Multiple sequence alignment - TraesCS2A01G014200

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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 TraesCS2A01G014200 chr2A 100.000 3908 0 0 1 3908 5675113 5679020 0.000000e+00 7217.0
1 TraesCS2A01G014200 chr2A 98.485 2839 36 5 1073 3908 62721903 62724737 0.000000e+00 4998.0
2 TraesCS2A01G014200 chr2A 86.687 646 24 23 410 1037 62721034 62721635 0.000000e+00 660.0
3 TraesCS2A01G014200 chr2A 97.414 232 2 2 137 364 62720122 62720353 3.660000e-105 392.0
4 TraesCS2A01G014200 chr2A 95.556 45 2 0 91 135 699427617 699427573 5.420000e-09 73.1
5 TraesCS2A01G014200 chr2A 92.308 52 0 1 3392 3443 12835691 12835738 1.950000e-08 71.3
6 TraesCS2A01G014200 chr2A 89.474 57 3 3 91 146 32141366 32141312 7.010000e-08 69.4
7 TraesCS2A01G014200 chr2A 92.000 50 3 1 703 751 71434040 71434089 7.010000e-08 69.4
8 TraesCS2A01G014200 chr2D 94.523 2976 113 24 968 3908 7167566 7170526 0.000000e+00 4547.0
9 TraesCS2A01G014200 chr2B 94.398 2249 92 13 843 3078 1831719 1833946 0.000000e+00 3424.0
10 TraesCS2A01G014200 chr2B 84.773 440 45 14 3216 3640 1834319 1834751 4.670000e-114 422.0
11 TraesCS2A01G014200 chr2B 96.104 77 1 1 15 91 583775806 583775880 1.470000e-24 124.0
12 TraesCS2A01G014200 chrUn 100.000 406 0 0 2575 2980 478150119 478150524 0.000000e+00 750.0
13 TraesCS2A01G014200 chr7A 78.205 546 73 33 234 758 432966602 432966082 1.360000e-79 307.0
14 TraesCS2A01G014200 chr3B 95.714 140 5 1 234 372 603492119 603492258 1.410000e-54 224.0
15 TraesCS2A01G014200 chr5B 88.827 179 11 6 234 408 606282304 606282477 1.100000e-50 211.0
16 TraesCS2A01G014200 chr1B 88.333 180 12 6 234 408 525829094 525829269 1.420000e-49 207.0
17 TraesCS2A01G014200 chr1B 91.837 147 8 2 234 376 29485310 29485164 6.620000e-48 202.0
18 TraesCS2A01G014200 chr1B 95.652 46 0 2 91 136 520262137 520262180 5.420000e-09 73.1
19 TraesCS2A01G014200 chr7D 92.414 145 7 3 234 374 458352615 458352471 1.840000e-48 204.0
20 TraesCS2A01G014200 chr4D 91.724 145 8 3 234 374 9595015 9595159 8.560000e-47 198.0
21 TraesCS2A01G014200 chr5A 85.714 182 14 8 234 408 401149460 401149284 8.630000e-42 182.0
22 TraesCS2A01G014200 chr5A 97.674 43 1 0 91 133 492468810 492468768 1.510000e-09 75.0
23 TraesCS2A01G014200 chr6B 97.260 73 2 0 19 91 502718410 502718482 1.470000e-24 124.0
24 TraesCS2A01G014200 chr6B 93.750 48 1 2 91 137 696412461 696412507 1.950000e-08 71.3
25 TraesCS2A01G014200 chr4A 97.260 73 2 0 19 91 7590726 7590798 1.470000e-24 124.0
26 TraesCS2A01G014200 chr4A 92.593 54 2 2 91 143 492941871 492941819 4.190000e-10 76.8
27 TraesCS2A01G014200 chr4A 95.556 45 2 0 91 135 446608050 446608006 5.420000e-09 73.1
28 TraesCS2A01G014200 chr4A 93.878 49 2 1 91 139 494007009 494006962 5.420000e-09 73.1
29 TraesCS2A01G014200 chr1A 97.260 73 1 1 20 91 203809009 203808937 5.300000e-24 122.0
