Multiple sequence alignment - TraesCS7B01G288900

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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 TraesCS7B01G288900 chr7B 100.000 3562 0 0 950 4511 524715375 524718936 0.000000e+00 6578.0
1 TraesCS7B01G288900 chr7B 100.000 385 0 0 1 385 524714426 524714810 0.000000e+00 712.0
2 TraesCS7B01G288900 chr7A 96.029 3576 128 5 950 4511 561877183 561880758 0.000000e+00 5805.0
3 TraesCS7B01G288900 chr7A 82.812 640 84 14 3779 4392 561799951 561800590 2.370000e-152 549.0
4 TraesCS7B01G288900 chr7A 94.545 220 11 1 1 220 690045627 690045409 5.590000e-89 339.0
5 TraesCS7B01G288900 chr7A 94.144 222 12 1 1 221 40794658 40794879 2.010000e-88 337.0
6 TraesCS7B01G288900 chr7A 94.091 220 13 0 1 220 663965238 663965457 7.230000e-88 335.0
7 TraesCS7B01G288900 chr7A 89.773 88 6 1 4422 4506 561801568 561801655 4.770000e-20 110.0
8 TraesCS7B01G288900 chr7A 97.368 38 1 0 4450 4487 561801742 561801779 1.050000e-06 65.8
9 TraesCS7B01G288900 chr7D 95.829 3524 114 6 988 4508 496363024 496366517 0.000000e+00 5662.0
10 TraesCS7B01G288900 chr7D 81.325 166 23 5 220 385 496362453 496362610 1.320000e-25 128.0
11 TraesCS7B01G288900 chr7D 89.773 88 6 1 4422 4506 496158304 496158391 4.770000e-20 110.0
12 TraesCS7B01G288900 chr7D 94.872 39 2 0 4449 4487 496158406 496158444 1.350000e-05 62.1
13 TraesCS7B01G288900 chr6B 95.000 220 11 0 1 220 557419188 557418969 3.340000e-91 346.0
14 TraesCS7B01G288900 chr1B 94.545 220 12 0 1 220 389004727 389004946 1.550000e-89 340.0
15 TraesCS7B01G288900 chr5D 94.091 220 13 0 1 220 525663149 525662930 7.230000e-88 335.0
16 TraesCS7B01G288900 chr5B 94.091 220 13 0 1 220 82463853 82463634 7.230000e-88 335.0
17 TraesCS7B01G288900 chr2D 94.091 220 13 0 1 220 2244474 2244693 7.230000e-88 335.0
18 TraesCS7B01G288900 chr1A 93.750 224 13 1 1 223 405146225 405146002 7.230000e-88 335.0
19 TraesCS7B01G288900 chr2A 91.667 48 2 2 255 301 500035583 500035629 1.050000e-06 65.8


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 TraesCS7B01G288900 chr7B 524714426 524718936 4510 False 3645.0 6578 100.000000 1 4511 2 chr7B.!!$F1 4510
1 TraesCS7B01G288900 chr7A 561877183 561880758 3575 False 5805.0 5805 96.029000 950 4511 1 chr7A.!!$F2 3561
2 TraesCS7B01G288900 chr7A 561799951 561801779 1828 False 241.6 549 89.984333 3779 4506 3 chr7A.!!$F4 727
3 TraesCS7B01G288900 chr7D 496362453 496366517 4064 False 2895.0 5662 88.577000 220 4508 2 chr7D.!!$F2 4288

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
215 216 0.179001 CCCGGGTTCCAAAGTGACTT 60.179 55.0 14.18 0.0 0.00 3.01 F
1284 1592 0.182299 GGGAATCCCTCCTGCTTCTG 59.818 60.0 11.95 0.0 44.68 3.02 F
1531 1839 0.250858 TGGTGCACTGGTCATTCAGG 60.251 55.0 17.98 0.0 38.98 3.86 F
2666 2974 0.609957 TGCTGGAAGGAAGCACATGG 60.610 55.0 0.00 0.0 45.50 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 2279 1.352017 ACTGGCATGGACTGTTCATGA 59.648 47.619 28.85 11.05 43.25 3.07 R
2970 3278 0.682532 TTTGCACCAGGTCTGCACAA 60.683 50.000 4.19 1.12 44.32 3.33 R
3199 3507 3.318839 TCAATTGTCAACTCAGGCTTTGG 59.681 43.478 5.13 0.00 0.00 3.28 R
