Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1174
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: 23757
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:8528 original size:20 final size:20
Alignment explanation
Indices: 8503--8552 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
8493 TGGCTTAAAA
8503 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
8523 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
8540 GTGGTAGTGGATT
1 TTGGTAGTGGATT
8553 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:13157 original size:20 final size:20
Alignment explanation
Indices: 13132--13181 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
13122 TGGCTTAAAA
13132 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
13152 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
13169 GTGGTAGTGGATT
1 TTGGTAGTGGATT
13182 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:13861 original size:21 final size:21
Alignment explanation
Indices: 13837--13878 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
13827 TTAATTTTTA
13837 AGTTATTAACTTTTTATATTT
1 AGTTATTAACTTTTTATATTT
13858 AGTTATTAACTTTTTATATTT
1 AGTTATTAACTTTTTATATTT
13879 TTAAATGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (21 bp):
AGTTATTAACTTTTTATATTT
Found at i:15766 original size:21 final size:21
Alignment explanation
Indices: 15726--15767 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
15716 ATATTCAATG
**
15726 TTCTAATAAACGCCTTCCCAA
1 TTCTAATAAACGCCCCCCCAA
15747 TTCTAATAAACGCCCCCCCAA
1 TTCTAATAAACGCCCCCCCAA
15768 ACATATCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.38, G:0.05, T:0.24
Consensus pattern (21 bp):
TTCTAATAAACGCCCCCCCAA
Found at i:16585 original size:30 final size:30
Alignment explanation
Indices: 16533--16591 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
16523 ACTTCCTTAA
*
16533 TTAATTTTTATTGAATATTATATATATTTT
1 TTAATATTTATTGAATATTATATATATTTT
*
16563 TTAATATTTACTTTAATATATATATATAT
1 TTAATATTTA-TTGAATAT-TATATATAT
16592 AACACTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.36
31 7 0.28
32 9 0.36
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (30 bp):
TTAATATTTATTGAATATTATATATATTTT
Found at i:16741 original size:17 final size:18
Alignment explanation
Indices: 16708--16759 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
16698 ATTTTAAATT
* *
16708 TATAAAAATATAAAAAAA
1 TATAAAATTAAAAAAAAA
*
16726 T-TGAAATTAAAAAAAAA
1 TATAAAATTAAAAAAAAA
16743 TCATAAAATTAAAAAAA
1 T-ATAAAATTAAAAAAA
16760 TATAGCATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 14 0.50
18 1 0.04
19 13 0.46
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (18 bp):
TATAAAATTAAAAAAAAA
Found at i:20638 original size:44 final size:44
Alignment explanation
Indices: 20589--20685 Score: 158
Period size: 44 Copynumber: 2.2 Consensus size: 44
20579 ATGATCACAG
*
20589 ACACAGATTTCAGAATATGGAAGCAAAAAAGGGAATGACCAGAA
1 ACACAGATTTCAGAATATGGAAGCAAAAAAGGAAATGACCAGAA
* **
20633 ACACAGATTTGAGAATATGGAAGCAAAAAAGGAAATGATGAGAA
1 ACACAGATTTCAGAATATGGAAGCAAAAAAGGAAATGACCAGAA
20677 ACACAGATT
1 ACACAGATT
20686 CGAGAATTAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.51, C:0.11, G:0.23, T:0.15
Consensus pattern (44 bp):
ACACAGATTTCAGAATATGGAAGCAAAAAAGGAAATGACCAGAA
Found at i:20706 original size:44 final size:44
Alignment explanation
Indices: 20589--20706 Score: 141
Period size: 44 Copynumber: 2.7 Consensus size: 44
20579 ATGATCACAG
* *
20589 ACACAGATTTC-AGAATATGGAAGCAAAAAAGGGAATGACCAGAA
1 ACACAGA-TTCGAGAATATGAAAGCAAAAAAGGAAATGACCAGAA
* * **
20633 ACACAGATTTGAGAATATGGAAGCAAAAAAGGAAATGATGAGAA
1 ACACAGATTCGAGAATATGAAAGCAAAAAAGGAAATGACCAGAA
*
20677 ACACAGATTCGAGAAT-TAGAAAGCCAAAAA
1 ACACAGATTCGAGAATAT-GAAAGCAAAAAA
20707 CAAAGAGTGG
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
43 3 0.05
44 62 0.95
ACGTcount: A:0.52, C:0.12, G:0.22, T:0.14
Consensus pattern (44 bp):
ACACAGATTCGAGAATATGAAAGCAAAAAAGGAAATGACCAGAA
Done.