Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022953.1 Corchorus olitorius cultivar O-4 contig22986, 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: 4673
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Found at i:1823 original size:58 final size:57
Alignment explanation
Indices: 1732--1840 Score: 173
Period size: 58 Copynumber: 1.9 Consensus size: 57
1722 ATCATGCCTC
*
1732 GGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGTCTT
1 GGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGTCTT
* * *
1789 GGTCCGAAAACGTCTTTTTTTATGCATCTAATAAAGAACATGTCACTTGATA
1 GGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAACATGTCACTCGATA
1841 TTTGATTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 13 0.28
58 34 0.72
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (57 bp):
GGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAAGTCTT
Found at i:3658 original size:24 final size:25
Alignment explanation
Indices: 3630--3676 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
3620 AATATTTACA
3630 TTAATT-AAATTCTTAGGTATTTTT
1 TTAATTCAAATTCTTAGGTATTTTT
3654 TTAATTCAAATTCTTAGGTATTT
1 TTAATTCAAATTCTTAGGTATTT
3677 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (25 bp):
TTAATTCAAATTCTTAGGTATTTTT
Found at i:3992 original size:205 final size:202
Alignment explanation
Indices: 3749--4160 Score: 738
Period size: 203 Copynumber: 2.0 Consensus size: 202
3739 TTCCTTAATA
3749 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
3814 ATTTAATAAATCAACC-ACTAATGTTCAACTAATTTTTTTTTGGTATACTTCTATATATATAATA
66 ATTTAATAAATCAACCTACTAATGTTCAACTAA-TTTTTTTTGGTATACTT-T-TATATATAATA
*
3878 GTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTGAAAAA-TTAATAAC
128 ATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTT-AAAAAGTTAATAAC
*
3942 ATTTACCATTG
192 ATTCACCATTG
3953 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
*
4018 AATTTAATAAATCAACCTACTAATGTTCAACTAATTTTTTTTGGTATAGTTTTATATATAATAAT
65 AATTTAATAAATCAACCTACTAATGTTCAACTAATTTTTTTTGGTATACTTTTATATATAATAAT
4083 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAGTTAATAACATT
130 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAGTTAATAACATT
4148 CACCATTG
195 CACCATTG
4156 ATAAA
1 ATAAA
4161 GTTATTAAGC
Statistics
Matches: 202, Mismatches: 3, Indels: 7
0.95 0.01 0.03
Matches are distributed among these distances:
202 5 0.02
203 83 0.41
204 17 0.08
205 81 0.40
206 16 0.08
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (202 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCTACTAATGTTCAACTAATTTTTTTTGGTATACTTTTATATATAATAATA
ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAGTTAATAACATTC
ACCATTG
Done.