Multiple sequence alignment - TraesCS2D01G230000

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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 TraesCS2D01G230000 chr2D 100.000 3611 0 0 1 3611 200913589 200917199 0 6669
1 TraesCS2D01G230000 chr7D 99.020 2347 22 1 1266 3611 579030321 579032667 0 4205
2 TraesCS2D01G230000 chr1A 98.935 2347 24 1 1266 3611 112004319 112001973 0 4194
3 TraesCS2D01G230000 chrUn 98.849 2346 27 0 1266 3611 86478642 86480987 0 4183
4 TraesCS2D01G230000 chrUn 98.722 2347 29 1 1266 3611 186190827 186188481 0 4167
5 TraesCS2D01G230000 chrUn 97.436 1209 29 2 68 1274 221548993 221547785 0 2060
6 TraesCS2D01G230000 chrUn 97.270 1209 31 2 68 1274 186191991 186190783 0 2049
7 TraesCS2D01G230000 chr7B 98.721 2346 30 0 1266 3611 743006652 743008997 0 4167
8 TraesCS2D01G230000 chr7B 97.273 1210 30 3 68 1274 743005487 743006696 0 2049
9 TraesCS2D01G230000 chr7B 94.210 1209 64 5 68 1274 247460473 247461677 0 1840
10 TraesCS2D01G230000 chr1D 98.466 2347 33 3 1266 3611 212467279 212464935 0 4132
11 TraesCS2D01G230000 chr4B 98.252 2346 39 2 1266 3611 209270720 209268377 0 4104
12 TraesCS2D01G230000 chr7A 98.210 2346 41 1 1266 3611 211292863 211295207 0 4098
13 TraesCS2D01G230000 chr7A 98.124 2346 44 0 1266 3611 120881035 120883380 0 4089
14 TraesCS2D01G230000 chr7A 96.857 1209 33 3 68 1274 120879874 120881079 0 2017
15 TraesCS2D01G230000 chr6D 97.027 1211 30 5 68 1274 458964374 458965582 0 2032
16 TraesCS2D01G230000 chr3A 96.694 1210 33 5 70 1274 51915585 51916792 0 2006
17 TraesCS2D01G230000 chr6A 95.702 1210 46 6 68 1274 79143101 79144307 0 1941
18 TraesCS2D01G230000 chr1B 95.443 1207 48 5 71 1274 499826615 499827817 0 1917


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 TraesCS2D01G230000 chr2D 200913589 200917199 3610 False 6669 6669 100.0000 1 3611 1 chr2D.!!$F1 3610
1 TraesCS2D01G230000 chr7D 579030321 579032667 2346 False 4205 4205 99.0200 1266 3611 1 chr7D.!!$F1 2345
2 TraesCS2D01G230000 chr1A 112001973 112004319 2346 True 4194 4194 98.9350 1266 3611 1 chr1A.!!$R1 2345
3 TraesCS2D01G230000 chrUn 86478642 86480987 2345 False 4183 4183 98.8490 1266 3611 1 chrUn.!!$F1 2345
4 TraesCS2D01G230000 chrUn 186188481 186191991 3510 True 3108 4167 97.9960 68 3611 2 chrUn.!!$R2 3543
5 TraesCS2D01G230000 chrUn 221547785 221548993 1208 True 2060 2060 97.4360 68 1274 1 chrUn.!!$R1 1206
6 TraesCS2D01G230000 chr7B 743005487 743008997 3510 False 3108 4167 97.9970 68 3611 2 chr7B.!!$F2 3543
