Multiple sequence alignment - TraesCS6B01G332000

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 TraesCS6B01G332000 chr6B 100.000 2866 0 0 1 2866 583445491 583442626 0.000000e+00 5293.0
1 TraesCS6B01G332000 chr6D 88.065 1483 104 47 1 1430 389700041 389698579 0.000000e+00 1690.0
2 TraesCS6B01G332000 chr6D 87.024 1472 96 41 1442 2866 389698531 389697108 0.000000e+00 1572.0
3 TraesCS6B01G332000 chr6A 84.319 1741 120 62 1 1622 536213978 536212272 0.000000e+00 1561.0
4 TraesCS6B01G332000 chr6A 83.557 967 74 36 1957 2866 536212241 536211303 0.000000e+00 826.0
5 TraesCS6B01G332000 chr2D 100.000 38 0 0 1828 1865 356726199 356726236 1.420000e-08 71.3
6 TraesCS6B01G332000 chr2B 100.000 38 0 0 1828 1865 424481617 424481654 1.420000e-08 71.3
7 TraesCS6B01G332000 chr2A 100.000 38 0 0 1828 1865 477108544 477108581 1.420000e-08 71.3


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 TraesCS6B01G332000 chr6B 583442626 583445491 2865 True 5293.0 5293 100.0000 1 2866 1 chr6B.!!$R1 2865
1 TraesCS6B01G332000 chr6D 389697108 389700041 2933 True 1631.0 1690 87.5445 1 2866 2 chr6D.!!$R1 2865
2 TraesCS6B01G332000 chr6A 536211303 536213978 2675 True 1193.5 1561 83.9380 1 2866 2 chr6A.!!$R1 2865

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
943 1019 0.166814 CGGGCTTCTTGCTTCTTTCG 59.833 55.0 0.0 0.0 42.39 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2270 0.106521 GCCATGCTTTGTTGGTTGGT 59.893 50.0 0.0 0.0 35.34 3.67 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 5.739358 GCCATCGAACTTACATAGGCTACTT 60.739 44.000 0.00 0.00 37.89 2.24
131 132 1.739196 CTGCTGCTCGCTGCTGTTA 60.739 57.895 19.07 1.31 43.37 2.41
220 221 4.707448 CCCCTGTATATCGCATAAGTCTCT 59.293 45.833 0.00 0.00 0.00 3.10
222 223 6.096036 CCCTGTATATCGCATAAGTCTCTTG 58.904 44.000 0.00 0.00 0.00 3.02
241 242 1.134521 TGTGTCAGCTGTTTCGGAAGT 60.135 47.619 14.67 0.00 0.00 3.01
265 266 0.819582 CCCGAGTTTAAGCGTAGGGA 59.180 55.000 12.11 0.00 39.71 4.20
268 269 3.551659 CCCGAGTTTAAGCGTAGGGATAC 60.552 52.174 12.11 0.00 39.71 2.24
302 305 2.579201 CGAATGGGTCACTCGCCT 59.421 61.111 0.00 0.00 0.00 5.52
308 311 2.027751 GGTCACTCGCCTATCGCC 59.972 66.667 0.00 0.00 38.27 5.54
313 316 4.685026 CTCGCCTATCGCCCGTCG 62.685 72.222 0.00 0.00 38.27 5.12
336 348 6.641314 TCGATCTTAAAAGAACACTGACAGAC 59.359 38.462 10.08 0.00 38.77 3.51
353 368 0.234884 GACCGGTTTGCTGAGAAACG 59.765 55.000 9.42 0.00 36.80 3.60
407 422 1.136110 AGGAAACGGTGCAAAAACCAG 59.864 47.619 0.00 0.00 40.53 4.00
417 432 1.036707 CAAAAACCAGGAAGCCGGAA 58.963 50.000 5.05 0.00 0.00 4.30
