Multiple sequence alignment - TraesCS2D01G169000

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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 TraesCS2D01G169000 chr2D 100.000 4744 0 0 1 4744 112875104 112870361 0.000000e+00 8761.0
1 TraesCS2D01G169000 chr2D 95.094 265 12 1 3893 4157 37526612 37526875 2.640000e-112 416.0
2 TraesCS2D01G169000 chr2D 94.139 273 15 1 3894 4165 644999133 644999405 9.500000e-112 414.0
3 TraesCS2D01G169000 chr2A 97.317 3317 68 10 591 3895 114313979 114310672 0.000000e+00 5613.0
4 TraesCS2D01G169000 chr2A 94.883 469 20 3 4260 4724 114310640 114310172 0.000000e+00 730.0
5 TraesCS2D01G169000 chr2A 91.837 98 5 2 4173 4267 78335722 78335819 2.980000e-27 134.0
6 TraesCS2D01G169000 chr2A 95.122 82 3 1 4181 4262 667018371 667018451 1.390000e-25 128.0
7 TraesCS2D01G169000 chr3B 96.286 3339 87 13 583 3895 103242909 103246236 0.000000e+00 5445.0
8 TraesCS2D01G169000 chr3B 95.344 494 22 1 52 544 607478201 607477708 0.000000e+00 784.0
9 TraesCS2D01G169000 chr3B 94.792 192 7 3 4260 4449 103246263 103246453 3.590000e-76 296.0
10 TraesCS2D01G169000 chr3B 89.423 104 2 4 4167 4262 88821669 88821771 6.450000e-24 122.0
11 TraesCS2D01G169000 chr5B 86.818 2951 297 50 990 3896 58898409 58895507 0.000000e+00 3210.0
12 TraesCS2D01G169000 chr5D 86.676 2837 308 43 1082 3893 56128547 56125756 0.000000e+00 3081.0
13 TraesCS2D01G169000 chr5D 93.333 90 1 3 4178 4262 255685631 255685720 1.390000e-25 128.0
14 TraesCS2D01G169000 chr2B 93.151 2015 125 8 1021 3035 163323672 163321671 0.000000e+00 2944.0
15 TraesCS2D01G169000 chr2B 93.961 861 42 3 3031 3891 163260465 163259615 0.000000e+00 1293.0
16 TraesCS2D01G169000 chr2B 93.686 491 21 7 4263 4744 163259585 163259096 0.000000e+00 726.0
17 TraesCS2D01G169000 chr2B 86.996 446 36 11 583 1025 163334164 163333738 2.570000e-132 483.0
18 TraesCS2D01G169000 chr2B 95.753 259 11 0 3897 4155 166592375 166592117 7.340000e-113 418.0
19 TraesCS2D01G169000 chr2B 97.143 35 1 0 549 583 545224974 545224940 5.130000e-05 60.2
20 TraesCS2D01G169000 chr2B 94.286 35 1 1 549 582 706196275 706196241 9.000000e-03 52.8
21 TraesCS2D01G169000 chr5A 88.006 2026 212 20 1897 3896 44950820 44948800 0.000000e+00 2366.0
22 TraesCS2D01G169000 chr5A 82.034 885 112 24 1024 1907 44951997 44951159 0.000000e+00 710.0
23 TraesCS2D01G169000 chr5A 95.785 261 9 1 3897 4155 34842165 34841905 2.040000e-113 420.0
24 TraesCS2D01G169000 chr5A 92.857 42 3 0 550 591 456462136 456462095 1.430000e-05 62.1
25 TraesCS2D01G169000 chr5A 100.000 31 0 0 552 582 674110328 674110358 1.840000e-04 58.4
26 TraesCS2D01G169000 chr7D 93.750 544 34 0 1 544 500989756 500990299 0.000000e+00 817.0
27 TraesCS2D01G169000 chr7D 91.837 98 2 3 4182 4273 414277599 414277696 1.070000e-26 132.0
28 TraesCS2D01G169000 chr3D 98.894 452 4 1 1 451 40995900 40995449 0.000000e+00 806.0
29 TraesCS2D01G169000 chr3D 96.899 258 8 0 3901 4158 62813854 62813597 2.620000e-117 433.0
30 TraesCS2D01G169000 chr3D 94.834 271 11 3 3886 4156 306029226 306028959 2.040000e-113 420.0
31 TraesCS2D01G169000 chr3D 94.757 267 13 1 3889 4155 91541205 91541470 9.500000e-112 414.0
32 TraesCS2D01G169000 chrUn 100.000 409 0 0 2248 2656 477841090 477840682 0.000000e+00 756.0
33 TraesCS2D01G169000 chrUn 91.489 94 2 2 4182 4270 108853549 108853457 1.790000e-24 124.0
34 TraesCS2D01G169000 chr4D 84.644 534 80 2 7 538 449345970 449346503 9.040000e-147 531.0
35 TraesCS2D01G169000 chr1D 96.578 263 8 1 3897 4159 365323987 365323726 7.290000e-118 435.0
36 TraesCS2D01G169000 chr1D 94.048 84 4 1 4179 4262 433188002 433188084 4.980000e-25 126.0
37 TraesCS2D01G169000 chr1D 96.970 33 1 0 549 581 9738602 9738570 6.630000e-04 56.5
38 TraesCS2D01G169000 chr1D 100.000 30 0 0 553 582 9739916 9739945 6.630000e-04 56.5
39 TraesCS2D01G169000 chr7B 95.437 263 12 0 3897 4159 598296405 598296143 2.040000e-113 420.0
40 TraesCS2D01G169000 chr7B 89.362 47 3 2 545 589 336595528 336595482 1.840000e-04 58.4
41 TraesCS2D01G169000 chr7B 100.000 30 0 0 553 582 593565317 593565346 6.630000e-04 56.5
42 TraesCS2D01G169000 chr4B 93.258 89 4 2 4179 4266 25847308 25847395 3.850000e-26 130.0
43 TraesCS2D01G169000 chr6B 89.899 99 3 3 4177 4270 617177295 617177199 2.320000e-23 121.0
44 TraesCS2D01G169000 chr1A 94.118 34 2 0 549 582 17075782 17075815 9.000000e-03 52.8


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 TraesCS2D01G169000 chr2D 112870361 112875104 4743 True 8761.0 8761 100.0000 1 4744 1 chr2D.!!$R1 4743
