Multiple sequence alignment - TraesCS7A01G275300

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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 TraesCS7A01G275300 chr7A 100.000 2439 0 0 1 2439 287860789 287863227 0.000000e+00 4505
1 TraesCS7A01G275300 chr7A 86.082 1164 86 27 628 1728 287888324 287889474 0.000000e+00 1182
2 TraesCS7A01G275300 chr7A 94.819 579 29 1 1861 2439 287890281 287890858 0.000000e+00 902
3 TraesCS7A01G275300 chr7A 85.124 363 38 9 330 690 287913023 287913371 8.290000e-95 357
4 TraesCS7A01G275300 chr7A 95.062 162 7 1 103 263 492528823 492528662 1.120000e-63 254
5 TraesCS7A01G275300 chr7A 92.941 170 11 1 96 264 32776502 32776671 1.870000e-61 246
6 TraesCS7A01G275300 chr7D 93.142 1531 65 13 262 1754 264324250 264325778 0.000000e+00 2209
7 TraesCS7A01G275300 chr7D 90.798 1304 75 13 317 1594 264369103 264370387 0.000000e+00 1701
8 TraesCS7A01G275300 chr7D 89.550 1311 90 13 317 1594 264359223 264360519 0.000000e+00 1618
9 TraesCS7A01G275300 chr7D 88.687 990 62 15 646 1594 264337504 264338484 0.000000e+00 1162
10 TraesCS7A01G275300 chr7D 95.337 579 27 0 1861 2439 264326714 264327292 0.000000e+00 920
11 TraesCS7A01G275300 chr7D 95.337 579 27 0 1861 2439 264361553 264362131 0.000000e+00 920
12 TraesCS7A01G275300 chr7D 94.819 579 30 0 1861 2439 264371422 264372000 0.000000e+00 904
13 TraesCS7A01G275300 chr7D 94.444 576 31 1 1861 2436 264339489 264340063 0.000000e+00 885
14 TraesCS7A01G275300 chr7D 95.062 162 7 1 103 263 453283663 453283502 1.120000e-63 254
15 TraesCS7A01G275300 chr7D 96.154 104 4 0 1 104 264324148 264324251 1.160000e-38 171
16 TraesCS7A01G275300 chr7B 86.137 1623 140 36 317 1882 244714754 244716348 0.000000e+00 1672
17 TraesCS7A01G275300 chr7B 89.740 1306 81 18 317 1594 244691244 244692524 0.000000e+00 1620
18 TraesCS7A01G275300 chr7B 89.437 1297 78 20 317 1594 244643180 244644436 0.000000e+00 1581
19 TraesCS7A01G275300 chr7B 86.914 1322 90 28 628 1877 244650210 244651520 0.000000e+00 1406
20 TraesCS7A01G275300 chr7B 95.509 579 26 0 1861 2439 244693545 244694123 0.000000e+00 926
21 TraesCS7A01G275300 chr7B 95.509 579 26 0 1861 2439 244717032 244717610 0.000000e+00 926
22 TraesCS7A01G275300 chr7B 95.164 579 28 0 1861 2439 244645756 244646334 0.000000e+00 915
23 TraesCS7A01G275300 chr7B 93.955 579 35 0 1861 2439 244652147 244652725 0.000000e+00 876
24 TraesCS7A01G275300 chr7B 81.250 304 41 9 1593 1882 244692573 244692874 5.240000e-57 231
25 TraesCS7A01G275300 chrUn 92.211 873 49 7 317 1189 284874376 284875229 0.000000e+00 1218
26 TraesCS7A01G275300 chr2D 93.976 166 9 1 102 266 56541157 56540992 1.450000e-62 250
27 TraesCS7A01G275300 chr5D 93.452 168 9 2 100 265 46311058 46310891 5.210000e-62 248
28 TraesCS7A01G275300 chr5D 92.941 170 11 1 100 268 296949355 296949524 1.870000e-61 246
29 TraesCS7A01G275300 chr5B 93.939 165 9 1 103 266 539322883 539322719 5.210000e-62 248
30 TraesCS7A01G275300 chr6B 92.941 170 11 1 95 263 469042124 469041955 1.870000e-61 246
