Multiple sequence alignment - TraesCS2A01G185300

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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 TraesCS2A01G185300 chr2A 100.000 8540 0 0 1 8540 146087264 146078725 0.000000e+00 15771.0
1 TraesCS2A01G185300 chr2D 96.607 6189 140 35 1551 7699 154624973 154631131 0.000000e+00 10202.0
2 TraesCS2A01G185300 chr2D 93.414 1078 60 7 464 1537 154623786 154624856 0.000000e+00 1587.0
3 TraesCS2A01G185300 chr2D 95.498 422 17 2 1 420 154623367 154623788 0.000000e+00 673.0
4 TraesCS2A01G185300 chr2D 96.861 223 6 1 7693 7915 154631168 154631389 1.050000e-98 372.0
5 TraesCS2A01G185300 chr2D 88.584 219 14 4 8021 8234 154631514 154631726 1.100000e-63 255.0
6 TraesCS2A01G185300 chr2B 97.793 5165 90 12 1897 7051 211869309 211874459 0.000000e+00 8885.0
7 TraesCS2A01G185300 chr2B 89.633 762 54 14 7068 7805 211874556 211875316 0.000000e+00 946.0
8 TraesCS2A01G185300 chr2B 92.574 606 33 8 811 1416 211865496 211866089 0.000000e+00 859.0
9 TraesCS2A01G185300 chr2B 90.974 421 16 5 1403 1817 211867581 211867985 1.620000e-151 547.0
10 TraesCS2A01G185300 chr2B 84.896 192 10 8 7803 7975 211875364 211875555 8.810000e-40 176.0
11 TraesCS2A01G185300 chr2B 95.122 82 4 0 1823 1904 211869177 211869258 6.960000e-26 130.0
12 TraesCS2A01G185300 chr2B 81.513 119 11 4 8284 8396 211875896 211876009 4.250000e-13 87.9
13 TraesCS2A01G185300 chr1A 95.745 94 4 0 8444 8537 49249739 49249646 1.480000e-32 152.0
14 TraesCS2A01G185300 chr1A 91.837 98 6 2 8436 8533 537892655 537892560 1.500000e-27 135.0
15 TraesCS2A01G185300 chr3D 96.552 87 3 0 8444 8530 571378037 571377951 2.480000e-30 145.0
16 TraesCS2A01G185300 chr3B 96.552 87 3 0 8444 8530 748777090 748777176 2.480000e-30 145.0
17 TraesCS2A01G185300 chr3A 95.556 90 4 0 8444 8533 646921641 646921552 2.480000e-30 145.0
18 TraesCS2A01G185300 chr6B 96.512 86 3 0 8444 8529 162181177 162181262 8.940000e-30 143.0
19 TraesCS2A01G185300 chr6B 89.091 110 9 3 8421 8529 24799100 24799207 5.380000e-27 134.0
20 TraesCS2A01G185300 chr5B 95.556 90 3 1 8445 8533 674496535 674496624 8.940000e-30 143.0
21 TraesCS2A01G185300 chr4D 94.565 92 5 0 8445 8536 509106377 509106468 8.940000e-30 143.0


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 TraesCS2A01G185300 chr2A 146078725 146087264 8539 True 15771.000000 15771 100.000000 1 8540 1 chr2A.!!$R1 8539
1 TraesCS2A01G185300 chr2D 154623367 154631726 8359 False 2617.800000 10202 94.192800 1 8234 5 chr2D.!!$F1 8233
2 TraesCS2A01G185300 chr2B 211865496 211876009 10513 False 1661.557143 8885 90.357857 811 8396 7 chr2B.!!$F1 7585

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
616 619 1.338769 GGCGTACTGACCAATTCCTGT 60.339 52.381 0.00 0.0 0.00 4.00 F
1080 1083 0.178068 AATCTCAACCCCGATCACCG 59.822 55.000 0.00 0.0 38.18 4.94 F
1204 1207 0.610232 CAAACCCCTGAGCCAGAAGG 60.610 60.000 4.00 6.7 32.44 3.46 F
1407 1410 1.208052 CCTCCCTCAATTTCTCGCTGA 59.792 52.381 0.00 0.0 0.00 4.26 F
2525 5392 2.037251 GGTTTCTGGCGCTAGGATCATA 59.963 50.000 21.43 0.0 0.00 2.15 F
3815 6682 0.647410 CGGCTGCTGTCTTTGATACG 59.353 55.000 0.00 0.0 0.00 3.06 F
5559 8433 3.439857 ACTTTGATGGTGTGCAGGTAT 57.560 42.857 0.00 0.0 0.00 2.73 F
6375 9252 1.903183 ACCAGGGCTCTGTCTAGTTTC 59.097 52.381 13.79 0.0 39.31 2.78 F
6922 9803 0.036164 TCCCATGTCCCGACACAAAG 59.964 55.000 0.00 0.0 45.05 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2525 5392 1.569072 AGGTGTCCAAAAGGTTCCTGT 59.431 47.619 0.0 0.00 0.00 4.00 R
2795 5662 6.828273 TCTTTCCTTTGTCTGTTGATTTCTCA 59.172 34.615 0.0 0.00 0.00 3.27 R
3648 6515 9.406828 GTCCAAGGTATTACAAGAATCAAAAAC 57.593 33.333 0.0 0.00 0.00 2.43 R
3815 6682 5.995897 ACTACCGCCAACTAATTCAATATCC 59.004 40.000 0.0 0.00 0.00 2.59 R
4446 7313 6.322456 TGGACATCAAAACAGTTTTCATGGTA 59.678 34.615 22.3 8.85 0.00 3.25 R
5649 8523 1.003118 CTCGTCCCCATCACCTTTTGA 59.997 52.381 0.0 0.00 39.11 2.69 R
6740 9617 0.108186 CCGCAGCAGGAGTAACATCA 60.108 55.000 0.0 0.00 0.00 3.07 R
7248 10212 0.868602 CGTCGTGTGTCCTCGTGTTT 60.869 55.000 0.0 0.00 0.00 2.83 R
8142 11327 1.425448 AGCCCTGCTTAGAAAACCAGT 59.575 47.619 0.0 0.00 33.89 4.00 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
88 90 6.892658 ATTTGTTGTTGCTATACTCCACAA 57.107 33.333 0.00 0.00 0.00 3.33
114 116 6.206634 AGTTAGGAACATAACACACACCAATG 59.793 38.462 10.98 0.00 37.98 2.82
128 130 9.171877 ACACACACCAATGAATTTTATGTTTTT 57.828 25.926 0.00 0.00 0.00 1.94
129 131 9.649024 CACACACCAATGAATTTTATGTTTTTC 57.351 29.630 0.00 0.00 0.00 2.29
353 356 6.365970 AGTCAATGTGATCAACTAGGTCTT 57.634 37.500 0.00 0.00 0.00 3.01
365 368 2.963782 ACTAGGTCTTGACGGAAAGTGT 59.036 45.455 0.00 0.00 0.00 3.55
366 369 2.240493 AGGTCTTGACGGAAAGTGTG 57.760 50.000 0.00 0.00 0.00 3.82
392 395 3.575630 TCTCTATGTGTTGCAACGTCTC 58.424 45.455 23.79 14.26 0.00 3.36
402 405 4.334203 TGTTGCAACGTCTCTTTGTTATGT 59.666 37.500 23.79 0.00 0.00 2.29
405 408 3.469629 CAACGTCTCTTTGTTATGTGCG 58.530 45.455 0.00 0.00 0.00 5.34
