Multiple sequence alignment - TraesCS5D01G347800

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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 TraesCS5D01G347800 chr5D 100.000 2438 0 0 1 2438 433189038 433191475 0.000000e+00 4503
1 TraesCS5D01G347800 chr5D 95.558 788 34 1 1 788 98580247 98579461 0.000000e+00 1260
2 TraesCS5D01G347800 chr5D 97.531 81 2 0 1226 1306 433190214 433190294 3.270000e-29 139
3 TraesCS5D01G347800 chr5D 97.531 81 2 0 1177 1257 433190263 433190343 3.270000e-29 139
4 TraesCS5D01G347800 chr5B 94.495 1199 47 7 1226 2418 526665958 526667143 0.000000e+00 1831
5 TraesCS5D01G347800 chr5B 98.294 469 7 1 790 1257 526665570 526666038 0.000000e+00 821
6 TraesCS5D01G347800 chr1D 96.958 789 24 0 1 789 238335439 238334651 0.000000e+00 1325
7 TraesCS5D01G347800 chr3A 96.015 778 31 0 4 781 363440611 363441388 0.000000e+00 1266
8 TraesCS5D01G347800 chr7B 95.396 782 34 2 1 780 28947127 28946346 0.000000e+00 1243
9 TraesCS5D01G347800 chr7B 95.013 782 37 2 1 780 648373208 648373989 0.000000e+00 1227
10 TraesCS5D01G347800 chr7A 95.178 788 36 2 1 787 76975730 76974944 0.000000e+00 1243
11 TraesCS5D01G347800 chr2B 95.275 783 34 2 1 780 687629038 687628256 0.000000e+00 1238
12 TraesCS5D01G347800 chr4A 94.036 788 44 3 1 787 661513279 661512494 0.000000e+00 1192
13 TraesCS5D01G347800 chr4A 94.110 781 45 1 1 780 663139901 663140681 0.000000e+00 1186


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 TraesCS5D01G347800 chr5D 433189038 433191475 2437 False 1593.666667 4503 98.3540 1 2438 3 chr5D.!!$F1 2437
1 TraesCS5D01G347800 chr5D 98579461 98580247 786 True 1260.000000 1260 95.5580 1 788 1 chr5D.!!$R1 787
2 TraesCS5D01G347800 chr5B 526665570 526667143 1573 False 1326.000000 1831 96.3945 790 2418 2 chr5B.!!$F1 1628
3 TraesCS5D01G347800 chr1D 238334651 238335439 788 True 1325.000000 1325 96.9580 1 789 1 chr1D.!!$R1 788
4 TraesCS5D01G347800 chr3A 363440611 363441388 777 False 1266.000000 1266 96.0150 4 781 1 chr3A.!!$F1 777
5 TraesCS5D01G347800 chr7B 28946346 28947127 781 True 1243.000000 1243 95.3960 1 780 1 chr7B.!!$R1 779
6 TraesCS5D01G347800 chr7B 648373208 648373989 781 False 1227.000000 1227 95.0130 1 780 1 chr7B.!!$F1 779
7 TraesCS5D01G347800 chr7A 76974944 76975730 786 True 1243.000000 1243 95.1780 1 787 1 chr7A.!!$R1 786
