Multiple sequence alignment - TraesCS7B01G131500

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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 TraesCS7B01G131500 chr7B 100.000 2234 0 0 1 2234 158556240 158554007 0.000000e+00 4126.0
1 TraesCS7B01G131500 chr7B 85.095 1362 105 47 421 1723 158936527 158937849 0.000000e+00 1301.0
2 TraesCS7B01G131500 chr7B 83.448 290 35 9 1917 2199 158937853 158938136 7.920000e-65 257.0
3 TraesCS7B01G131500 chr7A 89.547 1789 113 33 496 2234 204668684 204666920 0.000000e+00 2200.0
4 TraesCS7B01G131500 chr7A 86.088 1186 78 42 421 1542 205123906 205125068 0.000000e+00 1195.0
5 TraesCS7B01G131500 chr7A 84.375 96 11 3 319 413 204671107 204671015 8.500000e-15 91.6
6 TraesCS7B01G131500 chr7D 87.763 997 62 25 319 1285 194795321 194794355 0.000000e+00 1110.0
7 TraesCS7B01G131500 chr7D 84.710 1138 100 36 442 1542 195278932 195280032 0.000000e+00 1070.0
8 TraesCS7B01G131500 chr7D 94.675 338 17 1 1897 2234 194791248 194790912 7.070000e-145 523.0
9 TraesCS7B01G131500 chr7D 80.103 774 78 42 758 1499 194792618 194791889 7.120000e-140 507.0
10 TraesCS7B01G131500 chr7D 84.956 339 37 12 1900 2230 194793783 194793451 4.600000e-87 331.0
11 TraesCS7B01G131500 chr7D 82.199 382 32 16 1534 1911 194791613 194791264 1.680000e-76 296.0
12 TraesCS7B01G131500 chr7D 84.188 234 7 4 1333 1542 194794222 194793995 1.350000e-47 200.0
13 TraesCS7B01G131500 chr6D 88.356 292 24 4 1 291 390249254 390249536 2.120000e-90 342.0
14 TraesCS7B01G131500 chr6D 85.374 294 32 6 7 295 458749142 458749429 6.030000e-76 294.0
15 TraesCS7B01G131500 chrUn 87.415 294 25 6 1 294 50335467 50335186 5.950000e-86 327.0
16 TraesCS7B01G131500 chr1B 86.577 298 28 6 1 298 647623812 647623527 3.580000e-83 318.0
17 TraesCS7B01G131500 chr5D 87.273 275 27 3 1 275 226956737 226957003 7.750000e-80 307.0
18 TraesCS7B01G131500 chr5D 90.171 234 14 3 67 300 504003993 504003769 1.680000e-76 296.0
19 TraesCS7B01G131500 chr6A 91.441 222 15 3 73 294 604314456 604314673 3.610000e-78 302.0
20 TraesCS7B01G131500 chr1D 85.522 297 29 5 1 293 298578164 298577878 4.660000e-77 298.0
21 TraesCS7B01G131500 chr3D 88.306 248 20 3 47 294 537935459 537935697 2.810000e-74 289.0


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 TraesCS7B01G131500 chr7B 158554007 158556240 2233 True 4126.0 4126 100.000000 1 2234 1 chr7B.!!$R1 2233
1 TraesCS7B01G131500 chr7B 158936527 158938136 1609 False 779.0 1301 84.271500 421 2199 2 chr7B.!!$F1 1778
2 TraesCS7B01G131500 chr7A 205123906 205125068 1162 False 1195.0 1195 86.088000 421 1542 1 chr7A.!!$F1 1121
3 TraesCS7B01G131500 chr7A 204666920 204671107 4187 True 1145.8 2200 86.961000 319 2234 2 chr7A.!!$R1 1915
4 TraesCS7B01G131500 chr7D 195278932 195280032 1100 False 1070.0 1070 84.710000 442 1542 1 chr7D.!!$F1 1100
5 TraesCS7B01G131500 chr7D 194790912 194795321 4409 True 494.5 1110 85.647333 319 2234 6 chr7D.!!$R1 1915

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
80 81 0.325671 TCACTAGGGAGCAGGGGAAG 60.326 60.0 0.0 0.0 0.0 3.46 F
650 2932 0.392336 GAGGCGATGCAGATTCTCCT 59.608 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1147 3487 0.320073 TCCACGTCTTTTACCAGCCG 60.320 55.000 0.0 0.0 0.0 5.52 R
