Multiple sequence alignment - TraesCS2D01G442500

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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 TraesCS2D01G442500 chr2D 100.000 3982 0 0 1 3982 552960149 552964130 0.000000e+00 7354.0
1 TraesCS2D01G442500 chr2D 92.844 545 28 5 1 534 156022692 156023236 0.000000e+00 780.0
2 TraesCS2D01G442500 chr2D 92.764 539 27 5 1 528 156018370 156018907 0.000000e+00 769.0
3 TraesCS2D01G442500 chr2A 93.205 677 35 6 2662 3333 693285573 693286243 0.000000e+00 985.0
4 TraesCS2D01G442500 chr2A 82.101 1190 90 61 529 1667 693283485 693284602 0.000000e+00 904.0
5 TraesCS2D01G442500 chr2A 93.310 568 31 2 3415 3982 576652278 576652838 0.000000e+00 832.0
6 TraesCS2D01G442500 chr2A 84.150 612 42 27 1694 2289 693284685 693285257 3.500000e-150 542.0
7 TraesCS2D01G442500 chr2A 81.305 567 98 3 3415 3980 771683688 771684247 1.690000e-123 453.0
8 TraesCS2D01G442500 chr2A 78.022 546 110 4 3415 3959 47349633 47349097 6.380000e-88 335.0
9 TraesCS2D01G442500 chr2B 89.526 802 45 16 524 1308 658603396 658604175 0.000000e+00 979.0
10 TraesCS2D01G442500 chr2B 88.421 760 54 21 2669 3410 658605704 658606447 0.000000e+00 885.0
11 TraesCS2D01G442500 chr2B 84.330 970 77 26 1682 2592 658604563 658605516 0.000000e+00 880.0
12 TraesCS2D01G442500 chr2B 84.109 258 13 17 1378 1619 658604205 658604450 1.440000e-54 224.0
13 TraesCS2D01G442500 chr4A 94.728 569 23 2 3415 3982 453314592 453315154 0.000000e+00 878.0
14 TraesCS2D01G442500 chr4A 94.095 525 23 3 3410 3932 89936515 89937033 0.000000e+00 791.0
15 TraesCS2D01G442500 chr4A 92.778 540 26 6 1 528 80028377 80028915 0.000000e+00 769.0
16 TraesCS2D01G442500 chr4A 91.280 539 35 6 1 528 259869662 259870199 0.000000e+00 725.0
17 TraesCS2D01G442500 chr4A 90.149 538 39 9 1 527 398874217 398873683 0.000000e+00 688.0
18 TraesCS2D01G442500 chr4A 89.425 539 45 7 1 528 398885490 398884953 0.000000e+00 669.0
19 TraesCS2D01G442500 chr4A 89.054 539 46 8 1 528 398879850 398879314 0.000000e+00 656.0
20 TraesCS2D01G442500 chr6B 93.662 568 30 3 3415 3982 29967103 29966542 0.000000e+00 845.0
21 TraesCS2D01G442500 chr4B 93.206 574 33 1 3409 3982 488897056 488897623 0.000000e+00 839.0
22 TraesCS2D01G442500 chr4B 83.148 540 78 10 1 528 246840356 246839818 7.740000e-132 481.0
23 TraesCS2D01G442500 chr6D 93.135 539 26 5 1 528 454145569 454145031 0.000000e+00 780.0
24 TraesCS2D01G442500 chr6D 92.937 538 27 4 1 527 454130360 454129823 0.000000e+00 773.0
25 TraesCS2D01G442500 chr1D 92.764 539 28 4 1 528 213294785 213294247 0.000000e+00 769.0
26 TraesCS2D01G442500 chr1D 92.393 539 30 4 1 528 365976021 365976559 0.000000e+00 758.0
27 TraesCS2D01G442500 chr6A 92.579 539 29 6 1 528 40731552 40731014 0.000000e+00 763.0
28 TraesCS2D01G442500 chr3A 91.619 525 41 3 3459 3982 561049030 561048508 0.000000e+00 723.0
29 TraesCS2D01G442500 chr5B 88.930 542 43 11 1 528 30835714 30835176 0.000000e+00 652.0
30 TraesCS2D01G442500 chr1B 88.683 539 48 5 1 527 156445087 156445624 0.000000e+00 645.0
31 TraesCS2D01G442500 chr3B 87.985 541 45 8 1 527 30447670 30447136 4.370000e-174 621.0
32 TraesCS2D01G442500 chr5A 87.638 542 43 8 1 530 91162705 91162176 3.400000e-170 608.0
33 TraesCS2D01G442500 chr1A 84.889 450 66 2 3534 3982 277648163 277647715 1.690000e-123 453.0
34 TraesCS2D01G442500 chr7A 94.872 39 1 1 3944 3982 443171468 443171505 4.300000e-05 60.2


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G442500 chr2D 552960149 552964130 3981 False 7354.000000 7354 100.000000 1 3982 1 chr2D.!!$F1 3981
1 TraesCS2D01G442500 chr2D 156018370 156023236 4866 False 774.500000 780 92.804000 1 534 2 chr2D.!!$F2 533
2 TraesCS2D01G442500 chr2A 576652278 576652838 560 False 832.000000 832 93.310000 3415 3982 1 chr2A.!!$F1 567
3 TraesCS2D01G442500 chr2A 693283485 693286243 2758 False 810.333333 985 86.485333 529 3333 3 chr2A.!!$F3 2804
4 TraesCS2D01G442500 chr2A 771683688 771684247 559 False 453.000000 453 81.305000 3415 3980 1 chr2A.!!$F2 565
5 TraesCS2D01G442500 chr2A 47349097 47349633 536 True 335.000000 335 78.022000 3415 3959 1 chr2A.!!$R1 544
6 TraesCS2D01G442500 chr2B 658603396 658606447 3051 False 742.000000 979 86.596500 524 3410 4 chr2B.!!$F1 2886
7 TraesCS2D01G442500 chr4A 453314592 453315154 562 False 878.000000 878 94.728000 3415 3982 1 chr4A.!!$F4 567
8 TraesCS2D01G442500 chr4A 89936515 89937033 518 False 791.000000 791 94.095000 3410 3932 1 chr4A.!!$F2 522
9 TraesCS2D01G442500 chr4A 80028377 80028915 538 False 769.000000 769 92.778000 1 528 1 chr4A.!!$F1 527
10 TraesCS2D01G442500 chr4A 259869662 259870199 537 False 725.000000 725 91.280000 1 528 1 chr4A.!!$F3 527
