 189 1.479757 GCGAGGAGAGAGGAAGGGTAT 60.480 57.143 0.00 0.00 0.00 2.73
247 249 1.517832 CTCCAAGAAGGGACGCGAT 59.482 57.895 15.93 0.00 38.24 4.58
391 395 4.202111 CGCCCAAAAGAAAGGAAAGAGAAA 60.202 41.667 0.00 0.00 0.00 2.52
432 437 2.520982 CGACGATAGGGGCTGGGA 60.521 66.667 0.00 0.00 43.77 4.37
467 472 3.637911 TCCCCGCTTTGTATTACACAT 57.362 42.857 0.00 0.00 36.90 3.21
469 474 2.421073 GGTTCCCCGCTTTGTATTACAC 59.579 50.000 0.00 0.00 0.00 2.90
505 513 0.463116 ACGTGGCAGTTTTTCCGTCT 60.463 50.000 0.00 0.00 0.00 4.18
506 514 0.379316 AACGTGGCAGTTTTTCCGTC 59.621 50.000 0.00 0.00 0.00 4.79
507 515 0.099791 CAACGTGGCAGTTTTTCCGT 59.900 50.000 0.00 0.00 30.96 4.69
508 516 0.099791 ACAACGTGGCAGTTTTTCCG 59.900 50.000 0.00 0.00 30.96 4.30
509 517 1.555477 CACAACGTGGCAGTTTTTCC 58.445 50.000 0.00 0.00 30.96 3.13
510 518 0.920664 GCACAACGTGGCAGTTTTTC 59.079 50.000 0.00 0.00 33.64 2.29
511 519 0.244994 TGCACAACGTGGCAGTTTTT 59.755 45.000 5.79 0.00 34.58 1.94
512 520 1.886585 TGCACAACGTGGCAGTTTT 59.113 47.368 5.79 0.00 34.58 2.43
513 521 3.597072 TGCACAACGTGGCAGTTT 58.403 50.000 5.79 0.00 34.58 2.66
517 525 1.153269 TTCTCTGCACAACGTGGCA 60.153 52.632 9.12 9.12 38.52 4.92
518 526 1.160329 AGTTCTCTGCACAACGTGGC 61.160 55.000 0.00 0.00 33.64 5.01
519 527 0.583438 CAGTTCTCTGCACAACGTGG 59.417 55.000 0.00 0.00 34.79 4.94
529 537 1.891060 GAACGCACGGCAGTTCTCTG 61.891 60.000 17.30 0.00 43.87 3.35
530 538 1.664965 GAACGCACGGCAGTTCTCT 60.665 57.895 17.30 0.00 38.23 3.10
531 539 2.853914 GAACGCACGGCAGTTCTC 59.146 61.111 17.30 3.60 38.23 2.87
532 540 2.765250 ATCGAACGCACGGCAGTTCT 62.765 55.000 19.67 8.91 38.67 3.01
533 541 2.279937 GATCGAACGCACGGCAGTTC 62.280 60.000 15.91 15.91 38.05 3.01
534 542 2.357034 ATCGAACGCACGGCAGTT 60.357 55.556 0.00 0.00 0.00 3.16
535 543 2.809601 GATCGAACGCACGGCAGT 60.810 61.111 0.00 0.00 0.00 4.40
536 544 2.792290 CTGATCGAACGCACGGCAG 61.792 63.158 0.00 6.61 33.20 4.85
537 545 2.809174 CTGATCGAACGCACGGCA 60.809 61.111 0.00 1.46 0.00 5.69
538 546 3.554692 CCTGATCGAACGCACGGC 61.555 66.667 0.00 0.00 0.00 5.68
539 547 1.209275 GATCCTGATCGAACGCACGG 61.209 60.000 0.00 0.00 0.00 4.94
540 548 1.209275 GGATCCTGATCGAACGCACG 61.209 60.000 3.84 0.00 38.69 5.34
541 549 1.209275 CGGATCCTGATCGAACGCAC 61.209 60.000 10.75 0.00 38.69 5.34
542 550 1.065764 CGGATCCTGATCGAACGCA 59.934 57.895 10.75 0.00 38.69 5.24
543 551 1.661821 CCGGATCCTGATCGAACGC 60.662 63.158 10.75 0.00 38.69 4.84
