Multiple sequence alignment - TraesCS5D01G491300

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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 TraesCS5D01G491300 chr5D 100.000 2402 0 0 1 2402 525301605 525304006 0.000000e+00 4436.0
1 TraesCS5D01G491300 chr5D 81.476 664 87 20 766 1402 525250067 525250721 1.650000e-141 512.0
2 TraesCS5D01G491300 chr5D 80.157 635 81 25 996 1589 525317344 525317974 1.320000e-117 433.0
3 TraesCS5D01G491300 chr5A 89.388 735 63 8 745 1469 651744154 651744883 0.000000e+00 911.0
4 TraesCS5D01G491300 chr5A 80.192 626 72 22 1001 1582 651755060 651755677 2.850000e-114 422.0
5 TraesCS5D01G491300 chr5A 84.742 426 53 7 990 1403 651588588 651589013 1.330000e-112 416.0
6 TraesCS5D01G491300 chr5A 88.254 315 23 4 14 322 651741096 651741402 4.880000e-97 364.0
7 TraesCS5D01G491300 chr5A 89.256 242 25 1 2161 2402 651748086 651748326 3.880000e-78 302.0
8 TraesCS5D01G491300 chr5A 90.210 143 3 1 609 751 651743244 651743375 2.450000e-40 176.0
9 TraesCS5D01G491300 chr5A 90.909 77 6 1 1603 1678 651744958 651745034 4.220000e-18 102.0
10 TraesCS5D01G491300 chr5B 92.476 412 27 4 1993 2402 659623039 659623448 9.570000e-164 586.0
11 TraesCS5D01G491300 chr5B 80.173 807 109 29 631 1403 659604288 659605077 7.500000e-155 556.0
12 TraesCS5D01G491300 chr5B 82.459 610 73 22 996 1583 659679387 659679984 9.910000e-139 503.0
13 TraesCS5D01G491300 chr5B 94.118 323 19 0 2 324 659622428 659622750 2.150000e-135 492.0
14 TraesCS5D01G491300 chr5B 76.836 967 145 51 636 1561 659635405 659636333 2.800000e-129 472.0
15 TraesCS5D01G491300 chr5B 78.296 622 100 18 994 1583 659715532 659716150 3.770000e-98 368.0
16 TraesCS5D01G491300 chr5B 94.898 98 4 1 498 594 659622866 659622963 4.140000e-33 152.0
17 TraesCS5D01G491300 chr5B 94.737 76 2 1 596 669 659623039 659622964 1.510000e-22 117.0
18 TraesCS5D01G491300 chr1D 78.882 161 25 6 1755 1909 452257972 452257815 1.520000e-17 100.0
19 TraesCS5D01G491300 chrUn 83.495 103 8 6 1803 1899 1047945 1048044 1.180000e-13 87.9
20 TraesCS5D01G491300 chrUn 83.495 103 8 6 1803 1899 329633411 329633312 1.180000e-13 87.9
21 TraesCS5D01G491300 chr1A 83.495 103 8 6 1803 1899 547212671 547212572 1.180000e-13 87.9


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 TraesCS5D01G491300 chr5D 525301605 525304006 2401 False 4436 4436 100.000000 1 2402 1 chr5D.!!$F2 2401
1 TraesCS5D01G491300 chr5D 525250067 525250721 654 False 512 512 81.476000 766 1402 1 chr5D.!!$F1 636
2 TraesCS5D01G491300 chr5D 525317344 525317974 630 False 433 433 80.157000 996 1589 1 chr5D.!!$F3 593
3 TraesCS5D01G491300 chr5A 651755060 651755677 617 False 422 422 80.192000 1001 1582 1 chr5A.!!$F2 581
4 TraesCS5D01G491300 chr5A 651741096 651748326 7230 False 371 911 89.603400 14 2402 5 chr5A.!!$F3 2388
5 TraesCS5D01G491300 chr5B 659604288 659605077 789 False 556 556 80.173000 631 1403 1 chr5B.!!$F1 772
6 TraesCS5D01G491300 chr5B 659679387 659679984 597 False 503 503 82.459000 996 1583 1 chr5B.!!$F3 587
7 TraesCS5D01G491300 chr5B 659635405 659636333 928 False 472 472 76.836000 636 1561 1 chr5B.!!$F2 925
8 TraesCS5D01G491300 chr5B 659622428 659623448 1020 False 410 586 93.830667 2 2402 3 chr5B.!!$F5 2400
9 TraesCS5D01G491300 chr5B 659715532 659716150 618 False 368 368 78.296000 994 1583 1 chr5B.!!$F4 589

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
596 2182 0.031585 CCGCGCACCAGCTTATAGTA 59.968 55.0 8.75 0.0 39.1 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 4838 0.035439 ATGTCTTTTCCGCCGATGGT 60.035 50.0 0.0 0.0 0.0 3.55 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
45 46 4.112341 GGACGTCACGCCGTAGCT 62.112 66.667 18.91 0.00 41.98 3.32
77 78 1.086696 AATTGAGTTGGATCGGCGTG 58.913 50.000 6.85 0.00 0.00 5.34
104 105 4.518970 GCTATGGATCTTTCGAGAGTCTCT 59.481 45.833 17.91 0.70 0.00 3.10
137 138 1.126846 CTTGCCGTGCGAAAGAACTAG 59.873 52.381 0.00 0.00 37.57 2.57
172 175 5.812642 ACCGATGTTAGCTAGTCAGAATTTG 59.187 40.000 0.00 0.00 0.00 2.32
382 388 8.023706 GGAAAGCCATTTTTACACTAGAAGAAG 58.976 37.037 0.00 0.00 0.00 2.85
408 432 7.507829 AGAACAAAATTGGAAATGTGGAATCA 58.492 30.769 0.00 0.00 0.00 2.57
438 462 3.134804 AGGAATAGGAAGTGTGGAATCGG 59.865 47.826 0.00 0.00 0.00 4.18
458 482 3.554960 CGGGTGTGATCTCTTGTTCTTCA 60.555 47.826 0.00 0.00 0.00 3.02
465 489 1.202639 TCTCTTGTTCTTCAGGCGCAA 60.203 47.619 10.83 0.00 0.00 4.85
476 500 3.173240 GGCGCAAGTCTCGTCGTC 61.173 66.667 10.83 0.00 40.30 4.20
479 503 1.439858 CGCAAGTCTCGTCGTCGAA 60.440 57.895 6.19 0.00 45.61 3.71
510 561 7.164858 CGTCAAATCAGTAACGACAAATACTC 58.835 38.462 0.00 0.00 37.31 2.59
529 580 1.521450 CGACCACCACGACCAGTACT 61.521 60.000 0.00 0.00 0.00 2.73
594 2180 1.227263 ACCGCGCACCAGCTTATAG 60.227 57.895 8.75 0.00 39.10 1.31
596 2182 0.031585 CCGCGCACCAGCTTATAGTA 59.968 55.000 8.75 0.00 39.10 1.82
597 2183 1.129326 CGCGCACCAGCTTATAGTAC 58.871 55.000 8.75 0.00 39.10 2.73
598 2184 1.535226 CGCGCACCAGCTTATAGTACA 60.535 52.381 8.75 0.00 39.10 2.90
599 2185 2.755650 GCGCACCAGCTTATAGTACAT 58.244 47.619 0.30 0.00 39.10 2.29
600 2186 3.610821 CGCGCACCAGCTTATAGTACATA 60.611 47.826 8.75 0.00 39.10 2.29
602 2188 4.563184 GCGCACCAGCTTATAGTACATATC 59.437 45.833 0.30 0.00 39.10 1.63
603 2189 5.709966 CGCACCAGCTTATAGTACATATCA 58.290 41.667 0.00 0.00 39.10 2.15
604 2190 5.573282 CGCACCAGCTTATAGTACATATCAC 59.427 44.000 0.00 0.00 39.10 3.06
