Multiple sequence alignment - TraesCS2D01G323800

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 TraesCS2D01G323800 chr2D 100.000 2593 0 0 1 2593 416860560 416863152 0.000000e+00 4789
1 TraesCS2D01G323800 chr2B 87.998 1833 78 60 1 1785 488867741 488869479 0.000000e+00 2036
2 TraesCS2D01G323800 chr2B 88.303 607 24 17 1997 2593 488869885 488870454 0.000000e+00 684
3 TraesCS2D01G323800 chr2B 94.915 177 8 1 1818 1993 488869599 488869775 2.540000e-70 276
4 TraesCS2D01G323800 chr2A 92.564 901 49 5 1094 1993 573367314 573366431 0.000000e+00 1277
5 TraesCS2D01G323800 chr2A 86.019 1080 38 38 1 1039 573368337 573367330 0.000000e+00 1053
6 TraesCS2D01G323800 chr7D 88.511 235 16 6 2013 2244 548149750 548149976 9.140000e-70 274
7 TraesCS2D01G323800 chr7D 82.014 139 15 5 2112 2246 637532625 637532493 2.730000e-20 110
8 TraesCS2D01G323800 chr7B 87.917 240 19 6 2008 2245 591375075 591375306 9.140000e-70 274
9 TraesCS2D01G323800 chr7A 80.714 140 16 6 2112 2246 728153676 728153543 5.910000e-17 99
10 TraesCS2D01G323800 chr7A 80.714 140 16 6 2112 2246 728183286 728183153 5.910000e-17 99
11 TraesCS2D01G323800 chr7A 80.714 140 16 6 2112 2246 728214528 728214395 5.910000e-17 99
12 TraesCS2D01G323800 chr7A 80.714 140 16 6 2109 2243 728525823 728525956 5.910000e-17 99
13 TraesCS2D01G323800 chr7A 80.714 140 16 6 2109 2243 728527699 728527832 5.910000e-17 99


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 TraesCS2D01G323800 chr2D 416860560 416863152 2592 False 4789.000000 4789 100.000000 1 2593 1 chr2D.!!$F1 2592
1 TraesCS2D01G323800 chr2B 488867741 488870454 2713 False 998.666667 2036 90.405333 1 2593 3 chr2B.!!$F1 2592
2 TraesCS2D01G323800 chr2A 573366431 573368337 1906 True 1165.000000 1277 89.291500 1 1993 2 chr2A.!!$R1 1992

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
895 960 0.101939 GATCTTACCCGTCACCCGTC 59.898 60.0 0.0 0.0 33.66 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 2458 0.249114 TGCACGAGTTAACACAGCGA 60.249 50.0 8.61 0.0 0.0 4.93 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
39 40 1.338655 CCGAACAAAAACCCACGGAAT 59.661 47.619 0.00 0.00 42.40 3.01
66 67 0.456653 GGCATGCGTGGTGAATGAAC 60.457 55.000 12.44 0.00 0.00 3.18
176 177 1.217882 GGAATGGAATGTCGCTACCG 58.782 55.000 0.00 0.00 0.00 4.02
204 205 3.673484 CGTGGGGCTTTGGCTGTG 61.673 66.667 0.00 0.00 38.73 3.66
205 206 3.305516 GTGGGGCTTTGGCTGTGG 61.306 66.667 0.00 0.00 38.73 4.17
250 251 1.754226 GGGCTTTGTGTTTTGGACTGA 59.246 47.619 0.00 0.00 0.00 3.41
277 278 1.681327 AATCCAAGGCAGCAGCAGG 60.681 57.895 2.65 1.62 44.61 4.85
279 280 2.833604 ATCCAAGGCAGCAGCAGGAC 62.834 60.000 10.50 0.00 44.61 3.85
280 281 2.281970 CAAGGCAGCAGCAGGACA 60.282 61.111 2.65 0.00 44.61 4.02
282 283 2.827129 AAGGCAGCAGCAGGACAGT 61.827 57.895 2.65 0.00 44.61 3.55
285 286 2.359602 CAGCAGCAGGACAGTGGG 60.360 66.667 0.00 0.00 0.00 4.61
286 287 2.851102 AGCAGCAGGACAGTGGGT 60.851 61.111 0.00 0.00 0.00 4.51
287 288 2.670934 GCAGCAGGACAGTGGGTG 60.671 66.667 0.00 0.00 0.00 4.61
