Multiple sequence alignment - TraesCS2D01G368900

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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 TraesCS2D01G368900 chr2D 100.000 5786 0 0 1 5786 473282433 473276648 0.000000e+00 10685
1 TraesCS2D01G368900 chr2A 94.848 2271 82 13 1 2258 615350933 615348685 0.000000e+00 3513
2 TraesCS2D01G368900 chr2A 92.386 2075 80 25 2258 4278 615348495 615346445 0.000000e+00 2885
3 TraesCS2D01G368900 chr2A 87.492 1487 92 33 4327 5786 615346439 615345020 0.000000e+00 1629
4 TraesCS2D01G368900 chr2B 96.960 1875 41 7 1163 3028 553618299 553616432 0.000000e+00 3133
5 TraesCS2D01G368900 chr2B 90.728 2362 109 34 3485 5786 553616168 553613857 0.000000e+00 3048
6 TraesCS2D01G368900 chr2B 93.684 1140 39 8 1 1119 553619426 553618299 0.000000e+00 1676
7 TraesCS2D01G368900 chr2B 95.489 133 6 0 3095 3227 553616432 553616300 4.540000e-51 213
8 TraesCS2D01G368900 chr2B 90.511 137 7 2 3297 3432 553616301 553616170 5.960000e-40 176
9 TraesCS2D01G368900 chr1B 82.353 374 38 18 5054 5425 599469984 599469637 3.390000e-77 300
10 TraesCS2D01G368900 chr1B 89.623 106 7 3 3020 3125 301264584 301264483 1.310000e-26 132
11 TraesCS2D01G368900 chr1B 89.623 106 6 4 3018 3122 572529351 572529452 4.710000e-26 130
12 TraesCS2D01G368900 chr6A 89.815 108 6 3 3025 3132 8173803 8173701 3.640000e-27 134
13 TraesCS2D01G368900 chr4D 90.476 105 5 3 3025 3129 441512357 441512258 3.640000e-27 134
14 TraesCS2D01G368900 chr7D 89.091 110 7 3 3018 3126 190163223 190163118 1.310000e-26 132
15 TraesCS2D01G368900 chrUn 87.395 119 7 7 3016 3133 71312960 71312849 4.710000e-26 130
16 TraesCS2D01G368900 chr3D 89.623 106 6 5 3018 3122 110927759 110927860 4.710000e-26 130
17 TraesCS2D01G368900 chr3A 88.393 112 8 4 3016 3127 640348356 640348462 4.710000e-26 130


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 TraesCS2D01G368900 chr2D 473276648 473282433 5785 True 10685.000000 10685 100.000000 1 5786 1 chr2D.!!$R1 5785
1 TraesCS2D01G368900 chr2A 615345020 615350933 5913 True 2675.666667 3513 91.575333 1 5786 3 chr2A.!!$R1 5785
2 TraesCS2D01G368900 chr2B 553613857 553619426 5569 True 1649.200000 3133 93.474400 1 5786 5 chr2B.!!$R1 5785

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
762 777 0.460311 CACGTATTCCTCCTCGGCTT 59.540 55.000 0.00 0.0 0.00 4.35 F
1095 1131 0.176680 AGGTGAGCTCGTATGCCAAG 59.823 55.000 9.64 0.0 0.00 3.61 F
1131 1167 0.825425 CCTGCGCCATCTCTCCTCTA 60.825 60.000 4.18 0.0 0.00 2.43 F
2247 2284 2.862140 GCTTTTTAGTGCGTGCAACCAT 60.862 45.455 0.00 0.0 0.00 3.55 F
3161 3397 2.593925 TGGGACACCATTATGTTGCA 57.406 45.000 0.00 0.0 43.37 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1634 1670 3.963665 TGTTGCAAGCTATTGTCACAAC 58.036 40.909 0.0 0.0 37.4 3.32 R
2928 3161 1.227263 CGCAGTTGATACCTCCCGG 60.227 63.158 0.0 0.0 0.0 5.73 R
3106 3342 1.838077 AGTAATCCCTCCGTCCCAAAG 59.162 52.381 0.0 0.0 0.0 2.77 R
3331 3594 0.590682 CATAGCACAAACACGGCACA 59.409 50.000 0.0 0.0 0.0 4.57 R
5070 5394 0.371301 CATCGTGCATCTGTTCGGTG 59.629 55.000 0.0 0.0 0.0 4.94 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
57 58 3.771577 TCCTTCCGCTTCTTCTTCTTT 57.228 42.857 0.00 0.00 0.00 2.52
