Multiple sequence alignment - TraesCS6A01G266300

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 TraesCS6A01G266300 chr6A 100.000 5183 0 0 1880 7062 491564325 491569507 0.000000e+00 9572
1 TraesCS6A01G266300 chr6A 100.000 1581 0 0 1 1581 491562446 491564026 0.000000e+00 2920
2 TraesCS6A01G266300 chr6D 96.011 5214 140 31 1880 7062 351753063 351747887 0.000000e+00 8414
3 TraesCS6A01G266300 chr6D 95.154 1589 65 6 1 1581 351754711 351753127 0.000000e+00 2497
4 TraesCS6A01G266300 chr6B 97.389 3294 80 2 1880 5172 527566531 527569819 0.000000e+00 5602
5 TraesCS6A01G266300 chr6B 96.348 1369 36 6 5236 6593 527571254 527572619 0.000000e+00 2239
6 TraesCS6A01G266300 chr6B 96.277 1343 38 7 209 1540 527564755 527566096 0.000000e+00 2193
7 TraesCS6A01G266300 chr6B 96.516 287 9 1 6562 6848 527572618 527572903 2.310000e-129 473
8 TraesCS6A01G266300 chr6B 98.148 216 4 0 6847 7062 527573062 527573277 1.860000e-100 377
9 TraesCS6A01G266300 chr6B 90.116 172 9 3 1 172 527564598 527564761 4.290000e-52 217
10 TraesCS6A01G266300 chr5D 89.474 95 8 2 1880 1974 454025093 454025185 1.240000e-22 119
11 TraesCS6A01G266300 chr2D 87.379 103 10 3 1880 1980 592408629 592408528 1.610000e-21 115
12 TraesCS6A01G266300 chr4A 89.130 92 9 1 1886 1977 455925949 455925859 5.790000e-21 113
13 TraesCS6A01G266300 chr3B 88.421 95 10 1 1880 1974 24945194 24945287 5.790000e-21 113
14 TraesCS6A01G266300 chr3A 88.421 95 10 1 1883 1977 51452947 51452854 5.790000e-21 113
15 TraesCS6A01G266300 chr4B 88.043 92 10 1 1886 1977 180245219 180245129 2.690000e-19 108
16 TraesCS6A01G266300 chr4B 88.043 92 10 1 1886 1977 180245761 180245671 2.690000e-19 108


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 TraesCS6A01G266300 chr6A 491562446 491569507 7061 False 6246.000000 9572 100.0000 1 7062 2 chr6A.!!$F1 7061
1 TraesCS6A01G266300 chr6D 351747887 351754711 6824 True 5455.500000 8414 95.5825 1 7062 2 chr6D.!!$R1 7061
2 TraesCS6A01G266300 chr6B 527564598 527573277 8679 False 1850.166667 5602 95.7990 1 7062 6 chr6B.!!$F1 7061

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
172 217 0.249868 TCTCTGAACGCACTGGGTTG 60.250 55.0 15.67 3.48 38.76 3.77 F
174 219 0.396435 TCTGAACGCACTGGGTTGAT 59.604 50.0 15.67 0.00 38.76 2.57 F
