Multiple sequence alignment - TraesCS4B01G280800

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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 TraesCS4B01G280800 chr4B 100.000 3020 0 0 1 3020 563784408 563787427 0.000000e+00 5578.0
1 TraesCS4B01G280800 chr4B 85.185 270 39 1 2325 2594 72975059 72974791 2.970000e-70 276.0
2 TraesCS4B01G280800 chr4B 94.643 112 6 0 1133 1244 41177352 41177463 1.110000e-39 174.0
3 TraesCS4B01G280800 chr4D 91.703 916 42 13 734 1640 450501894 450502784 0.000000e+00 1240.0
4 TraesCS4B01G280800 chr4D 90.416 553 30 12 1765 2300 450502957 450503503 0.000000e+00 706.0
5 TraesCS4B01G280800 chr4D 78.510 349 60 14 85 427 477407069 477406730 6.560000e-52 215.0
6 TraesCS4B01G280800 chr4D 97.368 38 1 0 1347 1384 54807097 54807134 6.990000e-07 65.8
7 TraesCS4B01G280800 chr4A 88.713 886 66 12 762 1639 16206978 16206119 0.000000e+00 1051.0
8 TraesCS4B01G280800 chr4A 85.714 707 28 18 42 699 715077405 715076723 0.000000e+00 678.0
9 TraesCS4B01G280800 chr4A 94.393 428 20 4 1875 2300 16205789 16205364 0.000000e+00 654.0
10 TraesCS4B01G280800 chr4A 85.067 596 54 9 130 692 39586278 39585685 2.610000e-160 575.0
11 TraesCS4B01G280800 chr4A 88.462 364 18 11 42 404 715080116 715079776 4.660000e-113 418.0
12 TraesCS4B01G280800 chr4A 84.211 228 23 6 1647 1872 16206046 16205830 3.050000e-50 209.0
13 TraesCS4B01G280800 chr4A 77.895 190 34 6 1226 1413 439059196 439059013 8.850000e-21 111.0
14 TraesCS4B01G280800 chr4A 97.368 38 1 0 1347 1384 542265400 542265363 6.990000e-07 65.8
15 TraesCS4B01G280800 chr6B 87.278 676 35 8 42 667 37612549 37611875 0.000000e+00 725.0
16 TraesCS4B01G280800 chr6B 93.478 46 3 0 6 51 37612602 37612557 5.400000e-08 69.4
17 TraesCS4B01G280800 chr7B 92.578 512 23 4 44 542 641179796 641179287 0.000000e+00 721.0
18 TraesCS4B01G280800 chr7B 82.812 256 22 14 1134 1384 638445008 638444770 3.050000e-50 209.0
19 TraesCS4B01G280800 chr7B 97.321 112 3 0 1133 1244 678028779 678028890 1.110000e-44 191.0
20 TraesCS4B01G280800 chr7B 88.321 137 15 1 1884 2020 638443979 638443844 2.410000e-36 163.0
21 TraesCS4B01G280800 chr7B 83.660 153 22 2 2801 2953 703583653 703583504 1.130000e-29 141.0
22 TraesCS4B01G280800 chr7B 97.368 38 1 0 1347 1384 678029692 678029729 6.990000e-07 65.8
23 TraesCS4B01G280800 chr5D 84.435 726 41 16 39 692 515241935 515241210 0.000000e+00 649.0
24 TraesCS4B01G280800 chr5D 95.536 112 5 0 1133 1244 12360757 12360868 2.390000e-41 180.0
25 TraesCS4B01G280800 chr3B 85.918 632 44 12 108 698 749714652 749715279 1.530000e-177 632.0
26 TraesCS4B01G280800 chr3B 84.341 645 44 23 96 697 625622976 625623606 2.020000e-161 579.0
27 TraesCS4B01G280800 chr3B 84.962 266 39 1 2325 2590 452730109 452729845 4.960000e-68 268.0
28 TraesCS4B01G280800 chr3B 77.874 461 64 21 2593 3020 452729725 452729270 5.000000e-63 252.0
29 TraesCS4B01G280800 chr3B 83.226 155 17 2 2591 2736 173114079 173114233 1.890000e-27 134.0
30 TraesCS4B01G280800 chr3B 81.746 126 19 3 576 698 731261537 731261661 5.330000e-18 102.0
31 TraesCS4B01G280800 chr2B 83.333 624 54 16 85 664 100380018 100380635 5.730000e-147 531.0
32 TraesCS4B01G280800 chr2B 84.871 271 40 1 2325 2595 88410384 88410115 3.840000e-69 272.0
33 TraesCS4B01G280800 chr2B 80.357 224 35 7 2802 3020 561261268 561261049 8.660000e-36 161.0
34 TraesCS4B01G280800 chr3D 86.667 270 35 1 2325 2594 496175258 496174990 6.330000e-77 298.0
35 TraesCS4B01G280800 chr3D 83.613 238 36 3 2781 3017 526993935 526994170 1.410000e-53 220.0
36 TraesCS4B01G280800 chr3D 85.811 148 18 2 2593 2737 496174875 496174728 1.450000e-33 154.0
37 TraesCS4B01G280800 chr5A 85.338 266 38 1 2325 2590 502439050 502438786 1.070000e-69 274.0
38 TraesCS4B01G280800 chr7D 84.791 263 39 1 2332 2594 84181768 84181507 2.310000e-66 263.0
39 TraesCS4B01G280800 chr7D 84.444 270 38 4 2325 2594 118822490 118822225 2.310000e-66 263.0
40 TraesCS4B01G280800 chr7D 97.321 112 3 0 1133 1244 598613042 598613153 1.110000e-44 191.0
41 TraesCS4B01G280800 chr7D 81.457 151 19 3 2596 2737 84181391 84181241 6.840000e-22 115.0
42 TraesCS4B01G280800 chr1B 84.825 257 38 1 2335 2591 531695754 531695499 1.070000e-64 257.0
