Multiple sequence alignment - TraesCS7B01G099800

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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 TraesCS7B01G099800 chr7B 100.000 2950 0 0 1 2950 113921688 113924637 0.000000e+00 5448.0
1 TraesCS7B01G099800 chr7B 93.069 1111 66 7 830 1934 113802870 113801765 0.000000e+00 1615.0
2 TraesCS7B01G099800 chr7B 89.341 1229 122 6 729 1950 113627115 113625889 0.000000e+00 1535.0
3 TraesCS7B01G099800 chr7B 83.444 604 80 8 2364 2950 711189196 711188596 7.190000e-151 544.0
4 TraesCS7B01G099800 chr7B 83.557 596 72 7 2378 2950 654202409 654201817 4.330000e-148 534.0
5 TraesCS7B01G099800 chr7B 81.342 611 87 18 2364 2950 721656040 721655433 3.440000e-129 472.0
6 TraesCS7B01G099800 chr7D 92.838 1480 93 6 731 2205 151917098 151915627 0.000000e+00 2134.0
7 TraesCS7B01G099800 chr7D 92.361 1309 74 8 731 2036 151791582 151790297 0.000000e+00 1840.0
8 TraesCS7B01G099800 chr7D 90.751 173 15 1 2033 2205 151790115 151789944 2.290000e-56 230.0
9 TraesCS7B01G099800 chr7D 98.039 51 1 0 2236 2286 151789958 151789908 4.050000e-14 89.8
10 TraesCS7B01G099800 chr7A 90.598 1489 117 12 731 2205 151961686 151960207 0.000000e+00 1953.0
11 TraesCS7B01G099800 chr7A 92.626 990 72 1 1162 2151 151863053 151864041 0.000000e+00 1423.0
12 TraesCS7B01G099800 chr7A 94.573 737 34 5 1 734 579013408 579012675 0.000000e+00 1134.0
13 TraesCS7B01G099800 chr7A 86.072 359 20 8 2619 2950 32054851 32054496 2.800000e-95 359.0
14 TraesCS7B01G099800 chr7A 82.836 134 22 1 21 153 643649383 643649250 5.170000e-23 119.0
15 TraesCS7B01G099800 chr7A 84.444 90 12 2 641 729 579256875 579256963 1.460000e-13 87.9
16 TraesCS7B01G099800 chr7A 94.118 51 3 0 2236 2286 151868456 151868506 8.770000e-11 78.7
17 TraesCS7B01G099800 chr7A 82.558 86 14 1 645 730 678004749 678004833 1.130000e-09 75.0
18 TraesCS7B01G099800 chrUn 91.133 1139 93 5 803 1934 85701014 85702151 0.000000e+00 1537.0
19 TraesCS7B01G099800 chrUn 91.133 1139 93 5 803 1934 235702668 235701531 0.000000e+00 1537.0
20 TraesCS7B01G099800 chrUn 89.341 1229 122 6 729 1950 185555967 185554741 0.000000e+00 1535.0
21 TraesCS7B01G099800 chrUn 89.338 1088 107 6 729 1809 85624322 85625407 0.000000e+00 1358.0
22 TraesCS7B01G099800 chrUn 84.564 596 76 8 2365 2947 38495305 38495897 7.090000e-161 577.0
23 TraesCS7B01G099800 chrUn 89.906 426 38 5 2368 2790 48652651 48652228 7.190000e-151 544.0
24 TraesCS7B01G099800 chrUn 82.000 300 31 14 2672 2950 265349918 265349621 1.770000e-57 233.0
25 TraesCS7B01G099800 chrUn 81.081 74 13 1 2285 2358 345253606 345253534 1.140000e-04 58.4
26 TraesCS7B01G099800 chrUn 83.077 65 10 1 2285 2349 359392773 359392836 1.140000e-04 58.4
27 TraesCS7B01G099800 chr2A 94.973 736 36 1 3 738 667016865 667016131 0.000000e+00 1153.0
28 TraesCS7B01G099800 chr5A 94.384 730 37 4 1 729 622374744 622375470 0.000000e+00 1118.0
29 TraesCS7B01G099800 chr5A 82.714 619 69 11 2365 2950 544207556 544206943 1.570000e-142 516.0
30 TraesCS7B01G099800 chr5A 95.062 162 6 2 568 729 564983948 564983789 1.360000e-63 254.0
31 TraesCS7B01G099800 chr3B 93.175 718 46 3 1 718 735245444 735246158 0.000000e+00 1051.0
32 TraesCS7B01G099800 chr3B 89.535 430 40 5 2364 2790 50653242 50652815 9.300000e-150 540.0
33 TraesCS7B01G099800 chr3A 93.494 538 32 3 193 730 40812003 40811469 0.000000e+00 797.0
34 TraesCS7B01G099800 chr3A 96.135 207 7 1 1 207 40814508 40814303 1.310000e-88 337.0
35 TraesCS7B01G099800 chr4A 85.860 587 73 6 2365 2947 650905242 650905822 1.500000e-172 616.0
36 TraesCS7B01G099800 chr4A 90.654 428 33 5 2365 2790 718155150 718155572 1.990000e-156 562.0
37 TraesCS7B01G099800 chr4A 90.421 428 34 5 2365 2790 718051641 718052063 9.240000e-155 556.0
38 TraesCS7B01G099800 chr4A 89.953 428 39 4 2365 2790 719285649 719285224 1.550000e-152 549.0
39 TraesCS7B01G099800 chr1A 91.142 429 34 4 2364 2790 6510742 6510316 1.970000e-161 579.0
40 TraesCS7B01G099800 chr1A 80.000 155 23 6 590 738 494813231 494813079 1.120000e-19 108.0
41 TraesCS7B01G099800 chr6B 89.744 429 39 5 2365 2790 31717399 31717825 7.190000e-151 544.0
42 TraesCS7B01G099800 chr6B 77.570 428 71 14 1 411 204332186 204332605 4.920000e-58 235.0
43 TraesCS7B01G099800 chr4B 89.120 432 42 5 2362 2790 27288310 27288739 1.560000e-147 532.0
44 TraesCS7B01G099800 chr2B 82.708 613 75 18 2365 2947 56295592 56296203 1.570000e-142 516.0
45 TraesCS7B01G099800 chr2B 86.207 87 11 1 643 729 137438411 137438326 3.130000e-15 93.5
46 TraesCS7B01G099800 chr1B 95.600 250 11 0 1 250 633192242 633191993 4.580000e-108 401.0
