Multiple sequence alignment - TraesCS5B01G395800

Loading Multiple Alignment...

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 TraesCS5B01G395800 chr5B 100.000 5219 0 0 1 5219 572956439 572951221 0.000000e+00 9638.0
1 TraesCS5B01G395800 chr5B 84.553 246 33 3 4547 4791 479631202 479631443 6.750000e-59 239.0
2 TraesCS5B01G395800 chr5D 94.405 3110 90 35 2120 5219 465721909 465718874 0.000000e+00 4702.0
3 TraesCS5B01G395800 chr5D 89.766 1456 72 35 569 1988 465723496 465722082 0.000000e+00 1792.0
4 TraesCS5B01G395800 chr5D 89.501 381 26 8 15 388 465724323 465723950 2.200000e-128 470.0
5 TraesCS5B01G395800 chr5D 86.531 245 29 2 4547 4791 399222716 399222956 3.100000e-67 267.0
6 TraesCS5B01G395800 chr5A 94.024 2878 103 20 2344 5219 586152096 586149286 0.000000e+00 4298.0
7 TraesCS5B01G395800 chr5A 89.044 1433 75 37 569 1964 586153856 586152469 0.000000e+00 1701.0
8 TraesCS5B01G395800 chr5A 85.969 392 33 14 15 388 586163340 586162953 2.930000e-107 399.0
9 TraesCS5B01G395800 chr5A 87.778 270 12 11 1994 2260 586152407 586152156 3.950000e-76 296.0
10 TraesCS5B01G395800 chr5A 95.745 47 2 0 527 573 586153932 586153886 5.600000e-10 76.8
11 TraesCS5B01G395800 chr2B 73.322 596 120 35 3608 4182 660678294 660678871 3.210000e-42 183.0
12 TraesCS5B01G395800 chr2A 79.365 126 26 0 3367 3492 694633073 694633198 7.200000e-14 89.8
13 TraesCS5B01G395800 chr2D 78.571 126 27 0 3367 3492 554477080 554477205 3.350000e-12 84.2


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 TraesCS5B01G395800 chr5B 572951221 572956439 5218 True 9638.000000 9638 100.00000 1 5219 1 chr5B.!!$R1 5218
1 TraesCS5B01G395800 chr5D 465718874 465724323 5449 True 2321.333333 4702 91.22400 15 5219 3 chr5D.!!$R1 5204
2 TraesCS5B01G395800 chr5A 586149286 586153932 4646 True 1592.950000 4298 91.64775 527 5219 4 chr5A.!!$R2 4692

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
486 498 0.037734 AGGGTTCCCATTTCGGACAC 59.962 55.0 10.73 0.00 36.56 3.67 F
815 1097 0.042731 TGGGGAGTAGTGGAGGGAAG 59.957 60.0 0.00 0.00 0.00 3.46 F
820 1102 0.325765 AGTAGTGGAGGGAAGGGAGC 60.326 60.0 0.00 0.00 0.00 4.70 F
1773 2104 0.462581 GTCTGGCTGCCAATCGATGA 60.463 55.0 23.51 12.29 30.80 2.92 F
3140 3542 0.032813 CATGGTGGGGGATGCTCTTT 60.033 55.0 0.00 0.00 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2071 2439 0.249784 AAACGCCACATGCATGCAAA 60.250 45.0 26.68 1.26 41.33 3.68 R
2073 2441 0.249784 AAAAACGCCACATGCATGCA 60.250 45.0 26.53 25.04 41.33 3.96 R
2348 2746 0.609131 CCCTGCATTCGGTCCAAAGT 60.609 55.0 0.00 0.00 0.00 2.66 R
3568 3972 0.038526 CACGTCGGTTAGTTCAGCCT 60.039 55.0 0.00 0.00 0.00 4.58 R
4348 4756 0.391661 CAATGTGACTCAGGACGGGG 60.392 60.0 0.00 0.00 0.00 5.73 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
19 20 2.579738 GAGACGGCCCTGTTCCTC 59.420 66.667 0.00 0.00 0.00 3.71
31 32 0.836400 TGTTCCTCCACCCTCCACTC 60.836 60.000 0.00 0.00 0.00 3.51
41 42 2.496817 CTCCACTCGTGCCTAGCC 59.503 66.667 0.00 0.00 0.00 3.93
86 87 6.073222 GCCGATATCGAGTACAAAATCCAAAT 60.073 38.462 26.32 0.00 43.02 2.32
89 90 7.360101 CGATATCGAGTACAAAATCCAAATCCC 60.360 40.741 20.50 0.00 43.02 3.85
162 165 4.133796 GCGTGAGGCAAATGGGGC 62.134 66.667 0.00 0.00 42.87 5.80
171 174 1.692173 GCAAATGGGGCATGCATCCT 61.692 55.000 21.36 7.59 39.81 3.24
226 229 2.481104 GGATGAGGCAGAGAAGAGAACG 60.481 54.545 0.00 0.00 0.00 3.95
268 275 2.070262 TCATCAGACACGTCAAGCAG 57.930 50.000 0.00 0.00 0.00 4.24
271 278 1.595109 CAGACACGTCAAGCAGGCA 60.595 57.895 0.00 0.00 0.00 4.75
272 279 1.301244 AGACACGTCAAGCAGGCAG 60.301 57.895 0.00 0.00 0.00 4.85
273 280 2.281070 ACACGTCAAGCAGGCAGG 60.281 61.111 0.00 0.00 0.00 4.85
274 281 3.730761 CACGTCAAGCAGGCAGGC 61.731 66.667 0.00 0.00 0.00 4.85
279 286 1.904865 TCAAGCAGGCAGGCCAAAG 60.905 57.895 13.63 3.14 38.92 2.77
318 325 2.511600 CGGCACCTGATTCCCGTC 60.512 66.667 0.00 0.00 36.18 4.79
322 329 1.026718 GCACCTGATTCCCGTCCAAG 61.027 60.000 0.00 0.00 0.00 3.61
324 331 0.840722 ACCTGATTCCCGTCCAAGGT 60.841 55.000 0.00 0.00 0.00 3.50
326 333 0.107654 CTGATTCCCGTCCAAGGTCC 60.108 60.000 0.00 0.00 0.00 4.46
327 334 1.223763 GATTCCCGTCCAAGGTCCC 59.776 63.158 0.00 0.00 0.00 4.46
341 348 0.395312 GGTCCCAAGGTTTCGTCTCA 59.605 55.000 0.00 0.00 0.00 3.27
343 350 2.143925 GTCCCAAGGTTTCGTCTCAAG 58.856 52.381 0.00 0.00 0.00 3.02
346 353 2.290641 CCCAAGGTTTCGTCTCAAGTTG 59.709 50.000 0.00 0.00 0.00 3.16
349 356 4.495844 CCAAGGTTTCGTCTCAAGTTGTTC 60.496 45.833 2.11 0.00 0.00 3.18
351 358 3.621715 AGGTTTCGTCTCAAGTTGTTCAC 59.378 43.478 2.11 0.00 0.00 3.18
379 386 2.338809 ACTGATGTTCCCTGTTCTGGA 58.661 47.619 0.00 0.00 0.00 3.86
381 393 1.003580 TGATGTTCCCTGTTCTGGAGC 59.996 52.381 0.00 0.00 34.04 4.70
384 396 2.265367 TGTTCCCTGTTCTGGAGCATA 58.735 47.619 0.00 0.00 38.07 3.14
388 400 3.889815 TCCCTGTTCTGGAGCATAAATG 58.110 45.455 0.00 0.00 0.00 2.32
409 421 5.911378 TGCATGAACCACAATGCTAATTA 57.089 34.783 0.00 0.00 40.41 1.40
413 425 8.473219 TGCATGAACCACAATGCTAATTATTTA 58.527 29.630 0.00 0.00 40.41 1.40
414 426 8.755018 GCATGAACCACAATGCTAATTATTTAC 58.245 33.333 0.00 0.00 37.10 2.01
420 432 9.456147 ACCACAATGCTAATTATTTACTACACA 57.544 29.630 0.00 0.00 0.00 3.72
