Multiple sequence alignment - TraesCS5A01G522200

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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 TraesCS5A01G522200 chr5A 100.000 5071 0 0 1 5071 683348091 683353161 0.000000e+00 9365.0
1 TraesCS5A01G522200 chr4B 94.057 3803 170 29 962 4727 644789124 644785341 0.000000e+00 5720.0
2 TraesCS5A01G522200 chr4B 90.233 860 62 13 6 859 512735343 512736186 0.000000e+00 1103.0
3 TraesCS5A01G522200 chr4B 92.089 316 16 6 4761 5070 644785260 644784948 2.170000e-118 436.0
4 TraesCS5A01G522200 chr4B 95.918 49 2 0 2803 2851 644787326 644787278 4.210000e-11 80.5
5 TraesCS5A01G522200 chr4D 93.685 2011 79 10 1780 3748 500822210 500820206 0.000000e+00 2966.0
6 TraesCS5A01G522200 chr4D 90.196 969 54 17 4126 5070 500819844 500818893 0.000000e+00 1225.0
7 TraesCS5A01G522200 chr4D 95.364 755 22 7 962 1713 500823201 500822457 0.000000e+00 1188.0
8 TraesCS5A01G522200 chr4D 97.808 365 7 1 3805 4168 500820207 500819843 3.330000e-176 628.0
9 TraesCS5A01G522200 chr4D 97.015 67 2 0 2785 2851 500821233 500821167 4.150000e-21 113.0
10 TraesCS5A01G522200 chr1A 95.006 861 21 4 1 842 291968258 291969115 0.000000e+00 1332.0
11 TraesCS5A01G522200 chr1A 94.656 655 33 1 6 658 285423021 285422367 0.000000e+00 1014.0
12 TraesCS5A01G522200 chr6A 93.800 871 43 9 1 866 593677110 593677974 0.000000e+00 1299.0
13 TraesCS5A01G522200 chr2A 92.754 897 37 12 1 876 80462645 80461756 0.000000e+00 1271.0
14 TraesCS5A01G522200 chr5B 89.692 844 66 11 9 846 372204272 372203444 0.000000e+00 1057.0
15 TraesCS5A01G522200 chr7A 94.551 624 32 1 6 627 467523520 467522897 0.000000e+00 963.0
16 TraesCS5A01G522200 chr3B 90.762 682 34 3 9 688 17293066 17292412 0.000000e+00 883.0
17 TraesCS5A01G522200 chr2B 90.616 682 35 3 9 688 23155253 23154599 0.000000e+00 878.0
18 TraesCS5A01G522200 chr1B 90.511 685 35 9 6 688 632955473 632956129 0.000000e+00 878.0
19 TraesCS5A01G522200 chr7B 90.219 685 38 3 6 688 702232462 702233119 0.000000e+00 867.0


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 TraesCS5A01G522200 chr5A 683348091 683353161 5070 False 9365.000000 9365 100.000000 1 5071 1 chr5A.!!$F1 5070
1 TraesCS5A01G522200 chr4B 644784948 644789124 4176 True 2078.833333 5720 94.021333 962 5070 3 chr4B.!!$R1 4108
2 TraesCS5A01G522200 chr4B 512735343 512736186 843 False 1103.000000 1103 90.233000 6 859 1 chr4B.!!$F1 853
3 TraesCS5A01G522200 chr4D 500818893 500823201 4308 True 1224.000000 2966 94.813600 962 5070 5 chr4D.!!$R1 4108
4 TraesCS5A01G522200 chr1A 291968258 291969115 857 False 1332.000000 1332 95.006000 1 842 1 chr1A.!!$F1 841
5 TraesCS5A01G522200 chr1A 285422367 285423021 654 True 1014.000000 1014 94.656000 6 658 1 chr1A.!!$R1 652
6 TraesCS5A01G522200 chr6A 593677110 593677974 864 False 1299.000000 1299 93.800000 1 866 1 chr6A.!!$F1 865
7 TraesCS5A01G522200 chr2A 80461756 80462645 889 True 1271.000000 1271 92.754000 1 876 1 chr2A.!!$R1 875
