Multiple sequence alignment - TraesCS5D01G412600

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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 TraesCS5D01G412600 chr5D 100.000 2529 0 0 1 2529 475836493 475839021 0.000000e+00 4671.0
1 TraesCS5D01G412600 chr5D 92.473 93 4 3 1779 1870 354874451 354874361 2.040000e-26 130.0
2 TraesCS5D01G412600 chr5A 88.548 1563 88 48 171 1681 595371120 595372643 0.000000e+00 1810.0
3 TraesCS5D01G412600 chr5A 88.800 375 28 7 2159 2527 595372953 595373319 4.960000e-122 448.0
4 TraesCS5D01G412600 chr5B 91.107 1012 43 24 688 1681 583202787 583203769 0.000000e+00 1327.0
5 TraesCS5D01G412600 chr5B 91.402 535 34 7 1999 2527 583204083 583204611 0.000000e+00 723.0
6 TraesCS5D01G412600 chr5B 90.476 147 8 5 554 695 583202340 583202485 3.320000e-44 189.0
7 TraesCS5D01G412600 chr5B 93.548 62 4 0 171 232 583201647 583201708 2.680000e-15 93.5
8 TraesCS5D01G412600 chr6A 85.625 640 79 7 1 636 599651493 599652123 0.000000e+00 660.0
9 TraesCS5D01G412600 chr6A 90.099 101 7 3 1775 1872 15768248 15768148 7.340000e-26 128.0
10 TraesCS5D01G412600 chr4D 90.043 462 43 3 171 630 397672594 397672134 1.670000e-166 595.0
11 TraesCS5D01G412600 chr4D 100.000 173 0 0 1 173 74595213 74595385 1.130000e-83 320.0
12 TraesCS5D01G412600 chr4D 91.346 104 8 1 1776 1878 322674843 322674946 9.430000e-30 141.0
13 TraesCS5D01G412600 chr7A 88.985 463 47 4 171 630 694038428 694038889 1.020000e-158 569.0
14 TraesCS5D01G412600 chr7A 88.095 462 51 3 171 630 564349057 564349516 1.710000e-151 545.0
15 TraesCS5D01G412600 chr2D 87.527 465 50 7 171 630 545008497 545008036 4.790000e-147 531.0
16 TraesCS5D01G412600 chr2D 97.326 187 3 2 1 185 614967500 614967686 1.460000e-82 316.0
17 TraesCS5D01G412600 chr2D 96.791 187 2 3 1 187 449737046 449736864 2.440000e-80 309.0
18 TraesCS5D01G412600 chr2D 89.189 111 8 4 1769 1877 115111561 115111453 4.390000e-28 135.0
19 TraesCS5D01G412600 chr4A 83.871 465 65 7 171 628 51381723 51381262 3.860000e-118 435.0
20 TraesCS5D01G412600 chr4A 94.505 91 4 1 1784 1873 58913144 58913234 3.390000e-29 139.0
21 TraesCS5D01G412600 chr6D 86.337 344 38 7 294 631 301047375 301047715 1.430000e-97 366.0
22 TraesCS5D01G412600 chr6D 98.333 180 3 0 1 180 396546948 396546769 1.460000e-82 316.0
23 TraesCS5D01G412600 chr6D 89.109 101 9 2 1774 1873 208040714 208040813 9.500000e-25 124.0
24 TraesCS5D01G412600 chr7D 84.776 335 41 8 302 630 66982039 66982369 6.750000e-86 327.0
25 TraesCS5D01G412600 chr7D 100.000 174 0 0 1 174 148107271 148107444 3.140000e-84 322.0
26 TraesCS5D01G412600 chr3D 100.000 174 0 0 1 174 407634499 407634672 3.140000e-84 322.0
27 TraesCS5D01G412600 chr3D 100.000 174 0 0 1 174 599497715 599497888 3.140000e-84 322.0
28 TraesCS5D01G412600 chr1D 99.435 177 1 0 1 177 372803786 372803962 3.140000e-84 322.0
29 TraesCS5D01G412600 chr3A 96.392 194 5 2 1 192 130979760 130979567 4.060000e-83 318.0
30 TraesCS5D01G412600 chr3B 94.318 88 4 1 1787 1873 651725124 651725037 1.580000e-27 134.0
31 TraesCS5D01G412600 chr3B 92.391 92 6 1 1786 1876 551052696 551052605 2.040000e-26 130.0
32 TraesCS5D01G412600 chr6B 89.524 105 8 3 1779 1881 411238755 411238858 2.040000e-26 130.0


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 TraesCS5D01G412600 chr5D 475836493 475839021 2528 False 4671.000 4671 100.00000 1 2529 1 chr5D.!!$F1 2528
1 TraesCS5D01G412600 chr5A 595371120 595373319 2199 False 1129.000 1810 88.67400 171 2527 2 chr5A.!!$F1 2356
2 TraesCS5D01G412600 chr5B 583201647 583204611 2964 False 583.125 1327 91.63325 171 2527 4 chr5B.!!$F1 2356
3 TraesCS5D01G412600 chr6A 599651493 599652123 630 False 660.000 660 85.62500 1 636 1 chr6A.!!$F1 635

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
380 409 0.032815 TGACTGCGAACCGATTGTGA 59.967 50.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 2644 0.958091 TGTTCCGCATTTCCACCTTG 59.042 50.0 0.0 0.0 0.0 3.61 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
29 30 5.766174 GCTAGTCAAGTAGAGGCATACTAGT 59.234 44.000 0.00 0.00 38.02 2.57
36 37 5.127491 AGTAGAGGCATACTAGTGACACTC 58.873 45.833 12.39 8.31 34.21 3.51
42 43 4.627467 GGCATACTAGTGACACTCTGTTTG 59.373 45.833 12.39 16.63 0.00 2.93
43 44 5.230942 GCATACTAGTGACACTCTGTTTGT 58.769 41.667 12.39 5.61 0.00 2.83
61 63 7.877612 TCTGTTTGTCTATGTATTCACACATGT 59.122 33.333 0.00 0.00 39.46 3.21
174 176 1.499007 GGGCATATTTCCTTCAGGGGA 59.501 52.381 0.00 0.00 35.41 4.81
203 205 1.220749 GATGGGCGTGTTGGAGCTA 59.779 57.895 0.00 0.00 0.00 3.32