76 77 5.827756 TCTTTTTATCCTTTTCCCTCTCCC 58.172 41.667 0.00 0.00 0.00 4.30
239 240 2.011222 GTAGGACGACTCAGACTCTGG 58.989 57.143 6.20 0.24 31.51 3.86
361 362 2.123897 AGCTCTCGCTCTCCTCCC 60.124 66.667 0.00 0.00 45.15 4.30
387 388 1.961277 ACGCCTCTTTGACTTGCCG 60.961 57.895 0.00 0.00 0.00 5.69
511 518 4.738998 CCTTGCCGGCACCATCCA 62.739 66.667 32.95 13.16 0.00 3.41
569 576 1.356527 CCTAGGGTTTCGCCGTTTCG 61.357 60.000 0.00 0.00 38.44 3.46
676 683 2.164624 GTGTGAGAACGAGATAGCCTGT 59.835 50.000 0.00 0.00 0.00 4.00
682 689 2.693267 ACGAGATAGCCTGTTTTCCC 57.307 50.000 0.00 0.00 0.00 3.97
684 691 3.371965 ACGAGATAGCCTGTTTTCCCTA 58.628 45.455 0.00 0.00 0.00 3.53
758 773 2.033049 CCTGTACACGTATTCCTCCTCG 59.967 54.545 0.00 0.00 0.00 4.63
759 774 2.019249 TGTACACGTATTCCTCCTCGG 58.981 52.381 0.00 0.00 0.00 4.63
760 775 1.027357 TACACGTATTCCTCCTCGGC 58.973 55.000 0.00 0.00 0.00 5.54
761 776 0.683504 ACACGTATTCCTCCTCGGCT 60.684 55.000 0.00 0.00 0.00 5.52
762 777 0.460311 CACGTATTCCTCCTCGGCTT 59.540 55.000 0.00 0.00 0.00 4.35
793 822 1.429299 TGTCTGTCTCCCTCTCCTTCA 59.571 52.381 0.00 0.00 0.00 3.02
913 949 2.663188 CCTTATCAGCTCGCGGGC 60.663 66.667 26.87 26.87 0.00 6.13
1011 1047 1.079127 CTTGGCGATGTCGAGGGTT 60.079 57.895 6.60 0.00 43.02 4.11
1095 1131 0.176680 AGGTGAGCTCGTATGCCAAG 59.823 55.000 9.64 0.00 0.00 3.61
1131 1167 0.825425 CCTGCGCCATCTCTCCTCTA 60.825 60.000 4.18 0.00 0.00 2.43
1208 1244 8.522830 ACGATCCATTGTGTTGATTTTATTCTT 58.477 29.630 0.00 0.00 0.00 2.52
1351 1387 3.423154 GAGCGCAACAGGAACCGG 61.423 66.667 11.47 0.00 0.00 5.28
1562 1598 5.738619 TCAACCTTACTCTGCATTGTCTA 57.261 39.130 0.00 0.00 0.00 2.59
1774 1811 9.549078 CCTTGATTACTTTAGAAATCTAGGGTC 57.451 37.037 14.06 0.00 44.49 4.46
2193 2230 4.697514 TGTTCAGCTACTGCCAGATATTC 58.302 43.478 0.00 0.00 40.80 1.75
2237 2274 7.128976 GCTCTGATATTACTGCTTTTTAGTGC 58.871 38.462 0.00 0.00 0.00 4.40
2247 2284 2.862140 GCTTTTTAGTGCGTGCAACCAT 60.862 45.455 0.00 0.00 0.00 3.55
2373 2600 6.201044 GTCATTATACATGCGTTACTGAGCTT 59.799 38.462 0.00 0.00 0.00 3.74
2862 3095 5.697082 AGAAGATCAAGAAGAAGCCAGAT 57.303 39.130 0.00 0.00 0.00 2.90
2928 3161 3.914312 TGATGTCTCGAAGGTTGAAGAC 58.086 45.455 0.00 0.00 0.00 3.01
3008 3244 4.649674 ACGAGCTCTCCAGGTAATATTTGA 59.350 41.667 12.85 0.00 0.00 2.69
3018 3254 9.759473 CTCCAGGTAATATTTGAATGGGATATT 57.241 33.333 0.00 0.00 32.44 1.28
3042 3278 8.998957 TTATATATACTCCCTCCATCCCAAAA 57.001 34.615 0.00 0.00 0.00 2.44
3106 3342 9.310716 ACTTTGTACTAAAGTTGAGACACTTAC 57.689 33.333 14.04 0.00 37.18 2.34
3161 3397 2.593925 TGGGACACCATTATGTTGCA 57.406 45.000 0.00 0.00 43.37 4.08
3236 3499 5.353123 TGTTTTCTAGAATACGGTGCCATTC 59.647 40.000 17.68 0.00 0.00 2.67
3335 3598 8.795786 TTTCAGTTGATTAAAATAGTGTGTGC 57.204 30.769 0.00 0.00 0.00 4.57
3346 3609 1.871789 GTGTGTGCCGTGTTTGTGC 60.872 57.895 0.00 0.00 0.00 4.57
3364 3627 7.821846 TGTTTGTGCTATGTGTAGTGATATCAA 59.178 33.333 7.07 0.00 0.00 2.57
3376 3639 8.391106 GTGTAGTGATATCAACTGGTGAATTTC 58.609 37.037 7.07 0.00 40.50 2.17
3403 3667 4.836125 AAGGAATGACATGTGTGTTGAC 57.164 40.909 1.15 0.00 39.09 3.18
3433 3697 1.729586 TTGCTCAGGTAGGTTGGACT 58.270 50.000 0.00 0.00 0.00 3.85
3445 3709 4.332683 AGGTTGGACTGTAGGAGATACA 57.667 45.455 0.00 0.00 42.21 2.29
