Multiple sequence alignment - TraesCS2A01G011000

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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 TraesCS2A01G011000 chr2A 100.000 3394 0 0 965 4358 4161106 4164499 0.000000e+00 6268.0
1 TraesCS2A01G011000 chr2A 100.000 1314 0 0 4642 5955 4164783 4166096 0.000000e+00 2427.0
2 TraesCS2A01G011000 chr2A 100.000 538 0 0 1 538 4160142 4160679 0.000000e+00 994.0
3 TraesCS2A01G011000 chr2D 91.467 1254 86 16 2111 3362 5670783 5672017 0.000000e+00 1703.0
4 TraesCS2A01G011000 chr2D 90.034 1164 72 22 965 2099 5668875 5670023 0.000000e+00 1467.0
5 TraesCS2A01G011000 chr2D 92.842 922 51 10 4651 5570 5673766 5674674 0.000000e+00 1323.0
6 TraesCS2A01G011000 chr2D 90.273 915 73 9 3375 4280 5672441 5673348 0.000000e+00 1182.0
7 TraesCS2A01G011000 chr2D 96.992 532 10 2 1 532 5667940 5668465 0.000000e+00 889.0
8 TraesCS2A01G011000 chr2D 92.283 311 19 2 5647 5953 5675010 5675319 2.550000e-118 436.0
9 TraesCS2A01G011000 chr2B 93.518 1157 46 12 965 2099 5689416 5688267 0.000000e+00 1694.0
10 TraesCS2A01G011000 chr2B 89.514 1316 75 22 4675 5953 5685145 5683856 0.000000e+00 1607.0
11 TraesCS2A01G011000 chr2B 92.744 882 51 4 2119 2995 5687543 5686670 0.000000e+00 1262.0
12 TraesCS2A01G011000 chr2B 95.028 362 10 4 1 357 5690336 5689978 4.030000e-156 562.0
13 TraesCS2A01G011000 chr2B 86.873 518 33 17 3685 4196 5685986 5685498 1.130000e-151 547.0
14 TraesCS2A01G011000 chr2B 87.500 368 19 9 3022 3362 5686672 5686305 3.340000e-107 399.0
15 TraesCS2A01G011000 chr2B 89.320 309 32 1 3364 3672 5686263 5685956 2.600000e-103 387.0
16 TraesCS2A01G011000 chr2B 86.559 186 16 4 149 333 5695069 5694892 4.710000e-46 196.0
17 TraesCS2A01G011000 chr2B 89.706 136 7 3 402 530 5689969 5689834 3.690000e-37 167.0
18 TraesCS2A01G011000 chr1D 88.991 109 12 0 1292 1400 436713102 436712994 1.040000e-27 135.0
19 TraesCS2A01G011000 chr1D 93.443 61 2 2 4733 4792 436710661 436710602 8.220000e-14 89.8
20 TraesCS2A01G011000 chr1B 88.991 109 12 0 1292 1400 591512522 591512414 1.040000e-27 135.0
21 TraesCS2A01G011000 chr1B 91.667 60 5 0 4733 4792 591510627 591510568 3.820000e-12 84.2
22 TraesCS2A01G011000 chr1B 90.323 62 6 0 1326 1387 530779292 530779231 1.380000e-11 82.4
23 TraesCS2A01G011000 chr1A 88.991 109 12 0 1292 1400 533742366 533742258 1.040000e-27 135.0
24 TraesCS2A01G011000 chr1A 93.333 60 4 0 4733 4792 533741055 533740996 8.220000e-14 89.8
25 TraesCS2A01G011000 chr3A 91.304 92 8 0 1294 1385 509536390 509536299 6.270000e-25 126.0
26 TraesCS2A01G011000 chr3D 90.217 92 9 0 1294 1385 388442136 388442045 2.910000e-23 121.0
27 TraesCS2A01G011000 chr3B 88.235 85 8 2 1303 1385 505044201 505044117 3.800000e-17 100.0


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 TraesCS2A01G011000 chr2A 4160142 4166096 5954 False 3229.666667 6268 100.000000 1 5955 3 chr2A.!!$F1 5954
1 TraesCS2A01G011000 chr2D 5667940 5675319 7379 False 1166.666667 1703 92.315167 1 5953 6 chr2D.!!$F1 5952
2 TraesCS2A01G011000 chr2B 5683856 5690336 6480 True 828.125000 1694 90.525375 1 5953 8 chr2B.!!$R2 5952