544 552 1.661821 GCCGGATCCTGATCGAACG 60.662 63.158 5.05 0.26 38.69 3.95
545 553 1.661821 CGCCGGATCCTGATCGAAC 60.662 63.158 5.05 0.00 38.69 3.95
546 554 2.728180 CGCCGGATCCTGATCGAA 59.272 61.111 5.05 0.00 38.69 3.71
547 555 3.295273 CCGCCGGATCCTGATCGA 61.295 66.667 5.05 0.00 38.69 3.59
548 556 3.559657 GACCGCCGGATCCTGATCG 62.560 68.421 11.71 7.43 38.69 3.69
549 557 1.749334 AAGACCGCCGGATCCTGATC 61.749 60.000 11.71 0.00 37.11 2.92
550 558 0.469331 TAAGACCGCCGGATCCTGAT 60.469 55.000 11.71 0.00 0.00 2.90
551 559 0.685131 TTAAGACCGCCGGATCCTGA 60.685 55.000 11.71 0.00 0.00 3.86
552 560 0.249489 CTTAAGACCGCCGGATCCTG 60.249 60.000 11.71 4.14 0.00 3.86
553 561 1.400530 CCTTAAGACCGCCGGATCCT 61.401 60.000 11.71 0.12 0.00 3.24
554 562 1.069258 CCTTAAGACCGCCGGATCC 59.931 63.158 11.71 0.00 0.00 3.36
555 563 1.069258 CCCTTAAGACCGCCGGATC 59.931 63.158 11.71 3.56 0.00 3.36
556 564 1.688187 ACCCTTAAGACCGCCGGAT 60.688 57.895 11.71 0.00 0.00 4.18
557 565 2.284112 ACCCTTAAGACCGCCGGA 60.284 61.111 11.71 0.00 0.00 5.14
558 566 2.125269 CACCCTTAAGACCGCCGG 60.125 66.667 0.00 0.00 0.00 6.13
559 567 1.004200 AACACCCTTAAGACCGCCG 60.004 57.895 3.36 0.00 0.00 6.46
560 568 1.017701 CGAACACCCTTAAGACCGCC 61.018 60.000 3.36 0.00 0.00 6.13
561 569 0.320160 ACGAACACCCTTAAGACCGC 60.320 55.000 3.36 0.00 0.00 5.68
562 570 1.796459 CAACGAACACCCTTAAGACCG 59.204 52.381 3.36 0.94 0.00 4.79
563 571 2.148768 CCAACGAACACCCTTAAGACC 58.851 52.381 3.36 0.00 0.00 3.85
564 572 2.148768 CCCAACGAACACCCTTAAGAC 58.851 52.381 3.36 0.00 0.00 3.01
565 573 2.048601 TCCCAACGAACACCCTTAAGA 58.951 47.619 3.36 0.00 0.00 2.10
566 574 2.554370 TCCCAACGAACACCCTTAAG 57.446 50.000 0.00 0.00 0.00 1.85
567 575 3.150767 CAATCCCAACGAACACCCTTAA 58.849 45.455 0.00 0.00 0.00 1.85
568 576 2.785562 CAATCCCAACGAACACCCTTA 58.214 47.619 0.00 0.00 0.00 2.69
569 577 1.616159 CAATCCCAACGAACACCCTT 58.384 50.000 0.00 0.00 0.00 3.95
570 578 0.893727 GCAATCCCAACGAACACCCT 60.894 55.000 0.00 0.00 0.00 4.34
571 579 0.893727 AGCAATCCCAACGAACACCC 60.894 55.000 0.00 0.00 0.00 4.61
572 580 0.958822 AAGCAATCCCAACGAACACC 59.041 50.000 0.00 0.00 0.00 4.16
573 581 3.907894 TTAAGCAATCCCAACGAACAC 57.092 42.857 0.00 0.00 0.00 3.32
574 582 4.920640 TTTTAAGCAATCCCAACGAACA 57.079 36.364 0.00 0.00 0.00 3.18
575 583 5.174943 CAGTTTTTAAGCAATCCCAACGAAC 59.825 40.000 0.00 0.00 0.00 3.95
576 584 5.285651 CAGTTTTTAAGCAATCCCAACGAA 58.714 37.500 0.00 0.00 0.00 3.85
