Multiple sequence alignment - TraesCS5B01G322600

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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 TraesCS5B01G322600 chr5B 100.000 2213 0 0 1 2213 507341641 507343853 0.000000e+00 4087.0
1 TraesCS5B01G322600 chr5B 92.019 639 35 9 758 1391 707163799 707163172 0.000000e+00 883.0
2 TraesCS5B01G322600 chr5B 96.653 478 11 2 1687 2159 669373039 669372562 0.000000e+00 789.0
3 TraesCS5B01G322600 chr5B 97.007 401 12 0 209 609 441563315 441562915 0.000000e+00 675.0
4 TraesCS5B01G322600 chr5B 94.335 406 16 3 204 609 86478743 86478345 1.120000e-172 616.0
5 TraesCS5B01G322600 chr5B 99.091 220 0 2 1 219 666222907 666223125 5.730000e-106 394.0
6 TraesCS5B01G322600 chr5B 93.785 177 10 1 1499 1674 176794677 176794501 4.690000e-67 265.0
7 TraesCS5B01G322600 chr5B 92.655 177 12 1 1499 1674 204616775 204616599 1.010000e-63 254.0
8 TraesCS5B01G322600 chr5B 92.683 41 3 0 1391 1431 56367223 56367183 2.370000e-05 60.2
9 TraesCS5B01G322600 chr7B 97.143 1645 29 7 584 2213 616929371 616931012 0.000000e+00 2761.0
10 TraesCS5B01G322600 chr7B 96.058 482 16 3 1681 2159 230966513 230966994 0.000000e+00 782.0
11 TraesCS5B01G322600 chr7B 98.005 401 8 0 209 609 616928937 616929337 0.000000e+00 697.0
12 TraesCS5B01G322600 chr7B 99.087 219 2 0 1 219 614048034 614047816 5.730000e-106 394.0
13 TraesCS5B01G322600 chr7B 94.444 72 3 1 1431 1501 341991587 341991516 2.320000e-20 110.0
14 TraesCS5B01G322600 chr6B 95.599 568 22 2 937 1501 204852547 204853114 0.000000e+00 907.0
15 TraesCS5B01G322600 chr6B 97.095 482 11 3 1681 2159 267745957 267746438 0.000000e+00 809.0
16 TraesCS5B01G322600 chr6B 96.480 483 13 4 1681 2159 233925292 233925774 0.000000e+00 795.0
17 TraesCS5B01G322600 chr6B 95.480 177 7 1 1499 1674 204853326 204853502 4.650000e-72 281.0
18 TraesCS5B01G322600 chr4B 97.071 478 12 2 1684 2159 317036254 317035777 0.000000e+00 804.0
19 TraesCS5B01G322600 chr4B 92.683 41 3 0 1391 1431 242502694 242502654 2.370000e-05 60.2
20 TraesCS5B01G322600 chr4B 92.683 41 3 0 1391 1431 307976488 307976448 2.370000e-05 60.2
21 TraesCS5B01G322600 chr4B 92.683 41 3 0 1391 1431 401393233 401393273 2.370000e-05 60.2
22 TraesCS5B01G322600 chr2B 96.444 478 15 2 1684 2159 110276159 110275682 0.000000e+00 787.0
23 TraesCS5B01G322600 chr2B 94.581 406 16 2 204 609 58401858 58401459 6.710000e-175 623.0
24 TraesCS5B01G322600 chr2B 92.473 93 5 2 1584 1674 460569388 460569480 4.960000e-27 132.0
25 TraesCS5B01G322600 chr3B 95.859 483 16 3 1681 2159 274659393 274659875 0.000000e+00 778.0
26 TraesCS5B01G322600 chr3B 95.262 401 19 0 209 609 247080619 247080219 8.620000e-179 636.0
27 TraesCS5B01G322600 chr3B 96.341 82 2 1 584 665 247080185 247080105 1.380000e-27 134.0
28 TraesCS5B01G322600 chr3B 92.683 82 3 2 584 665 246971051 246970973 4.990000e-22 115.0
