Multiple sequence alignment - TraesCS1A01G061400

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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 TraesCS1A01G061400 chr1A 100.000 2607 0 0 1 2607 41918117 41920723 0.000000e+00 4815.0
1 TraesCS1A01G061400 chr1A 90.566 53 5 0 2185 2237 41907816 41907868 1.290000e-08 71.3
2 TraesCS1A01G061400 chr1D 91.642 1675 91 23 842 2478 41914539 41916202 0.000000e+00 2272.0
3 TraesCS1A01G061400 chr1D 85.970 335 30 10 526 855 41913103 41913425 2.480000e-90 342.0
4 TraesCS1A01G061400 chr1D 80.861 418 58 16 61 459 41912187 41912601 2.520000e-80 309.0
5 TraesCS1A01G061400 chr1D 94.231 104 6 0 2504 2607 41922043 41922146 2.690000e-35 159.0
6 TraesCS1A01G061400 chr1D 83.133 166 22 5 2290 2455 41863376 41863535 2.090000e-31 147.0
7 TraesCS1A01G061400 chr1D 84.127 63 8 2 179 240 494341759 494341820 2.800000e-05 60.2
8 TraesCS1A01G061400 chr1B 94.616 1263 54 7 853 2111 62284286 62285538 0.000000e+00 1943.0
9 TraesCS1A01G061400 chr1B 93.385 514 19 4 2109 2607 62285699 62286212 0.000000e+00 747.0
10 TraesCS1A01G061400 chr1B 82.872 397 39 14 464 855 62281017 62281389 1.930000e-86 329.0
11 TraesCS1A01G061400 chr1B 81.250 304 41 11 2312 2607 62003027 62003322 5.610000e-57 231.0
12 TraesCS1A01G061400 chr1B 82.000 150 20 6 2285 2432 62059398 62059542 1.270000e-23 121.0
13 TraesCS1A01G061400 chr1B 91.304 46 4 0 1 46 35401584 35401539 2.170000e-06 63.9
14 TraesCS1A01G061400 chr1B 85.714 56 2 2 2396 2447 61965312 61965365 1.000000e-03 54.7
15 TraesCS1A01G061400 chr4D 76.238 202 37 11 181 375 11293804 11294001 2.140000e-16 97.1
16 TraesCS1A01G061400 chrUn 86.765 68 5 3 178 243 340042920 340042985 3.600000e-09 73.1
17 TraesCS1A01G061400 chrUn 86.765 68 5 3 178 243 340045473 340045538 3.600000e-09 73.1
18 TraesCS1A01G061400 chrUn 86.765 68 5 3 178 243 449632508 449632443 3.600000e-09 73.1
19 TraesCS1A01G061400 chr7D 87.500 64 6 2 1 63 454844236 454844174 3.600000e-09 73.1
20 TraesCS1A01G061400 chr2A 91.304 46 4 0 1 46 137925327 137925372 2.170000e-06 63.9
21 TraesCS1A01G061400 chr2A 89.362 47 3 2 1 46 56944739 56944694 1.010000e-04 58.4
22 TraesCS1A01G061400 chr2D 100.000 30 0 0 17 46 39439448 39439477 3.620000e-04 56.5


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 TraesCS1A01G061400 chr1A 41918117 41920723 2606 False 4815.000000 4815 100.000000 1 2607 1 chr1A.!!$F2 2606
1 TraesCS1A01G061400 chr1D 41912187 41916202 4015 False 974.333333 2272 86.157667 61 2478 3 chr1D.!!$F4 2417
2 TraesCS1A01G061400 chr1B 62281017 62286212 5195 False 1006.333333 1943 90.291000 464 2607 3 chr1B.!!$F4 2143

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
20 21 0.036306 ATGGTGTCTTCGTTGGACCC 59.964 55.0 0.0 0.0 33.22 4.46 F
318 341 0.099791 CGCGGGTTGCCGAAATATTT 59.900 50.0 0.0 0.0 42.08 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1506 5119 0.748450 CGGGTTAATCTACCTCGGCA 59.252 55.0 0.00 0.0 38.3 5.69 R
