Multiple sequence alignment - TraesCS4B01G198000

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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 TraesCS4B01G198000 chr4B 100.000 2192 0 0 1 2192 427068517 427066326 0.000000e+00 4048.0
1 TraesCS4B01G198000 chr4A 84.154 2234 146 77 1 2114 120143382 120145527 0.000000e+00 1973.0
2 TraesCS4B01G198000 chr4A 100.000 42 0 0 1619 1660 120145078 120145119 6.490000e-11 78.7
3 TraesCS4B01G198000 chr4D 82.102 1732 119 83 1 1645 345415623 345413996 0.000000e+00 1304.0
4 TraesCS4B01G198000 chr4D 82.407 216 18 5 1959 2160 345413829 345413620 1.040000e-38 171.0
5 TraesCS4B01G198000 chr4D 89.011 91 10 0 1812 1902 345413929 345413839 1.780000e-21 113.0


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 TraesCS4B01G198000 chr4B 427066326 427068517 2191 True 4048.000000 4048 100.000000 1 2192 1 chr4B.!!$R1 2191
1 TraesCS4B01G198000 chr4A 120143382 120145527 2145 False 1025.850000 1973 92.077000 1 2114 2 chr4A.!!$F1 2113
2 TraesCS4B01G198000 chr4D 345413620 345415623 2003 True 529.333333 1304 84.506667 1 2160 3 chr4D.!!$R1 2159

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
519 564 0.034896 AACCTGGTCAGTTAGTGGCG 59.965 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 1891 0.035152 AATCTTGGACATGCAGGCGA 60.035 50.0 0.0 0.0 0.0 5.54 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
26 28 2.244510 TCTCCTGCTCCTCTGATCTCTT 59.755 50.000 0.00 0.00 0.00 2.85
31 36 4.202141 CCTGCTCCTCTGATCTCTTGTTAG 60.202 50.000 0.00 0.00 0.00 2.34
50 55 5.006552 TGTTAGTACTTTTGTTACCGTGCAC 59.993 40.000 6.82 6.82 0.00 4.57
58 63 1.076332 GTTACCGTGCACTGCCTTAG 58.924 55.000 16.19 0.00 0.00 2.18
155 169 5.638234 GCGAACAGAATATATAGGTTGGTCC 59.362 44.000 0.00 0.00 0.00 4.46
156 170 5.862323 CGAACAGAATATATAGGTTGGTCCG 59.138 44.000 2.41 0.00 41.99 4.79
157 171 6.294342 CGAACAGAATATATAGGTTGGTCCGA 60.294 42.308 2.41 0.00 41.99 4.55
158 172 6.989155 ACAGAATATATAGGTTGGTCCGAA 57.011 37.500 0.00 0.00 41.99 4.30
159 173 6.994221 ACAGAATATATAGGTTGGTCCGAAG 58.006 40.000 0.00 0.00 41.99 3.79
207 221 0.617413 TCCCCGGGCGTACAAAATAA 59.383 50.000 17.73 0.00 0.00 1.40
234 249 4.162320 TCCTTGTAACATCTCTGTCCATCC 59.838 45.833 0.00 0.00 33.36 3.51
256 271 2.285660 GCCGCTGTATTTTAGTTCGCTC 60.286 50.000 0.00 0.00 0.00 5.03
258 273 3.187700 CGCTGTATTTTAGTTCGCTCCT 58.812 45.455 0.00 0.00 0.00 3.69
266 281 3.438297 TTAGTTCGCTCCTAGTGCATC 57.562 47.619 0.00 0.00 0.00 3.91
294 309 2.728007 GGCTTTTCCTGCAGGTTATCT 58.272 47.619 31.58 0.00 36.34 1.98
337 376 2.032528 TTGCAAGCCCGACCTGAG 59.967 61.111 0.00 0.00 0.00 3.35
373 414 5.869753 AAGTTGTGATCCAGAAAATCTCG 57.130 39.130 0.00 0.00 0.00 4.04
374 415 4.256920 AGTTGTGATCCAGAAAATCTCGG 58.743 43.478 0.00 0.00 0.00 4.63
388 429 5.864628 AAATCTCGGTTTTCTTCTAGTGC 57.135 39.130 0.00 0.00 0.00 4.40
389 430 3.314541 TCTCGGTTTTCTTCTAGTGCC 57.685 47.619 0.00 0.00 0.00 5.01
390 431 2.631062 TCTCGGTTTTCTTCTAGTGCCA 59.369 45.455 0.00 0.00 0.00 4.92
391 432 3.260884 TCTCGGTTTTCTTCTAGTGCCAT 59.739 43.478 0.00 0.00 0.00 4.40
392 433 3.334691 TCGGTTTTCTTCTAGTGCCATG 58.665 45.455 0.00 0.00 0.00 3.66
393 434 2.420022 CGGTTTTCTTCTAGTGCCATGG 59.580 50.000 7.63 7.63 0.00 3.66
