Multiple sequence alignment - TraesCS6A01G275100

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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 TraesCS6A01G275100 chr6A 100.000 2582 0 0 1 2582 501802370 501799789 0.000000e+00 4769
1 TraesCS6A01G275100 chr6A 99.107 112 1 0 302 413 501802013 501801902 4.360000e-48 202
2 TraesCS6A01G275100 chr6A 99.107 112 1 0 358 469 501802069 501801958 4.360000e-48 202
3 TraesCS6A01G275100 chr6A 98.214 56 1 0 302 357 501801957 501801902 5.880000e-17 99
4 TraesCS6A01G275100 chr6A 98.214 56 1 0 414 469 501802069 501802014 5.880000e-17 99
5 TraesCS6A01G275100 chr6D 88.843 2196 112 62 414 2534 360688145 360686008 0.000000e+00 2575
6 TraesCS6A01G275100 chr6D 93.056 360 21 2 1 356 360688450 360688091 8.190000e-145 523
7 TraesCS6A01G275100 chr6B 91.533 874 38 12 414 1271 542232487 542231634 0.000000e+00 1171
8 TraesCS6A01G275100 chr6B 87.252 808 44 23 1314 2101 542231636 542230868 0.000000e+00 867
9 TraesCS6A01G275100 chr6B 89.474 361 31 7 1 360 542232783 542232429 1.410000e-122 449
10 TraesCS6A01G275100 chr6B 84.615 442 32 18 2086 2508 542229113 542228689 8.600000e-110 407


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 TraesCS6A01G275100 chr6A 501799789 501802370 2581 True 1074.2 4769 98.9284 1 2582 5 chr6A.!!$R1 2581
1 TraesCS6A01G275100 chr6D 360686008 360688450 2442 True 1549.0 2575 90.9495 1 2534 2 chr6D.!!$R1 2533
2 TraesCS6A01G275100 chr6B 542228689 542232783 4094 True 723.5 1171 88.2185 1 2508 4 chr6B.!!$R1 2507

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
978 1000 0.178935 CTCCCCCTCTCATCCTCCTC 60.179 65.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 1978 0.040425 GTGGTTACACAGCTTTGCCG 60.04 55.0 0.0 0.0 46.9 5.69 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
55 56 1.742308 TGTGGGTTAGGAAGAAGCCT 58.258 50.000 6.01 0.00 45.47 4.58
165 169 7.985634 TGTAATTTTTGTTTGAAGTGCTCTC 57.014 32.000 0.00 0.00 0.00 3.20
170 174 9.651913 AATTTTTGTTTGAAGTGCTCTCTTTTA 57.348 25.926 0.00 0.00 0.00 1.52
184 188 6.072119 TGCTCTCTTTTACTCGTATTCAGTGA 60.072 38.462 0.00 0.00 0.00 3.41
233 238 4.216257 ACAGTACATTTCGCTGCATTTTCT 59.784 37.500 0.00 0.00 33.87 2.52
246 251 3.512329 TGCATTTTCTCATGAGCATTGGT 59.488 39.130 18.36 0.00 0.00 3.67
337 342 9.753674 ATAATTTTCCTTTCTCAACCATAGTGA 57.246 29.630 0.00 0.00 0.00 3.41
338 343 8.655935 AATTTTCCTTTCTCAACCATAGTGAT 57.344 30.769 0.00 0.00 0.00 3.06
339 344 7.687941 TTTTCCTTTCTCAACCATAGTGATC 57.312 36.000 0.00 0.00 0.00 2.92
340 345 5.011090 TCCTTTCTCAACCATAGTGATCG 57.989 43.478 0.00 0.00 0.00 3.69
341 346 4.122776 CCTTTCTCAACCATAGTGATCGG 58.877 47.826 0.00 0.00 0.00 4.18
342 347 3.819564 TTCTCAACCATAGTGATCGGG 57.180 47.619 0.00 0.00 0.00 5.14
343 348 3.026707 TCTCAACCATAGTGATCGGGA 57.973 47.619 0.00 0.00 0.00 5.14
344 349 2.693591 TCTCAACCATAGTGATCGGGAC 59.306 50.000 0.00 0.00 0.00 4.46
345 350 2.695666 CTCAACCATAGTGATCGGGACT 59.304 50.000 0.00 0.00 0.00 3.85
346 351 2.693591 TCAACCATAGTGATCGGGACTC 59.306 50.000 0.00 0.00 0.00 3.36
347 352 1.705873 ACCATAGTGATCGGGACTCC 58.294 55.000 0.00 0.00 0.00 3.85
348 353 0.969894 CCATAGTGATCGGGACTCCC 59.030 60.000 3.63 3.63 41.09 4.30
357 362 3.721868 GGGACTCCCGGAATGACA 58.278 61.111 0.73 0.00 32.13 3.58
358 363 2.221918 GGGACTCCCGGAATGACAT 58.778 57.895 0.73 0.00 32.13 3.06