2168 5954 0.328258 ACTCTTTGGGCGTGCCTTAT 59.672 50.0 11.25 0.0 36.1 1.73 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
19 20 1.156736 CATGGTGTCTTCGTTGGACC 58.843 55.000 0.00 0.00 33.22 4.46
20 21 0.036306 ATGGTGTCTTCGTTGGACCC 59.964 55.000 0.00 0.00 33.22 4.46
21 22 1.338890 TGGTGTCTTCGTTGGACCCA 61.339 55.000 0.00 0.00 34.30 4.51
22 23 0.036306 GGTGTCTTCGTTGGACCCAT 59.964 55.000 0.00 0.00 33.22 4.00
23 24 1.156736 GTGTCTTCGTTGGACCCATG 58.843 55.000 0.00 0.00 33.22 3.66
24 25 0.762418 TGTCTTCGTTGGACCCATGT 59.238 50.000 0.00 0.00 33.22 3.21
25 26 1.972075 TGTCTTCGTTGGACCCATGTA 59.028 47.619 0.00 0.00 33.22 2.29
26 27 2.028476 TGTCTTCGTTGGACCCATGTAG 60.028 50.000 0.00 0.00 33.22 2.74
27 28 1.553248 TCTTCGTTGGACCCATGTAGG 59.447 52.381 0.00 0.00 37.03 3.18
41 42 5.993748 CCATGTAGGGTGTGGTAAAAATT 57.006 39.130 0.00 0.00 0.00 1.82
42 43 6.353404 CCATGTAGGGTGTGGTAAAAATTT 57.647 37.500 0.00 0.00 0.00 1.82
43 44 6.162777 CCATGTAGGGTGTGGTAAAAATTTG 58.837 40.000 0.00 0.00 0.00 2.32
44 45 6.015010 CCATGTAGGGTGTGGTAAAAATTTGA 60.015 38.462 0.00 0.00 0.00 2.69
45 46 6.642707 TGTAGGGTGTGGTAAAAATTTGAG 57.357 37.500 0.00 0.00 0.00 3.02
46 47 5.536916 TGTAGGGTGTGGTAAAAATTTGAGG 59.463 40.000 0.00 0.00 0.00 3.86
47 48 4.810345 AGGGTGTGGTAAAAATTTGAGGA 58.190 39.130 0.00 0.00 0.00 3.71
48 49 4.587262 AGGGTGTGGTAAAAATTTGAGGAC 59.413 41.667 0.00 0.00 0.00 3.85
49 50 4.587262 GGGTGTGGTAAAAATTTGAGGACT 59.413 41.667 0.00 0.00 0.00 3.85
50 51 5.069914 GGGTGTGGTAAAAATTTGAGGACTT 59.930 40.000 0.00 0.00 0.00 3.01
51 52 5.983118 GGTGTGGTAAAAATTTGAGGACTTG 59.017 40.000 0.00 0.00 0.00 3.16
52 53 6.183360 GGTGTGGTAAAAATTTGAGGACTTGA 60.183 38.462 0.00 0.00 0.00 3.02
53 54 7.433680 GTGTGGTAAAAATTTGAGGACTTGAT 58.566 34.615 0.00 0.00 0.00 2.57
54 55 7.382218 GTGTGGTAAAAATTTGAGGACTTGATG 59.618 37.037 0.00 0.00 0.00 3.07
55 56 6.868339 GTGGTAAAAATTTGAGGACTTGATGG 59.132 38.462 0.00 0.00 0.00 3.51
56 57 6.780031 TGGTAAAAATTTGAGGACTTGATGGA 59.220 34.615 0.00 0.00 0.00 3.41
57 58 7.288852 TGGTAAAAATTTGAGGACTTGATGGAA 59.711 33.333 0.00 0.00 0.00 3.53
58 59 8.147704 GGTAAAAATTTGAGGACTTGATGGAAA 58.852 33.333 0.00 0.00 0.00 3.13
59 60 9.541143 GTAAAAATTTGAGGACTTGATGGAAAA 57.459 29.630 0.00 0.00 0.00 2.29
83 84 1.344763 ACTCTCCGGTGAAGTTTCAGG 59.655 52.381 7.75 0.00 37.98 3.86
93 94 3.375922 GTGAAGTTTCAGGGTTTCGAACA 59.624 43.478 0.00 0.00 37.98 3.18
106 107 0.834612 TCGAACAGAAACCACCACCT 59.165 50.000 0.00 0.00 0.00 4.00
111 112 0.754957 CAGAAACCACCACCTGCCAA 60.755 55.000 0.00 0.00 0.00 4.52
113 114 0.104120 GAAACCACCACCTGCCAAAC 59.896 55.000 0.00 0.00 0.00 2.93
119 120 0.534873 ACCACCTGCCAAACACAAAC 59.465 50.000 0.00 0.00 0.00 2.93
128 129 5.355350 CCTGCCAAACACAAACCAATTTTTA 59.645 36.000 0.00 0.00 0.00 1.52
