Multiple sequence alignment - TraesCS4A01G262900

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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 TraesCS4A01G262900 chr4A 100.000 6090 0 0 1 6090 575026251 575032340 0.000000e+00 11247.0
1 TraesCS4A01G262900 chr4A 73.389 357 64 22 5308 5652 634423493 634423830 3.000000e-18 104.0
2 TraesCS4A01G262900 chr4A 73.389 357 64 22 5308 5652 634455762 634456099 3.000000e-18 104.0
3 TraesCS4A01G262900 chr4D 95.884 4495 159 8 759 5233 28460685 28456197 0.000000e+00 7252.0
4 TraesCS4A01G262900 chr4D 91.461 445 23 8 503 938 28461231 28460793 1.130000e-166 597.0
5 TraesCS4A01G262900 chr4D 87.589 419 28 9 14 415 28461644 28461233 1.200000e-126 464.0
6 TraesCS4A01G262900 chr4D 81.818 88 15 1 420 507 259494975 259494889 8.470000e-09 73.1
7 TraesCS4A01G262900 chr4B 96.248 4344 150 4 904 5238 40784044 40779705 0.000000e+00 7107.0
8 TraesCS4A01G262900 chr4B 88.439 346 23 11 82 423 40785007 40784675 9.510000e-108 401.0
9 TraesCS4A01G262900 chr4B 91.000 200 13 1 705 904 40784363 40784169 1.300000e-66 265.0
10 TraesCS4A01G262900 chr4B 88.095 210 14 5 503 704 40784678 40784472 7.890000e-59 239.0
11 TraesCS4A01G262900 chr4B 81.609 87 13 2 420 506 496467034 496466951 1.100000e-07 69.4
12 TraesCS4A01G262900 chr4B 78.571 98 19 2 5309 5404 377425581 377425484 5.100000e-06 63.9
13 TraesCS4A01G262900 chr2A 84.249 819 76 27 5308 6090 699445947 699445146 0.000000e+00 749.0
14 TraesCS4A01G262900 chr2A 89.980 489 37 5 5309 5795 699447143 699446665 6.700000e-174 621.0
15 TraesCS4A01G262900 chr2A 87.333 150 12 4 5920 6066 699446483 699446338 1.360000e-36 165.0
16 TraesCS4A01G262900 chr2A 80.899 89 17 0 418 506 690329334 690329422 3.050000e-08 71.3
17 TraesCS4A01G262900 chr7A 87.774 548 47 9 5308 5845 130786948 130787485 1.860000e-174 623.0
18 TraesCS4A01G262900 chr7A 86.207 87 10 2 418 504 445649430 445649514 6.500000e-15 93.5
19 TraesCS4A01G262900 chr3D 85.294 544 71 2 5307 5849 43658932 43659467 2.480000e-153 553.0
20 TraesCS4A01G262900 chr5D 84.191 544 76 3 5308 5849 15060517 15061052 2.520000e-143 520.0
21 TraesCS4A01G262900 chr5D 73.088 353 73 16 5311 5652 536718250 536717909 8.350000e-19 106.0
22 TraesCS4A01G262900 chr5D 93.750 48 3 0 464 511 464690683 464690730 8.470000e-09 73.1
23 TraesCS4A01G262900 chr1B 83.124 557 68 6 5311 5849 648249886 648250434 9.180000e-133 484.0
24 TraesCS4A01G262900 chr1B 80.531 339 56 9 5433 5763 31121250 31120914 1.010000e-62 252.0
25 TraesCS4A01G262900 chr3B 89.444 360 28 3 5329 5687 686121345 686121695 4.330000e-121 446.0
26 TraesCS4A01G262900 chr3B 100.000 29 0 0 416 444 90156428 90156456 3.000000e-03 54.7
27 TraesCS4A01G262900 chr3A 73.816 359 70 20 5308 5647 709443105 709443458 2.980000e-23 121.0
28 TraesCS4A01G262900 chr3A 82.955 88 15 0 420 507 161458362 161458275 5.060000e-11 80.5
29 TraesCS4A01G262900 chr3A 94.340 53 2 1 5307 5359 715645106 715645055 5.060000e-11 80.5
30 TraesCS4A01G262900 chr3A 80.899 89 17 0 419 507 303756877 303756789 3.050000e-08 71.3
31 TraesCS4A01G262900 chr5B 71.908 477 98 27 5313 5770 677401347 677400888 8.350000e-19 106.0
32 TraesCS4A01G262900 chr6A 83.871 93 15 0 420 512 63587128 63587036 8.410000e-14 89.8
33 TraesCS4A01G262900 chr1D 97.222 36 0 1 5306 5341 398461704 398461738 6.590000e-05 60.2
34 TraesCS4A01G262900 chr2B 78.161 87 19 0 420 506 18809611 18809697 8.530000e-04 56.5


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 TraesCS4A01G262900 chr4A 575026251 575032340 6089 False 11247.000000 11247 100.000000 1 6090 1 chr4A.!!$F1 6089
1 TraesCS4A01G262900 chr4D 28456197 28461644 5447 True 2771.000000 7252 91.644667 14 5233 3 chr4D.!!$R2 5219
2 TraesCS4A01G262900 chr4B 40779705 40785007 5302 True 2003.000000 7107 90.945500 82 5238 4 chr4B.!!$R3 5156
3 TraesCS4A01G262900 chr2A 699445146 699447143 1997 True 511.666667 749 87.187333 5308 6090 3 chr2A.!!$R1 782
4 TraesCS4A01G262900 chr7A 130786948 130787485 537 False 623.000000 623 87.774000 5308 5845 1 chr7A.!!$F1 537
5 TraesCS4A01G262900 chr3D 43658932 43659467 535 False 553.000000 553 85.294000 5307 5849 1 chr3D.!!$F1 542
6 TraesCS4A01G262900 chr5D 15060517 15061052 535 False 520.000000 520 84.191000 5308 5849 1 chr5D.!!$F1 541
7 TraesCS4A01G262900 chr1B 648249886 648250434 548 False 484.000000 484 83.124000 5311 5849 1 chr1B.!!$F1 538

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
295 311 0.182061 GGCCTCCTCTGCATCAATCA 59.818 55.0 0.00 0.0 0.00 2.57 F
957 1506 0.602106 CAGCAGGAGTGACACACAGG 60.602 60.0 8.59 0.0 36.74 4.00 F
2799 3348 0.400594 AGCCAACCGGAAAAGCTAGT 59.599 50.0 9.46 0.0 30.46 2.57 F
3501 4051 0.037447 TGGCGATCATTCACAACCCA 59.963 50.0 0.00 0.0 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 2451 0.252881 AGGGGAGTGCCTCATCTTCA 60.253 55.0 0.00 0.0 36.99 3.02 R