255 257 2.572104 ACTACCTTGGGTCCTCATCAAC 59.428 50.000 0.00 0.00 37.09 3.18
264 266 3.515901 GGGTCCTCATCAACTGTTCTACT 59.484 47.826 0.00 0.00 0.00 2.57
274 276 5.706916 TCAACTGTTCTACTCGGTGTTATC 58.293 41.667 0.00 0.00 0.00 1.75
284 313 3.579586 ACTCGGTGTTATCAACCCTACAA 59.420 43.478 0.00 0.00 0.00 2.41
335 364 2.767536 GCACTTGCGGCTGATCTAA 58.232 52.632 0.00 0.00 0.00 2.10
368 397 4.568359 ACTTGATAATTGCTAGTGACTGCG 59.432 41.667 0.00 0.00 0.00 5.18
380 409 0.032815 TGACTGCGAACCGATTGTGA 59.967 50.000 0.00 0.00 0.00 3.58
397 428 7.201723 CCGATTGTGAATGACATCATAAAAGGA 60.202 37.037 0.00 0.00 35.29 3.36
530 562 1.200484 TGTAAAATTTTCCGCCTCGCC 59.800 47.619 6.72 0.00 0.00 5.54
584 1005 3.713764 CCTCATGACCCTCTTTGTATCCT 59.286 47.826 0.00 0.00 0.00 3.24
676 1105 2.452767 GTGGATTCCACGAACGACC 58.547 57.895 19.65 0.00 44.95 4.79
694 1433 0.313987 CCCTCGAAACAACAAAGGGC 59.686 55.000 0.00 0.00 40.28 5.19
765 1504 3.507622 CACCAATTGGACCTTCTCCTTTC 59.492 47.826 31.22 0.00 40.26 2.62
824 1563 1.345715 CCCTCCCGCACCTTATCCTT 61.346 60.000 0.00 0.00 0.00 3.36
845 1584 1.004979 CCCTGATCCCCCGTACAAAAA 59.995 52.381 0.00 0.00 0.00 1.94
861 1604 3.052869 ACAAAAACCACTCCTTTCCCTCT 60.053 43.478 0.00 0.00 0.00 3.69
918 1670 1.684049 ACTCCTTCCTCCTCCAGCG 60.684 63.158 0.00 0.00 0.00 5.18
929 1681 2.048222 TCCAGCGCCAAGAACTCG 60.048 61.111 2.29 0.00 0.00 4.18
931 1683 2.383527 CCAGCGCCAAGAACTCGAC 61.384 63.158 2.29 0.00 0.00 4.20
934 1686 1.204312 GCGCCAAGAACTCGACAAC 59.796 57.895 0.00 0.00 0.00 3.32
935 1687 1.860078 CGCCAAGAACTCGACAACC 59.140 57.895 0.00 0.00 0.00 3.77
936 1688 0.878523 CGCCAAGAACTCGACAACCA 60.879 55.000 0.00 0.00 0.00 3.67
937 1689 0.586802 GCCAAGAACTCGACAACCAC 59.413 55.000 0.00 0.00 0.00 4.16
938 1690 1.226746 CCAAGAACTCGACAACCACC 58.773 55.000 0.00 0.00 0.00 4.61
939 1691 0.859232 CAAGAACTCGACAACCACCG 59.141 55.000 0.00 0.00 0.00 4.94
940 1692 0.249741 AAGAACTCGACAACCACCGG 60.250 55.000 0.00 0.00 0.00 5.28
941 1693 1.111116 AGAACTCGACAACCACCGGA 61.111 55.000 9.46 0.00 0.00 5.14
942 1694 0.666577 GAACTCGACAACCACCGGAG 60.667 60.000 9.46 0.00 0.00 4.63
973 1725 3.068064 CCAACCCACATTCCCCGC 61.068 66.667 0.00 0.00 0.00 6.13
982 1734 1.224315 CATTCCCCGCACCAGATCA 59.776 57.895 0.00 0.00 0.00 2.92
984 1736 0.109342 ATTCCCCGCACCAGATCATC 59.891 55.000 0.00 0.00 0.00 2.92
987 1739 2.202919 CCGCACCAGATCATCGCA 60.203 61.111 0.00 0.00 0.00 5.10
988 1740 2.242572 CCGCACCAGATCATCGCAG 61.243 63.158 0.00 0.00 0.00 5.18
989 1741 2.879070 CGCACCAGATCATCGCAGC 61.879 63.158 0.00 0.00 0.00 5.25
990 1742 1.523258 GCACCAGATCATCGCAGCT 60.523 57.895 0.00 0.00 0.00 4.24
1025 1785 2.549332 GCCCTTGCTTGTCTCTGAC 58.451 57.895 0.00 0.00 33.53 3.51
1026 1786 0.036022 GCCCTTGCTTGTCTCTGACT 59.964 55.000 0.00 0.00 31.79 3.41
1028 1788 1.345741 CCCTTGCTTGTCTCTGACTGA 59.654 52.381 0.00 0.00 33.15 3.41
1029 1789 2.411904 CCTTGCTTGTCTCTGACTGAC 58.588 52.381 0.00 0.00 33.15 3.51
1051 1816 2.507324 GGTTCAGCCGAGCTCGAC 60.507 66.667 36.59 26.65 43.02 4.20
1472 2237 1.940613 GCCGTTTCAGTTCAGTTCAGT 59.059 47.619 0.00 0.00 0.00 3.41
1473 2238 2.354821 GCCGTTTCAGTTCAGTTCAGTT 59.645 45.455 0.00 0.00 0.00 3.16
1474 2239 3.546218 GCCGTTTCAGTTCAGTTCAGTTC 60.546 47.826 0.00 0.00 0.00 3.01
1475 2240 3.621268 CCGTTTCAGTTCAGTTCAGTTCA 59.379 43.478 0.00 0.00 0.00 3.18
1476 2241 4.260375 CCGTTTCAGTTCAGTTCAGTTCAG 60.260 45.833 0.00 0.00 0.00 3.02
1560 2326 9.206870 ACATTTGGTTTTGTATCAATGACAATC 57.793 29.630 0.00 0.00 36.71 2.67
1630 2396 2.724977 TTGTCTCTCGATTGTTCGCT 57.275 45.000 0.00 0.00 45.10 4.93
1673 2439 3.586892 GAAGAGTACACTTCGAAAGGGG 58.413 50.000 15.81 0.00 37.20 4.79
1681 2447 3.958147 ACACTTCGAAAGGGGAAATGTTT 59.042 39.130 0.00 0.00 30.50 2.83
1686 2452 3.004944 TCGAAAGGGGAAATGTTTTTCGG 59.995 43.478 14.97 1.19 45.88 4.30
1687 2453 3.004944 CGAAAGGGGAAATGTTTTTCGGA 59.995 43.478 9.14 0.00 43.59 4.55
1689 2455 5.360649 AAAGGGGAAATGTTTTTCGGAAA 57.639 34.783 0.00 0.00 41.84 3.13
1691 2457 4.956085 AGGGGAAATGTTTTTCGGAAAAG 58.044 39.130 14.84 0.00 41.84 2.27
1692 2458 4.651962 AGGGGAAATGTTTTTCGGAAAAGA 59.348 37.500 14.84 0.64 41.84 2.52
1693 2459 5.129650 AGGGGAAATGTTTTTCGGAAAAGAA 59.870 36.000 14.84 8.71 41.84 2.52
1694 2460 5.818336 GGGGAAATGTTTTTCGGAAAAGAAA 59.182 36.000 14.84 6.53 41.84 2.52
1695 2461 6.316640 GGGGAAATGTTTTTCGGAAAAGAAAA 59.683 34.615 14.84 1.32 45.15 2.29
1696 2462 7.406553 GGGAAATGTTTTTCGGAAAAGAAAAG 58.593 34.615 14.84 0.00 46.61 2.27
1697 2463 7.279090 GGGAAATGTTTTTCGGAAAAGAAAAGA 59.721 33.333 14.84 1.18 46.61 2.52
