Multiple sequence alignment - TraesCS6D01G090000

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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 TraesCS6D01G090000 chr6D 100.000 4697 0 0 1 4697 55929252 55933948 0.000000e+00 8674.0
1 TraesCS6D01G090000 chr6A 93.426 4442 198 45 1 4406 70424477 70428860 0.000000e+00 6499.0
2 TraesCS6D01G090000 chr6A 91.154 260 13 5 4447 4697 70429442 70429700 1.250000e-90 344.0
3 TraesCS6D01G090000 chr6A 84.324 185 29 0 4219 4403 592521975 592521791 1.040000e-41 182.0
4 TraesCS6D01G090000 chr6B 91.010 2892 158 55 1 2857 126141549 126144373 0.000000e+00 3807.0
5 TraesCS6D01G090000 chr6B 91.769 899 54 12 3136 4018 126144810 126145704 0.000000e+00 1232.0
6 TraesCS6D01G090000 chr6B 91.518 224 9 3 4477 4697 126148427 126148643 2.750000e-77 300.0
7 TraesCS6D01G090000 chr6B 91.852 135 11 0 4274 4408 126145824 126145958 6.200000e-44 189.0
8 TraesCS6D01G090000 chr6B 90.598 117 8 3 4104 4219 126145710 126145824 8.140000e-33 152.0
9 TraesCS6D01G090000 chr5A 91.932 2008 138 16 1056 3057 700466654 700468643 0.000000e+00 2789.0
10 TraesCS6D01G090000 chr5A 79.670 182 31 5 4219 4394 20792873 20792692 4.930000e-25 126.0
11 TraesCS6D01G090000 chr2A 91.335 2008 136 22 1056 3057 585311692 585309717 0.000000e+00 2710.0
12 TraesCS6D01G090000 chr4A 89.637 1515 134 15 1059 2568 422206987 422205491 0.000000e+00 1906.0
13 TraesCS6D01G090000 chr4A 100.000 53 0 0 3005 3057 422204488 422204436 1.080000e-16 99.0
14 TraesCS6D01G090000 chr3B 89.591 1124 92 16 1056 2169 10904050 10905158 0.000000e+00 1404.0
15 TraesCS6D01G090000 chr3B 96.445 422 13 2 2636 3057 547647906 547648325 0.000000e+00 695.0
16 TraesCS6D01G090000 chr3B 95.735 422 16 2 2636 3057 10905156 10905575 0.000000e+00 678.0
17 TraesCS6D01G090000 chr3B 94.764 382 20 0 1788 2169 547647527 547647908 3.130000e-166 595.0
18 TraesCS6D01G090000 chr3B 83.696 184 30 0 4219 4402 30522640 30522457 1.740000e-39 174.0
19 TraesCS6D01G090000 chr1B 88.780 1123 103 14 1056 2169 86948686 86949794 0.000000e+00 1354.0
20 TraesCS6D01G090000 chr1B 96.682 422 11 3 2636 3057 86949792 86950210 0.000000e+00 699.0
21 TraesCS6D01G090000 chr7D 97.218 611 14 2 2447 3057 530088931 530088324 0.000000e+00 1031.0
22 TraesCS6D01G090000 chr7D 91.900 679 46 8 1111 1786 530089595 530088923 0.000000e+00 941.0
23 TraesCS6D01G090000 chr7D 96.774 31 1 0 357 387 603848065 603848035 8.000000e-03 52.8
24 TraesCS6D01G090000 chr7B 97.393 422 10 1 2636 3057 714860682 714860262 0.000000e+00 717.0
25 TraesCS6D01G090000 chr7B 94.269 349 20 0 1821 2169 714861028 714860680 6.920000e-148 534.0
26 TraesCS6D01G090000 chr7B 88.646 229 16 4 1057 1284 714861677 714861458 2.150000e-68 270.0
27 TraesCS6D01G090000 chr7B 85.946 185 26 0 4219 4403 490894767 490894583 1.030000e-46 198.0
