Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3124
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: 14757
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Found at i:1871 original size:27 final size:27
Alignment explanation
Indices: 1840--2017 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
1830 TAAATTGTAC
1840 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
1867 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
1893 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
1921 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
1949 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
1976 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2003 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2018 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:1954 original size:82 final size:81
Alignment explanation
Indices: 1841--1996 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
1831 AAATTGTACA
* *
1841 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
1905 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
1922 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
1987 TGCGAGTTGA
65 TGCGAATTGA
1997 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:2008 original size:82 final size:81
Alignment explanation
Indices: 1837--2017 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
1827 GATTAAATTG
* *
1837 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
1902 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
1918 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
1982 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
2000 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
2018 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:5286 original size:38 final size:40
Alignment explanation
Indices: 5188--5409 Score: 233
Period size: 39 Copynumber: 5.7 Consensus size: 40
5178 TTGAATGCTG
* * * *
5188 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
** *
5228 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
*
5267 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
5306 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
5345 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * *
5384 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
5410 AACGAGGAGC
Statistics
Matches: 156, Mismatches: 18, Indels: 16
0.82 0.09 0.08
Matches are distributed among these distances:
38 29 0.19
39 76 0.49
40 40 0.26
41 10 0.06
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:5431 original size:78 final size:79
Alignment explanation
Indices: 5267--5441 Score: 196
Period size: 78 Copynumber: 2.3 Consensus size: 79
5257 GAGATACAAT
* * *
5267 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
5331 GTGCGAGTATTAAA
66 GAACGAGGACTAAA
* * * *
5345 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
5409 GAACGAGGAGCTATA
66 GAACGAGGA-CTAAA
*
5424 TCC-GGTTAAAT-CCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
5442 TACGTGATTT
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
77 7 0.09
78 61 0.74
79 14 0.17
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGGACTAAA
Found at i:13232 original size:40 final size:40
Alignment explanation
Indices: 13085--13307 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
13075 TTGAATGCTG
* * * *
13085 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
** *
13125 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
*
13164 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * *
13203 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
13243 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * *
13282 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
13308 AACGAGGAGC
Statistics
Matches: 157, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
38 22 0.14
39 56 0.36
40 68 0.43
41 10 0.06
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:13269 original size:79 final size:78
Alignment explanation
Indices: 13085--13305 Score: 241
Period size: 79 Copynumber: 2.8 Consensus size: 78
13075 TTGAATGCTG
* * * * *
13085 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGA-T-ACTAAATCCGGGCTAAG-TCCCGAAGGCAT
* *
13148 TTGTGCGAGATACAAT
63 TCGTGCGAGATACAAA
*
13164 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGG-CTTTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTC
* *
13228 GTGCGAGTTATTAAA
65 GTGCGAGATA-CAAA
* * * * *
13243 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATT
13306 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
77 1 0.01
78 41 0.34
79 70 0.58
80 9 0.07
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGATACAAA
Found at i:13325 original size:79 final size:80
Alignment explanation
Indices: 13164--13340 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
13154 GAGATACAAT
* * *
13164 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
13228 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
13243 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
13307 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
13322 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
13341 TACGTGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
78 16 0.19
79 59 0.71
80 8 0.10
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Done.