Multiple sequence alignment - TraesCS6A01G079600

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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 TraesCS6A01G079600 chr6A 100.000 2231 0 0 1 2231 48869811 48872041 0.000000e+00 4120.0
1 TraesCS6A01G079600 chr6A 87.327 505 64 0 1533 2037 607404415 607403911 1.490000e-161 579.0
2 TraesCS6A01G079600 chr6A 78.728 865 133 36 585 1421 48880780 48881621 4.220000e-147 531.0
3 TraesCS6A01G079600 chr6B 86.144 1097 109 19 72 1141 87585390 87586470 0.000000e+00 1144.0
4 TraesCS6A01G079600 chr6B 81.818 352 46 14 1079 1421 87630595 87630937 1.690000e-71 279.0
5 TraesCS6A01G079600 chr6B 89.474 133 14 0 2099 2231 87588025 87588157 3.810000e-38 169.0
6 TraesCS6A01G079600 chr6B 86.905 84 10 1 600 683 87591956 87592038 2.360000e-15 93.5
7 TraesCS6A01G079600 chr6B 96.970 33 1 0 1036 1068 87560145 87560177 3.090000e-04 56.5
8 TraesCS6A01G079600 chr6D 88.984 817 60 17 633 1424 37454675 37455486 0.000000e+00 983.0
9 TraesCS6A01G079600 chr6D 85.669 635 72 12 1 630 37453768 37454388 0.000000e+00 651.0
10 TraesCS6A01G079600 chr6D 81.460 507 68 17 917 1402 37460932 37461433 2.080000e-105 392.0
11 TraesCS6A01G079600 chr6D 83.636 110 15 3 585 692 37460409 37460517 1.410000e-17 100.0
12 TraesCS6A01G079600 chr6D 74.172 151 34 4 1036 1182 37449701 37449850 8.610000e-05 58.4
13 TraesCS6A01G079600 chr4D 90.174 631 60 1 1471 2099 414047611 414048241 0.000000e+00 821.0
14 TraesCS6A01G079600 chr3D 88.608 632 68 3 1471 2099 349137095 349137725 0.000000e+00 765.0
15 TraesCS6A01G079600 chr7A 86.731 618 76 5 1484 2099 112447284 112447897 0.000000e+00 682.0
16 TraesCS6A01G079600 chr2B 87.216 485 60 2 1616 2099 680309989 680309506 3.240000e-153 551.0
17 TraesCS6A01G079600 chr1B 82.560 625 99 10 1482 2099 32016465 32015844 1.950000e-150 542.0
18 TraesCS6A01G079600 chr1D 82.258 620 104 6 1482 2099 17703410 17702795 4.220000e-147 531.0
19 TraesCS6A01G079600 chrUn 82.097 620 105 6 1482 2099 330530233 330529618 1.960000e-145 525.0
20 TraesCS6A01G079600 chr3A 82.496 577 98 3 1488 2062 704057075 704056500 9.200000e-139 503.0


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 TraesCS6A01G079600 chr6A 48869811 48872041 2230 False 4120.000000 4120 100.000000 1 2231 1 chr6A.!!$F1 2230
1 TraesCS6A01G079600 chr6A 607403911 607404415 504 True 579.000000 579 87.327000 1533 2037 1 chr6A.!!$R1 504
2 TraesCS6A01G079600 chr6A 48880780 48881621 841 False 531.000000 531 78.728000 585 1421 1 chr6A.!!$F2 836
3 TraesCS6A01G079600 chr6B 87585390 87592038 6648 False 468.833333 1144 87.507667 72 2231 3 chr6B.!!$F3 2159
