Multiple sequence alignment - TraesCS2D01G113800

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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 TraesCS2D01G113800 chr2D 100.000 2777 0 0 1 2777 63215552 63218328 0.000000e+00 5129.0
1 TraesCS2D01G113800 chr2D 81.034 232 26 10 695 920 67576109 67576328 4.760000e-38 169.0
2 TraesCS2D01G113800 chr2A 94.405 1841 55 25 671 2487 64348658 64350474 0.000000e+00 2785.0
3 TraesCS2D01G113800 chr2A 90.390 333 17 13 237 558 64013055 64012727 9.190000e-115 424.0
4 TraesCS2D01G113800 chr2A 90.390 333 17 13 237 558 64348325 64348653 9.190000e-115 424.0
5 TraesCS2D01G113800 chr2A 94.841 252 1 1 671 922 64012722 64012483 1.560000e-102 383.0
6 TraesCS2D01G113800 chr2A 93.277 238 4 7 1 238 64014135 64013910 9.530000e-90 340.0
7 TraesCS2D01G113800 chr2A 92.857 238 5 7 1 238 64347245 64347470 4.430000e-88 335.0
8 TraesCS2D01G113800 chr2A 91.943 211 9 4 2567 2777 64350537 64350739 3.500000e-74 289.0
9 TraesCS2D01G113800 chr2A 97.260 73 2 0 922 994 64012452 64012380 1.040000e-24 124.0
10 TraesCS2D01G113800 chr2A 100.000 30 0 0 2494 2523 64350517 64350546 3.860000e-04 56.5
11 TraesCS2D01G113800 chr5D 92.661 109 7 1 557 664 491692748 491692856 3.700000e-34 156.0
12 TraesCS2D01G113800 chr5A 91.892 111 8 1 557 666 663713754 663713644 1.330000e-33 154.0
13 TraesCS2D01G113800 chr6A 89.256 121 11 2 548 666 576195607 576195727 1.720000e-32 150.0
14 TraesCS2D01G113800 chr6A 89.256 121 11 2 548 666 576393134 576393254 1.720000e-32 150.0
15 TraesCS2D01G113800 chr4A 90.435 115 8 3 550 662 36368170 36368283 6.200000e-32 148.0
16 TraesCS2D01G113800 chr4A 87.037 108 12 2 2208 2315 742339615 742339720 1.350000e-23 121.0
17 TraesCS2D01G113800 chr1A 91.667 108 8 1 557 663 321876454 321876347 6.200000e-32 148.0
18 TraesCS2D01G113800 chr1A 89.565 115 10 2 557 670 42115758 42115871 8.020000e-31 145.0
19 TraesCS2D01G113800 chrUn 88.983 118 11 2 557 672 98087547 98087430 8.020000e-31 145.0
20 TraesCS2D01G113800 chr2B 89.565 115 11 1 553 666 706703621 706703735 8.020000e-31 145.0


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 TraesCS2D01G113800 chr2D 63215552 63218328 2776 False 5129.00 5129 100.000 1 2777 1 chr2D.!!$F1 2776
1 TraesCS2D01G113800 chr2A 64347245 64350739 3494 False 777.90 2785 93.919 1 2777 5 chr2A.!!$F1 2776
2 TraesCS2D01G113800 chr2A 64012380 64014135 1755 True 317.75 424 93.942 1 994 4 chr2A.!!$R1 993

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
262 1119 0.034059 CAGAACCTCACGCACCTTCT 59.966 55.0 0.00 0.0 0.0 2.85 F
1248 2149 0.101399 ACGACTCGGATGCTGATGAC 59.899 55.0 2.98 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 2518 0.185901 AACTTGCCAGAAGCCCAGAA 59.814 50.0 0.0 0.00 42.71 3.02 R
2487 3388 1.039068 TGTGTCCTGCAATTGTTGGG 58.961 50.0 7.4 7.16 0.00 4.12 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
178 179 2.408022 CGTAGTCGGCGAAGGAGG 59.592 66.667 12.92 1.40 0.00 4.30
262 1119 0.034059 CAGAACCTCACGCACCTTCT 59.966 55.000 0.00 0.00 0.00 2.85
263 1120 0.759346 AGAACCTCACGCACCTTCTT 59.241 50.000 0.00 0.00 0.00 2.52
264 1121 1.149148 GAACCTCACGCACCTTCTTC 58.851 55.000 0.00 0.00 0.00 2.87
265 1122 0.250338 AACCTCACGCACCTTCTTCC 60.250 55.000 0.00 0.00 0.00 3.46
266 1123 1.376037 CCTCACGCACCTTCTTCCC 60.376 63.158 0.00 0.00 0.00 3.97
285 1142 1.135960 CCTCCTTCATCCCCTTCTCC 58.864 60.000 0.00 0.00 0.00 3.71
291 1148 0.266152 TCATCCCCTTCTCCCTCTCC 59.734 60.000 0.00 0.00 0.00 3.71
293 1150 1.238896 ATCCCCTTCTCCCTCTCCCA 61.239 60.000 0.00 0.00 0.00 4.37
294 1151 1.082954 CCCCTTCTCCCTCTCCCAA 59.917 63.158 0.00 0.00 0.00 4.12
295 1152 0.550147 CCCCTTCTCCCTCTCCCAAA 60.550 60.000 0.00 0.00 0.00 3.28
299 1156 1.557371 CTTCTCCCTCTCCCAAACTCC 59.443 57.143 0.00 0.00 0.00 3.85
300 1157 0.491823 TCTCCCTCTCCCAAACTCCA 59.508 55.000 0.00 0.00 0.00 3.86
301 1158 0.908198 CTCCCTCTCCCAAACTCCAG 59.092 60.000 0.00 0.00 0.00 3.86
302 1159 0.193574 TCCCTCTCCCAAACTCCAGT 59.806 55.000 0.00 0.00 0.00 4.00
303 1160 1.435563 TCCCTCTCCCAAACTCCAGTA 59.564 52.381 0.00 0.00 0.00 2.74
305 1162 2.257207 CCTCTCCCAAACTCCAGTACA 58.743 52.381 0.00 0.00 0.00 2.90
306 1163 2.840651 CCTCTCCCAAACTCCAGTACAT 59.159 50.000 0.00 0.00 0.00 2.29
319 1189 5.885912 ACTCCAGTACATTTCTCTCTCTCTC 59.114 44.000 0.00 0.00 0.00 3.20
329 1199 2.511829 TCTCTCTCGCCGACTCCG 60.512 66.667 0.00 0.00 0.00 4.63
