Multiple sequence alignment - TraesCS6D01G133900

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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 TraesCS6D01G133900 chr6D 100.000 7670 0 0 1 7670 101488759 101496428 0.000000e+00 14164.0
1 TraesCS6D01G133900 chr6A 96.258 4089 104 10 3620 7670 121972545 121976622 0.000000e+00 6658.0
2 TraesCS6D01G133900 chr6A 96.000 2950 63 17 719 3625 121969336 121972273 0.000000e+00 4743.0
3 TraesCS6D01G133900 chr6A 88.365 318 28 8 399 715 121968149 121968458 2.610000e-99 374.0
4 TraesCS6D01G133900 chr6B 96.631 3977 103 17 3620 7580 186592598 186596559 0.000000e+00 6573.0
5 TraesCS6D01G133900 chr6B 96.010 2932 59 17 728 3625 186589218 186592125 0.000000e+00 4713.0
6 TraesCS6D01G133900 chr6B 88.531 715 56 7 1 694 186588514 186589223 0.000000e+00 843.0
7 TraesCS6D01G133900 chr7D 86.782 174 23 0 3315 3488 611714570 611714397 2.180000e-45 195.0
8 TraesCS6D01G133900 chr7A 86.782 174 23 0 3315 3488 701633601 701633428 2.180000e-45 195.0
9 TraesCS6D01G133900 chr7A 87.582 153 19 0 2100 2252 701634487 701634335 2.200000e-40 178.0
10 TraesCS6D01G133900 chr7B 86.207 174 24 0 3315 3488 701176280 701176107 1.020000e-43 189.0
11 TraesCS6D01G133900 chr2A 91.935 62 4 1 593 654 360703206 360703266 1.370000e-12 86.1
12 TraesCS6D01G133900 chr2B 91.667 60 4 1 593 652 379776519 379776461 1.770000e-11 82.4
13 TraesCS6D01G133900 chr2B 90.323 62 5 1 596 657 136801788 136801728 6.380000e-11 80.5
14 TraesCS6D01G133900 chr1D 90.000 60 3 3 593 652 63351399 63351455 2.970000e-09 75.0
15 TraesCS6D01G133900 chr1B 89.831 59 3 2 593 651 473484381 473484436 1.070000e-08 73.1
16 TraesCS6D01G133900 chr3D 93.333 45 3 0 593 637 16497977 16498021 4.970000e-07 67.6
17 TraesCS6D01G133900 chr2D 93.617 47 0 3 593 637 458923292 458923337 4.970000e-07 67.6


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 TraesCS6D01G133900 chr6D 101488759 101496428 7669 False 14164 14164 100.000 1 7670 1 chr6D.!!$F1 7669
1 TraesCS6D01G133900 chr6A 121968149 121976622 8473 False 3925 6658 93.541 399 7670 3 chr6A.!!$F1 7271
2 TraesCS6D01G133900 chr6B 186588514 186596559 8045 False 4043 6573 93.724 1 7580 3 chr6B.!!$F1 7579

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
541 562 0.391793 GTGCCCTTGAGCCTAGTGTC 60.392 60.000 0.00 0.00 0.00 3.67 F
1694 2624 1.069668 GTAGTATGGTTGGCGGGTAGG 59.930 57.143 0.00 0.00 0.00 3.18 F
2360 3290 0.172127 ATTTTGTGTGTGTGTGCGCA 59.828 45.000 5.66 5.66 0.00 6.09 F
