Multiple sequence alignment - TraesCS5D01G502900

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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 TraesCS5D01G502900 chr5D 100.000 2351 0 0 1 2351 530055914 530053564 0.000000e+00 4342
1 TraesCS5D01G502900 chr5B 89.792 1734 72 37 659 2347 669233285 669231612 0.000000e+00 2124
2 TraesCS5D01G502900 chr5B 86.975 238 22 9 4 235 669233803 669233569 2.320000e-65 259
3 TraesCS5D01G502900 chr5A 87.893 1718 92 48 662 2350 657779199 657777569 0.000000e+00 1914
4 TraesCS5D01G502900 chr5A 89.437 284 23 6 90 371 657780110 657779832 3.720000e-93 351
5 TraesCS5D01G502900 chr5A 96.190 105 1 1 394 498 657779307 657779206 4.020000e-38 169
6 TraesCS5D01G502900 chr7D 91.515 165 9 3 497 659 588621133 588621294 3.040000e-54 222
7 TraesCS5D01G502900 chr1B 90.964 166 10 3 497 660 623195683 623195845 3.930000e-53 219
8 TraesCS5D01G502900 chr1A 90.000 170 12 3 497 664 566481008 566481174 5.090000e-52 215
9 TraesCS5D01G502900 chr7B 89.941 169 11 4 494 659 339685438 339685603 1.830000e-51 213
10 TraesCS5D01G502900 chr7A 90.303 165 12 2 497 659 714613312 714613474 1.830000e-51 213
11 TraesCS5D01G502900 chr4A 90.361 166 11 3 496 659 517406470 517406632 1.830000e-51 213
12 TraesCS5D01G502900 chrUn 90.303 165 11 3 497 659 141680907 141680746 6.580000e-51 211
13 TraesCS5D01G502900 chr2D 90.303 165 11 3 497 659 362930808 362930969 6.580000e-51 211
14 TraesCS5D01G502900 chr1D 89.881 168 12 3 497 662 338937373 338937209 6.580000e-51 211


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 TraesCS5D01G502900 chr5D 530053564 530055914 2350 True 4342.000000 4342 100.000000 1 2351 1 chr5D.!!$R1 2350
1 TraesCS5D01G502900 chr5B 669231612 669233803 2191 True 1191.500000 2124 88.383500 4 2347 2 chr5B.!!$R1 2343
2 TraesCS5D01G502900 chr5A 657777569 657780110 2541 True 811.333333 1914 91.173333 90 2350 3 chr5A.!!$R1 2260

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
169 172 0.619543 ACTTACATGTAGGGCCCCGT 60.62 55.0 21.43 10.95 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 2098 2.036604 TCATTTGAGTAGTCACACCGCA 59.963 45.455 0.0 0.0 30.1 5.69 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
69 70 4.725790 ATCCTTGTAGAAATGCCTTTGC 57.274 40.909 0.00 0.00 38.26 3.68
75 76 2.422276 AGAAATGCCTTTGCGTGTTC 57.578 45.000 0.00 0.00 41.78 3.18
79 80 4.037446 AGAAATGCCTTTGCGTGTTCTTTA 59.963 37.500 0.00 0.00 41.78 1.85
80 81 2.766970 TGCCTTTGCGTGTTCTTTAC 57.233 45.000 0.00 0.00 41.78 2.01
101 102 4.412843 ACATCCGGTTAAAGGGTTTTGAT 58.587 39.130 0.00 0.00 0.00 2.57
