Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2147
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: 101772
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
File 2 of 2
Found at i:93598 original size:27 final size:27
Alignment explanation
Indices: 93560--93624 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
93550 TCAACAGGTA
* *
93560 ACAAAAATATATA-ACATTTATTTTTAT
1 ACAATAATATATATA-ATTTATTATTAT
93587 ACAATAATATATATAATTTATTATTAT
1 ACAATAATATATATAATTTATTATTAT
*
93614 AAAATTAATAT
1 ACAA-TAATAT
93625 GAATTAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 26 0.79
28 7 0.21
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.45
Consensus pattern (27 bp):
ACAATAATATATATAATTTATTATTAT
Found at i:94078 original size:13 final size:13
Alignment explanation
Indices: 94069--94104 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
94059 TATTAAAATT
94069 TAATTATAAAATAA
1 TAATT-TAAAATAA
94083 TAATTTAAAATAA
1 TAATTTAAAATAA
94096 TAATTTAAA
1 TAATTTAAA
94105 CTAAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAATTTAAAATAA
Found at i:95688 original size:9 final size:9
Alignment explanation
Indices: 95674--95759 Score: 59
Period size: 9 Copynumber: 9.6 Consensus size: 9
95664 TTATTTTTTT
95674 ATAATTATA
1 ATAATTATA
*
95683 ATAATTATT
1 ATAATTATA
*
95692 ATATTTTATA
1 ATA-ATTATA
*
95702 ATATTTATA
1 ATAATTATA
* *
95711 TAAAATTAAA
1 -ATAATTATA
*
95721 AAAATT-T-
1 ATAATTATA
* *
95728 ACAACTATA
1 ATAATTATA
95737 ATAATTATA
1 ATAATTATA
*
95746 ATAACTATA
1 ATAATTATA
95755 ATAAT
1 ATAAT
95760 ATTTATTATA
Statistics
Matches: 60, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
7 4 0.07
8 1 0.02
9 42 0.70
10 13 0.22
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (9 bp):
ATAATTATA
Found at i:96068 original size:2 final size:2
Alignment explanation
Indices: 96061--96103 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
96051 TCAACAAACA
96061 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
96103 A
1 A
96104 ATGAAATTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:96128 original size:19 final size:19
Alignment explanation
Indices: 96104--96141 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
96094 TATATATATA
*
96104 ATGAAATTCCTTTAAAAGC
1 ATGAAATTCCTTCAAAAGC
96123 ATGAAATTCCTTCAAAAGC
1 ATGAAATTCCTTCAAAAGC
96142 CCAAAAGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (19 bp):
ATGAAATTCCTTCAAAAGC
Found at i:96290 original size:11 final size:11
Alignment explanation
Indices: 96274--96329 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
96264 ATGTTAAAAA
96274 AATTTATTTAT
1 AATTTATTTAT
*
96285 AATTTATTTAA
1 AATTTATTTAT
*
96296 AACTTATTTATT
1 AATTTATTTA-T
*
96308 AATTTATTTAA
1 AATTTATTTAT
*
96319 AATTTGTTTAT
1 AATTTATTTAT
96330 TGTTTGAGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (11 bp):
AATTTATTTAT
Found at i:96310 original size:23 final size:23
Alignment explanation
Indices: 96272--96330 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
96262 TTATGTTAAA
96272 AAAATTTATTTA-TAATTTATTT
1 AAAATTTATTTATTAATTTATTT
*
96294 AAAACTTATTTATTAATTTATTT
1 AAAATTTATTTATTAATTTATTT
*
96317 AAAATTTGTTTATT
1 AAAATTTATTTATT
96331 GTTTGAGTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 11 0.33
23 22 0.67
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
AAAATTTATTTATTAATTTATTT
Found at i:97408 original size:13 final size:15
Alignment explanation
Indices: 97383--97421 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
97373 TTAATATGGC
97383 ATTTGATAATTTTGA-
1 ATTT-ATAATTTTGAT
97398 ATTTA-AATTTTGAT
1 ATTTATAATTTTGAT
97412 ATTTATAATT
1 ATTTATAATT
97422 CTATTGCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.36
14 6 0.27
15 8 0.36
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (15 bp):
ATTTATAATTTTGAT
Found at i:101007 original size:21 final size:21
Alignment explanation
Indices: 100981--101030 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
100971 ATATATTTTT
100981 ATAATTA-TATTTAAAATAAA-A
1 ATAATTATTATTT--AATAAATA
101002 ATAATTTATTATTTAATAAATA
1 ATAA-TTATTATTTAATAAATA
101024 ATAATTA
1 ATAATTA
101031 AATTAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 13 0.50
22 8 0.31
23 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATTATTATTTAATAAATA
Done.