2388 3318 4.753107 TGTCCGTTTGTTTGAGGAGATTAC 59.247 41.667 0.00 0.00 32.82 1.89 F
3342 4288 1.355720 ACTCCTTTACATTGGGCTGCT 59.644 47.619 0.00 0.00 0.00 4.24 F
3845 5270 3.632145 CCCCTGTGCTTTGGTGTATTATC 59.368 47.826 0.00 0.00 0.00 1.75 F
5351 6776 2.286418 GCAACGGCTGTCATAAGTATGC 60.286 50.000 0.00 0.00 36.96 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2360 3290 0.392729 TCAAACAAACGGACACGGGT 60.393 50.000 0.00 0.0 46.48 5.28 R
2513 3443 3.537580 TCTATCATGCCAAAACCGTACC 58.462 45.455 0.00 0.0 0.00 3.34 R
3342 4288 3.864328 TGACTCCATATTCCCCCGAATA 58.136 45.455 0.00 0.0 43.46 1.75 R
3660 5085 9.614792 AAATCTTACATTGAGGGTACTAATGAC 57.385 33.333 14.78 0.0 36.09 3.06 R
5222 6647 1.016130 AGACTGAACGATGCCGCAAG 61.016 55.000 0.00 0.0 39.95 4.01 R
5420 6845 2.348620 TGCGACTCCTGCAGCAAT 59.651 55.556 8.66 0.0 37.44 3.56 R
7287 8729 0.185901 TCAAAGGGCAGCAAACTCCT 59.814 50.000 0.00 0.0 0.00 3.69 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
45 46 6.536447 TCTCTTAGTTTTACGGAACCCAATT 58.464 36.000 0.00 0.00 0.00 2.32
46 47 7.678837 TCTCTTAGTTTTACGGAACCCAATTA 58.321 34.615 0.00 0.00 0.00 1.40
54 55 4.042271 ACGGAACCCAATTAAATCAGGT 57.958 40.909 0.00 0.00 0.00 4.00
60 61 8.856103 CGGAACCCAATTAAATCAGGTTTATAT 58.144 33.333 0.00 0.00 40.84 0.86
122 124 5.087323 TGCCTAGGACCTCTAATATTCCAG 58.913 45.833 14.75 0.00 0.00 3.86
167 169 2.649531 TGGGTGTAAAAGACCACAGG 57.350 50.000 0.00 0.00 34.89 4.00
240 242 3.691609 CCTGATTTGAGGTTACCAGAAGC 59.308 47.826 3.51 0.00 0.00 3.86
245 247 2.846193 TGAGGTTACCAGAAGCACAAC 58.154 47.619 3.51 0.00 0.00 3.32
257 259 1.242076 AGCACAACAAGATGGAGTGC 58.758 50.000 16.50 16.50 45.86 4.40
311 313 8.656806 TCAAACTAGAAGGTAAGGAGATTTCAA 58.343 33.333 0.00 0.00 0.00 2.69
312 314 8.940952 CAAACTAGAAGGTAAGGAGATTTCAAG 58.059 37.037 0.00 0.00 0.00 3.02
364 366 2.768253 TCTCAGCTACCACCATGTTG 57.232 50.000 0.00 0.00 0.00 3.33
375 377 6.531240 GCTACCACCATGTTGTCAATAATTTG 59.469 38.462 0.00 0.00 0.00 2.32
388 390 5.918011 GTCAATAATTTGTTTGCACTCGGAA 59.082 36.000 0.00 0.00 34.32 4.30
389 391 6.088085 GTCAATAATTTGTTTGCACTCGGAAG 59.912 38.462 0.00 0.00 34.32 3.46
417 438 5.404946 ACAACACAAGCATGATTATGAAGC 58.595 37.500 9.29 0.00 36.36 3.86
418 439 4.644103 ACACAAGCATGATTATGAAGCC 57.356 40.909 9.29 0.00 36.36 4.35
419 440 3.382546 ACACAAGCATGATTATGAAGCCC 59.617 43.478 9.29 0.00 36.36 5.19
428 449 5.128033 TGATTATGAAGCCCAGAAATGGA 57.872 39.130 0.00 0.00 28.87 3.41
488 509 9.147732 AGGAACTTCCACATTTTTCTTTATCTT 57.852 29.630 10.57 0.00 39.61 2.40
