Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3289
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: 16288
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Found at i:3370 original size:39 final size:39
Alignment explanation
Indices: 3318--3488 Score: 202
Period size: 39 Copynumber: 4.3 Consensus size: 39
3308 GGACTAAGAT
*
3318 CCGAAGGCATTTGTGCGAGATACAAGTTCCGGGTTAAG-C
1 CCGAAGGCATTTGTGCGAGATACAA-ATCCGGGTTAAGTC
*
3357 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGTC
* * *
3397 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
3437 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGTC
3476 CCGAAGGCATTTG
1 CCGAAGGCATTTG
3489 AACGAGGAGC
Statistics
Matches: 115, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
39 65 0.57
40 50 0.43
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:3401 original size:79 final size:79
Alignment explanation
Indices: 3265--3488 Score: 222
Period size: 79 Copynumber: 2.8 Consensus size: 79
3255 TTGAATGCTG
* * * * * * *
3265 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAAACCGGGCTAAG-TCCCGAAGGCAT
*
3328 TTGTGCGAGATA-CAAGT
63 TTGTGCGAGATATCAA-A
* * * *
3345 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTT
* *
3409 GTGCGAGTTATTAAA
65 GTGCGAGATATCAAA
* * *
3424 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
3489 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
78 1 0.01
79 90 0.74
80 30 0.25
81 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATATCAAA
Found at i:3506 original size:79 final size:80
Alignment explanation
Indices: 3345--3521 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
3335 AGATACAAGT
* * *
3345 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
3409 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
3424 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
3488 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
3503 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
3522 TACGTGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
78 16 0.19
79 59 0.71
80 8 0.10
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:10907 original size:80 final size:78
Alignment explanation
Indices: 10823--10994 Score: 213
Period size: 79 Copynumber: 2.2 Consensus size: 78
10813 GGACTAAGAT
*
10823 CCGAAGGCATTTGTGCGAG-A-TACAAGTTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATAC
1 CCGAAGGCATTTGTGCGAGCATTA-AA--TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATAC
* *
10886 TAAATCCGGGTTAAGTC
62 TAAAACCGGGCTAAGTC
* * * *
10903 CCGAAGGCATTCGTGCGAGTCATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAG-CATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
10968 AACCGGGCTATGTC
65 AACCGGGCTAAGTC
10982 CCGAAGGCATTTG
1 CCGAAGGCATTTG
10995 AACGAGGAGC
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
79 38 0.47
80 37 0.46
82 3 0.04
83 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGCATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
ACCGGGCTAAGTC
Found at i:10985 original size:39 final size:39
Alignment explanation
Indices: 10770--10992 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
10760 TTGAATGCTG
* * * * * *
10770 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
10810 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
10850 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
* *
10890 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
10930 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
10969 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
10993 TGAACGAGGA
Statistics
Matches: 152, Mismatches: 24, Indels: 15
0.80 0.13 0.08
Matches are distributed among these distances:
39 37 0.24
40 105 0.69
41 10 0.07
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:11012 original size:79 final size:80
Alignment explanation
Indices: 10850--11027 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
10840 AGATACAAGT
* * * *
10850 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** *
10915 GTGCGAGTCATTAAA
66 GAACGAGTCACTAAA
* * * *
10930 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* *
10994 GAACGAG-GAGCTATA
66 GAACGAGTCA-CTAAA
*
11009 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
11028 TATGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTCACTAAA
Found at i:14192 original size:40 final size:41
Alignment explanation
Indices: 14135--14282 Score: 176
Period size: 40 Copynumber: 3.6 Consensus size: 41
14125 GAGCTTGGTC
14135 TCGAAGGGCTTTTGAGCCAGTGCTAATAACC-AACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* * *
14175 TCGAAGGGCTTTAGAGCCAGTG-TCATAACCGGACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* * * * * *
14215 CCGAAGGGCCTTTGAGCCAGTGGTCTAAT-TCCGAGCTTGGTC
1 TCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGTT
14257 TCGAAGGGCTTTTGAGCCAGTGCTAA
1 TCGAAGGGCTTTTGAGCCAGTGCTAA
14283 GAATCGGGCT
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
39 7 0.08
40 51 0.57
41 2 0.02
42 27 0.30
43 3 0.03
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.28
Consensus pattern (41 bp):
TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
Done.