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
359 365 0.036010 ACCAATCTGCAACGCTAGCT 60.036 50.000 13.93 0.00 0.00 3.32 F
1095 1125 0.390492 CGAGCAGCCATGACCATCTA 59.610 55.000 0.00 0.00 0.00 1.98 F
1895 1950 1.334869 CACCTGGAGCACAAAAGACAC 59.665 52.381 0.00 0.00 0.00 3.67 F
2026 2082 0.317938 ACGCGGCTAGCTAGATTTCG 60.318 55.000 25.15 20.43 45.59 3.46 F
3744 5018 0.657840 ACATCGGCGCAAGAAATAGC 59.342 50.000 10.83 0.00 43.02 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1213 1246 0.038251 TGTGAGCTACTTCCTGCACG 60.038 55.000 0.00 0.00 0.00 5.34 R
1977 2033 1.023513 GCCAGTCTGCTAGTTGCCTG 61.024 60.000 0.00 0.00 42.00 4.85 R
2929 3760 2.609459 GCAATGATAGAGGACCAACACG 59.391 50.000 0.00 0.00 0.00 4.49 R
3818 5092 3.749665 TGGCCTGCCATAAATATTTGC 57.250 42.857 6.80 6.51 41.89 3.68 R
5192 6525 1.555075 CACTAGTGCACACATACCCCT 59.445 52.381 21.04 0.00 0.00 4.79 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
146 147 7.517417 CGTGATTAAGCTAACTAATCAAGCTGG 60.517 40.741 17.05 0.00 45.61 4.85
252 254 4.641645 TTCAGCTGCCCCCACACG 62.642 66.667 9.47 0.00 0.00 4.49
357 363 0.647410 CGACCAATCTGCAACGCTAG 59.353 55.000 0.00 0.00 0.00 3.42
358 364 0.375106 GACCAATCTGCAACGCTAGC 59.625 55.000 4.06 4.06 0.00 3.42
359 365 0.036010 ACCAATCTGCAACGCTAGCT 60.036 50.000 13.93 0.00 0.00 3.32
360 366 0.654683 CCAATCTGCAACGCTAGCTC 59.345 55.000 13.93 0.00 0.00 4.09
429 435 4.069232 TCTCTGGTCCGGCGCTTG 62.069 66.667 7.64 0.00 0.00 4.01
994 1024 1.981668 GCTCGAGCTCAACGTAACG 59.018 57.895 29.88 0.00 38.21 3.18
996 1026 0.728129 CTCGAGCTCAACGTAACGCA 60.728 55.000 15.40 0.00 0.00 5.24
1011 1041 2.645838 ACGCAGCCATGGAGAATTAT 57.354 45.000 18.40 0.00 0.00 1.28
1020 1050 4.461781 GCCATGGAGAATTATCCCATTCTG 59.538 45.833 18.40 6.28 42.52 3.02
1047 1077 1.743252 GCAGCCCTCTTCTTCCACG 60.743 63.158 0.00 0.00 0.00 4.94
1066 1096 4.000325 CACGTCCAATTCATACCACTTCA 59.000 43.478 0.00 0.00 0.00 3.02
1095 1125 0.390492 CGAGCAGCCATGACCATCTA 59.610 55.000 0.00 0.00 0.00 1.98
1213 1246 1.605710 CAAAGGATGGTGGCGATGATC 59.394 52.381 0.00 0.00 0.00 2.92
1227 1260 2.131183 GATGATCGTGCAGGAAGTAGC 58.869 52.381 13.87 2.05 0.00 3.58
1537 1573 8.923270 TCTAACCATTGATTGTTTCTCCTTTTT 58.077 29.630 0.00 0.00 0.00 1.94
1539 1575 6.888105 ACCATTGATTGTTTCTCCTTTTTGT 58.112 32.000 0.00 0.00 0.00 2.83
1540 1576 6.762661 ACCATTGATTGTTTCTCCTTTTTGTG 59.237 34.615 0.00 0.00 0.00 3.33
1542 1578 7.280652 CCATTGATTGTTTCTCCTTTTTGTGTT 59.719 33.333 0.00 0.00 0.00 3.32
1544 1580 7.169158 TGATTGTTTCTCCTTTTTGTGTTCT 57.831 32.000 0.00 0.00 0.00 3.01
1545 1581 7.610865 TGATTGTTTCTCCTTTTTGTGTTCTT 58.389 30.769 0.00 0.00 0.00 2.52
1589 1630 4.456566 GCAATTTCATGTTTTTGATGGGCT 59.543 37.500 0.00 0.00 0.00 5.19
1590 1631 5.391203 GCAATTTCATGTTTTTGATGGGCTC 60.391 40.000 0.00 0.00 0.00 4.70
1591 1632 4.952071 TTTCATGTTTTTGATGGGCTCA 57.048 36.364 0.00 0.00 0.00 4.26
1672 1721 4.327982 CATGGGATAACGACATGTCTCT 57.672 45.455 22.95 12.26 37.72 3.10
1673 1722 4.302455 CATGGGATAACGACATGTCTCTC 58.698 47.826 22.95 14.03 37.72 3.20
