Multiple sequence alignment - TraesCS5A01G184000

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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 TraesCS5A01G184000 chr5A 100.000 2901 0 0 1 2901 383874937 383877837 0.000000e+00 5358.0
1 TraesCS5A01G184000 chr5A 84.968 938 125 14 1937 2868 513205451 513206378 0.000000e+00 937.0
2 TraesCS5A01G184000 chr5A 81.592 804 127 12 1972 2766 655495300 655494509 0.000000e+00 645.0
3 TraesCS5A01G184000 chr5D 94.002 1217 46 10 731 1945 291496276 291497467 0.000000e+00 1818.0
4 TraesCS5A01G184000 chr5D 86.289 970 117 13 1920 2877 228261248 228262213 0.000000e+00 1040.0
5 TraesCS5A01G184000 chr5D 87.663 843 90 12 1933 2765 552631939 552631101 0.000000e+00 968.0
6 TraesCS5A01G184000 chr5D 88.423 691 47 8 1 666 291495593 291496275 0.000000e+00 802.0
7 TraesCS5A01G184000 chr1D 88.718 975 93 10 1938 2900 346392752 346391783 0.000000e+00 1175.0
8 TraesCS5A01G184000 chr1D 88.413 863 91 4 2020 2873 70580997 70581859 0.000000e+00 1031.0
9 TraesCS5A01G184000 chr7D 87.077 975 112 9 1938 2900 249618299 249619271 0.000000e+00 1090.0
10 TraesCS5A01G184000 chr2D 86.925 979 108 12 1938 2900 37012315 37013289 0.000000e+00 1081.0
11 TraesCS5A01G184000 chr2D 86.667 975 112 13 1937 2900 44466060 44467027 0.000000e+00 1064.0
12 TraesCS5A01G184000 chr6D 86.756 974 117 6 1938 2900 472759126 472758154 0.000000e+00 1074.0
13 TraesCS5A01G184000 chr5B 85.729 946 123 12 1939 2877 371906866 371907806 0.000000e+00 989.0
14 TraesCS5A01G184000 chr5B 91.542 733 33 9 1208 1940 332198677 332199380 0.000000e+00 983.0
15 TraesCS5A01G184000 chr5B 96.809 94 3 0 1087 1180 332198586 332198679 1.080000e-34 158.0
16 TraesCS5A01G184000 chr5B 89.552 67 3 1 455 521 332198522 332198584 6.660000e-12 82.4
17 TraesCS5A01G184000 chr6B 80.000 380 67 8 94 468 576366234 576366609 3.680000e-69 272.0
18 TraesCS5A01G184000 chr6B 97.143 35 0 1 1981 2015 136531298 136531331 1.120000e-04 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 TraesCS5A01G184000 chr5A 383874937 383877837 2900 False 5358.0 5358 100.000000 1 2901 1 chr5A.!!$F1 2900
1 TraesCS5A01G184000 chr5A 513205451 513206378 927 False 937.0 937 84.968000 1937 2868 1 chr5A.!!$F2 931
2 TraesCS5A01G184000 chr5A 655494509 655495300 791 True 645.0 645 81.592000 1972 2766 1 chr5A.!!$R1 794
3 TraesCS5A01G184000 chr5D 291495593 291497467 1874 False 1310.0 1818 91.212500 1 1945 2 chr5D.!!$F2 1944
4 TraesCS5A01G184000 chr5D 228261248 228262213 965 False 1040.0 1040 86.289000 1920 2877 1 chr5D.!!$F1 957
5 TraesCS5A01G184000 chr5D 552631101 552631939 838 True 968.0 968 87.663000 1933 2765 1 chr5D.!!$R1 832
6 TraesCS5A01G184000 chr1D 346391783 346392752 969 True 1175.0 1175 88.718000 1938 2900 1 chr1D.!!$R1 962
7 TraesCS5A01G184000 chr1D 70580997 70581859 862 False 1031.0 1031 88.413000 2020 2873 1 chr1D.!!$F1 853
8 TraesCS5A01G184000 chr7D 249618299 249619271 972 False 1090.0 1090 87.077000 1938 2900 1 chr7D.!!$F1 962
