Multiple sequence alignment - TraesCS5D01G140200

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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 TraesCS5D01G140200 chr5D 100.000 3533 0 0 1 3533 223886718 223890250 0.000000e+00 6525.0
1 TraesCS5D01G140200 chr5D 97.059 34 0 1 96 129 512531098 512531066 4.930000e-04 56.5
2 TraesCS5D01G140200 chr5B 96.260 3075 71 14 471 3533 247667394 247664352 0.000000e+00 5001.0
3 TraesCS5D01G140200 chr5B 89.744 390 28 6 62 449 247667770 247667391 4.100000e-134 488.0
4 TraesCS5D01G140200 chr5A 92.884 2656 99 36 892 3530 296468162 296470744 0.000000e+00 3775.0
5 TraesCS5D01G140200 chr5A 93.240 858 47 6 53 900 296467286 296468142 0.000000e+00 1253.0


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 TraesCS5D01G140200 chr5D 223886718 223890250 3532 False 6525.0 6525 100.000 1 3533 1 chr5D.!!$F1 3532
1 TraesCS5D01G140200 chr5B 247664352 247667770 3418 True 2744.5 5001 93.002 62 3533 2 chr5B.!!$R1 3471
2 TraesCS5D01G140200 chr5A 296467286 296470744 3458 False 2514.0 3775 93.062 53 3530 2 chr5A.!!$F1 3477

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
969 1037 0.031716 TCCACCTCCTCCTCCATCAG 60.032 60.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2766 2839 0.10852 GCTGCATGTGTTTCCATGGG 60.109 55.0 13.02 0.0 42.01 4.0 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
38 39 3.179939 GACGAAACGCGCCCTCTC 61.180 66.667 5.73 0.00 46.04 3.20
39 40 4.736896 ACGAAACGCGCCCTCTCC 62.737 66.667 5.73 0.00 46.04 3.71
48 49 4.516195 GCCCTCTCCGCGAAGGTC 62.516 72.222 8.23 0.00 41.99 3.85
49 50 4.194720 CCCTCTCCGCGAAGGTCG 62.195 72.222 8.23 0.00 43.89 4.79
98 99 2.018542 TATCGAGTCCCGGCAAAAAG 57.981 50.000 0.00 0.00 39.14 2.27
102 103 1.334689 CGAGTCCCGGCAAAAAGAAAC 60.335 52.381 0.00 0.00 33.91 2.78
106 109 2.100087 GTCCCGGCAAAAAGAAACTGAA 59.900 45.455 0.00 0.00 0.00 3.02
109 112 2.857748 CCGGCAAAAAGAAACTGAACAC 59.142 45.455 0.00 0.00 0.00 3.32
110 113 2.529894 CGGCAAAAAGAAACTGAACACG 59.470 45.455 0.00 0.00 0.00 4.49
236 239 5.182950 TCGCAACAACATAAATTGACATCCT 59.817 36.000 0.00 0.00 33.57 3.24
241 244 6.009589 ACAACATAAATTGACATCCTGGACA 58.990 36.000 0.00 0.00 33.57 4.02
258 261 4.507710 TGGACAGTCAGATTTGCTATGTC 58.492 43.478 2.17 6.71 0.00 3.06
386 392 2.847901 CTGGTCGTAACACGTCTGTAG 58.152 52.381 0.00 0.00 43.14 2.74
387 393 1.069022 TGGTCGTAACACGTCTGTAGC 60.069 52.381 0.00 0.00 43.14 3.58
445 451 5.948758 TGATGCACCACCAACAGATTTTATA 59.051 36.000 0.00 0.00 0.00 0.98
446 452 5.637006 TGCACCACCAACAGATTTTATAC 57.363 39.130 0.00 0.00 0.00 1.47
