Multiple sequence alignment - TraesCS1B01G228700

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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 TraesCS1B01G228700 chr1B 100.000 2333 0 0 1 2333 410047225 410044893 0.000000e+00 4309
1 TraesCS1B01G228700 chr1B 95.800 1643 68 1 3 1645 24201189 24202830 0.000000e+00 2651
2 TraesCS1B01G228700 chr6B 98.545 1650 24 0 1 1650 59939089 59940738 0.000000e+00 2915
3 TraesCS1B01G228700 chr4A 98.055 1645 32 0 1 1645 668642195 668640551 0.000000e+00 2861
4 TraesCS1B01G228700 chr4A 87.120 1646 205 7 3 1645 438690795 438689154 0.000000e+00 1858
5 TraesCS1B01G228700 chr5B 98.300 1588 27 0 59 1646 80274033 80272446 0.000000e+00 2784
6 TraesCS1B01G228700 chr5B 98.111 1588 30 0 59 1646 80678822 80677235 0.000000e+00 2767
7 TraesCS1B01G228700 chr7A 89.212 1650 166 11 3 1645 12891348 12892992 0.000000e+00 2050
8 TraesCS1B01G228700 chr6A 88.963 1649 173 8 3 1645 133819583 133821228 0.000000e+00 2028
9 TraesCS1B01G228700 chr5A 86.743 1652 204 14 3 1649 602240361 602242002 0.000000e+00 1823
10 TraesCS1B01G228700 chr1D 89.945 547 26 8 1790 2333 302999090 302998570 0.000000e+00 678
11 TraesCS1B01G228700 chr1A 91.008 367 21 5 1970 2333 380319064 380318707 3.490000e-133 484
12 TraesCS1B01G228700 chr1A 92.105 190 9 2 1767 1956 380323759 380323576 1.780000e-66 263


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 TraesCS1B01G228700 chr1B 410044893 410047225 2332 True 4309 4309 100.000 1 2333 1 chr1B.!!$R1 2332
1 TraesCS1B01G228700 chr1B 24201189 24202830 1641 False 2651 2651 95.800 3 1645 1 chr1B.!!$F1 1642
2 TraesCS1B01G228700 chr6B 59939089 59940738 1649 False 2915 2915 98.545 1 1650 1 chr6B.!!$F1 1649
3 TraesCS1B01G228700 chr4A 668640551 668642195 1644 True 2861 2861 98.055 1 1645 1 chr4A.!!$R2 1644
4 TraesCS1B01G228700 chr4A 438689154 438690795 1641 True 1858 1858 87.120 3 1645 1 chr4A.!!$R1 1642
5 TraesCS1B01G228700 chr5B 80272446 80274033 1587 True 2784 2784 98.300 59 1646 1 chr5B.!!$R1 1587
6 TraesCS1B01G228700 chr5B 80677235 80678822 1587 True 2767 2767 98.111 59 1646 1 chr5B.!!$R2 1587
7 TraesCS1B01G228700 chr7A 12891348 12892992 1644 False 2050 2050 89.212 3 1645 1 chr7A.!!$F1 1642
8 TraesCS1B01G228700 chr6A 133819583 133821228 1645 False 2028 2028 88.963 3 1645 1 chr6A.!!$F1 1642
9 TraesCS1B01G228700 chr5A 602240361 602242002 1641 False 1823 1823 86.743 3 1649 1 chr5A.!!$F1 1646
10 TraesCS1B01G228700 chr1D 302998570 302999090 520 True 678 678 89.945 1790 2333 1 chr1D.!!$R1 543

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
542 543 0.694771 ATGGCTGAGCAGTTTCCTCA 59.305 50.0 6.82 0.0 37.71 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 1678 0.03759 TAAAGCCAAGCCACATCCGT 59.962 50.0 0.0 0.0 0.0 4.69 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
118 119 9.860650 TTGCCTTTTATTATATGTCCATGTACT 57.139 29.630 0.00 0.00 0.00 2.73