1668 6562 1.078426 GGTTGGCTATGCTCGGTGT 60.078 57.895 0.0 0.0 0.0 4.16 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
30 31 3.186047 GGGACGACAACGCCGATG 61.186 66.667 0.00 0.00 43.96 3.84
31 32 3.186047 GGACGACAACGCCGATGG 61.186 66.667 0.00 0.00 43.96 3.51
32 33 3.849953 GACGACAACGCCGATGGC 61.850 66.667 0.00 0.00 46.75 4.40
42 43 4.529219 CCGATGGCAGCCGCTGTA 62.529 66.667 21.29 11.52 38.60 2.74
43 44 2.963854 CGATGGCAGCCGCTGTAG 60.964 66.667 21.29 5.46 38.60 2.74
44 45 2.501128 GATGGCAGCCGCTGTAGA 59.499 61.111 21.29 6.43 38.60 2.59
45 46 1.593750 GATGGCAGCCGCTGTAGAG 60.594 63.158 21.29 0.00 38.60 2.43
46 47 2.985512 GATGGCAGCCGCTGTAGAGG 62.986 65.000 21.29 0.00 38.60 3.69
47 48 4.537433 GGCAGCCGCTGTAGAGGG 62.537 72.222 21.29 0.00 38.60 4.30
55 56 3.541713 CTGTAGAGGGCCGGCCTC 61.542 72.222 42.70 34.19 36.10 4.70
66 67 3.129502 CGGCCTCGACGGTCACTA 61.130 66.667 9.10 0.00 37.17 2.74
67 68 2.799371 GGCCTCGACGGTCACTAG 59.201 66.667 9.10 2.38 37.34 2.57
68 69 2.772691 GGCCTCGACGGTCACTAGG 61.773 68.421 9.10 11.97 37.34 3.02
69 70 2.772691 GCCTCGACGGTCACTAGGG 61.773 68.421 17.79 9.26 34.25 3.53
70 71 1.077930 CCTCGACGGTCACTAGGGA 60.078 63.158 9.10 0.00 0.00 4.20
71 72 1.096386 CCTCGACGGTCACTAGGGAG 61.096 65.000 9.10 5.36 0.00 4.30
72 73 1.716826 CTCGACGGTCACTAGGGAGC 61.717 65.000 14.38 14.38 0.00 4.70
73 74 2.044555 CGACGGTCACTAGGGAGCA 61.045 63.158 23.23 0.00 35.06 4.26
74 75 1.810532 GACGGTCACTAGGGAGCAG 59.189 63.158 23.23 17.27 35.06 4.24
75 76 1.668101 GACGGTCACTAGGGAGCAGG 61.668 65.000 23.23 10.84 35.06 4.85
76 77 2.427245 CGGTCACTAGGGAGCAGGG 61.427 68.421 23.23 4.16 35.06 4.45
77 78 2.066999 GGTCACTAGGGAGCAGGGG 61.067 68.421 19.24 0.00 35.43 4.79
78 79 1.001760 GTCACTAGGGAGCAGGGGA 59.998 63.158 0.00 0.00 0.00 4.81
79 80 0.617820 GTCACTAGGGAGCAGGGGAA 60.618 60.000 0.00 0.00 0.00 3.97
80 81 0.325671 TCACTAGGGAGCAGGGGAAG 60.326 60.000 0.00 0.00 0.00 3.46
81 82 1.690985 ACTAGGGAGCAGGGGAAGC 60.691 63.158 0.00 0.00 0.00 3.86
82 83 2.764128 TAGGGAGCAGGGGAAGCG 60.764 66.667 0.00 0.00 37.01 4.68
124 125 2.936032 GTGGGGTGGAGGGCTCTT 60.936 66.667 0.00 0.00 0.00 2.85
125 126 2.610859 TGGGGTGGAGGGCTCTTC 60.611 66.667 0.00 0.00 0.00 2.87
126 127 2.610859 GGGGTGGAGGGCTCTTCA 60.611 66.667 0.00 0.00 0.00 3.02
127 128 2.674220 GGGGTGGAGGGCTCTTCAG 61.674 68.421 0.00 0.00 0.00 3.02
128 129 1.613630 GGGTGGAGGGCTCTTCAGA 60.614 63.158 0.00 0.00 0.00 3.27
129 130 1.621672 GGGTGGAGGGCTCTTCAGAG 61.622 65.000 0.00 0.00 44.75 3.35
130 131 1.621672 GGTGGAGGGCTCTTCAGAGG 61.622 65.000 0.00 0.00 42.29 3.69
131 132 0.907230 GTGGAGGGCTCTTCAGAGGT 60.907 60.000 0.00 0.00 42.29 3.85
132 133 0.616111 TGGAGGGCTCTTCAGAGGTC 60.616 60.000 0.00 0.00 42.29 3.85
133 134 1.671901 GGAGGGCTCTTCAGAGGTCG 61.672 65.000 5.97 0.00 42.29 4.79
134 135 0.681564 GAGGGCTCTTCAGAGGTCGA 60.682 60.000 5.97 0.00 42.29 4.20
135 136 0.682855 AGGGCTCTTCAGAGGTCGAG 60.683 60.000 5.97 0.00 42.29 4.04
136 137 1.671901 GGGCTCTTCAGAGGTCGAGG 61.672 65.000 5.97 0.00 42.29 4.63
137 138 1.140804 GCTCTTCAGAGGTCGAGGC 59.859 63.158 5.97 0.00 42.29 4.70
138 139 1.431440 CTCTTCAGAGGTCGAGGCG 59.569 63.158 0.00 0.00 38.48 5.52
139 140 1.999071 CTCTTCAGAGGTCGAGGCGG 61.999 65.000 0.00 0.00 38.48 6.13
