Multiple sequence alignment - TraesCS5D01G216000

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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 TraesCS5D01G216000 chr5D 100.000 3985 0 0 1 3985 324910882 324906898 0.000000e+00 7360.0
1 TraesCS5D01G216000 chr5D 83.598 189 30 1 3260 3447 63485554 63485366 4.090000e-40 176.0
2 TraesCS5D01G216000 chr5A 97.603 876 18 3 2321 3193 423042479 423041604 0.000000e+00 1498.0
3 TraesCS5D01G216000 chr5A 92.680 847 45 11 1491 2325 423043377 423042536 0.000000e+00 1205.0
4 TraesCS5D01G216000 chr5A 90.957 575 26 7 873 1427 423043946 423043378 0.000000e+00 750.0
5 TraesCS5D01G216000 chr5A 88.908 577 55 7 3408 3981 423040908 423040338 0.000000e+00 702.0
6 TraesCS5D01G216000 chr5A 90.787 445 27 5 170 602 423047694 423047252 2.060000e-162 582.0
7 TraesCS5D01G216000 chr5A 91.810 232 16 3 3188 3416 423041468 423041237 1.790000e-83 320.0
8 TraesCS5D01G216000 chr5A 92.442 172 13 0 1 172 423048086 423047915 3.080000e-61 246.0
9 TraesCS5D01G216000 chr5A 89.683 126 10 2 668 790 423046976 423046851 1.480000e-34 158.0
10 TraesCS5D01G216000 chr5A 92.537 67 3 1 807 871 423044160 423044094 1.180000e-15 95.3
11 TraesCS5D01G216000 chr5B 92.881 885 39 11 2317 3193 377345386 377344518 0.000000e+00 1264.0
12 TraesCS5D01G216000 chr5B 96.687 664 17 3 1665 2325 377346109 377345448 0.000000e+00 1099.0
13 TraesCS5D01G216000 chr5B 88.018 434 46 4 3549 3981 377342270 377341842 3.550000e-140 508.0
14 TraesCS5D01G216000 chr5B 89.896 386 31 2 1071 1448 377346500 377346115 1.290000e-134 490.0
15 TraesCS5D01G216000 chr5B 88.533 375 31 4 3190 3564 377344380 377344018 1.020000e-120 444.0
16 TraesCS5D01G216000 chr5B 90.774 336 14 9 736 1058 377346875 377346544 2.200000e-117 433.0
17 TraesCS5D01G216000 chr6D 86.513 304 40 1 3678 3981 38855752 38855450 2.300000e-87 333.0
18 TraesCS5D01G216000 chr1B 84.722 288 34 10 2040 2325 398651454 398651733 3.030000e-71 279.0
19 TraesCS5D01G216000 chr2B 84.375 288 35 10 2040 2325 409254846 409255125 1.410000e-69 274.0
20 TraesCS5D01G216000 chr2B 91.304 46 2 2 2316 2361 409255183 409255226 1.200000e-05 62.1
21 TraesCS5D01G216000 chr4B 84.028 288 36 10 2040 2325 311414545 311414824 6.560000e-68 268.0
22 TraesCS5D01G216000 chr1D 82.653 294 48 3 3258 3549 296517481 296517773 1.420000e-64 257.0
23 TraesCS5D01G216000 chr1D 83.835 266 39 4 3261 3524 296635444 296635707 2.380000e-62 250.0
24 TraesCS5D01G216000 chr3B 80.069 291 47 8 3258 3540 2158385 2158672 5.220000e-49 206.0
25 TraesCS5D01G216000 chr4A 80.385 260 46 4 3307 3562 625317123 625316865 4.060000e-45 193.0
26 TraesCS5D01G216000 chr7D 78.082 292 55 6 3695 3981 185800494 185800781 4.090000e-40 176.0
27 TraesCS5D01G216000 chr7D 91.837 49 4 0 3489 3537 41445045 41445093 7.150000e-08 69.4
28 TraesCS5D01G216000 chr7A 84.524 168 25 1 3260 3427 595801854 595802020 8.860000e-37 165.0
29 TraesCS5D01G216000 chr6B 82.105 190 29 3 3261 3449 591240364 591240549 1.480000e-34 158.0


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 TraesCS5D01G216000 chr5D 324906898 324910882 3984 True 7360.000000 7360 100.000000 1 3985 1 chr5D.!!$R2 3984
1 TraesCS5D01G216000 chr5A 423040338 423048086 7748 True 617.366667 1498 91.934111 1 3981 9 chr5A.!!$R1 3980
2 TraesCS5D01G216000 chr5B 377341842 377346875 5033 True 706.333333 1264 91.131500 736 3981 6 chr5B.!!$R1 3245

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
834 3993 0.327287 TCGTCCTCCTCCTCTCCCTA 60.327 60.0 0.00 0.0 0.00 3.53 F
1450 4818 0.030773 CTGCTCTCGTAATAGCGCCA 59.969 55.0 2.29 0.0 41.77 5.69 F
1473 4841 0.037697 ACCGCGTCTGCATTTCTGTA 60.038 50.0 4.92 0.0 42.97 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 5573 1.001974 AGCAGTTCGCAGACCATGTTA 59.998 47.619 0.00 0.0 46.13 2.41 R
2955 6404 0.252197 GCGGTATATTAGCCCCCAGG 59.748 60.000 0.00 0.0 0.00 4.45 R
3250 6845 1.000955 GTACGGATCCAGCCCACATAG 59.999 57.143 13.41 0.0 0.00 2.23 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
63 64 9.271828 CTTAAATGTTGGCCTAGAAAACAAATT 57.728 29.630 9.41 9.92 37.36 1.82
64 65 7.728847 AAATGTTGGCCTAGAAAACAAATTC 57.271 32.000 9.41 0.00 37.36 2.17
77 78 6.479990 AGAAAACAAATTCTGCTAGGCAAAAC 59.520 34.615 0.00 0.00 38.41 2.43
188 412 8.161425 ACTTTTCTACAAGCTTAGGGAATAACA 58.839 33.333 0.00 0.00 0.00 2.41
222 446 8.613060 TCATATCCATCAAGAGAACATAAAGC 57.387 34.615 0.00 0.00 0.00 3.51
223 447 7.663081 TCATATCCATCAAGAGAACATAAAGCC 59.337 37.037 0.00 0.00 0.00 4.35