30 TraesCS2A01G014200 chr7B 97.222 72 1 1 21 91 52907242 52907171 1.910000e-23 121.0
31 TraesCS2A01G014200 chr7B 92.683 82 3 2 11 91 703957282 703957203 8.870000e-22 115.0
32 TraesCS2A01G014200 chr4B 95.946 74 3 0 18 91 193970687 193970614 1.910000e-23 121.0
33 TraesCS2A01G014200 chr4B 94.805 77 3 1 15 91 396686411 396686336 6.860000e-23 119.0
34 TraesCS2A01G014200 chr6A 94.737 76 3 1 16 91 545147127 545147053 2.470000e-22 117.0
35 TraesCS2A01G014200 chr3A 89.655 58 1 5 91 148 594034478 594034426 7.010000e-08 69.4


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 TraesCS2A01G014200 chr2A 5675113 5679020 3907 False 7217.000000 7217 100.000000 1 3908 1 chr2A.!!$F1 3907
1 TraesCS2A01G014200 chr2A 62720122 62724737 4615 False 2016.666667 4998 94.195333 137 3908 3 chr2A.!!$F4 3771
2 TraesCS2A01G014200 chr2D 7167566 7170526 2960 False 4547.000000 4547 94.523000 968 3908 1 chr2D.!!$F1 2940
3 TraesCS2A01G014200 chr2B 1831719 1834751 3032 False 1923.000000 3424 89.585500 843 3640 2 chr2B.!!$F2 2797
4 TraesCS2A01G014200 chr7A 432966082 432966602 520 True 307.000000 307 78.205000 234 758 1 chr7A.!!$R1 524

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
70 71 0.181114 AAGCTGCTGTCTTGTGACCA 59.819 50.000 1.35 0.0 42.28 4.02 F
899 1587 0.250513 CCCGTCTCCTTCCTTCCTTG 59.749 60.000 0.00 0.0 0.00 3.61 F
966 1668 1.230281 ACATCCCCCACACCCAGAT 60.230 57.895 0.00 0.0 0.00 2.90 F
1245 2196 2.683859 CGTGGAGTCGCAGTACCGA 61.684 63.158 0.00 0.0 34.40 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1230 2181 1.428620 GACTCGGTACTGCGACTCC 59.571 63.158 0.00 0.0 0.00 3.85 R
2320 3274 0.107945 AGCCGGAATGAGAACTCTGC 60.108 55.000 5.05 0.0 0.00 4.26 R
2573 3527 1.533625 TGTAACATTGCTCAGTGGCC 58.466 50.000 0.00 0.0 0.00 5.36 R
3628 4845 5.358725 ACCGTGTTTCCAGAAATAAAGTGTT 59.641 36.000 0.00 0.0 32.36 3.32 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
22 23 4.487714 TGCCCCTCTCTAGTTAATTGTG 57.512 45.455 0.00 0.00 0.00 3.33
23 24 3.844211 TGCCCCTCTCTAGTTAATTGTGT 59.156 43.478 0.00 0.00 0.00 3.72
24 25 4.192317 GCCCCTCTCTAGTTAATTGTGTG 58.808 47.826 0.00 0.00 0.00 3.82
25 26 4.192317 CCCCTCTCTAGTTAATTGTGTGC 58.808 47.826 0.00 0.00 0.00 4.57
26 27 3.865745 CCCTCTCTAGTTAATTGTGTGCG 59.134 47.826 0.00 0.00 0.00 5.34
27 28 4.381612 CCCTCTCTAGTTAATTGTGTGCGA 60.382 45.833 0.00 0.00 0.00 5.10
28 29 5.168569 CCTCTCTAGTTAATTGTGTGCGAA 58.831 41.667 0.00 0.00 0.00 4.70
29 30 5.289675 CCTCTCTAGTTAATTGTGTGCGAAG 59.710 44.000 0.00 0.00 0.00 3.79
30 31 5.168569 TCTCTAGTTAATTGTGTGCGAAGG 58.831 41.667 0.00 0.00 0.00 3.46
31 32 4.250464 TCTAGTTAATTGTGTGCGAAGGG 58.750 43.478 0.00 0.00 0.00 3.95
32 33 2.159382 AGTTAATTGTGTGCGAAGGGG 58.841 47.619 0.00 0.00 0.00 4.79
33 34 2.156098 GTTAATTGTGTGCGAAGGGGA 58.844 47.619 0.00 0.00 0.00 4.81
