Multiple sequence alignment - TraesCS2B01G176300

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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 TraesCS2B01G176300 chr2B 100.000 2318 0 0 1 2318 151461688 151459371 0.000000e+00 4281
1 TraesCS2B01G176300 chr2B 90.955 597 48 5 1 597 787789521 787788931 0.000000e+00 798
2 TraesCS2B01G176300 chr2B 85.714 413 56 3 1824 2234 106830003 106830414 1.270000e-117 433
3 TraesCS2B01G176300 chr2B 92.627 217 16 0 1630 1846 106859979 106859763 1.730000e-81 313
4 TraesCS2B01G176300 chr2B 88.000 175 14 6 1613 1783 106829834 106830005 1.400000e-47 200
5 TraesCS2B01G176300 chr2A 95.257 1012 26 8 597 1602 98875065 98876060 0.000000e+00 1583
6 TraesCS2B01G176300 chr2A 93.645 598 34 4 1 597 765190768 765191362 0.000000e+00 891
7 TraesCS2B01G176300 chr2A 90.674 193 16 2 1625 1816 773263237 773263046 2.960000e-64 255
8 TraesCS2B01G176300 chr2A 91.908 173 13 1 1625 1796 773233624 773233796 8.280000e-60 241
9 TraesCS2B01G176300 chr2D 95.219 983 28 9 597 1568 99577965 99578939 0.000000e+00 1537
10 TraesCS2B01G176300 chr1B 91.457 597 44 6 1 597 561638523 561639112 0.000000e+00 813
11 TraesCS2B01G176300 chr1B 90.787 597 49 6 1 597 675546840 675546250 0.000000e+00 793
12 TraesCS2B01G176300 chr5B 90.955 597 48 6 1 597 244131992 244132582 0.000000e+00 798
13 TraesCS2B01G176300 chr7A 90.285 597 52 4 1 597 25045122 25044532 0.000000e+00 776
14 TraesCS2B01G176300 chr7A 91.367 139 12 0 1648 1786 703533463 703533601 8.450000e-45 191
15 TraesCS2B01G176300 chr4A 90.117 597 52 6 1 597 674455664 674456253 0.000000e+00 769
16 TraesCS2B01G176300 chr4A 88.294 598 65 5 1 597 717268925 717268332 0.000000e+00 712
17 TraesCS2B01G176300 chr4A 87.416 596 68 6 3 597 717763263 717763852 0.000000e+00 678
18 TraesCS2B01G176300 chr3A 89.379 499 47 6 1824 2318 697017940 697018436 7.030000e-175 623
19 TraesCS2B01G176300 chr3A 89.947 189 18 1 1629 1816 697023971 697023783 2.300000e-60 243
20 TraesCS2B01G176300 chr3A 91.720 157 13 0 1630 1786 697017789 697017945 3.880000e-53 219
21 TraesCS2B01G176300 chr5A 89.135 497 50 4 1824 2317 477828147 477828642 1.180000e-172 616
22 TraesCS2B01G176300 chr5A 92.661 218 13 3 1630 1846 477833217 477833002 6.220000e-81 311
23 TraesCS2B01G176300 chrUn 95.722 374 7 6 597 965 477877695 477877326 5.510000e-166 593
24 TraesCS2B01G176300 chr3B 76.400 250 56 3 1628 1876 5131767 5132014 5.200000e-27 132


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 TraesCS2B01G176300 chr2B 151459371 151461688 2317 True 4281.0 4281 100.0000 1 2318 1 chr2B.!!$R2 2317
1 TraesCS2B01G176300 chr2B 787788931 787789521 590 True 798.0 798 90.9550 1 597 1 chr2B.!!$R3 596
2 TraesCS2B01G176300 chr2B 106829834 106830414 580 False 316.5 433 86.8570 1613 2234 2 chr2B.!!$F1 621
