Multiple sequence alignment - TraesCS6B01G264200

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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 TraesCS6B01G264200 chr6B 100.000 3308 0 0 1 3308 475729869 475733176 0.000000e+00 6109
1 TraesCS6B01G264200 chr6D 92.257 2557 120 22 819 3306 308590485 308593032 0.000000e+00 3554
2 TraesCS6B01G264200 chr6D 95.157 351 16 1 94 443 308589532 308589882 1.340000e-153 553
3 TraesCS6B01G264200 chr6D 93.093 333 13 4 444 772 308590047 308590373 2.310000e-131 479
4 TraesCS6B01G264200 chr6A 93.364 1763 75 17 829 2551 445304234 445305994 0.000000e+00 2569
5 TraesCS6B01G264200 chr6A 86.924 673 41 20 132 768 445303493 445304154 0.000000e+00 712


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 TraesCS6B01G264200 chr6B 475729869 475733176 3307 False 6109.000000 6109 100.000000 1 3308 1 chr6B.!!$F1 3307
1 TraesCS6B01G264200 chr6D 308589532 308593032 3500 False 1528.666667 3554 93.502333 94 3306 3 chr6D.!!$F1 3212
2 TraesCS6B01G264200 chr6A 445303493 445305994 2501 False 1640.500000 2569 90.144000 132 2551 2 chr6A.!!$F1 2419

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
25 26 0.033601 ATTTGTATGCGGGGAAGGCA 60.034 50.0 0.00 0.0 45.71 4.75 F
36 37 0.249868 GGGAAGGCAACCAAACAAGC 60.250 55.0 2.72 0.0 37.17 4.01 F
58 59 0.261696 AAAACTGTTCACCAGGGCCT 59.738 50.0 0.00 0.0 46.06 5.19 F
88 89 0.317770 AATGCGAGCAACCAAACGTG 60.318 50.0 0.57 0.0 0.00 4.49 F
1032 1314 0.469331 TCCTGTCCCACGTTGTCTCT 60.469 55.0 0.00 0.0 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 1918 1.144936 GATGGAGCCGAAGAGGTGG 59.855 63.158 0.00 0.00 43.70 4.61 R
2070 2386 3.621394 GACATCTTCCTCGCGCGC 61.621 66.667 27.95 23.91 0.00 6.86 R
2187 2503 1.303317 GACGACCCAAACATGCCCT 60.303 57.895 0.00 0.00 0.00 5.19 R
2212 2528 1.868251 CGACTAGAACGCCGCTGAC 60.868 63.158 0.00 0.00 0.00 3.51 R
2672 3036 0.250901 CTCCAAACAGGTGGTGGGAG 60.251 60.000 3.94 3.94 42.22 4.30 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 3.576078 ATCAAGATTTGTATGCGGGGA 57.424 42.857 0.00 0.00 0.00 4.81
21 22 3.358111 TCAAGATTTGTATGCGGGGAA 57.642 42.857 0.00 0.00 0.00 3.97
22 23 3.278574 TCAAGATTTGTATGCGGGGAAG 58.721 45.455 0.00 0.00 0.00 3.46
23 24 2.348411 AGATTTGTATGCGGGGAAGG 57.652 50.000 0.00 0.00 0.00 3.46
24 25 0.668535 GATTTGTATGCGGGGAAGGC 59.331 55.000 0.00 0.00 0.00 4.35
25 26 0.033601 ATTTGTATGCGGGGAAGGCA 60.034 50.000 0.00 0.00 45.71 4.75
26 27 0.251386 TTTGTATGCGGGGAAGGCAA 60.251 50.000 0.00 0.00 44.66 4.52
27 28 0.963355 TTGTATGCGGGGAAGGCAAC 60.963 55.000 0.00 0.00 44.66 4.17
28 29 2.119029 GTATGCGGGGAAGGCAACC 61.119 63.158 0.00 0.00 44.66 3.77
29 30 2.607568 TATGCGGGGAAGGCAACCA 61.608 57.895 2.72 0.00 44.66 3.67
30 31 2.143575 TATGCGGGGAAGGCAACCAA 62.144 55.000 2.72 0.00 44.66 3.67
31 32 2.915137 GCGGGGAAGGCAACCAAA 60.915 61.111 2.72 0.00 37.17 3.28
32 33 3.047735 CGGGGAAGGCAACCAAAC 58.952 61.111 2.72 0.00 37.17 2.93
33 34 1.830408 CGGGGAAGGCAACCAAACA 60.830 57.895 2.72 0.00 37.17 2.83
34 35 1.395826 CGGGGAAGGCAACCAAACAA 61.396 55.000 2.72 0.00 37.17 2.83
35 36 0.392706 GGGGAAGGCAACCAAACAAG 59.607 55.000 2.72 0.00 37.17 3.16
36 37 0.249868 GGGAAGGCAACCAAACAAGC 60.250 55.000 2.72 0.00 37.17 4.01
37 38 0.752658 GGAAGGCAACCAAACAAGCT 59.247 50.000 0.00 0.00 37.17 3.74
38 39 1.538849 GGAAGGCAACCAAACAAGCTG 60.539 52.381 0.00 0.00 37.17 4.24
39 40 1.408702 GAAGGCAACCAAACAAGCTGA 59.591 47.619 0.00 0.00 37.17 4.26