9 TraesCS5A01G184000 chr2D 37012315 37013289 974 False 1081.0 1081 86.925000 1938 2900 1 chr2D.!!$F1 962
10 TraesCS5A01G184000 chr2D 44466060 44467027 967 False 1064.0 1064 86.667000 1937 2900 1 chr2D.!!$F2 963
11 TraesCS5A01G184000 chr6D 472758154 472759126 972 True 1074.0 1074 86.756000 1938 2900 1 chr6D.!!$R1 962
12 TraesCS5A01G184000 chr5B 371906866 371907806 940 False 989.0 989 85.729000 1939 2877 1 chr5B.!!$F1 938
13 TraesCS5A01G184000 chr5B 332198522 332199380 858 False 407.8 983 92.634333 455 1940 3 chr5B.!!$F2 1485

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
716 742 0.103026 CGAGATGATGCGTCTTCCCA 59.897 55.0 16.07 0.0 28.91 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2181 2219 0.249953 TGGCGGCTTCTAAAACGTGA 60.25 50.0 11.43 0.0 0.0 4.35 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
25 26 0.835276 CTGATGGTGCTCAGGATGGA 59.165 55.000 0.00 0.00 39.20 3.41
64 65 9.905713 TCTGCTATGTTAATCCAGTTTAAAGAT 57.094 29.630 0.00 0.00 0.00 2.40
97 98 7.264373 ACTATTATGATGTTAGCCTGTTTGC 57.736 36.000 0.00 0.00 0.00 3.68
99 100 6.720112 ATTATGATGTTAGCCTGTTTGCAT 57.280 33.333 0.00 0.00 0.00 3.96
101 102 4.177165 TGATGTTAGCCTGTTTGCATTG 57.823 40.909 0.00 0.00 0.00 2.82
103 104 1.962807 TGTTAGCCTGTTTGCATTGCT 59.037 42.857 10.49 0.00 36.79 3.91
104 105 3.153130 TGTTAGCCTGTTTGCATTGCTA 58.847 40.909 10.49 0.00 35.28 3.49
105 106 3.763360 TGTTAGCCTGTTTGCATTGCTAT 59.237 39.130 10.49 0.00 35.90 2.97
106 107 2.953466 AGCCTGTTTGCATTGCTATG 57.047 45.000 10.49 3.56 32.92 2.23
107 108 2.173519 AGCCTGTTTGCATTGCTATGT 58.826 42.857 10.49 0.00 32.92 2.29
108 109 2.564062 AGCCTGTTTGCATTGCTATGTT 59.436 40.909 10.49 0.00 32.92 2.71
121 122 6.144402 GCATTGCTATGTTTATGGTTATGCAC 59.856 38.462 9.87 0.00 35.68 4.57
150 151 7.745717 TGCTTATCCTATGGTTTAGCTTATGT 58.254 34.615 0.00 0.00 0.00 2.29
194 196 2.731976 GGTTACGCTATGTATGCTGCTC 59.268 50.000 0.00 0.00 31.81 4.26
196 198 0.319040 ACGCTATGTATGCTGCTCCG 60.319 55.000 0.00 0.00 0.00 4.63
242 244 3.447944 CACCACTCCTAGAAGAGGTTACC 59.552 52.174 0.00 0.00 46.76 2.85
272 274 8.687242 TCATTTGAGTTGTATGTAACCAAACAA 58.313 29.630 0.00 0.00 35.55 2.83
290 292 2.071540 CAACAGCTCTTTGCATCTCGA 58.928 47.619 0.00 0.00 45.94 4.04
296 298 4.208873 CAGCTCTTTGCATCTCGATAGAAC 59.791 45.833 0.00 0.00 45.68 3.01
335 337 0.534203 GGTTCCGGTGTTTCTGCTCA 60.534 55.000 0.00 0.00 0.00 4.26
348 350 1.605992 TGCTCAGGCAGATTGGAGG 59.394 57.895 0.00 0.00 44.28 4.30
351 353 1.918467 CTCAGGCAGATTGGAGGGCA 61.918 60.000 0.00 0.00 0.00 5.36
356 358 1.113517 GCAGATTGGAGGGCATGCAT 61.114 55.000 21.36 7.26 33.92 3.96
357 359 0.673985 CAGATTGGAGGGCATGCATG 59.326 55.000 22.70 22.70 0.00 4.06
370 372 2.893837 CATGCATGCAAACAAACAACG 58.106 42.857 26.68 0.00 0.00 4.10
382 384 6.529696 CAAACAAACAACGTGCAAAACTTAT 58.470 32.000 0.00 0.00 0.00 1.73
409 411 1.066858 ACGTGTATTCACTCAGCCAGG 60.067 52.381 0.77 0.00 41.89 4.45
430 432 2.749044 AGTTGGGCTGCAGATGCG 60.749 61.111 20.43 0.00 45.83 4.73
