Multiple sequence alignment - TraesCS6B01G125000

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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 TraesCS6B01G125000 chr6B 100.000 3642 0 0 1 3642 120014259 120010618 0.000000e+00 6726.0
1 TraesCS6B01G125000 chr6B 100.000 2211 0 0 4556 6766 120009704 120007494 0.000000e+00 4084.0
2 TraesCS6B01G125000 chr6B 91.364 220 19 0 4558 4777 120009660 120009441 1.100000e-77 302.0
3 TraesCS6B01G125000 chr6B 91.364 220 19 0 4600 4819 120009702 120009483 1.100000e-77 302.0
4 TraesCS6B01G125000 chr6B 96.104 154 6 0 4558 4711 120009618 120009465 1.130000e-62 252.0
5 TraesCS6B01G125000 chr6B 96.104 154 6 0 4642 4795 120009702 120009549 1.130000e-62 252.0
6 TraesCS6B01G125000 chr6B 83.333 84 9 3 6602 6684 713313991 713313912 9.410000e-09 73.1
7 TraesCS6B01G125000 chr6D 92.678 3715 154 42 1 3642 52872982 52869313 0.000000e+00 5245.0
8 TraesCS6B01G125000 chr6D 96.209 1609 50 7 4568 6172 52868895 52867294 0.000000e+00 2623.0
9 TraesCS6B01G125000 chr6D 84.873 628 39 20 6161 6766 52867241 52866648 3.520000e-162 582.0
10 TraesCS6B01G125000 chr6D 84.528 265 41 0 4558 4822 52869476 52869212 5.200000e-66 263.0
11 TraesCS6B01G125000 chr6D 88.182 220 23 1 4558 4777 52868863 52868647 6.730000e-65 259.0
12 TraesCS6B01G125000 chr6A 96.388 2547 56 15 1037 3578 63786515 63784000 0.000000e+00 4161.0
13 TraesCS6B01G125000 chr6A 92.510 2243 98 30 4561 6766 63783581 63781372 0.000000e+00 3147.0
14 TraesCS6B01G125000 chr6A 88.971 544 54 4 1 541 63787773 63787233 0.000000e+00 667.0
15 TraesCS6B01G125000 chr6A 86.224 392 15 12 613 968 63787185 63786797 8.230000e-104 388.0
16 TraesCS6B01G125000 chr6A 88.182 220 23 1 4558 4777 63783542 63783326 6.730000e-65 259.0
17 TraesCS6B01G125000 chr6A 87.097 217 25 1 4603 4819 63783581 63783368 6.780000e-60 243.0


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 TraesCS6B01G125000 chr6B 120007494 120014259 6765 True 1986.333333 6726 95.822667 1 6766 6 chr6B.!!$R2 6765
1 TraesCS6B01G125000 chr6D 52866648 52872982 6334 True 1794.400000 5245 89.294000 1 6766 5 chr6D.!!$R1 6765
2 TraesCS6B01G125000 chr6A 63781372 63787773 6401 True 1477.500000 4161 89.895333 1 6766 6 chr6A.!!$R1 6765

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
33 34 0.400213 AATGTTGGTTCGAGGGCTGA 59.600 50.000 0.00 0.00 0.00 4.26 F
1165 1446 0.249405 CAGCAAGGAGGAGATCGAGC 60.249 60.000 0.00 0.00 0.00 5.03 F
2006 2295 0.584876 GGGTTGTGTAACGTGTCTGC 59.415 55.000 0.00 0.00 42.39 4.26 F
2048 2337 1.606668 TGGTCACGGCAGACAAAATTC 59.393 47.619 8.99 0.00 40.29 2.17 F
3303 3593 0.179020 CTGCTATCGGGCCCATTCAA 60.179 55.000 24.92 0.78 0.00 2.69 F