227 228 5.484998 ACCCGGTTAAGTGGACTAGAATTTA 59.515 40.000 0.00 0.00 0.00 1.40
542 543 0.694771 ATGGCTGAGCAGTTTCCTCA 59.305 50.000 6.82 0.00 37.71 3.86
1287 1290 2.123342 CTGAAGGAGAATGCGTCGATC 58.877 52.381 0.00 0.00 37.83 3.69
1506 1514 2.675075 CGGGTTTTCGCCCCACAT 60.675 61.111 0.00 0.00 45.91 3.21
1590 1598 4.042934 CCCCTTTTCTCCTTTCTTGGACTA 59.957 45.833 0.00 0.00 31.94 2.59
1664 1672 6.441088 AAAAGAAGTATCTGGTTCAGGAGT 57.559 37.500 0.00 0.00 35.59 3.85
1665 1673 7.554959 AAAAGAAGTATCTGGTTCAGGAGTA 57.445 36.000 0.00 0.00 35.59 2.59
1666 1674 6.783708 AAGAAGTATCTGGTTCAGGAGTAG 57.216 41.667 0.00 0.00 35.59 2.57
1667 1675 5.205056 AGAAGTATCTGGTTCAGGAGTAGG 58.795 45.833 0.00 0.00 33.59 3.18
1668 1676 4.883021 AGTATCTGGTTCAGGAGTAGGA 57.117 45.455 0.00 0.00 31.51 2.94
1669 1677 5.208294 AGTATCTGGTTCAGGAGTAGGAA 57.792 43.478 0.00 0.00 31.51 3.36
1670 1678 5.590818 AGTATCTGGTTCAGGAGTAGGAAA 58.409 41.667 0.00 0.00 31.51 3.13
1671 1679 4.828072 ATCTGGTTCAGGAGTAGGAAAC 57.172 45.455 0.00 0.00 31.51 2.78
1672 1680 2.561419 TCTGGTTCAGGAGTAGGAAACG 59.439 50.000 0.00 0.00 33.43 3.60
1673 1681 1.621814 TGGTTCAGGAGTAGGAAACGG 59.378 52.381 0.00 0.00 33.43 4.44
1674 1682 1.897802 GGTTCAGGAGTAGGAAACGGA 59.102 52.381 0.00 0.00 0.00 4.69
1675 1683 2.500504 GGTTCAGGAGTAGGAAACGGAT 59.499 50.000 0.00 0.00 0.00 4.18
1676 1684 3.522553 GTTCAGGAGTAGGAAACGGATG 58.477 50.000 0.00 0.00 0.00 3.51
1677 1685 2.816411 TCAGGAGTAGGAAACGGATGT 58.184 47.619 0.00 0.00 0.00 3.06
1678 1686 2.496070 TCAGGAGTAGGAAACGGATGTG 59.504 50.000 0.00 0.00 0.00 3.21
1679 1687 1.831736 AGGAGTAGGAAACGGATGTGG 59.168 52.381 0.00 0.00 0.00 4.17
1680 1688 1.653151 GAGTAGGAAACGGATGTGGC 58.347 55.000 0.00 0.00 0.00 5.01
1681 1689 1.207329 GAGTAGGAAACGGATGTGGCT 59.793 52.381 0.00 0.00 0.00 4.75
1682 1690 1.628846 AGTAGGAAACGGATGTGGCTT 59.371 47.619 0.00 0.00 0.00 4.35
1683 1691 1.737793 GTAGGAAACGGATGTGGCTTG 59.262 52.381 0.00 0.00 0.00 4.01
1684 1692 0.609131 AGGAAACGGATGTGGCTTGG 60.609 55.000 0.00 0.00 0.00 3.61
1685 1693 1.212751 GAAACGGATGTGGCTTGGC 59.787 57.895 0.00 0.00 0.00 4.52
1686 1694 1.228552 AAACGGATGTGGCTTGGCT 60.229 52.632 0.00 0.00 0.00 4.75
1687 1695 0.827507 AAACGGATGTGGCTTGGCTT 60.828 50.000 0.00 0.00 0.00 4.35
1688 1696 0.827507 AACGGATGTGGCTTGGCTTT 60.828 50.000 0.00 0.00 0.00 3.51
1689 1697 0.037590 ACGGATGTGGCTTGGCTTTA 59.962 50.000 0.00 0.00 0.00 1.85
1690 1698 1.173043 CGGATGTGGCTTGGCTTTAA 58.827 50.000 0.00 0.00 0.00 1.52
1691 1699 1.543802 CGGATGTGGCTTGGCTTTAAA 59.456 47.619 0.00 0.00 0.00 1.52
1692 1700 2.415893 CGGATGTGGCTTGGCTTTAAAG 60.416 50.000 11.02 11.02 0.00 1.85
1707 1715 3.781079 TTAAAGCATGGGAATCGCTTG 57.219 42.857 8.50 8.50 44.93 4.01
1708 1716 0.174162 AAAGCATGGGAATCGCTTGC 59.826 50.000 23.93 23.93 44.93 4.01
1709 1717 1.077212 AGCATGGGAATCGCTTGCT 60.077 52.632 26.87 26.87 46.78 3.91
