Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1394
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: 17257
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Found at i:431 original size:52 final size:51
Alignment explanation
Indices: 370--559 Score: 186
Period size: 52 Copynumber: 3.6 Consensus size: 51
360 TATTTTCCGA
* * * *
370 GGGGATACTCCACACCCTGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCA-ACCCTGATTTTATTTCCAAAACACTAATTTTTCATAATC
* * * * *
422 GGGGATACTCCAACCCCGGTTTTATTGCTAAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCTGATTTTATTTC-CAAAACACTAATTTTT-CATAATC
* * * * *
475 GGGGATACTCCAA-CCTCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCT-GATTTTATTTCCAAAACACTAATTTTTC-ATAATC
527 GGGGATACTCCAACTCC-GATTTTATTTCCAAAA
1 GGGGATACTCCAAC-CCTGATTTTATTTCCAAAA
560 ATACCCAATT
Statistics
Matches: 113, Mismatches: 19, Indels: 12
0.78 0.13 0.08
Matches are distributed among these distances:
51 13 0.12
52 70 0.62
53 28 0.25
54 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.34
Consensus pattern (51 bp):
GGGGATACTCCAACCCTGATTTTATTTCCAAAACACTAATTTTTCATAATC
Found at i:485 original size:53 final size:52
Alignment explanation
Indices: 409--572 Score: 188
Period size: 52 Copynumber: 3.1 Consensus size: 52
399 CAAAATATTG
*
409 ATTTTT-CATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAAACACTA
1 ATTTTTCCATAATCGGGGATACTCCAACCCCGGTTTTATT-CTAAAAACACCA
* * * *
461 ATTTTTCCACAATCGGGGATACTCCAACCTCGGTTTTATTTTCAAAACACCA
1 ATTTTTCCATAATCGGGGATACTCCAACCCCGGTTTTATTCTAAAAACACCA
* * * * *
513 A-TTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCCA
1 ATTTTTCC-ATAATCGGGGATACTCCAACCCCGGTTTTA-TTCTAAAAACA-CCA
567 ATTTTT
1 ATTTTT
573 TCACAGTCGA
Statistics
Matches: 93, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
51 6 0.06
52 41 0.44
53 38 0.41
54 4 0.04
55 4 0.04
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (52 bp):
ATTTTTCCATAATCGGGGATACTCCAACCCCGGTTTTATTCTAAAAACACCA
Found at i:2086 original size:14 final size:14
Alignment explanation
Indices: 2067--2093 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2057 TTCTCCCTTA
2067 AACAAAATAATTTT
1 AACAAAATAATTTT
2081 AACAAAATAATTT
1 AACAAAATAATTT
2094 CTCCCTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (14 bp):
AACAAAATAATTTT
Found at i:4059 original size:13 final size:13
Alignment explanation
Indices: 4041--4079 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
4031 ATAATCCTCT
*
4041 TGTATCGATACAG
1 TGTATCGATACAA
4054 TGTATCGATACAA
1 TGTATCGATACAA
4067 TGTATCGATACAA
1 TGTATCGATACAA
4080 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:6166 original size:15 final size:15
Alignment explanation
Indices: 6146--6176 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6136 ATTTCGTTTG
*
6146 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
6161 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
6176 G
1 G
6177 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:8007 original size:21 final size:21
Alignment explanation
Indices: 7978--8022 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
7968 AAGTTTTCAT
*
7978 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
7998 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
8020 TTT
1 TTT
8023 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:10258 original size:13 final size:13
Alignment explanation
Indices: 10240--10265 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10230 CAATTTTTTG
10240 TGTATCGATACAT
1 TGTATCGATACAT
10253 TGTATCGATACAT
1 TGTATCGATACAT
10266 ACTTGCTGTA
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
Done.