Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021969.1 Corchorus olitorius cultivar O-4 contig22002, 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: 32400
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2514 original size:42 final size:43
Alignment explanation
Indices: 2467--2548 Score: 132
Period size: 43 Copynumber: 1.9 Consensus size: 43
2457 ATATTATTAA
*
2467 AATATATTTTAATTAAT-T-ATTATTAAAATATATAAAATTACC
1 AATATATTTTAATT-ATGTCACTATTAAAATATATAAAATTACC
2509 AATATATTTTAATTATGTCACTATTAAAATATATAAAATT
1 AATATATTTTAATTATGTCACTATTAAAATATATAAAATT
2549 GCCATTATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
41 2 0.05
42 15 0.41
43 20 0.54
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (43 bp):
AATATATTTTAATTATGTCACTATTAAAATATATAAAATTACC
Found at i:3460 original size:22 final size:22
Alignment explanation
Indices: 3342--3572 Score: 70
Period size: 22 Copynumber: 10.4 Consensus size: 22
3332 AATGATATAT
* *
3342 AATTTCATA-GAGAGATTATCGA
1 AATTTCATATGA-AGGTTATCAA
*
3364 AATTTCATACT-ATGG-TATCAAA
1 AATTTCATA-TGAAGGTTATC-AA
* * *
3386 AATTT-ATAGGGAGATTAAT-AA
1 AATTTCATATGAAGGTT-ATCAA
3407 AATTTCATA-GAGAGGGTTATCAAA
1 AATTTCATATGA-A-GGTTATC-AA
**
3431 AAAATCATATGAAGGTTATCAA
1 AATTTCATATGAAGGTTATCAA
* *
3453 AATTTCATA-GAAAAGTTTATTAA
1 AATTTCATATG--AAGGTTATCAA
* *
3476 AATTTCATAGTTAA-GTTATCAG
1 AATTTCATA-TGAAGGTTATCAA
* * * *
3498 TATTTCAT-TGGGAGTTTATCAC
1 AATTTCATAT-GAAGGTTATCAA
* ** *
3520 AATTTCATA-AAATAATCATCAA
1 AATTTCATATGAA-GGTTATCAA
* *
3542 AATTTCATAGTG-TGTTTATCAA
1 AATTTCATA-TGAAGGTTATCAA
3564 AATTTCATA
1 AATTTCATA
3573 AAAACATTTA
Statistics
Matches: 151, Mismatches: 36, Indels: 44
0.65 0.16 0.19
Matches are distributed among these distances:
20 1 0.01
21 19 0.13
22 86 0.57
23 33 0.22
24 10 0.07
25 2 0.01
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (22 bp):
AATTTCATATGAAGGTTATCAA
Found at i:8886 original size:16 final size:15
Alignment explanation
Indices: 8865--8913 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
8855 TTGAATCACC
8865 GTCATTCGGGTCTCGG
1 GTCATTCGGGT-TCGG
* *
8881 GTCATTCAGGTTATGG
1 GTCATTCGGGTT-CGG
*
8897 GTCATTCGAGTTCGG
1 GTCATTCGGGTTCGG
8912 GT
1 GT
8914 TTGTCAAGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.12, C:0.18, G:0.35, T:0.35
Consensus pattern (15 bp):
GTCATTCGGGTTCGG
Found at i:9151 original size:17 final size:17
Alignment explanation
Indices: 9115--9154 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
9105 GATCACCTCC
* **
9115 AGATCACTAGTGATTTA
1 AGATCACCAGTGATGCA
9132 AGATCACCAGTGATGCA
1 AGATCACCAGTGATGCA
9149 AGATCA
1 AGATCA
9155 TCGGTGATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (17 bp):
AGATCACCAGTGATGCA
Found at i:9680 original size:15 final size:16
Alignment explanation
Indices: 9660--9689 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9650 TTTTCTTAAG
9660 AAAAGAA-AAAGAAAA
1 AAAAGAAGAAAGAAAA
9675 AAAAGAAGAAAGAAA
1 AAAAGAAGAAAGAAA
9690 GTAAAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAGAAGAAAGAAAA
Found at i:18359 original size:20 final size:20
Alignment explanation
Indices: 18334--18379 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
18324 ATTGTCGCAG
18334 TACTTGCGGATGTCATCTGT
1 TACTTGCGGATGTCATCTGT
18354 TACTTGCGGATGTCATCTGT
1 TACTTGCGGATGTCATCTGT
18374 TACTTG
1 TACTTG
18380 TTTATACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (20 bp):
TACTTGCGGATGTCATCTGT
Found at i:20505 original size:18 final size:18
Alignment explanation
