Multiple sequence alignment - TraesCS6A01G371400

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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 TraesCS6A01G371400 chr6A 100.000 2225 0 0 1 2225 595647446 595649670 0.000000e+00 4109.0
1 TraesCS6A01G371400 chr6A 89.415 1247 65 45 49 1266 595658142 595659350 0.000000e+00 1509.0
2 TraesCS6A01G371400 chr6B 81.818 1782 146 93 264 1964 682587876 682589560 0.000000e+00 1332.0
3 TraesCS6A01G371400 chr6B 84.089 949 81 43 290 1195 682655528 682656449 0.000000e+00 852.0
4 TraesCS6A01G371400 chr6B 87.324 213 22 3 2002 2209 682589562 682589774 2.860000e-59 239.0
5 TraesCS6A01G371400 chr6B 89.041 73 4 4 1198 1266 682656482 682656554 1.090000e-13 87.9
6 TraesCS6A01G371400 chr6D 84.306 1319 75 53 265 1540 450136212 450137441 0.000000e+00 1168.0
7 TraesCS6A01G371400 chr6D 84.826 949 74 37 267 1195 450164337 450165235 0.000000e+00 891.0
8 TraesCS6A01G371400 chr6D 81.750 663 61 31 1569 2225 450137439 450138047 1.190000e-137 499.0
9 TraesCS6A01G371400 chr6D 89.041 73 4 4 1198 1266 450165268 450165340 1.090000e-13 87.9
10 TraesCS6A01G371400 chr6D 100.000 32 0 0 3 34 450136276 450136307 2.390000e-05 60.2
11 TraesCS6A01G371400 chr5B 97.674 43 1 0 1727 1769 50506213 50506171 8.520000e-10 75.0
12 TraesCS6A01G371400 chr5D 93.478 46 1 2 1730 1775 284162404 284162447 1.430000e-07 67.6


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 TraesCS6A01G371400 chr6A 595647446 595649670 2224 False 4109.000000 4109 100.000000 1 2225 1 chr6A.!!$F1 2224
1 TraesCS6A01G371400 chr6A 595658142 595659350 1208 False 1509.000000 1509 89.415000 49 1266 1 chr6A.!!$F2 1217
2 TraesCS6A01G371400 chr6B 682587876 682589774 1898 False 785.500000 1332 84.571000 264 2209 2 chr6B.!!$F1 1945
3 TraesCS6A01G371400 chr6B 682655528 682656554 1026 False 469.950000 852 86.565000 290 1266 2 chr6B.!!$F2 976
4 TraesCS6A01G371400 chr6D 450136212 450138047 1835 False 575.733333 1168 88.685333 3 2225 3 chr6D.!!$F1 2222
5 TraesCS6A01G371400 chr6D 450164337 450165340 1003 False 489.450000 891 86.933500 267 1266 2 chr6D.!!$F2 999

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
47 48 0.031616 GAGAGACTGGAGGGATGGGT 60.032 60.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1493 1629 0.249322 GTACGCTACGTGCCCATCAT 60.249 55.0 0.0 0.0 41.39 2.45 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
22 23 5.684550 GTTCCATAAGTTTGACCGTTTCT 57.315 39.130 0.00 0.00 0.00 2.52
23 24 5.449304 GTTCCATAAGTTTGACCGTTTCTG 58.551 41.667 0.00 0.00 0.00 3.02
24 25 4.069304 TCCATAAGTTTGACCGTTTCTGG 58.931 43.478 0.00 0.00 0.00 3.86
25 26 4.069304 CCATAAGTTTGACCGTTTCTGGA 58.931 43.478 0.00 0.00 0.00 3.86
26 27 4.154195 CCATAAGTTTGACCGTTTCTGGAG 59.846 45.833 0.00 0.00 0.00 3.86
27 28 3.553828 AAGTTTGACCGTTTCTGGAGA 57.446 42.857 0.00 0.00 0.00 3.71
28 29 3.113260 AGTTTGACCGTTTCTGGAGAG 57.887 47.619 0.00 0.00 0.00 3.20