3 TraesCS2B01G176300 chr2A 98875065 98876060 995 False 1583.0 1583 95.2570 597 1602 1 chr2A.!!$F1 1005
4 TraesCS2B01G176300 chr2A 765190768 765191362 594 False 891.0 891 93.6450 1 597 1 chr2A.!!$F2 596
5 TraesCS2B01G176300 chr2D 99577965 99578939 974 False 1537.0 1537 95.2190 597 1568 1 chr2D.!!$F1 971
6 TraesCS2B01G176300 chr1B 561638523 561639112 589 False 813.0 813 91.4570 1 597 1 chr1B.!!$F1 596
7 TraesCS2B01G176300 chr1B 675546250 675546840 590 True 793.0 793 90.7870 1 597 1 chr1B.!!$R1 596
8 TraesCS2B01G176300 chr5B 244131992 244132582 590 False 798.0 798 90.9550 1 597 1 chr5B.!!$F1 596
9 TraesCS2B01G176300 chr7A 25044532 25045122 590 True 776.0 776 90.2850 1 597 1 chr7A.!!$R1 596
10 TraesCS2B01G176300 chr4A 674455664 674456253 589 False 769.0 769 90.1170 1 597 1 chr4A.!!$F1 596
11 TraesCS2B01G176300 chr4A 717268332 717268925 593 True 712.0 712 88.2940 1 597 1 chr4A.!!$R1 596
12 TraesCS2B01G176300 chr4A 717763263 717763852 589 False 678.0 678 87.4160 3 597 1 chr4A.!!$F2 594
13 TraesCS2B01G176300 chr3A 697017789 697018436 647 False 421.0 623 90.5495 1630 2318 2 chr3A.!!$F1 688

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
646 651 0.598942 AACACGCACTGATGTACGCA 60.599 50.0 0.0 0.0 36.49 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 1738 0.031857 CACCCGCAATGCAAGTTCAA 59.968 50.0 5.91 0.0 0.0 2.69 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
24 25 3.067106 TCGGTTCTCAATGTCTTCTTGC 58.933 45.455 0.00 0.00 0.00 4.01
71 72 0.727398 CGTTCCGGCAATTCTTCCTC 59.273 55.000 0.00 0.00 0.00 3.71
143 144 2.281484 TGACTTGTTGGGCGAGCC 60.281 61.111 5.37 5.37 31.61 4.70
167 168 2.560105 GTTTCTTTCCAGATGCAGCCTT 59.440 45.455 0.00 0.00 0.00 4.35
266 271 2.250924 CAGGGGCCTTCTTTGACATTT 58.749 47.619 0.84 0.00 0.00 2.32
295 300 2.598787 GGATGTGTTGGGTCGGGGA 61.599 63.158 0.00 0.00 0.00 4.81
352 357 2.608506 CGTTGGACGTGTTGATCCAGTA 60.609 50.000 0.00 0.00 45.66 2.74
360 365 1.134521 TGTTGATCCAGTACGGGCATC 60.135 52.381 7.24 11.28 34.36 3.91
406 411 1.066858 GCGTTGAGGACCTCTTCATCA 60.067 52.381 22.14 0.00 43.29 3.07
427 432 2.604686 AGCGGTGCTTCTCCCTGA 60.605 61.111 0.00 0.00 33.89 3.86
432 437 1.134280 CGGTGCTTCTCCCTGATGATT 60.134 52.381 0.00 0.00 0.00 2.57
436 441 4.381292 GGTGCTTCTCCCTGATGATTTTTG 60.381 45.833 0.00 0.00 0.00 2.44
570 575 5.121221 CTTTGTTAATTCAAAGCCGGTCT 57.879 39.130 1.90 0.00 44.57 3.85
639 644 2.280797 ACGGCAACACGCACTGAT 60.281 55.556 0.00 0.00 45.17 2.90
646 651 0.598942 AACACGCACTGATGTACGCA 60.599 50.000 0.00 0.00 36.49 5.24
647 652 0.598942 ACACGCACTGATGTACGCAA 60.599 50.000 0.00 0.00 36.49 4.85
660 665 4.739587 TGTACGCAAACCCATCTGTATA 57.260 40.909 0.00 0.00 0.00 1.47
