Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024797.1 Corchorus olitorius cultivar O-4 contig24830, 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: 35281
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:5336 original size:15 final size:16
Alignment explanation
Indices: 5309--5338 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5299 CTTTGCTTTG
5309 TTTTCTAGTTTAATTA
1 TTTTCTAGTTTAATTA
5325 TTTTCT-GTTTAATT
1 TTTTCTAGTTTAATT
5339 GCTTTCTGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (16 bp):
TTTTCTAGTTTAATTA
Found at i:8211 original size:22 final size:21
Alignment explanation
Indices: 8159--8212 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
8149 GCTTCTTGGA
*
8159 AATAATTCTTC-AATTGTCTTC
1 AATAA-TCTTCAAATTATCTTC
8180 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATTATCTTC
8199 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
8213 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.41
Consensus pattern (21 bp):
AATAATCTTCAAATTATCTTC
Found at i:10665 original size:19 final size:18
Alignment explanation
Indices: 10641--10676 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10631 TGAAGACTTA
10641 TTGAAGATAATATGAAGAT
1 TTGAAGATAAT-TGAAGAT
*
10660 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
10677 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:17719 original size:62 final size:62
Alignment explanation
Indices: 17622--17750 Score: 231
Period size: 62 Copynumber: 2.1 Consensus size: 62
17612 TTGCTTGATA
*
17622 ATTGAGTCATATGTTACTTTGTCTTTGCATAAGAATTTAGGATTTAATTTGATTGTTTTCGG
1 ATTGAGTCATATGTTACTTTGTCTTTGCATAAGAATTTAGGATTTAATTTGATTGTCTTCGG
* *
17684 ATTGAGTCATATGTTAGTTTGTGTTTGCATAAGAATTTAGGATTTAATTTGATTGTCTTCGG
1 ATTGAGTCATATGTTACTTTGTCTTTGCATAAGAATTTAGGATTTAATTTGATTGTCTTCGG
17746 ATTGA
1 ATTGA
17751 TCTTTTATTT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.47
Consensus pattern (62 bp):
ATTGAGTCATATGTTACTTTGTCTTTGCATAAGAATTTAGGATTTAATTTGATTGTCTTCGG
Found at i:21818 original size:2 final size:2
Alignment explanation
Indices: 21813--21850 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
21803 CATATATGTG
21813 TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
21851 AGATAGGGAT
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):
TA
Found at i:22044 original size:41 final size:42
Alignment explanation
Indices: 21923--22203 Score: 397
Period size: 43 Copynumber: 6.6 Consensus size: 42
21913 GAAATGCCTA
**
21923 TGTGTTATATATGT-TTTAAGGACTTTGTAATAGAGATGCCCC
1 TGTGTTATATATGTGTTTGGGGACTTTG-AATAGAGATGCCCC
21965 TGTGTTATATATGTGTTTGGGGACTTTGATATAGAGATGCCCC
1 TGTGTTATATATGTGTTTGGGGACTTTGA-ATAGAGATGCCCC
* *
22008 TGTGTTATATATGTGTTTGGGGACTTTG-ATATAGATGCCTC
1 TGTGTTATATATGTGTTTGGGGACTTTGAATAGAGATGCCCC
* *
22049 TGTGTTATATATGTGTTTGAGGACTTTGAAATAGAGATGCCCA
1 TGTGTTATATATGTGTTTGGGGACTTTG-AATAGAGATGCCCC
* **
22092 TGTGTTATATATGTGTTTGGGGACTTTG-ATATAGATGCCTT
1 TGTGTTATATATGTGTTTGGGGACTTTGAATAGAGATGCCCC
* *
22133 TGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAGATGCCCA
1 TGTGTTATATATGTGTTTGGGGAC-TTT-GAATAGAGATGCCCC