359 364 0.179045 GGGACTCCCGGAATGACATG 60.179 60.000 0.73 0.00 32.13 3.21
360 365 0.830648 GGACTCCCGGAATGACATGA 59.169 55.000 0.73 0.00 0.00 3.07
361 366 1.209504 GGACTCCCGGAATGACATGAA 59.790 52.381 0.73 0.00 0.00 2.57
362 367 2.158755 GGACTCCCGGAATGACATGAAT 60.159 50.000 0.73 0.00 0.00 2.57
363 368 3.134458 GACTCCCGGAATGACATGAATC 58.866 50.000 0.73 0.00 0.00 2.52
364 369 2.774234 ACTCCCGGAATGACATGAATCT 59.226 45.455 0.73 0.00 0.00 2.40
365 370 3.967326 ACTCCCGGAATGACATGAATCTA 59.033 43.478 0.73 0.00 0.00 1.98
366 371 4.594920 ACTCCCGGAATGACATGAATCTAT 59.405 41.667 0.73 0.00 0.00 1.98
367 372 5.780282 ACTCCCGGAATGACATGAATCTATA 59.220 40.000 0.73 0.00 0.00 1.31
368 373 6.441924 ACTCCCGGAATGACATGAATCTATAT 59.558 38.462 0.73 0.00 0.00 0.86
369 374 7.619698 ACTCCCGGAATGACATGAATCTATATA 59.380 37.037 0.73 0.00 0.00 0.86
370 375 8.374184 TCCCGGAATGACATGAATCTATATAA 57.626 34.615 0.73 0.00 0.00 0.98
371 376 8.992349 TCCCGGAATGACATGAATCTATATAAT 58.008 33.333 0.73 0.00 0.00 1.28
372 377 9.618890 CCCGGAATGACATGAATCTATATAATT 57.381 33.333 0.73 0.00 0.00 1.40
393 398 7.595819 AATTTTCCTTTCACAACCATAGTGA 57.404 32.000 0.00 0.00 43.72 3.41
394 399 7.781324 ATTTTCCTTTCACAACCATAGTGAT 57.219 32.000 0.00 0.00 44.66 3.06
395 400 6.817765 TTTCCTTTCACAACCATAGTGATC 57.182 37.500 0.00 0.00 44.66 2.92
396 401 4.503910 TCCTTTCACAACCATAGTGATCG 58.496 43.478 0.00 0.00 44.66 3.69
397 402 3.623060 CCTTTCACAACCATAGTGATCGG 59.377 47.826 0.00 0.00 44.66 4.18
398 403 2.979814 TCACAACCATAGTGATCGGG 57.020 50.000 0.00 0.00 40.80 5.14
399 404 2.462723 TCACAACCATAGTGATCGGGA 58.537 47.619 0.00 0.00 40.80 5.14
400 405 2.167693 TCACAACCATAGTGATCGGGAC 59.832 50.000 0.00 0.00 40.80 4.46
401 406 2.168521 CACAACCATAGTGATCGGGACT 59.831 50.000 0.00 0.00 39.30 3.85
402 407 2.431057 ACAACCATAGTGATCGGGACTC 59.569 50.000 0.00 0.00 0.00 3.36
403 408 1.705873 ACCATAGTGATCGGGACTCC 58.294 55.000 0.00 0.00 0.00 3.85
404 409 0.969894 CCATAGTGATCGGGACTCCC 59.030 60.000 3.63 3.63 41.09 4.30
413 418 3.721868 GGGACTCCCGGAATGACA 58.278 61.111 0.73 0.00 32.13 3.58
414 419 2.221918 GGGACTCCCGGAATGACAT 58.778 57.895 0.73 0.00 32.13 3.06
415 420 0.179045 GGGACTCCCGGAATGACATG 60.179 60.000 0.73 0.00 32.13 3.21
416 421 0.830648 GGACTCCCGGAATGACATGA 59.169 55.000 0.73 0.00 0.00 3.07
417 422 1.209504 GGACTCCCGGAATGACATGAA 59.790 52.381 0.73 0.00 0.00 2.57
418 423 2.158755 GGACTCCCGGAATGACATGAAT 60.159 50.000 0.73 0.00 0.00 2.57
419 424 3.134458 GACTCCCGGAATGACATGAATC 58.866 50.000 0.73 0.00 0.00 2.52
420 425 2.774234 ACTCCCGGAATGACATGAATCT 59.226 45.455 0.73 0.00 0.00 2.40
421 426 3.967326 ACTCCCGGAATGACATGAATCTA 59.033 43.478 0.73 0.00 0.00 1.98
422 427 4.594920 ACTCCCGGAATGACATGAATCTAT 59.405 41.667 0.73 0.00 0.00 1.98
423 428 5.780282 ACTCCCGGAATGACATGAATCTATA 59.220 40.000 0.73 0.00 0.00 1.31
424 429 6.441924 ACTCCCGGAATGACATGAATCTATAT 59.558 38.462 0.73 0.00 0.00 0.86
425 430 7.619698 ACTCCCGGAATGACATGAATCTATATA 59.380 37.037 0.73 0.00 0.00 0.86
426 431 8.374184 TCCCGGAATGACATGAATCTATATAA 57.626 34.615 0.73 0.00 0.00 0.98
427 432 8.992349 TCCCGGAATGACATGAATCTATATAAT 58.008 33.333 0.73 0.00 0.00 1.28
428 433 9.618890 CCCGGAATGACATGAATCTATATAATT 57.381 33.333 0.73 0.00 0.00 1.40
460 465 0.969894 CCATAGTGATCGGGACTCCC 59.030 60.000 3.63 3.63 41.09 4.30
501 509 7.751646 TCATCTAAAAGGGGAAAGTTTGTCTA 58.248 34.615 0.00 0.00 0.00 2.59
