Multiple sequence alignment - TraesCS2B01G529200

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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 TraesCS2B01G529200 chr2B 100.000 2582 0 0 1 2582 723961757 723964338 0.000000e+00 4769
1 TraesCS2B01G529200 chr2B 86.486 111 14 1 2330 2439 724344448 724344558 1.250000e-23 121
2 TraesCS2B01G529200 chr2D 88.880 2581 233 31 1 2571 595660344 595657808 0.000000e+00 3127
3 TraesCS2B01G529200 chr2A 88.798 2571 239 22 11 2571 729628377 729625846 0.000000e+00 3107
4 TraesCS2B01G529200 chr1B 88.559 236 27 0 1049 1284 451134315 451134550 1.170000e-73 287
5 TraesCS2B01G529200 chr1A 88.559 236 27 0 1049 1284 432852158 432852393 1.170000e-73 287
6 TraesCS2B01G529200 chr1D 87.288 236 30 0 1049 1284 335287181 335287416 1.180000e-68 270


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 TraesCS2B01G529200 chr2B 723961757 723964338 2581 False 4769 4769 100.000 1 2582 1 chr2B.!!$F1 2581
1 TraesCS2B01G529200 chr2D 595657808 595660344 2536 True 3127 3127 88.880 1 2571 1 chr2D.!!$R1 2570
2 TraesCS2B01G529200 chr2A 729625846 729628377 2531 True 3107 3107 88.798 11 2571 1 chr2A.!!$R1 2560

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
873 878 0.108585 ATCTCCACCACACGTTGCTT 59.891 50.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 1686 0.171231 CAACGAGATCTGCAGACCGA 59.829 55.0 29.55 8.65 0.0 4.69 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
78 79 3.261933 GCAAGGAGCAGCAGTCAC 58.738 61.111 0.00 0.00 44.79 3.67
107 108 4.007457 GCAAGGAGCAGCAATGGA 57.993 55.556 0.00 0.00 44.79 3.41
111 112 0.251474 AAGGAGCAGCAATGGAAGCA 60.251 50.000 0.00 0.00 0.00 3.91
173 174 3.181367 GCAGTAGCAGCGCATGTT 58.819 55.556 11.47 5.78 41.58 2.71
174 175 1.503542 GCAGTAGCAGCGCATGTTT 59.496 52.632 11.47 1.13 41.58 2.83
175 176 0.726827 GCAGTAGCAGCGCATGTTTA 59.273 50.000 11.47 0.19 41.58 2.01
176 177 1.529826 GCAGTAGCAGCGCATGTTTAC 60.530 52.381 11.47 11.59 41.58 2.01
177 178 1.731709 CAGTAGCAGCGCATGTTTACA 59.268 47.619 11.47 0.00 0.00 2.41
178 179 2.159430 CAGTAGCAGCGCATGTTTACAA 59.841 45.455 11.47 0.00 0.00 2.41
179 180 2.416547 AGTAGCAGCGCATGTTTACAAG 59.583 45.455 11.47 0.00 0.00 3.16
180 181 0.109597 AGCAGCGCATGTTTACAAGC 60.110 50.000 11.47 0.26 37.23 4.01
181 182 0.109597 GCAGCGCATGTTTACAAGCT 60.110 50.000 11.47 6.75 38.31 3.74
182 183 1.130373 GCAGCGCATGTTTACAAGCTA 59.870 47.619 11.47 0.00 38.31 3.32
183 184 2.223340 GCAGCGCATGTTTACAAGCTAT 60.223 45.455 11.47 0.00 38.31 2.97
184 185 3.002246 GCAGCGCATGTTTACAAGCTATA 59.998 43.478 11.47 0.00 38.31 1.31
185 186 4.766007 CAGCGCATGTTTACAAGCTATAG 58.234 43.478 11.47 0.00 38.31 1.31
186 187 4.271049 CAGCGCATGTTTACAAGCTATAGT 59.729 41.667 11.47 0.00 38.31 2.12
187 188 5.462068 CAGCGCATGTTTACAAGCTATAGTA 59.538 40.000 11.47 0.00 38.31 1.82
188 189 5.692204 AGCGCATGTTTACAAGCTATAGTAG 59.308 40.000 11.47 0.00 38.31 2.57
204 205 0.804544 GTAGCAACGACGCATGGCTA 60.805 55.000 0.00 0.36 36.10 3.93