599 651 0.468029 CTGGGTTCAACAGCAGGGTT 60.468 55.0 0.00 0.00 0.00 4.11 F
965 1020 1.565305 CGTCAGCCAGTAATCTCAGC 58.435 55.0 0.00 0.00 0.00 4.26 F
2497 2680 0.901124 CTACCAGAGTGCAGCCTCTT 59.099 55.0 9.93 1.87 39.81 2.85 F
2951 3134 0.306533 AAGTTACGCAACGGCAACAG 59.693 50.0 8.68 0.00 41.24 3.16 F
4475 4660 1.479709 AATGTCTCGTGGCTCTAGCT 58.520 50.0 1.39 0.00 41.70 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1496 1551 1.388547 AAGCTCCGAAACTTGTGCAA 58.611 45.000 0.00 0.0 0.00 4.08 R
2049 2229 3.058639 GCTCCTAAACTTGTGCAGTGAAG 60.059 47.826 0.00 0.0 35.12 3.02 R
2497 2680 0.684535 TGGACCATTCAGCAAGACGA 59.315 50.000 0.00 0.0 0.00 4.20 R
2897 3080 7.209471 AGAAATGCGAAATAAAGTGTTACCA 57.791 32.000 0.00 0.0 0.00 3.25 R
3828 4013 4.744631 CAGTTAAAACCTGACATTGGTTGC 59.255 41.667 0.15 0.0 45.99 4.17 R
4541 4726 1.608055 TGAACTTCAGGTGGTGCATG 58.392 50.000 0.00 0.0 0.00 4.06 R
6170 7738 0.253044 AACCATCCATCACCGACTGG 59.747 55.000 0.00 0.0 42.84 4.00 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
24 25 7.820044 GTTGTTCCAACAGTTTGATTAAACA 57.180 32.000 14.74 0.00 46.76 2.83
75 76 0.375454 TTCCACGATTTTATGCGCGG 59.625 50.000 8.83 0.00 0.00 6.46
172 217 0.249868 TCTCTGAACGCACTGGGTTG 60.250 55.000 15.67 3.48 38.76 3.77
173 218 0.249868 CTCTGAACGCACTGGGTTGA 60.250 55.000 15.67 7.05 38.76 3.18
174 219 0.396435 TCTGAACGCACTGGGTTGAT 59.604 50.000 15.67 0.00 38.76 2.57
175 220 1.202758 TCTGAACGCACTGGGTTGATT 60.203 47.619 15.67 0.00 38.76 2.57
176 221 1.608590 CTGAACGCACTGGGTTGATTT 59.391 47.619 15.67 0.00 38.76 2.17
177 222 1.606668 TGAACGCACTGGGTTGATTTC 59.393 47.619 15.67 2.53 38.76 2.17
178 223 0.591170 AACGCACTGGGTTGATTTCG 59.409 50.000 10.50 0.00 37.32 3.46
179 224 0.534203 ACGCACTGGGTTGATTTCGT 60.534 50.000 0.00 0.00 0.00 3.85
180 225 1.270412 ACGCACTGGGTTGATTTCGTA 60.270 47.619 0.00 0.00 0.00 3.43
181 226 1.127951 CGCACTGGGTTGATTTCGTAC 59.872 52.381 0.00 0.00 0.00 3.67
182 227 1.127951 GCACTGGGTTGATTTCGTACG 59.872 52.381 9.53 9.53 0.00 3.67
183 228 1.730064 CACTGGGTTGATTTCGTACGG 59.270 52.381 16.52 0.00 0.00 4.02
184 229 1.619827 ACTGGGTTGATTTCGTACGGA 59.380 47.619 16.52 2.84 0.00 4.69
185 230 2.037511 ACTGGGTTGATTTCGTACGGAA 59.962 45.455 12.21 12.21 0.00 4.30
186 231 3.267483 CTGGGTTGATTTCGTACGGAAT 58.733 45.455 21.62 21.62 33.85 3.01