508 529 6.500589 TCTTATATAGGCTTCAGCTTTGGT 57.499 37.500 0.00 0.00 41.70 3.67
522 543 4.858692 CAGCTTTGGTTATCATGTTTTCCG 59.141 41.667 0.00 0.00 0.00 4.30
529 550 1.923356 ATCATGTTTTCCGTGCCCTT 58.077 45.000 0.00 0.00 0.00 3.95
541 562 0.391793 GTGCCCTTGAGCCTAGTGTC 60.392 60.000 0.00 0.00 0.00 3.67
583 604 3.213506 CCTATGACATGAAATTCGGCCA 58.786 45.455 2.24 0.00 0.00 5.36
711 732 8.635765 TGTTATTTCATCTTATATTCTGGCCC 57.364 34.615 0.00 0.00 0.00 5.80
715 736 5.661056 TCATCTTATATTCTGGCCCGTAG 57.339 43.478 0.00 0.00 0.00 3.51
716 737 5.084519 TCATCTTATATTCTGGCCCGTAGT 58.915 41.667 0.00 0.00 0.00 2.73
728 1623 1.952296 GCCCGTAGTAGTAGCTTGCTA 59.048 52.381 0.00 0.00 0.00 3.49
729 1624 2.557490 GCCCGTAGTAGTAGCTTGCTAT 59.443 50.000 5.59 0.00 0.00 2.97
808 1709 1.283321 GTGCAAAGATCCCCTTCTCCT 59.717 52.381 0.00 0.00 33.02 3.69
1112 2040 1.797933 CGCTCAAGGACGACGTCTG 60.798 63.158 25.87 17.69 32.47 3.51
1284 2212 2.897350 CGCCATTTCCCCGAGCTC 60.897 66.667 2.73 2.73 0.00 4.09
1302 2230 2.040178 CTCCCCCAATACGTAGCTTCT 58.960 52.381 0.08 0.00 0.00 2.85
1303 2231 1.760613 TCCCCCAATACGTAGCTTCTG 59.239 52.381 0.08 0.00 0.00 3.02
1342 2270 2.284625 TGACGATGGAGGGGTGCT 60.285 61.111 0.00 0.00 0.00 4.40
1345 2273 1.613630 ACGATGGAGGGGTGCTTCT 60.614 57.895 0.00 0.00 0.00 2.85
1694 2624 1.069668 GTAGTATGGTTGGCGGGTAGG 59.930 57.143 0.00 0.00 0.00 3.18
1738 2668 9.228949 CAAGGCTTCTTATATCTGCTTGATTAT 57.771 33.333 0.00 0.00 36.65 1.28
1838 2768 5.063880 GGACCAAACTGGATCATATACCAC 58.936 45.833 0.00 0.00 40.96 4.16
1969 2899 4.063998 TCATAGATGTAAGTGCCAGCTG 57.936 45.455 6.78 6.78 30.07 4.24
2051 2981 6.984474 TGCTATGCACTCCTTTACTGTTATAC 59.016 38.462 0.00 0.00 31.71 1.47
2108 3038 3.354948 TGCTTGTTATCTGGACAGCAT 57.645 42.857 0.00 0.00 31.26 3.79
2335 3265 3.002038 TGTTTTGGTTAGTTGACCCGT 57.998 42.857 0.00 0.00 39.01 5.28
2360 3290 0.172127 ATTTTGTGTGTGTGTGCGCA 59.828 45.000 5.66 5.66 0.00 6.09
2388 3318 4.753107 TGTCCGTTTGTTTGAGGAGATTAC 59.247 41.667 0.00 0.00 32.82 1.89
2389 3319 4.995487 GTCCGTTTGTTTGAGGAGATTACT 59.005 41.667 0.00 0.00 32.82 2.24
2390 3320 6.161381 GTCCGTTTGTTTGAGGAGATTACTA 58.839 40.000 0.00 0.00 32.82 1.82
2513 3443 4.985538 ATAACCTCTGTCTCTTACCGTG 57.014 45.455 0.00 0.00 0.00 4.94
2683 3627 4.883585 GCACATTTTGGATGGAGATGACTA 59.116 41.667 0.00 0.00 0.00 2.59
3342 4288 1.355720 ACTCCTTTACATTGGGCTGCT 59.644 47.619 0.00 0.00 0.00 4.24
3660 5085 6.797454 GTCTAGATTACAGACTTACAGTGGG 58.203 44.000 0.00 0.00 39.48 4.61