140 141 3.068691 TTCAGAGGTCGAGGCGGG 61.069 66.667 0.00 0.00 0.00 6.13
141 142 3.881019 TTCAGAGGTCGAGGCGGGT 62.881 63.158 0.00 0.00 0.00 5.28
142 143 4.135153 CAGAGGTCGAGGCGGGTG 62.135 72.222 0.00 0.00 0.00 4.61
224 225 4.798682 GGCGGGGGAGGAGGAGAA 62.799 72.222 0.00 0.00 0.00 2.87
225 226 3.157949 GCGGGGGAGGAGGAGAAG 61.158 72.222 0.00 0.00 0.00 2.85
226 227 2.444895 CGGGGGAGGAGGAGAAGG 60.445 72.222 0.00 0.00 0.00 3.46
227 228 2.040359 GGGGGAGGAGGAGAAGGG 60.040 72.222 0.00 0.00 0.00 3.95
228 229 2.770475 GGGGAGGAGGAGAAGGGC 60.770 72.222 0.00 0.00 0.00 5.19
229 230 2.041265 GGGAGGAGGAGAAGGGCA 59.959 66.667 0.00 0.00 0.00 5.36
230 231 2.069430 GGGAGGAGGAGAAGGGCAG 61.069 68.421 0.00 0.00 0.00 4.85
231 232 2.069430 GGAGGAGGAGAAGGGCAGG 61.069 68.421 0.00 0.00 0.00 4.85
232 233 2.690510 AGGAGGAGAAGGGCAGGC 60.691 66.667 0.00 0.00 0.00 4.85
233 234 3.803162 GGAGGAGAAGGGCAGGCC 61.803 72.222 4.33 4.33 0.00 5.19
234 235 4.168291 GAGGAGAAGGGCAGGCCG 62.168 72.222 7.51 0.00 36.85 6.13
253 254 4.832608 GGACCGGCGGCACCTAAG 62.833 72.222 28.71 0.00 35.61 2.18
254 255 4.832608 GACCGGCGGCACCTAAGG 62.833 72.222 28.71 2.91 35.61 2.69
256 257 4.404098 CCGGCGGCACCTAAGGTT 62.404 66.667 15.42 0.00 31.02 3.50
257 258 2.359478 CGGCGGCACCTAAGGTTT 60.359 61.111 10.53 0.00 31.02 3.27
258 259 2.396157 CGGCGGCACCTAAGGTTTC 61.396 63.158 10.53 0.00 31.02 2.78
259 260 2.396157 GGCGGCACCTAAGGTTTCG 61.396 63.158 3.07 0.00 31.02 3.46
260 261 3.035576 GCGGCACCTAAGGTTTCGC 62.036 63.158 0.00 0.00 43.23 4.70
261 262 2.396157 CGGCACCTAAGGTTTCGCC 61.396 63.158 0.00 0.00 38.45 5.54
262 263 2.044555 GGCACCTAAGGTTTCGCCC 61.045 63.158 0.00 0.00 36.61 6.13
263 264 2.396157 GCACCTAAGGTTTCGCCCG 61.396 63.158 0.00 0.00 38.26 6.13
264 265 2.046604 ACCTAAGGTTTCGCCCGC 60.047 61.111 0.00 0.00 38.26 6.13
265 266 3.192922 CCTAAGGTTTCGCCCGCG 61.193 66.667 0.00 0.00 38.26 6.46
307 308 3.151022 GGGGACCGAGAGCTGGAG 61.151 72.222 0.00 0.00 40.86 3.86
308 309 3.844090 GGGACCGAGAGCTGGAGC 61.844 72.222 0.00 0.00 42.49 4.70
470 2600 4.360951 ACGGTCCAAAGAAGAATTACCA 57.639 40.909 0.00 0.00 0.00 3.25
583 2864 6.670027 ACAAATAGTCTCAGTGAAGATAGGGT 59.330 38.462 0.00 0.00 0.00 4.34
605 2886 4.584743 GTGACAAAAAGAGATGAAAGGGGT 59.415 41.667 0.00 0.00 0.00 4.95
650 2932 0.392336 GAGGCGATGCAGATTCTCCT 59.608 55.000 0.00 0.00 0.00 3.69
712 3021 4.530161 CCTCTCCTCTCCTTTCTTCTTTCA 59.470 45.833 0.00 0.00 0.00 2.69
847 3156 5.482175 CCTCTCCTCCCACTATATAAGTTGG 59.518 48.000 0.00 0.00 41.49 3.77
859 3168 2.666272 TAAGTTGGACCATTGCCACA 57.334 45.000 0.00 0.00 34.56 4.17
875 3184 2.489329 GCCACACACTCTTGTTGCATAT 59.511 45.455 0.00 0.00 37.91 1.78
905 3219 0.811616 CAAGCCCGGTGATCTAGCAC 60.812 60.000 0.00 0.00 38.05 4.40
959 3299 1.202452 GCCATTGCAATCCACCTTAGC 60.202 52.381 9.53 0.00 37.47 3.09
964 3304 2.446435 TGCAATCCACCTTAGCTTTCC 58.554 47.619 0.00 0.00 0.00 3.13
985 3325 1.597742 TCTTGTTGAGAAGCCACAGC 58.402 50.000 0.00 0.00 40.32 4.40
1030 3370 1.136252 CGTGGACATTCAAGCAGAACG 60.136 52.381 0.00 0.00 39.49 3.95
1051 3391 1.664965 GTGTTCGAGAAGGCGCTGT 60.665 57.895 7.64 0.00 0.00 4.40
1055 3395 2.765250 TTCGAGAAGGCGCTGTCCAC 62.765 60.000 7.64 1.88 0.00 4.02
