Multiple sequence alignment - TraesCS2B01G461700

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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 TraesCS2B01G461700 chr2B 100.000 3678 0 0 1 3678 655217337 655213660 0.000000e+00 6793.0
1 TraesCS2B01G461700 chr2B 90.718 571 41 3 1 559 82423848 82423278 0.000000e+00 750.0
2 TraesCS2B01G461700 chr2B 78.947 95 9 7 481 565 42190109 42190202 2.000000e-03 54.7
3 TraesCS2B01G461700 chr2A 91.096 2235 120 34 566 2778 690909821 690911998 0.000000e+00 2952.0
4 TraesCS2B01G461700 chr2A 85.662 1911 171 63 924 2798 211335867 211334024 0.000000e+00 1916.0
5 TraesCS2B01G461700 chr2A 84.328 536 44 18 3157 3674 690912238 690912751 4.270000e-134 488.0
6 TraesCS2B01G461700 chrUn 91.652 1689 96 25 566 2242 319539205 319537550 0.000000e+00 2296.0
7 TraesCS2B01G461700 chrUn 89.358 545 24 9 2244 2778 307429158 307428638 0.000000e+00 654.0
8 TraesCS2B01G461700 chrUn 84.328 536 44 18 3157 3674 307428398 307427885 4.270000e-134 488.0
9 TraesCS2B01G461700 chrUn 89.796 49 2 3 3080 3125 196943398 196943350 3.970000e-05 60.2
10 TraesCS2B01G461700 chr2D 94.524 1333 64 6 663 1991 548259669 548258342 0.000000e+00 2049.0
11 TraesCS2B01G461700 chr2D 87.357 1226 107 27 756 1976 195731711 195730529 0.000000e+00 1362.0
12 TraesCS2B01G461700 chr2D 92.639 720 33 7 2056 2765 548258313 548257604 0.000000e+00 1018.0
13 TraesCS2B01G461700 chr2D 90.925 573 36 8 1 562 519143846 519144413 0.000000e+00 756.0
14 TraesCS2B01G461700 chr2D 83.470 732 80 23 2056 2778 195728716 195728017 0.000000e+00 643.0
15 TraesCS2B01G461700 chr2D 87.425 501 34 15 3146 3642 548257177 548256702 1.930000e-152 549.0
16 TraesCS2B01G461700 chr2D 91.626 406 14 7 3282 3678 548256629 548256235 8.980000e-151 544.0
17 TraesCS2B01G461700 chr2D 95.283 106 5 0 568 673 548261400 548261295 6.320000e-38 169.0
18 TraesCS2B01G461700 chr5D 86.583 1282 117 33 998 2274 372566637 372567868 0.000000e+00 1363.0
19 TraesCS2B01G461700 chr5D 92.114 317 19 2 2355 2671 372567925 372568235 3.370000e-120 442.0
20 TraesCS2B01G461700 chr5D 97.222 36 1 0 3083 3118 135719395 135719430 1.100000e-05 62.1
21 TraesCS2B01G461700 chr5D 94.872 39 2 0 3083 3121 408763874 408763836 1.100000e-05 62.1
22 TraesCS2B01G461700 chr6D 90.000 1030 77 17 982 1999 454649421 454648406 0.000000e+00 1308.0
23 TraesCS2B01G461700 chr6D 89.782 1008 81 15 995 1999 454653874 454654862 0.000000e+00 1271.0
24 TraesCS2B01G461700 chr6D 92.000 575 36 3 1 565 471362476 471361902 0.000000e+00 798.0
25 TraesCS2B01G461700 chr6D 91.319 576 37 5 1 565 62874960 62875533 0.000000e+00 774.0
26 TraesCS2B01G461700 chr6D 89.043 575 40 3 1 566 59104429 59103869 0.000000e+00 691.0
27 TraesCS2B01G461700 chr6D 86.656 637 60 19 2050 2675 454654875 454655497 0.000000e+00 682.0
28 TraesCS2B01G461700 chr6D 83.210 673 61 29 2027 2675 454648408 454647764 1.480000e-158 569.0
29 TraesCS2B01G461700 chr6D 80.412 485 56 24 95 559 59137955 59138420 2.120000e-87 333.0
30 TraesCS2B01G461700 chr6B 90.030 1013 81 12 994 1999 691338736 691337737 0.000000e+00 1293.0
31 TraesCS2B01G461700 chr6B 89.930 1003 81 14 976 1974 691617327 691618313 0.000000e+00 1275.0
32 TraesCS2B01G461700 chr6B 92.619 569 32 3 1 559 625076447 625075879 0.000000e+00 809.0
33 TraesCS2B01G461700 chr6B 83.283 658 66 24 2027 2675 691337739 691337117 1.920000e-157 566.0
34 TraesCS2B01G461700 chr6B 84.550 589 64 14 2099 2683 691627092 691627657 3.210000e-155 558.0
35 TraesCS2B01G461700 chr6A 88.487 1051 83 18 958 1999 600884162 600885183 0.000000e+00 1236.0
36 TraesCS2B01G461700 chr6A 85.758 653 63 16 2027 2675 600885181 600885807 0.000000e+00 664.0
37 TraesCS2B01G461700 chr6A 91.129 496 29 8 3183 3674 146499420 146499904 0.000000e+00 658.0
38 TraesCS2B01G461700 chr6A 92.857 42 2 1 3082 3123 481047034 481046994 3.970000e-05 60.2
39 TraesCS2B01G461700 chr5B 91.916 569 36 2 1 559 680249134 680249702 0.000000e+00 787.0
40 TraesCS2B01G461700 chr7D 91.783 572 35 5 1 562 514979296 514978727 0.000000e+00 785.0
41 TraesCS2B01G461700 chr7D 94.872 39 2 0 3083 3121 235581304 235581266 1.100000e-05 62.1
42 TraesCS2B01G461700 chr4A 91.084 572 40 4 1 562 695039104 695038534 0.000000e+00 763.0
43 TraesCS2B01G461700 chr4A 97.297 37 1 0 3085 3121 658953510 658953546 3.070000e-06 63.9
44 TraesCS2B01G461700 chr3B 91.037 569 41 3 1 559 92661690 92662258 0.000000e+00 760.0
45 TraesCS2B01G461700 chr7B 100.000 36 0 0 3083 3118 707519335 707519370 2.370000e-07 67.6
46 TraesCS2B01G461700 chr4D 97.222 36 1 0 3083 3118 98910478 98910513 1.100000e-05 62.1
47 TraesCS2B01G461700 chr3D 94.872 39 2 0 3083 3121 428545817 428545779 1.100000e-05 62.1


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 TraesCS2B01G461700 chr2B 655213660 655217337 3677 True 6793.0 6793 100.0000 1 3678 1 chr2B.!!$R2 3677
1 TraesCS2B01G461700 chr2B 82423278 82423848 570 True 750.0 750 90.7180 1 559 1 chr2B.!!$R1 558
2 TraesCS2B01G461700 chr2A 211334024 211335867 1843 True 1916.0 1916 85.6620 924 2798 1 chr2A.!!$R1 1874
3 TraesCS2B01G461700 chr2A 690909821 690912751 2930 False 1720.0 2952 87.7120 566 3674 2 chr2A.!!$F1 3108
4 TraesCS2B01G461700 chrUn 319537550 319539205 1655 True 2296.0 2296 91.6520 566 2242 1 chrUn.!!$R2 1676
5 TraesCS2B01G461700 chrUn 307427885 307429158 1273 True 571.0 654 86.8430 2244 3674 2 chrUn.!!$R3 1430