22177 TGTGTTATATATGTGTTTGGGGACTTT
1 TGTGTTATATATGTGTTTGGGGACTTT
22204 TAGTTATTGG
Statistics
Matches: 215, Mismatches: 17, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
41 71 0.33
42 18 0.08
43 93 0.43
44 33 0.15
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.42
Consensus pattern (42 bp):
TGTGTTATATATGTGTTTGGGGACTTTGAATAGAGATGCCCC
Found at i:22061 original size:84 final size:83
Alignment explanation
Indices: 21916--22203 Score: 443
Period size: 84 Copynumber: 3.4 Consensus size: 83
21906 ACAAAGAGAA
* ** * *
21916 ATGCCTATGTGTTATATATGT-TTTAAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
1 ATGCCCATGTGTTATATATGTGTTTGGGGACTTTG--ATATAGATGCCTCTGTGTTATATATGTG
*
21980 TTTGGGGACTTTGATATAGAG
64 TTTGAGGACTTTGA-ATAGAG
*
22001 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTT
1 ATGCCCATGTGTTATATATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTT
22066 TGAGGACTTTGAAATAGAG
66 TGAGGACTTTG-AATAGAG
*
22085 ATGCCCATGTGTTATATATGTGTTTGGGGACTTTGATATAGATGCCTTTGTGTTATATATGTGTT
1 ATGCCCATGTGTTATATATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTT
22150 TGAGGACTTTTGGAATAGAG
66 TGAGGAC-TTT-GAATAGAG
22170 ATGCCCATGTGTTATATATGTGTTTGGGGACTTT
1 ATGCCCATGTGTTATATATGTGTTTGGGGACTTT
22204 TAGTTATTGG
Statistics
Matches: 190, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
84 114 0.60
85 64 0.34
86 12 0.06
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.42
Consensus pattern (83 bp):
ATGCCCATGTGTTATATATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATATATGTGTT
TGAGGACTTTGAATAGAG
Found at i:24324 original size:40 final size:41
Alignment explanation
Indices: 24287--24747 Score: 235
Period size: 40 Copynumber: 10.9 Consensus size: 41
24277 GAAGGGAACA
*
24287 AGAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAT-T
1 AGAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAATCT
* * * * * * * *
24327 CA-AACGACACTTTCCAGTTATGAAGGGCAAGCTGGTAAACT
1 -AGAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAATCT
* * *
24368 A-AACAACACCTTCCGGCGAGGAAGGGCAAATTGGGGTAAAGC-
1 AGAACAACACCTTCCGGTGAGGAAGGGCAAACT-GGG--AATCT
* * * *
24410 AGACTTAAATAACACCTTCGGGTGGGGAAGGGCAAACTGGGAATTT
1 AG-----AACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAATCT
* * *
24456 AG-ACAACACCTTCCGGTGGGGAAGGGCAAACTGGTAATTT
1 AGAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAATCT
* * **
24496 AG-ACAACACCTTTCGGTGGGGAAGGGCAAACTGATAAACTAAACTT
1 AGAACAACACCTTCCGGTGAGGAAGGGCAAACTG-GGAA-T---C-T
* * ** *
24542 A-AACAACACCTTCCGGTGGGGAAGAGCAATTTGGTAAACTATACTT
1 AGAACAACACCTTCCGGTGAGGAAGGGCAAACTGG--GA--AT-C-T
* * *
24588 A-AACAACACCTTCCGGT-AGGGAGGGCAAATTGGGAATTT
1 AGAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAATCT
* * *
24627 AG-ACAACACCTTCCGGTGGGGAAGGGCAAATTGGTAAAGTGGACTT
1 AGAACAACACCTTCCGGTGAGGAAGGGCAAACTGG-GAA-T---C-T
* * *
24673 A-AACAACATCTTCCGATGAGGAAGGGCAAACTGGGAATTT
1 AGAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAATCT
* * *
24713 A-AACAATACCTTCCGGTGGGGAAGGGCAAATTGGG
1 AGAACAACACCTTCCGGTGAGGAAGGGCAAACTGGG
24748 TAAAGTAGAG
Statistics
Matches: 330, Mismatches: 59, Indels: 63
0.73 0.13 0.14