47 TraesCS7B01G099800 chr1B 91.770 243 18 2 243 485 633190252 633190012 1.310000e-88 337.0
48 TraesCS7B01G099800 chr1B 89.412 85 8 1 645 729 553900013 553899930 4.020000e-19 106.0
49 TraesCS7B01G099800 chr6A 79.059 425 71 10 1 411 143375612 143376032 2.900000e-70 276.0
50 TraesCS7B01G099800 chr6A 81.053 95 16 2 645 738 485760392 485760299 1.130000e-09 75.0
51 TraesCS7B01G099800 chr6A 81.176 85 15 1 645 729 48653033 48652950 1.900000e-07 67.6
52 TraesCS7B01G099800 chr6D 81.319 91 13 3 641 729 423817316 423817228 1.470000e-08 71.3
53 TraesCS7B01G099800 chr5B 81.081 74 13 1 2285 2358 516599770 516599698 1.140000e-04 58.4


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 TraesCS7B01G099800 chr7B 113921688 113924637 2949 False 5448.000000 5448 100.0000 1 2950 1 chr7B.!!$F1 2949
1 TraesCS7B01G099800 chr7B 113801765 113802870 1105 True 1615.000000 1615 93.0690 830 1934 1 chr7B.!!$R2 1104
2 TraesCS7B01G099800 chr7B 113625889 113627115 1226 True 1535.000000 1535 89.3410 729 1950 1 chr7B.!!$R1 1221
3 TraesCS7B01G099800 chr7B 711188596 711189196 600 True 544.000000 544 83.4440 2364 2950 1 chr7B.!!$R4 586
4 TraesCS7B01G099800 chr7B 654201817 654202409 592 True 534.000000 534 83.5570 2378 2950 1 chr7B.!!$R3 572
5 TraesCS7B01G099800 chr7B 721655433 721656040 607 True 472.000000 472 81.3420 2364 2950 1 chr7B.!!$R5 586
6 TraesCS7B01G099800 chr7D 151915627 151917098 1471 True 2134.000000 2134 92.8380 731 2205 1 chr7D.!!$R1 1474
7 TraesCS7B01G099800 chr7D 151789908 151791582 1674 True 719.933333 1840 93.7170 731 2286 3 chr7D.!!$R2 1555
8 TraesCS7B01G099800 chr7A 151960207 151961686 1479 True 1953.000000 1953 90.5980 731 2205 1 chr7A.!!$R2 1474
9 TraesCS7B01G099800 chr7A 151863053 151864041 988 False 1423.000000 1423 92.6260 1162 2151 1 chr7A.!!$F1 989
10 TraesCS7B01G099800 chr7A 579012675 579013408 733 True 1134.000000 1134 94.5730 1 734 1 chr7A.!!$R3 733
11 TraesCS7B01G099800 chrUn 85701014 85702151 1137 False 1537.000000 1537 91.1330 803 1934 1 chrUn.!!$F3 1131
12 TraesCS7B01G099800 chrUn 235701531 235702668 1137 True 1537.000000 1537 91.1330 803 1934 1 chrUn.!!$R3 1131
13 TraesCS7B01G099800 chrUn 185554741 185555967 1226 True 1535.000000 1535 89.3410 729 1950 1 chrUn.!!$R2 1221
14 TraesCS7B01G099800 chrUn 85624322 85625407 1085 False 1358.000000 1358 89.3380 729 1809 1 chrUn.!!$F2 1080
15 TraesCS7B01G099800 chrUn 38495305 38495897 592 False 577.000000 577 84.5640 2365 2947 1 chrUn.!!$F1 582
16 TraesCS7B01G099800 chr2A 667016131 667016865 734 True 1153.000000 1153 94.9730 3 738 1 chr2A.!!$R1 735
17 TraesCS7B01G099800 chr5A 622374744 622375470 726 False 1118.000000 1118 94.3840 1 729 1 chr5A.!!$F1 728
18 TraesCS7B01G099800 chr5A 544206943 544207556 613 True 516.000000 516 82.7140 2365 2950 1 chr5A.!!$R1 585
19 TraesCS7B01G099800 chr3B 735245444 735246158 714 False 1051.000000 1051 93.1750 1 718 1 chr3B.!!$F1 717
20 TraesCS7B01G099800 chr3A 40811469 40814508 3039 True 567.000000 797 94.8145 1 730 2 chr3A.!!$R1 729
21 TraesCS7B01G099800 chr4A 650905242 650905822 580 False 616.000000 616 85.8600 2365 2947 1 chr4A.!!$F1 582
22 TraesCS7B01G099800 chr2B 56295592 56296203 611 False 516.000000 516 82.7080 2365 2947 1 chr2B.!!$F1 582
23 TraesCS7B01G099800 chr1B 633190012 633192242 2230 True 369.000000 401 93.6850 1 485 2 chr1B.!!$R2 484

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
576 4637 0.031994 GTGTTGCATTTCCGCTGGTT 59.968 50.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2319 6891 0.534873 TGTATCCGCTTGCTGCTACA 59.465 50.0 0.0 0.0 40.11 2.74 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
132 133 3.766691 GCCTCCGTCAACGCCCTA 61.767 66.667 0.00 0.00 38.18 3.53
200 2513 4.083324 AGCTCATCCAAATGTACGTGTTTG 60.083 41.667 0.00 7.09 35.60 2.93
375 4436 2.375766 GCGTGCTCCTCTCGTTGTG 61.376 63.158 0.00 0.00 34.47 3.33
381 4442 1.903877 CTCCTCTCGTTGTGGGCCAT 61.904 60.000 10.70 0.00 0.00 4.40
412 4473 3.207669 GGCATCAAGGGCTCGCTG 61.208 66.667 0.00 0.00 0.00 5.18
509 4570 5.450818 TGCTATTAACCTGACAGGGAATT 57.549 39.130 25.34 13.06 40.58 2.17
510 4571 5.826643 TGCTATTAACCTGACAGGGAATTT 58.173 37.500 25.34 12.71 40.58 1.82
511 4572 5.885912 TGCTATTAACCTGACAGGGAATTTC 59.114 40.000 25.34 16.56 40.58 2.17
512 4573 5.885912 GCTATTAACCTGACAGGGAATTTCA 59.114 40.000 25.34 8.76 40.58 2.69
513 4574 6.038714 GCTATTAACCTGACAGGGAATTTCAG 59.961 42.308 25.34 16.93 40.58 3.02
514 4575 3.884037 AACCTGACAGGGAATTTCAGT 57.116 42.857 25.34 0.00 40.58 3.41
515 4576 3.884037 ACCTGACAGGGAATTTCAGTT 57.116 42.857 25.34 0.00 40.58 3.16
516 4577 4.184649 ACCTGACAGGGAATTTCAGTTT 57.815 40.909 25.34 0.00 40.58 2.66