40 41 1.484038 AGGCAACCAAACAAGCTGAA 58.516 45.000 0.00 0.00 37.17 3.02
41 42 1.830477 AGGCAACCAAACAAGCTGAAA 59.170 42.857 0.00 0.00 37.17 2.69
42 43 2.235898 AGGCAACCAAACAAGCTGAAAA 59.764 40.909 0.00 0.00 37.17 2.29
43 44 2.351418 GGCAACCAAACAAGCTGAAAAC 59.649 45.455 0.00 0.00 0.00 2.43
44 45 3.261580 GCAACCAAACAAGCTGAAAACT 58.738 40.909 0.00 0.00 0.00 2.66
45 46 3.062504 GCAACCAAACAAGCTGAAAACTG 59.937 43.478 0.00 0.00 0.00 3.16
46 47 4.244862 CAACCAAACAAGCTGAAAACTGT 58.755 39.130 0.00 0.00 0.00 3.55
47 48 4.535526 ACCAAACAAGCTGAAAACTGTT 57.464 36.364 0.00 0.00 0.00 3.16
48 49 4.494484 ACCAAACAAGCTGAAAACTGTTC 58.506 39.130 0.00 0.00 0.00 3.18
49 50 4.021544 ACCAAACAAGCTGAAAACTGTTCA 60.022 37.500 0.00 0.00 0.00 3.18
50 51 4.327087 CCAAACAAGCTGAAAACTGTTCAC 59.673 41.667 0.00 0.00 0.00 3.18
51 52 3.782889 ACAAGCTGAAAACTGTTCACC 57.217 42.857 0.00 0.00 0.00 4.02
52 53 3.088532 ACAAGCTGAAAACTGTTCACCA 58.911 40.909 0.00 0.00 0.00 4.17
54 55 2.301346 AGCTGAAAACTGTTCACCAGG 58.699 47.619 14.31 0.00 46.06 4.45
55 56 1.338020 GCTGAAAACTGTTCACCAGGG 59.662 52.381 14.31 0.00 46.06 4.45
56 57 1.338020 CTGAAAACTGTTCACCAGGGC 59.662 52.381 0.00 0.00 46.06 5.19
57 58 0.673985 GAAAACTGTTCACCAGGGCC 59.326 55.000 0.00 0.00 46.06 5.80
58 59 0.261696 AAAACTGTTCACCAGGGCCT 59.738 50.000 0.00 0.00 46.06 5.19
59 60 0.468029 AAACTGTTCACCAGGGCCTG 60.468 55.000 27.04 27.04 46.06 4.85
60 61 1.352622 AACTGTTCACCAGGGCCTGA 61.353 55.000 34.84 12.92 46.06 3.86
61 62 1.302832 CTGTTCACCAGGGCCTGAC 60.303 63.158 34.84 23.70 37.54 3.51
62 63 2.034221 GTTCACCAGGGCCTGACC 59.966 66.667 34.84 12.93 32.44 4.02
63 64 3.636231 TTCACCAGGGCCTGACCG 61.636 66.667 34.84 20.15 40.62 4.79
72 73 2.203209 GCCTGACCGGGCCTAATG 60.203 66.667 3.83 0.00 45.92 1.90
73 74 2.203209 CCTGACCGGGCCTAATGC 60.203 66.667 3.83 0.00 40.16 3.56
74 75 2.588877 CTGACCGGGCCTAATGCG 60.589 66.667 3.83 0.00 42.61 4.73
75 76 3.078196 TGACCGGGCCTAATGCGA 61.078 61.111 3.83 0.00 42.61 5.10
76 77 2.280186 GACCGGGCCTAATGCGAG 60.280 66.667 6.32 0.00 42.61 5.03
77 78 4.547367 ACCGGGCCTAATGCGAGC 62.547 66.667 6.32 0.00 42.61 5.03
78 79 4.545706 CCGGGCCTAATGCGAGCA 62.546 66.667 0.84 0.00 42.61 4.26
79 80 2.513666 CGGGCCTAATGCGAGCAA 60.514 61.111 0.84 0.00 42.61 3.91
80 81 2.823829 CGGGCCTAATGCGAGCAAC 61.824 63.158 0.84 0.00 42.61 4.17
81 82 2.481471 GGGCCTAATGCGAGCAACC 61.481 63.158 0.84 0.00 42.61 3.77
82 83 1.748879 GGCCTAATGCGAGCAACCA 60.749 57.895 0.57 0.00 42.61 3.67
83 84 1.312371 GGCCTAATGCGAGCAACCAA 61.312 55.000 0.57 0.00 42.61 3.67
84 85 0.525761 GCCTAATGCGAGCAACCAAA 59.474 50.000 0.57 0.00 0.00 3.28
85 86 1.732405 GCCTAATGCGAGCAACCAAAC 60.732 52.381 0.57 0.00 0.00 2.93
86 87 1.465689 CCTAATGCGAGCAACCAAACG 60.466 52.381 0.57 0.00 0.00 3.60
87 88 1.196808 CTAATGCGAGCAACCAAACGT 59.803 47.619 0.57 0.00 0.00 3.99
88 89 0.317770 AATGCGAGCAACCAAACGTG 60.318 50.000 0.57 0.00 0.00 4.49
104 105 1.883021 GTGGCCTTGATTTCCACCG 59.117 57.895 3.32 0.00 43.27 4.94
105 106 0.893727 GTGGCCTTGATTTCCACCGT 60.894 55.000 3.32 0.00 43.27 4.83
121 122 4.276431 TCCACCGTATTTTGGTTTCTTGTC 59.724 41.667 0.00 0.00 37.72 3.18
127 129 6.128499 CCGTATTTTGGTTTCTTGTCGTGATA 60.128 38.462 0.00 0.00 0.00 2.15
364 366 4.367023 TGTTCGAAGACCGCGGGG 62.367 66.667 31.76 18.33 34.32 5.73
468 635 6.103997 GGTGTATTCGTACTTCAGATTTGGA 58.896 40.000 0.00 0.00 0.00 3.53
