Multiple sequence alignment - TraesCS5B01G370700

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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 TraesCS5B01G370700 chr5B 100.000 3845 0 0 1 3845 549676337 549672493 0.000000e+00 7101.0
1 TraesCS5B01G370700 chr5B 80.928 582 76 18 2501 3066 549556876 549556314 9.870000e-116 427.0
2 TraesCS5B01G370700 chr5B 93.651 63 3 1 196 257 520411075 520411137 4.090000e-15 93.5
3 TraesCS5B01G370700 chr5B 90.909 66 4 2 193 256 402578136 402578201 1.900000e-13 87.9
4 TraesCS5B01G370700 chr5D 95.008 1222 49 5 2190 3410 449851676 449850466 0.000000e+00 1908.0
5 TraesCS5B01G370700 chr5D 90.815 773 33 15 807 1554 449852982 449852223 0.000000e+00 1000.0
6 TraesCS5B01G370700 chr5D 87.344 561 58 8 2296 2847 449654145 449653589 7.010000e-177 630.0
7 TraesCS5B01G370700 chr5D 92.671 423 11 2 3429 3845 449850392 449849984 3.310000e-165 592.0
8 TraesCS5B01G370700 chr5D 88.941 425 37 6 1769 2192 449852121 449851706 2.050000e-142 516.0
9 TraesCS5B01G370700 chr5D 92.758 359 23 3 1 357 449853333 449852976 2.050000e-142 516.0
10 TraesCS5B01G370700 chr5D 95.000 60 1 2 196 253 460171742 460171683 4.090000e-15 93.5
11 TraesCS5B01G370700 chr5A 87.902 1025 98 19 2270 3276 569074808 569073792 0.000000e+00 1182.0
12 TraesCS5B01G370700 chr5A 90.921 749 23 16 731 1461 569076422 569075701 0.000000e+00 965.0
13 TraesCS5B01G370700 chr5A 85.319 470 54 10 2190 2649 568675360 568674896 4.500000e-129 472.0
14 TraesCS5B01G370700 chr5A 86.510 341 22 8 199 536 569077755 569077436 1.700000e-93 353.0
15 TraesCS5B01G370700 chr5A 89.552 201 20 1 1 201 569078063 569077864 1.770000e-63 254.0
16 TraesCS5B01G370700 chr5A 83.462 260 35 4 1930 2189 569075198 569074947 6.420000e-58 235.0
17 TraesCS5B01G370700 chr5A 92.949 156 10 1 3437 3592 569073625 569073471 3.870000e-55 226.0
18 TraesCS5B01G370700 chr5A 89.855 138 8 4 2926 3062 568628531 568628399 5.110000e-39 172.0
19 TraesCS5B01G370700 chr5A 95.082 61 1 2 196 254 513846659 513846599 1.140000e-15 95.3
20 TraesCS5B01G370700 chr4B 84.138 145 21 1 2057 2201 603165601 603165459 5.180000e-29 139.0
21 TraesCS5B01G370700 chr4B 85.938 128 16 1 2071 2198 603167586 603167461 6.700000e-28 135.0
22 TraesCS5B01G370700 chr4B 85.345 116 17 0 2073 2188 603186904 603186789 1.880000e-23 121.0
23 TraesCS5B01G370700 chr4B 95.082 61 1 2 196 254 652917760 652917820 1.140000e-15 95.3
24 TraesCS5B01G370700 chr4B 95.000 60 1 2 196 253 358091445 358091504 4.090000e-15 93.5
25 TraesCS5B01G370700 chr4A 85.271 129 17 2 2061 2188 684505346 684505219 8.670000e-27 132.0
26 TraesCS5B01G370700 chr4A 85.345 116 17 0 2073 2188 684515748 684515633 1.880000e-23 121.0
27 TraesCS5B01G370700 chr4D 85.246 122 17 1 2067 2188 477580784 477580664 1.450000e-24 124.0
28 TraesCS5B01G370700 chr4D 84.127 126 18 1 2073 2198 477627371 477627248 1.880000e-23 121.0
29 TraesCS5B01G370700 chr3A 85.981 107 13 2 1345 1450 199707705 199707810 3.140000e-21 113.0
30 TraesCS5B01G370700 chr7B 79.221 154 26 3 2394 2541 590186774 590186927 6.800000e-18 102.0
31 TraesCS5B01G370700 chr7A 93.651 63 2 2 196 256 200511843 200511781 4.090000e-15 93.5
32 TraesCS5B01G370700 chr6B 95.000 60 1 2 196 253 654835340 654835281 4.090000e-15 93.5
33 TraesCS5B01G370700 chr7D 80.909 110 16 4 2762 2867 547295533 547295425 8.850000e-12 82.4
34 TraesCS5B01G370700 chr7D 83.784 74 10 2 2753 2825 547295947 547295875 6.890000e-08 69.4


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 TraesCS5B01G370700 chr5B 549672493 549676337 3844 True 7101.000000 7101 100.000000 1 3845 1 chr5B.!!$R2 3844
1 TraesCS5B01G370700 chr5B 549556314 549556876 562 True 427.000000 427 80.928000 2501 3066 1 chr5B.!!$R1 565
2 TraesCS5B01G370700 chr5D 449849984 449853333 3349 True 906.400000 1908 92.038600 1 3845 5 chr5D.!!$R3 3844
3 TraesCS5B01G370700 chr5D 449653589 449654145 556 True 630.000000 630 87.344000 2296 2847 1 chr5D.!!$R1 551
4 TraesCS5B01G370700 chr5A 569073471 569078063 4592 True 535.833333 1182 88.549333 1 3592 6 chr5A.!!$R4 3591

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
486 600 2.289002 CACTCAATATCGGCCAAGAAGC 59.711 50.0 2.24 0.00 0.0 3.86 F
1501 2523 0.035317 TTGCTAGGTGCCTGTCTGTG 59.965 55.0 0.12 0.00 42.0 3.66 F
