Multiple sequence alignment - TraesCS7A01G000900

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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 TraesCS7A01G000900 chr7A 100.000 5579 0 0 1 5579 630849 636427 0.000000e+00 10303.0
1 TraesCS7A01G000900 chr7A 87.000 1500 172 10 3161 4647 330935 332424 0.000000e+00 1668.0
2 TraesCS7A01G000900 chr7A 78.846 312 37 22 5269 5570 648518794 648518502 3.430000e-42 183.0
3 TraesCS7A01G000900 chr7A 78.205 312 40 22 5269 5570 648515227 648514934 2.070000e-39 174.0
4 TraesCS7A01G000900 chr7A 85.926 135 18 1 2738 2872 623866 623999 5.830000e-30 143.0
5 TraesCS7A01G000900 chr7A 85.393 89 6 2 5464 5547 718527909 718527823 9.960000e-13 86.1
6 TraesCS7A01G000900 chr7A 87.037 54 4 3 2760 2810 225043288 225043341 2.170000e-04 58.4
7 TraesCS7A01G000900 chr3A 95.757 2404 93 6 40 2437 719879652 719877252 0.000000e+00 3866.0
8 TraesCS7A01G000900 chr3A 94.259 2456 108 25 1 2437 212755313 212757754 0.000000e+00 3723.0
9 TraesCS7A01G000900 chr3A 86.606 1105 95 31 1 1070 677670704 677671790 0.000000e+00 1171.0
10 TraesCS7A01G000900 chr5A 94.685 2446 109 17 1 2437 598377673 598380106 0.000000e+00 3777.0
11 TraesCS7A01G000900 chr5A 94.433 2461 107 26 1 2442 671901212 671898763 0.000000e+00 3759.0
12 TraesCS7A01G000900 chr5A 94.431 2460 108 21 1 2446 603972842 603970398 0.000000e+00 3757.0
13 TraesCS7A01G000900 chr5A 94.338 2455 106 23 4 2437 385563383 385560941 0.000000e+00 3733.0
14 TraesCS7A01G000900 chr2A 94.546 2457 109 13 1 2437 457872278 457869827 0.000000e+00 3771.0
15 TraesCS7A01G000900 chr2A 100.000 30 0 0 5537 5566 767569653 767569682 7.810000e-04 56.5
16 TraesCS7A01G000900 chr4A 94.424 2457 102 24 1 2437 620203770 620201329 0.000000e+00 3746.0
17 TraesCS7A01G000900 chr4A 94.482 1649 76 7 3013 4647 743345639 743347286 0.000000e+00 2527.0
18 TraesCS7A01G000900 chr4A 91.712 1665 114 13 2926 4571 744013975 744012316 0.000000e+00 2289.0
19 TraesCS7A01G000900 chr4A 87.802 1492 163 12 3161 4641 744032131 744030648 0.000000e+00 1729.0
20 TraesCS7A01G000900 chr4A 87.118 1506 171 14 3154 4647 744416220 744417714 0.000000e+00 1685.0
21 TraesCS7A01G000900 chr4A 88.442 1367 157 1 3221 4586 743675113 743676479 0.000000e+00 1648.0
22 TraesCS7A01G000900 chr4A 85.845 219 13 3 4682 4882 743347380 743347598 3.380000e-52 217.0
23 TraesCS7A01G000900 chr4A 89.542 153 9 3 5014 5164 743348693 743348840 2.650000e-43 187.0
24 TraesCS7A01G000900 chr4A 93.878 49 2 1 4602 4650 744012318 744012271 7.750000e-09 73.1
25 TraesCS7A01G000900 chr1A 94.329 2451 108 21 1 2437 504516216 504518649 0.000000e+00 3727.0
26 TraesCS7A01G000900 chr1A 90.123 162 16 0 5164 5325 12601635 12601796 1.570000e-50 211.0
27 TraesCS7A01G000900 chr1A 92.683 41 3 0 3110 3150 578907274 578907234 6.040000e-05 60.2
28 TraesCS7A01G000900 chrUn 97.634 1606 36 2 2437 4040 51391597 51393202 0.000000e+00 2754.0
29 TraesCS7A01G000900 chrUn 96.932 1271 37 2 3307 4576 51384670 51385939 0.000000e+00 2130.0
30 TraesCS7A01G000900 chrUn 81.818 253 24 16 5319 5564 285731122 285731359 5.700000e-45 193.0
31 TraesCS7A01G000900 chrUn 81.467 259 26 16 5319 5570 304810793 304810550 5.700000e-45 193.0
32 TraesCS7A01G000900 chrUn 78.176 307 37 21 5269 5564 114391197 114391484 9.610000e-38 169.0
33 TraesCS7A01G000900 chrUn 93.878 98 6 0 2564 2661 51384570 51384667 1.250000e-31 148.0
34 TraesCS7A01G000900 chr7D 95.131 1376 61 3 3273 4642 1236143 1234768 0.000000e+00 2165.0
35 TraesCS7A01G000900 chr7D 85.430 151 20 2 2738 2887 1236864 1236715 7.480000e-34 156.0
36 TraesCS7A01G000900 chr7D 84.615 91 8 3 2648 2738 1236439 1236355 9.960000e-13 86.1
37 TraesCS7A01G000900 chr6B 92.038 314 18 7 5271 5579 23292868 23292557 8.580000e-118 435.0
38 TraesCS7A01G000900 chr6B 91.401 314 20 7 5271 5579 23296634 23296323 1.860000e-114 424.0
39 TraesCS7A01G000900 chr4D 79.805 307 32 22 5269 5564 484933914 484933627 4.410000e-46 196.0
40 TraesCS7A01G000900 chr3D 79.344 305 37 16 5269 5564 610658435 610658722 2.050000e-44 191.0
41 TraesCS7A01G000900 chr3D 79.412 306 35 19 5269 5564 610662089 610662376 2.050000e-44 191.0
42 TraesCS7A01G000900 chr3D 95.000 40 2 0 2770 2809 512613342 512613381 4.670000e-06 63.9
43 TraesCS7A01G000900 chr2B 86.164 159 18 2 5206 5361 6525949 6525792 9.610000e-38 169.0
44 TraesCS7A01G000900 chr2B 89.091 55 6 0 2775 2829 534201155 534201101 1.000000e-07 69.4
45 TraesCS7A01G000900 chr5D 79.253 241 29 12 5332 5564 549032060 549031833 1.250000e-31 148.0
46 TraesCS7A01G000900 chr5B 78.409 264 27 16 5324 5579 700599688 700599447 1.620000e-30 145.0
47 TraesCS7A01G000900 chr3B 97.917 48 1 0 2770 2817 675158388 675158341 3.580000e-12 84.2
48 TraesCS7A01G000900 chr4B 95.556 45 2 0 2770 2814 450041359 450041403 7.750000e-09 73.1
49 TraesCS7A01G000900 chr7B 100.000 30 0 0 2772 2801 188583718 188583689 7.810000e-04 56.5


