Multiple sequence alignment - TraesCS1A01G283300

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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 TraesCS1A01G283300 chr1A 100.000 2183 0 0 1 2183 480932628 480930446 0 4032
1 TraesCS1A01G283300 chr1B 87.740 2186 162 43 20 2183 509899411 509897310 0 2455
2 TraesCS1A01G283300 chr1D 88.214 1892 150 40 20 1882 379909722 379907875 0 2191


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 TraesCS1A01G283300 chr1A 480930446 480932628 2182 True 4032 4032 100.000 1 2183 1 chr1A.!!$R1 2182
1 TraesCS1A01G283300 chr1B 509897310 509899411 2101 True 2455 2455 87.740 20 2183 1 chr1B.!!$R1 2163
2 TraesCS1A01G283300 chr1D 379907875 379909722 1847 True 2191 2191 88.214 20 1882 1 chr1D.!!$R1 1862

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
290 302 0.271005 GGGGAGAGGGAAAGGGGATA 59.729 60.0 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1490 1536 0.701147 CCTGCCCCTCTCCTTTTTCT 59.299 55.0 0.0 0.0 0.0 2.52 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
43 44 2.683362 CAGCTCCTCGTCTGTATGTACA 59.317 50.000 0.00 0.00 34.56 2.90
56 57 0.844661 ATGTACAGCCTCCACCCCAA 60.845 55.000 0.33 0.00 0.00 4.12
77 78 2.031012 CCTCGTGGTGCAGCTCAA 59.969 61.111 18.08 0.00 0.00 3.02
85 86 2.666190 TGCAGCTCAACGTGCTCC 60.666 61.111 0.00 0.00 40.54 4.70
106 107 5.752036 CCAGTCCATCATCTGGTATATGT 57.248 43.478 3.38 0.00 46.08 2.29
107 108 6.857437 CCAGTCCATCATCTGGTATATGTA 57.143 41.667 3.38 0.00 46.08 2.29
108 109 6.634805 CCAGTCCATCATCTGGTATATGTAC 58.365 44.000 3.38 0.00 46.08 2.90
109 110 6.438741 CCAGTCCATCATCTGGTATATGTACT 59.561 42.308 0.00 0.00 46.08 2.73
110 111 7.318893 CAGTCCATCATCTGGTATATGTACTG 58.681 42.308 0.00 0.00 46.08 2.74
135 140 1.890489 TCCTCTTCGATTTCCACGTCA 59.110 47.619 0.00 0.00 0.00 4.35
223 235 4.988598 CGACAGCCACGCCAAGGT 62.989 66.667 0.00 0.00 0.00 3.50
245 257 4.778143 GCCAAGATCGCACCCGGT 62.778 66.667 0.00 0.00 34.56 5.28
264 276 2.023984 GGTGGGAGGAGGAAAATGGATT 60.024 50.000 0.00 0.00 0.00 3.01
290 302 0.271005 GGGGAGAGGGAAAGGGGATA 59.729 60.000 0.00 0.00 0.00 2.59
295 307 1.662623 AGAGGGAAAGGGGATAGGGAA 59.337 52.381 0.00 0.00 0.00 3.97
305 317 2.157926 GGGGATAGGGAAAGGAGAGGAT 60.158 54.545 0.00 0.00 0.00 3.24
321 333 7.831955 AGGAGAGGATAGAGGAAGAAGATAAA 58.168 38.462 0.00 0.00 0.00 1.40
322 334 7.950124 AGGAGAGGATAGAGGAAGAAGATAAAG 59.050 40.741 0.00 0.00 0.00 1.85
326 338 7.552750 AGGATAGAGGAAGAAGATAAAGGGAT 58.447 38.462 0.00 0.00 0.00 3.85
329 341 8.909423 ATAGAGGAAGAAGATAAAGGGATAGG 57.091 38.462 0.00 0.00 0.00 2.57
330 342 6.939617 AGAGGAAGAAGATAAAGGGATAGGA 58.060 40.000 0.00 0.00 0.00 2.94
375 394 5.592282 TCAGTGAGAGTAGATGATGAACCTC 59.408 44.000 0.00 0.00 0.00 3.85
380 399 2.101582 AGTAGATGATGAACCTCGCCAC 59.898 50.000 0.00 0.00 0.00 5.01
398 417 4.620567 CGCCACGATCATATCTTATCCCAA 60.621 45.833 0.00 0.00 0.00 4.12
408 427 6.491062 TCATATCTTATCCCAATGCACCAAAG 59.509 38.462 0.00 0.00 0.00 2.77
417 437 4.220382 CCCAATGCACCAAAGATGTTTAGA 59.780 41.667 0.00 0.00 0.00 2.10
433 453 9.702253 AGATGTTTAGAGTTAGGATAGACAGAA 57.298 33.333 0.00 0.00 0.00 3.02
