Multiple sequence alignment - TraesCS6B01G254200

Loading Multiple Alignment...

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 TraesCS6B01G254200 chr6B 100.000 3088 0 0 1 3088 457218304 457215217 0.000000e+00 5703.0
1 TraesCS6B01G254200 chr6B 93.982 914 44 7 2171 3081 198988765 198987860 0.000000e+00 1373.0
2 TraesCS6B01G254200 chr6D 92.092 2137 95 38 72 2173 292739200 292737103 0.000000e+00 2942.0
3 TraesCS6B01G254200 chr6D 86.364 88 9 3 1523 1608 309719543 309719629 3.280000e-15 93.5
4 TraesCS6B01G254200 chr6A 91.326 1199 55 18 31 1213 428425051 428426216 0.000000e+00 1592.0
5 TraesCS6B01G254200 chr6A 91.157 916 53 14 1267 2170 428426230 428427129 0.000000e+00 1218.0
6 TraesCS6B01G254200 chr2A 88.820 483 51 3 2166 2646 165003101 165002620 9.540000e-165 590.0
7 TraesCS6B01G254200 chr2A 87.662 154 14 3 1527 1679 607841870 607841721 1.140000e-39 174.0
8 TraesCS6B01G254200 chr7A 87.179 273 33 2 2171 2443 721233041 721233311 2.990000e-80 309.0
9 TraesCS6B01G254200 chr7A 83.273 275 41 3 2171 2441 207300419 207300146 6.610000e-62 248.0
10 TraesCS6B01G254200 chr7A 83.333 264 37 6 2171 2433 150152519 150152776 1.430000e-58 237.0
11 TraesCS6B01G254200 chr7A 82.524 206 20 8 2876 3081 721233337 721233526 1.900000e-37 167.0
12 TraesCS6B01G254200 chr2B 84.688 320 17 18 2470 2761 437386417 437386102 1.080000e-74 291.0
13 TraesCS6B01G254200 chr2B 88.312 154 13 4 1527 1679 545366056 545365907 2.450000e-41 180.0
14 TraesCS6B01G254200 chr4D 86.142 267 37 0 2171 2437 504260088 504259822 3.900000e-74 289.0
15 TraesCS6B01G254200 chr4D 86.022 93 13 0 1527 1619 497126484 497126576 1.960000e-17 100.0
16 TraesCS6B01G254200 chr3D 86.038 265 33 3 2171 2433 300922015 300921753 6.520000e-72 281.0
17 TraesCS6B01G254200 chr2D 83.481 339 17 19 2457 2761 368529686 368529353 2.340000e-71 279.0
18 TraesCS6B01G254200 chr2D 88.312 154 13 3 1527 1679 466723987 466723838 2.450000e-41 180.0
19 TraesCS6B01G254200 chr3B 85.227 264 29 9 2172 2432 521788137 521788393 2.360000e-66 263.0
20 TraesCS6B01G254200 chr5B 81.784 269 49 0 2171 2439 67330152 67330420 3.100000e-55 226.0
21 TraesCS6B01G254200 chr5A 86.022 93 13 0 1527 1619 676887309 676887401 1.960000e-17 100.0
22 TraesCS6B01G254200 chr4B 86.022 93 13 0 1527 1619 637622199 637622291 1.960000e-17 100.0


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 TraesCS6B01G254200 chr6B 457215217 457218304 3087 True 5703 5703 100.0000 1 3088 1 chr6B.!!$R2 3087
1 TraesCS6B01G254200 chr6B 198987860 198988765 905 True 1373 1373 93.9820 2171 3081 1 chr6B.!!$R1 910
2 TraesCS6B01G254200 chr6D 292737103 292739200 2097 True 2942 2942 92.0920 72 2173 1 chr6D.!!$R1 2101
3 TraesCS6B01G254200 chr6A 428425051 428427129 2078 False 1405 1592 91.2415 31 2170 2 chr6A.!!$F1 2139

