Multiple sequence alignment - TraesCS5A01G216100

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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 TraesCS5A01G216100 chr5A 100.000 7394 0 0 1 7394 432436230 432443623 0.000000e+00 13655.0
1 TraesCS5A01G216100 chr5A 95.745 47 2 0 6961 7007 432443141 432443187 7.960000e-10 76.8
2 TraesCS5A01G216100 chr5A 95.745 47 2 0 6912 6958 432443190 432443236 7.960000e-10 76.8
3 TraesCS5A01G216100 chr5D 95.385 4117 122 23 3217 7293 332036475 332040563 0.000000e+00 6488.0
4 TraesCS5A01G216100 chr5D 93.150 1708 52 21 1 1694 332033316 332034972 0.000000e+00 2446.0
5 TraesCS5A01G216100 chr5D 95.611 1481 33 12 1763 3218 332034967 332036440 0.000000e+00 2346.0
6 TraesCS5A01G216100 chr5D 90.909 99 9 0 7296 7394 232709291 232709193 4.650000e-27 134.0
7 TraesCS5A01G216100 chr5D 100.000 47 0 0 6961 7007 332040177 332040223 3.680000e-13 87.9
8 TraesCS5A01G216100 chr5D 97.872 47 1 0 6912 6958 332040226 332040272 1.710000e-11 82.4
9 TraesCS5A01G216100 chr5B 94.710 4121 144 27 3217 7291 387736378 387740470 0.000000e+00 6335.0
10 TraesCS5A01G216100 chr5B 93.329 1724 44 25 1 1694 387733196 387734878 0.000000e+00 2481.0
11 TraesCS5A01G216100 chr5B 95.273 1481 35 13 1763 3218 387734873 387736343 0.000000e+00 2314.0
12 TraesCS5A01G216100 chr5B 100.000 47 0 0 6961 7007 387740094 387740140 3.680000e-13 87.9
13 TraesCS5A01G216100 chrUn 85.294 476 51 12 6186 6650 83995135 83994668 2.410000e-129 473.0
14 TraesCS5A01G216100 chrUn 85.294 476 51 12 6186 6650 232033414 232032947 2.410000e-129 473.0
15 TraesCS5A01G216100 chrUn 85.294 476 51 12 6186 6650 232041621 232041154 2.410000e-129 473.0
16 TraesCS5A01G216100 chr7B 85.294 476 51 12 6186 6650 2315673 2315206 2.410000e-129 473.0
17 TraesCS5A01G216100 chr7B 86.957 115 14 1 7281 7394 492490676 492490562 2.170000e-25 128.0
18 TraesCS5A01G216100 chr7B 100.000 46 0 0 1614 1659 686818554 686818509 1.320000e-12 86.1
19 TraesCS5A01G216100 chr7B 97.826 46 1 0 1614 1659 246008162 246008117 6.150000e-11 80.5
20 TraesCS5A01G216100 chr4A 85.201 473 54 12 6186 6650 731999351 731998887 8.680000e-129 472.0
21 TraesCS5A01G216100 chr7A 89.091 110 11 1 7285 7394 494786996 494786888 1.290000e-27 135.0
22 TraesCS5A01G216100 chr7A 87.611 113 9 3 7284 7394 691723815 691723706 7.790000e-25 126.0
23 TraesCS5A01G216100 chr7A 100.000 59 0 0 1614 1672 290922172 290922114 7.840000e-20 110.0
24 TraesCS5A01G216100 chr7A 90.566 53 5 0 3546 3598 117981072 117981020 3.700000e-08 71.3
25 TraesCS5A01G216100 chr6D 88.889 108 11 1 7287 7394 57999641 57999747 1.670000e-26 132.0
26 TraesCS5A01G216100 chr6D 87.963 108 12 1 7287 7394 20298156 20298262 7.790000e-25 126.0
27 TraesCS5A01G216100 chr1B 89.423 104 10 1 7291 7394 540336682 540336580 6.020000e-26 130.0
28 TraesCS5A01G216100 chr1B 95.556 45 2 0 1617 1661 231643022 231642978 1.030000e-08 73.1
29 TraesCS5A01G216100 chr6B 87.963 108 12 1 7287 7394 130075220 130075326 7.790000e-25 126.0
30 TraesCS5A01G216100 chr6B 97.500 40 1 0 1614 1653 411102842 411102803 1.330000e-07 69.4
31 TraesCS5A01G216100 chr4B 87.387 111 13 1 7284 7394 512758572 512758681 7.790000e-25 126.0
32 TraesCS5A01G216100 chr7D 100.000 59 0 0 1614 1672 265703392 265703334 7.840000e-20 110.0
33 TraesCS5A01G216100 chr7D 100.000 55 0 0 1617 1671 604868051 604868105 1.310000e-17 102.0


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 TraesCS5A01G216100 chr5A 432436230 432443623 7393 False 4602.866667 13655 97.163333 1 7394 3 chr5A.!!$F1 7393
1 TraesCS5A01G216100 chr5D 332033316 332040563 7247 False 2290.060000 6488 96.403600 1 7293 5 chr5D.!!$F1 7292
2 TraesCS5A01G216100 chr5B 387733196 387740470 7274 False 2804.475000 6335 95.828000 1 7291 4 chr5B.!!$F1 7290

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
341 359 0.255890 TTATTGTCAGGCAGGGAGGC 59.744 55.000 0.00 0.00 44.61 4.70 F
374 392 0.329261 TGGTTGCTGCTAATCAGGCT 59.671 50.000 0.00 0.00 43.06 4.58 F
375 393 0.737219 GGTTGCTGCTAATCAGGCTG 59.263 55.000 8.58 8.58 43.06 4.85 F
1752 1792 0.773644 ACTTGCCCAAGGATGTCTGT 59.226 50.000 12.22 0.00 42.53 3.41 F
1943 2003 0.108396 TGTCTGTGTGTGGGTGATGG 59.892 55.000 0.00 0.00 0.00 3.51 F
2502 2564 0.245539 TTAAACTCGGCCCTCGTCTG 59.754 55.000 0.00 0.00 40.32 3.51 F
4198 4355 0.034380 AGCTAGTCCGTGCTCTACCA 60.034 55.000 0.00 0.00 33.90 3.25 F
4378 4551 0.305922 GTGTGCTGATATCGCTTGGC 59.694 55.000 16.64 8.52 0.00 4.52 F
5173 5347 2.005451 CTTTGAGCTTGATGAGGACGG 58.995 52.381 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1733 1773 0.773644 ACAGACATCCTTGGGCAAGT 59.226 50.000 0.00 0.00 36.72 3.16 R
1786 1826 0.916845 TACCCTAGTGGCATGGGCAA 60.917 55.000 18.82 8.31 44.56 4.52 R