394 435 2.164422 GGTTTTCTTCTAGTGCCATGGC 59.836 50.000 30.54 30.54 42.35 4.40
434 475 7.208080 AGGTTAGTGCTTAAACTATATCCACG 58.792 38.462 0.00 0.00 37.53 4.94
471 516 4.012374 AGACAGTGGCATGGTTTTCTATG 58.988 43.478 0.00 0.00 40.93 2.23
497 542 1.605710 CCAGCTGGAGTGTTGAACTTG 59.394 52.381 29.88 0.00 40.07 3.16
504 549 3.199946 TGGAGTGTTGAACTTGAGAACCT 59.800 43.478 0.00 0.00 40.07 3.50
505 550 3.561725 GGAGTGTTGAACTTGAGAACCTG 59.438 47.826 0.00 0.00 40.07 4.00
506 551 3.545703 AGTGTTGAACTTGAGAACCTGG 58.454 45.455 0.00 0.00 34.57 4.45
507 552 3.054361 AGTGTTGAACTTGAGAACCTGGT 60.054 43.478 0.00 0.00 34.57 4.00
508 553 3.312697 GTGTTGAACTTGAGAACCTGGTC 59.687 47.826 0.00 0.00 0.00 4.02
509 554 3.054728 TGTTGAACTTGAGAACCTGGTCA 60.055 43.478 0.00 0.00 0.00 4.02
510 555 3.475566 TGAACTTGAGAACCTGGTCAG 57.524 47.619 0.00 0.00 0.00 3.51
511 556 2.771943 TGAACTTGAGAACCTGGTCAGT 59.228 45.455 0.00 0.00 0.00 3.41
512 557 3.199946 TGAACTTGAGAACCTGGTCAGTT 59.800 43.478 0.00 4.07 0.00 3.16
513 558 4.407621 TGAACTTGAGAACCTGGTCAGTTA 59.592 41.667 0.00 0.00 0.00 2.24
514 559 4.608948 ACTTGAGAACCTGGTCAGTTAG 57.391 45.455 0.00 0.00 0.00 2.34
515 560 3.967987 ACTTGAGAACCTGGTCAGTTAGT 59.032 43.478 0.00 0.00 0.00 2.24
516 561 4.202264 ACTTGAGAACCTGGTCAGTTAGTG 60.202 45.833 0.00 0.00 0.00 2.74
517 562 2.632996 TGAGAACCTGGTCAGTTAGTGG 59.367 50.000 0.00 0.00 0.00 4.00
518 563 1.348036 AGAACCTGGTCAGTTAGTGGC 59.652 52.381 0.00 0.00 0.00 5.01
519 564 0.034896 AACCTGGTCAGTTAGTGGCG 59.965 55.000 0.00 0.00 0.00 5.69
520 565 1.741770 CCTGGTCAGTTAGTGGCGC 60.742 63.158 0.00 0.00 0.00 6.53
521 566 2.048597 TGGTCAGTTAGTGGCGCG 60.049 61.111 0.00 0.00 0.00 6.86
522 567 2.260434 GGTCAGTTAGTGGCGCGA 59.740 61.111 12.10 0.00 0.00 5.87
523 568 2.092882 GGTCAGTTAGTGGCGCGAC 61.093 63.158 15.38 15.38 0.00 5.19
524 569 2.092882 GTCAGTTAGTGGCGCGACC 61.093 63.158 19.50 11.50 39.84 4.79
525 570 2.813908 CAGTTAGTGGCGCGACCC 60.814 66.667 19.50 0.00 37.83 4.46
526 571 3.307906 AGTTAGTGGCGCGACCCA 61.308 61.111 19.50 5.14 37.83 4.51
527 572 2.813908 GTTAGTGGCGCGACCCAG 60.814 66.667 19.50 0.00 37.83 4.45
555 600 0.108424 AGACAGAATCCTGCAGCGAC 60.108 55.000 8.66 0.00 44.16 5.19
561 606 3.628646 ATCCTGCAGCGACCCAACC 62.629 63.158 8.66 0.00 0.00 3.77
574 627 2.171659 GACCCAACCCAAAACACCAATT 59.828 45.455 0.00 0.00 0.00 2.32
607 663 2.987547 GCCAGGCTTGCTTGCTGA 60.988 61.111 3.29 0.00 0.00 4.26
616 672 3.243002 GGCTTGCTTGCTGATGAGTTATC 60.243 47.826 1.96 0.00 36.29 1.75
618 674 4.496010 GCTTGCTTGCTGATGAGTTATCTG 60.496 45.833 0.00 0.00 36.71 2.90
640 700 3.790437 CGGGCTGGAGTGCTGGAT 61.790 66.667 0.00 0.00 0.00 3.41
686 746 2.962253 GGCTGGCGCGTATCTGAC 60.962 66.667 8.43 0.35 36.88 3.51
698 758 5.143660 CGCGTATCTGACTTAGATCTTCAG 58.856 45.833 14.36 14.36 42.54 3.02
714 778 3.844577 TTCAGTCTGAAGGTAGCGTAC 57.155 47.619 11.36 0.00 31.83 3.67
715 779 1.736126 TCAGTCTGAAGGTAGCGTACG 59.264 52.381 11.84 11.84 0.00 3.67
723 787 1.171308 AGGTAGCGTACGCAGAAAGA 58.829 50.000 38.58 15.62 44.88 2.52
731 795 1.810151 GTACGCAGAAAGATTTGCCCA 59.190 47.619 0.00 0.00 37.00 5.36
732 796 0.883833 ACGCAGAAAGATTTGCCCAG 59.116 50.000 0.00 0.00 37.00 4.45