6 TraesCS2B01G461700 chr2D 195728017 195731711 3694 True 1002.5 1362 85.4135 756 2778 2 chr2D.!!$R1 2022
7 TraesCS2B01G461700 chr2D 548256235 548261400 5165 True 865.8 2049 92.2994 568 3678 5 chr2D.!!$R2 3110
8 TraesCS2B01G461700 chr2D 519143846 519144413 567 False 756.0 756 90.9250 1 562 1 chr2D.!!$F1 561
9 TraesCS2B01G461700 chr5D 372566637 372568235 1598 False 902.5 1363 89.3485 998 2671 2 chr5D.!!$F2 1673
10 TraesCS2B01G461700 chr6D 454653874 454655497 1623 False 976.5 1271 88.2190 995 2675 2 chr6D.!!$F3 1680
11 TraesCS2B01G461700 chr6D 454647764 454649421 1657 True 938.5 1308 86.6050 982 2675 2 chr6D.!!$R3 1693
12 TraesCS2B01G461700 chr6D 471361902 471362476 574 True 798.0 798 92.0000 1 565 1 chr6D.!!$R2 564
13 TraesCS2B01G461700 chr6D 62874960 62875533 573 False 774.0 774 91.3190 1 565 1 chr6D.!!$F2 564
14 TraesCS2B01G461700 chr6D 59103869 59104429 560 True 691.0 691 89.0430 1 566 1 chr6D.!!$R1 565
15 TraesCS2B01G461700 chr6B 691617327 691618313 986 False 1275.0 1275 89.9300 976 1974 1 chr6B.!!$F1 998
16 TraesCS2B01G461700 chr6B 691337117 691338736 1619 True 929.5 1293 86.6565 994 2675 2 chr6B.!!$R2 1681
17 TraesCS2B01G461700 chr6B 625075879 625076447 568 True 809.0 809 92.6190 1 559 1 chr6B.!!$R1 558
18 TraesCS2B01G461700 chr6B 691627092 691627657 565 False 558.0 558 84.5500 2099 2683 1 chr6B.!!$F2 584
19 TraesCS2B01G461700 chr6A 600884162 600885807 1645 False 950.0 1236 87.1225 958 2675 2 chr6A.!!$F2 1717
20 TraesCS2B01G461700 chr5B 680249134 680249702 568 False 787.0 787 91.9160 1 559 1 chr5B.!!$F1 558
21 TraesCS2B01G461700 chr7D 514978727 514979296 569 True 785.0 785 91.7830 1 562 1 chr7D.!!$R2 561
22 TraesCS2B01G461700 chr4A 695038534 695039104 570 True 763.0 763 91.0840 1 562 1 chr4A.!!$R1 561
23 TraesCS2B01G461700 chr3B 92661690 92662258 568 False 760.0 760 91.0370 1 559 1 chr3B.!!$F1 558

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
537 557 0.098200 CGAAGTCAGATGTACGCCGA 59.902 55.000 0.00 0.0 0.00 5.54 F
1036 2708 0.318784 AGTCGTGGCACTCGTTCTTC 60.319 55.000 16.72 0.0 46.06 2.87 F
1992 3681 1.270625 TGACTGACCGGTGAATCAACC 60.271 52.381 14.63 0.0 36.82 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 5525 0.306840 TCTGTGTCACGAGTCACGAC 59.693 55.0 5.87 2.63 45.77 4.34 R
2069 5536 0.961753 TCATGCTCTGTGTCACGAGT 59.038 50.0 19.19 5.11 0.00 4.18 R
3113 6873 0.528470 GCCTAGTCTGTGAACGCTCT 59.472 55.0 0.00 0.00 0.00 4.09 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
172 176 2.534019 CGATCCACCGGCCAAATCG 61.534 63.158 0.00 8.08 34.06 3.34
198 202 0.952659 ATGGAGGGGGATCTAGTGGT 59.047 55.000 0.00 0.00 0.00 4.16
206 210 3.202151 GGGGGATCTAGTGGTTGATTTGA 59.798 47.826 0.00 0.00 0.00 2.69
307 326 2.576191 CTCCCCTCACAACCTTATCCAA 59.424 50.000 0.00 0.00 0.00 3.53
386 406 1.765074 GGTAGGTCCCTTTGCCACA 59.235 57.895 0.00 0.00 0.00 4.17
390 410 1.072266 AGGTCCCTTTGCCACATGTA 58.928 50.000 0.00 0.00 0.00 2.29
395 415 1.518325 CCTTTGCCACATGTACACGA 58.482 50.000 0.00 0.00 0.00 4.35
396 416 2.083774 CCTTTGCCACATGTACACGAT 58.916 47.619 0.00 0.00 0.00 3.73
405 425 3.001464 CACATGTACACGATCGTTAACGG 60.001 47.826 26.51 16.39 40.29 4.44
413 433 1.143969 GATCGTTAACGGCCAGACGG 61.144 60.000 26.51 0.00 40.29 4.79
468 488 1.379642 GCCTGTACGTACCTACCGCT 61.380 60.000 22.43 0.00 0.00 5.52
479 499 3.786884 CTACCGCTAGGGCCTCCGA 62.787 68.421 23.24 7.65 43.47 4.55
488 508 3.766691 GGCCTCCGACGGTAGCAA 61.767 66.667 24.94 3.03 0.00 3.91
489 509 2.263540 GCCTCCGACGGTAGCAAA 59.736 61.111 20.88 0.00 0.00 3.68
490 510 1.375013 GCCTCCGACGGTAGCAAAA 60.375 57.895 20.88 0.00 0.00 2.44
491 511 1.359459 GCCTCCGACGGTAGCAAAAG 61.359 60.000 20.88 7.59 0.00 2.27
492 512 0.739813 CCTCCGACGGTAGCAAAAGG 60.740 60.000 14.79 7.48 0.00 3.11
493 513 0.739813 CTCCGACGGTAGCAAAAGGG 60.740 60.000 14.79 0.00 0.00 3.95
494 514 1.004200 CCGACGGTAGCAAAAGGGT 60.004 57.895 5.48 0.00 0.00 4.34
495 515 1.017701 CCGACGGTAGCAAAAGGGTC 61.018 60.000 5.48 0.00 0.00 4.46
496 516 0.320073 CGACGGTAGCAAAAGGGTCA 60.320 55.000 0.00 0.00 0.00 4.02
497 517 1.874739 CGACGGTAGCAAAAGGGTCAA 60.875 52.381 0.00 0.00 0.00 3.18
498 518 2.223745 GACGGTAGCAAAAGGGTCAAA 58.776 47.619 0.00 0.00 0.00 2.69
499 519 2.817844 GACGGTAGCAAAAGGGTCAAAT 59.182 45.455 0.00 0.00 0.00 2.32
500 520 2.817844 ACGGTAGCAAAAGGGTCAAATC 59.182 45.455 0.00 0.00 0.00 2.17
501 521 3.081804 CGGTAGCAAAAGGGTCAAATCT 58.918 45.455 0.00 0.00 0.00 2.40
502 522 3.127030 CGGTAGCAAAAGGGTCAAATCTC 59.873 47.826 0.00 0.00 0.00 2.75
503 523 3.127030 GGTAGCAAAAGGGTCAAATCTCG 59.873 47.826 0.00 0.00 0.00 4.04
504 524 3.140325 AGCAAAAGGGTCAAATCTCGA 57.860 42.857 0.00 0.00 0.00 4.04
505 525 3.486383 AGCAAAAGGGTCAAATCTCGAA 58.514 40.909 0.00 0.00 0.00 3.71
506 526 3.888930 AGCAAAAGGGTCAAATCTCGAAA 59.111 39.130 0.00 0.00 0.00 3.46
507 527 4.524328 AGCAAAAGGGTCAAATCTCGAAAT 59.476 37.500 0.00 0.00 0.00 2.17
508 528 5.011023 AGCAAAAGGGTCAAATCTCGAAATT 59.989 36.000 0.00 0.00 0.00 1.82
509 529 5.696270 GCAAAAGGGTCAAATCTCGAAATTT 59.304 36.000 0.00 0.00 0.00 1.82
510 530 6.202762 GCAAAAGGGTCAAATCTCGAAATTTT 59.797 34.615 0.00 0.00 0.00 1.82
511 531 7.254761 GCAAAAGGGTCAAATCTCGAAATTTTT 60.255 33.333 0.00 0.00 0.00 1.94
512 532 7.946655 AAAGGGTCAAATCTCGAAATTTTTC 57.053 32.000 0.00 0.00 0.00 2.29
513 533 6.025749 AGGGTCAAATCTCGAAATTTTTCC 57.974 37.500 0.00 0.57 33.68 3.13