661 666 5.284861 TGTACGCAAACCCATCTGTATAT 57.715 39.130 0.00 0.00 0.00 0.86
667 672 7.152645 ACGCAAACCCATCTGTATATAACTAG 58.847 38.462 0.00 0.00 0.00 2.57
702 707 3.385749 ATCCCTACGCCACGCCAAG 62.386 63.158 0.00 0.00 0.00 3.61
942 952 7.333672 CACATTTCTCCTAACTTGGTAGTTACC 59.666 40.741 1.25 1.25 42.73 2.85
988 998 3.553105 ACAAACACCGACTCGTAACTTTC 59.447 43.478 0.00 0.00 0.00 2.62
997 1007 2.475487 ACTCGTAACTTTCGAAAGCAGC 59.525 45.455 32.49 21.75 39.63 5.25
1032 1042 1.004560 CTTCCACAAGAGCGGCTCA 60.005 57.895 29.88 7.06 32.06 4.26
1044 1054 1.395826 GCGGCTCACCAGAGGATACT 61.396 60.000 0.00 0.00 45.12 2.12
1140 1150 1.386525 GCGGGCACATGAACATCCAT 61.387 55.000 0.00 0.00 0.00 3.41
1319 1332 2.500504 GCCACTACCCTTACAACTAGCT 59.499 50.000 0.00 0.00 0.00 3.32
1543 1567 8.523658 CAGAGTATATGACCAATAATCGAGGAA 58.476 37.037 0.00 0.00 31.07 3.36
1544 1568 9.261035 AGAGTATATGACCAATAATCGAGGAAT 57.739 33.333 0.00 0.00 31.07 3.01
1591 1615 2.124736 ACGTCGATTGGGGCCATG 60.125 61.111 4.39 0.00 0.00 3.66
1599 1623 1.425066 GATTGGGGCCATGGATGAGTA 59.575 52.381 18.40 0.00 0.00 2.59
1600 1624 1.533187 TTGGGGCCATGGATGAGTAT 58.467 50.000 18.40 0.00 0.00 2.12
1601 1625 0.773014 TGGGGCCATGGATGAGTATG 59.227 55.000 18.40 0.00 0.00 2.39
1602 1626 1.067295 GGGGCCATGGATGAGTATGA 58.933 55.000 18.40 0.00 0.00 2.15
1603 1627 1.004044 GGGGCCATGGATGAGTATGAG 59.996 57.143 18.40 0.00 0.00 2.90
1604 1628 1.980765 GGGCCATGGATGAGTATGAGA 59.019 52.381 18.40 0.00 0.00 3.27
1605 1629 2.575279 GGGCCATGGATGAGTATGAGAT 59.425 50.000 18.40 0.00 0.00 2.75
1606 1630 3.370315 GGGCCATGGATGAGTATGAGATC 60.370 52.174 18.40 0.00 0.00 2.75
1607 1631 3.262660 GGCCATGGATGAGTATGAGATCA 59.737 47.826 18.40 0.00 0.00 2.92
1608 1632 4.505808 GCCATGGATGAGTATGAGATCAG 58.494 47.826 18.40 0.00 0.00 2.90
1609 1633 4.505808 CCATGGATGAGTATGAGATCAGC 58.494 47.826 5.56 0.00 0.00 4.26
1610 1634 4.223255 CCATGGATGAGTATGAGATCAGCT 59.777 45.833 5.56 0.00 32.52 4.24
1611 1635 4.868314 TGGATGAGTATGAGATCAGCTG 57.132 45.455 7.63 7.63 32.52 4.24
1612 1636 4.221530 TGGATGAGTATGAGATCAGCTGT 58.778 43.478 14.67 0.42 32.52 4.40
1613 1637 4.652881 TGGATGAGTATGAGATCAGCTGTT 59.347 41.667 14.67 5.03 32.52 3.16
1614 1638 4.989797 GGATGAGTATGAGATCAGCTGTTG 59.010 45.833 14.67 0.00 32.52 3.33
1615 1639 5.221402 GGATGAGTATGAGATCAGCTGTTGA 60.221 44.000 14.67 0.00 40.85 3.18
1616 1640 5.665916 TGAGTATGAGATCAGCTGTTGAA 57.334 39.130 14.67 0.00 39.77 2.69
1617 1641 6.231258 TGAGTATGAGATCAGCTGTTGAAT 57.769 37.500 14.67 0.00 39.77 2.57
1618 1642 6.047231 TGAGTATGAGATCAGCTGTTGAATG 58.953 40.000 14.67 0.00 39.77 2.67
1619 1643 4.815308 AGTATGAGATCAGCTGTTGAATGC 59.185 41.667 14.67 6.41 39.77 3.56
1620 1644 3.345508 TGAGATCAGCTGTTGAATGCT 57.654 42.857 14.67 0.00 39.77 3.79
