Multiple sequence alignment - TraesCS1B01G415100

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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 TraesCS1B01G415100 chr1B 100.000 3961 0 0 1 3961 640153741 640157701 0.000000e+00 7315.0
1 TraesCS1B01G415100 chr1D 93.776 3085 106 31 75 3147 464138552 464141562 0.000000e+00 4554.0
2 TraesCS1B01G415100 chr1D 95.477 619 25 2 3142 3760 464141597 464142212 0.000000e+00 985.0
3 TraesCS1B01G415100 chr1D 94.762 210 11 0 3752 3961 464142235 464142444 1.060000e-85 327.0
4 TraesCS1B01G415100 chr1A 94.026 3013 110 29 75 3072 556296419 556299376 0.000000e+00 4503.0
5 TraesCS1B01G415100 chr1A 94.184 619 29 4 3142 3760 556299512 556300123 0.000000e+00 937.0
6 TraesCS1B01G415100 chr1A 83.772 228 15 6 3752 3957 556300146 556300373 3.120000e-46 196.0
7 TraesCS1B01G415100 chr7A 88.953 172 15 4 3547 3717 85734993 85735161 4.010000e-50 209.0
8 TraesCS1B01G415100 chr7D 98.592 71 1 0 1722 1792 107135331 107135261 4.160000e-25 126.0
9 TraesCS1B01G415100 chr6D 97.183 71 2 0 1722 1792 421182432 421182502 1.930000e-23 121.0
10 TraesCS1B01G415100 chr4D 97.183 71 2 0 1722 1792 177515047 177514977 1.930000e-23 121.0
11 TraesCS1B01G415100 chr6B 95.775 71 3 0 1722 1792 7162436 7162506 8.990000e-22 115.0
12 TraesCS1B01G415100 chr6B 88.000 50 5 1 5 53 569048352 569048303 1.540000e-04 58.4
13 TraesCS1B01G415100 chr2B 95.775 71 3 0 1722 1792 754437614 754437544 8.990000e-22 115.0
14 TraesCS1B01G415100 chr2A 95.775 71 3 0 1722 1792 635080912 635080842 8.990000e-22 115.0
15 TraesCS1B01G415100 chr7B 94.366 71 4 0 1722 1792 644282211 644282281 4.180000e-20 110.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G415100 chr1B 640153741 640157701 3960 False 7315.000000 7315 100.000000 1 3961 1 chr1B.!!$F1 3960
1 TraesCS1B01G415100 chr1D 464138552 464142444 3892 False 1955.333333 4554 94.671667 75 3961 3 chr1D.!!$F1 3886
2 TraesCS1B01G415100 chr1A 556296419 556300373 3954 False 1878.666667 4503 90.660667 75 3957 3 chr1A.!!$F1 3882

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
930 938 0.336737 TCTGACCCCTTCTCCTCTCC 59.663 60.000 0.0 0.0 0.0 3.71 F
1679 1690 0.545548 ACCTTCTCCCAGTCCCAGTC 60.546 60.000 0.0 0.0 0.0 3.51 F
2084 2095 1.153086 ATCATCAGACAAGCCGCCC 60.153 57.895 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 2015 0.179084 CACACAGACACGGGTTGAGT 60.179 55.0 0.0 0.0 0.00 3.41 R
2942 2953 0.316204 TTCAAACCTCGTCGTCCTCC 59.684 55.0 0.0 0.0 0.00 4.30 R
3688 3774 0.180406 ACGGTGGAGCTGTTCTTTGT 59.820 50.0 0.0 0.0 31.36 2.83 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
23 24 6.603940 AAGGATAGCAAATTTAGTTGGCAA 57.396 33.333 0.00 0.00 39.36 4.52
24 25 6.212888 AGGATAGCAAATTTAGTTGGCAAG 57.787 37.500 0.00 0.00 39.36 4.01
25 26 4.805719 GGATAGCAAATTTAGTTGGCAAGC 59.194 41.667 0.00 0.00 39.36 4.01
26 27 3.749665 AGCAAATTTAGTTGGCAAGCA 57.250 38.095 0.00 0.00 39.36 3.91
27 28 4.276058 AGCAAATTTAGTTGGCAAGCAT 57.724 36.364 0.00 0.00 39.36 3.79