43 TraesCS4B01G280800 chr1B 84.000 175 27 1 2801 2975 618408296 618408123 1.860000e-37 167.0
44 TraesCS4B01G280800 chr1B 84.000 175 24 2 2801 2975 499243599 499243429 6.700000e-37 165.0
45 TraesCS4B01G280800 chr1B 83.007 153 18 4 2593 2737 469979983 469980135 6.790000e-27 132.0
46 TraesCS4B01G280800 chr1D 83.835 266 41 2 2325 2590 472335523 472335786 5.000000e-63 252.0
47 TraesCS4B01G280800 chr1D 84.038 213 33 1 2801 3013 451047405 451047616 1.420000e-48 204.0
48 TraesCS4B01G280800 chr1D 85.526 152 13 5 2595 2737 472336490 472336641 1.880000e-32 150.0
49 TraesCS4B01G280800 chr7A 97.321 112 3 0 1133 1244 691129107 691129218 1.110000e-44 191.0
50 TraesCS4B01G280800 chr7A 79.094 287 46 13 104 382 729586317 729586037 5.140000e-43 185.0
51 TraesCS4B01G280800 chr7A 100.000 38 0 0 1347 1384 691129830 691129867 1.500000e-08 71.3
52 TraesCS4B01G280800 chr6A 80.451 266 38 13 84 343 64566111 64566368 1.110000e-44 191.0
53 TraesCS4B01G280800 chr6A 83.784 148 21 1 2593 2737 554778956 554779103 1.460000e-28 137.0
54 TraesCS4B01G280800 chr2D 96.330 109 4 0 1136 1244 29677241 29677133 2.390000e-41 180.0
55 TraesCS4B01G280800 chr2D 82.065 184 32 1 2801 2984 478696884 478697066 4.030000e-34 156.0
56 TraesCS4B01G280800 chr2D 80.519 154 20 5 2593 2737 595408477 595408629 3.180000e-20 110.0
57 TraesCS4B01G280800 chr2D 97.368 38 1 0 1347 1384 462618572 462618609 6.990000e-07 65.8
58 TraesCS4B01G280800 chr5B 80.749 187 34 2 2801 2987 701206831 701207015 8.730000e-31 145.0
59 TraesCS4B01G280800 chr5B 97.368 38 1 0 1347 1384 499898953 499898916 6.990000e-07 65.8
60 TraesCS4B01G280800 chr3A 83.117 154 17 3 2593 2737 202579904 202580057 6.790000e-27 132.0
61 TraesCS4B01G280800 chr3A 82.468 154 18 3 2593 2737 30537970 30537817 3.160000e-25 126.0
62 TraesCS4B01G280800 chr6D 77.640 161 30 5 542 699 399416758 399416915 3.210000e-15 93.5


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 TraesCS4B01G280800 chr4B 563784408 563787427 3019 False 5578.0 5578 100.000000 1 3020 1 chr4B.!!$F2 3019
1 TraesCS4B01G280800 chr4D 450501894 450503503 1609 False 973.0 1240 91.059500 734 2300 2 chr4D.!!$F2 1566
2 TraesCS4B01G280800 chr4A 16205364 16206978 1614 True 638.0 1051 89.105667 762 2300 3 chr4A.!!$R4 1538
3 TraesCS4B01G280800 chr4A 39585685 39586278 593 True 575.0 575 85.067000 130 692 1 chr4A.!!$R1 562
4 TraesCS4B01G280800 chr4A 715076723 715080116 3393 True 548.0 678 87.088000 42 699 2 chr4A.!!$R5 657
5 TraesCS4B01G280800 chr6B 37611875 37612602 727 True 397.2 725 90.378000 6 667 2 chr6B.!!$R1 661
6 TraesCS4B01G280800 chr7B 641179287 641179796 509 True 721.0 721 92.578000 44 542 1 chr7B.!!$R1 498
7 TraesCS4B01G280800 chr5D 515241210 515241935 725 True 649.0 649 84.435000 39 692 1 chr5D.!!$R1 653
8 TraesCS4B01G280800 chr3B 749714652 749715279 627 False 632.0 632 85.918000 108 698 1 chr3B.!!$F4 590
9 TraesCS4B01G280800 chr3B 625622976 625623606 630 False 579.0 579 84.341000 96 697 1 chr3B.!!$F2 601
10 TraesCS4B01G280800 chr3B 452729270 452730109 839 True 260.0 268 81.418000 2325 3020 2 chr3B.!!$R1 695
11 TraesCS4B01G280800 chr2B 100380018 100380635 617 False 531.0 531 83.333000 85 664 1 chr2B.!!$F1 579
12 TraesCS4B01G280800 chr3D 496174728 496175258 530 True 226.0 298 86.239000 2325 2737 2 chr3D.!!$R1 412
13 TraesCS4B01G280800 chr1D 472335523 472336641 1118 False 201.0 252 84.680500 2325 2737 2 chr1D.!!$F2 412

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
701 3568 0.177141 CCGAATAGGAACCAGCGGAA 59.823 55.0 0.0 0.0 45.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2524 5577 0.030092 CCCCACCCTTCATCCCTCTA 60.03 60.0 0.0 0.0 0.0 2.43 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
610 3465 6.311690 GTGTGATAACTACAGAGAGAAAAGCC 59.688 42.308 0.00 0.00 0.00 4.35
699 3566 1.887707 GCCGAATAGGAACCAGCGG 60.888 63.158 0.00 0.00 45.00 5.52
700 3567 1.820581 CCGAATAGGAACCAGCGGA 59.179 57.895 0.00 0.00 45.00 5.54
701 3568 0.177141 CCGAATAGGAACCAGCGGAA 59.823 55.000 0.00 0.00 45.00 4.30
702 3569 1.571919 CGAATAGGAACCAGCGGAAG 58.428 55.000 1.50 0.00 0.00 3.46
716 3583 2.205307 CGGAAGCGACTACCCTTAAG 57.795 55.000 0.00 0.00 0.00 1.85
