Multiple sequence alignment - TraesCS3A01G038300

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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 TraesCS3A01G038300 chr3A 100.000 2561 0 0 1 2561 20591783 20589223 0.000000e+00 4730
1 TraesCS3A01G038300 chr3A 97.343 527 14 0 2035 2561 535087197 535086671 0.000000e+00 896
2 TraesCS3A01G038300 chr3A 96.768 526 17 0 2036 2561 446072527 446072002 0.000000e+00 878
3 TraesCS3A01G038300 chr3B 88.563 1775 103 40 83 1817 22859974 22861688 0.000000e+00 2061
4 TraesCS3A01G038300 chr3B 81.707 410 39 21 1647 2030 22862225 22862624 2.470000e-80 309
5 TraesCS3A01G038300 chr3D 87.764 1749 86 59 331 2034 15942591 15944256 0.000000e+00 1927
6 TraesCS3A01G038300 chr3D 87.170 795 57 27 838 1614 15937887 15937120 0.000000e+00 861
7 TraesCS3A01G038300 chr3D 92.276 246 13 4 1785 2030 15952886 15953125 6.780000e-91 344
8 TraesCS3A01G038300 chr3D 86.692 263 17 7 1618 1875 15945081 15945330 2.510000e-70 276
9 TraesCS3A01G038300 chr3D 85.572 201 19 6 1765 1962 15951217 15951410 4.320000e-48 202
10 TraesCS3A01G038300 chr3D 91.781 73 6 0 1182 1254 15952320 15952392 4.510000e-18 102
11 TraesCS3A01G038300 chr2A 97.533 527 13 0 2035 2561 643927543 643927017 0.000000e+00 902
12 TraesCS3A01G038300 chr7A 97.343 527 14 0 2035 2561 562192725 562193251 0.000000e+00 896
13 TraesCS3A01G038300 chr5A 97.343 527 14 0 2035 2561 240872687 240873213 0.000000e+00 896
14 TraesCS3A01G038300 chr5A 97.343 527 14 0 2035 2561 501902492 501903018 0.000000e+00 896
15 TraesCS3A01G038300 chr5A 96.828 536 15 2 2027 2561 20701359 20701893 0.000000e+00 894
16 TraesCS3A01G038300 chr4A 97.343 527 14 0 2035 2561 185612163 185611637 0.000000e+00 896
17 TraesCS3A01G038300 chr1A 97.343 527 14 0 2035 2561 305759177 305758651 0.000000e+00 896
18 TraesCS3A01G038300 chrUn 96.552 464 10 4 998 1461 470749643 470750100 0.000000e+00 763


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 TraesCS3A01G038300 chr3A 20589223 20591783 2560 True 4730.0 4730 100.000000 1 2561 1 chr3A.!!$R1 2560
1 TraesCS3A01G038300 chr3A 535086671 535087197 526 True 896.0 896 97.343000 2035 2561 1 chr3A.!!$R3 526
2 TraesCS3A01G038300 chr3A 446072002 446072527 525 True 878.0 878 96.768000 2036 2561 1 chr3A.!!$R2 525
3 TraesCS3A01G038300 chr3B 22859974 22862624 2650 False 1185.0 2061 85.135000 83 2030 2 chr3B.!!$F1 1947
4 TraesCS3A01G038300 chr3D 15942591 15945330 2739 False 1101.5 1927 87.228000 331 2034 2 chr3D.!!$F1 1703