234 236 4.402528 CCGGCGGTGGACCAATCA 62.403 66.667 19.97 0.00 35.14 2.57
238 240 2.100631 GCGGTGGACCAATCAGACG 61.101 63.158 0.00 0.00 35.14 4.18
244 246 1.338674 TGGACCAATCAGACGCGATTT 60.339 47.619 15.93 0.00 33.27 2.17
253 255 7.226720 ACCAATCAGACGCGATTTCTTTATTAT 59.773 33.333 15.93 0.00 33.27 1.28
264 266 8.534778 GCGATTTCTTTATTATTTTCTTGGCAG 58.465 33.333 0.00 0.00 0.00 4.85
265 267 9.787532 CGATTTCTTTATTATTTTCTTGGCAGA 57.212 29.630 0.00 0.00 0.00 4.26
284 286 5.220815 GGCAGAGACTTGATTGCTTTCTATG 60.221 44.000 0.00 0.00 36.79 2.23
288 290 8.176365 CAGAGACTTGATTGCTTTCTATGAAAG 58.824 37.037 13.77 13.77 28.87 2.62
290 292 8.804912 AGACTTGATTGCTTTCTATGAAAGAT 57.195 30.769 20.17 8.51 33.05 2.40
300 302 5.373812 TTCTATGAAAGATTCAGGGACCC 57.626 43.478 0.59 0.59 43.98 4.46
301 303 4.370776 TCTATGAAAGATTCAGGGACCCA 58.629 43.478 14.60 0.00 43.98 4.51
303 305 3.154827 TGAAAGATTCAGGGACCCAAC 57.845 47.619 14.60 0.00 34.08 3.77
363 367 1.076995 GCCCCACCTGTCATAACCC 60.077 63.158 0.00 0.00 0.00 4.11
403 407 3.561143 TGGTGTTGACTTTTATGCCACT 58.439 40.909 0.00 0.00 0.00 4.00
409 413 5.592282 TGTTGACTTTTATGCCACTTCAGAA 59.408 36.000 0.00 0.00 0.00 3.02
410 414 5.689383 TGACTTTTATGCCACTTCAGAAC 57.311 39.130 0.00 0.00 0.00 3.01
411 415 5.376625 TGACTTTTATGCCACTTCAGAACT 58.623 37.500 0.00 0.00 0.00 3.01
419 423 1.616865 CCACTTCAGAACTGACGGGTA 59.383 52.381 11.76 0.00 39.66 3.69
422 426 2.557490 ACTTCAGAACTGACGGGTAGAC 59.443 50.000 11.76 0.00 39.66 2.59
477 481 4.168922 ACACACTCATCAATGCAACATG 57.831 40.909 0.00 0.00 0.00 3.21
560 564 1.954382 GTTTTTCGGAACCCTTGCTCT 59.046 47.619 0.00 0.00 0.00 4.09
562 566 2.467566 TTTCGGAACCCTTGCTCTAC 57.532 50.000 0.00 0.00 0.00 2.59
565 569 2.811410 TCGGAACCCTTGCTCTACTTA 58.189 47.619 0.00 0.00 0.00 2.24
622 627 6.152323 CCATGAATGAAATGTCCAAAGAGACT 59.848 38.462 0.00 0.00 37.66 3.24
671 676 1.280133 AGCGAGCCATGCCATATGTAT 59.720 47.619 1.24 0.00 0.00 2.29
700 705 0.668535 GGAAACCAGGTGTGAGTTGC 59.331 55.000 0.00 0.00 0.00 4.17
701 706 1.388547 GAAACCAGGTGTGAGTTGCA 58.611 50.000 0.00 0.00 0.00 4.08
708 713 2.666190 TGTGAGTTGCAGAGGCGC 60.666 61.111 0.00 0.00 45.35 6.53
724 729 2.725699 CGCGACACTTGCATGCGTA 61.726 57.895 14.09 2.39 43.50 4.42
737 742 0.599558 ATGCGTACACACCTACACGT 59.400 50.000 0.00 0.00 36.78 4.49
772 777 3.052455 ACGCATGGAGAACACATGTAA 57.948 42.857 0.00 0.00 45.68 2.41
774 779 3.188460 ACGCATGGAGAACACATGTAAAC 59.812 43.478 0.00 0.00 45.68 2.01
779 784 3.064207 GGAGAACACATGTAAACGCTCA 58.936 45.455 0.00 0.00 0.00 4.26
781 786 3.728845 AGAACACATGTAAACGCTCACT 58.271 40.909 0.00 0.00 0.00 3.41
784 789 3.462982 ACACATGTAAACGCTCACTCAA 58.537 40.909 0.00 0.00 0.00 3.02
829 834 0.463295 TCGCTGACCGAGGTAGGTAG 60.463 60.000 0.00 0.00 46.09 3.18
849 854 3.095163 CAGCCCCTCCAGATGCCT 61.095 66.667 0.00 0.00 0.00 4.75
850 855 2.286732 AGCCCCTCCAGATGCCTT 60.287 61.111 0.00 0.00 0.00 4.35
854 859 1.565390 CCCCTCCAGATGCCTTGTCA 61.565 60.000 0.00 0.00 0.00 3.58
873 878 0.108585 ATCTCCACCACACGTTGCTT 59.891 50.000 0.00 0.00 0.00 3.91