717 3584 1.475682 CGGAAGCGACTACCCTTAAGT 59.524 52.381 0.97 0.00 0.00 2.24
718 3585 2.734492 CGGAAGCGACTACCCTTAAGTG 60.734 54.545 0.97 0.00 0.00 3.16
719 3586 2.494870 GGAAGCGACTACCCTTAAGTGA 59.505 50.000 0.97 0.00 0.00 3.41
720 3587 3.132467 GGAAGCGACTACCCTTAAGTGAT 59.868 47.826 0.97 0.00 0.00 3.06
721 3588 4.382793 GGAAGCGACTACCCTTAAGTGATT 60.383 45.833 0.97 0.00 0.00 2.57
722 3589 4.820894 AGCGACTACCCTTAAGTGATTT 57.179 40.909 0.97 0.00 0.00 2.17
723 3590 4.756502 AGCGACTACCCTTAAGTGATTTC 58.243 43.478 0.97 0.00 0.00 2.17
724 3591 3.550678 GCGACTACCCTTAAGTGATTTCG 59.449 47.826 0.97 5.37 0.00 3.46
725 3592 3.550678 CGACTACCCTTAAGTGATTTCGC 59.449 47.826 0.97 0.00 0.00 4.70
726 3593 3.869832 GACTACCCTTAAGTGATTTCGCC 59.130 47.826 0.97 0.00 0.00 5.54
727 3594 2.871096 ACCCTTAAGTGATTTCGCCA 57.129 45.000 0.97 0.00 0.00 5.69
728 3595 3.149005 ACCCTTAAGTGATTTCGCCAA 57.851 42.857 0.97 0.00 0.00 4.52
729 3596 3.492337 ACCCTTAAGTGATTTCGCCAAA 58.508 40.909 0.97 0.00 0.00 3.28
730 3597 3.506067 ACCCTTAAGTGATTTCGCCAAAG 59.494 43.478 0.97 0.00 0.00 2.77
731 3598 3.501950 CCTTAAGTGATTTCGCCAAAGC 58.498 45.455 0.97 0.00 0.00 3.51
756 3623 3.366052 ACCCTTAAGTGATTTCGCCAT 57.634 42.857 0.97 0.00 0.00 4.40
878 3750 0.249238 CAGATGCACCGAGCCTACTC 60.249 60.000 0.00 0.00 44.83 2.59
891 3763 2.780010 AGCCTACTCATAAAGCCACCAT 59.220 45.455 0.00 0.00 0.00 3.55
1029 3904 1.583054 GAGGATACATCGCGGCTTTT 58.417 50.000 6.13 0.00 41.41 2.27
1046 3921 5.109210 GGCTTTTATCCCCTTCGATTTTTG 58.891 41.667 0.00 0.00 0.00 2.44
1062 3937 2.679355 TTTGTCCGAATGTTTGCTCG 57.321 45.000 0.00 0.00 34.83 5.03
1091 3966 1.140589 CCGAGACTTGCGCATCTCT 59.859 57.895 28.91 22.79 39.43 3.10
1269 4144 2.030805 CGCATCAGATCACGTAGGATCA 60.031 50.000 15.82 0.00 44.89 2.92
1294 4169 0.892358 GGGGTTCCCGTTCCTTTGAC 60.892 60.000 1.48 0.00 32.13 3.18
1321 4196 4.794199 GGCTCGGCCCCTAATTAC 57.206 61.111 0.00 0.00 44.06 1.89
1341 4216 1.594518 CGTGCTTGTCTTTGTGTTCCG 60.595 52.381 0.00 0.00 0.00 4.30
1343 4218 1.668751 TGCTTGTCTTTGTGTTCCGTC 59.331 47.619 0.00 0.00 0.00 4.79
1386 4261 2.421424 GGGCTGCTTCAACATGTAAGAG 59.579 50.000 11.74 5.45 0.00 2.85
1388 4263 2.475187 GCTGCTTCAACATGTAAGAGCG 60.475 50.000 11.74 11.39 0.00 5.03
1404 4279 1.190323 GAGCGTATGATCTTTTCCGCG 59.810 52.381 0.00 0.00 45.20 6.46
1411 4286 2.695359 TGATCTTTTCCGCGCTTTAGT 58.305 42.857 5.56 0.00 0.00 2.24
1412 4287 2.671396 TGATCTTTTCCGCGCTTTAGTC 59.329 45.455 5.56 0.00 0.00 2.59
1413 4288 2.450609 TCTTTTCCGCGCTTTAGTCT 57.549 45.000 5.56 0.00 0.00 3.24
1483 4363 2.428530 GGATTGGATTCTTGACTTGGGC 59.571 50.000 0.00 0.00 0.00 5.36
1491 4371 2.507484 TCTTGACTTGGGCACTTGATG 58.493 47.619 0.00 0.00 0.00 3.07
1522 4402 9.909644 AAAGATGCTATCAATGATTTAGATTGC 57.090 29.630 0.00 0.00 39.71 3.56
1523 4403 8.865420 AGATGCTATCAATGATTTAGATTGCT 57.135 30.769 0.00 0.00 39.88 3.91
1524 4404 8.948145 AGATGCTATCAATGATTTAGATTGCTC 58.052 33.333 0.00 7.65 39.88 4.26
1532 4417 8.618677 TCAATGATTTAGATTGCTCTGCTTTAG 58.381 33.333 0.00 0.00 31.89 1.85
1540 4425 1.004628 TGCTCTGCTTTAGGAATGGCA 59.995 47.619 0.00 0.00 0.00 4.92
1605 4492 7.441157 TGAGAAAATATGTAGATTTAGCACCCG 59.559 37.037 0.00 0.00 0.00 5.28
1619 4506 1.079405 ACCCGGTGCATCTTGTACG 60.079 57.895 0.00 0.00 33.61 3.67
1621 4508 1.082117 CCCGGTGCATCTTGTACGAC 61.082 60.000 0.00 0.00 33.61 4.34
1640 4527 2.011222 ACGTTGTGGTTCGTTGATGTT 58.989 42.857 0.00 0.00 36.93 2.71
1642 4529 2.635444 GTTGTGGTTCGTTGATGTTCG 58.365 47.619 0.00 0.00 0.00 3.95
1643 4530 1.942677 TGTGGTTCGTTGATGTTCGT 58.057 45.000 0.00 0.00 0.00 3.85
1644 4531 1.862201 TGTGGTTCGTTGATGTTCGTC 59.138 47.619 0.00 0.00 0.00 4.20
1645 4532 1.133407 TGGTTCGTTGATGTTCGTCG 58.867 50.000 0.00 0.00 0.00 5.12
1668 4662 1.000717 GTTGGGTTAGTTTGCGTGCAT 60.001 47.619 0.00 0.00 0.00 3.96
1674 4668 5.032220 GGGTTAGTTTGCGTGCATTTATAC 58.968 41.667 0.00 0.00 0.00 1.47
1683 4677 6.183309 TGCGTGCATTTATACAACATACAA 57.817 33.333 0.00 0.00 0.00 2.41
1686 4680 6.290334 GCGTGCATTTATACAACATACAAACG 60.290 38.462 0.00 0.00 0.00 3.60
1694 4688 3.799366 ACAACATACAAACGTCACCTGA 58.201 40.909 0.00 0.00 0.00 3.86