29 30 2.698797 AGTTTGACCGTTTCTGGAGAGA 59.301 45.455 0.00 0.00 0.00 3.10
30 31 3.060602 GTTTGACCGTTTCTGGAGAGAG 58.939 50.000 0.00 0.00 0.00 3.20
31 32 2.287977 TGACCGTTTCTGGAGAGAGA 57.712 50.000 0.00 0.00 0.00 3.10
32 33 2.163509 TGACCGTTTCTGGAGAGAGAG 58.836 52.381 0.00 0.00 0.00 3.20
33 34 2.224793 TGACCGTTTCTGGAGAGAGAGA 60.225 50.000 0.00 0.00 0.00 3.10
34 35 2.162809 GACCGTTTCTGGAGAGAGAGAC 59.837 54.545 0.00 0.00 0.00 3.36
35 36 2.224917 ACCGTTTCTGGAGAGAGAGACT 60.225 50.000 0.00 0.00 0.00 3.24
36 37 2.163412 CCGTTTCTGGAGAGAGAGACTG 59.837 54.545 0.00 0.00 0.00 3.51
37 38 2.163412 CGTTTCTGGAGAGAGAGACTGG 59.837 54.545 0.00 0.00 0.00 4.00
38 39 3.426615 GTTTCTGGAGAGAGAGACTGGA 58.573 50.000 0.00 0.00 0.00 3.86
39 40 3.364460 TTCTGGAGAGAGAGACTGGAG 57.636 52.381 0.00 0.00 0.00 3.86
40 41 1.563879 TCTGGAGAGAGAGACTGGAGG 59.436 57.143 0.00 0.00 0.00 4.30
41 42 0.628522 TGGAGAGAGAGACTGGAGGG 59.371 60.000 0.00 0.00 0.00 4.30
42 43 0.923358 GGAGAGAGAGACTGGAGGGA 59.077 60.000 0.00 0.00 0.00 4.20
43 44 1.499007 GGAGAGAGAGACTGGAGGGAT 59.501 57.143 0.00 0.00 0.00 3.85
44 45 2.586425 GAGAGAGAGACTGGAGGGATG 58.414 57.143 0.00 0.00 0.00 3.51
45 46 1.217689 AGAGAGAGACTGGAGGGATGG 59.782 57.143 0.00 0.00 0.00 3.51
46 47 0.264359 AGAGAGACTGGAGGGATGGG 59.736 60.000 0.00 0.00 0.00 4.00
47 48 0.031616 GAGAGACTGGAGGGATGGGT 60.032 60.000 0.00 0.00 0.00 4.51
48 49 1.218196 GAGAGACTGGAGGGATGGGTA 59.782 57.143 0.00 0.00 0.00 3.69
49 50 1.062810 AGAGACTGGAGGGATGGGTAC 60.063 57.143 0.00 0.00 0.00 3.34
50 51 1.019650 AGACTGGAGGGATGGGTACT 58.980 55.000 0.00 0.00 0.00 2.73
605 646 5.334421 AGAACACTGGAGTAGTAACTGGAT 58.666 41.667 0.00 0.00 37.60 3.41
625 666 1.164411 TCGGTCACATGCACATTTCC 58.836 50.000 0.00 0.00 0.00 3.13
646 690 4.047059 CACTGCTTTGCTGGGGCG 62.047 66.667 1.90 0.00 42.25 6.13
666 710 1.356527 CGCGGGCCTATAAATACGCC 61.357 60.000 12.16 2.42 43.62 5.68
672 716 2.093606 GGCCTATAAATACGCCCTCTCC 60.094 54.545 0.00 0.00 35.23 3.71
702 753 1.286553 TCCCCACACCACAAGTTCTTT 59.713 47.619 0.00 0.00 0.00 2.52
706 757 2.618709 CCACACCACAAGTTCTTTCTCC 59.381 50.000 0.00 0.00 0.00 3.71
708 759 2.230660 CACCACAAGTTCTTTCTCCCC 58.769 52.381 0.00 0.00 0.00 4.81
710 761 1.144913 CCACAAGTTCTTTCTCCCCCA 59.855 52.381 0.00 0.00 0.00 4.96
711 762 2.230660 CACAAGTTCTTTCTCCCCCAC 58.769 52.381 0.00 0.00 0.00 4.61
712 763 2.136026 ACAAGTTCTTTCTCCCCCACT 58.864 47.619 0.00 0.00 0.00 4.00
714 765 0.977395 AGTTCTTTCTCCCCCACTCG 59.023 55.000 0.00 0.00 0.00 4.18
745 800 2.234908 GCCTTCTTCTTCCTCTGCTACA 59.765 50.000 0.00 0.00 0.00 2.74
760 832 1.714794 CTACAAGTGCCAGTCTTCCG 58.285 55.000 0.00 0.00 0.00 4.30
782 854 2.431057 AGCCCGAGTACTACCATTTCAG 59.569 50.000 0.00 0.00 0.00 3.02
783 855 2.822764 CCCGAGTACTACCATTTCAGC 58.177 52.381 0.00 0.00 0.00 4.26
835 911 4.619863 GCACTGCATTTTCACAATCCATCT 60.620 41.667 0.00 0.00 0.00 2.90
896 973 3.664107 TGCTAGGTGCTAGTTGTTCTTG 58.336 45.455 0.00 0.00 43.37 3.02
