Multiple sequence alignment - TraesCS2D01G318600

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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 TraesCS2D01G318600 chr2D 100.000 2462 0 0 1 2462 408361401 408363862 0.000000e+00 4547
1 TraesCS2D01G318600 chr2D 76.504 349 68 11 449 790 407982059 407981718 7.000000e-41 178
2 TraesCS2D01G318600 chr2A 93.579 2305 77 22 185 2462 576357629 576359889 0.000000e+00 3371
3 TraesCS2D01G318600 chr2A 75.522 335 74 6 460 790 575694661 575694331 9.110000e-35 158
4 TraesCS2D01G318600 chr2B 95.528 1789 47 16 355 2128 483681065 483682835 0.000000e+00 2830
5 TraesCS2D01G318600 chr2B 87.819 353 19 14 2133 2462 483683151 483683502 2.300000e-105 392
6 TraesCS2D01G318600 chr2B 76.119 335 72 6 460 790 483469788 483469458 4.210000e-38 169
7 TraesCS2D01G318600 chr2B 98.734 79 1 0 239 317 483680991 483681069 9.180000e-30 141
8 TraesCS2D01G318600 chr3A 90.625 128 11 1 60 187 685427584 685427710 4.210000e-38 169


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 TraesCS2D01G318600 chr2D 408361401 408363862 2461 False 4547 4547 100.000 1 2462 1 chr2D.!!$F1 2461
1 TraesCS2D01G318600 chr2A 576357629 576359889 2260 False 3371 3371 93.579 185 2462 1 chr2A.!!$F1 2277
2 TraesCS2D01G318600 chr2B 483680991 483683502 2511 False 1121 2830 94.027 239 2462 3 chr2B.!!$F1 2223


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
36 37 0.035881 CAGAAGCCTCTGTGCAAGGA 59.964 55.0 7.13 0.0 43.64 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 1872 0.16747 TTACTCAAGACGACGAGGCG 59.833 55.0 0.0 0.0 33.36 5.52 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
35 36 2.552802 CAGAAGCCTCTGTGCAAGG 58.447 57.895 4.01 0.00 43.64 3.61
36 37 0.035881 CAGAAGCCTCTGTGCAAGGA 59.964 55.000 7.13 0.00 43.64 3.36
37 38 0.767375 AGAAGCCTCTGTGCAAGGAA 59.233 50.000 7.13 0.00 35.83 3.36
38 39 0.877743 GAAGCCTCTGTGCAAGGAAC 59.122 55.000 7.13 0.00 35.83 3.62
39 40 0.886490 AAGCCTCTGTGCAAGGAACG 60.886 55.000 7.13 0.00 35.83 3.95
40 41 1.301716 GCCTCTGTGCAAGGAACGA 60.302 57.895 7.13 0.00 35.83 3.85
41 42 1.294659 GCCTCTGTGCAAGGAACGAG 61.295 60.000 7.13 0.00 35.83 4.18
42 43 0.671781 CCTCTGTGCAAGGAACGAGG 60.672 60.000 0.00 0.00 35.83 4.63
43 44 1.294659 CTCTGTGCAAGGAACGAGGC 61.295 60.000 0.00 0.00 0.00 4.70
44 45 2.664851 TGTGCAAGGAACGAGGCG 60.665 61.111 0.00 0.00 0.00 5.52
45 46 2.357034 GTGCAAGGAACGAGGCGA 60.357 61.111 0.00 0.00 0.00 5.54
46 47 2.048222 TGCAAGGAACGAGGCGAG 60.048 61.111 0.00 0.00 0.00 5.03
47 48 2.815647 GCAAGGAACGAGGCGAGG 60.816 66.667 0.00 0.00 0.00 4.63
48 49 2.125512 CAAGGAACGAGGCGAGGG 60.126 66.667 0.00 0.00 0.00 4.30
49 50 4.083862 AAGGAACGAGGCGAGGGC 62.084 66.667 0.00 0.00 38.90 5.19
51 52 3.145551 GGAACGAGGCGAGGGCTA 61.146 66.667 0.00 0.00 38.98 3.93
52 53 2.499827 GGAACGAGGCGAGGGCTAT 61.500 63.158 0.00 0.00 38.98 2.97
53 54 1.442148 GAACGAGGCGAGGGCTATT 59.558 57.895 0.00 0.00 38.98 1.73
54 55 0.672342 GAACGAGGCGAGGGCTATTA 59.328 55.000 0.00 0.00 38.98 0.98
55 56 0.674534 AACGAGGCGAGGGCTATTAG 59.325 55.000 0.00 0.00 38.98 1.73
56 57 1.080434 CGAGGCGAGGGCTATTAGC 60.080 63.158 7.16 7.16 38.98 3.09
