Multiple sequence alignment - TraesCS3D01G152400

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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 TraesCS3D01G152400 chr3D 100.000 4637 0 0 1 4637 116402395 116407031 0.000000e+00 8564
1 TraesCS3D01G152400 chr3B 89.612 4428 260 77 1 4322 171592499 171596832 0.000000e+00 5445
2 TraesCS3D01G152400 chr3B 86.061 330 23 9 4324 4635 171596913 171597237 2.670000e-87 333
3 TraesCS3D01G152400 chr3A 93.222 2272 113 19 1884 4148 125489017 125491254 0.000000e+00 3304
4 TraesCS3D01G152400 chr3A 88.213 1561 112 40 350 1848 125487462 125489012 0.000000e+00 1797
5 TraesCS3D01G152400 chr3A 85.000 260 23 7 40 290 125487180 125487432 2.770000e-62 250
6 TraesCS3D01G152400 chr3A 86.842 228 6 10 4380 4583 125494850 125495077 2.790000e-57 233
7 TraesCS3D01G152400 chr3A 84.672 137 13 3 4149 4283 125494453 125494583 3.770000e-26 130
8 TraesCS3D01G152400 chr4A 82.872 940 120 22 2746 3656 598709991 598710918 0.000000e+00 806
9 TraesCS3D01G152400 chr4A 82.714 538 60 16 2141 2671 598709440 598709951 9.150000e-122 448
10 TraesCS3D01G152400 chr4B 92.157 357 23 1 3966 4322 476236179 476236530 2.490000e-137 499
11 TraesCS3D01G152400 chr4B 87.970 266 28 2 2141 2403 7868505 7868241 1.250000e-80 311
12 TraesCS3D01G152400 chr4B 80.976 410 57 11 2264 2671 7804486 7804876 5.830000e-79 305
13 TraesCS3D01G152400 chr4B 95.376 173 7 1 4359 4531 476236605 476236776 1.640000e-69 274
14 TraesCS3D01G152400 chr4B 83.858 254 25 8 3441 3679 7806140 7806392 1.300000e-55 228
15 TraesCS3D01G152400 chr4D 82.119 453 66 11 2242 2690 4981223 4980782 1.580000e-99 374
16 TraesCS3D01G152400 chr1B 88.372 301 34 1 2962 3262 347560635 347560934 1.230000e-95 361


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 TraesCS3D01G152400 chr3D 116402395 116407031 4636 False 8564.0 8564 100.0000 1 4637 1 chr3D.!!$F1 4636
1 TraesCS3D01G152400 chr3B 171592499 171597237 4738 False 2889.0 5445 87.8365 1 4635 2 chr3B.!!$F1 4634
2 TraesCS3D01G152400 chr3A 125487180 125495077 7897 False 1142.8 3304 87.5898 40 4583 5 chr3A.!!$F1 4543
3 TraesCS3D01G152400 chr4A 598709440 598710918 1478 False 627.0 806 82.7930 2141 3656 2 chr4A.!!$F1 1515
4 TraesCS3D01G152400 chr4B 476236179 476236776 597 False 386.5 499 93.7665 3966 4531 2 chr4B.!!$F2 565
5 TraesCS3D01G152400 chr4B 7804486 7806392 1906 False 266.5 305 82.4170 2264 3679 2 chr4B.!!$F1 1415

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
310 338 0.037590 TTACTTTGGCGCCTGATGGT 59.962 50.0 29.7 19.74 35.27 3.55 F
311 339 0.392461 TACTTTGGCGCCTGATGGTC 60.392 55.0 29.7 0.00 35.27 4.02 F
1323 1435 0.106519 GCTCCCTCTCTCTCTGCTCT 60.107 60.0 0.0 0.00 0.00 4.09 F
1858 1995 0.038618 GGTGTTCGATTTGGCCCAAC 60.039 55.0 0.0 0.00 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1304 1416 0.106519 AGAGCAGAGAGAGAGGGAGC 60.107 60.0 0.0 0.0 0.00 4.70 R
1613 1750 0.179166 AGCAACACACACTGCAAACG 60.179 50.0 0.0 0.0 41.17 3.60 R
