Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3653
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: 31134
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3679 original size:43 final size:44
Alignment explanation
Indices: 3612--3781 Score: 192
Period size: 43 Copynumber: 3.9 Consensus size: 44
3602 GGCATTACAT
* * *
3612 GATTTCGTATAAGACCATAGCTGGGCTA-TGGCATCAATATATG
1 GATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATATATG
* *
3655 AGATTTTGTGTAA-ACCATATCTGGGATA-TGGCATCGATATATG
1 -GATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATATATG
**
3698 TGATTGCGTGTAAGACCAT-GTCTGGGAC-ATTGGCATCGATATAT-
1 -GATTTTGTGTAAGACCATAG-CTGGG-CTATTGGCATCGATATATG
3742 GA-TTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATAT
1 GATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATAT
3782 GTGATAACAT
Statistics
Matches: 108, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
41 1 0.01
42 32 0.30
43 40 0.37
44 21 0.19
45 14 0.13
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (44 bp):
GATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATATATG
Found at i:3765 original size:42 final size:41
Alignment explanation
Indices: 3610--3786 Score: 173
Period size: 42 Copynumber: 4.1 Consensus size: 41
3600 ATGGCATTAC
* *
3610 ATGATTTCGTATAAGACCATAGCTGGGC-TATGGCATCAATAT
1 ATGATTT-GTGTAAGACCATAGCTGGGCAT-TGGCATCGATAT
*
3652 ATGAGATTTTGTGTAA-ACCATATCTGGG-ATATGGCATCGATAT
1 AT--GA-TTTGTGTAAGACCATAGCTGGGCAT-TGGCATCGATAT
*
3695 ATGTGATTGCGTGTAAGACCAT-GTCTGGGACATTGGCATCGATAT
1 A--TGATT-TGTGTAAGACCATAG-CTGGG-CATTGGCATCGATAT
3740 ATGATTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATAT
1 ATGATTTGTGTAAGACCATAGCTGGGC-ATTGGCATCGATAT
*
3782 GTGAT
1 ATGAT
3787 AACATGTAAG
Statistics
Matches: 115, Mismatches: 7, Indels: 26
0.78 0.05 0.18
Matches are distributed among these distances:
41 1 0.01
42 39 0.34
43 39 0.34
44 17 0.15
45 17 0.15
46 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (41 bp):
ATGATTTGTGTAAGACCATAGCTGGGCATTGGCATCGATAT
Found at i:3774 original size:87 final size:86
Alignment explanation
Indices: 3611--3781 Score: 215
Period size: 87 Copynumber: 2.0 Consensus size: 86
3601 TGGCATTACA
* *
3611 TGATTTCGTATAAGACCATAGCTGGGCTATGGCATCAATATATGAGATTTTGTGTAAACCATATC
1 TGATTGCGTATAAGACCATAGCTGGGCTATGGCATCAATATAT-AGATTTTGTGTAAACCATAGC
3676 TGGGATATGGCATCGATATATG
65 TGGGATATGGCATCGATATATG
* *
3698 TGATTGCGTGTAAGACCAT-GTCTGGGAC-ATTGGCATCGATATAT-GA-TTTGTGTAAGACCAT
1 TGATTGCGTATAAGACCATAG-CTGGG-CTA-TGGCATCAATATATAGATTTTGTGTAA-ACCAT
*
3759 AGCTGGGCTATTGGCATCGATAT
62 AGCTGGGATA-TGGCATCGATAT
3782 GTGATAACAT
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
85 9 0.12
86 16 0.22
87 35 0.47
88 14 0.19
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (86 bp):
TGATTGCGTATAAGACCATAGCTGGGCTATGGCATCAATATATAGATTTTGTGTAAACCATAGCT
GGGATATGGCATCGATATATG
Found at i:3798 original size:85 final size:86
Alignment explanation
Indices: 3640--3798 Score: 207
Period size: 85 Copynumber: 1.8 Consensus size: 86
3630 AGCTGGGCTA
* **
3640 TGGCATCAATATATGAGATTTTGTGTAAACCATATCTGGGATATGGCATCGATATATGTGATTGC
1 TGGCATCAATATAT-AGATTTTGTGTAAACCATAGCTGGGATATGGCATCGA-ATATGTGATAAC
*
3705 GTGTAAGACCATGTCTGGGACAT
64 ATGTAAGACCATGTCTGGGACAT
* *
3728 TGGCATCGATATAT-GA-TTTGTGTAAGACCATAGCTGGGCTATTGGCATCG-ATATGTGATAAC
1 TGGCATCAATATATAGATTTTGTGTAA-ACCATAGCTGGGATA-TGGCATCGAATATGTGATAAC
3790 ATGTAAGAC
64 ATGTAAGAC
3799 TATATCTAGG
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
85 27 0.43
86 15 0.24
87 8 0.13
88 13 0.21
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (86 bp):
TGGCATCAATATATAGATTTTGTGTAAACCATAGCTGGGATATGGCATCGAATATGTGATAACAT
GTAAGACCATGTCTGGGACAT
Found at i:3816 original size:42 final size:42
Alignment explanation
Indices: 3662--3826 Score: 158
Period size: 42 Copynumber: 3.9 Consensus size: 42
3652 ATGAGATTTT
*
3662 GTGTAA-ACCATATCTGGGATA-TGGCATCGATATATGTGATTGC
1 GTGTAAGACCATATCTGGGATATTGGCATCG--ATATGTGA-TAC
* * * **
3705 GTGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTT
1 GTGTAAGACCATATCTGGGATATTGGCATCGATATGTGATAC
* *
3747 GTGTAAGACCATAGCTGGGCTATTGGCATCGATATGTGATAAC
1 GTGTAAGACCATATCTGGGATATTGGCATCGATATGTGAT-AC
* * * *
3790 ATGTAAGACTATATCTAGGATA-TGGCATTG-TATGTGA
1 GTGTAAGACCATATCTGGGATATTGGCATCGATATGTGA
3827 CATACGAGAC
Statistics
Matches: 101, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
41 7 0.07
42 43 0.43
43 30 0.30
44 13 0.13
45 8 0.08
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.32
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGATATTGGCATCGATATGTGATAC
Found at i:7014 original size:38 final size:38
Alignment explanation
Indices: 6972--7103 Score: 167
Period size: 38 Copynumber: 3.3 Consensus size: 38
6962 AAATTAAAAC
**
6972 AAAAATAAAAAATTTTATTTTAAAAATATTTTAAAATTA
1 AAAAATAAAAAA-AGTATTTTAAAAATATTTTAAAATTA
*
7011 AAAAA-AATTAAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAAATAA-AAAAAGTATTTTAAAAATATTTTAAAATT--A
*
7051 AAAAATTAAAAAAAGTATTTTAAAATTATTTTAAAATTTA
