Multiple sequence alignment - TraesCS1B01G208700

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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 TraesCS1B01G208700 chr1B 100.000 2576 0 0 1 2576 378461441 378464016 0.000000e+00 4758
1 TraesCS1B01G208700 chr1D 95.385 2232 58 20 241 2454 278945187 278947391 0.000000e+00 3509
2 TraesCS1B01G208700 chr1D 91.935 124 10 0 2453 2576 278947551 278947674 9.470000e-40 174
3 TraesCS1B01G208700 chr1A 95.779 1848 56 15 193 2027 351210878 351212716 0.000000e+00 2961
4 TraesCS1B01G208700 chr1A 91.886 456 25 5 2129 2576 351212999 351213450 6.050000e-176 627
5 TraesCS1B01G208700 chr2D 95.238 168 8 0 1 168 620450492 620450325 1.520000e-67 267
6 TraesCS1B01G208700 chr2D 94.706 170 9 0 1 170 289110650 289110481 5.470000e-67 265
7 TraesCS1B01G208700 chr2D 94.643 168 9 0 1 168 239791626 239791459 7.070000e-66 261
8 TraesCS1B01G208700 chr2D 93.064 173 11 1 1 173 174227759 174227930 4.260000e-63 252
9 TraesCS1B01G208700 chr3D 94.643 168 9 0 1 168 326280295 326280128 7.070000e-66 261
10 TraesCS1B01G208700 chr2A 94.643 168 9 0 1 168 500645496 500645663 7.070000e-66 261
11 TraesCS1B01G208700 chr2A 94.118 170 10 0 1 170 504535250 504535419 2.540000e-65 259
12 TraesCS1B01G208700 chr7D 93.642 173 11 0 1 173 375391082 375391254 2.540000e-65 259
13 TraesCS1B01G208700 chr4D 94.118 170 10 0 2 171 492511780 492511949 2.540000e-65 259


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 TraesCS1B01G208700 chr1B 378461441 378464016 2575 False 4758.0 4758 100.0000 1 2576 1 chr1B.!!$F1 2575
1 TraesCS1B01G208700 chr1D 278945187 278947674 2487 False 1841.5 3509 93.6600 241 2576 2 chr1D.!!$F1 2335
2 TraesCS1B01G208700 chr1A 351210878 351213450 2572 False 1794.0 2961 93.8325 193 2576 2 chr1A.!!$F1 2383

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
218 219 0.38539 ACGGCAGTTTGCTTCTTTGG 59.615 50.0 0.67 0.0 44.28 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2105 2150 1.218047 GACATGGTAGACGGCAGCA 59.782 57.895 0.0 0.0 0.0 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
23 24 6.173191 CGAGCTAATCTAGTAGAGGCTTAC 57.827 45.833 19.27 11.07 31.94 2.34
24 25 5.935789 CGAGCTAATCTAGTAGAGGCTTACT 59.064 44.000 19.27 12.02 37.61 2.24
25 26 7.098477 CGAGCTAATCTAGTAGAGGCTTACTA 58.902 42.308 19.27 12.72 35.57 1.82
27 28 7.399634 AGCTAATCTAGTAGAGGCTTACTAGG 58.600 42.308 26.08 18.07 46.84 3.02
28 29 6.600427 GCTAATCTAGTAGAGGCTTACTAGGG 59.400 46.154 26.08 19.33 46.84 3.53
29 30 6.783517 AATCTAGTAGAGGCTTACTAGGGA 57.216 41.667 26.08 17.18 46.84 4.20