8 TraesCS5A01G522200 chr5B 372203444 372204272 828 True 1057.000000 1057 89.692000 9 846 1 chr5B.!!$R1 837
9 TraesCS5A01G522200 chr7A 467522897 467523520 623 True 963.000000 963 94.551000 6 627 1 chr7A.!!$R1 621
10 TraesCS5A01G522200 chr3B 17292412 17293066 654 True 883.000000 883 90.762000 9 688 1 chr3B.!!$R1 679
11 TraesCS5A01G522200 chr2B 23154599 23155253 654 True 878.000000 878 90.616000 9 688 1 chr2B.!!$R1 679
12 TraesCS5A01G522200 chr1B 632955473 632956129 656 False 878.000000 878 90.511000 6 688 1 chr1B.!!$F1 682
13 TraesCS5A01G522200 chr7B 702232462 702233119 657 False 867.000000 867 90.219000 6 688 1 chr7B.!!$F1 682

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
722 738 0.104409 AAGGGAGTGGTTCCTGAGGT 60.104 55.0 0.00 0.00 45.98 3.85 F
983 1017 0.317854 GGCAACCGACTTGAGCAAAC 60.318 55.0 0.00 0.00 30.42 2.93 F
2194 2430 0.366871 GTGCGAGCTTACATGTGACG 59.633 55.0 9.11 7.94 0.00 4.35 F
3135 3395 0.617820 GAGGGAGTGGGGTCTGCTAA 60.618 60.0 0.00 0.00 0.00 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 1678 0.179124 GGGTGAACACGCAAAAGCAA 60.179 50.0 15.22 0.0 42.92 3.91 R
2777 3037 0.532862 CCTGCAACGGTGAGTCAACT 60.533 55.0 3.55 0.0 0.00 3.16 R
3326 3586 0.323360 GTGGGGCACAGGCAGATTTA 60.323 55.0 0.00 0.0 43.71 1.40 R
4487 4812 0.111253 AGCCAGTTTCAGACCAAGGG 59.889 55.0 0.00 0.0 0.00 3.95 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
373 380 9.886132 AACTGATAATATACGAAATCCATACCC 57.114 33.333 0.00 0.00 0.00 3.69
374 381 9.042450 ACTGATAATATACGAAATCCATACCCA 57.958 33.333 0.00 0.00 0.00 4.51
386 393 8.846211 CGAAATCCATACCCAATAACATAAGTT 58.154 33.333 0.00 0.00 41.74 2.66
576 583 1.196012 GGTCTGGGTTCGATCCTCTT 58.804 55.000 12.19 0.00 0.00 2.85
722 738 0.104409 AAGGGAGTGGTTCCTGAGGT 60.104 55.000 0.00 0.00 45.98 3.85
751 768 3.978876 AAAAATCAGGAGGGGTCGG 57.021 52.632 0.00 0.00 0.00 4.79
752 769 0.331616 AAAAATCAGGAGGGGTCGGG 59.668 55.000 0.00 0.00 0.00 5.14
753 770 1.571773 AAAATCAGGAGGGGTCGGGG 61.572 60.000 0.00 0.00 0.00 5.73
754 771 2.782997 AAATCAGGAGGGGTCGGGGT 62.783 60.000 0.00 0.00 0.00 4.95
755 772 3.698263 ATCAGGAGGGGTCGGGGTC 62.698 68.421 0.00 0.00 0.00 4.46
819 853 6.095440 GGTATGGTACTTTTGCAATCTGTCAT 59.905 38.462 0.00 3.70 0.00 3.06
834 868 2.671396 CTGTCATACGGTTGCCAGTTAC 59.329 50.000 0.00 0.00 0.00 2.50
847 881 3.007074 TGCCAGTTACGACAGTCCAATAA 59.993 43.478 0.00 0.00 0.00 1.40
852 886 7.148373 GCCAGTTACGACAGTCCAATAAATAAA 60.148 37.037 0.00 0.00 0.00 1.40
853 887 8.889717 CCAGTTACGACAGTCCAATAAATAAAT 58.110 33.333 0.00 0.00 0.00 1.40
854 888 9.702726 CAGTTACGACAGTCCAATAAATAAATG 57.297 33.333 0.00 0.00 0.00 2.32
855 889 9.661563 AGTTACGACAGTCCAATAAATAAATGA 57.338 29.630 0.00 0.00 0.00 2.57
889 923 9.959749 TTATTTGAAAAATAAAGTCGCTGAAGT 57.040 25.926 3.31 0.00 0.00 3.01
891 925 9.959749 ATTTGAAAAATAAAGTCGCTGAAGTAA 57.040 25.926 0.00 0.00 0.00 2.24
892 926 9.790389 TTTGAAAAATAAAGTCGCTGAAGTAAA 57.210 25.926 0.00 0.00 0.00 2.01
