Multiple sequence alignment - TraesCS5D01G054900

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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 TraesCS5D01G054900 chr5D 100.000 2312 0 0 1 2312 51851315 51853626 0.000000e+00 4270.0
1 TraesCS5D01G054900 chr5D 94.300 807 38 3 545 1349 51674851 51675651 0.000000e+00 1229.0
2 TraesCS5D01G054900 chr5D 88.158 912 57 24 553 1454 51860594 51861464 0.000000e+00 1038.0
3 TraesCS5D01G054900 chr5D 87.460 933 59 29 553 1466 51892561 51893454 0.000000e+00 1022.0
4 TraesCS5D01G054900 chr5D 87.108 861 61 28 612 1454 51637161 51637989 0.000000e+00 929.0
5 TraesCS5D01G054900 chr5D 85.314 892 71 36 568 1442 51697934 51698782 0.000000e+00 867.0
6 TraesCS5D01G054900 chr5D 83.850 452 49 8 1767 2199 51861766 51862212 2.140000e-110 409.0
7 TraesCS5D01G054900 chr5D 91.837 49 4 0 1582 1630 9395809 9395761 4.120000e-08 69.4
8 TraesCS5D01G054900 chr5A 87.514 1730 94 53 613 2269 40925041 40926721 0.000000e+00 1886.0
9 TraesCS5D01G054900 chr5A 92.129 775 48 6 545 1313 40684267 40685034 0.000000e+00 1081.0
10 TraesCS5D01G054900 chr5A 87.925 911 62 23 553 1454 40934387 40935258 0.000000e+00 1029.0
11 TraesCS5D01G054900 chr5A 87.925 911 62 23 553 1454 40968270 40969141 0.000000e+00 1029.0
12 TraesCS5D01G054900 chr5A 87.626 792 66 17 612 1382 40628623 40629403 0.000000e+00 891.0
13 TraesCS5D01G054900 chr5A 85.778 450 45 8 1767 2199 40969410 40969857 2.090000e-125 459.0
14 TraesCS5D01G054900 chr5A 85.556 450 46 8 1767 2199 41006292 41006739 9.740000e-124 453.0
15 TraesCS5D01G054900 chr5A 87.500 376 28 6 553 928 41045868 41046224 1.280000e-112 416.0
16 TraesCS5D01G054900 chr5A 89.384 292 23 3 1 286 40924259 40924548 6.070000e-96 361.0
17 TraesCS5D01G054900 chr5A 90.262 267 11 7 553 819 41087282 41087533 3.680000e-88 335.0
18 TraesCS5D01G054900 chr5A 86.932 176 12 6 292 465 40924747 40924913 1.090000e-43 187.0
19 TraesCS5D01G054900 chr5B 90.355 902 65 10 455 1349 54548967 54549853 0.000000e+00 1164.0
20 TraesCS5D01G054900 chr5B 88.022 910 61 23 553 1454 54859852 54860721 0.000000e+00 1033.0
21 TraesCS5D01G054900 chr5B 87.600 871 64 19 619 1454 54508308 54509169 0.000000e+00 970.0
22 TraesCS5D01G054900 chr5B 86.233 908 70 26 553 1444 55028079 55028947 0.000000e+00 933.0
23 TraesCS5D01G054900 chr5B 84.719 890 71 40 568 1442 54709897 54710736 0.000000e+00 830.0
24 TraesCS5D01G054900 chr5B 95.078 447 16 6 1043 1486 54850241 54850684 0.000000e+00 699.0
25 TraesCS5D01G054900 chr5B 88.988 563 41 10 1765 2312 54850979 54851535 0.000000e+00 676.0
