Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014308.1 Corchorus capsularis cultivar CVL-1 contig14329, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 39739
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:569 original size:40 final size:40
Alignment explanation
Indices: 524--647 Score: 96
Period size: 40 Copynumber: 3.1 Consensus size: 40
514 GTAAAATGGT
524 AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
1 AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
* * ** * * * * * *
564 AAAATAGAGTTTTTAGTTGAGTAAAATAG---TAA-AATGGT-
1 AAAATATAATAGTTA--TAAGGATATTAGATTTAATTAT-ATA
602 AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
1 AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
642 AAAATA
1 AAAATA
648 GAGTTTTTAG
Statistics
Matches: 56, Mismatches: 20, Indels: 16
0.61 0.22 0.17
Matches are distributed among these distances:
36 8 0.14
38 13 0.23
39 8 0.14
40 19 0.34
42 8 0.14
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (40 bp):
AAAATATAATAGTTATAAGGATATTAGATTTAATTATATA
Found at i:639 original size:78 final size:78
Alignment explanation
Indices: 510--753 Score: 427
Period size: 78 Copynumber: 3.1 Consensus size: 78
500 TTTTAATTAT
510 AATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTT
1 AATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTT
575 TTTAGTTGAGTAA
66 TTTAGTTGAGTAA
588 AATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTT
1 AATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTT
653 TTTAGTTGAGTAA
66 TTTAGTTGAGTAA
* * * * *
666 AATAGTAAAAAGGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGAGTT
1 AATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTT
731 TTTAGTTGAGTAA
66 TTTAGTTGAGTAA
744 AACTA-TAAAA
1 AA-TAGTAAAA
754 ACCTAAACAA
Statistics
Matches: 160, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
78 158 0.99
79 2 0.01
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (78 bp):
AATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTT
TTTAGTTGAGTAA
Found at i:873 original size:12 final size:11
Alignment explanation
Indices: 858--888 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
848 ATAGATATAG
858 ATATATATAAT
1 ATATATATAAT
869 AATATATATAAT
1 -ATATATATAAT
881 ATATATAT
1 ATATATAT
889 TAGGTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATATATATAAT
Found at i:5484 original size:17 final size:17
Alignment explanation
Indices: 5446--5480 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5436 GAAGAAGGAG
*
5446 AGAAAGGAAAGGAAAAA
1 AGAAAGGAAAAGAAAAA
5463 AGAAA-GAAAAGAAAAA
1 AGAAAGGAAAAGAAAAA
5479 AG
1 AG
5481 GAAAATAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AGAAAGGAAAAGAAAAA
Found at i:6196 original size:35 final size:35
Alignment explanation
Indices: 6150--6397 Score: 363
Period size: 35 Copynumber: 7.1 Consensus size: 35
6140 AGAGAGTTAG
6150 AATTGGTAATCAACTTAATTCGGTGTAATTAAGTA
1 AATTGGTAATCAACTTAATTCGGTGTAATTAAGTA
*
6185 AATTGGTAATCAAGTTAATTCGGTGTAATTAAGTA