1059 3399 1.153628 GAAGGCGCTGTCCACGTAT 60.154 57.895 7.64 0.00 0.00 3.06
1133 3473 1.208052 CAAGTCGGTGGAGGATGTGAT 59.792 52.381 0.00 0.00 0.00 3.06
1136 3476 1.114627 TCGGTGGAGGATGTGATGAG 58.885 55.000 0.00 0.00 0.00 2.90
1142 3482 2.042464 GGAGGATGTGATGAGGCACTA 58.958 52.381 0.00 0.00 41.55 2.74
1145 3485 3.311990 AGGATGTGATGAGGCACTATGA 58.688 45.455 0.00 0.00 41.55 2.15
1147 3487 2.609427 TGTGATGAGGCACTATGAGC 57.391 50.000 0.00 0.00 41.55 4.26
1148 3488 1.202452 TGTGATGAGGCACTATGAGCG 60.202 52.381 0.00 0.00 41.55 5.03
1188 3528 2.285026 CGAGATTCATACAAACGGTGCG 60.285 50.000 0.00 0.00 0.00 5.34
1279 3622 4.442375 AGTAGTCTGTCCGAAACTCATG 57.558 45.455 0.00 0.00 0.00 3.07
1280 3623 2.751166 AGTCTGTCCGAAACTCATGG 57.249 50.000 0.00 0.00 0.00 3.66
1282 3625 2.368875 AGTCTGTCCGAAACTCATGGTT 59.631 45.455 0.00 0.00 40.28 3.67
1283 3626 2.737252 GTCTGTCCGAAACTCATGGTTC 59.263 50.000 0.00 0.00 37.12 3.62
1285 3628 3.830178 TCTGTCCGAAACTCATGGTTCTA 59.170 43.478 0.00 0.00 37.12 2.10
1286 3629 4.466370 TCTGTCCGAAACTCATGGTTCTAT 59.534 41.667 0.00 0.00 37.12 1.98
1287 3630 4.755411 TGTCCGAAACTCATGGTTCTATC 58.245 43.478 0.00 0.00 37.12 2.08
1288 3631 4.120589 GTCCGAAACTCATGGTTCTATCC 58.879 47.826 0.00 0.00 37.12 2.59
1289 3632 3.772572 TCCGAAACTCATGGTTCTATCCA 59.227 43.478 0.00 0.00 42.01 3.41
1290 3633 4.224147 TCCGAAACTCATGGTTCTATCCAA 59.776 41.667 0.00 0.00 41.09 3.53
1291 3634 4.332819 CCGAAACTCATGGTTCTATCCAAC 59.667 45.833 0.00 0.00 41.09 3.77
1292 3635 4.935205 CGAAACTCATGGTTCTATCCAACA 59.065 41.667 0.00 0.00 41.09 3.33
1293 3636 5.586243 CGAAACTCATGGTTCTATCCAACAT 59.414 40.000 0.00 0.00 41.09 2.71
1294 3637 6.094048 CGAAACTCATGGTTCTATCCAACATT 59.906 38.462 0.00 0.00 41.09 2.71
1295 3638 7.362056 CGAAACTCATGGTTCTATCCAACATTT 60.362 37.037 0.00 0.00 41.09 2.32
1296 3639 8.877864 AAACTCATGGTTCTATCCAACATTTA 57.122 30.769 0.00 0.00 41.09 1.40
1297 3640 7.865706 ACTCATGGTTCTATCCAACATTTAC 57.134 36.000 0.00 0.00 41.09 2.01
1298 3641 6.828785 ACTCATGGTTCTATCCAACATTTACC 59.171 38.462 0.00 0.00 41.09 2.85
1319 3662 2.494471 CACTGTTCCATCCATGCACATT 59.506 45.455 0.00 0.00 0.00 2.71
1329 3672 2.953648 TCCATGCACATTCATCATCACC 59.046 45.455 0.00 0.00 0.00 4.02
1330 3673 2.287368 CCATGCACATTCATCATCACCG 60.287 50.000 0.00 0.00 0.00 4.94
1402 3844 1.817099 CGGCCTGGCTAGCTTTCTG 60.817 63.158 19.68 2.08 0.00 3.02
1461 3924 7.290014 TCCTTCACTAATATGCATGGTCTCTTA 59.710 37.037 10.16 0.00 0.00 2.10
1627 6513 7.833786 TCTTGAGAAGCAAATTTTAGCATGAT 58.166 30.769 0.00 0.00 35.74 2.45
1719 6617 6.607689 TGCTTTTTCACTTACGTATCATTGG 58.392 36.000 0.00 0.00 0.00 3.16
1734 6632 2.705658 TCATTGGGGAGATGTCGCTTAT 59.294 45.455 6.87 0.00 35.92 1.73
1736 6634 4.346709 TCATTGGGGAGATGTCGCTTATAA 59.653 41.667 6.87 0.00 35.92 0.98
1741 6639 4.932200 GGGGAGATGTCGCTTATAATTCAG 59.068 45.833 6.87 0.00 35.92 3.02
1750 6648 7.426410 TGTCGCTTATAATTCAGGACTTCTAG 58.574 38.462 0.00 0.00 0.00 2.43
1817 6716 3.828451 ACTACAGAAAAACATGGCATGCT 59.172 39.130 26.70 12.91 0.00 3.79
1854 6753 6.045318 TGCAAGCTAAACAGATCTCTATGTC 58.955 40.000 0.00 0.00 0.00 3.06
2068 7001 9.243105 GCCCTTTCTGATAAATATTAGCCAATA 57.757 33.333 0.00 0.00 0.00 1.90