3835 4148 1.134220 AGTTTCAGACTCGGCCACAAA 60.134 47.619 2.24 0.00 31.20 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 6.624352 AATAATGCATACGCTGTTCATCTT 57.376 33.333 0.00 0.00 39.64 2.40
24 25 4.970662 AATGCATACGCTGTTCATCTTT 57.029 36.364 0.00 0.00 39.64 2.52
25 26 4.542662 ATGCATACGCTGTTCATCTTTC 57.457 40.909 0.00 0.00 39.64 2.62
26 27 2.677836 TGCATACGCTGTTCATCTTTCC 59.322 45.455 0.00 0.00 39.64 3.13
27 28 2.677836 GCATACGCTGTTCATCTTTCCA 59.322 45.455 0.00 0.00 34.30 3.53
28 29 3.126858 GCATACGCTGTTCATCTTTCCAA 59.873 43.478 0.00 0.00 34.30 3.53
29 30 4.379394 GCATACGCTGTTCATCTTTCCAAA 60.379 41.667 0.00 0.00 34.30 3.28
30 31 5.698832 CATACGCTGTTCATCTTTCCAAAA 58.301 37.500 0.00 0.00 0.00 2.44
31 32 4.853924 ACGCTGTTCATCTTTCCAAAAT 57.146 36.364 0.00 0.00 0.00 1.82
32 33 4.798574 ACGCTGTTCATCTTTCCAAAATC 58.201 39.130 0.00 0.00 0.00 2.17
33 34 4.278170 ACGCTGTTCATCTTTCCAAAATCA 59.722 37.500 0.00 0.00 0.00 2.57
34 35 4.618489 CGCTGTTCATCTTTCCAAAATCAC 59.382 41.667 0.00 0.00 0.00 3.06
35 36 4.618489 GCTGTTCATCTTTCCAAAATCACG 59.382 41.667 0.00 0.00 0.00 4.35
36 37 5.562696 GCTGTTCATCTTTCCAAAATCACGA 60.563 40.000 0.00 0.00 0.00 4.35
37 38 6.573664 TGTTCATCTTTCCAAAATCACGAT 57.426 33.333 0.00 0.00 0.00 3.73
38 39 6.980593 TGTTCATCTTTCCAAAATCACGATT 58.019 32.000 0.00 0.00 0.00 3.34
39 40 7.432869 TGTTCATCTTTCCAAAATCACGATTT 58.567 30.769 0.00 0.00 42.35 2.17
41 42 9.405587 GTTCATCTTTCCAAAATCACGATTTTA 57.594 29.630 15.45 1.47 46.01 1.52
43 44 9.787532 TCATCTTTCCAAAATCACGATTTTATC 57.212 29.630 15.45 0.00 46.01 1.75
44 45 9.571810 CATCTTTCCAAAATCACGATTTTATCA 57.428 29.630 15.45 2.76 46.01 2.15
76 77 8.995220 GTGTAACTCACATGGTTACTTATTTCA 58.005 33.333 18.35 1.51 45.19 2.69
77 78 9.214957 TGTAACTCACATGGTTACTTATTTCAG 57.785 33.333 18.35 0.00 45.19 3.02
78 79 6.743575 ACTCACATGGTTACTTATTTCAGC 57.256 37.500 0.00 0.00 0.00 4.26
79 80 6.237901 ACTCACATGGTTACTTATTTCAGCA 58.762 36.000 0.00 0.00 0.00 4.41
80 81 6.886459 ACTCACATGGTTACTTATTTCAGCAT 59.114 34.615 0.00 0.00 0.00 3.79
81 82 7.066284 ACTCACATGGTTACTTATTTCAGCATC 59.934 37.037 0.00 0.00 0.00 3.91
82 83 6.883756 TCACATGGTTACTTATTTCAGCATCA 59.116 34.615 0.00 0.00 0.00 3.07
83 84 7.392953 TCACATGGTTACTTATTTCAGCATCAA 59.607 33.333 0.00 0.00 0.00 2.57
84 85 8.028354 CACATGGTTACTTATTTCAGCATCAAA 58.972 33.333 0.00 0.00 0.00 2.69
85 86 8.584157 ACATGGTTACTTATTTCAGCATCAAAA 58.416 29.630 0.00 0.00 0.00 2.44
86 87 9.079833 CATGGTTACTTATTTCAGCATCAAAAG 57.920 33.333 0.00 0.00 0.00 2.27
87 88 8.177119 TGGTTACTTATTTCAGCATCAAAAGT 57.823 30.769 0.00 0.00 0.00 2.66
88 89 8.637986 TGGTTACTTATTTCAGCATCAAAAGTT 58.362 29.630 0.00 0.00 0.00 2.66
93 94 8.629158 ACTTATTTCAGCATCAAAAGTTACACA 58.371 29.630 0.00 0.00 0.00 3.72
94 95 9.630098 CTTATTTCAGCATCAAAAGTTACACAT 57.370 29.630 0.00 0.00 0.00 3.21
95 96 7.878477 ATTTCAGCATCAAAAGTTACACATG 57.122 32.000 0.00 0.00 0.00 3.21
96 97 6.389830 TTCAGCATCAAAAGTTACACATGT 57.610 33.333 0.00 0.00 0.00 3.21
97 98 5.761003 TCAGCATCAAAAGTTACACATGTG 58.239 37.500 24.25 24.25 0.00 3.21
98 99 5.299028 TCAGCATCAAAAGTTACACATGTGT 59.701 36.000 32.47 32.47 46.87 3.72
99 100 6.484977 TCAGCATCAAAAGTTACACATGTGTA 59.515 34.615 30.31 30.31 44.42 2.90
167 168 6.606768 TGAAACTTCAAAACAACATTTTGGC 58.393 32.000 11.16 0.00 39.25 4.52
