Multiple sequence alignment - TraesCS5D01G120700

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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 TraesCS5D01G120700 chr5D 100.000 6765 0 0 1 6765 171305239 171312003 0.000000e+00 12493.0
1 TraesCS5D01G120700 chr5D 84.932 219 31 2 1 219 285022392 285022608 3.180000e-53 220.0
2 TraesCS5D01G120700 chr5D 97.619 84 2 0 1774 1857 171306904 171306987 1.970000e-30 145.0
3 TraesCS5D01G120700 chr5D 97.619 84 2 0 1666 1749 171307012 171307095 1.970000e-30 145.0
4 TraesCS5D01G120700 chr5A 96.523 4631 95 16 1563 6151 192426758 192422152 0.000000e+00 7600.0
5 TraesCS5D01G120700 chr5A 90.858 711 29 15 568 1273 192429431 192428752 0.000000e+00 920.0
6 TraesCS5D01G120700 chr5A 91.528 661 25 11 568 1226 192428245 192427614 0.000000e+00 881.0
7 TraesCS5D01G120700 chr5A 91.209 455 28 4 6313 6764 192422153 192421708 5.800000e-170 608.0
8 TraesCS5D01G120700 chr5A 85.606 396 30 15 206 576 192543242 192542849 2.290000e-104 390.0
9 TraesCS5D01G120700 chr5A 92.273 220 17 0 1 220 192543491 192543272 5.090000e-81 313.0
10 TraesCS5D01G120700 chr5A 96.875 160 2 1 1392 1551 192427105 192426949 1.450000e-66 265.0
11 TraesCS5D01G120700 chr5A 86.957 230 28 2 14 243 293861787 293862014 2.420000e-64 257.0
12 TraesCS5D01G120700 chr5A 97.391 115 3 0 1281 1395 192427350 192427236 5.350000e-46 196.0
13 TraesCS5D01G120700 chr5A 97.059 102 3 0 1666 1767 192426547 192426446 9.020000e-39 172.0
14 TraesCS5D01G120700 chr5A 97.701 87 2 0 1774 1860 192426655 192426569 4.230000e-32 150.0
15 TraesCS5D01G120700 chr5B 95.937 2363 60 9 1538 3875 187857109 187859460 0.000000e+00 3799.0
16 TraesCS5D01G120700 chr5B 95.072 1806 60 15 3876 5659 187859602 187861400 0.000000e+00 2815.0
17 TraesCS5D01G120700 chr5B 85.320 1015 70 29 226 1204 187855265 187856236 0.000000e+00 976.0
18 TraesCS5D01G120700 chr5B 91.781 584 29 11 5974 6552 187861753 187862322 0.000000e+00 795.0
19 TraesCS5D01G120700 chr5B 96.667 270 9 0 1272 1541 187856810 187857079 3.720000e-122 449.0
20 TraesCS5D01G120700 chr5B 96.596 235 4 2 5745 5979 187861445 187861675 2.960000e-103 387.0
21 TraesCS5D01G120700 chr5B 97.059 102 3 0 1666 1767 187857345 187857446 9.020000e-39 172.0
22 TraesCS5D01G120700 chr5B 97.619 84 2 0 1774 1857 187857237 187857320 1.970000e-30 145.0
23 TraesCS5D01G120700 chr5B 81.921 177 22 9 6372 6541 325963935 325963762 2.540000e-29 141.0
24 TraesCS5D01G120700 chr3A 87.915 331 27 4 6372 6699 156118322 156118002 1.780000e-100 377.0
25 TraesCS5D01G120700 chr3A 87.126 334 30 4 6369 6699 377235542 377235865 3.860000e-97 366.0
26 TraesCS5D01G120700 chr1B 87.349 332 26 6 6374 6699 612017197 612016876 3.860000e-97 366.0
27 TraesCS5D01G120700 chr4B 86.269 335 30 5 6371 6699 351513180 351512856 3.880000e-92 350.0
28 TraesCS5D01G120700 chr2D 85.417 336 34 8 6369 6699 109550373 109550698 1.090000e-87 335.0
29 TraesCS5D01G120700 chr2D 90.909 220 19 1 1 220 513019528 513019746 1.850000e-75 294.0
30 TraesCS5D01G120700 chr6A 90.455 220 20 1 1 220 65794361 65794143 8.580000e-74 289.0
31 TraesCS5D01G120700 chr6A 84.167 240 33 5 1 239 450110272 450110037 1.900000e-55 228.0
32 TraesCS5D01G120700 chr2B 91.257 183 15 1 1 183 603649978 603650159 1.460000e-61 248.0