1696 4690 4.213270 ACAACATACAAACGTCACCTGATG 59.787 41.667 0.00 0.00 37.11 3.07
1744 4738 5.378230 TGCTAGTTTCCATGATCATTCCT 57.622 39.130 5.16 0.49 0.00 3.36
1745 4739 5.371526 TGCTAGTTTCCATGATCATTCCTC 58.628 41.667 5.16 0.00 0.00 3.71
1746 4740 4.759183 GCTAGTTTCCATGATCATTCCTCC 59.241 45.833 5.16 0.00 0.00 4.30
1755 4749 1.696884 GATCATTCCTCCTCACCTCCC 59.303 57.143 0.00 0.00 0.00 4.30
1759 4753 0.719015 TTCCTCCTCACCTCCCTGAT 59.281 55.000 0.00 0.00 0.00 2.90
1762 4756 2.043227 CCTCCTCACCTCCCTGATTAC 58.957 57.143 0.00 0.00 0.00 1.89
1763 4757 2.043227 CTCCTCACCTCCCTGATTACC 58.957 57.143 0.00 0.00 0.00 2.85
1768 4762 0.846693 ACCTCCCTGATTACCCATGC 59.153 55.000 0.00 0.00 0.00 4.06
1801 4795 6.769512 TGGCCCTGACTTGAATTATATCTAC 58.230 40.000 0.00 0.00 0.00 2.59
1826 4822 6.905076 CGTATCAACCAATTCCAGTTTATTCG 59.095 38.462 0.00 0.00 0.00 3.34
1831 4827 8.798402 TCAACCAATTCCAGTTTATTCGTTATT 58.202 29.630 0.00 0.00 0.00 1.40
1846 4842 5.073311 TCGTTATTACTGAAGCTTGCTCT 57.927 39.130 2.10 0.00 0.00 4.09
1847 4843 5.479306 TCGTTATTACTGAAGCTTGCTCTT 58.521 37.500 2.10 0.00 0.00 2.85
1848 4844 5.348724 TCGTTATTACTGAAGCTTGCTCTTG 59.651 40.000 2.10 0.00 0.00 3.02
1882 4919 7.040409 ACGTATCATATATCTGACTCTGTTGCA 60.040 37.037 0.00 0.00 0.00 4.08
1888 4925 8.657729 CATATATCTGACTCTGTTGCATTGATC 58.342 37.037 0.00 0.00 0.00 2.92
1896 4933 1.878734 TGTTGCATTGATCGCAGAACA 59.121 42.857 0.00 0.00 43.58 3.18
2052 5090 4.424842 TGTTTATGGGAAAATGAAGCCCT 58.575 39.130 0.00 0.00 42.52 5.19
2148 5187 0.882927 TGCCAGCCTGAACGTTGTAC 60.883 55.000 5.00 0.00 0.00 2.90
2175 5214 5.008613 ACGTGTTCTATGTCATGCACTTTTT 59.991 36.000 0.00 0.00 0.00 1.94
2176 5215 5.340403 CGTGTTCTATGTCATGCACTTTTTG 59.660 40.000 0.00 0.00 0.00 2.44
2177 5216 6.437928 GTGTTCTATGTCATGCACTTTTTGA 58.562 36.000 0.00 0.00 0.00 2.69
2178 5217 6.580041 GTGTTCTATGTCATGCACTTTTTGAG 59.420 38.462 0.00 0.00 0.00 3.02
2194 5233 0.751277 TGAGTGGCCTGTTGTTGGTG 60.751 55.000 3.32 0.00 0.00 4.17
2268 5321 4.636249 AGTAGTAATAGCCTGCTGCATTC 58.364 43.478 1.31 0.00 44.83 2.67
2300 5353 7.552687 ACAGTGTTCAGTGTTTGGTATATATGG 59.447 37.037 7.37 0.00 0.00 2.74
2301 5354 6.542370 AGTGTTCAGTGTTTGGTATATATGGC 59.458 38.462 0.00 0.00 0.00 4.40
2302 5355 6.317642 GTGTTCAGTGTTTGGTATATATGGCA 59.682 38.462 0.00 0.00 0.00 4.92
2303 5356 6.887002 TGTTCAGTGTTTGGTATATATGGCAA 59.113 34.615 0.00 0.00 0.00 4.52
2304 5357 7.394641 TGTTCAGTGTTTGGTATATATGGCAAA 59.605 33.333 0.00 0.00 0.00 3.68
2305 5358 8.413229 GTTCAGTGTTTGGTATATATGGCAAAT 58.587 33.333 0.00 0.00 0.00 2.32
2306 5359 8.165239 TCAGTGTTTGGTATATATGGCAAATC 57.835 34.615 0.00 0.00 0.00 2.17
2307 5360 7.230510 TCAGTGTTTGGTATATATGGCAAATCC 59.769 37.037 0.00 0.00 0.00 3.01
2308 5361 6.206634 AGTGTTTGGTATATATGGCAAATCCG 59.793 38.462 0.00 0.00 37.80 4.18
2309 5362 6.205853 GTGTTTGGTATATATGGCAAATCCGA 59.794 38.462 0.00 0.00 37.80 4.55
2310 5363 6.205853 TGTTTGGTATATATGGCAAATCCGAC 59.794 38.462 0.00 0.00 37.80 4.79
2311 5364 4.839121 TGGTATATATGGCAAATCCGACC 58.161 43.478 0.00 0.00 37.80 4.79
2312 5365 4.196971 GGTATATATGGCAAATCCGACCC 58.803 47.826 0.00 0.00 37.80 4.46
2313 5366 2.871096 TATATGGCAAATCCGACCCC 57.129 50.000 0.00 0.00 37.80 4.95
2314 5367 1.149101 ATATGGCAAATCCGACCCCT 58.851 50.000 0.00 0.00 37.80 4.79
2315 5368 0.472471 TATGGCAAATCCGACCCCTC 59.528 55.000 0.00 0.00 37.80 4.30
2316 5369 1.570857 ATGGCAAATCCGACCCCTCA 61.571 55.000 0.00 0.00 37.80 3.86
2317 5370 1.001393 GGCAAATCCGACCCCTCAA 60.001 57.895 0.00 0.00 0.00 3.02
2318 5371 0.610785 GGCAAATCCGACCCCTCAAA 60.611 55.000 0.00 0.00 0.00 2.69
2319 5372 0.526211 GCAAATCCGACCCCTCAAAC 59.474 55.000 0.00 0.00 0.00 2.93
2320 5373 1.886655 GCAAATCCGACCCCTCAAACT 60.887 52.381 0.00 0.00 0.00 2.66
2321 5374 2.084546 CAAATCCGACCCCTCAAACTC 58.915 52.381 0.00 0.00 0.00 3.01
2322 5375 0.249398 AATCCGACCCCTCAAACTCG 59.751 55.000 0.00 0.00 0.00 4.18
2323 5376 1.614241 ATCCGACCCCTCAAACTCGG 61.614 60.000 0.00 0.00 45.86 4.63
2343 5396 1.588674 CGGGCACGCCTTATATTTCA 58.411 50.000 8.20 0.00 36.10 2.69
2348 5401 4.320494 GGGCACGCCTTATATTTCATCTTG 60.320 45.833 8.20 0.00 36.10 3.02
2364 5417 3.899981 TTGCATGCTCGCGTCCCTT 62.900 57.895 20.33 0.00 33.35 3.95