670 2282 1.817099 CTGGGGAGCAAGCTAAGCG 60.817 63.158 5.53 0.00 37.01 4.68
728 2358 3.569049 CTTCAAGTCGGGTCGCCGT 62.569 63.158 1.33 0.00 34.52 5.68
764 3179 1.313812 AAGTCGTGCCTCCTACCTCG 61.314 60.000 0.00 0.00 0.00 4.63
815 3236 1.002868 CACCTTGCTGCTACCTGCT 60.003 57.895 0.00 0.00 43.37 4.24
833 3254 5.370289 ACCTGCTAGTAGTAGTACTCCATCT 59.630 44.000 13.60 4.58 40.23 2.90
862 3295 0.609131 AAGGCCAACAATCCACGGAG 60.609 55.000 5.01 0.00 0.00 4.63
888 3321 1.617804 CCACATCCACAGCCAATTCCT 60.618 52.381 0.00 0.00 0.00 3.36
889 3322 1.747355 CACATCCACAGCCAATTCCTC 59.253 52.381 0.00 0.00 0.00 3.71
890 3323 1.637553 ACATCCACAGCCAATTCCTCT 59.362 47.619 0.00 0.00 0.00 3.69
901 3334 2.238144 CCAATTCCTCTGAGCTCTTCCA 59.762 50.000 16.19 0.00 0.00 3.53
940 3382 1.013005 CATCTCATCTCGCCCATCGC 61.013 60.000 0.00 0.00 38.27 4.58
976 3418 0.458543 ACGCGCGAACTCTCATTGAT 60.459 50.000 39.36 5.70 0.00 2.57
979 3421 1.863454 GCGCGAACTCTCATTGATCAT 59.137 47.619 12.10 0.00 0.00 2.45
1213 3694 2.356278 GTCATGGGCTTGCCCTCA 59.644 61.111 28.37 12.30 0.00 3.86
1255 3739 2.342279 CGACCAAGAAGGCCACGA 59.658 61.111 5.01 0.00 43.14 4.35
1263 3747 0.603975 AGAAGGCCACGAAGCAGAAC 60.604 55.000 5.01 0.00 0.00 3.01
1265 3749 2.032681 GGCCACGAAGCAGAACCT 59.967 61.111 0.00 0.00 0.00 3.50
1354 3838 3.936203 ACCGCGAACAGGAAGCCA 61.936 61.111 8.23 0.00 0.00 4.75
1361 3845 0.251341 GAACAGGAAGCCACCACCAT 60.251 55.000 0.00 0.00 0.00 3.55
1431 3941 5.047660 GCTGGTTCGATAAGGATAGACATCT 60.048 44.000 0.00 0.00 0.00 2.90
1437 3947 5.648526 TCGATAAGGATAGACATCTAGTGCC 59.351 44.000 0.00 0.00 0.00 5.01
1443 3953 2.386661 AGACATCTAGTGCCGGTTTG 57.613 50.000 1.90 0.00 0.00 2.93
1476 3998 1.396648 TGTGCGCGATTGGATTTGTAG 59.603 47.619 12.10 0.00 0.00 2.74
1482 4004 4.730613 GCGCGATTGGATTTGTAGATTTGT 60.731 41.667 12.10 0.00 0.00 2.83
1497 4019 4.003648 AGATTTGTTGCACACTAGTAGGC 58.996 43.478 10.22 10.22 0.00 3.93
1502 4031 0.037697 TGCACACTAGTAGGCGTTGG 60.038 55.000 11.86 0.00 0.00 3.77
1515 4045 1.673626 GGCGTTGGTCTCGGTTCATTA 60.674 52.381 0.00 0.00 0.00 1.90
1522 4052 4.948847 TGGTCTCGGTTCATTATCTCATG 58.051 43.478 0.00 0.00 0.00 3.07
1526 4056 6.238211 GGTCTCGGTTCATTATCTCATGTTTG 60.238 42.308 0.00 0.00 0.00 2.93
1561 4092 9.878667 TGTAAATATTTAGGACTCGTTCATTCA 57.121 29.630 8.18 0.00 0.00 2.57
1594 4125 9.698309 ACAGAGACTATATATGTGTTATTGTGC 57.302 33.333 0.00 0.00 0.00 4.57
1595 4126 9.920133 CAGAGACTATATATGTGTTATTGTGCT 57.080 33.333 0.00 0.00 0.00 4.40
1630 4161 1.533625 TGGGCGTTGATTTCTGGAAG 58.466 50.000 0.00 0.00 0.00 3.46
1631 4162 1.202879 TGGGCGTTGATTTCTGGAAGT 60.203 47.619 0.00 0.00 33.76 3.01
1633 4164 3.078837 GGGCGTTGATTTCTGGAAGTTA 58.921 45.455 0.00 0.00 33.76 2.24
1637 4168 5.147162 GCGTTGATTTCTGGAAGTTAGTTG 58.853 41.667 0.00 0.00 33.76 3.16
1645 4176 2.875933 CTGGAAGTTAGTTGCACGGAAA 59.124 45.455 0.00 0.00 32.22 3.13
1690 4616 4.776795 AAAAACACTCGGAAACACTGTT 57.223 36.364 0.00 0.00 0.00 3.16
1700 4626 4.082625 TCGGAAACACTGTTCGAAGCTATA 60.083 41.667 0.00 0.00 0.00 1.31
1715 4641 6.622549 CGAAGCTATATTCGGAAACCTAGAT 58.377 40.000 0.00 0.00 46.39 1.98
1716 4642 7.091443 CGAAGCTATATTCGGAAACCTAGATT 58.909 38.462 0.00 1.66 46.39 2.40
1717 4643 7.599245 CGAAGCTATATTCGGAAACCTAGATTT 59.401 37.037 0.00 0.00 46.39 2.17
1719 4645 7.963532 AGCTATATTCGGAAACCTAGATTTCA 58.036 34.615 11.76 0.00 39.85 2.69
1720 4646 8.429641 AGCTATATTCGGAAACCTAGATTTCAA 58.570 33.333 11.76 0.00 39.85 2.69
1721 4647 9.220767 GCTATATTCGGAAACCTAGATTTCAAT 57.779 33.333 11.76 6.21 39.85 2.57
1726 4652 9.627123 ATTCGGAAACCTAGATTTCAATATTCA 57.373 29.630 11.76 0.00 39.85 2.57
1727 4653 9.627123 TTCGGAAACCTAGATTTCAATATTCAT 57.373 29.630 11.76 0.00 39.85 2.57
1755 4681 9.448438 AAGTTATGCATGTGTACTAGATTTCAA 57.552 29.630 10.16 0.00 0.00 2.69
1765 4691 9.109393 TGTGTACTAGATTTCAATTTAGCATCC 57.891 33.333 0.00 0.00 28.89 3.51
1767 4693 9.109393 TGTACTAGATTTCAATTTAGCATCCAC 57.891 33.333 0.00 0.00 28.89 4.02
1768 4694 9.331282 GTACTAGATTTCAATTTAGCATCCACT 57.669 33.333 0.00 0.00 28.89 4.00
1769 4695 8.814038 ACTAGATTTCAATTTAGCATCCACTT 57.186 30.769 0.00 0.00 28.89 3.16
1770 4696 8.897752 ACTAGATTTCAATTTAGCATCCACTTC 58.102 33.333 0.00 0.00 28.89 3.01
1771 4697 7.707624 AGATTTCAATTTAGCATCCACTTCA 57.292 32.000 0.00 0.00 0.00 3.02
1772 4698 8.125978 AGATTTCAATTTAGCATCCACTTCAA 57.874 30.769 0.00 0.00 0.00 2.69
1773 4699 8.755977 AGATTTCAATTTAGCATCCACTTCAAT 58.244 29.630 0.00 0.00 0.00 2.57
1774 4700 8.937634 ATTTCAATTTAGCATCCACTTCAATC 57.062 30.769 0.00 0.00 0.00 2.67
1776 4702 7.707624 TCAATTTAGCATCCACTTCAATCTT 57.292 32.000 0.00 0.00 0.00 2.40
1777 4703 8.125978 TCAATTTAGCATCCACTTCAATCTTT 57.874 30.769 0.00 0.00 0.00 2.52
1778 4704 8.587608 TCAATTTAGCATCCACTTCAATCTTTT 58.412 29.630 0.00 0.00 0.00 2.27
1779 4705 9.211485 CAATTTAGCATCCACTTCAATCTTTTT 57.789 29.630 0.00 0.00 0.00 1.94
1801 4727 6.654793 TTTTTCACTTTCATTGTTTTCCCG 57.345 33.333 0.00 0.00 0.00 5.14
1802 4728 4.993029 TTCACTTTCATTGTTTTCCCGT 57.007 36.364 0.00 0.00 0.00 5.28
1803 4729 4.300189 TCACTTTCATTGTTTTCCCGTG 57.700 40.909 0.00 0.00 0.00 4.94
1804 4730 3.067461 TCACTTTCATTGTTTTCCCGTGG 59.933 43.478 0.00 0.00 0.00 4.94
1805 4731 2.223947 ACTTTCATTGTTTTCCCGTGGC 60.224 45.455 0.00 0.00 0.00 5.01
1806 4732 1.403814 TTCATTGTTTTCCCGTGGCA 58.596 45.000 0.00 0.00 0.00 4.92