168 169 6.205464 TGAAACTTCAAAACAACATTTTGGCA 59.795 30.769 11.16 0.00 39.25 4.92
169 170 5.544136 ACTTCAAAACAACATTTTGGCAC 57.456 34.783 11.16 0.00 39.25 5.01
170 171 4.999950 ACTTCAAAACAACATTTTGGCACA 59.000 33.333 11.16 0.00 39.25 4.57
171 172 5.122082 ACTTCAAAACAACATTTTGGCACAG 59.878 36.000 11.16 6.28 42.39 3.66
172 173 4.573900 TCAAAACAACATTTTGGCACAGT 58.426 34.783 11.16 0.00 42.39 3.55
173 174 4.999950 TCAAAACAACATTTTGGCACAGTT 59.000 33.333 11.16 0.00 42.39 3.16
174 175 5.121454 TCAAAACAACATTTTGGCACAGTTC 59.879 36.000 11.16 0.00 42.39 3.01
175 176 3.883830 ACAACATTTTGGCACAGTTCA 57.116 38.095 0.00 0.00 42.39 3.18
176 177 4.199432 ACAACATTTTGGCACAGTTCAA 57.801 36.364 0.00 0.00 42.39 2.69
177 178 4.573900 ACAACATTTTGGCACAGTTCAAA 58.426 34.783 0.00 0.00 42.39 2.69
178 179 4.999950 ACAACATTTTGGCACAGTTCAAAA 59.000 33.333 11.75 11.75 43.87 2.44
179 180 5.471456 ACAACATTTTGGCACAGTTCAAAAA 59.529 32.000 12.84 2.55 43.27 1.94
196 197 3.782889 AAAAATAGGGCTCGAATGCAC 57.217 42.857 0.00 0.00 36.44 4.57
197 198 1.680338 AAATAGGGCTCGAATGCACC 58.320 50.000 0.00 0.00 36.97 5.01
198 199 0.179018 AATAGGGCTCGAATGCACCC 60.179 55.000 0.00 0.00 43.17 4.61
202 203 4.778143 GCTCGAATGCACCCGGGT 62.778 66.667 24.16 24.16 0.00 5.28
203 204 2.046314 CTCGAATGCACCCGGGTT 60.046 61.111 27.83 10.09 0.00 4.11
204 205 2.046700 TCGAATGCACCCGGGTTC 60.047 61.111 27.83 22.19 0.00 3.62
205 206 3.131478 CGAATGCACCCGGGTTCC 61.131 66.667 27.83 19.07 0.00 3.62
206 207 2.034999 GAATGCACCCGGGTTCCA 59.965 61.111 27.83 24.48 0.00 3.53
207 208 1.605165 GAATGCACCCGGGTTCCAA 60.605 57.895 27.83 10.39 0.00 3.53
208 209 1.152440 AATGCACCCGGGTTCCAAA 60.152 52.632 27.83 3.17 0.00 3.28
209 210 1.184970 AATGCACCCGGGTTCCAAAG 61.185 55.000 27.83 13.42 0.00 2.77
210 211 2.203437 GCACCCGGGTTCCAAAGT 60.203 61.111 27.83 0.00 0.00 2.66
211 212 2.561037 GCACCCGGGTTCCAAAGTG 61.561 63.158 27.83 11.75 0.00 3.16
212 213 1.149627 CACCCGGGTTCCAAAGTGA 59.850 57.895 27.83 0.00 0.00 3.41
213 214 1.149854 ACCCGGGTTCCAAAGTGAC 59.850 57.895 24.16 0.00 0.00 3.67
214 215 1.350310 ACCCGGGTTCCAAAGTGACT 61.350 55.000 24.16 0.00 0.00 3.41
215 216 0.179001 CCCGGGTTCCAAAGTGACTT 60.179 55.000 14.18 0.00 0.00 3.01
216 217 1.687563 CCGGGTTCCAAAGTGACTTT 58.312 50.000 4.45 4.45 33.58 2.66
217 218 2.028876 CCGGGTTCCAAAGTGACTTTT 58.971 47.619 8.03 0.00 30.60 2.27
218 219 2.429250 CCGGGTTCCAAAGTGACTTTTT 59.571 45.455 8.03 0.00 30.60 1.94
298 299 9.337396 ACATGTTTGAAATGAAGTACTAGTTGA 57.663 29.630 0.00 0.00 0.00 3.18
301 302 9.607988 TGTTTGAAATGAAGTACTAGTTGAAGA 57.392 29.630 0.00 0.00 0.00 2.87
302 303 9.865484 GTTTGAAATGAAGTACTAGTTGAAGAC 57.135 33.333 0.00 0.00 0.00 3.01
328 351 3.596214 AGTATAGGAAAAGTGTGCACCG 58.404 45.455 15.69 0.00 0.00 4.94
329 352 1.821216 ATAGGAAAAGTGTGCACCGG 58.179 50.000 15.69 0.00 0.00 5.28
1190 1498 0.543277 GTCTGGCTCATGATGTCCCA 59.457 55.000 0.00 0.17 0.00 4.37
1284 1592 0.182299 GGGAATCCCTCCTGCTTCTG 59.818 60.000 11.95 0.00 44.68 3.02
1370 1678 0.324943 AAGAACAGTGGCCGCTACAT 59.675 50.000 20.73 8.02 0.00 2.29
1422 1730 1.522668 TTGGCAGGTTCGATGTTGAG 58.477 50.000 0.00 0.00 0.00 3.02
1429 1737 4.776743 CAGGTTCGATGTTGAGTTTCTTG 58.223 43.478 0.00 0.00 0.00 3.02