442 454 9.410556 ACACAAAATTCTGTTCTTATTATGCAC 57.589 29.630 0.00 0.00 0.00 4.57
450 462 7.854534 TCTGTTCTTATTATGCACAATGATCG 58.145 34.615 0.00 0.00 0.00 3.69
451 463 7.710475 TCTGTTCTTATTATGCACAATGATCGA 59.290 33.333 0.00 0.00 0.00 3.59
452 464 7.630026 TGTTCTTATTATGCACAATGATCGAC 58.370 34.615 0.00 0.00 0.00 4.20
453 465 7.279758 TGTTCTTATTATGCACAATGATCGACA 59.720 33.333 0.00 0.00 0.00 4.35
454 466 7.177498 TCTTATTATGCACAATGATCGACAC 57.823 36.000 0.00 0.00 0.00 3.67
458 470 3.311486 TGCACAATGATCGACACTGTA 57.689 42.857 2.64 0.00 36.81 2.74
460 472 3.865164 TGCACAATGATCGACACTGTATC 59.135 43.478 2.64 0.47 36.81 2.24
462 474 4.259970 GCACAATGATCGACACTGTATCAC 60.260 45.833 2.64 0.00 36.81 3.06
463 475 4.864247 CACAATGATCGACACTGTATCACA 59.136 41.667 2.64 0.00 36.81 3.58
474 486 3.252974 CTGTATCACAGTGAGGGTTCC 57.747 52.381 9.64 0.00 41.19 3.62
475 487 1.906574 TGTATCACAGTGAGGGTTCCC 59.093 52.381 9.64 0.00 0.00 3.97
476 488 1.906574 GTATCACAGTGAGGGTTCCCA 59.093 52.381 9.64 0.00 0.00 4.37
480 492 2.162681 CACAGTGAGGGTTCCCATTTC 58.837 52.381 10.73 0.00 0.00 2.17
481 493 1.271379 ACAGTGAGGGTTCCCATTTCG 60.271 52.381 10.73 0.00 0.00 3.46
482 494 0.328258 AGTGAGGGTTCCCATTTCGG 59.672 55.000 10.73 0.00 0.00 4.30
483 495 0.326927 GTGAGGGTTCCCATTTCGGA 59.673 55.000 10.73 0.00 36.56 4.55
485 497 0.326927 GAGGGTTCCCATTTCGGACA 59.673 55.000 10.73 0.00 36.56 4.02
486 498 0.037734 AGGGTTCCCATTTCGGACAC 59.962 55.000 10.73 0.00 36.56 3.67
487 499 0.250989 GGGTTCCCATTTCGGACACA 60.251 55.000 2.59 0.00 36.56 3.72
491 503 3.366985 GGTTCCCATTTCGGACACAATTC 60.367 47.826 0.00 0.00 36.56 2.17
495 507 5.505780 TCCCATTTCGGACACAATTCTATT 58.494 37.500 0.00 0.00 36.56 1.73
496 508 6.654959 TCCCATTTCGGACACAATTCTATTA 58.345 36.000 0.00 0.00 36.56 0.98
497 509 6.765989 TCCCATTTCGGACACAATTCTATTAG 59.234 38.462 0.00 0.00 36.56 1.73
498 510 6.430451 CCATTTCGGACACAATTCTATTAGC 58.570 40.000 0.00 0.00 36.56 3.09
499 511 6.038161 CCATTTCGGACACAATTCTATTAGCA 59.962 38.462 0.00 0.00 36.56 3.49
502 514 5.670485 TCGGACACAATTCTATTAGCATGT 58.330 37.500 0.00 0.00 0.00 3.21
505 517 6.203530 CGGACACAATTCTATTAGCATGTGAT 59.796 38.462 20.45 10.95 40.32 3.06
506 518 7.358066 GGACACAATTCTATTAGCATGTGATG 58.642 38.462 20.45 2.45 40.32 3.07
508 520 7.700505 ACACAATTCTATTAGCATGTGATGTG 58.299 34.615 20.45 13.31 40.32 3.21
509 521 7.337689 ACACAATTCTATTAGCATGTGATGTGT 59.662 33.333 20.45 13.75 40.32 3.72
510 522 8.829612 CACAATTCTATTAGCATGTGATGTGTA 58.170 33.333 13.54 0.00 40.32 2.90
511 523 9.565090 ACAATTCTATTAGCATGTGATGTGTAT 57.435 29.630 0.00 0.00 0.00 2.29
512 524 9.821662 CAATTCTATTAGCATGTGATGTGTATG 57.178 33.333 0.00 0.00 0.00 2.39
513 525 9.565090 AATTCTATTAGCATGTGATGTGTATGT 57.435 29.630 0.00 0.00 0.00 2.29
516 528 8.306761 TCTATTAGCATGTGATGTGTATGTAGG 58.693 37.037 0.00 0.00 0.00 3.18
518 530 2.221749 GCATGTGATGTGTATGTAGGCG 59.778 50.000 0.00 0.00 0.00 5.52
519 531 3.716601 CATGTGATGTGTATGTAGGCGA 58.283 45.455 0.00 0.00 0.00 5.54
520 532 3.159353 TGTGATGTGTATGTAGGCGAC 57.841 47.619 0.00 0.00 0.00 5.19
521 533 2.494073 TGTGATGTGTATGTAGGCGACA 59.506 45.455 2.11 2.11 43.97 4.35
522 534 3.116300 GTGATGTGTATGTAGGCGACAG 58.884 50.000 6.59 0.00 42.79 3.51
523 535 2.100749 TGATGTGTATGTAGGCGACAGG 59.899 50.000 6.59 0.00 42.79 4.00
524 536 0.821517 TGTGTATGTAGGCGACAGGG 59.178 55.000 6.59 0.00 42.79 4.45
525 537 0.529992 GTGTATGTAGGCGACAGGGC 60.530 60.000 6.59 0.00 42.79 5.19
747 1029 2.434884 CGGCCACGATGTGCTTCT 60.435 61.111 2.24 0.00 44.60 2.85
748 1030 2.456119 CGGCCACGATGTGCTTCTC 61.456 63.158 2.24 0.00 44.60 2.87
751 1033 0.723981 GCCACGATGTGCTTCTCTTC 59.276 55.000 0.00 0.00 31.34 2.87
753 1035 1.338105 CCACGATGTGCTTCTCTTCCA 60.338 52.381 0.00 0.00 31.34 3.53
754 1036 1.728971 CACGATGTGCTTCTCTTCCAC 59.271 52.381 0.00 0.00 0.00 4.02
755 1037 0.994995 CGATGTGCTTCTCTTCCACG 59.005 55.000 0.00 0.00 32.32 4.94
756 1038 1.363744 GATGTGCTTCTCTTCCACGG 58.636 55.000 0.00 0.00 32.32 4.94
757 1039 0.976641 ATGTGCTTCTCTTCCACGGA 59.023 50.000 0.00 0.00 32.32 4.69
758 1040 0.318441 TGTGCTTCTCTTCCACGGAG 59.682 55.000 0.00 0.00 32.32 4.63
759 1041 0.603569 GTGCTTCTCTTCCACGGAGA 59.396 55.000 0.00 0.00 37.96 3.71
760 1042 1.000955 GTGCTTCTCTTCCACGGAGAA 59.999 52.381 6.10 6.10 44.42 2.87
761 1043 1.691976 TGCTTCTCTTCCACGGAGAAA 59.308 47.619 7.42 0.00 45.40 2.52
762 1044 2.104111 TGCTTCTCTTCCACGGAGAAAA 59.896 45.455 7.42 0.00 45.40 2.29
763 1045 3.244561 TGCTTCTCTTCCACGGAGAAAAT 60.245 43.478 7.42 0.00 45.40 1.82
767 1049 4.315803 TCTCTTCCACGGAGAAAATCAAC 58.684 43.478 0.00 0.00 36.96 3.18
770 1052 1.422024 TCCACGGAGAAAATCAACCCA 59.578 47.619 0.00 0.00 0.00 4.51
799 1081 2.754658 AGGCGTACGAGGAGTGGG 60.755 66.667 21.65 0.00 0.00 4.61
801 1083 2.753043 GCGTACGAGGAGTGGGGA 60.753 66.667 21.65 0.00 0.00 4.81
803 1085 1.378250 CGTACGAGGAGTGGGGAGT 60.378 63.158 10.44 0.00 0.00 3.85
805 1087 1.677942 GTACGAGGAGTGGGGAGTAG 58.322 60.000 0.00 0.00 0.00 2.57
806 1088 1.064832 GTACGAGGAGTGGGGAGTAGT 60.065 57.143 0.00 0.00 0.00 2.73
807 1089 0.323542 ACGAGGAGTGGGGAGTAGTG 60.324 60.000 0.00 0.00 0.00 2.74
809 1091 0.335361 GAGGAGTGGGGAGTAGTGGA 59.665 60.000 0.00 0.00 0.00 4.02
