Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011441.1 Corchorus olitorius cultivar O-4 contig11474, 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: 23525
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1529 original size:10 final size:10
Alignment explanation
Indices: 1503--1538 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1493 GTAACACAAA
1503 TCACATACC-
1 TCACATACCT
1512 TCACATACCT
1 TCACATACCT
*
1522 TTACATACCT
1 TCACATACCT
1532 TCACATA
1 TCACATA
1539 ATTCTCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (10 bp):
TCACATACCT
Found at i:2357 original size:15 final size:16
Alignment explanation
Indices: 2324--2363 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
2314 TTACTTTGCT
2324 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
2340 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
2355 TTGTTTTCT
1 TTGTTTTCT
2364 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.15, C:0.07, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:4088 original size:137 final size:136
Alignment explanation
Indices: 3830--4453 Score: 759
Period size: 137 Copynumber: 4.6 Consensus size: 136
3820 CCAATAGTCA
* * ** *
3830 AATTGAATCCTTATCTATTCAACACCATATCCAAGATTTA-TCAGAAAACCTAACACAATATCCA
1 AATTGAATCCTTATCTCTTCCACA-CATATCCAAGA-AAAGTCAGAAAATCTAACACAATATCCA
* * * * *
3894 ATCAATTTAAGAGAATCTAACTTTATCTCAATCCAACTGTTGGATTAAAGATT-AGATTTAAATG
64 ATCAATTTCAGAGAATCTCACTTTATCTCTATCCAACTGTTGGA-TAAAAATTGAGATTCAAATG
3958 TGACCGTTG
128 TGACCGTTG
3967 AATTGAATCCTTATCTCTTCCACACCATATCCAAGAAAAGTCAGAAAATCTAACACAATATCCAA
1 AATTGAATCCTTATCTCTTCCACA-CATATCCAAGAAAAGTCAGAAAATCTAACACAATATCCAA
* * ** *
4032 TCAATTTCAGAGAATCTCACATTATTTCTATATAACTGTTGGATAAAAATTGAGATTTAAATGTG
65 TCAATTTCAGAGAATCTCACTTTATCTCTATCCAACTGTTGGATAAAAATTGAGATTCAAATGTG
*
4097 ATCGTTG
130 ACCGTTG
* * * * *
4104 AATTGAATCGTTATCTCTTCCACAACATATCTAAGAAAAGTCAAAAAATTTAACACAATACCCAA
1 AATTGAATCCTTATCTCTTCCAC-ACATATCCAAGAAAAGTCAGAAAATCTAACACAATATCCAA
* * * * *
4169 TCAA-TT----G-AT-TCACTTTATCTCTATCTAACCGTTAGATTAAAATTGAGATTCAAATATG
65 TCAATTTCAGAGAATCTCACTTTATCTCTATCCAACTGTTGGATAAAAATTGAGATTCAAATGTG
*
4227 ACTGTTG
130 ACCGTTG
*
4234 AATTGAATCCTTATCTCTTCCACTACATATCCAAGTAAAA-CCAGAAAATCTAACACAATATCCA
1 AATTGAATCCTTATCTCTTCCAC-ACATATCCAAG-AAAAGTCAGAAAATCTAACACAATATCCA
* * * * *
4298 ATCAATTTCGGAGAAACTTACTTTATCTCTATCCAACAGTTGGATTAAAATTGAGATTCAAATGT
64 ATCAATTTCAGAGAATCTCACTTTATCTCTATCCAACTGTTGGATAAAAATTGAGATTCAAATGT
*
4363 GACCATTG
129 GACCGTTG
* * *
4371 AATTGAATCCTTATCTTTTCCACTACATATCCAAGAAAAGTCATAAAATCTAACATAATATCC--
1 AATTGAATCCTTATCTCTTCCAC-ACATATCCAAGAAAAGTCAGAAAATCTAACACAATATCCAA
4434 TCAATTTCAGAGAATCTCAC
65 TCAATTTCAGAGAATCTCAC
4454 CAATACAACC
Statistics
Matches: 424, Mismatches: 51, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
130 103 0.24
131 8 0.02
132 1 0.00
135 18 0.04
136 15 0.04
137 278 0.66
138 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.32
Consensus pattern (136 bp):
AATTGAATCCTTATCTCTTCCACACATATCCAAGAAAAGTCAGAAAATCTAACACAATATCCAAT