34 35 2.107950 TAATTGTGTGCGAAGGGGAG 57.892 50.000 0.00 0.00 0.00 4.30
35 36 1.244019 AATTGTGTGCGAAGGGGAGC 61.244 55.000 0.00 0.00 0.00 4.70
36 37 3.842925 TTGTGTGCGAAGGGGAGCC 62.843 63.158 0.00 0.00 0.00 4.70
37 38 4.021925 GTGTGCGAAGGGGAGCCT 62.022 66.667 0.00 0.00 0.00 4.58
38 39 3.249189 TGTGCGAAGGGGAGCCTT 61.249 61.111 0.00 0.00 0.00 4.35
39 40 2.747855 GTGCGAAGGGGAGCCTTG 60.748 66.667 0.00 0.00 0.00 3.61
40 41 4.033776 TGCGAAGGGGAGCCTTGG 62.034 66.667 0.00 0.00 0.00 3.61
50 51 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
51 52 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
52 53 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
53 54 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
54 55 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
55 56 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
56 57 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
62 63 2.175878 CAGTGGTAAAGCTGCTGTCT 57.824 50.000 1.35 0.00 0.00 3.41
63 64 2.498167 CAGTGGTAAAGCTGCTGTCTT 58.502 47.619 1.35 0.00 0.00 3.01
64 65 2.225019 CAGTGGTAAAGCTGCTGTCTTG 59.775 50.000 1.35 0.00 0.00 3.02
65 66 2.158755 AGTGGTAAAGCTGCTGTCTTGT 60.159 45.455 1.35 0.00 0.00 3.16
66 67 2.031682 GTGGTAAAGCTGCTGTCTTGTG 60.032 50.000 1.35 0.00 0.00 3.33
67 68 2.158827 TGGTAAAGCTGCTGTCTTGTGA 60.159 45.455 1.35 0.00 0.00 3.58
68 69 2.224314 GGTAAAGCTGCTGTCTTGTGAC 59.776 50.000 1.35 0.00 43.20 3.67
69 70 1.312815 AAAGCTGCTGTCTTGTGACC 58.687 50.000 1.35 0.00 42.28 4.02
70 71 0.181114 AAGCTGCTGTCTTGTGACCA 59.819 50.000 1.35 0.00 42.28 4.02
71 72 0.399454 AGCTGCTGTCTTGTGACCAT 59.601 50.000 0.00 0.00 42.28 3.55
72 73 0.520404 GCTGCTGTCTTGTGACCATG 59.480 55.000 0.00 0.00 42.28 3.66
73 74 1.879372 GCTGCTGTCTTGTGACCATGA 60.879 52.381 0.00 0.00 42.28 3.07
74 75 2.074576 CTGCTGTCTTGTGACCATGAG 58.925 52.381 0.00 0.00 42.28 2.90
75 76 1.271001 TGCTGTCTTGTGACCATGAGG 60.271 52.381 0.00 0.00 42.28 3.86
90 91 2.859165 TGAGGTCATGGGTTCAAGTC 57.141 50.000 0.00 0.00 0.00 3.01
91 92 2.054021 TGAGGTCATGGGTTCAAGTCA 58.946 47.619 0.00 0.00 0.00 3.41
92 93 2.441375 TGAGGTCATGGGTTCAAGTCAA 59.559 45.455 0.00 0.00 0.00 3.18
93 94 3.077359 GAGGTCATGGGTTCAAGTCAAG 58.923 50.000 0.00 0.00 0.00 3.02
94 95 1.541588 GGTCATGGGTTCAAGTCAAGC 59.458 52.381 0.00 0.00 0.00 4.01
95 96 1.197721 GTCATGGGTTCAAGTCAAGCG 59.802 52.381 0.00 0.00 0.00 4.68
96 97 0.523072 CATGGGTTCAAGTCAAGCGG 59.477 55.000 0.00 0.00 0.00 5.52
97 98 0.609131 ATGGGTTCAAGTCAAGCGGG 60.609 55.000 0.00 0.00 0.00 6.13
98 99 1.072505 GGGTTCAAGTCAAGCGGGA 59.927 57.895 0.00 0.00 0.00 5.14
99 100 0.955919 GGGTTCAAGTCAAGCGGGAG 60.956 60.000 0.00 0.00 0.00 4.30
115 116 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
116 117 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
