Multiple sequence alignment - TraesCS5D01G064200

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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 TraesCS5D01G064200 chr5D 100.000 2339 0 0 1 2339 59569900 59567562 0.000000e+00 4320
1 TraesCS5D01G064200 chr5D 94.651 916 44 3 1 911 383585942 383586857 0.000000e+00 1415
2 TraesCS5D01G064200 chr5D 94.541 916 45 3 1 911 473452307 473453222 0.000000e+00 1410
3 TraesCS5D01G064200 chr5D 94.737 456 24 0 911 1366 383586889 383587344 0.000000e+00 710
4 TraesCS5D01G064200 chr6D 94.105 916 46 6 1 911 338919637 338920549 0.000000e+00 1386
5 TraesCS5D01G064200 chr6D 94.923 453 23 0 911 1363 338920581 338921033 0.000000e+00 710
6 TraesCS5D01G064200 chr2B 93.996 916 50 3 1 911 390803564 390802649 0.000000e+00 1382
7 TraesCS5D01G064200 chr2B 95.806 453 19 0 911 1363 793363875 793364327 0.000000e+00 732
8 TraesCS5D01G064200 chr2B 77.677 551 104 13 1765 2302 245164423 245163879 3.750000e-83 318
9 TraesCS5D01G064200 chr1B 93.996 916 49 4 1 911 92336360 92337274 0.000000e+00 1382
10 TraesCS5D01G064200 chr1B 75.758 561 99 22 1764 2302 308337057 308336512 4.990000e-62 248
11 TraesCS5D01G064200 chr1A 93.996 916 49 4 1 911 213935637 213936551 0.000000e+00 1382
12 TraesCS5D01G064200 chr5B 93.777 916 52 3 1 911 59780996 59780081 0.000000e+00 1371
13 TraesCS5D01G064200 chr5B 94.143 461 27 0 911 1371 677678319 677678779 0.000000e+00 702
14 TraesCS5D01G064200 chr3B 93.777 916 52 3 1 911 161678882 161677967 0.000000e+00 1371
15 TraesCS5D01G064200 chr3B 93.777 916 52 3 1 911 571263399 571262484 0.000000e+00 1371
16 TraesCS5D01G064200 chr3B 80.084 477 72 17 1764 2223 561694619 561695089 1.340000e-87 333
17 TraesCS5D01G064200 chr2D 96.009 451 18 0 914 1364 308681822 308681372 0.000000e+00 734
18 TraesCS5D01G064200 chr2D 95.787 451 19 0 914 1364 308678391 308677941 0.000000e+00 728
19 TraesCS5D01G064200 chr4D 94.714 454 23 1 914 1367 469444918 469444466 0.000000e+00 704
20 TraesCS5D01G064200 chr4B 94.530 457 24 1 907 1363 166833362 166832907 0.000000e+00 704
21 TraesCS5D01G064200 chr2A 94.702 453 24 0 911 1363 192002929 192003381 0.000000e+00 704
22 TraesCS5D01G064200 chr6A 76.445 467 88 14 1887 2336 1477881 1478342 1.400000e-57 233


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 TraesCS5D01G064200 chr5D 59567562 59569900 2338 True 4320.0 4320 100.000 1 2339 1 chr5D.!!$R1 2338
1 TraesCS5D01G064200 chr5D 473452307 473453222 915 False 1410.0 1410 94.541 1 911 1 chr5D.!!$F1 910
2 TraesCS5D01G064200 chr5D 383585942 383587344 1402 False 1062.5 1415 94.694 1 1366 2 chr5D.!!$F2 1365
3 TraesCS5D01G064200 chr6D 338919637 338921033 1396 False 1048.0 1386 94.514 1 1363 2 chr6D.!!$F1 1362
4 TraesCS5D01G064200 chr2B 390802649 390803564 915 True 1382.0 1382 93.996 1 911 1 chr2B.!!$R2 910
5 TraesCS5D01G064200 chr2B 245163879 245164423 544 True 318.0 318 77.677 1765 2302 1 chr2B.!!$R1 537
6 TraesCS5D01G064200 chr1B 92336360 92337274 914 False 1382.0 1382 93.996 1 911 1 chr1B.!!$F1 910
7 TraesCS5D01G064200 chr1B 308336512 308337057 545 True 248.0 248 75.758 1764 2302 1 chr1B.!!$R1 538
8 TraesCS5D01G064200 chr1A 213935637 213936551 914 False 1382.0 1382 93.996 1 911 1 chr1A.!!$F1 910
9 TraesCS5D01G064200 chr5B 59780081 59780996 915 True 1371.0 1371 93.777 1 911 1 chr5B.!!$R1 910
10 TraesCS5D01G064200 chr3B 161677967 161678882 915 True 1371.0 1371 93.777 1 911 1 chr3B.!!$R1 910
11 TraesCS5D01G064200 chr3B 571262484 571263399 915 True 1371.0 1371 93.777 1 911 1 chr3B.!!$R2 910
12 TraesCS5D01G064200 chr2D 308677941 308681822 3881 True 731.0 734 95.898 914 1364 2 chr2D.!!$R1 450

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
993 4430 0.396435 AGATTGACTGGTGTGCCGAA 59.604 50.0 0.0 0.0 37.67 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2122 5567 0.173481 AGCGCTGCTCTGTCGATTAA 59.827 50.0 10.39 0.0 30.62 1.4 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
33 34 1.742831 GAAGCGTGGTCATATTTGGCA 59.257 47.619 0.00 0.00 0.00 4.92
66 67 3.706086 GGGCAGAATATTGACATTTGGGT 59.294 43.478 0.00 0.00 0.00 4.51
210 211 4.343526 CAGACAGACTCTATGGCCTATTGT 59.656 45.833 3.32 0.00 0.00 2.71
394 397 2.297701 CACGGTCAATCCTATTTGGGG 58.702 52.381 0.00 0.00 36.20 4.96
420 423 4.442753 GGATTTGGAAACTTGCTTGTCCAA 60.443 41.667 0.00 0.00 46.02 3.53
458 461 1.890876 TTTGGCATACGCTTCACAGT 58.109 45.000 0.00 0.00 38.60 3.55
464 467 3.109619 GCATACGCTTCACAGTACTCTC 58.890 50.000 0.00 0.00 34.30 3.20
479 482 1.268899 ACTCTCCCGTGTCGTGTTAAG 59.731 52.381 0.00 0.00 0.00 1.85
511 517 1.412710 TGTGAAAGTCTCGCCTGAGTT 59.587 47.619 0.00 0.00 43.09 3.01
546 552 4.591321 TCTGGGCCAGAAGATACAAAAT 57.409 40.909 33.38 0.00 37.57 1.82
575 581 6.529829 TGTTGTTTCTATGTGACAAAGCAAAC 59.470 34.615 0.00 0.00 35.31 2.93
583 589 4.185394 TGTGACAAAGCAAACGAAGTCTA 58.815 39.130 0.00 0.00 45.00 2.59
