Multiple sequence alignment - TraesCS6A01G086300

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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 TraesCS6A01G086300 chr6A 100.000 2645 0 0 1 2645 55012647 55015291 0.000000e+00 4885.0
1 TraesCS6A01G086300 chrUn 91.507 1825 109 26 51 1867 69376421 69374635 0.000000e+00 2470.0
2 TraesCS6A01G086300 chrUn 89.560 728 66 5 1859 2576 69373356 69372629 0.000000e+00 915.0
3 TraesCS6A01G086300 chrUn 87.888 322 29 8 1548 1867 69373699 69373386 1.160000e-98 370.0
4 TraesCS6A01G086300 chr6B 91.976 1184 52 22 504 1685 101223253 101222111 0.000000e+00 1620.0
5 TraesCS6A01G086300 chr6B 90.753 465 33 6 2181 2645 101221815 101221361 1.740000e-171 612.0
6 TraesCS6A01G086300 chr6B 88.769 463 46 4 51 511 101223888 101223430 1.780000e-156 562.0
7 TraesCS6A01G086300 chr3B 75.644 505 109 12 2118 2613 786726576 786726077 3.400000e-59 239.0
8 TraesCS6A01G086300 chr7B 100.000 29 0 0 2019 2047 630315656 630315628 1.000000e-03 54.7


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 TraesCS6A01G086300 chr6A 55012647 55015291 2644 False 4885.000000 4885 100.000000 1 2645 1 chr6A.!!$F1 2644
1 TraesCS6A01G086300 chrUn 69372629 69376421 3792 True 1251.666667 2470 89.651667 51 2576 3 chrUn.!!$R1 2525
2 TraesCS6A01G086300 chr6B 101221361 101223888 2527 True 931.333333 1620 90.499333 51 2645 3 chr6B.!!$R1 2594

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
49 50 0.24912 TGGTGGCTATCCTTGTGTCG 59.751 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 1992 0.178981 ACACTGATTGGGCAGCTTGT 60.179 50.0 0.0 0.0 39.51 3.16 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
17 18 3.330853 GCCGCGACGATCCATGAC 61.331 66.667 8.23 0.00 0.00 3.06
18 19 2.413351 CCGCGACGATCCATGACT 59.587 61.111 8.23 0.00 0.00 3.41
19 20 1.652563 CCGCGACGATCCATGACTA 59.347 57.895 8.23 0.00 0.00 2.59
20 21 0.660595 CCGCGACGATCCATGACTAC 60.661 60.000 8.23 0.00 0.00 2.73
21 22 0.308068 CGCGACGATCCATGACTACT 59.692 55.000 0.00 0.00 0.00 2.57
22 23 1.529865 CGCGACGATCCATGACTACTA 59.470 52.381 0.00 0.00 0.00 1.82
23 24 2.159824 CGCGACGATCCATGACTACTAT 59.840 50.000 0.00 0.00 0.00 2.12
24 25 3.725305 CGCGACGATCCATGACTACTATC 60.725 52.174 0.00 0.00 0.00 2.08
25 26 3.188667 GCGACGATCCATGACTACTATCA 59.811 47.826 0.00 0.00 0.00 2.15
26 27 4.670478 GCGACGATCCATGACTACTATCAG 60.670 50.000 0.00 0.00 30.46 2.90
27 28 4.691216 CGACGATCCATGACTACTATCAGA 59.309 45.833 0.00 0.00 30.46 3.27
28 29 5.163903 CGACGATCCATGACTACTATCAGAG 60.164 48.000 0.00 0.00 30.46 3.35
29 30 5.626142 ACGATCCATGACTACTATCAGAGT 58.374 41.667 0.00 0.00 42.69 3.24
30 31 6.065374 ACGATCCATGACTACTATCAGAGTT 58.935 40.000 0.00 0.00 39.81 3.01
31 32 6.016693 ACGATCCATGACTACTATCAGAGTTG 60.017 42.308 0.00 0.00 39.81 3.16
32 33 6.569418 CGATCCATGACTACTATCAGAGTTGG 60.569 46.154 0.00 0.00 39.81 3.77
33 34 5.519808 TCCATGACTACTATCAGAGTTGGT 58.480 41.667 0.00 0.00 39.81 3.67
34 35 5.360999 TCCATGACTACTATCAGAGTTGGTG 59.639 44.000 0.00 0.00 39.81 4.17
35 36 5.452496 CCATGACTACTATCAGAGTTGGTGG 60.452 48.000 0.00 0.00 39.81 4.61
36 37 3.447586 TGACTACTATCAGAGTTGGTGGC 59.552 47.826 0.00 0.00 39.81 5.01
37 38 3.702045 GACTACTATCAGAGTTGGTGGCT 59.298 47.826 0.00 0.00 39.81 4.75
38 39 4.868268 ACTACTATCAGAGTTGGTGGCTA 58.132 43.478 0.00 0.00 39.81 3.93