3481 3745 7.870509 ATGTGTGCTTGATTACTTGTGATAT 57.129 32.000 0.00 0.00 0.00 1.63
3482 3746 8.962884 ATGTGTGCTTGATTACTTGTGATATA 57.037 30.769 0.00 0.00 0.00 0.86
3483 3747 8.196802 TGTGTGCTTGATTACTTGTGATATAC 57.803 34.615 0.00 0.00 0.00 1.47
3569 3834 7.971368 ATAGGTTAAAACATGGCTAAATGGT 57.029 32.000 0.00 0.00 31.46 3.55
3734 3999 4.833938 GGTACTGGGGAATTGGTGTTTTTA 59.166 41.667 0.00 0.00 0.00 1.52
3741 4006 5.186992 GGGGAATTGGTGTTTTTATACTGCT 59.813 40.000 0.00 0.00 0.00 4.24
3938 4213 5.459107 GCAAGCTCAGCAGATTCAATATTTG 59.541 40.000 0.00 0.00 0.00 2.32
3963 4238 3.579709 GACCAGGTATGATATCTGTGCG 58.420 50.000 11.48 0.00 35.10 5.34
4278 4563 3.611293 CGCACAACATTTGCTTATGTCCA 60.611 43.478 5.01 0.00 37.76 4.02
4308 4595 5.652452 GGTACTCCCTCTGCAAACAAATATT 59.348 40.000 0.00 0.00 0.00 1.28
4315 4602 6.128007 CCCTCTGCAAACAAATATTAGACGTT 60.128 38.462 0.00 0.00 0.00 3.99
4316 4603 7.305474 CCTCTGCAAACAAATATTAGACGTTT 58.695 34.615 0.00 0.00 0.00 3.60
4317 4604 7.807907 CCTCTGCAAACAAATATTAGACGTTTT 59.192 33.333 0.00 0.00 0.00 2.43
4318 4605 9.820229 CTCTGCAAACAAATATTAGACGTTTTA 57.180 29.630 0.00 0.00 0.00 1.52
4319 4606 9.820229 TCTGCAAACAAATATTAGACGTTTTAG 57.180 29.630 0.00 0.00 0.00 1.85
4320 4607 9.820229 CTGCAAACAAATATTAGACGTTTTAGA 57.180 29.630 0.00 0.00 0.00 2.10
4321 4608 9.820229 TGCAAACAAATATTAGACGTTTTAGAG 57.180 29.630 0.00 0.00 0.00 2.43
4362 4649 8.532819 ACTTCTTATACTTGTTTACAGAGGGAG 58.467 37.037 0.00 0.00 0.00 4.30
4365 4652 9.710818 TCTTATACTTGTTTACAGAGGGAGTAT 57.289 33.333 8.43 8.43 32.68 2.12
4556 4852 7.389053 AGGACACAAAGTTATCTGATTTGTCTC 59.611 37.037 4.57 3.70 43.37 3.36
4614 4910 3.055819 TCGCTGTTTGCTTCTCCTCTTAT 60.056 43.478 0.00 0.00 40.11 1.73
4618 4914 2.315925 TTGCTTCTCCTCTTATGGCG 57.684 50.000 0.00 0.00 0.00 5.69
4641 4937 2.564771 TCCTATGCATTTTCTCAGGCG 58.435 47.619 3.54 0.00 0.00 5.52
4653 4949 2.594303 CAGGCGGTGGAAGCAACA 60.594 61.111 0.00 0.00 36.08 3.33
4808 5107 7.198390 TGAATTAGCTCATGTAACCGTACTAC 58.802 38.462 0.00 0.00 0.00 2.73
4856 5155 2.959030 CCTCGTCTCTTGTGGGATGATA 59.041 50.000 0.00 0.00 0.00 2.15
4867 5166 4.441792 TGTGGGATGATAATCACTTGTCG 58.558 43.478 0.00 0.00 0.00 4.35
4883 5182 3.052455 TGTCGTGCATATTGGTCAGTT 57.948 42.857 0.00 0.00 0.00 3.16
4887 5186 5.645929 TGTCGTGCATATTGGTCAGTTTTAT 59.354 36.000 0.00 0.00 0.00 1.40
4891 5190 6.907212 CGTGCATATTGGTCAGTTTTATTCTC 59.093 38.462 0.00 0.00 0.00 2.87
4913 5212 8.408043 TCTCTTAAAATTCTGAGATTTTGCCA 57.592 30.769 14.90 0.00 39.05 4.92
4937 5236 8.134895 CCACCGTTTGCAAATATAATCAGTATT 58.865 33.333 16.21 0.00 0.00 1.89
5027 5326 3.738246 CTGTGCTGCTGCTGCTGG 61.738 66.667 27.67 15.67 40.48 4.85
5060 5384 3.813596 GCGGAGGCCACAATACTG 58.186 61.111 5.01 0.00 0.00 2.74
5061 5385 1.078426 GCGGAGGCCACAATACTGT 60.078 57.895 5.01 0.00 35.63 3.55
5062 5386 0.676782 GCGGAGGCCACAATACTGTT 60.677 55.000 5.01 0.00 31.64 3.16
5063 5387 1.821216 CGGAGGCCACAATACTGTTT 58.179 50.000 5.01 0.00 31.64 2.83
5064 5388 1.468520 CGGAGGCCACAATACTGTTTG 59.531 52.381 5.01 0.00 31.64 2.93
5065 5389 1.202348 GGAGGCCACAATACTGTTTGC 59.798 52.381 5.01 0.00 31.64 3.68
5066 5390 1.202348 GAGGCCACAATACTGTTTGCC 59.798 52.381 5.01 6.53 45.38 4.52