8 TraesCS5D01G347800 chr2B 687628256 687629038 782 True 1238.000000 1238 95.2750 1 780 1 chr2B.!!$R1 779
9 TraesCS5D01G347800 chr4A 661512494 661513279 785 True 1192.000000 1192 94.0360 1 787 1 chr4A.!!$R1 786
10 TraesCS5D01G347800 chr4A 663139901 663140681 780 False 1186.000000 1186 94.1100 1 780 1 chr4A.!!$F1 779

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
157 158 0.249699 CACAGCACACCGGACAACTA 60.25 55.0 9.46 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 1697 0.321564 TCTGACCAAAGCACCATCCG 60.322 55.0 0.0 0.0 0.0 4.18 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
107 108 4.999950 ACCTGACATCTCTTTTGCAGTTAG 59.000 41.667 0.00 0.00 0.00 2.34
148 149 1.966451 GCACCTACCACAGCACACC 60.966 63.158 0.00 0.00 0.00 4.16
157 158 0.249699 CACAGCACACCGGACAACTA 60.250 55.000 9.46 0.00 0.00 2.24
188 189 8.893219 TGAATTCTCAGGTATATAAGCAACAG 57.107 34.615 7.05 0.00 0.00 3.16
396 397 7.020914 AGCAGAATATAAAGCACTAGCAAAC 57.979 36.000 0.00 0.00 45.49 2.93
463 464 2.026262 GGGGTAATTCAGACTCAGCCAA 60.026 50.000 0.00 0.00 0.00 4.52
588 589 1.559831 GTGTTGCCAACAAACAGCTC 58.440 50.000 12.63 0.00 44.16 4.09
603 604 6.257411 ACAAACAGCTCGAGATCAGATTTATG 59.743 38.462 18.75 2.66 0.00 1.90
633 634 4.386867 AAATCAGCTTGCAGATGGATTG 57.613 40.909 1.40 0.00 31.42 2.67
744 748 3.898509 TGCAGGTTGTTGGCGTGC 61.899 61.111 0.00 0.00 44.84 5.34
913 918 5.964958 TTCAATCATGGAAACTGAAGGAC 57.035 39.130 0.00 0.00 0.00 3.85
972 977 3.181488 TGCGATTCCATATTGTGCAAAGG 60.181 43.478 0.00 0.00 0.00 3.11
984 989 3.440228 TGTGCAAAGGCTTTTTCGTTAC 58.560 40.909 10.36 4.27 41.91 2.50
1174 1180 6.483974 TGTTCATGTTATTGTTACCGACTTGT 59.516 34.615 0.00 0.00 0.00 3.16
1230 1236 9.962759 GACATCATTGAATTGTTTTAATTCAGC 57.037 29.630 12.95 0.00 44.49 4.26
1231 1237 9.715121 ACATCATTGAATTGTTTTAATTCAGCT 57.285 25.926 12.95 5.06 44.49 4.24
1234 1240 9.761504 TCATTGAATTGTTTTAATTCAGCTTGA 57.238 25.926 12.95 13.61 44.49 3.02
1237 1243 9.814899 TTGAATTGTTTTAATTCAGCTTGAAGA 57.185 25.926 12.95 0.00 44.49 2.87
1238 1244 9.248291 TGAATTGTTTTAATTCAGCTTGAAGAC 57.752 29.630 10.14 0.00 40.05 3.01
1239 1245 8.593492 AATTGTTTTAATTCAGCTTGAAGACC 57.407 30.769 0.00 0.00 40.05 3.85
1240 1246 6.959639 TGTTTTAATTCAGCTTGAAGACCT 57.040 33.333 0.00 0.00 40.05 3.85
1241 1247 6.738114 TGTTTTAATTCAGCTTGAAGACCTG 58.262 36.000 0.00 0.00 40.05 4.00