514 534 5.538433 AGGGTCAAATCTCGAAATTTTTCCA 59.462 36.000 13.15 0.00 33.68 3.53
515 535 6.211384 AGGGTCAAATCTCGAAATTTTTCCAT 59.789 34.615 13.15 6.36 33.68 3.41
516 536 7.396055 AGGGTCAAATCTCGAAATTTTTCCATA 59.604 33.333 13.15 0.00 33.68 2.74
517 537 7.488150 GGGTCAAATCTCGAAATTTTTCCATAC 59.512 37.037 13.15 0.30 33.68 2.39
518 538 7.488150 GGTCAAATCTCGAAATTTTTCCATACC 59.512 37.037 0.00 0.00 33.68 2.73
519 539 7.218204 GTCAAATCTCGAAATTTTTCCATACCG 59.782 37.037 0.00 0.00 33.68 4.02
520 540 6.995511 AATCTCGAAATTTTTCCATACCGA 57.004 33.333 0.00 0.00 33.68 4.69
521 541 6.995511 ATCTCGAAATTTTTCCATACCGAA 57.004 33.333 0.00 0.00 33.68 4.30
522 542 6.417191 TCTCGAAATTTTTCCATACCGAAG 57.583 37.500 0.00 0.00 33.68 3.79
523 543 5.935789 TCTCGAAATTTTTCCATACCGAAGT 59.064 36.000 0.00 0.00 33.68 3.01
524 544 6.091713 TCTCGAAATTTTTCCATACCGAAGTC 59.908 38.462 0.00 0.00 33.68 3.01
525 545 5.701750 TCGAAATTTTTCCATACCGAAGTCA 59.298 36.000 0.00 0.00 33.68 3.41
526 546 6.021596 CGAAATTTTTCCATACCGAAGTCAG 58.978 40.000 0.00 0.00 33.68 3.51
527 547 6.128391 CGAAATTTTTCCATACCGAAGTCAGA 60.128 38.462 0.00 0.00 33.68 3.27
528 548 7.414098 CGAAATTTTTCCATACCGAAGTCAGAT 60.414 37.037 0.00 0.00 33.68 2.90
529 549 6.683974 ATTTTTCCATACCGAAGTCAGATG 57.316 37.500 0.00 0.00 0.00 2.90
530 550 4.819105 TTTCCATACCGAAGTCAGATGT 57.181 40.909 0.00 0.00 0.00 3.06
531 551 5.925506 TTTCCATACCGAAGTCAGATGTA 57.074 39.130 0.00 0.00 0.00 2.29
532 552 4.913335 TCCATACCGAAGTCAGATGTAC 57.087 45.455 0.00 0.00 0.00 2.90
533 553 3.314357 TCCATACCGAAGTCAGATGTACG 59.686 47.826 0.00 0.00 0.00 3.67
534 554 2.838386 TACCGAAGTCAGATGTACGC 57.162 50.000 0.00 0.00 0.00 4.42
535 555 0.172803 ACCGAAGTCAGATGTACGCC 59.827 55.000 0.00 0.00 0.00 5.68
536 556 0.866061 CCGAAGTCAGATGTACGCCG 60.866 60.000 0.00 0.00 0.00 6.46
537 557 0.098200 CGAAGTCAGATGTACGCCGA 59.902 55.000 0.00 0.00 0.00 5.54
538 558 1.466866 CGAAGTCAGATGTACGCCGAA 60.467 52.381 0.00 0.00 0.00 4.30
539 559 2.602878 GAAGTCAGATGTACGCCGAAA 58.397 47.619 0.00 0.00 0.00 3.46
540 560 2.279582 AGTCAGATGTACGCCGAAAG 57.720 50.000 0.00 0.00 0.00 2.62
555 575 3.408288 CGAAAGGGTCAAAACACGAAA 57.592 42.857 0.00 0.00 32.44 3.46
556 576 3.959943 CGAAAGGGTCAAAACACGAAAT 58.040 40.909 0.00 0.00 32.44 2.17
557 577 4.356289 CGAAAGGGTCAAAACACGAAATT 58.644 39.130 0.00 0.00 32.44 1.82
558 578 4.801516 CGAAAGGGTCAAAACACGAAATTT 59.198 37.500 0.00 0.00 32.44 1.82
559 579 5.289917 CGAAAGGGTCAAAACACGAAATTTT 59.710 36.000 0.00 0.00 32.44 1.82
560 580 6.415798 AAAGGGTCAAAACACGAAATTTTG 57.584 33.333 3.73 3.73 44.74 2.44
561 581 3.868661 AGGGTCAAAACACGAAATTTTGC 59.131 39.130 5.27 11.02 43.62 3.68
562 582 3.868661 GGGTCAAAACACGAAATTTTGCT 59.131 39.130 5.27 0.00 43.62 3.91
563 583 4.026062 GGGTCAAAACACGAAATTTTGCTC 60.026 41.667 5.27 11.09 43.62 4.26
564 584 4.026062 GGTCAAAACACGAAATTTTGCTCC 60.026 41.667 5.27 14.34 43.62 4.70
590 610 1.106944 TCGCACTCCGCATCCATCTA 61.107 55.000 0.00 0.00 42.60 1.98
601 621 0.896019 ATCCATCTACTCCTCCGCCG 60.896 60.000 0.00 0.00 0.00 6.46
603 623 2.913060 ATCTACTCCTCCGCCGGC 60.913 66.667 19.07 19.07 0.00 6.13
673 2329 7.554959 AGTTGTCTGGACTCCTAAAAGAATA 57.445 36.000 0.00 0.00 0.00 1.75
773 2430 6.599244 TCAAGAGCATATACCCTTTTTGTCTG 59.401 38.462 0.00 0.00 0.00 3.51
777 2434 6.911308 AGCATATACCCTTTTTGTCTGGTAT 58.089 36.000 0.00 0.00 44.25 2.73
812 2472 1.064952 AGCGTTTTCAAGTTCGTTGGG 59.935 47.619 0.00 0.00 36.71 4.12
844 2504 7.093354 GGATTCTTTCTTGTTTGAAATCTCCC 58.907 38.462 0.00 0.00 35.68 4.30
848 2508 3.146066 TCTTGTTTGAAATCTCCCGTGG 58.854 45.455 0.00 0.00 0.00 4.94
849 2509 1.904287 TGTTTGAAATCTCCCGTGGG 58.096 50.000 0.00 0.00 0.00 4.61
855 2515 1.209504 GAAATCTCCCGTGGGTCATGA 59.790 52.381 4.53 0.00 36.47 3.07
937 2605 6.434340 TCATGCTCGCCTATATATTCCGATAT 59.566 38.462 0.00 0.00 33.17 1.63
938 2606 6.255596 TGCTCGCCTATATATTCCGATATC 57.744 41.667 0.00 0.00 31.09 1.63
1033 2705 1.269166 CATAGTCGTGGCACTCGTTC 58.731 55.000 16.72 1.56 46.06 3.95
1036 2708 0.318784 AGTCGTGGCACTCGTTCTTC 60.319 55.000 16.72 0.00 46.06 2.87
1053 2728 4.477975 CTCACCGCCTCGTCCGTC 62.478 72.222 0.00 0.00 0.00 4.79
1742 3421 3.971702 GAAGGCCAGCCAGGTGGT 61.972 66.667 16.71 0.00 40.09 4.16
1991 3680 1.798813 GTGACTGACCGGTGAATCAAC 59.201 52.381 14.63 0.00 0.00 3.18
1992 3681 1.270625 TGACTGACCGGTGAATCAACC 60.271 52.381 14.63 0.00 36.82 3.77
2012 5450 2.291465 CCATTCCACAATGTATCGGCAG 59.709 50.000 0.00 0.00 38.22 4.85
2014 5452 2.779755 TCCACAATGTATCGGCAGTT 57.220 45.000 0.00 0.00 0.00 3.16
2034 5490 1.687563 GGCAACAACTACCAACCTGT 58.312 50.000 0.00 0.00 0.00 4.00
2068 5535 4.176271 ACTCATGATATGTGTGTGTCGTG 58.824 43.478 0.00 0.00 35.84 4.35
2069 5536 4.082245 ACTCATGATATGTGTGTGTCGTGA 60.082 41.667 0.00 0.00 35.84 4.35
2070 5537 4.173256 TCATGATATGTGTGTGTCGTGAC 58.827 43.478 0.00 0.00 33.13 3.67
2104 5571 2.756760 GCATGAGGAGATTGCCAAGAAA 59.243 45.455 0.00 0.00 0.00 2.52
2683 6304 1.144936 GGCCTCTCCTTGATCGTGG 59.855 63.158 0.00 0.00 0.00 4.94
2688 6316 0.911769 TCTCCTTGATCGTGGCCAAT 59.088 50.000 7.24 0.00 0.00 3.16
2698 6326 0.888736 CGTGGCCAATCCTCACAACA 60.889 55.000 7.24 0.00 35.26 3.33
2705 6333 3.426695 GCCAATCCTCACAACAAATCTCG 60.427 47.826 0.00 0.00 0.00 4.04
2709 6337 6.238211 CCAATCCTCACAACAAATCTCGATAC 60.238 42.308 0.00 0.00 0.00 2.24
2715 6343 5.580691 TCACAACAAATCTCGATACCATGAC 59.419 40.000 0.00 0.00 0.00 3.06
