Multiple sequence alignment - TraesCS6A01G236100

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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 TraesCS6A01G236100 chr6A 100.000 2729 0 0 1 2729 445580343 445583071 0.000000e+00 5040
1 TraesCS6A01G236100 chr6B 93.330 1859 91 19 27 1881 476111946 476110117 0.000000e+00 2715
2 TraesCS6A01G236100 chr6B 86.150 361 23 7 2058 2418 476109772 476109439 5.550000e-97 364
3 TraesCS6A01G236100 chr6D 92.593 1863 73 27 27 1881 308880963 308879158 0.000000e+00 2615
4 TraesCS6A01G236100 chr6D 87.386 880 49 18 1882 2727 308879100 308878249 0.000000e+00 953
5 TraesCS6A01G236100 chr2B 77.389 314 51 14 1081 1381 553613204 553613510 4.670000e-38 169
6 TraesCS6A01G236100 chr2D 77.376 221 39 7 1081 1291 473275995 473276214 1.330000e-23 121


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 TraesCS6A01G236100 chr6A 445580343 445583071 2728 False 5040.0 5040 100.0000 1 2729 1 chr6A.!!$F1 2728
1 TraesCS6A01G236100 chr6B 476109439 476111946 2507 True 1539.5 2715 89.7400 27 2418 2 chr6B.!!$R1 2391
2 TraesCS6A01G236100 chr6D 308878249 308880963 2714 True 1784.0 2615 89.9895 27 2727 2 chr6D.!!$R1 2700

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
804 810 0.098376 CCGTCCCTCTCGTTAGTTCG 59.902 60.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 1886 0.599558 CCGTCGGTTTCCAGTACTGA 59.4 55.0 24.68 7.64 0.0 3.41 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
20 21 2.577449 AAGTCAAAAGTTGTTGGCCG 57.423 45.000 0.00 0.00 33.42 6.13
21 22 0.744281 AGTCAAAAGTTGTTGGCCGG 59.256 50.000 0.00 0.00 33.42 6.13
22 23 0.741915 GTCAAAAGTTGTTGGCCGGA 59.258 50.000 5.05 0.00 0.00 5.14
23 24 1.339929 GTCAAAAGTTGTTGGCCGGAT 59.660 47.619 5.05 0.00 0.00 4.18
24 25 2.035632 TCAAAAGTTGTTGGCCGGATT 58.964 42.857 5.05 0.00 0.00 3.01
25 26 3.004944 GTCAAAAGTTGTTGGCCGGATTA 59.995 43.478 5.05 0.00 0.00 1.75
54 55 6.481313 TGTTCTTGTCTTCTCAAAGATCACTG 59.519 38.462 0.00 0.00 43.26 3.66
105 106 4.804139 GTGTTCAGTCCCGTTGAGTATATG 59.196 45.833 0.00 0.00 0.00 1.78
115 116 1.593196 TGAGTATATGCCGCCAAAGC 58.407 50.000 0.00 0.00 0.00 3.51
116 117 1.140852 TGAGTATATGCCGCCAAAGCT 59.859 47.619 0.00 0.00 36.60 3.74
117 118 1.532868 GAGTATATGCCGCCAAAGCTG 59.467 52.381 0.00 0.00 36.60 4.24
118 119 1.134098 AGTATATGCCGCCAAAGCTGT 60.134 47.619 0.00 0.00 36.60 4.40
119 120 2.104111 AGTATATGCCGCCAAAGCTGTA 59.896 45.455 0.00 0.00 36.60 2.74