154 155 7.352079 ACATCATTTCAACTTCTTCAAACCT 57.648 32.000 0.00 0.00 0.00 3.50
234 256 8.514330 TTTTAAGCACTTTTCTGGACTTAAGA 57.486 30.769 10.09 0.00 32.84 2.10
248 270 1.873591 CTTAAGATATGTGTGGCGGGC 59.126 52.381 0.00 0.00 0.00 6.13
266 288 2.789249 GGCCGATACCGTTGCAAC 59.211 61.111 19.89 19.89 0.00 4.17
268 290 3.086309 CCGATACCGTTGCAACCG 58.914 61.111 23.42 19.08 0.00 4.44
269 291 1.738830 CCGATACCGTTGCAACCGT 60.739 57.895 23.62 23.62 0.00 4.83
274 297 2.237393 TACCGTTGCAACCGTAAAGT 57.763 45.000 22.92 13.95 0.00 2.66
283 306 4.174762 TGCAACCGTAAAGTTTTGGAAAC 58.825 39.130 12.17 0.00 0.00 2.78
288 311 6.519679 ACCGTAAAGTTTTGGAAACTTTCT 57.480 33.333 25.90 12.74 44.50 2.52
290 313 7.475015 ACCGTAAAGTTTTGGAAACTTTCTAC 58.525 34.615 25.90 20.18 44.50 2.59
293 316 9.511144 CGTAAAGTTTTGGAAACTTTCTACAAT 57.489 29.630 25.90 10.55 44.50 2.71
304 327 3.058501 ACTTTCTACAATTTTGACGCGGG 60.059 43.478 12.47 0.00 0.00 6.13
310 333 2.741116 AATTTTGACGCGGGTTGCCG 62.741 55.000 12.47 0.00 42.08 5.69
318 341 0.099791 CGCGGGTTGCCGAAATATTT 59.900 50.000 0.00 0.00 42.08 1.40
326 349 2.600731 TGCCGAAATATTTTTGTGGCG 58.399 42.857 20.28 11.60 42.11 5.69
328 351 1.923864 CCGAAATATTTTTGTGGCGGC 59.076 47.619 0.00 0.00 0.00 6.53
358 381 2.461110 CCCGCGACTGGTGCATAAC 61.461 63.158 8.23 0.00 0.00 1.89
370 393 2.817258 GGTGCATAACAAACCAGTAGCA 59.183 45.455 0.00 0.00 33.94 3.49
396 419 0.753479 TTTTCTTTGCCCGCCACTGA 60.753 50.000 0.00 0.00 0.00 3.41
399 422 1.973281 CTTTGCCCGCCACTGATGT 60.973 57.895 0.00 0.00 0.00 3.06
404 427 0.667184 GCCCGCCACTGATGTTTTTG 60.667 55.000 0.00 0.00 0.00 2.44
406 429 1.068434 CCCGCCACTGATGTTTTTGTT 59.932 47.619 0.00 0.00 0.00 2.83
407 430 2.482839 CCCGCCACTGATGTTTTTGTTT 60.483 45.455 0.00 0.00 0.00 2.83
411 434 4.432712 GCCACTGATGTTTTTGTTTCACT 58.567 39.130 0.00 0.00 0.00 3.41
416 439 7.543868 CCACTGATGTTTTTGTTTCACTTGTAA 59.456 33.333 0.00 0.00 0.00 2.41
438 461 9.719279 TGTAAATTTGTAAAAGTTTACGAGTGG 57.281 29.630 15.24 0.00 44.52 4.00
439 462 7.688478 AAATTTGTAAAAGTTTACGAGTGGC 57.312 32.000 8.90 0.00 44.52 5.01
440 463 5.814764 TTTGTAAAAGTTTACGAGTGGCA 57.185 34.783 8.90 0.00 44.52 4.92
459 482 3.552068 GGCAGGTTGTAATTTTTGCTCGT 60.552 43.478 0.00 0.00 0.00 4.18
461 484 3.906008 CAGGTTGTAATTTTTGCTCGTCG 59.094 43.478 0.00 0.00 0.00 5.12
500 577 3.138798 GCCTACTCGTCCTCGCCA 61.139 66.667 0.00 0.00 36.96 5.69
519 596 1.474077 CAGCCACTAAATTGAGCCCAC 59.526 52.381 0.00 0.00 0.00 4.61
520 597 1.075374 AGCCACTAAATTGAGCCCACA 59.925 47.619 0.00 0.00 0.00 4.17
521 598 1.202348 GCCACTAAATTGAGCCCACAC 59.798 52.381 0.00 0.00 0.00 3.82
529 606 4.862641 AATTGAGCCCACACCTATAAGT 57.137 40.909 0.00 0.00 0.00 2.24
535 999 4.844884 AGCCCACACCTATAAGTCTTTTC 58.155 43.478 0.00 0.00 0.00 2.29
537 1001 4.189231 CCCACACCTATAAGTCTTTTCCG 58.811 47.826 0.00 0.00 0.00 4.30
575 1039 8.789762 GGTCTTTGCCTAGTTTATTTAGTTTGA 58.210 33.333 0.00 0.00 0.00 2.69