28 29 5.404466 AGCAAATTTAGTTGGCAAGCATA 57.596 34.783 0.00 0.00 39.36 3.14
29 30 5.792741 AGCAAATTTAGTTGGCAAGCATAA 58.207 33.333 0.00 0.00 39.36 1.90
30 31 5.639082 AGCAAATTTAGTTGGCAAGCATAAC 59.361 36.000 0.00 0.00 39.36 1.89
31 32 5.407995 GCAAATTTAGTTGGCAAGCATAACA 59.592 36.000 0.00 0.00 36.71 2.41
32 33 6.073331 GCAAATTTAGTTGGCAAGCATAACAA 60.073 34.615 0.00 0.00 36.71 2.83
33 34 7.519649 GCAAATTTAGTTGGCAAGCATAACAAA 60.520 33.333 0.00 10.37 36.71 2.83
34 35 7.420184 AATTTAGTTGGCAAGCATAACAAAC 57.580 32.000 0.00 0.00 0.00 2.93
35 36 5.782893 TTAGTTGGCAAGCATAACAAACT 57.217 34.783 0.00 0.00 0.00 2.66
36 37 4.243007 AGTTGGCAAGCATAACAAACTC 57.757 40.909 0.00 0.00 0.00 3.01
37 38 2.979813 GTTGGCAAGCATAACAAACTCG 59.020 45.455 0.00 0.00 0.00 4.18
38 39 2.226330 TGGCAAGCATAACAAACTCGT 58.774 42.857 0.00 0.00 0.00 4.18
39 40 2.225491 TGGCAAGCATAACAAACTCGTC 59.775 45.455 0.00 0.00 0.00 4.20
40 41 2.484264 GGCAAGCATAACAAACTCGTCT 59.516 45.455 0.00 0.00 0.00 4.18
41 42 3.424962 GGCAAGCATAACAAACTCGTCTC 60.425 47.826 0.00 0.00 0.00 3.36
42 43 3.186409 GCAAGCATAACAAACTCGTCTCA 59.814 43.478 0.00 0.00 0.00 3.27
43 44 4.667668 GCAAGCATAACAAACTCGTCTCAG 60.668 45.833 0.00 0.00 0.00 3.35
44 45 4.521130 AGCATAACAAACTCGTCTCAGA 57.479 40.909 0.00 0.00 0.00 3.27
45 46 5.078411 AGCATAACAAACTCGTCTCAGAT 57.922 39.130 0.00 0.00 0.00 2.90
46 47 5.482908 AGCATAACAAACTCGTCTCAGATT 58.517 37.500 0.00 0.00 0.00 2.40
47 48 6.631016 AGCATAACAAACTCGTCTCAGATTA 58.369 36.000 0.00 0.00 0.00 1.75
48 49 7.268586 AGCATAACAAACTCGTCTCAGATTAT 58.731 34.615 0.00 0.00 0.00 1.28
49 50 7.766278 AGCATAACAAACTCGTCTCAGATTATT 59.234 33.333 0.00 0.00 0.00 1.40
50 51 8.391106 GCATAACAAACTCGTCTCAGATTATTT 58.609 33.333 0.00 0.00 0.00 1.40
54 55 8.608844 ACAAACTCGTCTCAGATTATTTTTCT 57.391 30.769 0.00 0.00 0.00 2.52
55 56 8.499162 ACAAACTCGTCTCAGATTATTTTTCTG 58.501 33.333 0.00 0.00 41.61 3.02
56 57 6.654793 ACTCGTCTCAGATTATTTTTCTGC 57.345 37.500 0.00 0.00 40.35 4.26
57 58 5.289675 ACTCGTCTCAGATTATTTTTCTGCG 59.710 40.000 0.00 0.00 40.35 5.18
58 59 5.407502 TCGTCTCAGATTATTTTTCTGCGA 58.592 37.500 0.00 0.00 40.35 5.10
59 60 5.516696 TCGTCTCAGATTATTTTTCTGCGAG 59.483 40.000 0.00 0.00 40.35 5.03
60 61 5.276584 CGTCTCAGATTATTTTTCTGCGAGG 60.277 44.000 0.00 0.00 40.35 4.63
61 62 5.812642 GTCTCAGATTATTTTTCTGCGAGGA 59.187 40.000 0.00 0.00 40.35 3.71
62 63 6.481644 GTCTCAGATTATTTTTCTGCGAGGAT 59.518 38.462 0.00 0.00 40.35 3.24
63 64 7.011857 GTCTCAGATTATTTTTCTGCGAGGATT 59.988 37.037 0.00 0.00 40.35 3.01
64 65 7.554118 TCTCAGATTATTTTTCTGCGAGGATTT 59.446 33.333 0.00 0.00 40.35 2.17
65 66 8.731275 TCAGATTATTTTTCTGCGAGGATTTA 57.269 30.769 0.00 0.00 40.35 1.40
66 67 9.342308 TCAGATTATTTTTCTGCGAGGATTTAT 57.658 29.630 0.00 0.00 40.35 1.40
67 68 9.604626 CAGATTATTTTTCTGCGAGGATTTATC 57.395 33.333 0.00 0.00 34.68 1.75
68 69 9.342308 AGATTATTTTTCTGCGAGGATTTATCA 57.658 29.630 0.00 0.00 0.00 2.15
70 71 9.903682 ATTATTTTTCTGCGAGGATTTATCATG 57.096 29.630 0.00 0.00 0.00 3.07
71 72 4.818534 TTTCTGCGAGGATTTATCATGC 57.181 40.909 0.00 0.00 0.00 4.06