185 186 2.072298 GCGCAACTCAGTCTCTGAAAT 58.928 47.619 0.30 0.00 40.18 2.17
291 293 2.978978 TGGTCAATTCTGTCTCCTTGGA 59.021 45.455 0.00 0.00 0.00 3.53
298 300 1.613925 TCTGTCTCCTTGGACTTGTCG 59.386 52.381 0.00 0.00 37.16 4.35
425 427 1.106285 GCAGGTTAGGGAAATGCCAG 58.894 55.000 0.00 0.00 38.95 4.85
461 463 9.733219 GTGAAAAGGCTTATGTAGTAGTACTAG 57.267 37.037 10.38 1.66 30.12 2.57
489 494 9.060347 AGTATAAATAATGACACAAGAGGCATG 57.940 33.333 0.00 0.00 0.00 4.06
544 549 5.272283 ACGTTTTCTACTCCTTGTCTGAA 57.728 39.130 0.00 0.00 0.00 3.02
545 550 5.667466 ACGTTTTCTACTCCTTGTCTGAAA 58.333 37.500 0.00 0.00 33.07 2.69
546 551 5.753921 ACGTTTTCTACTCCTTGTCTGAAAG 59.246 40.000 0.00 0.00 34.90 2.62
547 552 5.753921 CGTTTTCTACTCCTTGTCTGAAAGT 59.246 40.000 0.00 0.00 34.90 2.66
624 629 5.815222 TGATTACGACACAACAATATCCTGG 59.185 40.000 0.00 0.00 0.00 4.45
625 630 2.985896 ACGACACAACAATATCCTGGG 58.014 47.619 0.00 0.00 0.00 4.45
632 637 6.969043 ACACAACAATATCCTGGGAATTCTA 58.031 36.000 5.23 0.00 0.00 2.10
688 693 2.488153 GTTGTAGCATGTGTCCCTTTCC 59.512 50.000 0.00 0.00 0.00 3.13
727 733 2.100631 CCTTGTCACGACGGCATCC 61.101 63.158 0.00 0.00 0.00 3.51
803 809 1.401199 CTCCGTCCCTCTCGTTAGTTC 59.599 57.143 0.00 0.00 0.00 3.01
804 810 0.098376 CCGTCCCTCTCGTTAGTTCG 59.902 60.000 0.00 0.00 0.00 3.95
805 811 0.801251 CGTCCCTCTCGTTAGTTCGT 59.199 55.000 0.00 0.00 0.00 3.85
806 812 1.198637 CGTCCCTCTCGTTAGTTCGTT 59.801 52.381 0.00 0.00 0.00 3.85
816 822 2.067013 GTTAGTTCGTTGTCCTGCTCC 58.933 52.381 0.00 0.00 0.00 4.70
825 831 1.323271 TGTCCTGCTCCAGTCGGATC 61.323 60.000 0.00 0.00 41.79 3.36
849 855 6.038936 TCGATGATAATCTCACTACGGTTTGA 59.961 38.462 0.00 0.00 36.48 2.69
850 856 6.863645 CGATGATAATCTCACTACGGTTTGAT 59.136 38.462 0.00 0.00 36.48 2.57
851 857 7.061210 CGATGATAATCTCACTACGGTTTGATC 59.939 40.741 0.00 0.00 36.48 2.92
852 858 6.206498 TGATAATCTCACTACGGTTTGATCG 58.794 40.000 0.00 0.00 0.00 3.69
942 948 4.615223 CGTCTCTCTCGTTTGTGTAATCCA 60.615 45.833 0.00 0.00 0.00 3.41
978 984 3.477224 TTTTGCAGCGCCGTGAACC 62.477 57.895 2.29 0.00 0.00 3.62
1015 1021 2.158696 AGCAGGATGAATCAGGTTAGCC 60.159 50.000 0.00 0.00 39.69 3.93
1055 1061 1.984570 CCAAGAGAGTGAGCGGGGA 60.985 63.158 0.00 0.00 0.00 4.81
1125 1131 4.070552 GACTTCGCGGTGGAGCCT 62.071 66.667 6.13 0.00 34.25 4.58
1418 1424 2.180204 GCGTGATCATGGAACCCGG 61.180 63.158 16.59 0.00 0.00 5.73
1474 1480 2.096406 CCGCGCAGTTCAACATCG 59.904 61.111 8.75 0.00 0.00 3.84