749 827 1.406069 CCAGGCAGTACAGTGACATCC 60.406 57.143 0.00 0.00 0.00 3.51
753 831 2.552155 GGCAGTACAGTGACATCCCAAA 60.552 50.000 0.00 0.00 0.00 3.28
757 835 4.214119 CAGTACAGTGACATCCCAAAGTTG 59.786 45.833 0.00 0.00 0.00 3.16
760 838 2.816087 CAGTGACATCCCAAAGTTGAGG 59.184 50.000 0.00 0.00 0.00 3.86
805 883 2.036733 GCCCAAACCCTAAAGTTTCCAC 59.963 50.000 0.00 0.00 37.87 4.02
822 900 2.376808 CACAAGATGGAGCTCGAACT 57.623 50.000 7.83 5.01 0.00 3.01
823 901 1.998315 CACAAGATGGAGCTCGAACTG 59.002 52.381 9.24 6.43 0.00 3.16
824 902 1.620819 ACAAGATGGAGCTCGAACTGT 59.379 47.619 9.24 7.02 0.00 3.55
825 903 1.998315 CAAGATGGAGCTCGAACTGTG 59.002 52.381 9.24 6.55 0.00 3.66
826 904 0.534412 AGATGGAGCTCGAACTGTGG 59.466 55.000 7.72 0.00 0.00 4.17
827 905 0.532573 GATGGAGCTCGAACTGTGGA 59.467 55.000 7.83 0.00 0.00 4.02
828 906 0.534412 ATGGAGCTCGAACTGTGGAG 59.466 55.000 7.83 5.12 32.98 3.86
829 907 0.539669 TGGAGCTCGAACTGTGGAGA 60.540 55.000 7.83 0.00 31.52 3.71
830 908 0.172352 GGAGCTCGAACTGTGGAGAG 59.828 60.000 7.83 7.83 31.52 3.20
833 911 3.415237 CTCGAACTGTGGAGAGCAG 57.585 57.895 3.72 0.00 39.67 4.24
874 999 0.107606 TTGGCTATAAAAGGGCGCGA 60.108 50.000 12.10 0.00 0.00 5.87
879 1004 2.288030 GCTATAAAAGGGCGCGACTCTA 60.288 50.000 13.91 3.84 0.00 2.43
932 1057 2.203280 CCCACACGCCAACCTTCA 60.203 61.111 0.00 0.00 0.00 3.02
933 1058 2.551912 CCCACACGCCAACCTTCAC 61.552 63.158 0.00 0.00 0.00 3.18
934 1059 2.631428 CACACGCCAACCTTCACG 59.369 61.111 0.00 0.00 0.00 4.35
941 1068 1.961277 CCAACCTTCACGCGCTCTT 60.961 57.895 5.73 0.00 0.00 2.85
952 1084 2.411504 GCGCTCTTCTCTCGACCCT 61.412 63.158 0.00 0.00 0.00 4.34
953 1085 1.939769 GCGCTCTTCTCTCGACCCTT 61.940 60.000 0.00 0.00 0.00 3.95
954 1086 0.099791 CGCTCTTCTCTCGACCCTTC 59.900 60.000 0.00 0.00 0.00 3.46
966 1098 0.034960 GACCCTTCTTCTTCCTGGCC 60.035 60.000 0.00 0.00 0.00 5.36
1089 1230 4.069232 CTCTTCCCGTGCCTCGCA 62.069 66.667 0.00 0.00 38.35 5.10
1124 1265 4.521062 CGGAGGCGAGCAGAAGGG 62.521 72.222 0.00 0.00 0.00 3.95
1125 1266 3.077556 GGAGGCGAGCAGAAGGGA 61.078 66.667 0.00 0.00 0.00 4.20
1220 1379 1.918957 GGGGAAGGAGGGATGGATATG 59.081 57.143 0.00 0.00 0.00 1.78
1221 1380 1.918957 GGGAAGGAGGGATGGATATGG 59.081 57.143 0.00 0.00 0.00 2.74
1222 1381 2.497289 GGGAAGGAGGGATGGATATGGA 60.497 54.545 0.00 0.00 0.00 3.41
1223 1382 3.468850 GGAAGGAGGGATGGATATGGAT 58.531 50.000 0.00 0.00 0.00 3.41
1224 1383 4.577245 GGGAAGGAGGGATGGATATGGATA 60.577 50.000 0.00 0.00 0.00 2.59
1225 1384 5.230759 GGAAGGAGGGATGGATATGGATAT 58.769 45.833 0.00 0.00 0.00 1.63
1226 1385 6.393897 GGAAGGAGGGATGGATATGGATATA 58.606 44.000 0.00 0.00 0.00 0.86
1227 1386 7.028131 GGAAGGAGGGATGGATATGGATATAT 58.972 42.308 0.00 0.00 32.19 0.86
1228 1387 7.037730 GGAAGGAGGGATGGATATGGATATATG 60.038 44.444 0.00 0.00 29.67 1.78
1229 1388 6.337575 AGGAGGGATGGATATGGATATATGG 58.662 44.000 0.00 0.00 29.67 2.74
1230 1389 6.108320 AGGAGGGATGGATATGGATATATGGA 59.892 42.308 0.00 0.00 29.67 3.41
1231 1390 6.443206 GGAGGGATGGATATGGATATATGGAG 59.557 46.154 0.00 0.00 29.67 3.86
1232 1391 6.954642 AGGGATGGATATGGATATATGGAGT 58.045 40.000 0.00 0.00 29.67 3.85
1259 1418 8.774890 TGATGATCTCTGAAGAAAAGAAAGAG 57.225 34.615 0.00 0.00 34.49 2.85