577 585 4.261825 CCAGTTTTTAAGCAATCCCAACGA 60.262 41.667 0.00 0.00 0.00 3.85
578 586 3.987220 CCAGTTTTTAAGCAATCCCAACG 59.013 43.478 0.00 0.00 0.00 4.10
579 587 3.745975 GCCAGTTTTTAAGCAATCCCAAC 59.254 43.478 0.00 0.00 0.00 3.77
580 588 3.553922 CGCCAGTTTTTAAGCAATCCCAA 60.554 43.478 0.00 0.00 0.00 4.12
581 589 2.029470 CGCCAGTTTTTAAGCAATCCCA 60.029 45.455 0.00 0.00 0.00 4.37
582 590 2.029380 ACGCCAGTTTTTAAGCAATCCC 60.029 45.455 0.00 0.00 0.00 3.85
583 591 3.297830 ACGCCAGTTTTTAAGCAATCC 57.702 42.857 0.00 0.00 0.00 3.01
584 592 3.360758 CGAACGCCAGTTTTTAAGCAATC 59.639 43.478 0.00 0.00 41.34 2.67
585 593 3.305110 CGAACGCCAGTTTTTAAGCAAT 58.695 40.909 0.00 0.00 41.34 3.56
586 594 2.722071 CGAACGCCAGTTTTTAAGCAA 58.278 42.857 0.00 0.00 41.34 3.91
587 595 1.598430 GCGAACGCCAGTTTTTAAGCA 60.598 47.619 8.03 0.00 41.34 3.91
588 596 1.050009 GCGAACGCCAGTTTTTAAGC 58.950 50.000 8.03 0.00 41.34 3.09
589 597 2.307049 CAGCGAACGCCAGTTTTTAAG 58.693 47.619 15.44 0.00 41.34 1.85
590 598 1.002251 CCAGCGAACGCCAGTTTTTAA 60.002 47.619 15.44 0.00 41.34 1.52
591 599 0.589223 CCAGCGAACGCCAGTTTTTA 59.411 50.000 15.44 0.00 41.34 1.52
592 600 1.358759 CCAGCGAACGCCAGTTTTT 59.641 52.632 15.44 0.00 41.34 1.94
593 601 1.381165 AACCAGCGAACGCCAGTTTT 61.381 50.000 15.44 0.20 41.34 2.43
594 602 0.533308 TAACCAGCGAACGCCAGTTT 60.533 50.000 22.19 11.56 41.34 2.66
595 603 0.533308 TTAACCAGCGAACGCCAGTT 60.533 50.000 21.26 21.26 44.47 3.16
596 604 1.070105 TTAACCAGCGAACGCCAGT 59.930 52.632 15.44 10.31 43.17 4.00
597 605 0.949105 AGTTAACCAGCGAACGCCAG 60.949 55.000 15.44 9.69 43.17 4.85
598 606 1.070105 AGTTAACCAGCGAACGCCA 59.930 52.632 15.44 0.00 43.17 5.69
599 607 1.495951 CAGTTAACCAGCGAACGCC 59.504 57.895 15.44 0.00 43.17 5.68
600 608 1.226030 ACCAGTTAACCAGCGAACGC 61.226 55.000 11.31 11.31 42.33 4.84
601 609 1.223187 AACCAGTTAACCAGCGAACG 58.777 50.000 0.88 0.00 0.00 3.95
602 610 3.185797 CACTAACCAGTTAACCAGCGAAC 59.814 47.826 0.88 0.00 30.46 3.95
603 611 3.069872 TCACTAACCAGTTAACCAGCGAA 59.930 43.478 0.88 0.00 30.46 4.70
604 612 2.629137 TCACTAACCAGTTAACCAGCGA 59.371 45.455 0.88 0.00 30.46 4.93
605 613 2.735134 GTCACTAACCAGTTAACCAGCG 59.265 50.000 0.88 0.00 30.46 5.18
606 614 2.735134 CGTCACTAACCAGTTAACCAGC 59.265 50.000 0.88 0.00 30.46 4.85
607 615 3.986277 ACGTCACTAACCAGTTAACCAG 58.014 45.455 0.88 0.00 30.46 4.00
608 616 4.405116 AACGTCACTAACCAGTTAACCA 57.595 40.909 0.88 0.00 30.46 3.67
609 617 5.772521 TCTAACGTCACTAACCAGTTAACC 58.227 41.667 0.88 0.00 30.46 2.85