648 654 0.681733 ATACTATGCGGGTGAGGCAG 59.318 55.000 0.00 0.00 44.71 4.85
655 661 2.352805 GGGTGAGGCAGTCTTGGG 59.647 66.667 0.00 0.00 0.00 4.12
704 710 5.279306 GGAACTATGTATTATGGGCACTCGA 60.279 44.000 0.00 0.00 0.00 4.04
757 763 0.847373 TACTTGTGGTGGGAAAGGCA 59.153 50.000 0.00 0.00 0.00 4.75
847 853 4.041444 TGCCAATTTTGTTAATGCCTCCTT 59.959 37.500 0.00 0.00 0.00 3.36
926 932 4.194678 ACTTAAGAGGTATGATCGGGGA 57.805 45.455 10.09 0.00 0.00 4.81
930 936 2.071372 AGAGGTATGATCGGGGAGGTA 58.929 52.381 0.00 0.00 0.00 3.08
990 4427 2.084546 GGTAAGATTGACTGGTGTGCC 58.915 52.381 0.00 0.00 0.00 5.01
993 4430 0.396435 AGATTGACTGGTGTGCCGAA 59.604 50.000 0.00 0.00 37.67 4.30
1026 4463 4.143326 GCTGAAGCTTTGGCGTTAAAATTC 60.143 41.667 0.00 0.00 44.37 2.17
1035 4472 2.876550 GGCGTTAAAATTCGGCCTATCT 59.123 45.455 0.00 0.00 44.62 1.98
1125 4562 0.392729 ACGAAGGAGGACGATCGTCT 60.393 55.000 38.48 27.42 40.72 4.18
1138 4575 3.774528 CGTCTGGGGCAGCAGCTA 61.775 66.667 0.00 0.00 41.70 3.32
1185 4622 4.639135 AGCTTGCGATTTTCCTATTTCC 57.361 40.909 0.00 0.00 0.00 3.13
1262 4699 8.522830 CAAGTTGGCTAGATTTTCCTTCATTTA 58.477 33.333 0.00 0.00 0.00 1.40
1318 4755 7.207383 TGTACCAATCCTCATAAACGATGTAG 58.793 38.462 0.00 0.00 36.84 2.74
1377 4814 2.189594 AAAAAGGTAGCGTGTACCCC 57.810 50.000 11.30 0.00 38.33 4.95
1378 4815 0.325933 AAAAGGTAGCGTGTACCCCC 59.674 55.000 11.30 0.00 38.33 5.40
1379 4816 0.546027 AAAGGTAGCGTGTACCCCCT 60.546 55.000 11.30 0.00 38.33 4.79
1380 4817 0.336048 AAGGTAGCGTGTACCCCCTA 59.664 55.000 11.30 0.00 38.33 3.53
1381 4818 0.396278 AGGTAGCGTGTACCCCCTAC 60.396 60.000 11.30 0.00 38.33 3.18
1382 4819 1.395045 GGTAGCGTGTACCCCCTACC 61.395 65.000 13.72 13.72 41.95 3.18
1383 4820 0.684153 GTAGCGTGTACCCCCTACCA 60.684 60.000 0.00 0.00 0.00 3.25
1384 4821 0.396139 TAGCGTGTACCCCCTACCAG 60.396 60.000 0.00 0.00 0.00 4.00
1385 4822 2.897972 CGTGTACCCCCTACCAGC 59.102 66.667 0.00 0.00 0.00 4.85
1386 4823 2.897972 GTGTACCCCCTACCAGCG 59.102 66.667 0.00 0.00 0.00 5.18
1387 4824 2.364579 TGTACCCCCTACCAGCGG 60.365 66.667 0.00 0.00 0.00 5.52
1388 4825 3.159347 GTACCCCCTACCAGCGGG 61.159 72.222 0.00 0.00 43.05 6.13
1393 4830 3.717294 CCCTACCAGCGGGCAGTT 61.717 66.667 1.46 0.00 37.90 3.16
1394 4831 2.351276 CCTACCAGCGGGCAGTTT 59.649 61.111 1.46 0.00 37.90 2.66
1395 4832 1.303317 CCTACCAGCGGGCAGTTTT 60.303 57.895 1.46 0.00 37.90 2.43
1396 4833 0.893727 CCTACCAGCGGGCAGTTTTT 60.894 55.000 1.46 0.00 37.90 1.94
1397 4834 0.240945 CTACCAGCGGGCAGTTTTTG 59.759 55.000 1.46 0.00 37.90 2.44
1398 4835 0.179015 TACCAGCGGGCAGTTTTTGA 60.179 50.000 1.46 0.00 37.90 2.69
1399 4836 1.286880 CCAGCGGGCAGTTTTTGAG 59.713 57.895 0.00 0.00 0.00 3.02
1400 4837 1.286880 CAGCGGGCAGTTTTTGAGG 59.713 57.895 0.00 0.00 0.00 3.86
1401 4838 1.903404 AGCGGGCAGTTTTTGAGGG 60.903 57.895 0.00 0.00 0.00 4.30
1402 4839 2.650778 CGGGCAGTTTTTGAGGGC 59.349 61.111 0.00 0.00 0.00 5.19
1403 4840 1.903404 CGGGCAGTTTTTGAGGGCT 60.903 57.895 0.00 0.00 0.00 5.19
1404 4841 1.866853 CGGGCAGTTTTTGAGGGCTC 61.867 60.000 0.00 0.00 0.00 4.70
1405 4842 1.536073 GGGCAGTTTTTGAGGGCTCC 61.536 60.000 0.00 0.00 0.00 4.70
1406 4843 1.536073 GGCAGTTTTTGAGGGCTCCC 61.536 60.000 0.00 0.00 0.00 4.30
1407 4844 1.866853 GCAGTTTTTGAGGGCTCCCG 61.867 60.000 0.00 0.00 41.95 5.14
1408 4845 1.603739 AGTTTTTGAGGGCTCCCGC 60.604 57.895 1.40 1.40 41.95 6.13
1409 4846 1.901464 GTTTTTGAGGGCTCCCGCA 60.901 57.895 7.32 7.32 43.94 5.69
1410 4847 1.901464 TTTTTGAGGGCTCCCGCAC 60.901 57.895 11.00 2.36 45.23 5.34
1411 4848 2.632602 TTTTTGAGGGCTCCCGCACA 62.633 55.000 11.00 1.99 45.23 4.57
1412 4849 2.632602 TTTTGAGGGCTCCCGCACAA 62.633 55.000 11.00 8.42 45.23 3.33
1413 4850 3.842925 TTGAGGGCTCCCGCACAAC 62.843 63.158 11.00 0.00 45.23 3.32
1419 4856 3.345808 CTCCCGCACAACCACGTG 61.346 66.667 9.08 9.08 40.00 4.49
1420 4857 4.920112 TCCCGCACAACCACGTGG 62.920 66.667 32.83 32.83 37.37 4.94
1447 4884 4.262089 TGGCCACCACATGTCGCA 62.262 61.111 0.00 0.00 0.00 5.10
1448 4885 2.751436 GGCCACCACATGTCGCAT 60.751 61.111 0.00 0.00 0.00 4.73
1449 4886 1.451207 GGCCACCACATGTCGCATA 60.451 57.895 0.00 0.00 0.00 3.14
1450 4887 0.819259 GGCCACCACATGTCGCATAT 60.819 55.000 0.00 0.00 0.00 1.78
1451 4888 1.024271 GCCACCACATGTCGCATATT 58.976 50.000 0.00 0.00 0.00 1.28
1452 4889 1.268692 GCCACCACATGTCGCATATTG 60.269 52.381 0.00 0.00 0.00 1.90
1453 4890 1.268692 CCACCACATGTCGCATATTGC 60.269 52.381 0.00 0.00 40.69 3.56
1454 4891 1.024271 ACCACATGTCGCATATTGCC 58.976 50.000 0.00 0.00 41.12 4.52
1455 4892 0.041047 CCACATGTCGCATATTGCCG 60.041 55.000 0.00 0.00 41.12 5.69
1456 4893 0.658244 CACATGTCGCATATTGCCGC 60.658 55.000 0.00 0.00 41.12 6.53
1457 4894 1.094650 ACATGTCGCATATTGCCGCA 61.095 50.000 0.00 0.00 41.12 5.69
1458 4895 0.658244 CATGTCGCATATTGCCGCAC 60.658 55.000 0.00 0.00 41.12 5.34