542 710 8.564574 CCGTGGCAAATGTTAATATACTGTATT 58.435 33.333 5.52 0.00 0.00 1.89
543 711 9.381027 CGTGGCAAATGTTAATATACTGTATTG 57.619 33.333 5.52 0.00 0.00 1.90
554 722 0.535335 ACTGTATTGACGACGGCCAT 59.465 50.000 2.24 0.00 0.00 4.40
555 723 0.930310 CTGTATTGACGACGGCCATG 59.070 55.000 2.24 0.00 0.00 3.66
627 827 1.615392 AGCAGGACAAATTGAAGTGGC 59.385 47.619 0.00 0.00 0.00 5.01
628 828 1.340889 GCAGGACAAATTGAAGTGGCA 59.659 47.619 0.00 0.00 0.00 4.92
706 909 2.196749 GTGCTCGATACATGACACCTG 58.803 52.381 0.00 0.00 0.00 4.00
707 910 2.099405 TGCTCGATACATGACACCTGA 58.901 47.619 0.00 0.00 0.00 3.86
708 911 2.099756 TGCTCGATACATGACACCTGAG 59.900 50.000 0.00 0.00 0.00 3.35
709 912 2.736978 CTCGATACATGACACCTGAGC 58.263 52.381 0.00 0.00 0.00 4.26
818 1063 3.535280 TGTTACTCCGCATGCAATAGA 57.465 42.857 19.57 7.49 0.00 1.98
824 1069 4.060900 ACTCCGCATGCAATAGAGTAATG 58.939 43.478 21.40 1.71 36.08 1.90
825 1070 4.202253 ACTCCGCATGCAATAGAGTAATGA 60.202 41.667 21.40 0.00 36.08 2.57
826 1071 4.309933 TCCGCATGCAATAGAGTAATGAG 58.690 43.478 19.57 0.00 0.00 2.90
827 1072 3.120408 CCGCATGCAATAGAGTAATGAGC 60.120 47.826 19.57 0.00 0.00 4.26
902 1184 2.819595 GCACATCGCACATCCCGT 60.820 61.111 0.00 0.00 41.79 5.28
906 1188 1.141665 CATCGCACATCCCGTCTGA 59.858 57.895 0.00 0.00 0.00 3.27
907 1189 1.141881 ATCGCACATCCCGTCTGAC 59.858 57.895 0.00 0.00 0.00 3.51
912 1194 1.229209 ACATCCCGTCTGACCCACT 60.229 57.895 1.55 0.00 0.00 4.00
930 1212 4.351111 CCCACTTATAAATAGCCCTCACCT 59.649 45.833 0.00 0.00 0.00 4.00
963 1245 4.637489 CGCCTCATCCCGCTCTCG 62.637 72.222 0.00 0.00 0.00 4.04
1014 1296 1.647629 CAGAATGGCTGCGAGCATC 59.352 57.895 9.78 0.00 44.75 3.91
1032 1314 0.469331 TCCTGTCCCACGTTGTCTCT 60.469 55.000 0.00 0.00 0.00 3.10
1369 1677 2.736682 CGCCGCCGTACCTTTTGAG 61.737 63.158 0.00 0.00 0.00 3.02
1554 1870 2.335712 GGCCCGAAAGAAGCACCAG 61.336 63.158 0.00 0.00 32.68 4.00
1602 1918 3.084579 CAGCAAGACATCGTCCGC 58.915 61.111 0.00 0.00 33.46 5.54
2019 2335 2.029844 GGACGTTGCAGCTCTGTCC 61.030 63.158 9.63 9.63 41.98 4.02
2212 2528 0.037697 TGTTTGGGTCGTCGATGAGG 60.038 55.000 7.79 0.00 0.00 3.86
2282 2598 2.442272 CCGGGACCATCTCCGTCT 60.442 66.667 0.00 0.00 44.32 4.18
2290 2606 0.671251 CCATCTCCGTCTAGAGTGCC 59.329 60.000 0.00 0.00 35.28 5.01
2302 2618 2.257691 AGAGTGCCATGCAGATGATC 57.742 50.000 0.00 0.00 40.08 2.92
2310 2626 3.740115 CCATGCAGATGATCTGTGATCA 58.260 45.455 22.23 12.62 45.94 2.92
2314 2630 4.056050 TGCAGATGATCTGTGATCAATCG 58.944 43.478 22.23 6.69 45.94 3.34
2365 2682 2.585247 CTCGGCGATTTCCCGTCC 60.585 66.667 11.27 0.00 45.71 4.79
2401 2726 1.073897 GGTTGGAGACCTGCTGCTT 59.926 57.895 0.00 0.00 45.55 3.91
2486 2829 6.775629 GGGGTAGCCAAGTTTTATATTCATCA 59.224 38.462 14.06 0.00 0.00 3.07
2515 2864 1.806496 TCTCGGATCATGGGGTTGAT 58.194 50.000 0.00 0.00 39.04 2.57
2547 2896 1.906574 TGACGCCCTTGACCTAAAGAT 59.093 47.619 0.00 0.00 0.00 2.40
2567 2931 5.468592 AGATCGACTATGAGCTTTGCTATG 58.531 41.667 0.00 0.00 39.88 2.23
2575 2939 2.868583 TGAGCTTTGCTATGCGAATCTC 59.131 45.455 13.41 13.41 42.27 2.75
2590 2954 5.062183 TGCGAATCTCGACTTTCAAACATAG 59.938 40.000 0.00 0.00 43.74 2.23
2616 2980 8.507524 AATGACAAGTAAAACTAATAGCCCTC 57.492 34.615 0.00 0.00 0.00 4.30
2642 3006 9.522804 CTGAAGAATCTCACTAACAATAGTACC 57.477 37.037 0.00 0.00 40.44 3.34
2654 3018 1.446907 ATAGTACCGTATCTCCCGCG 58.553 55.000 0.00 0.00 0.00 6.46
