Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008886.1 Corchorus capsularis cultivar CVL-1 contig08907, 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: 45081
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:7809 original size:31 final size:31
Alignment explanation
Indices: 7740--7880 Score: 147
Period size: 31 Copynumber: 4.5 Consensus size: 31
7730 TCCTTTTGTG
* * * **
7740 CACGTGGCATGCGACATGTCACATTTTGAAA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * *
7771 CATGTGGCATGCCACGTGTCGCTTTTTAGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * *
7802 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* ** *
7833 CAGGTGGTGTGCCACATGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
7864 CACGTGGCATGCCACGT
1 CACGTGGCATGCCACGT
7881 CGGATACCGT
Statistics
Matches: 87, Mismatches: 23, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 87 1.00
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.31
Consensus pattern (31 bp):
CACGTGGCATGCCACGTGTCACTTTTTGGTA
Found at i:14220 original size:31 final size:30
Alignment explanation
Indices: 14177--14254 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
14167 GCTTATTGCT
*
14177 CAAAAAAGCCCCTGAACTTACACAAAACGGC
1 CAAATAAGCCCCTGAACTTACA-AAAACGGC
* * ***
14208 CAATTAAGCCCCTGAA-TTATAATTGCGGC
1 CAAATAAGCCCCTGAACTTACAAAAACGGC
14237 CAAATAAGCCCCTGAACT
1 CAAATAAGCCCCTGAACT
14255 CTTAAAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 20 0.51
30 5 0.13
31 14 0.36
ACGTcount: A:0.38, C:0.29, G:0.14, T:0.18
Consensus pattern (30 bp):
CAAATAAGCCCCTGAACTTACAAAAACGGC
Found at i:20866 original size:21 final size:22
Alignment explanation
Indices: 20842--20882 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
20832 TTAAATAAAT
20842 AATCTG-ACATACCAAAATTGA
1 AATCTGCACATACCAAAATTGA
**
20863 AATCTGCACATTGCAAAATT
1 AATCTGCACATACCAAAATT
20883 TGCAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.27
Consensus pattern (22 bp):
AATCTGCACATACCAAAATTGA
Found at i:24404 original size:27 final size:27
Alignment explanation
Indices: 24366--24420 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
24356 GACTAATTTG
24366 TTTTTATACATTTTTACTTCAGAGAGC
1 TTTTTATACATTTTTACTTCAGAGAGC
24393 TTTTTATACATTTTTACTTCAGAGAGC
1 TTTTTATACATTTTTACTTCAGAGAGC
24420 T
1 T
24421 GATCAGTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.49
Consensus pattern (27 bp):
TTTTTATACATTTTTACTTCAGAGAGC
Found at i:31759 original size:16 final size:17
Alignment explanation
Indices: 31738--31795 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 17
31728 ATGTCCATAC
*
31738 ATTATTTTAAT-TTTTT
1 ATTATTTTAATATTTTA
*
31754 ATTATTTTAGTATTTTA
1 ATTATTTTAATATTTTA
* *
31771 ATTATTCTAA-A-CTTA
1 ATTATTTTAATATTTTA
31786 ATTATTTTAA
1 ATTATTTTAA
31796 GGGTGATTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
15 12 0.34
16 11 0.31
17 12 0.34
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (17 bp):
ATTATTTTAATATTTTA
Found at i:33383 original size:17 final size:16
Alignment explanation