1476 1482 1.348538 CCGCGCAGTTCAACATCGTA 61.349 55.000 8.75 0.00 0.00 3.43
1489 1495 0.526662 CATCGTATACCCTCCTCCGC 59.473 60.000 0.00 0.00 0.00 5.54
1492 1498 1.155624 GTATACCCTCCTCCGCCCT 59.844 63.158 0.00 0.00 0.00 5.19
1499 1505 3.995809 CTCCTCCGCCCTTGGGGTA 62.996 68.421 7.91 0.00 46.51 3.69
1530 1536 1.505353 GATGAACTCGACGTCCGGT 59.495 57.895 10.58 6.10 39.14 5.28
1733 1739 2.538437 CCTGCTCTTGTTCTGATCTCG 58.462 52.381 0.00 0.00 0.00 4.04
1757 1763 2.157738 AGCACATTCCTGCAACTTCTC 58.842 47.619 0.00 0.00 39.86 2.87
1761 1767 3.369147 CACATTCCTGCAACTTCTCTACG 59.631 47.826 0.00 0.00 0.00 3.51
1768 1774 4.036971 CCTGCAACTTCTCTACGTATAGCT 59.963 45.833 3.19 0.00 0.00 3.32
1769 1775 4.921547 TGCAACTTCTCTACGTATAGCTG 58.078 43.478 0.00 1.86 0.00 4.24
1770 1776 4.398358 TGCAACTTCTCTACGTATAGCTGT 59.602 41.667 0.00 0.00 0.00 4.40
1771 1777 4.971220 GCAACTTCTCTACGTATAGCTGTC 59.029 45.833 0.00 0.00 0.00 3.51
1773 1779 4.440880 ACTTCTCTACGTATAGCTGTCGT 58.559 43.478 14.67 14.67 40.78 4.34
1774 1780 4.270566 ACTTCTCTACGTATAGCTGTCGTG 59.729 45.833 18.00 10.76 38.27 4.35
1775 1781 3.790091 TCTCTACGTATAGCTGTCGTGT 58.210 45.455 18.00 5.47 38.27 4.49
1776 1782 4.936891 TCTCTACGTATAGCTGTCGTGTA 58.063 43.478 18.00 6.20 38.27 2.90
1777 1783 4.742167 TCTCTACGTATAGCTGTCGTGTAC 59.258 45.833 18.00 0.00 38.27 2.90
1786 1792 4.617808 AGCTGTCGTGTACTACATAGTG 57.382 45.455 1.66 0.00 37.10 2.74
1806 1813 5.538067 GTGCAACTCTAAAAGAGGTCATC 57.462 43.478 8.69 0.00 37.92 2.92
1811 1818 6.205658 GCAACTCTAAAAGAGGTCATCTGTTT 59.794 38.462 8.69 0.00 37.92 2.83
1878 1885 4.968626 TGCGATCATACATGAACAAACAC 58.031 39.130 0.00 0.00 40.69 3.32
1879 1886 4.694982 TGCGATCATACATGAACAAACACT 59.305 37.500 0.00 0.00 40.69 3.55
1880 1887 5.163864 TGCGATCATACATGAACAAACACTC 60.164 40.000 0.00 0.00 40.69 3.51
1881 1888 5.163864 GCGATCATACATGAACAAACACTCA 60.164 40.000 0.00 0.00 40.69 3.41
1882 1889 6.472680 CGATCATACATGAACAAACACTCAG 58.527 40.000 0.00 0.00 40.69 3.35
1970 2036 9.787532 TCTGTTTTCAAAATGTAAACTCTCAAG 57.212 29.630 11.91 3.68 38.12 3.02
1991 2057 3.377656 GGCGGAGACAGACCAAGA 58.622 61.111 0.00 0.00 31.66 3.02
1992 2058 1.216710 GGCGGAGACAGACCAAGAG 59.783 63.158 0.00 0.00 31.66 2.85
1993 2059 1.536943 GGCGGAGACAGACCAAGAGT 61.537 60.000 0.00 0.00 31.66 3.24
1995 2061 1.133407 GCGGAGACAGACCAAGAGTAG 59.867 57.143 0.00 0.00 0.00 2.57
1997 2063 2.820787 CGGAGACAGACCAAGAGTAGTT 59.179 50.000 0.00 0.00 0.00 2.24
