Multiple sequence alignment - TraesCS5D01G133700

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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 TraesCS5D01G133700 chr5D 100.000 2483 0 0 1 2483 213469768 213472250 0.000000e+00 4586.0
1 TraesCS5D01G133700 chr5A 93.128 2343 84 33 180 2483 277717943 277720247 0.000000e+00 3363.0
2 TraesCS5D01G133700 chr5B 96.198 1736 42 12 586 2314 227831068 227832786 0.000000e+00 2819.0
3 TraesCS5D01G133700 chr5B 85.195 385 36 14 183 560 227808436 227808806 2.330000e-100 375.0
4 TraesCS5D01G133700 chr5B 97.701 174 2 1 2312 2483 227832868 227833041 5.190000e-77 298.0
5 TraesCS5D01G133700 chr4D 91.083 157 12 2 23 178 3590643 3590488 6.960000e-51 211.0
6 TraesCS5D01G133700 chrUn 91.391 151 11 2 29 178 41734378 41734229 3.240000e-49 206.0
7 TraesCS5D01G133700 chr3B 91.391 151 11 2 29 178 789487839 789487690 3.240000e-49 206.0
8 TraesCS5D01G133700 chr2B 90.000 160 14 2 20 178 379779240 379779082 3.240000e-49 206.0
9 TraesCS5D01G133700 chr2B 91.333 150 12 1 31 179 378686771 378686920 1.160000e-48 204.0
10 TraesCS5D01G133700 chr2B 100.000 28 0 0 1035 1062 751270554 751270581 4.000000e-03 52.8
11 TraesCS5D01G133700 chr4B 91.333 150 11 2 30 178 344463460 344463312 1.160000e-48 204.0
12 TraesCS5D01G133700 chr3D 90.000 160 12 4 20 178 595025146 595024990 1.160000e-48 204.0
13 TraesCS5D01G133700 chr7D 89.873 158 14 2 22 178 379768980 379768824 4.190000e-48 202.0
14 TraesCS5D01G133700 chr7B 91.275 149 11 2 31 178 677889233 677889380 4.190000e-48 202.0
15 TraesCS5D01G133700 chr2A 86.301 73 8 2 2329 2399 764097378 764097306 7.360000e-11 78.7
16 TraesCS5D01G133700 chr2D 82.667 75 7 5 2329 2399 638156237 638156309 7.410000e-06 62.1


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 TraesCS5D01G133700 chr5D 213469768 213472250 2482 False 4586.0 4586 100.0000 1 2483 1 chr5D.!!$F1 2482
1 TraesCS5D01G133700 chr5A 277717943 277720247 2304 False 3363.0 3363 93.1280 180 2483 1 chr5A.!!$F1 2303
2 TraesCS5D01G133700 chr5B 227831068 227833041 1973 False 1558.5 2819 96.9495 586 2483 2 chr5B.!!$F2 1897

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
629 669 0.251341 GAAACACAGCCCCATGGAGT 60.251 55.0 15.22 3.13 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1519 1563 1.066573 AGAGAATTCACGGAGGTGCAG 60.067 52.381 8.44 0.0 44.03 4.41 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
