Multiple sequence alignment - TraesCS1D01G177000

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G177000 chr1D 100.000 2366 0 0 1 2366 252300688 252303053 0.000000e+00 4370.0
1 TraesCS1D01G177000 chr1A 89.055 2202 109 52 29 2165 323206115 323203981 0.000000e+00 2610.0
2 TraesCS1D01G177000 chr1A 86.248 669 57 16 1515 2178 323203064 323202426 0.000000e+00 693.0
3 TraesCS1D01G177000 chr1B 90.413 1502 71 30 831 2320 361462357 361460917 0.000000e+00 1908.0
4 TraesCS1D01G177000 chr1B 86.755 453 25 16 354 788 361463070 361462635 2.750000e-129 472.0
5 TraesCS1D01G177000 chr1B 91.083 314 13 4 17 329 361463366 361463067 6.090000e-111 411.0
6 TraesCS1D01G177000 chr7A 87.037 54 3 4 2276 2327 138643497 138643548 9.130000e-05 58.4


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 TraesCS1D01G177000 chr1D 252300688 252303053 2365 False 4370.000000 4370 100.0000 1 2366 1 chr1D.!!$F1 2365
1 TraesCS1D01G177000 chr1A 323202426 323206115 3689 True 1651.500000 2610 87.6515 29 2178 2 chr1A.!!$R1 2149
2 TraesCS1D01G177000 chr1B 361460917 361463366 2449 True 930.333333 1908 89.4170 17 2320 3 chr1B.!!$R1 2303

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
292 310 0.466555 CCAAGTCAACCCCAAACCGA 60.467 55.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 2076 0.034896 TCCCGTCAAAAGAGTGAGGC 59.965 55.0 0.0 0.0 33.11 4.7 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
201 214 4.342378 GCCCCAGAAAGAATATCCTTTTCC 59.658 45.833 0.00 0.00 36.58 3.13
202 215 5.770919 CCCCAGAAAGAATATCCTTTTCCT 58.229 41.667 0.00 0.00 36.58 3.36
203 216 6.197903 CCCCAGAAAGAATATCCTTTTCCTT 58.802 40.000 0.00 0.00 36.58 3.36
204 217 6.322456 CCCCAGAAAGAATATCCTTTTCCTTC 59.678 42.308 0.00 0.00 36.58 3.46
221 234 5.857471 TCCTTCCGTTATTATCCTCGAAA 57.143 39.130 0.00 0.00 0.00 3.46
291 309 2.037871 CCAAGTCAACCCCAAACCG 58.962 57.895 0.00 0.00 0.00 4.44
292 310 0.466555 CCAAGTCAACCCCAAACCGA 60.467 55.000 0.00 0.00 0.00 4.69
334 356 2.669364 ACACGCGAGAAAAGAATACGT 58.331 42.857 15.93 0.00 0.00 3.57
359 381 0.612453 ACTCTCGAGTCCCAAGACCC 60.612 60.000 13.13 0.00 44.72 4.46
419 444 3.740128 CTGAACCCAGATCGGCCGG 62.740 68.421 27.83 10.66 43.02 6.13
495 532 0.543174 GACCTGACCTGACCTGACCT 60.543 60.000 0.00 0.00 0.00 3.85
633 686 2.031465 GCACGGGAAGGAAACGGA 59.969 61.111 0.00 0.00 0.00 4.69
634 687 2.033194 GCACGGGAAGGAAACGGAG 61.033 63.158 0.00 0.00 0.00 4.63
635 688 1.375523 CACGGGAAGGAAACGGAGG 60.376 63.158 0.00 0.00 0.00 4.30