1 AATTGGTAATCAACTTAATTCGGTGTAATTAAGTA
*
6220 AATTGGTAATCAAATTAATTCGGTGTAATTAAGTA
1 AATTGGTAATCAACTTAATTCGGTGTAATTAAGTA
* *
6255 AATTTGTAATCAACTTAATTCGGTGTAATTAAGCA
1 AATTGGTAATCAACTTAATTCGGTGTAATTAAGTA
* *
6290 AATTGGTAGGT-AACTTAATTCGGTGTAATTAAGCA
1 AATTGGTA-ATCAACTTAATTCGGTGTAATTAAGTA
* * *
6325 AATTGATAATTAACTTAATTTGGTGTAATTAAGTA
1 AATTGGTAATCAACTTAATTCGGTGTAATTAAGTA
** * *
6360 AATCAGTAATCAGCTTAATTCGGTGTAATTATGTA
1 AATTGGTAATCAACTTAATTCGGTGTAATTAAGTA
6395 AAT
1 AAT
6398 AATCAAATGG
Statistics
Matches: 193, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
34 1 0.01
35 191 0.99
36 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (35 bp):
AATTGGTAATCAACTTAATTCGGTGTAATTAAGTA
Found at i:6199 original size:16 final size:16
Alignment explanation
Indices: 6150--6267 Score: 74
Period size: 19 Copynumber: 6.8 Consensus size: 16
6140 AGAGAGTTAG
* *
6150 AATTGGTAATCAACTT
1 AATTGGTAATCAAGTA
*
6166 AATTCGGTGTAATTAAGTA
1 AATT--G-GTAATCAAGTA
*
6185 AATTGGTAATCAAGTT
1 AATTGGTAATCAAGTA
*
6201 AATTCGGTGTAATTAAGTA
1 AATT--G-GTAATCAAGTA
* *
6220 AATTGGTAATCAAATT
1 AATTGGTAATCAAGTA
*
6236 AATTCGGTGTAATTAAGTA
1 AATT--G-GTAATCAAGTA
*
6255 AATTTGTAATCAA
1 AATTGGTAATCAA
6268 CTTAATTCGG
Statistics
Matches: 78, Mismatches: 15, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
16 36 0.46
17 2 0.03
18 3 0.04
19 37 0.47
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (16 bp):
AATTGGTAATCAAGTA
Found at i:6274 original size:16 final size:16
Alignment explanation
Indices: 6150--6274 Score: 61
Period size: 16 Copynumber: 7.2 Consensus size: 16
6140 AGAGAGTTAG
* *
6150 AATTGGTAATCAACTT
1 AATTTGTAATCAAGTT
* *
6166 AATTCGGTGTAATTAAGTA
1 AATT---TGTAATCAAGTT
*
6185 AATTGGTAATCAAGTT
1 AATTTGTAATCAAGTT
* *
6201 AATTCGGTGTAATTAAGTA
1 AATT---TGTAATCAAGTT
* *
6220 AATTGGTAATCAAATT
1 AATTTGTAATCAAGTT
* *
6236 AATTCGGTGTAATTAAGTA
1 AATT---TGTAATCAAGTT
*
6255 AATTTGTAATCAACTT
1 AATTTGTAATCAAGTT
6271 AATT
1 AATT
6275 CGGTGTAATT
Statistics
Matches: 79, Mismatches: 21, Indels: 18
0.67 0.18 0.15
Matches are distributed among these distances:
16 42 0.53
19 37 0.47
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.38
Consensus pattern (16 bp):
AATTTGTAATCAAGTT
Found at i:6831 original size:67 final size:68
Alignment explanation
Indices: 6739--6870 Score: 189
Period size: 67 Copynumber: 2.0 Consensus size: 68
6729 CCATCGGTTT
* *
6739 AGTTTTTAGATTTAGGGAAAGATCCCA-CCAAGTCTTCAAAGTTTT-AGATTTAGGGAAAGATCC
1 AGTTTTTAGATTCAGGGAAAAATCCCATCC-AGTCTTCAAAGTTTTCA-ATTTAGGGAAAGATCC
6802 CGCCG
64 CGCCG
* *
6807 AGTTTTTA-ATTCAGGGAAAAATCCCATCCAGTTTTTAAAGTTTTCAATTTAGGGAAAGATCCCG
1 AGTTTTTAGATTCAGGGAAAAATCCCATCCAGTCTTCAAAGTTTTCAATTTAGGGAAAGATCCCG
6871 TCAAAAGGCA
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
67 47 0.81
68 11 0.19
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (68 bp):
AGTTTTTAGATTCAGGGAAAAATCCCATCCAGTCTTCAAAGTTTTCAATTTAGGGAAAGATCCCG
CCG
Found at i:6839 original size:29 final size:29
Alignment explanation