307 543 4.938832 CCGACATTACTAACATGGACCAAA 59.061 41.667 0.00 0.00 0.00 3.28
312 548 3.237268 ACTAACATGGACCAAAGCCAA 57.763 42.857 0.00 0.00 39.21 4.52
342 578 0.830648 TTTCTAGCTAGCGGGCACAT 59.169 50.000 16.35 0.00 34.17 3.21
354 590 1.766494 GGGCACATGAATCCACATCA 58.234 50.000 0.00 0.00 0.00 3.07
355 591 1.406539 GGGCACATGAATCCACATCAC 59.593 52.381 0.00 0.00 0.00 3.06
392 628 7.628234 ACCAATGGTTATGCATTAAAATCCAA 58.372 30.769 3.54 0.00 27.29 3.53
393 629 8.273605 ACCAATGGTTATGCATTAAAATCCAAT 58.726 29.630 3.54 0.00 27.29 3.16
396 632 7.551035 TGGTTATGCATTAAAATCCAATTGC 57.449 32.000 3.54 0.00 0.00 3.56
402 638 7.925043 TGCATTAAAATCCAATTGCAAAGAT 57.075 28.000 1.71 3.57 0.00 2.40
477 713 7.466455 GCTTCGAAATTCAGCTCTCAATGAATA 60.466 37.037 0.00 0.00 43.56 1.75
480 716 6.019559 CGAAATTCAGCTCTCAATGAATACGA 60.020 38.462 15.50 0.00 43.56 3.43
511 747 6.498304 CATGCTTCACATCCAAGTTTATACC 58.502 40.000 0.00 0.00 36.64 2.73
514 750 5.594317 GCTTCACATCCAAGTTTATACCCAT 59.406 40.000 0.00 0.00 0.00 4.00
524 760 6.350949 CCAAGTTTATACCCATTCCAGTTTGG 60.351 42.308 0.00 0.00 39.43 3.28
530 766 1.474330 CCATTCCAGTTTGGCTACCC 58.526 55.000 0.00 0.00 37.47 3.69
531 767 1.094785 CATTCCAGTTTGGCTACCCG 58.905 55.000 0.00 0.00 37.47 5.28
537 773 0.475044 AGTTTGGCTACCCGGTTTGA 59.525 50.000 0.00 0.00 0.00 2.69
549 785 6.072563 GCTACCCGGTTTGACTTGTATTTTTA 60.073 38.462 0.00 0.00 0.00 1.52
558 794 6.476243 TGACTTGTATTTTTAGAGCGGAAC 57.524 37.500 0.00 0.00 0.00 3.62
569 805 6.490566 TTTAGAGCGGAACTGGATTTTAAC 57.509 37.500 0.00 0.00 0.00 2.01
570 806 3.000727 AGAGCGGAACTGGATTTTAACG 58.999 45.455 0.00 0.00 0.00 3.18
588 824 2.344025 ACGAGCGAAATAGTCCCAAAC 58.656 47.619 0.00 0.00 0.00 2.93
589 825 2.289195 ACGAGCGAAATAGTCCCAAACA 60.289 45.455 0.00 0.00 0.00 2.83
590 826 2.348666 CGAGCGAAATAGTCCCAAACAG 59.651 50.000 0.00 0.00 0.00 3.16
591 827 3.596214 GAGCGAAATAGTCCCAAACAGA 58.404 45.455 0.00 0.00 0.00 3.41
592 828 3.335579 AGCGAAATAGTCCCAAACAGAC 58.664 45.455 0.00 0.00 34.31 3.51
593 829 2.418976 GCGAAATAGTCCCAAACAGACC 59.581 50.000 0.00 0.00 34.67 3.85
594 830 3.670625 CGAAATAGTCCCAAACAGACCA 58.329 45.455 0.00 0.00 34.67 4.02
595 831 3.435671 CGAAATAGTCCCAAACAGACCAC 59.564 47.826 0.00 0.00 34.67 4.16
596 832 4.394729 GAAATAGTCCCAAACAGACCACA 58.605 43.478 0.00 0.00 34.67 4.17
597 833 4.447138 AATAGTCCCAAACAGACCACAA 57.553 40.909 0.00 0.00 34.67 3.33
598 834 2.818751 AGTCCCAAACAGACCACAAA 57.181 45.000 0.00 0.00 34.67 2.83
599 835 2.654863 AGTCCCAAACAGACCACAAAG 58.345 47.619 0.00 0.00 34.67 2.77
600 836 2.025321 AGTCCCAAACAGACCACAAAGT 60.025 45.455 0.00 0.00 34.67 2.66
601 837 2.758423 GTCCCAAACAGACCACAAAGTT 59.242 45.455 0.00 0.00 0.00 2.66
602 838 3.194755 GTCCCAAACAGACCACAAAGTTT 59.805 43.478 0.00 0.00 34.78 2.66
603 839 3.835395 TCCCAAACAGACCACAAAGTTTT 59.165 39.130 0.00 0.00 32.34 2.43
604 840 4.284746 TCCCAAACAGACCACAAAGTTTTT 59.715 37.500 0.00 0.00 32.34 1.94
642 878 4.036734 ACAGACCACAAAGTTGCACTAATG 59.963 41.667 0.00 0.00 0.00 1.90
645 881 3.317993 ACCACAAAGTTGCACTAATGGAC 59.682 43.478 14.59 0.00 32.20 4.02
647 883 4.202101 CCACAAAGTTGCACTAATGGACAA 60.202 41.667 0.00 0.00 30.39 3.18
649 885 5.630680 CACAAAGTTGCACTAATGGACAATC 59.369 40.000 0.00 0.00 0.00 2.67
650 886 4.685169 AAGTTGCACTAATGGACAATCG 57.315 40.909 0.00 0.00 0.00 3.34
651 887 3.937814 AGTTGCACTAATGGACAATCGA 58.062 40.909 0.00 0.00 0.00 3.59
652 888 4.323417 AGTTGCACTAATGGACAATCGAA 58.677 39.130 0.00 0.00 0.00 3.71
653 889 4.759693 AGTTGCACTAATGGACAATCGAAA 59.240 37.500 0.00 0.00 0.00 3.46
656 892 4.517075 TGCACTAATGGACAATCGAAACAA 59.483 37.500 0.00 0.00 0.00 2.83
657 893 5.182950 TGCACTAATGGACAATCGAAACAAT 59.817 36.000 0.00 0.00 0.00 2.71
658 894 6.092748 GCACTAATGGACAATCGAAACAATT 58.907 36.000 0.00 0.00 0.00 2.32
659 895 6.251376 GCACTAATGGACAATCGAAACAATTC 59.749 38.462 0.00 0.00 0.00 2.17
660 896 7.304735 CACTAATGGACAATCGAAACAATTCA 58.695 34.615 0.00 0.00 35.15 2.57
663 899 9.357652 CTAATGGACAATCGAAACAATTCATTT 57.642 29.630 0.00 0.00 35.15 2.32
664 900 7.816945 ATGGACAATCGAAACAATTCATTTC 57.183 32.000 0.00 2.74 35.15 2.17
666 902 6.862608 TGGACAATCGAAACAATTCATTTCAG 59.137 34.615 10.75 5.47 36.09 3.02
671 1149 9.787626 CAATCGAAACAATTCATTTCAGAAAAG 57.212 29.630 0.00 0.00 36.09 2.27
689 1167 9.184523 TCAGAAAAGAAATGTCCAAAACTTAGA 57.815 29.630 0.00 0.00 0.00 2.10
690 1168 9.237846 CAGAAAAGAAATGTCCAAAACTTAGAC 57.762 33.333 0.00 0.00 0.00 2.59