517 4578 4.145052 ACCTGACAGGGAATTTCAGTTTC 58.855 43.478 25.34 0.00 40.58 2.78
518 4579 4.141158 ACCTGACAGGGAATTTCAGTTTCT 60.141 41.667 25.34 0.00 40.58 2.52
519 4580 4.829492 CCTGACAGGGAATTTCAGTTTCTT 59.171 41.667 14.26 0.00 35.89 2.52
520 4581 5.302823 CCTGACAGGGAATTTCAGTTTCTTT 59.697 40.000 14.26 0.00 35.89 2.52
521 4582 6.391227 TGACAGGGAATTTCAGTTTCTTTC 57.609 37.500 0.00 0.00 0.00 2.62
522 4583 5.890985 TGACAGGGAATTTCAGTTTCTTTCA 59.109 36.000 0.00 0.00 0.00 2.69
523 4584 6.149129 ACAGGGAATTTCAGTTTCTTTCAC 57.851 37.500 0.00 0.00 0.00 3.18
524 4585 5.656416 ACAGGGAATTTCAGTTTCTTTCACA 59.344 36.000 0.00 0.00 0.00 3.58
525 4586 6.324770 ACAGGGAATTTCAGTTTCTTTCACAT 59.675 34.615 0.00 0.00 0.00 3.21
526 4587 6.643770 CAGGGAATTTCAGTTTCTTTCACATG 59.356 38.462 0.00 0.00 0.00 3.21
527 4588 6.550854 AGGGAATTTCAGTTTCTTTCACATGA 59.449 34.615 0.00 0.00 0.00 3.07
528 4589 7.234166 AGGGAATTTCAGTTTCTTTCACATGAT 59.766 33.333 0.00 0.00 0.00 2.45
529 4590 8.522830 GGGAATTTCAGTTTCTTTCACATGATA 58.477 33.333 0.00 0.00 0.00 2.15
530 4591 9.346725 GGAATTTCAGTTTCTTTCACATGATAC 57.653 33.333 0.00 0.00 0.00 2.24
531 4592 9.897744 GAATTTCAGTTTCTTTCACATGATACA 57.102 29.630 0.00 0.00 0.00 2.29
534 4595 8.620116 TTCAGTTTCTTTCACATGATACATCA 57.380 30.769 0.00 0.00 41.70 3.07
535 4596 8.620116 TCAGTTTCTTTCACATGATACATCAA 57.380 30.769 0.00 0.00 40.69 2.57
536 4597 9.234827 TCAGTTTCTTTCACATGATACATCAAT 57.765 29.630 0.00 0.00 40.69 2.57
563 4624 9.703892 AAATATACAGAGATCTAGATGTGTTGC 57.296 33.333 10.74 0.00 0.00 4.17
564 4625 6.721704 ATACAGAGATCTAGATGTGTTGCA 57.278 37.500 10.74 0.00 0.00 4.08
565 4626 5.611128 ACAGAGATCTAGATGTGTTGCAT 57.389 39.130 10.74 0.00 41.24 3.96
566 4627 5.987098 ACAGAGATCTAGATGTGTTGCATT 58.013 37.500 10.74 0.00 38.06 3.56
567 4628 6.413052 ACAGAGATCTAGATGTGTTGCATTT 58.587 36.000 10.74 0.00 38.06 2.32
568 4629 6.538021 ACAGAGATCTAGATGTGTTGCATTTC 59.462 38.462 10.74 0.00 38.06 2.17
569 4630 6.018098 CAGAGATCTAGATGTGTTGCATTTCC 60.018 42.308 10.74 0.00 38.06 3.13
570 4631 4.813161 AGATCTAGATGTGTTGCATTTCCG 59.187 41.667 10.74 0.00 38.06 4.30
571 4632 2.677836 TCTAGATGTGTTGCATTTCCGC 59.322 45.455 0.00 0.00 38.06 5.54
572 4633 1.538047 AGATGTGTTGCATTTCCGCT 58.462 45.000 0.00 0.00 38.06 5.52
573 4634 1.200716 AGATGTGTTGCATTTCCGCTG 59.799 47.619 0.00 0.00 38.06 5.18
574 4635 0.244450 ATGTGTTGCATTTCCGCTGG 59.756 50.000 0.00 0.00 33.14 4.85
575 4636 1.106351 TGTGTTGCATTTCCGCTGGT 61.106 50.000 0.00 0.00 0.00 4.00
576 4637 0.031994 GTGTTGCATTTCCGCTGGTT 59.968 50.000 0.00 0.00 0.00 3.67
577 4638 0.749649 TGTTGCATTTCCGCTGGTTT 59.250 45.000 0.00 0.00 0.00 3.27
578 4639 1.269517 TGTTGCATTTCCGCTGGTTTC 60.270 47.619 0.00 0.00 0.00 2.78
579 4640 1.000274 GTTGCATTTCCGCTGGTTTCT 60.000 47.619 0.00 0.00 0.00 2.52
580 4641 1.327303 TGCATTTCCGCTGGTTTCTT 58.673 45.000 0.00 0.00 0.00 2.52
581 4642 1.269448 TGCATTTCCGCTGGTTTCTTC 59.731 47.619 0.00 0.00 0.00 2.87
582 4643 1.541588 GCATTTCCGCTGGTTTCTTCT 59.458 47.619 0.00 0.00 0.00 2.85
583 4644 2.747446 GCATTTCCGCTGGTTTCTTCTA 59.253 45.455 0.00 0.00 0.00 2.10
584 4645 3.426292 GCATTTCCGCTGGTTTCTTCTAC 60.426 47.826 0.00 0.00 0.00 2.59
585 4646 3.764237 TTTCCGCTGGTTTCTTCTACT 57.236 42.857 0.00 0.00 0.00 2.57
586 4647 4.877378 TTTCCGCTGGTTTCTTCTACTA 57.123 40.909 0.00 0.00 0.00 1.82
587 4648 5.416271 TTTCCGCTGGTTTCTTCTACTAT 57.584 39.130 0.00 0.00 0.00 2.12
588 4649 6.534475 TTTCCGCTGGTTTCTTCTACTATA 57.466 37.500 0.00 0.00 0.00 1.31
589 4650 6.534475 TTCCGCTGGTTTCTTCTACTATAA 57.466 37.500 0.00 0.00 0.00 0.98
590 4651 6.534475 TCCGCTGGTTTCTTCTACTATAAA 57.466 37.500 0.00 0.00 0.00 1.40
591 4652 7.120923 TCCGCTGGTTTCTTCTACTATAAAT 57.879 36.000 0.00 0.00 0.00 1.40
592 4653 8.241497 TCCGCTGGTTTCTTCTACTATAAATA 57.759 34.615 0.00 0.00 0.00 1.40
593 4654 8.867097 TCCGCTGGTTTCTTCTACTATAAATAT 58.133 33.333 0.00 0.00 0.00 1.28
594 4655 9.141400 CCGCTGGTTTCTTCTACTATAAATATC 57.859 37.037 0.00 0.00 0.00 1.63
595 4656 9.692749 CGCTGGTTTCTTCTACTATAAATATCA 57.307 33.333 0.00 0.00 0.00 2.15
617 4678 7.977789 TCAGTCTTTTCATAGCAACATTACA 57.022 32.000 0.00 0.00 0.00 2.41
618 4679 8.565896 TCAGTCTTTTCATAGCAACATTACAT 57.434 30.769 0.00 0.00 0.00 2.29
619 4680 8.453320 TCAGTCTTTTCATAGCAACATTACATG 58.547 33.333 0.00 0.00 0.00 3.21
621 4682 9.448438 AGTCTTTTCATAGCAACATTACATGTA 57.552 29.630 0.08 0.08 44.07 2.29
631 4692 8.964420 AGCAACATTACATGTATACAAAACAC 57.036 30.769 10.14 0.00 44.07 3.32
632 4693 8.572185 AGCAACATTACATGTATACAAAACACA 58.428 29.630 10.14 0.00 44.07 3.72