2090 7023 8.398665 CAATATGGTTAAACCTTTACTGAGAGC 58.601 37.037 0.00 0.00 39.58 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.789075 ATCGGCGTTGTCGTCCCG 62.789 66.667 6.85 0.00 41.51 5.14
13 14 3.186047 CATCGGCGTTGTCGTCCC 61.186 66.667 6.85 0.00 38.56 4.46
14 15 3.186047 CCATCGGCGTTGTCGTCC 61.186 66.667 15.96 0.00 38.56 4.79
15 16 3.849953 GCCATCGGCGTTGTCGTC 61.850 66.667 15.96 0.28 39.62 4.20
25 26 4.529219 TACAGCGGCTGCCATCGG 62.529 66.667 28.80 12.45 44.31 4.18
26 27 2.963854 CTACAGCGGCTGCCATCG 60.964 66.667 28.80 8.07 44.31 3.84
27 28 1.593750 CTCTACAGCGGCTGCCATC 60.594 63.158 28.80 9.67 44.31 3.51
28 29 2.503061 CTCTACAGCGGCTGCCAT 59.497 61.111 28.80 13.05 44.31 4.40
29 30 3.774528 CCTCTACAGCGGCTGCCA 61.775 66.667 28.80 16.26 44.31 4.92
30 31 4.537433 CCCTCTACAGCGGCTGCC 62.537 72.222 28.80 9.11 44.31 4.85
32 33 4.537433 GGCCCTCTACAGCGGCTG 62.537 72.222 27.43 27.43 42.58 4.85
49 50 3.109612 CTAGTGACCGTCGAGGCCG 62.110 68.421 0.00 0.00 46.52 6.13
50 51 2.772691 CCTAGTGACCGTCGAGGCC 61.773 68.421 0.00 0.00 46.52 5.19
51 52 2.772691 CCCTAGTGACCGTCGAGGC 61.773 68.421 0.00 0.00 46.52 4.70
53 54 1.716826 GCTCCCTAGTGACCGTCGAG 61.717 65.000 0.00 0.00 0.00 4.04
54 55 1.748122 GCTCCCTAGTGACCGTCGA 60.748 63.158 0.00 0.00 0.00 4.20
55 56 1.994507 CTGCTCCCTAGTGACCGTCG 61.995 65.000 0.00 0.00 0.00 5.12
56 57 1.668101 CCTGCTCCCTAGTGACCGTC 61.668 65.000 0.00 0.00 0.00 4.79
57 58 1.682684 CCTGCTCCCTAGTGACCGT 60.683 63.158 0.00 0.00 0.00 4.83
58 59 2.427245 CCCTGCTCCCTAGTGACCG 61.427 68.421 0.00 0.00 0.00 4.79
59 60 2.066999 CCCCTGCTCCCTAGTGACC 61.067 68.421 0.00 0.00 0.00 4.02
60 61 0.617820 TTCCCCTGCTCCCTAGTGAC 60.618 60.000 0.00 0.00 0.00 3.67
61 62 0.325671 CTTCCCCTGCTCCCTAGTGA 60.326 60.000 0.00 0.00 0.00 3.41
62 63 1.977293 GCTTCCCCTGCTCCCTAGTG 61.977 65.000 0.00 0.00 0.00 2.74
63 64 1.690985 GCTTCCCCTGCTCCCTAGT 60.691 63.158 0.00 0.00 0.00 2.57
64 65 2.801631 CGCTTCCCCTGCTCCCTAG 61.802 68.421 0.00 0.00 0.00 3.02
65 66 2.764128 CGCTTCCCCTGCTCCCTA 60.764 66.667 0.00 0.00 0.00 3.53
107 108 2.936032 AAGAGCCCTCCACCCCAC 60.936 66.667 0.00 0.00 0.00 4.61
108 109 2.610859 GAAGAGCCCTCCACCCCA 60.611 66.667 0.00 0.00 0.00 4.96
109 110 2.610859 TGAAGAGCCCTCCACCCC 60.611 66.667 0.00 0.00 0.00 4.95
110 111 1.613630 TCTGAAGAGCCCTCCACCC 60.614 63.158 0.00 0.00 0.00 4.61
111 112 1.621672 CCTCTGAAGAGCCCTCCACC 61.622 65.000 1.54 0.00 40.75 4.61
112 113 0.907230 ACCTCTGAAGAGCCCTCCAC 60.907 60.000 1.54 0.00 40.75 4.02
113 114 0.616111 GACCTCTGAAGAGCCCTCCA 60.616 60.000 1.54 0.00 40.75 3.86
114 115 1.671901 CGACCTCTGAAGAGCCCTCC 61.672 65.000 1.54 0.00 40.75 4.30
115 116 0.681564 TCGACCTCTGAAGAGCCCTC 60.682 60.000 1.54 0.00 40.75 4.30
116 117 0.682855 CTCGACCTCTGAAGAGCCCT 60.683 60.000 1.54 0.00 40.75 5.19
117 118 1.671901 CCTCGACCTCTGAAGAGCCC 61.672 65.000 1.54 0.00 40.75 5.19
118 119 1.813192 CCTCGACCTCTGAAGAGCC 59.187 63.158 1.54 0.00 40.75 4.70
119 120 1.140804 GCCTCGACCTCTGAAGAGC 59.859 63.158 1.54 0.00 40.75 4.09
120 121 1.431440 CGCCTCGACCTCTGAAGAG 59.569 63.158 0.00 0.00 41.71 2.85
121 122 2.046864 CCGCCTCGACCTCTGAAGA 61.047 63.158 0.00 0.00 0.00 2.87
122 123 2.492090 CCGCCTCGACCTCTGAAG 59.508 66.667 0.00 0.00 0.00 3.02