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 TraesCS7A01G000900 chr7A 630849 636427 5578 False 10303.000000 10303 100.000000 1 5579 1 chr7A.!!$F3 5578
1 TraesCS7A01G000900 chr7A 330935 332424 1489 False 1668.000000 1668 87.000000 3161 4647 1 chr7A.!!$F1 1486
2 TraesCS7A01G000900 chr3A 719877252 719879652 2400 True 3866.000000 3866 95.757000 40 2437 1 chr3A.!!$R1 2397
3 TraesCS7A01G000900 chr3A 212755313 212757754 2441 False 3723.000000 3723 94.259000 1 2437 1 chr3A.!!$F1 2436
4 TraesCS7A01G000900 chr3A 677670704 677671790 1086 False 1171.000000 1171 86.606000 1 1070 1 chr3A.!!$F2 1069
5 TraesCS7A01G000900 chr5A 598377673 598380106 2433 False 3777.000000 3777 94.685000 1 2437 1 chr5A.!!$F1 2436
6 TraesCS7A01G000900 chr5A 671898763 671901212 2449 True 3759.000000 3759 94.433000 1 2442 1 chr5A.!!$R3 2441
7 TraesCS7A01G000900 chr5A 603970398 603972842 2444 True 3757.000000 3757 94.431000 1 2446 1 chr5A.!!$R2 2445
8 TraesCS7A01G000900 chr5A 385560941 385563383 2442 True 3733.000000 3733 94.338000 4 2437 1 chr5A.!!$R1 2433
9 TraesCS7A01G000900 chr2A 457869827 457872278 2451 True 3771.000000 3771 94.546000 1 2437 1 chr2A.!!$R1 2436
10 TraesCS7A01G000900 chr4A 620201329 620203770 2441 True 3746.000000 3746 94.424000 1 2437 1 chr4A.!!$R1 2436
11 TraesCS7A01G000900 chr4A 744030648 744032131 1483 True 1729.000000 1729 87.802000 3161 4641 1 chr4A.!!$R2 1480
12 TraesCS7A01G000900 chr4A 744416220 744417714 1494 False 1685.000000 1685 87.118000 3154 4647 1 chr4A.!!$F2 1493
13 TraesCS7A01G000900 chr4A 743675113 743676479 1366 False 1648.000000 1648 88.442000 3221 4586 1 chr4A.!!$F1 1365
14 TraesCS7A01G000900 chr4A 744012271 744013975 1704 True 1181.050000 2289 92.795000 2926 4650 2 chr4A.!!$R3 1724
15 TraesCS7A01G000900 chr4A 743345639 743348840 3201 False 977.000000 2527 89.956333 3013 5164 3 chr4A.!!$F3 2151
16 TraesCS7A01G000900 chr1A 504516216 504518649 2433 False 3727.000000 3727 94.329000 1 2437 1 chr1A.!!$F2 2436
17 TraesCS7A01G000900 chrUn 51391597 51393202 1605 False 2754.000000 2754 97.634000 2437 4040 1 chrUn.!!$F1 1603
18 TraesCS7A01G000900 chrUn 51384570 51385939 1369 False 1139.000000 2130 95.405000 2564 4576 2 chrUn.!!$F4 2012
19 TraesCS7A01G000900 chr7D 1234768 1236864 2096 True 802.366667 2165 88.392000 2648 4642 3 chr7D.!!$R1 1994
20 TraesCS7A01G000900 chr6B 23292557 23296634 4077 True 429.500000 435 91.719500 5271 5579 2 chr6B.!!$R1 308

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
994 1042 1.425448 CAAGGGGAAAGGAGAGGTTGT 59.575 52.381 0.0 0.0 0.0 3.32 F
1439 1506 1.192803 GGTGACCCCGAAACTCTCCT 61.193 60.000 0.0 0.0 0.0 3.69 F
2733 2803 1.047801 ATCCACCAAAAGCAACCACC 58.952 50.000 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2578 2648 0.690762 TGAGAAGGGGCGCTTTTAGT 59.309 50.0 18.44 3.88 0.00 2.24 R
2987 3304 0.889994 GGGATTGTGCATGTGCTTGA 59.110 50.0 6.55 0.00 42.66 3.02 R
4672 5108 0.249573 ACGGTAACTTGTCCACGTGG 60.250 55.0 29.26 29.26 32.90 4.94 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
192 219 6.567602 AATAAAGACAACTCCTATGGCTCT 57.432 37.500 0.00 0.00 34.20 4.09
437 476 4.496673 GCCACAACGTGATTTGTCAACTTA 60.497 41.667 0.00 0.00 37.62 2.24
577 616 2.514205 AAGCGTACGTGTAAGGTTGT 57.486 45.000 17.90 0.00 34.84 3.32
602 641 1.609208 GCCGCTTCATCCCACAATAT 58.391 50.000 0.00 0.00 0.00 1.28
661 700 2.290008 TGACAACATCTACGCCCACAAT 60.290 45.455 0.00 0.00 0.00 2.71
994 1042 1.425448 CAAGGGGAAAGGAGAGGTTGT 59.575 52.381 0.00 0.00 0.00 3.32
1131 1182 3.486383 CACCAAAGGCAAAGGTAAGAGA 58.514 45.455 0.00 0.00 33.49 3.10
1238 1301 1.616628 CTGGAGTAGCCCCCAAGGT 60.617 63.158 0.00 0.00 38.26 3.50
1250 1313 2.750237 CAAGGTAAGGTGGGGCGC 60.750 66.667 0.00 0.00 0.00 6.53
1439 1506 1.192803 GGTGACCCCGAAACTCTCCT 61.193 60.000 0.00 0.00 0.00 3.69
1491 1558 6.394345 AATTCTTTACCTCAGGACCATTCT 57.606 37.500 0.00 0.00 0.00 2.40
1686 1753 2.443255 GGATCTGGATACCCATGTTGGT 59.557 50.000 0.00 0.00 42.59 3.67
1725 1792 2.765699 TGATCTCATCGGATGAACCACA 59.234 45.455 20.29 14.59 39.11 4.17
1742 1809 3.007940 ACCACAATGTCGAGGATTCAAGA 59.992 43.478 0.00 0.00 0.00 3.02
1834 1901 2.824341 ACCTCGTTCAATCTCGTTACCT 59.176 45.455 0.00 0.00 0.00 3.08
1994 2061 1.407258 CCGTGTCAACCCAACAAACAT 59.593 47.619 0.00 0.00 0.00 2.71
2223 2291 9.860898 CCTAATGATGTGATCTCGTTATCAATA 57.139 33.333 4.42 0.00 37.61 1.90
2249 2317 5.715439 TCCAATGTCCATAGTCAGGAAAT 57.285 39.130 0.00 0.00 36.80 2.17
2255 2323 6.505048 TGTCCATAGTCAGGAAATCATGAT 57.495 37.500 1.18 1.18 38.98 2.45
2340 2409 6.671614 TTCACACATGTATTACGATTTCCC 57.328 37.500 0.00 0.00 0.00 3.97
2465 2535 2.094286 CCACAGCGAGAGAATCAGACTT 60.094 50.000 0.00 0.00 37.82 3.01
2515 2585 2.851263 TGCCAAAACTAGACCGTCAT 57.149 45.000 0.00 0.00 0.00 3.06
2575 2645 6.128876 TGCGTTCTGAATAAATTTGCATTGTG 60.129 34.615 0.00 0.00 0.00 3.33
2578 2648 7.273164 CGTTCTGAATAAATTTGCATTGTGCTA 59.727 33.333 0.00 0.00 45.31 3.49
2733 2803 1.047801 ATCCACCAAAAGCAACCACC 58.952 50.000 0.00 0.00 0.00 4.61