187 232 3.264104 TGGGTTGATTTCGTACGGAATC 58.736 45.455 33.12 33.12 33.85 2.52
188 233 2.283351 GGGTTGATTTCGTACGGAATCG 59.717 50.000 33.21 3.43 43.02 3.34
201 246 3.354771 CGGAATCGTTCTGTTTTCGAG 57.645 47.619 0.00 0.00 37.04 4.04
202 247 2.984471 CGGAATCGTTCTGTTTTCGAGA 59.016 45.455 0.00 0.00 37.04 4.04
203 248 3.427528 CGGAATCGTTCTGTTTTCGAGAA 59.572 43.478 0.00 0.00 37.04 2.87
204 249 4.091509 CGGAATCGTTCTGTTTTCGAGAAT 59.908 41.667 0.00 0.00 37.04 2.40
205 250 5.389516 CGGAATCGTTCTGTTTTCGAGAATT 60.390 40.000 0.00 0.00 37.04 2.17
206 251 6.016111 GGAATCGTTCTGTTTTCGAGAATTC 58.984 40.000 0.00 0.00 37.04 2.17
207 252 6.128526 GGAATCGTTCTGTTTTCGAGAATTCT 60.129 38.462 7.95 7.95 37.04 2.40
208 253 5.824243 TCGTTCTGTTTTCGAGAATTCTC 57.176 39.130 23.20 23.20 39.55 2.87
209 254 5.529791 TCGTTCTGTTTTCGAGAATTCTCT 58.470 37.500 28.28 0.00 40.75 3.10
210 255 5.983720 TCGTTCTGTTTTCGAGAATTCTCTT 59.016 36.000 28.28 0.00 40.75 2.85
211 256 6.067669 CGTTCTGTTTTCGAGAATTCTCTTG 58.932 40.000 28.28 16.62 40.75 3.02
212 257 6.366630 GTTCTGTTTTCGAGAATTCTCTTGG 58.633 40.000 28.28 15.98 40.75 3.61
213 258 5.611374 TCTGTTTTCGAGAATTCTCTTGGT 58.389 37.500 28.28 0.00 40.75 3.67
214 259 6.755206 TCTGTTTTCGAGAATTCTCTTGGTA 58.245 36.000 28.28 12.48 40.75 3.25
215 260 7.386851 TCTGTTTTCGAGAATTCTCTTGGTAT 58.613 34.615 28.28 0.00 40.75 2.73
225 270 6.543831 AGAATTCTCTTGGTATATGTTGTGGC 59.456 38.462 0.88 0.00 0.00 5.01
226 271 5.435686 TTCTCTTGGTATATGTTGTGGCT 57.564 39.130 0.00 0.00 0.00 4.75
258 303 7.913674 AGAGCTGAGTTTAAAATGGTAGAAG 57.086 36.000 0.00 0.00 0.00 2.85
298 349 6.446318 TGATGTGTTTCCAAATTCTAACTGC 58.554 36.000 0.00 0.00 0.00 4.40
452 503 2.882876 GCGGGCGACAACTCTAGA 59.117 61.111 0.00 0.00 0.00 2.43
464 515 6.036083 GCGACAACTCTAGATGCTTAATTTGA 59.964 38.462 0.00 0.00 0.00 2.69
502 553 8.697507 AACAGATTCAGAAGTGTTTTCCTTAT 57.302 30.769 7.57 0.00 28.62 1.73
542 594 7.926018 GTGATTTGGTCTTAACTTTTTCATGGT 59.074 33.333 0.00 0.00 0.00 3.55
585 637 3.397955 ACTTAACTGTTGGATTCCTGGGT 59.602 43.478 2.69 0.00 0.00 4.51
593 645 1.177401 GGATTCCTGGGTTCAACAGC 58.823 55.000 0.00 0.00 34.65 4.40
598 650 1.151450 CTGGGTTCAACAGCAGGGT 59.849 57.895 0.00 0.00 0.00 4.34
599 651 0.468029 CTGGGTTCAACAGCAGGGTT 60.468 55.000 0.00 0.00 0.00 4.11