32 33 9.991906 TTACAACACCTAGGCAATATTATCTAC 57.008 33.333 9.30 0.00 0.00 2.59
33 34 8.263854 ACAACACCTAGGCAATATTATCTACT 57.736 34.615 9.30 0.00 0.00 2.57
34 35 8.368668 ACAACACCTAGGCAATATTATCTACTC 58.631 37.037 9.30 0.00 0.00 2.59
35 36 8.589338 CAACACCTAGGCAATATTATCTACTCT 58.411 37.037 9.30 0.00 0.00 3.24
36 37 8.356000 ACACCTAGGCAATATTATCTACTCTC 57.644 38.462 9.30 0.00 0.00 3.20
37 38 8.174085 ACACCTAGGCAATATTATCTACTCTCT 58.826 37.037 9.30 0.00 0.00 3.10
38 39 8.682710 CACCTAGGCAATATTATCTACTCTCTC 58.317 40.741 9.30 0.00 0.00 3.20
39 40 8.620177 ACCTAGGCAATATTATCTACTCTCTCT 58.380 37.037 9.30 0.00 0.00 3.10
40 41 8.902806 CCTAGGCAATATTATCTACTCTCTCTG 58.097 40.741 0.00 0.00 0.00 3.35
41 42 9.461312 CTAGGCAATATTATCTACTCTCTCTGT 57.539 37.037 0.00 0.00 0.00 3.41
42 43 8.719645 AGGCAATATTATCTACTCTCTCTGTT 57.280 34.615 0.00 0.00 0.00 3.16
43 44 9.153479 AGGCAATATTATCTACTCTCTCTGTTT 57.847 33.333 0.00 0.00 0.00 2.83
44 45 9.771534 GGCAATATTATCTACTCTCTCTGTTTT 57.228 33.333 0.00 0.00 0.00 2.43
86 87 7.481642 AGAGATTCCACTACAAACTACATACG 58.518 38.462 0.00 0.00 0.00 3.06
87 88 6.570692 AGATTCCACTACAAACTACATACGG 58.429 40.000 0.00 0.00 0.00 4.02
88 89 5.981088 TTCCACTACAAACTACATACGGA 57.019 39.130 0.00 0.00 0.00 4.69
89 90 6.534475 TTCCACTACAAACTACATACGGAT 57.466 37.500 0.00 0.00 0.00 4.18
90 91 5.898174 TCCACTACAAACTACATACGGATG 58.102 41.667 5.94 5.94 39.16 3.51
92 93 6.602803 TCCACTACAAACTACATACGGATGTA 59.397 38.462 19.32 19.32 44.77 2.29
93 94 7.286087 TCCACTACAAACTACATACGGATGTAT 59.714 37.037 20.64 8.38 45.42 2.29
94 95 8.570488 CCACTACAAACTACATACGGATGTATA 58.430 37.037 20.64 9.08 45.42 1.47
130 131 8.654230 TTAGAGTGTAGATTCATTGATTCTGC 57.346 34.615 17.35 16.40 0.00 4.26
131 132 6.887013 AGAGTGTAGATTCATTGATTCTGCT 58.113 36.000 20.13 14.71 30.23 4.24
132 133 7.337167 AGAGTGTAGATTCATTGATTCTGCTT 58.663 34.615 20.13 12.48 30.23 3.91
133 134 7.495279 AGAGTGTAGATTCATTGATTCTGCTTC 59.505 37.037 20.13 17.49 30.23 3.86
134 135 6.257411 AGTGTAGATTCATTGATTCTGCTTCG 59.743 38.462 20.13 0.00 30.23 3.79
135 136 6.036517 GTGTAGATTCATTGATTCTGCTTCGT 59.963 38.462 20.13 1.06 30.23 3.85
136 137 7.222805 GTGTAGATTCATTGATTCTGCTTCGTA 59.777 37.037 20.13 4.74 30.23 3.43