633 4694 8.635124 GCAACATTACATGTATACAAAACACAC 58.365 33.333 10.14 0.00 44.07 3.82
634 4695 9.891828 CAACATTACATGTATACAAAACACACT 57.108 29.630 10.14 0.00 44.07 3.55
660 4721 7.975608 ACTTTAAATAGGATAGTAGAAGGGGC 58.024 38.462 0.00 0.00 0.00 5.80
661 4722 6.600882 TTAAATAGGATAGTAGAAGGGGCG 57.399 41.667 0.00 0.00 0.00 6.13
662 4723 1.920610 TAGGATAGTAGAAGGGGCGC 58.079 55.000 0.00 0.00 0.00 6.53
663 4724 1.179814 AGGATAGTAGAAGGGGCGCG 61.180 60.000 0.00 0.00 0.00 6.86
664 4725 1.461911 GGATAGTAGAAGGGGCGCGT 61.462 60.000 8.43 0.00 0.00 6.01
665 4726 0.039346 GATAGTAGAAGGGGCGCGTC 60.039 60.000 8.43 4.38 0.00 5.19
666 4727 1.461911 ATAGTAGAAGGGGCGCGTCC 61.462 60.000 24.67 24.67 0.00 4.79
667 4728 2.563013 TAGTAGAAGGGGCGCGTCCT 62.563 60.000 31.31 22.51 35.88 3.85
668 4729 2.123428 GTAGAAGGGGCGCGTCCTA 61.123 63.158 31.31 11.48 33.58 2.94
669 4730 2.123428 TAGAAGGGGCGCGTCCTAC 61.123 63.158 31.31 20.08 33.58 3.18
670 4731 2.563013 TAGAAGGGGCGCGTCCTACT 62.563 60.000 31.31 25.47 33.58 2.57
671 4732 3.001406 AAGGGGCGCGTCCTACTT 61.001 61.111 31.31 22.15 33.58 2.24
672 4733 3.310860 AAGGGGCGCGTCCTACTTG 62.311 63.158 31.31 0.00 33.15 3.16
673 4734 4.832608 GGGGCGCGTCCTACTTGG 62.833 72.222 31.31 0.00 34.39 3.61
675 4736 4.752879 GGCGCGTCCTACTTGGCA 62.753 66.667 8.43 0.00 35.26 4.92
676 4737 3.488090 GCGCGTCCTACTTGGCAC 61.488 66.667 8.43 0.00 35.26 5.01
677 4738 2.813908 CGCGTCCTACTTGGCACC 60.814 66.667 0.00 0.00 35.26 5.01
678 4739 2.813908 GCGTCCTACTTGGCACCG 60.814 66.667 0.00 0.00 35.26 4.94
679 4740 2.813908 CGTCCTACTTGGCACCGC 60.814 66.667 0.00 0.00 35.26 5.68
689 4750 4.056125 GGCACCGCCTTTGCTTCC 62.056 66.667 0.00 0.00 46.69 3.46
690 4751 4.404654 GCACCGCCTTTGCTTCCG 62.405 66.667 0.00 0.00 37.00 4.30
691 4752 4.404654 CACCGCCTTTGCTTCCGC 62.405 66.667 0.00 0.00 34.43 5.54
692 4753 4.643387 ACCGCCTTTGCTTCCGCT 62.643 61.111 0.00 0.00 36.97 5.52
693 4754 3.804193 CCGCCTTTGCTTCCGCTC 61.804 66.667 0.00 0.00 36.97 5.03
694 4755 3.049674 CGCCTTTGCTTCCGCTCA 61.050 61.111 0.00 0.00 36.97 4.26
695 4756 2.616330 CGCCTTTGCTTCCGCTCAA 61.616 57.895 0.00 0.00 36.97 3.02
696 4757 1.211190 GCCTTTGCTTCCGCTCAAG 59.789 57.895 0.00 0.00 36.97 3.02
777 4838 0.606096 TGTACACACCATCCGTCCAG 59.394 55.000 0.00 0.00 0.00 3.86
796 4857 4.104261 TCCAGTTCCTCGACATAGATCCTA 59.896 45.833 0.00 0.00 0.00 2.94
800 4861 6.148150 CAGTTCCTCGACATAGATCCTACTAC 59.852 46.154 0.00 0.00 0.00 2.73
801 4862 5.163281 TCCTCGACATAGATCCTACTACC 57.837 47.826 0.00 0.00 0.00 3.18
816 4877 7.074653 TCCTACTACCACTGAAACATTCTTT 57.925 36.000 0.00 0.00 0.00 2.52
826 4887 5.241728 ACTGAAACATTCTTTTCTGTAGCCC 59.758 40.000 6.39 0.00 42.52 5.19
978 5052 3.706373 AAGACATGCCCCGACGCT 61.706 61.111 0.00 0.00 0.00 5.07
994 5068 1.590259 GCTGAGAAGATCGTCCGCC 60.590 63.158 4.93 0.00 0.00 6.13
1102 5186 7.096551 GGTACATAACTTACCCGTTCTTGTAA 58.903 38.462 0.00 0.00 33.98 2.41
1106 5190 7.335171 ACATAACTTACCCGTTCTTGTAATTCC 59.665 37.037 0.00 0.00 0.00 3.01
1287 5496 2.436109 GGGTGAAGGCCAAGCTCA 59.564 61.111 5.01 0.00 0.00 4.26
1364 5750 2.027073 CGCTGTCGTGCTGGCTAAA 61.027 57.895 0.00 0.00 0.00 1.85
1579 5965 4.849329 CGCCGACCGCCTCTACAC 62.849 72.222 0.00 0.00 0.00 2.90
1703 6089 0.252421 TGCTGTCTGAGATGGACCCT 60.252 55.000 0.00 0.00 33.22 4.34
1718 6104 1.903183 GACCCTGGTAGCTTCAAGACT 59.097 52.381 0.00 0.00 0.00 3.24
1720 6106 2.303311 ACCCTGGTAGCTTCAAGACTTC 59.697 50.000 0.00 0.00 0.00 3.01
1810 6196 2.669569 CGCCACCACCAAGGACTG 60.670 66.667 0.00 0.00 41.22 3.51
1842 6228 4.454948 CCACAGGCAAGTTCGACA 57.545 55.556 0.00 0.00 0.00 4.35
1952 6338 4.256920 AGTGTCATGTCCTCAATTAGTGC 58.743 43.478 0.00 0.00 0.00 4.40
1962 6348 6.939730 TGTCCTCAATTAGTGCTTGTTCATTA 59.060 34.615 0.00 0.00 0.00 1.90
1989 6375 2.287970 TGTAAGTGCACGAGTTCGATGT 60.288 45.455 12.01 0.00 43.02 3.06
1991 6377 2.717580 AGTGCACGAGTTCGATGTTA 57.282 45.000 12.01 0.00 43.02 2.41
2016 6402 8.561738 AGTTGTGTGGAACTATTTATTGTAGG 57.438 34.615 0.00 0.00 38.04 3.18
2021 6407 8.038944 GTGTGGAACTATTTATTGTAGGAGTGA 58.961 37.037 0.00 0.00 38.04 3.41
2058 6629 8.253810 TGAGTAAAAATCATTTGTTCACCAACA 58.746 29.630 0.00 0.00 40.97 3.33
2094 6666 1.352622 AAGCTTGTCCACCTCCACCA 61.353 55.000 0.00 0.00 0.00 4.17
2106 6678 1.663379 CTCCACCACGGCGATAGTCA 61.663 60.000 16.62 0.00 44.62 3.41
2107 6679 1.216977 CCACCACGGCGATAGTCAA 59.783 57.895 16.62 0.00 44.62 3.18
2128 6700 5.047731 TCAATCGCAAAACCATGATACCAAA 60.048 36.000 0.00 0.00 0.00 3.28
2129 6701 4.167554 TCGCAAAACCATGATACCAAAC 57.832 40.909 0.00 0.00 0.00 2.93
2136 6708 7.173047 GCAAAACCATGATACCAAACAGATTTT 59.827 33.333 0.00 0.00 0.00 1.82