1780 1833 4.150804 GGCGATCGAATTTGACTAGGAATC 59.849 45.833 21.57 0.00 0.00 2.52
1787 1840 8.201554 TCGAATTTGACTAGGAATCATTTGAG 57.798 34.615 0.00 0.00 0.00 3.02
1895 1950 1.334869 CACCTGGAGCACAAAAGACAC 59.665 52.381 0.00 0.00 0.00 3.67
1897 1952 2.438021 ACCTGGAGCACAAAAGACACTA 59.562 45.455 0.00 0.00 0.00 2.74
2026 2082 0.317938 ACGCGGCTAGCTAGATTTCG 60.318 55.000 25.15 20.43 45.59 3.46
2116 2189 8.819643 AGAATAAACTACTGAATAATCTCGGC 57.180 34.615 0.00 0.00 0.00 5.54
2117 2190 8.643324 AGAATAAACTACTGAATAATCTCGGCT 58.357 33.333 0.00 0.00 0.00 5.52
2143 2969 3.731652 TGCCATGAACTTTGAAAGTGG 57.268 42.857 11.83 9.42 41.91 4.00
2157 2983 3.318839 TGAAAGTGGCTGACAATTCAAGG 59.681 43.478 9.76 0.00 36.16 3.61
2175 3001 3.636153 AGGATTACCAAGCTTGACTCC 57.364 47.619 28.05 23.10 38.94 3.85
2184 3010 6.869206 ACCAAGCTTGACTCCTTTATACTA 57.131 37.500 28.05 0.00 0.00 1.82
2196 3022 9.478768 GACTCCTTTATACTAGAGTAAAATGGC 57.521 37.037 0.00 0.00 39.62 4.40
2203 3029 3.930848 ACTAGAGTAAAATGGCGTTTCCG 59.069 43.478 4.95 0.00 37.80 4.30
2210 3036 7.927629 AGAGTAAAATGGCGTTTCCGTATAATA 59.072 33.333 4.95 0.00 37.80 0.98
2265 3091 7.061566 TCCAAGAATGTTGATACATCGGATA 57.938 36.000 0.00 0.00 44.14 2.59
2957 3788 6.252599 TGGTCCTCTATCATTGCAAACTAT 57.747 37.500 1.71 0.00 0.00 2.12
3047 3878 9.959721 AATTGTACATATATACCCAATCACTCC 57.040 33.333 0.00 0.00 0.00 3.85
3049 3880 6.722590 TGTACATATATACCCAATCACTCCGT 59.277 38.462 0.00 0.00 0.00 4.69
3069 3900 8.838365 ACTCCGTGTAAACAATTAAATGTGTTA 58.162 29.630 0.00 0.00 36.97 2.41
3280 4139 3.194116 ACCTATTGCTTTGCATGAACTGG 59.806 43.478 0.00 0.00 38.76 4.00
3376 4275 8.888579 AAAAGGTCATAGGATTCGTATGTAAG 57.111 34.615 20.19 2.08 34.87 2.34
3396 4666 3.377573 AGCCATTGTCCAATTAATGCCT 58.622 40.909 0.00 0.00 33.92 4.75
3423 4693 7.211573 AGTCATTGTCAATTCAAATTCTTGCA 58.788 30.769 0.00 0.00 32.14 4.08
3439 4709 3.578282 TCTTGCAGATGTTAGAGGTGACA 59.422 43.478 0.00 0.00 0.00 3.58
3440 4710 3.319137 TGCAGATGTTAGAGGTGACAC 57.681 47.619 0.00 0.00 0.00 3.67
3488 4758 5.204409 ACAATGTGCTGATTTGTGATTGT 57.796 34.783 0.00 0.00 32.61 2.71
3585 4855 7.684317 TTACCACATATGATGGAAGGACTAA 57.316 36.000 23.07 11.89 39.87 2.24
3601 4871 7.945109 GGAAGGACTAATTTAGCCTATTTGGAT 59.055 37.037 15.37 3.69 38.35 3.41
3605 4875 8.568794 GGACTAATTTAGCCTATTTGGATGAAC 58.431 37.037 3.28 0.00 32.50 3.18
3609 4879 5.772825 TTAGCCTATTTGGATGAACATGC 57.227 39.130 0.00 0.00 38.35 4.06
3612 4882 3.633525 GCCTATTTGGATGAACATGCTGA 59.366 43.478 7.70 0.00 38.35 4.26
3621 4891 5.711506 TGGATGAACATGCTGACTTATTTGT 59.288 36.000 7.70 0.00 0.00 2.83
3622 4892 6.032094 GGATGAACATGCTGACTTATTTGTG 58.968 40.000 0.00 0.00 0.00 3.33
3624 4894 7.148255 GGATGAACATGCTGACTTATTTGTGTA 60.148 37.037 0.00 0.00 0.00 2.90
3627 4897 8.022550 TGAACATGCTGACTTATTTGTGTATTG 58.977 33.333 0.00 0.00 0.00 1.90
3628 4898 6.324819 ACATGCTGACTTATTTGTGTATTGC 58.675 36.000 0.00 0.00 0.00 3.56
3744 5018 0.657840 ACATCGGCGCAAGAAATAGC 59.342 50.000 10.83 0.00 43.02 2.97
3835 5109 9.683069 CTTAAAGTAGCAAATATTTATGGCAGG 57.317 33.333 10.56 0.00 0.00 4.85