1710 1718 2.706636 GCATGGGAATCGCTTGCTA 58.293 52.632 24.01 0.00 41.63 3.49
1711 1719 1.024271 GCATGGGAATCGCTTGCTAA 58.976 50.000 24.01 0.00 41.63 3.09
1712 1720 1.002033 GCATGGGAATCGCTTGCTAAG 60.002 52.381 24.01 0.00 41.63 2.18
1713 1721 2.564771 CATGGGAATCGCTTGCTAAGA 58.435 47.619 0.00 0.00 0.00 2.10
1714 1722 2.315925 TGGGAATCGCTTGCTAAGAG 57.684 50.000 0.00 0.00 0.00 2.85
1715 1723 0.940833 GGGAATCGCTTGCTAAGAGC 59.059 55.000 0.00 0.00 42.82 4.09
1726 1734 1.082690 GCTAAGAGCAGTGCTGTTCC 58.917 55.000 28.81 17.85 41.21 3.62
1727 1735 1.354040 CTAAGAGCAGTGCTGTTCCG 58.646 55.000 28.81 17.85 41.21 4.30
1728 1736 0.679505 TAAGAGCAGTGCTGTTCCGT 59.320 50.000 28.81 12.35 41.21 4.69
1729 1737 0.679505 AAGAGCAGTGCTGTTCCGTA 59.320 50.000 25.35 0.00 37.62 4.02
1730 1738 0.679505 AGAGCAGTGCTGTTCCGTAA 59.320 50.000 25.35 0.00 41.00 3.18
1731 1739 1.071605 GAGCAGTGCTGTTCCGTAAG 58.928 55.000 25.35 0.00 39.88 2.34
1732 1740 0.951040 AGCAGTGCTGTTCCGTAAGC 60.951 55.000 18.98 0.00 37.57 3.09
1733 1741 1.227999 GCAGTGCTGTTCCGTAAGCA 61.228 55.000 8.18 0.00 46.84 3.91
1736 1744 2.853159 TGCTGTTCCGTAAGCATGG 58.147 52.632 0.00 0.00 44.26 3.66
1737 1745 0.323302 TGCTGTTCCGTAAGCATGGA 59.677 50.000 0.00 0.00 44.26 3.41
1738 1746 1.271108 TGCTGTTCCGTAAGCATGGAA 60.271 47.619 0.00 0.00 45.77 3.53
1760 1768 3.375782 GCAAGGCCATTGATTGTATCC 57.624 47.619 16.28 0.00 41.83 2.59
1761 1769 2.694628 GCAAGGCCATTGATTGTATCCA 59.305 45.455 16.28 0.00 41.83 3.41
1762 1770 3.322828 GCAAGGCCATTGATTGTATCCAT 59.677 43.478 16.28 0.00 41.83 3.41
1763 1771 4.798263 GCAAGGCCATTGATTGTATCCATG 60.798 45.833 16.28 0.00 41.83 3.66
1764 1772 4.458256 AGGCCATTGATTGTATCCATGA 57.542 40.909 5.01 0.00 35.15 3.07
1765 1773 4.404640 AGGCCATTGATTGTATCCATGAG 58.595 43.478 5.01 0.00 35.15 2.90
1766 1774 4.141088 AGGCCATTGATTGTATCCATGAGT 60.141 41.667 5.01 0.00 35.15 3.41
1767 1775 4.586001 GGCCATTGATTGTATCCATGAGTT 59.414 41.667 0.00 0.00 35.15 3.01
1768 1776 5.508489 GGCCATTGATTGTATCCATGAGTTG 60.508 44.000 0.00 0.00 35.15 3.16
1769 1777 5.526115 CCATTGATTGTATCCATGAGTTGC 58.474 41.667 0.00 0.00 35.15 4.17
1770 1778 5.068067 CCATTGATTGTATCCATGAGTTGCA 59.932 40.000 0.00 0.00 35.15 4.08
1771 1779 5.823209 TTGATTGTATCCATGAGTTGCAG 57.177 39.130 0.00 0.00 0.00 4.41
1772 1780 4.847198 TGATTGTATCCATGAGTTGCAGT 58.153 39.130 0.00 0.00 0.00 4.40
1773 1781 4.637091 TGATTGTATCCATGAGTTGCAGTG 59.363 41.667 0.00 0.00 0.00 3.66
1774 1782 3.979101 TGTATCCATGAGTTGCAGTGA 57.021 42.857 0.00 0.00 0.00 3.41
1775 1783 3.865446 TGTATCCATGAGTTGCAGTGAG 58.135 45.455 0.00 0.00 0.00 3.51
1776 1784 3.515104 TGTATCCATGAGTTGCAGTGAGA 59.485 43.478 0.00 0.00 0.00 3.27
1777 1785 2.756840 TCCATGAGTTGCAGTGAGAG 57.243 50.000 0.00 0.00 0.00 3.20
1778 1786 2.250924 TCCATGAGTTGCAGTGAGAGA 58.749 47.619 0.00 0.00 0.00 3.10