2931 3480 0.322456 CCGCTTTCTGATTCCACCCA 60.322 55.0 0.00 0.0 0.00 4.51 R
4697 5255 0.729690 GCCTTGGCTGAAATCTCGAC 59.270 55.0 4.11 0.0 0.00 4.20 R
5292 5854 0.178861 CCCTGCTATCCATACCCCCT 60.179 60.0 0.00 0.0 0.00 4.79 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
30 31 3.897141 ACTAGCTAGAAAACCAGGAGC 57.103 47.619 27.45 0.00 0.00 4.70
40 42 1.003718 ACCAGGAGCTTTGGTACGC 60.004 57.895 19.06 0.00 46.80 4.42
66 68 3.926616 ACTCAAAATCCACACCTCTACG 58.073 45.455 0.00 0.00 0.00 3.51
67 69 3.576982 ACTCAAAATCCACACCTCTACGA 59.423 43.478 0.00 0.00 0.00 3.43
68 70 4.177026 CTCAAAATCCACACCTCTACGAG 58.823 47.826 0.00 0.00 0.00 4.18
183 197 2.509131 CCAATTTTGGCATGGGGGTATT 59.491 45.455 0.00 0.00 42.21 1.89
189 203 2.427872 TGGCATGGGGGTATTCTGTAT 58.572 47.619 0.00 0.00 0.00 2.29
293 309 1.147824 CGGCCTCCTCTGCATCAAT 59.852 57.895 0.00 0.00 0.00 2.57
294 310 0.883814 CGGCCTCCTCTGCATCAATC 60.884 60.000 0.00 0.00 0.00 2.67
295 311 0.182061 GGCCTCCTCTGCATCAATCA 59.818 55.000 0.00 0.00 0.00 2.57
296 312 1.409241 GGCCTCCTCTGCATCAATCAA 60.409 52.381 0.00 0.00 0.00 2.57
375 391 4.949856 GGCCACATTCTTTTTCTCCAGATA 59.050 41.667 0.00 0.00 0.00 1.98
389 405 9.838339 TTTTCTCCAGATAAGATAATTGACTCC 57.162 33.333 0.00 0.00 0.00 3.85
390 406 8.789767 TTCTCCAGATAAGATAATTGACTCCT 57.210 34.615 0.00 0.00 0.00 3.69
391 407 8.187913 TCTCCAGATAAGATAATTGACTCCTG 57.812 38.462 0.00 0.00 0.00 3.86
422 441 9.574516 AGAAATTGTTCCAACTGTTATTCTACT 57.425 29.630 0.00 0.00 33.92 2.57
423 442 9.827411 GAAATTGTTCCAACTGTTATTCTACTC 57.173 33.333 0.00 0.00 0.00 2.59
424 443 7.923414 ATTGTTCCAACTGTTATTCTACTCC 57.077 36.000 0.00 0.00 0.00 3.85
425 444 5.801380 TGTTCCAACTGTTATTCTACTCCC 58.199 41.667 0.00 0.00 0.00 4.30
426 445 5.546499 TGTTCCAACTGTTATTCTACTCCCT 59.454 40.000 0.00 0.00 0.00 4.20
427 446 5.934402 TCCAACTGTTATTCTACTCCCTC 57.066 43.478 0.00 0.00 0.00 4.30
428 447 5.590818 TCCAACTGTTATTCTACTCCCTCT 58.409 41.667 0.00 0.00 0.00 3.69
429 448 6.738635 TCCAACTGTTATTCTACTCCCTCTA 58.261 40.000 0.00 0.00 0.00 2.43
430 449 7.363031 TCCAACTGTTATTCTACTCCCTCTAT 58.637 38.462 0.00 0.00 0.00 1.98
431 450 8.508601 TCCAACTGTTATTCTACTCCCTCTATA 58.491 37.037 0.00 0.00 0.00 1.31
432 451 9.144298 CCAACTGTTATTCTACTCCCTCTATAA 57.856 37.037 0.00 0.00 0.00 0.98
435 454 9.939424 ACTGTTATTCTACTCCCTCTATAAACT 57.061 33.333 0.00 0.00 0.00 2.66
466 485 8.935614 AAGAAATTTTAGGCCACTAAAGTAGT 57.064 30.769 5.01 0.00 46.59 2.73
480 499 7.017319 ACTAAAGTAGTGGCCTAAAACATCT 57.983 36.000 3.32 0.00 37.69 2.90
481 500 7.459234 ACTAAAGTAGTGGCCTAAAACATCTT 58.541 34.615 3.32 0.00 37.69 2.40
482 501 8.599792 ACTAAAGTAGTGGCCTAAAACATCTTA 58.400 33.333 3.32 0.00 37.69 2.10
483 502 9.614792 CTAAAGTAGTGGCCTAAAACATCTTAT 57.385 33.333 3.32 0.00 0.00 1.73
485 504 9.969001 AAAGTAGTGGCCTAAAACATCTTATAA 57.031 29.630 3.32 0.00 0.00 0.98
486 505 9.969001 AAGTAGTGGCCTAAAACATCTTATAAA 57.031 29.630 3.32 0.00 0.00 1.40
487 506 9.969001 AGTAGTGGCCTAAAACATCTTATAAAA 57.031 29.630 3.32 0.00 0.00 1.52
489 508 8.879427 AGTGGCCTAAAACATCTTATAAAAGT 57.121 30.769 3.32 0.00 34.13 2.66
490 509 9.309224 AGTGGCCTAAAACATCTTATAAAAGTT 57.691 29.630 3.32 0.00 34.13 2.66
491 510 9.923143 GTGGCCTAAAACATCTTATAAAAGTTT 57.077 29.630 3.32 4.60 34.13 2.66
501 520 9.892130 ACATCTTATAAAAGTTTACAGAGGGAG 57.108 33.333 9.55 0.00 34.13 4.30
521 540 9.794719 GAGGGAGTACTTTTTATTAAGCCATAT 57.205 33.333 0.00 0.00 0.00 1.78
541 562 8.664798 GCCATATATTTTGTTTGGAAAAAGGAC 58.335 33.333 0.00 0.00 30.52 3.85
576 597 5.409826 CAGTAATGTTGAGAAGAGTGAACCC 59.590 44.000 0.00 0.00 0.00 4.11
586 607 1.229082 AGTGAACCCGACCCAGCTA 60.229 57.895 0.00 0.00 0.00 3.32
647 668 5.822519 GTGATGAATAGGATAAGTTGCACCA 59.177 40.000 0.00 0.00 0.00 4.17
651 672 6.422333 TGAATAGGATAAGTTGCACCATTGA 58.578 36.000 0.00 0.00 0.00 2.57
657 678 7.293073 AGGATAAGTTGCACCATTGAAGATAT 58.707 34.615 0.00 0.00 0.00 1.63
659 680 8.507249 GGATAAGTTGCACCATTGAAGATATAC 58.493 37.037 0.00 0.00 0.00 1.47
661 682 7.701539 AAGTTGCACCATTGAAGATATACAA 57.298 32.000 0.00 0.00 0.00 2.41
662 683 7.701539 AGTTGCACCATTGAAGATATACAAA 57.298 32.000 0.00 0.00 0.00 2.83
663 684 8.297470 AGTTGCACCATTGAAGATATACAAAT 57.703 30.769 0.00 0.00 0.00 2.32
664 685 8.752187 AGTTGCACCATTGAAGATATACAAATT 58.248 29.630 0.00 0.00 0.00 1.82
701 726 5.488341 GTTAGCATGGGAAGTCTCTTTACA 58.512 41.667 0.00 0.00 0.00 2.41
725 858 3.494924 GCTTTTTGGGTTTGCAGGAGATT 60.495 43.478 0.00 0.00 0.00 2.40
727 860 4.769345 TTTTGGGTTTGCAGGAGATTTT 57.231 36.364 0.00 0.00 0.00 1.82
781 914 4.992688 TGTCAAATTTGTTCACGCTTCTT 58.007 34.783 17.47 0.00 0.00 2.52
815 948 6.803154 AAGAAACACATCTTTAGTAGCACC 57.197 37.500 0.00 0.00 36.23 5.01
851 1275 3.987547 AGCCATTATGATCGTCTCTGTG 58.012 45.455 0.00 0.00 0.00 3.66