1459 4896 1.785041 ATGTCGCATATTGCCGCACC 61.785 55.000 0.00 0.00 41.12 5.01
1460 4897 2.899838 TCGCATATTGCCGCACCC 60.900 61.111 0.00 0.00 41.12 4.61
1461 4898 4.312231 CGCATATTGCCGCACCCG 62.312 66.667 0.00 0.00 41.12 5.28
1462 4899 3.209097 GCATATTGCCGCACCCGT 61.209 61.111 0.00 0.00 37.42 5.28
1463 4900 2.715005 CATATTGCCGCACCCGTG 59.285 61.111 0.00 0.00 0.00 4.94
1464 4901 1.817520 CATATTGCCGCACCCGTGA 60.818 57.895 0.00 0.00 0.00 4.35
1465 4902 1.523711 ATATTGCCGCACCCGTGAG 60.524 57.895 0.00 0.00 0.00 3.51
1466 4903 1.966901 ATATTGCCGCACCCGTGAGA 61.967 55.000 0.00 0.00 31.84 3.27
1467 4904 1.966901 TATTGCCGCACCCGTGAGAT 61.967 55.000 0.00 0.00 31.84 2.75
1468 4905 1.966901 ATTGCCGCACCCGTGAGATA 61.967 55.000 0.00 0.00 31.84 1.98
1469 4906 1.966901 TTGCCGCACCCGTGAGATAT 61.967 55.000 0.00 0.00 31.84 1.63
1470 4907 1.227556 GCCGCACCCGTGAGATATT 60.228 57.895 0.00 0.00 31.84 1.28
1471 4908 1.498865 GCCGCACCCGTGAGATATTG 61.499 60.000 0.00 0.00 31.84 1.90
1472 4909 0.179084 CCGCACCCGTGAGATATTGT 60.179 55.000 0.00 0.00 31.84 2.71
1473 4910 1.209128 CGCACCCGTGAGATATTGTC 58.791 55.000 0.00 0.00 31.84 3.18
1474 4911 1.202417 CGCACCCGTGAGATATTGTCT 60.202 52.381 0.00 0.00 40.81 3.41
1475 4912 2.738643 CGCACCCGTGAGATATTGTCTT 60.739 50.000 0.00 0.00 37.29 3.01
1476 4913 3.270877 GCACCCGTGAGATATTGTCTTT 58.729 45.455 0.00 0.00 37.29 2.52
1477 4914 3.689649 GCACCCGTGAGATATTGTCTTTT 59.310 43.478 0.00 0.00 37.29 2.27
1478 4915 4.156008 GCACCCGTGAGATATTGTCTTTTT 59.844 41.667 0.00 0.00 37.29 1.94
1506 4943 9.692749 TGTCCGTGTTCTCTGATATATATTTTC 57.307 33.333 0.00 0.00 0.00 2.29
1507 4944 9.141400 GTCCGTGTTCTCTGATATATATTTTCC 57.859 37.037 0.00 0.00 0.00 3.13
1508 4945 8.027189 TCCGTGTTCTCTGATATATATTTTCCG 58.973 37.037 0.00 0.00 0.00 4.30
1509 4946 7.275779 CCGTGTTCTCTGATATATATTTTCCGG 59.724 40.741 0.00 0.00 0.00 5.14
1510 4947 7.275779 CGTGTTCTCTGATATATATTTTCCGGG 59.724 40.741 0.00 0.00 0.00 5.73
1511 4948 8.095169 GTGTTCTCTGATATATATTTTCCGGGT 58.905 37.037 0.00 0.00 0.00 5.28
1512 4949 9.316594 TGTTCTCTGATATATATTTTCCGGGTA 57.683 33.333 0.00 0.00 0.00 3.69
1523 4960 5.963176 ATTTTCCGGGTAATTTTACGTGT 57.037 34.783 0.00 0.00 34.50 4.49
1524 4961 5.764487 TTTTCCGGGTAATTTTACGTGTT 57.236 34.783 0.00 0.00 34.50 3.32
1525 4962 5.764487 TTTCCGGGTAATTTTACGTGTTT 57.236 34.783 0.00 0.00 34.50 2.83
1526 4963 5.764487 TTCCGGGTAATTTTACGTGTTTT 57.236 34.783 0.00 0.00 34.50 2.43
1527 4964 6.867662 TTCCGGGTAATTTTACGTGTTTTA 57.132 33.333 0.00 0.00 34.50 1.52
1528 4965 6.867662 TCCGGGTAATTTTACGTGTTTTAA 57.132 33.333 0.00 0.00 34.50 1.52
1529 4966 7.446001 TCCGGGTAATTTTACGTGTTTTAAT 57.554 32.000 0.00 0.00 34.50 1.40
1530 4967 7.303998 TCCGGGTAATTTTACGTGTTTTAATG 58.696 34.615 0.00 0.00 34.50 1.90
1531 4968 7.040823 TCCGGGTAATTTTACGTGTTTTAATGT 60.041 33.333 0.00 0.00 34.50 2.71
1532 4969 7.594386 CCGGGTAATTTTACGTGTTTTAATGTT 59.406 33.333 0.00 0.00 34.50 2.71
1533 4970 8.966194 CGGGTAATTTTACGTGTTTTAATGTTT 58.034 29.630 0.00 0.00 34.50 2.83
1557 4994 9.819267 TTTTTATTGGTTTTCATAGGTTTTCGT 57.181 25.926 0.00 0.00 0.00 3.85
1562 4999 9.990360 ATTGGTTTTCATAGGTTTTCGTAATTT 57.010 25.926 0.00 0.00 0.00 1.82
1563 5000 9.819267 TTGGTTTTCATAGGTTTTCGTAATTTT 57.181 25.926 0.00 0.00 0.00 1.82
1564 5001 9.250624 TGGTTTTCATAGGTTTTCGTAATTTTG 57.749 29.630 0.00 0.00 0.00 2.44
1565 5002 9.251792 GGTTTTCATAGGTTTTCGTAATTTTGT 57.748 29.630 0.00 0.00 0.00 2.83
1646 5083 6.927933 ATTATGTTTTCTTGCGCAAAGTAC 57.072 33.333 25.01 18.36 37.18 2.73
1647 5084 3.766676 TGTTTTCTTGCGCAAAGTACA 57.233 38.095 25.01 20.52 37.18 2.90
1648 5085 4.300189 TGTTTTCTTGCGCAAAGTACAT 57.700 36.364 25.01 0.00 37.18 2.29
1649 5086 4.286910 TGTTTTCTTGCGCAAAGTACATC 58.713 39.130 25.01 11.50 37.18 3.06
1650 5087 3.552604 TTTCTTGCGCAAAGTACATCC 57.447 42.857 25.01 0.00 37.18 3.51
1651 5088 2.472695 TCTTGCGCAAAGTACATCCT 57.527 45.000 25.01 0.00 37.18 3.24
1652 5089 2.076100 TCTTGCGCAAAGTACATCCTG 58.924 47.619 25.01 8.31 37.18 3.86
1653 5090 1.806542 CTTGCGCAAAGTACATCCTGT 59.193 47.619 25.01 0.00 0.00 4.00
1654 5091 1.155889 TGCGCAAAGTACATCCTGTG 58.844 50.000 8.16 0.00 0.00 3.66
1655 5092 1.270571 TGCGCAAAGTACATCCTGTGA 60.271 47.619 8.16 0.00 0.00 3.58
1656 5093 1.804151 GCGCAAAGTACATCCTGTGAA 59.196 47.619 0.30 0.00 0.00 3.18
1657 5094 2.225491 GCGCAAAGTACATCCTGTGAAA 59.775 45.455 0.30 0.00 0.00 2.69
1658 5095 3.304391 GCGCAAAGTACATCCTGTGAAAA 60.304 43.478 0.30 0.00 0.00 2.29
1659 5096 4.791411 GCGCAAAGTACATCCTGTGAAAAA 60.791 41.667 0.30 0.00 0.00 1.94
1660 5097 4.911610 CGCAAAGTACATCCTGTGAAAAAG 59.088 41.667 0.00 0.00 0.00 2.27
1661 5098 4.681483 GCAAAGTACATCCTGTGAAAAAGC 59.319 41.667 0.00 0.00 0.00 3.51
1662 5099 5.735922 GCAAAGTACATCCTGTGAAAAAGCA 60.736 40.000 0.00 0.00 0.00 3.91
1663 5100 5.695851 AAGTACATCCTGTGAAAAAGCAG 57.304 39.130 0.00 0.00 0.00 4.24