810 1092 0.336737 AGGAGTGGGGAGTAGTGGAG 59.663 60.000 0.00 0.00 0.00 3.86
812 1094 0.688087 GAGTGGGGAGTAGTGGAGGG 60.688 65.000 0.00 0.00 0.00 4.30
813 1095 1.153695 AGTGGGGAGTAGTGGAGGGA 61.154 60.000 0.00 0.00 0.00 4.20
814 1096 0.252558 GTGGGGAGTAGTGGAGGGAA 60.253 60.000 0.00 0.00 0.00 3.97
815 1097 0.042731 TGGGGAGTAGTGGAGGGAAG 59.957 60.000 0.00 0.00 0.00 3.46
817 1099 0.691413 GGGAGTAGTGGAGGGAAGGG 60.691 65.000 0.00 0.00 0.00 3.95
819 1101 1.689892 GGAGTAGTGGAGGGAAGGGAG 60.690 61.905 0.00 0.00 0.00 4.30
820 1102 0.325765 AGTAGTGGAGGGAAGGGAGC 60.326 60.000 0.00 0.00 0.00 4.70
821 1103 1.003051 TAGTGGAGGGAAGGGAGCC 59.997 63.158 0.00 0.00 0.00 4.70
822 1104 2.873557 TAGTGGAGGGAAGGGAGCCG 62.874 65.000 0.00 0.00 0.00 5.52
905 1187 2.488545 AGTGTACTGAGCTACTTGTCCG 59.511 50.000 0.00 0.00 0.00 4.79
917 1200 0.527817 CTTGTCCGCCGGAGATACAC 60.528 60.000 5.82 0.00 29.39 2.90
953 1236 3.458163 CTTCGTAGCTCGGGGGCA 61.458 66.667 0.00 0.00 40.32 5.36
1008 1305 2.026879 GCGAGAGAGATGCCGTCC 59.973 66.667 0.00 0.00 0.00 4.79
1009 1306 2.329690 CGAGAGAGATGCCGTCCG 59.670 66.667 0.00 0.00 0.00 4.79
1479 1776 3.263170 TCATGAAGGCCTACTACAAGCAA 59.737 43.478 5.16 0.00 0.00 3.91
1482 1779 3.206964 GAAGGCCTACTACAAGCAATCC 58.793 50.000 5.16 0.00 0.00 3.01
1542 1847 2.419297 GCAGGTCCGTTCATCAATCTCT 60.419 50.000 0.00 0.00 0.00 3.10
1543 1848 3.452474 CAGGTCCGTTCATCAATCTCTC 58.548 50.000 0.00 0.00 0.00 3.20
1546 1851 3.383185 GGTCCGTTCATCAATCTCTCTCT 59.617 47.826 0.00 0.00 0.00 3.10
1548 1853 5.040635 GTCCGTTCATCAATCTCTCTCTTC 58.959 45.833 0.00 0.00 0.00 2.87
1549 1854 4.952957 TCCGTTCATCAATCTCTCTCTTCT 59.047 41.667 0.00 0.00 0.00 2.85
1550 1855 5.042593 CCGTTCATCAATCTCTCTCTTCTG 58.957 45.833 0.00 0.00 0.00 3.02
1551 1856 4.503734 CGTTCATCAATCTCTCTCTTCTGC 59.496 45.833 0.00 0.00 0.00 4.26
1552 1857 5.663456 GTTCATCAATCTCTCTCTTCTGCT 58.337 41.667 0.00 0.00 0.00 4.24
1599 1910 5.566623 CCATTCACAGAATCGAATGTTCAG 58.433 41.667 10.31 0.00 44.55 3.02
1602 1913 6.471976 TTCACAGAATCGAATGTTCAGAAG 57.528 37.500 0.00 0.00 0.00 2.85
1604 1915 6.223120 TCACAGAATCGAATGTTCAGAAGAA 58.777 36.000 0.00 0.00 0.00 2.52
1605 1916 6.705825 TCACAGAATCGAATGTTCAGAAGAAA 59.294 34.615 0.00 0.00 35.08 2.52
1607 1918 7.857389 CACAGAATCGAATGTTCAGAAGAAAAA 59.143 33.333 0.00 0.00 35.08 1.94
1634 1955 2.617308 AGCTCGATTGATCATTTGGCTG 59.383 45.455 14.75 5.30 0.00 4.85
1773 2104 0.462581 GTCTGGCTGCCAATCGATGA 60.463 55.000 23.51 12.29 30.80 2.92
1783 2114 3.313249 TGCCAATCGATGATGTGATGTTC 59.687 43.478 0.00 0.00 0.00 3.18
1886 2217 2.413837 CCCTACGAATAATTGGCGGAG 58.586 52.381 0.00 0.00 35.80 4.63
1935 2266 3.055675 CCATGCCACTGGTGAATTTCATT 60.056 43.478 1.78 0.00 0.00 2.57
1936 2267 3.940209 TGCCACTGGTGAATTTCATTC 57.060 42.857 1.78 0.00 39.70 2.67
1937 2268 2.228582 TGCCACTGGTGAATTTCATTCG 59.771 45.455 1.78 0.00 42.15 3.34
1938 2269 2.228822 GCCACTGGTGAATTTCATTCGT 59.771 45.455 1.78 0.00 42.15 3.85
1981 2312 1.672356 AGGTTGCGGTCATCAGTGC 60.672 57.895 0.00 0.00 0.00 4.40
1982 2313 1.965930 GGTTGCGGTCATCAGTGCA 60.966 57.895 0.00 0.00 35.15 4.57
1983 2314 1.514678 GGTTGCGGTCATCAGTGCAA 61.515 55.000 0.00 0.00 44.34 4.08
1984 2315 2.945510 TTGCGGTCATCAGTGCAAT 58.054 47.368 0.00 0.00 41.95 3.56
1986 2317 2.330440 TGCGGTCATCAGTGCAATAT 57.670 45.000 0.00 0.00 33.80 1.28
1989 2354 3.559655 TGCGGTCATCAGTGCAATATTAC 59.440 43.478 0.00 0.00 33.80 1.89
1992 2357 5.119279 GCGGTCATCAGTGCAATATTACTAG 59.881 44.000 0.00 0.00 0.00 2.57
2017 2382 2.361789 TGGATGCACTGTCATGTCATG 58.638 47.619 6.47 6.47 0.00 3.07
2018 2383 1.674441 GGATGCACTGTCATGTCATGG 59.326 52.381 12.90 0.00 0.00 3.66
2033 2401 6.257849 TCATGTCATGGAGCGATTAGTTAAAC 59.742 38.462 12.90 0.00 0.00 2.01
2058 2426 7.389053 ACATAATCCAGAAGAAAAGTGACTGTC 59.611 37.037 0.00 0.00 0.00 3.51
2062 2430 5.586243 TCCAGAAGAAAAGTGACTGTCTTTG 59.414 40.000 9.51 11.14 35.65 2.77
2064 2432 6.127897 CCAGAAGAAAAGTGACTGTCTTTGTT 60.128 38.462 9.51 6.27 35.65 2.83
2065 2433 7.308435 CAGAAGAAAAGTGACTGTCTTTGTTT 58.692 34.615 9.51 4.52 35.65 2.83
2067 2435 8.023706 AGAAGAAAAGTGACTGTCTTTGTTTTC 58.976 33.333 18.81 18.81 35.65 2.29
2068 2436 6.621613 AGAAAAGTGACTGTCTTTGTTTTCC 58.378 36.000 20.74 11.59 35.65 3.13
2069 2437 6.434340 AGAAAAGTGACTGTCTTTGTTTTCCT 59.566 34.615 20.74 12.76 35.65 3.36
2070 2438 5.567138 AAGTGACTGTCTTTGTTTTCCTG 57.433 39.130 9.51 0.00 0.00 3.86
2071 2439 4.589908 AGTGACTGTCTTTGTTTTCCTGT 58.410 39.130 9.51 0.00 0.00 4.00
2072 2440 5.010282 AGTGACTGTCTTTGTTTTCCTGTT 58.990 37.500 9.51 0.00 0.00 3.16
2073 2441 5.476945 AGTGACTGTCTTTGTTTTCCTGTTT 59.523 36.000 9.51 0.00 0.00 2.83
2074 2442 5.572896 GTGACTGTCTTTGTTTTCCTGTTTG 59.427 40.000 9.51 0.00 0.00 2.93
2075 2443 4.494484 ACTGTCTTTGTTTTCCTGTTTGC 58.506 39.130 0.00 0.00 0.00 3.68
2076 2444 4.021544 ACTGTCTTTGTTTTCCTGTTTGCA 60.022 37.500 0.00 0.00 0.00 4.08
2077 2445 5.083533 TGTCTTTGTTTTCCTGTTTGCAT 57.916 34.783 0.00 0.00 0.00 3.96
2078 2446 4.869297 TGTCTTTGTTTTCCTGTTTGCATG 59.131 37.500 0.00 0.00 0.00 4.06
2085 2453 0.604073 TCCTGTTTGCATGCATGTGG 59.396 50.000 26.79 19.88 0.00 4.17
