Multiple sequence alignment - TraesCS6A01G124200

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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 TraesCS6A01G124200 chr6A 100.000 2645 0 0 1 2645 98049574 98046930 0.000000e+00 4885.0
1 TraesCS6A01G124200 chr6B 92.087 1744 89 21 187 1920 156277171 156275467 0.000000e+00 2410.0
2 TraesCS6A01G124200 chr6B 88.598 649 56 5 1964 2601 156275473 156274832 0.000000e+00 773.0
3 TraesCS6A01G124200 chr6B 80.693 202 28 8 1 200 156277771 156277579 2.120000e-31 147.0
4 TraesCS6A01G124200 chr6D 95.684 1089 42 4 187 1275 81667108 81666025 0.000000e+00 1746.0
5 TraesCS6A01G124200 chr6D 86.607 448 32 6 2126 2573 81666025 81665606 1.110000e-128 470.0
6 TraesCS6A01G124200 chr6D 85.167 209 13 9 1 200 81667644 81667445 5.770000e-47 198.0
7 TraesCS6A01G124200 chr3B 78.783 1249 247 16 419 1659 747835536 747836774 0.000000e+00 822.0
8 TraesCS6A01G124200 chr3B 78.703 1249 248 16 419 1659 747823060 747824298 0.000000e+00 817.0
9 TraesCS6A01G124200 chr3B 78.703 1249 248 16 419 1659 747852063 747853301 0.000000e+00 817.0
10 TraesCS6A01G124200 chr3B 78.623 1249 249 16 419 1659 747839588 747840826 0.000000e+00 811.0
11 TraesCS6A01G124200 chrUn 78.543 1249 250 16 419 1659 331495094 331496332 0.000000e+00 806.0
12 TraesCS6A01G124200 chr3A 79.149 1175 230 14 480 1649 697262350 697263514 0.000000e+00 798.0
13 TraesCS6A01G124200 chr3D 78.383 1249 252 17 419 1659 561376221 561377459 0.000000e+00 795.0
14 TraesCS6A01G124200 chr2D 95.238 42 2 0 1915 1956 542365083 542365042 1.700000e-07 67.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G124200 chr6A 98046930 98049574 2644 True 4885.000000 4885 100.000000 1 2645 1 chr6A.!!$R1 2644
1 TraesCS6A01G124200 chr6B 156274832 156277771 2939 True 1110.000000 2410 87.126000 1 2601 3 chr6B.!!$R1 2600
2 TraesCS6A01G124200 chr6D 81665606 81667644 2038 True 804.666667 1746 89.152667 1 2573 3 chr6D.!!$R1 2572
3 TraesCS6A01G124200 chr3B 747823060 747824298 1238 False 817.000000 817 78.703000 419 1659 1 chr3B.!!$F1 1240
4 TraesCS6A01G124200 chr3B 747852063 747853301 1238 False 817.000000 817 78.703000 419 1659 1 chr3B.!!$F2 1240
5 TraesCS6A01G124200 chr3B 747835536 747840826 5290 False 816.500000 822 78.703000 419 1659 2 chr3B.!!$F3 1240
6 TraesCS6A01G124200 chrUn 331495094 331496332 1238 False 806.000000 806 78.543000 419 1659 1 chrUn.!!$F1 1240
7 TraesCS6A01G124200 chr3A 697262350 697263514 1164 False 798.000000 798 79.149000 480 1649 1 chr3A.!!$F1 1169
8 TraesCS6A01G124200 chr3D 561376221 561377459 1238 False 795.000000 795 78.383000 419 1659 1 chr3D.!!$F1 1240

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
403 839 0.665835 GGGAACACATTTGCACGACA 59.334 50.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2149 6653 0.258774 AGGCAACACACCAAGAACCT 59.741 50.0 0.0 0.0 41.41 3.5 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
42 44 4.629200 GTCACTGCCACTCTCAAGAAATAG 59.371 45.833 0.00 0.00 0.00 1.73
84 86 4.020928 TCCGTTACTCTGTTATTCAGCCAA 60.021 41.667 0.00 0.00 43.32 4.52
99 101 5.186256 TCAGCCAATATTGTCCCACTAAA 57.814 39.130 14.25 0.00 0.00 1.85
175 187 7.645402 CAATCAGCTAATTAGTGCAATCATGA 58.355 34.615 13.91 0.00 0.00 3.07