31 TraesCS7A01G275300 chr3D 92.000 175 12 2 91 264 410670052 410670225 6.740000e-61 244


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 TraesCS7A01G275300 chr7A 287860789 287863227 2438 False 4505.000000 4505 100.000000 1 2439 1 chr7A.!!$F2 2438
1 TraesCS7A01G275300 chr7A 287888324 287890858 2534 False 1042.000000 1182 90.450500 628 2439 2 chr7A.!!$F4 1811
2 TraesCS7A01G275300 chr7D 264369103 264372000 2897 False 1302.500000 1701 92.808500 317 2439 2 chr7D.!!$F4 2122
3 TraesCS7A01G275300 chr7D 264359223 264362131 2908 False 1269.000000 1618 92.443500 317 2439 2 chr7D.!!$F3 2122
4 TraesCS7A01G275300 chr7D 264324148 264327292 3144 False 1100.000000 2209 94.877667 1 2439 3 chr7D.!!$F1 2438
5 TraesCS7A01G275300 chr7D 264337504 264340063 2559 False 1023.500000 1162 91.565500 646 2436 2 chr7D.!!$F2 1790
6 TraesCS7A01G275300 chr7B 244714754 244717610 2856 False 1299.000000 1672 90.823000 317 2439 2 chr7B.!!$F3 2122
7 TraesCS7A01G275300 chr7B 244643180 244652725 9545 False 1194.500000 1581 91.367500 317 2439 4 chr7B.!!$F1 2122
8 TraesCS7A01G275300 chr7B 244691244 244694123 2879 False 925.666667 1620 88.833000 317 2439 3 chr7B.!!$F2 2122
9 TraesCS7A01G275300 chrUn 284874376 284875229 853 False 1218.000000 1218 92.211000 317 1189 1 chrUn.!!$F1 872

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
845 858 0.103026 CCATCAGCGACGAGATTCCA 59.897 55.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2042 3337 0.035458 CTTCGCCTTCTTCACCAGGT 59.965 55.0 0.0 0.0 32.06 4.0 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
36 37 5.240623 CCAGTTTATACCTGCAACACTTTGA 59.759 40.000 0.00 0.00 34.24 2.69
52 53 7.426929 ACACTTTGATGTGAGTTAATGAGAC 57.573 36.000 1.47 0.00 40.12 3.36
66 67 3.558931 ATGAGACGGTCATGCCAATTA 57.441 42.857 11.27 0.00 44.82 1.40
104 105 9.035607 CATCAAGACCTCAACACTATGTAATAC 57.964 37.037 0.00 0.00 0.00 1.89
105 106 8.362464 TCAAGACCTCAACACTATGTAATACT 57.638 34.615 0.00 0.00 0.00 2.12
106 107 8.467598 TCAAGACCTCAACACTATGTAATACTC 58.532 37.037 0.00 0.00 0.00 2.59
107 108 7.349412 AGACCTCAACACTATGTAATACTCC 57.651 40.000 0.00 0.00 0.00 3.85
108 109 7.126733 AGACCTCAACACTATGTAATACTCCT 58.873 38.462 0.00 0.00 0.00 3.69
109 110 7.285858 AGACCTCAACACTATGTAATACTCCTC 59.714 40.741 0.00 0.00 0.00 3.71
110 111 6.324254 ACCTCAACACTATGTAATACTCCTCC 59.676 42.308 0.00 0.00 0.00 4.30
111 112 6.387041 TCAACACTATGTAATACTCCTCCG 57.613 41.667 0.00 0.00 0.00 4.63
112 113 5.889853 TCAACACTATGTAATACTCCTCCGT 59.110 40.000 0.00 0.00 0.00 4.69
113 114 6.379133 TCAACACTATGTAATACTCCTCCGTT 59.621 38.462 0.00 0.00 0.00 4.44
114 115 6.388435 ACACTATGTAATACTCCTCCGTTC 57.612 41.667 0.00 0.00 0.00 3.95
115 116 5.301298 ACACTATGTAATACTCCTCCGTTCC 59.699 44.000 0.00 0.00 0.00 3.62
116 117 5.535406 CACTATGTAATACTCCTCCGTTCCT 59.465 44.000 0.00 0.00 0.00 3.36
117 118 6.713903 CACTATGTAATACTCCTCCGTTCCTA 59.286 42.308 0.00 0.00 0.00 2.94
118 119 7.230108 CACTATGTAATACTCCTCCGTTCCTAA 59.770 40.741 0.00 0.00 0.00 2.69
119 120 7.781693 ACTATGTAATACTCCTCCGTTCCTAAA 59.218 37.037 0.00 0.00 0.00 1.85