1943 2003 1.515081 TAACCAAGCCGCAGTGTTAC 58.485 50.000 0.00 0.00 0.00 2.50 R
3169 3234 1.585267 TTGGTGCCGCACATCATGAC 61.585 55.000 24.43 6.31 39.76 3.06 R
3918 4074 2.031012 TGGAGAAGCACTGCCACG 59.969 61.111 0.00 0.00 36.08 4.94 R
4469 4643 1.588674 TGTAAACAACTCAGGCGTGG 58.411 50.000 6.56 0.00 0.00 4.94 R
5045 5219 1.141657 GCATGAGATGGCCCTGAAGTA 59.858 52.381 0.00 0.00 0.00 2.24 R
6195 6376 1.307866 GAGAGGGGGTGGGGATCAA 60.308 63.158 0.00 0.00 0.00 2.57 R
6896 7080 0.457035 ACTTTGCCAGCAGTGTGTTG 59.543 50.000 0.00 0.00 0.00 3.33 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
28 29 0.465097 CCCCAGCAGCAGTAATGAGG 60.465 60.000 0.00 0.00 0.00 3.86
29 30 0.543277 CCCAGCAGCAGTAATGAGGA 59.457 55.000 0.00 0.00 0.00 3.71
30 31 1.661341 CCAGCAGCAGTAATGAGGAC 58.339 55.000 0.00 0.00 0.00 3.85
303 321 1.067974 CCCCTCCGGTTTGTTTTGTTC 59.932 52.381 0.00 0.00 0.00 3.18
328 346 4.328983 CGGCTCCGCGATAATTATTATTGT 59.671 41.667 8.23 0.00 31.00 2.71
337 355 6.403636 GCGATAATTATTATTGTCAGGCAGGG 60.404 42.308 12.30 0.00 33.00 4.45
338 356 6.878923 CGATAATTATTATTGTCAGGCAGGGA 59.121 38.462 0.00 0.00 33.00 4.20
339 357 7.065085 CGATAATTATTATTGTCAGGCAGGGAG 59.935 40.741 0.00 0.00 33.00 4.30
340 358 4.437682 TTATTATTGTCAGGCAGGGAGG 57.562 45.455 0.00 0.00 0.00 4.30
341 359 0.255890 TTATTGTCAGGCAGGGAGGC 59.744 55.000 0.00 0.00 44.61 4.70
374 392 0.329261 TGGTTGCTGCTAATCAGGCT 59.671 50.000 0.00 0.00 43.06 4.58
375 393 0.737219 GGTTGCTGCTAATCAGGCTG 59.263 55.000 8.58 8.58 43.06 4.85
455 473 9.579768 GCTTCTTTCTTTCTTTCTTTCTTTCTT 57.420 29.630 0.00 0.00 0.00 2.52
575 593 1.609210 CCAATTCCCCACCACCACC 60.609 63.158 0.00 0.00 0.00 4.61
578 596 2.380571 AATTCCCCACCACCACCACC 62.381 60.000 0.00 0.00 0.00 4.61
592 610 3.419759 CACCGCCACAAGTACGCC 61.420 66.667 0.00 0.00 0.00 5.68
663 683 1.149148 GGAGCTATTTCCGCGATTCC 58.851 55.000 8.23 0.00 0.00 3.01
689 715 1.388837 GGCTCCTCCCTCTTCGTCTC 61.389 65.000 0.00 0.00 0.00 3.36
794 821 3.395669 GGTTCGCCCTCGATTTCG 58.604 61.111 0.00 0.00 45.04 3.46
834 871 4.460683 CGCCGAAATCCGTCCCCA 62.461 66.667 0.00 0.00 36.31 4.96
1180 1220 1.066071 GGAGGTTGGAGGTCAGTTAGC 60.066 57.143 0.00 0.00 0.00 3.09
1213 1253 1.307647 GTTGTGCCTGGGGATGGAT 59.692 57.895 0.00 0.00 0.00 3.41
1486 1526 2.148768 TCTCAACTGTCTGCAATGCTG 58.851 47.619 6.82 6.24 0.00 4.41
1519 1559 2.594592 AGTGGTGGCGGCAAGTTC 60.595 61.111 15.50 0.00 0.00 3.01
1648 1688 2.452600 TGTTTGGGACTGAAAGGCTT 57.547 45.000 0.00 0.00 46.21 4.35
1649 1689 2.745968 TGTTTGGGACTGAAAGGCTTT 58.254 42.857 13.25 13.25 46.21 3.51
1650 1690 2.430332 TGTTTGGGACTGAAAGGCTTTG 59.570 45.455 18.79 6.49 46.21 2.77
1691 1731 6.472016 TGTTGATTCTAGTTCCATAACTGCA 58.528 36.000 1.11 0.00 45.63 4.41
1692 1732 6.939730 TGTTGATTCTAGTTCCATAACTGCAA 59.060 34.615 1.11 0.00 45.63 4.08
1693 1733 7.611467 TGTTGATTCTAGTTCCATAACTGCAAT 59.389 33.333 1.11 0.00 45.63 3.56
1694 1734 7.792374 TGATTCTAGTTCCATAACTGCAATC 57.208 36.000 12.55 12.55 45.63 2.67
1695 1735 6.479990 TGATTCTAGTTCCATAACTGCAATCG 59.520 38.462 13.60 0.00 45.63 3.34
1696 1736 4.693283 TCTAGTTCCATAACTGCAATCGG 58.307 43.478 1.11 0.00 45.63 4.18
1697 1737 2.017049 AGTTCCATAACTGCAATCGGC 58.983 47.619 0.00 0.00 44.40 5.54
1717 1757 3.722555 CAATTTTGATTGCAGCTGCTG 57.277 42.857 36.61 24.80 42.66 4.41
1718 1758 3.064207 CAATTTTGATTGCAGCTGCTGT 58.936 40.909 36.61 25.53 42.66 4.40
1719 1759 4.239304 CAATTTTGATTGCAGCTGCTGTA 58.761 39.130 36.61 23.01 42.66 2.74
1720 1760 4.730949 ATTTTGATTGCAGCTGCTGTAT 57.269 36.364 36.61 26.14 42.66 2.29
1721 1761 3.497297 TTTGATTGCAGCTGCTGTATG 57.503 42.857 36.61 6.88 42.66 2.39
1722 1762 2.406596 TGATTGCAGCTGCTGTATGA 57.593 45.000 36.61 19.56 42.66 2.15
1723 1763 2.713877 TGATTGCAGCTGCTGTATGAA 58.286 42.857 36.61 22.84 42.66 2.57
1724 1764 3.284617 TGATTGCAGCTGCTGTATGAAT 58.715 40.909 36.61 26.21 42.66 2.57
1725 1765 3.314357 TGATTGCAGCTGCTGTATGAATC 59.686 43.478 36.61 31.30 42.66 2.52
1726 1766 2.704464 TGCAGCTGCTGTATGAATCT 57.296 45.000 36.61 0.00 42.66 2.40
1727 1767 2.285977 TGCAGCTGCTGTATGAATCTG 58.714 47.619 36.61 2.76 42.66 2.90
1728 1768 2.093341 TGCAGCTGCTGTATGAATCTGA 60.093 45.455 36.61 11.32 42.66 3.27
1729 1769 2.941064 GCAGCTGCTGTATGAATCTGAA 59.059 45.455 31.33 0.00 38.21 3.02
1730 1770 3.002451 GCAGCTGCTGTATGAATCTGAAG 59.998 47.826 31.33 0.62 38.21 3.02
1731 1771 4.439968 CAGCTGCTGTATGAATCTGAAGA 58.560 43.478 21.21 0.00 0.00 2.87
1732 1772 4.874396 CAGCTGCTGTATGAATCTGAAGAA 59.126 41.667 21.21 0.00 0.00 2.52
1733 1773 5.353400 CAGCTGCTGTATGAATCTGAAGAAA 59.647 40.000 21.21 0.00 0.00 2.52
1734 1774 5.353678 AGCTGCTGTATGAATCTGAAGAAAC 59.646 40.000 0.00 0.00 0.00 2.78