420 423 8.039603 TGTTATGTGCGAAAATCTTGTATTCT 57.960 30.769 0.00 0.00 0.00 2.40
421 424 9.157104 TGTTATGTGCGAAAATCTTGTATTCTA 57.843 29.630 0.00 0.00 0.00 2.10
422 425 9.422196 GTTATGTGCGAAAATCTTGTATTCTAC 57.578 33.333 0.00 0.00 0.00 2.59
423 426 6.417191 TGTGCGAAAATCTTGTATTCTACC 57.583 37.500 0.00 0.00 0.00 3.18
424 427 5.935206 TGTGCGAAAATCTTGTATTCTACCA 59.065 36.000 0.00 0.00 0.00 3.25
425 428 6.128391 TGTGCGAAAATCTTGTATTCTACCAC 60.128 38.462 0.00 0.00 0.00 4.16
426 429 5.935206 TGCGAAAATCTTGTATTCTACCACA 59.065 36.000 0.00 0.00 0.00 4.17
427 430 6.128391 TGCGAAAATCTTGTATTCTACCACAC 60.128 38.462 0.00 0.00 0.00 3.82
428 431 6.128391 GCGAAAATCTTGTATTCTACCACACA 60.128 38.462 0.00 0.00 0.00 3.72
429 432 7.414098 GCGAAAATCTTGTATTCTACCACACAT 60.414 37.037 0.00 0.00 0.00 3.21
430 433 9.093970 CGAAAATCTTGTATTCTACCACACATA 57.906 33.333 0.00 0.00 0.00 2.29
432 435 8.420374 AAATCTTGTATTCTACCACACATACG 57.580 34.615 0.00 0.00 0.00 3.06
433 436 6.762702 TCTTGTATTCTACCACACATACGA 57.237 37.500 0.00 0.00 0.00 3.43
434 437 7.342769 TCTTGTATTCTACCACACATACGAT 57.657 36.000 0.00 0.00 0.00 3.73
435 438 7.200455 TCTTGTATTCTACCACACATACGATG 58.800 38.462 0.00 0.00 0.00 3.84
436 439 5.286438 TGTATTCTACCACACATACGATGC 58.714 41.667 0.00 0.00 0.00 3.91
437 440 2.882927 TCTACCACACATACGATGCC 57.117 50.000 0.00 0.00 0.00 4.40
438 441 2.384828 TCTACCACACATACGATGCCT 58.615 47.619 0.00 0.00 0.00 4.75
439 442 2.764010 TCTACCACACATACGATGCCTT 59.236 45.455 0.00 0.00 0.00 4.35
440 443 3.955551 TCTACCACACATACGATGCCTTA 59.044 43.478 0.00 0.00 0.00 2.69
441 444 3.838244 ACCACACATACGATGCCTTAT 57.162 42.857 0.00 0.00 0.00 1.73
442 445 4.948341 ACCACACATACGATGCCTTATA 57.052 40.909 0.00 0.00 0.00 0.98
443 446 5.483685 ACCACACATACGATGCCTTATAT 57.516 39.130 0.00 0.00 0.00 0.86
444 447 6.599356 ACCACACATACGATGCCTTATATA 57.401 37.500 0.00 0.00 0.00 0.86
445 448 6.999950 ACCACACATACGATGCCTTATATAA 58.000 36.000 0.00 0.00 0.00 0.98
446 449 6.872020 ACCACACATACGATGCCTTATATAAC 59.128 38.462 0.00 0.00 0.00 1.89
447 450 6.871492 CCACACATACGATGCCTTATATAACA 59.129 38.462 0.00 0.00 0.00 2.41
448 451 7.148639 CCACACATACGATGCCTTATATAACAC 60.149 40.741 0.00 0.00 0.00 3.32
449 452 7.598869 CACACATACGATGCCTTATATAACACT 59.401 37.037 0.00 0.00 0.00 3.55
450 453 7.598869 ACACATACGATGCCTTATATAACACTG 59.401 37.037 0.00 0.00 0.00 3.66
451 454 7.063426 CACATACGATGCCTTATATAACACTGG 59.937 40.741 0.00 0.00 0.00 4.00
452 455 5.546621 ACGATGCCTTATATAACACTGGT 57.453 39.130 0.00 0.00 0.00 4.00
453 456 6.659745 ACGATGCCTTATATAACACTGGTA 57.340 37.500 0.00 0.00 0.00 3.25
454 457 7.241042 ACGATGCCTTATATAACACTGGTAT 57.759 36.000 0.00 2.88 0.00 2.73
455 458 8.357290 ACGATGCCTTATATAACACTGGTATA 57.643 34.615 0.00 0.00 0.00 1.47
456 459 8.809066 ACGATGCCTTATATAACACTGGTATAA 58.191 33.333 0.00 0.00 0.00 0.98
457 460 9.647797 CGATGCCTTATATAACACTGGTATAAA 57.352 33.333 0.00 0.00 0.00 1.40
481 484 4.818534 AATTTCATGTCGATTCATCCGG 57.181 40.909 0.00 0.00 0.00 5.14
505 508 6.308675 GTGTCTAGAAGTAGAAGTCGAACTG 58.691 44.000 0.00 0.00 37.02 3.16
520 523 7.559590 AGTCGAACTGGTATATACGTTTACT 57.440 36.000 6.79 10.21 0.00 2.24
605 608 2.995283 TGCTTCTACTAGGCGTACTGA 58.005 47.619 0.00 0.00 0.00 3.41
616 619 1.338769 GGCGTACTGACCAATTCCTGT 60.339 52.381 0.00 0.00 0.00 4.00
618 621 2.870435 GCGTACTGACCAATTCCTGTGT 60.870 50.000 0.00 0.00 0.00 3.72
622 625 5.394224 CGTACTGACCAATTCCTGTGTCTAT 60.394 44.000 0.00 0.00 0.00 1.98
624 627 4.532126 ACTGACCAATTCCTGTGTCTATGA 59.468 41.667 0.00 0.00 0.00 2.15
630 633 8.193953 ACCAATTCCTGTGTCTATGAATTTTT 57.806 30.769 0.00 0.00 35.77 1.94
751 754 4.683832 AGAGTTAGGAATATGACACACGC 58.316 43.478 0.00 0.00 0.00 5.34
764 767 5.888691 TGACACACGCCAATAAATGTTAT 57.111 34.783 0.00 0.00 0.00 1.89
1052 1055 2.837291 CTGCTCCTCCTCCTCCGG 60.837 72.222 0.00 0.00 0.00 5.14
1080 1083 0.178068 AATCTCAACCCCGATCACCG 59.822 55.000 0.00 0.00 38.18 4.94
1204 1207 0.610232 CAAACCCCTGAGCCAGAAGG 60.610 60.000 4.00 6.70 32.44 3.46
1236 1239 2.741211 GCCGAACAACCGACCTCC 60.741 66.667 0.00 0.00 0.00 4.30
1407 1410 1.208052 CCTCCCTCAATTTCTCGCTGA 59.792 52.381 0.00 0.00 0.00 4.26
1426 2934 4.340381 GCTGATTACAATTCATGGCTCCTT 59.660 41.667 0.00 0.00 0.00 3.36
1466 2974 8.085296 CACATGGCAAAGTAAAACCTAAATACA 58.915 33.333 0.00 0.00 0.00 2.29
1479 2987 6.610075 ACCTAAATACACTCCGAAACCTAA 57.390 37.500 0.00 0.00 0.00 2.69
1504 3018 5.941948 TTGTTTAGACTTAGCAGGCTTTC 57.058 39.130 0.00 0.00 32.45 2.62
1521 3035 4.992951 GGCTTTCAGCATTTCAAAGATTGT 59.007 37.500 0.00 0.00 44.75 2.71
1538 3053 9.023967 CAAAGATTGTTCCTTACACTTTCAAAG 57.976 33.333 0.00 0.00 33.30 2.77
1729 3348 3.776969 TGAATGCTCACTGGACCTTCTAT 59.223 43.478 0.00 0.00 0.00 1.98
1759 3378 2.099263 CGCTTCTCTTCGATTCTACCCA 59.901 50.000 0.00 0.00 0.00 4.51
2525 5392 2.037251 GGTTTCTGGCGCTAGGATCATA 59.963 50.000 21.43 0.00 0.00 2.15
2616 5483 8.199449 CCACATGATTTTCTTAGGCATTTATGT 58.801 33.333 0.00 0.00 0.00 2.29
2617 5484 9.590451 CACATGATTTTCTTAGGCATTTATGTT 57.410 29.630 0.00 0.00 0.00 2.71