3845 5270 3.632145 CCCCTGTGCTTTGGTGTATTATC 59.368 47.826 0.00 0.00 0.00 1.75
4183 5608 4.571919 TCTTCTGTTTTGGTACCGTATGG 58.428 43.478 7.57 0.00 42.84 2.74
4977 6402 9.541884 TTGGTATGTTCTAGATATATGCCTACA 57.458 33.333 14.84 5.65 0.00 2.74
5351 6776 2.286418 GCAACGGCTGTCATAAGTATGC 60.286 50.000 0.00 0.00 36.96 3.14
5587 7012 4.623932 TCAAGCATCACAGGTAAGAACT 57.376 40.909 0.00 0.00 0.00 3.01
6049 7483 9.191995 CATGCTTGTGTCGATATATAACTGTAA 57.808 33.333 0.00 0.00 0.00 2.41
6303 7737 1.115467 ACAGTTATCTCAGAGGCCCG 58.885 55.000 0.00 0.00 0.00 6.13
6435 7869 4.261322 CCTGACGAGGAAATGGCAATTATG 60.261 45.833 0.00 0.00 42.93 1.90
6474 7908 0.889638 TCTCGCAGAACGGTGAGAGT 60.890 55.000 12.48 0.00 46.40 3.24
6567 8001 6.293244 GCCAAGTTAGTTCGTCTAAATGTTGT 60.293 38.462 4.91 0.00 39.88 3.32
6660 8094 3.843426 CGTTATGCACGGAATCTTCTC 57.157 47.619 0.00 0.00 45.89 2.87
6791 8225 4.522022 GGCTGGCTATTTCTTCATATTGCT 59.478 41.667 0.00 0.00 0.00 3.91
6828 8262 3.525537 CTGCACTGATATCGTCAAGGTT 58.474 45.455 0.00 0.00 36.14 3.50
6864 8298 4.029520 AGAGCCACAGATTCAGTGAGTAT 58.970 43.478 10.48 0.00 39.30 2.12
7033 8467 7.212976 TGATAGTTCAGATGCTGTCCTATTTC 58.787 38.462 0.00 0.00 31.36 2.17
7117 8551 6.252655 CGTGATTTTTCCTGTTTCTTTTTCGT 59.747 34.615 0.00 0.00 0.00 3.85
7134 8569 5.804692 TTTCGTTTTCAGTGTTGCTCTAA 57.195 34.783 0.00 0.00 0.00 2.10
7178 8613 8.744652 TCATTACCACTTTTTATGTAACCATGG 58.255 33.333 11.19 11.19 32.29 3.66
7187 8622 9.418045 CTTTTTATGTAACCATGGAACGAATTT 57.582 29.630 21.47 2.33 32.29 1.82
7222 8657 3.863424 GTGTTACATATGAGACGGTGTGG 59.137 47.826 10.38 0.00 0.00 4.17
7232 8674 1.743958 AGACGGTGTGGTCTCTAATCG 59.256 52.381 0.00 0.00 43.63 3.34
7287 8729 5.913137 AAAATGAACCTTGATATGGCGAA 57.087 34.783 0.00 0.00 0.00 4.70
7302 8746 1.302832 CGAAGGAGTTTGCTGCCCT 60.303 57.895 0.00 0.00 33.13 5.19
7363 8808 6.959639 AACCATTAATACCATTGCGATTCT 57.040 33.333 0.00 0.00 0.00 2.40
7366 8811 6.545666 ACCATTAATACCATTGCGATTCTTCA 59.454 34.615 0.00 0.00 0.00 3.02
7388 8833 2.099405 CACCCCATGCGGAACTTTATT 58.901 47.619 2.64 0.00 0.00 1.40
7390 8835 3.066203 CACCCCATGCGGAACTTTATTAC 59.934 47.826 2.64 0.00 0.00 1.89
7392 8837 3.888930 CCCCATGCGGAACTTTATTACAT 59.111 43.478 0.00 0.00 0.00 2.29
7447 8916 2.223852 GGAAGTTTTGCAGGCGGTAAAA 60.224 45.455 9.27 9.27 38.51 1.52
7486 8961 7.287061 TGGACGGATGGAATAATACTTCAATT 58.713 34.615 0.00 0.00 0.00 2.32
7487 8962 7.228507 TGGACGGATGGAATAATACTTCAATTG 59.771 37.037 0.00 0.00 0.00 2.32