5067 5391 0.246360 GGCCACAATACTGTTTGCCC 59.754 55.000 0.00 0.00 41.82 5.36
5068 5392 0.109319 GCCACAATACTGTTTGCCCG 60.109 55.000 0.00 0.00 31.64 6.13
5069 5393 0.525761 CCACAATACTGTTTGCCCGG 59.474 55.000 0.00 0.00 31.64 5.73
5070 5394 0.109319 CACAATACTGTTTGCCCGGC 60.109 55.000 1.04 1.04 31.64 6.13
5071 5395 0.538516 ACAATACTGTTTGCCCGGCA 60.539 50.000 8.43 8.43 36.47 5.69
5072 5396 0.109319 CAATACTGTTTGCCCGGCAC 60.109 55.000 13.00 1.73 38.71 5.01
5073 5397 1.248101 AATACTGTTTGCCCGGCACC 61.248 55.000 13.00 6.45 38.71 5.01
5076 5400 4.877619 TGTTTGCCCGGCACCGAA 62.878 61.111 13.00 0.37 38.71 4.30
5077 5401 4.337060 GTTTGCCCGGCACCGAAC 62.337 66.667 13.00 10.71 38.71 3.95
5078 5402 4.877619 TTTGCCCGGCACCGAACA 62.878 61.111 13.00 5.25 38.71 3.18
5114 5438 1.486310 TGACTTCTCCTTGCACAGTGT 59.514 47.619 1.61 0.00 0.00 3.55
5141 5465 0.901124 TGCAGTTGGGCAAACACTTT 59.099 45.000 7.64 0.00 41.65 2.66
5169 5493 1.670811 CAATAAAGTAGGGCACGGCTG 59.329 52.381 0.00 0.00 0.00 4.85
5191 5515 6.471519 GCTGCTAATTGAAATGTCTCAACATC 59.528 38.462 0.00 0.00 45.48 3.06
5192 5516 7.627939 GCTGCTAATTGAAATGTCTCAACATCT 60.628 37.037 0.00 0.00 45.48 2.90
5194 5518 8.668353 TGCTAATTGAAATGTCTCAACATCTAC 58.332 33.333 0.00 0.00 45.48 2.59
5205 5529 8.322906 TGTCTCAACATCTACAATAAAGTTGG 57.677 34.615 0.00 0.00 37.52 3.77
5206 5530 7.094805 TGTCTCAACATCTACAATAAAGTTGGC 60.095 37.037 0.00 0.00 37.52 4.52
5207 5531 6.374333 TCTCAACATCTACAATAAAGTTGGCC 59.626 38.462 0.00 0.00 37.52 5.36
5208 5532 6.007076 TCAACATCTACAATAAAGTTGGCCA 58.993 36.000 0.00 0.00 37.52 5.36
5209 5533 6.491745 TCAACATCTACAATAAAGTTGGCCAA 59.508 34.615 16.05 16.05 37.52 4.52
5210 5534 6.909550 ACATCTACAATAAAGTTGGCCAAA 57.090 33.333 22.47 4.55 0.00 3.28
5211 5535 6.687604 ACATCTACAATAAAGTTGGCCAAAC 58.312 36.000 22.47 14.58 39.24 2.93
5212 5536 6.266558 ACATCTACAATAAAGTTGGCCAAACA 59.733 34.615 22.47 5.86 41.61 2.83
5213 5537 6.079424 TCTACAATAAAGTTGGCCAAACAC 57.921 37.500 22.47 9.18 41.61 3.32
5214 5538 5.830991 TCTACAATAAAGTTGGCCAAACACT 59.169 36.000 22.47 11.82 41.61 3.55
5215 5539 5.351948 ACAATAAAGTTGGCCAAACACTT 57.648 34.783 22.47 17.77 41.61 3.16
5216 5540 5.739959 ACAATAAAGTTGGCCAAACACTTT 58.260 33.333 28.29 28.29 41.61 2.66
5217 5541 6.879400 ACAATAAAGTTGGCCAAACACTTTA 58.121 32.000 29.98 29.98 41.61 1.85
5218 5542 6.759356 ACAATAAAGTTGGCCAAACACTTTAC 59.241 34.615 30.26 15.46 41.61 2.01
5219 5543 6.724893 ATAAAGTTGGCCAAACACTTTACT 57.275 33.333 30.26 20.82 41.61 2.24
5223 5547 5.137551 AGTTGGCCAAACACTTTACTATGT 58.862 37.500 22.47 0.00 41.61 2.29
5224 5548 6.300703 AGTTGGCCAAACACTTTACTATGTA 58.699 36.000 22.47 0.00 41.61 2.29
5237 5561 7.060748 CACTTTACTATGTACGATATGCTTCGG 59.939 40.741 8.67 0.00 43.33 4.30
5357 5683 4.127171 ACGAATGGGGAGATTCATAAACG 58.873 43.478 0.00 0.00 32.67 3.60
5358 5684 4.127171 CGAATGGGGAGATTCATAAACGT 58.873 43.478 0.00 0.00 32.67 3.99
5375 5701 7.874016 TCATAAACGTGTAAATCCAGTAACAGT 59.126 33.333 0.00 0.00 0.00 3.55
5388 5714 1.536766 GTAACAGTAAACCGCCAACCC 59.463 52.381 0.00 0.00 0.00 4.11
5414 5740 3.675228 GCAAGAACAATGCAGATTCTGGG 60.675 47.826 15.28 7.44 43.29 4.45
5425 5751 4.264083 TGCAGATTCTGGGAAGAAAATCCT 60.264 41.667 15.28 0.00 39.57 3.24
5464 5814 0.603439 GGCAAACCAAACAGGCCATG 60.603 55.000 5.01 2.64 44.01 3.66