610 618 7.698836 TTTCTAACGTCACTAACCAGTTAAC 57.301 36.000 0.00 0.00 30.46 2.01
611 619 7.439056 CCTTTTCTAACGTCACTAACCAGTTAA 59.561 37.037 0.00 0.00 30.46 2.01
612 620 6.925165 CCTTTTCTAACGTCACTAACCAGTTA 59.075 38.462 0.00 0.00 30.46 2.24
613 621 5.756833 CCTTTTCTAACGTCACTAACCAGTT 59.243 40.000 0.00 0.00 30.46 3.16
614 622 5.069516 TCCTTTTCTAACGTCACTAACCAGT 59.930 40.000 0.00 0.00 34.42 4.00
615 623 5.535333 TCCTTTTCTAACGTCACTAACCAG 58.465 41.667 0.00 0.00 0.00 4.00
616 624 5.534207 TCCTTTTCTAACGTCACTAACCA 57.466 39.130 0.00 0.00 0.00 3.67
617 625 5.407691 CCTTCCTTTTCTAACGTCACTAACC 59.592 44.000 0.00 0.00 0.00 2.85
618 626 5.987953 ACCTTCCTTTTCTAACGTCACTAAC 59.012 40.000 0.00 0.00 0.00 2.34
619 627 6.165700 ACCTTCCTTTTCTAACGTCACTAA 57.834 37.500 0.00 0.00 0.00 2.24
620 628 5.796424 ACCTTCCTTTTCTAACGTCACTA 57.204 39.130 0.00 0.00 0.00 2.74
621 629 4.684484 ACCTTCCTTTTCTAACGTCACT 57.316 40.909 0.00 0.00 0.00 3.41
622 630 4.084693 CGAACCTTCCTTTTCTAACGTCAC 60.085 45.833 0.00 0.00 0.00 3.67
623 631 4.053295 CGAACCTTCCTTTTCTAACGTCA 58.947 43.478 0.00 0.00 0.00 4.35
624 632 3.120752 GCGAACCTTCCTTTTCTAACGTC 60.121 47.826 0.00 0.00 0.00 4.34
625 633 2.804527 GCGAACCTTCCTTTTCTAACGT 59.195 45.455 0.00 0.00 0.00 3.99
626 634 2.159037 GGCGAACCTTCCTTTTCTAACG 59.841 50.000 0.00 0.00 0.00 3.18
627 635 2.486982 GGGCGAACCTTCCTTTTCTAAC 59.513 50.000 0.00 0.00 35.85 2.34
628 636 2.553685 GGGGCGAACCTTCCTTTTCTAA 60.554 50.000 0.00 0.00 40.03 2.10
629 637 1.003928 GGGGCGAACCTTCCTTTTCTA 59.996 52.381 0.00 0.00 40.03 2.10
630 638 0.251209 GGGGCGAACCTTCCTTTTCT 60.251 55.000 0.00 0.00 40.03 2.52
631 639 1.248785 GGGGGCGAACCTTCCTTTTC 61.249 60.000 0.00 0.00 40.03 2.29
632 640 1.228769 GGGGGCGAACCTTCCTTTT 60.229 57.895 0.00 0.00 40.03 2.27
633 641 2.439245 GGGGGCGAACCTTCCTTT 59.561 61.111 0.00 0.00 40.03 3.11
647 655 1.373590 CGTGCCGTTATCTTTGGGGG 61.374 60.000 0.00 0.00 0.00 5.40
648 656 0.391927 TCGTGCCGTTATCTTTGGGG 60.392 55.000 0.00 0.00 0.00 4.96
649 657 1.597663 GATCGTGCCGTTATCTTTGGG 59.402 52.381 0.00 0.00 0.00 4.12
650 658 2.276201 TGATCGTGCCGTTATCTTTGG 58.724 47.619 0.00 0.00 0.00 3.28
651 659 4.745125 AGTATGATCGTGCCGTTATCTTTG 59.255 41.667 0.00 0.00 0.00 2.77
652 660 4.945246 AGTATGATCGTGCCGTTATCTTT 58.055 39.130 0.00 0.00 0.00 2.52
653 661 4.585955 AGTATGATCGTGCCGTTATCTT 57.414 40.909 0.00 0.00 0.00 2.40
654 662 4.585955 AAGTATGATCGTGCCGTTATCT 57.414 40.909 0.00 0.00 0.00 1.98