7 TraesCS2D01G230000 chr7B 247460473 247461677 1204 False 1840 1840 94.2100 68 1274 1 chr7B.!!$F1 1206
8 TraesCS2D01G230000 chr1D 212464935 212467279 2344 True 4132 4132 98.4660 1266 3611 1 chr1D.!!$R1 2345
9 TraesCS2D01G230000 chr4B 209268377 209270720 2343 True 4104 4104 98.2520 1266 3611 1 chr4B.!!$R1 2345
10 TraesCS2D01G230000 chr7A 211292863 211295207 2344 False 4098 4098 98.2100 1266 3611 1 chr7A.!!$F1 2345
11 TraesCS2D01G230000 chr7A 120879874 120883380 3506 False 3053 4089 97.4905 68 3611 2 chr7A.!!$F2 3543
12 TraesCS2D01G230000 chr6D 458964374 458965582 1208 False 2032 2032 97.0270 68 1274 1 chr6D.!!$F1 1206
13 TraesCS2D01G230000 chr3A 51915585 51916792 1207 False 2006 2006 96.6940 70 1274 1 chr3A.!!$F1 1204
14 TraesCS2D01G230000 chr6A 79143101 79144307 1206 False 1941 1941 95.7020 68 1274 1 chr6A.!!$F1 1206
15 TraesCS2D01G230000 chr1B 499826615 499827817 1202 False 1917 1917 95.4430 71 1274 1 chr1B.!!$F1 1203

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
975 991 0.546598 CGGCCCCTCTTTGATAAGGT 59.453 55.0 0.0 0.0 32.02 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2739 2796 1.465187 GGAATCGCTTTGGTTACGCAC 60.465 52.381 0.0 0.0 0.0 5.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.746045 TTCAGGATGTACGCTAATCCC 57.254 47.619 6.38 0.00 42.97 3.85
24 25 2.958818 TCAGGATGTACGCTAATCCCT 58.041 47.619 6.38 0.00 42.97 4.20
25 26 4.108501 TCAGGATGTACGCTAATCCCTA 57.891 45.455 6.38 0.00 42.97 3.53
26 27 4.476297 TCAGGATGTACGCTAATCCCTAA 58.524 43.478 6.38 0.00 42.97 2.69
27 28 4.897076 TCAGGATGTACGCTAATCCCTAAA 59.103 41.667 6.38 0.00 42.97 1.85
28 29 5.010719 TCAGGATGTACGCTAATCCCTAAAG 59.989 44.000 6.38 0.00 42.97 1.85
29 30 4.900054 AGGATGTACGCTAATCCCTAAAGT 59.100 41.667 6.38 0.00 42.97 2.66
30 31 5.365895 AGGATGTACGCTAATCCCTAAAGTT 59.634 40.000 6.38 0.00 42.97 2.66
31 32 5.465724 GGATGTACGCTAATCCCTAAAGTTG 59.534 44.000 0.00 0.00 37.04 3.16
32 33 5.664294 TGTACGCTAATCCCTAAAGTTGA 57.336 39.130 0.00 0.00 0.00 3.18
33 34 6.229936 TGTACGCTAATCCCTAAAGTTGAT 57.770 37.500 0.00 0.00 0.00 2.57
34 35 6.046593 TGTACGCTAATCCCTAAAGTTGATG 58.953 40.000 0.00 0.00 0.00 3.07
35 36 5.099042 ACGCTAATCCCTAAAGTTGATGT 57.901 39.130 0.00 0.00 0.00 3.06
36 37 5.497474 ACGCTAATCCCTAAAGTTGATGTT 58.503 37.500 0.00 0.00 0.00 2.71
37 38 5.585047 ACGCTAATCCCTAAAGTTGATGTTC 59.415 40.000 0.00 0.00 0.00 3.18
38 39 5.276868 CGCTAATCCCTAAAGTTGATGTTCG 60.277 44.000 0.00 0.00 0.00 3.95