1664 5101 4.973168 AGTACATCCTGTGAAAAAGCAGA 58.027 39.130 0.00 0.00 34.87 4.26
1665 5102 4.999950 AGTACATCCTGTGAAAAAGCAGAG 59.000 41.667 0.00 0.00 34.87 3.35
1666 5103 3.825328 ACATCCTGTGAAAAAGCAGAGT 58.175 40.909 0.00 0.00 34.87 3.24
1667 5104 4.210331 ACATCCTGTGAAAAAGCAGAGTT 58.790 39.130 0.00 0.00 34.87 3.01
1668 5105 4.037208 ACATCCTGTGAAAAAGCAGAGTTG 59.963 41.667 0.00 0.00 34.87 3.16
1669 5106 3.620488 TCCTGTGAAAAAGCAGAGTTGT 58.380 40.909 0.00 0.00 34.87 3.32
1670 5107 3.378112 TCCTGTGAAAAAGCAGAGTTGTG 59.622 43.478 0.00 0.00 34.87 3.33
1671 5108 3.378112 CCTGTGAAAAAGCAGAGTTGTGA 59.622 43.478 0.00 0.00 34.87 3.58
1672 5109 4.037208 CCTGTGAAAAAGCAGAGTTGTGAT 59.963 41.667 0.00 0.00 34.87 3.06
1673 5110 5.450965 CCTGTGAAAAAGCAGAGTTGTGATT 60.451 40.000 0.00 0.00 34.87 2.57
1674 5111 5.964758 TGTGAAAAAGCAGAGTTGTGATTT 58.035 33.333 0.00 0.00 37.64 2.17
1675 5112 6.397272 TGTGAAAAAGCAGAGTTGTGATTTT 58.603 32.000 0.15 0.15 45.50 1.82
1676 5113 6.531240 TGTGAAAAAGCAGAGTTGTGATTTTC 59.469 34.615 5.84 8.78 43.41 2.29
1677 5114 5.743398 TGAAAAAGCAGAGTTGTGATTTTCG 59.257 36.000 5.84 0.00 43.41 3.46
1678 5115 5.499139 AAAAGCAGAGTTGTGATTTTCGA 57.501 34.783 0.15 0.00 41.04 3.71
1679 5116 4.739046 AAGCAGAGTTGTGATTTTCGAG 57.261 40.909 0.00 0.00 0.00 4.04
1680 5117 3.995199 AGCAGAGTTGTGATTTTCGAGA 58.005 40.909 0.00 0.00 0.00 4.04
1681 5118 4.573900 AGCAGAGTTGTGATTTTCGAGAT 58.426 39.130 0.00 0.00 0.00 2.75
1682 5119 4.391216 AGCAGAGTTGTGATTTTCGAGATG 59.609 41.667 0.00 0.00 0.00 2.90
1683 5120 4.645956 CAGAGTTGTGATTTTCGAGATGC 58.354 43.478 0.00 0.00 0.00 3.91
1684 5121 4.152938 CAGAGTTGTGATTTTCGAGATGCA 59.847 41.667 0.00 0.00 0.00 3.96
1685 5122 4.153117 AGAGTTGTGATTTTCGAGATGCAC 59.847 41.667 0.00 0.00 0.00 4.57
1686 5123 4.067896 AGTTGTGATTTTCGAGATGCACT 58.932 39.130 0.00 0.00 0.00 4.40
1687 5124 4.083643 AGTTGTGATTTTCGAGATGCACTG 60.084 41.667 0.00 0.00 0.00 3.66
1688 5125 2.743664 TGTGATTTTCGAGATGCACTGG 59.256 45.455 0.00 0.00 0.00 4.00
1689 5126 2.744202 GTGATTTTCGAGATGCACTGGT 59.256 45.455 0.00 0.00 0.00 4.00
1690 5127 3.932710 GTGATTTTCGAGATGCACTGGTA 59.067 43.478 0.00 0.00 0.00 3.25
1691 5128 4.572389 GTGATTTTCGAGATGCACTGGTAT 59.428 41.667 0.00 0.00 0.00 2.73
1692 5129 5.065218 GTGATTTTCGAGATGCACTGGTATT 59.935 40.000 0.00 0.00 0.00 1.89
1693 5130 5.647658 TGATTTTCGAGATGCACTGGTATTT 59.352 36.000 0.00 0.00 0.00 1.40
1694 5131 5.545658 TTTTCGAGATGCACTGGTATTTC 57.454 39.130 0.00 0.00 0.00 2.17
1695 5132 4.471904 TTCGAGATGCACTGGTATTTCT 57.528 40.909 0.00 0.00 0.00 2.52
1696 5133 4.471904 TCGAGATGCACTGGTATTTCTT 57.528 40.909 0.00 0.00 0.00 2.52
1697 5134 4.832248 TCGAGATGCACTGGTATTTCTTT 58.168 39.130 0.00 0.00 0.00 2.52
1698 5135 4.870426 TCGAGATGCACTGGTATTTCTTTC 59.130 41.667 0.00 0.00 0.00 2.62
1699 5136 4.034510 CGAGATGCACTGGTATTTCTTTCC 59.965 45.833 0.00 0.00 0.00 3.13
1700 5137 5.184892 AGATGCACTGGTATTTCTTTCCT 57.815 39.130 0.00 0.00 0.00 3.36
1701 5138 6.313519 AGATGCACTGGTATTTCTTTCCTA 57.686 37.500 0.00 0.00 0.00 2.94
1702 5139 6.116126 AGATGCACTGGTATTTCTTTCCTAC 58.884 40.000 0.00 0.00 0.00 3.18
1703 5140 4.585879 TGCACTGGTATTTCTTTCCTACC 58.414 43.478 0.00 0.00 36.30 3.18
1704 5141 4.042311 TGCACTGGTATTTCTTTCCTACCA 59.958 41.667 0.00 0.00 41.93 3.25
1705 5142 5.193679 GCACTGGTATTTCTTTCCTACCAT 58.806 41.667 1.44 0.00 42.89 3.55
1706 5143 6.069905 TGCACTGGTATTTCTTTCCTACCATA 60.070 38.462 1.44 0.00 42.89 2.74
1707 5144 6.998673 GCACTGGTATTTCTTTCCTACCATAT 59.001 38.462 1.44 0.00 42.89 1.78
1708 5145 7.502561 GCACTGGTATTTCTTTCCTACCATATT 59.497 37.037 1.44 0.00 42.89 1.28
1709 5146 9.408648 CACTGGTATTTCTTTCCTACCATATTT 57.591 33.333 1.44 0.00 42.89 1.40
1710 5147 9.990868 ACTGGTATTTCTTTCCTACCATATTTT 57.009 29.630 1.44 0.00 42.89 1.82
1712 5149 9.762381 TGGTATTTCTTTCCTACCATATTTTGT 57.238 29.630 0.00 0.00 39.89 2.83
1751 5188 7.229581 AGTATTTTAGATCTAGGCTTACGGG 57.770 40.000 2.02 0.00 0.00 5.28
1752 5189 6.781507 AGTATTTTAGATCTAGGCTTACGGGT 59.218 38.462 2.02 0.00 0.00 5.28
1753 5190 5.526506 TTTTAGATCTAGGCTTACGGGTC 57.473 43.478 2.02 0.00 0.00 4.46
1754 5191 2.750141 AGATCTAGGCTTACGGGTCA 57.250 50.000 0.00 0.00 0.00 4.02
1755 5192 3.028094 AGATCTAGGCTTACGGGTCAA 57.972 47.619 0.00 0.00 0.00 3.18
1756 5193 3.371965 AGATCTAGGCTTACGGGTCAAA 58.628 45.455 0.00 0.00 0.00 2.69
1757 5194 3.773119 AGATCTAGGCTTACGGGTCAAAA 59.227 43.478 0.00 0.00 0.00 2.44
1758 5195 4.224370 AGATCTAGGCTTACGGGTCAAAAA 59.776 41.667 0.00 0.00 0.00 1.94
1808 5245 8.161699 TCATGTAAGAGTTTGGTCCTTTTTAC 57.838 34.615 0.00 0.00 0.00 2.01
1822 5259 9.223099 TGGTCCTTTTTACTGTTAATTAGCTAC 57.777 33.333 0.00 0.00 0.00 3.58
1870 5308 7.875327 AGGTATTTAATGAAGGTAAACGCAT 57.125 32.000 0.00 0.00 0.00 4.73
1877 5315 8.973835 TTAATGAAGGTAAACGCATTTAAAGG 57.026 30.769 0.00 0.00 32.04 3.11
1881 5319 4.805219 AGGTAAACGCATTTAAAGGCTTG 58.195 39.130 21.19 10.22 32.04 4.01