33 TraesCS5D01G120700 chr2B 82.036 167 27 3 6076 6239 59018911 59018745 9.150000e-29 139.0
34 TraesCS5D01G120700 chr6B 84.774 243 33 4 1 243 513133922 513134160 2.440000e-59 241.0
35 TraesCS5D01G120700 chr7B 87.019 208 24 3 14 219 426523108 426523314 1.470000e-56 231.0
36 TraesCS5D01G120700 chr7B 82.738 168 24 4 6076 6239 50358906 50358740 1.970000e-30 145.0
37 TraesCS5D01G120700 chr6D 89.831 118 11 1 197 314 389640655 389640771 4.230000e-32 150.0
38 TraesCS5D01G120700 chr3D 82.927 164 25 3 6076 6236 43646805 43646968 1.970000e-30 145.0
39 TraesCS5D01G120700 chr3D 97.222 36 0 1 206 241 581579534 581579500 7.330000e-05 60.2
40 TraesCS5D01G120700 chr3B 81.868 182 20 12 6369 6541 178481569 178481746 2.540000e-29 141.0
41 TraesCS5D01G120700 chr3B 81.176 170 29 3 6076 6242 661158025 661157856 4.260000e-27 134.0
42 TraesCS5D01G120700 chr4D 82.317 164 26 3 6076 6236 69497308 69497471 9.150000e-29 139.0
43 TraesCS5D01G120700 chrUn 82.099 162 24 4 6076 6233 85964520 85964680 4.260000e-27 134.0
44 TraesCS5D01G120700 chrUn 82.099 162 24 4 6076 6233 312297649 312297809 4.260000e-27 134.0
45 TraesCS5D01G120700 chr1A 80.791 177 24 9 6372 6541 442539447 442539274 5.510000e-26 130.0
46 TraesCS5D01G120700 chr7D 85.470 117 15 2 6122 6236 601495156 601495272 3.310000e-23 121.0


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 TraesCS5D01G120700 chr5D 171305239 171312003 6764 False 12493.00 12493 100.000000 1 6765 1 chr5D.!!$F1 6764
1 TraesCS5D01G120700 chr5A 192421708 192429431 7723 True 1349.00 7600 94.893000 568 6764 8 chr5A.!!$R1 6196
2 TraesCS5D01G120700 chr5A 192542849 192543491 642 True 351.50 390 88.939500 1 576 2 chr5A.!!$R2 575
3 TraesCS5D01G120700 chr5B 187855265 187862322 7057 False 1192.25 3799 94.506375 226 6552 8 chr5B.!!$F1 6326

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
926 1559 0.899720 AATTCGACTAGGCGACCCAA 59.100 50.000 23.03 6.33 40.42 4.12 F
1257 1890 0.107848 CGGCCATTCTTCGGGTTAGT 60.108 55.000 2.24 0.00 0.00 2.24 F
1270 1903 0.822811 GGTTAGTTCGACCCTCCTCC 59.177 60.000 0.00 0.00 0.00 4.30 F
2069 3577 0.875059 AGAAAAGTAGCAAGCACGCC 59.125 50.000 0.00 0.00 0.00 5.68 F
2686 4196 2.089201 CATGCAGTGATGCTTTCCTGA 58.911 47.619 0.00 0.00 35.49 3.86 F
3189 4699 3.211865 TCTTGATTCCAGATGCTCATGC 58.788 45.455 0.00 0.00 40.20 4.06 F
4468 6135 0.105760 TGGCCCAACATTGTCCAGTT 60.106 50.000 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 3382 0.616891 AGGGGTTCCGTGTTATGGAC 59.383 55.000 0.00 0.00 31.86 4.02 R
2069 3577 2.436646 AACCCAGCTCGCATTCCG 60.437 61.111 0.00 0.00 38.61 4.30 R
3189 4699 2.546789 GAGGTTGGTTAAGGTGAACACG 59.453 50.000 0.00 0.00 0.00 4.49 R
3712 5224 3.247648 CGAACCGCAATCCTTTCGAATAT 59.752 43.478 0.00 0.00 42.72 1.28 R
4208 5872 4.985538 TGAGTCCTAATCTTGCCAAGTTT 58.014 39.130 4.04 5.19 0.00 2.66 R
4939 6606 3.926527 CCTTCTCGTCGAACAATTCATCA 59.073 43.478 0.00 0.00 0.00 3.07 R
6160 7921 1.338107 TCACACTCAACACTCGGGAT 58.662 50.000 0.00 0.00 0.00 3.85 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
32 33 5.173774 TGAAAAATGTTGAGACTGAGCAC 57.826 39.130 0.00 0.00 0.00 4.40
61 62 1.323235 GGCAACGTTTGAACAGTTTGC 59.677 47.619 0.00 12.73 0.00 3.68
142 143 4.637534 GGTTGAGCACATGTAGAATCACAT 59.362 41.667 0.00 0.00 39.76 3.21
145 146 5.490159 TGAGCACATGTAGAATCACATTGA 58.510 37.500 0.00 0.00 37.02 2.57
