Multiple sequence alignment - TraesCS2B01G129900

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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 TraesCS2B01G129900 chr2B 100.000 2354 0 0 1 2354 97392255 97389902 0.000000e+00 4348.0
1 TraesCS2B01G129900 chr2A 90.224 982 61 20 509 1477 62366513 62365554 0.000000e+00 1249.0
2 TraesCS2B01G129900 chr2A 98.234 453 8 0 1 453 62366978 62366526 0.000000e+00 793.0
3 TraesCS2B01G129900 chr2A 85.636 550 51 8 1816 2352 62365068 62364534 9.510000e-154 553.0
4 TraesCS2B01G129900 chr2A 100.000 44 0 0 1706 1749 62365222 62365179 5.390000e-12 82.4
5 TraesCS2B01G129900 chr2D 81.780 1191 115 53 613 1749 62029124 62027982 0.000000e+00 904.0
6 TraesCS2B01G129900 chr2D 85.556 630 52 20 1742 2351 62027954 62027344 7.140000e-175 623.0
7 TraesCS2B01G129900 chr2D 80.000 90 18 0 1092 1181 572029046 572029135 1.510000e-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 TraesCS2B01G129900 chr2B 97389902 97392255 2353 True 4348.00 4348 100.0000 1 2354 1 chr2B.!!$R1 2353
1 TraesCS2B01G129900 chr2A 62364534 62366978 2444 True 669.35 1249 93.5235 1 2352 4 chr2A.!!$R1 2351
2 TraesCS2B01G129900 chr2D 62027344 62029124 1780 True 763.50 904 83.6680 613 2351 2 chr2D.!!$R1 1738

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
530 531 0.098552 TGTTTGTGCTTGTGCTCGTG 59.901 50.0 0.0 0.0 40.48 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2276 2511 0.113776 ACCTCCTTCGACCTGGTGTA 59.886 55.0 2.82 0.0 0.0 2.9 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
96 97 0.106894 CTTAGAAGGATGGTCGGGGC 59.893 60.000 0.00 0.00 0.00 5.80
132 133 1.652947 GTGGTAGGAGGTCAAAGGGA 58.347 55.000 0.00 0.00 0.00 4.20
138 139 1.377333 GAGGTCAAAGGGAAGGGCG 60.377 63.158 0.00 0.00 0.00 6.13
156 157 4.029809 GGGCGGTAAGGTGGCAGT 62.030 66.667 0.00 0.00 0.00 4.40
202 203 4.832608 GCGGTTAGGGCTGGGTCG 62.833 72.222 0.00 0.00 0.00 4.79
455 456 6.504398 CATCATTCCTTTGATTGATGTGAGG 58.496 40.000 14.65 0.00 45.57 3.86
456 457 5.818887 TCATTCCTTTGATTGATGTGAGGA 58.181 37.500 0.00 0.00 0.00 3.71
457 458 6.429151 TCATTCCTTTGATTGATGTGAGGAT 58.571 36.000 0.00 0.00 33.64 3.24
458 459 6.320418 TCATTCCTTTGATTGATGTGAGGATG 59.680 38.462 0.00 0.00 33.64 3.51
459 460 5.183530 TCCTTTGATTGATGTGAGGATGT 57.816 39.130 0.00 0.00 0.00 3.06
460 461 4.945543 TCCTTTGATTGATGTGAGGATGTG 59.054 41.667 0.00 0.00 0.00 3.21
461 462 4.439700 CCTTTGATTGATGTGAGGATGTGC 60.440 45.833 0.00 0.00 0.00 4.57
462 463 3.639672 TGATTGATGTGAGGATGTGCT 57.360 42.857 0.00 0.00 0.00 4.40
463 464 3.959293 TGATTGATGTGAGGATGTGCTT 58.041 40.909 0.00 0.00 0.00 3.91
464 465 3.692593 TGATTGATGTGAGGATGTGCTTG 59.307 43.478 0.00 0.00 0.00 4.01
465 466 3.421919 TTGATGTGAGGATGTGCTTGA 57.578 42.857 0.00 0.00 0.00 3.02