7488 8963 7.228706 GGACGGATGGAATAATACTTCAATTGT 59.771 37.037 5.13 0.00 0.00 2.71
7489 8964 7.930217 ACGGATGGAATAATACTTCAATTGTG 58.070 34.615 5.13 2.67 0.00 3.33
7490 8965 7.773224 ACGGATGGAATAATACTTCAATTGTGA 59.227 33.333 5.13 0.00 0.00 3.58
7491 8966 8.786898 CGGATGGAATAATACTTCAATTGTGAT 58.213 33.333 5.13 0.00 32.48 3.06
7512 8987 7.839705 TGTGATGATACCTAAGGTAAACTCTCT 59.160 37.037 0.00 0.00 41.85 3.10
7518 8993 5.652324 ACCTAAGGTAAACTCTCTGGAGAA 58.348 41.667 1.86 0.00 37.29 2.87
7542 9017 5.007682 GGTTACTCAGTTTAGGCCAATCAA 58.992 41.667 5.01 0.00 0.00 2.57
7551 9026 6.477688 CAGTTTAGGCCAATCAATTTATGCAG 59.522 38.462 5.01 0.00 0.00 4.41
7560 9035 4.937696 TCAATTTATGCAGTGTGGTACG 57.062 40.909 0.00 0.00 0.00 3.67
7561 9036 4.320023 TCAATTTATGCAGTGTGGTACGT 58.680 39.130 0.00 0.00 0.00 3.57
7590 9065 8.085296 AGTAATATCAAAGATGTTAGCCTCTCG 58.915 37.037 0.00 0.00 0.00 4.04
7598 9073 5.652518 AGATGTTAGCCTCTCGACTTAAAC 58.347 41.667 0.00 0.00 0.00 2.01
7600 9075 3.254166 TGTTAGCCTCTCGACTTAAACGT 59.746 43.478 0.00 0.00 0.00 3.99
7611 9086 6.199719 TCTCGACTTAAACGTTTTTCTTCCTC 59.800 38.462 20.19 4.07 0.00 3.71
7634 9115 3.763897 AGAGTCCAACACAAAGTGCTTTT 59.236 39.130 0.00 0.00 36.98 2.27
7644 9125 0.826062 AAGTGCTTTTGTGCCTTGCT 59.174 45.000 0.00 0.00 0.00 3.91
7646 9127 0.179103 GTGCTTTTGTGCCTTGCTGT 60.179 50.000 0.00 0.00 0.00 4.40
7654 9135 6.528537 TTTTGTGCCTTGCTGTATAATCAT 57.471 33.333 0.00 0.00 0.00 2.45
7658 9139 4.763793 GTGCCTTGCTGTATAATCATGGAT 59.236 41.667 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 6.350780 GGGTTCCGTAAAACTAAGAGAGATCA 60.351 42.308 0.00 0.00 0.00 2.92
33 34 4.042271 ACCTGATTTAATTGGGTTCCGT 57.958 40.909 0.00 0.00 0.00 4.69
34 35 5.400066 AAACCTGATTTAATTGGGTTCCG 57.600 39.130 12.96 0.00 39.05 4.30
60 61 6.116806 TGCCTTTTCTGACTTAGTGTGTTAA 58.883 36.000 0.00 0.00 0.00 2.01
93 95 2.856760 AGAGGTCCTAGGCAAGATGA 57.143 50.000 2.96 0.00 0.00 2.92
139 141 7.778853 TGTGGTCTTTTACACCCACTTAAAATA 59.221 33.333 8.91 0.00 46.02 1.40
189 191 6.700960 CACTGCTGATTTTGATGTTAAACCAA 59.299 34.615 0.00 0.00 0.00 3.67
190 192 6.215121 CACTGCTGATTTTGATGTTAAACCA 58.785 36.000 0.00 0.00 0.00 3.67
206 208 0.111061 AAATCAGGTGGCACTGCTGA 59.889 50.000 22.95 22.95 38.36 4.26
240 242 3.067180 AGTTTGCACTCCATCTTGTTGTG 59.933 43.478 0.00 0.00 0.00 3.33
364 366 5.457140 TCCGAGTGCAAACAAATTATTGAC 58.543 37.500 0.00 0.00 38.94 3.18
375 377 4.742438 TGTTAATCTTCCGAGTGCAAAC 57.258 40.909 0.00 0.00 0.00 2.93