1554 2579 0.106519 ATCAATTCTTCCGGGCCCTG 60.107 55.0 22.43 14.86 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1535 2560 0.106519 CAGGGCCCGGAAGAATTGAT 60.107 55.0 18.42 0.0 0.00 2.57 R
2740 3920 0.109272 TGAGACTCGACACGGCATTC 60.109 55.0 0.00 0.0 0.00 2.67 R
3541 4877 0.039618 ACCCAACAATCTTGGCCGAT 59.960 50.0 0.00 0.0 38.23 4.18 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
26 27 8.458843 CCTAGGTAAAATTATGTGTCCTTGTTG 58.541 37.037 0.00 0.00 0.00 3.33
32 33 2.291209 ATGTGTCCTTGTTGCCATCA 57.709 45.000 0.00 0.00 0.00 3.07
43 44 3.084039 TGTTGCCATCATTCCAAGAGAC 58.916 45.455 0.00 0.00 0.00 3.36
103 104 2.560981 GGTTTCGTCATCAACCCCATTT 59.439 45.455 0.00 0.00 37.11 2.32
105 106 2.577606 TCGTCATCAACCCCATTTGT 57.422 45.000 0.00 0.00 0.00 2.83
179 180 9.929722 TGTGCATGATTACGTCTTTATAAATTC 57.070 29.630 0.00 0.00 0.00 2.17
285 399 7.950512 TGTTGACCATTATTTTCTGTGACATT 58.049 30.769 0.00 0.00 0.00 2.71
321 435 7.333528 ACACTTTTAACTGACATGATTGTGT 57.666 32.000 0.00 0.00 35.79 3.72
436 550 4.223477 ACAGTCCATTTTTCCATGGGAATG 59.777 41.667 13.02 17.95 43.74 2.67
443 557 7.402650 TCCATTTTTCCATGGGAATGAAGTTAT 59.597 33.333 25.20 6.20 43.74 1.89
476 590 6.851222 AAAGAATAGCCACACTCAATATCG 57.149 37.500 0.00 0.00 0.00 2.92
486 600 2.289002 CACTCAATATCGGCCAAGAAGC 59.711 50.000 2.24 0.00 0.00 3.86
501 615 4.133078 CAAGAAGCTGAAGAACACTCCTT 58.867 43.478 0.00 0.00 0.00 3.36
524 638 4.994852 TGTTTGTGCCACTTAGATGTACTC 59.005 41.667 0.00 0.00 0.00 2.59
535 1499 8.830580 CCACTTAGATGTACTCCATAATGTTTG 58.169 37.037 0.00 0.00 32.56 2.93
540 1504 7.974675 AGATGTACTCCATAATGTTTGAAACG 58.025 34.615 3.37 0.00 32.56 3.60
545 1509 5.120208 ACTCCATAATGTTTGAAACGAGACG 59.880 40.000 12.93 0.00 0.00 4.18
564 1529 7.597743 ACGAGACGACTTGAAACTTAAATACAT 59.402 33.333 9.20 0.00 0.00 2.29
578 1543 8.951787 ACTTAAATACATAGGCGTCACATAAA 57.048 30.769 0.00 0.00 0.00 1.40
579 1544 9.555727 ACTTAAATACATAGGCGTCACATAAAT 57.444 29.630 0.00 0.00 0.00 1.40
590 1555 7.322664 AGGCGTCACATAAATTTTGAATGAAT 58.677 30.769 6.46 0.00 0.00 2.57
602 1567 8.826293 AATTTTGAATGAATGGGGCATAAAAT 57.174 26.923 0.00 0.00 30.81 1.82
621 1586 6.683974 AAAATCGTTGAACTATGCTATGCT 57.316 33.333 0.00 0.00 0.00 3.79
623 1588 5.914085 ATCGTTGAACTATGCTATGCTTC 57.086 39.130 0.00 0.00 0.00 3.86
624 1589 4.754322 TCGTTGAACTATGCTATGCTTCA 58.246 39.130 0.00 0.00 0.00 3.02
677 1642 4.398549 CGCGAGGTCTTATAGAGAAGAG 57.601 50.000 0.00 0.00 36.13 2.85
747 1713 9.921637 TTGAGACAATTGAACTTGTTTTTAGTT 57.078 25.926 13.59 0.00 39.40 2.24
748 1714 9.921637 TGAGACAATTGAACTTGTTTTTAGTTT 57.078 25.926 13.59 0.00 39.40 2.66
787 1753 8.718102 ATTGAACTTGTATTTAGTGTCGCTAT 57.282 30.769 0.00 0.00 0.00 2.97
824 1791 8.760980 TGTATTCTTATAAACCAAATGGAGGG 57.239 34.615 6.42 0.00 38.94 4.30
830 1797 2.397044 AACCAAATGGAGGGAAGCAA 57.603 45.000 6.42 0.00 38.94 3.91
878 1851 3.490348 CCAAATGCAGGATAAGGGGTAG 58.510 50.000 0.00 0.00 0.00 3.18
933 1906 3.056607 ACAAAATCCCGCAAAATCCTCAG 60.057 43.478 0.00 0.00 0.00 3.35
949 1931 2.499693 CCTCAGTCTCTTTCCTTCTCCC 59.500 54.545 0.00 0.00 0.00 4.30
1247 2235 2.043852 GGAGGACGAGGCTCTGGA 60.044 66.667 13.50 0.00 0.00 3.86
1248 2236 2.124693 GGAGGACGAGGCTCTGGAG 61.125 68.421 13.50 0.00 0.00 3.86
1249 2237 2.043450 AGGACGAGGCTCTGGAGG 60.043 66.667 13.50 0.00 0.00 4.30
1287 2284 3.083997 GCCGTGGTGGAGGAGGAT 61.084 66.667 0.00 0.00 42.00 3.24
1454 2460 1.374758 CCGAGGTGAGCGCTTCTTT 60.375 57.895 13.26 0.00 0.00 2.52
1475 2481 0.599558 CCCTTCATGCACACACCTTG 59.400 55.000 0.00 0.00 0.00 3.61
1480 2487 1.604593 ATGCACACACCTTGGCCTC 60.605 57.895 3.32 0.00 0.00 4.70
1501 2523 0.035317 TTGCTAGGTGCCTGTCTGTG 59.965 55.000 0.12 0.00 42.00 3.66
1527 2552 0.583438 CACACGTTGGCTCAGTCAAG 59.417 55.000 0.00 0.00 0.00 3.02
1535 2560 1.348696 TGGCTCAGTCAAGAGAATGCA 59.651 47.619 0.00 0.00 39.58 3.96
1547 2572 5.065602 TCAAGAGAATGCATCAATTCTTCCG 59.934 40.000 0.00 0.00 44.96 4.30
1554 2579 0.106519 ATCAATTCTTCCGGGCCCTG 60.107 55.000 22.43 14.86 0.00 4.45
1555 2580 1.204786 TCAATTCTTCCGGGCCCTGA 61.205 55.000 22.43 17.52 0.00 3.86
1556 2581 0.106519 CAATTCTTCCGGGCCCTGAT 60.107 55.000 22.43 0.00 0.00 2.90
1557 2582 0.631212 AATTCTTCCGGGCCCTGATT 59.369 50.000 22.43 7.11 0.00 2.57
1558 2583 1.518367 ATTCTTCCGGGCCCTGATTA 58.482 50.000 22.43 7.08 0.00 1.75
1560 2585 0.764890 TCTTCCGGGCCCTGATTATG 59.235 55.000 22.43 9.63 0.00 1.90