4 TraesCS6A01G079600 chr6D 37449701 37455486 5785 False 564.133333 983 82.941667 1 1424 3 chr6D.!!$F1 1423
5 TraesCS6A01G079600 chr6D 37460409 37461433 1024 False 246.000000 392 82.548000 585 1402 2 chr6D.!!$F2 817
6 TraesCS6A01G079600 chr4D 414047611 414048241 630 False 821.000000 821 90.174000 1471 2099 1 chr4D.!!$F1 628
7 TraesCS6A01G079600 chr3D 349137095 349137725 630 False 765.000000 765 88.608000 1471 2099 1 chr3D.!!$F1 628
8 TraesCS6A01G079600 chr7A 112447284 112447897 613 False 682.000000 682 86.731000 1484 2099 1 chr7A.!!$F1 615
9 TraesCS6A01G079600 chr1B 32015844 32016465 621 True 542.000000 542 82.560000 1482 2099 1 chr1B.!!$R1 617
10 TraesCS6A01G079600 chr1D 17702795 17703410 615 True 531.000000 531 82.258000 1482 2099 1 chr1D.!!$R1 617
11 TraesCS6A01G079600 chrUn 330529618 330530233 615 True 525.000000 525 82.097000 1482 2099 1 chrUn.!!$R1 617
12 TraesCS6A01G079600 chr3A 704056500 704057075 575 True 503.000000 503 82.496000 1488 2062 1 chr3A.!!$R1 574

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
503 4576 0.034756 TTAGCTTTGTGCCGCTCTGA 59.965 50.0 0.0 0.0 44.23 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1547 7443 0.756294 TTCGCAGGAGGACACTCAAA 59.244 50.0 0.0 0.0 45.81 2.69 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
20 4088 3.110447 CATGGTTTGGAAGGTTTGGTG 57.890 47.619 0.00 0.00 0.00 4.17
35 4103 0.847373 TGGTGACCCCTAAAGTGCAA 59.153 50.000 0.00 0.00 0.00 4.08
36 4104 1.215673 TGGTGACCCCTAAAGTGCAAA 59.784 47.619 0.00 0.00 0.00 3.68
70 4138 4.141688 CCTTAGTTACCCAGAACAGGATCC 60.142 50.000 2.48 2.48 28.35 3.36
77 4145 2.202892 GAACAGGATCCGGACGGC 60.203 66.667 19.55 0.00 34.68 5.68
78 4146 3.000819 AACAGGATCCGGACGGCA 61.001 61.111 19.55 0.00 34.68 5.69
91 4159 1.751924 GGACGGCAGATAGACTTCAGT 59.248 52.381 0.00 0.00 0.00 3.41
106 4174 0.608130 TCAGTGACAAGGATGACCCG 59.392 55.000 0.00 0.00 40.87 5.28
115 4183 1.573108 AGGATGACCCGACTGTGATT 58.427 50.000 0.00 0.00 40.87 2.57
150 4218 2.010817 GCAAGTGCAAGAAACGGCG 61.011 57.895 4.80 4.80 41.59 6.46
156 4224 2.953821 CAAGAAACGGCGGCACAT 59.046 55.556 13.24 0.00 0.00 3.21
160 4228 1.741770 GAAACGGCGGCACATCTCT 60.742 57.895 13.24 0.00 0.00 3.10
165 4233 1.503542 GGCGGCACATCTCTTGTTG 59.496 57.895 3.07 0.00 36.00 3.33
230 4298 8.117813 TCCTGGTTAAACCTTCAAATTGATAC 57.882 34.615 0.00 0.00 39.58 2.24
245 4313 0.384309 GATACGACGACATGGCAGGA 59.616 55.000 5.99 0.00 0.00 3.86
252 4320 1.450312 GACATGGCAGGACTTCCCG 60.450 63.158 5.99 0.00 40.87 5.14
284 4352 4.634199 CTTGTTGGCAAGGAACAATCAAT 58.366 39.130 0.00 0.00 46.17 2.57
288 4356 3.429492 TGGCAAGGAACAATCAATAGCA 58.571 40.909 0.00 0.00 0.00 3.49
310 4379 2.031120 CAACAAACAAAGGCCCTCTCA 58.969 47.619 0.00 0.00 0.00 3.27