30 31 5.565455 TCTAGTAGAGGCTTACTAGGGAC 57.435 47.826 26.08 5.42 46.84 4.46
31 32 4.973856 TCTAGTAGAGGCTTACTAGGGACA 59.026 45.833 26.08 14.79 46.84 4.02
32 33 4.817874 AGTAGAGGCTTACTAGGGACAT 57.182 45.455 7.35 0.00 32.25 3.06
33 34 5.926580 AGTAGAGGCTTACTAGGGACATA 57.073 43.478 7.35 0.00 32.25 2.29
34 35 5.883180 AGTAGAGGCTTACTAGGGACATAG 58.117 45.833 7.35 0.00 32.25 2.23
35 36 4.817874 AGAGGCTTACTAGGGACATAGT 57.182 45.455 2.09 2.09 39.35 2.12
36 37 4.475345 AGAGGCTTACTAGGGACATAGTG 58.525 47.826 6.89 0.00 36.66 2.74
37 38 4.079096 AGAGGCTTACTAGGGACATAGTGT 60.079 45.833 6.89 0.00 36.66 3.55
38 39 5.133999 AGAGGCTTACTAGGGACATAGTGTA 59.866 44.000 6.89 0.00 36.66 2.90
39 40 5.386924 AGGCTTACTAGGGACATAGTGTAG 58.613 45.833 6.89 5.61 36.66 2.74
40 41 5.103601 AGGCTTACTAGGGACATAGTGTAGT 60.104 44.000 6.89 0.00 36.66 2.73
41 42 5.597594 GGCTTACTAGGGACATAGTGTAGTT 59.402 44.000 6.89 0.00 36.66 2.24
42 43 6.097981 GGCTTACTAGGGACATAGTGTAGTTT 59.902 42.308 6.89 0.00 36.66 2.66
43 44 7.286316 GGCTTACTAGGGACATAGTGTAGTTTA 59.714 40.741 6.89 0.00 36.66 2.01
44 45 8.858094 GCTTACTAGGGACATAGTGTAGTTTAT 58.142 37.037 6.89 0.00 36.66 1.40
46 47 9.705103 TTACTAGGGACATAGTGTAGTTTATGT 57.295 33.333 6.89 0.00 41.78 2.29
48 49 9.878737 ACTAGGGACATAGTGTAGTTTATGTAT 57.121 33.333 0.00 0.00 39.81 2.29
51 52 9.209048 AGGGACATAGTGTAGTTTATGTATTCA 57.791 33.333 0.00 0.00 39.81 2.57
52 53 9.257651 GGGACATAGTGTAGTTTATGTATTCAC 57.742 37.037 0.00 0.00 39.81 3.18
53 54 9.811995 GGACATAGTGTAGTTTATGTATTCACA 57.188 33.333 0.00 0.00 39.81 3.58
72 73 8.964420 ATTCACACATGTATTTAAGTTTTCGG 57.036 30.769 0.00 0.00 0.00 4.30
73 74 7.499321 TCACACATGTATTTAAGTTTTCGGT 57.501 32.000 0.00 0.00 0.00 4.69
74 75 7.577979 TCACACATGTATTTAAGTTTTCGGTC 58.422 34.615 0.00 0.00 0.00 4.79
75 76 7.226918 TCACACATGTATTTAAGTTTTCGGTCA 59.773 33.333 0.00 0.00 0.00 4.02
76 77 7.858382 CACACATGTATTTAAGTTTTCGGTCAA 59.142 33.333 0.00 0.00 0.00 3.18
77 78 8.573035 ACACATGTATTTAAGTTTTCGGTCAAT 58.427 29.630 0.00 0.00 0.00 2.57
85 86 9.634163 ATTTAAGTTTTCGGTCAATACAATTCC 57.366 29.630 0.00 0.00 0.00 3.01
86 87 6.642707 AAGTTTTCGGTCAATACAATTCCA 57.357 33.333 0.00 0.00 0.00 3.53
87 88 6.254281 AGTTTTCGGTCAATACAATTCCAG 57.746 37.500 0.00 0.00 0.00 3.86
88 89 4.695217 TTTCGGTCAATACAATTCCAGC 57.305 40.909 0.00 0.00 0.00 4.85
89 90 3.342377 TCGGTCAATACAATTCCAGCA 57.658 42.857 0.00 0.00 0.00 4.41
90 91 3.884895 TCGGTCAATACAATTCCAGCAT 58.115 40.909 0.00 0.00 0.00 3.79
91 92 3.627123 TCGGTCAATACAATTCCAGCATG 59.373 43.478 0.00 0.00 0.00 4.06