1893 5331 8.302438 GCATTTAAAGGCTTGAATATAGCAGAT 58.698 33.333 17.15 0.00 40.42 2.90
1897 5335 9.712305 TTAAAGGCTTGAATATAGCAGATAGAC 57.288 33.333 0.00 0.00 40.42 2.59
1898 5336 7.552050 AAGGCTTGAATATAGCAGATAGACT 57.448 36.000 0.00 0.00 40.42 3.24
1899 5337 7.552050 AGGCTTGAATATAGCAGATAGACTT 57.448 36.000 0.00 0.00 40.42 3.01
1980 5425 2.457366 ACACTAACAAGGAAGGAGCG 57.543 50.000 0.00 0.00 0.00 5.03
1983 5428 1.697982 ACTAACAAGGAAGGAGCGGTT 59.302 47.619 0.00 0.00 0.00 4.44
2009 5454 6.385649 TTCGAAAGCAAACCAGTCTATTTT 57.614 33.333 0.00 0.00 0.00 1.82
2014 5459 8.638565 CGAAAGCAAACCAGTCTATTTTAAATG 58.361 33.333 0.00 0.00 0.00 2.32
2015 5460 7.889589 AAGCAAACCAGTCTATTTTAAATGC 57.110 32.000 0.00 0.00 0.00 3.56
2019 5464 7.702348 GCAAACCAGTCTATTTTAAATGCCTAG 59.298 37.037 0.00 0.00 0.00 3.02
2101 5546 8.662781 AAATCATACATGTAGTGGTGTGTATC 57.337 34.615 11.91 0.00 36.05 2.24
2136 5581 6.801539 AAAATCAAGTTAATCGACAGAGCA 57.198 33.333 0.00 0.00 0.00 4.26
2137 5582 6.414408 AAATCAAGTTAATCGACAGAGCAG 57.586 37.500 0.00 0.00 0.00 4.24
2140 5590 0.299003 GTTAATCGACAGAGCAGCGC 59.701 55.000 0.00 0.00 0.00 5.92
2146 5596 1.373999 GACAGAGCAGCGCTTCACT 60.374 57.895 7.50 3.45 39.88 3.41
2151 5601 2.428071 GCAGCGCTTCACTTGCAC 60.428 61.111 7.50 0.00 36.59 4.57
2159 5609 1.268743 GCTTCACTTGCACACTTGACC 60.269 52.381 0.00 0.00 0.00 4.02
2164 5614 0.738389 CTTGCACACTTGACCCGTTT 59.262 50.000 0.00 0.00 0.00 3.60
2170 5620 1.489230 ACACTTGACCCGTTTCCTCTT 59.511 47.619 0.00 0.00 0.00 2.85
2171 5621 2.701951 ACACTTGACCCGTTTCCTCTTA 59.298 45.455 0.00 0.00 0.00 2.10
2187 5637 9.117183 GTTTCCTCTTAAAACCTAGTTTCTTCA 57.883 33.333 0.00 0.00 34.43 3.02
2190 5640 7.817962 TCCTCTTAAAACCTAGTTTCTTCATCG 59.182 37.037 0.00 0.00 34.43 3.84
2210 5660 3.277142 GGAGATGGTCCGGTTTGTAAT 57.723 47.619 0.00 0.00 34.84 1.89
2211 5661 3.617284 GGAGATGGTCCGGTTTGTAATT 58.383 45.455 0.00 0.00 34.84 1.40
2214 5664 4.777463 AGATGGTCCGGTTTGTAATTAGG 58.223 43.478 0.00 0.00 0.00 2.69
2225 5675 6.183360 CGGTTTGTAATTAGGCTACGTGAAAT 60.183 38.462 0.00 0.00 0.00 2.17
2230 5680 8.556213 TGTAATTAGGCTACGTGAAATCTTTT 57.444 30.769 0.00 0.00 0.00 2.27
2236 5686 5.473504 AGGCTACGTGAAATCTTTTGTGAAT 59.526 36.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.629017 ATTCTGCCCATTTCCCACTT 57.371 45.000 0.00 0.00 0.00 3.16
66 67 0.331278 ATTTGGAATCCAGGCGTCCA 59.669 50.000 0.86 6.81 39.70 4.02
120 121 2.289257 GCTACCTTCCGTAACAACTGGT 60.289 50.000 0.00 0.00 0.00 4.00
228 229 2.298729 TCATGTTGCGATATCGGGATCA 59.701 45.455 25.51 12.55 40.23 2.92
394 397 3.321968 ACAAGCAAGTTTCCAAATCCTCC 59.678 43.478 0.00 0.00 0.00 4.30
445 448 2.688958 GGGAGAGTACTGTGAAGCGTAT 59.311 50.000 0.00 0.00 0.00 3.06
449 452 0.889306 ACGGGAGAGTACTGTGAAGC 59.111 55.000 0.00 0.00 0.00 3.86
458 461 2.183478 TAACACGACACGGGAGAGTA 57.817 50.000 0.00 0.00 32.98 2.59
464 467 1.723003 GCTAACTTAACACGACACGGG 59.277 52.381 0.00 0.00 35.82 5.28
479 482 5.513495 CGAGACTTTCACATGTCTAGCTAAC 59.487 44.000 0.00 0.00 42.79 2.34
511 517 1.605992 CCAGATGAGCAGGCAGGAA 59.394 57.895 0.00 0.00 0.00 3.36
546 552 7.443879 TGCTTTGTCACATAGAAACAACAGATA 59.556 33.333 0.00 0.00 32.94 1.98
583 589 2.510382 TCGTCCATCCCTAGTCTTCTCT 59.490 50.000 0.00 0.00 0.00 3.10
618 624 6.044046 CACCCGCATAGTATACTTTACAACA 58.956 40.000 11.40 0.00 0.00 3.33
619 625 6.275335 TCACCCGCATAGTATACTTTACAAC 58.725 40.000 11.40 0.00 0.00 3.32
627 633 1.616865 TGCCTCACCCGCATAGTATAC 59.383 52.381 0.00 0.00 0.00 1.47
630 636 0.686441 ACTGCCTCACCCGCATAGTA 60.686 55.000 0.00 0.00 35.25 1.82
648 654 9.403583 TGGTAATGAAAGTAAATATCCCAAGAC 57.596 33.333 0.00 0.00 0.00 3.01
704 710 2.598589 GCAATCATGTCACGCACATTT 58.401 42.857 0.00 0.00 43.89 2.32
757 763 7.224297 AGTAGTCTCATTGTGTACCAATTTGT 58.776 34.615 6.79 0.00 41.93 2.83
813 819 0.890542 AAATTGGCAGTGAGAGCGCA 60.891 50.000 11.47 0.00 0.00 6.09
911 917 2.599408 TACCTCCCCGATCATACCTC 57.401 55.000 0.00 0.00 0.00 3.85
912 918 3.562108 AATACCTCCCCGATCATACCT 57.438 47.619 0.00 0.00 0.00 3.08
917 923 4.464652 TCTCTTAATACCTCCCCGATCA 57.535 45.455 0.00 0.00 0.00 2.92
926 932 7.624077 ACCTACCTTTGTCATCTCTTAATACCT 59.376 37.037 0.00 0.00 0.00 3.08
930 936 7.918076 TGAACCTACCTTTGTCATCTCTTAAT 58.082 34.615 0.00 0.00 0.00 1.40
990 4427 1.135859 GCTTCAGCCATCAACACTTCG 60.136 52.381 0.00 0.00 34.31 3.79
993 4430 2.283145 AAGCTTCAGCCATCAACACT 57.717 45.000 0.00 0.00 43.38 3.55
1026 4463 1.089481 TTTGCGCAAGAGATAGGCCG 61.089 55.000 23.68 0.00 43.02 6.13
1035 4472 2.668212 CCCGTCCTTTGCGCAAGA 60.668 61.111 23.68 15.38 43.02 3.02
1087 4524 2.417379 CGTTCATGGTCTCGATCACCTT 60.417 50.000 13.42 5.91 34.66 3.50
1125 4562 0.251742 AAATTGTAGCTGCTGCCCCA 60.252 50.000 13.43 6.33 40.80 4.96
1147 4584 5.107104 CGCAAGCTAAGTGAAAACAGTCATA 60.107 40.000 0.00 0.00 0.00 2.15
