Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1589
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: 31518
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:187 original size:20 final size:22
Alignment explanation
Indices: 155--194 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
145 AGCCTAAGTC
155 AACCTTAATGTATC-GATACAA
1 AACCTTAATGTATCGGATACAA
176 AACCTT-ATGTATCGGATAC
1 AACCTTAATGTATCGGATAC
195 TTGATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (22 bp):
AACCTTAATGTATCGGATACAA
Found at i:6752 original size:42 final size:43
Alignment explanation
Indices: 6685--6786 Score: 136
Period size: 42 Copynumber: 2.4 Consensus size: 43
6675 TCATAATTGA
* *
6685 ATTGTATCGAT-CTATTAAGCCCAACGGCTATAA-TTCAACTAC
1 ATTGTATCGATAC-ATTAAGCCCAACGGCTAAAATTTCAAATAC
* * *
6727 ATTGTATCGATACATTGAGCTCAACGGCTAAAATTTCAAATGC
1 ATTGTATCGATACATTAAGCCCAACGGCTAAAATTTCAAATAC
6770 ATTGTATCGATACATTA
1 ATTGTATCGATACATTA
6787 TGAATTGTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 28 0.54
43 24 0.46
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (43 bp):
ATTGTATCGATACATTAAGCCCAACGGCTAAAATTTCAAATAC
Found at i:7239 original size:25 final size:26
Alignment explanation
Indices: 7211--7260 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
7201 TAAGTTATTG
*
7211 TCTTCGA-GGATACTCTAACCCCACT
1 TCTTCGAGGGATACTCCAACCCCACT
7236 TCTTCGAGGGGATACTCCAACCCCA
1 TCTTCGA-GGGATACTCCAACCCCA
7261 TTTTTCAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
27 15 0.68
ACGTcount: A:0.24, C:0.36, G:0.16, T:0.24
Consensus pattern (26 bp):
TCTTCGAGGGATACTCCAACCCCACT
Found at i:14524 original size:13 final size:14
Alignment explanation
Indices: 14499--14528 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
14489 AAAACACAAA
14499 TTTTAAAATTAATT
1 TTTTAAAATTAATT
14513 TTTTAAAA-TAATT
1 TTTTAAAATTAATT
14526 TTT
1 TTT
14529 AAATTTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTAAAATTAATT
Found at i:16868 original size:53 final size:54
Alignment explanation
Indices: 16811--16915 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 54
16801 GTGCATGATG
*
16811 ATGTTACCAGTATGAACTACAAAAATCACTTGAAAAAGAAA-TTAAAAAAAAGA
1 ATGTTACCAATATGAACTACAAAAATCACTTGAAAAAGAAATTTAAAAAAAAGA
*
16864 ATGTTACCAATATGAACTACAGAAATCACTTGAAAAAGAAATTTAAAAAAAA
1 ATGTTACCAATATGAACTACAAAAATCACTTGAAAAAGAAATTTAAAAAAAA
16916 AAAAAGAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
53 39 0.80
54 10 0.20
ACGTcount: A:0.56, C:0.11, G:0.10, T:0.22
Consensus pattern (54 bp):
ATGTTACCAATATGAACTACAAAAATCACTTGAAAAAGAAATTTAAAAAAAAGA
Found at i:17708 original size:45 final size:45
Alignment explanation
Indices: 17655--17759 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 45
17645 ATTTTTATTA
* *
17655 ATTTTA-TTTTATATATTTTATTCCTTTTA-TTTATTAAATTCATAT
1 ATTTTATTTTTA-AAATTTTAATCCTTTTATTTTATTAAATTC-TAT
* * *
17700 TTTTTATTTTTAAAATTTTAATCTTTTTATTTTATTTAATTCTAT
1 ATTTTATTTTTAAAATTTTAATCCTTTTATTTTATTAAATTCTAT
*
17745 AATTTATTTTTAAAA
1 ATTTTATTTTTAAAA
17760 AATTTTAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
45 35 0.69
46 16 0.31
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (45 bp):
ATTTTATTTTTAAAATTTTAATCCTTTTATTTTATTAAATTCTAT
Found at i:17715 original size:22 final size:21
Alignment explanation
Indices: 17679--17759 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 21
17669 ATTTTATTCC
17679 TTTTATTTATT-AAATTCATATT
1 TTTTATTT-TTAAAATTC-TATT
*
17701 TTTTATTTTTAAAATTTTAATCT
1 TTTTATTTTTAAAATTCT-AT-T
** *
17724 TTTTATTTTATTTAATTCTATA
1 TTTTATTTT-TAAAATTCTATT
*
17746 ATTTATTTTTAAAA
1 TTTTATTTTTAAAA
17760 AATTTTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
21 6 0.13
22 23 0.49
23 12 0.26
24 6 0.13
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTATTTTTAAAATTCTATT
Found at i:18528 original size:27 final size:27
Alignment explanation
Indices: 18498--18552 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
18488 AATTTTTGTT
18498 ACTTTGGTTCAGTCGCCAAATGACGCA
1 ACTTTGGTTCAGTCGCCAAATGACGCA
18525 ACTTTGGTTCAGTCGCCAAATGACGCA
1 ACTTTGGTTCAGTCGCCAAATGACGCA
18552 A
1 A
18553 GTTGTCTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (27 bp):
ACTTTGGTTCAGTCGCCAAATGACGCA
Found at i:19504 original size:20 final size:20
Alignment explanation
Indices: 19481--19533 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
19471 CACACCCAGA
19481 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
19501 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
19521 TGTATCGATACAT
1 TGTATCGATACAT
19534 GGACAATTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTATGCTT
Found at i:27759 original size:21 final size:23
Alignment explanation
Indices: 27719--27761 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
27709 TTTTAACCGG
*
27719 TTATCAAGGGGGAGAAATTTTTT
1 TTATCAAGAGGGAGAAATTTTTT
27742 TTATCAA-AGGGA-AAATTTTT
1 TTATCAAGAGGGAGAAATTTTT
27762 AACGAGAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
23 7 0.37
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
TTATCAAGAGGGAGAAATTTTTT
Found at i:28390 original size:20 final size:19
Alignment explanation
Indices: 28344--28400 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
28334 TTGAATCGAT
*
28344 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
28363 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
28382 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
28401 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:30754 original size:40 final size:40
Alignment explanation
Indices: 30703--30780 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
30693 ATTCTGGAAG
* * * *
30703 GAAATTGTATCGATACATTTTTTAATGTATTGATACATAA
1 GAAATTGTATCGAGACATTTCTCAATGTATTAATACATAA
*
30743 GAAATTGTATCGAGACATTTCTCATTGTATTAATACAT
1 GAAATTGTATCGAGACATTTCTCAATGTATTAATACAT
30781 TCTGGATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (40 bp):
GAAATTGTATCGAGACATTTCTCAATGTATTAATACATAA
Done.