Matches are distributed among these distances:
39 17 0.05
40 164 0.50
41 10 0.03
42 3 0.01
43 4 0.01
44 1 0.00
45 16 0.05
46 82 0.25
47 5 0.02
48 27 0.08
49 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (41 bp):
AGAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAATCT
Found at i:24552 original size:46 final size:45
Alignment explanation
Indices: 24498--24751 Score: 251
Period size: 46 Copynumber: 5.8 Consensus size: 45
24488 GGTAATTTAG
* * *
24498 ACAACACCTTTCGGTGGGGAAGGGCAAACTGATAAACTAAACTTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAATTGGTAAACT-AACTTAA
* *
24544 ACAACACCTTCCGGTGGGGAAGAGCAATTTGGTAAACTATACTTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAATTGGTAAACTA-ACTTAA
* * *
24590 ACAACACCTTCCGGTAGGG-AGGGCAAATTGG-GAA-T---TTAG
1 ACAACACCTTCCGGTGGGGAAGGGCAAATTGGTAAACTAACTTAA
* *
24629 ACAACACCTTCCGGTGGGGAAGGGCAAATTGGTAAAGTGGACTTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAATTGGTAAACT-AACTTAA
* * * * *
24675 ACAACATCTTCCGATGAGGAAGGGCAAACTGG-GAA-T---TTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAATTGGTAAACTAACTTAA
*
24715 ACAATACCTTCCGGTGGGGAAGGGCAAATTGGGTAAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAATT-GGTAAA
24752 GTAGAGGGCA
Statistics
Matches: 174, Mismatches: 24, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
39 21 0.12
40 41 0.24
41 4 0.02
42 3 0.02
43 1 0.01
44 3 0.02
45 13 0.07
46 88 0.51
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (45 bp):
ACAACACCTTCCGGTGGGGAAGGGCAAATTGGTAAACTAACTTAA
Found at i:24644 original size:131 final size:132
Alignment explanation
Indices: 24458--24701 Score: 364
Period size: 131 Copynumber: 1.9 Consensus size: 132
24448 GGGAATTTAG
* * *
24458 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGTAATTTAGACAACACCTTTCGGTGGGGAAGGGC
1 ACAACACCTTCCGGTAGGGAAGGGCAAACTGGGAATTTAGACAACACCTTCCGGTGGGGAAGGGC
* *
24523 AAACTGATAAACTAAACTTAAACAACACCTTCCGGTGGGGAAGAGCAATTTGGTAAACTATACTT
66 AAACTGATAAACTAAACTTAAACAACACCTTCCGATGAGGAAGAGCAATTTGGTAAACTATACTT
24588 AA
131 AA
*
24590 ACAACACCTTCCGGTAGGG-AGGGCAAATTGGGAATTTAGACAACACCTTCCGGTGGGGAAGGGC
1 ACAACACCTTCCGGTAGGGAAGGGCAAACTGGGAATTTAGACAACACCTTCCGGTGGGGAAGGGC
* * * ** * *
24654 AAATTGGTAAAGTGGACTTAAACAACATCTTCCGATGAGGAAGGGCAA
66 AAACTGATAAACTAAACTTAAACAACACCTTCCGATGAGGAAGAGCAA
24702 ACTGGGAATT
Statistics
Matches: 99, Mismatches: 13, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
131 81 0.82
132 18 0.18
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.20
Consensus pattern (132 bp):
ACAACACCTTCCGGTAGGGAAGGGCAAACTGGGAATTTAGACAACACCTTCCGGTGGGGAAGGGC
AAACTGATAAACTAAACTTAAACAACACCTTCCGATGAGGAAGAGCAATTTGGTAAACTATACTT
AA
Found at i:24735 original size:86 final size:85
Alignment explanation
Indices: 24348--24756 Score: 398
Period size: 86 Copynumber: 4.7 Consensus size: 85
24338 TTCCAGTTAT
* * ** * * *
24348 GAAGGGCAAGCTGGTAAACTAAACAACACCTTCCGGCGAGGAAGGGCAAATTGGGGTAAAGCAGA
1 GAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGCAAATT--GGTAAAGTAGA
* * * *
24413 CTTAAATAACACCTTCGGGTGGG
64 CTTAAACAACACCTTCCGAT-AG
* *
24436 GAAGGGCAAACTGGGAATTTAGACAACACCTTCCGGTGGGGAAGGGCAAACTGGT-AA-T----T