2086 2454 1.017177 CCTGTTTGCATGCATGTGGC 61.017 55.000 26.79 14.14 45.13 5.01
2153 2550 1.191096 GTGACTTGTGCAAAACTGCG 58.809 50.000 0.00 0.00 37.69 5.18
2260 2657 2.104170 CAGGTCTCCCTCTTCAGGTAC 58.896 57.143 0.00 0.00 39.89 3.34
2331 2729 5.913137 TTCTCAAGAAAACACACCATTGT 57.087 34.783 0.00 0.00 35.84 2.71
2332 2730 6.098679 TTTCTCAAGAAAACACACCATTGTG 58.901 36.000 2.74 3.22 46.50 3.33
2333 2731 7.338475 TTTCTCAAGAAAACACACCATTGTGC 61.338 38.462 4.68 0.00 45.86 4.57
2347 2745 4.835615 ACCATTGTGCTAATTTGGGTTACA 59.164 37.500 0.00 0.00 0.00 2.41
2348 2746 5.305644 ACCATTGTGCTAATTTGGGTTACAA 59.694 36.000 0.00 0.00 37.28 2.41
2349 2747 5.637387 CCATTGTGCTAATTTGGGTTACAAC 59.363 40.000 0.00 0.00 39.19 3.32
2351 2749 6.472686 TTGTGCTAATTTGGGTTACAACTT 57.527 33.333 0.00 0.00 39.19 2.66
2352 2750 6.472686 TGTGCTAATTTGGGTTACAACTTT 57.527 33.333 0.00 0.00 39.19 2.66
2353 2751 6.276847 TGTGCTAATTTGGGTTACAACTTTG 58.723 36.000 0.00 0.00 39.19 2.77
2354 2752 5.694458 GTGCTAATTTGGGTTACAACTTTGG 59.306 40.000 0.00 0.00 39.19 3.28
2355 2753 5.598830 TGCTAATTTGGGTTACAACTTTGGA 59.401 36.000 0.00 0.00 39.19 3.53
2356 2754 5.924254 GCTAATTTGGGTTACAACTTTGGAC 59.076 40.000 0.00 0.00 39.19 4.02
2357 2755 4.948341 ATTTGGGTTACAACTTTGGACC 57.052 40.909 7.79 7.79 39.19 4.46
2369 2771 2.705312 TTTGGACCGAATGCAGGGCA 62.705 55.000 0.00 0.00 44.86 5.36
3019 3421 2.437180 CGCCAGGCTCATGCAGAA 60.437 61.111 10.54 0.00 41.91 3.02
3140 3542 0.032813 CATGGTGGGGGATGCTCTTT 60.033 55.000 0.00 0.00 0.00 2.52
3215 3617 1.647545 CCAACCAGGTATGCGCACAG 61.648 60.000 14.90 0.07 0.00 3.66
3218 3620 0.179073 ACCAGGTATGCGCACAGATC 60.179 55.000 14.90 0.53 0.00 2.75
3219 3621 0.179076 CCAGGTATGCGCACAGATCA 60.179 55.000 14.90 0.00 0.00 2.92
3220 3622 1.541889 CCAGGTATGCGCACAGATCAT 60.542 52.381 14.90 0.00 0.00 2.45
3223 3625 2.158914 AGGTATGCGCACAGATCATCAA 60.159 45.455 14.90 0.00 0.00 2.57
3225 3627 1.019673 ATGCGCACAGATCATCAACC 58.980 50.000 14.90 0.00 0.00 3.77
3226 3628 1.349627 GCGCACAGATCATCAACCG 59.650 57.895 0.30 0.00 0.00 4.44
3227 3629 1.083806 GCGCACAGATCATCAACCGA 61.084 55.000 0.30 0.00 0.00 4.69
3228 3630 1.575244 CGCACAGATCATCAACCGAT 58.425 50.000 0.00 0.00 0.00 4.18
3230 3632 2.033407 CGCACAGATCATCAACCGATTC 60.033 50.000 0.00 0.00 0.00 2.52
3231 3633 2.938451 GCACAGATCATCAACCGATTCA 59.062 45.455 0.00 0.00 0.00 2.57
3233 3635 4.319333 GCACAGATCATCAACCGATTCATC 60.319 45.833 0.00 0.00 0.00 2.92
3234 3636 4.812626 CACAGATCATCAACCGATTCATCA 59.187 41.667 0.00 0.00 0.00 3.07
3235 3637 5.295045 CACAGATCATCAACCGATTCATCAA 59.705 40.000 0.00 0.00 0.00 2.57
3236 3638 5.295292 ACAGATCATCAACCGATTCATCAAC 59.705 40.000 0.00 0.00 0.00 3.18
3238 3640 2.935849 TCATCAACCGATTCATCAACCG 59.064 45.455 0.00 0.00 0.00 4.44
3239 3641 2.753055 TCAACCGATTCATCAACCGA 57.247 45.000 0.00 0.00 0.00 4.69
3240 3642 3.260475 TCAACCGATTCATCAACCGAT 57.740 42.857 0.00 0.00 0.00 4.18
3241 3643 3.605634 TCAACCGATTCATCAACCGATT 58.394 40.909 0.00 0.00 0.00 3.34
3242 3644 3.621268 TCAACCGATTCATCAACCGATTC 59.379 43.478 0.00 0.00 0.00 2.52
3243 3645 3.260475 ACCGATTCATCAACCGATTCA 57.740 42.857 0.00 0.00 0.00 2.57
3244 3646 3.605634 ACCGATTCATCAACCGATTCAA 58.394 40.909 0.00 0.00 0.00 2.69
3245 3647 3.623060 ACCGATTCATCAACCGATTCAAG 59.377 43.478 0.00 0.00 0.00 3.02
3246 3648 3.871006 CCGATTCATCAACCGATTCAAGA 59.129 43.478 0.00 0.00 0.00 3.02
3392 3794 2.905996 AAGCCCATCGCCAACCTGA 61.906 57.895 0.00 0.00 38.78 3.86
3546 3950 0.401356 TCTCAGCCTCCACAATGCAA 59.599 50.000 0.00 0.00 0.00 4.08
3547 3951 0.809385 CTCAGCCTCCACAATGCAAG 59.191 55.000 0.00 0.00 0.00 4.01
3563 3967 1.638133 CAAGAGGTGCTCATCACTCG 58.362 55.000 3.05 0.00 44.98 4.18
3564 3968 0.108424 AAGAGGTGCTCATCACTCGC 60.108 55.000 3.05 0.00 44.98 5.03
3565 3969 0.969917 AGAGGTGCTCATCACTCGCT 60.970 55.000 3.05 0.00 44.98 4.93
3566 3970 0.805322 GAGGTGCTCATCACTCGCTG 60.805 60.000 0.00 0.00 44.98 5.18
3567 3971 1.216444 GGTGCTCATCACTCGCTGA 59.784 57.895 0.00 0.00 44.98 4.26
3568 3972 0.390340 GGTGCTCATCACTCGCTGAA 60.390 55.000 0.00 0.00 44.98 3.02
3569 3973 0.997932 GTGCTCATCACTCGCTGAAG 59.002 55.000 0.00 0.00 42.38 3.02
3831 4235 1.822186 GGTGTGGCTGTTCGTGGTT 60.822 57.895 0.00 0.00 0.00 3.67
4344 4752 0.254462 TCAATTACCCGATGCAGCCA 59.746 50.000 0.00 0.00 0.00 4.75
4345 4753 0.381801 CAATTACCCGATGCAGCCAC 59.618 55.000 0.00 0.00 0.00 5.01
4346 4754 0.751643 AATTACCCGATGCAGCCACC 60.752 55.000 0.00 0.00 0.00 4.61
4347 4755 2.624674 ATTACCCGATGCAGCCACCC 62.625 60.000 0.00 0.00 0.00 4.61
4369 4777 1.548719 CCCGTCCTGAGTCACATTGTA 59.451 52.381 0.00 0.00 0.00 2.41
4374 4782 4.690748 CGTCCTGAGTCACATTGTAAACAT 59.309 41.667 0.00 0.00 0.00 2.71
4538 4946 4.152938 GCAAGCAAATCAATCCCAAAGAAC 59.847 41.667 0.00 0.00 0.00 3.01
4619 5027 4.511454 TCACACAACTGCACTATTCTCAAC 59.489 41.667 0.00 0.00 0.00 3.18
4673 5081 4.394712 GGGAGGCACCTGTGGTCG 62.395 72.222 0.00 0.00 38.98 4.79
4704 5112 3.845259 GGCACGCCGGAGTGGATA 61.845 66.667 34.76 0.00 42.09 2.59
4746 5154 2.820479 CTCGTCTCCTCTCGCGGT 60.820 66.667 6.13 0.00 0.00 5.68
4843 5251 0.984230 TGTCCATCCCTGTCAGAACC 59.016 55.000 0.00 0.00 0.00 3.62
4891 5299 1.451927 CTGCCTGGCCGCTTTCATA 60.452 57.895 17.53 0.00 0.00 2.15