26 TraesCS5D01G054900 chr5B 82.633 357 37 16 1863 2199 54866909 54867260 2.250000e-75 292.0
27 TraesCS5D01G054900 chr5B 87.500 144 14 3 508 649 54839871 54840012 1.840000e-36 163.0
28 TraesCS5D01G054900 chr5B 100.000 30 0 0 1657 1686 473770552 473770581 3.210000e-04 56.5
29 TraesCS5D01G054900 chrUn 93.750 48 3 0 1589 1636 110779145 110779192 3.190000e-09 73.1
30 TraesCS5D01G054900 chrUn 100.000 28 0 0 1659 1686 83939705 83939678 4.000000e-03 52.8
31 TraesCS5D01G054900 chr7A 88.136 59 6 1 1579 1637 501033493 501033550 4.120000e-08 69.4
32 TraesCS5D01G054900 chr6D 88.889 54 6 0 1584 1637 16866267 16866214 1.480000e-07 67.6
33 TraesCS5D01G054900 chr6D 94.595 37 2 0 1583 1619 129518190 129518226 8.920000e-05 58.4
34 TraesCS5D01G054900 chr3D 97.222 36 1 0 1591 1626 609632188 609632223 6.900000e-06 62.1
35 TraesCS5D01G054900 chr1A 94.737 38 2 0 1597 1634 8661904 8661867 2.480000e-05 60.2
36 TraesCS5D01G054900 chr1A 100.000 30 0 0 1659 1688 357431855 357431826 3.210000e-04 56.5
37 TraesCS5D01G054900 chr7B 100.000 31 0 0 1553 1583 65624784 65624754 8.920000e-05 58.4
38 TraesCS5D01G054900 chr7B 100.000 29 0 0 1555 1583 84650373 84650345 1.000000e-03 54.7
39 TraesCS5D01G054900 chr7B 100.000 28 0 0 1659 1686 2108930 2108957 4.000000e-03 52.8
40 TraesCS5D01G054900 chr4A 100.000 30 0 0 1554 1583 88091472 88091501 3.210000e-04 56.5
41 TraesCS5D01G054900 chr2B 84.375 64 1 1 1555 1609 490800341 490800404 1.000000e-03 54.7
42 TraesCS5D01G054900 chr1B 100.000 29 0 0 1555 1583 321874431 321874459 1.000000e-03 54.7
43 TraesCS5D01G054900 chr1D 100.000 28 0 0 1592 1619 467474699 467474672 4.000000e-03 52.8


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 TraesCS5D01G054900 chr5D 51851315 51853626 2311 False 4270.000000 4270 100.000000 1 2312 1 chr5D.!!$F4 2311
1 TraesCS5D01G054900 chr5D 51674851 51675651 800 False 1229.000000 1229 94.300000 545 1349 1 chr5D.!!$F2 804
2 TraesCS5D01G054900 chr5D 51892561 51893454 893 False 1022.000000 1022 87.460000 553 1466 1 chr5D.!!$F5 913
3 TraesCS5D01G054900 chr5D 51637161 51637989 828 False 929.000000 929 87.108000 612 1454 1 chr5D.!!$F1 842
4 TraesCS5D01G054900 chr5D 51697934 51698782 848 False 867.000000 867 85.314000 568 1442 1 chr5D.!!$F3 874
5 TraesCS5D01G054900 chr5D 51860594 51862212 1618 False 723.500000 1038 86.004000 553 2199 2 chr5D.!!$F6 1646
6 TraesCS5D01G054900 chr5A 40684267 40685034 767 False 1081.000000 1081 92.129000 545 1313 1 chr5A.!!$F2 768