117 118 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
118 119 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
119 120 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
120 121 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
121 122 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
122 123 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
123 124 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
124 125 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
200 201 8.443160 ACGAGAGTAATGAAAATGTTATGTGTG 58.557 33.333 0.00 0.00 46.88 3.82
220 223 3.547468 GTGTGTGTGTGTGAATGAAAAGC 59.453 43.478 0.00 0.00 0.00 3.51
575 1236 8.932945 AATGAAGAGAAAAACAGAAGAAAACC 57.067 30.769 0.00 0.00 0.00 3.27
576 1237 6.551736 TGAAGAGAAAAACAGAAGAAAACCG 58.448 36.000 0.00 0.00 0.00 4.44
577 1238 6.373216 TGAAGAGAAAAACAGAAGAAAACCGA 59.627 34.615 0.00 0.00 0.00 4.69
578 1239 6.753107 AGAGAAAAACAGAAGAAAACCGAA 57.247 33.333 0.00 0.00 0.00 4.30
641 1329 2.479837 CGGGAGCAATTACGCTAATGA 58.520 47.619 0.00 0.00 44.01 2.57
649 1337 1.682451 TTACGCTAATGAGCCGGCCT 61.682 55.000 26.15 10.99 46.86 5.19
651 1339 1.373497 CGCTAATGAGCCGGCCTAG 60.373 63.158 26.15 19.06 46.86 3.02
665 1353 1.138266 GGCCTAGTTCAGCGAATACCA 59.862 52.381 0.00 0.00 0.00 3.25
667 1355 2.474816 CCTAGTTCAGCGAATACCAGC 58.525 52.381 0.00 0.00 0.00 4.85
679 1367 3.665190 GAATACCAGCTAAATCCCCTCG 58.335 50.000 0.00 0.00 0.00 4.63
701 1389 3.183801 AGGTTCAAAATAGGTCGGGGTA 58.816 45.455 0.00 0.00 0.00 3.69
802 1490 9.125026 AGAGATGCTCAAAAGAGTTAAAAAGAA 57.875 29.630 0.00 0.00 32.06 2.52
844 1532 4.253257 GCGACCCCTAGCGTCTCG 62.253 72.222 6.62 1.25 0.00 4.04
847 1535 2.829458 ACCCCTAGCGTCTCGAGC 60.829 66.667 7.81 1.89 0.00 5.03
899 1587 0.250513 CCCGTCTCCTTCCTTCCTTG 59.749 60.000 0.00 0.00 0.00 3.61
959 1661 4.720902 CAGCGCACATCCCCCACA 62.721 66.667 11.47 0.00 0.00 4.17
964 1666 2.356278 CACATCCCCCACACCCAG 59.644 66.667 0.00 0.00 0.00 4.45
965 1667 2.209809 ACATCCCCCACACCCAGA 59.790 61.111 0.00 0.00 0.00 3.86
966 1668 1.230281 ACATCCCCCACACCCAGAT 60.230 57.895 0.00 0.00 0.00 2.90
1245 2196 2.683859 CGTGGAGTCGCAGTACCGA 61.684 63.158 0.00 0.00 34.40 4.69
2285 3239 5.048083 GTCTGAAGGGTACAATCATTTTGCA 60.048 40.000 0.00 0.00 0.00 4.08
2573 3527 4.160635 GAACCCGATGTTGCCGCG 62.161 66.667 0.00 0.00 37.29 6.46
2980 3934 3.211045 GCTTCTACAACAGGGTGTGAAA 58.789 45.455 0.00 0.00 32.75 2.69
3628 4845 6.016276 GCTGGGAAAAGATTCAAGTCAAGTAA 60.016 38.462 0.00 0.00 37.29 2.24
3780 4997 3.769739 AAAGCATGGAAAGGGGAAAAC 57.230 42.857 0.00 0.00 0.00 2.43
3787 5004 4.252570 TGGAAAGGGGAAAACACTTACA 57.747 40.909 0.00 0.00 43.63 2.41
3797 5014 5.278758 GGGAAAACACTTACATAGCTGCAAA 60.279 40.000 1.02 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.844211 ACACAATTAACTAGAGAGGGGCA 59.156 43.478 0.00 0.00 0.00 5.36