2987 3304 7.230510 ACACCACACACACATATTCACTAAAAT 59.769 33.333 0.00 0.00 0.00 1.82
3001 3318 4.277921 TCACTAAAATCAAGCACATGCACA 59.722 37.500 6.64 0.00 45.16 4.57
3363 3708 7.433680 TCTCGTGTATTTATGTGCTGATATGT 58.566 34.615 0.00 0.00 0.00 2.29
3449 3794 5.818678 AATTATGAGGCCATGATTGCATT 57.181 34.783 5.01 0.00 37.52 3.56
3480 3825 3.369052 CCCTAGCTCCAAAACGATACACA 60.369 47.826 0.00 0.00 0.00 3.72
3550 3899 2.579410 AGGTGGTTATGGTGTGGTTC 57.421 50.000 0.00 0.00 0.00 3.62
3651 4000 4.641989 GTGAATGAGGTTATGAGCATTGGT 59.358 41.667 0.00 0.00 31.65 3.67
3976 4326 7.222417 TGTGTCATACAAAAGAAAGCAATGTTG 59.778 33.333 0.00 0.00 36.06 3.33
4647 5015 4.040461 CCAACTCTTTGAGAAGGTGACCTA 59.960 45.833 3.68 0.00 34.24 3.08
4654 5090 9.137459 CTCTTTGAGAAGGTGACCTATATAAGA 57.863 37.037 3.68 9.78 31.13 2.10
4657 5093 8.603898 TTGAGAAGGTGACCTATATAAGACAA 57.396 34.615 3.68 1.13 31.13 3.18
4666 5102 7.327275 GTGACCTATATAAGACAAGAGCAATCG 59.673 40.741 0.00 0.00 0.00 3.34
4677 5113 3.814268 GCAATCGCATGCCCACGT 61.814 61.111 13.15 0.00 40.49 4.49
4678 5114 2.100797 CAATCGCATGCCCACGTG 59.899 61.111 13.15 9.08 35.78 4.49
4679 5115 3.133464 AATCGCATGCCCACGTGG 61.133 61.111 28.26 28.26 33.09 4.94
4680 5116 3.620419 AATCGCATGCCCACGTGGA 62.620 57.895 36.07 17.87 37.39 4.02
4754 5190 5.416952 CCAAAGATCCAACTGCTAGAACAAT 59.583 40.000 0.00 0.00 0.00 2.71
4798 5234 7.492352 AAACGATTTATGGTCTAAGTATGGC 57.508 36.000 0.00 0.00 0.00 4.40
4846 5300 7.280730 ACATTGCGACAATACATTTCAATTG 57.719 32.000 0.00 0.00 38.71 2.32
4850 5304 5.124617 TGCGACAATACATTTCAATTGGCTA 59.875 36.000 5.42 0.00 38.69 3.93
4872 5326 6.469275 GCTACAAGAAAATTAATCGTGGAAGC 59.531 38.462 14.33 14.33 34.79 3.86
4873 5327 6.325919 ACAAGAAAATTAATCGTGGAAGCA 57.674 33.333 10.36 0.00 31.67 3.91
4882 5336 0.176910 TCGTGGAAGCAGAACACACA 59.823 50.000 0.00 0.00 34.91 3.72
4883 5337 1.013596 CGTGGAAGCAGAACACACAA 58.986 50.000 0.00 0.00 34.91 3.33
4884 5338 1.400142 CGTGGAAGCAGAACACACAAA 59.600 47.619 0.00 0.00 34.91 2.83
4885 5339 2.791158 CGTGGAAGCAGAACACACAAAC 60.791 50.000 0.00 0.00 34.91 2.93
4886 5340 2.423538 GTGGAAGCAGAACACACAAACT 59.576 45.455 0.00 0.00 35.30 2.66
4887 5341 3.088532 TGGAAGCAGAACACACAAACTT 58.911 40.909 0.00 0.00 0.00 2.66
4888 5342 4.095782 GTGGAAGCAGAACACACAAACTTA 59.904 41.667 0.00 0.00 35.30 2.24
4889 5343 4.335315 TGGAAGCAGAACACACAAACTTAG 59.665 41.667 0.00 0.00 0.00 2.18
4890 5344 4.335594 GGAAGCAGAACACACAAACTTAGT 59.664 41.667 0.00 0.00 0.00 2.24
4891 5345 5.163652 GGAAGCAGAACACACAAACTTAGTT 60.164 40.000 0.00 0.00 0.00 2.24
4892 5346 5.235305 AGCAGAACACACAAACTTAGTTG 57.765 39.130 0.00 0.00 34.52 3.16
4893 5347 4.096382 AGCAGAACACACAAACTTAGTTGG 59.904 41.667 0.00 0.00 32.50 3.77
4894 5348 4.142469 GCAGAACACACAAACTTAGTTGGT 60.142 41.667 0.00 0.00 28.50 3.67
4895 5349 5.569413 CAGAACACACAAACTTAGTTGGTC 58.431 41.667 1.53 0.00 25.44 4.02
4896 5350 4.638865 AGAACACACAAACTTAGTTGGTCC 59.361 41.667 1.53 0.00 25.44 4.46
4897 5351 4.230745 ACACACAAACTTAGTTGGTCCT 57.769 40.909 1.53 0.00 25.44 3.85
4898 5352 4.196971 ACACACAAACTTAGTTGGTCCTC 58.803 43.478 1.53 0.00 25.44 3.71
4899 5353 4.080526 ACACACAAACTTAGTTGGTCCTCT 60.081 41.667 1.53 0.00 25.44 3.69
4900 5354 4.273480 CACACAAACTTAGTTGGTCCTCTG 59.727 45.833 1.53 0.00 25.44 3.35
4901 5355 3.251004 CACAAACTTAGTTGGTCCTCTGC 59.749 47.826 1.53 0.00 25.44 4.26
4902 5356 3.136626 ACAAACTTAGTTGGTCCTCTGCT 59.863 43.478 0.00 0.00 32.50 4.24
4903 5357 4.137543 CAAACTTAGTTGGTCCTCTGCTT 58.862 43.478 0.00 0.00 0.00 3.91
4904 5358 3.409026 ACTTAGTTGGTCCTCTGCTTG 57.591 47.619 0.00 0.00 0.00 4.01
4905 5359 2.079925 CTTAGTTGGTCCTCTGCTTGC 58.920 52.381 0.00 0.00 0.00 4.01
4906 5360 1.352083 TAGTTGGTCCTCTGCTTGCT 58.648 50.000 0.00 0.00 0.00 3.91
4907 5361 1.352083 AGTTGGTCCTCTGCTTGCTA 58.648 50.000 0.00 0.00 0.00 3.49
4908 5362 1.277557 AGTTGGTCCTCTGCTTGCTAG 59.722 52.381 0.00 0.00 0.00 3.42
4909 5363 0.615331 TTGGTCCTCTGCTTGCTAGG 59.385 55.000 0.00 7.83 0.00 3.02
4910 5364 0.545309 TGGTCCTCTGCTTGCTAGGT 60.545 55.000 12.05 0.00 0.00 3.08
4911 5365 0.107945 GGTCCTCTGCTTGCTAGGTG 60.108 60.000 12.05 0.00 0.00 4.00
4912 5366 0.107945 GTCCTCTGCTTGCTAGGTGG 60.108 60.000 12.05 5.52 0.00 4.61
4913 5367 1.451028 CCTCTGCTTGCTAGGTGGC 60.451 63.158 0.00 0.00 0.00 5.01
4914 5368 1.297689 CTCTGCTTGCTAGGTGGCA 59.702 57.895 0.00 0.00 40.74 4.92
4915 5369 0.107312 CTCTGCTTGCTAGGTGGCAT 60.107 55.000 0.00 0.00 42.09 4.40
4916 5370 0.107508 TCTGCTTGCTAGGTGGCATC 60.108 55.000 0.00 0.00 42.09 3.91
4917 5371 1.077501 TGCTTGCTAGGTGGCATCC 60.078 57.895 0.00 0.00 42.09 3.51
4918 5372 1.077501 GCTTGCTAGGTGGCATCCA 60.078 57.895 0.00 0.00 42.09 3.41
4928 5382 3.435846 TGGCATCCACTGAAGCAAA 57.564 47.368 0.00 0.00 36.94 3.68
4959 5413 1.885388 TTCCGTTCACACCTGCACG 60.885 57.895 0.00 0.00 0.00 5.34
4960 5414 3.345808 CCGTTCACACCTGCACGG 61.346 66.667 0.00 0.00 45.75 4.94
4965 5419 4.624364 CACACCTGCACGGCCTCA 62.624 66.667 0.00 0.00 35.61 3.86