655 663 5.233476 TGAAAAGTATGATCGTGCCGTTATC 59.767 40.000 0.00 0.00 0.00 1.75
656 664 5.113383 TGAAAAGTATGATCGTGCCGTTAT 58.887 37.500 0.00 0.00 0.00 1.89
657 665 4.496360 TGAAAAGTATGATCGTGCCGTTA 58.504 39.130 0.00 0.00 0.00 3.18
658 666 3.331150 TGAAAAGTATGATCGTGCCGTT 58.669 40.909 0.00 0.00 0.00 4.44
659 667 2.967362 TGAAAAGTATGATCGTGCCGT 58.033 42.857 0.00 0.00 0.00 5.68
660 668 5.405269 TGATATGAAAAGTATGATCGTGCCG 59.595 40.000 0.00 0.00 0.00 5.69
661 669 6.593978 GTGATATGAAAAGTATGATCGTGCC 58.406 40.000 0.00 0.00 0.00 5.01
662 670 6.074302 ACGTGATATGAAAAGTATGATCGTGC 60.074 38.462 0.00 0.00 0.00 5.34
663 671 7.043391 ACACGTGATATGAAAAGTATGATCGTG 60.043 37.037 25.01 0.00 44.60 4.35
664 672 6.978659 ACACGTGATATGAAAAGTATGATCGT 59.021 34.615 25.01 0.00 0.00 3.73
665 673 7.167468 TCACACGTGATATGAAAAGTATGATCG 59.833 37.037 25.01 0.00 34.14 3.69
666 674 8.269424 GTCACACGTGATATGAAAAGTATGATC 58.731 37.037 25.01 2.35 42.18 2.92
667 675 7.043391 CGTCACACGTGATATGAAAAGTATGAT 60.043 37.037 25.01 0.00 42.18 2.45
668 676 6.252655 CGTCACACGTGATATGAAAAGTATGA 59.747 38.462 25.01 7.57 42.18 2.15
669 677 6.252655 TCGTCACACGTGATATGAAAAGTATG 59.747 38.462 25.01 5.02 43.14 2.39
670 678 6.252869 GTCGTCACACGTGATATGAAAAGTAT 59.747 38.462 25.01 0.00 43.14 2.12
671 679 5.570206 GTCGTCACACGTGATATGAAAAGTA 59.430 40.000 25.01 0.00 43.14 2.24
672 680 4.384846 GTCGTCACACGTGATATGAAAAGT 59.615 41.667 25.01 0.00 43.14 2.66
673 681 4.621460 AGTCGTCACACGTGATATGAAAAG 59.379 41.667 25.01 10.43 43.14 2.27
674 682 4.384547 CAGTCGTCACACGTGATATGAAAA 59.615 41.667 25.01 4.47 43.14 2.29
675 683 3.917985 CAGTCGTCACACGTGATATGAAA 59.082 43.478 25.01 4.83 43.14 2.69
676 684 3.498082 CAGTCGTCACACGTGATATGAA 58.502 45.455 25.01 0.00 43.14 2.57
677 685 2.731027 GCAGTCGTCACACGTGATATGA 60.731 50.000 25.01 16.57 43.14 2.15
678 686 1.583856 GCAGTCGTCACACGTGATATG 59.416 52.381 25.01 14.49 43.14 1.78
679 687 1.472878 AGCAGTCGTCACACGTGATAT 59.527 47.619 25.01 0.00 43.14 1.63
680 688 0.879090 AGCAGTCGTCACACGTGATA 59.121 50.000 25.01 6.52 43.14 2.15
681 689 0.664466 CAGCAGTCGTCACACGTGAT 60.664 55.000 25.01 3.37 43.14 3.06
682 690 1.299089 CAGCAGTCGTCACACGTGA 60.299 57.895 25.01 0.00 43.14 4.35
683 691 0.317519 TACAGCAGTCGTCACACGTG 60.318 55.000 15.48 15.48 43.14 4.49
684 692 0.596577 ATACAGCAGTCGTCACACGT 59.403 50.000 0.00 0.00 43.14 4.49
685 693 0.984829 CATACAGCAGTCGTCACACG 59.015 55.000 0.00 0.00 44.19 4.49
