Multiple sequence alignment - TraesCS5B01G475200

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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 TraesCS5B01G475200 chr5B 100.000 3599 0 0 1 3599 648146873 648143275 0.000000e+00 6647.0
1 TraesCS5B01G475200 chr5B 84.833 1411 184 15 1017 2406 648135996 648134595 0.000000e+00 1393.0
2 TraesCS5B01G475200 chr5B 83.130 984 140 20 1445 2412 648180353 648179380 0.000000e+00 874.0
3 TraesCS5B01G475200 chr5B 83.078 981 137 19 1445 2407 648260039 648259070 0.000000e+00 865.0
4 TraesCS5B01G475200 chr5B 82.902 965 155 5 1445 2406 648130751 648129794 0.000000e+00 859.0
5 TraesCS5B01G475200 chr5B 87.075 441 45 1 1019 1447 648260591 648260151 4.180000e-134 488.0
6 TraesCS5B01G475200 chr5B 98.864 88 1 0 3228 3315 648143560 648143473 1.340000e-34 158.0
7 TraesCS5B01G475200 chr5B 98.864 88 1 0 3314 3401 648143646 648143559 1.340000e-34 158.0
8 TraesCS5B01G475200 chr5A 88.327 2707 185 48 1 2640 643628341 643625699 0.000000e+00 3127.0
9 TraesCS5B01G475200 chr5A 83.588 1438 199 18 1007 2417 643578530 643577103 0.000000e+00 1314.0
10 TraesCS5B01G475200 chr5A 83.150 908 137 15 1519 2417 643453257 643452357 0.000000e+00 815.0
11 TraesCS5B01G475200 chr5A 83.981 849 122 10 1544 2382 643854910 643854066 0.000000e+00 802.0
12 TraesCS5B01G475200 chr5A 81.903 967 151 16 1450 2401 643734545 643733588 0.000000e+00 795.0
13 TraesCS5B01G475200 chr5A 86.395 441 47 2 1019 1447 643855547 643855108 1.510000e-128 470.0
14 TraesCS5B01G475200 chr5A 86.744 430 41 5 1030 1447 643453882 643453457 7.040000e-127 464.0
15 TraesCS5B01G475200 chr5A 89.305 374 32 4 2943 3315 643625556 643625190 2.530000e-126 462.0
16 TraesCS5B01G475200 chr5A 92.578 256 13 5 3314 3568 643625273 643625023 2.640000e-96 363.0
17 TraesCS5B01G475200 chr5D 88.864 2218 142 52 736 2916 515412646 515410497 0.000000e+00 2630.0
18 TraesCS5B01G475200 chr5D 83.981 824 118 12 1582 2395 515568234 515567415 0.000000e+00 778.0
19 TraesCS5B01G475200 chr5D 83.724 811 118 12 1582 2382 551243463 551242657 0.000000e+00 754.0
20 TraesCS5B01G475200 chr5D 86.387 573 45 13 1 553 515413208 515412649 2.390000e-166 595.0
21 TraesCS5B01G475200 chr5D 85.845 438 44 4 1025 1447 515466254 515465820 1.970000e-122 449.0
22 TraesCS5B01G475200 chr5D 88.000 225 22 3 2952 3172 545779949 545780172 9.910000e-66 261.0
23 TraesCS5B01G475200 chr5D 85.259 251 31 4 2952 3198 515410429 515410181 1.660000e-63 254.0
24 TraesCS5B01G475200 chr5D 87.111 225 24 3 2952 3172 393679430 393679653 2.150000e-62 250.0
25 TraesCS5B01G475200 chr1B 85.495 455 57 7 1046 1491 136921848 136922302 1.960000e-127 466.0
26 TraesCS5B01G475200 chr1B 90.000 210 20 1 107 315 357924824 357924615 1.650000e-68 270.0
27 TraesCS5B01G475200 chr1B 88.940 217 22 2 101 315 622367247 622367463 2.130000e-67 267.0
28 TraesCS5B01G475200 chr1B 88.626 211 23 1 107 316 41839997 41839787 4.610000e-64 255.0
29 TraesCS5B01G475200 chr2B 83.333 306 38 6 27 319 566618234 566617929 1.650000e-68 270.0
30 TraesCS5B01G475200 chr2B 88.018 217 25 1 101 316 25697186 25697402 4.610000e-64 255.0
31 TraesCS5B01G475200 chr2D 88.444 225 21 3 2952 3172 4963152 4962929 2.130000e-67 267.0
32 TraesCS5B01G475200 chrUn 82.895 304 38 8 27 316 122294448 122294751 9.910000e-66 261.0
33 TraesCS5B01G475200 chr4A 82.838 303 39 6 27 316 605057863 605057561 3.560000e-65 259.0
34 TraesCS5B01G475200 chr1D 87.556 225 23 3 2952 3172 45886372 45886595 4.610000e-64 255.0
35 TraesCS5B01G475200 chr1D 87.556 225 23 3 2952 3172 481233192 481232969 4.610000e-64 255.0
36 TraesCS5B01G475200 chr3B 88.571 210 23 1 107 315 92929752 92929543 1.660000e-63 254.0
37 TraesCS5B01G475200 chr7D 87.054 224 25 3 2952 3172 603069324 603069102 2.150000e-62 250.0
38 TraesCS5B01G475200 chr4D 86.667 225 25 3 2952 3172 495759379 495759602 9.980000e-61 244.0
39 TraesCS5B01G475200 chr7A 85.714 91 13 0 346 436 195518773 195518863 2.960000e-16 97.1


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 TraesCS5B01G475200 chr5B 648143275 648146873 3598 True 2321.000000 6647 99.242667 1 3599 3 chr5B.!!$R3 3598
1 TraesCS5B01G475200 chr5B 648129794 648135996 6202 True 1126.000000 1393 83.867500 1017 2406 2 chr5B.!!$R2 1389
2 TraesCS5B01G475200 chr5B 648179380 648180353 973 True 874.000000 874 83.130000 1445 2412 1 chr5B.!!$R1 967
3 TraesCS5B01G475200 chr5B 648259070 648260591 1521 True 676.500000 865 85.076500 1019 2407 2 chr5B.!!$R4 1388
4 TraesCS5B01G475200 chr5A 643625023 643628341 3318 True 1317.333333 3127 90.070000 1 3568 3 chr5A.!!$R4 3567