1807 4733 1.626686 TCATTGTTTTCCCGTGGCAT 58.373 45.000 0.00 0.00 0.00 4.40
1808 4734 1.543802 TCATTGTTTTCCCGTGGCATC 59.456 47.619 0.00 0.00 0.00 3.91
1809 4735 1.271934 CATTGTTTTCCCGTGGCATCA 59.728 47.619 0.00 0.00 0.00 3.07
1810 4736 1.403814 TTGTTTTCCCGTGGCATCAA 58.596 45.000 0.00 0.00 0.00 2.57
1811 4737 1.403814 TGTTTTCCCGTGGCATCAAA 58.596 45.000 0.00 0.00 0.00 2.69
1812 4738 1.067821 TGTTTTCCCGTGGCATCAAAC 59.932 47.619 0.00 0.00 0.00 2.93
1813 4739 1.067821 GTTTTCCCGTGGCATCAAACA 59.932 47.619 0.00 0.00 0.00 2.83
1814 4740 0.671251 TTTCCCGTGGCATCAAACAC 59.329 50.000 0.00 0.00 0.00 3.32
1818 4744 4.539152 GTGGCATCAAACACGCTG 57.461 55.556 0.00 0.00 0.00 5.18
1819 4745 1.654220 GTGGCATCAAACACGCTGT 59.346 52.632 0.00 0.00 0.00 4.40
1820 4746 0.661187 GTGGCATCAAACACGCTGTG 60.661 55.000 7.07 7.07 39.75 3.66
1821 4747 1.730547 GGCATCAAACACGCTGTGC 60.731 57.895 8.31 0.00 36.98 4.57
1822 4748 1.283793 GCATCAAACACGCTGTGCT 59.716 52.632 8.31 0.00 36.98 4.40
1823 4749 0.516877 GCATCAAACACGCTGTGCTA 59.483 50.000 8.31 0.00 36.98 3.49
1824 4750 1.069296 GCATCAAACACGCTGTGCTAA 60.069 47.619 8.31 0.00 36.98 3.09
1825 4751 2.414559 GCATCAAACACGCTGTGCTAAT 60.415 45.455 8.31 0.00 36.98 1.73
1826 4752 3.825308 CATCAAACACGCTGTGCTAATT 58.175 40.909 8.31 0.00 36.98 1.40
1827 4753 3.536158 TCAAACACGCTGTGCTAATTC 57.464 42.857 8.31 0.00 36.98 2.17
1828 4754 3.138304 TCAAACACGCTGTGCTAATTCT 58.862 40.909 8.31 0.00 36.98 2.40
1829 4755 4.311606 TCAAACACGCTGTGCTAATTCTA 58.688 39.130 8.31 0.00 36.98 2.10
1830 4756 4.935205 TCAAACACGCTGTGCTAATTCTAT 59.065 37.500 8.31 0.00 36.98 1.98
1831 4757 4.864916 AACACGCTGTGCTAATTCTATG 57.135 40.909 8.31 0.00 36.98 2.23
1832 4758 4.123497 ACACGCTGTGCTAATTCTATGA 57.877 40.909 8.31 0.00 36.98 2.15
1833 4759 4.115516 ACACGCTGTGCTAATTCTATGAG 58.884 43.478 8.31 0.00 36.98 2.90
1834 4760 4.142160 ACACGCTGTGCTAATTCTATGAGA 60.142 41.667 8.31 0.00 36.98 3.27
1835 4761 4.987285 CACGCTGTGCTAATTCTATGAGAT 59.013 41.667 0.00 0.00 0.00 2.75
1836 4762 5.464722 CACGCTGTGCTAATTCTATGAGATT 59.535 40.000 0.00 0.00 0.00 2.40
1837 4763 5.694006 ACGCTGTGCTAATTCTATGAGATTC 59.306 40.000 0.00 0.00 0.00 2.52
1838 4764 5.693555 CGCTGTGCTAATTCTATGAGATTCA 59.306 40.000 0.00 0.00 0.00 2.57
1839 4765 6.201615 CGCTGTGCTAATTCTATGAGATTCAA 59.798 38.462 0.00 0.00 0.00 2.69
1840 4766 7.254556 CGCTGTGCTAATTCTATGAGATTCAAA 60.255 37.037 0.00 0.00 0.00 2.69
1841 4767 8.566260 GCTGTGCTAATTCTATGAGATTCAAAT 58.434 33.333 0.00 0.00 0.00 2.32
1842 4768 9.880064 CTGTGCTAATTCTATGAGATTCAAATG 57.120 33.333 0.00 0.00 0.00 2.32
1843 4769 8.843262 TGTGCTAATTCTATGAGATTCAAATGG 58.157 33.333 0.00 0.00 0.00 3.16
1844 4770 8.295288 GTGCTAATTCTATGAGATTCAAATGGG 58.705 37.037 0.00 0.00 0.00 4.00
1845 4771 7.040201 TGCTAATTCTATGAGATTCAAATGGGC 60.040 37.037 0.00 0.00 0.00 5.36
1846 4772 7.040201 GCTAATTCTATGAGATTCAAATGGGCA 60.040 37.037 0.00 0.00 0.00 5.36
1847 4773 7.850935 AATTCTATGAGATTCAAATGGGCAT 57.149 32.000 0.00 0.00 0.00 4.40
1848 4774 8.945195 AATTCTATGAGATTCAAATGGGCATA 57.055 30.769 0.00 0.00 0.00 3.14
1849 4775 9.543231 AATTCTATGAGATTCAAATGGGCATAT 57.457 29.630 0.00 0.00 0.00 1.78
1850 4776 7.933215 TCTATGAGATTCAAATGGGCATATG 57.067 36.000 0.00 0.00 0.00 1.78
1851 4777 4.859304 TGAGATTCAAATGGGCATATGC 57.141 40.909 19.79 19.79 41.14 3.14
1863 4789 2.283145 GCATATGCCACTCCAATCCT 57.717 50.000 17.26 0.00 34.31 3.24
1864 4790 2.590821 GCATATGCCACTCCAATCCTT 58.409 47.619 17.26 0.00 34.31 3.36
1865 4791 2.961062 GCATATGCCACTCCAATCCTTT 59.039 45.455 17.26 0.00 34.31 3.11
1866 4792 3.385755 GCATATGCCACTCCAATCCTTTT 59.614 43.478 17.26 0.00 34.31 2.27
1867 4793 4.141869 GCATATGCCACTCCAATCCTTTTT 60.142 41.667 17.26 0.00 34.31 1.94
1898 4824 9.760077 TCCTATGTTTTAAGAATCCTACGAATC 57.240 33.333 0.00 0.00 0.00 2.52
1899 4825 9.542462 CCTATGTTTTAAGAATCCTACGAATCA 57.458 33.333 0.00 0.00 0.00 2.57
1903 4829 9.496873 TGTTTTAAGAATCCTACGAATCAAAGA 57.503 29.630 0.00 0.00 0.00 2.52
1904 4830 9.974750 GTTTTAAGAATCCTACGAATCAAAGAG 57.025 33.333 0.00 0.00 0.00 2.85
1905 4831 9.938280 TTTTAAGAATCCTACGAATCAAAGAGA 57.062 29.630 0.00 0.00 0.00 3.10
1906 4832 9.587772 TTTAAGAATCCTACGAATCAAAGAGAG 57.412 33.333 0.00 0.00 0.00 3.20
1907 4833 5.596845 AGAATCCTACGAATCAAAGAGAGC 58.403 41.667 0.00 0.00 0.00 4.09
1908 4834 3.802948 TCCTACGAATCAAAGAGAGCC 57.197 47.619 0.00 0.00 0.00 4.70
1909 4835 3.366396 TCCTACGAATCAAAGAGAGCCT 58.634 45.455 0.00 0.00 0.00 4.58
1910 4836 3.131223 TCCTACGAATCAAAGAGAGCCTG 59.869 47.826 0.00 0.00 0.00 4.85
1911 4837 3.131223 CCTACGAATCAAAGAGAGCCTGA 59.869 47.826 0.00 0.00 0.00 3.86
1912 4838 3.685139 ACGAATCAAAGAGAGCCTGAA 57.315 42.857 0.00 0.00 0.00 3.02
1913 4839 3.330267 ACGAATCAAAGAGAGCCTGAAC 58.670 45.455 0.00 0.00 0.00 3.18
1914 4840 2.675348 CGAATCAAAGAGAGCCTGAACC 59.325 50.000 0.00 0.00 0.00 3.62
1915 4841 3.679389 GAATCAAAGAGAGCCTGAACCA 58.321 45.455 0.00 0.00 0.00 3.67
1916 4842 4.268359 GAATCAAAGAGAGCCTGAACCAT 58.732 43.478 0.00 0.00 0.00 3.55
1917 4843 3.340814 TCAAAGAGAGCCTGAACCATC 57.659 47.619 0.00 0.00 0.00 3.51
1918 4844 2.005451 CAAAGAGAGCCTGAACCATCG 58.995 52.381 0.00 0.00 0.00 3.84
1919 4845 0.539051 AAGAGAGCCTGAACCATCGG 59.461 55.000 0.00 0.00 0.00 4.18
1920 4846 1.522580 GAGAGCCTGAACCATCGGC 60.523 63.158 0.00 0.00 42.10 5.54
1921 4847 2.892425 GAGCCTGAACCATCGGCG 60.892 66.667 0.00 0.00 44.58 6.46