577 1041 9.344772 TCTTTGCCTAGTTTATTTAGTTTGACA 57.655 29.630 0.00 0.00 0.00 3.58
596 1060 5.761003 TGACATGTACTTTTCACTTGCATG 58.239 37.500 0.00 0.00 38.41 4.06
617 1081 5.204409 TGTCGGTAATGTACTGTCTTTGT 57.796 39.130 0.00 0.00 36.45 2.83
630 1094 1.461127 GTCTTTGTCGTGCTCCATGTC 59.539 52.381 0.00 0.00 0.00 3.06
668 1132 0.179078 AGGGTACAACGCGTTTGTCA 60.179 50.000 24.21 4.53 46.05 3.58
670 1134 1.595246 GGGTACAACGCGTTTGTCAAC 60.595 52.381 24.21 17.47 46.05 3.18
731 1195 3.061697 GGCGTACAACGATTTTCCAGTAG 59.938 47.826 3.22 0.00 46.05 2.57
746 1210 3.964688 TCCAGTAGTGTTGAGGACAAAGA 59.035 43.478 0.00 0.00 40.65 2.52
757 1221 1.342174 AGGACAAAGACGAACCGCTAA 59.658 47.619 0.00 0.00 0.00 3.09
773 1238 3.488489 CGCTAACCGTTGGATTTGAAAG 58.512 45.455 0.00 0.00 0.00 2.62
787 1252 8.624367 TGGATTTGAAAGGTCGACTTATTTAA 57.376 30.769 16.46 8.29 38.85 1.52
788 1253 9.069082 TGGATTTGAAAGGTCGACTTATTTAAA 57.931 29.630 16.46 15.58 38.85 1.52
789 1254 9.902196 GGATTTGAAAGGTCGACTTATTTAAAA 57.098 29.630 16.46 17.51 38.85 1.52
837 1308 6.159751 AGGTGGCCCTCAATTTTATAGTCTTA 59.840 38.462 0.00 0.00 35.62 2.10
864 4453 9.959749 GAGAAAATTACAAATCTTACCAACACA 57.040 29.630 0.00 0.00 0.00 3.72
886 4475 5.878116 ACAACTTGTTCAACTGTACTAGCAA 59.122 36.000 0.00 0.00 0.00 3.91
899 4490 1.015109 CTAGCAATGCAGCACTGAGG 58.985 55.000 8.35 0.00 36.85 3.86
910 4501 2.046892 ACTGAGGTGCACCATCGC 60.047 61.111 36.39 22.04 38.89 4.58
990 4587 1.703438 GCGCAAGATCAGTCTGCCAG 61.703 60.000 0.30 0.00 43.02 4.85
1137 4740 2.344203 CGCAACCGAGGAGGAGTCT 61.344 63.158 0.00 0.00 45.00 3.24
1146 4749 1.985116 GGAGGAGTCTCGGTGGCTT 60.985 63.158 0.00 0.00 40.85 4.35
1344 4947 4.782019 TGTCCACATACTGAATTTTGCC 57.218 40.909 0.00 0.00 0.00 4.52
1348 4951 3.511146 CCACATACTGAATTTTGCCCTGT 59.489 43.478 0.00 0.00 0.00 4.00
1357 4969 1.044611 TTTTGCCCTGTTTGCTACCC 58.955 50.000 0.00 0.00 0.00 3.69
1360 4972 0.842905 TGCCCTGTTTGCTACCCCTA 60.843 55.000 0.00 0.00 0.00 3.53
1361 4973 0.393944 GCCCTGTTTGCTACCCCTAC 60.394 60.000 0.00 0.00 0.00 3.18
1363 4975 0.988832 CCTGTTTGCTACCCCTACCA 59.011 55.000 0.00 0.00 0.00 3.25
1364 4976 1.339727 CCTGTTTGCTACCCCTACCAC 60.340 57.143 0.00 0.00 0.00 4.16
1365 4977 1.628846 CTGTTTGCTACCCCTACCACT 59.371 52.381 0.00 0.00 0.00 4.00
1366 4978 2.835764 CTGTTTGCTACCCCTACCACTA 59.164 50.000 0.00 0.00 0.00 2.74
1367 4979 3.249752 TGTTTGCTACCCCTACCACTAA 58.750 45.455 0.00 0.00 0.00 2.24
1370 4982 2.905246 TGCTACCCCTACCACTAAACA 58.095 47.619 0.00 0.00 0.00 2.83
1371 4983 3.456842 TGCTACCCCTACCACTAAACAT 58.543 45.455 0.00 0.00 0.00 2.71
1372 4984 3.199071 TGCTACCCCTACCACTAAACATG 59.801 47.826 0.00 0.00 0.00 3.21
1373 4985 2.801077 ACCCCTACCACTAAACATGC 57.199 50.000 0.00 0.00 0.00 4.06
1375 4987 2.580783 ACCCCTACCACTAAACATGCAT 59.419 45.455 0.00 0.00 0.00 3.96
1376 4988 2.951642 CCCCTACCACTAAACATGCATG 59.048 50.000 25.09 25.09 0.00 4.06