3858 5133 7.277098 CAGGCCAAAAATGAGATAAAATGACAG 59.723 37.037 5.01 0.00 0.00 3.51
3935 5212 7.355778 CGATATAGGCTTTTTCCAGAACAATC 58.644 38.462 0.00 0.00 0.00 2.67
3996 5276 7.348815 TCTCATGAACAATTATGAACCATCCT 58.651 34.615 0.00 0.00 33.30 3.24
4139 5419 8.416329 ACCAATTGATAATGCTTGGATAACTTC 58.584 33.333 7.12 0.00 40.48 3.01
4140 5420 7.869429 CCAATTGATAATGCTTGGATAACTTCC 59.131 37.037 7.12 0.00 45.69 3.46
4158 5438 0.035056 CCGTGAGCCTCCTTGGATTT 60.035 55.000 0.00 0.00 38.35 2.17
4167 5447 6.053632 AGCCTCCTTGGATTTTAAAAATGG 57.946 37.500 4.44 1.22 38.35 3.16
4168 5448 5.045651 AGCCTCCTTGGATTTTAAAAATGGG 60.046 40.000 4.44 4.05 38.35 4.00
4189 5469 6.369629 TGGGTAACATTGGAAGAAAAAGAGA 58.630 36.000 0.00 0.00 39.74 3.10
4199 5479 7.703058 TGGAAGAAAAAGAGAACAAGAGTTT 57.297 32.000 0.00 0.00 38.30 2.66
4209 5489 7.546250 AGAGAACAAGAGTTTGAGAGGAATA 57.454 36.000 0.00 0.00 38.30 1.75
4264 5545 7.231467 ACAATTGTAGGACAAACTGGTAAGAT 58.769 34.615 9.97 0.00 41.96 2.40
4280 5561 8.512138 ACTGGTAAGATAAAATACAACAAGCAC 58.488 33.333 0.00 0.00 0.00 4.40
4281 5562 7.822658 TGGTAAGATAAAATACAACAAGCACC 58.177 34.615 0.00 0.00 0.00 5.01
4283 5564 6.909550 AAGATAAAATACAACAAGCACCCA 57.090 33.333 0.00 0.00 0.00 4.51
4286 5567 6.663093 AGATAAAATACAACAAGCACCCATGA 59.337 34.615 0.00 0.00 0.00 3.07
4290 5571 5.743636 ATACAACAAGCACCCATGAAAAT 57.256 34.783 0.00 0.00 0.00 1.82
4291 5572 3.731089 ACAACAAGCACCCATGAAAATG 58.269 40.909 0.00 0.00 0.00 2.32
4292 5573 2.460757 ACAAGCACCCATGAAAATGC 57.539 45.000 0.00 0.00 38.39 3.56
4294 5575 1.276989 CAAGCACCCATGAAAATGCCT 59.723 47.619 0.00 0.00 38.92 4.75
4295 5576 1.188863 AGCACCCATGAAAATGCCTC 58.811 50.000 0.00 0.00 38.92 4.70
4312 5593 3.939592 TGCCTCGATCCTACATAGATACG 59.060 47.826 0.00 0.00 0.00 3.06
4336 5617 8.269317 ACGTATAAGAAATTGGTTGGATTCCTA 58.731 33.333 3.95 0.00 0.00 2.94
4338 5619 5.897377 AAGAAATTGGTTGGATTCCTACG 57.103 39.130 10.54 0.00 30.33 3.51
4340 5621 4.941873 AGAAATTGGTTGGATTCCTACGTC 59.058 41.667 10.54 0.07 30.33 4.34
4345 5626 3.262151 TGGTTGGATTCCTACGTCAATGA 59.738 43.478 10.54 0.00 30.33 2.57
4352 5633 5.462398 GGATTCCTACGTCAATGATGTACAC 59.538 44.000 10.98 0.00 33.52 2.90
4354 5635 5.394224 TCCTACGTCAATGATGTACACAA 57.606 39.130 10.98 0.00 33.52 3.33
4355 5636 5.407502 TCCTACGTCAATGATGTACACAAG 58.592 41.667 10.98 3.66 33.52 3.16
4357 5638 5.516696 CCTACGTCAATGATGTACACAAGAG 59.483 44.000 10.98 2.33 33.52 2.85
4707 6035 5.594317 CCCTGTAGCACAATAGCCTTTAAAT 59.406 40.000 0.00 0.00 34.23 1.40
4747 6075 1.032794 CATGCAGGAGCTACTACCGA 58.967 55.000 0.00 0.00 42.74 4.69
4825 6153 2.835764 AGGTGTGGTGGTAACGACATAT 59.164 45.455 0.00 0.00 45.26 1.78
4987 6315 2.405892 GGCTAAACAATGCCTATGCG 57.594 50.000 0.00 0.00 45.26 4.73
5057 6385 9.654417 GTGAAAACGTAAAAGAGTAATAAAGCA 57.346 29.630 0.00 0.00 0.00 3.91
5081 6409 3.790152 TGCCATAGCTAGATAGATGCG 57.210 47.619 0.00 0.00 40.80 4.73
5125 6454 6.601741 TTGCATTCCTTTGTTGATGTTTTC 57.398 33.333 0.00 0.00 0.00 2.29
5141 6470 9.695526 TTGATGTTTTCTTTCAATTGTAGATGG 57.304 29.630 5.13 0.00 0.00 3.51