441 443 1.865788 GCAGATGCGAAGTGCCCAAA 61.866 55.000 0.00 0.00 45.60 3.28
448 450 2.290387 TGCGAAGTGCCCAAAATAGGTA 60.290 45.455 0.00 0.00 45.60 3.08
487 489 0.257328 TGTTTGACCTGGCTTGTGGA 59.743 50.000 0.00 0.00 0.00 4.02
489 491 2.107378 TGTTTGACCTGGCTTGTGGATA 59.893 45.455 0.00 0.00 0.00 2.59
490 492 3.245229 TGTTTGACCTGGCTTGTGGATAT 60.245 43.478 0.00 0.00 0.00 1.63
636 662 9.822185 AAATGGCCATTATTTCTCAAGTTTATC 57.178 29.630 30.84 0.00 0.00 1.75
662 688 5.710099 CCAGGTATTTCTTTGAAGCAACCTA 59.290 40.000 0.00 0.00 0.00 3.08
666 692 8.329502 AGGTATTTCTTTGAAGCAACCTATACT 58.670 33.333 0.00 0.00 0.00 2.12
667 693 8.957466 GGTATTTCTTTGAAGCAACCTATACTT 58.043 33.333 0.00 0.00 0.00 2.24
668 694 9.989869 GTATTTCTTTGAAGCAACCTATACTTC 57.010 33.333 0.00 0.00 40.17 3.01
669 695 8.870075 ATTTCTTTGAAGCAACCTATACTTCT 57.130 30.769 0.00 0.00 40.36 2.85
670 696 8.691661 TTTCTTTGAAGCAACCTATACTTCTT 57.308 30.769 0.00 0.00 40.36 2.52
671 697 7.907214 TCTTTGAAGCAACCTATACTTCTTC 57.093 36.000 0.00 0.00 40.36 2.87
672 698 7.680730 TCTTTGAAGCAACCTATACTTCTTCT 58.319 34.615 0.00 0.00 40.36 2.85
673 699 7.604164 TCTTTGAAGCAACCTATACTTCTTCTG 59.396 37.037 0.00 0.00 40.36 3.02
674 700 6.605471 TGAAGCAACCTATACTTCTTCTGA 57.395 37.500 0.00 0.00 40.36 3.27
675 701 7.004555 TGAAGCAACCTATACTTCTTCTGAA 57.995 36.000 0.00 0.00 40.36 3.02
709 735 2.476873 GTACAGACGAGATGATGCGT 57.523 50.000 0.00 0.00 44.33 5.24
714 740 3.650409 ACGAGATGATGCGTCTTCC 57.350 52.632 16.07 8.55 35.59 3.46
715 741 0.103208 ACGAGATGATGCGTCTTCCC 59.897 55.000 16.07 5.84 35.59 3.97
716 742 0.103026 CGAGATGATGCGTCTTCCCA 59.897 55.000 16.07 0.00 28.91 4.37
717 743 1.576356 GAGATGATGCGTCTTCCCAC 58.424 55.000 16.07 6.79 28.91 4.61
718 744 1.137872 GAGATGATGCGTCTTCCCACT 59.862 52.381 16.07 0.49 28.91 4.00
719 745 1.137872 AGATGATGCGTCTTCCCACTC 59.862 52.381 16.07 0.00 30.83 3.51
720 746 1.137872 GATGATGCGTCTTCCCACTCT 59.862 52.381 7.58 0.00 0.00 3.24
721 747 0.976641 TGATGCGTCTTCCCACTCTT 59.023 50.000 7.58 0.00 0.00 2.85
722 748 1.338105 TGATGCGTCTTCCCACTCTTG 60.338 52.381 7.58 0.00 0.00 3.02
723 749 0.674895 ATGCGTCTTCCCACTCTTGC 60.675 55.000 0.00 0.00 0.00 4.01
724 750 1.301716 GCGTCTTCCCACTCTTGCA 60.302 57.895 0.00 0.00 0.00 4.08
725 751 0.884704 GCGTCTTCCCACTCTTGCAA 60.885 55.000 0.00 0.00 0.00 4.08
726 752 0.868406 CGTCTTCCCACTCTTGCAAC 59.132 55.000 0.00 0.00 0.00 4.17
727 753 1.239347 GTCTTCCCACTCTTGCAACC 58.761 55.000 0.00 0.00 0.00 3.77
728 754 0.843309 TCTTCCCACTCTTGCAACCA 59.157 50.000 0.00 0.00 0.00 3.67
729 755 1.214175 TCTTCCCACTCTTGCAACCAA 59.786 47.619 0.00 0.00 0.00 3.67
797 823 0.110238 GAATTGAAAGCGAGCGTGCA 60.110 50.000 6.01 0.00 37.31 4.57
807 833 1.391787 CGAGCGTGCATGCATTATTG 58.608 50.000 31.36 12.25 37.31 1.90
823 851 5.663456 CATTATTGCTACAATTTGGCAGGT 58.337 37.500 0.78 0.00 37.28 4.00
841 869 4.843728 CAGGTATCACACACAACCCTAAT 58.156 43.478 0.00 0.00 32.10 1.73
849 877 3.258123 ACACACAACCCTAATCAAATGGC 59.742 43.478 0.00 0.00 0.00 4.40