39 40 5.459505 ACTACTATCAGAGTTGGTGGCTAT 58.540 41.667 0.00 0.00 39.81 2.97
40 41 4.946478 ACTATCAGAGTTGGTGGCTATC 57.054 45.455 0.00 0.00 33.13 2.08
41 42 3.643792 ACTATCAGAGTTGGTGGCTATCC 59.356 47.826 0.00 0.00 33.13 2.59
42 43 2.254152 TCAGAGTTGGTGGCTATCCT 57.746 50.000 0.00 0.00 0.00 3.24
43 44 2.551270 TCAGAGTTGGTGGCTATCCTT 58.449 47.619 0.00 0.00 0.00 3.36
44 45 2.237143 TCAGAGTTGGTGGCTATCCTTG 59.763 50.000 0.00 0.00 0.00 3.61
45 46 2.026822 CAGAGTTGGTGGCTATCCTTGT 60.027 50.000 0.00 0.00 0.00 3.16
46 47 2.026822 AGAGTTGGTGGCTATCCTTGTG 60.027 50.000 0.00 0.00 0.00 3.33
47 48 1.705186 AGTTGGTGGCTATCCTTGTGT 59.295 47.619 0.00 0.00 0.00 3.72
48 49 2.084546 GTTGGTGGCTATCCTTGTGTC 58.915 52.381 0.00 0.00 0.00 3.67
49 50 0.249120 TGGTGGCTATCCTTGTGTCG 59.751 55.000 0.00 0.00 0.00 4.35
77 78 1.607467 GCAAAGGCATGGTCACCCT 60.607 57.895 0.00 0.00 40.72 4.34
102 103 0.827507 GGTGCACCATTTCCACCAGT 60.828 55.000 31.23 0.00 46.38 4.00
120 121 1.378646 TCGAGAGGCAGACGACCAT 60.379 57.895 0.00 0.00 0.00 3.55
128 129 3.041874 CAGACGACCATGACTGCTC 57.958 57.895 0.00 0.00 0.00 4.26
224 225 1.202639 CCTACACCAACAGCAGTGTGA 60.203 52.381 6.70 0.00 46.35 3.58
241 242 2.154462 GTGAAGTCCCTCCACACAATG 58.846 52.381 0.00 0.00 0.00 2.82
243 244 2.038952 TGAAGTCCCTCCACACAATGAG 59.961 50.000 0.00 0.00 0.00 2.90
244 245 1.734655 AGTCCCTCCACACAATGAGT 58.265 50.000 0.00 0.00 0.00 3.41
245 246 2.902608 AGTCCCTCCACACAATGAGTA 58.097 47.619 0.00 0.00 0.00 2.59
246 247 2.834549 AGTCCCTCCACACAATGAGTAG 59.165 50.000 0.00 0.00 0.00 2.57
271 272 9.930158 AGGATAGTAATAAGGATGGATAGAGTC 57.070 37.037 0.00 0.00 0.00 3.36
272 273 8.842280 GGATAGTAATAAGGATGGATAGAGTCG 58.158 40.741 0.00 0.00 0.00 4.18
276 277 1.917872 AGGATGGATAGAGTCGGAGC 58.082 55.000 0.00 0.00 0.00 4.70
334 335 4.081697 TCCGATGTAATCTGCAACTGAAGA 60.082 41.667 0.00 0.00 42.58 2.87
372 373 6.560711 GTGTCAAACCAACTTATCAACAACT 58.439 36.000 0.00 0.00 0.00 3.16
401 402 2.046313 GCGTGTTTGAATCTTGTGCAG 58.954 47.619 0.00 0.00 0.00 4.41
422 423 4.276678 CAGAGCAATGTTGGAAAAGACTCA 59.723 41.667 0.00 0.00 0.00 3.41
423 424 4.889409 AGAGCAATGTTGGAAAAGACTCAA 59.111 37.500 0.00 0.00 0.00 3.02
425 426 5.594926 AGCAATGTTGGAAAAGACTCAAAG 58.405 37.500 0.00 0.00 0.00 2.77
427 428 6.042143 GCAATGTTGGAAAAGACTCAAAGAA 58.958 36.000 0.00 0.00 0.00 2.52
432 435 3.117512 TGGAAAAGACTCAAAGAAGCCCT 60.118 43.478 0.00 0.00 0.00 5.19
439 442 1.543358 CTCAAAGAAGCCCTGAAAGCC 59.457 52.381 0.00 0.00 0.00 4.35
445 448 1.273606 GAAGCCCTGAAAGCCTTTTCC 59.726 52.381 0.00 0.00 41.62 3.13
458 461 1.394917 CCTTTTCCGAATCGACTGCAG 59.605 52.381 13.48 13.48 0.00 4.41
491 494 2.480845 CGACCCCCGAGAAATTCATAC 58.519 52.381 0.00 0.00 41.76 2.39
495 498 2.222027 CCCCGAGAAATTCATACAGGC 58.778 52.381 0.00 0.00 0.00 4.85
499 502 3.071023 CCGAGAAATTCATACAGGCCCTA 59.929 47.826 0.00 0.00 0.00 3.53
519 706 4.469945 CCTAGGTACCCAGAAATTCTCACA 59.530 45.833 9.15 0.00 0.00 3.58
520 707 4.993705 AGGTACCCAGAAATTCTCACAA 57.006 40.909 8.74 0.00 0.00 3.33
548 735 6.291796 GCCAAATATTTGAAAATACTGCTCGC 60.292 38.462 26.32 13.67 40.55 5.03
553 740 2.621338 TGAAAATACTGCTCGCTCCAG 58.379 47.619 0.00 0.00 36.41 3.86
585 772 2.708861 TGGTCCATTAATCCCGTATGCT 59.291 45.455 0.00 0.00 0.00 3.79
590 777 1.961793 TTAATCCCGTATGCTGTGCC 58.038 50.000 0.00 0.00 0.00 5.01