433 452 2.287909 CCGGAAGCGAGGATAAGAAGAG 60.288 54.545 0.00 0.00 0.00 2.85
434 453 2.287909 CGGAAGCGAGGATAAGAAGAGG 60.288 54.545 0.00 0.00 0.00 3.69
435 454 2.959707 GGAAGCGAGGATAAGAAGAGGA 59.040 50.000 0.00 0.00 0.00 3.71
436 455 3.005367 GGAAGCGAGGATAAGAAGAGGAG 59.995 52.174 0.00 0.00 0.00 3.69
437 456 2.593026 AGCGAGGATAAGAAGAGGAGG 58.407 52.381 0.00 0.00 0.00 4.30
438 457 2.175931 AGCGAGGATAAGAAGAGGAGGA 59.824 50.000 0.00 0.00 0.00 3.71
447 466 1.178276 GAAGAGGAGGAAGAGCGTGA 58.822 55.000 0.00 0.00 0.00 4.35
462 481 3.465701 TGACCGTGCAGTCATCCA 58.534 55.556 4.76 0.00 41.78 3.41
537 584 3.046087 CGGTCTGCACTGCACCTG 61.046 66.667 0.00 0.00 33.79 4.00
602 649 0.593128 GGCCTACTGCAACACACAAG 59.407 55.000 0.00 0.00 43.89 3.16
625 672 3.503363 GCACCGAGCCACTGCATC 61.503 66.667 0.00 0.00 41.13 3.91
626 673 2.267006 CACCGAGCCACTGCATCT 59.733 61.111 0.00 0.00 41.13 2.90
652 699 2.202146 GACCGTCGTCGTCGTCAG 60.202 66.667 10.76 0.00 38.33 3.51
653 700 2.947890 GACCGTCGTCGTCGTCAGT 61.948 63.158 10.76 2.02 38.33 3.41
654 701 2.202146 CCGTCGTCGTCGTCAGTC 60.202 66.667 10.76 0.00 38.33 3.51
655 702 2.547798 CGTCGTCGTCGTCAGTCA 59.452 61.111 3.67 0.00 38.33 3.41
656 703 1.787438 CGTCGTCGTCGTCAGTCAC 60.787 63.158 3.67 0.00 38.33 3.67
689 745 3.551496 CTCGCACCACCACCACCAT 62.551 63.158 0.00 0.00 0.00 3.55
771 847 4.204028 ACACACACACCAGCCCCC 62.204 66.667 0.00 0.00 0.00 5.40
825 901 1.443802 CCTTCTTCAGGTCGCCTTTC 58.556 55.000 0.00 0.00 37.99 2.62
891 967 2.800273 CGTGCCATTATGCATGCACAAT 60.800 45.455 28.72 21.56 44.30 2.71
920 996 0.691413 GCTACCTAGGCCCTCCACTT 60.691 60.000 9.30 0.00 33.74 3.16
943 1019 0.166814 CGGGCTTCTTGCTTCTTTCG 59.833 55.000 0.00 0.00 42.39 3.46
947 1023 1.463198 GCTTCTTGCTTCTTTCGCTCG 60.463 52.381 0.00 0.00 38.95 5.03
964 1040 0.448197 TCGCTCACTCGTCACTCATC 59.552 55.000 0.00 0.00 0.00 2.92
967 1043 1.135915 GCTCACTCGTCACTCATCCAT 59.864 52.381 0.00 0.00 0.00 3.41
1063 1143 4.270153 TGGGTGGAGGCCAGAGGT 62.270 66.667 5.01 0.00 32.34 3.85
1184 1267 2.673368 GCATCAGAGGTTAGTTCCGTTG 59.327 50.000 0.00 0.00 0.00 4.10
1185 1268 3.262420 CATCAGAGGTTAGTTCCGTTGG 58.738 50.000 0.00 0.00 0.00 3.77
1186 1269 2.322658 TCAGAGGTTAGTTCCGTTGGT 58.677 47.619 0.00 0.00 0.00 3.67
1187 1270 2.298163 TCAGAGGTTAGTTCCGTTGGTC 59.702 50.000 0.00 0.00 0.00 4.02
1188 1271 1.271656 AGAGGTTAGTTCCGTTGGTCG 59.728 52.381 0.00 0.00 39.52 4.79
1189 1272 0.320160 AGGTTAGTTCCGTTGGTCGC 60.320 55.000 0.00 0.00 38.35 5.19
1190 1273 0.320160 GGTTAGTTCCGTTGGTCGCT 60.320 55.000 0.00 0.00 38.35 4.93
