Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014316.1 Corchorus olitorius cultivar O-4 contig14349, 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: 35456
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3455 original size:18 final size:18
Alignment explanation
Indices: 3429--3464 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3419 CAGATAAACT
*
3429 ATCTCCTTGGTTTTGTGA
1 ATCTCCTTGGTTTAGTGA
*
3447 ATCTTCTTGGTTTAGTGA
1 ATCTCCTTGGTTTAGTGA
3465 GGAGTTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.50
Consensus pattern (18 bp):
ATCTCCTTGGTTTAGTGA
Found at i:3698 original size:30 final size:30
Alignment explanation
Indices: 3659--4158 Score: 600
Period size: 30 Copynumber: 17.1 Consensus size: 30
3649 ATTTATTTTA
*
3659 ATCTT-CAAATGACACCAGAAGTTGTCATG
1 ATCTTGCAATTGACACCAGAAGTTGTCATG
* * *
3688 ATCTTACAAATGACAGCAGAAGTTGTCATG
1 ATCTTGCAATTGACACCAGAAGTTGTCATG
*
3718 GTCTTGCAATTGACACCAGAAGTTGTCATG
1 ATCTTGCAATTGACACCAGAAGTTGTCATG
* *
3748 GTCTTGCAATTGACACCAAAAGTTGTCAATG
1 ATCTTGCAATTGACACCAGAAGTTGTC-ATG
3779 ATCTTGCAATTGACACCAGAAGTTGTCAATG
1 ATCTTGCAATTGACACCAGAAGTTGTC-ATG
3810 ATCTTGCAATTGACACC-GAAAGTTGTCATG
1 ATCTTGCAATTGACACCAG-AAGTTGTCATG
* *
3840 CTCTTGCAATTGACACAAG-AGTTGTCATG
1 ATCTTGCAATTGACACCAGAAGTTGTCATG
* *
3869 CTCTTGTAATTGACACCAG-AGTTGTCATG
1 ATCTTGCAATTGACACCAGAAGTTGTCATG
*
3898 CTCTTGCAATTGACACCAG-AGTTGTCATG
1 ATCTTGCAATTGACACCAGAAGTTGTCATG
* * *
3927 CTCTTGCAATTGACACCAAAAGCTGTCATG
1 ATCTTGCAATTGACACCAGAAGTTGTCATG
*
3957 CTCTTGCAATTGACACCAGAAGTTGTCATG
1 ATCTTGCAATTGACACCAGAAGTTGTCATG
*
3987 ATCTTACAATTGACACCAGAAGTTGTCATG
1 ATCTTGCAATTGACACCAGAAGTTGTCATG
**
4017 ATCTTATAATTGACACCAGAAGTTGTCAATG
1 ATCTTGCAATTGACACCAGAAGTTGTC-ATG
* * *
4048 GTCTTACAATTG--ACCAGAAGTTCTCAT-
1 ATCTTGCAATTGACACCAGAAGTTGTCATG
* * *
4075 A-ATT-AAATTGACACCAGAAGTTCTCAT-
1 ATCTTGCAATTGACACCAGAAGTTGTCATG
* *
4102 A-ATT-AAATTGACACCAGAAGTTGTCAT-
1 ATCTTGCAATTGACACCAGAAGTTGTCATG
*
4129 A-ATT-CAATTGACACCAGAAGTTGTCATG
1 ATCTTGCAATTGACACCAGAAGTTGTCATG
4157 AT
1 AT
4159 TTTACCTTTC
Statistics
Matches: 433, Mismatches: 28, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
25 5 0.01
26 2 0.00
27 67 0.15
28 3 0.01
29 100 0.23
30 185 0.43
31 71 0.16
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (30 bp):
ATCTTGCAATTGACACCAGAAGTTGTCATG
Found at i:8626 original size:26 final size:26
Alignment explanation
Indices: 8575--8627 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
8565 TATCTTTTCC
* *
8575 TTTTATCTTTTCTTTTATTTGGTACAT
1 TTTTATCTTCTCTTTTA-TTGCTACAT
8602 TTTTATCTTCTCTTTTA-TGACTACAT
1 TTTTATCTTCTCTTTTATTG-CTACAT
8628 GTTACTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 2 0.09
26 5 0.22
27 16 0.70
ACGTcount: A:0.17, C:0.15, G:0.06, T:0.62
Consensus pattern (26 bp):
TTTTATCTTCTCTTTTATTGCTACAT
Found at i:11927 original size:31 final size:31
Alignment explanation
Indices: 11880--12025 Score: 195
Period size: 31 Copynumber: 4.7 Consensus size: 31
11870 GCACGTATTC
11880 TTTT-GTACACGTGGCATGCCACGTGTCACT
1 TTTTGGTACACGTGGCATGCCACGTGTCACT
** *
11910 TTTTGAAACACATGGCATGCCACGTGTCACT
1 TTTTGGTACACGTGGCATGCCACGTGTCACT
* ** *
11941 TTTTGGTACACATGGCATGATATGTGTCACT
1 TTTTGGTACACGTGGCATGCCACGTGTCACT