931 1480 4.098416 GTGTTTGCCGCTTCTCATTTATC 58.902 43.478 0.00 0.00 0.00 1.75
957 1506 0.602106 CAGCAGGAGTGACACACAGG 60.602 60.000 8.59 0.00 36.74 4.00
961 1510 1.000283 CAGGAGTGACACACAGGAGAC 60.000 57.143 8.59 0.00 36.74 3.36
997 1546 1.351153 GTTCAAGTACTCGAGGCAGC 58.649 55.000 18.41 3.60 0.00 5.25
1013 1562 2.008329 GCAGCAGATGTCTTCCTCAAG 58.992 52.381 0.00 0.00 0.00 3.02
1015 1564 1.558756 AGCAGATGTCTTCCTCAAGGG 59.441 52.381 0.00 0.00 35.41 3.95
1020 1569 1.130054 TGTCTTCCTCAAGGGCTGCT 61.130 55.000 0.00 0.00 35.41 4.24
1029 1578 1.302832 AAGGGCTGCTTCCAGTTCG 60.303 57.895 0.00 0.00 41.26 3.95
1090 1639 2.746269 CACAAACAACCCTTGATGCTG 58.254 47.619 0.00 0.00 0.00 4.41
1170 1719 2.743718 CAGCGGGACACTCCAACT 59.256 61.111 0.00 0.00 38.64 3.16
1191 1740 4.020617 CTGCAGGAAGGGCGGTCA 62.021 66.667 5.57 0.00 32.96 4.02
1368 1917 2.998949 GACGATCCCCCAAGGCTT 59.001 61.111 0.00 0.00 34.51 4.35
1380 1929 1.073025 AAGGCTTGACATCGGCACA 59.927 52.632 0.00 0.00 0.00 4.57
1414 1963 3.177194 TTCACTGACCAGGGTGCCG 62.177 63.158 0.00 0.00 32.51 5.69
1731 2280 6.727394 TGATAGGGTTATGGCTTACAAGTTT 58.273 36.000 0.00 0.00 0.00 2.66
1758 2307 2.103263 AGATAACCATGGCGAGGTCTTC 59.897 50.000 13.04 0.00 38.76 2.87
1864 2413 1.266718 TCATGAAGAACAAAGTGCGGC 59.733 47.619 0.00 0.00 0.00 6.53
1869 2418 1.160137 AGAACAAAGTGCGGCTGATC 58.840 50.000 0.00 0.00 0.00 2.92
1998 2547 7.660030 TCAGTATATGGAGAACATGAACTCA 57.340 36.000 19.20 10.21 40.82 3.41
2097 2646 5.420421 ACAGCAGCAGAAGAAGAAGATACTA 59.580 40.000 0.00 0.00 0.00 1.82
2107 2656 5.727630 AGAAGAAGATACTATGGGGCCTTA 58.272 41.667 0.84 0.00 0.00 2.69
2130 2679 1.792757 TTTGCCACCATGAGAGCCCT 61.793 55.000 0.00 0.00 0.00 5.19
2229 2778 6.815142 AGTTTGAAGTACAGAAACAGTTACGT 59.185 34.615 13.61 0.00 0.00 3.57
2301 2850 2.158295 GGAAGCCTCTCCCCTGACTATA 60.158 54.545 0.00 0.00 0.00 1.31
2387 2936 2.277084 CAAAGTATGGCGTCTGGGTAC 58.723 52.381 0.00 0.00 0.00 3.34
2391 2940 0.973496 TATGGCGTCTGGGTACTGCA 60.973 55.000 0.00 0.00 0.00 4.41
2629 3178 2.945008 GCAAAGAATGATCCATCGGACA 59.055 45.455 0.00 0.00 32.98 4.02
2630 3179 3.567164 GCAAAGAATGATCCATCGGACAT 59.433 43.478 0.00 0.00 32.98 3.06
2761 3310 3.536956 TGCAACTTATACTTCGAGGGG 57.463 47.619 0.00 0.00 0.00 4.79
2799 3348 0.400594 AGCCAACCGGAAAAGCTAGT 59.599 50.000 9.46 0.00 30.46 2.57
2931 3480 3.649843 AGATGGCAATGGATTGGTCAAT 58.350 40.909 0.00 0.00 38.21 2.57
2940 3489 2.044215 TGGATTGGTCAATGGGTGGAAT 59.956 45.455 0.43 0.00 0.00 3.01
2970 3519 2.356125 GGCAGAATTGACTGGGCTAAGA 60.356 50.000 0.00 0.00 38.22 2.10
2982 3531 2.507058 TGGGCTAAGAGTTGATGATGCT 59.493 45.455 0.00 0.00 0.00 3.79
3045 3594 1.277273 TCAGTTGTCCAGAGGATGCTG 59.723 52.381 0.00 0.00 32.73 4.41
3269 3819 9.706691 TCGTTCATGGGTCTCTAATAAATATTC 57.293 33.333 0.00 0.00 0.00 1.75
3274 3824 7.786046 TGGGTCTCTAATAAATATTCCGCTA 57.214 36.000 0.00 0.00 0.00 4.26
3327 3877 5.046591 TCGATTTGAGGTAAAGACTCATGGT 60.047 40.000 0.00 0.00 43.82 3.55
3501 4051 0.037447 TGGCGATCATTCACAACCCA 59.963 50.000 0.00 0.00 0.00 4.51
3539 4089 6.373774 CCTCCTATATTTGGTGCTGATGAATC 59.626 42.308 0.00 0.00 0.00 2.52
3899 4449 2.046892 GCAAGCCTCGGAGCAGAA 60.047 61.111 0.00 0.00 34.23 3.02
4032 4582 2.508716 ACAGATGAGGCAGATCCATGTT 59.491 45.455 0.00 0.00 37.29 2.71
4033 4583 2.879026 CAGATGAGGCAGATCCATGTTG 59.121 50.000 0.00 0.00 37.29 3.33
4047 4597 6.776116 AGATCCATGTTGCAGATAATTGTCAT 59.224 34.615 4.92 0.00 0.00 3.06
4084 4634 1.523758 ACTTGCCGACTTGGATCAAC 58.476 50.000 0.00 0.00 42.00 3.18
4163 4713 6.533723 CGTTCTCATGTTTACTTATGGCTGTA 59.466 38.462 0.00 0.00 0.00 2.74
4216 4766 3.676540 GTTGATGTCGTTGTTCGTTGTT 58.323 40.909 0.00 0.00 40.80 2.83
4691 5249 3.711704 AGTGAAGTTCTCTCCTGTTGGAA 59.288 43.478 4.17 0.00 42.66 3.53
4697 5255 4.061596 GTTCTCTCCTGTTGGAAGTTCTG 58.938 47.826 2.25 0.00 42.66 3.02
4815 5376 9.249457 CCTGTTAATTTCTGAAAAGGAAGTTTC 57.751 33.333 6.95 0.00 37.89 2.78
4827 5388 5.993106 AAGGAAGTTTCGAAGTCTTCTTG 57.007 39.130 27.68 0.00 38.02 3.02
4863 5425 7.206981 AGTGATGGTTATTTTTGTCTCTGTG 57.793 36.000 0.00 0.00 0.00 3.66
4936 5498 2.886081 CAGATGTTTGAGGAGGACGAG 58.114 52.381 0.00 0.00 0.00 4.18
4937 5499 1.205893 AGATGTTTGAGGAGGACGAGC 59.794 52.381 0.00 0.00 0.00 5.03
4975 5537 2.610859 TTGGGCCTCCTGGTCTCC 60.611 66.667 4.53 0.00 38.23 3.71
5077 5639 4.043200 GCTTGTGCTCCAACGGCC 62.043 66.667 0.00 0.00 36.03 6.13
5108 5670 2.555325 TGATGAAGAAGCCAGTGCAAAG 59.445 45.455 0.00 0.00 41.13 2.77
5115 5677 0.321564 AGCCAGTGCAAAGCGTATGA 60.322 50.000 0.00 0.00 41.13 2.15
5156 5718 4.317671 ACAACTCTAACGCAGTACACTT 57.682 40.909 0.00 0.00 45.00 3.16
5234 5796 8.752005 TCTTAATTCATACTCCATCAAAAGGG 57.248 34.615 0.00 0.00 0.00 3.95
5256 5818 6.183309 GGTACCTGTGAAGATCATTGTTTC 57.817 41.667 4.06 0.00 0.00 2.78