123 124 5.011090 TCGTCTATGAGACATTCTTTGGG 57.989 43.478 7.36 0.00 45.30 4.12
124 125 3.557595 CGTCTATGAGACATTCTTTGGGC 59.442 47.826 7.36 0.00 45.30 5.36
126 127 1.098050 ATGAGACATTCTTTGGGCGC 58.902 50.000 0.00 0.00 0.00 6.53
167 170 1.134189 GTCACTTACATGTAGGGCCCC 60.134 57.143 21.43 4.15 0.00 5.80
169 172 0.619543 ACTTACATGTAGGGCCCCGT 60.620 55.000 21.43 10.95 0.00 5.28
170 173 1.343277 ACTTACATGTAGGGCCCCGTA 60.343 52.381 21.43 9.85 0.00 4.02
171 174 1.764134 CTTACATGTAGGGCCCCGTAA 59.236 52.381 21.43 16.67 0.00 3.18
211 214 0.845102 TCTTTCCCAACCCCCTCTCC 60.845 60.000 0.00 0.00 0.00 3.71
232 308 2.834549 CCTCTCTCACTTACATGTGGGT 59.165 50.000 9.11 4.09 39.33 4.51
250 326 1.600636 TCCAGGTCAAAGCTTGCCG 60.601 57.895 0.00 0.53 33.78 5.69
265 341 1.675641 GCCGAGTCAACAAGGGCAT 60.676 57.895 0.13 0.00 43.23 4.40
267 343 1.503542 CGAGTCAACAAGGGCATGC 59.496 57.895 9.90 9.90 0.00 4.06
366 447 4.615949 TGTGTGGATTGTTTGTATTGCAC 58.384 39.130 0.00 0.00 0.00 4.57
382 463 3.980646 TGCACATATATTCCCGCAAAC 57.019 42.857 0.00 0.00 0.00 2.93
385 466 4.158579 TGCACATATATTCCCGCAAACAAA 59.841 37.500 0.00 0.00 0.00 2.83
387 468 5.578727 GCACATATATTCCCGCAAACAAAAA 59.421 36.000 0.00 0.00 0.00 1.94
474 1057 8.136165 GGTATAAGAGTCTGTATCGTCATTTGT 58.864 37.037 0.00 0.00 0.00 2.83
510 1093 5.431179 TTTACTGGTACTTCCTCCATTCC 57.569 43.478 0.00 0.00 37.07 3.01
511 1094 3.207044 ACTGGTACTTCCTCCATTCCT 57.793 47.619 0.00 0.00 37.07 3.36
512 1095 4.348020 ACTGGTACTTCCTCCATTCCTA 57.652 45.455 0.00 0.00 37.07 2.94
513 1096 4.695606 ACTGGTACTTCCTCCATTCCTAA 58.304 43.478 0.00 0.00 37.07 2.69
514 1097 5.098663 ACTGGTACTTCCTCCATTCCTAAA 58.901 41.667 0.00 0.00 37.07 1.85
515 1098 5.731678 ACTGGTACTTCCTCCATTCCTAAAT 59.268 40.000 0.00 0.00 37.07 1.40
516 1099 6.906901 ACTGGTACTTCCTCCATTCCTAAATA 59.093 38.462 0.00 0.00 37.07 1.40
517 1100 7.572861 ACTGGTACTTCCTCCATTCCTAAATAT 59.427 37.037 0.00 0.00 37.07 1.28
518 1101 9.101325 CTGGTACTTCCTCCATTCCTAAATATA 57.899 37.037 0.00 0.00 37.07 0.86
519 1102 9.455144 TGGTACTTCCTCCATTCCTAAATATAA 57.545 33.333 0.00 0.00 37.07 0.98
520 1103 9.945904 GGTACTTCCTCCATTCCTAAATATAAG 57.054 37.037 0.00 0.00 0.00 1.73
523 1106 9.453830 ACTTCCTCCATTCCTAAATATAAGTCT 57.546 33.333 0.00 0.00 0.00 3.24
557 1140 8.680039 ATTCTACTATGGACTATATACGGAGC 57.320 38.462 0.00 0.00 0.00 4.70
558 1141 7.191593 TCTACTATGGACTATATACGGAGCA 57.808 40.000 0.00 0.00 0.00 4.26
559 1142 7.627311 TCTACTATGGACTATATACGGAGCAA 58.373 38.462 0.00 0.00 0.00 3.91