7 TraesCS5D01G054900 chr5A 40934387 40935258 871 False 1029.000000 1029 87.925000 553 1454 1 chr5A.!!$F3 901
8 TraesCS5D01G054900 chr5A 40628623 40629403 780 False 891.000000 891 87.626000 612 1382 1 chr5A.!!$F1 770
9 TraesCS5D01G054900 chr5A 40924259 40926721 2462 False 811.333333 1886 87.943333 1 2269 3 chr5A.!!$F7 2268
10 TraesCS5D01G054900 chr5A 40968270 40969857 1587 False 744.000000 1029 86.851500 553 2199 2 chr5A.!!$F8 1646
11 TraesCS5D01G054900 chr5B 54548967 54549853 886 False 1164.000000 1164 90.355000 455 1349 1 chr5B.!!$F2 894
12 TraesCS5D01G054900 chr5B 54859852 54860721 869 False 1033.000000 1033 88.022000 553 1454 1 chr5B.!!$F5 901
13 TraesCS5D01G054900 chr5B 54508308 54509169 861 False 970.000000 970 87.600000 619 1454 1 chr5B.!!$F1 835
14 TraesCS5D01G054900 chr5B 55028079 55028947 868 False 933.000000 933 86.233000 553 1444 1 chr5B.!!$F7 891
15 TraesCS5D01G054900 chr5B 54709897 54710736 839 False 830.000000 830 84.719000 568 1442 1 chr5B.!!$F3 874
16 TraesCS5D01G054900 chr5B 54850241 54851535 1294 False 687.500000 699 92.033000 1043 2312 2 chr5B.!!$F9 1269

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
307 507 0.382873 GGCGGCGGGTAAATTTAAGG 59.617 55.0 9.78 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 1982 0.031994 ACACCGGTGCTTGCATTTTC 59.968 50.0 34.26 0.0 0.0 2.29 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
21 22 4.657436 GGAACAAGAGAGTATCGACCAT 57.343 45.455 0.00 0.00 42.67 3.55
22 23 4.363999 GGAACAAGAGAGTATCGACCATG 58.636 47.826 0.00 0.00 42.67 3.66
62 69 4.416620 AGATCACTTTAGTTCGAAGCTCG 58.583 43.478 0.00 0.00 42.10 5.03
72 79 4.415332 GAAGCTCGGACGGCGTGA 62.415 66.667 21.19 8.87 34.52 4.35
80 87 4.736896 GACGGCGTGAGGACACCC 62.737 72.222 21.19 0.00 43.34 4.61
137 144 3.084579 GTGCATCTCGCTCCAACG 58.915 61.111 0.00 0.00 43.06 4.10
141 148 1.014044 GCATCTCGCTCCAACGAACA 61.014 55.000 0.00 0.00 42.39 3.18
142 149 0.716108 CATCTCGCTCCAACGAACAC 59.284 55.000 0.00 0.00 42.39 3.32
145 152 3.047877 CGCTCCAACGAACACCCC 61.048 66.667 0.00 0.00 34.06 4.95
146 153 2.671963 GCTCCAACGAACACCCCC 60.672 66.667 0.00 0.00 0.00 5.40
152 159 2.681400 AACGAACACCCCCACACCA 61.681 57.895 0.00 0.00 0.00 4.17
154 161 2.598467 GAACACCCCCACACCACA 59.402 61.111 0.00 0.00 0.00 4.17
171 178 4.024048 CACCACAAAGACCTACACACATTC 60.024 45.833 0.00 0.00 0.00 2.67
172 179 3.186409 CCACAAAGACCTACACACATTCG 59.814 47.826 0.00 0.00 0.00 3.34
184 191 2.616376 CACACATTCGTTTCCTTGGTCA 59.384 45.455 0.00 0.00 0.00 4.02
221 228 4.771590 AGCATAGAAACAACATGGTGTG 57.228 40.909 19.06 4.65 0.00 3.82