875 880 0.813610 CTCCACCACACGTTGCTTCA 60.814 55.000 0.00 0.00 0.00 3.02
893 898 4.037684 GCTTCATCCCTACACGTATGTACT 59.962 45.833 0.00 0.00 40.48 2.73
918 923 0.737219 GCAGTCTTCCATGCCATCAC 59.263 55.000 0.00 0.00 36.41 3.06
955 960 0.618968 GTGTCCATGGACCCTCTCCT 60.619 60.000 36.27 0.00 43.97 3.69
959 964 1.395826 CCATGGACCCTCTCCTCGAC 61.396 65.000 5.56 0.00 40.26 4.20
969 974 0.984995 TCTCCTCGACCAGAGTCAGA 59.015 55.000 0.00 0.00 45.44 3.27
978 983 1.177401 CCAGAGTCAGACGACATCCA 58.823 55.000 0.00 0.00 45.23 3.41
990 995 1.676916 CGACATCCATCTGCCACAGTT 60.677 52.381 0.00 0.00 32.61 3.16
998 1003 5.368145 TCCATCTGCCACAGTTATATCAAC 58.632 41.667 0.00 0.00 32.61 3.18
1014 1019 4.669206 ATCAACAATGAAGCAAACACCA 57.331 36.364 0.00 0.00 39.49 4.17
1018 1023 1.032014 AATGAAGCAAACACCAGCGT 58.968 45.000 0.00 0.00 35.48 5.07
1022 1027 3.276846 GCAAACACCAGCGTCGGT 61.277 61.111 0.00 0.00 41.07 4.69
1029 1034 2.280524 CCAGCGTCGGTGAACCAA 60.281 61.111 25.16 0.00 35.14 3.67
1032 1037 1.153329 AGCGTCGGTGAACCAACAA 60.153 52.632 0.00 0.00 35.14 2.83
1042 1047 4.394729 GGTGAACCAACAACAGAATAGGA 58.605 43.478 0.00 0.00 35.64 2.94
1043 1048 4.825085 GGTGAACCAACAACAGAATAGGAA 59.175 41.667 0.00 0.00 35.64 3.36
1047 1052 3.244422 ACCAACAACAGAATAGGAAGCGA 60.244 43.478 0.00 0.00 0.00 4.93
1062 1067 2.202932 CGATGCTTCCCACTCCGG 60.203 66.667 0.00 0.00 0.00 5.14
1239 1244 4.649954 GATGCCGCACGCGCATAC 62.650 66.667 5.73 10.00 42.08 2.39
1272 1277 1.517832 GGCGCTCTATGGTGACTGT 59.482 57.895 7.64 0.00 0.00 3.55
1284 1289 1.071299 TGACTGTGCACGCCTCAAT 59.929 52.632 13.13 0.00 0.00 2.57
1303 1308 3.185203 TGGCAGCACCTCCCCTTT 61.185 61.111 0.00 0.00 40.22 3.11
1304 1309 2.118294 GGCAGCACCTCCCCTTTT 59.882 61.111 0.00 0.00 34.51 2.27
1371 1376 3.900892 CCGGCTCGTAGCACCGAT 61.901 66.667 1.58 0.00 46.10 4.18
1374 1379 1.783031 CGGCTCGTAGCACCGATACT 61.783 60.000 8.71 0.00 46.10 2.12
1386 1391 2.997986 CACCGATACTAACAACACCACC 59.002 50.000 0.00 0.00 0.00 4.61
1392 1397 1.413445 ACTAACAACACCACCGCACTA 59.587 47.619 0.00 0.00 0.00 2.74
1394 1399 2.843401 AACAACACCACCGCACTATA 57.157 45.000 0.00 0.00 0.00 1.31
1399 1404 1.753073 ACACCACCGCACTATACTACC 59.247 52.381 0.00 0.00 0.00 3.18
1409 1414 4.161102 GCACTATACTACCCCTCCTCAAT 58.839 47.826 0.00 0.00 0.00 2.57
1422 1427 0.389817 CCTCAATCTCAACGGCGTCA 60.390 55.000 15.17 1.51 0.00 4.35
1437 1442 1.895231 GTCAACGACAACCCCCACC 60.895 63.158 0.00 0.00 32.09 4.61
1438 1443 2.073716 TCAACGACAACCCCCACCT 61.074 57.895 0.00 0.00 0.00 4.00
1445 1450 0.402272 ACAACCCCCACCTACTTGGA 60.402 55.000 0.00 0.00 39.24 3.53
1479 1484 4.260139 TGAGTGGTCTTATTACAACGCA 57.740 40.909 0.00 0.00 31.59 5.24
1520 1525 1.412710 GGACTTCGAGGCATATGTGGA 59.587 52.381 4.29 0.00 0.00 4.02
1578 1583 1.639722 TTCAGGAGGTGATGGACGAA 58.360 50.000 0.00 0.00 34.17 3.85
1584 1589 2.484889 GAGGTGATGGACGAATAAGGC 58.515 52.381 0.00 0.00 0.00 4.35
1604 1609 1.069823 CGGAGGAGGGATCAACATCTG 59.930 57.143 0.00 0.00 0.00 2.90