2543 2690 0.806492 GATTTCGGGAGTCAGGACGC 60.806 60.0 0.0 0.0 36.20 5.19 R
3730 4681 0.042581 TGACTATCCCCCTGTCAGCA 59.957 55.0 0.0 0.0 36.03 4.41 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
52 61 0.241749 TGTGTAGCGGTGAACGTAGG 59.758 55.000 0.00 0.00 46.52 3.18
56 65 2.531927 TAGCGGTGAACGTAGGTGCG 62.532 60.000 0.00 0.00 46.52 5.34
57 66 2.807895 CGGTGAACGTAGGTGCGG 60.808 66.667 0.00 0.00 37.93 5.69
62 71 3.243816 AACGTAGGTGCGGGGGTT 61.244 61.111 0.00 0.00 35.98 4.11
78 87 3.451540 GGGGGTTTTTGGACACTGTAAAA 59.548 43.478 0.00 0.00 0.00 1.52
90 100 5.476945 GGACACTGTAAAATCTCCAACCAAT 59.523 40.000 0.00 0.00 0.00 3.16
91 101 6.657541 GGACACTGTAAAATCTCCAACCAATA 59.342 38.462 0.00 0.00 0.00 1.90
97 107 9.410556 CTGTAAAATCTCCAACCAATAAAACAG 57.589 33.333 0.00 0.00 0.00 3.16
101 111 4.211125 TCTCCAACCAATAAAACAGTGCA 58.789 39.130 0.00 0.00 0.00 4.57
139 149 3.508845 TCCTGTTCTTTCCCCTTTCAG 57.491 47.619 0.00 0.00 0.00 3.02
170 187 8.190326 TGACAGAATTACCTAGTTTCAGAAGA 57.810 34.615 0.00 0.00 0.00 2.87
171 188 8.647796 TGACAGAATTACCTAGTTTCAGAAGAA 58.352 33.333 0.00 0.00 0.00 2.52
172 189 9.660180 GACAGAATTACCTAGTTTCAGAAGAAT 57.340 33.333 0.00 0.00 32.89 2.40
249 274 1.068474 CTTTCGCTCGACGGATTGTT 58.932 50.000 0.00 0.00 43.89 2.83
253 278 1.011968 CGCTCGACGGATTGTTTCCA 61.012 55.000 0.00 0.00 45.78 3.53
290 315 1.857217 GTGCGACACTGAGCTATGATG 59.143 52.381 0.00 0.00 0.00 3.07
297 325 5.807520 CGACACTGAGCTATGATGTTACTTT 59.192 40.000 0.00 0.00 0.00 2.66
310 338 0.037590 TTACTTTGGCGCCTGATGGT 59.962 50.000 29.70 19.74 35.27 3.55
311 339 0.392461 TACTTTGGCGCCTGATGGTC 60.392 55.000 29.70 0.00 35.27 4.02
327 355 2.161855 TGGTCATTGTCAACATGCTCC 58.838 47.619 0.00 0.00 0.00 4.70
346 374 1.097547 CGGCGCCTGAAATTGGAGAT 61.098 55.000 26.68 0.00 0.00 2.75
353 381 3.064545 GCCTGAAATTGGAGATCTGTTCG 59.935 47.826 0.00 0.00 0.00 3.95
367 396 2.282958 TTCGTCTCCACCGCTCCT 60.283 61.111 0.00 0.00 0.00 3.69
395 424 3.319122 GCATGTATTCCACTCATTTCCCC 59.681 47.826 0.00 0.00 0.00 4.81
441 472 4.505313 TCAAGCTCCGTATAGTGCATAG 57.495 45.455 0.00 0.00 0.00 2.23
610 646 7.119699 CCATTTTGACAGTATCTTTGCTCTGTA 59.880 37.037 0.00 0.00 40.53 2.74
620 656 3.753272 TCTTTGCTCTGTACTTGCATTCC 59.247 43.478 8.35 0.00 36.55 3.01
622 658 2.426522 TGCTCTGTACTTGCATTCCAC 58.573 47.619 0.00 0.00 0.00 4.02
631 667 0.537828 TTGCATTCCACAGCTGCAGA 60.538 50.000 20.43 8.03 45.72 4.26
644 695 3.077359 AGCTGCAGACATTTCCACTTAC 58.923 45.455 20.43 0.00 0.00 2.34
650 701 4.563580 GCAGACATTTCCACTTACTCCTGA 60.564 45.833 0.00 0.00 0.00 3.86
678 729 0.987294 TCCCCCTCTTGCAGAAGAAG 59.013 55.000 0.00 0.00 37.77 2.85
682 733 1.451067 CCTCTTGCAGAAGAAGCTGG 58.549 55.000 0.00 0.00 37.77 4.85
684 735 2.355920 CCTCTTGCAGAAGAAGCTGGAT 60.356 50.000 0.00 0.00 37.77 3.41
693 749 0.466124 AGAAGCTGGATACCCTTCGC 59.534 55.000 0.00 0.00 44.22 4.70
696 752 1.069935 GCTGGATACCCTTCGCTCC 59.930 63.158 0.00 0.00 0.00 4.70
708 764 4.767255 CGCTCCTGTCCACTGGCC 62.767 72.222 0.00 0.00 35.24 5.36