1 TraesCS2D01G169000 chr2A 114310172 114313979 3807 True 3171.5 5613 96.1000 591 4724 2 chr2A.!!$R1 4133
2 TraesCS2D01G169000 chr3B 103242909 103246453 3544 False 2870.5 5445 95.5390 583 4449 2 chr3B.!!$F2 3866
3 TraesCS2D01G169000 chr5B 58895507 58898409 2902 True 3210.0 3210 86.8180 990 3896 1 chr5B.!!$R1 2906
4 TraesCS2D01G169000 chr5D 56125756 56128547 2791 True 3081.0 3081 86.6760 1082 3893 1 chr5D.!!$R1 2811
5 TraesCS2D01G169000 chr2B 163321671 163323672 2001 True 2944.0 2944 93.1510 1021 3035 1 chr2B.!!$R1 2014
6 TraesCS2D01G169000 chr2B 163259096 163260465 1369 True 1009.5 1293 93.8235 3031 4744 2 chr2B.!!$R6 1713
7 TraesCS2D01G169000 chr5A 44948800 44951997 3197 True 1538.0 2366 85.0200 1024 3896 2 chr5A.!!$R3 2872
8 TraesCS2D01G169000 chr7D 500989756 500990299 543 False 817.0 817 93.7500 1 544 1 chr7D.!!$F2 543
9 TraesCS2D01G169000 chr4D 449345970 449346503 533 False 531.0 531 84.6440 7 538 1 chr4D.!!$F1 531

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
308 311 0.180406 GCACCATACTTCCACCCGAT 59.820 55.0 0.00 0.00 0.0 4.18 F
546 549 0.398318 ACACTCCTCCAAAGTCAGCC 59.602 55.0 0.00 0.00 0.0 4.85 F
551 554 0.543749 CCTCCAAAGTCAGCCTAGGG 59.456 60.0 11.72 0.00 0.0 3.53 F
563 566 0.767998 GCCTAGGGAGATTTGAGGGG 59.232 60.0 11.72 0.00 0.0 4.79 F
2656 3068 0.613853 AGTCGAATCTTGGGACCCGA 60.614 55.0 5.91 2.38 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1614 1.071471 CGTGTTGGACTCCAGGCTT 59.929 57.895 0.00 0.0 33.81 4.35 R
1882 1945 4.448732 GTCAATCACCTTTTGGACAAATGC 59.551 41.667 0.00 0.0 44.07 3.56 R
2656 3068 0.254178 ATTGGCACATTCTCGCTCCT 59.746 50.000 0.00 0.0 39.30 3.69 R
3429 3844 3.937079 CAGAGTCTATGCAAATGCTCACA 59.063 43.478 6.97 0.0 42.66 3.58 R
4633 5093 0.457851 CCTCAGGACGAAGCTCGAAT 59.542 55.000 11.64 0.0 43.74 3.34 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
17 18 4.655527 AGCTCACGTTGTTCCTCG 57.344 55.556 0.00 0.00 0.00 4.63
43 44 5.007921 GTCTTGCAAGTTTAAACCGGAGTAA 59.992 40.000 25.19 2.51 0.00 2.24
59 62 5.511888 CCGGAGTAACCCTTCTCTTTTAACA 60.512 44.000 0.00 0.00 34.64 2.41
98 101 3.579151 GTCTCCTCCTACAAGTTTCCAGT 59.421 47.826 0.00 0.00 0.00 4.00
107 110 6.766467 TCCTACAAGTTTCCAGTTCTTTCTTC 59.234 38.462 0.00 0.00 0.00 2.87
130 133 2.324541 CCGGGAGATCCTCTTCTCAAT 58.675 52.381 0.00 0.00 43.28 2.57
131 134 2.036992 CCGGGAGATCCTCTTCTCAATG 59.963 54.545 0.00 0.00 43.28 2.82
185 188 3.620966 GCTTGCTCATAACTCCCTTCAGT 60.621 47.826 0.00 0.00 0.00 3.41
206 209 3.931631 CTCCCCCACCCTCTGCTGA 62.932 68.421 0.00 0.00 0.00 4.26
242 245 6.006275 TCCCTCTCCCATTCTTCTTTAATG 57.994 41.667 0.00 0.00 34.71 1.90
297 300 4.455606 AGCTTCAAATCTAGGCACCATAC 58.544 43.478 0.00 0.00 0.00 2.39
308 311 0.180406 GCACCATACTTCCACCCGAT 59.820 55.000 0.00 0.00 0.00 4.18
356 359 5.124936 TGTGGTATCGATGATAATAGGACGG 59.875 44.000 8.54 0.00 0.00 4.79
365 368 6.349363 CGATGATAATAGGACGGTGATCAGAA 60.349 42.308 0.00 0.00 0.00 3.02
383 386 2.284515 AATGGCGGGGGTCTCCATTC 62.285 60.000 0.00 0.00 44.72 2.67
455 458 3.165875 CCTATCAAGCCTCTCCCGAATA 58.834 50.000 0.00 0.00 0.00 1.75
461 464 4.281182 TCAAGCCTCTCCCGAATATACTTC 59.719 45.833 0.00 0.00 0.00 3.01
466 469 4.551388 CTCTCCCGAATATACTTCTGTGC 58.449 47.826 0.00 0.00 0.00 4.57
514 517 4.974645 ATACATCTCCCATAAAGCCGAA 57.025 40.909 0.00 0.00 0.00 4.30
523 526 2.423185 CCATAAAGCCGAAGTCATGCAA 59.577 45.455 0.00 0.00 0.00 4.08
544 547 2.366916 ACTCACACTCCTCCAAAGTCAG 59.633 50.000 0.00 0.00 0.00 3.51
545 548 1.070758 TCACACTCCTCCAAAGTCAGC 59.929 52.381 0.00 0.00 0.00 4.26
546 549 0.398318 ACACTCCTCCAAAGTCAGCC 59.602 55.000 0.00 0.00 0.00 4.85
547 550 0.689623 CACTCCTCCAAAGTCAGCCT 59.310 55.000 0.00 0.00 0.00 4.58
548 551 1.902508 CACTCCTCCAAAGTCAGCCTA 59.097 52.381 0.00 0.00 0.00 3.93
549 552 2.093764 CACTCCTCCAAAGTCAGCCTAG 60.094 54.545 0.00 0.00 0.00 3.02
550 553 1.484240 CTCCTCCAAAGTCAGCCTAGG 59.516 57.143 3.67 3.67 0.00 3.02
551 554 0.543749 CCTCCAAAGTCAGCCTAGGG 59.456 60.000 11.72 0.00 0.00 3.53
552 555 1.573108 CTCCAAAGTCAGCCTAGGGA 58.427 55.000 11.72 0.00 0.00 4.20
553 556 1.484240 CTCCAAAGTCAGCCTAGGGAG 59.516 57.143 11.72 1.11 37.32 4.30
554 557 1.078823 TCCAAAGTCAGCCTAGGGAGA 59.921 52.381 11.72 0.00 0.00 3.71
555 558 2.122768 CCAAAGTCAGCCTAGGGAGAT 58.877 52.381 11.72 0.00 0.00 2.75
556 559 2.507471 CCAAAGTCAGCCTAGGGAGATT 59.493 50.000 11.72 0.00 0.00 2.40
557 560 3.054065 CCAAAGTCAGCCTAGGGAGATTT 60.054 47.826 11.72 2.17 0.00 2.17
558 561 3.922171 AAGTCAGCCTAGGGAGATTTG 57.078 47.619 11.72 0.00 0.00 2.32