560 1143 8.105197 TCTACTATGGACTATATACGGAGCAAA 58.895 37.037 0.00 0.00 0.00 3.68
561 1144 7.534723 ACTATGGACTATATACGGAGCAAAA 57.465 36.000 0.00 0.00 0.00 2.44
562 1145 8.135382 ACTATGGACTATATACGGAGCAAAAT 57.865 34.615 0.00 0.00 0.00 1.82
563 1146 8.035394 ACTATGGACTATATACGGAGCAAAATG 58.965 37.037 0.00 0.00 0.00 2.32
564 1147 6.413783 TGGACTATATACGGAGCAAAATGA 57.586 37.500 0.00 0.00 0.00 2.57
565 1148 6.455647 TGGACTATATACGGAGCAAAATGAG 58.544 40.000 0.00 0.00 0.00 2.90
566 1149 6.041637 TGGACTATATACGGAGCAAAATGAGT 59.958 38.462 0.00 0.00 0.00 3.41
567 1150 6.366332 GGACTATATACGGAGCAAAATGAGTG 59.634 42.308 0.00 0.00 0.00 3.51
568 1151 7.050970 ACTATATACGGAGCAAAATGAGTGA 57.949 36.000 0.00 0.00 0.00 3.41
569 1152 7.497595 ACTATATACGGAGCAAAATGAGTGAA 58.502 34.615 0.00 0.00 0.00 3.18
570 1153 8.150945 ACTATATACGGAGCAAAATGAGTGAAT 58.849 33.333 0.00 0.00 0.00 2.57
571 1154 5.741388 ATACGGAGCAAAATGAGTGAATC 57.259 39.130 0.00 0.00 0.00 2.52
572 1155 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
573 1156 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
574 1157 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
575 1158 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
576 1159 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
651 1234 9.558396 TTAAAAAGACTTATACTTTGGAACGGA 57.442 29.630 0.00 0.00 37.59 4.69
652 1235 7.668525 AAAAGACTTATACTTTGGAACGGAG 57.331 36.000 0.00 0.00 37.59 4.63
653 1236 5.340439 AGACTTATACTTTGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
654 1237 4.161754 AGACTTATACTTTGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
655 1238 4.098894 ACTTATACTTTGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
656 1239 4.161754 ACTTATACTTTGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
657 1240 2.019807 TACTTTGGAACGGAGGGAGT 57.980 50.000 0.00 0.00 0.00 3.85
671 1254 2.096248 AGGGAGTAAGAGACGAAGCAG 58.904 52.381 0.00 0.00 0.00 4.24
714 1301 3.594775 CCACTTGCGCTTGTGGCA 61.595 61.111 29.00 0.00 45.68 4.92
718 1305 4.283403 TTGCGCTTGTGGCAAGCC 62.283 61.111 22.93 17.13 44.79 4.35
727 1314 2.124109 TGGCAAGCCCACGTTGAA 60.124 55.556 8.89 0.00 39.18 2.69
728 1315 2.192861 TGGCAAGCCCACGTTGAAG 61.193 57.895 8.89 0.00 39.18 3.02
729 1316 1.896660 GGCAAGCCCACGTTGAAGA 60.897 57.895 0.00 0.00 0.00 2.87
730 1317 1.576421 GCAAGCCCACGTTGAAGAG 59.424 57.895 0.00 0.00 0.00 2.85
963 1566 1.745232 ACATTTCGCCGCCAAGAATA 58.255 45.000 0.00 0.00 0.00 1.75
964 1567 2.297701 ACATTTCGCCGCCAAGAATAT 58.702 42.857 0.00 0.00 0.00 1.28
970 1573 0.954452 GCCGCCAAGAATATCCAAGG 59.046 55.000 0.00 0.00 0.00 3.61