2663 3027 1.407656 TATCTCCCGCGATTGCCCTT 61.408 55.000 8.23 0.00 38.08 3.95
2664 3028 2.947938 ATCTCCCGCGATTGCCCTTG 62.948 60.000 8.23 0.00 38.08 3.61
2665 3029 3.976701 CTCCCGCGATTGCCCTTGT 62.977 63.158 8.23 0.00 38.08 3.16
2666 3030 3.508840 CCCGCGATTGCCCTTGTC 61.509 66.667 8.23 0.00 38.08 3.18
2667 3031 2.745884 CCGCGATTGCCCTTGTCA 60.746 61.111 8.23 0.00 38.08 3.58
2672 3036 1.468054 GCGATTGCCCTTGTCAATGTC 60.468 52.381 0.00 0.00 34.59 3.06
2682 3046 0.400213 TGTCAATGTCTCCCACCACC 59.600 55.000 0.00 0.00 0.00 4.61
2694 3058 0.537371 CCACCACCTGTTTGGAGTCC 60.537 60.000 0.73 0.73 39.24 3.85
2705 3071 4.083862 GGAGTCCGAGGCCACCAC 62.084 72.222 5.01 0.00 0.00 4.16
2717 3083 2.158638 AGGCCACCACAAAATTTTGCAT 60.159 40.909 26.94 12.44 41.79 3.96
2743 3109 3.503363 CTGCTGCCAGCGCTAACC 61.503 66.667 10.99 1.23 46.26 2.85
2745 3111 4.785453 GCTGCCAGCGCTAACCCT 62.785 66.667 10.99 0.00 35.36 4.34
2752 3118 2.824489 GCGCTAACCCTTCCCTGC 60.824 66.667 0.00 0.00 0.00 4.85
2754 3120 1.745489 CGCTAACCCTTCCCTGCAC 60.745 63.158 0.00 0.00 0.00 4.57
2761 3127 1.097547 CCCTTCCCTGCACGCAATAG 61.098 60.000 0.00 0.00 0.00 1.73
2774 3140 3.005261 CACGCAATAGCCTCTAGAGTCAT 59.995 47.826 18.42 6.44 37.52 3.06
2801 3167 1.150536 GGAGTCCAGGCACAACCAA 59.849 57.895 3.60 0.00 43.14 3.67
2882 3248 2.047274 CGATGGCGTTGACACCCT 60.047 61.111 0.00 0.00 0.00 4.34
2885 3251 2.748058 GATGGCGTTGACACCCTGGT 62.748 60.000 0.00 0.00 0.00 4.00
2949 3315 2.427506 CTTCTAACACCTCTTGGCACC 58.572 52.381 0.00 0.00 36.63 5.01
2950 3316 0.320374 TCTAACACCTCTTGGCACCG 59.680 55.000 0.00 0.00 36.63 4.94
2981 3347 1.448985 GTGTTTTGCATCGGCCTAGA 58.551 50.000 0.00 0.00 40.13 2.43
3000 3366 4.817318 AGACTCCTTCAGAATCTCCAAC 57.183 45.455 0.00 0.00 0.00 3.77
3056 3422 2.096268 GCTTGCGGCCTTTGAAAAATTC 60.096 45.455 0.00 0.00 34.27 2.17
3058 3424 1.691434 TGCGGCCTTTGAAAAATTCCT 59.309 42.857 0.00 0.00 0.00 3.36
3059 3425 2.288763 TGCGGCCTTTGAAAAATTCCTC 60.289 45.455 0.00 0.00 0.00 3.71
3060 3426 2.288763 GCGGCCTTTGAAAAATTCCTCA 60.289 45.455 0.00 0.00 0.00 3.86
3061 3427 3.617288 GCGGCCTTTGAAAAATTCCTCAT 60.617 43.478 0.00 0.00 0.00 2.90
3111 3477 1.574702 GCCCAAACAGTGACCGCTAC 61.575 60.000 0.00 0.00 0.00 3.58
3124 3490 2.469516 CGCTACCCGGGTGAATTGC 61.470 63.158 36.97 26.61 0.00 3.56
3143 3509 0.673985 CGTGTGTGGAAGAGACTCCA 59.326 55.000 0.00 0.00 43.45 3.86
3151 3517 2.493675 TGGAAGAGACTCCATCAACGAG 59.506 50.000 0.00 0.00 40.71 4.18
3158 3524 2.737252 GACTCCATCAACGAGAACAACC 59.263 50.000 0.00 0.00 0.00 3.77
3165 3531 2.093921 TCAACGAGAACAACCAGTGTCA 60.094 45.455 0.00 0.00 40.60 3.58
3177 3543 1.274167 CCAGTGTCATGCATTTGGCTT 59.726 47.619 0.00 0.00 45.15 4.35
3179 3545 3.056678 CCAGTGTCATGCATTTGGCTTTA 60.057 43.478 0.00 0.00 45.15 1.85
3215 3581 3.058293 GTGTTGAGCAATTTCGTCATCCA 60.058 43.478 0.00 0.00 0.00 3.41
3236 3602 1.134401 CCAGTGCCCACATACACCTAG 60.134 57.143 0.82 0.00 37.51 3.02
3292 3658 2.837498 TCTGGTGCATCACATAATCCG 58.163 47.619 0.00 0.00 35.86 4.18
3306 3672 2.927553 AATCCGCAAGCACTTGAATC 57.072 45.000 14.44 0.00 42.93 2.52
3307 3673 0.729116 ATCCGCAAGCACTTGAATCG 59.271 50.000 14.44 8.02 42.93 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.576078 TCCCCGCATACAAATCTTGAT 57.424 42.857 0.00 0.00 0.00 2.57
1 2 3.278574 CTTCCCCGCATACAAATCTTGA 58.721 45.455 0.00 0.00 0.00 3.02
2 3 2.358898 CCTTCCCCGCATACAAATCTTG 59.641 50.000 0.00 0.00 0.00 3.02
