Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017732.1 Corchorus olitorius cultivar O-4 contig17765, 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: 21861
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3460 original size:2 final size:2
Alignment explanation
Indices: 3453--3530 Score: 50
Period size: 2 Copynumber: 44.0 Consensus size: 2
3443 ACCGTTTAGT
* *
3453 TA TA TA TA TA -A T- TA AA TA TA TA T- TT TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
3491 -A TA T- TA GA TA TA TA TA -A T- TA TA CA TA TA -A TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3527 TA TA
1 TA TA
3531 ACTGTTAAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
1 10 0.17
2 49 0.83
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3494 original size:19 final size:20
Alignment explanation
Indices: 3467--3512 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
3457 TATATAATTA
**
3467 AATATATATTTTATATATAT
1 AATATATATTAGATATATAT
3487 AATA-ATATTAGATATATAT
1 AATATATATTAGATATATAT
3506 AAT-TATA
1 AATATATA
3513 CATATAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AATATATATTAGATATATAT
Found at i:3518 original size:31 final size:30
Alignment explanation
Indices: 3463--3525 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
3453 TATATATATA
* *
3463 ATTAAATATATATTTTATATATATAATAAT
1 ATTAAATATATATATTATACATATAATAAT
*
3493 ATTAGATATATATAATTATACATATAATAAT
1 ATTAAATATATAT-ATTATACATATAATAAT
3524 AT
1 AT
3526 ATATAACTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (30 bp):
ATTAAATATATATATTATACATATAATAAT
Found at i:4906 original size:24 final size:24
Alignment explanation
Indices: 4866--4921 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
4856 ACCTTGGTAT
*
4866 TTGGGCCTGTTGCAAGTTGAACAA
1 TTGGGCCTATTGCAAGTTGAACAA
* *
4890 TTGGGCCTATTGGAAGTTGAACAT
1 TTGGGCCTATTGCAAGTTGAACAA
4914 TTGGGCCT
1 TTGGGCCT
4922 TGGGCATCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.32
Consensus pattern (24 bp):
TTGGGCCTATTGCAAGTTGAACAA
Found at i:6018 original size:16 final size:15
Alignment explanation
Indices: 5996--6039 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
5986 TTAAAGTTTG
*
5996 AATTCAGTACTTATGA
1 AATTCAGTACTTA-AA
*
6012 GATTCAGTA-TTAAA
1 AATTCAGTACTTAAA
6026 AATTCAGTACTTAA
1 AATTCAGTACTTAA
6040 TCTTTCAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 9 0.38
15 7 0.29
16 8 0.33
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (15 bp):
AATTCAGTACTTAAA
Found at i:12037 original size:16 final size:16
Alignment explanation
Indices: 12016--12049 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
12006 CGGTCAAACG
12016 TATTTATACTTATGAC
1 TATTTATACTTATGAC
12032 TATTTATACTTATGAC
1 TATTTATACTTATGAC
12048 TA
1 TA
12050 GGGGTGTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.50
Consensus pattern (16 bp):
TATTTATACTTATGAC
Found at i:12127 original size:20 final size:22
Alignment explanation
Indices: 12091--12131 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
12081 CTATTCGGGC
12091 TCGACTCGAGAAAAATTCGAGT
1 TCGACTCGAGAAAAATTCGAGT
12113 TCGACTCG-G-AAAATTCGAG
1 TCGACTCGAGAAAAATTCGAG
12132 CCGAGCTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (22 bp):
TCGACTCGAGAAAAATTCGAGT
Found at i:12140 original size:20 final size:20
Alignment explanation
Indices: 12092--12140 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
12082 TATTCGGGCT
*
12092 CGACTCGAGAAAAATTCGAGTT
1 CGACTCG-G-AAAATTCGAGTC
12114 CGACTCGGAAAATTCGAG-C
1 CGACTCGGAAAATTCGAGTC
12133 CGAGCTCG
1 CGA-CTCG
12141 AGCTCGGGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 3 0.12
20 14 0.56
21 1 0.04
22 7 0.28
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.18
Consensus pattern (20 bp):
CGACTCGGAAAATTCGAGTC
Found at i:12965 original size:25 final size:24
Alignment explanation
Indices: 12937--12983 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
12927 TACTGCATTT
12937 TTTTTCTATTCATTTTGTAATTTCC
1 TTTTTCTATTCA-TTTGTAATTTCC