389 1259 2.612115 CTCCCTCCCTTGGCCAGT 60.612 66.667 5.11 0.00 0.00 4.00
409 1279 5.126067 CAGTTATGACCCTGATTTCCGATT 58.874 41.667 0.00 0.00 0.00 3.34
449 1319 4.509600 GTGGATTCTTCATTCGATCTCACC 59.490 45.833 0.00 0.00 0.00 4.02
498 1368 9.959721 AATTAACTAGTCCATGCTCTTCTTTTA 57.040 29.630 0.00 0.00 0.00 1.52
558 1428 8.499403 AAAGAAGCCAGATTTCTGTCTATTAC 57.501 34.615 6.81 0.00 42.27 1.89
559 1429 7.430760 AGAAGCCAGATTTCTGTCTATTACT 57.569 36.000 6.81 0.00 42.27 2.24
562 1432 6.587273 AGCCAGATTTCTGTCTATTACTTCC 58.413 40.000 6.81 0.00 42.27 3.46
563 1433 6.385467 AGCCAGATTTCTGTCTATTACTTCCT 59.615 38.462 6.81 0.00 42.27 3.36
564 1434 6.704050 GCCAGATTTCTGTCTATTACTTCCTC 59.296 42.308 6.81 0.00 42.27 3.71
565 1435 7.633772 GCCAGATTTCTGTCTATTACTTCCTCA 60.634 40.741 6.81 0.00 42.27 3.86
566 1436 8.260818 CCAGATTTCTGTCTATTACTTCCTCAA 58.739 37.037 6.81 0.00 42.27 3.02
567 1437 9.829507 CAGATTTCTGTCTATTACTTCCTCAAT 57.170 33.333 0.00 0.00 39.09 2.57
571 1441 8.703604 TTCTGTCTATTACTTCCTCAATTTCG 57.296 34.615 0.00 0.00 0.00 3.46
572 1442 8.063200 TCTGTCTATTACTTCCTCAATTTCGA 57.937 34.615 0.00 0.00 0.00 3.71
573 1443 8.528643 TCTGTCTATTACTTCCTCAATTTCGAA 58.471 33.333 0.00 0.00 0.00 3.71
574 1444 9.319143 CTGTCTATTACTTCCTCAATTTCGAAT 57.681 33.333 0.00 0.00 0.00 3.34
575 1445 9.667107 TGTCTATTACTTCCTCAATTTCGAATT 57.333 29.630 0.00 0.00 0.00 2.17
581 1451 7.745620 ACTTCCTCAATTTCGAATTACTTGT 57.254 32.000 0.00 0.00 0.00 3.16
582 1452 7.807680 ACTTCCTCAATTTCGAATTACTTGTC 58.192 34.615 0.00 0.00 0.00 3.18
583 1453 6.403333 TCCTCAATTTCGAATTACTTGTCG 57.597 37.500 0.00 0.00 38.62 4.35
584 1454 5.022021 CCTCAATTTCGAATTACTTGTCGC 58.978 41.667 0.00 0.00 37.19 5.19
585 1455 5.390461 CCTCAATTTCGAATTACTTGTCGCA 60.390 40.000 0.00 0.00 37.19 5.10
586 1456 6.176975 TCAATTTCGAATTACTTGTCGCAT 57.823 33.333 0.00 0.00 37.19 4.73
587 1457 6.020984 TCAATTTCGAATTACTTGTCGCATG 58.979 36.000 0.00 0.00 37.19 4.06
588 1458 5.545658 ATTTCGAATTACTTGTCGCATGT 57.454 34.783 0.00 4.39 37.19 3.21
589 1459 6.656314 ATTTCGAATTACTTGTCGCATGTA 57.344 33.333 0.00 2.87 37.19 2.29
590 1460 6.656314 TTTCGAATTACTTGTCGCATGTAT 57.344 33.333 0.00 0.00 37.19 2.29
591 1461 5.635549 TCGAATTACTTGTCGCATGTATG 57.364 39.130 0.00 0.00 37.19 2.39
592 1462 4.506288 TCGAATTACTTGTCGCATGTATGG 59.494 41.667 0.00 0.00 37.19 2.74
593 1463 4.506288 CGAATTACTTGTCGCATGTATGGA 59.494 41.667 0.00 0.00 0.00 3.41
594 1464 5.177511 CGAATTACTTGTCGCATGTATGGAT 59.822 40.000 0.00 0.00 0.00 3.41
595 1465 5.929697 ATTACTTGTCGCATGTATGGATG 57.070 39.130 0.00 0.00 0.00 3.51
596 1466 3.266510 ACTTGTCGCATGTATGGATGT 57.733 42.857 0.00 0.00 0.00 3.06
597 1467 4.400529 ACTTGTCGCATGTATGGATGTA 57.599 40.909 0.00 0.00 0.00 2.29
598 1468 4.960938 ACTTGTCGCATGTATGGATGTAT 58.039 39.130 0.00 0.00 0.00 2.29
599 1469 5.368145 ACTTGTCGCATGTATGGATGTATT 58.632 37.500 0.00 0.00 0.00 1.89
600 1470 5.822519 ACTTGTCGCATGTATGGATGTATTT 59.177 36.000 0.00 0.00 0.00 1.40
601 1471 6.989759 ACTTGTCGCATGTATGGATGTATTTA 59.010 34.615 0.00 0.00 0.00 1.40
602 1472 7.171508 ACTTGTCGCATGTATGGATGTATTTAG 59.828 37.037 0.00 0.00 0.00 1.85
603 1473 6.754193 TGTCGCATGTATGGATGTATTTAGA 58.246 36.000 0.00 0.00 0.00 2.10
604 1474 7.386059 TGTCGCATGTATGGATGTATTTAGAT 58.614 34.615 0.00 0.00 0.00 1.98
605 1475 7.331687 TGTCGCATGTATGGATGTATTTAGATG 59.668 37.037 0.00 0.00 0.00 2.90
606 1476 7.331934 GTCGCATGTATGGATGTATTTAGATGT 59.668 37.037 0.00 0.00 0.00 3.06
607 1477 8.527810 TCGCATGTATGGATGTATTTAGATGTA 58.472 33.333 0.00 0.00 0.00 2.29
608 1478 9.317936 CGCATGTATGGATGTATTTAGATGTAT 57.682 33.333 0.00 0.00 0.00 2.29
627 1497 9.080097 AGATGTATTGTAGTTCTAGGTACATCC 57.920 37.037 20.41 12.00 43.71 3.51
628 1498 8.777578 ATGTATTGTAGTTCTAGGTACATCCA 57.222 34.615 0.00 0.00 39.02 3.41
629 1499 8.777578 TGTATTGTAGTTCTAGGTACATCCAT 57.222 34.615 0.00 0.00 39.02 3.41
630 1500 9.209048 TGTATTGTAGTTCTAGGTACATCCATT 57.791 33.333 0.00 0.00 39.02 3.16
633 1503 7.973048 TGTAGTTCTAGGTACATCCATTTCT 57.027 36.000 0.00 0.00 39.02 2.52
634 1504 7.782049 TGTAGTTCTAGGTACATCCATTTCTG 58.218 38.462 0.00 0.00 39.02 3.02
635 1505 5.675538 AGTTCTAGGTACATCCATTTCTGC 58.324 41.667 0.00 0.00 39.02 4.26
636 1506 4.322080 TCTAGGTACATCCATTTCTGCG 57.678 45.455 0.00 0.00 39.02 5.18
637 1507 3.958147 TCTAGGTACATCCATTTCTGCGA 59.042 43.478 0.00 0.00 39.02 5.10