2155 6727 9.338291 CAGATTTTCAGATTGTGTTTCTACATG 57.662 33.333 0.00 0.00 36.50 3.21
2166 6738 8.763049 TTGTGTTTCTACATGATGTTCTAGAG 57.237 34.615 2.29 0.00 36.50 2.43
2205 6777 6.128795 CGAGACAACCACTAGAGATTTTGAAC 60.129 42.308 0.00 0.00 0.00 3.18
2206 6778 5.998363 AGACAACCACTAGAGATTTTGAACC 59.002 40.000 0.00 0.00 0.00 3.62
2207 6779 4.755123 ACAACCACTAGAGATTTTGAACCG 59.245 41.667 0.00 0.00 0.00 4.44
2208 6780 4.618920 ACCACTAGAGATTTTGAACCGT 57.381 40.909 0.00 0.00 0.00 4.83
2209 6781 4.969484 ACCACTAGAGATTTTGAACCGTT 58.031 39.130 0.00 0.00 0.00 4.44
2210 6782 5.374071 ACCACTAGAGATTTTGAACCGTTT 58.626 37.500 0.00 0.00 0.00 3.60
2211 6783 5.469084 ACCACTAGAGATTTTGAACCGTTTC 59.531 40.000 0.00 0.00 0.00 2.78
2212 6784 5.468746 CCACTAGAGATTTTGAACCGTTTCA 59.531 40.000 0.00 0.00 40.14 2.69
2247 6819 8.850454 TCCGTTTTGAAAAACTAGAGATTTTG 57.150 30.769 14.78 0.00 44.58 2.44
2248 6820 8.679100 TCCGTTTTGAAAAACTAGAGATTTTGA 58.321 29.630 14.78 0.00 44.58 2.69
2249 6821 9.296400 CCGTTTTGAAAAACTAGAGATTTTGAA 57.704 29.630 14.78 0.00 44.58 2.69
2286 6858 6.265196 ACCACATCATGTGTACAAAGTTGATT 59.735 34.615 16.74 0.00 46.45 2.57
2287 6859 7.147312 CCACATCATGTGTACAAAGTTGATTT 58.853 34.615 16.74 0.00 46.45 2.17
2288 6860 7.652909 CCACATCATGTGTACAAAGTTGATTTT 59.347 33.333 16.74 0.00 46.45 1.82
2289 6861 9.033481 CACATCATGTGTACAAAGTTGATTTTT 57.967 29.630 9.87 0.00 43.08 1.94
2324 6896 9.503427 AGCGTTTTTATTATCTCAAAATGTAGC 57.497 29.630 0.00 0.00 31.65 3.58
2325 6897 9.284594 GCGTTTTTATTATCTCAAAATGTAGCA 57.715 29.630 0.00 0.00 31.65 3.49
2331 6903 3.837213 TCTCAAAATGTAGCAGCAAGC 57.163 42.857 0.00 0.00 46.19 4.01
2341 6913 3.611433 GCAGCAAGCGGATACAAAG 57.389 52.632 0.00 0.00 0.00 2.77
2342 6914 0.804989 GCAGCAAGCGGATACAAAGT 59.195 50.000 0.00 0.00 0.00 2.66
2343 6915 2.006888 GCAGCAAGCGGATACAAAGTA 58.993 47.619 0.00 0.00 0.00 2.24
2344 6916 2.614057 GCAGCAAGCGGATACAAAGTAT 59.386 45.455 0.00 0.00 0.00 2.12
2345 6917 3.065371 GCAGCAAGCGGATACAAAGTATT 59.935 43.478 0.00 0.00 0.00 1.89
2346 6918 4.272504 GCAGCAAGCGGATACAAAGTATTA 59.727 41.667 0.00 0.00 0.00 0.98
2347 6919 5.049405 GCAGCAAGCGGATACAAAGTATTAT 60.049 40.000 0.00 0.00 0.00 1.28
2348 6920 6.365839 CAGCAAGCGGATACAAAGTATTATG 58.634 40.000 0.00 0.00 0.00 1.90
2349 6921 5.470098 AGCAAGCGGATACAAAGTATTATGG 59.530 40.000 0.00 0.00 0.00 2.74
2350 6922 5.238650 GCAAGCGGATACAAAGTATTATGGT 59.761 40.000 0.00 0.00 0.00 3.55
2351 6923 6.238648 GCAAGCGGATACAAAGTATTATGGTT 60.239 38.462 0.00 0.00 0.00 3.67
2352 6924 7.041644 GCAAGCGGATACAAAGTATTATGGTTA 60.042 37.037 0.00 0.00 0.00 2.85
2353 6925 8.832521 CAAGCGGATACAAAGTATTATGGTTAA 58.167 33.333 0.00 0.00 0.00 2.01
2354 6926 8.374327 AGCGGATACAAAGTATTATGGTTAAC 57.626 34.615 0.00 0.00 0.00 2.01
2355 6927 7.988599 AGCGGATACAAAGTATTATGGTTAACA 59.011 33.333 8.10 0.00 0.00 2.41
2356 6928 8.066000 GCGGATACAAAGTATTATGGTTAACAC 58.934 37.037 8.10 0.00 0.00 3.32
2357 6929 8.553696 CGGATACAAAGTATTATGGTTAACACC 58.446 37.037 8.10 0.00 44.56 4.16
2358 6930 8.843262 GGATACAAAGTATTATGGTTAACACCC 58.157 37.037 8.10 0.00 43.49 4.61
2359 6931 8.756486 ATACAAAGTATTATGGTTAACACCCC 57.244 34.615 8.10 0.00 43.49 4.95
2360 6932 5.648960 ACAAAGTATTATGGTTAACACCCCG 59.351 40.000 8.10 0.00 43.49 5.73
2361 6933 3.812262 AGTATTATGGTTAACACCCCGC 58.188 45.455 8.10 0.00 43.49 6.13
2362 6934 2.061509 ATTATGGTTAACACCCCGCC 57.938 50.000 8.10 0.00 43.49 6.13
2381 6953 2.240162 CTCACTACCGGAACAGGGCC 62.240 65.000 9.46 0.00 35.02 5.80
2385 6957 0.763223 CTACCGGAACAGGGCCCTAT 60.763 60.000 28.13 12.06 35.02 2.57
2411 6983 2.104170 TGGCCATATATATGCCGACGA 58.896 47.619 16.08 4.24 34.64 4.20
2431 7004 3.760035 CCCGTCGGTCCAGTCTGG 61.760 72.222 13.21 13.21 39.43 3.86
2539 7112 2.188469 GCCGTCGGCTTATCCCAA 59.812 61.111 28.98 0.00 46.69 4.12
2540 7113 1.887707 GCCGTCGGCTTATCCCAAG 60.888 63.158 28.98 0.00 46.69 3.61
2541 7114 1.520666 CCGTCGGCTTATCCCAAGT 59.479 57.895 0.00 0.00 0.00 3.16
2665 7255 3.458163 GAGATGGGTGGCCGTCGA 61.458 66.667 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 133 2.722201 GGCGACGACCCTCTGGAAT 61.722 63.158 0.00 0.00 34.81 3.01
175 176 2.282555 CACGTACATTTGGATGAGCTCG 59.717 50.000 9.64 0.00 36.73 5.03
200 2513 9.239002 GGATATCAATCGAGCACACTATAATAC 57.761 37.037 4.83 0.00 32.44 1.89
317 4378 3.535561 GCTACATCACCTAGTGCATGTT 58.464 45.455 13.88 0.00 36.51 2.71
320 4381 1.539065 GCGCTACATCACCTAGTGCAT 60.539 52.381 0.00 0.00 44.03 3.96
326 4387 2.724977 GCTATGCGCTACATCACCTA 57.275 50.000 9.73 0.00 40.38 3.08
350 4411 3.518998 GAGGAGCACGCTCGCCTA 61.519 66.667 12.65 0.00 43.59 3.93