3 4 2.654863 CCTTCCCCGCATACAAATCTT 58.345 47.619 0.00 0.00 0.00 2.40
4 5 1.750682 GCCTTCCCCGCATACAAATCT 60.751 52.381 0.00 0.00 0.00 2.40
5 6 0.668535 GCCTTCCCCGCATACAAATC 59.331 55.000 0.00 0.00 0.00 2.17
6 7 0.033601 TGCCTTCCCCGCATACAAAT 60.034 50.000 0.00 0.00 0.00 2.32
7 8 0.251386 TTGCCTTCCCCGCATACAAA 60.251 50.000 0.00 0.00 35.83 2.83
8 9 0.963355 GTTGCCTTCCCCGCATACAA 60.963 55.000 0.00 0.00 35.83 2.41
9 10 1.377987 GTTGCCTTCCCCGCATACA 60.378 57.895 0.00 0.00 35.83 2.29
10 11 2.119029 GGTTGCCTTCCCCGCATAC 61.119 63.158 0.00 0.00 35.83 2.39
11 12 2.143575 TTGGTTGCCTTCCCCGCATA 62.144 55.000 0.00 0.00 35.83 3.14
12 13 3.521765 TTGGTTGCCTTCCCCGCAT 62.522 57.895 0.00 0.00 35.83 4.73
13 14 3.740495 TTTGGTTGCCTTCCCCGCA 62.740 57.895 0.00 0.00 0.00 5.69
14 15 2.915137 TTTGGTTGCCTTCCCCGC 60.915 61.111 0.00 0.00 0.00 6.13
15 16 1.395826 TTGTTTGGTTGCCTTCCCCG 61.396 55.000 0.00 0.00 0.00 5.73
16 17 0.392706 CTTGTTTGGTTGCCTTCCCC 59.607 55.000 0.00 0.00 0.00 4.81
17 18 0.249868 GCTTGTTTGGTTGCCTTCCC 60.250 55.000 0.00 0.00 0.00 3.97
18 19 0.752658 AGCTTGTTTGGTTGCCTTCC 59.247 50.000 0.00 0.00 0.00 3.46
19 20 1.408702 TCAGCTTGTTTGGTTGCCTTC 59.591 47.619 0.00 0.00 0.00 3.46
20 21 1.484038 TCAGCTTGTTTGGTTGCCTT 58.516 45.000 0.00 0.00 0.00 4.35
21 22 1.484038 TTCAGCTTGTTTGGTTGCCT 58.516 45.000 0.00 0.00 0.00 4.75
22 23 2.307934 TTTCAGCTTGTTTGGTTGCC 57.692 45.000 0.00 0.00 0.00 4.52
23 24 3.062504 CAGTTTTCAGCTTGTTTGGTTGC 59.937 43.478 0.00 0.00 0.00 4.17
24 25 4.244862 ACAGTTTTCAGCTTGTTTGGTTG 58.755 39.130 0.00 0.00 0.00 3.77
25 26 4.535526 ACAGTTTTCAGCTTGTTTGGTT 57.464 36.364 0.00 0.00 0.00 3.67
26 27 4.021544 TGAACAGTTTTCAGCTTGTTTGGT 60.022 37.500 1.01 0.00 0.00 3.67
27 28 4.327087 GTGAACAGTTTTCAGCTTGTTTGG 59.673 41.667 1.01 0.00 0.00 3.28
28 29 4.327087 GGTGAACAGTTTTCAGCTTGTTTG 59.673 41.667 12.78 0.00 41.98 2.93
29 30 4.021544 TGGTGAACAGTTTTCAGCTTGTTT 60.022 37.500 18.96 0.00 44.58 2.83
30 31 3.509575 TGGTGAACAGTTTTCAGCTTGTT 59.490 39.130 18.96 0.00 44.58 2.83
31 32 3.088532 TGGTGAACAGTTTTCAGCTTGT 58.911 40.909 18.96 0.00 44.58 3.16
32 33 3.489738 CCTGGTGAACAGTTTTCAGCTTG 60.490 47.826 18.96 12.67 46.06 4.01
33 34 2.689983 CCTGGTGAACAGTTTTCAGCTT 59.310 45.455 18.96 0.00 46.06 3.74
34 35 2.301346 CCTGGTGAACAGTTTTCAGCT 58.699 47.619 18.96 0.00 46.06 4.24
35 36 1.338020 CCCTGGTGAACAGTTTTCAGC 59.662 52.381 13.09 13.09 46.06 4.26
36 37 1.338020 GCCCTGGTGAACAGTTTTCAG 59.662 52.381 0.00 0.00 46.06 3.02
37 38 1.398692 GCCCTGGTGAACAGTTTTCA 58.601 50.000 0.00 0.00 46.06 2.69
38 39 0.673985 GGCCCTGGTGAACAGTTTTC 59.326 55.000 0.00 0.00 46.06 2.29
39 40 0.261696 AGGCCCTGGTGAACAGTTTT 59.738 50.000 0.00 0.00 46.06 2.43
40 41 0.468029 CAGGCCCTGGTGAACAGTTT 60.468 55.000 1.63 0.00 46.06 2.66
41 42 1.151450 CAGGCCCTGGTGAACAGTT 59.849 57.895 1.63 0.00 46.06 3.16
42 43 1.770110 TCAGGCCCTGGTGAACAGT 60.770 57.895 11.68 0.00 46.06 3.55
44 45 2.829384 GGTCAGGCCCTGGTGAACA 61.829 63.158 11.68 0.00 30.20 3.18
45 46 2.034221 GGTCAGGCCCTGGTGAAC 59.966 66.667 11.68 0.84 31.51 3.18
46 47 3.636231 CGGTCAGGCCCTGGTGAA 61.636 66.667 11.68 0.00 31.51 3.18
56 57 2.203209 GCATTAGGCCCGGTCAGG 60.203 66.667 0.00 0.00 40.63 3.86
57 58 2.588877 CGCATTAGGCCCGGTCAG 60.589 66.667 0.00 0.00 40.31 3.51
58 59 3.078196 TCGCATTAGGCCCGGTCA 61.078 61.111 0.00 0.00 40.31 4.02
59 60 2.280186 CTCGCATTAGGCCCGGTC 60.280 66.667 0.00 0.00 40.31 4.79