39 40 4.965119 AATCCCTAAAGTTGATGTTCGC 57.035 40.909 0.00 0.00 0.00 4.70
40 41 2.706890 TCCCTAAAGTTGATGTTCGCC 58.293 47.619 0.00 0.00 0.00 5.54
41 42 1.743394 CCCTAAAGTTGATGTTCGCCC 59.257 52.381 0.00 0.00 0.00 6.13
42 43 2.618045 CCCTAAAGTTGATGTTCGCCCT 60.618 50.000 0.00 0.00 0.00 5.19
43 44 3.081804 CCTAAAGTTGATGTTCGCCCTT 58.918 45.455 0.00 0.00 0.00 3.95
44 45 3.506067 CCTAAAGTTGATGTTCGCCCTTT 59.494 43.478 0.00 0.00 0.00 3.11
45 46 3.643159 AAAGTTGATGTTCGCCCTTTC 57.357 42.857 0.00 0.00 0.00 2.62
46 47 2.568623 AGTTGATGTTCGCCCTTTCT 57.431 45.000 0.00 0.00 0.00 2.52
47 48 3.695830 AGTTGATGTTCGCCCTTTCTA 57.304 42.857 0.00 0.00 0.00 2.10
48 49 3.600388 AGTTGATGTTCGCCCTTTCTAG 58.400 45.455 0.00 0.00 0.00 2.43
49 50 2.678336 GTTGATGTTCGCCCTTTCTAGG 59.322 50.000 0.00 0.00 41.60 3.02
50 51 2.184533 TGATGTTCGCCCTTTCTAGGA 58.815 47.619 0.00 0.00 45.05 2.94
51 52 2.168521 TGATGTTCGCCCTTTCTAGGAG 59.831 50.000 0.00 0.00 45.05 3.69
52 53 1.933021 TGTTCGCCCTTTCTAGGAGA 58.067 50.000 0.00 0.00 45.05 3.71
53 54 1.549170 TGTTCGCCCTTTCTAGGAGAC 59.451 52.381 0.00 0.00 45.05 3.36
54 55 1.826096 GTTCGCCCTTTCTAGGAGACT 59.174 52.381 0.00 0.00 45.05 3.24
55 56 3.022406 GTTCGCCCTTTCTAGGAGACTA 58.978 50.000 0.00 0.00 45.05 2.59
56 57 3.596940 TCGCCCTTTCTAGGAGACTAT 57.403 47.619 0.00 0.00 45.05 2.12
57 58 3.912248 TCGCCCTTTCTAGGAGACTATT 58.088 45.455 0.00 0.00 45.05 1.73
58 59 4.287552 TCGCCCTTTCTAGGAGACTATTT 58.712 43.478 0.00 0.00 45.05 1.40
59 60 4.341520 TCGCCCTTTCTAGGAGACTATTTC 59.658 45.833 0.00 0.00 45.05 2.17
60 61 4.623002 GCCCTTTCTAGGAGACTATTTCG 58.377 47.826 0.00 0.00 45.05 3.46
61 62 4.099727 GCCCTTTCTAGGAGACTATTTCGT 59.900 45.833 0.00 0.00 45.05 3.85
62 63 5.593010 CCCTTTCTAGGAGACTATTTCGTG 58.407 45.833 0.00 0.00 45.05 4.35
63 64 5.360144 CCCTTTCTAGGAGACTATTTCGTGA 59.640 44.000 0.00 0.00 45.05 4.35
64 65 6.127423 CCCTTTCTAGGAGACTATTTCGTGAA 60.127 42.308 0.00 0.00 45.05 3.18
65 66 7.321153 CCTTTCTAGGAGACTATTTCGTGAAA 58.679 38.462 0.00 0.00 45.05 2.69
66 67 7.817962 CCTTTCTAGGAGACTATTTCGTGAAAA 59.182 37.037 0.00 0.00 45.05 2.29
379 387 7.220740 GGCTAAACTTCTATCTGAGCCTTTAT 58.779 38.462 2.77 0.00 43.77 1.40
500 508 3.639094 AGGAAAGCTGTCTAGTATGCGAT 59.361 43.478 3.34 0.00 0.00 4.58
521 529 7.074502 GCGATAAGATGTCATTCAGGAATTTC 58.925 38.462 0.00 0.00 0.00 2.17
655 663 5.828328 TCTCCAAGCGTCTTATCAAGATCTA 59.172 40.000 0.00 0.00 40.18 1.98
898 914 4.477249 AGCGGGGTAGCTTAGTAATTCTA 58.523 43.478 0.00 0.00 46.80 2.10