288 289 2.670934 CAGCAGGACAGTGGGTGC 60.671 66.667 5.69 5.69 38.27 5.01
289 290 3.958860 AGCAGGACAGTGGGTGCC 61.959 66.667 9.31 0.00 38.89 5.01
291 292 3.569210 CAGGACAGTGGGTGCCCA 61.569 66.667 5.73 5.73 45.02 5.36
300 301 4.284550 GGGTGCCCACTCTGCCAA 62.285 66.667 1.66 0.00 35.81 4.52
301 302 2.674380 GGTGCCCACTCTGCCAAG 60.674 66.667 0.00 0.00 0.00 3.61
302 303 3.368571 GTGCCCACTCTGCCAAGC 61.369 66.667 0.00 0.00 0.00 4.01
303 304 3.888460 TGCCCACTCTGCCAAGCA 61.888 61.111 0.00 0.00 36.92 3.91
308 309 1.321474 CCACTCTGCCAAGCAAAGAA 58.679 50.000 0.00 0.00 38.41 2.52
309 310 1.268899 CCACTCTGCCAAGCAAAGAAG 59.731 52.381 0.00 0.00 38.41 2.85
314 315 0.185901 TGCCAAGCAAAGAAGGGAGT 59.814 50.000 0.00 0.00 34.76 3.85
335 336 3.004171 TGAACATAACATAAAGCGGCGT 58.996 40.909 9.37 0.00 0.00 5.68
558 578 2.074729 GGCTCCAAGGCTAGTAGAGA 57.925 55.000 0.00 0.00 37.85 3.10
581 615 2.682155 TTTTGTTTTCCACCTGGCAC 57.318 45.000 0.00 0.00 34.44 5.01
655 692 3.220658 TGGTCACGGTCACGCTCA 61.221 61.111 0.00 0.00 46.04 4.26
665 702 0.663153 GTCACGCTCACTTGCCTTTT 59.337 50.000 0.00 0.00 0.00 2.27
753 790 2.576615 CCCCCACTAGATTTTAGCAGC 58.423 52.381 0.00 0.00 0.00 5.25
846 904 2.227865 GCACATCGTATCTCCCTCTCTC 59.772 54.545 0.00 0.00 0.00 3.20
848 906 4.141287 CACATCGTATCTCCCTCTCTCTT 58.859 47.826 0.00 0.00 0.00 2.85
849 907 4.582656 CACATCGTATCTCCCTCTCTCTTT 59.417 45.833 0.00 0.00 0.00 2.52
851 909 4.505324 TCGTATCTCCCTCTCTCTTTGA 57.495 45.455 0.00 0.00 0.00 2.69
852 910 4.456535 TCGTATCTCCCTCTCTCTTTGAG 58.543 47.826 0.00 0.00 43.96 3.02
853 911 3.004315 CGTATCTCCCTCTCTCTTTGAGC 59.996 52.174 0.00 0.00 42.38 4.26
855 913 3.182887 TCTCCCTCTCTCTTTGAGCTT 57.817 47.619 0.00 0.00 42.38 3.74
856 914 3.515562 TCTCCCTCTCTCTTTGAGCTTT 58.484 45.455 0.00 0.00 42.38 3.51
889 954 1.829222 GGACCAAGATCTTACCCGTCA 59.171 52.381 7.86 0.00 0.00 4.35
890 955 2.418334 GGACCAAGATCTTACCCGTCAC 60.418 54.545 7.86 3.23 0.00 3.67
891 956 1.553704 ACCAAGATCTTACCCGTCACC 59.446 52.381 7.86 0.00 0.00 4.02
892 957 1.134491 CCAAGATCTTACCCGTCACCC 60.134 57.143 7.86 0.00 0.00 4.61
893 958 0.822164 AAGATCTTACCCGTCACCCG 59.178 55.000 6.06 0.00 0.00 5.28
894 959 0.324091 AGATCTTACCCGTCACCCGT 60.324 55.000 0.00 0.00 33.66 5.28
895 960 0.101939 GATCTTACCCGTCACCCGTC 59.898 60.000 0.00 0.00 33.66 4.79
939 1004 2.597578 GGATACCCTCCTCTCCTCTC 57.402 60.000 0.00 0.00 41.29 3.20
940 1005 1.076513 GGATACCCTCCTCTCCTCTCC 59.923 61.905 0.00 0.00 41.29 3.71
941 1006 2.070573 GATACCCTCCTCTCCTCTCCT 58.929 57.143 0.00 0.00 0.00 3.69
942 1007 2.912459 TACCCTCCTCTCCTCTCCTA 57.088 55.000 0.00 0.00 0.00 2.94
943 1008 2.238819 ACCCTCCTCTCCTCTCCTAT 57.761 55.000 0.00 0.00 0.00 2.57
944 1009 3.387105 ACCCTCCTCTCCTCTCCTATA 57.613 52.381 0.00 0.00 0.00 1.31
945 1010 3.907460 ACCCTCCTCTCCTCTCCTATAT 58.093 50.000 0.00 0.00 0.00 0.86
946 1011 3.856206 ACCCTCCTCTCCTCTCCTATATC 59.144 52.174 0.00 0.00 0.00 1.63
975 1040 4.024893 ACAACAACAGAGACACGCAATAAG 60.025 41.667 0.00 0.00 0.00 1.73