466 467 2.703416 TGATGTGAGGATGTGCTTGAC 58.297 47.619 0.00 0.00 0.00 3.18
467 468 2.303890 TGATGTGAGGATGTGCTTGACT 59.696 45.455 0.00 0.00 0.00 3.41
468 469 2.936919 TGTGAGGATGTGCTTGACTT 57.063 45.000 0.00 0.00 0.00 3.01
469 470 3.213206 TGTGAGGATGTGCTTGACTTT 57.787 42.857 0.00 0.00 0.00 2.66
470 471 2.880268 TGTGAGGATGTGCTTGACTTTG 59.120 45.455 0.00 0.00 0.00 2.77
471 472 3.141398 GTGAGGATGTGCTTGACTTTGA 58.859 45.455 0.00 0.00 0.00 2.69
472 473 3.188048 GTGAGGATGTGCTTGACTTTGAG 59.812 47.826 0.00 0.00 0.00 3.02
473 474 2.746362 GAGGATGTGCTTGACTTTGAGG 59.254 50.000 0.00 0.00 0.00 3.86
474 475 2.107204 AGGATGTGCTTGACTTTGAGGT 59.893 45.455 0.00 0.00 0.00 3.85
475 476 2.887152 GGATGTGCTTGACTTTGAGGTT 59.113 45.455 0.00 0.00 0.00 3.50
476 477 3.304928 GGATGTGCTTGACTTTGAGGTTG 60.305 47.826 0.00 0.00 0.00 3.77
477 478 1.405105 TGTGCTTGACTTTGAGGTTGC 59.595 47.619 0.00 0.00 0.00 4.17
478 479 1.032014 TGCTTGACTTTGAGGTTGCC 58.968 50.000 0.00 0.00 0.00 4.52
479 480 1.032014 GCTTGACTTTGAGGTTGCCA 58.968 50.000 0.00 0.00 0.00 4.92
480 481 1.269257 GCTTGACTTTGAGGTTGCCAC 60.269 52.381 0.00 0.00 0.00 5.01
481 482 2.301346 CTTGACTTTGAGGTTGCCACT 58.699 47.619 0.00 0.00 0.00 4.00
482 483 1.679139 TGACTTTGAGGTTGCCACTG 58.321 50.000 0.00 0.00 0.00 3.66
495 496 1.633432 TGCCACTGTAATAGCCTGGTT 59.367 47.619 0.00 0.00 0.00 3.67
496 497 2.289565 GCCACTGTAATAGCCTGGTTC 58.710 52.381 0.00 0.00 0.00 3.62
497 498 2.550978 CCACTGTAATAGCCTGGTTCG 58.449 52.381 0.00 0.00 0.00 3.95
498 499 2.093658 CCACTGTAATAGCCTGGTTCGT 60.094 50.000 0.00 0.00 0.00 3.85
499 500 2.930040 CACTGTAATAGCCTGGTTCGTG 59.070 50.000 0.00 0.00 0.00 4.35
500 501 2.565834 ACTGTAATAGCCTGGTTCGTGT 59.434 45.455 0.00 0.00 0.00 4.49
501 502 3.007614 ACTGTAATAGCCTGGTTCGTGTT 59.992 43.478 0.00 0.00 0.00 3.32
502 503 3.592059 TGTAATAGCCTGGTTCGTGTTC 58.408 45.455 0.00 0.00 0.00 3.18
503 504 1.722011 AATAGCCTGGTTCGTGTTCG 58.278 50.000 0.00 0.00 38.55 3.95
504 505 0.606604 ATAGCCTGGTTCGTGTTCGT 59.393 50.000 0.00 0.00 38.33 3.85
505 506 0.319211 TAGCCTGGTTCGTGTTCGTG 60.319 55.000 0.00 0.00 38.33 4.35
506 507 1.593209 GCCTGGTTCGTGTTCGTGA 60.593 57.895 0.00 0.00 38.33 4.35
507 508 1.155424 GCCTGGTTCGTGTTCGTGAA 61.155 55.000 0.00 0.00 38.33 3.18
530 531 0.098552 TGTTTGTGCTTGTGCTCGTG 59.901 50.000 0.00 0.00 40.48 4.35
732 740 2.271777 TGGACCGGGGTAGAAATTTCT 58.728 47.619 23.53 23.53 41.24 2.52
775 783 2.123982 GGGATGGCCTGGAGCTTG 60.124 66.667 3.32 0.00 43.05 4.01
821 836 3.603857 CGTGTTTTTCGATTTCGTGCTCT 60.604 43.478 0.00 0.00 40.80 4.09
829 844 2.659757 CGATTTCGTGCTCTTGTTCGTA 59.340 45.455 0.00 0.00 34.11 3.43
834 849 1.578023 CGTGCTCTTGTTCGTATCGTC 59.422 52.381 0.00 0.00 0.00 4.20
845 860 2.132352 GTATCGTCTTCCCGGCCCT 61.132 63.158 0.00 0.00 0.00 5.19