316 4385 4.657814 AACAAAGGCCCTCTCATCTTTA 57.342 40.909 0.00 0.00 0.00 1.85
351 4420 6.594788 TGGATGGGAGATTTGAAAAGAAAG 57.405 37.500 0.00 0.00 0.00 2.62
352 4421 6.314120 TGGATGGGAGATTTGAAAAGAAAGA 58.686 36.000 0.00 0.00 0.00 2.52
360 4431 5.632347 AGATTTGAAAAGAAAGAAGCATGCG 59.368 36.000 13.01 0.00 0.00 4.73
379 4450 8.893727 AGCATGCGTCTTTAGAAATAATAAAGT 58.106 29.630 13.01 0.00 39.92 2.66
383 4455 7.119992 TGCGTCTTTAGAAATAATAAAGTGGCA 59.880 33.333 15.32 15.32 41.44 4.92
385 4457 8.665685 CGTCTTTAGAAATAATAAAGTGGCACT 58.334 33.333 15.88 15.88 39.92 4.40
391 4463 2.675658 AATAAAGTGGCACTGGTGGT 57.324 45.000 22.83 1.09 0.00 4.16
399 4471 0.676782 GGCACTGGTGGTGGTGATAC 60.677 60.000 2.84 0.00 45.44 2.24
403 4475 3.370527 GCACTGGTGGTGGTGATACTTAT 60.371 47.826 2.84 0.00 45.44 1.73
404 4476 4.191544 CACTGGTGGTGGTGATACTTATG 58.808 47.826 0.00 0.00 41.90 1.90
406 4478 2.843730 TGGTGGTGGTGATACTTATGCT 59.156 45.455 0.00 0.00 0.00 3.79
416 4488 7.171678 GTGGTGATACTTATGCTAATGAAGGAC 59.828 40.741 0.00 0.00 0.00 3.85
424 4496 1.066605 GCTAATGAAGGACGAGGCGTA 59.933 52.381 0.00 0.00 41.37 4.42
440 4513 2.793278 CGTAGCTTTGGGTTTTTGCT 57.207 45.000 0.00 0.00 37.72 3.91
445 4518 0.836606 CTTTGGGTTTTTGCTGGGGT 59.163 50.000 0.00 0.00 0.00 4.95
503 4576 0.034756 TTAGCTTTGTGCCGCTCTGA 59.965 50.000 0.00 0.00 44.23 3.27
523 4596 4.016444 TGAGGCATGTAATCCTTCAAACC 58.984 43.478 0.00 0.00 31.71 3.27
527 4600 4.706962 GGCATGTAATCCTTCAAACCTCTT 59.293 41.667 0.00 0.00 0.00 2.85
539 4612 8.656806 TCCTTCAAACCTCTTTCTTAATCAGTA 58.343 33.333 0.00 0.00 0.00 2.74
598 4671 9.646336 AATAAAAATAGAAAGTGTATAAGCGCG 57.354 29.630 0.00 0.00 0.00 6.86
631 4989 2.855953 GCATGACCGTAATGCTGCATTC 60.856 50.000 29.29 19.26 45.62 2.67
727 5087 0.464554 GAGCTATGGTGGTGAAGGCC 60.465 60.000 0.00 0.00 0.00 5.19
766 5134 5.295787 ACGCAAATGTAACATATGACCGAAT 59.704 36.000 10.38 0.00 0.00 3.34
774 5142 2.626266 ACATATGACCGAATGCCTACGA 59.374 45.455 10.38 0.00 0.00 3.43
829 5201 1.585267 CTGCACCATAACCGCAAGCA 61.585 55.000 0.00 0.00 34.75 3.91
846 5221 4.677779 GCAAGCAACCTTTCTTCTTGTCAA 60.678 41.667 0.00 0.00 37.17 3.18
1110 5750 0.911769 TCAAAGCCGACAGGATGGAT 59.088 50.000 0.00 0.00 43.62 3.41
1248 7093 2.911143 CCGGCCTATCCTGCTTGT 59.089 61.111 0.00 0.00 0.00 3.16
1254 7115 1.611673 GCCTATCCTGCTTGTGTGTGT 60.612 52.381 0.00 0.00 0.00 3.72
1257 7118 2.057137 ATCCTGCTTGTGTGTGTGTT 57.943 45.000 0.00 0.00 0.00 3.32
1306 7167 1.553248 GTGATGCACCTACCACCTACA 59.447 52.381 0.00 0.00 0.00 2.74
1308 7169 1.831736 GATGCACCTACCACCTACACT 59.168 52.381 0.00 0.00 0.00 3.55