3 4 4.192317 GCACACAATTAACTAGAGAGGGG 58.808 47.826 0.00 0.00 0.00 4.79
5 6 4.744570 TCGCACACAATTAACTAGAGAGG 58.255 43.478 0.00 0.00 0.00 3.69
6 7 5.289675 CCTTCGCACACAATTAACTAGAGAG 59.710 44.000 0.00 0.00 0.00 3.20
7 8 5.168569 CCTTCGCACACAATTAACTAGAGA 58.831 41.667 0.00 0.00 0.00 3.10
8 9 4.330074 CCCTTCGCACACAATTAACTAGAG 59.670 45.833 0.00 0.00 0.00 2.43
9 10 4.250464 CCCTTCGCACACAATTAACTAGA 58.750 43.478 0.00 0.00 0.00 2.43
10 11 3.374058 CCCCTTCGCACACAATTAACTAG 59.626 47.826 0.00 0.00 0.00 2.57
11 12 3.008157 TCCCCTTCGCACACAATTAACTA 59.992 43.478 0.00 0.00 0.00 2.24
12 13 2.159382 CCCCTTCGCACACAATTAACT 58.841 47.619 0.00 0.00 0.00 2.24
13 14 2.156098 TCCCCTTCGCACACAATTAAC 58.844 47.619 0.00 0.00 0.00 2.01
14 15 2.432444 CTCCCCTTCGCACACAATTAA 58.568 47.619 0.00 0.00 0.00 1.40
15 16 1.948611 GCTCCCCTTCGCACACAATTA 60.949 52.381 0.00 0.00 0.00 1.40
16 17 1.244019 GCTCCCCTTCGCACACAATT 61.244 55.000 0.00 0.00 0.00 2.32
17 18 1.675641 GCTCCCCTTCGCACACAAT 60.676 57.895 0.00 0.00 0.00 2.71
18 19 2.281484 GCTCCCCTTCGCACACAA 60.281 61.111 0.00 0.00 0.00 3.33
19 20 4.329545 GGCTCCCCTTCGCACACA 62.330 66.667 0.00 0.00 0.00 3.72
20 21 4.021925 AGGCTCCCCTTCGCACAC 62.022 66.667 0.00 0.00 38.74 3.82
32 33 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
33 34 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
34 35 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
35 36 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
36 37 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
37 38 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
38 39 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
39 40 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
43 44 2.175878 AGACAGCAGCTTTACCACTG 57.824 50.000 0.00 0.00 36.96 3.66
44 45 2.158755 ACAAGACAGCAGCTTTACCACT 60.159 45.455 0.00 0.00 0.00 4.00
45 46 2.031682 CACAAGACAGCAGCTTTACCAC 60.032 50.000 0.00 0.00 0.00 4.16
46 47 2.158827 TCACAAGACAGCAGCTTTACCA 60.159 45.455 0.00 0.00 0.00 3.25
47 48 2.224314 GTCACAAGACAGCAGCTTTACC 59.776 50.000 0.00 0.00 44.34 2.85
48 49 2.224314 GGTCACAAGACAGCAGCTTTAC 59.776 50.000 0.00 0.00 46.80 2.01
49 50 2.158827 TGGTCACAAGACAGCAGCTTTA 60.159 45.455 0.00 0.00 46.80 1.85
50 51 1.312815 GGTCACAAGACAGCAGCTTT 58.687 50.000 0.00 0.00 46.80 3.51
51 52 0.181114 TGGTCACAAGACAGCAGCTT 59.819 50.000 0.00 0.00 46.80 3.74
52 53 0.399454 ATGGTCACAAGACAGCAGCT 59.601 50.000 0.00 0.00 46.80 4.24
53 54 0.520404 CATGGTCACAAGACAGCAGC 59.480 55.000 0.00 0.00 46.80 5.25
54 55 2.074576 CTCATGGTCACAAGACAGCAG 58.925 52.381 0.00 0.00 46.80 4.24
55 56 1.271001 CCTCATGGTCACAAGACAGCA 60.271 52.381 0.00 0.00 46.80 4.41
56 57 1.271054 ACCTCATGGTCACAAGACAGC 60.271 52.381 0.00 0.00 44.78 4.40
57 58 2.847327 ACCTCATGGTCACAAGACAG 57.153 50.000 0.00 0.00 44.78 3.51