447 453 5.073428 TGCACCACCAACAGATTTTATACA 58.927 37.500 0.00 0.00 0.00 2.29
448 454 5.182950 TGCACCACCAACAGATTTTATACAG 59.817 40.000 0.00 0.00 0.00 2.74
449 455 5.393027 GCACCACCAACAGATTTTATACAGG 60.393 44.000 0.00 0.00 0.00 4.00
450 456 5.125417 CACCACCAACAGATTTTATACAGGG 59.875 44.000 0.00 0.00 0.00 4.45
451 457 5.014755 ACCACCAACAGATTTTATACAGGGA 59.985 40.000 0.00 0.00 0.00 4.20
452 458 5.590259 CCACCAACAGATTTTATACAGGGAG 59.410 44.000 0.00 0.00 0.00 4.30
453 459 5.590259 CACCAACAGATTTTATACAGGGAGG 59.410 44.000 0.00 0.00 0.00 4.30
454 460 5.133221 CCAACAGATTTTATACAGGGAGGG 58.867 45.833 0.00 0.00 0.00 4.30
455 461 5.133221 CAACAGATTTTATACAGGGAGGGG 58.867 45.833 0.00 0.00 0.00 4.79
456 462 4.641868 ACAGATTTTATACAGGGAGGGGA 58.358 43.478 0.00 0.00 0.00 4.81
457 463 5.043762 ACAGATTTTATACAGGGAGGGGAA 58.956 41.667 0.00 0.00 0.00 3.97
458 464 5.132816 ACAGATTTTATACAGGGAGGGGAAG 59.867 44.000 0.00 0.00 0.00 3.46
459 465 4.665483 AGATTTTATACAGGGAGGGGAAGG 59.335 45.833 0.00 0.00 0.00 3.46
460 466 2.507478 TTATACAGGGAGGGGAAGGG 57.493 55.000 0.00 0.00 0.00 3.95
461 467 1.640202 TATACAGGGAGGGGAAGGGA 58.360 55.000 0.00 0.00 0.00 4.20
462 468 0.728843 ATACAGGGAGGGGAAGGGAA 59.271 55.000 0.00 0.00 0.00 3.97
463 469 0.499147 TACAGGGAGGGGAAGGGAAA 59.501 55.000 0.00 0.00 0.00 3.13
464 470 0.404346 ACAGGGAGGGGAAGGGAAAA 60.404 55.000 0.00 0.00 0.00 2.29
465 471 0.783850 CAGGGAGGGGAAGGGAAAAA 59.216 55.000 0.00 0.00 0.00 1.94
625 662 3.951680 AGGCCAAGAAACGAGAAAGAAAA 59.048 39.130 5.01 0.00 0.00 2.29
627 664 4.036380 GGCCAAGAAACGAGAAAGAAAAGA 59.964 41.667 0.00 0.00 0.00 2.52
833 870 4.106987 CCCATATCTCCCTGGAATCCTTTT 59.893 45.833 0.00 0.00 34.24 2.27
936 1001 1.623834 CCTCCTGCCTTTCCTCTACCT 60.624 57.143 0.00 0.00 0.00 3.08
937 1002 1.760029 CTCCTGCCTTTCCTCTACCTC 59.240 57.143 0.00 0.00 0.00 3.85
938 1003 1.078823 TCCTGCCTTTCCTCTACCTCA 59.921 52.381 0.00 0.00 0.00 3.86
939 1004 2.122768 CCTGCCTTTCCTCTACCTCAT 58.877 52.381 0.00 0.00 0.00 2.90
940 1005 3.052109 TCCTGCCTTTCCTCTACCTCATA 60.052 47.826 0.00 0.00 0.00 2.15
941 1006 3.323403 CCTGCCTTTCCTCTACCTCATAG 59.677 52.174 0.00 0.00 0.00 2.23
942 1007 2.700897 TGCCTTTCCTCTACCTCATAGC 59.299 50.000 0.00 0.00 0.00 2.97
943 1008 2.700897 GCCTTTCCTCTACCTCATAGCA 59.299 50.000 0.00 0.00 0.00 3.49
944 1009 3.134804 GCCTTTCCTCTACCTCATAGCAA 59.865 47.826 0.00 0.00 0.00 3.91
946 1011 5.012148 GCCTTTCCTCTACCTCATAGCAATA 59.988 44.000 0.00 0.00 0.00 1.90
947 1012 6.696411 CCTTTCCTCTACCTCATAGCAATAG 58.304 44.000 0.00 0.00 0.00 1.73
