Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006671.1 Corchorus capsularis cultivar CVL-1 contig06692, 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: 40370
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:2598 original size:44 final size:44
Alignment explanation
Indices: 2535--2626 Score: 184
Period size: 44 Copynumber: 2.1 Consensus size: 44
2525 TATTCTTTCC
2535 AAAATTATCCCATTTAAAGTGTATGGAAAGTTGGAGTACAAAAT
1 AAAATTATCCCATTTAAAGTGTATGGAAAGTTGGAGTACAAAAT
2579 AAAATTATCCCATTTAAAGTGTATGGAAAGTTGGAGTACAAAAT
1 AAAATTATCCCATTTAAAGTGTATGGAAAGTTGGAGTACAAAAT
2623 AAAA
1 AAAA
2627 GAGGAGAGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (44 bp):
AAAATTATCCCATTTAAAGTGTATGGAAAGTTGGAGTACAAAAT
Found at i:7877 original size:9 final size:9
Alignment explanation
Indices: 7863--7897 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
7853 CCTGCGAGTG
7863 ATGGTGAGA
1 ATGGTGAGA
7872 ATGGTGAGCA
1 ATGGTGAG-A
7882 A-GGTGAGA
1 ATGGTGAGA
7890 ATGGTGAG
1 ATGGTGAG
7898 CAAGCAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 2 0.08
9 20 0.83
10 2 0.08
ACGTcount: A:0.31, C:0.03, G:0.46, T:0.20
Consensus pattern (9 bp):
ATGGTGAGA
Found at i:7888 original size:18 final size:18
Alignment explanation
Indices: 7865--7901 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
7855 TGCGAGTGAT
7865 GGTGAGAATGGTGAGCAA
1 GGTGAGAATGGTGAGCAA
7883 GGTGAGAATGGTGAGCAA
1 GGTGAGAATGGTGAGCAA
7901 G
1 G
7902 CAGAGAATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.46, T:0.16
Consensus pattern (18 bp):
GGTGAGAATGGTGAGCAA
Found at i:7907 original size:18 final size:18
Alignment explanation
Indices: 7868--7910 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
7858 GAGTGATGGT
**
7868 GAGAATGGTGAGCAAGGT
1 GAGAATGGTGAGCAAGCA
7886 GAGAATGGTGAGCAAGCA
1 GAGAATGGTGAGCAAGCA
7904 GAGAATG
1 GAGAATG
7911 CTGACAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.07, G:0.42, T:0.14
Consensus pattern (18 bp):
GAGAATGGTGAGCAAGCA
Found at i:9996 original size:16 final size:17
Alignment explanation
Indices: 9957--10007 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
9947 CCCGACCGAC
* *
9957 TATATATATATTAATAAA
1 TATATTTATATT-ATATA
9975 TATATTTATATTATATA
1 TATATTTATATTATATA
* *
9992 T-TATTAATAGTATATA
1 TATATTTATATTATATA
10008 AACTAAAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 13 0.45
17 5 0.17
18 11 0.38
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TATATTTATATTATATA
Found at i:11583 original size:15 final size:15
Alignment explanation
Indices: 11565--11610 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
11555 GCAGCTGCAT
11565 CAACATCAAACCAAG
1 CAACATCAAACCAAG
*
11580 CAACCTCAAACCAAG
1 CAACATCAAACCAAG
*
11595 CAACATCAACCCAAG
1 CAACATCAAACCAAG
11610 C
1 C
11611 TGCATCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.48, C:0.39, G:0.07, T:0.07
Consensus pattern (15 bp):
CAACATCAAACCAAG
Found at i:13399 original size:3 final size:3
Alignment explanation
Indices: 13391--13451 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
13381 GTCTCCAAGC
*
13391 AGA AGA AGA AGA AGA AGA AGA CGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
13439 AGA AGA AGA AGA A
1 AGA AGA AGA AGA A
13452 AATTGCAGCT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.02, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:19546 original size:36 final size:36
Alignment explanation
Indices: 19484--19631 Score: 161
Period size: 36 Copynumber: 4.1 Consensus size: 36
19474 GAATCTGAGC
* *
19484 CACCAGCTGTAACAGAGAAAATAAAGGAAGAAGAGG
1 CACCGGCTGTAACAGAGAAAACAAAGGAAGAAGAGG
* * *
19520 CACCGGCTGCAACAGAGAACACAAAGGACGAAGAGG
1 CACCGGCTGTAACAGAGAAAACAAAGGAAGAAGAGG
* * * * *
19556 CACCGGCTGTAACAGAGAAAGCAGAGGAAAAAGTGA
1 CACCGGCTGTAACAGAGAAAACAAAGGAAGAAGAGG
* ** * *
19592 TACCATCTGTAACAGAGAAAACGAAGGAAGAAGTGG
1 CACCGGCTGTAACAGAGAAAACAAAGGAAGAAGAGG
19628 CACC
1 CACC
19632 AGAAGCAACT
Statistics
Matches: 90, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 90 1.00