965 1020 1.565305 CGTCAGCCAGTAATCTCAGC 58.435 55.000 0.00 0.00 0.00 4.26
975 1030 3.019564 AGTAATCTCAGCATTTGTGGGC 58.980 45.455 0.00 0.00 0.00 5.36
1075 1130 2.479560 CGTAGGAGTCGTGATGCATCAA 60.480 50.000 30.24 14.00 38.75 2.57
1281 1336 8.417884 GGTATAAGTTCTTCTCTATGTTGCTCT 58.582 37.037 0.00 0.00 0.00 4.09
1356 1411 7.977853 ACAGAGAATTAATGATTGCCAAATGTC 59.022 33.333 0.00 0.00 0.00 3.06
1439 1494 7.908827 TCAAAGTCGTATTAAGTGGCAAATA 57.091 32.000 0.00 0.00 0.00 1.40
1496 1551 6.067217 ACTTTTAGACCTAAGTGATGCCAT 57.933 37.500 0.00 0.00 33.55 4.40
1509 1564 3.566273 TGCCATTGCACAAGTTTCG 57.434 47.368 0.00 0.00 44.23 3.46
2004 2184 3.866910 AGTTTTGTGTGCTTGCATGAAAG 59.133 39.130 9.31 9.31 0.00 2.62
2027 2207 5.885912 AGAGTTGACCATACACAAAACAAGT 59.114 36.000 0.00 0.00 0.00 3.16
2048 2228 9.403583 ACAAGTTTTTAGACCTAAGTGATTTCA 57.596 29.630 0.00 0.00 0.00 2.69
2049 2229 9.665264 CAAGTTTTTAGACCTAAGTGATTTCAC 57.335 33.333 2.41 2.41 46.77 3.18
2092 2272 6.257630 GGAGCTTCTAGTGCAATTTTCTCTAG 59.742 42.308 0.00 0.00 0.00 2.43
2127 2308 2.437200 TTGAAATGGCTCTTTTGGCG 57.563 45.000 0.00 0.00 35.06 5.69
2278 2461 5.069318 TCTTGCATGAAATAGTTGACCACA 58.931 37.500 0.00 0.00 0.00 4.17
2497 2680 0.901124 CTACCAGAGTGCAGCCTCTT 59.099 55.000 9.93 1.87 39.81 2.85
2897 3080 9.686683 AGAAATATTTATGTGCTAACCTCACTT 57.313 29.630 0.00 0.00 35.58 3.16
2951 3134 0.306533 AAGTTACGCAACGGCAACAG 59.693 50.000 8.68 0.00 41.24 3.16
3217 3402 5.163581 GCAATTCCAGTGAGTATGCTGAATT 60.164 40.000 0.00 0.00 34.87 2.17
3265 3450 8.361579 GTCGAGTACTAACTGTTTATTTTCGTC 58.638 37.037 0.00 0.00 35.56 4.20
3818 4003 9.123902 TCTCATTGGATAATTTATGAACACTGG 57.876 33.333 0.00 0.00 0.00 4.00
3828 4013 8.606040 AATTTATGAACACTGGGAAATGTTTG 57.394 30.769 0.00 0.00 39.13 2.93
3982 4167 4.968259 TCTTTGTAAAGAGGCAGCACTTA 58.032 39.130 3.05 0.00 39.95 2.24
4296 4481 6.017275 CAGATATCAACCTTTCTTGAGGCATC 60.017 42.308 5.32 0.00 40.65 3.91
4475 4660 1.479709 AATGTCTCGTGGCTCTAGCT 58.520 50.000 1.39 0.00 41.70 3.32
4541 4726 5.368145 TCCCATACTGCAAGATTCACATAC 58.632 41.667 0.00 0.00 37.43 2.39
4639 4824 9.532697 GATGCATCAACAATAACATTTTGTTTC 57.467 29.630 21.92 0.00 42.96 2.78
4687 4872 3.447586 GTGATGTAAGGCTCAGTCCTGTA 59.552 47.826 0.00 0.00 36.38 2.74
4893 5078 3.981211 TGAAAAATTGGCTGCAGAAGAC 58.019 40.909 20.43 4.47 0.00 3.01