29 TraesCS5B01G322600 chr1B 95.851 482 16 4 1681 2159 502363055 502363535 0.000000e+00 776.0
30 TraesCS5B01G322600 chr1B 98.190 221 3 1 1 221 541041441 541041660 3.450000e-103 385.0
31 TraesCS5B01G322600 chr1B 91.525 177 14 1 1499 1674 177157691 177157867 2.200000e-60 243.0
32 TraesCS5B01G322600 chr1B 91.525 177 14 1 1499 1674 192672986 192673162 2.200000e-60 243.0
33 TraesCS5B01G322600 chr2D 96.305 406 12 2 204 609 205892735 205892333 0.000000e+00 664.0
34 TraesCS5B01G322600 chr2D 96.341 82 2 1 584 665 205892299 205892219 1.380000e-27 134.0
35 TraesCS5B01G322600 chr2D 92.683 41 3 0 1391 1431 256893833 256893873 2.370000e-05 60.2
36 TraesCS5B01G322600 chr6A 95.823 407 13 3 204 609 443934530 443934933 0.000000e+00 654.0
37 TraesCS5B01G322600 chr6A 99.091 220 0 2 1 219 453270993 453270775 5.730000e-106 394.0
38 TraesCS5B01G322600 chr4D 96.474 397 13 1 213 609 266759822 266759427 0.000000e+00 654.0
39 TraesCS5B01G322600 chr3D 94.828 406 19 1 204 609 221278470 221278067 1.110000e-177 632.0
40 TraesCS5B01G322600 chr3D 92.655 177 11 2 1499 1674 288640316 288640491 1.010000e-63 254.0
41 TraesCS5B01G322600 chr4A 83.253 621 68 15 774 1391 607433206 607433793 2.500000e-149 538.0
42 TraesCS5B01G322600 chr4A 99.087 219 2 0 1 219 200321663 200321445 5.730000e-106 394.0
43 TraesCS5B01G322600 chr4A 98.222 225 2 2 1 224 443974046 443974269 2.060000e-105 392.0
44 TraesCS5B01G322600 chr5D 83.094 627 67 16 774 1391 565951802 565952398 3.230000e-148 534.0
45 TraesCS5B01G322600 chr5D 92.683 41 3 0 1391 1431 53760796 53760756 2.370000e-05 60.2
46 TraesCS5B01G322600 chr2A 99.539 217 0 1 1 217 78993955 78993740 5.730000e-106 394.0
47 TraesCS5B01G322600 chr2A 98.649 222 1 2 1 221 24455753 24455533 2.060000e-105 392.0
48 TraesCS5B01G322600 chr3A 99.087 219 1 1 1 219 565340732 565340949 2.060000e-105 392.0
49 TraesCS5B01G322600 chr1A 92.683 41 3 0 1391 1431 352915673 352915713 2.370000e-05 60.2


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 TraesCS5B01G322600 chr5B 507341641 507343853 2212 False 4087 4087 100.0000 1 2213 1 chr5B.!!$F1 2212
1 TraesCS5B01G322600 chr5B 707163172 707163799 627 True 883 883 92.0190 758 1391 1 chr5B.!!$R7 633
2 TraesCS5B01G322600 chr7B 616928937 616931012 2075 False 1729 2761 97.5740 209 2213 2 chr7B.!!$F2 2004
3 TraesCS5B01G322600 chr6B 204852547 204853502 955 False 594 907 95.5395 937 1674 2 chr6B.!!$F3 737
4 TraesCS5B01G322600 chr3B 247080105 247080619 514 True 385 636 95.8015 209 665 2 chr3B.!!$R2 456
5 TraesCS5B01G322600 chr2D 205892219 205892735 516 True 399 664 96.3230 204 665 2 chr2D.!!$R1 461
6 TraesCS5B01G322600 chr4A 607433206 607433793 587 False 538 538 83.2530 774 1391 1 chr4A.!!$F2 617
7 TraesCS5B01G322600 chr5D 565951802 565952398 596 False 534 534 83.0940 774 1391 1 chr5D.!!$F1 617

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