518 539 8.653191 TGTGAGGGTTTATTTCAGACTTTACTA 58.347 33.333 0.00 0.00 0.00 1.82
543 564 8.034313 AGAAGTGAATATAACCATTGCTCCTA 57.966 34.615 0.00 0.00 0.00 2.94
555 576 6.012745 ACCATTGCTCCTAGTCTTCATTTTT 58.987 36.000 0.00 0.00 0.00 1.94
559 580 9.912634 CATTGCTCCTAGTCTTCATTTTTAAAA 57.087 29.630 0.00 0.00 0.00 1.52
563 584 8.784043 GCTCCTAGTCTTCATTTTTAAAACTCA 58.216 33.333 0.00 0.00 0.00 3.41
623 645 6.237463 GGCGCATTACTAAATTGTTTGTTAGC 60.237 38.462 10.83 0.00 31.67 3.09
637 659 6.296026 TGTTTGTTAGCTAACTCAGGAACAT 58.704 36.000 31.14 0.00 37.12 2.71
645 667 0.952497 ACTCAGGAACATGCGTGCAG 60.952 55.000 5.64 0.00 0.00 4.41
652 674 2.126618 CATGCGTGCAGTGCCAAG 60.127 61.111 13.72 4.90 0.00 3.61
664 686 0.865769 GTGCCAAGGTACACGTGAAG 59.134 55.000 25.01 4.72 0.00 3.02
679 701 3.168193 CGTGAAGTTTGAACAACACACC 58.832 45.455 16.87 0.00 37.20 4.16
684 706 6.472163 GTGAAGTTTGAACAACACACCAATAG 59.528 38.462 14.00 0.00 37.26 1.73
729 751 2.124320 GGCGCATCAAGGCCCTAA 60.124 61.111 10.83 0.00 43.64 2.69
782 804 1.889105 CCGTCATCCCCGATTGCTG 60.889 63.158 0.00 0.00 0.00 4.41
858 884 2.285743 AACAGCCCTCCTCCCTCC 60.286 66.667 0.00 0.00 0.00 4.30
862 888 4.890306 GCCCTCCTCCCTCCCTCC 62.890 77.778 0.00 0.00 0.00 4.30
866 892 3.430497 TCCTCCCTCCCTCCCTCG 61.430 72.222 0.00 0.00 0.00 4.63
908 934 2.995574 CCCTCACGTCCTCCCGTT 60.996 66.667 0.00 0.00 39.45 4.44
945 971 1.153429 TCTCCGATCGAGCTCACGA 60.153 57.895 18.66 12.32 46.04 4.35
948 974 2.351322 CGATCGAGCTCACGACCG 60.351 66.667 15.40 5.79 42.63 4.79
980 1006 1.518302 GAAGGAAGGAGGCGGAGAC 59.482 63.158 0.00 0.00 0.00 3.36
1020 1046 3.414700 GACAAGTGCGGGCTGTCG 61.415 66.667 0.00 0.00 0.00 4.35
1030 1056 1.219393 GGGCTGTCGAAGAAGAGGG 59.781 63.158 0.00 0.00 39.69 4.30
1033 1059 1.893919 GCTGTCGAAGAAGAGGGGCT 61.894 60.000 0.00 0.00 39.69 5.19
1035 1061 1.219393 GTCGAAGAAGAGGGGCTGG 59.781 63.158 0.00 0.00 39.69 4.85
1210 1241 7.173735 TCCTGAAGCTGTAATGCATATGTATTG 59.826 37.037 24.26 12.06 32.67 1.90
1211 1242 7.173735 CCTGAAGCTGTAATGCATATGTATTGA 59.826 37.037 24.26 12.54 32.67 2.57
1212 1243 7.864686 TGAAGCTGTAATGCATATGTATTGAC 58.135 34.615 24.26 18.22 32.67 3.18
1213 1244 7.716560 TGAAGCTGTAATGCATATGTATTGACT 59.283 33.333 24.26 14.58 32.67 3.41
1214 1245 9.208022 GAAGCTGTAATGCATATGTATTGACTA 57.792 33.333 24.26 6.05 32.67 2.59
1215 1246 8.768957 AGCTGTAATGCATATGTATTGACTAG 57.231 34.615 24.26 17.38 32.67 2.57
1216 1247 8.370940 AGCTGTAATGCATATGTATTGACTAGT 58.629 33.333 24.26 0.00 32.67 2.57
1217 1248 9.639601 GCTGTAATGCATATGTATTGACTAGTA 57.360 33.333 24.26 4.44 32.67 1.82
1219 1250 9.639601 TGTAATGCATATGTATTGACTAGTAGC 57.360 33.333 24.26 7.62 32.67 3.58
1220 1251 9.862371 GTAATGCATATGTATTGACTAGTAGCT 57.138 33.333 24.26 0.00 32.67 3.32
1221 1252 8.768957 AATGCATATGTATTGACTAGTAGCTG 57.231 34.615 17.03 0.00 0.00 4.24
1222 1253 7.290110 TGCATATGTATTGACTAGTAGCTGT 57.710 36.000 4.29 0.00 0.00 4.40
1223 1254 8.404107 TGCATATGTATTGACTAGTAGCTGTA 57.596 34.615 4.29 0.00 0.00 2.74
1224 1255 8.856103 TGCATATGTATTGACTAGTAGCTGTAA 58.144 33.333 4.29 0.00 0.00 2.41