863 891 9.722056 CTAATCAAATGGCAAGTACAATTAGTC 57.278 33.333 0.00 0.00 0.00 2.59
934 962 3.575256 AGAGAAATGTGCATGCCAAAGAA 59.425 39.130 16.68 0.00 0.00 2.52
938 966 1.927487 TGTGCATGCCAAAGAAGGAT 58.073 45.000 16.68 0.00 0.00 3.24
939 967 1.820519 TGTGCATGCCAAAGAAGGATC 59.179 47.619 16.68 0.00 0.00 3.36
940 968 1.820519 GTGCATGCCAAAGAAGGATCA 59.179 47.619 16.68 0.00 0.00 2.92
941 969 1.820519 TGCATGCCAAAGAAGGATCAC 59.179 47.619 16.68 0.00 0.00 3.06
942 970 1.820519 GCATGCCAAAGAAGGATCACA 59.179 47.619 6.36 0.00 0.00 3.58
943 971 2.231964 GCATGCCAAAGAAGGATCACAA 59.768 45.455 6.36 0.00 0.00 3.33
944 972 3.118884 GCATGCCAAAGAAGGATCACAAT 60.119 43.478 6.36 0.00 0.00 2.71
1024 1052 3.137176 GGAGATGATTCACAAGGGATCCA 59.863 47.826 15.23 0.00 0.00 3.41
1032 1060 2.649312 TCACAAGGGATCCATGGACTTT 59.351 45.455 18.99 5.15 0.00 2.66
1047 1075 1.109323 ACTTTGTGCTGGTCCCTTGC 61.109 55.000 0.00 0.00 0.00 4.01
1180 1208 0.839277 CATGGTGCAGGTGGAGGATA 59.161 55.000 0.00 0.00 0.00 2.59
1181 1209 0.839946 ATGGTGCAGGTGGAGGATAC 59.160 55.000 0.00 0.00 0.00 2.24
1182 1210 1.144057 GGTGCAGGTGGAGGATACG 59.856 63.158 0.00 0.00 46.39 3.06
1183 1211 1.614241 GGTGCAGGTGGAGGATACGT 61.614 60.000 0.00 0.00 46.39 3.57
1184 1212 0.460284 GTGCAGGTGGAGGATACGTG 60.460 60.000 0.00 0.00 46.39 4.49
1185 1213 4.835927 CAGGTGGAGGATACGTGC 57.164 61.111 0.00 0.00 46.39 5.34
1186 1214 2.202866 CAGGTGGAGGATACGTGCT 58.797 57.895 0.00 0.00 46.39 4.40
1187 1215 0.103208 CAGGTGGAGGATACGTGCTC 59.897 60.000 0.00 0.00 41.65 4.26
1188 1216 0.324368 AGGTGGAGGATACGTGCTCA 60.324 55.000 0.00 0.00 43.92 4.26
1189 1217 0.179108 GGTGGAGGATACGTGCTCAC 60.179 60.000 0.00 0.00 43.92 3.51
1190 1218 0.818296 GTGGAGGATACGTGCTCACT 59.182 55.000 0.00 0.00 43.92 3.41
1191 1219 1.103803 TGGAGGATACGTGCTCACTC 58.896 55.000 0.00 4.45 43.92 3.51
1207 1235 3.653344 TCACTCCTCTTGTTGTTGATCG 58.347 45.455 0.00 0.00 0.00 3.69
1208 1236 3.320826 TCACTCCTCTTGTTGTTGATCGA 59.679 43.478 0.00 0.00 0.00 3.59
1209 1237 4.021104 TCACTCCTCTTGTTGTTGATCGAT 60.021 41.667 0.00 0.00 0.00 3.59
1210 1238 4.328440 CACTCCTCTTGTTGTTGATCGATC 59.672 45.833 18.72 18.72 0.00 3.69
1211 1239 3.861840 TCCTCTTGTTGTTGATCGATCC 58.138 45.455 22.31 8.72 0.00 3.36
1213 1241 3.620374 CCTCTTGTTGTTGATCGATCCTG 59.380 47.826 22.31 4.83 0.00 3.86
1214 1242 4.248859 CTCTTGTTGTTGATCGATCCTGT 58.751 43.478 22.31 0.00 0.00 4.00
1216 1244 5.063204 TCTTGTTGTTGATCGATCCTGTTT 58.937 37.500 22.31 0.00 0.00 2.83
1217 1245 5.179368 TCTTGTTGTTGATCGATCCTGTTTC 59.821 40.000 22.31 9.25 0.00 2.78
1218 1246 3.751175 TGTTGTTGATCGATCCTGTTTCC 59.249 43.478 22.31 5.48 0.00 3.13
1219 1247 3.981071 TGTTGATCGATCCTGTTTCCT 57.019 42.857 22.31 0.00 0.00 3.36
1220 1248 4.286297 TGTTGATCGATCCTGTTTCCTT 57.714 40.909 22.31 0.00 0.00 3.36
1239 1267 4.152402 TCCTTCTTTTCTTTTCTGCGATCG 59.848 41.667 11.69 11.69 0.00 3.69
1244 1272 1.019278 TCTTTTCTGCGATCGGTGCC 61.019 55.000 18.30 0.00 0.00 5.01