2365 5418 3.869272 GCATGCTCGCGTCCCTTG 61.869 66.667 11.37 5.56 0.00 3.61
2369 5422 0.249489 ATGCTCGCGTCCCTTGTATC 60.249 55.000 5.77 0.00 0.00 2.24
2453 5506 4.584874 TCATCGGATTAGCTGGACAAAAA 58.415 39.130 0.00 0.00 0.00 1.94
2455 5508 4.015872 TCGGATTAGCTGGACAAAAAGT 57.984 40.909 0.00 0.00 0.00 2.66
2492 5545 3.049674 CAACGGCGGACAGTGCAT 61.050 61.111 13.24 0.00 0.00 3.96
2542 5595 2.124560 ATAGAGGGATGAAGGGTGGG 57.875 55.000 0.00 0.00 0.00 4.61
2551 5604 1.392407 TGAAGGGTGGGGGAAATCAT 58.608 50.000 0.00 0.00 0.00 2.45
2572 5625 0.178894 ATTTCCTTGCTGGCCCCTTT 60.179 50.000 0.00 0.00 35.26 3.11
2578 5631 2.120496 GCTGGCCCCTTTCCCTTT 59.880 61.111 0.00 0.00 0.00 3.11
2582 5635 2.439245 GCCCCTTTCCCTTTCGGT 59.561 61.111 0.00 0.00 0.00 4.69
2586 5639 1.699730 CCCTTTCCCTTTCGGTTGTT 58.300 50.000 0.00 0.00 0.00 2.83
2591 5644 2.190841 CCCTTTCGGTTGTTGGCGT 61.191 57.895 0.00 0.00 0.00 5.68
2623 6375 3.982316 CTGCTCCTTGGCATGGCGA 62.982 63.158 15.27 12.23 41.63 5.54
2662 6426 0.886490 CCTTTGTTGCCTCGTGCTCT 60.886 55.000 1.74 0.00 42.00 4.09
2670 6434 1.287730 GCCTCGTGCTCTGACAGTTG 61.288 60.000 1.59 0.00 36.87 3.16
2671 6435 0.315251 CCTCGTGCTCTGACAGTTGA 59.685 55.000 1.59 0.00 0.00 3.18
2686 6450 0.389948 GTTGAATGGCGAGTCGGAGT 60.390 55.000 15.52 0.00 0.00 3.85
2737 6504 3.735029 GTCTCCGCCGTCGTGAGT 61.735 66.667 4.70 0.00 35.74 3.41
2739 6506 4.039357 CTCCGCCGTCGTGAGTGT 62.039 66.667 0.00 0.00 32.28 3.55
2740 6507 3.553437 CTCCGCCGTCGTGAGTGTT 62.553 63.158 0.00 0.00 32.28 3.32
2741 6508 3.403057 CCGCCGTCGTGAGTGTTG 61.403 66.667 0.00 0.00 0.00 3.33
2742 6509 4.059459 CGCCGTCGTGAGTGTTGC 62.059 66.667 0.00 0.00 0.00 4.17
2743 6510 3.712881 GCCGTCGTGAGTGTTGCC 61.713 66.667 0.00 0.00 0.00 4.52
2744 6511 2.029073 CCGTCGTGAGTGTTGCCT 59.971 61.111 0.00 0.00 0.00 4.75
2745 6512 2.022129 CCGTCGTGAGTGTTGCCTC 61.022 63.158 0.00 0.00 0.00 4.70
2746 6513 1.299850 CGTCGTGAGTGTTGCCTCA 60.300 57.895 0.00 0.00 39.11 3.86
2747 6514 1.278172 CGTCGTGAGTGTTGCCTCAG 61.278 60.000 0.00 0.00 41.93 3.35
2748 6515 0.946221 GTCGTGAGTGTTGCCTCAGG 60.946 60.000 4.89 4.89 44.66 3.86
2749 6516 1.367471 CGTGAGTGTTGCCTCAGGA 59.633 57.895 0.00 0.00 45.62 3.86
2750 6517 0.036952 CGTGAGTGTTGCCTCAGGAT 60.037 55.000 0.00 0.00 45.62 3.24
2751 6518 1.731720 GTGAGTGTTGCCTCAGGATC 58.268 55.000 0.00 0.00 41.93 3.36
2752 6519 0.247460 TGAGTGTTGCCTCAGGATCG 59.753 55.000 0.00 0.00 36.57 3.69
2753 6520 0.532573 GAGTGTTGCCTCAGGATCGA 59.467 55.000 0.00 0.00 0.00 3.59
2757 6524 0.385751 GTTGCCTCAGGATCGATCGA 59.614 55.000 21.86 21.86 0.00 3.59
2758 6525 1.000283 GTTGCCTCAGGATCGATCGAT 60.000 52.381 29.76 29.76 37.59 3.59
2762 6529 1.069924 CTCAGGATCGATCGATGCGC 61.070 60.000 34.27 21.35 45.68 6.09
2774 6541 2.580470 GATGCGCGGACATCGACTG 61.580 63.158 8.83 0.00 42.43 3.51
2778 6545 2.815308 GCGGACATCGACTGGGAT 59.185 61.111 0.00 0.00 42.43 3.85
2782 6549 1.592669 GACATCGACTGGGATGCCG 60.593 63.158 0.00 0.00 46.11 5.69
2783 6550 2.016393 GACATCGACTGGGATGCCGA 62.016 60.000 0.00 0.00 46.11 5.54
2813 6599 2.670934 CTGCCTGCTCGTGCCTTT 60.671 61.111 7.05 0.00 38.71 3.11
2826 6612 2.677979 GCCTTTGACTCGGGCGTTC 61.678 63.158 0.00 0.00 36.37 3.95
2837 6623 2.325082 GGGCGTTCGAGTGCATGTT 61.325 57.895 12.24 0.00 0.00 2.71
2900 6686 2.286523 CCTCCGAAGCAGAGGGTGT 61.287 63.158 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.906574 TCTGTTGAATCTAACGGGCCT 59.093 47.619 0.84 0.00 37.49 5.19
15 16 2.007608 GTCTGTTGAATCTAACGGGCC 58.992 52.381 0.00 0.00 35.92 5.80
18 19 2.268298 CGGGTCTGTTGAATCTAACGG 58.732 52.381 0.00 0.00 38.09 4.44
501 3325 8.246180 CCAACAAGACATGCTAACTTTCATATT 58.754 33.333 0.00 0.00 0.00 1.28
584 3434 7.093992 GCTTTTCTCTCTGTAGTTATCACACT 58.906 38.462 0.00 0.00 0.00 3.55
594 3449 4.440880 CCATCTGGCTTTTCTCTCTGTAG 58.559 47.826 0.00 0.00 0.00 2.74
699 3566 3.863142 TCACTTAAGGGTAGTCGCTTC 57.137 47.619 4.27 0.00 43.92 3.86
700 3567 4.820894 AATCACTTAAGGGTAGTCGCTT 57.179 40.909 4.27 3.36 46.13 4.68
701 3568 4.677250 CGAAATCACTTAAGGGTAGTCGCT 60.677 45.833 4.27 0.00 38.50 4.93
702 3569 3.550678 CGAAATCACTTAAGGGTAGTCGC 59.449 47.826 4.27 0.00 0.00 5.19
