Multiple sequence alignment - TraesCS6D01G178600

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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 TraesCS6D01G178600 chr6D 100.000 2983 0 0 1 2983 187206604 187203622 0.000000e+00 5509.0
1 TraesCS6D01G178600 chr6B 91.121 1802 80 31 367 2138 298488573 298486822 0.000000e+00 2368.0
2 TraesCS6D01G178600 chr6B 95.089 448 22 0 2536 2983 298486373 298485926 0.000000e+00 706.0
3 TraesCS6D01G178600 chr6B 91.639 299 19 3 11 303 298489411 298489113 2.770000e-110 409.0
4 TraesCS6D01G178600 chr6B 89.668 271 15 5 2127 2384 298486734 298486464 1.710000e-87 333.0
5 TraesCS6D01G178600 chr6A 93.276 1636 47 20 530 2138 223978840 223980439 0.000000e+00 2353.0
6 TraesCS6D01G178600 chr6A 89.013 892 53 11 2127 2980 223980553 223981437 0.000000e+00 1062.0
7 TraesCS6D01G178600 chr6A 91.573 178 11 3 359 535 223973715 223973889 2.970000e-60 243.0
8 TraesCS6D01G178600 chr6A 92.982 57 2 2 307 361 426605971 426605915 6.850000e-12 82.4
9 TraesCS6D01G178600 chr7A 94.737 57 2 1 304 359 339540513 339540457 1.470000e-13 87.9
10 TraesCS6D01G178600 chr3D 93.220 59 3 1 304 361 42250389 42250331 5.300000e-13 86.1
11 TraesCS6D01G178600 chr5B 94.340 53 1 1 306 358 277248010 277248060 2.460000e-11 80.5
12 TraesCS6D01G178600 chr5B 80.000 105 12 3 2443 2538 57130064 57129960 5.340000e-08 69.4
13 TraesCS6D01G178600 chr3B 92.857 56 3 1 304 358 338780058 338780003 2.460000e-11 80.5
14 TraesCS6D01G178600 chr5D 91.228 57 4 1 304 359 453824680 453824736 3.190000e-10 76.8
15 TraesCS6D01G178600 chr7B 90.000 50 4 1 2442 2490 723962114 723962163 2.480000e-06 63.9
16 TraesCS6D01G178600 chr4B 100.000 29 0 0 2458 2486 449811452 449811424 1.000000e-03 54.7


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 TraesCS6D01G178600 chr6D 187203622 187206604 2982 True 5509.0 5509 100.00000 1 2983 1 chr6D.!!$R1 2982
1 TraesCS6D01G178600 chr6B 298485926 298489411 3485 True 954.0 2368 91.87925 11 2983 4 chr6B.!!$R1 2972
2 TraesCS6D01G178600 chr6A 223978840 223981437 2597 False 1707.5 2353 91.14450 530 2980 2 chr6A.!!$F2 2450


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
426 910 0.173481 TCAGATTTCGAGCCCTCACG 59.827 55.0 0.00 0.00 0.00 4.35 F
428 912 0.173708 AGATTTCGAGCCCTCACGAC 59.826 55.0 0.00 0.00 38.24 4.34 F
863 1359 0.381089 CTAGGAACCGGTCTGCTACG 59.619 60.0 8.04 4.41 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 2398 0.467290 TGGCCAACAAGAAGGACACC 60.467 55.0 0.61 0.00 38.22 4.16 R
1892 2409 1.118965 TCTCTCGGTGGCCAACAAGA 61.119 55.0 23.36 17.64 0.00 3.02 R