3304 3594 0.179020 TGCTATCGGGCCCATTCAAG 60.179 55.000 24.92 12.24 0.00 3.02 F
3490 3780 0.255318 CTTCCTGAAGCCAGCTCCAT 59.745 55.000 0.00 0.00 39.07 3.41 F
3626 3916 1.079543 CAGCTCTGGTGGAGGAACG 60.080 63.158 0.00 0.00 42.08 3.95 F
4628 4918 1.301716 GGCGGAGAAACAGCAGACA 60.302 57.895 0.00 0.00 41.24 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1215 1496 0.924090 TGGAGTAGATGGACCGGAGA 59.076 55.000 9.46 0.00 0.00 3.71 R
2447 2737 0.033504 GCAACAGTCTGGAAGGACGA 59.966 55.000 4.53 0.00 40.76 4.20 R
3017 3307 1.255882 TCATGAAACTTGGCGGCAAT 58.744 45.000 25.71 10.76 0.00 3.56 R
3506 3796 2.111384 CAGGCTTCTGGGAGCTTACTA 58.889 52.381 0.63 0.00 42.32 1.82 R
4570 4860 0.601046 TGCTGTCTGCTGTTTCTCCG 60.601 55.000 3.20 0.00 43.37 4.63 R
4575 4865 0.950116 GAGCTTGCTGTCTGCTGTTT 59.050 50.000 0.00 0.00 43.37 2.83 R
5041 5731 1.073897 GAAGGGTGTGCTTGCCTCT 59.926 57.895 0.00 0.00 0.00 3.69 R
5405 6095 1.154093 CATTCGCAGTGGCTTGCTG 60.154 57.895 11.63 6.49 41.90 4.41 R
5824 6514 1.000385 CACAACCGCAATTCACATGGT 60.000 47.619 0.00 0.00 33.45 3.55 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
33 34 0.400213 AATGTTGGTTCGAGGGCTGA 59.600 50.000 0.00 0.00 0.00 4.26
63 64 4.038642 GCAGATCGAGGAGGTAAAGAAGAT 59.961 45.833 0.00 0.00 0.00 2.40
66 67 6.263392 CAGATCGAGGAGGTAAAGAAGATACA 59.737 42.308 0.00 0.00 0.00 2.29
74 75 7.039223 AGGAGGTAAAGAAGATACAAAACGAGA 60.039 37.037 0.00 0.00 0.00 4.04
79 80 4.894784 AGAAGATACAAAACGAGAGGCAA 58.105 39.130 0.00 0.00 0.00 4.52
91 92 0.460284 AGAGGCAATAGCACGGTTCG 60.460 55.000 0.00 0.00 44.61 3.95
191 192 2.799917 GCGTCACAGTCTCTGTCACTTT 60.800 50.000 2.90 0.00 43.43 2.66
198 199 5.117745 CACAGTCTCTGTCACTTTGTAATCG 59.882 44.000 0.00 0.00 43.43 3.34
201 202 6.587990 CAGTCTCTGTCACTTTGTAATCGATT 59.412 38.462 16.15 16.15 0.00 3.34
203 204 6.366332 GTCTCTGTCACTTTGTAATCGATTGT 59.634 38.462 20.87 6.58 0.00 2.71
213 214 1.359848 AATCGATTGTGAGGTGCGTC 58.640 50.000 10.50 0.00 0.00 5.19
291 294 2.760385 GGACGGGGGAGAGGTCTG 60.760 72.222 0.00 0.00 0.00 3.51
335 338 3.676291 TTGGAACATGAGATGTGACGA 57.324 42.857 0.00 0.00 44.07 4.20
340 343 0.873312 CATGAGATGTGACGAGCCGG 60.873 60.000 0.00 0.00 0.00 6.13
359 370 3.120442 CCGGTTGTGATTTACTTTCGACC 60.120 47.826 0.00 0.00 0.00 4.79
368 379 2.838386 TACTTTCGACCGAGGAATCG 57.162 50.000 0.00 0.00 39.72 3.34
388 399 3.637229 TCGCTTACTATTTCCTCCCTCTG 59.363 47.826 0.00 0.00 0.00 3.35
389 400 3.243907 CGCTTACTATTTCCTCCCTCTGG 60.244 52.174 0.00 0.00 0.00 3.86
390 401 3.967987 GCTTACTATTTCCTCCCTCTGGA 59.032 47.826 0.00 0.00 38.75 3.86
450 463 2.494059 CAAACACGAGACCCACTCAAT 58.506 47.619 0.00 0.00 45.14 2.57
491 504 1.130373 CCTGCTAAAGAAAATCGCGCA 59.870 47.619 8.75 0.00 0.00 6.09