1191 1274 1.066136 GTTAGTTCCGTTGGTCGCTC 58.934 55.000 0.00 0.00 38.35 5.03
1192 1275 0.387622 TTAGTTCCGTTGGTCGCTCG 60.388 55.000 0.00 0.00 38.35 5.03
1193 1276 2.807631 TAGTTCCGTTGGTCGCTCGC 62.808 60.000 0.00 0.00 38.35 5.03
1216 1299 0.736325 GTCGGTCGGTCACTCATTGG 60.736 60.000 0.00 0.00 0.00 3.16
1283 1410 0.322277 TGTTCCTCGCCGTCTAGAGT 60.322 55.000 0.00 0.00 32.88 3.24
1295 1425 3.752222 CCGTCTAGAGTGTAGACAACAGT 59.248 47.826 23.07 0.00 44.74 3.55
1298 1428 6.760298 CCGTCTAGAGTGTAGACAACAGTATA 59.240 42.308 23.07 0.00 42.02 1.47
1307 1437 7.446013 AGTGTAGACAACAGTATATAGCTCCTC 59.554 40.741 0.00 0.00 40.09 3.71
1349 1479 1.530323 TGTCCGCTTAAGCTTTTCCC 58.470 50.000 24.33 7.51 39.32 3.97
1350 1480 0.446616 GTCCGCTTAAGCTTTTCCCG 59.553 55.000 24.33 7.52 39.32 5.14
1370 1501 1.432251 CCCGTACACCTGTCGCTAG 59.568 63.158 0.00 0.00 0.00 3.42
1430 1561 1.466167 CCTTTTCGCACTCATGTCCAG 59.534 52.381 0.00 0.00 0.00 3.86
1431 1562 2.146342 CTTTTCGCACTCATGTCCAGT 58.854 47.619 0.00 0.00 0.00 4.00
1433 1564 1.511850 TTCGCACTCATGTCCAGTTG 58.488 50.000 0.00 0.00 0.00 3.16
1434 1565 0.678950 TCGCACTCATGTCCAGTTGA 59.321 50.000 0.00 0.00 0.00 3.18
1437 1568 2.094894 CGCACTCATGTCCAGTTGATTC 59.905 50.000 0.00 0.00 0.00 2.52
1446 1613 4.894784 TGTCCAGTTGATTCACTTAGTCC 58.105 43.478 0.00 0.00 0.00 3.85
1455 1622 4.041198 TGATTCACTTAGTCCCGTTTTCCT 59.959 41.667 0.00 0.00 0.00 3.36
1460 1627 4.577283 CACTTAGTCCCGTTTTCCTTTTCA 59.423 41.667 0.00 0.00 0.00 2.69
1461 1628 5.240844 CACTTAGTCCCGTTTTCCTTTTCAT 59.759 40.000 0.00 0.00 0.00 2.57
1462 1629 5.831525 ACTTAGTCCCGTTTTCCTTTTCATT 59.168 36.000 0.00 0.00 0.00 2.57
1463 1630 6.999871 ACTTAGTCCCGTTTTCCTTTTCATTA 59.000 34.615 0.00 0.00 0.00 1.90
1475 1642 8.776376 TTTCCTTTTCATTATGATTTGGCTTC 57.224 30.769 0.00 0.00 0.00 3.86
1477 1644 5.750067 CCTTTTCATTATGATTTGGCTTCGG 59.250 40.000 0.00 0.00 0.00 4.30
1485 1652 2.025793 TGATTTGGCTTCGGGTCCATTA 60.026 45.455 0.00 0.00 31.54 1.90
1487 1654 2.818751 TTGGCTTCGGGTCCATTATT 57.181 45.000 0.00 0.00 31.54 1.40
1514 1697 2.131183 GAGCACTGCTATTTAGGAGCG 58.869 52.381 2.71 0.00 44.50 5.03
1519 1705 3.746045 CTGCTATTTAGGAGCGGGTTA 57.254 47.619 0.00 0.00 43.19 2.85
1530 1716 4.850680 AGGAGCGGGTTATTTATTTGACA 58.149 39.130 0.00 0.00 0.00 3.58
1533 1719 5.124936 GGAGCGGGTTATTTATTTGACAAGT 59.875 40.000 0.00 0.00 0.00 3.16
1540 1726 9.984190 GGGTTATTTATTTGACAAGTGGTTTTA 57.016 29.630 0.00 0.00 0.00 1.52
1556 1742 5.236263 GTGGTTTTATTTTGAAGTTGCAGGG 59.764 40.000 0.00 0.00 0.00 4.45