2080 2256 6.924060 ACGAAATAACTATACTGCATCACTCC 59.076 38.462 0.00 0.00 0.00 3.85
2095 2271 0.038310 ACTCCAACAAGCTTAGCCCC 59.962 55.000 0.00 0.00 0.00 5.80
2145 2323 3.944087 TCTCTCAAGAGATCGACACTCA 58.056 45.455 19.06 3.19 45.48 3.41
2146 2324 4.522114 TCTCTCAAGAGATCGACACTCAT 58.478 43.478 19.06 8.31 45.48 2.90
2147 2325 4.335037 TCTCTCAAGAGATCGACACTCATG 59.665 45.833 19.06 17.34 45.48 3.07
2148 2326 4.013050 TCTCAAGAGATCGACACTCATGT 58.987 43.478 19.06 5.72 35.37 3.21
2149 2327 5.186198 TCTCAAGAGATCGACACTCATGTA 58.814 41.667 19.06 10.28 33.69 2.29
2150 2328 5.065346 TCTCAAGAGATCGACACTCATGTAC 59.935 44.000 19.06 0.00 33.69 2.90
2151 2329 4.944317 TCAAGAGATCGACACTCATGTACT 59.056 41.667 19.06 0.36 39.95 2.73
2152 2330 5.416013 TCAAGAGATCGACACTCATGTACTT 59.584 40.000 19.06 5.37 39.95 2.24
2153 2331 5.906113 AGAGATCGACACTCATGTACTTT 57.094 39.130 19.06 0.00 39.95 2.66
2154 2332 6.274157 AGAGATCGACACTCATGTACTTTT 57.726 37.500 19.06 0.00 39.95 2.27
2155 2333 6.692486 AGAGATCGACACTCATGTACTTTTT 58.308 36.000 19.06 0.00 39.95 1.94
2180 2358 5.529581 TGAGACAACTCACACTCATGTAA 57.470 39.130 0.00 0.00 46.55 2.41
2209 2387 7.788956 TTGAACAATCATAAGCAGAAAGCCTTC 60.789 37.037 0.00 0.00 38.76 3.46
2258 2436 7.415429 GCCTTAAGACTACGACTAAAGACATCT 60.415 40.741 3.36 0.00 0.00 2.90
2275 2453 1.210931 CTGAAGTCGTTCCGGCGTA 59.789 57.895 6.01 0.00 36.23 4.42
2292 2470 2.413897 GCGTACCTATACCTCGCTTAGC 60.414 54.545 0.00 0.00 42.88 3.09
2313 2491 2.343758 GGTTGGAGCGAGCACTCA 59.656 61.111 0.00 0.00 38.50 3.41
2335 2513 1.080569 CAGGCGTCACAAAATGGGC 60.081 57.895 0.00 0.00 0.00 5.36
2559 2742 8.431222 AGAAATGGAGAAAATCAATGAAAACCA 58.569 29.630 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.359531 CCGGCCAACAACTTTTGACTTA 59.640 45.455 2.24 0.00 0.00 2.24
1 2 1.136110 CCGGCCAACAACTTTTGACTT 59.864 47.619 2.24 0.00 0.00 3.01
2 3 0.744281 CCGGCCAACAACTTTTGACT 59.256 50.000 2.24 0.00 0.00 3.41
3 4 0.741915 TCCGGCCAACAACTTTTGAC 59.258 50.000 2.24 0.00 0.00 3.18
4 5 1.698506 ATCCGGCCAACAACTTTTGA 58.301 45.000 2.24 0.00 0.00 2.69
5 6 2.524569 AATCCGGCCAACAACTTTTG 57.475 45.000 2.24 0.00 0.00 2.44
6 7 6.071051 ACAATATAATCCGGCCAACAACTTTT 60.071 34.615 2.24 0.00 0.00 2.27
7 8 5.420739 ACAATATAATCCGGCCAACAACTTT 59.579 36.000 2.24 0.00 0.00 2.66
8 9 4.953579 ACAATATAATCCGGCCAACAACTT 59.046 37.500 2.24 0.00 0.00 2.66
9 10 4.532834 ACAATATAATCCGGCCAACAACT 58.467 39.130 2.24 0.00 0.00 3.16
10 11 4.911514 ACAATATAATCCGGCCAACAAC 57.088 40.909 2.24 0.00 0.00 3.32
