Multiple sequence alignment - TraesCS6B01G179700

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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 TraesCS6B01G179700 chr6B 100.000 3320 0 0 1 3320 199930282 199933601 0.000000e+00 6131.0
1 TraesCS6B01G179700 chr6B 83.021 1066 144 25 1258 2316 136101159 136100124 0.000000e+00 931.0
2 TraesCS6B01G179700 chr6B 82.519 1064 150 26 1258 2316 135996424 135995392 0.000000e+00 902.0
3 TraesCS6B01G179700 chr6D 93.711 2099 112 6 725 2823 111017771 111019849 0.000000e+00 3127.0
4 TraesCS6B01G179700 chr6D 83.068 1069 141 26 1258 2316 62425067 62424029 0.000000e+00 935.0
5 TraesCS6B01G179700 chr6D 82.755 1067 145 29 1258 2316 62325254 62324219 0.000000e+00 915.0
6 TraesCS6B01G179700 chr6D 91.260 492 28 4 1 492 111016423 111016899 0.000000e+00 656.0
7 TraesCS6B01G179700 chr6D 92.381 315 23 1 2818 3132 111022197 111022510 6.530000e-122 448.0
8 TraesCS6B01G179700 chr6D 84.211 133 9 6 532 661 111017647 111017770 5.820000e-23 119.0
9 TraesCS6B01G179700 chr6D 100.000 28 0 0 119 146 110986919 110986946 6.000000e-03 52.8
10 TraesCS6B01G179700 chr6A 88.871 1833 119 27 990 2761 135444912 135446720 0.000000e+00 2176.0
11 TraesCS6B01G179700 chr6A 82.386 1073 148 24 1258 2320 79703627 79702586 0.000000e+00 896.0
12 TraesCS6B01G179700 chr6A 82.056 1070 150 30 1258 2316 79814908 79813870 0.000000e+00 874.0
13 TraesCS6B01G179700 chr6A 86.129 310 23 9 433 738 135405937 135406230 1.920000e-82 316.0
14 TraesCS6B01G179700 chr7B 80.160 998 162 29 1328 2319 2329363 2328396 0.000000e+00 713.0
15 TraesCS6B01G179700 chr3D 85.897 156 20 2 238 392 610875783 610875937 7.370000e-37 165.0
16 TraesCS6B01G179700 chr2D 74.524 420 84 17 2592 2996 14646558 14646969 9.530000e-36 161.0
17 TraesCS6B01G179700 chr2D 73.282 393 89 13 2598 2977 14595059 14595448 2.690000e-26 130.0
18 TraesCS6B01G179700 chr2D 74.468 235 53 5 2592 2822 14441633 14441864 9.810000e-16 95.3
19 TraesCS6B01G179700 chr4A 84.076 157 21 4 235 389 690411287 690411441 7.420000e-32 148.0
20 TraesCS6B01G179700 chr4A 83.453 139 20 3 238 374 96018672 96018809 3.480000e-25 126.0
21 TraesCS6B01G179700 chr3A 83.221 149 23 2 244 391 568671527 568671380 5.780000e-28 135.0
22 TraesCS6B01G179700 chr7D 87.069 116 14 1 275 389 242791457 242791342 2.690000e-26 130.0
23 TraesCS6B01G179700 chr1A 83.824 136 18 3 255 389 546020595 546020463 3.480000e-25 126.0
24 TraesCS6B01G179700 chr5B 84.615 130 15 4 244 370 476927802 476927675 1.250000e-24 124.0
25 TraesCS6B01G179700 chr2B 77.251 211 47 1 2592 2801 26353166 26353376 4.500000e-24 122.0
26 TraesCS6B01G179700 chr4D 83.333 132 18 3 244 374 368870166 368870038 5.820000e-23 119.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G179700 chr6B 199930282 199933601 3319 False 6131.0 6131 100.00000 1 3320 1 chr6B.!!$F1 3319
1 TraesCS6B01G179700 chr6B 136100124 136101159 1035 True 931.0 931 83.02100 1258 2316 1 chr6B.!!$R2 1058
2 TraesCS6B01G179700 chr6B 135995392 135996424 1032 True 902.0 902 82.51900 1258 2316 1 chr6B.!!$R1 1058
3 TraesCS6B01G179700 chr6D 111016423 111022510 6087 False 1087.5 3127 90.39075 1 3132 4 chr6D.!!$F2 3131
4 TraesCS6B01G179700 chr6D 62424029 62425067 1038 True 935.0 935 83.06800 1258 2316 1 chr6D.!!$R2 1058
5 TraesCS6B01G179700 chr6D 62324219 62325254 1035 True 915.0 915 82.75500 1258 2316 1 chr6D.!!$R1 1058
6 TraesCS6B01G179700 chr6A 135444912 135446720 1808 False 2176.0 2176 88.87100 990 2761 1 chr6A.!!$F2 1771
7 TraesCS6B01G179700 chr6A 79702586 79703627 1041 True 896.0 896 82.38600 1258 2320 1 chr6A.!!$R1 1062
8 TraesCS6B01G179700 chr6A 79813870 79814908 1038 True 874.0 874 82.05600 1258 2316 1 chr6A.!!$R2 1058
9 TraesCS6B01G179700 chr7B 2328396 2329363 967 True 713.0 713 80.16000 1328 2319 1 chr7B.!!$R1 991

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
607 1316 0.034767 CCTGGTGATGTGGCATGACT 60.035 55.0 0.0 0.0 0.0 3.41 F
918 1628 0.179116 CCTCACACGAGCATGGAGAG 60.179 60.0 0.0 0.0 38.0 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1757 2485 0.321671 CCTGGTGTTGGACGACATCT 59.678 55.0 4.70 0.0 31.86 2.90 R
2755 3549 1.283736 GCGGTGTCGTTATTCCGATT 58.716 50.0 6.63 0.0 44.86 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
25 26 5.964958 TTCTTGAATTGACCACCTTCATC 57.035 39.130 0.00 0.00 0.00 2.92
70 71 7.048000 TCGCAATTATTTCATGTTCAAAAGC 57.952 32.000 0.00 0.00 0.00 3.51
81 82 4.589216 TGTTCAAAAGCATTCCTCCAAG 57.411 40.909 0.00 0.00 0.00 3.61
86 87 0.393537 AAGCATTCCTCCAAGCTCCG 60.394 55.000 0.00 0.00 36.07 4.63
91 92 1.892209 TTCCTCCAAGCTCCGAAAAC 58.108 50.000 0.00 0.00 0.00 2.43
110 111 7.478667 CCGAAAACTTCAGATTAAGTCGATTTG 59.521 37.037 3.04 0.00 38.76 2.32
111 112 8.221100 CGAAAACTTCAGATTAAGTCGATTTGA 58.779 33.333 3.04 0.00 38.76 2.69
172 173 9.906660 AAATTTCGCATATTTCTGTAGTTTTCA 57.093 25.926 0.00 0.00 0.00 2.69
190 191 5.705609 TTTCATTTTCTTCAGTAGCCACC 57.294 39.130 0.00 0.00 0.00 4.61
193 194 0.669318 TTTCTTCAGTAGCCACCGCG 60.669 55.000 0.00 0.00 41.18 6.46
194 195 1.812686 TTCTTCAGTAGCCACCGCGT 61.813 55.000 4.92 0.00 41.18 6.01