975 991 0.546598 CGGCCCCTCTTTGATAAGGT 59.453 55.000 0.00 0.00 32.02 3.50
1135 1152 1.418637 GTATGGAATTAGCCCGACCCA 59.581 52.381 0.00 0.00 0.00 4.51
1153 1170 2.098117 CCCAGCGATCAAATTCTTGGTC 59.902 50.000 0.00 0.00 39.03 4.02
1229 1247 2.264005 TTTATGGTTATGCCGGCGAT 57.736 45.000 23.90 18.31 41.21 4.58
1230 1248 1.518325 TTATGGTTATGCCGGCGATG 58.482 50.000 23.90 0.00 41.21 3.84
1231 1249 0.682292 TATGGTTATGCCGGCGATGA 59.318 50.000 23.90 10.48 41.21 2.92
1232 1250 0.036732 ATGGTTATGCCGGCGATGAT 59.963 50.000 23.90 12.40 41.21 2.45
1233 1251 0.682292 TGGTTATGCCGGCGATGATA 59.318 50.000 23.90 11.24 41.21 2.15
1234 1252 1.337728 TGGTTATGCCGGCGATGATAG 60.338 52.381 23.90 0.00 41.21 2.08
1235 1253 1.359848 GTTATGCCGGCGATGATAGG 58.640 55.000 23.90 0.00 0.00 2.57
1236 1254 0.973632 TTATGCCGGCGATGATAGGT 59.026 50.000 23.90 1.26 0.00 3.08
1237 1255 0.246360 TATGCCGGCGATGATAGGTG 59.754 55.000 23.90 0.00 0.00 4.00
1238 1256 2.357517 GCCGGCGATGATAGGTGG 60.358 66.667 12.58 0.00 0.00 4.61
1239 1257 2.867855 GCCGGCGATGATAGGTGGA 61.868 63.158 12.58 0.00 0.00 4.02
1240 1258 1.975327 CCGGCGATGATAGGTGGAT 59.025 57.895 9.30 0.00 0.00 3.41
1241 1259 0.321671 CCGGCGATGATAGGTGGATT 59.678 55.000 9.30 0.00 0.00 3.01
1242 1260 1.270839 CCGGCGATGATAGGTGGATTT 60.271 52.381 9.30 0.00 0.00 2.17
1243 1261 1.800586 CGGCGATGATAGGTGGATTTG 59.199 52.381 0.00 0.00 0.00 2.32
1244 1262 2.154462 GGCGATGATAGGTGGATTTGG 58.846 52.381 0.00 0.00 0.00 3.28
1245 1263 2.487265 GGCGATGATAGGTGGATTTGGT 60.487 50.000 0.00 0.00 0.00 3.67
1246 1264 3.244422 GGCGATGATAGGTGGATTTGGTA 60.244 47.826 0.00 0.00 0.00 3.25
1247 1265 4.385825 GCGATGATAGGTGGATTTGGTAA 58.614 43.478 0.00 0.00 0.00 2.85
1248 1266 5.003804 GCGATGATAGGTGGATTTGGTAAT 58.996 41.667 0.00 0.00 0.00 1.89
1249 1267 5.473504 GCGATGATAGGTGGATTTGGTAATT 59.526 40.000 0.00 0.00 0.00 1.40
1250 1268 6.568462 GCGATGATAGGTGGATTTGGTAATTG 60.568 42.308 0.00 0.00 0.00 2.32
1251 1269 6.072508 CGATGATAGGTGGATTTGGTAATTGG 60.073 42.308 0.00 0.00 0.00 3.16
1252 1270 6.086011 TGATAGGTGGATTTGGTAATTGGT 57.914 37.500 0.00 0.00 0.00 3.67
1253 1271 6.498538 TGATAGGTGGATTTGGTAATTGGTT 58.501 36.000 0.00 0.00 0.00 3.67
1254 1272 6.957020 TGATAGGTGGATTTGGTAATTGGTTT 59.043 34.615 0.00 0.00 0.00 3.27
1255 1273 5.482163 AGGTGGATTTGGTAATTGGTTTG 57.518 39.130 0.00 0.00 0.00 2.93
1256 1274 4.904853 AGGTGGATTTGGTAATTGGTTTGT 59.095 37.500 0.00 0.00 0.00 2.83
1257 1275 5.368230 AGGTGGATTTGGTAATTGGTTTGTT 59.632 36.000 0.00 0.00 0.00 2.83