176 188 6.856135 TCAGCTAATTAGTGCAATCATGAG 57.144 37.500 13.91 0.00 0.00 2.90
239 675 7.223584 TCTTCTTCACCACACAGATATTTTCA 58.776 34.615 0.00 0.00 0.00 2.69
321 757 5.331902 CATGCTACACAATACCGGAAAAAG 58.668 41.667 9.46 0.00 0.00 2.27
403 839 0.665835 GGGAACACATTTGCACGACA 59.334 50.000 0.00 0.00 0.00 4.35
415 851 1.204062 CACGACAAAGACGCGCATT 59.796 52.632 5.73 0.00 0.00 3.56
467 906 3.403968 TGTGTAATTTTGCAGGCTACGA 58.596 40.909 0.00 0.00 0.00 3.43
525 964 1.132262 GAGACTCGTGGAAGAGAGCAG 59.868 57.143 0.62 0.00 40.57 4.24
599 1038 2.722201 GGTAGCCAGGACGACCCAG 61.722 68.421 0.00 0.00 37.41 4.45
689 1128 1.597742 TTCAGAGCAAGCTGTTGGAC 58.402 50.000 0.00 0.00 37.20 4.02
877 1316 2.543637 TCTCCTTCCCCTCCCCCT 60.544 66.667 0.00 0.00 0.00 4.79
896 1335 5.952347 CCCCCTAAAGAATATATTTGAGGCC 59.048 44.000 0.00 0.00 0.00 5.19
911 1350 3.122480 TGAGGCCTTCCCTGATTATGAA 58.878 45.455 6.77 0.00 46.60 2.57
1033 1472 2.665165 CTCAGGCAGTCTACCATCTCT 58.335 52.381 0.00 0.00 0.00 3.10
1034 1473 3.030291 CTCAGGCAGTCTACCATCTCTT 58.970 50.000 0.00 0.00 0.00 2.85
1247 1686 4.256920 GCTTATCACCTGTCAGTGTTGAT 58.743 43.478 11.54 11.54 38.91 2.57
1299 1738 3.118186 TGTCCTTATTCACCGGTATTGGG 60.118 47.826 6.87 5.44 0.00 4.12
1314 1753 0.620700 TTGGGGGAGGAGAAGTAGCC 60.621 60.000 0.00 0.00 0.00 3.93
1439 1878 3.204526 GCAGTCTGATTGAGATTCCAGG 58.795 50.000 3.32 0.00 31.63 4.45
1441 1880 2.842496 AGTCTGATTGAGATTCCAGGCA 59.158 45.455 0.00 0.00 34.00 4.75
1476 1915 8.579682 TCACTAATGATACAATCGAGTCATTG 57.420 34.615 16.37 11.45 40.43 2.82
1670 6169 3.146066 TCCATTGTAGTGGCTGTTTGTC 58.854 45.455 0.00 0.00 39.19 3.18
1679 6178 4.980573 AGTGGCTGTTTGTCCATTTAGTA 58.019 39.130 0.00 0.00 34.47 1.82
1680 6179 5.003804 AGTGGCTGTTTGTCCATTTAGTAG 58.996 41.667 0.00 0.00 34.47 2.57
1681 6180 4.760204 GTGGCTGTTTGTCCATTTAGTAGT 59.240 41.667 0.00 0.00 34.47 2.73
1705 6205 9.646427 AGTGTTTATCTCTAGAAACTGAATGTC 57.354 33.333 6.59 0.00 37.62 3.06
1706 6206 8.874816 GTGTTTATCTCTAGAAACTGAATGTCC 58.125 37.037 6.59 0.00 37.62 4.02
1712 6212 5.551233 TCTAGAAACTGAATGTCCCAAGTG 58.449 41.667 0.00 0.00 0.00 3.16
1722 6222 3.485463 TGTCCCAAGTGTAAACAGAGG 57.515 47.619 0.00 0.00 0.00 3.69
1726 6226 3.139077 CCCAAGTGTAAACAGAGGTGAC 58.861 50.000 0.00 0.00 0.00 3.67
1745 6245 4.223032 GTGACTTGGAGGAGGTTTATCTGA 59.777 45.833 0.00 0.00 0.00 3.27
1762 6262 9.534565 GTTTATCTGAGAGTCACATTTAGCATA 57.465 33.333 0.00 0.00 0.00 3.14
1768 6268 8.599055 TGAGAGTCACATTTAGCATATGATTC 57.401 34.615 6.97 0.00 0.00 2.52
1772 6272 9.608617 GAGTCACATTTAGCATATGATTCATTG 57.391 33.333 6.97 4.77 0.00 2.82
1783 6283 8.781196 AGCATATGATTCATTGTTGCTAACTAG 58.219 33.333 20.70 0.00 34.27 2.57
1784 6284 8.562892 GCATATGATTCATTGTTGCTAACTAGT 58.437 33.333 6.97 0.00 0.00 2.57
1787 6287 7.520119 TGATTCATTGTTGCTAACTAGTACG 57.480 36.000 0.00 0.00 0.00 3.67
1788 6288 7.094631 TGATTCATTGTTGCTAACTAGTACGT 58.905 34.615 0.00 0.00 0.00 3.57
1789 6289 8.245491 TGATTCATTGTTGCTAACTAGTACGTA 58.755 33.333 0.00 0.00 0.00 3.57
1807 6307 8.754230 AGTACGTAATTTAGAACCTGTTCTTC 57.246 34.615 16.96 2.73 46.95 2.87
1814 6314 7.997773 ATTTAGAACCTGTTCTTCTTTACCC 57.002 36.000 16.96 0.00 46.95 3.69
1833 6333 2.224450 CCCAAAGAAAGTCTACCGTGGT 60.224 50.000 0.00 0.00 0.00 4.16