905 982 4.821260 TGCTAGTTGTTCTTGAATCAAGCA 59.179 37.500 17.58 4.55 40.84 3.91
1008 1094 3.838271 GCGTGGAGGATGGAGCGA 61.838 66.667 0.00 0.00 0.00 4.93
1266 1386 1.851021 CGTGAATGCAGCCGTGGAAA 61.851 55.000 0.00 0.00 0.00 3.13
1407 1543 1.275291 GAAGTAGTAGTGGTGGCAGCA 59.725 52.381 16.56 16.56 0.00 4.41
1408 1544 0.898320 AGTAGTAGTGGTGGCAGCAG 59.102 55.000 21.25 0.00 0.00 4.24
1409 1545 0.108138 GTAGTAGTGGTGGCAGCAGG 60.108 60.000 21.25 0.00 0.00 4.85
1443 1579 4.263287 GGGGGTTGTATTTGAATGGCTTTT 60.263 41.667 0.00 0.00 0.00 2.27
1465 1601 0.883833 CTCTGTGGCGCCATTTCTTT 59.116 50.000 35.23 0.00 0.00 2.52
1467 1603 1.269448 TCTGTGGCGCCATTTCTTTTC 59.731 47.619 35.23 17.70 0.00 2.29
1478 1614 5.447010 CGCCATTTCTTTTCTCAGTCTGATC 60.447 44.000 2.22 0.00 0.00 2.92
1479 1615 5.647225 GCCATTTCTTTTCTCAGTCTGATCT 59.353 40.000 2.22 0.00 0.00 2.75
1480 1616 6.403418 GCCATTTCTTTTCTCAGTCTGATCTG 60.403 42.308 2.22 0.00 36.85 2.90
1481 1617 6.877855 CCATTTCTTTTCTCAGTCTGATCTGA 59.122 38.462 2.22 0.00 41.40 3.27
1482 1618 7.553402 CCATTTCTTTTCTCAGTCTGATCTGAT 59.447 37.037 2.22 0.00 42.47 2.90
1483 1619 7.902387 TTTCTTTTCTCAGTCTGATCTGATG 57.098 36.000 2.22 5.81 42.47 3.07
1493 1629 1.697982 CTGATCTGATGGCCCTGATGA 59.302 52.381 0.00 0.00 0.00 2.92
1514 1654 2.287457 GATGGGCACGTAGCGTACCA 62.287 60.000 15.76 15.76 44.27 3.25
1515 1655 2.202703 GGGCACGTAGCGTACCAG 60.203 66.667 12.22 0.00 44.27 4.00
1516 1656 2.703798 GGGCACGTAGCGTACCAGA 61.704 63.158 12.22 0.00 44.27 3.86
1517 1657 1.515736 GGCACGTAGCGTACCAGAC 60.516 63.158 6.10 0.00 42.28 3.51
1518 1658 1.505353 GCACGTAGCGTACCAGACT 59.495 57.895 0.00 0.00 38.32 3.24
1537 1677 6.377429 CCAGACTTAGACTACCAGTAACATGA 59.623 42.308 0.00 0.00 0.00 3.07
1538 1678 7.093902 CCAGACTTAGACTACCAGTAACATGAA 60.094 40.741 0.00 0.00 0.00 2.57
1539 1679 8.304596 CAGACTTAGACTACCAGTAACATGAAA 58.695 37.037 0.00 0.00 0.00 2.69
1540 1680 8.524487 AGACTTAGACTACCAGTAACATGAAAG 58.476 37.037 0.00 0.00 0.00 2.62
1541 1681 8.418597 ACTTAGACTACCAGTAACATGAAAGA 57.581 34.615 0.00 0.00 0.00 2.52
1542 1682 9.036980 ACTTAGACTACCAGTAACATGAAAGAT 57.963 33.333 0.00 0.00 0.00 2.40
1545 1685 8.012957 AGACTACCAGTAACATGAAAGATAGG 57.987 38.462 0.00 0.00 0.00 2.57
1546 1686 7.620094 AGACTACCAGTAACATGAAAGATAGGT 59.380 37.037 0.00 1.07 0.00 3.08
1547 1687 7.783042 ACTACCAGTAACATGAAAGATAGGTC 58.217 38.462 0.00 0.00 0.00 3.85
1548 1688 6.875972 ACCAGTAACATGAAAGATAGGTCT 57.124 37.500 0.00 0.00 35.82 3.85
1549 1689 6.644347 ACCAGTAACATGAAAGATAGGTCTG 58.356 40.000 0.00 0.00 34.13 3.51
1550 1690 6.051717 CCAGTAACATGAAAGATAGGTCTGG 58.948 44.000 0.00 0.00 34.13 3.86
1551 1691 6.352222 CCAGTAACATGAAAGATAGGTCTGGT 60.352 42.308 0.00 0.00 34.13 4.00
1552 1692 7.106239 CAGTAACATGAAAGATAGGTCTGGTT 58.894 38.462 0.00 0.00 34.13 3.67
1553 1693 8.258007 CAGTAACATGAAAGATAGGTCTGGTTA 58.742 37.037 0.00 0.00 34.13 2.85