169 170 4.767578 ACCAGTAGATGCATCAGTTCAT 57.232 40.909 27.81 9.18 0.00 2.57
196 197 9.884636 TTTCTTTCCATCTATCGAAGACAATTA 57.115 29.630 0.00 0.00 42.51 1.40
204 205 6.213677 TCTATCGAAGACAATTACGATTGGG 58.786 40.000 0.00 0.00 45.56 4.12
315 360 3.370231 GGGCCAAATGCGTCCGTT 61.370 61.111 4.39 0.00 42.61 4.44
392 456 2.304751 ACGTCCGTTTGAAGTCTTGT 57.695 45.000 0.00 0.00 28.87 3.16
422 499 2.536365 ACATACGTGAATAGTGTGCGG 58.464 47.619 0.00 0.00 34.67 5.69
451 529 5.036117 TCTTCTGCAACCCCTTGTATATC 57.964 43.478 0.00 0.00 0.00 1.63
454 532 3.962063 TCTGCAACCCCTTGTATATCGTA 59.038 43.478 0.00 0.00 0.00 3.43
502 580 7.589587 TGACAATTTACAAGAACGCATAAACAG 59.410 33.333 0.00 0.00 0.00 3.16
503 581 7.644490 ACAATTTACAAGAACGCATAAACAGA 58.356 30.769 0.00 0.00 0.00 3.41
531 609 4.475944 GCGTTATGCAAAAACTGTCATCT 58.524 39.130 12.01 0.00 45.45 2.90
532 610 5.627172 GCGTTATGCAAAAACTGTCATCTA 58.373 37.500 12.01 0.00 45.45 1.98
573 654 7.757173 GGAAGCTTCAAACTCCATAATTTCTTC 59.243 37.037 27.02 0.00 0.00 2.87
608 1228 3.802948 AAGGATCCACTATGACGTGAC 57.197 47.619 15.82 0.00 37.06 3.67
633 1253 8.623030 ACGAGTTTAAACTTGCCTGTAAATAAA 58.377 29.630 28.30 0.00 42.94 1.40
639 1259 9.752961 TTAAACTTGCCTGTAAATAAAAGTTCC 57.247 29.630 0.00 0.00 36.98 3.62
700 1320 4.714308 ACACCATTCTTTTTCCCACAAGAA 59.286 37.500 0.00 0.00 41.97 2.52
701 1321 5.188751 ACACCATTCTTTTTCCCACAAGAAA 59.811 36.000 0.00 0.00 41.28 2.52
702 1322 6.112058 CACCATTCTTTTTCCCACAAGAAAA 58.888 36.000 0.00 0.00 41.28 2.29
703 1323 6.258507 CACCATTCTTTTTCCCACAAGAAAAG 59.741 38.462 0.00 0.00 44.27 2.27
704 1324 6.156083 ACCATTCTTTTTCCCACAAGAAAAGA 59.844 34.615 6.44 6.44 44.27 2.52
779 1408 1.449601 CCTCCGGGTTGTGATTCGG 60.450 63.158 0.00 0.00 43.42 4.30
841 1473 9.921637 TTTATTGAGAAATACATTCGGCTTTTT 57.078 25.926 0.00 0.00 43.15 1.94
890 1523 3.345508 AGGAAGGGGTTGTAATTCGAC 57.654 47.619 0.00 0.00 0.00 4.20
926 1559 0.899720 AATTCGACTAGGCGACCCAA 59.100 50.000 23.03 6.33 40.42 4.12
1232 1865 4.835891 CCTCCGGCGTACCCCTCT 62.836 72.222 6.01 0.00 0.00 3.69
1233 1866 3.217743 CTCCGGCGTACCCCTCTC 61.218 72.222 6.01 0.00 0.00 3.20
1234 1867 4.828296 TCCGGCGTACCCCTCTCC 62.828 72.222 6.01 0.00 0.00 3.71
1254 1887 2.750237 GCGGCCATTCTTCGGGTT 60.750 61.111 2.24 0.00 0.00 4.11
1255 1888 1.450669 GCGGCCATTCTTCGGGTTA 60.451 57.895 2.24 0.00 0.00 2.85
1256 1889 1.436983 GCGGCCATTCTTCGGGTTAG 61.437 60.000 2.24 0.00 0.00 2.34
1257 1890 0.107848 CGGCCATTCTTCGGGTTAGT 60.108 55.000 2.24 0.00 0.00 2.24
1258 1891 1.677820 CGGCCATTCTTCGGGTTAGTT 60.678 52.381 2.24 0.00 0.00 2.24
1259 1892 2.014857 GGCCATTCTTCGGGTTAGTTC 58.985 52.381 0.00 0.00 0.00 3.01
1260 1893 1.664151 GCCATTCTTCGGGTTAGTTCG 59.336 52.381 0.00 0.00 0.00 3.95
1261 1894 2.675889 GCCATTCTTCGGGTTAGTTCGA 60.676 50.000 0.00 0.00 0.00 3.71
1262 1895 2.928116 CCATTCTTCGGGTTAGTTCGAC 59.072 50.000 0.00 0.00 34.99 4.20
1263 1896 2.730550 TTCTTCGGGTTAGTTCGACC 57.269 50.000 0.00 0.00 34.99 4.79
1270 1903 0.822811 GGTTAGTTCGACCCTCCTCC 59.177 60.000 0.00 0.00 0.00 4.30
1288 2427 5.966684 TCCTCCTTAATCTCCTAACTAGGG 58.033 45.833 2.92 0.00 43.79 3.53
1401 2674 1.072331 CCAGGGATATTAGGTTGCGCT 59.928 52.381 9.73 0.00 0.00 5.92
1653 3138 5.505173 GACCATTGGTCCATTCATGTAAG 57.495 43.478 23.00 0.00 46.19 2.34
