Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1962
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: 23642
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Found at i:4020 original size:56 final size:56
Alignment explanation
Indices: 3929--4051 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 56
3919 GAGATTGGCG
* * *
3929 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATAGCA
* *
3986 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
*
4041 CTGAGTGTGCG
1 CTAAGTGTGCG
4052 GACTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 23 0.38
56 22 0.37
57 15 0.25
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
Found at i:4038 original size:27 final size:28
Alignment explanation
Indices: 3929--4051 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
3919 GAGATTGGCG
* * * *
3929 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
3958 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
3986 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
4014 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
4041 CTGAGTGTGCG
1 CTAAGTGTGCG
4052 GACTTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.28
28 48 0.55
29 15 0.17
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:4062 original size:27 final size:27
Alignment explanation
Indices: 3954--4064 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
3944 TAAATTGTAC
* * *
3954 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
3982 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
4010 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
4037 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
4064 A
1 A
4065 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:12171 original size:56 final size:56
Alignment explanation
Indices: 12080--12202 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 56
12070 GAGATTGGCG
* * *
12080 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATAGCA
* *
12137 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
*
12192 CTGAGTGTGCG
1 CTAAGTGTGCG
12203 GACTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 23 0.38
56 22 0.37
57 15 0.25
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
Found at i:12189 original size:27 final size:28
Alignment explanation
Indices: 12080--12202 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
12070 GAGATTGGCG
* * * *
12080 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
12109 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
12137 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
12165 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
12192 CTGAGTGTGCG
1 CTAAGTGTGCG
12203 GACTTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.28
28 48 0.55
29 15 0.17
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:12213 original size:27 final size:27
Alignment explanation
Indices: 12105--12215 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
12095 TAAATTGTAC
* * *
12105 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
12133 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
12161 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
12188 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
12215 A
1 A
12216 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:13891 original size:40 final size:40
Alignment explanation
Indices: 13854--14078 Score: 278
Period size: 40 Copynumber: 5.6 Consensus size: 40
13844 GCTACTCGTT
* *
13854 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
13894 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
13934 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** *
13974 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
** * * * *
14014 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACCTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGT-AACTCGCA
*
14055 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAACCCGG
14079 GCATCATTCA
Statistics
Matches: 170, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
39 3 0.02
40 153 0.90
41 14 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:21757 original size:40 final size:40
Alignment explanation
Indices: 21720--21940 Score: 260
Period size: 40 Copynumber: 5.7 Consensus size: 40
21710 GCTACTCGTT
* *
21720 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
21760 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
21800 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
21840 CAAATGCCTTC-GG-CTT-AGCCGGA-TTAGT-ACTCGTA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
21875 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
21916 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
21941 CATCATTCAA
Statistics
Matches: 162, Mismatches: 11, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
35 19 0.12
36 5 0.03
37 9 0.06
38 8 0.05
39 5 0.03
40 104 0.64
41 12 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:21824 original size:80 final size:78
Alignment explanation
Indices: 21687--21940 Score: 270
Period size: 80 Copynumber: 3.3 Consensus size: 78
21677 AAATCACGTA
* * ** *
21687 CCTTCGGAATTTAA-CCGGATATAGCTACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAG
1 CCTTCGGGACTTAACCCGGAT-TAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG
21751 TAACTCGCACAAATG
64 TAACTCGCACAAATG
*
21766 CCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT-TA
1 CCTTCGGGACTTAACCCGGA-TTAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATA
21830 GTAACTCGCACAAATG
63 GTAACTCGCACAAATG
* * * * *
21846 CCTTC-GG-CTT-AGCCGGATTAGTACTCGTACAAATGCCTTC-GGATCTTAGTCCGGATATGGT
1 CCTTCGGGACTTAACCCGGATTAGTACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGTTATAGT
* *
21907 CACTTAGCACAAA-G
65 AAC-TCGCACAAATG
*
21921 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
21941 CATCATTCAA
Statistics
Matches: 149, Mismatches: 16, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
74 4 0.03
75 36 0.24
76 15 0.10
77 9 0.06
78 8 0.05
79 15 0.10
80 59 0.40
81 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CCTTCGGGACTTAACCCGGATTAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
ACTCGCACAAATG
Found at i:21900 original size:115 final size:120
Alignment explanation
Indices: 21720--21940 Score: 285
Period size: 115 Copynumber: 1.9 Consensus size: 120
21710 GCTACTCGTT
*
21720 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
21785 ATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * **
21840 CAAATGCCTTC-GG-CTTAG-CCGGAT-TAGT-ACTCGTACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
* * *
21899 GATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
65 GATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
21941 CATCATTCAA
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
114 3 0.03
115 52 0.58
116 12 0.13
117 5 0.06
118 4 0.04
119 2 0.02
120 11 0.12
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Done.