893 927 9.790389 TTGAAAAATAAAGTCGCTGAAGTAAAA 57.210 25.926 0.00 0.00 0.00 1.52
894 928 9.790389 TGAAAAATAAAGTCGCTGAAGTAAAAA 57.210 25.926 0.00 0.00 0.00 1.94
917 951 2.568090 GCCCTGTGCATTTCCGTG 59.432 61.111 0.00 0.00 40.77 4.94
918 952 2.568090 CCCTGTGCATTTCCGTGC 59.432 61.111 0.00 0.00 45.25 5.34
925 959 3.996017 GCATTTCCGTGCGTTTTTG 57.004 47.368 0.00 0.00 35.10 2.44
926 960 1.204792 GCATTTCCGTGCGTTTTTGT 58.795 45.000 0.00 0.00 35.10 2.83
927 961 1.590698 GCATTTCCGTGCGTTTTTGTT 59.409 42.857 0.00 0.00 35.10 2.83
928 962 2.029849 GCATTTCCGTGCGTTTTTGTTT 59.970 40.909 0.00 0.00 35.10 2.83
929 963 3.484393 GCATTTCCGTGCGTTTTTGTTTT 60.484 39.130 0.00 0.00 35.10 2.43
930 964 4.642953 CATTTCCGTGCGTTTTTGTTTTT 58.357 34.783 0.00 0.00 0.00 1.94
948 982 1.497991 TTTTGAGAGAGAACCGTGCG 58.502 50.000 0.00 0.00 0.00 5.34
949 983 0.387929 TTTGAGAGAGAACCGTGCGT 59.612 50.000 0.00 0.00 0.00 5.24
950 984 0.318699 TTGAGAGAGAACCGTGCGTG 60.319 55.000 0.00 0.00 0.00 5.34
951 985 1.286260 GAGAGAGAACCGTGCGTGT 59.714 57.895 0.00 0.00 0.00 4.49
952 986 0.318784 GAGAGAGAACCGTGCGTGTT 60.319 55.000 0.00 0.00 0.00 3.32
953 987 0.597637 AGAGAGAACCGTGCGTGTTG 60.598 55.000 3.89 0.00 0.00 3.33
954 988 1.557443 GAGAGAACCGTGCGTGTTGG 61.557 60.000 3.89 0.00 0.00 3.77
955 989 2.590575 AGAACCGTGCGTGTTGGG 60.591 61.111 3.89 0.00 0.00 4.12
956 990 2.898343 GAACCGTGCGTGTTGGGT 60.898 61.111 3.89 0.00 0.00 4.51
957 991 2.438795 AACCGTGCGTGTTGGGTT 60.439 55.556 0.00 0.00 37.92 4.11
958 992 1.153208 AACCGTGCGTGTTGGGTTA 60.153 52.632 0.00 0.00 40.80 2.85
959 993 0.747283 AACCGTGCGTGTTGGGTTAA 60.747 50.000 0.00 0.00 40.80 2.01
960 994 0.747283 ACCGTGCGTGTTGGGTTAAA 60.747 50.000 0.00 0.00 0.00 1.52
965 999 2.224784 GTGCGTGTTGGGTTAAAGTAGG 59.775 50.000 0.00 0.00 0.00 3.18
978 1012 2.457366 AAGTAGGCAACCGACTTGAG 57.543 50.000 10.78 0.00 45.22 3.02
983 1017 0.317854 GGCAACCGACTTGAGCAAAC 60.318 55.000 0.00 0.00 30.42 2.93
1019 1056 2.366570 GCCTCCTCCCTCTCCAGT 59.633 66.667 0.00 0.00 0.00 4.00
1031 1068 1.307343 CTCCAGTCTCCACCCCCAT 60.307 63.158 0.00 0.00 0.00 4.00
1033 1070 2.735772 CCAGTCTCCACCCCCATCG 61.736 68.421 0.00 0.00 0.00 3.84
1034 1071 3.083997 AGTCTCCACCCCCATCGC 61.084 66.667 0.00 0.00 0.00 4.58
1086 1123 3.957435 ATGTGGCGAGACGAGGGGA 62.957 63.158 0.00 0.00 0.00 4.81
1635 1678 2.297701 CCGCTGCTGGTATTGGTTTAT 58.702 47.619 0.00 0.00 0.00 1.40
1709 1752 4.687018 TGTTTCATAGCTGCATTTGCTTTG 59.313 37.500 4.08 7.31 41.46 2.77
1734 1924 3.006537 GCTGTAGTAGAAGTGTGGGTTGA 59.993 47.826 0.00 0.00 0.00 3.18
1737 1927 5.547465 TGTAGTAGAAGTGTGGGTTGATTG 58.453 41.667 0.00 0.00 0.00 2.67
2018 2253 8.245195 ACAACTTTGGTTTATATCACCTGTTT 57.755 30.769 5.75 0.00 35.07 2.83
2030 2265 5.612725 ATCACCTGTTTGTTTGGTTCATT 57.387 34.783 0.00 0.00 30.72 2.57
2127 2362 6.207928 TGTTTGACATGTTGCTGAAGTATTG 58.792 36.000 0.00 0.00 0.00 1.90
2177 2413 9.687210 TGTTACTATGTGTTTTAGTGTAGAGTG 57.313 33.333 0.00 0.00 32.35 3.51
