Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3635
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: 59297
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2663 original size:13 final size:13
Alignment explanation
Indices: 2645--2669 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2635 AAACTAAGTA
2645 AAAATAAATAAAT
1 AAAATAAATAAAT
2658 AAAATAAATAAA
1 AAAATAAATAAA
2670 AATAAACTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:8415 original size:12 final size:12
Alignment explanation
Indices: 8398--8444 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
8388 AGACCGTATG
8398 CAATTTTTTTTT
1 CAATTTTTTTTT
*
8410 CAATTTTGTTTT
1 CAATTTTTTTTT
8422 CAA-TTTTTTTT
1 CAATTTTTTTTT
*
8433 CGATTTTTTTTT
1 CAATTTTTTTTT
8445 GAATCTACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
11 9 0.29
12 22 0.71
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.72
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:8432 original size:11 final size:11
Alignment explanation
Indices: 8402--8443 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
8392 CGTATGCAAT
8402 TTTTTTTTCAA
1 TTTTTTTTCAA
8413 TTTTGTTTTCAA
1 TTTT-TTTTCAA
*
8425 TTTTTTTTCGA
1 TTTTTTTTCAA
8436 TTTTTTTT
1 TTTTTTTT
8444 TGAATCTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.76
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:22340 original size:30 final size:29
Alignment explanation
Indices: 22306--22375 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
22296 GCAAGACTTT
22306 TCACTTTTTTTTTAACTTGAT-TTTTTTTGC
1 TCACTTTTTTTTT--CTTGATATTTTTTTGC
**
22336 TCACTTTTTTTTTCTTTCTATTTTTTTGC
1 TCACTTTTTTTTTCTTGATATTTTTTTGC
*
22365 TCAATTTTTTT
1 TCACTTTTTTT
22376 CACTTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.11
29 19 0.53
30 13 0.36
ACGTcount: A:0.11, C:0.14, G:0.04, T:0.70
Consensus pattern (29 bp):
TCACTTTTTTTTTCTTGATATTTTTTTGC
Found at i:22343 original size:14 final size:14
Alignment explanation
Indices: 22326--22375 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
22316 TTTAACTTGA
22326 TTTTTTTTGCTCAC
1 TTTTTTTTGCTCAC
* **
22340 TTTTTTTTTCTTTC
1 TTTTTTTTGCTCAC
*
22354 TATTTTTTTGCTCAA
1 T-TTTTTTTGCTCAC
22369 TTTTTTT
1 TTTTTTT
22376 CACTTTTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 18 0.64
15 10 0.36
ACGTcount: A:0.08, C:0.14, G:0.04, T:0.74
Consensus pattern (14 bp):
TTTTTTTTGCTCAC
Found at i:22383 original size:11 final size:11
Alignment explanation
Indices: 22344--22404 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
22334 GCTCACTTTT
*
22344 TTTTTCTTTCTA
1 TTTTT-TTTCAA
22356 TTTTTTTGCTCAA
1 TTTTTTT--TCAA
*
22369 -TTTTTTTCAC
1 TTTTTTTTCAA
*
22379 TTTTTTTTGAA
1 TTTTTTTTCAA
*
22390 TTTTTTTTGAA
1 TTTTTTTTCAA
22401 TTTT
1 TTTT
22405 GATTTTTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
10 3 0.07
11 25 0.60
12 11 0.26
13 3 0.07
ACGTcount: A:0.13, C:0.10, G:0.05, T:0.72
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:22393 original size:10 final size:11
Alignment explanation
Indices: 22369--22404 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
22359 TTTTGCTCAA
* *
22369 TTTTTTTCACT
1 TTTTTTTGAAT
22380 TTTTTTTGAAT
1 TTTTTTTGAAT
22391 TTTTTTTGAAT
1 TTTTTTTGAAT
22402 TTT
1 TTT
22405 GATTTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.75
Consensus pattern (11 bp):
TTTTTTTGAAT
Found at i:22823 original size:22 final size:22
Alignment explanation
Indices: 22793--22836 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
22783 TTTGGTATTT
22793 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
22815 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
22837 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:27465 original size:22 final size:22
Alignment explanation
Indices: 27437--27480 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
27427 TTTTGAACCA
27437 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
27459 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
27481 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:28745 original size:14 final size:14
Alignment explanation
Indices: 28728--28767 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
28718 CGAACGGAAT
*
28728 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
28742 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
28756 GATATGAACAAA
1 GGTAGGAACAAA
28768 TTGGTCAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Done.