4908 5093 4.370049 CAGAAGACGCTGATGATTCTGAT 58.630 43.478 7.32 0.00 46.22 2.90
4915 5100 4.117685 CGCTGATGATTCTGATTGTGAGA 58.882 43.478 0.00 0.00 0.00 3.27
4956 5141 2.102252 GTCTGGCATAACTCCTGAGAGG 59.898 54.545 0.22 0.00 45.11 3.69
5208 6651 6.701145 TTTGGACTTAATTTGCAGTGTACA 57.299 33.333 0.00 0.00 0.00 2.90
5224 6667 1.474077 GTACATGGAGCCCTTTTGCTG 59.526 52.381 0.00 0.00 42.95 4.41
5367 6923 4.606210 TCACAGGATAGTAAGGTGCTGTA 58.394 43.478 0.00 0.00 43.79 2.74
5449 7005 7.629222 GCTTCAATCCAGCATGTACTAAAATGT 60.629 37.037 0.00 0.00 37.22 2.71
5525 7082 4.209538 TGCATAAATCTGAAGGGACATGG 58.790 43.478 0.00 0.00 0.00 3.66
5603 7160 5.662674 TCATTTCATGGATTGATTGCACA 57.337 34.783 0.00 0.00 33.34 4.57
5604 7161 6.228616 TCATTTCATGGATTGATTGCACAT 57.771 33.333 0.00 0.00 33.34 3.21
5654 7222 5.645497 ACCTTCACATTGACTGCTTTATCTC 59.355 40.000 0.00 0.00 0.00 2.75
5867 7435 9.559958 CCAAATTGAAGATGTTACATCAACTAC 57.440 33.333 24.79 12.25 38.05 2.73
5896 7464 7.667557 CAAATATCATGGAGGATGAATTTGCT 58.332 34.615 0.11 0.00 44.50 3.91
6021 7589 5.911752 TGAGCTGGAAATCTCTTGTAGATC 58.088 41.667 0.00 0.00 44.56 2.75
6077 7645 5.502544 GCTCGATGAAGTATAACAAGGCAAC 60.503 44.000 0.00 0.00 0.00 4.17
6156 7724 0.250727 CCTTCGAGCCAAGGTTTCCA 60.251 55.000 0.00 0.00 38.58 3.53
6170 7738 2.035449 GGTTTCCAGTTTGTTGGTAGGC 59.965 50.000 0.00 0.00 39.35 3.93
6179 7747 1.375523 GTTGGTAGGCCAGTCGGTG 60.376 63.158 5.01 0.00 46.91 4.94
6232 7800 2.215907 CTCCAATAGAGGCACTGTCG 57.784 55.000 0.00 0.00 41.55 4.35
6434 8002 5.111989 CAGACACACATGTACCTAGAATGG 58.888 45.833 0.00 0.00 39.95 3.16
6549 8117 6.515272 TCAAGGCCATCAAACTTCTTATTC 57.485 37.500 5.01 0.00 0.00 1.75
6599 8198 7.867305 TTTTGTCTCCAGTGTGTTTATAACA 57.133 32.000 0.00 0.00 39.52 2.41
6648 8247 8.896744 TGCTGACAGGAAATTAATATCAAAGAG 58.103 33.333 4.26 0.00 0.00 2.85
6651 8250 9.177608 TGACAGGAAATTAATATCAAAGAGGTG 57.822 33.333 0.00 0.00 0.00 4.00
6861 8620 7.012421 GTCACAAATGATAGTTGTTAGATCCCC 59.988 40.741 0.00 0.00 37.09 4.81
6872 8631 8.568617 AGTTGTTAGATCCCCATCTACTAAAT 57.431 34.615 0.00 0.00 40.72 1.40
6920 8679 5.049267 TCCTTTAACTGCGTGGAAATACAAC 60.049 40.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.731612 CACCAGCAGTCGAGCGCT 62.732 66.667 11.27 11.27 39.66 5.92
