Multiple sequence alignment - TraesCS7A01G392700

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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 TraesCS7A01G392700 chr7A 100.000 3211 0 0 1 3211 570112313 570115523 0.000000e+00 5930.0
1 TraesCS7A01G392700 chr7A 99.310 145 1 0 1563 1707 570113730 570113874 2.460000e-66 263.0
2 TraesCS7A01G392700 chr7A 99.310 145 1 0 1418 1562 570113875 570114019 2.460000e-66 263.0
3 TraesCS7A01G392700 chr7D 95.266 845 26 6 1 832 502872806 502873649 0.000000e+00 1327.0
4 TraesCS7A01G392700 chr7D 96.122 722 26 2 833 1552 502873694 502874415 0.000000e+00 1177.0
5 TraesCS7A01G392700 chr7D 87.619 840 59 16 1565 2365 502874283 502875116 0.000000e+00 933.0
6 TraesCS7A01G392700 chr7D 78.426 343 64 8 464 802 27057229 27056893 6.980000e-52 215.0
7 TraesCS7A01G392700 chr7D 81.333 225 26 9 2364 2578 502875170 502875388 5.510000e-38 169.0
8 TraesCS7A01G392700 chr7B 94.645 803 23 7 2 784 531654151 531654953 0.000000e+00 1227.0
9 TraesCS7A01G392700 chr7B 95.902 732 27 3 833 1562 531655029 531655759 0.000000e+00 1182.0
10 TraesCS7A01G392700 chr7B 92.034 816 50 4 1563 2365 531655616 531656429 0.000000e+00 1133.0
11 TraesCS7A01G392700 chr7B 92.120 368 26 1 2844 3211 531657007 531657371 1.710000e-142 516.0
12 TraesCS7A01G392700 chr7B 90.395 354 18 8 2364 2713 531656484 531656825 4.880000e-123 451.0
13 TraesCS7A01G392700 chr7B 98.000 50 1 0 2758 2807 531656822 531656871 1.590000e-13 87.9
14 TraesCS7A01G392700 chr6B 81.628 811 104 30 58 831 272629531 272630333 5.850000e-177 630.0
15 TraesCS7A01G392700 chr5A 85.362 608 63 12 893 1495 320213679 320213093 9.850000e-170 606.0
16 TraesCS7A01G392700 chr5A 83.463 514 67 10 1866 2363 320213059 320212548 2.260000e-126 462.0
17 TraesCS7A01G392700 chr5D 85.500 600 60 12 893 1486 234145765 234146343 4.580000e-168 601.0
18 TraesCS7A01G392700 chr5D 82.227 512 71 8 1867 2361 234146388 234146896 1.060000e-114 424.0
19 TraesCS7A01G392700 chr5B 84.893 609 65 13 893 1496 270438245 270437659 9.920000e-165 590.0
20 TraesCS7A01G392700 chr5B 83.268 514 68 10 1866 2363 270437626 270437115 1.050000e-124 457.0
21 TraesCS7A01G392700 chr6D 79.826 689 115 14 162 832 384974121 384974803 6.230000e-132 481.0
22 TraesCS7A01G392700 chr4D 89.535 86 9 0 1658 1743 58141424 58141509 3.390000e-20 110.0
23 TraesCS7A01G392700 chr4D 96.000 50 2 0 1513 1562 58141424 58141473 7.380000e-12 82.4
24 TraesCS7A01G392700 chr4B 90.411 73 6 1 62 134 517988973 517989044 9.480000e-16 95.3


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 TraesCS7A01G392700 chr7A 570112313 570115523 3210 False 2152.00 5930 99.540000 1 3211 3 chr7A.!!$F1 3210
1 TraesCS7A01G392700 chr7D 502872806 502875388 2582 False 901.50 1327 90.085000 1 2578 4 chr7D.!!$F1 2577
2 TraesCS7A01G392700 chr7B 531654151 531657371 3220 False 766.15 1227 93.849333 2 3211 6 chr7B.!!$F1 3209
3 TraesCS7A01G392700 chr6B 272629531 272630333 802 False 630.00 630 81.628000 58 831 1 chr6B.!!$F1 773
4 TraesCS7A01G392700 chr5A 320212548 320213679 1131 True 534.00 606 84.412500 893 2363 2 chr5A.!!$R1 1470
5 TraesCS7A01G392700 chr5D 234145765 234146896 1131 False 512.50 601 83.863500 893 2361 2 chr5D.!!$F1 1468
6 TraesCS7A01G392700 chr5B 270437115 270438245 1130 True 523.50 590 84.080500 893 2363 2 chr5B.!!$R1 1470
7 TraesCS7A01G392700 chr6D 384974121 384974803 682 False 481.00 481 79.826000 162 832 1 chr6D.!!$F1 670

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
801 850 2.224967 GGCAGGGAATATTCTCAGGCAT 60.225 50.0 23.99 0.0 39.16 4.40 F
1707 1809 0.033601 TAGGGGTGGCATTTGCGAAT 60.034 50.0 0.00 0.0 43.26 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1688 1790 0.033601 ATTCGCAAATGCCACCCCTA 60.034 50.0 0.0 0.0 37.91 3.53 R
2697 2907 0.105246 ATCCTCTCTCTGCGGGGAAT 60.105 55.0 0.0 0.0 0.00 3.01 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
49 50 8.298854 TGACTTCAATTTTATGAACCATGTCAG 58.701 33.333 6.02 0.00 36.59 3.51
56 62 6.925610 TTTATGAACCATGTCAGTATCTGC 57.074 37.500 0.00 0.00 0.00 4.26
269 275 6.183360 GGTGTTGAATCATTTATCCGGTGATT 60.183 38.462 15.04 15.04 43.23 2.57
313 319 6.950842 TGATGATCCTATTGATGACCATACC 58.049 40.000 0.00 0.00 32.41 2.73