2691 5558 9.019764 CACCCAAATTTTGACATATATTCGTTC 57.980 33.333 10.72 0.00 0.00 3.95
2975 5842 2.312140 AGGTCAAGGACTAGAGGTGCTA 59.688 50.000 0.00 0.00 45.87 3.49
3654 6521 3.169355 AGCTTCAGCAGGTTGTTTTTG 57.831 42.857 0.75 0.00 45.16 2.44
3782 6649 5.524646 GGATGAGATTGAGAAGCAGAAGAAG 59.475 44.000 0.00 0.00 0.00 2.85
3815 6682 0.647410 CGGCTGCTGTCTTTGATACG 59.353 55.000 0.00 0.00 0.00 3.06
4143 7010 6.370166 CCTCAGTTAGAACCAAGAGATGTTTC 59.630 42.308 8.06 0.00 31.01 2.78
4298 7165 5.534207 TTTGGACATGCTTTCAGTCAAAT 57.466 34.783 0.00 0.00 34.04 2.32
4310 7177 9.388506 TGCTTTCAGTCAAATTTCCAAAATTTA 57.611 25.926 9.39 0.00 0.00 1.40
4451 7318 9.975218 AGAAATAAGTGGTCAAAGTTATACCAT 57.025 29.630 11.32 1.62 44.69 3.55
5247 8121 7.816995 CAGTCTATTCTGTGTTTAGAAAGCTCT 59.183 37.037 0.00 0.00 39.87 4.09
5559 8433 3.439857 ACTTTGATGGTGTGCAGGTAT 57.560 42.857 0.00 0.00 0.00 2.73
5649 8523 3.886123 ACAGTTGTGGACAAGTTAAGCT 58.114 40.909 0.00 0.00 37.41 3.74
5735 8609 9.359653 ACTGGAATCCTAATATTTGGAAGAATG 57.640 33.333 20.29 13.51 35.77 2.67
6375 9252 1.903183 ACCAGGGCTCTGTCTAGTTTC 59.097 52.381 13.79 0.00 39.31 2.78
6600 9477 4.220602 GGTACACAAGGGCAAATGAAATCT 59.779 41.667 0.00 0.00 0.00 2.40
6606 9483 3.509442 AGGGCAAATGAAATCTTCCACA 58.491 40.909 0.00 0.00 0.00 4.17
6650 9527 4.393239 AGGCATTGGCTGATTATGGTAT 57.607 40.909 12.53 0.00 40.87 2.73
6653 9530 4.281688 GGCATTGGCTGATTATGGTATGTT 59.718 41.667 2.42 0.00 40.87 2.71
6671 9548 7.765819 TGGTATGTTCTGTCAGTATCTTGATTG 59.234 37.037 0.00 0.00 0.00 2.67
6683 9560 7.552687 TCAGTATCTTGATTGAAACCGCTTTAT 59.447 33.333 0.00 0.00 0.00 1.40
6698 9575 4.381566 CCGCTTTATTTGCTGTGTTGTAAC 59.618 41.667 0.00 0.00 0.00 2.50
6739 9616 7.962995 TCAGATGGAGAAATGACTAAGTAGT 57.037 36.000 0.00 0.00 39.71 2.73
6740 9617 8.367660 TCAGATGGAGAAATGACTAAGTAGTT 57.632 34.615 0.00 0.00 36.50 2.24
6741 9618 8.253810 TCAGATGGAGAAATGACTAAGTAGTTG 58.746 37.037 0.00 0.00 36.50 3.16
6754 9631 6.631962 ACTAAGTAGTTGATGTTACTCCTGC 58.368 40.000 0.00 0.00 31.13 4.85
6757 9634 2.704572 AGTTGATGTTACTCCTGCTGC 58.295 47.619 0.00 0.00 0.00 5.25
6761 9638 1.264749 ATGTTACTCCTGCTGCGGGA 61.265 55.000 27.55 27.55 36.43 5.14
6766 9643 1.172812 ACTCCTGCTGCGGGAAAAAC 61.173 55.000 28.82 0.00 38.58 2.43
6778 9655 6.672836 GCTGCGGGAAAAACAATTTGATATTG 60.673 38.462 2.79 0.00 35.29 1.90
6780 9657 5.872070 GCGGGAAAAACAATTTGATATTGGA 59.128 36.000 2.79 0.00 33.56 3.53
6783 9660 8.227119 CGGGAAAAACAATTTGATATTGGAAAC 58.773 33.333 2.79 0.00 33.56 2.78
6796 9673 9.527157 TTGATATTGGAAACTAGGAATTGAACA 57.473 29.630 0.00 0.00 0.00 3.18
6850 9728 7.661536 ATACCTGCTCTAGTCATTTTGAGTA 57.338 36.000 0.00 0.00 31.49 2.59
6922 9803 0.036164 TCCCATGTCCCGACACAAAG 59.964 55.000 0.00 0.00 45.05 2.77
6933 9814 6.027749 GTCCCGACACAAAGCTTTAATATTG 58.972 40.000 12.25 1.26 0.00 1.90
6988 9869 7.219484 ACAAAATCCATTTTCTTGAGTCGAT 57.781 32.000 0.00 0.00 37.86 3.59
7164 10128 2.032528 TTGCGTGCCTGCTAAGCT 59.967 55.556 0.00 0.00 35.36 3.74
7193 10157 4.491676 TGAAACCGAGCACTTACTGATAC 58.508 43.478 0.00 0.00 0.00 2.24
7204 10168 5.701290 GCACTTACTGATACAGTTTGTTCCT 59.299 40.000 9.63 0.00 42.59 3.36
7440 10404 0.107214 CGGCCTGTGTGGGTATGAAT 60.107 55.000 0.00 0.00 36.00 2.57
7536 10500 7.014326 AGGAAGAAAAGAAGTATCACCAAAACC 59.986 37.037 0.00 0.00 0.00 3.27
7561 10528 0.739112 GACGCAGGGCTTCTTCAGAG 60.739 60.000 0.00 0.00 0.00 3.35
7607 10574 3.574396 TGTAAGACCTTGAGAGTGGAGTG 59.426 47.826 0.00 0.00 0.00 3.51
7638 10605 5.242393 AGCTTTCACATATGCTTTGTCTGTT 59.758 36.000 1.58 0.00 30.96 3.16
7640 10607 6.129009 GCTTTCACATATGCTTTGTCTGTTTG 60.129 38.462 1.58 0.00 0.00 2.93
7641 10608 6.631971 TTCACATATGCTTTGTCTGTTTGA 57.368 33.333 1.58 0.00 0.00 2.69
7700 10691 4.630644 ATCCATTAACATCAGGCGAGAT 57.369 40.909 0.00 0.00 0.00 2.75
7721 10755 6.241645 AGATTAAAGTTGGCTCTAAGCTTGT 58.758 36.000 9.86 0.00 41.99 3.16
7778 10812 0.529378 CCAGGGAACAGCAATGAAGC 59.471 55.000 0.00 0.00 0.00 3.86
7922 11024 5.629020 TGATTTGTTCTATTTTTGCACGAGC 59.371 36.000 0.00 0.00 42.57 5.03
7951 11053 5.682730 GCTTCTATTGTAGTCCTCCCTGTTC 60.683 48.000 0.00 0.00 0.00 3.18
7952 11054 4.942944 TCTATTGTAGTCCTCCCTGTTCA 58.057 43.478 0.00 0.00 0.00 3.18
7953 11055 4.956700 TCTATTGTAGTCCTCCCTGTTCAG 59.043 45.833 0.00 0.00 0.00 3.02
7954 11056 2.992847 TGTAGTCCTCCCTGTTCAGA 57.007 50.000 1.00 0.00 0.00 3.27
7955 11057 3.474798 TGTAGTCCTCCCTGTTCAGAT 57.525 47.619 1.00 0.00 0.00 2.90
7984 11092 8.833231 TTTTCTCTCATGTCTTTCGAAACTAT 57.167 30.769 6.47 0.00 0.00 2.12
7986 11094 8.467402 TTCTCTCATGTCTTTCGAAACTATTC 57.533 34.615 6.47 0.00 0.00 1.75
8005 11113 5.536497 ATTCCCTCTGTCCCAAATTACTT 57.464 39.130 0.00 0.00 0.00 2.24
8008 11116 4.019321 TCCCTCTGTCCCAAATTACTTCTG 60.019 45.833 0.00 0.00 0.00 3.02
8009 11117 3.691609 CCTCTGTCCCAAATTACTTCTGC 59.308 47.826 0.00 0.00 0.00 4.26
8010 11118 4.326826 CTCTGTCCCAAATTACTTCTGCA 58.673 43.478 0.00 0.00 0.00 4.41