1704 1890 1.065928 CATCCTGGCTACGACGACC 59.934 63.158 0.00 0.09 0.00 4.79
1772 1958 2.863484 AATGACAGGTGGGCCCCA 60.863 61.111 22.27 9.31 34.57 4.96
1786 1972 2.445845 CCCATCTCCCTACCGGCA 60.446 66.667 0.00 0.00 0.00 5.69
1826 2012 1.521010 CGAGCAGATCACCAGCCTG 60.521 63.158 0.00 0.00 0.00 4.85
1838 2024 2.091112 CAGCCTGTTCAGCGACGAG 61.091 63.158 0.00 0.00 34.64 4.18
1888 2074 1.202348 CCACAGCGTCTCATACAGAGG 60.202 57.143 0.00 0.00 44.81 3.69
1892 2078 2.020720 AGCGTCTCATACAGAGGAGTG 58.979 52.381 0.00 0.00 44.81 3.51
1906 2092 3.826729 AGAGGAGTGGTTGGTTTTTATGC 59.173 43.478 0.00 0.00 0.00 3.14
1907 2093 3.826729 GAGGAGTGGTTGGTTTTTATGCT 59.173 43.478 0.00 0.00 0.00 3.79
1908 2094 4.223144 AGGAGTGGTTGGTTTTTATGCTT 58.777 39.130 0.00 0.00 0.00 3.91
1909 2095 4.653801 AGGAGTGGTTGGTTTTTATGCTTT 59.346 37.500 0.00 0.00 0.00 3.51
1910 2096 5.130311 AGGAGTGGTTGGTTTTTATGCTTTT 59.870 36.000 0.00 0.00 0.00 2.27
1911 2097 5.820423 GGAGTGGTTGGTTTTTATGCTTTTT 59.180 36.000 0.00 0.00 0.00 1.94
1953 2140 5.702209 GCTTTAGCTAGATAGTCGTAGGAGT 59.298 44.000 0.00 0.00 38.21 3.85
1962 2153 2.553086 AGTCGTAGGAGTAGAAGCTCG 58.447 52.381 0.00 0.00 36.41 5.03
1995 2186 3.389329 TCTTGCCAATTTACCTTGCCAAA 59.611 39.130 0.00 0.00 0.00 3.28
2016 2207 2.159296 ACCTCACAAAACTTGCCGTTTC 60.159 45.455 2.24 0.00 44.77 2.78
2049 2240 0.928451 GACCTGCGAAACGTTGTTGC 60.928 55.000 0.00 7.16 0.00 4.17
2080 2272 6.829229 AAATTTTGGCTACCAAGTACTACC 57.171 37.500 0.00 0.00 44.84 3.18
2081 2273 4.978438 TTTTGGCTACCAAGTACTACCA 57.022 40.909 0.00 0.00 44.84 3.25
2082 2274 4.978438 TTTGGCTACCAAGTACTACCAA 57.022 40.909 0.00 1.29 44.84 3.67
2088 2280 4.503643 GCTACCAAGTACTACCAACCAACA 60.504 45.833 0.00 0.00 0.00 3.33
2129 2322 0.898789 ATCTCCGGTTGGTCTCGTGT 60.899 55.000 0.00 0.00 36.30 4.49
2130 2323 1.080705 CTCCGGTTGGTCTCGTGTC 60.081 63.158 0.00 0.00 36.30 3.67
2131 2324 1.802337 CTCCGGTTGGTCTCGTGTCA 61.802 60.000 0.00 0.00 36.30 3.58
2132 2325 1.183030 TCCGGTTGGTCTCGTGTCAT 61.183 55.000 0.00 0.00 36.30 3.06
2133 2326 0.528924 CCGGTTGGTCTCGTGTCATA 59.471 55.000 0.00 0.00 0.00 2.15
2134 2327 1.625616 CGGTTGGTCTCGTGTCATAC 58.374 55.000 0.00 0.00 0.00 2.39
2135 2328 1.201647 CGGTTGGTCTCGTGTCATACT 59.798 52.381 0.00 0.00 0.00 2.12
2136 2329 2.607187 GGTTGGTCTCGTGTCATACTG 58.393 52.381 0.00 0.00 0.00 2.74
2149 2342 3.179830 GTCATACTGTCATGTCGTCACC 58.820 50.000 0.00 0.00 0.00 4.02
2239 2440 1.792757 TTCCAACCAGAGGCAGCCAT 61.793 55.000 15.80 0.00 0.00 4.40
2291 2502 1.012841 AGATACTTCGACGACGGACC 58.987 55.000 7.55 0.00 40.21 4.46