559 562 3.121929 AGTCAGCCTAGGGAGATTTGA 57.878 47.619 11.72 0.00 0.00 2.69
560 563 3.037549 AGTCAGCCTAGGGAGATTTGAG 58.962 50.000 11.72 0.00 0.00 3.02
561 564 2.103941 GTCAGCCTAGGGAGATTTGAGG 59.896 54.545 11.72 0.00 0.00 3.86
562 565 1.419387 CAGCCTAGGGAGATTTGAGGG 59.581 57.143 11.72 0.00 0.00 4.30
563 566 0.767998 GCCTAGGGAGATTTGAGGGG 59.232 60.000 11.72 0.00 0.00 4.79
564 567 1.439543 CCTAGGGAGATTTGAGGGGG 58.560 60.000 0.00 0.00 0.00 5.40
565 568 1.061346 CCTAGGGAGATTTGAGGGGGA 60.061 57.143 0.00 0.00 0.00 4.81
566 569 2.632360 CCTAGGGAGATTTGAGGGGGAA 60.632 54.545 0.00 0.00 0.00 3.97
567 570 2.074922 AGGGAGATTTGAGGGGGAAA 57.925 50.000 0.00 0.00 0.00 3.13
568 571 2.368170 AGGGAGATTTGAGGGGGAAAA 58.632 47.619 0.00 0.00 0.00 2.29
569 572 2.313041 AGGGAGATTTGAGGGGGAAAAG 59.687 50.000 0.00 0.00 0.00 2.27
570 573 2.043115 GGGAGATTTGAGGGGGAAAAGT 59.957 50.000 0.00 0.00 0.00 2.66
571 574 3.268595 GGGAGATTTGAGGGGGAAAAGTA 59.731 47.826 0.00 0.00 0.00 2.24
572 575 4.079154 GGGAGATTTGAGGGGGAAAAGTAT 60.079 45.833 0.00 0.00 0.00 2.12
573 576 5.133830 GGGAGATTTGAGGGGGAAAAGTATA 59.866 44.000 0.00 0.00 0.00 1.47
574 577 6.062749 GGAGATTTGAGGGGGAAAAGTATAC 58.937 44.000 0.00 0.00 0.00 1.47
575 578 6.126449 GGAGATTTGAGGGGGAAAAGTATACT 60.126 42.308 0.00 0.00 0.00 2.12
576 579 7.285340 AGATTTGAGGGGGAAAAGTATACTT 57.715 36.000 12.50 12.50 37.91 2.24
578 581 7.834681 AGATTTGAGGGGGAAAAGTATACTTTC 59.165 37.037 26.87 19.79 44.69 2.62
579 582 6.713731 TTGAGGGGGAAAAGTATACTTTCT 57.286 37.500 26.87 19.73 44.69 2.52
580 583 6.713731 TGAGGGGGAAAAGTATACTTTCTT 57.286 37.500 26.87 15.23 44.69 2.52
581 584 6.718294 TGAGGGGGAAAAGTATACTTTCTTC 58.282 40.000 26.87 21.31 44.69 2.87
599 602 5.440207 TCTTCATTCCTCATCAACCATGA 57.560 39.130 0.00 0.00 39.39 3.07
632 636 4.571984 CACTTCGCCATTGACATTCTATCA 59.428 41.667 0.00 0.00 0.00 2.15
636 642 3.484407 GCCATTGACATTCTATCAGCCT 58.516 45.455 0.00 0.00 0.00 4.58
638 644 4.694509 GCCATTGACATTCTATCAGCCTAG 59.305 45.833 0.00 0.00 0.00 3.02
651 665 3.779444 TCAGCCTAGGTATCCATACAGG 58.221 50.000 11.31 0.00 34.98 4.00
695 709 4.695217 AAAGCCCATATTACACACAACG 57.305 40.909 0.00 0.00 0.00 4.10
701 715 3.869246 CCATATTACACACAACGGACCTC 59.131 47.826 0.00 0.00 0.00 3.85
874 907 3.373565 CCGCCACCCCTTTTCAGC 61.374 66.667 0.00 0.00 0.00 4.26
977 1010 2.105128 GTCGGCATCTCAGGTCGG 59.895 66.667 0.00 0.00 0.00 4.79
1301 1358 1.606531 CAAAGCCAGAGGAGGAGGG 59.393 63.158 0.00 0.00 0.00 4.30
1302 1359 1.617839 AAAGCCAGAGGAGGAGGGG 60.618 63.158 0.00 0.00 0.00 4.79
1303 1360 3.649652 AAGCCAGAGGAGGAGGGGG 62.650 68.421 0.00 0.00 0.00 5.40
1323 1380 3.397439 GAGCAGCAGAGGCCTGGA 61.397 66.667 12.00 0.00 42.56 3.86
1434 1491 4.028490 ACGGGATTTGGGCAGCGA 62.028 61.111 0.00 0.00 0.00 4.93
1882 1945 1.817099 GAACAGGATGAGCAGCCCG 60.817 63.158 0.38 0.00 39.69 6.13
2656 3068 0.613853 AGTCGAATCTTGGGACCCGA 60.614 55.000 5.91 2.38 0.00 5.14
3429 3844 2.151202 CCAGTGTACGAATTTGGCACT 58.849 47.619 15.32 15.32 40.54 4.40
3867 4313 2.923629 TGCCCTCCCACTAGGTTTATTT 59.076 45.455 0.00 0.00 34.56 1.40
3874 4320 6.321821 TCCCACTAGGTTTATTTATGTGCT 57.678 37.500 0.00 0.00 36.75 4.40
3896 4342 5.672321 GCTTCTAGCTTTTGTCACTATGTGC 60.672 44.000 0.00 0.00 38.45 4.57
3897 4343 5.152623 TCTAGCTTTTGTCACTATGTGCT 57.847 39.130 0.00 0.00 32.98 4.40
3898 4344 5.171476 TCTAGCTTTTGTCACTATGTGCTC 58.829 41.667 0.00 0.00 32.98 4.26
3899 4345 3.077359 AGCTTTTGTCACTATGTGCTCC 58.923 45.455 0.00 0.00 32.98 4.70
3900 4346 2.162408 GCTTTTGTCACTATGTGCTCCC 59.838 50.000 0.00 0.00 32.98 4.30
3901 4347 3.679389 CTTTTGTCACTATGTGCTCCCT 58.321 45.455 0.00 0.00 32.98 4.20
3902 4348 3.334583 TTTGTCACTATGTGCTCCCTC 57.665 47.619 0.00 0.00 32.98 4.30
3903 4349 1.195115 TGTCACTATGTGCTCCCTCC 58.805 55.000 0.00 0.00 32.98 4.30
3904 4350 0.103208 GTCACTATGTGCTCCCTCCG 59.897 60.000 0.00 0.00 32.98 4.63
3905 4351 0.324368 TCACTATGTGCTCCCTCCGT 60.324 55.000 0.00 0.00 32.98 4.69
3906 4352 0.537188 CACTATGTGCTCCCTCCGTT 59.463 55.000 0.00 0.00 0.00 4.44
3907 4353 1.066143 CACTATGTGCTCCCTCCGTTT 60.066 52.381 0.00 0.00 0.00 3.60
3908 4354 1.207329 ACTATGTGCTCCCTCCGTTTC 59.793 52.381 0.00 0.00 0.00 2.78
3909 4355 1.482593 CTATGTGCTCCCTCCGTTTCT 59.517 52.381 0.00 0.00 0.00 2.52
3910 4356 0.693049 ATGTGCTCCCTCCGTTTCTT 59.307 50.000 0.00 0.00 0.00 2.52
3911 4357 0.472471 TGTGCTCCCTCCGTTTCTTT 59.528 50.000 0.00 0.00 0.00 2.52
3912 4358 1.133915 TGTGCTCCCTCCGTTTCTTTT 60.134 47.619 0.00 0.00 0.00 2.27
3913 4359 1.954382 GTGCTCCCTCCGTTTCTTTTT 59.046 47.619 0.00 0.00 0.00 1.94