57 58 1.080434 GAGGCGAGGGCTATTAGCG 60.080 63.158 9.50 0.00 43.62 4.26
58 59 1.524863 GAGGCGAGGGCTATTAGCGA 61.525 60.000 9.50 0.00 43.62 4.93
59 60 1.373121 GGCGAGGGCTATTAGCGAC 60.373 63.158 9.50 5.40 43.62 5.19
60 61 1.660917 GCGAGGGCTATTAGCGACT 59.339 57.895 9.50 9.91 43.62 4.18
61 62 0.879765 GCGAGGGCTATTAGCGACTA 59.120 55.000 9.50 0.00 43.62 2.59
62 63 1.135632 GCGAGGGCTATTAGCGACTAG 60.136 57.143 9.50 10.93 43.62 2.57
63 64 2.152830 CGAGGGCTATTAGCGACTAGT 58.847 52.381 9.50 0.00 43.62 2.57
64 65 2.095668 CGAGGGCTATTAGCGACTAGTG 60.096 54.545 0.00 0.00 43.62 2.74
65 66 3.147629 GAGGGCTATTAGCGACTAGTGA 58.852 50.000 0.00 0.00 43.62 3.41
66 67 3.563223 AGGGCTATTAGCGACTAGTGAA 58.437 45.455 0.00 0.00 43.62 3.18
67 68 4.153411 AGGGCTATTAGCGACTAGTGAAT 58.847 43.478 0.00 0.00 43.62 2.57
68 69 4.218852 AGGGCTATTAGCGACTAGTGAATC 59.781 45.833 0.00 0.00 43.62 2.52
69 70 4.487019 GGCTATTAGCGACTAGTGAATCC 58.513 47.826 0.00 0.00 43.62 3.01
70 71 4.022242 GGCTATTAGCGACTAGTGAATCCA 60.022 45.833 0.00 0.00 43.62 3.41
71 72 5.509163 GGCTATTAGCGACTAGTGAATCCAA 60.509 44.000 0.00 0.00 43.62 3.53
72 73 5.983720 GCTATTAGCGACTAGTGAATCCAAA 59.016 40.000 0.00 0.00 0.00 3.28
73 74 6.647067 GCTATTAGCGACTAGTGAATCCAAAT 59.353 38.462 0.00 0.00 0.00 2.32
74 75 6.851222 ATTAGCGACTAGTGAATCCAAATG 57.149 37.500 0.00 0.00 0.00 2.32
75 76 4.471904 AGCGACTAGTGAATCCAAATGA 57.528 40.909 0.00 0.00 0.00 2.57
76 77 4.184629 AGCGACTAGTGAATCCAAATGAC 58.815 43.478 0.00 0.00 0.00 3.06
77 78 3.309954 GCGACTAGTGAATCCAAATGACC 59.690 47.826 0.00 0.00 0.00 4.02
78 79 4.503910 CGACTAGTGAATCCAAATGACCA 58.496 43.478 0.00 0.00 0.00 4.02
79 80 4.568359 CGACTAGTGAATCCAAATGACCAG 59.432 45.833 0.00 0.00 0.00 4.00
80 81 4.848357 ACTAGTGAATCCAAATGACCAGG 58.152 43.478 0.00 0.00 0.00 4.45
81 82 4.536090 ACTAGTGAATCCAAATGACCAGGA 59.464 41.667 0.00 0.00 35.59 3.86
82 83 4.387026 AGTGAATCCAAATGACCAGGAA 57.613 40.909 0.00 0.00 34.62 3.36
83 84 4.739793 AGTGAATCCAAATGACCAGGAAA 58.260 39.130 0.00 0.00 34.62 3.13
84 85 5.147032 AGTGAATCCAAATGACCAGGAAAA 58.853 37.500 0.00 0.00 34.62 2.29
85 86 5.602145 AGTGAATCCAAATGACCAGGAAAAA 59.398 36.000 0.00 0.00 34.62 1.94
134 135 9.411189 TCTTTTGTAGGTTTGTAAATTACACCT 57.589 29.630 16.32 16.32 38.63 4.00
135 136 9.458374 CTTTTGTAGGTTTGTAAATTACACCTG 57.542 33.333 19.55 4.32 36.29 4.00
136 137 8.522542 TTTGTAGGTTTGTAAATTACACCTGT 57.477 30.769 19.55 4.68 36.29 4.00
137 138 9.624373 TTTGTAGGTTTGTAAATTACACCTGTA 57.376 29.630 19.55 9.62 36.29 2.74
138 139 8.606040 TGTAGGTTTGTAAATTACACCTGTAC 57.394 34.615 19.55 13.49 36.29 2.90
139 140 8.209584 TGTAGGTTTGTAAATTACACCTGTACA 58.790 33.333 19.55 15.23 36.29 2.90
140 141 9.223099 GTAGGTTTGTAAATTACACCTGTACAT 57.777 33.333 19.55 8.70 36.29 2.29
142 143 9.796180 AGGTTTGTAAATTACACCTGTACATAA 57.204 29.630 12.71 0.00 38.63 1.90
151 152 8.833231 ATTACACCTGTACATAATCTACATGC 57.167 34.615 0.00 0.00 0.00 4.06
152 153 5.289595 ACACCTGTACATAATCTACATGCG 58.710 41.667 0.00 0.00 0.00 4.73
153 154 5.163447 ACACCTGTACATAATCTACATGCGT 60.163 40.000 0.00 0.00 0.00 5.24
154 155 6.040054 ACACCTGTACATAATCTACATGCGTA 59.960 38.462 0.00 0.00 0.00 4.42