1607 1612 0.475906 GGAGGGATCAACATCTGGGG 59.524 60.000 0.00 0.00 0.00 4.96
1628 1633 0.752658 CCCACCATCGCATCTGAGTA 59.247 55.000 0.00 0.00 0.00 2.59
1629 1634 1.138859 CCCACCATCGCATCTGAGTAA 59.861 52.381 0.00 0.00 0.00 2.24
1658 1663 3.933048 ATGGCTTGCAGGCGCTTCT 62.933 57.895 15.24 0.00 44.78 2.85
1672 1677 1.871126 GCTTCTTCCTGCAGCAACCC 61.871 60.000 8.66 0.00 35.04 4.11
1681 1686 0.467844 TGCAGCAACCCAGTTCATGT 60.468 50.000 0.00 0.00 0.00 3.21
1683 1688 0.518636 CAGCAACCCAGTTCATGTCG 59.481 55.000 0.00 0.00 0.00 4.35
1759 1764 7.229581 AGAAAAGTATATACTCCATCGGTCC 57.770 40.000 15.72 0.00 34.99 4.46
1763 1768 5.747342 AGTATATACTCCATCGGTCCTCTC 58.253 45.833 9.71 0.00 0.00 3.20
1766 1771 1.770294 ACTCCATCGGTCCTCTCTTC 58.230 55.000 0.00 0.00 0.00 2.87
1768 1773 0.631753 TCCATCGGTCCTCTCTTCCT 59.368 55.000 0.00 0.00 0.00 3.36
1770 1775 1.957877 CCATCGGTCCTCTCTTCCTAC 59.042 57.143 0.00 0.00 0.00 3.18
1773 1778 3.453059 TCGGTCCTCTCTTCCTACTTT 57.547 47.619 0.00 0.00 0.00 2.66
1777 1782 3.579151 GGTCCTCTCTTCCTACTTTGTGT 59.421 47.826 0.00 0.00 0.00 3.72
1796 1801 4.449405 TGTGTGTGTTGTATATGTTGGTCG 59.551 41.667 0.00 0.00 0.00 4.79
1799 1804 6.532302 GTGTGTGTTGTATATGTTGGTCGATA 59.468 38.462 0.00 0.00 0.00 2.92
1803 1808 9.819267 TGTGTTGTATATGTTGGTCGATATAAA 57.181 29.630 0.00 0.00 0.00 1.40
1814 1819 6.740944 TGGTCGATATAAATCTTGGAAGGA 57.259 37.500 0.00 0.00 0.00 3.36
1815 1820 7.316393 TGGTCGATATAAATCTTGGAAGGAT 57.684 36.000 0.00 0.00 0.00 3.24
1853 1858 2.744202 GGTCGATGAATATGCATCACCC 59.256 50.000 21.37 15.98 43.76 4.61
1873 1878 3.192001 CCCCATCTTGGCATAAATGATCG 59.808 47.826 6.00 0.00 35.79 3.69
1875 1880 4.155462 CCCATCTTGGCATAAATGATCGAG 59.845 45.833 0.00 0.00 35.79 4.04
1878 1883 2.238942 TGGCATAAATGATCGAGCGT 57.761 45.000 0.00 0.00 0.00 5.07
1889 1894 1.663643 GATCGAGCGTACATTTTGGCA 59.336 47.619 0.00 0.00 0.00 4.92
1890 1895 1.732941 TCGAGCGTACATTTTGGCAT 58.267 45.000 0.00 0.00 0.00 4.40
1903 1908 7.345422 ACATTTTGGCATGCATAGTACATTA 57.655 32.000 21.36 0.00 0.00 1.90
1964 1969 1.484240 TGCATCCCACATGTCGATGTA 59.516 47.619 23.75 19.72 41.12 2.29
1965 1970 1.867233 GCATCCCACATGTCGATGTAC 59.133 52.381 23.75 11.59 41.12 2.90
1972 1977 1.277842 ACATGTCGATGTACCAAGGCA 59.722 47.619 0.00 0.00 41.27 4.75
1981 1986 0.464554 GTACCAAGGCATCCTCCTGC 60.465 60.000 0.00 0.00 41.53 4.85
1989 1994 1.340405 GGCATCCTCCTGCTTTCTCAA 60.340 52.381 0.00 0.00 41.95 3.02
2003 2008 7.389884 CCTGCTTTCTCAAGTATGCATATATGT 59.610 37.037 10.16 0.00 31.86 2.29
2004 2009 8.681486 TGCTTTCTCAAGTATGCATATATGTT 57.319 30.769 10.16 5.26 31.86 2.71
2009 2014 9.836864 TTCTCAAGTATGCATATATGTTCACTT 57.163 29.630 10.16 15.27 0.00 3.16
2040 2045 5.243954 GGAGGTAAGGGCATTTCCAATAATC 59.756 44.000 10.18 0.00 36.21 1.75
2041 2046 6.030727 AGGTAAGGGCATTTCCAATAATCT 57.969 37.500 10.18 0.00 36.21 2.40
2042 2047 6.443832 AGGTAAGGGCATTTCCAATAATCTT 58.556 36.000 10.18 0.00 36.21 2.40
2043 2048 7.591821 AGGTAAGGGCATTTCCAATAATCTTA 58.408 34.615 10.18 0.00 36.21 2.10