2773 6405 4.037446 GCAGTGGACTAGAGAGATAAGTGG 59.963 50.000 0.00 0.00 0.00 4.00
2774 6406 5.441500 CAGTGGACTAGAGAGATAAGTGGA 58.558 45.833 0.00 0.00 0.00 4.02
2775 6407 5.888724 CAGTGGACTAGAGAGATAAGTGGAA 59.111 44.000 0.00 0.00 0.00 3.53
2776 6408 6.378564 CAGTGGACTAGAGAGATAAGTGGAAA 59.621 42.308 0.00 0.00 0.00 3.13
2777 6409 7.069331 CAGTGGACTAGAGAGATAAGTGGAAAT 59.931 40.741 0.00 0.00 0.00 2.17
2778 6410 8.282982 AGTGGACTAGAGAGATAAGTGGAAATA 58.717 37.037 0.00 0.00 0.00 1.40
2779 6411 8.915036 GTGGACTAGAGAGATAAGTGGAAATAA 58.085 37.037 0.00 0.00 0.00 1.40
2809 6487 0.953727 TGGAGACACACAATTGCAGC 59.046 50.000 5.05 0.00 33.40 5.25
2814 6492 1.002468 GACACACAATTGCAGCGTTCT 60.002 47.619 5.05 0.00 0.00 3.01
2815 6493 1.405105 ACACACAATTGCAGCGTTCTT 59.595 42.857 5.05 0.00 0.00 2.52
2816 6494 1.782569 CACACAATTGCAGCGTTCTTG 59.217 47.619 5.05 0.00 0.00 3.02
2817 6495 1.269206 ACACAATTGCAGCGTTCTTGG 60.269 47.619 5.05 0.00 0.00 3.61
2818 6496 0.318955 ACAATTGCAGCGTTCTTGGC 60.319 50.000 5.05 0.00 0.00 4.52
2824 6509 0.030638 GCAGCGTTCTTGGCTTTTCA 59.969 50.000 0.00 0.00 39.08 2.69
2828 6513 3.058293 CAGCGTTCTTGGCTTTTCATGTA 60.058 43.478 0.00 0.00 39.08 2.29
2863 6550 9.376075 ACATGTCTCAAGATAAGTAATCAACTG 57.624 33.333 0.00 0.00 38.88 3.16
2864 6551 8.824781 CATGTCTCAAGATAAGTAATCAACTGG 58.175 37.037 0.00 0.00 38.88 4.00
2875 6562 7.596749 AAGTAATCAACTGGTATTTGTCTCG 57.403 36.000 0.00 0.00 38.88 4.04
2895 6591 2.416547 CGCAAGATAAGTGTGGGAACAG 59.583 50.000 0.00 0.00 40.94 3.16
2898 6594 3.340814 AGATAAGTGTGGGAACAGCAG 57.659 47.619 0.00 0.00 44.46 4.24
2925 6621 5.782047 TGATTTGCTTCACAGTTATTTGGG 58.218 37.500 0.00 0.00 0.00 4.12
2929 6625 3.320541 TGCTTCACAGTTATTTGGGGTTG 59.679 43.478 0.00 0.00 0.00 3.77
2931 6627 4.038642 GCTTCACAGTTATTTGGGGTTGAA 59.961 41.667 0.00 0.00 0.00 2.69
2934 6652 4.339814 TCACAGTTATTTGGGGTTGAACAC 59.660 41.667 0.00 0.00 0.00 3.32
2940 6658 0.184933 TTGGGGTTGAACACTGGAGG 59.815 55.000 0.00 0.00 0.00 4.30
2954 6672 3.967326 CACTGGAGGTAGTATGGATCCAA 59.033 47.826 20.67 5.49 39.47 3.53
2993 6724 6.916440 AGTAGACCTCGTTTTGTTTTGTTTT 58.084 32.000 0.00 0.00 0.00 2.43
2994 6725 6.804783 AGTAGACCTCGTTTTGTTTTGTTTTG 59.195 34.615 0.00 0.00 0.00 2.44
2995 6726 5.534407 AGACCTCGTTTTGTTTTGTTTTGT 58.466 33.333 0.00 0.00 0.00 2.83
2996 6727 5.986741 AGACCTCGTTTTGTTTTGTTTTGTT 59.013 32.000 0.00 0.00 0.00 2.83
2997 6728 6.480651 AGACCTCGTTTTGTTTTGTTTTGTTT 59.519 30.769 0.00 0.00 0.00 2.83
2998 6729 7.011576 AGACCTCGTTTTGTTTTGTTTTGTTTT 59.988 29.630 0.00 0.00 0.00 2.43
2999 6730 7.473366 ACCTCGTTTTGTTTTGTTTTGTTTTT 58.527 26.923 0.00 0.00 0.00 1.94
3000 6731 7.429630 ACCTCGTTTTGTTTTGTTTTGTTTTTG 59.570 29.630 0.00 0.00 0.00 2.44
3001 6732 7.429630 CCTCGTTTTGTTTTGTTTTGTTTTTGT 59.570 29.630 0.00 0.00 0.00 2.83
3002 6733 8.669394 TCGTTTTGTTTTGTTTTGTTTTTGTT 57.331 23.077 0.00 0.00 0.00 2.83
3003 6734 9.124807 TCGTTTTGTTTTGTTTTGTTTTTGTTT 57.875 22.222 0.00 0.00 0.00 2.83
3042 6773 9.528018 TTTTGAAAGCAAAATGGAAACTACTAG 57.472 29.630 0.00 0.00 46.09 2.57
3043 6774 8.458573 TTGAAAGCAAAATGGAAACTACTAGA 57.541 30.769 0.00 0.00 0.00 2.43
3044 6775 7.871853 TGAAAGCAAAATGGAAACTACTAGAC 58.128 34.615 0.00 0.00 0.00 2.59
3045 6776 7.719633 TGAAAGCAAAATGGAAACTACTAGACT 59.280 33.333 0.00 0.00 0.00 3.24
3046 6777 9.216117 GAAAGCAAAATGGAAACTACTAGACTA 57.784 33.333 0.00 0.00 0.00 2.59
3047 6778 9.740710 AAAGCAAAATGGAAACTACTAGACTAT 57.259 29.630 0.00 0.00 0.00 2.12
3049 6780 9.819267 AGCAAAATGGAAACTACTAGACTATAC 57.181 33.333 0.00 0.00 0.00 1.47
3050 6781 9.819267 GCAAAATGGAAACTACTAGACTATACT 57.181 33.333 0.00 0.00 0.00 2.12
3095 6855 8.911918 AAAAAGGACAAATAAAAACATACCCC 57.088 30.769 0.00 0.00 0.00 4.95
3096 6856 6.614694 AAGGACAAATAAAAACATACCCCC 57.385 37.500 0.00 0.00 0.00 5.40
3097 6857 5.910931 AGGACAAATAAAAACATACCCCCT 58.089 37.500 0.00 0.00 0.00 4.79
3099 6859 5.955959 GGACAAATAAAAACATACCCCCTCT 59.044 40.000 0.00 0.00 0.00 3.69
3101 6861 6.319715 ACAAATAAAAACATACCCCCTCTGT 58.680 36.000 0.00 0.00 0.00 3.41
3102 6862 7.471890 ACAAATAAAAACATACCCCCTCTGTA 58.528 34.615 0.00 0.00 0.00 2.74
3103 6863 7.951245 ACAAATAAAAACATACCCCCTCTGTAA 59.049 33.333 0.00 0.00 0.00 2.41
3104 6864 8.808092 CAAATAAAAACATACCCCCTCTGTAAA 58.192 33.333 0.00 0.00 0.00 2.01
3106 6866 5.853572 AAAACATACCCCCTCTGTAAAGA 57.146 39.130 0.00 0.00 0.00 2.52
3107 6867 5.853572 AAACATACCCCCTCTGTAAAGAA 57.146 39.130 0.00 0.00 0.00 2.52
3109 6869 6.402981 AACATACCCCCTCTGTAAAGAAAT 57.597 37.500 0.00 0.00 0.00 2.17
3110 6870 7.519347 AACATACCCCCTCTGTAAAGAAATA 57.481 36.000 0.00 0.00 0.00 1.40
3111 6871 7.707467 ACATACCCCCTCTGTAAAGAAATAT 57.293 36.000 0.00 0.00 0.00 1.28
3112 6872 8.808240 ACATACCCCCTCTGTAAAGAAATATA 57.192 34.615 0.00 0.00 0.00 0.86
3113 6873 9.232882 ACATACCCCCTCTGTAAAGAAATATAA 57.767 33.333 0.00 0.00 0.00 0.98
3114 6874 9.726438 CATACCCCCTCTGTAAAGAAATATAAG 57.274 37.037 0.00 0.00 0.00 1.73
3115 6875 9.684702 ATACCCCCTCTGTAAAGAAATATAAGA 57.315 33.333 0.00 0.00 0.00 2.10
3116 6876 8.035448 ACCCCCTCTGTAAAGAAATATAAGAG 57.965 38.462 0.00 0.00 0.00 2.85
3117 6877 6.937465 CCCCCTCTGTAAAGAAATATAAGAGC 59.063 42.308 0.00 0.00 0.00 4.09
3118 6878 6.647067 CCCCTCTGTAAAGAAATATAAGAGCG 59.353 42.308 0.00 0.00 0.00 5.03
3119 6879 7.210873 CCCTCTGTAAAGAAATATAAGAGCGT 58.789 38.462 0.00 0.00 0.00 5.07