1922 4848 4.473520 AGCCTGAACCATCGGCGG 62.474 66.667 7.21 0.00 44.58 6.13
1923 4849 4.467084 GCCTGAACCATCGGCGGA 62.467 66.667 7.21 0.00 36.20 5.54
1924 4850 2.267642 CCTGAACCATCGGCGGAA 59.732 61.111 7.21 0.00 0.00 4.30
1925 4851 1.376683 CCTGAACCATCGGCGGAAA 60.377 57.895 7.21 0.00 0.00 3.13
1926 4852 0.958382 CCTGAACCATCGGCGGAAAA 60.958 55.000 7.21 0.00 0.00 2.29
1927 4853 0.447801 CTGAACCATCGGCGGAAAAG 59.552 55.000 7.21 0.00 0.00 2.27
1928 4854 0.035598 TGAACCATCGGCGGAAAAGA 59.964 50.000 7.21 0.00 0.00 2.52
1929 4855 0.446616 GAACCATCGGCGGAAAAGAC 59.553 55.000 7.21 0.00 0.00 3.01
1930 4856 0.250553 AACCATCGGCGGAAAAGACA 60.251 50.000 7.21 0.00 0.00 3.41
1931 4857 0.035439 ACCATCGGCGGAAAAGACAT 60.035 50.000 7.21 0.00 0.00 3.06
1932 4858 0.378257 CCATCGGCGGAAAAGACATG 59.622 55.000 7.21 0.00 0.00 3.21
1933 4859 1.368641 CATCGGCGGAAAAGACATGA 58.631 50.000 7.21 0.00 0.00 3.07
1934 4860 1.328680 CATCGGCGGAAAAGACATGAG 59.671 52.381 7.21 0.00 0.00 2.90
1935 4861 0.320374 TCGGCGGAAAAGACATGAGT 59.680 50.000 7.21 0.00 0.00 3.41
1936 4862 0.443869 CGGCGGAAAAGACATGAGTG 59.556 55.000 0.00 0.00 0.00 3.51
1937 4863 1.523758 GGCGGAAAAGACATGAGTGT 58.476 50.000 0.00 0.00 42.49 3.55
1938 4864 2.695359 GGCGGAAAAGACATGAGTGTA 58.305 47.619 0.00 0.00 39.09 2.90
1939 4865 3.270877 GGCGGAAAAGACATGAGTGTAT 58.729 45.455 0.00 0.00 39.09 2.29
1940 4866 3.309954 GGCGGAAAAGACATGAGTGTATC 59.690 47.826 0.00 0.00 39.09 2.24
1941 4867 3.309954 GCGGAAAAGACATGAGTGTATCC 59.690 47.826 0.00 0.00 39.09 2.59
1942 4868 4.503910 CGGAAAAGACATGAGTGTATCCA 58.496 43.478 0.00 0.00 39.09 3.41
1943 4869 4.935205 CGGAAAAGACATGAGTGTATCCAA 59.065 41.667 0.00 0.00 39.09 3.53
1944 4870 5.586243 CGGAAAAGACATGAGTGTATCCAAT 59.414 40.000 0.00 0.00 39.09 3.16
1945 4871 6.457392 CGGAAAAGACATGAGTGTATCCAATG 60.457 42.308 0.00 0.00 39.09 2.82
1946 4872 6.599244 GGAAAAGACATGAGTGTATCCAATGA 59.401 38.462 0.00 0.00 39.09 2.57
1947 4873 7.121168 GGAAAAGACATGAGTGTATCCAATGAA 59.879 37.037 0.00 0.00 39.09 2.57
1948 4874 8.408043 AAAAGACATGAGTGTATCCAATGAAA 57.592 30.769 0.00 0.00 39.09 2.69
1949 4875 7.621428 AAGACATGAGTGTATCCAATGAAAG 57.379 36.000 0.00 0.00 39.09 2.62
1950 4876 6.118170 AGACATGAGTGTATCCAATGAAAGG 58.882 40.000 0.00 0.00 39.09 3.11
1951 4877 6.065976 ACATGAGTGTATCCAATGAAAGGA 57.934 37.500 0.00 0.00 36.63 3.36
1952 4878 6.484288 ACATGAGTGTATCCAATGAAAGGAA 58.516 36.000 0.00 0.00 38.93 3.36
1953 4879 6.600822 ACATGAGTGTATCCAATGAAAGGAAG 59.399 38.462 0.00 0.00 38.93 3.46
1954 4880 6.373005 TGAGTGTATCCAATGAAAGGAAGA 57.627 37.500 0.00 0.00 38.93 2.87
1955 4881 6.409704 TGAGTGTATCCAATGAAAGGAAGAG 58.590 40.000 0.00 0.00 38.93 2.85
1956 4882 6.213397 TGAGTGTATCCAATGAAAGGAAGAGA 59.787 38.462 0.00 0.00 38.93 3.10
1957 4883 7.020827 AGTGTATCCAATGAAAGGAAGAGAA 57.979 36.000 0.00 0.00 38.93 2.87
1958 4884 7.637511 AGTGTATCCAATGAAAGGAAGAGAAT 58.362 34.615 0.00 0.00 38.93 2.40
1959 4885 7.555554 AGTGTATCCAATGAAAGGAAGAGAATG 59.444 37.037 0.00 0.00 38.93 2.67
1960 4886 7.554118 GTGTATCCAATGAAAGGAAGAGAATGA 59.446 37.037 0.00 0.00 38.93 2.57
1961 4887 7.772292 TGTATCCAATGAAAGGAAGAGAATGAG 59.228 37.037 0.00 0.00 38.93 2.90
1962 4888 6.131972 TCCAATGAAAGGAAGAGAATGAGT 57.868 37.500 0.00 0.00 30.71 3.41
1963 4889 5.942236 TCCAATGAAAGGAAGAGAATGAGTG 59.058 40.000 0.00 0.00 30.71 3.51
1964 4890 5.942236 CCAATGAAAGGAAGAGAATGAGTGA 59.058 40.000 0.00 0.00 0.00 3.41
1965 4891 6.093771 CCAATGAAAGGAAGAGAATGAGTGAG 59.906 42.308 0.00 0.00 0.00 3.51
1966 4892 4.573900 TGAAAGGAAGAGAATGAGTGAGC 58.426 43.478 0.00 0.00 0.00 4.26
1967 4893 2.957491 AGGAAGAGAATGAGTGAGCG 57.043 50.000 0.00 0.00 0.00 5.03
1968 4894 2.451490 AGGAAGAGAATGAGTGAGCGA 58.549 47.619 0.00 0.00 0.00 4.93
1969 4895 2.828520 AGGAAGAGAATGAGTGAGCGAA 59.171 45.455 0.00 0.00 0.00 4.70
1970 4896 3.119173 AGGAAGAGAATGAGTGAGCGAAG 60.119 47.826 0.00 0.00 0.00 3.79
1971 4897 3.119316 GGAAGAGAATGAGTGAGCGAAGA 60.119 47.826 0.00 0.00 0.00 2.87
1972 4898 3.781079 AGAGAATGAGTGAGCGAAGAG 57.219 47.619 0.00 0.00 0.00 2.85
1973 4899 3.088532 AGAGAATGAGTGAGCGAAGAGT 58.911 45.455 0.00 0.00 0.00 3.24
1974 4900 4.265893 AGAGAATGAGTGAGCGAAGAGTA 58.734 43.478 0.00 0.00 0.00 2.59
1975 4901 4.335315 AGAGAATGAGTGAGCGAAGAGTAG 59.665 45.833 0.00 0.00 0.00 2.57
1976 4902 3.380004 AGAATGAGTGAGCGAAGAGTAGG 59.620 47.826 0.00 0.00 0.00 3.18
1977 4903 0.811915 TGAGTGAGCGAAGAGTAGGC 59.188 55.000 0.00 0.00 0.00 3.93
1978 4904 0.248296 GAGTGAGCGAAGAGTAGGCG 60.248 60.000 0.00 0.00 0.00 5.52
1979 4905 0.677098 AGTGAGCGAAGAGTAGGCGA 60.677 55.000 0.00 0.00 0.00 5.54
1980 4906 0.523757 GTGAGCGAAGAGTAGGCGAC 60.524 60.000 0.00 0.00 0.00 5.19
1981 4907 0.958876 TGAGCGAAGAGTAGGCGACA 60.959 55.000 0.00 0.00 0.00 4.35
1982 4908 0.170561 GAGCGAAGAGTAGGCGACAA 59.829 55.000 0.00 0.00 0.00 3.18
1983 4909 0.601558 AGCGAAGAGTAGGCGACAAA 59.398 50.000 0.00 0.00 0.00 2.83
1984 4910 1.204941 AGCGAAGAGTAGGCGACAAAT 59.795 47.619 0.00 0.00 0.00 2.32
1985 4911 1.324736 GCGAAGAGTAGGCGACAAATG 59.675 52.381 0.00 0.00 0.00 2.32
1986 4912 1.324736 CGAAGAGTAGGCGACAAATGC 59.675 52.381 0.00 0.00 0.00 3.56
1987 4913 2.346803 GAAGAGTAGGCGACAAATGCA 58.653 47.619 0.00 0.00 0.00 3.96
1988 4914 1.726853 AGAGTAGGCGACAAATGCAC 58.273 50.000 0.00 0.00 0.00 4.57
1989 4915 1.276421 AGAGTAGGCGACAAATGCACT 59.724 47.619 0.00 0.00 0.00 4.40