1225 1256 9.862371 GCATATGTATTGACTAGTAGCTGTAAT 57.138 33.333 4.29 0.00 0.00 1.89
1227 1258 9.862371 ATATGTATTGACTAGTAGCTGTAATGC 57.138 33.333 0.00 0.00 0.00 3.56
1228 1259 7.107639 TGTATTGACTAGTAGCTGTAATGCA 57.892 36.000 0.00 0.00 34.99 3.96
1229 1260 7.726216 TGTATTGACTAGTAGCTGTAATGCAT 58.274 34.615 0.00 0.00 34.99 3.96
1230 1261 8.856103 TGTATTGACTAGTAGCTGTAATGCATA 58.144 33.333 0.00 0.00 34.99 3.14
1231 1262 9.862371 GTATTGACTAGTAGCTGTAATGCATAT 57.138 33.333 0.00 0.00 34.99 1.78
1232 1263 8.768957 ATTGACTAGTAGCTGTAATGCATATG 57.231 34.615 0.00 0.00 34.99 1.78
1233 1264 7.290110 TGACTAGTAGCTGTAATGCATATGT 57.710 36.000 0.00 0.00 34.99 2.29
1234 1265 8.404107 TGACTAGTAGCTGTAATGCATATGTA 57.596 34.615 0.00 0.00 34.99 2.29
1235 1266 9.025041 TGACTAGTAGCTGTAATGCATATGTAT 57.975 33.333 0.00 1.99 34.99 2.29
1236 1267 9.862371 GACTAGTAGCTGTAATGCATATGTATT 57.138 33.333 20.69 20.69 34.74 1.89
1237 1268 9.645059 ACTAGTAGCTGTAATGCATATGTATTG 57.355 33.333 24.26 12.06 32.67 1.90
1238 1269 9.860898 CTAGTAGCTGTAATGCATATGTATTGA 57.139 33.333 24.26 12.54 32.67 2.57
1239 1270 8.539770 AGTAGCTGTAATGCATATGTATTGAC 57.460 34.615 24.26 18.22 32.67 3.18
1240 1271 8.370940 AGTAGCTGTAATGCATATGTATTGACT 58.629 33.333 24.26 17.80 32.67 3.41
1241 1272 9.639601 GTAGCTGTAATGCATATGTATTGACTA 57.360 33.333 24.26 17.04 32.67 2.59
1242 1273 8.768957 AGCTGTAATGCATATGTATTGACTAG 57.231 34.615 24.26 17.38 32.67 2.57
1243 1274 8.370940 AGCTGTAATGCATATGTATTGACTAGT 58.629 33.333 24.26 0.00 32.67 2.57
1244 1275 9.639601 GCTGTAATGCATATGTATTGACTAGTA 57.360 33.333 24.26 4.44 32.67 1.82
1246 1277 9.639601 TGTAATGCATATGTATTGACTAGTAGC 57.360 33.333 24.26 7.62 32.67 3.58
1247 1278 9.862371 GTAATGCATATGTATTGACTAGTAGCT 57.138 33.333 24.26 0.00 32.67 3.32
1248 1279 8.768957 AATGCATATGTATTGACTAGTAGCTG 57.231 34.615 17.03 0.00 0.00 4.24
1249 1280 7.290110 TGCATATGTATTGACTAGTAGCTGT 57.710 36.000 4.29 0.00 0.00 4.40
1250 1281 8.404107 TGCATATGTATTGACTAGTAGCTGTA 57.596 34.615 4.29 0.00 0.00 2.74
1251 1282 8.856103 TGCATATGTATTGACTAGTAGCTGTAA 58.144 33.333 4.29 0.00 0.00 2.41
1268 1299 3.028850 TGTAATACAAGGGGAGACTCGG 58.971 50.000 0.00 0.00 34.16 4.63
1278 1309 3.053849 GAGACTCGGTCGGTGGAGC 62.054 68.421 0.00 0.00 37.67 4.70
1280 1311 3.628280 GACTCGGTCGGTGGAGCAC 62.628 68.421 0.00 0.00 40.71 4.40
1301 1341 6.261158 AGCACCTGTTTCTTTTCTTCTTCTAC 59.739 38.462 0.00 0.00 0.00 2.59
1302 1342 6.261158 GCACCTGTTTCTTTTCTTCTTCTACT 59.739 38.462 0.00 0.00 0.00 2.57
1303 1343 7.634522 CACCTGTTTCTTTTCTTCTTCTACTG 58.365 38.462 0.00 0.00 0.00 2.74
1304 1344 7.281100 CACCTGTTTCTTTTCTTCTTCTACTGT 59.719 37.037 0.00 0.00 0.00 3.55
1305 1345 8.483758 ACCTGTTTCTTTTCTTCTTCTACTGTA 58.516 33.333 0.00 0.00 0.00 2.74
1390 1432 3.191162 TGTGAATCCATTTTGCCTTCTCG 59.809 43.478 0.00 0.00 0.00 4.04
1391 1433 2.754552 TGAATCCATTTTGCCTTCTCGG 59.245 45.455 0.00 0.00 0.00 4.63
1392 1434 2.514458 ATCCATTTTGCCTTCTCGGT 57.486 45.000 0.00 0.00 34.25 4.69
1394 1436 2.985896 TCCATTTTGCCTTCTCGGTAG 58.014 47.619 0.00 0.00 34.25 3.18
1395 1437 2.569853 TCCATTTTGCCTTCTCGGTAGA 59.430 45.455 0.00 0.00 34.25 2.59