597 784 1.933853 CCGTATGCTGTGCCTACTTTC 59.066 52.381 0.00 0.00 29.73 2.62
598 785 1.933853 CGTATGCTGTGCCTACTTTCC 59.066 52.381 0.00 0.00 29.73 3.13
617 804 4.759516 TCCGTGGAAAAGAAAATGCTAC 57.240 40.909 0.00 0.00 0.00 3.58
624 811 4.406943 GAAAAGAAAATGCTACGCCTGAG 58.593 43.478 0.00 0.00 0.00 3.35
659 846 6.713762 TTTCACCTTTGTTTGTGATGAGAT 57.286 33.333 0.00 0.00 40.88 2.75
665 852 2.153645 TGTTTGTGATGAGATGCGCTT 58.846 42.857 9.73 0.55 0.00 4.68
686 873 5.051641 GCTTGATTAACTCTTCGATACCACG 60.052 44.000 0.00 0.00 0.00 4.94
691 878 2.165167 ACTCTTCGATACCACGGACAA 58.835 47.619 0.00 0.00 0.00 3.18
692 879 2.094854 ACTCTTCGATACCACGGACAAC 60.095 50.000 0.00 0.00 0.00 3.32
702 889 3.411351 CGGACAACGTGAAGGGCG 61.411 66.667 0.00 0.00 37.93 6.13
875 1063 0.392193 CTCACCTCAGCCATGTCACC 60.392 60.000 0.00 0.00 0.00 4.02
1039 1231 1.680522 ATTCCCAGCGCAGATCGTCT 61.681 55.000 11.47 0.00 41.07 4.18
1315 1507 1.533469 CGGACGTCAAGAAGGGGAGT 61.533 60.000 18.91 0.00 0.00 3.85
1398 1591 3.164269 CTGATCGTGGGGAGGGGG 61.164 72.222 0.00 0.00 0.00 5.40
1455 1648 6.681777 ACTACGTACGGTTTTATCTCTTGTT 58.318 36.000 21.06 0.00 0.00 2.83
1616 1809 2.673862 TCGTCTGTCGAGTGATCTTCTC 59.326 50.000 0.00 1.52 44.01 2.87
1617 1810 2.675844 CGTCTGTCGAGTGATCTTCTCT 59.324 50.000 13.53 0.22 42.86 3.10
1618 1811 3.866327 CGTCTGTCGAGTGATCTTCTCTA 59.134 47.826 13.53 3.81 42.86 2.43
1619 1812 4.330347 CGTCTGTCGAGTGATCTTCTCTAA 59.670 45.833 13.53 3.23 42.86 2.10
1621 1814 6.457663 CGTCTGTCGAGTGATCTTCTCTAATT 60.458 42.308 13.53 0.00 42.86 1.40
1622 1815 7.254488 CGTCTGTCGAGTGATCTTCTCTAATTA 60.254 40.741 13.53 0.00 42.86 1.40
1684 1877 1.177895 TGTCACGCCGTACTGGGTAA 61.178 55.000 6.67 0.00 38.63 2.85
1696 1889 4.502604 CGTACTGGGTAAGGATGGGTTATG 60.503 50.000 0.00 0.00 0.00 1.90
1705 1898 5.975988 AAGGATGGGTTATGTGACTATGT 57.024 39.130 0.00 0.00 0.00 2.29
1707 1900 7.446106 AAGGATGGGTTATGTGACTATGTAA 57.554 36.000 0.00 0.00 0.00 2.41
1734 1927 0.236449 ACGAACGAACAAAATCGCCC 59.764 50.000 0.14 0.00 46.51 6.13
1735 1928 0.787908 CGAACGAACAAAATCGCCCG 60.788 55.000 0.00 0.00 46.51 6.13
1748 1941 1.722011 TCGCCCGATCTTTGTTCTTC 58.278 50.000 0.00 0.00 0.00 2.87
1750 1943 2.494471 TCGCCCGATCTTTGTTCTTCTA 59.506 45.455 0.00 0.00 0.00 2.10
1752 1945 4.340097 TCGCCCGATCTTTGTTCTTCTATA 59.660 41.667 0.00 0.00 0.00 1.31
1753 1946 5.047847 CGCCCGATCTTTGTTCTTCTATAA 58.952 41.667 0.00 0.00 0.00 0.98
1754 1947 5.175856 CGCCCGATCTTTGTTCTTCTATAAG 59.824 44.000 0.00 0.00 0.00 1.73
1755 1948 6.281405 GCCCGATCTTTGTTCTTCTATAAGA 58.719 40.000 0.00 0.00 40.03 2.10
1756 1949 6.422400 GCCCGATCTTTGTTCTTCTATAAGAG 59.578 42.308 0.00 0.00 42.60 2.85
1757 1950 6.422400 CCCGATCTTTGTTCTTCTATAAGAGC 59.578 42.308 0.00 0.00 42.60 4.09
1777 1970 2.805657 GCATCTACATACAACCGGACCC 60.806 54.545 9.46 0.00 0.00 4.46
1778 1971 1.488390 TCTACATACAACCGGACCCC 58.512 55.000 9.46 0.00 0.00 4.95
1780 1973 1.766496 CTACATACAACCGGACCCCAT 59.234 52.381 9.46 0.00 0.00 4.00
1784 1977 2.767424 TACAACCGGACCCCATCCCA 62.767 60.000 9.46 0.00 46.04 4.37
1796 1989 0.409484 CCATCCCACCCCAAAAGTCT 59.591 55.000 0.00 0.00 0.00 3.24
1799 1992 0.699577 TCCCACCCCAAAAGTCTGGA 60.700 55.000 0.00 0.00 38.96 3.86
1811 2004 1.228245 GTCTGGACAAGCTGCCCAA 60.228 57.895 0.00 0.00 26.63 4.12
1819 2012 0.524862 CAAGCTGCCCAATCAGTGTC 59.475 55.000 0.00 0.00 36.49 3.67