CAATTTCAGAGAATCTCACTTTATCTCTATCCAACTGTTGGATAAAAATTGAGATTCAAATGTGA
CCGTTG
Found at i:4342 original size:267 final size:267
Alignment explanation
Indices: 3830--4430 Score: 751
Period size: 267 Copynumber: 2.2 Consensus size: 267
3820 CCAATAGTCA
* * * ** * * *
3830 AATTGAATCCTTATCTATTCAACACCATATCCAAGATTTA-TCAGAAAACCTAACACAATATCCA
1 AATTGAATCCTTATCTCTTCCACAACATATCCAAGA-AAAGTCAAAAAATCTAACACAATACCCA
* * * * *
3894 ATCAATTTAAGAGAATCTAACTTTATCTCAATCCAACTGTTGGATTAAAGATTAGATTTAAATGT
65 ATCAA-TT----G-AT-TCACTTTATCTCAATCCAACCGTTAGATTAAAGATTAGATTCAAATAT
*
3959 GACCGTTGAATTGAATCCTTATCTCTTCCACACCATATCCAAGAAAAGTCAGAAAATCTAACACA
123 GACCGTTGAATTGAATCCTTATCTCTTCCACACCATATCCAAGAAAAGCCAGAAAATCTAACACA
* * * *
4024 ATATCCAATCAATTTCAGAGAATCTCACATTATTTCTATATAACTGTTGGATAAAAATTGAGATT
188 ATATCCAATCAATTTCAGAGAAACTCACATTATCTCTATACAACAGTTGGATAAAAATTGAGATT
* * *
4089 TAAATGTGATCGTTG
253 CAAATGTGACCATTG
* * *
4104 AATTGAATCGTTATCTCTTCCACAACATATCTAAGAAAAGTCAAAAAATTTAACACAATACCCAA
1 AATTGAATCCTTATCTCTTCCACAACATATCCAAGAAAAGTCAAAAAATCTAACACAATACCCAA
* * *
4169 TCAATTGATTCACTTTATCTCTATCTAACCGTTAGATTAAA-ATTGAGATTCAAATATGACTGTT
66 TCAATTGATTCACTTTATCTCAATCCAACCGTTAGATTAAAGATT-AGATTCAAATATGACCGTT
4233 GAATTGAATCCTTATCTCTTCCACTA-CATATCCAAGTAAAA-CCAGAAAATCTAACACAATATC
130 GAATTGAATCCTTATCTCTTCCAC-ACCATATCCAAG-AAAAGCCAGAAAATCTAACACAATATC
* * * * *
4296 CAATCAATTTCGGAGAAACTTACTTTATCTCTATCCAACAGTTGGATTAAAATTGAGATTCAAAT
193 CAATCAATTTCAGAGAAACTCACATTATCTCTATACAACAGTTGGATAAAAATTGAGATTCAAAT
4361 GTGACCATTG
258 GTGACCATTG
* * * *
4371 AATTGAATCCTTATCTTTTCCACTACATATCCAAGAAAAGTCATAAAATCTAACATAATA
1 AATTGAATCCTTATCTCTTCCACAACATATCCAAGAAAAGTCAAAAAATCTAACACAATA
4431 TCCTCAATTT
Statistics
Matches: 284, Mismatches: 39, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
266 3 0.01
267 214 0.75
268 7 0.02
269 1 0.00
273 3 0.01
274 56 0.20
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (267 bp):
AATTGAATCCTTATCTCTTCCACAACATATCCAAGAAAAGTCAAAAAATCTAACACAATACCCAA
TCAATTGATTCACTTTATCTCAATCCAACCGTTAGATTAAAGATTAGATTCAAATATGACCGTTG
AATTGAATCCTTATCTCTTCCACACCATATCCAAGAAAAGCCAGAAAATCTAACACAATATCCAA
TCAATTTCAGAGAAACTCACATTATCTCTATACAACAGTTGGATAAAAATTGAGATTCAAATGTG
ACCATTG
Found at i:4722 original size:42 final size:42
Alignment explanation
Indices: 4676--4757 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
4666 ACATATATAT
*
4676 ATATATATGTTTCCTACCCTTTT-AGTGTTATGTCATTCAATA
1 ATATATATGTTTCCTA-CATTTTCAGTGTTATGTCATTCAATA
4718 ATATATATGTTTCCTACATTTTCAGTGTTATGTCATTCAA
1 ATATATATGTTTCCTACATTTTCAGTGTTATGTCATTCAA
4758 GTATCAAACT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 5 0.13
42 33 0.87
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.48
Consensus pattern (42 bp):
ATATATATGTTTCCTACATTTTCAGTGTTATGTCATTCAATA
Found at i:7489 original size:28 final size:28
Alignment explanation
Indices: 7457--7526 Score: 131
Period size: 28 Copynumber: 2.5 Consensus size: 28
7447 AGGACAAACA
7457 GTACGGATGCGCTAAAGCGATCAACGTC
1 GTACGGATGCGCTAAAGCGATCAACGTC
7485 GTACGGATGCGCTAAAGCGATCAACGTC
