Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017057.1 Corchorus olitorius cultivar O-4 contig17090, 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: 5383
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Found at i:1626 original size:39 final size:40
Alignment explanation
Indices: 1568--1648 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 40
1558 TTTAATTCTG
* *
1568 ATGTAATATAAATAATAACTAAAATAGGTATATTAATTAA
1 ATGTAATATAAATAATAACTAAAATACGTACATTAATTAA
* * *
1608 ATGTAATAT-TATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATAAATAATAACTAAAATACGTACATTAATTAA
1647 AT
1 AT
1649 TCTTAGGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 27 0.75
40 9 0.25
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.37
Consensus pattern (40 bp):
ATGTAATATAAATAATAACTAAAATACGTACATTAATTAA
Found at i:1666 original size:24 final size:25
Alignment explanation
Indices: 1639--1685 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1629 AATACTTACA
1639 TTAATT-AAATTCTTAGGTATTTTT
1 TTAATTCAAATTCTTAGGTATTTTT
1663 TTAATTCAAATTCTTAGGTATTT
1 TTAATTCAAATTCTTAGGTATTT
1686 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:2028 original size:207 final size:210
Alignment explanation
Indices: 1759--2182 Score: 709
Period size: 210 Copynumber: 2.0 Consensus size: 210
1749 TTCCTTAATA
1759 ATAAATAAATCGGATCTTAATATCTTTAATTTATAATTTTGAAATTTTGTTTGACATTGATCTAA
1 ATAAATAAATCGGATCTTAATATC-TT-ATTTATAATTTTGAAATTTTGTTTGACATTGATCTAA
1824 -TTTAATTTAATAAATCAACCACTAATGTTCAA-CTA-ATTTTTTTT-GGTATAGTTCTATATAT
64 TTTTAATTTAATAAATCAACCACTAATGTTCAATCTACATTTTTTTTCGGTATAG-T-TATATAT
*
1885 ATATAA-TAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACATAAAAAA
127 ATATAATTAATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACATAAAAAA
*
1949 TTAATAACATTCACCATTG
192 TTAATAACATTCACCATTC
1968 ATAAATAAATCGGATCATTAATATC-T-TTTATAATTTTGAAATTTTTGTTTGACATTGATCTAA
1 ATAAATAAATCGGATC-TTAATATCTTATTTATAATTTTGAAA-TTTTGTTTGACATTGATCTAA
*
2031 TTTTAATTTAATAAATCAACCACTAATGTTCAATCTACTTTTTTTTTCGGTATAGTTATATATAT
64 TTTTAATTTAATAAATCAACCACTAATGTTCAATCTACATTTTTTTTCGGTATAGTTATATATAT
*
2096 ATAATTAATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATT
129 ATAATTAATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACATAAAAAATT
2161 AATAACATTCACCATTC
194 AATAACATTCACCATTC
2178 ATAAA
1 ATAAA
2183 GTTATTAAGC
Statistics
Matches: 204, Mismatches: 4, Indels: 13
0.92 0.02 0.06
Matches are distributed among these distances:
206 15 0.07
207 21 0.10
208 33 0.16
209 32 0.16
210 96 0.47
211 7 0.03
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (210 bp):
ATAAATAAATCGGATCTTAATATCTTATTTATAATTTTGAAATTTTGTTTGACATTGATCTAATT
TTAATTTAATAAATCAACCACTAATGTTCAATCTACATTTTTTTTCGGTATAGTTATATATATAT
AATTAATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACATAAAAAATTAA
TAACATTCACCATTC
Done.