19 20 1.367346 TGTCCATAGCCAGGAAACCA 58.633 50.000 0.0 0.0 36.80 3.67 F
1061 1146 1.794437 CGAAGTCGTAAGGGAAGCTCG 60.794 57.143 0.0 0.0 38.47 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1111 1196 0.911769 AGATGGCCATCTTGGAACGA 59.088 50.000 37.67 0.0 45.31 3.85 R
2044 2351 6.899393 ATCATGGCTTTTACTTCAAACTGA 57.101 33.333 0.00 0.0 0.00 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
19 20 1.367346 TGTCCATAGCCAGGAAACCA 58.633 50.000 0.00 0.00 36.80 3.67
20 21 1.922447 TGTCCATAGCCAGGAAACCAT 59.078 47.619 0.00 0.00 36.80 3.55
21 22 2.301346 GTCCATAGCCAGGAAACCATG 58.699 52.381 0.00 0.00 36.80 3.66
22 23 2.092429 GTCCATAGCCAGGAAACCATGA 60.092 50.000 0.00 0.00 36.80 3.07
23 24 2.092429 TCCATAGCCAGGAAACCATGAC 60.092 50.000 0.00 0.00 30.71 3.06
24 25 2.092212 CCATAGCCAGGAAACCATGACT 60.092 50.000 0.00 0.00 0.00 3.41
25 26 3.136443 CCATAGCCAGGAAACCATGACTA 59.864 47.826 0.00 0.00 0.00 2.59
26 27 4.202503 CCATAGCCAGGAAACCATGACTAT 60.203 45.833 0.00 0.00 0.00 2.12
27 28 3.567478 AGCCAGGAAACCATGACTATC 57.433 47.619 0.00 0.00 0.00 2.08
28 29 3.118531 AGCCAGGAAACCATGACTATCT 58.881 45.455 0.00 0.00 0.00 1.98
29 30 3.118112 AGCCAGGAAACCATGACTATCTG 60.118 47.826 0.00 0.00 0.00 2.90
30 31 3.370953 GCCAGGAAACCATGACTATCTGT 60.371 47.826 0.00 0.00 0.00 3.41
31 32 4.848357 CCAGGAAACCATGACTATCTGTT 58.152 43.478 0.00 0.00 0.00 3.16
32 33 4.637534 CCAGGAAACCATGACTATCTGTTG 59.362 45.833 0.00 0.00 0.00 3.33
33 34 5.491070 CAGGAAACCATGACTATCTGTTGA 58.509 41.667 0.00 0.00 0.00 3.18
34 35 6.118170 CAGGAAACCATGACTATCTGTTGAT 58.882 40.000 0.00 0.00 36.74 2.57
35 36 6.259608 CAGGAAACCATGACTATCTGTTGATC 59.740 42.308 0.00 0.00 34.32 2.92
36 37 6.070021 AGGAAACCATGACTATCTGTTGATCA 60.070 38.462 0.00 0.00 34.32 2.92
37 38 6.037610 GGAAACCATGACTATCTGTTGATCAC 59.962 42.308 0.00 0.00 34.32 3.06
38 39 5.682234 ACCATGACTATCTGTTGATCACA 57.318 39.130 0.00 0.00 34.32 3.58
39 40 6.053632 ACCATGACTATCTGTTGATCACAA 57.946 37.500 0.00 0.00 33.87 3.33
50 51 3.575630 GTTGATCACAACGAGCTAGTCA 58.424 45.455 0.00 0.00 45.06 3.41
51 52 3.934457 TGATCACAACGAGCTAGTCAA 57.066 42.857 0.00 0.00 0.00 3.18
52 53 3.575630 TGATCACAACGAGCTAGTCAAC 58.424 45.455 0.00 0.00 0.00 3.18
53 54 3.255888 TGATCACAACGAGCTAGTCAACT 59.744 43.478 0.00 0.00 0.00 3.16
54 55 4.457949 TGATCACAACGAGCTAGTCAACTA 59.542 41.667 0.00 0.00 0.00 2.24
55 56 4.421033 TCACAACGAGCTAGTCAACTAG 57.579 45.455 11.99 11.99 46.63 2.57
56 57 4.070009 TCACAACGAGCTAGTCAACTAGA 58.930 43.478 19.03 0.00 46.80 2.43
57 58 4.154375 TCACAACGAGCTAGTCAACTAGAG 59.846 45.833 19.03 11.89 46.80 2.43
58 59 3.440872 ACAACGAGCTAGTCAACTAGAGG 59.559 47.826 19.03 10.05 46.80 3.69
59 60 2.018515 ACGAGCTAGTCAACTAGAGGC 58.981 52.381 19.03 6.58 46.80 4.70
60 61 2.294074 CGAGCTAGTCAACTAGAGGCT 58.706 52.381 19.03 10.84 46.80 4.58
61 62 2.289547 CGAGCTAGTCAACTAGAGGCTC 59.710 54.545 19.03 16.73 46.80 4.70