* * *
11972 TTTTGGTACACGTGGCGTGCCACATGTCGCT
1 TTTTGGTACACGTGGCATGCCACGTGTCACT
12003 TTTTGGTACACGTGGCATGCCAC
1 TTTTGGTACACGTGGCATGCCAC
12026 CGTCGGACAC
Statistics
Matches: 99, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
30 4 0.04
31 95 0.96
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (31 bp):
TTTTGGTACACGTGGCATGCCACGTGTCACT
Found at i:20824 original size:42 final size:42
Alignment explanation
Indices: 20776--20858 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
20766 GCTAAGAATC
20776 ATGATTTGAG-TCGAGTATTTCTTAATTTACAAAGAATTTTCT
1 ATGATTTGAGTTC-AGTATTTCTTAATTTACAAAGAATTTTCT
*
20818 ATGATTTGAGTTCAGTATTTCTTAATTTACAGAGAATTTTC
1 ATGATTTGAGTTCAGTATTTCTTAATTTACAAAGAATTTTC
20859 AAGACTTAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 37 0.95
43 2 0.05
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (42 bp):
ATGATTTGAGTTCAGTATTTCTTAATTTACAAAGAATTTTCT
Found at i:22109 original size:3 final size:3
Alignment explanation
Indices: 22101--22135 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
22091 GTTTAGAATT
22101 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
22136 TTAGATACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:25387 original size:2 final size:2
Alignment explanation
Indices: 25380--25417 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
25370 CTAATTGTTA
25380 AT AT 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 AT AT
25418 GTTATGGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26056 original size:41 final size:40
Alignment explanation
Indices: 26002--26104 Score: 111
Period size: 41 Copynumber: 2.5 Consensus size: 40
25992 CTTATAGTAA
**
26002 ATAATATTGAAAATTACCTTTGACACTAGAAGTTGTCATTTT
1 ATAA-ATT-AAAATTACCTTTGACACTAGAAGTTGTCACATT
26044 GATAAATTAAAATTA--TTGCTGACACTAGAAGTTGTCACATT
1 -ATAAATTAAAATTACCTT--TGACACTAGAAGTTGTCACATT
*
26085 AGTAAATTAAAACTACCTTT
1 A-TAAATTAAAATTACCTTT
26105 AACTCAGCAC
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
39 2 0.04
40 1 0.02
41 40 0.77
42 3 0.06
43 6 0.12
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.37
Consensus pattern (40 bp):
ATAAATTAAAATTACCTTTGACACTAGAAGTTGTCACATT
Found at i:26295 original size:226 final size:228
Alignment explanation
Indices: 25881--26333 Score: 784
Period size: 226 Copynumber: 2.0 Consensus size: 228
25871 ACGTTATCAA
*
25881 CAGCAAGAAAGCTCTGGTAATGCAACGCGAAGCTTCGATCTTCTGTTTAGGTTTGATCTTCCAAT
1 CAGCAAGAAAGCTCTGGTAATGCAACGCGAAGCTTCGATATTCTGTTTAGGTTTGATCTTCCAAT
*
25946 CTCTAGTTTTTATTTCTAAAATTGTTTATATTACTATCTTTTTACCCTTATAGTAAATAATATTG
66 CTCTAGTTTTTATTTCTAAAATTGTTTATATAACTATCTTTTTACCCTTATAGTAAATAATATTG
26011 AAAATTACCTTTGACACTAGAAGTTGTCATTTTGATAAATTAAAATTATTGCTGACACTAGAAGT
131 AAAATTACCTTTGACACTAGAAGTTGTCATTTTGATAAATTAAAATTATTGCTGACACTAGAAGT
*
26076 TGTCACATTAGTAAATTAAAACTACCTTTAACT
196 TGTCACATTAGTAAAGTAAAACTACCTTTAACT
* *
26109 CAGCACGAAAGCTCT-GTAATGCAACGCGAAGCTTTGATATTCTGTTTAGGTTTGATCTTCCAAT
1 CAGCAAGAAAGCTCTGGTAATGCAACGCGAAGCTTCGATATTCTGTTTAGGTTTGATCTTCCAAT
* *
26173 CTCTAG-TTTTATTTCTAAAGTTGTTTATATAATTATCTTTTTACCCTTATAGTAAATAATATTG
66 CTCTAGTTTTTATTTCTAAAATTGTTTATATAACTATCTTTTTACCCTTATAGTAAATAATATTG
* *
26237 AAAATTACCTTTGACACTAGAAGTTGTCATTTTGGTAAATTAAAATTATTGTTGACACTAGAAGT