2627 3324 0.392706 TCACACCTGTACTGCAGTGG 59.607 55.0 29.57 23.13 43.55 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
63 64 2.202756 GTAAGCGAGCTCCACGGG 60.203 66.667 8.47 0.00 0.00 5.28
84 85 0.877649 GCTCATCGATGTCGCCACAT 60.878 55.000 24.09 0.00 46.64 3.21
119 120 4.131088 GTCGGGCGAGGAGGTGTC 62.131 72.222 0.00 0.00 0.00 3.67
194 195 0.475044 GTGACCCCAACCACTGGTTA 59.525 55.000 13.33 0.00 45.01 2.85
247 249 3.041946 GGCTGAGAGGAAGAAGGGATAA 58.958 50.000 0.00 0.00 0.00 1.75
251 253 5.588246 GCTGAGAGGAAGAAGGGATAAAAAG 59.412 44.000 0.00 0.00 0.00 2.27
264 271 7.929941 AGGGATAAAAAGAAATCAGAGTGAC 57.070 36.000 0.00 0.00 0.00 3.67
280 287 0.614979 TGACTAGCACTCCCACTCCC 60.615 60.000 0.00 0.00 0.00 4.30
303 310 2.634600 CCCGGGATCAACATCGTTTAA 58.365 47.619 18.48 0.00 0.00 1.52
304 311 2.353579 CCCGGGATCAACATCGTTTAAC 59.646 50.000 18.48 0.00 0.00 2.01
305 312 3.267483 CCGGGATCAACATCGTTTAACT 58.733 45.455 0.00 0.00 0.00 2.24
309 316 5.106869 CGGGATCAACATCGTTTAACTTTGA 60.107 40.000 0.00 0.00 0.00 2.69
310 317 6.314784 GGGATCAACATCGTTTAACTTTGAG 58.685 40.000 0.00 0.00 0.00 3.02
312 319 7.118680 GGGATCAACATCGTTTAACTTTGAGTA 59.881 37.037 0.00 0.00 0.00 2.59
313 320 8.500773 GGATCAACATCGTTTAACTTTGAGTAA 58.499 33.333 0.00 0.00 0.00 2.24
331 652 9.455144 TTTGAGTAATATATTTAGGTGGAGGGA 57.545 33.333 2.68 0.00 0.00 4.20
332 653 8.431910 TGAGTAATATATTTAGGTGGAGGGAC 57.568 38.462 2.68 0.00 0.00 4.46
346 667 4.722389 GGACTCCTCCCCGGTAAT 57.278 61.111 0.00 0.00 0.00 1.89
347 668 2.926539 GGACTCCTCCCCGGTAATT 58.073 57.895 0.00 0.00 0.00 1.40
348 669 0.757512 GGACTCCTCCCCGGTAATTC 59.242 60.000 0.00 0.00 0.00 2.17
349 670 1.691801 GGACTCCTCCCCGGTAATTCT 60.692 57.143 0.00 0.00 0.00 2.40
351 672 3.303049 GACTCCTCCCCGGTAATTCTAA 58.697 50.000 0.00 0.00 0.00 2.10
352 673 3.708121 GACTCCTCCCCGGTAATTCTAAA 59.292 47.826 0.00 0.00 0.00 1.85
353 674 4.106324 ACTCCTCCCCGGTAATTCTAAAA 58.894 43.478 0.00 0.00 0.00 1.52
354 675 4.537288 ACTCCTCCCCGGTAATTCTAAAAA 59.463 41.667 0.00 0.00 0.00 1.94
381 864 2.027469 CAGCGTTTAGGGTTTAGGGACT 60.027 50.000 0.00 0.00 46.37 3.85
391 874 3.076621 GGTTTAGGGACTGTAAAACCCG 58.923 50.000 12.18 0.00 44.48 5.28
403 887 0.250338 AAAACCCGGAGTGTGAGAGC 60.250 55.000 0.73 0.00 0.00 4.09
404 888 1.407656 AAACCCGGAGTGTGAGAGCA 61.408 55.000 0.73 0.00 0.00 4.26
405 889 1.407656 AACCCGGAGTGTGAGAGCAA 61.408 55.000 0.73 0.00 0.00 3.91
415 899 4.314121 AGTGTGAGAGCAAGTCAGATTTC 58.686 43.478 0.00 0.00 0.00 2.17
416 900 3.122613 GTGTGAGAGCAAGTCAGATTTCG 59.877 47.826 0.00 0.00 0.00 3.46