195 196 2.048597 TTCAGTAGCCACCGCGTG 60.049 61.111 4.92 3.32 41.18 5.34
196 197 2.486636 CTTCAGTAGCCACCGCGTGA 62.487 60.000 4.92 0.00 41.18 4.35
197 198 2.758770 TTCAGTAGCCACCGCGTGAC 62.759 60.000 4.92 0.00 41.18 3.67
198 199 4.415332 AGTAGCCACCGCGTGACG 62.415 66.667 4.92 0.00 41.18 4.35
250 251 3.243301 TGTGTGTTGTAGTCTCTCCGTTC 60.243 47.826 0.00 0.00 0.00 3.95
342 343 3.792401 TCATTTCGATCCGTATGCAGTT 58.208 40.909 0.00 0.00 0.00 3.16
485 486 7.334858 AGAAAAAGGGTTTGTGCTTTGAATAA 58.665 30.769 0.00 0.00 0.00 1.40
492 493 4.884458 TTGTGCTTTGAATAACACGTCA 57.116 36.364 0.00 0.00 35.79 4.35
493 494 4.203950 TGTGCTTTGAATAACACGTCAC 57.796 40.909 0.00 0.00 35.79 3.67
494 495 3.874543 TGTGCTTTGAATAACACGTCACT 59.125 39.130 0.00 0.00 35.79 3.41
495 496 4.025229 TGTGCTTTGAATAACACGTCACTC 60.025 41.667 0.00 0.00 35.79 3.51
496 497 4.211374 GTGCTTTGAATAACACGTCACTCT 59.789 41.667 0.00 0.00 0.00 3.24
497 498 4.447724 TGCTTTGAATAACACGTCACTCTC 59.552 41.667 0.00 0.00 0.00 3.20
498 499 4.143094 GCTTTGAATAACACGTCACTCTCC 60.143 45.833 0.00 0.00 0.00 3.71
499 500 4.594123 TTGAATAACACGTCACTCTCCA 57.406 40.909 0.00 0.00 0.00 3.86
500 501 4.594123 TGAATAACACGTCACTCTCCAA 57.406 40.909 0.00 0.00 0.00 3.53
501 502 4.951254 TGAATAACACGTCACTCTCCAAA 58.049 39.130 0.00 0.00 0.00 3.28
502 503 5.361427 TGAATAACACGTCACTCTCCAAAA 58.639 37.500 0.00 0.00 0.00 2.44
503 504 5.995282 TGAATAACACGTCACTCTCCAAAAT 59.005 36.000 0.00 0.00 0.00 1.82
504 505 5.862924 ATAACACGTCACTCTCCAAAATG 57.137 39.130 0.00 0.00 0.00 2.32
505 506 3.194005 ACACGTCACTCTCCAAAATGT 57.806 42.857 0.00 0.00 0.00 2.71
506 507 3.131396 ACACGTCACTCTCCAAAATGTC 58.869 45.455 0.00 0.00 0.00 3.06
507 508 3.130633 CACGTCACTCTCCAAAATGTCA 58.869 45.455 0.00 0.00 0.00 3.58
508 509 3.748048 CACGTCACTCTCCAAAATGTCAT 59.252 43.478 0.00 0.00 0.00 3.06
509 510 4.214119 CACGTCACTCTCCAAAATGTCATT 59.786 41.667 0.00 0.00 0.00 2.57
510 511 5.408299 CACGTCACTCTCCAAAATGTCATTA 59.592 40.000 0.00 0.00 0.00 1.90
511 512 5.995282 ACGTCACTCTCCAAAATGTCATTAA 59.005 36.000 0.00 0.00 0.00 1.40
512 513 6.073222 ACGTCACTCTCCAAAATGTCATTAAC 60.073 38.462 0.00 0.00 0.00 2.01
513 514 6.147821 CGTCACTCTCCAAAATGTCATTAACT 59.852 38.462 0.00 0.00 0.00 2.24
514 515 7.330946 CGTCACTCTCCAAAATGTCATTAACTA 59.669 37.037 0.00 0.00 0.00 2.24
515 516 8.660373 GTCACTCTCCAAAATGTCATTAACTAG 58.340 37.037 0.00 0.00 0.00 2.57
516 517 8.593679 TCACTCTCCAAAATGTCATTAACTAGA 58.406 33.333 0.00 0.42 0.00 2.43
517 518 8.877779 CACTCTCCAAAATGTCATTAACTAGAG 58.122 37.037 17.77 17.77 33.50 2.43
518 519 8.043710 ACTCTCCAAAATGTCATTAACTAGAGG 58.956 37.037 20.68 9.08 31.95 3.69
519 520 8.146053 TCTCCAAAATGTCATTAACTAGAGGA 57.854 34.615 0.00 0.00 0.00 3.71
520 521 8.602424 TCTCCAAAATGTCATTAACTAGAGGAA 58.398 33.333 0.00 0.00 0.00 3.36
521 522 8.792830 TCCAAAATGTCATTAACTAGAGGAAG 57.207 34.615 0.00 0.00 0.00 3.46
522 523 8.383175 TCCAAAATGTCATTAACTAGAGGAAGT 58.617 33.333 0.00 0.00 0.00 3.01
523 524 9.667107 CCAAAATGTCATTAACTAGAGGAAGTA 57.333 33.333 0.00 0.00 0.00 2.24
530 531 9.881529 GTCATTAACTAGAGGAAGTAGTATTCG 57.118 37.037 0.00 0.00 30.26 3.34
571 1280 7.113658 TGGGCAATAAGTTTGTACTTTTCAA 57.886 32.000 0.00 0.00 41.85 2.69
572 1281 7.556844 TGGGCAATAAGTTTGTACTTTTCAAA 58.443 30.769 0.00 0.00 41.85 2.69
573 1282 8.041323 TGGGCAATAAGTTTGTACTTTTCAAAA 58.959 29.630 0.00 0.00 41.85 2.44
574 1283 8.884726 GGGCAATAAGTTTGTACTTTTCAAAAA 58.115 29.630 0.00 0.00 41.85 1.94
605 1314 1.284313 TACCTGGTGATGTGGCATGA 58.716 50.000 10.23 0.00 0.00 3.07
606 1315 0.322816 ACCTGGTGATGTGGCATGAC 60.323 55.000 0.00 0.00 0.00 3.06
607 1316 0.034767 CCTGGTGATGTGGCATGACT 60.035 55.000 0.00 0.00 0.00 3.41
614 1324 1.470098 GATGTGGCATGACTGGAACAC 59.530 52.381 0.00 0.00 0.00 3.32
628 1338 1.533625 GAACACACATAGCCTGCCAA 58.466 50.000 0.00 0.00 0.00 4.52
649 1359 3.788145 CGGGCCCGGTCATGGTAA 61.788 66.667 37.42 0.00 35.56 2.85
650 1360 2.923837 GGGCCCGGTCATGGTAAT 59.076 61.111 5.69 0.00 0.00 1.89
651 1361 1.528309 GGGCCCGGTCATGGTAATG 60.528 63.158 5.69 0.00 34.88 1.90
653 1363 1.226262 GCCCGGTCATGGTAATGGT 59.774 57.895 0.00 0.00 34.30 3.55
656 1366 1.065053 CCCGGTCATGGTAATGGTCAA 60.065 52.381 0.00 0.00 34.30 3.18
657 1367 2.288666 CCGGTCATGGTAATGGTCAAG 58.711 52.381 0.00 0.00 34.30 3.02
658 1368 2.093181 CCGGTCATGGTAATGGTCAAGA 60.093 50.000 0.00 0.00 34.30 3.02
659 1369 2.936498 CGGTCATGGTAATGGTCAAGAC 59.064 50.000 0.00 0.00 34.30 3.01
660 1370 3.618752 CGGTCATGGTAATGGTCAAGACA 60.619 47.826 2.29 0.00 34.48 3.41
661 1371 4.331968 GGTCATGGTAATGGTCAAGACAA 58.668 43.478 2.29 0.00 34.48 3.18
662 1372 4.396166 GGTCATGGTAATGGTCAAGACAAG 59.604 45.833 2.29 0.00 34.48 3.16
663 1373 4.009675 TCATGGTAATGGTCAAGACAAGC 58.990 43.478 2.29 0.00 34.30 4.01
664 1374 3.500448 TGGTAATGGTCAAGACAAGCA 57.500 42.857 2.29 0.00 0.00 3.91
665 1375 3.826524 TGGTAATGGTCAAGACAAGCAA 58.173 40.909 2.29 0.00 0.00 3.91
666 1376 3.820467 TGGTAATGGTCAAGACAAGCAAG 59.180 43.478 2.29 0.00 0.00 4.01
667 1377 3.821033 GGTAATGGTCAAGACAAGCAAGT 59.179 43.478 2.29 0.00 0.00 3.16