506 519 3.183754 TCGCGCAATTCGAATTCTCTAA 58.816 40.909 20.31 4.30 41.67 2.10
525 538 2.077687 ACAGGATCATGCAATTCCCC 57.922 50.000 7.40 0.00 0.00 4.81
533 546 1.624813 CATGCAATTCCCCCTTGTTGT 59.375 47.619 0.00 0.00 0.00 3.32
541 559 6.295632 GCAATTCCCCCTTGTTGTTTAGTAAT 60.296 38.462 0.00 0.00 0.00 1.89
543 561 4.581868 TCCCCCTTGTTGTTTAGTAATCG 58.418 43.478 0.00 0.00 0.00 3.34
554 572 7.042858 TGTTGTTTAGTAATCGCGTGTTTTCTA 60.043 33.333 5.77 3.98 0.00 2.10
556 574 7.849496 TGTTTAGTAATCGCGTGTTTTCTAAA 58.151 30.769 19.24 19.24 30.63 1.85
557 575 8.333908 TGTTTAGTAATCGCGTGTTTTCTAAAA 58.666 29.630 22.31 14.73 32.88 1.52
558 576 9.157259 GTTTAGTAATCGCGTGTTTTCTAAAAA 57.843 29.630 22.31 9.87 32.88 1.94
584 602 7.971183 AAAATTAGAGGAGTGAGAACTGAAC 57.029 36.000 0.00 0.00 0.00 3.18
592 610 5.819901 AGGAGTGAGAACTGAACTTCTTTTG 59.180 40.000 0.00 0.00 30.21 2.44
600 618 7.112779 AGAACTGAACTTCTTTTGAAAGAGGA 58.887 34.615 18.72 1.26 45.01 3.71
603 621 6.136541 TGAACTTCTTTTGAAAGAGGAAGC 57.863 37.500 18.72 9.80 45.01 3.86
605 623 6.152661 TGAACTTCTTTTGAAAGAGGAAGCAA 59.847 34.615 18.72 0.00 45.01 3.91
606 624 6.721704 ACTTCTTTTGAAAGAGGAAGCAAT 57.278 33.333 18.72 0.00 45.01 3.56
634 656 6.405278 TTTTTCAGGGCTAAAAGAGGAAAG 57.595 37.500 0.00 0.00 0.00 2.62
638 660 4.104102 TCAGGGCTAAAAGAGGAAAGTTCA 59.896 41.667 0.00 0.00 0.00 3.18
656 684 5.312079 AGTTCATCCTCAAACAGAAGGAAG 58.688 41.667 0.00 0.00 33.78 3.46
707 737 3.779444 TGTTCCCATCTATATCGAGCCT 58.221 45.455 0.00 0.00 0.00 4.58
973 1041 2.614013 GATCCCCACACCCACCCT 60.614 66.667 0.00 0.00 0.00 4.34
974 1042 2.614013 ATCCCCACACCCACCCTC 60.614 66.667 0.00 0.00 0.00 4.30
975 1043 4.995058 TCCCCACACCCACCCTCC 62.995 72.222 0.00 0.00 0.00 4.30
1074 1355 2.284151 GTCCCCTCCTCCTCCTCC 59.716 72.222 0.00 0.00 0.00 4.30
1075 1356 2.133201 TCCCCTCCTCCTCCTCCT 59.867 66.667 0.00 0.00 0.00 3.69
1076 1357 2.015726 TCCCCTCCTCCTCCTCCTC 61.016 68.421 0.00 0.00 0.00 3.71
1165 1446 0.249405 CAGCAAGGAGGAGATCGAGC 60.249 60.000 0.00 0.00 0.00 5.03
1225 1506 4.414956 AGGCCCATCTCCGGTCCA 62.415 66.667 0.00 0.00 0.00 4.02
1415 1702 1.533711 CTGGCCCCCGATGAAATCT 59.466 57.895 0.00 0.00 42.58 2.40
1481 1769 2.923426 ATCACAATCGCGACGGGCAT 62.923 55.000 12.93 0.00 43.84 4.40
1578 1866 3.388308 CCAACAATGGCAAATCGTTTCA 58.612 40.909 0.00 0.00 40.58 2.69
1596 1884 1.013596 CAGCACACACGACCTTGAAA 58.986 50.000 0.00 0.00 0.00 2.69
1597 1885 1.400142 CAGCACACACGACCTTGAAAA 59.600 47.619 0.00 0.00 0.00 2.29
1628 1916 2.281208 TAACCAGTTTGGCGCGCT 60.281 55.556 32.29 7.69 42.67 5.92
1650 1938 1.464023 CGTGTGTGTCGAATTCATGCC 60.464 52.381 6.22 0.00 0.00 4.40