420 904 1.663135 GAGCAAGTCAGATTTCGAGCC 59.337 52.381 0.00 0.00 0.00 4.70
426 910 0.173481 TCAGATTTCGAGCCCTCACG 59.827 55.000 0.00 0.00 0.00 4.35
428 912 0.173708 AGATTTCGAGCCCTCACGAC 59.826 55.000 0.00 0.00 38.24 4.34
440 924 3.627577 GCCCTCACGACATCATATTGTTT 59.372 43.478 0.00 0.00 0.00 2.83
479 963 5.987777 TTTTAGATGAAAACAACGTCCGA 57.012 34.783 0.00 0.00 31.90 4.55
488 972 1.578583 ACAACGTCCGAGAAACCTTG 58.421 50.000 0.00 0.00 0.00 3.61
498 982 2.224314 CGAGAAACCTTGTGCCTTTCTC 59.776 50.000 8.64 8.64 43.29 2.87
501 985 3.117888 AGAAACCTTGTGCCTTTCTCTGA 60.118 43.478 0.00 0.00 29.98 3.27
516 1000 7.470900 CCTTTCTCTGATATTGAAAGCAGAAC 58.529 38.462 10.14 0.00 42.89 3.01
517 1001 6.992063 TTCTCTGATATTGAAAGCAGAACC 57.008 37.500 0.00 0.00 36.99 3.62
559 1044 1.162800 GCCATCCTGCTGGTTCGATC 61.163 60.000 9.73 0.00 38.63 3.69
571 1065 2.948979 TGGTTCGATCAAAAAGCACTGT 59.051 40.909 0.00 0.00 0.00 3.55
739 1233 3.670627 GCGTTAGGCCAAAAGAACATCAG 60.671 47.826 5.01 0.00 34.80 2.90
740 1234 3.751175 CGTTAGGCCAAAAGAACATCAGA 59.249 43.478 5.01 0.00 0.00 3.27
743 1237 6.512297 GTTAGGCCAAAAGAACATCAGAAAA 58.488 36.000 5.01 0.00 0.00 2.29
744 1238 4.948847 AGGCCAAAAGAACATCAGAAAAC 58.051 39.130 5.01 0.00 0.00 2.43
745 1239 3.735746 GGCCAAAAGAACATCAGAAAACG 59.264 43.478 0.00 0.00 0.00 3.60
863 1359 0.381089 CTAGGAACCGGTCTGCTACG 59.619 60.000 8.04 4.41 0.00 3.51
879 1375 5.538813 TCTGCTACGATCCAAACCATATACT 59.461 40.000 0.00 0.00 0.00 2.12
880 1376 5.538118 TGCTACGATCCAAACCATATACTG 58.462 41.667 0.00 0.00 0.00 2.74
882 1378 6.265876 TGCTACGATCCAAACCATATACTGTA 59.734 38.462 0.00 0.00 0.00 2.74
883 1379 6.585322 GCTACGATCCAAACCATATACTGTAC 59.415 42.308 0.00 0.00 0.00 2.90
884 1380 6.726490 ACGATCCAAACCATATACTGTACT 57.274 37.500 0.00 0.00 0.00 2.73
885 1381 7.120923 ACGATCCAAACCATATACTGTACTT 57.879 36.000 0.00 0.00 0.00 2.24
886 1382 8.241497 ACGATCCAAACCATATACTGTACTTA 57.759 34.615 0.00 0.00 0.00 2.24
887 1383 8.139989 ACGATCCAAACCATATACTGTACTTAC 58.860 37.037 0.00 0.00 0.00 2.34
888 1384 8.358148 CGATCCAAACCATATACTGTACTTACT 58.642 37.037 0.00 0.00 0.00 2.24
954 1450 0.796312 CGATCAACACTTGGAACCCG 59.204 55.000 0.00 0.00 0.00 5.28
1427 1929 2.930019 CAGCCACCTGGTCCTCCA 60.930 66.667 0.00 0.00 42.05 3.86
1474 1976 1.677637 GCTACACCCCCTCCTTCTCG 61.678 65.000 0.00 0.00 0.00 4.04
1483 1985 0.745845 CCTCCTTCTCGGCATTGGTG 60.746 60.000 0.00 0.00 0.00 4.17
1782 2292 1.913685 CGCGCGTCTTGATCTTCTC 59.086 57.895 24.19 0.00 0.00 2.87
1839 2349 6.527423 TCTTGTAGTAGGATTTTTGACGGTT 58.473 36.000 0.00 0.00 0.00 4.44