5 TraesCS3A01G038300 chr3D 15937120 15937887 767 True 861.0 861 87.170000 838 1614 1 chr3D.!!$R1 776
6 TraesCS3A01G038300 chr3D 15951217 15953125 1908 False 216.0 344 89.876333 1182 2030 3 chr3D.!!$F2 848
7 TraesCS3A01G038300 chr2A 643927017 643927543 526 True 902.0 902 97.533000 2035 2561 1 chr2A.!!$R1 526
8 TraesCS3A01G038300 chr7A 562192725 562193251 526 False 896.0 896 97.343000 2035 2561 1 chr7A.!!$F1 526
9 TraesCS3A01G038300 chr5A 240872687 240873213 526 False 896.0 896 97.343000 2035 2561 1 chr5A.!!$F2 526
10 TraesCS3A01G038300 chr5A 501902492 501903018 526 False 896.0 896 97.343000 2035 2561 1 chr5A.!!$F3 526
11 TraesCS3A01G038300 chr5A 20701359 20701893 534 False 894.0 894 96.828000 2027 2561 1 chr5A.!!$F1 534
12 TraesCS3A01G038300 chr4A 185611637 185612163 526 True 896.0 896 97.343000 2035 2561 1 chr4A.!!$R1 526
13 TraesCS3A01G038300 chr1A 305758651 305759177 526 True 896.0 896 97.343000 2035 2561 1 chr1A.!!$R1 526

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
628 647 0.03496 GGAAAAGTCCTCCCTCAGCC 60.035 60.0 0.0 0.0 41.24 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 2794 1.597027 GCACACACAGCCGTTACCT 60.597 57.895 0.0 0.0 0.0 3.08 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
41 42 1.286880 GTGTGCACACCCTTCATGC 59.713 57.895 34.94 10.50 40.85 4.06
45 46 2.981560 GCACACCCTTCATGCCACG 61.982 63.158 0.00 0.00 33.06 4.94
46 47 2.034066 ACACCCTTCATGCCACGG 59.966 61.111 0.00 0.00 0.00 4.94
48 49 4.047125 ACCCTTCATGCCACGGGG 62.047 66.667 0.00 0.00 41.11 5.73
50 51 4.047125 CCTTCATGCCACGGGGGT 62.047 66.667 5.47 0.00 39.65 4.95
51 52 2.438434 CTTCATGCCACGGGGGTC 60.438 66.667 5.47 0.00 39.65 4.46
52 53 4.402528 TTCATGCCACGGGGGTCG 62.403 66.667 5.47 0.00 45.88 4.79
64 65 4.382320 GGGTCGCACGGCCTTGTA 62.382 66.667 14.08 0.00 40.34 2.41
65 66 2.357760 GGTCGCACGGCCTTGTAA 60.358 61.111 11.38 0.00 36.84 2.41
66 67 1.743995 GGTCGCACGGCCTTGTAAT 60.744 57.895 11.38 0.00 36.84 1.89
67 68 1.303091 GGTCGCACGGCCTTGTAATT 61.303 55.000 11.38 0.00 36.84 1.40
68 69 0.519961 GTCGCACGGCCTTGTAATTT 59.480 50.000 11.38 0.00 0.00 1.82
70 71 1.609555 TCGCACGGCCTTGTAATTTTT 59.390 42.857 11.38 0.00 0.00 1.94
71 72 1.718711 CGCACGGCCTTGTAATTTTTG 59.281 47.619 11.38 0.00 0.00 2.44
73 74 2.288518 GCACGGCCTTGTAATTTTTGGA 60.289 45.455 11.38 0.00 0.00 3.53
74 75 3.800604 GCACGGCCTTGTAATTTTTGGAA 60.801 43.478 11.38 0.00 0.00 3.53
75 76 4.372656 CACGGCCTTGTAATTTTTGGAAA 58.627 39.130 0.00 0.00 0.00 3.13