1851 6352 3.328637 GTGGTCCCCTTAAACTCTTACCA 59.671 47.826 0.00 0.00 33.53 3.25
1868 6369 7.125792 TCTTACCAGAGTCTAATTTCCATCC 57.874 40.000 0.00 0.00 0.00 3.51
1871 6372 5.032846 ACCAGAGTCTAATTTCCATCCTCA 58.967 41.667 0.00 0.00 0.00 3.86
1872 6373 5.488919 ACCAGAGTCTAATTTCCATCCTCAA 59.511 40.000 0.00 0.00 0.00 3.02
1873 6374 5.819901 CCAGAGTCTAATTTCCATCCTCAAC 59.180 44.000 0.00 0.00 0.00 3.18
1874 6375 6.352565 CCAGAGTCTAATTTCCATCCTCAACT 60.353 42.308 0.00 0.00 0.00 3.16
1875 6376 6.760770 CAGAGTCTAATTTCCATCCTCAACTC 59.239 42.308 0.00 0.00 0.00 3.01
1876 6377 5.995446 AGTCTAATTTCCATCCTCAACTCC 58.005 41.667 0.00 0.00 0.00 3.85
1877 6378 5.488919 AGTCTAATTTCCATCCTCAACTCCA 59.511 40.000 0.00 0.00 0.00 3.86
1878 6379 6.012508 AGTCTAATTTCCATCCTCAACTCCAA 60.013 38.462 0.00 0.00 0.00 3.53
1884 6385 2.229784 CCATCCTCAACTCCAAAACTGC 59.770 50.000 0.00 0.00 0.00 4.40
1891 6392 5.763204 CCTCAACTCCAAAACTGCTTACTTA 59.237 40.000 0.00 0.00 0.00 2.24
1904 6405 3.682858 TGCTTACTTAACATCGCCAACTC 59.317 43.478 0.00 0.00 0.00 3.01
1908 6409 6.622896 GCTTACTTAACATCGCCAACTCAAAT 60.623 38.462 0.00 0.00 0.00 2.32
1916 6417 5.123344 ACATCGCCAACTCAAATAAAGGTAC 59.877 40.000 0.00 0.00 0.00 3.34
1918 6419 6.040209 TCGCCAACTCAAATAAAGGTACTA 57.960 37.500 0.00 0.00 38.49 1.82
1919 6420 5.870978 TCGCCAACTCAAATAAAGGTACTAC 59.129 40.000 0.00 0.00 38.49 2.73
1920 6421 5.064325 CGCCAACTCAAATAAAGGTACTACC 59.936 44.000 0.00 0.00 38.49 3.18
1941 6442 9.187996 ACTACCTCTGTAAAGTAATAGAAGACC 57.812 37.037 0.00 0.00 0.00 3.85
1942 6443 9.411189 CTACCTCTGTAAAGTAATAGAAGACCT 57.589 37.037 0.00 0.00 0.00 3.85
1943 6444 8.667592 ACCTCTGTAAAGTAATAGAAGACCTT 57.332 34.615 0.00 0.00 0.00 3.50
1944 6445 9.102453 ACCTCTGTAAAGTAATAGAAGACCTTT 57.898 33.333 0.00 0.00 0.00 3.11
1945 6446 9.945904 CCTCTGTAAAGTAATAGAAGACCTTTT 57.054 33.333 0.00 0.00 0.00 2.27
1958 6459 9.702253 ATAGAAGACCTTTTAGATCACTACAGA 57.298 33.333 0.00 0.00 0.00 3.41
1959 6460 8.062065 AGAAGACCTTTTAGATCACTACAGAG 57.938 38.462 0.00 0.00 0.00 3.35
1960 6461 6.783708 AGACCTTTTAGATCACTACAGAGG 57.216 41.667 0.00 0.00 32.83 3.69
1961 6462 5.659079 AGACCTTTTAGATCACTACAGAGGG 59.341 44.000 0.00 0.00 31.82 4.30
1962 6463 5.590818 ACCTTTTAGATCACTACAGAGGGA 58.409 41.667 0.00 0.00 40.22 4.20
1963 6464 5.659079 ACCTTTTAGATCACTACAGAGGGAG 59.341 44.000 0.00 0.00 38.94 4.30
1964 6465 5.659079 CCTTTTAGATCACTACAGAGGGAGT 59.341 44.000 0.00 0.00 38.94 3.85
1965 6466 6.834451 CCTTTTAGATCACTACAGAGGGAGTA 59.166 42.308 0.00 0.00 38.94 2.59
2018 6519 6.006449 GGGATGATGAATGCCTACATAAAGT 58.994 40.000 0.00 0.00 43.36 2.66
2021 6522 7.013655 GGATGATGAATGCCTACATAAAGTTGT 59.986 37.037 0.00 0.00 34.62 3.32
2046 6547 8.671921 GTGATCTGATTGTTTAAGTGATGACAT 58.328 33.333 0.00 0.00 0.00 3.06
2047 6548 8.671028 TGATCTGATTGTTTAAGTGATGACATG 58.329 33.333 0.00 0.00 0.00 3.21
2049 6550 8.394971 TCTGATTGTTTAAGTGATGACATGTT 57.605 30.769 0.00 0.00 0.00 2.71
2052 6553 5.119931 TGTTTAAGTGATGACATGTTGCC 57.880 39.130 0.00 0.00 0.00 4.52
2053 6554 4.582240 TGTTTAAGTGATGACATGTTGCCA 59.418 37.500 0.00 0.00 0.00 4.92
2067 6568 7.042797 ACATGTTGCCATATTTCTCCAATAC 57.957 36.000 0.00 0.00 29.65 1.89
2100 6604 3.820557 ACACCTGCATTTGTACTCTTGT 58.179 40.909 0.00 0.00 0.00 3.16