796 3943 3.073735 CCCTCCAGCTCACGCTCT 61.074 66.667 0.00 0.00 45.15 4.09
797 3944 2.183811 CCTCCAGCTCACGCTCTG 59.816 66.667 0.00 0.00 45.15 3.35
800 3947 4.383861 CCAGCTCACGCTCTGCCA 62.384 66.667 0.00 0.00 45.15 4.92
801 3948 2.357881 CAGCTCACGCTCTGCCAA 60.358 61.111 0.00 0.00 45.15 4.52
802 3949 2.358003 AGCTCACGCTCTGCCAAC 60.358 61.111 0.00 0.00 45.15 3.77
805 3960 3.535629 CTCACGCTCTGCCAACCCA 62.536 63.158 0.00 0.00 0.00 4.51
834 3993 0.327287 TCGTCCTCCTCCTCTCCCTA 60.327 60.000 0.00 0.00 0.00 3.53
911 4216 4.436050 CGTGGCACAGTTATTCTTCATCAC 60.436 45.833 19.09 0.00 41.80 3.06
1004 4309 1.481363 CGACCTCCTCCTCCTTAAACC 59.519 57.143 0.00 0.00 0.00 3.27
1005 4310 1.481363 GACCTCCTCCTCCTTAAACCG 59.519 57.143 0.00 0.00 0.00 4.44
1006 4311 1.078324 ACCTCCTCCTCCTTAAACCGA 59.922 52.381 0.00 0.00 0.00 4.69
1152 4497 3.744719 TCGTCGTCGCTGGGGAAG 61.745 66.667 0.00 0.00 36.96 3.46
1296 4650 0.036294 GAGCAGAGCCCCTTTTACGT 60.036 55.000 0.00 0.00 0.00 3.57
1300 4656 2.351447 GCAGAGCCCCTTTTACGTTTTC 60.351 50.000 0.00 0.00 0.00 2.29
1312 4668 1.385528 ACGTTTTCTGTTTCGGCCTT 58.614 45.000 0.00 0.00 0.00 4.35
1315 4671 2.787129 CGTTTTCTGTTTCGGCCTTTTC 59.213 45.455 0.00 0.00 0.00 2.29
1316 4672 3.732471 CGTTTTCTGTTTCGGCCTTTTCA 60.732 43.478 0.00 0.00 0.00 2.69
1321 4677 4.616953 TCTGTTTCGGCCTTTTCAATTTC 58.383 39.130 0.00 0.00 0.00 2.17
1324 4680 2.723124 TCGGCCTTTTCAATTTCTGC 57.277 45.000 0.00 0.00 0.00 4.26
1332 4688 4.320788 CCTTTTCAATTTCTGCTCTCGCTT 60.321 41.667 0.00 0.00 36.97 4.68
1424 4792 2.031870 GGGGAAATAGGCACATTGGAC 58.968 52.381 0.00 0.00 0.00 4.02
1427 4795 4.469657 GGGAAATAGGCACATTGGACATA 58.530 43.478 0.00 0.00 0.00 2.29
1428 4796 5.079643 GGGAAATAGGCACATTGGACATAT 58.920 41.667 0.00 0.00 0.00 1.78
1429 4797 5.539955 GGGAAATAGGCACATTGGACATATT 59.460 40.000 0.00 0.00 0.00 1.28
1430 4798 6.449698 GGAAATAGGCACATTGGACATATTG 58.550 40.000 0.00 0.00 0.00 1.90
1431 4799 5.458041 AATAGGCACATTGGACATATTGC 57.542 39.130 0.00 0.00 0.00 3.56
1432 4800 3.022557 AGGCACATTGGACATATTGCT 57.977 42.857 0.00 0.00 0.00 3.91
1433 4801 2.691526 AGGCACATTGGACATATTGCTG 59.308 45.455 0.00 0.00 0.00 4.41
1434 4802 2.466846 GCACATTGGACATATTGCTGC 58.533 47.619 0.00 0.00 0.00 5.25
1435 4803 2.100252 GCACATTGGACATATTGCTGCT 59.900 45.455 0.00 0.00 0.00 4.24
1436 4804 3.794475 GCACATTGGACATATTGCTGCTC 60.794 47.826 0.00 0.00 0.00 4.26
1437 4805 3.630769 CACATTGGACATATTGCTGCTCT 59.369 43.478 0.00 0.00 0.00 4.09
1438 4806 3.881688 ACATTGGACATATTGCTGCTCTC 59.118 43.478 0.00 0.00 0.00 3.20
1439 4807 2.229675 TGGACATATTGCTGCTCTCG 57.770 50.000 0.00 0.00 0.00 4.04
1440 4808 1.482182 TGGACATATTGCTGCTCTCGT 59.518 47.619 0.00 0.00 0.00 4.18
1441 4809 2.693074 TGGACATATTGCTGCTCTCGTA 59.307 45.455 0.00 0.00 0.00 3.43
1442 4810 3.132111 TGGACATATTGCTGCTCTCGTAA 59.868 43.478 0.00 0.00 0.00 3.18
1443 4811 4.202253 TGGACATATTGCTGCTCTCGTAAT 60.202 41.667 0.00 0.00 0.00 1.89
1444 4812 5.010617 TGGACATATTGCTGCTCTCGTAATA 59.989 40.000 0.00 0.00 0.00 0.98
1445 4813 5.574830 GGACATATTGCTGCTCTCGTAATAG 59.425 44.000 0.00 0.00 0.00 1.73
1446 4814 4.926238 ACATATTGCTGCTCTCGTAATAGC 59.074 41.667 0.00 0.00 39.25 2.97
1447 4815 1.840181 TTGCTGCTCTCGTAATAGCG 58.160 50.000 0.00 0.00 41.77 4.26
1448 4816 0.595053 TGCTGCTCTCGTAATAGCGC 60.595 55.000 0.00 0.00 41.77 5.92
1449 4817 1.278849 GCTGCTCTCGTAATAGCGCC 61.279 60.000 2.29 0.00 41.77 6.53
1450 4818 0.030773 CTGCTCTCGTAATAGCGCCA 59.969 55.000 2.29 0.00 41.77 5.69
1451 4819 0.673985 TGCTCTCGTAATAGCGCCAT 59.326 50.000 2.29 0.00 41.77 4.40
1452 4820 1.063806 GCTCTCGTAATAGCGCCATG 58.936 55.000 2.29 0.00 0.00 3.66
1453 4821 1.335964 GCTCTCGTAATAGCGCCATGA 60.336 52.381 2.29 0.00 0.00 3.07
1454 4822 2.862530 GCTCTCGTAATAGCGCCATGAA 60.863 50.000 2.29 0.00 0.00 2.57
1455 4823 2.726760 CTCTCGTAATAGCGCCATGAAC 59.273 50.000 2.29 0.00 0.00 3.18
1456 4824 1.792949 CTCGTAATAGCGCCATGAACC 59.207 52.381 2.29 0.00 0.00 3.62
1457 4825 0.506932 CGTAATAGCGCCATGAACCG 59.493 55.000 2.29 0.00 0.00 4.44
1463 4831 3.853330 CGCCATGAACCGCGTCTG 61.853 66.667 4.92 0.00 43.35 3.51
1464 4832 4.166011 GCCATGAACCGCGTCTGC 62.166 66.667 4.92 0.00 37.91 4.26
1465 4833 2.741985 CCATGAACCGCGTCTGCA 60.742 61.111 4.92 0.00 42.97 4.41
1466 4834 2.108514 CCATGAACCGCGTCTGCAT 61.109 57.895 4.92 0.00 42.97 3.96
1467 4835 1.647545 CCATGAACCGCGTCTGCATT 61.648 55.000 4.92 0.00 42.97 3.56