72 73 3.758755 TCTGCGAGGATTTATCATGCT 57.241 42.857 0.00 0.00 0.00 3.79
73 74 4.077300 TCTGCGAGGATTTATCATGCTT 57.923 40.909 0.00 0.00 0.00 3.91
74 75 3.811497 TCTGCGAGGATTTATCATGCTTG 59.189 43.478 0.00 0.00 0.00 4.01
75 76 2.291465 TGCGAGGATTTATCATGCTTGC 59.709 45.455 8.28 8.28 44.20 4.01
76 77 2.291465 GCGAGGATTTATCATGCTTGCA 59.709 45.455 9.93 0.00 43.63 4.08
77 78 3.243168 GCGAGGATTTATCATGCTTGCAA 60.243 43.478 9.93 0.00 43.63 4.08
78 79 4.734402 GCGAGGATTTATCATGCTTGCAAA 60.734 41.667 9.93 0.00 43.63 3.68
98 99 6.192360 GCAAAGTAAAATTGCGAGACGATAT 58.808 36.000 0.00 0.00 43.14 1.63
99 100 6.139169 GCAAAGTAAAATTGCGAGACGATATG 59.861 38.462 0.00 0.00 43.14 1.78
149 151 2.749621 CCCCCAGCGAGCATTATAATTC 59.250 50.000 0.00 0.00 0.00 2.17
154 156 5.237815 CCAGCGAGCATTATAATTCAGGTA 58.762 41.667 0.00 0.00 0.00 3.08
158 160 6.936900 AGCGAGCATTATAATTCAGGTAATGT 59.063 34.615 0.00 0.00 37.84 2.71
161 163 8.438513 CGAGCATTATAATTCAGGTAATGTGAG 58.561 37.037 0.00 0.00 37.84 3.51
197 200 8.939201 TTTACTGTTTTGATTGCTCATTCAAA 57.061 26.923 12.97 12.97 38.28 2.69
227 230 6.665992 GGGAAAACCTCAACTTCCTAAATT 57.334 37.500 0.00 0.00 38.94 1.82
230 233 6.923508 GGAAAACCTCAACTTCCTAAATTGTG 59.076 38.462 0.00 0.00 36.48 3.33
233 236 3.193479 CCTCAACTTCCTAAATTGTGGCC 59.807 47.826 0.00 0.00 32.13 5.36
273 276 5.367060 AGGCCGAAGAAAGAATATTAGGAGT 59.633 40.000 0.00 0.00 0.00 3.85
278 281 7.810759 CCGAAGAAAGAATATTAGGAGTAGAGC 59.189 40.741 0.00 0.00 0.00 4.09
325 328 8.364142 AGTGATGTTCTAATCCTAAGCTCATAC 58.636 37.037 0.00 0.00 0.00 2.39
355 358 7.763356 TCGGTTGAACAGTAAAATCAAGAAAA 58.237 30.769 0.00 0.00 34.02 2.29
356 359 8.244802 TCGGTTGAACAGTAAAATCAAGAAAAA 58.755 29.630 0.00 0.00 34.02 1.94
430 433 4.952262 ATTTCAACACCAGATGACATCG 57.048 40.909 9.77 5.25 0.00 3.84
437 440 3.073678 CACCAGATGACATCGGTGAAAA 58.926 45.455 33.02 0.00 46.83 2.29
443 446 4.637534 AGATGACATCGGTGAAAAATCTGG 59.362 41.667 0.65 0.00 0.00 3.86
481 484 7.369607 TCAATGACATTCATGAAACGTTGATT 58.630 30.769 26.07 18.64 37.15 2.57
483 486 8.489559 CAATGACATTCATGAAACGTTGATTTT 58.510 29.630 24.73 10.64 37.15 1.82
532 535 1.734137 GCTTACGAGCTCGGGATCA 59.266 57.895 36.93 16.26 45.65 2.92
537 540 0.965866 ACGAGCTCGGGATCAGAACA 60.966 55.000 36.93 0.00 44.95 3.18
561 568 3.001939 CGGAAGCAAACACGTTTAAGACT 59.998 43.478 0.00 0.00 0.00 3.24
562 569 4.209703 CGGAAGCAAACACGTTTAAGACTA 59.790 41.667 0.00 0.00 0.00 2.59
563 570 5.611844 CGGAAGCAAACACGTTTAAGACTAG 60.612 44.000 0.00 0.00 0.00 2.57
564 571 5.464389 GGAAGCAAACACGTTTAAGACTAGA 59.536 40.000 0.00 0.00 0.00 2.43
565 572 5.902051 AGCAAACACGTTTAAGACTAGAC 57.098 39.130 0.00 0.00 0.00 2.59
566 573 5.598769 AGCAAACACGTTTAAGACTAGACT 58.401 37.500 0.00 0.00 0.00 3.24
585 592 5.729510 AGACTAGAAGACTTGGATTCTTGC 58.270 41.667 0.00 0.00 37.05 4.01
610 617 1.374125 TGACCGGTGAAGCATGACG 60.374 57.895 14.63 0.00 0.00 4.35
646 654 2.191354 TACTCGCGTCTGTTGACCGG 62.191 60.000 5.77 0.00 39.94 5.28
648 656 3.403057 CGCGTCTGTTGACCGGTG 61.403 66.667 14.63 0.00 39.94 4.94