521 530 0.438830 CGCTAGTTGACTGAAACCGC 59.561 55.000 0.00 0.00 0.00 5.68
599 616 5.489792 AGTCCAAGAATAGCTCTGAAACA 57.510 39.130 0.00 0.00 33.37 2.83
609 626 1.683385 GCTCTGAAACAGCACCCTTTT 59.317 47.619 0.00 0.00 36.82 2.27
649 666 0.328926 TCCGTTAACCAATCCACCCC 59.671 55.000 0.00 0.00 0.00 4.95
669 686 2.029649 CCAAGACACAAGAAAGGCCATG 60.030 50.000 5.01 0.00 0.00 3.66
705 722 1.923864 TGCACTCACATAATACGCGTG 59.076 47.619 24.59 7.13 0.00 5.34
854 876 1.254284 CCCCTCAAGTCACTCGAGCT 61.254 60.000 13.61 0.00 0.00 4.09
858 880 2.091112 CAAGTCACTCGAGCTGCCG 61.091 63.158 13.61 0.00 0.00 5.69
922 944 3.637229 TGCAGTTAGGCTAGCTAAGTAGG 59.363 47.826 15.72 0.00 34.04 3.18
934 956 5.102885 AGCTAAGTAGGCAAGCTCTAGCG 62.103 52.174 0.00 0.00 42.89 4.26
948 970 3.405093 TAGCGGCTGCCCATTCCTG 62.405 63.158 15.55 0.00 44.31 3.86
962 984 4.864334 CCTGCGTCCATGCCCTCC 62.864 72.222 0.00 0.00 0.00 4.30
970 992 2.367377 CATGCCCTCCCCCTCTCA 60.367 66.667 0.00 0.00 0.00 3.27
977 999 1.673928 CCTCCCCCTCTCATCCTCCT 61.674 65.000 0.00 0.00 0.00 3.69
978 1000 0.178935 CTCCCCCTCTCATCCTCCTC 60.179 65.000 0.00 0.00 0.00 3.71
979 1001 1.532794 CCCCCTCTCATCCTCCTCG 60.533 68.421 0.00 0.00 0.00 4.63
980 1002 1.231641 CCCCTCTCATCCTCCTCGT 59.768 63.158 0.00 0.00 0.00 4.18
981 1003 0.825840 CCCCTCTCATCCTCCTCGTC 60.826 65.000 0.00 0.00 0.00 4.20
982 1004 1.169661 CCCTCTCATCCTCCTCGTCG 61.170 65.000 0.00 0.00 0.00 5.12
983 1005 0.464735 CCTCTCATCCTCCTCGTCGT 60.465 60.000 0.00 0.00 0.00 4.34
984 1006 0.941542 CTCTCATCCTCCTCGTCGTC 59.058 60.000 0.00 0.00 0.00 4.20
985 1007 0.810426 TCTCATCCTCCTCGTCGTCG 60.810 60.000 0.00 0.00 38.55 5.12
1276 1301 1.741401 CTGCTGGACGGCGATTTCA 60.741 57.895 16.62 4.98 34.52 2.69
1347 1372 2.202756 GTCCGCGGTAGCTGGAAG 60.203 66.667 27.15 0.00 43.63 3.46
1374 1399 1.146358 GCTTCGCCATGGACGACTAC 61.146 60.000 24.55 15.63 39.67 2.73
1385 1410 2.262471 GACGACTACGATGGCGGTGT 62.262 60.000 11.63 0.00 43.17 4.16
1521 1549 4.754667 GGCGACCCCGTGTCTTCC 62.755 72.222 0.00 0.00 42.13 3.46
1540 1568 1.067060 CCGAGGATCAGATGTACGCAA 59.933 52.381 0.00 0.00 33.17 4.85
1549 1577 0.375106 GATGTACGCAAGCTTGAGCC 59.625 55.000 30.39 19.83 43.38 4.70
1560 1588 1.296715 CTTGAGCCTGCCGGTAGTT 59.703 57.895 18.86 6.15 0.00 2.24
1575 1603 2.614983 GGTAGTTCTAGAGAGAGTGCGG 59.385 54.545 0.00 0.00 31.77 5.69
1632 1666 1.203052 GGCTTGCATTGCAGCTTCTAA 59.797 47.619 23.08 5.25 40.61 2.10
1658 1692 2.422479 GGTTTCTACTTTTCCATCCGGC 59.578 50.000 0.00 0.00 0.00 6.13
1659 1693 2.413310 TTCTACTTTTCCATCCGGCC 57.587 50.000 0.00 0.00 0.00 6.13
1660 1694 1.281419 TCTACTTTTCCATCCGGCCA 58.719 50.000 2.24 0.00 0.00 5.36
1661 1695 1.631388 TCTACTTTTCCATCCGGCCAA 59.369 47.619 2.24 0.00 0.00 4.52
1662 1696 2.017049 CTACTTTTCCATCCGGCCAAG 58.983 52.381 2.24 0.00 0.00 3.61
1663 1697 0.611896 ACTTTTCCATCCGGCCAAGG 60.612 55.000 2.24 0.00 0.00 3.61
1664 1698 0.323360 CTTTTCCATCCGGCCAAGGA 60.323 55.000 2.24 1.76 45.54 3.36
1702 1736 5.530171 AGCAGCTATTACATCATTTGGTCAG 59.470 40.000 0.00 0.00 0.00 3.51
1750 1792 6.109156 TGTTATCATCATGGTACGCCTATT 57.891 37.500 0.00 0.00 35.27 1.73
1751 1793 7.234661 TGTTATCATCATGGTACGCCTATTA 57.765 36.000 0.00 0.00 35.27 0.98
1752 1794 7.847096 TGTTATCATCATGGTACGCCTATTAT 58.153 34.615 0.00 0.00 35.27 1.28
1769 1811 7.592533 CGCCTATTATCAATCAAAGGAACAATG 59.407 37.037 0.00 0.00 0.00 2.82