5494 5844 2.571653 TCAGGTAATGGAGTTCCTGGTG 59.428 50.000 9.66 0.00 45.07 4.17
5537 5887 6.418057 AAATTTGCATTTCACCTCCAAGTA 57.582 33.333 0.00 0.00 0.00 2.24
5541 5891 5.389859 TGCATTTCACCTCCAAGTATTTG 57.610 39.130 0.00 0.00 0.00 2.32
5595 5945 2.558795 ACGCATGCTTACCGATAGAGAT 59.441 45.455 17.13 0.00 39.76 2.75
5644 5994 7.475137 ACCCTCTCTTCATCACTATATAAGC 57.525 40.000 0.00 0.00 0.00 3.09
5645 5995 7.013220 ACCCTCTCTTCATCACTATATAAGCA 58.987 38.462 0.00 0.00 0.00 3.91
5646 5996 7.510685 ACCCTCTCTTCATCACTATATAAGCAA 59.489 37.037 0.00 0.00 0.00 3.91
5647 5997 7.816995 CCCTCTCTTCATCACTATATAAGCAAC 59.183 40.741 0.00 0.00 0.00 4.17
5648 5998 8.363390 CCTCTCTTCATCACTATATAAGCAACA 58.637 37.037 0.00 0.00 0.00 3.33
5652 6002 9.836864 TCTTCATCACTATATAAGCAACAACAT 57.163 29.630 0.00 0.00 0.00 2.71
5659 6009 8.292448 CACTATATAAGCAACAACATCCATTCC 58.708 37.037 0.00 0.00 0.00 3.01
5663 6013 5.391312 AAGCAACAACATCCATTCCTTAC 57.609 39.130 0.00 0.00 0.00 2.34
5689 6039 3.485463 TGCCTTCTTTTTCCTCGAGAA 57.515 42.857 15.71 3.49 0.00 2.87
5701 6051 6.656632 TTTCCTCGAGAAGCAGTATATCAT 57.343 37.500 15.71 0.00 35.40 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.336392 AGGATTTGGGGAAGAAGGCC 59.664 55.000 0.00 0.00 0.00 5.19
57 58 4.711055 AGAGGGAGAGGGAAAAGGATAAA 58.289 43.478 0.00 0.00 0.00 1.40
76 77 3.954258 GAGAAGAGGAAGAGGAAGGAGAG 59.046 52.174 0.00 0.00 0.00 3.20
361 362 1.738099 CAAAGAGGCGTGACGAGGG 60.738 63.158 10.10 0.00 0.00 4.30
579 586 1.651730 CGCTCTCGATCGTTCGTCC 60.652 63.158 15.94 0.00 45.65 4.79
581 588 2.403987 CCGCTCTCGATCGTTCGT 59.596 61.111 15.94 0.00 45.65 3.85
643 650 3.633094 CTCACACTCGGGCACTCGG 62.633 68.421 0.00 0.00 0.00 4.63
644 651 2.126307 CTCACACTCGGGCACTCG 60.126 66.667 0.00 0.00 0.00 4.18
645 652 0.667792 GTTCTCACACTCGGGCACTC 60.668 60.000 0.00 0.00 0.00 3.51
646 653 1.367840 GTTCTCACACTCGGGCACT 59.632 57.895 0.00 0.00 0.00 4.40
647 654 2.022129 CGTTCTCACACTCGGGCAC 61.022 63.158 0.00 0.00 0.00 5.01
648 655 2.142357 CTCGTTCTCACACTCGGGCA 62.142 60.000 0.00 0.00 0.00 5.36
649 656 1.444553 CTCGTTCTCACACTCGGGC 60.445 63.158 0.00 0.00 0.00 6.13
650 657 0.811915 ATCTCGTTCTCACACTCGGG 59.188 55.000 0.00 0.00 0.00 5.14
651 658 2.539953 GCTATCTCGTTCTCACACTCGG 60.540 54.545 0.00 0.00 0.00 4.63
676 683 0.407918 CAACTGGGCCCTAGGGAAAA 59.592 55.000 33.21 14.00 37.50 2.29
760 775 3.764466 AGACAGGGGCGCGAGAAG 61.764 66.667 12.10 0.00 0.00 2.85
761 776 4.069232 CAGACAGGGGCGCGAGAA 62.069 66.667 12.10 0.00 0.00 2.87
793 822 1.454539 CGAGGTGGGAGGTTTGGTT 59.545 57.895 0.00 0.00 0.00 3.67
873 909 0.808847 GCAAACCTCGTACGGGATCC 60.809 60.000 18.83 1.92 0.00 3.36
1011 1047 3.654143 TCCTCCGTCCTGTCCCGA 61.654 66.667 0.00 0.00 0.00 5.14
1095 1131 4.107051 GTGTGCGAGGTGGCATGC 62.107 66.667 9.90 9.90 45.99 4.06
1562 1598 8.923270 TCAAACAAGGAGAAAAGGTAAATCAAT 58.077 29.630 0.00 0.00 0.00 2.57
1634 1670 3.963665 TGTTGCAAGCTATTGTCACAAC 58.036 40.909 0.00 0.00 37.40 3.32
1774 1811 6.901887 CGTTGCTATGCTCTGTAACAAATTAG 59.098 38.462 0.00 0.00 0.00 1.73
2193 2230 6.025896 CAGAGCAATGCTGTATTTAACTGTG 58.974 40.000 14.48 0.00 39.88 3.66
2237 2274 5.106442 TGTTAGTATCTACATGGTTGCACG 58.894 41.667 0.00 0.00 0.00 5.34
