Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010369.1 Corchorus capsularis cultivar CVL-1 contig10390, 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: 17390
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:1017 original size:15 final size:16
Alignment explanation
Indices: 990--1023 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
980 TTTTCTTTGT
990 ATTTTATTTTTATACA
1 ATTTTATTTTTATACA
1006 ATTTTA-TTTTATACA
1 ATTTTATTTTTATACA
1021 ATT
1 ATT
1024 GACTCGGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTATTTTTATACA
Found at i:3913 original size:30 final size:29
Alignment explanation
Indices: 3851--3920 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
3841 ACCGAACCGT
****
3851 CAAATAAGCCCCTGAACTATTATTTCAGC
1 CAAATAAGCCCCTGAACTATTAAAAAAGC
*
3880 CAAATAAGCCCCTGAACTCTTAAAAAAAGC
1 CAAATAAGCCCCTGAACTATT-AAAAAAGC
3910 CAAATAAGCCC
1 CAAATAAGCCC
3921 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAAGC
Found at i:4969 original size:7 final size:7
Alignment explanation
Indices: 4957--4983 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4947 TTCAGAGCCA
4957 TATATAG
1 TATATAG
4964 TATATAG
1 TATATAG
4971 TATATAG
1 TATATAG
4978 TATATA
1 TATATA
4984 TAATATGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (7 bp):
TATATAG
Found at i:6305 original size:89 final size:89
Alignment explanation
Indices: 6212--6545 Score: 534
Period size: 89 Copynumber: 3.7 Consensus size: 89
6202 GTGGATTATA
6212 GAATAAACTTGATGATGCTATATGTATATATTCACATACCCATCTATCTCATTAGTAGATATACA
1 GAATAAACTTGATGATGCTATATGTATATATTCACATACCCATCTATCTCATTAGTAGATATACA
6277 TGAGATGAGGGTGTGTAATGGAGT
66 TGAGATGAGGGTGTGTAATGGAGT
6301 GAATAAACTTGATGATGCTATATGTATATATTCACATACCCATCTATCTCATTAGTAGATATACA
1 GAATAAACTTGATGATGCTATATGTATATATTCACATACCCATCTATCTCATTAGTAGATATACA
*
6366 TGAGATGAGGGTGTGTAATGGTGT
66 TGAGATGAGGGTGTGTAATGGAGT
6390 GAATAAACTTGATGATGCTATATGTATATATTCACATACCCATCTATCTCATTAGTAGATATAC-
1 GAATAAACTTGATGATGCTATATGTATATATTCACATACCCATCTATCTCATTAGTAGATATACA
6454 ----ATGAGGGTGTGTAATGGAGT
66 TGAGATGAGGGTGTGTAATGGAGT
6474 GAATAAACTTGATGATGCTATATGTATGTATGTACATTCACATACCCATATTCTATCTCATTAGT
1 GAATAAACTTGATGATGCTATATGTA--TA--T--ATTCACATACCC--A-TCTATCTCATTAGT
*
6539 AGGTATA
57 AGATATA
6546 TGTGGTGTGT
Statistics
Matches: 233, Mismatches: 3, Indels: 14
0.93 0.01 0.06
Matches are distributed among these distances:
84 45 0.19
86 2 0.01
88 1 0.00
89 152 0.65
90 12 0.05
92 1 0.00
93 20 0.09
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (89 bp):
GAATAAACTTGATGATGCTATATGTATATATTCACATACCCATCTATCTCATTAGTAGATATACA
TGAGATGAGGGTGTGTAATGGAGT
Found at i:8203 original size:33 final size:32
Alignment explanation
Indices: 8166--8272 Score: 117
Period size: 33 Copynumber: 3.2 Consensus size: 32
8156 CGCCTAGCGA
* *
8166 TGGCCGGT-TGTGACCGGACATGTCCATGTCGCG
1 TGGCCGGTGT-TGGCCGGACATCTCCA-GTCGCG
* *
8199 TGGCCGGTGTTGGCCGGGCATCTCCGAGTCACG
1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG
* *
8232 TGGCCGGTGTTGGCCGGACTTCTCCAAGTCGCA
1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG
8265 TGGCCGGT
1 TGGCCGGT
8273 CACTAGTGCT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
33 61 0.97
34 2 0.03
ACGTcount: A:0.10, C:0.29, G:0.37, T:0.23
Consensus pattern (32 bp):
TGGCCGGTGTTGGCCGGACATCTCCAGTCGCG
Found at i:13740 original size:8 final size:8
Alignment explanation
Indices: 13712--13745 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
13702 GAATCGGCTA
13712 TGAATTTT
1 TGAATTTT
*
13720 TGAAGTTTC
1 TGAA-TTTT
13729 TGAATTTT
1 TGAATTTT
13737 TGAATTTT
1 TGAATTTT
13745 T
1 T
13746 CAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:14747 original size:33 final size:32
Alignment explanation
Indices: 14710--14816 Score: 117
Period size: 33 Copynumber: 3.2 Consensus size: 32
14700 CGCCTAGCGA
* *
14710 TGGCCGGT-TGTGACCGGACATGTCCATGTCGCG
1 TGGCCGGTGT-TGGCCGGACATCTCCA-GTCGCG
* *
14743 TGGCCGGTGTTGGCCGGGCATCTCCGAGTCACG
1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG
* *
14776 TGGCCGGTGTTGGCCGGACTTCTCCAAGTCGCA
1 TGGCCGGTGTTGGCCGGACATCTCC-AGTCGCG
14809 TGGCCGGT
1 TGGCCGGT
14817 CACTAGTGCT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
33 61 0.97
34 2 0.03
ACGTcount: A:0.10, C:0.29, G:0.37, T:0.23
Consensus pattern (32 bp):
TGGCCGGTGTTGGCCGGACATCTCCAGTCGCG
Found at i:16827 original size:69 final size:69
Alignment explanation
Indices: 16715--16844 Score: 242
Period size: 69 Copynumber: 1.9 Consensus size: 69
16705 TGTCCTACTA
16715 TATATCCTAGTCTCCTAGATTTCGATTAAATAATAAATCAATAGATTGAAACTTTAATTTTTTAT
1 TATATCCTAGTCTCCTAGATTTCGATTAAATAATAAATCAATAGATTGAAACTTTAATTTTTTAT
16780 TTGG
66 TTGG
* *
16784 TATATCCTAGTCTCCTAGATTTCGATTAAATTATAAATTAATAGATTGAAACTTTAATTTT
1 TATATCCTAGTCTCCTAGATTTCGATTAAATAATAAATCAATAGATTGAAACTTTAATTTT
16845 ATTTTTATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (69 bp):
TATATCCTAGTCTCCTAGATTTCGATTAAATAATAAATCAATAGATTGAAACTTTAATTTTTTAT
TTGG
Done.