1315 1478 1.291877 CGGAAGCCGTTCTGTTGGAG 61.292 60.000 0.00 0.00 42.73 3.86
1375 1548 1.359818 GGGGTGTTGGAGGGGAATAAA 59.640 52.381 0.00 0.00 0.00 1.40
1438 1611 1.744014 CAGCAGCTTTTGGCCAACT 59.256 52.632 20.35 9.77 43.05 3.16
1467 1640 1.359848 CGTAGCCTCGCAGTGATTTT 58.640 50.000 0.00 0.00 0.00 1.82
1473 1646 1.672881 CCTCGCAGTGATTTTGGATCC 59.327 52.381 4.20 4.20 0.00 3.36
1480 1653 4.687483 GCAGTGATTTTGGATCCTTTGTTG 59.313 41.667 14.23 2.90 0.00 3.33
1481 1654 4.687483 CAGTGATTTTGGATCCTTTGTTGC 59.313 41.667 14.23 0.00 0.00 4.17
1482 1655 3.674753 GTGATTTTGGATCCTTTGTTGCG 59.325 43.478 14.23 0.00 0.00 4.85
1503 1676 3.013921 GGGTGGGTGTATGTATGTGTTG 58.986 50.000 0.00 0.00 0.00 3.33
1504 1677 3.560453 GGGTGGGTGTATGTATGTGTTGT 60.560 47.826 0.00 0.00 0.00 3.32
1505 1678 4.076394 GGTGGGTGTATGTATGTGTTGTT 58.924 43.478 0.00 0.00 0.00 2.83
1596 1769 4.663334 TGTCTGTCTATGGTGTGTACTCT 58.337 43.478 0.00 0.00 0.00 3.24
1665 1886 4.908601 TGGTACATTCACTCAATGACCT 57.091 40.909 1.36 0.00 44.40 3.85
1666 1887 5.241403 TGGTACATTCACTCAATGACCTT 57.759 39.130 1.36 0.00 44.40 3.50
1667 1888 5.630121 TGGTACATTCACTCAATGACCTTT 58.370 37.500 1.36 0.00 44.40 3.11
1668 1889 6.068010 TGGTACATTCACTCAATGACCTTTT 58.932 36.000 1.36 0.00 44.40 2.27
1669 1890 6.206634 TGGTACATTCACTCAATGACCTTTTC 59.793 38.462 1.36 0.00 44.40 2.29
1670 1891 6.431234 GGTACATTCACTCAATGACCTTTTCT 59.569 38.462 1.36 0.00 44.40 2.52
1671 1892 6.566197 ACATTCACTCAATGACCTTTTCTC 57.434 37.500 1.36 0.00 44.40 2.87
1672 1893 5.180117 ACATTCACTCAATGACCTTTTCTCG 59.820 40.000 1.36 0.00 44.40 4.04
1673 1894 3.067106 TCACTCAATGACCTTTTCTCGC 58.933 45.455 0.00 0.00 29.99 5.03
1674 1895 2.160417 CACTCAATGACCTTTTCTCGCC 59.840 50.000 0.00 0.00 0.00 5.54
1675 1896 2.039084 ACTCAATGACCTTTTCTCGCCT 59.961 45.455 0.00 0.00 0.00 5.52
1676 1897 2.417933 CTCAATGACCTTTTCTCGCCTG 59.582 50.000 0.00 0.00 0.00 4.85
1677 1898 1.135575 CAATGACCTTTTCTCGCCTGC 60.136 52.381 0.00 0.00 0.00 4.85
1678 1899 0.036732 ATGACCTTTTCTCGCCTGCA 59.963 50.000 0.00 0.00 0.00 4.41
1679 1900 0.036732 TGACCTTTTCTCGCCTGCAT 59.963 50.000 0.00 0.00 0.00 3.96
1680 1901 0.449388 GACCTTTTCTCGCCTGCATG 59.551 55.000 0.00 0.00 0.00 4.06
1681 1902 0.250901 ACCTTTTCTCGCCTGCATGT 60.251 50.000 0.00 0.00 0.00 3.21
1682 1903 0.449388 CCTTTTCTCGCCTGCATGTC 59.551 55.000 0.00 0.00 0.00 3.06
1683 1904 0.449388 CTTTTCTCGCCTGCATGTCC 59.551 55.000 0.00 0.00 0.00 4.02
1702 1923 1.737793 CCAAGATTGGCGAGGTTACAC 59.262 52.381 0.00 0.00 42.21 2.90
1703 1924 1.737793 CAAGATTGGCGAGGTTACACC 59.262 52.381 0.00 0.00 38.99 4.16
1704 1925 0.981183 AGATTGGCGAGGTTACACCA 59.019 50.000 0.00 0.00 41.95 4.17
1705 1926 1.559682 AGATTGGCGAGGTTACACCAT 59.440 47.619 0.00 0.00 41.95 3.55
1706 1927 1.940613 GATTGGCGAGGTTACACCATC 59.059 52.381 0.00 0.00 41.95 3.51
1772 1993 7.201688 GCTAACACCATGAACAAAACCAAATTT 60.202 33.333 0.00 0.00 0.00 1.82
1789 2010 5.799936 CCAAATTTATCAAGCTTGTGGTACG 59.200 40.000 25.19 8.94 0.00 3.67
1799 2020 1.218875 TTGTGGTACGACAAGCAGCG 61.219 55.000 18.20 0.00 32.05 5.18
1883 2104 0.675633 ACAACAACTCCTGCATTGCC 59.324 50.000 6.12 0.00 0.00 4.52
1921 2142 0.037697 TCGTTGACAAGTCATCCCCG 60.038 55.000 3.43 5.05 39.64 5.73