62 63 3.283751 GAGCTAGTCAACTAGAGGCTCA 58.716 50.000 18.26 1.80 46.80 4.26
63 64 3.020984 AGCTAGTCAACTAGAGGCTCAC 58.979 50.000 18.26 4.72 46.80 3.51
64 65 3.020984 GCTAGTCAACTAGAGGCTCACT 58.979 50.000 18.26 12.32 46.80 3.41
65 66 4.080243 AGCTAGTCAACTAGAGGCTCACTA 60.080 45.833 18.26 12.80 46.80 2.74
66 67 4.274950 GCTAGTCAACTAGAGGCTCACTAG 59.725 50.000 23.14 23.14 46.80 2.57
67 68 3.626930 AGTCAACTAGAGGCTCACTAGG 58.373 50.000 18.26 3.24 40.86 3.02
68 69 2.691011 GTCAACTAGAGGCTCACTAGGG 59.309 54.545 18.26 7.64 40.86 3.53
69 70 2.581246 TCAACTAGAGGCTCACTAGGGA 59.419 50.000 18.26 9.66 40.86 4.20
70 71 2.691011 CAACTAGAGGCTCACTAGGGAC 59.309 54.545 18.26 0.00 40.86 4.46
71 72 1.923850 ACTAGAGGCTCACTAGGGACA 59.076 52.381 18.26 0.00 40.86 4.02
72 73 2.516277 ACTAGAGGCTCACTAGGGACAT 59.484 50.000 18.26 0.00 40.86 3.06
73 74 3.722627 ACTAGAGGCTCACTAGGGACATA 59.277 47.826 18.26 0.00 40.86 2.29
74 75 3.913370 AGAGGCTCACTAGGGACATAT 57.087 47.619 18.26 0.00 0.00 1.78
75 76 4.206244 AGAGGCTCACTAGGGACATATT 57.794 45.455 18.26 0.00 0.00 1.28
76 77 3.900601 AGAGGCTCACTAGGGACATATTG 59.099 47.826 18.26 0.00 0.00 1.90
77 78 3.643792 GAGGCTCACTAGGGACATATTGT 59.356 47.826 10.25 0.00 0.00 2.71
78 79 3.389329 AGGCTCACTAGGGACATATTGTG 59.611 47.826 0.00 0.00 0.00 3.33
79 80 3.495100 GGCTCACTAGGGACATATTGTGG 60.495 52.174 0.00 0.00 0.00 4.17
80 81 3.134804 GCTCACTAGGGACATATTGTGGT 59.865 47.826 0.00 0.00 0.00 4.16
81 82 4.740934 GCTCACTAGGGACATATTGTGGTC 60.741 50.000 0.00 0.00 0.00 4.02
82 83 4.620723 TCACTAGGGACATATTGTGGTCT 58.379 43.478 0.00 0.00 34.49 3.85
83 84 5.773091 TCACTAGGGACATATTGTGGTCTA 58.227 41.667 0.00 0.00 34.49 2.59
84 85 6.382087 TCACTAGGGACATATTGTGGTCTAT 58.618 40.000 0.00 0.00 34.49 1.98
85 86 6.267699 TCACTAGGGACATATTGTGGTCTATG 59.732 42.308 0.00 0.00 34.49 2.23
86 87 6.042093 CACTAGGGACATATTGTGGTCTATGT 59.958 42.308 0.00 0.00 40.38 2.29
87 88 7.232737 CACTAGGGACATATTGTGGTCTATGTA 59.767 40.741 0.00 0.00 38.38 2.29
88 89 7.956315 ACTAGGGACATATTGTGGTCTATGTAT 59.044 37.037 0.00 0.00 38.38 2.29
89 90 7.633018 AGGGACATATTGTGGTCTATGTATT 57.367 36.000 0.00 0.00 38.38 1.89
90 91 7.680730 AGGGACATATTGTGGTCTATGTATTC 58.319 38.462 0.00 0.00 38.38 1.75
91 92 7.292356 AGGGACATATTGTGGTCTATGTATTCA 59.708 37.037 0.00 0.00 38.38 2.57
92 93 7.387948 GGGACATATTGTGGTCTATGTATTCAC 59.612 40.741 0.00 0.00 38.38 3.18
93 94 7.931407 GGACATATTGTGGTCTATGTATTCACA 59.069 37.037 0.00 0.00 38.38 3.58
94 95 8.662781 ACATATTGTGGTCTATGTATTCACAC 57.337 34.615 0.00 0.00 36.93 3.82
95 96 7.438160 ACATATTGTGGTCTATGTATTCACACG 59.562 37.037 0.00 0.00 36.93 4.49
96 97 4.794278 TGTGGTCTATGTATTCACACGT 57.206 40.909 0.00 0.00 37.54 4.49
97 98 4.490743 TGTGGTCTATGTATTCACACGTG 58.509 43.478 15.48 15.48 37.54 4.49
98 99 4.021807 TGTGGTCTATGTATTCACACGTGT 60.022 41.667 17.22 17.22 37.54 4.49