1698 2464 8.328146 GGAAATGTTTTTCGGAAAAGAAAAGAG 58.672 33.333 14.84 0.00 46.61 2.85
1699 2465 7.770801 AATGTTTTTCGGAAAAGAAAAGAGG 57.229 32.000 14.84 0.00 46.61 3.69
1700 2466 6.518208 TGTTTTTCGGAAAAGAAAAGAGGA 57.482 33.333 14.84 0.00 46.61 3.71
1701 2467 6.926313 TGTTTTTCGGAAAAGAAAAGAGGAA 58.074 32.000 14.84 0.00 46.61 3.36
1702 2468 7.379750 TGTTTTTCGGAAAAGAAAAGAGGAAA 58.620 30.769 14.84 0.00 46.61 3.13
1703 2469 7.873505 TGTTTTTCGGAAAAGAAAAGAGGAAAA 59.126 29.630 14.84 0.00 46.61 2.29
1704 2470 8.879759 GTTTTTCGGAAAAGAAAAGAGGAAAAT 58.120 29.630 14.84 0.00 46.61 1.82
1705 2471 8.419076 TTTTCGGAAAAGAAAAGAGGAAAATG 57.581 30.769 11.68 0.00 42.91 2.32
1706 2472 6.709018 TCGGAAAAGAAAAGAGGAAAATGT 57.291 33.333 0.00 0.00 0.00 2.71
1707 2473 7.107639 TCGGAAAAGAAAAGAGGAAAATGTT 57.892 32.000 0.00 0.00 0.00 2.71
1708 2474 8.228035 TCGGAAAAGAAAAGAGGAAAATGTTA 57.772 30.769 0.00 0.00 0.00 2.41
1709 2475 8.856103 TCGGAAAAGAAAAGAGGAAAATGTTAT 58.144 29.630 0.00 0.00 0.00 1.89
1710 2476 8.915654 CGGAAAAGAAAAGAGGAAAATGTTATG 58.084 33.333 0.00 0.00 0.00 1.90
1711 2477 8.712363 GGAAAAGAAAAGAGGAAAATGTTATGC 58.288 33.333 0.00 0.00 0.00 3.14
1712 2478 9.260002 GAAAAGAAAAGAGGAAAATGTTATGCA 57.740 29.630 0.00 0.00 0.00 3.96
1713 2479 9.612066 AAAAGAAAAGAGGAAAATGTTATGCAA 57.388 25.926 0.00 0.00 0.00 4.08
1714 2480 8.822652 AAGAAAAGAGGAAAATGTTATGCAAG 57.177 30.769 0.00 0.00 0.00 4.01
1715 2481 8.181904 AGAAAAGAGGAAAATGTTATGCAAGA 57.818 30.769 0.00 0.00 0.00 3.02
1716 2482 8.084684 AGAAAAGAGGAAAATGTTATGCAAGAC 58.915 33.333 0.00 0.00 0.00 3.01
1717 2483 7.530426 AAAGAGGAAAATGTTATGCAAGACT 57.470 32.000 0.00 0.00 0.00 3.24
1718 2484 6.506500 AGAGGAAAATGTTATGCAAGACTG 57.493 37.500 0.00 0.00 0.00 3.51
1726 2492 7.686438 AATGTTATGCAAGACTGATAACACA 57.314 32.000 8.53 0.00 42.44 3.72
1729 2495 7.529158 TGTTATGCAAGACTGATAACACAATG 58.471 34.615 3.32 0.00 37.55 2.82
1734 2500 6.039159 TGCAAGACTGATAACACAATGTTCAA 59.961 34.615 0.00 0.00 40.22 2.69
1751 2517 8.549548 CAATGTTCAAAAGTCATAATGCAACAA 58.450 29.630 0.00 0.00 0.00 2.83
1753 2519 9.926158 ATGTTCAAAAGTCATAATGCAACAATA 57.074 25.926 0.00 0.00 0.00 1.90
1757 2523 9.791820 TCAAAAGTCATAATGCAACAATATCTG 57.208 29.630 0.00 0.00 0.00 2.90
1761 2527 7.923888 AGTCATAATGCAACAATATCTGACAC 58.076 34.615 0.00 0.00 0.00 3.67
1768 2534 4.321156 GCAACAATATCTGACACCTTGCAA 60.321 41.667 0.00 0.00 34.05 4.08
1775 2541 1.067516 CTGACACCTTGCAAACCCAAG 59.932 52.381 0.00 0.00 41.40 3.61
1787 2553 7.936847 CCTTGCAAACCCAAGTCATATATACTA 59.063 37.037 0.00 0.00 40.40 1.82
1788 2554 8.671384 TTGCAAACCCAAGTCATATATACTAC 57.329 34.615 0.00 0.00 0.00 2.73
1789 2555 8.029782 TGCAAACCCAAGTCATATATACTACT 57.970 34.615 0.00 0.00 0.00 2.57
1790 2556 8.148351 TGCAAACCCAAGTCATATATACTACTC 58.852 37.037 0.00 0.00 0.00 2.59
1791 2557 7.603024 GCAAACCCAAGTCATATATACTACTCC 59.397 40.741 0.52 0.00 0.00 3.85
1792 2558 7.793948 AACCCAAGTCATATATACTACTCCC 57.206 40.000 0.52 0.00 0.00 4.30
1793 2559 7.117331 ACCCAAGTCATATATACTACTCCCT 57.883 40.000 0.52 0.00 0.00 4.20
1794 2560 7.183460 ACCCAAGTCATATATACTACTCCCTC 58.817 42.308 0.52 0.00 0.00 4.30
1795 2561 6.608002 CCCAAGTCATATATACTACTCCCTCC 59.392 46.154 0.52 0.00 0.00 4.30
1796 2562 6.319152 CCAAGTCATATATACTACTCCCTCCG 59.681 46.154 0.52 0.00 0.00 4.63
1797 2563 6.639590 AGTCATATATACTACTCCCTCCGT 57.360 41.667 0.00 0.00 0.00 4.69
1798 2564 6.652053 AGTCATATATACTACTCCCTCCGTC 58.348 44.000 0.00 0.00 0.00 4.79
1799 2565 5.821995 GTCATATATACTACTCCCTCCGTCC 59.178 48.000 0.00 0.00 0.00 4.79
1800 2566 3.735720 ATATACTACTCCCTCCGTCCC 57.264 52.381 0.00 0.00 0.00 4.46
1801 2567 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
1802 2568 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
1803 2569 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
1804 2570 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
1805 2571 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
1806 2572 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
1807 2573 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
1808 2574 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
1809 2575 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
1810 2576 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
1811 2577 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
1812 2578 5.021458 TCCCTCCGTCCCATAATATAAGAC 58.979 45.833 0.00 0.00 0.00 3.01
1814 2580 4.461781 CCTCCGTCCCATAATATAAGACGT 59.538 45.833 17.31 0.00 46.62 4.34