92 93 3.627123 CGGTCAATACAATTCCAGCATGA 59.373 43.478 0.00 0.00 39.69 3.07
93 94 4.096231 CGGTCAATACAATTCCAGCATGAA 59.904 41.667 0.00 0.00 39.69 2.57
94 95 5.221106 CGGTCAATACAATTCCAGCATGAAT 60.221 40.000 0.00 0.00 39.69 2.57
95 96 5.981315 GGTCAATACAATTCCAGCATGAATG 59.019 40.000 0.00 0.00 39.69 2.67
96 97 6.183360 GGTCAATACAATTCCAGCATGAATGA 60.183 38.462 0.00 0.00 39.69 2.57
97 98 7.431249 GTCAATACAATTCCAGCATGAATGAT 58.569 34.615 0.00 0.00 39.69 2.45
98 99 8.570488 GTCAATACAATTCCAGCATGAATGATA 58.430 33.333 0.00 0.00 39.69 2.15
99 100 9.134055 TCAATACAATTCCAGCATGAATGATAA 57.866 29.630 0.00 0.00 39.69 1.75
100 101 9.752961 CAATACAATTCCAGCATGAATGATAAA 57.247 29.630 0.00 0.00 39.69 1.40
126 127 9.753674 ATATTTATCATGAACGGGAAATATGGT 57.246 29.630 0.00 0.00 31.53 3.55
128 129 8.982091 TTTATCATGAACGGGAAATATGGTAA 57.018 30.769 0.00 0.00 0.00 2.85
129 130 9.581289 TTTATCATGAACGGGAAATATGGTAAT 57.419 29.630 0.00 0.00 28.04 1.89
132 133 8.385898 TCATGAACGGGAAATATGGTAATAAC 57.614 34.615 0.00 0.00 0.00 1.89
133 134 7.446013 TCATGAACGGGAAATATGGTAATAACC 59.554 37.037 0.00 0.00 46.98 2.85
167 168 4.437682 CCTCTAGGGCATATTTCCAACA 57.562 45.455 0.00 0.00 0.00 3.33
168 169 4.392940 CCTCTAGGGCATATTTCCAACAG 58.607 47.826 0.00 0.00 0.00 3.16
169 170 4.141390 CCTCTAGGGCATATTTCCAACAGT 60.141 45.833 0.00 0.00 0.00 3.55
170 171 5.440610 CTCTAGGGCATATTTCCAACAGTT 58.559 41.667 0.00 0.00 0.00 3.16
171 172 6.409234 CCTCTAGGGCATATTTCCAACAGTTA 60.409 42.308 0.00 0.00 0.00 2.24
172 173 6.964464 TCTAGGGCATATTTCCAACAGTTAA 58.036 36.000 0.00 0.00 0.00 2.01
173 174 7.054124 TCTAGGGCATATTTCCAACAGTTAAG 58.946 38.462 0.00 0.00 0.00 1.85
174 175 4.956075 AGGGCATATTTCCAACAGTTAAGG 59.044 41.667 0.00 0.00 0.00 2.69
175 176 4.441495 GGGCATATTTCCAACAGTTAAGGC 60.441 45.833 0.00 0.00 0.00 4.35
176 177 4.402474 GGCATATTTCCAACAGTTAAGGCT 59.598 41.667 0.00 0.00 0.00 4.58
177 178 5.450550 GGCATATTTCCAACAGTTAAGGCTC 60.451 44.000 0.00 0.00 0.00 4.70
178 179 5.730568 GCATATTTCCAACAGTTAAGGCTCG 60.731 44.000 0.00 0.00 0.00 5.03
179 180 2.178912 TTCCAACAGTTAAGGCTCGG 57.821 50.000 0.00 0.00 0.00 4.63
180 181 1.053424 TCCAACAGTTAAGGCTCGGT 58.947 50.000 0.00 0.00 0.00 4.69
181 182 1.001633 TCCAACAGTTAAGGCTCGGTC 59.998 52.381 0.00 0.00 0.00 4.79
182 183 1.270625 CCAACAGTTAAGGCTCGGTCA 60.271 52.381 0.00 0.00 0.00 4.02
183 184 2.069273 CAACAGTTAAGGCTCGGTCAG 58.931 52.381 0.00 0.00 0.00 3.51
184 185 1.629043 ACAGTTAAGGCTCGGTCAGA 58.371 50.000 0.00 0.00 0.00 3.27
195 196 2.411628 TCGGTCAGAGAGAAGGAGAG 57.588 55.000 0.00 0.00 0.00 3.20