Indices: 6780--6844 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
6770 GTCTTCAAAG
* *
6780 TTTTAGATTTAGGGAAAGATCCCGCCGAGT
1 TTTTA-ATTCAGGGAAAAATCCCGCCGAGT
*
6810 TTTTAATTCAGGGAAAAATCCCATCC-AGT
1 TTTTAATTCAGGGAAAAATCCC-GCCGAGT
6839 TTTTAA
1 TTTTAA
6845 AGTTTTCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 24 0.77
30 7 0.23
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (29 bp):
TTTTAATTCAGGGAAAAATCCCGCCGAGT
Found at i:10424 original size:11 final size:12
Alignment explanation
Indices: 10408--10446 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
10398 CAACGCAAAG
10408 GAAAAAAG-AAA
1 GAAAAAAGAAAA
10419 GAAAAAAGAAAA
1 GAAAAAAGAAAA
*
10431 GAAAGAAAAAAAA
1 GAAA-AAAGAAAA
10444 GAA
1 GAA
10447 GAATAAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 8 0.32
12 7 0.28
13 10 0.40
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
GAAAAAAGAAAA
Found at i:10448 original size:16 final size:15
Alignment explanation
Indices: 10409--10449 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 15
10399 AACGCAAAGG
10409 AAAAAAGAAAGAAAA
1 AAAAAAGAAAGAAAA
10424 AAGAAAAGAAAGAAAA
1 AA-AAAAGAAAGAAAA
10440 AAAAGAAGAA
1 AAAA-AAGAA
10450 TAAAACTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAGAAAA
Found at i:11087 original size:3 final size:3
Alignment explanation
Indices: 11067--11104 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
11057 ATGGTGAAAA
*
11067 AAG AAA AAG AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
11105 CTCTAGGGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12354 original size:54 final size:54
Alignment explanation
Indices: 12237--12606 Score: 618
Period size: 54 Copynumber: 6.8 Consensus size: 54
12227 TTCAGAAGAA
* *
12237 TAAGTTTATCTTCAAGTGA-CCTAGTGCGGTCAATCAA-AGAAGTATCCAGTGGTAT
1 TAAGTTTATCTTCAAGTGATCC-AGTGCGGTCAATCAAGA-AAGTTTCCAATGGT-T
* * *
12292 TAAGTTTATCTTCAAGTGATCCAGTGCAGTCAATAAAGAAAGTTTCCAATTGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTT
12346 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTT
* *
12400 TAAGTTTATCTTCAAGTGATCCACTGCGGTCAATCAAGAAAGTTTCCAGTGGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTT
*
12454 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCACTGGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTT
12508 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTT
*
12562 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAGTCAAGAAAGTTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTT
12607 GCAGTGCGGT
Statistics
Matches: 299, Mismatches: 14, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
54 253 0.85
55 43 0.14
56 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (54 bp):
TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTT
Found at i:12651 original size:108 final size:103
Alignment explanation
Indices: 12237--12651 Score: 492
Period size: 108 Copynumber: 3.8 Consensus size: 103
12227 TTCAGAAGAA
*
12237 TAAGTTTATCTTCAAGTGA-CCTAGTGCGGTCAATCAA-AGAAGTATCCAGTGGTATTAAGTTTA