155 156 7.090808 CACCTGTACATAATCTACATGCGTAT 58.909 38.462 0.00 0.00 0.00 3.06
156 157 7.598869 CACCTGTACATAATCTACATGCGTATT 59.401 37.037 0.00 0.00 0.00 1.89
157 158 8.799367 ACCTGTACATAATCTACATGCGTATTA 58.201 33.333 0.00 0.00 0.00 0.98
158 159 9.073368 CCTGTACATAATCTACATGCGTATTAC 57.927 37.037 0.00 0.00 0.00 1.89
159 160 9.841880 CTGTACATAATCTACATGCGTATTACT 57.158 33.333 0.00 0.00 0.00 2.24
166 167 8.589335 AATCTACATGCGTATTACTTTACAGG 57.411 34.615 0.00 0.00 0.00 4.00
167 168 7.104043 TCTACATGCGTATTACTTTACAGGT 57.896 36.000 0.00 0.00 0.00 4.00
168 169 7.198390 TCTACATGCGTATTACTTTACAGGTC 58.802 38.462 0.00 0.00 0.00 3.85
169 170 5.974108 ACATGCGTATTACTTTACAGGTCT 58.026 37.500 0.00 0.00 0.00 3.85
170 171 6.403878 ACATGCGTATTACTTTACAGGTCTT 58.596 36.000 0.00 0.00 0.00 3.01
171 172 6.534079 ACATGCGTATTACTTTACAGGTCTTC 59.466 38.462 0.00 0.00 0.00 2.87
172 173 5.413499 TGCGTATTACTTTACAGGTCTTCC 58.587 41.667 0.00 0.00 0.00 3.46
173 174 5.047164 TGCGTATTACTTTACAGGTCTTCCA 60.047 40.000 0.00 0.00 35.89 3.53
174 175 5.870978 GCGTATTACTTTACAGGTCTTCCAA 59.129 40.000 0.00 0.00 35.89 3.53
175 176 6.537660 GCGTATTACTTTACAGGTCTTCCAAT 59.462 38.462 0.00 0.00 35.89 3.16
176 177 7.254353 GCGTATTACTTTACAGGTCTTCCAATC 60.254 40.741 0.00 0.00 35.89 2.67
177 178 7.043590 CGTATTACTTTACAGGTCTTCCAATCG 60.044 40.741 0.00 0.00 35.89 3.34
178 179 3.939066 ACTTTACAGGTCTTCCAATCGG 58.061 45.455 0.00 0.00 35.89 4.18
179 180 3.270877 CTTTACAGGTCTTCCAATCGGG 58.729 50.000 0.00 0.00 35.89 5.14
180 181 1.200519 TACAGGTCTTCCAATCGGGG 58.799 55.000 0.00 0.00 37.22 5.73
181 182 1.452108 CAGGTCTTCCAATCGGGGC 60.452 63.158 0.00 0.00 37.22 5.80
182 183 2.124278 GGTCTTCCAATCGGGGCC 60.124 66.667 0.00 0.00 37.22 5.80
183 184 2.124278 GTCTTCCAATCGGGGCCC 60.124 66.667 15.76 15.76 37.22 5.80
201 202 2.863740 GCCCAAAAGTTTTTCGACAAGG 59.136 45.455 0.00 0.00 0.00 3.61
222 223 1.297598 GCATCGCGCACGCTAAAAT 60.298 52.632 13.70 0.00 41.79 1.82
223 224 1.255635 GCATCGCGCACGCTAAAATC 61.256 55.000 13.70 0.00 41.79 2.17
318 353 9.793245 CTAGCATTTTAATTTCGAGTTATACCG 57.207 33.333 0.00 0.00 0.00 4.02
319 354 7.636326 AGCATTTTAATTTCGAGTTATACCGG 58.364 34.615 0.00 0.00 0.00 5.28
320 355 7.496591 AGCATTTTAATTTCGAGTTATACCGGA 59.503 33.333 9.46 0.00 0.00 5.14
321 356 8.124199 GCATTTTAATTTCGAGTTATACCGGAA 58.876 33.333 9.46 0.00 0.00 4.30
325 360 6.998258 AATTTCGAGTTATACCGGAATACG 57.002 37.500 9.46 4.61 43.80 3.06
340 375 4.474113 GGAATACGAGTACCAATCTAGCG 58.526 47.826 0.00 0.00 0.00 4.26
341 376 3.555917 ATACGAGTACCAATCTAGCGC 57.444 47.619 0.00 0.00 0.00 5.92
342 377 1.390565 ACGAGTACCAATCTAGCGCT 58.609 50.000 17.26 17.26 0.00 5.92
343 378 2.569059 ACGAGTACCAATCTAGCGCTA 58.431 47.619 17.75 17.75 0.00 4.26
344 379 2.947652 ACGAGTACCAATCTAGCGCTAA 59.052 45.455 19.37 9.97 0.00 3.09
345 380 3.568853 ACGAGTACCAATCTAGCGCTAAT 59.431 43.478 19.37 11.81 0.00 1.73
346 381 4.758674 ACGAGTACCAATCTAGCGCTAATA 59.241 41.667 19.37 10.08 0.00 0.98
347 382 5.106634 ACGAGTACCAATCTAGCGCTAATAG 60.107 44.000 19.37 9.11 0.00 1.73
348 383 5.642686 GAGTACCAATCTAGCGCTAATAGG 58.357 45.833 19.37 18.57 0.00 2.57