1333 7194 6.158520 TCCTATACCAGTATACCACCGCTATA 59.841 42.308 0.00 0.00 0.00 1.31
1346 7208 5.595542 ACCACCGCTATAAGATGTGTACTAA 59.404 40.000 0.00 0.00 0.00 2.24
1349 7211 7.040892 CCACCGCTATAAGATGTGTACTAAGTA 60.041 40.741 0.00 0.00 0.00 2.24
1380 7244 7.134815 CACTAAAATGAAATAAGAGCCATCCG 58.865 38.462 0.00 0.00 0.00 4.18
1387 7251 3.674528 ATAAGAGCCATCCGTCTCATG 57.325 47.619 0.00 0.00 0.00 3.07
1397 7261 5.783111 CCATCCGTCTCATGTGTCATATAA 58.217 41.667 0.00 0.00 0.00 0.98
1399 7263 5.845391 TCCGTCTCATGTGTCATATAACA 57.155 39.130 0.00 0.00 0.00 2.41
1424 7290 9.376075 CATACATATTGCTAGAGGATAACTTGG 57.624 37.037 0.00 0.00 0.00 3.61
1426 7292 6.558775 ACATATTGCTAGAGGATAACTTGGGA 59.441 38.462 0.00 0.00 0.00 4.37
1427 7293 7.238514 ACATATTGCTAGAGGATAACTTGGGAT 59.761 37.037 0.00 0.00 0.00 3.85
1429 7295 5.296151 TGCTAGAGGATAACTTGGGATTG 57.704 43.478 0.00 0.00 0.00 2.67
1430 7296 4.068599 GCTAGAGGATAACTTGGGATTGC 58.931 47.826 0.00 0.00 0.00 3.56
1457 7351 7.246171 TCTTTCTCTAGCAGGTTATTCTGTT 57.754 36.000 0.00 0.00 37.12 3.16
1520 7416 7.636150 AATACTAGATGCTGCTTTTGTGATT 57.364 32.000 0.00 0.00 0.00 2.57
1529 7425 7.176285 TGCTGCTTTTGTGATTAAAATGAAC 57.824 32.000 0.00 0.00 0.00 3.18
1597 7493 7.686438 ATGGCGATCAATACATATTGCTTTA 57.314 32.000 6.73 0.00 42.06 1.85
1611 7507 9.019656 ACATATTGCTTTAAACATACACCTTCA 57.980 29.630 0.00 0.00 0.00 3.02
1637 7533 4.668289 GAGCATAAACACGTTATTTGGGG 58.332 43.478 5.07 0.00 29.38 4.96
1646 7542 1.747367 TTATTTGGGGCGTGGCTCG 60.747 57.895 4.32 4.32 43.12 5.03
1684 7581 6.017109 GTCACATAGCCAAACATATTCGGATT 60.017 38.462 0.00 0.00 0.00 3.01
1687 7584 3.897239 AGCCAAACATATTCGGATTGGA 58.103 40.909 9.41 0.00 42.46 3.53
1711 7610 8.150296 GGAATATGTGCTTTATTTTGGGCTATT 58.850 33.333 0.00 0.00 0.00 1.73
1713 7612 9.904198 AATATGTGCTTTATTTTGGGCTATTTT 57.096 25.926 0.00 0.00 0.00 1.82
1807 7706 1.134521 GCCTGAATCCGTATGTGGTCA 60.135 52.381 0.00 0.00 0.00 4.02
1879 7778 0.760567 AGGAGATGATAGCACGGGCA 60.761 55.000 14.57 0.00 44.61 5.36
1900 7799 4.512944 GCAATCTTCAGCCGATTTAGATGA 59.487 41.667 0.00 0.00 0.00 2.92
1902 7801 4.736126 TCTTCAGCCGATTTAGATGACA 57.264 40.909 0.00 0.00 0.00 3.58
1933 7832 2.472029 AGGCTAAGTGTGTAGGCATCT 58.528 47.619 8.29 0.00 46.43 2.90
1960 7859 5.690409 GTCTATTCTTTATCGCCGAATGTGA 59.310 40.000 0.00 0.00 38.00 3.58
1993 7893 4.603231 TTGTGTTTCGTTTTAAGCTCGT 57.397 36.364 0.00 0.00 0.00 4.18
2053 7953 7.555087 TGCTTTTATTTAACAATATGGCTGCT 58.445 30.769 0.00 0.00 0.00 4.24
2076 7976 0.554305 ATCCATTGATGCAGAGGCCA 59.446 50.000 5.01 0.00 40.13 5.36
2078 7978 0.106868 CCATTGATGCAGAGGCCAGA 60.107 55.000 5.01 0.00 40.13 3.86
2100 8000 5.959618 AGGTTATCCTCCTTTTCAAAACG 57.040 39.130 0.00 0.00 40.58 3.60