137 138 7.928167 TGTAGATTCATTGATTCTGCTTCGTAT 59.072 33.333 20.13 0.00 30.23 3.06
138 139 9.411801 GTAGATTCATTGATTCTGCTTCGTATA 57.588 33.333 17.35 0.00 0.00 1.47
142 143 9.935241 ATTCATTGATTCTGCTTCGTATATAGT 57.065 29.630 0.00 0.00 0.00 2.12
143 144 8.972262 TCATTGATTCTGCTTCGTATATAGTC 57.028 34.615 0.00 0.00 0.00 2.59
144 145 8.029522 TCATTGATTCTGCTTCGTATATAGTCC 58.970 37.037 0.00 0.00 0.00 3.85
145 146 6.894339 TGATTCTGCTTCGTATATAGTCCA 57.106 37.500 0.00 0.00 0.00 4.02
146 147 7.468141 TGATTCTGCTTCGTATATAGTCCAT 57.532 36.000 0.00 0.00 0.00 3.41
147 148 8.575649 TGATTCTGCTTCGTATATAGTCCATA 57.424 34.615 0.00 0.00 0.00 2.74
148 149 9.020731 TGATTCTGCTTCGTATATAGTCCATAA 57.979 33.333 0.00 0.00 0.00 1.90
150 151 9.809096 ATTCTGCTTCGTATATAGTCCATAATG 57.191 33.333 0.00 0.00 0.00 1.90
151 152 8.575649 TCTGCTTCGTATATAGTCCATAATGA 57.424 34.615 0.00 0.00 0.00 2.57
152 153 9.020731 TCTGCTTCGTATATAGTCCATAATGAA 57.979 33.333 0.00 0.00 0.00 2.57
153 154 9.639601 CTGCTTCGTATATAGTCCATAATGAAA 57.360 33.333 0.00 0.00 0.00 2.69
216 217 1.204704 ACTAGCAGCGAACATGCAGTA 59.795 47.619 0.00 0.00 46.31 2.74
227 228 5.460646 CGAACATGCAGTAATGAAAACCTT 58.539 37.500 0.00 0.00 0.00 3.50
322 352 4.780275 AACTACTACTTCCTCCGTTCAC 57.220 45.455 0.00 0.00 0.00 3.18
335 365 8.433421 TTCCTCCGTTCACAATAAGATATTTC 57.567 34.615 0.00 0.00 0.00 2.17
434 474 9.669887 TTTTTGACGGGTATATACATGTAAAGT 57.330 29.630 10.14 1.67 0.00 2.66
435 475 9.669887 TTTTGACGGGTATATACATGTAAAGTT 57.330 29.630 10.14 0.00 0.00 2.66
463 503 2.376109 TCTTAGTTAGCACTCCCTCCG 58.624 52.381 0.00 0.00 34.06 4.63
491 531 8.805145 CCATCTTATATTATGGGAGGGAGTAT 57.195 38.462 6.11 0.00 39.23 2.12
492 532 9.230477 CCATCTTATATTATGGGAGGGAGTATT 57.770 37.037 6.11 0.00 39.23 1.89
496 536 9.672673 CTTATATTATGGGAGGGAGTATTTGTG 57.327 37.037 0.00 0.00 0.00 3.33
497 537 7.888514 ATATTATGGGAGGGAGTATTTGTGA 57.111 36.000 0.00 0.00 0.00 3.58
498 538 6.590656 ATTATGGGAGGGAGTATTTGTGAA 57.409 37.500 0.00 0.00 0.00 3.18
499 539 4.946160 ATGGGAGGGAGTATTTGTGAAA 57.054 40.909 0.00 0.00 0.00 2.69
500 540 4.301072 TGGGAGGGAGTATTTGTGAAAG 57.699 45.455 0.00 0.00 0.00 2.62
502 542 3.265995 GGGAGGGAGTATTTGTGAAAGGA 59.734 47.826 0.00 0.00 0.00 3.36
503 543 4.079730 GGGAGGGAGTATTTGTGAAAGGAT 60.080 45.833 0.00 0.00 0.00 3.24
504 544 4.884164 GGAGGGAGTATTTGTGAAAGGATG 59.116 45.833 0.00 0.00 0.00 3.51