1455 1763 9.424319 GATCTTGAATATAGAGCGGTTGATTTA 57.576 33.333 0.00 0.00 0.00 1.40
1468 1776 3.754323 GGTTGATTTACACGGACCAATGA 59.246 43.478 0.00 0.00 0.00 2.57
1496 1804 4.428615 TGATAGACGACGTGTTTCATGA 57.571 40.909 12.95 0.00 0.00 3.07
1508 1816 7.533900 CGACGTGTTTCATGATAAACTTGATTT 59.466 33.333 10.75 0.00 39.57 2.17
1531 1839 0.250858 TGGTGCACTGGTCATTCAGG 60.251 55.000 17.98 0.00 38.98 3.86
1578 1886 7.534085 TGTGGAAACTTATAACACGATGATC 57.466 36.000 0.00 0.00 34.93 2.92
1676 1984 6.521162 TGCCAGACATATGTACGTTCAATAT 58.479 36.000 8.71 0.00 0.00 1.28
1724 2032 2.948720 GCGTCAAGGAGGCAGAGGT 61.949 63.158 6.08 0.00 42.14 3.85
1971 2279 3.641434 ATCAAGTCTGGCACTAGCATT 57.359 42.857 0.00 0.00 44.61 3.56
2220 2528 4.947388 GTGATGGTCAAGGCTTATGGTTTA 59.053 41.667 0.00 0.00 0.00 2.01
2229 2537 5.904362 AGGCTTATGGTTTAGCAAGAAAG 57.096 39.130 0.00 0.00 39.15 2.62
2270 2578 2.787994 ACTTGAGAACATGAAGGGCTG 58.212 47.619 0.00 0.00 0.00 4.85
2277 2585 0.625316 ACATGAAGGGCTGTGGCATA 59.375 50.000 0.00 0.00 40.87 3.14
2397 2705 3.058501 CAGGATTTAAACCGGTGTGTGAC 60.059 47.826 8.52 0.00 0.00 3.67
2487 2795 2.158475 TGAAATGAAGGCCTCAGGTGTT 60.158 45.455 5.23 0.00 37.52 3.32
2566 2874 1.065926 TGGAGAAGGCACTGCACTATG 60.066 52.381 2.82 0.00 40.86 2.23
2666 2974 0.609957 TGCTGGAAGGAAGCACATGG 60.610 55.000 0.00 0.00 45.50 3.66
2862 3170 3.834231 ACAAGAACATGGGCTTGCTTAAT 59.166 39.130 22.23 6.81 43.99 1.40
2925 3233 4.052159 ACTATCTGACTGTGCTGCATAC 57.948 45.455 5.27 0.00 0.00 2.39
2979 3287 3.364764 GCAACTTGAGAGATTGTGCAGAC 60.365 47.826 0.00 0.00 0.00 3.51
3199 3507 5.570589 GCATTAAATGTCTGTGAGCAACTTC 59.429 40.000 0.00 0.00 0.00 3.01
3267 3575 0.620556 AGGTGTATGCTTCCTGTGGG 59.379 55.000 0.00 0.00 0.00 4.61
3324 3632 2.495669 GCATGCTTTAGGGCTAAAACCA 59.504 45.455 11.37 0.00 34.95 3.67
3342 3650 3.820557 ACCAGACACTGTTACTTGCATT 58.179 40.909 0.00 0.00 0.00 3.56
3487 3795 6.715280 AGAGAAACTGGAAGCAATGATCTTA 58.285 36.000 0.00 0.00 37.60 2.10
3490 3798 6.944862 AGAAACTGGAAGCAATGATCTTACTT 59.055 34.615 0.00 0.00 37.60 2.24
3502 3810 7.761704 GCAATGATCTTACTTCTCAGTTAGTCA 59.238 37.037 0.00 0.00 32.41 3.41
3582 3891 3.644966 TGACTTTGTTGTGGACTTCCT 57.355 42.857 0.00 0.00 36.82 3.36
3646 3959 7.776969 AGGTGACACATATTTGCTTCAAGATAT 59.223 33.333 8.08 0.00 0.00 1.63
3680 3993 8.465201 GGGGATCAGAAATATTAATGAGATTGC 58.535 37.037 0.00 0.00 0.00 3.56
3687 4000 9.288576 AGAAATATTAATGAGATTGCCGATTGA 57.711 29.630 0.00 0.00 0.00 2.57
3761 4074 2.144833 CTGCCGCATGGAAACTGCAA 62.145 55.000 0.00 0.00 39.64 4.08
3766 4079 2.523015 CGCATGGAAACTGCAATTCTC 58.477 47.619 10.68 3.74 39.64 2.87
3793 4106 3.265221 TGAAGGCATTCTCAAGTCCATCT 59.735 43.478 12.92 0.00 36.33 2.90
3829 4142 4.101942 CGTCATAGAGTCTCTTGTGAAGC 58.898 47.826 7.89 2.46 0.00 3.86
3835 4148 1.683917 AGTCTCTTGTGAAGCGAGTGT 59.316 47.619 0.00 0.00 0.00 3.55
3871 4185 5.934625 TCTGAAACTGCTAATGAGAAAGGAC 59.065 40.000 0.00 0.00 0.00 3.85
3888 4202 3.791320 AGGACTGTGAGGATTAGGTTGA 58.209 45.455 0.00 0.00 0.00 3.18
3948 4262 1.178276 GGTGACAGTCGAGGAGATGT 58.822 55.000 0.00 0.00 0.00 3.06
3967 4281 6.245408 AGATGTAGAAATTTGCAGTGGGTAA 58.755 36.000 0.00 0.00 0.00 2.85