649 657 3.041940 GCGTCTGTTGACCGGTGG 61.042 66.667 14.63 0.00 39.94 4.61
650 658 2.420043 CGTCTGTTGACCGGTGGT 59.580 61.111 14.63 0.00 39.94 4.16
651 659 1.661480 CGTCTGTTGACCGGTGGTA 59.339 57.895 14.63 0.00 39.94 3.25
852 860 1.302832 GCTCCCACTCCCACACAAG 60.303 63.158 0.00 0.00 0.00 3.16
853 861 1.768684 GCTCCCACTCCCACACAAGA 61.769 60.000 0.00 0.00 0.00 3.02
854 862 0.764890 CTCCCACTCCCACACAAGAA 59.235 55.000 0.00 0.00 0.00 2.52
862 870 0.528901 CCCACACAAGAACGACACGA 60.529 55.000 0.00 0.00 0.00 4.35
869 877 3.456039 GAACGACACGACGACCGC 61.456 66.667 0.00 0.00 43.32 5.68
926 934 0.338120 CCTCTCTGACCCCTTCTCCT 59.662 60.000 0.00 0.00 0.00 3.69
928 936 1.287739 CTCTCTGACCCCTTCTCCTCT 59.712 57.143 0.00 0.00 0.00 3.69
929 937 1.286553 TCTCTGACCCCTTCTCCTCTC 59.713 57.143 0.00 0.00 0.00 3.20
930 938 0.336737 TCTGACCCCTTCTCCTCTCC 59.663 60.000 0.00 0.00 0.00 3.71
935 943 2.726351 CCCTTCTCCTCTCCGCACC 61.726 68.421 0.00 0.00 0.00 5.01
936 944 2.492090 CTTCTCCTCTCCGCACCG 59.508 66.667 0.00 0.00 0.00 4.94
985 993 1.090728 GAGCTTAACTGGCTTCTGGC 58.909 55.000 0.00 0.00 40.40 4.85
1107 1115 4.477975 GACCTCGCCGACGACCTG 62.478 72.222 0.00 0.00 45.12 4.00
1266 1277 4.717629 TTCCGCTCCGACGTGCTG 62.718 66.667 0.00 2.73 0.00 4.41
1273 1284 2.805353 CCGACGTGCTGTCCTTCG 60.805 66.667 0.00 0.00 45.23 3.79
1678 1689 0.838122 CACCTTCTCCCAGTCCCAGT 60.838 60.000 0.00 0.00 0.00 4.00
1679 1690 0.545548 ACCTTCTCCCAGTCCCAGTC 60.546 60.000 0.00 0.00 0.00 3.51
1680 1691 1.608717 CCTTCTCCCAGTCCCAGTCG 61.609 65.000 0.00 0.00 0.00 4.18
1681 1692 2.232298 CTTCTCCCAGTCCCAGTCGC 62.232 65.000 0.00 0.00 0.00 5.19
1682 1693 2.997315 CTCCCAGTCCCAGTCGCA 60.997 66.667 0.00 0.00 0.00 5.10
1683 1694 2.997315 TCCCAGTCCCAGTCGCAG 60.997 66.667 0.00 0.00 0.00 5.18
2001 2012 8.871629 ACCTCAGATGTACGATAATATCTTCT 57.128 34.615 0.00 0.00 0.00 2.85
2002 2013 8.952278 ACCTCAGATGTACGATAATATCTTCTC 58.048 37.037 0.00 0.00 0.00 2.87
2003 2014 8.951243 CCTCAGATGTACGATAATATCTTCTCA 58.049 37.037 0.00 0.00 0.00 3.27
2084 2095 1.153086 ATCATCAGACAAGCCGCCC 60.153 57.895 0.00 0.00 0.00 6.13
2804 2815 3.197790 CCCGTGCAGAAGATGGCG 61.198 66.667 0.00 0.00 0.00 5.69
2966 2977 1.390463 GACGACGAGGTTTGAATCAGC 59.610 52.381 0.00 0.00 0.00 4.26
3098 3137 8.768957 TGTGAGATGTTGAAATTTGTCAAAAA 57.231 26.923 1.31 0.00 39.18 1.94
3159 3243 3.243434 GCTGAAGATGGAATGGCATGAAG 60.243 47.826 0.00 0.00 0.00 3.02
3177 3261 0.813184 AGCAGCATCCACCGATTTTG 59.187 50.000 0.00 0.00 0.00 2.44
3203 3287 2.943033 ACAAAACCCGACAGAACTGAAG 59.057 45.455 8.87 2.25 0.00 3.02
3248 3332 4.025979 CGTCACACAAGTTCAGGTAAGAAC 60.026 45.833 0.00 0.00 46.35 3.01
3262 3346 5.412594 CAGGTAAGAACATACACAGTTGCAT 59.587 40.000 0.00 0.00 0.00 3.96
3458 3542 1.137513 GTTTCCTCGGTCAACAGTCG 58.862 55.000 0.00 0.00 0.00 4.18
3472 3556 2.201885 GTCGCGCTTCAAACGACG 60.202 61.111 5.56 0.00 45.52 5.12
3486 3570 1.028330 ACGACGAGAACCAGCGGATA 61.028 55.000 0.00 0.00 0.00 2.59