1841 2351 6.548441 TGTAGTAGGATTTTTGACGGTTTG 57.452 37.500 0.00 0.00 0.00 2.93
1843 2353 6.543100 TGTAGTAGGATTTTTGACGGTTTGTT 59.457 34.615 0.00 0.00 0.00 2.83
1844 2354 6.459670 AGTAGGATTTTTGACGGTTTGTTT 57.540 33.333 0.00 0.00 0.00 2.83
1845 2355 6.270064 AGTAGGATTTTTGACGGTTTGTTTG 58.730 36.000 0.00 0.00 0.00 2.93
1855 2369 2.223618 ACGGTTTGTTTGTGTGGCATAC 60.224 45.455 7.51 7.51 0.00 2.39
1861 2375 2.803386 TGTTTGTGTGGCATACGTACAG 59.197 45.455 14.29 0.00 32.72 2.74
1881 2395 2.543687 TAGTGTGAGCGGCGCTTCTC 62.544 60.000 36.73 27.81 39.88 2.87
1884 2398 4.441695 TGAGCGGCGCTTCTCCTG 62.442 66.667 36.73 0.00 39.88 3.86
1892 2409 1.674057 CGCTTCTCCTGGTGTCCTT 59.326 57.895 0.00 0.00 0.00 3.36
1908 2425 1.237285 CCTTCTTGTTGGCCACCGAG 61.237 60.000 11.34 11.34 0.00 4.63
1916 2433 1.768684 TTGGCCACCGAGAGAAGCTT 61.769 55.000 3.88 0.00 0.00 3.74
1918 2435 2.394563 GCCACCGAGAGAAGCTTGC 61.395 63.158 2.10 0.00 0.00 4.01
1952 2469 5.396436 CCTTGTACATACGGATCCTTTCCTT 60.396 44.000 10.75 0.00 42.99 3.36
1961 2478 3.681874 CGGATCCTTTCCTTCCCTTGTAC 60.682 52.174 10.75 0.00 42.99 2.90
1966 2483 3.010138 CCTTTCCTTCCCTTGTACCATCA 59.990 47.826 0.00 0.00 0.00 3.07
1970 2487 3.455910 TCCTTCCCTTGTACCATCATCTG 59.544 47.826 0.00 0.00 0.00 2.90
1971 2488 3.209410 CTTCCCTTGTACCATCATCTGC 58.791 50.000 0.00 0.00 0.00 4.26
1972 2489 2.481441 TCCCTTGTACCATCATCTGCT 58.519 47.619 0.00 0.00 0.00 4.24
2041 2565 8.851960 AATGACATACACATACTGTTACTACG 57.148 34.615 0.00 0.00 33.91 3.51
2198 2847 3.572604 AGTTCGCTAGTACAGTTGGTC 57.427 47.619 0.00 0.00 0.00 4.02
2217 2866 3.868077 GGTCAGCTGAAATGCTAGTACAG 59.132 47.826 20.19 0.00 41.98 2.74
2222 2871 3.372206 GCTGAAATGCTAGTACAGGTGTG 59.628 47.826 0.00 0.00 0.00 3.82
2223 2872 3.334691 TGAAATGCTAGTACAGGTGTGC 58.665 45.455 0.00 0.00 0.00 4.57
2224 2873 2.010145 AATGCTAGTACAGGTGTGCG 57.990 50.000 0.00 0.00 35.74 5.34
2340 3005 4.572389 AGCACAATCATCATCTTCGGTTAC 59.428 41.667 0.00 0.00 0.00 2.50
2343 3008 6.622679 GCACAATCATCATCTTCGGTTACAAA 60.623 38.462 0.00 0.00 0.00 2.83
2358 3023 1.808411 ACAAACATTCGGCGTGATCT 58.192 45.000 6.85 0.00 0.00 2.75
2446 3134 7.517417 CGAATCATGCACTCTGTTCCTAAATAC 60.517 40.741 0.00 0.00 0.00 1.89
2450 3138 5.974108 TGCACTCTGTTCCTAAATACTACC 58.026 41.667 0.00 0.00 0.00 3.18
2454 3142 5.593502 ACTCTGTTCCTAAATACTACCTCCG 59.406 44.000 0.00 0.00 0.00 4.63
2457 3145 6.096001 TCTGTTCCTAAATACTACCTCCGTTC 59.904 42.308 0.00 0.00 0.00 3.95
2458 3146 5.954150 TGTTCCTAAATACTACCTCCGTTCT 59.046 40.000 0.00 0.00 0.00 3.01
2472 3160 9.379791 CTACCTCCGTTCTAAAATAAATGTCTT 57.620 33.333 0.00 0.00 0.00 3.01