361 391 8.270744 ACTGATGATCCTGCTAATCTTTAAGTT 58.729 33.333 0.00 0.00 0.00 2.66
491 533 6.959639 AATGTGACTTTTGGACATGTTAGT 57.040 33.333 0.00 0.00 30.69 2.24
592 634 7.639113 TTGGATATGGTTATGTTTGGTCTTC 57.361 36.000 0.00 0.00 0.00 2.87
703 750 3.998913 TCCACACAGGCATATCTTCAA 57.001 42.857 0.00 0.00 37.29 2.69
718 767 7.415989 GCATATCTTCAAGACATCACCAAACAT 60.416 37.037 0.00 0.00 0.00 2.71
801 850 2.224967 GGCAGGGAATATTCTCAGGCAT 60.225 50.000 23.99 0.00 39.16 4.40
808 857 4.340381 GGAATATTCTCAGGCATGTTGCTT 59.660 41.667 14.95 0.00 44.28 3.91
811 860 3.423539 TTCTCAGGCATGTTGCTTAGT 57.576 42.857 0.00 0.00 44.28 2.24
816 865 2.679837 CAGGCATGTTGCTTAGTGTAGG 59.320 50.000 0.00 0.00 44.28 3.18
827 876 6.109156 TGCTTAGTGTAGGAATCAAACAGA 57.891 37.500 0.00 0.00 0.00 3.41
843 936 3.953542 ACAGACCCTGTTTCTTTCCTT 57.046 42.857 0.00 0.00 42.59 3.36
864 957 5.993441 CCTTGAATGGCATTTCTCTGTTTTT 59.007 36.000 14.93 0.00 0.00 1.94
887 980 5.988310 TTCATGCTTTGGTGATGATTTCT 57.012 34.783 0.00 0.00 0.00 2.52
942 1041 7.982354 AGCTGTTCTGTCTTATCTTGTATAACC 59.018 37.037 0.00 0.00 0.00 2.85
1303 1402 5.621197 TCACTTCAATTTCCGTATTGTGG 57.379 39.130 0.00 0.00 36.95 4.17
1390 1491 6.524101 TTCCTATAAAAACAATGGCCACTC 57.476 37.500 8.16 0.00 0.00 3.51
1557 1659 2.496942 CAGCTAGGGGTGGCATTTG 58.503 57.895 0.00 0.00 37.31 2.32
1558 1660 1.380380 AGCTAGGGGTGGCATTTGC 60.380 57.895 0.00 0.00 41.14 3.68
1559 1661 2.774799 GCTAGGGGTGGCATTTGCG 61.775 63.158 0.00 0.00 43.26 4.85
1560 1662 1.077787 CTAGGGGTGGCATTTGCGA 60.078 57.895 0.00 0.00 43.26 5.10
1561 1663 0.679640 CTAGGGGTGGCATTTGCGAA 60.680 55.000 0.00 0.00 43.26 4.70
1562 1664 0.251386 TAGGGGTGGCATTTGCGAAA 60.251 50.000 0.00 0.00 43.26 3.46
1563 1665 1.374125 GGGGTGGCATTTGCGAAAC 60.374 57.895 0.00 0.00 43.26 2.78
1564 1666 1.732683 GGGTGGCATTTGCGAAACG 60.733 57.895 0.00 0.00 43.26 3.60
1565 1667 1.007849 GGTGGCATTTGCGAAACGT 60.008 52.632 0.00 0.00 43.26 3.99
1566 1668 0.238817 GGTGGCATTTGCGAAACGTA 59.761 50.000 0.00 0.00 43.26 3.57
1567 1669 1.335142 GGTGGCATTTGCGAAACGTAA 60.335 47.619 0.00 0.00 43.26 3.18
1568 1670 2.386249 GTGGCATTTGCGAAACGTAAA 58.614 42.857 9.36 9.36 44.19 2.01
1569 1671 2.152301 GTGGCATTTGCGAAACGTAAAC 59.848 45.455 9.17 0.00 43.10 2.01
1570 1672 2.223502 TGGCATTTGCGAAACGTAAACA 60.224 40.909 9.17 2.11 43.10 2.83
1571 1673 2.789893 GGCATTTGCGAAACGTAAACAA 59.210 40.909 9.17 0.00 43.10 2.83
1572 1674 3.361243 GGCATTTGCGAAACGTAAACAAC 60.361 43.478 9.17 3.29 43.10 3.32
1582 1684 3.173247 GTAAACAACGGCCACTTGC 57.827 52.632 2.24 0.00 40.16 4.01
1583 1685 0.382515 GTAAACAACGGCCACTTGCA 59.617 50.000 2.24 0.00 43.89 4.08
1584 1686 0.382515 TAAACAACGGCCACTTGCAC 59.617 50.000 2.24 0.00 43.89 4.57
1585 1687 2.291457 AAACAACGGCCACTTGCACC 62.291 55.000 2.24 0.00 43.89 5.01
1586 1688 3.215568 CAACGGCCACTTGCACCA 61.216 61.111 2.24 0.00 43.89 4.17
1587 1689 3.216292 AACGGCCACTTGCACCAC 61.216 61.111 2.24 0.00 43.89 4.16
1588 1690 3.714487 AACGGCCACTTGCACCACT 62.714 57.895 2.24 0.00 43.89 4.00
1589 1691 3.663176 CGGCCACTTGCACCACTG 61.663 66.667 2.24 0.00 43.89 3.66
1590 1692 3.297620 GGCCACTTGCACCACTGG 61.298 66.667 0.00 0.00 43.89 4.00
1591 1693 2.203337 GCCACTTGCACCACTGGA 60.203 61.111 0.71 0.00 40.77 3.86
1592 1694 2.263741 GCCACTTGCACCACTGGAG 61.264 63.158 0.71 0.00 40.77 3.86
1593 1695 1.149174 CCACTTGCACCACTGGAGT 59.851 57.895 0.71 0.00 0.00 3.85
1594 1696 0.396435 CCACTTGCACCACTGGAGTA 59.604 55.000 0.71 0.00 0.00 2.59
1595 1697 1.202758 CCACTTGCACCACTGGAGTAA 60.203 52.381 0.71 0.00 0.00 2.24
1596 1698 2.553028 CCACTTGCACCACTGGAGTAAT 60.553 50.000 0.71 0.00 0.00 1.89
1597 1699 3.149196 CACTTGCACCACTGGAGTAATT 58.851 45.455 0.71 0.00 0.00 1.40
1598 1700 4.323417 CACTTGCACCACTGGAGTAATTA 58.677 43.478 0.71 0.00 0.00 1.40
1599 1701 4.759693 CACTTGCACCACTGGAGTAATTAA 59.240 41.667 0.71 0.00 0.00 1.40
1600 1702 5.003804 ACTTGCACCACTGGAGTAATTAAG 58.996 41.667 0.71 0.00 0.00 1.85
1601 1703 3.343617 TGCACCACTGGAGTAATTAAGC 58.656 45.455 0.71 0.00 0.00 3.09
1602 1704 3.244735 TGCACCACTGGAGTAATTAAGCA 60.245 43.478 0.71 0.00 0.00 3.91
1603 1705 3.947834 GCACCACTGGAGTAATTAAGCAT 59.052 43.478 0.71 0.00 0.00 3.79