1990 4916 2.076863 GAGTAGGCGACAAATGCACTT 58.923 47.619 0.00 0.00 0.00 3.16
1991 4917 3.056107 AGAGTAGGCGACAAATGCACTTA 60.056 43.478 0.00 0.00 0.00 2.24
2000 4926 4.840772 CGACAAATGCACTTAAAGACGAAG 59.159 41.667 0.00 0.00 0.00 3.79
2032 4959 3.362706 TGAAGCTAGGTTCGACTATGGT 58.637 45.455 25.22 0.00 0.00 3.55
2043 4970 6.038985 GGTTCGACTATGGTTACCTAACTTC 58.961 44.000 2.07 0.00 36.47 3.01
2201 7531 5.440610 GGGTTGACCACTGAATCTGATTAT 58.559 41.667 2.28 0.00 39.85 1.28
2205 7535 5.674525 TGACCACTGAATCTGATTATGTCC 58.325 41.667 2.28 0.00 0.00 4.02
2221 7551 2.100197 TGTCCACAGTAAGGGAGATCG 58.900 52.381 0.00 0.00 32.85 3.69
2226 7556 3.512680 CACAGTAAGGGAGATCGTCAAC 58.487 50.000 0.00 0.00 0.00 3.18
2229 7559 4.039973 ACAGTAAGGGAGATCGTCAACAAA 59.960 41.667 0.00 0.00 0.00 2.83
2280 7610 8.755696 TGATTCACTTTAACAAACAATATGCC 57.244 30.769 0.00 0.00 0.00 4.40
2350 7680 2.115343 CCCCCTCCGAAGAAAAGAAG 57.885 55.000 0.00 0.00 0.00 2.85
2355 7685 4.767409 CCCCTCCGAAGAAAAGAAGAAAAT 59.233 41.667 0.00 0.00 0.00 1.82
2377 7707 5.854010 TGAGATTGGTCATCACTAGGTAC 57.146 43.478 0.00 0.00 33.75 3.34
2390 7720 3.624861 CACTAGGTACGTCACGGTAGATT 59.375 47.826 0.35 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.764443 ACGTCCGTGTTCTATAGTTTACTAGTA 59.236 37.037 0.00 0.00 0.00 1.82
10 11 6.593770 TGACGTCCGTGTTCTATAGTTTACTA 59.406 38.462 14.12 0.00 0.00 1.82
28 29 4.112341 AGCTACGGCGTGACGTCC 62.112 66.667 24.86 6.18 45.08 4.79
45 46 5.255710 CAACTCAATTGTTGTTGGGTACA 57.744 39.130 25.07 0.00 41.78 2.90
77 78 2.293677 TCTCGAAAGATCCATAGCGACC 59.706 50.000 0.00 0.00 40.84 4.79
104 105 2.677524 GCAAGCCAGGACCATGCA 60.678 61.111 7.86 0.00 37.00 3.96
172 175 7.170320 TGTGTCTGTTTTTCTCCGAAATACTAC 59.830 37.037 9.94 8.83 0.00 2.73
343 349 2.159282 TGGCTTTCCGCACGTTTAAAAA 60.159 40.909 0.00 0.00 41.67 1.94
344 350 1.404391 TGGCTTTCCGCACGTTTAAAA 59.596 42.857 0.00 0.00 41.67 1.52
345 351 1.022735 TGGCTTTCCGCACGTTTAAA 58.977 45.000 0.00 0.00 41.67 1.52
346 352 1.240256 ATGGCTTTCCGCACGTTTAA 58.760 45.000 0.00 0.00 41.67 1.52
347 353 1.240256 AATGGCTTTCCGCACGTTTA 58.760 45.000 0.00 0.00 41.67 2.01
348 354 0.387565 AAATGGCTTTCCGCACGTTT 59.612 45.000 0.00 0.00 41.67 3.60
349 355 0.387565 AAAATGGCTTTCCGCACGTT 59.612 45.000 0.00 0.00 41.67 3.99
350 356 0.387565 AAAAATGGCTTTCCGCACGT 59.612 45.000 0.00 0.00 41.67 4.49
351 357 1.982913 GTAAAAATGGCTTTCCGCACG 59.017 47.619 0.00 0.00 41.67 5.34
352 358 2.729360 GTGTAAAAATGGCTTTCCGCAC 59.271 45.455 0.00 0.00 41.67 5.34
353 359 2.625790 AGTGTAAAAATGGCTTTCCGCA 59.374 40.909 0.00 0.00 41.67 5.69
354 360 3.297830 AGTGTAAAAATGGCTTTCCGC 57.702 42.857 0.00 0.00 38.13 5.54
355 361 5.873179 TCTAGTGTAAAAATGGCTTTCCG 57.127 39.130 0.00 0.00 34.14 4.30
356 362 7.448748 TCTTCTAGTGTAAAAATGGCTTTCC 57.551 36.000 0.00 0.00 0.00 3.13
357 363 8.784043 TCTTCTTCTAGTGTAAAAATGGCTTTC 58.216 33.333 0.00 0.00 0.00 2.62
358 364 8.691661 TCTTCTTCTAGTGTAAAAATGGCTTT 57.308 30.769 0.00 0.00 0.00 3.51
359 365 8.157476 TCTCTTCTTCTAGTGTAAAAATGGCTT 58.843 33.333 0.00 0.00 0.00 4.35
360 366 7.680730 TCTCTTCTTCTAGTGTAAAAATGGCT 58.319 34.615 0.00 0.00 0.00 4.75
361 367 7.907214 TCTCTTCTTCTAGTGTAAAAATGGC 57.093 36.000 0.00 0.00 0.00 4.40
362 368 9.273016 TGTTCTCTTCTTCTAGTGTAAAAATGG 57.727 33.333 0.00 0.00 0.00 3.16
382 388 7.656948 TGATTCCACATTTCCAATTTTGTTCTC 59.343 33.333 0.00 0.00 0.00 2.87
392 416 3.023119 CGGGATGATTCCACATTTCCAA 58.977 45.455 0.00 0.00 44.60 3.53
408 432 1.059913 CTTCCTATTCCTGCCGGGAT 58.940 55.000 2.18 0.00 44.66 3.85
421 445 1.553248 CACCCGATTCCACACTTCCTA 59.447 52.381 0.00 0.00 0.00 2.94
438 462 3.999663 CCTGAAGAACAAGAGATCACACC 59.000 47.826 0.00 0.00 0.00 4.16
458 482 3.612371 GACGACGAGACTTGCGCCT 62.612 63.158 4.18 0.00 0.00 5.52
470 494 4.789075 ACGGGCCATTCGACGACG 62.789 66.667 4.39 0.00 41.26 5.12
471 495 2.884207 GACGGGCCATTCGACGAC 60.884 66.667 4.39 0.00 0.00 4.34
473 497 1.366111 ATTTGACGGGCCATTCGACG 61.366 55.000 4.39 0.00 0.00 5.12
476 500 0.378257 CTGATTTGACGGGCCATTCG 59.622 55.000 4.39 0.56 0.00 3.34
479 503 2.365582 GTTACTGATTTGACGGGCCAT 58.634 47.619 4.39 0.00 0.00 4.40
510 561 1.080974 GTACTGGTCGTGGTGGTCG 60.081 63.158 0.00 0.00 0.00 4.79
587 2173 6.692486 AGCTGTGGTGATATGTACTATAAGC 58.308 40.000 0.00 0.00 0.00 3.09
604 2190 9.899226 GGAAGCTTAATTAATTATTAGCTGTGG 57.101 33.333 24.91 5.73 35.38 4.17
670 2282 4.503007 TGCTCGCGTCAGTTTAGAATAATC 59.497 41.667 5.77 0.00 0.00 1.75
833 3254 7.012894 CGTGGATTGTTGGCCTTTTATTCTATA 59.987 37.037 3.32 0.00 0.00 1.31
862 3295 2.821366 CTGTGGATGTGGCTCGGC 60.821 66.667 0.00 0.00 0.00 5.54
888 3321 2.298446 CAGTCACTTGGAAGAGCTCAGA 59.702 50.000 17.77 0.00 0.00 3.27
889 3322 2.298446 TCAGTCACTTGGAAGAGCTCAG 59.702 50.000 17.77 6.47 0.00 3.35
890 3323 2.319844 TCAGTCACTTGGAAGAGCTCA 58.680 47.619 17.77 0.00 0.00 4.26
901 3334 4.371624 TGTGGAATGGATTCAGTCACTT 57.628 40.909 3.46 0.00 39.50 3.16
940 3382 0.504384 CGTCTGTGCGAACTGTGAAG 59.496 55.000 0.00 0.00 0.00 3.02
976 3418 0.867746 GCGAGGCAAATGCGATATGA 59.132 50.000 0.00 0.00 43.26 2.15
1255 3739 2.980233 GTGCGCCAGGTTCTGCTT 60.980 61.111 4.18 0.00 0.00 3.91
1293 3777 2.922503 TGCCCCAGCTCGAACTCA 60.923 61.111 0.00 0.00 40.80 3.41
1344 3828 1.075482 CATGGTGGTGGCTTCCTGT 59.925 57.895 0.00 0.00 0.00 4.00
1419 3929 2.158445 ACCGGCACTAGATGTCTATCCT 60.158 50.000 0.00 0.00 33.64 3.24
1431 3941 0.887387 GAACCAGCAAACCGGCACTA 60.887 55.000 0.00 0.00 35.83 2.74