11 12 5.197451 AGAACAATATAATCCGGCCAACAA 58.803 37.500 2.24 0.00 0.00 2.83
12 13 4.787551 AGAACAATATAATCCGGCCAACA 58.212 39.130 2.24 0.00 0.00 3.33
13 14 5.067283 ACAAGAACAATATAATCCGGCCAAC 59.933 40.000 2.24 0.00 0.00 3.77
14 15 5.197451 ACAAGAACAATATAATCCGGCCAA 58.803 37.500 2.24 0.00 0.00 4.52
15 16 4.787551 ACAAGAACAATATAATCCGGCCA 58.212 39.130 2.24 0.00 0.00 5.36
16 17 5.063880 AGACAAGAACAATATAATCCGGCC 58.936 41.667 0.00 0.00 0.00 6.13
17 18 6.483640 AGAAGACAAGAACAATATAATCCGGC 59.516 38.462 0.00 0.00 0.00 6.13
18 19 7.710907 TGAGAAGACAAGAACAATATAATCCGG 59.289 37.037 0.00 0.00 0.00 5.14
19 20 8.648557 TGAGAAGACAAGAACAATATAATCCG 57.351 34.615 0.00 0.00 0.00 4.18
25 26 9.730705 TGATCTTTGAGAAGACAAGAACAATAT 57.269 29.630 0.00 0.00 44.27 1.28
105 106 0.672401 TACAGTACAGCTTTGGCGGC 60.672 55.000 0.00 0.00 44.37 6.53
115 116 8.483218 CAATCATAAAGAAGCGATACAGTACAG 58.517 37.037 0.00 0.00 0.00 2.74
116 117 7.979537 ACAATCATAAAGAAGCGATACAGTACA 59.020 33.333 0.00 0.00 0.00 2.90
117 118 8.354011 ACAATCATAAAGAAGCGATACAGTAC 57.646 34.615 0.00 0.00 0.00 2.73
118 119 8.942338 AACAATCATAAAGAAGCGATACAGTA 57.058 30.769 0.00 0.00 0.00 2.74
119 120 7.849804 AACAATCATAAAGAAGCGATACAGT 57.150 32.000 0.00 0.00 0.00 3.55
156 157 1.270518 ACTGAGTTGCGCATCACTTCT 60.271 47.619 19.92 8.08 0.00 2.85
242 244 0.465097 ATGGCAGGAAGGAGAATGCG 60.465 55.000 0.00 0.00 39.58 4.73
291 293 6.730960 TGTTTTCTTTAAGACACGACAAGT 57.269 33.333 0.00 0.00 0.00 3.16
461 463 9.542462 TGCCTCTTGTGTCATTATTTATACTAC 57.458 33.333 0.00 0.00 0.00 2.73
489 494 0.607489 ATGTGACTGACCTTGGCAGC 60.607 55.000 0.00 0.00 43.61 5.25
545 550 9.389755 GCTAAACAAGGTACTACTACTACTACT 57.610 37.037 0.00 0.00 38.49 2.57
546 551 9.167311 TGCTAAACAAGGTACTACTACTACTAC 57.833 37.037 0.00 0.00 38.49 2.73
547 552 9.167311 GTGCTAAACAAGGTACTACTACTACTA 57.833 37.037 0.00 0.00 38.49 1.82
581 586 2.236395 TCAGTCTAGCCAAACCCTAAGC 59.764 50.000 0.00 0.00 0.00 3.09
585 590 3.118738 CGTAATCAGTCTAGCCAAACCCT 60.119 47.826 0.00 0.00 0.00 4.34
586 591 3.118884 TCGTAATCAGTCTAGCCAAACCC 60.119 47.826 0.00 0.00 0.00 4.11
624 629 2.071778 TGCTTGGCCCATAGAATTCC 57.928 50.000 0.00 0.00 0.00 3.01
625 630 2.101415 GGTTGCTTGGCCCATAGAATTC 59.899 50.000 0.00 0.00 0.00 2.17
632 637 3.256941 ATGGGGTTGCTTGGCCCAT 62.257 57.895 0.00 0.00 46.59 4.00
688 693 1.021390 GGGCAGTGTCACCAAGATCG 61.021 60.000 0.00 0.00 0.00 3.69