5192 6525 7.663905 ACAAACACATAAACTATTAGCACCTCA 59.336 33.333 0.00 0.00 0.00 3.86
5226 6559 3.555168 GCACTAGTGTTGTACAGCTCCTT 60.555 47.826 23.44 0.00 0.00 3.36
5227 6560 3.990469 CACTAGTGTTGTACAGCTCCTTG 59.010 47.826 15.06 9.69 0.00 3.61
5344 6677 9.615295 TGACTTGTTTAAGTTGTACTTGTTTTC 57.385 29.630 2.45 0.00 46.79 2.29
5371 6704 9.812347 TTGTATTCCTATTTAGCATTGATCCAT 57.188 29.630 0.00 0.00 0.00 3.41
5487 6828 5.752955 GTGACCAAAACATACAAAACTGCAT 59.247 36.000 0.00 0.00 0.00 3.96
5534 6875 5.188948 TGAGTATAGAGCAAAGTTGGGCTTA 59.811 40.000 4.02 0.90 41.22 3.09
5541 6882 6.663734 AGAGCAAAGTTGGGCTTAGTATTAT 58.336 36.000 4.02 0.00 41.22 1.28
5546 6887 5.881923 AGTTGGGCTTAGTATTATCGGAA 57.118 39.130 0.00 0.00 0.00 4.30
5570 7136 6.924111 AGGTTTGATATTGATGTTGAACACC 58.076 36.000 0.00 0.00 0.00 4.16
5663 7261 1.626621 AGGGAGGGGTGTCTAGATCT 58.373 55.000 0.00 0.00 0.00 2.75
5729 7331 3.062099 CGTCTTTGTCACCGGATGTATTG 59.938 47.826 9.46 0.00 0.00 1.90
5744 7346 8.304596 CCGGATGTATTGTATTGACTAGTACAT 58.695 37.037 0.00 0.00 34.14 2.29
5786 7388 0.167470 CAGGAAATGCAGCACTCGTG 59.833 55.000 12.33 12.33 0.00 4.35
5790 7392 1.470098 GAAATGCAGCACTCGTGGAAT 59.530 47.619 0.00 0.00 0.00 3.01
5806 7408 7.495934 ACTCGTGGAATTCTATAATCAAACCAG 59.504 37.037 5.23 0.00 0.00 4.00
5828 7430 7.181125 ACCAGGTCTCATTGTCTACTTTTCTAT 59.819 37.037 0.00 0.00 0.00 1.98
5836 7439 9.031537 TCATTGTCTACTTTTCTATAGTGACCA 57.968 33.333 0.00 0.00 0.00 4.02
5877 7480 2.359981 AATCCACATCATCTGCTGGG 57.640 50.000 0.00 0.00 31.05 4.45
5881 7484 1.340308 CCACATCATCTGCTGGGTTGA 60.340 52.381 0.00 0.00 0.00 3.18
5898 7501 4.385310 GGGTTGAAGCCATGACTAGGTATT 60.385 45.833 8.81 0.00 35.40 1.89
5909 7512 3.958798 TGACTAGGTATTAGCACCTCCAC 59.041 47.826 0.00 0.00 46.34 4.02
5938 7541 0.468400 ATAGTGGACCGAGGAGAGCC 60.468 60.000 0.00 0.00 0.00 4.70
5953 7556 3.345808 GCCTGCGTCGACAAGCAA 61.346 61.111 17.16 2.44 43.31 3.91
5954 7557 2.551270 CCTGCGTCGACAAGCAAC 59.449 61.111 17.16 0.00 43.31 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 6.707440 TGTTCTAACTTTTGGAAGCATGAA 57.293 33.333 0.00 0.00 36.29 2.57
146 147 1.632589 AGGATTTTTCACTGTGGGGC 58.367 50.000 8.11 0.00 0.00 5.80
357 363 5.522460 TGCGTGTGTAGGAATTATTAAGAGC 59.478 40.000 0.00 0.00 0.00 4.09
358 364 6.533723 TGTGCGTGTGTAGGAATTATTAAGAG 59.466 38.462 0.00 0.00 0.00 2.85
359 365 6.399743 TGTGCGTGTGTAGGAATTATTAAGA 58.600 36.000 0.00 0.00 0.00 2.10
360 366 6.656314 TGTGCGTGTGTAGGAATTATTAAG 57.344 37.500 0.00 0.00 0.00 1.85
400 406 1.619332 GACCAGAGACGAACCTTCCTT 59.381 52.381 0.00 0.00 0.00 3.36
429 435 4.196193 TGACCATTCCCGTGATATTGTTC 58.804 43.478 0.00 0.00 0.00 3.18
487 495 1.181098 AGACTGTTTGCATGGTGGGC 61.181 55.000 0.00 0.00 0.00 5.36
989 1019 1.668419 ATTCTCCATGGCTGCGTTAC 58.332 50.000 6.96 0.00 0.00 2.50
992 1022 2.498167 GATAATTCTCCATGGCTGCGT 58.502 47.619 6.96 0.00 0.00 5.24
994 1024 2.165998 GGGATAATTCTCCATGGCTGC 58.834 52.381 6.96 0.00 37.01 5.25
996 1026 4.356190 AGAATGGGATAATTCTCCATGGCT 59.644 41.667 6.96 7.83 42.01 4.75
1038 1068 4.258543 GGTATGAATTGGACGTGGAAGAA 58.741 43.478 0.00 0.00 0.00 2.52
