Multiple sequence alignment - TraesCS3B01G382500

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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 TraesCS3B01G382500 chr3B 100.000 5404 0 0 1 5404 602359569 602364972 0.000000e+00 9980
1 TraesCS3B01G382500 chr3D 91.536 3887 174 72 1 3839 455874992 455878771 0.000000e+00 5212
2 TraesCS3B01G382500 chr3D 93.637 1493 46 10 3960 5404 455879056 455880547 0.000000e+00 2185
3 TraesCS3B01G382500 chr3A 89.351 2836 179 51 1 2768 598559043 598561823 0.000000e+00 3450
4 TraesCS3B01G382500 chr3A 90.972 1595 61 31 3862 5404 598563020 598564583 0.000000e+00 2071
5 TraesCS3B01G382500 chr3A 92.578 768 25 5 2770 3534 598561950 598562688 0.000000e+00 1074
6 TraesCS3B01G382500 chr3A 93.511 262 9 3 3580 3840 598562687 598562941 3.050000e-102 383


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 TraesCS3B01G382500 chr3B 602359569 602364972 5403 False 9980.0 9980 100.0000 1 5404 1 chr3B.!!$F1 5403
1 TraesCS3B01G382500 chr3D 455874992 455880547 5555 False 3698.5 5212 92.5865 1 5404 2 chr3D.!!$F1 5403
2 TraesCS3B01G382500 chr3A 598559043 598564583 5540 False 1744.5 3450 91.6030 1 5404 4 chr3A.!!$F1 5403

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
161 162 1.140589 CTTGAGCTCCGAGATGCGT 59.859 57.895 12.15 0.0 38.67 5.24 F
1514 1563 0.388520 CGCGTTGATCCTGTCAGTCA 60.389 55.000 0.00 0.0 38.29 3.41 F
1579 1628 0.533755 CGTGGAAGGGGATGATGCTC 60.534 60.000 0.00 0.0 0.00 4.26 F
1903 1971 0.767998 GGGGAAATCAGCTAGAGGGG 59.232 60.000 0.00 0.0 0.00 4.79 F
3761 3972 0.250513 AAGTTCTCCCAGCCTTAGCG 59.749 55.000 0.00 0.0 46.67 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 1910 0.486879 TGGCCCAAGGGAAATGAAGT 59.513 50.000 9.92 0.0 37.50 3.01 R
2844 3051 4.439974 CCAACAACAACACAGTGCAATAGT 60.440 41.667 0.00 0.0 0.00 2.12 R
3575 3786 0.036952 CCAACAGGCGACAGATCACT 60.037 55.000 0.00 0.0 0.00 3.41 R
3844 4055 0.317603 CTTTGCGCTGCTGCATATCC 60.318 55.000 16.29 0.0 45.78 2.59 R
4718 5115 0.792031 ATTCGCCGGACGTTTACAAC 59.208 50.000 5.05 0.0 44.19 3.32 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
47 48 2.037527 AGGGACTGGAGGTCGACC 59.962 66.667 27.67 27.67 45.35 4.79
161 162 1.140589 CTTGAGCTCCGAGATGCGT 59.859 57.895 12.15 0.00 38.67 5.24
164 165 2.824489 AGCTCCGAGATGCGTCGA 60.824 61.111 0.00 0.00 42.85 4.20
449 450 2.203788 AAGAGGGACGTGGAGGCA 60.204 61.111 0.00 0.00 0.00 4.75
659 692 4.164087 TGTGTCCACGGCGTTGGT 62.164 61.111 11.19 0.00 37.93 3.67
807 840 7.864379 CAGATTTTTCATCCTTCCATTTATCGG 59.136 37.037 0.00 0.00 0.00 4.18
1473 1522 2.428622 CCGGTTCCTCGGTTGGTT 59.571 61.111 0.00 0.00 44.60 3.67
1474 1523 1.670083 CCGGTTCCTCGGTTGGTTC 60.670 63.158 0.00 0.00 44.60 3.62
1511 1560 2.792290 CGCGCGTTGATCCTGTCAG 61.792 63.158 24.19 0.00 38.29 3.51
1512 1561 1.738099 GCGCGTTGATCCTGTCAGT 60.738 57.895 8.43 0.00 38.29 3.41
1513 1562 1.687494 GCGCGTTGATCCTGTCAGTC 61.687 60.000 8.43 0.00 38.29 3.51