668 1378 4.278419 GGTAATGGTCAAGACAAGCAAGTT 59.722 41.667 2.29 0.00 0.00 2.66
669 1379 3.996150 ATGGTCAAGACAAGCAAGTTG 57.004 42.857 0.00 0.00 42.48 3.16
670 1380 2.023673 TGGTCAAGACAAGCAAGTTGG 58.976 47.619 4.75 0.00 40.90 3.77
671 1381 2.024414 GGTCAAGACAAGCAAGTTGGT 58.976 47.619 0.63 0.63 40.90 3.67
672 1382 2.223572 GGTCAAGACAAGCAAGTTGGTG 60.224 50.000 8.61 5.73 40.90 4.17
673 1383 2.023673 TCAAGACAAGCAAGTTGGTGG 58.976 47.619 8.61 8.25 40.90 4.61
674 1384 2.023673 CAAGACAAGCAAGTTGGTGGA 58.976 47.619 16.33 0.00 40.90 4.02
675 1385 1.680338 AGACAAGCAAGTTGGTGGAC 58.320 50.000 16.33 9.95 40.90 4.02
676 1386 1.212935 AGACAAGCAAGTTGGTGGACT 59.787 47.619 16.33 12.13 40.90 3.85
677 1387 2.438021 AGACAAGCAAGTTGGTGGACTA 59.562 45.455 16.33 0.00 40.90 2.59
678 1388 2.548480 GACAAGCAAGTTGGTGGACTAC 59.452 50.000 16.33 1.62 40.90 2.73
686 1396 4.463043 GGTGGACTACCTCTGCCT 57.537 61.111 0.00 0.00 46.51 4.75
687 1397 1.901085 GGTGGACTACCTCTGCCTG 59.099 63.158 0.00 0.00 46.51 4.85
688 1398 1.617947 GGTGGACTACCTCTGCCTGG 61.618 65.000 0.00 0.00 46.51 4.45
689 1399 0.614979 GTGGACTACCTCTGCCTGGA 60.615 60.000 0.00 0.00 37.04 3.86
690 1400 0.324738 TGGACTACCTCTGCCTGGAG 60.325 60.000 0.00 0.00 37.04 3.86
691 1401 0.324830 GGACTACCTCTGCCTGGAGT 60.325 60.000 0.00 0.00 0.00 3.85
692 1402 1.107945 GACTACCTCTGCCTGGAGTC 58.892 60.000 0.00 0.00 0.00 3.36
693 1403 0.409876 ACTACCTCTGCCTGGAGTCA 59.590 55.000 0.00 0.00 0.00 3.41
694 1404 1.007721 ACTACCTCTGCCTGGAGTCAT 59.992 52.381 0.00 0.00 0.00 3.06
695 1405 2.114616 CTACCTCTGCCTGGAGTCATT 58.885 52.381 0.00 0.00 0.00 2.57
696 1406 0.908198 ACCTCTGCCTGGAGTCATTC 59.092 55.000 0.00 0.00 0.00 2.67
697 1407 1.202330 CCTCTGCCTGGAGTCATTCT 58.798 55.000 0.00 0.00 0.00 2.40
698 1408 1.558756 CCTCTGCCTGGAGTCATTCTT 59.441 52.381 0.00 0.00 0.00 2.52
699 1409 2.630158 CTCTGCCTGGAGTCATTCTTG 58.370 52.381 0.00 0.00 0.00 3.02
700 1410 1.980765 TCTGCCTGGAGTCATTCTTGT 59.019 47.619 0.00 0.00 0.00 3.16
701 1411 2.373169 TCTGCCTGGAGTCATTCTTGTT 59.627 45.455 0.00 0.00 0.00 2.83
702 1412 3.152341 CTGCCTGGAGTCATTCTTGTTT 58.848 45.455 0.00 0.00 0.00 2.83
703 1413 3.149196 TGCCTGGAGTCATTCTTGTTTC 58.851 45.455 0.00 0.00 0.00 2.78
704 1414 3.181440 TGCCTGGAGTCATTCTTGTTTCT 60.181 43.478 0.00 0.00 0.00 2.52
705 1415 3.823304 GCCTGGAGTCATTCTTGTTTCTT 59.177 43.478 0.00 0.00 0.00 2.52
706 1416 4.320788 GCCTGGAGTCATTCTTGTTTCTTG 60.321 45.833 0.00 0.00 0.00 3.02
707 1417 4.823989 CCTGGAGTCATTCTTGTTTCTTGT 59.176 41.667 0.00 0.00 0.00 3.16
708 1418 5.997746 CCTGGAGTCATTCTTGTTTCTTGTA 59.002 40.000 0.00 0.00 0.00 2.41
709 1419 6.656693 CCTGGAGTCATTCTTGTTTCTTGTAT 59.343 38.462 0.00 0.00 0.00 2.29
710 1420 7.175641 CCTGGAGTCATTCTTGTTTCTTGTATT 59.824 37.037 0.00 0.00 0.00 1.89
711 1421 8.099364 TGGAGTCATTCTTGTTTCTTGTATTC 57.901 34.615 0.00 0.00 0.00 1.75
712 1422 7.719193 TGGAGTCATTCTTGTTTCTTGTATTCA 59.281 33.333 0.00 0.00 0.00 2.57
713 1423 8.567948 GGAGTCATTCTTGTTTCTTGTATTCAA 58.432 33.333 0.00 0.00 0.00 2.69
716 1426 9.346725 GTCATTCTTGTTTCTTGTATTCAATCC 57.653 33.333 0.00 0.00 32.82 3.01
717 1427 9.076781 TCATTCTTGTTTCTTGTATTCAATCCA 57.923 29.630 0.00 0.00 32.82 3.41
718 1428 9.695526 CATTCTTGTTTCTTGTATTCAATCCAA 57.304 29.630 0.00 0.00 32.82 3.53
721 1431 9.695526 TCTTGTTTCTTGTATTCAATCCAATTG 57.304 29.630 0.00 0.00 41.57 2.32
722 1432 9.695526 CTTGTTTCTTGTATTCAATCCAATTGA 57.304 29.630 7.12 0.00 46.77 2.57
789 1499 2.095843 GCGCATTTGTCGACCGAC 59.904 61.111 14.12 14.88 44.77 4.79
903 1613 5.423931 TCACCAACTATATAAGCACACCTCA 59.576 40.000 0.00 0.00 0.00 3.86
904 1614 5.523916 CACCAACTATATAAGCACACCTCAC 59.476 44.000 0.00 0.00 0.00 3.51
918 1628 0.179116 CCTCACACGAGCATGGAGAG 60.179 60.000 0.00 0.00 38.00 3.20
953 1663 5.675575 GCATCATCAGAGTGGACATCAAAAC 60.676 44.000 0.00 0.00 0.00 2.43
1122 1832 1.585006 CGTCGGAGGTAACAGCACT 59.415 57.895 0.00 0.00 41.41 4.40
1125 1835 1.817447 GTCGGAGGTAACAGCACTAGT 59.183 52.381 0.00 0.00 41.41 2.57
1225 1941 4.175489 AGGACCGCGTCGTGATCG 62.175 66.667 7.51 0.00 32.65 3.69
1602 2330 3.066190 TCGTCCGCGACCAAGGAT 61.066 61.111 8.23 0.00 42.81 3.24
1742 2470 1.469335 AAGAAGAACCCGGCTCGTCA 61.469 55.000 16.22 0.00 0.00 4.35
1743 2471 1.737008 GAAGAACCCGGCTCGTCAC 60.737 63.158 11.19 0.00 0.00 3.67
1754 2482 4.600576 TCGTCACAGCGCCTGCAA 62.601 61.111 2.29 0.00 46.23 4.08
1755 2483 4.081030 CGTCACAGCGCCTGCAAG 62.081 66.667 2.29 0.00 46.23 4.01
1756 2484 2.666190 GTCACAGCGCCTGCAAGA 60.666 61.111 2.29 0.00 46.23 3.02
1757 2485 2.110835 TCACAGCGCCTGCAAGAA 59.889 55.556 2.29 0.00 46.23 2.52
1758 2486 1.962822 TCACAGCGCCTGCAAGAAG 60.963 57.895 2.29 0.00 46.23 2.85
1759 2487 1.962822 CACAGCGCCTGCAAGAAGA 60.963 57.895 2.29 0.00 46.23 2.87
1760 2488 1.002868 ACAGCGCCTGCAAGAAGAT 60.003 52.632 2.29 0.00 46.23 2.40
1776 2513 0.321671 AGATGTCGTCCAACACCAGG 59.678 55.000 0.00 0.00 30.55 4.45
1823 2568 3.041940 CGACAACGGCTGGACACC 61.042 66.667 0.00 0.00 35.72 4.16
1925 2670 3.877508 GTGGTGCTGAAACTTAACAGAGT 59.122 43.478 0.00 0.00 36.38 3.24