636 689 1.534717 ACGGGAAGGAAACGGAGGA 60.535 57.895 0.00 0.00 0.00 3.71
691 757 0.626916 ACCCGGGGCTGCTATAAAAA 59.373 50.000 27.92 0.00 0.00 1.94
729 796 1.662686 CCAACCTCCCCTCTTCTTCT 58.337 55.000 0.00 0.00 0.00 2.85
746 813 0.675083 TCTTCGCCAACAACGACCTA 59.325 50.000 0.00 0.00 39.67 3.08
747 814 0.788391 CTTCGCCAACAACGACCTAC 59.212 55.000 0.00 0.00 39.67 3.18
749 816 1.372004 CGCCAACAACGACCTACGA 60.372 57.895 0.00 0.00 45.77 3.43
758 825 1.224039 CGACCTACGACCTCCTCCT 59.776 63.158 0.00 0.00 45.77 3.69
910 1213 0.849540 CCTAACCCCAAACCCCTCCT 60.850 60.000 0.00 0.00 0.00 3.69
911 1214 0.624254 CTAACCCCAAACCCCTCCTC 59.376 60.000 0.00 0.00 0.00 3.71
914 1217 3.728373 CCCAAACCCCTCCTCCCG 61.728 72.222 0.00 0.00 0.00 5.14
927 1230 4.116585 TCCCGCCTCTCGAGCTCT 62.117 66.667 12.85 0.00 41.67 4.09
949 1252 4.220163 TCCGATCTCCCTCCCCCG 62.220 72.222 0.00 0.00 0.00 5.73
974 1278 2.037136 CCTTCCTCGCAACAGCCAG 61.037 63.158 0.00 0.00 0.00 4.85
1167 1474 2.496341 CTGCTCGATGAGGCCGAA 59.504 61.111 0.00 0.00 35.48 4.30
1439 1753 3.974642 AGGGTTGGTTGAGTAGTTCTCTT 59.025 43.478 0.00 0.00 43.13 2.85
1530 1848 3.370104 TGGTTGTTCTCCATTGGTTTGT 58.630 40.909 1.86 0.00 0.00 2.83
1588 1910 7.712797 TCCATGTTGATGATGATGATGAAAAG 58.287 34.615 0.00 0.00 0.00 2.27
1686 2010 1.801025 GCTCTCCGCAGAAGAAGTAGC 60.801 57.143 0.00 0.00 38.92 3.58
1687 2011 1.748493 CTCTCCGCAGAAGAAGTAGCT 59.252 52.381 0.00 0.00 0.00 3.32
1688 2012 1.474478 TCTCCGCAGAAGAAGTAGCTG 59.526 52.381 0.00 0.00 0.00 4.24
1689 2013 1.203523 CTCCGCAGAAGAAGTAGCTGT 59.796 52.381 0.00 0.00 32.39 4.40
1690 2014 1.067565 TCCGCAGAAGAAGTAGCTGTG 60.068 52.381 0.00 0.00 39.26 3.66
1691 2015 1.354040 CGCAGAAGAAGTAGCTGTGG 58.646 55.000 0.00 0.00 36.72 4.17
1692 2016 1.337260 CGCAGAAGAAGTAGCTGTGGT 60.337 52.381 0.00 0.00 36.72 4.16
1693 2017 2.772287 GCAGAAGAAGTAGCTGTGGTT 58.228 47.619 0.00 0.00 32.39 3.67
1694 2018 2.481952 GCAGAAGAAGTAGCTGTGGTTG 59.518 50.000 0.00 0.00 32.39 3.77
1695 2019 3.733337 CAGAAGAAGTAGCTGTGGTTGT 58.267 45.455 0.00 0.00 0.00 3.32
1696 2020 3.496130 CAGAAGAAGTAGCTGTGGTTGTG 59.504 47.826 0.00 0.00 0.00 3.33
1697 2021 1.884235 AGAAGTAGCTGTGGTTGTGC 58.116 50.000 0.00 0.00 0.00 4.57
1698 2022 0.875059 GAAGTAGCTGTGGTTGTGCC 59.125 55.000 0.00 0.00 37.90 5.01
1699 2023 0.474184 AAGTAGCTGTGGTTGTGCCT 59.526 50.000 0.00 0.00 38.35 4.75
1700 2024 0.474184 AGTAGCTGTGGTTGTGCCTT 59.526 50.000 0.00 0.00 38.35 4.35