75 76 1.396996 ACACATCTAAAATCACGCGCC 59.603 47.619 5.73 0.00 0.00 6.53
181 226 2.984471 TCTCGAAAACAGAACGATTCCG 59.016 45.455 0.00 0.00 42.50 4.30
182 227 4.985044 TTCTCGAAAACAGAACGATTCC 57.015 40.909 0.00 0.00 35.58 3.01
183 228 6.822506 AGAATTCTCGAAAACAGAACGATTC 58.177 36.000 0.88 0.00 32.65 2.52
184 229 6.787085 AGAATTCTCGAAAACAGAACGATT 57.213 33.333 0.88 0.00 32.65 3.34
185 230 6.396459 GAGAATTCTCGAAAACAGAACGAT 57.604 37.500 19.31 0.00 32.65 3.73
186 231 5.824243 GAGAATTCTCGAAAACAGAACGA 57.176 39.130 19.31 0.00 32.65 3.85
199 244 7.254932 GCCACAACATATACCAAGAGAATTCTC 60.255 40.741 25.20 25.20 43.17 2.87
200 245 6.543831 GCCACAACATATACCAAGAGAATTCT 59.456 38.462 7.95 7.95 34.29 2.40
201 246 6.543831 AGCCACAACATATACCAAGAGAATTC 59.456 38.462 0.00 0.00 0.00 2.17
202 247 6.319658 CAGCCACAACATATACCAAGAGAATT 59.680 38.462 0.00 0.00 0.00 2.17
203 248 5.824624 CAGCCACAACATATACCAAGAGAAT 59.175 40.000 0.00 0.00 0.00 2.40
204 249 5.045942 TCAGCCACAACATATACCAAGAGAA 60.046 40.000 0.00 0.00 0.00 2.87
205 250 4.469586 TCAGCCACAACATATACCAAGAGA 59.530 41.667 0.00 0.00 0.00 3.10
206 251 4.769688 TCAGCCACAACATATACCAAGAG 58.230 43.478 0.00 0.00 0.00 2.85
207 252 4.835284 TCAGCCACAACATATACCAAGA 57.165 40.909 0.00 0.00 0.00 3.02
208 253 4.096382 GGTTCAGCCACAACATATACCAAG 59.904 45.833 0.00 0.00 37.17 3.61
209 254 4.013728 GGTTCAGCCACAACATATACCAA 58.986 43.478 0.00 0.00 37.17 3.67
210 255 3.009584 TGGTTCAGCCACAACATATACCA 59.990 43.478 0.00 0.00 43.61 3.25
211 256 3.616219 TGGTTCAGCCACAACATATACC 58.384 45.455 0.00 0.00 43.61 2.73
225 270 7.672983 TTTTAAACTCAGCTCTATGGTTCAG 57.327 36.000 0.00 0.00 0.00 3.02
226 271 7.121168 CCATTTTAAACTCAGCTCTATGGTTCA 59.879 37.037 0.00 0.00 0.00 3.18
232 277 9.606631 CTTCTACCATTTTAAACTCAGCTCTAT 57.393 33.333 0.00 0.00 0.00 1.98
237 282 9.561270 GAAATCTTCTACCATTTTAAACTCAGC 57.439 33.333 0.00 0.00 0.00 4.26
258 303 5.451908 ACACATCAAACATGACACGAAATC 58.548 37.500 0.00 0.00 0.00 2.17
298 349 7.141363 CAGAAAAACTGGTCAAAACTATGGAG 58.859 38.462 0.00 0.00 42.39 3.86
502 553 4.648762 ACCAAATCACACAGGTCAAATTCA 59.351 37.500 0.00 0.00 0.00 2.57
542 594 6.839124 AGTGCCATCTCAATCATAAAACAA 57.161 33.333 0.00 0.00 0.00 2.83
585 637 2.435372 AGTCAAACCCTGCTGTTGAA 57.565 45.000 0.00 0.00 0.00 2.69
593 645 3.306019 GGGTGCAAATAAGTCAAACCCTG 60.306 47.826 0.00 0.00 42.13 4.45