ACGTcount: A:0.45, C:0.19, G:0.28, T:0.08
Consensus pattern (36 bp):
CACCGGCTGTAACAGAGAAAACAAAGGAAGAAGAGG
Found at i:25068 original size:31 final size:31
Alignment explanation
Indices: 25033--25139 Score: 142
Period size: 31 Copynumber: 3.5 Consensus size: 31
25023 TTTTGTGCAC
* **
25033 GTGGCATGCCACGTGTCATTTTTTGAAACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
*
25064 GTGGCATACCACGTGTCACTTTTTGGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
* * *
25095 GTGGCGTGTCACATGTCACTTTTTGGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
*
25126 GTGGCGTGCCACGT
1 GTGGCATGCCACGT
25140 CGGACACCGT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (31 bp):
GTGGCATGCCACGTGTCACTTTTTGGTACAT
Found at i:26054 original size:11 final size:11
Alignment explanation
Indices: 26038--26080 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
26028 TACACTATAT
26038 CTAATTAATAG
1 CTAATTAATAG
*
26049 CTAATTAATAT
1 CTAATTAATAG
26060 CTAATTAATAG
1 CTAATTAATAG
*
26071 TTAATTAATA
1 CTAATTAATA
26081 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:26059 original size:22 final size:22
Alignment explanation
Indices: 26034--26080 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
26024 CCATTACACT
26034 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
26056 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
26078 ATA
1 ATA
26081 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:31309 original size:52 final size:52
Alignment explanation
Indices: 31250--31353 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
31240 GTATTATTAC
31250 TATTTTTTTTAATGAAAGTATTTAGTGGCTACATTAAACCTGGTTAATTCAG
1 TATTTTTTTTAATGAAAGTATTTAGTGGCTACATTAAACCTGGTTAATTCAG
31302 TATTTTTTTTAATGAAAGTATTTAGTGGCTACATTAAACCTGGTTAATTCAG
1 TATTTTTTTTAATGAAAGTATTTAGTGGCTACATTAAACCTGGTTAATTCAG
31354 AATCAAGATG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (52 bp):
TATTTTTTTTAATGAAAGTATTTAGTGGCTACATTAAACCTGGTTAATTCAG
Found at i:31813 original size:31 final size:30
Alignment explanation
Indices: 31760--31918 Score: 127
Period size: 31 Copynumber: 5.4 Consensus size: 30
31750 TTTTGTGCAC
* * **
31760 GTGGCATGCACGTGCCATTTTTTGAAACAT
1 GTGGCATGCACGTGTCACTTTTTGGTACAT
*
31790 GTGGCATGCCACGTGTCACTTTTTGGTACAC
1 GTGGCATG-CACGTGTCACTTTTTGGTACAT
* *
31821 GTGGCGTGACATGTGTCACTTTTTGGTACAT
1 GTGGCATG-CACGTGTCACTTTTTGGTACAT
31852 GT-G---GCAC--G--ACTTTTTGGTACAT
1 GTGGCATGCACGTGTCACTTTTTGGTACAT
* * *
31874 GTGGCGTGCCACATGTCACTTTTTGGTACAC
1 GTGGCATG-CACGTGTCACTTTTTGGTACAT
*
31905 GTGGCGTGCCACGT
1 GTGGCATG-CACGT
31919 CGGACACCGT
Statistics
Matches: 107, Mismatches: 12, Indels: 19
0.78 0.09 0.14
Matches are distributed among these distances:
22 16 0.15
23 1 0.01
24 1 0.01
26 3 0.03
27 4 0.04
29 1 0.01
30 9 0.08
31 72 0.67
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (30 bp):
GTGGCATGCACGTGTCACTTTTTGGTACAT
Found at i:31869 original size:53 final size:53
Alignment explanation
Indices: 31807--31909 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
31797 GCCACGTGTC
** *
31807 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
* *
31860 ACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGC
31910 GTGCCACGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.36
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:32955 original size:2 final size:2
Alignment explanation
Indices: 32948--32973 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
32938 AGTATGTAAC
32948 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
32974 CACGCAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38530 original size:12 final size:12
Alignment explanation
Indices: 38513--38541 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
38503 CTCGCAAGCT
38513 TCAGCAGGAGCA
1 TCAGCAGGAGCA
38525 TCAGCAGGAGCA
1 TCAGCAGGAGCA
38537 TCAGC
1 TCAGC
38542 TTTCTCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.28, G:0.31, T:0.10
Consensus pattern (12 bp):
TCAGCAGGAGCA
Done.