1621 1645 3.682696 TGAGATCAGCTGTTGAATGCTT 58.317 40.909 14.67 0.00 39.77 3.91
1622 1646 4.835678 TGAGATCAGCTGTTGAATGCTTA 58.164 39.130 14.67 0.00 39.77 3.09
1623 1647 4.874396 TGAGATCAGCTGTTGAATGCTTAG 59.126 41.667 14.67 0.00 39.77 2.18
1624 1648 4.841422 AGATCAGCTGTTGAATGCTTAGT 58.159 39.130 14.67 0.00 39.77 2.24
1625 1649 5.251764 AGATCAGCTGTTGAATGCTTAGTT 58.748 37.500 14.67 0.00 39.77 2.24
1626 1650 5.709164 AGATCAGCTGTTGAATGCTTAGTTT 59.291 36.000 14.67 0.00 39.77 2.66
1627 1651 6.881065 AGATCAGCTGTTGAATGCTTAGTTTA 59.119 34.615 14.67 0.00 39.77 2.01
1628 1652 6.875948 TCAGCTGTTGAATGCTTAGTTTAA 57.124 33.333 14.67 0.00 37.44 1.52
1653 1677 2.337879 AAAGGCACTGGCGGTCAGAA 62.338 55.000 17.83 0.00 46.18 3.02
1662 1686 0.591659 GGCGGTCAGAAAACTTGTCC 59.408 55.000 0.00 0.00 0.00 4.02
1695 1719 6.192360 CACTTAAGTCACACTACTTGCAAAC 58.808 40.000 4.77 0.00 39.95 2.93
1698 1722 2.159014 AGTCACACTACTTGCAAACCGA 60.159 45.455 0.00 0.00 0.00 4.69
1699 1723 2.610374 GTCACACTACTTGCAAACCGAA 59.390 45.455 0.00 0.00 0.00 4.30
1700 1724 3.064271 GTCACACTACTTGCAAACCGAAA 59.936 43.478 0.00 0.00 0.00 3.46
1701 1725 3.690139 TCACACTACTTGCAAACCGAAAA 59.310 39.130 0.00 0.00 0.00 2.29
1784 1811 1.226746 CCGCTCGGTTTTCTCTGTTT 58.773 50.000 0.00 0.00 0.00 2.83
1785 1812 1.194772 CCGCTCGGTTTTCTCTGTTTC 59.805 52.381 0.00 0.00 0.00 2.78
1786 1813 1.136611 CGCTCGGTTTTCTCTGTTTCG 60.137 52.381 0.00 0.00 0.00 3.46
1787 1814 1.194772 GCTCGGTTTTCTCTGTTTCGG 59.805 52.381 0.00 0.00 0.00 4.30
1788 1815 1.798813 CTCGGTTTTCTCTGTTTCGGG 59.201 52.381 0.00 0.00 0.00 5.14
1789 1816 0.872388 CGGTTTTCTCTGTTTCGGGG 59.128 55.000 0.00 0.00 0.00 5.73
1790 1817 1.812708 CGGTTTTCTCTGTTTCGGGGT 60.813 52.381 0.00 0.00 0.00 4.95
1791 1818 1.878088 GGTTTTCTCTGTTTCGGGGTC 59.122 52.381 0.00 0.00 0.00 4.46
1792 1819 2.567985 GTTTTCTCTGTTTCGGGGTCA 58.432 47.619 0.00 0.00 0.00 4.02
1793 1820 2.249844 TTTCTCTGTTTCGGGGTCAC 57.750 50.000 0.00 0.00 0.00 3.67
1794 1821 0.032952 TTCTCTGTTTCGGGGTCACG 59.967 55.000 0.00 0.00 0.00 4.35
1795 1822 2.027625 CTCTGTTTCGGGGTCACGC 61.028 63.158 0.00 0.00 0.00 5.34
1823 1850 4.938756 TGACCTGGGTGGGGGCTT 62.939 66.667 0.00 0.00 41.11 4.35
1824 1851 4.366684 GACCTGGGTGGGGGCTTG 62.367 72.222 0.00 0.00 41.11 4.01
1826 1853 3.914713 CCTGGGTGGGGGCTTGTT 61.915 66.667 0.00 0.00 0.00 2.83
1846 1873 0.752054 TCTTTGCACAAAAGCCCCTG 59.248 50.000 0.00 0.00 44.30 4.45
1858 1885 4.346478 AAAGCCCCTGGTGGTTTATTAT 57.654 40.909 4.50 0.00 32.12 1.28
1866 1893 4.127171 CTGGTGGTTTATTATGAGGGTCG 58.873 47.826 0.00 0.00 0.00 4.79
1869 1896 5.367352 TGGTGGTTTATTATGAGGGTCGTAT 59.633 40.000 0.00 0.00 0.00 3.06
1876 1903 5.751243 ATTATGAGGGTCGTATTGCAAAC 57.249 39.130 1.71 2.39 0.00 2.93