1701 2025 0.593128 GTAGCTGTGGTTGTGCCTTG 59.407 55.000 0.00 0.00 38.35 3.61
1702 2026 0.537143 TAGCTGTGGTTGTGCCTTGG 60.537 55.000 0.00 0.00 38.35 3.61
1703 2027 2.859981 GCTGTGGTTGTGCCTTGGG 61.860 63.158 0.00 0.00 38.35 4.12
1714 2038 4.853468 TGTGCCTTGGGAGAATATGTTA 57.147 40.909 0.00 0.00 0.00 2.41
1733 2057 5.286438 TGTTATTGCTTGTCTACGCGATAT 58.714 37.500 15.93 0.00 33.71 1.63
1746 2070 7.273381 TGTCTACGCGATATATCATCAAACATG 59.727 37.037 15.93 0.00 0.00 3.21
1752 2076 8.201401 CGCGATATATCATCAAACATGTATACG 58.799 37.037 13.11 0.00 0.00 3.06
1774 2098 2.548480 CCTCACTCTTTTGACGGGAAAC 59.452 50.000 0.00 0.00 0.00 2.78
1775 2099 3.467803 CTCACTCTTTTGACGGGAAACT 58.532 45.455 0.00 0.00 0.00 2.66
1776 2100 4.502604 CCTCACTCTTTTGACGGGAAACTA 60.503 45.833 0.00 0.00 0.00 2.24
1777 2101 4.374399 TCACTCTTTTGACGGGAAACTAC 58.626 43.478 0.00 0.00 0.00 2.73
1780 2104 5.065474 CACTCTTTTGACGGGAAACTACAAA 59.935 40.000 0.00 0.00 0.00 2.83
1782 2106 4.577283 TCTTTTGACGGGAAACTACAAAGG 59.423 41.667 0.00 0.00 33.23 3.11
1785 2109 3.469739 TGACGGGAAACTACAAAGGAAC 58.530 45.455 0.00 0.00 0.00 3.62
1805 2129 5.490139 AACTTGTCGATAAATGCATCTGG 57.510 39.130 0.00 0.00 0.00 3.86
1807 2131 4.813161 ACTTGTCGATAAATGCATCTGGAG 59.187 41.667 0.00 0.00 0.00 3.86
1808 2132 4.406648 TGTCGATAAATGCATCTGGAGT 57.593 40.909 0.00 0.00 0.00 3.85
1809 2133 5.529581 TGTCGATAAATGCATCTGGAGTA 57.470 39.130 0.00 0.00 0.00 2.59
1815 2142 7.611855 TCGATAAATGCATCTGGAGTAGATAGA 59.388 37.037 0.00 0.00 44.34 1.98
1856 2183 7.277098 TCAAAATTAGTACTATCTCGCACCAAC 59.723 37.037 2.79 0.00 0.00 3.77
1858 2185 5.648178 TTAGTACTATCTCGCACCAACAA 57.352 39.130 2.79 0.00 0.00 2.83
1866 2193 2.161410 TCTCGCACCAACAAATACATGC 59.839 45.455 0.00 0.00 0.00 4.06
1983 2311 7.977818 TGGTGAGCATATCCAAGTAATATTCT 58.022 34.615 0.00 0.00 0.00 2.40
2001 2329 4.796038 TTCTGGGGTTCGTTCTTACTAG 57.204 45.455 0.00 0.00 0.00 2.57
2070 2398 9.474313 TCTAGGTGCCAAAATTAGTTAAATGAT 57.526 29.630 0.00 0.00 0.00 2.45
2097 2425 0.966920 TCTTGTCACCTCGGAAGGAC 59.033 55.000 0.00 0.00 46.67 3.85
2098 2426 0.679505 CTTGTCACCTCGGAAGGACA 59.320 55.000 0.00 0.00 46.67 4.02
2116 2444 8.803235 GGAAGGACAATTAAAGGTTTCACTAAT 58.197 33.333 0.00 0.00 0.00 1.73
2182 2511 2.340210 TTGCAGCACTACCAAAGACA 57.660 45.000 0.00 0.00 0.00 3.41
2190 2519 0.618981 CTACCAAAGACACCCCCTCC 59.381 60.000 0.00 0.00 0.00 4.30
2191 2520 0.843343 TACCAAAGACACCCCCTCCC 60.843 60.000 0.00 0.00 0.00 4.30