1514 1563 0.388520 CGCGTTGATCCTGTCAGTCA 60.389 55.000 0.00 0.00 38.29 3.41
1520 1569 1.967779 TGATCCTGTCAGTCAAACGGA 59.032 47.619 0.00 0.00 31.80 4.69
1576 1625 2.105477 AGATTCGTGGAAGGGGATGATG 59.895 50.000 0.00 0.00 0.00 3.07
1579 1628 0.533755 CGTGGAAGGGGATGATGCTC 60.534 60.000 0.00 0.00 0.00 4.26
1581 1630 2.050144 GTGGAAGGGGATGATGCTCTA 58.950 52.381 0.00 0.00 0.00 2.43
1607 1656 2.031333 CAGCTGTGCTTGACCTTTTCTC 60.031 50.000 5.25 0.00 36.40 2.87
1637 1686 1.071071 ACCACGTCCGATCTTTTTGGA 59.929 47.619 0.00 0.00 35.32 3.53
1644 1693 4.024048 CGTCCGATCTTTTTGGATATTGGG 60.024 45.833 0.00 0.00 40.21 4.12
1690 1739 2.019984 CTTTACTCCCATTCAGCAGGC 58.980 52.381 0.00 0.00 0.00 4.85
1712 1761 4.678044 GCGCTGCATGTCTATTAGCCTATA 60.678 45.833 0.00 0.00 0.00 1.31
1725 1774 2.285827 GCCTATAGCTCTATGTGGCG 57.714 55.000 14.91 0.00 37.05 5.69
1743 1809 2.288666 GCGGTGCTAATGGAATGAGAA 58.711 47.619 0.00 0.00 0.00 2.87
1757 1823 8.924511 ATGGAATGAGAAAGACAGAAAAGTTA 57.075 30.769 0.00 0.00 0.00 2.24
1805 1871 9.748708 TGACTTTGTGGATATTTTTCTTTTGAG 57.251 29.630 0.00 0.00 0.00 3.02
1806 1872 9.965824 GACTTTGTGGATATTTTTCTTTTGAGA 57.034 29.630 0.00 0.00 0.00 3.27
1807 1873 9.750125 ACTTTGTGGATATTTTTCTTTTGAGAC 57.250 29.630 0.00 0.00 0.00 3.36
1808 1874 9.748708 CTTTGTGGATATTTTTCTTTTGAGACA 57.251 29.630 0.00 0.00 0.00 3.41
1856 1922 7.021998 ACTAGCTTTAGAACTTCATTTCCCT 57.978 36.000 0.00 0.00 0.00 4.20
1858 1924 6.581171 AGCTTTAGAACTTCATTTCCCTTG 57.419 37.500 0.00 0.00 0.00 3.61
1867 1933 2.412591 TCATTTCCCTTGGGCCAAAAA 58.587 42.857 21.28 17.70 0.00 1.94
1868 1934 2.105649 TCATTTCCCTTGGGCCAAAAAC 59.894 45.455 21.28 0.00 0.00 2.43
1869 1935 1.886422 TTTCCCTTGGGCCAAAAACT 58.114 45.000 21.28 0.00 0.00 2.66
1870 1936 1.127343 TTCCCTTGGGCCAAAAACTG 58.873 50.000 21.28 7.97 0.00 3.16
1873 1939 1.202639 CCCTTGGGCCAAAAACTGTTC 60.203 52.381 21.28 0.00 0.00 3.18
1877 1943 2.114616 TGGGCCAAAAACTGTTCACAT 58.885 42.857 2.13 0.00 0.00 3.21
1878 1944 3.300388 TGGGCCAAAAACTGTTCACATA 58.700 40.909 2.13 0.00 0.00 2.29
1897 1965 2.871096 AAACACGGGGAAATCAGCTA 57.129 45.000 0.00 0.00 0.00 3.32
1898 1966 2.403252 AACACGGGGAAATCAGCTAG 57.597 50.000 0.00 0.00 0.00 3.42
1901 1969 1.123928 ACGGGGAAATCAGCTAGAGG 58.876 55.000 0.00 0.00 0.00 3.69
1903 1971 0.767998 GGGGAAATCAGCTAGAGGGG 59.232 60.000 0.00 0.00 0.00 4.79
1918 1991 1.613925 GAGGGGAAGGCAAACTTGTTC 59.386 52.381 0.00 0.00 40.21 3.18
1921 1994 2.368548 GGGGAAGGCAAACTTGTTCATT 59.631 45.455 0.00 0.00 40.21 2.57
1924 1997 5.454045 GGGGAAGGCAAACTTGTTCATTTTA 60.454 40.000 0.00 0.00 40.21 1.52
1925 1998 5.696270 GGGAAGGCAAACTTGTTCATTTTAG 59.304 40.000 0.00 0.00 40.21 1.85
1935 2008 9.868277 AAACTTGTTCATTTTAGTTCATCACAA 57.132 25.926 0.00 0.00 30.92 3.33
1942 2015 7.315142 TCATTTTAGTTCATCACAATTCAGGC 58.685 34.615 0.00 0.00 0.00 4.85