5257 5819 5.123979 GGTACCTGTGAAGATCATTGTTTCC 59.876 44.000 4.06 0.00 0.00 3.13
5258 5820 4.990526 ACCTGTGAAGATCATTGTTTCCT 58.009 39.130 0.00 0.00 0.00 3.36
5259 5821 6.126863 ACCTGTGAAGATCATTGTTTCCTA 57.873 37.500 0.00 0.00 0.00 2.94
5260 5822 6.542821 ACCTGTGAAGATCATTGTTTCCTAA 58.457 36.000 0.00 0.00 0.00 2.69
5261 5823 7.004086 ACCTGTGAAGATCATTGTTTCCTAAA 58.996 34.615 0.00 0.00 0.00 1.85
5262 5824 7.040409 ACCTGTGAAGATCATTGTTTCCTAAAC 60.040 37.037 0.00 0.00 41.73 2.01
5272 5834 4.582701 TGTTTCCTAAACACATTGGCTG 57.417 40.909 1.21 0.00 45.79 4.85
5273 5835 3.320541 TGTTTCCTAAACACATTGGCTGG 59.679 43.478 1.21 0.00 45.79 4.85
5274 5836 2.214376 TCCTAAACACATTGGCTGGG 57.786 50.000 0.00 0.00 0.00 4.45
5275 5837 1.185315 CCTAAACACATTGGCTGGGG 58.815 55.000 0.00 0.00 29.93 4.96
5276 5838 1.185315 CTAAACACATTGGCTGGGGG 58.815 55.000 0.00 0.00 29.93 5.40
5277 5839 0.902516 TAAACACATTGGCTGGGGGC 60.903 55.000 0.00 0.00 40.90 5.80
5278 5840 2.677968 AAACACATTGGCTGGGGGCT 62.678 55.000 0.00 0.00 41.46 5.19
5279 5841 1.799157 AACACATTGGCTGGGGGCTA 61.799 55.000 0.00 0.00 41.46 3.93
5280 5842 1.754234 CACATTGGCTGGGGGCTAC 60.754 63.158 0.00 0.00 41.46 3.58
5281 5843 2.237965 ACATTGGCTGGGGGCTACA 61.238 57.895 0.00 0.00 41.46 2.74
5282 5844 1.000233 CATTGGCTGGGGGCTACAA 60.000 57.895 0.00 0.00 41.46 2.41
5283 5845 1.000359 ATTGGCTGGGGGCTACAAC 60.000 57.895 0.00 0.00 41.46 3.32
5284 5846 2.837031 ATTGGCTGGGGGCTACAACG 62.837 60.000 0.00 0.00 41.46 4.10
5286 5848 4.410400 GCTGGGGGCTACAACGCT 62.410 66.667 0.00 0.00 38.06 5.07
5287 5849 2.436646 CTGGGGGCTACAACGCTG 60.437 66.667 0.00 0.00 0.00 5.18
5288 5850 2.925706 TGGGGGCTACAACGCTGA 60.926 61.111 0.00 0.00 0.00 4.26
5289 5851 2.349755 GGGGGCTACAACGCTGAA 59.650 61.111 0.00 0.00 0.00 3.02
5290 5852 1.077716 GGGGGCTACAACGCTGAAT 60.078 57.895 0.00 0.00 0.00 2.57
5291 5853 1.376609 GGGGGCTACAACGCTGAATG 61.377 60.000 0.00 0.00 0.00 2.67
5292 5854 0.392461 GGGGCTACAACGCTGAATGA 60.392 55.000 0.00 0.00 0.00 2.57
5293 5855 1.009829 GGGCTACAACGCTGAATGAG 58.990 55.000 0.00 0.00 0.00 2.90
5294 5856 1.009829 GGCTACAACGCTGAATGAGG 58.990 55.000 0.00 0.00 0.00 3.86
5295 5857 1.009829 GCTACAACGCTGAATGAGGG 58.990 55.000 0.00 0.00 40.53 4.30
5296 5858 1.656652 CTACAACGCTGAATGAGGGG 58.343 55.000 0.00 0.00 38.98 4.79
5297 5859 0.251916 TACAACGCTGAATGAGGGGG 59.748 55.000 0.00 0.00 38.98 5.40
5298 5860 1.002134 CAACGCTGAATGAGGGGGT 60.002 57.895 0.00 0.00 38.98 4.95
5299 5861 0.251916 CAACGCTGAATGAGGGGGTA 59.748 55.000 0.00 0.00 38.98 3.69
5300 5862 1.134098 CAACGCTGAATGAGGGGGTAT 60.134 52.381 0.00 0.00 38.98 2.73
5301 5863 0.469917 ACGCTGAATGAGGGGGTATG 59.530 55.000 0.00 0.00 38.98 2.39
5302 5864 0.250467 CGCTGAATGAGGGGGTATGG 60.250 60.000 0.00 0.00 0.00 2.74
5303 5865 1.140312 GCTGAATGAGGGGGTATGGA 58.860 55.000 0.00 0.00 0.00 3.41
5304 5866 1.707427 GCTGAATGAGGGGGTATGGAT 59.293 52.381 0.00 0.00 0.00 3.41
5305 5867 2.912956 GCTGAATGAGGGGGTATGGATA 59.087 50.000 0.00 0.00 0.00 2.59
5306 5868 3.054802 GCTGAATGAGGGGGTATGGATAG 60.055 52.174 0.00 0.00 0.00 2.08
5401 5969 7.918033 TGAATTTCGTTTCAAAAGTAGCATTGA 59.082 29.630 0.00 0.00 32.82 2.57
5402 5970 8.816640 AATTTCGTTTCAAAAGTAGCATTGAT 57.183 26.923 0.00 0.00 35.63 2.57
5403 5971 9.906660 AATTTCGTTTCAAAAGTAGCATTGATA 57.093 25.926 0.00 0.00 35.63 2.15
5404 5972 8.948853 TTTCGTTTCAAAAGTAGCATTGATAG 57.051 30.769 0.00 0.00 35.63 2.08
5405 5973 7.667043 TCGTTTCAAAAGTAGCATTGATAGT 57.333 32.000 0.00 0.00 35.63 2.12
5406 5974 8.094798 TCGTTTCAAAAGTAGCATTGATAGTT 57.905 30.769 0.00 0.00 35.63 2.24
5407 5975 8.564574 TCGTTTCAAAAGTAGCATTGATAGTTT 58.435 29.630 8.56 8.56 35.63 2.66
5408 5976 8.629986 CGTTTCAAAAGTAGCATTGATAGTTTG 58.370 33.333 13.82 11.68 35.63 2.93
5513 6082 8.485392 CATCAGGTGGATTTTTATTTTGGGTAT 58.515 33.333 0.00 0.00 32.57 2.73
5591 6161 4.689062 TCCTCCTCTTCATACTTCAACCT 58.311 43.478 0.00 0.00 0.00 3.50
5612 6183 5.163612 ACCTTTGAAACTTTGAACAGAGAGC 60.164 40.000 0.00 0.00 0.00 4.09
5614 6185 2.287915 TGAAACTTTGAACAGAGAGCGC 59.712 45.455 0.00 0.00 0.00 5.92
5615 6186 0.861837 AACTTTGAACAGAGAGCGCG 59.138 50.000 0.00 0.00 0.00 6.86
5620 6191 1.350193 TGAACAGAGAGCGCGATTTC 58.650 50.000 12.10 9.11 0.00 2.17
5636 6207 7.915397 AGCGCGATTTCAATTCTAAATTGTAAT 59.085 29.630 12.10 13.61 33.65 1.89
5712 6283 6.210385 AGTTCACTGTATGTGTCTCTGATCTT 59.790 38.462 0.00 0.00 46.27 2.40
5757 6345 8.084073 TGTTGTATTACGATAATACCAGTAGCC 58.916 37.037 17.57 4.24 33.37 3.93
5796 6384 0.911769 ATCGGTTGATGAAGGAGCCA 59.088 50.000 0.00 0.00 32.21 4.75
5832 7603 6.183360 GCTGGATTAGAAGCACAGAATGAATT 60.183 38.462 0.00 0.00 41.26 2.17
5833 7604 7.630082 GCTGGATTAGAAGCACAGAATGAATTT 60.630 37.037 0.00 0.00 41.26 1.82
5837 7608 4.553323 AGAAGCACAGAATGAATTTGCAC 58.447 39.130 0.00 0.00 39.69 4.57
