Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012559.1 Corchorus olitorius cultivar O-4 contig12592, 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: 16900
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1678 original size:27 final size:28
Alignment explanation
Indices: 1632--1693 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
1622 CTTTGTTTTC
1632 AAAT-ATATTTCTAAATTTCCATTATT-
1 AAATAATATTTCTAAATTTCCATTATTA
*
1658 AAATAATATTT-TAATTATTCCATTATTA
1 AAATAATATTTCTAAAT-TTCCATTATTA
1686 AAATAATA
1 AAATAATA
1694 GAAATTTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 8 0.25
27 16 0.50
28 8 0.25
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (28 bp):
AAATAATATTTCTAAATTTCCATTATTA
Found at i:3839 original size:23 final size:22
Alignment explanation
Indices: 3808--3872 Score: 94
Period size: 23 Copynumber: 2.9 Consensus size: 22
3798 TTTCATAAGG
*
3808 AGGTTATCAAAATTTTATAGGA
1 AGGTTATCAAAATTTTATAGCA
3830 AGGTTTATCAAAATTTTATAGCA
1 AGG-TTATCAAAATTTTATAGCA
* *
3853 AGGTTATCACAATTTCATAG
1 AGGTTATCAAAATTTTATAG
3873 TGTGATTATC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
22 18 0.46
23 21 0.54
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
AGGTTATCAAAATTTTATAGCA
Found at i:4039 original size:22 final size:22
Alignment explanation
Indices: 3788--4070 Score: 129
Period size: 22 Copynumber: 12.8 Consensus size: 22
3778 AAAATTTGTA
**
3788 GTTATCAAGCTTTCATAAG-GAG
1 GTTATCAAAATTTCAT-AGTGAG
*
3810 GTTATCAAAATTTTATAG-GAAG
1 GTTATCAAAATTTCATAGTG-AG
* **
3832 GTTTATCAAAATTTTATAGCAAG
1 G-TTATCAAAATTTCATAGTGAG
* *
3855 GTTATCACAATTTCATAGTGTG
1 GTTATCAAAATTTCATAGTGAG
* * *
3877 ATTATCAAAACTTT-AGAGTGTG
1 GTTATCAAAA-TTTCATAGTGAG
*
3899 ATTA-CTAACAA-TTCATA-TGGAG
1 GTTATC-AA-AATTTCATAGT-GAG
* * *
3921 GTTTTTAAATTTTCATGACGT--G
1 GTTATCAAAATTTCAT-A-GTGAG
* *
3943 GTTATCAATATATCATA-TGGAG
1 GTTATCAAAATTTCATAGT-GAG
* *
3965 GTTATCAACATCTCATAGT-ATTG
1 GTTATCAAAATTTCATAGTGA--G
* * *
3988 GTTATCAAAATTTCATTGGGAA
1 GTTATCAAAATTTCATAGTGAG
*
4010 ATTATCAAAATTTCATAGTGAG
1 GTTATCAAAATTTCATAGTGAG
* * *
4032 GTTTTCAAAATTCCTTAG-GAAG
1 GTTATCAAAATTTCATAGTG-AG
*
4054 GTTAACAAAATTTCATA
1 GTTATCAAAATTTCATA
4071 AGGTTAAAAA
Statistics
Matches: 198, Mismatches: 42, Indels: 42
0.70 0.15 0.15
Matches are distributed among these distances:
19 1 0.01
21 11 0.06
22 141 0.71
23 43 0.22
24 1 0.01
25 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.37
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGAG
Found at i:4085 original size:20 final size:18
Alignment explanation
Indices: 4051--4090 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
4041 ATTCCTTAGG
*
4051 AAGGTTAACAAAATTTCAT
1 AAGGTTAAAAAAATTT-AT
4070 AAGGTTAAAAAAAATTTAT
1 AAGGTT-AAAAAAATTTAT
4089 AA
1 AA
4091 AAACGTTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.30
Consensus pattern (18 bp):
AAGGTTAAAAAAATTTAT
Found at i:8745 original size:15 final size:15
Alignment explanation
Indices: 8727--8757 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
8717 CAAGGGCTGA
*
8727 AATTAAATAATTATT
1 AATTAAATAATAATT
8742 AATTAAATAATAATT
1 AATTAAATAATAATT
8757 A
1 A
8758 TTTTTATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTAAATAATAATT
Done.