1014 1088 3.496331 CACTCCCCCATAAAACTTGTGT 58.504 45.455 0.00 0.00 0.00 3.72
1022 1096 1.103803 TAAAACTTGTGTGCCGCCAA 58.896 45.000 0.00 0.00 0.00 4.52
1025 1103 3.289834 CTTGTGTGCCGCCAAGCT 61.290 61.111 0.00 0.00 32.46 3.74
1041 1119 3.084786 CAAGCTAAGCTAAGCCACCTTT 58.915 45.455 0.00 0.00 43.86 3.11
1044 1122 4.902595 AGCTAAGCTAAGCCACCTTTGGA 61.903 47.826 0.00 0.00 40.82 3.53
1056 1134 2.175878 CCTTTGGAGGTGTCTCACAG 57.824 55.000 2.41 0.00 41.69 3.66
1057 1135 1.517242 CTTTGGAGGTGTCTCACAGC 58.483 55.000 0.00 0.00 46.20 4.40
1064 1142 2.355717 GGTGTCTCACAGCTCACTAC 57.644 55.000 2.41 0.00 42.83 2.73
1065 1143 1.889829 GGTGTCTCACAGCTCACTACT 59.110 52.381 2.41 0.00 42.83 2.57
1066 1144 2.094957 GGTGTCTCACAGCTCACTACTC 60.095 54.545 2.41 0.00 42.83 2.59
1067 1145 2.554462 GTGTCTCACAGCTCACTACTCA 59.446 50.000 0.00 0.00 34.08 3.41
1068 1146 3.192422 GTGTCTCACAGCTCACTACTCAT 59.808 47.826 0.00 0.00 34.08 2.90
1069 1147 4.396478 GTGTCTCACAGCTCACTACTCATA 59.604 45.833 0.00 0.00 34.08 2.15
1070 1148 4.637977 TGTCTCACAGCTCACTACTCATAG 59.362 45.833 0.00 0.00 34.25 2.23
1071 1149 4.036262 GTCTCACAGCTCACTACTCATAGG 59.964 50.000 0.00 0.00 32.08 2.57
1072 1150 3.291584 TCACAGCTCACTACTCATAGGG 58.708 50.000 0.00 0.00 32.48 3.53
1073 1151 2.363680 CACAGCTCACTACTCATAGGGG 59.636 54.545 0.00 0.00 32.05 4.79
1074 1152 2.245028 ACAGCTCACTACTCATAGGGGA 59.755 50.000 0.00 0.00 32.05 4.81
1075 1153 2.890311 CAGCTCACTACTCATAGGGGAG 59.110 54.545 0.00 0.00 40.79 4.30
1076 1154 2.158385 AGCTCACTACTCATAGGGGAGG 60.158 54.545 0.00 0.00 39.27 4.30
1077 1155 2.158445 GCTCACTACTCATAGGGGAGGA 60.158 54.545 0.00 0.00 39.27 3.71
1079 1157 3.396276 CTCACTACTCATAGGGGAGGAGA 59.604 52.174 9.30 0.00 46.93 3.71
1080 1158 3.396276 TCACTACTCATAGGGGAGGAGAG 59.604 52.174 9.30 1.77 46.93 3.20
1081 1159 3.396276 CACTACTCATAGGGGAGGAGAGA 59.604 52.174 9.30 0.00 46.93 3.10
1082 1160 3.655777 ACTACTCATAGGGGAGGAGAGAG 59.344 52.174 9.30 0.00 46.93 3.20
1083 1161 2.795556 ACTCATAGGGGAGGAGAGAGA 58.204 52.381 0.00 0.00 38.28 3.10
1084 1162 2.716424 ACTCATAGGGGAGGAGAGAGAG 59.284 54.545 0.00 0.00 38.28 3.20
1085 1163 1.427368 TCATAGGGGAGGAGAGAGAGC 59.573 57.143 0.00 0.00 0.00 4.09
1086 1164 0.404040 ATAGGGGAGGAGAGAGAGCG 59.596 60.000 0.00 0.00 0.00 5.03
1087 1165 2.346284 TAGGGGAGGAGAGAGAGCGC 62.346 65.000 0.00 0.00 0.00 5.92
1088 1166 3.591835 GGGAGGAGAGAGAGCGCG 61.592 72.222 0.00 0.00 0.00 6.86
1089 1167 4.264638 GGAGGAGAGAGAGCGCGC 62.265 72.222 26.66 26.66 0.00 6.86
1090 1168 4.605967 GAGGAGAGAGAGCGCGCG 62.606 72.222 28.44 28.44 0.00 6.86
1106 1184 1.798368 CGCGCGCACACACTAGATAC 61.798 60.000 32.61 0.00 0.00 2.24
1111 1189 2.441462 CGCACACACTAGATACGACAG 58.559 52.381 0.00 0.00 0.00 3.51
1112 1190 2.791503 CGCACACACTAGATACGACAGG 60.792 54.545 0.00 0.00 0.00 4.00
1124 1202 5.870706 AGATACGACAGGATGATGAGAGTA 58.129 41.667 0.00 0.00 39.69 2.59
1450 1528 2.901840 CGGACCCATTGATGGCCG 60.902 66.667 12.55 12.55 46.70 6.13
1477 1555 4.809070 GCCACAGCCAACTCTCTT 57.191 55.556 0.00 0.00 0.00 2.85