2193 2429 1.656095 GAGTGCGAGCTTACATGTGAC 59.344 52.381 9.11 0.00 0.00 3.67
2194 2430 0.366871 GTGCGAGCTTACATGTGACG 59.633 55.000 9.11 7.94 0.00 4.35
2196 2432 1.068474 GCGAGCTTACATGTGACGTT 58.932 50.000 9.11 0.00 0.00 3.99
2197 2433 2.256174 GCGAGCTTACATGTGACGTTA 58.744 47.619 9.11 0.00 0.00 3.18
2198 2434 2.279136 GCGAGCTTACATGTGACGTTAG 59.721 50.000 9.11 0.00 0.00 2.34
2203 2439 5.907207 AGCTTACATGTGACGTTAGATCAT 58.093 37.500 9.11 0.00 0.00 2.45
2211 2447 6.465439 TGTGACGTTAGATCATAGAACCAT 57.535 37.500 0.00 0.00 0.00 3.55
2331 2567 8.739972 GGTCACATATTGTTCTCTGGTTAATTT 58.260 33.333 0.00 0.00 0.00 1.82
2456 2692 4.645535 TCAAAATCTGTGTTGAGGAGGAG 58.354 43.478 0.00 0.00 30.41 3.69
2463 2699 3.038280 TGTGTTGAGGAGGAGAAGTTCA 58.962 45.455 5.50 0.00 0.00 3.18
2466 2702 4.881850 GTGTTGAGGAGGAGAAGTTCAAAA 59.118 41.667 5.50 0.00 30.43 2.44
2477 2713 4.173256 AGAAGTTCAAAACCTTGTTTGCG 58.827 39.130 5.50 0.00 38.20 4.85
2485 2721 2.046285 CCTTGTTTGCGGCCCTAGG 61.046 63.158 0.06 0.06 0.00 3.02
2515 2751 3.805066 TGGTGGTGAATCTGGAAATGA 57.195 42.857 0.00 0.00 0.00 2.57
2777 3037 2.250924 TCATCAGAGACTGAAGCACCA 58.749 47.619 5.57 0.00 44.04 4.17
2879 3139 7.368480 TGTAAAACGCCTCTTAAAATACCTC 57.632 36.000 0.00 0.00 0.00 3.85
3059 3319 2.042464 CAGGATGAGGTTAGGCAGCTA 58.958 52.381 0.00 0.00 39.69 3.32
3135 3395 0.617820 GAGGGAGTGGGGTCTGCTAA 60.618 60.000 0.00 0.00 0.00 3.09
3416 3683 1.266989 AGTTTCCAAAGTGCTTAGCGC 59.733 47.619 10.07 10.07 39.59 5.92
3660 3932 4.521130 TTGCGTTATCTGAGAGACTGTT 57.479 40.909 0.00 0.00 0.00 3.16
3679 3951 6.936374 ACTGTTTGATTTTGCAGATTTTTCG 58.064 32.000 0.00 0.00 33.57 3.46
3712 3985 2.943033 CCTGTTTGAGACGAAAACCAGT 59.057 45.455 0.00 0.00 36.82 4.00
3737 4010 0.036010 CTTCCGCTGGTCATGGTTCT 60.036 55.000 0.00 0.00 0.00 3.01
3768 4041 6.375455 ACATCAGTGGGAGAAATGTAAATGTC 59.625 38.462 0.00 0.00 0.00 3.06
3848 4122 3.134458 GGCTATGACTACCAGATGCAAC 58.866 50.000 0.00 0.00 0.00 4.17
3870 4144 6.920569 ACGTCTGTCATTTTAAACTCTTGT 57.079 33.333 0.00 0.00 0.00 3.16
3960 4235 2.732500 CCGTTATGTACTGTCGCACAAA 59.267 45.455 0.00 0.00 0.00 2.83
4020 4295 6.526325 CGTTTCATGTTTTGTTTCTGAAGTCA 59.474 34.615 0.00 0.00 0.00 3.41
4313 4630 4.635765 CCATGATGACAAACGGTAGAATGT 59.364 41.667 0.00 0.00 0.00 2.71
4334 4651 5.851720 TGTTTTTGAGCATTTCCAGCATTA 58.148 33.333 0.00 0.00 0.00 1.90
4344 4661 5.335127 CATTTCCAGCATTACAGCAGTTAC 58.665 41.667 0.00 0.00 36.85 2.50
4346 4664 4.014569 TCCAGCATTACAGCAGTTACAA 57.985 40.909 0.00 0.00 36.85 2.41
4359 4677 8.311650 ACAGCAGTTACAAAACTCTTATACAG 57.688 34.615 0.00 0.00 44.28 2.74
4371 4691 3.392882 TCTTATACAGCGGTGCATGATG 58.607 45.455 15.82 5.72 0.00 3.07
4424 4744 5.590530 TTTCCAATGTTGCAACAACTACT 57.409 34.783 34.06 16.23 43.03 2.57
4429 4749 4.732285 ATGTTGCAACAACTACTTCTCG 57.268 40.909 34.06 0.00 43.03 4.04
4481 4806 6.586082 CACACATATCACAAAAAGCTAAACCC 59.414 38.462 0.00 0.00 0.00 4.11
4482 4807 6.266558 ACACATATCACAAAAAGCTAAACCCA 59.733 34.615 0.00 0.00 0.00 4.51