1561 2586 0.474184 CTTCCGGGCCCTGATTATGT 59.526 55.000 22.43 0.00 0.00 2.29
1562 2587 0.182537 TTCCGGGCCCTGATTATGTG 59.817 55.000 22.43 0.00 0.00 3.21
1564 2589 1.149174 CGGGCCCTGATTATGTGCT 59.851 57.895 22.43 0.00 0.00 4.40
1566 2591 1.780503 GGGCCCTGATTATGTGCTTT 58.219 50.000 17.04 0.00 0.00 3.51
1567 2592 1.410153 GGGCCCTGATTATGTGCTTTG 59.590 52.381 17.04 0.00 0.00 2.77
1568 2593 2.102578 GGCCCTGATTATGTGCTTTGT 58.897 47.619 0.00 0.00 0.00 2.83
1569 2594 2.497273 GGCCCTGATTATGTGCTTTGTT 59.503 45.455 0.00 0.00 0.00 2.83
1570 2595 3.055891 GGCCCTGATTATGTGCTTTGTTT 60.056 43.478 0.00 0.00 0.00 2.83
1572 2597 5.163416 GGCCCTGATTATGTGCTTTGTTTAT 60.163 40.000 0.00 0.00 0.00 1.40
1573 2598 5.750067 GCCCTGATTATGTGCTTTGTTTATG 59.250 40.000 0.00 0.00 0.00 1.90
1575 2600 5.456497 CCTGATTATGTGCTTTGTTTATGCG 59.544 40.000 0.00 0.00 0.00 4.73
1576 2601 4.797868 TGATTATGTGCTTTGTTTATGCGC 59.202 37.500 0.00 0.00 37.78 6.09
1578 2603 2.498807 TGTGCTTTGTTTATGCGCAA 57.501 40.000 17.11 0.11 42.36 4.85
1579 2604 2.123342 TGTGCTTTGTTTATGCGCAAC 58.877 42.857 17.11 9.37 42.36 4.17
1580 2605 2.223688 TGTGCTTTGTTTATGCGCAACT 60.224 40.909 17.11 0.00 42.36 3.16
1581 2606 2.153627 GTGCTTTGTTTATGCGCAACTG 59.846 45.455 17.11 4.50 37.37 3.16
1588 2660 4.615949 TGTTTATGCGCAACTGAAATTGT 58.384 34.783 17.11 0.00 31.83 2.71
1590 2662 4.495911 TTATGCGCAACTGAAATTGTCA 57.504 36.364 17.11 0.00 34.17 3.58
1592 2664 1.044725 GCGCAACTGAAATTGTCACG 58.955 50.000 0.30 0.00 31.13 4.35
1615 2688 0.179000 AGTCCTGGACGGAATGATGC 59.821 55.000 20.49 0.00 45.32 3.91
1630 2703 5.357878 GGAATGATGCCTAACTGAATGTTGA 59.642 40.000 0.00 0.00 39.55 3.18
1635 2708 2.680339 GCCTAACTGAATGTTGAGGCTC 59.320 50.000 7.79 7.79 43.70 4.70
1636 2709 3.869912 GCCTAACTGAATGTTGAGGCTCA 60.870 47.826 14.43 14.43 43.70 4.26
1637 2710 4.521146 CCTAACTGAATGTTGAGGCTCAT 58.479 43.478 19.50 2.42 39.55 2.90
1638 2711 5.674525 CCTAACTGAATGTTGAGGCTCATA 58.325 41.667 19.50 11.17 39.55 2.15
1641 2714 4.458397 ACTGAATGTTGAGGCTCATATGG 58.542 43.478 19.50 11.63 0.00 2.74
1653 2740 3.758755 CTCATATGGTGGAGCTGCTAA 57.241 47.619 6.82 0.00 0.00 3.09
1688 2775 1.134753 CTTTGCAACCTGCTTGTGTGA 59.865 47.619 0.00 0.00 45.31 3.58
1689 2776 1.401761 TTGCAACCTGCTTGTGTGAT 58.598 45.000 0.00 0.00 45.31 3.06
1690 2777 2.268762 TGCAACCTGCTTGTGTGATA 57.731 45.000 0.00 0.00 45.31 2.15
1691 2778 2.153645 TGCAACCTGCTTGTGTGATAG 58.846 47.619 0.00 0.00 45.31 2.08
1692 2779 1.470098 GCAACCTGCTTGTGTGATAGG 59.530 52.381 0.00 0.00 40.96 2.57
1693 2780 1.470098 CAACCTGCTTGTGTGATAGGC 59.530 52.381 0.00 0.00 31.69 3.93
1694 2781 0.987294 ACCTGCTTGTGTGATAGGCT 59.013 50.000 0.00 0.00 31.69 4.58
1695 2782 1.352352 ACCTGCTTGTGTGATAGGCTT 59.648 47.619 0.00 0.00 31.69 4.35
1696 2783 1.741706 CCTGCTTGTGTGATAGGCTTG 59.258 52.381 0.00 0.00 0.00 4.01
1697 2784 1.741706 CTGCTTGTGTGATAGGCTTGG 59.258 52.381 0.00 0.00 0.00 3.61
1698 2785 1.350684 TGCTTGTGTGATAGGCTTGGA 59.649 47.619 0.00 0.00 0.00 3.53
1699 2786 2.025981 TGCTTGTGTGATAGGCTTGGAT 60.026 45.455 0.00 0.00 0.00 3.41
1700 2787 2.357009 GCTTGTGTGATAGGCTTGGATG 59.643 50.000 0.00 0.00 0.00 3.51
1701 2788 2.042686 TGTGTGATAGGCTTGGATGC 57.957 50.000 0.00 0.00 0.00 3.91
1713 2800 0.323360 TTGGATGCAGTAGGTTGGCC 60.323 55.000 0.00 0.00 0.00 5.36
1714 2801 1.302949 GGATGCAGTAGGTTGGCCA 59.697 57.895 0.00 0.00 37.19 5.36
1717 2804 3.127533 GCAGTAGGTTGGCCAGCG 61.128 66.667 13.95 0.00 37.19 5.18
1721 2808 1.078426 GTAGGTTGGCCAGCGATGT 60.078 57.895 13.95 0.69 37.19 3.06
1723 2810 0.906066 TAGGTTGGCCAGCGATGTTA 59.094 50.000 13.95 0.00 37.19 2.41
1724 2811 0.255890 AGGTTGGCCAGCGATGTTAT 59.744 50.000 13.95 0.00 37.19 1.89
1725 2812 1.102978 GGTTGGCCAGCGATGTTATT 58.897 50.000 13.95 0.00 34.09 1.40
1726 2813 1.476488 GGTTGGCCAGCGATGTTATTT 59.524 47.619 13.95 0.00 34.09 1.40
1727 2814 2.529151 GTTGGCCAGCGATGTTATTTG 58.471 47.619 5.11 0.00 0.00 2.32
1728 2815 2.121291 TGGCCAGCGATGTTATTTGA 57.879 45.000 0.00 0.00 0.00 2.69
1729 2816 2.653726 TGGCCAGCGATGTTATTTGAT 58.346 42.857 0.00 0.00 0.00 2.57
1730 2817 2.358582 TGGCCAGCGATGTTATTTGATG 59.641 45.455 0.00 0.00 0.00 3.07
1731 2818 2.287788 GGCCAGCGATGTTATTTGATGG 60.288 50.000 0.00 0.00 0.00 3.51
1732 2819 2.287788 GCCAGCGATGTTATTTGATGGG 60.288 50.000 0.00 0.00 0.00 4.00