2192 2521 2.763902 CAAAGACACCCCCTCCCC 59.236 66.667 0.00 0.00 0.00 4.81
2193 2522 2.534533 AAAGACACCCCCTCCCCC 60.535 66.667 0.00 0.00 0.00 5.40
2194 2523 3.142715 AAAGACACCCCCTCCCCCT 62.143 63.158 0.00 0.00 0.00 4.79
2195 2524 3.581141 AAGACACCCCCTCCCCCTC 62.581 68.421 0.00 0.00 0.00 4.30
2208 2537 4.302930 CCTCCCCCTCTCTTTCTATCTTT 58.697 47.826 0.00 0.00 0.00 2.52
2209 2538 4.346709 CCTCCCCCTCTCTTTCTATCTTTC 59.653 50.000 0.00 0.00 0.00 2.62
2210 2539 4.299485 TCCCCCTCTCTTTCTATCTTTCC 58.701 47.826 0.00 0.00 0.00 3.13
2211 2540 4.040755 CCCCCTCTCTTTCTATCTTTCCA 58.959 47.826 0.00 0.00 0.00 3.53
2217 2745 6.597280 CCTCTCTTTCTATCTTTCCACTTTGG 59.403 42.308 0.00 0.00 39.43 3.28
2295 2823 3.765511 ACAAACATATTGAGCATGCACCT 59.234 39.130 21.98 6.50 0.00 4.00
2299 2827 0.752743 TATTGAGCATGCACCTGGCC 60.753 55.000 21.98 0.00 43.89 5.36
2320 2848 4.991687 GCCTCTACATAACTAAGATGCACC 59.008 45.833 0.00 0.00 32.95 5.01
2321 2849 5.221541 GCCTCTACATAACTAAGATGCACCT 60.222 44.000 0.00 0.00 32.95 4.00
2322 2850 6.451393 CCTCTACATAACTAAGATGCACCTC 58.549 44.000 0.00 0.00 0.00 3.85
2323 2851 6.040955 CCTCTACATAACTAAGATGCACCTCA 59.959 42.308 0.00 0.00 0.00 3.86
2325 2853 4.446371 ACATAACTAAGATGCACCTCAGC 58.554 43.478 0.00 0.00 0.00 4.26
2326 2854 2.409948 AACTAAGATGCACCTCAGCC 57.590 50.000 0.00 0.00 0.00 4.85
2327 2855 1.577736 ACTAAGATGCACCTCAGCCT 58.422 50.000 0.00 0.00 0.00 4.58
2328 2856 1.912043 ACTAAGATGCACCTCAGCCTT 59.088 47.619 0.00 0.00 0.00 4.35
2329 2857 2.286872 CTAAGATGCACCTCAGCCTTG 58.713 52.381 0.00 0.00 0.00 3.61
2330 2858 0.403271 AAGATGCACCTCAGCCTTGT 59.597 50.000 0.00 0.00 0.00 3.16
2332 2860 1.303888 ATGCACCTCAGCCTTGTGG 60.304 57.895 0.00 0.00 42.41 4.17
2342 2870 2.043652 CCTTGTGGCCTGATGGGG 60.044 66.667 3.32 0.00 35.12 4.96
2343 2871 2.765969 CTTGTGGCCTGATGGGGT 59.234 61.111 3.32 0.00 35.12 4.95
2344 2872 1.679977 CTTGTGGCCTGATGGGGTG 60.680 63.158 3.32 0.00 35.12 4.61
2345 2873 3.884704 TTGTGGCCTGATGGGGTGC 62.885 63.158 3.32 0.00 35.12 5.01
2348 2876 4.828296 GGCCTGATGGGGTGCCAG 62.828 72.222 0.00 0.00 43.46 4.85
2349 2877 3.731728 GCCTGATGGGGTGCCAGA 61.732 66.667 0.00 0.00 35.12 3.86
2350 2878 2.273449 CCTGATGGGGTGCCAGAC 59.727 66.667 0.00 0.00 0.00 3.51
2351 2879 2.304056 CCTGATGGGGTGCCAGACT 61.304 63.158 0.00 0.00 0.00 3.24
2352 2880 1.687612 CTGATGGGGTGCCAGACTT 59.312 57.895 0.00 0.00 0.00 3.01