273 280 5.431765 GTGATTGGCAAGATCCTAGAAGAA 58.568 41.667 5.96 0.00 0.00 2.52
280 287 4.102367 GCAAGATCCTAGAAGAAGGGACAT 59.898 45.833 0.00 0.00 37.24 3.06
286 293 5.788430 TCCTAGAAGAAGGGACATAATGGA 58.212 41.667 0.00 0.00 37.24 3.41
288 295 6.270927 TCCTAGAAGAAGGGACATAATGGATG 59.729 42.308 0.00 0.00 38.15 3.51
290 297 3.515602 AGAAGGGACATAATGGATGGC 57.484 47.619 0.00 0.00 43.77 4.40
294 494 1.577328 GGACATAATGGATGGCGGCG 61.577 60.000 0.51 0.51 45.73 6.46
307 507 0.382873 GGCGGCGGGTAAATTTAAGG 59.617 55.000 9.78 0.00 0.00 2.69
327 527 8.538409 TTAAGGAAGATGTAACTACGGTTTTC 57.462 34.615 0.00 0.00 36.92 2.29
368 568 1.809567 AACCGCGAGTAGTCCCGTTT 61.810 55.000 8.23 0.00 0.00 3.60
386 586 3.731717 CGTTTGTAAAATTGGTGAACGGG 59.268 43.478 0.00 0.00 35.93 5.28
387 587 4.684877 GTTTGTAAAATTGGTGAACGGGT 58.315 39.130 0.00 0.00 0.00 5.28
388 588 3.992260 TGTAAAATTGGTGAACGGGTG 57.008 42.857 0.00 0.00 0.00 4.61
389 589 2.623889 TGTAAAATTGGTGAACGGGTGG 59.376 45.455 0.00 0.00 0.00 4.61
390 590 1.783071 AAAATTGGTGAACGGGTGGT 58.217 45.000 0.00 0.00 0.00 4.16
391 591 1.783071 AAATTGGTGAACGGGTGGTT 58.217 45.000 0.00 0.00 42.96 3.67
415 615 4.872691 CCACGCTCTTCTTCTATGAATGTT 59.127 41.667 0.00 0.00 0.00 2.71
416 616 5.220548 CCACGCTCTTCTTCTATGAATGTTG 60.221 44.000 0.00 0.00 0.00 3.33
417 617 5.578336 CACGCTCTTCTTCTATGAATGTTGA 59.422 40.000 0.00 0.00 0.00 3.18
418 618 6.257411 CACGCTCTTCTTCTATGAATGTTGAT 59.743 38.462 0.00 0.00 0.00 2.57
419 619 7.436376 CACGCTCTTCTTCTATGAATGTTGATA 59.564 37.037 0.00 0.00 0.00 2.15
471 672 3.601443 ATATTCTCGTGCTCATAGGGC 57.399 47.619 0.00 0.00 0.00 5.19
472 673 0.394565 ATTCTCGTGCTCATAGGGCC 59.605 55.000 0.00 0.00 0.00 5.80
473 674 2.016393 TTCTCGTGCTCATAGGGCCG 62.016 60.000 0.00 0.00 0.00 6.13
474 675 3.506059 CTCGTGCTCATAGGGCCGG 62.506 68.421 0.00 0.00 0.00 6.13
486 687 2.708037 AGGGCCGGATAGGTTATGTA 57.292 50.000 5.05 0.00 43.70 2.29
494 695 2.666508 GGATAGGTTATGTATGCGTGCG 59.333 50.000 0.00 0.00 0.00 5.34
497 698 2.352388 AGGTTATGTATGCGTGCGTTT 58.648 42.857 0.00 0.00 0.00 3.60
499 700 3.933955 AGGTTATGTATGCGTGCGTTTAA 59.066 39.130 0.00 0.00 0.00 1.52
501 702 4.726704 GGTTATGTATGCGTGCGTTTAAAG 59.273 41.667 0.00 0.00 0.00 1.85
502 703 2.884663 TGTATGCGTGCGTTTAAAGG 57.115 45.000 3.51 3.51 0.00 3.11
503 704 2.414806 TGTATGCGTGCGTTTAAAGGA 58.585 42.857 11.95 0.00 0.00 3.36
504 705 2.806818 TGTATGCGTGCGTTTAAAGGAA 59.193 40.909 11.95 0.00 0.00 3.36
505 706 3.437395 TGTATGCGTGCGTTTAAAGGAAT 59.563 39.130 11.95 0.41 0.00 3.01