1468 4836 0.168788 CATGAACCGCGTCTGCATTT 59.831 50.000 4.92 0.00 42.97 2.32
1469 4837 0.447801 ATGAACCGCGTCTGCATTTC 59.552 50.000 4.92 0.00 42.97 2.17
1470 4838 0.602638 TGAACCGCGTCTGCATTTCT 60.603 50.000 4.92 0.00 42.97 2.52
1471 4839 0.179215 GAACCGCGTCTGCATTTCTG 60.179 55.000 4.92 0.00 42.97 3.02
1472 4840 0.884704 AACCGCGTCTGCATTTCTGT 60.885 50.000 4.92 0.00 42.97 3.41
1473 4841 0.037697 ACCGCGTCTGCATTTCTGTA 60.038 50.000 4.92 0.00 42.97 2.74
1474 4842 1.290203 CCGCGTCTGCATTTCTGTAT 58.710 50.000 4.92 0.00 42.97 2.29
1475 4843 1.004610 CCGCGTCTGCATTTCTGTATG 60.005 52.381 4.92 0.00 42.97 2.39
1476 4844 1.660607 CGCGTCTGCATTTCTGTATGT 59.339 47.619 0.00 0.00 42.97 2.29
1477 4845 2.094258 CGCGTCTGCATTTCTGTATGTT 59.906 45.455 0.00 0.00 42.97 2.71
1478 4846 3.424829 CGCGTCTGCATTTCTGTATGTTT 60.425 43.478 0.00 0.00 42.97 2.83
1479 4847 4.475944 GCGTCTGCATTTCTGTATGTTTT 58.524 39.130 0.00 0.00 42.15 2.43
1480 4848 4.321745 GCGTCTGCATTTCTGTATGTTTTG 59.678 41.667 0.00 0.00 42.15 2.44
1481 4849 5.451908 CGTCTGCATTTCTGTATGTTTTGT 58.548 37.500 0.00 0.00 0.00 2.83
1482 4850 5.914635 CGTCTGCATTTCTGTATGTTTTGTT 59.085 36.000 0.00 0.00 0.00 2.83
1483 4851 6.417635 CGTCTGCATTTCTGTATGTTTTGTTT 59.582 34.615 0.00 0.00 0.00 2.83
1484 4852 7.043458 CGTCTGCATTTCTGTATGTTTTGTTTT 60.043 33.333 0.00 0.00 0.00 2.43
1485 4853 8.603181 GTCTGCATTTCTGTATGTTTTGTTTTT 58.397 29.630 0.00 0.00 0.00 1.94
1486 4854 8.602328 TCTGCATTTCTGTATGTTTTGTTTTTG 58.398 29.630 0.00 0.00 0.00 2.44
1487 4855 7.185453 TGCATTTCTGTATGTTTTGTTTTTGC 58.815 30.769 0.00 0.00 0.00 3.68
1488 4856 7.148356 TGCATTTCTGTATGTTTTGTTTTTGCA 60.148 29.630 0.00 0.00 0.00 4.08
1489 4857 7.695618 GCATTTCTGTATGTTTTGTTTTTGCAA 59.304 29.630 0.00 0.00 0.00 4.08
1497 4865 9.980780 GTATGTTTTGTTTTTGCAACTGTAAAT 57.019 25.926 0.00 0.00 30.13 1.40
1514 4882 2.526888 AATGGGAGAGTAGGACGACA 57.473 50.000 0.00 0.00 0.00 4.35
1518 4886 1.891150 GGGAGAGTAGGACGACAAACA 59.109 52.381 0.00 0.00 0.00 2.83
1520 4888 3.698040 GGGAGAGTAGGACGACAAACATA 59.302 47.826 0.00 0.00 0.00 2.29
1524 4892 6.476053 GGAGAGTAGGACGACAAACATATTTC 59.524 42.308 0.00 0.00 0.00 2.17
1529 4897 5.547465 AGGACGACAAACATATTTCTGTGA 58.453 37.500 0.00 0.00 0.00 3.58
1535 4903 3.740044 AACATATTTCTGTGAACCGCG 57.260 42.857 0.00 0.00 0.00 6.46
1549 4917 0.953003 ACCGCGCTAGAGGATTACTC 59.047 55.000 5.56 0.00 46.98 2.59
1565 4933 9.145442 GAGGATTACTCCCAACTAGTAGTAAAT 57.855 37.037 16.23 8.48 43.21 1.40
1572 4940 9.317827 ACTCCCAACTAGTAGTAAATAAACTGA 57.682 33.333 2.50 0.00 0.00 3.41
1585 4953 8.677300 AGTAAATAAACTGATATTGCCACACAG 58.323 33.333 0.00 0.00 35.14 3.66
1587 4955 2.795231 ACTGATATTGCCACACAGCT 57.205 45.000 0.00 0.00 32.67 4.24
1590 4958 1.281577 TGATATTGCCACACAGCTGGA 59.718 47.619 19.93 0.00 32.30 3.86
1594 4962 1.383456 TTGCCACACAGCTGGACAAC 61.383 55.000 19.93 5.00 32.30 3.32
1595 4963 2.555547 GCCACACAGCTGGACAACC 61.556 63.158 19.93 0.00 32.30 3.77
1596 4964 1.898574 CCACACAGCTGGACAACCC 60.899 63.158 19.93 0.00 32.30 4.11
1616 4984 3.552068 CCCAAGGTTCCGATTCAACAAAC 60.552 47.826 0.00 0.00 0.00 2.93
1643 5011 1.902918 GTGGGCTGCCACATGTTGA 60.903 57.895 22.05 0.00 40.13 3.18
1650 5018 4.099266 GGGCTGCCACATGTTGAAATTATA 59.901 41.667 22.05 0.00 0.00 0.98
1651 5019 5.221501 GGGCTGCCACATGTTGAAATTATAT 60.222 40.000 22.05 0.00 0.00 0.86
1652 5020 6.015519 GGGCTGCCACATGTTGAAATTATATA 60.016 38.462 22.05 0.00 0.00 0.86
1653 5021 6.863126 GGCTGCCACATGTTGAAATTATATAC 59.137 38.462 15.17 0.00 0.00 1.47
1749 5118 4.275936 AGTGCTCCACATTGTTTAGTTGAC 59.724 41.667 0.00 0.00 36.74 3.18
1861 5235 1.444119 TTGTTGTGAGGTTGGCGAGC 61.444 55.000 0.00 0.00 0.00 5.03
1905 5279 7.851822 ATACTTGCACATTTTTCTACAAACG 57.148 32.000 0.00 0.00 0.00 3.60
1979 5353 5.351465 ACAGTACAACTCTTGACAACACAAG 59.649 40.000 0.00 0.00 45.73 3.16
1981 5355 3.686016 ACAACTCTTGACAACACAAGGT 58.314 40.909 0.00 0.00 44.84 3.50
2022 5396 2.394632 TCGCTGTATATGAACCCCACT 58.605 47.619 0.00 0.00 0.00 4.00
2196 5573 7.499232 TGAGAAGTAGCTTTAGTTTTTCTTGCT 59.501 33.333 0.00 0.00 33.39 3.91
2580 6027 2.416027 CGATCAGTCACAGATCACCGTT 60.416 50.000 10.53 0.00 41.49 4.44
2702 6149 2.658707 GCAGCGACGAAAACGAGCT 61.659 57.895 0.00 0.00 38.90 4.09
2817 6265 5.945784 GTCTAAGATATTGCCCATGCCAATA 59.054 40.000 15.16 15.16 36.33 1.90
2930 6378 5.848833 ATTCAAGAGGCATTTCCATCTTC 57.151 39.130 0.00 0.00 37.29 2.87
2937 6386 2.096496 GGCATTTCCATCTTCTCGTGTG 59.904 50.000 0.00 0.00 34.01 3.82