1995 2740 3.151710 TTCATCGGGTCCGGCGAT 61.152 61.111 9.30 9.33 40.25 4.58
2268 3013 0.846427 AGTTCAAGGGGATGGCCTCA 60.846 55.000 3.32 0.00 36.99 3.86
2292 3037 0.246635 CGTTCAGGGACGAGGACATT 59.753 55.000 0.00 0.00 45.47 2.71
2323 3068 2.355412 GCCGGGGAACTTTTCTAGCTAA 60.355 50.000 2.18 0.00 0.00 3.09
2324 3069 3.268330 CCGGGGAACTTTTCTAGCTAAC 58.732 50.000 0.00 0.00 0.00 2.34
2339 3118 4.065321 AGCTAACTAGTCATGATGGTGC 57.935 45.455 0.00 0.00 0.00 5.01
2344 3123 1.938577 CTAGTCATGATGGTGCAGTGC 59.061 52.381 8.58 8.58 0.00 4.40
2370 3153 8.017418 TGACTTTGTGGAACTGGAATTAAATT 57.983 30.769 0.00 0.00 38.04 1.82
2371 3154 9.137459 TGACTTTGTGGAACTGGAATTAAATTA 57.863 29.630 0.00 0.00 38.04 1.40
2446 3229 8.940768 TCAAACTCAAAATAAAGGAAAACTGG 57.059 30.769 0.00 0.00 0.00 4.00
2448 3231 6.419484 ACTCAAAATAAAGGAAAACTGGGG 57.581 37.500 0.00 0.00 0.00 4.96
2536 3321 6.783708 TGTCATTACCTTGGTTGTCTTTTT 57.216 33.333 0.00 0.00 0.00 1.94
2747 3541 4.236147 GTCAAGACTTCGGTAGAAAGACC 58.764 47.826 0.00 0.00 35.71 3.85
2755 3549 0.321298 GGTAGAAAGACCGCAGCCAA 60.321 55.000 0.00 0.00 0.00 4.52
2765 3559 1.021202 CCGCAGCCAAATCGGAATAA 58.979 50.000 0.00 0.00 45.53 1.40
2798 3592 3.129287 ACCCGTATACCTACACGAACTTG 59.871 47.826 0.00 0.00 40.56 3.16
2873 6020 0.034896 AAGACGTACTTGGGCTGTGG 59.965 55.000 0.00 0.00 37.45 4.17
2894 6041 6.057321 TGGATAACCACCTAACAGTAAAGG 57.943 41.667 1.01 1.01 41.77 3.11
2900 6047 3.744426 CCACCTAACAGTAAAGGTCGTTG 59.256 47.826 4.78 0.00 44.43 4.10
2904 6051 4.450080 CCTAACAGTAAAGGTCGTTGAACC 59.550 45.833 0.00 0.00 39.80 3.62
2912 6059 3.982576 AGGTCGTTGAACCACAAAATC 57.017 42.857 0.00 0.00 42.12 2.17
2934 6081 9.582431 AAATCTTCAATAGAACATCAAAGCATG 57.418 29.630 0.00 0.00 36.22 4.06
2945 6092 4.586001 ACATCAAAGCATGACTCCAAAGTT 59.414 37.500 0.00 0.00 41.93 2.66
2947 6094 5.947228 TCAAAGCATGACTCCAAAGTTAG 57.053 39.130 0.00 0.00 35.28 2.34
2956 6103 4.994852 TGACTCCAAAGTTAGAACCAATCG 59.005 41.667 0.00 0.00 35.28 3.34
2968 6115 4.549458 AGAACCAATCGCATCAACAAAAG 58.451 39.130 0.00 0.00 0.00 2.27
3056 6203 1.823169 TACGCAAGGTCCTGGACACC 61.823 60.000 26.94 12.58 46.39 4.16
3118 6265 1.616374 GTTGGGGCGATTTTCTTTCCA 59.384 47.619 0.00 0.00 0.00 3.53
3121 6268 2.040545 TGGGGCGATTTTCTTTCCAGTA 59.959 45.455 0.00 0.00 0.00 2.74
3132 6279 7.581213 TTTTCTTTCCAGTATCACAATGTGT 57.419 32.000 13.55 3.68 34.79 3.72
3142 6289 2.153366 CACAATGTGTGGGCCTTTTC 57.847 50.000 4.53 0.00 44.27 2.29
3143 6290 1.688197 CACAATGTGTGGGCCTTTTCT 59.312 47.619 4.53 0.00 44.27 2.52
3144 6291 2.102925 CACAATGTGTGGGCCTTTTCTT 59.897 45.455 4.53 0.00 44.27 2.52
3145 6292 2.771372 ACAATGTGTGGGCCTTTTCTTT 59.229 40.909 4.53 0.00 0.00 2.52
3146 6293 3.199727 ACAATGTGTGGGCCTTTTCTTTT 59.800 39.130 4.53 0.00 0.00 2.27
3147 6294 4.198530 CAATGTGTGGGCCTTTTCTTTTT 58.801 39.130 4.53 0.00 0.00 1.94
3148 6295 3.258971 TGTGTGGGCCTTTTCTTTTTG 57.741 42.857 4.53 0.00 0.00 2.44
3149 6296 2.093235 TGTGTGGGCCTTTTCTTTTTGG 60.093 45.455 4.53 0.00 0.00 3.28
3150 6297 2.093181 GTGTGGGCCTTTTCTTTTTGGT 60.093 45.455 4.53 0.00 0.00 3.67
3151 6298 2.573915 TGTGGGCCTTTTCTTTTTGGTT 59.426 40.909 4.53 0.00 0.00 3.67
3152 6299 3.009584 TGTGGGCCTTTTCTTTTTGGTTT 59.990 39.130 4.53 0.00 0.00 3.27
3153 6300 3.376859 GTGGGCCTTTTCTTTTTGGTTTG 59.623 43.478 4.53 0.00 0.00 2.93
3154 6301 2.357637 GGGCCTTTTCTTTTTGGTTTGC 59.642 45.455 0.84 0.00 0.00 3.68
3155 6302 2.357637 GGCCTTTTCTTTTTGGTTTGCC 59.642 45.455 0.00 0.00 0.00 4.52
3156 6303 3.278574 GCCTTTTCTTTTTGGTTTGCCT 58.721 40.909 0.00 0.00 35.27 4.75
3157 6304 3.694072 GCCTTTTCTTTTTGGTTTGCCTT 59.306 39.130 0.00 0.00 35.27 4.35
3158 6305 4.438608 GCCTTTTCTTTTTGGTTTGCCTTG 60.439 41.667 0.00 0.00 35.27 3.61
3159 6306 4.096231 CCTTTTCTTTTTGGTTTGCCTTGG 59.904 41.667 0.00 0.00 35.27 3.61
3160 6307 3.990959 TTCTTTTTGGTTTGCCTTGGT 57.009 38.095 0.00 0.00 35.27 3.67
3161 6308 3.535280 TCTTTTTGGTTTGCCTTGGTC 57.465 42.857 0.00 0.00 35.27 4.02
3162 6309 3.103742 TCTTTTTGGTTTGCCTTGGTCT 58.896 40.909 0.00 0.00 35.27 3.85
3163 6310 3.517500 TCTTTTTGGTTTGCCTTGGTCTT 59.482 39.130 0.00 0.00 35.27 3.01
3164 6311 3.990959 TTTTGGTTTGCCTTGGTCTTT 57.009 38.095 0.00 0.00 35.27 2.52
3165 6312 3.990959 TTTGGTTTGCCTTGGTCTTTT 57.009 38.095 0.00 0.00 35.27 2.27
3166 6313 3.990959 TTGGTTTGCCTTGGTCTTTTT 57.009 38.095 0.00 0.00 35.27 1.94
3167 6314 3.258971 TGGTTTGCCTTGGTCTTTTTG 57.741 42.857 0.00 0.00 35.27 2.44
3168 6315 2.569404 TGGTTTGCCTTGGTCTTTTTGT 59.431 40.909 0.00 0.00 35.27 2.83
3169 6316 3.008485 TGGTTTGCCTTGGTCTTTTTGTT 59.992 39.130 0.00 0.00 35.27 2.83
3170 6317 3.373748 GGTTTGCCTTGGTCTTTTTGTTG 59.626 43.478 0.00 0.00 0.00 3.33
3171 6318 4.249661 GTTTGCCTTGGTCTTTTTGTTGA 58.750 39.130 0.00 0.00 0.00 3.18
3172 6319 3.799281 TGCCTTGGTCTTTTTGTTGAG 57.201 42.857 0.00 0.00 0.00 3.02
3173 6320 3.096092 TGCCTTGGTCTTTTTGTTGAGT 58.904 40.909 0.00 0.00 0.00 3.41
3174 6321 3.513515 TGCCTTGGTCTTTTTGTTGAGTT 59.486 39.130 0.00 0.00 0.00 3.01
3175 6322 4.020662 TGCCTTGGTCTTTTTGTTGAGTTT 60.021 37.500 0.00 0.00 0.00 2.66