11 TraesCS2D01G442500 chr4A 398873683 398874217 534 True 688.000000 688 90.149000 1 527 1 chr4A.!!$R1 526
12 TraesCS2D01G442500 chr4A 398884953 398885490 537 True 669.000000 669 89.425000 1 528 1 chr4A.!!$R3 527
13 TraesCS2D01G442500 chr4A 398879314 398879850 536 True 656.000000 656 89.054000 1 528 1 chr4A.!!$R2 527
14 TraesCS2D01G442500 chr6B 29966542 29967103 561 True 845.000000 845 93.662000 3415 3982 1 chr6B.!!$R1 567
15 TraesCS2D01G442500 chr4B 488897056 488897623 567 False 839.000000 839 93.206000 3409 3982 1 chr4B.!!$F1 573
16 TraesCS2D01G442500 chr4B 246839818 246840356 538 True 481.000000 481 83.148000 1 528 1 chr4B.!!$R1 527
17 TraesCS2D01G442500 chr6D 454145031 454145569 538 True 780.000000 780 93.135000 1 528 1 chr6D.!!$R2 527
18 TraesCS2D01G442500 chr6D 454129823 454130360 537 True 773.000000 773 92.937000 1 527 1 chr6D.!!$R1 526
19 TraesCS2D01G442500 chr1D 213294247 213294785 538 True 769.000000 769 92.764000 1 528 1 chr1D.!!$R1 527
20 TraesCS2D01G442500 chr1D 365976021 365976559 538 False 758.000000 758 92.393000 1 528 1 chr1D.!!$F1 527
21 TraesCS2D01G442500 chr6A 40731014 40731552 538 True 763.000000 763 92.579000 1 528 1 chr6A.!!$R1 527
22 TraesCS2D01G442500 chr3A 561048508 561049030 522 True 723.000000 723 91.619000 3459 3982 1 chr3A.!!$R1 523
23 TraesCS2D01G442500 chr5B 30835176 30835714 538 True 652.000000 652 88.930000 1 528 1 chr5B.!!$R1 527
24 TraesCS2D01G442500 chr1B 156445087 156445624 537 False 645.000000 645 88.683000 1 527 1 chr1B.!!$F1 526
25 TraesCS2D01G442500 chr3B 30447136 30447670 534 True 621.000000 621 87.985000 1 527 1 chr3B.!!$R1 526
26 TraesCS2D01G442500 chr5A 91162176 91162705 529 True 608.000000 608 87.638000 1 530 1 chr5A.!!$R1 529

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
569 4913 0.237235 TCAAAACAACTGATCGCCGC 59.763 50.0 0.00 0.0 0.0 6.53 F
1313 5700 0.035152 CCCCTCACACAAGCATAGCA 60.035 55.0 0.00 0.0 0.0 3.49 F
2198 6759 0.035820 GGCACCGGTCTTATCCACAA 60.036 55.0 2.59 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1441 5861 0.034380 TGTGGGTGTTTCCAAACCGA 60.034 50.0 0.0 0.0 38.72 4.69 R
2512 7094 0.248012 TCGCTGTCCGCTTTCCATTA 59.752 50.0 0.0 0.0 36.73 1.90 R
3337 8131 0.167470 CCAAATGCAGCTCAGTCACG 59.833 55.0 0.0 0.0 0.00 4.35 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
79 91 1.146263 GATGTCGAAATCGGCCCCT 59.854 57.895 4.83 0.00 44.42 4.79
155 4489 0.323629 TCTGTTTAGCCCGGAACCTG 59.676 55.000 0.73 0.00 0.00 4.00
230 4564 4.513442 TGGCTCTAACTTTTGCATACGAT 58.487 39.130 0.00 0.00 0.00 3.73
405 4745 3.422796 GCCTTAGAGATGAGACCGGATA 58.577 50.000 9.46 0.00 0.00 2.59
481 4821 6.205464 CACTTTGAGCACTTCTCCATTTAAGA 59.795 38.462 0.00 0.00 41.18 2.10
504 4844 8.649973 AGACTATCTTAATTAAGTTCTTGGCG 57.350 34.615 21.69 8.13 34.93 5.69
561 4905 5.143660 TGCGAAATACGATCAAAACAACTG 58.856 37.500 0.00 0.00 45.77 3.16
569 4913 0.237235 TCAAAACAACTGATCGCCGC 59.763 50.000 0.00 0.00 0.00 6.53
619 4964 4.840288 TGATCCGGTGCGTACGCG 62.840 66.667 32.65 19.71 45.51 6.01
683 5041 0.954452 GCATGGCTAGCACCCAATAC 59.046 55.000 18.24 0.00 35.67 1.89
768 5131 4.265056 ACCCAGGGTTGCCGTCAC 62.265 66.667 4.76 0.00 27.29 3.67
806 5169 2.897350 CTCATTCGCTTCGCCCCC 60.897 66.667 0.00 0.00 0.00 5.40
819 5186 3.129362 GCCCCCGGTATTCCTTCCC 62.129 68.421 0.00 0.00 0.00 3.97
904 5281 1.265365 CACACACACACACACACACAA 59.735 47.619 0.00 0.00 0.00 3.33
905 5282 1.535028 ACACACACACACACACACAAG 59.465 47.619 0.00 0.00 0.00 3.16
918 5297 0.818040 ACACAAGCGAAACCCACTCC 60.818 55.000 0.00 0.00 0.00 3.85
919 5298 0.817634 CACAAGCGAAACCCACTCCA 60.818 55.000 0.00 0.00 0.00 3.86
921 5300 1.228154 AAGCGAAACCCACTCCACC 60.228 57.895 0.00 0.00 0.00 4.61
943 5324 2.101965 CGTCTCGGAGCAGAGCAG 59.898 66.667 0.00 0.00 38.12 4.24
944 5325 2.402572 CGTCTCGGAGCAGAGCAGA 61.403 63.158 0.00 0.00 38.12 4.26
945 5326 1.433064 GTCTCGGAGCAGAGCAGAG 59.567 63.158 0.00 0.00 38.12 3.35
947 5328 3.429080 CTCGGAGCAGAGCAGAGCC 62.429 68.421 0.00 0.00 0.00 4.70
948 5329 3.459965 CGGAGCAGAGCAGAGCCT 61.460 66.667 0.00 0.00 0.00 4.58
949 5330 2.500646 GGAGCAGAGCAGAGCCTC 59.499 66.667 0.00 0.00 0.00 4.70
950 5331 2.059786 GGAGCAGAGCAGAGCCTCT 61.060 63.158 0.00 0.00 42.75 3.69
951 5332 1.438814 GAGCAGAGCAGAGCCTCTC 59.561 63.158 0.00 0.00 40.11 3.20
952 5333 1.000739 AGCAGAGCAGAGCCTCTCT 59.999 57.895 0.00 0.00 42.11 3.10
953 5334 0.615544 AGCAGAGCAGAGCCTCTCTT 60.616 55.000 0.00 0.00 38.99 2.85
954 5335 0.249955 GCAGAGCAGAGCCTCTCTTT 59.750 55.000 0.00 0.00 38.99 2.52
955 5336 2.008045 GCAGAGCAGAGCCTCTCTTTG 61.008 57.143 0.00 0.00 38.99 2.77