60 61 4.547367 GCTCGCATTAGGCCCGGT 62.547 66.667 0.00 0.00 40.31 5.28
61 62 4.545706 TGCTCGCATTAGGCCCGG 62.546 66.667 0.00 0.00 40.31 5.73
62 63 2.513666 TTGCTCGCATTAGGCCCG 60.514 61.111 0.00 0.00 40.31 6.13
63 64 2.481471 GGTTGCTCGCATTAGGCCC 61.481 63.158 0.00 0.00 40.31 5.80
64 65 1.312371 TTGGTTGCTCGCATTAGGCC 61.312 55.000 0.00 0.00 40.31 5.19
65 66 0.525761 TTTGGTTGCTCGCATTAGGC 59.474 50.000 0.00 0.00 39.90 3.93
66 67 1.465689 CGTTTGGTTGCTCGCATTAGG 60.466 52.381 0.00 0.00 0.00 2.69
67 68 1.196808 ACGTTTGGTTGCTCGCATTAG 59.803 47.619 0.00 0.00 0.00 1.73
68 69 1.069568 CACGTTTGGTTGCTCGCATTA 60.070 47.619 0.00 0.00 0.00 1.90
69 70 0.317770 CACGTTTGGTTGCTCGCATT 60.318 50.000 0.00 0.00 0.00 3.56
70 71 1.282570 CACGTTTGGTTGCTCGCAT 59.717 52.632 0.00 0.00 0.00 4.73
71 72 2.712539 CACGTTTGGTTGCTCGCA 59.287 55.556 0.00 0.00 0.00 5.10
72 73 2.051345 CCACGTTTGGTTGCTCGC 60.051 61.111 0.00 0.00 38.23 5.03
73 74 2.051345 GCCACGTTTGGTTGCTCG 60.051 61.111 0.00 0.00 45.98 5.03
74 75 1.734388 AAGGCCACGTTTGGTTGCTC 61.734 55.000 5.01 0.00 45.98 4.26
75 76 1.756561 AAGGCCACGTTTGGTTGCT 60.757 52.632 5.01 0.00 45.98 3.91
76 77 1.591327 CAAGGCCACGTTTGGTTGC 60.591 57.895 5.01 0.00 45.98 4.17
77 78 0.673437 ATCAAGGCCACGTTTGGTTG 59.327 50.000 5.01 0.00 45.98 3.77
78 79 1.408969 AATCAAGGCCACGTTTGGTT 58.591 45.000 5.01 0.00 45.98 3.67
79 80 1.339929 GAAATCAAGGCCACGTTTGGT 59.660 47.619 5.01 0.00 45.98 3.67
81 82 1.339610 TGGAAATCAAGGCCACGTTTG 59.660 47.619 5.01 0.00 0.00 2.93
82 83 1.339929 GTGGAAATCAAGGCCACGTTT 59.660 47.619 5.01 0.00 42.20 3.60
83 84 0.958822 GTGGAAATCAAGGCCACGTT 59.041 50.000 5.01 0.00 42.20 3.99
84 85 2.641197 GTGGAAATCAAGGCCACGT 58.359 52.632 5.01 0.00 42.20 4.49
87 88 0.693622 TACGGTGGAAATCAAGGCCA 59.306 50.000 5.01 0.00 0.00 5.36
88 89 2.052782 ATACGGTGGAAATCAAGGCC 57.947 50.000 0.00 0.00 0.00 5.19
89 90 4.173256 CAAAATACGGTGGAAATCAAGGC 58.827 43.478 0.00 0.00 0.00 4.35
90 91 4.219725 ACCAAAATACGGTGGAAATCAAGG 59.780 41.667 0.00 0.00 38.36 3.61
91 92 5.385509 ACCAAAATACGGTGGAAATCAAG 57.614 39.130 0.00 0.00 38.36 3.02
92 93 5.793030 AACCAAAATACGGTGGAAATCAA 57.207 34.783 0.00 0.00 38.36 2.57
95 96 6.183360 ACAAGAAACCAAAATACGGTGGAAAT 60.183 34.615 0.00 0.00 38.36 2.17
104 105 7.908601 GGATATCACGACAAGAAACCAAAATAC 59.091 37.037 4.83 0.00 0.00 1.89
105 106 7.066525 GGGATATCACGACAAGAAACCAAAATA 59.933 37.037 4.83 0.00 0.00 1.40
121 122 1.037493 TGTTCCGAGGGGATATCACG 58.963 55.000 4.83 4.72 43.41 4.35
127 129 1.995626 CCCTGTGTTCCGAGGGGAT 60.996 63.158 0.00 0.00 44.88 3.85
231 233 0.249031 TATCGCTACGAGACGACGGA 60.249 55.000 0.00 0.00 41.76 4.69
311 313 2.031012 CCGTGCAGGAACAGCTGA 59.969 61.111 23.35 0.00 43.00 4.26
364 366 2.125793 GTCCCGGTAGACGCCAAC 60.126 66.667 0.00 0.00 42.52 3.77
468 635 1.203052 CCCCGTACGACACATTACAGT 59.797 52.381 18.76 0.00 0.00 3.55
542 710 2.356913 CACACATGGCCGTCGTCA 60.357 61.111 0.00 0.00 0.00 4.35
543 711 2.357034 ACACACATGGCCGTCGTC 60.357 61.111 0.00 0.00 0.00 4.20
554 722 0.108424 GCTTGCCCAAAACACACACA 60.108 50.000 0.00 0.00 0.00 3.72
555 723 0.809636 GGCTTGCCCAAAACACACAC 60.810 55.000 0.00 0.00 0.00 3.82
612 812 5.390991 GCTACTAGTGCCACTTCAATTTGTC 60.391 44.000 1.02 0.00 0.00 3.18
627 827 2.568696 ATCAGTGCGTGCTACTAGTG 57.431 50.000 5.39 0.00 0.00 2.74
628 828 2.417379 CCAATCAGTGCGTGCTACTAGT 60.417 50.000 0.00 0.00 0.00 2.57
676 876 3.064207 TGTATCGAGCACCAAACAACTC 58.936 45.455 0.00 0.00 0.00 3.01