1708 1997 2.675423 TCCGTCAGGGTCTGTCCG 60.675 66.667 0.00 0.00 38.33 4.79
1760 2049 4.036262 GCCATTTTTACTGTCACTGTGTCA 59.964 41.667 7.79 7.61 0.00 3.58
1794 2083 4.537135 TCTCTTACCTTTGTAGCACTGG 57.463 45.455 0.00 0.00 0.00 4.00
1968 2257 8.831000 AAATGTTGTCGTTTTCTGTTTAGTAC 57.169 30.769 0.00 0.00 29.63 2.73
2006 2295 0.584876 GGGTTGTGTAACGTGTCTGC 59.415 55.000 0.00 0.00 42.39 4.26
2048 2337 1.606668 TGGTCACGGCAGACAAAATTC 59.393 47.619 8.99 0.00 40.29 2.17
2070 2359 6.339587 TCTAACATGGGTTTTGGATCAAAC 57.660 37.500 0.00 0.00 38.45 2.93
2319 2609 3.118261 TCAAGTCCTGTTCTTCTTGCTGT 60.118 43.478 0.00 0.00 37.68 4.40
2323 2613 3.378427 GTCCTGTTCTTCTTGCTGTTGTT 59.622 43.478 0.00 0.00 0.00 2.83
2399 2689 2.665519 GCAGCAACACAACTTCATACCG 60.666 50.000 0.00 0.00 0.00 4.02
2527 2817 2.159382 CCTTGCCAATTAGGACGTGTT 58.841 47.619 0.00 0.00 41.22 3.32
2663 2953 5.890334 TGTTTCTTGTGATGTTTCTGTTCC 58.110 37.500 0.00 0.00 0.00 3.62
2968 3258 2.093106 CTGTACAGGCTTCGGACTACT 58.907 52.381 15.49 0.00 0.00 2.57
3153 3443 6.228273 TCATTGAGTTAGTTTTCTTCTGCG 57.772 37.500 0.00 0.00 0.00 5.18
3279 3569 4.572571 AGAAACCAACGCCCCGCA 62.573 61.111 0.00 0.00 0.00 5.69
3300 3590 1.770110 TCCTGCTATCGGGCCCATT 60.770 57.895 24.92 11.03 38.67 3.16
3301 3591 1.302832 CCTGCTATCGGGCCCATTC 60.303 63.158 24.92 6.06 30.75 2.67
3302 3592 1.451504 CTGCTATCGGGCCCATTCA 59.548 57.895 24.92 10.66 0.00 2.57
3303 3593 0.179020 CTGCTATCGGGCCCATTCAA 60.179 55.000 24.92 0.78 0.00 2.69
3304 3594 0.179020 TGCTATCGGGCCCATTCAAG 60.179 55.000 24.92 12.24 0.00 3.02
3305 3595 1.518903 GCTATCGGGCCCATTCAAGC 61.519 60.000 24.92 18.30 0.00 4.01
3382 3672 0.675633 GGTGGCAAAACAGCAGACAT 59.324 50.000 0.00 0.00 38.65 3.06
3421 3711 2.192861 CCGGTGGCAAAACAGCAGA 61.193 57.895 0.00 0.00 38.72 4.26
3490 3780 0.255318 CTTCCTGAAGCCAGCTCCAT 59.745 55.000 0.00 0.00 39.07 3.41
3506 3796 2.232941 CTCCATTGGCAAAACAGCAGAT 59.767 45.455 3.01 0.00 35.83 2.90
3555 3845 3.515502 TGGAGGAACATCAGACAGTAAGG 59.484 47.826 0.00 0.00 0.00 2.69
3626 3916 1.079543 CAGCTCTGGTGGAGGAACG 60.080 63.158 0.00 0.00 42.08 3.95
4584 4874 2.048222 CGGCGGAGAAACAGCAGA 60.048 61.111 0.00 0.00 41.24 4.26
4588 4878 1.905922 GCGGAGAAACAGCAGACAGC 61.906 60.000 0.00 0.00 46.19 4.40
4609 4899 3.080121 CTCCCCGAAGCCTGCTCT 61.080 66.667 0.00 0.00 0.00 4.09
4628 4918 1.301716 GGCGGAGAAACAGCAGACA 60.302 57.895 0.00 0.00 41.24 3.41
4630 4920 1.905922 GCGGAGAAACAGCAGACAGC 61.906 60.000 0.00 0.00 46.19 4.40
4693 5302 3.080121 CTCCCCGAAGCCTGCTCT 61.080 66.667 0.00 0.00 0.00 4.09
4723 5413 2.350514 GCAGACAGCAAGCTCCCT 59.649 61.111 0.00 0.00 44.79 4.20
4759 5449 3.390135 CGGAGAAACAGCAGACAGTAAA 58.610 45.455 0.00 0.00 0.00 2.01