850 865 2.203938 TCTTCCCGGCCCTGTCTT 60.204 61.111 0.00 0.00 0.00 3.01
853 868 4.649705 TCCCGGCCCTGTCTTCCA 62.650 66.667 0.00 0.00 0.00 3.53
856 871 2.046892 CGGCCCTGTCTTCCAGTG 60.047 66.667 0.00 0.00 39.74 3.66
863 878 2.358737 GTCTTCCAGTGCACCCCG 60.359 66.667 14.63 1.99 0.00 5.73
876 891 3.126343 GTGCACCCCGTTGTCTATAAAAG 59.874 47.826 5.22 0.00 0.00 2.27
877 892 3.244630 TGCACCCCGTTGTCTATAAAAGT 60.245 43.478 0.00 0.00 0.00 2.66
878 893 3.373130 GCACCCCGTTGTCTATAAAAGTC 59.627 47.826 0.00 0.00 0.00 3.01
880 895 3.583966 ACCCCGTTGTCTATAAAAGTCCA 59.416 43.478 0.00 0.00 0.00 4.02
881 896 4.226620 ACCCCGTTGTCTATAAAAGTCCAT 59.773 41.667 0.00 0.00 0.00 3.41
882 897 4.574828 CCCCGTTGTCTATAAAAGTCCATG 59.425 45.833 0.00 0.00 0.00 3.66
883 898 4.574828 CCCGTTGTCTATAAAAGTCCATGG 59.425 45.833 4.97 4.97 0.00 3.66
884 899 4.035208 CCGTTGTCTATAAAAGTCCATGGC 59.965 45.833 6.96 2.00 0.00 4.40
888 903 3.138468 GTCTATAAAAGTCCATGGCCCCT 59.862 47.826 6.96 0.00 0.00 4.79
889 904 2.755952 ATAAAAGTCCATGGCCCCTC 57.244 50.000 6.96 0.00 0.00 4.30
925 941 1.808945 ACGCTCTGAAGCTCCAAATTG 59.191 47.619 0.00 0.00 46.91 2.32
927 943 2.681848 CGCTCTGAAGCTCCAAATTGAT 59.318 45.455 0.00 0.00 46.91 2.57
932 948 6.127786 GCTCTGAAGCTCCAAATTGATAGTTT 60.128 38.462 0.00 0.00 45.55 2.66
947 964 0.323957 AGTTTTCCCCTCTACACGCC 59.676 55.000 0.00 0.00 0.00 5.68
952 969 4.077184 CCCTCTACACGCCGCCAA 62.077 66.667 0.00 0.00 0.00 4.52
987 1004 8.737175 TCACAAATCACAAGTAGTAGTAGTAGG 58.263 37.037 0.00 0.00 0.00 3.18
988 1005 8.737175 CACAAATCACAAGTAGTAGTAGTAGGA 58.263 37.037 0.00 0.00 0.00 2.94
989 1006 9.305555 ACAAATCACAAGTAGTAGTAGTAGGAA 57.694 33.333 0.00 0.00 0.00 3.36
990 1007 9.570488 CAAATCACAAGTAGTAGTAGTAGGAAC 57.430 37.037 0.00 0.00 0.00 3.62
991 1008 9.531158 AAATCACAAGTAGTAGTAGTAGGAACT 57.469 33.333 0.00 0.00 46.37 3.01
1059 1076 3.782244 CGCGACTGCCACAAGCTC 61.782 66.667 0.00 0.00 44.23 4.09
1092 1109 1.228429 CCCTGGAGGCGTTTTCCAA 60.228 57.895 0.00 0.00 43.79 3.53
1134 1151 0.895530 TCGTCTTCAAGAAGCCCGAT 59.104 50.000 15.49 0.00 36.95 4.18
1144 1161 1.837439 AGAAGCCCGATGGTATGTTCA 59.163 47.619 0.00 0.00 0.00 3.18
1162 1179 0.387929 CATCCATCATGGCAAGGTGC 59.612 55.000 0.00 0.00 44.08 5.01
1294 1311 2.763215 GGAAGGTGGCCATGGTGA 59.237 61.111 9.72 0.00 0.00 4.02
1312 1329 1.285078 TGATCTCCGTCCTCTTCCTCA 59.715 52.381 0.00 0.00 0.00 3.86
1436 1462 4.503910 CAGTAAGTTTGTCCATCGATCCA 58.496 43.478 0.00 0.00 0.00 3.41
1439 1465 3.417069 AGTTTGTCCATCGATCCACAA 57.583 42.857 12.64 12.64 0.00 3.33
1462 1488 2.353803 GGAACACTGTTGATCTAGCGGT 60.354 50.000 0.00 0.00 0.00 5.68
1478 1504 6.213677 TCTAGCGGTTCATGTCATGTTATAC 58.786 40.000 12.54 7.04 0.00 1.47
1479 1505 4.127171 AGCGGTTCATGTCATGTTATACC 58.873 43.478 12.54 13.44 0.00 2.73