956 5337 1.275856 CAGAGCAGAGCCTCTCTTTGT 59.724 52.381 0.00 0.00 38.99 2.83
988 5369 3.077556 TTCCTCCCTCTCGGCAGC 61.078 66.667 0.00 0.00 0.00 5.25
1159 5540 8.157476 AGTACATGTTCCAAGTAAATCAGTTCT 58.843 33.333 2.30 0.00 0.00 3.01
1163 5544 7.962964 TGTTCCAAGTAAATCAGTTCTAGTG 57.037 36.000 0.00 0.00 0.00 2.74
1215 5602 4.645535 TCTTGTTCTTGTTCTCATGGAGG 58.354 43.478 0.00 0.00 0.00 4.30
1217 5604 4.008074 TGTTCTTGTTCTCATGGAGGTC 57.992 45.455 0.00 0.00 0.00 3.85
1241 5628 5.106237 CCGTAGTGCTAGTTCTAGTTCTTGT 60.106 44.000 8.38 0.00 0.00 3.16
1242 5629 6.093219 CCGTAGTGCTAGTTCTAGTTCTTGTA 59.907 42.308 8.38 0.00 0.00 2.41
1243 5630 6.960431 CGTAGTGCTAGTTCTAGTTCTTGTAC 59.040 42.308 8.38 9.56 0.00 2.90
1244 5631 7.148440 CGTAGTGCTAGTTCTAGTTCTTGTACT 60.148 40.741 17.72 17.72 36.70 2.73
1245 5632 7.148355 AGTGCTAGTTCTAGTTCTTGTACTC 57.852 40.000 8.38 0.00 30.53 2.59
1258 5645 8.535690 AGTTCTTGTACTCTACTTGTTATTGC 57.464 34.615 0.00 0.00 0.00 3.56
1308 5695 1.150536 GGTTCCCCTCACACAAGCA 59.849 57.895 0.00 0.00 0.00 3.91
1309 5696 0.251341 GGTTCCCCTCACACAAGCAT 60.251 55.000 0.00 0.00 0.00 3.79
1310 5697 1.004277 GGTTCCCCTCACACAAGCATA 59.996 52.381 0.00 0.00 0.00 3.14
1311 5698 2.359900 GTTCCCCTCACACAAGCATAG 58.640 52.381 0.00 0.00 0.00 2.23
1312 5699 0.253044 TCCCCTCACACAAGCATAGC 59.747 55.000 0.00 0.00 0.00 2.97
1313 5700 0.035152 CCCCTCACACAAGCATAGCA 60.035 55.000 0.00 0.00 0.00 3.49
1314 5701 1.409241 CCCCTCACACAAGCATAGCAT 60.409 52.381 0.00 0.00 0.00 3.79
1326 5720 1.994074 GCATAGCATCATCTCGCTCTG 59.006 52.381 0.00 0.00 39.70 3.35
1337 5731 5.906073 TCATCTCGCTCTGTGAATGATTAA 58.094 37.500 0.00 0.00 0.00 1.40
1348 5742 5.640147 TGTGAATGATTAACCCCTGTTCTT 58.360 37.500 0.00 0.00 35.87 2.52
1353 5747 6.840780 ATGATTAACCCCTGTTCTTTGAAG 57.159 37.500 0.00 0.00 35.87 3.02
1366 5760 3.758973 TTGAAGCGGCGTTGTGGGA 62.759 57.895 9.37 0.00 0.00 4.37
1389 5791 1.672737 GGCACCATGCTAAAACTTGCC 60.673 52.381 0.13 0.00 44.28 4.52
1390 5792 1.273327 GCACCATGCTAAAACTTGCCT 59.727 47.619 0.00 0.00 40.96 4.75
1391 5793 2.491693 GCACCATGCTAAAACTTGCCTA 59.508 45.455 0.00 0.00 40.96 3.93
1392 5794 3.056891 GCACCATGCTAAAACTTGCCTAA 60.057 43.478 0.00 0.00 40.96 2.69
1393 5795 4.560513 GCACCATGCTAAAACTTGCCTAAA 60.561 41.667 0.00 0.00 40.96 1.85
1430 5832 7.809806 CCCAAAGATAGAAAGATTGTGTGTTTC 59.190 37.037 0.00 0.00 39.66 2.78
1431 5833 8.352201 CCAAAGATAGAAAGATTGTGTGTTTCA 58.648 33.333 0.00 0.00 41.29 2.69
1432 5834 9.390795 CAAAGATAGAAAGATTGTGTGTTTCAG 57.609 33.333 0.00 0.00 41.29 3.02
1434 5836 8.682936 AGATAGAAAGATTGTGTGTTTCAGTT 57.317 30.769 0.00 0.00 41.29 3.16
1437 5857 7.396540 AGAAAGATTGTGTGTTTCAGTTTCT 57.603 32.000 0.00 0.00 41.29 2.52
1439 5859 8.306761 AGAAAGATTGTGTGTTTCAGTTTCTTT 58.693 29.630 0.00 0.00 41.29 2.52
1440 5860 9.567848 GAAAGATTGTGTGTTTCAGTTTCTTTA 57.432 29.630 0.00 0.00 39.29 1.85
1444 5864 6.055231 TGTGTGTTTCAGTTTCTTTATCGG 57.945 37.500 0.00 0.00 0.00 4.18
1453 5873 6.731164 TCAGTTTCTTTATCGGTTTGGAAAC 58.269 36.000 0.00 0.00 41.24 2.78
1456 5876 5.441709 TTCTTTATCGGTTTGGAAACACC 57.558 39.130 4.71 0.00 42.67 4.16
1463 5883 2.737039 CGGTTTGGAAACACCCACAAAG 60.737 50.000 4.71 0.00 42.67 2.77
1464 5884 2.235155 GGTTTGGAAACACCCACAAAGT 59.765 45.455 4.71 0.00 42.67 2.66
1472 5892 5.983118 GGAAACACCCACAAAGTTCTTTATG 59.017 40.000 0.00 0.00 0.00 1.90
1473 5893 6.406512 GGAAACACCCACAAAGTTCTTTATGT 60.407 38.462 3.48 0.00 0.00 2.29
1474 5894 7.201839 GGAAACACCCACAAAGTTCTTTATGTA 60.202 37.037 3.48 0.00 0.00 2.29
1475 5895 7.833285 AACACCCACAAAGTTCTTTATGTAT 57.167 32.000 3.48 0.00 0.00 2.29
1476 5896 8.927675 AACACCCACAAAGTTCTTTATGTATA 57.072 30.769 3.48 0.00 0.00 1.47
1477 5897 8.927675 ACACCCACAAAGTTCTTTATGTATAA 57.072 30.769 3.48 0.00 0.00 0.98
1496 5916 1.050204 AAAAGCAGGGCAGAAATGCA 58.950 45.000 2.29 0.00 42.45 3.96
1510 5941 5.800941 GCAGAAATGCATTTTTCTCTCTCTG 59.199 40.000 24.81 22.68 42.58 3.35
1553 5984 3.838903 ACTTGTTTAGTCAGTCCCTAGGG 59.161 47.826 23.22 23.22 28.23 3.53
1554 5985 3.839323 TGTTTAGTCAGTCCCTAGGGA 57.161 47.619 27.73 27.73 42.90 4.20
1555 5986 5.934671 ACTTGTTTAGTCAGTCCCTAGGGAA 60.935 44.000 32.73 14.80 38.24 3.97
1556 5987 7.381171 ACTTGTTTAGTCAGTCCCTAGGGAAA 61.381 42.308 32.73 18.63 38.24 3.13
1557 5988 8.794046 ACTTGTTTAGTCAGTCCCTAGGGAAAA 61.794 40.741 32.73 23.18 38.24 2.29
1627 6070 1.748122 CACAGCCACAGGATGCCTC 60.748 63.158 0.49 0.00 43.70 4.70
1629 6072 3.790437 AGCCACAGGATGCCTCGG 61.790 66.667 0.00 0.00 42.53 4.63
1637 6080 1.134280 CAGGATGCCTCGGTGAATCTT 60.134 52.381 0.00 0.00 0.00 2.40
1638 6081 1.134280 AGGATGCCTCGGTGAATCTTG 60.134 52.381 0.00 0.00 0.00 3.02