811 1056 6.092670 TGTTTCACTGCTCATTACTCTATTGC 59.907 38.462 0.00 0.00 0.00 3.56
818 1063 3.067106 CCGTGTTTCACTGCTCATTACT 58.933 45.455 0.00 0.00 31.34 2.24
824 1069 2.143122 TCAATCCGTGTTTCACTGCTC 58.857 47.619 0.00 0.00 31.34 4.26
825 1070 2.254546 TCAATCCGTGTTTCACTGCT 57.745 45.000 0.00 0.00 31.34 4.24
826 1071 3.189287 AGAATCAATCCGTGTTTCACTGC 59.811 43.478 0.00 0.00 38.09 4.40
827 1072 4.214119 ACAGAATCAATCCGTGTTTCACTG 59.786 41.667 0.00 0.00 38.09 3.66
902 1184 5.224441 AGGGCTATTTATAAGTGGGTCAGA 58.776 41.667 0.00 0.00 0.00 3.27
906 1188 4.104261 GGTGAGGGCTATTTATAAGTGGGT 59.896 45.833 0.00 0.00 0.00 4.51
907 1189 4.351111 AGGTGAGGGCTATTTATAAGTGGG 59.649 45.833 0.00 0.00 0.00 4.61
912 1194 5.473273 TGGAGAGGTGAGGGCTATTTATAA 58.527 41.667 0.00 0.00 0.00 0.98
930 1212 3.181443 TGAGGCGATACTAGTCATGGAGA 60.181 47.826 0.00 0.00 0.00 3.71
963 1245 4.734917 AGTGCAGAGAACGTGTATTACTC 58.265 43.478 0.00 0.00 0.00 2.59
1014 1296 4.790436 GTCAGAGACAACGTGGGACAGG 62.790 59.091 0.00 0.00 40.26 4.00
1131 1413 2.970324 GGTGCAGCGTCCACGAAA 60.970 61.111 0.00 0.00 43.02 3.46
1369 1677 7.478520 TTTCAGAACAAAGTAGTAGCAAGAC 57.521 36.000 0.00 0.00 0.00 3.01
1404 1712 1.559682 GGGTTGGTATGGCTGAGAGAA 59.440 52.381 0.00 0.00 0.00 2.87
1602 1918 1.144936 GATGGAGCCGAAGAGGTGG 59.855 63.158 0.00 0.00 43.70 4.61
2067 2383 4.880537 ATCTTCCTCGCGCGCCTG 62.881 66.667 27.95 18.12 0.00 4.85
2070 2386 3.621394 GACATCTTCCTCGCGCGC 61.621 66.667 27.95 23.91 0.00 6.86
2187 2503 1.303317 GACGACCCAAACATGCCCT 60.303 57.895 0.00 0.00 0.00 5.19
2212 2528 1.868251 CGACTAGAACGCCGCTGAC 60.868 63.158 0.00 0.00 0.00 3.51
2222 2538 1.085091 GCTGACGACTCCGACTAGAA 58.915 55.000 0.00 0.00 39.50 2.10
2257 2573 2.607750 ATGGTCCCGGAGCACAGT 60.608 61.111 21.45 3.33 42.86 3.55
2282 2598 2.970640 AGATCATCTGCATGGCACTCTA 59.029 45.455 0.00 0.00 33.79 2.43
2302 2618 3.925299 CAGGCTATAGCGATTGATCACAG 59.075 47.826 18.30 0.00 43.26 3.66
2310 2626 2.934364 GCATCTGCAGGCTATAGCGATT 60.934 50.000 18.30 4.04 40.78 3.34
2314 2630 0.320247 ACGCATCTGCAGGCTATAGC 60.320 55.000 16.78 16.78 42.21 2.97
2409 2734 2.693267 AAGCTGGACCGATCCTTAAC 57.307 50.000 0.00 0.00 46.43 2.01
2410 2735 3.713826 AAAAGCTGGACCGATCCTTAA 57.286 42.857 0.00 0.00 46.43 1.85
2411 2736 3.713826 AAAAAGCTGGACCGATCCTTA 57.286 42.857 0.00 0.00 46.43 2.69
2460 2803 6.335781 TGAATATAAAACTTGGCTACCCCT 57.664 37.500 0.00 0.00 0.00 4.79
2486 2829 5.365025 CCCCATGATCCGAGATGTATTCTAT 59.635 44.000 0.00 0.00 33.74 1.98
2515 2864 0.463654 GGGCGTCATATGTGGCTTGA 60.464 55.000 18.38 0.00 0.00 3.02
2525 2874 3.101437 TCTTTAGGTCAAGGGCGTCATA 58.899 45.455 0.00 0.00 0.00 2.15
2547 2896 3.384668 GCATAGCAAAGCTCATAGTCGA 58.615 45.455 0.00 0.00 40.44 4.20
2561 2925 2.871182 AAGTCGAGATTCGCATAGCA 57.129 45.000 0.00 0.00 40.21 3.49
2567 2931 3.788434 TGTTTGAAAGTCGAGATTCGC 57.212 42.857 5.84 1.08 40.21 4.70
2575 2939 7.576236 ACTTGTCATTCTATGTTTGAAAGTCG 58.424 34.615 0.00 0.00 0.00 4.18
2590 2954 8.507524 AGGGCTATTAGTTTTACTTGTCATTC 57.492 34.615 0.00 0.00 0.00 2.67
2608 2972 4.555689 AGTGAGATTCTTCAGAGGGCTAT 58.444 43.478 0.00 0.00 0.00 2.97
2613 2977 8.474025 ACTATTGTTAGTGAGATTCTTCAGAGG 58.526 37.037 0.00 0.00 37.28 3.69
2616 2980 9.522804 GGTACTATTGTTAGTGAGATTCTTCAG 57.477 37.037 0.00 0.00 39.08 3.02
2642 3006 2.022129 GGCAATCGCGGGAGATACG 61.022 63.158 6.13 0.00 39.92 3.06