514 715 6.035220 CGTGCGTTTAAAGGAATGAGTGTATA 59.965 38.462 11.95 0.00 0.00 1.47
520 721 7.946655 TTAAAGGAATGAGTGTATATGAGCG 57.053 36.000 0.00 0.00 0.00 5.03
525 726 6.072397 AGGAATGAGTGTATATGAGCGTCTAC 60.072 42.308 0.00 0.00 0.00 2.59
526 727 4.727235 TGAGTGTATATGAGCGTCTACG 57.273 45.455 0.00 0.00 43.27 3.51
537 738 1.463831 AGCGTCTACGTCTGTACTGTG 59.536 52.381 4.24 0.00 42.22 3.66
538 739 1.879646 CGTCTACGTCTGTACTGTGC 58.120 55.000 0.00 0.00 34.11 4.57
540 741 2.095869 CGTCTACGTCTGTACTGTGCTT 60.096 50.000 0.00 0.00 34.11 3.91
541 742 3.608707 CGTCTACGTCTGTACTGTGCTTT 60.609 47.826 0.00 0.00 34.11 3.51
543 749 4.850470 GTCTACGTCTGTACTGTGCTTTAC 59.150 45.833 0.00 0.00 0.00 2.01
821 1073 0.751452 GAACCCTCCCGTATCACCTC 59.249 60.000 0.00 0.00 0.00 3.85
999 1290 4.081142 TCACTAGCATTGGCACTAAGCTTA 60.081 41.667 5.94 5.94 44.61 3.09
1085 1376 3.335534 GTGCCACACCGTGACGAC 61.336 66.667 6.54 0.00 35.23 4.34
1319 1612 2.030412 CTGGGTGTAGTGCGTGCA 59.970 61.111 0.00 0.00 0.00 4.57
1320 1613 1.375908 CTGGGTGTAGTGCGTGCAT 60.376 57.895 0.00 0.00 0.00 3.96
1444 1765 3.330701 AGACTTAAGGAAACCATGCAGGA 59.669 43.478 7.53 0.00 41.22 3.86
1459 1780 7.962441 ACCATGCAGGACTTTTTACTAATTTT 58.038 30.769 0.00 0.00 41.22 1.82
1488 1809 6.380995 ACATTTAACACAGTACATGCACATG 58.619 36.000 9.06 9.06 44.15 3.21
1537 1894 6.484308 CCTACATGCACATCATCTTGACATTA 59.516 38.462 0.00 0.00 31.79 1.90
1543 1900 5.163864 GCACATCATCTTGACATTAACGTGA 60.164 40.000 0.00 0.00 0.00 4.35
1545 1902 6.903479 CACATCATCTTGACATTAACGTGATG 59.097 38.462 9.84 9.84 44.29 3.07
1556 1918 0.238289 AACGTGATGGCAAGCTTTCG 59.762 50.000 0.00 0.00 0.00 3.46
1583 1945 0.613260 CGGAAATGTCTCCTCCCACA 59.387 55.000 0.00 0.00 32.82 4.17
1584 1946 1.210478 CGGAAATGTCTCCTCCCACAT 59.790 52.381 0.00 0.00 34.58 3.21
1585 1947 2.743183 CGGAAATGTCTCCTCCCACATC 60.743 54.545 0.00 0.00 31.79 3.06
1586 1948 2.555199 GAAATGTCTCCTCCCACATCG 58.445 52.381 0.00 0.00 31.79 3.84
1611 1982 7.218204 CGTCGAAAAGCCTAAAATAAATTCAGG 59.782 37.037 0.00 0.00 0.00 3.86
1619 1990 8.320617 AGCCTAAAATAAATTCAGGAAAATGCA 58.679 29.630 0.00 0.00 0.00 3.96
1649 2047 2.026729 TGTCAAGTCAAACCACTGTCCA 60.027 45.455 0.00 0.00 0.00 4.02
1671 2069 4.225267 CACCTAAGTCCTAACCATCCAACT 59.775 45.833 0.00 0.00 0.00 3.16
1700 2099 5.257082 TGGTTTGCAGGTCTTTTTACTTC 57.743 39.130 0.00 0.00 0.00 3.01
1725 2124 2.567169 TGGGAGTACCTGTCATGTCAAG 59.433 50.000 0.00 0.00 41.11 3.02
1753 2152 9.866798 TGTTAAGCATTATAATTTGTGCATTCA 57.133 25.926 10.54 3.16 39.94 2.57