1 AAAAA-TAAAAAAAGTATTTTAAAAATATTTTAAAA-TTA
7091 AAAAATAAAAAAA
1 AAAAATAAAAAAA
7104 CAAAAAAAAT
Statistics
Matches: 82, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
38 25 0.30
39 16 0.20
40 12 0.15
41 25 0.30
42 4 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (38 bp):
AAAAATAAAAAAAGTATTTTAAAAATATTTTAAAATTA
Found at i:7570 original size:43 final size:43
Alignment explanation
Indices: 7518--7604 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
7508 TTCATATTTC
* * *
7518 TTTTCTCATCTCATAATCATTTCTTATCTTTTCCATTTCAATA
1 TTTTCTCATCTCATAATCATTTCTCACCTTTGCCATTTCAATA
*
7561 TTTTCTCATCTCATATTCATTTCTCACCTTTGCCATTTCAATA
1 TTTTCTCATCTCATAATCATTTCTCACCTTTGCCATTTCAATA
7604 T
1 T
7605 CAGTCACATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.22, C:0.25, G:0.01, T:0.52
Consensus pattern (43 bp):
TTTTCTCATCTCATAATCATTTCTCACCTTTGCCATTTCAATA
Found at i:8794 original size:24 final size:23
Alignment explanation
Indices: 8762--8816 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
8752 TCATTTCATT
*
8762 TTATATATTTTAGTATAA-ATATTA
1 TTATATA-TTTAATATAACATA-TA
*
8786 TTATTTATTTAATATAACATATA
1 TTATATATTTAATATAACATATA
*
8809 TTAAATAT
1 TTATATAT
8817 ATATACATGC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TTATATATTTAATATAACATATA
Found at i:16961 original size:40 final size:40
Alignment explanation
Indices: 16878--17140 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
16868 TTGAATGCTG
* * * * * *
16878 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
16918 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
16958 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
16998 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
17038 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
17078 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
17117 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
17141 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:17160 original size:79 final size:80
Alignment explanation
Indices: 16917--17175 Score: 238
Period size: 80 Copynumber: 3.3 Consensus size: 80
16907 AAGTGAATAT
* * * * * * *
16917 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAG
** * *
16981 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
16997 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
** ** *
17062 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * * *
17077 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
* *
17141 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
17156 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
17176 TACGTGATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 47 0.31
80 93 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
CGAACGAGGAGCTAA
Found at i:24960 original size:40 final size:40
Alignment explanation
Indices: 24847--24966 Score: 179
Period size: 40 Copynumber: 3.0 Consensus size: 40
24837 AAGTGAATAT
* * * * *
24847 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAA
24887 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
24927 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
24967 GTCCCGAAGG
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
39 1 0.01
40 73 0.99
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
Found at i:24983 original size:25 final size:27
Alignment explanation
Indices: 24934--24991 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
24924 TAAATCCGGG
24934 TTAAGTCCCGAAGGCATTCGTGCGAGTTA
1 TTAAGTCCCGAAGG-A-TCGTGCGAGTTA
*
24963 TTAAGTCCCGAAGG-TCG-GCGAGTTG
1 TTAAGTCCCGAAGGATCGTGCGAGTTA
24988 TTAA
1 TTAA
24992 ATCCGGGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 11 0.39
26 3 0.11
29 14 0.50
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (27 bp):
TTAAGTCCCGAAGGATCGTGCGAGTTA
Found at i:24995 original size:65 final size:66
Alignment explanation
Indices: 24894--25026 Score: 198
Period size: 65 Copynumber: 2.0 Consensus size: 66
24884 TAAATCCGGG
24894 TTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGA
1 TTAAGTCCCGAAGG-A-TCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT-GTGCGA
24959 GTTA
63 GTTA
* * *
24963 TTAAGTCCCGAAGG-TCG-GCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTT
1 TTAAGTCCCGAAGGATCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTT
25026 A
66 A
25027 CTAAAACCGG
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
64 9 0.15
65 35 0.57
66 3 0.05
69 14 0.23
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (66 bp):
TTAAGTCCCGAAGGATCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTT
A
Found at i:26604 original size:17 final size:19
Alignment explanation
Indices: 26582--26619 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
26572 AAGGTGGCAA
26582 TTTTTC-TAT-CACTTCAT
1 TTTTTCTTATGCACTTCAT
26599 TTTTTCTTTATGCACTTCAT
1 TTTTTC-TTATGCACTTCAT
26619 T
1 T
26620 CCTCTCTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
19 3 0.17
20 9 0.50
ACGTcount: A:0.16, C:0.21, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTTTCTTATGCACTTCAT
Done.