1396 1438 3.199946 TCCATTTTGCCTTCTCGGTAGAT 59.800 43.478 0.00 0.00 34.25 1.98
1397 1439 3.561725 CCATTTTGCCTTCTCGGTAGATC 59.438 47.826 0.00 0.00 34.25 2.75
1458 1503 7.596749 AAATGTACTGTACTATGTTCTGCAC 57.403 36.000 17.98 0.00 0.00 4.57
1723 1769 2.301346 CAGCCATTACAGCTAAAGGGG 58.699 52.381 12.15 5.75 38.95 4.79
1725 1771 2.580783 AGCCATTACAGCTAAAGGGGAA 59.419 45.455 12.15 0.00 39.29 3.97
1749 1795 2.747855 CTCCCCGCTTTGGACAGC 60.748 66.667 0.00 0.00 42.00 4.40
1861 1907 2.202440 CCGTCGAGCACCAGTACG 60.202 66.667 0.00 0.00 0.00 3.67
1887 1933 6.430962 TGCTCAGATAAGCATCTCCTTAAT 57.569 37.500 0.00 0.00 47.00 1.40
1888 1934 6.228995 TGCTCAGATAAGCATCTCCTTAATG 58.771 40.000 0.00 0.00 47.00 1.90
1889 1935 6.183361 TGCTCAGATAAGCATCTCCTTAATGT 60.183 38.462 0.00 0.00 47.00 2.71
1890 1936 7.015584 TGCTCAGATAAGCATCTCCTTAATGTA 59.984 37.037 0.00 0.00 47.00 2.29
1891 1937 7.875041 GCTCAGATAAGCATCTCCTTAATGTAA 59.125 37.037 0.00 0.00 39.62 2.41
1892 1938 9.941325 CTCAGATAAGCATCTCCTTAATGTAAT 57.059 33.333 0.00 0.00 39.62 1.89
1963 2009 9.150348 GGTTTGGTTTAAATTACATCAATGGAG 57.850 33.333 0.00 0.00 0.00 3.86
1978 2024 1.271856 TGGAGCTTCGGGTACAATCA 58.728 50.000 0.00 0.00 32.78 2.57
1983 2029 4.879545 GGAGCTTCGGGTACAATCAAATTA 59.120 41.667 0.00 0.00 0.00 1.40
1999 2046 9.104965 CAATCAAATTATGGTAACGGAACTCTA 57.895 33.333 0.00 0.00 42.51 2.43
2006 2053 3.244181 TGGTAACGGAACTCTAAACCCAC 60.244 47.826 0.00 0.00 42.51 4.61
2008 2055 2.833631 ACGGAACTCTAAACCCACAG 57.166 50.000 0.00 0.00 0.00 3.66
2009 2056 1.346722 ACGGAACTCTAAACCCACAGG 59.653 52.381 0.00 0.00 40.04 4.00
2019 2066 1.270907 AACCCACAGGCACAAAAACA 58.729 45.000 0.00 0.00 36.11 2.83
2022 2069 2.238395 ACCCACAGGCACAAAAACAAAT 59.762 40.909 0.00 0.00 36.11 2.32
2024 2071 2.539274 CCACAGGCACAAAAACAAATCG 59.461 45.455 0.00 0.00 0.00 3.34
2033 2080 5.163903 GCACAAAAACAAATCGAAACCAAGT 60.164 36.000 0.00 0.00 0.00 3.16
2037 2084 4.568152 AACAAATCGAAACCAAGTGGAG 57.432 40.909 3.83 0.00 38.94 3.86
2039 2086 4.398319 ACAAATCGAAACCAAGTGGAGAT 58.602 39.130 3.83 1.08 38.94 2.75
2042 2089 6.072673 ACAAATCGAAACCAAGTGGAGATTAC 60.073 38.462 3.83 0.00 38.94 1.89
2043 2090 4.610605 TCGAAACCAAGTGGAGATTACA 57.389 40.909 3.83 0.00 38.94 2.41
2053 2100 7.093858 ACCAAGTGGAGATTACAACTAGACTAC 60.094 40.741 3.83 0.00 38.94 2.73
2060 2107 7.650104 GGAGATTACAACTAGACTACAAGCATC 59.350 40.741 0.00 0.00 0.00 3.91
2062 2109 8.531982 AGATTACAACTAGACTACAAGCATCAA 58.468 33.333 0.00 0.00 0.00 2.57
2074 2121 4.634199 ACAAGCATCAAAAAGAACCATGG 58.366 39.130 11.19 11.19 0.00 3.66
2085 2132 0.802607 GAACCATGGCTCTCGTCGAC 60.803 60.000 13.04 5.18 0.00 4.20
2110 2157 3.057596 TGGACAACATCGAAAAATCCAGC 60.058 43.478 5.06 0.00 31.25 4.85
2113 2160 3.511146 ACAACATCGAAAAATCCAGCCAT 59.489 39.130 0.00 0.00 0.00 4.40
2127 2174 2.223829 CCAGCCATCGAAGTACCTACAG 60.224 54.545 0.00 0.00 0.00 2.74
2146 2193 4.023980 ACAGAGGACCGTAGATGATCAAA 58.976 43.478 0.00 0.00 0.00 2.69
2172 2219 6.424176 TTGTTGAATCGATGCGGTAATAAA 57.576 33.333 0.00 0.00 0.00 1.40