120 121 7.613551 ATGTAATACTCCTCCGTTCCTAAAT 57.386 36.000 0.00 0.00 0.00 1.40
121 122 8.716674 ATGTAATACTCCTCCGTTCCTAAATA 57.283 34.615 0.00 0.00 0.00 1.40
122 123 8.716674 TGTAATACTCCTCCGTTCCTAAATAT 57.283 34.615 0.00 0.00 0.00 1.28
123 124 9.812347 TGTAATACTCCTCCGTTCCTAAATATA 57.188 33.333 0.00 0.00 0.00 0.86
126 127 8.953223 ATACTCCTCCGTTCCTAAATATAAGT 57.047 34.615 0.00 0.00 0.00 2.24
127 128 7.287512 ACTCCTCCGTTCCTAAATATAAGTC 57.712 40.000 0.00 0.00 0.00 3.01
128 129 7.068061 ACTCCTCCGTTCCTAAATATAAGTCT 58.932 38.462 0.00 0.00 0.00 3.24
129 130 7.564292 ACTCCTCCGTTCCTAAATATAAGTCTT 59.436 37.037 0.00 0.00 0.00 3.01
130 131 8.315220 TCCTCCGTTCCTAAATATAAGTCTTT 57.685 34.615 0.00 0.00 0.00 2.52
131 132 8.202137 TCCTCCGTTCCTAAATATAAGTCTTTG 58.798 37.037 0.00 0.00 0.00 2.77
132 133 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
147 148 7.678947 AAGTCTTTGTAGAGATTTCACCATG 57.321 36.000 0.00 0.00 0.00 3.66
148 149 6.176183 AGTCTTTGTAGAGATTTCACCATGG 58.824 40.000 11.19 11.19 0.00 3.66
149 150 6.013379 AGTCTTTGTAGAGATTTCACCATGGA 60.013 38.462 21.47 0.00 0.00 3.41
150 151 6.092807 GTCTTTGTAGAGATTTCACCATGGAC 59.907 42.308 21.47 1.95 0.00 4.02
151 152 4.487714 TGTAGAGATTTCACCATGGACC 57.512 45.455 21.47 0.27 0.00 4.46
152 153 2.698855 AGAGATTTCACCATGGACCG 57.301 50.000 21.47 6.49 0.00 4.79
153 154 1.017387 GAGATTTCACCATGGACCGC 58.983 55.000 21.47 2.32 0.00 5.68
154 155 0.327924 AGATTTCACCATGGACCGCA 59.672 50.000 21.47 0.00 0.00 5.69
155 156 1.064463 AGATTTCACCATGGACCGCAT 60.064 47.619 21.47 3.22 0.00 4.73
156 157 2.172505 AGATTTCACCATGGACCGCATA 59.827 45.455 21.47 0.00 0.00 3.14
157 158 1.745232 TTTCACCATGGACCGCATAC 58.255 50.000 21.47 0.00 0.00 2.39
158 159 0.461163 TTCACCATGGACCGCATACG 60.461 55.000 21.47 0.00 39.67 3.06
180 181 7.658179 ACGGATGTATGTAGATGCATTTTAG 57.342 36.000 0.00 1.10 35.26 1.85
181 182 7.441836 ACGGATGTATGTAGATGCATTTTAGA 58.558 34.615 0.00 0.00 35.26 2.10
182 183 7.600375 ACGGATGTATGTAGATGCATTTTAGAG 59.400 37.037 0.00 0.00 35.26 2.43
183 184 7.600375 CGGATGTATGTAGATGCATTTTAGAGT 59.400 37.037 0.00 0.00 35.26 3.24
184 185 8.715998 GGATGTATGTAGATGCATTTTAGAGTG 58.284 37.037 0.00 0.00 35.26 3.51
185 186 9.265901 GATGTATGTAGATGCATTTTAGAGTGT 57.734 33.333 0.00 0.00 35.26 3.55
187 188 9.750125 TGTATGTAGATGCATTTTAGAGTGTAG 57.250 33.333 0.00 0.00 0.00 2.74
188 189 9.967346 GTATGTAGATGCATTTTAGAGTGTAGA 57.033 33.333 0.00 0.00 0.00 2.59
191 192 9.534565 TGTAGATGCATTTTAGAGTGTAGATTC 57.465 33.333 0.00 0.00 0.00 2.52
192 193 9.534565 GTAGATGCATTTTAGAGTGTAGATTCA 57.465 33.333 0.00 0.00 0.00 2.57
193 194 8.430801 AGATGCATTTTAGAGTGTAGATTCAC 57.569 34.615 0.00 0.00 38.46 3.18
204 205 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
205 206 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
206 207 5.412594 GTGTAGATTCACTCATTTTGCTCCA 59.587 40.000 0.00 0.00 35.68 3.86
207 208 6.094603 GTGTAGATTCACTCATTTTGCTCCAT 59.905 38.462 0.00 0.00 35.68 3.41