3120 6880 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
3121 6881 8.756864 CCTCTGTAAAGAAATATAAGAGCGTTC 58.243 37.037 0.00 0.00 0.00 3.95
3122 6882 9.302345 CTCTGTAAAGAAATATAAGAGCGTTCA 57.698 33.333 1.01 0.00 0.00 3.18
3123 6883 9.084164 TCTGTAAAGAAATATAAGAGCGTTCAC 57.916 33.333 1.01 0.00 0.00 3.18
3124 6884 8.766000 TGTAAAGAAATATAAGAGCGTTCACA 57.234 30.769 1.01 0.00 0.00 3.58
3125 6885 8.869897 TGTAAAGAAATATAAGAGCGTTCACAG 58.130 33.333 1.01 0.00 0.00 3.66
3126 6886 9.084164 GTAAAGAAATATAAGAGCGTTCACAGA 57.916 33.333 1.01 0.00 0.00 3.41
3127 6887 7.527084 AAGAAATATAAGAGCGTTCACAGAC 57.473 36.000 1.01 0.00 0.00 3.51
3128 6888 6.868622 AGAAATATAAGAGCGTTCACAGACT 58.131 36.000 1.01 0.00 0.00 3.24
3129 6889 7.997482 AGAAATATAAGAGCGTTCACAGACTA 58.003 34.615 1.01 0.00 0.00 2.59
3130 6890 8.132362 AGAAATATAAGAGCGTTCACAGACTAG 58.868 37.037 1.01 0.00 0.00 2.57
3131 6891 4.640789 ATAAGAGCGTTCACAGACTAGG 57.359 45.455 1.01 0.00 0.00 3.02
3132 6892 0.528470 AGAGCGTTCACAGACTAGGC 59.472 55.000 1.01 0.00 0.00 3.93
3133 6893 0.528470 GAGCGTTCACAGACTAGGCT 59.472 55.000 0.00 0.00 35.89 4.58
3134 6894 0.969894 AGCGTTCACAGACTAGGCTT 59.030 50.000 0.00 0.00 29.54 4.35
3135 6895 1.067495 AGCGTTCACAGACTAGGCTTC 60.067 52.381 0.00 0.00 29.54 3.86
3136 6896 1.067495 GCGTTCACAGACTAGGCTTCT 60.067 52.381 0.00 0.00 0.00 2.85
3137 6897 2.869897 CGTTCACAGACTAGGCTTCTC 58.130 52.381 0.00 0.00 0.00 2.87
3138 6898 2.229062 CGTTCACAGACTAGGCTTCTCA 59.771 50.000 0.00 0.00 0.00 3.27
3139 6899 3.305403 CGTTCACAGACTAGGCTTCTCAA 60.305 47.826 0.00 0.00 0.00 3.02
3140 6900 4.241681 GTTCACAGACTAGGCTTCTCAAG 58.758 47.826 0.00 0.00 0.00 3.02
3141 6901 3.501349 TCACAGACTAGGCTTCTCAAGT 58.499 45.455 0.00 0.00 0.00 3.16
3142 6902 4.663334 TCACAGACTAGGCTTCTCAAGTA 58.337 43.478 0.00 0.00 0.00 2.24
3143 6903 4.702612 TCACAGACTAGGCTTCTCAAGTAG 59.297 45.833 0.00 0.00 0.00 2.57
3144 6904 3.445805 ACAGACTAGGCTTCTCAAGTAGC 59.554 47.826 0.00 0.40 37.67 3.58
3165 6925 3.841643 CAACCACAGAGATTCCAAATGC 58.158 45.455 0.00 0.00 0.00 3.56
3175 6935 7.386848 ACAGAGATTCCAAATGCAATTTCTTTG 59.613 33.333 0.00 0.00 44.81 2.77
3201 6962 2.771089 TGCTCTTGTGTTTAGGCTCAG 58.229 47.619 0.00 0.00 0.00 3.35
3203 6964 3.323691 TGCTCTTGTGTTTAGGCTCAGTA 59.676 43.478 0.00 0.00 0.00 2.74
3204 6965 4.202315 TGCTCTTGTGTTTAGGCTCAGTAA 60.202 41.667 0.00 0.00 0.00 2.24
3205 6966 4.938226 GCTCTTGTGTTTAGGCTCAGTAAT 59.062 41.667 0.00 0.00 0.00 1.89
3207 6968 6.109156 TCTTGTGTTTAGGCTCAGTAATGA 57.891 37.500 0.00 0.00 0.00 2.57
3257 7018 6.844388 ACATAAGGTGGAGGTCAACATATCTA 59.156 38.462 0.00 0.00 34.94 1.98
3258 7019 7.347222 ACATAAGGTGGAGGTCAACATATCTAA 59.653 37.037 0.00 0.00 34.94 2.10
3458 7679 6.365520 AGGTTTACTTCATTTTCCACAGACT 58.634 36.000 0.00 0.00 0.00 3.24
3459 7680 6.486993 AGGTTTACTTCATTTTCCACAGACTC 59.513 38.462 0.00 0.00 0.00 3.36
3465 7686 1.967319 TTTTCCACAGACTCCACTGC 58.033 50.000 0.00 0.00 41.06 4.40
3479 7700 2.304761 TCCACTGCTTTCCCGAATTAGT 59.695 45.455 0.00 0.00 0.00 2.24
3488 7709 6.921307 TGCTTTCCCGAATTAGTTTTTCTTTC 59.079 34.615 0.00 0.00 0.00 2.62
3494 7715 7.021790 CCCGAATTAGTTTTTCTTTCTGCTAC 58.978 38.462 0.00 0.00 0.00 3.58
3495 7716 7.308348 CCCGAATTAGTTTTTCTTTCTGCTACA 60.308 37.037 0.00 0.00 0.00 2.74
3496 7717 8.073768 CCGAATTAGTTTTTCTTTCTGCTACAA 58.926 33.333 0.00 0.00 0.00 2.41
3497 7718 9.612620 CGAATTAGTTTTTCTTTCTGCTACAAT 57.387 29.630 0.00 0.00 0.00 2.71
3515 7736 3.074985 ACAATAGCCATCCTGCCACATAT 59.925 43.478 0.00 0.00 0.00 1.78
3516 7737 4.289410 ACAATAGCCATCCTGCCACATATA 59.711 41.667 0.00 0.00 0.00 0.86
3517 7738 5.044624 ACAATAGCCATCCTGCCACATATAT 60.045 40.000 0.00 0.00 0.00 0.86
3518 7739 6.158520 ACAATAGCCATCCTGCCACATATATA 59.841 38.462 0.00 0.00 0.00 0.86
3541 7762 3.181443 CCTACTGTCCAAGACCAAACCTT 60.181 47.826 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 5.156355 CCTTCATTTGGTCAGTTCAAATCG 58.844 41.667 0.00 0.00 41.28 3.34
103 104 1.006998 CCATCCCCCTTCATTTGGTCA 59.993 52.381 0.00 0.00 0.00 4.02
172 176 1.075748 ATCCCCCTCCATTGCTTGC 60.076 57.895 0.00 0.00 0.00 4.01
198 202 3.053395 CCTCTTCTCCCCCATCAAATCAA 60.053 47.826 0.00 0.00 0.00 2.57
206 210 2.272170 TCCCCCTCTTCTCCCCCAT 61.272 63.158 0.00 0.00 0.00 4.00
307 326 1.324005 GCTCTCTGGCGGTAGGTTCT 61.324 60.000 0.00 0.00 0.00 3.01
386 406 2.187707 GCCGTTAACGATCGTGTACAT 58.812 47.619 28.79 8.18 43.02 2.29
390 410 0.734942 CTGGCCGTTAACGATCGTGT 60.735 55.000 28.79 14.14 43.02 4.49
395 415 1.153706 CCGTCTGGCCGTTAACGAT 60.154 57.895 28.79 0.00 43.02 3.73
396 416 2.259204 CCGTCTGGCCGTTAACGA 59.741 61.111 28.79 8.63 43.02 3.85
413 433 2.435410 CGGTAGGTTCCCCAACGC 60.435 66.667 0.00 0.00 32.68 4.84
415 435 2.045634 GGCGGTAGGTTCCCCAAC 60.046 66.667 0.00 0.00 0.00 3.77
417 437 3.324108 GTGGCGGTAGGTTCCCCA 61.324 66.667 0.00 0.00 0.00 4.96
418 438 4.462280 CGTGGCGGTAGGTTCCCC 62.462 72.222 0.00 0.00 0.00 4.81
440 460 1.656818 TACGTACAGGCTACCACCGC 61.657 60.000 0.00 0.00 33.69 5.68
441 461 0.099436 GTACGTACAGGCTACCACCG 59.901 60.000 20.67 0.00 33.69 4.94
444 464 2.643551 GTAGGTACGTACAGGCTACCA 58.356 52.381 26.02 0.00 33.54 3.25
445 465 1.950216 GGTAGGTACGTACAGGCTACC 59.050 57.143 28.52 28.52 34.12 3.18
453 473 1.230324 CCCTAGCGGTAGGTACGTAC 58.770 60.000 32.70 17.56 44.27 3.67
468 488 2.194056 CTACCGTCGGAGGCCCTA 59.806 66.667 20.51 0.00 33.69 3.53