1879 3382 4.584029 ATGCTTCGTTACAGTCGAATTG 57.416 40.909 1.48 0.00 44.29 2.32
1911 3414 3.623703 CGGAACCCCTTTATGGTCATGAA 60.624 47.826 0.00 0.00 34.15 2.57
2069 3577 0.875059 AGAAAAGTAGCAAGCACGCC 59.125 50.000 0.00 0.00 0.00 5.68
2354 3862 6.265196 GGTTGCTGAATATGGTATGGAATTGA 59.735 38.462 0.00 0.00 0.00 2.57
2475 3983 6.690957 TGTGATTTTAGTCAAGCTTTTGTTCG 59.309 34.615 0.00 0.00 0.00 3.95
2566 4074 5.866207 ACTAACTTGGAAGTAAAGACCTGG 58.134 41.667 8.19 0.00 38.57 4.45
2686 4196 2.089201 CATGCAGTGATGCTTTCCTGA 58.911 47.619 0.00 0.00 35.49 3.86
3050 4560 4.129757 TCGCTCGCGAGGTACATA 57.870 55.556 35.10 8.93 44.01 2.29
3065 4575 6.693545 CGAGGTACATATTTTCTCTGACACTC 59.306 42.308 0.00 0.00 0.00 3.51
3189 4699 3.211865 TCTTGATTCCAGATGCTCATGC 58.788 45.455 0.00 0.00 40.20 4.06
3332 4842 8.008513 TGATTTCGCTTCCTAGTTAGACTATT 57.991 34.615 0.00 0.00 29.08 1.73
3496 5006 5.418310 TTCAGCTTTGTAGGAAAAACTCG 57.582 39.130 0.00 0.00 0.00 4.18
3712 5224 8.956426 AGATTTCTGTTGTAACAACAAGAAGAA 58.044 29.630 14.78 14.78 38.66 2.52
4072 5736 4.212213 GAATGCTCTATTCAGCTTGCAG 57.788 45.455 0.00 0.00 43.79 4.41
4093 5757 7.441017 TGCAGATTGCTTATTGGTTTAACTTT 58.559 30.769 2.48 0.00 45.31 2.66
4205 5869 5.117592 GCATGCATGTGTAAAGAACTTGTTC 59.882 40.000 26.79 5.44 0.00 3.18
4206 5870 6.441274 CATGCATGTGTAAAGAACTTGTTCT 58.559 36.000 18.91 9.93 0.00 3.01
4208 5872 7.561021 TGCATGTGTAAAGAACTTGTTCTTA 57.439 32.000 23.61 11.93 40.14 2.10
4243 5910 7.351166 AGATTAGGACTCAGAAAGTAGCTAGT 58.649 38.462 0.00 0.00 38.74 2.57
4298 5965 6.385649 TCAACAAAAGTAAAGCCTAAGTGG 57.614 37.500 0.00 0.00 39.35 4.00
4420 6087 1.214062 GAGCACTCCTCACTGTCGG 59.786 63.158 0.00 0.00 40.45 4.79
4468 6135 0.105760 TGGCCCAACATTGTCCAGTT 60.106 50.000 0.00 0.00 0.00 3.16
4530 6197 5.106555 GCTTGCTAGCTACATTTTCTGTCAA 60.107 40.000 17.23 0.00 44.27 3.18
4567 6234 3.402628 AAGTTACGCCATGTTCTGTCT 57.597 42.857 0.00 0.00 0.00 3.41
4801 6468 0.877071 AAGATTTGCCTGCAGTGTCG 59.123 50.000 13.81 0.00 0.00 4.35
4820 6487 5.625311 GTGTCGCTTTTCCTTCTGTAAATTG 59.375 40.000 0.00 0.00 0.00 2.32
4931 6598 7.594758 ACAAATGTTTTATTCGTCAACCTGATG 59.405 33.333 0.00 0.00 34.78 3.07
4939 6606 4.677673 TCGTCAACCTGATGATGATGAT 57.322 40.909 0.00 0.00 39.73 2.45
4943 6610 5.107065 CGTCAACCTGATGATGATGATGATG 60.107 44.000 0.00 0.00 38.37 3.07
4944 6611 5.995897 GTCAACCTGATGATGATGATGATGA 59.004 40.000 0.00 0.00 0.00 2.92
5323 6994 2.029110 TGCAGCCTTTTATGTTGGAAGC 60.029 45.455 0.00 0.00 0.00 3.86
5396 7070 4.913335 ATGGCTTGAAGCACAGATATTG 57.087 40.909 19.89 0.00 44.75 1.90
5470 7144 6.321181 TGTTCTTCTGTCCATTAGTTTGCTTT 59.679 34.615 0.00 0.00 0.00 3.51
5918 7596 2.042520 TTCGTTGCCGTGCTTCACAC 62.043 55.000 0.00 0.00 46.45 3.82
6039 7800 2.031120 CCCTCTTTGTTTGAGCCACAA 58.969 47.619 0.00 0.00 36.65 3.33
6160 7921 4.819630 GGAGGTTGTGAAATGTCAGTAACA 59.180 41.667 12.59 0.00 43.51 2.41
6234 7997 7.377131 GCTGTTTTGACTTGATAAAGTGAGAAC 59.623 37.037 8.39 8.39 33.72 3.01
6242 8005 6.651225 ACTTGATAAAGTGAGAACTGGCTAAC 59.349 38.462 0.00 0.00 0.00 2.34
6250 8013 6.354130 AGTGAGAACTGGCTAACTTGTTTTA 58.646 36.000 0.00 0.00 0.00 1.52
6306 8069 7.385778 TGCACCAACCATTAGTTTTAGATAC 57.614 36.000 0.00 0.00 36.18 2.24
6309 8072 7.012044 GCACCAACCATTAGTTTTAGATACGAT 59.988 37.037 0.00 0.00 36.18 3.73