1484 1562 3.378112 CACAGCCAACTCTCTTTGTTTCA 59.622 43.478 0.00 0.00 0.00 2.69
1518 1596 7.553044 TCTCGTTTTCTTCTTCTTCTTCCTTTT 59.447 33.333 0.00 0.00 0.00 2.27
1616 1697 3.930336 ACATGTACATAGATGCCGATGG 58.070 45.455 8.32 0.00 30.76 3.51
1637 1718 2.186826 GGATGGGCGCATGTGTACC 61.187 63.158 22.33 11.69 0.00 3.34
1638 1719 1.153168 GATGGGCGCATGTGTACCT 60.153 57.895 22.33 0.00 0.00 3.08
1639 1720 0.105964 GATGGGCGCATGTGTACCTA 59.894 55.000 22.33 7.39 0.00 3.08
1709 1793 4.690122 ACGCAACTCAGTTTTACAGTAGT 58.310 39.130 0.00 0.00 0.00 2.73
1993 2165 3.255379 GGCGCTGCGTGCTACTAC 61.255 66.667 24.04 3.64 39.23 2.73
1995 2167 2.224885 GCGCTGCGTGCTACTACTC 61.225 63.158 24.04 0.00 40.11 2.59
2005 2283 4.974888 GCGTGCTACTACTCCAGTATTTAC 59.025 45.833 0.00 0.00 39.06 2.01
2063 2341 2.114825 CGGCCTAAATAACGAGACGAC 58.885 52.381 0.00 0.00 0.00 4.34
2067 2345 3.239254 GCCTAAATAACGAGACGACGAAC 59.761 47.826 0.00 0.00 37.03 3.95
2078 2356 0.454600 ACGACGAACCATGTATCGCT 59.545 50.000 14.98 5.20 42.61 4.93
2079 2357 0.846401 CGACGAACCATGTATCGCTG 59.154 55.000 14.98 6.28 42.61 5.18
2080 2358 1.533129 CGACGAACCATGTATCGCTGA 60.533 52.381 14.98 0.00 42.61 4.26
2081 2359 1.852895 GACGAACCATGTATCGCTGAC 59.147 52.381 14.98 4.03 42.61 3.51
2082 2360 0.846401 CGAACCATGTATCGCTGACG 59.154 55.000 4.70 0.00 42.01 4.35
2104 2382 1.884926 CAAGGCTGGCGCTAGCTAC 60.885 63.158 38.90 26.17 43.22 3.58
2180 2458 1.916181 AGCAGCCTGTTGTTACCCTAT 59.084 47.619 0.00 0.00 0.00 2.57
2181 2459 2.092914 AGCAGCCTGTTGTTACCCTATC 60.093 50.000 0.00 0.00 0.00 2.08
2182 2460 2.550978 CAGCCTGTTGTTACCCTATCG 58.449 52.381 0.00 0.00 0.00 2.92
2184 2462 1.134491 GCCTGTTGTTACCCTATCGCT 60.134 52.381 0.00 0.00 0.00 4.93
2185 2463 2.550978 CCTGTTGTTACCCTATCGCTG 58.449 52.381 0.00 0.00 0.00 5.18
2204 2482 3.548014 GCTGTGTTAACTCGTGCATGTTT 60.548 43.478 7.22 3.47 0.00 2.83
2205 2483 3.946402 TGTGTTAACTCGTGCATGTTTG 58.054 40.909 7.22 0.61 0.00 2.93
2226 2504 1.153349 GGGCTAAGAAGTGCGGAGG 60.153 63.158 0.00 0.00 0.00 4.30
2228 2506 1.614241 GGCTAAGAAGTGCGGAGGGA 61.614 60.000 0.00 0.00 0.00 4.20
2232 2510 2.126031 GAAGTGCGGAGGGACGTC 60.126 66.667 7.13 7.13 39.82 4.34
2436 2717 5.604758 TTAGATCACAGACTTGGGAGATG 57.395 43.478 0.00 0.00 40.81 2.90
2539 2825 4.655762 TCCATGTACAGTAGTGATCTGC 57.344 45.455 4.09 0.00 36.50 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.720902 CACGCATGCCCTCACCCA 62.721 66.667 13.15 0.00 0.00 4.51
44 45 1.750399 ATTCACCACGCATGCCCTC 60.750 57.895 13.15 0.00 0.00 4.30
205 206 0.453390 CAAAGATCCAAAGGCTCGGC 59.547 55.000 0.00 0.00 0.00 5.54
206 207 2.113860 TCAAAGATCCAAAGGCTCGG 57.886 50.000 0.00 0.00 0.00 4.63
207 208 2.159653 CGTTCAAAGATCCAAAGGCTCG 60.160 50.000 0.00 0.00 0.00 5.03
208 209 2.162408 CCGTTCAAAGATCCAAAGGCTC 59.838 50.000 0.00 0.00 0.00 4.70
209 210 2.162681 CCGTTCAAAGATCCAAAGGCT 58.837 47.619 0.00 0.00 0.00 4.58
210 211 1.202348 CCCGTTCAAAGATCCAAAGGC 59.798 52.381 0.00 0.00 0.00 4.35