2353 2881 0.038744 CTGATGGGGTGCCAGACTTT 59.961 55.000 0.00 0.00 0.00 2.66
2354 2882 0.251297 TGATGGGGTGCCAGACTTTG 60.251 55.000 0.00 0.00 0.00 2.77
2355 2883 0.251341 GATGGGGTGCCAGACTTTGT 60.251 55.000 0.00 0.00 0.00 2.83
2356 2884 0.188342 ATGGGGTGCCAGACTTTGTT 59.812 50.000 0.00 0.00 0.00 2.83
2359 2887 1.620822 GGGTGCCAGACTTTGTTCAT 58.379 50.000 0.00 0.00 0.00 2.57
2360 2888 1.270550 GGGTGCCAGACTTTGTTCATG 59.729 52.381 0.00 0.00 0.00 3.07
2362 2890 0.592637 TGCCAGACTTTGTTCATGCG 59.407 50.000 0.00 0.00 0.00 4.73
2364 2892 1.470098 GCCAGACTTTGTTCATGCGAT 59.530 47.619 0.00 0.00 0.00 4.58
2365 2893 2.730090 GCCAGACTTTGTTCATGCGATG 60.730 50.000 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.787334 ATTCCTATCTGATCTGAATTCTCCTAT 57.213 33.333 7.05 0.00 0.00 2.57
2 3 9.612879 AATTCCTATCTGATCTGAATTCTCCTA 57.387 33.333 15.83 0.00 31.83 2.94
3 4 8.508969 AATTCCTATCTGATCTGAATTCTCCT 57.491 34.615 15.83 0.00 31.83 3.69
4 5 9.571816 AAAATTCCTATCTGATCTGAATTCTCC 57.428 33.333 19.26 0.00 35.28 3.71
6 7 9.917887 ACAAAATTCCTATCTGATCTGAATTCT 57.082 29.630 19.26 9.65 35.28 2.40
8 9 9.690913 TGACAAAATTCCTATCTGATCTGAATT 57.309 29.630 15.83 15.83 37.27 2.17
9 10 9.863650 ATGACAAAATTCCTATCTGATCTGAAT 57.136 29.630 6.37 1.32 0.00 2.57
11 12 9.770097 GTATGACAAAATTCCTATCTGATCTGA 57.230 33.333 4.63 4.63 0.00 3.27
12 13 9.551734 TGTATGACAAAATTCCTATCTGATCTG 57.448 33.333 0.00 0.00 0.00 2.90
44 46 3.249320 CCGGATTCAGACAGTTGCATATG 59.751 47.826 0.00 0.00 0.00 1.78
121 123 1.516042 GGTATTCGTTCGCTCGTTAGC 59.484 52.381 0.00 0.00 45.86 3.09
122 124 3.034562 GAGGTATTCGTTCGCTCGTTAG 58.965 50.000 0.00 0.00 0.00 2.34
123 125 2.419673 TGAGGTATTCGTTCGCTCGTTA 59.580 45.455 0.00 0.00 0.00 3.18
124 126 1.200716 TGAGGTATTCGTTCGCTCGTT 59.799 47.619 0.00 0.00 0.00 3.85
125 127 0.806868 TGAGGTATTCGTTCGCTCGT 59.193 50.000 0.00 0.00 0.00 4.18
177 187 3.602205 AAGGATATTCTTTCTGGGGCC 57.398 47.619 0.00 0.00 0.00 5.80
201 214 6.200475 GGTTCTTTCGAGGATAATAACGGAAG 59.800 42.308 0.00 0.00 41.06 3.46
202 215 6.044682 GGTTCTTTCGAGGATAATAACGGAA 58.955 40.000 0.00 0.00 0.00 4.30
203 216 5.452356 GGGTTCTTTCGAGGATAATAACGGA 60.452 44.000 0.00 0.00 0.00 4.69
204 217 4.748600 GGGTTCTTTCGAGGATAATAACGG 59.251 45.833 0.00 0.00 0.00 4.44
291 309 5.705609 ACTGTTTGTTCTCTCTCTCTCTC 57.294 43.478 0.00 0.00 0.00 3.20
292 310 6.016610 GTGTACTGTTTGTTCTCTCTCTCTCT 60.017 42.308 0.00 0.00 0.00 3.10
334 356 3.893200 TCTTGGGACTCGAGAGTTTGTTA 59.107 43.478 21.68 0.00 42.66 2.41