1488 1581 8.487313 TCATGTCATGTTATACCTGTTTACAC 57.513 34.615 12.54 0.00 0.00 2.90
1613 1747 7.599998 GCTGAATTTTGTTACACTTTGATCCAT 59.400 33.333 0.00 0.00 0.00 3.41
1665 1822 2.017049 GCAGTTGTATGGTGGATGGAC 58.983 52.381 0.00 0.00 0.00 4.02
1666 1823 2.356125 GCAGTTGTATGGTGGATGGACT 60.356 50.000 0.00 0.00 0.00 3.85
1667 1824 3.535561 CAGTTGTATGGTGGATGGACTC 58.464 50.000 0.00 0.00 0.00 3.36
1668 1825 3.055167 CAGTTGTATGGTGGATGGACTCA 60.055 47.826 0.00 0.00 0.00 3.41
1669 1826 3.782523 AGTTGTATGGTGGATGGACTCAT 59.217 43.478 0.00 0.00 36.09 2.90
1670 1827 3.843893 TGTATGGTGGATGGACTCATG 57.156 47.619 0.00 0.00 32.98 3.07
1671 1828 2.439135 TGTATGGTGGATGGACTCATGG 59.561 50.000 0.00 0.00 32.98 3.66
1672 1829 1.897473 ATGGTGGATGGACTCATGGA 58.103 50.000 0.00 0.00 32.98 3.41
1696 1853 3.168628 GCATTCCGTGTATGCATGC 57.831 52.632 11.82 11.82 45.93 4.06
1697 1854 0.664761 GCATTCCGTGTATGCATGCT 59.335 50.000 20.33 7.07 45.93 3.79
1698 1855 1.598676 GCATTCCGTGTATGCATGCTG 60.599 52.381 20.33 5.55 45.93 4.41
1699 1856 0.664761 ATTCCGTGTATGCATGCTGC 59.335 50.000 20.33 9.35 45.29 5.25
1749 1906 3.805422 ACGCGTGAACTGAATTTTGAGTA 59.195 39.130 12.93 0.00 0.00 2.59
1753 1943 6.199393 GCGTGAACTGAATTTTGAGTAAAGT 58.801 36.000 0.00 0.00 0.00 2.66
1757 1947 9.651718 GTGAACTGAATTTTGAGTAAAGTAGTG 57.348 33.333 0.00 0.00 0.00 2.74
1761 1951 4.680171 ATTTTGAGTAAAGTAGTGCGCC 57.320 40.909 4.18 0.00 0.00 6.53
1768 1958 2.185004 AAAGTAGTGCGCCACAGAAT 57.815 45.000 4.18 0.00 36.74 2.40
1783 1976 3.057315 CACAGAATTTTGCGTTCCCTCAT 60.057 43.478 0.00 0.00 0.00 2.90
1787 1980 5.801947 CAGAATTTTGCGTTCCCTCATAAAG 59.198 40.000 0.00 0.00 0.00 1.85
1837 2056 0.742505 CCAGCCCACATATGCACTTG 59.257 55.000 1.58 0.00 0.00 3.16
1838 2057 0.101759 CAGCCCACATATGCACTTGC 59.898 55.000 1.58 0.00 42.50 4.01
1839 2058 1.064621 GCCCACATATGCACTTGCG 59.935 57.895 1.58 0.00 45.83 4.85
1841 2060 1.064621 CCACATATGCACTTGCGGC 59.935 57.895 1.58 0.00 45.83 6.53
1875 2104 2.804933 GCTTGCTTAAGAGAGATCCCCG 60.805 54.545 6.67 0.00 0.00 5.73
1877 2106 0.034198 GCTTAAGAGAGATCCCCGGC 59.966 60.000 6.67 0.00 0.00 6.13
1879 2108 0.264955 TTAAGAGAGATCCCCGGCCT 59.735 55.000 0.00 0.00 0.00 5.19
1881 2110 1.051556 AAGAGAGATCCCCGGCCTTC 61.052 60.000 0.00 0.00 0.00 3.46
1882 2111 1.458588 GAGAGATCCCCGGCCTTCT 60.459 63.158 0.00 0.00 0.00 2.85
1884 2113 1.147153 GAGATCCCCGGCCTTCTTG 59.853 63.158 0.00 0.00 0.00 3.02
1987 2222 4.587891 CTTTGAGATGGAGGAAGAAGCTT 58.412 43.478 0.00 0.00 0.00 3.74
2043 2278 3.876198 GTTCAATGGCGCGCGGAT 61.876 61.111 33.06 16.87 0.00 4.18
2076 2311 1.522092 CCTGCGGATGGACAAGCTA 59.478 57.895 0.00 0.00 0.00 3.32
2091 2326 1.364171 GCTAGATGCGTGGATCCGT 59.636 57.895 7.39 0.00 0.00 4.69
2104 2339 1.616628 ATCCGTGGAGAGGGGCTTT 60.617 57.895 0.00 0.00 0.00 3.51