208 209 7.280876 GTGTAGATTCACTCATTTTGCTCCATA 59.719 37.037 0.00 0.00 35.68 2.74
209 210 7.994911 TGTAGATTCACTCATTTTGCTCCATAT 59.005 33.333 0.00 0.00 0.00 1.78
210 211 9.494271 GTAGATTCACTCATTTTGCTCCATATA 57.506 33.333 0.00 0.00 0.00 0.86
215 216 9.494271 TTCACTCATTTTGCTCCATATATAGTC 57.506 33.333 0.00 0.00 0.00 2.59
216 217 8.097038 TCACTCATTTTGCTCCATATATAGTCC 58.903 37.037 0.00 0.00 0.00 3.85
217 218 7.879677 CACTCATTTTGCTCCATATATAGTCCA 59.120 37.037 0.00 0.00 0.00 4.02
218 219 8.609483 ACTCATTTTGCTCCATATATAGTCCAT 58.391 33.333 0.00 0.00 0.00 3.41
221 222 9.896645 CATTTTGCTCCATATATAGTCCATAGT 57.103 33.333 0.00 0.00 0.00 2.12
222 223 9.896645 ATTTTGCTCCATATATAGTCCATAGTG 57.103 33.333 0.00 0.00 0.00 2.74
223 224 8.664669 TTTGCTCCATATATAGTCCATAGTGA 57.335 34.615 0.00 0.00 0.00 3.41
224 225 7.888250 TGCTCCATATATAGTCCATAGTGAG 57.112 40.000 0.00 0.00 0.00 3.51
225 226 7.643123 TGCTCCATATATAGTCCATAGTGAGA 58.357 38.462 0.00 0.00 0.00 3.27
226 227 8.285163 TGCTCCATATATAGTCCATAGTGAGAT 58.715 37.037 0.00 0.00 0.00 2.75
227 228 8.792633 GCTCCATATATAGTCCATAGTGAGATC 58.207 40.741 0.00 0.00 0.00 2.75
236 237 7.581213 AGTCCATAGTGAGATCTCTACAAAG 57.419 40.000 22.95 8.76 0.00 2.77
237 238 7.350382 AGTCCATAGTGAGATCTCTACAAAGA 58.650 38.462 22.95 10.78 0.00 2.52
238 239 7.284489 AGTCCATAGTGAGATCTCTACAAAGAC 59.716 40.741 22.95 19.93 0.00 3.01
239 240 7.284489 GTCCATAGTGAGATCTCTACAAAGACT 59.716 40.741 22.95 17.16 0.00 3.24
240 241 7.836685 TCCATAGTGAGATCTCTACAAAGACTT 59.163 37.037 22.95 5.47 0.00 3.01
241 242 9.126151 CCATAGTGAGATCTCTACAAAGACTTA 57.874 37.037 22.95 7.25 0.00 2.24
256 257 8.943909 ACAAAGACTTATATTTAGGAACCGAG 57.056 34.615 0.00 0.00 0.00 4.63
257 258 7.985752 ACAAAGACTTATATTTAGGAACCGAGG 59.014 37.037 0.00 0.00 0.00 4.63
258 259 6.667558 AGACTTATATTTAGGAACCGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
259 260 6.379579 AGACTTATATTTAGGAACCGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
260 261 6.494146 AGACTTATATTTAGGAACCGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
261 262 6.141790 ACTTATATTTAGGAACCGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
262 263 7.300658 ACTTATATTTAGGAACCGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
393 394 4.770795 AGCAATAATCGAGTAAACTGCCT 58.229 39.130 16.46 6.37 0.00 4.75
521 524 1.004745 CCCTAGTGGAAACATGCCAGT 59.995 52.381 0.00 0.00 46.14 4.00
548 551 2.159028 TCACCAGACAAACACATCGTGA 60.159 45.455 0.24 0.00 36.96 4.35
629 632 3.384467 GCTCTTTCTCTCCACTAGCTCAT 59.616 47.826 0.00 0.00 0.00 2.90
670 679 3.945921 CTGGATCTGACATCAAACTGCAT 59.054 43.478 0.00 0.00 0.00 3.96
672 681 3.943381 GGATCTGACATCAAACTGCATGA 59.057 43.478 0.00 0.00 0.00 3.07
845 858 0.103026 CCATCAGCGACGAGATTCCA 59.897 55.000 0.00 0.00 0.00 3.53
865 878 2.047061 AGTTGTCTACAAGGTCAGCCA 58.953 47.619 0.00 0.00 36.39 4.75
1175 1199 2.307098 ACAAAGATAGGCTGTGGAGCTT 59.693 45.455 0.00 0.00 45.44 3.74
1284 1330 2.836981 AGACCAAGATCCAGTCCTTCAG 59.163 50.000 4.27 0.00 0.00 3.02
1419 1484 2.189594 TCAATGCTTCAGTCACCCAG 57.810 50.000 0.00 0.00 0.00 4.45
