Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015336.1 Corchorus capsularis cultivar CVL-1 contig15357, 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: 27871
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1788 original size:109 final size:110
Alignment explanation
Indices: 1659--1871 Score: 349
Period size: 109 Copynumber: 1.9 Consensus size: 110
1649 GTATCAAGTG
*
1659 TTGGATATACTAAAAATTTTTCTAATATACAATTTTATTCTACTAAAAACTCTATTTTCATTTAA
1 TTGGATATACTAAAAATTTTTCTAATATACAACTTTATTCTACTAAAAACTCTATTTTCATTTAA
1724 TTAAA-TCTAATATCTT-TATAATTACTTTATTTTTACCAAAAAAT
66 TTAAATTC-AATATCTTATATAATTACTTTATTTTTACCAAAAAAT
* *
1768 TTGGATATATTAAAATTTTTTCTAATATACAACTTTATTCTACTAAAAACTCTATTTTCATTTAA
1 TTGGATATACTAAAAATTTTTCTAATATACAACTTTATTCTACTAAAAACTCTATTTTCATTTAA
* **
1833 TTAAATTCAATATTTTATATAATTTTTTTATTTTTACCA
66 TTAAATTCAATATCTTATATAATTACTTTATTTTTACCA
1872 TTTTAATTTA
Statistics
Matches: 96, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
109 74 0.77
110 22 0.23
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (110 bp):
TTGGATATACTAAAAATTTTTCTAATATACAACTTTATTCTACTAAAAACTCTATTTTCATTTAA
TTAAATTCAATATCTTATATAATTACTTTATTTTTACCAAAAAAT
Found at i:4037 original size:17 final size:18
Alignment explanation
Indices: 4001--4039 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3991 ATATTAAAAT
* *
4001 TTTTAATATACAATTTTA
1 TTTTAATATAAAACTTTA
4019 TTTTAATA-AAAACTTTA
1 TTTTAATATAAAACTTTA
4036 TTTT
1 TTTT
4040 CATTTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTAATATAAAACTTTA
Found at i:4917 original size:28 final size:25
Alignment explanation
Indices: 4885--4959 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 25
4875 ACATATATAC
4885 AGTGTATAAAGTGTGTATATATATCTAT
1 AGTGTAT-AA-TG-GTATATATATCTAT
* *
4913 GGTGTAT-ATGGTGTATATATCTAT
1 AGTGTATAATGGTATATATATCTAT
*
4937 AGTGTAT-AT-ATATATATAT-TAT
1 AGTGTATAATGGTATATATATCTAT
4959 A
1 A
4960 TATTATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
22 4 0.10
23 8 0.19
24 21 0.50
25 2 0.05
26 1 0.02
28 6 0.14
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (25 bp):
AGTGTATAATGGTATATATATCTAT
Found at i:4937 original size:17 final size:16
Alignment explanation
Indices: 4917--4969 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 16
4907 ATCTATGGTG
*
4917 TATATGGTGTATATATC
1 TATAT-GTGTATATATA
4934 TATA-GTGTATATATA
1 TATATGTGTATATATA
*
4949 TATATAT-TATATATTA
1 TATATGTGTATATA-TA
4965 TATAT
1 TATAT
4970 AATATTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 20 0.62
16 8 0.25
17 4 0.12
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (16 bp):
TATATGTGTATATATA
Found at i:4946 original size:2 final size:2
Alignment explanation
Indices: 4926--5006 Score: 79
Period size: 2 Copynumber: 44.0 Consensus size: 2
4916 GTATATGGTG
* *
4926 TA TA TA TC TA TA GTG TA TA TA TA TA TA TA T- TA TA TA T- TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4967 TA TA -A TA T- TA TA T- TA -A TA T- TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5003 TA TA
1 TA TA