70 71 2.644299 TGACTTGAACCCATGACCTCAT 59.356 45.455 0.00 0.00 36.96 2.90
71 72 2.054021 TGACTTGAACCCATGACCTCA 58.946 47.619 0.00 0.00 0.00 3.86
72 73 2.859165 TGACTTGAACCCATGACCTC 57.141 50.000 0.00 0.00 0.00 3.85
73 74 2.815589 GCTTGACTTGAACCCATGACCT 60.816 50.000 0.00 0.00 0.00 3.85
74 75 1.541588 GCTTGACTTGAACCCATGACC 59.458 52.381 0.00 0.00 0.00 4.02
75 76 1.197721 CGCTTGACTTGAACCCATGAC 59.802 52.381 0.00 0.00 0.00 3.06
76 77 1.522668 CGCTTGACTTGAACCCATGA 58.477 50.000 0.00 0.00 0.00 3.07
77 78 0.523072 CCGCTTGACTTGAACCCATG 59.477 55.000 0.00 0.00 0.00 3.66
78 79 0.609131 CCCGCTTGACTTGAACCCAT 60.609 55.000 0.00 0.00 0.00 4.00
79 80 1.228124 CCCGCTTGACTTGAACCCA 60.228 57.895 0.00 0.00 0.00 4.51
80 81 0.955919 CTCCCGCTTGACTTGAACCC 60.956 60.000 0.00 0.00 0.00 4.11
81 82 1.578206 GCTCCCGCTTGACTTGAACC 61.578 60.000 0.00 0.00 0.00 3.62
82 83 0.603975 AGCTCCCGCTTGACTTGAAC 60.604 55.000 0.00 0.00 46.47 3.18
83 84 0.973632 TAGCTCCCGCTTGACTTGAA 59.026 50.000 0.00 0.00 46.47 2.69
84 85 0.246635 GTAGCTCCCGCTTGACTTGA 59.753 55.000 0.00 0.00 46.47 3.02
85 86 0.037326 TGTAGCTCCCGCTTGACTTG 60.037 55.000 0.00 0.00 46.47 3.16
86 87 0.905357 ATGTAGCTCCCGCTTGACTT 59.095 50.000 0.00 0.00 46.47 3.01
87 88 0.176680 CATGTAGCTCCCGCTTGACT 59.823 55.000 0.00 0.00 46.47 3.41
88 89 1.432270 GCATGTAGCTCCCGCTTGAC 61.432 60.000 0.00 0.00 46.47 3.18
89 90 1.153369 GCATGTAGCTCCCGCTTGA 60.153 57.895 0.00 0.00 46.47 3.02
90 91 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
91 92 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
97 98 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
98 99 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
99 100 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
100 101 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
101 102 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
122 123 4.333095 TGCGCACACAACTAACTAGAAAAA 59.667 37.500 5.66 0.00 0.00 1.94
123 124 3.872182 TGCGCACACAACTAACTAGAAAA 59.128 39.130 5.66 0.00 0.00 2.29
124 125 3.459145 TGCGCACACAACTAACTAGAAA 58.541 40.909 5.66 0.00 0.00 2.52
125 126 3.100658 TGCGCACACAACTAACTAGAA 57.899 42.857 5.66 0.00 0.00 2.10
126 127 2.804697 TGCGCACACAACTAACTAGA 57.195 45.000 5.66 0.00 0.00 2.43
127 128 3.679980 AGATTGCGCACACAACTAACTAG 59.320 43.478 11.12 0.00 31.03 2.57
128 129 3.431912 CAGATTGCGCACACAACTAACTA 59.568 43.478 11.12 0.00 31.03 2.24
129 130 2.224079 CAGATTGCGCACACAACTAACT 59.776 45.455 11.12 0.00 31.03 2.24
130 131 2.223144 TCAGATTGCGCACACAACTAAC 59.777 45.455 11.12 0.00 31.03 2.34
131 132 2.488952 TCAGATTGCGCACACAACTAA 58.511 42.857 11.12 0.00 31.03 2.24
132 133 2.162319 TCAGATTGCGCACACAACTA 57.838 45.000 11.12 0.00 31.03 2.24
133 134 1.002468 GTTCAGATTGCGCACACAACT 60.002 47.619 11.12 0.00 31.03 3.16