1452 1517 4.943705 ACTGAAGTAAATTGTGATGCCGAT 59.056 37.500 0.00 0.00 0.00 4.18
1659 1798 2.839486 TGGACAGCGTCTTCAAGAAT 57.161 45.000 8.26 0.00 32.47 2.40
1763 2322 9.976511 GTCATACAAGCTAATACCATACTGTTA 57.023 33.333 0.00 0.00 0.00 2.41
1770 2330 7.333323 AGCTAATACCATACTGTTAAAACCGT 58.667 34.615 0.00 0.00 0.00 4.83
1796 2356 8.154203 TGTTTTGGAATGTGTCTCTACAAGATA 58.846 33.333 0.00 0.00 37.36 1.98
1823 2383 5.565592 TGTTATTCAGATGCCATGTGTTC 57.434 39.130 1.40 0.00 0.00 3.18
1856 2418 5.041191 AGCAAAGGATCCTTATACAGTGG 57.959 43.478 27.29 10.33 34.84 4.00
1857 2419 4.721776 AGCAAAGGATCCTTATACAGTGGA 59.278 41.667 27.29 0.00 34.84 4.02
1867 3162 7.233389 TCCTTATACAGTGGATCTTGCTATC 57.767 40.000 0.00 0.00 0.00 2.08
1899 3194 3.888930 GGAAGATGTTGGAAGGTGAAACA 59.111 43.478 0.00 0.00 39.98 2.83
1956 3251 0.684535 TGCATGAGGACTTCACCGAA 59.315 50.000 0.00 0.00 38.99 4.30
2042 3337 3.516586 TCAAGATCCAGTCTTACACCCA 58.483 45.455 0.00 0.00 45.35 4.51
2095 3390 0.952010 GGCCGCGAAGAAGGTTACAA 60.952 55.000 8.23 0.00 0.00 2.41
2187 3482 3.050619 GTCAACAGTACACCTCTTGTCG 58.949 50.000 0.00 0.00 39.91 4.35
2200 3495 1.870402 TCTTGTCGAAGCAAATCGCAA 59.130 42.857 0.00 12.11 46.13 4.85
2235 3530 0.690192 TCGTCTCCAAGGCATTCCAA 59.310 50.000 0.00 0.00 33.74 3.53
2245 3540 4.309933 CAAGGCATTCCAAAAGAAGAACC 58.690 43.478 0.00 0.00 38.07 3.62
2314 3609 0.540923 AGATCTTGAGGCTGGAGCAC 59.459 55.000 0.00 0.00 44.36 4.40
2408 3703 0.460987 ATCTGCTACTCTTGCACCGC 60.461 55.000 0.00 0.00 36.37 5.68
2410 3705 2.432628 GCTACTCTTGCACCGCGT 60.433 61.111 4.92 0.00 0.00 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.801330 TGACCGTCTCATTAACTCACAT 57.199 40.909 0.00 0.00 0.00 3.21
71 72 5.104610 AGTGTTGAGGTCTTGATGAGCATAT 60.105 40.000 0.42 0.00 44.98 1.78
104 105 7.527568 AGACTTATATTTAGGAACGGAGGAG 57.472 40.000 0.00 0.00 0.00 3.69
105 106 7.909485 AAGACTTATATTTAGGAACGGAGGA 57.091 36.000 0.00 0.00 0.00 3.71
106 107 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
107 108 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
121 122 9.388506 CATGGTGAAATCTCTACAAAGACTTAT 57.611 33.333 0.00 0.00 0.00 1.73
122 123 7.824289 CCATGGTGAAATCTCTACAAAGACTTA 59.176 37.037 2.57 0.00 0.00 2.24
123 124 6.656693 CCATGGTGAAATCTCTACAAAGACTT 59.343 38.462 2.57 0.00 0.00 3.01
124 125 6.013379 TCCATGGTGAAATCTCTACAAAGACT 60.013 38.462 12.58 0.00 0.00 3.24
125 126 6.092807 GTCCATGGTGAAATCTCTACAAAGAC 59.907 42.308 12.58 0.00 0.00 3.01
126 127 6.173339 GTCCATGGTGAAATCTCTACAAAGA 58.827 40.000 12.58 0.00 0.00 2.52
127 128 5.355350 GGTCCATGGTGAAATCTCTACAAAG 59.645 44.000 12.58 0.00 0.00 2.77
128 129 5.253330 GGTCCATGGTGAAATCTCTACAAA 58.747 41.667 12.58 0.00 0.00 2.83
129 130 4.622933 CGGTCCATGGTGAAATCTCTACAA 60.623 45.833 12.58 0.00 0.00 2.41
130 131 3.118775 CGGTCCATGGTGAAATCTCTACA 60.119 47.826 12.58 0.00 0.00 2.74
131 132 3.458189 CGGTCCATGGTGAAATCTCTAC 58.542 50.000 12.58 0.00 0.00 2.59
132 133 2.158957 GCGGTCCATGGTGAAATCTCTA 60.159 50.000 12.58 0.00 0.00 2.43