686 694 2.254459 CTCATACAGCAGTCGTCACAC 58.746 52.381 0.00 0.00 0.00 3.82
687 695 2.636768 CTCATACAGCAGTCGTCACA 57.363 50.000 0.00 0.00 0.00 3.58
723 733 7.413657 CGTGACCCGAGATATGTTTATTGTTTT 60.414 37.037 0.00 0.00 39.56 2.43
743 753 1.677637 GGGAGAGATGGGACGTGACC 61.678 65.000 0.00 0.00 0.00 4.02
797 823 3.119779 AGAGACGGAGAAGAAATGTCGAC 60.120 47.826 9.11 9.11 34.82 4.20
853 894 1.586541 CTCGCACCTGCACAGACTA 59.413 57.895 0.00 0.00 42.21 2.59
854 895 2.341543 CTCGCACCTGCACAGACT 59.658 61.111 0.00 0.00 42.21 3.24
855 896 2.715532 TTCCTCGCACCTGCACAGAC 62.716 60.000 0.00 0.00 42.21 3.51
856 897 2.440385 CTTCCTCGCACCTGCACAGA 62.440 60.000 0.00 0.00 42.21 3.41
857 898 2.031012 TTCCTCGCACCTGCACAG 59.969 61.111 0.00 0.00 42.21 3.66
858 899 2.031012 CTTCCTCGCACCTGCACA 59.969 61.111 0.00 0.00 42.21 4.57
859 900 3.426568 GCTTCCTCGCACCTGCAC 61.427 66.667 0.00 0.00 42.21 4.57
860 901 3.596066 GAGCTTCCTCGCACCTGCA 62.596 63.158 0.00 0.00 42.21 4.41
898 939 0.307760 GGTGCACAGACGGAAAACAG 59.692 55.000 20.43 0.00 0.00 3.16
939 980 3.488678 CGCTACAACTGAGCTACATCATG 59.511 47.826 0.00 0.00 37.81 3.07
982 1023 2.202864 GGCCTCTGCTCTCGCTTC 60.203 66.667 0.00 0.00 37.74 3.86
1329 1378 1.671379 GAGAAAGCCGGCGAAAGGT 60.671 57.895 23.20 4.57 0.00 3.50
1488 1792 1.334779 CGTACTACCTACTCGCCATGC 60.335 57.143 0.00 0.00 0.00 4.06
1489 1793 1.945394 ACGTACTACCTACTCGCCATG 59.055 52.381 0.00 0.00 0.00 3.66
1490 1794 2.216898 GACGTACTACCTACTCGCCAT 58.783 52.381 0.00 0.00 0.00 4.40
1493 1797 0.579156 CGGACGTACTACCTACTCGC 59.421 60.000 0.00 0.00 0.00 5.03
1521 2133 1.589716 GCATGGAGTGTTGGAGCCAC 61.590 60.000 0.00 0.00 32.42 5.01
1750 3199 2.202690 CGGAAGGCGTCGCATACA 60.203 61.111 20.50 0.00 0.00 2.29
2502 3999 1.748122 TCGACGTACTCCTCCTGCC 60.748 63.158 0.00 0.00 0.00 4.85
2574 4074 0.532573 TTTCACCTAGAGGCTGCGAG 59.467 55.000 0.00 0.00 39.32 5.03
2576 4076 2.029838 ATTTTCACCTAGAGGCTGCG 57.970 50.000 0.00 0.00 39.32 5.18
2577 4077 3.313803 GCTTATTTTCACCTAGAGGCTGC 59.686 47.826 0.00 0.00 39.32 5.25
2598 4098 1.824230 TCCATGGTTTTATGGCACTGC 59.176 47.619 12.58 0.00 45.83 4.40
2623 4123 1.669115 GACACGAGTGGCAGTGCAT 60.669 57.895 18.61 1.36 41.72 3.96
2625 4125 1.560860 GAAGACACGAGTGGCAGTGC 61.561 60.000 12.04 6.55 42.32 4.40
2739 4268 7.309194 GGCAAGGTAGTGTTTTTACATCATCTT 60.309 37.037 0.00 0.00 0.00 2.40
2748 6913 6.937392 AGTTTTTGGCAAGGTAGTGTTTTTA 58.063 32.000 0.00 0.00 0.00 1.52