948 1013 5.730296 TTCCTCTACCTCATAGCAATAGC 57.270 43.478 0.00 0.00 42.56 2.97
949 1014 4.740902 TCCTCTACCTCATAGCAATAGCA 58.259 43.478 0.00 0.00 45.49 3.49
950 1015 5.336945 TCCTCTACCTCATAGCAATAGCAT 58.663 41.667 0.00 0.00 45.49 3.79
951 1016 5.420421 TCCTCTACCTCATAGCAATAGCATC 59.580 44.000 0.00 0.00 45.49 3.91
954 1019 4.013267 ACCTCATAGCAATAGCATCCAC 57.987 45.455 0.00 0.00 45.49 4.02
955 1020 3.244700 ACCTCATAGCAATAGCATCCACC 60.245 47.826 0.00 0.00 45.49 4.61
969 1037 0.031716 TCCACCTCCTCCTCCATCAG 60.032 60.000 0.00 0.00 0.00 2.90
970 1038 1.053264 CCACCTCCTCCTCCATCAGG 61.053 65.000 0.00 0.00 45.15 3.86
985 1053 1.369209 CAGGCAAAACACACGCTCG 60.369 57.895 0.00 0.00 0.00 5.03
1074 1143 1.107114 TCCTCGACAGGAAGCTCATC 58.893 55.000 0.00 0.00 46.84 2.92
1242 1314 0.620556 GAGTTCTTGGGGCTCCATGA 59.379 55.000 17.03 17.03 43.63 3.07
1312 1384 6.101650 AGATAGATGGTTTATCATGTGCGA 57.898 37.500 0.00 0.00 38.31 5.10
1333 1405 3.367646 AGCCACAGTACTAGTGCTCTA 57.632 47.619 10.90 0.00 35.69 2.43
1351 1423 9.899226 AGTGCTCTAAAATTGTTTCTGATTAAC 57.101 29.630 0.00 0.00 0.00 2.01
1365 1437 8.301720 GTTTCTGATTAACTAATTCCGGGTTTT 58.698 33.333 0.00 0.00 0.00 2.43
1409 1481 3.006859 TGAACGTGAACCTCATCATCACT 59.993 43.478 0.00 0.00 40.95 3.41
1467 1539 3.055094 GCTCAAGAAGATCAAGGTACCCA 60.055 47.826 8.74 0.00 0.00 4.51
1481 1553 4.377762 GGTACCCACCTTTTCTTTACCT 57.622 45.455 0.00 0.00 42.11 3.08
1482 1554 4.077108 GGTACCCACCTTTTCTTTACCTG 58.923 47.826 0.00 0.00 42.11 4.00
1483 1555 4.202493 GGTACCCACCTTTTCTTTACCTGA 60.202 45.833 0.00 0.00 42.11 3.86
1484 1556 4.529716 ACCCACCTTTTCTTTACCTGAA 57.470 40.909 0.00 0.00 0.00 3.02
1485 1557 5.074746 ACCCACCTTTTCTTTACCTGAAT 57.925 39.130 0.00 0.00 0.00 2.57
1486 1558 4.832823 ACCCACCTTTTCTTTACCTGAATG 59.167 41.667 0.00 0.00 0.00 2.67
1487 1559 5.076873 CCCACCTTTTCTTTACCTGAATGA 58.923 41.667 0.00 0.00 0.00 2.57
1488 1560 5.538433 CCCACCTTTTCTTTACCTGAATGAA 59.462 40.000 0.00 0.00 31.26 2.57
1489 1561 6.041523 CCCACCTTTTCTTTACCTGAATGAAA 59.958 38.462 0.00 0.00 38.65 2.69
1490 1562 7.256296 CCCACCTTTTCTTTACCTGAATGAAAT 60.256 37.037 0.00 0.00 39.56 2.17
1491 1563 7.599998 CCACCTTTTCTTTACCTGAATGAAATG 59.400 37.037 0.00 0.00 39.56 2.32
1492 1564 8.143835 CACCTTTTCTTTACCTGAATGAAATGT 58.856 33.333 0.00 0.00 39.56 2.71
1493 1565 8.704668 ACCTTTTCTTTACCTGAATGAAATGTT 58.295 29.630 0.00 0.00 39.56 2.71
1494 1566 9.196552 CCTTTTCTTTACCTGAATGAAATGTTC 57.803 33.333 0.00 0.00 39.56 3.18
1495 1567 9.971922 CTTTTCTTTACCTGAATGAAATGTTCT 57.028 29.630 0.00 0.00 39.56 3.01