6310 8073 8.889717 CACCAACCATTAGTTTTAGATACGATT 58.110 33.333 0.00 0.00 36.18 3.34
6311 8074 9.457436 ACCAACCATTAGTTTTAGATACGATTT 57.543 29.630 0.00 0.00 36.18 2.17
6327 8090 9.140286 AGATACGATTTATCATATGTGAAACCG 57.860 33.333 13.74 13.74 38.01 4.44
6416 8180 9.034800 ACCAATTCAACAAGGATATTGTAATGT 57.965 29.630 0.00 0.00 31.50 2.71
6450 8214 6.282930 CAAATTCACTTGTTTGGATGTCCTT 58.717 36.000 0.09 0.00 36.82 3.36
6467 8231 5.776358 TGTCCTTAATTGGCCTATGGAATT 58.224 37.500 3.32 3.57 0.00 2.17
6516 8280 8.627208 ATGTTTGGATGACATACTATGGAATC 57.373 34.615 0.00 3.61 36.04 2.52
6517 8281 7.572814 TGTTTGGATGACATACTATGGAATCA 58.427 34.615 0.00 4.02 32.94 2.57
6518 8282 8.219868 TGTTTGGATGACATACTATGGAATCAT 58.780 33.333 0.00 7.51 37.40 2.45
6583 8349 8.333908 TGAATCAAAACAAAATTTGTGATTCCG 58.666 29.630 28.20 13.53 43.15 4.30
6595 8361 4.844998 TGTGATTCCGATTTTCAGCAAA 57.155 36.364 0.00 0.00 0.00 3.68
6658 8424 9.959721 AAGTAGAAAAACAAATCTATGCCTCTA 57.040 29.630 0.00 0.00 31.29 2.43
6666 8432 7.736447 ACAAATCTATGCCTCTATTTACAGC 57.264 36.000 0.00 0.00 0.00 4.40
6699 8465 3.448686 CACAACCGATGTAGCCTAGAAG 58.551 50.000 0.00 0.00 41.46 2.85
6700 8466 2.431057 ACAACCGATGTAGCCTAGAAGG 59.569 50.000 0.00 0.00 41.63 3.46
6714 8480 3.259625 CCTAGAAGGCTAGAACTATGCCC 59.740 52.174 14.09 3.44 45.71 5.36
6717 8483 6.457351 CTAGAAGGCTAGAACTATGCCCCTT 61.457 48.000 14.09 0.00 45.71 3.95
6744 8510 5.621193 ACCTGTACAAAGCATGAACTACTT 58.379 37.500 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.772233 TCAGTCTCAACATTTTTCATCCTGAA 59.228 34.615 0.00 0.00 34.03 3.02
7 8 5.048504 TGCTCAGTCTCAACATTTTTCATCC 60.049 40.000 0.00 0.00 0.00 3.51
24 25 1.071471 CCGGTTCTTGGTGCTCAGT 59.929 57.895 0.00 0.00 0.00 3.41
32 33 0.593773 CAAACGTTGCCGGTTCTTGG 60.594 55.000 0.00 0.00 40.81 3.61
61 62 1.442769 CACTTCACGATGGAGTTGGG 58.557 55.000 0.00 0.00 0.00 4.12
142 143 4.256110 CTGATGCATCTACTGGTTGTCAA 58.744 43.478 26.32 1.49 0.00 3.18
145 146 3.988976 ACTGATGCATCTACTGGTTGT 57.011 42.857 26.32 9.87 0.00 3.32
196 197 6.153756 GCAAATAGTTTTACAACCCAATCGT 58.846 36.000 0.00 0.00 32.70 3.73
315 360 2.123988 GACCGTTTTGTGGATGCGCA 62.124 55.000 14.96 14.96 0.00 6.09
343 406 2.553466 CCGTTTGGGTTGGACAATAGGA 60.553 50.000 0.00 0.00 30.92 2.94
422 499 1.745653 GGGGTTGCAGAAGATACAAGC 59.254 52.381 0.00 0.00 40.22 4.01
471 549 8.841444 ATGCGTTCTTGTAAATTGTCATATTC 57.159 30.769 0.00 0.00 0.00 1.75
480 558 9.522804 TTTTCTGTTTATGCGTTCTTGTAAATT 57.477 25.926 0.00 0.00 0.00 1.82
502 580 7.114247 TGACAGTTTTTGCATAACGCTATTTTC 59.886 33.333 6.58 0.00 43.06 2.29
503 581 6.920758 TGACAGTTTTTGCATAACGCTATTTT 59.079 30.769 6.58 0.00 43.06 1.82
573 654 3.503748 GGATCCTTTCCGCATCCTATTTG 59.496 47.826 3.84 0.00 34.31 2.32
608 1228 9.453325 TTTTATTTACAGGCAAGTTTAAACTCG 57.547 29.630 20.78 11.63 38.57 4.18
633 1253 1.144093 TGTTCGACAATGGGGGAACTT 59.856 47.619 12.16 0.00 39.50 2.66
639 1259 1.890876 TTCAGTGTTCGACAATGGGG 58.109 50.000 12.94 0.00 43.60 4.96
700 1320 6.926826 ACAAAGAACGGTGTTTTCTTTTCTTT 59.073 30.769 7.70 3.41 46.47 2.52
701 1321 6.452242 ACAAAGAACGGTGTTTTCTTTTCTT 58.548 32.000 7.70 0.00 46.47 2.52
702 1322 6.020971 ACAAAGAACGGTGTTTTCTTTTCT 57.979 33.333 7.70 0.00 46.47 2.52
703 1323 5.859648 TGACAAAGAACGGTGTTTTCTTTTC 59.140 36.000 7.70 9.21 46.47 2.29