1416 5029 0.389426 GCAGCTTTGGCAGAATGGTG 60.389 55.000 7.86 7.86 41.70 4.17
1443 5056 0.961358 CCTTCCACTCTCGACCTCGT 60.961 60.000 0.00 0.00 40.80 4.18
1495 5108 1.905894 AGAAGAAGAACCTGGAGGAGC 59.094 52.381 0.00 0.00 38.94 4.70
1506 5119 1.379309 GGAGGAGCCTCACTCTCGT 60.379 63.158 17.68 0.00 45.48 4.18
1522 5135 2.857592 TCGTGCCGAGGTAGATTAAC 57.142 50.000 0.00 0.00 0.00 2.01
1542 5155 1.153647 CGACCGGCACTGCATTAGA 60.154 57.895 0.00 0.00 0.00 2.10
1553 5166 5.586243 GGCACTGCATTAGAGATTCAACTTA 59.414 40.000 2.82 0.00 0.00 2.24
1695 5308 5.220815 GGAGTTCGTGTCGTCTATCATTAGT 60.221 44.000 0.00 0.00 0.00 2.24
1735 5348 4.211125 TCGGCTCAAGAGAGATTAGTCAT 58.789 43.478 0.32 0.00 44.98 3.06
1831 5449 7.393234 GCCCACCTAATATAAGTGATATGCAAA 59.607 37.037 0.00 0.00 33.21 3.68
1895 5514 5.478233 TGAAATCATGTAAAACGCGCTAT 57.522 34.783 5.73 0.00 0.00 2.97
1973 5593 2.923020 CAAACACAACAAGGACAACTGC 59.077 45.455 0.00 0.00 0.00 4.40
1980 5600 0.386352 CAAGGACAACTGCACATGCG 60.386 55.000 0.00 0.00 45.83 4.73
2144 5927 2.159128 TGCATTCAACACACACTTTGGG 60.159 45.455 0.00 0.00 33.17 4.12
2168 5954 3.827302 GGTGGTACTTCTCTTGAGACAGA 59.173 47.826 0.00 0.00 0.00 3.41
2170 5956 5.652891 GGTGGTACTTCTCTTGAGACAGATA 59.347 44.000 0.00 0.00 0.00 1.98
2478 6265 5.767670 AGACAATACAGGTAGCTAGGAGAA 58.232 41.667 0.00 0.00 0.00 2.87
2479 6266 6.377912 AGACAATACAGGTAGCTAGGAGAAT 58.622 40.000 0.00 0.00 0.00 2.40
2543 6344 5.050091 CCTCATGCTACAAATATCCACGAAC 60.050 44.000 0.00 0.00 0.00 3.95
2555 6356 3.134574 TCCACGAACAGCCTTTTACAT 57.865 42.857 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.156736 GGTCCAACGAAGACACCATG 58.843 55.000 0.00 0.00 35.89 3.66
1 2 0.036306 GGGTCCAACGAAGACACCAT 59.964 55.000 0.00 0.00 35.89 3.55
2 3 1.338890 TGGGTCCAACGAAGACACCA 61.339 55.000 0.00 0.27 36.80 4.17
3 4 0.036306 ATGGGTCCAACGAAGACACC 59.964 55.000 0.00 0.00 36.80 4.16
4 5 1.156736 CATGGGTCCAACGAAGACAC 58.843 55.000 0.00 0.00 38.19 3.67
5 6 0.762418 ACATGGGTCCAACGAAGACA 59.238 50.000 0.00 0.00 35.89 3.41
6 7 2.618053 CTACATGGGTCCAACGAAGAC 58.382 52.381 0.00 0.00 0.00 3.01
7 8 1.553248 CCTACATGGGTCCAACGAAGA 59.447 52.381 0.00 0.00 0.00 2.87
8 9 2.024176 CCTACATGGGTCCAACGAAG 57.976 55.000 0.00 0.00 0.00 3.79
19 20 5.993748 AATTTTTACCACACCCTACATGG 57.006 39.130 0.00 0.00 39.57 3.66
20 21 6.987386 TCAAATTTTTACCACACCCTACATG 58.013 36.000 0.00 0.00 0.00 3.21
21 22 6.210584 CCTCAAATTTTTACCACACCCTACAT 59.789 38.462 0.00 0.00 0.00 2.29
22 23 5.536916 CCTCAAATTTTTACCACACCCTACA 59.463 40.000 0.00 0.00 0.00 2.74
23 24 5.771165 TCCTCAAATTTTTACCACACCCTAC 59.229 40.000 0.00 0.00 0.00 3.18
24 25 5.771165 GTCCTCAAATTTTTACCACACCCTA 59.229 40.000 0.00 0.00 0.00 3.53
25 26 4.587262 GTCCTCAAATTTTTACCACACCCT 59.413 41.667 0.00 0.00 0.00 4.34
26 27 4.587262 AGTCCTCAAATTTTTACCACACCC 59.413 41.667 0.00 0.00 0.00 4.61