2147 2382 7.223582 GCTAAAATCTGAGATCGATGAAGTCAA 59.776 37.037 0.54 0.00 0.00 3.18
2161 2396 1.444553 GTCAAGGCGACGGTCTCTG 60.445 63.158 6.57 0.00 34.19 3.35
2166 2401 0.393944 AGGCGACGGTCTCTGATGTA 60.394 55.000 6.57 0.00 0.00 2.29
2179 2414 0.619255 TGATGTAAAGGGGAGGGCGA 60.619 55.000 0.00 0.00 0.00 5.54
2181 2416 0.765510 ATGTAAAGGGGAGGGCGATC 59.234 55.000 0.00 0.00 0.00 3.69
2276 2511 4.186159 GAGCTCGACTACTACAGACTTCT 58.814 47.826 0.00 0.00 0.00 2.85
2298 2542 1.204941 CACCAGGTCGAAGGAGGTAAG 59.795 57.143 6.80 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 2.438951 TAACAACTCCGCGACACCCC 62.439 60.000 8.23 0.00 0.00 4.95
96 97 3.663176 CCGTTGTGCTGGCCACTG 61.663 66.667 0.00 0.00 44.92 3.66
138 139 4.796495 CTGCCACCTTACCGCCCC 62.796 72.222 0.00 0.00 0.00 5.80
177 178 2.804912 GCCCTAACCGCCTACCTCC 61.805 68.421 0.00 0.00 0.00 4.30
453 454 2.107204 ACCTCAAAGTCAAGCACATCCT 59.893 45.455 0.00 0.00 0.00 3.24
454 455 2.508526 ACCTCAAAGTCAAGCACATCC 58.491 47.619 0.00 0.00 0.00 3.51
455 456 3.854784 GCAACCTCAAAGTCAAGCACATC 60.855 47.826 0.00 0.00 0.00 3.06
456 457 2.035066 GCAACCTCAAAGTCAAGCACAT 59.965 45.455 0.00 0.00 0.00 3.21
457 458 1.405105 GCAACCTCAAAGTCAAGCACA 59.595 47.619 0.00 0.00 0.00 4.57
458 459 1.269257 GGCAACCTCAAAGTCAAGCAC 60.269 52.381 0.00 0.00 0.00 4.40
459 460 1.032014 GGCAACCTCAAAGTCAAGCA 58.968 50.000 0.00 0.00 0.00 3.91
460 461 1.032014 TGGCAACCTCAAAGTCAAGC 58.968 50.000 0.00 0.00 0.00 4.01
461 462 2.033801 CAGTGGCAACCTCAAAGTCAAG 59.966 50.000 0.00 0.00 0.00 3.02
462 463 2.023673 CAGTGGCAACCTCAAAGTCAA 58.976 47.619 0.00 0.00 0.00 3.18
463 464 1.064758 ACAGTGGCAACCTCAAAGTCA 60.065 47.619 0.00 0.00 0.00 3.41
464 465 1.680338 ACAGTGGCAACCTCAAAGTC 58.320 50.000 0.00 0.00 0.00 3.01
465 466 3.290948 TTACAGTGGCAACCTCAAAGT 57.709 42.857 0.00 0.00 0.00 2.66
466 467 4.142600 GCTATTACAGTGGCAACCTCAAAG 60.143 45.833 0.00 0.00 0.00 2.77
467 468 3.756434 GCTATTACAGTGGCAACCTCAAA 59.244 43.478 0.00 0.00 0.00 2.69
468 469 3.343617 GCTATTACAGTGGCAACCTCAA 58.656 45.455 0.00 0.00 0.00 3.02
469 470 2.355716 GGCTATTACAGTGGCAACCTCA 60.356 50.000 0.00 0.00 0.00 3.86
470 471 2.092914 AGGCTATTACAGTGGCAACCTC 60.093 50.000 0.00 0.00 0.00 3.85
471 472 1.916181 AGGCTATTACAGTGGCAACCT 59.084 47.619 0.00 0.00 0.00 3.50
472 473 2.017049 CAGGCTATTACAGTGGCAACC 58.983 52.381 0.00 0.00 0.00 3.77
473 474 2.017049 CCAGGCTATTACAGTGGCAAC 58.983 52.381 0.00 0.00 0.00 4.17
474 475 1.633432 ACCAGGCTATTACAGTGGCAA 59.367 47.619 0.00 0.00 0.00 4.52
475 476 1.285280 ACCAGGCTATTACAGTGGCA 58.715 50.000 0.00 0.00 0.00 4.92
476 477 2.289565 GAACCAGGCTATTACAGTGGC 58.710 52.381 0.00 0.00 0.00 5.01
477 478 2.093658 ACGAACCAGGCTATTACAGTGG 60.094 50.000 0.00 0.00 0.00 4.00
478 479 2.930040 CACGAACCAGGCTATTACAGTG 59.070 50.000 0.00 0.00 0.00 3.66