211 212 1.818674 CCCCGTTCAAAGATCCAAAGG 59.181 52.381 0.00 0.00 0.00 3.11
250 251 1.384191 GCCTTGGATTGAGTGGGGT 59.616 57.895 0.00 0.00 0.00 4.95
285 286 3.368571 GCTTGGCAGAGTGGGCAC 61.369 66.667 0.00 0.00 43.63 5.01
286 287 2.925416 TTTGCTTGGCAGAGTGGGCA 62.925 55.000 0.00 0.00 40.61 5.36
287 288 2.151049 CTTTGCTTGGCAGAGTGGGC 62.151 60.000 2.50 0.00 40.61 5.36
288 289 0.538057 TCTTTGCTTGGCAGAGTGGG 60.538 55.000 9.31 0.00 40.85 4.61
289 290 1.268899 CTTCTTTGCTTGGCAGAGTGG 59.731 52.381 9.31 1.96 40.85 4.00
290 291 1.268899 CCTTCTTTGCTTGGCAGAGTG 59.731 52.381 9.31 5.03 40.85 3.51
291 292 1.613836 CCTTCTTTGCTTGGCAGAGT 58.386 50.000 9.31 0.00 40.85 3.24
292 293 0.886563 CCCTTCTTTGCTTGGCAGAG 59.113 55.000 4.05 4.05 41.30 3.35
293 294 0.478072 TCCCTTCTTTGCTTGGCAGA 59.522 50.000 0.00 0.00 40.61 4.26
294 295 0.886563 CTCCCTTCTTTGCTTGGCAG 59.113 55.000 0.00 0.00 40.61 4.85
295 296 0.185901 ACTCCCTTCTTTGCTTGGCA 59.814 50.000 0.00 0.00 36.47 4.92
296 297 0.600057 CACTCCCTTCTTTGCTTGGC 59.400 55.000 0.00 0.00 0.00 4.52
297 298 2.276732 TCACTCCCTTCTTTGCTTGG 57.723 50.000 0.00 0.00 0.00 3.61
298 299 2.951642 TGTTCACTCCCTTCTTTGCTTG 59.048 45.455 0.00 0.00 0.00 4.01
299 300 3.297134 TGTTCACTCCCTTCTTTGCTT 57.703 42.857 0.00 0.00 0.00 3.91
300 301 3.515602 ATGTTCACTCCCTTCTTTGCT 57.484 42.857 0.00 0.00 0.00 3.91
301 302 4.518970 TGTTATGTTCACTCCCTTCTTTGC 59.481 41.667 0.00 0.00 0.00 3.68
302 303 6.824305 ATGTTATGTTCACTCCCTTCTTTG 57.176 37.500 0.00 0.00 0.00 2.77
303 304 8.934023 TTTATGTTATGTTCACTCCCTTCTTT 57.066 30.769 0.00 0.00 0.00 2.52
308 309 4.876107 CGCTTTATGTTATGTTCACTCCCT 59.124 41.667 0.00 0.00 0.00 4.20
309 310 4.035208 CCGCTTTATGTTATGTTCACTCCC 59.965 45.833 0.00 0.00 0.00 4.30
314 315 3.004171 ACGCCGCTTTATGTTATGTTCA 58.996 40.909 0.00 0.00 0.00 3.18
556 576 4.683129 GCCAGGTGGAAAACAAAAATGTCT 60.683 41.667 0.00 0.00 37.39 3.41
557 577 3.559655 GCCAGGTGGAAAACAAAAATGTC 59.440 43.478 0.00 0.00 37.39 3.06
558 578 3.054802 TGCCAGGTGGAAAACAAAAATGT 60.055 39.130 0.00 0.00 37.39 2.71
581 615 2.408704 GCGCTGCTAAATAGTATGGTCG 59.591 50.000 0.00 0.00 0.00 4.79
655 692 5.659440 TCACAGAAAAGAAAAAGGCAAGT 57.341 34.783 0.00 0.00 0.00 3.16
665 702 6.072508 GCAGTAATCCACATCACAGAAAAGAA 60.073 38.462 0.00 0.00 0.00 2.52
753 790 5.534207 TGTAAACCCCGTATACATACAGG 57.466 43.478 3.32 2.86 34.30 4.00
774 824 2.288334 TGGCTTTACACTTGCTTGCATG 60.288 45.455 6.90 6.90 0.00 4.06
846 904 7.276438 GTCCAAAGGCATAAATAAAGCTCAAAG 59.724 37.037 0.00 0.00 0.00 2.77
848 906 6.350949 GGTCCAAAGGCATAAATAAAGCTCAA 60.351 38.462 0.00 0.00 0.00 3.02
849 907 5.127031 GGTCCAAAGGCATAAATAAAGCTCA 59.873 40.000 0.00 0.00 0.00 4.26
851 909 5.022787 TGGTCCAAAGGCATAAATAAAGCT 58.977 37.500 0.00 0.00 0.00 3.74
852 910 5.337578 TGGTCCAAAGGCATAAATAAAGC 57.662 39.130 0.00 0.00 0.00 3.51
853 911 7.169158 TCTTGGTCCAAAGGCATAAATAAAG 57.831 36.000 5.64 0.00 0.00 1.85
855 913 7.125391 AGATCTTGGTCCAAAGGCATAAATAA 58.875 34.615 5.64 0.00 0.00 1.40
856 914 6.672593 AGATCTTGGTCCAAAGGCATAAATA 58.327 36.000 5.64 0.00 0.00 1.40