3914 4360 3.143728 GTGCTCCCTCCGTTTCTTTTTA 58.856 45.455 0.00 0.00 0.00 1.52
3915 4361 3.188667 GTGCTCCCTCCGTTTCTTTTTAG 59.811 47.826 0.00 0.00 0.00 1.85
3916 4362 3.181448 TGCTCCCTCCGTTTCTTTTTAGT 60.181 43.478 0.00 0.00 0.00 2.24
3917 4363 3.436015 GCTCCCTCCGTTTCTTTTTAGTC 59.564 47.826 0.00 0.00 0.00 2.59
3918 4364 4.803253 GCTCCCTCCGTTTCTTTTTAGTCT 60.803 45.833 0.00 0.00 0.00 3.24
3919 4365 4.638304 TCCCTCCGTTTCTTTTTAGTCTG 58.362 43.478 0.00 0.00 0.00 3.51
3920 4366 3.188667 CCCTCCGTTTCTTTTTAGTCTGC 59.811 47.826 0.00 0.00 0.00 4.26
3921 4367 3.813166 CCTCCGTTTCTTTTTAGTCTGCA 59.187 43.478 0.00 0.00 0.00 4.41
3922 4368 4.455877 CCTCCGTTTCTTTTTAGTCTGCAT 59.544 41.667 0.00 0.00 0.00 3.96
3923 4369 5.642063 CCTCCGTTTCTTTTTAGTCTGCATA 59.358 40.000 0.00 0.00 0.00 3.14
3924 4370 6.316390 CCTCCGTTTCTTTTTAGTCTGCATAT 59.684 38.462 0.00 0.00 0.00 1.78
3925 4371 7.494625 CCTCCGTTTCTTTTTAGTCTGCATATA 59.505 37.037 0.00 0.00 0.00 0.86
3926 4372 8.780846 TCCGTTTCTTTTTAGTCTGCATATAA 57.219 30.769 0.00 0.00 0.00 0.98
3927 4373 8.879759 TCCGTTTCTTTTTAGTCTGCATATAAG 58.120 33.333 0.00 0.00 0.00 1.73
3928 4374 8.879759 CCGTTTCTTTTTAGTCTGCATATAAGA 58.120 33.333 0.00 0.00 0.00 2.10
3940 4386 9.624373 AGTCTGCATATAAGATTTGATCAAAGT 57.376 29.630 24.17 14.86 33.32 2.66
3941 4387 9.875675 GTCTGCATATAAGATTTGATCAAAGTC 57.124 33.333 24.17 19.70 33.32 3.01
3942 4388 9.617523 TCTGCATATAAGATTTGATCAAAGTCA 57.382 29.630 24.17 11.02 33.32 3.41
3976 4422 6.844097 AGTTTGACCAACTTTGTAGGAAAA 57.156 33.333 0.00 0.00 43.89 2.29
3977 4423 7.234661 AGTTTGACCAACTTTGTAGGAAAAA 57.765 32.000 0.00 0.00 43.89 1.94
4146 4592 8.879759 TCTTATATGCAGACTAAAAAGAAACGG 58.120 33.333 0.00 0.00 0.00 4.44
4147 4593 8.780846 TTATATGCAGACTAAAAAGAAACGGA 57.219 30.769 0.00 0.00 0.00 4.69
4148 4594 5.613358 ATGCAGACTAAAAAGAAACGGAG 57.387 39.130 0.00 0.00 0.00 4.63
4149 4595 3.813166 TGCAGACTAAAAAGAAACGGAGG 59.187 43.478 0.00 0.00 0.00 4.30
4150 4596 3.188667 GCAGACTAAAAAGAAACGGAGGG 59.811 47.826 0.00 0.00 0.00 4.30
4151 4597 4.638304 CAGACTAAAAAGAAACGGAGGGA 58.362 43.478 0.00 0.00 0.00 4.20
4173 4619 9.907229 AGGGAGTATTAAAGATTTAGGAAACTG 57.093 33.333 0.00 0.00 43.88 3.16
4180 4631 5.649782 AAGATTTAGGAAACTGCCACATG 57.350 39.130 0.00 0.00 43.88 3.21
4181 4632 4.666512 AGATTTAGGAAACTGCCACATGT 58.333 39.130 0.00 0.00 43.88 3.21
4182 4633 5.815581 AGATTTAGGAAACTGCCACATGTA 58.184 37.500 0.00 0.00 43.88 2.29
4183 4634 5.648092 AGATTTAGGAAACTGCCACATGTAC 59.352 40.000 0.00 0.00 43.88 2.90
4184 4635 4.634012 TTAGGAAACTGCCACATGTACT 57.366 40.909 0.00 0.00 43.88 2.73
4185 4636 3.059352 AGGAAACTGCCACATGTACTC 57.941 47.619 0.00 0.00 41.13 2.59
4186 4637 2.084546 GGAAACTGCCACATGTACTCC 58.915 52.381 0.00 0.00 0.00 3.85
4187 4638 2.084546 GAAACTGCCACATGTACTCCC 58.915 52.381 0.00 0.00 0.00 4.30
4188 4639 1.362224 AACTGCCACATGTACTCCCT 58.638 50.000 0.00 0.00 0.00 4.20
4189 4640 0.905357 ACTGCCACATGTACTCCCTC 59.095 55.000 0.00 0.00 0.00 4.30
4190 4641 1.198713 CTGCCACATGTACTCCCTCT 58.801 55.000 0.00 0.00 0.00 3.69
4191 4642 0.904649 TGCCACATGTACTCCCTCTG 59.095 55.000 0.00 0.00 0.00 3.35
4192 4643 0.905357 GCCACATGTACTCCCTCTGT 59.095 55.000 0.00 0.00 0.00 3.41
4193 4644 1.134670 GCCACATGTACTCCCTCTGTC 60.135 57.143 0.00 0.00 0.00 3.51
4194 4645 1.482593 CCACATGTACTCCCTCTGTCC 59.517 57.143 0.00 0.00 0.00 4.02
4195 4646 1.482593 CACATGTACTCCCTCTGTCCC 59.517 57.143 0.00 0.00 0.00 4.46
4196 4647 1.078823 ACATGTACTCCCTCTGTCCCA 59.921 52.381 0.00 0.00 0.00 4.37
4197 4648 2.187958 CATGTACTCCCTCTGTCCCAA 58.812 52.381 0.00 0.00 0.00 4.12
4198 4649 2.409064 TGTACTCCCTCTGTCCCAAA 57.591 50.000 0.00 0.00 0.00 3.28
4199 4650 2.696775 TGTACTCCCTCTGTCCCAAAA 58.303 47.619 0.00 0.00 0.00 2.44
4200 4651 3.256704 TGTACTCCCTCTGTCCCAAAAT 58.743 45.455 0.00 0.00 0.00 1.82
4201 4652 4.431378 TGTACTCCCTCTGTCCCAAAATA 58.569 43.478 0.00 0.00 0.00 1.40
4202 4653 4.847512 TGTACTCCCTCTGTCCCAAAATAA 59.152 41.667 0.00 0.00 0.00 1.40
4203 4654 4.576330 ACTCCCTCTGTCCCAAAATAAG 57.424 45.455 0.00 0.00 0.00 1.73
4204 4655 3.916989 ACTCCCTCTGTCCCAAAATAAGT 59.083 43.478 0.00 0.00 0.00 2.24
4205 4656 4.263506 ACTCCCTCTGTCCCAAAATAAGTG 60.264 45.833 0.00 0.00 0.00 3.16
4206 4657 3.913799 TCCCTCTGTCCCAAAATAAGTGA 59.086 43.478 0.00 0.00 0.00 3.41
4207 4658 4.010349 CCCTCTGTCCCAAAATAAGTGAC 58.990 47.826 0.00 0.00 0.00 3.67
4208 4659 4.263506 CCCTCTGTCCCAAAATAAGTGACT 60.264 45.833 0.00 0.00 0.00 3.41
4209 4660 4.938226 CCTCTGTCCCAAAATAAGTGACTC 59.062 45.833 0.00 0.00 0.00 3.36