638 1508 3.185246 AGGTACATCCATTTCTGCGAG 57.815 47.619 0.00 0.00 39.02 5.03
639 1509 2.766263 AGGTACATCCATTTCTGCGAGA 59.234 45.455 0.00 0.00 39.02 4.04
640 1510 3.126831 GGTACATCCATTTCTGCGAGAG 58.873 50.000 0.00 0.00 35.97 3.20
641 1511 3.430929 GGTACATCCATTTCTGCGAGAGT 60.431 47.826 0.00 0.00 35.97 3.24
642 1512 4.202121 GGTACATCCATTTCTGCGAGAGTA 60.202 45.833 0.00 0.00 35.97 2.59
643 1513 4.471904 ACATCCATTTCTGCGAGAGTAA 57.528 40.909 0.00 0.00 0.00 2.24
644 1514 5.028549 ACATCCATTTCTGCGAGAGTAAT 57.971 39.130 0.00 0.00 0.00 1.89
645 1515 5.431765 ACATCCATTTCTGCGAGAGTAATT 58.568 37.500 0.00 0.00 0.00 1.40
646 1516 5.882557 ACATCCATTTCTGCGAGAGTAATTT 59.117 36.000 0.00 0.00 0.00 1.82
647 1517 5.801350 TCCATTTCTGCGAGAGTAATTTG 57.199 39.130 0.00 0.00 0.00 2.32
648 1518 5.487433 TCCATTTCTGCGAGAGTAATTTGA 58.513 37.500 0.00 0.00 0.00 2.69
649 1519 5.937540 TCCATTTCTGCGAGAGTAATTTGAA 59.062 36.000 0.00 0.00 0.00 2.69
650 1520 6.429692 TCCATTTCTGCGAGAGTAATTTGAAA 59.570 34.615 0.00 0.00 0.00 2.69
651 1521 6.524586 CCATTTCTGCGAGAGTAATTTGAAAC 59.475 38.462 0.00 0.00 0.00 2.78
652 1522 4.903638 TCTGCGAGAGTAATTTGAAACG 57.096 40.909 0.00 0.00 0.00 3.60
653 1523 3.678072 TCTGCGAGAGTAATTTGAAACGG 59.322 43.478 0.00 0.00 0.00 4.44
654 1524 3.655486 TGCGAGAGTAATTTGAAACGGA 58.345 40.909 0.00 0.00 0.00 4.69
655 1525 3.678072 TGCGAGAGTAATTTGAAACGGAG 59.322 43.478 0.00 0.00 0.00 4.63
656 1526 3.062234 GCGAGAGTAATTTGAAACGGAGG 59.938 47.826 0.00 0.00 0.00 4.30
657 1527 3.617263 CGAGAGTAATTTGAAACGGAGGG 59.383 47.826 0.00 0.00 0.00 4.30
658 1528 4.619863 CGAGAGTAATTTGAAACGGAGGGA 60.620 45.833 0.00 0.00 0.00 4.20
659 1529 4.833390 AGAGTAATTTGAAACGGAGGGAG 58.167 43.478 0.00 0.00 0.00 4.30
660 1530 4.286291 AGAGTAATTTGAAACGGAGGGAGT 59.714 41.667 0.00 0.00 0.00 3.85
661 1531 5.482878 AGAGTAATTTGAAACGGAGGGAGTA 59.517 40.000 0.00 0.00 0.00 2.59
662 1532 5.731591 AGTAATTTGAAACGGAGGGAGTAG 58.268 41.667 0.00 0.00 0.00 2.57
663 1533 4.903045 AATTTGAAACGGAGGGAGTAGA 57.097 40.909 0.00 0.00 0.00 2.59
664 1534 5.437191 AATTTGAAACGGAGGGAGTAGAT 57.563 39.130 0.00 0.00 0.00 1.98
665 1535 4.467198 TTTGAAACGGAGGGAGTAGATC 57.533 45.455 0.00 0.00 0.00 2.75
666 1536 2.022195 TGAAACGGAGGGAGTAGATCG 58.978 52.381 0.00 0.00 0.00 3.69
667 1537 1.337387 GAAACGGAGGGAGTAGATCGG 59.663 57.143 0.00 0.00 0.00 4.18
668 1538 0.467659 AACGGAGGGAGTAGATCGGG 60.468 60.000 0.00 0.00 0.00 5.14
669 1539 1.604023 CGGAGGGAGTAGATCGGGG 60.604 68.421 0.00 0.00 0.00 5.73
836 1706 1.952296 CAGATCCAGCTGCCATAAACC 59.048 52.381 8.66 0.00 0.00 3.27
842 1712 1.137404 GCTGCCATAAACCACAGCG 59.863 57.895 0.00 0.00 45.23 5.18
843 1713 1.137404 CTGCCATAAACCACAGCGC 59.863 57.895 0.00 0.00 0.00 5.92
844 1714 1.303236 TGCCATAAACCACAGCGCT 60.303 52.632 2.64 2.64 0.00 5.92
845 1715 1.305219 TGCCATAAACCACAGCGCTC 61.305 55.000 7.13 0.00 0.00 5.03
846 1716 1.993369 GCCATAAACCACAGCGCTCC 61.993 60.000 7.13 0.00 0.00 4.70
847 1717 0.676466 CCATAAACCACAGCGCTCCA 60.676 55.000 7.13 0.00 0.00 3.86
848 1718 0.729116 CATAAACCACAGCGCTCCAG 59.271 55.000 7.13 0.00 0.00 3.86
849 1719 1.026718 ATAAACCACAGCGCTCCAGC 61.027 55.000 7.13 0.00 37.78 4.85
1067 1968 0.179073 AGCCTGTATGTCATGGCGAC 60.179 55.000 6.94 0.00 45.61 5.19
1196 2097 3.382546 CCTTGCTTTGATTATGAGGGTGG 59.617 47.826 0.00 0.00 0.00 4.61
1198 2099 3.620488 TGCTTTGATTATGAGGGTGGTC 58.380 45.455 0.00 0.00 0.00 4.02
1227 2128 0.385029 CGGATCTGCCTCACTCTGAG 59.615 60.000 2.45 2.45 43.91 3.35
1248 2149 0.101399 ACGACTCGGATGCTGATGAC 59.899 55.000 2.98 0.00 0.00 3.06
1283 2184 3.610040 TTACACGGATTCTGCAGATGT 57.390 42.857 19.04 19.88 0.00 3.06
1302 2203 4.804608 TGTTACAAACACCAATGAGTCG 57.195 40.909 0.00 0.00 36.25 4.18
1396 2297 2.611971 GGCACGTACTCCTTTGACATCA 60.612 50.000 0.00 0.00 0.00 3.07
1424 2325 3.050275 GTGGAGCAAGGTCGGCAC 61.050 66.667 0.00 0.00 0.00 5.01
1617 2518 4.347607 CTTCCCATCTTCTTCATTTGGGT 58.652 43.478 6.21 0.00 45.96 4.51
1618 2519 4.402616 TCCCATCTTCTTCATTTGGGTT 57.597 40.909 6.21 0.00 45.96 4.11
1619 2520 4.344104 TCCCATCTTCTTCATTTGGGTTC 58.656 43.478 6.21 0.00 45.96 3.62
1620 2521 4.044571 TCCCATCTTCTTCATTTGGGTTCT 59.955 41.667 6.21 0.00 45.96 3.01
1621 2522 4.159135 CCCATCTTCTTCATTTGGGTTCTG 59.841 45.833 0.00 0.00 41.78 3.02
1622 2523 4.159135 CCATCTTCTTCATTTGGGTTCTGG 59.841 45.833 0.00 0.00 0.00 3.86