479 480 2.565834 ACACGAACCAGGCTATTACAGT 59.434 45.455 0.00 0.00 0.00 3.55
480 481 3.247006 ACACGAACCAGGCTATTACAG 57.753 47.619 0.00 0.00 0.00 2.74
481 482 3.592059 GAACACGAACCAGGCTATTACA 58.408 45.455 0.00 0.00 0.00 2.41
482 483 2.601763 CGAACACGAACCAGGCTATTAC 59.398 50.000 0.00 0.00 0.00 1.89
495 496 1.842720 AACACGATTCACGAACACGA 58.157 45.000 12.73 0.00 45.77 4.35
496 497 2.285371 ACAAACACGATTCACGAACACG 60.285 45.455 0.00 6.65 45.77 4.49
497 498 3.026349 CACAAACACGATTCACGAACAC 58.974 45.455 0.00 0.00 45.77 3.32
498 499 2.537931 GCACAAACACGATTCACGAACA 60.538 45.455 0.00 0.00 45.77 3.18
499 500 2.034076 GCACAAACACGATTCACGAAC 58.966 47.619 0.00 0.00 45.77 3.95
500 501 1.937223 AGCACAAACACGATTCACGAA 59.063 42.857 0.00 0.00 45.77 3.85
501 502 1.577468 AGCACAAACACGATTCACGA 58.423 45.000 0.00 0.00 45.77 4.35
503 504 2.783284 CACAAGCACAAACACGATTCAC 59.217 45.455 0.00 0.00 0.00 3.18
504 505 2.794282 GCACAAGCACAAACACGATTCA 60.794 45.455 0.00 0.00 41.58 2.57
505 506 1.780860 GCACAAGCACAAACACGATTC 59.219 47.619 0.00 0.00 41.58 2.52
506 507 1.405105 AGCACAAGCACAAACACGATT 59.595 42.857 0.00 0.00 45.49 3.34
507 508 1.002468 GAGCACAAGCACAAACACGAT 60.002 47.619 0.00 0.00 45.49 3.73
530 531 1.355066 GCAGCTAGCGTCACAAGACC 61.355 60.000 9.55 0.00 41.87 3.85
595 599 4.678287 GTCACATGTCACATCAAAGCTTTG 59.322 41.667 29.53 29.53 39.48 2.77
694 702 1.136252 CCAAATGAGCACGAACACGAG 60.136 52.381 0.00 0.00 0.00 4.18
775 783 2.012673 CCATGTTAAGAGTCAGCTGCC 58.987 52.381 9.47 0.00 0.00 4.85
821 836 1.135315 CCGGGAAGACGATACGAACAA 60.135 52.381 0.00 0.00 35.47 2.83
829 844 3.470888 CAGGGCCGGGAAGACGAT 61.471 66.667 2.18 0.00 35.47 3.73
834 849 2.269241 GAAGACAGGGCCGGGAAG 59.731 66.667 8.94 0.00 0.00 3.46
845 860 2.836154 GGGGTGCACTGGAAGACA 59.164 61.111 17.98 0.00 37.43 3.41
850 865 3.469863 GACAACGGGGTGCACTGGA 62.470 63.158 17.98 0.00 0.00 3.86
853 868 1.563924 TATAGACAACGGGGTGCACT 58.436 50.000 17.98 0.00 0.00 4.40
856 871 3.340928 ACTTTTATAGACAACGGGGTGC 58.659 45.455 0.00 0.00 0.00 5.01
863 878 4.338400 GGGCCATGGACTTTTATAGACAAC 59.662 45.833 19.55 0.00 0.00 3.32
876 891 2.692368 TGGAGAGGGGCCATGGAC 60.692 66.667 18.40 14.40 0.00 4.02
877 892 2.692368 GTGGAGAGGGGCCATGGA 60.692 66.667 18.40 0.00 37.81 3.41
878 893 3.813724 GGTGGAGAGGGGCCATGG 61.814 72.222 7.63 7.63 37.81 3.66
880 895 1.224003 AAATGGTGGAGAGGGGCCAT 61.224 55.000 4.39 0.00 42.90 4.40
881 896 1.442886 AAAATGGTGGAGAGGGGCCA 61.443 55.000 4.39 0.00 35.28 5.36
882 897 0.684479 GAAAATGGTGGAGAGGGGCC 60.684 60.000 0.00 0.00 0.00 5.80
883 898 1.032114 CGAAAATGGTGGAGAGGGGC 61.032 60.000 0.00 0.00 0.00 5.80
884 899 1.032114 GCGAAAATGGTGGAGAGGGG 61.032 60.000 0.00 0.00 0.00 4.79
888 903 0.953471 CGTGGCGAAAATGGTGGAGA 60.953 55.000 0.00 0.00 0.00 3.71