8011 11119 4.326826 TCTGTCCCAAATTACTTCTGCAG 58.673 43.478 7.63 7.63 0.00 4.41
8012 11120 4.041567 TCTGTCCCAAATTACTTCTGCAGA 59.958 41.667 13.74 13.74 0.00 4.26
8017 11125 6.995091 GTCCCAAATTACTTCTGCAGATAGAT 59.005 38.462 19.04 6.89 0.00 1.98
8018 11126 6.994496 TCCCAAATTACTTCTGCAGATAGATG 59.006 38.462 19.04 10.24 0.00 2.90
8019 11127 6.994496 CCCAAATTACTTCTGCAGATAGATGA 59.006 38.462 19.04 0.00 0.00 2.92
8101 11284 4.390264 AGGTCCAGTTCTTTTCAGCTTAC 58.610 43.478 0.00 0.00 0.00 2.34
8108 11291 2.253610 TCTTTTCAGCTTACGGAGGGA 58.746 47.619 0.00 0.00 0.00 4.20
8116 11300 3.056035 CAGCTTACGGAGGGACTTAGTTT 60.056 47.826 0.00 0.00 41.55 2.66
8119 11303 4.400567 GCTTACGGAGGGACTTAGTTTAGA 59.599 45.833 0.00 0.00 41.55 2.10
8142 11327 5.948742 ATTTCAGGTCAAACCCAAAAGAA 57.051 34.783 0.00 0.00 39.75 2.52
8230 11419 1.453148 GTCAACTTTCGACGTAACCCG 59.547 52.381 0.00 0.00 44.03 5.28
8234 11423 1.200020 ACTTTCGACGTAACCCGGTAG 59.800 52.381 0.00 0.00 42.24 3.18
8235 11424 1.200020 CTTTCGACGTAACCCGGTAGT 59.800 52.381 0.00 0.00 42.24 2.73
8237 11426 1.514873 CGACGTAACCCGGTAGTGC 60.515 63.158 0.00 0.00 42.24 4.40
8238 11427 1.885871 GACGTAACCCGGTAGTGCT 59.114 57.895 0.00 0.00 42.24 4.40
8239 11428 1.094785 GACGTAACCCGGTAGTGCTA 58.905 55.000 0.00 0.00 42.24 3.49
8240 11429 1.064654 GACGTAACCCGGTAGTGCTAG 59.935 57.143 0.00 0.00 42.24 3.42
8241 11430 0.383231 CGTAACCCGGTAGTGCTAGG 59.617 60.000 0.00 0.00 0.00 3.02
8242 11431 1.478631 GTAACCCGGTAGTGCTAGGT 58.521 55.000 0.00 0.00 0.00 3.08
8243 11432 2.654863 GTAACCCGGTAGTGCTAGGTA 58.345 52.381 0.00 0.00 0.00 3.08
8244 11433 2.236489 AACCCGGTAGTGCTAGGTAA 57.764 50.000 0.00 0.00 0.00 2.85
8245 11434 2.236489 ACCCGGTAGTGCTAGGTAAA 57.764 50.000 0.00 0.00 0.00 2.01
8246 11435 2.539302 ACCCGGTAGTGCTAGGTAAAA 58.461 47.619 0.00 0.00 0.00 1.52
8247 11436 3.109928 ACCCGGTAGTGCTAGGTAAAAT 58.890 45.455 0.00 0.00 0.00 1.82
8248 11437 3.118519 ACCCGGTAGTGCTAGGTAAAATG 60.119 47.826 0.00 0.00 0.00 2.32
8249 11438 3.463944 CCGGTAGTGCTAGGTAAAATGG 58.536 50.000 0.00 0.00 0.00 3.16
8250 11439 3.463944 CGGTAGTGCTAGGTAAAATGGG 58.536 50.000 0.00 0.00 0.00 4.00
8251 11440 3.133362 CGGTAGTGCTAGGTAAAATGGGA 59.867 47.826 0.00 0.00 0.00 4.37
8252 11441 4.449131 GGTAGTGCTAGGTAAAATGGGAC 58.551 47.826 0.00 0.00 0.00 4.46
8253 11442 4.163649 GGTAGTGCTAGGTAAAATGGGACT 59.836 45.833 0.00 0.00 34.35 3.85
8254 11443 4.929146 AGTGCTAGGTAAAATGGGACTT 57.071 40.909 0.00 0.00 0.00 3.01
8255 11444 4.844884 AGTGCTAGGTAAAATGGGACTTC 58.155 43.478 0.00 0.00 0.00 3.01
8256 11445 4.536489 AGTGCTAGGTAAAATGGGACTTCT 59.464 41.667 0.00 0.00 0.00 2.85
8319 11508 6.373759 AGGAAGTGGAAAAACTGGAAATAGT 58.626 36.000 0.00 0.00 0.00 2.12
8321 11510 8.002459 AGGAAGTGGAAAAACTGGAAATAGTAA 58.998 33.333 0.00 0.00 0.00 2.24
8322 11511 8.635328 GGAAGTGGAAAAACTGGAAATAGTAAA 58.365 33.333 0.00 0.00 0.00 2.01
8377 11566 8.528044 ACAAAAAGTACAAGGATTCAAAGGTA 57.472 30.769 0.00 0.00 0.00 3.08
8380 11569 6.697641 AAGTACAAGGATTCAAAGGTAGGA 57.302 37.500 0.00 0.00 0.00 2.94
8389 11578 6.834168 GATTCAAAGGTAGGAATCCACAAA 57.166 37.500 0.61 0.00 42.14 2.83
8417 11606 8.985315 AAATCATATGCAGTTTCAATCCTAGA 57.015 30.769 0.00 0.00 0.00 2.43
8418 11607 8.985315 AATCATATGCAGTTTCAATCCTAGAA 57.015 30.769 0.00 0.00 0.00 2.10
8419 11608 8.985315 ATCATATGCAGTTTCAATCCTAGAAA 57.015 30.769 0.00 0.00 32.93 2.52
8420 11609 8.985315 TCATATGCAGTTTCAATCCTAGAAAT 57.015 30.769 0.00 0.00 37.33 2.17
8421 11610 9.412460 TCATATGCAGTTTCAATCCTAGAAATT 57.588 29.630 0.00 0.00 37.33 1.82
8422 11611 9.674824 CATATGCAGTTTCAATCCTAGAAATTC 57.325 33.333 0.00 0.00 37.33 2.17
8423 11612 7.951347 ATGCAGTTTCAATCCTAGAAATTCT 57.049 32.000 0.00 0.00 37.33 2.40
8424 11613 7.765695 TGCAGTTTCAATCCTAGAAATTCTT 57.234 32.000 0.00 0.00 37.33 2.52
8425 11614 8.181904 TGCAGTTTCAATCCTAGAAATTCTTT 57.818 30.769 0.00 0.00 37.33 2.52
8426 11615 8.641541 TGCAGTTTCAATCCTAGAAATTCTTTT 58.358 29.630 0.00 0.00 37.33 2.27
8427 11616 8.919661 GCAGTTTCAATCCTAGAAATTCTTTTG 58.080 33.333 0.00 1.69 37.33 2.44
8428 11617 8.919661 CAGTTTCAATCCTAGAAATTCTTTTGC 58.080 33.333 0.00 0.00 37.33 3.68
8429 11618 8.641541 AGTTTCAATCCTAGAAATTCTTTTGCA 58.358 29.630 0.00 0.00 37.33 4.08
8430 11619 9.428097 GTTTCAATCCTAGAAATTCTTTTGCAT 57.572 29.630 0.00 0.00 37.33 3.96
8431 11620 8.991243 TTCAATCCTAGAAATTCTTTTGCATG 57.009 30.769 0.00 0.00 0.00 4.06
8432 11621 8.352137 TCAATCCTAGAAATTCTTTTGCATGA 57.648 30.769 0.00 0.00 0.00 3.07
8433 11622 8.974238 TCAATCCTAGAAATTCTTTTGCATGAT 58.026 29.630 0.00 0.00 0.00 2.45
8434 11623 9.031360 CAATCCTAGAAATTCTTTTGCATGATG 57.969 33.333 0.00 0.00 0.00 3.07
8435 11624 7.943079 TCCTAGAAATTCTTTTGCATGATGA 57.057 32.000 0.00 0.00 0.00 2.92
8436 11625 8.529424 TCCTAGAAATTCTTTTGCATGATGAT 57.471 30.769 0.00 0.00 0.00 2.45
8437 11626 8.627403 TCCTAGAAATTCTTTTGCATGATGATC 58.373 33.333 0.00 0.00 0.00 2.92
8438 11627 7.866393 CCTAGAAATTCTTTTGCATGATGATCC 59.134 37.037 0.00 0.00 0.00 3.36
8439 11628 7.177832 AGAAATTCTTTTGCATGATGATCCA 57.822 32.000 0.00 0.00 0.00 3.41