1948 2021 4.842531 TCATCACAATTCAGGCCTTCTA 57.157 40.909 0.00 0.00 0.00 2.10
1949 2022 4.517285 TCATCACAATTCAGGCCTTCTAC 58.483 43.478 0.00 0.00 0.00 2.59
1952 2025 4.985538 TCACAATTCAGGCCTTCTACTTT 58.014 39.130 0.00 0.00 0.00 2.66
2038 2111 5.770663 TGGCATTACTTACCTTTGCTTGTTA 59.229 36.000 0.00 0.00 33.86 2.41
2128 2205 7.392953 CACTCCTCAGCATCTCTATCACTATAA 59.607 40.741 0.00 0.00 0.00 0.98
2139 2216 6.665680 TCTCTATCACTATAAGAGGGAATGGC 59.334 42.308 0.00 0.00 42.36 4.40
2155 2232 5.166398 GGAATGGCTCTTCACAATTTTGAG 58.834 41.667 0.00 0.00 0.00 3.02
2158 2235 2.589014 GCTCTTCACAATTTTGAGCGG 58.411 47.619 0.00 0.00 40.25 5.52
2176 2253 6.927416 TGAGCGGTAGACATTTACTTAAGAA 58.073 36.000 10.09 0.00 0.00 2.52
2218 2295 5.598005 TCAATTTTGGAGGAACAACATGAGT 59.402 36.000 0.00 0.00 0.00 3.41
2219 2296 4.916983 TTTTGGAGGAACAACATGAGTG 57.083 40.909 0.00 0.00 0.00 3.51
2241 2318 5.067805 GTGTTTCTCATTTTCTTCCCACAGT 59.932 40.000 0.00 0.00 0.00 3.55
2246 2323 6.805713 TCTCATTTTCTTCCCACAGTTTTTC 58.194 36.000 0.00 0.00 0.00 2.29
2251 2328 3.146066 TCTTCCCACAGTTTTTCCATCG 58.854 45.455 0.00 0.00 0.00 3.84
2261 2338 7.812191 CCACAGTTTTTCCATCGATTTATTCAA 59.188 33.333 0.00 0.00 0.00 2.69
2266 2343 8.860128 GTTTTTCCATCGATTTATTCAAACTCC 58.140 33.333 0.00 0.00 0.00 3.85
2268 2345 7.553881 TTCCATCGATTTATTCAAACTCCTC 57.446 36.000 0.00 0.00 0.00 3.71
2272 2349 4.876107 TCGATTTATTCAAACTCCTCTGGC 59.124 41.667 0.00 0.00 0.00 4.85
2286 2363 2.358267 CCTCTGGCTTCAGATTGATTGC 59.642 50.000 0.00 0.00 45.45 3.56
2295 2372 3.515630 TCAGATTGATTGCGAGACAGTC 58.484 45.455 0.00 0.00 35.64 3.51
2530 2607 9.593134 CAGCTCAATATGTATCTAATTACCCTC 57.407 37.037 0.00 0.00 0.00 4.30
2557 2637 6.741358 GGCACAAAGTCGTCAATTATTACTTC 59.259 38.462 0.00 0.00 30.37 3.01
2561 2641 3.795101 AGTCGTCAATTATTACTTCCGCG 59.205 43.478 0.00 0.00 0.00 6.46
2562 2642 3.549070 GTCGTCAATTATTACTTCCGCGT 59.451 43.478 4.92 0.00 0.00 6.01
2563 2643 3.548668 TCGTCAATTATTACTTCCGCGTG 59.451 43.478 4.92 0.00 0.00 5.34
2567 2647 3.668596 ATTATTACTTCCGCGTGTTGC 57.331 42.857 4.92 0.00 41.47 4.17
2574 2654 2.356313 CCGCGTGTTGCTGTCTCT 60.356 61.111 4.92 0.00 43.27 3.10
2583 2663 4.864806 CGTGTTGCTGTCTCTGTATAATGT 59.135 41.667 0.00 0.00 0.00 2.71
2633 2714 4.083217 ACAGTTGCGTGTACTTTTTGTTCA 60.083 37.500 0.00 0.00 0.00 3.18
2679 2761 7.960262 TGTCATCTCTCATATGCTTCATTACT 58.040 34.615 0.00 0.00 0.00 2.24
2761 2843 5.664457 TCTCAGAATATACCTTGTGTGCAG 58.336 41.667 0.00 0.00 0.00 4.41
3096 3306 0.933097 CATCCTTCGATGTTCGCCTG 59.067 55.000 0.00 0.00 40.97 4.85
3263 3474 6.482308 GGGAACATGATGTACATAGTTGGTAC 59.518 42.308 19.50 12.41 41.11 3.34
3562 3773 7.795482 TTACATAGTTTATTGATTGGACCCG 57.205 36.000 0.00 0.00 0.00 5.28
3563 3774 4.578928 ACATAGTTTATTGATTGGACCCGC 59.421 41.667 0.00 0.00 0.00 6.13
3564 3775 2.014128 AGTTTATTGATTGGACCCGCG 58.986 47.619 0.00 0.00 0.00 6.46
3719 3930 1.321474 CTGTTGGTGATTGCTGTGGT 58.679 50.000 0.00 0.00 0.00 4.16