1242 1248 5.964958 TTTAATTCAGCTTGAAGACCTGG 57.035 39.130 0.00 0.00 40.05 4.45
1243 1249 3.795688 AATTCAGCTTGAAGACCTGGA 57.204 42.857 0.00 0.00 40.05 3.86
1244 1250 2.847327 TTCAGCTTGAAGACCTGGAG 57.153 50.000 0.00 0.00 31.83 3.86
1245 1251 0.322975 TCAGCTTGAAGACCTGGAGC 59.677 55.000 0.00 0.00 0.00 4.70
1246 1252 0.035881 CAGCTTGAAGACCTGGAGCA 59.964 55.000 0.00 0.00 35.86 4.26
1247 1253 0.990374 AGCTTGAAGACCTGGAGCAT 59.010 50.000 0.00 0.00 35.86 3.79
1248 1254 1.093159 GCTTGAAGACCTGGAGCATG 58.907 55.000 0.00 0.00 33.68 4.06
1249 1255 1.339438 GCTTGAAGACCTGGAGCATGA 60.339 52.381 0.00 0.00 33.68 3.07
1250 1256 2.877300 GCTTGAAGACCTGGAGCATGAA 60.877 50.000 0.00 0.00 33.68 2.57
1251 1257 3.415212 CTTGAAGACCTGGAGCATGAAA 58.585 45.455 0.00 0.00 0.00 2.69
1252 1258 3.726557 TGAAGACCTGGAGCATGAAAT 57.273 42.857 0.00 0.00 0.00 2.17
1316 1322 4.261572 GCAAGAAATGACAACACCAAGCTA 60.262 41.667 0.00 0.00 0.00 3.32
1414 1420 7.624549 TGCATCTTCTCCAACTAAATCTTACT 58.375 34.615 0.00 0.00 0.00 2.24
1454 1460 3.610911 ACTAGGTGGCTGAAAGTAATGC 58.389 45.455 0.00 0.00 35.30 3.56
1476 1482 3.261981 ACTGACCTTGGGTTATAAGCG 57.738 47.619 8.49 0.00 35.25 4.68
1554 1560 8.245195 TGCTAGTTTTCTGTTAAAAGGGAATT 57.755 30.769 0.00 0.00 0.00 2.17
1632 1638 4.477975 CGTCACCGTCGAGCCCTC 62.478 72.222 0.00 0.00 0.00 4.30
1665 1671 6.073873 CGTATTTTGGAGATCTCTGATCTTGC 60.074 42.308 21.81 3.72 0.00 4.01
1691 1697 8.592998 CGTCAAGTATGAAGGTTATGAAGTTAC 58.407 37.037 0.00 0.00 37.30 2.50
1728 1736 1.077993 AGAGAGTGAGGCTACTTGGGT 59.922 52.381 0.00 0.00 0.00 4.51
1838 1846 7.386848 GCTATTAGTTTGTTGGTGTGAGTAGAA 59.613 37.037 0.00 0.00 0.00 2.10
1870 1878 2.642807 CTGTGTTCCTTAAAGGAGGGGA 59.357 50.000 0.00 0.00 46.73 4.81
1874 1882 2.239150 GTTCCTTAAAGGAGGGGAGACC 59.761 54.545 0.00 0.00 46.73 3.85
1891 1899 4.701171 GGAGACCGTAATATCTGGACTAGG 59.299 50.000 0.00 0.00 0.00 3.02
1916 1924 6.596309 ATTTAAGGAGCAAGGAAGGAAAAG 57.404 37.500 0.00 0.00 0.00 2.27
1920 1928 3.395941 AGGAGCAAGGAAGGAAAAGAAGA 59.604 43.478 0.00 0.00 0.00 2.87
1926 1934 5.244851 GCAAGGAAGGAAAAGAAGAAGGAAT 59.755 40.000 0.00 0.00 0.00 3.01
1928 1936 7.039714 GCAAGGAAGGAAAAGAAGAAGGAATAA 60.040 37.037 0.00 0.00 0.00 1.40
1932 1940 8.246871 GGAAGGAAAAGAAGAAGGAATAACATG 58.753 37.037 0.00 0.00 0.00 3.21
1944 1952 7.776969 AGAAGGAATAACATGCATATTCAGTGT 59.223 33.333 23.06 12.24 40.13 3.55