388 390 8.959548 TCATAATCATGCTTGTGTTGTTAATCT 58.040 29.630 6.02 0.00 31.73 2.40
389 391 9.571810 TTCATAATCATGCTTGTGTTGTTAATC 57.428 29.630 6.02 0.00 31.73 1.75
417 438 2.097825 CCTGAGCTTTCCATTTCTGGG 58.902 52.381 0.00 0.00 43.34 4.45
418 439 2.097825 CCCTGAGCTTTCCATTTCTGG 58.902 52.381 0.00 0.00 44.64 3.86
419 440 3.077484 TCCCTGAGCTTTCCATTTCTG 57.923 47.619 0.00 0.00 0.00 3.02
428 449 4.917906 AGTAAGTCATTCCCTGAGCTTT 57.082 40.909 0.00 0.00 33.51 3.51
488 509 7.973402 TGATAACCAAAGCTGAAGCCTATATA 58.027 34.615 0.00 0.00 43.38 0.86
489 510 6.841601 TGATAACCAAAGCTGAAGCCTATAT 58.158 36.000 0.00 0.00 43.38 0.86
508 529 3.080300 AGGGCACGGAAAACATGATAA 57.920 42.857 0.00 0.00 0.00 1.75
522 543 0.391793 GACACTAGGCTCAAGGGCAC 60.392 60.000 0.00 0.00 43.56 5.01
529 550 5.426689 AAGATGAAATGACACTAGGCTCA 57.573 39.130 0.00 0.00 0.00 4.26
541 562 5.923204 AGGTCTACCTGCTAAGATGAAATG 58.077 41.667 0.00 0.00 46.55 2.32
583 604 1.662517 TACAATCATTCGCCACGCAT 58.337 45.000 0.00 0.00 0.00 4.73
687 708 7.390718 ACGGGCCAGAATATAAGATGAAATAAC 59.609 37.037 10.86 0.00 0.00 1.89
693 714 5.084519 ACTACGGGCCAGAATATAAGATGA 58.915 41.667 10.86 0.00 0.00 2.92
694 715 5.407407 ACTACGGGCCAGAATATAAGATG 57.593 43.478 10.86 0.00 0.00 2.90
695 716 6.254522 ACTACTACGGGCCAGAATATAAGAT 58.745 40.000 10.86 0.00 0.00 2.40
696 717 5.638133 ACTACTACGGGCCAGAATATAAGA 58.362 41.667 10.86 0.00 0.00 2.10
697 718 5.979288 ACTACTACGGGCCAGAATATAAG 57.021 43.478 10.86 1.77 0.00 1.73
698 719 5.416952 GCTACTACTACGGGCCAGAATATAA 59.583 44.000 10.86 0.00 0.00 0.98
699 720 4.946157 GCTACTACTACGGGCCAGAATATA 59.054 45.833 10.86 0.00 0.00 0.86
700 721 3.762823 GCTACTACTACGGGCCAGAATAT 59.237 47.826 10.86 0.00 0.00 1.28
711 732 6.750501 TGACAAAATAGCAAGCTACTACTACG 59.249 38.462 3.55 0.00 0.00 3.51
743 1638 5.674525 CCTCATTTGACCATACTAGCTGAA 58.325 41.667 0.00 0.00 0.00 3.02
749 1644 3.490249 CGACGCCTCATTTGACCATACTA 60.490 47.826 0.00 0.00 0.00 1.82
752 1647 1.934589 CGACGCCTCATTTGACCATA 58.065 50.000 0.00 0.00 0.00 2.74
1085 2010 0.968393 GTCCTTGAGCGACTCCTCCT 60.968 60.000 4.73 0.00 0.00 3.69
1086 2011 1.513622 GTCCTTGAGCGACTCCTCC 59.486 63.158 4.73 0.00 0.00 4.30
1087 2012 1.137825 CGTCCTTGAGCGACTCCTC 59.862 63.158 4.73 0.00 0.00 3.71
1284 2212 1.760613 TCAGAAGCTACGTATTGGGGG 59.239 52.381 0.00 0.00 0.00 5.40
1302 2230 6.206438 TCACAGTTTATAACAAGCAGCAATCA 59.794 34.615 0.00 0.00 0.00 2.57
1303 2231 6.524586 GTCACAGTTTATAACAAGCAGCAATC 59.475 38.462 0.00 0.00 0.00 2.67