1047 1077 5.505173 CCATGAAGTGGTATGAATTGGAC 57.495 43.478 0.00 0.00 43.44 4.02
1066 1096 4.853050 GCTGCTCGCTCCTGCCAT 62.853 66.667 0.00 0.00 35.36 4.40
1095 1125 1.830279 CTGCTTGACCATGGTGATGT 58.170 50.000 25.52 0.00 0.00 3.06
1147 1177 2.124942 CGAGAAGAGGCCTTGGCC 60.125 66.667 22.29 22.29 31.62 5.36
1148 1178 2.124942 CCGAGAAGAGGCCTTGGC 60.125 66.667 6.77 2.49 31.62 4.52
1162 1192 3.003173 CTCCTGCTTGGACCCCGA 61.003 66.667 0.00 0.00 40.56 5.14
1213 1246 0.038251 TGTGAGCTACTTCCTGCACG 60.038 55.000 0.00 0.00 0.00 5.34
1254 1290 1.672145 CCTTTCTTCTTCCCGACGACC 60.672 57.143 0.00 0.00 0.00 4.79
1486 1522 7.074653 AGTCCCAAACAACATCTAGAAGTAA 57.925 36.000 0.17 0.00 0.00 2.24
1589 1630 5.544176 ACTCCATCTCACCTACTTTCTTTGA 59.456 40.000 0.00 0.00 0.00 2.69
1590 1631 5.799213 ACTCCATCTCACCTACTTTCTTTG 58.201 41.667 0.00 0.00 0.00 2.77
1591 1632 5.046231 GGACTCCATCTCACCTACTTTCTTT 60.046 44.000 0.00 0.00 0.00 2.52
1672 1721 5.260424 GCCTAGACTAGATGATGAGGATGA 58.740 45.833 11.27 0.00 0.00 2.92
1673 1722 4.096231 CGCCTAGACTAGATGATGAGGATG 59.904 50.000 11.27 0.00 0.00 3.51
1780 1833 3.012518 CCTCTAACTGGTGGCTCAAATG 58.987 50.000 0.00 0.00 0.00 2.32
1977 2033 1.023513 GCCAGTCTGCTAGTTGCCTG 61.024 60.000 0.00 0.00 42.00 4.85
2099 2172 4.855715 TGGAGCCGAGATTATTCAGTAG 57.144 45.455 0.00 0.00 0.00 2.57
2101 2174 4.696479 ATTGGAGCCGAGATTATTCAGT 57.304 40.909 0.00 0.00 0.00 3.41
2102 2175 4.320057 GCAATTGGAGCCGAGATTATTCAG 60.320 45.833 7.72 0.00 0.00 3.02
2104 2177 3.057946 GGCAATTGGAGCCGAGATTATTC 60.058 47.826 7.72 0.00 43.15 1.75
2105 2178 2.887152 GGCAATTGGAGCCGAGATTATT 59.113 45.455 7.72 0.00 43.15 1.40
2106 2179 2.508526 GGCAATTGGAGCCGAGATTAT 58.491 47.619 7.72 0.00 43.15 1.28
2107 2180 1.967319 GGCAATTGGAGCCGAGATTA 58.033 50.000 7.72 0.00 43.15 1.75
2108 2181 2.799176 GGCAATTGGAGCCGAGATT 58.201 52.632 7.72 0.00 43.15 2.40
2109 2182 4.567318 GGCAATTGGAGCCGAGAT 57.433 55.556 7.72 0.00 43.15 2.75
2115 2188 2.997986 CAAAGTTCATGGCAATTGGAGC 59.002 45.455 7.72 0.00 0.00 4.70
2116 2189 4.524316 TCAAAGTTCATGGCAATTGGAG 57.476 40.909 7.72 0.00 0.00 3.86
2117 2190 4.952071 TTCAAAGTTCATGGCAATTGGA 57.048 36.364 7.72 0.00 0.00 3.53
2143 2969 5.643379 TTGGTAATCCTTGAATTGTCAGC 57.357 39.130 0.00 0.00 34.49 4.26
2157 2983 7.988028 AGTATAAAGGAGTCAAGCTTGGTAATC 59.012 37.037 25.73 15.65 0.00 1.75
2252 3078 3.259123 AGCAGCACATATCCGATGTATCA 59.741 43.478 0.00 0.00 0.00 2.15
2265 3091 1.608590 GTTACACACCAAGCAGCACAT 59.391 47.619 0.00 0.00 0.00 3.21
2399 3225 3.259876 TCACATACTACGAAGCAAAGGGT 59.740 43.478 0.00 0.00 0.00 4.34
2494 3320 8.989131 TGTACTAGACCTGGAAGCTAAATATTT 58.011 33.333 5.89 5.89 0.00 1.40
2925 3756 4.819105 TGATAGAGGACCAACACGAAAT 57.181 40.909 0.00 0.00 0.00 2.17
2929 3760 2.609459 GCAATGATAGAGGACCAACACG 59.391 50.000 0.00 0.00 0.00 4.49
2995 3826 6.894339 TCTAAAACTGAAAATGGAGAACCC 57.106 37.500 0.00 0.00 34.81 4.11
3047 3878 9.176181 AGCTTAACACATTTAATTGTTTACACG 57.824 29.630 0.25 0.00 37.19 4.49
3266 4125 4.201990 GCTATTCTCCCAGTTCATGCAAAG 60.202 45.833 0.00 0.00 0.00 2.77