4210 4661 5.513094 CCTCTGTCCCAAAATAAGTGACTCA 60.513 44.000 0.00 0.00 0.00 3.41
4211 4662 5.935945 TCTGTCCCAAAATAAGTGACTCAA 58.064 37.500 0.00 0.00 0.00 3.02
4212 4663 5.763204 TCTGTCCCAAAATAAGTGACTCAAC 59.237 40.000 0.00 0.00 0.00 3.18
4213 4664 5.690865 TGTCCCAAAATAAGTGACTCAACT 58.309 37.500 0.00 0.00 0.00 3.16
4214 4665 6.126409 TGTCCCAAAATAAGTGACTCAACTT 58.874 36.000 0.00 0.00 42.89 2.66
4215 4666 6.605594 TGTCCCAAAATAAGTGACTCAACTTT 59.394 34.615 0.00 0.00 40.77 2.66
4216 4667 7.776030 TGTCCCAAAATAAGTGACTCAACTTTA 59.224 33.333 0.00 0.00 40.77 1.85
4217 4668 8.626526 GTCCCAAAATAAGTGACTCAACTTTAA 58.373 33.333 0.00 0.00 40.77 1.52
4218 4669 9.191479 TCCCAAAATAAGTGACTCAACTTTAAA 57.809 29.630 0.00 0.00 40.77 1.52
4219 4670 9.463443 CCCAAAATAAGTGACTCAACTTTAAAG 57.537 33.333 13.76 13.76 40.77 1.85
4220 4671 8.968242 CCAAAATAAGTGACTCAACTTTAAAGC 58.032 33.333 15.24 0.00 40.77 3.51
4221 4672 9.736023 CAAAATAAGTGACTCAACTTTAAAGCT 57.264 29.630 15.24 0.00 40.77 3.74
4224 4675 9.780186 AATAAGTGACTCAACTTTAAAGCTAGT 57.220 29.630 15.24 14.66 40.77 2.57
4226 4677 8.590719 AAGTGACTCAACTTTAAAGCTAGTAC 57.409 34.615 15.24 12.77 37.05 2.73
4227 4678 7.723324 AGTGACTCAACTTTAAAGCTAGTACA 58.277 34.615 15.24 11.85 0.00 2.90
4228 4679 8.202137 AGTGACTCAACTTTAAAGCTAGTACAA 58.798 33.333 15.24 3.72 0.00 2.41
4229 4680 8.823818 GTGACTCAACTTTAAAGCTAGTACAAA 58.176 33.333 15.24 1.70 0.00 2.83
4230 4681 9.042008 TGACTCAACTTTAAAGCTAGTACAAAG 57.958 33.333 15.24 0.00 33.45 2.77
4231 4682 8.959705 ACTCAACTTTAAAGCTAGTACAAAGT 57.040 30.769 15.24 0.00 40.25 2.66
4232 4683 9.392259 ACTCAACTTTAAAGCTAGTACAAAGTT 57.608 29.630 15.24 15.05 45.48 2.66
4236 4687 8.959705 ACTTTAAAGCTAGTACAAAGTTGAGT 57.040 30.769 15.24 0.00 36.33 3.41
4237 4688 9.043079 ACTTTAAAGCTAGTACAAAGTTGAGTC 57.957 33.333 15.24 0.00 36.33 3.36
4238 4689 8.951787 TTTAAAGCTAGTACAAAGTTGAGTCA 57.048 30.769 0.00 0.00 0.00 3.41
4239 4690 6.846325 AAAGCTAGTACAAAGTTGAGTCAC 57.154 37.500 0.00 0.00 0.00 3.67
4240 4691 5.793030 AGCTAGTACAAAGTTGAGTCACT 57.207 39.130 0.00 0.00 0.00 3.41
4241 4692 6.163135 AGCTAGTACAAAGTTGAGTCACTT 57.837 37.500 0.00 0.00 38.74 3.16
4242 4693 7.286215 AGCTAGTACAAAGTTGAGTCACTTA 57.714 36.000 0.00 0.00 35.87 2.24
4243 4694 7.897864 AGCTAGTACAAAGTTGAGTCACTTAT 58.102 34.615 0.00 0.00 35.87 1.73
4244 4695 8.368668 AGCTAGTACAAAGTTGAGTCACTTATT 58.631 33.333 0.00 0.00 35.87 1.40
4245 4696 8.989980 GCTAGTACAAAGTTGAGTCACTTATTT 58.010 33.333 0.00 0.00 35.87 1.40
4248 4699 8.621286 AGTACAAAGTTGAGTCACTTATTTTGG 58.379 33.333 12.94 0.78 35.87 3.28
4249 4700 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
4250 4701 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
4251 4702 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
4252 4703 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
4253 4704 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
4254 4705 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
4255 4706 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
4256 4707 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
4257 4708 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
4258 4709 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
4333 4784 9.040939 GTTAATATGACATTTTGGGTTATTGCC 57.959 33.333 0.00 0.00 0.00 4.52
4347 4798 4.201970 GGTTATTGCCGTGCATAGCTTTTA 60.202 41.667 11.61 0.02 38.76 1.52
4407 4864 7.426606 TGTAGCATTTTATCCAGTACCACTA 57.573 36.000 0.00 0.00 0.00 2.74
4410 4867 7.136822 AGCATTTTATCCAGTACCACTATCA 57.863 36.000 0.00 0.00 0.00 2.15
4633 5093 3.569194 TGTCAACCCTTGCTTTCAGTA 57.431 42.857 0.00 0.00 0.00 2.74
4726 5186 7.816995 GCCTGATCTGGTAAGAGATACTTTATG 59.183 40.741 18.82 0.00 39.72 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.562557 TCCGGTTTAAACTTGCAAGACTC 59.437 43.478 32.50 14.74 0.00 3.36
43 44 6.183347 CCAGATCATGTTAAAAGAGAAGGGT 58.817 40.000 0.00 0.00 0.00 4.34
59 62 3.294214 GAGACAAATTGGGCCAGATCAT 58.706 45.455 6.23 0.00 0.00 2.45
98 101 1.348064 TCTCCCGGCTGAAGAAAGAA 58.652 50.000 0.00 0.00 0.00 2.52
131 134 7.290014 ATATGGAATAAAAATGTCCTTGGGGAC 59.710 37.037 8.11 8.11 46.55 4.46
198 201 3.509442 AGATAGGGGAGAATCAGCAGAG 58.491 50.000 0.00 0.00 36.25 3.35
206 209 2.385417 GGAGAGGGAGATAGGGGAGAAT 59.615 54.545 0.00 0.00 0.00 2.40
242 245 6.098982 TGGAGGAAGAAGAATGTAAGGAGATC 59.901 42.308 0.00 0.00 0.00 2.75
297 300 1.479709 AGAGTGAGATCGGGTGGAAG 58.520 55.000 0.00 0.00 0.00 3.46
308 311 3.495100 GGTTGGCAGAAAGAAGAGTGAGA 60.495 47.826 0.00 0.00 0.00 3.27