2654 3018 2.424956 GGAGACATTGACAAGGGCAATC 59.575 50.000 8.64 0.00 33.93 2.67
2663 3027 0.400213 GGTGGTGGGAGACATTGACA 59.600 55.000 0.00 0.00 0.00 3.58
2664 3028 0.693049 AGGTGGTGGGAGACATTGAC 59.307 55.000 0.00 0.00 0.00 3.18
2665 3029 0.692476 CAGGTGGTGGGAGACATTGA 59.308 55.000 0.00 0.00 0.00 2.57
2666 3030 0.401738 ACAGGTGGTGGGAGACATTG 59.598 55.000 0.00 0.00 0.00 2.82
2667 3031 1.149101 AACAGGTGGTGGGAGACATT 58.851 50.000 0.00 0.00 0.00 2.71
2672 3036 0.250901 CTCCAAACAGGTGGTGGGAG 60.251 60.000 3.94 3.94 42.22 4.30
2682 3046 1.376037 GGCCTCGGACTCCAAACAG 60.376 63.158 0.00 0.00 0.00 3.16
2694 3058 2.134346 CAAAATTTTGTGGTGGCCTCG 58.866 47.619 20.57 0.00 33.59 4.63
2728 3094 4.785453 AGGGTTAGCGCTGGCAGC 62.785 66.667 29.22 29.22 43.41 5.25
2735 3101 2.824489 GCAGGGAAGGGTTAGCGC 60.824 66.667 0.00 0.00 0.00 5.92
2743 3109 1.718757 GCTATTGCGTGCAGGGAAGG 61.719 60.000 18.14 13.80 0.00 3.46
2745 3111 1.748879 GGCTATTGCGTGCAGGGAA 60.749 57.895 15.75 15.75 40.82 3.97
2752 3118 2.359214 TGACTCTAGAGGCTATTGCGTG 59.641 50.000 25.95 0.00 40.82 5.34
2754 3120 3.669290 CGATGACTCTAGAGGCTATTGCG 60.669 52.174 25.95 16.84 40.82 4.85
2761 3127 0.955905 GACCCGATGACTCTAGAGGC 59.044 60.000 23.50 21.63 36.85 4.70
2774 3140 1.609501 CCTGGACTCCAAGACCCGA 60.610 63.158 0.00 0.00 30.80 5.14
2801 3167 5.104485 GGGAATTATATGGGAAGCTCGGTAT 60.104 44.000 0.00 0.00 0.00 2.73
2851 3217 4.195334 ATCGAGGGGTGGCATGGC 62.195 66.667 13.29 13.29 0.00 4.40
2920 3286 2.237392 GAGGTGTTAGAAGGCAGATGGT 59.763 50.000 0.00 0.00 0.00 3.55
2928 3294 2.427506 GTGCCAAGAGGTGTTAGAAGG 58.572 52.381 0.00 0.00 37.19 3.46
2949 3315 2.058829 AAAACACCGGAACTGCAGCG 62.059 55.000 15.27 9.57 0.00 5.18
2950 3316 0.594796 CAAAACACCGGAACTGCAGC 60.595 55.000 15.27 0.00 0.00 5.25
2961 3327 0.451783 CTAGGCCGATGCAAAACACC 59.548 55.000 0.00 0.00 40.13 4.16
2981 3347 4.424842 AGAGTTGGAGATTCTGAAGGAGT 58.575 43.478 0.00 0.00 0.00 3.85
3012 3378 7.318141 AGCCACTCATATTTTCATTGACAAAG 58.682 34.615 0.00 0.00 0.00 2.77
3020 3386 3.067180 CCGCAAGCCACTCATATTTTCAT 59.933 43.478 0.00 0.00 0.00 2.57
3056 3422 3.117360 AGGGGGAAAGCTATTCAATGAGG 60.117 47.826 9.75 0.00 0.00 3.86
3058 3424 3.433598 CGAGGGGGAAAGCTATTCAATGA 60.434 47.826 9.75 0.00 0.00 2.57
3059 3425 2.880890 CGAGGGGGAAAGCTATTCAATG 59.119 50.000 9.75 0.00 0.00 2.82
3060 3426 2.777692 TCGAGGGGGAAAGCTATTCAAT 59.222 45.455 9.75 0.00 0.00 2.57
3061 3427 2.193127 TCGAGGGGGAAAGCTATTCAA 58.807 47.619 9.75 0.00 0.00 2.69
3111 3477 2.671619 ACACGCAATTCACCCGGG 60.672 61.111 22.25 22.25 0.00 5.73
3115 3481 0.665835 TTCCACACACGCAATTCACC 59.334 50.000 0.00 0.00 0.00 4.02
3116 3482 1.601903 TCTTCCACACACGCAATTCAC 59.398 47.619 0.00 0.00 0.00 3.18
3124 3490 0.673985 TGGAGTCTCTTCCACACACG 59.326 55.000 0.00 0.00 42.24 4.49
3143 3509 3.131396 GACACTGGTTGTTCTCGTTGAT 58.869 45.455 0.00 0.00 39.17 2.57
3151 3517 3.648339 AATGCATGACACTGGTTGTTC 57.352 42.857 0.00 0.00 39.17 3.18
3158 3524 2.736144 AAGCCAAATGCATGACACTG 57.264 45.000 0.00 0.00 44.83 3.66
3165 3531 4.325119 TGCAACAATAAAGCCAAATGCAT 58.675 34.783 0.00 0.00 44.83 3.96
3177 3543 6.155827 GCTCAACACCTTATTGCAACAATAA 58.844 36.000 0.00 11.20 0.00 1.40
3179 3545 4.039004 TGCTCAACACCTTATTGCAACAAT 59.961 37.500 0.00 0.00 0.00 2.71
3215 3581 1.133809 AGGTGTATGTGGGCACTGGT 61.134 55.000 0.00 0.00 36.03 4.00


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

AutoCloner maintained by Alex Coulton.