1822 1864 4.227864 TCACTGCAGAGAGACAGATAGA 57.772 45.455 23.35 0.00 37.35 1.98
1877 1919 0.528684 GAACGCTGATCCTTCTCCGG 60.529 60.000 0.00 0.00 0.00 5.14
1920 1975 3.828786 GTTATGTAACCACGCCTTTTGG 58.171 45.455 0.00 0.00 44.18 3.28
1921 1976 1.253100 ATGTAACCACGCCTTTTGGG 58.747 50.000 0.00 0.00 38.59 4.12
1931 1986 2.357396 CTTTTGGGGCGGCAAAGC 60.357 61.111 12.47 0.00 0.00 3.51
1961 2016 1.670811 ACCTCGTGTTGCTTTGTTCAG 59.329 47.619 0.00 0.00 0.00 3.02
1965 2021 4.688879 CCTCGTGTTGCTTTGTTCAGTATA 59.311 41.667 0.00 0.00 0.00 1.47
1967 2023 4.449743 TCGTGTTGCTTTGTTCAGTATACC 59.550 41.667 0.00 0.00 0.00 2.73
1977 2033 4.901868 TGTTCAGTATACCTGGTTTGGAC 58.098 43.478 3.84 4.86 41.83 4.02
2101 3955 1.751924 ACTTCATCCCGTAGCTGTCTC 59.248 52.381 0.00 0.00 0.00 3.36
2113 3967 1.479730 AGCTGTCTCGCTGATGATTGA 59.520 47.619 0.00 0.00 39.16 2.57
2134 3988 4.047059 CTTGTTGCCCGCCAGCTG 62.047 66.667 6.78 6.78 0.00 4.24
2214 4086 2.005960 ATGACCACCGCGCTCTACTC 62.006 60.000 5.56 0.00 0.00 2.59
2215 4087 2.361357 ACCACCGCGCTCTACTCT 60.361 61.111 5.56 0.00 0.00 3.24
2216 4088 1.077930 ACCACCGCGCTCTACTCTA 60.078 57.895 5.56 0.00 0.00 2.43
2217 4089 1.355916 CCACCGCGCTCTACTCTAC 59.644 63.158 5.56 0.00 0.00 2.59
2218 4090 1.355916 CACCGCGCTCTACTCTACC 59.644 63.158 5.56 0.00 0.00 3.18
2264 4136 2.510948 GCGTATGGCGACTCAGATG 58.489 57.895 0.00 0.00 44.77 2.90
2271 4155 0.108424 GGCGACTCAGATGAGCAACT 60.108 55.000 9.75 0.00 45.79 3.16
2287 4171 2.353208 GCAACTGGACGAAGATCTCACT 60.353 50.000 0.00 0.00 0.00 3.41
2290 4174 2.894126 ACTGGACGAAGATCTCACTGTT 59.106 45.455 0.00 0.00 0.00 3.16
2291 4175 3.057174 ACTGGACGAAGATCTCACTGTTC 60.057 47.826 0.00 0.00 0.00 3.18
2292 4176 2.890945 TGGACGAAGATCTCACTGTTCA 59.109 45.455 0.00 0.00 0.00 3.18
2293 4177 3.057245 TGGACGAAGATCTCACTGTTCAG 60.057 47.826 0.00 0.00 0.00 3.02
2294 4178 3.506810 GACGAAGATCTCACTGTTCAGG 58.493 50.000 0.00 0.00 0.00 3.86
2295 4179 2.232452 ACGAAGATCTCACTGTTCAGGG 59.768 50.000 0.00 0.00 0.00 4.45
2296 4180 2.626840 GAAGATCTCACTGTTCAGGGC 58.373 52.381 0.00 0.00 0.00 5.19
2297 4181 0.908198 AGATCTCACTGTTCAGGGCC 59.092 55.000 0.00 0.00 0.00 5.80
2298 4182 0.107459 GATCTCACTGTTCAGGGCCC 60.107 60.000 16.46 16.46 0.00 5.80
2299 4183 0.842030 ATCTCACTGTTCAGGGCCCA 60.842 55.000 27.56 0.00 0.00 5.36
2300 4184 1.302832 CTCACTGTTCAGGGCCCAC 60.303 63.158 27.56 14.86 0.00 4.61
2301 4185 2.282462 CACTGTTCAGGGCCCACC 60.282 66.667 27.56 8.92 40.67 4.61
2354 4238 3.741476 CTTCGGCCCTGCTGCAAC 61.741 66.667 3.02 0.00 34.49 4.17
2355 4239 4.269523 TTCGGCCCTGCTGCAACT 62.270 61.111 3.02 0.00 34.49 3.16
2374 4271 3.392440 CGCCGTACGCCGAATAGC 61.392 66.667 14.10 6.57 39.56 2.97
2492 4389 1.666189 GCAGCCAGAATCCTTCGTAAC 59.334 52.381 0.00 0.00 34.02 2.50
2529 4426 2.413351 CGTCTCATCCGTGCCGAT 59.587 61.111 0.00 0.00 0.00 4.18
2544 4441 4.166011 GATGCCGCGGAAGTGCAC 62.166 66.667 33.48 9.40 42.14 4.57
2563 4460 4.456253 GCGACGCCGACGAGAAGA 62.456 66.667 13.88 0.00 43.93 2.87
2564 4461 2.573689 CGACGCCGACGAGAAGAC 60.574 66.667 2.16 0.00 43.93 3.01
2565 4462 2.573689 GACGCCGACGAGAAGACG 60.574 66.667 0.00 0.00 43.93 4.18
2566 4463 4.755614 ACGCCGACGAGAAGACGC 62.756 66.667 0.00 0.00 43.93 5.19
2567 4464 4.753877 CGCCGACGAGAAGACGCA 62.754 66.667 0.00 0.00 43.93 5.24
2568 4465 3.173240 GCCGACGAGAAGACGCAC 61.173 66.667 0.00 0.00 36.73 5.34
2569 4466 2.870161 CCGACGAGAAGACGCACG 60.870 66.667 0.00 0.00 36.73 5.34