2173 2220 6.424176 TGTTGAATCGATGCGGTAATAAAA 57.576 33.333 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.288188 TCTTGGATGCCCATCACTGA 58.712 50.000 10.17 2.45 43.12 3.41
1 2 2.228059 GATCTTGGATGCCCATCACTG 58.772 52.381 10.17 0.36 43.12 3.66
2 3 1.144503 GGATCTTGGATGCCCATCACT 59.855 52.381 10.17 0.00 43.12 3.41
3 4 1.133699 TGGATCTTGGATGCCCATCAC 60.134 52.381 10.17 1.29 43.12 3.06
4 5 1.144298 CTGGATCTTGGATGCCCATCA 59.856 52.381 10.17 0.00 43.12 3.07
5 6 1.906990 CTGGATCTTGGATGCCCATC 58.093 55.000 0.00 0.00 43.12 3.51
6 7 0.178970 GCTGGATCTTGGATGCCCAT 60.179 55.000 0.00 0.00 43.12 4.00
7 8 1.228228 GCTGGATCTTGGATGCCCA 59.772 57.895 0.00 0.00 41.64 5.36
8 9 0.536915 GAGCTGGATCTTGGATGCCC 60.537 60.000 0.00 0.00 0.00 5.36
9 10 0.536915 GGAGCTGGATCTTGGATGCC 60.537 60.000 0.00 0.00 0.00 4.40
10 11 0.473326 AGGAGCTGGATCTTGGATGC 59.527 55.000 0.00 0.00 0.00 3.91
11 12 1.270199 CGAGGAGCTGGATCTTGGATG 60.270 57.143 0.00 0.00 0.00 3.51
12 13 1.047002 CGAGGAGCTGGATCTTGGAT 58.953 55.000 0.00 0.00 0.00 3.41
13 14 0.324738 ACGAGGAGCTGGATCTTGGA 60.325 55.000 0.00 0.00 0.00 3.53
14 15 0.103937 GACGAGGAGCTGGATCTTGG 59.896 60.000 0.00 0.00 0.00 3.61
15 16 1.110442 AGACGAGGAGCTGGATCTTG 58.890 55.000 0.00 0.00 0.00 3.02
16 17 1.110442 CAGACGAGGAGCTGGATCTT 58.890 55.000 0.00 0.00 0.00 2.40
17 18 0.033601 ACAGACGAGGAGCTGGATCT 60.034 55.000 0.00 0.00 36.47 2.75
18 19 1.681538 TACAGACGAGGAGCTGGATC 58.318 55.000 0.00 0.00 36.47 3.36
77 78 0.176680 GATGATGGACTGGAGCACGT 59.823 55.000 0.00 0.00 0.00 4.49
102 103 5.970317 TCGAAGAGGAACAACAGTACATA 57.030 39.130 0.00 0.00 0.00 2.29
106 107 5.221561 TGGAAATCGAAGAGGAACAACAGTA 60.222 40.000 0.00 0.00 43.63 2.74
107 108 4.065789 GGAAATCGAAGAGGAACAACAGT 58.934 43.478 0.00 0.00 43.63 3.55
108 109 4.065088 TGGAAATCGAAGAGGAACAACAG 58.935 43.478 0.00 0.00 43.63 3.16
109 110 3.813166 GTGGAAATCGAAGAGGAACAACA 59.187 43.478 0.00 0.00 43.63 3.33
110 111 3.120649 CGTGGAAATCGAAGAGGAACAAC 60.121 47.826 0.00 0.00 43.63 3.32
135 140 0.108662 TTCGAGATGAGCATGCACGT 60.109 50.000 21.98 15.77 0.00 4.49
219 231 2.044946 GATCTTGGCCCGCACCTT 60.045 61.111 0.00 0.00 0.00 3.50
231 243 4.096003 CCCACCGGGTGCGATCTT 62.096 66.667 21.88 0.00 38.25 2.40
245 257 2.925653 TCAATCCATTTTCCTCCTCCCA 59.074 45.455 0.00 0.00 0.00 4.37
255 267 3.053693 TCTCCCCATCGTCAATCCATTTT 60.054 43.478 0.00 0.00 0.00 1.82
264 276 0.252513 TTTCCCTCTCCCCATCGTCA 60.253 55.000 0.00 0.00 0.00 4.35
290 302 3.143406 TCCTCTATCCTCTCCTTTCCCT 58.857 50.000 0.00 0.00 0.00 4.20
295 307 5.742562 TCTTCTTCCTCTATCCTCTCCTT 57.257 43.478 0.00 0.00 0.00 3.36
305 317 8.070062 TCCTATCCCTTTATCTTCTTCCTCTA 57.930 38.462 0.00 0.00 0.00 2.43
321 333 3.491766 TCCACAAGTCTTCCTATCCCT 57.508 47.619 0.00 0.00 0.00 4.20
322 334 3.071747 GGATCCACAAGTCTTCCTATCCC 59.928 52.174 6.95 0.00 0.00 3.85
326 338 6.386927 ACAATATGGATCCACAAGTCTTCCTA 59.613 38.462 18.99 1.28 0.00 2.94
329 341 6.115446 TGACAATATGGATCCACAAGTCTTC 58.885 40.000 25.94 15.52 0.00 2.87
330 342 6.065976 TGACAATATGGATCCACAAGTCTT 57.934 37.500 25.94 11.79 0.00 3.01
375 394 3.119137 TGGGATAAGATATGATCGTGGCG 60.119 47.826 0.00 0.00 0.00 5.69