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
932 963 0.464735 TCGCCTCACTAGCTCTCTCC 60.465 60.0 0.0 0.0 0.0 3.71 F
1254 1291 0.105964 TCTACTGGGGCTCTAGCTGG 60.106 60.0 0.0 0.0 41.7 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 1905 0.034337 GGTGGTCGTACTGCAGGAAA 59.966 55.0 19.93 0.0 0.0 3.13 R
2244 2297 0.517316 CGCTACACAAAAGGGTCAGC 59.483 55.0 0.00 0.0 0.0 4.26 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
97 98 4.080526 AGGAAAAGGCTAACGTGGATATGT 60.081 41.667 0.00 0.00 0.00 2.29
129 130 3.230522 AACCCCCGTACACGACAGC 62.231 63.158 2.76 0.00 43.02 4.40
159 160 1.206132 CCTCTTGTATGGCCACACGTA 59.794 52.381 8.16 0.00 0.00 3.57
189 190 4.033702 TGCACATAAAACGTACGAAACACA 59.966 37.500 24.41 5.22 0.00 3.72
193 194 2.314323 AAACGTACGAAACACACCCT 57.686 45.000 24.41 0.00 0.00 4.34
197 198 1.068055 CGTACGAAACACACCCTAGCT 60.068 52.381 10.44 0.00 0.00 3.32
216 217 6.915843 CCTAGCTCTTTCTAGAACGAATCTTC 59.084 42.308 12.27 1.54 39.71 2.87
429 436 6.652062 ACTTCATGCGATATTATTGCTGATCA 59.348 34.615 15.34 0.00 40.43 2.92
499 507 5.672051 CAAGAGTCAGTAGTACGATCGATC 58.328 45.833 24.34 15.68 0.00 3.69
602 610 2.378445 ACACAAAGCAACACCCAAAC 57.622 45.000 0.00 0.00 0.00 2.93
603 611 1.620819 ACACAAAGCAACACCCAAACA 59.379 42.857 0.00 0.00 0.00 2.83
604 612 2.037772 ACACAAAGCAACACCCAAACAA 59.962 40.909 0.00 0.00 0.00 2.83
605 613 3.070018 CACAAAGCAACACCCAAACAAA 58.930 40.909 0.00 0.00 0.00 2.83
659 667 0.611618 TCGGCAGGAAACCTACGGTA 60.612 55.000 11.83 0.00 33.12 4.02
687 695 3.878237 AATCCATCATCATGCCTGTCT 57.122 42.857 0.00 0.00 0.00 3.41
709 717 4.926140 AGAAAAAGAGGAGCAAAAGGTG 57.074 40.909 0.00 0.00 0.00 4.00
713 721 2.797177 AGAGGAGCAAAAGGTGGATC 57.203 50.000 0.00 0.00 0.00 3.36
883 895 2.796383 GCGCGCTAGTATATATGCAGCT 60.796 50.000 26.67 0.00 0.00 4.24
923 944 1.228769 ACACCACCTCGCCTCACTA 60.229 57.895 0.00 0.00 0.00 2.74
932 963 0.464735 TCGCCTCACTAGCTCTCTCC 60.465 60.000 0.00 0.00 0.00 3.71
933 964 0.465460 CGCCTCACTAGCTCTCTCCT 60.465 60.000 0.00 0.00 0.00 3.69
937 968 2.487265 CCTCACTAGCTCTCTCCTCCTC 60.487 59.091 0.00 0.00 0.00 3.71
938 969 1.493022 TCACTAGCTCTCTCCTCCTCC 59.507 57.143 0.00 0.00 0.00 4.30
940 971 1.149101 CTAGCTCTCTCCTCCTCCCT 58.851 60.000 0.00 0.00 0.00 4.20
944 975 2.285180 CTCTCCTCCTCCCTGGGG 59.715 72.222 14.00 2.42 36.20 4.96
1104 1135 1.841302 ATGTTCGGCAGCAGGGAGAA 61.841 55.000 0.00 0.00 0.00 2.87
1175 1212 8.105097 TGATCATTCGTGTTCTTTAATTTGGA 57.895 30.769 0.00 0.00 0.00 3.53
1187 1224 5.356751 TCTTTAATTTGGACTGCATGCGTAT 59.643 36.000 14.09 0.00 0.00 3.06
1188 1225 6.540551 TCTTTAATTTGGACTGCATGCGTATA 59.459 34.615 14.09 4.07 0.00 1.47
1189 1226 4.552166 AATTTGGACTGCATGCGTATAC 57.448 40.909 14.09 1.77 0.00 1.47