1964 1972 3.446873 TGTTGAACTGTTGATTTGTGCCT 59.553 39.130 0.00 0.00 0.00 4.75
1984 1992 2.042639 GGGCTGCCCAATGATGGT 60.043 61.111 32.46 0.00 46.01 3.55
1993 2001 5.186409 GCTGCCCAATGATGGTCATTTATAT 59.814 40.000 2.59 0.00 44.03 0.86
1999 2007 9.128404 CCCAATGATGGTCATTTATATGGATAG 57.872 37.037 2.59 0.00 44.03 2.08
2000 2008 9.128404 CCAATGATGGTCATTTATATGGATAGG 57.872 37.037 2.59 0.00 44.03 2.57
2017 2025 4.816925 GGATAGGTGTAAATGGTCTTCTGC 59.183 45.833 0.00 0.00 0.00 4.26
2021 2029 2.162408 GTGTAAATGGTCTTCTGCAGGC 59.838 50.000 15.13 1.96 0.00 4.85
2085 2093 4.920376 AGTTCCAACATGACTTGTTTTCG 58.080 39.130 0.00 0.00 46.51 3.46
2099 2108 7.711772 TGACTTGTTTTCGTTTTCCTGTATCTA 59.288 33.333 0.00 0.00 0.00 1.98
2100 2109 8.084590 ACTTGTTTTCGTTTTCCTGTATCTAG 57.915 34.615 0.00 0.00 0.00 2.43
2102 2111 6.228258 TGTTTTCGTTTTCCTGTATCTAGCT 58.772 36.000 0.00 0.00 0.00 3.32
2103 2112 6.708949 TGTTTTCGTTTTCCTGTATCTAGCTT 59.291 34.615 0.00 0.00 0.00 3.74
2104 2113 7.874016 TGTTTTCGTTTTCCTGTATCTAGCTTA 59.126 33.333 0.00 0.00 0.00 3.09
2105 2114 8.715088 GTTTTCGTTTTCCTGTATCTAGCTTAA 58.285 33.333 0.00 0.00 0.00 1.85
2106 2115 8.475331 TTTCGTTTTCCTGTATCTAGCTTAAG 57.525 34.615 0.00 0.00 0.00 1.85
2107 2116 6.040878 TCGTTTTCCTGTATCTAGCTTAAGC 58.959 40.000 20.09 20.09 42.49 3.09
2148 2157 9.507329 AAGTGATACTTGTATCTTTGTTGATGT 57.493 29.630 18.08 0.00 37.00 3.06
2165 2174 7.312154 TGTTGATGTTGTGCTAATAACATTCC 58.688 34.615 0.00 0.00 45.09 3.01
2176 2185 5.758296 GCTAATAACATTCCGGATGACTTCA 59.242 40.000 4.15 0.00 39.15 3.02
2212 2221 1.107114 TCGAGAGAAGCCCATGAGAC 58.893 55.000 0.00 0.00 37.03 3.36
2234 2243 3.259902 CAAGTTTCGTCTACCCTTAGCC 58.740 50.000 0.00 0.00 0.00 3.93
2241 2250 7.124750 AGTTTCGTCTACCCTTAGCCTAATAAA 59.875 37.037 0.00 0.00 0.00 1.40
2253 2262 7.445707 CCTTAGCCTAATAAATCAGAAAGGGTC 59.554 40.741 0.00 0.00 36.35 4.46
2254 2263 6.327386 AGCCTAATAAATCAGAAAGGGTCA 57.673 37.500 0.00 0.00 29.10 4.02
2290 2299 2.159043 TCAACGGGATCTTCAGATGCTC 60.159 50.000 8.09 0.00 41.79 4.26
2350 2359 2.945668 GGCATGTACTTCTGTTGGGATC 59.054 50.000 0.00 0.00 0.00 3.36
2383 2392 6.027131 TGATTTCACTGAACTGTTTGTTTCG 58.973 36.000 0.00 0.00 39.30 3.46
2424 2436 9.807386 GACGTGTGAACTATATATATTTTTGGC 57.193 33.333 0.00 0.00 0.00 4.52
2425 2437 8.780249 ACGTGTGAACTATATATATTTTTGGCC 58.220 33.333 0.00 0.00 0.00 5.36