99 100 5.183522 TGTGGTCTATGTATTCACACGTGTA 59.816 40.000 22.90 7.35 37.54 2.90
100 101 6.127563 TGTGGTCTATGTATTCACACGTGTAT 60.128 38.462 22.90 14.96 37.54 2.29
101 102 6.755141 GTGGTCTATGTATTCACACGTGTATT 59.245 38.462 22.90 11.42 37.54 1.89
102 103 7.916977 GTGGTCTATGTATTCACACGTGTATTA 59.083 37.037 22.90 9.93 37.54 0.98
103 104 7.916977 TGGTCTATGTATTCACACGTGTATTAC 59.083 37.037 22.90 20.91 37.54 1.89
120 121 8.746922 GTGTATTACGATTTCCGGATAATACA 57.253 34.615 28.04 28.04 43.07 2.29
121 122 8.857216 GTGTATTACGATTTCCGGATAATACAG 58.143 37.037 30.32 18.57 44.29 2.74
122 123 8.579006 TGTATTACGATTTCCGGATAATACAGT 58.421 33.333 28.04 20.31 41.92 3.55
123 124 9.415544 GTATTACGATTTCCGGATAATACAGTT 57.584 33.333 26.02 11.20 39.68 3.16
128 129 7.758528 ACGATTTCCGGATAATACAGTTATAGC 59.241 37.037 4.15 0.00 43.93 2.97
129 130 7.758076 CGATTTCCGGATAATACAGTTATAGCA 59.242 37.037 4.15 0.00 33.91 3.49
130 131 9.601217 GATTTCCGGATAATACAGTTATAGCAT 57.399 33.333 4.15 0.00 0.00 3.79
131 132 8.771920 TTTCCGGATAATACAGTTATAGCATG 57.228 34.615 4.15 0.00 0.00 4.06
132 133 7.712204 TCCGGATAATACAGTTATAGCATGA 57.288 36.000 0.00 0.00 0.00 3.07
133 134 8.129496 TCCGGATAATACAGTTATAGCATGAA 57.871 34.615 0.00 0.00 0.00 2.57
134 135 8.758829 TCCGGATAATACAGTTATAGCATGAAT 58.241 33.333 0.00 0.00 0.00 2.57
217 218 4.887071 GGCATATTTCCAACACATAGGTCA 59.113 41.667 0.00 0.00 0.00 4.02
284 285 2.031420 CGTCCTCAACTAGTTCGTCACA 60.031 50.000 4.77 0.00 0.00 3.58
371 372 6.128391 CCTCGTACTTGCACTTGCTTATTTTA 60.128 38.462 2.33 0.00 42.66 1.52
496 497 5.716228 ACATATGAAAACCATTCTGGCTTCA 59.284 36.000 10.38 11.52 42.90 3.02
500 501 3.795688 AAACCATTCTGGCTTCAGAGA 57.204 42.857 0.00 0.00 46.84 3.10
951 1025 3.561725 AGAAAGCACAACACTAGTTCTGC 59.438 43.478 0.00 1.17 46.15 4.26
1035 1120 2.681064 GCATCAGGGCTTGGGCAA 60.681 61.111 8.77 0.00 40.87 4.52
1061 1146 1.794437 CGAAGTCGTAAGGGAAGCTCG 60.794 57.143 0.00 0.00 38.47 5.03
1094 1179 5.930837 AAACTTTGGAATGTGAGGTTTGA 57.069 34.783 0.00 0.00 0.00 2.69
1111 1196 2.112297 ACGACGCAATGGGGTTGT 59.888 55.556 4.31 4.31 46.48 3.32
1503 1807 3.177228 ACTATTCCTGTTGCTCTCACCT 58.823 45.455 0.00 0.00 0.00 4.00
1622 1927 5.197682 ACCAGACATAGTATTAGTTCGGC 57.802 43.478 0.00 0.00 0.00 5.54
1733 2038 2.584835 TTGCTGTGCAGGAAATAGGT 57.415 45.000 3.67 0.00 40.61 3.08
1779 2084 8.246180 GTGGGTGCTATGGATAATATGAAAATG 58.754 37.037 0.00 0.00 0.00 2.32
1799 2104 2.028020 TGTGCAATCGGTGTGGTGTATA 60.028 45.455 0.00 0.00 0.00 1.47
1891 2196 8.514594 TGTGTGGAAAATTTTCTGTCTATGATC 58.485 33.333 25.86 9.44 37.35 2.92
2192 2499 4.503910 AGCTCAAACAAAAAGAAACCCAC 58.496 39.130 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.367346 TGGTTTCCTGGCTATGGACA 58.633 50.000 0.00 0.00 32.65 4.02
1 2 2.092429 TCATGGTTTCCTGGCTATGGAC 60.092 50.000 0.00 0.00 32.65 4.02
2 3 2.092429 GTCATGGTTTCCTGGCTATGGA 60.092 50.000 0.00 0.00 0.00 3.41
