Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016722.1 Corchorus olitorius cultivar O-4 contig16755, 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: 40687
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:7300 original size:5 final size:5
Alignment explanation
Indices: 7290--7323 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
7280 TTCAGCCGGT
7290 TTTTC TTTTC TTTTC TTTTC TTTTCC TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTT-C TTTTC TTTT
7324 TAAATACTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:7689 original size:20 final size:20
Alignment explanation
Indices: 7664--7702 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7654 CATATAAAAT
* *
7664 AATAATAATTAATTTTTAAA
1 AATAATAACTAATTATTAAA
7684 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
7703 TTTTAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:7701 original size:27 final size:26
Alignment explanation
Indices: 7661--7712 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
7651 AATCATATAA
*
7661 AATAATAATAATTAATTTTTAAAAAT
1 AATAATAATAATTAATTTTAAAAAAT
*
7687 AATAACTAATTATTAATTTTAAAAAA
1 AATAA-TAATAATTAATTTTAAAAAA
7713 AAAGTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
AATAATAATAATTAATTTTAAAAAAT
Found at i:7800 original size:32 final size:33
Alignment explanation
Indices: 7740--7808 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 33
7730 GATGGCTGGT
* *
7740 CGCGAGCCGATTGCGACCATGCCGCGGCTCGGA
1 CGCGAGCCGATTGCGACCAAGCCACGGCTCGGA
*
7773 CGCGAGCCGA-TGCGACCAAGCCACGGCTCGGT
1 CGCGAGCCGATTGCGACCAAGCCACGGCTCGGA
7805 CGCG
1 CGCG
7809 CGCGGCTGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 23 0.70
33 10 0.30
ACGTcount: A:0.16, C:0.38, G:0.36, T:0.10
Consensus pattern (33 bp):
CGCGAGCCGATTGCGACCAAGCCACGGCTCGGA
Found at i:8053 original size:17 final size:18
Alignment explanation
Indices: 8028--8074 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
8018 ATTGAGGTTT
*
8028 GAAAGTTTGAA-AATTGA
1 GAAAATTTGAAGAATTGA
8045 GAAAATTTGAGAGAATTGA
1 GAAAATTTGA-AGAATTGA
*
8064 -AAATTTTGAAG
1 GAAAATTTGAAG
8075 TTTGAACGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 11 0.42
18 9 0.35
19 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (18 bp):
GAAAATTTGAAGAATTGA
Found at i:11259 original size:177 final size:177
Alignment explanation
Indices: 10978--11306 Score: 441
Period size: 177 Copynumber: 1.9 Consensus size: 177
10968 AGGTGATTTA
*
10978 AGTGTCTATTAAAAGATTATTCAATGATCTACAATTTTCATAAGGACTCGAAAACTAAATTTAAT
1 AGTGTCTATTAAAAGATTATTCAATGATCTACAACTTTCATAAGGACTCGAAAACTAAATTTAAT
* * * * **
11043 GTTTCAAGTATCAAAAATGCTTCCGAAAAATTTGTTGTTTCCATTAACGGGAATAGACGGTCCAC
66 GTTTCAAGTATCAAAAATGCTTCCAAAAAATTAGTTGTTTCCAGTAACGGAAATAGACAATCCAC
*
11108 TTAATATTATATAACTTT-TGCTCCAGATGTCTGATTGAGATGATTCG
131 TTAATATTACATAA-TTTGTGCTCCAGATGTCTGATTGAGATGATTCG
* * * *
11155 AGTGTCTCTTGAAAGGTTATTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTAA
1 AGTGTCTATTAAAAGATTATTCAATGATCTACAACTTTCAT-AAGGACTCGAAAACTAAATTTAA
* ** *
11220 TG-TTCAAGGTAT-AAAATTG-TTTTAAAAGAATTAGTTGTTTCGAGTAACGGAAATAGACAATC
65 TGTTTCAA-GTATCAAAAATGCTTCCAAAA-AATTAGTTGTTTCCAGTAACGGAAATAGACAATC
*
11282 TACTTAATATTACATAATTTGTGCT
128 CACTTAATATTACATAATTTGTGCT
11307 TCTGGTGGAA
Statistics
Matches: 131, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
176 8 0.06
177 94 0.72
178 29 0.22
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (177 bp):
