Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012344.1 Corchorus capsularis cultivar CVL-1 contig12365, 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: 17675
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Found at i:402 original size:120 final size:120
Alignment explanation
Indices: 180--661 Score: 724
Period size: 120 Copynumber: 4.1 Consensus size: 120
170 AAGCCCACTG
** * * * *
180 TGATGAAACCTGCGGTGTTTGATAATGGTTTGATGAAACCTAGGGTTCAACATGGACCGATGATG
1 TGATGAAACCTGATGTGTTTGAAAATGGTTTGATGAAACCCAGAGTTCGACATGGACCGATGATG
* * *
245 ATGAAACCCATGGTTCGACATGGACCAATAATAAAACCCACGGTTGGACATGGGA
66 ATGAAATCCATGGTTCGACATGGACCAATGATGAAACCCACGGTTGGACATGGGA
* * * *
300 TGATGAAACTTGATATGTTTGAAAATGGTTTGATGAAACCCAGAGTTCGACATAGACCGATGACG
1 TGATGAAACCTGATGTGTTTGAAAATGGTTTGATGAAACCCAGAGTTCGACATGGACCGATGATG
* * ** *
365 ATGAAATTCACGGTTCGGTATGGACCGATGATGAAACCCACGGTTGGACATGGGA
66 ATGAAATCCATGGTTCGACATGGACCAATGATGAAACCCACGGTTGGACATGGGA
420 TGATGAAACCTGATGTGTTTGAAAATGGTTTGATGAAACCCAGAGTTCGACATGGACCGATGATG
1 TGATGAAACCTGATGTGTTTGAAAATGGTTTGATGAAACCCAGAGTTCGACATGGACCGATGATG
*
485 ATGAAATCCATGGTTCGACATGGACC---GAT---ACCCATGGTTGGACATGGGA
66 ATGAAATCCATGGTTCGACATGGACCAATGATGAAACCCACGGTTGGACATGGGA
534 TGATGAAACCTGATGTGTTTGAAAATGGTTTGATGAAACCCAGAGTTCGACATGGACCGATGATG
1 TGATGAAACCTGATGTGTTTGAAAATGGTTTGATGAAACCCAGAGTTCGACATGGACCGATGATG
** *
599 ATGAAATCCATGGTTCGACATGTTCCAATGATGAAACCCACGGTTGGACATGAGA
66 ATGAAATCCATGGTTCGACATGGACCAATGATGAAACCCACGGTTGGACATGGGA
654 TGATGAAA
1 TGATGAAA
662 TTTGAAAACG
Statistics
Matches: 325, Mismatches: 31, Indels: 12
0.88 0.08 0.03
Matches are distributed among these distances:
114 108 0.33
117 6 0.02
120 211 0.65
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (120 bp):
TGATGAAACCTGATGTGTTTGAAAATGGTTTGATGAAACCCAGAGTTCGACATGGACCGATGATG
ATGAAATCCATGGTTCGACATGGACCAATGATGAAACCCACGGTTGGACATGGGA
Found at i:487 original size:33 final size:33
Alignment explanation
Indices: 450--513 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
440 GAAAATGGTT
450 TGATGAAACCCA-GAGTTCGACATGGACCGATGA
1 TGATGAAACCCATG-GTTCGACATGGACCGATGA
*
483 TGATGAAATCCATGGTTCGACATGGACCGAT
1 TGATGAAACCCATGGTTCGACATGGACCGAT
514 ACCCATGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (33 bp):
TGATGAAACCCATGGTTCGACATGGACCGATGA
Found at i:596 original size:57 final size:57
Alignment explanation
Indices: 278--596 Score: 153
Period size: 57 Copynumber: 5.5 Consensus size: 57
268 ACCAATAATA
* * * *
278 AAACCCACGGTTGGACATGGGATGATGAAACTTGATATGTTTGAAAATGGTTTGATG
1 AAACCCACGGTTCGACATGGGACGATGAAACCTGATGTGTTTGAAAATGGTTTGATG
* * * * ** **
335 AAACCCA-GAGTTCGACATAGACCGATGACGATGAAA-TTCACG-GTTCG-GTATGGACCGATGA