1623 2524 3.766545 TCTTCTTCATTTGGGTTCTGGG 58.233 45.455 0.00 0.00 0.00 4.45
1624 2525 1.923356 TCTTCATTTGGGTTCTGGGC 58.077 50.000 0.00 0.00 0.00 5.36
1625 2526 1.428912 TCTTCATTTGGGTTCTGGGCT 59.571 47.619 0.00 0.00 0.00 5.19
1727 2628 1.000274 GATGAAGGTTTTGCCGTGCTT 60.000 47.619 0.00 0.00 43.70 3.91
1778 2679 3.564644 GCATTGGAGACCTTCAGATGATG 59.435 47.826 0.00 0.00 0.00 3.07
1795 2696 0.806868 ATGAAGCACAAGTCCATGCG 59.193 50.000 0.00 0.00 46.74 4.73
1844 2745 0.734309 TGCTGTGATATTGCAAGCGG 59.266 50.000 4.94 0.00 33.48 5.52
1850 2751 3.759086 TGTGATATTGCAAGCGGGTTTAA 59.241 39.130 4.94 0.00 0.00 1.52
1867 2768 6.238814 CGGGTTTAAAGCAAGGACTTCTTTTA 60.239 38.462 18.43 4.95 32.41 1.52
2076 2977 1.847890 TTTGCTGCGCCCGTAAAGAC 61.848 55.000 4.18 0.00 0.00 3.01
2084 2985 2.870411 GCGCCCGTAAAGACTAATGAAT 59.130 45.455 0.00 0.00 0.00 2.57
2196 3097 8.669946 TTACGGATACATCAAAATATGAAGCA 57.330 30.769 0.00 0.00 42.54 3.91
2268 3169 3.069300 TGAGTATCATCAAGGCAGCTCTC 59.931 47.826 0.00 0.00 42.56 3.20
2330 3231 5.042593 TGCAAAGCTTACTCACAAACAATG 58.957 37.500 0.00 0.00 0.00 2.82
2401 3302 9.003658 ACAGATAGTGATAAAAGGTTGTTCAAG 57.996 33.333 0.00 0.00 0.00 3.02
2465 3366 1.668751 GTTCGCTTCCTGTCACACAAA 59.331 47.619 0.00 0.00 0.00 2.83
2472 3373 4.036262 GCTTCCTGTCACACAAACATACAA 59.964 41.667 0.00 0.00 0.00 2.41
2523 3460 6.486657 CAGGACACAATTTGTAAGGAAGAGAA 59.513 38.462 0.86 0.00 39.17 2.87
2524 3461 6.712547 AGGACACAATTTGTAAGGAAGAGAAG 59.287 38.462 0.86 0.00 39.17 2.85
2525 3462 6.710744 GGACACAATTTGTAAGGAAGAGAAGA 59.289 38.462 0.86 0.00 39.17 2.87
2526 3463 7.228706 GGACACAATTTGTAAGGAAGAGAAGAA 59.771 37.037 0.86 0.00 39.17 2.52
2527 3464 8.519799 ACACAATTTGTAAGGAAGAGAAGAAA 57.480 30.769 0.86 0.00 36.32 2.52
2528 3465 9.136323 ACACAATTTGTAAGGAAGAGAAGAAAT 57.864 29.630 0.86 0.00 36.32 2.17
2529 3466 9.971922 CACAATTTGTAAGGAAGAGAAGAAATT 57.028 29.630 0.86 0.00 0.00 1.82
2530 3467 9.971922 ACAATTTGTAAGGAAGAGAAGAAATTG 57.028 29.630 0.00 0.00 43.09 2.32
2531 3468 9.971922 CAATTTGTAAGGAAGAGAAGAAATTGT 57.028 29.630 0.00 0.00 37.59 2.71
2535 3472 9.847224 TTGTAAGGAAGAGAAGAAATTGTTAGT 57.153 29.630 0.00 0.00 0.00 2.24
2558 3495 8.635765 AGTACATAATGTGAGAACAATTTGGT 57.364 30.769 0.78 0.00 0.00 3.67
2559 3496 8.514594 AGTACATAATGTGAGAACAATTTGGTG 58.485 33.333 0.78 0.00 0.00 4.17
2560 3497 7.523293 ACATAATGTGAGAACAATTTGGTGA 57.477 32.000 0.78 0.00 0.00 4.02
2561 3498 7.596494 ACATAATGTGAGAACAATTTGGTGAG 58.404 34.615 0.78 0.00 0.00 3.51
2562 3499 5.458041 AATGTGAGAACAATTTGGTGAGG 57.542 39.130 0.78 0.00 0.00 3.86
2563 3500 4.163441 TGTGAGAACAATTTGGTGAGGA 57.837 40.909 0.78 0.00 0.00 3.71
2564 3501 4.531854 TGTGAGAACAATTTGGTGAGGAA 58.468 39.130 0.78 0.00 0.00 3.36
2565 3502 4.338118 TGTGAGAACAATTTGGTGAGGAAC 59.662 41.667 0.78 0.00 0.00 3.62
2566 3503 4.338118 GTGAGAACAATTTGGTGAGGAACA 59.662 41.667 0.78 0.00 0.00 3.18
2567 3504 4.952957 TGAGAACAATTTGGTGAGGAACAA 59.047 37.500 0.78 0.00 0.00 2.83
2568 3505 5.598005 TGAGAACAATTTGGTGAGGAACAAT 59.402 36.000 0.78 0.00 0.00 2.71
2569 3506 5.846203 AGAACAATTTGGTGAGGAACAATG 58.154 37.500 0.78 0.00 0.00 2.82
2570 3507 5.598005 AGAACAATTTGGTGAGGAACAATGA 59.402 36.000 0.78 0.00 0.00 2.57
2571 3508 5.867903 ACAATTTGGTGAGGAACAATGAA 57.132 34.783 0.78 0.00 0.00 2.57
2572 3509 5.846203 ACAATTTGGTGAGGAACAATGAAG 58.154 37.500 0.78 0.00 0.00 3.02
2573 3510 5.221501 ACAATTTGGTGAGGAACAATGAAGG 60.222 40.000 0.78 0.00 0.00 3.46
2574 3511 3.874383 TTGGTGAGGAACAATGAAGGA 57.126 42.857 0.00 0.00 0.00 3.36
2575 3512 3.423539 TGGTGAGGAACAATGAAGGAG 57.576 47.619 0.00 0.00 0.00 3.69
2576 3513 2.978978 TGGTGAGGAACAATGAAGGAGA 59.021 45.455 0.00 0.00 0.00 3.71
2726 3663 8.893563 ATAATAAAACTGATTGACCAAGGGAA 57.106 30.769 0.00 0.00 0.00 3.97
2736 3673 3.420893 TGACCAAGGGAAATGCTTACTG 58.579 45.455 0.00 0.00 0.00 2.74
2768 3705 3.266772 ACTTGGGGACTTCTATTGATGCA 59.733 43.478 0.00 0.00 0.00 3.96
2770 3707 2.225467 GGGGACTTCTATTGATGCAGC 58.775 52.381 0.00 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 8.487970 GTTTCTGCTAGGCTTTTTATTTTTGTC 58.512 33.333 0.00 0.00 0.00 3.18
96 97 6.934645 GGGTTTCTGCTAGGCTTTTTATTTTT 59.065 34.615 0.00 0.00 0.00 1.94
163 164 2.441532 CCCCTCCTTCGCCGACTA 60.442 66.667 0.00 0.00 0.00 2.59
167 168 2.436115 GTTTCCCCTCCTTCGCCG 60.436 66.667 0.00 0.00 0.00 6.46