2570 4467 3.524759 CGACGAGAAGACGCACGC 61.525 66.667 0.00 0.00 36.70 5.34
2571 4468 3.173240 GACGAGAAGACGCACGCC 61.173 66.667 0.00 0.00 36.70 5.68
2572 4469 4.719369 ACGAGAAGACGCACGCCC 62.719 66.667 0.00 0.00 36.70 6.13
2574 4471 4.373116 GAGAAGACGCACGCCCCA 62.373 66.667 0.00 0.00 0.00 4.96
2575 4472 4.681978 AGAAGACGCACGCCCCAC 62.682 66.667 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 8.137437 CCACAAGACAAAATAAAACAGAGTGAT 58.863 33.333 0.00 0.00 0.00 3.06
15 16 7.416213 CCCACAAGACAAAATAAAACAGAGTGA 60.416 37.037 0.00 0.00 0.00 3.41
55 56 8.641541 AGAAAGGAAATTAAAGATTGTTCAGCA 58.358 29.630 0.00 0.00 0.00 4.41
150 154 5.234329 CGAGTAAAAGAGAGCACTTCAAACA 59.766 40.000 0.00 0.00 0.00 2.83
165 169 9.569167 TTCATACTCACTGAATACGAGTAAAAG 57.431 33.333 0.00 0.00 43.46 2.27
170 174 7.489435 CACAATTCATACTCACTGAATACGAGT 59.511 37.037 0.00 0.00 41.33 4.18
205 210 2.672874 GCAGCGAAATGTACTGTCATCA 59.327 45.455 0.00 0.00 33.87 3.07
233 238 1.005097 AGGCTCAACCAATGCTCATGA 59.995 47.619 0.00 0.00 43.14 3.07
271 276 1.195115 GGGGCGCTAGATATGATCCA 58.805 55.000 7.64 0.00 0.00 3.41
323 328 2.693591 GTCCCGATCACTATGGTTGAGA 59.306 50.000 0.00 0.00 0.00 3.27
324 329 2.695666 AGTCCCGATCACTATGGTTGAG 59.304 50.000 0.00 0.00 0.00 3.02
325 330 2.693591 GAGTCCCGATCACTATGGTTGA 59.306 50.000 0.00 0.00 0.00 3.18
326 331 2.224066 GGAGTCCCGATCACTATGGTTG 60.224 54.545 0.00 0.00 0.00 3.77
327 332 2.040178 GGAGTCCCGATCACTATGGTT 58.960 52.381 0.00 0.00 0.00 3.67
328 333 1.705873 GGAGTCCCGATCACTATGGT 58.294 55.000 0.00 0.00 0.00 3.55
329 334 0.969894 GGGAGTCCCGATCACTATGG 59.030 60.000 13.89 0.00 32.13 2.74
340 345 0.179045 CATGTCATTCCGGGAGTCCC 60.179 60.000 19.37 19.37 41.09 4.46
341 346 0.830648 TCATGTCATTCCGGGAGTCC 59.169 55.000 0.00 0.00 0.00 3.85
342 347 2.691409 TTCATGTCATTCCGGGAGTC 57.309 50.000 0.00 0.00 0.00 3.36
343 348 2.774234 AGATTCATGTCATTCCGGGAGT 59.226 45.455 0.00 0.00 0.00 3.85
344 349 3.482156 AGATTCATGTCATTCCGGGAG 57.518 47.619 0.00 0.00 0.00 4.30
345 350 6.874278 ATATAGATTCATGTCATTCCGGGA 57.126 37.500 0.00 0.00 0.00 5.14
346 351 9.618890 AATTATATAGATTCATGTCATTCCGGG 57.381 33.333 0.00 0.00 0.00 5.73
367 372 9.308000 TCACTATGGTTGTGAAAGGAAAATTAT 57.692 29.630 0.00 0.00 40.89 1.28
368 373 8.698973 TCACTATGGTTGTGAAAGGAAAATTA 57.301 30.769 0.00 0.00 40.89 1.40
369 374 7.595819 TCACTATGGTTGTGAAAGGAAAATT 57.404 32.000 0.00 0.00 40.89 1.82
370 375 7.362056 CGATCACTATGGTTGTGAAAGGAAAAT 60.362 37.037 0.66 0.00 45.82 1.82
371 376 6.072728 CGATCACTATGGTTGTGAAAGGAAAA 60.073 38.462 0.66 0.00 45.82 2.29
372 377 5.411361 CGATCACTATGGTTGTGAAAGGAAA 59.589 40.000 0.66 0.00 45.82 3.13
373 378 4.935205 CGATCACTATGGTTGTGAAAGGAA 59.065 41.667 0.66 0.00 45.82 3.36
374 379 4.503910 CGATCACTATGGTTGTGAAAGGA 58.496 43.478 0.66 0.00 45.82 3.36
375 380 3.623060 CCGATCACTATGGTTGTGAAAGG 59.377 47.826 0.66 4.18 45.82 3.11
376 381 3.623060 CCCGATCACTATGGTTGTGAAAG 59.377 47.826 0.66 0.00 45.82 2.62
377 382 3.262151 TCCCGATCACTATGGTTGTGAAA 59.738 43.478 0.66 0.00 45.82 2.69
378 383 2.835156 TCCCGATCACTATGGTTGTGAA 59.165 45.455 0.66 0.00 45.82 3.18
379 384 2.167693 GTCCCGATCACTATGGTTGTGA 59.832 50.000 0.00 0.00 46.58 3.58
380 385 2.168521 AGTCCCGATCACTATGGTTGTG 59.831 50.000 0.00 0.00 36.82 3.33
381 386 2.431057 GAGTCCCGATCACTATGGTTGT 59.569 50.000 0.00 0.00 0.00 3.32