2134 6638 6.611642 TCTGAAGTTCTGTATATAGGTTGCCT 59.388 38.462 4.17 0.00 37.71 4.75
2139 6643 8.671987 AGTTCTGTATATAGGTTGCCTATGAT 57.328 34.615 15.75 9.04 45.40 2.45
2149 6653 8.995027 ATAGGTTGCCTATGATAACATTTTGA 57.005 30.769 6.88 0.00 44.30 2.69
2177 6681 1.065854 GGTGTGTTGCCTATGAGCTCT 60.066 52.381 16.19 3.04 0.00 4.09
2186 6690 6.268617 TGTTGCCTATGAGCTCTATCATTACT 59.731 38.462 16.19 0.00 40.40 2.24
2205 6709 8.514594 TCATTACTTTGGCTTCTTTGAAGTATG 58.485 33.333 8.78 0.00 34.06 2.39
2206 6710 8.514594 CATTACTTTGGCTTCTTTGAAGTATGA 58.485 33.333 8.78 0.00 34.06 2.15
2228 6732 8.931385 ATGATTAAATGGATTTCGTTTTCAGG 57.069 30.769 0.00 0.00 36.18 3.86
2250 6754 9.924650 TCAGGTGAGTTCTATTAACTTAAACTC 57.075 33.333 11.87 11.87 43.80 3.01
2258 6762 9.295214 GTTCTATTAACTTAAACTCGGGTAGTC 57.705 37.037 0.00 0.00 37.50 2.59
2263 6767 5.796424 ACTTAAACTCGGGTAGTCTTGAA 57.204 39.130 0.00 0.00 37.50 2.69
2270 6774 3.071479 TCGGGTAGTCTTGAAATGTTGC 58.929 45.455 0.00 0.00 0.00 4.17
2272 6776 3.440173 CGGGTAGTCTTGAAATGTTGCAT 59.560 43.478 0.00 0.00 0.00 3.96
2273 6777 4.082787 CGGGTAGTCTTGAAATGTTGCATT 60.083 41.667 0.00 0.00 0.00 3.56
2274 6778 5.163513 GGGTAGTCTTGAAATGTTGCATTG 58.836 41.667 0.00 0.00 0.00 2.82
2275 6779 4.622740 GGTAGTCTTGAAATGTTGCATTGC 59.377 41.667 0.46 0.46 0.00 3.56
2284 6788 5.345472 TGAAATGTTGCATTGCGTTCTATTG 59.655 36.000 3.84 0.00 0.00 1.90
2290 6794 3.179048 GCATTGCGTTCTATTGTTTCCC 58.821 45.455 0.00 0.00 0.00 3.97
2326 6830 7.878127 TCCTGTTGACTGAAAATAGAGGTAAAG 59.122 37.037 0.00 0.00 0.00 1.85
2332 6836 7.824289 TGACTGAAAATAGAGGTAAAGTCATGG 59.176 37.037 0.00 0.00 38.23 3.66
2358 6870 5.097234 AGGGTAGCTATTCTAGGATGCATT 58.903 41.667 0.00 0.00 0.00 3.56
2360 6872 6.905776 AGGGTAGCTATTCTAGGATGCATTAT 59.094 38.462 0.00 0.00 0.00 1.28
2395 6907 3.751479 TTCAGTCTCTGTTTGCTAGCA 57.249 42.857 14.93 14.93 32.61 3.49
2396 6908 3.309961 TCAGTCTCTGTTTGCTAGCAG 57.690 47.619 18.45 6.43 32.61 4.24
2397 6909 1.731160 CAGTCTCTGTTTGCTAGCAGC 59.269 52.381 18.45 15.06 42.82 5.25
2398 6910 1.622811 AGTCTCTGTTTGCTAGCAGCT 59.377 47.619 18.45 0.00 42.97 4.24
2399 6911 2.828520 AGTCTCTGTTTGCTAGCAGCTA 59.171 45.455 18.45 1.13 42.97 3.32
2400 6912 2.926838 GTCTCTGTTTGCTAGCAGCTAC 59.073 50.000 18.45 16.77 42.97 3.58
2401 6913 2.828520 TCTCTGTTTGCTAGCAGCTACT 59.171 45.455 18.45 0.00 42.97 2.57
2562 7074 2.133195 TGTCTCGTGAGGCAAAGGT 58.867 52.632 0.86 0.00 40.54 3.50
2585 7097 9.783256 AGGTAAAATTGTAATTTTATCAGACGC 57.217 29.630 24.13 12.26 46.74 5.19
2601 7113 3.970610 CAGACGCATTTGTCTTGTTCTTG 59.029 43.478 0.00 0.00 46.85 3.02
2602 7114 3.003689 AGACGCATTTGTCTTGTTCTTGG 59.996 43.478 0.00 0.00 46.85 3.61
2603 7115 2.687935 ACGCATTTGTCTTGTTCTTGGT 59.312 40.909 0.00 0.00 0.00 3.67
2604 7116 3.130340 ACGCATTTGTCTTGTTCTTGGTT 59.870 39.130 0.00 0.00 0.00 3.67
2605 7117 3.730715 CGCATTTGTCTTGTTCTTGGTTC 59.269 43.478 0.00 0.00 0.00 3.62
2606 7118 4.498009 CGCATTTGTCTTGTTCTTGGTTCT 60.498 41.667 0.00 0.00 0.00 3.01
2607 7119 4.741676 GCATTTGTCTTGTTCTTGGTTCTG 59.258 41.667 0.00 0.00 0.00 3.02
2608 7120 4.981806 TTTGTCTTGTTCTTGGTTCTGG 57.018 40.909 0.00 0.00 0.00 3.86
2609 7121 2.297701 TGTCTTGTTCTTGGTTCTGGC 58.702 47.619 0.00 0.00 0.00 4.85
2610 7122 1.609072 GTCTTGTTCTTGGTTCTGGCC 59.391 52.381 0.00 0.00 0.00 5.36