28 TraesCS6D01G090000 chr4D 85.946 185 26 0 4219 4403 196883214 196883398 1.030000e-46 198.0
29 TraesCS6D01G090000 chr5D 91.071 56 5 0 4306 4361 486824631 486824576 5.040000e-10 76.8


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 TraesCS6D01G090000 chr6D 55929252 55933948 4696 False 8674.0 8674 100.0000 1 4697 1 chr6D.!!$F1 4696
1 TraesCS6D01G090000 chr6A 70424477 70429700 5223 False 3421.5 6499 92.2900 1 4697 2 chr6A.!!$F1 4696
2 TraesCS6D01G090000 chr6B 126141549 126148643 7094 False 1136.0 3807 91.3494 1 4697 5 chr6B.!!$F1 4696
3 TraesCS6D01G090000 chr5A 700466654 700468643 1989 False 2789.0 2789 91.9320 1056 3057 1 chr5A.!!$F1 2001
4 TraesCS6D01G090000 chr2A 585309717 585311692 1975 True 2710.0 2710 91.3350 1056 3057 1 chr2A.!!$R1 2001
5 TraesCS6D01G090000 chr4A 422204436 422206987 2551 True 1002.5 1906 94.8185 1059 3057 2 chr4A.!!$R1 1998
6 TraesCS6D01G090000 chr3B 10904050 10905575 1525 False 1041.0 1404 92.6630 1056 3057 2 chr3B.!!$F1 2001
7 TraesCS6D01G090000 chr3B 547647527 547648325 798 False 645.0 695 95.6045 1788 3057 2 chr3B.!!$F2 1269
8 TraesCS6D01G090000 chr1B 86948686 86950210 1524 False 1026.5 1354 92.7310 1056 3057 2 chr1B.!!$F1 2001
9 TraesCS6D01G090000 chr7D 530088324 530089595 1271 True 986.0 1031 94.5590 1111 3057 2 chr7D.!!$R2 1946
10 TraesCS6D01G090000 chr7B 714860262 714861677 1415 True 507.0 717 93.4360 1057 3057 3 chr7B.!!$R2 2000

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
774 790 1.003812 TCGGATAGGTTGGTTGGTTGG 59.996 52.381 0.0 0.0 0.0 3.77 F
1103 1141 0.039764 GGAAAGGGGAAGGGGAACTG 59.960 60.000 0.0 0.0 0.0 3.16 F
1507 1636 0.246635 TTGCGTCAGGAGGAAGTAGC 59.753 55.000 0.0 0.0 0.0 3.58 F
1531 1660 0.310854 GAGAGGGTTTGTGTTTGCGG 59.689 55.000 0.0 0.0 0.0 5.69 F
1693 1829 0.394192 TGTGAGGACTGACTTGCTGG 59.606 55.000 0.0 0.0 0.0 4.85 F
3305 4923 0.036010 ACATTCTCACAGCTTCCCCG 60.036 55.000 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1708 1850 0.105504 TAGCAGCTCTCAGCCCCATA 60.106 55.000 0.00 0.00 43.77 2.74 R
2882 4374 2.024414 GGGAGAACTGCAGTGTTTGTT 58.976 47.619 22.49 2.42 0.00 2.83 R
3127 4640 0.246360 CACGTCACCATCCAGTAGCA 59.754 55.000 0.00 0.00 0.00 3.49 R
3305 4923 1.001293 TGACCAGATGAGCACACAGAC 59.999 52.381 0.00 0.00 0.00 3.51 R
3335 4954 1.298953 ACATGGTGGGAAGCATAGGT 58.701 50.000 0.00 0.00 0.00 3.08 R
4215 5850 0.035317 TGTGGCACTACTCCTGCTTG 59.965 55.000 19.83 0.00 34.84 4.01 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
101 102 4.216257 AGCAATTAATTGAAGTGTGTCGCT 59.784 37.500 28.33 13.07 40.14 4.93
241 242 2.822255 GGGCGCGCAGTTATCCAA 60.822 61.111 34.42 0.00 0.00 3.53
245 246 2.808958 CGCGCAGTTATCCAACCCG 61.809 63.158 8.75 0.00 35.05 5.28
263 264 2.042843 TCCTCCTTCTCGGCCTCC 60.043 66.667 0.00 0.00 0.00 4.30