3612 3696 2.304180 GTGCCTCCATGCCTATGATAGT 59.696 50.000 0.00 0.00 36.36 2.12
3613 3697 3.515502 GTGCCTCCATGCCTATGATAGTA 59.484 47.826 0.00 0.00 36.36 1.82
3663 3749 8.691661 ACAGTTGGTTCAGTAAACAGAATATT 57.308 30.769 0.00 0.00 39.81 1.28
3668 3754 8.800370 TGGTTCAGTAAACAGAATATTGCATA 57.200 30.769 0.00 0.00 39.81 3.14
3688 3774 5.528690 GCATAGTTCATGACTGGATTAGCAA 59.471 40.000 0.00 0.00 39.48 3.91
3704 3790 1.678101 AGCAACAAAGAACAGCTCCAC 59.322 47.619 0.00 0.00 0.00 4.02
3735 3821 2.034878 AGAGCCAATGATGCTACGAGA 58.965 47.619 0.00 0.00 39.69 4.04
3749 3835 3.066900 GCTACGAGATCAGAAGGCAGTTA 59.933 47.826 0.00 0.00 0.00 2.24
3807 3924 4.195225 TGTGTAAGCATTATGTCACCGA 57.805 40.909 0.00 0.00 30.46 4.69
3825 3942 2.157668 CCGACAACGAACTCCAAATCAG 59.842 50.000 0.00 0.00 42.66 2.90
3923 4062 8.352201 TGTATGCTTTTATAAGGAATGACATGC 58.648 33.333 0.00 0.00 35.22 4.06
3925 4064 5.068987 TGCTTTTATAAGGAATGACATGCCC 59.931 40.000 9.05 4.03 31.76 5.36
3929 4068 7.759489 TTTATAAGGAATGACATGCCCATAC 57.241 36.000 9.05 0.00 0.00 2.39
3944 4083 4.881273 TGCCCATACTTACTGCATTTAGTG 59.119 41.667 6.03 0.00 32.19 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.603940 TTGCCAACTAAATTTGCTATCCTT 57.396 33.333 0.00 0.00 0.00 3.36
1 2 5.394553 GCTTGCCAACTAAATTTGCTATCCT 60.395 40.000 0.00 0.00 0.00 3.24
2 3 4.805719 GCTTGCCAACTAAATTTGCTATCC 59.194 41.667 0.00 0.00 0.00 2.59
3 4 5.410067 TGCTTGCCAACTAAATTTGCTATC 58.590 37.500 0.00 0.00 0.00 2.08
5 6 4.862902 TGCTTGCCAACTAAATTTGCTA 57.137 36.364 0.00 0.00 0.00 3.49
6 7 3.749665 TGCTTGCCAACTAAATTTGCT 57.250 38.095 0.00 0.00 0.00 3.91
7 8 5.407995 TGTTATGCTTGCCAACTAAATTTGC 59.592 36.000 0.00 0.00 0.00 3.68
8 9 7.418840 TTGTTATGCTTGCCAACTAAATTTG 57.581 32.000 0.00 0.00 0.00 2.32
9 10 7.714813 AGTTTGTTATGCTTGCCAACTAAATTT 59.285 29.630 0.00 0.00 0.00 1.82
10 11 7.216494 AGTTTGTTATGCTTGCCAACTAAATT 58.784 30.769 8.09 0.00 0.00 1.82
11 12 6.758254 AGTTTGTTATGCTTGCCAACTAAAT 58.242 32.000 8.09 4.59 0.00 1.40
12 13 6.155475 AGTTTGTTATGCTTGCCAACTAAA 57.845 33.333 8.09 5.45 0.00 1.85
13 14 5.561919 CGAGTTTGTTATGCTTGCCAACTAA 60.562 40.000 8.09 5.06 0.00 2.24
14 15 4.083537 CGAGTTTGTTATGCTTGCCAACTA 60.084 41.667 8.09 0.28 0.00 2.24
15 16 3.304659 CGAGTTTGTTATGCTTGCCAACT 60.305 43.478 8.09 0.00 0.00 3.16
16 17 2.979813 CGAGTTTGTTATGCTTGCCAAC 59.020 45.455 0.00 0.00 0.00 3.77
17 18 2.621055 ACGAGTTTGTTATGCTTGCCAA 59.379 40.909 0.00 0.00 0.00 4.52
18 19 2.225491 GACGAGTTTGTTATGCTTGCCA 59.775 45.455 0.00 0.00 0.00 4.92
19 20 2.484264 AGACGAGTTTGTTATGCTTGCC 59.516 45.455 0.00 0.00 0.00 4.52
20 21 3.186409 TGAGACGAGTTTGTTATGCTTGC 59.814 43.478 0.00 0.00 0.00 4.01
21 22 4.686091 TCTGAGACGAGTTTGTTATGCTTG 59.314 41.667 0.00 0.00 0.00 4.01
22 23 4.883083 TCTGAGACGAGTTTGTTATGCTT 58.117 39.130 0.00 0.00 0.00 3.91
23 24 4.521130 TCTGAGACGAGTTTGTTATGCT 57.479 40.909 0.00 0.00 0.00 3.79
24 25 5.786401 AATCTGAGACGAGTTTGTTATGC 57.214 39.130 0.00 0.00 0.00 3.14
28 29 9.057089 AGAAAAATAATCTGAGACGAGTTTGTT 57.943 29.630 0.00 0.00 0.00 2.83