1295 1404 1.168714 CCCTTCAACTGGTAAGCTGC 58.831 55.000 0.00 0.00 0.00 5.25
1297 1406 1.808945 CCTTCAACTGGTAAGCTGCTG 59.191 52.381 1.35 0.00 0.00 4.41
1298 1407 2.498167 CTTCAACTGGTAAGCTGCTGT 58.502 47.619 1.35 0.00 0.00 4.40
1299 1408 2.638480 TCAACTGGTAAGCTGCTGTT 57.362 45.000 1.35 0.00 0.00 3.16
1304 1416 1.745489 GGTAAGCTGCTGTTCCCCG 60.745 63.158 1.35 0.00 0.00 5.73
1319 1431 1.827789 CCCGCTCCCTCTCTCTCTG 60.828 68.421 0.00 0.00 0.00 3.35
1320 1432 2.489275 CCGCTCCCTCTCTCTCTGC 61.489 68.421 0.00 0.00 0.00 4.26
1321 1433 1.453745 CGCTCCCTCTCTCTCTGCT 60.454 63.158 0.00 0.00 0.00 4.24
1322 1434 1.447317 CGCTCCCTCTCTCTCTGCTC 61.447 65.000 0.00 0.00 0.00 4.26
1323 1435 0.106519 GCTCCCTCTCTCTCTGCTCT 60.107 60.000 0.00 0.00 0.00 4.09
1332 1444 0.819259 CTCTCTGCTCTCTCTCCCGG 60.819 65.000 0.00 0.00 0.00 5.73
1368 1492 3.727970 GCGGGTCTGTCGATTTGAATTTC 60.728 47.826 0.00 0.00 0.00 2.17
1473 1598 0.257328 TGGTTCTGGAACTTGGTGCA 59.743 50.000 12.34 0.00 40.94 4.57
1478 1603 1.303236 TGGAACTTGGTGCATCGGG 60.303 57.895 0.00 0.00 0.00 5.14
1505 1630 1.379044 AGGGAATTGGGCTTGAGCG 60.379 57.895 0.00 0.00 43.26 5.03
1535 1660 4.704540 TGATGAATCCGTGCAAATTACCTT 59.295 37.500 0.00 0.00 0.00 3.50
1553 1690 7.624360 TTACCTTCTGAATTGCGTATTGAAT 57.376 32.000 0.00 0.00 0.00 2.57
1588 1725 1.300971 TGCTGTGAATCGAGCTTGGC 61.301 55.000 0.00 0.00 36.11 4.52
1590 1727 1.376543 CTGTGAATCGAGCTTGGCAT 58.623 50.000 0.00 0.00 0.00 4.40
1592 1729 2.938451 CTGTGAATCGAGCTTGGCATTA 59.062 45.455 0.00 0.00 0.00 1.90
1601 1738 2.849880 GCTTGGCATTAAAGCGATCA 57.150 45.000 0.00 0.00 40.56 2.92
1613 1750 2.109425 AGCGATCACAACTTAACCCC 57.891 50.000 0.00 0.00 0.00 4.95
1649 1786 2.783135 TGCTGTTTGAATCCTCTGGAC 58.217 47.619 0.00 0.00 32.98 4.02
1739 1876 3.102097 CTGCGCCCTCGAAATTCC 58.898 61.111 4.18 0.00 38.10 3.01
1850 1987 4.002906 TGAAGCAGTAGGTGTTCGATTT 57.997 40.909 0.00 0.00 0.00 2.17
1853 1990 1.130561 GCAGTAGGTGTTCGATTTGGC 59.869 52.381 0.00 0.00 0.00 4.52
1857 1994 0.178975 AGGTGTTCGATTTGGCCCAA 60.179 50.000 0.00 0.00 0.00 4.12
1858 1995 0.038618 GGTGTTCGATTTGGCCCAAC 60.039 55.000 0.00 0.00 0.00 3.77
1878 2015 2.338015 CGCCCTCTGCATTGCTGTT 61.338 57.895 10.49 0.00 41.33 3.16
1882 2019 1.336517 CCCTCTGCATTGCTGTTTGTG 60.337 52.381 10.49 0.63 0.00 3.33
1890 2027 2.050985 GCTGTTTGTGGTCGCAGC 60.051 61.111 0.00 0.00 45.70 5.25
1893 2030 0.317269 CTGTTTGTGGTCGCAGCTTG 60.317 55.000 0.00 0.00 0.00 4.01
1904 2041 3.987404 CAGCTTGGGTGTACTGCC 58.013 61.111 0.00 0.00 0.00 4.85
1916 2053 1.265635 TGTACTGCCGTGTCATTTTGC 59.734 47.619 0.00 0.00 0.00 3.68
1940 2080 6.565811 GCTTTTTGGGTTCGAATTCAAATTCC 60.566 38.462 21.19 8.58 41.30 3.01
1954 2094 0.613012 AATTCCCTGGAGCCAAGTGC 60.613 55.000 0.00 0.00 41.71 4.40
1982 2122 4.127171 GACCAATGTATAATGCCTGACGT 58.873 43.478 0.00 0.00 0.00 4.34
2027 2167 3.181471 CGATGCTTCAGGGATTCTACTGT 60.181 47.826 0.08 0.00 36.17 3.55