359 381 1.465689 CGGTTACGATTTGCTTGGCTG 60.466 52.381 0.00 0.00 44.60 4.85
495 532 2.765705 GAAGGGAGGGGAGGTGGTCA 62.766 65.000 0.00 0.00 0.00 4.02
589 638 2.110967 TCTCCGTTACCCGAGCGAG 61.111 63.158 0.00 0.00 39.56 5.03
671 727 0.106918 TTTTATAGCAGCCCCGGGTG 60.107 55.000 21.85 13.78 45.36 4.61
672 728 0.626916 TTTTTATAGCAGCCCCGGGT 59.373 50.000 21.85 1.96 0.00 5.28
673 729 1.318576 CTTTTTATAGCAGCCCCGGG 58.681 55.000 15.80 15.80 0.00 5.73
676 742 0.668535 CCGCTTTTTATAGCAGCCCC 59.331 55.000 0.00 0.00 41.28 5.80
729 796 0.940519 CGTAGGTCGTTGTTGGCGAA 60.941 55.000 0.00 0.00 40.19 4.70
746 813 1.304547 CTGGTGAGGAGGAGGTCGT 60.305 63.158 0.00 0.00 0.00 4.34
747 814 0.612174 TTCTGGTGAGGAGGAGGTCG 60.612 60.000 0.00 0.00 0.00 4.79
748 815 1.645710 TTTCTGGTGAGGAGGAGGTC 58.354 55.000 0.00 0.00 0.00 3.85
749 816 2.118403 TTTTCTGGTGAGGAGGAGGT 57.882 50.000 0.00 0.00 0.00 3.85
773 841 0.600057 CCACCTTGCCTGCTTTCTTC 59.400 55.000 0.00 0.00 0.00 2.87
775 843 0.251077 CTCCACCTTGCCTGCTTTCT 60.251 55.000 0.00 0.00 0.00 2.52
910 1213 4.116585 AGAGCTCGAGAGGCGGGA 62.117 66.667 18.75 0.00 45.56 5.14
911 1214 3.898509 CAGAGCTCGAGAGGCGGG 61.899 72.222 18.75 0.00 45.45 6.13
914 1217 4.567385 CGGCAGAGCTCGAGAGGC 62.567 72.222 18.75 12.69 0.00 4.70
927 1230 2.833582 GAGGGAGATCGGACGGCA 60.834 66.667 0.00 0.00 0.00 5.69
949 1252 0.108567 GTTGCGAGGAAGGAGGAGAC 60.109 60.000 0.00 0.00 0.00 3.36
974 1278 1.801983 GAGGACCGGACGAGTCTTC 59.198 63.158 9.46 0.00 33.86 2.87
1149 1456 3.081311 TTCGGCCTCATCGAGCAGG 62.081 63.158 0.00 7.90 37.93 4.85
1158 1465 3.057548 TACTCGCGTTCGGCCTCA 61.058 61.111 5.77 0.00 38.94 3.86
1167 1474 2.178521 CTGAAGCCGTACTCGCGT 59.821 61.111 5.77 0.00 35.54 6.01
1530 1848 2.559698 TCGATTCTCCCAGCACAAAA 57.440 45.000 0.00 0.00 0.00 2.44
1679 2003 0.875059 GGCACAACCACAGCTACTTC 59.125 55.000 0.00 0.00 38.86 3.01
1686 2010 1.152777 TCCCAAGGCACAACCACAG 60.153 57.895 0.00 0.00 43.14 3.66
1687 2011 1.152777 CTCCCAAGGCACAACCACA 60.153 57.895 0.00 0.00 43.14 4.17
1688 2012 0.467290 TTCTCCCAAGGCACAACCAC 60.467 55.000 0.00 0.00 43.14 4.16
1689 2013 0.482446 ATTCTCCCAAGGCACAACCA 59.518 50.000 0.00 0.00 43.14 3.67
1690 2014 2.507407 TATTCTCCCAAGGCACAACC 57.493 50.000 0.00 0.00 39.61 3.77
1691 2015 3.356290 ACATATTCTCCCAAGGCACAAC 58.644 45.455 0.00 0.00 0.00 3.32
1692 2016 3.737559 ACATATTCTCCCAAGGCACAA 57.262 42.857 0.00 0.00 0.00 3.33