5849 7620 1.940883 ATTTGCACGGCTCCAGCATG 61.941 55.000 0.03 0.00 44.36 4.06
5868 7679 4.007940 GCGCACGAAGCCACGAAA 62.008 61.111 0.30 0.00 41.38 3.46
5871 7682 1.259544 CGCACGAAGCCACGAAAAAC 61.260 55.000 7.12 0.00 41.38 2.43
5873 7684 1.599419 GCACGAAGCCACGAAAAACAT 60.599 47.619 7.12 0.00 37.23 2.71
5891 7702 6.541111 AAACATTAGGAACGAAACTGACTC 57.459 37.500 0.00 0.00 0.00 3.36
5892 7703 5.470047 ACATTAGGAACGAAACTGACTCT 57.530 39.130 0.00 0.00 0.00 3.24
5893 7704 5.471257 ACATTAGGAACGAAACTGACTCTC 58.529 41.667 0.00 0.00 0.00 3.20
5897 7709 2.917971 GGAACGAAACTGACTCTCGATG 59.082 50.000 0.00 0.00 36.45 3.84
5900 7712 2.095161 ACGAAACTGACTCTCGATGGAC 60.095 50.000 0.00 0.00 36.45 4.02
5906 7718 2.279120 CTCTCGATGGACGGCTGC 60.279 66.667 0.00 0.00 42.82 5.25
5931 7744 2.373735 CGCTATTTTCCTGATGCGTG 57.626 50.000 0.00 0.00 38.81 5.34
5960 7773 1.586154 CGATTCTGTGTGTTGGGCCC 61.586 60.000 17.59 17.59 0.00 5.80
5965 7778 2.917227 GTGTGTTGGGCCCTTGGG 60.917 66.667 25.70 0.32 0.00 4.12
5974 7787 2.386935 GGCCCTTGGGCTGGAGTAT 61.387 63.158 27.45 0.00 45.39 2.12
5992 7805 6.211184 TGGAGTATTGGGTCGTTTAACTCTAA 59.789 38.462 0.00 0.00 33.92 2.10
5994 7807 7.767659 GGAGTATTGGGTCGTTTAACTCTAAAT 59.232 37.037 0.00 0.00 33.92 1.40
5995 7808 9.807649 GAGTATTGGGTCGTTTAACTCTAAATA 57.192 33.333 0.00 0.00 31.41 1.40
6020 7833 7.563888 AAATAGTACGTCAGCTATGTCTACA 57.436 36.000 0.00 0.00 0.00 2.74
6023 7836 6.542574 AGTACGTCAGCTATGTCTACATAC 57.457 41.667 0.00 0.00 37.76 2.39
6042 7858 7.776933 ACATACGATATATTTATGCTGCCAG 57.223 36.000 12.19 0.00 0.00 4.85
6047 7863 8.873215 ACGATATATTTATGCTGCCAGTATAC 57.127 34.615 1.66 0.00 0.00 1.47
6067 7883 4.380841 ACGAATACCTAGCGAACATTCA 57.619 40.909 0.00 0.00 0.00 2.57
6068 7884 4.110482 ACGAATACCTAGCGAACATTCAC 58.890 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.783119 TCCTGGTTTTCTAGCTAGTACATCATA 59.217 37.037 20.10 0.22 0.00 2.15
3 4 6.611642 TCCTGGTTTTCTAGCTAGTACATCAT 59.388 38.462 20.10 0.00 0.00 2.45
4 5 5.955959 TCCTGGTTTTCTAGCTAGTACATCA 59.044 40.000 20.10 9.67 0.00 3.07
6 7 5.163395 GCTCCTGGTTTTCTAGCTAGTACAT 60.163 44.000 20.10 0.00 0.00 2.29
7 8 4.159879 GCTCCTGGTTTTCTAGCTAGTACA 59.840 45.833 20.10 11.63 0.00 2.90
8 9 4.403113 AGCTCCTGGTTTTCTAGCTAGTAC 59.597 45.833 20.10 15.39 41.56 2.73
9 10 4.611367 AGCTCCTGGTTTTCTAGCTAGTA 58.389 43.478 20.10 8.39 41.56 1.82
10 11 3.445987 AGCTCCTGGTTTTCTAGCTAGT 58.554 45.455 20.10 0.00 41.56 2.57
11 12 4.479786 AAGCTCCTGGTTTTCTAGCTAG 57.520 45.455 15.01 15.01 42.49 3.42
12 13 4.565652 CCAAAGCTCCTGGTTTTCTAGCTA 60.566 45.833 5.84 0.00 42.49 3.32
23 24 2.100631 CGCGTACCAAAGCTCCTGG 61.101 63.158 12.25 12.25 40.05 4.45
30 31 3.595709 TTGAGTTTTCGCGTACCAAAG 57.404 42.857 5.77 0.00 0.00 2.77
38 40 2.719046 GTGTGGATTTTGAGTTTTCGCG 59.281 45.455 0.00 0.00 0.00 5.87
40 42 4.275936 AGAGGTGTGGATTTTGAGTTTTCG 59.724 41.667 0.00 0.00 0.00 3.46
71 73 9.605275 CGGATCATGGTTCTATTTCATATGTAT 57.395 33.333 1.90 0.87 0.00 2.29
74 76 6.317140 CCCGGATCATGGTTCTATTTCATATG 59.683 42.308 0.73 0.00 0.00 1.78
76 78 5.546110 TCCCGGATCATGGTTCTATTTCATA 59.454 40.000 0.73 0.00 0.00 2.15
77 79 4.350816 TCCCGGATCATGGTTCTATTTCAT 59.649 41.667 0.73 0.00 0.00 2.57
78 80 3.714280 TCCCGGATCATGGTTCTATTTCA 59.286 43.478 0.73 0.00 0.00 2.69
80 82 4.446311 CCTTCCCGGATCATGGTTCTATTT 60.446 45.833 0.73 0.00 33.16 1.40
84 98 0.839946 CCTTCCCGGATCATGGTTCT 59.160 55.000 0.73 0.00 33.16 3.01
123 137 3.739167 GCACGGCCAACACTTACA 58.261 55.556 2.24 0.00 0.00 2.41
163 177 3.455543 AGAATACCCCCATGCCAAAATTG 59.544 43.478 0.00 0.00 0.00 2.32
402 418 5.546499 AGGGAGTAGAATAACAGTTGGAACA 59.454 40.000 0.00 0.00 0.00 3.18
403 419 6.051179 AGGGAGTAGAATAACAGTTGGAAC 57.949 41.667 0.00 0.00 0.00 3.62
405 421 5.590818 AGAGGGAGTAGAATAACAGTTGGA 58.409 41.667 0.00 0.00 0.00 3.53
441 460 8.935614 ACTACTTTAGTGGCCTAAAATTTCTT 57.064 30.769 3.32 0.00 41.41 2.52
456 475 7.017319 AGATGTTTTAGGCCACTACTTTAGT 57.983 36.000 5.01 0.00 40.28 2.24
457 476 7.923414 AAGATGTTTTAGGCCACTACTTTAG 57.077 36.000 5.01 0.00 0.00 1.85
459 478 9.969001 TTATAAGATGTTTTAGGCCACTACTTT 57.031 29.630 5.01 0.00 0.00 2.66
460 479 9.969001 TTTATAAGATGTTTTAGGCCACTACTT 57.031 29.630 5.01 6.93 0.00 2.24
461 480 9.969001 TTTTATAAGATGTTTTAGGCCACTACT 57.031 29.630 5.01 0.00 0.00 2.57
463 482 9.969001 ACTTTTATAAGATGTTTTAGGCCACTA 57.031 29.630 5.01 0.00 35.30 2.74
464 483 8.879427 ACTTTTATAAGATGTTTTAGGCCACT 57.121 30.769 5.01 0.00 35.30 4.00
465 484 9.923143 AAACTTTTATAAGATGTTTTAGGCCAC 57.077 29.630 5.01 0.00 35.30 5.01
475 494 9.892130 CTCCCTCTGTAAACTTTTATAAGATGT 57.108 33.333 0.00 0.00 35.30 3.06
476 495 9.892130 ACTCCCTCTGTAAACTTTTATAAGATG 57.108 33.333 0.00 0.00 35.30 2.90
483 502 9.910267 AAAAAGTACTCCCTCTGTAAACTTTTA 57.090 29.630 9.83 0.00 34.93 1.52