3007 6456 3.245087 TGCTAACCTAAGGTTGCATTGGA 60.245 43.478 3.47 0.00 46.35 3.53
3104 6558 8.746922 ATAGCTTGTTTGACAATGTGTAAATG 57.253 30.769 0.00 0.00 37.48 2.32
3250 6845 5.529791 ACTGATATGAGCGTTATGTGGTAC 58.470 41.667 0.00 0.00 0.00 3.34
3251 6846 5.302059 ACTGATATGAGCGTTATGTGGTACT 59.698 40.000 0.00 0.00 0.00 2.73
3252 6847 6.489022 ACTGATATGAGCGTTATGTGGTACTA 59.511 38.462 0.00 0.00 0.00 1.82
3272 6870 2.363276 TGGGCTGGATCCGTACGT 60.363 61.111 15.21 0.00 0.00 3.57
3508 7443 8.846211 GGCTACTTTGTTTAATAATATGGCTCA 58.154 33.333 0.00 0.00 0.00 4.26
3532 7467 2.119801 ATCGTTTTGATGCAGAGGCT 57.880 45.000 0.00 0.00 41.91 4.58
3599 9297 1.521749 CTCGTCGCGCTCGTTATGTC 61.522 60.000 19.02 0.00 36.96 3.06
3620 9318 0.108329 AGGGACGCAACCTCATAACG 60.108 55.000 0.00 0.00 31.01 3.18
3669 9367 7.670605 AGTCTATAGTATTTGCCAACTACCA 57.329 36.000 0.00 0.00 31.30 3.25
3676 9374 7.826918 AGTATTTGCCAACTACCACTTTTTA 57.173 32.000 1.73 0.00 0.00 1.52
3745 9444 5.393866 AGGGTTCAGAACATACAACCAAAT 58.606 37.500 15.36 0.00 40.21 2.32
3749 9448 7.175990 GGGTTCAGAACATACAACCAAATAGAA 59.824 37.037 15.36 0.00 40.21 2.10
3775 9474 8.255206 ACGAGATTAAGACAATATGGTTACACA 58.745 33.333 0.00 0.00 0.00 3.72
3794 9493 3.689161 CACAACATGAAAGCCGGAATAGA 59.311 43.478 5.05 0.00 0.00 1.98
3846 9545 4.394610 GGCACAACAAACCAAAAAGAACAT 59.605 37.500 0.00 0.00 0.00 2.71
3873 9572 1.377202 AGCATCGGCATGGTCGTTT 60.377 52.632 0.00 0.00 44.61 3.60
3891 9590 2.814336 GTTTTGGAGCAAGGAAGACGAT 59.186 45.455 0.00 0.00 0.00 3.73
3903 9602 6.565234 CAAGGAAGACGATGTAGAATGTACT 58.435 40.000 0.00 0.00 0.00 2.73
3905 9604 5.886474 AGGAAGACGATGTAGAATGTACTCA 59.114 40.000 0.00 0.00 0.00 3.41
3964 9663 5.885912 TCCTTAGTCAATAATTTCCACTGCC 59.114 40.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 5.295431 GGCCAACATTTAAGCCATTTTTC 57.705 39.130 0.00 0.00 45.07 2.29
37 38 8.831715 ATTTGTTTTCTAGGCCAACATTTAAG 57.168 30.769 5.01 0.00 30.64 1.85
43 44 5.738783 GCAGAATTTGTTTTCTAGGCCAACA 60.739 40.000 5.01 2.97 34.21 3.33
63 64 1.877443 GGTTTCGTTTTGCCTAGCAGA 59.123 47.619 0.00 0.00 40.61 4.26
64 65 1.880027 AGGTTTCGTTTTGCCTAGCAG 59.120 47.619 0.00 0.00 40.61 4.24
77 78 9.692749 TCTAGCTTATTGATATTGTAGGTTTCG 57.307 33.333 0.00 0.00 0.00 3.46
104 105 4.737855 TGCTCTAAATGGTCCTACAGTC 57.262 45.455 0.00 0.00 0.00 3.51
105 106 5.248477 TCTTTGCTCTAAATGGTCCTACAGT 59.752 40.000 0.00 0.00 0.00 3.55
106 107 5.734720 TCTTTGCTCTAAATGGTCCTACAG 58.265 41.667 0.00 0.00 0.00 2.74
147 148 7.152645 TGTAGAAAAGTTCATGTGTACCTCTC 58.847 38.462 0.00 0.00 0.00 3.20
153 154 7.801716 AAGCTTGTAGAAAAGTTCATGTGTA 57.198 32.000 0.00 0.00 0.00 2.90
222 446 4.796231 CGGAGCCACGGAACTCGG 62.796 72.222 0.00 0.00 44.45 4.63
223 447 2.558554 AATCGGAGCCACGGAACTCG 62.559 60.000 0.00 0.00 45.88 4.18
307 543 2.356135 AGAAACGCGTATGATTTGGCT 58.644 42.857 14.46 0.00 0.00 4.75
312 548 3.982058 GCTAGCTAGAAACGCGTATGATT 59.018 43.478 25.15 1.82 0.00 2.57
354 590 9.762933 GCATAACCATTGGTAATTCAAATATGT 57.237 29.630 9.20 0.00 33.12 2.29
355 591 9.761504 TGCATAACCATTGGTAATTCAAATATG 57.238 29.630 9.20 11.32 33.12 1.78
427 663 6.016276 GCTGGTCAATTTTCCTCAAGAGTAAA 60.016 38.462 0.00 0.00 0.00 2.01
431 667 4.077822 AGCTGGTCAATTTTCCTCAAGAG 58.922 43.478 0.00 0.00 0.00 2.85
433 669 4.614535 CGAAGCTGGTCAATTTTCCTCAAG 60.615 45.833 0.00 0.00 0.00 3.02
445 681 1.806542 GCTGAATTTCGAAGCTGGTCA 59.193 47.619 0.00 0.00 34.05 4.02
477 713 1.002257 TGAAGCATGCCATGGTCGT 60.002 52.632 15.66 4.27 40.65 4.34
480 716 1.108776 GATGTGAAGCATGCCATGGT 58.891 50.000 15.66 2.99 43.93 3.55
511 747 1.474330 GGGTAGCCAAACTGGAATGG 58.526 55.000 5.96 0.00 40.96 3.16
514 750 1.377229 CCGGGTAGCCAAACTGGAA 59.623 57.895 12.31 0.00 40.96 3.53
524 760 2.460757 TACAAGTCAAACCGGGTAGC 57.539 50.000 6.32 0.00 0.00 3.58
530 766 5.788531 CGCTCTAAAAATACAAGTCAAACCG 59.211 40.000 0.00 0.00 0.00 4.44
531 767 6.072893 TCCGCTCTAAAAATACAAGTCAAACC 60.073 38.462 0.00 0.00 0.00 3.27
537 773 5.411669 CCAGTTCCGCTCTAAAAATACAAGT 59.588 40.000 0.00 0.00 0.00 3.16
549 785 3.000727 CGTTAAAATCCAGTTCCGCTCT 58.999 45.455 0.00 0.00 0.00 4.09
558 794 6.345920 ACTATTTCGCTCGTTAAAATCCAG 57.654 37.500 0.00 0.00 0.00 3.86
569 805 2.343101 TGTTTGGGACTATTTCGCTCG 58.657 47.619 0.00 0.00 38.04 5.03
570 806 3.371285 GTCTGTTTGGGACTATTTCGCTC 59.629 47.826 0.00 0.00 38.04 5.03
605 841 3.951680 GTGGTCTGTTTCTCCCTCAAAAA 59.048 43.478 0.00 0.00 0.00 1.94