5 TraesCS5B01G475200 chr5A 643577103 643578530 1427 True 1314.000000 1314 83.588000 1007 2417 1 chr5A.!!$R1 1410
6 TraesCS5B01G475200 chr5A 643733588 643734545 957 True 795.000000 795 81.903000 1450 2401 1 chr5A.!!$R2 951
7 TraesCS5B01G475200 chr5A 643452357 643453882 1525 True 639.500000 815 84.947000 1030 2417 2 chr5A.!!$R3 1387
8 TraesCS5B01G475200 chr5A 643854066 643855547 1481 True 636.000000 802 85.188000 1019 2382 2 chr5A.!!$R5 1363
9 TraesCS5B01G475200 chr5D 515410181 515413208 3027 True 1159.666667 2630 86.836667 1 3198 3 chr5D.!!$R4 3197
10 TraesCS5B01G475200 chr5D 515567415 515568234 819 True 778.000000 778 83.981000 1582 2395 1 chr5D.!!$R2 813
11 TraesCS5B01G475200 chr5D 551242657 551243463 806 True 754.000000 754 83.724000 1582 2382 1 chr5D.!!$R3 800

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
776 808 0.037734 ACTCCCCCAAACATTCGTCC 59.962 55.0 0.0 0.0 0.0 4.79 F
846 879 0.039180 TGAAGGTGAGGCCGAGTAGA 59.961 55.0 0.0 0.0 43.7 2.59 F
931 971 0.665298 GGAATCTCATTTCGCCCAGC 59.335 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 2532 0.038166 TTCTTCGCCTCCATTTGCCT 59.962 50.0 0.0 0.0 0.00 4.75 R
2479 2857 0.478072 ACTTGAATCAGTGCCCCACA 59.522 50.0 0.0 0.0 36.74 4.17 R
2798 5175 0.679002 GGAGTTTTACCCCCGAAGCC 60.679 60.0 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
25 26 2.677542 TCCTGTGAGACACTACCACT 57.322 50.000 0.00 0.00 35.11 4.00
30 31 2.891580 TGTGAGACACTACCACTTCCTC 59.108 50.000 0.00 0.00 35.11 3.71
36 37 2.633481 ACACTACCACTTCCTCTGGTTC 59.367 50.000 0.00 0.00 42.35 3.62
40 41 4.712337 ACTACCACTTCCTCTGGTTCATAG 59.288 45.833 0.00 0.00 42.35 2.23
41 42 2.840651 ACCACTTCCTCTGGTTCATAGG 59.159 50.000 0.00 0.00 39.07 2.57
42 43 3.107601 CCACTTCCTCTGGTTCATAGGA 58.892 50.000 0.00 0.00 35.42 2.94
43 44 3.713764 CCACTTCCTCTGGTTCATAGGAT 59.286 47.826 3.42 0.00 36.78 3.24
44 45 4.901849 CCACTTCCTCTGGTTCATAGGATA 59.098 45.833 3.42 0.00 36.78 2.59
46 47 6.126768 CCACTTCCTCTGGTTCATAGGATAAA 60.127 42.308 3.42 0.00 36.78 1.40
47 48 7.338710 CACTTCCTCTGGTTCATAGGATAAAA 58.661 38.462 3.42 0.00 36.78 1.52
130 151 4.437682 AGAGATGTCCTTTGGTTCACAA 57.562 40.909 0.00 0.00 37.28 3.33
135 156 5.707298 AGATGTCCTTTGGTTCACAACATAG 59.293 40.000 0.00 0.00 39.19 2.23
240 263 7.710907 GGATTTTATTCCTACCAATCAAAAGGC 59.289 37.037 0.00 0.00 32.68 4.35
248 271 5.358160 CCTACCAATCAAAAGGCTCTAAAGG 59.642 44.000 0.00 0.00 0.00 3.11
302 325 8.250332 TGAAATTCCTACATAATTCCTGCAAAC 58.750 33.333 0.00 0.00 0.00 2.93
310 333 6.825610 ACATAATTCCTGCAAACCAAAAGAA 58.174 32.000 0.00 0.00 0.00 2.52
363 386 5.599656 CCTCATTCTCTCTTCTCTCTTCCAT 59.400 44.000 0.00 0.00 0.00 3.41
375 398 4.164221 TCTCTCTTCCATACAAATCCACCC 59.836 45.833 0.00 0.00 0.00 4.61
406 429 7.086685 TCCACCTTTCCTAACTTAAATCAGT 57.913 36.000 0.00 0.00 0.00 3.41
597 627 9.893305 AACTTTTAAAATAGAGTGAAATCGGTG 57.107 29.630 0.09 0.00 0.00 4.94
598 628 9.063615 ACTTTTAAAATAGAGTGAAATCGGTGT 57.936 29.630 0.09 0.00 0.00 4.16
599 629 9.893305 CTTTTAAAATAGAGTGAAATCGGTGTT 57.107 29.630 0.09 0.00 0.00 3.32
605 635 9.840427 AAATAGAGTGAAATCGGTGTTAAAATG 57.160 29.630 0.00 0.00 0.00 2.32
627 657 8.472683 AATGAGTGAAATTTGTTTTCGAAACA 57.527 26.923 10.79 9.37 45.63 2.83
630 660 7.062839 TGAGTGAAATTTGTTTTCGAAACAAGG 59.937 33.333 10.79 0.00 45.63 3.61
719 750 8.977505 ACTGAAATATGTTTTTCAAAATGACCG 58.022 29.630 1.78 0.00 43.12 4.79
720 751 8.304202 TGAAATATGTTTTTCAAAATGACCGG 57.696 30.769 0.00 0.00 41.39 5.28
721 752 8.144478 TGAAATATGTTTTTCAAAATGACCGGA 58.856 29.630 9.46 0.00 41.39 5.14
722 753 8.894768 AAATATGTTTTTCAAAATGACCGGAA 57.105 26.923 9.46 0.00 0.00 4.30
723 754 9.500785 AAATATGTTTTTCAAAATGACCGGAAT 57.499 25.926 9.46 0.00 0.00 3.01
726 757 8.702163 ATGTTTTTCAAAATGACCGGAATATC 57.298 30.769 9.46 0.00 0.00 1.63
727 758 6.804295 TGTTTTTCAAAATGACCGGAATATCG 59.196 34.615 9.46 0.00 0.00 2.92
734 765 7.170828 TCAAAATGACCGGAATATCGACAATAG 59.829 37.037 9.46 0.00 0.00 1.73
749 780 2.950309 ACAATAGCACCTCGTAGTCGAT 59.050 45.455 0.00 0.00 45.21 3.59
757 788 4.386652 GCACCTCGTAGTCGATAAAAACAA 59.613 41.667 0.00 0.00 45.21 2.83
764 795 3.682696 AGTCGATAAAAACAACTCCCCC 58.317 45.455 0.00 0.00 0.00 5.40
771 803 4.853468 AAAAACAACTCCCCCAAACATT 57.147 36.364 0.00 0.00 0.00 2.71
776 808 0.037734 ACTCCCCCAAACATTCGTCC 59.962 55.000 0.00 0.00 0.00 4.79
827 860 3.568007 TGCAAGAACAAGATTTACCGCTT 59.432 39.130 0.00 0.00 0.00 4.68
828 861 3.914364 GCAAGAACAAGATTTACCGCTTG 59.086 43.478 0.00 0.00 45.27 4.01