1815 2581 5.047519 CCTCCGTCCCATAATATAAGACGTT 60.048 44.000 17.31 0.00 46.62 3.99
1816 2582 6.409524 TCCGTCCCATAATATAAGACGTTT 57.590 37.500 17.31 0.00 46.62 3.60
1817 2583 6.819284 TCCGTCCCATAATATAAGACGTTTT 58.181 36.000 17.31 0.00 46.62 2.43
1818 2584 7.274447 TCCGTCCCATAATATAAGACGTTTTT 58.726 34.615 17.31 0.00 46.62 1.94
1843 2609 8.738199 TTGACTTAGTATAGTGTCAAGAAACG 57.262 34.615 8.63 0.00 39.28 3.60
1844 2610 7.879070 TGACTTAGTATAGTGTCAAGAAACGT 58.121 34.615 0.00 0.00 34.58 3.99
1845 2611 8.019669 TGACTTAGTATAGTGTCAAGAAACGTC 58.980 37.037 0.00 0.00 34.58 4.34
1846 2612 8.108551 ACTTAGTATAGTGTCAAGAAACGTCT 57.891 34.615 0.00 0.00 34.72 4.18
1847 2613 8.574737 ACTTAGTATAGTGTCAAGAAACGTCTT 58.425 33.333 0.00 0.00 45.36 3.01
1849 2615 9.831737 TTAGTATAGTGTCAAGAAACGTCTTAC 57.168 33.333 0.00 0.00 42.45 2.34
1850 2616 7.879070 AGTATAGTGTCAAGAAACGTCTTACA 58.121 34.615 0.00 0.00 42.45 2.41
1851 2617 8.521176 AGTATAGTGTCAAGAAACGTCTTACAT 58.479 33.333 0.00 0.00 42.45 2.29
1852 2618 9.136952 GTATAGTGTCAAGAAACGTCTTACATT 57.863 33.333 0.00 0.00 42.45 2.71
1854 2620 9.871238 ATAGTGTCAAGAAACGTCTTACATTAT 57.129 29.630 0.00 0.12 42.45 1.28
1855 2621 8.018677 AGTGTCAAGAAACGTCTTACATTATG 57.981 34.615 0.00 0.00 42.45 1.90
1856 2622 7.117812 AGTGTCAAGAAACGTCTTACATTATGG 59.882 37.037 0.00 0.00 42.45 2.74
1857 2623 7.117236 GTGTCAAGAAACGTCTTACATTATGGA 59.883 37.037 0.00 0.00 42.45 3.41
1858 2624 7.658167 TGTCAAGAAACGTCTTACATTATGGAA 59.342 33.333 0.00 0.00 42.45 3.53
1859 2625 7.955864 GTCAAGAAACGTCTTACATTATGGAAC 59.044 37.037 0.00 0.00 42.45 3.62
1860 2626 6.642683 AGAAACGTCTTACATTATGGAACG 57.357 37.500 0.62 0.62 0.00 3.95
1861 2627 5.579511 AGAAACGTCTTACATTATGGAACGG 59.420 40.000 6.60 0.00 0.00 4.44
1862 2628 4.724074 ACGTCTTACATTATGGAACGGA 57.276 40.909 6.60 0.00 0.00 4.69
1863 2629 4.679662 ACGTCTTACATTATGGAACGGAG 58.320 43.478 6.60 0.00 0.00 4.63
1864 2630 4.049186 CGTCTTACATTATGGAACGGAGG 58.951 47.826 0.00 0.00 0.00 4.30
1865 2631 4.377897 GTCTTACATTATGGAACGGAGGG 58.622 47.826 0.00 0.00 0.00 4.30
1866 2632 4.100498 GTCTTACATTATGGAACGGAGGGA 59.900 45.833 0.00 0.00 0.00 4.20
1867 2633 4.344102 TCTTACATTATGGAACGGAGGGAG 59.656 45.833 0.00 0.00 0.00 4.30
1874 2640 1.203087 TGGAACGGAGGGAGTACTTGA 60.203 52.381 0.00 0.00 0.00 3.02
1878 2644 2.308690 ACGGAGGGAGTACTTGATAGC 58.691 52.381 0.00 0.00 0.00 2.97
1899 2666 1.698506 AGGTGGAAATGCGGAACAAA 58.301 45.000 0.00 0.00 0.00 2.83
1919 2686 5.703130 ACAAAAGTGTATTCTCTCTTCAGGC 59.297 40.000 0.00 0.00 35.72 4.85
1947 2789 7.757279 ATTCGACTCACAAGAATGGAGGTACT 61.757 42.308 0.00 0.00 35.58 2.73
1958 2800 8.875168 CAAGAATGGAGGTACTAGATTCCTTAT 58.125 37.037 0.00 0.00 41.55 1.73
1974 2816 8.784880 AGATTCCTTATGATGATTATGCCCATA 58.215 33.333 0.00 0.00 0.00 2.74
1982 2824 5.947566 TGATGATTATGCCCATATTGACCTG 59.052 40.000 0.00 0.00 0.00 4.00
1990 2833 4.889409 TGCCCATATTGACCTGATTTCTTC 59.111 41.667 0.00 0.00 0.00 2.87
1992 2835 5.126067 CCCATATTGACCTGATTTCTTCGT 58.874 41.667 0.00 0.00 0.00 3.85
1993 2836 5.590259 CCCATATTGACCTGATTTCTTCGTT 59.410 40.000 0.00 0.00 0.00 3.85
1997 2884 6.884280 ATTGACCTGATTTCTTCGTTTTCT 57.116 33.333 0.00 0.00 0.00 2.52
2009 2896 9.734984 ATTTCTTCGTTTTCTTAGGAGGAATAA 57.265 29.630 0.00 0.00 31.19 1.40
2022 2909 3.945921 GGAGGAATAAACTTCGAAAGGGG 59.054 47.826 0.00 0.00 0.00 4.79
2036 2923 3.653344 GAAAGGGGAAATGTTCTGCAAC 58.347 45.455 0.00 0.00 0.00 4.17
2052 2939 4.277921 TCTGCAACATTGATAGCACAACAA 59.722 37.500 0.00 0.00 32.87 2.83
2107 2994 5.014123 TCTCTTCCTGACCAAAACCATGTAT 59.986 40.000 0.00 0.00 0.00 2.29
2108 2995 5.253330 TCTTCCTGACCAAAACCATGTATC 58.747 41.667 0.00 0.00 0.00 2.24
2109 2996 3.605634 TCCTGACCAAAACCATGTATCG 58.394 45.455 0.00 0.00 0.00 2.92
2110 2997 3.008594 TCCTGACCAAAACCATGTATCGT 59.991 43.478 0.00 0.00 0.00 3.73
2111 2998 4.223255 TCCTGACCAAAACCATGTATCGTA 59.777 41.667 0.00 0.00 0.00 3.43
2112 2999 4.331717 CCTGACCAAAACCATGTATCGTAC 59.668 45.833 0.00 0.00 0.00 3.67
2113 3000 4.255301 TGACCAAAACCATGTATCGTACC 58.745 43.478 0.00 0.00 0.00 3.34
2117 3008 5.182380 ACCAAAACCATGTATCGTACCAAAG 59.818 40.000 0.00 0.00 0.00 2.77
2141 3032 6.929049 AGATGAAACGACAGTGTATTTTCTCA 59.071 34.615 21.28 10.73 0.00 3.27
2152 3043 7.492669 ACAGTGTATTTTCTCATAATCTGTCGG 59.507 37.037 0.00 0.00 0.00 4.79
2154 3045 6.257849 GTGTATTTTCTCATAATCTGTCGGCA 59.742 38.462 0.00 0.00 0.00 5.69
2167 3058 3.195610 TCTGTCGGCATAAGTGAATGTCT 59.804 43.478 0.00 0.00 28.98 3.41
2219 3110 9.264719 CTATTGAGCAGAATATGTGATACAACA 57.735 33.333 0.00 0.00 0.00 3.33