704 1324 5.774630 TGACAAAGAACGGTGTTTTCTTTT 58.225 33.333 7.70 2.07 46.47 2.27
706 1326 5.048294 ACTTGACAAAGAACGGTGTTTTCTT 60.048 36.000 0.00 0.00 43.67 2.52
707 1327 4.457949 ACTTGACAAAGAACGGTGTTTTCT 59.542 37.500 0.00 0.00 36.84 2.52
708 1328 4.557301 CACTTGACAAAGAACGGTGTTTTC 59.443 41.667 0.00 0.00 36.84 2.29
788 1417 8.831715 AAAGCCGAATGTTTCTCAAAAATAAT 57.168 26.923 0.00 0.00 0.00 1.28
791 1420 7.552458 AAAAAGCCGAATGTTTCTCAAAAAT 57.448 28.000 0.00 0.00 0.00 1.82
842 1474 5.975693 AAAGCCGAATGTGATCCTAAAAA 57.024 34.783 0.00 0.00 0.00 1.94
843 1475 5.710099 AGAAAAGCCGAATGTGATCCTAAAA 59.290 36.000 0.00 0.00 0.00 1.52
844 1476 5.253330 AGAAAAGCCGAATGTGATCCTAAA 58.747 37.500 0.00 0.00 0.00 1.85
845 1477 4.843728 AGAAAAGCCGAATGTGATCCTAA 58.156 39.130 0.00 0.00 0.00 2.69
846 1478 4.487714 AGAAAAGCCGAATGTGATCCTA 57.512 40.909 0.00 0.00 0.00 2.94
847 1479 3.356529 AGAAAAGCCGAATGTGATCCT 57.643 42.857 0.00 0.00 0.00 3.24
848 1480 5.449177 CCTTAAGAAAAGCCGAATGTGATCC 60.449 44.000 3.36 0.00 0.00 3.36
849 1481 5.354234 TCCTTAAGAAAAGCCGAATGTGATC 59.646 40.000 3.36 0.00 0.00 2.92
850 1482 5.253330 TCCTTAAGAAAAGCCGAATGTGAT 58.747 37.500 3.36 0.00 0.00 3.06
851 1483 4.647611 TCCTTAAGAAAAGCCGAATGTGA 58.352 39.130 3.36 0.00 0.00 3.58
852 1484 5.371115 TTCCTTAAGAAAAGCCGAATGTG 57.629 39.130 3.36 0.00 0.00 3.21
853 1485 4.459337 CCTTCCTTAAGAAAAGCCGAATGT 59.541 41.667 3.36 0.00 34.37 2.71
854 1486 4.142381 CCCTTCCTTAAGAAAAGCCGAATG 60.142 45.833 3.36 0.00 34.37 2.67
855 1487 4.017126 CCCTTCCTTAAGAAAAGCCGAAT 58.983 43.478 3.36 0.00 34.37 3.34
856 1488 3.418047 CCCTTCCTTAAGAAAAGCCGAA 58.582 45.455 3.36 0.00 34.37 4.30
857 1489 2.290705 CCCCTTCCTTAAGAAAAGCCGA 60.291 50.000 3.36 0.00 34.37 5.54
858 1490 2.092323 CCCCTTCCTTAAGAAAAGCCG 58.908 52.381 3.36 1.15 34.37 5.52
859 1491 3.170991 ACCCCTTCCTTAAGAAAAGCC 57.829 47.619 3.36 0.00 34.37 4.35
860 1492 3.895656 ACAACCCCTTCCTTAAGAAAAGC 59.104 43.478 3.36 0.00 34.37 3.51
890 1523 3.356658 CGAATTACAAAACACTTTCCGCG 59.643 43.478 0.00 0.00 0.00 6.46
926 1559 4.895297 CCTGTTTTATATTGGGCAGGTGAT 59.105 41.667 0.00 0.00 38.80 3.06
1237 1870 1.436983 CTAACCCGAAGAATGGCCGC 61.437 60.000 0.00 0.00 0.00 6.53
1238 1871 0.107848 ACTAACCCGAAGAATGGCCG 60.108 55.000 0.00 0.00 0.00 6.13
1239 1872 2.014857 GAACTAACCCGAAGAATGGCC 58.985 52.381 0.00 0.00 0.00 5.36
1240 1873 1.664151 CGAACTAACCCGAAGAATGGC 59.336 52.381 0.00 0.00 0.00 4.40
1241 1874 2.928116 GTCGAACTAACCCGAAGAATGG 59.072 50.000 0.00 0.00 36.50 3.16
1242 1875 2.928116 GGTCGAACTAACCCGAAGAATG 59.072 50.000 0.00 0.00 36.50 2.67
1243 1876 2.093816 GGGTCGAACTAACCCGAAGAAT 60.094 50.000 0.00 0.00 46.66 2.40
1244 1877 1.273327 GGGTCGAACTAACCCGAAGAA 59.727 52.381 0.00 0.00 46.66 2.52
1245 1878 0.890683 GGGTCGAACTAACCCGAAGA 59.109 55.000 0.00 0.00 46.66 2.87
1246 1879 3.430779 GGGTCGAACTAACCCGAAG 57.569 57.895 0.00 0.00 46.66 3.79
1251 1884 0.822811 GGAGGAGGGTCGAACTAACC 59.177 60.000 0.00 1.52 35.97 2.85
1252 1885 1.849977 AGGAGGAGGGTCGAACTAAC 58.150 55.000 0.00 0.00 0.00 2.34
1253 1886 2.617840 AAGGAGGAGGGTCGAACTAA 57.382 50.000 0.00 0.00 0.00 2.24
1254 1887 3.744940 TTAAGGAGGAGGGTCGAACTA 57.255 47.619 0.00 0.00 0.00 2.24
1255 1888 2.617840 TTAAGGAGGAGGGTCGAACT 57.382 50.000 0.00 0.00 0.00 3.01