1213 1250 2.555782 GCGCATGCAAGTTCGTCA 59.444 55.556 19.57 0.00 42.15 4.35
1215 1252 0.454957 GCGCATGCAAGTTCGTCAAT 60.455 50.000 19.57 0.00 42.15 2.57
1216 1253 1.253116 CGCATGCAAGTTCGTCAATG 58.747 50.000 19.57 0.00 0.00 2.82
1217 1254 0.986992 GCATGCAAGTTCGTCAATGC 59.013 50.000 14.21 0.00 39.22 3.56
1218 1255 1.621107 CATGCAAGTTCGTCAATGCC 58.379 50.000 0.00 0.00 38.00 4.40
1219 1256 0.527565 ATGCAAGTTCGTCAATGCCC 59.472 50.000 0.00 0.00 38.00 5.36
1223 1260 2.163412 GCAAGTTCGTCAATGCCCAATA 59.837 45.455 0.00 0.00 32.73 1.90
1224 1261 3.731867 GCAAGTTCGTCAATGCCCAATAG 60.732 47.826 0.00 0.00 32.73 1.73
1225 1262 3.350219 AGTTCGTCAATGCCCAATAGT 57.650 42.857 0.00 0.00 0.00 2.12
1226 1263 3.009723 AGTTCGTCAATGCCCAATAGTG 58.990 45.455 0.00 0.00 0.00 2.74
1227 1264 1.378531 TCGTCAATGCCCAATAGTGC 58.621 50.000 0.00 0.00 0.00 4.40
1228 1265 1.065491 TCGTCAATGCCCAATAGTGCT 60.065 47.619 0.00 0.00 0.00 4.40
1229 1266 1.064505 CGTCAATGCCCAATAGTGCTG 59.935 52.381 0.00 0.00 0.00 4.41
1230 1267 1.105457 TCAATGCCCAATAGTGCTGC 58.895 50.000 0.00 0.00 0.00 5.25
1231 1268 1.108776 CAATGCCCAATAGTGCTGCT 58.891 50.000 0.00 0.00 0.00 4.24
1232 1269 1.479323 CAATGCCCAATAGTGCTGCTT 59.521 47.619 0.00 0.00 0.00 3.91
1235 1272 1.026718 GCCCAATAGTGCTGCTTCGT 61.027 55.000 0.00 0.00 0.00 3.85
1236 1273 1.009829 CCCAATAGTGCTGCTTCGTC 58.990 55.000 0.00 0.00 0.00 4.20
1240 1277 3.429547 CCAATAGTGCTGCTTCGTCTACT 60.430 47.826 0.00 0.00 0.00 2.57
1241 1278 2.921634 TAGTGCTGCTTCGTCTACTG 57.078 50.000 0.00 0.00 0.00 2.74
1243 1280 0.737715 GTGCTGCTTCGTCTACTGGG 60.738 60.000 0.00 0.00 0.00 4.45
1244 1281 1.153549 GCTGCTTCGTCTACTGGGG 60.154 63.158 0.00 0.00 0.00 4.96
1246 1283 1.608717 CTGCTTCGTCTACTGGGGCT 61.609 60.000 0.00 0.00 0.00 5.19
1247 1284 1.142097 GCTTCGTCTACTGGGGCTC 59.858 63.158 0.00 0.00 0.00 4.70
1248 1285 1.324005 GCTTCGTCTACTGGGGCTCT 61.324 60.000 0.00 0.00 0.00 4.09
1249 1286 2.022754 GCTTCGTCTACTGGGGCTCTA 61.023 57.143 0.00 0.00 0.00 2.43
1251 1288 0.465824 TCGTCTACTGGGGCTCTAGC 60.466 60.000 0.00 0.00 41.14 3.42
1252 1289 0.466555 CGTCTACTGGGGCTCTAGCT 60.467 60.000 0.00 0.00 41.70 3.32
1253 1290 1.036707 GTCTACTGGGGCTCTAGCTG 58.963 60.000 0.00 0.00 41.70 4.24
1254 1291 0.105964 TCTACTGGGGCTCTAGCTGG 60.106 60.000 0.00 0.00 41.70 4.85
1255 1292 1.075226 TACTGGGGCTCTAGCTGGG 60.075 63.158 0.00 0.00 41.70 4.45
1256 1293 1.590339 TACTGGGGCTCTAGCTGGGA 61.590 60.000 0.00 0.00 41.70 4.37
1257 1294 2.041508 TGGGGCTCTAGCTGGGAG 60.042 66.667 12.37 12.37 41.70 4.30
1289 1326 1.609208 ATCTCGTTTTGCTGCAGGTT 58.391 45.000 17.12 0.00 0.00 3.50
1381 1418 0.251653 TTACGCCACAGGAGGAGAGT 60.252 55.000 0.00 0.00 32.29 3.24
1421 1458 1.546998 CCTTGTGGGGAAACAGGTACC 60.547 57.143 2.73 2.73 0.00 3.34
1422 1459 1.144093 CTTGTGGGGAAACAGGTACCA 59.856 52.381 15.94 0.00 0.00 3.25