1924 2145 0.762418 TTGACAAGTCATCCCCGTGT 59.238 50.000 3.43 0.00 39.64 4.49
1925 2146 0.320374 TGACAAGTCATCCCCGTGTC 59.680 55.000 0.00 0.00 40.35 3.67
1929 2150 0.042131 AAGTCATCCCCGTGTCCCTA 59.958 55.000 0.00 0.00 0.00 3.53
2028 2249 3.901797 GAGGCAACGACACCTGGGG 62.902 68.421 0.00 0.00 46.39 4.96
2029 2250 4.265056 GGCAACGACACCTGGGGT 62.265 66.667 0.00 0.00 35.62 4.95
2133 2368 4.426416 CGCAATCAACATCATCCACAAAT 58.574 39.130 0.00 0.00 0.00 2.32
2138 2373 4.567971 TCAACATCATCCACAAATTTGCC 58.432 39.130 18.12 0.00 0.00 4.52
2146 2381 3.190874 TCCACAAATTTGCCAACGAAAC 58.809 40.909 18.12 0.00 0.00 2.78
2160 2395 3.764237 ACGAAACCCTAGAAAGCAGAA 57.236 42.857 0.00 0.00 0.00 3.02
2161 2396 4.081322 ACGAAACCCTAGAAAGCAGAAA 57.919 40.909 0.00 0.00 0.00 2.52
2162 2397 4.652822 ACGAAACCCTAGAAAGCAGAAAT 58.347 39.130 0.00 0.00 0.00 2.17
2163 2398 5.070685 ACGAAACCCTAGAAAGCAGAAATT 58.929 37.500 0.00 0.00 0.00 1.82
2164 2399 5.048713 ACGAAACCCTAGAAAGCAGAAATTG 60.049 40.000 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.363038 CAAGAGATCAGAGGAGCAGGAG 59.637 54.545 0.00 0.00 0.00 3.69
19 21 8.645487 CGGTAACAAAAGTACTAACAAGAGATC 58.355 37.037 0.00 0.00 0.00 2.75
26 28 5.006552 GTGCACGGTAACAAAAGTACTAACA 59.993 40.000 0.00 0.00 0.00 2.41
31 36 3.847105 GCAGTGCACGGTAACAAAAGTAC 60.847 47.826 18.34 0.00 0.00 2.73
50 55 3.450457 AGTGTCTGGAATCTCTAAGGCAG 59.550 47.826 0.00 0.00 0.00 4.85
155 169 2.169832 ATTCCACACTGTGACCTTCG 57.830 50.000 15.86 0.00 35.23 3.79
156 170 3.476552 TGAATTCCACACTGTGACCTTC 58.523 45.455 15.86 9.79 35.23 3.46
157 171 3.576078 TGAATTCCACACTGTGACCTT 57.424 42.857 15.86 0.84 35.23 3.50
158 172 3.117888 ACTTGAATTCCACACTGTGACCT 60.118 43.478 15.86 0.00 35.23 3.85
159 173 3.214328 ACTTGAATTCCACACTGTGACC 58.786 45.455 15.86 0.00 35.23 4.02
160 174 3.876914 TGACTTGAATTCCACACTGTGAC 59.123 43.478 15.86 0.00 35.23 3.67
161 175 4.149511 TGACTTGAATTCCACACTGTGA 57.850 40.909 15.86 0.00 35.23 3.58
162 176 4.336433 AGTTGACTTGAATTCCACACTGTG 59.664 41.667 6.19 6.19 0.00 3.66
163 177 4.336433 CAGTTGACTTGAATTCCACACTGT 59.664 41.667 2.27 0.00 0.00 3.55
164 178 4.790766 GCAGTTGACTTGAATTCCACACTG 60.791 45.833 2.27 10.27 0.00 3.66
207 221 6.542821 TGGACAGAGATGTTACAAGGAAAAT 58.457 36.000 0.00 0.00 0.00 1.82
229 244 1.531149 CTAAAATACAGCGGCGGATGG 59.469 52.381 14.32 0.00 32.67 3.51
234 249 1.591394 GCGAACTAAAATACAGCGGCG 60.591 52.381 0.51 0.51 0.00 6.46
256 271 1.867233 GCCGTACAATGATGCACTAGG 59.133 52.381 0.00 0.00 0.00 3.02
258 273 2.979814 AGCCGTACAATGATGCACTA 57.020 45.000 0.00 0.00 0.00 2.74
266 281 1.539388 TGCAGGAAAAGCCGTACAATG 59.461 47.619 0.00 0.00 43.43 2.82
294 309 5.413309 CCCAAACACAGGGCATAAAATAA 57.587 39.130 0.00 0.00 39.96 1.40
337 376 0.179215 CAACTTTCAGCATCGACCGC 60.179 55.000 0.36 0.36 0.00 5.68
373 414 2.164422 GCCATGGCACTAGAAGAAAACC 59.836 50.000 32.08 0.00 41.49 3.27
374 415 2.164422 GGCCATGGCACTAGAAGAAAAC 59.836 50.000 36.56 11.88 44.11 2.43
434 475 4.082523 TCTGCCTGCCTACGGTGC 62.083 66.667 0.00 0.00 0.00 5.01
459 500 5.359009 CAGCTGGAATGACATAGAAAACCAT 59.641 40.000 5.57 0.00 0.00 3.55
461 502 4.096984 CCAGCTGGAATGACATAGAAAACC 59.903 45.833 29.88 0.00 37.39 3.27
471 516 1.808945 CAACACTCCAGCTGGAATGAC 59.191 52.381 42.23 0.00 43.66 3.06