29 30 8.499162 CAGAAAAATAATCTGAGACGAGTTTGT 58.501 33.333 0.00 0.00 45.74 2.83
30 31 7.479916 GCAGAAAAATAATCTGAGACGAGTTTG 59.520 37.037 7.67 0.00 45.74 2.93
31 32 7.522374 GCAGAAAAATAATCTGAGACGAGTTT 58.478 34.615 7.67 0.00 45.74 2.66
32 33 6.183360 CGCAGAAAAATAATCTGAGACGAGTT 60.183 38.462 7.67 0.00 45.74 3.01
33 34 5.289675 CGCAGAAAAATAATCTGAGACGAGT 59.710 40.000 7.67 0.00 45.74 4.18
34 35 5.516696 TCGCAGAAAAATAATCTGAGACGAG 59.483 40.000 7.67 0.00 45.00 4.18
35 36 5.407502 TCGCAGAAAAATAATCTGAGACGA 58.592 37.500 7.67 4.59 45.00 4.20
36 37 5.276584 CCTCGCAGAAAAATAATCTGAGACG 60.277 44.000 7.67 2.46 45.00 4.18
37 38 5.812642 TCCTCGCAGAAAAATAATCTGAGAC 59.187 40.000 7.67 0.00 45.00 3.36
38 39 5.977635 TCCTCGCAGAAAAATAATCTGAGA 58.022 37.500 7.67 8.47 46.78 3.27
39 40 6.857777 ATCCTCGCAGAAAAATAATCTGAG 57.142 37.500 7.67 4.50 45.74 3.35
40 41 7.630242 AAATCCTCGCAGAAAAATAATCTGA 57.370 32.000 7.67 0.00 45.74 3.27
41 42 9.604626 GATAAATCCTCGCAGAAAAATAATCTG 57.395 33.333 0.00 0.00 45.65 2.90
42 43 9.342308 TGATAAATCCTCGCAGAAAAATAATCT 57.658 29.630 0.00 0.00 34.09 2.40
44 45 9.903682 CATGATAAATCCTCGCAGAAAAATAAT 57.096 29.630 0.00 0.00 34.09 1.28
45 46 7.862372 GCATGATAAATCCTCGCAGAAAAATAA 59.138 33.333 0.00 0.00 34.09 1.40
46 47 7.229306 AGCATGATAAATCCTCGCAGAAAAATA 59.771 33.333 0.00 0.00 34.09 1.40
47 48 6.040166 AGCATGATAAATCCTCGCAGAAAAAT 59.960 34.615 0.00 0.00 34.09 1.82
48 49 5.357878 AGCATGATAAATCCTCGCAGAAAAA 59.642 36.000 0.00 0.00 34.09 1.94
49 50 4.883585 AGCATGATAAATCCTCGCAGAAAA 59.116 37.500 0.00 0.00 34.09 2.29
50 51 4.454678 AGCATGATAAATCCTCGCAGAAA 58.545 39.130 0.00 0.00 34.09 2.52
51 52 4.077300 AGCATGATAAATCCTCGCAGAA 57.923 40.909 0.00 0.00 34.09 3.02
52 53 3.758755 AGCATGATAAATCCTCGCAGA 57.241 42.857 0.00 0.00 0.00 4.26
53 54 3.608707 GCAAGCATGATAAATCCTCGCAG 60.609 47.826 0.00 0.00 0.00 5.18
54 55 2.291465 GCAAGCATGATAAATCCTCGCA 59.709 45.455 0.00 0.00 0.00 5.10
55 56 2.291465 TGCAAGCATGATAAATCCTCGC 59.709 45.455 0.00 0.00 0.00 5.03
56 57 4.556942 TTGCAAGCATGATAAATCCTCG 57.443 40.909 0.00 0.00 0.00 4.63
57 58 5.899299 ACTTTGCAAGCATGATAAATCCTC 58.101 37.500 0.00 0.00 0.00 3.71
58 59 5.927281 ACTTTGCAAGCATGATAAATCCT 57.073 34.783 0.00 0.00 0.00 3.24
59 60 8.477984 TTTTACTTTGCAAGCATGATAAATCC 57.522 30.769 0.00 0.00 0.00 3.01
62 63 8.229137 GCAATTTTACTTTGCAAGCATGATAAA 58.771 29.630 0.00 0.00 46.78 1.40
63 64 7.741198 GCAATTTTACTTTGCAAGCATGATAA 58.259 30.769 0.00 0.00 46.78 1.75
64 65 7.293402 GCAATTTTACTTTGCAAGCATGATA 57.707 32.000 0.00 0.00 46.78 2.15
65 66 6.173191 GCAATTTTACTTTGCAAGCATGAT 57.827 33.333 0.00 0.00 46.78 2.45
66 67 5.594724 GCAATTTTACTTTGCAAGCATGA 57.405 34.783 0.00 0.00 46.78 3.07
74 75 3.805823 TCGTCTCGCAATTTTACTTTGC 58.194 40.909 0.00 0.00 44.68 3.68
75 76 7.398746 TCATATCGTCTCGCAATTTTACTTTG 58.601 34.615 0.00 0.00 0.00 2.77
76 77 7.534085 TCATATCGTCTCGCAATTTTACTTT 57.466 32.000 0.00 0.00 0.00 2.66
77 78 7.534085 TTCATATCGTCTCGCAATTTTACTT 57.466 32.000 0.00 0.00 0.00 2.24