1554 1694 8.993424 AGTAACATGAAAGATAGGTCTGGTTAT 58.007 33.333 0.00 0.00 34.13 1.89
1555 1695 9.614792 GTAACATGAAAGATAGGTCTGGTTATT 57.385 33.333 0.00 0.00 34.13 1.40
1556 1696 8.738645 AACATGAAAGATAGGTCTGGTTATTC 57.261 34.615 0.00 0.00 34.13 1.75
1557 1697 7.283329 ACATGAAAGATAGGTCTGGTTATTCC 58.717 38.462 0.00 0.00 34.13 3.01
1558 1698 6.884472 TGAAAGATAGGTCTGGTTATTCCA 57.116 37.500 0.00 0.00 45.01 3.53
1559 1699 6.650120 TGAAAGATAGGTCTGGTTATTCCAC 58.350 40.000 0.00 0.00 41.93 4.02
1560 1700 6.443849 TGAAAGATAGGTCTGGTTATTCCACT 59.556 38.462 0.00 0.00 41.93 4.00
1561 1701 7.622081 TGAAAGATAGGTCTGGTTATTCCACTA 59.378 37.037 0.00 0.00 41.93 2.74
1562 1702 6.980416 AGATAGGTCTGGTTATTCCACTAC 57.020 41.667 0.00 0.00 41.93 2.73
1563 1703 6.684538 AGATAGGTCTGGTTATTCCACTACT 58.315 40.000 0.00 0.00 41.93 2.57
1564 1704 7.133483 AGATAGGTCTGGTTATTCCACTACTT 58.867 38.462 0.00 0.00 41.93 2.24
1565 1705 5.422214 AGGTCTGGTTATTCCACTACTTG 57.578 43.478 0.00 0.00 41.93 3.16
1566 1706 3.939592 GGTCTGGTTATTCCACTACTTGC 59.060 47.826 0.00 0.00 41.93 4.01
1567 1707 3.939592 GTCTGGTTATTCCACTACTTGCC 59.060 47.826 0.00 0.00 41.93 4.52
1592 1763 9.912634 CCAAAATCTGTAGTTTAATGTGAACAT 57.087 29.630 0.00 0.00 38.41 2.71
1597 1768 9.912634 ATCTGTAGTTTAATGTGAACATTTTGG 57.087 29.630 13.53 0.00 43.48 3.28
1620 1791 8.477419 TGGGAAAATCTCTCTTTTACAAACAT 57.523 30.769 0.00 0.00 31.67 2.71
1622 1793 8.576442 GGGAAAATCTCTCTTTTACAAACATGA 58.424 33.333 0.00 0.00 31.67 3.07
1669 1840 0.886490 CCAGACAGGTGTGTGAAGGC 60.886 60.000 8.76 0.00 41.29 4.35
1681 1852 3.242936 TGTGTGAAGGCGTTTTAGAAAGC 60.243 43.478 0.00 0.00 39.18 3.51
1788 2011 8.191534 ACATAATAGAGTCTGTTATACCACCC 57.808 38.462 18.52 0.00 29.13 4.61
1789 2012 7.787904 ACATAATAGAGTCTGTTATACCACCCA 59.212 37.037 18.52 0.00 29.13 4.51
1790 2013 8.816894 CATAATAGAGTCTGTTATACCACCCAT 58.183 37.037 18.52 0.00 29.13 4.00
1791 2014 6.919775 ATAGAGTCTGTTATACCACCCATC 57.080 41.667 1.86 0.00 0.00 3.51
1792 2015 4.620723 AGAGTCTGTTATACCACCCATCA 58.379 43.478 0.00 0.00 0.00 3.07
1793 2016 5.219739 AGAGTCTGTTATACCACCCATCAT 58.780 41.667 0.00 0.00 0.00 2.45
1794 2017 5.667626 AGAGTCTGTTATACCACCCATCATT 59.332 40.000 0.00 0.00 0.00 2.57
1795 2018 6.844388 AGAGTCTGTTATACCACCCATCATTA 59.156 38.462 0.00 0.00 0.00 1.90
1796 2019 7.347222 AGAGTCTGTTATACCACCCATCATTAA 59.653 37.037 0.00 0.00 0.00 1.40
1797 2020 8.045720 AGTCTGTTATACCACCCATCATTAAT 57.954 34.615 0.00 0.00 0.00 1.40
1798 2021 8.502738 AGTCTGTTATACCACCCATCATTAATT 58.497 33.333 0.00 0.00 0.00 1.40
1799 2022 9.787435 GTCTGTTATACCACCCATCATTAATTA 57.213 33.333 0.00 0.00 0.00 1.40
1837 2060 8.774183 AGAGTTTGTTATACCACCCATATTACA 58.226 33.333 0.00 0.00 0.00 2.41
1855 2080 0.038526 CACGCGAAGGTGGAACTAGT 60.039 55.000 15.93 0.00 36.74 2.57
1874 2100 4.535526 AGTTGTTTGGTGCTCAGTTTTT 57.464 36.364 0.00 0.00 0.00 1.94
1916 2142 3.743396 GCTCACATCGTTCTCTTGTTCTT 59.257 43.478 0.00 0.00 0.00 2.52