4967 5421 4.320456 CACCTGCACGGCCTCACT 62.320 66.667 0.00 0.00 35.61 3.41
4968 5422 4.008933 ACCTGCACGGCCTCACTC 62.009 66.667 0.00 0.00 35.61 3.51
4976 5430 4.373116 GGCCTCACTCGCGGTCAA 62.373 66.667 6.13 0.00 0.00 3.18
4977 5431 2.125512 GCCTCACTCGCGGTCAAT 60.126 61.111 6.13 0.00 0.00 2.57
4980 5434 1.446792 CTCACTCGCGGTCAATGCT 60.447 57.895 6.13 0.00 0.00 3.79
4981 5435 0.179137 CTCACTCGCGGTCAATGCTA 60.179 55.000 6.13 0.00 0.00 3.49
4982 5436 0.245266 TCACTCGCGGTCAATGCTAA 59.755 50.000 6.13 0.00 0.00 3.09
4984 5438 1.665679 CACTCGCGGTCAATGCTAAAT 59.334 47.619 6.13 0.00 0.00 1.40
4986 5440 2.747446 ACTCGCGGTCAATGCTAAATTT 59.253 40.909 6.13 0.00 0.00 1.82
4989 5443 3.189495 TCGCGGTCAATGCTAAATTTTGA 59.811 39.130 6.13 0.00 0.00 2.69
4996 6448 7.447430 GGTCAATGCTAAATTTTGATTTGTCG 58.553 34.615 3.69 0.00 32.48 4.35
5005 6457 9.781834 CTAAATTTTGATTTGTCGTTATGGCTA 57.218 29.630 0.00 0.00 0.00 3.93
5006 6458 8.687824 AAATTTTGATTTGTCGTTATGGCTAG 57.312 30.769 0.00 0.00 0.00 3.42
5007 6459 5.811399 TTTGATTTGTCGTTATGGCTAGG 57.189 39.130 0.00 0.00 0.00 3.02
5008 6460 4.746535 TGATTTGTCGTTATGGCTAGGA 57.253 40.909 0.00 0.00 0.00 2.94
5009 6461 5.092554 TGATTTGTCGTTATGGCTAGGAA 57.907 39.130 0.00 0.00 0.00 3.36
5011 6463 5.941058 TGATTTGTCGTTATGGCTAGGAAAA 59.059 36.000 0.00 0.00 0.00 2.29
5012 6464 6.601613 TGATTTGTCGTTATGGCTAGGAAAAT 59.398 34.615 0.00 0.00 0.00 1.82
5021 6478 9.665264 CGTTATGGCTAGGAAAATTAATTCTTC 57.335 33.333 0.10 7.63 0.00 2.87
5041 6498 2.423185 TCCGCATATTGTTTTGAGCCTG 59.577 45.455 0.00 0.00 0.00 4.85
5084 6542 5.949354 TGGATTGGAGTAAATGTAAGGTTGG 59.051 40.000 0.00 0.00 0.00 3.77
5123 6581 2.586425 ACACAACTCTCCATTTGGGTG 58.414 47.619 0.00 0.00 37.96 4.61
5150 6609 3.304257 CCACATCACAACTCACAAGCTTC 60.304 47.826 0.00 0.00 0.00 3.86
5191 6650 9.967451 TTTGGAGTTAAACATGAATAGTATCCA 57.033 29.630 0.00 1.94 0.00 3.41
5192 6651 9.967451 TTGGAGTTAAACATGAATAGTATCCAA 57.033 29.630 0.00 8.12 39.06 3.53
5193 6652 9.391006 TGGAGTTAAACATGAATAGTATCCAAC 57.609 33.333 0.00 0.00 0.00 3.77
5194 6653 8.548721 GGAGTTAAACATGAATAGTATCCAACG 58.451 37.037 0.00 0.00 0.00 4.10
5195 6654 9.095065 GAGTTAAACATGAATAGTATCCAACGT 57.905 33.333 0.00 0.00 0.00 3.99
5196 6655 8.879759 AGTTAAACATGAATAGTATCCAACGTG 58.120 33.333 0.00 0.00 0.00 4.49
5197 6656 8.662141 GTTAAACATGAATAGTATCCAACGTGT 58.338 33.333 0.00 0.00 0.00 4.49
5198 6657 6.903883 AACATGAATAGTATCCAACGTGTC 57.096 37.500 0.00 0.00 0.00 3.67
5199 6658 5.357257 ACATGAATAGTATCCAACGTGTCC 58.643 41.667 0.00 0.00 0.00 4.02
5200 6659 4.036567 TGAATAGTATCCAACGTGTCCG 57.963 45.455 0.00 0.00 40.83 4.79
5201 6660 3.181484 TGAATAGTATCCAACGTGTCCGG 60.181 47.826 0.00 0.00 38.78 5.14
5202 6661 0.457035 TAGTATCCAACGTGTCCGGC 59.543 55.000 0.00 0.00 38.78 6.13
5203 6662 1.217244 GTATCCAACGTGTCCGGCT 59.783 57.895 0.00 0.00 38.78 5.52
5204 6663 0.804933 GTATCCAACGTGTCCGGCTC 60.805 60.000 0.00 0.00 38.78 4.70
5205 6664 1.952102 TATCCAACGTGTCCGGCTCC 61.952 60.000 0.00 0.00 38.78 4.70
5207 6666 4.657824 CAACGTGTCCGGCTCCGT 62.658 66.667 7.59 0.64 38.78 4.69
5208 6667 4.657824 AACGTGTCCGGCTCCGTG 62.658 66.667 11.84 0.00 38.78 4.94
5210 6669 3.740397 CGTGTCCGGCTCCGTGTA 61.740 66.667 7.59 0.00 37.81 2.90
5211 6670 2.126189 GTGTCCGGCTCCGTGTAC 60.126 66.667 7.59 3.58 37.81 2.90
5212 6671 3.740397 TGTCCGGCTCCGTGTACG 61.740 66.667 7.59 0.00 37.81 3.67
5213 6672 3.741476 GTCCGGCTCCGTGTACGT 61.741 66.667 7.59 0.00 37.74 3.57
5214 6673 2.985282 TCCGGCTCCGTGTACGTT 60.985 61.111 7.59 0.00 37.74 3.99
5215 6674 1.673993 TCCGGCTCCGTGTACGTTA 60.674 57.895 7.59 0.00 37.74 3.18
5216 6675 1.514873 CCGGCTCCGTGTACGTTAC 60.515 63.158 7.59 0.00 37.74 2.50
5217 6676 1.209898 CGGCTCCGTGTACGTTACA 59.790 57.895 0.00 0.00 37.74 2.41
5235 6694 3.550656 CGAGTCCGTGTTGGCTTC 58.449 61.111 0.00 0.00 37.80 3.86
5236 6695 1.300620 CGAGTCCGTGTTGGCTTCA 60.301 57.895 0.00 0.00 37.80 3.02
5237 6696 0.878523 CGAGTCCGTGTTGGCTTCAA 60.879 55.000 0.00 0.00 37.80 2.69
5238 6697 1.305201 GAGTCCGTGTTGGCTTCAAA 58.695 50.000 0.00 0.00 37.80 2.69
5239 6698 1.264288 GAGTCCGTGTTGGCTTCAAAG 59.736 52.381 0.00 0.00 37.80 2.77
5240 6699 1.021968 GTCCGTGTTGGCTTCAAAGT 58.978 50.000 0.00 0.00 37.80 2.66
5241 6700 1.002792 GTCCGTGTTGGCTTCAAAGTC 60.003 52.381 0.00 0.00 37.80 3.01
5242 6701 1.021202 CCGTGTTGGCTTCAAAGTCA 58.979 50.000 0.00 0.00 39.20 3.41
5243 6702 1.608590 CCGTGTTGGCTTCAAAGTCAT 59.391 47.619 0.00 0.00 40.84 3.06
5244 6703 2.034558 CCGTGTTGGCTTCAAAGTCATT 59.965 45.455 0.00 0.00 40.84 2.57
5245 6704 3.044986 CGTGTTGGCTTCAAAGTCATTG 58.955 45.455 0.00 0.00 40.84 2.82
5246 6705 2.796593 GTGTTGGCTTCAAAGTCATTGC 59.203 45.455 0.00 0.00 40.84 3.56
5247 6706 2.224018 TGTTGGCTTCAAAGTCATTGCC 60.224 45.455 0.00 0.00 40.84 4.52
5248 6707 0.597568 TGGCTTCAAAGTCATTGCCG 59.402 50.000 0.00 0.00 42.87 5.69
5249 6708 0.881118 GGCTTCAAAGTCATTGCCGA 59.119 50.000 0.00 0.00 38.98 5.54
5250 6709 1.135575 GGCTTCAAAGTCATTGCCGAG 60.136 52.381 0.00 0.00 38.98 4.63