703 3570 3.550678 GCGAAATCACTTAAGGGTAGTCG 59.449 47.826 16.84 16.84 0.00 4.18
704 3571 3.869832 GGCGAAATCACTTAAGGGTAGTC 59.130 47.826 4.27 0.00 0.00 2.59
705 3572 3.262405 TGGCGAAATCACTTAAGGGTAGT 59.738 43.478 4.27 0.00 0.00 2.73
706 3573 3.869065 TGGCGAAATCACTTAAGGGTAG 58.131 45.455 4.27 0.00 0.00 3.18
707 3574 3.985019 TGGCGAAATCACTTAAGGGTA 57.015 42.857 4.27 0.00 0.00 3.69
708 3575 2.871096 TGGCGAAATCACTTAAGGGT 57.129 45.000 4.27 0.00 0.00 4.34
709 3576 3.673323 GCTTTGGCGAAATCACTTAAGGG 60.673 47.826 7.53 2.06 0.00 3.95
710 3577 3.501950 GCTTTGGCGAAATCACTTAAGG 58.498 45.455 7.53 0.00 0.00 2.69
724 3591 2.007608 CTTAAGGGTAGTCGCTTTGGC 58.992 52.381 0.00 0.00 42.78 4.52
725 3592 3.000727 CACTTAAGGGTAGTCGCTTTGG 58.999 50.000 7.53 0.95 42.78 3.28
726 3593 3.921677 TCACTTAAGGGTAGTCGCTTTG 58.078 45.455 4.27 0.00 42.78 2.77
727 3594 4.820894 ATCACTTAAGGGTAGTCGCTTT 57.179 40.909 4.27 0.00 42.78 3.51
728 3595 4.820894 AATCACTTAAGGGTAGTCGCTT 57.179 40.909 4.27 3.36 46.13 4.68
729 3596 4.677250 CGAAATCACTTAAGGGTAGTCGCT 60.677 45.833 4.27 0.00 38.50 4.93
730 3597 3.550678 CGAAATCACTTAAGGGTAGTCGC 59.449 47.826 4.27 0.00 0.00 5.19
731 3598 3.550678 GCGAAATCACTTAAGGGTAGTCG 59.449 47.826 16.84 16.84 0.00 4.18
732 3599 3.869832 GGCGAAATCACTTAAGGGTAGTC 59.130 47.826 4.27 0.00 0.00 2.59
733 3600 3.262405 TGGCGAAATCACTTAAGGGTAGT 59.738 43.478 4.27 0.00 0.00 2.73
734 3601 3.869065 TGGCGAAATCACTTAAGGGTAG 58.131 45.455 4.27 0.00 0.00 3.18
735 3602 3.985019 TGGCGAAATCACTTAAGGGTA 57.015 42.857 4.27 0.00 0.00 3.69
736 3603 2.871096 TGGCGAAATCACTTAAGGGT 57.129 45.000 4.27 0.00 0.00 4.34
737 3604 2.358898 CCATGGCGAAATCACTTAAGGG 59.641 50.000 7.53 2.06 0.00 3.95
756 3623 2.669229 CATGTGTCGCAGTGGCCA 60.669 61.111 0.00 0.00 36.38 5.36
836 3708 1.290203 CGTCCATCCCGTTTGATCTG 58.710 55.000 0.00 0.00 0.00 2.90
878 3750 2.689983 GGGACTTCATGGTGGCTTTATG 59.310 50.000 0.00 0.00 0.00 1.90
891 3763 3.948719 GTGGGCGTGGGGACTTCA 61.949 66.667 0.00 0.00 0.00 3.02
955 3827 3.551407 GGGAGAGGATGCGGGGAC 61.551 72.222 0.00 0.00 0.00 4.46
966 3838 2.182030 GGTCTTCGCGTGGGAGAG 59.818 66.667 5.77 0.00 0.00 3.20
1029 3904 3.198200 TCGGACAAAAATCGAAGGGGATA 59.802 43.478 0.00 0.00 0.00 2.59
1046 3921 1.461888 CGAACGAGCAAACATTCGGAC 60.462 52.381 0.00 0.00 40.11 4.79
1062 3937 2.159827 GCAAGTCTCGGATCAAACGAAC 60.160 50.000 0.00 0.00 40.16 3.95
1091 3966 6.997655 AGACAACAGACAGATTAGATCACAA 58.002 36.000 0.00 0.00 0.00 3.33
1294 4169 4.527583 GCCGAGCCAGGAGAGCAG 62.528 72.222 0.00 0.00 0.00 4.24
1320 4195 1.400494 GGAACACAAAGACAAGCACGT 59.600 47.619 0.00 0.00 0.00 4.49
1321 4196 1.594518 CGGAACACAAAGACAAGCACG 60.595 52.381 0.00 0.00 0.00 5.34
1341 4216 0.320771 ACTTGACATCCTGCACGGAC 60.321 55.000 7.00 0.00 46.80 4.79
1343 4218 1.915614 GCACTTGACATCCTGCACGG 61.916 60.000 0.00 0.00 0.00 4.94
1386 4261 0.383124 GCGCGGAAAAGATCATACGC 60.383 55.000 8.83 11.46 43.15 4.42
1388 4263 3.675467 AAAGCGCGGAAAAGATCATAC 57.325 42.857 8.83 0.00 0.00 2.39
1401 4276 1.792949 ACACAAGAAGACTAAAGCGCG 59.207 47.619 0.00 0.00 0.00 6.86
1404 4279 7.659652 ACTATGAACACAAGAAGACTAAAGC 57.340 36.000 0.00 0.00 0.00 3.51
1434 4309 9.494271 CCATCTTAATGTTACTGTGCAGTATAT 57.506 33.333 12.18 7.93 42.83 0.86
1435 4310 8.482943 ACCATCTTAATGTTACTGTGCAGTATA 58.517 33.333 12.18 6.19 42.83 1.47
1436 4311 7.280876 CACCATCTTAATGTTACTGTGCAGTAT 59.719 37.037 12.18 1.52 42.83 2.12
1438 4313 5.412594 CACCATCTTAATGTTACTGTGCAGT 59.587 40.000 9.90 9.90 45.02 4.40
1518 4398 2.692041 GCCATTCCTAAAGCAGAGCAAT 59.308 45.455 0.00 0.00 0.00 3.56
1520 4400 1.004628 TGCCATTCCTAAAGCAGAGCA 59.995 47.619 0.00 0.00 0.00 4.26
1521 4401 1.755179 TGCCATTCCTAAAGCAGAGC 58.245 50.000 0.00 0.00 0.00 4.09
1522 4402 5.009410 CCTTTATGCCATTCCTAAAGCAGAG 59.991 44.000 0.00 0.00 38.89 3.35
1523 4403 4.889409 CCTTTATGCCATTCCTAAAGCAGA 59.111 41.667 0.00 0.00 38.89 4.26
1524 4404 4.646492 ACCTTTATGCCATTCCTAAAGCAG 59.354 41.667 0.00 0.00 38.89 4.24
1532 4417 5.932619 AAACCTAACCTTTATGCCATTCC 57.067 39.130 0.00 0.00 0.00 3.01
1540 4425 9.914834 TTCTATGTGCATAAACCTAACCTTTAT 57.085 29.630 0.00 0.00 0.00 1.40