27 28 5.784578 AGTCCTCAAATTTTTACCACACC 57.215 39.130 0.00 0.00 0.00 4.16
28 29 6.801575 TCAAGTCCTCAAATTTTTACCACAC 58.198 36.000 0.00 0.00 0.00 3.82
29 30 7.432869 CATCAAGTCCTCAAATTTTTACCACA 58.567 34.615 0.00 0.00 0.00 4.17
30 31 6.868339 CCATCAAGTCCTCAAATTTTTACCAC 59.132 38.462 0.00 0.00 0.00 4.16
31 32 6.780031 TCCATCAAGTCCTCAAATTTTTACCA 59.220 34.615 0.00 0.00 0.00 3.25
32 33 7.227049 TCCATCAAGTCCTCAAATTTTTACC 57.773 36.000 0.00 0.00 0.00 2.85
33 34 9.541143 TTTTCCATCAAGTCCTCAAATTTTTAC 57.459 29.630 0.00 0.00 0.00 2.01
57 58 3.277142 ACTTCACCGGAGAGTGTTTTT 57.723 42.857 9.46 0.00 38.91 1.94
58 59 3.277142 AACTTCACCGGAGAGTGTTTT 57.723 42.857 9.46 0.00 38.91 2.43
59 60 3.203716 GAAACTTCACCGGAGAGTGTTT 58.796 45.455 23.76 23.76 38.91 2.83
72 73 3.611970 TGTTCGAAACCCTGAAACTTCA 58.388 40.909 0.00 0.00 35.57 3.02
93 94 0.032615 TTTGGCAGGTGGTGGTTTCT 60.033 50.000 0.00 0.00 0.00 2.52
103 104 1.270907 TTGGTTTGTGTTTGGCAGGT 58.729 45.000 0.00 0.00 0.00 4.00
106 107 7.552687 TGTATAAAAATTGGTTTGTGTTTGGCA 59.447 29.630 0.00 0.00 0.00 4.92
128 129 9.082313 AGGTTTGAAGAAGTTGAAATGATGTAT 57.918 29.630 0.00 0.00 0.00 2.29
159 160 6.533723 GTCTCAATGGTGTGTATTAATCGTGA 59.466 38.462 0.00 0.00 0.00 4.35
162 163 8.818141 ATAGTCTCAATGGTGTGTATTAATCG 57.182 34.615 0.00 0.00 0.00 3.34
213 235 7.885399 ACATATCTTAAGTCCAGAAAAGTGCTT 59.115 33.333 1.63 0.00 0.00 3.91
215 237 7.119846 ACACATATCTTAAGTCCAGAAAAGTGC 59.880 37.037 1.63 0.00 0.00 4.40
216 238 8.446273 CACACATATCTTAAGTCCAGAAAAGTG 58.554 37.037 1.63 0.00 0.00 3.16
217 239 7.607991 CCACACATATCTTAAGTCCAGAAAAGT 59.392 37.037 1.63 0.00 0.00 2.66
218 240 7.414540 GCCACACATATCTTAAGTCCAGAAAAG 60.415 40.741 1.63 0.00 0.00 2.27
223 245 3.804325 CGCCACACATATCTTAAGTCCAG 59.196 47.826 1.63 0.00 0.00 3.86
224 246 3.431626 CCGCCACACATATCTTAAGTCCA 60.432 47.826 1.63 0.00 0.00 4.02
227 249 2.745152 GCCCGCCACACATATCTTAAGT 60.745 50.000 1.63 0.00 0.00 2.24
252 274 1.348276 TTACGGTTGCAACGGTATCG 58.652 50.000 35.82 28.01 42.02 2.92
258 280 2.532317 CCAAAACTTTACGGTTGCAACG 59.468 45.455 22.67 19.11 37.36 4.10
260 282 4.451629 TTCCAAAACTTTACGGTTGCAA 57.548 36.364 0.00 0.00 0.00 4.08
261 283 4.082136 AGTTTCCAAAACTTTACGGTTGCA 60.082 37.500 0.00 0.00 0.00 4.08
262 284 4.426416 AGTTTCCAAAACTTTACGGTTGC 58.574 39.130 0.00 0.00 0.00 4.17
263 285 6.809689 AGAAAGTTTCCAAAACTTTACGGTTG 59.190 34.615 23.28 0.00 46.81 3.77
264 286 6.927416 AGAAAGTTTCCAAAACTTTACGGTT 58.073 32.000 23.28 7.35 46.81 4.44
265 287 6.519679 AGAAAGTTTCCAAAACTTTACGGT 57.480 33.333 23.28 7.93 46.81 4.83
266 288 7.474190 TGTAGAAAGTTTCCAAAACTTTACGG 58.526 34.615 23.28 0.00 46.81 4.02
274 297 8.865001 CGTCAAAATTGTAGAAAGTTTCCAAAA 58.135 29.630 12.05 0.35 0.00 2.44
283 306 3.058501 ACCCGCGTCAAAATTGTAGAAAG 60.059 43.478 4.92 0.00 0.00 2.62
288 311 1.335142 GCAACCCGCGTCAAAATTGTA 60.335 47.619 4.92 0.00 0.00 2.41