1 TAAGTTTATCTTCAAGTGATCC-AGTGCGGTCAATCAAGA-AAGTTTCCAGTGGT-TTAAGTTTA
* *
12300 TCTTCAAGTGATCCAGTGCAGTCAATAAAGAAAGTTTCCAATTGTT
63 TCTTCAAGTGAT----T-CAGTCAATCAAGAAAGTTTCCAATGGTT
*
12346 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTTTAAGTTTATCT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATCT
* *
12411 TCAAGTGATCCACTGCGGTCAATCAAGAAAGTTTCCAGTGGTT
66 TCAAGTGAT----T-CAGTCAATCAAGAAAGTTTCCAATGGTT
*
12454 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCACTGGTTTAAGTTTATCT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATCT
*
12519 TCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTT
66 TCAAGTGAT----T-CAGTCAATCAAGAAAGTTTCCAATGGTT
* * *
12562 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAGTCAAGAAAGTTTGCAGTGCGGTTAATTAGGTT
1 TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGT--GG-T--TTAAGTT
* *
12627 TATCTTCAAGTGGTTCAGTGAATCA
61 TATCTTCAAGTGATTCAGTCAATCA
12652 GATGAATCGG
Statistics
Matches: 282, Mismatches: 17, Indels: 15
0.90 0.05 0.05
Matches are distributed among these distances:
108 210 0.74
109 47 0.17
110 5 0.02
111 1 0.00
113 19 0.07
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.33
Consensus pattern (103 bp):
TAAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATCT
TCAAGTGATTCAGTCAATCAAGAAAGTTTCCAATGGTT
Found at i:12859 original size:88 final size:88
Alignment explanation
Indices: 12680--13064 Score: 488
Period size: 88 Copynumber: 4.3 Consensus size: 88
12670 CCTCATAGGA
* * *
12680 TGATTCGGTGAATCAAGTCAATGCGATGCATTTCTTCAAAGATTGGAATTCGGTGAGCTCGGTGC
1 TGATTCGGTGAATCAAGTTAATGCGGTGCATTTATTCAAAGATTGG-ATTCGGTGAGCTCGGTGC
* *
12745 AACAAATTTTCAAATAGTTCATGG
65 AGCAAATTTTCAAACAGTTCATGG
*
12769 TGATTCGGTGAATCAAGTTAATGCGGTGCATTTATTCAAATATTGGATTCGGTGAGCTCGGTGCA
1 TGATTCGGTGAATCAAGTTAATGCGGTGCATTTATTCAAAGATTGGATTCGGTGAGCTCGGTGCA
12834 GCAAATTTTCAAACAGTTCATGG
66 GCAAATTTTCAAACAGTTCATGG
*
12857 TGATTCGGTGAATCAAGTTAATGCGGTGCATTCATTCAAAGATTGGATTCGGTGAGCTCGGTGCA
1 TGATTCGGTGAATCAAGTTAATGCGGTGCATTTATTCAAAGATTGGATTCGGTGAGCTCGGTGCA
*
12922 GCAAA-TTTCAAAATAGTTCA-GG
66 GCAAATTTTC-AAACAGTTCATGG
** *** * *
12944 ACCATTCGGTGAATCAAGTTAATTTAGTGCCTTATTTCTTC-AAGATTGGATTCAGTGAGCTCGG
1 -TGATTCGGTGAATCAAGTTAATGCGGTG-C--ATTTATTCAAAGATTGGATTCGGTGAGCTCGG
* * * * *
13008 TTCAGCACATTTTCAGACAGTTCAAAGTT
62 TGCAGCAAATTTTCAAACAGTTC-ATG-G
*
13037 TGATTCGGTGGATCAAGTTAATGCGGTG
1 TGATTCGGTGAATCAAGTTAATGCGGTG
13065 TAATATTTCT
Statistics
Matches: 259, Mismatches: 28, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
87 6 0.02
88 140 0.54
89 43 0.17
90 36 0.14
91 11 0.04
92 23 0.09
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (88 bp):
TGATTCGGTGAATCAAGTTAATGCGGTGCATTTATTCAAAGATTGGATTCGGTGAGCTCGGTGCA
GCAAATTTTCAAACAGTTCATGG
Found at i:16220 original size:17 final size:17
Alignment explanation
Indices: 16184--16216 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16174 AGAAGGAGAA
*
16184 AAAGGAAAGTAAAAAAG
1 AAAGAAAAGTAAAAAAG
16201 AAAGAAAAG-AAAAAAG
1 AAAGAAAAGTAAAAAAG