479 499 2.351706 TTTGACCCTTTTGCTACCGT 57.648 45.000 0.00 0.00 0.00 4.83
486 506 7.713764 AAAATTTCGAGATTTGACCCTTTTG 57.286 32.000 14.03 0.00 30.06 2.44
487 507 7.441157 GGAAAAATTTCGAGATTTGACCCTTTT 59.559 33.333 14.03 3.78 38.06 2.27
488 508 6.929049 GGAAAAATTTCGAGATTTGACCCTTT 59.071 34.615 14.03 4.43 38.06 3.11
489 509 6.041523 TGGAAAAATTTCGAGATTTGACCCTT 59.958 34.615 22.24 12.05 38.06 3.95
490 510 5.538433 TGGAAAAATTTCGAGATTTGACCCT 59.462 36.000 22.24 5.96 38.06 4.34
491 511 5.778862 TGGAAAAATTTCGAGATTTGACCC 58.221 37.500 22.24 18.55 38.06 4.46
492 512 7.488150 GGTATGGAAAAATTTCGAGATTTGACC 59.512 37.037 14.03 17.83 38.06 4.02
493 513 7.218204 CGGTATGGAAAAATTTCGAGATTTGAC 59.782 37.037 14.03 10.81 38.06 3.18
494 514 7.119992 TCGGTATGGAAAAATTTCGAGATTTGA 59.880 33.333 14.03 2.27 38.06 2.69
495 515 7.247728 TCGGTATGGAAAAATTTCGAGATTTG 58.752 34.615 14.03 0.08 38.06 2.32
496 516 7.385778 TCGGTATGGAAAAATTTCGAGATTT 57.614 32.000 8.04 8.04 38.06 2.17
497 517 6.995511 TCGGTATGGAAAAATTTCGAGATT 57.004 33.333 0.00 0.00 38.06 2.40
498 518 6.598064 ACTTCGGTATGGAAAAATTTCGAGAT 59.402 34.615 0.00 0.00 38.06 2.75
499 519 5.935789 ACTTCGGTATGGAAAAATTTCGAGA 59.064 36.000 0.00 0.00 38.06 4.04
500 520 6.128391 TGACTTCGGTATGGAAAAATTTCGAG 60.128 38.462 0.00 0.00 38.06 4.04
501 521 5.701750 TGACTTCGGTATGGAAAAATTTCGA 59.298 36.000 0.00 0.00 38.06 3.71
502 522 5.933790 TGACTTCGGTATGGAAAAATTTCG 58.066 37.500 0.00 0.00 38.06 3.46
503 523 7.141100 TCTGACTTCGGTATGGAAAAATTTC 57.859 36.000 0.00 0.00 36.46 2.17
504 524 7.176690 ACATCTGACTTCGGTATGGAAAAATTT 59.823 33.333 0.00 0.00 0.00 1.82
505 525 6.659242 ACATCTGACTTCGGTATGGAAAAATT 59.341 34.615 0.00 0.00 0.00 1.82
506 526 6.180472 ACATCTGACTTCGGTATGGAAAAAT 58.820 36.000 0.00 0.00 0.00 1.82
507 527 5.556915 ACATCTGACTTCGGTATGGAAAAA 58.443 37.500 0.00 0.00 0.00 1.94
508 528 5.160607 ACATCTGACTTCGGTATGGAAAA 57.839 39.130 0.00 0.00 0.00 2.29
509 529 4.819105 ACATCTGACTTCGGTATGGAAA 57.181 40.909 0.00 0.00 0.00 3.13
510 530 4.201980 CGTACATCTGACTTCGGTATGGAA 60.202 45.833 0.00 0.00 0.00 3.53
511 531 3.314357 CGTACATCTGACTTCGGTATGGA 59.686 47.826 0.00 0.00 0.00 3.41
512 532 3.629058 CGTACATCTGACTTCGGTATGG 58.371 50.000 0.00 0.00 0.00 2.74
513 533 3.043586 GCGTACATCTGACTTCGGTATG 58.956 50.000 0.00 0.00 0.00 2.39
514 534 2.034305 GGCGTACATCTGACTTCGGTAT 59.966 50.000 0.00 0.00 0.00 2.73
515 535 1.402968 GGCGTACATCTGACTTCGGTA 59.597 52.381 0.00 0.00 0.00 4.02
516 536 0.172803 GGCGTACATCTGACTTCGGT 59.827 55.000 0.00 0.00 0.00 4.69
517 537 0.866061 CGGCGTACATCTGACTTCGG 60.866 60.000 0.00 0.00 0.00 4.30
518 538 0.098200 TCGGCGTACATCTGACTTCG 59.902 55.000 6.85 0.00 0.00 3.79
519 539 2.273370 TTCGGCGTACATCTGACTTC 57.727 50.000 6.85 0.00 0.00 3.01
520 540 2.607187 CTTTCGGCGTACATCTGACTT 58.393 47.619 6.85 0.00 0.00 3.01
521 541 1.135083 CCTTTCGGCGTACATCTGACT 60.135 52.381 6.85 0.00 0.00 3.41
522 542 1.278238 CCTTTCGGCGTACATCTGAC 58.722 55.000 6.85 0.00 0.00 3.51
523 543 0.174845 CCCTTTCGGCGTACATCTGA 59.825 55.000 6.85 0.00 0.00 3.27
524 544 0.108329 ACCCTTTCGGCGTACATCTG 60.108 55.000 6.85 0.00 33.26 2.90
525 545 0.175073 GACCCTTTCGGCGTACATCT 59.825 55.000 6.85 0.00 33.26 2.90
526 546 0.108520 TGACCCTTTCGGCGTACATC 60.109 55.000 6.85 0.00 33.26 3.06
527 547 0.322322 TTGACCCTTTCGGCGTACAT 59.678 50.000 6.85 0.00 33.26 2.29
528 548 0.106335 TTTGACCCTTTCGGCGTACA 59.894 50.000 6.85 0.00 33.26 2.90
529 549 1.069703 GTTTTGACCCTTTCGGCGTAC 60.070 52.381 6.85 0.00 33.26 3.67
530 550 1.228533 GTTTTGACCCTTTCGGCGTA 58.771 50.000 6.85 0.00 33.26 4.42
531 551 0.748729 TGTTTTGACCCTTTCGGCGT 60.749 50.000 6.85 0.00 33.26 5.68
532 552 0.317519 GTGTTTTGACCCTTTCGGCG 60.318 55.000 0.00 0.00 33.26 6.46
533 553 0.317519 CGTGTTTTGACCCTTTCGGC 60.318 55.000 0.00 0.00 33.26 5.54
534 554 1.301423 TCGTGTTTTGACCCTTTCGG 58.699 50.000 0.00 0.00 37.81 4.30
535 555 3.408288 TTTCGTGTTTTGACCCTTTCG 57.592 42.857 0.00 0.00 0.00 3.46
536 556 6.474364 CAAAATTTCGTGTTTTGACCCTTTC 58.526 36.000 13.46 0.00 45.02 2.62
537 557 5.163804 GCAAAATTTCGTGTTTTGACCCTTT 60.164 36.000 19.19 0.00 45.02 3.11
538 558 4.331443 GCAAAATTTCGTGTTTTGACCCTT 59.669 37.500 19.19 0.00 45.02 3.95
539 559 3.868661 GCAAAATTTCGTGTTTTGACCCT 59.131 39.130 19.19 0.00 45.02 4.34
540 560 3.868661 AGCAAAATTTCGTGTTTTGACCC 59.131 39.130 19.19 7.93 45.02 4.46
541 561 4.026062 GGAGCAAAATTTCGTGTTTTGACC 60.026 41.667 19.19 16.87 45.02 4.02
542 562 4.564769 TGGAGCAAAATTTCGTGTTTTGAC 59.435 37.500 19.19 13.77 45.02 3.18
543 563 4.564769 GTGGAGCAAAATTTCGTGTTTTGA 59.435 37.500 19.19 3.75 45.02 2.69
544 564 4.547966 CGTGGAGCAAAATTTCGTGTTTTG 60.548 41.667 14.02 14.02 45.01 2.44
545 565 3.549873 CGTGGAGCAAAATTTCGTGTTTT 59.450 39.130 0.00 0.00 0.00 2.43
546 566 3.112580 CGTGGAGCAAAATTTCGTGTTT 58.887 40.909 0.00 0.00 0.00 2.83
547 567 2.542824 CCGTGGAGCAAAATTTCGTGTT 60.543 45.455 0.00 0.00 0.00 3.32
548 568 1.001815 CCGTGGAGCAAAATTTCGTGT 60.002 47.619 0.00 0.00 0.00 4.49
549 569 1.265635 TCCGTGGAGCAAAATTTCGTG 59.734 47.619 0.00 0.00 0.00 4.35
550 570 1.535462 CTCCGTGGAGCAAAATTTCGT 59.465 47.619 2.38 0.00 35.31 3.85
551 571 1.535462 ACTCCGTGGAGCAAAATTTCG 59.465 47.619 15.80 0.00 45.54 3.46
552 572 2.412847 CGACTCCGTGGAGCAAAATTTC 60.413 50.000 15.80 3.42 45.54 2.17
553 573 1.535462 CGACTCCGTGGAGCAAAATTT 59.465 47.619 15.80 0.00 45.54 1.82