264 265 2.364317 CCTCCTTCTCGGCCTCCA 60.364 66.667 0.00 0.00 0.00 3.86
265 266 1.764054 CCTCCTTCTCGGCCTCCAT 60.764 63.158 0.00 0.00 0.00 3.41
303 307 3.930012 CGCGATCCCCCTCTTCCC 61.930 72.222 0.00 0.00 0.00 3.97
756 772 2.897350 GCTTCTTCCCGGCCATCG 60.897 66.667 2.24 0.00 38.88 3.84
771 787 1.211949 CCATCGGATAGGTTGGTTGGT 59.788 52.381 0.00 0.00 0.00 3.67
772 788 2.356741 CCATCGGATAGGTTGGTTGGTT 60.357 50.000 0.00 0.00 0.00 3.67
773 789 2.483014 TCGGATAGGTTGGTTGGTTG 57.517 50.000 0.00 0.00 0.00 3.77
774 790 1.003812 TCGGATAGGTTGGTTGGTTGG 59.996 52.381 0.00 0.00 0.00 3.77
775 791 1.182667 GGATAGGTTGGTTGGTTGGC 58.817 55.000 0.00 0.00 0.00 4.52
1004 1036 2.187946 GAGACCATCAGGCCCGTG 59.812 66.667 0.00 0.00 39.06 4.94
1101 1139 0.784495 AAGGAAAGGGGAAGGGGAAC 59.216 55.000 0.00 0.00 0.00 3.62
1102 1140 0.103337 AGGAAAGGGGAAGGGGAACT 60.103 55.000 0.00 0.00 0.00 3.01
1103 1141 0.039764 GGAAAGGGGAAGGGGAACTG 59.960 60.000 0.00 0.00 0.00 3.16
1104 1142 0.039764 GAAAGGGGAAGGGGAACTGG 59.960 60.000 0.00 0.00 0.00 4.00
1105 1143 1.443729 AAAGGGGAAGGGGAACTGGG 61.444 60.000 0.00 0.00 0.00 4.45
1106 1144 2.204244 GGGGAAGGGGAACTGGGA 60.204 66.667 0.00 0.00 0.00 4.37
1109 1147 1.000771 GGAAGGGGAACTGGGAAGC 60.001 63.158 0.00 0.00 0.00 3.86
1298 1424 2.601299 GGTACCAATCCAGCCCCC 59.399 66.667 7.15 0.00 0.00 5.40
1299 1425 2.313427 GGTACCAATCCAGCCCCCA 61.313 63.158 7.15 0.00 0.00 4.96
1366 1494 4.702131 CCATTAAACTGAGAGGTTTCTGGG 59.298 45.833 0.00 0.00 39.66 4.45
1388 1516 3.119280 GCTTGTCTCTCAACCTAGAGGAC 60.119 52.174 1.60 0.00 42.78 3.85
1450 1578 0.861866 CTGCTCGACGTGTACGATGG 60.862 60.000 11.79 0.13 43.02 3.51
1499 1628 2.742372 CCGGGTTTGCGTCAGGAG 60.742 66.667 0.00 0.00 0.00 3.69
1507 1636 0.246635 TTGCGTCAGGAGGAAGTAGC 59.753 55.000 0.00 0.00 0.00 3.58
1531 1660 0.310854 GAGAGGGTTTGTGTTTGCGG 59.689 55.000 0.00 0.00 0.00 5.69
1553 1683 4.549458 GTGCTGATTGTATTTGTTGCACT 58.451 39.130 0.00 0.00 43.95 4.40
1629 1760 3.935993 CGAGAGGTTGGATTGTGGT 57.064 52.632 0.00 0.00 0.00 4.16
1632 1767 2.162681 GAGAGGTTGGATTGTGGTTGG 58.837 52.381 0.00 0.00 0.00 3.77
1641 1776 2.547855 GGATTGTGGTTGGTCTTTTGCC 60.548 50.000 0.00 0.00 0.00 4.52
1649 1784 4.837860 TGGTTGGTCTTTTGCCTTGATTAT 59.162 37.500 0.00 0.00 0.00 1.28
1650 1785 5.306678 TGGTTGGTCTTTTGCCTTGATTATT 59.693 36.000 0.00 0.00 0.00 1.40
1651 1786 5.639082 GGTTGGTCTTTTGCCTTGATTATTG 59.361 40.000 0.00 0.00 0.00 1.90
1652 1787 6.223120 GTTGGTCTTTTGCCTTGATTATTGT 58.777 36.000 0.00 0.00 0.00 2.71
1681 1816 6.597562 AGTTTAACCATTGTAACTGTGAGGA 58.402 36.000 0.00 0.00 30.17 3.71
1688 1823 5.300752 CATTGTAACTGTGAGGACTGACTT 58.699 41.667 0.00 0.00 0.00 3.01
1693 1829 0.394192 TGTGAGGACTGACTTGCTGG 59.606 55.000 0.00 0.00 0.00 4.85
1744 1886 1.024271 CTATGGTCACCAATTGCCCG 58.976 55.000 0.00 0.00 36.95 6.13