1687 2617 2.427245 CCCTGCTCAGACCTACCCG 61.427 68.421 0.00 0.00 0.00 5.28
1694 2624 2.267324 GACTGGCCCTGCTCAGAC 59.733 66.667 0.00 2.79 33.40 3.51
1838 2768 2.546195 TTGAAACGAACCAACCAACG 57.454 45.000 0.00 0.00 0.00 4.10
2051 2981 4.104776 CACCATATAGCAAACAAAAGGCG 58.895 43.478 0.00 0.00 0.00 5.52
2108 3038 6.459066 GTCTATAGCATTTACATCTGCTCCA 58.541 40.000 0.00 0.00 45.30 3.86
2335 3265 2.096657 CACACACACACAAAATCGACCA 59.903 45.455 0.00 0.00 0.00 4.02
2360 3290 0.392729 TCAAACAAACGGACACGGGT 60.393 50.000 0.00 0.00 46.48 5.28
2368 3298 6.164176 AGTAGTAATCTCCTCAAACAAACGG 58.836 40.000 0.00 0.00 0.00 4.44
2388 3318 6.313905 CACTTATTTTGTGCCAGAGGTAGTAG 59.686 42.308 0.00 0.00 0.00 2.57
2389 3319 6.014070 TCACTTATTTTGTGCCAGAGGTAGTA 60.014 38.462 0.00 0.00 35.58 1.82
2390 3320 5.003804 CACTTATTTTGTGCCAGAGGTAGT 58.996 41.667 0.00 0.00 0.00 2.73
2513 3443 3.537580 TCTATCATGCCAAAACCGTACC 58.462 45.455 0.00 0.00 0.00 3.34
2683 3627 9.642327 AAATTCAAAGTTAACGTAAACCAAACT 57.358 25.926 0.00 0.00 31.94 2.66
3096 4041 4.459337 AGCAGCCCTACAAATGTTAAGAAC 59.541 41.667 0.00 0.00 0.00 3.01
3342 4288 3.864328 TGACTCCATATTCCCCCGAATA 58.136 45.455 0.00 0.00 43.46 1.75
3660 5085 9.614792 AAATCTTACATTGAGGGTACTAATGAC 57.385 33.333 14.78 0.00 36.09 3.06
3845 5270 9.911138 TGTATATATGCAACAATTAAGCCAATG 57.089 29.630 0.45 0.00 0.00 2.82
4104 5529 9.985730 CCCGACAAAAGGTTACTATGTAATATA 57.014 33.333 0.00 0.00 29.93 0.86
4757 6182 8.458573 AGTTCCACATACAAAAACACTGAATA 57.541 30.769 0.00 0.00 0.00 1.75
5222 6647 1.016130 AGACTGAACGATGCCGCAAG 61.016 55.000 0.00 0.00 39.95 4.01
5351 6776 7.373493 ACAGGCAAAAGAAAAGAAGATGTATG 58.627 34.615 0.00 0.00 0.00 2.39
5420 6845 2.348620 TGCGACTCCTGCAGCAAT 59.651 55.556 8.66 0.00 37.44 3.56
5587 7012 6.403049 TGATGAAAAGGTAAACGCAGAGATA 58.597 36.000 0.00 0.00 0.00 1.98
6049 7483 6.824553 TGTCATCTGCAGAAGCTATTATCTT 58.175 36.000 22.50 0.00 42.74 2.40
6303 7737 1.450025 GATTTCTGAACCGACCACCC 58.550 55.000 0.00 0.00 0.00 4.61
6474 7908 2.093890 CCATTAGCATGAAGTGGCACA 58.906 47.619 21.41 0.00 31.07 4.57
6567 8001 6.405278 TTGTCAGTCTTCTTACTGTGATCA 57.595 37.500 0.00 0.00 45.78 2.92
6660 8094 2.040278 TCTCCAAATGAGTCACAAGGGG 59.960 50.000 0.00 0.00 42.12 4.79
6791 8225 1.066215 TGCAGCCAGAAAGAAGCGATA 60.066 47.619 0.00 0.00 0.00 2.92
6828 8262 2.102084 GTGGCTCTGCATCTAGTCATCA 59.898 50.000 2.04 0.00 28.60 3.07
6864 8298 2.275134 TTGTGCTCTTGCCATCTCAA 57.725 45.000 0.00 0.00 38.71 3.02
7033 8467 6.489127 TCCAATGTACAACTGTATTTTCCG 57.511 37.500 0.00 0.00 32.54 4.30