382 387 2.224066 GGAGTCCCGATCACTATGGTTG 60.224 54.545 0.00 0.00 0.00 3.77
383 388 2.040178 GGAGTCCCGATCACTATGGTT 58.960 52.381 0.00 0.00 0.00 3.67
384 389 1.705873 GGAGTCCCGATCACTATGGT 58.294 55.000 0.00 0.00 0.00 3.55
385 390 0.969894 GGGAGTCCCGATCACTATGG 59.030 60.000 13.89 0.00 32.13 2.74
396 401 0.179045 CATGTCATTCCGGGAGTCCC 60.179 60.000 19.37 19.37 41.09 4.46
397 402 0.830648 TCATGTCATTCCGGGAGTCC 59.169 55.000 0.00 0.00 0.00 3.85
398 403 2.691409 TTCATGTCATTCCGGGAGTC 57.309 50.000 0.00 0.00 0.00 3.36
399 404 2.774234 AGATTCATGTCATTCCGGGAGT 59.226 45.455 0.00 0.00 0.00 3.85
400 405 3.482156 AGATTCATGTCATTCCGGGAG 57.518 47.619 0.00 0.00 0.00 4.30
401 406 6.874278 ATATAGATTCATGTCATTCCGGGA 57.126 37.500 0.00 0.00 0.00 5.14
402 407 9.618890 AATTATATAGATTCATGTCATTCCGGG 57.381 33.333 0.00 0.00 0.00 5.73
423 428 9.308000 TCACTATGGTTGTGAAAGGAAAATTAT 57.692 29.630 0.00 0.00 40.89 1.28
424 429 8.698973 TCACTATGGTTGTGAAAGGAAAATTA 57.301 30.769 0.00 0.00 40.89 1.40
425 430 7.595819 TCACTATGGTTGTGAAAGGAAAATT 57.404 32.000 0.00 0.00 40.89 1.82
426 431 7.362056 CGATCACTATGGTTGTGAAAGGAAAAT 60.362 37.037 0.66 0.00 45.82 1.82
427 432 6.072728 CGATCACTATGGTTGTGAAAGGAAAA 60.073 38.462 0.66 0.00 45.82 2.29
428 433 5.411361 CGATCACTATGGTTGTGAAAGGAAA 59.589 40.000 0.66 0.00 45.82 3.13
429 434 4.935205 CGATCACTATGGTTGTGAAAGGAA 59.065 41.667 0.66 0.00 45.82 3.36
430 435 4.503910 CGATCACTATGGTTGTGAAAGGA 58.496 43.478 0.66 0.00 45.82 3.36
431 436 3.623060 CCGATCACTATGGTTGTGAAAGG 59.377 47.826 0.66 4.18 45.82 3.11
432 437 3.623060 CCCGATCACTATGGTTGTGAAAG 59.377 47.826 0.66 0.00 45.82 2.62
433 438 3.262151 TCCCGATCACTATGGTTGTGAAA 59.738 43.478 0.66 0.00 45.82 2.69
434 439 2.835156 TCCCGATCACTATGGTTGTGAA 59.165 45.455 0.66 0.00 45.82 3.18
435 440 2.167693 GTCCCGATCACTATGGTTGTGA 59.832 50.000 0.00 0.00 46.58 3.58
460 465 2.710297 GATGAAGTCGGCGTCATTCCG 61.710 57.143 19.28 0.00 42.36 4.30
468 475 1.933853 CCCTTTTAGATGAAGTCGGCG 59.066 52.381 0.00 0.00 0.00 6.46
501 509 1.779569 CGGTTTCAGTCAACTAGCGT 58.220 50.000 0.00 0.00 0.00 5.07
521 530 4.437794 CGACATCCAACATGAGAAATGTGG 60.438 45.833 0.00 2.07 31.80 4.17
561 570 1.542987 GGACTAGTCGATCGGGTAGCT 60.543 57.143 16.41 8.50 0.00 3.32
599 616 0.661020 CGTCGAACAAAAAGGGTGCT 59.339 50.000 0.00 0.00 0.00 4.40
609 626 2.702898 TTCCGTGTATCGTCGAACAA 57.297 45.000 0.00 0.00 37.94 2.83
649 666 2.608752 GCATGGCCTTTCTTGTGTCTTG 60.609 50.000 3.32 0.00 0.00 3.02
782 799 1.529796 CACCCCGCTTATTAGGCCA 59.470 57.895 5.01 0.00 0.00 5.36
783 800 1.228154 CCACCCCGCTTATTAGGCC 60.228 63.158 0.00 0.00 0.00 5.19
784 801 1.897137 GCCACCCCGCTTATTAGGC 60.897 63.158 0.00 0.00 0.00 3.93
785 802 0.110486 ATGCCACCCCGCTTATTAGG 59.890 55.000 0.00 0.00 0.00 2.69
858 880 1.866853 CGGAGGCTTTGGGTTGCTTC 61.867 60.000 0.00 0.00 35.05 3.86
922 944 3.571588 GCAGCCGCTAGAGCTTGC 61.572 66.667 5.05 8.72 38.95 4.01
962 984 0.825840 GACGAGGAGGATGAGAGGGG 60.826 65.000 0.00 0.00 0.00 4.79
970 992 1.818785 GGACGACGACGAGGAGGAT 60.819 63.158 15.32 0.00 42.66 3.24
1026 1048 2.753043 CAGTCCATGGCCACCAGC 60.753 66.667 8.16 0.00 36.75 4.85
1276 1301 2.334023 GATATCCCTGAAGGTGGCTCT 58.666 52.381 0.00 0.00 36.75 4.09
1385 1410 2.604686 ACCTCTGCTTCCAGCCGA 60.605 61.111 0.00 0.00 41.51 5.54
1454 1482 2.690510 AGAAGAGCCCCTCCTGCC 60.691 66.667 0.00 0.00 0.00 4.85