889 954 0.670546 CATCTGAAACAGCGACGGGT 60.671 55.000 0.00 0.00 0.00 5.28
890 955 0.670546 ACATCTGAAACAGCGACGGG 60.671 55.000 0.00 0.00 0.00 5.28
891 956 0.439985 CACATCTGAAACAGCGACGG 59.560 55.000 0.00 0.00 0.00 4.79
892 957 1.125021 GTCACATCTGAAACAGCGACG 59.875 52.381 0.00 0.00 0.00 5.12
893 958 1.461127 GGTCACATCTGAAACAGCGAC 59.539 52.381 0.00 0.00 0.00 5.19
894 959 1.608025 GGGTCACATCTGAAACAGCGA 60.608 52.381 0.00 0.00 0.00 4.93
895 960 0.798776 GGGTCACATCTGAAACAGCG 59.201 55.000 0.00 0.00 0.00 5.18
926 991 6.851836 AGATAGATATAGGAGAGGAGAGGAGG 59.148 46.154 0.00 0.00 0.00 4.30
932 997 9.967451 TTGTTGTAGATAGATATAGGAGAGGAG 57.033 37.037 0.00 0.00 0.00 3.69
933 998 9.742144 GTTGTTGTAGATAGATATAGGAGAGGA 57.258 37.037 0.00 0.00 0.00 3.71
934 999 9.521841 TGTTGTTGTAGATAGATATAGGAGAGG 57.478 37.037 0.00 0.00 0.00 3.69
942 1007 8.346300 CGTGTCTCTGTTGTTGTAGATAGATAT 58.654 37.037 0.00 0.00 0.00 1.63
943 1008 7.678927 GCGTGTCTCTGTTGTTGTAGATAGATA 60.679 40.741 0.00 0.00 0.00 1.98
944 1009 6.556212 CGTGTCTCTGTTGTTGTAGATAGAT 58.444 40.000 0.00 0.00 0.00 1.98
945 1010 5.619309 GCGTGTCTCTGTTGTTGTAGATAGA 60.619 44.000 0.00 0.00 0.00 1.98
946 1011 4.559251 GCGTGTCTCTGTTGTTGTAGATAG 59.441 45.833 0.00 0.00 0.00 2.08
961 1026 2.866762 GGACCATCTTATTGCGTGTCTC 59.133 50.000 0.00 0.00 0.00 3.36
975 1040 0.620556 TGGAGGAAGCTTGGACCATC 59.379 55.000 2.10 0.00 0.00 3.51
1014 1088 0.744414 CTTAGCTTAGCTTGGCGGCA 60.744 55.000 13.44 7.97 40.44 5.69
1022 1096 2.619074 CCAAAGGTGGCTTAGCTTAGCT 60.619 50.000 22.83 12.67 45.88 3.32
1025 1103 2.026262 CCTCCAAAGGTGGCTTAGCTTA 60.026 50.000 3.59 0.00 45.88 3.09
1041 1119 0.469892 TGAGCTGTGAGACACCTCCA 60.470 55.000 0.00 0.00 38.66 3.86
1044 1122 1.889829 GTAGTGAGCTGTGAGACACCT 59.110 52.381 0.00 0.00 32.73 4.00
1046 1124 2.554462 TGAGTAGTGAGCTGTGAGACAC 59.446 50.000 0.00 0.00 34.56 3.67
1047 1125 2.863809 TGAGTAGTGAGCTGTGAGACA 58.136 47.619 0.00 0.00 0.00 3.41
1048 1126 4.036262 CCTATGAGTAGTGAGCTGTGAGAC 59.964 50.000 0.00 0.00 0.00 3.36
1049 1127 4.203226 CCTATGAGTAGTGAGCTGTGAGA 58.797 47.826 0.00 0.00 0.00 3.27
1050 1128 3.317711 CCCTATGAGTAGTGAGCTGTGAG 59.682 52.174 0.00 0.00 0.00 3.51
1051 1129 3.291584 CCCTATGAGTAGTGAGCTGTGA 58.708 50.000 0.00 0.00 0.00 3.58
1053 1131 2.245028 TCCCCTATGAGTAGTGAGCTGT 59.755 50.000 0.00 0.00 0.00 4.40
1055 1133 2.158385 CCTCCCCTATGAGTAGTGAGCT 60.158 54.545 0.00 0.00 0.00 4.09
1056 1134 2.158445 TCCTCCCCTATGAGTAGTGAGC 60.158 54.545 0.00 0.00 0.00 4.26
1057 1135 3.396276 TCTCCTCCCCTATGAGTAGTGAG 59.604 52.174 0.00 0.00 0.00 3.51
1058 1136 3.396276 CTCTCCTCCCCTATGAGTAGTGA 59.604 52.174 0.00 0.00 0.00 3.41
1059 1137 3.396276 TCTCTCCTCCCCTATGAGTAGTG 59.604 52.174 0.00 0.00 0.00 2.74
1060 1138 3.655777 CTCTCTCCTCCCCTATGAGTAGT 59.344 52.174 0.00 0.00 0.00 2.73
1061 1139 3.913799 TCTCTCTCCTCCCCTATGAGTAG 59.086 52.174 0.00 0.00 0.00 2.57
1062 1140 3.913799 CTCTCTCTCCTCCCCTATGAGTA 59.086 52.174 0.00 0.00 0.00 2.59