1185 4622 7.359097 GCTTCTCTATTACAATGCTCGAATCTG 60.359 40.741 0.00 0.00 0.00 2.90
1262 4699 0.911769 TGGTTCCTCGAGCCAATCAT 59.088 50.000 6.99 0.00 39.86 2.45
1366 4803 1.684734 CTGGTAGGGGGTACACGCT 60.685 63.158 19.57 19.57 37.42 5.07
1367 4804 2.897972 CTGGTAGGGGGTACACGC 59.102 66.667 3.50 3.50 32.62 5.34
1368 4805 2.897972 GCTGGTAGGGGGTACACG 59.102 66.667 0.00 0.00 32.62 4.49
1369 4806 2.728435 CCGCTGGTAGGGGGTACAC 61.728 68.421 4.16 0.00 43.90 2.90
1370 4807 2.364579 CCGCTGGTAGGGGGTACA 60.365 66.667 4.16 0.00 43.90 2.90
1379 4816 0.179015 TCAAAAACTGCCCGCTGGTA 60.179 50.000 0.00 0.00 0.00 3.25
1380 4817 1.454847 TCAAAAACTGCCCGCTGGT 60.455 52.632 0.00 0.00 0.00 4.00
1381 4818 1.286880 CTCAAAAACTGCCCGCTGG 59.713 57.895 0.00 0.00 0.00 4.85
1382 4819 1.286880 CCTCAAAAACTGCCCGCTG 59.713 57.895 0.00 0.00 0.00 5.18
1383 4820 1.903404 CCCTCAAAAACTGCCCGCT 60.903 57.895 0.00 0.00 0.00 5.52
1384 4821 2.650778 CCCTCAAAAACTGCCCGC 59.349 61.111 0.00 0.00 0.00 6.13
1385 4822 1.866853 GAGCCCTCAAAAACTGCCCG 61.867 60.000 0.00 0.00 0.00 6.13
1386 4823 1.536073 GGAGCCCTCAAAAACTGCCC 61.536 60.000 0.00 0.00 0.00 5.36
1387 4824 1.536073 GGGAGCCCTCAAAAACTGCC 61.536 60.000 0.00 0.00 33.29 4.85
1388 4825 1.866853 CGGGAGCCCTCAAAAACTGC 61.867 60.000 3.70 0.00 0.00 4.40
1389 4826 2.257353 CGGGAGCCCTCAAAAACTG 58.743 57.895 3.70 0.00 0.00 3.16
1390 4827 4.821935 CGGGAGCCCTCAAAAACT 57.178 55.556 3.70 0.00 0.00 2.66
1402 4839 3.345808 CACGTGGTTGTGCGGGAG 61.346 66.667 7.95 0.00 32.58 4.30
1403 4840 4.920112 CCACGTGGTTGTGCGGGA 62.920 66.667 26.95 0.00 38.55 5.14
1433 4870 1.268692 GCAATATGCGACATGTGGTGG 60.269 52.381 1.15 0.00 31.71 4.61
1434 4871 1.268692 GGCAATATGCGACATGTGGTG 60.269 52.381 1.15 0.00 46.21 4.17
1435 4872 1.024271 GGCAATATGCGACATGTGGT 58.976 50.000 1.15 0.00 46.21 4.16
1436 4873 0.041047 CGGCAATATGCGACATGTGG 60.041 55.000 1.15 2.26 46.21 4.17
1437 4874 0.658244 GCGGCAATATGCGACATGTG 60.658 55.000 1.15 0.00 46.21 3.21
1438 4875 1.094650 TGCGGCAATATGCGACATGT 61.095 50.000 0.00 0.00 46.21 3.21
1439 4876 0.658244 GTGCGGCAATATGCGACATG 60.658 55.000 3.23 0.00 46.21 3.21
1440 4877 1.648720 GTGCGGCAATATGCGACAT 59.351 52.632 3.23 0.00 46.21 3.06
1441 4878 2.468670 GGTGCGGCAATATGCGACA 61.469 57.895 3.23 0.00 46.21 4.35
1442 4879 2.327940 GGTGCGGCAATATGCGAC 59.672 61.111 3.23 0.00 46.21 5.19
1443 4880 2.899838 GGGTGCGGCAATATGCGA 60.900 61.111 3.23 0.00 46.21 5.10
1444 4881 4.312231 CGGGTGCGGCAATATGCG 62.312 66.667 3.23 0.00 46.21 4.73
1445 4882 3.209097 ACGGGTGCGGCAATATGC 61.209 61.111 3.23 0.00 44.08 3.14
1446 4883 1.775039 CTCACGGGTGCGGCAATATG 61.775 60.000 3.23 1.12 0.00 1.78
1447 4884 1.523711 CTCACGGGTGCGGCAATAT 60.524 57.895 3.23 0.00 0.00 1.28
1448 4885 1.966901 ATCTCACGGGTGCGGCAATA 61.967 55.000 3.23 0.00 0.00 1.90
1449 4886 1.966901 TATCTCACGGGTGCGGCAAT 61.967 55.000 3.23 0.00 0.00 3.56
1450 4887 1.966901 ATATCTCACGGGTGCGGCAA 61.967 55.000 3.23 0.00 0.00 4.52
1451 4888 1.966901 AATATCTCACGGGTGCGGCA 61.967 55.000 0.00 0.00 0.00 5.69
1452 4889 1.227556 AATATCTCACGGGTGCGGC 60.228 57.895 0.00 0.00 0.00 6.53
1453 4890 0.179084 ACAATATCTCACGGGTGCGG 60.179 55.000 0.00 0.00 0.00 5.69
1454 4891 1.202417 AGACAATATCTCACGGGTGCG 60.202 52.381 0.00 0.00 28.16 5.34
1455 4892 2.604046 AGACAATATCTCACGGGTGC 57.396 50.000 0.00 0.00 28.16 5.01
1456 4893 5.880054 AAAAAGACAATATCTCACGGGTG 57.120 39.130 0.00 0.00 36.27 4.61
1480 4917 9.692749 GAAAATATATATCAGAGAACACGGACA 57.307 33.333 0.00 0.00 0.00 4.02
1481 4918 9.141400 GGAAAATATATATCAGAGAACACGGAC 57.859 37.037 0.00 0.00 0.00 4.79
1482 4919 8.027189 CGGAAAATATATATCAGAGAACACGGA 58.973 37.037 0.00 0.00 0.00 4.69
1483 4920 7.275779 CCGGAAAATATATATCAGAGAACACGG 59.724 40.741 0.00 0.00 0.00 4.94
1484 4921 7.275779 CCCGGAAAATATATATCAGAGAACACG 59.724 40.741 0.73 0.00 0.00 4.49
1485 4922 8.095169 ACCCGGAAAATATATATCAGAGAACAC 58.905 37.037 0.73 0.00 0.00 3.32
1486 4923 8.202461 ACCCGGAAAATATATATCAGAGAACA 57.798 34.615 0.73 0.00 0.00 3.18
1497 4934 9.341078 ACACGTAAAATTACCCGGAAAATATAT 57.659 29.630 0.73 0.00 0.00 0.86
1498 4935 8.729805 ACACGTAAAATTACCCGGAAAATATA 57.270 30.769 0.73 0.00 0.00 0.86
1499 4936 7.628769 ACACGTAAAATTACCCGGAAAATAT 57.371 32.000 0.73 0.00 0.00 1.28
1500 4937 7.446001 AACACGTAAAATTACCCGGAAAATA 57.554 32.000 0.73 0.00 0.00 1.40
1501 4938 5.963176 ACACGTAAAATTACCCGGAAAAT 57.037 34.783 0.73 0.00 0.00 1.82
1502 4939 5.764487 AACACGTAAAATTACCCGGAAAA 57.236 34.783 0.73 0.00 0.00 2.29
1503 4940 5.764487 AAACACGTAAAATTACCCGGAAA 57.236 34.783 0.73 0.00 0.00 3.13
1504 4941 5.764487 AAAACACGTAAAATTACCCGGAA 57.236 34.783 0.73 0.00 0.00 4.30
1505 4942 6.867662 TTAAAACACGTAAAATTACCCGGA 57.132 33.333 0.73 0.00 0.00 5.14
1506 4943 7.083230 ACATTAAAACACGTAAAATTACCCGG 58.917 34.615 0.00 0.00 0.00 5.73
1507 4944 8.504812 AACATTAAAACACGTAAAATTACCCG 57.495 30.769 0.00 0.00 0.00 5.28