1667 6110 0.681733 GAGAGCTCCACCACACAAGA 59.318 55.000 10.93 0.00 0.00 3.02
1719 6219 2.979649 GAGGAAGGGACGGTGGAC 59.020 66.667 0.00 0.00 0.00 4.02
1749 6249 6.614694 TTATTGCTCCTTGTACTCCAGTAA 57.385 37.500 0.00 0.00 31.52 2.24
1753 6255 4.705507 TGCTCCTTGTACTCCAGTAAGTAG 59.294 45.833 0.00 0.00 32.52 2.57
1755 6257 5.185442 GCTCCTTGTACTCCAGTAAGTAGTT 59.815 44.000 0.00 0.00 32.52 2.24
1758 6260 6.552350 TCCTTGTACTCCAGTAAGTAGTTGTT 59.448 38.462 0.00 0.00 32.52 2.83
1759 6261 6.645415 CCTTGTACTCCAGTAAGTAGTTGTTG 59.355 42.308 0.00 0.00 32.52 3.33
1767 6269 5.815740 CCAGTAAGTAGTTGTTGTTCACAGT 59.184 40.000 0.00 0.00 36.48 3.55
1774 6281 1.009675 GTTGTTCACAGTGCGCAGG 60.010 57.895 12.22 9.27 0.00 4.85
1849 6375 2.428925 GCGAATGGGAGGACGGGTA 61.429 63.158 0.00 0.00 0.00 3.69
1993 6532 0.906756 TGCAAGGGAGGAGAGAGGTG 60.907 60.000 0.00 0.00 0.00 4.00
2054 6593 0.907704 ATGAGCCCTGTACGGTTCCA 60.908 55.000 0.00 0.00 32.42 3.53
2180 6741 2.231529 CTAGGGTGAGTAGGATGACGG 58.768 57.143 0.00 0.00 0.00 4.79
2182 6743 1.327690 GGGTGAGTAGGATGACGGCA 61.328 60.000 0.00 0.00 0.00 5.69
2198 6759 0.035820 GGCACCGGTCTTATCCACAA 60.036 55.000 2.59 0.00 0.00 3.33
2208 6769 1.633432 CTTATCCACAAGACCCACCCA 59.367 52.381 0.00 0.00 0.00 4.51
2209 6770 0.988832 TATCCACAAGACCCACCCAC 59.011 55.000 0.00 0.00 0.00 4.61
2210 6771 1.065410 ATCCACAAGACCCACCCACA 61.065 55.000 0.00 0.00 0.00 4.17
2213 6774 2.115266 CAAGACCCACCCACACCC 59.885 66.667 0.00 0.00 0.00 4.61
2214 6775 2.369015 AAGACCCACCCACACCCA 60.369 61.111 0.00 0.00 0.00 4.51
2215 6776 2.763645 AAGACCCACCCACACCCAC 61.764 63.158 0.00 0.00 0.00 4.61
2216 6777 4.280019 GACCCACCCACACCCACC 62.280 72.222 0.00 0.00 0.00 4.61
2279 6843 0.551396 CCCCCTACTTTGTCATCCCC 59.449 60.000 0.00 0.00 0.00 4.81
2313 6877 3.406361 CCAGACGTGCGTGTGAGC 61.406 66.667 20.74 0.00 41.22 4.26
2316 6880 4.046998 GACGTGCGTGTGAGCGTG 62.047 66.667 0.67 0.00 40.67 5.34
2423 7005 1.262166 GCACTCTTTGCGTGCGTTTC 61.262 55.000 0.00 0.00 46.81 2.78
2425 7007 0.582005 ACTCTTTGCGTGCGTTTCTC 59.418 50.000 0.00 0.00 0.00 2.87
2428 7010 0.861837 CTTTGCGTGCGTTTCTCTCT 59.138 50.000 0.00 0.00 0.00 3.10
2431 7013 0.879090 TGCGTGCGTTTCTCTCTAGA 59.121 50.000 0.00 0.00 0.00 2.43
2437 7019 1.469423 GCGTTTCTCTCTAGAACCCGG 60.469 57.143 0.00 0.00 41.48 5.73
2441 7023 0.323178 TCTCTCTAGAACCCGGCGTT 60.323 55.000 6.01 7.90 37.41 4.84
2454 7036 2.125793 GCGTTCCGGACACCTACC 60.126 66.667 1.83 0.00 0.00 3.18
2455 7037 2.934570 GCGTTCCGGACACCTACCA 61.935 63.158 1.83 0.00 0.00 3.25
2456 7038 1.080298 CGTTCCGGACACCTACCAC 60.080 63.158 1.83 0.00 0.00 4.16
2457 7039 1.808531 CGTTCCGGACACCTACCACA 61.809 60.000 1.83 0.00 0.00 4.17
2458 7040 0.320160 GTTCCGGACACCTACCACAC 60.320 60.000 1.83 0.00 0.00 3.82
2459 7041 0.470456 TTCCGGACACCTACCACACT 60.470 55.000 1.83 0.00 0.00 3.55
2460 7042 0.470456 TCCGGACACCTACCACACTT 60.470 55.000 0.00 0.00 0.00 3.16
2461 7043 0.395312 CCGGACACCTACCACACTTT 59.605 55.000 0.00 0.00 0.00 2.66
2462 7044 1.508632 CGGACACCTACCACACTTTG 58.491 55.000 0.00 0.00 0.00 2.77
2463 7045 1.202604 CGGACACCTACCACACTTTGT 60.203 52.381 0.00 0.00 0.00 2.83
2472 7054 1.009675 CACACTTTGTGGTCTGCGC 60.010 57.895 0.00 0.00 44.27 6.09
2473 7055 1.153168 ACACTTTGTGGTCTGCGCT 60.153 52.632 9.73 0.00 37.94 5.92
2474 7056 1.280746 CACTTTGTGGTCTGCGCTG 59.719 57.895 9.73 8.88 0.00 5.18
2545 7146 1.202580 ACAGCGATCTGGCCAAGATAC 60.203 52.381 7.01 8.01 46.12 2.24
2592 7196 7.739498 ATCTTAACGTTCACTTATTGGTTGT 57.261 32.000 2.82 0.00 0.00 3.32
2595 7199 3.811083 ACGTTCACTTATTGGTTGTCCA 58.189 40.909 0.00 0.00 42.66 4.02
2596 7200 3.562557 ACGTTCACTTATTGGTTGTCCAC 59.437 43.478 0.00 0.00 44.22 4.02
2612 7330 6.438763 GTTGTCCACCTTTAAGATCTTGTTG 58.561 40.000 18.47 7.24 0.00 3.33
2618 7336 7.283127 TCCACCTTTAAGATCTTGTTGATATGC 59.717 37.037 18.47 0.00 35.14 3.14
2622 7340 8.778358 CCTTTAAGATCTTGTTGATATGCTACC 58.222 37.037 18.47 0.00 35.14 3.18
2623 7341 9.330063 CTTTAAGATCTTGTTGATATGCTACCA 57.670 33.333 18.47 0.00 35.14 3.25
2642 7360 1.724623 CATCAAGTCAACGTGGTACCG 59.275 52.381 7.57 0.00 0.00 4.02
2644 7362 0.856641 CAAGTCAACGTGGTACCGTG 59.143 55.000 7.57 4.41 41.65 4.94
2645 7363 0.249573 AAGTCAACGTGGTACCGTGG 60.250 55.000 7.57 0.00 41.65 4.94
2648 7366 1.067635 GTCAACGTGGTACCGTGGTAT 60.068 52.381 7.57 0.00 41.65 2.73
2650 7368 2.423185 TCAACGTGGTACCGTGGTATAG 59.577 50.000 7.57 0.00 41.65 1.31
2652 7370 1.064758 ACGTGGTACCGTGGTATAGGA 60.065 52.381 7.57 0.00 40.08 2.94
2653 7371 2.023673 CGTGGTACCGTGGTATAGGAA 58.976 52.381 7.57 0.00 32.82 3.36
2654 7372 2.624838 CGTGGTACCGTGGTATAGGAAT 59.375 50.000 7.57 0.00 32.82 3.01