4484 4809 7.818930 CACATATCACAAAAAGCTAAACCCATT 59.181 33.333 0.00 0.00 0.00 3.16
4487 4812 3.498018 CACAAAAAGCTAAACCCATTGGC 59.502 43.478 0.00 0.00 45.19 4.52
4508 4833 1.882623 CCTTGGTCTGAAACTGGCTTC 59.117 52.381 0.00 0.00 0.00 3.86
4512 4837 2.218603 GGTCTGAAACTGGCTTCGAAA 58.781 47.619 0.00 0.00 0.00 3.46
4513 4838 2.814336 GGTCTGAAACTGGCTTCGAAAT 59.186 45.455 0.00 0.00 0.00 2.17
4515 4840 4.454504 GGTCTGAAACTGGCTTCGAAATAA 59.545 41.667 0.00 0.00 0.00 1.40
4680 5007 0.403271 ACTTCACATCAAGGCCAGCT 59.597 50.000 5.01 0.00 0.00 4.24
4749 5076 2.743664 TGATTTCATCGCCTTCACACAG 59.256 45.455 0.00 0.00 0.00 3.66
4828 5216 6.464222 TCTGACAGTAGTTAACAATCCAAGG 58.536 40.000 8.61 0.00 0.00 3.61
4846 5234 3.014304 AGGGCAGACTCGTAATACAGA 57.986 47.619 0.00 0.00 0.00 3.41
4854 5242 5.457148 CAGACTCGTAATACAGAGAACATGC 59.543 44.000 15.35 0.00 37.87 4.06
4970 5365 5.702670 ACATCAATATCAATCTTAGCCACCG 59.297 40.000 0.00 0.00 0.00 4.94
4980 5375 2.438021 TCTTAGCCACCGGATTAGCAAT 59.562 45.455 9.46 0.00 0.00 3.56
4987 5382 4.320494 GCCACCGGATTAGCAATTCTAATG 60.320 45.833 9.46 0.00 45.45 1.90
5070 5465 3.891366 CTGGTTTTCCACAACAGAGGAAT 59.109 43.478 0.00 0.00 46.22 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.306953 ACCGCGTTGTTTGTATGTAAATTATT 58.693 30.769 4.92 0.00 0.00 1.40
284 291 6.593382 ACATAAGTTACCGGCGTATGTTTTTA 59.407 34.615 6.01 0.00 37.95 1.52
373 380 6.402118 CCGTGGTGTCTGAACTTATGTTATTG 60.402 42.308 0.00 0.00 36.39 1.90
374 381 5.642063 CCGTGGTGTCTGAACTTATGTTATT 59.358 40.000 0.00 0.00 36.39 1.40
751 768 4.735599 ACCCCCTCCCTTCGACCC 62.736 72.222 0.00 0.00 0.00 4.46
752 769 3.082055 GACCCCCTCCCTTCGACC 61.082 72.222 0.00 0.00 0.00 4.79
753 770 1.900545 CTTGACCCCCTCCCTTCGAC 61.901 65.000 0.00 0.00 0.00 4.20
754 771 1.612442 CTTGACCCCCTCCCTTCGA 60.612 63.158 0.00 0.00 0.00 3.71
755 772 2.670148 CCTTGACCCCCTCCCTTCG 61.670 68.421 0.00 0.00 0.00 3.79
756 773 2.985116 GCCTTGACCCCCTCCCTTC 61.985 68.421 0.00 0.00 0.00 3.46
757 774 2.941583 GCCTTGACCCCCTCCCTT 60.942 66.667 0.00 0.00 0.00 3.95
819 853 0.672889 TGTCGTAACTGGCAACCGTA 59.327 50.000 0.00 0.00 0.00 4.02
863 897 9.959749 ACTTCAGCGACTTTATTTTTCAAATAA 57.040 25.926 0.00 0.00 0.00 1.40
865 899 9.959749 TTACTTCAGCGACTTTATTTTTCAAAT 57.040 25.926 0.00 0.00 0.00 2.32
866 900 9.790389 TTTACTTCAGCGACTTTATTTTTCAAA 57.210 25.926 0.00 0.00 0.00 2.69
867 901 9.790389 TTTTACTTCAGCGACTTTATTTTTCAA 57.210 25.926 0.00 0.00 0.00 2.69
868 902 9.790389 TTTTTACTTCAGCGACTTTATTTTTCA 57.210 25.926 0.00 0.00 0.00 2.69
900 934 2.568090 CACGGAAATGCACAGGGC 59.432 61.111 0.00 0.00 45.13 5.19
901 935 2.568090 GCACGGAAATGCACAGGG 59.432 61.111 0.00 0.00 45.39 4.45
902 936 2.128853 AACGCACGGAAATGCACAGG 62.129 55.000 0.00 0.00 46.47 4.00
903 937 0.317770 AAACGCACGGAAATGCACAG 60.318 50.000 0.00 0.00 46.47 3.66
904 938 0.101399 AAAACGCACGGAAATGCACA 59.899 45.000 0.00 0.00 46.47 4.57
905 939 1.071568 CAAAAACGCACGGAAATGCAC 60.072 47.619 0.00 0.00 46.47 4.57