168 169 1.377333 CAGTTTCCCCTCCTTCGCC 60.377 63.158 0.00 0.00 0.00 5.54
171 172 1.073098 TTCCCAGTTTCCCCTCCTTC 58.927 55.000 0.00 0.00 0.00 3.46
172 173 1.147191 GTTTCCCAGTTTCCCCTCCTT 59.853 52.381 0.00 0.00 0.00 3.36
173 174 0.778083 GTTTCCCAGTTTCCCCTCCT 59.222 55.000 0.00 0.00 0.00 3.69
174 175 0.481128 TGTTTCCCAGTTTCCCCTCC 59.519 55.000 0.00 0.00 0.00 4.30
175 176 2.375014 TTGTTTCCCAGTTTCCCCTC 57.625 50.000 0.00 0.00 0.00 4.30
176 177 2.677914 CTTTGTTTCCCAGTTTCCCCT 58.322 47.619 0.00 0.00 0.00 4.79
177 178 1.691976 CCTTTGTTTCCCAGTTTCCCC 59.308 52.381 0.00 0.00 0.00 4.81
178 179 1.691976 CCCTTTGTTTCCCAGTTTCCC 59.308 52.381 0.00 0.00 0.00 3.97
262 1119 0.123266 AAGGGGATGAAGGAGGGGAA 59.877 55.000 0.00 0.00 0.00 3.97
263 1120 0.327576 GAAGGGGATGAAGGAGGGGA 60.328 60.000 0.00 0.00 0.00 4.81
264 1121 0.327964 AGAAGGGGATGAAGGAGGGG 60.328 60.000 0.00 0.00 0.00 4.79
265 1122 1.135960 GAGAAGGGGATGAAGGAGGG 58.864 60.000 0.00 0.00 0.00 4.30
266 1123 1.135960 GGAGAAGGGGATGAAGGAGG 58.864 60.000 0.00 0.00 0.00 4.30
285 1142 2.257207 TGTACTGGAGTTTGGGAGAGG 58.743 52.381 0.00 0.00 0.00 3.69
291 1148 5.799213 AGAGAGAAATGTACTGGAGTTTGG 58.201 41.667 0.00 0.00 0.00 3.28
293 1150 6.723977 AGAGAGAGAGAAATGTACTGGAGTTT 59.276 38.462 0.00 0.00 0.00 2.66
294 1151 6.252995 AGAGAGAGAGAAATGTACTGGAGTT 58.747 40.000 0.00 0.00 0.00 3.01
295 1152 5.826643 AGAGAGAGAGAAATGTACTGGAGT 58.173 41.667 0.00 0.00 0.00 3.85
299 1156 4.497340 GGCGAGAGAGAGAGAAATGTACTG 60.497 50.000 0.00 0.00 0.00 2.74
300 1157 3.630312 GGCGAGAGAGAGAGAAATGTACT 59.370 47.826 0.00 0.00 0.00 2.73
301 1158 3.547214 CGGCGAGAGAGAGAGAAATGTAC 60.547 52.174 0.00 0.00 0.00 2.90
302 1159 2.614520 CGGCGAGAGAGAGAGAAATGTA 59.385 50.000 0.00 0.00 0.00 2.29
303 1160 1.403679 CGGCGAGAGAGAGAGAAATGT 59.596 52.381 0.00 0.00 0.00 2.71
305 1162 1.673920 GTCGGCGAGAGAGAGAGAAAT 59.326 52.381 11.20 0.00 0.00 2.17
306 1163 1.088306 GTCGGCGAGAGAGAGAGAAA 58.912 55.000 11.20 0.00 0.00 2.52
319 1189 4.570663 GGGATGTCGGAGTCGGCG 62.571 72.222 0.00 0.00 45.11 6.46
389 1259 5.630415 AGAATCGGAAATCAGGGTCATAA 57.370 39.130 0.00 0.00 0.00 1.90
449 1319 1.609072 TGATATCGGCGTCTTCTCCAG 59.391 52.381 6.85 0.00 0.00 3.86
505 1375 9.573166 TCCTTTCTTCTATTTGAATGAACTGAA 57.427 29.630 0.00 0.00 33.71 3.02
558 1428 6.955963 CGACAAGTAATTCGAAATTGAGGAAG 59.044 38.462 17.33 1.66 37.43 3.46
559 1429 6.619874 GCGACAAGTAATTCGAAATTGAGGAA 60.620 38.462 17.33 0.00 37.43 3.36
562 1432 5.617609 TGCGACAAGTAATTCGAAATTGAG 58.382 37.500 17.33 12.88 37.43 3.02
563 1433 5.599359 TGCGACAAGTAATTCGAAATTGA 57.401 34.783 17.33 0.00 37.43 2.57
564 1434 5.794945 ACATGCGACAAGTAATTCGAAATTG 59.205 36.000 0.00 7.96 37.43 2.32
565 1435 5.938322 ACATGCGACAAGTAATTCGAAATT 58.062 33.333 0.00 0.00 37.43 1.82
566 1436 5.545658 ACATGCGACAAGTAATTCGAAAT 57.454 34.783 0.00 0.00 37.43 2.17
567 1437 6.456315 CCATACATGCGACAAGTAATTCGAAA 60.456 38.462 0.00 0.00 37.43 3.46
568 1438 5.006261 CCATACATGCGACAAGTAATTCGAA 59.994 40.000 0.00 0.00 37.43 3.71
569 1439 4.506288 CCATACATGCGACAAGTAATTCGA 59.494 41.667 0.00 0.00 37.43 3.71
570 1440 4.506288 TCCATACATGCGACAAGTAATTCG 59.494 41.667 0.00 0.00 38.31 3.34
571 1441 5.984233 TCCATACATGCGACAAGTAATTC 57.016 39.130 0.00 0.00 0.00 2.17
572 1442 5.822519 ACATCCATACATGCGACAAGTAATT 59.177 36.000 0.00 0.00 0.00 1.40
573 1443 5.368145 ACATCCATACATGCGACAAGTAAT 58.632 37.500 0.00 0.00 0.00 1.89
574 1444 4.765273 ACATCCATACATGCGACAAGTAA 58.235 39.130 0.00 0.00 0.00 2.24
575 1445 4.400529 ACATCCATACATGCGACAAGTA 57.599 40.909 0.00 0.00 0.00 2.24
576 1446 3.266510 ACATCCATACATGCGACAAGT 57.733 42.857 0.00 0.00 0.00 3.16
577 1447 5.929697 AATACATCCATACATGCGACAAG 57.070 39.130 0.00 0.00 0.00 3.16
578 1448 7.213678 TCTAAATACATCCATACATGCGACAA 58.786 34.615 0.00 0.00 0.00 3.18
579 1449 6.754193 TCTAAATACATCCATACATGCGACA 58.246 36.000 0.00 0.00 0.00 4.35
580 1450 7.331934 ACATCTAAATACATCCATACATGCGAC 59.668 37.037 0.00 0.00 0.00 5.19
581 1451 7.386059 ACATCTAAATACATCCATACATGCGA 58.614 34.615 0.00 0.00 0.00 5.10
582 1452 7.601073 ACATCTAAATACATCCATACATGCG 57.399 36.000 0.00 0.00 0.00 4.73
601 1471 9.080097 GGATGTACCTAGAACTACAATACATCT 57.920 37.037 16.69 0.00 43.38 2.90
602 1472 8.857098 TGGATGTACCTAGAACTACAATACATC 58.143 37.037 11.32 11.32 43.24 3.06
603 1473 8.777578 TGGATGTACCTAGAACTACAATACAT 57.222 34.615 0.00 0.00 39.86 2.29