606 842 3.053991 TGTGGTCTGTTTCTCCCTCAAAA 60.054 43.478 0.00 0.00 0.00 2.44
607 843 2.507886 TGTGGTCTGTTTCTCCCTCAAA 59.492 45.455 0.00 0.00 0.00 2.69
608 844 2.123589 TGTGGTCTGTTTCTCCCTCAA 58.876 47.619 0.00 0.00 0.00 3.02
609 845 1.801242 TGTGGTCTGTTTCTCCCTCA 58.199 50.000 0.00 0.00 0.00 3.86
610 846 2.930826 TTGTGGTCTGTTTCTCCCTC 57.069 50.000 0.00 0.00 0.00 4.30
611 847 2.509964 ACTTTGTGGTCTGTTTCTCCCT 59.490 45.455 0.00 0.00 0.00 4.20
612 848 2.932261 ACTTTGTGGTCTGTTTCTCCC 58.068 47.619 0.00 0.00 0.00 4.30
613 849 3.489229 GCAACTTTGTGGTCTGTTTCTCC 60.489 47.826 0.00 0.00 0.00 3.71
614 850 3.128589 TGCAACTTTGTGGTCTGTTTCTC 59.871 43.478 0.00 0.00 0.00 2.87
615 851 3.088532 TGCAACTTTGTGGTCTGTTTCT 58.911 40.909 0.00 0.00 0.00 2.52
616 852 3.179048 GTGCAACTTTGTGGTCTGTTTC 58.821 45.455 0.00 0.00 0.00 2.78
617 853 3.230743 GTGCAACTTTGTGGTCTGTTT 57.769 42.857 0.00 0.00 0.00 2.83
618 854 2.939460 GTGCAACTTTGTGGTCTGTT 57.061 45.000 0.00 0.00 0.00 3.16
642 878 7.083858 TCTGAAATGAATTGTTTCGATTGTCC 58.916 34.615 7.86 0.00 38.18 4.02
645 881 9.787626 CTTTTCTGAAATGAATTGTTTCGATTG 57.212 29.630 9.69 1.49 38.18 2.67
647 883 9.748708 TTCTTTTCTGAAATGAATTGTTTCGAT 57.251 25.926 20.87 0.00 38.18 3.59
660 896 9.671279 AAGTTTTGGACATTTCTTTTCTGAAAT 57.329 25.926 3.31 0.00 44.57 2.17
663 899 9.184523 TCTAAGTTTTGGACATTTCTTTTCTGA 57.815 29.630 0.00 0.00 0.00 3.27
664 900 9.237846 GTCTAAGTTTTGGACATTTCTTTTCTG 57.762 33.333 1.12 0.00 40.46 3.02
793 3940 0.758685 TTTGGGTTGGGTTGGCAGAG 60.759 55.000 0.00 0.00 0.00 3.35
796 3943 2.066999 GGTTTGGGTTGGGTTGGCA 61.067 57.895 0.00 0.00 0.00 4.92
797 3944 1.754380 GAGGTTTGGGTTGGGTTGGC 61.754 60.000 0.00 0.00 0.00 4.52
800 3947 0.466739 GACGAGGTTTGGGTTGGGTT 60.467 55.000 0.00 0.00 0.00 4.11
801 3948 1.149854 GACGAGGTTTGGGTTGGGT 59.850 57.895 0.00 0.00 0.00 4.51
802 3949 1.602605 GGACGAGGTTTGGGTTGGG 60.603 63.158 0.00 0.00 0.00 4.12
805 3960 0.767060 AGGAGGACGAGGTTTGGGTT 60.767 55.000 0.00 0.00 0.00 4.11
834 3993 3.681835 GTCAGAGACGTGCGGGGT 61.682 66.667 0.00 0.00 0.00 4.95
911 4216 1.083489 TAATGAAGGCGAGCCGTTTG 58.917 50.000 8.63 0.00 41.95 2.93
1004 4309 3.984212 CTCGTCGTCGTCGTCGTCG 62.984 68.421 20.39 20.39 45.27 5.12
1005 4310 2.275081 CTCGTCGTCGTCGTCGTC 60.275 66.667 18.44 5.52 45.27 4.20
1006 4311 2.714871 CTCTCGTCGTCGTCGTCGT 61.715 63.158 18.44 0.00 45.27 4.34
1296 4650 4.457834 TTGAAAAGGCCGAAACAGAAAA 57.542 36.364 0.00 0.00 0.00 2.29
1300 4656 4.445385 CAGAAATTGAAAAGGCCGAAACAG 59.555 41.667 0.00 0.00 0.00 3.16
1368 4724 0.591659 CGTCCAGCGAAGATCGGATA 59.408 55.000 1.64 0.00 44.77 2.59
1424 4792 4.031089 CGCTATTACGAGAGCAGCAATATG 59.969 45.833 0.00 0.00 40.10 1.78
1427 4795 2.398498 CGCTATTACGAGAGCAGCAAT 58.602 47.619 0.00 0.00 40.10 3.56
1428 4796 1.840181 CGCTATTACGAGAGCAGCAA 58.160 50.000 0.00 0.00 40.10 3.91
1429 4797 0.595053 GCGCTATTACGAGAGCAGCA 60.595 55.000 0.00 0.00 40.10 4.41
1430 4798 1.278849 GGCGCTATTACGAGAGCAGC 61.279 60.000 7.64 0.71 43.34 5.25
1431 4799 0.030773 TGGCGCTATTACGAGAGCAG 59.969 55.000 7.64 0.00 43.34 4.24
1432 4800 0.673985 ATGGCGCTATTACGAGAGCA 59.326 50.000 7.64 0.00 43.34 4.26
1433 4801 1.063806 CATGGCGCTATTACGAGAGC 58.936 55.000 7.64 0.00 41.09 4.09
1434 4802 2.706555 TCATGGCGCTATTACGAGAG 57.293 50.000 7.64 0.00 34.06 3.20
1435 4803 2.545113 GGTTCATGGCGCTATTACGAGA 60.545 50.000 7.64 0.00 34.06 4.04
1436 4804 1.792949 GGTTCATGGCGCTATTACGAG 59.207 52.381 7.64 0.00 34.06 4.18
1437 4805 1.860676 GGTTCATGGCGCTATTACGA 58.139 50.000 7.64 0.00 34.06 3.43
1438 4806 0.506932 CGGTTCATGGCGCTATTACG 59.493 55.000 7.64 4.54 0.00 3.18
1439 4807 0.234884 GCGGTTCATGGCGCTATTAC 59.765 55.000 7.64 7.30 0.00 1.89
1440 4808 1.218875 CGCGGTTCATGGCGCTATTA 61.219 55.000 7.64 0.00 46.26 0.98
1441 4809 2.534019 CGCGGTTCATGGCGCTATT 61.534 57.895 7.64 0.00 46.26 1.73
1442 4810 2.967076 CGCGGTTCATGGCGCTAT 60.967 61.111 7.64 2.85 46.26 2.97
1447 4815 4.166011 GCAGACGCGGTTCATGGC 62.166 66.667 12.47 1.68 0.00 4.40
1448 4816 1.647545 AATGCAGACGCGGTTCATGG 61.648 55.000 12.47 0.00 42.97 3.66
1449 4817 0.168788 AAATGCAGACGCGGTTCATG 59.831 50.000 12.47 2.27 42.97 3.07
1450 4818 0.447801 GAAATGCAGACGCGGTTCAT 59.552 50.000 12.47 5.29 42.97 2.57
1451 4819 0.602638 AGAAATGCAGACGCGGTTCA 60.603 50.000 12.47 2.74 42.97 3.18
1452 4820 0.179215 CAGAAATGCAGACGCGGTTC 60.179 55.000 12.47 0.00 42.97 3.62
1453 4821 0.884704 ACAGAAATGCAGACGCGGTT 60.885 50.000 12.47 0.00 42.97 4.44