1604 1706 4.201950 GCACCACTGGAGTAATTAAGCATG 60.202 45.833 0.71 0.00 0.00 4.06
1605 1707 4.336433 CACCACTGGAGTAATTAAGCATGG 59.664 45.833 0.71 0.00 0.00 3.66
1606 1708 4.018415 ACCACTGGAGTAATTAAGCATGGT 60.018 41.667 0.71 0.00 31.91 3.55
1607 1709 4.336433 CCACTGGAGTAATTAAGCATGGTG 59.664 45.833 0.00 0.00 0.00 4.17
1608 1710 3.947834 ACTGGAGTAATTAAGCATGGTGC 59.052 43.478 0.00 0.00 45.46 5.01
1665 1767 4.579647 TCCTACAAAAATAGGACCCCAC 57.420 45.455 0.00 0.00 44.86 4.61
1666 1768 4.180723 TCCTACAAAAATAGGACCCCACT 58.819 43.478 0.00 0.00 44.86 4.00
1667 1769 5.352264 TCCTACAAAAATAGGACCCCACTA 58.648 41.667 0.00 0.00 44.86 2.74
1668 1770 5.427481 TCCTACAAAAATAGGACCCCACTAG 59.573 44.000 0.00 0.00 44.86 2.57
1669 1771 3.964411 ACAAAAATAGGACCCCACTAGC 58.036 45.455 0.00 0.00 0.00 3.42
1670 1772 3.591977 ACAAAAATAGGACCCCACTAGCT 59.408 43.478 0.00 0.00 0.00 3.32
1671 1773 3.933861 AAAATAGGACCCCACTAGCTG 57.066 47.619 0.00 0.00 0.00 4.24
1672 1774 1.807814 AATAGGACCCCACTAGCTGG 58.192 55.000 0.00 0.00 40.26 4.85
1673 1775 0.764752 ATAGGACCCCACTAGCTGGC 60.765 60.000 0.00 0.00 39.01 4.85
1674 1776 4.162690 GGACCCCACTAGCTGGCG 62.163 72.222 0.00 0.00 39.01 5.69
1675 1777 3.075005 GACCCCACTAGCTGGCGA 61.075 66.667 0.00 0.00 39.01 5.54
1676 1778 3.372554 GACCCCACTAGCTGGCGAC 62.373 68.421 0.00 0.00 39.01 5.19
1677 1779 4.162690 CCCCACTAGCTGGCGACC 62.163 72.222 0.00 0.00 39.01 4.79
1678 1780 4.514577 CCCACTAGCTGGCGACCG 62.515 72.222 0.00 0.00 39.01 4.79
1679 1781 3.760035 CCACTAGCTGGCGACCGT 61.760 66.667 0.00 0.00 31.36 4.83
1680 1782 2.261671 CACTAGCTGGCGACCGTT 59.738 61.111 0.00 0.00 0.00 4.44
1681 1783 1.805945 CACTAGCTGGCGACCGTTC 60.806 63.158 0.00 0.00 0.00 3.95
1690 1792 2.579787 CGACCGTTCGCCAGCTAG 60.580 66.667 0.00 0.00 38.71 3.42
1691 1793 2.202756 GACCGTTCGCCAGCTAGG 60.203 66.667 0.00 0.00 41.84 3.02
1692 1794 3.718210 GACCGTTCGCCAGCTAGGG 62.718 68.421 4.65 0.00 38.09 3.53
1707 1809 0.033601 TAGGGGTGGCATTTGCGAAT 60.034 50.000 0.00 0.00 43.26 3.34
1813 1935 0.388520 CTTGATCGAGTGGCGTGTGA 60.389 55.000 1.30 0.00 41.80 3.58
1901 2023 3.313526 CCACTTGCATTACTGGAGTATGC 59.686 47.826 0.00 0.00 36.50 3.14
1905 2027 3.544684 TGCATTACTGGAGTATGCAAGG 58.455 45.455 15.53 0.00 39.56 3.61
1909 2031 2.814805 ACTGGAGTATGCAAGGCAAT 57.185 45.000 0.00 0.00 43.62 3.56
1930 2052 9.893305 GGCAATGTTTACTGTTGATATATAACC 57.107 33.333 0.00 0.00 0.00 2.85
1977 2100 0.382873 GACGAAACAGGCCCGTTTTT 59.617 50.000 18.03 8.72 39.17 1.94
2015 2138 3.181491 TGCTGAAAACAGAACTTTTCCCG 60.181 43.478 0.00 0.00 38.76 5.14
2042 2165 3.444034 TCTGCATCTCTACTGTTACGCTT 59.556 43.478 0.00 0.00 0.00 4.68
2067 2192 7.974675 TGAAACAAATTATCTCGCTCTTTAGG 58.025 34.615 0.00 0.00 0.00 2.69
2075 2214 3.422796 TCTCGCTCTTTAGGACTGTTCT 58.577 45.455 0.00 0.00 0.00 3.01
2087 2226 5.367945 AGGACTGTTCTACTTTCCAAACA 57.632 39.130 0.00 0.00 0.00 2.83
2090 2229 5.500645 ACTGTTCTACTTTCCAAACAAGC 57.499 39.130 0.00 0.00 31.75 4.01
2097 2238 9.556030 GTTCTACTTTCCAAACAAGCATATAAC 57.444 33.333 0.00 0.00 0.00 1.89
2278 2419 8.819974 ACAGCAAGAACAAAAATATGAAACTTG 58.180 29.630 0.00 0.00 34.73 3.16
2279 2420 8.277713 CAGCAAGAACAAAAATATGAAACTTGG 58.722 33.333 0.00 0.00 33.63 3.61
2282 2423 9.533253 CAAGAACAAAAATATGAAACTTGGTCT 57.467 29.630 0.00 0.00 44.00 3.85
2284 2425 8.912988 AGAACAAAAATATGAAACTTGGTCTCA 58.087 29.630 0.00 0.00 39.29 3.27
2338 2479 7.980099 AGTACTACAAATAGTTGACATGTAGGC 59.020 37.037 10.35 7.83 44.79 3.93
2429 2638 9.975218 ATTGGTGTTTTGGAGTTACTTAGATAT 57.025 29.630 0.00 0.00 0.00 1.63
2495 2704 4.098349 TGTTCTGTTTTGCTTGCTGAAGAT 59.902 37.500 0.00 0.00 0.00 2.40
2496 2705 5.299028 TGTTCTGTTTTGCTTGCTGAAGATA 59.701 36.000 0.00 0.00 0.00 1.98
2498 2707 5.065914 TCTGTTTTGCTTGCTGAAGATACT 58.934 37.500 0.00 0.00 0.00 2.12
2499 2708 6.230472 TCTGTTTTGCTTGCTGAAGATACTA 58.770 36.000 0.00 0.00 0.00 1.82
2500 2709 6.369890 TCTGTTTTGCTTGCTGAAGATACTAG 59.630 38.462 0.00 0.00 0.00 2.57
2501 2710 5.997746 TGTTTTGCTTGCTGAAGATACTAGT 59.002 36.000 0.00 0.00 0.00 2.57
2502 2711 7.158697 TGTTTTGCTTGCTGAAGATACTAGTA 58.841 34.615 4.77 4.77 0.00 1.82