2426 2438 8.999431 CGTGTGAACTATATATATTTTTGGCCT 58.001 33.333 3.32 0.00 0.00 5.19
2432 2444 9.569122 AACTATATATATTTTTGGCCTTGTCGT 57.431 29.630 3.32 0.00 0.00 4.34
2433 2445 8.999431 ACTATATATATTTTTGGCCTTGTCGTG 58.001 33.333 3.32 0.00 0.00 4.35
2434 2446 9.214957 CTATATATATTTTTGGCCTTGTCGTGA 57.785 33.333 3.32 0.00 0.00 4.35
2435 2447 2.793278 ATTTTTGGCCTTGTCGTGAC 57.207 45.000 3.32 0.00 0.00 3.67
2436 2448 1.464734 TTTTTGGCCTTGTCGTGACA 58.535 45.000 3.32 0.00 39.98 3.58
2437 2449 1.021202 TTTTGGCCTTGTCGTGACAG 58.979 50.000 3.32 0.00 42.94 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 5.292101 GCATGAAGATACTGACACACCTTAC 59.708 44.000 0.00 0.00 0.00 2.34
148 149 6.898041 TGAGAATTCATTTTGTAGTTGTCCG 58.102 36.000 8.44 0.00 0.00 4.79
188 189 4.219944 TGAGTGTGAGACCCAAGTGTATAC 59.780 45.833 0.00 0.00 0.00 1.47
247 248 0.896940 CAACCAGCCCAGTCTGCATT 60.897 55.000 0.00 0.00 32.87 3.56
396 397 2.664568 CCAAATGATTTCTGCTGTTGCG 59.335 45.455 0.00 0.00 43.34 4.85
463 464 3.055385 AGGTTATCACACCATAAGCACGT 60.055 43.478 5.47 0.00 38.62 4.49
588 589 4.572909 TGGATGGCATAAATCTGATCTCG 58.427 43.478 0.00 0.00 0.00 4.04
603 604 2.004733 GCAAGCTGATTTTTGGATGGC 58.995 47.619 0.00 0.00 0.00 4.40
633 634 3.403038 TCTGACTGGCAAAGCTTTAGTC 58.597 45.455 24.43 24.43 35.93 2.59
744 748 1.622607 TATGCCGTGGACCTCAAGGG 61.623 60.000 0.29 0.00 43.83 3.95
863 868 8.811994 CAAGGAAATTAAAAGGGAGAATAACCA 58.188 33.333 0.00 0.00 0.00 3.67
873 878 9.895138 ATGATTGAATCAAGGAAATTAAAAGGG 57.105 29.630 12.36 0.00 43.50 3.95
913 918 2.398498 CCAGTTCAGAGACAGAACACG 58.602 52.381 8.54 0.08 45.93 4.49
984 989 7.224753 AGGTTTAGCATACTGTATGTGATTTCG 59.775 37.037 24.32 2.18 38.43 3.46
1228 1234 0.990374 ATGCTCCAGGTCTTCAAGCT 59.010 50.000 0.00 0.00 35.64 3.74
1229 1235 1.093159 CATGCTCCAGGTCTTCAAGC 58.907 55.000 0.00 0.00 0.00 4.01
1230 1236 2.775911 TCATGCTCCAGGTCTTCAAG 57.224 50.000 0.00 0.00 0.00 3.02
1231 1237 3.507162 TTTCATGCTCCAGGTCTTCAA 57.493 42.857 0.00 0.00 0.00 2.69
1232 1238 3.009363 TCATTTCATGCTCCAGGTCTTCA 59.991 43.478 0.00 0.00 0.00 3.02
1233 1239 3.376546 GTCATTTCATGCTCCAGGTCTTC 59.623 47.826 0.00 0.00 0.00 2.87
1234 1240 3.245016 TGTCATTTCATGCTCCAGGTCTT 60.245 43.478 0.00 0.00 0.00 3.01
1235 1241 2.306805 TGTCATTTCATGCTCCAGGTCT 59.693 45.455 0.00 0.00 0.00 3.85
1236 1242 2.715046 TGTCATTTCATGCTCCAGGTC 58.285 47.619 0.00 0.00 0.00 3.85
