Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1708
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: 19648
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:8484 original size:20 final size:21
Alignment explanation
Indices: 8459--8501 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
8449 GTACTAGGTA
8459 GATAAAAA-AATGAATAC-TAC
1 GATAAAAAGAAT-AATACATAC
8479 GATAAAAAGAATAATACATAC
1 GATAAAAAGAATAATACATAC
8500 GA
1 GA
8502 AGCAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.60, C:0.09, G:0.12, T:0.19
Consensus pattern (21 bp):
GATAAAAAGAATAATACATAC
Found at i:11897 original size:47 final size:47
Alignment explanation
Indices: 11838--12137 Score: 492
Period size: 47 Copynumber: 6.4 Consensus size: 47
11828 GATGTACAAG
* * *
11838 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
11885 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
11932 GTGTATATATGTGATAAGGCCGAATGGCCAACGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
11979 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* * * * * *
12026 GTGTATATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAG
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
12073 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
12120 GTGTATAAATGTGATAAG
1 GTGTATATATGTGATAAG
12138 TCCCGAAGGG
Statistics
Matches: 236, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 236 1.00
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (47 bp):
GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
Found at i:11921 original size:22 final size:22
Alignment explanation
Indices: 11893--12015 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
11883 AAGTGTATAT
11893 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * ***
11915 ATGTGATGAATG-TGAAAGTGTATA
1 ATGTGAT-AAGGCCG-AA-TGGCCA
11939 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
* * * ***
11962 ACGTGATGAATG-TGAAAGTGTATA
1 ATGTGAT-AAGGCCG-AA-TGGCCA
11986 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
12009 ATGTGAT
1 ATGTGAT
12016 GAATGTGAAA
Statistics
Matches: 69, Mismatches: 22, Indels: 20
0.62 0.20 0.18
Matches are distributed among these distances:
22 22 0.32
23 16 0.23
24 16 0.23
25 15 0.22
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:14131 original size:79 final size:79
Alignment explanation
Indices: 13990--14256 Score: 479
Period size: 79 Copynumber: 3.4 Consensus size: 79
13980 CAGTATGTTA
13990 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG--ATATCCGGGCTAAGTCCCGAAGAGCA
1 TATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGAGCA
14053 TTCGTGCTGGTGATG
65 TTCGTGCTGGTGATG
14068 TATCCGGGCTAAGTCCGAAGAGCATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGAGCAT
1 TATCCGGGCTAAGTCCGAAGAGCATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGAGCAT
14133 TCGTGCTGGTGATG
66 TCGTGCTGGTGATG
14147 TATCCGGGCTAAGTCCGAAGAGCATTCGTGCTGGTGATATATCCGGGCTAAGTCCC-AAGAGCAT
1 TATCCGGGCTAAGTCCGAAGAGCATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGAGCAT
14211 TCGTGCTGGTGATG
66 TCGTGCTGGTGATG
*
14225 TATCCGGGCTAAGCCCCGAAG-GCATTCGTGCT
1 TATCCGGGCTAAG-TCCGAAGAGCATTCGTGCT
14257 TGGACAAAAT
Statistics
Matches: 185, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
77 22 0.12
78 60 0.32
79 103 0.56
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (79 bp):
TATCCGGGCTAAGTCCGAAGAGCATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGAGCAT
TCGTGCTGGTGATG
Found at i:14207 original size:118 final size:117
Alignment explanation
Indices: 13988--14256 Score: 470
Period size: 118 Copynumber: 2.3 Consensus size: 117
13978 TTCAGTATGT
13988 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATATCCGGGCTAAGTCCCGAAGAGCA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATATCCGGGCTAAGTCCCGAAGAGCA
* *
14053 TTCGTGCTGGTGATGTATCCGGGCTAAGTCCGAAGAGCATTCGTGCTGGTGA
66 TTCGTGCTGGTGATATATCCGGGCTAAGTCCCAAGAGCATTCGTGCTGGTGA
14105 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATGTATCCGGGCTAAGT-CCGAAGAG
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA--TATCCGGGCTAAGTCCCGAAGAG
14169 CATTCGTGCTGGTGATATATCCGGGCTAAGTCCCAAGAGCATTCGTGCTGGTGA
64 CATTCGTGCTGGTGATATATCCGGGCTAAGTCCCAAGAGCATTCGTGCTGGTGA
* *
14223 TGTATCCGGGCTAAGCCCCGAAG-GCATTCGTGCT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
14257 TGGACAAAAT
Statistics
Matches: 146, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
117 51 0.35
118 81 0.55
119 14 0.10
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (117 bp):
TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATATCCGGGCTAAGTCCCGAAGAGCA
TTCGTGCTGGTGATATATCCGGGCTAAGTCCCAAGAGCATTCGTGCTGGTGA
Found at i:14270 original size:39 final size:40
Alignment explanation
Indices: 13988--14256 Score: 460
Period size: 39 Copynumber: 6.9 Consensus size: 40
13978 TTCAGTATGT
13988 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG-
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
14027 -ATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
*
14066 TGTATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
14105 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
*
14145 TGTATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
14184 TATATCCGGGCTAAGTCCC-AAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
* *
14223 TGTATCCGGGCTAAGCCCCGAAG-GCATTCGTGCT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
14257 TGGACAAAAT
Statistics
Matches: 219, Mismatches: 6, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
38 38 0.17
39 124 0.57
40 57 0.26
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (40 bp):
TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
Found at i:18248 original size:47 final size:47
Alignment explanation
Indices: 18189--18487 Score: 483
Period size: 47 Copynumber: 6.4 Consensus size: 47
18179 GATGTACAAG
* * *
18189 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
18236 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
18283 GTGTATATATGTGATAAGGCCG-ATGGCCAACGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
18329 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* * * * * *
18376 GTGTATATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAG
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
18423 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
18470 GTGTATAAATGTGATAAG
1 GTGTATATATGTGATAAG
18488 TCCCGAAGGG
Statistics
Matches: 234, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
46 45 0.19
47 189 0.81
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (47 bp):
GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
Done.