1807 1949 1.079503 GAACTGAAGATTTCGCCGCT 58.920 50.000 0.00 0.00 0.00 5.52
1918 2273 1.855360 GCGTCTGAATTCGATCTGGTC 59.145 52.381 0.04 0.00 0.00 4.02
2032 2387 4.722700 ATGGAAGCTGCGCCGGTT 62.723 61.111 16.23 16.23 0.00 4.44
2221 2576 5.984725 ACGTTGGATGATGTCAGGTAAATA 58.015 37.500 0.00 0.00 0.00 1.40
2235 2590 7.885922 TGTCAGGTAAATATTGTTCTTGGCTAA 59.114 33.333 0.00 0.00 0.00 3.09
2268 2623 6.969366 TGTCATAACAGATGTTTTGAAGTGG 58.031 36.000 16.86 0.00 43.75 4.00
2298 2653 9.374838 CTTTATTGCAGAAAAATGCTCCTTTAT 57.625 29.630 0.00 0.00 46.63 1.40
2450 2805 2.076100 TCATGAAAGCTAACAGCCACG 58.924 47.619 0.00 0.00 43.77 4.94
2838 4287 8.807948 AATACTGTATATGCAAGTTTGTTCCT 57.192 30.769 0.00 0.00 0.00 3.36
2943 4436 2.533266 GTGCCAGCATTAGAAACATGC 58.467 47.619 0.00 0.00 46.39 4.06
3179 4796 3.784511 AGGATGCCCTAGATGATTGTG 57.215 47.619 0.00 0.00 42.15 3.33
3226 4843 4.389077 ACAACAGTAAATCGCAGTAGCTTC 59.611 41.667 0.00 0.00 39.10 3.86
3305 4923 0.036010 ACATTCTCACAGCTTCCCCG 60.036 55.000 0.00 0.00 0.00 5.73
3335 4954 4.406649 TGCTCATCTGGTCATGATGTAGAA 59.593 41.667 0.00 0.00 41.30 2.10
3347 4966 4.689612 TGATGTAGAACCTATGCTTCCC 57.310 45.455 0.00 0.00 0.00 3.97
3364 4985 4.220602 GCTTCCCACCATGTTATGTTTCTT 59.779 41.667 0.00 0.00 0.00 2.52
3395 5016 5.241506 TGAAGTTTTGGCTGGTGATTCTTAG 59.758 40.000 0.00 0.00 0.00 2.18
3514 5136 2.095059 CGGAAACTTTGCTATGCTTGCT 60.095 45.455 0.00 0.00 0.00 3.91
3592 5214 4.323104 GCATAGTTCTGTCTGAGGAGGTTT 60.323 45.833 0.00 0.00 0.00 3.27
3627 5249 4.879545 GGCGTGGAATCACCTAATAAAAGA 59.120 41.667 0.00 0.00 40.65 2.52
3796 5422 4.699257 CCAGTAGTAGTTACTTCGTGGAGT 59.301 45.833 0.00 0.00 40.68 3.85
3822 5448 2.443416 TGTGAGCCTCTCTAACGCTTA 58.557 47.619 0.00 0.00 31.61 3.09
3823 5449 2.823747 TGTGAGCCTCTCTAACGCTTAA 59.176 45.455 0.00 0.00 31.61 1.85
3828 5454 4.496360 AGCCTCTCTAACGCTTAACTTTC 58.504 43.478 0.00 0.00 0.00 2.62
3829 5455 4.021368 AGCCTCTCTAACGCTTAACTTTCA 60.021 41.667 0.00 0.00 0.00 2.69
3844 5470 7.095102 GCTTAACTTTCATGAAACAATGCCATT 60.095 33.333 16.91 1.74 0.00 3.16
3934 5560 1.486310 ACCATGTGCGGATCACTGTAT 59.514 47.619 0.00 0.00 45.81 2.29
3935 5561 1.869132 CCATGTGCGGATCACTGTATG 59.131 52.381 0.00 0.00 45.81 2.39
3936 5562 2.554142 CATGTGCGGATCACTGTATGT 58.446 47.619 0.00 0.00 45.81 2.29
3937 5563 3.492482 CCATGTGCGGATCACTGTATGTA 60.492 47.826 0.00 0.00 45.81 2.29
3938 5564 4.309933 CATGTGCGGATCACTGTATGTAT 58.690 43.478 0.00 0.00 45.81 2.29
3939 5565 4.400529 TGTGCGGATCACTGTATGTATT 57.599 40.909 0.00 0.00 45.81 1.89
3940 5566 4.119136 TGTGCGGATCACTGTATGTATTG 58.881 43.478 0.00 0.00 45.81 1.90
4035 5669 4.289238 TGAATTTCTTAAGGCGGTACCA 57.711 40.909 13.54 0.00 43.14 3.25
4061 5696 4.006319 ACCTTTACTTGCAGCTTCAGATC 58.994 43.478 0.00 0.00 0.00 2.75
4072 5707 4.671250 GCAGCTTCAGATCTGTGCTTTTAC 60.671 45.833 29.32 20.05 38.53 2.01