4122 4438 5.772825 ATGTCAGCACACTTGTTAATGTT 57.227 34.783 0.00 0.00 34.48 2.71
4144 4460 6.702723 TGTTAGAGAAAATCTTTTTCCGTCGA 59.297 34.615 8.65 0.00 39.64 4.20
4259 4584 2.566724 TGATGGGTTCATTTTCCTTGCC 59.433 45.455 0.00 0.00 32.98 4.52
4279 4625 8.522830 CCTTGCCAAACTCTTATAAGAAAATGA 58.477 33.333 15.85 0.00 34.03 2.57
4342 4688 2.212869 TTTGAACAAAGCAGCAGCAG 57.787 45.000 3.17 0.00 45.49 4.24
4492 5791 6.691508 TCAGCTATGCATCGAACTATGTAAT 58.308 36.000 0.19 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.624352 AAGATGAACAGCGTATGCATTATT 57.376 33.333 3.54 0.00 46.23 1.40
1 2 6.293626 GGAAAGATGAACAGCGTATGCATTAT 60.294 38.462 3.54 0.00 46.23 1.28
2 3 5.007626 GGAAAGATGAACAGCGTATGCATTA 59.992 40.000 3.54 0.00 46.23 1.90
3 4 4.201950 GGAAAGATGAACAGCGTATGCATT 60.202 41.667 3.54 2.76 46.23 3.56
4 5 3.313526 GGAAAGATGAACAGCGTATGCAT 59.686 43.478 10.11 3.79 46.23 3.96
5 6 2.677836 GGAAAGATGAACAGCGTATGCA 59.322 45.455 10.11 0.00 46.23 3.96
6 7 2.677836 TGGAAAGATGAACAGCGTATGC 59.322 45.455 0.00 0.00 43.24 3.14
7 8 4.944962 TTGGAAAGATGAACAGCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
8 9 5.957842 TTTTGGAAAGATGAACAGCGTAT 57.042 34.783 0.00 0.00 0.00 3.06
9 10 5.471797 TGATTTTGGAAAGATGAACAGCGTA 59.528 36.000 0.00 0.00 0.00 4.42
10 11 4.278170 TGATTTTGGAAAGATGAACAGCGT 59.722 37.500 0.00 0.00 0.00 5.07
11 12 4.618489 GTGATTTTGGAAAGATGAACAGCG 59.382 41.667 0.00 0.00 0.00 5.18
12 13 4.618489 CGTGATTTTGGAAAGATGAACAGC 59.382 41.667 0.00 0.00 0.00 4.40
13 14 6.000891 TCGTGATTTTGGAAAGATGAACAG 57.999 37.500 0.00 0.00 0.00 3.16
14 15 6.573664 ATCGTGATTTTGGAAAGATGAACA 57.426 33.333 0.00 0.00 0.00 3.18
15 16 7.873739 AAATCGTGATTTTGGAAAGATGAAC 57.126 32.000 2.04 0.00 37.74 3.18
17 18 9.787532 GATAAAATCGTGATTTTGGAAAGATGA 57.212 29.630 23.90 7.15 46.80 2.92
18 19 9.571810 TGATAAAATCGTGATTTTGGAAAGATG 57.428 29.630 23.90 0.00 46.80 2.90
52 53 8.175716 GCTGAAATAAGTAACCATGTGAGTTAC 58.824 37.037 12.83 12.83 46.45 2.50
53 54 7.880713 TGCTGAAATAAGTAACCATGTGAGTTA 59.119 33.333 0.00 0.00 0.00 2.24
54 55 6.714810 TGCTGAAATAAGTAACCATGTGAGTT 59.285 34.615 0.00 0.00 0.00 3.01
55 56 6.237901 TGCTGAAATAAGTAACCATGTGAGT 58.762 36.000 0.00 0.00 0.00 3.41
56 57 6.741992 TGCTGAAATAAGTAACCATGTGAG 57.258 37.500 0.00 0.00 0.00 3.51
57 58 6.883756 TGATGCTGAAATAAGTAACCATGTGA 59.116 34.615 0.00 0.00 0.00 3.58
58 59 7.087409 TGATGCTGAAATAAGTAACCATGTG 57.913 36.000 0.00 0.00 0.00 3.21
59 60 7.701539 TTGATGCTGAAATAAGTAACCATGT 57.298 32.000 0.00 0.00 0.00 3.21
60 61 8.984891 TTTTGATGCTGAAATAAGTAACCATG 57.015 30.769 0.00 0.00 0.00 3.66
61 62 8.806146 ACTTTTGATGCTGAAATAAGTAACCAT 58.194 29.630 0.00 0.00 0.00 3.55
62 63 8.177119 ACTTTTGATGCTGAAATAAGTAACCA 57.823 30.769 0.00 0.00 0.00 3.67
67 68 8.629158 TGTGTAACTTTTGATGCTGAAATAAGT 58.371 29.630 0.00 0.00 38.04 2.24
68 69 9.630098 ATGTGTAACTTTTGATGCTGAAATAAG 57.370 29.630 0.00 0.00 38.04 1.73
69 70 9.409312 CATGTGTAACTTTTGATGCTGAAATAA 57.591 29.630 0.00 0.00 38.04 1.40
70 71 8.575589 ACATGTGTAACTTTTGATGCTGAAATA 58.424 29.630 0.00 0.00 38.04 1.40
71 72 7.383029 CACATGTGTAACTTTTGATGCTGAAAT 59.617 33.333 18.03 0.00 38.04 2.17
72 73 6.696583 CACATGTGTAACTTTTGATGCTGAAA 59.303 34.615 18.03 0.00 38.04 2.69