829 862 4.320202 GCAAGAACAAGATTTACCGCTTGA 60.320 41.667 9.31 0.00 43.11 3.02
846 879 0.039180 TGAAGGTGAGGCCGAGTAGA 59.961 55.000 0.00 0.00 43.70 2.59
847 880 0.741915 GAAGGTGAGGCCGAGTAGAG 59.258 60.000 0.00 0.00 43.70 2.43
931 971 0.665298 GGAATCTCATTTCGCCCAGC 59.335 55.000 0.00 0.00 0.00 4.85
1002 1042 3.918253 GATTCCAGGCCACGCACCA 62.918 63.158 5.01 0.00 0.00 4.17
1569 1893 2.122167 CGAACGAGAGGGGAGGGAG 61.122 68.421 0.00 0.00 0.00 4.30
1919 2255 3.849951 GGAGCGCTCCGGGATTGA 61.850 66.667 38.78 0.00 40.36 2.57
2160 2513 1.452651 CATGCTGCCCATCTTCGGT 60.453 57.895 0.00 0.00 29.71 4.69
2235 2588 3.680338 GAGGGACGAGAACGACGGC 62.680 68.421 0.00 0.00 42.66 5.68
2252 2605 4.695231 CTCGTTCGACCGCCGTGT 62.695 66.667 0.00 0.00 39.75 4.49
2343 2696 1.626356 GGATGCAGGAGGTGGTAGCA 61.626 60.000 0.00 0.00 39.79 3.49
2374 2727 2.669670 CGGCATGAGAGATACATCGACC 60.670 54.545 0.00 0.00 0.00 4.79
2408 2761 1.407258 GCTCAGATCTTACTCCGCTGT 59.593 52.381 0.00 0.00 0.00 4.40
2421 2774 1.019278 CCGCTGTAGGTGCAACGAAT 61.019 55.000 0.00 0.00 38.12 3.34
2427 2780 2.161410 TGTAGGTGCAACGAATTGATGC 59.839 45.455 0.00 0.00 45.84 3.91
2444 2822 6.403866 TTGATGCCAATTTCACTACTGTTT 57.596 33.333 0.00 0.00 0.00 2.83
2458 2836 6.426937 TCACTACTGTTTCAGATTACTTTGGC 59.573 38.462 3.70 0.00 35.18 4.52
2460 2838 5.695851 ACTGTTTCAGATTACTTTGGCAG 57.304 39.130 3.70 0.00 35.18 4.85
2462 2840 3.888323 TGTTTCAGATTACTTTGGCAGCA 59.112 39.130 0.00 0.00 0.00 4.41
2465 2843 2.819608 TCAGATTACTTTGGCAGCAACC 59.180 45.455 0.00 0.00 0.00 3.77
2478 2856 3.195396 GGCAGCAACCCATTCAAAGAATA 59.805 43.478 0.00 0.00 0.00 1.75
2479 2857 4.141869 GGCAGCAACCCATTCAAAGAATAT 60.142 41.667 0.00 0.00 0.00 1.28
2504 2886 3.010420 GGGCACTGATTCAAGTTCCTAC 58.990 50.000 0.00 0.00 34.30 3.18
2506 2888 3.686726 GGCACTGATTCAAGTTCCTACAG 59.313 47.826 0.00 0.00 31.49 2.74
2509 3367 5.470098 GCACTGATTCAAGTTCCTACAGAAA 59.530 40.000 0.00 0.00 35.85 2.52
2594 3554 5.825593 TCTGAGAAATAACCACAGGAACT 57.174 39.130 0.00 0.00 43.88 3.01
2597 3557 6.013379 TCTGAGAAATAACCACAGGAACTCAT 60.013 38.462 0.00 0.00 34.60 2.90
2642 3606 4.162320 TCCAAACAGCAGGAAGGTAGATAG 59.838 45.833 0.00 0.00 0.00 2.08
2643 3607 4.446371 CAAACAGCAGGAAGGTAGATAGG 58.554 47.826 0.00 0.00 0.00 2.57
2644 3608 3.406512 ACAGCAGGAAGGTAGATAGGT 57.593 47.619 0.00 0.00 0.00 3.08
2645 3609 4.537945 ACAGCAGGAAGGTAGATAGGTA 57.462 45.455 0.00 0.00 0.00 3.08
2648 3612 5.080337 CAGCAGGAAGGTAGATAGGTATGA 58.920 45.833 0.00 0.00 0.00 2.15
2649 3613 5.719085 CAGCAGGAAGGTAGATAGGTATGAT 59.281 44.000 0.00 0.00 0.00 2.45
2650 3614 6.892456 CAGCAGGAAGGTAGATAGGTATGATA 59.108 42.308 0.00 0.00 0.00 2.15
2657 3621 9.914834 GAAGGTAGATAGGTATGATATGACTCT 57.085 37.037 0.00 0.00 0.00 3.24
2658 3622 9.693739 AAGGTAGATAGGTATGATATGACTCTG 57.306 37.037 0.00 0.00 0.00 3.35
2659 3623 7.777910 AGGTAGATAGGTATGATATGACTCTGC 59.222 40.741 0.00 0.00 0.00 4.26
2672 3636 9.230122 TGATATGACTCTGCTGAAATTAACAAA 57.770 29.630 0.00 0.00 0.00 2.83
2727 3694 6.596309 TCGATTCATACTGCCAGATAATCT 57.404 37.500 0.00 0.00 0.00 2.40
2730 3697 7.040494 CGATTCATACTGCCAGATAATCTCAT 58.960 38.462 0.00 0.00 0.00 2.90
2731 3698 7.548427 CGATTCATACTGCCAGATAATCTCATT 59.452 37.037 0.00 0.00 0.00 2.57
2732 3699 8.789825 ATTCATACTGCCAGATAATCTCATTC 57.210 34.615 0.00 0.00 0.00 2.67
2733 3700 6.705302 TCATACTGCCAGATAATCTCATTCC 58.295 40.000 0.00 0.00 0.00 3.01
2734 3701 4.363991 ACTGCCAGATAATCTCATTCCC 57.636 45.455 0.00 0.00 0.00 3.97
2735 3702 3.718434 ACTGCCAGATAATCTCATTCCCA 59.282 43.478 0.00 0.00 0.00 4.37
2736 3703 4.353191 ACTGCCAGATAATCTCATTCCCAT 59.647 41.667 0.00 0.00 0.00 4.00
2739 3706 5.310331 TGCCAGATAATCTCATTCCCATGTA 59.690 40.000 0.00 0.00 0.00 2.29
2740 3707 6.183361 TGCCAGATAATCTCATTCCCATGTAA 60.183 38.462 0.00 0.00 0.00 2.41
2771 4416 6.896307 AGTTAATGCTCTACTAACAGGTAGGT 59.104 38.462 0.00 0.00 39.50 3.08
2772 4417 7.399478 AGTTAATGCTCTACTAACAGGTAGGTT 59.601 37.037 0.00 0.00 39.50 3.50
2781 4426 7.952368 TCTACTAACAGGTAGGTTTTCTAGGTT 59.048 37.037 0.00 0.00 39.50 3.50
2791 4436 7.013942 GGTAGGTTTTCTAGGTTTTGACATTGT 59.986 37.037 0.00 0.00 0.00 2.71
2796 4441 9.744468 GTTTTCTAGGTTTTGACATTGTTGTAT 57.256 29.630 0.00 0.00 35.79 2.29
2809 5186 0.835276 GTTGTATAGGCTTCGGGGGT 59.165 55.000 0.00 0.00 0.00 4.95
2869 5962 6.453943 CCATCTGAGACATCCTGTATAGTTG 58.546 44.000 0.00 0.00 0.00 3.16
2884 5977 9.273016 CCTGTATAGTTGTATTAACCTCATTGG 57.727 37.037 0.00 0.00 42.93 3.16
2885 5978 8.671384 TGTATAGTTGTATTAACCTCATTGGC 57.329 34.615 0.00 0.00 40.22 4.52