2656 7374 4.460382 CGTGGTACCGTGGTATAGGAATAT 59.540 45.833 7.57 0.00 32.82 1.28
2657 7375 5.620654 CGTGGTACCGTGGTATAGGAATATG 60.621 48.000 7.57 0.00 32.82 1.78
2659 7377 6.154021 GTGGTACCGTGGTATAGGAATATGAT 59.846 42.308 7.57 0.00 32.82 2.45
2700 7458 0.818938 GGTCCGGTTTTGGTGTTTGT 59.181 50.000 0.00 0.00 0.00 2.83
2701 7459 1.205179 GGTCCGGTTTTGGTGTTTGTT 59.795 47.619 0.00 0.00 0.00 2.83
3005 7768 3.103911 GCGACCACCAAGACGACG 61.104 66.667 0.00 0.00 0.00 5.12
3052 7815 2.202946 GCTTAGCTGGGCTCGACC 60.203 66.667 0.00 0.00 40.44 4.79
3077 7846 9.096823 CCACCCACCTAATTATAATCTACAGTA 57.903 37.037 0.00 0.00 0.00 2.74
3130 7904 3.705072 GGCACCAGAACCAGTAGTAGTAT 59.295 47.826 0.00 0.00 0.00 2.12
3189 7966 5.758784 AGATGTGTGATGATGATGATGACAC 59.241 40.000 7.57 7.57 34.22 3.67
3222 7999 2.426024 GCTGTGATGTACTCCCGTCTTA 59.574 50.000 0.00 0.00 0.00 2.10
3227 8004 3.119388 TGATGTACTCCCGTCTTAAACCG 60.119 47.826 0.00 0.00 0.00 4.44
3250 8027 5.179742 CGGTACTATTGCAAGTGTTTGGTAA 59.820 40.000 4.94 0.00 34.79 2.85
3269 8046 1.016130 ACCGCTGCGTCTCTTGATTG 61.016 55.000 21.59 3.70 0.00 2.67
3314 8108 2.611473 CGTTCTCTGTCAGGCATTCAGT 60.611 50.000 0.00 0.00 0.00 3.41
3317 8111 5.450550 CGTTCTCTGTCAGGCATTCAGTATA 60.451 44.000 0.00 0.00 0.00 1.47
3335 8129 5.047306 CAGTATAGACAGGGACTTGAACACA 60.047 44.000 0.00 0.00 34.60 3.72
3337 8131 3.409026 AGACAGGGACTTGAACACATC 57.591 47.619 0.00 0.00 34.60 3.06
3341 8135 1.691976 AGGGACTTGAACACATCGTGA 59.308 47.619 0.24 0.00 33.03 4.35
3346 8140 3.384668 ACTTGAACACATCGTGACTGAG 58.615 45.455 0.24 0.00 36.96 3.35
3347 8141 1.783284 TGAACACATCGTGACTGAGC 58.217 50.000 0.24 0.00 36.96 4.26
3357 8151 0.109412 GTGACTGAGCTGCATTTGGC 60.109 55.000 1.02 0.00 45.13 4.52
3358 8152 0.251033 TGACTGAGCTGCATTTGGCT 60.251 50.000 1.02 0.00 45.15 4.75
3361 8158 1.945354 CTGAGCTGCATTTGGCTGGG 61.945 60.000 2.49 0.00 45.15 4.45
3377 8174 2.773487 CTGGGGTTTGATCAACGTGTA 58.227 47.619 7.89 0.00 36.05 2.90
3395 8192 3.073678 TGTATCACGCTGTGAATTTGCT 58.926 40.909 13.81 1.78 45.96 3.91
3396 8193 2.624316 ATCACGCTGTGAATTTGCTG 57.376 45.000 13.81 0.00 45.96 4.41
3397 8194 1.308047 TCACGCTGTGAATTTGCTGT 58.692 45.000 8.59 0.00 39.78 4.40
3398 8195 1.002576 TCACGCTGTGAATTTGCTGTG 60.003 47.619 8.59 0.00 39.78 3.66
3399 8196 1.024271 ACGCTGTGAATTTGCTGTGT 58.976 45.000 0.00 2.23 0.00 3.72
3400 8197 1.268692 ACGCTGTGAATTTGCTGTGTG 60.269 47.619 0.00 0.00 0.00 3.82
3401 8198 1.774639 GCTGTGAATTTGCTGTGTGG 58.225 50.000 0.00 0.00 0.00 4.17
3402 8199 1.067516 GCTGTGAATTTGCTGTGTGGT 59.932 47.619 0.00 0.00 0.00 4.16
3403 8200 2.859806 GCTGTGAATTTGCTGTGTGGTC 60.860 50.000 0.00 0.00 0.00 4.02
3404 8201 1.680735 TGTGAATTTGCTGTGTGGTCC 59.319 47.619 0.00 0.00 0.00 4.46
3405 8202 1.680735 GTGAATTTGCTGTGTGGTCCA 59.319 47.619 0.00 0.00 0.00 4.02
3406 8203 1.955778 TGAATTTGCTGTGTGGTCCAG 59.044 47.619 0.00 0.00 0.00 3.86
3407 8204 2.229792 GAATTTGCTGTGTGGTCCAGA 58.770 47.619 0.00 0.00 31.38 3.86
3408 8205 1.609208 ATTTGCTGTGTGGTCCAGAC 58.391 50.000 12.26 12.26 31.38 3.51
3452 8249 6.670233 GCAAAAGATTTGCCATTTTCATTGA 58.330 32.000 15.12 0.00 39.38 2.57
3453 8250 7.140048 GCAAAAGATTTGCCATTTTCATTGAA 58.860 30.769 15.12 0.00 39.38 2.69
3454 8251 7.810759 GCAAAAGATTTGCCATTTTCATTGAAT 59.189 29.630 15.12 0.00 39.38 2.57
3544 8341 4.495911 TGAATTACACAAATGCTTCGCA 57.504 36.364 0.00 0.00 44.86 5.10
3571 8368 3.057526 CGAGACACCACAGATTACACTCA 60.058 47.826 0.00 0.00 0.00 3.41
3627 8424 0.823356 GCCAAGTTGCAGAAGACCCA 60.823 55.000 0.00 0.00 0.00 4.51
3704 8501 1.873903 GCTTTCTGGACTGCGTCTTCA 60.874 52.381 8.26 0.01 32.47 3.02
3718 8515 0.601057 TCTTCATGGTCGCGTTGAGA 59.399 50.000 5.77 0.00 0.00 3.27
3756 8553 3.181429 ACTGAATTCATGTGACCCCACTT 60.181 43.478 8.96 0.00 43.55 3.16
3824 8621 4.081420 CCCAAACTCTAGCTGTGTATCTGT 60.081 45.833 0.00 0.00 0.00 3.41
3837 8634 6.989169 GCTGTGTATCTGTATTGGAAGAGAAT 59.011 38.462 0.00 0.00 0.00 2.40
3897 8695 2.834638 AGGTTGCAATTAGGCCATCT 57.165 45.000 5.01 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 4489 4.050934 CGGGCAAAACTTCCGGGC 62.051 66.667 0.00 0.00 40.07 6.13
230 4564 8.843262 TGATATAAAGAACGTCTAAATCGGAGA 58.157 33.333 0.00 0.00 45.75 3.71
405 4745 7.494922 AAACTTTGATATTTGGGCCATAGTT 57.505 32.000 7.26 4.72 34.12 2.24
481 4821 7.280205 CACCGCCAAGAACTTAATTAAGATAGT 59.720 37.037 27.92 12.17 37.08 2.12
520 4860 4.992688 TCGCAAAACAAAAGAGTGTTGAT 58.007 34.783 1.41 0.00 40.86 2.57
587 4932 3.150647 ATCACGCGCCGATCATGGA 62.151 57.895 5.73 0.00 0.00 3.41
588 4933 2.661566 GATCACGCGCCGATCATGG 61.662 63.158 25.84 1.77 39.30 3.66