73 74 6.183360 ACACATGTGTAACTTTTGATGCTGAA 60.183 34.615 29.66 0.00 42.90 3.02
74 75 5.299028 ACACATGTGTAACTTTTGATGCTGA 59.701 36.000 29.66 0.00 42.90 4.26
75 76 5.522456 ACACATGTGTAACTTTTGATGCTG 58.478 37.500 29.66 0.00 42.90 4.41
76 77 5.772825 ACACATGTGTAACTTTTGATGCT 57.227 34.783 29.66 0.00 42.90 3.79
141 142 7.592903 GCCAAAATGTTGTTTTGAAGTTTCAAA 59.407 29.630 14.27 14.27 42.08 2.69
142 143 7.080724 GCCAAAATGTTGTTTTGAAGTTTCAA 58.919 30.769 13.20 3.28 40.73 2.69
143 144 6.205464 TGCCAAAATGTTGTTTTGAAGTTTCA 59.795 30.769 13.20 0.00 40.73 2.69
144 145 6.522855 GTGCCAAAATGTTGTTTTGAAGTTTC 59.477 34.615 13.20 0.00 40.73 2.78
145 146 6.016777 TGTGCCAAAATGTTGTTTTGAAGTTT 60.017 30.769 13.20 0.00 40.73 2.66
146 147 5.471456 TGTGCCAAAATGTTGTTTTGAAGTT 59.529 32.000 13.20 0.00 40.73 2.66
147 148 4.999950 TGTGCCAAAATGTTGTTTTGAAGT 59.000 33.333 13.20 0.00 40.73 3.01
148 149 5.122082 ACTGTGCCAAAATGTTGTTTTGAAG 59.878 36.000 13.20 8.38 40.73 3.02
149 150 4.999950 ACTGTGCCAAAATGTTGTTTTGAA 59.000 33.333 13.20 1.18 40.73 2.69
150 151 4.573900 ACTGTGCCAAAATGTTGTTTTGA 58.426 34.783 13.20 0.00 40.73 2.69
151 152 4.943142 ACTGTGCCAAAATGTTGTTTTG 57.057 36.364 6.33 6.33 38.68 2.44
152 153 4.999950 TGAACTGTGCCAAAATGTTGTTTT 59.000 33.333 0.00 0.00 32.40 2.43
153 154 4.573900 TGAACTGTGCCAAAATGTTGTTT 58.426 34.783 0.00 0.00 32.40 2.83
154 155 4.199432 TGAACTGTGCCAAAATGTTGTT 57.801 36.364 0.00 0.00 32.40 2.83
155 156 3.883830 TGAACTGTGCCAAAATGTTGT 57.116 38.095 0.00 0.00 32.40 3.32
156 157 5.542616 TTTTGAACTGTGCCAAAATGTTG 57.457 34.783 13.72 0.00 37.35 3.33
176 177 2.427095 GGTGCATTCGAGCCCTATTTTT 59.573 45.455 0.00 0.00 0.00 1.94
177 178 2.024414 GGTGCATTCGAGCCCTATTTT 58.976 47.619 0.00 0.00 0.00 1.82
178 179 1.680338 GGTGCATTCGAGCCCTATTT 58.320 50.000 0.00 0.00 0.00 1.40
179 180 0.179018 GGGTGCATTCGAGCCCTATT 60.179 55.000 0.56 0.00 38.12 1.73
180 181 1.451936 GGGTGCATTCGAGCCCTAT 59.548 57.895 0.56 0.00 38.12 2.57
181 182 2.908015 GGGTGCATTCGAGCCCTA 59.092 61.111 0.56 0.00 38.12 3.53
182 183 4.473520 CGGGTGCATTCGAGCCCT 62.474 66.667 6.28 0.00 38.97 5.19
185 186 4.778143 ACCCGGGTGCATTCGAGC 62.778 66.667 29.69 0.00 0.00 5.03
186 187 2.046314 AACCCGGGTGCATTCGAG 60.046 61.111 31.05 0.00 0.00 4.04
187 188 2.046700 GAACCCGGGTGCATTCGA 60.047 61.111 31.05 0.00 0.00 3.71
188 189 3.131478 GGAACCCGGGTGCATTCG 61.131 66.667 33.33 0.47 0.00 3.34
189 190 1.182385 TTTGGAACCCGGGTGCATTC 61.182 55.000 33.33 23.19 0.00 2.67
190 191 1.152440 TTTGGAACCCGGGTGCATT 60.152 52.632 33.33 15.52 0.00 3.56
191 192 1.606313 CTTTGGAACCCGGGTGCAT 60.606 57.895 33.33 15.95 0.00 3.96
192 193 2.203422 CTTTGGAACCCGGGTGCA 60.203 61.111 33.33 21.88 0.00 4.57
193 194 2.203437 ACTTTGGAACCCGGGTGC 60.203 61.111 31.05 28.06 0.00 5.01
194 195 1.149627 TCACTTTGGAACCCGGGTG 59.850 57.895 31.05 16.58 0.00 4.61
195 196 1.149854 GTCACTTTGGAACCCGGGT 59.850 57.895 24.16 24.16 0.00 5.28
196 197 0.179001 AAGTCACTTTGGAACCCGGG 60.179 55.000 22.25 22.25 0.00 5.73
197 198 1.687563 AAAGTCACTTTGGAACCCGG 58.312 50.000 0.68 0.00 31.98 5.73
198 199 3.119280 ACAAAAAGTCACTTTGGAACCCG 60.119 43.478 2.78 0.00 37.96 5.28