16217 GAAAATAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (17 bp):
AAAGAAAAGTAAAAAAG
Found at i:16922 original size:19 final size:19
Alignment explanation
Indices: 16900--16991 Score: 88
Period size: 19 Copynumber: 5.2 Consensus size: 19
16890 TAATCAGTTT
16900 AATTCGGTGTAATTAAGTA
1 AATTCGGTGTAATTAAGTA
* *
16919 AATT--G-GTAATCAAGTT
1 AATTCGGTGTAATTAAGTA
*
16935 AGTTCGGTGTAATTAAGTA
1 AATTCGGTGTAATTAAGTA
* * *
16954 AATT--G-GTAATCAACTT
1 AATTCGGTGTAATTAAGTA
16970 AATTCGGTGTAATTAAGTA
1 AATTCGGTGTAATTAAGTA
16989 AAT
1 AAT
16992 GGAGTCAGTT
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
16 24 0.44
17 2 0.04
18 2 0.04
19 27 0.49
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (19 bp):
AATTCGGTGTAATTAAGTA
Found at i:16930 original size:35 final size:34
Alignment explanation
Indices: 16884--17003 Score: 172
Period size: 35 Copynumber: 3.5 Consensus size: 34
16874 AGAGAGTTAG
16884 AATTGGTAATCAGTTTAATTCGGTGTAATTAAGTA
1 AATTGGTAATCAG-TTAATTCGGTGTAATTAAGTA
*
16919 AATTGGTAATCAAGTTAGTTCGGTGTAATTAAGTA
1 AATTGGTAATC-AGTTAATTCGGTGTAATTAAGTA
*
16954 AATTGGTAATCAACTTAATTCGGTGTAATTAAGTA
1 AATTGGTAATC-AGTTAATTCGGTGTAATTAAGTA
*
16989 AA-TGG-AGTCAGTTAA
1 AATTGGTAATCAGTTAA
17004 GAATCAAGGA
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
32 5 0.06
33 3 0.04
34 3 0.04
35 66 0.84
36 2 0.03
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.37
Consensus pattern (34 bp):
AATTGGTAATCAGTTAATTCGGTGTAATTAAGTA
Found at i:16933 original size:16 final size:16
Alignment explanation
Indices: 16908--16966 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
16898 TTAATTCGGT
*
16908 GTAATTAAGTAAATTG
1 GTAATCAAGTAAATTG
* *
16924 GTAATCAAGTTAGTTCGG
1 GTAATCAAGTAAATT--G
*
16942 TGTAATTAAGTAAATTG
1 -GTAATCAAGTAAATTG
16959 GTAATCAA
1 GTAATCAA
16967 CTTAATTCGG
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
16 19 0.58
17 1 0.03
18 1 0.03
19 12 0.36
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (16 bp):
GTAATCAAGTAAATTG
Found at i:17413 original size:29 final size:29
Alignment explanation
Indices: 17354--17418 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
17344 GTCTTCAAAG
* *
17354 TTTTAGATTTAGGGAAAGATCCCGCCGAGT
1 TTTTA-ATTCAGGGAAAAATCCCGCCGAGT
*
17384 TTTTAATTCAGGGAAAAATCCCATCC-AGT
1 TTTTAATTCAGGGAAAAATCCC-GCCGAGT
17413 TTTTAA
1 TTTTAA
17419 AGTTTTCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 24 0.77
30 7 0.23
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (29 bp):
TTTTAATTCAGGGAAAAATCCCGCCGAGT
Found at i:17421 original size:67 final size:68
Alignment explanation
Indices: 17313--17443 Score: 178
Period size: 67 Copynumber: 1.9 Consensus size: 68
17303 CCATCGGTTT
* * *
17313 AGTTTTTAGATTTAGGGATAGATCCCACCAAGTCTTCAAAGTTTT-AGATTTAGGGAAAGATCCC
1 AGTTTTTAGATTCAGGGAAAAATCCCACCAAGTCTTCAAAGTTTTCA-ATTTAGGGAAAGATCCC
17377 GCCG
65 GCCG
* *
17381 AGTTTTTA-ATTCAGGGAAAAATCCCATCC-AGTTTTTAAAGTTTTCAATTTAGGGAAAGATCCC
1 AGTTTTTAGATTCAGGGAAAAATCCCA-CCAAGTCTTCAAAGTTTTCAATTTAGGGAAAGATCCC