3176 6323 5.186021 TGCCTTGGTCTTTTTGTTGAGTTTA 59.814 36.000 0.00 0.00 0.00 2.01
3177 6324 6.127196 TGCCTTGGTCTTTTTGTTGAGTTTAT 60.127 34.615 0.00 0.00 0.00 1.40
3178 6325 6.761242 GCCTTGGTCTTTTTGTTGAGTTTATT 59.239 34.615 0.00 0.00 0.00 1.40
3179 6326 7.279981 GCCTTGGTCTTTTTGTTGAGTTTATTT 59.720 33.333 0.00 0.00 0.00 1.40
3180 6327 9.161629 CCTTGGTCTTTTTGTTGAGTTTATTTT 57.838 29.630 0.00 0.00 0.00 1.82
3182 6329 9.712305 TTGGTCTTTTTGTTGAGTTTATTTTCA 57.288 25.926 0.00 0.00 0.00 2.69
3183 6330 9.883142 TGGTCTTTTTGTTGAGTTTATTTTCAT 57.117 25.926 0.00 0.00 0.00 2.57
3205 6352 9.677567 TTCATTTTATGTTTTGTGAGCTAGTTC 57.322 29.630 0.00 0.00 0.00 3.01
3206 6353 9.066892 TCATTTTATGTTTTGTGAGCTAGTTCT 57.933 29.630 8.15 0.00 0.00 3.01
3207 6354 9.683069 CATTTTATGTTTTGTGAGCTAGTTCTT 57.317 29.630 8.15 0.00 0.00 2.52
3210 6357 9.515020 TTTATGTTTTGTGAGCTAGTTCTTTTG 57.485 29.630 8.15 0.00 0.00 2.44
3211 6358 6.509418 TGTTTTGTGAGCTAGTTCTTTTGT 57.491 33.333 8.15 0.00 0.00 2.83
3212 6359 6.551736 TGTTTTGTGAGCTAGTTCTTTTGTC 58.448 36.000 8.15 0.00 0.00 3.18
3213 6360 6.150307 TGTTTTGTGAGCTAGTTCTTTTGTCA 59.850 34.615 8.15 0.00 0.00 3.58
3214 6361 6.942532 TTTGTGAGCTAGTTCTTTTGTCAT 57.057 33.333 8.15 0.00 0.00 3.06
3215 6362 5.929697 TGTGAGCTAGTTCTTTTGTCATG 57.070 39.130 8.15 0.00 0.00 3.07
3216 6363 5.368145 TGTGAGCTAGTTCTTTTGTCATGT 58.632 37.500 8.15 0.00 0.00 3.21
3217 6364 5.822519 TGTGAGCTAGTTCTTTTGTCATGTT 59.177 36.000 8.15 0.00 0.00 2.71
3218 6365 6.318648 TGTGAGCTAGTTCTTTTGTCATGTTT 59.681 34.615 8.15 0.00 0.00 2.83
3219 6366 6.853362 GTGAGCTAGTTCTTTTGTCATGTTTC 59.147 38.462 8.15 0.00 0.00 2.78
3220 6367 6.767902 TGAGCTAGTTCTTTTGTCATGTTTCT 59.232 34.615 8.15 0.00 0.00 2.52
3221 6368 7.283127 TGAGCTAGTTCTTTTGTCATGTTTCTT 59.717 33.333 8.15 0.00 0.00 2.52
3222 6369 8.000780 AGCTAGTTCTTTTGTCATGTTTCTTT 57.999 30.769 0.00 0.00 0.00 2.52
3223 6370 8.470002 AGCTAGTTCTTTTGTCATGTTTCTTTT 58.530 29.630 0.00 0.00 0.00 2.27
3224 6371 9.087424 GCTAGTTCTTTTGTCATGTTTCTTTTT 57.913 29.630 0.00 0.00 0.00 1.94
3277 6424 9.921637 TTTATTTTGTGTTTCTCTTTGTCTGTT 57.078 25.926 0.00 0.00 0.00 3.16
3278 6425 9.921637 TTATTTTGTGTTTCTCTTTGTCTGTTT 57.078 25.926 0.00 0.00 0.00 2.83
3279 6426 8.831715 ATTTTGTGTTTCTCTTTGTCTGTTTT 57.168 26.923 0.00 0.00 0.00 2.43
3280 6427 8.655651 TTTTGTGTTTCTCTTTGTCTGTTTTT 57.344 26.923 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.466922 GGCCCATGAGATGAAGGTGG 60.467 60.000 0.00 0.00 0.00 4.61
70 71 2.113860 TTTCGGAGCTTGGAGGAATG 57.886 50.000 0.00 0.00 0.00 2.67
131 132 6.738114 TGCGAAATTTCTGAAGTTCTTTCAT 58.262 32.000 15.92 0.00 44.48 2.57
162 163 7.500892 TGGCTACTGAAGAAAATGAAAACTACA 59.499 33.333 0.00 0.00 0.00 2.74
167 168 5.278266 CGGTGGCTACTGAAGAAAATGAAAA 60.278 40.000 2.19 0.00 35.05 2.29
172 173 2.084546 GCGGTGGCTACTGAAGAAAAT 58.915 47.619 14.03 0.00 35.05 1.82
193 194 2.279252 ACACACTCACGCCGTCAC 60.279 61.111 0.00 0.00 0.00 3.67
194 195 2.027024 GACACACTCACGCCGTCA 59.973 61.111 0.00 0.00 0.00 4.35
195 196 2.733593 GGACACACTCACGCCGTC 60.734 66.667 0.00 0.00 0.00 4.79
196 197 4.640855 CGGACACACTCACGCCGT 62.641 66.667 0.00 0.00 37.35 5.68
197 198 4.640855 ACGGACACACTCACGCCG 62.641 66.667 0.00 0.00 46.83 6.46
198 199 3.036084 CACGGACACACTCACGCC 61.036 66.667 0.00 0.00 0.00 5.68
199 200 3.702555 GCACGGACACACTCACGC 61.703 66.667 0.00 0.00 0.00 5.34
200 201 2.279186 TGCACGGACACACTCACG 60.279 61.111 0.00 0.00 0.00 4.35
201 202 1.227263 ACTGCACGGACACACTCAC 60.227 57.895 0.00 0.00 0.00 3.51
290 291 8.828644 ACAAACACAATAAAACGTGTCTATACA 58.171 29.630 0.00 0.00 45.37 2.29
301 302 9.900264 GAAATGAGTGAACAAACACAATAAAAC 57.100 29.630 0.00 0.00 42.45 2.43
366 367 9.509956 CAAATACTCCCCCATTCGTAAATATAA 57.490 33.333 0.00 0.00 0.00 0.98
374 375 1.920351 ACCAAATACTCCCCCATTCGT 59.080 47.619 0.00 0.00 0.00 3.85
375 376 2.729028 ACCAAATACTCCCCCATTCG 57.271 50.000 0.00 0.00 0.00 3.34
379 380 4.357313 AGTAGTACCAAATACTCCCCCA 57.643 45.455 0.00 0.00 43.47 4.96
467 468 3.733727 CGTGTTATTCAAAGCACAAACCC 59.266 43.478 0.00 0.00 32.62 4.11
476 477 4.988540 TGGAGAGTGACGTGTTATTCAAAG 59.011 41.667 0.00 0.00 0.00 2.77
485 486 3.131396 GACATTTTGGAGAGTGACGTGT 58.869 45.455 0.00 0.00 0.00 4.49
492 493 8.043710 CCTCTAGTTAATGACATTTTGGAGAGT 58.956 37.037 5.89 0.00 0.00 3.24
493 494 8.260818 TCCTCTAGTTAATGACATTTTGGAGAG 58.739 37.037 5.89 12.61 0.00 3.20
494 495 8.146053 TCCTCTAGTTAATGACATTTTGGAGA 57.854 34.615 5.89 4.56 0.00 3.71
495 496 8.792830 TTCCTCTAGTTAATGACATTTTGGAG 57.207 34.615 5.89 9.06 0.00 3.86
496 497 8.383175 ACTTCCTCTAGTTAATGACATTTTGGA 58.617 33.333 5.89 2.07 0.00 3.53
497 498 8.567285 ACTTCCTCTAGTTAATGACATTTTGG 57.433 34.615 5.89 0.00 0.00 3.28
504 505 9.881529 CGAATACTACTTCCTCTAGTTAATGAC 57.118 37.037 0.00 0.00 0.00 3.06
505 506 9.842775 TCGAATACTACTTCCTCTAGTTAATGA 57.157 33.333 0.00 0.00 0.00 2.57
507 508 9.850198 ACTCGAATACTACTTCCTCTAGTTAAT 57.150 33.333 0.00 0.00 0.00 1.40
508 509 9.323985 GACTCGAATACTACTTCCTCTAGTTAA 57.676 37.037 0.00 0.00 0.00 2.01
509 510 7.651304 CGACTCGAATACTACTTCCTCTAGTTA 59.349 40.741 0.00 0.00 0.00 2.24
