Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5880.1
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: 16515
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Found at i:251 original size:76 final size:76
Alignment explanation
Indices: 125--274 Score: 282
Period size: 76 Copynumber: 2.0 Consensus size: 76
115 ATTATAAATT
125 AACCAGAGATAATTAGGAGTCATGCCATATATGTATAGATTCCTATTTGAGTCTAGTTTCTATAG
1 AACCAGAGATAATTAGGAGTCATGCCATATATGTATAGATTCCTATTTGAGTCTAGTTTCTATAG
190 AAACAAACGGG
66 AAACAAACGGG
* *
201 AACCAGAGATAATTAGGAGTCATGCCATATATTTATAGATTCCTATTTGAGTTTAGTTTCTATAG
1 AACCAGAGATAATTAGGAGTCATGCCATATATGTATAGATTCCTATTTGAGTCTAGTTTCTATAG
266 AAACAAACG
66 AAACAAACG
275 ACATCTGTAT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (76 bp):
AACCAGAGATAATTAGGAGTCATGCCATATATGTATAGATTCCTATTTGAGTCTAGTTTCTATAG
AAACAAACGGG
Found at i:6386 original size:39 final size:39
Alignment explanation
Indices: 6251--6433 Score: 224
Period size: 40 Copynumber: 4.6 Consensus size: 39
6241 TCGGATGATA
* * * **
6251 ACCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAAT
1 ACCGGGCTAAGTCCCGAAG-GCATTCGTGCGAGTTACT-AT
* *
6291 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTAT
1 ACCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTAT
* * *
6330 ATCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTATTAT
1 A-CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTAT
*
6370 ACCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAT
1 ACCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTAT
6409 AACCGGGCTAAGTCCCGAAGGCATT
1 -ACCGGGCTAAGTCCCGAAGGCATT
6434 TGAGCTAGTG
Statistics
Matches: 124, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
39 36 0.29
40 86 0.69
41 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (39 bp):
ACCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTAT
Found at i:6449 original size:40 final size:40
Alignment explanation
Indices: 6248--6458 Score: 209
Period size: 40 Copynumber: 5.3 Consensus size: 40
6238 TGTTCGGATG
* *
6248 ATAACCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCT
1 ATAACCGGGCTAAGTCCCGAAG-GCATTTGAGCGAGTGACT
* * *
6288 A-ATTCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCT-ACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TGACT
* * *
6328 ATATCCGGGCTAAGTCCCGAAGGCATTTGTA-CGAGTTATT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG-AGCGAGTGACT
* * * *
6368 AT-ACCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGACT
* *
6407 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGACT
*
6447 ATATCC-GGCTAA
1 ATAACCGGGCTAA
6459 ACTCCGAAGG
Statistics
Matches: 144, Mismatches: 19, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
39 41 0.28
40 99 0.69
41 4 0.03
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGACT
Found at i:6468 original size:79 final size:80
Alignment explanation
Indices: 6248--6458 Score: 297
Period size: 79 Copynumber: 2.7 Consensus size: 80
6238 TGTTCGGATG
6248 ATAACCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTA-ATTCCGGGCTAAGTCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAG-GCATTTGAGCTAGTGGCTATA-TCCGGGCTAAGTCCCGAAGG
*
6311 CATTCGTGCGAGCTACT
64 CATTCGTGCAAGCTACT
* * ***
6328 ATATCCGGGCTAAGTCCCGAAGGCATTTGTA-CGAGTTATTATA-CCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG-AGCTAGTGGCTATATCCGGGCTAAGTCCCGAAGGC
*
6391 ATTCGTGCAAGTTACT
65 ATTCGTGCAAGCTACT
6407 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCC-GGCTAA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCCGGGCTAA
6459 ACTCCGAAGG
Statistics
Matches: 114, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
78 1 0.01
79 76 0.67
80 33 0.29
81 4 0.04
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCCGGGCTAAGTCCCGAAGGCA
TTCGTGCAAGCTACT
Found at i:9278 original size:27 final size:27
Alignment explanation
Indices: 9248--9398 Score: 160
Period size: 27 Copynumber: 5.6 Consensus size: 27
9238 AAATTGTACA
* *
9248 GCACTAAGGGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTG
** *
9275 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGATTTGACTATG-TG
* * *
9302 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTG
* * *
9329 GCACTAAGAGTGCGAGTCTGACTATGTA
1 GCACTAAGTGTGCGA-TTTGACTATGTG
* *
9357 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGATTTGACTATGTG
9384 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
9399 GATGATTATA
Statistics
Matches: 102, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
27 80 0.78
28 22 0.22
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTG
Found at i:9361 original size:82 final size:81
Alignment explanation
Indices: 9248--9398 Score: 214
Period size: 82 Copynumber: 1.9 Consensus size: 81
9238 AAATTGTACA
* * * *
9248 GCACTAAGGGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGAGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
9312 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
9329 GCACTAAGAGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGAGTGCGA-TCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
9394 TGCGA
65 TGCGA
9399 GATGATTATA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 15 0.25
82 46 0.75
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (81 bp):
GCACTAAGAGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:9404 original size:27 final size:27
Alignment explanation
Indices: 9247--9424 Score: 144
Period size: 27 Copynumber: 6.6 Consensus size: 27
9237 TAAATTGTAC
* **
9247 AGCACTAAGGGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAGATGACTATGT
* * *
9274 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGATGACTATGT
* *
9300 ATGCACTAAGTGTGCGA-ATTGACCATGC
1 A-GCACTAAGTGTGCGAGA-TGACTATGT
* * *
9328 GGCACTAAGAGTGCGAGTCTGACTATGT
1 AGCACTAAGTGTGCGAG-ATGACTATGT
** * *
9356 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGATGACTATGT
* * *
9383 GGCACTAAGTGTGCGAGATGATTATAT
1 AGCACTAAGTGTGCGAGATGACTATGT
*
9410 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
9425 GGCTCAATAT
Statistics
Matches: 120, Mismatches: 26, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
26 1 0.01
27 98 0.82
28 21 0.17
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGATGACTATGT
Done.