123 124 3.068691 CCCGCCTCGACCTCTGAA 61.069 66.667 0.00 0.00 0.00 3.02
124 125 4.361971 ACCCGCCTCGACCTCTGA 62.362 66.667 0.00 0.00 0.00 3.27
125 126 4.135153 CACCCGCCTCGACCTCTG 62.135 72.222 0.00 0.00 0.00 3.35
207 208 4.798682 TTCTCCTCCTCCCCCGCC 62.799 72.222 0.00 0.00 0.00 6.13
208 209 3.157949 CTTCTCCTCCTCCCCCGC 61.158 72.222 0.00 0.00 0.00 6.13
209 210 2.444895 CCTTCTCCTCCTCCCCCG 60.445 72.222 0.00 0.00 0.00 5.73
210 211 2.040359 CCCTTCTCCTCCTCCCCC 60.040 72.222 0.00 0.00 0.00 5.40
211 212 2.770475 GCCCTTCTCCTCCTCCCC 60.770 72.222 0.00 0.00 0.00 4.81
212 213 2.041265 TGCCCTTCTCCTCCTCCC 59.959 66.667 0.00 0.00 0.00 4.30
213 214 2.069430 CCTGCCCTTCTCCTCCTCC 61.069 68.421 0.00 0.00 0.00 4.30
214 215 2.741055 GCCTGCCCTTCTCCTCCTC 61.741 68.421 0.00 0.00 0.00 3.71
215 216 2.690510 GCCTGCCCTTCTCCTCCT 60.691 66.667 0.00 0.00 0.00 3.69
216 217 3.803162 GGCCTGCCCTTCTCCTCC 61.803 72.222 0.00 0.00 0.00 4.30
217 218 4.168291 CGGCCTGCCCTTCTCCTC 62.168 72.222 0.00 0.00 0.00 3.71
236 237 4.832608 CTTAGGTGCCGCCGGTCC 62.833 72.222 4.45 8.25 43.70 4.46
237 238 4.832608 CCTTAGGTGCCGCCGGTC 62.833 72.222 4.45 0.00 43.70 4.79
239 240 3.912745 AAACCTTAGGTGCCGCCGG 62.913 63.158 3.99 0.00 43.70 6.13
240 241 2.359478 AAACCTTAGGTGCCGCCG 60.359 61.111 3.99 0.00 43.70 6.46
241 242 2.396157 CGAAACCTTAGGTGCCGCC 61.396 63.158 3.99 0.00 35.34 6.13
242 243 3.035576 GCGAAACCTTAGGTGCCGC 62.036 63.158 25.94 25.94 44.74 6.53
243 244 2.396157 GGCGAAACCTTAGGTGCCG 61.396 63.158 14.23 15.92 33.66 5.69
244 245 2.044555 GGGCGAAACCTTAGGTGCC 61.045 63.158 19.41 19.41 40.30 5.01
245 246 2.396157 CGGGCGAAACCTTAGGTGC 61.396 63.158 3.99 3.93 35.34 5.01
246 247 2.396157 GCGGGCGAAACCTTAGGTG 61.396 63.158 3.99 0.00 35.34 4.00
247 248 2.046604 GCGGGCGAAACCTTAGGT 60.047 61.111 0.00 0.00 39.10 3.08
248 249 3.192922 CGCGGGCGAAACCTTAGG 61.193 66.667 7.38 0.00 42.83 2.69
249 250 2.125832 TCGCGGGCGAAACCTTAG 60.126 61.111 14.01 0.00 46.01 2.18
289 290 4.779733 TCCAGCTCTCGGTCCCCC 62.780 72.222 0.00 0.00 0.00 5.40
290 291 3.151022 CTCCAGCTCTCGGTCCCC 61.151 72.222 0.00 0.00 0.00 4.81
291 292 3.844090 GCTCCAGCTCTCGGTCCC 61.844 72.222 0.00 0.00 38.21 4.46
292 293 4.200283 CGCTCCAGCTCTCGGTCC 62.200 72.222 0.00 0.00 39.32 4.46
293 294 3.134792 TCGCTCCAGCTCTCGGTC 61.135 66.667 0.00 0.00 39.32 4.79
294 295 3.444805 GTCGCTCCAGCTCTCGGT 61.445 66.667 0.00 0.00 39.32 4.69
295 296 2.705821 AAGTCGCTCCAGCTCTCGG 61.706 63.158 0.00 0.00 39.32 4.63
296 297 1.515952 CAAGTCGCTCCAGCTCTCG 60.516 63.158 0.00 0.00 39.32 4.04
297 298 1.153667 CCAAGTCGCTCCAGCTCTC 60.154 63.158 0.00 0.00 39.32 3.20
298 299 1.603236 CTCCAAGTCGCTCCAGCTCT 61.603 60.000 0.00 0.00 39.32 4.09
299 300 1.153667 CTCCAAGTCGCTCCAGCTC 60.154 63.158 0.00 0.00 39.32 4.09
300 301 1.476007 AACTCCAAGTCGCTCCAGCT 61.476 55.000 0.00 0.00 39.32 4.24
301 302 0.603975 AAACTCCAAGTCGCTCCAGC 60.604 55.000 0.00 0.00 37.78 4.85
302 303 1.801178 GAAAACTCCAAGTCGCTCCAG 59.199 52.381 0.00 0.00 0.00 3.86
303 304 1.140052 TGAAAACTCCAAGTCGCTCCA 59.860 47.619 0.00 0.00 0.00 3.86
304 305 1.531578 GTGAAAACTCCAAGTCGCTCC 59.468 52.381 0.00 0.00 0.00 4.70
305 306 2.484889 AGTGAAAACTCCAAGTCGCTC 58.515 47.619 0.00 0.00 0.00 5.03