349 384 5.322754 AGTACCAATCTAGCGCTAATAGGA 58.677 41.667 19.37 12.43 0.00 2.94
350 385 4.792521 ACCAATCTAGCGCTAATAGGAG 57.207 45.455 19.37 7.48 0.00 3.69
351 386 4.153411 ACCAATCTAGCGCTAATAGGAGT 58.847 43.478 19.37 8.54 0.00 3.85
352 387 5.322754 ACCAATCTAGCGCTAATAGGAGTA 58.677 41.667 19.37 0.00 0.00 2.59
353 388 5.416326 ACCAATCTAGCGCTAATAGGAGTAG 59.584 44.000 19.37 7.12 0.00 2.57
354 389 5.416326 CCAATCTAGCGCTAATAGGAGTAGT 59.584 44.000 19.37 0.00 0.00 2.73
355 390 6.598457 CCAATCTAGCGCTAATAGGAGTAGTA 59.402 42.308 19.37 0.00 0.00 1.82
356 391 7.283580 CCAATCTAGCGCTAATAGGAGTAGTAT 59.716 40.741 19.37 0.00 0.00 2.12
357 392 9.327628 CAATCTAGCGCTAATAGGAGTAGTATA 57.672 37.037 19.37 0.00 0.00 1.47
358 393 8.891671 ATCTAGCGCTAATAGGAGTAGTATAC 57.108 38.462 19.37 0.00 43.47 1.47
807 842 1.755783 CCCCTTGGGCATCTTGCTC 60.756 63.158 0.00 0.00 46.11 4.26
871 906 1.580815 CAACCAAACGCAAAGCCATT 58.419 45.000 0.00 0.00 0.00 3.16
883 918 3.420893 CAAAGCCATTAGTGTCCCAGAA 58.579 45.455 0.00 0.00 0.00 3.02
922 969 6.183360 GGATGGAAAATGTAGTAGGTCTTTGC 60.183 42.308 0.00 0.00 0.00 3.68
1485 1532 1.153823 CAGGTTGGCGACGAGGTAG 60.154 63.158 0.00 0.00 0.00 3.18
1806 1853 1.518325 CCTGGTCGTTGTACATGCAA 58.482 50.000 0.00 0.00 0.00 4.08
1901 1948 0.872021 GACACACCGCCTGATCGATC 60.872 60.000 18.72 18.72 0.00 3.69
1909 1957 1.132588 GCCTGATCGATCACGTTAGC 58.867 55.000 23.99 16.52 40.69 3.09
1930 1978 3.126858 GCGCCATGAACAAGATTCACTTA 59.873 43.478 0.00 0.00 37.03 2.24
1998 2046 6.837992 ACGTACGATAAAATGTCATTTTGCT 58.162 32.000 26.74 16.84 42.08 3.91
1999 2047 7.966111 ACGTACGATAAAATGTCATTTTGCTA 58.034 30.769 26.74 12.53 42.08 3.49
2000 2048 8.444715 ACGTACGATAAAATGTCATTTTGCTAA 58.555 29.630 26.74 12.22 42.08 3.09
2067 2120 1.467342 GCGGATGACTGTAAACCCAAC 59.533 52.381 0.00 0.00 0.00 3.77
2083 2136 5.897377 ACCCAACTGTTGATATTTACTGC 57.103 39.130 21.49 0.00 0.00 4.40
2172 2536 0.609151 TCTGGCAACCGGATTCGTTA 59.391 50.000 9.46 0.00 33.41 3.18
2318 2694 6.813649 TCTCATAAAAGTCCGATCTTGTCAAG 59.186 38.462 6.21 6.21 0.00 3.02
2329 2712 3.986996 TCTTGTCAAGCTCATCCATCA 57.013 42.857 7.78 0.00 0.00 3.07
2330 2713 3.603532 TCTTGTCAAGCTCATCCATCAC 58.396 45.455 7.78 0.00 0.00 3.06
2340 2723 1.827344 TCATCCATCACTCACTCGCTT 59.173 47.619 0.00 0.00 0.00 4.68
2410 2793 6.427974 CGAGAGCACAATCGACTAATAACTA 58.572 40.000 0.00 0.00 41.40 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.436824 GCCTCGGGCTTGTTCTCC 60.437 66.667 7.58 0.00 46.69 3.71
18 19 0.767375 TTCCTTGCACAGAGGCTTCT 59.233 50.000 0.00 0.00 34.17 2.85
19 20 0.877743 GTTCCTTGCACAGAGGCTTC 59.122 55.000 0.00 0.00 34.17 3.86
20 21 0.886490 CGTTCCTTGCACAGAGGCTT 60.886 55.000 0.00 0.00 34.17 4.35
21 22 1.302033 CGTTCCTTGCACAGAGGCT 60.302 57.895 0.00 0.00 34.17 4.58
22 23 1.294659 CTCGTTCCTTGCACAGAGGC 61.295 60.000 0.00 0.00 34.17 4.70
23 24 0.671781 CCTCGTTCCTTGCACAGAGG 60.672 60.000 0.00 0.00 39.18 3.69
24 25 1.294659 GCCTCGTTCCTTGCACAGAG 61.295 60.000 0.00 0.00 0.00 3.35
25 26 1.301716 GCCTCGTTCCTTGCACAGA 60.302 57.895 0.00 0.00 0.00 3.41
26 27 2.671177 CGCCTCGTTCCTTGCACAG 61.671 63.158 0.00 0.00 0.00 3.66
27 28 2.664851 CGCCTCGTTCCTTGCACA 60.665 61.111 0.00 0.00 0.00 4.57