505 545 4.860022 AGGGAGTATTTGTGAAAGGATGG 58.140 43.478 0.00 0.00 0.00 3.51
506 546 4.540099 AGGGAGTATTTGTGAAAGGATGGA 59.460 41.667 0.00 0.00 0.00 3.41
507 547 4.884164 GGGAGTATTTGTGAAAGGATGGAG 59.116 45.833 0.00 0.00 0.00 3.86
508 548 5.501156 GGAGTATTTGTGAAAGGATGGAGT 58.499 41.667 0.00 0.00 0.00 3.85
509 549 6.352737 GGGAGTATTTGTGAAAGGATGGAGTA 60.353 42.308 0.00 0.00 0.00 2.59
548 588 4.273148 ACCATAAGACGCAGGGAATATC 57.727 45.455 0.00 0.00 0.00 1.63
562 602 6.432162 GCAGGGAATATCTAATTTCTGATGCA 59.568 38.462 0.00 0.00 31.30 3.96
629 669 0.251341 GAAACACAGCCCCATGGAGT 60.251 55.000 15.22 3.13 0.00 3.85
836 876 3.073735 AGAGCAGCCTCCGACCAG 61.074 66.667 0.00 0.00 38.96 4.00
873 914 9.988815 ATTTATATACTCGAGTGAATTGCTTCT 57.011 29.630 28.12 0.00 32.29 2.85
906 950 3.309296 TCTCTCTCTCTCTCTCCTCTCC 58.691 54.545 0.00 0.00 0.00 3.71
911 955 2.520741 CTCTCTCCTCTCCCCCGC 60.521 72.222 0.00 0.00 0.00 6.13
1046 1090 4.176851 GGACTCTCCGTCGCCGTC 62.177 72.222 0.00 0.00 43.79 4.79
1047 1091 4.517703 GACTCTCCGTCGCCGTCG 62.518 72.222 0.00 0.00 32.04 5.12
1248 1292 2.491022 GGACATCCTAGCGTCGCCT 61.491 63.158 14.86 3.94 32.74 5.52
1464 1508 2.124983 TGCCTCAGCTTCATCGGC 60.125 61.111 0.00 0.00 40.80 5.54
1519 1563 1.675641 ACCTCCATGCGGTTCTTGC 60.676 57.895 0.00 0.00 0.00 4.01
1599 1643 6.296803 AGATTCTTTTGTAGAGTTTTCCGGT 58.703 36.000 0.00 0.00 33.51 5.28
1661 1705 7.052873 AGGATTAGACACAAAGAGGAATGATG 58.947 38.462 0.00 0.00 0.00 3.07
2138 2189 1.671742 GTCGCAAAGGGACTCCAGA 59.328 57.895 6.92 0.00 41.34 3.86
2360 2495 3.702045 CAGTTTTTACCCCTGGTTTCACA 59.298 43.478 0.00 0.00 37.09 3.58
2419 2556 3.435105 TTAGCAAAACTTGTGCCACAG 57.565 42.857 0.00 0.00 43.27 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.991906 GTAGATAATATTGCCTAGGTGTTGTAA 57.008 33.333 11.31 0.00 0.00 2.41
7 8 9.375974 AGTAGATAATATTGCCTAGGTGTTGTA 57.624 33.333 11.31 0.00 0.00 2.41
8 9 8.263854 AGTAGATAATATTGCCTAGGTGTTGT 57.736 34.615 11.31 0.00 0.00 3.32
9 10 8.589338 AGAGTAGATAATATTGCCTAGGTGTTG 58.411 37.037 11.31 0.00 0.00 3.33
10 11 8.728596 AGAGTAGATAATATTGCCTAGGTGTT 57.271 34.615 11.31 0.00 0.00 3.32
11 12 8.174085 AGAGAGTAGATAATATTGCCTAGGTGT 58.826 37.037 11.31 0.00 0.00 4.16
12 13 8.588290 AGAGAGTAGATAATATTGCCTAGGTG 57.412 38.462 11.31 0.00 0.00 4.00