1519 1547 0.952280 GCGTACATCTGATCCTCGGA 59.048 55.000 0.00 0.00 36.02 4.55
1521 1549 2.389059 CTTGCGTACATCTGATCCTCG 58.611 52.381 0.00 0.00 0.00 4.63
1540 1568 3.003173 TACCGGCAGGCTCAAGCT 61.003 61.111 0.00 0.00 42.76 3.74
1549 1577 2.875933 CTCTCTCTAGAACTACCGGCAG 59.124 54.545 0.00 0.00 0.00 4.85
1560 1588 2.738587 AATCCCGCACTCTCTCTAGA 57.261 50.000 0.00 0.00 0.00 2.43
1575 1603 2.839486 TCATCATCGGTGCCTAATCC 57.161 50.000 0.00 0.00 0.00 3.01
1632 1666 5.648092 CGGATGGAAAAGTAGAAACCTCATT 59.352 40.000 0.00 0.00 0.00 2.57
1663 1697 9.145865 GTAATAGCTGCTACTCTGGATAAAATC 57.854 37.037 12.26 0.00 0.00 2.17
1664 1698 8.651389 TGTAATAGCTGCTACTCTGGATAAAAT 58.349 33.333 12.26 0.00 0.00 1.82
1665 1699 8.018537 TGTAATAGCTGCTACTCTGGATAAAA 57.981 34.615 12.26 0.00 0.00 1.52
1666 1700 7.597288 TGTAATAGCTGCTACTCTGGATAAA 57.403 36.000 12.26 0.00 0.00 1.40
1667 1701 7.451566 TGATGTAATAGCTGCTACTCTGGATAA 59.548 37.037 12.26 0.00 0.00 1.75
1668 1702 6.948309 TGATGTAATAGCTGCTACTCTGGATA 59.052 38.462 12.26 0.00 0.00 2.59
1669 1703 5.777223 TGATGTAATAGCTGCTACTCTGGAT 59.223 40.000 12.26 0.00 0.00 3.41
1670 1704 5.140454 TGATGTAATAGCTGCTACTCTGGA 58.860 41.667 12.26 0.00 0.00 3.86
1671 1705 5.459536 TGATGTAATAGCTGCTACTCTGG 57.540 43.478 12.26 0.00 0.00 3.86
1672 1706 7.095313 CCAAATGATGTAATAGCTGCTACTCTG 60.095 40.741 12.26 0.00 0.00 3.35
1673 1707 6.933521 CCAAATGATGTAATAGCTGCTACTCT 59.066 38.462 12.26 2.39 0.00 3.24
1674 1708 6.708054 ACCAAATGATGTAATAGCTGCTACTC 59.292 38.462 12.26 6.13 0.00 2.59
1675 1709 6.595682 ACCAAATGATGTAATAGCTGCTACT 58.404 36.000 12.26 3.22 0.00 2.57
1676 1710 6.483307 TGACCAAATGATGTAATAGCTGCTAC 59.517 38.462 12.26 2.54 0.00 3.58
1677 1711 6.591001 TGACCAAATGATGTAATAGCTGCTA 58.409 36.000 12.40 12.40 0.00 3.49
1678 1712 5.439721 TGACCAAATGATGTAATAGCTGCT 58.560 37.500 7.57 7.57 0.00 4.24
1679 1713 5.297776 ACTGACCAAATGATGTAATAGCTGC 59.702 40.000 0.00 0.00 0.00 5.25
1680 1714 6.722301 CACTGACCAAATGATGTAATAGCTG 58.278 40.000 0.00 0.00 0.00 4.24
1681 1715 5.297776 GCACTGACCAAATGATGTAATAGCT 59.702 40.000 0.00 0.00 0.00 3.32
1682 1716 5.066375 TGCACTGACCAAATGATGTAATAGC 59.934 40.000 0.00 0.00 0.00 2.97
1683 1717 6.317140 AGTGCACTGACCAAATGATGTAATAG 59.683 38.462 20.97 0.00 0.00 1.73
1684 1718 6.093909 CAGTGCACTGACCAAATGATGTAATA 59.906 38.462 38.12 0.00 46.59 0.98
1685 1719 5.012239 AGTGCACTGACCAAATGATGTAAT 58.988 37.500 20.97 0.00 0.00 1.89
1686 1720 4.216042 CAGTGCACTGACCAAATGATGTAA 59.784 41.667 38.12 0.00 46.59 2.41
1687 1721 3.752747 CAGTGCACTGACCAAATGATGTA 59.247 43.478 38.12 0.00 46.59 2.29
1688 1722 2.555325 CAGTGCACTGACCAAATGATGT 59.445 45.455 38.12 0.00 46.59 3.06
1702 1736 1.296715 CAGTAGGGGGTCAGTGCAC 59.703 63.158 9.40 9.40 0.00 4.57
1711 1745 6.928348 TGATAACATATGTACAGTAGGGGG 57.072 41.667 9.21 0.00 0.00 5.40
1712 1746 8.134202 TGATGATAACATATGTACAGTAGGGG 57.866 38.462 9.21 0.00 36.82 4.79
1713 1747 9.591792 CATGATGATAACATATGTACAGTAGGG 57.408 37.037 9.21 0.00 36.82 3.53
1714 1748 9.591792 CCATGATGATAACATATGTACAGTAGG 57.408 37.037 9.21 7.48 36.82 3.18
1750 1792 5.951148 TCAGGCATTGTTCCTTTGATTGATA 59.049 36.000 0.00 0.00 0.00 2.15
1751 1793 4.773674 TCAGGCATTGTTCCTTTGATTGAT 59.226 37.500 0.00 0.00 0.00 2.57
1752 1794 4.151121 TCAGGCATTGTTCCTTTGATTGA 58.849 39.130 0.00 0.00 0.00 2.57
1769 1811 1.135402 CCCGCTGTTTATTGTTCAGGC 60.135 52.381 0.00 0.00 0.00 4.85