510 511 6.479660 CGACTCGAATACTACTTCCTCTAGTT 59.520 42.308 0.00 0.00 0.00 2.24
511 512 5.984926 CGACTCGAATACTACTTCCTCTAGT 59.015 44.000 0.00 0.00 0.00 2.57
512 513 6.215121 TCGACTCGAATACTACTTCCTCTAG 58.785 44.000 0.00 0.00 31.06 2.43
513 514 6.154203 TCGACTCGAATACTACTTCCTCTA 57.846 41.667 0.00 0.00 31.06 2.43
514 515 5.021033 TCGACTCGAATACTACTTCCTCT 57.979 43.478 0.00 0.00 31.06 3.69
515 516 5.106987 GGATCGACTCGAATACTACTTCCTC 60.107 48.000 5.00 0.00 39.99 3.71
516 517 4.756135 GGATCGACTCGAATACTACTTCCT 59.244 45.833 5.00 0.00 39.99 3.36
517 518 4.756135 AGGATCGACTCGAATACTACTTCC 59.244 45.833 5.00 5.38 39.99 3.46
518 519 5.697633 AGAGGATCGACTCGAATACTACTTC 59.302 44.000 5.00 0.00 42.67 3.01
519 520 5.467399 CAGAGGATCGACTCGAATACTACTT 59.533 44.000 5.00 0.00 42.67 2.24
520 521 4.992319 CAGAGGATCGACTCGAATACTACT 59.008 45.833 5.00 0.00 42.67 2.57
521 522 4.989797 TCAGAGGATCGACTCGAATACTAC 59.010 45.833 5.00 0.00 42.67 2.73
522 523 5.211174 TCAGAGGATCGACTCGAATACTA 57.789 43.478 5.00 0.00 42.67 1.82
523 524 4.074627 TCAGAGGATCGACTCGAATACT 57.925 45.455 5.00 4.07 42.67 2.12
524 525 4.273969 AGTTCAGAGGATCGACTCGAATAC 59.726 45.833 5.00 0.00 42.67 1.89
525 526 4.273724 CAGTTCAGAGGATCGACTCGAATA 59.726 45.833 5.00 0.00 42.67 1.75
526 527 3.066064 CAGTTCAGAGGATCGACTCGAAT 59.934 47.826 5.00 0.00 42.67 3.34
527 528 2.420372 CAGTTCAGAGGATCGACTCGAA 59.580 50.000 5.00 0.00 42.67 3.71
528 529 2.010497 CAGTTCAGAGGATCGACTCGA 58.990 52.381 3.06 3.06 42.67 4.04
529 530 1.064803 CCAGTTCAGAGGATCGACTCG 59.935 57.143 0.00 0.00 42.67 4.18
530 531 1.407258 CCCAGTTCAGAGGATCGACTC 59.593 57.143 0.00 0.00 42.67 3.36
574 1283 7.503566 CCACATCACCAGGTATATGAGATTTTT 59.496 37.037 17.39 0.00 0.00 1.94
575 1284 7.000472 CCACATCACCAGGTATATGAGATTTT 59.000 38.462 17.39 0.00 0.00 1.82
576 1285 6.537355 CCACATCACCAGGTATATGAGATTT 58.463 40.000 17.39 0.00 0.00 2.17
577 1286 5.513788 GCCACATCACCAGGTATATGAGATT 60.514 44.000 17.39 0.00 0.00 2.40
578 1287 4.019860 GCCACATCACCAGGTATATGAGAT 60.020 45.833 17.39 2.20 0.00 2.75
579 1288 3.324846 GCCACATCACCAGGTATATGAGA 59.675 47.826 17.39 0.00 0.00 3.27
580 1289 3.071457 TGCCACATCACCAGGTATATGAG 59.929 47.826 17.39 11.15 0.00 2.90
605 1314 1.611673 GCAGGCTATGTGTGTTCCAGT 60.612 52.381 0.00 0.00 0.00 4.00
606 1315 1.089920 GCAGGCTATGTGTGTTCCAG 58.910 55.000 0.00 0.00 0.00 3.86
607 1316 0.322456 GGCAGGCTATGTGTGTTCCA 60.322 55.000 0.00 0.00 0.00 3.53
614 1324 2.123428 GGGCTTGGCAGGCTATGTG 61.123 63.158 21.41 0.00 45.26 3.21
635 1345 0.818040 GACCATTACCATGACCGGGC 60.818 60.000 6.32 1.57 31.07 6.13
637 1347 2.093181 TCTTGACCATTACCATGACCGG 60.093 50.000 0.00 0.00 31.07 5.28
638 1348 2.936498 GTCTTGACCATTACCATGACCG 59.064 50.000 0.00 0.00 33.79 4.79
642 1352 3.758023 TGCTTGTCTTGACCATTACCATG 59.242 43.478 0.00 0.00 0.00 3.66
648 1358 3.068590 CCAACTTGCTTGTCTTGACCATT 59.931 43.478 0.00 0.00 0.00 3.16
649 1359 2.624838 CCAACTTGCTTGTCTTGACCAT 59.375 45.455 0.00 0.00 0.00 3.55
650 1360 2.023673 CCAACTTGCTTGTCTTGACCA 58.976 47.619 0.00 0.00 0.00 4.02
651 1361 2.024414 ACCAACTTGCTTGTCTTGACC 58.976 47.619 0.00 0.00 0.00 4.02
653 1363 2.023673 CCACCAACTTGCTTGTCTTGA 58.976 47.619 0.00 0.00 0.00 3.02
656 1366 1.212935 AGTCCACCAACTTGCTTGTCT 59.787 47.619 0.00 0.00 0.00 3.41
657 1367 1.680338 AGTCCACCAACTTGCTTGTC 58.320 50.000 0.00 0.00 0.00 3.18
658 1368 2.572290 GTAGTCCACCAACTTGCTTGT 58.428 47.619 0.00 0.00 0.00 3.16
670 1380 0.614979 TCCAGGCAGAGGTAGTCCAC 60.615 60.000 0.00 0.00 35.89 4.02
671 1381 0.324738 CTCCAGGCAGAGGTAGTCCA 60.325 60.000 0.00 0.00 35.89 4.02
672 1382 0.324830 ACTCCAGGCAGAGGTAGTCC 60.325 60.000 9.08 0.00 38.26 3.85
673 1383 1.107945 GACTCCAGGCAGAGGTAGTC 58.892 60.000 9.08 7.94 38.26 2.59
674 1384 0.409876 TGACTCCAGGCAGAGGTAGT 59.590 55.000 9.08 3.44 38.26 2.73
675 1385 1.786937 ATGACTCCAGGCAGAGGTAG 58.213 55.000 9.08 0.77 38.26 3.18
676 1386 2.111384 GAATGACTCCAGGCAGAGGTA 58.889 52.381 9.08 0.00 38.26 3.08
677 1387 0.908198 GAATGACTCCAGGCAGAGGT 59.092 55.000 9.08 0.00 38.26 3.85
678 1388 1.202330 AGAATGACTCCAGGCAGAGG 58.798 55.000 9.08 0.00 38.26 3.69
679 1389 2.027377 ACAAGAATGACTCCAGGCAGAG 60.027 50.000 3.28 3.28 39.91 3.35
680 1390 1.980765 ACAAGAATGACTCCAGGCAGA 59.019 47.619 0.00 0.00 0.00 4.26
681 1391 2.486472 ACAAGAATGACTCCAGGCAG 57.514 50.000 0.00 0.00 0.00 4.85
682 1392 2.957402 AACAAGAATGACTCCAGGCA 57.043 45.000 0.00 0.00 0.00 4.75
683 1393 3.416156 AGAAACAAGAATGACTCCAGGC 58.584 45.455 0.00 0.00 0.00 4.85
684 1394 4.823989 ACAAGAAACAAGAATGACTCCAGG 59.176 41.667 0.00 0.00 0.00 4.45
685 1395 7.678947 ATACAAGAAACAAGAATGACTCCAG 57.321 36.000 0.00 0.00 0.00 3.86
686 1396 7.719193 TGAATACAAGAAACAAGAATGACTCCA 59.281 33.333 0.00 0.00 0.00 3.86
687 1397 8.099364 TGAATACAAGAAACAAGAATGACTCC 57.901 34.615 0.00 0.00 0.00 3.85
690 1400 9.346725 GGATTGAATACAAGAAACAAGAATGAC 57.653 33.333 0.00 0.00 39.46 3.06
691 1401 9.076781 TGGATTGAATACAAGAAACAAGAATGA 57.923 29.630 0.00 0.00 39.46 2.57
692 1402 9.695526 TTGGATTGAATACAAGAAACAAGAATG 57.304 29.630 0.00 0.00 39.46 2.67