199 200 4.465632 ACAAAAAGTCACTTTGGAACCC 57.534 40.909 2.78 0.00 37.96 4.11
200 201 6.203808 ACTACAAAAAGTCACTTTGGAACC 57.796 37.500 2.78 0.00 37.96 3.62
201 202 7.309920 TCAACTACAAAAAGTCACTTTGGAAC 58.690 34.615 2.78 0.00 37.96 3.62
202 203 7.455641 TCAACTACAAAAAGTCACTTTGGAA 57.544 32.000 2.78 0.00 37.96 3.53
203 204 7.455641 TTCAACTACAAAAAGTCACTTTGGA 57.544 32.000 2.78 0.00 37.96 3.53
204 205 8.702163 AATTCAACTACAAAAAGTCACTTTGG 57.298 30.769 2.78 2.07 37.96 3.28
205 206 9.956797 CAAATTCAACTACAAAAAGTCACTTTG 57.043 29.630 2.78 0.00 39.26 2.77
206 207 8.655970 GCAAATTCAACTACAAAAAGTCACTTT 58.344 29.630 0.00 0.00 34.94 2.66
207 208 8.034804 AGCAAATTCAACTACAAAAAGTCACTT 58.965 29.630 0.00 0.00 0.00 3.16
208 209 7.547227 AGCAAATTCAACTACAAAAAGTCACT 58.453 30.769 0.00 0.00 0.00 3.41
209 210 7.755582 AGCAAATTCAACTACAAAAAGTCAC 57.244 32.000 0.00 0.00 0.00 3.67
210 211 9.462174 CATAGCAAATTCAACTACAAAAAGTCA 57.538 29.630 0.00 0.00 0.00 3.41
211 212 9.463443 ACATAGCAAATTCAACTACAAAAAGTC 57.537 29.630 0.00 0.00 0.00 3.01
212 213 9.816354 AACATAGCAAATTCAACTACAAAAAGT 57.184 25.926 0.00 0.00 0.00 2.66
215 216 9.809096 TCAAACATAGCAAATTCAACTACAAAA 57.191 25.926 0.00 0.00 0.00 2.44
216 217 9.809096 TTCAAACATAGCAAATTCAACTACAAA 57.191 25.926 0.00 0.00 0.00 2.83
217 218 9.979578 ATTCAAACATAGCAAATTCAACTACAA 57.020 25.926 0.00 0.00 0.00 2.41
218 219 9.979578 AATTCAAACATAGCAAATTCAACTACA 57.020 25.926 0.00 0.00 0.00 2.74
255 256 9.755804 TCAAACATGTAATTCAAACTATGCAAA 57.244 25.926 0.00 0.00 0.00 3.68
256 257 9.755804 TTCAAACATGTAATTCAAACTATGCAA 57.244 25.926 0.00 0.00 0.00 4.08
257 258 9.755804 TTTCAAACATGTAATTCAAACTATGCA 57.244 25.926 0.00 0.00 0.00 3.96
272 273 9.337396 TCAACTAGTACTTCATTTCAAACATGT 57.663 29.630 0.00 0.00 0.00 3.21
275 276 9.607988 TCTTCAACTAGTACTTCATTTCAAACA 57.392 29.630 0.00 0.00 0.00 2.83
276 277 9.865484 GTCTTCAACTAGTACTTCATTTCAAAC 57.135 33.333 0.00 0.00 0.00 2.93
277 278 9.832445 AGTCTTCAACTAGTACTTCATTTCAAA 57.168 29.630 0.00 0.00 36.07 2.69
278 279 9.832445 AAGTCTTCAACTAGTACTTCATTTCAA 57.168 29.630 0.00 0.00 37.17 2.69
297 298 8.713271 CACACTTTTCCTATACTTCAAGTCTTC 58.287 37.037 0.00 0.00 0.00 2.87
298 299 7.173390 GCACACTTTTCCTATACTTCAAGTCTT 59.827 37.037 0.00 0.00 0.00 3.01
299 300 6.651225 GCACACTTTTCCTATACTTCAAGTCT 59.349 38.462 0.00 0.00 0.00 3.24
300 301 6.426937 TGCACACTTTTCCTATACTTCAAGTC 59.573 38.462 0.00 0.00 0.00 3.01
301 302 6.204882 GTGCACACTTTTCCTATACTTCAAGT 59.795 38.462 13.17 0.00 0.00 3.16
302 303 6.348540 GGTGCACACTTTTCCTATACTTCAAG 60.349 42.308 20.43 0.00 0.00 3.02
328 351 1.446366 GGGGGAGAGTTGCGTATCC 59.554 63.158 0.00 0.00 0.00 2.59
329 352 1.067582 CGGGGGAGAGTTGCGTATC 59.932 63.158 0.00 0.00 0.00 2.24
1190 1498 4.162690 GCGGGATGGCGTCTTCCT 62.163 66.667 20.08 0.00 37.37 3.36
1422 1730 7.439655 ACCGCTCTATATTCAAGATCAAGAAAC 59.560 37.037 0.00 0.00 0.00 2.78
1429 1737 7.897575 AATCAACCGCTCTATATTCAAGATC 57.102 36.000 0.00 0.00 0.00 2.75
1440 1748 2.492881 TCCGTGTAAATCAACCGCTCTA 59.507 45.455 0.00 0.00 0.00 2.43
1455 1763 4.141287 TCAAGAATTTCATTGGTCCGTGT 58.859 39.130 0.00 0.00 0.00 4.49
1468 1776 6.422701 TGAAACACGTCGTCTATCAAGAATTT 59.577 34.615 0.00 0.00 32.16 1.82