2101 8001 5.382616 AGGTTATCCTCCTTTTCAAAACGT 58.617 37.500 0.00 0.00 40.58 3.99
2102 8002 5.831525 AGGTTATCCTCCTTTTCAAAACGTT 59.168 36.000 0.00 0.00 40.58 3.99
2103 8003 6.322969 AGGTTATCCTCCTTTTCAAAACGTTT 59.677 34.615 7.96 7.96 40.58 3.60
2104 8004 6.982141 GGTTATCCTCCTTTTCAAAACGTTTT 59.018 34.615 20.26 20.26 0.00 2.43
2105 8005 8.136800 GGTTATCCTCCTTTTCAAAACGTTTTA 58.863 33.333 24.79 8.99 0.00 1.52
2121 8021 7.815398 AACGTTTTAGTTTTACTTGGGTTTG 57.185 32.000 0.00 0.00 0.00 2.93
2141 8041 7.934665 GGGTTTGTTGGGTTTTAATTATGTTCT 59.065 33.333 0.00 0.00 0.00 3.01
2182 8082 4.335315 CGTTCATATATTGTGTTGGGTGCT 59.665 41.667 0.00 0.00 0.00 4.40
2196 8096 3.609853 TGGGTGCTGCTAAAGACAATAG 58.390 45.455 0.00 0.00 0.00 1.73
2199 8099 4.459337 GGGTGCTGCTAAAGACAATAGTTT 59.541 41.667 0.00 0.00 0.00 2.66
2204 8104 7.324616 GTGCTGCTAAAGACAATAGTTTTTCTG 59.675 37.037 0.00 0.00 34.35 3.02
2206 8106 8.239998 GCTGCTAAAGACAATAGTTTTTCTGAT 58.760 33.333 0.00 0.00 34.35 2.90
2215 8115 9.092876 GACAATAGTTTTTCTGATAGGAGAGTG 57.907 37.037 0.00 0.00 0.00 3.51
2226 8126 6.267699 TCTGATAGGAGAGTGAAGTTGTTTGA 59.732 38.462 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.697751 TCACCAAACCTTCCAAACCATG 59.302 45.455 0.00 0.00 0.00 3.66
2 3 2.104170 GTCACCAAACCTTCCAAACCA 58.896 47.619 0.00 0.00 0.00 3.67
4 5 1.411246 GGGTCACCAAACCTTCCAAAC 59.589 52.381 0.00 0.00 39.42 2.93
47 4115 4.141688 GGATCCTGTTCTGGGTAACTAAGG 60.142 50.000 3.84 0.00 0.00 2.69
48 4116 4.441634 CGGATCCTGTTCTGGGTAACTAAG 60.442 50.000 10.75 0.00 0.00 2.18
70 4138 0.738975 TGAAGTCTATCTGCCGTCCG 59.261 55.000 0.00 0.00 0.00 4.79
77 4145 5.651387 TCCTTGTCACTGAAGTCTATCTG 57.349 43.478 0.00 0.00 0.00 2.90
78 4146 5.954752 TCATCCTTGTCACTGAAGTCTATCT 59.045 40.000 0.00 0.00 0.00 1.98
91 4159 0.608130 CAGTCGGGTCATCCTTGTCA 59.392 55.000 0.00 0.00 0.00 3.58
106 4174 4.125703 CAGAGAGGGCATTAATCACAGTC 58.874 47.826 0.00 0.00 0.00 3.51
115 4183 3.519510 ACTTGCTTACAGAGAGGGCATTA 59.480 43.478 0.00 0.00 32.87 1.90
150 4218 3.549299 CACTTCAACAAGAGATGTGCC 57.451 47.619 0.00 0.00 42.99 5.01
156 4224 0.468226 ACCGGCACTTCAACAAGAGA 59.532 50.000 0.00 0.00 33.34 3.10
160 4228 2.018544 CGAACCGGCACTTCAACAA 58.981 52.632 0.00 0.00 0.00 2.83
165 4233 3.774702 GTCGCGAACCGGCACTTC 61.775 66.667 12.06 0.00 42.23 3.01
187 4255 4.144297 CAGGAGAACACATCCTTCCAAAA 58.856 43.478 0.00 0.00 45.13 2.44
230 4298 1.078759 GAAGTCCTGCCATGTCGTCG 61.079 60.000 0.00 0.00 0.00 5.12
252 4320 1.080772 GCCAACAAGCTTTACCCGC 60.081 57.895 0.00 0.00 0.00 6.13
284 4352 1.410882 GGCCTTTGTTTGTTGGTGCTA 59.589 47.619 0.00 0.00 0.00 3.49