497 542 2.613223 GCCACTAACTGACCAGGTTCTC 60.613 54.545 0.00 0.00 0.00 2.87
504 549 2.048597 CGCGCCACTAACTGACCA 60.049 61.111 0.00 0.00 0.00 4.02
505 550 2.092882 GTCGCGCCACTAACTGACC 61.093 63.158 0.00 0.00 0.00 4.02
506 551 2.092882 GGTCGCGCCACTAACTGAC 61.093 63.158 13.61 2.07 37.17 3.51
507 552 2.260434 GGTCGCGCCACTAACTGA 59.740 61.111 13.61 0.00 37.17 3.41
508 553 2.813908 GGGTCGCGCCACTAACTG 60.814 66.667 18.87 0.00 39.65 3.16
509 554 3.296709 CTGGGTCGCGCCACTAACT 62.297 63.158 18.87 0.00 39.65 2.24
510 555 2.813908 CTGGGTCGCGCCACTAAC 60.814 66.667 18.87 3.52 39.65 2.34
511 556 4.752879 GCTGGGTCGCGCCACTAA 62.753 66.667 18.87 0.00 39.65 2.24
516 561 3.281359 AAAAATGCTGGGTCGCGCC 62.281 57.895 0.00 6.06 0.00 6.53
517 562 1.801512 GAAAAATGCTGGGTCGCGC 60.802 57.895 0.00 0.00 0.00 6.86
518 563 0.454957 CTGAAAAATGCTGGGTCGCG 60.455 55.000 0.00 0.00 0.00 5.87
519 564 0.881118 TCTGAAAAATGCTGGGTCGC 59.119 50.000 0.00 0.00 0.00 5.19
520 565 1.879380 TGTCTGAAAAATGCTGGGTCG 59.121 47.619 0.00 0.00 0.00 4.79
521 566 3.149196 TCTGTCTGAAAAATGCTGGGTC 58.851 45.455 0.00 0.00 0.00 4.46
522 567 3.228188 TCTGTCTGAAAAATGCTGGGT 57.772 42.857 0.00 0.00 0.00 4.51
523 568 4.381292 GGATTCTGTCTGAAAAATGCTGGG 60.381 45.833 0.00 0.00 38.29 4.45
524 569 4.461781 AGGATTCTGTCTGAAAAATGCTGG 59.538 41.667 0.00 0.00 38.29 4.85
525 570 5.399858 CAGGATTCTGTCTGAAAAATGCTG 58.600 41.667 11.91 11.91 39.88 4.41
526 571 4.082354 GCAGGATTCTGTCTGAAAAATGCT 60.082 41.667 2.16 0.00 42.78 3.79
527 572 4.171754 GCAGGATTCTGTCTGAAAAATGC 58.828 43.478 2.16 9.02 42.78 3.56
555 600 3.289407 AAATTGGTGTTTTGGGTTGGG 57.711 42.857 0.00 0.00 0.00 4.12
607 663 1.344763 GCCCGGTAGCAGATAACTCAT 59.655 52.381 0.00 0.00 0.00 2.90
616 672 3.077556 ACTCCAGCCCGGTAGCAG 61.078 66.667 0.00 0.00 35.57 4.24
618 674 4.840005 GCACTCCAGCCCGGTAGC 62.840 72.222 0.00 0.00 35.57 3.58
639 699 5.825679 TGTTTAGCCACTGTTACTTGTCAAT 59.174 36.000 0.00 0.00 0.00 2.57
640 700 5.065474 GTGTTTAGCCACTGTTACTTGTCAA 59.935 40.000 0.00 0.00 32.50 3.18
698 758 0.169672 TGCGTACGCTACCTTCAGAC 59.830 55.000 36.99 7.91 42.51 3.51
714 778 0.171903 CCTGGGCAAATCTTTCTGCG 59.828 55.000 0.00 0.00 39.55 5.18
715 779 0.108472 GCCTGGGCAAATCTTTCTGC 60.108 55.000 6.75 0.00 41.49 4.26
731 795 0.905357 GGGATGTCACTGTACTGCCT 59.095 55.000 0.00 0.00 0.00 4.75
732 796 0.613260 TGGGATGTCACTGTACTGCC 59.387 55.000 0.00 0.00 0.00 4.85
749 827 2.166270 GCTCGAGCCTCAACTTTGG 58.834 57.895 27.22 0.00 34.31 3.28
779 857 1.266178 CTTTAGGGTTTGGGCTTGGG 58.734 55.000 0.00 0.00 0.00 4.12
780 858 2.009681 ACTTTAGGGTTTGGGCTTGG 57.990 50.000 0.00 0.00 0.00 3.61
781 859 3.244078 GGAAACTTTAGGGTTTGGGCTTG 60.244 47.826 0.00 0.00 39.20 4.01
782 860 2.969950 GGAAACTTTAGGGTTTGGGCTT 59.030 45.455 0.00 0.00 39.20 4.35
783 861 2.090999 TGGAAACTTTAGGGTTTGGGCT 60.091 45.455 0.00 0.00 39.20 5.19
786 864 4.647399 TCTTGTGGAAACTTTAGGGTTTGG 59.353 41.667 0.00 0.00 39.20 3.28
805 883 1.998315 CACAGTTCGAGCTCCATCTTG 59.002 52.381 8.47 3.39 0.00 3.02
815 893 0.735632 GCTGCTCTCCACAGTTCGAG 60.736 60.000 0.00 0.00 37.47 4.04
830 908 2.558554 CTTGGGATGCAAGCAGCTGC 62.559 60.000 31.53 31.53 45.94 5.25
831 909 1.511305 CTTGGGATGCAAGCAGCTG 59.489 57.895 10.11 10.11 45.94 4.24