484 503 8.818622 AAAAAGTACTCCCTCTGTAAACTTTT 57.181 30.769 0.00 0.00 36.74 2.27
490 509 9.662947 GCTTAATAAAAAGTACTCCCTCTGTAA 57.337 33.333 0.00 0.00 0.00 2.41
491 510 8.262933 GGCTTAATAAAAAGTACTCCCTCTGTA 58.737 37.037 0.00 0.00 0.00 2.74
492 511 7.110810 GGCTTAATAAAAAGTACTCCCTCTGT 58.889 38.462 0.00 0.00 0.00 3.41
493 512 7.110155 TGGCTTAATAAAAAGTACTCCCTCTG 58.890 38.462 0.00 0.00 0.00 3.35
494 513 7.266905 TGGCTTAATAAAAAGTACTCCCTCT 57.733 36.000 0.00 0.00 0.00 3.69
495 514 9.794719 ATATGGCTTAATAAAAAGTACTCCCTC 57.205 33.333 0.00 0.00 0.00 4.30
521 540 7.930865 CAGATGGTCCTTTTTCCAAACAAAATA 59.069 33.333 0.00 0.00 37.27 1.40
523 542 6.112058 CAGATGGTCCTTTTTCCAAACAAAA 58.888 36.000 0.00 0.00 37.27 2.44
541 562 6.406370 TCTCAACATTACTGTAACCAGATGG 58.594 40.000 1.73 0.00 41.50 3.51
576 597 1.398390 GCTGTGATTTTAGCTGGGTCG 59.602 52.381 0.00 0.00 36.99 4.79
586 607 2.002586 CGATCAGTCGGCTGTGATTTT 58.997 47.619 18.04 0.00 44.00 1.82
642 663 9.023967 GTCAAATTTGTATATCTTCAATGGTGC 57.976 33.333 17.47 0.00 0.00 5.01
657 678 7.338449 GCTAACCATAGGGAAGTCAAATTTGTA 59.662 37.037 17.47 1.83 38.05 2.41
659 680 6.152661 TGCTAACCATAGGGAAGTCAAATTTG 59.847 38.462 12.15 12.15 38.05 2.32
661 682 5.826643 TGCTAACCATAGGGAAGTCAAATT 58.173 37.500 0.00 0.00 38.05 1.82
662 683 5.450818 TGCTAACCATAGGGAAGTCAAAT 57.549 39.130 0.00 0.00 38.05 2.32
663 684 4.919774 TGCTAACCATAGGGAAGTCAAA 57.080 40.909 0.00 0.00 38.05 2.69
664 685 4.385199 CCATGCTAACCATAGGGAAGTCAA 60.385 45.833 0.00 0.00 38.05 3.18
701 726 1.836802 TCCTGCAAACCCAAAAAGCTT 59.163 42.857 0.00 0.00 0.00 3.74
756 889 4.214980 AGCGTGAACAAATTTGACAGAG 57.785 40.909 24.64 17.91 0.00 3.35
781 914 7.654022 AAGATGTGTTTCTTTTCCTGGTTTA 57.346 32.000 0.00 0.00 31.94 2.01
931 1480 1.827344 TGTCACTCCTGCTGGACATAG 59.173 52.381 8.48 1.57 37.46 2.23
957 1506 1.153862 CTCTCAGCAGCGGTGTCTC 60.154 63.158 17.07 0.00 32.43 3.36
982 1531 1.135915 CATCTGCTGCCTCGAGTACTT 59.864 52.381 12.31 0.00 0.00 2.24
997 1546 1.558756 AGCCCTTGAGGAAGACATCTG 59.441 52.381 0.00 0.00 38.24 2.90
1013 1562 2.032681 ACGAACTGGAAGCAGCCC 59.967 61.111 0.00 0.00 37.60 5.19
1015 1564 1.294659 CTGGACGAACTGGAAGCAGC 61.295 60.000 0.00 0.00 37.60 5.25
1020 1569 1.118965 TCCTGCTGGACGAACTGGAA 61.119 55.000 8.48 0.00 37.46 3.53
1029 1578 4.329545 TGGCGGTTCCTGCTGGAC 62.330 66.667 12.53 7.64 43.06 4.02
1191 1740 3.386402 GCAAGTAGGCTATGACCTTCTCT 59.614 47.826 0.00 0.00 41.50 3.10
1368 1917 1.729517 CGTACATTTGTGCCGATGTCA 59.270 47.619 0.00 0.00 37.62 3.58
1380 1929 4.038763 TCAGTGAACAGAGACCGTACATTT 59.961 41.667 0.00 0.00 0.00 2.32
1527 2076 3.821033 GCTCAAAGTCTACCACCAAACAT 59.179 43.478 0.00 0.00 0.00 2.71
1731 2280 3.494924 CCTCGCCATGGTTATCTTCATGA 60.495 47.826 14.67 0.00 42.25 3.07
1758 2307 1.448540 AGGCTTTGTGATCTCGGCG 60.449 57.895 0.00 0.00 0.00 6.46
1888 2437 5.533903 CCTCATCTTCAATGACCTTTATGGG 59.466 44.000 0.00 0.00 41.11 4.00
1902 2451 0.252881 AGGGGAGTGCCTCATCTTCA 60.253 55.000 0.00 0.00 36.99 3.02
1998 2547 1.483415 GCCATGACAAGGGATGCAATT 59.517 47.619 0.00 0.00 0.00 2.32
2097 2646 1.203237 GGCAAACAATAAGGCCCCAT 58.797 50.000 0.00 0.00 40.55 4.00
2107 2656 1.547372 GCTCTCATGGTGGCAAACAAT 59.453 47.619 0.00 0.00 0.00 2.71
2130 2679 3.494398 GCAGCGGAAAAGGGACATATCTA 60.494 47.826 0.00 0.00 0.00 1.98
2301 2850 2.206322 TATTGGGTGCCCCTGATACT 57.794 50.000 11.10 0.00 45.70 2.12
2387 2936 0.668706 CTGAGACTCGGTTGGTGCAG 60.669 60.000 2.84 0.00 0.00 4.41
2391 2940 1.743958 CGTATCTGAGACTCGGTTGGT 59.256 52.381 11.11 0.00 0.00 3.67
2579 3128 5.762218 CCCCATCTGATTTCTTTAGCTGTAG 59.238 44.000 0.00 0.00 0.00 2.74
2629 3178 2.748798 GCATCCTTCTGCTGTCATCCAT 60.749 50.000 0.00 0.00 39.12 3.41
2630 3179 1.407851 GCATCCTTCTGCTGTCATCCA 60.408 52.381 0.00 0.00 39.12 3.41
2761 3310 2.813908 GACGACACCATCCACCGC 60.814 66.667 0.00 0.00 0.00 5.68
2799 3348 9.958180 TTTAGATCACCAATCTGTTCATCTAAA 57.042 29.630 6.99 6.99 44.69 1.85
2907 3456 3.202818 TGACCAATCCATTGCCATCTACT 59.797 43.478 0.00 0.00 36.48 2.57
2931 3480 0.322456 CCGCTTTCTGATTCCACCCA 60.322 55.000 0.00 0.00 0.00 4.51
2940 3489 1.806542 GTCAATTCTGCCGCTTTCTGA 59.193 47.619 0.00 0.00 0.00 3.27
2970 3519 4.349048 TGCCTTCCTATAGCATCATCAACT 59.651 41.667 0.00 0.00 0.00 3.16
2982 3531 5.723355 AGGGTAAGTATGTGCCTTCCTATA 58.277 41.667 0.00 0.00 0.00 1.31
3045 3594 3.118592 ACTCACCCTGCAAAGCTAGATAC 60.119 47.826 0.00 0.00 0.00 2.24
3106 3655 1.829849 GGAGGAAGGTAAAGTAGGCGT 59.170 52.381 0.00 0.00 0.00 5.68
3240 3789 6.724893 TTATTAGAGACCCATGAACGATCA 57.275 37.500 0.00 0.00 40.57 2.92
3269 3819 2.487762 TCTTTGCCTGTTTGATTAGCGG 59.512 45.455 0.00 0.00 0.00 5.52
3274 3824 6.322201 TCTTTCTCTTCTTTGCCTGTTTGATT 59.678 34.615 0.00 0.00 0.00 2.57
3327 3877 1.492176 GGGCCATCATCTCTCTTTGGA 59.508 52.381 4.39 0.00 0.00 3.53
