Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3427
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: 42596
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:3769 original size:40 final size:40
Alignment explanation
Indices: 3524--3983 Score: 562
Period size: 40 Copynumber: 11.7 Consensus size: 40
3514 GAGCATTGGA
*
3524 ATATATCCGGGCGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCC-GG-GCTAAGACCCGAAGGCAATTATGCGAGTTG
*
3566 ATATATCCGTCGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCG--GGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
3608 ATATATCC-GG-TAAGACCCGAAGGCAATTAT-TGAGTTT
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
3645 ATATATCCGGG-TAAGACCCGAAGGCAATTATGCGAGTT-
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * * *
3683 A-ATATTCGCAGCTATGA-CCG-AGGCAATTTATGCGAGATG
1 ATATATCCG-GGCTAAGACCCGAAGGCAA-TTATGCGAGTTG
* *
3722 ATATATCCGGGCTAAGACCCGAAGGCATTTATGGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTAT-GCGAGTTG
*
3763 AT-TATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTT
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
3802 ATATATCCGGGCT-AGACCCGAAGGCAATTATGCGAGTTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAG-TTG
*
3842 ATATATCCGGGCTAAGA-CCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
3881 ATAT-TCCGGTG-TATGACCCGAA-GCAATTATGCGAG-TG
1 ATATATCCGG-GCTAAGACCCGAAGGCAATTATGCGAGTTG
3918 ATATATCC-GGCTAAGA-CCGAAGGCAATT-TGC-AGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
3954 ATATATTCCGGAGTTAAGACCCGAAGGCAA
1 ATATA-TCCGG-GCTAAGACCCGAAGGCAA
3984 ATGTGTTTGC
Statistics
Matches: 369, Mismatches: 24, Indels: 52
0.83 0.05 0.12
Matches are distributed among these distances:
35 2 0.01
36 16 0.04
37 44 0.12
38 83 0.22
39 67 0.18
40 95 0.26
41 17 0.05
42 44 0.12
43 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:3778 original size:118 final size:116
Alignment explanation
Indices: 3527--3983 Score: 512
Period size: 118 Copynumber: 3.9 Consensus size: 116
3517 CATTGGAATA
* *
3527 TATCCGGGCGCTAAGACCCGAAGGCAATTATGCGAGATGATATATCCGTCGGCTAAGACCCGAAG
1 TATCC-GGCG-TAAGACCCGAAGGCAATTATGCGAGTTAATATAT-C--CGGCTAAGACCCGAAG
*
3592 GCAATTATGCGAGTTAATATATCC-GG-TAAGACCCGAAGGCAATTATTG-AGTTTAT
61 GCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAATTA-TGCAG-TTAT
* *
3647 ATATCCGG-GTAAGACCCGAAGGCAATTATGCGAGTTAATAT-TCGCAGCTATGA-CCG-AGGCA
1 -TATCCGGCGTAAGACCCGAAGGCAATTATGCGAGTTAATATATC-CGGCTAAGACCCGAAGGCA
* *
3708 ATTTATGCGAGATGATATATCCGGGCTAAGACCCGAAGGCATTTATGGCAAGTTGAT
64 A-TTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAATTAT-GC-AGTT-AT
*
3765 TATCCGG-GCTAAGACCCGAAGGCAATTATGCGAGTTTATATATCCGGGCT-AGACCCGAAGGCA
1 TATCCGGCG-TAAGACCCGAAGGCAATTATGCGAGTTAATATATCC-GGCTAAGACCCGAAGGCA
*
3828 ATTATGCGAGTTTGATATATCCGGGCTAAGA-CCGAAGGCAATTATGCGAGTTAA
64 ATTATGCGAG-TTGATATATCCGGGCTAAGACCCGAAGGCAATTATGC-AGTTAT
* * *
3882 TATTCCGGTGTATGACCCGAA-GCAATTATGCGAG-TGATATATCCGGCTAAGA-CCGAAGGCAA
1 TA-TCCGGCGTAAGACCCGAAGGCAATTATGCGAGTTAATATATCCGGCTAAGACCCGAAGGCAA
*
3944 TT-TGC-AGTTGATATATTCCGGAGTTAAGACCCGAAGGCAA
65 TTATGCGAGTTGATATA-TCCGG-GCTAAGACCCGAAGGCAA
3984 ATGTGTTTGC
Statistics
Matches: 299, Mismatches: 18, Indels: 44
0.83 0.05 0.12
Matches are distributed among these distances:
112 8 0.03
113 13 0.04
114 30 0.10
115 36 0.12
116 32 0.11
117 27 0.09
118 89 0.30
119 32 0.11
120 27 0.09
121 5 0.02
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.24
Consensus pattern (116 bp):
TATCCGGCGTAAGACCCGAAGGCAATTATGCGAGTTAATATATCCGGCTAAGACCCGAAGGCAAT
TATGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAATTATGCAGTTAT
Found at i:12197 original size:40 final size:40
Alignment explanation
Indices: 12142--12609 Score: 801
Period size: 40 Copynumber: 11.7 Consensus size: 40
12132 GAGCATTGGA
*
