Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1183
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: 24368
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Found at i:5638 original size:13 final size:13
Alignment explanation
Indices: 5620--5644 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5610 TGACTAATCT
5620 TTATTATTTTATG
1 TTATTATTTTATG
5633 TTATTATTTTAT
1 TTATTATTTTAT
5645 CTTAACATAA
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:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTATTATTTTATG
Found at i:6958 original size:35 final size:36
Alignment explanation
Indices: 6905--7032 Score: 117
Period size: 35 Copynumber: 3.6 Consensus size: 36
6895 ACCCGCGACT
6905 GTCCGAAGGCATTTGTGCT-GTGACTATATCGGCTAA
1 GTCCGAAGGCATTTGTGCTAGT-ACTATATCGGCTAA
* *
6941 GTCCGAAGG-ATTTGTGCTAGTTCTATATCGGGTAA
1 GTCCGAAGGCATTTGTGCTAGTACTATATCGGCTAA
*
6976 GGCCCG-AGGCATTTGTG-TAGTGA--ATATCGGGCTAA
1 -GTCCGAAGGCATTTGTGCTAGT-ACTATATC-GGCTAA
* *
7011 TTCC-AAGGCCTTCTGTGCTAGT
1 GTCCGAAGGCATT-TGTGCTAGT
7033 GATTATTACG
Statistics
Matches: 76, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
34 13 0.17
35 37 0.49
36 26 0.34
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (36 bp):
GTCCGAAGGCATTTGTGCTAGTACTATATCGGCTAA
Found at i:13457 original size:13 final size:13
Alignment explanation
Indices: 13439--13464 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13429 ATATTATAAT
13439 TATTTTATGTTAA
1 TATTTTATGTTAA
13452 TATTTTATGTTAA
1 TATTTTATGTTAA
13465 AAATAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTTATGTTAA
Found at i:14850 original size:40 final size:40
Alignment explanation
Indices: 14802--15007 Score: 353
Period size: 40 Copynumber: 5.2 Consensus size: 40
14792 GGACTAAGAT
14802 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
14842 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
14882 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
14922 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
14962 CCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTC
15001 CCGAAGG
1 CCGAAGG
15008 TACTTGGGTT
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
39 15 0.09
40 142 0.89
41 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
Found at i:21489 original size:13 final size:13
Alignment explanation
Indices: 21471--21496 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21461 ATATTATAAT
21471 TATTTTATGTTAA
1 TATTTTATGTTAA
21484 TATTTTATGTTAA
1 TATTTTATGTTAA
21497 AAATAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTTATGTTAA
Found at i:22882 original size:40 final size:40
Alignment explanation
Indices: 22827--23028 Score: 317
Period size: 40 Copynumber: 5.2 Consensus size: 40
22817 GGACTAAGAT
22827 CCGAA-GCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
22866 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
22906 CCGAA-GCATTTGTGCTAGTGAC-A-ATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
22943 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
22983 CCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTC
23022 CCGAAGG
1 CCGAAGG
23029 TACTTGGGTT
Statistics
Matches: 152, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
37 19 0.12
38 17 0.11
39 37 0.24
40 77 0.51
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
Found at i:22955 original size:77 final size:79
Alignment explanation
Indices: 22827--23028 Score: 322
Period size: 77 Copynumber: 2.6 Consensus size: 79
22817 GGACTAAGAT
*
22827 CCGAAGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTAT
1 CCGAAGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
22892 ATCCGGGCTAAGTC
66 ATCCGGGCTAAGTC
*
22906 CCGAAGCATTTGTGCTAGTGAC-A-ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTAT
1 CCGAAGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
22969 ATCCGGGCTAAGTC
66 ATCCGGGCTAAGTC
* *
22983 CCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAGG
1 CCGAA-GCATTTGTGCTAG-TGACTATATCCGGGCTAAGTCCCGAAGG
23029 TACTTGGGTT
Statistics
Matches: 115, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
77 57 0.50
78 14 0.12
79 40 0.35
80 4 0.03
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGAAGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAT
ATCCGGGCTAAGTC
Done.