1878 1905 2.852449 TGAGGGTCGTATTGCAAACAA 58.148 42.857 1.71 0.00 40.87 2.83
1907 1934 3.490060 ATAAAACATGCCCTTTCCCCT 57.510 42.857 0.00 0.00 0.00 4.79
1929 1956 2.764269 TCCCCTTCTCGATCCAGAATT 58.236 47.619 3.07 0.00 31.84 2.17
1934 1961 5.163301 CCCCTTCTCGATCCAGAATTAGAAA 60.163 44.000 3.07 0.00 31.84 2.52
1956 1984 4.930696 ACCCTAGTTCCCAAATCGAAAAT 58.069 39.130 0.00 0.00 0.00 1.82
1975 2003 1.595382 CAAATCCCTAGCCGGCGAG 60.595 63.158 27.80 27.80 0.00 5.03
2010 2040 3.444805 GGCAGCGAGACCGAGAGT 61.445 66.667 0.00 0.00 38.22 3.24
2017 2047 1.666011 GAGACCGAGAGTTGTGGCA 59.334 57.895 0.00 0.00 0.00 4.92
2019 2049 1.115930 AGACCGAGAGTTGTGGCAGT 61.116 55.000 0.00 0.00 0.00 4.40
2022 2052 0.317160 CCGAGAGTTGTGGCAGTGTA 59.683 55.000 0.00 0.00 0.00 2.90
2031 2061 1.488812 TGTGGCAGTGTACCTTCTGTT 59.511 47.619 0.00 0.00 34.57 3.16
2039 2070 3.134804 AGTGTACCTTCTGTTTGAGCAGT 59.865 43.478 0.00 0.00 37.70 4.40
2063 2094 1.728672 CTCTCCCGTCGGAAGTAGC 59.271 63.158 14.39 0.00 37.86 3.58
2096 2127 2.395988 CTGTGGTAGGCAGTGTGGCA 62.396 60.000 3.09 0.00 46.46 4.92
2127 2158 4.521062 GCGAGGAGAGCGTGGCAT 62.521 66.667 0.00 0.00 34.39 4.40
2140 2171 3.124921 GGCATTGTGTAGCCGCGT 61.125 61.111 4.92 0.00 41.70 6.01
2142 2173 2.387445 GCATTGTGTAGCCGCGTCA 61.387 57.895 4.92 0.00 0.00 4.35
2160 2191 1.134310 TCATCGTCGCTGGAGGTAGTA 60.134 52.381 0.00 0.00 0.00 1.82
2168 2199 3.524606 GGAGGTAGTAGCGGCGCA 61.525 66.667 35.02 17.29 0.00 6.09
2186 2217 0.038159 CAGTCGTTCCAGTGAGGTCC 60.038 60.000 0.00 0.00 39.02 4.46
2212 2243 2.418910 CGCTCGTGGGATGGTCTCT 61.419 63.158 0.00 0.00 0.00 3.10
2213 2244 1.901085 GCTCGTGGGATGGTCTCTT 59.099 57.895 0.00 0.00 0.00 2.85
2226 2257 2.022934 GGTCTCTTATCCCGAACTCGT 58.977 52.381 0.00 0.00 37.74 4.18
2298 2330 3.701604 GAGGCCGCGTTCTCATCGT 62.702 63.158 17.39 0.00 0.00 3.73
2301 2333 2.092291 GCCGCGTTCTCATCGTTCA 61.092 57.895 4.92 0.00 0.00 3.18
2304 2336 0.363512 CGCGTTCTCATCGTTCACAG 59.636 55.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.135660 TCGAGCAACAGCTAGAACTCG 60.136 52.381 17.49 17.49 46.17 4.18
63 64 5.256474 GGATTGGTCATGAAAGAGGAAGAA 58.744 41.667 0.00 0.00 0.00 2.52
71 72 1.745087 CCCACGGATTGGTCATGAAAG 59.255 52.381 0.00 0.00 45.25 2.62
105 106 1.731720 GAACAGATCACCAGGAGCAC 58.268 55.000 0.00 0.00 33.23 4.40
245 250 0.040204 ATGTCAAAGAAGGCCCCTGG 59.960 55.000 0.00 0.00 0.00 4.45
266 271 4.100084 CACATCCGCCCAGCTCCA 62.100 66.667 0.00 0.00 0.00 3.86
295 300 0.541392 TGTCGCCTAATCACCAGCAT 59.459 50.000 0.00 0.00 0.00 3.79
352 357 0.253327 GGAAGAAGAAGGATGCCCGT 59.747 55.000 0.00 0.00 37.58 5.28
360 365 0.602905 AACGCCGTGGAAGAAGAAGG 60.603 55.000 0.00 0.00 0.00 3.46
427 432 6.160576 ACACACCAAGCTAACAAAAATCAT 57.839 33.333 0.00 0.00 0.00 2.45