1822 1864 4.854587 AGACTGCTCTTCCGGTCT 57.145 55.556 0.00 0.00 44.50 3.85
1862 1904 1.045911 AGGTCCGGAGAAGGATCAGC 61.046 60.000 3.06 0.00 43.79 4.26
1877 1919 1.137282 GTTTCCTCCGAGGATCAGGTC 59.863 57.143 18.16 2.41 45.34 3.85
1913 1968 2.343387 CTTTGCCGCCCCAAAAGG 59.657 61.111 0.00 0.00 34.59 3.11
1914 1969 2.357396 GCTTTGCCGCCCCAAAAG 60.357 61.111 0.00 0.00 34.59 2.27
1915 1970 2.841988 AGCTTTGCCGCCCCAAAA 60.842 55.556 0.00 0.00 34.59 2.44
1916 1971 3.614698 CAGCTTTGCCGCCCCAAA 61.615 61.111 0.00 0.00 33.93 3.28
1917 1972 4.912395 ACAGCTTTGCCGCCCCAA 62.912 61.111 0.00 0.00 0.00 4.12
1920 1975 2.265182 TTACACAGCTTTGCCGCCC 61.265 57.895 0.00 0.00 0.00 6.13
1921 1976 1.081442 GTTACACAGCTTTGCCGCC 60.081 57.895 0.00 0.00 0.00 6.13
1922 1977 1.081442 GGTTACACAGCTTTGCCGC 60.081 57.895 0.00 0.00 0.00 6.53
1923 1978 0.040425 GTGGTTACACAGCTTTGCCG 60.040 55.000 0.00 0.00 46.90 5.69
1961 2016 8.115490 AGTATATACGTCCAAACCAGGTATAC 57.885 38.462 7.23 0.00 32.59 1.47
1965 2021 5.945144 AAGTATATACGTCCAAACCAGGT 57.055 39.130 7.23 0.00 0.00 4.00
1967 2023 5.007332 GGCAAAGTATATACGTCCAAACCAG 59.993 44.000 7.23 0.00 0.00 4.00
1977 2033 2.409975 CGGGTGGGCAAAGTATATACG 58.590 52.381 7.23 0.00 0.00 3.06
2101 3955 3.416119 ACAAGCAATCAATCATCAGCG 57.584 42.857 0.00 0.00 0.00 5.18
2180 4052 1.375908 TCATCAGGCAAGCGTGTCC 60.376 57.895 13.59 2.78 33.97 4.02
2188 4060 2.359850 GCGGTGGTCATCAGGCAA 60.360 61.111 0.00 0.00 0.00 4.52
2214 4086 1.883084 CGCGGCTGCTTTAGGGTAG 60.883 63.158 17.03 0.00 39.65 3.18
2215 4087 1.682451 ATCGCGGCTGCTTTAGGGTA 61.682 55.000 17.03 0.00 39.65 3.69
2216 4088 1.682451 TATCGCGGCTGCTTTAGGGT 61.682 55.000 17.03 0.00 39.65 4.34
2217 4089 0.320771 ATATCGCGGCTGCTTTAGGG 60.321 55.000 17.03 0.00 39.65 3.53
2218 4090 1.071605 GATATCGCGGCTGCTTTAGG 58.928 55.000 17.03 0.00 39.65 2.69
2259 4131 1.998315 CTTCGTCCAGTTGCTCATCTG 59.002 52.381 1.90 1.90 0.00 2.90
2260 4132 1.895798 TCTTCGTCCAGTTGCTCATCT 59.104 47.619 0.00 0.00 0.00 2.90
2262 4134 2.499289 AGATCTTCGTCCAGTTGCTCAT 59.501 45.455 0.00 0.00 0.00 2.90
2263 4135 1.895798 AGATCTTCGTCCAGTTGCTCA 59.104 47.619 0.00 0.00 0.00 4.26
2264 4136 2.094494 TGAGATCTTCGTCCAGTTGCTC 60.094 50.000 0.00 0.00 0.00 4.26
2271 4155 2.890945 TGAACAGTGAGATCTTCGTCCA 59.109 45.455 0.00 0.00 0.00 4.02
2346 4230 4.978863 TACGGCGCAGTTGCAGCA 62.979 61.111 20.39 0.00 42.21 4.41
2509 4406 4.492160 GGCACGGATGAGACGCGA 62.492 66.667 15.93 0.00 34.00 5.87
2546 4443 4.456253 TCTTCTCGTCGGCGTCGC 62.456 66.667 20.97 9.22 39.49 5.19
2547 4444 2.573689 GTCTTCTCGTCGGCGTCG 60.574 66.667 19.85 19.85 39.49 5.12
2548 4445 2.573689 CGTCTTCTCGTCGGCGTC 60.574 66.667 10.18 0.00 39.49 5.19
2549 4446 4.755614 GCGTCTTCTCGTCGGCGT 62.756 66.667 10.18 0.00 39.49 5.68
2550 4447 4.753877 TGCGTCTTCTCGTCGGCG 62.754 66.667 1.15 1.15 39.92 6.46
2551 4448 3.173240 GTGCGTCTTCTCGTCGGC 61.173 66.667 0.00 0.00 0.00 5.54
2552 4449 2.870161 CGTGCGTCTTCTCGTCGG 60.870 66.667 0.00 0.00 0.00 4.79
2553 4450 3.524759 GCGTGCGTCTTCTCGTCG 61.525 66.667 0.00 0.00 35.25 5.12
2554 4451 3.173240 GGCGTGCGTCTTCTCGTC 61.173 66.667 0.00 0.00 0.00 4.20
2555 4452 4.719369 GGGCGTGCGTCTTCTCGT 62.719 66.667 0.00 0.00 0.00 4.18
2557 4454 4.373116 TGGGGCGTGCGTCTTCTC 62.373 66.667 0.00 0.00 0.00 2.87
2558 4455 4.681978 GTGGGGCGTGCGTCTTCT 62.682 66.667 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.