1926 2152 4.277515 TCTCTTGTTCTTCCACATCAGG 57.722 45.455 0.00 0.00 0.00 3.86
1932 2158 0.321564 TCTTCCACATCAGGCCGTTG 60.322 55.000 0.00 0.00 0.00 4.10
1957 2183 2.623878 TCCTTTCCGTAACACTTGCA 57.376 45.000 0.00 0.00 0.00 4.08
1960 2186 3.695060 TCCTTTCCGTAACACTTGCAAAA 59.305 39.130 0.00 0.00 0.00 2.44
2000 2227 4.560739 ACCCTAACTACATAACCCCCTAC 58.439 47.826 0.00 0.00 0.00 3.18
2006 2233 4.839589 ACTACATAACCCCCTACCATCAT 58.160 43.478 0.00 0.00 0.00 2.45
2013 2240 3.130450 ACCCCCTACCATCATTTCATCA 58.870 45.455 0.00 0.00 0.00 3.07
2014 2241 3.728990 ACCCCCTACCATCATTTCATCAT 59.271 43.478 0.00 0.00 0.00 2.45
2034 2261 1.847328 AAACTTTAGCCCATTCCCCG 58.153 50.000 0.00 0.00 0.00 5.73
2073 2300 3.493350 CGCCATAGTAGATTTGCCTCACT 60.493 47.826 0.00 0.00 0.00 3.41
2075 2302 4.684485 GCCATAGTAGATTTGCCTCACTGT 60.684 45.833 0.00 0.00 0.00 3.55
2086 2313 1.972872 CCTCACTGTTGCCAACTCTT 58.027 50.000 9.30 0.00 0.00 2.85
2094 2323 0.878523 TTGCCAACTCTTCGTCACGG 60.879 55.000 0.00 0.00 0.00 4.94
2099 2328 2.049433 CTCTTCGTCACGGCCGTT 60.049 61.111 32.11 11.80 0.00 4.44
2137 2366 2.124529 TTGCCGGTTGTCACTGCA 60.125 55.556 1.90 0.00 0.00 4.41
2209 2441 0.536687 AACTCTCTCCGTCACCGTCA 60.537 55.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.517453 CCAGAAACGGTCAAACTTATGGAA 59.483 41.667 0.00 0.00 32.97 3.53
2 3 4.069304 CCAGAAACGGTCAAACTTATGGA 58.931 43.478 0.00 0.00 32.97 3.41
3 4 4.069304 TCCAGAAACGGTCAAACTTATGG 58.931 43.478 0.00 0.00 32.58 2.74
4 5 4.994852 TCTCCAGAAACGGTCAAACTTATG 59.005 41.667 0.00 0.00 0.00 1.90
5 6 5.011738 TCTCTCCAGAAACGGTCAAACTTAT 59.988 40.000 0.00 0.00 0.00 1.73
6 7 4.342951 TCTCTCCAGAAACGGTCAAACTTA 59.657 41.667 0.00 0.00 0.00 2.24
7 8 3.134081 TCTCTCCAGAAACGGTCAAACTT 59.866 43.478 0.00 0.00 0.00 2.66
8 9 2.698797 TCTCTCCAGAAACGGTCAAACT 59.301 45.455 0.00 0.00 0.00 2.66
9 10 3.060602 CTCTCTCCAGAAACGGTCAAAC 58.939 50.000 0.00 0.00 0.00 2.93
10 11 2.963101 TCTCTCTCCAGAAACGGTCAAA 59.037 45.455 0.00 0.00 0.00 2.69
11 12 2.558795 CTCTCTCTCCAGAAACGGTCAA 59.441 50.000 0.00 0.00 0.00 3.18
12 13 2.163509 CTCTCTCTCCAGAAACGGTCA 58.836 52.381 0.00 0.00 0.00 4.02
13 14 2.162809 GTCTCTCTCTCCAGAAACGGTC 59.837 54.545 0.00 0.00 0.00 4.79
14 15 2.164338 GTCTCTCTCTCCAGAAACGGT 58.836 52.381 0.00 0.00 0.00 4.83
15 16 2.163412 CAGTCTCTCTCTCCAGAAACGG 59.837 54.545 0.00 0.00 0.00 4.44
16 17 2.163412 CCAGTCTCTCTCTCCAGAAACG 59.837 54.545 0.00 0.00 0.00 3.60
17 18 3.426615 TCCAGTCTCTCTCTCCAGAAAC 58.573 50.000 0.00 0.00 0.00 2.78
18 19 3.563261 CCTCCAGTCTCTCTCTCCAGAAA 60.563 52.174 0.00 0.00 0.00 2.52
19 20 2.025416 CCTCCAGTCTCTCTCTCCAGAA 60.025 54.545 0.00 0.00 0.00 3.02
20 21 1.563879 CCTCCAGTCTCTCTCTCCAGA 59.436 57.143 0.00 0.00 0.00 3.86
21 22 1.410083 CCCTCCAGTCTCTCTCTCCAG 60.410 61.905 0.00 0.00 0.00 3.86
22 23 0.628522 CCCTCCAGTCTCTCTCTCCA 59.371 60.000 0.00 0.00 0.00 3.86
23 24 0.923358 TCCCTCCAGTCTCTCTCTCC 59.077 60.000 0.00 0.00 0.00 3.71