2220 3111 7.543947 TTGAGCAGAATATGTGATACAACAG 57.456 36.000 0.00 0.00 32.52 3.16
2221 3112 6.051074 TGAGCAGAATATGTGATACAACAGG 58.949 40.000 0.00 0.00 32.52 4.00
2224 3115 5.822519 GCAGAATATGTGATACAACAGGGAA 59.177 40.000 0.00 0.00 32.52 3.97
2225 3116 6.488006 GCAGAATATGTGATACAACAGGGAAT 59.512 38.462 0.00 0.00 32.52 3.01
2273 3169 4.219944 CCTACAAGAGCACCTGTTACAGTA 59.780 45.833 11.68 0.00 0.00 2.74
2276 3172 2.248248 AGAGCACCTGTTACAGTAGCA 58.752 47.619 21.90 0.00 33.75 3.49
2277 3173 2.232452 AGAGCACCTGTTACAGTAGCAG 59.768 50.000 21.90 15.74 36.85 4.24
2278 3174 1.971357 AGCACCTGTTACAGTAGCAGT 59.029 47.619 21.90 7.10 35.53 4.40
2279 3175 3.162666 AGCACCTGTTACAGTAGCAGTA 58.837 45.455 21.90 0.00 35.53 2.74
2280 3176 3.193691 AGCACCTGTTACAGTAGCAGTAG 59.806 47.826 21.90 13.66 35.53 2.57
2281 3177 3.512680 CACCTGTTACAGTAGCAGTAGC 58.487 50.000 19.75 0.00 42.56 3.58
2282 3178 3.056821 CACCTGTTACAGTAGCAGTAGCA 60.057 47.826 19.75 0.00 45.49 3.49
2288 3184 3.791973 ACAGTAGCAGTAGCACTCATC 57.208 47.619 0.00 0.00 45.49 2.92
2311 3207 5.583457 TCAGATCATGTGTTTCTGCACTATG 59.417 40.000 0.00 0.00 39.89 2.23
2363 3259 9.503427 GCAACTGAACCTCAAAATATATGTTAC 57.497 33.333 0.00 0.00 0.00 2.50
2527 3423 3.444742 CAGCTGATGAAAGCCATAACCAA 59.555 43.478 8.42 0.00 44.68 3.67
2528 3424 3.698040 AGCTGATGAAAGCCATAACCAAG 59.302 43.478 0.00 0.00 44.68 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.017782 TGCCTCTACTTGACTAGCTCG 58.982 52.381 0.00 0.00 0.00 5.03
12 13 5.511363 AGTGTCACTAGTATGCCTCTACTT 58.489 41.667 2.87 0.00 33.96 2.24
29 30 7.598869 GTGAATACATAGACAAACAGAGTGTCA 59.401 37.037 7.26 0.00 46.44 3.58
36 37 8.032952 ACATGTGTGAATACATAGACAAACAG 57.967 34.615 0.00 0.00 39.17 3.16
153 155 1.500736 CCCCTGAAGGAAATATGCCCT 59.499 52.381 0.00 0.00 38.24 5.19
174 176 2.092429 ACACGCCCATCATAGGACAAAT 60.092 45.455 0.00 0.00 0.00 2.32
203 205 4.838152 CCTGCATACTGCCGCCGT 62.838 66.667 0.00 0.00 44.23 5.68
255 257 4.863131 GGTTGATAACACCGAGTAGAACAG 59.137 45.833 0.00 0.00 0.00 3.16
264 266 4.829872 ATTGTAGGGTTGATAACACCGA 57.170 40.909 0.00 0.00 34.56 4.69
274 276 7.538575 CAATGGTCTCTAAAATTGTAGGGTTG 58.461 38.462 2.34 0.00 0.00 3.77
284 313 3.129287 CGGCAAGCAATGGTCTCTAAAAT 59.871 43.478 0.00 0.00 0.00 1.82
335 364 7.831193 ACTAGCAATTATCAAGTGATCCAAAGT 59.169 33.333 0.00 0.00 36.05 2.66
368 397 4.944962 TGATGTCATTCACAATCGGTTC 57.055 40.909 0.00 0.00 38.97 3.62
380 409 7.512992 CCTCCTACTCCTTTTATGATGTCATT 58.487 38.462 0.19 0.00 37.76 2.57
397 428 2.180086 TGTGATATGAGGGCCTCCTACT 59.820 50.000 30.03 14.55 45.05 2.57
530 562 2.883828 AAGTGGTGACCCTGCGGAG 61.884 63.158 0.00 0.00 0.00 4.63
631 1055 5.070047 GCTGGCCTAGGAGTAGTACATTTTA 59.930 44.000 14.75 0.00 0.00 1.52
676 1105 0.040425 CGCCCTTTGTTGTTTCGAGG 60.040 55.000 0.00 0.00 0.00 4.63
694 1433 0.179181 GTCCACATGTGCATGCTTCG 60.179 55.000 20.81 7.31 42.39 3.79
765 1504 1.936547 GCAGTTTATCCTTGCTCCTCG 59.063 52.381 0.00 0.00 35.05 4.63
805 1544 1.345715 AAGGATAAGGTGCGGGAGGG 61.346 60.000 0.00 0.00 0.00 4.30
824 1563 0.252789 TTTGTACGGGGGATCAGGGA 60.253 55.000 0.00 0.00 0.00 4.20
845 1584 2.840651 CACATAGAGGGAAAGGAGTGGT 59.159 50.000 0.00 0.00 0.00 4.16
861 1604 1.502527 GGGGTTGGGTGGGTCACATA 61.503 60.000 0.38 0.00 35.86 2.29
905 1648 2.927856 TTGGCGCTGGAGGAGGAA 60.928 61.111 7.64 0.00 0.00 3.36
918 1670 0.586802 GTGGTTGTCGAGTTCTTGGC 59.413 55.000 0.00 0.00 0.00 4.52
929 1681 0.672711 GCTTACCTCCGGTGGTTGTC 60.673 60.000 31.68 16.98 41.22 3.18
931 1683 0.250553 TTGCTTACCTCCGGTGGTTG 60.251 55.000 31.68 23.91 41.22 3.77
934 1686 1.745489 GCTTGCTTACCTCCGGTGG 60.745 63.158 21.02 21.02 36.19 4.61
935 1687 0.605319 TTGCTTGCTTACCTCCGGTG 60.605 55.000 0.00 0.00 36.19 4.94
936 1688 0.605589 GTTGCTTGCTTACCTCCGGT 60.606 55.000 0.00 0.00 40.16 5.28
937 1689 1.305930 GGTTGCTTGCTTACCTCCGG 61.306 60.000 0.00 0.00 0.00 5.14
938 1690 1.305930 GGGTTGCTTGCTTACCTCCG 61.306 60.000 13.85 0.00 32.46 4.63
939 1691 0.251165 TGGGTTGCTTGCTTACCTCC 60.251 55.000 13.85 3.58 32.46 4.30
940 1692 1.269723 GTTGGGTTGCTTGCTTACCTC 59.730 52.381 13.85 7.63 32.46 3.85
941 1693 1.328279 GTTGGGTTGCTTGCTTACCT 58.672 50.000 13.85 0.00 32.46 3.08
942 1694 0.317160 GGTTGGGTTGCTTGCTTACC 59.683 55.000 8.31 8.31 0.00 2.85
943 1695 0.317160 GGGTTGGGTTGCTTGCTTAC 59.683 55.000 0.00 0.00 0.00 2.34
944 1696 0.105964 TGGGTTGGGTTGCTTGCTTA 60.106 50.000 0.00 0.00 0.00 3.09
945 1697 1.382420 TGGGTTGGGTTGCTTGCTT 60.382 52.632 0.00 0.00 0.00 3.91
946 1698 2.133641 GTGGGTTGGGTTGCTTGCT 61.134 57.895 0.00 0.00 0.00 3.91