356 359 1.526917 CCCCCGCCATTCTGATCAC 60.527 63.158 0.00 0.00 0.00 3.06
455 458 0.673644 GCCACACCGCACAGAAGTAT 60.674 55.000 0.00 0.00 0.00 2.12
461 464 2.108514 CCATAGCCACACCGCACAG 61.109 63.158 0.00 0.00 0.00 3.66
466 469 1.426041 GCGTAACCATAGCCACACCG 61.426 60.000 0.00 0.00 0.00 4.94
494 497 3.709653 ACTTCGGCTTTATGGGAGATGTA 59.290 43.478 0.00 0.00 0.00 2.29
514 517 1.696336 AGGAGTGTGAGTTGCATGACT 59.304 47.619 0.00 0.00 0.00 3.41
523 526 2.366916 CTGACTTTGGAGGAGTGTGAGT 59.633 50.000 0.00 0.00 0.00 3.41
544 547 0.767998 CCCCTCAAATCTCCCTAGGC 59.232 60.000 2.05 0.00 0.00 3.93
545 548 1.061346 TCCCCCTCAAATCTCCCTAGG 60.061 57.143 0.06 0.06 0.00 3.02
546 549 2.496679 TCCCCCTCAAATCTCCCTAG 57.503 55.000 0.00 0.00 0.00 3.02
547 550 2.982842 TTCCCCCTCAAATCTCCCTA 57.017 50.000 0.00 0.00 0.00 3.53
548 551 2.074922 TTTCCCCCTCAAATCTCCCT 57.925 50.000 0.00 0.00 0.00 4.20
549 552 2.043115 ACTTTTCCCCCTCAAATCTCCC 59.957 50.000 0.00 0.00 0.00 4.30
550 553 3.458044 ACTTTTCCCCCTCAAATCTCC 57.542 47.619 0.00 0.00 0.00 3.71
551 554 6.901300 AGTATACTTTTCCCCCTCAAATCTC 58.099 40.000 0.00 0.00 0.00 2.75
552 555 6.910259 AGTATACTTTTCCCCCTCAAATCT 57.090 37.500 0.00 0.00 0.00 2.40
553 556 7.834681 AGAAAGTATACTTTTCCCCCTCAAATC 59.165 37.037 27.27 12.90 45.37 2.17
554 557 7.709601 AGAAAGTATACTTTTCCCCCTCAAAT 58.290 34.615 27.27 5.00 45.37 2.32
555 558 7.098845 AGAAAGTATACTTTTCCCCCTCAAA 57.901 36.000 27.27 0.00 45.37 2.69
556 559 6.713731 AGAAAGTATACTTTTCCCCCTCAA 57.286 37.500 27.27 0.00 45.37 3.02
557 560 6.273730 TGAAGAAAGTATACTTTTCCCCCTCA 59.726 38.462 27.27 17.70 45.37 3.86
558 561 6.718294 TGAAGAAAGTATACTTTTCCCCCTC 58.282 40.000 27.27 15.36 45.37 4.30
559 562 6.713731 TGAAGAAAGTATACTTTTCCCCCT 57.286 37.500 27.27 17.95 45.37 4.79
560 563 7.068348 GGAATGAAGAAAGTATACTTTTCCCCC 59.932 40.741 27.27 18.13 45.37 5.40
561 564 7.834681 AGGAATGAAGAAAGTATACTTTTCCCC 59.165 37.037 27.27 20.47 45.37 4.81
562 565 8.809468 AGGAATGAAGAAAGTATACTTTTCCC 57.191 34.615 27.27 18.31 45.37 3.97
563 566 9.449719 TGAGGAATGAAGAAAGTATACTTTTCC 57.550 33.333 27.27 25.74 45.37 3.13
568 571 9.606631 GTTGATGAGGAATGAAGAAAGTATACT 57.393 33.333 0.00 0.00 0.00 2.12
569 572 8.831550 GGTTGATGAGGAATGAAGAAAGTATAC 58.168 37.037 0.00 0.00 0.00 1.47
570 573 8.548025 TGGTTGATGAGGAATGAAGAAAGTATA 58.452 33.333 0.00 0.00 0.00 1.47
571 574 7.405292 TGGTTGATGAGGAATGAAGAAAGTAT 58.595 34.615 0.00 0.00 0.00 2.12
572 575 6.778821 TGGTTGATGAGGAATGAAGAAAGTA 58.221 36.000 0.00 0.00 0.00 2.24
573 576 5.634118 TGGTTGATGAGGAATGAAGAAAGT 58.366 37.500 0.00 0.00 0.00 2.66
574 577 6.376299 TCATGGTTGATGAGGAATGAAGAAAG 59.624 38.462 0.00 0.00 36.06 2.62
575 578 6.247676 TCATGGTTGATGAGGAATGAAGAAA 58.752 36.000 0.00 0.00 36.06 2.52
576 579 5.818887 TCATGGTTGATGAGGAATGAAGAA 58.181 37.500 0.00 0.00 36.06 2.52
577 580 5.440207 TCATGGTTGATGAGGAATGAAGA 57.560 39.130 0.00 0.00 36.06 2.87
599 602 2.980233 GCGAAGTGTGCTTGGGCT 60.980 61.111 0.00 0.00 39.59 5.19
632 636 2.541466 GCCTGTATGGATACCTAGGCT 58.459 52.381 9.30 0.00 43.61 4.58
636 642 2.984435 TCGGCCTGTATGGATACCTA 57.016 50.000 0.00 0.00 38.35 3.08
638 644 2.674177 CGATTCGGCCTGTATGGATACC 60.674 54.545 0.00 0.00 38.35 2.73
727 741 1.070577 CACGAGCGACTGTTTTTCTGG 60.071 52.381 0.00 0.00 0.00 3.86
729 743 1.202486 TCCACGAGCGACTGTTTTTCT 60.202 47.619 0.00 0.00 0.00 2.52
835 868 3.599285 CTACCTTGCCGCCCGTGAA 62.599 63.158 0.00 0.00 0.00 3.18
963 996 0.318762 GATACCCGACCTGAGATGCC 59.681 60.000 0.00 0.00 0.00 4.40
1301 1358 4.173924 GCCTCTGCTGCTCCTCCC 62.174 72.222 0.00 0.00 33.53 4.30
1302 1359 4.173924 GGCCTCTGCTGCTCCTCC 62.174 72.222 0.00 0.00 37.74 4.30
1303 1360 3.082701 AGGCCTCTGCTGCTCCTC 61.083 66.667 0.00 0.00 37.74 3.71
1554 1614 1.071471 CGTGTTGGACTCCAGGCTT 59.929 57.895 0.00 0.00 33.81 4.35
1758 1818 4.659172 TTCTTGGCAGGCGGTGGG 62.659 66.667 0.00 0.00 0.00 4.61
1882 1945 4.448732 GTCAATCACCTTTTGGACAAATGC 59.551 41.667 0.00 0.00 44.07 3.56
2656 3068 0.254178 ATTGGCACATTCTCGCTCCT 59.746 50.000 0.00 0.00 39.30 3.69
3429 3844 3.937079 CAGAGTCTATGCAAATGCTCACA 59.063 43.478 6.97 0.00 42.66 3.58
3867 4313 5.551233 AGTGACAAAAGCTAGAAGCACATA 58.449 37.500 1.22 0.00 45.56 2.29
3874 4320 5.551233 AGCACATAGTGACAAAAGCTAGAA 58.449 37.500 0.58 0.00 35.23 2.10
3896 4342 4.691216 CAGACTAAAAAGAAACGGAGGGAG 59.309 45.833 0.00 0.00 0.00 4.30
3897 4343 4.638304 CAGACTAAAAAGAAACGGAGGGA 58.362 43.478 0.00 0.00 0.00 4.20
3898 4344 3.188667 GCAGACTAAAAAGAAACGGAGGG 59.811 47.826 0.00 0.00 0.00 4.30
3899 4345 3.813166 TGCAGACTAAAAAGAAACGGAGG 59.187 43.478 0.00 0.00 0.00 4.30