2886 5979 8.268605 TGTATAGTTGTATTAACCTCATTGGCA 58.731 33.333 0.00 0.00 40.22 4.92
2941 6075 2.569853 TGGTCATGTCACCTTTACCGAT 59.430 45.455 5.27 0.00 37.34 4.18
2942 6076 3.195661 GGTCATGTCACCTTTACCGATC 58.804 50.000 0.00 0.00 33.08 3.69
2943 6077 3.118738 GGTCATGTCACCTTTACCGATCT 60.119 47.826 0.00 0.00 33.08 2.75
2944 6078 4.504858 GTCATGTCACCTTTACCGATCTT 58.495 43.478 0.00 0.00 0.00 2.40
2945 6079 4.567159 GTCATGTCACCTTTACCGATCTTC 59.433 45.833 0.00 0.00 0.00 2.87
2946 6080 3.604875 TGTCACCTTTACCGATCTTCC 57.395 47.619 0.00 0.00 0.00 3.46
2947 6081 2.094390 TGTCACCTTTACCGATCTTCCG 60.094 50.000 0.00 0.00 0.00 4.30
2963 6139 0.106569 TCCGGCGACACCCTAATCTA 60.107 55.000 9.30 0.00 33.26 1.98
2967 6143 2.223971 CGGCGACACCCTAATCTAACAT 60.224 50.000 0.00 0.00 33.26 2.71
2968 6144 3.005050 CGGCGACACCCTAATCTAACATA 59.995 47.826 0.00 0.00 33.26 2.29
3026 6202 4.616181 AGCACAAGTGTCTTTACAACAC 57.384 40.909 1.79 0.00 45.86 3.32
3070 6246 4.336713 TGCTACTGTACTCAGCATCTACAG 59.663 45.833 11.10 8.51 44.77 2.74
3074 6250 7.255312 GCTACTGTACTCAGCATCTACAGTAAT 60.255 40.741 17.38 3.32 46.16 1.89
3089 6265 4.929479 ACAGTAATTTATGGTGCCCTTCA 58.071 39.130 0.00 0.00 0.00 3.02
3100 6276 2.417243 GGTGCCCTTCAAAATCATTCCG 60.417 50.000 0.00 0.00 0.00 4.30
3144 6324 6.038356 GTGTTGATCATTTCTAAAGCCCATG 58.962 40.000 0.00 0.00 0.00 3.66
3198 6396 3.132289 CAGGGATACTCGCTAAACAGGAA 59.868 47.826 0.00 0.00 37.59 3.36
3200 6398 4.058817 GGGATACTCGCTAAACAGGAATG 58.941 47.826 0.00 0.00 0.00 2.67
3246 6444 9.677567 TCAGTCTAAACAAGTTTAAATCATTGC 57.322 29.630 6.82 0.00 34.95 3.56
3247 6445 9.683069 CAGTCTAAACAAGTTTAAATCATTGCT 57.317 29.630 6.82 0.00 34.95 3.91
3253 6451 5.777732 ACAAGTTTAAATCATTGCTACCCCA 59.222 36.000 9.42 0.00 0.00 4.96
3254 6452 6.268847 ACAAGTTTAAATCATTGCTACCCCAA 59.731 34.615 9.42 0.00 0.00 4.12
3256 6454 5.105351 AGTTTAAATCATTGCTACCCCAAGC 60.105 40.000 0.00 0.00 43.08 4.01
3263 6461 3.577389 GCTACCCCAAGCAATCACT 57.423 52.632 0.00 0.00 42.30 3.41
3265 6463 3.214696 GCTACCCCAAGCAATCACTAT 57.785 47.619 0.00 0.00 42.30 2.12
3266 6464 2.880890 GCTACCCCAAGCAATCACTATG 59.119 50.000 0.00 0.00 42.30 2.23
3267 6465 3.433598 GCTACCCCAAGCAATCACTATGA 60.434 47.826 0.00 0.00 42.30 2.15
3269 6467 2.308570 ACCCCAAGCAATCACTATGACA 59.691 45.455 0.00 0.00 0.00 3.58
3270 6468 3.053395 ACCCCAAGCAATCACTATGACAT 60.053 43.478 0.00 0.00 0.00 3.06
3271 6469 3.567164 CCCCAAGCAATCACTATGACATC 59.433 47.826 0.00 0.00 0.00 3.06
3272 6470 3.567164 CCCAAGCAATCACTATGACATCC 59.433 47.826 0.00 0.00 0.00 3.51
3274 6472 4.201657 CAAGCAATCACTATGACATCCCA 58.798 43.478 0.00 0.00 0.00 4.37
3275 6473 4.719026 AGCAATCACTATGACATCCCAT 57.281 40.909 0.00 0.00 0.00 4.00
3277 6475 6.384342 AGCAATCACTATGACATCCCATAT 57.616 37.500 0.00 0.00 0.00 1.78
3278 6476 6.787170 AGCAATCACTATGACATCCCATATT 58.213 36.000 0.00 0.00 0.00 1.28
3279 6477 6.883217 AGCAATCACTATGACATCCCATATTC 59.117 38.462 0.00 0.00 0.00 1.75
3280 6478 6.883217 GCAATCACTATGACATCCCATATTCT 59.117 38.462 0.00 0.00 0.00 2.40
3281 6479 7.392673 GCAATCACTATGACATCCCATATTCTT 59.607 37.037 0.00 0.00 0.00 2.52
3283 6481 8.859236 ATCACTATGACATCCCATATTCTTTG 57.141 34.615 0.00 0.00 0.00 2.77
3284 6482 6.712095 TCACTATGACATCCCATATTCTTTGC 59.288 38.462 0.00 0.00 0.00 3.68
3285 6483 6.713903 CACTATGACATCCCATATTCTTTGCT 59.286 38.462 0.00 0.00 0.00 3.91
3286 6484 7.879677 CACTATGACATCCCATATTCTTTGCTA 59.120 37.037 0.00 0.00 0.00 3.49
3287 6485 8.439971 ACTATGACATCCCATATTCTTTGCTAA 58.560 33.333 0.00 0.00 0.00 3.09
3288 6486 9.288576 CTATGACATCCCATATTCTTTGCTAAA 57.711 33.333 0.00 0.00 0.00 1.85
3289 6487 7.572523 TGACATCCCATATTCTTTGCTAAAG 57.427 36.000 0.00 0.00 39.88 1.85
3290 6488 6.039717 TGACATCCCATATTCTTTGCTAAAGC 59.960 38.462 0.00 0.00 38.39 3.51
3309 6507 5.644977 AAGCATACTGTAAAAGAAAGGCC 57.355 39.130 0.00 0.00 0.00 5.19
3310 6508 4.662278 AGCATACTGTAAAAGAAAGGCCA 58.338 39.130 5.01 0.00 0.00 5.36
3311 6509 5.264395 AGCATACTGTAAAAGAAAGGCCAT 58.736 37.500 5.01 0.00 0.00 4.40
3312 6510 5.358160 AGCATACTGTAAAAGAAAGGCCATC 59.642 40.000 5.01 2.29 0.00 3.51
3315 6513 7.601856 CATACTGTAAAAGAAAGGCCATCAAA 58.398 34.615 5.01 0.00 0.00 2.69
3316 6514 5.842907 ACTGTAAAAGAAAGGCCATCAAAC 58.157 37.500 5.01 1.11 0.00 2.93
3319 6517 6.279882 TGTAAAAGAAAGGCCATCAAACAAG 58.720 36.000 5.01 0.00 0.00 3.16
3321 6519 5.357742 AAAGAAAGGCCATCAAACAAGTT 57.642 34.783 5.01 0.00 0.00 2.66
3322 6520 5.357742 AAGAAAGGCCATCAAACAAGTTT 57.642 34.783 5.01 0.00 0.00 2.66
3323 6521 6.478512 AAGAAAGGCCATCAAACAAGTTTA 57.521 33.333 5.01 0.00 0.00 2.01