1733 2820 2.294233 CCAGCGATGTTATTTGATGGGG 59.706 50.000 0.00 0.00 0.00 4.96
1734 2821 2.951642 CAGCGATGTTATTTGATGGGGT 59.048 45.455 0.00 0.00 0.00 4.95
1735 2822 2.951642 AGCGATGTTATTTGATGGGGTG 59.048 45.455 0.00 0.00 0.00 4.61
1736 2823 2.543653 GCGATGTTATTTGATGGGGTGC 60.544 50.000 0.00 0.00 0.00 5.01
1737 2824 2.687425 CGATGTTATTTGATGGGGTGCA 59.313 45.455 0.00 0.00 0.00 4.57
1738 2825 3.318839 CGATGTTATTTGATGGGGTGCAT 59.681 43.478 0.00 0.00 0.00 3.96
1739 2826 4.557296 CGATGTTATTTGATGGGGTGCATC 60.557 45.833 0.00 0.00 0.00 3.91
1740 2827 2.687425 TGTTATTTGATGGGGTGCATCG 59.313 45.455 0.00 0.00 32.04 3.84
1741 2828 2.687935 GTTATTTGATGGGGTGCATCGT 59.312 45.455 0.00 0.00 32.04 3.73
1742 2829 1.105457 ATTTGATGGGGTGCATCGTG 58.895 50.000 0.00 0.00 32.04 4.35
1743 2830 0.251121 TTTGATGGGGTGCATCGTGT 60.251 50.000 0.00 0.00 32.04 4.49
1744 2831 0.251121 TTGATGGGGTGCATCGTGTT 60.251 50.000 0.00 0.00 32.04 3.32
1745 2832 0.615850 TGATGGGGTGCATCGTGTTA 59.384 50.000 0.00 0.00 32.04 2.41
1746 2833 1.211703 TGATGGGGTGCATCGTGTTAT 59.788 47.619 0.00 0.00 32.04 1.89
1747 2834 2.436173 TGATGGGGTGCATCGTGTTATA 59.564 45.455 0.00 0.00 32.04 0.98
1748 2835 2.613026 TGGGGTGCATCGTGTTATAG 57.387 50.000 0.00 0.00 0.00 1.31
1749 2836 1.834896 TGGGGTGCATCGTGTTATAGT 59.165 47.619 0.00 0.00 0.00 2.12
1756 2843 4.151689 GTGCATCGTGTTATAGTTGTGTGT 59.848 41.667 0.00 0.00 0.00 3.72
1757 2844 4.151512 TGCATCGTGTTATAGTTGTGTGTG 59.848 41.667 0.00 0.00 0.00 3.82
1759 2846 4.587584 TCGTGTTATAGTTGTGTGTGGA 57.412 40.909 0.00 0.00 0.00 4.02
1760 2847 4.552355 TCGTGTTATAGTTGTGTGTGGAG 58.448 43.478 0.00 0.00 0.00 3.86
1763 2850 3.007635 GTTATAGTTGTGTGTGGAGGCC 58.992 50.000 0.00 0.00 0.00 5.19
1767 2854 1.148273 TTGTGTGTGGAGGCCAGTC 59.852 57.895 5.01 0.00 32.34 3.51
1774 2861 1.168714 GTGGAGGCCAGTCATTTCAC 58.831 55.000 5.01 0.00 32.34 3.18
1784 2871 4.391830 GCCAGTCATTTCACGTCTTTATCA 59.608 41.667 0.00 0.00 0.00 2.15
1796 2884 7.552459 TCACGTCTTTATCAGAATTATGTCCA 58.448 34.615 0.00 0.00 31.28 4.02
1808 2896 7.933577 TCAGAATTATGTCCATTAACCTGCTAG 59.066 37.037 0.00 0.00 0.00 3.42
1819 2907 2.402388 CTGCTAGCGCATGCACAC 59.598 61.111 19.57 6.36 46.74 3.82
1823 2921 0.864377 GCTAGCGCATGCACACAATG 60.864 55.000 19.57 0.00 46.23 2.82
1891 3000 9.893634 TTCTAATATGAAGTTTCGGTCCAATTA 57.106 29.630 0.00 0.00 0.00 1.40
1924 3033 8.795842 TTTCCTTCCACGTAACAATGTATTAT 57.204 30.769 0.00 0.00 0.00 1.28
1931 3040 7.334671 TCCACGTAACAATGTATTATTTGCTGA 59.665 33.333 0.00 0.00 0.00 4.26
1934 3043 6.910433 CGTAACAATGTATTATTTGCTGACCC 59.090 38.462 0.00 0.00 0.00 4.46
1951 3060 5.106673 GCTGACCCTGTTACTGTTAATTCAC 60.107 44.000 0.00 0.00 0.00 3.18
1953 3062 5.217978 ACCCTGTTACTGTTAATTCACGA 57.782 39.130 0.00 0.00 0.00 4.35
1975 3084 2.740714 GCGTGGTGTCGGCTTCATC 61.741 63.158 0.00 0.00 0.00 2.92
1976 3085 1.374125 CGTGGTGTCGGCTTCATCA 60.374 57.895 0.00 0.00 0.00 3.07
1977 3086 1.354337 CGTGGTGTCGGCTTCATCAG 61.354 60.000 0.00 0.00 0.00 2.90
1978 3087 0.320771 GTGGTGTCGGCTTCATCAGT 60.321 55.000 0.00 0.00 0.00 3.41
1979 3088 1.067142 GTGGTGTCGGCTTCATCAGTA 60.067 52.381 0.00 0.00 0.00 2.74
1980 3089 1.621317 TGGTGTCGGCTTCATCAGTAA 59.379 47.619 0.00 0.00 0.00 2.24
1981 3090 2.236146 TGGTGTCGGCTTCATCAGTAAT 59.764 45.455 0.00 0.00 0.00 1.89
1982 3091 3.270877 GGTGTCGGCTTCATCAGTAATT 58.729 45.455 0.00 0.00 0.00 1.40
2010 3119 1.059584 TTGGAGGGGCAGTCAGACAA 61.060 55.000 2.66 0.00 0.00 3.18
2041 3150 5.036117 TGGATACTGTATGCCTTTTCTCC 57.964 43.478 15.42 4.48 37.61 3.71
2047 3156 3.420893 TGTATGCCTTTTCTCCCTGTTG 58.579 45.455 0.00 0.00 0.00 3.33
2051 3160 4.112634 TGCCTTTTCTCCCTGTTGTAAT 57.887 40.909 0.00 0.00 0.00 1.89
2063 3172 9.483489 TCTCCCTGTTGTAATATGTAGTTTCTA 57.517 33.333 0.00 0.00 0.00 2.10
2145 3254 4.632327 TGTCACCATGAGTACCATTGAA 57.368 40.909 0.00 0.00 31.94 2.69
2233 3374 1.064166 ACCTGCATAGAATGGCTGCTT 60.064 47.619 0.00 0.00 36.84 3.91
2280 3453 5.776716 CCTGTCATAGGGCATTAATTCCAAT 59.223 40.000 6.47 0.00 43.33 3.16
2288 3461 7.926674 AGGGCATTAATTCCAATTTCAAAAG 57.073 32.000 6.47 0.00 0.00 2.27
2345 3519 7.546358 TCTAAAGAATGCACCAAAATGTATGG 58.454 34.615 0.00 0.00 43.84 2.74
2672 3851 5.428253 TGGACAGGTTAGTTAGCAATCATC 58.572 41.667 0.00 0.00 0.00 2.92
2699 3879 4.200874 TGCCCTACCATTTTTACATACCG 58.799 43.478 0.00 0.00 0.00 4.02