24 25 2.586425 CATCCCTCCAGTCTCTCTCTC 58.414 57.143 0.00 0.00 0.00 3.20
25 26 1.217689 CCATCCCTCCAGTCTCTCTCT 59.782 57.143 0.00 0.00 0.00 3.10
26 27 1.703411 CCATCCCTCCAGTCTCTCTC 58.297 60.000 0.00 0.00 0.00 3.20
27 28 0.264359 CCCATCCCTCCAGTCTCTCT 59.736 60.000 0.00 0.00 0.00 3.10
28 29 0.031616 ACCCATCCCTCCAGTCTCTC 60.032 60.000 0.00 0.00 0.00 3.20
29 30 1.062810 GTACCCATCCCTCCAGTCTCT 60.063 57.143 0.00 0.00 0.00 3.10
30 31 1.062810 AGTACCCATCCCTCCAGTCTC 60.063 57.143 0.00 0.00 0.00 3.36
31 32 1.019650 AGTACCCATCCCTCCAGTCT 58.980 55.000 0.00 0.00 0.00 3.24
32 33 2.091222 AGTAGTACCCATCCCTCCAGTC 60.091 54.545 0.00 0.00 0.00 3.51
33 34 1.938069 AGTAGTACCCATCCCTCCAGT 59.062 52.381 0.00 0.00 0.00 4.00
34 35 2.777459 AGTAGTACCCATCCCTCCAG 57.223 55.000 0.00 0.00 0.00 3.86
35 36 3.246203 TGAAAGTAGTACCCATCCCTCCA 60.246 47.826 0.00 0.00 0.00 3.86
36 37 3.381335 TGAAAGTAGTACCCATCCCTCC 58.619 50.000 0.00 0.00 0.00 4.30
37 38 4.902448 AGATGAAAGTAGTACCCATCCCTC 59.098 45.833 17.35 6.68 35.48 4.30
38 39 4.656112 CAGATGAAAGTAGTACCCATCCCT 59.344 45.833 17.35 4.99 35.48 4.20
39 40 4.409247 ACAGATGAAAGTAGTACCCATCCC 59.591 45.833 17.35 3.22 35.48 3.85
40 41 5.615925 ACAGATGAAAGTAGTACCCATCC 57.384 43.478 17.35 6.72 35.48 3.51
41 42 8.475639 TCTAAACAGATGAAAGTAGTACCCATC 58.524 37.037 14.94 14.94 35.21 3.51
42 43 8.258708 GTCTAAACAGATGAAAGTAGTACCCAT 58.741 37.037 0.00 0.00 0.00 4.00
43 44 7.453752 AGTCTAAACAGATGAAAGTAGTACCCA 59.546 37.037 0.00 0.00 0.00 4.51
44 45 7.838884 AGTCTAAACAGATGAAAGTAGTACCC 58.161 38.462 0.00 0.00 0.00 3.69
605 646 1.539388 GGAAATGTGCATGTGACCGAA 59.461 47.619 0.00 0.00 0.00 4.30
625 666 1.601419 CCCCAGCAAAGCAGTGGATG 61.601 60.000 0.00 0.00 32.60 3.51
646 690 1.963190 GCGTATTTATAGGCCCGCGC 61.963 60.000 0.00 0.00 37.99 6.86
647 691 2.075761 GCGTATTTATAGGCCCGCG 58.924 57.895 0.00 0.00 37.99 6.46
666 710 1.152839 GGAGAGGAGACGGGAGAGG 60.153 68.421 0.00 0.00 0.00 3.69
672 716 2.037367 TGTGGGGAGAGGAGACGG 59.963 66.667 0.00 0.00 0.00 4.79
702 753 1.227664 CTAGCTCGAGTGGGGGAGA 59.772 63.158 15.13 0.00 31.90 3.71
706 757 1.801309 GCTAGCTAGCTCGAGTGGGG 61.801 65.000 33.71 1.21 45.62 4.96
745 800 1.004440 GCTCGGAAGACTGGCACTT 60.004 57.895 0.00 0.00 35.39 3.16
760 832 2.429610 TGAAATGGTAGTACTCGGGCTC 59.570 50.000 0.00 0.00 0.00 4.70
896 973 6.203338 ACATTCCAAATGTTTGTGCTTGATTC 59.797 34.615 4.92 0.00 36.45 2.52
947 1028 8.588472 CCACATTCACATCCATCTATAGTTAGA 58.412 37.037 0.00 0.00 38.79 2.10
1008 1094 1.080705 GTACAGCTCCGTGTTCGCT 60.081 57.895 0.00 0.00 35.54 4.93
1243 1363 4.465512 CGGCTGCATTCACGCACC 62.466 66.667 0.50 0.00 36.86 5.01
1251 1371 2.953821 CGTTTCCACGGCTGCATT 59.046 55.556 0.50 0.00 43.16 3.56
1266 1386 7.401955 AGTGCTACTTAATTAACTACTCCGT 57.598 36.000 0.00 0.00 0.00 4.69
1407 1543 2.076597 AACCCCCAAAAGCGCTACCT 62.077 55.000 12.05 0.00 0.00 3.08
1408 1544 1.605451 AACCCCCAAAAGCGCTACC 60.605 57.895 12.05 0.00 0.00 3.18