971 1574 1.609208 CCGCCAAGAATATCCAAGGG 58.391 55.000 0.00 0.00 0.00 3.95
977 1580 4.692496 GCCAAGAATATCCAAGGGATCCAA 60.692 45.833 15.23 0.00 42.11 3.53
978 1581 4.829492 CCAAGAATATCCAAGGGATCCAAC 59.171 45.833 15.23 0.00 42.11 3.77
979 1582 4.731313 AGAATATCCAAGGGATCCAACC 57.269 45.455 15.23 0.00 42.11 3.77
980 1583 4.054369 AGAATATCCAAGGGATCCAACCA 58.946 43.478 15.23 0.00 42.11 3.67
981 1584 4.482025 AGAATATCCAAGGGATCCAACCAA 59.518 41.667 15.23 0.00 42.11 3.67
988 1591 0.915364 GGGATCCAACCAAGAGAGCT 59.085 55.000 15.23 0.00 0.00 4.09
997 1603 6.014647 TCCAACCAAGAGAGCTAGTAGTTAA 58.985 40.000 0.00 0.00 0.00 2.01
1400 2027 4.043200 GCTTGGGTGCGTGCTTCC 62.043 66.667 0.00 0.00 0.00 3.46
1452 2079 4.701651 TCCATGAAAAACATCGCAGAGATT 59.298 37.500 0.00 0.00 43.63 2.40
1465 2096 7.767659 ACATCGCAGAGATTTGCATATATGTAT 59.232 33.333 14.14 5.84 43.63 2.29
1467 2098 9.993454 ATCGCAGAGATTTGCATATATGTATAT 57.007 29.630 14.14 10.08 43.63 0.86
1554 2185 7.605691 CACAACTTCTGGAGTAATTTCTCTCAT 59.394 37.037 11.35 0.00 37.72 2.90
1555 2186 7.605691 ACAACTTCTGGAGTAATTTCTCTCATG 59.394 37.037 11.35 6.05 37.72 3.07
1556 2187 7.251321 ACTTCTGGAGTAATTTCTCTCATGT 57.749 36.000 11.35 3.33 36.65 3.21
1643 2292 7.121168 TCTGGGACTGCTGATTTTAAACATAAG 59.879 37.037 0.00 0.00 0.00 1.73
1646 2295 8.903820 GGGACTGCTGATTTTAAACATAAGTAT 58.096 33.333 0.00 0.00 0.00 2.12
1800 2449 1.586028 CCGGTGTTGAAATGGCCAG 59.414 57.895 13.05 0.00 0.00 4.85
1809 2458 4.021192 TGTTGAAATGGCCAGATCTTTTCC 60.021 41.667 20.72 10.58 31.42 3.13
1810 2459 3.777087 TGAAATGGCCAGATCTTTTCCA 58.223 40.909 20.72 10.74 31.42 3.53
1811 2460 3.511146 TGAAATGGCCAGATCTTTTCCAC 59.489 43.478 20.72 3.53 31.42 4.02
1812 2461 3.463048 AATGGCCAGATCTTTTCCACT 57.537 42.857 13.05 0.00 0.00 4.00
1875 2524 6.541641 GCAGAGATCAACAATTGGATAGAGTT 59.458 38.462 10.83 0.00 0.00 3.01
1925 2574 3.558505 CATGCTTGCTTGACACAGTTAC 58.441 45.455 2.83 0.00 0.00 2.50
1981 2630 0.029035 CGAAATCCCGATCGACTCGT 59.971 55.000 18.66 0.00 46.18 4.18
2127 2780 4.734695 GCGAAGAATATCCCAGCAAAAAGG 60.735 45.833 0.00 0.00 0.00 3.11
2155 2808 6.752351 TGCAGATGTTAAGATCGAGTAGAAAC 59.248 38.462 6.93 0.00 0.00 2.78
2199 2852 0.177141 GGGTAGCGAGGTAACATGCA 59.823 55.000 0.00 0.00 40.97 3.96
2200 2853 1.406341 GGGTAGCGAGGTAACATGCAA 60.406 52.381 0.00 0.00 40.97 4.08
2345 2998 2.555757 CCAACAAGGCTGAGAAAAGGAG 59.444 50.000 0.00 0.00 0.00 3.69
2348 3001 4.170468 ACAAGGCTGAGAAAAGGAGAAA 57.830 40.909 0.00 0.00 0.00 2.52
2349 3002 4.536765 ACAAGGCTGAGAAAAGGAGAAAA 58.463 39.130 0.00 0.00 0.00 2.29