78 79 4.923281 CGGCCTTGTAATTTTTGGAAAGAG 59.077 41.667 0.00 0.00 0.00 2.85
79 80 4.690748 GGCCTTGTAATTTTTGGAAAGAGC 59.309 41.667 0.00 0.00 0.00 4.09
80 81 5.296748 GCCTTGTAATTTTTGGAAAGAGCA 58.703 37.500 0.00 0.00 0.00 4.26
81 82 5.757808 GCCTTGTAATTTTTGGAAAGAGCAA 59.242 36.000 0.00 0.00 0.00 3.91
82 83 6.259829 GCCTTGTAATTTTTGGAAAGAGCAAA 59.740 34.615 0.00 0.00 0.00 3.68
83 84 7.518848 GCCTTGTAATTTTTGGAAAGAGCAAAG 60.519 37.037 0.00 0.00 0.00 2.77
84 85 6.843069 TGTAATTTTTGGAAAGAGCAAAGC 57.157 33.333 0.00 0.00 0.00 3.51
85 86 6.344500 TGTAATTTTTGGAAAGAGCAAAGCA 58.656 32.000 0.00 0.00 0.00 3.91
86 87 5.739752 AATTTTTGGAAAGAGCAAAGCAC 57.260 34.783 0.00 0.00 0.00 4.40
87 88 2.490328 TTTGGAAAGAGCAAAGCACG 57.510 45.000 0.00 0.00 0.00 5.34
88 89 1.388547 TTGGAAAGAGCAAAGCACGT 58.611 45.000 0.00 0.00 0.00 4.49
89 90 0.944386 TGGAAAGAGCAAAGCACGTC 59.056 50.000 0.00 0.00 0.00 4.34
90 91 0.238553 GGAAAGAGCAAAGCACGTCC 59.761 55.000 0.00 0.00 0.00 4.79
132 133 4.980434 GCGAACGACTTTAGCAATCCTATA 59.020 41.667 0.00 0.00 35.96 1.31
133 134 5.117287 GCGAACGACTTTAGCAATCCTATAG 59.883 44.000 0.00 0.00 35.96 1.31
135 136 9.798416 GCGAACGACTTTAGCAATCCTATAGGA 62.798 44.444 23.76 23.76 40.88 2.94
146 147 2.525877 TATAGGACCAGGGGGCGC 60.526 66.667 0.00 0.00 37.90 6.53
177 179 4.421479 CAACGGCGGAGAGAGCGT 62.421 66.667 13.24 0.00 35.00 5.07
192 194 4.636435 CGTTCGCCAGGGTTGGGT 62.636 66.667 0.00 0.00 45.16 4.51
193 195 2.671963 GTTCGCCAGGGTTGGGTC 60.672 66.667 0.00 0.00 45.16 4.46
223 226 1.659098 GTTCGCCAGACAGTATTTCCG 59.341 52.381 0.00 0.00 0.00 4.30
253 256 5.160511 ACCTATATGTACCCCCACACTAA 57.839 43.478 0.00 0.00 0.00 2.24
263 267 4.266714 ACCCCCACACTAATAAAATCACG 58.733 43.478 0.00 0.00 0.00 4.35
264 268 4.019141 ACCCCCACACTAATAAAATCACGA 60.019 41.667 0.00 0.00 0.00 4.35
279 283 0.993746 CACGAGCGCAGTGAAAAAGC 60.994 55.000 25.36 0.00 41.83 3.51
286 290 0.663153 GCAGTGAAAAAGCGAGTGGT 59.337 50.000 0.00 0.00 0.00 4.16
297 301 1.160329 GCGAGTGGTGGCCATGATAC 61.160 60.000 9.72 6.10 35.28 2.24
376 380 3.508840 GCAAAGGATGGGACGCCG 61.509 66.667 0.00 0.00 0.00 6.46
521 540 4.116961 GGCAAAGGAATAAATAAACCGGC 58.883 43.478 0.00 0.00 0.00 6.13
623 642 2.168666 GACGCGGAAAAGTCCTCCCT 62.169 60.000 12.47 0.00 42.44 4.20
626 645 0.391793 GCGGAAAAGTCCTCCCTCAG 60.392 60.000 0.00 0.00 42.44 3.35
628 647 0.034960 GGAAAAGTCCTCCCTCAGCC 60.035 60.000 0.00 0.00 41.24 4.85
751 774 2.330393 GCTCGCCGCGTACTGATA 59.670 61.111 13.39 0.00 0.00 2.15