3325 6523 6.883744 AGAAAGGCCATCAAACAAGTTTAAA 58.116 32.000 5.01 0.00 0.00 1.52
3326 6524 7.508687 AGAAAGGCCATCAAACAAGTTTAAAT 58.491 30.769 5.01 0.00 0.00 1.40
3357 6555 3.567164 CCCCAAGCAATCACTATGACATC 59.433 47.826 0.00 0.00 0.00 3.06
3365 6563 6.883217 AGCAATCACTATGACATCCCATATTC 59.117 38.462 0.00 0.00 0.00 1.75
3369 6567 8.859236 ATCACTATGACATCCCATATTCTTTG 57.141 34.615 0.00 0.00 0.00 2.77
3370 6568 6.712095 TCACTATGACATCCCATATTCTTTGC 59.288 38.462 0.00 0.00 0.00 3.68
3371 6569 6.713903 CACTATGACATCCCATATTCTTTGCT 59.286 38.462 0.00 0.00 0.00 3.91
3372 6570 7.879677 CACTATGACATCCCATATTCTTTGCTA 59.120 37.037 0.00 0.00 0.00 3.49
3375 6573 7.572523 TGACATCCCATATTCTTTGCTAAAG 57.427 36.000 0.00 0.00 39.88 1.85
3376 6574 6.039717 TGACATCCCATATTCTTTGCTAAAGC 59.960 38.462 0.00 0.00 38.39 3.51
3481 6806 4.828939 AGAAAGGTGCATCAAGTGAATTCA 59.171 37.500 3.38 3.38 0.00 2.57
3524 6849 9.936759 TTTCCTCTTCTCTAAAGAAATCTTCTC 57.063 33.333 0.00 0.00 40.95 2.87
3525 6850 8.073467 TCCTCTTCTCTAAAGAAATCTTCTCC 57.927 38.462 0.00 0.00 40.95 3.71
3540 6865 5.815233 TCTTCTCCAAGGGATGATATGTC 57.185 43.478 0.00 0.00 0.00 3.06
3558 6883 2.435805 TGTCAGGTCTGTTCTCAAAGCT 59.564 45.455 0.00 0.00 0.00 3.74
3568 6893 7.550906 GGTCTGTTCTCAAAGCTAACAAGATAT 59.449 37.037 0.99 0.00 33.05 1.63
3569 6894 8.940952 GTCTGTTCTCAAAGCTAACAAGATATT 58.059 33.333 0.99 0.00 33.05 1.28
3570 6895 9.507329 TCTGTTCTCAAAGCTAACAAGATATTT 57.493 29.630 0.99 0.00 33.05 1.40
3571 6896 9.552114 CTGTTCTCAAAGCTAACAAGATATTTG 57.448 33.333 0.99 0.00 33.05 2.32
3572 6897 9.066892 TGTTCTCAAAGCTAACAAGATATTTGT 57.933 29.630 0.00 0.00 30.54 2.83
3575 6900 9.944376 TCTCAAAGCTAACAAGATATTTGTAGT 57.056 29.630 0.00 0.00 31.50 2.73
3586 6911 9.672673 ACAAGATATTTGTAGTAATCAGTTGCT 57.327 29.630 2.63 0.00 34.50 3.91
3589 6914 9.765795 AGATATTTGTAGTAATCAGTTGCTACC 57.234 33.333 11.91 0.00 46.62 3.18
3590 6915 9.765795 GATATTTGTAGTAATCAGTTGCTACCT 57.234 33.333 11.91 2.96 46.62 3.08
3592 6917 6.852420 TTGTAGTAATCAGTTGCTACCTCT 57.148 37.500 11.91 0.00 46.62 3.69
3593 6918 7.949690 TTGTAGTAATCAGTTGCTACCTCTA 57.050 36.000 11.91 0.00 46.62 2.43
3594 6919 8.534954 TTGTAGTAATCAGTTGCTACCTCTAT 57.465 34.615 11.91 0.00 46.62 1.98
3596 6921 6.320494 AGTAATCAGTTGCTACCTCTATCG 57.680 41.667 0.00 0.00 0.00 2.92
3597 6922 5.828859 AGTAATCAGTTGCTACCTCTATCGT 59.171 40.000 0.00 0.00 0.00 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 131 3.882888 TGTTGTGAACCAAAGGACATCTC 59.117 43.478 0.00 0.00 34.07 2.75
117 138 4.398319 AGTCCTATGTTGTGAACCAAAGG 58.602 43.478 0.00 0.00 34.07 3.11
219 242 6.731467 AGAGCCTTTTGATTGGTAGGAATAA 58.269 36.000 0.00 0.00 0.00 1.40
229 252 8.837788 AAAATTCCTTTAGAGCCTTTTGATTG 57.162 30.769 0.00 0.00 0.00 2.67
297 320 3.726291 TGTAGGCTTCTTTTGGTTTGC 57.274 42.857 0.00 0.00 0.00 3.68
302 325 4.137543 ACTCTGTTGTAGGCTTCTTTTGG 58.862 43.478 0.00 0.00 0.00 3.28
310 333 2.430465 CATGCAACTCTGTTGTAGGCT 58.570 47.619 11.35 0.00 0.00 4.58
363 386 5.717654 GGTGGAATAAAAGGGTGGATTTGTA 59.282 40.000 0.00 0.00 0.00 2.41
450 473 1.504359 TTACGCGAGGAGTTTGGTTG 58.496 50.000 15.93 0.00 0.00 3.77
458 481 2.409975 TGAAGGTTTTTACGCGAGGAG 58.590 47.619 15.93 0.00 0.00 3.69
482 506 4.870363 AGATTGGAACCACACAAAAATCG 58.130 39.130 0.00 0.00 0.00 3.34
571 601 9.893305 CACCGATTTCACTCTATTTTAAAAGTT 57.107 29.630 6.79 0.00 0.00 2.66
600 630 9.753669 GTTTCGAAAACAAATTTCACTCATTTT 57.246 25.926 13.10 0.00 46.42 1.82
601 631 8.930760 TGTTTCGAAAACAAATTTCACTCATTT 58.069 25.926 13.10 0.00 46.42 2.32
602 632 8.472683 TGTTTCGAAAACAAATTTCACTCATT 57.527 26.923 13.10 0.00 46.42 2.57
603 633 8.472683 TTGTTTCGAAAACAAATTTCACTCAT 57.527 26.923 13.10 0.00 46.42 2.90
604 634 7.062839 CCTTGTTTCGAAAACAAATTTCACTCA 59.937 33.333 13.10 0.00 46.42 3.41
605 635 7.391016 CCTTGTTTCGAAAACAAATTTCACTC 58.609 34.615 13.10 0.00 46.42 3.51
627 657 7.768582 CACTCTTTTTAAAACATGGTTTCCCTT 59.231 33.333 13.07 0.00 0.00 3.95
630 660 8.710835 TTCACTCTTTTTAAAACATGGTTTCC 57.289 30.769 13.07 0.00 0.00 3.13
696 727 8.527567 TCCGGTCATTTTGAAAAACATATTTC 57.472 30.769 0.00 0.00 39.28 2.17
697 728 8.894768 TTCCGGTCATTTTGAAAAACATATTT 57.105 26.923 0.00 0.00 0.00 1.40
700 731 9.796120 GATATTCCGGTCATTTTGAAAAACATA 57.204 29.630 0.00 0.00 0.00 2.29
701 732 7.487829 CGATATTCCGGTCATTTTGAAAAACAT 59.512 33.333 0.00 0.00 0.00 2.71
702 733 6.804295 CGATATTCCGGTCATTTTGAAAAACA 59.196 34.615 0.00 0.00 0.00 2.83
703 734 7.007995 GTCGATATTCCGGTCATTTTGAAAAAC 59.992 37.037 0.00 0.00 0.00 2.43