889 904 1.501741 CGTGGCGAAAATGGTGGAG 59.498 57.895 0.00 0.00 0.00 3.86
925 941 3.455327 GCGTGTAGAGGGGAAAACTATC 58.545 50.000 0.00 0.00 0.00 2.08
927 943 1.551883 GGCGTGTAGAGGGGAAAACTA 59.448 52.381 0.00 0.00 0.00 2.24
932 948 3.766691 GCGGCGTGTAGAGGGGAA 61.767 66.667 9.37 0.00 0.00 3.97
947 964 0.813610 TTGTGAGTGGTCTGTTGGCG 60.814 55.000 0.00 0.00 0.00 5.69
952 969 3.558931 TGTGATTTGTGAGTGGTCTGT 57.441 42.857 0.00 0.00 0.00 3.41
987 1004 1.133976 ACATCCATGGCTGGCTAGTTC 60.134 52.381 19.40 0.00 42.80 3.01
988 1005 0.921896 ACATCCATGGCTGGCTAGTT 59.078 50.000 19.40 0.00 42.80 2.24
989 1006 0.182061 CACATCCATGGCTGGCTAGT 59.818 55.000 19.40 0.00 42.80 2.57
990 1007 0.536687 CCACATCCATGGCTGGCTAG 60.537 60.000 19.40 6.58 42.80 3.42
991 1008 0.987613 TCCACATCCATGGCTGGCTA 60.988 55.000 19.40 1.62 42.80 3.93
1134 1151 3.117587 TGCCATGATGGATGAACATACCA 60.118 43.478 17.22 0.00 40.96 3.25
1144 1161 2.816746 GCACCTTGCCATGATGGAT 58.183 52.632 17.22 0.00 40.96 3.41
1162 1179 1.680207 GGCGTAGTACAGGTAGAAGGG 59.320 57.143 0.38 0.00 0.00 3.95
1270 1287 0.406361 ATGGCCACCTTCCCGTAAAA 59.594 50.000 8.16 0.00 0.00 1.52
1271 1288 0.322997 CATGGCCACCTTCCCGTAAA 60.323 55.000 8.16 0.00 0.00 2.01
1294 1311 2.593026 GATGAGGAAGAGGACGGAGAT 58.407 52.381 0.00 0.00 0.00 2.75
1312 1329 2.671070 CAGGCCACCAACGAGGAT 59.329 61.111 5.01 0.00 41.22 3.24
1344 1361 2.092914 GGCTCATGGCTACTACTTTGGT 60.093 50.000 6.20 0.00 41.46 3.67
1397 1423 5.872070 ACTTACTGCATGAGCTTCTTCTAAC 59.128 40.000 0.00 0.00 42.74 2.34
1436 1462 3.864789 AGATCAACAGTGTTCCCTTGT 57.135 42.857 5.27 0.00 0.00 3.16
1439 1465 2.093973 CGCTAGATCAACAGTGTTCCCT 60.094 50.000 5.27 6.10 0.00 4.20
1445 1471 2.959516 TGAACCGCTAGATCAACAGTG 58.040 47.619 0.00 0.00 0.00 3.66
1462 1488 8.941977 GTGTAAACAGGTATAACATGACATGAA 58.058 33.333 22.19 9.75 33.56 2.57
1513 1606 7.619512 ACAAACCTTGGTAAAATAATCCCAA 57.380 32.000 0.00 0.00 35.72 4.12
1549 1647 5.623368 GCCATGGAATTTACCGTGATCAAAA 60.623 40.000 18.40 0.00 46.43 2.44
1551 1649 3.380004 GCCATGGAATTTACCGTGATCAA 59.620 43.478 18.40 0.00 46.43 2.57
1552 1650 2.948979 GCCATGGAATTTACCGTGATCA 59.051 45.455 18.40 0.00 46.43 2.92
1554 1652 3.297134 AGCCATGGAATTTACCGTGAT 57.703 42.857 18.40 0.00 46.43 3.06
1555 1653 2.752354 CAAGCCATGGAATTTACCGTGA 59.248 45.455 18.40 0.00 46.43 4.35
1556 1654 2.491693 ACAAGCCATGGAATTTACCGTG 59.508 45.455 18.40 6.79 44.04 4.94
1617 1751 9.349713 ACAGTTCTTCAGTTTTCCATTACATAA 57.650 29.630 0.00 0.00 0.00 1.90
1640 1797 1.167851 CCACCATACAACTGCCACAG 58.832 55.000 0.00 0.00 37.52 3.66
1665 1822 4.276678 ACACGGAATGCAAATATCCATGAG 59.723 41.667 12.30 0.45 31.23 2.90
1666 1823 4.206375 ACACGGAATGCAAATATCCATGA 58.794 39.130 12.30 0.00 31.23 3.07
1667 1824 4.572985 ACACGGAATGCAAATATCCATG 57.427 40.909 10.58 8.30 32.89 3.66