1 AAACCCACG-GTTCGACAT-G---G--GACGATGAAACCTGATGTGTTTGAAAATGG---TTTGA
396 TG
56 TG
* *
398 AAACCCACGGTTGGACATGGGATGATGAAACCTGATGTGTTTGAAAATGGTTTGATG
1 AAACCCACGGTTCGACATGGGACGATGAAACCTGATGTGTTTGAAAATGGTTTGATG
* * * ***
455 AAACCCA-GAGTTCGACATGGACCGATGATGATGAAATCC--ATG-GTTCG-ACATGGACCGAT-
1 AAACCCACG-GTTCGACAT-G---G--GACGATGAAA-CCTGATGTGTTTGAAAATGGTTTGATG
* * *
514 --ACCCATGGTTGGACATGGGATGATGAAACCTGATGTGTTTGAAAATGGTTTGATG
1 AAACCCACGGTTCGACATGGGACGATGAAACCTGATGTGTTTGAAAATGGTTTGATG
569 AAACCCA-GAGTTCGACAT-GGACCGATGA
1 AAACCCACG-GTTCGACATGGGA-CGATGA
597 TGATGAAATC
Statistics
Matches: 196, Mismatches: 34, Indels: 64
0.67 0.12 0.22
Matches are distributed among these distances:
50 2 0.01
51 10 0.05
52 3 0.02
53 5 0.03
54 8 0.04
56 7 0.04
57 75 0.38
58 6 0.03
59 5 0.03
60 16 0.08
61 10 0.05
62 7 0.04
63 39 0.20
64 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (57 bp):
AAACCCACGGTTCGACATGGGACGATGAAACCTGATGTGTTTGAAAATGGTTTGATG
Found at i:605 original size:234 final size:236
Alignment explanation
Indices: 180--661 Score: 725
Period size: 234 Copynumber: 2.0 Consensus size: 236
170 AAGCCCACTG
* * * *
180 TGATGAAACCTGCGGTGTTTGATAATGGTTTGATGAAACCTAGGGTTCAACATGGACCGATGATG
1 TGATGAAACCTGAGGTGTTTGAAAATGGTTTGATGAAACCCAGAGTTCAACATGGACCGATGATG
*
245 ATGAAACCCATGGTTCGACATGGACCAATAATAAAACCCACGGTTGGACATGGGATGATGAAACT
66 ATGAAACCCATGGTTCGACATGGACC-A-AAT--AACCCACGGTTGGACATGGGATGATGAAACC
*
310 TGATATGTTTGAAAATGGTTTGATGAAACCCAGAGTTCGACATAGACCGATGACGATGAAATTCA
127 TGATATGTTTGAAAATGGTTTGATGAAACCCAGAGTTCGACATAGACCGATGACGATGAAATCCA
** * *
375 CGGTTCGGTATGGACCGATGATGAAACCCACGGTTGGACATGGGA
192 CGGTTCGACATGGACCAATGATGAAACCCACGGTTGGACATGAGA
* *
420 TGATGAAACCTGATGTGTTTGAAAATGGTTTGATGAAACCCAGAGTTCGACATGGACCGATGATG
1 TGATGAAACCTGAGGTGTTTGAAAATGGTTTGATGAAACCCAGAGTTCAACATGGACCGATGATG
* * *
485 ATGAAATCCATGGTTCGACATGGACC-GAT-ACCCATGGTTGGACATGGGATGATGAAACCTGAT
66 ATGAAACCCATGGTTCGACATGGACCAAATAACCCACGGTTGGACATGGGATGATGAAACCTGAT
* * * *
548 GTGTTTGAAAATGGTTTGATGAAACCCAGAGTTCGACATGGACCGATGATGATGAAATCCATGGT
131 ATGTTTGAAAATGGTTTGATGAAACCCAGAGTTCGACATAGACCGATGACGATGAAATCCACGGT
**
613 TCGACATGTTCCAATGATGAAACCCACGGTTGGACATGAGA
196 TCGACATGGACCAATGATGAAACCCACGGTTGGACATGAGA
654 TGATGAAA
1 TGATGAAA
662 TTTGAAAACG
Statistics
Matches: 221, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
234 135 0.61
237 2 0.01
240 84 0.38
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (236 bp):
TGATGAAACCTGAGGTGTTTGAAAATGGTTTGATGAAACCCAGAGTTCAACATGGACCGATGATG
ATGAAACCCATGGTTCGACATGGACCAAATAACCCACGGTTGGACATGGGATGATGAAACCTGAT
ATGTTTGAAAATGGTTTGATGAAACCCAGAGTTCGACATAGACCGATGACGATGAAATCCACGGT