3761 3972 0.250513 AAGTTCTCCCAGCCTTAGCG 59.749 55.000 0.00 0.00 46.67 4.26
3857 4068 1.335145 AAATGGGGATATGCAGCAGC 58.665 50.000 0.00 0.00 42.57 5.25
3858 4069 0.892358 AATGGGGATATGCAGCAGCG 60.892 55.000 0.00 0.00 46.23 5.18
3863 4131 0.317603 GGATATGCAGCAGCGCAAAG 60.318 55.000 11.47 0.00 46.87 2.77
3869 4137 1.226323 CAGCAGCGCAAAGAGATGC 60.226 57.895 11.47 9.07 42.94 3.91
3876 4144 3.806521 CAGCGCAAAGAGATGCTTATACT 59.193 43.478 11.47 0.00 44.21 2.12
3882 4150 5.008118 GCAAAGAGATGCTTATACTTCCCAC 59.992 44.000 0.00 0.00 43.06 4.61
3902 4170 3.255642 CACCAAATTACAGACACTTGGGG 59.744 47.826 4.33 0.00 40.74 4.96
3935 4226 5.043903 TGACATAAGACTATCTCTTTGCGC 58.956 41.667 0.00 0.00 40.04 6.09
4046 4421 1.462283 CTGCTCAACCGTGTGATGAAG 59.538 52.381 0.00 0.00 0.00 3.02
4081 4456 0.171231 GCAAATTCCCAGGTCGAAGC 59.829 55.000 0.00 0.00 0.00 3.86
4410 4798 4.639310 ACATAAGCCGTATCTAGGGTATCG 59.361 45.833 0.00 0.00 38.73 2.92
4423 4819 7.260387 TCTAGGGTATCGATCTGTAGATCTT 57.740 40.000 17.19 9.01 46.58 2.40
4481 4877 3.314357 AGGCCACGAACACTAAAAGAAAC 59.686 43.478 5.01 0.00 0.00 2.78
4500 4896 7.621428 AGAAACATAGGTCTTGATCACATTG 57.379 36.000 0.00 0.00 0.00 2.82
4510 4906 6.309737 GGTCTTGATCACATTGCATCTTTTTC 59.690 38.462 0.00 0.00 0.00 2.29
4578 4974 5.291971 GTGAGTTCCAAATGCACAATCTTT 58.708 37.500 0.00 0.00 0.00 2.52
4619 5015 8.880878 TGAATAAATGAGATGCAATTTGATGG 57.119 30.769 0.00 0.00 0.00 3.51
4684 5081 4.816925 ACTGTAGTTTCTTTGCTCAGGAAC 59.183 41.667 0.00 0.00 32.90 3.62
4685 5082 5.036117 TGTAGTTTCTTTGCTCAGGAACT 57.964 39.130 12.46 12.46 43.86 3.01
4718 5115 4.398358 TCTCCAAGAACCTCACTATACACG 59.602 45.833 0.00 0.00 0.00 4.49
4790 5187 4.238761 TCAGAAAGACTACACGAACCAG 57.761 45.455 0.00 0.00 0.00 4.00
4807 5204 1.727880 CCAGCAAATGAAACAATGCCG 59.272 47.619 0.00 0.00 39.59 5.69
4832 5229 5.612351 AGTCAGGTGTTTCTTTAGAGGTTC 58.388 41.667 0.00 0.00 0.00 3.62
4852 5249 5.293324 GGTTCCATTTCCAGTTTGTTGTTTC 59.707 40.000 0.00 0.00 0.00 2.78
4928 5356 3.366679 CGAAAATGATGAGTTGGCTTGCT 60.367 43.478 0.00 0.00 0.00 3.91
5033 5461 2.869233 TCTCAAGCAACAAAGGCAAC 57.131 45.000 0.00 0.00 0.00 4.17
5240 5668 5.680619 TGACCAACAGTTTGACAGACTAAT 58.319 37.500 0.00 0.00 34.24 1.73
5304 5732 8.770010 TCTAGTAAACAAATGGAAAGGGAAAA 57.230 30.769 0.00 0.00 0.00 2.29
5329 5757 4.878971 ACATTGTTACACTACAACACAGCA 59.121 37.500 0.00 0.00 40.53 4.41
5370 5798 6.414732 ACGAAATGGAATAACTGGAATCAGA 58.585 36.000 0.00 0.00 43.49 3.27
5372 5800 7.148239 ACGAAATGGAATAACTGGAATCAGAAC 60.148 37.037 0.00 0.00 43.49 3.01
5376 5807 5.887598 TGGAATAACTGGAATCAGAACCATG 59.112 40.000 0.00 0.00 43.49 3.66
5381 5812 4.583871 ACTGGAATCAGAACCATGAAGTC 58.416 43.478 0.00 0.00 43.49 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.862147 CGACAACGTCTACTCGCCG 60.862 63.158 0.00 0.00 34.56 6.46
164 165 3.382832 CTCTCCGAGGCCACCGTT 61.383 66.667 5.01 0.00 0.00 4.44
