Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020453.1 Corchorus olitorius cultivar O-4 contig20486, 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: 32503
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:8154 original size:36 final size:36
Alignment explanation
Indices: 8107--8201 Score: 172
Period size: 36 Copynumber: 2.6 Consensus size: 36
8097 ACTGACTTCA
*
8107 CTCAGCATAATCAACTCCAGCAGATCAATCGTCATC
1 CTCATCATAATCAACTCCAGCAGATCAATCGTCATC
8143 CTCATCATAATCAACTCCAGCAGATCAATCGTCATC
1 CTCATCATAATCAACTCCAGCAGATCAATCGTCATC
*
8179 CTCATCATAATCATCTCCAGCAG
1 CTCATCATAATCAACTCCAGCAG
8202 CTGAATTGAG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.33, C:0.34, G:0.09, T:0.24
Consensus pattern (36 bp):
CTCATCATAATCAACTCCAGCAGATCAATCGTCATC
Found at i:14863 original size:18 final size:17
Alignment explanation
Indices: 14840--14884 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
14830 GAGGATTATG
14840 GGGTCCTGGGAATCCAT
1 GGGTCCTGGGAATCCAT
*
14857 CGGGTCCTGGGAGTCCAT
1 -GGGTCCTGGGAATCCAT
14875 GAGGTCCTGG
1 G-GGTCCTGG
14885 TTGATTTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.13, C:0.24, G:0.40, T:0.22
Consensus pattern (17 bp):
GGGTCCTGGGAATCCAT
Found at i:16108 original size:15 final size:15
Alignment explanation
Indices: 16084--16116 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
16074 GCCACCGTAA
*
16084 CCACCCCCATACATT
1 CCACCACCATACATT
16099 CCACCACCATACATT
1 CCACCACCATACATT
16114 CCA
1 CCA
16117 GAATTCCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.52, G:0.00, T:0.18
Consensus pattern (15 bp):
CCACCACCATACATT
Found at i:26483 original size:21 final size:24
Alignment explanation
Indices: 26459--26509 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
26449 AACTCATTAT
26459 TTATC-ATTTAA-AATATAT-TTA
1 TTATCTATTTAATAATATATGTTA
26480 TTATCTATTTAATAATATATGTTA
1 TTATCTATTTAATAATATATGTTA
26504 -TATCTA
1 TTATCTA
26510 AGATAGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.19
22 6 0.22
23 13 0.48
24 3 0.11
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (24 bp):
TTATCTATTTAATAATATATGTTA
Found at i:28079 original size:3 final size:3
Alignment explanation
Indices: 28061--28209 Score: 259
Period size: 3 Copynumber: 50.3 Consensus size: 3
28051 CAAATGAACG
28061 AAT ATAT AAT AA- AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28105 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
28153 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28201 AAT AA- AAT A
1 AAT AAT AAT A
28210 TAAGAAGTAT
Statistics
Matches: 140, Mismatches: 2, Indels: 8
0.93 0.01 0.05
Matches are distributed among these distances:
2 6 0.04
3 131 0.94
4 3 0.02
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28484 original size:29 final size:28
Alignment explanation
Indices: 28447--28531 Score: 111
Period size: 29 Copynumber: 3.0 Consensus size: 28
28437 CAATATGTTA
28447 AACAAAATATACAATACTGTATATCGAT
1 AACAAAATATACAATACTGTATATCGAT
*
28475 ATACAAAATATACAATACTGTA-AGTAGCA-
1 A-ACAAAATATACAATACTGTATA-TCG-AT
*
28504 AAAAAAATATACAATACTGTATATCGAT
1 AACAAAATATACAATACTGTATATCGAT
28532 CTATGTACCG
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
27 1 0.02
28 23 0.47
29 24 0.49
30 1 0.02
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.27
Consensus pattern (28 bp):
AACAAAATATACAATACTGTATATCGAT
Found at i:32476 original size:32 final size:32
Alignment explanation
Indices: 32420--32481 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
32410 TTTTGAAAGG
**
32420 TAAAATCATGACAACTTCTGGTGTCAATTGAA
1 TAAAATCATGACAACTTCAAGTGTCAATTGAA
* * *
32452 TAAAATTATGACATCTTCAAGTGTCTATTG
1 TAAAATCATGACAACTTCAAGTGTCAATTG
32482 GAAATTTATC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (32 bp):
TAAAATCATGACAACTTCAAGTGTCAATTGAA
Done.