600 4945 2.947621 CGTACGCACCGGATCACG 60.948 66.667 9.46 8.65 43.80 4.35
619 4964 2.044860 GAGTAGTCATGCACGTATCGC 58.955 52.381 0.00 0.00 0.00 4.58
701 5059 1.528586 CTGCACACCGTTTCTTCTCAG 59.471 52.381 0.00 0.00 0.00 3.35
753 5116 4.263572 TGGTGACGGCAACCCTGG 62.264 66.667 2.41 0.00 0.00 4.45
806 5169 1.148498 GGGCAGGGAAGGAATACCG 59.852 63.158 0.00 0.00 36.96 4.02
904 5281 2.430367 GGTGGAGTGGGTTTCGCT 59.570 61.111 0.00 0.00 39.23 4.93
905 5282 2.671963 GGGTGGAGTGGGTTTCGC 60.672 66.667 0.00 0.00 0.00 4.70
942 5323 2.301583 GTGAAGGACAAAGAGAGGCTCT 59.698 50.000 18.80 18.80 43.37 4.09
943 5324 2.614229 GGTGAAGGACAAAGAGAGGCTC 60.614 54.545 6.34 6.34 0.00 4.70
944 5325 1.349357 GGTGAAGGACAAAGAGAGGCT 59.651 52.381 0.00 0.00 0.00 4.58
945 5326 1.349357 AGGTGAAGGACAAAGAGAGGC 59.651 52.381 0.00 0.00 0.00 4.70
947 5328 3.243907 ACGAAGGTGAAGGACAAAGAGAG 60.244 47.826 0.00 0.00 0.00 3.20
948 5329 2.698797 ACGAAGGTGAAGGACAAAGAGA 59.301 45.455 0.00 0.00 0.00 3.10
949 5330 3.060602 GACGAAGGTGAAGGACAAAGAG 58.939 50.000 0.00 0.00 0.00 2.85
950 5331 2.698797 AGACGAAGGTGAAGGACAAAGA 59.301 45.455 0.00 0.00 0.00 2.52
951 5332 3.113260 AGACGAAGGTGAAGGACAAAG 57.887 47.619 0.00 0.00 0.00 2.77
952 5333 3.463944 GAAGACGAAGGTGAAGGACAAA 58.536 45.455 0.00 0.00 0.00 2.83
953 5334 2.224209 GGAAGACGAAGGTGAAGGACAA 60.224 50.000 0.00 0.00 0.00 3.18
954 5335 1.343465 GGAAGACGAAGGTGAAGGACA 59.657 52.381 0.00 0.00 0.00 4.02
955 5336 1.619332 AGGAAGACGAAGGTGAAGGAC 59.381 52.381 0.00 0.00 0.00 3.85
956 5337 1.893801 GAGGAAGACGAAGGTGAAGGA 59.106 52.381 0.00 0.00 0.00 3.36
988 5369 1.798735 CTGCCATGCAAAGGTCGAG 59.201 57.895 9.94 1.53 38.41 4.04
1159 5540 6.482898 AGAGTAGCAGTAGTACTAGCACTA 57.517 41.667 19.92 0.00 30.60 2.74
1215 5602 4.635324 AGAACTAGAACTAGCACTACGGAC 59.365 45.833 8.54 0.00 36.66 4.79
1217 5604 5.106237 ACAAGAACTAGAACTAGCACTACGG 60.106 44.000 8.54 5.33 36.66 4.02
1241 5628 3.449737 AGGGCGCAATAACAAGTAGAGTA 59.550 43.478 10.83 0.00 0.00 2.59
1242 5629 2.236395 AGGGCGCAATAACAAGTAGAGT 59.764 45.455 10.83 0.00 0.00 3.24
1243 5630 2.866762 GAGGGCGCAATAACAAGTAGAG 59.133 50.000 10.83 0.00 0.00 2.43
1244 5631 2.737359 CGAGGGCGCAATAACAAGTAGA 60.737 50.000 10.83 0.00 0.00 2.59
1245 5632 1.593006 CGAGGGCGCAATAACAAGTAG 59.407 52.381 10.83 0.00 0.00 2.57
1275 5662 2.070654 GAACCAACCAGTGCCAACGG 62.071 60.000 0.00 0.00 0.00 4.44
1276 5663 1.358759 GAACCAACCAGTGCCAACG 59.641 57.895 0.00 0.00 0.00 4.10
1277 5664 1.739667 GGAACCAACCAGTGCCAAC 59.260 57.895 0.00 0.00 35.23 3.77
1278 5665 4.268720 GGAACCAACCAGTGCCAA 57.731 55.556 0.00 0.00 35.23 4.52
1308 5695 2.889678 TCACAGAGCGAGATGATGCTAT 59.110 45.455 0.00 0.00 42.60 2.97
1309 5696 2.301346 TCACAGAGCGAGATGATGCTA 58.699 47.619 0.00 0.00 42.60 3.49
1310 5697 1.109609 TCACAGAGCGAGATGATGCT 58.890 50.000 0.00 0.00 45.90 3.79
1311 5698 1.931906 TTCACAGAGCGAGATGATGC 58.068 50.000 0.00 0.00 0.00 3.91
1312 5699 3.714391 TCATTCACAGAGCGAGATGATG 58.286 45.455 0.00 0.00 0.00 3.07
1313 5700 4.603989 ATCATTCACAGAGCGAGATGAT 57.396 40.909 0.00 0.00 0.00 2.45
1314 5701 4.397481 AATCATTCACAGAGCGAGATGA 57.603 40.909 0.00 0.00 0.00 2.92
1326 5720 6.208599 TCAAAGAACAGGGGTTAATCATTCAC 59.791 38.462 0.00 0.00 37.36 3.18
1337 5731 0.537371 CCGCTTCAAAGAACAGGGGT 60.537 55.000 0.00 0.00 36.20 4.95
1348 5742 3.283684 CCCACAACGCCGCTTCAA 61.284 61.111 0.00 0.00 0.00 2.69
1353 5747 2.895372 CCTATCCCACAACGCCGC 60.895 66.667 0.00 0.00 0.00 6.53
1366 5760 3.131046 GCAAGTTTTAGCATGGTGCCTAT 59.869 43.478 7.89 0.00 46.52 2.57
1389 5791 8.802267 TCTATCTTTGGGTTGGAAAATGTTTAG 58.198 33.333 0.00 0.00 0.00 1.85
1390 5792 8.713708 TCTATCTTTGGGTTGGAAAATGTTTA 57.286 30.769 0.00 0.00 0.00 2.01
1391 5793 7.610580 TCTATCTTTGGGTTGGAAAATGTTT 57.389 32.000 0.00 0.00 0.00 2.83
1392 5794 7.610580 TTCTATCTTTGGGTTGGAAAATGTT 57.389 32.000 0.00 0.00 0.00 2.71
1393 5795 7.508977 TCTTTCTATCTTTGGGTTGGAAAATGT 59.491 33.333 0.00 0.00 0.00 2.71
1430 5832 6.416750 GTGTTTCCAAACCGATAAAGAAACTG 59.583 38.462 12.88 0.00 42.12 3.16
1431 5833 6.460537 GGTGTTTCCAAACCGATAAAGAAACT 60.461 38.462 12.88 0.00 42.12 2.66
1432 5834 5.688621 GGTGTTTCCAAACCGATAAAGAAAC 59.311 40.000 6.50 6.50 42.02 2.78
1434 5836 4.278919 GGGTGTTTCCAAACCGATAAAGAA 59.721 41.667 0.00 0.00 38.11 2.52
1437 5857 3.318557 GTGGGTGTTTCCAAACCGATAAA 59.681 43.478 0.00 0.00 38.72 1.40
1439 5859 2.158652 TGTGGGTGTTTCCAAACCGATA 60.159 45.455 0.00 0.00 38.72 2.92
1440 5860 1.324383 GTGGGTGTTTCCAAACCGAT 58.676 50.000 0.00 0.00 38.72 4.18
1441 5861 0.034380 TGTGGGTGTTTCCAAACCGA 60.034 50.000 0.00 0.00 38.72 4.69
1444 5864 3.603158 ACTTTGTGGGTGTTTCCAAAC 57.397 42.857 0.00 0.00 38.72 2.93
