Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3030
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: 16924
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Found at i:1127 original size:13 final size:13
Alignment explanation
Indices: 1109--1133 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1099 TAATGGTATA
1109 TTGAATCCATGAT
1 TTGAATCCATGAT
1122 TTGAATCCATGA
1 TTGAATCCATGA
1134 AAATTTAGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:3018 original size:25 final size:25
Alignment explanation
Indices: 2990--3068 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
2980 CTAATGGCTG
2990 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* * * *
3015 ATGTGAT-AAGGCCGAATG-GCA-A-
1 ATGTGATGAATG-TGAAAGTGTATAT
*
3037 ATGTGATGAATGTGAAAGTGTGTAT
1 ATGTGATGAATGTGAAAGTGTATAT
3062 ATGTGAT
1 ATGTGAT
3069 AAGGCCTAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.12
24 6 0.15
25 18 0.45
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:3018 original size:47 final size:47
Alignment explanation
Indices: 2965--3118 Score: 254
Period size: 47 Copynumber: 3.3 Consensus size: 47
2955 ACAAGATATG
*
2965 TATATGTGATAAGGCCTAATGGCTGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCAGATGTGATGAATGTGAAAGTGTA
* * *
3012 TATATGTGATAAGGCCGAATGGCAAATGTGATGAATGTGAAAGTGTG
1 TATATGTGATAAGGCCTAATGGCAGATGTGATGAATGTGAAAGTGTA
* *
3059 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGGGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCAGATGTGATGAATGTGAAAGTGTA
3106 TATATGTGATAAG
1 TATATGTGATAAG
3119 TCCCGAAGGA
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 98 1.00
ACGTcount: A:0.33, C:0.06, G:0.31, T:0.30
Consensus pattern (47 bp):
TATATGTGATAAGGCCTAATGGCAGATGTGATGAATGTGAAAGTGTA
Found at i:6070 original size:79 final size:79
Alignment explanation
Indices: 5926--6144 Score: 257
Period size: 79 Copynumber: 2.7 Consensus size: 79
5916 GAATCACATA
* * * * * *
5926 CCTTCGGAATTTAACCGGATATAGCTACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTATAG
1 CCTTCGGGACTTAACCGGATTTAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATATAG
5990 TAACTCGCACAAATG
65 TAACTCGCACAAATG
*
6005 CCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGGAAT-TA
1 CCTTCGGGACTTAA-CCGGATTTAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATATA
6068 GTAACTCGCACAAATG
64 GTAACTCGCACAAATG
* * *
6084 CCTTC-GGATCTTAGTCCGGATTTAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTA-ACCGGATTTAGT-AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
6145 TATCATTCGA
Statistics
Matches: 121, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
78 3 0.02
79 62 0.51
80 45 0.37
81 11 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CCTTCGGGACTTAACCGGATTTAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATATAGT
AACTCGCACAAATG
Found at i:6073 original size:39 final size:40
Alignment explanation
Indices: 5952--6145 Score: 259
Period size: 40 Copynumber: 4.8 Consensus size: 40
5942 GGATATAGCT
* *
5952 ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
*
5992 ACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
6032 ACTCGCACCAATGCCTTCGGG-CTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
6071 ACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATTTAGTC
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTA
* *
6111 ACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGAT
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGAT
6146 ATCATTCGAA
Statistics
Matches: 136, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 71 0.52
41 27 0.20
42 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:14242 original size:39 final size:40
Alignment explanation
Indices: 14121--14313 Score: 232
Period size: 40 Copynumber: 4.8 Consensus size: 40
14111 CGATATAGCT
* *
14121 ACTCGCTCAAATGCCTTCGGGACATAGCCC-GATTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
*
14161 ACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
14201 ACTCGCACCAATGCCTTTGGG-CTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
14240 ACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATAG-C
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTA
* *
14279 ACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGAT
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGAT
14314 ATCATTCGAA
Statistics
Matches: 132, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
38 2 0.02
39 34 0.26
40 89 0.67
41 7 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:14272 original size:79 final size:80
Alignment explanation
Indices: 14121--14315 Score: 218
Period size: 79 Copynumber: 2.5 Consensus size: 80
14111 CGATATAGCT
* *
14121 ACTCGCTCAAATGCCTTCGGGACATAGCCCGATTATAGTAACTCGCACAAATGCCTTCGGGACTT
1 ACTCGCACAAATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTT
14186 AACCCGGATTTAGTA
66 AACCCGGATTTAGTA
* * *
14201 ACTCGCACCAATGCCTTTGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATC
1 ACTCGCACAAATGCCTTCGGGACATAGCCC-GAATATAGTAACTCGCACAAATGCCTTCGGGA-C
** * *
14263 TTAGTCCGGATATAG-C
64 TTAACCCGGATTTAGTA
* * * *
14279 ACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGATAT
1 AC-TCGCACAAATGCCTTCGGGACATAGCCCGAATAT
14316 CATTCGAATA
Statistics
Matches: 96, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
78 5 0.05
79 61 0.64
80 30 0.31
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
ACTCGCACAAATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTT
AACCCGGATTTAGTA
Done.