1735 1775 5.353678 GCTGCTGTATGAATCTGAAGAAACT 59.646 40.000 0.00 0.00 0.00 2.66
1736 1776 6.128063 GCTGCTGTATGAATCTGAAGAAACTT 60.128 38.462 0.00 0.00 0.00 2.66
1737 1777 7.137490 TGCTGTATGAATCTGAAGAAACTTG 57.863 36.000 0.00 0.00 0.00 3.16
1738 1778 6.026513 GCTGTATGAATCTGAAGAAACTTGC 58.973 40.000 0.00 0.00 0.00 4.01
1739 1779 6.500684 TGTATGAATCTGAAGAAACTTGCC 57.499 37.500 0.00 0.00 0.00 4.52
1740 1780 5.415701 TGTATGAATCTGAAGAAACTTGCCC 59.584 40.000 0.00 0.00 0.00 5.36
1741 1781 3.831323 TGAATCTGAAGAAACTTGCCCA 58.169 40.909 0.00 0.00 0.00 5.36
1742 1782 4.214310 TGAATCTGAAGAAACTTGCCCAA 58.786 39.130 0.00 0.00 0.00 4.12
1743 1783 4.279169 TGAATCTGAAGAAACTTGCCCAAG 59.721 41.667 6.48 6.48 43.79 3.61
1744 1784 2.586425 TCTGAAGAAACTTGCCCAAGG 58.414 47.619 12.22 0.00 42.53 3.61
1745 1785 2.174639 TCTGAAGAAACTTGCCCAAGGA 59.825 45.455 12.22 0.00 42.53 3.36
1746 1786 3.160269 CTGAAGAAACTTGCCCAAGGAT 58.840 45.455 12.22 0.96 42.53 3.24
1747 1787 2.892852 TGAAGAAACTTGCCCAAGGATG 59.107 45.455 12.22 0.00 42.53 3.51
1748 1788 2.683211 AGAAACTTGCCCAAGGATGT 57.317 45.000 12.22 0.00 42.53 3.06
1749 1789 2.519013 AGAAACTTGCCCAAGGATGTC 58.481 47.619 12.22 4.35 42.53 3.06
1750 1790 2.108952 AGAAACTTGCCCAAGGATGTCT 59.891 45.455 12.22 6.21 42.53 3.41
1751 1791 1.915141 AACTTGCCCAAGGATGTCTG 58.085 50.000 12.22 0.00 42.53 3.51
1752 1792 0.773644 ACTTGCCCAAGGATGTCTGT 59.226 50.000 12.22 0.00 42.53 3.41
1753 1793 1.145738 ACTTGCCCAAGGATGTCTGTT 59.854 47.619 12.22 0.00 42.53 3.16
1754 1794 2.242043 CTTGCCCAAGGATGTCTGTTT 58.758 47.619 0.06 0.00 34.87 2.83
1755 1795 1.619654 TGCCCAAGGATGTCTGTTTG 58.380 50.000 0.00 0.00 0.00 2.93
1756 1796 1.144708 TGCCCAAGGATGTCTGTTTGA 59.855 47.619 0.00 0.00 0.00 2.69
1757 1797 2.225091 TGCCCAAGGATGTCTGTTTGAT 60.225 45.455 0.00 0.00 0.00 2.57
1758 1798 2.827921 GCCCAAGGATGTCTGTTTGATT 59.172 45.455 0.00 0.00 0.00 2.57
1759 1799 3.259123 GCCCAAGGATGTCTGTTTGATTT 59.741 43.478 0.00 0.00 0.00 2.17
1760 1800 4.813027 CCCAAGGATGTCTGTTTGATTTG 58.187 43.478 0.00 0.00 0.00 2.32
1761 1801 4.281688 CCCAAGGATGTCTGTTTGATTTGT 59.718 41.667 0.00 0.00 0.00 2.83
1762 1802 5.221501 CCCAAGGATGTCTGTTTGATTTGTT 60.222 40.000 0.00 0.00 0.00 2.83
1763 1803 5.693104 CCAAGGATGTCTGTTTGATTTGTTG 59.307 40.000 0.00 0.00 0.00 3.33
1764 1804 4.874970 AGGATGTCTGTTTGATTTGTTGC 58.125 39.130 0.00 0.00 0.00 4.17
1872 1912 7.761249 GCTATTATGTTTTCACAGGCAGATTTT 59.239 33.333 0.00 0.00 35.94 1.82
1912 1972 7.301868 TGGATTTTCTTTGCCTTGTATTCTT 57.698 32.000 0.00 0.00 0.00 2.52
1943 2003 0.108396 TGTCTGTGTGTGGGTGATGG 59.892 55.000 0.00 0.00 0.00 3.51
2123 2185 3.619038 GGTTGCACACAGAAGTATCTAGC 59.381 47.826 0.00 0.00 33.50 3.42
2321 2383 0.395724 CAAAGGTACTGCCATCCCCC 60.396 60.000 0.00 0.00 40.86 5.40
2328 2390 1.142688 ACTGCCATCCCCCTTTCACT 61.143 55.000 0.00 0.00 0.00 3.41
2335 2397 3.448660 CCATCCCCCTTTCACTTTTCATC 59.551 47.826 0.00 0.00 0.00 2.92
2502 2564 0.245539 TTAAACTCGGCCCTCGTCTG 59.754 55.000 0.00 0.00 40.32 3.51
2508 2570 4.021925 GGCCCTCGTCTGCTTGGT 62.022 66.667 0.00 0.00 0.00 3.67
2646 2708 1.546476 CTTCTCTGCGGAGTACCAAGT 59.454 52.381 21.88 0.00 40.29 3.16
2713 2775 8.796475 ACATCTCTTGCATATTGTTTGTTACTT 58.204 29.630 0.00 0.00 0.00 2.24
2903 2965 7.192148 CATGATTTCTGAGTCATGGAATCTC 57.808 40.000 19.29 9.70 44.94 2.75
3072 3135 7.122501 TGCATGGATGTTATCACATTTACACTT 59.877 33.333 0.00 0.00 44.22 3.16
3073 3136 7.433131 GCATGGATGTTATCACATTTACACTTG 59.567 37.037 0.00 0.00 44.22 3.16
3148 3213 3.820467 CTGGACAATGGTTACAAGCAAGA 59.180 43.478 0.00 0.00 40.14 3.02
3271 3408 0.968405 ATGTGAAGCGGCAAAACCAT 59.032 45.000 1.45 0.00 39.03 3.55
3580 3735 4.097892 GTGTTGATTTTCTGTCTGTTGGGT 59.902 41.667 0.00 0.00 0.00 4.51
3590 3745 5.935945 TCTGTCTGTTGGGTTTGAGAATTA 58.064 37.500 0.00 0.00 0.00 1.40
3621 3776 2.609747 ACCTTCCTGTAGAGTGCTGAA 58.390 47.619 0.00 0.00 0.00 3.02
3669 3824 6.800543 TGTATTCTCAGCTAGCTCTTAACTG 58.199 40.000 16.15 2.51 0.00 3.16
3830 3985 3.131046 CACCCTGTGCAAGAAGTCTTTTT 59.869 43.478 0.00 0.00 33.11 1.94
3836 3991 6.016777 CCTGTGCAAGAAGTCTTTTTATCTGT 60.017 38.462 0.00 0.00 33.11 3.41
3872 4027 2.222819 GCTGCCAACTTTATCTTCGTCG 60.223 50.000 0.00 0.00 0.00 5.12
3918 4074 3.802948 ACTGATCGGGTGTTCTCATAC 57.197 47.619 6.47 0.00 0.00 2.39
4058 4214 5.663456 AGTGCACAAACTTGTTTTGATGAT 58.337 33.333 21.04 0.00 46.76 2.45
4198 4355 0.034380 AGCTAGTCCGTGCTCTACCA 60.034 55.000 0.00 0.00 33.90 3.25
4378 4551 0.305922 GTGTGCTGATATCGCTTGGC 59.694 55.000 16.64 8.52 0.00 4.52
4400 4573 7.646314 TGGCTACTTCTATTCGTATTGTCTAC 58.354 38.462 0.00 0.00 0.00 2.59
4497 4671 6.258727 CGCCTGAGTTGTTTACATATGAATCT 59.741 38.462 10.38 0.00 0.00 2.40
4498 4672 7.201644 CGCCTGAGTTGTTTACATATGAATCTT 60.202 37.037 10.38 0.00 0.00 2.40