752 775 1.081376 GCTCGCCGCGTACTGATAT 60.081 57.895 13.39 0.00 0.00 1.63
753 776 1.337817 GCTCGCCGCGTACTGATATG 61.338 60.000 13.39 0.00 0.00 1.78
754 777 0.237498 CTCGCCGCGTACTGATATGA 59.763 55.000 13.39 0.00 0.00 2.15
755 778 0.040692 TCGCCGCGTACTGATATGAC 60.041 55.000 13.39 0.00 0.00 3.06
756 779 0.040336 CGCCGCGTACTGATATGACT 60.040 55.000 4.92 0.00 0.00 3.41
798 821 5.425862 AGTTACTCCTCCACTTCTTTATCCC 59.574 44.000 0.00 0.00 0.00 3.85
824 847 4.148825 GAGGATGGTCGGTGCGCT 62.149 66.667 9.73 0.00 0.00 5.92
825 848 4.148825 AGGATGGTCGGTGCGCTC 62.149 66.667 9.73 4.47 0.00 5.03
894 917 1.746615 CTGCAACCTCCACCCATCG 60.747 63.158 0.00 0.00 0.00 3.84
897 923 1.682849 CAACCTCCACCCATCGGAA 59.317 57.895 0.00 0.00 30.33 4.30
908 937 3.081804 ACCCATCGGAACATTCAAGTTC 58.918 45.455 0.00 0.00 45.50 3.01
918 947 1.821136 CATTCAAGTTCAAGCTCCCCC 59.179 52.381 0.00 0.00 0.00 5.40
945 982 0.685097 TCACTACAACCAGCCACCTC 59.315 55.000 0.00 0.00 0.00 3.85
989 1026 2.559840 GCGACCGTCGAGTCTCAA 59.440 61.111 24.78 0.00 43.74 3.02
990 1027 1.512310 GCGACCGTCGAGTCTCAAG 60.512 63.158 24.78 0.00 43.74 3.02
991 1028 1.867615 CGACCGTCGAGTCTCAAGT 59.132 57.895 16.03 0.00 43.74 3.16
992 1029 0.179220 CGACCGTCGAGTCTCAAGTC 60.179 60.000 16.03 0.30 43.74 3.01
995 1032 1.267261 ACCGTCGAGTCTCAAGTCTTG 59.733 52.381 6.21 6.21 0.00 3.02
1554 1909 1.480137 CCTGACAGCAACAAACCCAAA 59.520 47.619 0.00 0.00 0.00 3.28
1581 1944 7.253422 AGTGATACATGCTTGCTTGTAAATTC 58.747 34.615 19.96 15.03 32.46 2.17
1658 2034 3.265791 GGCATAGTGTTCTGGTCTGAAG 58.734 50.000 0.00 0.00 0.00 3.02
1660 2036 4.383552 GGCATAGTGTTCTGGTCTGAAGAT 60.384 45.833 0.00 0.00 0.00 2.40
1701 2077 2.728690 TCAATGTGCAATTGCCACTC 57.271 45.000 26.94 14.78 41.18 3.51
1718 2794 3.258372 CCACTCTTGTGCTGTACCTCTAA 59.742 47.826 0.00 0.00 42.54 2.10
1883 2993 1.614996 ACCCAATGCATCGTCAACAA 58.385 45.000 0.00 0.00 0.00 2.83
2076 3187 9.408648 CTCTAGGTGGTTTTGGTAATTCATAAT 57.591 33.333 0.00 0.00 0.00 1.28
2124 3235 7.795047 TGCTATTCCAAGATGACTATTTCAGA 58.205 34.615 0.00 0.00 37.77 3.27
2149 3260 3.568443 ACTCAATGATTGGCATGGCATA 58.432 40.909 23.96 14.03 37.28 3.14
2162 3273 3.628942 GCATGGCATAGATGTGAAAGTGA 59.371 43.478 0.00 0.00 0.00 3.41
2369 3480 5.741011 TCAACTACTTTCCCATATCCACAC 58.259 41.667 0.00 0.00 0.00 3.82
2468 3579 2.299867 CACTGCCAAACCCTAGCAATTT 59.700 45.455 0.00 0.00 35.79 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.286880 GCATGAAGGGTGTGCACAC 59.713 57.895 36.56 36.56 45.72 3.82