8440 11629 7.265673 AGAAATTCTTTTGCATGATGATCCAG 58.734 34.615 0.00 0.00 0.00 3.86
8441 11630 6.540438 AATTCTTTTGCATGATGATCCAGT 57.460 33.333 0.00 0.00 0.00 4.00
8442 11631 5.571784 TTCTTTTGCATGATGATCCAGTC 57.428 39.130 0.00 0.00 0.00 3.51
8443 11632 4.591929 TCTTTTGCATGATGATCCAGTCA 58.408 39.130 0.00 0.00 42.06 3.41
8453 11642 3.981516 TGATCCAGTCATACTCCCTCT 57.018 47.619 0.00 0.00 0.00 3.69
8454 11643 3.570540 TGATCCAGTCATACTCCCTCTG 58.429 50.000 0.00 0.00 0.00 3.35
8455 11644 3.052566 TGATCCAGTCATACTCCCTCTGT 60.053 47.826 0.00 0.00 0.00 3.41
8456 11645 4.168088 TGATCCAGTCATACTCCCTCTGTA 59.832 45.833 0.00 0.00 0.00 2.74
8457 11646 4.603094 TCCAGTCATACTCCCTCTGTAA 57.397 45.455 0.00 0.00 0.00 2.41
8458 11647 4.942944 TCCAGTCATACTCCCTCTGTAAA 58.057 43.478 0.00 0.00 0.00 2.01
8459 11648 4.710375 TCCAGTCATACTCCCTCTGTAAAC 59.290 45.833 0.00 0.00 0.00 2.01
8460 11649 4.712337 CCAGTCATACTCCCTCTGTAAACT 59.288 45.833 0.00 0.00 0.00 2.66
8461 11650 5.892119 CCAGTCATACTCCCTCTGTAAACTA 59.108 44.000 0.00 0.00 0.00 2.24
8462 11651 6.380274 CCAGTCATACTCCCTCTGTAAACTAA 59.620 42.308 0.00 0.00 0.00 2.24
8463 11652 7.070074 CCAGTCATACTCCCTCTGTAAACTAAT 59.930 40.741 0.00 0.00 0.00 1.73
8464 11653 9.132923 CAGTCATACTCCCTCTGTAAACTAATA 57.867 37.037 0.00 0.00 0.00 0.98
8465 11654 9.884814 AGTCATACTCCCTCTGTAAACTAATAT 57.115 33.333 0.00 0.00 0.00 1.28
8471 11660 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
8473 11662 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
8534 11723 5.224821 AGTTTACAGAGGGAGTACAAACC 57.775 43.478 0.00 0.00 0.00 3.27
8535 11724 4.657039 AGTTTACAGAGGGAGTACAAACCA 59.343 41.667 0.00 0.00 0.00 3.67
8536 11725 5.131475 AGTTTACAGAGGGAGTACAAACCAA 59.869 40.000 0.00 0.00 0.00 3.67
8537 11726 3.771577 ACAGAGGGAGTACAAACCAAG 57.228 47.619 0.00 0.00 0.00 3.61
8538 11727 2.224548 ACAGAGGGAGTACAAACCAAGC 60.225 50.000 0.00 0.00 0.00 4.01
8539 11728 2.054799 AGAGGGAGTACAAACCAAGCA 58.945 47.619 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 8.820831 ACTATGAAGATATGGGATTTAGGTCTG 58.179 37.037 0.00 0.00 0.00 3.51
88 90 5.686753 TGGTGTGTGTTATGTTCCTAACTT 58.313 37.500 0.00 0.00 33.62 2.66
128 130 8.531146 AGAAAAATGAGTTGAAAAAGACAAGGA 58.469 29.630 0.00 0.00 0.00 3.36
129 131 8.707938 AGAAAAATGAGTTGAAAAAGACAAGG 57.292 30.769 0.00 0.00 0.00 3.61
174 177 7.278203 TCAATTACTTACGACACAGACAAAACA 59.722 33.333 0.00 0.00 0.00 2.83
180 183 7.168637 TGAAACTCAATTACTTACGACACAGAC 59.831 37.037 0.00 0.00 0.00 3.51
280 283 4.562757 GGCGTTGGGTATATAAGAGCATCA 60.563 45.833 0.00 0.00 37.82 3.07
325 328 5.352569 CCTAGTTGATCACATTGACTTCCAC 59.647 44.000 0.00 0.00 0.00 4.02
326 329 5.013079 ACCTAGTTGATCACATTGACTTCCA 59.987 40.000 0.00 0.00 0.00 3.53
353 356 2.231478 GAGATCTCCACACTTTCCGTCA 59.769 50.000 12.00 0.00 0.00 4.35
365 368 4.507710 GTTGCAACACATAGAGATCTCCA 58.492 43.478 24.52 6.16 0.00 3.86
366 369 3.553511 CGTTGCAACACATAGAGATCTCC 59.446 47.826 28.01 1.63 0.00 3.71
392 395 6.991485 ACAAGATTTTCGCACATAACAAAG 57.009 33.333 0.00 0.00 0.00 2.77
402 405 5.935206 TGTGGTAGAATACAAGATTTTCGCA 59.065 36.000 0.00 0.00 45.43 5.10
420 423 4.948341 ATAAGGCATCGTATGTGTGGTA 57.052 40.909 0.00 0.00 0.00 3.25
421 424 3.838244 ATAAGGCATCGTATGTGTGGT 57.162 42.857 0.00 0.00 0.00 4.16
422 425 6.871492 TGTTATATAAGGCATCGTATGTGTGG 59.129 38.462 0.00 0.00 0.00 4.17
423 426 7.598869 AGTGTTATATAAGGCATCGTATGTGTG 59.401 37.037 0.00 0.00 0.00 3.82
424 427 7.598869 CAGTGTTATATAAGGCATCGTATGTGT 59.401 37.037 0.00 0.00 0.00 3.72
425 428 7.063426 CCAGTGTTATATAAGGCATCGTATGTG 59.937 40.741 0.00 0.00 0.00 3.21
426 429 7.097192 CCAGTGTTATATAAGGCATCGTATGT 58.903 38.462 0.00 0.00 0.00 2.29
427 430 7.097192 ACCAGTGTTATATAAGGCATCGTATG 58.903 38.462 0.00 0.00 0.00 2.39
428 431 7.241042 ACCAGTGTTATATAAGGCATCGTAT 57.759 36.000 0.00 0.00 0.00 3.06
429 432 6.659745 ACCAGTGTTATATAAGGCATCGTA 57.340 37.500 0.00 0.00 0.00 3.43
430 433 5.546621 ACCAGTGTTATATAAGGCATCGT 57.453 39.130 0.00 0.00 0.00 3.73
431 434 9.647797 TTTATACCAGTGTTATATAAGGCATCG 57.352 33.333 0.00 0.00 0.00 3.84
445 448 8.450964 CGACATGAAATTTCTTTATACCAGTGT 58.549 33.333 18.64 4.14 0.00 3.55
446 449 8.664798 TCGACATGAAATTTCTTTATACCAGTG 58.335 33.333 18.64 1.24 0.00 3.66
447 450 8.786826 TCGACATGAAATTTCTTTATACCAGT 57.213 30.769 18.64 5.42 0.00 4.00
453 456 9.956720 GGATGAATCGACATGAAATTTCTTTAT 57.043 29.630 18.64 5.59 0.00 1.40
454 457 8.122330 CGGATGAATCGACATGAAATTTCTTTA 58.878 33.333 18.64 0.00 0.00 1.85
455 458 6.968904 CGGATGAATCGACATGAAATTTCTTT 59.031 34.615 18.64 4.28 0.00 2.52
456 459 6.458751 CCGGATGAATCGACATGAAATTTCTT 60.459 38.462 18.64 10.06 0.00 2.52
457 460 5.008019 CCGGATGAATCGACATGAAATTTCT 59.992 40.000 18.64 0.00 0.00 2.52
458 461 5.207768 CCGGATGAATCGACATGAAATTTC 58.792 41.667 11.41 11.41 0.00 2.17
459 462 4.640201 ACCGGATGAATCGACATGAAATTT 59.360 37.500 9.46 0.00 0.00 1.82
460 463 4.035558 CACCGGATGAATCGACATGAAATT 59.964 41.667 9.46 0.00 0.00 1.82