17444 ATCAAAAGGC
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
67 45 0.80
68 11 0.20
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (68 bp):
AGTTTTTAGATTCAGGGAAAAATCCCACCAAGTCTTCAAAGTTTTCAATTTAGGGAAAGATCCCG
CCG
Found at i:17700 original size:19 final size:18
Alignment explanation
Indices: 17678--17769 Score: 75
Period size: 19 Copynumber: 5.2 Consensus size: 18
17668 TAATCAGCTT
17678 AATTAGGTGTAATTAAGTA
1 AATT-GGTGTAATTAAGTA
* *
17697 AATT-G-GTAATCAAGTT
1 AATTGGTGTAATTAAGTA
*
17713 AGTTCGGTGTAATTAAGTA
1 AATT-GGTGTAATTAAGTA
* * *
17732 AATT-G-GTAATCAATTT
1 AATTGGTGTAATTAAGTA
17748 AATTCGGTGTAATTAAGTA
1 AATT-GGTGTAATTAAGTA
17767 AAT
1 AAT
17770 GGAGTCAGTT
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
16 24 0.44
17 2 0.04
18 2 0.04
19 27 0.49
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (18 bp):
AATTGGTGTAATTAAGTA
Found at i:17708 original size:35 final size:34
Alignment explanation
Indices: 17662--17781 Score: 163
Period size: 35 Copynumber: 3.5 Consensus size: 34
17652 GAGAGTTTAG
*
17662 AATTGGTAATCAGCTTAATTAGGTGTAATTAAGTA
1 AATTGGTAATCAG-TTAATTCGGTGTAATTAAGTA
*
17697 AATTGGTAATCAAGTTAGTTCGGTGTAATTAAGTA
1 AATTGGTAATC-AGTTAATTCGGTGTAATTAAGTA
*
17732 AATTGGTAATCAATTTAATTCGGTGTAATTAAGTA
1 AATTGGTAATC-AGTTAATTCGGTGTAATTAAGTA
*
17767 AA-TGG-AGTCAGTTAA
1 AATTGGTAATCAGTTAA
17782 GAATCAAGGA
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
32 5 0.06
33 3 0.04
34 3 0.04
35 65 0.83
36 2 0.03
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.37
Consensus pattern (34 bp):
AATTGGTAATCAGTTAATTCGGTGTAATTAAGTA
Found at i:17711 original size:16 final size:16
Alignment explanation
Indices: 17686--17744 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
17676 TTAATTAGGT
*
17686 GTAATTAAGTAAATTG
1 GTAATCAAGTAAATTG
* *
17702 GTAATCAAGTTAGTTCGG
1 GTAATCAAGTAAATT--G
*
17720 TGTAATTAAGTAAATTG
1 -GTAATCAAGTAAATTG
17737 GTAATCAA
1 GTAATCAA
17745 TTTAATTCGG
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
16 19 0.58
17 1 0.03
18 1 0.03
19 12 0.36
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (16 bp):
GTAATCAAGTAAATTG
Found at i:17921 original size:778 final size:780
Alignment explanation
Indices: 16798--18354 Score: 2926
Period size: 780 Copynumber: 2.0 Consensus size: 780
16788 ATGCATCATA
* *
16798 TGCATCCATGCATTTCAGGACAAAATTCAGTGATTAATTAAAGAATAAAATTCCCATAAAAAAAA
1 TGCATCCATGCATTTCAGGACAAAATTCAGTGATTAATCAAAGAATAAAATTCACATAAAAAAAA
* *
16863 GAAGAAAAGAAAGAGAGTTAGAATTGGTAATCAGTTTAATTCGGTGTAATTAAGTAAATTGGTAA
66 GAAGAAAAGAAAGAGAGTTAGAATTGGTAATCAGCTTAATTAGGTGTAATTAAGTAAATTGGTAA
16928 TCAAGTTAGTTCGGTGTAATTAAGTAAATTGGTAATCAACTTAATTCGGTGTAATTAAGTAAATG
131 TCAAGTTAGTTCGGTGTAATTAAGTAAATTGGTAATCAACTTAATTCGGTGTAATTAAGTAAATG
16993 GAGTCAGTTAAGAATCAAGGAAAGATAATAATATGTAATAAAAGGTCTAATTCAGGATCATCGAG
196 GAGTCAGTTAAGAATCAAGGAAAGATAATAATATGTAATAAAAGGTCTAATTCAGGATCATCGAG
17058 TCAATCAAAATTAAAAAAAAACAAAGAAGAAGAAGAATTTATCGTTAAAGAAAAAAACTAAAAAG
