Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018586.1 Corchorus olitorius cultivar O-4 contig18619, 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: 5272
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Found at i:715 original size:22 final size:22
Alignment explanation
Indices: 670--832 Score: 99
Period size: 22 Copynumber: 7.4 Consensus size: 22
660 TTGGAAACAT
* *
670 CTTTGCAGAG-ATT-CTTTCTT
1 CTTTGCAGAGCATTATTTTCTA
690 CTTTGCAGAGCATTATTTTCTA
1 CTTTGCAGAGCATTATTTTCTA
712 CTTTGCAGAGCATTATTTTCTTCAA
1 CTTTGCAGAGCATTATTTTC-T--A
* *** * **
737 CTTCAGCTTTGCACTATTGGAAAC-A
1 CTT-TGCAGAGCATTATT---TTCTA
*
762 TCTTTGCAGAG-A-T-TCTT-T-
1 -CTTTGCAGAGCATTATTTTCTA
780 CTTTGCAGAGCATTATTTTCTA
1 CTTTGCAGAGCATTATTTTCTA
*
802 CTTTGCAGAGCATTATTTTCCA
1 CTTTGCAGAGCATTATTTTCTA
824 CTTTGCAGA
1 CTTTGCAGA
833 ACACTTCTTG
Statistics
Matches: 109, Mismatches: 18, Indels: 30
0.69 0.11 0.19
Matches are distributed among these distances:
17 10 0.09
18 1 0.01
19 1 0.01
20 13 0.12
21 4 0.04
22 56 0.51
23 2 0.02
24 1 0.01
25 8 0.07
26 12 0.11
29 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (22 bp):
CTTTGCAGAGCATTATTTTCTA
Found at i:917 original size:2 final size:2
Alignment explanation
Indices: 879--903 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
869 AGGATGATTT
879 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
904 CATTCTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1953 original size:12 final size:12
Alignment explanation
Indices: 1936--1961 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1926 TTTAGATTTA
1936 TTCTTCTAGTTT
1 TTCTTCTAGTTT
1948 TTCTTCTAGTTT
1 TTCTTCTAGTTT
1960 TT
1 TT
1962 AGGCAAGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (12 bp):
TTCTTCTAGTTT
Found at i:3905 original size:20 final size:20
Alignment explanation
Indices: 3877--3914 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3867 CGCTTTTTCT
*
3877 CATCTTTTTCCTTCATTTTA
1 CATCATTTTCCTTCATTTTA
*
3897 CATCATTTTCTTTCATTT
1 CATCATTTTCCTTCATTT
3915 CCTTTCTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.61
Consensus pattern (20 bp):
CATCATTTTCCTTCATTTTA
Found at i:4151 original size:391 final size:387
Alignment explanation
Indices: 3430--4217 Score: 1380
Period size: 391 Copynumber: 2.0 Consensus size: 387
3420 AAATTCTCTC
* *
3430 AAGTGGAGACGGTTTCTTCTCAGATCTGAGATTTTCTTTGACGGTTACTTCGCTTTCTCTTATCT