290 313 1.281566 GGCAACCCGCGTCAAAATTG 61.282 55.000 4.92 1.21 43.84 2.32
304 327 3.181535 CGCCACAAAAATATTTCGGCAAC 60.182 43.478 21.26 5.44 41.27 4.17
310 333 2.966050 TGGCCGCCACAAAAATATTTC 58.034 42.857 8.43 0.00 0.00 2.17
318 341 0.179000 AAAAACATGGCCGCCACAAA 59.821 45.000 16.16 0.00 35.80 2.83
348 371 2.817258 GCTACTGGTTTGTTATGCACCA 59.183 45.455 0.00 0.00 38.30 4.17
349 372 2.817258 TGCTACTGGTTTGTTATGCACC 59.183 45.455 0.00 0.00 0.00 5.01
358 381 1.609208 AAGTGCCTGCTACTGGTTTG 58.391 50.000 0.00 0.00 0.00 2.93
387 410 2.507339 AACAAAAACATCAGTGGCGG 57.493 45.000 0.00 0.00 0.00 6.13
389 412 4.432712 AGTGAAACAAAAACATCAGTGGC 58.567 39.130 0.00 0.00 41.43 5.01
416 439 6.797454 TGCCACTCGTAAACTTTTACAAATT 58.203 32.000 11.45 0.00 42.34 1.82
421 444 3.811497 ACCTGCCACTCGTAAACTTTTAC 59.189 43.478 2.29 2.29 39.62 2.01
433 456 3.740832 GCAAAAATTACAACCTGCCACTC 59.259 43.478 0.00 0.00 0.00 3.51
438 461 3.638484 ACGAGCAAAAATTACAACCTGC 58.362 40.909 0.00 0.00 0.00 4.85
439 462 3.906008 CGACGAGCAAAAATTACAACCTG 59.094 43.478 0.00 0.00 0.00 4.00
440 463 4.141855 CGACGAGCAAAAATTACAACCT 57.858 40.909 0.00 0.00 0.00 3.50
459 482 1.086696 GCCACTGCTATTTTGAGCGA 58.913 50.000 0.00 0.00 45.99 4.93
461 484 2.229784 ACTTGCCACTGCTATTTTGAGC 59.770 45.455 0.00 0.00 43.16 4.26
485 562 2.409651 GCTGGCGAGGACGAGTAG 59.590 66.667 0.00 0.00 42.66 2.57
488 565 4.803426 GTGGCTGGCGAGGACGAG 62.803 72.222 0.00 0.00 42.66 4.18
489 566 3.931190 TAGTGGCTGGCGAGGACGA 62.931 63.158 0.00 0.00 42.66 4.20
490 567 2.501223 TTTAGTGGCTGGCGAGGACG 62.501 60.000 0.00 0.00 42.93 4.79
500 577 1.075374 TGTGGGCTCAATTTAGTGGCT 59.925 47.619 0.00 0.00 0.00 4.75
519 596 6.973474 CACTACTCGGAAAAGACTTATAGGTG 59.027 42.308 0.00 0.00 0.00 4.00
520 597 6.888632 TCACTACTCGGAAAAGACTTATAGGT 59.111 38.462 0.00 0.00 0.00 3.08
521 598 7.194962 GTCACTACTCGGAAAAGACTTATAGG 58.805 42.308 0.00 0.00 0.00 2.57
535 999 0.964358 AAGACCCCGTCACTACTCGG 60.964 60.000 0.00 0.00 45.42 4.63
537 1001 1.672145 GCAAAGACCCCGTCACTACTC 60.672 57.143 0.00 0.00 34.60 2.59
575 1039 5.560760 CGACATGCAAGTGAAAAGTACATGT 60.561 40.000 2.69 2.69 46.67 3.21
577 1041 4.083324 CCGACATGCAAGTGAAAAGTACAT 60.083 41.667 0.00 0.00 0.00 2.29
578 1042 3.249799 CCGACATGCAAGTGAAAAGTACA 59.750 43.478 0.00 0.00 0.00 2.90
596 1060 4.322804 CGACAAAGACAGTACATTACCGAC 59.677 45.833 0.00 0.00 0.00 4.79
617 1081 1.375908 GGCAAGACATGGAGCACGA 60.376 57.895 0.00 0.00 0.00 4.35
668 1132 1.279271 AGAGCTAAATCACCGGCTGTT 59.721 47.619 0.00 0.00 35.01 3.16
670 1134 1.576356 GAGAGCTAAATCACCGGCTG 58.424 55.000 0.00 0.00 35.01 4.85
731 1195 2.287103 GGTTCGTCTTTGTCCTCAACAC 59.713 50.000 0.00 0.00 37.70 3.32
746 1210 1.665599 CCAACGGTTAGCGGTTCGT 60.666 57.895 9.04 0.00 36.25 3.85
757 1221 1.877443 CGACCTTTCAAATCCAACGGT 59.123 47.619 0.00 0.00 0.00 4.83