5251 6710 1.537202 GCTTCAAAGTCATTGCCGAGT 59.463 47.619 0.00 0.00 38.98 4.18
5252 6711 2.742053 GCTTCAAAGTCATTGCCGAGTA 59.258 45.455 0.00 0.00 38.98 2.59
5253 6712 3.181516 GCTTCAAAGTCATTGCCGAGTAG 60.182 47.826 0.00 0.00 38.98 2.57
5254 6713 3.953712 TCAAAGTCATTGCCGAGTAGA 57.046 42.857 0.00 0.00 38.98 2.59
5255 6714 4.265904 TCAAAGTCATTGCCGAGTAGAA 57.734 40.909 0.00 0.00 38.98 2.10
5256 6715 4.832248 TCAAAGTCATTGCCGAGTAGAAT 58.168 39.130 0.00 0.00 38.98 2.40
5257 6716 5.245531 TCAAAGTCATTGCCGAGTAGAATT 58.754 37.500 0.00 0.00 38.98 2.17
5258 6717 5.122239 TCAAAGTCATTGCCGAGTAGAATTG 59.878 40.000 0.00 0.00 38.98 2.32
5259 6718 2.939103 AGTCATTGCCGAGTAGAATTGC 59.061 45.455 0.00 0.00 0.00 3.56
5260 6719 2.939103 GTCATTGCCGAGTAGAATTGCT 59.061 45.455 0.00 0.00 0.00 3.91
5261 6720 2.938451 TCATTGCCGAGTAGAATTGCTG 59.062 45.455 0.00 0.00 0.00 4.41
5262 6721 1.737838 TTGCCGAGTAGAATTGCTGG 58.262 50.000 0.00 0.00 0.00 4.85
5263 6722 0.613260 TGCCGAGTAGAATTGCTGGT 59.387 50.000 0.00 0.00 0.00 4.00
5264 6723 1.828595 TGCCGAGTAGAATTGCTGGTA 59.171 47.619 0.00 0.00 0.00 3.25
5265 6724 2.159099 TGCCGAGTAGAATTGCTGGTAG 60.159 50.000 0.00 0.00 0.00 3.18
5266 6725 2.100916 GCCGAGTAGAATTGCTGGTAGA 59.899 50.000 0.00 0.00 0.00 2.59
5267 6726 3.707793 CCGAGTAGAATTGCTGGTAGAC 58.292 50.000 0.00 0.00 0.00 2.59
5268 6727 3.130516 CCGAGTAGAATTGCTGGTAGACA 59.869 47.826 0.00 0.00 0.00 3.41
5269 6728 4.202161 CCGAGTAGAATTGCTGGTAGACAT 60.202 45.833 0.00 0.00 0.00 3.06
5270 6729 5.009710 CCGAGTAGAATTGCTGGTAGACATA 59.990 44.000 0.00 0.00 0.00 2.29
5271 6730 6.146216 CGAGTAGAATTGCTGGTAGACATAG 58.854 44.000 0.00 0.00 0.00 2.23
5272 6731 6.412362 AGTAGAATTGCTGGTAGACATAGG 57.588 41.667 0.00 0.00 0.00 2.57
5273 6732 5.900123 AGTAGAATTGCTGGTAGACATAGGT 59.100 40.000 0.00 0.00 0.00 3.08
5274 6733 5.700402 AGAATTGCTGGTAGACATAGGTT 57.300 39.130 0.00 0.00 0.00 3.50
5275 6734 6.808321 AGAATTGCTGGTAGACATAGGTTA 57.192 37.500 0.00 0.00 0.00 2.85
5276 6735 6.821388 AGAATTGCTGGTAGACATAGGTTAG 58.179 40.000 0.00 0.00 0.00 2.34
5277 6736 4.402056 TTGCTGGTAGACATAGGTTAGC 57.598 45.455 0.00 0.00 0.00 3.09
5278 6737 3.643237 TGCTGGTAGACATAGGTTAGCT 58.357 45.455 0.00 0.00 0.00 3.32
5279 6738 4.800023 TGCTGGTAGACATAGGTTAGCTA 58.200 43.478 0.00 0.00 0.00 3.32
5283 6742 6.149807 GCTGGTAGACATAGGTTAGCTACTAG 59.850 46.154 11.47 11.47 41.04 2.57
5313 6772 5.641789 ACTTGACTACCCCTGTAAACTTT 57.358 39.130 0.00 0.00 0.00 2.66
5314 6773 5.618236 ACTTGACTACCCCTGTAAACTTTC 58.382 41.667 0.00 0.00 0.00 2.62
5315 6774 5.368816 ACTTGACTACCCCTGTAAACTTTCT 59.631 40.000 0.00 0.00 0.00 2.52
5327 6788 6.051646 TGTAAACTTTCTAAAACCGTGAGC 57.948 37.500 0.00 0.00 0.00 4.26
5340 6801 7.807977 AAAACCGTGAGCTGAATCAATATAT 57.192 32.000 0.00 0.00 0.00 0.86
5409 6870 3.764693 CGTACGTGTGTGTTTAGTTTCG 58.235 45.455 7.22 0.00 0.00 3.46
5441 6902 3.758755 ATCCAGCGATTGATTCAGCTA 57.241 42.857 0.00 0.00 37.94 3.32
5447 6908 5.410746 CCAGCGATTGATTCAGCTATTGTAT 59.589 40.000 0.00 0.00 37.94 2.29
5472 6933 2.076863 GCGTGCTTGTGTAGGAGATTT 58.923 47.619 0.00 0.00 0.00 2.17
5478 6939 4.994852 TGCTTGTGTAGGAGATTTGTGTAC 59.005 41.667 0.00 0.00 0.00 2.90
5499 6960 4.010224 TGCAACTCGCCGGGCTAA 62.010 61.111 18.34 4.02 41.33 3.09
5549 7010 1.734137 GACGGATCGAGCCAGCTTA 59.266 57.895 21.44 0.00 0.00 3.09
5572 7033 1.202698 GCAGGAACCAAGTCAGTCAGT 60.203 52.381 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.745489 GCCGGTGACAAGGTGATCC 60.745 63.158 1.90 0.00 0.00 3.36
86 111 4.336433 ACGCGTTAGCCATAGTAGTAGAAA 59.664 41.667 5.58 0.00 41.18 2.52
192 219 2.627945 GATGAGTATGACAACCGGCAA 58.372 47.619 0.00 0.00 0.00 4.52
457 496 2.550978 GAGCGGATTCGATGAAAAGGA 58.449 47.619 0.00 0.00 39.00 3.36
577 616 4.483243 GGATGAAGCGGCCCGGAA 62.483 66.667 4.77 0.00 0.00 4.30
602 641 6.268825 ACTAGTCTTATCTTGCTTCAACGA 57.731 37.500 0.00 0.00 0.00 3.85
661 700 3.318886 TGCGCGAGTAGAACACAATTTA 58.681 40.909 12.10 0.00 0.00 1.40
994 1042 1.605992 CTGCTGGAGCCATCTTCCA 59.394 57.895 0.00 0.00 41.18 3.53
1439 1506 0.537143 AAGTGCAGTTTCGGCCATCA 60.537 50.000 2.24 0.00 0.00 3.07
1491 1558 1.521450 GGACGTCACGAGGAGTTCCA 61.521 60.000 18.91 0.00 38.89 3.53
1686 1753 0.178767 CATCGAGGAGCATGTGGGAA 59.821 55.000 0.00 0.00 0.00 3.97
1725 1792 4.010349 GGGTTTCTTGAATCCTCGACATT 58.990 43.478 9.49 0.00 35.49 2.71
1742 1809 4.596354 AAGGGAATTGTATACGGGGTTT 57.404 40.909 0.00 0.00 0.00 3.27
1834 1901 3.645884 GGTACGAGTAAAGTGACTTGCA 58.354 45.455 0.00 0.00 34.59 4.08
1878 1945 2.945668 GAGCTCAAAGTGACCAAGTGTT 59.054 45.455 9.40 0.00 0.00 3.32
2223 2291 4.474651 TCCTGACTATGGACATTGGATGTT 59.525 41.667 0.00 0.00 45.03 2.71
2249 2317 7.066163 AGCTCGTTGATCAACAAATAATCATGA 59.934 33.333 32.06 18.25 41.20 3.07
2255 2323 6.871492 TGACTAGCTCGTTGATCAACAAATAA 59.129 34.615 32.06 16.47 41.20 1.40
2465 2535 3.196901 TGGCTTTAGTAGGATTGAAGCGA 59.803 43.478 0.00 0.00 42.63 4.93