947 1699 1.757423 ATGTGGGTTGGGTTGCTTGC 61.757 55.000 0.00 0.00 0.00 4.01
948 1700 0.758123 AATGTGGGTTGGGTTGCTTG 59.242 50.000 0.00 0.00 0.00 4.01
955 1707 2.362375 CGGGGAATGTGGGTTGGG 60.362 66.667 0.00 0.00 0.00 4.12
973 1725 1.213733 CGAGCTGCGATGATCTGGTG 61.214 60.000 0.00 0.00 44.57 4.17
987 1739 2.024305 CGTAATCCGTCGCGAGCT 59.976 61.111 10.24 0.00 0.00 4.09
988 1740 3.679326 GCGTAATCCGTCGCGAGC 61.679 66.667 10.24 2.25 42.79 5.03
994 1746 1.153429 AAGGGCTGCGTAATCCGTC 60.153 57.895 0.00 0.00 39.32 4.79
1017 1777 0.965439 ACCTGCAGTCAGTCAGAGAC 59.035 55.000 13.81 0.00 38.66 3.36
1018 1778 1.615883 GAACCTGCAGTCAGTCAGAGA 59.384 52.381 13.81 0.00 38.66 3.10
1019 1779 1.342496 TGAACCTGCAGTCAGTCAGAG 59.658 52.381 13.81 0.00 38.66 3.35
1021 1781 1.793258 CTGAACCTGCAGTCAGTCAG 58.207 55.000 20.81 17.70 37.21 3.51
1022 1782 0.250038 GCTGAACCTGCAGTCAGTCA 60.250 55.000 26.38 16.67 38.66 3.41
1023 1783 0.952984 GGCTGAACCTGCAGTCAGTC 60.953 60.000 26.38 23.19 40.18 3.51
1024 1784 1.072159 GGCTGAACCTGCAGTCAGT 59.928 57.895 26.38 11.32 40.18 3.41
1025 1785 2.031516 CGGCTGAACCTGCAGTCAG 61.032 63.158 23.47 23.47 40.45 3.51
1026 1786 2.031012 CGGCTGAACCTGCAGTCA 59.969 61.111 13.81 9.88 40.45 3.41
1028 1788 2.345244 CTCGGCTGAACCTGCAGT 59.655 61.111 13.81 0.00 38.17 4.40
1029 1789 3.123620 GCTCGGCTGAACCTGCAG 61.124 66.667 6.78 6.78 38.91 4.41
1472 2237 1.152694 AGCCAAACAGCAGCCTGAA 60.153 52.632 0.00 0.00 41.77 3.02
1473 2238 1.900016 CAGCCAAACAGCAGCCTGA 60.900 57.895 0.00 0.00 41.77 3.86
1474 2239 2.649034 CAGCCAAACAGCAGCCTG 59.351 61.111 0.00 0.00 44.80 4.85
1475 2240 2.599578 CCAGCCAAACAGCAGCCT 60.600 61.111 0.00 0.00 34.23 4.58
1476 2241 4.368543 GCCAGCCAAACAGCAGCC 62.369 66.667 0.00 0.00 34.23 4.85
1560 2326 2.831685 TCCGGGGTATTCATCAATCG 57.168 50.000 0.00 0.00 0.00 3.34
1630 2396 5.019470 TCCTAGAGAAGAATCAGACAAGCA 58.981 41.667 0.00 0.00 0.00 3.91
1673 2439 8.328146 CCTCTTTTCTTTTCCGAAAAACATTTC 58.672 33.333 7.67 0.00 40.99 2.17
1681 2447 7.552459 ACATTTTCCTCTTTTCTTTTCCGAAA 58.448 30.769 0.00 0.00 0.00 3.46
1686 2452 9.260002 TGCATAACATTTTCCTCTTTTCTTTTC 57.740 29.630 0.00 0.00 0.00 2.29
1687 2453 9.612066 TTGCATAACATTTTCCTCTTTTCTTTT 57.388 25.926 0.00 0.00 0.00 2.27
1689 2455 8.641541 TCTTGCATAACATTTTCCTCTTTTCTT 58.358 29.630 0.00 0.00 0.00 2.52
1691 2457 8.084684 AGTCTTGCATAACATTTTCCTCTTTTC 58.915 33.333 0.00 0.00 0.00 2.29
1692 2458 7.869429 CAGTCTTGCATAACATTTTCCTCTTTT 59.131 33.333 0.00 0.00 0.00 2.27
1693 2459 7.231317 TCAGTCTTGCATAACATTTTCCTCTTT 59.769 33.333 0.00 0.00 0.00 2.52
1694 2460 6.716628 TCAGTCTTGCATAACATTTTCCTCTT 59.283 34.615 0.00 0.00 0.00 2.85
1695 2461 6.240894 TCAGTCTTGCATAACATTTTCCTCT 58.759 36.000 0.00 0.00 0.00 3.69
1696 2462 6.500684 TCAGTCTTGCATAACATTTTCCTC 57.499 37.500 0.00 0.00 0.00 3.71
1697 2463 8.462016 GTTATCAGTCTTGCATAACATTTTCCT 58.538 33.333 0.00 0.00 34.45 3.36
1698 2464 8.243426 TGTTATCAGTCTTGCATAACATTTTCC 58.757 33.333 3.32 0.00 37.83 3.13
1699 2465 9.065871 GTGTTATCAGTCTTGCATAACATTTTC 57.934 33.333 9.36 0.00 42.25 2.29
1700 2466 8.575589 TGTGTTATCAGTCTTGCATAACATTTT 58.424 29.630 9.36 0.00 42.25 1.82
1701 2467 8.109705 TGTGTTATCAGTCTTGCATAACATTT 57.890 30.769 9.36 0.00 42.25 2.32
1702 2468 7.686438 TGTGTTATCAGTCTTGCATAACATT 57.314 32.000 9.36 0.00 42.25 2.71
1703 2469 7.686438 TTGTGTTATCAGTCTTGCATAACAT 57.314 32.000 9.36 0.00 42.25 2.71
1704 2470 7.174772 ACATTGTGTTATCAGTCTTGCATAACA 59.825 33.333 3.32 3.32 39.55 2.41
1705 2471 7.530010 ACATTGTGTTATCAGTCTTGCATAAC 58.470 34.615 0.00 0.00 34.75 1.89
1706 2472 7.686438 ACATTGTGTTATCAGTCTTGCATAA 57.314 32.000 0.00 0.00 0.00 1.90
1707 2473 7.390162 TGAACATTGTGTTATCAGTCTTGCATA 59.610 33.333 0.00 0.00 41.28 3.14
1708 2474 6.207221 TGAACATTGTGTTATCAGTCTTGCAT 59.793 34.615 0.00 0.00 41.28 3.96
1709 2475 5.530543 TGAACATTGTGTTATCAGTCTTGCA 59.469 36.000 0.00 0.00 41.28 4.08
1710 2476 6.000891 TGAACATTGTGTTATCAGTCTTGC 57.999 37.500 0.00 0.00 41.28 4.01
1711 2477 8.854979 TTTTGAACATTGTGTTATCAGTCTTG 57.145 30.769 0.00 0.00 41.28 3.02
1712 2478 8.686334 ACTTTTGAACATTGTGTTATCAGTCTT 58.314 29.630 0.00 0.00 41.28 3.01
1713 2479 8.225603 ACTTTTGAACATTGTGTTATCAGTCT 57.774 30.769 0.00 0.00 41.28 3.24
1714 2480 8.128582 TGACTTTTGAACATTGTGTTATCAGTC 58.871 33.333 12.41 12.41 41.28 3.51
1715 2481 7.995289 TGACTTTTGAACATTGTGTTATCAGT 58.005 30.769 0.00 0.00 41.28 3.41
1726 2492 8.659925 TTGTTGCATTATGACTTTTGAACATT 57.340 26.923 0.00 0.00 0.00 2.71