4810 5500 5.699143 ACAGCAGATTATAAGCTTCCCAAT 58.301 37.500 0.00 0.60 36.26 3.16
5041 5731 2.310779 AGCACCCTAGACTCTGTTCA 57.689 50.000 0.00 0.00 0.00 3.18
5072 5762 1.421646 CACCCTTCAGTTGGAGGAGTT 59.578 52.381 8.09 0.00 0.00 3.01
5101 5791 5.335897 GCACTAGATCTCCAGCTCAAGATAG 60.336 48.000 0.00 5.57 32.43 2.08
5174 5864 1.518056 ATGCACGCCCTTCAGTTGTG 61.518 55.000 0.00 0.00 0.00 3.33
5345 6035 1.301716 TGCTCTGGCGAGGAAACAC 60.302 57.895 0.00 0.00 42.25 3.32
5678 6368 0.953471 CAAGTTTGATCGTCGCCCCA 60.953 55.000 0.00 0.00 0.00 4.96
5757 6447 7.285401 CCCATTGGTACTGCTATTAAAGACAAT 59.715 37.037 1.20 0.00 0.00 2.71
5818 6508 6.601613 TGTGGAAAGTGAACAGTGATTAAGTT 59.398 34.615 0.00 0.00 0.00 2.66
5819 6509 7.771361 TGTGGAAAGTGAACAGTGATTAAGTTA 59.229 33.333 0.00 0.00 0.00 2.24
5820 6510 8.784043 GTGGAAAGTGAACAGTGATTAAGTTAT 58.216 33.333 0.00 0.00 0.00 1.89
5830 6520 9.905713 AACAGTGATTAAGTTATGATACCATGT 57.094 29.630 0.00 0.00 34.31 3.21
5839 6529 5.239306 AGTTATGATACCATGTGAATTGCGG 59.761 40.000 0.00 0.00 34.31 5.69
5928 6618 1.061570 CTCGAAGGCGCTTGATTGC 59.938 57.895 7.64 0.00 37.46 3.56
5935 6625 1.937846 GCGCTTGATTGCTCGCATG 60.938 57.895 0.00 0.00 45.99 4.06
6192 6949 2.159212 TGCGGAGGCATTCATTCATTTG 60.159 45.455 0.00 0.00 46.21 2.32
6316 7074 4.347813 GTGCAAACGTATGTTGTTGTCTT 58.652 39.130 0.00 0.00 38.62 3.01
6341 7099 5.690865 TCTGGAGGTTATGTTTGTCTGTTT 58.309 37.500 0.00 0.00 0.00 2.83
6367 7125 5.348451 CAGTTTTTCCTTGTGTTTTGTCTGG 59.652 40.000 0.00 0.00 0.00 3.86
6369 7127 5.930837 TTTTCCTTGTGTTTTGTCTGGAT 57.069 34.783 0.00 0.00 0.00 3.41
6384 7142 9.489084 TTTTGTCTGGATACTATATGTATGTGC 57.511 33.333 3.48 0.00 41.55 4.57
6576 7334 9.831054 CGTAAATATAGACGTTGATCAAACTTC 57.169 33.333 10.35 6.89 37.32 3.01
6584 7342 7.707104 AGACGTTGATCAAACTTCTTTTTCAT 58.293 30.769 10.35 0.00 42.96 2.57
6586 7344 9.445786 GACGTTGATCAAACTTCTTTTTCATAA 57.554 29.630 10.35 0.00 34.89 1.90
6688 7470 7.391148 AAGTATCAACATCCACAATACCAAC 57.609 36.000 0.00 0.00 0.00 3.77
6705 7487 9.224267 CAATACCAACTCAATATCCTTATCCAG 57.776 37.037 0.00 0.00 0.00 3.86
6739 7521 8.205131 AGTTTTTCATATGTATTACCACCGTC 57.795 34.615 1.90 0.00 0.00 4.79
6745 7527 3.056588 TGTATTACCACCGTCCCAAAC 57.943 47.619 0.00 0.00 0.00 2.93
6757 7539 5.470777 CACCGTCCCAAACTAATTGTCTTAA 59.529 40.000 0.00 0.00 37.32 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.200020 CAGCCCTCGAACCAACATTTC 59.800 52.381 0.00 0.00 0.00 2.17
16 17 1.371183 CTCAGCCCTCGAACCAACA 59.629 57.895 0.00 0.00 0.00 3.33
33 34 1.305297 TCCTCGATCTGCACACCCT 60.305 57.895 0.00 0.00 0.00 4.34
63 64 3.682858 GTGCTATTGCCTCTCGTTTTGTA 59.317 43.478 0.00 0.00 38.71 2.41