3 4 2.092212 AGTCATGGTTTCCTGGCTATGG 60.092 50.000 0.00 0.00 0.00 2.74
6 7 4.101585 CAGATAGTCATGGTTTCCTGGCTA 59.898 45.833 0.00 0.00 34.35 3.93
7 8 3.118112 CAGATAGTCATGGTTTCCTGGCT 60.118 47.826 0.00 0.00 0.00 4.75
8 9 3.209410 CAGATAGTCATGGTTTCCTGGC 58.791 50.000 0.00 0.00 0.00 4.85
9 10 4.494091 ACAGATAGTCATGGTTTCCTGG 57.506 45.455 0.00 0.00 0.00 4.45
10 11 5.491070 TCAACAGATAGTCATGGTTTCCTG 58.509 41.667 0.00 0.00 0.00 3.86
11 12 5.762179 TCAACAGATAGTCATGGTTTCCT 57.238 39.130 0.00 0.00 0.00 3.36
12 13 6.037610 GTGATCAACAGATAGTCATGGTTTCC 59.962 42.308 0.00 0.00 0.00 3.13
13 14 6.595326 TGTGATCAACAGATAGTCATGGTTTC 59.405 38.462 0.00 0.00 33.78 2.78
14 15 6.475504 TGTGATCAACAGATAGTCATGGTTT 58.524 36.000 0.00 0.00 33.78 3.27
15 16 6.053632 TGTGATCAACAGATAGTCATGGTT 57.946 37.500 0.00 0.00 33.78 3.67
16 17 5.682234 TGTGATCAACAGATAGTCATGGT 57.318 39.130 0.00 0.00 33.78 3.55
29 30 8.771523 CTAGTTGACTAGCTCGTTGTGATCAAC 61.772 44.444 0.00 9.17 42.66 3.18
30 31 3.934457 TGACTAGCTCGTTGTGATCAA 57.066 42.857 0.00 0.00 0.00 2.57
31 32 3.255888 AGTTGACTAGCTCGTTGTGATCA 59.744 43.478 0.00 0.00 0.00 2.92
32 33 3.839293 AGTTGACTAGCTCGTTGTGATC 58.161 45.455 0.00 0.00 0.00 2.92
33 34 3.944055 AGTTGACTAGCTCGTTGTGAT 57.056 42.857 0.00 0.00 0.00 3.06
34 35 4.070009 TCTAGTTGACTAGCTCGTTGTGA 58.930 43.478 12.30 0.00 44.24 3.58
35 36 4.407818 CTCTAGTTGACTAGCTCGTTGTG 58.592 47.826 12.30 0.00 44.24 3.33
36 37 3.440872 CCTCTAGTTGACTAGCTCGTTGT 59.559 47.826 12.30 0.00 44.24 3.32
37 38 3.732471 GCCTCTAGTTGACTAGCTCGTTG 60.732 52.174 12.30 0.75 44.24 4.10
38 39 2.424246 GCCTCTAGTTGACTAGCTCGTT 59.576 50.000 12.30 0.00 44.24 3.85
39 40 2.018515 GCCTCTAGTTGACTAGCTCGT 58.981 52.381 12.30 0.00 44.24 4.18
40 41 2.289547 GAGCCTCTAGTTGACTAGCTCG 59.710 54.545 12.30 0.00 44.24 5.03
41 42 3.066203 GTGAGCCTCTAGTTGACTAGCTC 59.934 52.174 17.34 17.34 44.24 4.09
42 43 3.020984 GTGAGCCTCTAGTTGACTAGCT 58.979 50.000 12.30 7.92 44.24 3.32
43 44 3.020984 AGTGAGCCTCTAGTTGACTAGC 58.979 50.000 12.30 3.61 44.24 3.42
44 45 4.819630 CCTAGTGAGCCTCTAGTTGACTAG 59.180 50.000 11.14 11.14 45.57 2.57
45 46 4.385421 CCCTAGTGAGCCTCTAGTTGACTA 60.385 50.000 0.00 0.00 34.72 2.59
46 47 3.626222 CCCTAGTGAGCCTCTAGTTGACT 60.626 52.174 0.00 0.00 34.72 3.41
47 48 2.691011 CCCTAGTGAGCCTCTAGTTGAC 59.309 54.545 0.00 0.00 34.72 3.18
48 49 2.581246 TCCCTAGTGAGCCTCTAGTTGA 59.419 50.000 0.00 4.76 34.72 3.18
49 50 2.691011 GTCCCTAGTGAGCCTCTAGTTG 59.309 54.545 0.00 3.20 34.72 3.16
50 51 2.312140 TGTCCCTAGTGAGCCTCTAGTT 59.688 50.000 0.00 0.00 34.72 2.24
51 52 1.923850 TGTCCCTAGTGAGCCTCTAGT 59.076 52.381 0.00 0.00 34.72 2.57
52 53 2.738587 TGTCCCTAGTGAGCCTCTAG 57.261 55.000 0.00 0.00 35.86 2.43
53 54 5.080337 CAATATGTCCCTAGTGAGCCTCTA 58.920 45.833 0.00 0.00 0.00 2.43
54 55 3.900601 CAATATGTCCCTAGTGAGCCTCT 59.099 47.826 0.00 0.00 0.00 3.69
