Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2117
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: 3912
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Found at i:125 original size:1 final size:1
Alignment explanation
Indices: 119--162 Score: 61
Period size: 1 Copynumber: 44.0 Consensus size: 1
109 AAAGTGTTTG
***
119 AAAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
163 TTTAAATGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.93, C:0.00, G:0.02, T:0.05
Consensus pattern (1 bp):
A
Found at i:141 original size:20 final size:20
Alignment explanation
Indices: 116--155 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
106 GATAAAGTGT
116 TTGAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAA
136 TTGAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAA
156 AAAAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (20 bp):
TTGAAAAAAAAAAAAAAAAA
Found at i:218 original size:22 final size:21
Alignment explanation
Indices: 167--222 Score: 80
Period size: 19 Copynumber: 2.7 Consensus size: 21
157 AAAAAATTTA
167 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
188 -A-GTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
207 AATGCTATCGATACAT
1 AATG-TATCGATACAT
223 CCTACAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 17 0.55
20 2 0.06
21 1 0.03
22 11 0.35
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:300 original size:19 final size:19
Alignment explanation
Indices: 276--343 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
266 AATTCAACAA
276 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
295 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
310 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
327 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
344 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:315 original size:13 final size:13
Alignment explanation
Indices: 297--321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
287 ACATAAGTTT
297 TGTATCGATACAA
1 TGTATCGATACAA
310 TGTATCGATACA
1 TGTATCGATACA
322 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:315 original size:32 final size:32
Alignment explanation
Indices: 278--340 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
268 TTCAACAATT
*
278 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
310 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
341 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:401 original size:13 final size:13
Alignment explanation
Indices: 383--408 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
373 CATTTTTCTG
383 TGTATCGATACAT
1 TGTATCGATACAT
396 TGTATCGATACAT
1 TGTATCGATACAT
409 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:405 original size:33 final size:33
Alignment explanation
Indices: 363--429 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
353 GCCAAGGAAA
***
363 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
396 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
429 T
1 T
430 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2902 original size:28 final size:27
Alignment explanation
Indices: 2835--2907 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
2825 CTTCACAATC
* *
2835 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
2862 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
2890 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
2908 ACTTTATTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:3078 original size:28 final size:28
Alignment explanation
Indices: 3042--3123 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
3032 ATTTTTCACA
*
3042 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
3070 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
3098 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
3124 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Done.