4083 5718 6.426980 TCTGTGCTTTTACATATCAGCTTG 57.573 37.500 0.00 0.00 33.15 4.01
4103 5738 1.349627 GTCCGCATGATTGTGCTCG 59.650 57.895 0.00 0.00 42.88 5.03
4104 5739 1.079197 TCCGCATGATTGTGCTCGT 60.079 52.632 0.00 0.00 42.88 4.18
4105 5740 1.061411 CCGCATGATTGTGCTCGTG 59.939 57.895 0.00 0.00 42.88 4.35
4106 5741 1.638388 CCGCATGATTGTGCTCGTGT 61.638 55.000 0.00 0.00 42.88 4.49
4107 5742 0.247419 CGCATGATTGTGCTCGTGTC 60.247 55.000 0.00 0.00 42.88 3.67
4108 5743 0.798159 GCATGATTGTGCTCGTGTCA 59.202 50.000 0.00 0.00 41.82 3.58
4169 5804 7.881775 AGAATCCCTGTGGTACAAAATTATC 57.118 36.000 0.00 0.00 44.16 1.75
4176 5811 5.502079 TGTGGTACAAAATTATCCATCCGT 58.498 37.500 0.00 0.00 44.16 4.69
4215 5850 1.506493 CTATCCTGATTGAGTGCGCC 58.494 55.000 4.18 0.00 0.00 6.53
4232 5867 1.679311 CCAAGCAGGAGTAGTGCCA 59.321 57.895 0.00 0.00 42.24 4.92
4242 5877 0.033504 AGTAGTGCCACACCTTGTCG 59.966 55.000 0.00 0.00 34.49 4.35
4253 5888 1.002134 CCTTGTCGATGGTGGCCTT 60.002 57.895 3.32 0.00 0.00 4.35
4256 5891 0.109532 TTGTCGATGGTGGCCTTTCA 59.890 50.000 3.32 0.00 0.00 2.69
4273 5908 3.713858 TTCAATCTTGCAATATGCCGG 57.286 42.857 0.00 0.00 44.23 6.13
4279 5914 3.138304 TCTTGCAATATGCCGGTGATAC 58.862 45.455 1.90 0.00 44.23 2.24
4280 5915 2.629336 TGCAATATGCCGGTGATACA 57.371 45.000 1.90 0.00 44.23 2.29
4281 5916 2.217750 TGCAATATGCCGGTGATACAC 58.782 47.619 1.90 0.00 44.23 2.90
4319 5954 4.386867 TGACCTCGATAAAGCTCGAAAT 57.613 40.909 0.00 0.00 46.14 2.17
4338 5973 6.038161 TCGAAATCTGAAACTCTTGCTTTCAA 59.962 34.615 0.51 0.00 37.22 2.69
4415 6073 4.202060 TGCTTCGAAGAGACCAGACATATC 60.202 45.833 28.95 6.06 38.43 1.63
4521 8573 5.127682 AGGCCTGTGCTTTGGAAAAATATAG 59.872 40.000 3.11 0.00 37.74 1.31
4524 8576 5.337578 TGTGCTTTGGAAAAATATAGGGC 57.662 39.130 0.00 0.00 0.00 5.19
4552 8604 9.529823 AAACAGAATGAGCATGGATATATCAAT 57.470 29.630 14.60 5.91 39.69 2.57
4561 8613 4.219264 TGGATATATCAATGCGCATGGA 57.781 40.909 28.89 28.89 0.00 3.41
4594 8653 5.551760 AAACAAGATATTTCAGCTCACCG 57.448 39.130 0.00 0.00 0.00 4.94
4601 8661 1.221466 TTTCAGCTCACCGCAGTTCG 61.221 55.000 0.00 0.00 42.61 3.95
4633 8693 3.417069 AGCTAGTGCAACATACACCAA 57.583 42.857 0.00 0.00 41.43 3.67
4674 8734 0.035630 GGCACAGGCATGAGAAGACT 60.036 55.000 4.84 0.00 43.71 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 3.342719 TGGAATGATTAAACTGCAGCGA 58.657 40.909 15.27 0.00 0.00 4.93
101 102 8.190122 GTGATGTAATGGAATGATTAAACTGCA 58.810 33.333 0.00 0.00 0.00 4.41
241 242 2.362632 CCGAGAAGGAGGACGGGT 60.363 66.667 0.00 0.00 45.00 5.28
245 246 2.428085 GGAGGCCGAGAAGGAGGAC 61.428 68.421 0.00 0.00 45.00 3.85
263 264 2.249535 CGGCCCTTCGCAGATGATG 61.250 63.158 0.00 0.00 40.31 3.07
264 265 2.109799 CGGCCCTTCGCAGATGAT 59.890 61.111 0.00 0.00 40.31 2.45