695 1405 9.695526 CAATTGGATTGAATACAAGAAACAAGA 57.304 29.630 8.96 0.00 42.83 3.02
696 1406 9.695526 TCAATTGGATTGAATACAAGAAACAAG 57.304 29.630 8.96 0.00 45.57 3.16
710 1420 4.626287 GCTGGGTCTACTCAATTGGATTGA 60.626 45.833 5.42 3.60 46.30 2.57
711 1421 3.629398 GCTGGGTCTACTCAATTGGATTG 59.371 47.826 5.42 0.00 41.57 2.67
712 1422 3.372025 GGCTGGGTCTACTCAATTGGATT 60.372 47.826 5.42 0.00 0.00 3.01
713 1423 2.173569 GGCTGGGTCTACTCAATTGGAT 59.826 50.000 5.42 0.00 0.00 3.41
714 1424 1.559682 GGCTGGGTCTACTCAATTGGA 59.440 52.381 5.42 0.00 0.00 3.53
715 1425 1.281867 TGGCTGGGTCTACTCAATTGG 59.718 52.381 5.42 0.00 0.00 3.16
716 1426 2.636830 CTGGCTGGGTCTACTCAATTG 58.363 52.381 0.00 0.00 0.00 2.32
717 1427 1.065126 GCTGGCTGGGTCTACTCAATT 60.065 52.381 0.00 0.00 0.00 2.32
718 1428 0.543749 GCTGGCTGGGTCTACTCAAT 59.456 55.000 0.00 0.00 0.00 2.57
719 1429 0.835971 TGCTGGCTGGGTCTACTCAA 60.836 55.000 0.00 0.00 0.00 3.02
720 1430 1.229177 TGCTGGCTGGGTCTACTCA 60.229 57.895 0.00 0.00 0.00 3.41
721 1431 1.219393 GTGCTGGCTGGGTCTACTC 59.781 63.158 0.00 0.00 0.00 2.59
722 1432 2.294078 GGTGCTGGCTGGGTCTACT 61.294 63.158 0.00 0.00 0.00 2.57
723 1433 2.269241 GGTGCTGGCTGGGTCTAC 59.731 66.667 0.00 0.00 0.00 2.59
776 1486 1.295423 CTGGGGTCGGTCGACAAAT 59.705 57.895 22.35 0.00 46.20 2.32
806 1516 1.886861 CTTGTTGACGAGGGCGAACG 61.887 60.000 0.00 0.00 41.64 3.95
882 1592 5.523916 GTGTGAGGTGTGCTTATATAGTTGG 59.476 44.000 0.00 0.00 0.00 3.77
886 1596 5.183014 TCGTGTGAGGTGTGCTTATATAG 57.817 43.478 0.00 0.00 0.00 1.31
903 1613 0.247736 GTTCCTCTCCATGCTCGTGT 59.752 55.000 0.00 0.00 0.00 4.49
904 1614 0.803768 CGTTCCTCTCCATGCTCGTG 60.804 60.000 0.00 0.00 0.00 4.35
918 1628 1.083806 TGATGATGCGTGCTCGTTCC 61.084 55.000 10.18 0.07 39.49 3.62
953 1663 3.414700 GACACGCAACTCTGCCCG 61.415 66.667 0.00 0.00 46.56 6.13
972 1682 1.200252 CTGTCACGTAGTCTGTCCCAG 59.800 57.143 0.00 0.00 41.61 4.45
1111 1821 2.564062 TGGTGGTACTAGTGCTGTTACC 59.436 50.000 10.95 13.43 0.00 2.85
1113 1823 2.229543 CGTGGTGGTACTAGTGCTGTTA 59.770 50.000 10.95 0.00 0.00 2.41
1122 1832 0.960364 GGTCGGACGTGGTGGTACTA 60.960 60.000 0.00 0.00 0.00 1.82
1125 1835 2.203466 TGGTCGGACGTGGTGGTA 60.203 61.111 0.00 0.00 0.00 3.25
1225 1941 2.202892 GCCGTCATCTCCCGTTCC 60.203 66.667 0.00 0.00 0.00 3.62
1226 1942 2.582498 CGCCGTCATCTCCCGTTC 60.582 66.667 0.00 0.00 0.00 3.95
1246 1962 3.003763 GAGCTTCCCCACCTCCGT 61.004 66.667 0.00 0.00 0.00 4.69
1602 2330 0.473694 TGGCCTCCTGGAAGAAGTCA 60.474 55.000 3.32 0.00 34.07 3.41
1710 2438 3.883744 CTTCTTCGGCCACCAGCGT 62.884 63.158 2.24 0.00 45.17 5.07
1723 2451 1.292541 GACGAGCCGGGTTCTTCTT 59.707 57.895 8.00 0.00 0.00 2.52
1742 2470 1.002868 ATCTTCTTGCAGGCGCTGT 60.003 52.632 7.64 0.00 39.64 4.40
1743 2471 1.303799 ACATCTTCTTGCAGGCGCTG 61.304 55.000 7.64 4.78 39.64 5.18
1749 2477 2.084610 TGGACGACATCTTCTTGCAG 57.915 50.000 0.00 0.00 0.00 4.41
1750 2478 2.143122 GTTGGACGACATCTTCTTGCA 58.857 47.619 0.00 0.00 0.00 4.08
1751 2479 2.096218 GTGTTGGACGACATCTTCTTGC 60.096 50.000 0.00 0.00 0.00 4.01
1752 2480 2.480419 GGTGTTGGACGACATCTTCTTG 59.520 50.000 0.00 0.00 0.00 3.02
1753 2481 2.104111 TGGTGTTGGACGACATCTTCTT 59.896 45.455 4.70 0.00 31.86 2.52
1754 2482 1.691976 TGGTGTTGGACGACATCTTCT 59.308 47.619 4.70 0.00 31.86 2.85
1755 2483 2.069273 CTGGTGTTGGACGACATCTTC 58.931 52.381 4.70 0.00 31.86 2.87
1756 2484 1.270839 CCTGGTGTTGGACGACATCTT 60.271 52.381 4.70 0.00 31.86 2.40
1757 2485 0.321671 CCTGGTGTTGGACGACATCT 59.678 55.000 4.70 0.00 31.86 2.90
1758 2486 1.298859 GCCTGGTGTTGGACGACATC 61.299 60.000 0.00 0.00 0.00 3.06
1759 2487 1.302511 GCCTGGTGTTGGACGACAT 60.303 57.895 0.00 0.00 0.00 3.06
1760 2488 2.050836 ATGCCTGGTGTTGGACGACA 62.051 55.000 0.00 0.00 0.00 4.35
1821 2566 4.163427 TCATCTCTTCTTCCAGTTCTGGT 58.837 43.478 17.00 0.00 0.00 4.00
1823 2568 5.394443 CCTCTCATCTCTTCTTCCAGTTCTG 60.394 48.000 0.00 0.00 0.00 3.02
2026 2771 3.842923 CAGAGTGCCGCCGAGGAT 61.843 66.667 0.91 0.00 45.00 3.24
2292 3037 1.356398 AGTTCCCCGGCAAAATTCCTA 59.644 47.619 0.00 0.00 0.00 2.94
2323 3068 2.679059 GCACTGCACCATCATGACTAGT 60.679 50.000 0.00 0.00 0.00 2.57
2324 3069 1.938577 GCACTGCACCATCATGACTAG 59.061 52.381 0.00 0.00 0.00 2.57
2339 3118 2.032550 CAGTTCCACAAAGTCAGCACTG 59.967 50.000 0.00 0.00 31.06 3.66
2344 3123 6.633500 TTAATTCCAGTTCCACAAAGTCAG 57.367 37.500 0.00 0.00 0.00 3.51
2400 3183 9.921637 GTTTGAGTCCCATTTTATGTTTATTCA 57.078 29.630 0.00 0.00 0.00 2.57
2446 3229 7.450225 GAAATAATTTCTCGGCCAAGAGCCC 62.450 48.000 2.24 0.00 46.65 5.19
2448 3231 4.336713 AGAAATAATTTCTCGGCCAAGAGC 59.663 41.667 2.24 0.00 46.62 4.09
2505 3288 6.207417 ACAACCAAGGTAATGACAATTCAGAG 59.793 38.462 0.00 0.00 34.35 3.35
2747 3541 1.594518 CGTTATTCCGATTTGGCTGCG 60.595 52.381 0.00 0.00 37.80 5.18
2755 3549 1.283736 GCGGTGTCGTTATTCCGATT 58.716 50.000 6.63 0.00 44.86 3.34
2836 5983 9.031360 GTACGTCTTCTTATTCTTTATCATGCA 57.969 33.333 0.00 0.00 0.00 3.96
2844 5991 5.642491 GCCCAAGTACGTCTTCTTATTCTTT 59.358 40.000 0.00 0.00 33.63 2.52