13 14 8.620177 AGAGAGAGTAGATAATATTGCCTAGGT 58.380 37.037 11.31 0.00 0.00 3.08
14 15 8.902806 CAGAGAGAGTAGATAATATTGCCTAGG 58.097 40.741 3.67 3.67 0.00 3.02
15 16 9.461312 ACAGAGAGAGTAGATAATATTGCCTAG 57.539 37.037 0.00 0.00 0.00 3.02
16 17 9.815306 AACAGAGAGAGTAGATAATATTGCCTA 57.185 33.333 0.00 0.00 0.00 3.93
17 18 8.719645 AACAGAGAGAGTAGATAATATTGCCT 57.280 34.615 0.00 0.00 0.00 4.75
18 19 9.771534 AAAACAGAGAGAGTAGATAATATTGCC 57.228 33.333 0.00 0.00 0.00 4.52
60 61 8.618677 CGTATGTAGTTTGTAGTGGAATCTCTA 58.381 37.037 0.00 0.00 0.00 2.43
61 62 7.416438 CCGTATGTAGTTTGTAGTGGAATCTCT 60.416 40.741 0.00 0.00 0.00 3.10
62 63 6.696148 CCGTATGTAGTTTGTAGTGGAATCTC 59.304 42.308 0.00 0.00 0.00 2.75
63 64 6.379133 TCCGTATGTAGTTTGTAGTGGAATCT 59.621 38.462 0.00 0.00 0.00 2.40
64 65 6.567050 TCCGTATGTAGTTTGTAGTGGAATC 58.433 40.000 0.00 0.00 0.00 2.52
65 66 6.534475 TCCGTATGTAGTTTGTAGTGGAAT 57.466 37.500 0.00 0.00 0.00 3.01
66 67 5.981088 TCCGTATGTAGTTTGTAGTGGAA 57.019 39.130 0.00 0.00 0.00 3.53
67 68 5.419788 ACATCCGTATGTAGTTTGTAGTGGA 59.580 40.000 0.00 0.00 44.66 4.02
68 69 5.657474 ACATCCGTATGTAGTTTGTAGTGG 58.343 41.667 0.00 0.00 44.66 4.00
104 105 9.102757 GCAGAATCAATGAATCTACACTCTAAA 57.897 33.333 0.00 0.00 0.00 1.85
105 106 8.481314 AGCAGAATCAATGAATCTACACTCTAA 58.519 33.333 0.00 0.00 0.00 2.10
106 107 8.016301 AGCAGAATCAATGAATCTACACTCTA 57.984 34.615 0.00 0.00 0.00 2.43
107 108 6.887013 AGCAGAATCAATGAATCTACACTCT 58.113 36.000 0.00 0.00 0.00 3.24
108 109 7.516470 CGAAGCAGAATCAATGAATCTACACTC 60.516 40.741 0.00 0.00 0.00 3.51
109 110 6.257411 CGAAGCAGAATCAATGAATCTACACT 59.743 38.462 0.00 0.00 0.00 3.55
110 111 6.036517 ACGAAGCAGAATCAATGAATCTACAC 59.963 38.462 0.00 0.00 0.00 2.90
111 112 6.108687 ACGAAGCAGAATCAATGAATCTACA 58.891 36.000 0.00 0.00 0.00 2.74
112 113 6.595772 ACGAAGCAGAATCAATGAATCTAC 57.404 37.500 0.00 0.00 0.00 2.59
116 117 9.935241 ACTATATACGAAGCAGAATCAATGAAT 57.065 29.630 0.00 0.00 0.00 2.57
117 118 9.411801 GACTATATACGAAGCAGAATCAATGAA 57.588 33.333 0.00 0.00 0.00 2.57
118 119 8.029522 GGACTATATACGAAGCAGAATCAATGA 58.970 37.037 0.00 0.00 0.00 2.57
119 120 7.814587 TGGACTATATACGAAGCAGAATCAATG 59.185 37.037 0.00 0.00 0.00 2.82
120 121 7.896811 TGGACTATATACGAAGCAGAATCAAT 58.103 34.615 0.00 0.00 0.00 2.57
121 122 7.284919 TGGACTATATACGAAGCAGAATCAA 57.715 36.000 0.00 0.00 0.00 2.57