2373 2600 5.859495 TCCACCGAAATATGTGCACATATA 58.141 37.500 39.28 24.77 45.85 0.86
2693 2926 6.765036 ACACATCTTATTGGAAGTGAGCATAG 59.235 38.462 6.81 0.00 38.03 2.23
2862 3095 7.924541 ACTTGGATGGTTCAGTAGGTTTTATA 58.075 34.615 0.00 0.00 0.00 0.98
2928 3161 1.227263 CGCAGTTGATACCTCCCGG 60.227 63.158 0.00 0.00 0.00 5.73
3034 3270 7.839680 AAAGTTGAGACACTTATTTTGGGAT 57.160 32.000 0.00 0.00 35.87 3.85
3075 3311 9.880157 TGTCTCAACTTTAGTACAAAGTACTTT 57.120 29.630 15.22 15.22 39.36 2.66
3076 3312 9.310716 GTGTCTCAACTTTAGTACAAAGTACTT 57.689 33.333 14.27 1.12 39.36 2.24
3077 3313 8.693625 AGTGTCTCAACTTTAGTACAAAGTACT 58.306 33.333 17.85 13.64 39.36 2.73
3078 3314 8.868635 AGTGTCTCAACTTTAGTACAAAGTAC 57.131 34.615 17.85 14.12 39.36 2.73
3080 3316 9.310716 GTAAGTGTCTCAACTTTAGTACAAAGT 57.689 33.333 14.04 14.04 40.77 2.66
3081 3317 9.530633 AGTAAGTGTCTCAACTTTAGTACAAAG 57.469 33.333 13.08 13.08 40.77 2.77
3082 3318 9.880157 AAGTAAGTGTCTCAACTTTAGTACAAA 57.120 29.630 0.00 0.00 40.77 2.83
3083 3319 9.880157 AAAGTAAGTGTCTCAACTTTAGTACAA 57.120 29.630 0.00 0.00 39.67 2.41
3084 3320 9.309516 CAAAGTAAGTGTCTCAACTTTAGTACA 57.690 33.333 0.00 0.00 39.50 2.90
3085 3321 8.762426 CCAAAGTAAGTGTCTCAACTTTAGTAC 58.238 37.037 0.00 0.00 39.50 2.73
3086 3322 7.929785 CCCAAAGTAAGTGTCTCAACTTTAGTA 59.070 37.037 0.00 0.00 39.50 1.82
3087 3323 6.766467 CCCAAAGTAAGTGTCTCAACTTTAGT 59.234 38.462 0.00 0.00 39.50 2.24
3088 3324 6.990349 TCCCAAAGTAAGTGTCTCAACTTTAG 59.010 38.462 0.00 0.00 39.50 1.85
3089 3325 6.764560 GTCCCAAAGTAAGTGTCTCAACTTTA 59.235 38.462 0.00 0.00 39.50 1.85
3106 3342 1.838077 AGTAATCCCTCCGTCCCAAAG 59.162 52.381 0.00 0.00 0.00 2.77
3217 3480 6.474140 TTAAGAATGGCACCGTATTCTAGA 57.526 37.500 1.04 0.00 41.45 2.43
3331 3594 0.590682 CATAGCACAAACACGGCACA 59.409 50.000 0.00 0.00 0.00 4.57
3332 3595 0.591170 ACATAGCACAAACACGGCAC 59.409 50.000 0.00 0.00 0.00 5.01
3333 3596 0.590682 CACATAGCACAAACACGGCA 59.409 50.000 0.00 0.00 0.00 5.69
3334 3597 0.591170 ACACATAGCACAAACACGGC 59.409 50.000 0.00 0.00 0.00 5.68
3335 3598 3.064207 ACTACACATAGCACAAACACGG 58.936 45.455 0.00 0.00 30.75 4.94
3346 3609 7.716612 TCACCAGTTGATATCACTACACATAG 58.283 38.462 4.48 0.00 34.25 2.23
3376 3639 6.331369 ACACACATGTCATTCCTTTTAAGG 57.669 37.500 0.00 1.95 40.57 2.69
3403 3667 6.924111 ACCTACCTGAGCAATTTAACAAATG 58.076 36.000 0.00 0.00 0.00 2.32
3433 3697 9.379791 CATATATCACTACGTGTATCTCCTACA 57.620 37.037 0.00 0.00 38.02 2.74
3445 3709 6.144078 TCAAGCACACATATATCACTACGT 57.856 37.500 0.00 0.00 0.00 3.57
3453 3717 8.962884 TCACAAGTAATCAAGCACACATATAT 57.037 30.769 0.00 0.00 0.00 0.86
3481 3745 8.715190 TCACCAGCTAATATAACCACATAGTA 57.285 34.615 0.00 0.00 0.00 1.82
3482 3746 7.612065 TCACCAGCTAATATAACCACATAGT 57.388 36.000 0.00 0.00 0.00 2.12
3483 3747 9.507329 AATTCACCAGCTAATATAACCACATAG 57.493 33.333 0.00 0.00 0.00 2.23
3569 3834 7.041303 TGTGTATCCGTTTATTTTACTTGCACA 60.041 33.333 0.00 0.00 0.00 4.57
3741 4006 5.076182 TCTGAGACAACATTAATTGCCCAA 58.924 37.500 0.00 0.00 32.47 4.12
3938 4213 5.700846 CACAGATATCATACCTGGTCGTAC 58.299 45.833 0.63 0.00 32.52 3.67
3963 4238 4.425577 CCAGATGTTGGCTTAAACTGTC 57.574 45.455 0.00 0.00 40.87 3.51
3987 4262 8.287439 TGTCCTAGTCTCTTCTCTTGAATAAG 57.713 38.462 0.00 0.00 35.16 1.73