1437 3947 3.009723 ACATAGATGAACCAGCAAACCG 58.990 45.455 0.00 0.00 0.00 4.44
1443 3953 0.305922 GCGCACATAGATGAACCAGC 59.694 55.000 0.30 0.00 0.00 4.85
1482 4004 1.606994 CCAACGCCTACTAGTGTGCAA 60.607 52.381 5.39 0.00 0.00 4.08
1497 4019 3.782046 AGATAATGAACCGAGACCAACG 58.218 45.455 0.00 0.00 0.00 4.10
1502 4031 6.313905 ACAAACATGAGATAATGAACCGAGAC 59.686 38.462 0.00 0.00 0.00 3.36
1515 4045 8.487313 TTTACATAAGCGTACAAACATGAGAT 57.513 30.769 0.00 0.00 0.00 2.75
1589 4120 1.669604 TAGTGTCCGCAAAAGCACAA 58.330 45.000 0.00 0.00 34.59 3.33
1590 4121 1.890876 ATAGTGTCCGCAAAAGCACA 58.109 45.000 0.00 0.00 34.59 4.57
1591 4122 3.242739 CCATATAGTGTCCGCAAAAGCAC 60.243 47.826 0.00 0.00 0.00 4.40
1592 4123 2.942376 CCATATAGTGTCCGCAAAAGCA 59.058 45.455 0.00 0.00 0.00 3.91
1593 4124 2.290641 CCCATATAGTGTCCGCAAAAGC 59.709 50.000 0.00 0.00 0.00 3.51
1594 4125 2.290641 GCCCATATAGTGTCCGCAAAAG 59.709 50.000 0.00 0.00 0.00 2.27
1595 4126 2.294074 GCCCATATAGTGTCCGCAAAA 58.706 47.619 0.00 0.00 0.00 2.44
1596 4127 1.808512 CGCCCATATAGTGTCCGCAAA 60.809 52.381 0.00 0.00 0.00 3.68
1597 4128 0.249699 CGCCCATATAGTGTCCGCAA 60.250 55.000 0.00 0.00 0.00 4.85
1598 4129 1.365999 CGCCCATATAGTGTCCGCA 59.634 57.895 0.00 0.00 0.00 5.69
1599 4130 0.249741 AACGCCCATATAGTGTCCGC 60.250 55.000 0.00 0.00 0.00 5.54
1600 4131 1.067974 TCAACGCCCATATAGTGTCCG 59.932 52.381 0.00 0.00 0.00 4.79
1601 4132 2.902705 TCAACGCCCATATAGTGTCC 57.097 50.000 0.00 0.00 0.00 4.02
1602 4133 5.050091 CAGAAATCAACGCCCATATAGTGTC 60.050 44.000 0.00 0.00 0.00 3.67
1603 4134 4.816385 CAGAAATCAACGCCCATATAGTGT 59.184 41.667 0.00 0.00 0.00 3.55
1604 4135 4.214119 CCAGAAATCAACGCCCATATAGTG 59.786 45.833 0.00 0.00 0.00 2.74
1630 4161 1.601166 AGGGTTTCCGTGCAACTAAC 58.399 50.000 0.00 0.00 38.33 2.34
1631 4162 2.351706 AAGGGTTTCCGTGCAACTAA 57.648 45.000 0.00 0.00 38.33 2.24
1633 4164 2.159382 CATAAGGGTTTCCGTGCAACT 58.841 47.619 0.00 0.00 38.33 3.16
1637 4168 4.196971 ACTATTCATAAGGGTTTCCGTGC 58.803 43.478 0.00 0.00 38.33 5.34
1645 4176 7.451731 TTCAGAATGGACTATTCATAAGGGT 57.548 36.000 13.36 0.00 46.20 4.34
1674 4205 1.847818 TCGAACAGTGTTTCCGAGTG 58.152 50.000 10.45 0.00 0.00 3.51
1675 4206 2.470821 CTTCGAACAGTGTTTCCGAGT 58.529 47.619 16.38 0.00 0.00 4.18
1676 4207 1.192534 GCTTCGAACAGTGTTTCCGAG 59.807 52.381 16.38 12.74 0.00 4.63
1700 4626 9.627123 TGAATATTGAAATCTAGGTTTCCGAAT 57.373 29.630 22.75 18.33 37.31 3.34
1729 4655 9.448438 TTGAAATCTAGTACACATGCATAACTT 57.552 29.630 0.00 0.00 0.00 2.66
1730 4656 9.618890 ATTGAAATCTAGTACACATGCATAACT 57.381 29.630 0.00 3.71 0.00 2.24
1736 4662 8.397906 TGCTAAATTGAAATCTAGTACACATGC 58.602 33.333 0.00 0.00 0.00 4.06
1739 4665 9.109393 GGATGCTAAATTGAAATCTAGTACACA 57.891 33.333 0.00 0.00 0.00 3.72
1740 4666 9.109393 TGGATGCTAAATTGAAATCTAGTACAC 57.891 33.333 0.00 0.00 0.00 2.90
1742 4668 9.331282 AGTGGATGCTAAATTGAAATCTAGTAC 57.669 33.333 0.00 0.00 0.00 2.73
1744 4670 8.814038 AAGTGGATGCTAAATTGAAATCTAGT 57.186 30.769 0.00 0.00 0.00 2.57
1746 4672 8.806429 TGAAGTGGATGCTAAATTGAAATCTA 57.194 30.769 0.00 0.00 0.00 1.98
1747 4673 7.707624 TGAAGTGGATGCTAAATTGAAATCT 57.292 32.000 0.00 0.00 0.00 2.40
1748 4674 8.937634 ATTGAAGTGGATGCTAAATTGAAATC 57.062 30.769 0.00 0.00 0.00 2.17
1750 4676 8.125978 AGATTGAAGTGGATGCTAAATTGAAA 57.874 30.769 0.00 0.00 0.00 2.69
1752 4678 7.707624 AAGATTGAAGTGGATGCTAAATTGA 57.292 32.000 0.00 0.00 0.00 2.57
1753 4679 8.767478 AAAAGATTGAAGTGGATGCTAAATTG 57.233 30.769 0.00 0.00 0.00 2.32
1778 4704 6.091441 CACGGGAAAACAATGAAAGTGAAAAA 59.909 34.615 0.00 0.00 34.17 1.94
1779 4705 5.578727 CACGGGAAAACAATGAAAGTGAAAA 59.421 36.000 0.00 0.00 34.17 2.29
1780 4706 5.105752 CACGGGAAAACAATGAAAGTGAAA 58.894 37.500 0.00 0.00 34.17 2.69
1781 4707 4.440802 CCACGGGAAAACAATGAAAGTGAA 60.441 41.667 0.00 0.00 34.17 3.18
1782 4708 3.067461 CCACGGGAAAACAATGAAAGTGA 59.933 43.478 0.00 0.00 34.17 3.41
1783 4709 3.380142 CCACGGGAAAACAATGAAAGTG 58.620 45.455 0.00 0.00 38.30 3.16
1784 4710 2.223947 GCCACGGGAAAACAATGAAAGT 60.224 45.455 0.00 0.00 0.00 2.66
1785 4711 2.223923 TGCCACGGGAAAACAATGAAAG 60.224 45.455 0.00 0.00 0.00 2.62
1788 4714 1.543802 GATGCCACGGGAAAACAATGA 59.456 47.619 0.00 0.00 0.00 2.57
1789 4715 1.271934 TGATGCCACGGGAAAACAATG 59.728 47.619 0.00 0.00 0.00 2.82
1790 4716 1.626686 TGATGCCACGGGAAAACAAT 58.373 45.000 0.00 0.00 0.00 2.71
1791 4717 1.403814 TTGATGCCACGGGAAAACAA 58.596 45.000 0.00 0.00 0.00 2.83
1792 4718 1.067821 GTTTGATGCCACGGGAAAACA 59.932 47.619 0.00 0.00 0.00 2.83
1793 4719 1.067821 TGTTTGATGCCACGGGAAAAC 59.932 47.619 0.00 0.00 0.00 2.43
1794 4720 1.067821 GTGTTTGATGCCACGGGAAAA 59.932 47.619 0.00 0.00 0.00 2.29
1795 4721 0.671251 GTGTTTGATGCCACGGGAAA 59.329 50.000 0.00 0.00 0.00 3.13
1796 4722 2.336341 GTGTTTGATGCCACGGGAA 58.664 52.632 0.00 0.00 0.00 3.97
1797 4723 4.073052 GTGTTTGATGCCACGGGA 57.927 55.556 0.00 0.00 0.00 5.14
1801 4727 0.661187 CACAGCGTGTTTGATGCCAC 60.661 55.000 1.24 0.00 37.28 5.01
1802 4728 1.653667 CACAGCGTGTTTGATGCCA 59.346 52.632 1.24 0.00 37.28 4.92
1803 4729 1.730547 GCACAGCGTGTTTGATGCC 60.731 57.895 9.76 0.00 37.28 4.40
1804 4730 0.516877 TAGCACAGCGTGTTTGATGC 59.483 50.000 9.76 0.00 35.75 3.91
1805 4731 2.967459 TTAGCACAGCGTGTTTGATG 57.033 45.000 9.76 0.00 35.75 3.07
1806 4732 3.753272 AGAATTAGCACAGCGTGTTTGAT 59.247 39.130 9.76 1.39 35.75 2.57