2031 2171 4.141846 TGCTTCAGGGATTCTACTGTGATC 60.142 45.833 8.17 0.00 36.17 2.92
2037 2177 3.243569 GGGATTCTACTGTGATCGGAGTG 60.244 52.174 6.68 0.00 0.00 3.51
2041 2181 1.474478 CTACTGTGATCGGAGTGCTGT 59.526 52.381 6.68 0.00 0.00 4.40
2046 2186 1.126846 GTGATCGGAGTGCTGTTTTCG 59.873 52.381 0.00 0.00 0.00 3.46
2056 2196 1.201181 TGCTGTTTTCGTGCTTTGTGT 59.799 42.857 0.00 0.00 0.00 3.72
2057 2197 2.258755 GCTGTTTTCGTGCTTTGTGTT 58.741 42.857 0.00 0.00 0.00 3.32
2058 2198 2.027926 GCTGTTTTCGTGCTTTGTGTTG 59.972 45.455 0.00 0.00 0.00 3.33
2059 2199 3.241701 CTGTTTTCGTGCTTTGTGTTGT 58.758 40.909 0.00 0.00 0.00 3.32
2060 2200 2.983136 TGTTTTCGTGCTTTGTGTTGTG 59.017 40.909 0.00 0.00 0.00 3.33
2061 2201 3.238441 GTTTTCGTGCTTTGTGTTGTGA 58.762 40.909 0.00 0.00 0.00 3.58
2062 2202 3.560902 TTTCGTGCTTTGTGTTGTGAA 57.439 38.095 0.00 0.00 0.00 3.18
2063 2203 2.535934 TCGTGCTTTGTGTTGTGAAC 57.464 45.000 0.00 0.00 0.00 3.18
2118 2258 1.068895 TGATTTGTGCTGCAGGTTTGG 59.931 47.619 17.12 0.00 0.00 3.28
2403 2543 2.442084 GGTACGCACCAAGTCTTCG 58.558 57.895 0.00 0.00 45.04 3.79
2414 2556 2.213499 CAAGTCTTCGGTGTGCTTCTT 58.787 47.619 0.00 0.00 0.00 2.52
2416 2558 1.149148 GTCTTCGGTGTGCTTCTTCC 58.851 55.000 0.00 0.00 0.00 3.46
2420 2562 1.376037 CGGTGTGCTTCTTCCTCCC 60.376 63.158 0.00 0.00 0.00 4.30
2453 2596 0.732880 GTCGCACGTACTGACATGCT 60.733 55.000 8.59 0.00 42.60 3.79
2543 2690 3.720193 GTGAGCACAGCACAGCGG 61.720 66.667 0.00 0.00 36.31 5.52
2586 2733 1.898574 CCGGCCTGTTTCTTGCTGT 60.899 57.895 0.00 0.00 0.00 4.40
2595 2742 5.036737 CCTGTTTCTTGCTGTTTTACTGTG 58.963 41.667 0.00 0.00 0.00 3.66
2601 2748 4.275689 TCTTGCTGTTTTACTGTGATGTGG 59.724 41.667 0.00 0.00 0.00 4.17
2869 3792 4.445385 CACTTGCTGGTCTTGTTAAAATGC 59.555 41.667 0.00 0.00 0.00 3.56
2906 3833 3.569701 TGTTCTTTGGTCCTCTTGAATGC 59.430 43.478 0.00 0.00 0.00 3.56
2913 3840 2.641305 GTCCTCTTGAATGCTGCAGAT 58.359 47.619 20.43 5.31 0.00 2.90
2978 3905 0.471617 GGTGATGATGCTAGGCTGGT 59.528 55.000 0.00 0.00 0.00 4.00
3029 3957 4.273235 GCTTGTTTCTGAATTTGGTTTGGG 59.727 41.667 0.00 0.00 0.00 4.12
3070 4002 0.741221 GGACGATGCAGGTTCTGGAC 60.741 60.000 0.00 0.00 34.07 4.02
3156 4088 1.527034 GGCAGTCACTTCAGCAATGA 58.473 50.000 0.00 0.00 0.00 2.57
3311 4247 1.665916 CACTCACGCTGACTGTGGG 60.666 63.158 0.00 0.00 43.57 4.61
3312 4248 2.740055 CTCACGCTGACTGTGGGC 60.740 66.667 0.00 0.00 37.91 5.36
3679 4630 2.054453 GGCTGGGTTCCTTGATGCC 61.054 63.158 0.00 0.00 0.00 4.40
3730 4681 6.763610 GGTATTTAGTTTGCTCTGATGCTAGT 59.236 38.462 0.00 0.00 0.00 2.57
3767 4718 1.073284 TCACAAAGGAAGGGGTACAGC 59.927 52.381 0.00 0.00 0.00 4.40
3790 4741 4.394729 GGGGTAGATAAATTCCATCGCAA 58.605 43.478 0.00 0.00 0.00 4.85
3833 4789 8.885302 AGTAATTAAATCGGCGTTTAGAAAAC 57.115 30.769 6.85 6.44 0.00 2.43
3874 4830 2.659610 GAGCGGGCTCTCTGTTGT 59.340 61.111 13.25 0.00 39.80 3.32
3882 4838 3.447742 GGGCTCTCTGTTGTTTGTTTTG 58.552 45.455 0.00 0.00 0.00 2.44
3886 4842 4.342772 CTCTCTGTTGTTTGTTTTGTCGG 58.657 43.478 0.00 0.00 0.00 4.79