554 574 1.156736 CGACTCCGTGGAGCAAAATT 58.843 50.000 15.80 0.00 45.54 1.82
555 575 1.298859 GCGACTCCGTGGAGCAAAAT 61.299 55.000 15.80 0.00 45.54 1.82
556 576 1.959226 GCGACTCCGTGGAGCAAAA 60.959 57.895 15.80 0.00 45.54 2.44
557 577 2.357034 GCGACTCCGTGGAGCAAA 60.357 61.111 15.80 0.00 45.54 3.68
558 578 3.611674 TGCGACTCCGTGGAGCAA 61.612 61.111 15.80 0.00 45.54 3.91
559 579 4.357947 GTGCGACTCCGTGGAGCA 62.358 66.667 15.80 6.52 45.54 4.26
560 580 3.973267 GAGTGCGACTCCGTGGAGC 62.973 68.421 15.80 7.87 45.54 4.70
561 581 2.179517 GAGTGCGACTCCGTGGAG 59.820 66.667 14.35 14.35 46.91 3.86
601 621 2.279784 CTTCGAGGAGCATCGGCC 60.280 66.667 4.67 0.00 42.93 6.13
673 2329 0.533491 ATGCACGCATGAAATTGGCT 59.467 45.000 3.17 0.00 35.03 4.75
812 2472 4.440839 AACAAGAAAGAATCCGCCATTC 57.559 40.909 0.00 0.00 41.37 2.67
844 2504 2.004583 ACACGTAATCATGACCCACG 57.995 50.000 18.70 18.70 38.52 4.94
848 2508 5.220154 CGTAGTTCAACACGTAATCATGACC 60.220 44.000 0.00 0.00 33.56 4.02
849 2509 5.720433 GCGTAGTTCAACACGTAATCATGAC 60.720 44.000 0.00 0.00 40.25 3.06
855 2515 3.029320 TGGCGTAGTTCAACACGTAAT 57.971 42.857 12.16 0.00 40.25 1.89
937 2605 1.458398 CTGGAGCTGAAGACGAGAGA 58.542 55.000 0.00 0.00 0.00 3.10
938 2606 0.179140 GCTGGAGCTGAAGACGAGAG 60.179 60.000 0.00 0.00 38.21 3.20
964 2632 3.124297 GTGTTAAGATGACACTGCTGCTC 59.876 47.826 0.00 0.00 43.07 4.26
1033 2705 2.182030 GGACGAGGCGGTGAGAAG 59.818 66.667 0.00 0.00 0.00 2.85
1036 2708 4.477975 GACGGACGAGGCGGTGAG 62.478 72.222 0.00 0.00 0.00 3.51
1053 2728 4.899239 GCGAGGAGGTGGATGGCG 62.899 72.222 0.00 0.00 0.00 5.69
1182 2861 2.121781 ATCCGGGCCTGGATCCAT 60.122 61.111 36.72 19.24 45.80 3.41
1193 2872 2.719979 CGTACCTGTCGATCCGGG 59.280 66.667 0.00 0.00 0.00 5.73
1750 3429 4.999939 CTTGCCGTTGCCGTTGCC 63.000 66.667 0.00 0.00 36.33 4.52
1751 3430 4.999939 CCTTGCCGTTGCCGTTGC 63.000 66.667 0.00 0.00 36.33 4.17
1752 3431 4.999939 GCCTTGCCGTTGCCGTTG 63.000 66.667 0.00 0.00 36.33 4.10
1991 3680 2.291465 CTGCCGATACATTGTGGAATGG 59.709 50.000 0.00 0.00 43.00 3.16
1992 3681 2.945008 ACTGCCGATACATTGTGGAATG 59.055 45.455 0.00 0.00 44.11 2.67
2014 5452 1.064314 ACAGGTTGGTAGTTGTTGCCA 60.064 47.619 0.00 0.00 40.09 4.92
2063 5525 0.306840 TCTGTGTCACGAGTCACGAC 59.693 55.000 5.87 2.63 45.77 4.34
2068 5535 1.068264 TCATGCTCTGTGTCACGAGTC 60.068 52.381 19.19 14.19 0.00 3.36
2069 5536 0.961753 TCATGCTCTGTGTCACGAGT 59.038 50.000 19.19 5.11 0.00 4.18
2070 5537 1.626747 CTCATGCTCTGTGTCACGAG 58.373 55.000 15.93 15.93 0.00 4.18
2104 5571 2.668550 GCCTCGCCGTCACCTTTT 60.669 61.111 0.00 0.00 0.00 2.27
2304 5810 1.899814 TCTCGGCAAGTTGGTAGTGAT 59.100 47.619 4.75 0.00 0.00 3.06
2306 5812 2.163818 TTCTCGGCAAGTTGGTAGTG 57.836 50.000 4.75 0.00 0.00 2.74
2683 6304 3.426695 CGAGATTTGTTGTGAGGATTGGC 60.427 47.826 0.00 0.00 0.00 4.52
2688 6316 4.221924 TGGTATCGAGATTTGTTGTGAGGA 59.778 41.667 0.00 0.00 0.00 3.71
2698 6326 2.698797 ACCGGTCATGGTATCGAGATTT 59.301 45.455 0.00 0.00 41.55 2.17
2779 6411 4.460263 TGTGTGTCTCCAGCTACATTTTT 58.540 39.130 0.00 0.00 0.00 1.94
2809 6487 3.914364 GCTTACATGAAAAGCCAAGAACG 59.086 43.478 20.07 0.00 42.85 3.95
2838 6523 8.824781 CCAGTTGATTACTTATCTTGAGACATG 58.175 37.037 0.00 0.00 33.85 3.21
2839 6524 8.543774 ACCAGTTGATTACTTATCTTGAGACAT 58.456 33.333 0.00 0.00 33.85 3.06
2862 6549 5.580691 CACTTATCTTGCGAGACAAATACCA 59.419 40.000 5.59 0.00 37.96 3.25
2863 6550 5.581085 ACACTTATCTTGCGAGACAAATACC 59.419 40.000 5.59 0.00 37.96 2.73
2864 6551 6.455646 CCACACTTATCTTGCGAGACAAATAC 60.456 42.308 5.59 0.00 37.96 1.89
2875 6562 2.162408 GCTGTTCCCACACTTATCTTGC 59.838 50.000 0.00 0.00 0.00 4.01
2881 6568 2.325484 TCTCTGCTGTTCCCACACTTA 58.675 47.619 0.00 0.00 0.00 2.24
2882 6569 1.131638 TCTCTGCTGTTCCCACACTT 58.868 50.000 0.00 0.00 0.00 3.16
2884 6571 1.002430 TCATCTCTGCTGTTCCCACAC 59.998 52.381 0.00 0.00 0.00 3.82
2885 6572 1.351076 TCATCTCTGCTGTTCCCACA 58.649 50.000 0.00 0.00 0.00 4.17
2886 6573 2.706339 ATCATCTCTGCTGTTCCCAC 57.294 50.000 0.00 0.00 0.00 4.61
2895 6591 3.439476 ACTGTGAAGCAAATCATCTCTGC 59.561 43.478 0.00 0.00 36.29 4.26
2898 6594 7.487189 CCAAATAACTGTGAAGCAAATCATCTC 59.513 37.037 0.00 0.00 0.00 2.75
2925 6621 4.504858 CATACTACCTCCAGTGTTCAACC 58.495 47.826 0.00 0.00 0.00 3.77
2929 6625 4.039366 GGATCCATACTACCTCCAGTGTTC 59.961 50.000 6.95 0.00 0.00 3.18
2931 6627 3.052109 TGGATCCATACTACCTCCAGTGT 60.052 47.826 11.44 0.00 32.39 3.55
2934 6652 3.967326 TGTTGGATCCATACTACCTCCAG 59.033 47.826 17.06 0.00 37.32 3.86
2940 6658 3.996480 GAGCCTGTTGGATCCATACTAC 58.004 50.000 17.06 11.43 42.60 2.73
2954 6672 1.630369 TCTACTTGCCAATGAGCCTGT 59.370 47.619 0.00 0.00 0.00 4.00
2999 6730 9.875675 GCTTTCAAAACAATGCAATAATAAACA 57.124 25.926 0.00 0.00 0.00 2.83
3000 6731 9.875675 TGCTTTCAAAACAATGCAATAATAAAC 57.124 25.926 0.00 0.00 34.46 2.01
3021 6752 9.740710 ATAGTCTAGTAGTTTCCATTTTGCTTT 57.259 29.630 0.00 0.00 0.00 3.51
3086 6846 5.853572 TTTCTTTACAGAGGGGGTATGTT 57.146 39.130 0.00 0.00 31.40 2.71
3092 6852 6.937465 GCTCTTATATTTCTTTACAGAGGGGG 59.063 42.308 0.00 0.00 0.00 5.40
3094 6854 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
3095 6855 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
3096 6856 9.302345 TGAACGCTCTTATATTTCTTTACAGAG 57.698 33.333 0.00 0.00 0.00 3.35
3097 6857 9.084164 GTGAACGCTCTTATATTTCTTTACAGA 57.916 33.333 0.00 0.00 0.00 3.41
3099 6859 8.766000 TGTGAACGCTCTTATATTTCTTTACA 57.234 30.769 0.00 0.00 0.00 2.41