Indices: 33327--33379 Score: 70
Period size: 17 Copynumber: 3.2 Consensus size: 16
33317 GAATCACCCC
*
33327 CAAGATCACTAGTGAT
1 CAAGATCACCAGTGAT
33343 CTAAGATCACCAGTGAT
1 C-AAGATCACCAGTGAT
*
33360 GCAAGATCACCGGTGAT
1 -CAAGATCACCAGTGAT
33377 CAA
1 CAA
33380 AGATTACATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 4 0.12
17 28 0.85
18 1 0.03
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (16 bp):
CAAGATCACCAGTGAT
Found at i:34979 original size:36 final size:36
Alignment explanation
Indices: 34930--35008 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
34920 GTGTAATATC
* *
34930 TATGTAATCTTGTTATCTTTGACAATGTGGATGCTT
1 TATGTAATATTGTTATATTTGACAATGTGGATGCTT
34966 TATGTAATATTGTTATATTTGACAATGTGGATGCTT
1 TATGTAATATTGTTATATTTGACAATGTGGATGCTT
35002 TATGTAA
1 TATGTAA
35009 ATGTTTACTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.47
Consensus pattern (36 bp):
TATGTAATATTGTTATATTTGACAATGTGGATGCTT
Found at i:35754 original size:18 final size:18
Alignment explanation
Indices: 35731--35765 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35721 ATGAAGAGTG
*
35731 TCAAATTGAGGCAGTGGT
1 TCAAATTGAGGAAGTGGT
35749 TCAAATTGAGGAAGTGG
1 TCAAATTGAGGAAGTGG
35766 ATTAGTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TCAAATTGAGGAAGTGGT
Found at i:35803 original size:20 final size:20
Alignment explanation
Indices: 35780--35823 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
35770 GTTATAGGTC
**
35780 ATGGCTTTAGGGTTTAGGAA
1 ATGGCTTTAGGAATTAGGAA
35800 ATGGCTTTAGGAATTAGGAA
1 ATGGCTTTAGGAATTAGGAA
35820 ATGG
1 ATGG
35824 GTATTGTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.32
Consensus pattern (20 bp):
ATGGCTTTAGGAATTAGGAA
Found at i:42357 original size:62 final size:62
Alignment explanation
Indices: 42268--42390 Score: 192
Period size: 62 Copynumber: 2.0 Consensus size: 62
42258 CGTTATTATC
*
42268 GTGTCCAAGTAATAGAACACAAACAAAAATTTGTTCAATTACCGTGTTTAACTAACATAAAG
1 GTGTCCAAGTAATAGAACACAAACAAAAATTTGTTCAATTACCGTGTTTAACTAAAATAAAG
* * * * *
42330 GTGTCCAAGTGATTGAACTCAAGCAAAAATTTGTTCAATTACCTTGTTTAACTAAAATAAA
1 GTGTCCAAGTAATAGAACACAAACAAAAATTTGTTCAATTACCGTGTTTAACTAAAATAAA
42391 AATGTCTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (62 bp):
GTGTCCAAGTAATAGAACACAAACAAAAATTTGTTCAATTACCGTGTTTAACTAAAATAAAG
Found at i:44476 original size:69 final size:68
Alignment explanation
Indices: 44360--44498 Score: 251
Period size: 69 Copynumber: 2.0 Consensus size: 68
44350 AGGTTGTTGC
*
44360 TTTTAAAATGTTTATGCTTTTCTTAATATAGCTTTGAGTAATTGAGAGCTCTTGAAGCAAAAGTA
1 TTTTAAAATGTTTATGCTTTTCTTAATACAGCTTTGAGTAATTGAGAGCTCTTGAAGCAAAAGTA
44425 TTAT
66 -TAT
*
44429 TTTTGAAATGTTTATGCTTTTCTTAATACAGCTTTGAGTAATTGAGAGCTCTTGAAGCAAAAGTA
1 TTTTAAAATGTTTATGCTTTTCTTAATACAGCTTTGAGTAATTGAGAGCTCTTGAAGCAAAAGTA
44494 TAT
66 TAT
44497 TT
1 TT
44499 GCATACATTT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
68 5 0.07
69 63 0.93
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (68 bp):
TTTTAAAATGTTTATGCTTTTCTTAATACAGCTTTGAGTAATTGAGAGCTCTTGAAGCAAAAGTA
TAT
Done.