Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2607
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: 19739
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Found at i:1648 original size:13 final size:13
Alignment explanation
Indices: 1629--1668 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1619 ACAATTCACC
1629 ATGTATCGATACA
1 ATGTATCGATACA
* * *
1642 TTGTATCAATATA
1 ATGTATCGATACA
1655 ATGTATCGATACA
1 ATGTATCGATACA
1668 A
1 A
1669 AGTGAGTTTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1752 original size:32 final size:33
Alignment explanation
Indices: 1716--1780 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1706 TAATTCGAAT
*
1716 ATGTATCGATACTAAG-AACATGTATCAATACA
1 ATGTATCGACACTAAGCAACATGTATCAATACA
* *
1748 ATGTATCGACACTAAGCAATATGTATCGATACA
1 ATGTATCGACACTAAGCAACATGTATCAATACA
1781 TTCTAGGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
ATGTATCGACACTAAGCAACATGTATCAATACA
Found at i:1859 original size:20 final size:21
Alignment explanation
Indices: 1836--1879 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
1826 GATACTTTGA
1836 ATTATTTTTA-CTTGAAAAAC
1 ATTATTTTTAGCTTGAAAAAC
1856 ATTATTTTTATGCTTGAAAAAC
1 ATTATTTTTA-GCTTGAAAAAC
1878 AT
1 AT
1880 CTATACTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (21 bp):
ATTATTTTTAGCTTGAAAAAC
Found at i:3215 original size:23 final size:22
Alignment explanation
Indices: 3187--3229 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3177 TTTATAATTT
3187 TTTAATTATAAAATTATAAAAAA
1 TTTAATTATAAAATT-TAAAAAA
*
3210 TTTAATTTTAAAATTTAAAA
1 TTTAATTATAAAATTTAAAA
3230 TTTTCAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTAATTATAAAATTTAAAAAA
Found at i:3650 original size:21 final size:21
Alignment explanation
Indices: 3634--3676 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3624 GAATGAAATG
3634 ATGCATTGGTTGGATGAAAAA
1 ATGCATTGGTTGGATGAAAAA
**
3655 ATGCATTTTTTGGATGAAAAA
1 ATGCATTGGTTGGATGAAAAA
3676 A
1 A
3677 GGTAACTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.33
Consensus pattern (21 bp):
ATGCATTGGTTGGATGAAAAA
Found at i:3686 original size:21 final size:21
Alignment explanation
Indices: 3643--3686 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3633 GATGCATTGG
* **
3643 TTGGATGAAAAAATGCATTTT
1 TTGGATGAAAAAAGGCAACTT
*
3664 TTGGATGAAAAAAGGTAACTT
1 TTGGATGAAAAAAGGCAACTT
3685 TT
1 TT
3687 AATAACCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (21 bp):
TTGGATGAAAAAAGGCAACTT
Found at i:4951 original size:13 final size:13
Alignment explanation
Indices: 4933--4957 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4923 CATGCTGCCT
4933 TGTATCGATACAA
1 TGTATCGATACAA
4946 TGTATCGATACA
1 TGTATCGATACA
4958 TGTTCAATGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4957 original size:33 final size:32
Alignment explanation
Indices: 4915--4976 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
4905 CACCCAGATA
**
4915 TATCGATACATGCTGCCTTGTATCGATACAATG
1 TATCGATACATG-TGCAATGTATCGATACAATG
*
4948 TATCGATACATGTTCAATGTATCGATACA
1 TATCGATACATGTGCAATGTATCGATACA
4977 TGGACAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (32 bp):
TATCGATACATGTGCAATGTATCGATACAATG
Found at i:4991 original size:21 final size:19
Alignment explanation
Indices: 4942--4998 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
4932 TTGTATCGAT
*
4942 ACAATGTATCGATACATGT
1 ACAATGTATCGATACATGG
*
4961 TCAATGTATCGATACATGG
1 ACAATGTATCGATACATGG
4980 ACAAATTGTATCGATACAT
1 AC-AA-TGTATCGATACAT
4999 AAAACTGGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.55
20 2 0.06
21 13 0.39
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
ACAATGTATCGATACATGG
Found at i:5064 original size:13 final size:13
Alignment explanation
Indices: 5043--5073 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5033 CGATACATGG
*
5043 TACAATGTATCGA
1 TACATTGTATCGA
5056 TACATTGTATCGA
1 TACATTGTATCGA
5069 TACAT
1 TACAT
5074 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:5069 original size:33 final size:32
Alignment explanation
Indices: 5027--5090 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 32