2504 2713 7.776933 TTTGCTTGCTGAAGATACTAGTATG 57.223 36.000 20.13 6.47 0.00 2.39
2550 2759 5.863397 CGTGGTTTCTGTCAATTGCATTATT 59.137 36.000 0.00 0.00 0.00 1.40
2559 2768 8.549548 TCTGTCAATTGCATTATTGTTTTTGTG 58.450 29.630 10.20 0.00 36.95 3.33
2599 2808 3.365265 GCAAAGGGACGCTGTGGG 61.365 66.667 11.39 0.00 0.00 4.61
2622 2831 0.109735 GCTTCAGTTTAACTGGCGGC 60.110 55.000 22.82 19.06 45.94 6.53
2671 2880 1.267121 GTGTCCCAGCTACTCCTTCA 58.733 55.000 0.00 0.00 0.00 3.02
2690 2900 2.621526 TCAGTGCTACGACTCTTGTCAA 59.378 45.455 0.00 0.00 43.06 3.18
2693 2903 2.030185 GTGCTACGACTCTTGTCAAGGA 60.030 50.000 12.66 0.00 43.06 3.36
2697 2907 4.510340 GCTACGACTCTTGTCAAGGAAAAA 59.490 41.667 12.66 0.00 43.06 1.94
2703 2913 5.279006 GACTCTTGTCAAGGAAAAATTCCCC 60.279 44.000 12.66 0.00 45.32 4.81
2713 2923 2.409948 AAAATTCCCCGCAGAGAGAG 57.590 50.000 0.00 0.00 0.00 3.20
2714 2924 0.543749 AAATTCCCCGCAGAGAGAGG 59.456 55.000 0.00 0.00 36.87 3.69
2715 2925 0.325671 AATTCCCCGCAGAGAGAGGA 60.326 55.000 0.00 0.00 40.01 3.71
2716 2926 0.105246 ATTCCCCGCAGAGAGAGGAT 60.105 55.000 0.00 0.00 40.01 3.24
2717 2927 1.045350 TTCCCCGCAGAGAGAGGATG 61.045 60.000 0.00 0.00 40.01 3.51
2718 2928 1.760086 CCCCGCAGAGAGAGGATGT 60.760 63.158 0.00 0.00 40.01 3.06
2719 2929 1.440893 CCCGCAGAGAGAGGATGTG 59.559 63.158 0.00 0.00 40.01 3.21
2720 2930 1.227205 CCGCAGAGAGAGGATGTGC 60.227 63.158 0.00 0.00 40.01 4.57
2721 2931 1.514553 CGCAGAGAGAGGATGTGCA 59.485 57.895 0.00 0.00 36.79 4.57
2722 2932 0.104487 CGCAGAGAGAGGATGTGCAT 59.896 55.000 0.00 0.00 36.79 3.96
2723 2933 1.584175 GCAGAGAGAGGATGTGCATG 58.416 55.000 0.00 0.00 36.95 4.06
2724 2934 1.584175 CAGAGAGAGGATGTGCATGC 58.416 55.000 11.82 11.82 0.00 4.06
2725 2935 1.134491 CAGAGAGAGGATGTGCATGCA 60.134 52.381 18.46 18.46 0.00 3.96
2726 2936 1.139256 AGAGAGAGGATGTGCATGCAG 59.861 52.381 23.41 0.00 0.00 4.41
2727 2937 0.910338 AGAGAGGATGTGCATGCAGT 59.090 50.000 23.41 13.39 0.00 4.40
2728 2938 1.015109 GAGAGGATGTGCATGCAGTG 58.985 55.000 23.41 0.00 0.00 3.66
2729 2939 0.616891 AGAGGATGTGCATGCAGTGA 59.383 50.000 23.41 8.66 0.00 3.41
2730 2940 1.212195 AGAGGATGTGCATGCAGTGAT 59.788 47.619 23.41 13.55 0.00 3.06
2731 2941 2.436911 AGAGGATGTGCATGCAGTGATA 59.563 45.455 23.41 5.80 0.00 2.15
2732 2942 3.072622 AGAGGATGTGCATGCAGTGATAT 59.927 43.478 23.41 10.61 0.00 1.63
2733 2943 3.146847 AGGATGTGCATGCAGTGATATG 58.853 45.455 23.41 0.00 0.00 1.78
2734 2944 2.228103 GGATGTGCATGCAGTGATATGG 59.772 50.000 23.41 0.00 0.00 2.74
2735 2945 1.026584 TGTGCATGCAGTGATATGGC 58.973 50.000 23.41 6.40 0.00 4.40
2736 2946 0.313043 GTGCATGCAGTGATATGGCC 59.687 55.000 23.41 0.56 0.00 5.36
2737 2947 0.106619 TGCATGCAGTGATATGGCCA 60.107 50.000 18.46 8.56 0.00 5.36
2738 2948 0.313043 GCATGCAGTGATATGGCCAC 59.687 55.000 8.16 0.00 34.89 5.01
2739 2949 1.682740 CATGCAGTGATATGGCCACA 58.317 50.000 8.16 0.00 37.01 4.17
2740 2950 1.335810 CATGCAGTGATATGGCCACAC 59.664 52.381 8.16 12.86 37.01 3.82
2741 2951 0.394216 TGCAGTGATATGGCCACACC 60.394 55.000 18.61 7.17 37.01 4.16
2742 2952 1.103398 GCAGTGATATGGCCACACCC 61.103 60.000 18.61 8.81 37.83 4.61
2743 2953 0.466189 CAGTGATATGGCCACACCCC 60.466 60.000 18.61 3.70 37.83 4.95
2744 2954 0.918799 AGTGATATGGCCACACCCCA 60.919 55.000 18.61 6.25 37.83 4.96
2745 2955 0.033601 GTGATATGGCCACACCCCAA 60.034 55.000 8.16 0.00 37.83 4.12
2746 2956 0.258484 TGATATGGCCACACCCCAAG 59.742 55.000 8.16 0.00 37.83 3.61
2747 2957 0.468029 GATATGGCCACACCCCAAGG 60.468 60.000 8.16 0.00 37.83 3.61
2748 2958 0.923729 ATATGGCCACACCCCAAGGA 60.924 55.000 8.16 0.00 37.83 3.36
2749 2959 1.143329 TATGGCCACACCCCAAGGAA 61.143 55.000 8.16 0.00 37.83 3.36
2750 2960 2.283173 GGCCACACCCCAAGGAAG 60.283 66.667 0.00 0.00 36.73 3.46
2751 2961 2.840753 GGCCACACCCCAAGGAAGA 61.841 63.158 0.00 0.00 36.73 2.87
2752 2962 1.303643 GCCACACCCCAAGGAAGAG 60.304 63.158 0.00 0.00 36.73 2.85
2753 2963 1.303643 CCACACCCCAAGGAAGAGC 60.304 63.158 0.00 0.00 36.73 4.09
2754 2964 1.455849 CACACCCCAAGGAAGAGCA 59.544 57.895 0.00 0.00 36.73 4.26
2755 2965 0.178992 CACACCCCAAGGAAGAGCAA 60.179 55.000 0.00 0.00 36.73 3.91
2756 2966 0.779997 ACACCCCAAGGAAGAGCAAT 59.220 50.000 0.00 0.00 36.73 3.56