2069 2074 7.961351 TGGGAATAAATTGTGTGAACTTGAAT 58.039 30.769 0.00 0.00 0.00 2.57
2072 2077 9.132521 GGAATAAATTGTGTGAACTTGAATCAG 57.867 33.333 0.00 0.00 0.00 2.90
2166 2176 2.031314 CCAATGCTCTAACATGTGCTCG 59.969 50.000 0.00 0.00 0.00 5.03
2173 2183 4.106029 TCTAACATGTGCTCGGTCTAAC 57.894 45.455 0.00 0.00 0.00 2.34
2174 2184 2.831685 AACATGTGCTCGGTCTAACA 57.168 45.000 0.00 0.00 0.00 2.41
2200 2210 8.004215 ACATGCCACCTAGATAAAAATCCAATA 58.996 33.333 0.00 0.00 0.00 1.90
2227 2237 7.064134 TGACACCATATTTAATGAGACACGAAC 59.936 37.037 0.00 0.00 0.00 3.95
2230 2240 8.450964 CACCATATTTAATGAGACACGAACTTT 58.549 33.333 0.00 0.00 0.00 2.66
2319 2329 0.579630 TGCACTGCGTCTAAAACACG 59.420 50.000 0.00 0.00 40.35 4.49
2343 2353 6.397998 CGTCATCTCAATAGAAATCTAACGCG 60.398 42.308 3.53 3.53 34.73 6.01
2344 2354 5.920840 TCATCTCAATAGAAATCTAACGCGG 59.079 40.000 12.47 0.00 34.73 6.46
2360 2370 3.146066 ACGCGGCACCATATTTAATGAT 58.854 40.909 12.47 0.00 0.00 2.45
2405 2415 8.232913 TCTTAGTTCTTAGCACAAAAACCAAT 57.767 30.769 0.00 0.00 0.00 3.16
2500 2512 7.925993 TCATTTCACGAAACAAGATACAACTT 58.074 30.769 0.00 0.00 32.51 2.66
2502 2514 9.019764 CATTTCACGAAACAAGATACAACTTTT 57.980 29.630 0.00 0.00 32.51 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 4.711949 ACTGCTGCTCCTTGCCCG 62.712 66.667 0.00 0.00 42.00 6.13
99 100 2.629656 GCCGTGTGCTTCCATTGCT 61.630 57.895 0.00 0.00 36.87 3.91
180 181 2.980476 CCATGCGTCGTTGCTACTATAG 59.020 50.000 0.00 0.00 35.36 1.31
181 182 2.860971 GCCATGCGTCGTTGCTACTATA 60.861 50.000 0.00 0.00 35.36 1.31
182 183 1.852942 CCATGCGTCGTTGCTACTAT 58.147 50.000 0.00 0.00 35.36 2.12
183 184 0.804544 GCCATGCGTCGTTGCTACTA 60.805 55.000 0.00 0.00 35.36 1.82
184 185 2.100631 GCCATGCGTCGTTGCTACT 61.101 57.895 0.00 0.00 35.36 2.57
185 186 0.804544 TAGCCATGCGTCGTTGCTAC 60.805 55.000 0.00 0.00 33.63 3.58
186 187 0.804544 GTAGCCATGCGTCGTTGCTA 60.805 55.000 0.00 0.00 33.63 3.49
187 188 2.100631 GTAGCCATGCGTCGTTGCT 61.101 57.895 0.00 0.00 36.11 3.91
188 189 1.906994 TTGTAGCCATGCGTCGTTGC 61.907 55.000 0.00 0.00 0.00 4.17
189 190 0.095245 CTTGTAGCCATGCGTCGTTG 59.905 55.000 0.00 0.00 0.00 4.10
190 191 1.019278 CCTTGTAGCCATGCGTCGTT 61.019 55.000 0.00 0.00 0.00 3.85
191 192 1.447838 CCTTGTAGCCATGCGTCGT 60.448 57.895 0.00 0.00 0.00 4.34
192 193 1.148157 CTCCTTGTAGCCATGCGTCG 61.148 60.000 0.00 0.00 0.00 5.12
193 194 1.432270 GCTCCTTGTAGCCATGCGTC 61.432 60.000 0.00 0.00 36.45 5.19
194 195 1.450312 GCTCCTTGTAGCCATGCGT 60.450 57.895 0.00 0.00 36.45 5.24
195 196 1.434622 CTGCTCCTTGTAGCCATGCG 61.435 60.000 0.00 0.00 42.05 4.73
196 197 1.722636 GCTGCTCCTTGTAGCCATGC 61.723 60.000 0.00 0.00 46.56 4.06
197 198 2.401967 GCTGCTCCTTGTAGCCATG 58.598 57.895 0.00 0.00 46.56 3.66
198 199 4.972875 GCTGCTCCTTGTAGCCAT 57.027 55.556 0.00 0.00 46.56 4.40
231 233 9.651718 GAAAATAATAAAGAAATCGCGTCTGAT 57.348 29.630 5.77 0.00 0.00 2.90
232 234 8.879759 AGAAAATAATAAAGAAATCGCGTCTGA 58.120 29.630 5.77 0.00 0.00 3.27
234 236 9.490663 CAAGAAAATAATAAAGAAATCGCGTCT 57.509 29.630 5.77 0.00 0.00 4.18