1779 1787 2.836372 TCCATGAGTTGCAGTGAGAGAT 59.164 45.455 0.00 0.00 0.00 2.75
1780 1788 3.262660 TCCATGAGTTGCAGTGAGAGATT 59.737 43.478 0.00 0.00 0.00 2.40
1781 1789 3.374367 CCATGAGTTGCAGTGAGAGATTG 59.626 47.826 0.00 0.00 0.00 2.67
1782 1790 2.420642 TGAGTTGCAGTGAGAGATTGC 58.579 47.619 0.00 0.00 37.80 3.56
1783 1791 2.038164 TGAGTTGCAGTGAGAGATTGCT 59.962 45.455 0.00 0.00 38.14 3.91
1784 1792 2.672381 GAGTTGCAGTGAGAGATTGCTC 59.328 50.000 0.00 0.00 38.14 4.26
1785 1793 1.736681 GTTGCAGTGAGAGATTGCTCC 59.263 52.381 0.00 0.00 42.30 4.70
1786 1794 0.978907 TGCAGTGAGAGATTGCTCCA 59.021 50.000 0.00 0.00 42.30 3.86
1787 1795 1.066358 TGCAGTGAGAGATTGCTCCAG 60.066 52.381 0.00 0.00 42.30 3.86
1788 1796 1.206610 GCAGTGAGAGATTGCTCCAGA 59.793 52.381 0.00 0.00 42.30 3.86
1810 1818 3.260100 ACCTCCCAACTGCAGGGG 61.260 66.667 19.93 19.57 46.77 4.79
1831 1839 2.639286 GCAACAACTGGTCCAGCG 59.361 61.111 19.40 12.72 34.37 5.18
1911 1919 2.787680 CGGTCTATTCGTTCGCCTTTAG 59.212 50.000 0.00 0.00 0.00 1.85
1940 1948 4.451900 TCTCTTGTTGTTTTCCTGAGGAC 58.548 43.478 0.00 0.00 0.00 3.85
1956 1964 5.205056 CTGAGGACTACTCTTGGGTAGATT 58.795 45.833 13.94 0.06 46.72 2.40
1958 1966 5.202004 GAGGACTACTCTTGGGTAGATTCA 58.798 45.833 13.94 0.00 43.14 2.57
2008 2016 8.830915 ACAGATATAGGAGTATATGTTGGGAG 57.169 38.462 0.00 0.00 33.93 4.30
2009 2017 7.343316 ACAGATATAGGAGTATATGTTGGGAGC 59.657 40.741 0.00 0.00 33.93 4.70
2034 2042 1.821753 AGATCGAGTGAGGGTTGACAG 59.178 52.381 0.00 0.00 0.00 3.51
2045 2053 1.160137 GGTTGACAGAGCATGGTGAC 58.840 55.000 0.00 0.00 0.00 3.67
2078 2086 3.614092 GATGGAGAATCAAAGTGAGCCA 58.386 45.455 0.00 0.00 36.25 4.75
2111 2122 4.336433 ACACACACATGCTGATATAAAGCC 59.664 41.667 7.28 0.00 40.06 4.35
2141 2152 1.789078 CGGCAGTGCTCAGCAAAGTT 61.789 55.000 16.11 0.00 41.47 2.66
2147 2158 1.174712 TGCTCAGCAAAGTTGGGCTC 61.175 55.000 0.00 0.00 42.56 4.70
2148 2159 1.871772 CTCAGCAAAGTTGGGCTCG 59.128 57.895 0.00 0.00 38.56 5.03
2150 2161 1.898574 CAGCAAAGTTGGGCTCGGT 60.899 57.895 0.00 0.00 38.56 4.69
2159 2170 0.766131 TTGGGCTCGGTTCAACCTAA 59.234 50.000 4.68 0.00 35.66 2.69
2174 2185 5.101529 TCAACCTAAGATTCTTCCTTCCCT 58.898 41.667 1.27 0.00 0.00 4.20
2181 2192 4.434195 AGATTCTTCCTTCCCTTGAGAGT 58.566 43.478 0.00 0.00 0.00 3.24
2186 2197 6.301169 TCTTCCTTCCCTTGAGAGTAATTC 57.699 41.667 0.00 0.00 0.00 2.17
2187 2198 5.189934 TCTTCCTTCCCTTGAGAGTAATTCC 59.810 44.000 0.00 0.00 0.00 3.01
2188 2199 4.435137 TCCTTCCCTTGAGAGTAATTCCA 58.565 43.478 0.00 0.00 0.00 3.53
2216 2227 6.901300 TCTACTCTCTCTTGGAGTATGCTAA 58.099 40.000 4.40 0.00 42.85 3.09
2217 2228 6.995686 TCTACTCTCTCTTGGAGTATGCTAAG 59.004 42.308 4.40 0.00 42.85 2.18
2218 2229 4.892934 ACTCTCTCTTGGAGTATGCTAAGG 59.107 45.833 0.00 0.00 41.56 2.69
2240 2251 1.346197 CACGCACTAGCAGCATTCG 59.654 57.895 8.31 0.00 42.27 3.34
2247 2258 2.098934 CACTAGCAGCATTCGAGAGTCT 59.901 50.000 0.00 0.00 0.00 3.24