2334 2560 3.692257 AGTTTATGCTCTGCTGTCTGT 57.308 42.857 0.00 0.00 0.00 3.41
2335 2561 3.594134 AGTTTATGCTCTGCTGTCTGTC 58.406 45.455 0.00 0.00 0.00 3.51
2336 2562 3.260380 AGTTTATGCTCTGCTGTCTGTCT 59.740 43.478 0.00 0.00 0.00 3.41
2337 2563 2.955477 TATGCTCTGCTGTCTGTCTG 57.045 50.000 0.00 0.00 0.00 3.51
2338 2564 0.975135 ATGCTCTGCTGTCTGTCTGT 59.025 50.000 0.00 0.00 0.00 3.41
2339 2565 0.316522 TGCTCTGCTGTCTGTCTGTC 59.683 55.000 0.00 0.00 0.00 3.51
2340 2566 0.602562 GCTCTGCTGTCTGTCTGTCT 59.397 55.000 0.00 0.00 0.00 3.41
2341 2567 1.000731 GCTCTGCTGTCTGTCTGTCTT 59.999 52.381 0.00 0.00 0.00 3.01
2353 2579 4.646945 TCTGTCTGTCTTTCTGTCTCTGTT 59.353 41.667 0.00 0.00 0.00 3.16
2522 2756 0.753111 CTGGATGGTAAAGCAGGCCC 60.753 60.000 0.00 0.00 0.00 5.80
2585 2820 1.645710 GTCAGGTCCTTCCTTGGAGA 58.354 55.000 0.00 0.00 45.67 3.71
2669 2912 1.523758 GCCTCCTTTTGAGCTCGAAA 58.476 50.000 24.49 24.49 39.98 3.46
2745 2992 0.661552 CATGTATGGCTCTGTGCTGC 59.338 55.000 1.44 0.00 42.39 5.25
2752 3008 2.359602 CTCTGTGCTGCTGGGTGG 60.360 66.667 0.00 0.00 0.00 4.61
2770 3026 2.586635 GTGCGTGGGTTGACGACA 60.587 61.111 0.00 0.00 42.10 4.35
2779 3035 1.066430 GGGTTGACGACAGATTGGCTA 60.066 52.381 0.00 0.00 0.00 3.93
2804 3070 2.088763 AACGACGATGAGCTGCGTG 61.089 57.895 10.17 6.11 41.34 5.34
2839 3105 4.222589 CGCACGCGGCCACTAATG 62.223 66.667 12.47 0.00 40.31 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 5.290386 GCAAGTAGCCTATGTAAGTTCGAT 58.710 41.667 0.00 0.00 37.23 3.59
131 132 0.832135 ACACGGTGGAGATGGTCAGT 60.832 55.000 13.48 0.00 0.00 3.41
220 221 1.939934 CTTCCGAAACAGCTGACACAA 59.060 47.619 23.35 4.20 0.00 3.33
222 223 1.261619 CACTTCCGAAACAGCTGACAC 59.738 52.381 23.35 9.55 0.00 3.67
241 242 0.034337 ACGCTTAAACTCGGGAAGCA 59.966 50.000 7.84 0.00 44.71 3.91
265 266 1.279271 GCTGGTGGAGTGGAGTTGTAT 59.721 52.381 0.00 0.00 0.00 2.29
268 269 1.669115 CGCTGGTGGAGTGGAGTTG 60.669 63.158 0.00 0.00 0.00 3.16
308 311 4.921515 TCAGTGTTCTTTTAAGATCGACGG 59.078 41.667 0.00 0.00 34.49 4.79
313 316 6.128795 CGGTCTGTCAGTGTTCTTTTAAGATC 60.129 42.308 0.00 0.00 34.49 2.75
320 326 1.485066 ACCGGTCTGTCAGTGTTCTTT 59.515 47.619 0.00 0.00 0.00 2.52
336 348 0.234884 GACGTTTCTCAGCAAACCGG 59.765 55.000 0.00 0.00 33.37 5.28
407 422 1.745320 TATCCTCGCTTCCGGCTTCC 61.745 60.000 0.00 0.00 39.13 3.46
417 432 2.175931 TCCTCCTCTTCTTATCCTCGCT 59.824 50.000 0.00 0.00 0.00 4.93
433 452 2.182030 CGGTCACGCTCTTCCTCC 59.818 66.667 0.00 0.00 0.00 4.30
434 453 1.444553 CACGGTCACGCTCTTCCTC 60.445 63.158 0.00 0.00 46.04 3.71
435 454 2.651361 CACGGTCACGCTCTTCCT 59.349 61.111 0.00 0.00 46.04 3.36
