Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1458
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: 19502
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:4398 original size:15 final size:15
Alignment explanation
Indices: 4378--4408 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4368 TAAAAATGTC
*
4378 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
4393 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
4408 C
1 C
4409 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:6511 original size:13 final size:13
Alignment explanation
Indices: 6493--6556 Score: 110
Period size: 13 Copynumber: 4.9 Consensus size: 13
6483 CATTTTTCTT
6493 TGTATCGATACAA
1 TGTATCGATACAA
*
6506 TGTATCGATACAC
1 TGTATCGATACAA
6519 TGTATCGATACAA
1 TGTATCGATACAA
*
6532 TGTATCGATACAC
1 TGTATCGATACAA
6545 TGTATCGATACA
1 TGTATCGATACA
6557 GGGGGATTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:6529 original size:26 final size:26
Alignment explanation
Indices: 6493--6556 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
6483 CATTTTTCTT
6493 TGTATCGATACAATGTATCGATACAC
1 TGTATCGATACAATGTATCGATACAC
6519 TGTATCGATACAATGTATCGATACAC
1 TGTATCGATACAATGTATCGATACAC
6545 TGTATCGATACA
1 TGTATCGATACA
6557 GGGGGATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (26 bp):
TGTATCGATACAATGTATCGATACAC
Found at i:9032 original size:20 final size:19
Alignment explanation
Indices: 8978--9033 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
8968 AAAACCCTTA
*
8978 AAAGTATCGATACACAGTTC
1 AAAGTATCGATACA-TGTTC
8998 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
9018 AATGTATCGATACATG
1 AAAGTATCGATACATG
9034 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:9121 original size:13 final size:13
Alignment explanation
Indices: 9103--9128 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9093 TACACAAAAT
9103 ATGTATCGATACA
1 ATGTATCGATACA
9116 ATGTATCGATACA
1 ATGTATCGATACA
9129 CAAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:9149 original size:34 final size:32
Alignment explanation
Indices: 9085--9149 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
9075 TAGCCAAACT
* *
9085 TGTATCGATACACAAAATATGTATCGATACAA
1 TGTATCGATACACAAAAAATATATCGATACAA
9117 TGTATCGATACACAAAAAAATTATATCGATACA
1 TGTATCGATACAC-AAAAAA-TATATCGATACA
9150 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 5 0.17
34 11 0.38
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATATATCGATACAA
Found at i:15270 original size:79 final size:79
Alignment explanation
Indices: 15180--15336 Score: 224
Period size: 79 Copynumber: 2.0 Consensus size: 79
15170 ATGGTGTAAA
* * * ** * *
15180 TGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGGAAAATTGATGT
1 TGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCAAAAGTGGAAAATGGATAT
15245 TTTAAAAATAAAAC
66 TTTAAAAATAAAAC
* *
15259 TGGGGTTGGAGTATCCCCTTGGAAATAACAGGGTTGGAGTATCCCCAAAAGTGGAAAATGGATAT
1 TGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCAAAAGTGGAAAATGGATAT
*
15324 TTTAGAAATAAAA
66 TTTAAAAATAAAA
15337 ACATCAATGA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 68 1.00
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (79 bp):
TGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCAAAAGTGGAAAATGGATAT
TTTAAAAATAAAAC
Found at i:17684 original size:20 final size:20
Alignment explanation
Indices: 17639--17684 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
17629 ATTAACAGCC
*
17639 CATGATTCATGCATTTTGAG
1 CATGTTTCATGCATTTTGAG
17659 CTATGTTTCATGCA-TTTGCAG
1 C-ATGTTTCATGCATTTTG-AG
17680 CATGT
1 CATGT
17685 CCAGCACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (20 bp):
CATGTTTCATGCATTTTGAG
Done.