1531 4968 9.819267 ACGAAAACCTATGAAAACCAATAAAAA 57.181 25.926 0.00 0.00 0.00 1.94
1536 4973 9.990360 AAATTACGAAAACCTATGAAAACCAAT 57.010 25.926 0.00 0.00 0.00 3.16
1537 4974 9.819267 AAAATTACGAAAACCTATGAAAACCAA 57.181 25.926 0.00 0.00 0.00 3.67
1538 4975 9.250624 CAAAATTACGAAAACCTATGAAAACCA 57.749 29.630 0.00 0.00 0.00 3.67
1539 4976 9.251792 ACAAAATTACGAAAACCTATGAAAACC 57.748 29.630 0.00 0.00 0.00 3.27
1620 5057 9.710979 GTACTTTGCGCAAGAAAACATAATATA 57.289 29.630 23.68 1.89 40.83 0.86
1621 5058 8.240682 TGTACTTTGCGCAAGAAAACATAATAT 58.759 29.630 23.68 0.00 40.83 1.28
1622 5059 7.585867 TGTACTTTGCGCAAGAAAACATAATA 58.414 30.769 23.68 2.58 40.83 0.98
1623 5060 6.442952 TGTACTTTGCGCAAGAAAACATAAT 58.557 32.000 23.68 0.00 40.83 1.28
1624 5061 5.822278 TGTACTTTGCGCAAGAAAACATAA 58.178 33.333 23.68 3.94 40.83 1.90
1625 5062 5.425577 TGTACTTTGCGCAAGAAAACATA 57.574 34.783 23.68 4.73 40.83 2.29
1626 5063 4.300189 TGTACTTTGCGCAAGAAAACAT 57.700 36.364 23.68 7.39 40.83 2.71
1627 5064 3.766676 TGTACTTTGCGCAAGAAAACA 57.233 38.095 23.68 20.97 40.83 2.83
1628 5065 3.668656 GGATGTACTTTGCGCAAGAAAAC 59.331 43.478 23.68 18.83 40.83 2.43
1629 5066 3.568007 AGGATGTACTTTGCGCAAGAAAA 59.432 39.130 23.68 7.56 44.36 2.29
1630 5067 3.058293 CAGGATGTACTTTGCGCAAGAAA 60.058 43.478 23.68 7.96 43.02 2.52
1631 5068 2.483877 CAGGATGTACTTTGCGCAAGAA 59.516 45.455 23.68 8.77 43.02 2.52
1632 5069 2.076100 CAGGATGTACTTTGCGCAAGA 58.924 47.619 23.68 13.19 43.02 3.02
1633 5070 2.532531 CAGGATGTACTTTGCGCAAG 57.467 50.000 23.68 18.71 38.64 4.01
1646 5083 4.037208 ACAACTCTGCTTTTTCACAGGATG 59.963 41.667 0.00 0.00 46.00 3.51
1647 5084 4.037208 CACAACTCTGCTTTTTCACAGGAT 59.963 41.667 0.00 0.00 34.57 3.24
1648 5085 3.378112 CACAACTCTGCTTTTTCACAGGA 59.622 43.478 0.00 0.00 34.57 3.86
1649 5086 3.378112 TCACAACTCTGCTTTTTCACAGG 59.622 43.478 0.00 0.00 34.57 4.00
1650 5087 4.621068 TCACAACTCTGCTTTTTCACAG 57.379 40.909 0.00 0.00 35.15 3.66
1651 5088 5.581126 AATCACAACTCTGCTTTTTCACA 57.419 34.783 0.00 0.00 0.00 3.58
1652 5089 6.291269 CGAAAATCACAACTCTGCTTTTTCAC 60.291 38.462 0.00 0.00 32.70 3.18
1653 5090 5.743398 CGAAAATCACAACTCTGCTTTTTCA 59.257 36.000 0.00 0.00 32.70 2.69
1654 5091 5.971202 TCGAAAATCACAACTCTGCTTTTTC 59.029 36.000 0.00 0.00 31.34 2.29
1655 5092 5.890334 TCGAAAATCACAACTCTGCTTTTT 58.110 33.333 0.00 0.00 0.00 1.94
1656 5093 5.296780 TCTCGAAAATCACAACTCTGCTTTT 59.703 36.000 0.00 0.00 0.00 2.27
1657 5094 4.816385 TCTCGAAAATCACAACTCTGCTTT 59.184 37.500 0.00 0.00 0.00 3.51
1658 5095 4.380531 TCTCGAAAATCACAACTCTGCTT 58.619 39.130 0.00 0.00 0.00 3.91
1659 5096 3.995199 TCTCGAAAATCACAACTCTGCT 58.005 40.909 0.00 0.00 0.00 4.24
1660 5097 4.645956 CATCTCGAAAATCACAACTCTGC 58.354 43.478 0.00 0.00 0.00 4.26
1661 5098 4.152938 TGCATCTCGAAAATCACAACTCTG 59.847 41.667 0.00 0.00 0.00 3.35
1662 5099 4.153117 GTGCATCTCGAAAATCACAACTCT 59.847 41.667 0.00 0.00 0.00 3.24
1663 5100 4.153117 AGTGCATCTCGAAAATCACAACTC 59.847 41.667 0.00 0.00 0.00 3.01
1664 5101 4.067896 AGTGCATCTCGAAAATCACAACT 58.932 39.130 0.00 0.00 0.00 3.16
1665 5102 4.153986 CAGTGCATCTCGAAAATCACAAC 58.846 43.478 0.00 0.00 0.00 3.32
1666 5103 3.189080 CCAGTGCATCTCGAAAATCACAA 59.811 43.478 0.00 0.00 0.00 3.33
1667 5104 2.743664 CCAGTGCATCTCGAAAATCACA 59.256 45.455 0.00 0.00 0.00 3.58
1668 5105 2.744202 ACCAGTGCATCTCGAAAATCAC 59.256 45.455 0.00 0.00 0.00 3.06
1669 5106 3.057969 ACCAGTGCATCTCGAAAATCA 57.942 42.857 0.00 0.00 0.00 2.57
1670 5107 5.741388 AATACCAGTGCATCTCGAAAATC 57.259 39.130 0.00 0.00 0.00 2.17
1671 5108 5.882557 AGAAATACCAGTGCATCTCGAAAAT 59.117 36.000 0.00 0.00 0.00 1.82
1672 5109 5.245531 AGAAATACCAGTGCATCTCGAAAA 58.754 37.500 0.00 0.00 0.00 2.29
1673 5110 4.832248 AGAAATACCAGTGCATCTCGAAA 58.168 39.130 0.00 0.00 0.00 3.46
1674 5111 4.471904 AGAAATACCAGTGCATCTCGAA 57.528 40.909 0.00 0.00 0.00 3.71
1675 5112 4.471904 AAGAAATACCAGTGCATCTCGA 57.528 40.909 0.00 0.00 0.00 4.04
1676 5113 4.034510 GGAAAGAAATACCAGTGCATCTCG 59.965 45.833 0.00 0.00 0.00 4.04
1677 5114 5.189180 AGGAAAGAAATACCAGTGCATCTC 58.811 41.667 0.00 0.00 0.00 2.75
1678 5115 5.184892 AGGAAAGAAATACCAGTGCATCT 57.815 39.130 0.00 0.00 0.00 2.90
1679 5116 5.297029 GGTAGGAAAGAAATACCAGTGCATC 59.703 44.000 0.00 0.00 39.05 3.91
1680 5117 5.193679 GGTAGGAAAGAAATACCAGTGCAT 58.806 41.667 0.00 0.00 39.05 3.96
1681 5118 4.042311 TGGTAGGAAAGAAATACCAGTGCA 59.958 41.667 0.00 0.00 43.06 4.57
1682 5119 4.585879 TGGTAGGAAAGAAATACCAGTGC 58.414 43.478 0.00 0.00 43.06 4.40
1725 5162 8.800332 CCCGTAAGCCTAGATCTAAAATACTAA 58.200 37.037 3.57 0.00 0.00 2.24
1726 5163 7.946776 ACCCGTAAGCCTAGATCTAAAATACTA 59.053 37.037 3.57 0.00 0.00 1.82
1727 5164 6.781507 ACCCGTAAGCCTAGATCTAAAATACT 59.218 38.462 3.57 0.00 0.00 2.12
1728 5165 6.990798 ACCCGTAAGCCTAGATCTAAAATAC 58.009 40.000 3.57 4.67 0.00 1.89