1854 2047 1.303309 CATCCAATCGGCCTCTTCAC 58.697 55.000 0.00 0.00 0.00 3.18
1857 3337 1.281867 TCCAATCGGCCTCTTCACATT 59.718 47.619 0.00 0.00 0.00 2.71
1871 3351 3.694043 TCACATTCGGTCCAAATCTGA 57.306 42.857 0.00 0.00 0.00 3.27
1876 3356 1.218047 CGGTCCAAATCTGAGGCGA 59.782 57.895 0.00 0.00 0.00 5.54
1891 3372 0.606604 GGCGAATATAAGAGGCCCGA 59.393 55.000 0.00 0.00 37.82 5.14
1894 3375 2.547218 GCGAATATAAGAGGCCCGAACA 60.547 50.000 0.00 0.00 0.00 3.18
1917 3398 2.358247 GGACACGCCCGTCATGTT 60.358 61.111 2.87 0.00 37.66 2.71
1924 3405 2.040544 GCCCGTCATGTTGGACTGG 61.041 63.158 7.44 0.00 42.91 4.00
1925 3406 1.374947 CCCGTCATGTTGGACTGGT 59.625 57.895 7.44 0.00 37.39 4.00
1933 3414 0.618458 TGTTGGACTGGTGGATAGGC 59.382 55.000 0.00 0.00 0.00 3.93
1934 3415 0.912486 GTTGGACTGGTGGATAGGCT 59.088 55.000 0.00 0.00 0.00 4.58
1957 3438 1.668151 GCAGGAACGCGGAGAAACT 60.668 57.895 12.47 0.00 0.00 2.66
1966 3447 0.391661 GCGGAGAAACTGCTGATCCA 60.392 55.000 0.00 0.00 46.39 3.41
1968 3449 2.636830 CGGAGAAACTGCTGATCCAAT 58.363 47.619 0.00 0.00 0.00 3.16
1977 3458 1.454479 CTGATCCAATGGGCGCCTT 60.454 57.895 28.56 11.36 0.00 4.35
2020 3510 4.821589 GCCGCACGAGGGAGGAAG 62.822 72.222 0.00 0.00 0.00 3.46
2022 3512 4.821589 CGCACGAGGGAGGAAGCC 62.822 72.222 0.00 0.00 0.00 4.35
2034 3524 2.104281 GGAGGAAGCCGGCTATTTAAGA 59.896 50.000 33.07 0.00 0.00 2.10
2044 3534 1.484356 CTATTTAAGACGGACGGCGG 58.516 55.000 13.24 0.00 0.00 6.13
2062 3552 2.971598 GCAGCAGAACCCTAGCCCA 61.972 63.158 0.00 0.00 0.00 5.36
2065 3555 2.602676 GCAGAACCCTAGCCCACCA 61.603 63.158 0.00 0.00 0.00 4.17
2087 3577 3.399305 ACATTTCTTCCCCTTTCTCCACT 59.601 43.478 0.00 0.00 0.00 4.00
2092 3582 2.269241 CCCTTTCTCCACTCCGCC 59.731 66.667 0.00 0.00 0.00 6.13
2108 3598 1.378762 GCCCCAGCACTTCCACTTA 59.621 57.895 0.00 0.00 39.53 2.24
2110 3600 0.400213 CCCCAGCACTTCCACTTACA 59.600 55.000 0.00 0.00 0.00 2.41
2113 3603 2.026822 CCCAGCACTTCCACTTACATCT 60.027 50.000 0.00 0.00 0.00 2.90
2117 3607 5.395657 CCAGCACTTCCACTTACATCTGATA 60.396 44.000 0.00 0.00 0.00 2.15
2120 3610 8.093307 CAGCACTTCCACTTACATCTGATATAT 58.907 37.037 0.00 0.00 0.00 0.86
2122 3612 8.715998 GCACTTCCACTTACATCTGATATATTG 58.284 37.037 0.00 0.00 0.00 1.90
2130 3620 5.494390 ACATCTGATATATTGCTGCCTCA 57.506 39.130 0.00 0.00 0.00 3.86
2150 3640 2.034939 CACAACACATGCAACACCTCAT 59.965 45.455 0.00 0.00 0.00 2.90
2170 3660 1.266446 TGCACCACATCATCAACAACG 59.734 47.619 0.00 0.00 0.00 4.10
2202 3692 9.613428 CCAATAGTGTTTATAGAAGACCATTGA 57.387 33.333 8.12 0.00 0.00 2.57
2242 3732 4.457834 AGCTTTTCGATCCCCTATATCG 57.542 45.455 0.00 0.00 45.88 2.92
2278 3768 0.462047 CCTCCTTCGGGGTGAATTCG 60.462 60.000 0.04 0.00 35.63 3.34
2354 3844 4.827835 GGATGTCACTAGTATCAGCACCTA 59.172 45.833 13.83 0.00 0.00 3.08
2432 3922 3.792114 TCCTCCTCTACCAGAACTCCATA 59.208 47.826 0.00 0.00 0.00 2.74
2452 3942 5.131142 CCATACTCCCTCCTCAACTAATTGT 59.869 44.000 0.00 0.00 37.11 2.71
2477 3967 6.653526 TTCTTTTTCTTCCATTCTGATGCA 57.346 33.333 0.00 0.00 31.67 3.96
2542 4032 5.461526 CCAATTTGCATGATCTATCTGCTG 58.538 41.667 0.00 0.00 34.37 4.41
2599 4089 8.480643 TCTAGCTTAAAGCATAGAGTTTGTTC 57.519 34.615 0.00 0.00 45.56 3.18
2624 4114 2.691011 GCTAACTTGGTTGTCCCACAAA 59.309 45.455 0.00 0.00 45.19 2.83