375 4436 1.153756 CCCTCCAACCATATGGCCC 59.846 63.158 22.18 0.00 40.46 5.80
381 4442 1.140312 GATGCCTCCCTCCAACCATA 58.860 55.000 0.00 0.00 0.00 2.74
468 4529 4.515361 AGCATCAGGAGCATATATCTTGC 58.485 43.478 3.01 3.01 40.45 4.01
509 4570 8.620116 TGATGTATCATGTGAAAGAAACTGAA 57.380 30.769 0.00 0.00 0.00 3.02
510 4571 8.620116 TTGATGTATCATGTGAAAGAAACTGA 57.380 30.769 0.00 0.00 36.56 3.41
537 4598 9.703892 GCAACACATCTAGATCTCTGTATATTT 57.296 33.333 1.03 0.00 0.00 1.40
538 4599 8.864087 TGCAACACATCTAGATCTCTGTATATT 58.136 33.333 1.03 0.00 0.00 1.28
539 4600 8.414629 TGCAACACATCTAGATCTCTGTATAT 57.585 34.615 1.03 0.00 0.00 0.86
540 4601 7.823745 TGCAACACATCTAGATCTCTGTATA 57.176 36.000 1.03 0.00 0.00 1.47
541 4602 6.721704 TGCAACACATCTAGATCTCTGTAT 57.278 37.500 1.03 0.00 0.00 2.29
542 4603 6.721704 ATGCAACACATCTAGATCTCTGTA 57.278 37.500 1.03 0.00 31.52 2.74
543 4604 5.611128 ATGCAACACATCTAGATCTCTGT 57.389 39.130 1.03 2.00 31.52 3.41
544 4605 6.018098 GGAAATGCAACACATCTAGATCTCTG 60.018 42.308 1.03 1.37 38.34 3.35
545 4606 6.054295 GGAAATGCAACACATCTAGATCTCT 58.946 40.000 1.03 0.00 38.34 3.10
546 4607 5.050499 CGGAAATGCAACACATCTAGATCTC 60.050 44.000 1.03 0.00 38.34 2.75
547 4608 4.813161 CGGAAATGCAACACATCTAGATCT 59.187 41.667 1.03 0.00 38.34 2.75
548 4609 4.553547 GCGGAAATGCAACACATCTAGATC 60.554 45.833 1.03 0.00 38.34 2.75
549 4610 3.313526 GCGGAAATGCAACACATCTAGAT 59.686 43.478 0.00 0.00 38.34 1.98
550 4611 2.677836 GCGGAAATGCAACACATCTAGA 59.322 45.455 0.00 0.00 38.34 2.43
551 4612 2.679837 AGCGGAAATGCAACACATCTAG 59.320 45.455 0.00 0.00 38.34 2.43
552 4613 2.419673 CAGCGGAAATGCAACACATCTA 59.580 45.455 0.00 0.00 38.34 1.98
553 4614 1.200716 CAGCGGAAATGCAACACATCT 59.799 47.619 0.00 0.00 38.34 2.90
554 4615 1.621107 CAGCGGAAATGCAACACATC 58.379 50.000 0.00 0.00 38.34 3.06
555 4616 0.244450 CCAGCGGAAATGCAACACAT 59.756 50.000 0.00 0.00 42.30 3.21
556 4617 1.106351 ACCAGCGGAAATGCAACACA 61.106 50.000 0.00 0.00 37.31 3.72
557 4618 0.031994 AACCAGCGGAAATGCAACAC 59.968 50.000 0.00 0.00 37.31 3.32
558 4619 0.749649 AAACCAGCGGAAATGCAACA 59.250 45.000 0.00 0.00 37.31 3.33
559 4620 1.000274 AGAAACCAGCGGAAATGCAAC 60.000 47.619 0.00 0.00 37.31 4.17
560 4621 1.327303 AGAAACCAGCGGAAATGCAA 58.673 45.000 0.00 0.00 37.31 4.08
561 4622 1.269448 GAAGAAACCAGCGGAAATGCA 59.731 47.619 0.00 0.00 37.31 3.96
562 4623 1.541588 AGAAGAAACCAGCGGAAATGC 59.458 47.619 1.50 0.00 0.00 3.56
563 4624 4.003648 AGTAGAAGAAACCAGCGGAAATG 58.996 43.478 1.50 0.00 0.00 2.32
564 4625 4.287766 AGTAGAAGAAACCAGCGGAAAT 57.712 40.909 1.50 0.00 0.00 2.17
565 4626 3.764237 AGTAGAAGAAACCAGCGGAAA 57.236 42.857 1.50 0.00 0.00 3.13
566 4627 6.534475 TTATAGTAGAAGAAACCAGCGGAA 57.466 37.500 1.50 0.00 0.00 4.30
567 4628 6.534475 TTTATAGTAGAAGAAACCAGCGGA 57.466 37.500 1.50 0.00 0.00 5.54
568 4629 9.141400 GATATTTATAGTAGAAGAAACCAGCGG 57.859 37.037 0.00 0.00 0.00 5.52
569 4630 9.692749 TGATATTTATAGTAGAAGAAACCAGCG 57.307 33.333 0.00 0.00 0.00 5.18
591 4652 9.665719 TGTAATGTTGCTATGAAAAGACTGATA 57.334 29.630 0.00 0.00 0.00 2.15
592 4653 8.565896 TGTAATGTTGCTATGAAAAGACTGAT 57.434 30.769 0.00 0.00 0.00 2.90
593 4654 7.977789 TGTAATGTTGCTATGAAAAGACTGA 57.022 32.000 0.00 0.00 0.00 3.41
594 4655 8.610855 CATGTAATGTTGCTATGAAAAGACTG 57.389 34.615 0.00 0.00 40.20 3.51
634 4695 9.097946 GCCCCTTCTACTATCCTATTTAAAGTA 57.902 37.037 0.00 0.00 0.00 2.24
635 4696 7.256225 CGCCCCTTCTACTATCCTATTTAAAGT 60.256 40.741 0.00 0.00 0.00 2.66
636 4697 7.097834 CGCCCCTTCTACTATCCTATTTAAAG 58.902 42.308 0.00 0.00 0.00 1.85
637 4698 6.519551 GCGCCCCTTCTACTATCCTATTTAAA 60.520 42.308 0.00 0.00 0.00 1.52
638 4699 5.046807 GCGCCCCTTCTACTATCCTATTTAA 60.047 44.000 0.00 0.00 0.00 1.52
639 4700 4.465305 GCGCCCCTTCTACTATCCTATTTA 59.535 45.833 0.00 0.00 0.00 1.40
640 4701 3.261137 GCGCCCCTTCTACTATCCTATTT 59.739 47.826 0.00 0.00 0.00 1.40
641 4702 2.832733 GCGCCCCTTCTACTATCCTATT 59.167 50.000 0.00 0.00 0.00 1.73
642 4703 2.458620 GCGCCCCTTCTACTATCCTAT 58.541 52.381 0.00 0.00 0.00 2.57
643 4704 1.885359 CGCGCCCCTTCTACTATCCTA 60.885 57.143 0.00 0.00 0.00 2.94
644 4705 1.179814 CGCGCCCCTTCTACTATCCT 61.180 60.000 0.00 0.00 0.00 3.24
645 4706 1.289380 CGCGCCCCTTCTACTATCC 59.711 63.158 0.00 0.00 0.00 2.59
646 4707 0.039346 GACGCGCCCCTTCTACTATC 60.039 60.000 5.73 0.00 0.00 2.08
647 4708 1.461911 GGACGCGCCCCTTCTACTAT 61.462 60.000 5.73 0.00 0.00 2.12
648 4709 2.123428 GGACGCGCCCCTTCTACTA 61.123 63.158 5.73 0.00 0.00 1.82
649 4710 2.563013 TAGGACGCGCCCCTTCTACT 62.563 60.000 23.03 3.31 37.37 2.57
650 4711 2.123428 TAGGACGCGCCCCTTCTAC 61.123 63.158 23.03 0.00 37.37 2.59