2515 2585 1.077858 TGGACGCAATGGCTATGCA 60.078 52.632 13.87 0.00 44.01 3.96
2575 2645 1.015109 GAAGGGGCGCTTTTAGTAGC 58.985 55.000 18.44 0.00 37.80 3.58
2578 2648 0.690762 TGAGAAGGGGCGCTTTTAGT 59.309 50.000 18.44 3.88 0.00 2.24
2733 2803 2.857489 GCTGCTTGTCTCAACTTTGCAG 60.857 50.000 13.33 13.33 41.70 4.41
2866 2936 2.473891 TAGACGTCTGGACCGCTCCA 62.474 60.000 28.12 0.00 45.11 3.86
2987 3304 0.889994 GGGATTGTGCATGTGCTTGA 59.110 50.000 6.55 0.00 42.66 3.02
3001 3318 1.503347 GGAGAGAGGAGAGGAGGGATT 59.497 57.143 0.00 0.00 0.00 3.01
3363 3708 8.380742 ACCATAGTCTTCTTCCTTTTCTATGA 57.619 34.615 0.00 0.00 36.89 2.15
3550 3899 4.265073 CCATGAAGTAGGGTTCCTTTGAG 58.735 47.826 0.00 0.00 34.61 3.02
3568 3917 0.747255 ACTGCTACTAGACGGCCATG 59.253 55.000 2.24 0.00 0.00 3.66
3651 4000 9.653287 CTAACAACATTAACATGAGAAGTCCTA 57.347 33.333 0.00 0.00 34.11 2.94
3972 4322 0.250510 TAGCACCGGTCATTGCAACA 60.251 50.000 16.21 0.00 41.48 3.33
3976 4326 0.811616 CCTCTAGCACCGGTCATTGC 60.812 60.000 2.59 5.11 39.16 3.56
4325 4678 2.158842 GGCATGTCCAGCTCATCTAAGT 60.159 50.000 0.00 0.00 34.01 2.24
4647 5015 5.106791 GCATGCGATTGCTCTTGTCTTATAT 60.107 40.000 0.00 0.00 43.34 0.86
4654 5090 1.660560 GGGCATGCGATTGCTCTTGT 61.661 55.000 12.44 0.00 40.09 3.16
4657 5093 2.117156 GTGGGCATGCGATTGCTCT 61.117 57.895 12.44 0.00 43.77 4.09
4672 5108 0.249573 ACGGTAACTTGTCCACGTGG 60.250 55.000 29.26 29.26 32.90 4.94
4673 5109 1.134226 GACGGTAACTTGTCCACGTG 58.866 55.000 9.08 9.08 34.43 4.49
4674 5110 3.575399 GACGGTAACTTGTCCACGT 57.425 52.632 0.00 0.00 37.26 4.49
4679 5115 3.004002 CCTTTTTGGGACGGTAACTTGTC 59.996 47.826 0.00 0.00 0.00 3.18
4680 5116 2.953648 CCTTTTTGGGACGGTAACTTGT 59.046 45.455 0.00 0.00 0.00 3.16
4727 5163 4.836825 TCTAGCAGTTGGATCTTTGGAAG 58.163 43.478 0.00 0.00 0.00 3.46
4784 5220 4.377021 CTTTATGCGCCATACTTAGACCA 58.623 43.478 4.18 0.00 0.00 4.02
4813 5267 7.603963 TGTATTGTCGCAATGTTTATACACT 57.396 32.000 13.17 0.00 37.03 3.55
4846 5300 6.431198 TCCACGATTAATTTTCTTGTAGCC 57.569 37.500 0.00 0.00 0.00 3.93
4850 5304 6.206634 TCTGCTTCCACGATTAATTTTCTTGT 59.793 34.615 0.00 0.00 0.00 3.16
4859 5313 3.496884 GTGTGTTCTGCTTCCACGATTAA 59.503 43.478 0.00 0.00 31.75 1.40
4872 5326 5.448632 GGACCAACTAAGTTTGTGTGTTCTG 60.449 44.000 0.00 0.00 0.00 3.02
4873 5327 4.638865 GGACCAACTAAGTTTGTGTGTTCT 59.361 41.667 0.00 0.00 0.00 3.01
4882 5336 4.137543 CAAGCAGAGGACCAACTAAGTTT 58.862 43.478 0.00 0.00 0.00 2.66
4883 5337 3.744660 CAAGCAGAGGACCAACTAAGTT 58.255 45.455 0.00 0.00 0.00 2.66
4884 5338 2.551071 GCAAGCAGAGGACCAACTAAGT 60.551 50.000 0.00 0.00 0.00 2.24
4885 5339 2.079925 GCAAGCAGAGGACCAACTAAG 58.920 52.381 0.00 0.00 0.00 2.18
4886 5340 1.699634 AGCAAGCAGAGGACCAACTAA 59.300 47.619 0.00 0.00 0.00 2.24
4887 5341 1.352083 AGCAAGCAGAGGACCAACTA 58.648 50.000 0.00 0.00 0.00 2.24
4888 5342 1.277557 CTAGCAAGCAGAGGACCAACT 59.722 52.381 0.00 0.00 0.00 3.16
4889 5343 1.677217 CCTAGCAAGCAGAGGACCAAC 60.677 57.143 7.11 0.00 31.45 3.77
4890 5344 0.615331 CCTAGCAAGCAGAGGACCAA 59.385 55.000 7.11 0.00 31.45 3.67
4891 5345 0.545309 ACCTAGCAAGCAGAGGACCA 60.545 55.000 16.93 0.00 34.24 4.02
4892 5346 0.107945 CACCTAGCAAGCAGAGGACC 60.108 60.000 16.93 0.00 34.24 4.46
4893 5347 0.107945 CCACCTAGCAAGCAGAGGAC 60.108 60.000 16.93 0.00 34.24 3.85
4894 5348 1.903877 GCCACCTAGCAAGCAGAGGA 61.904 60.000 16.93 0.00 34.24 3.71
4895 5349 1.451028 GCCACCTAGCAAGCAGAGG 60.451 63.158 10.45 10.45 36.36 3.69
4896 5350 1.297689 TGCCACCTAGCAAGCAGAG 59.702 57.895 0.00 0.00 40.56 3.35
4897 5351 3.482383 TGCCACCTAGCAAGCAGA 58.518 55.556 0.00 0.00 40.56 4.26
4909 5363 6.741116 GCTATTTGCTTCAGTGGATGCCAC 62.741 50.000 8.51 8.51 45.68 5.01
4910 5364 1.927487 ATTTGCTTCAGTGGATGCCA 58.073 45.000 0.00 0.00 42.00 4.92
4911 5365 2.223665 GCTATTTGCTTCAGTGGATGCC 60.224 50.000 0.00 0.00 42.00 4.40
4912 5366 2.540361 CGCTATTTGCTTCAGTGGATGC 60.540 50.000 0.00 0.00 42.75 3.91
4913 5367 2.540361 GCGCTATTTGCTTCAGTGGATG 60.540 50.000 0.00 0.00 40.11 3.51
4914 5368 1.672881 GCGCTATTTGCTTCAGTGGAT 59.327 47.619 0.00 0.00 40.11 3.41
4915 5369 1.086696 GCGCTATTTGCTTCAGTGGA 58.913 50.000 0.00 0.00 40.11 4.02
4916 5370 0.099436 GGCGCTATTTGCTTCAGTGG 59.901 55.000 7.64 0.00 40.11 4.00
4917 5371 0.804364 TGGCGCTATTTGCTTCAGTG 59.196 50.000 7.64 0.00 40.11 3.66
4918 5372 0.804989 GTGGCGCTATTTGCTTCAGT 59.195 50.000 7.64 0.00 40.11 3.41
4919 5373 0.247814 CGTGGCGCTATTTGCTTCAG 60.248 55.000 7.64 0.00 40.11 3.02
4920 5374 0.953471 ACGTGGCGCTATTTGCTTCA 60.953 50.000 7.64 0.00 40.11 3.02
4921 5375 0.521242 CACGTGGCGCTATTTGCTTC 60.521 55.000 7.95 0.00 40.11 3.86
4922 5376 1.234615 ACACGTGGCGCTATTTGCTT 61.235 50.000 21.57 0.00 40.11 3.91
4928 5382 2.508439 CGGAACACGTGGCGCTAT 60.508 61.111 21.57 0.00 37.93 2.97
4939 5393 1.092921 GTGCAGGTGTGAACGGAACA 61.093 55.000 0.00 0.00 0.00 3.18
4959 5413 3.665675 ATTGACCGCGAGTGAGGCC 62.666 63.158 8.23 0.00 38.90 5.19
4960 5414 2.125512 ATTGACCGCGAGTGAGGC 60.126 61.111 8.23 0.00 38.90 4.70