131 AAAATTACCTTTGACACTAGAAGTTGTCATTTTGATAAATTAAAATTATTGCTGACACTAGAAGT
* * *
26302 TGTCACCTTGGTAAAGTAAAATTACCTTTAAC
196 TGTCACATTAGTAAAGTAAAACTACCTTTAAC
26334 ACCAGAAGTG
Statistics
Matches: 213, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
226 146 0.69
227 53 0.25
228 14 0.07
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (228 bp):
CAGCAAGAAAGCTCTGGTAATGCAACGCGAAGCTTCGATATTCTGTTTAGGTTTGATCTTCCAAT
CTCTAGTTTTTATTTCTAAAATTGTTTATATAACTATCTTTTTACCCTTATAGTAAATAATATTG
AAAATTACCTTTGACACTAGAAGTTGTCATTTTGATAAATTAAAATTATTGCTGACACTAGAAGT
TGTCACATTAGTAAAGTAAAACTACCTTTAACT
Found at i:26341 original size:41 final size:41
Alignment explanation
Indices: 26237--26342 Score: 142
Period size: 41 Copynumber: 2.6 Consensus size: 41
26227 AATAATATTG
** *
26237 AAAATTACCTTTGACACTAGAAGTTGTCATTTTGGTAAATT
1 AAAATTACCTTTGACACTAGAAGTTGTCACCTTGGTAAAGT
*
26278 AAAATTA-TTGTTGACACTAGAAGTTGTCACCTTGGTAAAGT
1 AAAATTACCT-TTGACACTAGAAGTTGTCACCTTGGTAAAGT
* *
26319 AAAATTACCTTTAACACCAGAAGT
1 AAAATTACCTTTGACACTAGAAGT
26343 GTTACTGCAG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 1 0.02
41 54 0.96
42 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (41 bp):
AAAATTACCTTTGACACTAGAAGTTGTCACCTTGGTAAAGT
Found at i:28502 original size:1 final size:1
Alignment explanation
Indices: 28496--28525 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
28486 TCTCATAGAT
28496 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28526 TCACTTTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30926 original size:11 final size:11
Alignment explanation
Indices: 30910--30938 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
30900 TTTCAACTGA
30910 AGATTATCTGG
1 AGATTATCTGG
30921 AGATTATCTGG
1 AGATTATCTGG
30932 AGATTAT
1 AGATTAT
30939 ATGAAGATTT
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:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (11 bp):
AGATTATCTGG
Found at i:32553 original size:51 final size:50
Alignment explanation
Indices: 32475--32574 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 50
32465 TCAATGAAAA
* *
32475 AAATTAGAAATACAAACTACATACACTAGCTTAATTAATAAA-GATAACAAG
1 AAATTACAAATACAAACTACATACACTA-ATTAATTAATAAATG-TAACAAG
*
32526 AAATTACAAATACAAACTAACAT-CACTAATTATTTAATAAATGTAACAA
1 AAATTACAAATACAAACT-ACATACACTAATTAATTAATAAATGTAACAA
32575 AGTAACCAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
50 17 0.39
51 23 0.52
52 4 0.09
ACGTcount: A:0.55, C:0.14, G:0.05, T:0.26
Consensus pattern (50 bp):
AAATTACAAATACAAACTACATACACTAATTAATTAATAAATGTAACAAG
Found at i:33803 original size:42 final size:42
Alignment explanation
Indices: 33752--33841 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 42
33742 AGTGCATTAC
* *
33752 CTAA-ATTCTACTCCATCTCTAGCTAATTTATCAAAATAAAG
1 CTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAAAG
*
33793 CTAATATTCTAGTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAAAG
*
33835 GTAATAT
1 CTAATAT
33842 CAATTGTTGC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 4 0.09
42 40 0.91
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.34
Consensus pattern (42 bp):
CTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAAAG
Done.