306 307 2.614057 CAAGTGAAAACTCCAAGTCGCT 59.386 45.455 0.00 0.00 32.34 4.93
307 308 2.612212 TCAAGTGAAAACTCCAAGTCGC 59.388 45.455 0.00 0.00 0.00 5.19
308 309 4.332819 ACTTCAAGTGAAAACTCCAAGTCG 59.667 41.667 0.00 0.00 33.07 4.18
309 310 5.819825 ACTTCAAGTGAAAACTCCAAGTC 57.180 39.130 0.00 0.00 33.07 3.01
310 311 6.590234 AAACTTCAAGTGAAAACTCCAAGT 57.410 33.333 0.00 0.00 33.07 3.16
311 312 8.458843 TCTTAAACTTCAAGTGAAAACTCCAAG 58.541 33.333 0.00 0.00 33.07 3.61
312 313 8.343168 TCTTAAACTTCAAGTGAAAACTCCAA 57.657 30.769 0.00 0.00 33.07 3.53
313 314 7.610305 ACTCTTAAACTTCAAGTGAAAACTCCA 59.390 33.333 0.00 0.00 33.07 3.86
314 315 7.986562 ACTCTTAAACTTCAAGTGAAAACTCC 58.013 34.615 0.00 0.00 33.07 3.85
315 316 8.123575 GGACTCTTAAACTTCAAGTGAAAACTC 58.876 37.037 0.00 0.00 33.07 3.01
316 317 7.610305 TGGACTCTTAAACTTCAAGTGAAAACT 59.390 33.333 0.00 0.00 33.07 2.66
317 318 7.758495 TGGACTCTTAAACTTCAAGTGAAAAC 58.242 34.615 0.00 0.00 33.07 2.43
419 421 9.945633 AGCTTTAAGGGGGACATAAAATTATTA 57.054 29.630 0.00 0.00 0.00 0.98
421 423 8.854237 AAGCTTTAAGGGGGACATAAAATTAT 57.146 30.769 0.00 0.00 0.00 1.28
422 424 7.896496 TGAAGCTTTAAGGGGGACATAAAATTA 59.104 33.333 0.00 0.00 0.00 1.40
423 425 6.728632 TGAAGCTTTAAGGGGGACATAAAATT 59.271 34.615 0.00 0.00 0.00 1.82
424 426 6.260663 TGAAGCTTTAAGGGGGACATAAAAT 58.739 36.000 0.00 0.00 0.00 1.82
425 427 5.646215 TGAAGCTTTAAGGGGGACATAAAA 58.354 37.500 0.00 0.00 0.00 1.52
433 435 1.173913 CCGTTGAAGCTTTAAGGGGG 58.826 55.000 26.68 15.01 0.00 5.40
583 2864 4.803452 ACCCCTTTCATCTCTTTTTGTCA 58.197 39.130 0.00 0.00 0.00 3.58
650 2932 6.993786 TCATTGTACGAAATGAAATGCCTA 57.006 33.333 6.23 0.00 42.22 3.93
689 2998 4.530161 TGAAAGAAGAAAGGAGAGGAGAGG 59.470 45.833 0.00 0.00 0.00 3.69
712 3021 4.379302 AGGAGCCACAAGAAGAAAGAAT 57.621 40.909 0.00 0.00 0.00 2.40
847 3156 1.267806 CAAGAGTGTGTGGCAATGGTC 59.732 52.381 0.00 0.00 0.00 4.02
859 3168 6.875948 TGTGTTTATATGCAACAAGAGTGT 57.124 33.333 0.00 0.00 40.75 3.55
875 3184 1.175983 CCGGGCTTGGCTTGTGTTTA 61.176 55.000 0.00 0.00 0.00 2.01
905 3219 8.356657 ACTACTACTACTAGTACTATCACACGG 58.643 40.741 2.33 0.00 34.79 4.94
915 3234 9.471084 GGCTACTGTTACTACTACTACTAGTAC 57.529 40.741 0.00 0.00 34.79 2.73
918 3237 9.558396 AATGGCTACTGTTACTACTACTACTAG 57.442 37.037 0.00 0.00 0.00 2.57
940 3280 2.381911 AGCTAAGGTGGATTGCAATGG 58.618 47.619 18.59 0.00 0.00 3.16
985 3325 1.209019 ACTCATGCTTGACTGGGCTAG 59.791 52.381 0.00 0.00 0.00 3.42
986 3326 1.279496 ACTCATGCTTGACTGGGCTA 58.721 50.000 0.00 0.00 0.00 3.93
987 3327 0.403271 AACTCATGCTTGACTGGGCT 59.597 50.000 0.00 0.00 0.00 5.19
988 3328 0.807496 GAACTCATGCTTGACTGGGC 59.193 55.000 0.00 0.00 0.00 5.36
1030 3370 2.095252 GCGCCTTCTCGAACACCTC 61.095 63.158 0.00 0.00 0.00 3.85
1042 3382 1.447838 CATACGTGGACAGCGCCTT 60.448 57.895 2.29 0.00 0.00 4.35
1051 3391 1.068125 CGTGTCCTTGTCATACGTGGA 60.068 52.381 0.00 0.00 0.00 4.02
1055 3395 0.389296 TGGCGTGTCCTTGTCATACG 60.389 55.000 0.00 0.00 37.77 3.06
1059 3399 1.069090 GTCTGGCGTGTCCTTGTCA 59.931 57.895 0.00 0.00 35.26 3.58
1133 3473 2.060383 AGCCGCTCATAGTGCCTCA 61.060 57.895 0.00 0.00 0.00 3.86
1136 3476 2.028125 TACCAGCCGCTCATAGTGCC 62.028 60.000 0.00 0.00 0.00 5.01
1142 3482 1.739067 GTCTTTTACCAGCCGCTCAT 58.261 50.000 0.00 0.00 0.00 2.90