28 29 2.357034 TCGCCTCGTTCCTTGCAC 60.357 61.111 0.00 0.00 0.00 4.57
29 30 2.048222 CTCGCCTCGTTCCTTGCA 60.048 61.111 0.00 0.00 0.00 4.08
30 31 2.815647 CCTCGCCTCGTTCCTTGC 60.816 66.667 0.00 0.00 0.00 4.01
31 32 2.125512 CCCTCGCCTCGTTCCTTG 60.126 66.667 0.00 0.00 0.00 3.61
32 33 4.083862 GCCCTCGCCTCGTTCCTT 62.084 66.667 0.00 0.00 0.00 3.36
33 34 2.930777 ATAGCCCTCGCCTCGTTCCT 62.931 60.000 0.00 0.00 34.57 3.36
34 35 2.029307 AATAGCCCTCGCCTCGTTCC 62.029 60.000 0.00 0.00 34.57 3.62
35 36 0.672342 TAATAGCCCTCGCCTCGTTC 59.328 55.000 0.00 0.00 34.57 3.95
36 37 0.674534 CTAATAGCCCTCGCCTCGTT 59.325 55.000 0.00 0.00 34.57 3.85
37 38 1.807495 GCTAATAGCCCTCGCCTCGT 61.807 60.000 0.00 0.00 34.48 4.18
38 39 1.080434 GCTAATAGCCCTCGCCTCG 60.080 63.158 0.00 0.00 34.48 4.63
39 40 1.080434 CGCTAATAGCCCTCGCCTC 60.080 63.158 6.69 0.00 38.18 4.70
40 41 1.530891 TCGCTAATAGCCCTCGCCT 60.531 57.895 6.69 0.00 38.18 5.52
41 42 1.373121 GTCGCTAATAGCCCTCGCC 60.373 63.158 6.69 0.00 38.18 5.54
42 43 0.879765 TAGTCGCTAATAGCCCTCGC 59.120 55.000 6.69 0.00 38.18 5.03
43 44 2.095668 CACTAGTCGCTAATAGCCCTCG 60.096 54.545 6.69 2.18 38.18 4.63
44 45 3.147629 TCACTAGTCGCTAATAGCCCTC 58.852 50.000 6.69 0.00 38.18 4.30
45 46 3.225177 TCACTAGTCGCTAATAGCCCT 57.775 47.619 6.69 5.60 38.18 5.19
46 47 4.487019 GATTCACTAGTCGCTAATAGCCC 58.513 47.826 6.69 0.00 38.18 5.19
47 48 4.022242 TGGATTCACTAGTCGCTAATAGCC 60.022 45.833 6.69 0.00 38.18 3.93
48 49 5.122512 TGGATTCACTAGTCGCTAATAGC 57.877 43.478 1.41 1.41 38.02 2.97
49 50 7.867909 TCATTTGGATTCACTAGTCGCTAATAG 59.132 37.037 0.00 0.00 0.00 1.73
50 51 7.652105 GTCATTTGGATTCACTAGTCGCTAATA 59.348 37.037 0.00 0.00 0.00 0.98
51 52 6.480320 GTCATTTGGATTCACTAGTCGCTAAT 59.520 38.462 0.00 0.00 0.00 1.73
52 53 5.810587 GTCATTTGGATTCACTAGTCGCTAA 59.189 40.000 0.00 0.00 0.00 3.09
53 54 5.348986 GTCATTTGGATTCACTAGTCGCTA 58.651 41.667 0.00 0.00 0.00 4.26
54 55 4.184629 GTCATTTGGATTCACTAGTCGCT 58.815 43.478 0.00 0.00 0.00 4.93
55 56 3.309954 GGTCATTTGGATTCACTAGTCGC 59.690 47.826 0.00 0.00 0.00 5.19
56 57 4.503910 TGGTCATTTGGATTCACTAGTCG 58.496 43.478 0.00 0.00 0.00 4.18
57 58 4.878397 CCTGGTCATTTGGATTCACTAGTC 59.122 45.833 0.00 0.00 0.00 2.59
58 59 4.536090 TCCTGGTCATTTGGATTCACTAGT 59.464 41.667 0.00 0.00 0.00 2.57
59 60 5.102953 TCCTGGTCATTTGGATTCACTAG 57.897 43.478 0.00 0.00 0.00 2.57
60 61 5.512942 TTCCTGGTCATTTGGATTCACTA 57.487 39.130 0.00 0.00 0.00 2.74
61 62 4.387026 TTCCTGGTCATTTGGATTCACT 57.613 40.909 0.00 0.00 0.00 3.41
62 63 5.467035 TTTTCCTGGTCATTTGGATTCAC 57.533 39.130 0.00 0.00 0.00 3.18
108 109 9.411189 AGGTGTAATTTACAAACCTACAAAAGA 57.589 29.630 14.10 0.00 40.93 2.52
109 110 9.458374 CAGGTGTAATTTACAAACCTACAAAAG 57.542 33.333 14.91 3.07 40.93 2.27
110 111 8.968969 ACAGGTGTAATTTACAAACCTACAAAA 58.031 29.630 14.91 0.00 40.93 2.44
111 112 8.522542 ACAGGTGTAATTTACAAACCTACAAA 57.477 30.769 14.91 0.00 40.93 2.83
112 113 9.054922 GTACAGGTGTAATTTACAAACCTACAA 57.945 33.333 14.91 5.09 40.93 2.41
113 114 8.209584 TGTACAGGTGTAATTTACAAACCTACA 58.790 33.333 14.91 13.87 40.93 2.74
114 115 8.606040 TGTACAGGTGTAATTTACAAACCTAC 57.394 34.615 14.91 12.16 40.93 3.18