196 197 1.631388 TCGGTCAGAGAGAAGGAGAGT 59.369 52.381 0.00 0.00 0.00 3.24
197 198 2.014128 CGGTCAGAGAGAAGGAGAGTC 58.986 57.143 0.00 0.00 0.00 3.36
203 204 0.968393 AGAGAAGGAGAGTCCACGGC 60.968 60.000 0.00 0.00 39.61 5.68
209 210 0.951040 GGAGAGTCCACGGCAGTTTG 60.951 60.000 0.00 0.00 36.28 2.93
218 219 0.385390 ACGGCAGTTTGCTTCTTTGG 59.615 50.000 0.67 0.00 44.28 3.28
226 227 3.005155 AGTTTGCTTCTTTGGAGACATGC 59.995 43.478 0.00 0.00 42.32 4.06
234 235 1.236616 TTGGAGACATGCGCACTTGG 61.237 55.000 14.90 5.30 42.32 3.61
235 236 1.672356 GGAGACATGCGCACTTGGT 60.672 57.895 14.90 9.16 0.00 3.67
236 237 0.391130 GGAGACATGCGCACTTGGTA 60.391 55.000 14.90 0.00 0.00 3.25
238 239 1.594862 GAGACATGCGCACTTGGTATC 59.405 52.381 14.90 12.10 0.00 2.24
253 254 4.229304 TGGTATCCAATGAATGAACCGT 57.771 40.909 0.00 0.00 32.12 4.83
300 302 0.538287 AACTGGAGCAAAGGAGTGCC 60.538 55.000 0.00 0.00 46.14 5.01
302 304 1.228245 TGGAGCAAAGGAGTGCCAC 60.228 57.895 0.00 0.00 46.14 5.01
303 305 1.228245 GGAGCAAAGGAGTGCCACA 60.228 57.895 0.00 0.00 46.14 4.17
358 360 4.857037 GTGCGTGGGTGATATTTTCTTTTC 59.143 41.667 0.00 0.00 0.00 2.29
684 691 6.480763 TGTCCGGATATGCAATAATTGGTAT 58.519 36.000 7.81 0.00 29.06 2.73
688 695 8.865090 TCCGGATATGCAATAATTGGTATTTTT 58.135 29.630 0.00 0.00 29.38 1.94
817 824 3.449528 TCAATTGATCAGAGGAGCTCG 57.550 47.619 7.83 0.00 35.36 5.03
1179 1195 1.003839 CAACAAGGACGGCAGCCTA 60.004 57.895 10.54 0.00 33.76 3.93
1545 1561 4.812476 TTCTCCCGCGCCATCACG 62.812 66.667 0.00 0.00 0.00 4.35
1667 1683 2.710971 CGTCATCATCGATCGCGCC 61.711 63.158 11.09 0.00 37.46 6.53
1853 1869 5.716703 ACTTTAGGGGTCAAGGAATGAATTG 59.283 40.000 0.00 0.00 40.50 2.32
2237 2447 0.521242 GTTGAACGGATCATGCGTGC 60.521 55.000 4.42 3.11 45.62 5.34
2253 2467 0.250727 GTGCCTTTCACCACCAGCTA 60.251 55.000 0.00 0.00 39.79 3.32
2291 2505 2.158475 TGGCCAGATTCCAGTGAAAAGT 60.158 45.455 0.00 0.00 33.32 2.66
2332 2546 6.881067 ATGATTTGGCCAGATAGATAGCTA 57.119 37.500 9.11 0.00 0.00 3.32
2351 2565 3.386402 GCTATCTGCTGGTCCCTATATCC 59.614 52.174 0.00 0.00 38.95 2.59
2459 2673 9.463443 AAGAAGTTGAGTTGTATGTTATTTTGC 57.537 29.630 0.00 0.00 0.00 3.68
2500 2875 1.551883 GGGCCATTCACAATTGAGCTT 59.448 47.619 13.59 0.00 31.71 3.74
2509 2884 4.245660 TCACAATTGAGCTTAGAAGACGG 58.754 43.478 13.59 0.00 0.00 4.79
2516 2891 6.465439 TTGAGCTTAGAAGACGGATATGAA 57.535 37.500 0.00 0.00 0.00 2.57
2571 2946 7.348033 TGGTACTTTAAAGGAAGACTTGGAAA 58.652 34.615 19.14 0.00 39.96 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.935789 AGTAAGCCTCTACTAGATTAGCTCG 59.064 44.000 0.00 0.00 30.13 5.03