1409 1545 1.176619 ACAACCCCCAAAAGCGCTAC 61.177 55.000 12.05 0.00 0.00 3.58
1478 1614 2.437413 CATCATCATCAGGGCCATCAG 58.563 52.381 6.18 0.00 0.00 2.90
1479 1615 1.074889 CCATCATCATCAGGGCCATCA 59.925 52.381 6.18 0.00 0.00 3.07
1480 1616 1.616187 CCCATCATCATCAGGGCCATC 60.616 57.143 6.18 0.00 33.91 3.51
1481 1617 0.408309 CCCATCATCATCAGGGCCAT 59.592 55.000 6.18 0.00 33.91 4.40
1482 1618 1.848400 CCCATCATCATCAGGGCCA 59.152 57.895 6.18 0.00 33.91 5.36
1483 1619 4.837085 CCCATCATCATCAGGGCC 57.163 61.111 0.00 0.00 33.91 5.80
1493 1629 0.249322 GTACGCTACGTGCCCATCAT 60.249 55.000 0.00 0.00 41.39 2.45
1501 1641 2.674852 TCTAAGTCTGGTACGCTACGTG 59.325 50.000 0.00 0.00 41.39 4.49
1513 1653 7.392494 TCATGTTACTGGTAGTCTAAGTCTG 57.608 40.000 0.00 0.00 0.00 3.51
1514 1654 8.418597 TTTCATGTTACTGGTAGTCTAAGTCT 57.581 34.615 0.00 0.00 0.00 3.24
1515 1655 8.521176 TCTTTCATGTTACTGGTAGTCTAAGTC 58.479 37.037 0.00 0.00 0.00 3.01
1516 1656 8.418597 TCTTTCATGTTACTGGTAGTCTAAGT 57.581 34.615 0.00 0.00 0.00 2.24
1549 1689 5.715434 TTTTGGCAAGTAGTGGAATAACC 57.285 39.130 0.00 0.00 39.54 2.85
1550 1690 7.029563 CAGATTTTGGCAAGTAGTGGAATAAC 58.970 38.462 0.00 0.00 0.00 1.89
1551 1691 6.719370 ACAGATTTTGGCAAGTAGTGGAATAA 59.281 34.615 0.00 0.00 0.00 1.40
1552 1692 6.245408 ACAGATTTTGGCAAGTAGTGGAATA 58.755 36.000 0.00 0.00 0.00 1.75
1553 1693 5.079643 ACAGATTTTGGCAAGTAGTGGAAT 58.920 37.500 0.00 0.00 0.00 3.01
1554 1694 4.469657 ACAGATTTTGGCAAGTAGTGGAA 58.530 39.130 0.00 0.00 0.00 3.53
1555 1695 4.098914 ACAGATTTTGGCAAGTAGTGGA 57.901 40.909 0.00 0.00 0.00 4.02
1556 1696 5.003804 ACTACAGATTTTGGCAAGTAGTGG 58.996 41.667 21.40 12.56 40.23 4.00
1557 1697 6.560253 AACTACAGATTTTGGCAAGTAGTG 57.440 37.500 22.26 12.73 40.68 2.74
1558 1698 8.685838 TTAAACTACAGATTTTGGCAAGTAGT 57.314 30.769 18.24 18.24 42.64 2.73
1559 1699 9.559958 CATTAAACTACAGATTTTGGCAAGTAG 57.440 33.333 17.23 17.23 36.08 2.57
1560 1700 9.073475 ACATTAAACTACAGATTTTGGCAAGTA 57.927 29.630 0.00 0.00 0.00 2.24
1561 1701 7.867403 CACATTAAACTACAGATTTTGGCAAGT 59.133 33.333 0.00 0.00 0.00 3.16
1562 1702 8.081633 TCACATTAAACTACAGATTTTGGCAAG 58.918 33.333 0.00 0.00 0.00 4.01
1563 1703 7.946207 TCACATTAAACTACAGATTTTGGCAA 58.054 30.769 0.00 0.00 0.00 4.52
1564 1704 7.517614 TCACATTAAACTACAGATTTTGGCA 57.482 32.000 0.00 0.00 0.00 4.92
1565 1705 7.865385 TGTTCACATTAAACTACAGATTTTGGC 59.135 33.333 0.00 0.00 0.00 4.52
1566 1706 9.912634 ATGTTCACATTAAACTACAGATTTTGG 57.087 29.630 0.00 0.00 31.37 3.28
1592 1763 9.594478 GTTTGTAAAAGAGAGATTTTCCCAAAA 57.406 29.630 9.40 0.00 36.25 2.44
1597 1768 9.399403 GTCATGTTTGTAAAAGAGAGATTTTCC 57.601 33.333 0.00 0.00 34.35 3.13
1620 1791 3.498018 GCCATTGCATATACATCACGTCA 59.502 43.478 0.00 0.00 37.47 4.35
1622 1793 3.743521 AGCCATTGCATATACATCACGT 58.256 40.909 0.00 0.00 41.13 4.49
1669 1840 1.393883 GGAGCCTCGCTTTCTAAAACG 59.606 52.381 0.00 0.00 39.88 3.60