2350 3003 5.143369 ACAAGGCTGAGAAAAGGAGAAAAT 58.857 37.500 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.661847 AGCATAATAAATGTTAGTGGTAGGCTC 59.338 37.037 0.00 0.00 0.00 4.70
1 2 7.518188 AGCATAATAAATGTTAGTGGTAGGCT 58.482 34.615 0.00 0.00 0.00 4.58
2 3 7.444183 TGAGCATAATAAATGTTAGTGGTAGGC 59.556 37.037 0.00 0.00 0.00 3.93
12 13 9.880157 AGAGCAAATTTGAGCATAATAAATGTT 57.120 25.926 22.31 0.00 0.00 2.71
20 21 7.218228 TGAGAAAGAGCAAATTTGAGCATAA 57.782 32.000 22.31 0.00 0.00 1.90
69 70 5.390145 CCTTTAACCGGATGTAAAGAACACG 60.390 44.000 25.28 12.89 42.09 4.49
75 76 5.970317 AAACCCTTTAACCGGATGTAAAG 57.030 39.130 9.46 17.48 0.00 1.85
79 80 3.834938 TCAAAACCCTTTAACCGGATGT 58.165 40.909 9.46 0.00 0.00 3.06
80 81 4.438200 CGATCAAAACCCTTTAACCGGATG 60.438 45.833 9.46 0.00 0.00 3.51
123 124 1.369839 GCAGAGAGGGGTAAAAGCGC 61.370 60.000 0.00 0.00 0.00 5.92
124 125 0.036388 TGCAGAGAGGGGTAAAAGCG 60.036 55.000 0.00 0.00 0.00 4.68
126 127 5.041191 ACATATGCAGAGAGGGGTAAAAG 57.959 43.478 1.58 0.00 0.00 2.27
160 162 3.743092 TTCTTTTTATTACGGGGCCCT 57.257 42.857 24.38 10.47 0.00 5.19
163 165 5.648178 TCCTTTTCTTTTTATTACGGGGC 57.352 39.130 0.00 0.00 0.00 5.80
195 198 2.204244 GGGAGAGGGGGTTGGGAA 60.204 66.667 0.00 0.00 0.00 3.97
211 214 2.834549 ACCCACATGTAAGTGAGAGAGG 59.165 50.000 0.00 0.00 42.05 3.69
232 308 1.600636 CGGCAAGCTTTGACCTGGA 60.601 57.895 0.00 0.00 34.26 3.86
250 326 0.895100 TGGCATGCCCTTGTTGACTC 60.895 55.000 33.44 4.70 34.56 3.36
267 343 0.469892 GGACATATGGGCCCCTTTGG 60.470 60.000 22.27 7.73 37.09 3.28
387 468 6.932356 ATGACGATACAGATGCAAGATTTT 57.068 33.333 0.00 0.00 0.00 1.82
388 469 6.932356 AATGACGATACAGATGCAAGATTT 57.068 33.333 0.00 0.00 0.00 2.17
389 470 6.317140 ACAAATGACGATACAGATGCAAGATT 59.683 34.615 0.00 0.00 0.00 2.40
390 471 5.819379 ACAAATGACGATACAGATGCAAGAT 59.181 36.000 0.00 0.00 0.00 2.40
391 472 5.178061 ACAAATGACGATACAGATGCAAGA 58.822 37.500 0.00 0.00 0.00 3.02
392 473 5.292834 AGACAAATGACGATACAGATGCAAG 59.707 40.000 0.00 0.00 0.00 4.01
440 1023 8.554528 CGATACAGACTCTTATACCGTAAAAGA 58.445 37.037 0.00 0.00 0.00 2.52
442 1025 8.213518 ACGATACAGACTCTTATACCGTAAAA 57.786 34.615 0.00 0.00 0.00 1.52
531 1114 8.776470 GCTCCGTATATAGTCCATAGTAGAATC 58.224 40.741 0.00 0.00 0.00 2.52
532 1115 8.272889 TGCTCCGTATATAGTCCATAGTAGAAT 58.727 37.037 0.00 0.00 0.00 2.40
533 1116 7.627311 TGCTCCGTATATAGTCCATAGTAGAA 58.373 38.462 0.00 0.00 0.00 2.10
534 1117 7.191593 TGCTCCGTATATAGTCCATAGTAGA 57.808 40.000 0.00 0.00 0.00 2.59