3501 4051 6.848562 AATATAGGAGGAATGAGTGGGTTT 57.151 37.500 0.00 0.00 0.00 3.27
3539 4089 1.072173 TCCACTCACAACACCATCCAG 59.928 52.381 0.00 0.00 0.00 3.86
3633 4183 2.355108 GCAGGAGGCATTTCTACTGTCA 60.355 50.000 6.04 0.00 45.25 3.58
3899 4449 4.464947 AGCTTTCAGCCTTTTTAGTGACT 58.535 39.130 0.00 0.00 43.77 3.41
4032 4582 3.628942 GCTGGTGATGACAATTATCTGCA 59.371 43.478 0.00 0.00 0.00 4.41
4033 4583 3.881688 AGCTGGTGATGACAATTATCTGC 59.118 43.478 0.00 0.00 0.00 4.26
4047 4597 4.695455 GCAAGTATCTTGTTTAGCTGGTGA 59.305 41.667 0.00 0.00 0.00 4.02
4216 4766 4.158394 GGCATGAAAGCAGGTGAAATTAGA 59.842 41.667 0.00 0.00 35.83 2.10
4322 4880 4.201920 GGCTAAATTTTCCGGAAGCAGTAG 60.202 45.833 21.73 18.94 0.00 2.57
4402 4960 9.486497 AGATGATAACAGTGAACTATTATGCAG 57.514 33.333 0.00 0.00 26.71 4.41
4448 5006 4.576053 TCTGTGACCACAAATGACAGAAAG 59.424 41.667 4.30 0.00 41.33 2.62
4691 5249 2.300152 TGGCTGAAATCTCGACAGAACT 59.700 45.455 4.30 0.00 34.07 3.01
4697 5255 0.729690 GCCTTGGCTGAAATCTCGAC 59.270 55.000 4.11 0.00 0.00 4.20
4720 5278 3.685139 TTCTCTCCGATGCTGTTCTTT 57.315 42.857 0.00 0.00 0.00 2.52
4815 5376 2.160417 GCATTCCCACAAGAAGACTTCG 59.840 50.000 9.53 0.00 33.70 3.79
4827 5388 3.004752 ACCATCACTAAGCATTCCCAC 57.995 47.619 0.00 0.00 0.00 4.61
4863 5425 2.622942 TGGTGCTTGATCCTGAAAACAC 59.377 45.455 0.00 0.00 0.00 3.32
4900 5462 1.816679 CTGCGCCATTAGCTCTGCA 60.817 57.895 4.18 0.00 40.39 4.41
4918 5480 1.646189 GCTCGTCCTCCTCAAACATC 58.354 55.000 0.00 0.00 0.00 3.06
4936 5498 4.074526 TCCTCTGACTGCTGCGGC 62.075 66.667 11.65 11.65 39.26 6.53
4937 5499 2.183811 CTCCTCTGACTGCTGCGG 59.816 66.667 6.98 6.98 0.00 5.69
4975 5537 2.260844 TGAGCCTCAACAGGTTTCTG 57.739 50.000 0.00 0.00 42.74 3.02
5077 5639 2.355132 GCTTCTTCATCAGTGCTCCATG 59.645 50.000 0.00 0.00 0.00 3.66
5108 5670 5.290400 CACATACCATCTGATGATCATACGC 59.710 44.000 18.92 0.00 0.00 4.42
5115 5677 7.114754 AGTTGTTTCACATACCATCTGATGAT 58.885 34.615 18.92 4.22 0.00 2.45
5156 5718 3.254411 TGACAAAAGAAACACACTGCACA 59.746 39.130 0.00 0.00 0.00 4.57
5234 5796 5.940470 AGGAAACAATGATCTTCACAGGTAC 59.060 40.000 0.00 0.00 0.00 3.34
5252 5814 3.306019 CCCAGCCAATGTGTTTAGGAAAC 60.306 47.826 0.00 0.00 41.73 2.78
5253 5815 2.896685 CCCAGCCAATGTGTTTAGGAAA 59.103 45.455 0.00 0.00 0.00 3.13
5254 5816 2.524306 CCCAGCCAATGTGTTTAGGAA 58.476 47.619 0.00 0.00 0.00 3.36
5255 5817 1.272425 CCCCAGCCAATGTGTTTAGGA 60.272 52.381 0.00 0.00 0.00 2.94
5256 5818 1.185315 CCCCAGCCAATGTGTTTAGG 58.815 55.000 0.00 0.00 0.00 2.69
5257 5819 1.185315 CCCCCAGCCAATGTGTTTAG 58.815 55.000 0.00 0.00 0.00 1.85
5258 5820 0.902516 GCCCCCAGCCAATGTGTTTA 60.903 55.000 0.00 0.00 34.35 2.01
5259 5821 2.216331 GCCCCCAGCCAATGTGTTT 61.216 57.895 0.00 0.00 34.35 2.83
5260 5822 1.799157 TAGCCCCCAGCCAATGTGTT 61.799 55.000 0.00 0.00 45.47 3.32
5261 5823 2.237965 TAGCCCCCAGCCAATGTGT 61.238 57.895 0.00 0.00 45.47 3.72
5262 5824 1.754234 GTAGCCCCCAGCCAATGTG 60.754 63.158 0.00 0.00 45.47 3.21
5263 5825 1.799157 TTGTAGCCCCCAGCCAATGT 61.799 55.000 0.00 0.00 45.47 2.71
5264 5826 1.000233 TTGTAGCCCCCAGCCAATG 60.000 57.895 0.00 0.00 45.47 2.82
5265 5827 1.000359 GTTGTAGCCCCCAGCCAAT 60.000 57.895 0.00 0.00 45.47 3.16
5266 5828 2.438795 GTTGTAGCCCCCAGCCAA 59.561 61.111 0.00 0.00 45.47 4.52
5267 5829 4.028490 CGTTGTAGCCCCCAGCCA 62.028 66.667 0.00 0.00 45.47 4.75
5269 5831 4.410400 AGCGTTGTAGCCCCCAGC 62.410 66.667 0.00 0.00 44.25 4.85
5270 5832 2.436646 CAGCGTTGTAGCCCCCAG 60.437 66.667 0.00 0.00 38.01 4.45
5271 5833 1.847798 ATTCAGCGTTGTAGCCCCCA 61.848 55.000 0.00 0.00 38.01 4.96
5272 5834 1.077716 ATTCAGCGTTGTAGCCCCC 60.078 57.895 0.00 0.00 38.01 5.40
5273 5835 0.392461 TCATTCAGCGTTGTAGCCCC 60.392 55.000 0.00 0.00 38.01 5.80
5274 5836 1.009829 CTCATTCAGCGTTGTAGCCC 58.990 55.000 0.00 0.00 38.01 5.19
5275 5837 1.009829 CCTCATTCAGCGTTGTAGCC 58.990 55.000 0.00 0.00 38.01 3.93
5276 5838 1.009829 CCCTCATTCAGCGTTGTAGC 58.990 55.000 0.00 0.00 37.41 3.58
5277 5839 1.656652 CCCCTCATTCAGCGTTGTAG 58.343 55.000 0.00 0.00 0.00 2.74
5278 5840 0.251916 CCCCCTCATTCAGCGTTGTA 59.748 55.000 0.00 0.00 0.00 2.41
5279 5841 1.002134 CCCCCTCATTCAGCGTTGT 60.002 57.895 0.00 0.00 0.00 3.32
5280 5842 0.251916 TACCCCCTCATTCAGCGTTG 59.748 55.000 0.00 0.00 0.00 4.10
5281 5843 1.134098 CATACCCCCTCATTCAGCGTT 60.134 52.381 0.00 0.00 0.00 4.84
5282 5844 0.469917 CATACCCCCTCATTCAGCGT 59.530 55.000 0.00 0.00 0.00 5.07
5283 5845 0.250467 CCATACCCCCTCATTCAGCG 60.250 60.000 0.00 0.00 0.00 5.18
5284 5846 1.140312 TCCATACCCCCTCATTCAGC 58.860 55.000 0.00 0.00 0.00 4.26
5285 5847 3.054802 GCTATCCATACCCCCTCATTCAG 60.055 52.174 0.00 0.00 0.00 3.02
5286 5848 2.912956 GCTATCCATACCCCCTCATTCA 59.087 50.000 0.00 0.00 0.00 2.57
5287 5849 2.912956 TGCTATCCATACCCCCTCATTC 59.087 50.000 0.00 0.00 0.00 2.67