133 134 1.407437 GCGGTCCATGGTGAAATCTCT 60.407 52.381 12.58 0.00 0.00 3.10
134 135 1.017387 GCGGTCCATGGTGAAATCTC 58.983 55.000 12.58 0.00 0.00 2.75
135 136 0.327924 TGCGGTCCATGGTGAAATCT 59.672 50.000 12.58 0.00 0.00 2.40
136 137 1.392589 ATGCGGTCCATGGTGAAATC 58.607 50.000 12.58 0.00 31.48 2.17
137 138 2.297701 GTATGCGGTCCATGGTGAAAT 58.702 47.619 12.58 3.51 35.34 2.17
138 139 1.745232 GTATGCGGTCCATGGTGAAA 58.255 50.000 12.58 0.00 35.34 2.69
139 140 0.461163 CGTATGCGGTCCATGGTGAA 60.461 55.000 12.58 0.00 35.34 3.18
140 141 1.142965 CGTATGCGGTCCATGGTGA 59.857 57.895 12.58 0.00 35.34 4.02
141 142 3.717899 CGTATGCGGTCCATGGTG 58.282 61.111 12.58 4.31 35.34 4.17
154 155 9.371136 CTAAAATGCATCTACATACATCCGTAT 57.629 33.333 0.00 0.00 38.96 3.06
155 156 8.581578 TCTAAAATGCATCTACATACATCCGTA 58.418 33.333 0.00 0.00 0.00 4.02
156 157 7.441836 TCTAAAATGCATCTACATACATCCGT 58.558 34.615 0.00 0.00 0.00 4.69
157 158 7.600375 ACTCTAAAATGCATCTACATACATCCG 59.400 37.037 0.00 0.00 0.00 4.18
158 159 8.715998 CACTCTAAAATGCATCTACATACATCC 58.284 37.037 0.00 0.00 0.00 3.51
159 160 9.265901 ACACTCTAAAATGCATCTACATACATC 57.734 33.333 0.00 0.00 0.00 3.06
161 162 9.750125 CTACACTCTAAAATGCATCTACATACA 57.250 33.333 0.00 0.00 0.00 2.29
162 163 9.967346 TCTACACTCTAAAATGCATCTACATAC 57.033 33.333 0.00 0.00 0.00 2.39
165 166 9.534565 GAATCTACACTCTAAAATGCATCTACA 57.465 33.333 0.00 0.00 0.00 2.74
166 167 9.534565 TGAATCTACACTCTAAAATGCATCTAC 57.465 33.333 0.00 0.00 0.00 2.59
167 168 9.534565 GTGAATCTACACTCTAAAATGCATCTA 57.465 33.333 0.00 0.00 37.73 1.98
168 169 8.263640 AGTGAATCTACACTCTAAAATGCATCT 58.736 33.333 0.00 0.00 46.36 2.90
169 170 8.430801 AGTGAATCTACACTCTAAAATGCATC 57.569 34.615 0.00 0.00 46.36 3.91
182 183 5.412594 TGGAGCAAAATGAGTGAATCTACAC 59.587 40.000 0.00 0.00 40.60 2.90
183 184 5.559770 TGGAGCAAAATGAGTGAATCTACA 58.440 37.500 0.00 0.00 0.00 2.74
184 185 6.690194 ATGGAGCAAAATGAGTGAATCTAC 57.310 37.500 0.00 0.00 0.00 2.59
189 190 9.494271 GACTATATATGGAGCAAAATGAGTGAA 57.506 33.333 2.68 0.00 0.00 3.18
190 191 8.097038 GGACTATATATGGAGCAAAATGAGTGA 58.903 37.037 2.68 0.00 0.00 3.41
191 192 7.879677 TGGACTATATATGGAGCAAAATGAGTG 59.120 37.037 2.68 0.00 0.00 3.51
192 193 7.977818 TGGACTATATATGGAGCAAAATGAGT 58.022 34.615 2.68 0.00 0.00 3.41
195 196 9.896645 ACTATGGACTATATATGGAGCAAAATG 57.103 33.333 2.68 0.00 0.00 2.32
196 197 9.896645 CACTATGGACTATATATGGAGCAAAAT 57.103 33.333 2.68 0.00 0.00 1.82
197 198 9.100197 TCACTATGGACTATATATGGAGCAAAA 57.900 33.333 2.68 0.00 0.00 2.44
198 199 8.664669 TCACTATGGACTATATATGGAGCAAA 57.335 34.615 2.68 0.00 0.00 3.68
199 200 8.116026 TCTCACTATGGACTATATATGGAGCAA 58.884 37.037 2.68 0.00 0.00 3.91
200 201 7.643123 TCTCACTATGGACTATATATGGAGCA 58.357 38.462 2.68 0.00 0.00 4.26
201 202 8.704849 ATCTCACTATGGACTATATATGGAGC 57.295 38.462 2.68 0.00 0.00 4.70
210 211 9.295825 CTTTGTAGAGATCTCACTATGGACTAT 57.704 37.037 24.39 1.90 0.00 2.12
211 212 8.495260 TCTTTGTAGAGATCTCACTATGGACTA 58.505 37.037 24.39 2.17 0.00 2.59