261 TCAATCAAAATTAAAAAAAAACAAAGAAGAAGAAGAATTTATCGTTAAAGAAAAAAACTAAAAAG
17123 AAAGAATAAAATCCTTTTTTTCGAAAATTAAAAAGAGTTTGTGCTTGCATTTGTTCTCTTTGGTT
326 AAAGAATAAAATCCTTTTTTTCGAAAATTAAAAAGAGTTTGTGCTTGCATTTGTTCTCTTTGGTT
* *
17188 TTTCGAAAGA-ATAAAA-AAAATTAATCAATAAAAAAAAGAGTC-TTTTTTCTCAAAGTTTTCAA
391 TTTCAAAAGATAAAAAAGAAAATTAATCAAT-AAAAAAAGAGTCTTTTTTTCTCAAAGTTTTCAA
*
17250 AAGAGGGAAAGTTACCATCAGTCTCGGCTTTCATCTTCATTTAGGGAAAGTTCCCATCGGTTTAG
455 AAGAGGGAAAGTTACCATCAATCTCGGCTTTCATCTTCATTTAGGGAAAGTTCCCATCGGTTTAG
*
17315 TTTTTAGATTTAGGGATAGATCCCACCAAGTCTTCAAAGTTTTAGATTTAGGGAAAGATCCCGCC
520 TTTTTAGATTTAGGGAAAGATCCCACCAAGTCTTCAAAGTTTTAGATTTAGGGAAAGATCCCGCC
17380 GAGTTTTTAATTCAGGGAAAAATCCCATCCAGTTTTTAAAGTTTTCAATTTAGGGAAAGATCCCA
585 GAGTTTTTAATTCAGGGAAAAATCCCATCCAGTTTTTAAAGTTTTCAATTTAGGGAAAGATCCCA
17445 TCAAAAGGCATTTTTCAAAAAGAGTCGTTTTCATGGTAAGTTTTAAAGAAAATCCTCTAATGAGG
650 TCAAAAGGCATTTTTCAAAAAGAGTCGTTTTCATGGTAAGTTTTAAAGAAAATCCTCTAATGAGG
*
17510 AACCTAAAAAGAGAGCAAAATAGAAAATGGGAAAGTTCCCAACATTCCTATTTCAAAAAAAAAAA
715 AACCCAAAAAGAGAGCAAAATAGAAAATGGGAAAGTTCCCAACATTCCTATTTCAAAAAAAAAAA
17575 G
780 G
17576 TGCATCCATGCATTTCAGGACAAAATTCAGTGATTAATCAAAGAATAAAATTCACATAAAAAAAA
1 TGCATCCATGCATTTCAGGACAAAATTCAGTGATTAATCAAAGAATAAAATTCACATAAAAAAAA
17641 G-AGAAAAGAAAGAGAGTTTAGAATTGGTAATCAGCTTAATTAGGTGTAATTAAGTAAATTGGTA
66 GAAGAAAAGAAAGAGAG-TTAGAATTGGTAATCAGCTTAATTAGGTGTAATTAAGTAAATTGGTA
*
17705 ATCAAGTTAGTTCGGTGTAATTAAGTAAATTGGTAATCAATTTAATTCGGTGTAATTAAGTAAAT
130 ATCAAGTTAGTTCGGTGTAATTAAGTAAATTGGTAATCAACTTAATTCGGTGTAATTAAGTAAAT
17770 GGAGTCAGTTAAGAATCAAGGAAAGATAATAATATGTAATAAAAGGTCTAATTCAGGATCATCGA
195 GGAGTCAGTTAAGAATCAAGGAAAGATAATAATATGTAATAAAAGGTCTAATTCAGGATCATCGA
17835 GTCAATCAAAATTAAAAAAAAA-AAAGAAGAAGAAGAATTTATCGTTAAAGAAAAAAACTAAAAA
260 GTCAATCAAAATTAAAAAAAAACAAAGAAGAAGAAGAATTTATCGTTAAAGAAAAAAACTAAAAA
17899 GAAAGAATAAAATCCTTTTTTTTCGAAAATTAAAAAGAGTTTGTGCTTGCATTTGTTCTCTTTGG
325 GAAAGAATAAAATCC-TTTTTTTCGAAAATTAAAAAGAGTTTGTGCTTGCATTTGTTCTCTTTGG
17964 TTTTTCAAAAGATAAAAAAGAAAATTAATCAATAAAAAAAGAGTCTTTTTTTCTCAAAGTTTTCA
389 TTTTTCAAAAGATAAAAAAGAAAATTAATCAATAAAAAAAGAGTCTTTTTTTCTCAAAGTTTTCA
* *
18029 AAAGAGGGAAAGTTCCCTTCAATCTCGGCTTTCATCTTCATTTAGGGAAAGTTCCCATCGGTTTA
454 AAAGAGGGAAAGTTACCATCAATCTCGGCTTTCATCTTCATTTAGGGAAAGTTCCCATCGGTTTA
*
18094 GTTTTTAGATTTAGGGAAAGATCCCACCAAGTCTTCAAAGTTTTAGATTTAGGGAAAGATCTCGC
519 GTTTTTAGATTTAGGGAAAGATCCCACCAAGTCTTCAAAGTTTTAGATTTAGGGAAAGATCCCGC
18159 CGAGTTTTTAATTCAGGGAAAAATCCCATCCAGTTTTTAAAGTTTTCAATTTAGGGAAAGATCCC
584 CGAGTTTTTAATTCAGGGAAAAATCCCATCCAGTTTTTAAAGTTTTCAATTTAGGGAAAGATCCC
*
18224 GTCAAAAGGCATTTTTCAAAAAGAGTCGTTTTCATGGTAAGTTTTAAAGAAAATCCTCTAATGAG
649 ATCAAAAGGCATTTTTCAAAAAGAGTCGTTTTCATGGTAAGTTTTAAAGAAAATCCTCTAATGAG
18289 GAACCCAAAAAGAGAGCAAAATAGAAAATGGGAAAGTTCCCAACATTCCTATTTCAAAAAAAAAA
714 GAACCCAAAAAGAGAGCAAAATAGAAAATGGGAAAGTTCCCAACATTCCTATTTCAAAAAAAAAA
18354 A
779 A
18355 AACCATTTGT
Statistics
Matches: 760, Mismatches: 14, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
777 72 0.09