1237 1243 2.885135 TGTCATTTCATGCTCCAGGT 57.115 45.000 0.00 0.00 0.00 4.00
1238 1244 3.284617 TGATGTCATTTCATGCTCCAGG 58.715 45.455 0.00 0.00 0.00 4.45
1239 1245 5.067283 TCAATGATGTCATTTCATGCTCCAG 59.933 40.000 5.53 0.00 43.48 3.86
1240 1246 4.951094 TCAATGATGTCATTTCATGCTCCA 59.049 37.500 5.53 0.00 43.48 3.86
1241 1247 5.509716 TCAATGATGTCATTTCATGCTCC 57.490 39.130 5.53 0.00 43.48 4.70
1242 1248 7.491372 ACAATTCAATGATGTCATTTCATGCTC 59.509 33.333 5.53 0.00 43.48 4.26
1243 1249 7.327975 ACAATTCAATGATGTCATTTCATGCT 58.672 30.769 5.53 0.00 43.48 3.79
1244 1250 7.534085 ACAATTCAATGATGTCATTTCATGC 57.466 32.000 5.53 0.00 43.48 4.06
1253 1259 9.962759 GCTGAATTAAAACAATTCAATGATGTC 57.037 29.630 12.13 0.00 43.55 3.06
1254 1260 9.715121 AGCTGAATTAAAACAATTCAATGATGT 57.285 25.926 12.13 0.00 43.55 3.06
1257 1263 9.761504 TCAAGCTGAATTAAAACAATTCAATGA 57.238 25.926 12.13 12.71 43.55 2.57
1260 1266 9.814899 TCTTCAAGCTGAATTAAAACAATTCAA 57.185 25.926 12.13 0.00 43.55 2.69
1261 1267 9.248291 GTCTTCAAGCTGAATTAAAACAATTCA 57.752 29.630 10.92 10.92 42.44 2.57
1262 1268 8.703336 GGTCTTCAAGCTGAATTAAAACAATTC 58.297 33.333 0.00 3.34 35.59 2.17
1263 1269 8.424133 AGGTCTTCAAGCTGAATTAAAACAATT 58.576 29.630 0.00 0.00 35.59 2.32
1264 1270 7.955918 AGGTCTTCAAGCTGAATTAAAACAAT 58.044 30.769 0.00 0.00 35.59 2.71
1265 1271 7.346751 AGGTCTTCAAGCTGAATTAAAACAA 57.653 32.000 0.00 0.00 35.59 2.83
1266 1272 6.959639 AGGTCTTCAAGCTGAATTAAAACA 57.040 33.333 0.00 0.00 35.59 2.83
1316 1322 6.705825 GGCAATCAAAACCTCACTTGTAAAAT 59.294 34.615 0.00 0.00 0.00 1.82
1363 1369 0.733909 GACTTGAAATTGCCAGCGCC 60.734 55.000 2.29 0.00 0.00 6.53
1454 1460 3.374058 CGCTTATAACCCAAGGTCAGTTG 59.626 47.826 0.00 0.00 33.12 3.16
1516 1522 6.016777 CAGAAAACTAGCATCCTGAAACAAGT 60.017 38.462 0.00 0.00 0.00 3.16
1521 1527 8.458573 TTTAACAGAAAACTAGCATCCTGAAA 57.541 30.769 9.01 2.49 0.00 2.69
1554 1560 1.697432 CTGAACTACACCTGGGACCAA 59.303 52.381 0.00 0.00 0.00 3.67
1624 1630 4.504916 CGCACCAGAGAGGGCTCG 62.505 72.222 0.00 0.00 45.98 5.03
1632 1638 2.972625 TCTCCAAAATACGCACCAGAG 58.027 47.619 0.00 0.00 0.00 3.35
1665 1671 7.596749 AACTTCATAACCTTCATACTTGACG 57.403 36.000 0.00 0.00 0.00 4.35
1691 1697 0.321564 TCTGACCAAAGCACCATCCG 60.322 55.000 0.00 0.00 0.00 4.18
1838 1846 3.884037 AGGAACACAGTCCCAAATTCT 57.116 42.857 0.00 0.00 38.59 2.40