604 1474 8.777578 ATGGATGTACCTAGAACTACAATACA 57.222 34.615 0.00 0.00 39.86 2.29
607 1477 8.993424 AGAAATGGATGTACCTAGAACTACAAT 58.007 33.333 0.00 0.00 39.86 2.71
608 1478 8.258007 CAGAAATGGATGTACCTAGAACTACAA 58.742 37.037 0.00 0.00 39.86 2.41
609 1479 7.632898 GCAGAAATGGATGTACCTAGAACTACA 60.633 40.741 0.00 0.00 39.86 2.74
610 1480 6.702282 GCAGAAATGGATGTACCTAGAACTAC 59.298 42.308 0.00 0.00 39.86 2.73
611 1481 6.461092 CGCAGAAATGGATGTACCTAGAACTA 60.461 42.308 0.00 0.00 39.86 2.24
612 1482 5.675538 GCAGAAATGGATGTACCTAGAACT 58.324 41.667 0.00 0.00 39.86 3.01
613 1483 4.508124 CGCAGAAATGGATGTACCTAGAAC 59.492 45.833 0.00 0.00 39.86 3.01
614 1484 4.404394 TCGCAGAAATGGATGTACCTAGAA 59.596 41.667 0.00 0.00 39.86 2.10
615 1485 3.958147 TCGCAGAAATGGATGTACCTAGA 59.042 43.478 0.00 0.00 39.86 2.43
616 1486 4.038042 TCTCGCAGAAATGGATGTACCTAG 59.962 45.833 0.00 0.00 36.07 3.02
617 1487 3.958147 TCTCGCAGAAATGGATGTACCTA 59.042 43.478 0.00 0.00 36.07 3.08
618 1488 2.766263 TCTCGCAGAAATGGATGTACCT 59.234 45.455 0.00 0.00 36.07 3.08
619 1489 3.126831 CTCTCGCAGAAATGGATGTACC 58.873 50.000 0.00 0.00 34.09 3.34
620 1490 3.786635 ACTCTCGCAGAAATGGATGTAC 58.213 45.455 0.00 0.00 34.09 2.90
621 1491 5.592104 TTACTCTCGCAGAAATGGATGTA 57.408 39.130 0.00 0.00 34.09 2.29
622 1492 4.471904 TTACTCTCGCAGAAATGGATGT 57.528 40.909 0.00 0.00 34.09 3.06
623 1493 5.998454 AATTACTCTCGCAGAAATGGATG 57.002 39.130 0.00 0.00 34.09 3.51
624 1494 6.115446 TCAAATTACTCTCGCAGAAATGGAT 58.885 36.000 0.00 0.00 34.09 3.41
625 1495 5.487433 TCAAATTACTCTCGCAGAAATGGA 58.513 37.500 0.00 0.00 34.09 3.41
626 1496 5.801350 TCAAATTACTCTCGCAGAAATGG 57.199 39.130 0.00 0.00 34.09 3.16
627 1497 6.247165 CGTTTCAAATTACTCTCGCAGAAATG 59.753 38.462 0.00 0.00 34.09 2.32
628 1498 6.307155 CGTTTCAAATTACTCTCGCAGAAAT 58.693 36.000 0.00 0.00 34.09 2.17
629 1499 5.333798 CCGTTTCAAATTACTCTCGCAGAAA 60.334 40.000 0.00 0.00 34.09 2.52
630 1500 4.151689 CCGTTTCAAATTACTCTCGCAGAA 59.848 41.667 0.00 0.00 34.09 3.02
631 1501 3.678072 CCGTTTCAAATTACTCTCGCAGA 59.322 43.478 0.00 0.00 0.00 4.26
632 1502 3.678072 TCCGTTTCAAATTACTCTCGCAG 59.322 43.478 0.00 0.00 0.00 5.18
633 1503 3.655486 TCCGTTTCAAATTACTCTCGCA 58.345 40.909 0.00 0.00 0.00 5.10
634 1504 3.062234 CCTCCGTTTCAAATTACTCTCGC 59.938 47.826 0.00 0.00 0.00 5.03
635 1505 3.617263 CCCTCCGTTTCAAATTACTCTCG 59.383 47.826 0.00 0.00 0.00 4.04
636 1506 4.828829 TCCCTCCGTTTCAAATTACTCTC 58.171 43.478 0.00 0.00 0.00 3.20
637 1507 4.286291 ACTCCCTCCGTTTCAAATTACTCT 59.714 41.667 0.00 0.00 0.00 3.24
638 1508 4.576879 ACTCCCTCCGTTTCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
639 1509 4.635699 ACTCCCTCCGTTTCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
640 1510 5.727434 TCTACTCCCTCCGTTTCAAATTAC 58.273 41.667 0.00 0.00 0.00 1.89
641 1511 6.555463 ATCTACTCCCTCCGTTTCAAATTA 57.445 37.500 0.00 0.00 0.00 1.40
642 1512 4.903045 TCTACTCCCTCCGTTTCAAATT 57.097 40.909 0.00 0.00 0.00 1.82
643 1513 4.441634 CGATCTACTCCCTCCGTTTCAAAT 60.442 45.833 0.00 0.00 0.00 2.32
644 1514 3.119245 CGATCTACTCCCTCCGTTTCAAA 60.119 47.826 0.00 0.00 0.00 2.69
645 1515 2.426024 CGATCTACTCCCTCCGTTTCAA 59.574 50.000 0.00 0.00 0.00 2.69
646 1516 2.022195 CGATCTACTCCCTCCGTTTCA 58.978 52.381 0.00 0.00 0.00 2.69
647 1517 1.337387 CCGATCTACTCCCTCCGTTTC 59.663 57.143 0.00 0.00 0.00 2.78
648 1518 1.400737 CCGATCTACTCCCTCCGTTT 58.599 55.000 0.00 0.00 0.00 3.60
649 1519 0.467659 CCCGATCTACTCCCTCCGTT 60.468 60.000 0.00 0.00 0.00 4.44
650 1520 1.150992 CCCGATCTACTCCCTCCGT 59.849 63.158 0.00 0.00 0.00 4.69
651 1521 1.604023 CCCCGATCTACTCCCTCCG 60.604 68.421 0.00 0.00 0.00 4.63
652 1522 1.228925 CCCCCGATCTACTCCCTCC 60.229 68.421 0.00 0.00 0.00 4.30
653 1523 0.251430 CTCCCCCGATCTACTCCCTC 60.251 65.000 0.00 0.00 0.00 4.30
654 1524 1.731324 CCTCCCCCGATCTACTCCCT 61.731 65.000 0.00 0.00 0.00 4.20
655 1525 1.228925 CCTCCCCCGATCTACTCCC 60.229 68.421 0.00 0.00 0.00 4.30
656 1526 1.909287 GCCTCCCCCGATCTACTCC 60.909 68.421 0.00 0.00 0.00 3.85
657 1527 1.152525 TGCCTCCCCCGATCTACTC 60.153 63.158 0.00 0.00 0.00 2.59
658 1528 1.152440 CTGCCTCCCCCGATCTACT 60.152 63.158 0.00 0.00 0.00 2.57
659 1529 1.152525 TCTGCCTCCCCCGATCTAC 60.153 63.158 0.00 0.00 0.00 2.59
660 1530 1.153989 CTCTGCCTCCCCCGATCTA 59.846 63.158 0.00 0.00 0.00 1.98