778 320 0.42
779 17 0.02
780 351 0.46
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (780 bp):
TGCATCCATGCATTTCAGGACAAAATTCAGTGATTAATCAAAGAATAAAATTCACATAAAAAAAA
GAAGAAAAGAAAGAGAGTTAGAATTGGTAATCAGCTTAATTAGGTGTAATTAAGTAAATTGGTAA
TCAAGTTAGTTCGGTGTAATTAAGTAAATTGGTAATCAACTTAATTCGGTGTAATTAAGTAAATG
GAGTCAGTTAAGAATCAAGGAAAGATAATAATATGTAATAAAAGGTCTAATTCAGGATCATCGAG
TCAATCAAAATTAAAAAAAAACAAAGAAGAAGAAGAATTTATCGTTAAAGAAAAAAACTAAAAAG
AAAGAATAAAATCCTTTTTTTCGAAAATTAAAAAGAGTTTGTGCTTGCATTTGTTCTCTTTGGTT
TTTCAAAAGATAAAAAAGAAAATTAATCAATAAAAAAAGAGTCTTTTTTTCTCAAAGTTTTCAAA
AGAGGGAAAGTTACCATCAATCTCGGCTTTCATCTTCATTTAGGGAAAGTTCCCATCGGTTTAGT
TTTTAGATTTAGGGAAAGATCCCACCAAGTCTTCAAAGTTTTAGATTTAGGGAAAGATCCCGCCG
AGTTTTTAATTCAGGGAAAAATCCCATCCAGTTTTTAAAGTTTTCAATTTAGGGAAAGATCCCAT
CAAAAGGCATTTTTCAAAAAGAGTCGTTTTCATGGTAAGTTTTAAAGAAAATCCTCTAATGAGGA
ACCCAAAAAGAGAGCAAAATAGAAAATGGGAAAGTTCCCAACATTCCTATTTCAAAAAAAAAAAG
Found at i:18185 original size:67 final size:68
Alignment explanation
Indices: 18093--18221 Score: 183
Period size: 67 Copynumber: 1.9 Consensus size: 68
18083 CCATCGGTTT
* *
18093 AGTTTTTAGATTTAGGGAAAGATCCCA-CCAAGTCTTCAAAGTTTT-AGATTTAGGGAAAGATCT
1 AGTTTTTAGATTCAGGGAAAAATCCCATCC-AGTCTTCAAAGTTTTCA-ATTTAGGGAAAGATCT
18156 CGCCG
64 CGCCG
* *
18161 AGTTTTTA-ATTCAGGGAAAAATCCCATCCAGTTTTTAAAGTTTTCAATTTAGGGAAAGATC
1 AGTTTTTAGATTCAGGGAAAAATCCCATCCAGTCTTCAAAGTTTTCAATTTAGGGAAAGATC
18222 CCGTCAAAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
67 44 0.80
68 11 0.20
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (68 bp):
AGTTTTTAGATTCAGGGAAAAATCCCATCCAGTCTTCAAAGTTTTCAATTTAGGGAAAGATCTCG
CCG
Found at i:19920 original size:31 final size:31
Alignment explanation
Indices: 19885--19946 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
19875 GCCACCCATA
* *
19885 ACATCAATCCTATGTACATTTTCTTCATATG
1 ACATCAATCCTATCTACATGTTCTTCATATG
* *
19916 ACATCAATCTTATCTACCTGTTCTTCATATG
1 ACATCAATCCTATCTACATGTTCTTCATATG
19947 CTTATAGACC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.42
Consensus pattern (31 bp):
ACATCAATCCTATCTACATGTTCTTCATATG
Found at i:21037 original size:15 final size:15
Alignment explanation
Indices: 21019--21049 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21009 TTTAAGTTTC
21019 AGGGACTTAATTGAA
1 AGGGACTTAATTGAA
*
21034 AGGGACTTATTTGAA
1 AGGGACTTAATTGAA
21049 A
1 A
21050 AGAAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (15 bp):
AGGGACTTAATTGAA
Found at i:25062 original size:21 final size:21
Alignment explanation
Indices: 24996--25062 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
24986 ATGTTCATAA
*
24996 CTTGGAATCGGTTGGAATATT
1 CTTGGAATCGATTGGAATATT
* * *
25017 CCTAGAATCGATTGTGAGA-A-G
1 CTTGGAATCGATTG-GA-ATATT
25038 CTTGGAATCGATTGGAATATT
1 CTTGGAATCGATTGGAATATT
25059 CTTG
1 CTTG
25063 CTCAAAACAT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
19 1 0.03
20 3 0.09
21 27 0.77
22 3 0.09
23 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (21 bp):
CTTGGAATCGATTGGAATATT
Done.