2757 2967 1.180029 CACCCCAAGGAAGAGCAATG 58.820 55.000 0.00 0.00 36.73 2.82
2758 2968 1.075601 ACCCCAAGGAAGAGCAATGA 58.924 50.000 0.00 0.00 36.73 2.57
2759 2969 1.005215 ACCCCAAGGAAGAGCAATGAG 59.995 52.381 0.00 0.00 36.73 2.90
2760 2970 1.283029 CCCCAAGGAAGAGCAATGAGA 59.717 52.381 0.00 0.00 33.47 3.27
2813 3106 4.109766 TCTCGTCAAGTTGTACACTGTTG 58.890 43.478 2.11 0.00 35.12 3.33
2815 3108 2.350192 CGTCAAGTTGTACACTGTTGCA 59.650 45.455 2.11 0.00 35.12 4.08
2818 3111 1.295792 AGTTGTACACTGTTGCACCG 58.704 50.000 0.00 0.00 32.83 4.94
2820 3113 1.004292 GTTGTACACTGTTGCACCGTC 60.004 52.381 0.00 0.00 0.00 4.79
2831 3124 2.033194 GCACCGTCTGCTAACCACC 61.033 63.158 0.00 0.00 43.33 4.61
2833 3126 2.125673 CCGTCTGCTAACCACCGG 60.126 66.667 0.00 0.00 0.00 5.28
2834 3127 2.642254 CCGTCTGCTAACCACCGGA 61.642 63.158 9.46 0.00 35.78 5.14
2835 3128 1.445582 CGTCTGCTAACCACCGGAC 60.446 63.158 9.46 0.00 34.72 4.79
2836 3129 1.079336 GTCTGCTAACCACCGGACC 60.079 63.158 9.46 0.00 32.48 4.46
2838 3131 0.907704 TCTGCTAACCACCGGACCAT 60.908 55.000 9.46 0.00 0.00 3.55
2841 3134 0.462047 GCTAACCACCGGACCATCAG 60.462 60.000 9.46 0.00 0.00 2.90
2926 3235 8.890410 TCAAGTACCTACTTACTACATTCCTT 57.110 34.615 0.00 0.00 44.19 3.36
2937 3246 8.962679 ACTTACTACATTCCTTGAAACAAACAA 58.037 29.630 0.00 0.00 0.00 2.83
2938 3247 9.796120 CTTACTACATTCCTTGAAACAAACAAA 57.204 29.630 0.00 0.00 0.00 2.83
2939 3248 9.575783 TTACTACATTCCTTGAAACAAACAAAC 57.424 29.630 0.00 0.00 0.00 2.93
2940 3249 7.607250 ACTACATTCCTTGAAACAAACAAACA 58.393 30.769 0.00 0.00 0.00 2.83
2976 3285 6.596621 ACTCTAAAGGTTTCTTTCTCAAGCT 58.403 36.000 0.00 0.00 41.82 3.74
2989 3298 0.603439 TCAAGCTGCTGCATTGACGA 60.603 50.000 18.42 1.92 42.74 4.20
2994 3303 0.524816 CTGCTGCATTGACGATTGGC 60.525 55.000 1.31 0.00 0.00 4.52
3003 3312 0.959867 TGACGATTGGCCACATGGTG 60.960 55.000 3.88 0.00 37.57 4.17
3007 3316 0.532115 GATTGGCCACATGGTGAACC 59.468 55.000 3.88 0.00 35.23 3.62
3017 3326 2.166829 CATGGTGAACCGGGAATCAAA 58.833 47.619 6.32 0.00 39.43 2.69
3019 3328 0.885879 GGTGAACCGGGAATCAAACC 59.114 55.000 6.32 2.35 0.00 3.27
3021 3330 1.539827 GTGAACCGGGAATCAAACCAG 59.460 52.381 6.32 0.00 0.00 4.00
3025 3334 1.185315 CCGGGAATCAAACCAGCAAT 58.815 50.000 0.00 0.00 0.00 3.56
3032 3341 4.380867 GGAATCAAACCAGCAATTGACGAT 60.381 41.667 10.34 0.00 38.29 3.73
3045 3354 5.277683 GCAATTGACGATCTGCTGATAATGT 60.278 40.000 10.34 5.78 32.19 2.71
3059 3368 0.179100 TAATGTGGCTCGCTCTCTGC 60.179 55.000 0.00 0.00 38.57 4.26
3070 3379 3.669036 CTCTCTGCCGTGGTCGTCG 62.669 68.421 0.00 0.00 35.01 5.12
3101 3410 1.493950 GCATGGCGAGAATGGTCGAG 61.494 60.000 0.00 0.00 42.85 4.04
3152 3461 2.534298 CAAATTGCAACCGTGTCAACA 58.466 42.857 0.00 0.00 0.00 3.33
3154 3463 0.383949 ATTGCAACCGTGTCAACACC 59.616 50.000 0.00 0.00 43.66 4.16
3156 3465 2.841160 GCAACCGTGTCAACACCCC 61.841 63.158 7.66 0.00 43.66 4.95
3157 3466 2.190841 CAACCGTGTCAACACCCCC 61.191 63.158 7.66 0.00 43.66 5.40
3204 3513 0.521735 AAAATGACGCCTCTTTCGCC 59.478 50.000 0.00 0.00 0.00 5.54
3205 3514 1.635663 AAATGACGCCTCTTTCGCCG 61.636 55.000 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 4.379499 GGTTGTGTAAGGCTTTGCAGATAC 60.379 45.833 4.45 0.00 29.18 2.24
56 62 5.446143 TGTATTGGTTGTGTAAGGCTTTG 57.554 39.130 4.45 0.00 0.00 2.77
269 275 0.679505 GTACGGCCATCAGCAGGATA 59.320 55.000 2.24 0.00 46.50 2.59
313 319 2.554462 ACGACCATGAGTAGGATCATCG 59.446 50.000 0.00 0.00 37.84 3.84
388 419 2.572290 AGTCCACCAAAAGGAAACTCG 58.428 47.619 0.00 0.00 42.68 4.18
491 533 8.812972 ACAGATCAGTACTTAGATTGTTAACCA 58.187 33.333 2.48 0.00 0.00 3.67
574 616 6.126863 TCAGAGAAGACCAAACATAACCAT 57.873 37.500 0.00 0.00 0.00 3.55
703 750 1.076024 AGGCCATGTTTGGTGATGTCT 59.924 47.619 5.01 0.00 45.57 3.41
718 767 2.879756 GCACACAAAGAATCCTAGGCCA 60.880 50.000 5.01 0.00 0.00 5.36
801 850 6.058833 TGTTTGATTCCTACACTAAGCAACA 58.941 36.000 0.00 0.00 31.32 3.33
808 857 5.046591 CAGGGTCTGTTTGATTCCTACACTA 60.047 44.000 0.00 0.00 32.56 2.74
811 860 3.650942 ACAGGGTCTGTTTGATTCCTACA 59.349 43.478 0.00 0.00 42.59 2.74
827 876 3.897505 CCATTCAAGGAAAGAAACAGGGT 59.102 43.478 0.00 0.00 0.00 4.34
864 957 6.349243 AGAAATCATCACCAAAGCATGAAA 57.651 33.333 0.00 0.00 30.43 2.69