1531 1839 2.750166 GCTTTGGCTTCCTAGGAACTTC 59.250 50.000 20.72 12.54 36.04 3.01
1578 1886 1.873591 CCGGCCTTTCCATAAAGATCG 59.126 52.381 0.00 3.53 44.14 3.69
1676 1984 8.640651 CACATGACCCAAATCCATAAATCATTA 58.359 33.333 0.00 0.00 0.00 1.90
1683 1991 3.030291 GCCACATGACCCAAATCCATAA 58.970 45.455 0.00 0.00 0.00 1.90
1724 2032 1.471501 CGACCATGTTAGCTAGCAGCA 60.472 52.381 18.83 12.59 45.56 4.41
1971 2279 1.352017 ACTGGCATGGACTGTTCATGA 59.648 47.619 28.85 11.05 43.25 3.07
2270 2578 3.136763 CACTCATCTGGTGATATGCCAC 58.863 50.000 0.00 0.00 35.97 5.01
2277 2585 3.261643 TGTAAGTGCACTCATCTGGTGAT 59.738 43.478 21.95 2.37 35.97 3.06
2363 2671 6.389906 GGTTTAAATCCTGTGTCCTTCATTG 58.610 40.000 0.00 0.00 0.00 2.82
2397 2705 4.744137 GCTCTCATAACAGCAGAGTATGTG 59.256 45.833 0.00 0.00 36.75 3.21
2566 2874 3.129988 CCAGATTCTTCCATCAAGTTGCC 59.870 47.826 0.00 0.00 33.27 4.52
2661 2969 6.069673 TCCTCATCCTTGTATACAAACCATGT 60.070 38.462 18.55 0.81 46.36 3.21
2664 2972 6.177610 GTTCCTCATCCTTGTATACAAACCA 58.822 40.000 18.55 6.52 35.15 3.67
2666 2974 7.201732 CCATGTTCCTCATCCTTGTATACAAAC 60.202 40.741 18.55 11.04 33.15 2.93
2862 3170 5.993055 TCATGAGCAATCTTAATGGACTCA 58.007 37.500 0.00 0.00 37.13 3.41
2970 3278 0.682532 TTTGCACCAGGTCTGCACAA 60.683 50.000 4.19 1.12 44.32 3.33
3199 3507 3.318839 TCAATTGTCAACTCAGGCTTTGG 59.681 43.478 5.13 0.00 0.00 3.28
3267 3575 3.956744 ACTGAAAGCTTTATCCACCTCC 58.043 45.455 12.68 0.00 37.60 4.30
3324 3632 6.039717 ACAAATCAATGCAAGTAACAGTGTCT 59.960 34.615 0.00 0.00 34.83 3.41
3342 3650 8.821686 ATATCCCATAACAAGTTGACAAATCA 57.178 30.769 10.54 0.00 0.00 2.57
3487 3795 7.500992 TCTCATTTGTTGACTAACTGAGAAGT 58.499 34.615 0.00 0.00 40.09 3.01
3490 3798 7.445121 ACATCTCATTTGTTGACTAACTGAGA 58.555 34.615 9.27 9.27 43.62 3.27
3582 3891 6.123651 ACATTACCACAACAAAGTTAGACCA 58.876 36.000 0.00 0.00 0.00 4.02
3680 3993 3.270877 CCAGACCCTTAACTTCAATCGG 58.729 50.000 0.00 0.00 0.00 4.18
3687 4000 1.616994 GCATGCCCAGACCCTTAACTT 60.617 52.381 6.36 0.00 0.00 2.66
3761 4074 4.165565 TGAGAATGCCTTCATCCAGAGAAT 59.834 41.667 4.48 0.00 33.56 2.40
3766 4079 3.618351 ACTTGAGAATGCCTTCATCCAG 58.382 45.455 4.48 3.55 33.56 3.86
3829 4142 1.557443 GACTCGGCCACAAACACTCG 61.557 60.000 2.24 0.00 0.00 4.18
3835 4148 1.134220 AGTTTCAGACTCGGCCACAAA 60.134 47.619 2.24 0.00 31.20 2.83
3871 4185 6.042638 TCTCTTTCAACCTAATCCTCACAG 57.957 41.667 0.00 0.00 0.00 3.66
3888 4202 3.517500 GTGGTCTTCCTCCTGATCTCTTT 59.482 47.826 0.00 0.00 34.23 2.52
3948 4262 7.158021 CCATTTTTACCCACTGCAAATTTCTA 58.842 34.615 0.00 0.00 0.00 2.10
3991 4305 2.441750 GCCCCACATCTTCAACCCTATA 59.558 50.000 0.00 0.00 0.00 1.31
4067 4383 4.153117 GCGAGTCAAAGTCATTCTTCACAT 59.847 41.667 0.00 0.00 35.02 3.21
4122 4438 7.149973 TCTTCGACGGAAAAAGATTTTCTCTA 58.850 34.615 13.46 0.00 32.41 2.43
4135 4451 3.562141 TCAAATTGCTTCTTCGACGGAAA 59.438 39.130 0.00 0.00 0.00 3.13
4144 4460 5.771666 TCTCCATTGTCTCAAATTGCTTCTT 59.228 36.000 0.00 0.00 0.00 2.52
4311 4657 5.129485 TGCTTTGTTCAAAATTGGGAGGTTA 59.871 36.000 0.00 0.00 0.00 2.85
4342 4688 7.653311 GCCAGAATTTATGGAATGAATGGTTAC 59.347 37.037 14.18 0.00 40.51 2.50


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

AutoCloner maintained by Alex Coulton.