Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold706
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: 50228
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.31
Found at i:106 original size:9 final size:9
Alignment explanation
Indices: 92--168 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
82 ATCTCGTGTG
92 CATATCATA
1 CATATCATA
*
101 CATATCATGTG
1 CATATCA--TA
112 CATATCATA
1 CATATCATA
* *
121 CATGTCATGTG
1 CATATCA--TA
132 CATATCATA
1 CATATCATA
*
141 CATATCATGTG
1 CATATCA--TA
152 CATATCATA
1 CATATCATA
161 CATATCAT
1 CATATCAT
169 GTTTATCAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 31 0.57
11 23 0.43
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:111 original size:20 final size:20
Alignment explanation
Indices: 88--170 Score: 157
Period size: 20 Copynumber: 4.2 Consensus size: 20
78 GAACATCTCG
88 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
108 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
128 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
148 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
168 TGT
1 TGT
171 TTATCAAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:117 original size:11 final size:11
Alignment explanation
Indices: 88--159 Score: 66
Period size: 11 Copynumber: 7.1 Consensus size: 11
78 GAACATCTCG
88 TGTGCATATCA
1 TGTGCATATCA
*
99 --TACATATCA
1 TGTGCATATCA
108 TGTGCATATCA
1 TGTGCATATCA
* *
119 --TACATGTCA
1 TGTGCATATCA
128 TGTGCATATCA
1 TGTGCATATCA
*
139 --TACATATCA
1 TGTGCATATCA
148 TGTGCATATCA
1 TGTGCATATCA
159 T
1 T
160 ACATATCATG
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 23 0.49
11 24 0.51
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (11 bp):
TGTGCATATCA
Found at i:7246 original size:31 final size:31
Alignment explanation
Indices: 7203--7266 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
7193 CCTTTTCATA
7203 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* **
7234 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
7265 TT
1 TT
7267 ACGGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:7504 original size:24 final size:24
Alignment explanation
Indices: 7457--7599 Score: 195
Period size: 23 Copynumber: 6.0 Consensus size: 24
7447 GCTTTATCAT
*
7457 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
7482 ATAACTAGGGCA-AAGCCCTTTTTTA
1 ATAACTGGGGCATAAGCCC--TTTTA
7507 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
7530 ATAACTGGGGTATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
7554 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
7577 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
7600 GCACTTCCTC
Statistics
Matches: 107, Mismatches: 5, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
23 46 0.43
24 32 0.30
25 23 0.21
26 6 0.06
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:7558 original size:47 final size:47
Alignment explanation
Indices: 7478--7599 Score: 201
Period size: 47 Copynumber: 2.6 Consensus size: 47
7468 CCTAGCCTCT
*
7478 TTTAATAACTAGGGCA-AAGCCCTTTTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC--TTTTAATAACTGGGGCATAAGCCC
*
7526 TTTAATAACTGGGGTATAAGCCCTTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
7573 TTTAATAACTGGGGCATAAGCCCTTTT
1 TTTAATAACTGGGGCATAAGCCCTTTT
7600 GCACTTCCTC
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
47 50 0.71
48 14 0.20
49 6 0.09
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (47 bp):
TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
Found at i:7671 original size:9 final size:9
Alignment explanation
Indices: 7657--7733 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
7647 ATCTCGTGTG
7657 CATATCATA
1 CATATCATA
*
7666 CATATCATGTG
1 CATATCA--TA
7677 CATATCATA
1 CATATCATA
* *
7686 CATGTCATGTG
1 CATATCA--TA
7697 CATATCATA
1 CATATCATA
*
7706 CATATCATGTG
1 CATATCA--TA
7717 CATATCATA
1 CATATCATA
7726 CATATCAT
1 CATATCAT
7734 GTTTATCAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 31 0.57
11 23 0.43
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:7676 original size:20 final size:20
Alignment explanation
Indices: 7653--7735 Score: 157
Period size: 20 Copynumber: 4.2 Consensus size: 20
7643 GAACATCTCG
7653 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
7673 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
7693 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
7713 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
7733 TGT
1 TGT
7736 TTATCAAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:7682 original size:11 final size:11
Alignment explanation
Indices: 7653--7724 Score: 66
Period size: 11 Copynumber: 7.1 Consensus size: 11
7643 GAACATCTCG
7653 TGTGCATATCA
1 TGTGCATATCA
*
7664 --TACATATCA
1 TGTGCATATCA
7673 TGTGCATATCA
1 TGTGCATATCA
* *
7684 --TACATGTCA
1 TGTGCATATCA
7693 TGTGCATATCA
1 TGTGCATATCA
*
7704 --TACATATCA
1 TGTGCATATCA
7713 TGTGCATATCA
1 TGTGCATATCA
7724 T
1 T
7725 ACATATCATG
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 23 0.49
11 24 0.51
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (11 bp):
TGTGCATATCA
Found at i:26865 original size:44 final size:43
Alignment explanation
Indices: 26802--26918 Score: 155
Period size: 44 Copynumber: 2.7 Consensus size: 43
26792 TGTAACCCGC
* * * *
26802 CCATAAGCGAACTCGGACTCAACTCAACGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGCTCAGACATT-GCAT
*
26846 CCATAAGTGAACTCGGACTCAACTCAACCAGTTCAGACATTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAA-C-GCTCAGACATTGCAT
26891 CCATAAGTGAACTC-GACTCAACTCAACG
1 CCATAAGTGAACTCGGACTCAACTCAACG
26919 AGTTCGGATG
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
42 1 0.02
43 1 0.02
44 38 0.58
45 19 0.29
46 7 0.11
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.20
Consensus pattern (43 bp):
CCATAAGTGAACTCGGACTCAACTCAACGCTCAGACATTGCAT
Found at i:34380 original size:46 final size:46
Alignment explanation
Indices: 34313--34441 Score: 195
Period size: 46 Copynumber: 2.8 Consensus size: 46
34303 TGTAACCCGC
* * * * *
34313 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
34359 CCATAAGTGAACTCGGACTCAACTCAACCAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
34405 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
34442 TGCTCAACCA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 75 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:34460 original size:46 final size:45
Alignment explanation
Indices: 34321--34460 Score: 122
Period size: 46 Copynumber: 3.0 Consensus size: 45
34311 GCCCATAAGC
* * ** *
34321 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTC-GCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCC-T-AGT
* ** **
34367 GAACTCGGACTCAACTCAACCAGTTCGGACATT-TGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCC-T-AGT
*
34413 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGTTC-ACCATCCTAGT
34459 GA
1 GA
34461 CATGTCACTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
46 74 0.93
47 1 0.01
48 5 0.06
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCCTAGT
Found at i:37810 original size:13 final size:13
Alignment explanation
Indices: 37792--37816 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37782 CCGTGCCCTT
37792 CACATGGCTGTGA
1 CACATGGCTGTGA
37805 CACATGGCTGTG
1 CACATGGCTGTG
37817 TCTCTGCCCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (13 bp):
CACATGGCTGTGA
Done.