Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009484.1 Corchorus capsularis cultivar CVL-1 contig09505, whole genome shotgun sequence
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: 35088
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3903 original size:15 final size:16
Alignment explanation
Indices: 3883--3912 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3873 TTAATTGATT
3883 TCTTAGTTA-ATTTAC
1 TCTTAGTTAGATTTAC
3898 TCTTAGTTAGATTTA
1 TCTTAGTTAGATTTA
3913 ATTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.53
Consensus pattern (16 bp):
TCTTAGTTAGATTTAC
Found at i:10460 original size:24 final size:24
Alignment explanation
Indices: 10428--10475 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
10418 ATATATTTTG
10428 AACATTAAAAGGCCACCCTAAAGT
1 AACATTAAAAGGCCACCCTAAAGT
10452 AACATTAAAAGGCCACCCTAAAGT
1 AACATTAAAAGGCCACCCTAAAGT
10476 TTATAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.25, G:0.12, T:0.17
Consensus pattern (24 bp):
AACATTAAAAGGCCACCCTAAAGT
Found at i:10632 original size:17 final size:17
Alignment explanation
Indices: 10610--10645 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
10600 GTTACGGAAT
10610 TTTTTCATT-TTTTTTTC
1 TTTTTC-TTCTTTTTTTC
10627 TTTTTCTTCTTTTTTTC
1 TTTTTCTTCTTTTTTTC
10644 TT
1 TT
10646 CAATCATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 16 0.89
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTCTTTTTTTC
Found at i:10765 original size:33 final size:33
Alignment explanation
Indices: 10723--10794 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
10713 ATGTGAATAC
10723 GGGACTCCTTGTGAGAGCTTTTGTATTGTCTTT
1 GGGACTCCTTGTGAGAGCTTTTGTATTGTCTTT
10756 GGGACTCCTTGTGAGAGCTTTTGTATTGTCTTT
1 GGGACTCCTTGTGAGAGCTTTTGTATTGTCTTT
10789 GGGACT
1 GGGACT
10795 GTACAATCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.12, C:0.15, G:0.29, T:0.43
Consensus pattern (33 bp):
GGGACTCCTTGTGAGAGCTTTTGTATTGTCTTT
Found at i:14236 original size:3 final size:3
Alignment explanation
Indices: 14228--14257 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
14218 CCCATTGCTA
*
14228 CTT CTT CTT CTT CTT CTT CTT GTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
14258 GTTCCCCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.30, G:0.03, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:14258 original size:9 final size:9
Alignment explanation
Indices: 14232--14261 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
14222 TTGCTACTTC
*
14232 TTCTTCTTC
1 TTCTTCTTG
14241 TTCTTCTTG
1 TTCTTCTTG
14250 TTCTTCTTG
1 TTCTTCTTG
14259 TTC
1 TTC
14262 CCCTGTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.27, G:0.07, T:0.67
Consensus pattern (9 bp):
TTCTTCTTG
Found at i:17606 original size:56 final size:56
Alignment explanation
Indices: 17539--17651 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
17529 GTGTAATAGA
17539 ATACTTGTTAAACAACATCAATGGAAACTTCAAAAGAATGTCATCCTTGTCCCCAC
1 ATACTTGTTAAACAACATCAATGGAAACTTCAAAAGAATGTCATCCTTGTCCCCAC
*
17595 ATACTTGTTAAACAACATCAATGGAAACTTCAATAGAATGTCATCCTTGTCCCCAC
1 ATACTTGTTAAACAACATCAATGGAAACTTCAAAAGAATGTCATCCTTGTCCCCAC
17651 A
1 A
17652 GAGCACATTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (56 bp):
ATACTTGTTAAACAACATCAATGGAAACTTCAAAAGAATGTCATCCTTGTCCCCAC
Found at i:25214 original size:7 final size:7
Alignment explanation
Indices: 25202--25230 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
25192 AAACATTGCC
25202 CAAAAAA
1 CAAAAAA
25209 CAAAAAA
1 CAAAAAA
25216 C-AAAAA
1 CAAAAAA
25222 CAAAAAA
1 CAAAAAA
25229 CA
1 CA
25231 TTGCTAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (7 bp):
CAAAAAA
Found at i:25220 original size:13 final size:13
Alignment explanation
Indices: 25204--25230 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25194 ACATTGCCCA
25204 AAAAACAAAAAAC
1 AAAAACAAAAAAC
25217 AAAAACAAAAAAC
1 AAAAACAAAAAAC
25230 A
1 A
25231 TTGCTAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAAAC
Found at i:33691 original size:31 final size:31
Alignment explanation
Indices: 33656--33721 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
33646 AACTTTATGT
*
33656 TTTCCGATTGTACCCTTATT-TTTAAAACATA
1 TTTCCAATTGTACCCTT-TTCTTTAAAACATA
*
33687 TTTCCAATTGTACCGTTTTCTTTAAAACATA
1 TTTCCAATTGTACCCTTTTCTTTAAAACATA
33718 TTTC
1 TTTC
33722 TAAATTGTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTCTTTAAAACATA
Done.