4965 5419 2.024176 ATTTAGCATTGACCGCGAGT 57.976 45.000 8.23 3.14 0.00 4.18
4967 5421 3.189495 TCAAAATTTAGCATTGACCGCGA 59.811 39.130 8.23 0.00 0.00 5.87
4968 5422 3.497118 TCAAAATTTAGCATTGACCGCG 58.503 40.909 0.00 0.00 0.00 6.46
4970 5424 7.350110 ACAAATCAAAATTTAGCATTGACCG 57.650 32.000 11.40 0.00 36.03 4.79
4972 5426 8.006741 ACGACAAATCAAAATTTAGCATTGAC 57.993 30.769 11.40 6.47 36.03 3.18
4973 5427 8.586570 AACGACAAATCAAAATTTAGCATTGA 57.413 26.923 11.40 3.60 37.47 2.57
4976 5430 9.086336 CCATAACGACAAATCAAAATTTAGCAT 57.914 29.630 0.00 0.00 33.27 3.79
4977 5431 7.062839 GCCATAACGACAAATCAAAATTTAGCA 59.937 33.333 0.00 0.00 33.27 3.49
4980 5434 9.781834 CTAGCCATAACGACAAATCAAAATTTA 57.218 29.630 0.00 0.00 33.27 1.40
4981 5435 7.759433 CCTAGCCATAACGACAAATCAAAATTT 59.241 33.333 0.00 0.00 35.43 1.82
4982 5436 7.122055 TCCTAGCCATAACGACAAATCAAAATT 59.878 33.333 0.00 0.00 0.00 1.82
4984 5438 5.941058 TCCTAGCCATAACGACAAATCAAAA 59.059 36.000 0.00 0.00 0.00 2.44
4986 5440 5.092554 TCCTAGCCATAACGACAAATCAA 57.907 39.130 0.00 0.00 0.00 2.57
4989 5443 7.404671 AATTTTCCTAGCCATAACGACAAAT 57.595 32.000 0.00 0.00 0.00 2.32
4996 6448 9.967346 GGAAGAATTAATTTTCCTAGCCATAAC 57.033 33.333 22.08 2.12 37.86 1.89
5005 6457 8.695456 ACAATATGCGGAAGAATTAATTTTCCT 58.305 29.630 24.22 15.88 38.55 3.36
5006 6458 8.871686 ACAATATGCGGAAGAATTAATTTTCC 57.128 30.769 20.74 20.74 37.58 3.13
5011 6463 9.520204 CTCAAAACAATATGCGGAAGAATTAAT 57.480 29.630 0.00 0.00 0.00 1.40
5012 6464 7.487829 GCTCAAAACAATATGCGGAAGAATTAA 59.512 33.333 0.00 0.00 0.00 1.40
5021 6478 2.423185 TCAGGCTCAAAACAATATGCGG 59.577 45.455 0.00 0.00 0.00 5.69
5041 6498 3.118738 TCCACGGAATTAAGAGAGGCTTC 60.119 47.826 0.00 0.00 38.05 3.86
5084 6542 2.594592 GTGTGTGTGGCTCCACCC 60.595 66.667 15.76 5.61 45.63 4.61
5098 6556 3.381272 CCAAATGGAGAGTTGTGTTGTGT 59.619 43.478 0.00 0.00 37.39 3.72
5099 6557 3.243501 CCCAAATGGAGAGTTGTGTTGTG 60.244 47.826 0.00 0.00 37.39 3.33
5100 6558 2.958355 CCCAAATGGAGAGTTGTGTTGT 59.042 45.455 0.00 0.00 37.39 3.32
5101 6559 2.958355 ACCCAAATGGAGAGTTGTGTTG 59.042 45.455 0.00 0.00 37.39 3.33
5102 6560 2.958355 CACCCAAATGGAGAGTTGTGTT 59.042 45.455 0.00 0.00 37.39 3.32
5123 6581 0.890542 TGAGTTGTGATGTGGCTGCC 60.891 55.000 12.87 12.87 0.00 4.85
5133 6591 2.595124 TCGAAGCTTGTGAGTTGTGA 57.405 45.000 2.10 0.00 0.00 3.58
5134 6592 3.244670 CTTCGAAGCTTGTGAGTTGTG 57.755 47.619 13.09 0.00 0.00 3.33
5165 6624 9.967451 TGGATACTATTCATGTTTAACTCCAAA 57.033 29.630 0.00 0.00 37.61 3.28
5166 6625 9.967451 TTGGATACTATTCATGTTTAACTCCAA 57.033 29.630 10.19 10.19 35.99 3.53
5167 6626 9.391006 GTTGGATACTATTCATGTTTAACTCCA 57.609 33.333 0.00 0.00 37.61 3.86
5168 6627 8.548721 CGTTGGATACTATTCATGTTTAACTCC 58.451 37.037 0.00 0.00 37.61 3.85
5169 6628 9.095065 ACGTTGGATACTATTCATGTTTAACTC 57.905 33.333 0.00 0.00 37.61 3.01
5170 6629 8.879759 CACGTTGGATACTATTCATGTTTAACT 58.120 33.333 0.00 0.00 37.61 2.24
5171 6630 8.662141 ACACGTTGGATACTATTCATGTTTAAC 58.338 33.333 0.00 0.00 37.61 2.01
5172 6631 8.780846 ACACGTTGGATACTATTCATGTTTAA 57.219 30.769 0.00 0.00 37.61 1.52
5173 6632 7.493320 GGACACGTTGGATACTATTCATGTTTA 59.507 37.037 0.00 0.00 37.61 2.01
5174 6633 6.315393 GGACACGTTGGATACTATTCATGTTT 59.685 38.462 0.00 0.00 37.61 2.83
5175 6634 5.815740 GGACACGTTGGATACTATTCATGTT 59.184 40.000 0.00 0.00 37.61 2.71
5176 6635 5.357257 GGACACGTTGGATACTATTCATGT 58.643 41.667 0.00 0.00 37.61 3.21
5177 6636 4.444388 CGGACACGTTGGATACTATTCATG 59.556 45.833 0.00 0.00 34.81 3.07
5178 6637 4.500887 CCGGACACGTTGGATACTATTCAT 60.501 45.833 0.00 0.00 38.78 2.57
5179 6638 3.181484 CCGGACACGTTGGATACTATTCA 60.181 47.826 0.00 0.00 38.78 2.57
5180 6639 3.378339 CCGGACACGTTGGATACTATTC 58.622 50.000 0.00 0.00 38.78 1.75
5181 6640 2.482490 GCCGGACACGTTGGATACTATT 60.482 50.000 5.05 0.00 38.78 1.73
5182 6641 1.068127 GCCGGACACGTTGGATACTAT 59.932 52.381 5.05 0.00 38.78 2.12
5183 6642 0.457035 GCCGGACACGTTGGATACTA 59.543 55.000 5.05 0.00 38.78 1.82
5184 6643 1.217244 GCCGGACACGTTGGATACT 59.783 57.895 5.05 0.00 38.78 2.12
5185 6644 0.804933 GAGCCGGACACGTTGGATAC 60.805 60.000 5.05 0.00 38.78 2.24
5186 6645 1.514087 GAGCCGGACACGTTGGATA 59.486 57.895 5.05 0.00 38.78 2.59
5187 6646 2.264794 GAGCCGGACACGTTGGAT 59.735 61.111 5.05 0.00 38.78 3.41
5188 6647 3.998672 GGAGCCGGACACGTTGGA 61.999 66.667 5.05 0.00 38.78 3.53
5190 6649 4.657824 ACGGAGCCGGACACGTTG 62.658 66.667 5.05 0.00 44.69 4.10
5191 6650 4.657824 CACGGAGCCGGACACGTT 62.658 66.667 5.05 0.00 44.69 3.99
5193 6652 3.740397 TACACGGAGCCGGACACG 61.740 66.667 5.05 8.27 44.69 4.49
5194 6653 2.126189 GTACACGGAGCCGGACAC 60.126 66.667 5.05 3.83 44.69 3.67
5195 6654 3.740397 CGTACACGGAGCCGGACA 61.740 66.667 5.05 0.00 44.69 4.02
5196 6655 1.922135 TAACGTACACGGAGCCGGAC 61.922 60.000 5.05 7.26 44.95 4.79
5197 6656 1.673993 TAACGTACACGGAGCCGGA 60.674 57.895 5.05 0.00 44.95 5.14
5198 6657 1.514873 GTAACGTACACGGAGCCGG 60.515 63.158 14.07 0.00 44.95 6.13