704 735 7.024768 GTCGATATTCCGGTCATTTTGAAAAA 58.975 34.615 0.00 0.00 0.00 1.94
705 736 6.149640 TGTCGATATTCCGGTCATTTTGAAAA 59.850 34.615 0.00 0.00 0.00 2.29
706 737 5.644206 TGTCGATATTCCGGTCATTTTGAAA 59.356 36.000 0.00 0.00 0.00 2.69
707 738 5.179533 TGTCGATATTCCGGTCATTTTGAA 58.820 37.500 0.00 0.00 0.00 2.69
708 739 4.760878 TGTCGATATTCCGGTCATTTTGA 58.239 39.130 0.00 0.00 0.00 2.69
709 740 5.478233 TTGTCGATATTCCGGTCATTTTG 57.522 39.130 0.00 0.00 0.00 2.44
710 741 6.073222 GCTATTGTCGATATTCCGGTCATTTT 60.073 38.462 0.00 0.00 0.00 1.82
711 742 5.408604 GCTATTGTCGATATTCCGGTCATTT 59.591 40.000 0.00 0.00 0.00 2.32
712 743 4.929808 GCTATTGTCGATATTCCGGTCATT 59.070 41.667 0.00 0.00 0.00 2.57
713 744 4.021456 TGCTATTGTCGATATTCCGGTCAT 60.021 41.667 0.00 0.00 0.00 3.06
714 745 3.319689 TGCTATTGTCGATATTCCGGTCA 59.680 43.478 0.00 0.00 0.00 4.02
715 746 3.673809 GTGCTATTGTCGATATTCCGGTC 59.326 47.826 0.00 0.00 0.00 4.79
716 747 3.554337 GGTGCTATTGTCGATATTCCGGT 60.554 47.826 0.00 0.00 0.00 5.28
717 748 2.993899 GGTGCTATTGTCGATATTCCGG 59.006 50.000 0.00 0.00 0.00 5.14
718 749 3.914312 AGGTGCTATTGTCGATATTCCG 58.086 45.455 0.00 0.00 0.00 4.30
719 750 3.921021 CGAGGTGCTATTGTCGATATTCC 59.079 47.826 0.00 0.00 34.28 3.01
720 751 4.547532 ACGAGGTGCTATTGTCGATATTC 58.452 43.478 0.00 0.00 36.30 1.75
721 752 4.585955 ACGAGGTGCTATTGTCGATATT 57.414 40.909 0.00 0.00 36.30 1.28
722 753 4.760715 ACTACGAGGTGCTATTGTCGATAT 59.239 41.667 0.00 0.00 36.30 1.63
723 754 4.132336 ACTACGAGGTGCTATTGTCGATA 58.868 43.478 0.00 0.00 36.30 2.92
724 755 2.950309 ACTACGAGGTGCTATTGTCGAT 59.050 45.455 0.00 0.00 36.30 3.59
725 756 2.353889 GACTACGAGGTGCTATTGTCGA 59.646 50.000 0.00 0.00 36.30 4.20
726 757 2.717530 GACTACGAGGTGCTATTGTCG 58.282 52.381 0.00 0.00 38.40 4.35
727 758 2.353889 TCGACTACGAGGTGCTATTGTC 59.646 50.000 0.00 0.00 43.81 3.18
749 780 5.452077 CGAATGTTTGGGGGAGTTGTTTTTA 60.452 40.000 0.00 0.00 0.00 1.52
757 788 0.037734 GGACGAATGTTTGGGGGAGT 59.962 55.000 0.00 0.00 0.00 3.85
808 841 5.048713 CCTTCAAGCGGTAAATCTTGTTCTT 60.049 40.000 0.00 0.00 40.27 2.52
827 860 0.039180 TCTACTCGGCCTCACCTTCA 59.961 55.000 0.00 0.00 35.61 3.02
828 861 0.741915 CTCTACTCGGCCTCACCTTC 59.258 60.000 0.00 0.00 35.61 3.46
829 862 0.331954 TCTCTACTCGGCCTCACCTT 59.668 55.000 0.00 0.00 35.61 3.50
846 879 3.345414 CGTAGTGGTCAAGTAGGACTCT 58.655 50.000 0.00 0.00 37.91 3.24
847 880 2.422832 CCGTAGTGGTCAAGTAGGACTC 59.577 54.545 0.00 0.00 37.91 3.36
957 997 1.374758 GGTGGTGCTCTCTGTTCGG 60.375 63.158 0.00 0.00 0.00 4.30
1002 1042 0.256464 AGCTAGCTCGTCCACTAGGT 59.744 55.000 12.68 0.00 41.21 3.08
1005 1045 1.489649 AGGTAGCTAGCTCGTCCACTA 59.510 52.381 23.26 0.00 0.00 2.74
1569 1893 1.063469 CCATGGTCGTTGTAAATCGGC 59.937 52.381 2.57 0.00 0.00 5.54
1774 2104 3.397439 ATGCTCTGCTCCGCTGGT 61.397 61.111 0.00 0.00 0.00 4.00
1835 2171 4.360964 TCCCCAACGCCACGTACG 62.361 66.667 15.01 15.01 39.99 3.67
1870 2206 2.898738 CTCGTGCTCCTGCTCCAT 59.101 61.111 0.00 0.00 40.48 3.41
1907 2243 0.179070 GAGGAAGTCAATCCCGGAGC 60.179 60.000 0.73 0.00 40.59 4.70
1909 2245 1.195115 CAGAGGAAGTCAATCCCGGA 58.805 55.000 0.73 0.00 40.59 5.14
1916 2252 1.270907 GAGAGCCCAGAGGAAGTCAA 58.729 55.000 0.00 0.00 33.47 3.18
1917 2253 0.115152 TGAGAGCCCAGAGGAAGTCA 59.885 55.000 0.00 0.00 33.47 3.41
1918 2254 0.823460 CTGAGAGCCCAGAGGAAGTC 59.177 60.000 0.00 0.00 36.29 3.01
1919 2255 0.617249 CCTGAGAGCCCAGAGGAAGT 60.617 60.000 0.00 0.00 36.29 3.01
2179 2532 0.038166 TTCTTCGCCTCCATTTGCCT 59.962 50.000 0.00 0.00 0.00 4.75
2235 2588 4.695231 ACACGGCGGTCGAACGAG 62.695 66.667 29.97 21.61 42.43 4.18
2343 2696 1.612950 CTCTCATGCCGCTCTGTATCT 59.387 52.381 0.00 0.00 0.00 1.98
2374 2727 2.759191 TCTGAGCTGCTGTACAAACTG 58.241 47.619 7.01 0.00 0.00 3.16
2408 2761 1.742831 GGCATCAATTCGTTGCACCTA 59.257 47.619 0.00 0.00 41.35 3.08
2421 2774 6.040278 TGAAACAGTAGTGAAATTGGCATCAA 59.960 34.615 4.09 0.00 37.28 2.57
2427 2780 9.003658 AGTAATCTGAAACAGTAGTGAAATTGG 57.996 33.333 4.09 0.00 32.61 3.16
2444 2822 2.819608 GGTTGCTGCCAAAGTAATCTGA 59.180 45.455 0.00 0.00 32.72 3.27
2458 2836 5.808540 CACATATTCTTTGAATGGGTTGCTG 59.191 40.000 3.35 0.00 0.00 4.41
2460 2838 5.111293 CCACATATTCTTTGAATGGGTTGC 58.889 41.667 3.35 0.00 0.00 4.17
2462 2840 4.716287 CCCCACATATTCTTTGAATGGGTT 59.284 41.667 12.79 0.00 43.28 4.11
2465 2843 3.705579 TGCCCCACATATTCTTTGAATGG 59.294 43.478 3.35 0.00 0.00 3.16
2478 2856 1.076024 ACTTGAATCAGTGCCCCACAT 59.924 47.619 0.00 0.00 36.74 3.21
2479 2857 0.478072 ACTTGAATCAGTGCCCCACA 59.522 50.000 0.00 0.00 36.74 4.17