66 67 1.732259 CGTGCTATTGCCTCTCGTTTT 59.268 47.619 0.00 0.00 38.71 2.43
74 75 2.106683 GCGAACCGTGCTATTGCCT 61.107 57.895 0.00 0.00 38.71 4.75
91 92 3.774702 GACGAAACTCGCCCACGC 61.775 66.667 0.00 0.00 45.12 5.34
100 101 2.049433 CCTGTCCGCGACGAAACT 60.049 61.111 8.23 0.00 34.95 2.66
168 169 2.049985 ACAGAGACTGTGACGCGC 60.050 61.111 5.73 0.00 43.63 6.86
191 192 2.267426 CGCACCTCACAATCGATTACA 58.733 47.619 10.97 0.00 0.00 2.41
198 199 1.080093 TCCGACGCACCTCACAATC 60.080 57.895 0.00 0.00 0.00 2.67
201 202 4.337060 CGTCCGACGCACCTCACA 62.337 66.667 8.21 0.00 33.65 3.58
213 214 1.378124 AAAACCACAACCACCGTCCG 61.378 55.000 0.00 0.00 0.00 4.79
302 305 6.499699 TCTCATGTTCCAATCTATATCCAGCT 59.500 38.462 0.00 0.00 0.00 4.24
335 338 2.482721 CGAAAGTAAATCACAACCGGCT 59.517 45.455 0.00 0.00 0.00 5.52
340 343 4.143179 CCTCGGTCGAAAGTAAATCACAAC 60.143 45.833 0.00 0.00 0.00 3.32
368 379 3.967987 TCCAGAGGGAGGAAATAGTAAGC 59.032 47.826 0.00 0.00 38.64 3.09
450 463 3.938963 GGATCATGCGGTTCTTCTTGTTA 59.061 43.478 0.00 0.00 0.00 2.41
491 504 7.041508 GCATGATCCTGTTAGAGAATTCGAATT 60.042 37.037 22.93 22.93 0.00 2.17
506 519 1.412074 GGGGGAATTGCATGATCCTGT 60.412 52.381 11.40 0.00 33.61 4.00
525 538 4.084223 ACACGCGATTACTAAACAACAAGG 60.084 41.667 15.93 0.00 0.00 3.61
559 577 8.214364 AGTTCAGTTCTCACTCCTCTAATTTTT 58.786 33.333 0.00 0.00 0.00 1.94
560 578 7.740805 AGTTCAGTTCTCACTCCTCTAATTTT 58.259 34.615 0.00 0.00 0.00 1.82
561 579 7.309770 AGTTCAGTTCTCACTCCTCTAATTT 57.690 36.000 0.00 0.00 0.00 1.82
562 580 6.926630 AGTTCAGTTCTCACTCCTCTAATT 57.073 37.500 0.00 0.00 0.00 1.40
563 581 6.723977 AGAAGTTCAGTTCTCACTCCTCTAAT 59.276 38.462 5.50 0.00 30.55 1.73
584 602 6.510536 ACATTGCTTCCTCTTTCAAAAGAAG 58.489 36.000 6.64 1.32 43.84 2.85
634 656 4.083057 GCTTCCTTCTGTTTGAGGATGAAC 60.083 45.833 8.86 0.00 0.00 3.18
638 660 2.704572 CGCTTCCTTCTGTTTGAGGAT 58.295 47.619 0.00 0.00 0.00 3.24
666 694 2.336945 TGAGATGTGATGTGATGGGC 57.663 50.000 0.00 0.00 0.00 5.36
752 800 0.178967 GGGGGTTTAAAACGTGGGGA 60.179 55.000 0.00 0.00 0.00 4.81
753 801 0.469518 TGGGGGTTTAAAACGTGGGG 60.470 55.000 0.00 0.00 0.00 4.96
1165 1446 4.796231 CCTCGACGGCGACCCTTG 62.796 72.222 10.67 0.00 42.51 3.61
1179 1460 2.514824 GGCATGCCGTCCTTCCTC 60.515 66.667 23.48 0.00 0.00 3.71
1215 1496 0.924090 TGGAGTAGATGGACCGGAGA 59.076 55.000 9.46 0.00 0.00 3.71
1225 1506 1.889829 GCGGATGTAGCTGGAGTAGAT 59.110 52.381 0.00 0.00 0.00 1.98
1415 1702 1.532437 CATCAGCGTCAAAAGACTGCA 59.468 47.619 12.32 0.00 0.00 4.41
1433 1720 2.931325 CTGCAGCAACAACAAACAACAT 59.069 40.909 0.00 0.00 0.00 2.71
1578 1866 1.745232 TTTTCAAGGTCGTGTGTGCT 58.255 45.000 0.00 0.00 0.00 4.40
1596 1884 3.323979 ACTGGTTAGTCAGTCACGGAATT 59.676 43.478 0.00 0.00 43.82 2.17