5288 5850 2.915604 CTGCTATCCATACCCCCTCATT 59.084 50.000 0.00 0.00 0.00 2.57
5289 5851 2.555664 CTGCTATCCATACCCCCTCAT 58.444 52.381 0.00 0.00 0.00 2.90
5290 5852 1.485019 CCTGCTATCCATACCCCCTCA 60.485 57.143 0.00 0.00 0.00 3.86
5291 5853 1.280457 CCTGCTATCCATACCCCCTC 58.720 60.000 0.00 0.00 0.00 4.30
5292 5854 0.178861 CCCTGCTATCCATACCCCCT 60.179 60.000 0.00 0.00 0.00 4.79
5293 5855 1.208165 CCCCTGCTATCCATACCCCC 61.208 65.000 0.00 0.00 0.00 5.40
5294 5856 1.853250 GCCCCTGCTATCCATACCCC 61.853 65.000 0.00 0.00 33.53 4.95
5295 5857 1.685820 GCCCCTGCTATCCATACCC 59.314 63.158 0.00 0.00 33.53 3.69
5296 5858 1.296715 CGCCCCTGCTATCCATACC 59.703 63.158 0.00 0.00 34.43 2.73
5297 5859 1.192146 TCCGCCCCTGCTATCCATAC 61.192 60.000 0.00 0.00 34.43 2.39
5298 5860 0.904865 CTCCGCCCCTGCTATCCATA 60.905 60.000 0.00 0.00 34.43 2.74
5299 5861 2.122413 TCCGCCCCTGCTATCCAT 60.122 61.111 0.00 0.00 34.43 3.41
5300 5862 2.844362 CTCCGCCCCTGCTATCCA 60.844 66.667 0.00 0.00 34.43 3.41
5301 5863 4.321966 GCTCCGCCCCTGCTATCC 62.322 72.222 0.00 0.00 34.43 2.59
5302 5864 4.321966 GGCTCCGCCCCTGCTATC 62.322 72.222 0.00 0.00 44.06 2.08
5401 5969 6.934056 TGCCAATGCTTTTGTATCAAACTAT 58.066 32.000 0.00 0.00 38.71 2.12
5402 5970 6.338214 TGCCAATGCTTTTGTATCAAACTA 57.662 33.333 0.00 0.00 38.71 2.24
5403 5971 5.212532 TGCCAATGCTTTTGTATCAAACT 57.787 34.783 0.00 0.00 38.71 2.66
5404 5972 5.466393 AGTTGCCAATGCTTTTGTATCAAAC 59.534 36.000 0.00 0.00 38.71 2.93
5405 5973 5.609423 AGTTGCCAATGCTTTTGTATCAAA 58.391 33.333 0.00 0.00 38.71 2.69
5406 5974 5.212532 AGTTGCCAATGCTTTTGTATCAA 57.787 34.783 0.00 0.00 38.71 2.57
5407 5975 4.870123 AGTTGCCAATGCTTTTGTATCA 57.130 36.364 0.00 0.00 38.71 2.15
5408 5976 9.533253 AATATTAGTTGCCAATGCTTTTGTATC 57.467 29.630 0.00 0.00 38.71 2.24
5413 5981 9.717942 TGTTAAATATTAGTTGCCAATGCTTTT 57.282 25.926 0.00 0.00 38.71 2.27
5479 6047 9.533831 AATAAAAATCCACCTGATGTACTCTTT 57.466 29.630 0.00 0.00 32.68 2.52
5481 6049 9.533831 AAAATAAAAATCCACCTGATGTACTCT 57.466 29.630 0.00 0.00 32.68 3.24
5513 6082 4.080129 AGGCTTCCAGCTCAAATATTCAGA 60.080 41.667 0.00 0.00 41.99 3.27
5591 6161 4.730613 GCGCTCTCTGTTCAAAGTTTCAAA 60.731 41.667 0.00 0.00 0.00 2.69
5599 6169 1.795768 AATCGCGCTCTCTGTTCAAA 58.204 45.000 5.56 0.00 0.00 2.69
5612 6183 9.438291 AGATTACAATTTAGAATTGAAATCGCG 57.562 29.630 17.51 0.00 33.51 5.87
5636 6207 8.547481 TGATCAACCTATTAGATGTGGTAAGA 57.453 34.615 0.00 0.00 31.82 2.10
5796 6384 5.180868 GCTTCTAATCCAGCGATTGAATCAT 59.819 40.000 5.95 0.00 39.14 2.45
5832 7603 3.057548 CATGCTGGAGCCGTGCAA 61.058 61.111 10.22 0.00 40.24 4.08
5851 7622 2.975167 TTTTTCGTGGCTTCGTGCGC 62.975 55.000 0.00 0.00 44.05 6.09
5862 7673 6.140108 CAGTTTCGTTCCTAATGTTTTTCGTG 59.860 38.462 0.00 0.00 0.00 4.35
5868 7679 6.289064 AGAGTCAGTTTCGTTCCTAATGTTT 58.711 36.000 0.00 0.00 0.00 2.83
5871 7682 4.559251 CGAGAGTCAGTTTCGTTCCTAATG 59.441 45.833 0.00 0.00 0.00 1.90
5873 7684 3.817084 TCGAGAGTCAGTTTCGTTCCTAA 59.183 43.478 0.00 0.00 35.90 2.69
5891 7702 2.887568 GTGCAGCCGTCCATCGAG 60.888 66.667 0.00 0.00 42.86 4.04
5892 7703 4.794439 CGTGCAGCCGTCCATCGA 62.794 66.667 0.00 0.00 42.86 3.59
5893 7704 3.693382 TACGTGCAGCCGTCCATCG 62.693 63.158 11.56 0.00 42.00 3.84
5900 7712 1.418342 AAATAGCGTACGTGCAGCCG 61.418 55.000 17.90 0.00 37.31 5.52
5906 7718 3.302480 GCATCAGGAAAATAGCGTACGTG 60.302 47.826 17.90 3.74 0.00 4.49
5929 7742 3.187700 CACAGAATCGCTAGTTACCCAC 58.812 50.000 0.00 0.00 0.00 4.61
5931 7744 3.187700 CACACAGAATCGCTAGTTACCC 58.812 50.000 0.00 0.00 0.00 3.69
5960 7773 0.625849 ACCCAATACTCCAGCCCAAG 59.374 55.000 0.00 0.00 0.00 3.61
5965 7778 2.109425 AAACGACCCAATACTCCAGC 57.891 50.000 0.00 0.00 0.00 4.85
5994 7807 9.112725 TGTAGACATAGCTGACGTACTATTTTA 57.887 33.333 0.00 0.00 0.00 1.52
5995 7808 7.993101 TGTAGACATAGCTGACGTACTATTTT 58.007 34.615 0.00 0.00 0.00 1.82
5996 7809 7.563888 TGTAGACATAGCTGACGTACTATTT 57.436 36.000 0.00 0.00 0.00 1.40
5997 7810 7.747155 ATGTAGACATAGCTGACGTACTATT 57.253 36.000 0.00 0.00 34.26 1.73
5998 7811 7.063191 CGTATGTAGACATAGCTGACGTACTAT 59.937 40.741 0.00 0.00 39.29 2.12
5999 7812 6.364435 CGTATGTAGACATAGCTGACGTACTA 59.636 42.308 0.00 0.00 39.29 1.82
6019 7832 7.776933 ACTGGCAGCATAAATATATCGTATG 57.223 36.000 15.89 10.18 0.00 2.39
6023 7836 7.860872 TCGTATACTGGCAGCATAAATATATCG 59.139 37.037 15.89 9.51 0.00 2.92
6034 7850 2.963101 AGGTATTCGTATACTGGCAGCA 59.037 45.455 15.89 0.71 37.39 4.41
6038 7854 3.438087 TCGCTAGGTATTCGTATACTGGC 59.562 47.826 11.37 11.30 37.39 4.85
6042 7858 7.060403 GTGAATGTTCGCTAGGTATTCGTATAC 59.940 40.741 3.75 3.75 34.73 1.47
6047 7863 4.109766 TGTGAATGTTCGCTAGGTATTCG 58.890 43.478 7.70 0.00 38.47 3.34


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

AutoCloner maintained by Alex Coulton.