1423 1460 3.334413 GTGGGGAAACAGGTACCAC 57.666 57.895 15.94 0.00 43.98 4.16
1456 1493 0.881118 TTTCTTTGGTCTGCGGATGC 59.119 50.000 0.00 0.00 43.20 3.91
1610 1659 0.955919 GGACGCACTTCAAGAAGGGG 60.956 60.000 13.49 12.11 41.99 4.79
1685 1734 1.590932 GCGAGATCATGCAAGGTCAT 58.409 50.000 4.82 0.00 0.00 3.06
1791 1840 4.595538 AAGCGACGACACGGCCAA 62.596 61.111 2.24 0.00 0.00 4.52
1832 1884 1.282875 CGACCTAGCGATGATGCGA 59.717 57.895 0.00 0.00 40.67 5.10
1846 1898 3.188786 GCGAGACATGGCGGACAC 61.189 66.667 0.00 0.00 0.00 3.67
1853 1905 3.458163 ATGGCGGACACGGACGAT 61.458 61.111 0.00 0.00 41.36 3.73
1956 2008 2.765807 CCAGCGGGGAGATCACCT 60.766 66.667 9.20 0.00 40.01 4.00
2108 2161 4.927049 AGCCTAGCATATACAATGGCAAT 58.073 39.130 0.00 0.00 41.12 3.56
2109 2162 5.327732 AGCCTAGCATATACAATGGCAATT 58.672 37.500 0.00 0.00 41.12 2.32
2181 2234 4.651045 GGTGGATAAGGAGGCAAAAATGAT 59.349 41.667 0.00 0.00 0.00 2.45
2193 2246 7.105241 AGGCAAAAATGATAAATCTGACCTC 57.895 36.000 0.00 0.00 0.00 3.85
2196 2249 6.976925 GCAAAAATGATAAATCTGACCTCAGG 59.023 38.462 2.45 0.00 43.91 3.86
2215 2268 6.295039 TCAGGACGAAACTAATTCACAAAC 57.705 37.500 0.00 0.00 37.96 2.93
2222 2275 8.428186 ACGAAACTAATTCACAAACTGAACTA 57.572 30.769 0.00 0.00 41.87 2.24
2258 2311 1.605710 CACTCAGCTGACCCTTTTGTG 59.394 52.381 13.74 13.61 0.00 3.33
2266 2319 1.583495 GACCCTTTTGTGTAGCGCCC 61.583 60.000 2.29 0.00 0.00 6.13
2274 2327 1.153628 GTGTAGCGCCCGACATCTT 60.154 57.895 2.29 0.00 0.00 2.40
2276 2329 1.141019 GTAGCGCCCGACATCTTGA 59.859 57.895 2.29 0.00 0.00 3.02
2278 2331 1.600511 TAGCGCCCGACATCTTGACA 61.601 55.000 2.29 0.00 0.00 3.58
2296 2349 1.416030 ACATCACACTACACTGTGCCA 59.584 47.619 7.90 0.00 41.27 4.92
2299 2352 1.594293 ACACTACACTGTGCCACGC 60.594 57.895 7.90 0.00 41.30 5.34
2319 2372 0.174389 CTGACTCACAGGCGCTACAT 59.826 55.000 7.64 0.00 42.39 2.29
2336 2389 3.017771 ATGCCTGACCATCGTCGCA 62.018 57.895 0.00 0.00 42.37 5.10
2338 2391 2.240500 GCCTGACCATCGTCGCATC 61.241 63.158 0.00 0.00 42.37 3.91
2339 2392 1.592669 CCTGACCATCGTCGCATCC 60.593 63.158 0.00 0.00 42.37 3.51
2341 2394 0.873312 CTGACCATCGTCGCATCCAG 60.873 60.000 0.00 0.00 42.37 3.86
2357 2410 4.380233 GCATCCAGGACTGACTGAAAAATG 60.380 45.833 0.00 5.61 40.97 2.32
2374 2427 5.458041 AAAATGCTAAGTCAGTGTGCAAT 57.542 34.783 0.00 0.00 37.20 3.56
2460 2513 2.049802 ACGCGGTACACTTCCACG 60.050 61.111 12.47 0.00 36.70 4.94
2468 2521 0.398696 TACACTTCCACGGCCATTGT 59.601 50.000 2.24 0.00 0.00 2.71
2542 2595 3.055591 GTGACGTGATGATGGATAGCTG 58.944 50.000 0.00 0.00 0.00 4.24
2582 2636 3.181522 CGATCCCTATTCGCGTAGTAGTC 60.182 52.174 5.77 1.00 0.00 2.59
2597 2651 3.547746 AGTAGTCGCTTTGGGTTTTTCA 58.452 40.909 0.00 0.00 0.00 2.69