1597 1885 2.897969 ACTGGTTAGTCAGTCACGGAAT 59.102 45.455 0.00 0.00 43.82 3.01
1628 1916 2.065512 CATGAATTCGACACACACGGA 58.934 47.619 0.04 0.00 0.00 4.69
1650 1938 4.082571 AGGAGAACAATTGCTCAATTTCGG 60.083 41.667 11.27 0.00 38.84 4.30
1708 1997 1.272480 ACATTTTACCCCCAGGAGCAC 60.272 52.381 0.00 0.00 36.73 4.40
1760 2049 9.628500 ACAAAGGTAAGAGAAAATGTTAGTTCT 57.372 29.630 0.00 0.00 36.80 3.01
1794 2083 2.103263 AGAGAAACAGTCAGTCCACACC 59.897 50.000 0.00 0.00 0.00 4.16
1968 2257 2.356135 CCTCGACTACCCCAAAATGTG 58.644 52.381 0.00 0.00 0.00 3.21
2048 2337 5.160641 CGTTTGATCCAAAACCCATGTTAG 58.839 41.667 3.75 0.00 36.83 2.34
2070 2359 3.059570 GCGTGAAACATCTCAACTCTACG 59.940 47.826 0.00 0.00 35.74 3.51
2319 2609 5.719173 CTTTTTCAGGAAGACAACCAACAA 58.281 37.500 0.00 0.00 0.00 2.83
2399 2689 6.966435 ATGGCAAGTGCATAATTACAAAAC 57.034 33.333 5.52 0.00 44.36 2.43
2447 2737 0.033504 GCAACAGTCTGGAAGGACGA 59.966 55.000 4.53 0.00 40.76 4.20
2527 2817 3.282885 TGTTTCATGTGCCACAGTAACA 58.717 40.909 14.40 14.40 0.00 2.41
2663 2953 9.897744 TTTAGTTCAGAAAAGTTGAGCAATATG 57.102 29.630 0.00 0.00 0.00 1.78
2968 3258 6.043411 GTGTGGTTTAAATTGCACTACCAAA 58.957 36.000 0.00 0.00 37.41 3.28
3017 3307 1.255882 TCATGAAACTTGGCGGCAAT 58.744 45.000 25.71 10.76 0.00 3.56
3153 3443 4.113354 GGTAAATGACTGTCTCGATGGAC 58.887 47.826 9.51 0.00 36.81 4.02
3279 3569 2.844839 GGCCCGATAGCAGGACCT 60.845 66.667 0.00 0.00 0.00 3.85
3476 3766 4.749323 CCAATGGAGCTGGCTTCA 57.251 55.556 6.00 6.00 35.79 3.02
3490 3780 4.082787 GCTTACTATCTGCTGTTTTGCCAA 60.083 41.667 0.00 0.00 0.00 4.52
3506 3796 2.111384 CAGGCTTCTGGGAGCTTACTA 58.889 52.381 0.63 0.00 42.32 1.82
3555 3845 2.361737 GGAGCAGGCTTTGGGGAC 60.362 66.667 0.00 0.00 0.00 4.46
4566 4856 3.121030 CTGCTGTTTCTCCGCCGG 61.121 66.667 0.00 0.00 0.00 6.13
4570 4860 0.601046 TGCTGTCTGCTGTTTCTCCG 60.601 55.000 3.20 0.00 43.37 4.63
4575 4865 0.950116 GAGCTTGCTGTCTGCTGTTT 59.050 50.000 0.00 0.00 43.37 2.83
4584 4874 2.348998 CTTCGGGGAGCTTGCTGT 59.651 61.111 0.00 0.00 0.00 4.40
4588 4878 2.437359 CAGGCTTCGGGGAGCTTG 60.437 66.667 0.00 0.00 42.21 4.01
4594 4884 4.479993 CCAGAGCAGGCTTCGGGG 62.480 72.222 0.00 0.00 0.00 5.73
4609 4899 1.301716 GTCTGCTGTTTCTCCGCCA 60.302 57.895 0.00 0.00 0.00 5.69
4612 4902 1.294659 GGCTGTCTGCTGTTTCTCCG 61.295 60.000 1.44 0.00 42.39 4.63
4630 4920 4.479993 CAGGCTTCGGGGAGCTGG 62.480 72.222 0.00 0.00 42.32 4.85
4634 4924 4.168291 GGAGCAGGCTTCGGGGAG 62.168 72.222 0.00 0.00 0.00 4.30
4661 5270 1.302351 GGAGCTTGCTGTCTGCTGT 60.302 57.895 0.00 0.00 43.37 4.40
4693 5302 1.301716 GTCTGCTGTTTCTCCGCCA 60.302 57.895 0.00 0.00 0.00 5.69