535 1118 7.860918 TTGCTCCGTATATAGTCCATAGTAG 57.139 40.000 0.00 0.00 0.00 2.57
536 1119 8.640063 TTTTGCTCCGTATATAGTCCATAGTA 57.360 34.615 0.00 0.00 0.00 1.82
537 1120 7.534723 TTTTGCTCCGTATATAGTCCATAGT 57.465 36.000 0.00 0.00 0.00 2.12
538 1121 8.251026 TCATTTTGCTCCGTATATAGTCCATAG 58.749 37.037 0.00 0.00 0.00 2.23
539 1122 8.129496 TCATTTTGCTCCGTATATAGTCCATA 57.871 34.615 0.00 0.00 0.00 2.74
540 1123 7.004555 TCATTTTGCTCCGTATATAGTCCAT 57.995 36.000 0.00 0.00 0.00 3.41
541 1124 6.041637 ACTCATTTTGCTCCGTATATAGTCCA 59.958 38.462 0.00 0.00 0.00 4.02
542 1125 6.366332 CACTCATTTTGCTCCGTATATAGTCC 59.634 42.308 0.00 0.00 0.00 3.85
543 1126 7.145985 TCACTCATTTTGCTCCGTATATAGTC 58.854 38.462 0.00 0.00 0.00 2.59
544 1127 7.050970 TCACTCATTTTGCTCCGTATATAGT 57.949 36.000 0.00 0.00 0.00 2.12
545 1128 7.946655 TTCACTCATTTTGCTCCGTATATAG 57.053 36.000 0.00 0.00 0.00 1.31
546 1129 8.367911 AGATTCACTCATTTTGCTCCGTATATA 58.632 33.333 0.00 0.00 0.00 0.86
547 1130 7.220030 AGATTCACTCATTTTGCTCCGTATAT 58.780 34.615 0.00 0.00 0.00 0.86
548 1131 6.582636 AGATTCACTCATTTTGCTCCGTATA 58.417 36.000 0.00 0.00 0.00 1.47
549 1132 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
550 1133 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
551 1134 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
552 1135 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
553 1136 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
554 1137 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
555 1138 8.621532 TTTAGTGTAGATTCACTCATTTTGCT 57.378 30.769 2.59 0.00 45.79 3.91
556 1139 9.846248 ATTTTAGTGTAGATTCACTCATTTTGC 57.154 29.630 2.59 0.00 45.79 3.68
625 1208 9.558396 TCCGTTCCAAAGTATAAGTCTTTTTAA 57.442 29.630 0.00 0.00 33.58 1.52
626 1209 9.211485 CTCCGTTCCAAAGTATAAGTCTTTTTA 57.789 33.333 0.00 0.00 33.58 1.52
627 1210 7.174426 CCTCCGTTCCAAAGTATAAGTCTTTTT 59.826 37.037 0.00 0.00 33.58 1.94
628 1211 6.653740 CCTCCGTTCCAAAGTATAAGTCTTTT 59.346 38.462 0.00 0.00 33.58 2.27
629 1212 6.171213 CCTCCGTTCCAAAGTATAAGTCTTT 58.829 40.000 0.00 0.00 35.82 2.52
630 1213 5.338137 CCCTCCGTTCCAAAGTATAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
631 1214 4.161754 CCCTCCGTTCCAAAGTATAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
632 1215 4.161001 TCCCTCCGTTCCAAAGTATAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
633 1216 4.098894 TCCCTCCGTTCCAAAGTATAAGT 58.901 43.478 0.00 0.00 0.00 2.24
634 1217 4.161754 ACTCCCTCCGTTCCAAAGTATAAG 59.838 45.833 0.00 0.00 0.00 1.73
635 1218 4.098894 ACTCCCTCCGTTCCAAAGTATAA 58.901 43.478 0.00 0.00 0.00 0.98