432 437 4.783055 TCCTACACACCAAGCTAACAAAA 58.217 39.130 0.00 0.00 0.00 2.44
436 441 2.935676 GCCTCCTACACACCAAGCTAAC 60.936 54.545 0.00 0.00 0.00 2.34
568 573 3.555168 GGAACGAAGGCTCAAGAAGAAGA 60.555 47.826 0.00 0.00 0.00 2.87
570 575 2.104111 TGGAACGAAGGCTCAAGAAGAA 59.896 45.455 0.00 0.00 0.00 2.52
639 644 3.620427 ATACAGATGGGTTTGCGTACA 57.380 42.857 0.00 0.00 0.00 2.90
646 651 8.157476 CCAAGCTAGTTATATACAGATGGGTTT 58.843 37.037 0.00 0.00 0.00 3.27
647 652 7.680730 CCAAGCTAGTTATATACAGATGGGTT 58.319 38.462 0.00 0.00 0.00 4.11
660 665 3.134458 GCGAGAATGCCAAGCTAGTTAT 58.866 45.455 0.00 0.00 0.00 1.89
661 666 2.550978 GCGAGAATGCCAAGCTAGTTA 58.449 47.619 0.00 0.00 0.00 2.24
702 707 0.179134 ATACAGGACGACGCTCTTGC 60.179 55.000 0.00 0.00 0.00 4.01
712 717 0.457166 TCGTTGGCGAATACAGGACG 60.457 55.000 0.00 0.00 44.92 4.79
942 952 2.437413 GAGCTTCTAGGGTTTTGGGTG 58.563 52.381 0.00 0.00 0.00 4.61
988 998 1.202687 TCCCTCCATATGCTGCTTTCG 60.203 52.381 0.00 0.00 0.00 3.46
997 1007 1.981495 GAAGTCCCCTCCCTCCATATG 59.019 57.143 0.00 0.00 0.00 1.78
1267 1280 2.663196 CAAGTCCACGTCCTCCCC 59.337 66.667 0.00 0.00 0.00 4.81
1338 1359 0.904649 TGATCTATATGGCCTGCCGG 59.095 55.000 3.32 0.00 39.42 6.13
1339 1360 2.996249 ATGATCTATATGGCCTGCCG 57.004 50.000 3.32 0.00 39.42 5.69
1340 1361 6.125029 ACATTAATGATCTATATGGCCTGCC 58.875 40.000 22.16 0.00 0.00 4.85
1341 1362 7.636150 AACATTAATGATCTATATGGCCTGC 57.364 36.000 22.16 0.00 0.00 4.85
1342 1363 9.017509 ACAAACATTAATGATCTATATGGCCTG 57.982 33.333 22.16 4.15 0.00 4.85
1343 1364 9.592196 AACAAACATTAATGATCTATATGGCCT 57.408 29.630 22.16 0.00 0.00 5.19
1543 1567 5.947228 ACACGAAAAATCACACATCAGAT 57.053 34.783 0.00 0.00 0.00 2.90
1544 1568 6.852858 TTACACGAAAAATCACACATCAGA 57.147 33.333 0.00 0.00 0.00 3.27
1576 1600 1.151450 ATCCATGGCCCCAATCGAC 59.849 57.895 6.96 0.00 0.00 4.20
1581 1605 1.145531 CATACTCATCCATGGCCCCAA 59.854 52.381 6.96 0.00 0.00 4.12
1591 1615 4.870123 ACAGCTGATCTCATACTCATCC 57.130 45.455 23.35 0.00 0.00 3.51
1599 1623 3.887352 AGCATTCAACAGCTGATCTCAT 58.113 40.909 23.35 2.49 40.13 2.90
1600 1624 3.345508 AGCATTCAACAGCTGATCTCA 57.654 42.857 23.35 0.00 40.13 3.27
1601 1625 4.874966 ACTAAGCATTCAACAGCTGATCTC 59.125 41.667 23.35 2.47 41.70 2.75
1602 1626 4.841422 ACTAAGCATTCAACAGCTGATCT 58.159 39.130 23.35 0.71 41.70 2.75
1603 1627 5.557891 AACTAAGCATTCAACAGCTGATC 57.442 39.130 23.35 0.00 41.70 2.92
1604 1628 5.972107 AAACTAAGCATTCAACAGCTGAT 57.028 34.783 23.35 5.41 41.70 2.90
1605 1629 6.710295 TCTTAAACTAAGCATTCAACAGCTGA 59.290 34.615 23.35 0.00 41.70 4.26
1606 1630 6.902341 TCTTAAACTAAGCATTCAACAGCTG 58.098 36.000 13.48 13.48 41.70 4.24
1607 1631 6.712547 ACTCTTAAACTAAGCATTCAACAGCT 59.287 34.615 0.00 0.00 44.31 4.24
1608 1632 6.903419 ACTCTTAAACTAAGCATTCAACAGC 58.097 36.000 0.00 0.00 35.76 4.40