2767 6932 3.844640 AGTGCCCTAAATGGTGAGTTTT 58.155 40.909 0.00 0.00 0.00 2.43
2808 6973 3.864686 CAGTGGCGGCCGAAATCG 61.865 66.667 33.48 9.91 39.44 3.34
2848 7013 0.405198 TTGAGTGGATGTGGTGGCAT 59.595 50.000 0.00 0.00 0.00 4.40
2849 7014 0.405198 ATTGAGTGGATGTGGTGGCA 59.595 50.000 0.00 0.00 0.00 4.92
2854 7019 2.698803 TCGACAATTGAGTGGATGTGG 58.301 47.619 13.59 0.00 0.00 4.17
2855 7020 5.178252 GGATATCGACAATTGAGTGGATGTG 59.822 44.000 13.59 0.00 37.49 3.21
2864 7029 1.136690 GCGCGGATATCGACAATTGA 58.863 50.000 13.59 0.00 42.43 2.57
2866 7031 1.282248 CGGCGCGGATATCGACAATT 61.282 55.000 9.72 0.00 42.43 2.32
2869 7034 4.994201 GCGGCGCGGATATCGACA 62.994 66.667 19.09 0.00 42.43 4.35
2871 7036 3.964221 GATGCGGCGCGGATATCGA 62.964 63.158 28.09 7.12 38.17 3.59
2872 7037 3.545481 GATGCGGCGCGGATATCG 61.545 66.667 28.09 8.22 38.17 2.92
2885 7050 0.525668 CAGGTGGACTACGTCGATGC 60.526 60.000 4.06 0.00 32.65 3.91
2890 7055 0.032952 TGTTGCAGGTGGACTACGTC 59.967 55.000 0.00 0.00 0.00 4.34
2895 7060 1.525995 CGGTTGTTGCAGGTGGACT 60.526 57.895 0.00 0.00 0.00 3.85
2897 7062 2.904866 GCGGTTGTTGCAGGTGGA 60.905 61.111 0.00 0.00 0.00 4.02
2903 7068 3.053291 GGATCGGCGGTTGTTGCA 61.053 61.111 7.21 0.00 0.00 4.08
2955 7120 2.181021 GGCGTGGATTCGACGACT 59.819 61.111 22.90 0.00 41.84 4.18
2959 7124 0.876342 GATGAGGGCGTGGATTCGAC 60.876 60.000 0.00 0.00 38.22 4.20
2962 7127 1.227973 GGGATGAGGGCGTGGATTC 60.228 63.158 0.00 0.00 0.00 2.52
2967 7132 2.965716 GATTGGGGGATGAGGGCGTG 62.966 65.000 0.00 0.00 0.00 5.34
2973 7138 5.413833 CGAAATCAATAGATTGGGGGATGAG 59.586 44.000 2.52 0.00 43.52 2.90
3116 7283 0.736636 ACATGATCTCGACGGCGTAA 59.263 50.000 14.74 2.97 38.98 3.18
3133 7300 3.356639 GATGTCTCGCCCTCGCACA 62.357 63.158 0.00 0.00 34.35 4.57
3177 7368 0.596577 TCGTACCTCCATGCTATCGC 59.403 55.000 0.00 0.00 0.00 4.58
3237 7428 2.223340 CCTCAGCGGTGCATTTTACATC 60.223 50.000 10.38 0.00 0.00 3.06
3243 7434 3.064324 GGCCTCAGCGGTGCATTT 61.064 61.111 10.38 0.00 41.24 2.32
3254 7445 0.618458 ATAACGCTTTCCTGGCCTCA 59.382 50.000 3.32 0.00 0.00 3.86
3260 7451 3.871006 TCTGCATGTATAACGCTTTCCTG 59.129 43.478 0.00 0.00 0.00 3.86
3264 7455 3.941483 AGCTTCTGCATGTATAACGCTTT 59.059 39.130 0.00 0.00 42.74 3.51
3266 7457 3.126831 GAGCTTCTGCATGTATAACGCT 58.873 45.455 0.00 0.59 42.74 5.07
3394 7585 2.104928 CTCGGCGCTGATACTGCA 59.895 61.111 21.31 0.00 0.00 4.41
3507 7708 8.950208 ATAGTTTCATTAGCTCTTGGAAGTAC 57.050 34.615 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.