1497 1569 9.748708 TTTCTTTACCTGAATGAAATGTTCTTG 57.251 29.630 0.00 0.00 36.68 3.02
1498 1570 8.690203 TCTTTACCTGAATGAAATGTTCTTGA 57.310 30.769 0.00 0.00 0.00 3.02
1499 1571 9.300681 TCTTTACCTGAATGAAATGTTCTTGAT 57.699 29.630 0.00 0.00 0.00 2.57
1500 1572 9.350357 CTTTACCTGAATGAAATGTTCTTGATG 57.650 33.333 0.00 0.00 0.00 3.07
1501 1573 6.906157 ACCTGAATGAAATGTTCTTGATGT 57.094 33.333 0.00 0.00 0.00 3.06
1502 1574 6.684686 ACCTGAATGAAATGTTCTTGATGTG 58.315 36.000 0.00 0.00 0.00 3.21
1503 1575 6.491062 ACCTGAATGAAATGTTCTTGATGTGA 59.509 34.615 0.00 0.00 0.00 3.58
1504 1576 7.177921 ACCTGAATGAAATGTTCTTGATGTGAT 59.822 33.333 0.00 0.00 0.00 3.06
1505 1577 7.488150 CCTGAATGAAATGTTCTTGATGTGATG 59.512 37.037 0.00 0.00 0.00 3.07
1506 1578 8.113173 TGAATGAAATGTTCTTGATGTGATGA 57.887 30.769 0.00 0.00 0.00 2.92
1507 1579 8.241367 TGAATGAAATGTTCTTGATGTGATGAG 58.759 33.333 0.00 0.00 0.00 2.90
1548 1620 0.694771 AAGCCTGAAGAGCATGGTGA 59.305 50.000 0.00 0.00 0.00 4.02
1566 1639 2.492484 GTGACTAATGGTCTCCGTCTGT 59.508 50.000 0.00 0.00 44.74 3.41
1664 1737 0.320771 ATCAACAGGTGAGCACGGTC 60.321 55.000 0.00 0.00 40.43 4.79
1714 1787 6.599244 TGGAAACCAGATTGATTACTGATGAC 59.401 38.462 0.00 0.00 36.38 3.06
1734 1807 8.390354 TGATGACGCTGATTTAGAAACTTTATG 58.610 33.333 0.00 0.00 0.00 1.90
2083 2156 9.930693 GTAAAAACCCAAATATATGGACACAAA 57.069 29.630 0.00 0.00 43.54 2.83
2385 2458 0.666913 CCATTACCATCAGCAGCAGC 59.333 55.000 0.00 0.00 42.56 5.25
2393 2466 2.509931 ATCAGCAGCAGCAACCCCAT 62.510 55.000 3.17 0.00 45.49 4.00
2525 2598 1.748493 GACAAGCAGACCAAACCACAA 59.252 47.619 0.00 0.00 0.00 3.33
2766 2839 2.222027 ACAGCTTGCTACACCTTTCAC 58.778 47.619 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.179939 GAGAGGGCGCGTTTCGTC 61.180 66.667 8.43 9.20 43.18 4.20
22 23 4.736896 GGAGAGGGCGCGTTTCGT 62.737 66.667 8.43 0.00 41.07 3.85
41 42 0.647410 GTCATGTCATGCGACCTTCG 59.353 55.000 8.03 0.00 41.85 3.79
42 43 1.725641 TGTCATGTCATGCGACCTTC 58.274 50.000 8.03 0.00 41.85 3.46
43 44 2.183478 TTGTCATGTCATGCGACCTT 57.817 45.000 8.03 0.00 41.85 3.50
44 45 2.408271 ATTGTCATGTCATGCGACCT 57.592 45.000 8.03 0.00 41.85 3.85
45 46 3.492421 AAATTGTCATGTCATGCGACC 57.508 42.857 8.03 0.00 41.85 4.79
67 68 3.181465 GGGACTCGATATGCTTCCTGAAA 60.181 47.826 0.00 0.00 0.00 2.69
73 74 0.667792 GCCGGGACTCGATATGCTTC 60.668 60.000 2.18 0.00 42.43 3.86
83 84 1.954382 AGTTTCTTTTTGCCGGGACTC 59.046 47.619 2.18 0.00 0.00 3.36
98 99 1.305201 TCCTTGCCGTGTTCAGTTTC 58.695 50.000 0.00 0.00 0.00 2.78
102 103 2.336554 CAAATCCTTGCCGTGTTCAG 57.663 50.000 0.00 0.00 0.00 3.02