5083 5491 2.174319 GCCGATCTTCAGGGCGAAC 61.174 63.158 0.00 0.00 37.06 3.95
5161 5569 0.249784 CCACCTGGATCAGATCGCAG 60.250 60.000 16.46 16.46 37.39 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.319198 GGAACAGGGCCGTCTCCA 61.319 66.667 15.36 0.00 0.00 3.86
1 2 3.003763 AGGAACAGGGCCGTCTCC 61.004 66.667 13.19 13.19 0.00 3.71
2 3 2.579738 GAGGAACAGGGCCGTCTC 59.420 66.667 0.00 0.00 0.00 3.36
3 4 3.003763 GGAGGAACAGGGCCGTCT 61.004 66.667 0.00 0.00 0.00 4.18
4 5 3.319198 TGGAGGAACAGGGCCGTC 61.319 66.667 0.00 0.00 0.00 4.79
5 6 3.637273 GTGGAGGAACAGGGCCGT 61.637 66.667 0.00 0.00 0.00 5.68
6 7 4.410400 GGTGGAGGAACAGGGCCG 62.410 72.222 0.00 0.00 0.00 6.13
7 8 4.048470 GGGTGGAGGAACAGGGCC 62.048 72.222 0.00 0.00 0.00 5.80
8 9 2.936032 AGGGTGGAGGAACAGGGC 60.936 66.667 0.00 0.00 0.00 5.19
9 10 2.301738 GGAGGGTGGAGGAACAGGG 61.302 68.421 0.00 0.00 0.00 4.45
10 11 1.538876 TGGAGGGTGGAGGAACAGG 60.539 63.158 0.00 0.00 0.00 4.00
11 12 0.838122 AGTGGAGGGTGGAGGAACAG 60.838 60.000 0.00 0.00 0.00 3.16
12 13 0.836400 GAGTGGAGGGTGGAGGAACA 60.836 60.000 0.00 0.00 0.00 3.18
13 14 1.889530 CGAGTGGAGGGTGGAGGAAC 61.890 65.000 0.00 0.00 0.00 3.62
19 20 4.394712 GGCACGAGTGGAGGGTGG 62.395 72.222 5.32 0.00 32.42 4.61
58 59 1.596603 TTGTACTCGATATCGGCGGA 58.403 50.000 24.12 10.37 40.29 5.54
63 64 7.360101 GGGATTTGGATTTTGTACTCGATATCG 60.360 40.741 19.14 19.14 41.45 2.92
86 87 0.764890 CACAGGACTGTTCAAGGGGA 59.235 55.000 1.49 0.00 42.83 4.81
89 90 2.038952 TCATCCACAGGACTGTTCAAGG 59.961 50.000 1.49 1.38 42.83 3.61
126 127 5.941058 TCACGCCTCAAACCAAATATCTAAA 59.059 36.000 0.00 0.00 0.00 1.85
154 157 1.210967 CAAAGGATGCATGCCCCATTT 59.789 47.619 23.05 17.35 0.00 2.32
155 158 0.834612 CAAAGGATGCATGCCCCATT 59.165 50.000 23.05 16.62 0.00 3.16
156 159 2.523440 CAAAGGATGCATGCCCCAT 58.477 52.632 23.05 12.25 0.00 4.00
226 229 0.608035 TTTCACATGCCCCGACCTTC 60.608 55.000 0.00 0.00 0.00 3.46
268 275 1.216444 GCTAAAGCTTTGGCCTGCC 59.784 57.895 30.97 8.57 38.53 4.85
273 280 1.677633 TCCCGGCTAAAGCTTTGGC 60.678 57.895 32.57 32.57 43.00 4.52
274 281 1.644786 CGTCCCGGCTAAAGCTTTGG 61.645 60.000 22.02 19.70 41.70 3.28
275 282 1.794222 CGTCCCGGCTAAAGCTTTG 59.206 57.895 22.02 12.32 41.70 2.77
279 286 1.583495 AAAAGCGTCCCGGCTAAAGC 61.583 55.000 0.00 0.00 43.93 3.51
303 310 1.002624 TTGGACGGGAATCAGGTGC 60.003 57.895 0.00 0.00 0.00 5.01
317 324 0.109723 CGAAACCTTGGGACCTTGGA 59.890 55.000 7.09 0.00 0.00 3.53
318 325 0.179001 ACGAAACCTTGGGACCTTGG 60.179 55.000 0.00 0.00 0.00 3.61
322 329 0.395312 TGAGACGAAACCTTGGGACC 59.605 55.000 0.00 0.00 0.00 4.46
324 331 1.766496 ACTTGAGACGAAACCTTGGGA 59.234 47.619 0.00 0.00 0.00 4.37
326 333 2.943033 ACAACTTGAGACGAAACCTTGG 59.057 45.455 0.00 0.00 0.00 3.61
327 334 4.094294 TGAACAACTTGAGACGAAACCTTG 59.906 41.667 0.00 0.00 0.00 3.61
341 348 1.489230 AGTTCCCTCGGTGAACAACTT 59.511 47.619 15.11 0.00 43.57 2.66
343 350 1.202604 TCAGTTCCCTCGGTGAACAAC 60.203 52.381 15.11 0.00 43.57 3.32
346 353 1.002087 ACATCAGTTCCCTCGGTGAAC 59.998 52.381 8.40 8.40 41.89 3.18
349 356 1.726853 GAACATCAGTTCCCTCGGTG 58.273 55.000 0.00 0.00 46.68 4.94
381 393 5.113383 AGCATTGTGGTTCATGCATTTATG 58.887 37.500 0.00 0.00 42.06 1.90
384 396 3.688694 AGCATTGTGGTTCATGCATTT 57.311 38.095 0.00 0.00 42.06 2.32
388 400 7.775397 AAATAATTAGCATTGTGGTTCATGC 57.225 32.000 0.00 0.00 40.09 4.06
416 428 9.410556 GTGCATAATAAGAACAGAATTTTGTGT 57.589 29.630 1.85 0.00 36.08 3.72
425 437 7.710475 TCGATCATTGTGCATAATAAGAACAGA 59.290 33.333 8.49 0.84 0.00 3.41
426 438 7.795734 GTCGATCATTGTGCATAATAAGAACAG 59.204 37.037 8.49 0.00 0.00 3.16
427 439 7.279758 TGTCGATCATTGTGCATAATAAGAACA 59.720 33.333 8.49 7.27 0.00 3.18
428 440 7.584123 GTGTCGATCATTGTGCATAATAAGAAC 59.416 37.037 8.49 5.01 0.00 3.01
429 441 7.495606 AGTGTCGATCATTGTGCATAATAAGAA 59.504 33.333 8.49 0.00 0.00 2.52
430 442 6.986231 AGTGTCGATCATTGTGCATAATAAGA 59.014 34.615 8.49 3.67 0.00 2.10
431 443 7.067728 CAGTGTCGATCATTGTGCATAATAAG 58.932 38.462 8.49 0.00 0.00 1.73
432 444 6.538381 ACAGTGTCGATCATTGTGCATAATAA 59.462 34.615 8.49 0.00 43.57 1.40
434 446 4.877823 ACAGTGTCGATCATTGTGCATAAT 59.122 37.500 2.38 2.38 43.57 1.28
436 448 3.860641 ACAGTGTCGATCATTGTGCATA 58.139 40.909 12.74 0.00 43.57 3.14
438 450 2.168326 ACAGTGTCGATCATTGTGCA 57.832 45.000 12.74 0.00 43.57 4.57
439 451 3.865164 TGATACAGTGTCGATCATTGTGC 59.135 43.478 19.02 13.73 44.58 4.57
440 452 4.864247 TGTGATACAGTGTCGATCATTGTG 59.136 41.667 19.02 8.71 44.58 3.33
441 453 5.072040 TGTGATACAGTGTCGATCATTGT 57.928 39.130 11.05 16.05 46.16 2.71
442 454 5.632445 CTGTGATACAGTGTCGATCATTG 57.368 43.478 11.05 8.28 41.19 2.82
470 482 3.506067 AGAATTGTGTCCGAAATGGGAAC 59.494 43.478 0.00 0.00 37.96 3.62
473 485 5.835113 AATAGAATTGTGTCCGAAATGGG 57.165 39.130 0.00 0.00 38.76 4.00
474 486 6.038161 TGCTAATAGAATTGTGTCCGAAATGG 59.962 38.462 0.00 0.00 40.09 3.16
475 487 7.015226 TGCTAATAGAATTGTGTCCGAAATG 57.985 36.000 0.00 0.00 0.00 2.32
476 488 7.283127 ACATGCTAATAGAATTGTGTCCGAAAT 59.717 33.333 0.00 0.00 0.00 2.17
480 492 5.523552 TCACATGCTAATAGAATTGTGTCCG 59.476 40.000 13.45 0.00 0.00 4.79