2850 5997 2.895404 ACAGCCCAAGTACGTCTTCTTA 59.105 45.455 0.00 0.00 33.63 2.10
2873 6020 5.809051 CGACCTTTACTGTTAGGTGGTTATC 59.191 44.000 16.16 3.58 44.65 1.75
2891 6038 3.951680 AGATTTTGTGGTTCAACGACCTT 59.048 39.130 0.00 0.00 40.47 3.50
2893 6040 3.982576 AGATTTTGTGGTTCAACGACC 57.017 42.857 0.00 0.00 40.23 4.79
2894 6041 4.915704 TGAAGATTTTGTGGTTCAACGAC 58.084 39.130 0.00 0.00 35.61 4.34
2900 6047 9.346725 GATGTTCTATTGAAGATTTTGTGGTTC 57.653 33.333 1.33 0.00 36.48 3.62
2912 6059 7.759465 AGTCATGCTTTGATGTTCTATTGAAG 58.241 34.615 0.00 0.00 36.54 3.02
2934 6081 4.142881 GCGATTGGTTCTAACTTTGGAGTC 60.143 45.833 0.00 0.00 34.21 3.36
2945 6092 5.697473 TTTTGTTGATGCGATTGGTTCTA 57.303 34.783 0.00 0.00 0.00 2.10
2947 6094 3.121778 GCTTTTGTTGATGCGATTGGTTC 59.878 43.478 0.00 0.00 0.00 3.62
3024 6171 9.268268 CAGGACCTTGCGTATTTTAGATTTATA 57.732 33.333 0.00 0.00 0.00 0.98
3029 6176 4.163458 TCCAGGACCTTGCGTATTTTAGAT 59.837 41.667 0.00 0.00 0.00 1.98
3030 6177 3.516300 TCCAGGACCTTGCGTATTTTAGA 59.484 43.478 0.00 0.00 0.00 2.10
3038 6185 2.426023 GTGTCCAGGACCTTGCGT 59.574 61.111 17.59 0.00 0.00 5.24
3056 6203 2.604373 CCACGCACACATTGTAGGTTTG 60.604 50.000 0.00 0.00 0.00 2.93
3132 6279 3.615155 CAAACCAAAAAGAAAAGGCCCA 58.385 40.909 0.00 0.00 0.00 5.36
3133 6280 2.357637 GCAAACCAAAAAGAAAAGGCCC 59.642 45.455 0.00 0.00 0.00 5.80
3134 6281 2.357637 GGCAAACCAAAAAGAAAAGGCC 59.642 45.455 0.00 0.00 35.26 5.19
3135 6282 3.278574 AGGCAAACCAAAAAGAAAAGGC 58.721 40.909 0.00 0.00 39.06 4.35
3136 6283 4.096231 CCAAGGCAAACCAAAAAGAAAAGG 59.904 41.667 0.00 0.00 39.06 3.11
3137 6284 4.699735 ACCAAGGCAAACCAAAAAGAAAAG 59.300 37.500 0.00 0.00 39.06 2.27
3138 6285 4.657013 ACCAAGGCAAACCAAAAAGAAAA 58.343 34.783 0.00 0.00 39.06 2.29
3139 6286 4.019771 AGACCAAGGCAAACCAAAAAGAAA 60.020 37.500 0.00 0.00 39.06 2.52
3140 6287 3.517500 AGACCAAGGCAAACCAAAAAGAA 59.482 39.130 0.00 0.00 39.06 2.52
3141 6288 3.103742 AGACCAAGGCAAACCAAAAAGA 58.896 40.909 0.00 0.00 39.06 2.52
3142 6289 3.541996 AGACCAAGGCAAACCAAAAAG 57.458 42.857 0.00 0.00 39.06 2.27
3143 6290 3.990959 AAGACCAAGGCAAACCAAAAA 57.009 38.095 0.00 0.00 39.06 1.94
3144 6291 3.990959 AAAGACCAAGGCAAACCAAAA 57.009 38.095 0.00 0.00 39.06 2.44
3145 6292 3.990959 AAAAGACCAAGGCAAACCAAA 57.009 38.095 0.00 0.00 39.06 3.28
3146 6293 3.008485 ACAAAAAGACCAAGGCAAACCAA 59.992 39.130 0.00 0.00 39.06 3.67
3147 6294 2.569404 ACAAAAAGACCAAGGCAAACCA 59.431 40.909 0.00 0.00 39.06 3.67
3148 6295 3.260475 ACAAAAAGACCAAGGCAAACC 57.740 42.857 0.00 0.00 0.00 3.27
3149 6296 4.249661 TCAACAAAAAGACCAAGGCAAAC 58.750 39.130 0.00 0.00 0.00 2.93
3150 6297 4.020662 ACTCAACAAAAAGACCAAGGCAAA 60.021 37.500 0.00 0.00 0.00 3.68
3151 6298 3.513515 ACTCAACAAAAAGACCAAGGCAA 59.486 39.130 0.00 0.00 0.00 4.52
3152 6299 3.096092 ACTCAACAAAAAGACCAAGGCA 58.904 40.909 0.00 0.00 0.00 4.75
3153 6300 3.801114 ACTCAACAAAAAGACCAAGGC 57.199 42.857 0.00 0.00 0.00 4.35
3154 6301 8.716646 AAATAAACTCAACAAAAAGACCAAGG 57.283 30.769 0.00 0.00 0.00 3.61
3156 6303 9.712305 TGAAAATAAACTCAACAAAAAGACCAA 57.288 25.926 0.00 0.00 0.00 3.67
3157 6304 9.883142 ATGAAAATAAACTCAACAAAAAGACCA 57.117 25.926 0.00 0.00 0.00 4.02
3179 6326 9.677567 GAACTAGCTCACAAAACATAAAATGAA 57.322 29.630 0.00 0.00 0.00 2.57
3180 6327 9.066892 AGAACTAGCTCACAAAACATAAAATGA 57.933 29.630 0.00 0.00 0.00 2.57
3181 6328 9.683069 AAGAACTAGCTCACAAAACATAAAATG 57.317 29.630 0.00 0.00 0.00 2.32
3184 6331 9.515020 CAAAAGAACTAGCTCACAAAACATAAA 57.485 29.630 0.00 0.00 0.00 1.40
3185 6332 8.682710 ACAAAAGAACTAGCTCACAAAACATAA 58.317 29.630 0.00 0.00 0.00 1.90
3186 6333 8.220755 ACAAAAGAACTAGCTCACAAAACATA 57.779 30.769 0.00 0.00 0.00 2.29
3187 6334 7.100458 ACAAAAGAACTAGCTCACAAAACAT 57.900 32.000 0.00 0.00 0.00 2.71
3188 6335 6.150307 TGACAAAAGAACTAGCTCACAAAACA 59.850 34.615 0.00 0.00 0.00 2.83
3189 6336 6.551736 TGACAAAAGAACTAGCTCACAAAAC 58.448 36.000 0.00 0.00 0.00 2.43
3190 6337 6.751514 TGACAAAAGAACTAGCTCACAAAA 57.248 33.333 0.00 0.00 0.00 2.44
3191 6338 6.318648 ACATGACAAAAGAACTAGCTCACAAA 59.681 34.615 0.00 0.00 0.00 2.83
3192 6339 5.822519 ACATGACAAAAGAACTAGCTCACAA 59.177 36.000 0.00 0.00 0.00 3.33
3193 6340 5.368145 ACATGACAAAAGAACTAGCTCACA 58.632 37.500 0.00 0.00 0.00 3.58
3194 6341 5.931441 ACATGACAAAAGAACTAGCTCAC 57.069 39.130 0.00 0.00 0.00 3.51
3195 6342 6.767902 AGAAACATGACAAAAGAACTAGCTCA 59.232 34.615 0.00 0.00 0.00 4.26
3196 6343 7.195839 AGAAACATGACAAAAGAACTAGCTC 57.804 36.000 0.00 0.00 0.00 4.09
3197 6344 7.573968 AAGAAACATGACAAAAGAACTAGCT 57.426 32.000 0.00 0.00 0.00 3.32
3198 6345 8.634475 AAAAGAAACATGACAAAAGAACTAGC 57.366 30.769 0.00 0.00 0.00 3.42
3251 6398 9.921637 AACAGACAAAGAGAAACACAAAATAAA 57.078 25.926 0.00 0.00 0.00 1.40
3252 6399 9.921637 AAACAGACAAAGAGAAACACAAAATAA 57.078 25.926 0.00 0.00 0.00 1.40
3253 6400 9.921637 AAAACAGACAAAGAGAAACACAAAATA 57.078 25.926 0.00 0.00 0.00 1.40
3254 6401 8.831715 AAAACAGACAAAGAGAAACACAAAAT 57.168 26.923 0.00 0.00 0.00 1.82
3255 6402 8.655651 AAAAACAGACAAAGAGAAACACAAAA 57.344 26.923 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.