1454 4822 0.037697 TACAGAAATGCAGACGCGGT 60.038 50.000 12.47 0.00 42.97 5.68
1455 4823 1.004610 CATACAGAAATGCAGACGCGG 60.005 52.381 12.47 0.00 42.97 6.46
1456 4824 1.660607 ACATACAGAAATGCAGACGCG 59.339 47.619 3.53 3.53 42.97 6.01
1457 4825 3.747099 AACATACAGAAATGCAGACGC 57.253 42.857 0.00 0.00 39.24 5.19
1458 4826 5.451908 ACAAAACATACAGAAATGCAGACG 58.548 37.500 0.00 0.00 0.00 4.18
1459 4827 7.698836 AAACAAAACATACAGAAATGCAGAC 57.301 32.000 0.00 0.00 0.00 3.51
1460 4828 8.602328 CAAAAACAAAACATACAGAAATGCAGA 58.398 29.630 0.00 0.00 0.00 4.26
1461 4829 7.373966 GCAAAAACAAAACATACAGAAATGCAG 59.626 33.333 0.00 0.00 0.00 4.41
1462 4830 7.148356 TGCAAAAACAAAACATACAGAAATGCA 60.148 29.630 0.00 0.00 34.55 3.96
1463 4831 7.185453 TGCAAAAACAAAACATACAGAAATGC 58.815 30.769 0.00 0.00 0.00 3.56
1464 4832 8.997960 GTTGCAAAAACAAAACATACAGAAATG 58.002 29.630 0.00 0.00 0.00 2.32
1465 4833 8.945057 AGTTGCAAAAACAAAACATACAGAAAT 58.055 25.926 0.00 0.00 0.00 2.17
1466 4834 8.226448 CAGTTGCAAAAACAAAACATACAGAAA 58.774 29.630 0.00 0.00 0.00 2.52
1467 4835 7.386299 ACAGTTGCAAAAACAAAACATACAGAA 59.614 29.630 0.00 0.00 0.00 3.02
1468 4836 6.870965 ACAGTTGCAAAAACAAAACATACAGA 59.129 30.769 0.00 0.00 0.00 3.41
1469 4837 7.059448 ACAGTTGCAAAAACAAAACATACAG 57.941 32.000 0.00 0.00 0.00 2.74
1470 4838 8.534333 TTACAGTTGCAAAAACAAAACATACA 57.466 26.923 0.00 0.00 0.00 2.29
1471 4839 9.980780 ATTTACAGTTGCAAAAACAAAACATAC 57.019 25.926 0.00 0.00 0.00 2.39
1472 4840 9.979270 CATTTACAGTTGCAAAAACAAAACATA 57.021 25.926 0.00 0.00 0.00 2.29
1473 4841 7.967303 CCATTTACAGTTGCAAAAACAAAACAT 59.033 29.630 0.00 0.00 0.00 2.71
1474 4842 7.301054 CCATTTACAGTTGCAAAAACAAAACA 58.699 30.769 0.00 0.00 0.00 2.83
1475 4843 6.744993 CCCATTTACAGTTGCAAAAACAAAAC 59.255 34.615 0.00 0.00 0.00 2.43
1476 4844 6.655003 TCCCATTTACAGTTGCAAAAACAAAA 59.345 30.769 0.00 0.00 0.00 2.44
1477 4845 6.173339 TCCCATTTACAGTTGCAAAAACAAA 58.827 32.000 0.00 0.18 0.00 2.83
1478 4846 5.734720 TCCCATTTACAGTTGCAAAAACAA 58.265 33.333 0.00 0.00 0.00 2.83
1479 4847 5.127845 TCTCCCATTTACAGTTGCAAAAACA 59.872 36.000 0.00 0.00 0.00 2.83
1480 4848 5.596845 TCTCCCATTTACAGTTGCAAAAAC 58.403 37.500 0.00 0.00 0.00 2.43
1481 4849 5.362430 ACTCTCCCATTTACAGTTGCAAAAA 59.638 36.000 0.00 0.00 0.00 1.94
1482 4850 4.892934 ACTCTCCCATTTACAGTTGCAAAA 59.107 37.500 0.00 0.00 0.00 2.44
1483 4851 4.469657 ACTCTCCCATTTACAGTTGCAAA 58.530 39.130 0.00 0.00 0.00 3.68
1484 4852 4.098914 ACTCTCCCATTTACAGTTGCAA 57.901 40.909 0.00 0.00 0.00 4.08
1485 4853 3.788227 ACTCTCCCATTTACAGTTGCA 57.212 42.857 0.00 0.00 0.00 4.08
1486 4854 4.081087 TCCTACTCTCCCATTTACAGTTGC 60.081 45.833 0.00 0.00 0.00 4.17
1487 4855 5.420409 GTCCTACTCTCCCATTTACAGTTG 58.580 45.833 0.00 0.00 0.00 3.16
1488 4856 4.159879 CGTCCTACTCTCCCATTTACAGTT 59.840 45.833 0.00 0.00 0.00 3.16
1489 4857 3.700038 CGTCCTACTCTCCCATTTACAGT 59.300 47.826 0.00 0.00 0.00 3.55
1497 4865 1.891150 GTTTGTCGTCCTACTCTCCCA 59.109 52.381 0.00 0.00 0.00 4.37
1514 4882 3.669557 GCGCGGTTCACAGAAATATGTTT 60.670 43.478 8.83 0.00 0.00 2.83
1518 4886 2.024176 AGCGCGGTTCACAGAAATAT 57.976 45.000 4.23 0.00 0.00 1.28
1520 4888 1.067142 TCTAGCGCGGTTCACAGAAAT 60.067 47.619 19.09 0.00 0.00 2.17
1524 4892 1.517257 CCTCTAGCGCGGTTCACAG 60.517 63.158 19.09 7.97 0.00 3.66
1529 4897 1.337387 GAGTAATCCTCTAGCGCGGTT 59.663 52.381 19.09 0.00 37.22 4.44
1535 4903 5.141910 ACTAGTTGGGAGTAATCCTCTAGC 58.858 45.833 22.88 10.10 40.30 3.42
1557 4925 9.931210 GTGTGGCAATATCAGTTTATTTACTAC 57.069 33.333 0.00 0.00 0.00 2.73
1558 4926 9.674068 TGTGTGGCAATATCAGTTTATTTACTA 57.326 29.630 0.00 0.00 0.00 1.82
1559 4927 8.574251 TGTGTGGCAATATCAGTTTATTTACT 57.426 30.769 0.00 0.00 0.00 2.24
1560 4928 7.432252 GCTGTGTGGCAATATCAGTTTATTTAC 59.568 37.037 0.00 0.00 0.00 2.01
1561 4929 7.339212 AGCTGTGTGGCAATATCAGTTTATTTA 59.661 33.333 0.00 0.00 34.17 1.40
1562 4930 6.153340 AGCTGTGTGGCAATATCAGTTTATTT 59.847 34.615 0.00 0.00 34.17 1.40
1563 4931 5.653769 AGCTGTGTGGCAATATCAGTTTATT 59.346 36.000 0.00 0.00 34.17 1.40
1565 4933 4.395854 CAGCTGTGTGGCAATATCAGTTTA 59.604 41.667 5.25 0.00 34.17 2.01
1567 4935 2.751259 CAGCTGTGTGGCAATATCAGTT 59.249 45.455 5.25 0.00 34.17 3.16
1568 4936 2.362736 CAGCTGTGTGGCAATATCAGT 58.637 47.619 5.25 0.00 34.17 3.41
1569 4937 1.674441 CCAGCTGTGTGGCAATATCAG 59.326 52.381 13.81 0.00 34.17 2.90
1570 4938 1.281577 TCCAGCTGTGTGGCAATATCA 59.718 47.619 13.81 0.00 37.53 2.15
