Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1596
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: 10061
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Found at i:1319 original size:46 final size:45
Alignment explanation
Indices: 1269--1444 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 45
1259 TGGTTGAGCA
*
1269 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-AAACG
* *** * ** *
1315 TCCGAACTTGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACT-AGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-TGAAACG
* *
1362 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTGTGGATGAGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGA-AACG
* *
1408 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1445 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 21, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
44 1 0.01
45 2 0.02
46 67 0.64
47 32 0.31
48 1 0.01
49 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAACG
Found at i:1382 original size:93 final size:93
Alignment explanation
Indices: 1266--1436 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
1256 GGATGGTTGA
* * *
1266 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCA-AATGTCCGAACTTGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-AGAACGCCCGAACTCGTTGAG
1330 TTGAGTCCGAGTTCGAGAGATGTAACTAG
65 TTGAGTCCGAGTTCGAGAGATGTAACTAG
* * *
1359 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTGTGGATGAGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAACGCCCGAACTCGTTGAGT
1424 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
1437 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 1 0.01
93 70 0.99
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:4364 original size:15 final size:15
Alignment explanation
Indices: 4344--4396 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
4334 GTATCTTGGG
4344 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
4359 TCTCTTTATTCTGG-
1 TTTCTTTATCCTGGA
* *
4373 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
4388 TTTCTTTAT
1 TTTCTTTAT
4397 TCGGTTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
14 10 0.33
15 20 0.67
ACGTcount: A:0.11, C:0.19, G:0.11, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:4406 original size:29 final size:29
Alignment explanation
Indices: 4342--4403 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
4332 TCGTATCTTG
*
4342 GGTTTCTTTATCCTGGATCTCTTTATTCT
1 GGTTTCTCTATCCTGGATCTCTTTATTCT
* *
4371 GGTTTCTCTATCTTGGATTTCTTTATTC-
1 GGTTTCTCTATCCTGGATCTCTTTATTCT
4399 GGTTT
1 GGTTT
4404 TCTTGTTATC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 5 0.17
29 25 0.83
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (29 bp):
GGTTTCTCTATCCTGGATCTCTTTATTCT
Found at i:6826 original size:46 final size:48
Alignment explanation
Indices: 6775--6905 Score: 157
Period size: 46 Copynumber: 2.8 Consensus size: 48
6765 GGATGTTGGC
*
6775 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA-ATG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACAGG
* *
6822 -TCCGAACTCGTTGAGTTGAGTCCGAGTT--C-GA-GAGATGTAACTAGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCAAC-AGG
*
6867 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
6906 GCGGTTACAT
Statistics
Matches: 70, Mismatches: 5, Indels: 15
0.78 0.06 0.17
Matches are distributed among these distances:
42 1 0.01
43 7 0.10
44 1 0.01
45 2 0.03
46 28 0.40
47 27 0.39
49 1 0.01
50 2 0.03
51 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (48 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACAGG
Found at i:9381 original size:40 final size:40
Alignment explanation
Indices: 9326--9547 Score: 252
Period size: 40 Copynumber: 5.5 Consensus size: 40
9316 TATTCGGATG
9326 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
9366 ATATCTGGGCTAAGTCTCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * * *
9409 ATACCCGGGCTAAGTTCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * *
9449 ATATCCGGGCTAAGT-CCGAAGGCATTCATGC-TGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
9487 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
9527 ATATCC-GGCTAAATCTCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
9548 ATACTTGGGT
Statistics
Matches: 154, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
38 20 0.13
39 40 0.26
40 59 0.38
41 1 0.01
43 34 0.22
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:9529 original size:78 final size:81
Alignment explanation
Indices: 9326--9547 Score: 276
Period size: 83 Copynumber: 2.8 Consensus size: 81
9316 TATTCGGATG
* *
9326 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCTGGGCTAAGTCTCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTGCTATATCCGGGCTAAGTCTCGAAGGCA
**
9391 TTTGTGCGAGTAGTTGCT
66 TTCATGC--GTAGTTGCT
* * *
9409 ATACCCGGGCTAAGTTCCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTC-CGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTG-CTATATCCGGGCTAAGTCTCGAAGGC
9472 ATTCATGC-T-G-TGACT
65 ATTCATGCGTAGTTG-CT
* * *
9487 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCC-GGCTAAATCTCGAAG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTGCTATATCCGGGCTAAGTCTCGAAG
9548 ATACTTGGGT
Statistics
Matches: 123, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
77 10 0.08
78 47 0.38
79 3 0.02
82 14 0.11
83 49 0.40
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (81 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTGCTATATCCGGGCTAAGTCTCGAAGGCA
TTCATGCGTAGTTGCT
Done.