4759 5449 3.394836 GAGCAGGCTTCGGGGAGT 61.395 66.667 0.00 0.00 0.00 3.85
4810 5500 7.791029 TGAATATGTATACTTCAGAACAGGCA 58.209 34.615 4.17 0.00 0.00 4.75
5041 5731 1.073897 GAAGGGTGTGCTTGCCTCT 59.926 57.895 0.00 0.00 0.00 3.69
5072 5762 1.338337 GCTGGAGATCTAGTGCGCTTA 59.662 52.381 9.73 0.00 0.00 3.09
5101 5791 3.208747 TCTGTTTCTTCACCAGGGTTC 57.791 47.619 0.00 0.00 0.00 3.62
5316 6006 1.612395 GCCAGAGCACTAGCAGGAGT 61.612 60.000 0.00 0.00 45.49 3.85
5336 6026 3.572255 TGCTTATTGTTGGGTGTTTCCTC 59.428 43.478 0.00 0.00 36.25 3.71
5345 6035 1.185315 CTGGGGTGCTTATTGTTGGG 58.815 55.000 0.00 0.00 0.00 4.12
5405 6095 1.154093 CATTCGCAGTGGCTTGCTG 60.154 57.895 11.63 6.49 41.90 4.41
5678 6368 1.420430 TCTGTTTCTTCCAGGACGGT 58.580 50.000 0.00 0.00 35.57 4.83
5757 6447 4.157246 TCTAGTTCTCTACAGGCAAACCA 58.843 43.478 0.00 0.00 39.06 3.67
5818 6508 4.713553 ACCGCAATTCACATGGTATCATA 58.286 39.130 0.00 0.00 31.33 2.15
5819 6509 3.554934 ACCGCAATTCACATGGTATCAT 58.445 40.909 0.00 0.00 0.00 2.45
5820 6510 2.997980 ACCGCAATTCACATGGTATCA 58.002 42.857 0.00 0.00 0.00 2.15
5824 6514 1.000385 CACAACCGCAATTCACATGGT 60.000 47.619 0.00 0.00 33.45 3.55
5830 6520 0.874390 GAGCTCACAACCGCAATTCA 59.126 50.000 9.40 0.00 0.00 2.57
5839 6529 1.194781 TCCTCCCTGGAGCTCACAAC 61.195 60.000 17.19 0.00 40.56 3.32
5928 6618 4.038522 TCTCTATTTCCTTCTCCATGCGAG 59.961 45.833 5.18 5.18 40.30 5.03
5935 6625 5.455469 GGTTCCCATCTCTATTTCCTTCTCC 60.455 48.000 0.00 0.00 0.00 3.71
5997 6687 6.113411 TCCTAGGCTTAAATTAGACAACAGC 58.887 40.000 2.96 0.00 0.00 4.40
6041 6732 8.856490 ACAACATCAAATTTACAGAACAACTC 57.144 30.769 0.00 0.00 0.00 3.01
6118 6811 2.584236 TCTCGGCTACCACCTCTATTC 58.416 52.381 0.00 0.00 0.00 1.75
6175 6932 8.937634 AAATTAGACAAATGAATGAATGCCTC 57.062 30.769 0.00 0.00 0.00 4.70
6188 6945 9.528489 TTGTTTCCTAGGCTAAATTAGACAAAT 57.472 29.630 8.76 0.00 35.81 2.32
6316 7074 5.690865 ACAGACAAACATAACCTCCAGAAA 58.309 37.500 0.00 0.00 0.00 2.52
6341 7099 6.644592 CAGACAAAACACAAGGAAAAACTGAA 59.355 34.615 0.00 0.00 0.00 3.02
6562 7320 9.450807 AGTTATGAAAAAGAAGTTTGATCAACG 57.549 29.630 7.89 0.00 40.75 4.10
6672 7452 6.772716 GGATATTGAGTTGGTATTGTGGATGT 59.227 38.462 0.00 0.00 0.00 3.06
6673 7453 7.000472 AGGATATTGAGTTGGTATTGTGGATG 59.000 38.462 0.00 0.00 0.00 3.51
6688 7470 7.991084 TTTCATGCTGGATAAGGATATTGAG 57.009 36.000 0.00 0.00 34.11 3.02
6734 7516 3.782656 AGACAATTAGTTTGGGACGGT 57.217 42.857 0.00 0.00 39.80 4.83
6737 7519 9.758651 ACAAATTTAAGACAATTAGTTTGGGAC 57.241 29.630 0.00 0.00 39.80 4.46
6739 7521 9.981114 AGACAAATTTAAGACAATTAGTTTGGG 57.019 29.630 0.00 0.00 39.80 4.12


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

AutoCloner maintained by Alex Coulton.