5199 6658 1.209898 TGTAACGTACACGGAGCCG 59.790 57.895 7.48 7.48 44.95 5.52
5218 6677 0.878523 TTGAAGCCAACACGGACTCG 60.879 55.000 0.00 0.00 43.02 4.18
5219 6678 1.264288 CTTTGAAGCCAACACGGACTC 59.736 52.381 0.00 0.00 36.56 3.36
5220 6679 1.308998 CTTTGAAGCCAACACGGACT 58.691 50.000 0.00 0.00 36.56 3.85
5221 6680 1.002792 GACTTTGAAGCCAACACGGAC 60.003 52.381 0.00 0.00 36.56 4.79
5222 6681 1.305201 GACTTTGAAGCCAACACGGA 58.695 50.000 0.00 0.00 36.56 4.69
5223 6682 1.021202 TGACTTTGAAGCCAACACGG 58.979 50.000 0.00 0.00 38.11 4.94
5224 6683 3.044986 CAATGACTTTGAAGCCAACACG 58.955 45.455 0.00 0.00 37.53 4.49
5225 6684 2.796593 GCAATGACTTTGAAGCCAACAC 59.203 45.455 5.31 0.00 37.53 3.32
5226 6685 2.224018 GGCAATGACTTTGAAGCCAACA 60.224 45.455 5.31 0.00 41.63 3.33
5227 6686 2.407090 GGCAATGACTTTGAAGCCAAC 58.593 47.619 5.31 0.00 41.63 3.77
5228 6687 1.000385 CGGCAATGACTTTGAAGCCAA 60.000 47.619 5.31 0.00 42.10 4.52
5229 6688 0.597568 CGGCAATGACTTTGAAGCCA 59.402 50.000 5.31 0.00 42.10 4.75
5230 6689 0.881118 TCGGCAATGACTTTGAAGCC 59.119 50.000 5.31 0.00 37.53 4.35
5231 6690 1.537202 ACTCGGCAATGACTTTGAAGC 59.463 47.619 5.31 0.00 37.53 3.86
5232 6691 4.245660 TCTACTCGGCAATGACTTTGAAG 58.754 43.478 5.31 2.27 37.53 3.02
5233 6692 4.265904 TCTACTCGGCAATGACTTTGAA 57.734 40.909 5.31 0.00 37.53 2.69
5234 6693 3.953712 TCTACTCGGCAATGACTTTGA 57.046 42.857 5.31 0.00 37.53 2.69
5235 6694 5.327091 CAATTCTACTCGGCAATGACTTTG 58.673 41.667 0.00 0.00 38.43 2.77
5236 6695 4.142600 GCAATTCTACTCGGCAATGACTTT 60.143 41.667 0.00 0.00 0.00 2.66
5237 6696 3.375299 GCAATTCTACTCGGCAATGACTT 59.625 43.478 0.00 0.00 0.00 3.01
5238 6697 2.939103 GCAATTCTACTCGGCAATGACT 59.061 45.455 0.00 0.00 0.00 3.41
5239 6698 2.939103 AGCAATTCTACTCGGCAATGAC 59.061 45.455 0.00 0.00 0.00 3.06
5240 6699 2.938451 CAGCAATTCTACTCGGCAATGA 59.062 45.455 0.00 0.00 0.00 2.57
5241 6700 2.032550 CCAGCAATTCTACTCGGCAATG 59.967 50.000 0.00 0.00 0.00 2.82
5242 6701 2.292267 CCAGCAATTCTACTCGGCAAT 58.708 47.619 0.00 0.00 0.00 3.56
5243 6702 1.003118 ACCAGCAATTCTACTCGGCAA 59.997 47.619 0.00 0.00 0.00 4.52
5244 6703 0.613260 ACCAGCAATTCTACTCGGCA 59.387 50.000 0.00 0.00 0.00 5.69
5245 6704 2.100916 TCTACCAGCAATTCTACTCGGC 59.899 50.000 0.00 0.00 0.00 5.54
5246 6705 3.130516 TGTCTACCAGCAATTCTACTCGG 59.869 47.826 0.00 0.00 0.00 4.63
5247 6706 4.371855 TGTCTACCAGCAATTCTACTCG 57.628 45.455 0.00 0.00 0.00 4.18
5248 6707 6.041069 ACCTATGTCTACCAGCAATTCTACTC 59.959 42.308 0.00 0.00 0.00 2.59
5249 6708 5.900123 ACCTATGTCTACCAGCAATTCTACT 59.100 40.000 0.00 0.00 0.00 2.57
5250 6709 6.163135 ACCTATGTCTACCAGCAATTCTAC 57.837 41.667 0.00 0.00 0.00 2.59
5251 6710 6.808321 AACCTATGTCTACCAGCAATTCTA 57.192 37.500 0.00 0.00 0.00 2.10
5252 6711 5.700402 AACCTATGTCTACCAGCAATTCT 57.300 39.130 0.00 0.00 0.00 2.40
5253 6712 5.467063 GCTAACCTATGTCTACCAGCAATTC 59.533 44.000 0.00 0.00 0.00 2.17
5254 6713 5.131142 AGCTAACCTATGTCTACCAGCAATT 59.869 40.000 0.00 0.00 0.00 2.32
5255 6714 4.656112 AGCTAACCTATGTCTACCAGCAAT 59.344 41.667 0.00 0.00 0.00 3.56
5256 6715 4.030913 AGCTAACCTATGTCTACCAGCAA 58.969 43.478 0.00 0.00 0.00 3.91
5257 6716 3.643237 AGCTAACCTATGTCTACCAGCA 58.357 45.455 0.00 0.00 0.00 4.41
5258 6717 4.828387 AGTAGCTAACCTATGTCTACCAGC 59.172 45.833 0.00 0.00 32.31 4.85
5259 6718 7.225725 ACTAGTAGCTAACCTATGTCTACCAG 58.774 42.308 0.00 0.00 32.31 4.00
5260 6719 7.146715 ACTAGTAGCTAACCTATGTCTACCA 57.853 40.000 0.00 0.00 32.31 3.25
5288 6747 8.439964 AAAGTTTACAGGGGTAGTCAAGTATA 57.560 34.615 0.00 0.00 0.00 1.47
5289 6748 6.947376 AAGTTTACAGGGGTAGTCAAGTAT 57.053 37.500 0.00 0.00 0.00 2.12
5294 6753 6.999705 TTAGAAAGTTTACAGGGGTAGTCA 57.000 37.500 0.00 0.00 0.00 3.41
5295 6754 7.173907 GGTTTTAGAAAGTTTACAGGGGTAGTC 59.826 40.741 0.00 0.00 0.00 2.59
5296 6755 7.000472 GGTTTTAGAAAGTTTACAGGGGTAGT 59.000 38.462 0.00 0.00 0.00 2.73
5297 6756 6.148315 CGGTTTTAGAAAGTTTACAGGGGTAG 59.852 42.308 0.00 0.00 0.00 3.18
5305 6764 6.018507 TCAGCTCACGGTTTTAGAAAGTTTAC 60.019 38.462 0.00 0.00 0.00 2.01
5306 6765 6.050432 TCAGCTCACGGTTTTAGAAAGTTTA 58.950 36.000 0.00 0.00 0.00 2.01
5307 6766 4.879545 TCAGCTCACGGTTTTAGAAAGTTT 59.120 37.500 0.00 0.00 0.00 2.66
5313 6772 4.265904 TGATTCAGCTCACGGTTTTAGA 57.734 40.909 0.00 0.00 0.00 2.10
5314 6773 5.551760 ATTGATTCAGCTCACGGTTTTAG 57.448 39.130 0.00 0.00 0.00 1.85
5315 6774 8.902540 ATATATTGATTCAGCTCACGGTTTTA 57.097 30.769 0.00 0.00 0.00 1.52
5327 6788 8.939201 ATCGAGCCTTGTATATATTGATTCAG 57.061 34.615 0.00 0.00 0.00 3.02
5409 6870 1.729881 GCTGGATTGAATCACGCCC 59.270 57.895 7.56 0.00 0.00 6.13
5441 6902 2.093625 CACAAGCACGCACGTATACAAT 59.906 45.455 3.32 0.00 0.00 2.71
5447 6908 0.665068 CCTACACAAGCACGCACGTA 60.665 55.000 0.00 0.00 0.00 3.57
5472 6933 1.484227 GCGAGTTGCACACGTACACA 61.484 55.000 0.00 0.00 45.45 3.72
5549 7010 1.062488 ACTGACTTGGTTCCTGCCCT 61.062 55.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.