1256 1889 3.032459 AGATTAAGGAGGAGGGTCGAAC 58.968 50.000 0.00 0.00 0.00 3.95
1257 1890 3.297736 GAGATTAAGGAGGAGGGTCGAA 58.702 50.000 0.00 0.00 0.00 3.71
1258 1891 2.424523 GGAGATTAAGGAGGAGGGTCGA 60.425 54.545 0.00 0.00 0.00 4.20
1259 1892 1.964933 GGAGATTAAGGAGGAGGGTCG 59.035 57.143 0.00 0.00 0.00 4.79
1260 1893 3.338110 AGGAGATTAAGGAGGAGGGTC 57.662 52.381 0.00 0.00 0.00 4.46
1261 1894 4.235636 AGTTAGGAGATTAAGGAGGAGGGT 59.764 45.833 0.00 0.00 0.00 4.34
1262 1895 4.821940 AGTTAGGAGATTAAGGAGGAGGG 58.178 47.826 0.00 0.00 0.00 4.30
1263 1896 6.014012 CCTAGTTAGGAGATTAAGGAGGAGG 58.986 48.000 0.00 0.00 46.63 4.30
1264 1897 6.014012 CCCTAGTTAGGAGATTAAGGAGGAG 58.986 48.000 6.77 0.00 46.63 3.69
1265 1898 5.162859 CCCCTAGTTAGGAGATTAAGGAGGA 60.163 48.000 6.77 0.00 46.63 3.71
1266 1899 5.088026 CCCCTAGTTAGGAGATTAAGGAGG 58.912 50.000 6.77 0.00 46.63 4.30
1267 1900 4.528987 GCCCCTAGTTAGGAGATTAAGGAG 59.471 50.000 6.77 0.00 46.63 3.69
1268 1901 4.490706 GCCCCTAGTTAGGAGATTAAGGA 58.509 47.826 6.77 0.00 46.63 3.36
1269 1902 3.258622 CGCCCCTAGTTAGGAGATTAAGG 59.741 52.174 6.77 0.00 46.63 2.69
1270 1903 3.896272 ACGCCCCTAGTTAGGAGATTAAG 59.104 47.826 6.77 0.00 46.63 1.85
1288 2427 5.396484 GGAGTAGGAAATAACAAAAACGCC 58.604 41.667 0.00 0.00 0.00 5.68
1844 3329 3.181497 ACGAAGCATTATGATGTTGCACC 60.181 43.478 0.00 0.00 38.84 5.01
1879 3382 0.616891 AGGGGTTCCGTGTTATGGAC 59.383 55.000 0.00 0.00 31.86 4.02
1911 3414 7.006509 CCCCTCATCCAATTTACATCTTACAT 58.993 38.462 0.00 0.00 0.00 2.29
2069 3577 2.436646 AACCCAGCTCGCATTCCG 60.437 61.111 0.00 0.00 38.61 4.30
2573 4081 5.738619 TCACATAAGGCAGTGAAGAGTTA 57.261 39.130 0.00 0.00 41.42 2.24
2686 4196 5.388654 ACAGTGAATCCTGGAAAACTGAAT 58.611 37.500 28.80 14.46 38.66 2.57
2794 4304 9.573166 TTTATCGGTAATTGGAGATCATGAATT 57.427 29.630 0.00 0.00 0.00 2.17
3050 4560 7.768807 ACTGTACTAGAGTGTCAGAGAAAAT 57.231 36.000 17.45 0.00 36.22 1.82
3065 4575 4.790123 GCAGGAATCACGCTACTGTACTAG 60.790 50.000 0.00 0.00 0.00 2.57
3158 4668 4.711399 TCTGGAATCAAGATACTGGCATG 58.289 43.478 0.00 0.00 0.00 4.06
3162 4672 4.970711 AGCATCTGGAATCAAGATACTGG 58.029 43.478 0.00 0.00 0.00 4.00
3189 4699 2.546789 GAGGTTGGTTAAGGTGAACACG 59.453 50.000 0.00 0.00 0.00 4.49
3287 4797 7.470289 AATCAACAAGTCAAGTATAGCGATC 57.530 36.000 0.00 0.00 0.00 3.69
3496 5006 4.248058 CCCAAATGGTTTCAGCTGATTTC 58.752 43.478 19.04 10.67 0.00 2.17
3712 5224 3.247648 CGAACCGCAATCCTTTCGAATAT 59.752 43.478 0.00 0.00 42.72 1.28
4072 5736 8.601845 ACCAAAAGTTAAACCAATAAGCAATC 57.398 30.769 0.00 0.00 0.00 2.67
4205 5869 6.655003 TGAGTCCTAATCTTGCCAAGTTTAAG 59.345 38.462 4.04 1.40 0.00 1.85
4206 5870 6.539173 TGAGTCCTAATCTTGCCAAGTTTAA 58.461 36.000 4.04 0.00 0.00 1.52
4208 5872 4.985538 TGAGTCCTAATCTTGCCAAGTTT 58.014 39.130 4.04 5.19 0.00 2.66
4298 5965 7.332182 AGCTCTAATTAGACAAACTGTGTTAGC 59.668 37.037 11.24 8.42 41.96 3.09
4487 6154 7.355778 AGCAAGCGTATCTAAGATAAATTTGC 58.644 34.615 0.00 11.33 37.03 3.68
4530 6197 6.018180 GCGTAACTTATTGGTAAGCTAGCATT 60.018 38.462 18.83 10.75 39.64 3.56
4567 6234 6.288294 ACTAATGTGTTAGACAGAAGCAACA 58.712 36.000 2.47 0.00 39.77 3.33
4683 6350 7.434307 CGATGATTTTGCAGCATCTTTAGAAAT 59.566 33.333 0.00 0.00 37.00 2.17
4801 6468 7.491048 TGAACAACAATTTACAGAAGGAAAAGC 59.509 33.333 0.00 0.00 0.00 3.51