598 650 6.535540 TGTAGTAGGGTGCAAATAAGTCAAA 58.464 36.000 0.00 0.00 0.00 2.69
599 651 6.116711 TGTAGTAGGGTGCAAATAAGTCAA 57.883 37.500 0.00 0.00 0.00 3.18
965 1020 1.126948 AACCCCTTGGCCCACAAATG 61.127 55.000 0.00 0.00 38.91 2.32
975 1030 2.440409 CTGAAGACATCAACCCCTTGG 58.560 52.381 0.00 0.00 37.67 3.61
1075 1130 4.653341 CCTCATGGACACTTCCTCTCTTAT 59.347 45.833 0.00 0.00 43.31 1.73
1281 1336 6.597672 TGCCTTAAGAGAAGAAAATAATCGCA 59.402 34.615 3.36 0.00 0.00 5.10
1439 1494 2.719705 TGGTGGGTCCCTAAACTTGAAT 59.280 45.455 10.00 0.00 34.77 2.57
1496 1551 1.388547 AAGCTCCGAAACTTGTGCAA 58.611 45.000 0.00 0.00 0.00 4.08
2004 2184 6.131544 ACTTGTTTTGTGTATGGTCAACTC 57.868 37.500 0.00 0.00 0.00 3.01
2045 2225 4.335315 CCTAAACTTGTGCAGTGAAGTGAA 59.665 41.667 6.49 0.00 35.12 3.18
2046 2226 3.876914 CCTAAACTTGTGCAGTGAAGTGA 59.123 43.478 6.49 0.00 35.12 3.41
2047 2227 3.876914 TCCTAAACTTGTGCAGTGAAGTG 59.123 43.478 6.49 0.00 35.12 3.16
2048 2228 4.130118 CTCCTAAACTTGTGCAGTGAAGT 58.870 43.478 0.00 0.00 35.12 3.01
2049 2229 3.058639 GCTCCTAAACTTGTGCAGTGAAG 60.059 47.826 0.00 0.00 35.12 3.02
2278 2461 2.983229 TGGCAATGCTTGTTTTTGTGT 58.017 38.095 4.82 0.00 0.00 3.72
2497 2680 0.684535 TGGACCATTCAGCAAGACGA 59.315 50.000 0.00 0.00 0.00 4.20
2887 3070 8.983702 AAATAAAGTGTTACCAAGTGAGGTTA 57.016 30.769 0.00 0.00 43.08 2.85
2897 3080 7.209471 AGAAATGCGAAATAAAGTGTTACCA 57.791 32.000 0.00 0.00 0.00 3.25
2913 3096 8.147172 CGTAACTTCACAAAATAAAGAAATGCG 58.853 33.333 0.00 0.00 0.00 4.73
2951 3134 8.652810 AAAGGAAATGCAAAGCAATCATATAC 57.347 30.769 0.00 0.00 43.62 1.47
3081 3264 5.593095 AGCACATGCAACAGATAAGATCATT 59.407 36.000 6.64 0.00 45.16 2.57
3217 3402 6.568271 CGACAACAAAGGATGTGAATTCATCA 60.568 38.462 12.12 11.70 42.99 3.07
3235 3420 8.876275 AAATAAACAGTTAGTACTCGACAACA 57.124 30.769 0.00 0.00 30.26 3.33
3236 3421 9.789029 GAAAATAAACAGTTAGTACTCGACAAC 57.211 33.333 0.00 0.00 30.26 3.32
3265 3450 3.522553 GTCAGTTACTCCCTGGAAATCG 58.477 50.000 0.00 0.00 0.00 3.34
3828 4013 4.744631 CAGTTAAAACCTGACATTGGTTGC 59.255 41.667 0.15 0.00 45.99 4.17
4260 4445 9.109393 GAAAGGTTGATATCTGCACTTAATGTA 57.891 33.333 3.98 0.00 0.00 2.29
4269 4454 5.188434 CCTCAAGAAAGGTTGATATCTGCA 58.812 41.667 3.98 0.00 35.88 4.41