2254 2265 3.555139 CAGCATTCGAGAGTCTTTGATCC 59.445 47.826 0.00 0.00 0.00 3.36
2256 2267 4.081198 AGCATTCGAGAGTCTTTGATCCTT 60.081 41.667 0.00 0.00 0.00 3.36
2278 2289 1.353022 TGGCGAATAAAAGTGGGGAGT 59.647 47.619 0.00 0.00 0.00 3.85
2285 2296 5.648092 CGAATAAAAGTGGGGAGTTCAATCT 59.352 40.000 0.00 0.00 0.00 2.40
2300 2311 7.038154 AGTTCAATCTCCGAAATCAACAAAA 57.962 32.000 0.00 0.00 0.00 2.44
2324 2335 3.905249 CGCCTCTTTGGGGCTAAC 58.095 61.111 6.90 0.00 46.73 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 8.527810 CCTGGCAAGTATAGTTTTGGATAAAAA 58.472 33.333 0.00 0.00 37.51 1.94
250 251 5.415701 GCTTATGAAGATCTTTCACACCCAA 59.584 40.000 9.87 0.00 0.00 4.12
1179 1182 6.630444 ATTAAAGCACAGGCAGAGAATATG 57.370 37.500 0.00 0.00 44.61 1.78
1287 1290 1.874231 GCAGCACAGATCCTCATCATG 59.126 52.381 0.00 0.00 0.00 3.07
1590 1598 6.509418 ACTGCAACATAACGGAAATACAAT 57.491 33.333 0.00 0.00 0.00 2.71
1650 1658 3.195825 CGTTTCCTACTCCTGAACCAGAT 59.804 47.826 0.00 0.00 32.44 2.90
1651 1659 2.561419 CGTTTCCTACTCCTGAACCAGA 59.439 50.000 0.00 0.00 32.44 3.86
1652 1660 2.353803 CCGTTTCCTACTCCTGAACCAG 60.354 54.545 0.00 0.00 0.00 4.00
1653 1661 1.621814 CCGTTTCCTACTCCTGAACCA 59.378 52.381 0.00 0.00 0.00 3.67
1654 1662 1.897802 TCCGTTTCCTACTCCTGAACC 59.102 52.381 0.00 0.00 0.00 3.62
1655 1663 3.056035 ACATCCGTTTCCTACTCCTGAAC 60.056 47.826 0.00 0.00 0.00 3.18
1656 1664 3.056107 CACATCCGTTTCCTACTCCTGAA 60.056 47.826 0.00 0.00 0.00 3.02
1657 1665 2.496070 CACATCCGTTTCCTACTCCTGA 59.504 50.000 0.00 0.00 0.00 3.86
1658 1666 2.418746 CCACATCCGTTTCCTACTCCTG 60.419 54.545 0.00 0.00 0.00 3.86
1659 1667 1.831736 CCACATCCGTTTCCTACTCCT 59.168 52.381 0.00 0.00 0.00 3.69
1660 1668 1.742750 GCCACATCCGTTTCCTACTCC 60.743 57.143 0.00 0.00 0.00 3.85
1661 1669 1.207329 AGCCACATCCGTTTCCTACTC 59.793 52.381 0.00 0.00 0.00 2.59
1662 1670 1.276622 AGCCACATCCGTTTCCTACT 58.723 50.000 0.00 0.00 0.00 2.57
1663 1671 1.737793 CAAGCCACATCCGTTTCCTAC 59.262 52.381 0.00 0.00 0.00 3.18
1664 1672 1.339631 CCAAGCCACATCCGTTTCCTA 60.340 52.381 0.00 0.00 0.00 2.94
1665 1673 0.609131 CCAAGCCACATCCGTTTCCT 60.609 55.000 0.00 0.00 0.00 3.36
1666 1674 1.883021 CCAAGCCACATCCGTTTCC 59.117 57.895 0.00 0.00 0.00 3.13
1667 1675 1.212751 GCCAAGCCACATCCGTTTC 59.787 57.895 0.00 0.00 0.00 2.78
1668 1676 0.827507 AAGCCAAGCCACATCCGTTT 60.828 50.000 0.00 0.00 0.00 3.60
1669 1677 0.827507 AAAGCCAAGCCACATCCGTT 60.828 50.000 0.00 0.00 0.00 4.44
1670 1678 0.037590 TAAAGCCAAGCCACATCCGT 59.962 50.000 0.00 0.00 0.00 4.69
1671 1679 1.173043 TTAAAGCCAAGCCACATCCG 58.827 50.000 0.00 0.00 0.00 4.18
1672 1680 2.675032 GCTTTAAAGCCAAGCCACATCC 60.675 50.000 26.60 0.00 46.20 3.51
1673 1681 2.610433 GCTTTAAAGCCAAGCCACATC 58.390 47.619 26.60 0.00 46.20 3.06
1674 1682 2.749280 GCTTTAAAGCCAAGCCACAT 57.251 45.000 26.60 0.00 46.20 3.21