1937 2604 7.589958 TTTTTCCTGTAACCTTGCTCAAATA 57.410 32.000 0.00 0.00 0.00 1.40
2127 2815 4.362279 ACATTGTGATGAACTTTGCACAC 58.638 39.130 0.00 0.00 40.57 3.82
2142 2830 9.926158 AACTTTGCACACAAATGAAATATATGA 57.074 25.926 0.00 0.00 44.54 2.15
2215 2904 4.700213 AGCTCCTAAACAAAATGCGTATGT 59.300 37.500 0.00 0.00 0.00 2.29
2277 2966 2.161609 CCAACCGACAAAATGCCTCTAC 59.838 50.000 0.00 0.00 0.00 2.59
2281 2970 1.076332 GACAAAATGCCTCTACGCGT 58.924 50.000 19.17 19.17 0.00 6.01
2282 2971 0.796312 ACAAAATGCCTCTACGCGTG 59.204 50.000 24.59 12.26 0.00 5.34
2302 2991 1.001376 GAAGACCCCCTACGGAGGT 59.999 63.158 14.11 0.00 41.95 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 52 2.667724 CGTCCGAGCTTCGAACTAAAGT 60.668 50.000 0.00 0.00 43.74 2.66
50 57 2.567049 CCGTCCGAGCTTCGAACT 59.433 61.111 0.00 0.00 43.74 3.01
62 69 4.736896 GGTGTCCTCACGCCGTCC 62.737 72.222 0.00 0.00 43.38 4.79
72 79 0.543174 GAGTCCACTCTGGGTGTCCT 60.543 60.000 6.95 1.42 43.94 3.85
105 112 1.805945 GCACCACGCTAGAAGTCGG 60.806 63.158 0.00 0.46 37.77 4.79
108 115 0.898320 AGATGCACCACGCTAGAAGT 59.102 50.000 0.00 0.00 43.06 3.01
125 132 1.006571 GGTGTTCGTTGGAGCGAGA 60.007 57.895 0.00 0.00 42.10 4.04
137 144 0.684805 TTTGTGGTGTGGGGGTGTTC 60.685 55.000 0.00 0.00 0.00 3.18
141 148 1.229076 GTCTTTGTGGTGTGGGGGT 59.771 57.895 0.00 0.00 0.00 4.95
142 149 1.530655 GGTCTTTGTGGTGTGGGGG 60.531 63.158 0.00 0.00 0.00 5.40
145 152 2.218603 GTGTAGGTCTTTGTGGTGTGG 58.781 52.381 0.00 0.00 0.00 4.17
146 153 2.612212 GTGTGTAGGTCTTTGTGGTGTG 59.388 50.000 0.00 0.00 0.00 3.82
152 159 4.067972 ACGAATGTGTGTAGGTCTTTGT 57.932 40.909 0.00 0.00 0.00 2.83
154 161 4.514066 GGAAACGAATGTGTGTAGGTCTTT 59.486 41.667 0.00 0.00 0.00 2.52
171 178 0.240945 GCCACATGACCAAGGAAACG 59.759 55.000 0.00 0.00 0.00 3.60
172 179 1.327303 TGCCACATGACCAAGGAAAC 58.673 50.000 0.00 0.00 0.00 2.78
184 191 2.268076 GCTTCCACGGTTGCCACAT 61.268 57.895 0.00 0.00 0.00 3.21
221 228 1.450312 CACGGGATGGCCTTCTCAC 60.450 63.158 18.08 6.07 0.00 3.51
273 280 0.401738 CCGCCATCCATTATGTCCCT 59.598 55.000 0.00 0.00 33.34 4.20
280 287 1.697082 TTACCCGCCGCCATCCATTA 61.697 55.000 0.00 0.00 0.00 1.90
286 293 1.679153 CTTAAATTTACCCGCCGCCAT 59.321 47.619 0.00 0.00 0.00 4.40
288 295 0.382873 CCTTAAATTTACCCGCCGCC 59.617 55.000 0.00 0.00 0.00 6.13
290 297 3.272581 TCTTCCTTAAATTTACCCGCCG 58.727 45.455 0.00 0.00 0.00 6.46
307 507 6.790285 TTGGAAAACCGTAGTTACATCTTC 57.210 37.500 0.00 0.00 34.19 2.87
321 521 4.055360 GCACATACAACCTTTGGAAAACC 58.945 43.478 0.00 0.00 34.12 3.27