2636 4126 0.607489 CCCACAAAGGCAGACTCCTG 60.607 60.000 0.00 0.00 43.22 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.402282 TAGTCATGGATCGTCGCGGC 62.402 60.000 6.13 1.93 0.00 6.53
1 2 0.660595 GTAGTCATGGATCGTCGCGG 60.661 60.000 6.13 0.00 0.00 6.46
2 3 0.308068 AGTAGTCATGGATCGTCGCG 59.692 55.000 0.00 0.00 0.00 5.87
3 4 3.188667 TGATAGTAGTCATGGATCGTCGC 59.811 47.826 0.00 0.00 0.00 5.19
4 5 4.691216 TCTGATAGTAGTCATGGATCGTCG 59.309 45.833 0.00 0.00 0.00 5.12
5 6 5.703592 ACTCTGATAGTAGTCATGGATCGTC 59.296 44.000 0.00 0.00 36.36 4.20
6 7 5.626142 ACTCTGATAGTAGTCATGGATCGT 58.374 41.667 0.00 0.00 36.36 3.73
7 8 6.377780 CAACTCTGATAGTAGTCATGGATCG 58.622 44.000 0.00 0.00 37.50 3.69
8 9 6.266558 ACCAACTCTGATAGTAGTCATGGATC 59.733 42.308 0.00 0.00 37.50 3.36
9 10 6.041409 CACCAACTCTGATAGTAGTCATGGAT 59.959 42.308 0.00 0.00 37.50 3.41
10 11 5.360999 CACCAACTCTGATAGTAGTCATGGA 59.639 44.000 0.00 0.00 37.50 3.41
11 12 5.452496 CCACCAACTCTGATAGTAGTCATGG 60.452 48.000 0.00 0.00 37.50 3.66
12 13 5.595885 CCACCAACTCTGATAGTAGTCATG 58.404 45.833 0.00 0.00 37.50 3.07
13 14 4.100189 GCCACCAACTCTGATAGTAGTCAT 59.900 45.833 0.00 0.00 37.50 3.06
14 15 3.447586 GCCACCAACTCTGATAGTAGTCA 59.552 47.826 0.00 0.00 37.50 3.41
15 16 3.702045 AGCCACCAACTCTGATAGTAGTC 59.298 47.826 0.00 0.00 37.50 2.59
16 17 3.714144 AGCCACCAACTCTGATAGTAGT 58.286 45.455 0.00 0.00 37.50 2.73
17 18 5.047660 GGATAGCCACCAACTCTGATAGTAG 60.048 48.000 0.00 0.00 37.50 2.57
18 19 4.833380 GGATAGCCACCAACTCTGATAGTA 59.167 45.833 0.00 0.00 37.50 1.82
19 20 3.643792 GGATAGCCACCAACTCTGATAGT 59.356 47.826 0.00 0.00 41.49 2.12
20 21 3.900601 AGGATAGCCACCAACTCTGATAG 59.099 47.826 0.00 0.00 36.29 2.08
21 22 3.928754 AGGATAGCCACCAACTCTGATA 58.071 45.455 0.00 0.00 36.29 2.15
22 23 2.769209 AGGATAGCCACCAACTCTGAT 58.231 47.619 0.00 0.00 36.29 2.90
23 24 2.237143 CAAGGATAGCCACCAACTCTGA 59.763 50.000 0.00 0.00 36.29 3.27
24 25 2.026822 ACAAGGATAGCCACCAACTCTG 60.027 50.000 0.00 0.00 36.29 3.35
25 26 2.026822 CACAAGGATAGCCACCAACTCT 60.027 50.000 0.00 0.00 36.29 3.24
26 27 2.290323 ACACAAGGATAGCCACCAACTC 60.290 50.000 0.00 0.00 36.29 3.01
27 28 1.705186 ACACAAGGATAGCCACCAACT 59.295 47.619 0.00 0.00 36.29 3.16
28 29 2.084546 GACACAAGGATAGCCACCAAC 58.915 52.381 0.00 0.00 36.29 3.77
29 30 1.338674 CGACACAAGGATAGCCACCAA 60.339 52.381 0.00 0.00 36.29 3.67
30 31 0.249120 CGACACAAGGATAGCCACCA 59.751 55.000 0.00 0.00 36.29 4.17
31 32 0.535335 TCGACACAAGGATAGCCACC 59.465 55.000 0.00 0.00 36.29 4.61
32 33 2.205074 CATCGACACAAGGATAGCCAC 58.795 52.381 0.00 0.00 36.29 5.01
33 34 1.138859 CCATCGACACAAGGATAGCCA 59.861 52.381 0.00 0.00 36.29 4.75
34 35 1.412710 TCCATCGACACAAGGATAGCC 59.587 52.381 0.00 0.00 0.00 3.93
35 36 2.748605 CTCCATCGACACAAGGATAGC 58.251 52.381 0.00 0.00 0.00 2.97
36 37 2.748605 GCTCCATCGACACAAGGATAG 58.251 52.381 0.00 0.00 0.00 2.08
37 38 1.067060 CGCTCCATCGACACAAGGATA 59.933 52.381 0.00 0.00 0.00 2.59
38 39 0.179100 CGCTCCATCGACACAAGGAT 60.179 55.000 0.00 0.00 0.00 3.24
39 40 1.215382 CGCTCCATCGACACAAGGA 59.785 57.895 0.00 0.00 0.00 3.36
40 41 1.811266 CCGCTCCATCGACACAAGG 60.811 63.158 0.00 0.00 0.00 3.61
41 42 1.811266 CCCGCTCCATCGACACAAG 60.811 63.158 0.00 0.00 0.00 3.16
42 43 2.264480 CCCGCTCCATCGACACAA 59.736 61.111 0.00 0.00 0.00 3.33
43 44 4.451150 GCCCGCTCCATCGACACA 62.451 66.667 0.00 0.00 0.00 3.72