265 266 3.371097 GACGGCCCTTCGCAGATGA 62.371 63.158 0.00 0.00 40.31 2.92
285 286 2.838225 GGAAGAGGGGGATCGCGA 60.838 66.667 13.09 13.09 0.00 5.87
286 287 3.930012 GGGAAGAGGGGGATCGCG 61.930 72.222 0.00 0.00 0.00 5.87
287 288 3.561241 GGGGAAGAGGGGGATCGC 61.561 72.222 0.06 0.06 0.00 4.58
756 772 1.182667 GCCAACCAACCAACCTATCC 58.817 55.000 0.00 0.00 0.00 2.59
762 778 1.744320 GACCCAGCCAACCAACCAAC 61.744 60.000 0.00 0.00 0.00 3.77
860 882 6.070366 AGCAAAAACCCTAACCCTAGTAGTAG 60.070 42.308 0.00 0.00 0.00 2.57
861 883 5.786975 AGCAAAAACCCTAACCCTAGTAGTA 59.213 40.000 0.00 0.00 0.00 1.82
862 884 4.600547 AGCAAAAACCCTAACCCTAGTAGT 59.399 41.667 0.00 0.00 0.00 2.73
915 942 1.003580 CTTGGGCTGGCTTCAGTAGAA 59.996 52.381 0.00 0.00 40.51 2.10
962 989 2.761208 CCGGGATAACTGGGCTATAGAG 59.239 54.545 3.21 0.00 42.34 2.43
963 990 2.816411 CCGGGATAACTGGGCTATAGA 58.184 52.381 3.21 0.00 42.34 1.98
964 991 1.207329 GCCGGGATAACTGGGCTATAG 59.793 57.143 2.18 0.00 46.45 1.31
965 992 1.272807 GCCGGGATAACTGGGCTATA 58.727 55.000 2.18 0.00 46.45 1.31
966 993 2.067197 GCCGGGATAACTGGGCTAT 58.933 57.895 2.18 0.00 46.45 2.97
967 994 3.558475 GCCGGGATAACTGGGCTA 58.442 61.111 2.18 0.00 46.45 3.93
980 1007 4.227134 CTGATGGTCTCGGGCCGG 62.227 72.222 27.98 17.02 0.00 6.13
1004 1036 3.814283 CCTGCCAGAGAGAATTAATGCTC 59.186 47.826 14.87 14.87 0.00 4.26
1101 1139 2.738521 CCGACACACGCTTCCCAG 60.739 66.667 0.00 0.00 41.07 4.45
1102 1140 4.980805 GCCGACACACGCTTCCCA 62.981 66.667 0.00 0.00 41.07 4.37
1388 1516 2.982130 CTGTTCCTGTCCCCTCCG 59.018 66.667 0.00 0.00 0.00 4.63
1450 1578 2.301738 ACCTTGGCAGGGTAGAGGC 61.302 63.158 21.01 0.00 46.01 4.70
1499 1628 0.463620 CCCTCTCTGCAGCTACTTCC 59.536 60.000 9.47 0.00 0.00 3.46
1507 1636 1.972872 AACACAAACCCTCTCTGCAG 58.027 50.000 7.63 7.63 0.00 4.41
1531 1660 4.891277 GTGCAACAAATACAATCAGCAC 57.109 40.909 0.00 0.00 43.27 4.40
1553 1683 1.006639 GGGCAGTTTCCCCATCCTAAA 59.993 52.381 0.00 0.00 42.36 1.85
1620 1750 2.547855 GGCAAAAGACCAACCACAATCC 60.548 50.000 0.00 0.00 0.00 3.01
1628 1759 6.223120 ACAATAATCAAGGCAAAAGACCAAC 58.777 36.000 0.00 0.00 0.00 3.77
1629 1760 6.418057 ACAATAATCAAGGCAAAAGACCAA 57.582 33.333 0.00 0.00 0.00 3.67
1660 1795 5.995282 CAGTCCTCACAGTTACAATGGTTAA 59.005 40.000 0.00 0.00 0.00 2.01
1663 1798 3.646162 TCAGTCCTCACAGTTACAATGGT 59.354 43.478 0.00 0.00 0.00 3.55
1681 1816 2.887152 GGATTTTCACCAGCAAGTCAGT 59.113 45.455 0.00 0.00 0.00 3.41
1693 1829 3.118775 GCCCCATAAACCTGGATTTTCAC 60.119 47.826 0.00 0.00 38.69 3.18
1708 1850 0.105504 TAGCAGCTCTCAGCCCCATA 60.106 55.000 0.00 0.00 43.77 2.74
1744 1886 1.429148 CCGCGAATGAGCTAACACCC 61.429 60.000 8.23 0.00 34.40 4.61
1807 1949 1.372683 GCTGCCTGAACCTGACTGA 59.627 57.895 0.00 0.00 0.00 3.41
1883 2238 0.107703 GACGCATCCTGGACATTCCA 60.108 55.000 0.00 0.00 45.98 3.53