2727 3907 1.999735 TGCATGAATCGAACCTCGTTC 59.000 47.619 0.00 0.00 41.35 3.95
2740 3920 1.334779 CCTCGTTCTAGCGGGATAACG 60.335 57.143 5.94 5.94 44.46 3.18
2909 4092 1.878522 GACACGATAGCACGCCCAG 60.879 63.158 0.00 0.00 42.67 4.45
2963 4157 0.998928 TGTCTGCCTCCTCTCTCTCT 59.001 55.000 0.00 0.00 0.00 3.10
2964 4158 1.064758 TGTCTGCCTCCTCTCTCTCTC 60.065 57.143 0.00 0.00 0.00 3.20
3107 4301 0.529337 AGATTCGTGCTCGCCTGATG 60.529 55.000 2.69 0.00 36.96 3.07
3136 4330 5.487861 AAGGATCCAAAATCCCCTTATGT 57.512 39.130 15.82 0.00 38.98 2.29
3137 4331 5.487861 AGGATCCAAAATCCCCTTATGTT 57.512 39.130 15.82 0.00 38.98 2.71
3227 4421 1.290203 AGCAGTGCAATACCGATTCG 58.710 50.000 19.20 0.00 0.00 3.34
3259 4454 0.905809 TAAAGGGACCCTAGCGTGCA 60.906 55.000 15.29 0.00 31.13 4.57
3270 4465 2.995939 CCTAGCGTGCATATATGTGTGG 59.004 50.000 14.14 3.31 0.00 4.17
3308 4503 3.128415 TCTGCAACTCAGATCTCGAGAAG 59.872 47.826 20.91 14.55 46.34 2.85
3370 4565 4.124351 CAACTGCTGGCCATGGCG 62.124 66.667 29.90 18.44 43.06 5.69
3371 4566 4.666253 AACTGCTGGCCATGGCGT 62.666 61.111 29.90 18.81 43.06 5.68
3396 4592 1.672854 CCGATGTCCCTGGCGAAGTA 61.673 60.000 0.00 0.00 0.00 2.24
3407 4603 2.098831 GCGAAGTAGCGAACCACCC 61.099 63.158 0.00 0.00 0.00 4.61
3410 4606 0.035739 GAAGTAGCGAACCACCCCAA 59.964 55.000 0.00 0.00 0.00 4.12
3541 4877 0.595588 CGCCATTGTTGCCTGTGTTA 59.404 50.000 0.00 0.00 0.00 2.41
3555 4891 3.009723 CTGTGTTATCGGCCAAGATTGT 58.990 45.455 2.24 0.00 32.39 2.71
3575 4911 0.246086 TGGGTCGATGCAAAAATGCC 59.754 50.000 0.00 0.00 0.00 4.40
3597 4933 4.393990 CCGAATTTTTACGACTTAAGGGCT 59.606 41.667 7.53 0.00 0.00 5.19
3641 4983 2.180017 GCACCATCAAGCGCCAAG 59.820 61.111 2.29 0.00 0.00 3.61
3643 4985 1.503542 CACCATCAAGCGCCAAGAC 59.496 57.895 2.29 0.00 0.00 3.01
3648 4990 1.674441 CATCAAGCGCCAAGACATCAT 59.326 47.619 2.29 0.00 0.00 2.45
3659 5001 5.107182 CGCCAAGACATCATTCATCTCATAC 60.107 44.000 0.00 0.00 0.00 2.39
3668 5010 6.828502 TCATTCATCTCATACGCAAAGTAC 57.171 37.500 0.00 0.00 38.29 2.73
3683 5025 4.436523 GCAAAGTACAACGTGAATCACAAC 59.563 41.667 14.24 3.41 33.40 3.32
3684 5026 5.564768 CAAAGTACAACGTGAATCACAACA 58.435 37.500 14.24 0.00 33.40 3.33
3799 5141 5.113446 AGAATTGAGAACCTGATGAGCAT 57.887 39.130 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.501445 GCTATGTCTCTTGGAATGATGGC 59.499 47.826 0.00 0.00 0.00 4.40
32 33 7.449247 GGATCTTAAGCTATGTCTCTTGGAAT 58.551 38.462 0.00 0.00 0.00 3.01
43 44 4.158764 CGAGGTAGGGGATCTTAAGCTATG 59.841 50.000 0.00 0.00 0.00 2.23
103 104 4.157849 TGGAATACACCACTCAAACACA 57.842 40.909 0.00 0.00 34.77 3.72
105 106 4.724399 ACATGGAATACACCACTCAAACA 58.276 39.130 0.00 0.00 43.03 2.83
179 180 0.834612 TAGTATTCCGGGGTTGCTGG 59.165 55.000 0.00 0.00 0.00 4.85
420 534 9.050154 AGAATAACTTCATTCCCATGGAAAAAT 57.950 29.630 15.22 7.23 45.41 1.82
476 590 1.268079 GTGTTCTTCAGCTTCTTGGCC 59.732 52.381 0.00 0.00 0.00 5.36
501 615 4.968259 AGTACATCTAAGTGGCACAAACA 58.032 39.130 21.41 0.77 44.16 2.83
524 638 5.120208 AGTCGTCTCGTTTCAAACATTATGG 59.880 40.000 0.22 0.00 0.00 2.74
535 1499 4.773742 AAGTTTCAAGTCGTCTCGTTTC 57.226 40.909 0.00 0.00 0.00 2.78
545 1509 7.971455 ACGCCTATGTATTTAAGTTTCAAGTC 58.029 34.615 0.00 0.00 0.00 3.01
564 1529 7.384439 TCATTCAAAATTTATGTGACGCCTA 57.616 32.000 0.00 0.00 0.00 3.93
578 1543 7.227116 CGATTTTATGCCCCATTCATTCAAAAT 59.773 33.333 0.00 0.00 30.71 1.82
579 1544 6.538021 CGATTTTATGCCCCATTCATTCAAAA 59.462 34.615 0.00 0.00 0.00 2.44
582 1547 4.648762 ACGATTTTATGCCCCATTCATTCA 59.351 37.500 0.00 0.00 0.00 2.57
590 1555 3.426615 AGTTCAACGATTTTATGCCCCA 58.573 40.909 0.00 0.00 0.00 4.96
602 1567 4.754322 TGAAGCATAGCATAGTTCAACGA 58.246 39.130 0.00 0.00 0.00 3.85
637 1602 1.077716 GCCGGGCTTCACTACCATT 60.078 57.895 12.87 0.00 0.00 3.16
755 1721 9.337396 ACACTAAATACAAGTTCAATTGTCTCA 57.663 29.630 5.13 0.00 42.33 3.27
756 1722 9.813080 GACACTAAATACAAGTTCAATTGTCTC 57.187 33.333 5.13 0.00 42.33 3.36
757 1723 8.495949 CGACACTAAATACAAGTTCAATTGTCT 58.504 33.333 5.13 2.91 42.33 3.41
758 1724 7.268447 GCGACACTAAATACAAGTTCAATTGTC 59.732 37.037 5.13 0.51 42.33 3.18
759 1725 7.041372 AGCGACACTAAATACAAGTTCAATTGT 60.041 33.333 5.13 0.00 45.19 2.71
760 1726 7.298122 AGCGACACTAAATACAAGTTCAATTG 58.702 34.615 0.00 0.00 36.22 2.32
761 1727 7.435068 AGCGACACTAAATACAAGTTCAATT 57.565 32.000 0.00 0.00 0.00 2.32