322 522 3.733727 CGCACATACAACCTTTGGAAAAC 59.266 43.478 0.00 0.00 34.12 2.43
327 527 1.529226 TCCGCACATACAACCTTTGG 58.471 50.000 0.00 0.00 34.12 3.28
358 558 5.374921 TCACCAATTTTACAAACGGGACTA 58.625 37.500 0.00 0.00 0.00 2.59
359 559 4.208746 TCACCAATTTTACAAACGGGACT 58.791 39.130 0.00 0.00 0.00 3.85
360 560 4.571372 TCACCAATTTTACAAACGGGAC 57.429 40.909 0.00 0.00 0.00 4.46
361 561 4.497674 CGTTCACCAATTTTACAAACGGGA 60.498 41.667 0.00 0.00 35.61 5.14
368 568 2.623889 CCACCCGTTCACCAATTTTACA 59.376 45.455 0.00 0.00 0.00 2.41
386 586 1.149148 GAAGAAGAGCGTGGAACCAC 58.851 55.000 13.32 13.32 43.01 4.16
387 587 1.048601 AGAAGAAGAGCGTGGAACCA 58.951 50.000 0.00 0.00 0.00 3.67
388 588 3.119101 TCATAGAAGAAGAGCGTGGAACC 60.119 47.826 0.00 0.00 0.00 3.62
389 589 4.111375 TCATAGAAGAAGAGCGTGGAAC 57.889 45.455 0.00 0.00 0.00 3.62
390 590 4.801330 TTCATAGAAGAAGAGCGTGGAA 57.199 40.909 0.00 0.00 0.00 3.53
391 591 4.160439 ACATTCATAGAAGAAGAGCGTGGA 59.840 41.667 0.00 0.00 0.00 4.02
396 596 7.568497 GCGTATCAACATTCATAGAAGAAGAGC 60.568 40.741 0.00 0.00 0.00 4.09
452 653 1.618837 GGCCCTATGAGCACGAGAATA 59.381 52.381 0.00 0.00 0.00 1.75
453 654 0.394565 GGCCCTATGAGCACGAGAAT 59.605 55.000 0.00 0.00 0.00 2.40
471 672 3.250744 CACGCATACATAACCTATCCGG 58.749 50.000 0.00 0.00 39.35 5.14
472 673 2.666508 GCACGCATACATAACCTATCCG 59.333 50.000 0.00 0.00 0.00 4.18
473 674 2.666508 CGCACGCATACATAACCTATCC 59.333 50.000 0.00 0.00 0.00 2.59
474 675 3.314553 ACGCACGCATACATAACCTATC 58.685 45.455 0.00 0.00 0.00 2.08
486 687 2.486203 TCATTCCTTTAAACGCACGCAT 59.514 40.909 0.00 0.00 0.00 4.73
494 695 8.276325 CGCTCATATACACTCATTCCTTTAAAC 58.724 37.037 0.00 0.00 0.00 2.01
497 698 7.014326 AGACGCTCATATACACTCATTCCTTTA 59.986 37.037 0.00 0.00 0.00 1.85
499 700 5.303078 AGACGCTCATATACACTCATTCCTT 59.697 40.000 0.00 0.00 0.00 3.36
501 702 5.127693 AGACGCTCATATACACTCATTCC 57.872 43.478 0.00 0.00 0.00 3.01
502 703 5.790988 CGTAGACGCTCATATACACTCATTC 59.209 44.000 0.00 0.00 0.00 2.67
503 704 5.238868 ACGTAGACGCTCATATACACTCATT 59.761 40.000 1.14 0.00 44.43 2.57
504 705 4.755629 ACGTAGACGCTCATATACACTCAT 59.244 41.667 1.14 0.00 44.43 2.90
505 706 4.124970 ACGTAGACGCTCATATACACTCA 58.875 43.478 1.14 0.00 44.43 3.41
514 715 2.352034 CAGTACAGACGTAGACGCTCAT 59.648 50.000 1.14 0.00 44.43 2.90
520 721 3.555917 AAGCACAGTACAGACGTAGAC 57.444 47.619 0.00 0.00 0.00 2.59
525 726 5.398176 TTTTGTAAAGCACAGTACAGACG 57.602 39.130 0.00 0.00 38.72 4.18
821 1073 1.804151 TCGAGCAATTTGACCCGAAAG 59.196 47.619 0.00 0.00 0.00 2.62
