Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015666.1 Corchorus olitorius cultivar O-4 contig15699, 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: 33496
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--32 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33 TGCATAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1062 original size:28 final size:29
Alignment explanation
Indices: 1023--1085 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
1013 ACTTGTAGCG
1023 TTTGGACATTTG-TCTCCTGAACT-TCAAT
1 TTTGGACATTTGCTCTCC-GAACTCTCAAT
*
1051 TTTGGACATTTGCTCTCCGGACTCTCAAT
1 TTTGGACATTTGCTCTCCGAACTCTCAAT
1080 TTTGGA
1 TTTGGA
1086 TGTTTTTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 16 0.50
29 16 0.50
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.41
Consensus pattern (29 bp):
TTTGGACATTTGCTCTCCGAACTCTCAAT
Found at i:9687 original size:40 final size:39
Alignment explanation
Indices: 9643--9766 Score: 169
Period size: 40 Copynumber: 3.1 Consensus size: 39
9633 TCGCCATTGG
9643 TCATATCTTGTCTCGGTATAAACACTCTAGTATCCGGTAA
1 TCATAT-TTGTCTCGGTATAAACACTCTAGTATCCGGTAA
*
9683 TCATATTTTGTCTCGGTATAAACACTCTAATATCCGGTAA
1 TCATA-TTTGTCTCGGTATAAACACTCTAGTATCCGGTAA
* **
9723 TCATATTTCGT-TACGATATAAACACTCCGGTATCCGGTAA
1 TCATATTT-GTCT-CGGTATAAACACTCTAGTATCCGGTAA
9763 TCAT
1 TCAT
9767 GGTATAAACA
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
39 4 0.05
40 71 0.93
41 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (39 bp):
TCATATTTGTCTCGGTATAAACACTCTAGTATCCGGTAA
Found at i:9936 original size:48 final size:49
Alignment explanation
Indices: 9842--9936 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 49
9832 TAAGACTCGA
* * * **
9842 ATAAGACTCGAATCGGAATAGATATTGCATTTCTTCTATTTTTCCATTT
1 ATAAGACTCGAATCCGAATAGATATTGAATTTCTTCTACTCATCCATTT
*
9891 ATAAGACTCGAATCCGAAT-GGTATTGAATTTCTTCTACTCATCCAT
1 ATAAGACTCGAATCCGAATAGATATTGAATTTCTTCTACTCATCCAT
9937 GTCAAAAAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 22 0.55
49 18 0.45
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (49 bp):
ATAAGACTCGAATCCGAATAGATATTGAATTTCTTCTACTCATCCATTT
Found at i:19254 original size:16 final size:16
Alignment explanation
Indices: 19233--19280 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
19223 CTTCTTTCTC
19233 TTTCTTTTTTCTTTTT
1 TTTCTTTTTTCTTTTT
19249 TTTC-TTTTTC-TTTT
1 TTTCTTTTTTCTTTTT
* *
19263 ATTCTAATTTTCTTTTT
1 TTTCT-TTTTTCTTTTT
19280 T
1 T
19281 GGGTTTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 7 0.27
15 6 0.23
16 9 0.35
17 4 0.15
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTCTTTTTTCTTTTT
Found at i:26027 original size:19 final size:19
Alignment explanation
Indices: 25992--26028 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
25982 CTTATATGTA
* *
25992 ATCGTTTCACTATCGTTTG
1 ATCGTTTCACCACCGTTTG
26011 ATCGTTTCACCACCGTTT
1 ATCGTTTCACCACCGTTT
26029 TAGGTCCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.27, G:0.14, T:0.43
Consensus pattern (19 bp):
ATCGTTTCACCACCGTTTG
Found at i:29283 original size:49 final size:47
Alignment explanation
Indices: 29215--29349 Score: 159
Period size: 49 Copynumber: 2.9 Consensus size: 47
29205 ATATTAATTT
* **
29215 TTTTATAATTTCCTTTTTATTAATAAATTCCACATAACTCATTTTTGTA
1 TTTTATAATTTCCTGTTTATTAATAAATTCCACATAACTCA--TGGGTA
29264 TTTTATAATTTCCTGTTTATTAAT-AATATCCACATAACTCATGGGTA
1 TTTTATAATTTCCTGTTTATTAATAAAT-TCCACATAACTCATGGGTA
* * **
29311 --TTATAATATCCTGTTTATTAATAATTTCCATGTAACTCA
1 TTTTATAATTTCCTGTTTATTAATAAATTCCACATAACTCA
29350 ACTACCAATG
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
45 32 0.42
46 2 0.03
47 4 0.05
48 3 0.04
49 36 0.47
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.48
Consensus pattern (47 bp):
TTTTATAATTTCCTGTTTATTAATAAATTCCACATAACTCATGGGTA
Done.