44 45 3.950794 TTGCCCGCTCCATCGACAC 62.951 63.158 0.00 0.00 0.00 3.67
45 46 3.247056 TTTGCCCGCTCCATCGACA 62.247 57.895 0.00 0.00 0.00 4.35
46 47 2.435938 TTTGCCCGCTCCATCGAC 60.436 61.111 0.00 0.00 0.00 4.20
47 48 2.125147 CTTTGCCCGCTCCATCGA 60.125 61.111 0.00 0.00 0.00 3.59
48 49 3.204827 CCTTTGCCCGCTCCATCG 61.205 66.667 0.00 0.00 0.00 3.84
49 50 3.521796 GCCTTTGCCCGCTCCATC 61.522 66.667 0.00 0.00 0.00 3.51
91 92 0.250513 GCCTCTCGACTGGTGGAAAT 59.749 55.000 1.54 0.00 0.00 2.17
102 103 1.378646 ATGGTCGTCTGCCTCTCGA 60.379 57.895 0.00 0.00 0.00 4.04
185 186 0.108585 GGCCCACCATACATCGACAT 59.891 55.000 0.00 0.00 35.26 3.06
222 223 2.038952 CTCATTGTGTGGAGGGACTTCA 59.961 50.000 0.00 0.00 45.05 3.02
224 225 2.057922 ACTCATTGTGTGGAGGGACTT 58.942 47.619 0.00 0.00 41.55 3.01
245 246 9.930158 GACTCTATCCATCCTTATTACTATCCT 57.070 37.037 0.00 0.00 0.00 3.24
246 247 8.842280 CGACTCTATCCATCCTTATTACTATCC 58.158 40.741 0.00 0.00 0.00 2.59
266 267 1.769026 TATCTGCTTGCTCCGACTCT 58.231 50.000 0.00 0.00 0.00 3.24
271 272 2.292267 ACCATTTATCTGCTTGCTCCG 58.708 47.619 0.00 0.00 0.00 4.63
272 273 3.696051 TCAACCATTTATCTGCTTGCTCC 59.304 43.478 0.00 0.00 0.00 4.70
276 277 6.446781 AGTCATCAACCATTTATCTGCTTG 57.553 37.500 0.00 0.00 0.00 4.01
311 312 3.885724 TCAGTTGCAGATTACATCGGA 57.114 42.857 0.00 0.00 0.00 4.55
312 313 4.183865 TCTTCAGTTGCAGATTACATCGG 58.816 43.478 0.00 0.00 0.00 4.18
334 335 4.383661 GGTTTGACACCATTTCCCAAACTT 60.384 41.667 13.59 0.00 46.42 2.66
361 362 3.064207 GCTCGACACCAGTTGTTGATAA 58.936 45.455 0.00 0.00 45.99 1.75
372 373 0.460459 TTCAAACACGCTCGACACCA 60.460 50.000 0.00 0.00 0.00 4.17
401 402 4.836125 TGAGTCTTTTCCAACATTGCTC 57.164 40.909 0.00 0.00 0.00 4.26
422 423 2.388526 AAGGCTTTCAGGGCTTCTTT 57.611 45.000 0.00 0.00 46.76 2.52
427 428 0.895559 CGGAAAAGGCTTTCAGGGCT 60.896 55.000 13.76 0.00 42.44 5.19
432 435 2.482721 GTCGATTCGGAAAAGGCTTTCA 59.517 45.455 13.76 0.00 42.44 2.69
439 442 1.201965 GCTGCAGTCGATTCGGAAAAG 60.202 52.381 16.64 0.01 0.00 2.27
445 448 0.179215 GTTTGGCTGCAGTCGATTCG 60.179 55.000 14.71 0.00 0.00 3.34
458 461 1.592400 GGGGTCGGCTTAAGTTTGGC 61.592 60.000 4.02 0.00 0.00 4.52
519 706 9.452287 AGCAGTATTTTCAAATATTTGGCATTT 57.548 25.926 24.40 11.02 38.66 2.32
520 707 9.101655 GAGCAGTATTTTCAAATATTTGGCATT 57.898 29.630 24.40 12.17 38.66 3.56
548 735 3.084786 GGACCAAAATGGAGTTCTGGAG 58.915 50.000 2.85 0.00 40.96 3.86
553 740 6.406961 GGGATTAATGGACCAAAATGGAGTTC 60.407 42.308 9.53 0.00 40.96 3.01
585 772 0.759959 TTCCACGGAAAGTAGGCACA 59.240 50.000 0.00 0.00 0.00 4.57
590 777 5.629435 GCATTTTCTTTTCCACGGAAAGTAG 59.371 40.000 10.95 7.47 43.75 2.57
597 784 3.488489 CGTAGCATTTTCTTTTCCACGG 58.512 45.455 0.00 0.00 0.00 4.94
617 804 4.988598 AACGTGGGTGCTCAGGCG 62.989 66.667 0.00 0.00 42.25 5.52
639 826 4.232221 GCATCTCATCACAAACAAAGGTG 58.768 43.478 0.00 0.00 36.36 4.00
640 827 3.058016 CGCATCTCATCACAAACAAAGGT 60.058 43.478 0.00 0.00 0.00 3.50
641 828 3.495193 CGCATCTCATCACAAACAAAGG 58.505 45.455 0.00 0.00 0.00 3.11
642 829 2.912967 GCGCATCTCATCACAAACAAAG 59.087 45.455 0.30 0.00 0.00 2.77
643 830 2.553602 AGCGCATCTCATCACAAACAAA 59.446 40.909 11.47 0.00 0.00 2.83
650 837 4.272018 AGTTAATCAAGCGCATCTCATCAC 59.728 41.667 11.47 0.00 0.00 3.06
655 842 4.317698 CGAAGAGTTAATCAAGCGCATCTC 60.318 45.833 11.47 1.43 0.00 2.75