238 240 8.406172 TGCCAAGAAAATAATAAAGAAATCGC 57.594 30.769 0.00 0.00 0.00 4.58
244 246 9.520515 AAGTCTCTGCCAAGAAAATAATAAAGA 57.479 29.630 0.00 0.00 30.03 2.52
253 255 4.261741 GCAATCAAGTCTCTGCCAAGAAAA 60.262 41.667 0.00 0.00 30.03 2.29
264 266 8.261492 TCTTTCATAGAAAGCAATCAAGTCTC 57.739 34.615 13.23 0.00 0.00 3.36
265 267 8.804912 ATCTTTCATAGAAAGCAATCAAGTCT 57.195 30.769 13.23 0.00 36.22 3.24
266 268 9.500864 GAATCTTTCATAGAAAGCAATCAAGTC 57.499 33.333 13.23 2.64 36.22 3.01
284 286 3.084786 CAGTTGGGTCCCTGAATCTTTC 58.915 50.000 10.00 0.00 0.00 2.62
288 290 0.329596 AGCAGTTGGGTCCCTGAATC 59.670 55.000 10.00 0.00 0.00 2.52
290 292 0.555769 AAAGCAGTTGGGTCCCTGAA 59.444 50.000 10.00 0.00 0.00 3.02
338 342 1.984026 GACAGGTGGGGCCCAAATG 60.984 63.158 30.70 29.14 38.26 2.32
363 367 3.056891 ACCATTAGTTTTGGCCATTGACG 60.057 43.478 6.09 0.00 37.81 4.35
403 407 1.891150 GGTCTACCCGTCAGTTCTGAA 59.109 52.381 3.99 0.00 0.00 3.02
419 423 1.202533 CGATTATGGCAGAACGGGTCT 60.203 52.381 0.00 0.00 36.88 3.85
422 426 0.937304 CACGATTATGGCAGAACGGG 59.063 55.000 16.69 11.40 0.00 5.28
452 456 4.161333 GTTGCATTGATGAGTGTGTTAGC 58.839 43.478 0.00 0.00 0.00 3.09
562 566 9.654663 GGAGTAATAGCATAAACCTACCATAAG 57.345 37.037 0.00 0.00 0.00 1.73
565 569 7.680730 CAGGAGTAATAGCATAAACCTACCAT 58.319 38.462 0.00 0.00 0.00 3.55
622 627 0.672091 AACACATCGCGCACATACCA 60.672 50.000 8.75 0.00 0.00 3.25
671 676 1.039068 CCTGGTTTCCATGTGTTGCA 58.961 50.000 0.00 0.00 30.82 4.08
700 705 3.782244 GCAAGTGTCGCGCCTCTG 61.782 66.667 0.00 0.00 0.00 3.35
701 706 3.596066 ATGCAAGTGTCGCGCCTCT 62.596 57.895 0.00 0.00 0.00 3.69
708 713 0.179250 GTGTACGCATGCAAGTGTCG 60.179 55.000 19.57 6.95 33.64 4.35
722 727 0.032403 TGGCACGTGTAGGTGTGTAC 59.968 55.000 18.38 0.00 40.08 2.90
724 729 1.227438 GTGGCACGTGTAGGTGTGT 60.227 57.895 18.38 0.00 40.08 3.72
737 742 1.891919 GCGTTGAGGTGAAGTGGCA 60.892 57.895 0.00 0.00 0.00 4.92
772 777 3.191371 GGATTTGGATTTGAGTGAGCGTT 59.809 43.478 0.00 0.00 0.00 4.84
774 779 2.749076 TGGATTTGGATTTGAGTGAGCG 59.251 45.455 0.00 0.00 0.00 5.03
779 784 6.950041 TCTCTTTGATGGATTTGGATTTGAGT 59.050 34.615 0.00 0.00 0.00 3.41
781 786 6.153340 GGTCTCTTTGATGGATTTGGATTTGA 59.847 38.462 0.00 0.00 0.00 2.69
784 789 4.641989 CGGTCTCTTTGATGGATTTGGATT 59.358 41.667 0.00 0.00 0.00 3.01
813 818 2.023318 CGCTACCTACCTCGGTCAG 58.977 63.158 0.00 0.00 38.49 3.51
849 854 0.756294 ACGTGTGGTGGAGATGACAA 59.244 50.000 0.00 0.00 0.00 3.18
850 855 0.756294 AACGTGTGGTGGAGATGACA 59.244 50.000 0.00 0.00 0.00 3.58
854 859 0.108585 AAGCAACGTGTGGTGGAGAT 59.891 50.000 0.00 0.00 38.21 2.75
873 878 5.066893 GTGAAGTACATACGTGTAGGGATGA 59.933 44.000 0.00 0.00 41.29 2.92
875 880 4.340381 GGTGAAGTACATACGTGTAGGGAT 59.660 45.833 0.00 0.00 41.29 3.85
893 898 0.955428 GCATGGAAGACTGCGGTGAA 60.955 55.000 0.80 0.00 0.00 3.18
955 960 0.250166 TGTCGTCTGACTCTGGTCGA 60.250 55.000 6.21 0.00 45.70 4.20
959 964 1.177401 TGGATGTCGTCTGACTCTGG 58.823 55.000 6.21 0.00 45.70 3.86