490 507 3.164269 CTCATCCCACCCCTCCCG 61.164 72.222 0.00 0.00 0.00 5.14
561 584 1.071385 CTCTCCCTGTCAACAACTGCT 59.929 52.381 0.00 0.00 0.00 4.24
659 692 1.538876 CCTCCCTGGACCTGGTTCA 60.539 63.158 15.72 7.76 38.35 3.18
968 1017 1.582937 ACGAGATGCGAACGCTACG 60.583 57.895 19.32 18.55 44.57 3.51
969 1018 0.522705 TCACGAGATGCGAACGCTAC 60.523 55.000 19.32 12.85 44.57 3.58
970 1019 0.248094 CTCACGAGATGCGAACGCTA 60.248 55.000 19.32 7.19 44.57 4.26
971 1020 1.515088 CTCACGAGATGCGAACGCT 60.515 57.895 19.32 5.89 44.57 5.07
1388 1437 3.698263 AAGTAGGAGCCGGGGGAGG 62.698 68.421 2.18 0.00 0.00 4.30
1465 1514 1.503818 CTCACCAACCGAACCAACCG 61.504 60.000 0.00 0.00 0.00 4.44
1470 1519 1.671379 GCCTCTCACCAACCGAACC 60.671 63.158 0.00 0.00 0.00 3.62
1471 1520 2.027625 CGCCTCTCACCAACCGAAC 61.028 63.158 0.00 0.00 0.00 3.95
1472 1521 2.342279 CGCCTCTCACCAACCGAA 59.658 61.111 0.00 0.00 0.00 4.30
1473 1522 4.373116 GCGCCTCTCACCAACCGA 62.373 66.667 0.00 0.00 0.00 4.69
1511 1560 0.942252 AAAAGCGACCTCCGTTTGAC 59.058 50.000 0.00 0.00 40.80 3.18
1512 1561 2.137523 GTAAAAGCGACCTCCGTTTGA 58.862 47.619 0.00 0.00 40.80 2.69
1513 1562 1.868498 TGTAAAAGCGACCTCCGTTTG 59.132 47.619 0.00 0.00 40.80 2.93
1514 1563 2.140717 CTGTAAAAGCGACCTCCGTTT 58.859 47.619 0.00 0.00 43.50 3.60
1520 1569 2.301870 TCCACATCTGTAAAAGCGACCT 59.698 45.455 0.00 0.00 0.00 3.85
1576 1625 3.012399 CACAGCTGCGCATAGAGC 58.988 61.111 12.24 11.55 40.87 4.09
1589 1638 3.567164 ACATGAGAAAAGGTCAAGCACAG 59.433 43.478 0.00 0.00 0.00 3.66
1607 1656 1.134936 TCGGACGTGGTTATGGACATG 60.135 52.381 0.00 0.00 0.00 3.21
1637 1686 3.600617 TCTTCCTTTTCCCCACCCAATAT 59.399 43.478 0.00 0.00 0.00 1.28
1644 1693 2.971901 TTCCTCTTCCTTTTCCCCAC 57.028 50.000 0.00 0.00 0.00 4.61
1690 1739 2.160822 AGGCTAATAGACATGCAGCG 57.839 50.000 0.00 0.00 32.97 5.18
1712 1761 1.043116 TAGCACCGCCACATAGAGCT 61.043 55.000 0.00 0.00 34.84 4.09
1722 1771 0.947244 CTCATTCCATTAGCACCGCC 59.053 55.000 0.00 0.00 0.00 6.13
1725 1774 4.943705 TGTCTTTCTCATTCCATTAGCACC 59.056 41.667 0.00 0.00 0.00 5.01
1743 1809 5.625150 AGCTGGTGATAACTTTTCTGTCTT 58.375 37.500 0.00 0.00 0.00 3.01
1757 1823 1.293062 AATGAGTGGGAGCTGGTGAT 58.707 50.000 0.00 0.00 0.00 3.06
1811 1877 9.595823 GCTAGTACAGTTAGAAAAATATCCACA 57.404 33.333 0.00 0.00 0.00 4.17
1812 1878 9.819267 AGCTAGTACAGTTAGAAAAATATCCAC 57.181 33.333 0.00 0.00 0.00 4.02
1823 1889 9.293404 TGAAGTTCTAAAGCTAGTACAGTTAGA 57.707 33.333 4.17 0.00 30.02 2.10
1827 1893 9.425577 GAAATGAAGTTCTAAAGCTAGTACAGT 57.574 33.333 4.17 0.00 30.02 3.55
1829 1895 7.822822 GGGAAATGAAGTTCTAAAGCTAGTACA 59.177 37.037 4.17 0.00 30.02 2.90
1840 1906 3.563479 GGCCCAAGGGAAATGAAGTTCTA 60.563 47.826 9.92 0.00 37.50 2.10
1841 1907 2.529632 GCCCAAGGGAAATGAAGTTCT 58.470 47.619 9.92 0.00 37.50 3.01
1842 1908 1.550524 GGCCCAAGGGAAATGAAGTTC 59.449 52.381 9.92 0.00 37.50 3.01