2523 3211 6.329496 ACTTGAAACACATATTTTATGGCGG 58.671 36.000 0.10 0.00 0.00 6.13
2525 3213 6.130298 TGAAACACATATTTTATGGCGGAG 57.870 37.500 0.10 0.00 0.00 4.63
2526 3214 5.067153 TGAAACACATATTTTATGGCGGAGG 59.933 40.000 0.10 0.00 0.00 4.30
2527 3215 3.486383 ACACATATTTTATGGCGGAGGG 58.514 45.455 0.10 0.00 0.00 4.30
2528 3216 3.137544 ACACATATTTTATGGCGGAGGGA 59.862 43.478 0.10 0.00 0.00 4.20
2572 3263 6.879276 AGCAGTTCAAATCATCTGGATATG 57.121 37.500 0.00 0.00 34.28 1.78
2666 3363 1.048601 TTCTGCCCGTCACTTCTTCT 58.951 50.000 0.00 0.00 0.00 2.85
2703 3400 1.786441 TCATTCCCCAACTGTTCCCTT 59.214 47.619 0.00 0.00 0.00 3.95
2741 3438 1.408702 TCAAGCCCACACAGAAAAAGC 59.591 47.619 0.00 0.00 0.00 3.51
2751 3448 0.033920 CAGAAAAAGCAGGTTGGGCC 59.966 55.000 0.00 0.00 37.58 5.80
2830 3527 8.242729 ACTTGAATTCTCCATGACTTCTTTTT 57.757 30.769 7.05 0.00 35.95 1.94
2881 3578 4.342665 GGGTTTCTACTCCTAGTGAGATGG 59.657 50.000 13.28 5.11 44.42 3.51
2882 3579 4.202172 GGTTTCTACTCCTAGTGAGATGGC 60.202 50.000 13.28 0.00 44.42 4.40
2894 3591 1.953231 GAGATGGCCTGCCTTTTGCC 61.953 60.000 9.97 0.00 45.56 4.52
2980 3677 4.026558 CGACAATCATCTTCACGTATGTGG 60.027 45.833 15.02 0.25 46.42 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.455682 GCGCTATCTCTTCTGTAACTAGATAAT 58.544 37.037 0.00 0.00 30.84 1.28
2 3 7.444487 TGCGCTATCTCTTCTGTAACTAGATAA 59.556 37.037 9.73 0.00 30.84 1.75
3 4 6.935208 TGCGCTATCTCTTCTGTAACTAGATA 59.065 38.462 9.73 0.00 0.00 1.98
4 5 5.765677 TGCGCTATCTCTTCTGTAACTAGAT 59.234 40.000 9.73 0.00 0.00 1.98
5 6 5.123936 TGCGCTATCTCTTCTGTAACTAGA 58.876 41.667 9.73 0.00 0.00 2.43
6 7 5.425577 TGCGCTATCTCTTCTGTAACTAG 57.574 43.478 9.73 0.00 0.00 2.57
7 8 5.531287 TGATGCGCTATCTCTTCTGTAACTA 59.469 40.000 9.73 0.00 36.71 2.24
8 9 4.339530 TGATGCGCTATCTCTTCTGTAACT 59.660 41.667 9.73 0.00 36.71 2.24
9 10 4.611943 TGATGCGCTATCTCTTCTGTAAC 58.388 43.478 9.73 0.00 36.71 2.50
60 61 1.371022 CGACATCGATGAGCTCCCG 60.371 63.158 31.33 17.99 43.02 5.14
63 64 1.066422 TGGCGACATCGATGAGCTC 59.934 57.895 32.16 25.80 43.02 4.09
70 71 1.671901 TAGGCATGTGGCGACATCGA 61.672 55.000 11.83 0.00 46.14 3.59
71 72 0.809636 TTAGGCATGTGGCGACATCG 60.810 55.000 11.83 8.82 46.14 3.84
84 85 2.434185 CGCTCGCAAGGTTAGGCA 60.434 61.111 0.00 0.00 38.47 4.75
136 137 1.384643 CCTCTAGGGGAAGGGGTGG 60.385 68.421 0.73 0.00 31.85 4.61
137 138 4.401657 CCTCTAGGGGAAGGGGTG 57.598 66.667 0.73 0.00 31.85 4.61
149 150 3.000819 CCACGGTGGTGCCCTCTA 61.001 66.667 19.15 0.00 43.00 2.43
161 162 1.577328 GGTCACTGTTCATGCCACGG 61.577 60.000 2.90 2.90 0.00 4.94