1870 1878 5.321934 ACCTAGTCCAGATATTACGGTCT 57.678 43.478 0.00 0.00 0.00 3.85
1891 1899 7.393515 TCTTTTCCTTCCTTGCTCCTTAAATAC 59.606 37.037 0.00 0.00 0.00 1.89
1916 1924 8.844244 ACTGAATATGCATGTTATTCCTTCTTC 58.156 33.333 10.16 0.00 35.92 2.87
1920 1928 7.886629 ACACTGAATATGCATGTTATTCCTT 57.113 32.000 10.16 0.00 35.92 3.36
1926 1934 7.686438 AGTTCAACACTGAATATGCATGTTA 57.314 32.000 10.16 0.00 43.39 2.41
1944 1952 3.698539 TCAGGCACAAATCAACAGTTCAA 59.301 39.130 0.00 0.00 0.00 2.69
1964 1972 1.076559 CATCATTGGGCAGCCCTCA 60.077 57.895 31.51 18.37 45.70 3.86
1973 1981 7.966339 ATCCATATAAATGACCATCATTGGG 57.034 36.000 4.86 3.45 45.57 4.12
1993 2001 5.629133 GCAGAAGACCATTTACACCTATCCA 60.629 44.000 0.00 0.00 0.00 3.41
1999 2007 2.749621 CCTGCAGAAGACCATTTACACC 59.250 50.000 17.39 0.00 0.00 4.16
2000 2008 2.162408 GCCTGCAGAAGACCATTTACAC 59.838 50.000 17.39 0.00 0.00 2.90
2007 2015 1.203441 ATGAGGCCTGCAGAAGACCA 61.203 55.000 12.00 6.76 0.00 4.02
2017 2025 2.165167 TGAAAGAAGCAATGAGGCCTG 58.835 47.619 12.00 0.00 0.00 4.85
2021 2029 6.808008 TCTACTTTGAAAGAAGCAATGAGG 57.192 37.500 12.53 0.00 0.00 3.86
2129 2138 6.039717 AGCACAACATCAACAAAGATACAAGT 59.960 34.615 0.00 0.00 0.00 3.16
2148 2157 5.295787 GTCATCCGGAATGTTATTAGCACAA 59.704 40.000 9.01 0.00 36.68 3.33
2165 2174 3.443099 TCTGCAGTATGAAGTCATCCG 57.557 47.619 14.67 0.00 44.37 4.18
2176 2185 5.069648 TCTCTCGATCCATTTTCTGCAGTAT 59.930 40.000 14.67 3.31 0.00 2.12
2212 2221 3.259902 GCTAAGGGTAGACGAAACTTGG 58.740 50.000 0.00 0.00 0.00 3.61
2234 2243 6.015940 GGCCATGACCCTTTCTGATTTATTAG 60.016 42.308 0.00 0.00 0.00 1.73
2241 2250 1.064166 CAGGCCATGACCCTTTCTGAT 60.064 52.381 5.01 0.00 0.00 2.90
2253 2262 1.270550 GTTGACAACCTTCAGGCCATG 59.729 52.381 5.01 0.00 39.32 3.66
2254 2263 1.620822 GTTGACAACCTTCAGGCCAT 58.379 50.000 5.01 0.00 39.32 4.40
2290 2299 3.578282 ACCAGGGCAAAAAGGATAAACAG 59.422 43.478 0.00 0.00 0.00 3.16
2350 2359 2.349590 TCAGTGAAATCAGCATCCACG 58.650 47.619 0.00 0.00 33.37 4.94
2383 2392 5.224888 TCACACGTCCATACTTGAAACTAC 58.775 41.667 0.00 0.00 0.00 2.73
2418 2430 1.021202 CTGTCACGACAAGGCCAAAA 58.979 50.000 5.01 0.00 41.33 2.44
2419 2431 2.701587 CTGTCACGACAAGGCCAAA 58.298 52.632 5.01 0.00 41.33 3.28
2420 2432 4.454948 CTGTCACGACAAGGCCAA 57.545 55.556 5.01 0.00 41.33 4.52


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

AutoCloner maintained by Alex Coulton.