AGTGTCTATTAAAAGATTATTCAATGATCTACAACTTTCATAAGGACTCGAAAACTAAATTTAAT
GTTTCAAGTATCAAAAATGCTTCCAAAAAATTAGTTGTTTCCAGTAACGGAAATAGACAATCCAC
TTAATATTACATAATTTGTGCTCCAGATGTCTGATTGAGATGATTCG
Found at i:11865 original size:7 final size:7
Alignment explanation
Indices: 11853--11877 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11843 ACATCAACTT
11853 CAATTTC
1 CAATTTC
11860 CAATTTC
1 CAATTTC
11867 CAATTTC
1 CAATTTC
11874 CAAT
1 CAAT
11878 CTGAACTTGA
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:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (7 bp):
CAATTTC
Found at i:13346 original size:42 final size:42
Alignment explanation
Indices: 13287--13366 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
13277 AAGGATCATG
13287 ATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTATA
1 ATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTATA
*
13329 ATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 ATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
13367 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.47
Consensus pattern (42 bp):
ATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTATA
Found at i:13351 original size:21 final size:21
Alignment explanation
Indices: 13287--13353 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
13277 AAGGATCATG
13287 ATTTGAGTTGAGTATTTCTTA
1 ATTTGAGTTGAGTATTTCTTA
*** *
13308 ATTT-A-CAAAGAATTTTCTATA
1 ATTTGAGTTGAGTA-TTTCT-TA
13329 ATTTGAGTTGAGTATTTCTTA
1 ATTTGAGTTGAGTATTTCTTA
13350 ATTT
1 ATTT
13354 ACAGAGAATT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 3 0.09
20 6 0.18
21 16 0.47
22 6 0.18
23 3 0.09
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (21 bp):
ATTTGAGTTGAGTATTTCTTA
Found at i:30671 original size:2 final size:2
Alignment explanation
Indices: 30664--30697 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30654 TTTCTACTTT
30664 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
30698 AAAGAGAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34107 original size:8 final size:9
Alignment explanation
Indices: 34086--34120 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
34076 GGTATACAGA
34086 AAAAAATAC
1 AAAAAATAC
34095 AAAAAATAC
1 AAAAAATAC
34104 AAAAAAGATAC
1 -AAAAA-ATAC
34115 AAAAAA
1 AAAAAA
34121 GAAAAACGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 10 0.42
10 10 0.42
11 4 0.17
ACGTcount: A:0.80, C:0.09, G:0.03, T:0.09
Consensus pattern (9 bp):
AAAAAATAC
Found at i:34114 original size:20 final size:21
Alignment explanation
Indices: 34079--34120 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
34069 CAAAAAAGGT
34079 ATACAGAAAAAAATACAAAAA
1 ATACAGAAAAAAATACAAAAA
*
34100 ATACA-AAAAAGATACAAAAA
1 ATACAGAAAAAAATACAAAAA
34120 A
1 A
34121 GAAAAACGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.76, C:0.10, G:0.05, T:0.10
Consensus pattern (21 bp):
ATACAGAAAAAAATACAAAAA
Found at i:34121 original size:11 final size:11
Alignment explanation
Indices: 34069--34122 Score: 58
Period size: 11 Copynumber: 4.8 Consensus size: 11
34059 TTTTTTTTGG
34069 CAAAAAAGGTATA
1 CAAAAAA-G-ATA
*
34082 CAGAAAAAAATA
1 CA-AAAAAGATA
34094 C-AAAAA-ATA
1 CAAAAAAGATA
34103 CAAAAAAGATA
1 CAAAAAAGATA
34114 CAAAAAAGA
1 CAAAAAAGA
34123 AAAACGAGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
9 4 0.11
10 10 0.27
11 12 0.32
12 4 0.11
13 2 0.05
14 5 0.14
ACGTcount: A:0.72, C:0.09, G:0.09, T:0.09
Consensus pattern (11 bp):
CAAAAAAGATA
Done.