116 117 9.796180 TTATGTACAGGTGTAATTTACAAACCT 57.204 29.630 10.73 11.00 40.93 3.50
125 126 9.273016 GCATGTAGATTATGTACAGGTGTAATT 57.727 33.333 13.97 0.00 35.19 1.40
126 127 7.598869 CGCATGTAGATTATGTACAGGTGTAAT 59.401 37.037 16.05 0.22 37.71 1.89
127 128 6.921307 CGCATGTAGATTATGTACAGGTGTAA 59.079 38.462 16.05 0.00 37.71 2.41
128 129 6.443792 CGCATGTAGATTATGTACAGGTGTA 58.556 40.000 16.05 0.00 37.71 2.90
129 130 5.163447 ACGCATGTAGATTATGTACAGGTGT 60.163 40.000 21.59 21.59 45.85 4.16
130 131 5.289595 ACGCATGTAGATTATGTACAGGTG 58.710 41.667 20.54 20.54 44.33 4.00
131 132 5.531122 ACGCATGTAGATTATGTACAGGT 57.469 39.130 13.97 6.85 35.19 4.00
132 133 9.073368 GTAATACGCATGTAGATTATGTACAGG 57.927 37.037 9.34 9.34 35.71 4.00
133 134 9.841880 AGTAATACGCATGTAGATTATGTACAG 57.158 33.333 8.16 2.57 33.94 2.74
140 141 9.687210 CCTGTAAAGTAATACGCATGTAGATTA 57.313 33.333 0.00 0.00 33.17 1.75
141 142 8.202137 ACCTGTAAAGTAATACGCATGTAGATT 58.798 33.333 0.00 0.00 33.17 2.40
142 143 7.723324 ACCTGTAAAGTAATACGCATGTAGAT 58.277 34.615 0.00 0.00 33.17 1.98
143 144 7.067859 AGACCTGTAAAGTAATACGCATGTAGA 59.932 37.037 0.00 0.00 33.17 2.59
144 145 7.201145 AGACCTGTAAAGTAATACGCATGTAG 58.799 38.462 0.00 0.00 33.17 2.74
145 146 7.104043 AGACCTGTAAAGTAATACGCATGTA 57.896 36.000 0.00 0.00 34.45 2.29
146 147 5.974108 AGACCTGTAAAGTAATACGCATGT 58.026 37.500 0.00 0.00 0.00 3.21
147 148 6.018994 GGAAGACCTGTAAAGTAATACGCATG 60.019 42.308 0.00 0.00 0.00 4.06
148 149 6.047231 GGAAGACCTGTAAAGTAATACGCAT 58.953 40.000 0.00 0.00 0.00 4.73
149 150 5.047164 TGGAAGACCTGTAAAGTAATACGCA 60.047 40.000 0.00 0.00 37.04 5.24
150 151 5.413499 TGGAAGACCTGTAAAGTAATACGC 58.587 41.667 0.00 0.00 37.04 4.42
151 152 7.043590 CGATTGGAAGACCTGTAAAGTAATACG 60.044 40.741 0.00 0.00 37.04 3.06
152 153 7.224167 CCGATTGGAAGACCTGTAAAGTAATAC 59.776 40.741 0.00 0.00 37.49 1.89
153 154 7.270047 CCGATTGGAAGACCTGTAAAGTAATA 58.730 38.462 0.00 0.00 37.49 0.98
154 155 6.113411 CCGATTGGAAGACCTGTAAAGTAAT 58.887 40.000 0.00 0.00 37.49 1.89
155 156 5.484715 CCGATTGGAAGACCTGTAAAGTAA 58.515 41.667 0.00 0.00 37.49 2.24
156 157 4.081309 CCCGATTGGAAGACCTGTAAAGTA 60.081 45.833 0.00 0.00 37.49 2.24
157 158 3.307480 CCCGATTGGAAGACCTGTAAAGT 60.307 47.826 0.00 0.00 37.49 2.66
158 159 3.270877 CCCGATTGGAAGACCTGTAAAG 58.729 50.000 0.00 0.00 37.49 1.85
159 160 2.026636 CCCCGATTGGAAGACCTGTAAA 60.027 50.000 0.00 0.00 37.49 2.01
160 161 1.557832 CCCCGATTGGAAGACCTGTAA 59.442 52.381 0.00 0.00 37.49 2.41
161 162 1.200519 CCCCGATTGGAAGACCTGTA 58.799 55.000 0.00 0.00 37.49 2.74
162 163 1.991230 CCCCGATTGGAAGACCTGT 59.009 57.895 0.00 0.00 37.49 4.00
163 164 1.452108 GCCCCGATTGGAAGACCTG 60.452 63.158 0.00 0.00 37.49 4.00
164 165 2.680370 GGCCCCGATTGGAAGACCT 61.680 63.158 0.00 0.00 37.49 3.85
165 166 2.124278 GGCCCCGATTGGAAGACC 60.124 66.667 0.00 0.00 37.49 3.85
166 167 2.124278 GGGCCCCGATTGGAAGAC 60.124 66.667 12.23 0.00 37.49 3.01
167 168 1.794885 TTTGGGCCCCGATTGGAAGA 61.795 55.000 22.27 0.00 37.49 2.87
168 169 0.902516 TTTTGGGCCCCGATTGGAAG 60.903 55.000 22.27 0.00 37.49 3.46
169 170 0.902516 CTTTTGGGCCCCGATTGGAA 60.903 55.000 22.27 0.75 37.49 3.53