2268 2623 7.763071 AGGAGCATTTTTCTGCAATAAAGATTC 59.237 33.333 0.00 0.00 44.77 2.52
2298 2653 8.720562 CAACTCACATCAAACACATACAGAATA 58.279 33.333 0.00 0.00 0.00 1.75
2352 2707 8.408043 AATATTGACTGGAAATGACAAACAGA 57.592 30.769 0.00 0.00 33.57 3.41
2450 2805 6.422400 TCAACTTCACTTCACAAAACCAAAAC 59.578 34.615 0.00 0.00 0.00 2.43
2622 3593 7.578169 AAGTTATTTGTGTAAGTCTAGACGC 57.422 36.000 17.07 11.77 36.20 5.19
2663 4108 6.470278 CAGTAGCATTGGATGATGATTCCTA 58.530 40.000 0.00 0.00 34.17 2.94
2819 4265 6.494893 TCACAGGAACAAACTTGCATATAC 57.505 37.500 0.00 0.00 0.00 1.47
2838 4287 8.918202 AAACAGAAGTAATAAACAGGATCACA 57.082 30.769 0.00 0.00 0.00 3.58
2882 4374 2.024414 GGGAGAACTGCAGTGTTTGTT 58.976 47.619 22.49 2.42 0.00 2.83
3127 4640 0.246360 CACGTCACCATCCAGTAGCA 59.754 55.000 0.00 0.00 0.00 3.49
3130 4643 3.358118 TGATACACGTCACCATCCAGTA 58.642 45.455 0.00 0.00 0.00 2.74
3179 4796 4.367450 GAGCATACTCATTCTGGTCAGTC 58.633 47.826 0.00 0.00 42.93 3.51
3305 4923 1.001293 TGACCAGATGAGCACACAGAC 59.999 52.381 0.00 0.00 0.00 3.51
3335 4954 1.298953 ACATGGTGGGAAGCATAGGT 58.701 50.000 0.00 0.00 0.00 3.08
3347 4966 7.490725 TCAAACACAAAGAAACATAACATGGTG 59.509 33.333 0.00 0.00 33.60 4.17
3364 4985 3.007398 ACCAGCCAAAACTTCAAACACAA 59.993 39.130 0.00 0.00 0.00 3.33
3395 5016 6.263617 TGGTAAGACCTGTGTTTGGAAATAAC 59.736 38.462 0.00 0.00 39.58 1.89
3514 5136 1.550524 ACCTCATGTAGAAAGCGCTCA 59.449 47.619 12.06 3.76 0.00 4.26
3579 5201 7.766738 CCTTATTAAGAGAAAACCTCCTCAGAC 59.233 40.741 4.96 0.00 42.97 3.51
3592 5214 5.815740 GTGATTCCACGCCTTATTAAGAGAA 59.184 40.000 4.96 1.49 33.10 2.87
3627 5249 7.120923 TGAAAGAAGTACTTGTCTAACACCT 57.879 36.000 14.14 0.00 38.98 4.00
3632 5254 7.996644 ACCCATTTGAAAGAAGTACTTGTCTAA 59.003 33.333 14.14 10.58 38.98 2.10
3635 5257 6.635030 ACCCATTTGAAAGAAGTACTTGTC 57.365 37.500 14.14 8.10 38.98 3.18
3702 5324 2.241176 GGGTGATACCAAATGAGGACCA 59.759 50.000 0.00 0.00 41.02 4.02
3706 5328 2.624838 GCATGGGTGATACCAAATGAGG 59.375 50.000 13.79 0.00 45.13 3.86
3796 5422 3.305403 CGTTAGAGAGGCTCACAACAGAA 60.305 47.826 18.26 0.00 31.58 3.02
3822 5448 6.527423 AGAATGGCATTGTTTCATGAAAGTT 58.473 32.000 21.05 6.40 0.00 2.66
3823 5449 6.105397 AGAATGGCATTGTTTCATGAAAGT 57.895 33.333 21.05 7.85 0.00 2.66
3828 5454 3.305094 GCGAAGAATGGCATTGTTTCATG 59.695 43.478 21.67 13.64 0.00 3.07
3829 5455 3.056678 TGCGAAGAATGGCATTGTTTCAT 60.057 39.130 21.67 1.60 35.17 2.57
3934 5560 3.627123 CGGTCATCATTTCCAGCAATACA 59.373 43.478 0.00 0.00 0.00 2.29
3935 5561 3.003689 CCGGTCATCATTTCCAGCAATAC 59.996 47.826 0.00 0.00 0.00 1.89
3936 5562 3.213506 CCGGTCATCATTTCCAGCAATA 58.786 45.455 0.00 0.00 0.00 1.90
3937 5563 2.026641 CCGGTCATCATTTCCAGCAAT 58.973 47.619 0.00 0.00 0.00 3.56
3938 5564 1.462616 CCGGTCATCATTTCCAGCAA 58.537 50.000 0.00 0.00 0.00 3.91