1684 1692 3.429410 AAGCGATTCCCATGCTTTAAAGC 60.429 43.478 29.36 29.36 46.12 3.51
1685 1693 4.107622 CAAGCGATTCCCATGCTTTAAAG 58.892 43.478 11.02 11.02 46.12 1.85
1686 1694 3.675775 GCAAGCGATTCCCATGCTTTAAA 60.676 43.478 0.00 0.00 46.12 1.52
1687 1695 2.159254 GCAAGCGATTCCCATGCTTTAA 60.159 45.455 0.00 0.00 46.12 1.52
1688 1696 1.405105 GCAAGCGATTCCCATGCTTTA 59.595 47.619 0.00 0.00 46.12 1.85
1689 1697 0.174162 GCAAGCGATTCCCATGCTTT 59.826 50.000 0.00 0.00 46.12 3.51
1691 1699 1.077212 AGCAAGCGATTCCCATGCT 60.077 52.632 0.00 0.00 42.19 3.79
1692 1700 1.002033 CTTAGCAAGCGATTCCCATGC 60.002 52.381 0.00 0.00 37.28 4.06
1693 1701 2.547211 CTCTTAGCAAGCGATTCCCATG 59.453 50.000 0.00 0.00 0.00 3.66
1694 1702 2.843701 CTCTTAGCAAGCGATTCCCAT 58.156 47.619 0.00 0.00 0.00 4.00
1695 1703 1.743772 GCTCTTAGCAAGCGATTCCCA 60.744 52.381 0.00 0.00 41.89 4.37
1696 1704 0.940833 GCTCTTAGCAAGCGATTCCC 59.059 55.000 0.00 0.00 41.89 3.97
1707 1715 1.082690 GGAACAGCACTGCTCTTAGC 58.917 55.000 0.00 0.00 42.82 3.09
1708 1716 1.337260 ACGGAACAGCACTGCTCTTAG 60.337 52.381 0.00 0.00 36.40 2.18
1709 1717 0.679505 ACGGAACAGCACTGCTCTTA 59.320 50.000 0.00 0.00 36.40 2.10
1710 1718 0.679505 TACGGAACAGCACTGCTCTT 59.320 50.000 0.00 0.00 36.40 2.85
1711 1719 0.679505 TTACGGAACAGCACTGCTCT 59.320 50.000 0.00 0.00 36.40 4.09
1712 1720 1.071605 CTTACGGAACAGCACTGCTC 58.928 55.000 0.00 0.00 36.40 4.26
1713 1721 0.951040 GCTTACGGAACAGCACTGCT 60.951 55.000 0.00 0.00 40.77 4.24
1714 1722 1.227999 TGCTTACGGAACAGCACTGC 61.228 55.000 0.00 0.00 41.20 4.40
1715 1723 2.912986 TGCTTACGGAACAGCACTG 58.087 52.632 0.00 0.00 41.20 3.66
1719 1727 1.398390 CTTCCATGCTTACGGAACAGC 59.602 52.381 0.00 0.00 36.36 4.40
1720 1728 2.009774 CCTTCCATGCTTACGGAACAG 58.990 52.381 0.00 0.00 36.36 3.16
1721 1729 1.948611 GCCTTCCATGCTTACGGAACA 60.949 52.381 0.00 0.00 36.36 3.18
1722 1730 0.733150 GCCTTCCATGCTTACGGAAC 59.267 55.000 0.00 0.00 36.36 3.62
1723 1731 0.326595 TGCCTTCCATGCTTACGGAA 59.673 50.000 0.00 0.00 38.99 4.30
1724 1732 0.326595 TTGCCTTCCATGCTTACGGA 59.673 50.000 0.00 0.00 0.00 4.69
1725 1733 0.734889 CTTGCCTTCCATGCTTACGG 59.265 55.000 0.00 0.00 0.00 4.02
1726 1734 0.734889 CCTTGCCTTCCATGCTTACG 59.265 55.000 0.00 0.00 0.00 3.18
1727 1735 0.457443 GCCTTGCCTTCCATGCTTAC 59.543 55.000 0.00 0.00 0.00 2.34
1728 1736 0.684153 GGCCTTGCCTTCCATGCTTA 60.684 55.000 0.00 0.00 46.69 3.09
1729 1737 1.986210 GGCCTTGCCTTCCATGCTT 60.986 57.895 0.00 0.00 46.69 3.91
1730 1738 2.363406 GGCCTTGCCTTCCATGCT 60.363 61.111 0.00 0.00 46.69 3.79
1740 1748 3.375782 GGATACAATCAATGGCCTTGC 57.624 47.619 3.32 0.00 34.66 4.01
1755 1763 4.118410 CTCTCACTGCAACTCATGGATAC 58.882 47.826 0.00 0.00 0.00 2.24
1756 1764 4.026052 TCTCTCACTGCAACTCATGGATA 58.974 43.478 0.00 0.00 0.00 2.59
1757 1765 2.836372 TCTCTCACTGCAACTCATGGAT 59.164 45.455 0.00 0.00 0.00 3.41
1758 1766 2.250924 TCTCTCACTGCAACTCATGGA 58.749 47.619 0.00 0.00 0.00 3.41