870 963 5.967674 CACGATAAGAAATCATCACCAAAGC 59.032 40.000 0.00 0.00 0.00 3.51
1112 1211 0.179111 TGCTAGGGCAATCGACTTCG 60.179 55.000 0.00 0.00 46.36 3.79
1289 1388 5.009610 GGCATATCAACCACAATACGGAAAT 59.990 40.000 0.00 0.00 0.00 2.17
1303 1402 5.824904 AGATGAAACAGTGGCATATCAAC 57.175 39.130 0.00 0.00 0.00 3.18
1390 1491 7.337942 AGGAAGTTTTTACAGGAAGCATATGAG 59.662 37.037 6.97 0.00 0.00 2.90
1504 1606 3.947834 CAGCTAGTGGGGTCCTATTTTTG 59.052 47.826 0.00 0.00 0.00 2.44
1519 1621 2.572284 GAACGGTCGCCAGCTAGT 59.428 61.111 0.00 0.00 0.00 2.57
1552 1654 4.005316 CGTTGTTTACGTTTCGCAAATG 57.995 40.909 0.00 0.00 45.14 2.32
1564 1666 0.382515 TGCAAGTGGCCGTTGTTTAC 59.617 50.000 16.74 0.00 43.89 2.01
1565 1667 0.382515 GTGCAAGTGGCCGTTGTTTA 59.617 50.000 16.74 4.15 43.89 2.01
1566 1668 1.140804 GTGCAAGTGGCCGTTGTTT 59.859 52.632 16.74 0.00 43.89 2.83
1567 1669 2.781158 GGTGCAAGTGGCCGTTGTT 61.781 57.895 16.74 0.00 43.89 2.83
1568 1670 3.216292 GGTGCAAGTGGCCGTTGT 61.216 61.111 16.74 0.00 43.89 3.32
1569 1671 3.215568 TGGTGCAAGTGGCCGTTG 61.216 61.111 12.35 12.35 43.89 4.10
1570 1672 3.216292 GTGGTGCAAGTGGCCGTT 61.216 61.111 0.00 0.00 43.89 4.44
1571 1673 4.189580 AGTGGTGCAAGTGGCCGT 62.190 61.111 0.00 0.00 43.89 5.68
1572 1674 3.663176 CAGTGGTGCAAGTGGCCG 61.663 66.667 0.00 0.00 43.89 6.13
1573 1675 3.297620 CCAGTGGTGCAAGTGGCC 61.298 66.667 0.00 0.00 43.89 5.36
1574 1676 2.203337 TCCAGTGGTGCAAGTGGC 60.203 61.111 9.54 0.00 40.04 5.01
1575 1677 0.396435 TACTCCAGTGGTGCAAGTGG 59.604 55.000 9.54 5.97 41.37 4.00
1576 1678 2.254546 TTACTCCAGTGGTGCAAGTG 57.745 50.000 9.54 0.00 0.00 3.16
1577 1679 3.508845 AATTACTCCAGTGGTGCAAGT 57.491 42.857 9.54 7.77 0.00 3.16
1578 1680 4.142600 GCTTAATTACTCCAGTGGTGCAAG 60.143 45.833 9.54 1.09 0.00 4.01
1579 1681 3.756434 GCTTAATTACTCCAGTGGTGCAA 59.244 43.478 9.54 4.01 0.00 4.08
1580 1682 3.244735 TGCTTAATTACTCCAGTGGTGCA 60.245 43.478 9.54 0.00 0.00 4.57
1581 1683 3.343617 TGCTTAATTACTCCAGTGGTGC 58.656 45.455 9.54 2.21 0.00 5.01
1582 1684 4.336433 CCATGCTTAATTACTCCAGTGGTG 59.664 45.833 9.54 9.64 0.00 4.17
1583 1685 4.018415 ACCATGCTTAATTACTCCAGTGGT 60.018 41.667 9.54 0.00 0.00 4.16
1584 1686 4.336433 CACCATGCTTAATTACTCCAGTGG 59.664 45.833 1.40 1.40 0.00 4.00
1585 1687 4.201950 GCACCATGCTTAATTACTCCAGTG 60.202 45.833 0.00 0.00 40.96 3.66
1586 1688 3.947834 GCACCATGCTTAATTACTCCAGT 59.052 43.478 0.00 0.00 40.96 4.00
1587 1689 3.947196 TGCACCATGCTTAATTACTCCAG 59.053 43.478 2.02 0.00 45.31 3.86
1588 1690 3.947196 CTGCACCATGCTTAATTACTCCA 59.053 43.478 2.02 0.00 45.31 3.86
1589 1691 3.947834 ACTGCACCATGCTTAATTACTCC 59.052 43.478 2.02 0.00 45.31 3.85
1590 1692 5.567138 AACTGCACCATGCTTAATTACTC 57.433 39.130 2.02 0.00 45.31 2.59
1591 1693 5.982890 AAACTGCACCATGCTTAATTACT 57.017 34.783 2.02 0.00 45.31 2.24
1644 1746 4.180723 AGTGGGGTCCTATTTTTGTAGGA 58.819 43.478 0.00 0.00 46.14 2.94
1645 1747 4.586306 AGTGGGGTCCTATTTTTGTAGG 57.414 45.455 0.00 0.00 42.19 3.18
1646 1748 5.104485 AGCTAGTGGGGTCCTATTTTTGTAG 60.104 44.000 0.00 0.00 0.00 2.74
1647 1749 4.786454 AGCTAGTGGGGTCCTATTTTTGTA 59.214 41.667 0.00 0.00 0.00 2.41
1648 1750 3.591977 AGCTAGTGGGGTCCTATTTTTGT 59.408 43.478 0.00 0.00 0.00 2.83
1649 1751 3.947834 CAGCTAGTGGGGTCCTATTTTTG 59.052 47.826 0.00 0.00 0.00 2.44
1650 1752 3.053619 CCAGCTAGTGGGGTCCTATTTTT 60.054 47.826 0.00 0.00 43.63 1.94
1651 1753 2.509964 CCAGCTAGTGGGGTCCTATTTT 59.490 50.000 0.00 0.00 43.63 1.82
1652 1754 2.127708 CCAGCTAGTGGGGTCCTATTT 58.872 52.381 0.00 0.00 43.63 1.40
1653 1755 1.807814 CCAGCTAGTGGGGTCCTATT 58.192 55.000 0.00 0.00 43.63 1.73
1654 1756 3.560226 CCAGCTAGTGGGGTCCTAT 57.440 57.895 0.00 0.00 43.63 2.57
1663 1765 1.805945 GAACGGTCGCCAGCTAGTG 60.806 63.158 0.00 0.00 0.00 2.74
1664 1766 2.572284 GAACGGTCGCCAGCTAGT 59.428 61.111 0.00 0.00 0.00 2.57
1665 1767 2.579787 CGAACGGTCGCCAGCTAG 60.580 66.667 11.19 0.00 41.08 3.42
1674 1776 2.202756 CCTAGCTGGCGAACGGTC 60.203 66.667 0.00 0.00 0.00 4.79
1675 1777 3.771160 CCCTAGCTGGCGAACGGT 61.771 66.667 0.00 0.00 0.00 4.83
1676 1778 4.530857 CCCCTAGCTGGCGAACGG 62.531 72.222 0.00 0.00 0.00 4.44
