Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold474
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: 24726
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Found at i:2023 original size:40 final size:40
Alignment explanation
Indices: 1939--2160 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
1929 TTGAATGATG
* * *
1939 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
1978 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
2019 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
2058 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
2097 AACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCA-TAA-
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
2136 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
2161 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 14, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
37 24 0.15
39 37 0.23
40 90 0.56
41 10 0.06
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:2075 original size:79 final size:80
Alignment explanation
Indices: 1939--2179 Score: 282
Period size: 79 Copynumber: 3.1 Consensus size: 80
1929 TTGAATGATG
* * * * *
1939 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTCACTAAATCCGGGCTAAG-TCCCGAAGGCAT
2002 TTGTGCGAGTTACTA-A
64 TTGTGCGAGTTACTATA
* * *
2018 TTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAATCCGGGCTAAGTCCCGAAGGCATT
2082 TGTGCGAGTTACTATA
65 TGTGCGAGTTACTATA
* *
2098 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCA-T-AA-CCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAATCCGGGCTAAGTCCCGAAGGCATTT
**
2160 GAACGAG-TAGCTATA
66 GTGCGAGTTA-CTATA
2175 TCCGG
1 TCCGG
2180 TTAAATTCCG
Statistics
Matches: 141, Mismatches: 15, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
76 2 0.01
77 36 0.26
78 3 0.02
79 61 0.43
80 39 0.28
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGTTACTATA
Found at i:6127 original size:31 final size:31
Alignment explanation
Indices: 6089--6152 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
6079 GGATAAGCAG
6089 TATGCTAAGTTCAGTAAGTGTGAGTTCTGGT
1 TATGCTAAGTTCAGTAAGTGTGAGTTCTGGT
6120 TATGCTAAGTTCAGTAAGTGTGAGTTCTGGT
1 TATGCTAAGTTCAGTAAGTGTGAGTTCTGGT
6151 TA
1 TA
6153 AGAGAGGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.23, C:0.09, G:0.28, T:0.39
Consensus pattern (31 bp):
TATGCTAAGTTCAGTAAGTGTGAGTTCTGGT
Found at i:17944 original size:40 final size:40
Alignment explanation
Indices: 17707--17937 Score: 220
Period size: 40 Copynumber: 5.8 Consensus size: 40
17697 TGAATGATGT
* * * * *
17707 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTAC-GAGTTACTATAA
* * * * *
17747 CCAGACTAAGAT-CCGAAGGCATTTATGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTACGAGTTACTATA-A
* *
17787 CCAGGCTAAG-CCCGAAGGCATTGGTACGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAA
* * *
17825 TCCGGGTTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAA
* *
17866 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAA
* *
17906 CCGGGCTATGTCCCGAAGGCATTTGAACGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGT
17938 AGCTATATCC
Statistics
Matches: 162, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
39 32 0.20
40 121 0.75
41 9 0.06
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAA
Found at i:17952 original size:119 final size:119
Alignment explanation
Indices: 17706--17963 Score: 292
Period size: 119 Copynumber: 2.2 Consensus size: 119
17696 TTGAATGATG
* *
17706 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCAGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCAGACTAAGATCCGAAGGCATTT
* * *
17771 ATGCGAGTTACTAATTCCAGGCTAAGCCCGAAGGCATTGGTACGAGTTACTAAA
66 ATGCGAGTCACTAATACCAGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
* * * *
17825 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-AAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCAGACTAAGAT-CCGAAGGCAT
* * * * *
17888 TTGTGCGAGTCACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTATGCGAGTCACTAAT-ACCAGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAA
* *
17945 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
17964 TACGTGATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
118 3 0.03
119 83 0.70
120 32 0.27
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCAGACTAAGATCCGAAGGCATTT
ATGCGAGTCACTAATACCAGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
Done.