651 4712 2.123428 GTAGGACGCGCCCCTTCTA 61.123 63.158 23.03 2.18 37.37 2.10
652 4713 3.459063 GTAGGACGCGCCCCTTCT 61.459 66.667 23.03 3.21 37.37 2.85
653 4714 3.015312 AAGTAGGACGCGCCCCTTC 62.015 63.158 23.03 18.33 37.37 3.46
654 4715 3.001406 AAGTAGGACGCGCCCCTT 61.001 61.111 23.03 17.24 37.37 3.95
655 4716 3.771160 CAAGTAGGACGCGCCCCT 61.771 66.667 21.83 21.83 37.37 4.79
656 4717 4.832608 CCAAGTAGGACGCGCCCC 62.833 72.222 8.22 9.17 41.22 5.80
658 4719 4.752879 TGCCAAGTAGGACGCGCC 62.753 66.667 5.73 9.03 41.22 6.53
659 4720 3.488090 GTGCCAAGTAGGACGCGC 61.488 66.667 5.73 0.00 41.22 6.86
660 4721 2.813908 GGTGCCAAGTAGGACGCG 60.814 66.667 3.53 3.53 41.22 6.01
661 4722 2.813908 CGGTGCCAAGTAGGACGC 60.814 66.667 0.00 0.00 41.22 5.19
662 4723 2.813908 GCGGTGCCAAGTAGGACG 60.814 66.667 0.00 0.00 41.22 4.79
711 4772 2.306255 ATACTAGTGGTTGGGGCGCG 62.306 60.000 5.39 0.00 0.00 6.86
712 4773 0.814010 CATACTAGTGGTTGGGGCGC 60.814 60.000 5.39 0.00 0.00 6.53
713 4774 0.539986 ACATACTAGTGGTTGGGGCG 59.460 55.000 5.39 0.00 0.00 6.13
714 4775 5.556006 TTATACATACTAGTGGTTGGGGC 57.444 43.478 5.39 0.00 0.00 5.80
715 4776 8.653191 TGTATTTATACATACTAGTGGTTGGGG 58.347 37.037 5.39 0.00 38.28 4.96
716 4777 9.706691 CTGTATTTATACATACTAGTGGTTGGG 57.293 37.037 5.39 0.00 41.92 4.12
717 4778 9.706691 CCTGTATTTATACATACTAGTGGTTGG 57.293 37.037 5.39 0.00 41.92 3.77
718 4779 9.706691 CCCTGTATTTATACATACTAGTGGTTG 57.293 37.037 5.39 3.28 41.92 3.77
719 4780 9.664777 TCCCTGTATTTATACATACTAGTGGTT 57.335 33.333 5.39 0.00 41.92 3.67
720 4781 9.310449 CTCCCTGTATTTATACATACTAGTGGT 57.690 37.037 5.39 6.45 41.92 4.16
721 4782 9.310449 ACTCCCTGTATTTATACATACTAGTGG 57.690 37.037 5.39 0.00 41.92 4.00
724 4785 9.640963 GCAACTCCCTGTATTTATACATACTAG 57.359 37.037 9.78 6.22 41.92 2.57
725 4786 8.301720 CGCAACTCCCTGTATTTATACATACTA 58.698 37.037 9.78 0.00 41.92 1.82
726 4787 7.014905 TCGCAACTCCCTGTATTTATACATACT 59.985 37.037 9.78 0.00 41.92 2.12
727 4788 7.149973 TCGCAACTCCCTGTATTTATACATAC 58.850 38.462 3.23 2.60 41.92 2.39
777 4838 5.412286 GGTAGTAGGATCTATGTCGAGGAAC 59.588 48.000 0.00 0.00 0.00 3.62
796 4857 6.828785 ACAGAAAAGAATGTTTCAGTGGTAGT 59.171 34.615 0.97 0.00 39.52 2.73
800 4861 6.145535 GCTACAGAAAAGAATGTTTCAGTGG 58.854 40.000 6.11 4.69 37.66 4.00
801 4862 6.145535 GGCTACAGAAAAGAATGTTTCAGTG 58.854 40.000 6.11 0.00 37.66 3.66
978 5052 1.667154 CCTGGCGGACGATCTTCTCA 61.667 60.000 0.00 0.00 0.00 3.27
994 5068 2.780714 GATGATCTTGGCCATCTCCTG 58.219 52.381 6.09 0.00 36.97 3.86
1102 5186 3.079578 CCATGATCAATAGCAGCGGAAT 58.920 45.455 0.00 0.00 0.00 3.01
1106 5190 3.501062 ACATTCCATGATCAATAGCAGCG 59.499 43.478 0.00 0.00 0.00 5.18
1157 5241 5.395103 GGCATCACAACCCTGCAATTTAATA 60.395 40.000 0.00 0.00 37.64 0.98
1364 5750 4.658786 ACCGGCCAGAAGGGTCCT 62.659 66.667 0.00 0.00 38.37 3.85
1548 5934 2.263540 GGCGAAAGACGGGCAGTA 59.736 61.111 0.00 0.00 42.83 2.74
1571 5957 1.296715 GCTGGTGGTGGTGTAGAGG 59.703 63.158 0.00 0.00 0.00 3.69
1579 5965 2.738521 CGTTCTCGCTGGTGGTGG 60.739 66.667 0.00 0.00 0.00 4.61
1703 6089 5.105310 GGTATCAGAAGTCTTGAAGCTACCA 60.105 44.000 0.00 0.00 0.00 3.25
1718 6104 2.621998 GCGGTAGTAGCTGGTATCAGAA 59.378 50.000 7.33 0.00 43.49 3.02
1720 6106 1.269998 GGCGGTAGTAGCTGGTATCAG 59.730 57.143 0.00 0.00 43.64 2.90
1788 6174 2.738521 CTTGGTGGTGGCGTCGAG 60.739 66.667 0.00 0.00 0.00 4.04
1842 6228 1.273886 GAAGTCCCTGAAGAACTCGCT 59.726 52.381 0.00 0.00 0.00 4.93
1952 6338 9.329913 GTGCACTTACAGTAAATAATGAACAAG 57.670 33.333 10.32 0.00 0.00 3.16
1962 6348 4.384846 CGAACTCGTGCACTTACAGTAAAT 59.615 41.667 16.19 0.00 34.11 1.40
1980 6366 4.330944 TCCACACAACTAACATCGAACT 57.669 40.909 0.00 0.00 0.00 3.01
1991 6377 8.380099 TCCTACAATAAATAGTTCCACACAACT 58.620 33.333 0.00 0.00 39.94 3.16
2048 6619 4.697352 AGCAGATCATTAGTGTTGGTGAAC 59.303 41.667 0.00 0.00 0.00 3.18
2106 6678 5.167845 GTTTGGTATCATGGTTTTGCGATT 58.832 37.500 0.00 0.00 0.00 3.34
2107 6679 4.219507 TGTTTGGTATCATGGTTTTGCGAT 59.780 37.500 0.00 0.00 0.00 4.58
2115 6687 6.947733 TCTGAAAATCTGTTTGGTATCATGGT 59.052 34.615 0.00 0.00 0.00 3.55
2128 6700 8.450578 TGTAGAAACACAATCTGAAAATCTGT 57.549 30.769 0.00 0.00 0.00 3.41
2129 6701 9.338291 CATGTAGAAACACAATCTGAAAATCTG 57.662 33.333 0.00 0.00 38.78 2.90
2136 6708 7.879677 AGAACATCATGTAGAAACACAATCTGA 59.120 33.333 0.00 0.00 38.78 3.27
2155 6727 6.981559 GTGTAAACATCCTCCTCTAGAACATC 59.018 42.308 0.00 0.00 0.00 3.06
2166 6738 3.587797 TGTCTCGTGTAAACATCCTCC 57.412 47.619 0.00 0.00 0.00 4.30
2244 6816 4.825422 TGTGGTGCATTTTTGTCTTCAAA 58.175 34.783 0.00 0.00 41.10 2.69