762 1728 8.718102 ATAGCGACACTAAATACAAGTTCAAT 57.282 30.769 0.00 0.00 33.57 2.57
763 1729 7.815549 TGATAGCGACACTAAATACAAGTTCAA 59.184 33.333 0.00 0.00 33.57 2.69
764 1730 7.317390 TGATAGCGACACTAAATACAAGTTCA 58.683 34.615 0.00 0.00 33.57 3.18
765 1731 7.751047 TGATAGCGACACTAAATACAAGTTC 57.249 36.000 0.00 0.00 33.57 3.01
766 1732 7.817962 AGTTGATAGCGACACTAAATACAAGTT 59.182 33.333 0.34 0.00 33.57 2.66
767 1733 7.321153 AGTTGATAGCGACACTAAATACAAGT 58.679 34.615 0.34 0.00 33.57 3.16
768 1734 7.757097 AGTTGATAGCGACACTAAATACAAG 57.243 36.000 0.34 0.00 33.57 3.16
769 1735 8.440059 CAAAGTTGATAGCGACACTAAATACAA 58.560 33.333 0.34 0.00 33.57 2.41
770 1736 7.815549 TCAAAGTTGATAGCGACACTAAATACA 59.184 33.333 0.34 0.00 33.57 2.29
771 1737 8.181487 TCAAAGTTGATAGCGACACTAAATAC 57.819 34.615 0.34 0.00 33.57 1.89
772 1738 8.653338 GTTCAAAGTTGATAGCGACACTAAATA 58.347 33.333 0.34 0.00 37.00 1.40
773 1739 7.387948 AGTTCAAAGTTGATAGCGACACTAAAT 59.612 33.333 0.34 0.00 37.00 1.40
774 1740 6.704493 AGTTCAAAGTTGATAGCGACACTAAA 59.296 34.615 0.34 0.00 37.00 1.85
775 1741 6.145534 CAGTTCAAAGTTGATAGCGACACTAA 59.854 38.462 0.34 0.00 37.00 2.24
776 1742 5.633601 CAGTTCAAAGTTGATAGCGACACTA 59.366 40.000 0.34 0.00 37.00 2.74
777 1743 4.449068 CAGTTCAAAGTTGATAGCGACACT 59.551 41.667 0.34 0.00 37.00 3.55
778 1744 4.211374 ACAGTTCAAAGTTGATAGCGACAC 59.789 41.667 0.34 0.00 37.00 3.67
779 1745 4.377021 ACAGTTCAAAGTTGATAGCGACA 58.623 39.130 0.34 0.00 37.00 4.35
860 1827 2.982488 CTCCTACCCCTTATCCTGCATT 59.018 50.000 0.00 0.00 0.00 3.56
862 1829 1.414538 CCTCCTACCCCTTATCCTGCA 60.415 57.143 0.00 0.00 0.00 4.41
878 1851 0.105709 CTCTTCCCTCTCCCTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
949 1931 1.275666 GGATTTTCTGGGTTTGGGGG 58.724 55.000 0.00 0.00 0.00 5.40
1079 2067 4.814294 CGAGGAACGGCTTCGGGG 62.814 72.222 4.54 0.00 41.82 5.73
1277 2274 1.132913 CATCCTCCTCATCCTCCTCCA 60.133 57.143 0.00 0.00 0.00 3.86
1278 2275 1.132881 ACATCCTCCTCATCCTCCTCC 60.133 57.143 0.00 0.00 0.00 4.30
1279 2276 1.969923 CACATCCTCCTCATCCTCCTC 59.030 57.143 0.00 0.00 0.00 3.71
1280 2277 1.414245 CCACATCCTCCTCATCCTCCT 60.414 57.143 0.00 0.00 0.00 3.69
1281 2278 1.055040 CCACATCCTCCTCATCCTCC 58.945 60.000 0.00 0.00 0.00 4.30
1287 2284 2.993008 GCTGCCACATCCTCCTCA 59.007 61.111 0.00 0.00 0.00 3.86
1454 2460 1.074775 GGTGTGTGCATGAAGGGGA 59.925 57.895 0.00 0.00 0.00 4.81
1475 2481 3.911137 GCACCTAGCAAAGAGGCC 58.089 61.111 0.00 0.00 44.79 5.19
1501 2523 2.277884 GCCAACGTGTGTGTGCAC 60.278 61.111 10.75 10.75 45.44 4.57
1516 2538 2.105006 TGCATTCTCTTGACTGAGCC 57.895 50.000 0.00 0.00 34.29 4.70
1527 2552 3.004106 CCCGGAAGAATTGATGCATTCTC 59.996 47.826 0.73 0.00 36.22 2.87
1535 2560 0.106519 CAGGGCCCGGAAGAATTGAT 60.107 55.000 18.42 0.00 0.00 2.57
1547 2572 1.410153 CAAAGCACATAATCAGGGCCC 59.590 52.381 16.46 16.46 0.00 5.80
1554 2579 4.797868 TGCGCATAAACAAAGCACATAATC 59.202 37.500 5.66 0.00 32.43 1.75
1555 2580 4.742417 TGCGCATAAACAAAGCACATAAT 58.258 34.783 5.66 0.00 32.43 1.28
1556 2581 4.166187 TGCGCATAAACAAAGCACATAA 57.834 36.364 5.66 0.00 32.43 1.90
1557 2582 3.839051 TGCGCATAAACAAAGCACATA 57.161 38.095 5.66 0.00 32.43 2.29
1558 2583 2.721274 TGCGCATAAACAAAGCACAT 57.279 40.000 5.66 0.00 32.43 3.21
1560 2585 2.153627 CAGTTGCGCATAAACAAAGCAC 59.846 45.455 12.75 1.38 37.57 4.40
1561 2586 2.033927 TCAGTTGCGCATAAACAAAGCA 59.966 40.909 12.75 0.00 35.90 3.91
1562 2587 2.660490 TCAGTTGCGCATAAACAAAGC 58.340 42.857 12.75 0.00 0.00 3.51
1564 2589 5.521735 ACAATTTCAGTTGCGCATAAACAAA 59.478 32.000 12.75 7.71 32.32 2.83
1566 2591 4.615949 ACAATTTCAGTTGCGCATAAACA 58.384 34.783 12.75 0.00 32.32 2.83
1567 2592 4.679197 TGACAATTTCAGTTGCGCATAAAC 59.321 37.500 12.75 6.79 32.32 2.01
1568 2593 4.679197 GTGACAATTTCAGTTGCGCATAAA 59.321 37.500 12.75 10.46 33.71 1.40
1569 2594 4.225984 GTGACAATTTCAGTTGCGCATAA 58.774 39.130 12.75 0.25 33.71 1.90
1570 2595 3.666638 CGTGACAATTTCAGTTGCGCATA 60.667 43.478 12.75 0.00 33.71 3.14
1572 2597 1.596709 CGTGACAATTTCAGTTGCGCA 60.597 47.619 5.66 5.66 33.71 6.09
1573 2598 1.044725 CGTGACAATTTCAGTTGCGC 58.955 50.000 0.00 0.00 33.71 6.09
1575 2600 3.690422 TGAACGTGACAATTTCAGTTGC 58.310 40.909 0.00 0.00 33.71 4.17
1580 2605 3.559655 CAGGACTGAACGTGACAATTTCA 59.440 43.478 0.00 1.19 0.00 2.69
1581 2606 3.058914 CCAGGACTGAACGTGACAATTTC 60.059 47.826 0.00 0.00 0.00 2.17