1463 5883 7.543756 TGCCCTGCTTTTTATACATAAAGAAC 58.456 34.615 0.00 0.00 34.11 3.01
1464 5884 7.613801 TCTGCCCTGCTTTTTATACATAAAGAA 59.386 33.333 0.00 0.00 34.11 2.52
1472 5892 4.805719 GCATTTCTGCCCTGCTTTTTATAC 59.194 41.667 0.00 0.00 42.88 1.47
1473 5893 5.009854 GCATTTCTGCCCTGCTTTTTATA 57.990 39.130 0.00 0.00 42.88 0.98
1474 5894 3.865446 GCATTTCTGCCCTGCTTTTTAT 58.135 40.909 0.00 0.00 42.88 1.40
1475 5895 3.317603 GCATTTCTGCCCTGCTTTTTA 57.682 42.857 0.00 0.00 42.88 1.52
1476 5896 2.174363 GCATTTCTGCCCTGCTTTTT 57.826 45.000 0.00 0.00 42.88 1.94
1477 5897 3.921257 GCATTTCTGCCCTGCTTTT 57.079 47.368 0.00 0.00 42.88 2.27
1553 5984 7.978414 GGAGATCAATCAATCCTTTTCCTTTTC 59.022 37.037 0.00 0.00 0.00 2.29
1554 5985 7.677319 AGGAGATCAATCAATCCTTTTCCTTTT 59.323 33.333 0.00 0.00 39.14 2.27
1555 5986 7.123847 CAGGAGATCAATCAATCCTTTTCCTTT 59.876 37.037 0.00 0.00 40.23 3.11
1556 5987 6.606395 CAGGAGATCAATCAATCCTTTTCCTT 59.394 38.462 0.00 0.00 40.23 3.36
1557 5988 6.127793 CAGGAGATCAATCAATCCTTTTCCT 58.872 40.000 0.00 0.00 40.23 3.36
1558 5989 5.221204 GCAGGAGATCAATCAATCCTTTTCC 60.221 44.000 0.00 0.00 40.23 3.13
1559 5990 5.221204 GGCAGGAGATCAATCAATCCTTTTC 60.221 44.000 0.00 0.00 40.23 2.29
1627 6070 1.361668 CGTGGGCTCAAGATTCACCG 61.362 60.000 0.00 0.00 0.00 4.94
1629 6072 1.026718 CCCGTGGGCTCAAGATTCAC 61.027 60.000 0.00 0.00 0.00 3.18
1637 6080 4.704103 AGCTCTCCCGTGGGCTCA 62.704 66.667 0.00 0.00 34.68 4.26
1638 6081 3.844090 GAGCTCTCCCGTGGGCTC 61.844 72.222 6.43 3.09 43.07 4.70
1719 6219 6.369065 GGAGTACAAGGAGCAATAAATATCCG 59.631 42.308 0.00 0.00 36.91 4.18
1749 6249 2.607635 CGCACTGTGAACAACAACTACT 59.392 45.455 12.86 0.00 38.67 2.57
1753 6255 0.179176 TGCGCACTGTGAACAACAAC 60.179 50.000 5.66 0.00 38.67 3.32
1755 6257 1.713937 CCTGCGCACTGTGAACAACA 61.714 55.000 5.66 0.61 37.22 3.33
1758 6260 3.279116 GCCTGCGCACTGTGAACA 61.279 61.111 5.66 7.46 34.03 3.18
1759 6261 3.279116 TGCCTGCGCACTGTGAAC 61.279 61.111 5.66 2.64 41.12 3.18
1828 6350 3.833645 CGTCCTCCCATTCGCCGA 61.834 66.667 0.00 0.00 0.00 5.54
1829 6351 4.891727 CCGTCCTCCCATTCGCCG 62.892 72.222 0.00 0.00 0.00 6.46
1886 6412 4.947147 AAACCAAGGGAGCGCGCA 62.947 61.111 35.10 0.00 0.00 6.09
1891 6424 2.871453 TGGAGTAAAAACCAAGGGAGC 58.129 47.619 0.00 0.00 32.93 4.70
1969 6508 1.352352 TCTCTCCTCCCTTGCAAAAGG 59.648 52.381 13.51 13.51 39.68 3.11
2118 6679 0.321298 CGTACACCCCAGGAACAAGG 60.321 60.000 0.00 0.00 0.00 3.61
2123 6684 2.608368 CCCCGTACACCCCAGGAA 60.608 66.667 0.00 0.00 0.00 3.36
2158 6719 2.750135 CGTCATCCTACTCACCCTAGCT 60.750 54.545 0.00 0.00 0.00 3.32
2180 6741 1.066430 TCTTGTGGATAAGACCGGTGC 60.066 52.381 14.63 3.40 32.02 5.01
2198 6759 3.175710 GTGGGTGTGGGTGGGTCT 61.176 66.667 0.00 0.00 0.00 3.85
2202 6763 4.636435 GTCGGTGGGTGTGGGTGG 62.636 72.222 0.00 0.00 0.00 4.61
2203 6764 4.980805 CGTCGGTGGGTGTGGGTG 62.981 72.222 0.00 0.00 0.00 4.61
2205 6766 4.675029 GTCGTCGGTGGGTGTGGG 62.675 72.222 0.00 0.00 0.00 4.61
2213 6774 4.778415 CAGGAGGCGTCGTCGGTG 62.778 72.222 3.90 0.00 37.56 4.94
2217 6778 4.070552 AAGGCAGGAGGCGTCGTC 62.071 66.667 0.00 0.00 46.16 4.20
2218 6779 4.379243 CAAGGCAGGAGGCGTCGT 62.379 66.667 0.00 0.00 46.16 4.34
2272 6836 1.210204 AGGCAGCAAAGAGGGGATGA 61.210 55.000 0.00 0.00 0.00 2.92
2279 6843 3.066814 GGGCCAGGCAGCAAAGAG 61.067 66.667 15.19 0.00 0.00 2.85
2423 7005 2.190756 AACGCCGGGTTCTAGAGAG 58.809 57.895 2.18 0.00 31.79 3.20
2441 7023 0.470456 AAGTGTGGTAGGTGTCCGGA 60.470 55.000 0.00 0.00 0.00 5.14
2455 7037 1.153168 AGCGCAGACCACAAAGTGT 60.153 52.632 11.47 0.00 0.00 3.55
2456 7038 1.280746 CAGCGCAGACCACAAAGTG 59.719 57.895 11.47 0.00 0.00 3.16
2457 7039 2.546494 GCAGCGCAGACCACAAAGT 61.546 57.895 11.47 0.00 0.00 2.66
2458 7040 2.253452 GCAGCGCAGACCACAAAG 59.747 61.111 11.47 0.00 0.00 2.77
2459 7041 3.286751 GGCAGCGCAGACCACAAA 61.287 61.111 11.47 0.00 0.00 2.83
2505 7087 5.523438 TGTCCGCTTTCCATTAAGTTTTT 57.477 34.783 0.00 0.00 0.00 1.94
2510 7092 1.062587 CGCTGTCCGCTTTCCATTAAG 59.937 52.381 0.00 0.00 36.13 1.85
2511 7093 1.083489 CGCTGTCCGCTTTCCATTAA 58.917 50.000 0.00 0.00 36.13 1.40
2512 7094 0.248012 TCGCTGTCCGCTTTCCATTA 59.752 50.000 0.00 0.00 36.73 1.90
2513 7095 0.392998 ATCGCTGTCCGCTTTCCATT 60.393 50.000 0.00 0.00 36.73 3.16
2515 7097 1.447838 GATCGCTGTCCGCTTTCCA 60.448 57.895 0.00 0.00 36.73 3.53
2518 7100 1.448540 CCAGATCGCTGTCCGCTTT 60.449 57.895 0.00 0.00 40.63 3.51
2519 7101 2.185350 CCAGATCGCTGTCCGCTT 59.815 61.111 0.00 0.00 40.63 4.68
2520 7102 4.521062 GCCAGATCGCTGTCCGCT 62.521 66.667 0.00 0.00 40.63 5.52
2592 7196 7.283127 GCATATCAACAAGATCTTAAAGGTGGA 59.717 37.037 7.86 5.46 38.19 4.02