170 171 1.304879 CTTTTGGGCCCCGATTGGA 60.305 57.895 22.27 0.00 37.49 3.53
171 172 1.191489 AACTTTTGGGCCCCGATTGG 61.191 55.000 22.27 7.18 0.00 3.16
172 173 0.684535 AAACTTTTGGGCCCCGATTG 59.315 50.000 22.27 8.38 0.00 2.67
173 174 1.429930 AAAACTTTTGGGCCCCGATT 58.570 45.000 22.27 3.41 0.00 3.34
174 175 1.346395 GAAAAACTTTTGGGCCCCGAT 59.654 47.619 22.27 0.00 0.00 4.18
175 176 0.753867 GAAAAACTTTTGGGCCCCGA 59.246 50.000 22.27 4.75 0.00 5.14
176 177 0.598942 CGAAAAACTTTTGGGCCCCG 60.599 55.000 22.27 7.42 0.00 5.73
177 178 0.753867 TCGAAAAACTTTTGGGCCCC 59.246 50.000 22.27 0.85 0.00 5.80
178 179 1.137282 TGTCGAAAAACTTTTGGGCCC 59.863 47.619 17.59 17.59 30.78 5.80
179 180 2.588027 TGTCGAAAAACTTTTGGGCC 57.412 45.000 0.00 0.00 30.78 5.80
180 181 2.863740 CCTTGTCGAAAAACTTTTGGGC 59.136 45.455 0.00 0.00 32.20 5.36
181 182 3.131400 TCCCTTGTCGAAAAACTTTTGGG 59.869 43.478 2.30 2.30 30.97 4.12
182 183 4.359706 CTCCCTTGTCGAAAAACTTTTGG 58.640 43.478 0.00 0.00 0.00 3.28
183 184 3.796717 GCTCCCTTGTCGAAAAACTTTTG 59.203 43.478 0.00 0.00 0.00 2.44
317 352 4.474113 GCTAGATTGGTACTCGTATTCCG 58.526 47.826 0.00 0.00 38.13 4.30
318 353 4.474113 CGCTAGATTGGTACTCGTATTCC 58.526 47.826 0.00 0.00 0.00 3.01
319 354 3.913163 GCGCTAGATTGGTACTCGTATTC 59.087 47.826 0.00 0.00 0.00 1.75
320 355 3.568853 AGCGCTAGATTGGTACTCGTATT 59.431 43.478 8.99 0.00 0.00 1.89
321 356 3.147629 AGCGCTAGATTGGTACTCGTAT 58.852 45.455 8.99 0.00 0.00 3.06
322 357 2.569059 AGCGCTAGATTGGTACTCGTA 58.431 47.619 8.99 0.00 0.00 3.43
323 358 1.390565 AGCGCTAGATTGGTACTCGT 58.609 50.000 8.99 0.00 0.00 4.18
324 359 3.620929 TTAGCGCTAGATTGGTACTCG 57.379 47.619 17.98 0.00 0.00 4.18
325 360 5.415077 TCCTATTAGCGCTAGATTGGTACTC 59.585 44.000 24.27 0.00 0.00 2.59
326 361 5.322754 TCCTATTAGCGCTAGATTGGTACT 58.677 41.667 24.27 4.57 0.00 2.73
327 362 5.183522 ACTCCTATTAGCGCTAGATTGGTAC 59.816 44.000 24.27 0.00 0.00 3.34
328 363 5.322754 ACTCCTATTAGCGCTAGATTGGTA 58.677 41.667 24.27 10.93 0.00 3.25
329 364 4.153411 ACTCCTATTAGCGCTAGATTGGT 58.847 43.478 24.27 16.33 0.00 3.67
330 365 4.792521 ACTCCTATTAGCGCTAGATTGG 57.207 45.455 17.98 20.53 0.00 3.16
331 366 6.503589 ACTACTCCTATTAGCGCTAGATTG 57.496 41.667 17.98 13.69 0.00 2.67
332 367 9.328845 GTATACTACTCCTATTAGCGCTAGATT 57.671 37.037 17.98 8.20 0.00 2.40
333 368 8.484575 TGTATACTACTCCTATTAGCGCTAGAT 58.515 37.037 17.98 15.49 0.00 1.98
334 369 7.845037 TGTATACTACTCCTATTAGCGCTAGA 58.155 38.462 17.98 10.41 0.00 2.43
335 370 8.665643 ATGTATACTACTCCTATTAGCGCTAG 57.334 38.462 17.98 9.23 0.00 3.42
336 371 7.714377 GGATGTATACTACTCCTATTAGCGCTA 59.286 40.741 14.45 14.45 0.00 4.26
337 372 6.543100 GGATGTATACTACTCCTATTAGCGCT 59.457 42.308 17.26 17.26 0.00 5.92
338 373 6.318144 TGGATGTATACTACTCCTATTAGCGC 59.682 42.308 0.00 0.00 31.49 5.92
339 374 7.860918 TGGATGTATACTACTCCTATTAGCG 57.139 40.000 15.90 0.00 31.49 4.26
340 375 9.409918 TGATGGATGTATACTACTCCTATTAGC 57.590 37.037 15.90 4.71 31.49 3.09
343 378 9.026121 GTGTGATGGATGTATACTACTCCTATT 57.974 37.037 15.90 6.02 31.49 1.73
344 379 8.170730 TGTGTGATGGATGTATACTACTCCTAT 58.829 37.037 15.90 10.31 31.49 2.57