436 455 3.112709 GCACGGTCACGCTCTTCC 61.113 66.667 0.00 0.00 46.04 3.46
437 456 2.355837 TGCACGGTCACGCTCTTC 60.356 61.111 0.00 0.00 46.04 2.87
438 457 2.356313 CTGCACGGTCACGCTCTT 60.356 61.111 0.00 0.00 46.04 2.85
447 466 1.153568 CGATGGATGACTGCACGGT 60.154 57.895 0.00 0.00 0.00 4.83
462 481 2.369394 GAAAAAGGGACTGCCATCGAT 58.631 47.619 0.00 0.00 40.86 3.59
537 584 4.996434 AGTGCAGAGTGCCCGTGC 62.996 66.667 0.00 0.00 44.23 5.34
539 586 4.996434 GCAGTGCAGAGTGCCCGT 62.996 66.667 11.09 0.00 44.23 5.28
541 588 3.360340 GTGCAGTGCAGAGTGCCC 61.360 66.667 20.42 0.14 46.58 5.36
542 589 3.360340 GGTGCAGTGCAGAGTGCC 61.360 66.667 20.42 12.26 46.58 5.01
624 671 2.432456 GACGGTCGTGCATGCAGA 60.432 61.111 23.41 17.44 0.00 4.26
625 672 3.842126 CGACGGTCGTGCATGCAG 61.842 66.667 23.41 15.31 34.72 4.41
648 695 2.426738 CCTCTCCTCTCATGTGACTGAC 59.573 54.545 0.00 0.00 0.00 3.51
649 696 2.732763 CCTCTCCTCTCATGTGACTGA 58.267 52.381 0.00 0.00 0.00 3.41
650 697 1.136695 GCCTCTCCTCTCATGTGACTG 59.863 57.143 0.00 0.00 0.00 3.51
651 698 1.484038 GCCTCTCCTCTCATGTGACT 58.516 55.000 0.00 0.00 0.00 3.41
652 699 0.463620 GGCCTCTCCTCTCATGTGAC 59.536 60.000 0.00 0.00 0.00 3.67
653 700 0.337773 AGGCCTCTCCTCTCATGTGA 59.662 55.000 0.00 0.00 43.20 3.58
654 701 2.913463 AGGCCTCTCCTCTCATGTG 58.087 57.895 0.00 0.00 43.20 3.21
771 847 2.760385 GGGGACAGGAGAGACGGG 60.760 72.222 0.00 0.00 0.00 5.28
772 848 1.755008 GAGGGGACAGGAGAGACGG 60.755 68.421 0.00 0.00 0.00 4.79
773 849 2.115911 CGAGGGGACAGGAGAGACG 61.116 68.421 0.00 0.00 0.00 4.18
891 967 2.385803 GCCTAGGTAGCTAGTGTTGGA 58.614 52.381 23.74 0.00 0.00 3.53
943 1019 1.513160 GAGTGACGAGTGAGCGAGC 60.513 63.158 0.00 0.00 34.83 5.03
947 1023 0.528017 TGGATGAGTGACGAGTGAGC 59.472 55.000 0.00 0.00 0.00 4.26
1167 1250 2.685100 GACCAACGGAACTAACCTCTG 58.315 52.381 0.00 0.00 0.00 3.35
1168 1251 1.271656 CGACCAACGGAACTAACCTCT 59.728 52.381 0.00 0.00 38.46 3.69
1216 1299 4.580580 AGAGAAAACAAGACAATGTGACCC 59.419 41.667 0.00 0.00 32.81 4.46
1283 1410 7.287810 TGAGGAGCTATATACTGTTGTCTACA 58.712 38.462 0.00 0.00 34.95 2.74
1295 1425 7.471959 CGGGCATTATTGATGAGGAGCTATATA 60.472 40.741 0.00 0.00 38.03 0.86
1298 1428 4.624843 CGGGCATTATTGATGAGGAGCTAT 60.625 45.833 0.00 0.00 38.03 2.97
1307 1437 1.939934 ACACGACGGGCATTATTGATG 59.060 47.619 0.00 0.00 38.85 3.07
1349 1479 4.789075 CGACAGGTGTACGGGCCG 62.789 72.222 27.06 27.06 0.00 6.13
1430 1561 5.334646 GGAAAACGGGACTAAGTGAATCAAC 60.335 44.000 0.00 0.00 0.00 3.18
1431 1562 4.758165 GGAAAACGGGACTAAGTGAATCAA 59.242 41.667 0.00 0.00 0.00 2.57