1677 1779 3.771160 ACCCCTAGCTGGCGAACG 61.771 66.667 0.00 0.00 0.00 3.95
1678 1780 2.125106 CACCCCTAGCTGGCGAAC 60.125 66.667 0.00 0.00 0.00 3.95
1679 1781 3.399181 CCACCCCTAGCTGGCGAA 61.399 66.667 0.00 0.00 0.00 4.70
1683 1785 1.039233 CAAATGCCACCCCTAGCTGG 61.039 60.000 0.00 0.00 0.00 4.85
1684 1786 1.669999 GCAAATGCCACCCCTAGCTG 61.670 60.000 0.00 0.00 34.31 4.24
1685 1787 1.380380 GCAAATGCCACCCCTAGCT 60.380 57.895 0.00 0.00 34.31 3.32
1686 1788 2.774799 CGCAAATGCCACCCCTAGC 61.775 63.158 0.00 0.00 37.91 3.42
1687 1789 0.679640 TTCGCAAATGCCACCCCTAG 60.680 55.000 0.00 0.00 37.91 3.02
1688 1790 0.033601 ATTCGCAAATGCCACCCCTA 60.034 50.000 0.00 0.00 37.91 3.53
1689 1791 0.904394 AATTCGCAAATGCCACCCCT 60.904 50.000 0.00 0.00 37.91 4.79
1690 1792 0.740516 CAATTCGCAAATGCCACCCC 60.741 55.000 0.00 0.00 37.91 4.95
1691 1793 1.360931 GCAATTCGCAAATGCCACCC 61.361 55.000 0.00 0.00 41.79 4.61
1692 1794 1.360931 GGCAATTCGCAAATGCCACC 61.361 55.000 17.70 0.00 45.17 4.61
1735 1837 7.605691 CACTAAAATTAAACAAATGCCATCCCA 59.394 33.333 0.00 0.00 0.00 4.37
1771 1893 1.001181 CTGATGGTGGCAGTTTTTGGG 59.999 52.381 0.00 0.00 0.00 4.12
1930 2052 5.808366 TGGAAGAGCCTATACCAGTTATG 57.192 43.478 0.00 0.00 37.63 1.90
1931 2053 7.394144 AAATGGAAGAGCCTATACCAGTTAT 57.606 36.000 0.00 0.00 37.20 1.89
1977 2100 8.468399 TGTTTTCAGCATAATAATTGAGATGCA 58.532 29.630 17.36 0.00 45.72 3.96
2015 2138 5.513495 CGTAACAGTAGAGATGCAGAAGAAC 59.487 44.000 0.00 0.00 0.00 3.01
2042 2165 7.822334 TCCTAAAGAGCGAGATAATTTGTTTCA 59.178 33.333 0.00 0.00 0.00 2.69
2067 2192 5.065988 TGCTTGTTTGGAAAGTAGAACAGTC 59.934 40.000 0.00 0.00 33.97 3.51
2075 2214 9.515226 AAGAGTTATATGCTTGTTTGGAAAGTA 57.485 29.630 0.00 0.00 0.00 2.24
2278 2419 2.096496 CGTGCTCATTCCATTTGAGACC 59.904 50.000 4.93 0.00 42.63 3.85
2279 2420 2.744202 ACGTGCTCATTCCATTTGAGAC 59.256 45.455 4.93 0.60 42.63 3.36
2282 2423 2.503331 ACACGTGCTCATTCCATTTGA 58.497 42.857 17.22 0.00 0.00 2.69
2284 2425 2.622942 ACAACACGTGCTCATTCCATTT 59.377 40.909 17.22 0.00 0.00 2.32
2338 2479 0.868406 GTCAACAGAAGGTGGCTTCG 59.132 55.000 0.00 0.00 38.31 3.79
2502 2711 9.275572 ACGGATAAAGTATGGGGTAATATACAT 57.724 33.333 0.00 0.00 33.30 2.29
2504 2713 7.983484 CCACGGATAAAGTATGGGGTAATATAC 59.017 40.741 0.00 0.00 0.00 1.47
2526 2735 2.772568 TGCAATTGACAGAAACCACG 57.227 45.000 10.34 0.00 0.00 4.94
2550 2759 6.149142 AGCAATTGAAAGAAAGCACAAAAACA 59.851 30.769 10.34 0.00 0.00 2.83
2559 2768 5.614013 GCAATGTCAGCAATTGAAAGAAAGC 60.614 40.000 10.34 0.00 37.61 3.51
2572 2781 0.961019 GTCCCTTTGCAATGTCAGCA 59.039 50.000 0.00 0.00 40.85 4.41
2622 2831 2.782192 GTCCGAAGATTACATCGTGACG 59.218 50.000 0.00 0.00 35.83 4.35
2632 2841 5.957798 ACACGTTAGATTGTCCGAAGATTA 58.042 37.500 0.00 0.00 0.00 1.75
2659 2868 1.746220 CGTAGCACTGAAGGAGTAGCT 59.254 52.381 0.00 0.00 40.22 3.32
2693 2903 2.619074 CCTCTCTCTGCGGGGAATTTTT 60.619 50.000 0.00 0.00 0.00 1.94
2697 2907 0.105246 ATCCTCTCTCTGCGGGGAAT 60.105 55.000 0.00 0.00 0.00 3.01
2703 2913 0.104487 ATGCACATCCTCTCTCTGCG 59.896 55.000 0.00 0.00 0.00 5.18
2713 2923 2.228103 CCATATCACTGCATGCACATCC 59.772 50.000 18.46 0.00 0.00 3.51
2714 2924 2.351447 GCCATATCACTGCATGCACATC 60.351 50.000 18.46 0.00 0.00 3.06
2715 2925 1.611977 GCCATATCACTGCATGCACAT 59.388 47.619 18.46 11.49 0.00 3.21
2716 2926 1.026584 GCCATATCACTGCATGCACA 58.973 50.000 18.46 3.75 0.00 4.57
2717 2927 0.313043 GGCCATATCACTGCATGCAC 59.687 55.000 18.46 3.18 0.00 4.57
2718 2928 0.106619 TGGCCATATCACTGCATGCA 60.107 50.000 21.29 21.29 0.00 3.96
2719 2929 0.313043 GTGGCCATATCACTGCATGC 59.687 55.000 9.72 11.82 32.78 4.06
2720 2930 1.335810 GTGTGGCCATATCACTGCATG 59.664 52.381 9.72 0.00 36.21 4.06
2721 2931 1.683943 GTGTGGCCATATCACTGCAT 58.316 50.000 9.72 0.00 36.21 3.96
2722 2932 0.394216 GGTGTGGCCATATCACTGCA 60.394 55.000 20.70 4.76 36.21 4.41
2723 2933 1.103398 GGGTGTGGCCATATCACTGC 61.103 60.000 20.70 8.33 39.65 4.40
2724 2934 0.466189 GGGGTGTGGCCATATCACTG 60.466 60.000 20.70 0.00 39.65 3.66
2725 2935 0.918799 TGGGGTGTGGCCATATCACT 60.919 55.000 16.80 0.00 39.65 3.41
2726 2936 0.033601 TTGGGGTGTGGCCATATCAC 60.034 55.000 15.38 12.07 39.65 3.06
2727 2937 0.258484 CTTGGGGTGTGGCCATATCA 59.742 55.000 15.38 2.31 39.65 2.15