1759 1767 2.756840 TCTCTCACTGCAACTCATGG 57.243 50.000 0.00 0.00 0.00 3.66
1760 1768 3.181509 GCAATCTCTCACTGCAACTCATG 60.182 47.826 0.00 0.00 36.09 3.07
1761 1769 3.008330 GCAATCTCTCACTGCAACTCAT 58.992 45.455 0.00 0.00 36.09 2.90
1762 1770 2.038164 AGCAATCTCTCACTGCAACTCA 59.962 45.455 0.00 0.00 38.58 3.41
1763 1771 2.672381 GAGCAATCTCTCACTGCAACTC 59.328 50.000 0.00 0.00 38.58 3.01
1764 1772 2.614987 GGAGCAATCTCTCACTGCAACT 60.615 50.000 0.00 0.00 39.31 3.16
1765 1773 1.736681 GGAGCAATCTCTCACTGCAAC 59.263 52.381 0.00 0.00 39.31 4.17
1766 1774 1.348696 TGGAGCAATCTCTCACTGCAA 59.651 47.619 0.00 0.00 39.31 4.08
1767 1775 0.978907 TGGAGCAATCTCTCACTGCA 59.021 50.000 0.00 0.00 39.31 4.41
1768 1776 1.206610 TCTGGAGCAATCTCTCACTGC 59.793 52.381 0.00 0.00 39.31 4.40
1769 1777 2.418471 GGTCTGGAGCAATCTCTCACTG 60.418 54.545 0.00 0.00 39.31 3.66
1770 1778 1.830477 GGTCTGGAGCAATCTCTCACT 59.170 52.381 0.00 0.00 39.31 3.41
1771 1779 1.552337 TGGTCTGGAGCAATCTCTCAC 59.448 52.381 0.00 0.00 39.31 3.51
1772 1780 1.829849 CTGGTCTGGAGCAATCTCTCA 59.170 52.381 4.09 0.00 38.46 3.27
1773 1781 2.106566 TCTGGTCTGGAGCAATCTCTC 58.893 52.381 4.09 0.00 38.46 3.20
1774 1782 1.830477 GTCTGGTCTGGAGCAATCTCT 59.170 52.381 4.09 0.00 38.46 3.10
1775 1783 1.134551 GGTCTGGTCTGGAGCAATCTC 60.135 57.143 4.09 0.00 38.46 2.75
1776 1784 0.908198 GGTCTGGTCTGGAGCAATCT 59.092 55.000 4.09 0.00 38.46 2.40
1777 1785 0.908198 AGGTCTGGTCTGGAGCAATC 59.092 55.000 4.09 0.96 38.46 2.67
1778 1786 0.908198 GAGGTCTGGTCTGGAGCAAT 59.092 55.000 4.09 0.00 38.46 3.56
1779 1787 1.194781 GGAGGTCTGGTCTGGAGCAA 61.195 60.000 4.09 0.00 38.46 3.91
1780 1788 1.610673 GGAGGTCTGGTCTGGAGCA 60.611 63.158 2.52 2.52 37.27 4.26
1781 1789 2.363172 GGGAGGTCTGGTCTGGAGC 61.363 68.421 0.00 0.00 0.00 4.70
1782 1790 0.545309 TTGGGAGGTCTGGTCTGGAG 60.545 60.000 0.00 0.00 0.00 3.86
1783 1791 0.836400 GTTGGGAGGTCTGGTCTGGA 60.836 60.000 0.00 0.00 0.00 3.86
1784 1792 0.838122 AGTTGGGAGGTCTGGTCTGG 60.838 60.000 0.00 0.00 0.00 3.86
1785 1793 0.322975 CAGTTGGGAGGTCTGGTCTG 59.677 60.000 0.00 0.00 0.00 3.51
1786 1794 1.484444 GCAGTTGGGAGGTCTGGTCT 61.484 60.000 0.00 0.00 0.00 3.85
1787 1795 1.003233 GCAGTTGGGAGGTCTGGTC 60.003 63.158 0.00 0.00 0.00 4.02
1788 1796 1.770110 TGCAGTTGGGAGGTCTGGT 60.770 57.895 0.00 0.00 0.00 4.00
1810 1818 0.883833 CTGGACCAGTTGTTGCCATC 59.116 55.000 13.84 0.00 0.00 3.51
1828 1836 1.028905 GGATCTGACTGTAGCTCGCT 58.971 55.000 0.00 0.00 0.00 4.93
1831 1839 1.068434 GCCTGGATCTGACTGTAGCTC 59.932 57.143 0.00 0.00 0.00 4.09
1911 1919 7.257722 TCAGGAAAACAACAAGAGAAAATCAC 58.742 34.615 0.00 0.00 0.00 3.06
1940 1948 4.503991 GGCCATGAATCTACCCAAGAGTAG 60.504 50.000 0.00 0.00 40.98 2.57
1956 1964 5.447757 TCATCATAATGTTCAAGGCCATGA 58.552 37.500 6.57 6.57 34.32 3.07
1958 1966 6.989155 AATCATCATAATGTTCAAGGCCAT 57.011 33.333 5.01 0.00 34.32 4.40