1613 1637 8.512138 GCCTTTTACTCTTAAACTAAGCATTCA 58.488 33.333 0.00 0.00 35.76 2.57
1614 1638 8.512138 TGCCTTTTACTCTTAAACTAAGCATTC 58.488 33.333 0.00 0.00 35.76 2.67
1615 1639 8.297426 GTGCCTTTTACTCTTAAACTAAGCATT 58.703 33.333 0.00 0.00 35.76 3.56
1616 1640 7.665974 AGTGCCTTTTACTCTTAAACTAAGCAT 59.334 33.333 0.00 0.00 35.76 3.79
1617 1641 6.996282 AGTGCCTTTTACTCTTAAACTAAGCA 59.004 34.615 0.00 0.00 35.76 3.91
1618 1642 7.298854 CAGTGCCTTTTACTCTTAAACTAAGC 58.701 38.462 0.00 0.00 35.76 3.09
1619 1643 7.573283 GCCAGTGCCTTTTACTCTTAAACTAAG 60.573 40.741 0.00 0.00 37.13 2.18
1620 1644 6.206048 GCCAGTGCCTTTTACTCTTAAACTAA 59.794 38.462 0.00 0.00 0.00 2.24
1621 1645 5.704053 GCCAGTGCCTTTTACTCTTAAACTA 59.296 40.000 0.00 0.00 0.00 2.24
1622 1646 4.519350 GCCAGTGCCTTTTACTCTTAAACT 59.481 41.667 0.00 0.00 0.00 2.66
1623 1647 4.612939 CGCCAGTGCCTTTTACTCTTAAAC 60.613 45.833 0.00 0.00 0.00 2.01
1624 1648 3.500680 CGCCAGTGCCTTTTACTCTTAAA 59.499 43.478 0.00 0.00 0.00 1.52
1625 1649 3.071479 CGCCAGTGCCTTTTACTCTTAA 58.929 45.455 0.00 0.00 0.00 1.85
1626 1650 2.614481 CCGCCAGTGCCTTTTACTCTTA 60.614 50.000 0.00 0.00 0.00 2.10
1627 1651 1.523758 CGCCAGTGCCTTTTACTCTT 58.476 50.000 0.00 0.00 0.00 2.85
1628 1652 0.321653 CCGCCAGTGCCTTTTACTCT 60.322 55.000 0.00 0.00 0.00 3.24
1662 1686 1.798813 GTGACTTAAGTGCACCCGAAG 59.201 52.381 14.14 16.19 0.00 3.79
1699 1723 4.992688 TGCAAGTTCAATGACGAGTTTTT 58.007 34.783 0.00 0.00 0.00 1.94
1700 1724 4.630894 TGCAAGTTCAATGACGAGTTTT 57.369 36.364 0.00 0.00 0.00 2.43
1701 1725 4.836125 ATGCAAGTTCAATGACGAGTTT 57.164 36.364 0.00 0.00 0.00 2.66
1705 1732 2.665245 CGCAATGCAAGTTCAATGACGA 60.665 45.455 5.91 0.00 0.00 4.20
1711 1738 0.031857 CACCCGCAATGCAAGTTCAA 59.968 50.000 5.91 0.00 0.00 2.69
1712 1739 1.659233 CACCCGCAATGCAAGTTCA 59.341 52.632 5.91 0.00 0.00 3.18
1763 1790 1.667830 CAGAGAAAACCGAGCGGCA 60.668 57.895 9.14 0.00 39.32 5.69
1769 1796 1.541670 CCCCGAAACAGAGAAAACCGA 60.542 52.381 0.00 0.00 0.00 4.69
1796 1823 4.767255 CCAGGTCAGGTGCGCCTC 62.767 72.222 18.11 6.09 44.97 4.70
1806 1833 4.938756 AAGCCCCCACCCAGGTCA 62.939 66.667 0.00 0.00 34.66 4.02
1807 1834 4.366684 CAAGCCCCCACCCAGGTC 62.367 72.222 0.00 0.00 34.66 3.85
1809 1836 3.466803 AAACAAGCCCCCACCCAGG 62.467 63.158 0.00 0.00 37.03 4.45
1810 1837 1.908299 GAAACAAGCCCCCACCCAG 60.908 63.158 0.00 0.00 0.00 4.45
1811 1838 1.955458 AAGAAACAAGCCCCCACCCA 61.955 55.000 0.00 0.00 0.00 4.51
1812 1839 0.762842 AAAGAAACAAGCCCCCACCC 60.763 55.000 0.00 0.00 0.00 4.61
1813 1840 0.392706 CAAAGAAACAAGCCCCCACC 59.607 55.000 0.00 0.00 0.00 4.61
1814 1841 0.249868 GCAAAGAAACAAGCCCCCAC 60.250 55.000 0.00 0.00 0.00 4.61
1815 1842 0.689080 TGCAAAGAAACAAGCCCCCA 60.689 50.000 0.00 0.00 0.00 4.96