TCGACATGGACCAATGATGAAACCCACGGTTGGACATGAGA
Found at i:630 original size:33 final size:33
Alignment explanation
Indices: 564--632 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
554 GAAAATGGTT
*
564 TGATGAAACCCAGAGTTCGACATGGACCGATGA
1 TGATGAAACCCAGAGTTCGACATGGACCAATGA
* **
597 TGATGAAATCCATG-GTTCGACATGTTCCAATGA
1 TGATGAAACCCA-GAGTTCGACATGGACCAATGA
630 TGA
1 TGA
633 AACCCACGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (33 bp):
TGATGAAACCCAGAGTTCGACATGGACCAATGA
Found at i:1948 original size:2 final size:2
Alignment explanation
Indices: 1941--1965 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1931 ATATAATGAA
1941 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 A
1966 ATTCATAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11159 original size:13 final size:13
Alignment explanation
Indices: 11141--11165 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11131 CGGACCCAAC
11141 AAAAATGGACTGG
1 AAAAATGGACTGG
11154 AAAAATGGACTG
1 AAAAATGGACTG
11166 AAGAAGGAAA
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:0.48, C:0.08, G:0.28, T:0.16
Consensus pattern (13 bp):
AAAAATGGACTGG
Found at i:13467 original size:2 final size:2
Alignment explanation
Indices: 13454--13485 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
13444 TATTCAAATA
13454 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A
13486 CACACATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:14409 original size:86 final size:86
Alignment explanation
Indices: 14264--14438 Score: 350
Period size: 86 Copynumber: 2.0 Consensus size: 86
14254 ATATTTCTTA
14264 TAACTTTCATAACCTTTCATTAGTGATGAAGAAAGTTACTAATATTCTTATTCAATGTTACTAAA
1 TAACTTTCATAACCTTTCATTAGTGATGAAGAAAGTTACTAATATTCTTATTCAATGTTACTAAA
14329 AATGCAGTTATTCAAGGTTAC
66 AATGCAGTTATTCAAGGTTAC
14350 TAACTTTCATAACCTTTCATTAGTGATGAAGAAAGTTACTAATATTCTTATTCAATGTTACTAAA
1 TAACTTTCATAACCTTTCATTAGTGATGAAGAAAGTTACTAATATTCTTATTCAATGTTACTAAA
14415 AATGCAGTTATTCAAGGTTAC
66 AATGCAGTTATTCAAGGTTAC
14436 TAA
1 TAA
14439 AAAATGCAGT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 89 1.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (86 bp):
TAACTTTCATAACCTTTCATTAGTGATGAAGAAAGTTACTAATATTCTTATTCAATGTTACTAAA
AATGCAGTTATTCAAGGTTAC
Found at i:14429 original size:25 final size:26
Alignment explanation
Indices: 14397--14449 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 26
14387 ACTAATATTC
*
14397 TTATTCAATGTTACT-AAAAATGCAG
1 TTATTCAAGGTTACTAAAAAATGCAG
14422 TTATTCAAGGTTACTAAAAAATGCAG
1 TTATTCAAGGTTACTAAAAAATGCAG
14448 TT
1 TT
14450 GTTATTAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (26 bp):
TTATTCAAGGTTACTAAAAAATGCAG
Done.