345 380 7.523415 TGTGTGATGGATGTATACTACTCCTA 58.477 38.462 15.90 7.34 31.49 2.94
346 381 6.373759 TGTGTGATGGATGTATACTACTCCT 58.626 40.000 15.90 6.42 31.49 3.69
347 382 6.650427 TGTGTGATGGATGTATACTACTCC 57.350 41.667 4.17 8.30 0.00 3.85
348 383 7.116948 GCATTGTGTGATGGATGTATACTACTC 59.883 40.741 4.17 0.00 0.00 2.59
349 384 6.931281 GCATTGTGTGATGGATGTATACTACT 59.069 38.462 4.17 0.00 0.00 2.57
350 385 6.128822 CGCATTGTGTGATGGATGTATACTAC 60.129 42.308 4.17 0.00 0.00 2.73
351 386 5.925969 CGCATTGTGTGATGGATGTATACTA 59.074 40.000 4.17 0.00 0.00 1.82
352 387 4.751600 CGCATTGTGTGATGGATGTATACT 59.248 41.667 4.17 0.00 0.00 2.12
353 388 4.749598 TCGCATTGTGTGATGGATGTATAC 59.250 41.667 0.00 0.00 31.05 1.47
354 389 4.954875 TCGCATTGTGTGATGGATGTATA 58.045 39.130 0.00 0.00 31.05 1.47
355 390 3.807553 TCGCATTGTGTGATGGATGTAT 58.192 40.909 0.00 0.00 31.05 2.29
356 391 3.258971 TCGCATTGTGTGATGGATGTA 57.741 42.857 0.00 0.00 31.05 2.29
357 392 2.112380 TCGCATTGTGTGATGGATGT 57.888 45.000 0.00 0.00 31.05 3.06
358 393 3.173599 GTTTCGCATTGTGTGATGGATG 58.826 45.455 0.00 0.00 36.69 3.51
552 587 2.126618 TACGCGTTCTGGCTCGTG 60.127 61.111 20.78 0.00 42.16 4.35
855 890 2.288152 ACACTAATGGCTTTGCGTTTGG 60.288 45.455 0.00 0.00 0.00 3.28
871 906 3.374988 CGTACGTATGTTCTGGGACACTA 59.625 47.826 7.22 0.00 31.30 2.74
883 918 0.387929 CCATCCCAGCGTACGTATGT 59.612 55.000 17.90 0.00 0.00 2.29
1485 1532 1.416813 CTCTGTTCATCAGCGTCGGC 61.417 60.000 0.00 0.00 43.32 5.54
1806 1853 1.516386 CGCGAGCAAGGACGTGTAT 60.516 57.895 0.00 0.00 35.70 2.29
1825 1872 0.167470 TTACTCAAGACGACGAGGCG 59.833 55.000 0.00 0.00 33.36 5.52
1869 1916 0.888619 GTGTGTCGGAGATGGAGTCA 59.111 55.000 0.00 0.00 40.67 3.41
1901 1948 0.515127 TTGTTCATGGCGCTAACGTG 59.485 50.000 7.64 2.23 42.83 4.49
1909 1957 3.837213 AAGTGAATCTTGTTCATGGCG 57.163 42.857 0.00 0.00 34.77 5.69
1945 1993 8.780249 ACGTACTAACTTTGCAAATGATTTAGT 58.220 29.630 24.22 24.22 31.94 2.24
1975 2023 8.814733 TTAGCAAAATGACATTTTATCGTACG 57.185 30.769 22.46 9.53 40.27 3.67
1993 2041 3.369756 CGCTCGTTCCAGTTATTAGCAAA 59.630 43.478 0.00 0.00 0.00 3.68
1998 2046 3.853831 TCACGCTCGTTCCAGTTATTA 57.146 42.857 0.00 0.00 0.00 0.98
1999 2047 2.736144 TCACGCTCGTTCCAGTTATT 57.264 45.000 0.00 0.00 0.00 1.40
2000 2048 2.961526 ATCACGCTCGTTCCAGTTAT 57.038 45.000 0.00 0.00 0.00 1.89
2083 2136 9.880157 AATTTGGTTCAAGGAATATGAAGAATG 57.120 29.630 0.00 0.00 37.46 2.67
2172 2536 3.441572 GCCAGTGAGTGTCAAATAATGCT 59.558 43.478 0.00 0.00 0.00 3.79
2318 2694 1.850377 CGAGTGAGTGATGGATGAGC 58.150 55.000 0.00 0.00 0.00 4.26
2329 2712 2.224281 TGTCATTTCCAAGCGAGTGAGT 60.224 45.455 0.00 0.00 0.00 3.41
2330 2713 2.158449 GTGTCATTTCCAAGCGAGTGAG 59.842 50.000 0.00 0.00 0.00 3.51
2340 2723 3.531538 GATTAGGAGCGTGTCATTTCCA 58.468 45.455 3.87 0.00 32.02 3.53
2410 2793 8.689707 AGTAGAACTATAGGCTACTCTCCTAT 57.310 38.462 22.14 6.76 45.92 2.57
2429 2820 5.408356 GTTTATTCGAGCAGTGGAGTAGAA 58.592 41.667 0.00 0.00 0.00 2.10
2430 2821 4.142227 GGTTTATTCGAGCAGTGGAGTAGA 60.142 45.833 0.00 0.00 0.00 2.59



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

AutoCloner maintained by Alex Coulton.