3930 4886 0.179197 TACTTCGTCGAAGAGCTGCG 60.179 55.000 35.22 13.28 41.71 5.18
4023 4983 7.235193 TGGTATGTACTGGGTTTACTCTGTTTA 59.765 37.037 0.00 0.00 0.00 2.01
4029 4989 4.139038 TGGGTTTACTCTGTTTACTTGGC 58.861 43.478 0.00 0.00 0.00 4.52
4068 5028 5.599242 TGTATCTACCGTGTGGATAATGGAA 59.401 40.000 10.23 0.00 37.65 3.53
4123 5083 1.609208 AACATGGCACTGGTGAACTC 58.391 50.000 4.79 0.00 0.00 3.01
4326 8584 3.758023 TGTGAAACAGATGGGCATTAGTG 59.242 43.478 0.00 0.00 45.67 2.74
4356 8614 1.729881 GCCAATCGATCTTGTGGGC 59.270 57.895 14.23 9.76 0.00 5.36
4368 8626 0.035739 TTGTGGGCTTCTTCGTACCC 59.964 55.000 0.00 0.00 43.14 3.69
4424 8785 6.447084 TCCCACAAGACCTATATTTCTCCTTT 59.553 38.462 0.00 0.00 0.00 3.11
4536 8909 0.957362 AACCTGAAAGCAGAAGCAGC 59.043 50.000 0.00 0.00 45.17 5.25
4542 8915 1.849976 AAAGCAGAAGCAGCGCAGAC 61.850 55.000 11.47 0.00 45.49 3.51
4544 8917 2.736236 CAGAAGCAGCGCAGACGT 60.736 61.111 11.47 0.00 42.83 4.34
4583 8970 7.010160 TCACTGGTAATTTTTCTTCCTTGGAT 58.990 34.615 0.00 0.00 0.00 3.41
4584 8971 7.039784 TCACTGGTAATTTTTCTTCCTTGGATG 60.040 37.037 0.00 0.00 0.00 3.51
4585 8972 6.211384 ACTGGTAATTTTTCTTCCTTGGATGG 59.789 38.462 3.24 0.00 0.00 3.51
4586 8973 6.318913 TGGTAATTTTTCTTCCTTGGATGGA 58.681 36.000 3.24 0.00 0.00 3.41
4605 8992 1.324736 GAAAGGCGCACACTAGAATCG 59.675 52.381 10.83 0.00 0.00 3.34
4622 9009 4.529769 AGAATCGATCTCCTGCCATTCATA 59.470 41.667 0.00 0.00 30.46 2.15
4635 9022 1.863454 CATTCATACGCAGTGGAGCTC 59.137 52.381 4.71 4.71 45.73 4.09
4636 9023 1.186200 TTCATACGCAGTGGAGCTCT 58.814 50.000 14.64 0.00 45.73 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 8.547894 CGCTACACATTTTTAAGTGCTATATCA 58.452 33.333 0.00 0.00 39.30 2.15
21 22 3.818773 ACCGCTACACATTTTTAAGTGCT 59.181 39.130 0.00 0.00 39.30 4.40
22 23 3.911964 CACCGCTACACATTTTTAAGTGC 59.088 43.478 0.00 0.00 39.30 4.40
31 32 2.602878 CTACGTTCACCGCTACACATT 58.397 47.619 0.00 0.00 41.42 2.71
52 61 2.128507 TGTCCAAAAACCCCCGCAC 61.129 57.895 0.00 0.00 0.00 5.34
56 65 2.368311 TACAGTGTCCAAAAACCCCC 57.632 50.000 0.00 0.00 0.00 5.40
57 66 4.739587 TTTTACAGTGTCCAAAAACCCC 57.260 40.909 0.00 0.00 0.00 4.95
62 71 6.183360 GGTTGGAGATTTTACAGTGTCCAAAA 60.183 38.462 10.86 8.69 45.69 2.44
78 87 4.832266 TGCACTGTTTTATTGGTTGGAGAT 59.168 37.500 0.00 0.00 0.00 2.75
90 100 7.161404 AGAGATACAATCAGTGCACTGTTTTA 58.839 34.615 38.41 27.89 44.12 1.52
91 101 6.000219 AGAGATACAATCAGTGCACTGTTTT 59.000 36.000 38.41 30.07 44.12 2.43
97 107 6.989169 AGGAAATAGAGATACAATCAGTGCAC 59.011 38.462 9.40 9.40 0.00 4.57
101 111 8.986991 AGAACAGGAAATAGAGATACAATCAGT 58.013 33.333 0.00 0.00 0.00 3.41
139 149 7.656137 TGAAACTAGGTAATTCTGTCAGTTGAC 59.344 37.037 5.33 5.33 44.97 3.18
170 187 7.582719 TGGTCAGGTAATTCTGCCTTATTATT 58.417 34.615 0.00 0.00 35.03 1.40
171 188 7.149202 TGGTCAGGTAATTCTGCCTTATTAT 57.851 36.000 0.00 0.00 35.03 1.28
172 189 6.569127 TGGTCAGGTAATTCTGCCTTATTA 57.431 37.500 0.00 0.00 35.03 0.98
