Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4698
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: 13825
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Found at i:2134 original size:200 final size:200
Alignment explanation
Indices: 1645--2178 Score: 691
Period size: 206 Copynumber: 2.6 Consensus size: 200
1635 AAATCTGCTT
* *
1645 CTTCGATTTGTTCTCTGACAATACAGAGTTGCCAAATCATCTTAGATTTGCTTCAGCGTTAGCAC
1 CTTCGATTTG-T-TCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
** * * * *
1710 GCAAAAACCAAATCAGCTATGCCTTCGATTTGCTCCTTGTAAGCACAAGGATACCAAACTATCTT
64 GTGAAAGCCAAATCAGCTATG-TTTCGATTTG-TCCTTGTAAACACAAGGATGCCAAAC-ATCTT
* * * ** * * *
1775 GGATCTGCTTCAGTCTAATCATCTGAAGGTTAGATCTGCTATGTGTTTGCCCTCCGTCCAATATG
126 GGATATGCTTCAGTATAAACATCTGAAGGCCAGA-CTGCTATGTATATGCCCTCCGTCAAATATG
1840 GAGACGCCAAA
190 GAGACGCCAAA
* *
1851 CTTCGATTTGTTCTTTGACAATACAGAGATGCCAAATCATCTTAGACTTGCTTCAGCATAAGCAC
1 CTTCGATTTGTTC--TGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* * *
1916 ATGAAAGCTAAGTCAGCTATGATTTCGATTTGTCCTTGTAAACACAAGGATGCCAAATCATCTTG
64 GTGAAAGCCAAATCAGCTATG-TTTCGATTTGTCCTTGTAAACACAAGGATGCCAAA-CATCTTG
*
1981 GATATGCTTCAGTATAAACATCTGAAGGCCAG-CTGC-ATGTATATGCTCTCCGTCAAATATGGA
127 GATATGCTTCAGTATAAACATCTGAAGGCCAGACTGCTATGTATATGCCCTCCGTCAAATATGGA
*
2044 GACGCCGAA
192 GACGCCAAA
* * *
2053 CTTTGATTTGTTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTTATCGTAAGCACGT
1 CTTCGATTTGTTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACGT
*
2118 GAAAGCCAAATCAGCTATGTTTCGATTTATTCC-TGT-AACACAAGGATGCC-AACATCTTGGA
66 GAAAGCCAAATCAGCTATGTTTCGATTT-GTCCTTGTAAACACAAGGATGCCAAACATCTTGGA
2179 ATCTTGCGTC
Statistics
Matches: 291, Mismatches: 33, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
196 9 0.03
197 2 0.01
198 14 0.05
199 12 0.04
200 67 0.23
202 43 0.15
203 4 0.01
204 2 0.01
205 57 0.20
206 81 0.28
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (200 bp):
CTTCGATTTGTTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACGT
GAAAGCCAAATCAGCTATGTTTCGATTTGTCCTTGTAAACACAAGGATGCCAAACATCTTGGATA
TGCTTCAGTATAAACATCTGAAGGCCAGACTGCTATGTATATGCCCTCCGTCAAATATGGAGACG
CCAAA
Found at i:5559 original size:39 final size:40
Alignment explanation
Indices: 5464--5725 Score: 328
Period size: 39 Copynumber: 6.7 Consensus size: 40
5454 TTGAATGATG
*
5464 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
5502 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
5543 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
5582 TCCGGGCTAAG-CCCGAAGGCATTTGTGTGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
5621 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
5660 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
5699 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
5726 AACGAGGAGC
Statistics
Matches: 201, Mismatches: 13, Indels: 17
0.87 0.06 0.07
Matches are distributed among these distances:
39 130 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:12120 original size:39 final size:39
Alignment explanation
Indices: 12071--12240 Score: 220
Period size: 39 Copynumber: 4.3 Consensus size: 39
12061 GGACTAAGAT
*
12071 CCGAAGGCATTTGTGCGAGATACTAATTCCAGGCTAAGC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
12110 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
* * *
12149 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAG-C
* *
12189 CCG-AGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-TCCGGGCTAAG-C
*
12228 TCGAAGGCATTTG
1 CCGAAGGCATTTG
12241 AACGAGGAGC
Statistics
Matches: 117, Mismatches: 10, Indels: 7
0.87 0.07 0.05
Matches are distributed among these distances:
38 1 0.01
39 103 0.88
40 13 0.11
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
Found at i:12164 original size:78 final size:79
Alignment explanation
Indices: 12025--12240 Score: 223
Period size: 78 Copynumber: 2.8 Consensus size: 79
12015 ATGATGTCCG
* * * * *
12025 GGCTAAGTCCCAAGGC--TTGTGCTAAGTGAC-ATATCCGGACTAAGAT-CCGAAGGCATTTGTG
1 GGCTAAGTCCCGAGGCATTTGTGCGAA-TTACTATAACCGGGCTAAG-TCCCGAAGGCATTTGTG
*
12086 CGAGATACTAATTCCA
64 CGAGATACTAAATCCA
*
12102 GGCTAAG-CCCGAAGGCATTTGTGCGAGA-TACTA-ATTCCGGGCTAAG-CCCGAAGGCATTTGT
1 GGCTAAGTCCCG-AGGCATTTGTGCGA-ATTACTATA-ACCGGGCTAAGTCCCGAAGGCATTTGT
* *
12163 GCGAGTTACTAAATCCG
63 GCGAGATACTAAATCCA
* * *
12180 GGTTAAGTCCCGAGGCATTTGTGCGAATTACTATAACCGGGCTATGTCTCGAAGGCATTTG
1 GGCTAAGTCCCGAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
12241 AACGAGGAGC
Statistics
Matches: 117, Mismatches: 11, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
76 3 0.03
77 12 0.10
78 65 0.56
79 36 0.31
80 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
GGCTAAGTCCCGAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTTGTGCG
AGATACTAAATCCA
Found at i:12262 original size:78 final size:78
Alignment explanation
Indices: 12071--12263 Score: 182
Period size: 78 Copynumber: 2.5 Consensus size: 78
12061 GGACTAAGAT
** * * *
12071 CCGAAGGCATTTGTGCGAGAT-ACTAATTCCAGGCTAAGCCCGAAGGCATTTGTGCGAGATACTA
1 CCGAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAGCCCGAAGGCATTTGTGCGAGATACTA
*
12135 ATTCCGGGCTAAGC
65 ATACCGGGCTAAGC
** *
12149 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCG-AGGCATTTGTGCGA-ATTACT
1 CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAG-CCCGAAGGCATTTGTGCGAGA-TACT
*
12212 -ATAACCGGGCTATGTC
64 AAT-ACCGGGCTAAG-C
* *
12228 TCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAA
1 CCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAA
12264 ATTCCGAAGG
Statistics
Matches: 99, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
77 4 0.04
78 67 0.68
79 28 0.28
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (78 bp):
CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGCCCGAAGGCATTTGTGCGAGATACTAA
TACCGGGCTAAGC
Done.