24 25 1.902918 GGCATGAAGGGTGTGCACA 60.903 57.895 17.42 17.42 40.53 4.57
25 26 1.902918 TGGCATGAAGGGTGTGCAC 60.903 57.895 10.75 10.75 40.53 4.57
26 27 1.902918 GTGGCATGAAGGGTGTGCA 60.903 57.895 0.00 0.00 40.53 4.57
27 28 2.964978 GTGGCATGAAGGGTGTGC 59.035 61.111 0.00 0.00 38.12 4.57
28 29 2.334946 CCGTGGCATGAAGGGTGTG 61.335 63.158 8.63 0.00 0.00 3.82
29 30 2.034066 CCGTGGCATGAAGGGTGT 59.966 61.111 8.63 0.00 0.00 4.16
31 32 4.047125 CCCCGTGGCATGAAGGGT 62.047 66.667 8.63 0.00 42.26 4.34
32 33 4.820744 CCCCCGTGGCATGAAGGG 62.821 72.222 17.17 17.17 43.41 3.95
34 35 2.438434 GACCCCCGTGGCATGAAG 60.438 66.667 8.63 0.00 37.83 3.02
48 49 1.303091 AATTACAAGGCCGTGCGACC 61.303 55.000 19.37 0.00 0.00 4.79
50 51 1.240256 AAAATTACAAGGCCGTGCGA 58.760 45.000 19.37 7.82 0.00 5.10
51 52 1.718711 CAAAAATTACAAGGCCGTGCG 59.281 47.619 19.37 0.00 0.00 5.34
52 53 2.065512 CCAAAAATTACAAGGCCGTGC 58.934 47.619 19.37 0.00 0.00 5.34
53 54 3.651803 TCCAAAAATTACAAGGCCGTG 57.348 42.857 17.83 17.83 0.00 4.94
54 55 4.342665 TCTTTCCAAAAATTACAAGGCCGT 59.657 37.500 0.00 0.00 0.00 5.68
55 56 4.877282 TCTTTCCAAAAATTACAAGGCCG 58.123 39.130 0.00 0.00 0.00 6.13
56 57 4.690748 GCTCTTTCCAAAAATTACAAGGCC 59.309 41.667 0.00 0.00 0.00 5.19
57 58 5.296748 TGCTCTTTCCAAAAATTACAAGGC 58.703 37.500 0.00 0.00 0.00 4.35
58 59 7.518848 GCTTTGCTCTTTCCAAAAATTACAAGG 60.519 37.037 0.00 0.00 32.37 3.61
59 60 7.011295 TGCTTTGCTCTTTCCAAAAATTACAAG 59.989 33.333 0.00 0.00 32.37 3.16
61 62 6.257630 GTGCTTTGCTCTTTCCAAAAATTACA 59.742 34.615 0.00 0.00 32.37 2.41
62 63 6.562086 CGTGCTTTGCTCTTTCCAAAAATTAC 60.562 38.462 0.00 0.00 32.37 1.89
63 64 5.461737 CGTGCTTTGCTCTTTCCAAAAATTA 59.538 36.000 0.00 0.00 32.37 1.40
64 65 4.270808 CGTGCTTTGCTCTTTCCAAAAATT 59.729 37.500 0.00 0.00 32.37 1.82
65 66 3.803778 CGTGCTTTGCTCTTTCCAAAAAT 59.196 39.130 0.00 0.00 32.37 1.82
66 67 3.186119 CGTGCTTTGCTCTTTCCAAAAA 58.814 40.909 0.00 0.00 32.37 1.94
67 68 2.165437 ACGTGCTTTGCTCTTTCCAAAA 59.835 40.909 0.00 0.00 32.37 2.44
68 69 1.748493 ACGTGCTTTGCTCTTTCCAAA 59.252 42.857 0.00 0.00 0.00 3.28
70 71 0.944386 GACGTGCTTTGCTCTTTCCA 59.056 50.000 0.00 0.00 0.00 3.53
71 72 0.238553 GGACGTGCTTTGCTCTTTCC 59.761 55.000 0.00 0.00 0.00 3.13
73 74 1.941812 CGGACGTGCTTTGCTCTTT 59.058 52.632 5.27 0.00 0.00 2.52
74 75 2.607892 GCGGACGTGCTTTGCTCTT 61.608 57.895 5.27 0.00 0.00 2.85
75 76 3.044305 GCGGACGTGCTTTGCTCT 61.044 61.111 5.27 0.00 0.00 4.09
78 79 4.389576 CTGGCGGACGTGCTTTGC 62.390 66.667 5.27 0.66 34.52 3.68