5007 AGGTGGGAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
1 8 0.12
2 57 0.86
3 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4960 original size:30 final size:27
Alignment explanation
Indices: 4926--5005 Score: 96
Period size: 24 Copynumber: 3.0 Consensus size: 27
4916 GTATATGGTG
4926 TATATATCTATAGTGTATATATATATATAT
1 TATATAT-TATA-T-TATATATATATATAT
4956 TATATATTATA-TATA-ATAT-TATAT
1 TATATATTATATTATATATATATATAT
*
4980 TA-ATATTATATAATATATATATATAT
1 TATATATTATATTATATATATATATAT
5006 AAGGTGGGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
23 8 0.17
24 10 0.22
25 8 0.17
26 9 0.20
29 4 0.09
30 7 0.15
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (27 bp):
TATATATTATATTATATATATATATAT
Found at i:4961 original size:24 final size:22
Alignment explanation
Indices: 4941--5006 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 22
4931 ATCTATAGTG
4941 TATATATATATATATTATATAT
1 TATATATATATATATTATATAT
4963 TATATATAATATTATATTA-ATAT
1 TATATAT-ATA-TATATTATATAT
4986 TATATA-ATATATATATATATA
1 TATATATATATATAT-TATATA
5007 AGGTGGGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.12
21 5 0.12
22 10 0.25
23 13 0.32
24 7 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATATATATATATATTATATAT
Found at i:12475 original size:210 final size:210
Alignment explanation
Indices: 12181--12581 Score: 475
Period size: 210 Copynumber: 1.9 Consensus size: 210
12171 TAAATCCCAA
* * * *
12181 ACCTCAATGGCTTCTTCAGCTCTCTTTTCCTTGCAAAGAGCATCAATTATAGAGTTGAAAGTCTT
1 ACCTCAATGGCCTCTTCAGCTCTCCTTTCCTTGCAAAGAGCATCAATTAAAGAGTTGAAAGTCTC
* * ** * * *
12246 GAGATTTGGCTGCACTCCTTCATTTATCATTCTGTCCAAA-AAGATCATTGCTTCCTTCCATTGA
66 CAGATTCGGCTGCACTCCTTCATCCACCATTAT-TCCAAACAAGATCATCGCTTCCTTCCATTGA
* * * * ** *
12310 CCTGAACGAAAAAATCCATGGATTATAGAATTATATGTGATGACATTAGGTTTCACACCTTTGTC
130 CCTGAACGAAAAAATCCATGGATCATACAACTATAGGTGACCACATCAGGTTTCACACCTTTGTC
12375 AACCATCAGATCGAAT
195 AACCATCAGATCGAAT
* * *
12391 ACCTCAATTGCCTCTTCAGTTCTCCTTTCCTTGCAAAGAGCATCAATTAAAGTGTTGAAAGT-TA
1 ACCTCAATGGCCTCTTCAGCTCTCCTTTCCTTGCAAAGAGCATCAATTAAAGAGTTGAAAGTCT-
* * * ** *
12455 CCACG-TTCGGCTGTACTCCTTCATCCACCATTATTTCAAACAAGCTTGTCGCTTCTTTCCATTG
65 CCA-GATTCGGCTGCACTCCTTCATCCACCATTATTCCAAACAAGATCATCGCTTCCTTCCATTG
* * * *
12519 ACTTGAACGACAAAATCCTTGGATCATACAACTATAGGTGACCACATCGGGTTTCACACCTTT
129 ACCTGAACGAAAAAATCCATGGATCATACAACTATAGGTGACCACATCAGGTTTCACACCTTT
12582 ATGAGTCATC
Statistics
Matches: 157, Mismatches: 31, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
209 6 0.04
210 150 0.96
211 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (210 bp):
ACCTCAATGGCCTCTTCAGCTCTCCTTTCCTTGCAAAGAGCATCAATTAAAGAGTTGAAAGTCTC
CAGATTCGGCTGCACTCCTTCATCCACCATTATTCCAAACAAGATCATCGCTTCCTTCCATTGAC
CTGAACGAAAAAATCCATGGATCATACAACTATAGGTGACCACATCAGGTTTCACACCTTTGTCA
ACCATCAGATCGAAT
Found at i:22967 original size:135 final size:138
Alignment explanation
Indices: 22639--22967 Score: 495
Period size: 142 Copynumber: 2.4 Consensus size: 138
22629 TACAACTTTG
* * * * *
22639 ATTAGATAATGATCAATCAATTACAACTTTGATTGGCAAAATTAATTAACAACATGTTCAATAAT