9 10 5.307544 TGTCCCTAGTAAGCCTCTACTAG 57.692 47.826 14.24 14.24 45.92 2.57
10 11 5.926580 ATGTCCCTAGTAAGCCTCTACTA 57.073 43.478 0.00 0.00 34.03 1.82
11 12 4.817874 ATGTCCCTAGTAAGCCTCTACT 57.182 45.455 0.00 0.00 36.16 2.57
12 13 5.474189 CACTATGTCCCTAGTAAGCCTCTAC 59.526 48.000 0.00 0.00 30.78 2.59
13 14 5.133999 ACACTATGTCCCTAGTAAGCCTCTA 59.866 44.000 0.00 0.00 30.78 2.43
14 15 4.079096 ACACTATGTCCCTAGTAAGCCTCT 60.079 45.833 0.00 0.00 30.78 3.69
15 16 4.216708 ACACTATGTCCCTAGTAAGCCTC 58.783 47.826 0.00 0.00 30.78 4.70
16 17 4.267341 ACACTATGTCCCTAGTAAGCCT 57.733 45.455 0.00 0.00 30.78 4.58
17 18 5.139001 ACTACACTATGTCCCTAGTAAGCC 58.861 45.833 0.00 0.00 30.78 4.35
18 19 6.712179 AACTACACTATGTCCCTAGTAAGC 57.288 41.667 0.00 0.00 30.78 3.09
20 21 9.705103 ACATAAACTACACTATGTCCCTAGTAA 57.295 33.333 0.00 0.00 34.37 2.24
22 23 9.878737 ATACATAAACTACACTATGTCCCTAGT 57.121 33.333 0.00 0.00 39.08 2.57
25 26 9.209048 TGAATACATAAACTACACTATGTCCCT 57.791 33.333 0.00 0.00 39.08 4.20
26 27 9.257651 GTGAATACATAAACTACACTATGTCCC 57.742 37.037 0.00 0.00 39.08 4.46
27 28 9.811995 TGTGAATACATAAACTACACTATGTCC 57.188 33.333 0.00 0.00 39.08 4.02
47 48 8.573035 ACCGAAAACTTAAATACATGTGTGAAT 58.427 29.630 9.11 0.00 0.00 2.57
48 49 7.932335 ACCGAAAACTTAAATACATGTGTGAA 58.068 30.769 9.11 0.00 0.00 3.18
49 50 7.226918 TGACCGAAAACTTAAATACATGTGTGA 59.773 33.333 9.11 0.00 0.00 3.58
50 51 7.356540 TGACCGAAAACTTAAATACATGTGTG 58.643 34.615 9.11 0.00 0.00 3.82
51 52 7.499321 TGACCGAAAACTTAAATACATGTGT 57.501 32.000 9.11 0.00 0.00 3.72
52 53 8.964420 ATTGACCGAAAACTTAAATACATGTG 57.036 30.769 9.11 0.00 0.00 3.21
59 60 9.634163 GGAATTGTATTGACCGAAAACTTAAAT 57.366 29.630 0.00 0.00 0.00 1.40
60 61 8.630917 TGGAATTGTATTGACCGAAAACTTAAA 58.369 29.630 0.00 0.00 0.00 1.52
61 62 8.167605 TGGAATTGTATTGACCGAAAACTTAA 57.832 30.769 0.00 0.00 0.00 1.85
62 63 7.574217 GCTGGAATTGTATTGACCGAAAACTTA 60.574 37.037 0.00 0.00 0.00 2.24
63 64 6.642707 TGGAATTGTATTGACCGAAAACTT 57.357 33.333 0.00 0.00 0.00 2.66
64 65 5.335661 GCTGGAATTGTATTGACCGAAAACT 60.336 40.000 0.00 0.00 0.00 2.66
65 66 4.857037 GCTGGAATTGTATTGACCGAAAAC 59.143 41.667 0.00 0.00 0.00 2.43
66 67 4.520874 TGCTGGAATTGTATTGACCGAAAA 59.479 37.500 0.00 0.00 0.00 2.29
67 68 4.075682 TGCTGGAATTGTATTGACCGAAA 58.924 39.130 0.00 0.00 0.00 3.46
68 69 3.680490 TGCTGGAATTGTATTGACCGAA 58.320 40.909 0.00 0.00 0.00 4.30
69 70 3.342377 TGCTGGAATTGTATTGACCGA 57.658 42.857 0.00 0.00 0.00 4.69
70 71 3.627123 TCATGCTGGAATTGTATTGACCG 59.373 43.478 0.00 0.00 0.00 4.79
71 72 5.581126 TTCATGCTGGAATTGTATTGACC 57.419 39.130 0.00 0.00 0.00 4.02