134 135 1.002468 AGTTCAGATTGCGCACACAAC 60.002 47.619 11.12 9.16 31.03 3.32
135 136 1.264020 GAGTTCAGATTGCGCACACAA 59.736 47.619 11.12 0.00 0.00 3.33
200 201 2.783284 CGCTTTTCATTCACACACACAC 59.217 45.455 0.00 0.00 0.00 3.82
220 223 2.607771 CCCAGTTTTGAAATGCCACTCG 60.608 50.000 0.00 0.00 0.00 4.18
637 1325 0.179000 CTGAACTAGGCCGGCTCATT 59.821 55.000 28.56 15.65 0.00 2.57
641 1329 4.148825 CGCTGAACTAGGCCGGCT 62.149 66.667 28.56 15.07 32.74 5.52
649 1337 4.994907 TTAGCTGGTATTCGCTGAACTA 57.005 40.909 0.00 0.00 37.05 2.24
651 1339 4.024809 GGATTTAGCTGGTATTCGCTGAAC 60.025 45.833 0.00 0.00 35.10 3.18
665 1353 1.763545 GAACCTCGAGGGGATTTAGCT 59.236 52.381 34.04 8.06 40.27 3.32
667 1355 3.906720 TTGAACCTCGAGGGGATTTAG 57.093 47.619 34.04 7.95 40.27 1.85
679 1367 2.026542 ACCCCGACCTATTTTGAACCTC 60.027 50.000 0.00 0.00 0.00 3.85
701 1389 7.094463 CCTTAAATCAGCACATCAAACTCTCTT 60.094 37.037 0.00 0.00 0.00 2.85
802 1490 8.450964 GCCTTAAACTTGCTTTTCTTTCTTTTT 58.549 29.630 0.00 0.00 0.00 1.94
806 1494 5.067283 TCGCCTTAAACTTGCTTTTCTTTCT 59.933 36.000 0.00 0.00 0.00 2.52
807 1495 5.173312 GTCGCCTTAAACTTGCTTTTCTTTC 59.827 40.000 0.00 0.00 0.00 2.62
844 1532 2.433318 GACTCAGTGCACGGGCTC 60.433 66.667 17.13 7.64 41.91 4.70
847 1535 2.357517 GTGGACTCAGTGCACGGG 60.358 66.667 14.29 11.69 44.01 5.28
899 1587 4.097361 GGGTGCGGGGAAGGAGTC 62.097 72.222 0.00 0.00 0.00 3.36
955 1657 4.489771 GGGCGGATCTGGGTGTGG 62.490 72.222 3.14 0.00 0.00 4.17
956 1658 4.489771 GGGGCGGATCTGGGTGTG 62.490 72.222 3.14 0.00 0.00 3.82
958 1660 4.181010 CTGGGGCGGATCTGGGTG 62.181 72.222 3.14 0.00 0.00 4.61
959 1661 3.721172 ATCTGGGGCGGATCTGGGT 62.721 63.158 3.14 0.00 0.00 4.51
961 1663 2.746359 GATCTGGGGCGGATCTGG 59.254 66.667 3.14 0.00 41.55 3.86
962 1664 2.746359 GGATCTGGGGCGGATCTG 59.254 66.667 0.00 0.00 43.56 2.90
964 1666 4.008933 CCGGATCTGGGGCGGATC 62.009 72.222 13.34 0.00 43.38 3.36
1230 2181 1.428620 GACTCGGTACTGCGACTCC 59.571 63.158 0.00 0.00 0.00 3.85
1467 2418 4.458829 TGGGAGAGGCGGACGGAT 62.459 66.667 0.00 0.00 0.00 4.18
2285 3239 2.224793 GCCTTCTTTGGTGGTAAGGTCT 60.225 50.000 0.00 0.00 40.55 3.85
2320 3274 0.107945 AGCCGGAATGAGAACTCTGC 60.108 55.000 5.05 0.00 0.00 4.26
2573 3527 1.533625 TGTAACATTGCTCAGTGGCC 58.466 50.000 0.00 0.00 0.00 5.36
3628 4845 5.358725 ACCGTGTTTCCAGAAATAAAGTGTT 59.641 36.000 0.00 0.00 32.36 3.32
3780 4997 3.609853 TCCCTTTGCAGCTATGTAAGTG 58.390 45.455 0.00 0.00 32.32 3.16
3787 5004 3.457380 TGATCTCTTCCCTTTGCAGCTAT 59.543 43.478 0.00 0.00 0.00 2.97
3797 5014 9.620259 GTTTTTGTATAGATTGATCTCTTCCCT 57.380 33.333 0.00 0.00 38.32 4.20
3860 5077 1.134699 ACCAGGCATCATACTGACACG 60.135 52.381 0.00 0.00 36.86 4.49
3863 5080 4.265073 AGAAAACCAGGCATCATACTGAC 58.735 43.478 0.00 0.00 36.86 3.51


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

AutoCloner maintained by Alex Coulton.