1796 1824 1.898574 CTGCACCACCACCAGTTCC 60.899 63.158 0.00 0.00 0.00 3.62
1816 1844 2.049063 GACAGAACGAGCGGCACT 60.049 61.111 1.45 0.00 0.00 4.40
1932 1960 5.862924 AAGTTTCTGGTGTATGATGTTCG 57.137 39.130 0.00 0.00 0.00 3.95
1965 1994 2.894763 AAAAAGGTTAAACCACCGGC 57.105 45.000 0.00 0.00 41.95 6.13
2076 2113 5.778241 TCACTCACACCTATAAACTCAGGAA 59.222 40.000 0.00 0.00 35.76 3.36
2086 2123 9.939424 ACCTATAAACTCAGGAATACTCTTACT 57.061 33.333 0.00 0.00 35.76 2.24
2136 2174 6.524734 GCCGATCCATCCACATAATATATCA 58.475 40.000 0.00 0.00 0.00 2.15
2181 2219 1.399440 CTAAAGCGCACATCACATGCT 59.601 47.619 11.47 0.00 41.10 3.79
2222 2260 1.676678 ATCATCGGACCACTGACCCG 61.677 60.000 0.00 0.00 44.22 5.28
2246 2284 2.087646 TCAGGAGAGATATCCGCATCG 58.912 52.381 0.00 0.00 44.65 3.84
2329 2369 1.375396 CATCCGCCCAGACGTGAAA 60.375 57.895 0.00 0.00 0.00 2.69
2336 2376 1.810412 GCCCAGACGTGAAAACTCTGT 60.810 52.381 0.00 0.00 31.16 3.41
2437 2481 1.664649 CGAAGCTCCGTGCAAGACA 60.665 57.895 0.00 0.00 45.94 3.41
2443 2487 1.153066 TCCGTGCAAGACAAAGCCA 60.153 52.632 0.00 0.00 0.00 4.75
2492 2536 2.882761 GCTGCTCCATAAATGATGCTCA 59.117 45.455 0.00 0.00 33.79 4.26
2510 2555 3.797184 GCTCACAAGAGAGAAACGACACT 60.797 47.826 0.00 0.00 44.98 3.55
2558 2603 1.413077 GACCAGATCCTAGGGTTTCCG 59.587 57.143 9.46 0.00 38.33 4.30
2631 2677 0.110554 GTAACGATGCAAAACGCCGT 60.111 50.000 10.33 0.00 39.73 5.68
2635 2681 0.454285 CGATGCAAAACGCCGTCATT 60.454 50.000 0.00 0.00 41.33 2.57
2683 2730 0.259065 AGCTATGTCTCCCCGACTCA 59.741 55.000 0.00 0.00 43.25 3.41
2785 2833 1.300620 TCGACTGCACCGGTCAAAG 60.301 57.895 2.59 4.97 39.51 2.77
2801 2850 3.096852 TCAAAGCAGATCTAACCGGAGA 58.903 45.455 9.46 0.43 0.00 3.71
2805 2854 1.342819 GCAGATCTAACCGGAGATGCT 59.657 52.381 9.46 4.04 36.27 3.79
2807 2856 2.363680 CAGATCTAACCGGAGATGCTGT 59.636 50.000 9.46 0.00 36.27 4.40
2812 2861 1.532604 AACCGGAGATGCTGTCGACA 61.533 55.000 18.88 18.88 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 5.804944 ACATAGCAGAGATAGCAGTGATT 57.195 39.130 0.00 0.00 0.00 2.57
64 65 9.938280 GGCTAACATCATAATAGTACCACATAA 57.062 33.333 0.00 0.00 0.00 1.90
65 66 9.321532 AGGCTAACATCATAATAGTACCACATA 57.678 33.333 0.00 0.00 0.00 2.29
66 67 8.097038 CAGGCTAACATCATAATAGTACCACAT 58.903 37.037 0.00 0.00 0.00 3.21
79 80 4.751060 CAATGCAAACAGGCTAACATCAT 58.249 39.130 0.00 0.00 34.04 2.45
97 98 7.428020 AGTGCATAACCATAAACATAGCAATG 58.572 34.615 0.00 0.00 39.17 2.82
99 100 7.403312 AAGTGCATAACCATAAACATAGCAA 57.597 32.000 0.00 0.00 0.00 3.91
101 102 8.955061 CATAAGTGCATAACCATAAACATAGC 57.045 34.615 0.00 0.00 0.00 2.97
121 122 8.854614 AAGCTAAACCATAGGATAAGCATAAG 57.145 34.615 0.00 0.00 0.00 1.73
196 198 0.033781 TACAAGTACACGGGCACACC 59.966 55.000 0.00 0.00 0.00 4.16
205 207 4.304939 GAGTGGTGAGGTTACAAGTACAC 58.695 47.826 0.00 0.00 0.00 2.90
210 212 4.087182 TCTAGGAGTGGTGAGGTTACAAG 58.913 47.826 0.00 0.00 0.00 3.16
212 214 3.820195 TCTAGGAGTGGTGAGGTTACA 57.180 47.619 0.00 0.00 0.00 2.41