1734 2500 8.959548 TGTCAGATATTGTTGCATTATGACTTT 58.040 29.630 0.00 0.00 0.00 2.66
1751 2517 3.245229 TGGGTTTGCAAGGTGTCAGATAT 60.245 43.478 0.00 0.00 0.00 1.63
1753 2519 1.133513 TGGGTTTGCAAGGTGTCAGAT 60.134 47.619 0.00 0.00 0.00 2.90
1757 2523 1.067060 GACTTGGGTTTGCAAGGTGTC 59.933 52.381 0.00 0.80 33.05 3.67
1761 2527 6.772716 AGTATATATGACTTGGGTTTGCAAGG 59.227 38.462 0.00 0.00 33.05 3.61
1768 2534 7.545546 AGGGAGTAGTATATATGACTTGGGTT 58.454 38.462 0.00 0.00 0.00 4.11
1775 2541 5.821995 GGACGGAGGGAGTAGTATATATGAC 59.178 48.000 0.00 0.00 0.00 3.06
1787 2553 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
1788 2554 5.127356 GTCTTATATTATGGGACGGAGGGAG 59.873 48.000 0.00 0.00 0.00 4.30
1789 2555 5.021458 GTCTTATATTATGGGACGGAGGGA 58.979 45.833 0.00 0.00 0.00 4.20
1790 2556 4.142227 CGTCTTATATTATGGGACGGAGGG 60.142 50.000 17.59 0.46 43.69 4.30
1791 2557 4.995124 CGTCTTATATTATGGGACGGAGG 58.005 47.826 17.59 0.00 43.69 4.30
1817 2583 9.188588 CGTTTCTTGACACTATACTAAGTCAAA 57.811 33.333 8.03 0.00 46.56 2.69
1818 2584 8.355169 ACGTTTCTTGACACTATACTAAGTCAA 58.645 33.333 0.00 0.00 45.57 3.18
1819 2585 7.879070 ACGTTTCTTGACACTATACTAAGTCA 58.121 34.615 0.00 0.00 39.06 3.41
1820 2586 8.235905 AGACGTTTCTTGACACTATACTAAGTC 58.764 37.037 0.00 0.00 0.00 3.01
1821 2587 8.108551 AGACGTTTCTTGACACTATACTAAGT 57.891 34.615 0.00 0.00 0.00 2.24
1822 2588 8.967552 AAGACGTTTCTTGACACTATACTAAG 57.032 34.615 0.00 0.00 40.82 2.18
1823 2589 9.831737 GTAAGACGTTTCTTGACACTATACTAA 57.168 33.333 0.00 0.00 42.41 2.24
1824 2590 9.002600 TGTAAGACGTTTCTTGACACTATACTA 57.997 33.333 0.00 0.00 42.41 1.82
1825 2591 7.879070 TGTAAGACGTTTCTTGACACTATACT 58.121 34.615 0.00 0.00 42.41 2.12
1826 2592 8.684973 ATGTAAGACGTTTCTTGACACTATAC 57.315 34.615 0.00 0.00 42.41 1.47
1828 2594 9.871238 ATAATGTAAGACGTTTCTTGACACTAT 57.129 29.630 0.00 0.00 42.41 2.12
1829 2595 9.135843 CATAATGTAAGACGTTTCTTGACACTA 57.864 33.333 0.00 0.00 42.41 2.74
1830 2596 7.117812 CCATAATGTAAGACGTTTCTTGACACT 59.882 37.037 0.00 0.00 42.41 3.55
1831 2597 7.117236 TCCATAATGTAAGACGTTTCTTGACAC 59.883 37.037 0.00 0.00 42.41 3.67
1832 2598 7.156000 TCCATAATGTAAGACGTTTCTTGACA 58.844 34.615 0.00 0.00 42.41 3.58
1833 2599 7.591006 TCCATAATGTAAGACGTTTCTTGAC 57.409 36.000 0.00 0.00 42.41 3.18
1834 2600 7.148705 CGTTCCATAATGTAAGACGTTTCTTGA 60.149 37.037 0.00 0.00 42.41 3.02
1835 2601 6.953743 CGTTCCATAATGTAAGACGTTTCTTG 59.046 38.462 0.00 0.00 42.41 3.02
1836 2602 6.091713 CCGTTCCATAATGTAAGACGTTTCTT 59.908 38.462 0.00 0.00 44.70 2.52
1837 2603 5.579511 CCGTTCCATAATGTAAGACGTTTCT 59.420 40.000 0.00 0.00 0.00 2.52
1838 2604 5.577945 TCCGTTCCATAATGTAAGACGTTTC 59.422 40.000 0.00 0.00 0.00 2.78
1839 2605 5.481105 TCCGTTCCATAATGTAAGACGTTT 58.519 37.500 0.00 0.00 0.00 3.60
1840 2606 5.075858 TCCGTTCCATAATGTAAGACGTT 57.924 39.130 0.00 0.00 0.00 3.99
1841 2607 4.441079 CCTCCGTTCCATAATGTAAGACGT 60.441 45.833 0.00 0.00 0.00 4.34
1842 2608 4.049186 CCTCCGTTCCATAATGTAAGACG 58.951 47.826 0.00 0.00 0.00 4.18
1843 2609 4.100498 TCCCTCCGTTCCATAATGTAAGAC 59.900 45.833 0.00 0.00 0.00 3.01
1844 2610 4.291792 TCCCTCCGTTCCATAATGTAAGA 58.708 43.478 0.00 0.00 0.00 2.10
1845 2611 4.101119 ACTCCCTCCGTTCCATAATGTAAG 59.899 45.833 0.00 0.00 0.00 2.34
1846 2612 4.035112 ACTCCCTCCGTTCCATAATGTAA 58.965 43.478 0.00 0.00 0.00 2.41
1847 2613 3.649843 ACTCCCTCCGTTCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
1848 2614 2.478292 ACTCCCTCCGTTCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
1849 2615 3.641906 AGTACTCCCTCCGTTCCATAATG 59.358 47.826 0.00 0.00 0.00 1.90
1850 2616 3.924922 AGTACTCCCTCCGTTCCATAAT 58.075 45.455 0.00 0.00 0.00 1.28
1851 2617 3.393426 AGTACTCCCTCCGTTCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
1852 2618 3.028850 CAAGTACTCCCTCCGTTCCATA 58.971 50.000 0.00 0.00 0.00 2.74
1853 2619 1.831736 CAAGTACTCCCTCCGTTCCAT 59.168 52.381 0.00 0.00 0.00 3.41
1854 2620 1.203087 TCAAGTACTCCCTCCGTTCCA 60.203 52.381 0.00 0.00 0.00 3.53
1855 2621 1.553706 TCAAGTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 0.00 3.62
1856 2622 3.243468 GCTATCAAGTACTCCCTCCGTTC 60.243 52.174 0.00 0.00 0.00 3.95
1857 2623 2.694109 GCTATCAAGTACTCCCTCCGTT 59.306 50.000 0.00 0.00 0.00 4.44
1858 2624 2.308690 GCTATCAAGTACTCCCTCCGT 58.691 52.381 0.00 0.00 0.00 4.69
1859 2625 2.307768 TGCTATCAAGTACTCCCTCCG 58.692 52.381 0.00 0.00 0.00 4.63
1860 2626 3.070302 CCTTGCTATCAAGTACTCCCTCC 59.930 52.174 5.64 0.00 46.33 4.30
1861 2627 3.707102 ACCTTGCTATCAAGTACTCCCTC 59.293 47.826 5.64 0.00 46.33 4.30