1 GAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGTAAAGTAGACT
* * * *
24495 TAGACAACACCTTTCGGTGGG
66 TAAACAACACCTTCCGAT-AG
** * * *
24516 GAAGGGCAAACTGATAAACTAAACTTAAACAACACCTTCCGGTGGGGAAGAGCAATTTGGTAAAC
1 GAAGGGCAAACTG-GGAA-T----TTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGTAAAG
* *
24581 TATACTTAAACAACACCTTCCGGTAG
60 TAGACTTAAACAACACCTTCCGATAG
* * * *
24607 GGAGGGCAAATTGGGAATTTAGACAACACCTTCCGGTGGGGAAGGGCAAATTGGTAAAGTGGACT
1 GAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGTAAAGTAGACT
*
24672 TAAACAACATCTTCCGATGAG
66 TAAACAACACCTTCCGAT-AG
*
24693 GAAGGGCAAACTGGGAATTTAAACAATACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAGTAGA
1 GAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGCAAATT-GGTAAAGTAGA
24757 GGGCAAACTG
Statistics
Matches: 268, Mismatches: 39, Indels: 29
0.80 0.12 0.09
Matches are distributed among these distances:
80 31 0.12
81 2 0.01
82 1 0.00
85 59 0.22
86 86 0.32
87 12 0.04
88 45 0.17
89 1 0.00
90 2 0.01
91 12 0.04
92 17 0.06
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (85 bp):
GAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGTAAAGTAGACT
TAAACAACACCTTCCGATAG
Found at i:24790 original size:61 final size:61
Alignment explanation
Indices: 24695--24814 Score: 222
Period size: 61 Copynumber: 2.0 Consensus size: 61
24685 CCGATGAGGA
*
24695 AGGGCAAACTGGGAATTTAAACAATACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAGTAG
1 AGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAGTAG
*
24756 AGGGCAAACTGGGAATTTAGACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAGT
1 AGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAGT
24815 GGACTTAAAC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.33, C:0.14, G:0.33, T:0.19
Consensus pattern (61 bp):
AGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAGTAG
Found at i:24879 original size:148 final size:147
Alignment explanation
Indices: 24608--24893 Score: 500
Period size: 148 Copynumber: 1.9 Consensus size: 147
24598 TTCCGGTAGG
*
24608 GAGGGCAAATTGGGAATTTAGACAACACCTTCCGGTGGGGAAGGGCAAATTGGTAAAGTGGACTT
1 GAGGGCAAACTGGGAATTTAGACAACACCTTCCGGTGGGGAAGGGCAAATTGGTAAAGTGGACTT
* * * *
24673 AAACAACATCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAATACCTTCCGGTGGGGAAGG
66 AAACAACACCTTCCGATGAGGAAAGGCAAACTGGGAATCTAAACAACACCTTCCGGTGGGGAAGG
24738 GCAAATTGGGTAAAGTA
131 GCAAATTGGGTAAAGTA
24755 GAGGGCAAACTGGGAATTTAGACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAGTGGACT
1 GAGGGCAAACTGGGAATTTAGACAACACCTTCCGGTGGGGAAGGGCAAATT-GGTAAAGTGGACT
* *
24820 TAAACAACACCTTCCGATGAGGAAAGGCAAACTGGGAATCTAAACGACACCTTCTGGTGGGGAAG
65 TAAACAACACCTTCCGATGAGGAAAGGCAAACTGGGAATCTAAACAACACCTTCCGGTGGGGAAG
24885 GGCAAATTG
130 GGCAAATTG
24894 CGTATTTAGA
Statistics
Matches: 131, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
147 50 0.38
148 81 0.62
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (147 bp):
GAGGGCAAACTGGGAATTTAGACAACACCTTCCGGTGGGGAAGGGCAAATTGGTAAAGTGGACTT
AAACAACACCTTCCGATGAGGAAAGGCAAACTGGGAATCTAAACAACACCTTCCGGTGGGGAAGG
GCAAATTGGGTAAAGTA
Done.