3101 6861 9.084164 GTCTGTGAACGCTCTTATATTTCTTTA 57.916 33.333 0.00 0.00 0.00 1.85
3102 6862 7.819900 AGTCTGTGAACGCTCTTATATTTCTTT 59.180 33.333 0.00 0.00 0.00 2.52
3103 6863 7.324178 AGTCTGTGAACGCTCTTATATTTCTT 58.676 34.615 0.00 0.00 0.00 2.52
3104 6864 6.868622 AGTCTGTGAACGCTCTTATATTTCT 58.131 36.000 0.00 0.00 0.00 2.52
3106 6866 7.203910 CCTAGTCTGTGAACGCTCTTATATTT 58.796 38.462 0.00 0.00 0.00 1.40
3107 6867 6.736243 GCCTAGTCTGTGAACGCTCTTATATT 60.736 42.308 0.00 0.00 0.00 1.28
3109 6869 4.036498 GCCTAGTCTGTGAACGCTCTTATA 59.964 45.833 0.00 0.00 0.00 0.98
3110 6870 3.181485 GCCTAGTCTGTGAACGCTCTTAT 60.181 47.826 0.00 0.00 0.00 1.73
3111 6871 2.163815 GCCTAGTCTGTGAACGCTCTTA 59.836 50.000 0.00 0.00 0.00 2.10
3112 6872 1.067495 GCCTAGTCTGTGAACGCTCTT 60.067 52.381 0.00 0.00 0.00 2.85
3113 6873 0.528470 GCCTAGTCTGTGAACGCTCT 59.472 55.000 0.00 0.00 0.00 4.09
3114 6874 0.528470 AGCCTAGTCTGTGAACGCTC 59.472 55.000 0.00 0.00 0.00 5.03
3115 6875 0.969894 AAGCCTAGTCTGTGAACGCT 59.030 50.000 0.00 0.00 0.00 5.07
3116 6876 1.067495 AGAAGCCTAGTCTGTGAACGC 60.067 52.381 0.00 0.00 0.00 4.84
3117 6877 2.229062 TGAGAAGCCTAGTCTGTGAACG 59.771 50.000 0.00 0.00 0.00 3.95
3118 6878 3.944055 TGAGAAGCCTAGTCTGTGAAC 57.056 47.619 0.00 0.00 0.00 3.18
3119 6879 3.898123 ACTTGAGAAGCCTAGTCTGTGAA 59.102 43.478 0.00 0.00 0.00 3.18
3120 6880 3.501349 ACTTGAGAAGCCTAGTCTGTGA 58.499 45.455 0.00 0.00 0.00 3.58
3121 6881 3.951775 ACTTGAGAAGCCTAGTCTGTG 57.048 47.619 0.00 0.00 0.00 3.66
3122 6882 3.445805 GCTACTTGAGAAGCCTAGTCTGT 59.554 47.826 0.00 0.00 32.40 3.41
3123 6883 3.445450 TGCTACTTGAGAAGCCTAGTCTG 59.555 47.826 0.00 0.00 37.97 3.51
3124 6884 3.702792 TGCTACTTGAGAAGCCTAGTCT 58.297 45.455 0.00 0.00 37.97 3.24
3125 6885 4.177783 GTTGCTACTTGAGAAGCCTAGTC 58.822 47.826 0.00 0.00 37.97 2.59
3126 6886 3.055747 GGTTGCTACTTGAGAAGCCTAGT 60.056 47.826 0.00 0.00 37.97 2.57
3127 6887 3.055819 TGGTTGCTACTTGAGAAGCCTAG 60.056 47.826 0.00 0.00 37.97 3.02
3128 6888 2.903784 TGGTTGCTACTTGAGAAGCCTA 59.096 45.455 0.00 0.00 37.97 3.93
3129 6889 1.699634 TGGTTGCTACTTGAGAAGCCT 59.300 47.619 0.00 0.00 37.97 4.58
3130 6890 1.807142 GTGGTTGCTACTTGAGAAGCC 59.193 52.381 0.00 0.00 37.97 4.35
3131 6891 2.481952 CTGTGGTTGCTACTTGAGAAGC 59.518 50.000 0.00 0.00 39.25 3.86
3132 6892 3.993081 CTCTGTGGTTGCTACTTGAGAAG 59.007 47.826 0.00 0.00 0.00 2.85
3133 6893 3.641436 TCTCTGTGGTTGCTACTTGAGAA 59.359 43.478 0.00 0.00 31.16 2.87
3134 6894 3.230976 TCTCTGTGGTTGCTACTTGAGA 58.769 45.455 0.00 4.16 0.00 3.27
3135 6895 3.667497 TCTCTGTGGTTGCTACTTGAG 57.333 47.619 0.00 2.05 0.00 3.02
3136 6896 4.563580 GGAATCTCTGTGGTTGCTACTTGA 60.564 45.833 0.00 0.00 0.00 3.02
3137 6897 3.686726 GGAATCTCTGTGGTTGCTACTTG 59.313 47.826 0.00 0.00 0.00 3.16
3138 6898 3.327757 TGGAATCTCTGTGGTTGCTACTT 59.672 43.478 0.00 0.00 0.00 2.24
3139 6899 2.906389 TGGAATCTCTGTGGTTGCTACT 59.094 45.455 0.00 0.00 0.00 2.57
3140 6900 3.334583 TGGAATCTCTGTGGTTGCTAC 57.665 47.619 0.00 0.00 0.00 3.58
3141 6901 4.365514 TTTGGAATCTCTGTGGTTGCTA 57.634 40.909 0.00 0.00 0.00 3.49
3142 6902 2.957402 TTGGAATCTCTGTGGTTGCT 57.043 45.000 0.00 0.00 0.00 3.91
3143 6903 3.841643 CATTTGGAATCTCTGTGGTTGC 58.158 45.455 0.00 0.00 0.00 4.17
3144 6904 3.256383 TGCATTTGGAATCTCTGTGGTTG 59.744 43.478 0.00 0.00 0.00 3.77
3175 6935 3.429881 GCCTAAACACAAGAGCAAAATGC 59.570 43.478 0.00 0.00 45.46 3.56
3178 6938 3.951037 TGAGCCTAAACACAAGAGCAAAA 59.049 39.130 0.00 0.00 0.00 2.44
3179 6939 3.550820 TGAGCCTAAACACAAGAGCAAA 58.449 40.909 0.00 0.00 0.00 3.68
3201 6962 8.831715 ATGTGTTTCCCTTGATTTTTCATTAC 57.168 30.769 0.00 0.00 0.00 1.89
3203 6964 9.492973 CTTATGTGTTTCCCTTGATTTTTCATT 57.507 29.630 0.00 0.00 0.00 2.57
3204 6965 8.869109 TCTTATGTGTTTCCCTTGATTTTTCAT 58.131 29.630 0.00 0.00 0.00 2.57
3205 6966 8.141268 GTCTTATGTGTTTCCCTTGATTTTTCA 58.859 33.333 0.00 0.00 0.00 2.69
3207 6968 7.926018 GTGTCTTATGTGTTTCCCTTGATTTTT 59.074 33.333 0.00 0.00 0.00 1.94
3257 7018 6.670695 ATGCCTTTGGAAACTAGTGAATTT 57.329 33.333 0.00 0.00 0.00 1.82
3258 7019 6.670695 AATGCCTTTGGAAACTAGTGAATT 57.329 33.333 0.00 0.00 0.00 2.17
3268 7029 6.769822 TTTCAAAAGCATAATGCCTTTGGAAA 59.230 30.769 17.47 17.47 44.67 3.13
3341 7533 4.097286 GGCTTCAGAAACTGTGTTAAACCA 59.903 41.667 0.00 0.00 32.61 3.67
3435 7654 6.294010 GGAGTCTGTGGAAAATGAAGTAAACC 60.294 42.308 0.00 0.00 0.00 3.27
3436 7655 6.262273 TGGAGTCTGTGGAAAATGAAGTAAAC 59.738 38.462 0.00 0.00 0.00 2.01
3450 7671 1.517242 GAAAGCAGTGGAGTCTGTGG 58.483 55.000 0.00 0.00 37.70 4.17
3458 7679 2.304761 ACTAATTCGGGAAAGCAGTGGA 59.695 45.455 0.00 0.00 0.00 4.02
3459 7680 2.711542 ACTAATTCGGGAAAGCAGTGG 58.288 47.619 0.00 0.00 0.00 4.00
3465 7686 7.114953 GCAGAAAGAAAAACTAATTCGGGAAAG 59.885 37.037 0.00 0.00 32.04 2.62
3515 7736 5.188359 GGTTTGGTCTTGGACAGTAGGTATA 59.812 44.000 0.14 0.00 33.68 1.47
3516 7737 4.019591 GGTTTGGTCTTGGACAGTAGGTAT 60.020 45.833 0.14 0.00 33.68 2.73
3517 7738 3.325716 GGTTTGGTCTTGGACAGTAGGTA 59.674 47.826 0.14 0.00 33.68 3.08
3518 7739 2.105993 GGTTTGGTCTTGGACAGTAGGT 59.894 50.000 0.14 0.00 33.68 3.08
3541 7762 1.067142 CAAAGCTACGACCTGCCTACA 60.067 52.381 0.00 0.00 0.00 2.74
3629 7850 3.637273 GGCACGGAAGGAGGGTGT 61.637 66.667 0.00 0.00 34.25 4.16


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

AutoCloner maintained by Alex Coulton.