72 73 6.798482 TCATTCATGCTGGAATTGTATTGAC 58.202 36.000 1.36 0.00 35.37 3.18
73 74 7.591421 ATCATTCATGCTGGAATTGTATTGA 57.409 32.000 1.36 0.00 35.37 2.57
74 75 9.752961 TTTATCATTCATGCTGGAATTGTATTG 57.247 29.630 1.36 0.00 35.37 1.90
100 101 9.753674 ACCATATTTCCCGTTCATGATAAATAT 57.246 29.630 0.00 5.67 32.50 1.28
102 103 9.581289 TTACCATATTTCCCGTTCATGATAAAT 57.419 29.630 0.00 1.62 0.00 1.40
103 104 8.982091 TTACCATATTTCCCGTTCATGATAAA 57.018 30.769 0.00 0.00 0.00 1.40
106 107 9.010029 GTTATTACCATATTTCCCGTTCATGAT 57.990 33.333 0.00 0.00 0.00 2.45
107 108 7.446013 GGTTATTACCATATTTCCCGTTCATGA 59.554 37.037 0.00 0.00 44.36 3.07
108 109 7.590279 GGTTATTACCATATTTCCCGTTCATG 58.410 38.462 0.00 0.00 44.36 3.07
109 110 7.754851 GGTTATTACCATATTTCCCGTTCAT 57.245 36.000 0.00 0.00 44.36 2.57
146 147 4.141390 ACTGTTGGAAATATGCCCTAGAGG 60.141 45.833 0.00 0.00 39.47 3.69
147 148 5.041191 ACTGTTGGAAATATGCCCTAGAG 57.959 43.478 0.00 0.00 0.00 2.43
148 149 5.450818 AACTGTTGGAAATATGCCCTAGA 57.549 39.130 0.00 0.00 0.00 2.43
149 150 6.263168 CCTTAACTGTTGGAAATATGCCCTAG 59.737 42.308 2.69 0.00 0.00 3.02
150 151 6.126409 CCTTAACTGTTGGAAATATGCCCTA 58.874 40.000 2.69 0.00 0.00 3.53
151 152 4.956075 CCTTAACTGTTGGAAATATGCCCT 59.044 41.667 2.69 0.00 0.00 5.19
152 153 4.441495 GCCTTAACTGTTGGAAATATGCCC 60.441 45.833 2.69 0.00 0.00 5.36
153 154 4.402474 AGCCTTAACTGTTGGAAATATGCC 59.598 41.667 2.69 0.00 0.00 4.40
154 155 5.582550 GAGCCTTAACTGTTGGAAATATGC 58.417 41.667 2.69 0.00 0.00 3.14
155 156 5.220854 CCGAGCCTTAACTGTTGGAAATATG 60.221 44.000 2.69 0.00 0.00 1.78
156 157 4.881850 CCGAGCCTTAACTGTTGGAAATAT 59.118 41.667 2.69 0.00 0.00 1.28
157 158 4.258543 CCGAGCCTTAACTGTTGGAAATA 58.741 43.478 2.69 0.00 0.00 1.40
158 159 3.081804 CCGAGCCTTAACTGTTGGAAAT 58.918 45.455 2.69 0.00 0.00 2.17
159 160 2.158726 ACCGAGCCTTAACTGTTGGAAA 60.159 45.455 2.69 0.00 0.00 3.13
160 161 1.418637 ACCGAGCCTTAACTGTTGGAA 59.581 47.619 2.69 0.00 0.00 3.53
161 162 1.001633 GACCGAGCCTTAACTGTTGGA 59.998 52.381 2.69 0.00 0.00 3.53
162 163 1.270625 TGACCGAGCCTTAACTGTTGG 60.271 52.381 2.69 0.00 0.00 3.77
163 164 2.069273 CTGACCGAGCCTTAACTGTTG 58.931 52.381 2.69 0.00 0.00 3.33
164 165 1.968493 TCTGACCGAGCCTTAACTGTT 59.032 47.619 0.00 0.00 0.00 3.16
165 166 1.546476 CTCTGACCGAGCCTTAACTGT 59.454 52.381 0.00 0.00 31.99 3.55
166 167 1.819288 TCTCTGACCGAGCCTTAACTG 59.181 52.381 0.00 0.00 39.70 3.16
167 168 2.096248 CTCTCTGACCGAGCCTTAACT 58.904 52.381 0.00 0.00 39.70 2.24
168 169 2.093106 TCTCTCTGACCGAGCCTTAAC 58.907 52.381 0.00 0.00 39.70 2.01