1807 4733 3.138304 AGAATTAGCACAGCGTGTTTGA 58.862 40.909 9.76 0.00 35.75 2.69
1808 4734 3.542712 AGAATTAGCACAGCGTGTTTG 57.457 42.857 9.76 0.00 35.75 2.93
1809 4735 4.935205 TCATAGAATTAGCACAGCGTGTTT 59.065 37.500 9.76 3.05 35.75 2.83
1810 4736 4.503910 TCATAGAATTAGCACAGCGTGTT 58.496 39.130 9.76 6.85 35.75 3.32
1811 4737 4.115516 CTCATAGAATTAGCACAGCGTGT 58.884 43.478 9.76 0.00 35.75 4.49
1812 4738 4.363138 TCTCATAGAATTAGCACAGCGTG 58.637 43.478 4.61 4.61 36.51 5.34
1813 4739 4.655762 TCTCATAGAATTAGCACAGCGT 57.344 40.909 0.00 0.00 0.00 5.07
1814 4740 5.693555 TGAATCTCATAGAATTAGCACAGCG 59.306 40.000 0.00 0.00 0.00 5.18
1815 4741 7.488187 TTGAATCTCATAGAATTAGCACAGC 57.512 36.000 0.00 0.00 0.00 4.40
1816 4742 9.880064 CATTTGAATCTCATAGAATTAGCACAG 57.120 33.333 0.00 0.00 0.00 3.66
1817 4743 8.843262 CCATTTGAATCTCATAGAATTAGCACA 58.157 33.333 0.00 0.00 0.00 4.57
1818 4744 8.295288 CCCATTTGAATCTCATAGAATTAGCAC 58.705 37.037 0.00 0.00 0.00 4.40
1819 4745 7.040201 GCCCATTTGAATCTCATAGAATTAGCA 60.040 37.037 0.00 0.00 0.00 3.49
1820 4746 7.040201 TGCCCATTTGAATCTCATAGAATTAGC 60.040 37.037 0.00 0.00 0.00 3.09
1821 4747 8.400184 TGCCCATTTGAATCTCATAGAATTAG 57.600 34.615 0.00 0.00 0.00 1.73
1822 4748 8.945195 ATGCCCATTTGAATCTCATAGAATTA 57.055 30.769 0.00 0.00 0.00 1.40
1823 4749 7.850935 ATGCCCATTTGAATCTCATAGAATT 57.149 32.000 0.00 0.00 0.00 2.17
1824 4750 8.967918 CATATGCCCATTTGAATCTCATAGAAT 58.032 33.333 0.00 0.00 0.00 2.40
1825 4751 7.094075 GCATATGCCCATTTGAATCTCATAGAA 60.094 37.037 17.26 0.00 34.31 2.10
1826 4752 6.376299 GCATATGCCCATTTGAATCTCATAGA 59.624 38.462 17.26 0.00 34.31 1.98
1827 4753 6.561614 GCATATGCCCATTTGAATCTCATAG 58.438 40.000 17.26 0.00 34.31 2.23
1828 4754 6.519679 GCATATGCCCATTTGAATCTCATA 57.480 37.500 17.26 0.00 34.31 2.15
1829 4755 5.401531 GCATATGCCCATTTGAATCTCAT 57.598 39.130 17.26 0.00 34.31 2.90
1830 4756 4.859304 GCATATGCCCATTTGAATCTCA 57.141 40.909 17.26 0.00 34.31 3.27
1844 4770 2.283145 AGGATTGGAGTGGCATATGC 57.717 50.000 19.79 19.79 41.14 3.14
1845 4771 5.603170 AAAAAGGATTGGAGTGGCATATG 57.397 39.130 0.00 0.00 0.00 1.78
1872 4798 9.760077 GATTCGTAGGATTCTTAAAACATAGGA 57.240 33.333 1.11 0.00 0.00 2.94
1873 4799 9.542462 TGATTCGTAGGATTCTTAAAACATAGG 57.458 33.333 8.35 0.00 0.00 2.57
1877 4803 9.496873 TCTTTGATTCGTAGGATTCTTAAAACA 57.503 29.630 8.35 0.00 0.00 2.83
1878 4804 9.974750 CTCTTTGATTCGTAGGATTCTTAAAAC 57.025 33.333 8.35 0.00 0.00 2.43
1879 4805 9.938280 TCTCTTTGATTCGTAGGATTCTTAAAA 57.062 29.630 8.35 1.96 0.00 1.52
1880 4806 9.587772 CTCTCTTTGATTCGTAGGATTCTTAAA 57.412 33.333 8.35 2.49 0.00 1.52
1881 4807 7.707035 GCTCTCTTTGATTCGTAGGATTCTTAA 59.293 37.037 8.35 3.52 0.00 1.85
1882 4808 7.203910 GCTCTCTTTGATTCGTAGGATTCTTA 58.796 38.462 8.35 0.00 0.00 2.10
1883 4809 6.045955 GCTCTCTTTGATTCGTAGGATTCTT 58.954 40.000 8.35 0.00 0.00 2.52
1884 4810 5.452636 GGCTCTCTTTGATTCGTAGGATTCT 60.453 44.000 8.35 0.00 0.00 2.40
1885 4811 4.747605 GGCTCTCTTTGATTCGTAGGATTC 59.252 45.833 1.32 1.32 0.00 2.52
1886 4812 4.407296 AGGCTCTCTTTGATTCGTAGGATT 59.593 41.667 0.00 0.00 0.00 3.01
1887 4813 3.964031 AGGCTCTCTTTGATTCGTAGGAT 59.036 43.478 0.00 0.00 0.00 3.24
1888 4814 3.131223 CAGGCTCTCTTTGATTCGTAGGA 59.869 47.826 0.00 0.00 0.00 2.94
1889 4815 3.131223 TCAGGCTCTCTTTGATTCGTAGG 59.869 47.826 0.00 0.00 0.00 3.18
1890 4816 4.377839 TCAGGCTCTCTTTGATTCGTAG 57.622 45.455 0.00 0.00 0.00 3.51
1891 4817 4.495422 GTTCAGGCTCTCTTTGATTCGTA 58.505 43.478 0.00 0.00 0.00 3.43
1892 4818 3.330267 GTTCAGGCTCTCTTTGATTCGT 58.670 45.455 0.00 0.00 0.00 3.85
1893 4819 2.675348 GGTTCAGGCTCTCTTTGATTCG 59.325 50.000 0.00 0.00 0.00 3.34
1894 4820 3.679389 TGGTTCAGGCTCTCTTTGATTC 58.321 45.455 0.00 0.00 0.00 2.52
1895 4821 3.795688 TGGTTCAGGCTCTCTTTGATT 57.204 42.857 0.00 0.00 0.00 2.57
1896 4822 3.681034 CGATGGTTCAGGCTCTCTTTGAT 60.681 47.826 0.00 0.00 0.00 2.57
1897 4823 2.354103 CGATGGTTCAGGCTCTCTTTGA 60.354 50.000 0.00 0.00 0.00 2.69
1898 4824 2.005451 CGATGGTTCAGGCTCTCTTTG 58.995 52.381 0.00 0.00 0.00 2.77
1899 4825 1.065854 CCGATGGTTCAGGCTCTCTTT 60.066 52.381 0.00 0.00 0.00 2.52
1900 4826 0.539051 CCGATGGTTCAGGCTCTCTT 59.461 55.000 0.00 0.00 0.00 2.85
1901 4827 1.965754 GCCGATGGTTCAGGCTCTCT 61.966 60.000 0.00 0.00 46.83 3.10
1902 4828 1.522580 GCCGATGGTTCAGGCTCTC 60.523 63.158 0.00 0.00 46.83 3.20
1903 4829 2.586792 GCCGATGGTTCAGGCTCT 59.413 61.111 0.00 0.00 46.83 4.09
1906 4832 3.969250 TTCCGCCGATGGTTCAGGC 62.969 63.158 0.00 0.00 46.88 4.85
1907 4833 0.958382 TTTTCCGCCGATGGTTCAGG 60.958 55.000 0.00 0.00 0.00 3.86
1908 4834 0.447801 CTTTTCCGCCGATGGTTCAG 59.552 55.000 0.00 0.00 0.00 3.02
1909 4835 0.035598 TCTTTTCCGCCGATGGTTCA 59.964 50.000 0.00 0.00 0.00 3.18
1910 4836 0.446616 GTCTTTTCCGCCGATGGTTC 59.553 55.000 0.00 0.00 0.00 3.62
1911 4837 0.250553 TGTCTTTTCCGCCGATGGTT 60.251 50.000 0.00 0.00 0.00 3.67
1912 4838 0.035439 ATGTCTTTTCCGCCGATGGT 60.035 50.000 0.00 0.00 0.00 3.55
1913 4839 0.378257 CATGTCTTTTCCGCCGATGG 59.622 55.000 0.00 0.00 0.00 3.51
1914 4840 1.328680 CTCATGTCTTTTCCGCCGATG 59.671 52.381 0.00 0.00 0.00 3.84
1915 4841 1.066143 ACTCATGTCTTTTCCGCCGAT 60.066 47.619 0.00 0.00 0.00 4.18
1916 4842 0.320374 ACTCATGTCTTTTCCGCCGA 59.680 50.000 0.00 0.00 0.00 5.54
1917 4843 0.443869 CACTCATGTCTTTTCCGCCG 59.556 55.000 0.00 0.00 0.00 6.46