969 974 0.107993 CTGTGGCAGATGGATGTCGT 60.108 55.000 0.00 0.00 32.44 4.34
978 983 7.056006 TCATTGTTGATATAACTGTGGCAGAT 58.944 34.615 2.91 0.00 35.18 2.90
990 995 7.459795 TGGTGTTTGCTTCATTGTTGATATA 57.540 32.000 0.00 0.00 0.00 0.86
998 1003 1.269206 ACGCTGGTGTTTGCTTCATTG 60.269 47.619 0.00 0.00 0.00 2.82
1018 1023 2.404923 TTCTGTTGTTGGTTCACCGA 57.595 45.000 0.00 0.00 39.43 4.69
1022 1027 4.518970 GCTTCCTATTCTGTTGTTGGTTCA 59.481 41.667 0.00 0.00 0.00 3.18
1024 1029 3.502211 CGCTTCCTATTCTGTTGTTGGTT 59.498 43.478 0.00 0.00 0.00 3.67
1029 1034 2.939103 GCATCGCTTCCTATTCTGTTGT 59.061 45.455 0.00 0.00 0.00 3.32
1032 1037 3.550437 AAGCATCGCTTCCTATTCTGT 57.450 42.857 0.00 0.00 46.77 3.41
1043 1048 2.586792 GGAGTGGGAAGCATCGCT 59.413 61.111 7.54 0.00 42.56 4.93
1047 1052 2.905996 TTGCCGGAGTGGGAAGCAT 61.906 57.895 5.05 0.00 44.07 3.79
1052 1057 4.467084 GCGATTGCCGGAGTGGGA 62.467 66.667 5.05 0.00 38.63 4.37
1062 1067 4.481112 CACCCCTTGCGCGATTGC 62.481 66.667 12.10 0.00 37.91 3.56
1149 1154 3.083997 ATCTCGGCCACCCACCTC 61.084 66.667 2.24 0.00 0.00 3.85
1272 1277 2.747460 GCCAGATTGAGGCGTGCA 60.747 61.111 0.00 0.00 43.15 4.57
1284 1289 4.664267 AGGGGAGGTGCTGCCAGA 62.664 66.667 0.00 0.00 44.05 3.86
1303 1308 4.321966 TGTCGCGGTCATGGGCAA 62.322 61.111 6.13 0.00 0.00 4.52
1304 1309 4.758251 CTGTCGCGGTCATGGGCA 62.758 66.667 6.13 0.00 0.00 5.36
1361 1366 3.861689 GGTGTTGTTAGTATCGGTGCTAC 59.138 47.826 0.00 0.00 0.00 3.58
1371 1376 1.413445 AGTGCGGTGGTGTTGTTAGTA 59.587 47.619 0.00 0.00 0.00 1.82
1374 1379 2.843401 ATAGTGCGGTGGTGTTGTTA 57.157 45.000 0.00 0.00 0.00 2.41
1386 1391 2.161030 GAGGAGGGGTAGTATAGTGCG 58.839 57.143 0.00 0.00 0.00 5.34
1392 1397 4.834406 TGAGATTGAGGAGGGGTAGTAT 57.166 45.455 0.00 0.00 0.00 2.12
1394 1399 3.108376 GTTGAGATTGAGGAGGGGTAGT 58.892 50.000 0.00 0.00 0.00 2.73
1399 1404 0.462759 GCCGTTGAGATTGAGGAGGG 60.463 60.000 0.00 0.00 0.00 4.30
1409 1414 1.659335 GTCGTTGACGCCGTTGAGA 60.659 57.895 0.00 0.00 39.60 3.27
1422 1427 0.765519 AGTAGGTGGGGGTTGTCGTT 60.766 55.000 0.00 0.00 0.00 3.85
1437 1442 6.205464 ACTCAATGTCAAATGTGTCCAAGTAG 59.795 38.462 0.00 0.00 0.00 2.57
1438 1443 6.017192 CACTCAATGTCAAATGTGTCCAAGTA 60.017 38.462 0.00 0.00 0.00 2.24
1445 1450 4.464008 AGACCACTCAATGTCAAATGTGT 58.536 39.130 0.00 0.00 33.89 3.72
1479 1484 3.001406 AACTCTAACGCCCCCGCT 61.001 61.111 0.00 0.00 38.22 5.52
1537 1542 0.400594 CCCTCCAACCCGAAGTCTTT 59.599 55.000 0.00 0.00 0.00 2.52
1545 1550 1.303317 CTGAAACCCCTCCAACCCG 60.303 63.158 0.00 0.00 0.00 5.28
1578 1583 0.191064 TGATCCCTCCTCCGCCTTAT 59.809 55.000 0.00 0.00 0.00 1.73
1584 1589 1.069823 CAGATGTTGATCCCTCCTCCG 59.930 57.143 0.00 0.00 0.00 4.63
1607 1612 2.903855 CAGATGCGATGGTGGGGC 60.904 66.667 0.00 0.00 0.00 5.80
1646 1651 2.359107 CAGGAAGAAGCGCCTGCA 60.359 61.111 2.29 0.00 44.53 4.41
1658 1663 0.823356 GAACTGGGTTGCTGCAGGAA 60.823 55.000 17.55 17.55 0.00 3.36
1672 1677 1.073964 CTGCAGACCGACATGAACTG 58.926 55.000 8.42 2.64 0.00 3.16