380 399 5.295292 GGTGCATTGGGATAAGATATGATCG 59.705 44.000 0.00 0.00 0.00 3.69
398 417 6.375455 CCTAACTCTAAACATCTTTGGTGCAT 59.625 38.462 0.00 0.00 0.00 3.96
417 437 8.830915 TTCTCTGATTTCTGTCTATCCTAACT 57.169 34.615 0.00 0.00 0.00 2.24
431 451 4.811557 CGGTACCCTGAATTCTCTGATTTC 59.188 45.833 6.25 0.00 0.00 2.17
433 453 4.030913 TCGGTACCCTGAATTCTCTGATT 58.969 43.478 6.25 0.00 0.00 2.57
436 456 2.761208 AGTCGGTACCCTGAATTCTCTG 59.239 50.000 6.25 0.00 0.00 3.35
459 480 3.557054 CGACCCTCACCTTCAAATCTTCA 60.557 47.826 0.00 0.00 0.00 3.02
461 482 2.637872 TCGACCCTCACCTTCAAATCTT 59.362 45.455 0.00 0.00 0.00 2.40
492 513 7.514721 AGTAAAGTCTGAAATAAACCCTCACA 58.485 34.615 0.00 0.00 0.00 3.58
518 539 6.904626 AGGAGCAATGGTTATATTCACTTCT 58.095 36.000 0.00 0.00 0.00 2.85
543 564 7.898014 AGGGTGAGTTTTAAAAATGAAGACT 57.102 32.000 5.49 0.00 0.00 3.24
555 576 1.892474 GCATGCCAAGGGTGAGTTTTA 59.108 47.619 6.36 0.00 0.00 1.52
559 580 2.036256 GGCATGCCAAGGGTGAGT 59.964 61.111 32.08 0.00 35.81 3.41
563 584 0.114168 TTTACTGGCATGCCAAGGGT 59.886 50.000 37.47 31.83 46.63 4.34
585 607 0.674895 ATGCGCCAGGAGTGAGTTTC 60.675 55.000 4.18 0.00 0.00 2.78
623 645 1.394917 GCACGCATGTTCCTGAGTTAG 59.605 52.381 0.00 0.00 0.00 2.34
637 659 3.468326 TACCTTGGCACTGCACGCA 62.468 57.895 2.82 0.00 0.00 5.24
645 667 0.865769 CTTCACGTGTACCTTGGCAC 59.134 55.000 16.51 0.00 0.00 5.01
652 674 4.142859 TGTTGTTCAAACTTCACGTGTACC 60.143 41.667 16.51 0.00 0.00 3.34
664 686 7.010091 CCTTTTCTATTGGTGTGTTGTTCAAAC 59.990 37.037 0.00 0.00 33.73 2.93
679 701 4.157840 GCCACTTGGTACCCTTTTCTATTG 59.842 45.833 10.07 0.00 37.57 1.90
684 706 0.879090 CGCCACTTGGTACCCTTTTC 59.121 55.000 10.07 0.00 37.57 2.29
782 804 4.214437 GCATTTGTCTGCTTATATCGTGC 58.786 43.478 0.00 0.00 39.12 5.34
817 839 1.880894 CGACGAGCCAAGTGGTAGA 59.119 57.895 0.00 0.00 37.57 2.59
858 884 4.200283 GCGACAGAGCGAGGGAGG 62.200 72.222 0.00 0.00 0.00 4.30
862 888 2.101965 CAGAGCGACAGAGCGAGG 59.898 66.667 0.00 0.00 43.00 4.63
866 892 1.516821 CAGAGCAGAGCGACAGAGC 60.517 63.158 0.00 0.00 37.41 4.09
906 932 0.040692 GAAACTTGGTCGGCGGAAAC 60.041 55.000 7.21 0.00 0.00 2.78
908 934 1.957186 CGAAACTTGGTCGGCGGAA 60.957 57.895 7.21 0.00 34.85 4.30
1020 1046 1.340502 CCTTTCCAGCCCCTCTTCTTC 60.341 57.143 0.00 0.00 0.00 2.87
1030 1056 1.953231 GCCATTGCTCCTTTCCAGCC 61.953 60.000 0.00 0.00 35.89 4.85
1033 1059 0.899717 GTGGCCATTGCTCCTTTCCA 60.900 55.000 9.72 0.00 37.74 3.53
1035 1061 1.508088 CGTGGCCATTGCTCCTTTC 59.492 57.895 9.72 0.00 37.74 2.62
1122 1148 3.320078 CGCGCGATGTAGAACCGG 61.320 66.667 28.94 0.00 0.00 5.28
1210 1241 9.862371 AATACATATGCATTACAGCTACTAGTC 57.138 33.333 3.54 0.00 34.99 2.59
1211 1242 9.645059 CAATACATATGCATTACAGCTACTAGT 57.355 33.333 3.54 0.00 34.99 2.57
1212 1243 9.860898 TCAATACATATGCATTACAGCTACTAG 57.139 33.333 3.54 0.00 34.99 2.57
1213 1244 9.639601 GTCAATACATATGCATTACAGCTACTA 57.360 33.333 3.54 0.00 34.99 1.82
1214 1245 8.370940 AGTCAATACATATGCATTACAGCTACT 58.629 33.333 3.54 0.00 34.99 2.57
1215 1246 8.539770 AGTCAATACATATGCATTACAGCTAC 57.460 34.615 3.54 0.00 34.99 3.58