242 244 7.815641 TGGTTACATACAACTCAAATGATGTG 58.184 34.615 0.00 0.00 0.00 3.21
272 274 2.687700 ATCGAGATGCAAAGAGCTGT 57.312 45.000 0.00 0.00 45.94 4.40
290 292 6.207221 TGTGTTTGATTGTCTGCATGTTCTAT 59.793 34.615 0.00 0.00 0.00 1.98
296 298 3.005050 ACCTGTGTTTGATTGTCTGCATG 59.995 43.478 0.00 0.00 0.00 4.06
303 305 1.953686 CCGGAACCTGTGTTTGATTGT 59.046 47.619 0.00 0.00 33.97 2.71
307 309 0.253610 ACACCGGAACCTGTGTTTGA 59.746 50.000 9.46 0.00 40.54 2.69
335 337 1.229359 CATGCCCTCCAATCTGCCT 59.771 57.895 0.00 0.00 0.00 4.75
351 353 2.284684 CACGTTGTTTGTTTGCATGCAT 59.715 40.909 23.37 0.00 0.00 3.96
356 358 1.783284 TTGCACGTTGTTTGTTTGCA 58.217 40.000 0.00 0.00 41.33 4.08
357 359 2.863658 TTTGCACGTTGTTTGTTTGC 57.136 40.000 0.00 0.00 0.00 3.68
391 393 1.065854 AGCCTGGCTGAGTGAATACAC 60.066 52.381 22.71 0.00 41.50 2.90
409 411 1.378250 ATCTGCAGCCCAACTCAGC 60.378 57.895 9.47 0.00 0.00 4.26
422 424 1.865788 TTTGGGCACTTCGCATCTGC 61.866 55.000 0.00 0.00 45.17 4.26
430 432 3.694566 CCTGTACCTATTTTGGGCACTTC 59.305 47.826 0.00 0.00 0.00 3.01
441 443 5.999600 GTGTGTTTGGTTACCTGTACCTATT 59.000 40.000 2.07 0.00 36.60 1.73
448 450 3.020984 CAAGGTGTGTTTGGTTACCTGT 58.979 45.455 2.07 0.00 42.47 4.00
472 474 6.127451 CGTATATATATCCACAAGCCAGGTCA 60.127 42.308 0.00 0.00 0.00 4.02
476 478 5.660460 TGCGTATATATATCCACAAGCCAG 58.340 41.667 0.00 0.00 0.00 4.85
523 549 1.462283 CTTGCACTCAAGGATGACACG 59.538 52.381 0.00 0.00 44.53 4.49
636 662 5.335976 GGTTGCTTCAAAGAAATACCTGGAG 60.336 44.000 0.00 0.00 0.00 3.86
690 716 2.476873 ACGCATCATCTCGTCTGTAC 57.523 50.000 0.00 0.00 33.09 2.90
696 722 0.103208 GGGAAGACGCATCATCTCGT 59.897 55.000 0.00 0.00 42.09 4.18
697 723 0.103026 TGGGAAGACGCATCATCTCG 59.897 55.000 0.00 0.00 34.12 4.04
698 724 1.137872 AGTGGGAAGACGCATCATCTC 59.862 52.381 0.00 0.00 40.82 2.75
699 725 1.137872 GAGTGGGAAGACGCATCATCT 59.862 52.381 0.00 0.00 40.82 2.90
700 726 1.137872 AGAGTGGGAAGACGCATCATC 59.862 52.381 0.00 0.00 40.82 2.92
701 727 1.198713 AGAGTGGGAAGACGCATCAT 58.801 50.000 0.00 0.00 40.82 2.45
702 728 0.976641 AAGAGTGGGAAGACGCATCA 59.023 50.000 0.00 0.00 40.82 3.07
703 729 1.363744 CAAGAGTGGGAAGACGCATC 58.636 55.000 0.00 0.00 40.82 3.91
704 730 0.674895 GCAAGAGTGGGAAGACGCAT 60.675 55.000 0.00 0.00 40.82 4.73
705 731 1.301716 GCAAGAGTGGGAAGACGCA 60.302 57.895 0.00 0.00 36.64 5.24
706 732 0.884704 TTGCAAGAGTGGGAAGACGC 60.885 55.000 0.00 0.00 0.00 5.19
707 733 0.868406 GTTGCAAGAGTGGGAAGACG 59.132 55.000 0.00 0.00 0.00 4.18
708 734 1.239347 GGTTGCAAGAGTGGGAAGAC 58.761 55.000 0.00 0.00 0.00 3.01
709 735 0.843309 TGGTTGCAAGAGTGGGAAGA 59.157 50.000 0.00 0.00 0.00 2.87
710 736 1.691196 TTGGTTGCAAGAGTGGGAAG 58.309 50.000 0.00 0.00 0.00 3.46
711 737 2.151502 TTTGGTTGCAAGAGTGGGAA 57.848 45.000 0.00 0.00 0.00 3.97
712 738 2.151502 TTTTGGTTGCAAGAGTGGGA 57.848 45.000 0.00 0.00 0.00 4.37
713 739 2.093764 TGTTTTTGGTTGCAAGAGTGGG 60.094 45.455 0.00 0.00 0.00 4.61
714 740 2.929398 GTGTTTTTGGTTGCAAGAGTGG 59.071 45.455 0.00 0.00 0.00 4.00