3346 4205 5.915175 ACGAATCCTATGACCTTTTCTACC 58.085 41.667 0.00 0.00 0.00 3.18
3362 4221 4.213482 GGACAATGGCTTACATACGAATCC 59.787 45.833 0.00 0.00 39.40 3.01
3396 4666 9.195411 GCAAGAATTTGAATTGACAATGACTTA 57.805 29.630 0.34 0.00 36.36 2.24
3423 4693 5.519808 TGGATAGTGTCACCTCTAACATCT 58.480 41.667 0.00 0.00 0.00 2.90
3439 4709 4.464951 TGACAACGGTAGAACATGGATAGT 59.535 41.667 0.00 0.00 0.00 2.12
3440 4710 5.006153 TGACAACGGTAGAACATGGATAG 57.994 43.478 0.00 0.00 0.00 2.08
3585 4855 6.552350 AGCATGTTCATCCAAATAGGCTAAAT 59.448 34.615 0.00 0.00 35.96 1.40
3601 4871 7.686438 ATACACAAATAAGTCAGCATGTTCA 57.314 32.000 0.00 0.00 37.40 3.18
3605 4875 6.558009 AGCAATACACAAATAAGTCAGCATG 58.442 36.000 0.00 0.00 37.54 4.06
3744 5018 4.570369 TGCATCAACATACACATAAGTCGG 59.430 41.667 0.00 0.00 0.00 4.79
3818 5092 3.749665 TGGCCTGCCATAAATATTTGC 57.250 42.857 6.80 6.51 41.89 3.68
3835 5109 8.937634 ATCTGTCATTTTATCTCATTTTTGGC 57.062 30.769 0.00 0.00 0.00 4.52
3897 5172 5.804639 AGCCTATATCGCAATGGTAAATCA 58.195 37.500 0.00 0.00 0.00 2.57
3910 5185 6.677781 TTGTTCTGGAAAAAGCCTATATCG 57.322 37.500 0.00 0.00 0.00 2.92
3950 5227 3.895025 GCGTGATGTGCCATCACT 58.105 55.556 29.43 0.00 44.50 3.41
3967 5247 7.774134 TGGTTCATAATTGTTCATGAGATTGG 58.226 34.615 0.00 0.00 32.96 3.16
3968 5248 9.459640 GATGGTTCATAATTGTTCATGAGATTG 57.540 33.333 0.00 0.00 32.96 2.67
4139 5419 0.035056 AAATCCAAGGAGGCTCACGG 60.035 55.000 17.69 12.87 37.29 4.94
4140 5420 1.826385 AAAATCCAAGGAGGCTCACG 58.174 50.000 17.69 3.42 37.29 4.35
4145 5425 5.185454 CCCATTTTTAAAATCCAAGGAGGC 58.815 41.667 0.55 0.00 37.29 4.70
4167 5447 7.712797 TGTTCTCTTTTTCTTCCAATGTTACC 58.287 34.615 0.00 0.00 0.00 2.85
4168 5448 9.237846 CTTGTTCTCTTTTTCTTCCAATGTTAC 57.762 33.333 0.00 0.00 0.00 2.50
4189 5469 7.227512 CACTTGTATTCCTCTCAAACTCTTGTT 59.772 37.037 0.00 0.00 38.16 2.83
4199 5479 4.346709 TGTTCCACACTTGTATTCCTCTCA 59.653 41.667 0.00 0.00 0.00 3.27
4209 5489 2.880890 GCAATCTCTGTTCCACACTTGT 59.119 45.455 0.00 0.00 0.00 3.16
4258 5539 7.822658 TGGGTGCTTGTTGTATTTTATCTTAC 58.177 34.615 0.00 0.00 0.00 2.34
4260 5541 6.909550 TGGGTGCTTGTTGTATTTTATCTT 57.090 33.333 0.00 0.00 0.00 2.40
4264 5545 6.656632 TTCATGGGTGCTTGTTGTATTTTA 57.343 33.333 0.00 0.00 0.00 1.52
4280 5561 1.610522 GGATCGAGGCATTTTCATGGG 59.389 52.381 0.00 0.00 0.00 4.00
4281 5562 2.579873 AGGATCGAGGCATTTTCATGG 58.420 47.619 0.00 0.00 0.00 3.66
4283 5564 4.422073 TGTAGGATCGAGGCATTTTCAT 57.578 40.909 0.00 0.00 0.00 2.57
4286 5567 5.808366 TCTATGTAGGATCGAGGCATTTT 57.192 39.130 0.00 0.00 0.00 1.82
4290 5571 3.939592 CGTATCTATGTAGGATCGAGGCA 59.060 47.826 0.00 0.00 0.00 4.75
4291 5572 3.940221 ACGTATCTATGTAGGATCGAGGC 59.060 47.826 0.00 0.00 0.00 4.70
4292 5573 8.883954 TTATACGTATCTATGTAGGATCGAGG 57.116 38.462 12.24 0.00 31.81 4.63
4312 5593 8.557029 CGTAGGAATCCAACCAATTTCTTATAC 58.443 37.037 0.61 0.00 0.00 1.47
4641 5922 4.416516 AGCCTTTTAGCAATAAGGTGGTT 58.583 39.130 11.04 0.00 42.37 3.67
4642 5923 4.047627 AGCCTTTTAGCAATAAGGTGGT 57.952 40.909 11.04 0.00 42.37 4.16