481 493 6.925610 TCACATGCTAATAGAATTGTGTCC 57.074 37.500 13.45 0.00 0.00 4.02
482 494 7.854422 CACATCACATGCTAATAGAATTGTGTC 59.146 37.037 13.45 0.00 0.00 3.67
483 495 7.337689 ACACATCACATGCTAATAGAATTGTGT 59.662 33.333 9.53 9.53 38.27 3.72
485 497 7.870509 ACACATCACATGCTAATAGAATTGT 57.129 32.000 0.00 0.00 0.00 2.71
486 498 9.821662 CATACACATCACATGCTAATAGAATTG 57.178 33.333 0.00 0.00 0.00 2.32
487 499 9.565090 ACATACACATCACATGCTAATAGAATT 57.435 29.630 0.00 0.00 0.00 2.17
491 503 7.063898 GCCTACATACACATCACATGCTAATAG 59.936 40.741 0.00 0.00 0.00 1.73
495 507 4.631131 GCCTACATACACATCACATGCTA 58.369 43.478 0.00 0.00 0.00 3.49
496 508 3.470709 GCCTACATACACATCACATGCT 58.529 45.455 0.00 0.00 0.00 3.79
497 509 2.221749 CGCCTACATACACATCACATGC 59.778 50.000 0.00 0.00 0.00 4.06
498 510 3.490896 GTCGCCTACATACACATCACATG 59.509 47.826 0.00 0.00 0.00 3.21
499 511 3.132111 TGTCGCCTACATACACATCACAT 59.868 43.478 0.00 0.00 31.43 3.21
502 514 2.100749 CCTGTCGCCTACATACACATCA 59.899 50.000 0.00 0.00 37.50 3.07
505 517 0.821517 CCCTGTCGCCTACATACACA 59.178 55.000 0.00 0.00 37.50 3.72
506 518 0.529992 GCCCTGTCGCCTACATACAC 60.530 60.000 0.00 0.00 37.50 2.90
508 520 1.069258 GGCCCTGTCGCCTACATAC 59.931 63.158 0.00 0.00 46.10 2.39
509 521 3.546009 GGCCCTGTCGCCTACATA 58.454 61.111 0.00 0.00 46.10 2.29
524 536 0.251608 TTTTTAGTCCTGGCCCTGGC 60.252 55.000 0.00 0.00 41.06 4.85
525 537 1.839424 CTTTTTAGTCCTGGCCCTGG 58.161 55.000 0.00 2.20 0.00 4.45
747 1029 3.408634 GGTTGATTTTCTCCGTGGAAGA 58.591 45.455 0.00 0.00 0.00 2.87
748 1030 2.488153 GGGTTGATTTTCTCCGTGGAAG 59.512 50.000 0.00 0.00 0.00 3.46
751 1033 1.904287 TGGGTTGATTTTCTCCGTGG 58.096 50.000 0.00 0.00 0.00 4.94
753 1035 2.890945 CCTTTGGGTTGATTTTCTCCGT 59.109 45.455 0.00 0.00 0.00 4.69
754 1036 2.352715 GCCTTTGGGTTGATTTTCTCCG 60.353 50.000 0.00 0.00 34.45 4.63
755 1037 2.352715 CGCCTTTGGGTTGATTTTCTCC 60.353 50.000 0.00 0.00 34.45 3.71
756 1038 2.352715 CCGCCTTTGGGTTGATTTTCTC 60.353 50.000 0.00 0.00 34.45 2.87
757 1039 1.618343 CCGCCTTTGGGTTGATTTTCT 59.382 47.619 0.00 0.00 34.45 2.52
758 1040 1.939381 GCCGCCTTTGGGTTGATTTTC 60.939 52.381 0.00 0.00 34.45 2.29
759 1041 0.034756 GCCGCCTTTGGGTTGATTTT 59.965 50.000 0.00 0.00 34.45 1.82
760 1042 1.671166 GCCGCCTTTGGGTTGATTT 59.329 52.632 0.00 0.00 34.45 2.17
761 1043 2.635443 CGCCGCCTTTGGGTTGATT 61.635 57.895 0.00 0.00 34.45 2.57
762 1044 3.061848 CGCCGCCTTTGGGTTGAT 61.062 61.111 0.00 0.00 34.45 2.57
785 1067 0.107508 TACTCCCCACTCCTCGTACG 60.108 60.000 9.53 9.53 0.00 3.67
799 1081 0.338814 TCCCTTCCCTCCACTACTCC 59.661 60.000 0.00 0.00 0.00 3.85
801 1083 0.325765 GCTCCCTTCCCTCCACTACT 60.326 60.000 0.00 0.00 0.00 2.57
803 1085 1.003051 GGCTCCCTTCCCTCCACTA 59.997 63.158 0.00 0.00 0.00 2.74
805 1087 3.787001 CGGCTCCCTTCCCTCCAC 61.787 72.222 0.00 0.00 0.00 4.02
810 1092 4.840005 CTTCGCGGCTCCCTTCCC 62.840 72.222 6.13 0.00 0.00 3.97
812 1094 2.815647 CACTTCGCGGCTCCCTTC 60.816 66.667 6.13 0.00 0.00 3.46
813 1095 4.394712 CCACTTCGCGGCTCCCTT 62.395 66.667 6.13 0.00 0.00 3.95
815 1097 2.306255 TATTCCACTTCGCGGCTCCC 62.306 60.000 6.13 0.00 0.00 4.30
817 1099 2.433868 TATATTCCACTTCGCGGCTC 57.566 50.000 6.13 0.00 0.00 4.70
819 1101 4.219033 CAATTTATATTCCACTTCGCGGC 58.781 43.478 6.13 0.00 0.00 6.53
820 1102 4.320202 CCCAATTTATATTCCACTTCGCGG 60.320 45.833 6.13 0.00 0.00 6.46
821 1103 4.513692 TCCCAATTTATATTCCACTTCGCG 59.486 41.667 0.00 0.00 0.00 5.87
822 1104 5.560183 CGTCCCAATTTATATTCCACTTCGC 60.560 44.000 0.00 0.00 0.00 4.70
823 1105 5.756347 TCGTCCCAATTTATATTCCACTTCG 59.244 40.000 0.00 0.00 0.00 3.79
824 1106 6.017357 GGTCGTCCCAATTTATATTCCACTTC 60.017 42.308 0.00 0.00 0.00 3.01
825 1107 5.826208 GGTCGTCCCAATTTATATTCCACTT 59.174 40.000 0.00 0.00 0.00 3.16
826 1108 5.104277 TGGTCGTCCCAATTTATATTCCACT 60.104 40.000 0.00 0.00 41.50 4.00
859 1141 2.139118 GAGATTCTTGGATGGTAGCGC 58.861 52.381 0.00 0.00 0.00 5.92
905 1187 1.068250 GCTCCTGTGTATCTCCGGC 59.932 63.158 0.00 0.00 0.00 6.13
917 1200 4.495349 CGAAGCTACAATGATTTGCTCCTG 60.495 45.833 0.00 0.00 36.22 3.86
992 1289 2.329690 CGGACGGCATCTCTCTCG 59.670 66.667 0.00 0.00 0.00 4.04
1434 1731 1.069090 GATGGCGCCGATGGAGTAA 59.931 57.895 23.90 0.00 0.00 2.24
1479 1776 1.684386 CGCAGAGGAAGCTGAGGGAT 61.684 60.000 0.00 0.00 38.14 3.85
1482 1779 2.511145 GCGCAGAGGAAGCTGAGG 60.511 66.667 0.30 0.00 38.14 3.86
1542 1847 4.080863 GGTCCAGGAAATTAGCAGAAGAGA 60.081 45.833 0.00 0.00 0.00 3.10
1543 1848 4.195416 GGTCCAGGAAATTAGCAGAAGAG 58.805 47.826 0.00 0.00 0.00 2.85
1546 1851 4.272489 CATGGTCCAGGAAATTAGCAGAA 58.728 43.478 0.00 0.00 0.00 3.02
1548 1853 2.954318 CCATGGTCCAGGAAATTAGCAG 59.046 50.000 4.74 0.00 0.00 4.24
1549 1854 2.311542 ACCATGGTCCAGGAAATTAGCA 59.688 45.455 13.00 0.00 0.00 3.49
1550 1855 3.018423 ACCATGGTCCAGGAAATTAGC 57.982 47.619 13.00 0.00 0.00 3.09
1551 1856 4.580580 GCTAACCATGGTCCAGGAAATTAG 59.419 45.833 20.07 13.43 0.00 1.73
1552 1857 4.532834 GCTAACCATGGTCCAGGAAATTA 58.467 43.478 20.07 2.21 0.00 1.40
1605 1916 9.090692 CCAAATGATCAATCGAGCTTAAATTTT 57.909 29.630 0.00 0.00 0.00 1.82
1607 1918 6.698766 GCCAAATGATCAATCGAGCTTAAATT 59.301 34.615 0.00 0.00 0.00 1.82
1608 1919 6.040166 AGCCAAATGATCAATCGAGCTTAAAT 59.960 34.615 0.00 0.00 0.00 1.40