79 80 3.726517 CCTGGCGGACGTGCTTTG 61.727 66.667 5.27 0.00 34.52 2.77
90 91 2.374830 CTATCAGCTGACCCCTGGCG 62.375 65.000 20.97 0.00 0.00 5.69
97 98 0.100682 TCGTTCGCTATCAGCTGACC 59.899 55.000 20.97 9.62 39.60 4.02
146 147 1.416049 CGTTGCACGGATCTTGACG 59.584 57.895 0.00 0.00 38.08 4.35
166 168 4.116328 TGGCGAACGCTCTCTCCG 62.116 66.667 18.14 0.00 41.60 4.63
168 170 2.202676 CCTGGCGAACGCTCTCTC 60.203 66.667 18.14 2.64 41.60 3.20
177 179 3.961414 GGACCCAACCCTGGCGAA 61.961 66.667 0.00 0.00 41.99 4.70
223 226 8.439172 TGTGGGGGTACATATAGGTTAATTTAC 58.561 37.037 0.00 0.00 0.00 2.01
238 241 6.181908 GTGATTTTATTAGTGTGGGGGTACA 58.818 40.000 0.00 0.00 0.00 2.90
253 256 2.616960 TCACTGCGCTCGTGATTTTAT 58.383 42.857 22.95 0.00 36.54 1.40
263 267 4.121490 CGCTTTTTCACTGCGCTC 57.879 55.556 9.73 0.00 43.08 5.03
279 283 0.532862 GGTATCATGGCCACCACTCG 60.533 60.000 8.16 0.00 35.80 4.18
286 290 1.227102 GTGCAGGGTATCATGGCCA 59.773 57.895 8.56 8.56 0.00 5.36
297 301 0.030638 CAACAAAGGTTCGTGCAGGG 59.969 55.000 6.56 0.00 34.21 4.45
376 380 3.173240 GAGGTCGTCGTTGCTCGC 61.173 66.667 0.00 0.00 39.67 5.03
623 642 2.369257 GATGCGAATCTCGGGGCTGA 62.369 60.000 0.00 0.00 40.84 4.26
626 645 3.038417 CGATGCGAATCTCGGGGC 61.038 66.667 0.96 0.00 40.84 5.80
743 766 2.229302 GGAGGCGGAGTCATATCAGTAC 59.771 54.545 0.00 0.00 0.00 2.73
744 767 2.515854 GGAGGCGGAGTCATATCAGTA 58.484 52.381 0.00 0.00 0.00 2.74
746 769 0.605589 GGGAGGCGGAGTCATATCAG 59.394 60.000 0.00 0.00 0.00 2.90
747 770 0.832135 GGGGAGGCGGAGTCATATCA 60.832 60.000 0.00 0.00 0.00 2.15
748 771 1.878656 CGGGGAGGCGGAGTCATATC 61.879 65.000 0.00 0.00 0.00 1.63
750 773 2.520982 CGGGGAGGCGGAGTCATA 60.521 66.667 0.00 0.00 0.00 2.15
783 806 3.446968 TCCTTCGGGATAAAGAAGTGGA 58.553 45.455 4.78 0.00 41.51 4.02
785 808 3.798202 CCTCCTTCGGGATAAAGAAGTG 58.202 50.000 4.78 0.00 44.11 3.16
798 821 1.739338 CGACCATCCTCCCTCCTTCG 61.739 65.000 0.00 0.00 0.00 3.79
864 887 1.676384 GTTGCAGTGGGCTCTCTCT 59.324 57.895 0.00 0.00 45.15 3.10
865 888 1.376553 GGTTGCAGTGGGCTCTCTC 60.377 63.158 0.00 0.00 45.15 3.20
866 889 1.835927 GAGGTTGCAGTGGGCTCTCT 61.836 60.000 0.00 0.00 45.15 3.10
867 890 1.376553 GAGGTTGCAGTGGGCTCTC 60.377 63.158 0.00 0.00 45.15 3.20
894 917 3.057245 GGGAGCTTGAACTTGAATGTTCC 60.057 47.826 5.15 0.00 43.96 3.62
897 923 2.519013 GGGGAGCTTGAACTTGAATGT 58.481 47.619 0.00 0.00 0.00 2.71
908 937 0.110104 GATGGAGATGGGGGAGCTTG 59.890 60.000 0.00 0.00 0.00 4.01
918 947 3.201290 GCTGGTTGTAGTGATGGAGATG 58.799 50.000 0.00 0.00 0.00 2.90