4538 4712 6.828273 TGATGACCGAACATTATTTTCTGGAT 59.172 34.615 8.24 0.00 0.00 3.41
4680 4854 2.045561 TTTCTTCTGCACCGGTCAAA 57.954 45.000 2.59 0.00 0.00 2.69
4694 4868 3.077359 CGGTCAAAGGAAAGATTCAGCT 58.923 45.455 0.00 0.00 0.00 4.24
5045 5219 2.991250 ACAACAGCGCATAGGAAATCT 58.009 42.857 11.47 0.00 0.00 2.40
5090 5264 3.825143 TCGATCATTCAGCTGAATCCA 57.175 42.857 33.95 24.62 42.41 3.41
5173 5347 2.005451 CTTTGAGCTTGATGAGGACGG 58.995 52.381 0.00 0.00 0.00 4.79
5177 5351 3.031013 TGAGCTTGATGAGGACGGAATA 58.969 45.455 0.00 0.00 0.00 1.75
5401 5575 5.181245 GGTAATTCTGCACTTCTGCTTACAA 59.819 40.000 0.00 0.00 44.57 2.41
5677 5855 2.422945 GGAGAACAAGGGAACAACCTGT 60.423 50.000 0.00 0.00 40.87 4.00
5682 5860 2.099405 CAAGGGAACAACCTGTGTGTT 58.901 47.619 0.00 0.00 40.60 3.32
5694 5872 2.890311 CCTGTGTGTTGGCCATTTCTAA 59.110 45.455 6.09 0.00 0.00 2.10
5735 5914 9.906660 TTCAATTTTAACATGTGCTTACTTAGG 57.093 29.630 0.00 0.00 0.00 2.69
5887 6066 4.620982 GTGTTCTAATTTTGCACTTGCCT 58.379 39.130 0.00 0.00 41.18 4.75
5888 6067 4.445385 GTGTTCTAATTTTGCACTTGCCTG 59.555 41.667 0.00 0.00 41.18 4.85
5965 6144 5.350914 GCTGGAATATGAGCTATCACATGAC 59.649 44.000 0.00 0.00 38.57 3.06
6195 6376 8.803235 ACTTTCAAGGTAAAAACTTGTCTTCTT 58.197 29.630 4.72 0.00 44.29 2.52
6246 6427 4.458295 TCGTCTAACGATTGGTCTTCTTCT 59.542 41.667 0.00 0.00 46.73 2.85
6247 6428 5.645067 TCGTCTAACGATTGGTCTTCTTCTA 59.355 40.000 0.00 0.00 46.73 2.10
6248 6429 5.738225 CGTCTAACGATTGGTCTTCTTCTAC 59.262 44.000 0.00 0.00 46.05 2.59
6273 6454 2.186076 CAGGATTACGCGAAGACAGAC 58.814 52.381 15.93 0.00 0.00 3.51
6330 6511 3.307242 CGAATTACAAGAAGAAGCCTCCG 59.693 47.826 0.00 0.00 0.00 4.63
6417 6598 5.449553 TCCTCTTCTTTTCTTGCTTTTCCT 58.550 37.500 0.00 0.00 0.00 3.36
6560 6744 5.029807 AGGAGCTCAAGTCTTTTATAGCC 57.970 43.478 17.19 0.00 0.00 3.93
6686 6870 2.289002 CAGACTGCTTGTGTTGTCCTTC 59.711 50.000 0.00 0.00 0.00 3.46
6712 6896 2.355132 GCTCTAGTCGTCTCGGAATTCA 59.645 50.000 7.93 0.00 0.00 2.57
6717 6901 3.283751 AGTCGTCTCGGAATTCAGATCT 58.716 45.455 8.79 0.00 0.00 2.75
6781 6965 2.290641 ACATTGAACTGCCAGTTTCGTC 59.709 45.455 12.09 0.00 38.80 4.20
6782 6966 2.031258 TTGAACTGCCAGTTTCGTCA 57.969 45.000 12.09 1.95 38.80 4.35
6784 6968 0.232303 GAACTGCCAGTTTCGTCACG 59.768 55.000 12.09 0.00 38.80 4.35
6785 6969 0.179094 AACTGCCAGTTTCGTCACGA 60.179 50.000 3.74 0.00 34.11 4.35
6823 7007 1.310933 GGCAATGAGACAGGCAGGTG 61.311 60.000 0.00 0.00 0.00 4.00
6824 7008 1.310933 GCAATGAGACAGGCAGGTGG 61.311 60.000 0.00 0.00 0.00 4.61
6844 7028 4.523083 TGGATATACCAGGTTTGCACTTC 58.477 43.478 0.00 0.00 44.64 3.01
6864 7048 3.932822 TCGCAGAGCCAAAGTGTATTAA 58.067 40.909 0.00 0.00 0.00 1.40
6896 7080 3.952323 GGCTTAATTTACAGGGAAGGACC 59.048 47.826 0.00 0.00 38.08 4.46
6904 7088 0.474184 CAGGGAAGGACCAACACACT 59.526 55.000 0.00 0.00 41.20 3.55
6909 7093 0.466189 AAGGACCAACACACTGCTGG 60.466 55.000 0.00 0.00 39.43 4.85
6925 7109 7.171337 CACACTGCTGGCAAAGTTTATTTATTT 59.829 33.333 0.00 0.00 0.00 1.40
6976 7160 9.020731 CAGGGTAGTGAAAGTTTATTTATTGGT 57.979 33.333 0.00 0.00 0.00 3.67
7026 7215 0.535335 GGTAGATCACACCGCCTTCA 59.465 55.000 0.00 0.00 0.00 3.02
7066 7255 2.079158 GCTTGTGTAGCTGAAGATGCA 58.921 47.619 0.00 0.00 46.77 3.96
7133 7322 2.374830 CTTGAGGCGCGGGATCATCT 62.375 60.000 8.83 0.00 0.00 2.90
7153 7342 0.105778 CCTTGATCTTCTCCTCGCCC 59.894 60.000 0.00 0.00 0.00 6.13
7177 7366 0.317160 GGATCGTGCACCGGATATGA 59.683 55.000 9.46 5.01 37.11 2.15
7258 7447 1.915141 ACAAGATCAAAGGCCACCAG 58.085 50.000 5.01 0.00 0.00 4.00
7294 7483 9.865321 ACTAACAACATCTTGTAACATATACGT 57.135 29.630 0.00 0.00 39.88 3.57
7296 7485 7.766219 ACAACATCTTGTAACATATACGTCC 57.234 36.000 0.00 0.00 38.95 4.79
7297 7486 7.553334 ACAACATCTTGTAACATATACGTCCT 58.447 34.615 0.00 0.00 38.95 3.85
7298 7487 7.705325 ACAACATCTTGTAACATATACGTCCTC 59.295 37.037 0.00 0.00 38.95 3.71
7299 7488 6.746120 ACATCTTGTAACATATACGTCCTCC 58.254 40.000 0.00 0.00 0.00 4.30
7300 7489 6.322969 ACATCTTGTAACATATACGTCCTCCA 59.677 38.462 0.00 0.00 0.00 3.86
7301 7490 6.971726 TCTTGTAACATATACGTCCTCCAT 57.028 37.500 0.00 0.00 0.00 3.41
7302 7491 7.356089 TCTTGTAACATATACGTCCTCCATT 57.644 36.000 0.00 0.00 0.00 3.16
7303 7492 7.788026 TCTTGTAACATATACGTCCTCCATTT 58.212 34.615 0.00 0.00 0.00 2.32
7304 7493 7.924412 TCTTGTAACATATACGTCCTCCATTTC 59.076 37.037 0.00 0.00 0.00 2.17
7305 7494 7.356089 TGTAACATATACGTCCTCCATTTCT 57.644 36.000 0.00 0.00 0.00 2.52
7306 7495 8.467963 TGTAACATATACGTCCTCCATTTCTA 57.532 34.615 0.00 0.00 0.00 2.10
7307 7496 8.916062 TGTAACATATACGTCCTCCATTTCTAA 58.084 33.333 0.00 0.00 0.00 2.10
7308 7497 9.754382 GTAACATATACGTCCTCCATTTCTAAA 57.246 33.333 0.00 0.00 0.00 1.85
