Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007270.1 Corchorus capsularis cultivar CVL-1 contig07291, 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: 45324
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:263 original size:10 final size:10
Alignment explanation
Indices: 248--274 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
238 AGTTTGAAGG
248 TTGAGAGAAT
1 TTGAGAGAAT
258 TTGAGAGAAT
1 TTGAGAGAAT
268 TTGAGAG
1 TTGAGAG
275 TTTAAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (10 bp):
TTGAGAGAAT
Found at i:495 original size:2 final size:2
Alignment explanation
Indices: 490--520 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
480 CAGTGGGAAG
490 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
521 GTTGAAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1305 original size:1 final size:1
Alignment explanation
Indices: 1299--1326 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1289 CTGTCACGAT
1299 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1327 CAAGTCATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:8040 original size:12 final size:12
Alignment explanation
Indices: 8008--8047 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
7998 ATACAGGTAA
8008 CGACGGATATAT
1 CGACGGATATAT
8020 CGAACGGATATAT
1 CG-ACGGATATAT
8033 CGACGGATATAT
1 CGACGGATATAT
8045 CGA
1 CGA
8048 GGTATCGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (12 bp):
CGACGGATATAT
Found at i:9498 original size:10 final size:10
Alignment explanation
Indices: 9483--9508 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
9473 AATTTAATAT
9483 GGATATTTAC
1 GGATATTTAC
9493 GGATATTTAC
1 GGATATTTAC
9503 GGATAT
1 GGATAT
9509 ATCGAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Found at i:9636 original size:12 final size:12
Alignment explanation
Indices: 9619--9657 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
9609 GTACAGATAT
9619 CGGATATATCGA
1 CGGATATATCGA
9631 CGGATATATCGA
1 CGGATATATCGA
9643 -GG---TATCGA
1 CGGATATATCGA
9651 CGGATAT
1 CGGATAT
9658 TTAATTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Found at i:14935 original size:22 final size:22
Alignment explanation
Indices: 14890--14960 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 22
14880 TGAAAAGAGT
*
14890 TTAAAATTAAATCT-AGTAAACAA
1 TTAAAATT-AAT-TAAGAAAACAA
14913 TTAAAATTAATTAAGAAAACAA
1 TTAAAATTAATTAAGAAAACAA
*
14935 TTAAAA-AAATTAAAGAAAACAA
1 TTAAAATTAATT-AAGAAAACAA
14957 TTAA
1 TTAA
14961 TTAAAAAGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
21 5 0.11
22 31 0.70
23 8 0.18
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (22 bp):
TTAAAATTAATTAAGAAAACAA
Found at i:14958 original size:13 final size:12
Alignment explanation
Indices: 14921--14960 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
14911 AATTAAAATT
14921 AATTAAGAAAAC
1 AATTAAGAAAAC
14933 AATT-A-AAAA-
1 AATTAAGAAAAC
14942 AATTAAAGAAAAC
1 AATT-AAGAAAAC
14955 AATTAA
1 AATTAA
14961 TTAAAAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 4 0.17
10 4 0.17
11 2 0.08
12 10 0.42
13 4 0.17
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (12 bp):
AATTAAGAAAAC
Found at i:14966 original size:13 final size:13
Alignment explanation
Indices: 14915--14967 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
14905 GTAAACAATT
*
14915 AAAATTAATTAAG
1 AAAATTAATTAAA
*
14928 AAAA-CAATTAAA
1 AAAATTAATTAAA
**
14940 AAAATTAAAGAAA
1 AAAATTAATTAAA
*
14953 ACAATTAATTAAA
1 AAAATTAATTAAA
14966 AA
1 AA
14968 GCAGAGAATA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (13 bp):
AAAATTAATTAAA
Found at i:17642 original size:2 final size:2
Alignment explanation
Indices: 17635--17663 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17625 ATACTATCAA
17635 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17664 ATAAGTTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18046 original size:20 final size:20
Alignment explanation
Indices: 18021--18061 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
18011 AAAATCTTGA
18021 TTACTAAACACCGCCCCCTT
1 TTACTAAACACCGCCCCCTT
*
18041 TTACTAACCACCGCCCCCTT
1 TTACTAAACACCGCCCCCTT
18061 T
1 T
18062 GAATTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.46, G:0.05, T:0.27
Consensus pattern (20 bp):
TTACTAAACACCGCCCCCTT
Found at i:19739 original size:2 final size:2
Alignment explanation
Indices: 19734--19763 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19724 ACACACACAC
19734 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
19764 GTAGAGACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25568 original size:19 final size:20
Alignment explanation
Indices: 25550--25585 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
25540 AATTAATTAT
25550 TTTA-ATATTA-ATTTTTTA
1 TTTATATATTATATTTTTTA
25568 TTTATATATTATATTTTT
1 TTTATATATTATATTTTT
25586 ACTTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 6 0.38
20 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATATATTATATTTTTTA
Found at i:34154 original size:17 final size:18
Alignment explanation
Indices: 34121--34154 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
34111 AAATTTATGG
*
34121 ATGTTTGATGTTGGTTTT
1 ATGTTTGATGATGGTTTT
34139 ATGTTT-ATGATGGTTT
1 ATGTTTGATGATGGTTT
34155 GGGGTTGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (18 bp):
ATGTTTGATGATGGTTTT
Found at i:35116 original size:27 final size:27
Alignment explanation
Indices: 35045--35119 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 27
35035 TCCCTTTTGG
* *
35045 GTAAAAATACAA-TGTTACCCTCGATTA
1 GTAAAATTACAACT-TTACCCTCGATGA
* *
35072 GTGAAAATTACCATTTTACCCTCGAATGA
1 GT-AAAATTACAACTTTACCCTCG-ATGA
35101 GT-AAATTACAACTTTACCC
1 GTAAAATTACAACTTTACCC
35120 CTAGGAAAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 17 0.43
28 17 0.43
29 6 0.15
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (27 bp):
GTAAAATTACAACTTTACCCTCGATGA
Done.