906 940 1.203928 CAAAAACGCACGGAAATGCA 58.796 45.000 0.00 0.00 46.47 3.96
907 941 1.204792 ACAAAAACGCACGGAAATGC 58.795 45.000 0.00 0.00 42.48 3.56
908 942 3.916405 AAACAAAAACGCACGGAAATG 57.084 38.095 0.00 0.00 0.00 2.32
909 943 4.930463 AAAAACAAAAACGCACGGAAAT 57.070 31.818 0.00 0.00 0.00 2.17
928 962 1.864711 CGCACGGTTCTCTCTCAAAAA 59.135 47.619 0.00 0.00 0.00 1.94
929 963 1.202486 ACGCACGGTTCTCTCTCAAAA 60.202 47.619 0.00 0.00 0.00 2.44
930 964 0.387929 ACGCACGGTTCTCTCTCAAA 59.612 50.000 0.00 0.00 0.00 2.69
931 965 0.318699 CACGCACGGTTCTCTCTCAA 60.319 55.000 0.00 0.00 0.00 3.02
932 966 1.285950 CACGCACGGTTCTCTCTCA 59.714 57.895 0.00 0.00 0.00 3.27
933 967 0.318784 AACACGCACGGTTCTCTCTC 60.319 55.000 0.00 0.00 0.00 3.20
934 968 0.597637 CAACACGCACGGTTCTCTCT 60.598 55.000 0.00 0.00 0.00 3.10
935 969 1.557443 CCAACACGCACGGTTCTCTC 61.557 60.000 0.00 0.00 0.00 3.20
936 970 1.594293 CCAACACGCACGGTTCTCT 60.594 57.895 0.00 0.00 0.00 3.10
937 971 2.604174 CCCAACACGCACGGTTCTC 61.604 63.158 0.00 0.00 0.00 2.87
938 972 2.590575 CCCAACACGCACGGTTCT 60.591 61.111 0.00 0.00 0.00 3.01
939 973 1.159098 TAACCCAACACGCACGGTTC 61.159 55.000 0.00 0.00 39.33 3.62
940 974 0.747283 TTAACCCAACACGCACGGTT 60.747 50.000 0.00 0.00 41.43 4.44
941 975 0.747283 TTTAACCCAACACGCACGGT 60.747 50.000 0.00 0.00 0.00 4.83
942 976 0.040781 CTTTAACCCAACACGCACGG 60.041 55.000 0.00 0.00 0.00 4.94
943 977 0.658897 ACTTTAACCCAACACGCACG 59.341 50.000 0.00 0.00 0.00 5.34
944 978 2.224784 CCTACTTTAACCCAACACGCAC 59.775 50.000 0.00 0.00 0.00 5.34
945 979 2.496111 CCTACTTTAACCCAACACGCA 58.504 47.619 0.00 0.00 0.00 5.24
946 980 1.198408 GCCTACTTTAACCCAACACGC 59.802 52.381 0.00 0.00 0.00 5.34
947 981 2.496111 TGCCTACTTTAACCCAACACG 58.504 47.619 0.00 0.00 0.00 4.49
948 982 3.005050 GGTTGCCTACTTTAACCCAACAC 59.995 47.826 0.00 0.00 38.29 3.32
949 983 3.224269 GGTTGCCTACTTTAACCCAACA 58.776 45.455 0.00 0.00 38.29 3.33
950 984 2.227149 CGGTTGCCTACTTTAACCCAAC 59.773 50.000 0.00 0.00 40.52 3.77
951 985 2.106166 TCGGTTGCCTACTTTAACCCAA 59.894 45.455 0.00 0.00 40.52 4.12
952 986 1.698532 TCGGTTGCCTACTTTAACCCA 59.301 47.619 0.00 0.00 40.52 4.51
953 987 2.079158 GTCGGTTGCCTACTTTAACCC 58.921 52.381 0.00 0.00 40.52 4.11
954 988 3.049708 AGTCGGTTGCCTACTTTAACC 57.950 47.619 0.00 0.00 40.29 2.85
955 989 4.060205 TCAAGTCGGTTGCCTACTTTAAC 58.940 43.478 2.83 0.00 37.42 2.01
956 990 4.312443 CTCAAGTCGGTTGCCTACTTTAA 58.688 43.478 2.83 0.00 37.42 1.52
957 991 3.863400 GCTCAAGTCGGTTGCCTACTTTA 60.863 47.826 2.83 0.00 37.42 1.85
958 992 2.767505 CTCAAGTCGGTTGCCTACTTT 58.232 47.619 2.83 0.00 37.42 2.66
959 993 1.608283 GCTCAAGTCGGTTGCCTACTT 60.608 52.381 0.03 0.03 39.61 2.24
960 994 0.037232 GCTCAAGTCGGTTGCCTACT 60.037 55.000 0.00 0.00 35.94 2.57
965 999 0.317854 GGTTTGCTCAAGTCGGTTGC 60.318 55.000 0.00 0.00 35.94 4.17
978 1012 1.454201 GAAGGTAGCAGAGGGTTTGC 58.546 55.000 0.00 0.00 41.83 3.68