7317 7506 8.925338 ACGTCCTCCATTTCTAAATATAAGTCT 58.075 33.333 0.00 0.00 0.00 3.24
7318 7507 9.765795 CGTCCTCCATTTCTAAATATAAGTCTT 57.234 33.333 0.00 0.00 0.00 3.01
7352 7541 7.719871 TCCTATAAGGAACTACATATGGAGC 57.280 40.000 15.30 0.00 42.51 4.70
7353 7542 7.246027 TCCTATAAGGAACTACATATGGAGCA 58.754 38.462 15.30 0.00 42.51 4.26
7354 7543 7.733047 TCCTATAAGGAACTACATATGGAGCAA 59.267 37.037 15.30 0.00 42.51 3.91
7355 7544 8.375506 CCTATAAGGAACTACATATGGAGCAAA 58.624 37.037 15.30 0.00 38.49 3.68
7356 7545 9.778741 CTATAAGGAACTACATATGGAGCAAAA 57.221 33.333 15.30 0.00 38.49 2.44
7358 7547 6.949352 AGGAACTACATATGGAGCAAAATG 57.051 37.500 15.30 0.00 36.02 2.32
7359 7548 6.662755 AGGAACTACATATGGAGCAAAATGA 58.337 36.000 15.30 0.00 36.02 2.57
7360 7549 6.769822 AGGAACTACATATGGAGCAAAATGAG 59.230 38.462 15.30 0.00 36.02 2.90
7361 7550 6.543831 GGAACTACATATGGAGCAAAATGAGT 59.456 38.462 15.30 0.00 0.00 3.41
7362 7551 6.932356 ACTACATATGGAGCAAAATGAGTG 57.068 37.500 15.30 0.00 0.00 3.51
7363 7552 6.653020 ACTACATATGGAGCAAAATGAGTGA 58.347 36.000 15.30 0.00 0.00 3.41
7364 7553 7.112122 ACTACATATGGAGCAAAATGAGTGAA 58.888 34.615 15.30 0.00 0.00 3.18
7365 7554 7.776969 ACTACATATGGAGCAAAATGAGTGAAT 59.223 33.333 15.30 0.00 0.00 2.57
7366 7555 7.035840 ACATATGGAGCAAAATGAGTGAATC 57.964 36.000 7.80 0.00 0.00 2.52
7367 7556 4.996788 ATGGAGCAAAATGAGTGAATCC 57.003 40.909 0.00 0.00 0.00 3.01
7368 7557 2.749076 TGGAGCAAAATGAGTGAATCCG 59.251 45.455 0.00 0.00 0.00 4.18
7369 7558 2.749621 GGAGCAAAATGAGTGAATCCGT 59.250 45.455 0.00 0.00 0.00 4.69
7370 7559 3.938963 GGAGCAAAATGAGTGAATCCGTA 59.061 43.478 0.00 0.00 0.00 4.02
7371 7560 4.201822 GGAGCAAAATGAGTGAATCCGTAC 60.202 45.833 0.00 0.00 0.00 3.67
7372 7561 4.579869 AGCAAAATGAGTGAATCCGTACT 58.420 39.130 0.00 0.00 0.00 2.73
7373 7562 4.631813 AGCAAAATGAGTGAATCCGTACTC 59.368 41.667 0.00 0.00 42.77 2.59
7374 7563 4.631813 GCAAAATGAGTGAATCCGTACTCT 59.368 41.667 0.00 0.00 42.86 3.24
7375 7564 5.810587 GCAAAATGAGTGAATCCGTACTCTA 59.189 40.000 0.00 0.00 42.86 2.43
7376 7565 6.312918 GCAAAATGAGTGAATCCGTACTCTAA 59.687 38.462 0.00 0.00 42.86 2.10
7377 7566 7.148474 GCAAAATGAGTGAATCCGTACTCTAAA 60.148 37.037 0.00 0.00 42.86 1.85
7378 7567 8.717821 CAAAATGAGTGAATCCGTACTCTAAAA 58.282 33.333 0.00 0.00 42.86 1.52
7379 7568 9.449719 AAAATGAGTGAATCCGTACTCTAAAAT 57.550 29.630 0.00 0.00 42.86 1.82
7382 7571 9.698309 ATGAGTGAATCCGTACTCTAAAATATG 57.302 33.333 0.00 0.00 42.86 1.78
7383 7572 8.692710 TGAGTGAATCCGTACTCTAAAATATGT 58.307 33.333 0.00 0.00 42.86 2.29
7384 7573 9.182933 GAGTGAATCCGTACTCTAAAATATGTC 57.817 37.037 0.00 0.00 40.06 3.06
7385 7574 8.915036 AGTGAATCCGTACTCTAAAATATGTCT 58.085 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.135915 CTCGTCCTCATTACTGCTGCT 59.864 52.381 0.00 0.00 0.00 4.24
14 15 1.565305 CTCGTCCTCATTACTGCTGC 58.435 55.000 0.00 0.00 0.00 5.25
30 31 3.939837 TTTCTCTGCCGCTGCCTCG 62.940 63.158 0.00 0.00 36.33 4.63
190 194 6.375736 GGGACTTTTTCTTTCTCTATCCCTTG 59.624 42.308 0.00 0.00 40.21 3.61
337 355 4.748144 CCAACCAGGGGCTGCCTC 62.748 72.222 19.68 15.99 0.00 4.70
341 359 3.451056 AACCACCAACCAGGGGCTG 62.451 63.158 0.00 0.00 40.60 4.85
342 360 3.110031 AACCACCAACCAGGGGCT 61.110 61.111 0.00 0.00 40.60 5.19
343 361 2.917227 CAACCACCAACCAGGGGC 60.917 66.667 0.00 0.00 40.60 5.80
455 473 3.461831 TCCAAGGAACCTCCAAGAAAGAA 59.538 43.478 0.00 0.00 39.61 2.52
456 474 3.053077 TCCAAGGAACCTCCAAGAAAGA 58.947 45.455 0.00 0.00 39.61 2.52
457 475 3.508845 TCCAAGGAACCTCCAAGAAAG 57.491 47.619 0.00 0.00 39.61 2.62
458 476 4.141041 TGAATCCAAGGAACCTCCAAGAAA 60.141 41.667 0.00 0.00 39.61 2.52
575 593 3.419759 GGCGTACTTGTGGCGGTG 61.420 66.667 0.00 0.00 0.00 4.94
578 596 0.949105 AAAGAGGCGTACTTGTGGCG 60.949 55.000 0.00 0.00 35.52 5.69
579 597 1.235724 AAAAGAGGCGTACTTGTGGC 58.764 50.000 0.00 0.00 0.00 5.01
689 715 1.221021 GAGTAAAGCGTGGGGGAGG 59.779 63.158 0.00 0.00 0.00 4.30
821 858 1.489230 ACATACCTGGGGACGGATTTC 59.511 52.381 0.00 0.00 39.98 2.17
822 859 1.591768 ACATACCTGGGGACGGATTT 58.408 50.000 0.00 0.00 39.98 2.17
829 866 0.539986 GCGAGAAACATACCTGGGGA 59.460 55.000 0.00 0.00 0.00 4.81
831 868 1.429148 GCGCGAGAAACATACCTGGG 61.429 60.000 12.10 0.00 0.00 4.45
834 871 1.518572 CGGCGCGAGAAACATACCT 60.519 57.895 12.10 0.00 0.00 3.08
865 902 0.250234 TCCGACCAAATCTGAGGCAG 59.750 55.000 0.00 0.00 0.00 4.85
1155 1195 4.658786 ACCTCCAACCTCCCCGCT 62.659 66.667 0.00 0.00 0.00 5.52
1180 1220 1.283793 CAACAAAGTGAGGGCGCTG 59.716 57.895 8.56 0.00 34.49 5.18
1486 1526 4.022329 CCACCACTCAACCAAGGAATAAAC 60.022 45.833 0.00 0.00 0.00 2.01
1519 1559 1.335324 GCTAACAGCACTGCAACTTGG 60.335 52.381 3.30 0.00 41.89 3.61