3900 4346 5.613358 ATGCAGACTAAAAAGAAACGGAG 57.387 39.130 0.00 0.00 0.00 4.63
3901 4347 8.780846 TTATATGCAGACTAAAAAGAAACGGA 57.219 30.769 0.00 0.00 0.00 4.69
3902 4348 8.879759 TCTTATATGCAGACTAAAAAGAAACGG 58.120 33.333 0.00 0.00 0.00 4.44
3914 4360 9.624373 ACTTTGATCAAATCTTATATGCAGACT 57.376 29.630 20.76 0.00 0.00 3.24
3915 4361 9.875675 GACTTTGATCAAATCTTATATGCAGAC 57.124 33.333 20.76 2.27 0.00 3.51
3916 4362 9.617523 TGACTTTGATCAAATCTTATATGCAGA 57.382 29.630 20.76 0.00 0.00 4.26
4120 4566 8.879759 CCGTTTCTTTTTAGTCTGCATATAAGA 58.120 33.333 0.00 0.00 0.00 2.10
4121 4567 8.879759 TCCGTTTCTTTTTAGTCTGCATATAAG 58.120 33.333 0.00 0.00 0.00 1.73
4122 4568 8.780846 TCCGTTTCTTTTTAGTCTGCATATAA 57.219 30.769 0.00 0.00 0.00 0.98
4123 4569 7.494625 CCTCCGTTTCTTTTTAGTCTGCATATA 59.505 37.037 0.00 0.00 0.00 0.86
4124 4570 6.316390 CCTCCGTTTCTTTTTAGTCTGCATAT 59.684 38.462 0.00 0.00 0.00 1.78
4125 4571 5.642063 CCTCCGTTTCTTTTTAGTCTGCATA 59.358 40.000 0.00 0.00 0.00 3.14
4126 4572 4.455877 CCTCCGTTTCTTTTTAGTCTGCAT 59.544 41.667 0.00 0.00 0.00 3.96
4127 4573 3.813166 CCTCCGTTTCTTTTTAGTCTGCA 59.187 43.478 0.00 0.00 0.00 4.41
4128 4574 3.188667 CCCTCCGTTTCTTTTTAGTCTGC 59.811 47.826 0.00 0.00 0.00 4.26
4129 4575 4.638304 TCCCTCCGTTTCTTTTTAGTCTG 58.362 43.478 0.00 0.00 0.00 3.51
4130 4576 4.347292 ACTCCCTCCGTTTCTTTTTAGTCT 59.653 41.667 0.00 0.00 0.00 3.24
4131 4577 4.639334 ACTCCCTCCGTTTCTTTTTAGTC 58.361 43.478 0.00 0.00 0.00 2.59
4132 4578 4.701651 ACTCCCTCCGTTTCTTTTTAGT 57.298 40.909 0.00 0.00 0.00 2.24
4133 4579 8.782339 TTAATACTCCCTCCGTTTCTTTTTAG 57.218 34.615 0.00 0.00 0.00 1.85
4134 4580 9.223099 CTTTAATACTCCCTCCGTTTCTTTTTA 57.777 33.333 0.00 0.00 0.00 1.52
4135 4581 7.940688 TCTTTAATACTCCCTCCGTTTCTTTTT 59.059 33.333 0.00 0.00 0.00 1.94
4136 4582 7.455891 TCTTTAATACTCCCTCCGTTTCTTTT 58.544 34.615 0.00 0.00 0.00 2.27
4137 4583 7.012661 TCTTTAATACTCCCTCCGTTTCTTT 57.987 36.000 0.00 0.00 0.00 2.52
4138 4584 6.616237 TCTTTAATACTCCCTCCGTTTCTT 57.384 37.500 0.00 0.00 0.00 2.52
4139 4585 6.809976 ATCTTTAATACTCCCTCCGTTTCT 57.190 37.500 0.00 0.00 0.00 2.52
4140 4586 7.860918 AAATCTTTAATACTCCCTCCGTTTC 57.139 36.000 0.00 0.00 0.00 2.78
4141 4587 7.991460 CCTAAATCTTTAATACTCCCTCCGTTT 59.009 37.037 0.00 0.00 0.00 3.60
4142 4588 7.346436 TCCTAAATCTTTAATACTCCCTCCGTT 59.654 37.037 0.00 0.00 0.00 4.44
4143 4589 6.842807 TCCTAAATCTTTAATACTCCCTCCGT 59.157 38.462 0.00 0.00 0.00 4.69
4144 4590 7.299246 TCCTAAATCTTTAATACTCCCTCCG 57.701 40.000 0.00 0.00 0.00 4.63
4145 4591 9.339850 GTTTCCTAAATCTTTAATACTCCCTCC 57.660 37.037 0.00 0.00 0.00 4.30
4147 4593 9.907229 CAGTTTCCTAAATCTTTAATACTCCCT 57.093 33.333 0.00 0.00 0.00 4.20
4148 4594 8.622157 GCAGTTTCCTAAATCTTTAATACTCCC 58.378 37.037 0.00 0.00 0.00 4.30
4149 4595 8.622157 GGCAGTTTCCTAAATCTTTAATACTCC 58.378 37.037 0.00 0.00 0.00 3.85
4150 4596 9.174166 TGGCAGTTTCCTAAATCTTTAATACTC 57.826 33.333 0.00 0.00 0.00 2.59
4151 4597 8.957466 GTGGCAGTTTCCTAAATCTTTAATACT 58.043 33.333 0.00 0.00 0.00 2.12
4173 4619 0.905357 ACAGAGGGAGTACATGTGGC 59.095 55.000 9.11 1.02 0.00 5.01
4180 4631 5.045797 ACTTATTTTGGGACAGAGGGAGTAC 60.046 44.000 0.00 0.00 42.39 2.73
4181 4632 5.045869 CACTTATTTTGGGACAGAGGGAGTA 60.046 44.000 0.00 0.00 42.39 2.59
4182 4633 3.916989 ACTTATTTTGGGACAGAGGGAGT 59.083 43.478 0.00 0.00 42.39 3.85
4183 4634 4.019321 TCACTTATTTTGGGACAGAGGGAG 60.019 45.833 0.00 0.00 42.39 4.30
4184 4635 3.913799 TCACTTATTTTGGGACAGAGGGA 59.086 43.478 0.00 0.00 42.39 4.20
4185 4636 4.010349 GTCACTTATTTTGGGACAGAGGG 58.990 47.826 0.00 0.00 42.39 4.30
4186 4637 4.911390 AGTCACTTATTTTGGGACAGAGG 58.089 43.478 0.00 0.00 42.39 3.69
4187 4638 5.551233 TGAGTCACTTATTTTGGGACAGAG 58.449 41.667 0.00 0.00 42.39 3.35
4188 4639 5.560722 TGAGTCACTTATTTTGGGACAGA 57.439 39.130 0.00 0.00 42.39 3.41
4189 4640 5.765182 AGTTGAGTCACTTATTTTGGGACAG 59.235 40.000 0.00 0.00 42.39 3.51
4190 4641 5.690865 AGTTGAGTCACTTATTTTGGGACA 58.309 37.500 0.00 0.00 0.00 4.02
4191 4642 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
4192 4643 8.754991 TTAAAGTTGAGTCACTTATTTTGGGA 57.245 30.769 0.00 0.00 35.87 4.37
4193 4644 9.463443 CTTTAAAGTTGAGTCACTTATTTTGGG 57.537 33.333 7.07 0.00 35.87 4.12
4194 4645 8.968242 GCTTTAAAGTTGAGTCACTTATTTTGG 58.032 33.333 16.38 0.00 35.87 3.28
4195 4646 9.736023 AGCTTTAAAGTTGAGTCACTTATTTTG 57.264 29.630 16.38 0.00 35.87 2.44
4198 4649 9.780186 ACTAGCTTTAAAGTTGAGTCACTTATT 57.220 29.630 16.38 0.00 35.87 1.40