1588 2660 1.658114 CGTCCAGGACTGAACGTGA 59.342 57.895 17.95 0.00 0.00 4.35
1590 2662 1.529948 TCCGTCCAGGACTGAACGT 60.530 57.895 17.95 0.00 45.98 3.99
1607 2679 6.441093 TCAACATTCAGTTAGGCATCATTC 57.559 37.500 0.00 0.00 38.74 2.67
1615 2688 3.942829 TGAGCCTCAACATTCAGTTAGG 58.057 45.455 0.00 0.00 38.74 2.69
1635 2708 5.068636 AGATTTTAGCAGCTCCACCATATG 58.931 41.667 0.00 0.00 0.00 1.78
1636 2709 5.316158 AGATTTTAGCAGCTCCACCATAT 57.684 39.130 0.00 0.00 0.00 1.78
1637 2710 4.778213 AGATTTTAGCAGCTCCACCATA 57.222 40.909 0.00 0.00 0.00 2.74
1638 2711 3.659183 AGATTTTAGCAGCTCCACCAT 57.341 42.857 0.00 0.00 0.00 3.55
1641 2714 5.674820 GCAAACTAGATTTTAGCAGCTCCAC 60.675 44.000 0.00 0.00 0.00 4.02
1676 2763 1.741706 CAAGCCTATCACACAAGCAGG 59.258 52.381 0.00 0.00 0.00 4.85
1688 2775 2.412591 ACCTACTGCATCCAAGCCTAT 58.587 47.619 0.00 0.00 0.00 2.57
1689 2776 1.879575 ACCTACTGCATCCAAGCCTA 58.120 50.000 0.00 0.00 0.00 3.93
1690 2777 0.995024 AACCTACTGCATCCAAGCCT 59.005 50.000 0.00 0.00 0.00 4.58
1691 2778 1.098050 CAACCTACTGCATCCAAGCC 58.902 55.000 0.00 0.00 0.00 4.35
1692 2779 1.098050 CCAACCTACTGCATCCAAGC 58.902 55.000 0.00 0.00 0.00 4.01
1693 2780 1.098050 GCCAACCTACTGCATCCAAG 58.902 55.000 0.00 0.00 0.00 3.61
1694 2781 0.323360 GGCCAACCTACTGCATCCAA 60.323 55.000 0.00 0.00 0.00 3.53
1695 2782 1.302949 GGCCAACCTACTGCATCCA 59.697 57.895 0.00 0.00 0.00 3.41
1696 2783 0.749454 CTGGCCAACCTACTGCATCC 60.749 60.000 7.01 0.00 36.63 3.51
1697 2784 1.379642 GCTGGCCAACCTACTGCATC 61.380 60.000 7.01 0.00 36.63 3.91
1698 2785 1.379044 GCTGGCCAACCTACTGCAT 60.379 57.895 7.01 0.00 36.63 3.96
1699 2786 2.034066 GCTGGCCAACCTACTGCA 59.966 61.111 7.01 0.00 36.63 4.41
1700 2787 2.876368 ATCGCTGGCCAACCTACTGC 62.876 60.000 7.01 3.43 36.63 4.40
1701 2788 1.091771 CATCGCTGGCCAACCTACTG 61.092 60.000 7.01 0.00 36.63 2.74
1713 2800 2.951642 ACCCCATCAAATAACATCGCTG 59.048 45.455 0.00 0.00 0.00 5.18
1714 2801 2.951642 CACCCCATCAAATAACATCGCT 59.048 45.455 0.00 0.00 0.00 4.93
1717 2804 4.942761 ATGCACCCCATCAAATAACATC 57.057 40.909 0.00 0.00 0.00 3.06
1727 2814 1.967319 ATAACACGATGCACCCCATC 58.033 50.000 0.00 0.00 45.58 3.51
1728 2815 2.438021 ACTATAACACGATGCACCCCAT 59.562 45.455 0.00 0.00 36.70 4.00
1729 2816 1.834896 ACTATAACACGATGCACCCCA 59.165 47.619 0.00 0.00 0.00 4.96
1730 2817 2.612212 CAACTATAACACGATGCACCCC 59.388 50.000 0.00 0.00 0.00 4.95
1731 2818 3.063452 CACAACTATAACACGATGCACCC 59.937 47.826 0.00 0.00 0.00 4.61
1732 2819 3.682858 ACACAACTATAACACGATGCACC 59.317 43.478 0.00 0.00 0.00 5.01
1733 2820 4.151689 ACACACAACTATAACACGATGCAC 59.848 41.667 0.00 0.00 0.00 4.57
1734 2821 4.151512 CACACACAACTATAACACGATGCA 59.848 41.667 0.00 0.00 0.00 3.96
1735 2822 4.435518 CCACACACAACTATAACACGATGC 60.436 45.833 0.00 0.00 0.00 3.91
1736 2823 4.926832 TCCACACACAACTATAACACGATG 59.073 41.667 0.00 0.00 0.00 3.84
1737 2824 5.142061 TCCACACACAACTATAACACGAT 57.858 39.130 0.00 0.00 0.00 3.73
1738 2825 4.552355 CTCCACACACAACTATAACACGA 58.448 43.478 0.00 0.00 0.00 4.35
1739 2826 3.678072 CCTCCACACACAACTATAACACG 59.322 47.826 0.00 0.00 0.00 4.49
1740 2827 3.435671 GCCTCCACACACAACTATAACAC 59.564 47.826 0.00 0.00 0.00 3.32
1741 2828 3.558321 GGCCTCCACACACAACTATAACA 60.558 47.826 0.00 0.00 0.00 2.41
1742 2829 3.007635 GGCCTCCACACACAACTATAAC 58.992 50.000 0.00 0.00 0.00 1.89
1743 2830 2.640332 TGGCCTCCACACACAACTATAA 59.360 45.455 3.32 0.00 0.00 0.98
1744 2831 2.236146 CTGGCCTCCACACACAACTATA 59.764 50.000 3.32 0.00 0.00 1.31
1745 2832 1.003580 CTGGCCTCCACACACAACTAT 59.996 52.381 3.32 0.00 0.00 2.12
1746 2833 0.396435 CTGGCCTCCACACACAACTA 59.604 55.000 3.32 0.00 0.00 2.24
1747 2834 1.149174 CTGGCCTCCACACACAACT 59.851 57.895 3.32 0.00 0.00 3.16
1748 2835 1.152963 ACTGGCCTCCACACACAAC 60.153 57.895 3.32 0.00 0.00 3.32
1749 2836 1.148273 GACTGGCCTCCACACACAA 59.852 57.895 3.32 0.00 0.00 3.33
1756 2843 0.321564 CGTGAAATGACTGGCCTCCA 60.322 55.000 3.32 0.00 0.00 3.86
1757 2844 0.321653 ACGTGAAATGACTGGCCTCC 60.322 55.000 3.32 0.00 0.00 4.30
1759 2846 0.687354 AGACGTGAAATGACTGGCCT 59.313 50.000 3.32 0.00 0.00 5.19
1760 2847 1.523758 AAGACGTGAAATGACTGGCC 58.476 50.000 0.00 0.00 0.00 5.36
1763 2850 6.951256 TCTGATAAAGACGTGAAATGACTG 57.049 37.500 0.00 0.00 0.00 3.51