1648 1688 5.580691 TCAACAACAACAACAACAACAACAA 59.419 32.000 0.00 0.00 0.00 2.83
1649 1689 5.109210 TCAACAACAACAACAACAACAACA 58.891 33.333 0.00 0.00 0.00 3.33
1650 1690 5.643339 TCAACAACAACAACAACAACAAC 57.357 34.783 0.00 0.00 0.00 3.32
1697 1737 3.064207 ACAGCAGCTGCAATCAAAATTG 58.936 40.909 38.24 25.72 44.31 2.32
1698 1738 3.396260 ACAGCAGCTGCAATCAAAATT 57.604 38.095 38.24 13.55 45.16 1.82
1699 1739 4.158949 TCATACAGCAGCTGCAATCAAAAT 59.841 37.500 38.24 18.66 45.16 1.82
1700 1740 3.506844 TCATACAGCAGCTGCAATCAAAA 59.493 39.130 38.24 17.30 45.16 2.44
1701 1741 3.083293 TCATACAGCAGCTGCAATCAAA 58.917 40.909 38.24 17.86 45.16 2.69
1702 1742 2.713877 TCATACAGCAGCTGCAATCAA 58.286 42.857 38.24 19.73 45.16 2.57
1703 1743 2.406596 TCATACAGCAGCTGCAATCA 57.593 45.000 38.24 21.18 45.16 2.57
1704 1744 3.564644 AGATTCATACAGCAGCTGCAATC 59.435 43.478 38.24 31.80 45.16 2.67
1705 1745 3.315470 CAGATTCATACAGCAGCTGCAAT 59.685 43.478 38.24 26.89 45.16 3.56
1706 1746 2.681344 CAGATTCATACAGCAGCTGCAA 59.319 45.455 38.24 23.53 45.16 4.08
1707 1747 2.093341 TCAGATTCATACAGCAGCTGCA 60.093 45.455 38.24 20.45 45.16 4.41
1708 1748 2.558378 TCAGATTCATACAGCAGCTGC 58.442 47.619 31.53 31.53 42.49 5.25
1709 1749 4.439968 TCTTCAGATTCATACAGCAGCTG 58.560 43.478 21.54 21.54 37.52 4.24
1710 1750 4.750021 TCTTCAGATTCATACAGCAGCT 57.250 40.909 0.00 0.00 0.00 4.24
1711 1751 5.353678 AGTTTCTTCAGATTCATACAGCAGC 59.646 40.000 0.00 0.00 0.00 5.25
1712 1752 6.981762 AGTTTCTTCAGATTCATACAGCAG 57.018 37.500 0.00 0.00 0.00 4.24
1713 1753 6.348786 GCAAGTTTCTTCAGATTCATACAGCA 60.349 38.462 0.00 0.00 0.00 4.41
1714 1754 6.026513 GCAAGTTTCTTCAGATTCATACAGC 58.973 40.000 0.00 0.00 0.00 4.40
1715 1755 6.404074 GGGCAAGTTTCTTCAGATTCATACAG 60.404 42.308 0.00 0.00 0.00 2.74
1716 1756 5.415701 GGGCAAGTTTCTTCAGATTCATACA 59.584 40.000 0.00 0.00 0.00 2.29
1717 1757 5.415701 TGGGCAAGTTTCTTCAGATTCATAC 59.584 40.000 0.00 0.00 0.00 2.39
1718 1758 5.569355 TGGGCAAGTTTCTTCAGATTCATA 58.431 37.500 0.00 0.00 0.00 2.15
1719 1759 4.410099 TGGGCAAGTTTCTTCAGATTCAT 58.590 39.130 0.00 0.00 0.00 2.57
1720 1760 3.831323 TGGGCAAGTTTCTTCAGATTCA 58.169 40.909 0.00 0.00 0.00 2.57
1721 1761 4.321527 CCTTGGGCAAGTTTCTTCAGATTC 60.322 45.833 0.00 0.00 36.72 2.52
1722 1762 3.575687 CCTTGGGCAAGTTTCTTCAGATT 59.424 43.478 0.00 0.00 36.72 2.40
1723 1763 3.160269 CCTTGGGCAAGTTTCTTCAGAT 58.840 45.455 0.00 0.00 36.72 2.90
1724 1764 2.174639 TCCTTGGGCAAGTTTCTTCAGA 59.825 45.455 0.00 0.00 36.72 3.27
1725 1765 2.586425 TCCTTGGGCAAGTTTCTTCAG 58.414 47.619 0.00 0.00 36.72 3.02
1726 1766 2.746279 TCCTTGGGCAAGTTTCTTCA 57.254 45.000 0.00 0.00 36.72 3.02
1727 1767 2.893489 ACATCCTTGGGCAAGTTTCTTC 59.107 45.455 0.00 0.00 36.72 2.87
1728 1768 2.893489 GACATCCTTGGGCAAGTTTCTT 59.107 45.455 0.00 0.00 36.72 2.52
1729 1769 2.108952 AGACATCCTTGGGCAAGTTTCT 59.891 45.455 0.00 0.00 36.72 2.52
1730 1770 2.229784 CAGACATCCTTGGGCAAGTTTC 59.770 50.000 0.00 0.00 36.72 2.78
1731 1771 2.242043 CAGACATCCTTGGGCAAGTTT 58.758 47.619 0.00 0.00 36.72 2.66
1732 1772 1.145738 ACAGACATCCTTGGGCAAGTT 59.854 47.619 0.00 0.00 36.72 2.66
1733 1773 0.773644 ACAGACATCCTTGGGCAAGT 59.226 50.000 0.00 0.00 36.72 3.16
1734 1774 1.915141 AACAGACATCCTTGGGCAAG 58.085 50.000 0.00 0.00 38.14 4.01
1735 1775 1.962807 CAAACAGACATCCTTGGGCAA 59.037 47.619 0.00 0.00 0.00 4.52
1736 1776 1.144708 TCAAACAGACATCCTTGGGCA 59.855 47.619 0.00 0.00 0.00 5.36
1737 1777 1.909700 TCAAACAGACATCCTTGGGC 58.090 50.000 0.00 0.00 0.00 5.36
1738 1778 4.281688 ACAAATCAAACAGACATCCTTGGG 59.718 41.667 0.00 0.00 0.00 4.12
1739 1779 5.458041 ACAAATCAAACAGACATCCTTGG 57.542 39.130 0.00 0.00 0.00 3.61
1740 1780 5.176223 GCAACAAATCAAACAGACATCCTTG 59.824 40.000 0.00 0.00 0.00 3.61
1741 1781 5.163426 TGCAACAAATCAAACAGACATCCTT 60.163 36.000 0.00 0.00 0.00 3.36
1742 1782 4.341806 TGCAACAAATCAAACAGACATCCT 59.658 37.500 0.00 0.00 0.00 3.24
1743 1783 4.619973 TGCAACAAATCAAACAGACATCC 58.380 39.130 0.00 0.00 0.00 3.51
1744 1784 6.774354 ATTGCAACAAATCAAACAGACATC 57.226 33.333 0.00 0.00 0.00 3.06
1745 1785 8.143193 TCTTATTGCAACAAATCAAACAGACAT 58.857 29.630 0.00 0.00 0.00 3.06
1746 1786 7.434897 GTCTTATTGCAACAAATCAAACAGACA 59.565 33.333 0.00 0.00 36.43 3.41
1747 1787 7.434897 TGTCTTATTGCAACAAATCAAACAGAC 59.565 33.333 0.00 0.00 36.67 3.51
1748 1788 7.487484 TGTCTTATTGCAACAAATCAAACAGA 58.513 30.769 0.00 0.00 0.00 3.41
1749 1789 7.436080 ACTGTCTTATTGCAACAAATCAAACAG 59.564 33.333 0.00 10.13 33.18 3.16
1750 1790 7.264221 ACTGTCTTATTGCAACAAATCAAACA 58.736 30.769 0.00 0.00 0.00 2.83
1751 1791 7.698836 ACTGTCTTATTGCAACAAATCAAAC 57.301 32.000 0.00 0.00 0.00 2.93
1752 1792 8.602328 CAAACTGTCTTATTGCAACAAATCAAA 58.398 29.630 0.00 0.00 0.00 2.69