4643 5924 5.170748 CAAAGCCTTTTAGCAATAAGGTGG 58.829 41.667 11.04 0.00 42.37 4.61
4644 5925 5.783111 ACAAAGCCTTTTAGCAATAAGGTG 58.217 37.500 11.04 5.80 42.37 4.00
4645 5926 6.183360 ACAACAAAGCCTTTTAGCAATAAGGT 60.183 34.615 11.04 0.00 42.37 3.50
4646 5927 6.223120 ACAACAAAGCCTTTTAGCAATAAGG 58.777 36.000 6.43 6.43 43.08 2.69
4647 5928 7.224557 ACAACAACAAAGCCTTTTAGCAATAAG 59.775 33.333 0.00 0.00 34.23 1.73
4648 5929 7.044798 ACAACAACAAAGCCTTTTAGCAATAA 58.955 30.769 0.00 0.00 34.23 1.40
4649 5930 6.578023 ACAACAACAAAGCCTTTTAGCAATA 58.422 32.000 0.00 0.00 34.23 1.90
4657 5985 6.872920 TCATAAGAACAACAACAAAGCCTTT 58.127 32.000 0.00 0.00 0.00 3.11
4707 6035 9.327628 TGCATGTAACAAACAAGTTAGTACTTA 57.672 29.630 0.00 0.00 42.67 2.24
4747 6075 2.703798 GCATCCTTGGTGCGTGCAT 61.704 57.895 0.00 0.00 35.93 3.96
4825 6153 4.182433 TGCGTGTGGGTGCCTTCA 62.182 61.111 0.00 0.00 0.00 3.02
4987 6315 4.864916 TCAAAATAATCTCTGCGAGTGC 57.135 40.909 5.66 0.00 43.20 4.40
5004 6332 9.747898 ATGTCTAGGGTTAATGTACAAATCAAA 57.252 29.630 0.00 0.00 0.00 2.69
5057 6385 5.509332 CGCATCTATCTAGCTATGGCATCAT 60.509 44.000 1.65 0.00 41.70 2.45
5104 6433 6.849588 AAGAAAACATCAACAAAGGAATGC 57.150 33.333 0.00 0.00 0.00 3.56
5192 6525 1.555075 CACTAGTGCACACATACCCCT 59.445 52.381 21.04 0.00 0.00 4.79
5226 6559 9.958180 TTTTTACTAGATCTGAAATGGATGACA 57.042 29.630 5.18 0.00 0.00 3.58
5253 6586 6.709397 GCATCGTGGATATGATATGGATGATT 59.291 38.462 12.61 0.00 33.63 2.57
5343 6676 9.507329 GGATCAATGCTAAATAGGAATACAAGA 57.493 33.333 0.00 0.00 0.00 3.02
5344 6677 9.288576 TGGATCAATGCTAAATAGGAATACAAG 57.711 33.333 0.00 0.00 0.00 3.16
5430 6763 3.272581 CTCATGTGGTCATATGTGCACA 58.727 45.455 24.08 24.08 34.37 4.57
5431 6764 2.615447 CCTCATGTGGTCATATGTGCAC 59.385 50.000 10.75 10.75 32.61 4.57
5476 6817 8.825745 CACCAAGTAAAATTAATGCAGTTTTGT 58.174 29.630 0.00 0.00 0.00 2.83
5477 6818 8.825745 ACACCAAGTAAAATTAATGCAGTTTTG 58.174 29.630 0.00 0.00 0.00 2.44
5541 6882 6.176896 TCAACATCAATATCAAACCTTCCGA 58.823 36.000 0.00 0.00 0.00 4.55
5546 6887 6.721208 AGGTGTTCAACATCAATATCAAACCT 59.279 34.615 2.99 0.00 29.79 3.50
5570 7136 7.653713 CCACACTATATTAAGCCTCTGTTACAG 59.346 40.741 5.94 5.94 0.00 2.74
5663 7261 3.730028 CTGGCCAACCACCACACCA 62.730 63.158 7.01 0.00 42.67 4.17
5729 7331 6.726490 TTCTCCCCATGTACTAGTCAATAC 57.274 41.667 0.00 0.00 0.00 1.89
5744 7346 0.991920 CCCTTACTTGCTTCTCCCCA 59.008 55.000 0.00 0.00 0.00 4.96
5786 7388 7.993183 TGAGACCTGGTTTGATTATAGAATTCC 59.007 37.037 0.00 0.00 0.00 3.01
5790 7392 8.328758 ACAATGAGACCTGGTTTGATTATAGAA 58.671 33.333 14.23 0.00 0.00 2.10
5806 7408 9.522804 CACTATAGAAAAGTAGACAATGAGACC 57.477 37.037 6.78 0.00 0.00 3.85
5836 7439 9.732130 GGATTTATGCTAGGAATTTAGTGATCT 57.268 33.333 0.00 0.00 0.00 2.75
5877 7480 5.467063 GCTAATACCTAGTCATGGCTTCAAC 59.533 44.000 4.49 0.00 0.00 3.18
5881 7484 4.202367 GGTGCTAATACCTAGTCATGGCTT 60.202 45.833 4.49 0.00 37.74 4.35
5898 7501 3.628989 CATCCCGTGGAGGTGCTA 58.371 61.111 0.00 0.00 38.74 3.49
5909 7512 0.969894 GGTCCACTATCTCCATCCCG 59.030 60.000 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.