2824 2880 2.831770 CATGCATAGGGGAGCGGT 59.168 61.111 0.00 0.00 0.00 5.68
2832 2888 2.451462 TAGGGGAGCGGTATAGGCCC 62.451 65.000 0.00 0.00 38.08 5.80
2866 2922 0.966920 CCAGCCCGAGAACCGTATAT 59.033 55.000 0.00 0.00 36.31 0.86
2867 2923 2.165167 CCAGCCCGAGAACCGTATATA 58.835 52.381 0.00 0.00 36.31 0.86
2868 2924 2.758979 CCAGCCCGAGAACCGTATATAT 59.241 50.000 0.00 0.00 36.31 0.86
2869 2925 3.949754 CCAGCCCGAGAACCGTATATATA 59.050 47.826 0.00 0.00 36.31 0.86
2870 2926 4.583489 CCAGCCCGAGAACCGTATATATAT 59.417 45.833 0.00 0.00 36.31 0.86
2912 2968 1.308998 CATGGGGGTCGCTAAACATC 58.691 55.000 0.00 0.00 0.00 3.06
2941 2997 4.056125 GGCTTTGCTGGTTCGCCC 62.056 66.667 0.00 0.00 34.75 6.13
3017 3073 1.639298 GCACAAGCTAGCCAGTTCCG 61.639 60.000 12.13 0.09 37.91 4.30
3033 3089 4.012895 CGCGTGTGTTGGCCACTC 62.013 66.667 3.88 1.78 44.81 3.51
3081 3137 3.744987 CACGACATAGTATAGCGCCTAC 58.255 50.000 2.29 6.71 0.00 3.18
3082 3138 2.746362 ACGACATAGTATAGCGCCTACC 59.254 50.000 2.29 0.00 0.00 3.18
3083 3139 2.097142 CGACATAGTATAGCGCCTACCC 59.903 54.545 2.29 0.00 0.00 3.69
3084 3140 3.354467 GACATAGTATAGCGCCTACCCT 58.646 50.000 2.29 0.00 0.00 4.34
3085 3141 3.354467 ACATAGTATAGCGCCTACCCTC 58.646 50.000 2.29 0.00 0.00 4.30
3086 3142 3.245158 ACATAGTATAGCGCCTACCCTCA 60.245 47.826 2.29 0.00 0.00 3.86
3087 3143 1.912417 AGTATAGCGCCTACCCTCAG 58.088 55.000 2.29 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 6.726490 AGTCCCTACATTCATGTTACGTAT 57.274 37.500 0.00 0.00 41.97 3.06
44 45 6.534475 AAGTCCCTACATTCATGTTACGTA 57.466 37.500 0.00 0.00 41.97 3.57
45 46 5.416271 AAGTCCCTACATTCATGTTACGT 57.584 39.130 0.00 0.00 41.97 3.57
46 47 5.642063 ACAAAGTCCCTACATTCATGTTACG 59.358 40.000 0.00 0.00 41.97 3.18
47 48 8.556213 TTACAAAGTCCCTACATTCATGTTAC 57.444 34.615 0.00 0.00 41.97 2.50
48 49 9.575868 TTTTACAAAGTCCCTACATTCATGTTA 57.424 29.630 0.00 0.00 41.97 2.41
49 50 8.472007 TTTTACAAAGTCCCTACATTCATGTT 57.528 30.769 0.00 0.00 41.97 2.71
50 51 7.176690 CCTTTTACAAAGTCCCTACATTCATGT 59.823 37.037 0.00 0.00 44.48 3.21
51 52 7.393234 TCCTTTTACAAAGTCCCTACATTCATG 59.607 37.037 0.00 0.00 0.00 3.07
97 98 1.602323 GGGTTGTGGATCGTGGCAA 60.602 57.895 0.00 0.00 0.00 4.52
106 107 2.870119 CGTGTACGGGGGTTGTGGA 61.870 63.158 0.00 0.00 35.37 4.02
129 130 3.770666 CCATACAAGAGGACGTGTAGTG 58.229 50.000 0.00 0.00 42.17 2.74
159 160 4.435518 CGTACGTTTTATGTGCATTGCTCT 60.436 41.667 7.22 0.00 0.00 4.09
189 190 3.965694 TCGTTCTAGAAAGAGCTAGGGT 58.034 45.455 15.95 0.00 38.68 4.34
193 194 6.487960 CGAAGATTCGTTCTAGAAAGAGCTA 58.512 40.000 18.49 7.34 45.09 3.32
378 379 8.896722 TTGGGCTTAATAATTTTTGGGTACTA 57.103 30.769 0.00 0.00 0.00 1.82
382 383 7.085476 AGTTTGGGCTTAATAATTTTTGGGT 57.915 32.000 0.00 0.00 0.00 4.51
429 436 2.477825 CTTCGTGCGATGGAGATGATT 58.522 47.619 0.00 0.00 0.00 2.57