1 AAGTGGACACGGTTTCTTCTCAGATCTGAGATTTTCTTTGACGGTTACTTCGCTTTCTCTCATCT
*
3495 TTTTCCTTCATTTTACATCATTTTCTTTCATTTCCTTTTTTTGTTTGTTTCTCTCTGTTTCTCGC
66 TTTTCCTTCATTTTACATCATTTTCTTTCATTTCCTTTTTTTGTTTGTTTCTCTATGTTTCTCGC
3560 TCATTTGATCTTGTTTCTTTATATGATTGCTCACTTCTTGATCTTTGCCGCTCTTTTTGATTGAG
131 TCATTTGATCTTGTTTCTTTATATGATTGCTCACTTCTTGATCTTTGCCGCTCTTTTTGATTGAG
3625 TCTTTGCGTCTTTTCTTGTGTTTATGAGTTGTTTGTTTTTCTAAGGTTTGTTTTTTCAATTTTCT
196 TCTTTGCGTCTTTTCTTGTGTTTATGAGTTGTTTGTTTTTCTAAGGTTTGTTTTTTCAATTTTCT
3690 GGGGAATTATAGATTGTCTCATTCGCCATTGATAGGGACATAGAATTTAAGGTTGTTGATTCTAA
261 GGGGAATTATAGATTGTCTCATTCGCCATTGATAGGGACATAGAATTTAAGGTTGTTGATTCTAA
* *
3755 ATATAAGGCTGGTAGAAATAAGAAGAGCTTTAACTTTGAAATTTTGTGGCCTGAAAGTGTAG
326 ATATAAGGCTGGTAGAAATAAGAAGAGCTTTAAATTTGAAATTTTGTGGACTGAAAGTGTAG
* *
3817 AAGTGGACACGGTTTCTTCTCGGATCTGAGATTTTCTTTGACGGTTACTTCGCTTTTTCTCATCT
1 AAGTGGACACGGTTTCTTCTCAGATCTGAGATTTTCTTTGACGGTTACTTCGCTTTCTCTCATCT
3882 TTTTCCTTCATTTTACATCATTTTCTTTCATTTCCTTTCTGTTTTTGTTTGTTTCTCTATGTTTC
66 TTTTCCTTCATTTTACATCATTTTCTTTCATTTCC--T-T-TTTTTGTTTGTTTCTCTATGTTTC
* *
3947 TCGCTCATTTGATCTTGTTTCTTTATATGATTGTTCACTTCTTGATCTTTGCTGCTCTTTTTGAT
127 TCGCTCATTTGATCTTGTTTCTTTATATGATTGCTCACTTCTTGATCTTTGCCGCTCTTTTTGAT
*
4012 TGAGTCTTTGCGTCTTTTCTTGTGTTTATGAGTTGTTTGTTTTTCTAAGGTTTGTTTTTTTTAAT
192 TGAGTCTTTGCGTCTTTTCTTGTGTTTATGAGTTGTTTGTTTTTCTAAGGTTTG-TTTTTTCAAT
* *
4077 TTT-TGGGGAATTATAGGTTGTCTGATTCGCCATTGATAGGGACATAGAATTTAAGGTTGTTGAT
256 TTTCTGGGGAATTATAGATTGTCTCATTCGCCATTGATAGGGACATAGAATTTAAGGTTGTTGAT
* * *
4141 TTTGAATATAAGGCTGGTAGAAATAAGAAGAGCTTTAAATTTGAAATTTTGTGGACTGGAAGTGT
321 TCTAAATATAAGGCTGGTAGAAATAAGAAGAGCTTTAAATTTGAAATTTTGTGGACTGAAAGTGT
4206 AG
386 AG
4208 AATGTGGACA
1 AA-GTGGACA
4218 GGTGATACAA
Statistics
Matches: 380, Mismatches: 15, Indels: 7
0.95 0.04 0.02
Matches are distributed among these distances:
387 96 0.25
389 1 0.00
390 1 0.00
391 263 0.69
392 19 0.05
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.48
Consensus pattern (387 bp):
AAGTGGACACGGTTTCTTCTCAGATCTGAGATTTTCTTTGACGGTTACTTCGCTTTCTCTCATCT
TTTTCCTTCATTTTACATCATTTTCTTTCATTTCCTTTTTTTGTTTGTTTCTCTATGTTTCTCGC
TCATTTGATCTTGTTTCTTTATATGATTGCTCACTTCTTGATCTTTGCCGCTCTTTTTGATTGAG
TCTTTGCGTCTTTTCTTGTGTTTATGAGTTGTTTGTTTTTCTAAGGTTTGTTTTTTCAATTTTCT
GGGGAATTATAGATTGTCTCATTCGCCATTGATAGGGACATAGAATTTAAGGTTGTTGATTCTAA
ATATAAGGCTGGTAGAAATAAGAAGAGCTTTAAATTTGAAATTTTGTGGACTGAAAGTGTAG
Done.