727 733 2.032634 CCGTCCGGGTTCATGTGTG 61.033 63.158 0.00 0.00 0.00 3.82
803 809 1.734477 CGACTGGAGCAGGACAACG 60.734 63.158 0.00 0.00 35.51 4.10
804 810 1.374758 CCGACTGGAGCAGGACAAC 60.375 63.158 0.00 0.00 37.49 3.32
805 811 1.533033 TCCGACTGGAGCAGGACAA 60.533 57.895 0.00 0.00 40.17 3.18
806 812 2.117423 TCCGACTGGAGCAGGACA 59.883 61.111 0.00 0.00 40.17 4.02
816 822 5.092105 GTGAGATTATCATCGATCCGACTG 58.908 45.833 0.00 0.00 40.92 3.51
825 831 6.206498 TCAAACCGTAGTGAGATTATCATCG 58.794 40.000 0.00 0.00 40.92 3.84
849 855 6.471233 TTCAAGGTAGACATCTTGATCGAT 57.529 37.500 0.00 0.00 45.69 3.59
850 856 5.914898 TTCAAGGTAGACATCTTGATCGA 57.085 39.130 6.60 0.00 45.69 3.59
851 857 8.824159 ATAATTCAAGGTAGACATCTTGATCG 57.176 34.615 6.60 0.00 45.69 3.69
978 984 0.601046 TGCTCTTGCACCTTCAGACG 60.601 55.000 0.00 0.00 45.31 4.18
1015 1021 2.288457 ACGGATCATTATCACGCTCCTG 60.288 50.000 0.00 0.00 33.41 3.86
1022 1028 5.201713 TCTCTTGGACGGATCATTATCAC 57.798 43.478 0.00 0.00 33.41 3.06
1024 1030 5.010112 TCACTCTCTTGGACGGATCATTATC 59.990 44.000 0.00 0.00 0.00 1.75
1025 1031 4.895889 TCACTCTCTTGGACGGATCATTAT 59.104 41.667 0.00 0.00 0.00 1.28
1026 1032 4.278310 TCACTCTCTTGGACGGATCATTA 58.722 43.478 0.00 0.00 0.00 1.90
1027 1033 3.099905 TCACTCTCTTGGACGGATCATT 58.900 45.455 0.00 0.00 0.00 2.57
1418 1424 1.411493 GGATGAACGAGTCGGCGAAC 61.411 60.000 18.30 8.31 34.83 3.95
1455 1461 2.669569 ATGTTGAACTGCGCGGCT 60.670 55.556 18.15 3.02 0.00 5.52
1468 1474 2.236766 CGGAGGAGGGTATACGATGTT 58.763 52.381 0.00 0.00 0.00 2.71
1474 1480 0.471401 AAGGGCGGAGGAGGGTATAC 60.471 60.000 0.00 0.00 0.00 1.47
1476 1482 1.766461 CAAGGGCGGAGGAGGGTAT 60.766 63.158 0.00 0.00 0.00 2.73
1492 1498 3.183130 CATTCATGCCGTACCCCAA 57.817 52.632 0.00 0.00 0.00 4.12
1733 1739 2.334946 TTGCAGGAATGTGCTCCGC 61.335 57.895 0.00 0.00 44.32 5.54
1746 1752 4.973051 CAGCTATACGTAGAGAAGTTGCAG 59.027 45.833 20.95 0.00 0.00 4.41
1757 1763 5.460091 TGTAGTACACGACAGCTATACGTAG 59.540 44.000 0.08 8.59 38.47 3.51
1761 1767 7.289395 CACTATGTAGTACACGACAGCTATAC 58.711 42.308 4.80 0.00 35.07 1.47
1768 1774 4.216902 AGTTGCACTATGTAGTACACGACA 59.783 41.667 4.80 0.00 36.01 4.35
1769 1775 4.730657 AGTTGCACTATGTAGTACACGAC 58.269 43.478 4.80 2.85 34.13 4.34
1770 1776 4.698780 AGAGTTGCACTATGTAGTACACGA 59.301 41.667 4.80 0.00 34.13 4.35
1771 1777 4.982999 AGAGTTGCACTATGTAGTACACG 58.017 43.478 4.80 2.55 34.13 4.49
1773 1779 8.799367 TCTTTTAGAGTTGCACTATGTAGTACA 58.201 33.333 5.24 5.24 34.13 2.90