162 163 1.577328 GGGTCACTGTTCATGCCACG 61.577 60.000 0.00 0.00 0.00 4.94
194 195 3.241530 TGGCCGCTCTCACCTTGT 61.242 61.111 0.00 0.00 0.00 3.16
247 249 6.793492 GTGCTAGTCACTCTGATTTCTTTT 57.207 37.500 9.26 0.00 42.38 2.27
264 271 2.427245 CGGGGAGTGGGAGTGCTAG 61.427 68.421 0.00 0.00 0.00 3.42
280 287 2.591715 GATGTTGATCCCGGGCGG 60.592 66.667 18.49 0.00 0.00 6.13
304 311 9.726438 CCCTCCACCTAAATATATTACTCAAAG 57.274 37.037 0.00 0.00 0.00 2.77
305 312 9.455144 TCCCTCCACCTAAATATATTACTCAAA 57.545 33.333 0.00 0.00 0.00 2.69
309 316 8.667592 GAGTCCCTCCACCTAAATATATTACT 57.332 38.462 0.00 0.00 0.00 2.24
331 652 3.409804 TTAGAATTACCGGGGAGGAGT 57.590 47.619 6.32 0.00 45.00 3.85
332 653 4.765813 TTTTAGAATTACCGGGGAGGAG 57.234 45.455 6.32 0.00 45.00 3.69
355 676 4.038282 CCCTAAACCCTAAACGCTGTTTTT 59.962 41.667 10.96 3.69 33.36 1.94
356 677 3.570975 CCCTAAACCCTAAACGCTGTTTT 59.429 43.478 10.96 0.00 33.36 2.43
357 678 3.151554 CCCTAAACCCTAAACGCTGTTT 58.848 45.455 10.61 10.61 35.32 2.83
360 681 2.027469 AGTCCCTAAACCCTAAACGCTG 60.027 50.000 0.00 0.00 0.00 5.18
361 682 2.027469 CAGTCCCTAAACCCTAAACGCT 60.027 50.000 0.00 0.00 0.00 5.07
362 683 2.289882 ACAGTCCCTAAACCCTAAACGC 60.290 50.000 0.00 0.00 0.00 4.84
363 684 3.690475 ACAGTCCCTAAACCCTAAACG 57.310 47.619 0.00 0.00 0.00 3.60
364 685 6.207417 GGTTTTACAGTCCCTAAACCCTAAAC 59.793 42.308 0.00 0.00 42.22 2.01
365 686 6.306199 GGTTTTACAGTCCCTAAACCCTAAA 58.694 40.000 0.00 0.00 42.22 1.85
371 854 3.076621 CCGGGTTTTACAGTCCCTAAAC 58.923 50.000 0.00 0.00 39.10 2.01
381 864 2.036733 CTCTCACACTCCGGGTTTTACA 59.963 50.000 0.00 0.00 0.00 2.41
391 874 1.615883 TCTGACTTGCTCTCACACTCC 59.384 52.381 0.00 0.00 0.00 3.85
403 887 2.275318 GAGGGCTCGAAATCTGACTTG 58.725 52.381 0.00 0.00 0.00 3.16
404 888 1.902508 TGAGGGCTCGAAATCTGACTT 59.097 47.619 0.00 0.00 0.00 3.01
405 889 1.205893 GTGAGGGCTCGAAATCTGACT 59.794 52.381 0.00 0.00 0.00 3.41
415 899 0.668535 TATGATGTCGTGAGGGCTCG 59.331 55.000 0.00 0.00 0.00 5.03
416 900 3.062763 CAATATGATGTCGTGAGGGCTC 58.937 50.000 0.00 0.00 0.00 4.70
420 904 6.037062 TGCTTAAACAATATGATGTCGTGAGG 59.963 38.462 0.00 0.00 31.81 3.86
426 910 7.489113 CCAAACCTGCTTAAACAATATGATGTC 59.511 37.037 0.00 0.00 31.81 3.06
428 912 6.256321 GCCAAACCTGCTTAAACAATATGATG 59.744 38.462 0.00 0.00 0.00 3.07
440 924 7.559533 TCATCTAAAATATGCCAAACCTGCTTA 59.440 33.333 0.00 0.00 0.00 3.09
479 963 3.117888 TCAGAGAAAGGCACAAGGTTTCT 60.118 43.478 0.00 0.00 42.02 2.52
488 972 5.124457 TGCTTTCAATATCAGAGAAAGGCAC 59.876 40.000 13.88 1.46 45.09 5.01