659 846 2.954316 TCGAAGAGTTAATCAAGCGCA 58.046 42.857 11.47 0.00 0.00 6.09
665 852 4.641541 TCCGTGGTATCGAAGAGTTAATCA 59.358 41.667 0.00 0.00 43.63 2.57
686 873 3.723348 GCGCCCTTCACGTTGTCC 61.723 66.667 0.00 0.00 0.00 4.02
691 878 1.381165 AACAAAAGCGCCCTTCACGT 61.381 50.000 2.29 0.00 0.00 4.49
692 879 0.248866 AAACAAAAGCGCCCTTCACG 60.249 50.000 2.29 0.00 0.00 4.35
693 880 2.034179 AGTAAACAAAAGCGCCCTTCAC 59.966 45.455 2.29 0.00 0.00 3.18
694 881 2.292292 GAGTAAACAAAAGCGCCCTTCA 59.708 45.455 2.29 0.00 0.00 3.02
695 882 2.552743 AGAGTAAACAAAAGCGCCCTTC 59.447 45.455 2.29 0.00 0.00 3.46
697 884 2.271944 AGAGTAAACAAAAGCGCCCT 57.728 45.000 2.29 0.00 0.00 5.19
698 885 2.607038 CCAAGAGTAAACAAAAGCGCCC 60.607 50.000 2.29 0.00 0.00 6.13
702 889 4.870363 TGATGCCAAGAGTAAACAAAAGC 58.130 39.130 0.00 0.00 0.00 3.51
1039 1231 0.601046 CGGAGCTGCTGAGTTGTTGA 60.601 55.000 7.01 0.00 0.00 3.18
1315 1507 0.836400 ACTTCTTCTTGGCCTCGGGA 60.836 55.000 3.32 0.00 0.00 5.14
1398 1591 2.610694 CCACCCGCATCATCATCGC 61.611 63.158 0.00 0.00 0.00 4.58
1455 1648 3.592898 TGCATCTAAGCTCGAACTTCA 57.407 42.857 3.95 0.00 34.99 3.02
1616 1809 7.201232 CGTTGTGCTCGGTTCATTTTTAATTAG 60.201 37.037 0.00 0.00 0.00 1.73
1617 1810 6.579292 CGTTGTGCTCGGTTCATTTTTAATTA 59.421 34.615 0.00 0.00 0.00 1.40
1618 1811 5.401079 CGTTGTGCTCGGTTCATTTTTAATT 59.599 36.000 0.00 0.00 0.00 1.40
1619 1812 4.915085 CGTTGTGCTCGGTTCATTTTTAAT 59.085 37.500 0.00 0.00 0.00 1.40
1621 1814 3.850374 GCGTTGTGCTCGGTTCATTTTTA 60.850 43.478 0.00 0.00 41.73 1.52
1622 1815 2.726633 CGTTGTGCTCGGTTCATTTTT 58.273 42.857 0.00 0.00 0.00 1.94
1635 1828 2.320587 CCTGAGGTCAGCGTTGTGC 61.321 63.158 1.08 0.00 42.47 4.57
1684 1877 6.043243 CCTTACATAGTCACATAACCCATCCT 59.957 42.308 0.00 0.00 0.00 3.24
1696 1889 5.808042 TCGTACACTCCTTACATAGTCAC 57.192 43.478 0.00 0.00 0.00 3.67
1705 1898 4.566545 TTGTTCGTTCGTACACTCCTTA 57.433 40.909 4.35 0.00 0.00 2.69
1707 1900 3.441496 TTTGTTCGTTCGTACACTCCT 57.559 42.857 4.35 0.00 0.00 3.69
1734 1927 7.993821 TGCTCTTATAGAAGAACAAAGATCG 57.006 36.000 0.78 0.00 41.23 3.69
1735 1928 9.762933 AGATGCTCTTATAGAAGAACAAAGATC 57.237 33.333 7.24 1.49 40.31 2.75
1748 1941 7.030165 CCGGTTGTATGTAGATGCTCTTATAG 58.970 42.308 0.00 0.00 0.00 1.31
1750 1943 5.538813 TCCGGTTGTATGTAGATGCTCTTAT 59.461 40.000 0.00 0.00 0.00 1.73
1752 1945 3.704566 TCCGGTTGTATGTAGATGCTCTT 59.295 43.478 0.00 0.00 0.00 2.85
1753 1946 3.068307 GTCCGGTTGTATGTAGATGCTCT 59.932 47.826 0.00 0.00 0.00 4.09
1754 1947 3.381949 GTCCGGTTGTATGTAGATGCTC 58.618 50.000 0.00 0.00 0.00 4.26
1755 1948 2.102588 GGTCCGGTTGTATGTAGATGCT 59.897 50.000 0.00 0.00 0.00 3.79
1756 1949 2.480845 GGTCCGGTTGTATGTAGATGC 58.519 52.381 0.00 0.00 0.00 3.91
1757 1950 2.224209 GGGGTCCGGTTGTATGTAGATG 60.224 54.545 0.00 0.00 0.00 2.90
1758 1951 2.044758 GGGGTCCGGTTGTATGTAGAT 58.955 52.381 0.00 0.00 0.00 1.98
1759 1952 1.273154 TGGGGTCCGGTTGTATGTAGA 60.273 52.381 0.00 0.00 0.00 2.59
1760 1953 1.196911 TGGGGTCCGGTTGTATGTAG 58.803 55.000 0.00 0.00 0.00 2.74
1761 1954 1.764134 GATGGGGTCCGGTTGTATGTA 59.236 52.381 0.00 0.00 0.00 2.29
1762 1955 0.544697 GATGGGGTCCGGTTGTATGT 59.455 55.000 0.00 0.00 0.00 2.29
1763 1956 0.179029 GGATGGGGTCCGGTTGTATG 60.179 60.000 0.00 0.00 37.23 2.39
1764 1957 2.227737 GGATGGGGTCCGGTTGTAT 58.772 57.895 0.00 0.00 37.23 2.29