212 213 7.284489 GTCTTTGTAGAGATCTCACTATGGACT 59.716 40.741 24.39 3.15 0.00 3.85
213 214 7.284489 AGTCTTTGTAGAGATCTCACTATGGAC 59.716 40.741 24.39 21.06 0.00 4.02
214 215 7.350382 AGTCTTTGTAGAGATCTCACTATGGA 58.650 38.462 24.39 12.20 0.00 3.41
215 216 7.581213 AGTCTTTGTAGAGATCTCACTATGG 57.419 40.000 24.39 10.24 0.00 2.74
231 232 7.985752 CCTCGGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
232 233 7.441458 CCCTCGGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
233 234 7.346436 TCCCTCGGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
234 235 6.842807 TCCCTCGGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
235 236 6.379579 TCCCTCGGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
236 237 6.267242 ACTCCCTCGGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
237 238 6.141790 ACTCCCTCGGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
238 239 6.667558 ACTCCCTCGGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
239 240 7.529555 TCTACTCCCTCGGTTCCTAAATATAA 58.470 38.462 0.00 0.00 0.00 0.98
240 241 7.095183 TCTACTCCCTCGGTTCCTAAATATA 57.905 40.000 0.00 0.00 0.00 0.86
241 242 5.961897 TCTACTCCCTCGGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
242 243 5.393068 TCTACTCCCTCGGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
243 244 4.261411 TCTACTCCCTCGGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
244 245 3.744940 TCTACTCCCTCGGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
245 246 3.744940 TTCTACTCCCTCGGTTCCTAA 57.255 47.619 0.00 0.00 0.00 2.69
246 247 3.626729 CCTTTCTACTCCCTCGGTTCCTA 60.627 52.174 0.00 0.00 0.00 2.94
247 248 2.458620 CTTTCTACTCCCTCGGTTCCT 58.541 52.381 0.00 0.00 0.00 3.36
248 249 1.481363 CCTTTCTACTCCCTCGGTTCC 59.519 57.143 0.00 0.00 0.00 3.62
249 250 2.454538 TCCTTTCTACTCCCTCGGTTC 58.545 52.381 0.00 0.00 0.00 3.62
250 251 2.617840 TCCTTTCTACTCCCTCGGTT 57.382 50.000 0.00 0.00 0.00 4.44
251 252 2.292323 ACATCCTTTCTACTCCCTCGGT 60.292 50.000 0.00 0.00 0.00 4.69
252 253 2.389715 ACATCCTTTCTACTCCCTCGG 58.610 52.381 0.00 0.00 0.00 4.63
253 254 3.786635 CAACATCCTTTCTACTCCCTCG 58.213 50.000 0.00 0.00 0.00 4.63
254 255 3.198853 AGCAACATCCTTTCTACTCCCTC 59.801 47.826 0.00 0.00 0.00 4.30
255 256 3.185455 AGCAACATCCTTTCTACTCCCT 58.815 45.455 0.00 0.00 0.00 4.20
256 257 3.198853 AGAGCAACATCCTTTCTACTCCC 59.801 47.826 0.00 0.00 0.00 4.30
257 258 4.438148 GAGAGCAACATCCTTTCTACTCC 58.562 47.826 0.00 0.00 0.00 3.85
258 259 4.161377 AGGAGAGCAACATCCTTTCTACTC 59.839 45.833 0.00 0.00 43.62 2.59
259 260 4.100373 AGGAGAGCAACATCCTTTCTACT 58.900 43.478 0.00 0.00 43.62 2.57
260 261 4.438148 GAGGAGAGCAACATCCTTTCTAC 58.562 47.826 0.00 0.00 46.12 2.59
261 262 3.131223 CGAGGAGAGCAACATCCTTTCTA 59.869 47.826 0.00 0.00 46.12 2.10
262 263 2.093764 CGAGGAGAGCAACATCCTTTCT 60.094 50.000 0.00 0.00 46.12 2.52
393 394 0.603707 CTGACAGCAAGGAAAGGCGA 60.604 55.000 0.00 0.00 34.54 5.54
548 551 2.158623 TCACCTTTGAGCTCCAACACAT 60.159 45.455 12.15 0.00 33.85 3.21
