Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006528.1 Corchorus olitorius cultivar O-4 contig06553, 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: 3317
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Found at i:1821 original size:42 final size:40
Alignment explanation
Indices: 1762--1845 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 40
1752 TTTAATTCCT
*
1762 ATGTAATATATATAATAACTAAAATACTTACATTATTTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
1802 ATGTAATAATACTATAATAACTAGAATACTTGCATTAATTAA
1 ATGTAAT-ATA-TATAATAACTAAAATACTTACATTAATTAA
1844 AT
1 AT
1846 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
40 7 0.18
41 3 0.08
42 29 0.74
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:1872 original size:25 final size:24
Alignment explanation
Indices: 1836--1882 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
1826 AATACTTGCA
1836 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
1860 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
1883 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 (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Found at i:2203 original size:201 final size:194
Alignment explanation
Indices: 1958--2358 Score: 642
Period size: 201 Copynumber: 2.0 Consensus size: 194
1948 TTCCTTAATA
*
1958 ATAAATAAATCAGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCAGATCTTTAATATCCTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
2023 AATTTAATAAATCAACCACTAATGTTCAACTAA-TTTTTTTGGTATAGTTCTATATATAATAGTA
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAG---T-T-T-T-ATA-TA
*
2087 ATGTGTTGTATTTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
123 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
2152 ACAATTG
188 ACAATTG
* *
2159 ATAAATAAATCGGATCTTTAATATCCTTTATAATTTTGAAATTTTTTTTGACATTGATCTAATTT
1 ATAAATAAATCAGATCTTTAATATCCTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* *
2224 AATTTAATAATTCGACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTTTTATATAATGTGTT
66 AATTTAATAAATCAACCACTAATGTTCAACTAA-TTTTTTTTGGTATAGTTTTATATAATGTGTT
* *
2289 GTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTGAAAAATTAATAACATTCACCATTG
130 GTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACAATTG
2354 ATAAA
1 ATAAA
2359 GTTATTAAGC
Statistics
Matches: 190, Mismatches: 8, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
195 76 0.40
196 3 0.02
197 1 0.01
198 1 0.01
199 1 0.01
200 1 0.01
201 93 0.49
203 14 0.07
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.45
Consensus pattern (194 bp):
ATAAATAAATCAGATCTTTAATATCCTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTTTATATAATGTGTTG
TATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCACAATTG
Found at i:2916 original size:36 final size:36
Alignment explanation
Indices: 2869--2939 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
2859 TGAGATTTTG
* *
2869 AAGAAATATGATAATCAAAATTACAAAAAATGTAAT
1 AAGAAATATGATAACCAAAATCACAAAAAATGTAAT
*
2905 AAGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AAGAAATATGATAACCAAAATCACAAAAAATGTAA
2940 GGTTATTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.61, C:0.08, G:0.10, T:0.21
Consensus pattern (36 bp):
AAGAAATATGATAACCAAAATCACAAAAAATGTAAT
Done.