715 741 3.583806 TGTGTTTTTGGTTGCAAGAGTG 58.416 40.909 0.00 0.00 0.00 3.51
716 742 3.951775 TGTGTTTTTGGTTGCAAGAGT 57.048 38.095 0.00 0.00 0.00 3.24
717 743 5.447548 CCAAATGTGTTTTTGGTTGCAAGAG 60.448 40.000 0.00 0.00 46.94 2.85
718 744 4.394300 CCAAATGTGTTTTTGGTTGCAAGA 59.606 37.500 0.00 0.00 46.94 3.02
719 745 4.660105 CCAAATGTGTTTTTGGTTGCAAG 58.340 39.130 0.00 0.00 46.94 4.01
720 746 4.691860 CCAAATGTGTTTTTGGTTGCAA 57.308 36.364 0.00 0.00 46.94 4.08
741 767 6.417930 GCGGATTTCCAGCTAATTAAATGAAC 59.582 38.462 0.00 0.00 34.38 3.18
807 833 3.694072 TGTGATACCTGCCAAATTGTAGC 59.306 43.478 0.00 0.00 0.00 3.58
809 835 4.457603 GTGTGTGATACCTGCCAAATTGTA 59.542 41.667 0.00 0.00 0.00 2.41
823 851 6.376864 CCATTTGATTAGGGTTGTGTGTGATA 59.623 38.462 0.00 0.00 0.00 2.15
841 869 5.703592 ACGACTAATTGTACTTGCCATTTGA 59.296 36.000 0.00 0.00 0.00 2.69
849 877 7.484007 ACGAGATTGTACGACTAATTGTACTTG 59.516 37.037 3.54 0.00 43.64 3.16
863 891 1.921243 TGATGGCACGAGATTGTACG 58.079 50.000 0.00 0.00 0.00 3.67
934 962 6.611613 TCTAGTCTTGTGAATTGTGATCCT 57.388 37.500 0.00 0.00 0.00 3.24
938 966 7.290110 TCTCTTCTAGTCTTGTGAATTGTGA 57.710 36.000 0.00 0.00 0.00 3.58
939 967 7.869937 TCTTCTCTTCTAGTCTTGTGAATTGTG 59.130 37.037 0.00 0.00 0.00 3.33
940 968 7.957002 TCTTCTCTTCTAGTCTTGTGAATTGT 58.043 34.615 0.00 0.00 0.00 2.71
941 969 8.303156 TCTCTTCTCTTCTAGTCTTGTGAATTG 58.697 37.037 0.00 0.00 0.00 2.32
942 970 8.415950 TCTCTTCTCTTCTAGTCTTGTGAATT 57.584 34.615 0.00 0.00 0.00 2.17
943 971 7.888021 TCTCTCTTCTCTTCTAGTCTTGTGAAT 59.112 37.037 0.00 0.00 0.00 2.57
944 972 7.227873 TCTCTCTTCTCTTCTAGTCTTGTGAA 58.772 38.462 0.00 0.00 0.00 3.18
1047 1075 2.890109 GAGCATGATCGCAAGCCCG 61.890 63.158 0.00 0.00 39.44 6.13
1116 1144 0.591741 GGTTCTCGTAGCCGATGACG 60.592 60.000 0.00 0.00 43.27 4.35
1180 1208 0.753262 AACAAGAGGAGTGAGCACGT 59.247 50.000 0.00 0.00 36.20 4.49
1181 1209 1.143305 CAACAAGAGGAGTGAGCACG 58.857 55.000 0.00 0.00 36.20 5.34
1182 1210 2.246719 ACAACAAGAGGAGTGAGCAC 57.753 50.000 0.00 0.00 0.00 4.40
1183 1211 2.170397 TCAACAACAAGAGGAGTGAGCA 59.830 45.455 0.00 0.00 0.00 4.26
1184 1212 2.838736 TCAACAACAAGAGGAGTGAGC 58.161 47.619 0.00 0.00 0.00 4.26
1185 1213 3.677121 CGATCAACAACAAGAGGAGTGAG 59.323 47.826 0.00 0.00 0.00 3.51
1186 1214 3.320826 TCGATCAACAACAAGAGGAGTGA 59.679 43.478 0.00 0.00 0.00 3.41
1187 1215 3.653344 TCGATCAACAACAAGAGGAGTG 58.347 45.455 0.00 0.00 0.00 3.51
1188 1216 4.499183 GATCGATCAACAACAAGAGGAGT 58.501 43.478 20.52 0.00 0.00 3.85
1189 1217 3.868077 GGATCGATCAACAACAAGAGGAG 59.132 47.826 25.93 0.00 0.00 3.69
1190 1218 3.515502 AGGATCGATCAACAACAAGAGGA 59.484 43.478 25.93 0.00 0.00 3.71
1191 1219 3.620374 CAGGATCGATCAACAACAAGAGG 59.380 47.826 25.93 0.00 0.00 3.69
1207 1235 7.864882 CAGAAAAGAAAAGAAGGAAACAGGATC 59.135 37.037 0.00 0.00 0.00 3.36
1208 1236 7.685398 GCAGAAAAGAAAAGAAGGAAACAGGAT 60.685 37.037 0.00 0.00 0.00 3.24
1209 1237 6.405842 GCAGAAAAGAAAAGAAGGAAACAGGA 60.406 38.462 0.00 0.00 0.00 3.86
