Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3723_ERROPOS41587
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: 41587
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:8622 original size:29 final size:29
Alignment explanation
Indices: 8588--8661 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
8578 TAATCAACCG
*
8588 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
8617 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
8646 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
8662 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:12138 original size:22 final size:22
Alignment explanation
Indices: 12113--12165 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
12103 GCTTTTGTTC
* *
12113 AAAACATTTGATTTAATGGCTA
1 AAAACATTTGATTTAAAGACTA
* *
12135 AAAAC-TTGGTTTTAAAGACTA
1 AAAACATTTGATTTAAAGACTA
12156 AATAACATTT
1 AA-AACATTT
12166 AAAACTAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 14 0.58
22 8 0.33
23 2 0.08
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (22 bp):
AAAACATTTGATTTAAAGACTA
Found at i:15347 original size:18 final size:18
Alignment explanation
Indices: 15324--15361 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
15314 ATGTGATTGG
15324 TAAGTTTAATTCTTGTTA
1 TAAGTTTAATTCTTGTTA
15342 TAAGTTTAATTCTTGTTA
1 TAAGTTTAATTCTTGTTA
15360 TA
1 TA
15362 CAAACTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (18 bp):
TAAGTTTAATTCTTGTTA
Found at i:23455 original size:19 final size:20
Alignment explanation
Indices: 23412--23457 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
23402 GTTGGGCCTC
23412 GCCCATATTAACACAGTTGG
1 GCCCATATTAACACAGTTGG
* *
23432 GCCCATTTTAATACAGTT-G
1 GCCCATATTAACACAGTTGG
23451 GCCCATA
1 GCCCATA
23458 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (20 bp):
GCCCATATTAACACAGTTGG
Found at i:29134 original size:40 final size:39
Alignment explanation
Indices: 28946--29127 Score: 199
Period size: 40 Copynumber: 4.6 Consensus size: 39
28936 AATGATGTCT
* * * *
28946 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AACC
* *
28986 GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-ACC
* *
29026 GGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA-CC
*
29065 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AACC
*
29105 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
29128 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 34 0.28
40 78 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (39 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAACC
Found at i:29149 original size:79 final size:79
Alignment explanation
Indices: 28996--29150 Score: 199
Period size: 79 Copynumber: 2.0 Consensus size: 79
28986 GGACTAAGAT
* **
28996 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
29061 ATCTGGGTTAAGTC
66 ATCTCGGTTAAGTC
* *
29075 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
*
29138 TATATC-CGGTTAA
63 TAAATCTCGGTTAA
29151 ATTCTGAAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
78 2 0.03
79 41 0.62
80 23 0.35
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCTCGGTTAAGTC
Found at i:37230 original size:40 final size:40
Alignment explanation
Indices: 37036--37216 Score: 210
Period size: 40 Copynumber: 4.5 Consensus size: 40
37026 ATGATGTCCA
* * * *
37036 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCG
* *
37076 GACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATTCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-ACCG
*
37116 GGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCG
*
37155 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCG
*
37195 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
37217 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 78 0.63
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCG
Found at i:37238 original size:79 final size:79
Alignment explanation
Indices: 37085--37249 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
37075 GGACTAAGAT
* **
37085 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
37150 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
37164 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
37227 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
37243 CCGAAGG
1 CCGAAGG
37250 TACGTGATTC
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Done.