2245 6817 4.462508 TGTGGTGCATTTTTGTCTTCAA 57.537 36.364 0.00 0.00 0.00 2.69
2246 6818 4.099113 TGATGTGGTGCATTTTTGTCTTCA 59.901 37.500 0.00 0.00 38.06 3.02
2247 6819 4.619973 TGATGTGGTGCATTTTTGTCTTC 58.380 39.130 0.00 0.00 38.06 2.87
2248 6820 4.669206 TGATGTGGTGCATTTTTGTCTT 57.331 36.364 0.00 0.00 38.06 3.01
2249 6821 4.039488 ACATGATGTGGTGCATTTTTGTCT 59.961 37.500 0.00 0.00 38.06 3.41
2250 6822 4.150980 CACATGATGTGGTGCATTTTTGTC 59.849 41.667 17.51 0.00 44.27 3.18
2251 6823 4.059511 CACATGATGTGGTGCATTTTTGT 58.940 39.130 17.51 0.00 44.27 2.83
2252 6824 4.655440 CACATGATGTGGTGCATTTTTG 57.345 40.909 17.51 0.00 44.27 2.44
2298 6870 9.503427 GCTACATTTTGAGATAATAAAAACGCT 57.497 29.630 0.00 0.00 30.50 5.07
2299 6871 9.284594 TGCTACATTTTGAGATAATAAAAACGC 57.715 29.630 0.00 0.00 30.50 4.84
2305 6877 8.131100 GCTTGCTGCTACATTTTGAGATAATAA 58.869 33.333 0.00 0.00 38.95 1.40
2306 6878 7.518848 CGCTTGCTGCTACATTTTGAGATAATA 60.519 37.037 0.00 0.00 40.11 0.98
2307 6879 6.501781 GCTTGCTGCTACATTTTGAGATAAT 58.498 36.000 0.00 0.00 38.95 1.28
2308 6880 5.447683 CGCTTGCTGCTACATTTTGAGATAA 60.448 40.000 0.00 0.00 40.11 1.75
2309 6881 4.034394 CGCTTGCTGCTACATTTTGAGATA 59.966 41.667 0.00 0.00 40.11 1.98
2310 6882 3.181503 CGCTTGCTGCTACATTTTGAGAT 60.182 43.478 0.00 0.00 40.11 2.75
2311 6883 2.160219 CGCTTGCTGCTACATTTTGAGA 59.840 45.455 0.00 0.00 40.11 3.27
2312 6884 2.512885 CGCTTGCTGCTACATTTTGAG 58.487 47.619 0.00 0.00 40.11 3.02
2313 6885 1.199789 CCGCTTGCTGCTACATTTTGA 59.800 47.619 0.00 0.00 40.11 2.69
2314 6886 1.199789 TCCGCTTGCTGCTACATTTTG 59.800 47.619 0.00 0.00 40.11 2.44
2315 6887 1.533625 TCCGCTTGCTGCTACATTTT 58.466 45.000 0.00 0.00 40.11 1.82
2316 6888 1.755179 ATCCGCTTGCTGCTACATTT 58.245 45.000 0.00 0.00 40.11 2.32
2317 6889 2.213499 GTATCCGCTTGCTGCTACATT 58.787 47.619 0.00 0.00 40.11 2.71
2318 6890 1.138859 TGTATCCGCTTGCTGCTACAT 59.861 47.619 0.00 0.00 40.11 2.29
2319 6891 0.534873 TGTATCCGCTTGCTGCTACA 59.465 50.000 0.00 0.00 40.11 2.74
2320 6892 1.651987 TTGTATCCGCTTGCTGCTAC 58.348 50.000 0.00 0.00 40.11 3.58
2321 6893 2.279741 CTTTGTATCCGCTTGCTGCTA 58.720 47.619 0.00 0.00 40.11 3.49
2322 6894 1.089920 CTTTGTATCCGCTTGCTGCT 58.910 50.000 0.00 0.00 40.11 4.24
2323 6895 0.804989 ACTTTGTATCCGCTTGCTGC 59.195 50.000 0.00 0.00 38.57 5.25
2324 6896 4.882671 AATACTTTGTATCCGCTTGCTG 57.117 40.909 0.00 0.00 0.00 4.41
2325 6897 5.470098 CCATAATACTTTGTATCCGCTTGCT 59.530 40.000 0.00 0.00 0.00 3.91
2326 6898 5.238650 ACCATAATACTTTGTATCCGCTTGC 59.761 40.000 0.00 0.00 0.00 4.01
2327 6899 6.861065 ACCATAATACTTTGTATCCGCTTG 57.139 37.500 0.00 0.00 0.00 4.01
2328 6900 8.833493 GTTAACCATAATACTTTGTATCCGCTT 58.167 33.333 0.00 0.00 0.00 4.68
2329 6901 7.988599 TGTTAACCATAATACTTTGTATCCGCT 59.011 33.333 2.48 0.00 0.00 5.52
2330 6902 8.066000 GTGTTAACCATAATACTTTGTATCCGC 58.934 37.037 2.48 0.00 32.24 5.54
2331 6903 8.553696 GGTGTTAACCATAATACTTTGTATCCG 58.446 37.037 2.48 0.00 46.75 4.18
2348 6920 1.673337 GTGAGGCGGGGTGTTAACC 60.673 63.158 2.48 0.00 46.81 2.85
2349 6921 0.609662 TAGTGAGGCGGGGTGTTAAC 59.390 55.000 0.00 0.00 0.00 2.01
2350 6922 0.609662 GTAGTGAGGCGGGGTGTTAA 59.390 55.000 0.00 0.00 0.00 2.01
2351 6923 1.259840 GGTAGTGAGGCGGGGTGTTA 61.260 60.000 0.00 0.00 0.00 2.41
2352 6924 2.590114 GGTAGTGAGGCGGGGTGTT 61.590 63.158 0.00 0.00 0.00 3.32
2353 6925 3.001406 GGTAGTGAGGCGGGGTGT 61.001 66.667 0.00 0.00 0.00 4.16
2354 6926 4.143333 CGGTAGTGAGGCGGGGTG 62.143 72.222 0.00 0.00 0.00 4.61
2357 6929 3.072468 TTCCGGTAGTGAGGCGGG 61.072 66.667 0.00 0.00 0.00 6.13
2358 6930 2.183555 GTTCCGGTAGTGAGGCGG 59.816 66.667 0.00 0.00 0.00 6.13
2359 6931 1.153823 CTGTTCCGGTAGTGAGGCG 60.154 63.158 0.00 0.00 0.00 5.52
2360 6932 1.218316 CCTGTTCCGGTAGTGAGGC 59.782 63.158 0.00 0.00 0.00 4.70
2361 6933 1.898154 CCCTGTTCCGGTAGTGAGG 59.102 63.158 0.00 0.96 0.00 3.86
2362 6934 1.218316 GCCCTGTTCCGGTAGTGAG 59.782 63.158 0.00 0.00 0.00 3.51
2397 6969 1.477553 GGGGGTCGTCGGCATATATA 58.522 55.000 0.00 0.00 0.00 0.86
2422 6995 3.647367 GGCATAGCCCAGACTGGA 58.353 61.111 23.77 3.13 44.06 3.86
2504 7077 4.418328 TGATTTGGGCCGACGGGG 62.418 66.667 17.22 0.00 39.58 5.73
2505 7078 2.824041 CTGATTTGGGCCGACGGG 60.824 66.667 17.22 0.00 0.00 5.28
2625 7215 1.729838 GTCGGCATAGATCGGACGC 60.730 63.158 5.58 0.00 0.00 5.19
2652 7242 2.680707 TATGTCGACGGCCACCCA 60.681 61.111 11.62 0.00 0.00 4.51
2665 7255 1.325355 CGTGTCCCCCGTATCTATGT 58.675 55.000 0.00 0.00 0.00 2.29
2678 7268 2.509336 CTGGATCGGTGCGTGTCC 60.509 66.667 0.00 0.00 34.98 4.02


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

AutoCloner maintained by Alex Coulton.