661 1531 2.123077 CTCTGCCTCCCCCGATCT 60.123 66.667 0.00 0.00 0.00 2.75
662 1532 2.123251 TCTCTGCCTCCCCCGATC 60.123 66.667 0.00 0.00 0.00 3.69
663 1533 2.123077 CTCTCTGCCTCCCCCGAT 60.123 66.667 0.00 0.00 0.00 4.18
664 1534 3.347590 TCTCTCTGCCTCCCCCGA 61.348 66.667 0.00 0.00 0.00 5.14
665 1535 2.655077 ATCTCTCTCTGCCTCCCCCG 62.655 65.000 0.00 0.00 0.00 5.73
666 1536 0.399806 AATCTCTCTCTGCCTCCCCC 60.400 60.000 0.00 0.00 0.00 5.40
667 1537 1.140652 CAAATCTCTCTCTGCCTCCCC 59.859 57.143 0.00 0.00 0.00 4.81
668 1538 2.114616 TCAAATCTCTCTCTGCCTCCC 58.885 52.381 0.00 0.00 0.00 4.30
669 1539 3.795877 CTTCAAATCTCTCTCTGCCTCC 58.204 50.000 0.00 0.00 0.00 4.30
981 1882 3.961414 GGGTTCAAGGCCCGGACA 61.961 66.667 0.73 0.00 36.30 4.02
1067 1968 4.845580 ATCGCAAGCCAGCCTCGG 62.846 66.667 0.00 0.00 37.18 4.63
1081 1982 2.618053 GAACCATATAAGCCGGGATCG 58.382 52.381 2.18 0.00 0.00 3.69
1128 2029 3.135530 AGTCCTGCTGACCTATGAAATCC 59.864 47.826 3.72 0.00 45.68 3.01
1196 2097 2.866762 GGCAGATCCGACTTGTAATGAC 59.133 50.000 0.00 0.00 0.00 3.06
1198 2099 3.126831 GAGGCAGATCCGACTTGTAATG 58.873 50.000 0.00 0.00 40.77 1.90
1227 2128 1.333931 TCATCAGCATCCGAGTCGTAC 59.666 52.381 12.31 0.00 0.00 3.67
1248 2149 2.282555 CGTGTAATCAGCATTCCAGTCG 59.717 50.000 0.00 0.00 0.00 4.18
1283 2184 2.550606 GGCGACTCATTGGTGTTTGTAA 59.449 45.455 0.00 0.00 0.00 2.41
1396 2297 2.046892 GCTCCACGTGCCACTCAT 60.047 61.111 10.91 0.00 0.00 2.90
1545 2446 2.038557 TGGGTCTTCTAACACCTTCTGC 59.961 50.000 0.00 0.00 32.69 4.26
1617 2518 0.185901 AACTTGCCAGAAGCCCAGAA 59.814 50.000 0.00 0.00 42.71 3.02
1618 2519 0.538057 CAACTTGCCAGAAGCCCAGA 60.538 55.000 0.00 0.00 42.71 3.86
1619 2520 0.825010 ACAACTTGCCAGAAGCCCAG 60.825 55.000 0.00 0.00 42.71 4.45
1620 2521 1.108727 CACAACTTGCCAGAAGCCCA 61.109 55.000 0.00 0.00 42.71 5.36
1621 2522 1.662044 CACAACTTGCCAGAAGCCC 59.338 57.895 0.00 0.00 42.71 5.19
1622 2523 1.006922 GCACAACTTGCCAGAAGCC 60.007 57.895 0.00 0.00 46.63 4.35
1623 2524 4.641777 GCACAACTTGCCAGAAGC 57.358 55.556 0.00 0.00 46.63 3.86
1727 2628 1.227823 CCGAACTTCCACACCAGCA 60.228 57.895 0.00 0.00 0.00 4.41
1778 2679 0.593128 AACGCATGGACTTGTGCTTC 59.407 50.000 0.00 0.00 39.16 3.86
1795 2696 5.637387 ACGCCATTTTCATCAAAACCATAAC 59.363 36.000 0.00 0.00 34.24 1.89
1844 2745 8.936070 TTTAAAAGAAGTCCTTGCTTTAAACC 57.064 30.769 0.00 0.00 34.79 3.27
1873 2774 6.043854 ACAAACAAAAACTGGCCTAAAAGA 57.956 33.333 3.32 0.00 0.00 2.52
1876 2777 9.699703 GAATATACAAACAAAAACTGGCCTAAA 57.300 29.630 3.32 0.00 0.00 1.85
1923 2824 6.364165 CACAGTAATTCAACAAATCAGCCAAG 59.636 38.462 0.00 0.00 0.00 3.61
2044 2945 4.929198 GCAAAGCGCGCATATCAT 57.071 50.000 35.10 8.46 0.00 2.45
2170 3071 9.114952 TGCTTCATATTTTGATGTATCCGTAAA 57.885 29.630 0.00 0.00 33.34 2.01
2173 3074 7.566760 TTGCTTCATATTTTGATGTATCCGT 57.433 32.000 0.00 0.00 33.34 4.69
2218 3119 6.767524 TGTAAAATGTTCAGTGTCTTTGGT 57.232 33.333 0.00 0.00 0.00 3.67
2260 3161 1.471287 TGCATGAATGTTGAGAGCTGC 59.529 47.619 0.00 0.00 0.00 5.25
2261 3162 3.628032 AGATGCATGAATGTTGAGAGCTG 59.372 43.478 2.46 0.00 0.00 4.24
2268 3169 4.142752 ACGAGTGAAGATGCATGAATGTTG 60.143 41.667 2.46 0.00 0.00 3.33
2302 3203 5.574891 TTGTGAGTAAGCTTTGCAGAAAA 57.425 34.783 3.20 0.00 0.00 2.29
2303 3204 5.105957 TGTTTGTGAGTAAGCTTTGCAGAAA 60.106 36.000 3.20 8.94 0.00 2.52
2318 3219 9.817365 CTACTGATTAACTTCATTGTTTGTGAG 57.183 33.333 0.00 0.00 0.00 3.51
2330 3231 5.001232 TGTTGCCCACTACTGATTAACTTC 58.999 41.667 0.00 0.00 0.00 3.01
2341 3242 3.885297 AGATATTGCATGTTGCCCACTAC 59.115 43.478 0.00 0.00 44.23 2.73
2401 3302 3.855858 ACTCTCGAAAAGCCAGAGAATC 58.144 45.455 2.22 0.00 40.09 2.52
2472 3373 8.575589 GCAATTGTTGGGATTAAATTTTCCTTT 58.424 29.630 7.40 0.00 32.34 3.11
2487 3388 1.039068 TGTGTCCTGCAATTGTTGGG 58.961 50.000 7.40 7.16 0.00 4.12
2488 3389 2.886862 TTGTGTCCTGCAATTGTTGG 57.113 45.000 7.40 9.62 0.00 3.77
2489 3390 4.571580 ACAAATTGTGTCCTGCAATTGTTG 59.428 37.500 7.40 1.75 43.30 3.33
2490 3391 4.768583 ACAAATTGTGTCCTGCAATTGTT 58.231 34.783 7.40 0.00 43.30 2.83
2491 3392 4.405116 ACAAATTGTGTCCTGCAATTGT 57.595 36.364 7.40 3.27 43.30 2.71
2492 3393 5.406175 CCTTACAAATTGTGTCCTGCAATTG 59.594 40.000 9.15 0.00 43.30 2.32
2532 3469 9.733556 ACCAAATTGTTCTCACATTATGTACTA 57.266 29.630 0.00 0.00 31.06 1.82
2533 3470 8.514594 CACCAAATTGTTCTCACATTATGTACT 58.485 33.333 0.00 0.00 31.06 2.73