1258 1276 5.699001 GGTGGATTTGGTAATTGGTTTGTTC 59.301 40.000 0.00 0.00 0.00 3.18
1259 1277 5.699001 GTGGATTTGGTAATTGGTTTGTTCC 59.301 40.000 0.00 0.00 0.00 3.62
1260 1278 4.926832 GGATTTGGTAATTGGTTTGTTCCG 59.073 41.667 0.00 0.00 0.00 4.30
1261 1279 5.279056 GGATTTGGTAATTGGTTTGTTCCGA 60.279 40.000 0.00 0.00 0.00 4.55
1262 1280 5.793030 TTTGGTAATTGGTTTGTTCCGAT 57.207 34.783 0.00 0.00 33.36 4.18
1263 1281 5.793030 TTGGTAATTGGTTTGTTCCGATT 57.207 34.783 0.00 0.00 42.34 3.34
1264 1282 5.379732 TGGTAATTGGTTTGTTCCGATTC 57.620 39.130 1.99 0.00 40.72 2.52
1296 1314 5.366768 TGGATTTGGTAATTGGTTTGTTCCA 59.633 36.000 0.00 0.00 35.49 3.53
1417 1471 4.586235 AAGTGGGCAGCGGCACTT 62.586 61.111 13.50 10.59 46.28 3.16
1434 1488 2.567169 CACTTGGTGGACAGTCTATCCA 59.433 50.000 0.00 0.00 44.20 3.41
1615 1669 0.677288 TGTGTGGTCCGTTCTAGTGG 59.323 55.000 0.00 0.00 0.00 4.00
2258 2312 6.540914 GGTAAAATCTTTGGTCGGACATATCA 59.459 38.462 10.76 0.00 0.00 2.15
2739 2796 3.136808 GGCTTTTATCGCCAACTGAAG 57.863 47.619 0.00 0.00 46.77 3.02
3087 3144 0.174389 CTCGCGGATATAGCTGCCAT 59.826 55.000 15.89 0.00 36.83 4.40
3181 3238 5.656859 TGCTATCAGAGTAGGAAAGTTAGCA 59.343 40.000 0.00 0.00 36.01 3.49
3603 3660 1.174783 AGCTCTTCGTTCCGCTCTTA 58.825 50.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.063880 GGGATTAGCGTACATCCTGAAAAT 58.936 41.667 9.21 0.00 39.30 1.82
1 2 4.163458 AGGGATTAGCGTACATCCTGAAAA 59.837 41.667 9.21 0.00 39.30 2.29
2 3 3.709653 AGGGATTAGCGTACATCCTGAAA 59.290 43.478 9.21 0.00 39.30 2.69
3 4 3.305720 AGGGATTAGCGTACATCCTGAA 58.694 45.455 9.21 0.00 39.30 3.02
4 5 2.958818 AGGGATTAGCGTACATCCTGA 58.041 47.619 9.21 0.00 39.30 3.86
5 6 4.866508 TTAGGGATTAGCGTACATCCTG 57.133 45.455 9.21 0.00 39.30 3.86
6 7 4.900054 ACTTTAGGGATTAGCGTACATCCT 59.100 41.667 9.21 0.00 39.30 3.24
7 8 5.211174 ACTTTAGGGATTAGCGTACATCC 57.789 43.478 2.04 2.04 38.68 3.51
8 9 6.278363 TCAACTTTAGGGATTAGCGTACATC 58.722 40.000 0.00 0.00 0.00 3.06
9 10 6.229936 TCAACTTTAGGGATTAGCGTACAT 57.770 37.500 0.00 0.00 0.00 2.29
10 11 5.664294 TCAACTTTAGGGATTAGCGTACA 57.336 39.130 0.00 0.00 0.00 2.90
11 12 6.047231 ACATCAACTTTAGGGATTAGCGTAC 58.953 40.000 0.00 0.00 0.00 3.67
12 13 6.229936 ACATCAACTTTAGGGATTAGCGTA 57.770 37.500 0.00 0.00 0.00 4.42
13 14 5.099042 ACATCAACTTTAGGGATTAGCGT 57.901 39.130 0.00 0.00 0.00 5.07
14 15 5.276868 CGAACATCAACTTTAGGGATTAGCG 60.277 44.000 0.00 0.00 0.00 4.26
15 16 5.504173 GCGAACATCAACTTTAGGGATTAGC 60.504 44.000 0.00 0.00 0.00 3.09