1681 1852 0.744874 TATTTCGGTCAGGAGCCTCG 59.255 55.000 0.00 0.00 0.00 4.63
1723 1894 3.582714 GCAAAGCTTATGCCTTCAGTT 57.417 42.857 17.56 0.00 40.80 3.16
1763 1986 7.787904 TGGGTGGTATAACAGACTCTATTATGT 59.212 37.037 0.00 0.00 0.00 2.29
1764 1987 8.190326 TGGGTGGTATAACAGACTCTATTATG 57.810 38.462 0.00 0.00 0.00 1.90
1765 1988 8.974292 ATGGGTGGTATAACAGACTCTATTAT 57.026 34.615 0.00 0.00 0.00 1.28
1766 1989 8.008332 TGATGGGTGGTATAACAGACTCTATTA 58.992 37.037 0.00 0.00 0.00 0.98
1767 1990 6.844388 TGATGGGTGGTATAACAGACTCTATT 59.156 38.462 0.00 0.00 0.00 1.73
1768 1991 6.382087 TGATGGGTGGTATAACAGACTCTAT 58.618 40.000 0.00 0.00 0.00 1.98
1769 1992 5.773091 TGATGGGTGGTATAACAGACTCTA 58.227 41.667 0.00 0.00 0.00 2.43
1770 1993 4.620723 TGATGGGTGGTATAACAGACTCT 58.379 43.478 0.00 0.00 0.00 3.24
1771 1994 5.552870 ATGATGGGTGGTATAACAGACTC 57.447 43.478 0.00 0.00 0.00 3.36
1772 1995 5.975988 AATGATGGGTGGTATAACAGACT 57.024 39.130 0.00 0.00 0.00 3.24
1773 1996 8.691661 AATTAATGATGGGTGGTATAACAGAC 57.308 34.615 0.00 0.00 0.00 3.51
1804 2027 9.220906 TGGGTGGTATAACAAACTCTATTATCT 57.779 33.333 0.00 0.00 0.00 1.98
1822 2045 2.030371 TCGCGTGTAATATGGGTGGTA 58.970 47.619 5.77 0.00 0.00 3.25
1837 2060 0.677842 AACTAGTTCCACCTTCGCGT 59.322 50.000 5.77 0.00 0.00 6.01
1875 2101 4.989797 TGAGCCGAAATTTACACGAAGTAA 59.010 37.500 0.00 0.00 41.61 2.24
1891 2117 0.888619 AAGAGAACGATGTGAGCCGA 59.111 50.000 0.00 0.00 0.00 5.54
1916 2142 2.350895 CCAACGGCCTGATGTGGA 59.649 61.111 0.00 0.00 0.00 4.02
1932 2158 3.805207 AGTGTTACGGAAAGGATATGCC 58.195 45.455 0.00 0.00 0.00 4.40
1935 2161 4.839121 TGCAAGTGTTACGGAAAGGATAT 58.161 39.130 0.00 0.00 0.00 1.63
1936 2162 4.274602 TGCAAGTGTTACGGAAAGGATA 57.725 40.909 0.00 0.00 0.00 2.59
1960 2186 4.595986 AGGGTATAACAGTGCCGATTTTT 58.404 39.130 0.00 0.00 0.00 1.94
1964 2190 3.965347 AGTTAGGGTATAACAGTGCCGAT 59.035 43.478 0.00 0.00 0.00 4.18
1966 2192 3.814005 AGTTAGGGTATAACAGTGCCG 57.186 47.619 0.00 0.00 0.00 5.69
1970 2197 7.290948 GGGGTTATGTAGTTAGGGTATAACAGT 59.709 40.741 0.00 0.00 36.45 3.55
2000 2227 7.869429 GGGCTAAAGTTTATGATGAAATGATGG 59.131 37.037 0.00 0.00 0.00 3.51
2006 2233 7.147742 GGGAATGGGCTAAAGTTTATGATGAAA 60.148 37.037 0.00 0.00 0.00 2.69
2013 2240 3.562182 CGGGGAATGGGCTAAAGTTTAT 58.438 45.455 0.00 0.00 0.00 1.40
2014 2241 2.946791 GCGGGGAATGGGCTAAAGTTTA 60.947 50.000 0.00 0.00 0.00 2.01
2034 2261 2.125106 GGTCGGGGTGTGAGATGC 60.125 66.667 0.00 0.00 0.00 3.91
2075 2302 0.878523 CCGTGACGAAGAGTTGGCAA 60.879 55.000 6.54 0.00 0.00 4.52
2086 2313 2.974489 GAGAGAACGGCCGTGACGA 61.974 63.158 34.95 0.00 35.20 4.20
2094 2323 1.140407 CGTCAATCGGAGAGAACGGC 61.140 60.000 0.00 0.00 43.63 5.68
2149 2378 4.681643 AACAACATGCCGTGCGCG 62.682 61.111 13.88 13.88 42.08 6.86
2150 2379 3.098958 CAACAACATGCCGTGCGC 61.099 61.111 0.00 0.00 38.31 6.09


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

AutoCloner maintained by Alex Coulton.