78 79 7.715265 ATTCATATCGTCTCGCAATTTTACT 57.285 32.000 0.00 0.00 0.00 2.24
79 80 9.302773 GTAATTCATATCGTCTCGCAATTTTAC 57.697 33.333 0.00 0.00 0.00 2.01
125 127 0.037303 ATAATGCTCGCTGGGGGATG 59.963 55.000 0.00 0.00 0.00 3.51
184 186 4.778958 TCCCTTGGATTTTGAATGAGCAAT 59.221 37.500 0.00 0.00 0.00 3.56
193 196 4.551671 TGAGGTTTTCCCTTGGATTTTGA 58.448 39.130 0.00 0.00 46.51 2.69
197 200 4.199002 AGTTGAGGTTTTCCCTTGGATT 57.801 40.909 0.00 0.00 46.51 3.01
216 219 2.433436 GTCGGCCACAATTTAGGAAGT 58.567 47.619 2.24 0.00 0.00 3.01
219 222 0.391927 CGGTCGGCCACAATTTAGGA 60.392 55.000 6.96 0.00 34.09 2.94
233 236 2.125912 CTTGCCTGGTCTCGGTCG 60.126 66.667 0.00 0.00 0.00 4.79
273 276 1.656587 TGCTTCCTCCCTTTGCTCTA 58.343 50.000 0.00 0.00 0.00 2.43
278 281 1.604604 TCGTTTGCTTCCTCCCTTTG 58.395 50.000 0.00 0.00 0.00 2.77
303 306 7.526142 TCGTATGAGCTTAGGATTAGAACAT 57.474 36.000 0.00 0.00 0.00 2.71
304 307 6.954487 TCGTATGAGCTTAGGATTAGAACA 57.046 37.500 0.00 0.00 0.00 3.18
325 328 2.060326 TTACTGTTCAACCGAGCTCG 57.940 50.000 29.06 29.06 39.44 5.03
331 334 7.979115 TTTTCTTGATTTTACTGTTCAACCG 57.021 32.000 0.00 0.00 0.00 4.44
405 408 6.088483 CGATGTCATCTGGTGTTGAAATTTTG 59.912 38.462 11.04 0.00 0.00 2.44
490 493 9.515226 AGCTCAGGTGAACAGTAAAATAAATAA 57.485 29.630 0.00 0.00 0.00 1.40
491 494 9.515226 AAGCTCAGGTGAACAGTAAAATAAATA 57.485 29.630 0.00 0.00 0.00 1.40
492 495 8.409358 AAGCTCAGGTGAACAGTAAAATAAAT 57.591 30.769 0.00 0.00 0.00 1.40
493 496 7.817418 AAGCTCAGGTGAACAGTAAAATAAA 57.183 32.000 0.00 0.00 0.00 1.40
494 497 7.117236 CGTAAGCTCAGGTGAACAGTAAAATAA 59.883 37.037 0.00 0.00 0.00 1.40
495 498 6.588756 CGTAAGCTCAGGTGAACAGTAAAATA 59.411 38.462 0.00 0.00 0.00 1.40
496 499 5.408604 CGTAAGCTCAGGTGAACAGTAAAAT 59.591 40.000 0.00 0.00 0.00 1.82
532 535 1.021968 GTGTTTGCTTCCGGTGTTCT 58.978 50.000 0.00 0.00 0.00 3.01
537 540 1.666054 TAAACGTGTTTGCTTCCGGT 58.334 45.000 0.00 0.00 34.23 5.28
561 568 6.437477 TGCAAGAATCCAAGTCTTCTAGTCTA 59.563 38.462 0.00 0.00 32.96 2.59
562 569 5.247110 TGCAAGAATCCAAGTCTTCTAGTCT 59.753 40.000 0.00 0.00 32.96 3.24
563 570 5.482908 TGCAAGAATCCAAGTCTTCTAGTC 58.517 41.667 0.00 0.00 32.96 2.59
564 571 5.489792 TGCAAGAATCCAAGTCTTCTAGT 57.510 39.130 0.00 0.00 32.96 2.57
565 572 5.526846 GGATGCAAGAATCCAAGTCTTCTAG 59.473 44.000 2.01 0.00 44.85 2.43
566 573 5.431765 GGATGCAAGAATCCAAGTCTTCTA 58.568 41.667 2.01 0.00 44.85 2.10
604 611 5.702865 AGAAAATCAATCAACACCGTCATG 58.297 37.500 0.00 0.00 0.00 3.07
610 617 5.324697 GCGAGTAGAAAATCAATCAACACC 58.675 41.667 0.00 0.00 0.00 4.16
852 860 3.456039 GCGGTCGTCGTGTCGTTC 61.456 66.667 0.00 0.00 41.72 3.95
853 861 4.988486 GGCGGTCGTCGTGTCGTT 62.988 66.667 0.00 0.00 41.72 3.85
869 877 4.394712 GTCGGTGTCTGGGCAGGG 62.395 72.222 0.00 0.00 0.00 4.45
894 902 2.126882 CAGAGAGGAGGGAGAGAGAGA 58.873 57.143 0.00 0.00 0.00 3.10
935 943 1.130613 GAGCGCGCATTATAAGCCG 59.869 57.895 35.10 3.86 0.00 5.52
936 944 1.130613 CGAGCGCGCATTATAAGCC 59.869 57.895 35.10 8.90 0.00 4.35
985 993 4.227134 CATCCCCGCTCCACTCCG 62.227 72.222 0.00 0.00 0.00 4.63