1693 2017 3.737559 AACATATTCTCCCAAGGCACA 57.262 42.857 0.00 0.00 0.00 4.57
1694 2018 5.507985 GCAATAACATATTCTCCCAAGGCAC 60.508 44.000 0.00 0.00 0.00 5.01
1695 2019 4.584325 GCAATAACATATTCTCCCAAGGCA 59.416 41.667 0.00 0.00 0.00 4.75
1696 2020 4.829492 AGCAATAACATATTCTCCCAAGGC 59.171 41.667 0.00 0.00 0.00 4.35
1697 2021 6.322201 ACAAGCAATAACATATTCTCCCAAGG 59.678 38.462 0.00 0.00 0.00 3.61
1698 2022 7.284034 AGACAAGCAATAACATATTCTCCCAAG 59.716 37.037 0.00 0.00 0.00 3.61
1699 2023 7.118723 AGACAAGCAATAACATATTCTCCCAA 58.881 34.615 0.00 0.00 0.00 4.12
1700 2024 6.662755 AGACAAGCAATAACATATTCTCCCA 58.337 36.000 0.00 0.00 0.00 4.37
1701 2025 7.095607 CGTAGACAAGCAATAACATATTCTCCC 60.096 40.741 0.00 0.00 0.00 4.30
1702 2026 7.569591 GCGTAGACAAGCAATAACATATTCTCC 60.570 40.741 0.00 0.00 0.00 3.71
1703 2027 7.284351 GCGTAGACAAGCAATAACATATTCTC 58.716 38.462 0.00 0.00 0.00 2.87
1714 2038 5.709966 TGATATATCGCGTAGACAAGCAAT 58.290 37.500 5.77 0.00 0.00 3.56
1733 2057 6.645003 GTGAGGCGTATACATGTTTGATGATA 59.355 38.462 2.30 0.00 0.00 2.15
1746 2070 3.546670 CGTCAAAAGAGTGAGGCGTATAC 59.453 47.826 0.00 0.00 0.00 1.47
1752 2076 0.034896 TCCCGTCAAAAGAGTGAGGC 59.965 55.000 0.00 0.00 33.11 4.70
1774 2098 6.961554 GCATTTATCGACAAGTTCCTTTGTAG 59.038 38.462 0.00 0.00 41.15 2.74
1775 2099 6.428465 TGCATTTATCGACAAGTTCCTTTGTA 59.572 34.615 0.00 0.00 41.15 2.41
1776 2100 5.240623 TGCATTTATCGACAAGTTCCTTTGT 59.759 36.000 0.00 0.00 43.61 2.83
1777 2101 5.698832 TGCATTTATCGACAAGTTCCTTTG 58.301 37.500 0.00 0.00 0.00 2.77
1780 2104 5.295292 CAGATGCATTTATCGACAAGTTCCT 59.705 40.000 0.00 0.00 32.33 3.36
1782 2106 5.294306 TCCAGATGCATTTATCGACAAGTTC 59.706 40.000 0.00 0.00 32.33 3.01
1785 2109 4.813161 ACTCCAGATGCATTTATCGACAAG 59.187 41.667 0.00 0.00 32.33 3.16
1789 2113 6.596309 ATCTACTCCAGATGCATTTATCGA 57.404 37.500 0.00 0.00 42.69 3.59
1831 2158 7.064134 TGTTGGTGCGAGATAGTACTAATTTTG 59.936 37.037 6.70 1.20 31.21 2.44
1832 2159 7.101054 TGTTGGTGCGAGATAGTACTAATTTT 58.899 34.615 6.70 0.00 31.21 1.82
1836 2163 5.648178 TTGTTGGTGCGAGATAGTACTAA 57.352 39.130 6.70 0.00 0.00 2.24
1840 2167 5.968254 TGTATTTGTTGGTGCGAGATAGTA 58.032 37.500 0.00 0.00 0.00 1.82
1866 2193 0.950836 TTGTGAATTGTGCCGTCTGG 59.049 50.000 0.00 0.00 38.77 3.86
1983 2311 6.211184 TCAATTACTAGTAAGAACGAACCCCA 59.789 38.462 19.58 0.00 0.00 4.96
2168 2496 0.608308 GGGGGTGTCTTTGGTAGTGC 60.608 60.000 0.00 0.00 0.00 4.40
2169 2497 1.003233 GAGGGGGTGTCTTTGGTAGTG 59.997 57.143 0.00 0.00 0.00 2.74