173 190 5.450818 TGGTCAGGTAATTCTGCCTTATT 57.549 39.130 0.00 0.00 35.03 1.40
174 191 5.380043 CATGGTCAGGTAATTCTGCCTTAT 58.620 41.667 0.00 0.00 35.03 1.73
175 192 4.780815 CATGGTCAGGTAATTCTGCCTTA 58.219 43.478 0.00 0.00 35.03 2.69
270 295 1.857217 CATCATAGCTCAGTGTCGCAC 59.143 52.381 0.00 2.28 34.10 5.34
290 315 0.451783 CCATCAGGCGCCAAAGTAAC 59.548 55.000 31.54 0.00 0.00 2.50
297 325 1.750018 CAATGACCATCAGGCGCCA 60.750 57.895 31.54 9.64 39.06 5.69
310 338 1.452110 CCGGAGCATGTTGACAATGA 58.548 50.000 0.00 0.00 0.00 2.57
311 339 0.179156 GCCGGAGCATGTTGACAATG 60.179 55.000 5.05 0.00 39.53 2.82
327 355 1.097547 ATCTCCAATTTCAGGCGCCG 61.098 55.000 23.20 16.49 0.00 6.46
335 363 5.710613 GAGACGAACAGATCTCCAATTTC 57.289 43.478 0.00 0.00 36.18 2.17
346 374 1.863662 GAGCGGTGGAGACGAACAGA 61.864 60.000 0.00 0.00 0.00 3.41
353 381 3.655810 CTGCAGGAGCGGTGGAGAC 62.656 68.421 5.57 0.00 46.23 3.36
395 424 5.097529 CCGTCCATCATTCATCAACAAAAG 58.902 41.667 0.00 0.00 0.00 2.27
441 472 0.588252 AGTGTTGCTCGTGTTGCATC 59.412 50.000 0.00 0.00 40.34 3.91
446 477 5.034152 CACAAATAAAGTGTTGCTCGTGTT 58.966 37.500 0.00 0.00 32.44 3.32
455 486 4.610945 GTGAGCTGCACAAATAAAGTGTT 58.389 39.130 0.25 0.00 46.91 3.32
557 593 7.451255 ACAGGTAAACAAATGGAATCTGATTCA 59.549 33.333 26.60 15.70 41.03 2.57
595 631 6.428385 AATGCAAGTACAGAGCAAAGATAC 57.572 37.500 10.27 0.00 42.15 2.24
610 646 0.824595 TGCAGCTGTGGAATGCAAGT 60.825 50.000 16.64 0.00 46.31 3.16
620 656 1.068748 GTGGAAATGTCTGCAGCTGTG 60.069 52.381 16.64 9.01 0.00 3.66
622 658 1.531423 AGTGGAAATGTCTGCAGCTG 58.469 50.000 10.11 10.11 0.00 4.24
631 667 5.568620 AGTTCAGGAGTAAGTGGAAATGT 57.431 39.130 0.00 0.00 0.00 2.71
644 695 2.310052 AGGGGGATGAAAAGTTCAGGAG 59.690 50.000 0.00 0.00 43.98 3.69
650 701 2.158325 TGCAAGAGGGGGATGAAAAGTT 60.158 45.455 0.00 0.00 0.00 2.66
678 729 1.069935 GGAGCGAAGGGTATCCAGC 59.930 63.158 0.00 0.00 34.83 4.85
682 733 0.389757 GGACAGGAGCGAAGGGTATC 59.610 60.000 0.00 0.00 0.00 2.24
684 735 1.077805 TGGACAGGAGCGAAGGGTA 59.922 57.895 0.00 0.00 0.00 3.69
693 749 2.667418 CAGGCCAGTGGACAGGAG 59.333 66.667 19.84 0.00 29.21 3.69
998 1101 4.434685 GCTTCCTCAGCTCCATCG 57.565 61.111 0.00 0.00 46.27 3.84
1295 1404 2.685380 AGAGGGAGCGGGGAACAG 60.685 66.667 0.00 0.00 0.00 3.16
1297 1406 2.364448 AGAGAGGGAGCGGGGAAC 60.364 66.667 0.00 0.00 0.00 3.62
1298 1407 2.042843 GAGAGAGGGAGCGGGGAA 60.043 66.667 0.00 0.00 0.00 3.97
1299 1408 3.024356 AGAGAGAGGGAGCGGGGA 61.024 66.667 0.00 0.00 0.00 4.81
1304 1416 0.106519 AGAGCAGAGAGAGAGGGAGC 60.107 60.000 0.00 0.00 0.00 4.70
1319 1431 2.430610 ATGCACCGGGAGAGAGAGC 61.431 63.158 6.32 0.00 0.00 4.09
1320 1432 1.440893 CATGCACCGGGAGAGAGAG 59.559 63.158 6.32 0.00 0.00 3.20
1321 1433 2.725312 GCATGCACCGGGAGAGAGA 61.725 63.158 14.21 0.00 0.00 3.10
1322 1434 2.202987 GCATGCACCGGGAGAGAG 60.203 66.667 14.21 0.00 0.00 3.20
1323 1435 4.147449 CGCATGCACCGGGAGAGA 62.147 66.667 19.57 0.00 0.00 3.10