1571 4939 1.672881 GTCCAGCTGTGTGGCAATATC 59.327 52.381 13.81 0.00 37.53 1.63
1572 4940 1.004628 TGTCCAGCTGTGTGGCAATAT 59.995 47.619 13.81 0.00 37.53 1.28
1578 4946 1.898574 GGGTTGTCCAGCTGTGTGG 60.899 63.158 13.81 0.00 39.19 4.17
1585 4953 1.179174 GGAACCTTGGGTTGTCCAGC 61.179 60.000 6.69 0.00 46.95 4.85
1587 4955 1.149627 CGGAACCTTGGGTTGTCCA 59.850 57.895 6.69 0.00 46.95 4.02
1590 4958 1.144093 TGAATCGGAACCTTGGGTTGT 59.856 47.619 6.69 0.00 46.95 3.32
1594 4962 1.904287 TGTTGAATCGGAACCTTGGG 58.096 50.000 0.00 0.00 0.00 4.12
1595 4963 3.638484 GTTTGTTGAATCGGAACCTTGG 58.362 45.455 0.00 0.00 0.00 3.61
1596 4964 3.002862 TCGTTTGTTGAATCGGAACCTTG 59.997 43.478 0.00 0.00 0.00 3.61
1652 5020 8.883731 GTTGTAATCAAGAACATGCACTATAGT 58.116 33.333 0.00 0.00 33.97 2.12
1653 5021 9.102757 AGTTGTAATCAAGAACATGCACTATAG 57.897 33.333 0.00 0.00 33.82 1.31
1749 5118 1.656652 CAAATAGCAGACCTGTCCCG 58.343 55.000 0.00 0.00 0.00 5.14
1861 5235 9.689976 CAAGTATTCATGAGAAGATAGGTACAG 57.310 37.037 0.00 0.00 37.14 2.74
1905 5279 4.336433 TGCTATTTCCTCTACAAGCAATGC 59.664 41.667 0.00 0.00 37.05 3.56
1979 5353 4.600062 AGGATCCCAACATGAAACTTACC 58.400 43.478 8.55 0.00 0.00 2.85
1981 5355 4.941263 CGAAGGATCCCAACATGAAACTTA 59.059 41.667 8.55 0.00 0.00 2.24
2022 5396 8.461222 CAAACATATCAAATGGAGCACTCTTTA 58.539 33.333 0.00 0.00 0.00 1.85
2196 5573 1.001974 AGCAGTTCGCAGACCATGTTA 59.998 47.619 0.00 0.00 46.13 2.41
2323 5769 2.827652 TGAACACACACATGAAGCGTA 58.172 42.857 0.00 0.00 0.00 4.42
2580 6027 1.171308 CGTTCTTGTAGGTCTCCGGA 58.829 55.000 2.93 2.93 0.00 5.14
2817 6265 2.536761 TCACCATCGAAAACGACCTT 57.463 45.000 0.00 0.00 0.00 3.50
2944 6393 0.623723 GCCCCCAGGATAAACACAGA 59.376 55.000 0.00 0.00 33.47 3.41
2945 6394 0.625849 AGCCCCCAGGATAAACACAG 59.374 55.000 0.00 0.00 33.47 3.66
2953 6402 2.478292 CGGTATATTAGCCCCCAGGAT 58.522 52.381 0.00 0.00 34.71 3.24
2955 6404 0.252197 GCGGTATATTAGCCCCCAGG 59.748 60.000 0.00 0.00 0.00 4.45
3007 6456 5.501156 CTCCCTCTTATTTAGGCAAACACT 58.499 41.667 0.00 0.00 32.34 3.55
3138 6592 4.037208 AGTGTGATTTCTGCCTTTGACTTG 59.963 41.667 0.00 0.00 0.00 3.16
3250 6845 1.000955 GTACGGATCCAGCCCACATAG 59.999 57.143 13.41 0.00 0.00 2.23
3251 6846 1.045407 GTACGGATCCAGCCCACATA 58.955 55.000 13.41 0.00 0.00 2.29
3252 6847 1.830145 GTACGGATCCAGCCCACAT 59.170 57.895 13.41 0.00 0.00 3.21
3272 6870 1.340889 AGCACGGTTAAGTAACGACCA 59.659 47.619 0.00 0.00 37.07 4.02
3283 6881 3.575256 TCTCCTTAACTTCAGCACGGTTA 59.425 43.478 0.00 0.00 0.00 2.85
3285 6883 1.968493 TCTCCTTAACTTCAGCACGGT 59.032 47.619 0.00 0.00 0.00 4.83
3288 6886 5.008118 GCCATATTCTCCTTAACTTCAGCAC 59.992 44.000 0.00 0.00 0.00 4.40
3326 6924 1.445582 GTGCTACCGTCTCCCAACG 60.446 63.158 0.00 0.00 42.24 4.10
3370 6968 6.420913 ACACCTATCCTATTATTTGAGCGT 57.579 37.500 0.00 0.00 0.00 5.07
3397 6995 4.101585 TCGGCAGAAATAGGACAAGATGAT 59.898 41.667 0.00 0.00 0.00 2.45
3448 7383 8.999431 ACGTAGTTTGATACAACTTCATGAATT 58.001 29.630 8.96 0.00 37.78 2.17
3607 9305 1.087771 CCGGTCCGTTATGAGGTTGC 61.088 60.000 11.06 0.00 0.00 4.17
3645 9343 7.344871 AGTGGTAGTTGGCAAATACTATAGACT 59.655 37.037 29.69 21.17 0.00 3.24
3676 9374 0.727398 GGCGCGTGCTTTTTCTCTAT 59.273 50.000 21.89 0.00 42.25 1.98
3686 9385 2.287457 TATAAAGTCGGGCGCGTGCT 62.287 55.000 23.19 18.24 42.25 4.40
3713 9412 6.670464 TGTATGTTCTGAACCCTACCTATTGA 59.330 38.462 17.26 1.37 0.00 2.57
3716 9415 6.126854 GGTTGTATGTTCTGAACCCTACCTAT 60.127 42.308 17.26 5.47 33.11 2.57
3723 9422 5.722021 ATTTGGTTGTATGTTCTGAACCC 57.278 39.130 17.26 10.48 37.63 4.11
3749 9448 8.255206 TGTGTAACCATATTGTCTTAATCTCGT 58.745 33.333 0.00 0.00 34.36 4.18
3766 9465 2.292016 CGGCTTTCATGTTGTGTAACCA 59.708 45.455 0.00 0.00 35.92 3.67
3767 9466 2.351350 CCGGCTTTCATGTTGTGTAACC 60.351 50.000 0.00 0.00 35.92 2.85
3775 9474 3.689649 GTGTCTATTCCGGCTTTCATGTT 59.310 43.478 0.00 0.00 0.00 2.71
3794 9493 0.611200 TAGGTAGTTGGCATGCGTGT 59.389 50.000 12.44 0.00 0.00 4.49
3846 9545 2.359850 GCCGATGCTGGTTGACCA 60.360 61.111 2.40 2.40 45.30 4.02
3860 9559 1.501741 CTCCAAAACGACCATGCCG 59.498 57.895 0.00 4.51 0.00 5.69
3873 9572 1.347707 ACATCGTCTTCCTTGCTCCAA 59.652 47.619 0.00 0.00 0.00 3.53
3891 9590 5.507985 CCTGATCGCATGAGTACATTCTACA 60.508 44.000 0.00 0.00 34.15 2.74
3903 9602 1.827344 ACTGAAGACCTGATCGCATGA 59.173 47.619 0.00 0.00 0.00 3.07
3905 9604 2.625737 CAACTGAAGACCTGATCGCAT 58.374 47.619 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.