1545 4430 6.458342 GCAGTTCTATGTGCATAAACCTAACC 60.458 42.308 0.00 0.00 39.62 2.85
1602 4487 1.082117 GTCGTACAAGATGCACCGGG 61.082 60.000 6.32 0.00 0.00 5.73
1605 4492 1.126113 CAACGTCGTACAAGATGCACC 59.874 52.381 0.00 0.00 0.00 5.01
1619 4506 1.595794 ACATCAACGAACCACAACGTC 59.404 47.619 0.00 0.00 41.87 4.34
1621 4508 2.635444 GAACATCAACGAACCACAACG 58.365 47.619 0.00 0.00 0.00 4.10
1640 4527 3.125316 CAAACTAACCCAACTTCGACGA 58.875 45.455 0.00 0.00 0.00 4.20
1642 4529 2.349155 CGCAAACTAACCCAACTTCGAC 60.349 50.000 0.00 0.00 0.00 4.20
1643 4530 1.868498 CGCAAACTAACCCAACTTCGA 59.132 47.619 0.00 0.00 0.00 3.71
1644 4531 1.600485 ACGCAAACTAACCCAACTTCG 59.400 47.619 0.00 0.00 0.00 3.79
1645 4532 2.857104 GCACGCAAACTAACCCAACTTC 60.857 50.000 0.00 0.00 0.00 3.01
1668 4662 7.656542 TCAGGTGACGTTTGTATGTTGTATAAA 59.343 33.333 0.00 0.00 0.00 1.40
1674 4668 4.378356 CCATCAGGTGACGTTTGTATGTTG 60.378 45.833 0.00 0.00 0.00 3.33
1694 4688 3.411446 TCAACATTTCGAGCTGAACCAT 58.589 40.909 0.00 0.00 35.97 3.55
1696 4690 3.461946 CTCAACATTTCGAGCTGAACC 57.538 47.619 0.00 0.00 35.97 3.62
1727 4721 4.578105 GTGAGGAGGAATGATCATGGAAAC 59.422 45.833 9.46 0.51 0.00 2.78
1732 4726 3.244491 GGAGGTGAGGAGGAATGATCATG 60.244 52.174 9.46 0.00 0.00 3.07
1733 4727 2.978278 GGAGGTGAGGAGGAATGATCAT 59.022 50.000 1.18 1.18 0.00 2.45
1736 4730 1.296523 AGGGAGGTGAGGAGGAATGAT 59.703 52.381 0.00 0.00 0.00 2.45
1744 4738 1.344087 GGGTAATCAGGGAGGTGAGGA 60.344 57.143 0.00 0.00 0.00 3.71
1745 4739 1.132500 GGGTAATCAGGGAGGTGAGG 58.868 60.000 0.00 0.00 0.00 3.86
1746 4740 1.879575 TGGGTAATCAGGGAGGTGAG 58.120 55.000 0.00 0.00 0.00 3.51
1755 4749 3.155093 GCAAACAGCATGGGTAATCAG 57.845 47.619 0.00 0.00 43.62 2.90
1768 4762 2.115910 TCAGGGCCAGGCAAACAG 59.884 61.111 15.19 0.00 0.00 3.16
1801 4795 6.905076 CGAATAAACTGGAATTGGTTGATACG 59.095 38.462 0.00 0.00 0.00 3.06
1826 4822 6.487689 ACAAGAGCAAGCTTCAGTAATAAC 57.512 37.500 0.00 0.00 0.00 1.89
1831 4827 4.071961 TGAACAAGAGCAAGCTTCAGTA 57.928 40.909 0.00 0.00 0.00 2.74
1847 4843 9.626045 GTCAGATATATGATACGTGAATGAACA 57.374 33.333 2.87 0.00 0.00 3.18
1848 4844 9.847706 AGTCAGATATATGATACGTGAATGAAC 57.152 33.333 2.87 0.00 0.00 3.18
1882 4919 3.565482 AACACAGTTGTTCTGCGATCAAT 59.435 39.130 0.00 0.00 42.67 2.57
1896 4933 1.486310 TGAGAGTGGCTGAACACAGTT 59.514 47.619 0.00 0.00 43.72 3.16
2086 5124 7.106439 ACAAAATTTGACCAGTACACATTCA 57.894 32.000 13.19 0.00 0.00 2.57
2087 5125 9.522804 TTAACAAAATTTGACCAGTACACATTC 57.477 29.630 13.19 0.00 0.00 2.67
2148 5187 2.741517 TGCATGACATAGAACACGTTGG 59.258 45.455 0.00 0.00 0.00 3.77
2175 5214 0.751277 CACCAACAACAGGCCACTCA 60.751 55.000 5.01 0.00 0.00 3.41
2176 5215 2.032981 CACCAACAACAGGCCACTC 58.967 57.895 5.01 0.00 0.00 3.51
2177 5216 2.127232 GCACCAACAACAGGCCACT 61.127 57.895 5.01 0.00 0.00 4.00
2178 5217 1.675720 AAGCACCAACAACAGGCCAC 61.676 55.000 5.01 0.00 0.00 5.01
2180 5219 1.109323 AGAAGCACCAACAACAGGCC 61.109 55.000 0.00 0.00 0.00 5.19
2194 5233 0.039708 GCAGCCAGACAAACAGAAGC 60.040 55.000 0.00 0.00 0.00 3.86
2268 5321 4.201851 CCAAACACTGAACACTGTCAAGAG 60.202 45.833 0.00 0.00 0.00 2.85
2300 5353 0.526211 GTTTGAGGGGTCGGATTTGC 59.474 55.000 0.00 0.00 0.00 3.68
2301 5354 2.084546 GAGTTTGAGGGGTCGGATTTG 58.915 52.381 0.00 0.00 0.00 2.32
2302 5355 1.338769 CGAGTTTGAGGGGTCGGATTT 60.339 52.381 0.00 0.00 0.00 2.17
2303 5356 0.249398 CGAGTTTGAGGGGTCGGATT 59.751 55.000 0.00 0.00 0.00 3.01
2304 5357 1.898154 CGAGTTTGAGGGGTCGGAT 59.102 57.895 0.00 0.00 0.00 4.18
2305 5358 3.373226 CGAGTTTGAGGGGTCGGA 58.627 61.111 0.00 0.00 0.00 4.55
2306 5359 2.264794 CCGAGTTTGAGGGGTCGG 59.735 66.667 0.00 0.00 45.48 4.79
2307 5360 2.434359 GCCGAGTTTGAGGGGTCG 60.434 66.667 0.00 0.00 0.00 4.79
2308 5361 2.434359 CGCCGAGTTTGAGGGGTC 60.434 66.667 0.00 0.00 35.95 4.46
2309 5362 4.016706 CCGCCGAGTTTGAGGGGT 62.017 66.667 0.00 0.00 38.61 4.95
2310 5363 4.778143 CCCGCCGAGTTTGAGGGG 62.778 72.222 0.00 0.00 38.44 4.79
2312 5365 4.697756 TGCCCGCCGAGTTTGAGG 62.698 66.667 0.00 0.00 0.00 3.86
2313 5366 3.423154 GTGCCCGCCGAGTTTGAG 61.423 66.667 0.00 0.00 0.00 3.02
2335 5388 4.143052 CGCGAGCATGCAAGATGAAATATA 60.143 41.667 21.98 0.00 34.15 0.86