1216 1247 9.860898 CTAGTCAATACATATGCATTACAGCTA 57.139 33.333 3.54 2.62 34.99 3.32
1217 1248 8.370940 ACTAGTCAATACATATGCATTACAGCT 58.629 33.333 3.54 1.66 34.99 4.24
1218 1249 8.539770 ACTAGTCAATACATATGCATTACAGC 57.460 34.615 3.54 0.00 0.00 4.40
1220 1251 9.639601 GCTACTAGTCAATACATATGCATTACA 57.360 33.333 3.54 0.00 0.00 2.41
1221 1252 9.862371 AGCTACTAGTCAATACATATGCATTAC 57.138 33.333 3.54 2.18 0.00 1.89
1222 1253 9.860898 CAGCTACTAGTCAATACATATGCATTA 57.139 33.333 3.54 0.00 0.00 1.90
1223 1254 8.370940 ACAGCTACTAGTCAATACATATGCATT 58.629 33.333 3.54 0.00 0.00 3.56
1224 1255 7.901029 ACAGCTACTAGTCAATACATATGCAT 58.099 34.615 3.79 3.79 0.00 3.96
1225 1256 7.290110 ACAGCTACTAGTCAATACATATGCA 57.710 36.000 0.00 0.00 0.00 3.96
1226 1257 9.862371 ATTACAGCTACTAGTCAATACATATGC 57.138 33.333 0.00 0.00 0.00 3.14
1232 1263 9.680315 CCTTGTATTACAGCTACTAGTCAATAC 57.320 37.037 0.00 6.15 0.00 1.89
1233 1264 8.857098 CCCTTGTATTACAGCTACTAGTCAATA 58.143 37.037 0.00 0.00 0.00 1.90
1234 1265 7.202011 CCCCTTGTATTACAGCTACTAGTCAAT 60.202 40.741 0.00 0.00 0.00 2.57
1235 1266 6.097839 CCCCTTGTATTACAGCTACTAGTCAA 59.902 42.308 0.00 0.00 0.00 3.18
1236 1267 5.597182 CCCCTTGTATTACAGCTACTAGTCA 59.403 44.000 0.00 0.00 0.00 3.41
1237 1268 5.832060 TCCCCTTGTATTACAGCTACTAGTC 59.168 44.000 0.00 0.00 0.00 2.59
1238 1269 5.774179 TCCCCTTGTATTACAGCTACTAGT 58.226 41.667 0.00 0.00 0.00 2.57
1239 1270 6.016108 GTCTCCCCTTGTATTACAGCTACTAG 60.016 46.154 0.00 0.00 0.00 2.57
1240 1271 5.832060 GTCTCCCCTTGTATTACAGCTACTA 59.168 44.000 0.00 0.00 0.00 1.82
1241 1272 4.650131 GTCTCCCCTTGTATTACAGCTACT 59.350 45.833 0.00 0.00 0.00 2.57
1242 1273 4.650131 AGTCTCCCCTTGTATTACAGCTAC 59.350 45.833 0.00 0.00 0.00 3.58
1243 1274 4.880164 AGTCTCCCCTTGTATTACAGCTA 58.120 43.478 0.00 0.00 0.00 3.32
1244 1275 3.707102 GAGTCTCCCCTTGTATTACAGCT 59.293 47.826 0.00 0.00 0.00 4.24
1245 1276 3.491104 CGAGTCTCCCCTTGTATTACAGC 60.491 52.174 0.00 0.00 0.00 4.40
1246 1277 3.068307 CCGAGTCTCCCCTTGTATTACAG 59.932 52.174 0.00 0.00 0.00 2.74
1247 1278 3.028850 CCGAGTCTCCCCTTGTATTACA 58.971 50.000 0.00 0.00 0.00 2.41
1248 1279 3.029570 ACCGAGTCTCCCCTTGTATTAC 58.970 50.000 0.00 0.00 0.00 1.89
1249 1280 3.294214 GACCGAGTCTCCCCTTGTATTA 58.706 50.000 0.00 0.00 0.00 0.98
1250 1281 2.108970 GACCGAGTCTCCCCTTGTATT 58.891 52.381 0.00 0.00 0.00 1.89
1251 1282 1.777941 GACCGAGTCTCCCCTTGTAT 58.222 55.000 0.00 0.00 0.00 2.29
1278 1309 7.281100 ACAGTAGAAGAAGAAAAGAAACAGGTG 59.719 37.037 0.00 0.00 0.00 4.00
1280 1311 7.793927 ACAGTAGAAGAAGAAAAGAAACAGG 57.206 36.000 0.00 0.00 0.00 4.00
1301 1341 7.035612 TCAAGCACATACTATGTCAACTACAG 58.964 38.462 0.00 0.00 42.70 2.74
1302 1342 6.930731 TCAAGCACATACTATGTCAACTACA 58.069 36.000 0.00 0.00 42.70 2.74
1303 1343 8.425577 AATCAAGCACATACTATGTCAACTAC 57.574 34.615 0.00 0.00 42.70 2.73
1304 1344 9.448438 AAAATCAAGCACATACTATGTCAACTA 57.552 29.630 0.00 0.00 42.70 2.24
1305 1345 7.928307 AAATCAAGCACATACTATGTCAACT 57.072 32.000 0.00 0.00 42.70 3.16
1337 1377 1.750193 TGGCGATTCCACAAATCTCC 58.250 50.000 0.00 0.85 45.67 3.71