122 123 6.894339 TGGACTATATACGAAGCAGAATCA 57.106 37.500 0.00 0.00 0.00 2.57
124 125 9.809096 CATTATGGACTATATACGAAGCAGAAT 57.191 33.333 0.00 0.00 0.00 2.40
125 126 9.020731 TCATTATGGACTATATACGAAGCAGAA 57.979 33.333 0.00 0.00 0.00 3.02
126 127 8.575649 TCATTATGGACTATATACGAAGCAGA 57.424 34.615 0.00 0.00 0.00 4.26
127 128 9.639601 TTTCATTATGGACTATATACGAAGCAG 57.360 33.333 0.00 0.00 0.00 4.24
171 172 9.982651 GTCTCAGCCATTTGTATAGTCTAAATA 57.017 33.333 0.00 0.00 0.00 1.40
172 173 8.709308 AGTCTCAGCCATTTGTATAGTCTAAAT 58.291 33.333 0.00 0.00 0.00 1.40
173 174 8.079211 AGTCTCAGCCATTTGTATAGTCTAAA 57.921 34.615 0.00 0.00 0.00 1.85
174 175 7.661536 AGTCTCAGCCATTTGTATAGTCTAA 57.338 36.000 0.00 0.00 0.00 2.10
175 176 7.040340 GCTAGTCTCAGCCATTTGTATAGTCTA 60.040 40.741 0.00 0.00 35.40 2.59
176 177 6.239176 GCTAGTCTCAGCCATTTGTATAGTCT 60.239 42.308 0.00 0.00 35.40 3.24
177 178 5.923684 GCTAGTCTCAGCCATTTGTATAGTC 59.076 44.000 0.00 0.00 35.40 2.59
178 179 5.363868 TGCTAGTCTCAGCCATTTGTATAGT 59.636 40.000 0.00 0.00 41.04 2.12
191 192 2.191802 CATGTTCGCTGCTAGTCTCAG 58.808 52.381 0.00 0.00 34.79 3.35
231 232 9.144298 TCGACCACTAGAGATTTTTAAGGATAT 57.856 33.333 0.00 0.00 0.00 1.63
234 235 6.845758 TCGACCACTAGAGATTTTTAAGGA 57.154 37.500 0.00 0.00 0.00 3.36
243 244 6.071984 AGGAACATATTCGACCACTAGAGAT 58.928 40.000 0.00 0.00 35.48 2.75
244 245 5.446860 AGGAACATATTCGACCACTAGAGA 58.553 41.667 0.00 0.00 35.48 3.10
297 298 7.776969 TGTGAACGGAGGAAGTAGTAGTTATAT 59.223 37.037 0.00 0.00 0.00 0.86
335 365 9.639601 TCTGTATAGGCTACATTGAAATATTCG 57.360 33.333 0.00 0.00 0.00 3.34
408 448 9.669887 ACTTTACATGTATATACCCGTCAAAAA 57.330 29.630 6.36 4.82 0.00 1.94
409 449 9.669887 AACTTTACATGTATATACCCGTCAAAA 57.330 29.630 6.36 5.39 0.00 2.44
430 470 9.740710 AGTGCTAACTAAGATGGATTTAACTTT 57.259 29.630 0.00 0.00 33.79 2.66
431 471 9.384764 GAGTGCTAACTAAGATGGATTTAACTT 57.615 33.333 0.00 0.00 36.52 2.66
432 472 7.988028 GGAGTGCTAACTAAGATGGATTTAACT 59.012 37.037 0.00 0.00 36.52 2.24
433 473 7.226918 GGGAGTGCTAACTAAGATGGATTTAAC 59.773 40.741 0.00 0.00 36.52 2.01
434 474 7.127339 AGGGAGTGCTAACTAAGATGGATTTAA 59.873 37.037 0.00 0.00 36.52 1.52
435 475 6.615726 AGGGAGTGCTAACTAAGATGGATTTA 59.384 38.462 0.00 0.00 36.52 1.40
436 476 5.430089 AGGGAGTGCTAACTAAGATGGATTT 59.570 40.000 0.00 0.00 36.52 2.17