983 1017 1.524482 GCTGGAAGGTAGCAGAGGG 59.476 63.158 0.00 0.00 40.81 4.30
1055 1092 2.436646 CACATGGCGGTGGAGGAC 60.437 66.667 0.00 0.00 35.13 3.85
1086 1123 1.152922 GGGTCTCCTCGTCCTCGAT 60.153 63.158 0.00 0.00 45.21 3.59
1623 1664 4.926832 ACGCAAAAGCAATAAACCAATACC 59.073 37.500 0.00 0.00 0.00 2.73
1635 1678 0.179124 GGGTGAACACGCAAAAGCAA 60.179 50.000 15.22 0.00 42.92 3.91
1709 1752 2.611518 CCACACTTCTACTACAGCTGC 58.388 52.381 15.27 0.00 0.00 5.25
1713 1756 4.866508 TCAACCCACACTTCTACTACAG 57.133 45.455 0.00 0.00 0.00 2.74
1734 1924 8.370182 AGGATTCATAAAAACAAACAGCTCAAT 58.630 29.630 0.00 0.00 0.00 2.57
1737 1927 7.653311 ACAAGGATTCATAAAAACAAACAGCTC 59.347 33.333 0.00 0.00 0.00 4.09
1983 2218 1.134936 ACCAAAGTTGTCCAAAACCGC 60.135 47.619 0.00 0.00 0.00 5.68
2018 2253 5.728471 TGCTTCAGAAAAATGAACCAAACA 58.272 33.333 0.00 0.00 35.40 2.83
2110 2345 4.456911 ACTGACCAATACTTCAGCAACATG 59.543 41.667 0.00 0.00 42.67 3.21
2127 2362 3.674997 TCCAACTATCAAGCAACTGACC 58.325 45.455 0.00 0.00 0.00 4.02
2177 2413 1.068474 AACGTCACATGTAAGCTCGC 58.932 50.000 0.00 0.00 0.00 5.03
2193 2429 8.735315 AGTCAGATATGGTTCTATGATCTAACG 58.265 37.037 0.00 0.00 0.00 3.18
2196 2432 9.593565 ACAAGTCAGATATGGTTCTATGATCTA 57.406 33.333 0.00 0.00 0.00 1.98
2197 2433 8.489676 ACAAGTCAGATATGGTTCTATGATCT 57.510 34.615 0.00 0.00 0.00 2.75
2198 2434 8.986847 CAACAAGTCAGATATGGTTCTATGATC 58.013 37.037 0.00 0.00 0.00 2.92
2203 2439 7.331026 CCTTCAACAAGTCAGATATGGTTCTA 58.669 38.462 0.00 0.00 0.00 2.10
2211 2447 6.899393 AAATTGCCTTCAACAAGTCAGATA 57.101 33.333 0.00 0.00 34.60 1.98
2243 2479 9.961265 CTAACTATAACATTCGATTAGTCACCA 57.039 33.333 0.00 0.00 0.00 4.17
2244 2480 9.962783 ACTAACTATAACATTCGATTAGTCACC 57.037 33.333 0.00 0.00 27.77 4.02
2304 2540 4.908601 ACCAGAGAACAATATGTGACCA 57.091 40.909 0.00 0.00 0.00 4.02
2331 2567 7.342799 CCAAGGAGAAAATGGGAGAATCAAATA 59.657 37.037 0.00 0.00 36.25 1.40
2456 2692 3.305897 CCGCAAACAAGGTTTTGAACTTC 59.694 43.478 0.00 0.00 38.54 3.01
2463 2699 1.145156 GGGCCGCAAACAAGGTTTT 59.855 52.632 0.00 0.00 0.00 2.43
2466 2702 1.303317 CTAGGGCCGCAAACAAGGT 60.303 57.895 0.00 0.00 0.00 3.50
2477 2713 1.408822 CCATCAGTTGAACCTAGGGCC 60.409 57.143 14.81 4.66 0.00 5.80
2485 2721 4.074970 AGATTCACCACCATCAGTTGAAC 58.925 43.478 0.00 0.00 0.00 3.18
2515 2751 2.189594 TGCATGCTTAGCACTGAACT 57.810 45.000 20.33 0.00 43.04 3.01
2777 3037 0.532862 CCTGCAACGGTGAGTCAACT 60.533 55.000 3.55 0.00 0.00 3.16
2879 3139 4.785453 GGGGGCTCAAGCTCACCG 62.785 72.222 3.95 0.00 45.20 4.94
3017 3277 2.364970 CACCTGTTTCCTTCCATGCAAA 59.635 45.455 0.00 0.00 0.00 3.68
3059 3319 4.020396 TGCAACAGCAACATAATCCCATTT 60.020 37.500 0.00 0.00 34.85 2.32
3135 3395 9.034544 GTTTTCTTCAAGCAAATATTTCACAGT 57.965 29.630 0.00 0.00 0.00 3.55
3326 3586 0.323360 GTGGGGCACAGGCAGATTTA 60.323 55.000 0.00 0.00 43.71 1.40
3327 3587 1.607467 GTGGGGCACAGGCAGATTT 60.607 57.895 0.00 0.00 43.71 2.17
3382 3649 6.153680 ACTTTGGAAACTGTATGTGAACCAAA 59.846 34.615 0.00 0.00 40.19 3.28