2595 7199 9.331282 GTAGCATATCAACAAGATCTTAAAGGT 57.669 33.333 7.86 0.00 38.19 3.50
2596 7200 8.778358 GGTAGCATATCAACAAGATCTTAAAGG 58.222 37.037 7.86 0.00 38.19 3.11
2597 7201 9.330063 TGGTAGCATATCAACAAGATCTTAAAG 57.670 33.333 7.86 0.00 38.19 1.85
2599 7203 9.494271 GATGGTAGCATATCAACAAGATCTTAA 57.506 33.333 7.86 0.00 33.90 1.85
2612 7330 5.050490 ACGTTGACTTGATGGTAGCATATC 58.950 41.667 7.54 4.45 0.00 1.63
2618 7336 3.040147 ACCACGTTGACTTGATGGTAG 57.960 47.619 0.00 0.00 41.90 3.18
2622 7340 1.724623 CGGTACCACGTTGACTTGATG 59.275 52.381 13.54 0.00 0.00 3.07
2623 7341 1.342174 ACGGTACCACGTTGACTTGAT 59.658 47.619 13.54 0.00 46.25 2.57
2642 7360 7.758528 GGTCGTTGTATCATATTCCTATACCAC 59.241 40.741 0.00 0.00 0.00 4.16
2644 7362 8.064336 AGGTCGTTGTATCATATTCCTATACC 57.936 38.462 0.00 0.00 0.00 2.73
2645 7363 8.737175 TGAGGTCGTTGTATCATATTCCTATAC 58.263 37.037 0.00 0.00 0.00 1.47
2648 7366 7.776618 ATGAGGTCGTTGTATCATATTCCTA 57.223 36.000 0.00 0.00 30.78 2.94
2650 7368 8.709646 GTTAATGAGGTCGTTGTATCATATTCC 58.290 37.037 0.00 0.00 32.25 3.01
2652 7370 8.208224 TGGTTAATGAGGTCGTTGTATCATATT 58.792 33.333 0.00 0.00 32.25 1.28
2653 7371 7.732025 TGGTTAATGAGGTCGTTGTATCATAT 58.268 34.615 0.00 0.00 32.25 1.78
2654 7372 7.114866 TGGTTAATGAGGTCGTTGTATCATA 57.885 36.000 0.00 0.00 32.25 2.15
2656 7374 5.408880 TGGTTAATGAGGTCGTTGTATCA 57.591 39.130 0.00 0.00 0.00 2.15
2657 7375 5.220340 CGTTGGTTAATGAGGTCGTTGTATC 60.220 44.000 0.00 0.00 0.00 2.24
2659 7377 3.989167 CGTTGGTTAATGAGGTCGTTGTA 59.011 43.478 0.00 0.00 0.00 2.41
2700 7458 1.901464 GCACCGCCCTCCTGAAAAA 60.901 57.895 0.00 0.00 0.00 1.94
2701 7459 2.282180 GCACCGCCCTCCTGAAAA 60.282 61.111 0.00 0.00 0.00 2.29
2993 7751 0.527817 GGGCTATCGTCGTCTTGGTG 60.528 60.000 0.00 0.00 0.00 4.17
2994 7752 0.968901 TGGGCTATCGTCGTCTTGGT 60.969 55.000 0.00 0.00 0.00 3.67
2995 7753 0.249073 CTGGGCTATCGTCGTCTTGG 60.249 60.000 0.00 0.00 0.00 3.61
2996 7754 0.872021 GCTGGGCTATCGTCGTCTTG 60.872 60.000 0.00 0.00 0.00 3.02
2997 7755 1.038130 AGCTGGGCTATCGTCGTCTT 61.038 55.000 0.00 0.00 36.99 3.01
2998 7756 1.448922 GAGCTGGGCTATCGTCGTCT 61.449 60.000 0.00 0.00 39.88 4.18
3005 7768 0.965439 AGATGTCGAGCTGGGCTATC 59.035 55.000 0.97 3.57 39.88 2.08
3077 7846 4.462834 TCTGTACTATAGCACAAGCACACT 59.537 41.667 7.22 0.00 45.49 3.55
3085 7854 3.704061 TGCCATGTCTGTACTATAGCACA 59.296 43.478 5.67 5.67 0.00 4.57
3130 7904 3.594775 CAGGCAGCAACACCGCAA 61.595 61.111 0.00 0.00 0.00 4.85
3146 7920 2.760650 TCTTCTGCTCGCTCTTATTCCA 59.239 45.455 0.00 0.00 0.00 3.53
3189 7966 1.471287 CATCACAGCCACCAACATCAG 59.529 52.381 0.00 0.00 0.00 2.90
3222 7999 3.746940 ACACTTGCAATAGTACCGGTTT 58.253 40.909 15.04 4.12 0.00 3.27
3227 8004 6.376177 GTTACCAAACACTTGCAATAGTACC 58.624 40.000 0.00 0.00 35.56 3.34
3250 8027 1.016130 CAATCAAGAGACGCAGCGGT 61.016 55.000 21.15 5.56 0.00 5.68
3292 8086 1.344438 TGAATGCCTGACAGAGAACGT 59.656 47.619 3.32 0.00 0.00 3.99
3314 8108 5.163550 CGATGTGTTCAAGTCCCTGTCTATA 60.164 44.000 0.00 0.00 0.00 1.31
3317 8111 2.289072 CGATGTGTTCAAGTCCCTGTCT 60.289 50.000 0.00 0.00 0.00 3.41
3335 8129 1.736126 CAAATGCAGCTCAGTCACGAT 59.264 47.619 0.00 0.00 0.00 3.73
3337 8131 0.167470 CCAAATGCAGCTCAGTCACG 59.833 55.000 0.00 0.00 0.00 4.35
3341 8135 1.248785 CCAGCCAAATGCAGCTCAGT 61.249 55.000 0.00 0.00 44.83 3.41
3346 8140 2.115734 AAACCCCAGCCAAATGCAGC 62.116 55.000 0.00 0.00 44.83 5.25
3347 8141 0.320946 CAAACCCCAGCCAAATGCAG 60.321 55.000 0.00 0.00 44.83 4.41
3357 8151 1.604604 ACACGTTGATCAAACCCCAG 58.395 50.000 10.35 0.25 35.13 4.45
3358 8152 2.932855 TACACGTTGATCAAACCCCA 57.067 45.000 10.35 0.00 35.13 4.96
3377 8174 1.881973 ACAGCAAATTCACAGCGTGAT 59.118 42.857 11.23 0.00 42.40 3.06
3388 8185 1.956477 GTCTGGACCACACAGCAAATT 59.044 47.619 0.00 0.00 35.94 1.82
3457 8254 9.642343 ACAAACTCTAAACCTTCTTCCTTATTT 57.358 29.630 0.00 0.00 0.00 1.40
3544 8341 3.991051 CTGTGGTGTCTCGCCGGT 61.991 66.667 1.90 0.00 36.72 5.28
3571 8368 7.067494 GGTGTTATTGTTGCTAGGATCAAAGAT 59.933 37.037 11.20 0.00 0.00 2.40
3704 8501 1.215647 GGAGTCTCAACGCGACCAT 59.784 57.895 15.93 0.00 31.83 3.55
3718 8515 7.004086 TGAATTCAGTTAAAGATTGGTGGAGT 58.996 34.615 3.38 0.00 0.00 3.85
3756 8553 0.955905 TCATGACGTGAACCTCGTGA 59.044 50.000 0.00 0.00 41.64 4.35
3824 8621 3.270027 CGGCACACATTCTCTTCCAATA 58.730 45.455 0.00 0.00 0.00 1.90
3837 8634 1.236616 CCAAGAATCAGCGGCACACA 61.237 55.000 1.45 0.00 0.00 3.72
3897 8695 4.308458 ACCGGCTGCAGCAACGTA 62.308 61.111 37.63 0.00 44.36 3.57


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

AutoCloner maintained by Alex Coulton.