1844 1910 0.486879 TGGCCCAAGGGAAATGAAGT 59.513 50.000 9.92 0.00 37.50 3.01
1845 1911 1.643310 TTGGCCCAAGGGAAATGAAG 58.357 50.000 9.92 0.00 37.50 3.02
1856 1922 1.902508 TGTGAACAGTTTTTGGCCCAA 59.097 42.857 0.00 0.00 0.00 4.12
1858 1924 2.908688 ATGTGAACAGTTTTTGGCCC 57.091 45.000 0.00 0.00 0.00 5.80
1867 1933 2.105134 TCCCCGTGTTTATGTGAACAGT 59.895 45.455 0.00 0.00 39.97 3.55
1868 1934 2.773487 TCCCCGTGTTTATGTGAACAG 58.227 47.619 0.00 0.00 39.97 3.16
1869 1935 2.932855 TCCCCGTGTTTATGTGAACA 57.067 45.000 0.00 0.00 37.20 3.18
1870 1936 4.216687 TGATTTCCCCGTGTTTATGTGAAC 59.783 41.667 0.00 0.00 0.00 3.18
1873 1939 3.427503 GCTGATTTCCCCGTGTTTATGTG 60.428 47.826 0.00 0.00 0.00 3.21
1877 1943 2.871096 AGCTGATTTCCCCGTGTTTA 57.129 45.000 0.00 0.00 0.00 2.01
1878 1944 2.304761 TCTAGCTGATTTCCCCGTGTTT 59.695 45.455 0.00 0.00 0.00 2.83
1897 1965 0.853530 ACAAGTTTGCCTTCCCCTCT 59.146 50.000 0.00 0.00 0.00 3.69
1898 1966 1.613925 GAACAAGTTTGCCTTCCCCTC 59.386 52.381 0.00 0.00 0.00 4.30
1901 1969 3.751479 AATGAACAAGTTTGCCTTCCC 57.249 42.857 0.00 0.00 0.00 3.97
1903 1971 7.491048 TGAACTAAAATGAACAAGTTTGCCTTC 59.509 33.333 0.00 0.00 32.51 3.46
1918 1991 6.532657 GGCCTGAATTGTGATGAACTAAAATG 59.467 38.462 0.00 0.00 0.00 2.32
1921 1994 5.324409 AGGCCTGAATTGTGATGAACTAAA 58.676 37.500 3.11 0.00 0.00 1.85
1924 1997 3.446442 AGGCCTGAATTGTGATGAACT 57.554 42.857 3.11 0.00 0.00 3.01
1925 1998 3.760684 AGAAGGCCTGAATTGTGATGAAC 59.239 43.478 5.69 0.00 0.00 3.18
1960 2033 5.063060 GTCTCAGGTGTATAACGCGATTTTT 59.937 40.000 15.93 0.00 0.00 1.94
1961 2034 4.565564 GTCTCAGGTGTATAACGCGATTTT 59.434 41.667 15.93 0.00 0.00 1.82
1962 2035 4.110482 GTCTCAGGTGTATAACGCGATTT 58.890 43.478 15.93 0.00 0.00 2.17
1964 2037 2.950309 AGTCTCAGGTGTATAACGCGAT 59.050 45.455 15.93 2.34 0.00 4.58
1965 2038 2.362736 AGTCTCAGGTGTATAACGCGA 58.637 47.619 15.93 0.00 0.00 5.87
1967 2040 4.373348 AGAAGTCTCAGGTGTATAACGC 57.627 45.455 0.00 0.00 0.00 4.84
1968 2041 9.000486 TGATATAGAAGTCTCAGGTGTATAACG 58.000 37.037 0.00 0.00 0.00 3.18
1999 2072 2.133281 TGCCAATGCATGAACTAGCT 57.867 45.000 0.00 0.00 44.23 3.32
2013 2086 4.586841 ACAAGCAAAGGTAAGTAATGCCAA 59.413 37.500 0.00 0.00 37.73 4.52
2015 2088 4.783764 ACAAGCAAAGGTAAGTAATGCC 57.216 40.909 0.00 0.00 37.73 4.40
2020 2093 7.656137 CAGACTCTTAACAAGCAAAGGTAAGTA 59.344 37.037 7.46 0.00 0.00 2.24
2022 2095 6.483640 ACAGACTCTTAACAAGCAAAGGTAAG 59.516 38.462 2.52 2.52 0.00 2.34
2023 2096 6.354130 ACAGACTCTTAACAAGCAAAGGTAA 58.646 36.000 0.00 0.00 0.00 2.85
2026 2099 5.059833 AGACAGACTCTTAACAAGCAAAGG 58.940 41.667 0.00 0.00 0.00 3.11
2038 2111 8.107095 AGTGAGTCTTCTATTAGACAGACTCTT 58.893 37.037 32.76 26.31 46.00 2.85
2059 2133 4.250116 ACTGTCTAAGTTGCAGAGTGAG 57.750 45.455 9.78 0.00 34.57 3.51
2109 2186 6.889177 TCCCTCTTATAGTGATAGAGATGCTG 59.111 42.308 0.00 0.00 0.00 4.41
2128 2205 1.661463 TGTGAAGAGCCATTCCCTCT 58.339 50.000 0.00 0.00 41.25 3.69