832 910 1.681327 CCTTGGGATGCAAGCAGCT 60.681 57.895 10.32 0.00 45.94 4.24
833 911 1.252904 TTCCTTGGGATGCAAGCAGC 61.253 55.000 0.94 0.94 45.96 5.25
874 999 1.380112 GGGGAGTGACCGCTAGAGT 60.380 63.158 0.00 0.00 46.34 3.24
932 1057 2.481464 GTCGAGAGAAGAGCGCGT 59.519 61.111 8.43 0.00 45.01 6.01
933 1058 2.277628 GGTCGAGAGAAGAGCGCG 60.278 66.667 0.00 0.00 45.01 6.86
934 1059 1.939769 AAGGGTCGAGAGAAGAGCGC 61.940 60.000 0.00 0.00 45.01 5.92
936 1061 1.470051 AGAAGGGTCGAGAGAAGAGC 58.530 55.000 0.00 0.00 45.01 4.09
938 1063 3.443145 AGAAGAAGGGTCGAGAGAAGA 57.557 47.619 0.00 0.00 45.01 2.87
941 1068 2.041891 AGGAAGAAGAAGGGTCGAGAGA 59.958 50.000 0.00 0.00 38.16 3.10
952 1084 0.324943 CCGAAGGCCAGGAAGAAGAA 59.675 55.000 5.01 0.00 46.14 2.52
953 1085 1.983224 CCGAAGGCCAGGAAGAAGA 59.017 57.895 5.01 0.00 46.14 2.87
954 1086 4.625800 CCGAAGGCCAGGAAGAAG 57.374 61.111 5.01 0.00 46.14 2.85
966 1098 2.744768 GCGCCTTCTTGCTCCGAAG 61.745 63.158 0.00 0.00 38.05 3.79
985 1117 2.181777 CATTGCTGGCTGCTGCTG 59.818 61.111 17.45 9.71 43.37 4.41
986 1118 3.068691 CCATTGCTGGCTGCTGCT 61.069 61.111 17.45 0.00 43.37 4.24
987 1119 3.064987 CTCCATTGCTGGCTGCTGC 62.065 63.158 17.45 7.10 42.80 5.25
1110 1251 3.080121 CCTCCCTTCTGCTCGCCT 61.080 66.667 0.00 0.00 0.00 5.52
1199 1340 0.178903 TATCCATCCCTCCTTCCCCG 60.179 60.000 0.00 0.00 0.00 5.73
1202 1343 2.921221 TCCATATCCATCCCTCCTTCC 58.079 52.381 0.00 0.00 0.00 3.46
1203 1344 7.037730 CCATATATCCATATCCATCCCTCCTTC 60.038 44.444 0.00 0.00 0.00 3.46
1204 1345 6.796523 CCATATATCCATATCCATCCCTCCTT 59.203 42.308 0.00 0.00 0.00 3.36
1205 1346 6.108320 TCCATATATCCATATCCATCCCTCCT 59.892 42.308 0.00 0.00 0.00 3.69
1220 1379 7.779326 TCAGAGATCATCAGACTCCATATATCC 59.221 40.741 0.00 0.00 0.00 2.59
1221 1380 8.750515 TCAGAGATCATCAGACTCCATATATC 57.249 38.462 0.00 0.00 0.00 1.63
1222 1381 9.192642 CTTCAGAGATCATCAGACTCCATATAT 57.807 37.037 0.00 0.00 0.00 0.86
1223 1382 8.389366 TCTTCAGAGATCATCAGACTCCATATA 58.611 37.037 0.00 0.00 0.00 0.86
1224 1383 7.240167 TCTTCAGAGATCATCAGACTCCATAT 58.760 38.462 0.00 0.00 0.00 1.78
1225 1384 6.608922 TCTTCAGAGATCATCAGACTCCATA 58.391 40.000 0.00 0.00 0.00 2.74
1226 1385 5.456779 TCTTCAGAGATCATCAGACTCCAT 58.543 41.667 0.00 0.00 0.00 3.41
1227 1386 4.864726 TCTTCAGAGATCATCAGACTCCA 58.135 43.478 0.00 0.00 0.00 3.86
1228 1387 5.850557 TTCTTCAGAGATCATCAGACTCC 57.149 43.478 0.00 0.00 0.00 3.85
1229 1388 7.546358 TCTTTTCTTCAGAGATCATCAGACTC 58.454 38.462 0.00 0.00 0.00 3.36
1230 1389 7.479352 TCTTTTCTTCAGAGATCATCAGACT 57.521 36.000 0.00 0.00 0.00 3.24
1231 1390 8.545229 TTTCTTTTCTTCAGAGATCATCAGAC 57.455 34.615 0.00 0.00 0.00 3.51
1232 1391 8.591940 TCTTTCTTTTCTTCAGAGATCATCAGA 58.408 33.333 0.00 0.00 0.00 3.27
1259 1418 0.108945 GGCCTGCAGCAATTCTTGAC 60.109 55.000 8.66 0.00 46.50 3.18
1277 1439 0.875059 GCTCAAGAACAAGAACCGGG 59.125 55.000 6.32 0.00 0.00 5.73
1344 1517 0.906282 CAACACCCCCTACCGTACCT 60.906 60.000 0.00 0.00 0.00 3.08
1398 1571 2.159572 CGGAATCACAACGGAATTCCAC 60.160 50.000 24.09 0.00 40.44 4.02
1438 1611 1.592400 CGAGGCTACGGACTCCACAA 61.592 60.000 0.00 0.00 44.49 3.33
1467 1640 0.893270 CACCCGCAACAAAGGATCCA 60.893 55.000 15.82 0.00 0.00 3.41