636 1219 3.716431 ACTCCCTCCGTTCCAAAGTATA 58.284 45.455 0.00 0.00 0.00 1.47
637 1220 2.547990 ACTCCCTCCGTTCCAAAGTAT 58.452 47.619 0.00 0.00 0.00 2.12
638 1221 2.019807 ACTCCCTCCGTTCCAAAGTA 57.980 50.000 0.00 0.00 0.00 2.24
639 1222 2.019807 TACTCCCTCCGTTCCAAAGT 57.980 50.000 0.00 0.00 0.00 2.66
640 1223 2.565834 TCTTACTCCCTCCGTTCCAAAG 59.434 50.000 0.00 0.00 0.00 2.77
641 1224 2.565834 CTCTTACTCCCTCCGTTCCAAA 59.434 50.000 0.00 0.00 0.00 3.28
642 1225 2.176889 CTCTTACTCCCTCCGTTCCAA 58.823 52.381 0.00 0.00 0.00 3.53
643 1226 1.356738 TCTCTTACTCCCTCCGTTCCA 59.643 52.381 0.00 0.00 0.00 3.53
644 1227 1.750206 GTCTCTTACTCCCTCCGTTCC 59.250 57.143 0.00 0.00 0.00 3.62
645 1228 1.401199 CGTCTCTTACTCCCTCCGTTC 59.599 57.143 0.00 0.00 0.00 3.95
646 1229 1.004044 TCGTCTCTTACTCCCTCCGTT 59.996 52.381 0.00 0.00 0.00 4.44
647 1230 0.617413 TCGTCTCTTACTCCCTCCGT 59.383 55.000 0.00 0.00 0.00 4.69
648 1231 1.671845 CTTCGTCTCTTACTCCCTCCG 59.328 57.143 0.00 0.00 0.00 4.63
649 1232 1.406180 GCTTCGTCTCTTACTCCCTCC 59.594 57.143 0.00 0.00 0.00 4.30
650 1233 2.093106 TGCTTCGTCTCTTACTCCCTC 58.907 52.381 0.00 0.00 0.00 4.30
651 1234 2.096248 CTGCTTCGTCTCTTACTCCCT 58.904 52.381 0.00 0.00 0.00 4.20
652 1235 1.470112 GCTGCTTCGTCTCTTACTCCC 60.470 57.143 0.00 0.00 0.00 4.30
653 1236 1.795889 CGCTGCTTCGTCTCTTACTCC 60.796 57.143 0.00 0.00 0.00 3.85
654 1237 1.540407 CGCTGCTTCGTCTCTTACTC 58.460 55.000 0.00 0.00 0.00 2.59
655 1238 0.456995 GCGCTGCTTCGTCTCTTACT 60.457 55.000 0.00 0.00 0.00 2.24
656 1239 0.456995 AGCGCTGCTTCGTCTCTTAC 60.457 55.000 10.39 0.00 33.89 2.34
657 1240 0.456824 CAGCGCTGCTTCGTCTCTTA 60.457 55.000 26.68 0.00 36.40 2.10
712 1299 1.576421 CTCTTCAACGTGGGCTTGC 59.424 57.895 0.00 0.00 0.00 4.01
714 1301 1.600916 GGCTCTTCAACGTGGGCTT 60.601 57.895 0.00 0.00 0.00 4.35
718 1305 2.954753 GCGTGGCTCTTCAACGTGG 61.955 63.158 0.00 0.00 0.00 4.94
719 1306 2.551270 GCGTGGCTCTTCAACGTG 59.449 61.111 0.00 0.00 0.00 4.49
720 1307 2.665185 GGCGTGGCTCTTCAACGT 60.665 61.111 0.00 0.00 0.00 3.99
721 1308 3.777925 CGGCGTGGCTCTTCAACG 61.778 66.667 0.00 0.00 0.00 4.10
722 1309 2.357034 TCGGCGTGGCTCTTCAAC 60.357 61.111 6.85 0.00 0.00 3.18
723 1310 2.357034 GTCGGCGTGGCTCTTCAA 60.357 61.111 6.85 0.00 0.00 2.69
724 1311 4.373116 GGTCGGCGTGGCTCTTCA 62.373 66.667 6.85 0.00 0.00 3.02
725 1312 3.991536 GAGGTCGGCGTGGCTCTTC 62.992 68.421 6.85 0.00 0.00 2.87
726 1313 4.070552 GAGGTCGGCGTGGCTCTT 62.071 66.667 6.85 0.00 0.00 2.85
728 1315 4.500116 GAGAGGTCGGCGTGGCTC 62.500 72.222 6.85 6.43 0.00 4.70