1784 2871 6.712547 GCTAGCAGGTTAATGGACATAATTCT 59.287 38.462 10.63 0.00 0.00 2.40
1808 2896 0.860533 AAAACATTGTGTGCATGCGC 59.139 45.000 24.25 24.25 39.24 6.09
1819 2907 9.299963 TGTATTTCACAGTTTCTGAAAACATTG 57.700 29.630 4.09 4.42 45.94 2.82
1891 3000 2.795329 ACGTGGAAGGAAATGCATCTT 58.205 42.857 0.00 0.00 0.00 2.40
1924 3033 3.290948 AACAGTAACAGGGTCAGCAAA 57.709 42.857 0.00 0.00 0.00 3.68
1931 3040 4.992951 GTCGTGAATTAACAGTAACAGGGT 59.007 41.667 0.00 0.00 0.00 4.34
1934 3043 6.237227 CGCTAGTCGTGAATTAACAGTAACAG 60.237 42.308 0.00 0.00 0.00 3.16
1953 3062 2.488087 GAAGCCGACACCACGCTAGT 62.488 60.000 0.00 0.00 0.00 2.57
1964 3073 4.184629 ACTGAATTACTGATGAAGCCGAC 58.815 43.478 0.00 0.00 0.00 4.79
1966 3075 5.178252 CCATACTGAATTACTGATGAAGCCG 59.822 44.000 0.00 0.00 0.00 5.52
1975 3084 5.126067 CCCTCCAACCATACTGAATTACTG 58.874 45.833 0.00 0.00 0.00 2.74
1976 3085 4.166144 CCCCTCCAACCATACTGAATTACT 59.834 45.833 0.00 0.00 0.00 2.24
1977 3086 4.461198 CCCCTCCAACCATACTGAATTAC 58.539 47.826 0.00 0.00 0.00 1.89
1978 3087 3.117663 GCCCCTCCAACCATACTGAATTA 60.118 47.826 0.00 0.00 0.00 1.40
1979 3088 2.358195 GCCCCTCCAACCATACTGAATT 60.358 50.000 0.00 0.00 0.00 2.17
1980 3089 1.215423 GCCCCTCCAACCATACTGAAT 59.785 52.381 0.00 0.00 0.00 2.57
1981 3090 0.623723 GCCCCTCCAACCATACTGAA 59.376 55.000 0.00 0.00 0.00 3.02
1982 3091 0.548926 TGCCCCTCCAACCATACTGA 60.549 55.000 0.00 0.00 0.00 3.41
2010 3119 3.885297 GCATACAGTATCCAAGCAACCAT 59.115 43.478 0.00 0.00 0.00 3.55
2063 3172 6.916360 AAATGACCTGTACATCCACAAAAT 57.084 33.333 0.00 0.00 0.00 1.82
2198 3339 7.728148 TCTATGCAGGTTCCATTACGTAAATA 58.272 34.615 12.81 0.98 0.00 1.40
2205 3346 4.022849 GCCATTCTATGCAGGTTCCATTAC 60.023 45.833 0.00 0.00 0.00 1.89
2208 3349 2.176364 AGCCATTCTATGCAGGTTCCAT 59.824 45.455 0.00 0.00 0.00 3.41
2233 3374 6.267471 AGGAAACATAGAAAATGCAAACTGGA 59.733 34.615 0.00 0.00 0.00 3.86
2267 3409 9.628746 AAATGCTTTTGAAATTGGAATTAATGC 57.371 25.926 0.00 0.00 0.00 3.56
2334 3508 5.630680 GTCAGTCAGCAAACCATACATTTTG 59.369 40.000 0.00 0.00 36.06 2.44
2345 3519 3.311596 ACGTTAAAGGTCAGTCAGCAAAC 59.688 43.478 0.00 0.00 0.00 2.93
2672 3851 5.913137 TGTAAAAATGGTAGGGCAATCAG 57.087 39.130 0.00 0.00 0.00 2.90
2699 3879 4.572389 AGGTTCGATTCATGCAGTTATCAC 59.428 41.667 0.00 0.00 0.00 3.06
2727 3907 1.429463 GGCATTCGTTATCCCGCTAG 58.571 55.000 0.00 0.00 0.00 3.42
2740 3920 0.109272 TGAGACTCGACACGGCATTC 60.109 55.000 0.00 0.00 0.00 2.67
2909 4092 3.224230 GGGGGTCTAAGCCGGTAC 58.776 66.667 1.90 0.00 36.39 3.34
2963 4157 6.772716 AGATAGCAAAAGAGAAAAACACTGGA 59.227 34.615 0.00 0.00 0.00 3.86
2964 4158 6.860023 CAGATAGCAAAAGAGAAAAACACTGG 59.140 38.462 0.00 0.00 0.00 4.00
3078 4272 1.874019 CACGAATCTCAGGGCGACG 60.874 63.158 0.00 0.00 0.00 5.12
3081 4275 1.880340 GAGCACGAATCTCAGGGCG 60.880 63.158 0.00 0.00 0.00 6.13
3086 4280 1.153765 CAGGCGAGCACGAATCTCA 60.154 57.895 8.01 0.00 42.66 3.27
3107 4301 3.511699 GGATTTTGGATCCTTTTCGCAC 58.488 45.455 14.23 0.00 35.36 5.34
3136 4330 8.937835 TCACAAGGAGATTTCAGATCCATATAA 58.062 33.333 0.00 0.00 35.45 0.98
3137 4331 8.370940 GTCACAAGGAGATTTCAGATCCATATA 58.629 37.037 0.00 0.00 35.45 0.86
3227 4421 1.210478 TCCCTTTAGCATCAGGACTGC 59.790 52.381 0.00 0.00 39.97 4.40
3259 4454 2.176798 CACCCAACCCCCACACATATAT 59.823 50.000 0.00 0.00 0.00 0.86
3270 4465 1.228862 AGATGCAACACCCAACCCC 60.229 57.895 0.00 0.00 0.00 4.95
3308 4503 1.616872 CGCGGCAATGGAGCAAAAAC 61.617 55.000 0.00 0.00 35.83 2.43
3396 4592 4.660938 GGCTTGGGGTGGTTCGCT 62.661 66.667 0.00 0.00 0.00 4.93
3541 4877 0.039618 ACCCAACAATCTTGGCCGAT 59.960 50.000 0.00 0.00 38.23 4.18
3555 4891 1.337635 GGCATTTTTGCATCGACCCAA 60.338 47.619 0.00 0.00 36.33 4.12
3575 4911 5.541098 AGCCCTTAAGTCGTAAAAATTCG 57.459 39.130 0.97 0.00 0.00 3.34
3641 4983 5.912360 TTGCGTATGAGATGAATGATGTC 57.088 39.130 0.00 0.00 0.00 3.06
3643 4985 6.296365 ACTTTGCGTATGAGATGAATGATG 57.704 37.500 0.00 0.00 0.00 3.07
3648 4990 5.061684 CGTTGTACTTTGCGTATGAGATGAA 59.938 40.000 0.00 0.00 0.00 2.57
3659 5001 3.215244 GTGATTCACGTTGTACTTTGCG 58.785 45.455 0.13 0.00 0.00 4.85
3668 5010 1.946768 AGGGTGTTGTGATTCACGTTG 59.053 47.619 11.97 0.00 37.14 4.10
3684 5026 2.176798 TCACAACTTCCAAATGGAGGGT 59.823 45.455 15.10 6.41 46.36 4.34


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

AutoCloner maintained by Alex Coulton.