Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2289
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: 43217
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:3605 original size:22 final size:22
Alignment explanation
Indices: 3577--3620 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3567 TTTTGAACCA
3577 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
* *
3599 TTACCATTTTGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
3621 AAATACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.34, G:0.05, T:0.36
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:13693 original size:19 final size:19
Alignment explanation
Indices: 13669--13706 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
13659 TGGCTTAGAA
13669 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
13688 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
13707 TTGGCTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
AATGACTCTTGAGTTGTCC
Found at i:20863 original size:19 final size:18
Alignment explanation
Indices: 20827--20866 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
20817 TTTCCACTCG
*
20827 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
20845 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
20864 TTT
1 TTT
20867 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:21939 original size:12 final size:13
Alignment explanation
Indices: 21921--21955 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
21911 AACTAGCTCT
*
21921 TTTTTTTTCACAAT
1 TTTTTTTTCA-AAA
21935 TTTTTTTTCAAAA
1 TTTTTTTTCAAAA
21948 TTTTTTTT
1 TTTTTTTT
21956 TCACAACTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTTTTCAAAA
Found at i:21939 original size:14 final size:14
Alignment explanation
Indices: 21920--21961 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
21910 AAACTAGCTC
21920 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
*
21934 TTTTTTTTTCAAAA
1 TTTTTTTTTCACAA
21948 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
21962 CTTGATATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTTTTTCACAA
Found at i:22017 original size:11 final size:11
Alignment explanation
Indices: 22001--22040 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
21991 GAAACTAGTT
22001 TTTTTTTCGAA
1 TTTTTTTCGAA
*
22012 TTTTTTTTGAA
1 TTTTTTTCGAA
*
22023 TTTTTTTCGAG
1 TTTTTTTCGAA
22034 TTTTTTT
1 TTTTTTT
22041 TCGAGAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.12, C:0.05, G:0.10, T:0.72
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:22017 original size:12 final size:12
Alignment explanation
Indices: 22000--22044 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
21990 GGAAACTAGT
22000 TTTTTTTTCGAA
1 TTTTTTTTCGAA
22012 TTTTTTTT-GAA
1 TTTTTTTTCGAA
*
22023 -TTTTTTTCGAG
1 TTTTTTTTCGAA
22034 TTTTTTTTCGA
1 TTTTTTTTCGA
22045 GAAACTACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 7 0.23
11 5 0.17
12 18 0.60
ACGTcount: A:0.13, C:0.07, G:0.11, T:0.69
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:29247 original size:20 final size:19
Alignment explanation
Indices: 29224--29288 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
29214 AAGCTCAAAC
29224 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
29244 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
29264 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
29284 GAGCT
1 GAGCT
29289 GGGTAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:41126 original size:11 final size:12
Alignment explanation
Indices: 41109--41150 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
41099 TAGTTTCTCG
*
41109 AAAAAAAACTCG
1 AAAAAAAACTCA
*
41121 AAAAAAAATTC-
1 AAAAAAAACTCA
*
41132 AAAAAAAATTCA
1 AAAAAAAACTCA
41144 AAAAAAA
1 AAAAAAA
41151 CTAGTTTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 11 0.39
12 17 0.61
ACGTcount: A:0.76, C:0.10, G:0.02, T:0.12
Consensus pattern (12 bp):
AAAAAAAACTCA
Found at i:41127 original size:13 final size:12
Alignment explanation
Indices: 41105--41152 Score: 64
Period size: 11 Copynumber: 4.2 Consensus size: 12
41095 ATAGTAGTTT
41105 CTCGAAAAAAAA
1 CTCGAAAAAAAA
41117 CTCGAAAAAAAA
1 CTCGAAAAAAAA
*
41129 TTC-AAAAAAAA
1 CTCGAAAAAAAA
*
41140 TTC-AAAAAAAA
1 CTCGAAAAAAAA
41151 CT
1 CT
41153 AGTTTCCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
11 20 0.59
12 14 0.41
ACGTcount: A:0.67, C:0.15, G:0.04, T:0.15
Consensus pattern (12 bp):
CTCGAAAAAAAA
Found at i:41135 original size:10 final size:11
Alignment explanation
Indices: 41109--41150 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
41099 TAGTTTCTCG
*
41109 AAAAAAAACTC
1 AAAAAAAATTC
41120 GAAAAAAAATTC
1 -AAAAAAAATTC
41132 AAAAAAAATTC
1 AAAAAAAATTC
41143 AAAAAAAA
1 AAAAAAAA
41151 CTAGTTTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.76, C:0.10, G:0.02, T:0.12
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:41209 original size:13 final size:13
Alignment explanation
Indices: 41191--41239 Score: 73
Period size: 14 Copynumber: 3.7 Consensus size: 13
41181 TATCAAGTTG
41191 TGAAAAAAAAATT
1 TGAAAAAAAAATT
41204 TGAAAAAAAAAATT
1 TG-AAAAAAAAATT
41218 GTGAAAAAAAAA-T
1 -TGAAAAAAAAATT
41231 TGAAAAAAA
1 TGAAAAAAA
41240 GAGAGAGCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
12 9 0.26
13 3 0.09
14 20 0.59
15 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.18
Consensus pattern (13 bp):
TGAAAAAAAAATT
Found at i:42184 original size:17 final size:17
Alignment explanation
Indices: 42162--42207 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
42152 AAAAGAAACC
42162 GAAAAAGAAACAAAATT-
1 GAAAAAGAAA-AAAATTG
42179 GAAAAAGAGAAAAAATTG
1 GAAAAAGA-AAAAAATTG
*
42197 GAGAAAGAAAA
1 GAAAAAGAAAA
42208 GAAAGAGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.09
Consensus pattern (17 bp):
GAAAAAGAAAAAAATTG
Done.