55 56 3.643792 ACAATATGTCCCTAGTGAGCCTC 59.356 47.826 0.00 0.00 0.00 4.70
56 57 3.389329 CACAATATGTCCCTAGTGAGCCT 59.611 47.826 0.00 0.00 0.00 4.58
57 58 3.495100 CCACAATATGTCCCTAGTGAGCC 60.495 52.174 0.00 0.00 0.00 4.70
58 59 3.134804 ACCACAATATGTCCCTAGTGAGC 59.865 47.826 0.00 0.00 0.00 4.26
59 60 4.651503 AGACCACAATATGTCCCTAGTGAG 59.348 45.833 0.00 0.00 31.76 3.51
60 61 4.620723 AGACCACAATATGTCCCTAGTGA 58.379 43.478 0.00 0.00 31.76 3.41
61 62 6.042093 ACATAGACCACAATATGTCCCTAGTG 59.958 42.308 0.00 0.00 37.98 2.74
62 63 6.143915 ACATAGACCACAATATGTCCCTAGT 58.856 40.000 0.00 0.00 37.98 2.57
63 64 6.672266 ACATAGACCACAATATGTCCCTAG 57.328 41.667 0.00 0.00 37.98 3.02
64 65 8.736097 AATACATAGACCACAATATGTCCCTA 57.264 34.615 1.37 0.00 40.78 3.53
65 66 7.292356 TGAATACATAGACCACAATATGTCCCT 59.708 37.037 1.37 0.00 40.78 4.20
66 67 7.387948 GTGAATACATAGACCACAATATGTCCC 59.612 40.741 1.37 0.00 40.78 4.46
67 68 7.931407 TGTGAATACATAGACCACAATATGTCC 59.069 37.037 1.37 0.00 40.78 4.02
68 69 8.765219 GTGTGAATACATAGACCACAATATGTC 58.235 37.037 0.00 0.00 40.78 3.06
69 70 7.438160 CGTGTGAATACATAGACCACAATATGT 59.562 37.037 0.00 3.60 43.31 2.29
70 71 7.438160 ACGTGTGAATACATAGACCACAATATG 59.562 37.037 0.00 0.00 39.13 1.78
71 72 7.438160 CACGTGTGAATACATAGACCACAATAT 59.562 37.037 7.58 0.00 39.13 1.28
72 73 6.754675 CACGTGTGAATACATAGACCACAATA 59.245 38.462 7.58 0.00 39.13 1.90
73 74 5.580691 CACGTGTGAATACATAGACCACAAT 59.419 40.000 7.58 0.00 39.13 2.71
74 75 4.926832 CACGTGTGAATACATAGACCACAA 59.073 41.667 7.58 0.00 39.13 3.33
75 76 4.021807 ACACGTGTGAATACATAGACCACA 60.022 41.667 22.71 0.00 39.39 4.17
76 77 4.491676 ACACGTGTGAATACATAGACCAC 58.508 43.478 22.71 0.00 39.39 4.16
77 78 4.794278 ACACGTGTGAATACATAGACCA 57.206 40.909 22.71 0.00 39.39 4.02
78 79 7.112565 CGTAATACACGTGTGAATACATAGACC 59.887 40.741 30.83 6.57 45.82 3.85
79 80 7.979037 CGTAATACACGTGTGAATACATAGAC 58.021 38.462 30.83 14.41 45.82 2.59
95 96 8.746922 TGTATTATCCGGAAATCGTAATACAC 57.253 34.615 28.04 16.29 42.13 2.90
96 97 8.579006 ACTGTATTATCCGGAAATCGTAATACA 58.421 33.333 28.89 28.89 43.27 2.29
97 98 8.976986 ACTGTATTATCCGGAAATCGTAATAC 57.023 34.615 25.06 25.06 40.20 1.89
102 103 7.758528 GCTATAACTGTATTATCCGGAAATCGT 59.241 37.037 9.01 5.81 37.11 3.73
103 104 7.758076 TGCTATAACTGTATTATCCGGAAATCG 59.242 37.037 9.01 5.25 38.88 3.34
104 105 8.997621 TGCTATAACTGTATTATCCGGAAATC 57.002 34.615 9.01 5.33 0.00 2.17
105 106 9.383519 CATGCTATAACTGTATTATCCGGAAAT 57.616 33.333 9.01 12.31 0.00 2.17
106 107 8.590204 TCATGCTATAACTGTATTATCCGGAAA 58.410 33.333 9.01 4.74 0.00 3.13
107 108 8.129496 TCATGCTATAACTGTATTATCCGGAA 57.871 34.615 9.01 0.00 0.00 4.30
108 109 7.712204 TCATGCTATAACTGTATTATCCGGA 57.288 36.000 6.61 6.61 0.00 5.14
109 110 8.948631 ATTCATGCTATAACTGTATTATCCGG 57.051 34.615 0.00 0.00 0.00 5.14
187 188 4.137543 GTGTTGGAAATATGCCCTAGAGG 58.862 47.826 0.00 0.00 39.47 3.69