1729 5166 6.779049 TGACCCGTAAGCCTAGATCTAAAATA 59.221 38.462 3.57 0.00 0.00 1.40
1730 5167 5.601313 TGACCCGTAAGCCTAGATCTAAAAT 59.399 40.000 3.57 0.00 0.00 1.82
1731 5168 4.957954 TGACCCGTAAGCCTAGATCTAAAA 59.042 41.667 3.57 0.00 0.00 1.52
1732 5169 4.539726 TGACCCGTAAGCCTAGATCTAAA 58.460 43.478 3.57 0.00 0.00 1.85
1733 5170 4.174704 TGACCCGTAAGCCTAGATCTAA 57.825 45.455 3.57 0.00 0.00 2.10
1734 5171 3.870538 TGACCCGTAAGCCTAGATCTA 57.129 47.619 1.69 1.69 0.00 1.98
1735 5172 2.750141 TGACCCGTAAGCCTAGATCT 57.250 50.000 0.00 0.00 0.00 2.75
1736 5173 3.814005 TTTGACCCGTAAGCCTAGATC 57.186 47.619 0.00 0.00 0.00 2.75
1737 5174 4.563140 TTTTTGACCCGTAAGCCTAGAT 57.437 40.909 0.00 0.00 0.00 1.98
1759 5196 9.253832 TGAATGTTTAAATGATGTACCTTCCAT 57.746 29.630 0.00 0.00 0.00 3.41
1760 5197 8.642935 TGAATGTTTAAATGATGTACCTTCCA 57.357 30.769 0.00 0.00 0.00 3.53
1761 5198 9.520204 CATGAATGTTTAAATGATGTACCTTCC 57.480 33.333 0.00 0.00 0.00 3.46
1780 5217 6.824305 AAGGACCAAACTCTTACATGAATG 57.176 37.500 0.00 0.00 0.00 2.67
1781 5218 7.839680 AAAAGGACCAAACTCTTACATGAAT 57.160 32.000 0.00 0.00 0.00 2.57
1784 5221 8.076178 CAGTAAAAAGGACCAAACTCTTACATG 58.924 37.037 0.00 0.00 0.00 3.21
1858 5296 5.010213 TCAAGCCTTTAAATGCGTTTACCTT 59.990 36.000 10.66 8.31 29.82 3.50
1866 5304 6.437928 TGCTATATTCAAGCCTTTAAATGCG 58.562 36.000 9.43 0.00 39.30 4.73
1867 5305 7.651808 TCTGCTATATTCAAGCCTTTAAATGC 58.348 34.615 7.32 7.32 39.30 3.56
1877 5315 8.824159 TTCAAGTCTATCTGCTATATTCAAGC 57.176 34.615 0.00 0.00 40.50 4.01
1893 5331 6.705381 CCAAATTTGGCATTGTTTCAAGTCTA 59.295 34.615 23.81 0.00 42.21 2.59
1895 5333 5.750650 CCAAATTTGGCATTGTTTCAAGTC 58.249 37.500 23.81 0.00 42.21 3.01
1954 5398 7.521585 CGCTCCTTCCTTGTTAGTGTTTTAATT 60.522 37.037 0.00 0.00 0.00 1.40
1955 5399 6.072673 CGCTCCTTCCTTGTTAGTGTTTTAAT 60.073 38.462 0.00 0.00 0.00 1.40
1956 5400 5.237779 CGCTCCTTCCTTGTTAGTGTTTTAA 59.762 40.000 0.00 0.00 0.00 1.52
1957 5401 4.753107 CGCTCCTTCCTTGTTAGTGTTTTA 59.247 41.667 0.00 0.00 0.00 1.52
1958 5402 3.564225 CGCTCCTTCCTTGTTAGTGTTTT 59.436 43.478 0.00 0.00 0.00 2.43
1959 5403 3.139077 CGCTCCTTCCTTGTTAGTGTTT 58.861 45.455 0.00 0.00 0.00 2.83
1990 5435 7.387673 GGCATTTAAAATAGACTGGTTTGCTTT 59.612 33.333 0.00 0.00 0.00 3.51
1992 5437 6.211384 AGGCATTTAAAATAGACTGGTTTGCT 59.789 34.615 0.00 0.00 0.00 3.91
1999 5444 9.455847 GCATTTCTAGGCATTTAAAATAGACTG 57.544 33.333 4.75 6.16 0.00 3.51
2000 5445 9.189156 TGCATTTCTAGGCATTTAAAATAGACT 57.811 29.630 0.00 0.00 35.91 3.24
2070 5515 9.461312 ACACCACTACATGTATGATTTACAAAT 57.539 29.630 5.91 0.00 0.00 2.32
2074 5519 7.843490 ACACACCACTACATGTATGATTTAC 57.157 36.000 5.91 0.00 0.00 2.01
2075 5520 9.758651 GATACACACCACTACATGTATGATTTA 57.241 33.333 5.91 0.00 38.16 1.40
2077 5522 6.923508 CGATACACACCACTACATGTATGATT 59.076 38.462 5.91 0.00 38.16 2.57
2080 5525 5.827666 TCGATACACACCACTACATGTATG 58.172 41.667 5.91 4.34 38.16 2.39
2090 5535 2.717580 TCACACTCGATACACACCAC 57.282 50.000 0.00 0.00 0.00 4.16
2116 5561 3.868077 GCTGCTCTGTCGATTAACTTGAT 59.132 43.478 0.00 0.00 0.00 2.57
2122 5567 0.173481 AGCGCTGCTCTGTCGATTAA 59.827 50.000 10.39 0.00 30.62 1.40
2124 5569 1.079543 AAGCGCTGCTCTGTCGATT 60.080 52.632 12.58 0.00 38.25 3.34
2126 5571 2.126307 GAAGCGCTGCTCTGTCGA 60.126 61.111 12.58 0.00 38.25 4.20
2128 5573 0.948141 AAGTGAAGCGCTGCTCTGTC 60.948 55.000 20.36 9.14 38.25 3.51
2130 5575 1.496393 CAAGTGAAGCGCTGCTCTG 59.504 57.895 20.36 10.84 38.25 3.35
2131 5576 2.323580 GCAAGTGAAGCGCTGCTCT 61.324 57.895 18.27 16.19 38.25 4.09
2132 5577 2.175322 GCAAGTGAAGCGCTGCTC 59.825 61.111 18.27 13.77 38.25 4.26
2134 5579 2.428071 GTGCAAGTGAAGCGCTGC 60.428 61.111 12.58 10.71 39.31 5.25
2135 5580 1.369689 GTGTGCAAGTGAAGCGCTG 60.370 57.895 12.58 0.00 42.68 5.18
2136 5581 1.097547 AAGTGTGCAAGTGAAGCGCT 61.098 50.000 2.64 2.64 42.68 5.92
2137 5582 0.931662 CAAGTGTGCAAGTGAAGCGC 60.932 55.000 0.00 0.00 42.56 5.92
2140 5590 1.334869 GGGTCAAGTGTGCAAGTGAAG 59.665 52.381 0.00 0.00 0.00 3.02
2146 5596 0.736053 GAAACGGGTCAAGTGTGCAA 59.264 50.000 0.00 0.00 0.00 4.08
2151 5601 2.256117 AAGAGGAAACGGGTCAAGTG 57.744 50.000 0.00 0.00 0.00 3.16
2159 5609 6.709397 AGAAACTAGGTTTTAAGAGGAAACGG 59.291 38.462 0.00 0.00 35.77 4.44
2164 5614 7.817962 CGATGAAGAAACTAGGTTTTAAGAGGA 59.182 37.037 0.00 0.00 35.77 3.71
2170 5620 7.235935 TCTCCGATGAAGAAACTAGGTTTTA 57.764 36.000 0.00 0.00 35.77 1.52
2171 5621 6.110411 TCTCCGATGAAGAAACTAGGTTTT 57.890 37.500 0.00 0.00 35.77 2.43
2190 5640 2.773993 TTACAAACCGGACCATCTCC 57.226 50.000 9.46 0.00 35.33 3.71
2210 5660 5.992829 TCACAAAAGATTTCACGTAGCCTAA 59.007 36.000 0.00 0.00 0.00 2.69
2211 5661 5.543714 TCACAAAAGATTTCACGTAGCCTA 58.456 37.500 0.00 0.00 0.00 3.93
2214 5664 6.370593 TGATTCACAAAAGATTTCACGTAGC 58.629 36.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.