498 982 4.096984 GGTGGGTTCTGCTTTCAATATCAG 59.903 45.833 0.00 0.00 0.00 2.90
501 985 3.016736 CGGTGGGTTCTGCTTTCAATAT 58.983 45.455 0.00 0.00 0.00 1.28
559 1044 3.636764 AGGGGTTTCTACAGTGCTTTTTG 59.363 43.478 0.00 0.00 0.00 2.44
571 1065 2.543635 GTGGGAGTGTAGGGGTTTCTA 58.456 52.381 0.00 0.00 0.00 2.10
739 1233 3.466836 CTCGGTTCATTCGTTCGTTTTC 58.533 45.455 0.00 0.00 0.00 2.29
740 1234 2.349155 GCTCGGTTCATTCGTTCGTTTT 60.349 45.455 0.00 0.00 0.00 2.43
743 1237 0.038526 AGCTCGGTTCATTCGTTCGT 60.039 50.000 0.00 0.00 0.00 3.85
744 1238 0.640768 GAGCTCGGTTCATTCGTTCG 59.359 55.000 0.00 0.00 0.00 3.95
745 1239 1.390463 GTGAGCTCGGTTCATTCGTTC 59.610 52.381 9.64 0.00 0.00 3.95
879 1375 5.819379 ACGCTGCTACAGTATAGTAAGTACA 59.181 40.000 0.00 0.00 33.43 2.90
880 1376 6.134730 CACGCTGCTACAGTATAGTAAGTAC 58.865 44.000 0.00 0.00 33.43 2.73
882 1378 4.497674 GCACGCTGCTACAGTATAGTAAGT 60.498 45.833 0.00 0.00 40.96 2.24
883 1379 3.975670 GCACGCTGCTACAGTATAGTAAG 59.024 47.826 0.00 0.00 40.96 2.34
884 1380 3.379057 TGCACGCTGCTACAGTATAGTAA 59.621 43.478 10.54 0.00 45.31 2.24
885 1381 2.946990 TGCACGCTGCTACAGTATAGTA 59.053 45.455 10.54 0.00 45.31 1.82
886 1382 1.749063 TGCACGCTGCTACAGTATAGT 59.251 47.619 10.54 0.00 45.31 2.12
887 1383 2.120232 GTGCACGCTGCTACAGTATAG 58.880 52.381 0.00 0.00 45.31 1.31
888 1384 1.202371 GGTGCACGCTGCTACAGTATA 60.202 52.381 11.45 0.00 45.31 1.47
954 1450 5.147330 AGCCTTTTTATAAAAGTGGGTGC 57.853 39.130 23.69 15.56 34.88 5.01
1004 1500 2.456119 GCGTGAGGAACTGATGGCG 61.456 63.158 0.00 0.00 41.55 5.69
1072 1568 0.392461 TTGGCATCTTGTACCGCTCC 60.392 55.000 0.00 0.00 0.00 4.70
1079 1575 2.846206 ACCTCTCCATTGGCATCTTGTA 59.154 45.455 0.00 0.00 0.00 2.41
1342 1844 0.621082 AGAAAGGCTTGTAGGAGGCC 59.379 55.000 0.00 0.00 45.57 5.19
1474 1976 1.586154 CCTCGTTGTCCACCAATGCC 61.586 60.000 0.00 0.00 39.49 4.40
1508 2016 4.796231 CTCGTCCGTCTTGGCCGG 62.796 72.222 0.00 0.00 46.83 6.13
1509 2017 4.796231 CCTCGTCCGTCTTGGCCG 62.796 72.222 0.00 0.00 37.80 6.13
1512 2020 4.796231 CCGCCTCGTCCGTCTTGG 62.796 72.222 0.00 0.00 40.09 3.61
1513 2021 3.685214 CTCCGCCTCGTCCGTCTTG 62.685 68.421 0.00 0.00 0.00 3.02
1678 2186 1.028868 GCAGAGCAACCTGGATGGAC 61.029 60.000 0.00 0.00 39.71 4.02
1719 2228 1.516161 TAGCTCAGCTGCACAACAAG 58.484 50.000 10.31 0.00 40.10 3.16
1720 2229 2.189594 ATAGCTCAGCTGCACAACAA 57.810 45.000 10.31 0.00 40.10 2.83
1721 2230 2.028203 TGTATAGCTCAGCTGCACAACA 60.028 45.455 10.31 3.38 40.10 3.33
1782 2292 1.077858 GGAGGAAGCAGAAGGGCAG 60.078 63.158 0.00 0.00 35.83 4.85
1839 2349 3.203716 TGTACGTATGCCACACAAACAA 58.796 40.909 0.00 0.00 0.00 2.83