2139 2216 3.904136 ACCGCTCAAAATTGTGAAGAG 57.096 42.857 0.00 0.00 0.00 2.85
2155 2232 6.335777 TCCTTCTTAAGTAAATGTCTACCGC 58.664 40.000 1.63 0.00 0.00 5.68
2176 2253 5.818678 ATTGATGCAATATGCCAAATCCT 57.181 34.783 0.00 0.00 44.23 3.24
2195 2272 5.693104 CACTCATGTTGTTCCTCCAAAATTG 59.307 40.000 0.00 0.00 0.00 2.32
2197 2274 4.895297 ACACTCATGTTGTTCCTCCAAAAT 59.105 37.500 0.00 0.00 34.46 1.82
2218 2295 5.200483 ACTGTGGGAAGAAAATGAGAAACA 58.800 37.500 0.00 0.00 0.00 2.83
2219 2296 5.774498 ACTGTGGGAAGAAAATGAGAAAC 57.226 39.130 0.00 0.00 0.00 2.78
2226 2303 5.948742 TGGAAAAACTGTGGGAAGAAAAT 57.051 34.783 0.00 0.00 0.00 1.82
2227 2304 5.451242 CGATGGAAAAACTGTGGGAAGAAAA 60.451 40.000 0.00 0.00 0.00 2.29
2228 2305 4.037446 CGATGGAAAAACTGTGGGAAGAAA 59.963 41.667 0.00 0.00 0.00 2.52
2229 2306 3.568007 CGATGGAAAAACTGTGGGAAGAA 59.432 43.478 0.00 0.00 0.00 2.52
2230 2307 3.146066 CGATGGAAAAACTGTGGGAAGA 58.854 45.455 0.00 0.00 0.00 2.87
2231 2308 3.146066 TCGATGGAAAAACTGTGGGAAG 58.854 45.455 0.00 0.00 0.00 3.46
2232 2309 3.216187 TCGATGGAAAAACTGTGGGAA 57.784 42.857 0.00 0.00 0.00 3.97
2233 2310 2.940994 TCGATGGAAAAACTGTGGGA 57.059 45.000 0.00 0.00 0.00 4.37
2241 2318 8.802267 AGGAGTTTGAATAAATCGATGGAAAAA 58.198 29.630 0.00 0.00 0.00 1.94
2246 2323 6.017605 CCAGAGGAGTTTGAATAAATCGATGG 60.018 42.308 0.00 0.00 0.00 3.51
2251 2328 6.375455 TGAAGCCAGAGGAGTTTGAATAAATC 59.625 38.462 0.00 0.00 0.00 2.17
2268 2345 2.011947 TCGCAATCAATCTGAAGCCAG 58.988 47.619 0.00 0.00 41.74 4.85
2272 2349 3.931468 ACTGTCTCGCAATCAATCTGAAG 59.069 43.478 0.00 0.00 0.00 3.02
2530 2607 4.685169 ATAATTGACGACTTTGTGCCAG 57.315 40.909 0.00 0.00 0.00 4.85
2561 2641 6.727824 AACATTATACAGAGACAGCAACAC 57.272 37.500 0.00 0.00 0.00 3.32
2562 2642 7.744087 AAAACATTATACAGAGACAGCAACA 57.256 32.000 0.00 0.00 0.00 3.33
2649 2730 8.186709 TGAAGCATATGAGAGATGACATAGAA 57.813 34.615 6.97 0.00 33.46 2.10
2679 2761 7.201679 CCCAAAATGCATTGAACAAAAAGTACA 60.202 33.333 13.82 0.00 31.84 2.90
2844 3051 4.439974 CCAACAACAACACAGTGCAATAGT 60.440 41.667 0.00 0.00 0.00 2.12
3096 3306 5.368989 AGTTGGTTTATAGCATACTGCCTC 58.631 41.667 0.00 0.00 46.52 4.70
3263 3474 9.190858 GAGAGAATGATACACAGCTATTACAAG 57.809 37.037 0.00 0.00 0.00 3.16
3573 3784 0.247736 AACAGGCGACAGATCACTCC 59.752 55.000 0.00 0.00 0.00 3.85
3575 3786 0.036952 CCAACAGGCGACAGATCACT 60.037 55.000 0.00 0.00 0.00 3.41
3577 3788 1.375908 GCCAACAGGCGACAGATCA 60.376 57.895 0.00 0.00 38.93 2.92
3719 3930 0.753479 TGCCGGTGCTTTCAAGGAAA 60.753 50.000 1.90 0.00 38.71 3.13
3761 3972 8.125448 GTCAAGATAGTTCATGAAATTACCTGC 58.875 37.037 14.34 0.00 31.84 4.85
3840 4051 1.303074 CGCTGCTGCATATCCCCAT 60.303 57.895 16.29 0.00 39.64 4.00
3841 4052 2.111669 CGCTGCTGCATATCCCCA 59.888 61.111 16.29 0.00 39.64 4.96
3844 4055 0.317603 CTTTGCGCTGCTGCATATCC 60.318 55.000 16.29 0.00 45.78 2.59
3845 4056 0.659427 TCTTTGCGCTGCTGCATATC 59.341 50.000 16.29 2.22 45.78 1.63