1382 1506 1.732259 CGAAGCGCAGTCCAATTAAGT 59.268 47.619 11.47 0.00 0.00 2.24
1473 1598 4.541648 CCCTCCCTCCGACCCGAT 62.542 72.222 0.00 0.00 0.00 4.18
1478 1603 1.527370 CCAATTCCCTCCCTCCGAC 59.473 63.158 0.00 0.00 0.00 4.79
1505 1630 2.031245 TGCACGGATTCATCACACAAAC 60.031 45.455 0.00 0.00 0.00 2.93
1535 1660 5.895636 ACCAATTCAATACGCAATTCAGA 57.104 34.783 0.00 0.00 0.00 3.27
1553 1690 2.694628 ACAGCAGCAGAATTCAAACCAA 59.305 40.909 8.44 0.00 0.00 3.67
1588 1725 6.027749 GGGTTAAGTTGTGATCGCTTTAATG 58.972 40.000 7.94 0.00 0.00 1.90
1590 1727 4.456566 GGGGTTAAGTTGTGATCGCTTTAA 59.543 41.667 7.94 7.31 0.00 1.52
1592 1729 2.817844 GGGGTTAAGTTGTGATCGCTTT 59.182 45.455 7.94 2.60 0.00 3.51
1601 1738 1.679153 CTGCAAACGGGGTTAAGTTGT 59.321 47.619 0.00 0.00 0.00 3.32
1613 1750 0.179166 AGCAACACACACTGCAAACG 60.179 50.000 0.00 0.00 41.17 3.60
1649 1786 2.356382 CTCCAAGCTCCAGTCTACTACG 59.644 54.545 0.00 0.00 0.00 3.51
1739 1876 1.834188 AATTGGGAACACTAAGCCCG 58.166 50.000 0.00 0.00 45.08 6.13
1875 2012 1.723608 CCAAGCTGCGACCACAAACA 61.724 55.000 0.00 0.00 0.00 2.83
1878 2015 2.594303 CCCAAGCTGCGACCACAA 60.594 61.111 0.00 0.00 0.00 3.33
1882 2019 2.033194 GTACACCCAAGCTGCGACC 61.033 63.158 0.00 0.00 0.00 4.79
1890 2027 0.949105 GACACGGCAGTACACCCAAG 60.949 60.000 0.00 0.00 0.00 3.61
1893 2030 0.321298 AATGACACGGCAGTACACCC 60.321 55.000 0.00 0.00 0.00 4.61
1904 2041 3.194062 ACCCAAAAAGCAAAATGACACG 58.806 40.909 0.00 0.00 0.00 4.49
1916 2053 6.073276 GGGAATTTGAATTCGAACCCAAAAAG 60.073 38.462 21.57 0.00 44.43 2.27
1954 2094 4.581824 AGGCATTATACATTGGTCAGCAAG 59.418 41.667 0.00 0.00 0.00 4.01
1982 2122 5.751509 CGGAATCACAAGTAATCGGTTCATA 59.248 40.000 0.00 0.00 0.00 2.15
2027 2167 1.270094 ACGAAAACAGCACTCCGATCA 60.270 47.619 0.00 0.00 0.00 2.92
2031 2171 1.082756 GCACGAAAACAGCACTCCG 60.083 57.895 0.00 0.00 0.00 4.63
2037 2177 1.908065 ACACAAAGCACGAAAACAGC 58.092 45.000 0.00 0.00 0.00 4.40
2041 2181 3.560902 TCACAACACAAAGCACGAAAA 57.439 38.095 0.00 0.00 0.00 2.29
2046 2186 3.364621 CACAAGTTCACAACACAAAGCAC 59.635 43.478 0.00 0.00 0.00 4.40
2056 2196 6.513230 CGAATTCCTGAATCACAAGTTCACAA 60.513 38.462 0.00 0.00 32.55 3.33
2057 2197 5.049474 CGAATTCCTGAATCACAAGTTCACA 60.049 40.000 0.00 0.00 32.55 3.58
2058 2198 5.049405 ACGAATTCCTGAATCACAAGTTCAC 60.049 40.000 0.00 0.00 32.55 3.18
2059 2199 5.063204 ACGAATTCCTGAATCACAAGTTCA 58.937 37.500 0.00 0.00 34.63 3.18
2060 2200 5.613358 ACGAATTCCTGAATCACAAGTTC 57.387 39.130 0.00 0.00 0.00 3.01
2061 2201 7.607991 AGATAACGAATTCCTGAATCACAAGTT 59.392 33.333 0.00 0.00 0.00 2.66
2062 2202 7.106239 AGATAACGAATTCCTGAATCACAAGT 58.894 34.615 0.00 0.00 0.00 3.16
2063 2203 7.545362 AGATAACGAATTCCTGAATCACAAG 57.455 36.000 0.00 0.00 0.00 3.16
2403 2543 1.002011 GGGGAGGAAGAAGCACACC 60.002 63.158 0.00 0.00 0.00 4.16
2453 2596 1.722034 AACAGAGGACAGAGGAGCAA 58.278 50.000 0.00 0.00 0.00 3.91
2537 2683 4.057428 GAGTCAGGACGCCGCTGT 62.057 66.667 0.00 0.00 36.20 4.40