3660 3932 6.420588 CAAAGCGAAAAATCTGCAAAATCAA 58.579 32.000 0.00 0.00 0.00 2.57
3679 3951 2.510551 AAACAGGGCAGGCCAAAGC 61.511 57.895 16.94 5.81 37.98 3.51
3712 3985 2.354704 CCATGACCAGCGGAAGTTTCTA 60.355 50.000 0.00 0.00 0.00 2.10
3737 4010 5.485353 ACATTTCTCCCACTGATGTCTAGAA 59.515 40.000 0.00 0.00 0.00 2.10
3784 4057 6.407613 TGAGAATATAACCCCTATTTCCCCT 58.592 40.000 0.00 0.00 0.00 4.79
3848 4122 5.621228 GCACAAGAGTTTAAAATGACAGACG 59.379 40.000 0.00 0.00 0.00 4.18
3870 4144 4.102996 TGAATCTGTAATCATAGCCCAGCA 59.897 41.667 0.00 0.00 0.00 4.41
3960 4235 1.915489 TGCCTATTCCCACATCACTGT 59.085 47.619 0.00 0.00 35.44 3.55
4020 4295 5.125417 AGTTCATGTTGTTTTACTGCACACT 59.875 36.000 0.00 0.00 0.00 3.55
4147 4464 1.809684 AGCAGGTCGAGCTTTTTACC 58.190 50.000 15.83 0.00 39.87 2.85
4313 4630 5.851720 TGTAATGCTGGAAATGCTCAAAAA 58.148 33.333 0.00 0.00 0.00 1.94
4334 4651 7.095187 GCTGTATAAGAGTTTTGTAACTGCTGT 60.095 37.037 0.00 0.00 44.51 4.40
4344 4661 3.435327 TGCACCGCTGTATAAGAGTTTTG 59.565 43.478 0.00 0.00 0.00 2.44
4346 4664 3.328382 TGCACCGCTGTATAAGAGTTT 57.672 42.857 0.00 0.00 0.00 2.66
4359 4677 1.137404 GTGTTCCATCATGCACCGC 59.863 57.895 0.00 0.00 0.00 5.68
4371 4691 5.639082 CCTGCCTAATCAAAAATTGTGTTCC 59.361 40.000 0.00 0.00 0.00 3.62
4388 4708 2.124320 GAAATGCCGGCCTGCCTA 60.124 61.111 26.77 3.54 0.00 3.93
4424 4744 2.093128 GCCCCAGAGGTAAAATCGAGAA 60.093 50.000 0.00 0.00 38.26 2.87
4429 4749 3.282885 CAGAAGCCCCAGAGGTAAAATC 58.717 50.000 0.00 0.00 38.26 2.17
4481 4806 1.273327 GTTTCAGACCAAGGGCCAATG 59.727 52.381 6.18 4.03 0.00 2.82
4482 4807 1.147817 AGTTTCAGACCAAGGGCCAAT 59.852 47.619 6.18 0.00 0.00 3.16
4484 4809 0.178992 CAGTTTCAGACCAAGGGCCA 60.179 55.000 6.18 0.00 0.00 5.36
4487 4812 0.111253 AGCCAGTTTCAGACCAAGGG 59.889 55.000 0.00 0.00 0.00 3.95
4508 4833 6.022251 CGTGTTTGCTTAGCTGAATTATTTCG 60.022 38.462 5.60 0.00 34.39 3.46
4512 4837 5.445939 CGTCGTGTTTGCTTAGCTGAATTAT 60.446 40.000 5.60 0.00 0.00 1.28
4513 4838 4.143200 CGTCGTGTTTGCTTAGCTGAATTA 60.143 41.667 5.60 0.00 0.00 1.40
4515 4840 2.157668 CGTCGTGTTTGCTTAGCTGAAT 59.842 45.455 5.60 0.00 0.00 2.57
4670 4997 2.413142 GCCAAGCTAGCTGGCCTTG 61.413 63.158 31.71 21.24 42.52 3.61
4680 5007 0.758734 ACACTGTCACTGCCAAGCTA 59.241 50.000 0.00 0.00 0.00 3.32
4749 5076 2.099756 GCCTTGTGAAATATCCTGGTGC 59.900 50.000 0.00 0.00 0.00 5.01
4807 5181 4.395231 GCCCTTGGATTGTTAACTACTGTC 59.605 45.833 7.22 0.00 0.00 3.51
4828 5216 4.142447 TGTTCTCTGTATTACGAGTCTGCC 60.142 45.833 12.28 3.22 0.00 4.85
4846 5234 3.388308 GAGTATGAGATGCGCATGTTCT 58.612 45.455 30.76 20.49 0.00 3.01
4874 5262 7.563020 AGAATTATGTCTGCTGAGAAATCAGA 58.437 34.615 9.38 0.00 39.99 3.27
4970 5365 7.148255 TGTCACACACATTAGAATTGCTAATCC 60.148 37.037 0.00 0.00 44.55 3.01
4980 5375 6.252281 GTTTCGTTTGTCACACACATTAGAA 58.748 36.000 0.00 0.00 33.90 2.10
4987 5382 2.904011 TGGTTTCGTTTGTCACACAC 57.096 45.000 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.