1433 1564 4.576879 AGGAAAACGGGACTAAGTGAATC 58.423 43.478 0.00 0.00 0.00 2.52
1434 1565 4.635699 AGGAAAACGGGACTAAGTGAAT 57.364 40.909 0.00 0.00 0.00 2.57
1437 1568 4.577283 TGAAAAGGAAAACGGGACTAAGTG 59.423 41.667 0.00 0.00 0.00 3.16
1446 1613 7.412891 GCCAAATCATAATGAAAAGGAAAACGG 60.413 37.037 0.00 0.00 0.00 4.44
1455 1622 5.186797 ACCCGAAGCCAAATCATAATGAAAA 59.813 36.000 0.00 0.00 0.00 2.29
1460 1627 3.222603 GGACCCGAAGCCAAATCATAAT 58.777 45.455 0.00 0.00 0.00 1.28
1461 1628 2.025793 TGGACCCGAAGCCAAATCATAA 60.026 45.455 0.00 0.00 0.00 1.90
1462 1629 1.562008 TGGACCCGAAGCCAAATCATA 59.438 47.619 0.00 0.00 0.00 2.15
1463 1630 0.331278 TGGACCCGAAGCCAAATCAT 59.669 50.000 0.00 0.00 0.00 2.45
1487 1654 5.767665 TCCTAAATAGCAGTGCTCACAAAAA 59.232 36.000 23.64 1.66 40.44 1.94
1504 1673 7.558444 TGTCAAATAAATAACCCGCTCCTAAAT 59.442 33.333 0.00 0.00 0.00 1.40
1514 1697 8.896320 AAAACCACTTGTCAAATAAATAACCC 57.104 30.769 0.00 0.00 0.00 4.11
1530 1716 6.538381 CCTGCAACTTCAAAATAAAACCACTT 59.462 34.615 0.00 0.00 0.00 3.16
1533 1719 5.363939 CCCTGCAACTTCAAAATAAAACCA 58.636 37.500 0.00 0.00 0.00 3.67
1540 1726 1.693606 CCACCCCTGCAACTTCAAAAT 59.306 47.619 0.00 0.00 0.00 1.82
1546 1732 2.116125 GCTCCACCCCTGCAACTT 59.884 61.111 0.00 0.00 0.00 2.66
1556 1742 3.450115 ACCTCTACGCGCTCCACC 61.450 66.667 5.73 0.00 0.00 4.61
1598 1784 4.337060 TCCACGACGCCAGTGACG 62.337 66.667 0.00 0.00 41.83 4.35
1755 1941 2.228841 GATGGGGCCCACCTGTCATT 62.229 60.000 31.54 9.61 35.80 2.57
1818 2004 2.031163 GTCGCTGAACAGGCTGGT 59.969 61.111 20.34 13.55 0.00 4.00
1826 2012 2.087009 CGGGTTCTCGTCGCTGAAC 61.087 63.158 16.99 16.99 41.08 3.18
1838 2024 3.119096 GAGCAGGCGTTCGGGTTC 61.119 66.667 0.00 0.00 0.00 3.62
1877 2063 2.834549 ACCAACCACTCCTCTGTATGAG 59.165 50.000 0.00 0.00 42.30 2.90
1888 2074 6.918892 AAAAAGCATAAAAACCAACCACTC 57.081 33.333 0.00 0.00 0.00 3.51
1944 2131 1.134461 AGCGAGCTTCTACTCCTACGA 60.134 52.381 0.00 0.00 32.79 3.43
1945 2132 1.003331 CAGCGAGCTTCTACTCCTACG 60.003 57.143 0.00 0.00 32.79 3.51
1953 2140 1.511305 CGAACCCAGCGAGCTTCTA 59.489 57.895 0.00 0.00 0.00 2.10
1962 2153 3.435186 GGCAAGAGCGAACCCAGC 61.435 66.667 0.00 0.00 43.41 4.85
1995 2186 1.470051 AACGGCAAGTTTTGTGAGGT 58.530 45.000 0.00 0.00 40.88 3.85
2031 2222 1.063488 GCAACAACGTTTCGCAGGT 59.937 52.632 0.00 0.00 0.00 4.00
2037 2228 1.942223 GGCACGGCAACAACGTTTC 60.942 57.895 0.00 0.00 43.58 2.78
2073 2265 4.320935 CCATGCTTTGTTGGTTGGTAGTAC 60.321 45.833 0.00 0.00 0.00 2.73
2074 2266 3.823873 CCATGCTTTGTTGGTTGGTAGTA 59.176 43.478 0.00 0.00 0.00 1.82