4285 4572 6.759497 AATATTTGTTTGCAGAGGGAGTAC 57.241 37.500 0.00 0.00 0.00 2.73
4338 4625 8.431910 ACTCCCTCTGTAAACAAGTATAAGAA 57.568 34.615 0.00 0.00 0.00 2.52
4440 4727 9.886132 GTAGATTTCCTAGACCAGACAAAATAA 57.114 33.333 0.00 0.00 0.00 1.40
4441 4728 9.042450 TGTAGATTTCCTAGACCAGACAAAATA 57.958 33.333 0.00 0.00 0.00 1.40
4465 4752 9.914834 TGGCAGGTTATTAAGTAAAGATATTGT 57.085 29.630 0.00 0.00 0.00 2.71
4480 4770 3.573967 CCTGTTGAACTTGGCAGGTTATT 59.426 43.478 15.43 0.00 42.47 1.40
4523 4819 7.930217 TCAGATAACTTTGTGTCCTTTTTCTG 58.070 34.615 0.00 0.00 0.00 3.02
4568 4864 8.446273 CGACTGAAAACTTATCATGAGTCATTT 58.554 33.333 1.86 0.00 0.00 2.32
4577 4873 6.373779 CAAACAGCGACTGAAAACTTATCAT 58.626 36.000 12.77 0.00 35.18 2.45
4641 4937 1.135228 ACGTTGTTTGTTGCTTCCACC 60.135 47.619 0.00 0.00 0.00 4.61
4808 5107 4.913335 ATAGCTCAATCCATTTGCACAG 57.087 40.909 0.00 0.00 35.16 3.66
4867 5166 7.989826 AGAGAATAAAACTGACCAATATGCAC 58.010 34.615 0.00 0.00 0.00 4.57
4887 5186 8.859090 TGGCAAAATCTCAGAATTTTAAGAGAA 58.141 29.630 0.00 0.00 40.19 2.87
4891 5190 6.308766 CGGTGGCAAAATCTCAGAATTTTAAG 59.691 38.462 0.00 0.00 36.86 1.85
4913 5212 8.682710 ACAATACTGATTATATTTGCAAACGGT 58.317 29.630 15.41 13.65 0.00 4.83
5056 5380 2.281900 GGTGCCGGGCAAACAGTA 60.282 61.111 25.70 0.00 41.47 2.74
5059 5383 4.877619 TTCGGTGCCGGGCAAACA 62.878 61.111 25.70 7.14 41.47 2.83
5060 5384 4.337060 GTTCGGTGCCGGGCAAAC 62.337 66.667 25.70 20.40 41.47 2.93
5061 5385 4.877619 TGTTCGGTGCCGGGCAAA 62.878 61.111 25.70 12.25 41.47 3.68
5064 5388 4.778143 ATCTGTTCGGTGCCGGGC 62.778 66.667 13.32 13.32 40.25 6.13
5065 5389 2.819595 CATCTGTTCGGTGCCGGG 60.820 66.667 10.94 0.00 40.25 5.73
5066 5390 3.499737 GCATCTGTTCGGTGCCGG 61.500 66.667 10.94 0.00 40.25 6.13
5067 5391 2.741985 TGCATCTGTTCGGTGCCG 60.742 61.111 3.94 3.94 38.06 5.69
5068 5392 2.870372 GTGCATCTGTTCGGTGCC 59.130 61.111 0.00 0.00 38.06 5.01
5069 5393 1.361668 ATCGTGCATCTGTTCGGTGC 61.362 55.000 0.00 0.00 39.26 5.01
5070 5394 0.371301 CATCGTGCATCTGTTCGGTG 59.629 55.000 0.00 0.00 0.00 4.94
5071 5395 1.361668 GCATCGTGCATCTGTTCGGT 61.362 55.000 0.00 0.00 44.26 4.69
5072 5396 1.349627 GCATCGTGCATCTGTTCGG 59.650 57.895 0.00 0.00 44.26 4.30
5073 5397 4.961622 GCATCGTGCATCTGTTCG 57.038 55.556 0.00 0.00 44.26 3.95
5092 5416 3.144506 CACTGTGCAAGGAGAAGTCATT 58.855 45.455 0.00 0.00 0.00 2.57
5114 5438 2.877097 TGCCCAACTGCATCTTTCTA 57.123 45.000 0.00 0.00 36.04 2.10
5141 5465 7.388500 GCCGTGCCCTACTTTATTGTATAATAA 59.612 37.037 0.87 0.87 37.06 1.40
5169 5493 8.668353 TGTAGATGTTGAGACATTTCAATTAGC 58.332 33.333 0.00 0.00 46.27 3.09
5191 5515 6.084326 AGTGTTTGGCCAACTTTATTGTAG 57.916 37.500 20.35 0.00 36.21 2.74
5192 5516 6.472686 AAGTGTTTGGCCAACTTTATTGTA 57.527 33.333 20.35 0.00 36.21 2.41
5194 5518 6.983890 AGTAAAGTGTTTGGCCAACTTTATTG 59.016 34.615 30.27 0.00 44.09 1.90
5197 5521 7.285858 ACATAGTAAAGTGTTTGGCCAACTTTA 59.714 33.333 26.66 26.66 42.52 1.85
5201 5525 5.447624 ACATAGTAAAGTGTTTGGCCAAC 57.552 39.130 20.35 14.11 35.71 3.77
5204 5528 4.931002 TCGTACATAGTAAAGTGTTTGGCC 59.069 41.667 0.00 0.00 0.00 5.36
5205 5529 6.657836 ATCGTACATAGTAAAGTGTTTGGC 57.342 37.500 0.00 0.00 0.00 4.52