16 17 5.007724 GGCGAACATCAACTTTAGGGATTAG 59.992 44.000 0.00 0.00 0.00 1.73
17 18 4.879545 GGCGAACATCAACTTTAGGGATTA 59.120 41.667 0.00 0.00 0.00 1.75
18 19 3.694566 GGCGAACATCAACTTTAGGGATT 59.305 43.478 0.00 0.00 0.00 3.01
19 20 3.279434 GGCGAACATCAACTTTAGGGAT 58.721 45.455 0.00 0.00 0.00 3.85
20 21 2.617021 GGGCGAACATCAACTTTAGGGA 60.617 50.000 0.00 0.00 0.00 4.20
21 22 1.743394 GGGCGAACATCAACTTTAGGG 59.257 52.381 0.00 0.00 0.00 3.53
22 23 2.711542 AGGGCGAACATCAACTTTAGG 58.288 47.619 0.00 0.00 0.00 2.69
23 24 4.455877 AGAAAGGGCGAACATCAACTTTAG 59.544 41.667 0.00 0.00 0.00 1.85
24 25 4.394729 AGAAAGGGCGAACATCAACTTTA 58.605 39.130 0.00 0.00 0.00 1.85
25 26 3.222603 AGAAAGGGCGAACATCAACTTT 58.777 40.909 0.00 0.00 0.00 2.66
26 27 2.863809 AGAAAGGGCGAACATCAACTT 58.136 42.857 0.00 0.00 0.00 2.66
27 28 2.568623 AGAAAGGGCGAACATCAACT 57.431 45.000 0.00 0.00 0.00 3.16
28 29 2.678336 CCTAGAAAGGGCGAACATCAAC 59.322 50.000 0.00 0.00 39.48 3.18
29 30 2.569853 TCCTAGAAAGGGCGAACATCAA 59.430 45.455 0.00 0.00 43.84 2.57
30 31 2.168521 CTCCTAGAAAGGGCGAACATCA 59.831 50.000 0.00 0.00 43.84 3.07
31 32 2.431057 TCTCCTAGAAAGGGCGAACATC 59.569 50.000 0.00 0.00 43.84 3.06
32 33 2.168728 GTCTCCTAGAAAGGGCGAACAT 59.831 50.000 0.00 0.00 43.84 2.71
33 34 1.549170 GTCTCCTAGAAAGGGCGAACA 59.451 52.381 0.00 0.00 43.84 3.18
34 35 1.826096 AGTCTCCTAGAAAGGGCGAAC 59.174 52.381 0.00 0.00 43.84 3.95
35 36 2.233305 AGTCTCCTAGAAAGGGCGAA 57.767 50.000 0.00 0.00 43.84 4.70
36 37 3.596940 ATAGTCTCCTAGAAAGGGCGA 57.403 47.619 0.00 0.00 43.84 5.54
37 38 4.623002 GAAATAGTCTCCTAGAAAGGGCG 58.377 47.826 0.00 0.00 43.84 6.13
38 39 4.099727 ACGAAATAGTCTCCTAGAAAGGGC 59.900 45.833 0.00 0.00 43.84 5.19
39 40 5.360144 TCACGAAATAGTCTCCTAGAAAGGG 59.640 44.000 0.00 0.00 43.84 3.95
40 41 6.452494 TCACGAAATAGTCTCCTAGAAAGG 57.548 41.667 0.00 0.00 45.21 3.11
41 42 8.758633 TTTTCACGAAATAGTCTCCTAGAAAG 57.241 34.615 0.00 0.00 0.00 2.62
42 43 9.204570 CTTTTTCACGAAATAGTCTCCTAGAAA 57.795 33.333 0.00 0.00 0.00 2.52
43 44 7.331193 GCTTTTTCACGAAATAGTCTCCTAGAA 59.669 37.037 10.39 0.00 33.69 2.10
44 45 6.812160 GCTTTTTCACGAAATAGTCTCCTAGA 59.188 38.462 10.39 0.00 33.69 2.43
45 46 6.036191 GGCTTTTTCACGAAATAGTCTCCTAG 59.964 42.308 10.39 0.00 33.29 3.02
46 47 5.873164 GGCTTTTTCACGAAATAGTCTCCTA 59.127 40.000 10.39 0.00 33.29 2.94
47 48 4.695928 GGCTTTTTCACGAAATAGTCTCCT 59.304 41.667 10.39 0.00 33.29 3.69
48 49 4.142665 GGGCTTTTTCACGAAATAGTCTCC 60.143 45.833 12.29 8.12 35.36 3.71