12142 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
12182 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
12222 ATATATCCGGGCTAAGACCCGAAGGCAATTATGTGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
12262 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
12302 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
12342 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
12382 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
12422 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
12462 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
12502 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
12542 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
12582 ATATATCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
12610 ATGTGTTTGC
Statistics
Matches: 401, Mismatches: 27, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 401 1.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:17206 original size:40 final size:40
Alignment explanation
Indices: 17162--17309 Score: 260
Period size: 40 Copynumber: 3.7 Consensus size: 40
17152 GCAAACACAT
* *
17162 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
17202 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
* *
17242 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
17282 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
17310 TCCAATGCTC
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 104 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
Found at i:25827 original size:39 final size:40
Alignment explanation
Indices: 25719--25865 Score: 251
Period size: 40 Copynumber: 3.7 Consensus size: 40
25709 GCAAACACAT
* * *
25719 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
25759 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
25799 TTGCCTTCGGGTC-TAGCCCGGATATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
25838 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
25866 TCCATGCTCA
Statistics
Matches: 102, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
39 38 0.37
40 64 0.63
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:25839 original size:79 final size:80
Alignment explanation
Indices: 25719--25865 Score: 251
Period size: 79 Copynumber: 1.9 Consensus size: 80
25709 GCAAACACAT
*
25719 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
25784 TATCAACTCGCATAA
66 TATCAACTCGCATAA
* * *
25799 TTGCCTTCGGGTC-TAGCCCGGATATATCAACTCGCGTAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
25863 TAT
66 TAT
25866 TCCATGCTCA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
79 50 0.79
80 13 0.21
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (80 bp):
TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
TATCAACTCGCATAA
Found at i:27020 original size:30 final size:29
Alignment explanation
Indices: 26986--27051 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 29
26976 TTAATTTAAC
26986 ATATAATTCACACATAT-CATATTCAGCTAT
1 ATATAATTCACACATATCCAT-TTCAGC-AT
* * *
27016 ATATACATTTACATATTTCCATTTCAGCAT
1 ATATA-ATTCACACATATCCATTTCAGCAT
27046 ATATAA
1 ATATAA
27052 CTAACATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 1 0.03
30 12 0.39
31 15 0.48
32 3 0.10
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.39
Consensus pattern (29 bp):
ATATAATTCACACATATCCATTTCAGCAT
Found at i:35656 original size:30 final size:30
Alignment explanation
Indices: 35597--35653 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
35587 CCACTATCAT
* *
35597 ATTCAGCTATATATAGCCTATCATATTTAC
1 ATTCAGCTATATATAGACTAACATATTTAC
35627 ATTCAGC-ATATATA-ACTAACATTATTT
1 ATTCAGCTATATATAGACTAACA-TATTT
35654 TACCGAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.21
29 12 0.50
30 7 0.29
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (30 bp):
ATTCAGCTATATATAGACTAACATATTTAC
Done.