5206 5530 8.273557 GCATATCGTACATAGTAAAGTGTTTGG 58.726 37.037 0.00 0.00 0.00 3.28
5207 5531 9.031360 AGCATATCGTACATAGTAAAGTGTTTG 57.969 33.333 0.00 0.00 0.00 2.93
5208 5532 9.595823 AAGCATATCGTACATAGTAAAGTGTTT 57.404 29.630 0.00 0.00 0.00 2.83
5209 5533 9.245962 GAAGCATATCGTACATAGTAAAGTGTT 57.754 33.333 0.00 0.00 0.00 3.32
5210 5534 7.590322 CGAAGCATATCGTACATAGTAAAGTGT 59.410 37.037 0.00 0.00 38.01 3.55
5211 5535 7.060748 CCGAAGCATATCGTACATAGTAAAGTG 59.939 40.741 5.96 0.00 41.16 3.16
5212 5536 7.082602 CCGAAGCATATCGTACATAGTAAAGT 58.917 38.462 5.96 0.00 41.16 2.66
5213 5537 6.527023 CCCGAAGCATATCGTACATAGTAAAG 59.473 42.308 5.96 0.00 41.16 1.85
5214 5538 6.016024 ACCCGAAGCATATCGTACATAGTAAA 60.016 38.462 5.96 0.00 41.16 2.01
5215 5539 5.474532 ACCCGAAGCATATCGTACATAGTAA 59.525 40.000 5.96 0.00 41.16 2.24
5216 5540 5.005740 ACCCGAAGCATATCGTACATAGTA 58.994 41.667 5.96 0.00 41.16 1.82
5217 5541 3.825014 ACCCGAAGCATATCGTACATAGT 59.175 43.478 5.96 0.00 41.16 2.12
5218 5542 4.082949 TGACCCGAAGCATATCGTACATAG 60.083 45.833 5.96 0.00 41.16 2.23
5219 5543 3.822167 TGACCCGAAGCATATCGTACATA 59.178 43.478 5.96 0.00 41.16 2.29
5223 5547 3.319689 TGAATGACCCGAAGCATATCGTA 59.680 43.478 5.96 0.00 41.16 3.43
5224 5548 2.102420 TGAATGACCCGAAGCATATCGT 59.898 45.455 5.96 0.00 41.16 3.73
5237 5561 7.887996 TTGTAGATTTGCAAATTGAATGACC 57.112 32.000 24.81 10.16 0.00 4.02
5327 5653 0.953471 CTCCCCATTCGTTGTTCGCA 60.953 55.000 0.00 0.00 39.67 5.10
5328 5654 0.672401 TCTCCCCATTCGTTGTTCGC 60.672 55.000 0.00 0.00 39.67 4.70
5330 5656 3.343617 TGAATCTCCCCATTCGTTGTTC 58.656 45.455 0.00 0.00 35.78 3.18
5357 5683 6.619232 GCGGTTTACTGTTACTGGATTTACAC 60.619 42.308 0.00 0.00 0.00 2.90
5358 5684 5.409214 GCGGTTTACTGTTACTGGATTTACA 59.591 40.000 0.00 0.00 0.00 2.41
5375 5701 0.827925 TGCATTGGGTTGGCGGTTTA 60.828 50.000 0.00 0.00 0.00 2.01
5414 5740 6.173339 TGTCACTACCATGAGGATTTTCTTC 58.827 40.000 0.00 0.00 38.69 2.87
5425 5751 2.169144 CCTGCATCTGTCACTACCATGA 59.831 50.000 0.00 0.00 0.00 3.07
5464 5814 5.099042 ACTCCATTACCTGAACCATACAC 57.901 43.478 0.00 0.00 0.00 2.90
5494 5844 2.430465 TCATTCTTGTCTTGCCTCAGC 58.570 47.619 0.00 0.00 40.48 4.26
5570 5920 2.423926 ATCGGTAAGCATGCGTCTAG 57.576 50.000 10.11 4.26 0.00 2.43
5595 5945 5.741011 AGGAATGGTTAATGCTCTTAACGA 58.259 37.500 13.01 10.90 36.13 3.85
5644 5994 8.400947 CAAGATAGTAAGGAATGGATGTTGTTG 58.599 37.037 0.00 0.00 0.00 3.33
5645 5995 7.067494 GCAAGATAGTAAGGAATGGATGTTGTT 59.933 37.037 0.00 0.00 0.00 2.83
5646 5996 6.543831 GCAAGATAGTAAGGAATGGATGTTGT 59.456 38.462 0.00 0.00 0.00 3.32
5647 5997 6.016777 GGCAAGATAGTAAGGAATGGATGTTG 60.017 42.308 0.00 0.00 0.00 3.33
5648 5998 6.064717 GGCAAGATAGTAAGGAATGGATGTT 58.935 40.000 0.00 0.00 0.00 2.71
5652 6002 5.667626 AGAAGGCAAGATAGTAAGGAATGGA 59.332 40.000 0.00 0.00 0.00 3.41
5659 6009 7.201565 CGAGGAAAAAGAAGGCAAGATAGTAAG 60.202 40.741 0.00 0.00 0.00 2.34
5663 6013 5.178797 TCGAGGAAAAAGAAGGCAAGATAG 58.821 41.667 0.00 0.00 0.00 2.08
5689 6039 4.712051 TTGGAAGGCATGATATACTGCT 57.288 40.909 0.00 0.00 38.45 4.24
5701 6051 5.070001 GGCTTGTGTATATATTGGAAGGCA 58.930 41.667 0.00 0.00 35.30 4.75


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

AutoCloner maintained by Alex Coulton.