Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016197.1 Corchorus capsularis cultivar CVL-1 contig16218, 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: 52328
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:6652 original size:25 final size:25
Alignment explanation
Indices: 6618--6666 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
6608 TGTTTGGTTG
6618 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
6643 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
6667 GATTGTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.33, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:7564 original size:25 final size:25
Alignment explanation
Indices: 7530--7578 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
7520 TGTTTGTTTG
7530 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
7555 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
7579 GATTGTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.33, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:15196 original size:20 final size:20
Alignment explanation
Indices: 15171--15210 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
15161 GAGAGATCGG
15171 ACAAAAG-ATAATAGTAAAAA
1 ACAAAAGCA-AATAGTAAAAA
15191 ACAAAAGCAAATAGTAAAAA
1 ACAAAAGCAAATAGTAAAAA
15211 GCTAGCATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.70, C:0.07, G:0.10, T:0.12
Consensus pattern (20 bp):
ACAAAAGCAAATAGTAAAAA
Found at i:15910 original size:13 final size:13
Alignment explanation
Indices: 15892--15921 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
15882 AATCTCTGTT
15892 TTTTCAATTTTCA
1 TTTTCAATTTTCA
*
15905 TTTTCATTTTTCA
1 TTTTCAATTTTCA
15918 TTTT
1 TTTT
15922 TCATTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTCAATTTTCA
Found at i:15925 original size:7 final size:7
Alignment explanation
Indices: 15891--15927 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
15881 CAATCTCTGT
15891 TTTTTCA
1 TTTTTCA
*
15898 ATTTTCA
1 TTTTTCA
15905 -TTTTCA
1 TTTTTCA
15911 TTTTTCA
1 TTTTTCA
15918 TTTTTCA
1 TTTTTCA
15925 TTT
1 TTT
15928 ATATGTGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTTCA
Found at i:17381 original size:22 final size:22
Alignment explanation
Indices: 17356--17398 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
17346 TACTTGTTAA
* *
17356 AATTGTAAAATAAATTAGCAAT
1 AATTGAAAAATAAAATAGCAAT
17378 AATTGAAAAATAAAATAGCAA
1 AATTGAAAAATAAAATAGCAA
17399 AAATGCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (22 bp):
AATTGAAAAATAAAATAGCAAT
Found at i:19349 original size:12 final size:11
Alignment explanation
Indices: 19313--19341 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
19303 ACCTAAACGG
19313 AGAAAAATAAA
1 AGAAAAATAAA
19324 AGAAAAATAAA
1 AGAAAAATAAA
19335 AGAAAAA
1 AGAAAAA
19342 AAGAAAGACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (11 bp):
AGAAAAATAAA
Found at i:27979 original size:73 final size:73
Alignment explanation
Indices: 27860--28034 Score: 235
Period size: 73 Copynumber: 2.4 Consensus size: 73
27850 AAAATGGACT
*
27860 ATTTCAGTCGACTAAAACCGAAGTTGAAAGCGCCCAGCCTGTTGTGCCCATTCTGCATAAACAGT
1 ATTTCAGTCGACTAAAACAGAAGTTGAAAGCGCCCAGCCTGTTGTGCCCATTCTGCATAAACAGT
* *
27925 GAATTACC
66 AAAATACC
* * * *
27933 ATTTCAGTC-AGCTAAAACAGAAGTTGAAAGTGCTCTGCCTGTTGTGCCCATTCTGTATAAACAG
1 ATTTCAGTCGA-CTAAAACAGAAGTTGAAAGCGCCCAGCCTGTTGTGCCCATTCTGCATAAACAG
*
27997 TAAAATGCC
65 TAAAATACC
* **
28006 ATTTCAGTCGACTGAAACTTAAGTTGAAA
1 ATTTCAGTCGACTAAAACAGAAGTTGAAA
28035 TGAGCCGGGT
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
72 1 0.01
73 87 0.98
74 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (73 bp):
ATTTCAGTCGACTAAAACAGAAGTTGAAAGCGCCCAGCCTGTTGTGCCCATTCTGCATAAACAGT
AAAATACC
Found at i:30364 original size:25 final size:25
Alignment explanation
Indices: 30330--30382 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
30320 AAAATAAACT
30330 ATGTTGAGTTAAAACAAGAGCAACC
1 ATGTTGAGTTAAAACAAGAGCAACC
*
30355 ATGTTGAGTTAAAACATGAGCAACC
1 ATGTTGAGTTAAAACAAGAGCAACC
30380 ATG
1 ATG
30383 GTTCCATTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.23
Consensus pattern (25 bp):
ATGTTGAGTTAAAACAAGAGCAACC
Found at i:35983 original size:45 final size:45
Alignment explanation
Indices: 35928--36017 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
35918 AGATTACTTC
*
35928 TCCAGCTCATCATTAGTACGGGGTAGGGATCTTTTAGTAATTCCA
1 TCCAGCTCATCATTAATACGGGGTAGGGATCTTTTAGTAATTCCA
* * *
35973 TCCAGGTCATCATTAATTCGGGGTAGGGATTTTTTAGTAATTCCA
1 TCCAGCTCATCATTAATACGGGGTAGGGATCTTTTAGTAATTCCA
36018 CTATTCTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (45 bp):
TCCAGCTCATCATTAATACGGGGTAGGGATCTTTTAGTAATTCCA
Found at i:39689 original size:6 final size:6
Alignment explanation
Indices: 39678--39702 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
39668 CCTCCGAGAG
39678 TAAGAT TAAGAT TAAGAT TAAGAT T
1 TAAGAT TAAGAT TAAGAT TAAGAT T
39703 CATATCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (6 bp):
TAAGAT
Found at i:43117 original size:24 final size:24
Alignment explanation
Indices: 43085--43130 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
43075 CACGTGAAAG
43085 TTTTCCTCTGTCAAATGGCCAGAA
1 TTTTCCTCTGTCAAATGGCCAGAA
43109 TTTTCCTCTGTCAAATGGCCAG
1 TTTTCCTCTGTCAAATGGCCAG
43131 TGGCACCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (24 bp):
TTTTCCTCTGTCAAATGGCCAGAA
Done.