1145 3485 0.949105 CACGTCTTTTACCAGCCGCT 60.949 55.000 0.00 0.00 0.00 5.52
1147 3487 0.320073 TCCACGTCTTTTACCAGCCG 60.320 55.000 0.00 0.00 0.00 5.52
1148 3488 1.154197 GTCCACGTCTTTTACCAGCC 58.846 55.000 0.00 0.00 0.00 4.85
1198 3541 2.336088 CCCTTTGGTGCTGTTGCG 59.664 61.111 0.00 0.00 43.34 4.85
1205 3548 3.680786 GGAACCGCCCTTTGGTGC 61.681 66.667 0.00 0.00 40.35 5.01
1279 3622 5.944007 ACAGTGGTAAATGTTGGATAGAACC 59.056 40.000 0.00 0.00 0.00 3.62
1280 3623 7.361799 GGAACAGTGGTAAATGTTGGATAGAAC 60.362 40.741 0.00 0.00 39.66 3.01
1282 3625 6.177610 GGAACAGTGGTAAATGTTGGATAGA 58.822 40.000 0.00 0.00 39.66 1.98
1283 3626 5.943416 TGGAACAGTGGTAAATGTTGGATAG 59.057 40.000 0.00 0.00 39.66 2.08
1285 3628 4.735369 TGGAACAGTGGTAAATGTTGGAT 58.265 39.130 0.00 0.00 39.66 3.41
1286 3629 4.171878 TGGAACAGTGGTAAATGTTGGA 57.828 40.909 0.00 0.00 39.66 3.53
1319 3662 1.040646 GTAGAGGGCGGTGATGATGA 58.959 55.000 0.00 0.00 0.00 2.92
1329 3672 1.338337 CCACATGAGTAGTAGAGGGCG 59.662 57.143 0.00 0.00 0.00 6.13
1330 3673 2.101582 CACCACATGAGTAGTAGAGGGC 59.898 54.545 0.00 0.00 0.00 5.19
1418 3860 6.264067 AGTGAAGGAATATAAAAGCATCCAGC 59.736 38.462 0.00 0.00 46.19 4.85
1461 3924 2.357836 CATGCCCAAGGGAGCAGT 59.642 61.111 9.92 0.00 43.38 4.40
1518 3981 8.150945 TCAGTCAAGAGATAACCAAATATAGCC 58.849 37.037 0.00 0.00 0.00 3.93
1568 4096 4.493547 GCCAATGCTACTACATTTGCAAA 58.506 39.130 15.44 15.44 44.14 3.68
1627 6513 9.887629 ACAAAAATATGTTCATGCATGGATTAA 57.112 25.926 25.97 10.51 0.00 1.40
1660 6550 3.248602 GGCTATGCTCGGTGTAAATGAAG 59.751 47.826 0.00 0.00 0.00 3.02
1661 6551 3.202906 GGCTATGCTCGGTGTAAATGAA 58.797 45.455 0.00 0.00 0.00 2.57
1662 6552 2.169561 TGGCTATGCTCGGTGTAAATGA 59.830 45.455 0.00 0.00 0.00 2.57
1663 6553 2.560504 TGGCTATGCTCGGTGTAAATG 58.439 47.619 0.00 0.00 0.00 2.32
1664 6554 2.943033 GTTGGCTATGCTCGGTGTAAAT 59.057 45.455 0.00 0.00 0.00 1.40
1665 6555 2.352388 GTTGGCTATGCTCGGTGTAAA 58.648 47.619 0.00 0.00 0.00 2.01
1668 6562 1.078426 GGTTGGCTATGCTCGGTGT 60.078 57.895 0.00 0.00 0.00 4.16
1719 6617 4.932200 CCTGAATTATAAGCGACATCTCCC 59.068 45.833 0.00 0.00 0.00 4.30
1734 6632 6.261435 TCCTGAACCTAGAAGTCCTGAATTA 58.739 40.000 0.00 0.00 0.00 1.40
1736 6634 4.689062 TCCTGAACCTAGAAGTCCTGAAT 58.311 43.478 0.00 0.00 0.00 2.57
1741 6639 4.282496 TGATCTCCTGAACCTAGAAGTCC 58.718 47.826 0.00 0.00 0.00 3.85
1750 6648 9.886132 TTACTATAAAACTTGATCTCCTGAACC 57.114 33.333 0.00 0.00 0.00 3.62
1817 6716 7.429633 TGTTTAGCTTGCAATTAGTTAAGCAA 58.570 30.769 0.00 0.00 45.90 3.91
1825 6724 7.551035 AGAGATCTGTTTAGCTTGCAATTAG 57.449 36.000 0.00 0.00 0.00 1.73
1854 6753 9.503399 GGTAGTTCATCCTATAAGTAAAATGGG 57.497 37.037 0.00 0.00 0.00 4.00
1890 6789 5.086727 CACGTACGAGCATGTACTATATGG 58.913 45.833 24.41 3.32 42.00 2.74
1950 6880 5.686771 CGATAACACAATGATATCGCGAT 57.313 39.130 26.78 26.78 44.40 4.58
2068 7001 5.876357 TGCTCTCAGTAAAGGTTTAACCAT 58.124 37.500 17.10 0.59 41.95 3.55
2128 7061 8.977505 CCAATGATTTCGTTTATGACAAGTTTT 58.022 29.630 0.00 0.00 0.00 2.43
2134 7067 7.807433 CAGAAACCAATGATTTCGTTTATGACA 59.193 33.333 13.10 0.00 38.88 3.58


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

AutoCloner maintained by Alex Coulton.