1615 1926 2.287427 GCCAGCCAAATGATCAATCGAG 60.287 50.000 0.00 0.00 0.00 4.04
1618 1929 3.746045 ATGCCAGCCAAATGATCAATC 57.254 42.857 0.00 0.00 0.00 2.67
1619 1930 3.005050 CGTATGCCAGCCAAATGATCAAT 59.995 43.478 0.00 0.00 0.00 2.57
1634 1955 2.618241 TCAATTCCTTGATGCGTATGCC 59.382 45.455 4.05 0.00 37.04 4.40
1773 2104 0.740868 CGCGGACCAGAACATCACAT 60.741 55.000 0.00 0.00 0.00 3.21
1783 2114 1.063764 GTAACTCTCTACGCGGACCAG 59.936 57.143 12.47 0.00 0.00 4.00
1886 2217 3.866496 GCATACGCAAGAATAACAGAGC 58.134 45.455 0.00 0.00 43.62 4.09
1935 2266 2.296831 TTCAAAGTTGACCACGACGA 57.703 45.000 0.00 0.00 36.83 4.20
1936 2267 3.602390 ATTTCAAAGTTGACCACGACG 57.398 42.857 0.00 0.00 36.83 5.12
1937 2268 4.970003 CAGAATTTCAAAGTTGACCACGAC 59.030 41.667 0.00 0.00 36.83 4.34
1938 2269 4.638421 ACAGAATTTCAAAGTTGACCACGA 59.362 37.500 0.00 0.00 36.83 4.35
1981 2312 8.880750 CAGTGCATCCATGATCTAGTAATATTG 58.119 37.037 0.00 0.00 0.00 1.90
1982 2313 8.600668 ACAGTGCATCCATGATCTAGTAATATT 58.399 33.333 0.00 0.00 0.00 1.28
1983 2314 8.143673 ACAGTGCATCCATGATCTAGTAATAT 57.856 34.615 0.00 0.00 0.00 1.28
1984 2315 7.233348 TGACAGTGCATCCATGATCTAGTAATA 59.767 37.037 0.00 0.00 0.00 0.98
1986 2317 5.363580 TGACAGTGCATCCATGATCTAGTAA 59.636 40.000 0.00 0.00 0.00 2.24
1989 2354 4.332428 TGACAGTGCATCCATGATCTAG 57.668 45.455 0.00 0.00 0.00 2.43
1992 2357 3.211865 ACATGACAGTGCATCCATGATC 58.788 45.455 19.94 0.00 38.83 2.92
2017 2382 7.656137 TCTGGATTATGTTTAACTAATCGCTCC 59.344 37.037 14.69 8.23 35.91 4.70
2018 2383 8.589335 TCTGGATTATGTTTAACTAATCGCTC 57.411 34.615 14.69 7.46 35.91 5.03
2033 2401 7.605691 AGACAGTCACTTTTCTTCTGGATTATG 59.394 37.037 2.66 0.00 0.00 1.90
2053 2421 4.021544 TGCAAACAGGAAAACAAAGACAGT 60.022 37.500 0.00 0.00 0.00 3.55
2058 2426 3.622163 TGCATGCAAACAGGAAAACAAAG 59.378 39.130 20.30 0.00 0.00 2.77
2062 2430 3.059461 CACATGCATGCAAACAGGAAAAC 60.059 43.478 26.68 0.00 0.00 2.43
2064 2432 2.548280 CCACATGCATGCAAACAGGAAA 60.548 45.455 26.68 0.00 0.00 3.13
2065 2433 1.001068 CCACATGCATGCAAACAGGAA 59.999 47.619 26.68 0.00 0.00 3.36
2067 2435 1.017177 GCCACATGCATGCAAACAGG 61.017 55.000 26.68 23.05 40.77 4.00
2068 2436 1.348538 CGCCACATGCATGCAAACAG 61.349 55.000 26.68 16.81 41.33 3.16
2069 2437 1.373121 CGCCACATGCATGCAAACA 60.373 52.632 26.68 0.00 41.33 2.83
2070 2438 0.945265 AACGCCACATGCATGCAAAC 60.945 50.000 26.68 12.42 41.33 2.93
2071 2439 0.249784 AAACGCCACATGCATGCAAA 60.250 45.000 26.68 1.26 41.33 3.68
2072 2440 0.249784 AAAACGCCACATGCATGCAA 60.250 45.000 26.68 8.49 41.33 4.08
2073 2441 0.249784 AAAAACGCCACATGCATGCA 60.250 45.000 26.53 25.04 41.33 3.96
2074 2442 2.531055 AAAAACGCCACATGCATGC 58.469 47.368 26.53 11.82 41.33 4.06
2096 2464 9.677567 CAGTGTTTGCTTTTGTACTGTTATATT 57.322 29.630 0.00 0.00 32.92 1.28
2097 2465 8.296713 CCAGTGTTTGCTTTTGTACTGTTATAT 58.703 33.333 0.00 0.00 35.09 0.86
2098 2466 7.499563 TCCAGTGTTTGCTTTTGTACTGTTATA 59.500 33.333 0.00 0.00 35.09 0.98
2099 2467 6.320164 TCCAGTGTTTGCTTTTGTACTGTTAT 59.680 34.615 0.00 0.00 35.09 1.89
2103 2471 4.335315 TCTCCAGTGTTTGCTTTTGTACTG 59.665 41.667 0.00 0.00 36.27 2.74
2153 2550 1.602311 CCATAGCCCAGAATCTGCAC 58.398 55.000 4.40 0.00 0.00 4.57
2263 2660 2.420628 TCCTGCGTTGCAAAGATTTG 57.579 45.000 16.93 0.84 38.41 2.32
2264 2661 2.622942 TCTTCCTGCGTTGCAAAGATTT 59.377 40.909 16.93 0.00 38.41 2.17
2308 2706 6.279513 ACAATGGTGTGTTTTCTTGAGAAA 57.720 33.333 2.16 2.16 38.20 2.52
2309 2707 5.913137 ACAATGGTGTGTTTTCTTGAGAA 57.087 34.783 0.00 0.00 36.31 2.87
2326 2724 6.454795 AGTTGTAACCCAAATTAGCACAATG 58.545 36.000 0.00 0.00 34.07 2.82
2327 2725 6.664428 AGTTGTAACCCAAATTAGCACAAT 57.336 33.333 0.00 0.00 34.07 2.71
2330 2728 5.694458 CCAAAGTTGTAACCCAAATTAGCAC 59.306 40.000 0.00 0.00 40.24 4.40
2331 2729 5.598830 TCCAAAGTTGTAACCCAAATTAGCA 59.401 36.000 0.00 0.00 40.24 3.49
2332 2730 5.924254 GTCCAAAGTTGTAACCCAAATTAGC 59.076 40.000 0.00 0.00 40.24 3.09
2333 2731 6.452242 GGTCCAAAGTTGTAACCCAAATTAG 58.548 40.000 2.79 0.00 40.24 1.73
2347 2745 1.247567 CCTGCATTCGGTCCAAAGTT 58.752 50.000 0.00 0.00 0.00 2.66
2348 2746 0.609131 CCCTGCATTCGGTCCAAAGT 60.609 55.000 0.00 0.00 0.00 2.66
2349 2747 1.937546 GCCCTGCATTCGGTCCAAAG 61.938 60.000 0.00 0.00 0.00 2.77
2351 2749 2.361104 GCCCTGCATTCGGTCCAA 60.361 61.111 0.00 0.00 0.00 3.53
2352 2750 3.645660 TGCCCTGCATTCGGTCCA 61.646 61.111 0.00 0.00 31.71 4.02
2353 2751 3.134127 GTGCCCTGCATTCGGTCC 61.134 66.667 0.00 0.00 41.91 4.46
2354 2752 2.045926 AGTGCCCTGCATTCGGTC 60.046 61.111 0.00 0.00 41.91 4.79
2355 2753 2.360350 CAGTGCCCTGCATTCGGT 60.360 61.111 0.00 0.00 41.91 4.69
2369 2771 1.581954 CTCCTTCGTCTCGTGCAGT 59.418 57.895 0.00 0.00 0.00 4.40
2483 2885 0.827368 AGAAGAAGGTCAGGATCGGC 59.173 55.000 0.00 0.00 0.00 5.54
2486 2888 2.159170 CCACGAGAAGAAGGTCAGGATC 60.159 54.545 0.00 0.00 0.00 3.36
3019 3421 2.358737 GCGGCACCTGCTTGTACT 60.359 61.111 0.00 0.00 41.70 2.73
3080 3482 0.952497 ACACGAAGCACATGAGCAGG 60.952 55.000 17.61 8.03 36.85 4.85
3210 3612 2.938451 TGAATCGGTTGATGATCTGTGC 59.062 45.455 0.00 0.00 34.24 4.57
3215 3617 4.319046 CGGTTGATGAATCGGTTGATGATC 60.319 45.833 0.00 0.00 34.24 2.92