1681 1686 0.171231 CAACGAGATCTGCAGACCGA 59.829 55.000 29.55 8.65 0.00 4.69
1683 1688 1.728971 CAACAACGAGATCTGCAGACC 59.271 52.381 20.97 10.07 0.00 3.85
1759 1764 4.950050 ACACACACAAAGTAGGAAGAGAG 58.050 43.478 0.00 0.00 0.00 3.20
1763 1768 6.861065 ATACAACACACACAAAGTAGGAAG 57.139 37.500 0.00 0.00 0.00 3.46
1766 1771 7.667043 ACATATACAACACACACAAAGTAGG 57.333 36.000 0.00 0.00 0.00 3.18
1768 1773 7.499563 ACCAACATATACAACACACACAAAGTA 59.500 33.333 0.00 0.00 0.00 2.24
1770 1775 6.734137 ACCAACATATACAACACACACAAAG 58.266 36.000 0.00 0.00 0.00 2.77
1773 1778 4.449405 CGACCAACATATACAACACACACA 59.551 41.667 0.00 0.00 0.00 3.72
1777 1782 9.819267 TTTATATCGACCAACATATACAACACA 57.181 29.630 0.00 0.00 0.00 3.72
1803 1808 8.906867 CAACACAACATTATATCCTTCCAAGAT 58.093 33.333 0.00 0.00 0.00 2.40
1814 1819 7.335673 TCATCGACCAACAACACAACATTATAT 59.664 33.333 0.00 0.00 0.00 0.86
1815 1820 6.651225 TCATCGACCAACAACACAACATTATA 59.349 34.615 0.00 0.00 0.00 0.98
1853 1858 4.379186 GCTCGATCATTTATGCCAAGATGG 60.379 45.833 0.00 0.00 41.55 3.51
1873 1878 1.135431 TGCATGCCAAAATGTACGCTC 60.135 47.619 16.68 0.00 0.00 5.03
1875 1880 1.925229 ATGCATGCCAAAATGTACGC 58.075 45.000 16.68 0.00 0.00 4.42
1878 1883 6.957920 ATGTACTATGCATGCCAAAATGTA 57.042 33.333 16.68 7.05 0.00 2.29
1903 1908 8.193953 TGTAGGATCATGTGATATATGTGTGT 57.806 34.615 0.00 0.00 34.37 3.72
1964 1969 2.679716 GCAGGAGGATGCCTTGGT 59.320 61.111 0.00 0.00 40.43 3.67
1972 1977 4.685575 GCATACTTGAGAAAGCAGGAGGAT 60.686 45.833 0.00 0.00 0.00 3.24
1989 1994 7.806409 TTGCAAGTGAACATATATGCATACT 57.194 32.000 8.99 10.75 42.64 2.12
2003 2008 3.826157 CCTTACCTCCATTTGCAAGTGAA 59.174 43.478 22.24 1.58 0.00 3.18
2004 2009 3.420893 CCTTACCTCCATTTGCAAGTGA 58.579 45.455 22.24 8.71 0.00 3.41
2009 2014 0.407528 TGCCCTTACCTCCATTTGCA 59.592 50.000 0.00 0.00 0.00 4.08
2040 2045 9.357652 CAAGTTCACACAATTTATTCCCATAAG 57.642 33.333 0.00 0.00 0.00 1.73
2041 2046 9.083422 TCAAGTTCACACAATTTATTCCCATAA 57.917 29.630 0.00 0.00 0.00 1.90
2042 2047 8.642935 TCAAGTTCACACAATTTATTCCCATA 57.357 30.769 0.00 0.00 0.00 2.74
2043 2048 7.537596 TCAAGTTCACACAATTTATTCCCAT 57.462 32.000 0.00 0.00 0.00 4.00
2058 2063 5.562890 GCAAGGGTTACTGATTCAAGTTCAC 60.563 44.000 0.00 0.00 0.00 3.18
2069 2074 3.857157 AGTTCTTGCAAGGGTTACTGA 57.143 42.857 25.73 1.40 0.00 3.41
2072 2077 7.307160 GCATTTTAAAGTTCTTGCAAGGGTTAC 60.307 37.037 25.73 17.34 0.00 2.50
2166 2176 2.500098 TCTAGGTGGCATGTGTTAGACC 59.500 50.000 0.00 0.00 0.00 3.85
2173 2183 5.593909 TGGATTTTTATCTAGGTGGCATGTG 59.406 40.000 0.00 0.00 0.00 3.21
2174 2184 5.765510 TGGATTTTTATCTAGGTGGCATGT 58.234 37.500 0.00 0.00 0.00 3.21
2200 2210 7.272244 TCGTGTCTCATTAAATATGGTGTCAT 58.728 34.615 0.00 0.00 37.40 3.06
2227 2237 9.255304 GTAGTCCTATCTCTTTGCATCTTAAAG 57.745 37.037 0.00 0.00 36.67 1.85
2230 2240 8.001875 AGAGTAGTCCTATCTCTTTGCATCTTA 58.998 37.037 0.00 0.00 35.37 2.10
2319 2329 6.129062 CCGCGTTAGATTTCTATTGAGATGAC 60.129 42.308 4.92 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.