461 464 3.561310 CACCGGATGAATCGACATGAAAT 59.439 43.478 9.46 0.00 0.00 2.17
462 465 2.935849 CACCGGATGAATCGACATGAAA 59.064 45.455 9.46 0.00 0.00 2.69
463 466 2.093711 ACACCGGATGAATCGACATGAA 60.094 45.455 9.46 0.00 0.00 2.57
464 467 1.480545 ACACCGGATGAATCGACATGA 59.519 47.619 9.46 0.00 0.00 3.07
465 468 1.860950 GACACCGGATGAATCGACATG 59.139 52.381 9.46 0.00 0.00 3.21
474 477 4.498894 TCTACTTCTAGACACCGGATGA 57.501 45.455 9.46 0.00 0.00 2.92
475 478 4.641094 ACTTCTACTTCTAGACACCGGATG 59.359 45.833 9.46 5.32 0.00 3.51
481 484 6.308675 CAGTTCGACTTCTACTTCTAGACAC 58.691 44.000 0.00 0.00 0.00 3.67
570 573 9.322773 CTAGTAGAAGCATCATCAATCAAGAAA 57.677 33.333 0.00 0.00 0.00 2.52
572 575 7.440198 CCTAGTAGAAGCATCATCAATCAAGA 58.560 38.462 0.00 0.00 0.00 3.02
577 580 4.039730 ACGCCTAGTAGAAGCATCATCAAT 59.960 41.667 0.00 0.00 0.00 2.57
579 582 2.959030 ACGCCTAGTAGAAGCATCATCA 59.041 45.455 0.00 0.00 0.00 3.07
605 608 7.781324 AAAATTCATAGACACAGGAATTGGT 57.219 32.000 0.00 0.00 39.26 3.67
751 754 9.500785 ACAAAAGGGAAACATAACATTTATTGG 57.499 29.630 0.00 0.00 0.00 3.16
813 816 7.223777 ACCACACAAAGGAAAACGAAAAATATG 59.776 33.333 0.00 0.00 0.00 1.78
828 831 1.925229 CTTTGCACACCACACAAAGG 58.075 50.000 6.78 0.00 44.10 3.11
923 926 8.891720 ACTTCAAAACACCTTTTATACAACGTA 58.108 29.630 0.00 0.00 0.00 3.57
924 927 7.698970 CACTTCAAAACACCTTTTATACAACGT 59.301 33.333 0.00 0.00 0.00 3.99
929 932 6.508777 TGCCACTTCAAAACACCTTTTATAC 58.491 36.000 0.00 0.00 0.00 1.47
1407 1410 6.189859 TGAAGAAGGAGCCATGAATTGTAAT 58.810 36.000 0.00 0.00 0.00 1.89
1426 2934 2.687614 GCCATGTGAATCCCCATGAAGA 60.688 50.000 10.40 0.00 40.70 2.87
1466 2974 8.537858 AGTCTAAACAATATTAGGTTTCGGAGT 58.462 33.333 7.07 7.50 38.17 3.85
1479 2987 7.829211 TGAAAGCCTGCTAAGTCTAAACAATAT 59.171 33.333 0.00 0.00 0.00 1.28
1504 3018 7.115378 GTGTAAGGAACAATCTTTGAAATGCTG 59.885 37.037 0.00 0.00 40.63 4.41
1521 3035 7.340743 TGGATTTGTCTTTGAAAGTGTAAGGAA 59.659 33.333 4.68 0.00 0.00 3.36
1624 3243 3.182538 TGCGCATGAGCAAACTTTG 57.817 47.368 22.42 0.00 45.06 2.77
1729 3348 3.021695 TCGAAGAGAAGCGAATCCCTAA 58.978 45.455 0.00 0.00 33.04 2.69
1824 4633 3.916761 ACACTCGCGGTCTGTTTTATAA 58.083 40.909 6.13 0.00 0.00 0.98
1825 4634 3.581024 ACACTCGCGGTCTGTTTTATA 57.419 42.857 6.13 0.00 0.00 0.98
1837 4646 4.201812 ACAAATAATGGATGAACACTCGCG 60.202 41.667 0.00 0.00 0.00 5.87
2525 5392 1.569072 AGGTGTCCAAAAGGTTCCTGT 59.431 47.619 0.00 0.00 0.00 4.00
2795 5662 6.828273 TCTTTCCTTTGTCTGTTGATTTCTCA 59.172 34.615 0.00 0.00 0.00 3.27
3648 6515 9.406828 GTCCAAGGTATTACAAGAATCAAAAAC 57.593 33.333 0.00 0.00 0.00 2.43
3654 6521 7.923414 AACTGTCCAAGGTATTACAAGAATC 57.077 36.000 0.00 0.00 0.00 2.52
3815 6682 5.995897 ACTACCGCCAACTAATTCAATATCC 59.004 40.000 0.00 0.00 0.00 2.59
4446 7313 6.322456 TGGACATCAAAACAGTTTTCATGGTA 59.678 34.615 22.30 8.85 0.00 3.25
5221 8095 7.816995 AGAGCTTTCTAAACACAGAATAGACTG 59.183 37.037 0.00 0.00 42.78 3.51
5222 8096 7.816995 CAGAGCTTTCTAAACACAGAATAGACT 59.183 37.037 0.00 0.00 34.59 3.24
5232 8106 9.899226 AATAAATTCACAGAGCTTTCTAAACAC 57.101 29.630 0.00 0.00 0.00 3.32
5559 8433 2.694628 AGTTCTGAAGCAAATGTGGCAA 59.305 40.909 0.00 0.00 0.00 4.52
5649 8523 1.003118 CTCGTCCCCATCACCTTTTGA 59.997 52.381 0.00 0.00 39.11 2.69
5735 8609 6.699642 TGGTTCTTATGTTTAAAACTTGCTGC 59.300 34.615 0.00 0.00 0.00 5.25
6600 9477 1.350684 TCACCTATTGCTGCTGTGGAA 59.649 47.619 0.00 0.00 0.00 3.53
6606 9483 4.951715 TGATTTTCATCACCTATTGCTGCT 59.048 37.500 0.00 0.00 34.22 4.24
6650 9527 7.173218 GGTTTCAATCAAGATACTGACAGAACA 59.827 37.037 10.08 0.00 0.00 3.18
6653 9530 5.869344 CGGTTTCAATCAAGATACTGACAGA 59.131 40.000 10.08 0.00 30.36 3.41
6671 9548 3.638484 ACACAGCAAATAAAGCGGTTTC 58.362 40.909 17.03 1.52 38.32 2.78
6683 9560 5.512753 ACATCATGTTACAACACAGCAAA 57.487 34.783 0.00 0.00 42.51 3.68
6698 9575 6.485648 TCCATCTGAAGCTTTCATACATCATG 59.514 38.462 0.00 0.00 39.30 3.07
6739 9616 1.675714 CCGCAGCAGGAGTAACATCAA 60.676 52.381 0.00 0.00 0.00 2.57
6740 9617 0.108186 CCGCAGCAGGAGTAACATCA 60.108 55.000 0.00 0.00 0.00 3.07
6741 9618 0.811616 CCCGCAGCAGGAGTAACATC 60.812 60.000 4.99 0.00 0.00 3.06
6754 9631 6.183360 CCAATATCAAATTGTTTTTCCCGCAG 60.183 38.462 0.00 0.00 0.00 5.18
6757 9634 7.897575 TTCCAATATCAAATTGTTTTTCCCG 57.102 32.000 0.00 0.00 0.00 5.14
6785 9662 9.657419 GACATGGAAATTAAATGTTCAATTCCT 57.343 29.630 0.00 0.00 34.74 3.36
6786 9663 9.434420 TGACATGGAAATTAAATGTTCAATTCC 57.566 29.630 0.00 0.00 34.74 3.01
6791 9668 9.246670 AGAGATGACATGGAAATTAAATGTTCA 57.753 29.630 0.00 3.81 34.74 3.18
6794 9671 9.246670 TGAAGAGATGACATGGAAATTAAATGT 57.753 29.630 0.00 1.39 37.24 2.71
6896 9777 2.774809 TGTCGGGACATGGGATGAAATA 59.225 45.455 0.00 0.00 36.21 1.40
6933 9814 8.696175 CGACCTTGTAAAATAAAACATTTCACC 58.304 33.333 0.00 0.00 0.00 4.02
6988 9869 4.688879 CGTGAGGCTAATGAAGTGTAAACA 59.311 41.667 0.00 0.00 0.00 2.83
7024 9905 8.794335 AAAACTGAAGAGTGGAAATATAGGAC 57.206 34.615 0.00 0.00 30.61 3.85