49 50 4.142665 GGGGCTTTTTCACGAAATAGTCTC 60.143 45.833 12.29 6.62 35.36 3.36
50 51 3.756963 GGGGCTTTTTCACGAAATAGTCT 59.243 43.478 12.29 0.00 35.36 3.24
51 52 3.119602 GGGGGCTTTTTCACGAAATAGTC 60.120 47.826 10.39 8.36 34.62 2.59
52 53 2.823747 GGGGGCTTTTTCACGAAATAGT 59.176 45.455 10.39 0.00 33.69 2.12
53 54 3.503827 GGGGGCTTTTTCACGAAATAG 57.496 47.619 5.83 5.83 34.09 1.73
281 289 1.290134 AGGAAGGAGGCTCCGAAAAT 58.710 50.000 27.11 12.58 42.75 1.82
351 359 4.141597 GGCTCAGATAGAAGTTTAGCCCTT 60.142 45.833 0.00 0.00 41.73 3.95
379 387 1.058428 CCCATCCAGGATCCTGCTCA 61.058 60.000 32.97 20.03 42.35 4.26
480 488 6.439599 TCTTATCGCATACTAGACAGCTTTC 58.560 40.000 0.00 0.00 0.00 2.62
500 508 6.319658 GCCAGAAATTCCTGAATGACATCTTA 59.680 38.462 0.00 0.00 36.29 2.10
521 529 4.023707 CCCTATTCTTTGATAAAGCGCCAG 60.024 45.833 2.29 0.00 38.39 4.85
655 663 0.266152 ATCCTCCCTCATTCTCCCGT 59.734 55.000 0.00 0.00 0.00 5.28
735 743 0.322008 CACTTCCAGGCACCTCCTTC 60.322 60.000 0.00 0.00 44.75 3.46
873 886 1.978454 TACTAAGCTACCCCGCTCTC 58.022 55.000 0.00 0.00 39.86 3.20
898 914 3.435275 GGGGCTGGAAGAGAAAAGAATT 58.565 45.455 0.00 0.00 34.07 2.17
926 942 3.245087 GGAAGAGAAAAGAAAGAGGGGCT 60.245 47.826 0.00 0.00 0.00 5.19
1004 1021 5.440610 AGAAGAGCCATCGAACCATATTTT 58.559 37.500 0.00 0.00 0.00 1.82
1135 1152 2.009774 CCGACCAAGAATTTGATCGCT 58.990 47.619 0.00 0.00 46.74 4.93
1229 1247 6.086011 ACCAATTACCAAATCCACCTATCA 57.914 37.500 0.00 0.00 0.00 2.15
1230 1248 7.093509 ACAAACCAATTACCAAATCCACCTATC 60.094 37.037 0.00 0.00 0.00 2.08
1231 1249 6.728632 ACAAACCAATTACCAAATCCACCTAT 59.271 34.615 0.00 0.00 0.00 2.57
1232 1250 6.078664 ACAAACCAATTACCAAATCCACCTA 58.921 36.000 0.00 0.00 0.00 3.08
1233 1251 4.904853 ACAAACCAATTACCAAATCCACCT 59.095 37.500 0.00 0.00 0.00 4.00
1234 1252 5.222079 ACAAACCAATTACCAAATCCACC 57.778 39.130 0.00 0.00 0.00 4.61
1235 1253 5.699001 GGAACAAACCAATTACCAAATCCAC 59.301 40.000 0.00 0.00 0.00 4.02
1236 1254 5.509840 CGGAACAAACCAATTACCAAATCCA 60.510 40.000 0.00 0.00 0.00 3.41
1237 1255 4.926832 CGGAACAAACCAATTACCAAATCC 59.073 41.667 0.00 0.00 0.00 3.01
1238 1256 5.774630 TCGGAACAAACCAATTACCAAATC 58.225 37.500 0.00 0.00 0.00 2.17
1239 1257 5.793030 TCGGAACAAACCAATTACCAAAT 57.207 34.783 0.00 0.00 0.00 2.32
1240 1258 5.793030 ATCGGAACAAACCAATTACCAAA 57.207 34.783 0.00 0.00 0.00 3.28
1241 1259 5.536916 AGAATCGGAACAAACCAATTACCAA 59.463 36.000 0.00 0.00 0.00 3.67
1242 1260 5.048364 CAGAATCGGAACAAACCAATTACCA 60.048 40.000 0.00 0.00 0.00 3.25