2515 3373 6.647334 TGCATATGAAGAAACCACTTGAAA 57.353 33.333 6.97 0.00 0.00 2.69
2581 3540 4.974645 ACTTCATGAGTTCCTGTGGTTA 57.025 40.909 0.00 0.00 33.92 2.85
2594 3554 4.202567 ACTGAAAGCCCCTAAACTTCATGA 60.203 41.667 0.00 0.00 37.60 3.07
2597 3557 3.876309 ACTGAAAGCCCCTAAACTTCA 57.124 42.857 0.00 0.00 37.60 3.02
2609 3573 3.118542 CTGCTGTTTGGAAACTGAAAGC 58.881 45.455 11.94 8.68 39.36 3.51
2642 3606 7.976135 AATTTCAGCAGAGTCATATCATACC 57.024 36.000 0.00 0.00 0.00 2.73
2645 3609 8.969260 TGTTAATTTCAGCAGAGTCATATCAT 57.031 30.769 0.00 0.00 0.00 2.45
2650 3614 9.768662 AATTTTTGTTAATTTCAGCAGAGTCAT 57.231 25.926 0.00 0.00 0.00 3.06
2698 3665 2.146342 GGCAGTATGAATCGATGGGTG 58.854 52.381 0.00 0.00 39.69 4.61
2730 3697 8.133024 AGCATTAACTTTTCATTACATGGGAA 57.867 30.769 0.00 0.00 0.00 3.97
2731 3698 7.615365 AGAGCATTAACTTTTCATTACATGGGA 59.385 33.333 0.00 0.00 0.00 4.37
2732 3699 7.775120 AGAGCATTAACTTTTCATTACATGGG 58.225 34.615 0.00 0.00 0.00 4.00
2733 3700 9.722056 GTAGAGCATTAACTTTTCATTACATGG 57.278 33.333 0.00 0.00 0.00 3.66
2740 3707 9.167311 CCTGTTAGTAGAGCATTAACTTTTCAT 57.833 33.333 0.00 0.00 32.14 2.57
2752 4132 5.778750 AGAAAACCTACCTGTTAGTAGAGCA 59.221 40.000 0.32 0.00 41.98 4.26
2754 4134 7.614974 ACCTAGAAAACCTACCTGTTAGTAGAG 59.385 40.741 0.00 0.00 41.98 2.43
2755 4135 7.473593 ACCTAGAAAACCTACCTGTTAGTAGA 58.526 38.462 0.00 0.00 41.98 2.59
2758 4138 7.384524 AAACCTAGAAAACCTACCTGTTAGT 57.615 36.000 0.00 0.00 0.00 2.24
2781 4426 5.123186 CCGAAGCCTATACAACAATGTCAAA 59.877 40.000 0.00 0.00 41.05 2.69
2791 4436 2.475339 TACCCCCGAAGCCTATACAA 57.525 50.000 0.00 0.00 0.00 2.41
2796 4441 1.556451 GAGTTTTACCCCCGAAGCCTA 59.444 52.381 0.00 0.00 0.00 3.93
2798 5175 0.679002 GGAGTTTTACCCCCGAAGCC 60.679 60.000 0.00 0.00 0.00 4.35
2809 5186 8.819974 CAACTGTACTTTTTCGTAGGAGTTTTA 58.180 33.333 0.00 0.00 0.00 1.52
2869 5962 5.049828 GCCATTTGCCAATGAGGTTAATAC 58.950 41.667 11.92 0.00 42.35 1.89
2882 5975 5.363292 ACTTGTATCATATTGCCATTTGCCA 59.637 36.000 0.00 0.00 40.16 4.92
2884 5977 5.922544 GGACTTGTATCATATTGCCATTTGC 59.077 40.000 0.00 0.00 41.77 3.68
2885 5978 6.040729 TGGGACTTGTATCATATTGCCATTTG 59.959 38.462 0.00 0.00 0.00 2.32
2886 5979 6.135454 TGGGACTTGTATCATATTGCCATTT 58.865 36.000 0.00 0.00 0.00 2.32
2929 6063 1.935933 CCGGAAGATCGGTAAAGGTG 58.064 55.000 0.00 0.00 44.60 4.00
2941 6075 0.974010 ATTAGGGTGTCGCCGGAAGA 60.974 55.000 5.05 0.00 38.44 2.87
2942 6076 0.529992 GATTAGGGTGTCGCCGGAAG 60.530 60.000 5.05 0.00 38.44 3.46
2943 6077 0.974010 AGATTAGGGTGTCGCCGGAA 60.974 55.000 5.05 0.00 38.44 4.30
2944 6078 0.106569 TAGATTAGGGTGTCGCCGGA 60.107 55.000 5.05 0.00 38.44 5.14
2945 6079 0.748450 TTAGATTAGGGTGTCGCCGG 59.252 55.000 0.00 0.00 38.44 6.13
2946 6080 1.135527 TGTTAGATTAGGGTGTCGCCG 59.864 52.381 0.00 0.00 38.44 6.46
2947 6081 2.973694 TGTTAGATTAGGGTGTCGCC 57.026 50.000 0.00 0.00 0.00 5.54
3026 6202 5.815740 AGCAAATACTAAACCCGATGTAGTG 59.184 40.000 0.97 0.00 30.81 2.74
3089 6265 3.255725 CAACTGCATGCGGAATGATTTT 58.744 40.909 32.80 11.83 38.72 1.82
3100 6276 0.037139 TCAATTGGCCAACTGCATGC 60.037 50.000 23.27 11.82 43.89 4.06
3172 6352 0.750850 TTAGCGAGTATCCCTGTGCC 59.249 55.000 0.00 0.00 0.00 5.01
3173 6353 2.202566 GTTTAGCGAGTATCCCTGTGC 58.797 52.381 0.00 0.00 0.00 4.57
3174 6354 3.448686 CTGTTTAGCGAGTATCCCTGTG 58.551 50.000 0.00 0.00 0.00 3.66
3198 6396 6.233434 TGAACTTTGTCATGCTTACTCTCAT 58.767 36.000 0.00 0.00 0.00 2.90
3200 6398 5.698545 ACTGAACTTTGTCATGCTTACTCTC 59.301 40.000 0.00 0.00 0.00 3.20
3245 6443 2.710096 TAGTGATTGCTTGGGGTAGC 57.290 50.000 0.00 0.00 41.59 3.58
3246 6444 4.130118 GTCATAGTGATTGCTTGGGGTAG 58.870 47.826 0.00 0.00 0.00 3.18
3247 6445 3.521531 TGTCATAGTGATTGCTTGGGGTA 59.478 43.478 0.00 0.00 0.00 3.69
3248 6446 2.308570 TGTCATAGTGATTGCTTGGGGT 59.691 45.455 0.00 0.00 0.00 4.95
3250 6448 3.567164 GGATGTCATAGTGATTGCTTGGG 59.433 47.826 0.00 0.00 0.00 4.12
3253 6451 4.508551 TGGGATGTCATAGTGATTGCTT 57.491 40.909 0.00 0.00 0.00 3.91
3254 6452 4.719026 ATGGGATGTCATAGTGATTGCT 57.281 40.909 0.00 0.00 0.00 3.91
3256 6454 8.859236 AAGAATATGGGATGTCATAGTGATTG 57.141 34.615 0.00 0.00 33.69 2.67
3259 6457 6.712095 GCAAAGAATATGGGATGTCATAGTGA 59.288 38.462 0.00 0.00 33.69 3.41
3260 6458 6.713903 AGCAAAGAATATGGGATGTCATAGTG 59.286 38.462 0.00 0.00 33.69 2.74
3262 6460 8.853077 TTAGCAAAGAATATGGGATGTCATAG 57.147 34.615 0.00 0.00 33.69 2.23
3263 6461 9.288576 CTTTAGCAAAGAATATGGGATGTCATA 57.711 33.333 3.41 0.00 41.02 2.15
3265 6463 6.039717 GCTTTAGCAAAGAATATGGGATGTCA 59.960 38.462 11.34 0.00 41.02 3.58
