Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1522
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: 24911
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Found at i:3803 original size:40 final size:40
Alignment explanation
Indices: 3703--3922 Score: 340
Period size: 40 Copynumber: 5.5 Consensus size: 40
3693 GGATGATAAT
* * *
3703 CGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-TC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATC
*
3743 CGAGC-AAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
*
3782 CGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
3822 CGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTTACTATATC
*
3862 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
3902 CGGGCTAAGT-CCGAAGGCATT
1 CGGGCTAAGTCCCGAAGGCATT
3923 GAGCAGTAGC
Statistics
Matches: 168, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
38 1 0.01
39 46 0.27
40 119 0.71
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:12021 original size:40 final size:40
Alignment explanation
Indices: 11921--12142 Score: 344
Period size: 40 Copynumber: 5.6 Consensus size: 40
11911 GGATGATAAT
* * *
11921 CGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-TC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATC
*
11961 CGAGC-AAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
*
12000 CGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
12040 CGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTTACTATATC
*
12080 CGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAAC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
12119 CGGGCTAAGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTG
12143 AGCAGTAGCT
Statistics
Matches: 169, Mismatches: 8, Indels: 10
0.90 0.04 0.05
Matches are distributed among these distances:
38 3 0.02
39 68 0.40
40 96 0.57
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:12095 original size:79 final size:80
Alignment explanation
Indices: 11921--12142 Score: 344
Period size: 79 Copynumber: 2.8 Consensus size: 80
11911 GGATGATAAT
* * * *
11921 CGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-TCCGAGC-AAGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCCGGGCTAAGTCCCGAAGGCATTTG
11984 TGCGAGTTACTATATC
65 TGCGAGTTACTATATC
*
12000 CGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
12065 GCGAAG-TACTATATC
66 GCG-AGTTACTATATC
*
12080 CGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
12143 AGCAGTAGCT
Statistics
Matches: 133, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
78 1 0.01
79 89 0.67
80 41 0.31
81 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (80 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
GCGAGTTACTATATC
Found at i:12132 original size:119 final size:119
Alignment explanation
Indices: 11921--12140 Score: 356
Period size: 119 Copynumber: 1.8 Consensus size: 119
11911 GGATGATAAT
*
11921 CGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTTCCGAGCAAGTCCCGAAGGCATTTGTG
1 CGGGCTAAGTCCCGAAGGCATTTGCGCAAGTGACTAGTTCCGAGCAAGTCCCGAAGGCATTTGTG
*
11986 CGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATC
66 CGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATC
* *
12040 CGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTA-TATCCGGGCTAAGT-CCGAAGGCATTT
1 CGGGCTAAGTCCCGAAGGCATTTGCGC-AAGTGACTAGT-TCCGAGC-AAGTCCCGAAGGCATTT
12102 GTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATT
63 GTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATT
12141 TGAGCAGTAG
Statistics
Matches: 94, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
118 1 0.01
119 86 0.91
120 7 0.07
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.25
Consensus pattern (119 bp):
CGGGCTAAGTCCCGAAGGCATTTGCGCAAGTGACTAGTTCCGAGCAAGTCCCGAAGGCATTTGTG
CGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATC
Found at i:15496 original size:40 final size:40
Alignment explanation
Indices: 15420--15563 Score: 125
Period size: 40 Copynumber: 3.6 Consensus size: 40
15410 TAACTCATTC
* *
15420 AATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACA
* *
15460 AATGCCTTCGGGACTTAACCCGGA-ATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATATTA-AAACTCGCACA
* ** ** *
15500 AAGGCCTTC-GGATCTTAGTCCGGATA-TAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGATATTA-AAAC-TCGCACA
*
15541 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
15564 CAGCATTCAA
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
39 6 0.07
40 70 0.80
41 12 0.14
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACA
Found at i:23348 original size:40 final size:40
Alignment explanation
Indices: 23272--23415 Score: 125
Period size: 40 Copynumber: 3.6 Consensus size: 40
23262 TAACTCATTC
* *
23272 AATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACA
* *
23312 AATGCCTTCGGGACTTAACCCGGA-ATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATATTA-AAACTCGCACA
* ** ** *
23352 AAGGCCTTC-GGATCTTAGTCCGGATA-TAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGATATTA-AAAC-TCGCACA
*
23393 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
23416 CAGCATTCAA
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
39 6 0.07
40 70 0.80
41 12 0.14
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACA
Done.