Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1005
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: 80285
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:8953 original size:13 final size:13
Alignment explanation
Indices: 8932--8974 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
8922 CAAACATGGG
8932 ACATAAGAAATTA
1 ACATAAGAAATTA
* *
8945 ACATCAGAATATGA
1 ACATAAGAA-ATTA
8959 A-ATAAGAAATTA
1 ACATAAGAAATTA
8971 ACAT
1 ACAT
8975 TAAAATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 4 0.17
13 16 0.67
14 4 0.17
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.23
Consensus pattern (13 bp):
ACATAAGAAATTA
Found at i:18575 original size:15 final size:15
Alignment explanation
Indices: 18543--18571 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
18533 ACTATTAGTA
18543 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
18558 ATTTTTT-AATATTT
1 ATTTTTTAAATATTT
18572 TATTGTACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTTAAATATTT
Found at i:33400 original size:28 final size:28
Alignment explanation
Indices: 33368--33427 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
33358 TTGTTTTGGT
33368 CACTTAATTAAAAAAAATACTATTTAGC
1 CACTTAATTAAAAAAAATACTATTTAGC
*
33396 CACTTAATTAAAAAAAATACTATTTGGC
1 CACTTAATTAAAAAAAATACTATTTAGC
33424 CACT
1 CACT
33428 AAACTCTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.32
Consensus pattern (28 bp):
CACTTAATTAAAAAAAATACTATTTAGC
Found at i:39709 original size:23 final size:23
Alignment explanation
Indices: 39679--39723 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
39669 CCTTCTGGCA
39679 TAGTACTTAT-ATACTTTTGTTAT
1 TAGTACTT-TGATACTTTTGTTAT
*
39702 TAGTACTTTGGTACTTTTGTTA
1 TAGTACTTTGATACTTTTGTTA
39724 CTATCACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.22, C:0.09, G:0.13, T:0.56
Consensus pattern (23 bp):
TAGTACTTTGATACTTTTGTTAT
Found at i:39735 original size:23 final size:23
Alignment explanation
Indices: 39690--39748 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
39680 AGTACTTATA
* *
39690 TACTTTTGTTATTAGTACTTTGG
1 TACTTTTGTTACTAGTACATTGG
39713 TACTTTTGTTACTA-TCACATTGG
1 TACTTTTGTTACTAGT-ACATTGG
* *
39736 TGCTTTTTTTACT
1 TACTTTTGTTACT
39749 GACACTTCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.56
Consensus pattern (23 bp):
TACTTTTGTTACTAGTACATTGG
Found at i:41961 original size:28 final size:27
Alignment explanation
Indices: 41903--41961 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
41893 CATCTGATAT
* ** *
41903 TGATTCTGTATTGGGCTTAGGCCTTCT
1 TGATTCTGTATTGGGCTAAGGCCCACC
41930 TGATTCTGTTATTGGGCTAAGGCCCACC
1 TGATTCTG-TATTGGGCTAAGGCCCACC
41958 TGAT
1 TGAT
41962 ACTATTTCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.39
Consensus pattern (27 bp):
TGATTCTGTATTGGGCTAAGGCCCACC
Found at i:51988 original size:17 final size:17
Alignment explanation
Indices: 51976--52011 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
51966 AGAGAAATGG
51976 ATCATATTCAGAAATAA
1 ATCATATTCAGAAATAA
51993 ATCATATTCAGAAATAA
1 ATCATATTCAGAAATAA
52010 AT
1 AT
52012 GTGTTTTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.31
Consensus pattern (17 bp):
ATCATATTCAGAAATAA
Found at i:52656 original size:20 final size:20
Alignment explanation
Indices: 52619--52656 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52609 ATAATGAGAA
*
52619 TTTATTTTCTAAGTATAAAT
1 TTTATTTTCTAAGAATAAAT
*
52639 TTTATTTTCTAGGAATAA
1 TTTATTTTCTAAGAATAA
52657 CAATTCTATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (20 bp):
TTTATTTTCTAAGAATAAAT
Found at i:56833 original size:16 final size:16
Alignment explanation
Indices: 56812--56860 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
56802 TTCGCTGTAT
56812 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
**
56828 TGGAATAGAGAAGTAA
1 TGGAATAGAGGCGTAA
56844 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
56860 T
1 T
56861 AGCAAATCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.41, C:0.04, G:0.35, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:60614 original size:19 final size:20
Alignment explanation
Indices: 60592--60632 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
60582 AAGAAGAAAA
60592 TTATATAACATT-AAAAATT
1 TTATATAACATTCAAAAATT
* *
60611 TTATATAATATTCTAAAATT
1 TTATATAACATTCAAAAATT
60631 TT
1 TT
60633 CAATATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATATAACATTCAAAAATT
Found at i:60645 original size:22 final size:20
Alignment explanation
Indices: 60592--60645 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
60582 AAGAAGAAAA
* *
60592 TTATATAACATT-AAAAATT
1 TTATATAAAATTCTAAAATT
*
60611 TTATATAATATTCTAAAATT
1 TTATATAAAATTCTAAAATT
60631 TTCAATATAAAATTC
1 TT--ATATAAAATTC
60646 CATAGAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 11 0.38
20 8 0.28
22 10 0.34
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATATAAAATTCTAAAATT
Found at i:73758 original size:25 final size:25
Alignment explanation
Indices: 73725--73773 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
73715 TGTGAAAAGG
*
73725 GGGTTGCTATGTGCTGATTCCCCGA
1 GGGTTGCTAAGTGCTGATTCCCCGA
*
73750 GGGTTGCTAAGTGTTGATTCCCCG
1 GGGTTGCTAAGTGCTGATTCCCCG
73774 GTTCATTGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.12, C:0.22, G:0.33, T:0.33
Consensus pattern (25 bp):
GGGTTGCTAAGTGCTGATTCCCCGA
Found at i:73859 original size:26 final size:26
Alignment explanation
Indices: 73824--73874 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
73814 AATGTGAAAG
*
73824 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
73850 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
73875 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:73944 original size:102 final size:103
Alignment explanation
Indices: 73645--73951 Score: 516
Period size: 101 Copynumber: 3.0 Consensus size: 103
73635 TTGTATATAA
** *
73645 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGC-ATGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTATGTGCGAT-ATCCACCATATCT
73709 TTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCG
65 TTGAAATGTG-AAAGGGGGTTGCTATGTGCTGATTCCCCG
*
73749 A-GGGTTGCTAAGTGTTGATTCCCCGGTTCATTGGTGGTGCTATGTGCG--ATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTATGTGCGATATCCACCATATCTT
73811 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
*
73849 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGT-GTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTATGTGCGATATCCACCATATCTT
73913 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
73951 A
1 A
73952 TTCAGCTGGT
Statistics
Matches: 193, Mismatches: 6, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
100 41 0.21
101 56 0.29
102 53 0.27
103 42 0.22
104 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTATGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
Done.