1064 1142 2.555227 GCTCTCTCTCCTCCCCTATGAG 60.555 59.091 0.00 0.00 0.00 2.90
1065 1143 1.427368 GCTCTCTCTCCTCCCCTATGA 59.573 57.143 0.00 0.00 0.00 2.15
1066 1144 1.886222 CGCTCTCTCTCCTCCCCTATG 60.886 61.905 0.00 0.00 0.00 2.23
1067 1145 0.404040 CGCTCTCTCTCCTCCCCTAT 59.596 60.000 0.00 0.00 0.00 2.57
1068 1146 1.840598 CGCTCTCTCTCCTCCCCTA 59.159 63.158 0.00 0.00 0.00 3.53
1069 1147 2.600731 CGCTCTCTCTCCTCCCCT 59.399 66.667 0.00 0.00 0.00 4.79
1070 1148 3.223589 GCGCTCTCTCTCCTCCCC 61.224 72.222 0.00 0.00 0.00 4.81
1071 1149 3.591835 CGCGCTCTCTCTCCTCCC 61.592 72.222 5.56 0.00 0.00 4.30
1072 1150 4.264638 GCGCGCTCTCTCTCCTCC 62.265 72.222 26.67 0.00 0.00 4.30
1073 1151 4.605967 CGCGCGCTCTCTCTCCTC 62.606 72.222 30.48 0.00 0.00 3.71
1087 1165 1.585261 TATCTAGTGTGTGCGCGCG 60.585 57.895 28.44 28.44 0.00 6.86
1088 1166 1.798368 CGTATCTAGTGTGTGCGCGC 61.798 60.000 27.26 27.26 0.00 6.86
1089 1167 0.247934 TCGTATCTAGTGTGTGCGCG 60.248 55.000 0.00 0.00 0.00 6.86
1090 1168 1.189403 GTCGTATCTAGTGTGTGCGC 58.811 55.000 0.00 0.00 0.00 6.09
1091 1169 2.441462 CTGTCGTATCTAGTGTGTGCG 58.559 52.381 0.00 0.00 0.00 5.34
1092 1170 2.422479 TCCTGTCGTATCTAGTGTGTGC 59.578 50.000 0.00 0.00 0.00 4.57
1103 1181 4.762765 GGTACTCTCATCATCCTGTCGTAT 59.237 45.833 0.00 0.00 0.00 3.06
1106 1184 2.294791 GGGTACTCTCATCATCCTGTCG 59.705 54.545 0.00 0.00 0.00 4.35
1111 1189 1.346068 GGCTGGGTACTCTCATCATCC 59.654 57.143 0.00 0.00 0.00 3.51
1112 1190 2.324541 AGGCTGGGTACTCTCATCATC 58.675 52.381 0.00 0.00 0.00 2.92
1255 1333 1.747367 CCAGCCTCGACGAGTCTCT 60.747 63.158 22.61 13.54 0.00 3.10
1439 1517 1.402968 CTTCAAGTCCGGCCATCAATG 59.597 52.381 2.24 0.00 0.00 2.82
1441 1519 0.322456 CCTTCAAGTCCGGCCATCAA 60.322 55.000 2.24 0.00 0.00 2.57
1450 1528 3.673599 GCTGTGGCCTTCAAGTCC 58.326 61.111 3.32 0.00 0.00 3.85
1461 1539 1.972872 ACAAAGAGAGTTGGCTGTGG 58.027 50.000 0.00 0.00 32.50 4.17
1463 1541 3.378427 GTGAAACAAAGAGAGTTGGCTGT 59.622 43.478 0.00 0.00 36.32 4.40
1477 1555 2.639065 ACGAGAGGCAAAGTGAAACAA 58.361 42.857 0.00 0.00 41.43 2.83
1484 1562 3.809905 AGAAGAAAACGAGAGGCAAAGT 58.190 40.909 0.00 0.00 0.00 2.66
1616 1697 0.463654 TACACATGCGCCCATCCTTC 60.464 55.000 4.18 0.00 0.00 3.46
1639 1720 9.175312 TCGATTCAGACTCAAGTAATAAGTAGT 57.825 33.333 0.00 0.00 0.00 2.73
1709 1793 9.449719 GGAACTGAAGGAATCTTGAAAAGTATA 57.550 33.333 0.00 0.00 46.34 1.47
1718 1802 3.265791 CTCGGGAACTGAAGGAATCTTG 58.734 50.000 0.00 0.00 46.55 3.02
1726 1810 0.891373 TCTCAGCTCGGGAACTGAAG 59.109 55.000 3.65 0.00 46.55 3.02
1898 2070 1.019805 GGCAGCCAAGAACTACGGAC 61.020 60.000 6.55 0.00 0.00 4.79
1957 2129 1.548973 CGTCAAGCGTGCTCGTCTTT 61.549 55.000 10.18 0.00 39.49 2.52
1993 2165 9.095065 GTGTGGTACTAAATGTAAATACTGGAG 57.905 37.037 0.00 0.00 32.25 3.86
1995 2167 7.010738 CGGTGTGGTACTAAATGTAAATACTGG 59.989 40.741 0.00 0.00 32.25 4.00
2005 2283 1.924524 CGAGCGGTGTGGTACTAAATG 59.075 52.381 0.00 0.00 0.00 2.32
2044 2322 2.114825 CGTCGTCTCGTTATTTAGGCC 58.885 52.381 0.00 0.00 0.00 5.19