2728 2938 0.468029 CCTTGGGGTGTGGCCATATC 60.468 60.000 9.72 6.41 39.65 1.63
2729 2939 0.923729 TCCTTGGGGTGTGGCCATAT 60.924 55.000 9.72 0.00 39.65 1.78
2730 2940 1.143329 TTCCTTGGGGTGTGGCCATA 61.143 55.000 9.72 1.91 39.65 2.74
2731 2941 2.445492 CTTCCTTGGGGTGTGGCCAT 62.445 60.000 9.72 0.00 39.65 4.40
2732 2942 3.106609 TTCCTTGGGGTGTGGCCA 61.107 61.111 0.00 0.00 39.65 5.36
2733 2943 2.283173 CTTCCTTGGGGTGTGGCC 60.283 66.667 0.00 0.00 0.00 5.36
2734 2944 1.303643 CTCTTCCTTGGGGTGTGGC 60.304 63.158 0.00 0.00 0.00 5.01
2735 2945 1.303643 GCTCTTCCTTGGGGTGTGG 60.304 63.158 0.00 0.00 0.00 4.17
2736 2946 0.178992 TTGCTCTTCCTTGGGGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
2737 2947 0.779997 ATTGCTCTTCCTTGGGGTGT 59.220 50.000 0.00 0.00 0.00 4.16
2738 2948 1.180029 CATTGCTCTTCCTTGGGGTG 58.820 55.000 0.00 0.00 0.00 4.61
2739 2949 1.005215 CTCATTGCTCTTCCTTGGGGT 59.995 52.381 0.00 0.00 0.00 4.95
2740 2950 1.283029 TCTCATTGCTCTTCCTTGGGG 59.717 52.381 0.00 0.00 0.00 4.96
2741 2951 2.795231 TCTCATTGCTCTTCCTTGGG 57.205 50.000 0.00 0.00 0.00 4.12
2742 2952 5.184479 TCAAATTCTCATTGCTCTTCCTTGG 59.816 40.000 0.00 0.00 0.00 3.61
2743 2953 6.263516 TCAAATTCTCATTGCTCTTCCTTG 57.736 37.500 0.00 0.00 0.00 3.61
2744 2954 5.105837 GCTCAAATTCTCATTGCTCTTCCTT 60.106 40.000 0.00 0.00 0.00 3.36
2745 2955 4.398673 GCTCAAATTCTCATTGCTCTTCCT 59.601 41.667 0.00 0.00 0.00 3.36
2746 2956 4.157289 TGCTCAAATTCTCATTGCTCTTCC 59.843 41.667 0.00 0.00 0.00 3.46
2747 2957 5.306532 TGCTCAAATTCTCATTGCTCTTC 57.693 39.130 0.00 0.00 0.00 2.87
2748 2958 4.380655 GCTGCTCAAATTCTCATTGCTCTT 60.381 41.667 0.00 0.00 0.00 2.85
2749 2959 3.128938 GCTGCTCAAATTCTCATTGCTCT 59.871 43.478 0.00 0.00 0.00 4.09
2750 2960 3.128938 AGCTGCTCAAATTCTCATTGCTC 59.871 43.478 0.00 0.00 0.00 4.26
2751 2961 3.090037 AGCTGCTCAAATTCTCATTGCT 58.910 40.909 0.00 0.00 0.00 3.91
2752 2962 3.179830 CAGCTGCTCAAATTCTCATTGC 58.820 45.455 0.00 0.00 0.00 3.56
2753 2963 3.770666 CCAGCTGCTCAAATTCTCATTG 58.229 45.455 8.66 0.00 0.00 2.82
2754 2964 2.165845 GCCAGCTGCTCAAATTCTCATT 59.834 45.455 8.66 0.00 36.87 2.57
2755 2965 1.749634 GCCAGCTGCTCAAATTCTCAT 59.250 47.619 8.66 0.00 36.87 2.90
2756 2966 1.171308 GCCAGCTGCTCAAATTCTCA 58.829 50.000 8.66 0.00 36.87 3.27
2785 2995 4.150098 GTGTACAACTTGACGAGATGGAAC 59.850 45.833 0.00 3.64 32.79 3.62
2815 3108 2.654877 CGGTGGTTAGCAGACGGT 59.345 61.111 1.37 0.00 0.00 4.83
2818 3111 1.079336 GGTCCGGTGGTTAGCAGAC 60.079 63.158 0.00 0.00 32.34 3.51
2820 3113 0.462047 GATGGTCCGGTGGTTAGCAG 60.462 60.000 0.00 0.00 0.00 4.24
2831 3124 0.803768 CTGTCGAAGCTGATGGTCCG 60.804 60.000 0.00 0.00 0.00 4.79
2833 3126 0.460987 CCCTGTCGAAGCTGATGGTC 60.461 60.000 0.00 0.00 0.00 4.02
2834 3127 0.904865 TCCCTGTCGAAGCTGATGGT 60.905 55.000 0.00 0.00 0.00 3.55
2835 3128 0.460987 GTCCCTGTCGAAGCTGATGG 60.461 60.000 0.00 0.00 0.00 3.51
2836 3129 0.247460 TGTCCCTGTCGAAGCTGATG 59.753 55.000 0.00 0.00 0.00 3.07
2838 3131 1.666011 GTGTCCCTGTCGAAGCTGA 59.334 57.895 0.00 0.00 0.00 4.26
2841 3134 3.112709 GCGTGTCCCTGTCGAAGC 61.113 66.667 0.00 0.00 0.00 3.86
2976 3285 1.507630 GCCAATCGTCAATGCAGCA 59.492 52.632 0.00 0.00 0.00 4.41
2989 3298 1.250154 CGGTTCACCATGTGGCCAAT 61.250 55.000 7.24 0.00 39.32 3.16
2994 3303 0.323360 ATTCCCGGTTCACCATGTGG 60.323 55.000 0.00 0.00 42.17 4.17
3003 3312 0.526211 GCTGGTTTGATTCCCGGTTC 59.474 55.000 0.00 0.00 0.00 3.62
3007 3316 2.230992 TCAATTGCTGGTTTGATTCCCG 59.769 45.455 0.00 0.00 0.00 5.14
3017 3326 1.089920 GCAGATCGTCAATTGCTGGT 58.910 50.000 0.00 0.00 33.88 4.00
3021 3330 4.801147 TTATCAGCAGATCGTCAATTGC 57.199 40.909 0.00 0.00 35.67 3.56
3025 3334 4.122046 CCACATTATCAGCAGATCGTCAA 58.878 43.478 0.00 0.00 35.67 3.18
3032 3341 1.807755 GCGAGCCACATTATCAGCAGA 60.808 52.381 0.00 0.00 0.00 4.26
3059 3368 2.880879 CATCAGCGACGACCACGG 60.881 66.667 0.00 0.00 44.46 4.94
3168 3477 6.038356 GTCATTTTTCTTGGATGCTATGGTG 58.962 40.000 0.00 0.00 0.00 4.17
3179 3488 3.923017 AAGAGGCGTCATTTTTCTTGG 57.077 42.857 9.41 0.00 0.00 3.61
3180 3489 3.908382 CGAAAGAGGCGTCATTTTTCTTG 59.092 43.478 9.41 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.