437 477 4.971924 AGGGAGTGCTAACTAAGATGGATT 59.028 41.667 0.00 0.00 36.52 3.01
438 478 4.561752 AGGGAGTGCTAACTAAGATGGAT 58.438 43.478 0.00 0.00 36.52 3.41
439 479 3.961408 GAGGGAGTGCTAACTAAGATGGA 59.039 47.826 0.00 0.00 36.52 3.41
440 480 3.070302 GGAGGGAGTGCTAACTAAGATGG 59.930 52.174 0.00 0.00 36.52 3.51
441 481 3.243569 CGGAGGGAGTGCTAACTAAGATG 60.244 52.174 0.00 0.00 36.52 2.90
442 482 2.959707 CGGAGGGAGTGCTAACTAAGAT 59.040 50.000 0.00 0.00 36.52 2.40
443 483 2.291411 ACGGAGGGAGTGCTAACTAAGA 60.291 50.000 0.00 0.00 36.52 2.10
484 524 4.855340 TCCATCCTTTCACAAATACTCCC 58.145 43.478 0.00 0.00 0.00 4.30
537 577 6.432162 TGCATCAGAAATTAGATATTCCCTGC 59.568 38.462 0.00 0.00 0.00 4.85
548 588 8.725148 GGGACTGTATATTGCATCAGAAATTAG 58.275 37.037 0.00 0.00 0.00 1.73
562 602 6.663734 AGCTGCTTTTTAGGGACTGTATATT 58.336 36.000 0.00 0.00 41.52 1.28
568 608 5.461526 GTTTTAGCTGCTTTTTAGGGACTG 58.538 41.667 7.79 0.00 41.52 3.51
629 669 1.001048 CCACGAGTGAACGTTGTCCTA 60.001 52.381 5.00 0.00 44.76 2.94
793 833 3.295785 CGCATGTCATCGAACACAAAAA 58.704 40.909 4.09 0.00 30.55 1.94
794 834 2.350293 CCGCATGTCATCGAACACAAAA 60.350 45.455 4.09 0.00 30.55 2.44
801 841 2.513666 GGCCCGCATGTCATCGAA 60.514 61.111 0.00 0.00 0.00 3.71
836 876 9.654663 ACTCGAGTATATAAATTGGGAAATAGC 57.345 33.333 18.46 0.00 0.00 2.97
873 914 1.010793 AGAGAGAGAGGGAGAGAGGGA 59.989 57.143 0.00 0.00 0.00 4.20
906 950 2.809601 CGACGACTTTGAGCGGGG 60.810 66.667 0.00 0.00 0.00 5.73
911 955 1.716581 GAGCAAGACGACGACTTTGAG 59.283 52.381 9.84 1.21 0.00 3.02
940 984 7.012327 TGGTGGATTGATAAGAATCGAATCAAC 59.988 37.037 10.76 0.28 41.14 3.18
1311 1355 3.492656 GGTGGCGTATCATGTGTATGTCT 60.493 47.826 0.00 0.00 35.73 3.41
1499 1543 1.675641 AAGAACCGCATGGAGGTGC 60.676 57.895 0.00 0.00 41.95 5.01
1500 1544 1.926511 GCAAGAACCGCATGGAGGTG 61.927 60.000 0.00 0.00 41.95 4.00
1519 1563 1.066573 AGAGAATTCACGGAGGTGCAG 60.067 52.381 8.44 0.00 44.03 4.41
1599 1643 8.258007 TCACACAAATTACAACCCAAACATAAA 58.742 29.630 0.00 0.00 0.00 1.40
1661 1705 5.717119 ACATTCATCATTTCTCTTGTTGCC 58.283 37.500 0.00 0.00 0.00 4.52
1679 1723 8.703604 TCAGCTTTGTTAGTAGTATGACATTC 57.296 34.615 0.00 0.00 0.00 2.67
2138 2189 4.774726 TCAGCAGAGGAACAAGAAGTCTAT 59.225 41.667 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.