1266 1277 3.567797 GCCATCTGCGCGAAGGAC 61.568 66.667 15.70 12.22 32.13 3.85
1680 1691 4.803426 CTCTGCCGTCGGTCCTGC 62.803 72.222 13.94 0.00 0.00 4.85
1681 1692 4.803426 GCTCTGCCGTCGGTCCTG 62.803 72.222 13.94 1.30 0.00 3.86
1683 1694 4.500116 GAGCTCTGCCGTCGGTCC 62.500 72.222 13.94 0.00 0.00 4.46
2000 2011 1.202533 ACAGACACGGGTTGAGTTGAG 60.203 52.381 0.00 0.00 0.00 3.02
2001 2012 0.828022 ACAGACACGGGTTGAGTTGA 59.172 50.000 0.00 0.00 0.00 3.18
2002 2013 0.937304 CACAGACACGGGTTGAGTTG 59.063 55.000 0.00 0.00 0.00 3.16
2003 2014 0.539986 ACACAGACACGGGTTGAGTT 59.460 50.000 0.00 0.00 0.00 3.01
2004 2015 0.179084 CACACAGACACGGGTTGAGT 60.179 55.000 0.00 0.00 0.00 3.41
2084 2095 1.412079 ACTGCTCCAGCTCCTCTATG 58.588 55.000 0.00 0.00 42.66 2.23
2555 2566 2.069273 CGTAGGAACAGCACCTTCTTG 58.931 52.381 0.00 0.00 38.76 3.02
2567 2578 0.810016 AGAAGCCGAGACGTAGGAAC 59.190 55.000 8.21 0.00 0.00 3.62
2804 2815 1.129251 TCCGTCGTGTCGATGTACTTC 59.871 52.381 9.84 0.00 40.74 3.01
2942 2953 0.316204 TTCAAACCTCGTCGTCCTCC 59.684 55.000 0.00 0.00 0.00 4.30
3002 3013 3.259374 AGTCTGTACCACCTCTTGATGTG 59.741 47.826 0.00 0.12 0.00 3.21
3015 3027 6.238538 GCACTCTCTAATCTACAGTCTGTACC 60.239 46.154 8.70 0.00 0.00 3.34
3132 3174 1.407979 CCATTCCATCTTCAGCAAGGC 59.592 52.381 0.00 0.00 0.00 4.35
3159 3243 0.527565 ACAAAATCGGTGGATGCTGC 59.472 50.000 0.00 0.00 31.83 5.25
3177 3261 4.062991 AGTTCTGTCGGGTTTTGTGATAC 58.937 43.478 0.00 0.00 0.00 2.24
3203 3287 5.163530 ACGAGGATGATGATGATATCAGAGC 60.164 44.000 11.78 3.86 43.53 4.09
3248 3332 7.538303 TGTACATTAGATGCAACTGTGTATG 57.462 36.000 19.48 13.78 29.11 2.39
3298 3382 1.517475 GAGCTCTTCGGCCGAGAAC 60.517 63.158 29.20 21.02 0.00 3.01
3374 3458 2.036604 CCTATCTTTCCGAGAAGAGGCC 59.963 54.545 0.00 0.00 38.90 5.19
3458 3542 0.449022 GTTCTCGTCGTTTGAAGCGC 60.449 55.000 0.00 0.00 0.00 5.92
3472 3556 2.930682 GTTCTTGTATCCGCTGGTTCTC 59.069 50.000 0.00 0.00 0.00 2.87
3486 3570 0.616891 GGTATGTCCCCGGTTCTTGT 59.383 55.000 0.00 0.00 0.00 3.16
3612 3696 7.496747 TCTGATGATGACATTGGTTCGTTATA 58.503 34.615 0.00 0.00 36.82 0.98
3613 3697 6.348498 TCTGATGATGACATTGGTTCGTTAT 58.652 36.000 0.00 0.00 36.82 1.89
3663 3749 5.059161 GCTAATCCAGTCATGAACTATGCA 58.941 41.667 0.00 0.00 36.07 3.96
3668 3754 4.910195 TGTTGCTAATCCAGTCATGAACT 58.090 39.130 0.00 0.00 39.44 3.01
3688 3774 0.180406 ACGGTGGAGCTGTTCTTTGT 59.820 50.000 0.00 0.00 31.36 2.83
3704 3790 4.635769 TGGCTCTTGGCAATACGG 57.364 55.556 0.00 0.00 46.03 4.02
3735 3821 4.946157 CCAAATGTCTAACTGCCTTCTGAT 59.054 41.667 0.00 0.00 0.00 2.90
3749 3835 2.840651 ACTTCCCTCGATCCAAATGTCT 59.159 45.455 0.00 0.00 0.00 3.41
3807 3924 5.995282 TCATAACTGATTTGGAGTTCGTTGT 59.005 36.000 0.00 0.00 35.30 3.32
3923 4062 5.437060 ACCACTAAATGCAGTAAGTATGGG 58.563 41.667 0.00 0.00 0.00 4.00
3925 4064 8.942338 TTCTACCACTAAATGCAGTAAGTATG 57.058 34.615 0.00 0.00 0.00 2.39
3929 4068 8.251721 AGTACTTCTACCACTAAATGCAGTAAG 58.748 37.037 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.