2611 7123 1.494721 TCTTGTTCTTGGTTCTGGCCT 59.505 47.619 3.32 0.00 0.00 5.19
2612 7124 1.882623 CTTGTTCTTGGTTCTGGCCTC 59.117 52.381 3.32 0.00 0.00 4.70
2613 7125 1.140312 TGTTCTTGGTTCTGGCCTCT 58.860 50.000 3.32 0.00 0.00 3.69
2614 7126 1.494721 TGTTCTTGGTTCTGGCCTCTT 59.505 47.619 3.32 0.00 0.00 2.85
2615 7127 2.155279 GTTCTTGGTTCTGGCCTCTTC 58.845 52.381 3.32 0.00 0.00 2.87
2616 7128 1.434188 TCTTGGTTCTGGCCTCTTCA 58.566 50.000 3.32 0.00 0.00 3.02
2617 7129 1.774254 TCTTGGTTCTGGCCTCTTCAA 59.226 47.619 3.32 1.69 0.00 2.69
2618 7130 2.157738 CTTGGTTCTGGCCTCTTCAAG 58.842 52.381 3.32 8.05 0.00 3.02
2631 7143 2.159382 TCTTCAAGGAAATTGTCGGGC 58.841 47.619 0.00 0.00 40.05 6.13
2632 7144 1.885887 CTTCAAGGAAATTGTCGGGCA 59.114 47.619 0.00 0.00 40.05 5.36
2633 7145 1.988293 TCAAGGAAATTGTCGGGCAA 58.012 45.000 0.00 0.00 40.05 4.52
2643 7155 4.701956 ATTGTCGGGCAATTTAAGACTG 57.298 40.909 1.15 0.00 44.82 3.51
2644 7156 2.432444 TGTCGGGCAATTTAAGACTGG 58.568 47.619 0.00 0.00 33.40 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.681733 TCTTGAGAGTGGCAGTGACC 59.318 55.000 0.00 0.00 0.00 4.02
26 28 6.003950 TCCAAAACCTATTTCTTGAGAGTGG 58.996 40.000 0.00 0.00 0.00 4.00
68 70 8.336873 TGGGACAATATTGGCTGAATAACAGAG 61.337 40.741 20.60 0.00 42.31 3.35
69 71 6.580051 TGGGACAATATTGGCTGAATAACAGA 60.580 38.462 20.60 0.00 42.31 3.41
70 72 5.593909 TGGGACAATATTGGCTGAATAACAG 59.406 40.000 20.60 0.00 42.51 3.16
175 187 2.398588 TGGGGCTCAAGTTATCGATCT 58.601 47.619 0.00 0.00 0.00 2.75
176 188 2.910688 TGGGGCTCAAGTTATCGATC 57.089 50.000 0.00 0.00 0.00 3.69
239 675 0.326264 CTGGGTGCTAACTTCCAGCT 59.674 55.000 0.00 0.00 40.04 4.24
376 812 2.738743 CAAATGTGTTCCCAGGGCTAT 58.261 47.619 0.00 0.00 0.00 2.97
403 839 1.523758 AGAAGGAAATGCGCGTCTTT 58.476 45.000 8.43 7.92 0.00 2.52
415 851 3.513912 TCCTTGCATCGAACTAGAAGGAA 59.486 43.478 10.59 0.00 36.80 3.36
467 906 4.834496 TCCAAAGGAATCAATGAAGCTGTT 59.166 37.500 0.00 0.00 0.00 3.16
525 964 6.183360 ACCTCCATATCGTTTCCTCTTCTTAC 60.183 42.308 0.00 0.00 0.00 2.34
599 1038 1.207811 CATTGGATTTGGAAGGGGCAC 59.792 52.381 0.00 0.00 0.00 5.01
877 1316 7.944554 CAGGGAAGGCCTCAAATATATTCTTTA 59.055 37.037 5.23 0.00 0.00 1.85
896 1335 5.126061 CCACCACTTTTCATAATCAGGGAAG 59.874 44.000 0.00 0.00 0.00 3.46
911 1350 1.153756 CCAGGAAGGCCACCACTTT 59.846 57.895 18.84 0.00 36.29 2.66
1033 1472 7.676004 TCCATGACATACTTCTGAACACTTAA 58.324 34.615 0.00 0.00 0.00 1.85
1034 1473 7.239763 TCCATGACATACTTCTGAACACTTA 57.760 36.000 0.00 0.00 0.00 2.24
1200 1639 7.301054 CAACTGTATCCACTTGAAATGAGTTC 58.699 38.462 0.00 0.00 36.70 3.01
1234 1673 3.405831 ACATGTCCATCAACACTGACAG 58.594 45.455 0.00 0.00 40.70 3.51
1247 1686 4.860802 ATACCATCAGGAAACATGTCCA 57.139 40.909 0.00 0.00 40.48 4.02
1299 1738 1.691195 GCAGGGCTACTTCTCCTCCC 61.691 65.000 0.00 0.00 37.24 4.30
1314 1753 2.203538 ACCCCAAGCTTGTGCAGG 60.204 61.111 24.35 19.75 42.74 4.85
1439 1878 4.662468 TCATTAGTGAGAGTCTCCATGC 57.338 45.455 17.57 5.50 0.00 4.06
1441 1880 7.904558 TTGTATCATTAGTGAGAGTCTCCAT 57.095 36.000 17.57 8.41 37.87 3.41
1476 1915 5.181433 GTCAAAACCACCCAATCTTCTAGTC 59.819 44.000 0.00 0.00 0.00 2.59
1679 6178 9.646427 GACATTCAGTTTCTAGAGATAAACACT 57.354 33.333 7.57 0.00 37.92 3.55