1753 1793 7.763528 ACAAACTGTCTTATTGCAACAAATCAA 59.236 29.630 0.00 0.00 0.00 2.57
1754 1794 7.264221 ACAAACTGTCTTATTGCAACAAATCA 58.736 30.769 0.00 0.00 0.00 2.57
1755 1795 7.698836 ACAAACTGTCTTATTGCAACAAATC 57.301 32.000 0.00 0.00 0.00 2.17
1756 1796 7.698836 GACAAACTGTCTTATTGCAACAAAT 57.301 32.000 0.00 0.00 43.73 2.32
1786 1826 0.916845 TACCCTAGTGGCATGGGCAA 60.917 55.000 18.82 8.31 44.56 4.52
1912 1972 6.098679 CCACACACAGACAAAAAGAATCAAA 58.901 36.000 0.00 0.00 0.00 2.69
1943 2003 1.515081 TAACCAAGCCGCAGTGTTAC 58.485 50.000 0.00 0.00 0.00 2.50
2123 2185 7.535139 TCTTTTGTGAAACTTAAGACAGGTTG 58.465 34.615 10.09 0.00 38.04 3.77
2196 2258 5.049828 CCCTGAAATGAAACAACCAAAGTC 58.950 41.667 0.00 0.00 0.00 3.01
2198 2260 5.022282 ACCCTGAAATGAAACAACCAAAG 57.978 39.130 0.00 0.00 0.00 2.77
2199 2261 6.739331 ATACCCTGAAATGAAACAACCAAA 57.261 33.333 0.00 0.00 0.00 3.28
2321 2383 8.188799 ACATATGATGCTGATGAAAAGTGAAAG 58.811 33.333 10.38 0.00 0.00 2.62
2328 2390 8.132995 GTCATTGACATATGATGCTGATGAAAA 58.867 33.333 10.38 0.00 36.94 2.29
2362 2424 7.530010 AGCATAAACACATTGTTACATGTCTC 58.470 34.615 0.00 0.00 40.14 3.36
2377 2439 6.021596 CCGAACTACATTCAAGCATAAACAC 58.978 40.000 0.00 0.00 37.12 3.32
2502 2564 0.529378 CCTTTGGAGCATCACCAAGC 59.471 55.000 0.00 0.00 46.05 4.01
2508 2570 5.815581 ACTACATTTACCTTTGGAGCATCA 58.184 37.500 0.00 0.00 36.25 3.07
2899 2961 7.889469 AGCAAATAGTTGAACATTTGTGAGAT 58.111 30.769 22.09 10.11 41.87 2.75
2900 2962 7.275888 AGCAAATAGTTGAACATTTGTGAGA 57.724 32.000 22.09 0.00 41.87 3.27
2901 2963 9.462174 TTTAGCAAATAGTTGAACATTTGTGAG 57.538 29.630 22.09 8.31 41.87 3.51
2902 2964 9.462174 CTTTAGCAAATAGTTGAACATTTGTGA 57.538 29.630 22.09 13.95 41.87 3.58
2903 2965 9.462174 TCTTTAGCAAATAGTTGAACATTTGTG 57.538 29.630 22.09 13.60 41.87 3.33
2948 3011 7.284261 TGTCAATGAAGGTTGTTGTTAGAATCA 59.716 33.333 0.00 0.00 0.00 2.57
3003 3066 8.999431 TGACAAAATGTAACCTAGTCAAATCTC 58.001 33.333 0.00 0.00 32.26 2.75
3004 3067 8.918202 TGACAAAATGTAACCTAGTCAAATCT 57.082 30.769 0.00 0.00 32.26 2.40
3047 3110 7.031226 AGTGTAAATGTGATAACATCCATGC 57.969 36.000 0.00 0.00 0.00 4.06
3072 3135 8.715191 AAACAAGAGCATAAATGTTTTGAACA 57.285 26.923 0.00 0.00 41.75 3.18
3073 3136 8.816144 TGAAACAAGAGCATAAATGTTTTGAAC 58.184 29.630 4.47 0.00 43.77 3.18
3169 3234 1.585267 TTGGTGCCGCACATCATGAC 61.585 55.000 24.43 6.31 39.76 3.06
3232 3369 9.625747 TTCACATATAAGACAAAAGGATGCATA 57.374 29.630 0.00 0.00 0.00 3.14
3430 3585 5.359576 ACAGAATTACAGAAGTGGCACAAAA 59.640 36.000 21.41 4.74 44.16 2.44
3494 3649 6.915300 TCCAAAACAGAATCAAACGTTACATG 59.085 34.615 0.00 0.00 0.00 3.21
3590 3745 7.070074 CACTCTACAGGAAGGTTATCAGGTAAT 59.930 40.741 0.00 0.00 0.00 1.89
3786 3941 7.320399 GGTGACCCCAATATTTACAAAGAAAG 58.680 38.462 0.00 0.00 0.00 2.62
3872 4027 5.473504 TCTGCTTTACCCACAAAGAATCTTC 59.526 40.000 0.00 0.00 37.66 2.87
3918 4074 2.031012 TGGAGAAGCACTGCCACG 59.969 61.111 0.00 0.00 36.08 4.94
4058 4214 4.816126 AGTATGGGCTAATCTGTACCTGA 58.184 43.478 0.00 0.00 0.00 3.86
4198 4355 2.497675 TGAGAGCTTATCCTCGCTGTTT 59.502 45.455 0.00 0.00 36.45 2.83
4378 4551 7.350467 TGCGTAGACAATACGAATAGAAGTAG 58.650 38.462 11.30 0.00 42.94 2.57
4400 4573 2.624316 AGCAAACTGAATCACATGCG 57.376 45.000 0.00 0.00 37.18 4.73
4469 4643 1.588674 TGTAAACAACTCAGGCGTGG 58.411 50.000 6.56 0.00 0.00 4.94
4498 4672 8.385111 GTTCGGTCATCAGATATAAACGAAAAA 58.615 33.333 11.87 0.00 39.14 1.94
4538 4712 7.067008 GGTGCTAGATGCTTCAAAACCTAAATA 59.933 37.037 2.07 0.00 43.37 1.40
4680 4854 3.560882 CCTTCACCAGCTGAATCTTTCCT 60.561 47.826 17.39 0.00 38.26 3.36
4694 4868 1.006813 AATATGGGCCACCTTCACCA 58.993 50.000 9.28 0.00 37.76 4.17
4701 4875 2.036346 GCAGATGAAAATATGGGCCACC 59.964 50.000 9.28 0.00 37.24 4.61
4792 4966 4.141505 TGTCCTCTGAAGTTCCATTCACAA 60.142 41.667 0.00 0.00 35.40 3.33
5028 5202 4.141937 TGAAGTAGATTTCCTATGCGCTGT 60.142 41.667 9.73 0.00 0.00 4.40
5045 5219 1.141657 GCATGAGATGGCCCTGAAGTA 59.858 52.381 0.00 0.00 0.00 2.24
5177 5351 7.813331 TGGTGTAGTGGTCTTAGTATAGAGAT 58.187 38.462 0.00 0.00 0.00 2.75
5418 5592 9.853555 CAAAATGCACATTTATTTGTACCTCTA 57.146 29.630 8.92 0.00 39.88 2.43
5650 5828 2.158475 TGTTCCCTTGTTCTCCAGCATT 60.158 45.455 0.00 0.00 0.00 3.56
5651 5829 1.425066 TGTTCCCTTGTTCTCCAGCAT 59.575 47.619 0.00 0.00 0.00 3.79
5657 5835 2.618709 CACAGGTTGTTCCCTTGTTCTC 59.381 50.000 0.00 0.00 36.75 2.87
5677 5855 6.909550 ATACTTTTAGAAATGGCCAACACA 57.090 33.333 10.96 0.00 0.00 3.72
5682 5860 7.967908 TGGAAAAATACTTTTAGAAATGGCCA 58.032 30.769 8.56 8.56 34.83 5.36
5718 5896 6.942576 AGATCAAACCTAAGTAAGCACATGTT 59.057 34.615 0.00 0.00 0.00 2.71
5735 5914 6.115446 TGTTATCATGGAGACCAGATCAAAC 58.885 40.000 0.00 0.00 36.75 2.93