188 189 4.780815 TGTGTTGGAAATATGCCCTAGAG 58.219 43.478 0.00 0.00 0.00 2.43
189 190 4.853468 TGTGTTGGAAATATGCCCTAGA 57.147 40.909 0.00 0.00 0.00 2.43
190 191 5.707298 CCTATGTGTTGGAAATATGCCCTAG 59.293 44.000 0.00 0.00 0.00 3.02
191 192 5.133660 ACCTATGTGTTGGAAATATGCCCTA 59.866 40.000 0.00 0.00 0.00 3.53
192 193 4.079212 ACCTATGTGTTGGAAATATGCCCT 60.079 41.667 0.00 0.00 0.00 5.19
193 194 4.215109 ACCTATGTGTTGGAAATATGCCC 58.785 43.478 0.00 0.00 0.00 5.36
194 195 4.887071 TGACCTATGTGTTGGAAATATGCC 59.113 41.667 0.00 0.00 0.00 4.40
195 196 6.639632 ATGACCTATGTGTTGGAAATATGC 57.360 37.500 0.00 0.00 0.00 3.14
196 197 6.919662 GCAATGACCTATGTGTTGGAAATATG 59.080 38.462 0.00 0.00 0.00 1.78
197 198 6.040842 GGCAATGACCTATGTGTTGGAAATAT 59.959 38.462 0.00 0.00 0.00 1.28
198 199 5.359576 GGCAATGACCTATGTGTTGGAAATA 59.640 40.000 0.00 0.00 0.00 1.40
199 200 4.160252 GGCAATGACCTATGTGTTGGAAAT 59.840 41.667 0.00 0.00 0.00 2.17
200 201 3.509575 GGCAATGACCTATGTGTTGGAAA 59.490 43.478 0.00 0.00 0.00 3.13
201 202 3.088532 GGCAATGACCTATGTGTTGGAA 58.911 45.455 0.00 0.00 0.00 3.53
202 203 2.620367 GGGCAATGACCTATGTGTTGGA 60.620 50.000 0.00 0.00 0.00 3.53
203 204 1.750778 GGGCAATGACCTATGTGTTGG 59.249 52.381 0.00 0.00 0.00 3.77
204 205 1.750778 GGGGCAATGACCTATGTGTTG 59.249 52.381 4.56 0.00 0.00 3.33
205 206 1.640670 AGGGGCAATGACCTATGTGTT 59.359 47.619 4.56 0.00 34.71 3.32
206 207 1.298953 AGGGGCAATGACCTATGTGT 58.701 50.000 4.56 0.00 34.71 3.72
207 208 2.442236 AAGGGGCAATGACCTATGTG 57.558 50.000 4.56 0.00 35.64 3.21
217 218 0.108396 GTTGTGGCAAAAGGGGCAAT 59.892 50.000 0.00 0.00 45.54 3.56
496 497 8.046708 TGCACATGTACTGGTTATATTTTCTCT 58.953 33.333 0.00 0.00 0.00 3.10
500 501 9.585099 CAATTGCACATGTACTGGTTATATTTT 57.415 29.630 0.00 0.00 0.00 1.82
645 705 6.428083 TCTAGACCAACATGGACTTTGTTA 57.572 37.500 6.68 0.00 39.42 2.41
951 1025 7.226128 AGTGAGCATATCAACATCATTACTGTG 59.774 37.037 0.00 0.00 40.43 3.66
1035 1120 4.022503 GCTTCCCTTACGACTTCGGTATAT 60.023 45.833 3.30 0.00 44.95 0.86
1061 1146 6.873605 CACATTCCAAAGTTTTAATCCCTTCC 59.126 38.462 0.00 0.00 0.00 3.46
1094 1179 1.964373 GACAACCCCATTGCGTCGT 60.964 57.895 0.00 0.00 42.62 4.34
1111 1196 0.911769 AGATGGCCATCTTGGAACGA 59.088 50.000 37.67 0.00 45.31 3.85
1263 1348 6.536941 GCGAAGAGTTGAGAGAGGAAATTAAT 59.463 38.462 0.00 0.00 0.00 1.40
1622 1927 6.681777 TCATGGACTGATGATAGATTACACG 58.318 40.000 0.00 0.00 0.00 4.49
1684 1989 4.219115 ACCACACCCACATGACAATAAAA 58.781 39.130 0.00 0.00 0.00 1.52
1733 2038 2.425312 ACCGCAACACAAAAATCACAGA 59.575 40.909 0.00 0.00 0.00 3.41
1779 2084 1.448985 ATACACCACACCGATTGCAC 58.551 50.000 0.00 0.00 0.00 4.57
1799 2104 8.002984 TGCACATTTTCATAGATGAATGACAT 57.997 30.769 11.14 0.00 45.30 3.06
2044 2351 6.899393 ATCATGGCTTTTACTTCAAACTGA 57.101 33.333 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.