1774 1780 9.291664 CTCTTTTAGAGTTGCACTATGTAGTAC 57.708 37.037 0.00 0.00 37.57 2.73
1775 1781 8.467598 CCTCTTTTAGAGTTGCACTATGTAGTA 58.532 37.037 3.27 0.00 40.72 1.82
1776 1782 7.038941 ACCTCTTTTAGAGTTGCACTATGTAGT 60.039 37.037 3.27 0.00 40.72 2.73
1777 1783 7.324178 ACCTCTTTTAGAGTTGCACTATGTAG 58.676 38.462 3.27 0.00 40.72 2.74
1786 1792 5.241662 ACAGATGACCTCTTTTAGAGTTGC 58.758 41.667 3.27 0.00 40.72 4.17
1806 1813 6.586082 GGACATTTGGTTAATAGTGCAAACAG 59.414 38.462 0.00 0.00 0.00 3.16
1811 1818 4.157656 GCTGGACATTTGGTTAATAGTGCA 59.842 41.667 0.00 0.00 30.88 4.57
1878 1885 1.402456 CCGTCGGTTTCCAGTACTGAG 60.402 57.143 24.68 13.96 31.84 3.35
1879 1886 0.599558 CCGTCGGTTTCCAGTACTGA 59.400 55.000 24.68 7.64 0.00 3.41
1880 1887 0.599558 TCCGTCGGTTTCCAGTACTG 59.400 55.000 16.34 16.34 0.00 2.74
1881 1888 0.886563 CTCCGTCGGTTTCCAGTACT 59.113 55.000 11.88 0.00 0.00 2.73
1882 1889 0.600057 ACTCCGTCGGTTTCCAGTAC 59.400 55.000 11.88 0.00 0.00 2.73
1970 2036 1.816863 TTGGTCTGTCTCCGCCACTC 61.817 60.000 0.00 0.00 0.00 3.51
2080 2256 1.598701 GCCTGGGGCTAAGCTTGTTG 61.599 60.000 9.86 0.19 46.69 3.33
2095 2271 5.333513 GGAGATAGTATCGAATTACGCCTG 58.666 45.833 4.48 0.00 42.26 4.85
2158 2336 5.529581 TTACATGAGTGTGAGTTGTCTCA 57.470 39.130 0.00 0.00 46.85 3.27
2159 2337 5.986135 AGTTTACATGAGTGTGAGTTGTCTC 59.014 40.000 0.00 0.00 39.39 3.36
2160 2338 5.918608 AGTTTACATGAGTGTGAGTTGTCT 58.081 37.500 0.00 0.00 39.39 3.41
2161 2339 6.257849 TCAAGTTTACATGAGTGTGAGTTGTC 59.742 38.462 0.00 0.00 39.39 3.18
2162 2340 6.112734 TCAAGTTTACATGAGTGTGAGTTGT 58.887 36.000 0.00 0.00 39.39 3.32
2163 2341 6.603237 TCAAGTTTACATGAGTGTGAGTTG 57.397 37.500 0.00 0.00 39.39 3.16
2164 2342 6.597672 TGTTCAAGTTTACATGAGTGTGAGTT 59.402 34.615 0.00 0.00 39.39 3.01
2165 2343 6.112734 TGTTCAAGTTTACATGAGTGTGAGT 58.887 36.000 0.00 0.00 39.39 3.41
2166 2344 6.603237 TGTTCAAGTTTACATGAGTGTGAG 57.397 37.500 0.00 0.00 39.39 3.51
2179 2357 7.383300 GCTTTCTGCTTATGATTGTTCAAGTTT 59.617 33.333 0.00 0.00 38.95 2.66
2180 2358 6.865205 GCTTTCTGCTTATGATTGTTCAAGTT 59.135 34.615 0.00 0.00 38.95 2.66
2209 2387 3.521524 GAACTGTTGTTCTAACGCTGG 57.478 47.619 0.00 0.00 46.56 4.85
2313 2491 1.541147 CCATTTTGTGACGCCTGATGT 59.459 47.619 0.00 0.00 0.00 3.06
2524 2703 9.981114 TTGATTTTCTCCATTTCTTTTTCTACC 57.019 29.630 0.00 0.00 0.00 3.18
2687 2893 5.013547 TCACAGGTTTTCTTCAGTTTTCCA 58.986 37.500 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.