1210 1238 5.750547 GCAGAAAAGAAAAGAAGGAAACAGG 59.249 40.000 0.00 0.00 0.00 4.00
1211 1239 5.456822 CGCAGAAAAGAAAAGAAGGAAACAG 59.543 40.000 0.00 0.00 0.00 3.16
1213 1241 5.578776 TCGCAGAAAAGAAAAGAAGGAAAC 58.421 37.500 0.00 0.00 0.00 2.78
1214 1242 5.828299 TCGCAGAAAAGAAAAGAAGGAAA 57.172 34.783 0.00 0.00 0.00 3.13
1216 1244 4.152402 CGATCGCAGAAAAGAAAAGAAGGA 59.848 41.667 0.26 0.00 43.58 3.36
1217 1245 4.398247 CGATCGCAGAAAAGAAAAGAAGG 58.602 43.478 0.26 0.00 43.58 3.46
1218 1246 4.083802 ACCGATCGCAGAAAAGAAAAGAAG 60.084 41.667 10.32 0.00 43.58 2.85
1219 1247 3.813166 ACCGATCGCAGAAAAGAAAAGAA 59.187 39.130 10.32 0.00 43.58 2.52
1220 1248 3.186409 CACCGATCGCAGAAAAGAAAAGA 59.814 43.478 10.32 0.00 43.58 2.52
1239 1267 3.056328 GCCAGAAGAACCGGCACC 61.056 66.667 0.00 0.00 45.52 5.01
1244 1272 1.424493 GCGATCAGCCAGAAGAACCG 61.424 60.000 0.00 0.00 40.81 4.44
1750 1778 2.047844 CTGGTGTCGAGCAGGTGG 60.048 66.667 0.00 0.00 42.93 4.61
1796 1824 2.811317 GCCGCTCGTTCTGTCCAG 60.811 66.667 0.00 0.00 0.00 3.86
1884 1912 1.807226 CGTCACCTGAGATACGGCA 59.193 57.895 0.00 0.00 0.00 5.69
1885 1913 4.711980 CGTCACCTGAGATACGGC 57.288 61.111 0.00 0.00 0.00 5.68
1910 1938 5.547465 TCGAACATCATACACCAGAAACTT 58.453 37.500 0.00 0.00 0.00 2.66
1948 1976 0.828762 GGGCCGGTGGTTTAACCTTT 60.829 55.000 15.68 0.00 39.58 3.11
1949 1977 1.228644 GGGCCGGTGGTTTAACCTT 60.229 57.895 15.68 0.00 39.58 3.50
1960 1989 2.215451 AATTGATGCAGAGGGCCGGT 62.215 55.000 1.90 0.00 43.89 5.28
1963 1992 1.340248 CATCAATTGATGCAGAGGGCC 59.660 52.381 30.11 0.00 44.44 5.80
2086 2123 7.116662 CGACGATACCGATTTTAAATATGGGAA 59.883 37.037 14.01 2.46 39.50 3.97
2136 2174 4.643387 GCACCGGCTGTTGGTCCT 62.643 66.667 0.00 0.00 37.72 3.85
2181 2219 0.249953 TGGCGGCTTCTAAAACGTGA 60.250 50.000 11.43 0.00 0.00 4.35
2222 2260 2.887783 TGCGGATATCTCTCCTGAAGAC 59.112 50.000 2.05 0.00 32.77 3.01
2246 2284 4.703703 GTCCAGACTGGCAAGGAC 57.296 61.111 17.33 9.04 43.18 3.85
2329 2369 3.670895 CGCACGACAGATCTTACAGAGTT 60.671 47.826 0.00 0.00 0.00 3.01
2336 2376 1.741145 TGCTACGCACGACAGATCTTA 59.259 47.619 0.00 0.00 31.71 2.10
2365 2405 0.457443 CTACGCTGAGTCATGCCTGA 59.543 55.000 0.00 0.00 0.00 3.86
2437 2481 1.763770 CAGGAGGTGGAGTGGCTTT 59.236 57.895 0.00 0.00 0.00 3.51
2443 2487 1.611851 CAGAGGCAGGAGGTGGAGT 60.612 63.158 0.00 0.00 0.00 3.85
2492 2536 3.802948 ACAGTGTCGTTTCTCTCTTGT 57.197 42.857 0.00 0.00 0.00 3.16
2510 2555 1.404748 TCGAACGATGGCGGTATTACA 59.595 47.619 0.00 0.00 37.73 2.41
2558 2603 3.782244 CACTCGTGCTGCTTCGGC 61.782 66.667 14.88 0.00 42.19 5.54
2631 2677 3.053291 GTCGTTGGCGGGCAATGA 61.053 61.111 28.78 28.78 38.89 2.57
2683 2730 5.998981 AGATTCGTCATCTAGTCTCGGTTAT 59.001 40.000 0.00 0.00 40.85 1.89
2785 2833 1.342819 AGCATCTCCGGTTAGATCTGC 59.657 52.381 5.18 5.99 33.87 4.26
2807 2856 2.558286 GGTCTGGTGGTCGTGTCGA 61.558 63.158 0.00 0.00 0.00 4.20
2812 2861 2.603776 GGAGGGTCTGGTGGTCGT 60.604 66.667 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.