* *
12962 TTTTTCTTTTTATTTGTAATTT
1 TTTTTCTATTCATTTGTAATTT
12984 GGGTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.15, C:0.11, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTTTCTATTCATTTGTAATTTCC
Found at i:18552 original size:26 final size:28
Alignment explanation
Indices: 18508--18559 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
18498 TTGAGCTTTT
18508 TTTTTTGGACCTTATTAAACTTTTTTCC
1 TTTTTTGGACCTTATTAAACTTTTTTCC
*
18536 TTTTTTGG-CCTTA-TAAAGTTTTTT
1 TTTTTTGGACCTTATTAAACTTTTTT
18560 AGTCACCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 10 0.43
27 5 0.22
28 8 0.35
ACGTcount: A:0.17, C:0.13, G:0.10, T:0.60
Consensus pattern (28 bp):
TTTTTTGGACCTTATTAAACTTTTTTCC
Found at i:19140 original size:85 final size:86
Alignment explanation
Indices: 19045--19213 Score: 304
Period size: 86 Copynumber: 2.0 Consensus size: 86
19035 AATTATCTTC
19045 GTAAGCTTATAAATTTCTCATTAAACTTAAAAG-TTTTTAAATAGTTTTCTTAAATTTATTCAAT
1 GTAAGCTTATAAATTTCTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATTTATTCAAT
*
19109 CACCTCGTTTAAGATTTTTTG
66 CACCTCATTTAAGATTTTTTG
* *
19130 GTAAGCTTATAAATTTTTCATTAAATTTAAAAGCTTTTTAAATAGTTTTCTTAAATTTATTCAAT
1 GTAAGCTTATAAATTTCTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATTTATTCAAT
19195 CACCTCATTTAAGATTTTT
66 CACCTCATTTAAGATTTTT
19214 AGTGATCTTA
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
85 31 0.39
86 49 0.61
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (86 bp):
GTAAGCTTATAAATTTCTCATTAAACTTAAAAGCTTTTTAAATAGTTTTCTTAAATTTATTCAAT
CACCTCATTTAAGATTTTTTG
Found at i:19227 original size:21 final size:22
Alignment explanation
Indices: 19203--19257 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
19193 ATCACCTCAT
* *
19203 TTAAGATTTTTAGTGATCTTA-
1 TTAAGATTTTTAGAGACCTTAC
*
19224 TTAACATATTTTAGAGACCTTAC
1 TTAAGAT-TTTTAGAGACCTTAC
19247 TTAAG-TTTTTA
1 TTAAGATTTTTA
19258 TTTAGTGACC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 11 0.39
22 13 0.46
23 4 0.14
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (22 bp):
TTAAGATTTTTAGAGACCTTAC
Found at i:19310 original size:20 final size:21
Alignment explanation
Indices: 19287--19334 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
19277 TTATCGTTAA
19287 CTTATGAA-TTTTATAGTAAC
1 CTTATGAATTTTTATAGTAAC
*
19307 CTTATGAAGTTTTTTTTAGTAAC
1 CTTATGAA--TTTTTATAGTAAC
19330 CTTAT
1 CTTAT
19335 TGAGTGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
23 16 0.67
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
CTTATGAATTTTTATAGTAAC
Found at i:19344 original size:23 final size:23
Alignment explanation
Indices: 19295--19345 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
19285 AACTTATGAA
*
19295 TTTTATAGTAACCTTATGAAGTT
1 TTTTATAGTAACCTTATGAAGTG
*
19318 TTTTTTAGTAACCTTATTG-AGTG
1 TTTTATAGTAACCTTA-TGAAGTG
19341 TTTTA
1 TTTTA
19346 GAAATCTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.53
Consensus pattern (23 bp):
TTTTATAGTAACCTTATGAAGTG
Found at i:19646 original size:21 final size:22
Alignment explanation
Indices: 19622--19673 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
19612 TTACTAAACG
*
19622 TTTTAGTAACCTTTATTACAAT
1 TTTTAGTAACCTTTATTAAAAT
19644 TTTTAGTAACCTTTATTAAAA-
1 TTTTAGTAACCTTTATTAAAAT
19665 TTTTAGTAA
1 TTTTAGTAA
19674 TCTTGTAAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 9 0.31
22 20 0.69
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.50
Consensus pattern (22 bp):
TTTTAGTAACCTTTATTAAAAT
Found at i:19971 original size:21 final size:20
Alignment explanation
Indices: 19933--19982 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
19923 TTTCAATATA
19933 TAACTTAGTAAGCATTTTAG
1 TAACTTAGTAAGCATTTTAG
* *
19953 TAACTTTATTAAGCTTTTTAG
1 TAAC-TTAGTAAGCATTTTAG
19974 TAATCTTAG
1 TAA-CTTAG
19983 ATAGTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 4 0.16
21 20 0.80
22 1 0.04
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (20 bp):
TAACTTAGTAAGCATTTTAG
Done.