3266 6464 6.442112 GCTTTAGCAAAGAATATGGGATGTC 58.558 40.000 11.34 0.00 41.02 3.06
3267 6465 6.396829 GCTTTAGCAAAGAATATGGGATGT 57.603 37.500 11.34 0.00 41.02 3.06
3283 6481 6.747739 GCCTTTCTTTTACAGTATGCTTTAGC 59.252 38.462 0.00 0.00 42.53 3.09
3284 6482 7.094377 TGGCCTTTCTTTTACAGTATGCTTTAG 60.094 37.037 3.32 0.00 42.53 1.85
3285 6483 6.717540 TGGCCTTTCTTTTACAGTATGCTTTA 59.282 34.615 3.32 0.00 42.53 1.85
3286 6484 5.538433 TGGCCTTTCTTTTACAGTATGCTTT 59.462 36.000 3.32 0.00 42.53 3.51
3287 6485 5.076873 TGGCCTTTCTTTTACAGTATGCTT 58.923 37.500 3.32 0.00 42.53 3.91
3288 6486 4.662278 TGGCCTTTCTTTTACAGTATGCT 58.338 39.130 3.32 0.00 42.53 3.79
3289 6487 5.125417 TGATGGCCTTTCTTTTACAGTATGC 59.875 40.000 3.32 0.00 42.53 3.14
3290 6488 6.757897 TGATGGCCTTTCTTTTACAGTATG 57.242 37.500 3.32 0.00 46.00 2.39
3291 6489 7.232534 TGTTTGATGGCCTTTCTTTTACAGTAT 59.767 33.333 3.32 0.00 0.00 2.12
3292 6490 6.547880 TGTTTGATGGCCTTTCTTTTACAGTA 59.452 34.615 3.32 0.00 0.00 2.74
3293 6491 5.362430 TGTTTGATGGCCTTTCTTTTACAGT 59.638 36.000 3.32 0.00 0.00 3.55
3295 6493 5.860941 TGTTTGATGGCCTTTCTTTTACA 57.139 34.783 3.32 2.48 0.00 2.41
3296 6494 6.280643 ACTTGTTTGATGGCCTTTCTTTTAC 58.719 36.000 3.32 0.06 0.00 2.01
3297 6495 6.478512 ACTTGTTTGATGGCCTTTCTTTTA 57.521 33.333 3.32 0.00 0.00 1.52
3300 6498 5.357742 AAACTTGTTTGATGGCCTTTCTT 57.642 34.783 3.32 0.00 0.00 2.52
3301 6499 6.478512 TTAAACTTGTTTGATGGCCTTTCT 57.521 33.333 3.32 0.00 0.00 2.52
3302 6500 7.440856 TGATTTAAACTTGTTTGATGGCCTTTC 59.559 33.333 3.32 1.19 0.00 2.62
3304 6502 6.825610 TGATTTAAACTTGTTTGATGGCCTT 58.174 32.000 3.32 0.00 0.00 4.35
3305 6503 6.418057 TGATTTAAACTTGTTTGATGGCCT 57.582 33.333 3.32 0.00 0.00 5.19
3307 6505 7.017055 GCAATGATTTAAACTTGTTTGATGGC 58.983 34.615 8.79 0.41 0.00 4.40
3309 6507 9.801714 GAAGCAATGATTTAAACTTGTTTGATG 57.198 29.630 8.79 0.00 0.00 3.07
3310 6508 8.992073 GGAAGCAATGATTTAAACTTGTTTGAT 58.008 29.630 8.79 3.53 0.00 2.57
3311 6509 7.440856 GGGAAGCAATGATTTAAACTTGTTTGA 59.559 33.333 8.79 0.00 0.00 2.69
3312 6510 7.307930 GGGGAAGCAATGATTTAAACTTGTTTG 60.308 37.037 8.79 4.71 0.00 2.93
3315 6513 5.306678 TGGGGAAGCAATGATTTAAACTTGT 59.693 36.000 0.00 0.00 0.00 3.16
3316 6514 5.792741 TGGGGAAGCAATGATTTAAACTTG 58.207 37.500 0.00 0.00 0.00 3.16
3319 6517 4.631377 GCTTGGGGAAGCAATGATTTAAAC 59.369 41.667 1.90 0.00 44.85 2.01
3321 6519 4.470334 GCTTGGGGAAGCAATGATTTAA 57.530 40.909 1.90 0.00 44.85 1.52
3350 6548 7.255730 GCTTTAGCAAAGAATATGGGATGTCAT 60.256 37.037 11.34 0.00 41.02 3.06
3369 6567 6.747739 GCCTTTCTTTTACAGTATGCTTTAGC 59.252 38.462 0.00 0.00 42.53 3.09
3370 6568 7.094377 TGGCCTTTCTTTTACAGTATGCTTTAG 60.094 37.037 3.32 0.00 42.53 1.85
3371 6569 6.717540 TGGCCTTTCTTTTACAGTATGCTTTA 59.282 34.615 3.32 0.00 42.53 1.85
3372 6570 5.538433 TGGCCTTTCTTTTACAGTATGCTTT 59.462 36.000 3.32 0.00 42.53 3.51
3375 6573 5.125417 TGATGGCCTTTCTTTTACAGTATGC 59.875 40.000 3.32 0.00 42.53 3.14
3376 6574 6.757897 TGATGGCCTTTCTTTTACAGTATG 57.242 37.500 3.32 0.00 46.00 2.39
3378 6576 5.710099 CCTTGATGGCCTTTCTTTTACAGTA 59.290 40.000 3.32 0.00 0.00 2.74
3379 6577 4.524328 CCTTGATGGCCTTTCTTTTACAGT 59.476 41.667 3.32 0.00 0.00 3.55
3380 6578 5.064441 CCTTGATGGCCTTTCTTTTACAG 57.936 43.478 3.32 0.00 0.00 2.74
3517 6842 5.848369 TGACATATCATCCCTTGGAGAAGAT 59.152 40.000 0.00 0.00 34.05 2.40
3524 6849 3.649981 AGACCTGACATATCATCCCTTGG 59.350 47.826 0.00 0.00 33.22 3.61
3525 6850 4.102210 ACAGACCTGACATATCATCCCTTG 59.898 45.833 3.76 0.00 33.22 3.61
3540 6865 4.380531 TGTTAGCTTTGAGAACAGACCTG 58.619 43.478 0.00 0.00 0.00 4.00
3568 6893 7.241042 AGAGGTAGCAACTGATTACTACAAA 57.759 36.000 0.00 0.00 36.67 2.83
3569 6894 6.852420 AGAGGTAGCAACTGATTACTACAA 57.148 37.500 0.00 0.00 36.67 2.41
3570 6895 7.041303 CGATAGAGGTAGCAACTGATTACTACA 60.041 40.741 0.00 0.00 35.89 2.74
3571 6896 7.041235 ACGATAGAGGTAGCAACTGATTACTAC 60.041 40.741 0.00 0.00 35.61 2.73
3572 6897 6.996879 ACGATAGAGGTAGCAACTGATTACTA 59.003 38.462 0.00 0.00 41.38 1.82
3573 6898 5.828859 ACGATAGAGGTAGCAACTGATTACT 59.171 40.000 0.00 0.00 41.38 2.24
3574 6899 6.074544 ACGATAGAGGTAGCAACTGATTAC 57.925 41.667 0.00 0.00 41.38 1.89
3575 6900 6.315091 GACGATAGAGGTAGCAACTGATTA 57.685 41.667 0.00 0.00 41.38 1.75
3576 6901 5.189659 GACGATAGAGGTAGCAACTGATT 57.810 43.478 0.00 0.00 41.38 2.57
3577 6902 4.839668 GACGATAGAGGTAGCAACTGAT 57.160 45.455 0.00 0.00 41.38 2.90


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

AutoCloner maintained by Alex Coulton.