1918 4844 1.523758 ACACTCATGTCTTTTCCGCC 58.476 50.000 0.00 0.00 31.55 6.13
1919 4845 3.309954 GGATACACTCATGTCTTTTCCGC 59.690 47.826 0.00 0.00 40.48 5.54
1920 4846 4.503910 TGGATACACTCATGTCTTTTCCG 58.496 43.478 0.00 0.00 46.17 4.30
1936 4862 7.772757 ACTCATTCTCTTCCTTTCATTGGATAC 59.227 37.037 0.00 0.00 33.09 2.24
1937 4863 7.772292 CACTCATTCTCTTCCTTTCATTGGATA 59.228 37.037 0.00 0.00 33.09 2.59
1938 4864 6.602406 CACTCATTCTCTTCCTTTCATTGGAT 59.398 38.462 0.00 0.00 33.09 3.41
1939 4865 5.942236 CACTCATTCTCTTCCTTTCATTGGA 59.058 40.000 0.00 0.00 0.00 3.53
1940 4866 5.942236 TCACTCATTCTCTTCCTTTCATTGG 59.058 40.000 0.00 0.00 0.00 3.16
1941 4867 6.403418 GCTCACTCATTCTCTTCCTTTCATTG 60.403 42.308 0.00 0.00 0.00 2.82
1942 4868 5.647225 GCTCACTCATTCTCTTCCTTTCATT 59.353 40.000 0.00 0.00 0.00 2.57
1943 4869 5.184711 GCTCACTCATTCTCTTCCTTTCAT 58.815 41.667 0.00 0.00 0.00 2.57
1944 4870 4.573900 GCTCACTCATTCTCTTCCTTTCA 58.426 43.478 0.00 0.00 0.00 2.69
1945 4871 3.616379 CGCTCACTCATTCTCTTCCTTTC 59.384 47.826 0.00 0.00 0.00 2.62
1946 4872 3.259374 TCGCTCACTCATTCTCTTCCTTT 59.741 43.478 0.00 0.00 0.00 3.11
1947 4873 2.828520 TCGCTCACTCATTCTCTTCCTT 59.171 45.455 0.00 0.00 0.00 3.36
1948 4874 2.451490 TCGCTCACTCATTCTCTTCCT 58.549 47.619 0.00 0.00 0.00 3.36
1949 4875 2.949451 TCGCTCACTCATTCTCTTCC 57.051 50.000 0.00 0.00 0.00 3.46
1950 4876 4.103365 TCTTCGCTCACTCATTCTCTTC 57.897 45.455 0.00 0.00 0.00 2.87
1951 4877 3.509575 ACTCTTCGCTCACTCATTCTCTT 59.490 43.478 0.00 0.00 0.00 2.85
1952 4878 3.088532 ACTCTTCGCTCACTCATTCTCT 58.911 45.455 0.00 0.00 0.00 3.10
1953 4879 3.502191 ACTCTTCGCTCACTCATTCTC 57.498 47.619 0.00 0.00 0.00 2.87
1954 4880 3.380004 CCTACTCTTCGCTCACTCATTCT 59.620 47.826 0.00 0.00 0.00 2.40
1955 4881 3.701241 CCTACTCTTCGCTCACTCATTC 58.299 50.000 0.00 0.00 0.00 2.67
1956 4882 2.159170 GCCTACTCTTCGCTCACTCATT 60.159 50.000 0.00 0.00 0.00 2.57
1957 4883 1.407258 GCCTACTCTTCGCTCACTCAT 59.593 52.381 0.00 0.00 0.00 2.90
1958 4884 0.811915 GCCTACTCTTCGCTCACTCA 59.188 55.000 0.00 0.00 0.00 3.41
1959 4885 0.248296 CGCCTACTCTTCGCTCACTC 60.248 60.000 0.00 0.00 0.00 3.51
1960 4886 0.677098 TCGCCTACTCTTCGCTCACT 60.677 55.000 0.00 0.00 0.00 3.41
1961 4887 0.523757 GTCGCCTACTCTTCGCTCAC 60.524 60.000 0.00 0.00 0.00 3.51
1962 4888 0.958876 TGTCGCCTACTCTTCGCTCA 60.959 55.000 0.00 0.00 0.00 4.26
1963 4889 0.170561 TTGTCGCCTACTCTTCGCTC 59.829 55.000 0.00 0.00 0.00 5.03
1964 4890 0.601558 TTTGTCGCCTACTCTTCGCT 59.398 50.000 0.00 0.00 0.00 4.93
1965 4891 1.324736 CATTTGTCGCCTACTCTTCGC 59.675 52.381 0.00 0.00 0.00 4.70
1966 4892 1.324736 GCATTTGTCGCCTACTCTTCG 59.675 52.381 0.00 0.00 0.00 3.79
1967 4893 2.094417 GTGCATTTGTCGCCTACTCTTC 59.906 50.000 0.00 0.00 0.00 2.87
1968 4894 2.076863 GTGCATTTGTCGCCTACTCTT 58.923 47.619 0.00 0.00 0.00 2.85
1969 4895 1.276421 AGTGCATTTGTCGCCTACTCT 59.724 47.619 0.00 0.00 0.00 3.24
1970 4896 1.726853 AGTGCATTTGTCGCCTACTC 58.273 50.000 0.00 0.00 0.00 2.59
1971 4897 2.185004 AAGTGCATTTGTCGCCTACT 57.815 45.000 0.00 0.00 0.00 2.57
1972 4898 4.153475 TCTTTAAGTGCATTTGTCGCCTAC 59.847 41.667 4.47 0.00 0.00 3.18
1973 4899 4.153475 GTCTTTAAGTGCATTTGTCGCCTA 59.847 41.667 4.47 0.00 0.00 3.93
1974 4900 3.058224 GTCTTTAAGTGCATTTGTCGCCT 60.058 43.478 4.47 0.00 0.00 5.52
1975 4901 3.234386 GTCTTTAAGTGCATTTGTCGCC 58.766 45.455 4.47 0.00 0.00 5.54
1976 4902 2.902484 CGTCTTTAAGTGCATTTGTCGC 59.098 45.455 4.47 0.00 0.00 5.19
1977 4903 4.383774 TCGTCTTTAAGTGCATTTGTCG 57.616 40.909 4.47 0.00 0.00 4.35
1978 4904 5.621228 CACTTCGTCTTTAAGTGCATTTGTC 59.379 40.000 4.47 0.00 45.15 3.18
1979 4905 5.510671 CACTTCGTCTTTAAGTGCATTTGT 58.489 37.500 4.47 0.00 45.15 2.83
1987 4913 8.737175 TCATGTATACTCACTTCGTCTTTAAGT 58.263 33.333 4.17 0.00 37.67 2.24
1988 4914 9.569167 TTCATGTATACTCACTTCGTCTTTAAG 57.431 33.333 4.17 0.00 0.00 1.85
1989 4915 9.569167 CTTCATGTATACTCACTTCGTCTTTAA 57.431 33.333 4.17 0.00 0.00 1.52
1990 4916 7.701078 GCTTCATGTATACTCACTTCGTCTTTA 59.299 37.037 4.17 0.00 0.00 1.85
1991 4917 6.531948 GCTTCATGTATACTCACTTCGTCTTT 59.468 38.462 4.17 0.00 0.00 2.52
2000 4926 5.915758 CGAACCTAGCTTCATGTATACTCAC 59.084 44.000 4.17 0.00 0.00 3.51
2006 4932 6.294787 CCATAGTCGAACCTAGCTTCATGTAT 60.295 42.308 0.00 0.00 0.00 2.29
2032 4959 6.201425 CACGCACAGTAAAAGAAGTTAGGTAA 59.799 38.462 0.00 0.00 0.00 2.85
2043 4970 2.800544 ACACTAGCACGCACAGTAAAAG 59.199 45.455 0.00 0.00 0.00 2.27
2080 5110 1.959042 AATCGCGCAGGATCTTTCAT 58.041 45.000 8.75 0.00 0.00 2.57
2201 7531 2.100197 CGATCTCCCTTACTGTGGACA 58.900 52.381 0.00 0.00 0.00 4.02
2205 7535 3.056821 TGTTGACGATCTCCCTTACTGTG 60.057 47.826 0.00 0.00 0.00 3.66
2244 7574 7.726079 TGTTAAAGTGAATCAGAACGTAATCG 58.274 34.615 0.00 0.00 43.34 3.34
2280 7610 0.108615 CTACGGCCACTCTTCACTGG 60.109 60.000 2.24 0.00 0.00 4.00
2335 7665 7.426929 TCTCATTTTCTTCTTTTCTTCGGAG 57.573 36.000 0.00 0.00 0.00 4.63
2338 7668 8.078596 ACCAATCTCATTTTCTTCTTTTCTTCG 58.921 33.333 0.00 0.00 0.00 3.79
2347 7677 7.388460 AGTGATGACCAATCTCATTTTCTTC 57.612 36.000 0.00 0.00 36.15 2.87
2349 7679 7.052873 CCTAGTGATGACCAATCTCATTTTCT 58.947 38.462 0.00 0.00 36.15 2.52
2350 7680 6.825721 ACCTAGTGATGACCAATCTCATTTTC 59.174 38.462 0.00 0.00 36.15 2.29
2355 7685 4.338400 CGTACCTAGTGATGACCAATCTCA 59.662 45.833 0.00 0.00 36.15 3.27


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

AutoCloner maintained by Alex Coulton.