526 534 2.520982 TAGCTAGCCGGCCATCGT 60.521 61.111 26.15 6.59 37.11 3.73
604 612 1.468914 GCCTAGCTTAGCTGCGTTTTT 59.531 47.619 17.97 0.00 40.10 1.94
605 613 1.087501 GCCTAGCTTAGCTGCGTTTT 58.912 50.000 17.97 0.00 40.10 2.43
659 667 4.067896 GCATGATGATGGATTACCGACTT 58.932 43.478 0.00 0.00 39.42 3.01
687 695 4.827284 CCACCTTTTGCTCCTCTTTTTCTA 59.173 41.667 0.00 0.00 0.00 2.10
709 717 1.140816 GTCGCGGCTAATTCTGATCC 58.859 55.000 1.90 0.00 0.00 3.36
713 721 1.752501 CGGTGTCGCGGCTAATTCTG 61.753 60.000 13.81 0.00 0.00 3.02
883 895 2.095466 GCAACAAACCAAGCGTGCTATA 60.095 45.455 0.00 0.00 0.00 1.31
923 944 1.620259 CAGGGAGGAGGAGAGAGCT 59.380 63.158 0.00 0.00 0.00 4.09
937 968 0.340208 AGACTTAGACTCCCCCAGGG 59.660 60.000 0.00 0.00 46.11 4.45
938 969 2.024273 TGTAGACTTAGACTCCCCCAGG 60.024 54.545 0.00 0.00 0.00 4.45
940 971 2.623502 GCTGTAGACTTAGACTCCCCCA 60.624 54.545 0.00 0.00 0.00 4.96
944 975 3.533547 TCGAGCTGTAGACTTAGACTCC 58.466 50.000 0.00 0.00 0.00 3.85
945 976 5.744666 AATCGAGCTGTAGACTTAGACTC 57.255 43.478 0.00 0.00 0.00 3.36
946 977 5.234757 CGTAATCGAGCTGTAGACTTAGACT 59.765 44.000 0.00 0.00 39.71 3.24
947 978 5.233902 TCGTAATCGAGCTGTAGACTTAGAC 59.766 44.000 0.00 0.00 41.35 2.59
948 979 5.354767 TCGTAATCGAGCTGTAGACTTAGA 58.645 41.667 0.00 0.00 41.35 2.10
949 980 5.654317 TCGTAATCGAGCTGTAGACTTAG 57.346 43.478 0.00 0.00 41.35 2.18
974 1005 5.984926 CCAACAATCACTTGCAACAATTACT 59.015 36.000 0.00 0.00 35.69 2.24
981 1012 3.742369 CCATTCCAACAATCACTTGCAAC 59.258 43.478 0.00 0.00 35.69 4.17
1104 1135 0.905357 CGACAGAATTCCACCTCCCT 59.095 55.000 0.65 0.00 0.00 4.20
1165 1201 3.932545 ACGCATGCAGTCCAAATTAAA 57.067 38.095 19.57 0.00 0.00 1.52
1187 1224 2.126424 TGCATGCGCACGTACGTA 60.126 55.556 22.34 5.61 45.36 3.57
1213 1250 1.753073 GAAGCAGCACTATTGGGCATT 59.247 47.619 3.74 0.00 0.00 3.56
1215 1252 1.026182 CGAAGCAGCACTATTGGGCA 61.026 55.000 3.74 0.00 0.00 5.36
1216 1253 1.026718 ACGAAGCAGCACTATTGGGC 61.027 55.000 0.00 0.00 0.00 5.36
1217 1254 1.009829 GACGAAGCAGCACTATTGGG 58.990 55.000 0.00 0.00 0.00 4.12
1218 1255 2.015736 AGACGAAGCAGCACTATTGG 57.984 50.000 0.00 0.00 0.00 3.16
1219 1256 3.549471 CAGTAGACGAAGCAGCACTATTG 59.451 47.826 0.00 0.00 0.00 1.90
1223 1260 0.244994 CCAGTAGACGAAGCAGCACT 59.755 55.000 0.00 0.00 0.00 4.40
1224 1261 0.737715 CCCAGTAGACGAAGCAGCAC 60.738 60.000 0.00 0.00 0.00 4.40
1225 1262 1.591703 CCCAGTAGACGAAGCAGCA 59.408 57.895 0.00 0.00 0.00 4.41
1226 1263 1.153549 CCCCAGTAGACGAAGCAGC 60.154 63.158 0.00 0.00 0.00 5.25
1227 1264 1.153549 GCCCCAGTAGACGAAGCAG 60.154 63.158 0.00 0.00 0.00 4.24
1228 1265 1.605058 GAGCCCCAGTAGACGAAGCA 61.605 60.000 0.00 0.00 0.00 3.91
1229 1266 1.142097 GAGCCCCAGTAGACGAAGC 59.858 63.158 0.00 0.00 0.00 3.86