790 1255 8.458843 CACCTATTTATCAGTTGTCCGATTTTT 58.541 33.333 0.00 0.00 0.00 1.94
797 1265 3.883489 GGCCACCTATTTATCAGTTGTCC 59.117 47.826 0.00 0.00 0.00 4.02
864 4453 6.513393 GCATTGCTAGTACAGTTGAACAAGTT 60.513 38.462 0.16 0.00 0.00 2.66
899 4490 2.113860 ATATATGGGCGATGGTGCAC 57.886 50.000 8.80 8.80 39.27 4.57
910 4501 3.432186 CCGCCTGGATGTGTATATATGGG 60.432 52.174 0.00 0.00 37.49 4.00
990 4587 2.476320 GCGGGCCATCTTGCTTCTC 61.476 63.158 4.39 0.00 0.00 2.87
1272 4875 1.273455 GGTGGTCGTCGTCAAACTCG 61.273 60.000 0.00 0.00 0.00 4.18
1344 4947 0.988832 TGGTAGGGGTAGCAAACAGG 59.011 55.000 0.00 0.00 0.00 4.00
1348 4951 3.651904 TGTTTAGTGGTAGGGGTAGCAAA 59.348 43.478 0.00 0.00 0.00 3.68
1370 4982 4.171005 CAGAAGCGAAATTCAACATGCAT 58.829 39.130 0.00 0.00 0.00 3.96
1371 4983 3.567530 CAGAAGCGAAATTCAACATGCA 58.432 40.909 0.00 0.00 0.00 3.96
1372 4984 2.919229 CCAGAAGCGAAATTCAACATGC 59.081 45.455 0.00 0.00 0.00 4.06
1373 4985 4.083110 ACTCCAGAAGCGAAATTCAACATG 60.083 41.667 0.00 0.00 0.00 3.21
1375 4987 3.250762 CACTCCAGAAGCGAAATTCAACA 59.749 43.478 0.00 0.00 0.00 3.33
1376 4988 3.814945 CACTCCAGAAGCGAAATTCAAC 58.185 45.455 0.00 0.00 0.00 3.18
1443 5056 2.366480 TTTCGTTCGGCTTGGACGGA 62.366 55.000 9.83 0.00 37.39 4.69
1506 5119 0.748450 CGGGTTAATCTACCTCGGCA 59.252 55.000 0.00 0.00 38.30 5.69
1522 5135 3.673956 TAATGCAGTGCCGGTCGGG 62.674 63.158 13.72 2.06 39.58 5.14
1553 5166 5.362430 ACAATCACAAGGGTTAACACAACAT 59.638 36.000 11.16 0.00 0.00 2.71
1695 5308 4.888239 AGCCGAGCTACTAAATAAGACAGA 59.112 41.667 0.00 0.00 36.99 3.41
1711 5324 2.360801 ACTAATCTCTCTTGAGCCGAGC 59.639 50.000 0.00 0.00 40.03 5.03
1735 5348 4.826274 AGCCAGAATTACTGCTAGAACA 57.174 40.909 0.00 0.00 44.52 3.18
1831 5449 7.496346 TTAGATTGTAGAAGGAACAGGTGAT 57.504 36.000 0.00 0.00 0.00 3.06
1888 5507 2.707039 CGGGTTTTCCATAGCGCG 59.293 61.111 0.00 0.00 42.91 6.86
1994 5614 5.212745 TGAACCTAAACCATGTTTCCCTTT 58.787 37.500 0.00 0.00 0.00 3.11
1995 5615 4.810345 TGAACCTAAACCATGTTTCCCTT 58.190 39.130 0.00 0.00 0.00 3.95
1996 5616 4.463050 TGAACCTAAACCATGTTTCCCT 57.537 40.909 0.00 0.00 0.00 4.20
2066 5686 4.698780 ACAGCCCGTAAAATTCTTTACTCC 59.301 41.667 6.28 0.00 43.20 3.85
2117 5900 5.512753 AGTGTGTGTTGAATGCATGTAAA 57.487 34.783 0.00 0.00 0.00 2.01
2118 5901 5.512753 AAGTGTGTGTTGAATGCATGTAA 57.487 34.783 0.00 0.00 0.00 2.41
2144 5927 3.321111 TGTCTCAAGAGAAGTACCACCAC 59.679 47.826 0.57 0.00 39.48 4.16
2168 5954 0.328258 ACTCTTTGGGCGTGCCTTAT 59.672 50.000 11.25 0.00 36.10 1.73
2170 5956 1.152756 AACTCTTTGGGCGTGCCTT 60.153 52.632 11.25 0.00 36.10 4.35
2506 6307 2.985896 GCATGAGGCTTTGTACCTACA 58.014 47.619 0.00 0.00 37.77 2.74
2543 6344 2.618709 GGGGAATCGATGTAAAAGGCTG 59.381 50.000 0.00 0.00 0.00 4.85
2555 6356 2.546899 TCTCTCTTTTGGGGGAATCGA 58.453 47.619 0.00 0.00 0.00 3.59


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

AutoCloner maintained by Alex Coulton.