1816 1843 0.249868 GTGCAAAGAAACAAGCCCCC 60.250 55.000 0.00 0.00 0.00 5.40
1817 1844 0.463620 TGTGCAAAGAAACAAGCCCC 59.536 50.000 0.00 0.00 0.00 5.80
1818 1845 2.307934 TTGTGCAAAGAAACAAGCCC 57.692 45.000 0.00 0.00 32.66 5.19
1819 1846 3.485711 GCTTTTGTGCAAAGAAACAAGCC 60.486 43.478 0.71 0.00 44.40 4.35
1820 1847 3.485711 GGCTTTTGTGCAAAGAAACAAGC 60.486 43.478 0.71 7.74 44.40 4.01
1821 1848 3.063861 GGGCTTTTGTGCAAAGAAACAAG 59.936 43.478 0.71 0.00 44.40 3.16
1822 1849 3.006247 GGGCTTTTGTGCAAAGAAACAA 58.994 40.909 0.71 0.00 44.40 2.83
1823 1850 2.626840 GGGCTTTTGTGCAAAGAAACA 58.373 42.857 0.71 0.00 44.40 2.83
1824 1851 1.939934 GGGGCTTTTGTGCAAAGAAAC 59.060 47.619 0.71 0.00 44.40 2.78
1825 1852 1.836802 AGGGGCTTTTGTGCAAAGAAA 59.163 42.857 0.71 0.00 44.40 2.52
1826 1853 1.138661 CAGGGGCTTTTGTGCAAAGAA 59.861 47.619 0.71 0.00 44.40 2.52
1846 1873 4.146745 ACGACCCTCATAATAAACCACC 57.853 45.455 0.00 0.00 0.00 4.61
1858 1885 2.552599 TGTTTGCAATACGACCCTCA 57.447 45.000 0.00 0.00 0.00 3.86
1907 1934 2.247699 TCTGGATCGAGAAGGGGAAA 57.752 50.000 4.77 0.00 0.00 3.13
1929 1956 4.778958 TCGATTTGGGAACTAGGGTTTCTA 59.221 41.667 0.00 0.00 35.58 2.10
1934 1961 4.376225 TTTTCGATTTGGGAACTAGGGT 57.624 40.909 0.00 0.00 0.00 4.34
1956 1984 2.028125 CTCGCCGGCTAGGGATTTGA 62.028 60.000 26.68 9.86 41.48 2.69
1991 2021 3.408501 CTCTCGGTCTCGCTGCCAG 62.409 68.421 0.00 0.00 36.13 4.85
2010 2040 1.488812 ACAGAAGGTACACTGCCACAA 59.511 47.619 11.85 0.00 38.22 3.33
2017 2047 3.134804 ACTGCTCAAACAGAAGGTACACT 59.865 43.478 0.00 0.00 40.25 3.55
2019 2049 3.466836 CACTGCTCAAACAGAAGGTACA 58.533 45.455 0.00 0.00 40.25 2.90
2022 2052 1.212935 ACCACTGCTCAAACAGAAGGT 59.787 47.619 0.00 3.48 41.42 3.50
2039 2070 2.439701 CCGACGGGAGAGCTACCA 60.440 66.667 5.81 0.00 31.13 3.25
2083 2114 2.358615 CGCTTGCCACACTGCCTA 60.359 61.111 0.00 0.00 0.00 3.93
2105 2136 2.673341 ACGCTCTCCTCGCTGACA 60.673 61.111 0.00 0.00 0.00 3.58
2127 2158 1.803922 CGATGACGCGGCTACACAA 60.804 57.895 15.80 0.00 0.00 3.33
2140 2171 0.393944 ACTACCTCCAGCGACGATGA 60.394 55.000 15.87 0.00 0.00 2.92
2142 2173 1.595466 CTACTACCTCCAGCGACGAT 58.405 55.000 0.00 0.00 0.00 3.73
2150 2181 3.524606 GCGCCGCTACTACCTCCA 61.525 66.667 0.00 0.00 0.00 3.86
2168 2199 0.178958 AGGACCTCACTGGAACGACT 60.179 55.000 0.00 0.00 39.71 4.18
2172 2203 1.592223 CGGAGGACCTCACTGGAAC 59.408 63.158 23.06 2.84 39.71 3.62
2196 2227 2.297597 GGATAAGAGACCATCCCACGAG 59.702 54.545 0.00 0.00 35.61 4.18
2220 2251 1.341531 CTGAGGGAAGACACACGAGTT 59.658 52.381 0.00 0.00 0.00 3.01
2226 2257 3.073228 CCTCCTGAGGGAAGACACA 57.927 57.895 5.22 0.00 44.87 3.72
2298 2330 2.270257 GCCATGCCAGCACTGTGAA 61.270 57.895 12.86 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.