3218 3620 2.935849 TCGGTTGATGAATCGGTTGATG 59.064 45.455 0.00 0.00 36.28 3.07
3219 3621 3.260475 TCGGTTGATGAATCGGTTGAT 57.740 42.857 0.00 0.00 36.28 2.57
3220 3622 2.753055 TCGGTTGATGAATCGGTTGA 57.247 45.000 0.00 0.00 36.28 3.18
3223 3625 3.260475 TGAATCGGTTGATGAATCGGT 57.740 42.857 0.00 0.00 36.28 4.69
3225 3627 5.234972 TGATCTTGAATCGGTTGATGAATCG 59.765 40.000 0.00 0.00 37.01 3.34
3226 3628 6.609237 TGATCTTGAATCGGTTGATGAATC 57.391 37.500 0.00 0.00 34.24 2.52
3227 3629 6.769341 TGATGATCTTGAATCGGTTGATGAAT 59.231 34.615 0.00 0.00 34.24 2.57
3228 3630 6.114767 TGATGATCTTGAATCGGTTGATGAA 58.885 36.000 0.00 0.00 34.24 2.57
3230 3632 5.526479 ACTGATGATCTTGAATCGGTTGATG 59.474 40.000 0.00 0.00 38.92 3.07
3231 3633 5.678583 ACTGATGATCTTGAATCGGTTGAT 58.321 37.500 0.00 0.00 38.92 2.57
3233 3635 6.908870 TTACTGATGATCTTGAATCGGTTG 57.091 37.500 9.74 0.00 41.53 3.77
3234 3636 6.017605 GCATTACTGATGATCTTGAATCGGTT 60.018 38.462 9.74 0.00 41.53 4.44
3235 3637 5.468072 GCATTACTGATGATCTTGAATCGGT 59.532 40.000 9.47 9.47 43.28 4.69
3236 3638 5.699915 AGCATTACTGATGATCTTGAATCGG 59.300 40.000 0.00 0.00 38.03 4.18
3238 3640 8.599055 TGTAGCATTACTGATGATCTTGAATC 57.401 34.615 0.00 0.00 38.03 2.52
3239 3641 8.969260 TTGTAGCATTACTGATGATCTTGAAT 57.031 30.769 0.00 0.00 38.03 2.57
3240 3642 8.969260 ATTGTAGCATTACTGATGATCTTGAA 57.031 30.769 0.00 0.00 38.03 2.69
3241 3643 8.969260 AATTGTAGCATTACTGATGATCTTGA 57.031 30.769 0.00 0.00 38.03 3.02
3245 3647 8.749499 GCAAAAATTGTAGCATTACTGATGATC 58.251 33.333 0.00 0.00 38.03 2.92
3246 3648 8.472413 AGCAAAAATTGTAGCATTACTGATGAT 58.528 29.630 0.00 0.00 38.03 2.45
3392 3794 1.341531 CCGGCCGTAGATCTTGAAGAT 59.658 52.381 26.12 7.53 37.73 2.40
3433 3835 3.066233 GAGGTCGGCGAGGAAGGAC 62.066 68.421 11.20 0.00 0.00 3.85
3509 3911 1.906757 GAGCGATCTCTGTCAGTGTG 58.093 55.000 0.00 0.00 36.42 3.82
3563 3967 1.079503 CGGTTAGTTCAGCCTTCAGC 58.920 55.000 0.00 0.00 44.25 4.26
3564 3968 2.338500 GTCGGTTAGTTCAGCCTTCAG 58.662 52.381 0.00 0.00 0.00 3.02
3565 3969 1.336517 CGTCGGTTAGTTCAGCCTTCA 60.337 52.381 0.00 0.00 0.00 3.02
3566 3970 1.336609 ACGTCGGTTAGTTCAGCCTTC 60.337 52.381 0.00 0.00 0.00 3.46
3567 3971 0.677842 ACGTCGGTTAGTTCAGCCTT 59.322 50.000 0.00 0.00 0.00 4.35
3568 3972 0.038526 CACGTCGGTTAGTTCAGCCT 60.039 55.000 0.00 0.00 0.00 4.58
3569 3973 1.623973 GCACGTCGGTTAGTTCAGCC 61.624 60.000 0.00 0.00 0.00 4.85
4074 4478 4.066139 AGCACCCCCATGAAGGCC 62.066 66.667 0.00 0.00 35.39 5.19
4347 4755 1.553690 AATGTGACTCAGGACGGGGG 61.554 60.000 0.00 0.00 0.00 5.40
4348 4756 0.391661 CAATGTGACTCAGGACGGGG 60.392 60.000 0.00 0.00 0.00 5.73
4374 4782 6.203723 CCTTGGAGAAAAACAAAACACACAAA 59.796 34.615 0.00 0.00 0.00 2.83
4443 4851 5.606749 AGGGTGTGATTTGCCTATGAGTATA 59.393 40.000 0.00 0.00 0.00 1.47
4444 4852 4.413520 AGGGTGTGATTTGCCTATGAGTAT 59.586 41.667 0.00 0.00 0.00 2.12
4445 4853 3.780294 AGGGTGTGATTTGCCTATGAGTA 59.220 43.478 0.00 0.00 0.00 2.59
4446 4854 2.578021 AGGGTGTGATTTGCCTATGAGT 59.422 45.455 0.00 0.00 0.00 3.41
4538 4946 6.017192 TCTGTCAAATTGTGTGTATTCCTGTG 60.017 38.462 0.00 0.00 0.00 3.66
4593 5001 3.438087 AGAATAGTGCAGTTGTGTGATGC 59.562 43.478 0.00 0.00 40.40 3.91
4594 5002 4.692155 TGAGAATAGTGCAGTTGTGTGATG 59.308 41.667 0.00 0.00 0.00 3.07
4595 5003 4.898320 TGAGAATAGTGCAGTTGTGTGAT 58.102 39.130 0.00 0.00 0.00 3.06
4596 5004 4.335400 TGAGAATAGTGCAGTTGTGTGA 57.665 40.909 0.00 0.00 0.00 3.58
4597 5005 4.512944 AGTTGAGAATAGTGCAGTTGTGTG 59.487 41.667 0.00 0.00 0.00 3.82
4598 5006 4.512944 CAGTTGAGAATAGTGCAGTTGTGT 59.487 41.667 0.00 0.00 0.00 3.72
4599 5007 4.512944 ACAGTTGAGAATAGTGCAGTTGTG 59.487 41.667 0.00 0.00 0.00 3.33
4600 5008 4.708177 ACAGTTGAGAATAGTGCAGTTGT 58.292 39.130 0.00 0.00 0.00 3.32
4601 5009 4.751600 TGACAGTTGAGAATAGTGCAGTTG 59.248 41.667 0.00 0.00 0.00 3.16
4602 5010 4.752101 GTGACAGTTGAGAATAGTGCAGTT 59.248 41.667 0.00 0.00 0.00 3.16
4603 5011 4.310769 GTGACAGTTGAGAATAGTGCAGT 58.689 43.478 0.00 0.00 0.00 4.40
4604 5012 3.681897 GGTGACAGTTGAGAATAGTGCAG 59.318 47.826 0.00 0.00 0.00 4.41
4605 5013 3.324846 AGGTGACAGTTGAGAATAGTGCA 59.675 43.478 0.00 0.00 0.00 4.57
4606 5014 3.931578 AGGTGACAGTTGAGAATAGTGC 58.068 45.455 0.00 0.00 0.00 4.40
4619 5027 3.305950 GCTGATAGCCTGATAGGTGACAG 60.306 52.174 0.00 0.00 37.80 3.51
4694 5102 1.067821 GCTCTGAACCTATCCACTCCG 59.932 57.143 0.00 0.00 0.00 4.63
4704 5112 3.317571 AGCTGCCGCTCTGAACCT 61.318 61.111 0.00 0.00 45.15 3.50
4843 5251 0.627986 ATTTCCTGAGAGGGCAAGGG 59.372 55.000 0.00 0.00 35.59 3.95
4891 5299 1.635817 CCAACGACATGGGGGAGGAT 61.636 60.000 0.00 0.00 36.79 3.24
4975 5383 4.075854 TCGGCCATGTACAGCGCA 62.076 61.111 11.47 0.00 0.00 6.09
4976 5384 3.264897 CTCGGCCATGTACAGCGC 61.265 66.667 2.24 0.00 0.00 5.92
4980 5388 0.613572 TGACTCCTCGGCCATGTACA 60.614 55.000 2.24 0.00 0.00 2.90
5032 5440 1.500736 GTTGGGATGGGGGAGATGATT 59.499 52.381 0.00 0.00 0.00 2.57
5083 5491 4.153117 AGCAAGTTCATGAAGCTCTTAACG 59.847 41.667 8.80 0.00 0.00 3.18
5161 5569 1.369321 GGTGGAGGATCAGATCGGC 59.631 63.158 4.23 0.00 36.25 5.54


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

AutoCloner maintained by Alex Coulton.