169 170 2.509166 TCTCTCTGACCGAGCCTTAA 57.491 50.000 0.00 0.00 39.70 1.85
170 171 2.370349 CTTCTCTCTGACCGAGCCTTA 58.630 52.381 0.00 0.00 39.70 2.69
171 172 1.181786 CTTCTCTCTGACCGAGCCTT 58.818 55.000 0.00 0.00 39.70 4.35
172 173 0.682855 CCTTCTCTCTGACCGAGCCT 60.683 60.000 0.00 0.00 39.70 4.58
173 174 0.681564 TCCTTCTCTCTGACCGAGCC 60.682 60.000 0.00 0.00 39.70 4.70
174 175 0.738389 CTCCTTCTCTCTGACCGAGC 59.262 60.000 0.00 0.00 39.70 5.03
175 176 2.288666 CTCTCCTTCTCTCTGACCGAG 58.711 57.143 0.00 0.00 41.30 4.63
176 177 1.631388 ACTCTCCTTCTCTCTGACCGA 59.369 52.381 0.00 0.00 0.00 4.69
177 178 2.014128 GACTCTCCTTCTCTCTGACCG 58.986 57.143 0.00 0.00 0.00 4.79
178 179 2.291282 TGGACTCTCCTTCTCTCTGACC 60.291 54.545 0.00 0.00 37.46 4.02
179 180 2.752903 GTGGACTCTCCTTCTCTCTGAC 59.247 54.545 0.00 0.00 37.46 3.51
180 181 2.616765 CGTGGACTCTCCTTCTCTCTGA 60.617 54.545 0.00 0.00 37.46 3.27
181 182 1.742831 CGTGGACTCTCCTTCTCTCTG 59.257 57.143 0.00 0.00 37.46 3.35
182 183 1.340600 CCGTGGACTCTCCTTCTCTCT 60.341 57.143 0.00 0.00 37.46 3.10
183 184 1.099689 CCGTGGACTCTCCTTCTCTC 58.900 60.000 0.00 0.00 37.46 3.20
184 185 0.968393 GCCGTGGACTCTCCTTCTCT 60.968 60.000 0.00 0.00 37.46 3.10
185 186 1.251527 TGCCGTGGACTCTCCTTCTC 61.252 60.000 0.00 0.00 37.46 2.87
186 187 1.228894 TGCCGTGGACTCTCCTTCT 60.229 57.895 0.00 0.00 37.46 2.85
187 188 1.216710 CTGCCGTGGACTCTCCTTC 59.783 63.158 0.00 0.00 37.46 3.46
188 189 1.122019 AACTGCCGTGGACTCTCCTT 61.122 55.000 0.00 0.00 37.46 3.36
189 190 1.122019 AAACTGCCGTGGACTCTCCT 61.122 55.000 0.00 0.00 37.46 3.69
190 191 0.951040 CAAACTGCCGTGGACTCTCC 60.951 60.000 0.00 0.00 36.96 3.71
191 192 1.569479 GCAAACTGCCGTGGACTCTC 61.569 60.000 0.00 0.00 37.42 3.20
192 193 1.598130 GCAAACTGCCGTGGACTCT 60.598 57.895 0.00 0.00 37.42 3.24
193 194 1.166531 AAGCAAACTGCCGTGGACTC 61.167 55.000 0.00 0.00 46.52 3.36
194 195 1.152963 AAGCAAACTGCCGTGGACT 60.153 52.632 0.00 0.00 46.52 3.85
195 196 1.166531 AGAAGCAAACTGCCGTGGAC 61.167 55.000 0.00 0.00 46.52 4.02
196 197 0.465460 AAGAAGCAAACTGCCGTGGA 60.465 50.000 0.00 0.00 46.52 4.02
197 198 0.385390 AAAGAAGCAAACTGCCGTGG 59.615 50.000 0.00 0.00 46.52 4.94
203 204 4.543692 CATGTCTCCAAAGAAGCAAACTG 58.456 43.478 0.00 0.00 31.93 3.16
209 210 0.179179 GCGCATGTCTCCAAAGAAGC 60.179 55.000 0.30 0.00 31.93 3.86
218 219 1.594862 GATACCAAGTGCGCATGTCTC 59.405 52.381 15.91 7.58 0.00 3.36
234 235 4.273480 CCTCACGGTTCATTCATTGGATAC 59.727 45.833 0.00 0.00 0.00 2.24
235 236 4.163268 TCCTCACGGTTCATTCATTGGATA 59.837 41.667 0.00 0.00 0.00 2.59