5770 5949 8.369218 TGAAATTTCAGAGAAAAATTGAAGGC 57.631 30.769 16.91 0.00 36.65 4.35
5887 6066 4.288398 TCCCGACACCCTAAATATACACA 58.712 43.478 0.00 0.00 0.00 3.72
5888 6067 4.942761 TCCCGACACCCTAAATATACAC 57.057 45.455 0.00 0.00 0.00 2.90
5965 6144 2.180204 GCATTCCCCATCCACGTCG 61.180 63.158 0.00 0.00 0.00 5.12
6195 6376 1.307866 GAGAGGGGGTGGGGATCAA 60.308 63.158 0.00 0.00 0.00 2.57
6235 6416 3.685139 CTGCAAGGTAGAAGAAGACCA 57.315 47.619 0.00 0.00 38.27 4.02
6273 6454 1.308998 GGCAGATGTATTCCAACCCG 58.691 55.000 0.00 0.00 0.00 5.28
6330 6511 2.824489 GCTACTTTCTGGGGCGGC 60.824 66.667 0.00 0.00 0.00 6.53
6493 6675 9.391006 GGGATAATACAGATCAACACTACAAAA 57.609 33.333 0.00 0.00 0.00 2.44
6494 6676 8.544622 TGGGATAATACAGATCAACACTACAAA 58.455 33.333 0.00 0.00 0.00 2.83
6560 6744 2.286833 CCTGTGTTGTCGGTTGTTACAG 59.713 50.000 0.00 0.00 35.17 2.74
6686 6870 1.274476 GAGACGACTAGAGCGAGCG 59.726 63.158 14.71 0.00 0.00 5.03
6712 6896 6.150641 CACAACATCCAACATTCAGAAGATCT 59.849 38.462 0.00 0.00 0.00 2.75
6717 6901 6.653526 ATTCACAACATCCAACATTCAGAA 57.346 33.333 0.00 0.00 0.00 3.02
6781 6965 4.435877 CGCGATGATCATAGTCATATCGTG 59.564 45.833 16.00 12.56 38.88 4.35
6782 6966 4.496507 CCGCGATGATCATAGTCATATCGT 60.497 45.833 8.23 0.00 38.88 3.73
6784 6968 3.733224 GCCGCGATGATCATAGTCATATC 59.267 47.826 8.23 0.00 38.88 1.63
6785 6969 3.131046 TGCCGCGATGATCATAGTCATAT 59.869 43.478 8.23 0.00 38.88 1.78
6823 7007 3.560068 CGAAGTGCAAACCTGGTATATCC 59.440 47.826 0.00 0.00 0.00 2.59
6824 7008 3.002348 GCGAAGTGCAAACCTGGTATATC 59.998 47.826 0.00 0.00 45.45 1.63
6844 7028 4.651994 CTTTAATACACTTTGGCTCTGCG 58.348 43.478 0.00 0.00 0.00 5.18
6896 7080 0.457035 ACTTTGCCAGCAGTGTGTTG 59.543 50.000 0.00 0.00 0.00 3.33
6904 7088 6.479095 GCAAATAAATAAACTTTGCCAGCA 57.521 33.333 7.76 0.00 45.57 4.41
6925 7109 2.920724 TAAGCCTGTGTTGTACTGCA 57.079 45.000 0.00 0.00 32.46 4.41
6927 7111 7.197071 TGTAAATTAAGCCTGTGTTGTACTG 57.803 36.000 0.00 0.00 0.00 2.74
6976 7160 7.604927 CCTGTAAATTAAGCCTGTGTTGTACTA 59.395 37.037 0.00 0.00 0.00 1.82
7066 7255 2.507102 CGCGACCGAAGCTGATGT 60.507 61.111 0.00 0.00 36.29 3.06
7133 7322 1.115467 GGCGAGGAGAAGATCAAGGA 58.885 55.000 0.00 0.00 0.00 3.36
7258 7447 4.319177 AGATGTTGTTAGTTGCCTGACTC 58.681 43.478 0.00 0.00 0.00 3.36
7328 7517 7.246027 TGCTCCATATGTAGTTCCTTATAGGA 58.754 38.462 1.24 0.00 44.10 2.94
7329 7518 7.482169 TGCTCCATATGTAGTTCCTTATAGG 57.518 40.000 1.24 0.00 36.46 2.57
7330 7519 9.778741 TTTTGCTCCATATGTAGTTCCTTATAG 57.221 33.333 1.24 0.00 0.00 1.31
7332 7521 9.071276 CATTTTGCTCCATATGTAGTTCCTTAT 57.929 33.333 1.24 0.00 0.00 1.73
7333 7522 8.271458 TCATTTTGCTCCATATGTAGTTCCTTA 58.729 33.333 1.24 0.00 0.00 2.69
7334 7523 7.118723 TCATTTTGCTCCATATGTAGTTCCTT 58.881 34.615 1.24 0.00 0.00 3.36
7335 7524 6.662755 TCATTTTGCTCCATATGTAGTTCCT 58.337 36.000 1.24 0.00 0.00 3.36
7336 7525 6.543831 ACTCATTTTGCTCCATATGTAGTTCC 59.456 38.462 1.24 0.00 0.00 3.62
7337 7526 7.280876 TCACTCATTTTGCTCCATATGTAGTTC 59.719 37.037 1.24 0.00 0.00 3.01
7338 7527 7.112122 TCACTCATTTTGCTCCATATGTAGTT 58.888 34.615 1.24 0.00 0.00 2.24
7339 7528 6.653020 TCACTCATTTTGCTCCATATGTAGT 58.347 36.000 1.24 0.00 0.00 2.73
7340 7529 7.558161 TTCACTCATTTTGCTCCATATGTAG 57.442 36.000 1.24 0.00 0.00 2.74
7341 7530 7.229306 GGATTCACTCATTTTGCTCCATATGTA 59.771 37.037 1.24 0.00 0.00 2.29
7342 7531 6.040166 GGATTCACTCATTTTGCTCCATATGT 59.960 38.462 1.24 0.00 0.00 2.29
7343 7532 6.444633 GGATTCACTCATTTTGCTCCATATG 58.555 40.000 0.00 0.00 0.00 1.78
7344 7533 5.240183 CGGATTCACTCATTTTGCTCCATAT 59.760 40.000 0.00 0.00 0.00 1.78
7345 7534 4.576053 CGGATTCACTCATTTTGCTCCATA 59.424 41.667 0.00 0.00 0.00 2.74
7346 7535 3.379372 CGGATTCACTCATTTTGCTCCAT 59.621 43.478 0.00 0.00 0.00 3.41
7347 7536 2.749076 CGGATTCACTCATTTTGCTCCA 59.251 45.455 0.00 0.00 0.00 3.86
7348 7537 2.749621 ACGGATTCACTCATTTTGCTCC 59.250 45.455 0.00 0.00 0.00 4.70
7349 7538 4.631813 AGTACGGATTCACTCATTTTGCTC 59.368 41.667 0.00 0.00 0.00 4.26
7350 7539 4.579869 AGTACGGATTCACTCATTTTGCT 58.420 39.130 0.00 0.00 0.00 3.91
7351 7540 4.631813 AGAGTACGGATTCACTCATTTTGC 59.368 41.667 4.70 0.00 42.99 3.68
7352 7541 7.827819 TTAGAGTACGGATTCACTCATTTTG 57.172 36.000 4.70 0.00 42.99 2.44
7353 7542 8.842358 TTTTAGAGTACGGATTCACTCATTTT 57.158 30.769 4.70 0.00 42.99 1.82
7356 7545 9.698309 CATATTTTAGAGTACGGATTCACTCAT 57.302 33.333 4.70 0.00 42.99 2.90
7357 7546 8.692710 ACATATTTTAGAGTACGGATTCACTCA 58.307 33.333 4.70 0.00 42.99 3.41
7358 7547 9.182933 GACATATTTTAGAGTACGGATTCACTC 57.817 37.037 0.00 0.00 41.25 3.51
7359 7548 8.915036 AGACATATTTTAGAGTACGGATTCACT 58.085 33.333 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.