1 GTACGGATGCGCTAAAGCGATCAACGTC
*
7513 GTACGGACGCGCTA
1 GTACGGATGCGCTA
7527 GAGTTGTCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.27, C:0.26, G:0.30, T:0.17
Consensus pattern (28 bp):
GTACGGATGCGCTAAAGCGATCAACGTC
Found at i:8559 original size:4 final size:4
Alignment explanation
Indices: 8545--8596 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
8535 TGTATTCTCT
* * * * *
8545 TATA GTATA TATA TACA TACA TACA TACA TACA TATA TATA TATA TATA
1 TATA -TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
8594 TAT
1 TAT
8597 GATACCCTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
4 41 0.91
5 4 0.09
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (4 bp):
TATA
Found at i:8588 original size:8 final size:8
Alignment explanation
Indices: 8553--8601 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
8543 CTTATAGTAT
8553 ATATATAC
1 ATATATAC
*
8561 ATACATAC
1 ATATATAC
*
8569 ATACATAC
1 ATATATAC
*
8577 ATATATAT
1 ATATATAC
*
8585 ATATATAT
1 ATATATAC
8593 ATATGATAC
1 ATAT-ATAC
8602 CCTAGTCTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
8 33 0.92
9 3 0.08
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (8 bp):
ATATATAC
Found at i:8596 original size:12 final size:12
Alignment explanation
Indices: 8550--8595 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
8540 TCTCTTATAG
8550 TATATATATACA
1 TATATATATACA
* *
8562 TACATACATACA
1 TATATATATACA
* *
8574 TACATATATATA
1 TATATATATACA
8586 TATATATATA
1 TATATATATA
8596 TGATACCCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (12 bp):
TATATATATACA
Found at i:8674 original size:12 final size:12
Alignment explanation
Indices: 8653--8689 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
8643 CCACCGTTTC
*
8653 CACCTTCATCAT
1 CACCTCCATCAT
*
8665 CACCTCCATCTT
1 CACCTCCATCAT
8677 CACCTCCATCAT
1 CACCTCCATCAT
8689 C
1 C
8690 CAAATGCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.22, C:0.49, G:0.00, T:0.30
Consensus pattern (12 bp):
CACCTCCATCAT
Found at i:11870 original size:35 final size:35
Alignment explanation
Indices: 11824--11891 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
11814 CAAAGACTAC
*
11824 AAACCCACACAATAATTACTTTGAAAATGTCAAGT
1 AAACCCACACAATAATTACTTCGAAAATGTCAAGT
11859 AAACCCACACAATAATTACTTCGAAAATGTCAA
1 AAACCCACACAATAATTACTTCGAAAATGTCAA
11892 AAATCAAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.47, C:0.22, G:0.07, T:0.24
Consensus pattern (35 bp):
AAACCCACACAATAATTACTTCGAAAATGTCAAGT
Found at i:15074 original size:32 final size:32
Alignment explanation
Indices: 15004--15083 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
14994 ATTCCTAAAC
* *
15004 CAGTTATGA-CAAAACAGTTTCAAACTCAATA
1 CAGTTAAGATCAAAACAATTTCAAACTCAATA
* * * *
15035 AAATTAAGATCAAAACAATTTCAAATTTAATA
1 CAGTTAAGATCAAAACAATTTCAAACTCAATA
* *
15067 CAGTTAAGCTCAGAACA
1 CAGTTAAGATCAAAACA
15084 TCCTAAATTT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 6 0.16
32 32 0.84
ACGTcount: A:0.49, C:0.16, G:0.09, T:0.26
Consensus pattern (32 bp):
CAGTTAAGATCAAAACAATTTCAAACTCAATA
Done.