1243 1261 5.182380 TCAGAATCGGAACAAACCAATTACC 59.818 40.000 0.00 0.00 0.00 2.85
1244 1262 6.249035 TCAGAATCGGAACAAACCAATTAC 57.751 37.500 0.00 0.00 0.00 1.89
1245 1263 7.282224 CCTATCAGAATCGGAACAAACCAATTA 59.718 37.037 0.00 0.00 0.00 1.40
1246 1264 5.982890 ATCAGAATCGGAACAAACCAATT 57.017 34.783 0.00 0.00 0.00 2.32
1247 1265 5.590259 CCTATCAGAATCGGAACAAACCAAT 59.410 40.000 0.00 0.00 0.00 3.16
1248 1266 4.941263 CCTATCAGAATCGGAACAAACCAA 59.059 41.667 0.00 0.00 0.00 3.67
1249 1267 4.019681 ACCTATCAGAATCGGAACAAACCA 60.020 41.667 0.00 0.00 0.00 3.67
1250 1268 4.332819 CACCTATCAGAATCGGAACAAACC 59.667 45.833 0.00 0.00 0.00 3.27
1251 1269 4.332819 CCACCTATCAGAATCGGAACAAAC 59.667 45.833 0.00 0.00 0.00 2.93
1252 1270 4.224147 TCCACCTATCAGAATCGGAACAAA 59.776 41.667 0.00 0.00 0.00 2.83
1253 1271 3.772572 TCCACCTATCAGAATCGGAACAA 59.227 43.478 0.00 0.00 0.00 2.83
1254 1272 3.371034 TCCACCTATCAGAATCGGAACA 58.629 45.455 0.00 0.00 0.00 3.18
1255 1273 4.608948 ATCCACCTATCAGAATCGGAAC 57.391 45.455 0.00 0.00 0.00 3.62
1256 1274 5.368145 CAAATCCACCTATCAGAATCGGAA 58.632 41.667 0.00 0.00 0.00 4.30
1257 1275 4.202357 CCAAATCCACCTATCAGAATCGGA 60.202 45.833 0.00 0.00 0.00 4.55
1258 1276 4.067896 CCAAATCCACCTATCAGAATCGG 58.932 47.826 0.00 0.00 0.00 4.18
1259 1277 4.708177 ACCAAATCCACCTATCAGAATCG 58.292 43.478 0.00 0.00 0.00 3.34
1260 1278 8.571336 CAATTACCAAATCCACCTATCAGAATC 58.429 37.037 0.00 0.00 0.00 2.52
1261 1279 7.506938 CCAATTACCAAATCCACCTATCAGAAT 59.493 37.037 0.00 0.00 0.00 2.40
1262 1280 6.833416 CCAATTACCAAATCCACCTATCAGAA 59.167 38.462 0.00 0.00 0.00 3.02
1263 1281 6.069088 ACCAATTACCAAATCCACCTATCAGA 60.069 38.462 0.00 0.00 0.00 3.27
1264 1282 6.129179 ACCAATTACCAAATCCACCTATCAG 58.871 40.000 0.00 0.00 0.00 2.90
1296 1314 3.264193 TGTCAGGTGCACCTATCAGAATT 59.736 43.478 37.27 10.61 46.65 2.17
1434 1488 3.201487 GGCTGGTAATACCACTTAAGGGT 59.799 47.826 8.27 16.71 44.79 4.34
1615 1669 8.159344 AGTGATAATAAAAGTAGGAATGCTGC 57.841 34.615 0.00 0.00 0.00 5.25
2258 2312 6.625532 AATGGATTTGGCCTAAAGTTTCAT 57.374 33.333 3.32 0.00 0.00 2.57
2557 2611 4.594970 TCTCCAAAATTATGAAAGGCCGA 58.405 39.130 0.00 0.00 0.00 5.54
2739 2796 1.465187 GGAATCGCTTTGGTTACGCAC 60.465 52.381 0.00 0.00 0.00 5.34
2819 2876 3.193691 AGAGATTCTCCACACGAACGAAT 59.806 43.478 10.09 0.00 0.00 3.34
3152 3209 5.538433 ACTTTCCTACTCTGATAGCATCTCC 59.462 44.000 0.00 0.00 0.00 3.71
3337 3394 4.999950 CACTGCTGATTACTGAGAACCTTT 59.000 41.667 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.