1680 6179 8.874816 GGACATTCAGTTTCTAGAGATAAACAC 58.125 37.037 7.57 0.00 37.92 3.32
1681 6180 8.041323 GGGACATTCAGTTTCTAGAGATAAACA 58.959 37.037 7.57 0.00 37.92 2.83
1705 6205 3.139077 GTCACCTCTGTTTACACTTGGG 58.861 50.000 0.00 0.00 0.00 4.12
1706 6206 4.073293 AGTCACCTCTGTTTACACTTGG 57.927 45.455 0.00 0.00 0.00 3.61
1712 6212 3.323979 TCCTCCAAGTCACCTCTGTTTAC 59.676 47.826 0.00 0.00 0.00 2.01
1722 6222 4.223032 TCAGATAAACCTCCTCCAAGTCAC 59.777 45.833 0.00 0.00 0.00 3.67
1726 6226 4.714308 ACTCTCAGATAAACCTCCTCCAAG 59.286 45.833 0.00 0.00 0.00 3.61
1727 6227 4.689062 ACTCTCAGATAAACCTCCTCCAA 58.311 43.478 0.00 0.00 0.00 3.53
1745 6245 9.570468 AATGAATCATATGCTAAATGTGACTCT 57.430 29.630 0.00 0.00 0.00 3.24
1762 6262 7.764443 ACGTACTAGTTAGCAACAATGAATCAT 59.236 33.333 0.00 0.00 0.00 2.45
1795 6295 5.826208 TCTTTGGGTAAAGAAGAACAGGTTC 59.174 40.000 4.00 4.00 46.87 3.62
1807 6307 5.178809 CACGGTAGACTTTCTTTGGGTAAAG 59.821 44.000 0.00 0.00 43.72 1.85
1812 6312 2.224450 ACCACGGTAGACTTTCTTTGGG 60.224 50.000 0.00 0.00 0.00 4.12
1813 6313 3.064931 GACCACGGTAGACTTTCTTTGG 58.935 50.000 0.00 0.00 0.00 3.28
1814 6314 3.064931 GGACCACGGTAGACTTTCTTTG 58.935 50.000 0.00 0.00 0.00 2.77
1851 6352 6.126911 GGAGTTGAGGATGGAAATTAGACTCT 60.127 42.308 0.00 0.00 32.57 3.24
1857 6358 7.010160 AGTTTTGGAGTTGAGGATGGAAATTA 58.990 34.615 0.00 0.00 0.00 1.40
1864 6365 3.152341 AGCAGTTTTGGAGTTGAGGATG 58.848 45.455 0.00 0.00 0.00 3.51
1867 6368 4.137543 AGTAAGCAGTTTTGGAGTTGAGG 58.862 43.478 0.00 0.00 0.00 3.86
1868 6369 5.757850 AAGTAAGCAGTTTTGGAGTTGAG 57.242 39.130 0.00 0.00 0.00 3.02
1871 6372 7.519970 CGATGTTAAGTAAGCAGTTTTGGAGTT 60.520 37.037 0.00 0.00 0.00 3.01
1872 6373 6.073222 CGATGTTAAGTAAGCAGTTTTGGAGT 60.073 38.462 0.00 0.00 0.00 3.85
1873 6374 6.307155 CGATGTTAAGTAAGCAGTTTTGGAG 58.693 40.000 0.00 0.00 0.00 3.86
1874 6375 5.334569 GCGATGTTAAGTAAGCAGTTTTGGA 60.335 40.000 0.00 0.00 0.00 3.53
1875 6376 4.851558 GCGATGTTAAGTAAGCAGTTTTGG 59.148 41.667 0.00 0.00 0.00 3.28
1876 6377 4.851558 GGCGATGTTAAGTAAGCAGTTTTG 59.148 41.667 0.00 0.00 0.00 2.44
1877 6378 4.517453 TGGCGATGTTAAGTAAGCAGTTTT 59.483 37.500 0.00 0.00 0.00 2.43
1878 6379 4.069304 TGGCGATGTTAAGTAAGCAGTTT 58.931 39.130 0.00 0.00 0.00 2.66
1884 6385 5.856126 TTGAGTTGGCGATGTTAAGTAAG 57.144 39.130 0.00 0.00 0.00 2.34
1891 6392 4.522789 ACCTTTATTTGAGTTGGCGATGTT 59.477 37.500 0.00 0.00 0.00 2.71
1916 6417 9.411189 AGGTCTTCTATTACTTTACAGAGGTAG 57.589 37.037 0.00 0.00 0.00 3.18
1917 6418 9.765295 AAGGTCTTCTATTACTTTACAGAGGTA 57.235 33.333 0.00 0.00 0.00 3.08
1918 6419 8.667592 AAGGTCTTCTATTACTTTACAGAGGT 57.332 34.615 0.00 0.00 0.00 3.85
1919 6420 9.945904 AAAAGGTCTTCTATTACTTTACAGAGG 57.054 33.333 0.00 0.00 31.71 3.69
1932 6433 9.702253 TCTGTAGTGATCTAAAAGGTCTTCTAT 57.298 33.333 0.00 0.00 0.00 1.98
1933 6434 9.179909 CTCTGTAGTGATCTAAAAGGTCTTCTA 57.820 37.037 0.00 0.00 0.00 2.10
1934 6435 7.123547 CCTCTGTAGTGATCTAAAAGGTCTTCT 59.876 40.741 0.00 0.00 0.00 2.85
1935 6436 7.262048 CCTCTGTAGTGATCTAAAAGGTCTTC 58.738 42.308 0.00 0.00 0.00 2.87
1936 6437 6.155393 CCCTCTGTAGTGATCTAAAAGGTCTT 59.845 42.308 0.00 0.00 0.00 3.01
1937 6438 5.659079 CCCTCTGTAGTGATCTAAAAGGTCT 59.341 44.000 0.00 0.00 0.00 3.85