288 4356 1.119684 GAGGGCCTTTGTTTGTTGGT 58.880 50.000 7.89 0.00 0.00 3.67
351 4420 9.716507 TTTATTATTTCTAAAGACGCATGCTTC 57.283 29.630 15.97 15.97 0.00 3.86
352 4421 9.722056 CTTTATTATTTCTAAAGACGCATGCTT 57.278 29.630 17.13 6.17 38.07 3.91
360 4431 9.774742 CAGTGCCACTTTATTATTTCTAAAGAC 57.225 33.333 0.00 0.00 38.07 3.01
379 4450 1.130678 TATCACCACCACCAGTGCCA 61.131 55.000 0.00 0.00 45.83 4.92
383 4455 3.370527 GCATAAGTATCACCACCACCAGT 60.371 47.826 0.00 0.00 0.00 4.00
385 4457 2.843730 AGCATAAGTATCACCACCACCA 59.156 45.455 0.00 0.00 0.00 4.17
391 4463 7.217200 GTCCTTCATTAGCATAAGTATCACCA 58.783 38.462 0.00 0.00 0.00 4.17
399 4471 3.743396 GCCTCGTCCTTCATTAGCATAAG 59.257 47.826 0.00 0.00 0.00 1.73
403 4475 0.179111 CGCCTCGTCCTTCATTAGCA 60.179 55.000 0.00 0.00 0.00 3.49
404 4476 0.179108 ACGCCTCGTCCTTCATTAGC 60.179 55.000 0.00 0.00 33.69 3.09
406 4478 1.066605 GCTACGCCTCGTCCTTCATTA 59.933 52.381 0.00 0.00 41.54 1.90
416 4488 0.953960 AAACCCAAAGCTACGCCTCG 60.954 55.000 0.00 0.00 0.00 4.63
424 4496 0.469494 CCCAGCAAAAACCCAAAGCT 59.531 50.000 0.00 0.00 35.63 3.74
433 4506 0.463620 GTGCTTGACCCCAGCAAAAA 59.536 50.000 0.00 0.00 40.45 1.94
440 4513 1.429930 TACTCAAGTGCTTGACCCCA 58.570 50.000 10.26 0.00 43.90 4.96
445 4518 7.604927 ACGGTATTAAATTACTCAAGTGCTTGA 59.395 33.333 13.22 13.22 46.27 3.02
462 4535 7.645340 GCTAACGAATTACTCTCACGGTATTAA 59.355 37.037 0.00 0.00 0.00 1.40
467 4540 3.442977 AGCTAACGAATTACTCTCACGGT 59.557 43.478 0.00 0.00 0.00 4.83
503 4576 4.018050 AGAGGTTTGAAGGATTACATGCCT 60.018 41.667 0.00 0.00 35.61 4.75
507 4580 9.807921 TTAAGAAAGAGGTTTGAAGGATTACAT 57.192 29.630 0.00 0.00 0.00 2.29
573 4646 8.823818 ACGCGCTTATACACTTTCTATTTTTAT 58.176 29.630 5.73 0.00 0.00 1.40
574 4647 8.188531 ACGCGCTTATACACTTTCTATTTTTA 57.811 30.769 5.73 0.00 0.00 1.52
575 4648 7.068692 ACGCGCTTATACACTTTCTATTTTT 57.931 32.000 5.73 0.00 0.00 1.94
576 4649 6.657836 ACGCGCTTATACACTTTCTATTTT 57.342 33.333 5.73 0.00 0.00 1.82
577 4650 7.568861 GCATACGCGCTTATACACTTTCTATTT 60.569 37.037 5.73 0.00 0.00 1.40
578 4651 6.128902 GCATACGCGCTTATACACTTTCTATT 60.129 38.462 5.73 0.00 0.00 1.73
579 4652 5.345202 GCATACGCGCTTATACACTTTCTAT 59.655 40.000 5.73 0.00 0.00 1.98
580 4653 4.678287 GCATACGCGCTTATACACTTTCTA 59.322 41.667 5.73 0.00 0.00 2.10
581 4654 3.489785 GCATACGCGCTTATACACTTTCT 59.510 43.478 5.73 0.00 0.00 2.52
582 4655 3.244345 TGCATACGCGCTTATACACTTTC 59.756 43.478 5.73 0.00 42.97 2.62
583 4656 3.000925 GTGCATACGCGCTTATACACTTT 59.999 43.478 23.10 0.00 45.49 2.66
631 4989 0.958091 TTGTTTTCCCATGGACGCAG 59.042 50.000 15.22 0.00 0.00 5.18
637 4995 3.256631 CCTCTTGACTTGTTTTCCCATGG 59.743 47.826 4.14 4.14 0.00 3.66