2170 2498 1.359168 GAGGGGGTGTCTTTGGTAGT 58.641 55.000 0.00 0.00 0.00 2.73
2171 2499 0.618981 GGAGGGGGTGTCTTTGGTAG 59.381 60.000 0.00 0.00 0.00 3.18
2182 2511 2.494151 GAAAGAGAGGGGGAGGGGGT 62.494 65.000 0.00 0.00 0.00 4.95
2190 2519 4.719273 AGTGGAAAGATAGAAAGAGAGGGG 59.281 45.833 0.00 0.00 0.00 4.79
2191 2520 5.948742 AGTGGAAAGATAGAAAGAGAGGG 57.051 43.478 0.00 0.00 0.00 4.30
2192 2521 6.597280 CCAAAGTGGAAAGATAGAAAGAGAGG 59.403 42.308 0.00 0.00 40.96 3.69
2193 2522 7.164803 ACCAAAGTGGAAAGATAGAAAGAGAG 58.835 38.462 0.18 0.00 40.96 3.20
2194 2523 7.079451 ACCAAAGTGGAAAGATAGAAAGAGA 57.921 36.000 0.18 0.00 40.96 3.10
2195 2524 7.751768 AACCAAAGTGGAAAGATAGAAAGAG 57.248 36.000 0.18 0.00 40.96 2.85
2273 2801 3.765511 AGGTGCATGCTCAATATGTTTGT 59.234 39.130 20.33 0.00 0.00 2.83
2286 2814 1.821332 GTAGAGGCCAGGTGCATGC 60.821 63.158 11.82 11.82 43.89 4.06
2290 2818 1.486726 AGTTATGTAGAGGCCAGGTGC 59.513 52.381 5.01 0.00 40.16 5.01
2295 2823 4.653801 TGCATCTTAGTTATGTAGAGGCCA 59.346 41.667 5.01 0.00 43.05 5.36
2299 2827 7.043961 TGAGGTGCATCTTAGTTATGTAGAG 57.956 40.000 0.00 0.00 0.00 2.43
2325 2853 2.043652 CCCCATCAGGCCACAAGG 60.044 66.667 5.01 0.65 38.23 3.61
2326 2854 1.679977 CACCCCATCAGGCCACAAG 60.680 63.158 5.01 0.00 0.00 3.16
2327 2855 2.440147 CACCCCATCAGGCCACAA 59.560 61.111 5.01 0.00 0.00 3.33
2328 2856 4.365111 GCACCCCATCAGGCCACA 62.365 66.667 5.01 0.00 0.00 4.17
2332 2860 3.731728 TCTGGCACCCCATCAGGC 61.732 66.667 0.00 0.00 41.21 4.85
2333 2861 1.856539 AAGTCTGGCACCCCATCAGG 61.857 60.000 0.00 0.00 41.21 3.86
2334 2862 0.038744 AAAGTCTGGCACCCCATCAG 59.961 55.000 0.00 0.00 41.21 2.90
2335 2863 0.251297 CAAAGTCTGGCACCCCATCA 60.251 55.000 0.00 0.00 41.21 3.07
2336 2864 0.251341 ACAAAGTCTGGCACCCCATC 60.251 55.000 0.00 0.00 41.21 3.51
2338 2866 0.467290 GAACAAAGTCTGGCACCCCA 60.467 55.000 0.00 0.00 39.32 4.96
2339 2867 0.467290 TGAACAAAGTCTGGCACCCC 60.467 55.000 0.00 0.00 0.00 4.95
2340 2868 1.270550 CATGAACAAAGTCTGGCACCC 59.729 52.381 0.00 0.00 0.00 4.61
2341 2869 1.336240 GCATGAACAAAGTCTGGCACC 60.336 52.381 0.00 0.00 0.00 5.01
2342 2870 1.664016 CGCATGAACAAAGTCTGGCAC 60.664 52.381 0.00 0.00 0.00 5.01
2343 2871 0.592637 CGCATGAACAAAGTCTGGCA 59.407 50.000 0.00 0.00 0.00 4.92
2344 2872 0.874390 TCGCATGAACAAAGTCTGGC 59.126 50.000 0.00 0.00 0.00 4.85
2345 2873 3.127081 CATCGCATGAACAAAGTCTGG 57.873 47.619 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.