2534 3471 8.511321 TCACCAAATTGTTCTCACATTATGTAC 58.489 33.333 0.00 0.00 31.06 2.90
2535 3472 8.628630 TCACCAAATTGTTCTCACATTATGTA 57.371 30.769 0.00 0.00 31.06 2.29
2536 3473 7.309377 CCTCACCAAATTGTTCTCACATTATGT 60.309 37.037 0.00 0.00 31.06 2.29
2537 3474 7.031372 CCTCACCAAATTGTTCTCACATTATG 58.969 38.462 0.00 0.00 31.06 1.90
2538 3475 6.947733 TCCTCACCAAATTGTTCTCACATTAT 59.052 34.615 0.00 0.00 31.06 1.28
2539 3476 6.303054 TCCTCACCAAATTGTTCTCACATTA 58.697 36.000 0.00 0.00 31.06 1.90
2540 3477 5.139727 TCCTCACCAAATTGTTCTCACATT 58.860 37.500 0.00 0.00 31.06 2.71
2541 3478 4.728772 TCCTCACCAAATTGTTCTCACAT 58.271 39.130 0.00 0.00 31.06 3.21
2542 3479 4.163441 TCCTCACCAAATTGTTCTCACA 57.837 40.909 0.00 0.00 0.00 3.58
2543 3480 4.338118 TGTTCCTCACCAAATTGTTCTCAC 59.662 41.667 0.00 0.00 0.00 3.51
2544 3481 4.531854 TGTTCCTCACCAAATTGTTCTCA 58.468 39.130 0.00 0.00 0.00 3.27
2545 3482 5.514274 TTGTTCCTCACCAAATTGTTCTC 57.486 39.130 0.00 0.00 0.00 2.87
2546 3483 5.598005 TCATTGTTCCTCACCAAATTGTTCT 59.402 36.000 0.00 0.00 0.00 3.01
2547 3484 5.841810 TCATTGTTCCTCACCAAATTGTTC 58.158 37.500 0.00 0.00 0.00 3.18
2548 3485 5.867903 TCATTGTTCCTCACCAAATTGTT 57.132 34.783 0.00 0.00 0.00 2.83
2549 3486 5.221501 CCTTCATTGTTCCTCACCAAATTGT 60.222 40.000 0.00 0.00 0.00 2.71
2550 3487 5.010922 TCCTTCATTGTTCCTCACCAAATTG 59.989 40.000 0.00 0.00 0.00 2.32
2551 3488 5.147032 TCCTTCATTGTTCCTCACCAAATT 58.853 37.500 0.00 0.00 0.00 1.82
2552 3489 4.739793 TCCTTCATTGTTCCTCACCAAAT 58.260 39.130 0.00 0.00 0.00 2.32
2553 3490 4.141274 TCTCCTTCATTGTTCCTCACCAAA 60.141 41.667 0.00 0.00 0.00 3.28
2554 3491 3.394274 TCTCCTTCATTGTTCCTCACCAA 59.606 43.478 0.00 0.00 0.00 3.67
2555 3492 2.978978 TCTCCTTCATTGTTCCTCACCA 59.021 45.455 0.00 0.00 0.00 4.17
2556 3493 3.703001 TCTCCTTCATTGTTCCTCACC 57.297 47.619 0.00 0.00 0.00 4.02
2557 3494 4.080638 AGGATCTCCTTCATTGTTCCTCAC 60.081 45.833 0.00 0.00 46.09 3.51
2558 3495 4.080695 CAGGATCTCCTTCATTGTTCCTCA 60.081 45.833 0.00 0.00 46.09 3.86
2559 3496 4.450053 CAGGATCTCCTTCATTGTTCCTC 58.550 47.826 0.00 0.00 46.09 3.71
2560 3497 3.371380 GCAGGATCTCCTTCATTGTTCCT 60.371 47.826 0.00 0.00 46.09 3.36
2561 3498 2.948315 GCAGGATCTCCTTCATTGTTCC 59.052 50.000 0.00 0.00 46.09 3.62
2562 3499 2.948315 GGCAGGATCTCCTTCATTGTTC 59.052 50.000 0.00 0.00 46.09 3.18
2563 3500 2.309755 TGGCAGGATCTCCTTCATTGTT 59.690 45.455 0.00 0.00 46.09 2.83
2564 3501 1.918262 TGGCAGGATCTCCTTCATTGT 59.082 47.619 0.00 0.00 46.09 2.71
2565 3502 2.723322 TGGCAGGATCTCCTTCATTG 57.277 50.000 0.00 0.00 46.09 2.82
2566 3503 3.744940 TTTGGCAGGATCTCCTTCATT 57.255 42.857 0.00 0.00 46.09 2.57
2567 3504 3.011032 ACTTTTGGCAGGATCTCCTTCAT 59.989 43.478 0.00 0.00 46.09 2.57
2568 3505 2.376518 ACTTTTGGCAGGATCTCCTTCA 59.623 45.455 0.00 0.00 46.09 3.02
2569 3506 2.751806 CACTTTTGGCAGGATCTCCTTC 59.248 50.000 0.00 0.00 46.09 3.46
2570 3507 2.108952 ACACTTTTGGCAGGATCTCCTT 59.891 45.455 0.00 0.00 46.09 3.36
2571 3508 8.002680 AAGATACACTTTTGGCAGGATCTCCT 62.003 42.308 0.00 0.00 40.75 3.69
2572 3509 2.206576 ACACTTTTGGCAGGATCTCC 57.793 50.000 0.00 0.00 0.00 3.71
2573 3510 4.775236 AGATACACTTTTGGCAGGATCTC 58.225 43.478 0.00 0.00 0.00 2.75
2574 3511 4.851639 AGATACACTTTTGGCAGGATCT 57.148 40.909 0.00 0.00 0.00 2.75
2575 3512 4.943705 TCAAGATACACTTTTGGCAGGATC 59.056 41.667 0.00 0.00 36.61 3.36
2576 3513 4.702131 GTCAAGATACACTTTTGGCAGGAT 59.298 41.667 0.00 0.00 36.61 3.24
2717 3654 3.525800 ACAGTAAGCATTTCCCTTGGT 57.474 42.857 0.00 0.00 0.00 3.67
2718 3655 4.589908 AGTACAGTAAGCATTTCCCTTGG 58.410 43.478 0.00 0.00 0.00 3.61
2719 3656 7.201732 CCAATAGTACAGTAAGCATTTCCCTTG 60.202 40.741 0.00 0.00 0.00 3.61
2720 3657 6.828785 CCAATAGTACAGTAAGCATTTCCCTT 59.171 38.462 0.00 0.00 0.00 3.95
2721 3658 6.157994 TCCAATAGTACAGTAAGCATTTCCCT 59.842 38.462 0.00 0.00 0.00 4.20
2722 3659 6.260271 GTCCAATAGTACAGTAAGCATTTCCC 59.740 42.308 0.00 0.00 0.00 3.97
2723 3660 7.048512 AGTCCAATAGTACAGTAAGCATTTCC 58.951 38.462 0.00 0.00 0.00 3.13
2724 3661 8.391106 CAAGTCCAATAGTACAGTAAGCATTTC 58.609 37.037 0.00 0.00 0.00 2.17
2725 3662 7.336931 CCAAGTCCAATAGTACAGTAAGCATTT 59.663 37.037 0.00 0.00 0.00 2.32
2726 3663 6.823689 CCAAGTCCAATAGTACAGTAAGCATT 59.176 38.462 0.00 0.00 0.00 3.56
2736 3673 4.470304 AGAAGTCCCCAAGTCCAATAGTAC 59.530 45.833 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.