122 125 1.468520 ACGTCGGATTTTTGAGCATGG 59.531 47.619 0.00 0.00 0.00 3.66
236 239 4.223700 AGACATAGCAAATCTGACTGTCCA 59.776 41.667 5.17 0.00 33.88 4.02
241 244 5.641209 GTGAACAGACATAGCAAATCTGACT 59.359 40.000 12.52 1.95 42.07 3.41
296 299 3.278574 CAGTTCACTTGAAAGGGTGTGA 58.721 45.455 0.00 0.00 37.62 3.58
350 356 0.391661 CCAGCTGCGAGTTATGTGGT 60.392 55.000 8.66 0.00 0.00 4.16
386 392 3.774702 GGGACGTCGAGTTTGCGC 61.775 66.667 9.92 0.00 0.00 6.09
445 451 0.404346 TTTTCCCTTCCCCTCCCTGT 60.404 55.000 0.00 0.00 0.00 4.00
446 452 0.783850 TTTTTCCCTTCCCCTCCCTG 59.216 55.000 0.00 0.00 0.00 4.45
447 453 3.309953 TTTTTCCCTTCCCCTCCCT 57.690 52.632 0.00 0.00 0.00 4.20
462 468 5.337009 GCATCCATCTGATCTGTTGGTTTTT 60.337 40.000 22.16 9.14 0.00 1.94
463 469 4.159135 GCATCCATCTGATCTGTTGGTTTT 59.841 41.667 22.16 10.91 0.00 2.43
464 470 3.698040 GCATCCATCTGATCTGTTGGTTT 59.302 43.478 22.16 12.70 0.00 3.27
465 471 3.285484 GCATCCATCTGATCTGTTGGTT 58.715 45.455 22.16 14.93 0.00 3.67
466 472 2.744166 CGCATCCATCTGATCTGTTGGT 60.744 50.000 22.16 11.72 0.00 3.67
467 473 1.871676 CGCATCCATCTGATCTGTTGG 59.128 52.381 18.87 18.87 0.00 3.77
468 474 1.263484 GCGCATCCATCTGATCTGTTG 59.737 52.381 0.30 0.00 0.00 3.33
469 475 1.134310 TGCGCATCCATCTGATCTGTT 60.134 47.619 5.66 0.00 0.00 3.16
625 662 4.352298 ACCATTTTCTCTTGTTCCCTCTCT 59.648 41.667 0.00 0.00 0.00 3.10
627 664 4.401925 CACCATTTTCTCTTGTTCCCTCT 58.598 43.478 0.00 0.00 0.00 3.69
833 870 0.608856 ATGCACCCGAAGCACATGAA 60.609 50.000 0.00 0.00 45.95 2.57
936 1001 3.008375 GGAGGTGGATGCTATTGCTATGA 59.992 47.826 0.00 0.00 40.48 2.15
937 1002 3.008813 AGGAGGTGGATGCTATTGCTATG 59.991 47.826 0.00 0.00 40.48 2.23
938 1003 3.254960 AGGAGGTGGATGCTATTGCTAT 58.745 45.455 0.00 0.00 40.48 2.97
939 1004 2.634940 GAGGAGGTGGATGCTATTGCTA 59.365 50.000 0.00 0.00 40.48 3.49
940 1005 1.419387 GAGGAGGTGGATGCTATTGCT 59.581 52.381 0.00 0.00 40.48 3.91
941 1006 1.544314 GGAGGAGGTGGATGCTATTGC 60.544 57.143 0.00 0.00 40.20 3.56
942 1007 2.038295 GAGGAGGAGGTGGATGCTATTG 59.962 54.545 0.00 0.00 0.00 1.90
943 1008 2.334023 GAGGAGGAGGTGGATGCTATT 58.666 52.381 0.00 0.00 0.00 1.73
944 1009 1.484065 GGAGGAGGAGGTGGATGCTAT 60.484 57.143 0.00 0.00 0.00 2.97
946 1011 1.383803 GGAGGAGGAGGTGGATGCT 60.384 63.158 0.00 0.00 0.00 3.79
947 1012 1.059006 ATGGAGGAGGAGGTGGATGC 61.059 60.000 0.00 0.00 0.00 3.91
948 1013 1.055040 GATGGAGGAGGAGGTGGATG 58.945 60.000 0.00 0.00 0.00 3.51
949 1014 0.644380 TGATGGAGGAGGAGGTGGAT 59.356 55.000 0.00 0.00 0.00 3.41