3846 4057 0.661552 CTCTTTGCGCTGCTGCATAT 59.338 50.000 16.29 0.00 45.78 1.78
3848 4059 1.030488 ATCTCTTTGCGCTGCTGCAT 61.030 50.000 16.29 0.00 45.78 3.96
3850 4061 1.226323 CATCTCTTTGCGCTGCTGC 60.226 57.895 9.73 5.34 0.00 5.25
3851 4062 1.226323 GCATCTCTTTGCGCTGCTG 60.226 57.895 9.73 0.00 32.06 4.41
3852 4063 3.185155 GCATCTCTTTGCGCTGCT 58.815 55.556 9.73 0.00 32.06 4.24
3858 4069 5.008118 GTGGGAAGTATAAGCATCTCTTTGC 59.992 44.000 0.00 0.00 43.09 3.68
3860 4071 5.191722 TGGTGGGAAGTATAAGCATCTCTTT 59.808 40.000 0.00 0.00 36.25 2.52
3863 4131 4.689612 TGGTGGGAAGTATAAGCATCTC 57.310 45.455 0.00 0.00 0.00 2.75
3869 4137 7.827236 TGTCTGTAATTTGGTGGGAAGTATAAG 59.173 37.037 0.00 0.00 0.00 1.73
3876 4144 4.447138 AGTGTCTGTAATTTGGTGGGAA 57.553 40.909 0.00 0.00 0.00 3.97
3882 4150 3.255642 CACCCCAAGTGTCTGTAATTTGG 59.744 47.826 0.00 0.00 41.93 3.28
3902 4170 3.347216 AGTCTTATGTCATGCCCAACAC 58.653 45.455 0.00 0.00 0.00 3.32
4081 4456 3.684788 CACAAACTTTGGACCTAGATCGG 59.315 47.826 6.47 0.00 34.12 4.18
4178 4553 1.151668 CACAAAGAACGGAGGAGCAG 58.848 55.000 0.00 0.00 0.00 4.24
4423 4819 2.906389 ACTCATACAGTTCAGAGCCCAA 59.094 45.455 0.00 0.00 26.56 4.12
4454 4850 6.046593 TCTTTTAGTGTTCGTGGCCTATATG 58.953 40.000 3.32 0.00 0.00 1.78
4481 4877 5.763698 AGATGCAATGTGATCAAGACCTATG 59.236 40.000 0.00 0.00 0.00 2.23
4500 4896 1.478631 CAGGAGGGGGAAAAAGATGC 58.521 55.000 0.00 0.00 0.00 3.91
4510 4906 2.445654 GAGAGGAGCAGGAGGGGG 60.446 72.222 0.00 0.00 0.00 5.40
4619 5015 6.200475 GTCTACACACCAAGTAACTTGAAGAC 59.800 42.308 0.00 0.00 43.42 3.01
4684 5081 3.181485 GGTTCTTGGAGACCGATCACTAG 60.181 52.174 0.00 0.00 0.00 2.57
4685 5082 2.758979 GGTTCTTGGAGACCGATCACTA 59.241 50.000 0.00 0.00 0.00 2.74
4718 5115 0.792031 ATTCGCCGGACGTTTACAAC 59.208 50.000 5.05 0.00 44.19 3.32
4790 5187 3.574614 ACTACGGCATTGTTTCATTTGC 58.425 40.909 0.00 0.00 0.00 3.68
4807 5204 6.099159 ACCTCTAAAGAAACACCTGACTAC 57.901 41.667 0.00 0.00 0.00 2.73
4832 5229 5.022282 AGGAAACAACAAACTGGAAATGG 57.978 39.130 0.00 0.00 0.00 3.16
4852 5249 5.873164 AGAGCAAGTTAAAACGTGGTATAGG 59.127 40.000 12.28 0.00 46.17 2.57
4928 5356 4.824479 TCATTCACTGATAGTTCTGGCA 57.176 40.909 0.00 0.00 0.00 4.92
5129 5557 7.255173 GCATTCAGAGCAATGAGATTTCTATGT 60.255 37.037 0.00 0.00 36.03 2.29
5240 5668 1.462432 TGGGGCCTGTTGTACCTCA 60.462 57.895 0.84 0.00 0.00 3.86
5304 5732 6.127869 TGCTGTGTTGTAGTGTAACAATGTTT 60.128 34.615 3.17 0.00 41.18 2.83
5329 5757 6.095440 CCATTTCGTTTCTTTGGATGGTATCT 59.905 38.462 0.00 0.00 0.00 1.98
5370 5798 4.584743 GGAGTTTCTTTGGACTTCATGGTT 59.415 41.667 0.00 0.00 0.00 3.67
5372 5800 3.189287 CGGAGTTTCTTTGGACTTCATGG 59.811 47.826 0.00 0.00 0.00 3.66
5376 5807 1.194772 CGCGGAGTTTCTTTGGACTTC 59.805 52.381 0.00 0.00 0.00 3.01
5381 5812 1.866925 GGTCGCGGAGTTTCTTTGG 59.133 57.895 6.13 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.