1938 6439 5.657302 TCCCTCTGTAGTGATCTAAAAGGTC 59.343 44.000 0.00 0.00 0.00 3.85
1939 6440 5.590818 TCCCTCTGTAGTGATCTAAAAGGT 58.409 41.667 0.00 0.00 0.00 3.50
1940 6441 5.659079 ACTCCCTCTGTAGTGATCTAAAAGG 59.341 44.000 0.00 0.00 0.00 3.11
1941 6442 6.783708 ACTCCCTCTGTAGTGATCTAAAAG 57.216 41.667 0.00 0.00 0.00 2.27
1942 6443 7.411808 AGTACTCCCTCTGTAGTGATCTAAAA 58.588 38.462 0.00 0.00 0.00 1.52
1943 6444 6.971340 AGTACTCCCTCTGTAGTGATCTAAA 58.029 40.000 0.00 0.00 0.00 1.85
1944 6445 6.578313 AGTACTCCCTCTGTAGTGATCTAA 57.422 41.667 0.00 0.00 0.00 2.10
1945 6446 6.845446 AGTAGTACTCCCTCTGTAGTGATCTA 59.155 42.308 0.00 0.00 0.00 1.98
1946 6447 5.668535 AGTAGTACTCCCTCTGTAGTGATCT 59.331 44.000 0.00 0.00 0.00 2.75
1947 6448 5.761234 CAGTAGTACTCCCTCTGTAGTGATC 59.239 48.000 0.00 0.00 0.00 2.92
1948 6449 5.429109 TCAGTAGTACTCCCTCTGTAGTGAT 59.571 44.000 0.00 0.00 0.00 3.06
1949 6450 4.781621 TCAGTAGTACTCCCTCTGTAGTGA 59.218 45.833 0.00 0.00 0.00 3.41
1950 6451 5.100344 TCAGTAGTACTCCCTCTGTAGTG 57.900 47.826 0.00 0.00 0.00 2.74
1951 6452 5.775813 TTCAGTAGTACTCCCTCTGTAGT 57.224 43.478 0.00 0.00 0.00 2.73
1952 6453 6.358178 TGATTCAGTAGTACTCCCTCTGTAG 58.642 44.000 0.00 0.00 0.00 2.74
1953 6454 6.323210 TGATTCAGTAGTACTCCCTCTGTA 57.677 41.667 0.00 0.00 0.00 2.74
1954 6455 5.194473 TGATTCAGTAGTACTCCCTCTGT 57.806 43.478 0.00 0.00 0.00 3.41
1955 6456 5.419155 TGTTGATTCAGTAGTACTCCCTCTG 59.581 44.000 0.00 4.92 0.00 3.35
1956 6457 5.580998 TGTTGATTCAGTAGTACTCCCTCT 58.419 41.667 0.00 0.00 0.00 3.69
1957 6458 5.419471 ACTGTTGATTCAGTAGTACTCCCTC 59.581 44.000 0.00 0.00 45.31 4.30
1958 6459 5.186021 CACTGTTGATTCAGTAGTACTCCCT 59.814 44.000 0.00 0.00 45.37 4.20
1959 6460 5.047235 ACACTGTTGATTCAGTAGTACTCCC 60.047 44.000 0.00 0.00 45.37 4.30
1960 6461 5.864474 CACACTGTTGATTCAGTAGTACTCC 59.136 44.000 0.00 0.00 45.37 3.85
1961 6462 6.363626 CACACACTGTTGATTCAGTAGTACTC 59.636 42.308 0.00 0.00 45.37 2.59
1962 6463 6.183360 ACACACACTGTTGATTCAGTAGTACT 60.183 38.462 0.00 0.00 45.37 2.73
1963 6464 5.983720 ACACACACTGTTGATTCAGTAGTAC 59.016 40.000 0.00 0.00 45.37 2.73
1964 6465 5.983118 CACACACACTGTTGATTCAGTAGTA 59.017 40.000 0.00 0.00 45.37 1.82
1965 6466 4.811024 CACACACACTGTTGATTCAGTAGT 59.189 41.667 0.00 0.58 45.37 2.73
1981 6482 3.148412 CATCATCCCAAACTCACACACA 58.852 45.455 0.00 0.00 0.00 3.72
2018 6519 8.506437 GTCATCACTTAAACAATCAGATCACAA 58.494 33.333 0.00 0.00 0.00 3.33
2021 6522 8.671028 CATGTCATCACTTAAACAATCAGATCA 58.329 33.333 0.00 0.00 0.00 2.92
2079 6580 3.820557 ACAAGAGTACAAATGCAGGTGT 58.179 40.909 9.73 9.73 0.00 4.16
2080 6581 4.836125 AACAAGAGTACAAATGCAGGTG 57.164 40.909 0.00 0.00 0.00 4.00
2081 6582 6.003950 ACATAACAAGAGTACAAATGCAGGT 58.996 36.000 0.00 0.00 0.00 4.00
2082 6583 6.500684 ACATAACAAGAGTACAAATGCAGG 57.499 37.500 0.00 0.00 0.00 4.85
2110 6614 6.821388 AGGCAACCTATATACAGAACTTCAG 58.179 40.000 0.00 0.00 28.47 3.02
2113 6617 8.492415 TCATAGGCAACCTATATACAGAACTT 57.508 34.615 5.84 0.00 44.19 2.66
2124 6628 8.995027 TCAAAATGTTATCATAGGCAACCTAT 57.005 30.769 0.10 0.10 46.66 2.57
2131 6635 7.573968 AGAACCTCAAAATGTTATCATAGGC 57.426 36.000 0.00 0.00 32.32 3.93
2134 6638 8.739039 CACCAAGAACCTCAAAATGTTATCATA 58.261 33.333 0.00 0.00 33.49 2.15