1988 1996 5.823312 TCGCTCCCAACATATACTCCTATA 58.177 41.667 0.00 0.00 0.00 1.31
1989 1997 4.673968 TCGCTCCCAACATATACTCCTAT 58.326 43.478 0.00 0.00 0.00 2.57
1990 1998 4.108501 TCGCTCCCAACATATACTCCTA 57.891 45.455 0.00 0.00 0.00 2.94
1991 1999 2.958818 TCGCTCCCAACATATACTCCT 58.041 47.619 0.00 0.00 0.00 3.69
1992 2000 3.746045 TTCGCTCCCAACATATACTCC 57.254 47.619 0.00 0.00 0.00 3.85
1993 2001 5.357257 TCTTTTCGCTCCCAACATATACTC 58.643 41.667 0.00 0.00 0.00 2.59
1994 2002 5.353394 TCTTTTCGCTCCCAACATATACT 57.647 39.130 0.00 0.00 0.00 2.12
1995 2003 5.107453 CGATCTTTTCGCTCCCAACATATAC 60.107 44.000 0.00 0.00 41.69 1.47
1996 2004 4.988540 CGATCTTTTCGCTCCCAACATATA 59.011 41.667 0.00 0.00 41.69 0.86
1997 2005 3.809832 CGATCTTTTCGCTCCCAACATAT 59.190 43.478 0.00 0.00 41.69 1.78
1998 2006 3.194861 CGATCTTTTCGCTCCCAACATA 58.805 45.455 0.00 0.00 41.69 2.29
1999 2007 2.009774 CGATCTTTTCGCTCCCAACAT 58.990 47.619 0.00 0.00 41.69 2.71
2000 2008 1.438651 CGATCTTTTCGCTCCCAACA 58.561 50.000 0.00 0.00 41.69 3.33
2045 2053 2.512692 TCTCCATCCAACAACCATGG 57.487 50.000 11.19 11.19 38.83 3.66
2078 2086 2.291465 GCATGTGTGTGTCAACTGTCAT 59.709 45.455 0.00 0.00 0.00 3.06
2124 2135 0.318445 CCAACTTTGCTGAGCACTGC 60.318 55.000 6.64 6.07 38.71 4.40
2141 2152 0.323629 CTTAGGTTGAACCGAGCCCA 59.676 55.000 8.98 0.00 44.90 5.36
2147 2158 4.833390 AGGAAGAATCTTAGGTTGAACCG 58.167 43.478 8.98 0.00 44.90 4.44
2148 2159 5.648526 GGAAGGAAGAATCTTAGGTTGAACC 59.351 44.000 6.16 6.16 38.99 3.62
2150 2161 5.551977 AGGGAAGGAAGAATCTTAGGTTGAA 59.448 40.000 0.00 0.00 0.00 2.69
2159 2170 4.434195 ACTCTCAAGGGAAGGAAGAATCT 58.566 43.478 0.00 0.00 0.00 2.40
2174 2185 6.897966 AGAGTAGATGGTGGAATTACTCTCAA 59.102 38.462 6.65 0.00 44.26 3.02
2181 2192 6.325028 CCAAGAGAGAGTAGATGGTGGAATTA 59.675 42.308 0.00 0.00 0.00 1.40
2186 2197 3.636300 CTCCAAGAGAGAGTAGATGGTGG 59.364 52.174 0.00 0.00 46.50 4.61
2187 2198 4.277476 ACTCCAAGAGAGAGTAGATGGTG 58.723 47.826 0.00 0.00 46.50 4.17
2188 2199 4.601406 ACTCCAAGAGAGAGTAGATGGT 57.399 45.455 0.00 0.00 46.50 3.55
2216 2227 1.890894 CTGCTAGTGCGTGGTACCT 59.109 57.895 14.36 0.00 43.34 3.08
2217 2228 1.810030 GCTGCTAGTGCGTGGTACC 60.810 63.158 4.43 4.43 43.34 3.34
2218 2229 0.460284 ATGCTGCTAGTGCGTGGTAC 60.460 55.000 0.00 0.00 43.34 3.34
2240 2251 3.006247 GCCACAAGGATCAAAGACTCTC 58.994 50.000 0.00 0.00 36.89 3.20
2247 2258 5.242838 ACTTTTATTCGCCACAAGGATCAAA 59.757 36.000 0.00 0.00 36.89 2.69
2254 2265 2.094752 CCCCACTTTTATTCGCCACAAG 60.095 50.000 0.00 0.00 0.00 3.16
2256 2267 1.074084 TCCCCACTTTTATTCGCCACA 59.926 47.619 0.00 0.00 0.00 4.17
2278 2289 5.920273 GCTTTTGTTGATTTCGGAGATTGAA 59.080 36.000 0.00 0.00 35.04 2.69
2285 2296 3.801594 GCAAAGCTTTTGTTGATTTCGGA 59.198 39.130 9.53 0.00 0.00 4.55


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

AutoCloner maintained by Alex Coulton.