7166 10130 5.407387 TCAGTAAGTGCTCGGTTTCATAAAC 59.593 40.000 0.00 0.00 40.65 2.01
7193 10157 5.357032 ACTCCTGTTTACAAGGAACAAACTG 59.643 40.000 0.00 0.00 36.64 3.16
7204 10168 5.373222 AGCATACACAACTCCTGTTTACAA 58.627 37.500 0.00 0.00 35.47 2.41
7248 10212 0.868602 CGTCGTGTGTCCTCGTGTTT 60.869 55.000 0.00 0.00 0.00 2.83
7440 10404 2.564771 CACTTGCTGAACTCAAGGTCA 58.435 47.619 7.52 0.00 43.77 4.02
7469 10433 2.346541 CGCTGCAGAGGAGAGACCA 61.347 63.158 20.43 0.00 42.04 4.02
7536 10500 2.029838 AGAAGCCCTGCGTCATTTAG 57.970 50.000 4.91 0.00 39.36 1.85
7587 10554 3.165875 CCACTCCACTCTCAAGGTCTTA 58.834 50.000 0.00 0.00 0.00 2.10
7607 10574 1.331756 CATATGTGAAAGCTCGGCACC 59.668 52.381 10.02 0.00 0.00 5.01
7638 10605 5.012458 ACAGAGAAACATGGAGATGTCTCAA 59.988 40.000 11.78 0.85 42.30 3.02
7640 10607 5.083533 ACAGAGAAACATGGAGATGTCTC 57.916 43.478 0.00 1.33 42.30 3.36
7641 10608 5.495926 AACAGAGAAACATGGAGATGTCT 57.504 39.130 0.00 0.00 42.30 3.41
7700 10691 5.008613 CACACAAGCTTAGAGCCAACTTTAA 59.991 40.000 0.00 0.00 43.77 1.52
7721 10755 2.080693 GGCGTCATGTTTATGGTCACA 58.919 47.619 0.00 0.00 34.97 3.58
7871 10973 1.990563 CGTCGAACCACACAATACTCC 59.009 52.381 0.00 0.00 0.00 3.85
7922 11024 4.442192 GGAGGACTACAATAGAAGCACCTG 60.442 50.000 0.00 0.00 0.00 4.00
7964 11067 6.070767 AGGGAATAGTTTCGAAAGACATGAGA 60.071 38.462 11.66 0.00 41.84 3.27
7979 11087 5.536497 AATTTGGGACAGAGGGAATAGTT 57.464 39.130 0.00 0.00 42.39 2.24
7984 11092 4.601857 AGAAGTAATTTGGGACAGAGGGAA 59.398 41.667 0.00 0.00 42.39 3.97
7986 11094 4.265073 CAGAAGTAATTTGGGACAGAGGG 58.735 47.826 0.00 0.00 42.39 4.30
8044 11227 7.922811 GTGATGAAAGGAGTGAACAAGATTTTT 59.077 33.333 0.00 0.00 0.00 1.94
8045 11228 7.286316 AGTGATGAAAGGAGTGAACAAGATTTT 59.714 33.333 0.00 0.00 0.00 1.82
8046 11229 6.774656 AGTGATGAAAGGAGTGAACAAGATTT 59.225 34.615 0.00 0.00 0.00 2.17
8047 11230 6.302269 AGTGATGAAAGGAGTGAACAAGATT 58.698 36.000 0.00 0.00 0.00 2.40
8048 11231 5.874093 AGTGATGAAAGGAGTGAACAAGAT 58.126 37.500 0.00 0.00 0.00 2.40
8050 11233 6.382869 AAAGTGATGAAAGGAGTGAACAAG 57.617 37.500 0.00 0.00 0.00 3.16
8101 11284 6.403878 TGAAATTCTAAACTAAGTCCCTCCG 58.596 40.000 0.00 0.00 0.00 4.63
8108 11291 8.847196 GGTTTGACCTGAAATTCTAAACTAAGT 58.153 33.333 0.00 0.00 34.73 2.24
8116 11300 6.836527 TCTTTTGGGTTTGACCTGAAATTCTA 59.163 34.615 0.00 0.00 38.64 2.10
8119 11303 5.948742 TCTTTTGGGTTTGACCTGAAATT 57.051 34.783 0.00 0.00 38.64 1.82
8142 11327 1.425448 AGCCCTGCTTAGAAAACCAGT 59.575 47.619 0.00 0.00 33.89 4.00
8230 11419 4.163649 AGTCCCATTTTACCTAGCACTACC 59.836 45.833 0.00 0.00 0.00 3.18
8234 11423 4.844884 AGAAGTCCCATTTTACCTAGCAC 58.155 43.478 0.00 0.00 0.00 4.40
8235 11424 5.104652 GGTAGAAGTCCCATTTTACCTAGCA 60.105 44.000 0.00 0.00 0.00 3.49
8237 11426 6.809976 AGGTAGAAGTCCCATTTTACCTAG 57.190 41.667 6.86 0.00 39.17 3.02
8238 11427 6.731919 TGAAGGTAGAAGTCCCATTTTACCTA 59.268 38.462 8.59 0.00 39.83 3.08
8239 11428 5.550403 TGAAGGTAGAAGTCCCATTTTACCT 59.450 40.000 3.55 3.55 41.87 3.08
8240 11429 5.812286 TGAAGGTAGAAGTCCCATTTTACC 58.188 41.667 0.00 0.00 0.00 2.85
8241 11430 6.473758 ACTGAAGGTAGAAGTCCCATTTTAC 58.526 40.000 0.00 0.00 0.00 2.01
8242 11431 6.697641 ACTGAAGGTAGAAGTCCCATTTTA 57.302 37.500 0.00 0.00 0.00 1.52
8243 11432 5.584551 ACTGAAGGTAGAAGTCCCATTTT 57.415 39.130 0.00 0.00 0.00 1.82
8275 11464 5.430007 TCCTACTGAAGGTCGTTTTCAAAA 58.570 37.500 0.00 0.00 46.62 2.44
8276 11465 5.026038 TCCTACTGAAGGTCGTTTTCAAA 57.974 39.130 0.00 0.00 46.62 2.69
8277 11466 4.675976 TCCTACTGAAGGTCGTTTTCAA 57.324 40.909 0.00 0.00 46.62 2.69
8278 11467 4.628074 CTTCCTACTGAAGGTCGTTTTCA 58.372 43.478 0.00 0.00 45.66 2.69
8289 11478 5.104277 TCCAGTTTTTCCACTTCCTACTGAA 60.104 40.000 0.00 0.00 34.87 3.02
8290 11479 4.410883 TCCAGTTTTTCCACTTCCTACTGA 59.589 41.667 0.00 0.00 34.87 3.41
8291 11480 4.714632 TCCAGTTTTTCCACTTCCTACTG 58.285 43.478 0.00 0.00 33.21 2.74
8292 11481 5.382664 TTCCAGTTTTTCCACTTCCTACT 57.617 39.130 0.00 0.00 0.00 2.57
8293 11482 6.650427 ATTTCCAGTTTTTCCACTTCCTAC 57.350 37.500 0.00 0.00 0.00 3.18
8294 11483 7.523415 ACTATTTCCAGTTTTTCCACTTCCTA 58.477 34.615 0.00 0.00 0.00 2.94
8295 11484 6.373759 ACTATTTCCAGTTTTTCCACTTCCT 58.626 36.000 0.00 0.00 0.00 3.36
8296 11485 6.650427 ACTATTTCCAGTTTTTCCACTTCC 57.350 37.500 0.00 0.00 0.00 3.46
8330 11519 2.794103 TGACACAGCAATGCTATGGTT 58.206 42.857 18.33 0.00 37.40 3.67
8331 11520 2.495155 TGACACAGCAATGCTATGGT 57.505 45.000 18.33 11.46 37.40 3.55
8332 11521 3.878699 TGTATGACACAGCAATGCTATGG 59.121 43.478 18.33 8.30 37.40 2.74
8336 11525 4.852134 TTTTGTATGACACAGCAATGCT 57.148 36.364 0.00 0.00 40.77 3.79
8339 11528 7.270757 TGTACTTTTTGTATGACACAGCAAT 57.729 32.000 0.00 0.00 38.72 3.56
8340 11529 6.685527 TGTACTTTTTGTATGACACAGCAA 57.314 33.333 0.00 0.00 38.72 3.91
8341 11530 6.238621 CCTTGTACTTTTTGTATGACACAGCA 60.239 38.462 0.00 0.00 38.72 4.41
8342 11531 6.017440 TCCTTGTACTTTTTGTATGACACAGC 60.017 38.462 0.00 0.00 38.72 4.40
8343 11532 7.490962 TCCTTGTACTTTTTGTATGACACAG 57.509 36.000 0.00 0.00 38.72 3.66