984 1021 1.003580 GACATGGCCCAAGACTTGAGA 59.996 52.381 16.99 0.00 0.00 3.27
985 1022 1.457346 GACATGGCCCAAGACTTGAG 58.543 55.000 16.99 4.36 0.00 3.02
989 1026 1.599047 CTCGACATGGCCCAAGACT 59.401 57.895 0.00 0.00 0.00 3.24
990 1027 2.109126 GCTCGACATGGCCCAAGAC 61.109 63.158 0.00 0.00 0.00 3.01
991 1028 2.268920 GCTCGACATGGCCCAAGA 59.731 61.111 0.00 0.00 0.00 3.02
992 1029 3.197790 CGCTCGACATGGCCCAAG 61.198 66.667 0.00 0.00 0.00 3.61
1015 1052 3.441290 CTGCTGCTGCTGCTTCCC 61.441 66.667 27.67 3.96 40.48 3.97
1395 1747 2.740055 CAGTCCTCGGTGCTGCAC 60.740 66.667 24.02 24.02 0.00 4.57
1554 1909 3.947868 ACAAGCAAGCATGTATCACTCT 58.052 40.909 0.54 0.00 0.00 3.24
1601 1964 6.657541 TGACAATTAACATACACCTTCCCTTC 59.342 38.462 0.00 0.00 0.00 3.46
1603 1966 6.134535 TGACAATTAACATACACCTTCCCT 57.865 37.500 0.00 0.00 0.00 4.20
1604 1967 5.944007 ACTGACAATTAACATACACCTTCCC 59.056 40.000 0.00 0.00 0.00 3.97
1606 1969 7.822822 AGGTACTGACAATTAACATACACCTTC 59.177 37.037 0.00 0.00 37.18 3.46
1607 1970 7.686434 AGGTACTGACAATTAACATACACCTT 58.314 34.615 0.00 0.00 37.18 3.50
1658 2034 8.923270 TGATCCTTATTCCCAATTTTTACCATC 58.077 33.333 0.00 0.00 0.00 3.51
1660 2036 8.671987 TTGATCCTTATTCCCAATTTTTACCA 57.328 30.769 0.00 0.00 0.00 3.25
1718 2794 1.597027 GCACACACAGCCGTTACCT 60.597 57.895 0.00 0.00 0.00 3.08
1794 2875 6.916440 TCCATTCTCATGTGAAAATGAAGTG 58.084 36.000 13.74 6.25 36.16 3.16
1883 2993 8.640651 TGCATTGTCAAGTGCCAATATAAATAT 58.359 29.630 13.79 0.00 40.56 1.28
1951 3062 7.049754 GTCCCCATGAAATCATTTTAAAGCAT 58.950 34.615 0.00 0.00 33.61 3.79
1952 3063 6.213195 AGTCCCCATGAAATCATTTTAAAGCA 59.787 34.615 0.00 0.00 33.61 3.91
1970 3081 2.668144 AATTTTCGTTGGAGTCCCCA 57.332 45.000 6.74 0.00 44.93 4.96
2023 3134 2.454055 GCACTTTCAAGCGGATAATGC 58.546 47.619 0.00 0.00 0.00 3.56
2124 3235 4.004982 GCCATGCCAATCATTGAGTTTTT 58.995 39.130 0.00 0.00 31.79 1.94
2128 3239 1.855295 TGCCATGCCAATCATTGAGT 58.145 45.000 0.00 0.00 31.79 3.41
2149 3260 4.437682 TGAGGGTTTCACTTTCACATCT 57.562 40.909 0.00 0.00 0.00 2.90
2162 3273 4.479158 TGTCCTTAGCATTTTGAGGGTTT 58.521 39.130 0.00 0.00 0.00 3.27
2229 3340 9.911788 ACTTAATGTGATCTTGGATCACTAAAT 57.088 29.630 28.84 17.90 46.25 1.40
2369 3480 3.644966 TGGCTTAGGGTTTAGGTCATG 57.355 47.619 0.00 0.00 0.00 3.07
2468 3579 3.764218 GAGATCCCTATCGGTAGAACCA 58.236 50.000 3.68 0.00 38.47 3.67


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

AutoCloner maintained by Alex Coulton.