7134 8569 0.737715 GAAGCCGACACTTCGCTCAT 60.738 55.000 0.00 0.00 44.43 2.90
7143 8578 2.094762 AGTGGTAATGAAGCCGACAC 57.905 50.000 0.00 0.00 0.00 3.67
7178 8613 2.032799 TGGCACTCACACAAATTCGTTC 59.967 45.455 0.00 0.00 0.00 3.95
7187 8622 1.208293 TGTAACACTGGCACTCACACA 59.792 47.619 0.00 0.00 0.00 3.72
7222 8657 2.609916 GCTGGAAAAGGCGATTAGAGAC 59.390 50.000 0.00 0.00 0.00 3.36
7260 8702 7.936847 TCGCCATATCAAGGTTCATTTTAGTAT 59.063 33.333 0.00 0.00 0.00 2.12
7265 8707 5.163519 CCTTCGCCATATCAAGGTTCATTTT 60.164 40.000 0.00 0.00 33.24 1.82
7287 8729 0.185901 TCAAAGGGCAGCAAACTCCT 59.814 50.000 0.00 0.00 0.00 3.69
7302 8746 1.658596 CGCTTGCGCACTATACTCAAA 59.341 47.619 11.12 0.00 35.30 2.69
7351 8796 1.202222 GGTGCTGAAGAATCGCAATGG 60.202 52.381 0.00 0.00 37.04 3.16
7380 8825 9.108284 GCATTGGCCAAAATATGTAATAAAGTT 57.892 29.630 24.71 0.00 29.06 2.66
7382 8827 8.891671 AGCATTGGCCAAAATATGTAATAAAG 57.108 30.769 24.71 0.00 42.56 1.85
7447 8916 3.420893 TCCGTCCAGAATCTTGCAATTT 58.579 40.909 0.00 0.00 0.00 1.82
7465 8934 8.153479 TCACAATTGAAGTATTATTCCATCCG 57.847 34.615 13.59 0.00 0.00 4.18
7486 8961 7.839705 AGAGAGTTTACCTTAGGTATCATCACA 59.160 37.037 12.36 0.00 38.05 3.58
7487 8962 8.138712 CAGAGAGTTTACCTTAGGTATCATCAC 58.861 40.741 12.36 8.75 38.05 3.06
7488 8963 7.287927 CCAGAGAGTTTACCTTAGGTATCATCA 59.712 40.741 12.36 0.00 38.05 3.07
7489 8964 7.506261 TCCAGAGAGTTTACCTTAGGTATCATC 59.494 40.741 12.36 9.95 38.05 2.92
7490 8965 7.363031 TCCAGAGAGTTTACCTTAGGTATCAT 58.637 38.462 12.36 0.86 38.05 2.45
7491 8966 6.738635 TCCAGAGAGTTTACCTTAGGTATCA 58.261 40.000 12.36 0.00 38.05 2.15
7495 8970 5.272405 TCTCCAGAGAGTTTACCTTAGGT 57.728 43.478 9.57 9.57 41.26 3.08
7512 8987 4.020485 GCCTAAACTGAGTAACCTTCTCCA 60.020 45.833 0.00 0.00 0.00 3.86
7518 8993 4.288626 TGATTGGCCTAAACTGAGTAACCT 59.711 41.667 3.32 0.00 0.00 3.50
7542 9017 5.935789 ACTTTACGTACCACACTGCATAAAT 59.064 36.000 0.00 0.00 0.00 1.40
7551 9026 9.357652 TCTTTGATATTACTTTACGTACCACAC 57.642 33.333 0.00 0.00 0.00 3.82
7590 9065 7.011202 ACTCTGAGGAAGAAAAACGTTTAAGTC 59.989 37.037 15.03 11.93 33.37 3.01
7598 9073 3.728845 TGGACTCTGAGGAAGAAAAACG 58.271 45.455 9.85 0.00 33.37 3.60
7600 9075 4.881850 GTGTTGGACTCTGAGGAAGAAAAA 59.118 41.667 9.85 0.00 33.37 1.94
7611 9086 2.292267 AGCACTTTGTGTTGGACTCTG 58.708 47.619 0.00 0.00 35.75 3.35
7634 9115 3.884693 CCATGATTATACAGCAAGGCACA 59.115 43.478 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.