4931 6598 6.069563 CGTCGAACAATTCATCATCATCATC 58.930 40.000 0.00 0.00 0.00 2.92
4939 6606 3.926527 CCTTCTCGTCGAACAATTCATCA 59.073 43.478 0.00 0.00 0.00 3.07
4943 6610 4.985044 TTTCCTTCTCGTCGAACAATTC 57.015 40.909 0.00 0.00 0.00 2.17
4944 6611 5.296035 AGTTTTTCCTTCTCGTCGAACAATT 59.704 36.000 0.00 0.00 0.00 2.32
5201 6869 8.888579 AAGATATCTTTATCACCAACGTAAGG 57.111 34.615 12.37 5.48 38.36 2.69
5298 6967 2.730928 CCAACATAAAAGGCTGCAAACG 59.269 45.455 0.50 0.00 0.00 3.60
5396 7070 9.502145 GGGAAGAAAATTTGAAATGAAACAAAC 57.498 29.630 0.00 0.00 38.50 2.93
5419 7093 9.684702 AAATAGAACCTTGGTATATCTTAGGGA 57.315 33.333 8.88 0.00 0.00 4.20
5470 7144 3.396276 TGGTGGTGTCCTAAATTCCTTCA 59.604 43.478 0.00 0.00 0.00 3.02
5722 7396 2.235898 AGGAGCTCCACTTCATGTTCTC 59.764 50.000 33.90 1.99 38.89 2.87
5918 7596 7.223387 CAGAAAATGTTCCTTTGAGTCCAAAAG 59.777 37.037 0.00 0.00 41.28 2.27
5922 7600 5.200483 ACAGAAAATGTTCCTTTGAGTCCA 58.800 37.500 0.00 0.00 39.96 4.02
5923 7601 5.278512 GGACAGAAAATGTTCCTTTGAGTCC 60.279 44.000 0.00 0.00 44.17 3.85
5924 7602 5.299279 TGGACAGAAAATGTTCCTTTGAGTC 59.701 40.000 0.00 0.00 44.17 3.36
6039 7800 3.009916 AGCCACAGTGATTCTCAGGAATT 59.990 43.478 0.62 0.00 41.68 2.17
6133 7894 3.213506 TGACATTTCACAACCTCCACAG 58.786 45.455 0.00 0.00 0.00 3.66
6160 7921 1.338107 TCACACTCAACACTCGGGAT 58.662 50.000 0.00 0.00 0.00 3.85
6262 8025 3.065233 GCATTTCGTATGCAAGACCATCA 59.935 43.478 16.59 0.00 44.00 3.07
6306 8069 8.294341 AGTACGGTTTCACATATGATAAATCG 57.706 34.615 24.90 24.90 33.85 3.34
6309 8072 9.607988 ATCAAGTACGGTTTCACATATGATAAA 57.392 29.630 10.38 6.44 33.85 1.40
6311 8074 9.687210 GTATCAAGTACGGTTTCACATATGATA 57.313 33.333 10.38 0.00 33.85 2.15
6312 8075 8.589335 GTATCAAGTACGGTTTCACATATGAT 57.411 34.615 10.38 0.00 33.85 2.45
6313 8076 7.997107 GTATCAAGTACGGTTTCACATATGA 57.003 36.000 10.38 0.00 0.00 2.15
6347 8110 6.209192 ACAGACATCCAAACAAAGCATAATGA 59.791 34.615 0.00 0.00 0.00 2.57
6425 8189 4.448732 GGACATCCAAACAAGTGAATTTGC 59.551 41.667 0.00 0.00 34.99 3.68
6450 8214 4.141287 CACCGAATTCCATAGGCCAATTA 58.859 43.478 5.01 0.00 0.00 1.40
6467 8231 3.773418 TTGGTATTGAAACCTCACCGA 57.227 42.857 0.00 0.00 40.44 4.69
6558 8322 8.547069 TCGGAATCACAAATTTTGTTTTGATTC 58.453 29.630 26.62 26.62 43.11 2.52
6559 8323 8.430801 TCGGAATCACAAATTTTGTTTTGATT 57.569 26.923 18.77 18.77 43.23 2.57
6647 8413 3.258372 CCGGCTGTAAATAGAGGCATAGA 59.742 47.826 10.94 0.00 41.40 1.98
6666 8432 3.964875 GTTGTGCACTGCCACCGG 61.965 66.667 19.41 0.00 34.85 5.28
6700 8466 4.021280 GGTACTAAGGGGCATAGTTCTAGC 60.021 50.000 0.00 0.00 35.34 3.42
6701 8467 5.244178 CAGGTACTAAGGGGCATAGTTCTAG 59.756 48.000 0.00 0.00 36.02 2.43
6702 8468 5.145564 CAGGTACTAAGGGGCATAGTTCTA 58.854 45.833 0.00 0.00 36.02 2.10
6703 8469 3.967987 CAGGTACTAAGGGGCATAGTTCT 59.032 47.826 0.00 0.45 36.02 3.01
6704 8470 3.710165 ACAGGTACTAAGGGGCATAGTTC 59.290 47.826 0.00 0.00 36.02 3.01
6705 8471 3.732595 ACAGGTACTAAGGGGCATAGTT 58.267 45.455 0.00 0.00 36.02 2.24
6706 8472 3.416414 ACAGGTACTAAGGGGCATAGT 57.584 47.619 0.00 3.02 36.02 2.12
6714 8480 5.730550 TCATGCTTTGTACAGGTACTAAGG 58.269 41.667 24.58 14.31 43.82 2.69
6717 8483 6.354794 AGTTCATGCTTTGTACAGGTACTA 57.645 37.500 10.62 0.72 36.02 1.82


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

AutoCloner maintained by Alex Coulton.