1841 2351 2.803956 ACTGTACGTATGCCACACAAAC 59.196 45.455 0.00 0.00 0.00 2.93
1843 2353 2.823924 ACTGTACGTATGCCACACAA 57.176 45.000 0.00 0.00 0.00 3.33
1844 2354 2.821378 ACTACTGTACGTATGCCACACA 59.179 45.455 0.00 0.00 0.00 3.72
1845 2355 3.176708 CACTACTGTACGTATGCCACAC 58.823 50.000 0.00 0.00 0.00 3.82
1855 2369 0.797249 GCCGCTCACACTACTGTACG 60.797 60.000 0.00 0.00 0.00 3.67
1861 2375 2.432628 AAGCGCCGCTCACACTAC 60.433 61.111 14.01 0.00 38.25 2.73
1881 2395 1.609208 CCAACAAGAAGGACACCAGG 58.391 55.000 0.00 0.00 0.00 4.45
1884 2398 0.467290 TGGCCAACAAGAAGGACACC 60.467 55.000 0.61 0.00 38.22 4.16
1892 2409 1.118965 TCTCTCGGTGGCCAACAAGA 61.119 55.000 23.36 17.64 0.00 3.02
1908 2425 1.265365 GACAACACAGGCAAGCTTCTC 59.735 52.381 0.00 0.00 0.00 2.87
1916 2433 1.210722 TGTACAAGGACAACACAGGCA 59.789 47.619 0.00 0.00 0.00 4.75
1918 2435 3.678072 CGTATGTACAAGGACAACACAGG 59.322 47.826 0.00 0.00 31.83 4.00
1961 2478 8.715998 GTGTCTATATTACAAAGCAGATGATGG 58.284 37.037 0.00 0.00 0.00 3.51
2041 2565 4.585162 ACATGGCCAGTATGTAGTCTAGTC 59.415 45.833 13.05 0.00 37.02 2.59
2198 2847 3.620374 CACCTGTACTAGCATTTCAGCTG 59.380 47.826 7.63 7.63 46.11 4.24
2340 3005 1.202065 CCAGATCACGCCGAATGTTTG 60.202 52.381 0.00 0.00 0.00 2.93
2343 3008 1.815421 GCCAGATCACGCCGAATGT 60.815 57.895 0.00 0.00 0.00 2.71
2358 3023 1.377202 GAGAAATCCCACAGCGCCA 60.377 57.895 2.29 0.00 0.00 5.69
2446 3134 8.943909 AGACATTTATTTTAGAACGGAGGTAG 57.056 34.615 0.00 0.00 0.00 3.18
2497 3185 7.330700 CCGCCATAAAATATGTGTTTCAAGTTT 59.669 33.333 0.00 0.00 0.00 2.66
2505 3193 3.888930 CCCTCCGCCATAAAATATGTGTT 59.111 43.478 0.00 0.00 0.00 3.32
2510 3198 7.504926 TTATACTCCCTCCGCCATAAAATAT 57.495 36.000 0.00 0.00 0.00 1.28
2516 3204 8.063153 TCTTATATTTATACTCCCTCCGCCATA 58.937 37.037 0.00 0.00 0.00 2.74
2518 3206 6.154021 GTCTTATATTTATACTCCCTCCGCCA 59.846 42.308 0.00 0.00 0.00 5.69
2520 3208 6.127786 ACGTCTTATATTTATACTCCCTCCGC 60.128 42.308 0.00 0.00 0.00 5.54
2525 3213 9.786105 GCTAGAACGTCTTATATTTATACTCCC 57.214 37.037 0.00 0.00 0.00 4.30
2627 3324 0.392706 TCACACCTGTACTGCAGTGG 59.607 55.000 29.57 23.13 43.55 4.00
2632 3329 1.734465 GCAGAATCACACCTGTACTGC 59.266 52.381 0.00 0.00 41.33 4.40
2666 3363 2.655090 TGACCTGGTCAAATTGCTCA 57.345 45.000 26.54 0.75 39.78 4.26
2751 3448 2.719739 ACTGAGCAATCACCCATTCAG 58.280 47.619 0.00 0.00 38.34 3.02
2894 3591 2.230992 TCCCAAATGGTTCAAGCAATCG 59.769 45.455 0.00 0.00 34.77 3.34



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

AutoCloner maintained by Alex Coulton.