999 1290 0.674895 GCTTCGTCACCTGCTCCATT 60.675 55.000 0.00 0.00 0.00 3.16
1319 1612 3.412386 GCCGAATATCTACAAAGCCCAT 58.588 45.455 0.00 0.00 0.00 4.00
1320 1613 2.486548 GGCCGAATATCTACAAAGCCCA 60.487 50.000 0.00 0.00 32.93 5.36
1459 1780 9.239002 GTGCATGTACTGTGTTAAATGTTTAAA 57.761 29.630 6.69 0.00 34.71 1.52
1461 1782 7.931275 TGTGCATGTACTGTGTTAAATGTTTA 58.069 30.769 15.25 0.00 0.00 2.01
1462 1783 6.800543 TGTGCATGTACTGTGTTAAATGTTT 58.199 32.000 15.25 0.00 0.00 2.83
1463 1784 6.384258 TGTGCATGTACTGTGTTAAATGTT 57.616 33.333 15.25 0.00 0.00 2.71
1464 1785 6.380995 CATGTGCATGTACTGTGTTAAATGT 58.619 36.000 15.25 0.00 34.23 2.71
1465 1786 5.286797 GCATGTGCATGTACTGTGTTAAATG 59.713 40.000 15.25 8.53 40.80 2.32
1466 1787 5.401550 GCATGTGCATGTACTGTGTTAAAT 58.598 37.500 15.25 0.00 40.80 1.40
1488 1809 2.983229 AGAATGTGTGAGGATGAGTGC 58.017 47.619 0.00 0.00 0.00 4.40
1537 1894 0.238289 CGAAAGCTTGCCATCACGTT 59.762 50.000 0.00 0.00 0.00 3.99
1543 1900 1.067142 TCGACTACGAAAGCTTGCCAT 60.067 47.619 0.00 0.00 45.74 4.40
1545 1902 3.117589 TCGACTACGAAAGCTTGCC 57.882 52.632 0.00 0.00 45.74 4.52
1556 1918 2.422832 AGGAGACATTTCCGTCGACTAC 59.577 50.000 14.70 0.00 42.29 2.73
1570 1932 1.313091 CGACGATGTGGGAGGAGACA 61.313 60.000 0.00 0.00 0.00 3.41
1583 1945 8.455682 TGAATTTATTTTAGGCTTTTCGACGAT 58.544 29.630 0.00 0.00 0.00 3.73
1584 1946 7.808672 TGAATTTATTTTAGGCTTTTCGACGA 58.191 30.769 0.00 0.00 0.00 4.20
1585 1947 7.218204 CCTGAATTTATTTTAGGCTTTTCGACG 59.782 37.037 0.00 0.00 0.00 5.12
1586 1948 8.241367 TCCTGAATTTATTTTAGGCTTTTCGAC 58.759 33.333 0.00 0.00 0.00 4.20
1611 1982 0.031994 ACACCGGTGCTTGCATTTTC 59.968 50.000 34.26 0.00 0.00 2.29
1619 1990 0.107410 TTGACTTGACACCGGTGCTT 60.107 50.000 34.26 16.70 0.00 3.91
1649 2047 4.436079 AGTTGGATGGTTAGGACTTAGGT 58.564 43.478 0.00 0.00 0.00 3.08
1671 2069 1.493022 AGACCTGCAAACCAACCTGTA 59.507 47.619 0.00 0.00 0.00 2.74
1700 2099 2.768527 ACATGACAGGTACTCCCATCAG 59.231 50.000 0.00 0.00 34.60 2.90
1761 2184 8.986477 AGACACCACAAATTATAATGCTTTTC 57.014 30.769 0.00 0.00 0.00 2.29
1911 2576 7.589958 TTTGAGCAAGGTTACAGGAAAAATA 57.410 32.000 0.00 0.00 0.00 1.40
1912 2577 6.478512 TTTGAGCAAGGTTACAGGAAAAAT 57.521 33.333 0.00 0.00 0.00 1.82
2006 2678 2.507407 AAGTTCATGTACCCGCCAAT 57.493 45.000 0.00 0.00 0.00 3.16
2202 2891 2.746904 TGAGGTGGACATACGCATTTTG 59.253 45.455 0.00 0.00 0.00 2.44
2277 2966 2.642254 TAGGGGGTCTTCACACGCG 61.642 63.158 3.53 3.53 43.75 6.01


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

AutoCloner maintained by Alex Coulton.