1862 2628 3.452627 CACCTTGCTATCAAGTACTCCCT 59.547 47.826 5.64 0.00 46.33 4.20
1863 2629 3.432326 CCACCTTGCTATCAAGTACTCCC 60.432 52.174 5.64 0.00 46.33 4.30
1864 2630 3.451178 TCCACCTTGCTATCAAGTACTCC 59.549 47.826 5.64 0.00 46.33 3.85
1865 2631 4.737855 TCCACCTTGCTATCAAGTACTC 57.262 45.455 5.64 0.00 46.33 2.59
1866 2632 5.499004 TTTCCACCTTGCTATCAAGTACT 57.501 39.130 5.64 0.00 46.33 2.73
1867 2633 5.449177 GCATTTCCACCTTGCTATCAAGTAC 60.449 44.000 5.64 0.00 46.33 2.73
1874 2640 1.064758 TCCGCATTTCCACCTTGCTAT 60.065 47.619 0.00 0.00 34.23 2.97
1878 2644 0.958091 TGTTCCGCATTTCCACCTTG 59.042 50.000 0.00 0.00 0.00 3.61
1899 2666 4.774726 TGAGCCTGAAGAGAGAATACACTT 59.225 41.667 0.00 0.00 0.00 3.16
1919 2686 4.498241 TCCATTCTTGTGAGTCGAATGAG 58.502 43.478 15.87 8.98 44.06 2.90
1939 2781 8.602472 ATCATCATAAGGAATCTAGTACCTCC 57.398 38.462 0.00 1.32 33.16 4.30
1947 2789 8.161640 TGGGCATAATCATCATAAGGAATCTA 57.838 34.615 0.00 0.00 0.00 1.98
1958 2800 5.947566 CAGGTCAATATGGGCATAATCATCA 59.052 40.000 0.00 0.00 0.00 3.07
1974 2816 6.884280 AGAAAACGAAGAAATCAGGTCAAT 57.116 33.333 0.00 0.00 0.00 2.57
1982 2824 7.668525 TTCCTCCTAAGAAAACGAAGAAATC 57.331 36.000 0.00 0.00 0.00 2.17
1990 2833 7.330208 TCGAAGTTTATTCCTCCTAAGAAAACG 59.670 37.037 0.00 0.00 0.00 3.60
1992 2835 9.563748 TTTCGAAGTTTATTCCTCCTAAGAAAA 57.436 29.630 0.00 0.00 0.00 2.29
1993 2836 9.216117 CTTTCGAAGTTTATTCCTCCTAAGAAA 57.784 33.333 0.00 0.00 0.00 2.52
1997 2884 6.412214 CCCTTTCGAAGTTTATTCCTCCTAA 58.588 40.000 0.00 0.00 0.00 2.69
2009 2896 4.278419 CAGAACATTTCCCCTTTCGAAGTT 59.722 41.667 0.00 0.00 0.00 2.66
2036 2923 6.849502 ACTTCTGATTGTTGTGCTATCAATG 58.150 36.000 0.00 0.00 38.48 2.82
2038 2925 5.997129 TGACTTCTGATTGTTGTGCTATCAA 59.003 36.000 0.00 0.00 38.48 2.57
2052 2939 5.412594 ACAACGTTGCATTATGACTTCTGAT 59.587 36.000 27.61 0.00 0.00 2.90
2107 2994 3.979948 TGTCGTTTCATCTTTGGTACGA 58.020 40.909 0.00 0.00 37.01 3.43
2108 2995 3.739300 ACTGTCGTTTCATCTTTGGTACG 59.261 43.478 0.00 0.00 33.93 3.67
2109 2996 4.510340 ACACTGTCGTTTCATCTTTGGTAC 59.490 41.667 0.00 0.00 0.00 3.34
2110 2997 4.699637 ACACTGTCGTTTCATCTTTGGTA 58.300 39.130 0.00 0.00 0.00 3.25
2111 2998 3.541632 ACACTGTCGTTTCATCTTTGGT 58.458 40.909 0.00 0.00 0.00 3.67
2112 2999 5.862924 ATACACTGTCGTTTCATCTTTGG 57.137 39.130 0.00 0.00 0.00 3.28
2113 3000 8.070171 AGAAAATACACTGTCGTTTCATCTTTG 58.930 33.333 15.08 0.00 31.94 2.77
2117 3008 7.117241 TGAGAAAATACACTGTCGTTTCATC 57.883 36.000 15.08 11.34 31.94 2.92
2141 3032 6.291377 ACATTCACTTATGCCGACAGATTAT 58.709 36.000 0.00 0.00 0.00 1.28
2152 3043 4.156556 TGAAGCCAAGACATTCACTTATGC 59.843 41.667 0.00 0.00 0.00 3.14
2154 3045 5.645497 GTCTGAAGCCAAGACATTCACTTAT 59.355 40.000 6.24 0.00 33.20 1.73
2167 3058 3.261643 TGCATCTTCTAGTCTGAAGCCAA 59.738 43.478 0.00 0.00 42.15 4.52
2210 3101 4.227300 AGCACCTTATTCCCTGTTGTATCA 59.773 41.667 0.00 0.00 0.00 2.15
2211 3102 4.781934 AGCACCTTATTCCCTGTTGTATC 58.218 43.478 0.00 0.00 0.00 2.24
2217 3108 2.185387 ACGTAGCACCTTATTCCCTGT 58.815 47.619 0.00 0.00 0.00 4.00
2218 3109 2.981859 ACGTAGCACCTTATTCCCTG 57.018 50.000 0.00 0.00 0.00 4.45
2219 3110 3.994931 AAACGTAGCACCTTATTCCCT 57.005 42.857 0.00 0.00 0.00 4.20
2220 3111 4.034858 GCTAAAACGTAGCACCTTATTCCC 59.965 45.833 3.93 0.00 40.14 3.97
2221 3112 4.874396 AGCTAAAACGTAGCACCTTATTCC 59.126 41.667 11.19 0.00 42.68 3.01
2224 3115 4.110482 CGAGCTAAAACGTAGCACCTTAT 58.890 43.478 11.19 0.00 42.68 1.73
2225 3116 3.191162 TCGAGCTAAAACGTAGCACCTTA 59.809 43.478 11.19 0.00 42.68 2.69
2273 3169 3.029570 TGATCTGATGAGTGCTACTGCT 58.970 45.455 0.00 0.00 40.48 4.24
2276 3172 4.405036 ACACATGATCTGATGAGTGCTACT 59.595 41.667 0.00 0.00 0.00 2.57
2277 3173 4.691175 ACACATGATCTGATGAGTGCTAC 58.309 43.478 0.00 0.00 0.00 3.58
2278 3174 5.349061 AACACATGATCTGATGAGTGCTA 57.651 39.130 0.00 0.00 28.96 3.49
2279 3175 3.908643 ACACATGATCTGATGAGTGCT 57.091 42.857 0.00 0.00 0.00 4.40
2280 3176 4.634883 AGAAACACATGATCTGATGAGTGC 59.365 41.667 0.00 0.00 28.96 4.40
2281 3177 5.447413 GCAGAAACACATGATCTGATGAGTG 60.447 44.000 19.30 3.72 42.48 3.51
2282 3178 4.634883 GCAGAAACACATGATCTGATGAGT 59.365 41.667 19.30 0.00 42.48 3.41
2288 3184 5.220796 CCATAGTGCAGAAACACATGATCTG 60.221 44.000 0.00 8.75 43.23 2.90
2311 3207 4.786507 ACGTTTTACTTTATTTGTCGGCC 58.213 39.130 0.00 0.00 0.00 6.13
2373 3269 2.618442 AGAATGCTGCTTAGAGCCTC 57.382 50.000 0.00 0.00 41.51 4.70
2430 3326 1.474330 GGATTTGCCGGAGATTTGGT 58.526 50.000 5.05 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.