2139 6643 5.654650 ACACACCAAGAACCTCAAAATGTTA 59.345 36.000 0.00 0.00 0.00 2.41
2149 6653 0.258774 AGGCAACACACCAAGAACCT 59.741 50.000 0.00 0.00 41.41 3.50
2177 6681 8.635765 ACTTCAAAGAAGCCAAAGTAATGATA 57.364 30.769 6.67 0.00 0.00 2.15
2205 6709 8.026607 TCACCTGAAAACGAAATCCATTTAATC 58.973 33.333 0.00 0.00 0.00 1.75
2206 6710 7.891561 TCACCTGAAAACGAAATCCATTTAAT 58.108 30.769 0.00 0.00 0.00 1.40
2228 6732 7.816513 ACCCGAGTTTAAGTTAATAGAACTCAC 59.183 37.037 18.55 4.60 43.85 3.51
2248 6752 3.125316 GCAACATTTCAAGACTACCCGAG 59.875 47.826 0.00 0.00 0.00 4.63
2250 6754 2.811431 TGCAACATTTCAAGACTACCCG 59.189 45.455 0.00 0.00 0.00 5.28
2258 6762 3.737266 AGAACGCAATGCAACATTTCAAG 59.263 39.130 5.91 0.00 0.00 3.02
2263 6767 4.808558 ACAATAGAACGCAATGCAACATT 58.191 34.783 5.91 0.00 0.00 2.71
2270 6774 4.701956 AGGGAAACAATAGAACGCAATG 57.298 40.909 0.00 0.00 0.00 2.82
2272 6776 3.504520 GGAAGGGAAACAATAGAACGCAA 59.495 43.478 0.00 0.00 0.00 4.85
2273 6777 3.078837 GGAAGGGAAACAATAGAACGCA 58.921 45.455 0.00 0.00 0.00 5.24
2274 6778 3.078837 TGGAAGGGAAACAATAGAACGC 58.921 45.455 0.00 0.00 0.00 4.84
2275 6779 6.995511 TTATGGAAGGGAAACAATAGAACG 57.004 37.500 0.00 0.00 0.00 3.95
2284 6788 5.714806 TCAACAGGAATTATGGAAGGGAAAC 59.285 40.000 0.00 0.00 0.00 2.78
2290 6794 7.452880 TTTCAGTCAACAGGAATTATGGAAG 57.547 36.000 0.00 0.00 0.00 3.46
2326 6830 3.648545 AGAATAGCTACCCTTCCCATGAC 59.351 47.826 0.00 0.00 0.00 3.06
2332 6836 4.081365 GCATCCTAGAATAGCTACCCTTCC 60.081 50.000 0.00 0.00 37.37 3.46
2358 6870 5.822519 AGACTGAAAGACACAACAAGCAATA 59.177 36.000 0.00 0.00 37.43 1.90
2360 6872 4.009675 AGACTGAAAGACACAACAAGCAA 58.990 39.130 0.00 0.00 37.43 3.91
2422 6934 5.937975 ATATAAACAGCAAAGGCCACAAT 57.062 34.783 5.01 0.00 42.56 2.71
2456 6968 8.669243 CAGAAATATAAACAGTTCTCACTTCCC 58.331 37.037 0.00 0.00 0.00 3.97
2522 7034 8.587608 AGACAAATGCTGAAAATTCTGGAATTA 58.412 29.630 8.69 0.00 39.88 1.40
2577 7089 4.067896 AGAACAAGACAAATGCGTCTGAT 58.932 39.130 0.00 0.00 45.56 2.90
2585 7097 5.284079 CCAGAACCAAGAACAAGACAAATG 58.716 41.667 0.00 0.00 0.00 2.32
2601 7113 0.693049 TCCTTGAAGAGGCCAGAACC 59.307 55.000 5.01 0.00 45.87 3.62
2602 7114 2.568623 TTCCTTGAAGAGGCCAGAAC 57.431 50.000 5.01 0.00 45.87 3.01
2603 7115 3.814504 ATTTCCTTGAAGAGGCCAGAA 57.185 42.857 5.01 0.00 45.87 3.02
2604 7116 3.181429 ACAATTTCCTTGAAGAGGCCAGA 60.181 43.478 5.01 0.00 45.87 3.86
2605 7117 3.160269 ACAATTTCCTTGAAGAGGCCAG 58.840 45.455 5.01 0.00 45.87 4.85
2606 7118 3.157087 GACAATTTCCTTGAAGAGGCCA 58.843 45.455 5.01 0.00 45.87 5.36
2607 7119 2.162408 CGACAATTTCCTTGAAGAGGCC 59.838 50.000 0.00 0.00 45.87 5.19
2608 7120 2.162408 CCGACAATTTCCTTGAAGAGGC 59.838 50.000 0.00 0.00 45.87 4.70
2610 7122 2.162408 GCCCGACAATTTCCTTGAAGAG 59.838 50.000 0.00 0.00 38.29 2.85
2611 7123 2.159382 GCCCGACAATTTCCTTGAAGA 58.841 47.619 0.00 0.00 38.29 2.87
2612 7124 1.885887 TGCCCGACAATTTCCTTGAAG 59.114 47.619 0.00 0.00 38.29 3.02
2613 7125 1.988293 TGCCCGACAATTTCCTTGAA 58.012 45.000 0.00 0.00 38.29 2.69
2614 7126 1.988293 TTGCCCGACAATTTCCTTGA 58.012 45.000 0.00 0.00 38.29 3.02
2623 7135 2.817258 CCAGTCTTAAATTGCCCGACAA 59.183 45.455 0.00 0.00 44.01 3.18
2624 7136 2.432444 CCAGTCTTAAATTGCCCGACA 58.568 47.619 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.