1765 1958 3.730158 GGATGGGGTCCGGTTGTA 58.270 61.111 0.00 0.00 37.23 2.41
1777 1970 0.409484 AGACTTTTGGGGTGGGATGG 59.591 55.000 0.00 0.00 0.00 3.51
1778 1971 1.549203 CAGACTTTTGGGGTGGGATG 58.451 55.000 0.00 0.00 0.00 3.51
1780 1973 0.699577 TCCAGACTTTTGGGGTGGGA 60.700 55.000 0.00 0.00 38.81 4.37
1784 1977 1.754201 GCTTGTCCAGACTTTTGGGGT 60.754 52.381 0.00 0.00 38.81 4.95
1799 1992 0.178981 ACACTGATTGGGCAGCTTGT 60.179 50.000 0.00 0.00 39.51 3.16
1811 2004 2.198827 TTTTGCATCCGGACACTGAT 57.801 45.000 6.12 0.00 0.00 2.90
1819 2012 1.215117 ATGCCGTTTTTGCATCCGG 59.785 52.632 0.00 0.00 46.04 5.14
1834 2027 0.464373 TGAAGAGGCCGATTGGATGC 60.464 55.000 1.98 0.00 37.49 3.91
1854 2047 1.672881 GCCTCAGATTTGGACCGAATG 59.327 52.381 11.98 0.16 0.00 2.67
1857 3337 1.218047 CGCCTCAGATTTGGACCGA 59.782 57.895 0.00 0.00 0.00 4.69
1871 3351 0.608640 CGGGCCTCTTATATTCGCCT 59.391 55.000 0.84 0.00 39.64 5.52
1876 3356 2.805657 GCGTGTTCGGGCCTCTTATATT 60.806 50.000 0.84 0.00 37.56 1.28
1917 3398 2.916355 GAGCCTATCCACCAGTCCA 58.084 57.895 0.00 0.00 0.00 4.02
1954 3435 1.033746 CGCCCATTGGATCAGCAGTT 61.034 55.000 3.62 0.00 0.00 3.16
1957 3438 2.829914 GCGCCCATTGGATCAGCA 60.830 61.111 3.62 0.00 0.00 4.41
2020 3510 1.215244 GTCCGTCTTAAATAGCCGGC 58.785 55.000 21.89 21.89 38.54 6.13
2022 3512 1.484356 CCGTCCGTCTTAAATAGCCG 58.516 55.000 0.00 0.00 0.00 5.52
2044 3534 2.124529 GGGCTAGGGTTCTGCTGC 60.125 66.667 0.00 0.00 0.00 5.25
2048 3538 1.299976 GTGGTGGGCTAGGGTTCTG 59.700 63.158 0.00 0.00 0.00 3.02
2062 3552 3.500471 GGAGAAAGGGGAAGAAATGTGGT 60.500 47.826 0.00 0.00 0.00 4.16
2065 3555 3.399305 AGTGGAGAAAGGGGAAGAAATGT 59.601 43.478 0.00 0.00 0.00 2.71
2092 3582 2.026822 AGATGTAAGTGGAAGTGCTGGG 60.027 50.000 0.00 0.00 0.00 4.45
2108 3598 5.221783 TGTGAGGCAGCAATATATCAGATGT 60.222 40.000 0.00 0.00 0.00 3.06
2110 3600 5.494390 TGTGAGGCAGCAATATATCAGAT 57.506 39.130 0.00 0.00 0.00 2.90
2113 3603 4.576053 GTGTTGTGAGGCAGCAATATATCA 59.424 41.667 0.00 0.00 39.96 2.15
2117 3607 2.794103 TGTGTTGTGAGGCAGCAATAT 58.206 42.857 0.00 0.00 39.96 1.28
2120 3610 0.669619 CATGTGTTGTGAGGCAGCAA 59.330 50.000 0.00 0.00 39.96 3.91
2122 3612 1.080974 GCATGTGTTGTGAGGCAGC 60.081 57.895 0.00 0.00 0.00 5.25
2130 3620 1.761449 TGAGGTGTTGCATGTGTTGT 58.239 45.000 0.00 0.00 0.00 3.32
2150 3640 1.266446 CGTTGTTGATGATGTGGTGCA 59.734 47.619 0.00 0.00 0.00 4.57
2154 3644 3.486375 GCATCTCGTTGTTGATGATGTGG 60.486 47.826 7.09 0.00 41.69 4.17
2170 3660 8.983724 GTCTTCTATAAACACTATTGGCATCTC 58.016 37.037 0.00 0.00 0.00 2.75
2202 3692 2.173569 GCTACTGGGATGGATGGTTTCT 59.826 50.000 0.00 0.00 0.00 2.52
2242 3732 2.158885 GGAGGTTAAGAGAGCCCATGAC 60.159 54.545 0.00 0.00 0.00 3.06
2278 3768 2.288961 TGAACGAGTTTCTATCGGCC 57.711 50.000 0.00 0.00 44.36 6.13
2432 3922 6.674419 AGAATACAATTAGTTGAGGAGGGAGT 59.326 38.462 4.81 0.00 38.71 3.85
2452 3942 8.352137 TGCATCAGAATGGAAGAAAAAGAATA 57.648 30.769 0.00 0.00 36.16 1.75
2477 3967 7.095355 CGTAACACACACTATTTCTAGGCTTTT 60.095 37.037 0.00 0.00 0.00 2.27
2542 4032 1.146263 CGGGAGGACCTTATGTGGC 59.854 63.158 0.00 0.00 36.97 5.01
2599 4089 1.534729 GGACAACCAAGTTAGCAGGG 58.465 55.000 0.00 0.00 35.97 4.45
2624 4114 1.915769 GGTGGTCAGGAGTCTGCCT 60.916 63.158 0.00 0.00 40.69 4.75


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

AutoCloner maintained by Alex Coulton.