641 4999 2.554462 GAGCCTCTTGACTTGTTTTCCC 59.446 50.000 0.00 0.00 0.00 3.97
766 5134 0.812549 TACTCGTGCATTCGTAGGCA 59.187 50.000 0.00 0.00 39.01 4.75
829 5201 4.580580 AGCGAATTGACAAGAAGAAAGGTT 59.419 37.500 0.00 0.00 0.00 3.50
846 5221 0.679960 GTTTGCCCCTACCAGCGAAT 60.680 55.000 0.00 0.00 34.96 3.34
940 5567 2.362397 TGGCTGCAAAATACGAACCAAA 59.638 40.909 0.50 0.00 0.00 3.28
947 5574 1.453155 ACCTCTGGCTGCAAAATACG 58.547 50.000 0.50 0.00 0.00 3.06
1056 5696 4.280019 AAACCGTCCCAGCCCACC 62.280 66.667 0.00 0.00 0.00 4.61
1110 5750 5.726397 ACGGTGTGCAACTCTATATAAACA 58.274 37.500 0.00 0.00 38.04 2.83
1248 7093 1.288350 CGTAAACGGGAACACACACA 58.712 50.000 0.00 0.00 35.37 3.72
1306 7167 4.660168 CGGTGGTATACTGGTATAGGAGT 58.340 47.826 2.25 0.00 31.71 3.85
1308 7169 3.074985 AGCGGTGGTATACTGGTATAGGA 59.925 47.826 2.25 0.00 44.25 2.94
1349 7211 9.301897 GGCTCTTATTTCATTTTAGTGGGATAT 57.698 33.333 0.00 0.00 0.00 1.63
1352 7214 6.489603 TGGCTCTTATTTCATTTTAGTGGGA 58.510 36.000 0.00 0.00 0.00 4.37
1354 7216 7.428826 GGATGGCTCTTATTTCATTTTAGTGG 58.571 38.462 0.00 0.00 0.00 4.00
1357 7219 7.227512 AGACGGATGGCTCTTATTTCATTTTAG 59.772 37.037 0.00 0.00 0.00 1.85
1358 7220 7.054124 AGACGGATGGCTCTTATTTCATTTTA 58.946 34.615 0.00 0.00 0.00 1.52
1359 7221 5.888161 AGACGGATGGCTCTTATTTCATTTT 59.112 36.000 0.00 0.00 0.00 1.82
1397 7261 9.935241 CAAGTTATCCTCTAGCAATATGTATGT 57.065 33.333 0.00 0.00 0.00 2.29
1399 7263 8.543774 CCCAAGTTATCCTCTAGCAATATGTAT 58.456 37.037 0.00 0.00 0.00 2.29
1408 7274 4.068599 GCAATCCCAAGTTATCCTCTAGC 58.931 47.826 0.00 0.00 0.00 3.42
1424 7290 3.813443 TGCTAGAGAAAGATGGCAATCC 58.187 45.455 0.00 0.00 32.77 3.01
1426 7292 3.201708 ACCTGCTAGAGAAAGATGGCAAT 59.798 43.478 0.00 0.00 0.00 3.56
1427 7293 2.573462 ACCTGCTAGAGAAAGATGGCAA 59.427 45.455 0.00 0.00 0.00 4.52
1429 7295 2.998316 ACCTGCTAGAGAAAGATGGC 57.002 50.000 0.00 0.00 0.00 4.40
1430 7296 6.705381 CAGAATAACCTGCTAGAGAAAGATGG 59.295 42.308 0.00 0.00 0.00 3.51
1457 7351 6.282167 TCTGTCAGATTAAACGTAACAACCA 58.718 36.000 0.00 0.00 0.00 3.67
1491 7387 6.540189 ACAAAAGCAGCATCTAGTATTACCAG 59.460 38.462 0.00 0.00 0.00 4.00
1547 7443 0.756294 TTCGCAGGAGGACACTCAAA 59.244 50.000 0.00 0.00 45.81 2.69
1560 7456 5.281693 TGATCGCCATAATAATTTCGCAG 57.718 39.130 0.00 0.00 0.00 5.18
1597 7493 4.827692 TGCTCGTATGAAGGTGTATGTTT 58.172 39.130 0.00 0.00 0.00 2.83
1608 7504 7.528481 AATAACGTGTTTATGCTCGTATGAA 57.472 32.000 0.00 0.00 37.56 2.57
1611 7507 6.238266 CCCAAATAACGTGTTTATGCTCGTAT 60.238 38.462 0.00 0.00 37.56 3.06
1637 7533 1.878522 CCACTACATCGAGCCACGC 60.879 63.158 0.00 0.00 42.26 5.34
1646 7542 4.363999 GCTATGTGACTGTCCACTACATC 58.636 47.826 12.90 0.32 37.50 3.06