950 1015 0.031716 CTGATGGAGGAGGAGGTGGA 60.032 60.000 0.00 0.00 0.00 4.02
951 1016 1.053264 CCTGATGGAGGAGGAGGTGG 61.053 65.000 0.00 0.00 46.33 4.61
954 1019 0.984961 TTGCCTGATGGAGGAGGAGG 60.985 60.000 0.00 0.00 46.33 4.30
955 1020 0.914644 TTTGCCTGATGGAGGAGGAG 59.085 55.000 0.00 0.00 46.33 3.69
969 1037 2.725815 GCGAGCGTGTGTTTTGCC 60.726 61.111 0.00 0.00 0.00 4.52
970 1038 1.722507 GAGCGAGCGTGTGTTTTGC 60.723 57.895 0.00 0.00 0.00 3.68
985 1053 1.294857 GCCATCGGAGAAGAAAGAGC 58.705 55.000 0.00 0.00 43.58 4.09
1074 1143 1.066908 GATGTCTTGAGGAGCCTCTCG 59.933 57.143 16.87 8.33 43.12 4.04
1165 1237 2.587522 GAAACAAAGAGACCCTGCCTT 58.412 47.619 0.00 0.00 0.00 4.35
1172 1244 1.594331 ACTGCGGAAACAAAGAGACC 58.406 50.000 0.00 0.00 0.00 3.85
1312 1384 2.530701 AGAGCACTAGTACTGTGGCTT 58.469 47.619 20.02 9.06 36.08 4.35
1349 1421 4.108501 AGGACAAAACCCGGAATTAGTT 57.891 40.909 0.73 0.00 0.00 2.24
1351 1423 4.095932 GCTTAGGACAAAACCCGGAATTAG 59.904 45.833 0.73 0.00 0.00 1.73
1357 1429 1.165270 CTGCTTAGGACAAAACCCGG 58.835 55.000 0.00 0.00 0.00 5.73
1358 1430 1.165270 CCTGCTTAGGACAAAACCCG 58.835 55.000 0.00 0.00 0.00 5.28
1409 1481 0.909133 TCCCAGGCATGCAGTAGTCA 60.909 55.000 21.36 0.00 0.00 3.41
1467 1539 8.250143 ACATTTCATTCAGGTAAAGAAAAGGT 57.750 30.769 0.00 0.00 38.05 3.50
1474 1546 9.350357 CATCAAGAACATTTCATTCAGGTAAAG 57.650 33.333 0.00 0.00 0.00 1.85
1479 1551 6.916440 TCACATCAAGAACATTTCATTCAGG 58.084 36.000 0.00 0.00 0.00 3.86
1480 1552 8.241367 TCATCACATCAAGAACATTTCATTCAG 58.759 33.333 0.00 0.00 0.00 3.02
1481 1553 8.113173 TCATCACATCAAGAACATTTCATTCA 57.887 30.769 0.00 0.00 0.00 2.57
1482 1554 8.242053 ACTCATCACATCAAGAACATTTCATTC 58.758 33.333 0.00 0.00 0.00 2.67
1483 1555 8.118976 ACTCATCACATCAAGAACATTTCATT 57.881 30.769 0.00 0.00 0.00 2.57
1484 1556 7.698506 ACTCATCACATCAAGAACATTTCAT 57.301 32.000 0.00 0.00 0.00 2.57
1485 1557 7.514784 AACTCATCACATCAAGAACATTTCA 57.485 32.000 0.00 0.00 0.00 2.69
1486 1558 8.725148 ACTAACTCATCACATCAAGAACATTTC 58.275 33.333 0.00 0.00 0.00 2.17
1487 1559 8.627208 ACTAACTCATCACATCAAGAACATTT 57.373 30.769 0.00 0.00 0.00 2.32
1488 1560 8.627208 AACTAACTCATCACATCAAGAACATT 57.373 30.769 0.00 0.00 0.00 2.71
1489 1561 8.509690 CAAACTAACTCATCACATCAAGAACAT 58.490 33.333 0.00 0.00 0.00 2.71
1490 1562 7.714813 TCAAACTAACTCATCACATCAAGAACA 59.285 33.333 0.00 0.00 0.00 3.18
1491 1563 8.087982 TCAAACTAACTCATCACATCAAGAAC 57.912 34.615 0.00 0.00 0.00 3.01
1492 1564 8.853077 ATCAAACTAACTCATCACATCAAGAA 57.147 30.769 0.00 0.00 0.00 2.52