4200 4651 9.688592 GTACTAGCTTTAAAGTTGAGTCACTTA 57.311 33.333 16.38 0.82 35.87 2.24
4201 4652 8.202137 TGTACTAGCTTTAAAGTTGAGTCACTT 58.798 33.333 16.38 0.00 38.74 3.16
4202 4653 7.723324 TGTACTAGCTTTAAAGTTGAGTCACT 58.277 34.615 16.38 5.23 0.00 3.41
4203 4654 7.941795 TGTACTAGCTTTAAAGTTGAGTCAC 57.058 36.000 16.38 13.74 0.00 3.67
4204 4655 8.951787 TTTGTACTAGCTTTAAAGTTGAGTCA 57.048 30.769 16.38 12.61 0.00 3.41
4205 4656 9.043079 ACTTTGTACTAGCTTTAAAGTTGAGTC 57.957 33.333 16.38 10.81 38.11 3.36
4206 4657 8.959705 ACTTTGTACTAGCTTTAAAGTTGAGT 57.040 30.769 16.38 16.93 38.11 3.41
4210 4661 9.392259 ACTCAACTTTGTACTAGCTTTAAAGTT 57.608 29.630 16.38 13.03 46.53 2.66
4211 4662 8.959705 ACTCAACTTTGTACTAGCTTTAAAGT 57.040 30.769 16.38 6.35 41.74 2.66
4212 4663 9.042008 TGACTCAACTTTGTACTAGCTTTAAAG 57.958 33.333 11.02 11.02 35.18 1.85
4213 4664 8.823818 GTGACTCAACTTTGTACTAGCTTTAAA 58.176 33.333 0.00 0.00 0.00 1.52
4214 4665 8.202137 AGTGACTCAACTTTGTACTAGCTTTAA 58.798 33.333 0.00 0.00 0.00 1.52
4215 4666 7.723324 AGTGACTCAACTTTGTACTAGCTTTA 58.277 34.615 0.00 0.00 0.00 1.85
4216 4667 6.583562 AGTGACTCAACTTTGTACTAGCTTT 58.416 36.000 0.00 0.00 0.00 3.51
4217 4668 6.163135 AGTGACTCAACTTTGTACTAGCTT 57.837 37.500 0.00 0.00 0.00 3.74
4218 4669 5.793030 AGTGACTCAACTTTGTACTAGCT 57.207 39.130 0.00 0.00 0.00 3.32
4219 4670 8.535690 AATAAGTGACTCAACTTTGTACTAGC 57.464 34.615 0.00 0.00 40.77 3.42
4222 4673 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
4223 4674 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
4224 4675 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
4225 4676 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
4226 4677 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
4227 4678 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
4228 4679 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
4229 4680 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
4230 4681 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
4231 4682 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
4232 4683 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
4233 4684 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
4234 4685 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
4235 4686 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
4236 4687 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
4237 4688 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
4238 4689 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
4239 4690 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
4240 4691 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
4241 4692 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
4242 4693 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
4243 4694 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
4244 4695 1.961133 ATTACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
4245 4696 2.023695 AGTATTACTCCCTCCGTCCCAA 60.024 50.000 0.00 0.00 0.00 4.12
4246 4697 1.572415 AGTATTACTCCCTCCGTCCCA 59.428 52.381 0.00 0.00 0.00 4.37
4247 4698 2.378378 AGTATTACTCCCTCCGTCCC 57.622 55.000 0.00 0.00 0.00 4.46
4248 4699 4.439968 CAAAAGTATTACTCCCTCCGTCC 58.560 47.826 0.00 0.00 0.00 4.79
4249 4700 4.161001 TCCAAAAGTATTACTCCCTCCGTC 59.839 45.833 0.00 0.00 0.00 4.79
4250 4701 4.098894 TCCAAAAGTATTACTCCCTCCGT 58.901 43.478 0.00 0.00 0.00 4.69
4251 4702 4.748277 TCCAAAAGTATTACTCCCTCCG 57.252 45.455 0.00 0.00 0.00 4.63
4252 4703 5.132144 TCCATCCAAAAGTATTACTCCCTCC 59.868 44.000 0.00 0.00 0.00 4.30
4253 4704 6.248569 TCCATCCAAAAGTATTACTCCCTC 57.751 41.667 0.00 0.00 0.00 4.30
4254 4705 6.389869 TCATCCATCCAAAAGTATTACTCCCT 59.610 38.462 0.00 0.00 0.00 4.20
4255 4706 6.601332 TCATCCATCCAAAAGTATTACTCCC 58.399 40.000 0.00 0.00 0.00 4.30
4256 4707 8.697507 ATTCATCCATCCAAAAGTATTACTCC 57.302 34.615 0.00 0.00 0.00 3.85
4289 4740 8.727910 CATATTAACAGCTGAACATAGCATCAT 58.272 33.333 23.35 1.29 46.07 2.45
4290 4741 7.933033 TCATATTAACAGCTGAACATAGCATCA 59.067 33.333 23.35 0.00 46.07 3.07
4333 4784 4.151070 CAACACAGTAAAAGCTATGCACG 58.849 43.478 0.00 0.00 0.00 5.34
4347 4798 6.603940 AAAATTATATGCACCCAACACAGT 57.396 33.333 0.00 0.00 0.00 3.55
4506 4965 3.756082 AGATGGGCCATTTACTTTCCA 57.244 42.857 22.20 0.00 0.00 3.53
4515 4974 6.721208 CCTTGTATACAAATAGATGGGCCATT 59.279 38.462 22.20 12.92 35.15 3.16
4633 5093 0.457851 CCTCAGGACGAAGCTCGAAT 59.542 55.000 11.64 0.00 43.74 3.34


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

AutoCloner maintained by Alex Coulton.