551 554 2.092429 ACTTCACCTTTGAGCTCCAACA 60.092 45.455 12.15 0.00 33.85 3.33
629 632 5.152934 TCCAGATCCAGATCATGAGATTGA 58.847 41.667 10.17 0.00 40.22 2.57
670 679 1.733912 GCAAACTCATCTGCACGATCA 59.266 47.619 0.00 0.00 38.48 2.92
672 681 1.736126 CAGCAAACTCATCTGCACGAT 59.264 47.619 0.00 0.00 41.17 3.73
821 833 2.994995 TCGTCGCTGATGGGGTGT 60.995 61.111 0.00 0.00 0.00 4.16
845 858 2.047061 TGGCTGACCTTGTAGACAACT 58.953 47.619 0.00 0.00 36.63 3.16
865 878 6.005823 TCTATATAAGCACAAGCCATGCAAT 58.994 36.000 7.14 3.30 45.92 3.56
1018 1034 3.393800 TGTTCGCCTTCAGAGAAAAGAG 58.606 45.455 0.00 0.00 0.00 2.85
1113 1137 4.980339 TTGGCTGCATATGATCTCCTTA 57.020 40.909 6.97 0.00 0.00 2.69
1175 1199 2.497273 TGCAAGATAGTGCTGTAGCTCA 59.503 45.455 5.38 0.00 45.17 4.26
1273 1309 1.079543 CAGACGGCTGAAGGACTGG 60.080 63.158 14.96 0.00 45.17 4.00
1284 1330 1.450312 CCCATCTTGGTCAGACGGC 60.450 63.158 0.00 0.00 32.99 5.68
1419 1484 0.822164 TTACTTCAGTAGGAGCCGCC 59.178 55.000 0.00 0.00 0.00 6.13
1614 1748 8.174733 AGCTATCAGCAGCATAAACATTAAAT 57.825 30.769 0.00 0.00 45.56 1.40
1619 1753 4.277672 CCAAGCTATCAGCAGCATAAACAT 59.722 41.667 0.00 0.00 45.56 2.71
1659 1798 7.500892 TGAGTTAAATGCTCCAGAGTTGTTTTA 59.499 33.333 0.00 0.00 32.31 1.52
1705 1844 7.011763 GCAATGATGAGCATTTCAGAGTAACTA 59.988 37.037 0.00 0.00 44.68 2.24
1714 2152 2.159156 GCCAGCAATGATGAGCATTTCA 60.159 45.455 0.00 0.00 44.68 2.69
1763 2322 4.081917 AGACACATTCCAAAACACGGTTTT 60.082 37.500 8.40 8.40 0.00 2.43
1770 2330 6.353323 TCTTGTAGAGACACATTCCAAAACA 58.647 36.000 0.00 0.00 34.48 2.83
1796 2356 3.301794 TGGCATCTGAATAACATGGCT 57.698 42.857 0.00 0.00 35.83 4.75
1823 2383 1.321474 TCCTTTGCTTGTTGCTGAGG 58.679 50.000 0.00 0.00 42.05 3.86
1856 2418 1.953559 TTGCCGTGGATAGCAAGATC 58.046 50.000 0.00 0.00 43.74 2.75
1865 3160 1.004745 ACATCTTCCTTTGCCGTGGAT 59.995 47.619 0.00 0.00 31.76 3.41
1867 3162 1.068333 CAACATCTTCCTTTGCCGTGG 60.068 52.381 0.00 0.00 0.00 4.94
1871 3166 2.232208 CCTTCCAACATCTTCCTTTGCC 59.768 50.000 0.00 0.00 0.00 4.52
1956 3251 5.773680 CAGATCTTGGATAATGGCCTTCAAT 59.226 40.000 3.32 0.00 0.00 2.57
2042 3337 0.035458 CTTCGCCTTCTTCACCAGGT 59.965 55.000 0.00 0.00 32.06 4.00
2095 3390 1.821061 CTGCAGTCCTCCTTGTCGGT 61.821 60.000 5.25 0.00 0.00 4.69
2137 3432 1.219213 AGAGGTGGTGATCTCCCTAGG 59.781 57.143 11.24 0.06 28.07 3.02
2187 3482 1.712401 TTGGCATTGCGATTTGCTTC 58.288 45.000 1.91 0.00 46.63 3.86
2200 3495 2.026822 AGACGAGAGACCATTTTGGCAT 60.027 45.455 0.00 0.00 42.67 4.40
2235 3530 2.159156 GCAAACAACCGGGTTCTTCTTT 60.159 45.455 10.04 2.85 0.00 2.52
2245 3540 0.821711 TCCTCCTTGCAAACAACCGG 60.822 55.000 0.00 0.00 0.00 5.28
2314 3609 2.609459 CCAATCTCCGGAACAGAATTCG 59.391 50.000 5.23 0.00 0.00 3.34
2382 3677 3.748048 TGCAAGAGTAGCAGATGTTGAAC 59.252 43.478 0.00 0.00 37.02 3.18
2408 3703 1.247567 AAAGGTGGAAGCCAATCACG 58.752 50.000 0.00 0.00 34.18 4.35
2410 3705 4.283212 CCTTTAAAAGGTGGAAGCCAATCA 59.717 41.667 0.00 0.00 43.95 2.57


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

AutoCloner maintained by Alex Coulton.