809 1396 2.829043 TATCCTCACCACGCGTGTGC 62.829 60.000 34.81 0.00 45.04 4.57
811 1398 0.108804 CTTATCCTCACCACGCGTGT 60.109 55.000 34.81 21.36 43.51 4.49
963 1566 2.243221 CTCTTGGTTGGATCCCTTGGAT 59.757 50.000 9.90 0.00 46.28 3.41
964 1567 1.635487 CTCTTGGTTGGATCCCTTGGA 59.365 52.381 9.90 0.00 35.55 3.53
970 1573 2.769095 ACTAGCTCTCTTGGTTGGATCC 59.231 50.000 4.20 4.20 0.00 3.36
971 1574 4.647399 ACTACTAGCTCTCTTGGTTGGATC 59.353 45.833 0.00 0.00 0.00 3.36
977 1580 6.912951 TTGTTAACTACTAGCTCTCTTGGT 57.087 37.500 7.22 0.00 0.00 3.67
978 1581 6.758886 CCATTGTTAACTACTAGCTCTCTTGG 59.241 42.308 7.22 0.00 0.00 3.61
979 1582 6.256757 GCCATTGTTAACTACTAGCTCTCTTG 59.743 42.308 7.22 0.00 0.00 3.02
980 1583 6.342111 GCCATTGTTAACTACTAGCTCTCTT 58.658 40.000 7.22 0.00 0.00 2.85
981 1584 5.450688 CGCCATTGTTAACTACTAGCTCTCT 60.451 44.000 7.22 0.00 0.00 3.10
988 1591 5.165676 CACAGACGCCATTGTTAACTACTA 58.834 41.667 7.22 0.00 0.00 1.82
997 1603 2.034066 CCCCACAGACGCCATTGT 59.966 61.111 0.00 0.00 0.00 2.71
1400 2027 6.368243 ACAGCAATAAATCGAGCTATGAGATG 59.632 38.462 0.00 0.00 35.19 2.90
1465 2096 3.945981 TTTGAGTAGTCACACCGCATA 57.054 42.857 0.00 0.00 30.10 3.14
1467 2098 2.036604 TCATTTGAGTAGTCACACCGCA 59.963 45.455 0.00 0.00 30.10 5.69
1554 2185 4.457603 GCTTAACATGGGTACATCACAACA 59.542 41.667 0.00 0.00 34.35 3.33
1555 2186 4.700213 AGCTTAACATGGGTACATCACAAC 59.300 41.667 0.00 0.00 34.35 3.32
1556 2187 4.917385 AGCTTAACATGGGTACATCACAA 58.083 39.130 0.00 0.00 34.35 3.33
1731 2380 5.359576 GCTTCCTCTGTTTCTCTCTCTGATA 59.640 44.000 0.00 0.00 0.00 2.15
1809 2458 7.176690 AGGACAACCATACAAAATAAAGGAGTG 59.823 37.037 0.00 0.00 38.94 3.51
1810 2459 7.176690 CAGGACAACCATACAAAATAAAGGAGT 59.823 37.037 0.00 0.00 38.94 3.85
1811 2460 7.538575 CAGGACAACCATACAAAATAAAGGAG 58.461 38.462 0.00 0.00 38.94 3.69
1812 2461 6.071616 GCAGGACAACCATACAAAATAAAGGA 60.072 38.462 0.00 0.00 38.94 3.36
1909 2558 3.685272 TGTTTCGTAACTGTGTCAAGCAA 59.315 39.130 6.48 0.00 35.24 3.91
1925 2574 7.865385 TGTTTATTCTTTCCCAGATTTGTTTCG 59.135 33.333 0.00 0.00 0.00 3.46
1981 2630 3.812156 TCAGAGTCCGTTTGAACTTGA 57.188 42.857 0.00 0.00 0.00 3.02
2066 2719 4.884164 CCAAGTCCTAATGTTCATTCTCCC 59.116 45.833 1.11 0.00 0.00 4.30
2127 2780 2.799412 CTCGATCTTAACATCTGCAGGC 59.201 50.000 15.13 0.00 0.00 4.85
2199 2852 8.450578 TCTTTCATCAAGTGTTGAGTTATGTT 57.549 30.769 0.00 0.00 43.98 2.71
2200 2853 8.450578 TTCTTTCATCAAGTGTTGAGTTATGT 57.549 30.769 0.00 0.00 43.98 2.29


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

AutoCloner maintained by Alex Coulton.