236 237 3.054434 TCCTCACGGTTCATTCATTGGAT 60.054 43.478 0.00 0.00 0.00 3.41
238 239 2.420022 GTCCTCACGGTTCATTCATTGG 59.580 50.000 0.00 0.00 0.00 3.16
253 254 3.773418 TTATTTGTTGACCCGTCCTCA 57.227 42.857 0.00 0.00 0.00 3.86
298 300 0.875059 CTCCGAGTTTTTCCTGTGGC 59.125 55.000 0.00 0.00 0.00 5.01
300 302 1.873591 CCACTCCGAGTTTTTCCTGTG 59.126 52.381 0.00 0.00 0.00 3.66
302 304 1.071699 TCCCACTCCGAGTTTTTCCTG 59.928 52.381 0.00 0.00 0.00 3.86
303 305 1.348036 CTCCCACTCCGAGTTTTTCCT 59.652 52.381 0.00 0.00 0.00 3.36
655 658 3.576078 ATTGCATATCCGGACAAAGGA 57.424 42.857 6.12 0.00 42.69 3.36
656 659 5.964958 ATTATTGCATATCCGGACAAAGG 57.035 39.130 6.12 0.00 0.00 3.11
688 695 6.125327 TCGAATTTATCTTGCCGCATTTAA 57.875 33.333 0.00 0.00 0.00 1.52
809 816 1.402259 CACGATTGTACTCGAGCTCCT 59.598 52.381 13.61 0.00 41.12 3.69
817 824 2.915738 AGACGGACACGATTGTACTC 57.084 50.000 0.00 0.00 44.60 2.59
856 863 2.814183 CTACGAGGAAGTTGGCGCGT 62.814 60.000 8.43 0.00 35.95 6.01
1515 1531 2.545537 GGGAGAACTCACGGAAGTTT 57.454 50.000 6.21 0.00 46.40 2.66
1667 1683 1.507141 GAAGCACGGACACCAACAGG 61.507 60.000 0.00 0.00 0.00 4.00
1968 1984 8.101309 TCATGGACAAATTCTCCTTATCCTTA 57.899 34.615 0.00 0.00 0.00 2.69
2105 2150 1.218047 GACATGGTAGACGGCAGCA 59.782 57.895 0.00 0.00 0.00 4.41
2172 2378 6.058833 TCAACAGCTCACACAAAACCTAATA 58.941 36.000 0.00 0.00 0.00 0.98
2173 2379 4.887071 TCAACAGCTCACACAAAACCTAAT 59.113 37.500 0.00 0.00 0.00 1.73
2237 2447 2.565841 GCTATAGCTGGTGGTGAAAGG 58.434 52.381 17.75 0.00 38.21 3.11
2253 2467 3.081409 AGGCAACCCGACGGCTAT 61.081 61.111 8.86 0.00 36.06 2.97
2291 2505 6.456795 AATCATAGTCGAGACACATTGAGA 57.543 37.500 5.99 0.00 0.00 3.27
2332 2546 3.862600 AGGATATAGGGACCAGCAGAT 57.137 47.619 0.00 0.00 0.00 2.90
2348 2562 0.689623 GCAGCTACAGGGCATAGGAT 59.310 55.000 0.00 0.00 34.17 3.24
2351 2565 2.149578 GATTGCAGCTACAGGGCATAG 58.850 52.381 0.00 0.00 37.39 2.23
2454 2668 6.007936 ACAAAATATAGTCGTGCAGCAAAA 57.992 33.333 0.00 0.00 0.00 2.44
2456 2670 5.621197 AACAAAATATAGTCGTGCAGCAA 57.379 34.783 0.00 0.00 0.00 3.91
2457 2671 5.389778 CAAACAAAATATAGTCGTGCAGCA 58.610 37.500 0.00 0.00 0.00 4.41
2458 2672 4.793216 CCAAACAAAATATAGTCGTGCAGC 59.207 41.667 0.00 0.00 0.00 5.25
2459 2673 5.331902 CCCAAACAAAATATAGTCGTGCAG 58.668 41.667 0.00 0.00 0.00 4.41
2500 2875 3.323979 GGGGCTTTCATATCCGTCTTCTA 59.676 47.826 0.00 0.00 0.00 2.10
2509 2884 0.476771 TTCCCCGGGGCTTTCATATC 59.523 55.000 36.68 0.00 34.68 1.63


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

AutoCloner maintained by Alex Coulton.