1650 7546 2.815158 TGGCTATGTGACTGTCCACTA 58.185 47.619 5.17 0.00 37.89 2.74
1684 7581 5.424895 AGCCCAAAATAAAGCACATATTCCA 59.575 36.000 0.00 0.00 0.00 3.53
1687 7584 9.904198 AAAATAGCCCAAAATAAAGCACATATT 57.096 25.926 0.00 0.00 0.00 1.28
1765 7664 5.279356 GGCTGTAGCTTTATAGATAACCCGT 60.279 44.000 3.63 0.00 41.70 5.28
1767 7666 6.014499 TCAGGCTGTAGCTTTATAGATAACCC 60.014 42.308 15.27 0.00 41.70 4.11
1777 7676 2.500098 ACGGATTCAGGCTGTAGCTTTA 59.500 45.455 15.27 0.00 41.70 1.85
1807 7706 5.339008 TGAAGTCCGCATGAGTTAGTAAT 57.661 39.130 0.00 0.00 36.74 1.89
1860 7759 0.760567 TGCCCGTGCTATCATCTCCT 60.761 55.000 0.00 0.00 38.71 3.69
1879 7778 5.674525 TGTCATCTAAATCGGCTGAAGATT 58.325 37.500 0.00 0.00 39.75 2.40
1895 7794 8.875168 ACTTAGCCTATTATTAGCTTGTCATCT 58.125 33.333 0.00 0.00 0.00 2.90
1900 7799 7.565680 ACACACTTAGCCTATTATTAGCTTGT 58.434 34.615 0.00 0.00 0.00 3.16
1902 7801 8.368668 CCTACACACTTAGCCTATTATTAGCTT 58.631 37.037 0.00 0.00 0.00 3.74
1919 7818 6.836527 AGAATAGACTAAGATGCCTACACACT 59.163 38.462 0.00 0.00 0.00 3.55
1933 7832 7.381408 CACATTCGGCGATAAAGAATAGACTAA 59.619 37.037 11.76 0.00 33.75 2.24
1960 7859 3.508402 ACGAAACACAAAGGGAAAAGTGT 59.492 39.130 0.00 0.00 46.24 3.55
1993 7893 9.201989 TCTCAAGGTCTAGAAAAGCTCATAATA 57.798 33.333 0.00 0.00 0.00 0.98
2099 7999 7.201453 CCAACAAACCCAAGTAAAACTAAAACG 60.201 37.037 0.00 0.00 0.00 3.60
2100 8000 7.064847 CCCAACAAACCCAAGTAAAACTAAAAC 59.935 37.037 0.00 0.00 0.00 2.43
2101 8001 7.104290 CCCAACAAACCCAAGTAAAACTAAAA 58.896 34.615 0.00 0.00 0.00 1.52
2102 8002 6.212993 ACCCAACAAACCCAAGTAAAACTAAA 59.787 34.615 0.00 0.00 0.00 1.85
2103 8003 5.720520 ACCCAACAAACCCAAGTAAAACTAA 59.279 36.000 0.00 0.00 0.00 2.24
2104 8004 5.270794 ACCCAACAAACCCAAGTAAAACTA 58.729 37.500 0.00 0.00 0.00 2.24
2105 8005 4.098155 ACCCAACAAACCCAAGTAAAACT 58.902 39.130 0.00 0.00 0.00 2.66
2112 8012 7.717436 ACATAATTAAAACCCAACAAACCCAAG 59.283 33.333 0.00 0.00 0.00 3.61
2116 8016 8.769891 CAGAACATAATTAAAACCCAACAAACC 58.230 33.333 0.00 0.00 0.00 3.27
2117 8017 9.320352 ACAGAACATAATTAAAACCCAACAAAC 57.680 29.630 0.00 0.00 0.00 2.93
2121 8021 8.799367 ACCTACAGAACATAATTAAAACCCAAC 58.201 33.333 0.00 0.00 0.00 3.77
2141 8041 3.581265 ACGGGAAAAAGGAAACCTACA 57.419 42.857 0.00 0.00 31.13 2.74
2196 8096 7.442666 ACAACTTCACTCTCCTATCAGAAAAAC 59.557 37.037 0.00 0.00 0.00 2.43
2199 8099 6.672266 ACAACTTCACTCTCCTATCAGAAA 57.328 37.500 0.00 0.00 0.00 2.52
2204 8104 6.876257 ACATCAAACAACTTCACTCTCCTATC 59.124 38.462 0.00 0.00 0.00 2.08
2206 8106 5.991606 CACATCAAACAACTTCACTCTCCTA 59.008 40.000 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.