Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1375
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: 43111
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Found at i:24344 original size:40 final size:40
Alignment explanation
Indices: 24289--24511 Score: 310
Period size: 40 Copynumber: 5.6 Consensus size: 40
24279 GATGATAACG
*
24289 GGGCTAAGTCTCGAAGGCATTTGTGCTAGTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
*
24329 GGGCTAAGTCCCGAAGGCATTTGTGCTAATGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
* *
24369 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
* *
24409 GGGCTAAGTCCCGAAGGCATTTGTG-TGAGTTACT-ATATCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCT-AGTGACTAAT-TCC
* *
24449 GGGCTAAGTCCCGAAGGCATTTGTGCGAACT-ACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-TAGTGACTAAT-TCC
24489 GGGCTAAGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
24512 AGTGAGTAGC
Statistics
Matches: 169, Mismatches: 10, Indels: 8
0.90 0.05 0.04
Matches are distributed among these distances:
39 2 0.01
40 165 0.98
41 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
Found at i:24422 original size:80 final size:80
Alignment explanation
Indices: 24289--24544 Score: 333
Period size: 80 Copynumber: 3.2 Consensus size: 80
24279 GATGATAACG
* * *
24289 GGGCTAAGTCTCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
24354 CT-AATGACTA-ATTCC
66 -TGAATGACTATA-TCC
24369 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
* * *
24434 TGAGTTACTATATCT
66 TGAATGACTATATCC
** *
24449 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACT-ATATCCGGGCTAAGTCCCGAAGGCATTTGA
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTGT
*
24513 GTGAGT-AGCTATATCC
65 GTGAATGA-CTATATCC
* *
24529 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
24545 TACTTGGTTT
Statistics
Matches: 160, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
79 18 0.11
80 141 0.88
81 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (80 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
TGAATGACTATATCC
Found at i:24502 original size:120 final size:120
Alignment explanation
Indices: 24289--24511 Score: 346
Period size: 120 Copynumber: 1.9 Consensus size: 120
24279 GATGATAACG
*
24289 GGGCTAAGTCTCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
*
24354 CTAATGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
66 CGAATGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
* *
24409 GGGCTAAGTCCCGAAGGCATTTGTG-TGAGTTACT-ATATCTGGGCTAAGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCT-AGTGACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTG
24472 TGCGAACT-ACT-ATATCCGGGCTAAGTCCCGAAGGCATTTG
64 TGCGAA-TGACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTG
24512 AGTGAGTAGC
Statistics
Matches: 95, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
119 5 0.05
120 89 0.94
121 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (120 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
CGAATGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
Found at i:24525 original size:40 final size:39
Alignment explanation
Indices: 24289--24544 Score: 290
Period size: 40 Copynumber: 6.4 Consensus size: 39
24279 GATGATAACG
*
24289 GGGCTAAGTCTCGAAGGCATTTGTGCT-AGTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTG-TGAGT-ACTAATTCC
*
24329 GGGCTAAGTCCCGAAGGCATTTGTGCT-AATGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTG-TGAGT-ACTAATTCC
*
24369 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGTGAG-TACTAATTCC
*
24409 GGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACT-ATATCT
1 GGGCTAAGTCCCGAAGGCATTTGTGTGAG-TACTAAT-TCC
* *
24449 GGGCTAAGTCCCGAAGGCATTTGTGCGAACTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGTG-AGTACTAAT-TCC
*
24489 GGGCTAAGTCCCGAAGGCATTTGAGTGAGTAGCT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGTGAGTA-CTAAT-TCC
* *
24529 -GGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
24545 TACTTGGTTT
Statistics
Matches: 197, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
39 19 0.10
40 176 0.89
41 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
GGGCTAAGTCCCGAAGGCATTTGTGTGAGTACTAATTCC
Found at i:39203 original size:43 final size:40
Alignment explanation
Indices: 39077--39312 Score: 159
Period size: 39 Copynumber: 5.8 Consensus size: 40
39067 GAATATAGCT
*
39077 ACTCACATCAAACCTGCCTTCGGTGACTTAGCCC-GATATAAGTA
1 ACTCACAACAAA--TGCCTTCGG-GACTTAGCCCGGAT-T-AGTA
** * * * *
39121 GTTCGCGACAACTGCCTTCGGGACTTAG-CCAGATATAGTA
1 ACTCACAACAAATGCCTTCGGGACTTAGCCCGGAT-TAGTA
39161 ACTCACAAAAAACAAATGCCTTCGGG-CTTAGCCCGGATTAGTA
1 ACTCAC----AACAAATGCCTTCGGGACTTAGCCCGGATTAGTA
* * *
39204 ACTCGCCACAAATGCCTTCGGGAACTTAGCCCGGAATTAGTC
1 ACTCACAACAAATGCCTTCGGG-ACTTAGCCCGG-ATTAGTA
* *
39246 A-TTAGC-AC-AATGCCTTCGGGACTTAG-CCGGAATTAGTC
1 ACTCA-CAACAAATGCCTTCGGGACTTAGCCCGG-ATTAGTA
39284 ACT-AGC-ACAAATGCCTTC-GGACTTAGCCC
1 ACTCA-CAACAAATGCCTTCGGGACTTAGCCC
39313 CGTTATCATC
Statistics
Matches: 162, Mismatches: 17, Indels: 31
0.77 0.08 0.15
Matches are distributed among these distances:
38 26 0.16
39 33 0.20
40 21 0.13
41 25 0.15
42 17 0.10
43 15 0.09
44 25 0.15
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
ACTCACAACAAATGCCTTCGGGACTTAGCCCGGATTAGTA
Found at i:39297 original size:39 final size:40
Alignment explanation
Indices: 39172--39312 Score: 202
Period size: 39 Copynumber: 3.6 Consensus size: 40
39162 CTCACAAAAA
* *
39172 ACAAATGCCTTCGGG-CTTAGCCCGG-ATTAGTAACTCGCC
1 ACAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAG-C
*
39211 ACAAATGCCTTCGGGAACTTAGCCCGGAATTAGTCATTAGC
1 ACAAATGCCTTCGGG-ACTTAGCCCGGAATTAGTCACTAGC
39252 AC-AATGCCTTCGGGACTTAG-CCGGAATTAGTCACTAGC
1 ACAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGC
39290 ACAAATGCCTTC-GGACTTAGCCC
1 ACAAATGCCTTCGGGACTTAGCCC
39313 CGTTATCATC
Statistics
Matches: 93, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
38 27 0.29
39 32 0.34
40 12 0.13
41 13 0.14
42 9 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
ACAAATGCCTTCGGGACTTAGCCCGGAATTAGTCACTAGC
Done.