1473 1646 0.820074 TACACCCACCCGCAACAAAG 60.820 55.000 0.00 0.00 0.00 2.77
1480 1653 0.179468 ACATACATACACCCACCCGC 59.821 55.000 0.00 0.00 0.00 6.13
1481 1654 1.208535 ACACATACATACACCCACCCG 59.791 52.381 0.00 0.00 0.00 5.28
1482 1655 3.013921 CAACACATACATACACCCACCC 58.986 50.000 0.00 0.00 0.00 4.61
1503 1676 8.212495 GCAATTACGTACAGTAGCATATACAAC 58.788 37.037 0.00 0.00 36.56 3.32
1504 1677 7.383029 GGCAATTACGTACAGTAGCATATACAA 59.617 37.037 0.00 0.00 36.56 2.41
1505 1678 6.864685 GGCAATTACGTACAGTAGCATATACA 59.135 38.462 0.00 0.00 36.56 2.29
1596 1769 5.360714 AGAAGAAATTCAAGTGCAGAAACCA 59.639 36.000 0.00 0.00 0.00 3.67
1658 1879 1.168714 GCAGGCGAGAAAAGGTCATT 58.831 50.000 0.00 0.00 0.00 2.57
1659 1880 0.036732 TGCAGGCGAGAAAAGGTCAT 59.963 50.000 0.00 0.00 0.00 3.06
1660 1881 0.036732 ATGCAGGCGAGAAAAGGTCA 59.963 50.000 0.00 0.00 0.00 4.02
1661 1882 0.449388 CATGCAGGCGAGAAAAGGTC 59.551 55.000 0.00 0.00 0.00 3.85
1662 1883 0.250901 ACATGCAGGCGAGAAAAGGT 60.251 50.000 0.00 0.00 0.00 3.50
1663 1884 0.449388 GACATGCAGGCGAGAAAAGG 59.551 55.000 0.00 0.00 0.00 3.11
1664 1885 0.449388 GGACATGCAGGCGAGAAAAG 59.551 55.000 0.00 0.00 0.00 2.27
1665 1886 0.250684 TGGACATGCAGGCGAGAAAA 60.251 50.000 0.00 0.00 0.00 2.29
1666 1887 0.250684 TTGGACATGCAGGCGAGAAA 60.251 50.000 0.00 0.00 0.00 2.52
1667 1888 0.674581 CTTGGACATGCAGGCGAGAA 60.675 55.000 0.00 0.00 0.00 2.87
1668 1889 1.078918 CTTGGACATGCAGGCGAGA 60.079 57.895 0.00 0.00 0.00 4.04
1669 1890 0.463295 ATCTTGGACATGCAGGCGAG 60.463 55.000 0.00 0.00 0.00 5.03
1670 1891 0.035152 AATCTTGGACATGCAGGCGA 60.035 50.000 0.00 0.00 0.00 5.54
1671 1892 0.099968 CAATCTTGGACATGCAGGCG 59.900 55.000 0.00 0.00 0.00 5.52
1702 1923 4.875536 TGTTTCGTTATCCTGTGATGATGG 59.124 41.667 0.00 0.00 32.18 3.51
1703 1924 5.503031 GCTGTTTCGTTATCCTGTGATGATG 60.503 44.000 0.00 0.00 32.18 3.07
1704 1925 4.572389 GCTGTTTCGTTATCCTGTGATGAT 59.428 41.667 0.00 0.00 32.18 2.45
1705 1926 3.932710 GCTGTTTCGTTATCCTGTGATGA 59.067 43.478 0.00 0.00 32.18 2.92
1706 1927 3.684305 TGCTGTTTCGTTATCCTGTGATG 59.316 43.478 0.00 0.00 32.18 3.07
1772 1993 3.945981 TGTCGTACCACAAGCTTGATA 57.054 42.857 32.50 17.59 0.00 2.15
1789 2010 2.742053 TGATTACCTTTCGCTGCTTGTC 59.258 45.455 0.00 0.00 0.00 3.18
1799 2020 2.436417 TGCAGCCTGTGATTACCTTTC 58.564 47.619 0.00 0.00 0.00 2.62
1869 2090 2.361610 CGGGGCAATGCAGGAGTT 60.362 61.111 7.79 0.00 0.00 3.01
1921 2142 3.011818 CCACCGGTAAAAATAGGGACAC 58.988 50.000 6.87 0.00 0.00 3.67
1924 2145 1.634459 TGCCACCGGTAAAAATAGGGA 59.366 47.619 6.87 0.00 0.00 4.20
1925 2146 2.131776 TGCCACCGGTAAAAATAGGG 57.868 50.000 6.87 2.13 0.00 3.53
1929 2150 0.534873 GCCATGCCACCGGTAAAAAT 59.465 50.000 6.87 0.00 0.00 1.82
2036 2257 3.428282 GTTTACACGCCCGCCTGG 61.428 66.667 0.00 0.00 37.09 4.45
2038 2261 1.743995 GATGTTTACACGCCCGCCT 60.744 57.895 0.00 0.00 0.00 5.52
2043 2266 0.997196 GACCTCGATGTTTACACGCC 59.003 55.000 0.00 0.00 0.00 5.68
2114 2349 5.644636 GGCAAATTTGTGGATGATGTTGATT 59.355 36.000 19.03 0.00 0.00 2.57
2133 2368 2.642154 TCTAGGGTTTCGTTGGCAAA 57.358 45.000 0.00 0.00 0.00 3.68
2138 2373 3.399330 TCTGCTTTCTAGGGTTTCGTTG 58.601 45.455 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.