5017 CCTATCACTT
5027 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
5060 TTGTATCGATACATGAAGAAATGTATCGATA
1 TTGTATCGATACATG-AGAAATGTATCGATA
5091 AATAGCTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:10490 original size:18 final size:18
Alignment explanation
Indices: 10469--10503 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10459 TCCAAGTCAC
10469 CATCATCATCATCATTGT
1 CATCATCATCATCATTGT
*
10487 CATCTTCATCATCATTG
1 CATCATCATCATCATTG
10504 ATGGTTGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.40
Consensus pattern (18 bp):
CATCATCATCATCATTGT
Found at i:12189 original size:20 final size:20
Alignment explanation
Indices: 12164--12223 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
12154 CTGCCAGTTT
*
12164 CATGTATTGATATAATTATC
1 CATGTATCGATATAATTATC
* *
12184 CATGTATCGATACAATGAT-
1 CATGTATCGATATAATTATC
12203 CATGTATCGATATAATGTATC
1 CATGTATCGATATAAT-TATC
12224 GATACAAAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (20 bp):
CATGTATCGATATAATTATC
Found at i:12208 original size:19 final size:19
Alignment explanation
Indices: 12163--12219 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
12153 ACTGCCAGTT
* *
12163 TCATGTATTGATATAATTA
1 TCATGTATCGATATAATGA
*
12182 TCCATGTATCGATACAATGA
1 T-CATGTATCGATATAATGA
12202 TCATGTATCGATATAATG
1 TCATGTATCGATATAATG
12220 TATCGATACA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (19 bp):
TCATGTATCGATATAATGA
Found at i:12221 original size:32 final size:33
Alignment explanation
Indices: 12185--12247 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
12175 ATAATTATCC
* *
12185 ATGTATCGATACAATG-ATCATGTATCGATATA
1 ATGTATCGATACAAAGCATAATGTATCGATATA
12217 ATGTATCGATACAAAGCATAATGTATCGATA
1 ATGTATCGATACAAAGCATAATGTATCGATA
12248 CATCTGGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATATA
Found at i:13799 original size:15 final size:15
Alignment explanation
Indices: 13779--13811 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
13769 TTATATTATC
13779 ATAAGGATTCCACCT
1 ATAAGGATTCCACCT
13794 ATAAGGATTCCACCT
1 ATAAGGATTCCACCT
13809 ATA
1 ATA
13812 TGAATATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.27
Consensus pattern (15 bp):
ATAAGGATTCCACCT
Found at i:14167 original size:12 final size:12
Alignment explanation
Indices: 14150--14178 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
14140 TTAACCAGAT
14150 AAATGTTATCAA
1 AAATGTTATCAA
14162 AAATGTTATCAA
1 AAATGTTATCAA
14174 AAATG
1 AAATG
14179 CAATTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (12 bp):
AAATGTTATCAA
Found at i:14962 original size:2 final size:2
Alignment explanation
Indices: 14955--14988 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
14945 TTGTTTGCAA
14955 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14989 TAGAAAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15187 original size:25 final size:25
Alignment explanation
Indices: 15141--15202 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
15131 TTTATTAATT
* *
15141 TTTAATTCATTACTTTTTAATACATA
1 TTTAA-TCATTACTTTTAAATACAAA
*
15167 TTTAATCATTA-TTTATAAATATAAA
1 TTTAATCATTACTTT-TAAATACAAA
*
15192 TTTAATAATTA
1 TTTAATCATTA
15203 ATAAATGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 3 0.10
25 23 0.74
26 5 0.16
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTAATCATTACTTTTAAATACAAA
Found at i:18225 original size:2 final size:2
Alignment explanation
Indices: 18213--18257 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
18203 CAGGGGAAAA
*
18213 AG AG GG AG AG AG AG AG -G AG AG -G AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
18253 AG AG A
1 AG AG A
18258 AATGCAAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19590 original size:15 final size:15
Alignment explanation
Indices: 19570--19610 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
19560 TTATATTTTT
*
19570 TATTAAATTTAATAA
1 TATTAAATATAATAA
*
19585 TATTAAATATAATTA
1 TATTAAATATAATAA
19600 TATT-AATATAA
1 TATTAAATATAA
19611 CATACATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TATTAAATATAATAA
Done.