1668 1825 6.258230 CATACACGGAATGCAAATATCCAT 57.742 37.500 10.58 0.00 32.58 3.41
1669 1826 5.687770 CATACACGGAATGCAAATATCCA 57.312 39.130 10.58 0.00 32.58 3.41
1693 1850 5.008811 GCATTCTCTATTTCTCTTGCAGCAT 59.991 40.000 0.00 0.00 0.00 3.79
1694 1851 4.334759 GCATTCTCTATTTCTCTTGCAGCA 59.665 41.667 0.00 0.00 0.00 4.41
1695 1852 4.575645 AGCATTCTCTATTTCTCTTGCAGC 59.424 41.667 0.00 0.00 0.00 5.25
1696 1853 5.816258 TCAGCATTCTCTATTTCTCTTGCAG 59.184 40.000 0.00 0.00 0.00 4.41
1697 1854 5.737860 TCAGCATTCTCTATTTCTCTTGCA 58.262 37.500 0.00 0.00 0.00 4.08
1698 1855 6.674694 TTCAGCATTCTCTATTTCTCTTGC 57.325 37.500 0.00 0.00 0.00 4.01
1699 1856 7.133513 GCATTCAGCATTCTCTATTTCTCTTG 58.866 38.462 0.00 0.00 44.79 3.02
1749 1906 2.185004 ATTCTGTGGCGCACTACTTT 57.815 45.000 10.83 0.00 35.11 2.66
1753 1943 1.068610 GCAAAATTCTGTGGCGCACTA 60.069 47.619 10.83 0.00 35.11 2.74
1757 1947 3.451250 CGCAAAATTCTGTGGCGC 58.549 55.556 0.00 0.00 41.27 6.53
1761 1951 2.293122 TGAGGGAACGCAAAATTCTGTG 59.707 45.455 0.00 0.00 37.13 3.66
1768 1958 5.776173 TTTCTTTATGAGGGAACGCAAAA 57.224 34.783 0.00 0.00 45.56 2.44
1795 1988 4.475135 GGGCTCCTGGCGGAACTC 62.475 72.222 0.00 0.00 42.94 3.01
1837 2056 2.426023 CTATAGGTGGTGGGCCGC 59.574 66.667 9.05 9.05 44.31 6.53
1838 2057 1.696097 AAGCTATAGGTGGTGGGCCG 61.696 60.000 4.96 0.00 37.67 6.13
1839 2058 0.179018 CAAGCTATAGGTGGTGGGCC 60.179 60.000 4.96 0.00 0.00 5.80
1841 2060 0.839946 AGCAAGCTATAGGTGGTGGG 59.160 55.000 4.96 0.00 0.00 4.61
1877 2106 2.485814 GAGCAGTTAACAGGCAAGAAGG 59.514 50.000 20.07 0.00 0.00 3.46
1879 2108 3.403038 GAGAGCAGTTAACAGGCAAGAA 58.597 45.455 20.07 0.00 0.00 2.52
1881 2110 2.079925 GGAGAGCAGTTAACAGGCAAG 58.920 52.381 20.07 0.87 0.00 4.01
1882 2111 1.699634 AGGAGAGCAGTTAACAGGCAA 59.300 47.619 20.07 0.00 0.00 4.52
1884 2113 3.828875 ATAGGAGAGCAGTTAACAGGC 57.171 47.619 8.61 11.02 0.00 4.85
1889 2119 4.467795 AGTGCTGAATAGGAGAGCAGTTAA 59.532 41.667 0.00 0.00 42.48 2.01
1890 2120 4.026744 AGTGCTGAATAGGAGAGCAGTTA 58.973 43.478 0.00 0.00 42.48 2.24
1987 2222 3.680620 CTTCCATCGCCGCCCTCAA 62.681 63.158 0.00 0.00 0.00 3.02
2043 2278 0.691078 GCAGGGTCTGGAGGATGGTA 60.691 60.000 0.00 0.00 31.21 3.25
2076 2311 2.021068 CTCCACGGATCCACGCATCT 62.021 60.000 13.41 0.00 37.37 2.90
2091 2326 1.306997 ATCGGAAAGCCCCTCTCCA 60.307 57.895 0.00 0.00 0.00 3.86
2124 2359 6.538021 CCTTGACTTCATCGATCTCAGATTTT 59.462 38.462 0.00 0.00 0.00 1.82
2147 2382 0.393944 TACATCAGAGACCGTCGCCT 60.394 55.000 0.00 0.00 0.00 5.52
2161 2396 0.765510 ATCGCCCTCCCCTTTACATC 59.234 55.000 0.00 0.00 0.00 3.06
2166 2401 3.480133 CCGATCGCCCTCCCCTTT 61.480 66.667 10.32 0.00 0.00 3.11
2276 2511 0.113776 ACCTCCTTCGACCTGGTGTA 59.886 55.000 2.82 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.