3939 5565 1.031571 GCCGGTCATCATTTCCAGCA 61.032 55.000 1.90 0.00 0.00 4.41
3940 5566 0.749454 AGCCGGTCATCATTTCCAGC 60.749 55.000 1.90 0.00 0.00 4.85
4018 5652 4.004982 GTGATTGGTACCGCCTTAAGAAA 58.995 43.478 7.57 0.00 38.35 2.52
4019 5653 3.602483 GTGATTGGTACCGCCTTAAGAA 58.398 45.455 7.57 0.00 38.35 2.52
4020 5654 2.093341 GGTGATTGGTACCGCCTTAAGA 60.093 50.000 7.57 0.00 38.35 2.10
4021 5655 2.093128 AGGTGATTGGTACCGCCTTAAG 60.093 50.000 7.57 0.00 40.09 1.85
4023 5657 1.575419 AGGTGATTGGTACCGCCTTA 58.425 50.000 7.57 0.00 40.09 2.69
4024 5658 0.696501 AAGGTGATTGGTACCGCCTT 59.303 50.000 7.57 12.10 45.45 4.35
4025 5659 0.696501 AAAGGTGATTGGTACCGCCT 59.303 50.000 7.57 6.68 44.47 5.52
4035 5669 4.144297 TGAAGCTGCAAGTAAAGGTGATT 58.856 39.130 1.02 0.00 35.30 2.57
4061 5696 6.025896 CACAAGCTGATATGTAAAAGCACAG 58.974 40.000 0.00 0.00 38.14 3.66
4072 5707 1.655484 TGCGGACACAAGCTGATATG 58.345 50.000 0.00 0.00 0.00 1.78
4083 5718 4.771684 GCACAATCATGCGGACAC 57.228 55.556 0.00 0.00 35.50 3.67
4103 5738 6.756542 TGCATGTATATACTTGACACTGACAC 59.243 38.462 25.27 10.06 34.39 3.67
4104 5739 6.872920 TGCATGTATATACTTGACACTGACA 58.127 36.000 25.27 12.99 34.39 3.58
4105 5740 7.770801 TTGCATGTATATACTTGACACTGAC 57.229 36.000 25.27 11.13 34.39 3.51
4106 5741 8.040727 AGTTTGCATGTATATACTTGACACTGA 58.959 33.333 25.27 10.37 34.39 3.41
4107 5742 8.201554 AGTTTGCATGTATATACTTGACACTG 57.798 34.615 25.27 9.22 34.39 3.66
4108 5743 8.668353 CAAGTTTGCATGTATATACTTGACACT 58.332 33.333 25.27 19.61 42.99 3.55
4176 5811 6.096423 GGATAGCCAACATATAGGACGACATA 59.904 42.308 0.00 0.00 0.00 2.29
4215 5850 0.035317 TGTGGCACTACTCCTGCTTG 59.965 55.000 19.83 0.00 34.84 4.01
4242 5877 2.417787 GCAAGATTGAAAGGCCACCATC 60.418 50.000 5.01 3.11 0.00 3.51
4304 5939 6.254589 AGAGTTTCAGATTTCGAGCTTTATCG 59.745 38.462 0.00 0.00 44.07 2.92
4319 5954 6.515272 AAAGTTGAAAGCAAGAGTTTCAGA 57.485 33.333 0.00 0.00 43.11 3.27
4338 5973 1.000274 GCCCGACATTTGCTCAAAAGT 60.000 47.619 3.28 3.28 35.28 2.66
4388 6023 2.828520 TCTGGTCTCTTCGAAGCAGAAT 59.171 45.455 22.86 0.00 44.51 2.40
4415 6073 4.460382 AGAATTGACCTTATGCACAACCAG 59.540 41.667 0.00 0.00 0.00 4.00
4521 8573 2.613691 CATGCTCATTCTGTTTTGCCC 58.386 47.619 0.00 0.00 0.00 5.36
4524 8576 8.789762 TGATATATCCATGCTCATTCTGTTTTG 58.210 33.333 10.25 0.00 0.00 2.44
4552 8604 1.006337 GGTTTGCTTTCCATGCGCA 60.006 52.632 14.96 14.96 0.00 6.09
4561 8613 8.729805 TGAAATATCTTGTTTTGGTTTGCTTT 57.270 26.923 0.00 0.00 0.00 3.51
4594 8653 0.388134 TACTCGGTCTTGCGAACTGC 60.388 55.000 0.00 0.00 46.70 4.40
4601 8661 1.799548 GCACTAGCTACTCGGTCTTGC 60.800 57.143 0.00 0.00 37.91 4.01
4633 8693 4.499019 CCCTAACTGTTGTTGCAATCGTTT 60.499 41.667 0.59 0.00 37.59 3.60


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

AutoCloner maintained by Alex Coulton.