1230 1267 1.950909 CTAGAGCCCCAGTAGACGAAG 59.049 57.143 0.00 0.00 0.00 3.79
1231 1268 2.022754 GCTAGAGCCCCAGTAGACGAA 61.023 57.143 0.00 0.00 34.31 3.85
1232 1269 0.465824 GCTAGAGCCCCAGTAGACGA 60.466 60.000 0.00 0.00 34.31 4.20
1235 1272 0.105964 CCAGCTAGAGCCCCAGTAGA 60.106 60.000 0.00 0.00 43.38 2.59
1236 1273 1.118356 CCCAGCTAGAGCCCCAGTAG 61.118 65.000 0.00 0.00 43.38 2.57
1240 1277 2.041508 CTCCCAGCTAGAGCCCCA 60.042 66.667 0.00 0.00 43.38 4.96
1258 1295 5.751028 AGCAAAACGAGATTAGCTTAGCTAG 59.249 40.000 13.93 5.09 42.34 3.42
1259 1296 5.520288 CAGCAAAACGAGATTAGCTTAGCTA 59.480 40.000 10.21 10.21 40.44 3.32
1260 1297 4.331168 CAGCAAAACGAGATTAGCTTAGCT 59.669 41.667 12.67 12.67 43.41 3.32
1261 1298 4.582459 CAGCAAAACGAGATTAGCTTAGC 58.418 43.478 0.00 0.00 31.38 3.09
1262 1299 4.093408 TGCAGCAAAACGAGATTAGCTTAG 59.907 41.667 0.00 0.00 31.38 2.18
1263 1300 4.000325 TGCAGCAAAACGAGATTAGCTTA 59.000 39.130 0.00 0.00 31.38 3.09
1264 1301 2.813754 TGCAGCAAAACGAGATTAGCTT 59.186 40.909 0.00 0.00 31.38 3.74
1271 1308 1.065401 CAAACCTGCAGCAAAACGAGA 59.935 47.619 8.66 0.00 0.00 4.04
1289 1326 1.338200 GCTCTTCCCGCTTCTCTTCAA 60.338 52.381 0.00 0.00 0.00 2.69
1363 1400 0.965866 CACTCTCCTCCTGTGGCGTA 60.966 60.000 0.00 0.00 0.00 4.42
1381 1418 1.067669 GCATGGAGCTCGAGTATGACA 59.932 52.381 15.13 7.06 41.15 3.58
1429 1466 4.622740 CCGCAGACCAAAGAAAATGATTTC 59.377 41.667 0.00 0.00 44.34 2.17
1433 1470 2.857483 TCCGCAGACCAAAGAAAATGA 58.143 42.857 0.00 0.00 0.00 2.57
1434 1471 3.504863 CATCCGCAGACCAAAGAAAATG 58.495 45.455 0.00 0.00 0.00 2.32
1435 1472 2.094545 GCATCCGCAGACCAAAGAAAAT 60.095 45.455 0.00 0.00 38.36 1.82
1436 1473 1.269448 GCATCCGCAGACCAAAGAAAA 59.731 47.619 0.00 0.00 38.36 2.29
1437 1474 0.881118 GCATCCGCAGACCAAAGAAA 59.119 50.000 0.00 0.00 38.36 2.52
1438 1475 1.298157 CGCATCCGCAGACCAAAGAA 61.298 55.000 0.00 0.00 38.40 2.52
1456 1493 2.051614 GATCATGGCGTGCATGCG 60.052 61.111 23.96 11.15 35.06 4.73
1488 1533 8.741101 TCACAAATTAAGTGCATGTGTTTATC 57.259 30.769 12.64 0.00 41.52 1.75
1490 1535 8.355913 TCATCACAAATTAAGTGCATGTGTTTA 58.644 29.630 12.64 0.00 41.52 2.01
1610 1659 0.599204 TGTTCTTGGACGACGGCTTC 60.599 55.000 0.00 0.00 0.00 3.86
1706 1755 4.338539 GTGCCGTCGTCGTCCTGT 62.339 66.667 0.71 0.00 35.01 4.00
1722 1771 2.432628 GTTGTCCGCGCTAGCAGT 60.433 61.111 16.45 0.00 45.49 4.40
1757 1806 0.935898 CTTCATCTGCGTGCTGGATC 59.064 55.000 0.00 0.00 0.00 3.36
1759 1808 1.742880 GCTTCATCTGCGTGCTGGA 60.743 57.895 0.00 0.00 0.00 3.86
1820 1872 0.599466 CCATGTCTCGCATCATCGCT 60.599 55.000 0.00 0.00 35.19 4.93
1832 1884 2.994995 TCCGTGTCCGCCATGTCT 60.995 61.111 0.00 0.00 0.00 3.41
1853 1905 0.034337 GGTGGTCGTACTGCAGGAAA 59.966 55.000 19.93 0.00 0.00 3.13
1970 2022 3.970410 TTCCACAGGCTGCCCCAG 61.970 66.667 16.57 8.49 35.39 4.45