2543 2690 0.806492 GATTTCGGGAGTCAGGACGC 60.806 60.000 0.00 0.00 36.20 5.19
2551 2698 1.043673 CGGGAGAGGATTTCGGGAGT 61.044 60.000 0.00 0.00 0.00 3.85
2586 2733 5.761234 GTCAGGTAACCACATCACAGTAAAA 59.239 40.000 0.00 0.00 37.17 1.52
2595 2742 1.732259 CAAGCGTCAGGTAACCACATC 59.268 52.381 0.00 0.00 37.17 3.06
2601 2748 0.865769 CACACCAAGCGTCAGGTAAC 59.134 55.000 0.00 0.00 36.07 2.50
2781 3704 2.681706 CATGTACCAGCGATCCAGATC 58.318 52.381 0.00 0.00 34.56 2.75
2869 3792 5.336213 CCAAAGAACAATGAGGAATGTCAGG 60.336 44.000 0.00 0.00 0.00 3.86
2879 3802 5.065914 TCAAGAGGACCAAAGAACAATGAG 58.934 41.667 0.00 0.00 0.00 2.90
2906 3833 2.032290 CGCACCATGTTCATATCTGCAG 60.032 50.000 7.63 7.63 0.00 4.41
2913 3840 1.308047 GGCATCGCACCATGTTCATA 58.692 50.000 0.00 0.00 0.00 2.15
2978 3905 1.398692 GGCAGGACCAAGAACAAACA 58.601 50.000 0.00 0.00 38.86 2.83
3029 3957 2.616842 CTGTACCACAGGTTGTTCCAAC 59.383 50.000 0.00 0.00 42.35 3.77
3156 4088 1.144936 GCGGCAGTATCCAGCTTCT 59.855 57.895 0.00 0.00 0.00 2.85
3175 4107 1.275010 TCGTAGTTGAAGATGGCAGCA 59.725 47.619 5.19 0.00 0.00 4.41
3312 4248 1.005867 GCACAAACCATGCCACAGG 60.006 57.895 0.00 0.00 37.08 4.00
3322 4258 5.163713 GGAGTTGAGAATATCTGCACAAACC 60.164 44.000 0.00 0.00 0.00 3.27
3679 4630 2.672188 TAACACATTTCCACAACGCG 57.328 45.000 3.53 3.53 0.00 6.01
3730 4681 0.042581 TGACTATCCCCCTGTCAGCA 59.957 55.000 0.00 0.00 36.03 4.41
3767 4718 3.000727 GCGATGGAATTTATCTACCCCG 58.999 50.000 0.00 0.00 0.00 5.73
3833 4789 6.589523 TCCATTTGTGCAATTTCCTATTTTCG 59.410 34.615 0.00 0.00 0.00 3.46
3874 4830 7.464710 GCATTAAACATTGACCGACAAAACAAA 60.465 33.333 0.00 0.00 42.03 2.83
3882 4838 4.419522 ACTGCATTAAACATTGACCGAC 57.580 40.909 0.00 0.00 0.00 4.79
3886 4842 8.519492 ACAAACATACTGCATTAAACATTGAC 57.481 30.769 0.00 0.00 0.00 3.18
4023 4983 3.300765 GCAGCAAGCCAGCCAAGT 61.301 61.111 0.00 0.00 37.23 3.16
4151 8317 7.779326 TCATGATCTAATAGTGCATGGGAAAAA 59.221 33.333 17.76 3.40 37.51 1.94
4156 8322 6.882678 TCAATCATGATCTAATAGTGCATGGG 59.117 38.462 9.06 11.64 37.51 4.00
4230 8396 7.701539 ATGAGTGGACAAAATACATAAGCAA 57.298 32.000 0.00 0.00 0.00 3.91
4322 8501 4.523083 GATTGGCCATAAACAGACCACTA 58.477 43.478 6.09 0.00 0.00 2.74
4326 8584 2.639065 TCGATTGGCCATAAACAGACC 58.361 47.619 6.09 0.00 0.00 3.85
4356 8614 3.292460 AGGATCTCAGGGTACGAAGAAG 58.708 50.000 0.00 0.00 0.00 2.85
4368 8626 2.290514 TGCCAACAAGGAAGGATCTCAG 60.291 50.000 0.00 0.00 41.22 3.35
4542 8915 1.672030 TGATCCTTGCTGCACCACG 60.672 57.895 0.00 0.00 0.00 4.94
4544 8917 0.607217 CAGTGATCCTTGCTGCACCA 60.607 55.000 0.00 0.00 31.85 4.17
4583 8970 0.394938 TTCTAGTGTGCGCCTTTCCA 59.605 50.000 4.18 0.00 0.00 3.53
4584 8971 1.666189 GATTCTAGTGTGCGCCTTTCC 59.334 52.381 4.18 0.00 0.00 3.13
4585 8972 1.324736 CGATTCTAGTGTGCGCCTTTC 59.675 52.381 4.18 0.00 0.00 2.62
4586 8973 1.067142 TCGATTCTAGTGTGCGCCTTT 60.067 47.619 4.18 0.00 0.00 3.11
4605 8992 2.072298 GCGTATGAATGGCAGGAGATC 58.928 52.381 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.