2075 2267 2.627699 CCATGCTTTGTTGGTTGGTAGT 59.372 45.455 0.00 0.00 0.00 2.73
2076 2268 2.610232 GCCATGCTTTGTTGGTTGGTAG 60.610 50.000 0.00 0.00 35.34 3.18
2077 2269 1.342819 GCCATGCTTTGTTGGTTGGTA 59.657 47.619 0.00 0.00 35.34 3.25
2078 2270 0.106521 GCCATGCTTTGTTGGTTGGT 59.893 50.000 0.00 0.00 35.34 3.67
2079 2271 0.603439 GGCCATGCTTTGTTGGTTGG 60.603 55.000 0.00 0.00 35.34 3.77
2080 2272 0.393820 AGGCCATGCTTTGTTGGTTG 59.606 50.000 5.01 0.00 35.34 3.77
2081 2273 1.130777 AAGGCCATGCTTTGTTGGTT 58.869 45.000 5.01 0.00 35.34 3.67
2082 2274 0.393820 CAAGGCCATGCTTTGTTGGT 59.606 50.000 5.01 0.00 40.07 3.67
2088 2280 0.112995 TCTCACCAAGGCCATGCTTT 59.887 50.000 5.01 0.00 0.00 3.51
2129 2322 3.503827 GGTGACGACATGACAGTATGA 57.496 47.619 0.00 0.00 39.69 2.15
2239 2440 4.101585 GGTGATTGATGGTGGTCTAGATCA 59.898 45.833 0.14 0.14 0.00 2.92
2306 2529 3.006323 AGCAGAGCATAAACTATAGCGCT 59.994 43.478 17.26 17.26 37.62 5.92
2311 2534 6.322456 AGACAGACAGCAGAGCATAAACTATA 59.678 38.462 0.00 0.00 0.00 1.31
2334 2560 4.646945 AGTGAACAGAGACAGAAAGACAGA 59.353 41.667 0.00 0.00 0.00 3.41
2335 2561 4.942852 AGTGAACAGAGACAGAAAGACAG 58.057 43.478 0.00 0.00 0.00 3.51
2336 2562 4.202161 GGAGTGAACAGAGACAGAAAGACA 60.202 45.833 0.00 0.00 0.00 3.41
2337 2563 4.038642 AGGAGTGAACAGAGACAGAAAGAC 59.961 45.833 0.00 0.00 0.00 3.01
2338 2564 4.219115 AGGAGTGAACAGAGACAGAAAGA 58.781 43.478 0.00 0.00 0.00 2.52
2339 2565 4.555262 GAGGAGTGAACAGAGACAGAAAG 58.445 47.826 0.00 0.00 0.00 2.62
2340 2566 3.004839 CGAGGAGTGAACAGAGACAGAAA 59.995 47.826 0.00 0.00 0.00 2.52
2341 2567 2.554462 CGAGGAGTGAACAGAGACAGAA 59.446 50.000 0.00 0.00 0.00 3.02
2353 2579 0.391597 AAAAGAACGGCGAGGAGTGA 59.608 50.000 16.62 0.00 0.00 3.41
2502 2736 0.753111 GGCCTGCTTTACCATCCAGG 60.753 60.000 0.00 0.00 45.93 4.45
2507 2741 2.275418 CCGGGCCTGCTTTACCAT 59.725 61.111 5.85 0.00 0.00 3.55
2522 2756 1.731433 CTCCATTGGCATTGCTCCCG 61.731 60.000 8.82 0.00 0.00 5.14
2533 2767 1.926511 GCGCACTGAACCTCCATTGG 61.927 60.000 0.30 0.00 0.00 3.16
2585 2820 4.279169 ACAGCATCTGCACAAATACTGTTT 59.721 37.500 4.79 0.00 45.16 2.83
2621 2856 1.866853 GCAGAAAAGCGAGGGGGTTG 61.867 60.000 0.00 0.00 36.26 3.77
2624 2859 2.751837 GGCAGAAAAGCGAGGGGG 60.752 66.667 0.00 0.00 34.64 5.40
2752 3008 3.343421 GTCGTCAACCCACGCACC 61.343 66.667 0.00 0.00 39.74 5.01
2770 3026 5.172934 TCGTCGTTGTTAATTAGCCAATCT 58.827 37.500 0.00 0.00 0.00 2.40
2779 3035 3.181520 GCAGCTCATCGTCGTTGTTAATT 60.182 43.478 3.38 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.