2181 2234 4.527038 AGTTTCGTCCTGAGGTCAGATTTA 59.473 41.667 8.64 0.00 46.59 1.40
2193 2246 6.018262 TCAGTTTGTGAATTAGTTTCGTCCTG 60.018 38.462 0.00 0.00 37.13 3.86
2196 2249 7.407337 AGTTCAGTTTGTGAATTAGTTTCGTC 58.593 34.615 0.00 0.00 46.99 4.20
2237 2290 1.490490 ACAAAAGGGTCAGCTGAGTGA 59.510 47.619 18.89 0.00 0.00 3.41
2244 2297 0.517316 CGCTACACAAAAGGGTCAGC 59.483 55.000 0.00 0.00 0.00 4.26
2248 2301 1.602605 GGGCGCTACACAAAAGGGT 60.603 57.895 7.64 0.00 0.00 4.34
2258 2311 1.141019 TCAAGATGTCGGGCGCTAC 59.859 57.895 7.64 4.10 0.00 3.58
2266 2319 4.324669 GTGTAGTGTGATGTCAAGATGTCG 59.675 45.833 0.00 0.00 0.00 4.35
2319 2372 2.906182 GATGCGACGATGGTCAGGCA 62.906 60.000 11.59 11.59 43.61 4.75
2325 2378 2.058001 TCCTGGATGCGACGATGGT 61.058 57.895 0.00 0.00 0.00 3.55
2326 2379 1.592669 GTCCTGGATGCGACGATGG 60.593 63.158 0.00 0.00 0.00 3.51
2336 2389 3.760684 GCATTTTTCAGTCAGTCCTGGAT 59.239 43.478 0.00 0.00 33.14 3.41
2338 2391 3.152341 AGCATTTTTCAGTCAGTCCTGG 58.848 45.455 0.00 0.00 33.14 4.45
2339 2392 5.471456 ACTTAGCATTTTTCAGTCAGTCCTG 59.529 40.000 0.00 0.00 0.00 3.86
2341 2394 5.470098 TGACTTAGCATTTTTCAGTCAGTCC 59.530 40.000 0.00 0.00 39.12 3.85
2357 2410 1.135575 GGCATTGCACACTGACTTAGC 60.136 52.381 11.39 0.00 0.00 3.09
2468 2521 2.210013 AGAGGCGCAGAGGACACAA 61.210 57.895 10.83 0.00 0.00 3.33
2542 2595 1.599240 GGATCGATGGGGAAGCAGC 60.599 63.158 0.54 0.00 0.00 5.25
2582 2636 5.232414 TCGTAAAAATGAAAAACCCAAAGCG 59.768 36.000 0.00 0.00 0.00 4.68
2597 2651 9.647797 AACAAGGTTTTCTTTTCTCGTAAAAAT 57.352 25.926 0.00 0.00 32.41 1.82
2765 2821 6.312426 CCACTGCACAATGTCTTTGTTTAAAA 59.688 34.615 1.48 0.00 46.51 1.52
2770 2826 3.023119 TCCACTGCACAATGTCTTTGTT 58.977 40.909 1.48 0.00 46.51 2.83
2780 2836 2.741985 CGCCGATCCACTGCACAA 60.742 61.111 0.00 0.00 0.00 3.33
2786 2842 2.486663 TATGACGCGCCGATCCACT 61.487 57.895 5.73 0.00 0.00 4.00
2849 2905 5.198965 ACATATATATACGGTTCTCGGGCT 58.801 41.667 0.00 0.00 44.45 5.19
2866 2922 0.961019 GACCCGCACCGGTACATATA 59.039 55.000 6.87 0.00 46.80 0.86
2867 2923 1.744014 GACCCGCACCGGTACATAT 59.256 57.895 6.87 0.00 46.80 1.78
2868 2924 2.773745 CGACCCGCACCGGTACATA 61.774 63.158 6.87 0.00 46.80 2.29
2869 2925 4.137872 CGACCCGCACCGGTACAT 62.138 66.667 6.87 0.00 46.80 2.29
2899 2955 5.853282 GCAATGATTATGATGTTTAGCGACC 59.147 40.000 0.00 0.00 0.00 4.79
2900 2956 5.561499 CGCAATGATTATGATGTTTAGCGAC 59.439 40.000 0.00 0.00 42.47 5.19
2912 2968 2.792674 CAGCAAAGCCGCAATGATTATG 59.207 45.455 0.00 0.00 0.00 1.90
2941 2997 0.525668 CTCGCCGCTAACTGTACCTG 60.526 60.000 0.00 0.00 0.00 4.00
3044 3100 1.963338 GTGCAACGCCTGAGCTCTT 60.963 57.895 16.19 0.00 36.60 2.85


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

AutoCloner maintained by Alex Coulton.