8344 11533 8.458573 AATCCTTGTACTTTTTGTATGACACA 57.541 30.769 0.00 0.00 33.23 3.72
8345 11534 8.564574 TGAATCCTTGTACTTTTTGTATGACAC 58.435 33.333 0.00 0.00 33.23 3.67
8396 11585 9.674824 GAATTTCTAGGATTGAAACTGCATATG 57.325 33.333 0.00 0.00 36.43 1.78
8397 11586 9.638176 AGAATTTCTAGGATTGAAACTGCATAT 57.362 29.630 0.00 0.00 36.43 1.78
8398 11587 9.466497 AAGAATTTCTAGGATTGAAACTGCATA 57.534 29.630 0.00 0.00 36.43 3.14
8399 11588 7.951347 AGAATTTCTAGGATTGAAACTGCAT 57.049 32.000 0.00 0.00 36.43 3.96
8400 11589 7.765695 AAGAATTTCTAGGATTGAAACTGCA 57.234 32.000 0.00 0.00 36.43 4.41
8401 11590 8.919661 CAAAAGAATTTCTAGGATTGAAACTGC 58.080 33.333 0.00 0.00 37.28 4.40
8402 11591 8.919661 GCAAAAGAATTTCTAGGATTGAAACTG 58.080 33.333 0.00 0.00 37.28 3.16
8403 11592 8.641541 TGCAAAAGAATTTCTAGGATTGAAACT 58.358 29.630 0.00 0.00 37.28 2.66
8404 11593 8.816640 TGCAAAAGAATTTCTAGGATTGAAAC 57.183 30.769 0.00 0.00 37.28 2.78
8405 11594 9.426837 CATGCAAAAGAATTTCTAGGATTGAAA 57.573 29.630 0.00 0.00 37.28 2.69
8406 11595 8.805175 TCATGCAAAAGAATTTCTAGGATTGAA 58.195 29.630 0.00 0.00 37.28 2.69
8407 11596 8.352137 TCATGCAAAAGAATTTCTAGGATTGA 57.648 30.769 0.00 0.00 37.28 2.57
8408 11597 9.031360 CATCATGCAAAAGAATTTCTAGGATTG 57.969 33.333 0.00 4.94 37.28 2.67
8409 11598 8.974238 TCATCATGCAAAAGAATTTCTAGGATT 58.026 29.630 0.00 0.00 37.28 3.01
8410 11599 8.529424 TCATCATGCAAAAGAATTTCTAGGAT 57.471 30.769 0.00 0.00 37.28 3.24
8411 11600 7.943079 TCATCATGCAAAAGAATTTCTAGGA 57.057 32.000 0.00 0.00 37.28 2.94
8412 11601 7.866393 GGATCATCATGCAAAAGAATTTCTAGG 59.134 37.037 0.00 0.00 37.28 3.02
8413 11602 8.410912 TGGATCATCATGCAAAAGAATTTCTAG 58.589 33.333 0.00 0.00 37.28 2.43
8414 11603 8.296211 TGGATCATCATGCAAAAGAATTTCTA 57.704 30.769 0.00 0.00 37.28 2.10
8415 11604 7.093465 ACTGGATCATCATGCAAAAGAATTTCT 60.093 33.333 0.00 0.00 37.28 2.52
8416 11605 7.039882 ACTGGATCATCATGCAAAAGAATTTC 58.960 34.615 0.00 0.00 37.28 2.17
8417 11606 6.942976 ACTGGATCATCATGCAAAAGAATTT 58.057 32.000 0.00 0.00 42.41 1.82
8418 11607 6.153851 TGACTGGATCATCATGCAAAAGAATT 59.846 34.615 0.00 0.00 28.45 2.17
8419 11608 5.655090 TGACTGGATCATCATGCAAAAGAAT 59.345 36.000 0.00 0.00 28.45 2.40
8420 11609 5.011586 TGACTGGATCATCATGCAAAAGAA 58.988 37.500 0.00 0.00 28.45 2.52
8421 11610 4.591929 TGACTGGATCATCATGCAAAAGA 58.408 39.130 0.00 0.00 28.45 2.52
8422 11611 4.976224 TGACTGGATCATCATGCAAAAG 57.024 40.909 0.00 0.00 28.45 2.27
8423 11612 6.124340 AGTATGACTGGATCATCATGCAAAA 58.876 36.000 17.83 0.00 45.52 2.44
8424 11613 5.687780 AGTATGACTGGATCATCATGCAAA 58.312 37.500 17.83 0.00 45.52 3.68
8425 11614 5.300411 AGTATGACTGGATCATCATGCAA 57.700 39.130 17.83 0.23 45.52 4.08
8426 11615 4.262765 GGAGTATGACTGGATCATCATGCA 60.263 45.833 17.83 0.00 45.52 3.96
8427 11616 4.252073 GGAGTATGACTGGATCATCATGC 58.748 47.826 13.72 12.59 45.52 4.06
8428 11617 4.531339 AGGGAGTATGACTGGATCATCATG 59.469 45.833 13.72 0.00 45.52 3.07
8429 11618 4.761086 AGGGAGTATGACTGGATCATCAT 58.239 43.478 10.23 10.23 45.52 2.45
8430 11619 4.140829 AGAGGGAGTATGACTGGATCATCA 60.141 45.833 0.00 0.00 45.52 3.07
8431 11620 4.220382 CAGAGGGAGTATGACTGGATCATC 59.780 50.000 0.00 0.00 45.52 2.92
8433 11622 3.052566 ACAGAGGGAGTATGACTGGATCA 60.053 47.826 0.00 0.00 43.13 2.92
8434 11623 3.571590 ACAGAGGGAGTATGACTGGATC 58.428 50.000 0.00 0.00 33.57 3.36
8435 11624 3.697190 ACAGAGGGAGTATGACTGGAT 57.303 47.619 0.00 0.00 33.57 3.41
8436 11625 4.603094 TTACAGAGGGAGTATGACTGGA 57.397 45.455 0.00 0.00 33.57 3.86
8437 11626 4.712337 AGTTTACAGAGGGAGTATGACTGG 59.288 45.833 0.00 0.00 33.57 4.00
8438 11627 5.923733 AGTTTACAGAGGGAGTATGACTG 57.076 43.478 0.00 0.00 35.14 3.51
8439 11628 9.884814 ATATTAGTTTACAGAGGGAGTATGACT 57.115 33.333 0.00 0.00 0.00 3.41
8445 11634 9.939424 ACTCTTATATTAGTTTACAGAGGGAGT 57.061 33.333 0.00 0.00 32.21 3.85
8447 11636 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
8508 11697 8.534496 GGTTTGTACTCCCTCTGTAAACTAATA 58.466 37.037 0.00 0.00 0.00 0.98
8509 11698 7.016858 TGGTTTGTACTCCCTCTGTAAACTAAT 59.983 37.037 0.00 0.00 0.00 1.73
8510 11699 6.327104 TGGTTTGTACTCCCTCTGTAAACTAA 59.673 38.462 0.00 0.00 0.00 2.24
8511 11700 5.840149 TGGTTTGTACTCCCTCTGTAAACTA 59.160 40.000 0.00 0.00 0.00 2.24
8512 11701 4.657039 TGGTTTGTACTCCCTCTGTAAACT 59.343 41.667 0.00 0.00 0.00 2.66
8513 11702 4.964593 TGGTTTGTACTCCCTCTGTAAAC 58.035 43.478 0.00 0.00 0.00 2.01
8514 11703 5.617252 CTTGGTTTGTACTCCCTCTGTAAA 58.383 41.667 0.00 0.00 0.00 2.01
8515 11704 4.504340 GCTTGGTTTGTACTCCCTCTGTAA 60.504 45.833 0.00 0.00 0.00 2.41
8516 11705 3.007614 GCTTGGTTTGTACTCCCTCTGTA 59.992 47.826 0.00 0.00 0.00 2.74
8517 11706 2.224548 GCTTGGTTTGTACTCCCTCTGT 60.225 50.000 0.00 0.00 0.00 3.41
8518 11707 2.224523 TGCTTGGTTTGTACTCCCTCTG 60.225 50.000 0.00 0.00 0.00 3.35
8519 11708 2.054799 TGCTTGGTTTGTACTCCCTCT 58.945 47.619 0.00 0.00 0.00 3.69
8520 11709 2.561478 TGCTTGGTTTGTACTCCCTC 57.439 50.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.