1493 1565 8.853077 AATCAAACTAACTCATCACATCAAGA 57.147 30.769 0.00 0.00 0.00 3.02
1494 1566 9.338291 CAAATCAAACTAACTCATCACATCAAG 57.662 33.333 0.00 0.00 0.00 3.02
1495 1567 8.298854 CCAAATCAAACTAACTCATCACATCAA 58.701 33.333 0.00 0.00 0.00 2.57
1496 1568 7.448161 ACCAAATCAAACTAACTCATCACATCA 59.552 33.333 0.00 0.00 0.00 3.07
1497 1569 7.820648 ACCAAATCAAACTAACTCATCACATC 58.179 34.615 0.00 0.00 0.00 3.06
1498 1570 7.667219 AGACCAAATCAAACTAACTCATCACAT 59.333 33.333 0.00 0.00 0.00 3.21
1499 1571 6.998074 AGACCAAATCAAACTAACTCATCACA 59.002 34.615 0.00 0.00 0.00 3.58
1500 1572 7.301054 CAGACCAAATCAAACTAACTCATCAC 58.699 38.462 0.00 0.00 0.00 3.06
1501 1573 6.072508 GCAGACCAAATCAAACTAACTCATCA 60.073 38.462 0.00 0.00 0.00 3.07
1502 1574 6.150140 AGCAGACCAAATCAAACTAACTCATC 59.850 38.462 0.00 0.00 0.00 2.92
1503 1575 6.006449 AGCAGACCAAATCAAACTAACTCAT 58.994 36.000 0.00 0.00 0.00 2.90
1504 1576 5.376625 AGCAGACCAAATCAAACTAACTCA 58.623 37.500 0.00 0.00 0.00 3.41
1505 1577 5.470098 TGAGCAGACCAAATCAAACTAACTC 59.530 40.000 0.00 0.00 0.00 3.01
1506 1578 5.376625 TGAGCAGACCAAATCAAACTAACT 58.623 37.500 0.00 0.00 0.00 2.24
1507 1579 5.689383 TGAGCAGACCAAATCAAACTAAC 57.311 39.130 0.00 0.00 0.00 2.34
1548 1620 3.088789 AGACAGACGGAGACCATTAGT 57.911 47.619 0.00 0.00 0.00 2.24
1561 1634 5.529060 ACTCCTGATTCAACAAAAGACAGAC 59.471 40.000 0.00 0.00 0.00 3.51
1566 1639 4.703897 ACGACTCCTGATTCAACAAAAGA 58.296 39.130 0.00 0.00 0.00 2.52
1664 1737 3.181480 ACAAACAAGATTTTGGGTCCGTG 60.181 43.478 0.57 0.00 40.25 4.94
1714 1787 5.967674 CAGCCATAAAGTTTCTAAATCAGCG 59.032 40.000 0.00 0.00 0.00 5.18
1734 1807 1.886886 TTTCTAACGGTGGTTCAGCC 58.113 50.000 0.00 0.00 37.58 4.85
1796 1869 7.336931 TCTTGGTGTCTAAATTTAGATCAAGGC 59.663 37.037 33.60 22.91 41.43 4.35
2385 2458 0.827089 TGCTGTTGTCCATGGGGTTG 60.827 55.000 13.02 0.00 34.93 3.77
2497 2570 3.126001 TGGTCTGCTTGTCTTGGTTAG 57.874 47.619 0.00 0.00 0.00 2.34
2766 2839 0.108520 GCTGCATGTGTTTCCATGGG 60.109 55.000 13.02 0.00 42.01 4.00
3046 3126 2.988493 CCTGTTGGATTTTTCACATGCG 59.012 45.455 0.00 0.00 34.57 4.73
3293 3377 2.353704 CCTGACCACTTGCGTCTCATAA 60.354 50.000 0.00 0.00 0.00 1.90
3454 3546 1.517242 CTTCACAGAACAGCCTGGTC 58.483 55.000 0.10 0.10 38.44 4.02
3455 3547 0.109342 CCTTCACAGAACAGCCTGGT 59.891 55.000 0.00 0.00 38.44 4.00
3456 3548 0.397941 TCCTTCACAGAACAGCCTGG 59.602 55.000 0.00 0.00 38.44 4.45
3457 3549 2.260844 TTCCTTCACAGAACAGCCTG 57.739 50.000 0.00 0.00 39.93 4.85
3458 3550 3.515602 ATTTCCTTCACAGAACAGCCT 57.484 42.857 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.