2063 2341 0.846401 CGTCAGCGATACATGGTTCG 59.154 55.000 13.37 13.37 41.33 3.95
2085 2363 3.740128 TAGCTAGCGCCAGCCTTGC 62.740 63.158 24.31 8.07 46.67 4.01
2086 2364 1.884926 GTAGCTAGCGCCAGCCTTG 60.885 63.158 24.31 0.00 46.67 3.61
2087 2365 2.501610 GTAGCTAGCGCCAGCCTT 59.498 61.111 24.31 9.54 46.67 4.35
2136 2414 2.221299 AAGCCCGGCCAGAAGTACA 61.221 57.895 5.55 0.00 0.00 2.90
2165 2443 2.093658 ACAGCGATAGGGTAACAACAGG 60.094 50.000 0.00 0.00 39.74 4.00
2167 2445 2.300723 ACACAGCGATAGGGTAACAACA 59.699 45.455 0.00 0.00 39.74 3.33
2168 2446 2.968675 ACACAGCGATAGGGTAACAAC 58.031 47.619 0.00 0.00 39.74 3.32
2169 2447 3.688694 AACACAGCGATAGGGTAACAA 57.311 42.857 0.00 0.00 39.74 2.83
2180 2458 0.249114 TGCACGAGTTAACACAGCGA 60.249 50.000 8.61 0.00 0.00 4.93
2181 2459 0.790207 ATGCACGAGTTAACACAGCG 59.210 50.000 8.61 8.30 0.00 5.18
2182 2460 1.531149 ACATGCACGAGTTAACACAGC 59.469 47.619 8.61 9.14 0.00 4.40
2184 2462 3.242903 CCAAACATGCACGAGTTAACACA 60.243 43.478 8.61 0.00 0.00 3.72
2185 2463 3.296628 CCAAACATGCACGAGTTAACAC 58.703 45.455 8.61 0.00 0.00 3.32
2212 2490 0.896940 ACGTCCCTCCGCACTTCTTA 60.897 55.000 0.00 0.00 0.00 2.10
2250 2528 9.693739 ACCATGTATAAATGAGTCAAAATGGTA 57.306 29.630 12.98 0.00 41.61 3.25
2251 2529 8.469200 CACCATGTATAAATGAGTCAAAATGGT 58.531 33.333 9.86 9.86 43.61 3.55
2252 2530 8.685427 TCACCATGTATAAATGAGTCAAAATGG 58.315 33.333 4.31 8.78 37.46 3.16
2253 2531 9.726232 CTCACCATGTATAAATGAGTCAAAATG 57.274 33.333 4.31 0.00 33.58 2.32
2254 2532 9.466497 ACTCACCATGTATAAATGAGTCAAAAT 57.534 29.630 4.31 0.00 45.25 1.82
2255 2533 8.729756 CACTCACCATGTATAAATGAGTCAAAA 58.270 33.333 4.31 0.00 45.25 2.44
2256 2534 7.336679 CCACTCACCATGTATAAATGAGTCAAA 59.663 37.037 4.31 0.00 45.25 2.69
2257 2535 6.823182 CCACTCACCATGTATAAATGAGTCAA 59.177 38.462 4.31 0.00 45.25 3.18
2258 2536 6.070251 ACCACTCACCATGTATAAATGAGTCA 60.070 38.462 4.31 0.00 45.25 3.41
2259 2537 6.258727 CACCACTCACCATGTATAAATGAGTC 59.741 42.308 4.31 0.00 45.25 3.36
2261 2539 5.008019 GCACCACTCACCATGTATAAATGAG 59.992 44.000 4.31 0.00 42.07 2.90
2262 2540 4.881273 GCACCACTCACCATGTATAAATGA 59.119 41.667 4.31 0.00 0.00 2.57
2263 2541 4.036734 GGCACCACTCACCATGTATAAATG 59.963 45.833 0.00 0.00 0.00 2.32
2264 2542 4.079787 AGGCACCACTCACCATGTATAAAT 60.080 41.667 0.00 0.00 0.00 1.40
2265 2543 3.265737 AGGCACCACTCACCATGTATAAA 59.734 43.478 0.00 0.00 0.00 1.40
2266 2544 2.843730 AGGCACCACTCACCATGTATAA 59.156 45.455 0.00 0.00 0.00 0.98
2267 2545 2.477245 AGGCACCACTCACCATGTATA 58.523 47.619 0.00 0.00 0.00 1.47
2268 2546 1.289160 AGGCACCACTCACCATGTAT 58.711 50.000 0.00 0.00 0.00 2.29
2269 2547 1.553248 GTAGGCACCACTCACCATGTA 59.447 52.381 0.00 0.00 0.00 2.29
2270 2548 0.324943 GTAGGCACCACTCACCATGT 59.675 55.000 0.00 0.00 0.00 3.21
2320 2598 0.591170 AAACGAAACTGATGTGGCCG 59.409 50.000 0.00 0.00 0.00 6.13
2390 2671 4.566426 AAGCTGGAGTTTTGCTAGATCT 57.434 40.909 0.00 0.00 35.85 2.75
2436 2717 2.846193 TGAACCAACTAAGCTGTCACC 58.154 47.619 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.