4417 4602 5.348986 TCGACTATTCCATTTTCCTCTTCG 58.651 41.667 0.00 0.00 0.00 3.79
4475 4660 5.895636 ATGCGGTTGAAATAAGAATGTGA 57.104 34.783 0.00 0.00 0.00 3.58
4541 4726 1.608055 TGAACTTCAGGTGGTGCATG 58.392 50.000 0.00 0.00 0.00 4.06
4639 4824 2.963101 TGTAGAATACTCATGGGGTCCG 59.037 50.000 0.00 0.00 43.54 4.79
4893 5078 4.117685 TCTCACAATCAGAATCATCAGCG 58.882 43.478 0.00 0.00 0.00 5.18
4908 5093 7.733773 TCTCTTCACCCTAAATATCTCACAA 57.266 36.000 0.00 0.00 0.00 3.33
4915 5100 6.100424 CCAGACCTTCTCTTCACCCTAAATAT 59.900 42.308 0.00 0.00 0.00 1.28
4956 5141 4.517285 TGGTTGAATCTTCTGTATGCCTC 58.483 43.478 0.00 0.00 0.00 4.70
5014 5199 2.760634 ATACATGAGTGGCGTCACAA 57.239 45.000 24.06 10.69 45.91 3.33
5098 5283 9.269453 GTCACCATTAGTTTCTAGTGTTACTTT 57.731 33.333 0.00 0.00 0.00 2.66
5099 5284 8.648693 AGTCACCATTAGTTTCTAGTGTTACTT 58.351 33.333 0.00 0.00 0.00 2.24
5100 5285 8.191534 AGTCACCATTAGTTTCTAGTGTTACT 57.808 34.615 0.00 0.00 0.00 2.24
5208 6651 0.407139 AGACAGCAAAAGGGCTCCAT 59.593 50.000 0.00 0.00 43.68 3.41
5250 6806 2.639347 TGAACTGAGGATTCCAGCAAGA 59.361 45.455 5.29 0.00 35.14 3.02
5367 6923 5.184864 TCATAGTTTTGATTGCCCAATTCGT 59.815 36.000 0.00 0.00 0.00 3.85
5418 6974 3.960571 ACATGCTGGATTGAAGCTAAGT 58.039 40.909 0.00 0.00 41.42 2.24
5560 7117 4.595762 AACTTGCCGTTCACTAACTAGA 57.404 40.909 0.00 0.00 33.15 2.43
5867 7435 6.584185 TTCATCCTCCATGATATTTGCATG 57.416 37.500 0.00 0.00 41.42 4.06
6021 7589 0.322975 CAAGTCACTGTCCTCCTGGG 59.677 60.000 0.00 0.00 0.00 4.45
6170 7738 0.253044 AACCATCCATCACCGACTGG 59.747 55.000 0.00 0.00 42.84 4.00
6179 7747 4.643784 AGAATTGCTTCTGAACCATCCATC 59.356 41.667 0.00 0.00 40.28 3.51
6232 7800 1.820519 TGCAATCAAGAATCCAGCCAC 59.179 47.619 0.00 0.00 0.00 5.01
6299 7867 6.729187 ACAACTAAAGAACATCAGAAACTGC 58.271 36.000 0.00 0.00 0.00 4.40
6575 8144 7.867305 TGTTATAAACACACTGGAGACAAAA 57.133 32.000 0.00 0.00 36.67 2.44
6599 8198 7.552687 AGCATCAATCAATTCATTGCTTTTCAT 59.447 29.630 0.00 0.00 35.57 2.57
6648 8247 3.243839 ACACATCTGGAAACAAATGCACC 60.244 43.478 0.00 0.00 42.74 5.01
6651 8250 8.647226 GTTATTAACACATCTGGAAACAAATGC 58.353 33.333 1.62 0.00 42.74 3.56
6872 8631 9.561069 GGAGAAAGTAAATCTTATATGCCAGAA 57.439 33.333 0.00 0.00 35.02 3.02


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

AutoCloner maintained by Alex Coulton.