Indices: 20482--20526 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
20472 AAAATAGTAA
20482 GACTTTCCCGGGAAAGTT
1 GACTTTCCCGGGAAAGTT
20500 GACTTTCCCGGGAAAGTT
1 GACTTTCCCGGGAAAGTT
*
20518 AACTTTCCC
1 GACTTTCCC
20527 ACCATTTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (18 bp):
GACTTTCCCGGGAAAGTT
Found at i:21744 original size:10 final size:11
Alignment explanation
Indices: 21728--21752 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21718 CAGTTATCCA
21728 AAAAAAAAAAG
1 AAAAAAAAAAG
21739 AAAAAAAAAAG
1 AAAAAAAAAAG
21750 AAA
1 AAA
21753 TCTATGGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:26085 original size:2 final size:2
Alignment explanation
Indices: 26078--26102 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26068 CGACCCCGAA
26078 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
26103 CACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26293 original size:29 final size:29
Alignment explanation
Indices: 26251--26306 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
26241 CCTTGTACGG
*
26251 TGTTGAAAGCTTGTAATTGTGGTGTTGAT
1 TGTTGAAAACTTGTAATTGTGGTGTTGAT
26280 TGTTGAAAACTTGTAATTGTGGTGTTG
1 TGTTGAAAACTTGTAATTGTGGTGTTG
26307 TAAACTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.04, G:0.30, T:0.45
Consensus pattern (29 bp):
TGTTGAAAACTTGTAATTGTGGTGTTGAT
Found at i:26781 original size:7 final size:7
Alignment explanation
Indices: 26769--26793 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
26759 AGAATTTGCT
26769 CAAAGAG
1 CAAAGAG
26776 CAAAGAG
1 CAAAGAG
26783 CAAAGAG
1 CAAAGAG
26790 CAAA
1 CAAA
26794 TTGACAAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.16, G:0.24, T:0.00
Consensus pattern (7 bp):
CAAAGAG
Found at i:27436 original size:20 final size:21
Alignment explanation
Indices: 27411--27465 Score: 87
Period size: 19 Copynumber: 2.7 Consensus size: 21
27401 CCCCCCAATA
27411 TTTTTTAATTTGGCCTAATTT
1 TTTTTTAATTTGGCCTAATTT
27432 TTTTTTAATTT-GCCTAA-TT
1 TTTTTTAATTTGGCCTAATTT
*
27451 TTTTTGAATTTGGCC
1 TTTTTTAATTTGGCC
27466 CCTTAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 12 0.38
20 9 0.28
21 11 0.34
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.60
Consensus pattern (21 bp):
TTTTTTAATTTGGCCTAATTT
Found at i:30459 original size:45 final size:42
Alignment explanation
Indices: 30410--30503 Score: 127
Period size: 45 Copynumber: 2.2 Consensus size: 42
30400 AGCAACAATT
* *
30410 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAAAGAT--A-GAGTAG
*
30455 AATATCAGCTTTATTTTGATGAATTACCTAAAGATAGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAAAGATAGAGTAG
30497 AAT-TTAG
1 AATATTAG
30504 ATAATGCACT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 3 0.07
42 9 0.20
43 1 0.02
45 32 0.71
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.37
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAAAGATAGAGTAG
Found at i:31686 original size:49 final size:47
Alignment explanation
Indices: 31585--31714 Score: 165
Period size: 49 Copynumber: 2.7 Consensus size: 47
31575 GAGCGTGCCA
* *
31585 ATCAATTTTGTC-AAAAGATTGATAAAAAGTGCAATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAA-ATTGAGAAAAAGTGCAATGAAAAATAAAAG
31632 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* *
31681 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCA
31715 GAAAAGTAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
47 12 0.16
48 16 0.22
49 46 0.62
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.28
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Done.