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACGACATGTTCAATAAT
*
22704 TTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTGGTGGCGAT
66 TTATTTTTTTGGTAACATAATTACTAATTG---TATTTATTTATGGTAATCTTTTTGGTAGCGA-
22769 TTTTATGGTAAA
127 TTTTATGGTAAA
*
22781 ATTATATAATCATCAATCAATTACAACTTTGATT-GACAAAATTAACTAACGACATGTTCAATAA
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGA-AAAATTAACTAACGACATGTTCAATAA
* *
22845 TTTATTTTTTTGGTAACATAATTACTAATTG-ATTTATTTATGTTAAT-TTTTTTGTAGCGA-TT
65 TTTATTTTTTTGGTAACATAATTACTAATTGTATTTATTTATGGTAATCTTTTTGGTAGCGATTT
22907 TATGGTAAA
130 TATGGTAAA
*
22916 ATTAAATAATTATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACGA
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACGA
22968 TCACTAACTT
Statistics
Matches: 175, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
135 58 0.33
136 2 0.01
137 11 0.06
138 15 0.09
141 1 0.01
142 88 0.50
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (138 bp):
ATTAAATAATCATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACGACATGTTCAATAAT
TTATTTTTTTGGTAACATAATTACTAATTGTATTTATTTATGGTAATCTTTTTGGTAGCGATTTT
ATGGTAAA
Found at i:23519 original size:139 final size:139
Alignment explanation
Indices: 23252--23645 Score: 447
Period size: 139 Copynumber: 2.8 Consensus size: 139
23242 TTTTTGGCAA
* * ** * * *
23252 TTAATTAACGACTAATTTGATTCCCTAATTTATTTAGTATGTTCAATCAATCTATTTTTTTTTCT
1 TTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATC-A---ATTTTTTTTTGT
*
23317 AACATAATTACTAATTGATTCATTTATTTAT-GACAAAATCAAATAATCATCAATCAATTATAAC
62 AACATAATTACTAATTGATTCATTTATTTATGGAAAAAAT-AAATAATCATCAATCAATTATAAC
23381 TTTAATTGACAAAG
126 TTTAATTGACAAAG
* * *
23395 TTGA-TCAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAA-TTTTTTTGGTAAT
1 TTAACT-AACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTTTTTTTGTAAC
* *
23458 ATAATTAGTAATTGAATT-ATTTATTTATGGAAAAAAATAAATAATCATCCATCAATTATAACTT
65 ATAATTACTAATTG-ATTCATTTATTTATGG-AAAAAATAAATAATCATCAATCAATTATAACTT
* **
23522 TGATTGGTAAAG
128 TAATTGACAAAG
* * * *
23534 TTAACTAAGGACTAACTTGATTCATTTACTTATTTTGGATGTTCAATCAATTTATTTTTTTGTAA
1 TTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAA-TT-TTTTTTTGTAA
* * * *
23599 CATAA-TATTAATTGATTCATTTATTTGTGGCAAAATTAAATAATCAT
64 CATAATTACTAATTGATTCATTTATTTATGGAAAAAATAAATAATCAT
23646 TAGCTTTTGG
Statistics
Matches: 216, Mismatches: 26, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
138 33 0.15
139 82 0.38
140 25 0.12
141 20 0.09
142 16 0.07
143 40 0.19
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (139 bp):
TTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTTTTTTTGTAACA
TAATTACTAATTGATTCATTTATTTATGGAAAAAATAAATAATCATCAATCAATTATAACTTTAA
TTGACAAAG
Found at i:25283 original size:2 final size:2
Alignment explanation
Indices: 25276--25309 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
25266 TACAGTTTTA
25276 AT AT 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 AT AT
25310 GATGTGAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.