1351 1391 4.670896 TCACAGAAGATGAATATGGCGA 57.329 40.909 0.00 0.00 0.00 5.54
1353 1393 5.766670 TGGATTCACAGAAGATGAATATGGC 59.233 40.000 0.40 0.00 44.85 4.40
1412 1457 3.631250 TGAAGCCTTTCCAGTGTTTCTT 58.369 40.909 0.00 0.00 32.09 2.52
1472 1518 8.642432 CCTTTTTCTCTTTTCCCTCTTACAAAT 58.358 33.333 0.00 0.00 0.00 2.32
1484 1530 3.508012 GCCCCTCTCCTTTTTCTCTTTTC 59.492 47.826 0.00 0.00 0.00 2.29
1488 1534 1.632920 CTGCCCCTCTCCTTTTTCTCT 59.367 52.381 0.00 0.00 0.00 3.10
1489 1535 1.340502 CCTGCCCCTCTCCTTTTTCTC 60.341 57.143 0.00 0.00 0.00 2.87
1490 1536 0.701147 CCTGCCCCTCTCCTTTTTCT 59.299 55.000 0.00 0.00 0.00 2.52
1491 1537 0.967887 GCCTGCCCCTCTCCTTTTTC 60.968 60.000 0.00 0.00 0.00 2.29
1492 1538 1.077445 GCCTGCCCCTCTCCTTTTT 59.923 57.895 0.00 0.00 0.00 1.94
1736 1782 2.032528 TCCTGCTGTCCAAAGCGG 59.967 61.111 0.00 0.00 46.65 5.52
1738 1784 1.228245 TGGTCCTGCTGTCCAAAGC 60.228 57.895 3.09 0.00 43.82 3.51
1749 1795 4.862902 ACATCGATCTTATCTGGTCCTG 57.137 45.455 0.00 0.00 0.00 3.86
1918 1964 8.318412 ACCAAACCTATGGCTATTTTTAAAAGG 58.682 33.333 0.14 0.00 44.75 3.11
1937 1983 9.150348 CTCCATTGATGTAATTTAAACCAAACC 57.850 33.333 0.00 0.00 0.00 3.27
1963 2009 5.067283 ACCATAATTTGATTGTACCCGAAGC 59.933 40.000 0.00 0.00 0.00 3.86
1978 2024 7.337689 GGGTTTAGAGTTCCGTTACCATAATTT 59.662 37.037 0.00 0.00 0.00 1.82
1983 2029 3.583966 TGGGTTTAGAGTTCCGTTACCAT 59.416 43.478 0.00 0.00 0.00 3.55
1999 2046 1.625818 TGTTTTTGTGCCTGTGGGTTT 59.374 42.857 0.00 0.00 34.45 3.27
2006 2053 4.260172 GGTTTCGATTTGTTTTTGTGCCTG 60.260 41.667 0.00 0.00 0.00 4.85
2008 2055 3.619038 TGGTTTCGATTTGTTTTTGTGCC 59.381 39.130 0.00 0.00 0.00 5.01
2009 2056 4.849111 TGGTTTCGATTTGTTTTTGTGC 57.151 36.364 0.00 0.00 0.00 4.57
2019 2066 6.001460 TGTAATCTCCACTTGGTTTCGATTT 58.999 36.000 0.00 0.00 36.34 2.17
2022 2069 4.610605 TGTAATCTCCACTTGGTTTCGA 57.389 40.909 0.00 0.00 36.34 3.71
2024 2071 7.117956 GTCTAGTTGTAATCTCCACTTGGTTTC 59.882 40.741 0.00 0.00 36.34 2.78
2033 2080 6.436218 TGCTTGTAGTCTAGTTGTAATCTCCA 59.564 38.462 0.00 0.00 0.00 3.86
2037 2084 8.703604 TTGATGCTTGTAGTCTAGTTGTAATC 57.296 34.615 0.00 0.00 0.00 1.75
2039 2086 8.896320 TTTTGATGCTTGTAGTCTAGTTGTAA 57.104 30.769 0.00 0.00 0.00 2.41
2042 2089 8.087982 TCTTTTTGATGCTTGTAGTCTAGTTG 57.912 34.615 0.00 0.00 0.00 3.16
2043 2090 8.560374 GTTCTTTTTGATGCTTGTAGTCTAGTT 58.440 33.333 0.00 0.00 0.00 2.24
2053 2100 3.434299 GCCATGGTTCTTTTTGATGCTTG 59.566 43.478 14.67 0.00 0.00 4.01
2060 2107 2.554032 ACGAGAGCCATGGTTCTTTTTG 59.446 45.455 29.31 20.98 35.85 2.44
2062 2109 2.427506 GACGAGAGCCATGGTTCTTTT 58.572 47.619 29.31 19.82 35.85 2.27
2092 2139 3.574284 TGGCTGGATTTTTCGATGTTG 57.426 42.857 0.00 0.00 0.00 3.33
2110 2157 3.315749 GTCCTCTGTAGGTACTTCGATGG 59.684 52.174 3.12 0.00 44.09 3.51
2113 2160 2.679059 CGGTCCTCTGTAGGTACTTCGA 60.679 54.545 0.00 0.00 44.09 3.71
2127 2174 3.385111 AGGTTTGATCATCTACGGTCCTC 59.615 47.826 0.00 0.00 0.00 3.71
2134 2181 7.064609 TCGATTCAACAAGGTTTGATCATCTAC 59.935 37.037 0.00 0.00 35.42 2.59
2146 2193 1.086696 CCGCATCGATTCAACAAGGT 58.913 50.000 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.