2343 5396 2.176273 GGACGCGAGCATGCAAGAT 61.176 57.895 21.98 0.00 34.15 2.40
2348 5401 3.869272 CAAGGGACGCGAGCATGC 61.869 66.667 15.93 10.51 0.00 4.06
2364 5417 5.417580 GCATGGTTTTGAGGTTTAGGATACA 59.582 40.000 0.00 0.00 41.41 2.29
2365 5418 5.417580 TGCATGGTTTTGAGGTTTAGGATAC 59.582 40.000 0.00 0.00 0.00 2.24
2369 5422 4.599047 TTGCATGGTTTTGAGGTTTAGG 57.401 40.909 0.00 0.00 0.00 2.69
2405 5458 7.517320 ACTGGGCTATGATCATGTATTTTACA 58.483 34.615 18.72 5.71 43.80 2.41
2412 5465 5.567423 CGATGAACTGGGCTATGATCATGTA 60.567 44.000 18.72 0.00 0.00 2.29
2426 5479 2.103094 TCCAGCTAATCCGATGAACTGG 59.897 50.000 8.47 8.47 43.65 4.00
2453 5506 4.100035 TGAGCTCCGATGAATCATGTTACT 59.900 41.667 12.15 0.00 0.00 2.24
2455 5508 4.670896 TGAGCTCCGATGAATCATGTTA 57.329 40.909 12.15 0.00 0.00 2.41
2524 5577 0.030092 CCCCACCCTTCATCCCTCTA 60.030 60.000 0.00 0.00 0.00 2.43
2528 5581 1.514864 TTTCCCCCACCCTTCATCCC 61.515 60.000 0.00 0.00 0.00 3.85
2529 5582 0.636647 ATTTCCCCCACCCTTCATCC 59.363 55.000 0.00 0.00 0.00 3.51
2532 5585 1.287739 GATGATTTCCCCCACCCTTCA 59.712 52.381 0.00 0.00 0.00 3.02
2551 5604 1.305213 GGGGCCAGCAAGGAAATGA 60.305 57.895 4.39 0.00 41.22 2.57
2560 5613 2.730129 GAAAGGGAAAGGGGCCAGCA 62.730 60.000 4.39 0.00 0.00 4.41
2563 5616 2.438795 CGAAAGGGAAAGGGGCCA 59.561 61.111 4.39 0.00 0.00 5.36
2578 5631 2.280524 CTCCACGCCAACAACCGA 60.281 61.111 0.00 0.00 0.00 4.69
2582 5635 2.594303 CCTGCTCCACGCCAACAA 60.594 61.111 0.00 0.00 38.05 2.83
2635 6399 3.294493 GCAACAAAGGAGGCGGCA 61.294 61.111 13.08 0.00 0.00 5.69
2662 6426 1.795768 GACTCGCCATTCAACTGTCA 58.204 50.000 0.00 0.00 0.00 3.58
2670 6434 2.167861 GCACTCCGACTCGCCATTC 61.168 63.158 0.00 0.00 0.00 2.67
2671 6435 2.125512 GCACTCCGACTCGCCATT 60.126 61.111 0.00 0.00 0.00 3.16
2712 6479 0.319900 GACGGCGGAGACATATGCAT 60.320 55.000 13.24 3.79 27.25 3.96
2718 6485 3.052620 CTCACGACGGCGGAGACAT 62.053 63.158 18.49 0.00 43.17 3.06
2719 6486 3.733960 CTCACGACGGCGGAGACA 61.734 66.667 18.49 0.00 43.17 3.41
2737 6504 0.103026 CGATCGATCCTGAGGCAACA 59.897 55.000 19.51 0.00 41.41 3.33
2739 6506 1.000171 CATCGATCGATCCTGAGGCAA 60.000 52.381 27.20 0.00 31.62 4.52
2740 6507 0.600057 CATCGATCGATCCTGAGGCA 59.400 55.000 27.20 0.00 31.62 4.75
2741 6508 0.735632 GCATCGATCGATCCTGAGGC 60.736 60.000 27.20 21.32 31.62 4.70
2742 6509 0.455802 CGCATCGATCGATCCTGAGG 60.456 60.000 27.20 15.90 31.62 3.86
2743 6510 1.069924 GCGCATCGATCGATCCTGAG 61.070 60.000 27.20 19.92 31.62 3.35
2744 6511 1.081175 GCGCATCGATCGATCCTGA 60.081 57.895 27.20 12.17 31.62 3.86
2745 6512 2.431738 CGCGCATCGATCGATCCTG 61.432 63.158 27.20 18.99 41.67 3.86
2746 6513 2.126696 CGCGCATCGATCGATCCT 60.127 61.111 27.20 5.68 41.67 3.24
2747 6514 3.175240 CCGCGCATCGATCGATCC 61.175 66.667 27.20 18.40 41.67 3.36
2748 6515 2.126850 TCCGCGCATCGATCGATC 60.127 61.111 27.20 19.40 41.67 3.69
2749 6516 2.429236 GTCCGCGCATCGATCGAT 60.429 61.111 24.60 24.60 41.67 3.59
2750 6517 3.194272 ATGTCCGCGCATCGATCGA 62.194 57.895 21.86 21.86 41.67 3.59
2751 6518 2.710971 GATGTCCGCGCATCGATCG 61.711 63.158 9.36 9.36 41.67 3.69
2752 6519 3.150895 GATGTCCGCGCATCGATC 58.849 61.111 8.75 0.00 41.67 3.69
2757 6524 2.583319 CAGTCGATGTCCGCGCAT 60.583 61.111 8.75 0.00 38.37 4.73
2758 6525 4.794439 CCAGTCGATGTCCGCGCA 62.794 66.667 8.75 0.00 38.37 6.09
2762 6529 1.592669 GCATCCCAGTCGATGTCCG 60.593 63.158 0.00 0.00 41.49 4.79
2797 6564 2.979676 CAAAGGCACGAGCAGGCA 60.980 61.111 7.26 0.00 44.61 4.75
2798 6565 2.669569 TCAAAGGCACGAGCAGGC 60.670 61.111 7.26 0.00 44.61 4.85
2826 6612 2.360350 AGGGCCAACATGCACTCG 60.360 61.111 6.18 0.00 42.73 4.18
2872 6658 3.172106 TTCGGAGGTTGGTGCCCA 61.172 61.111 0.00 0.00 0.00 5.36
2886 6672 1.071471 ACCAACACCCTCTGCTTCG 59.929 57.895 0.00 0.00 0.00 3.79
2888 6674 1.151450 CCACCAACACCCTCTGCTT 59.849 57.895 0.00 0.00 0.00 3.91
2962 6748 1.750018 TCGACATCGCCGGTCCTTA 60.750 57.895 1.90 0.00 39.60 2.69
2987 6787 2.338620 CACTTCGACAGTGCCCGA 59.661 61.111 12.60 4.36 46.70 5.14
2997 6797 2.184322 GCGGCAGATCCACTTCGA 59.816 61.111 0.00 0.00 34.01 3.71


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

AutoCloner maintained by Alex Coulton.