Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021168.1 Corchorus olitorius cultivar O-4 contig21201, 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: 36456
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:2959 original size:9 final size:9
Alignment explanation
Indices: 2943--2973 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
2933 GAAAAATATC
2943 AAAA-AAAA
1 AAAATAAAA
2951 AAAATAAAA
1 AAAATAAAA
2960 AAAATAAAA
1 AAAATAAAA
2969 AAAAT
1 AAAAT
2974 TTTGACCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.18
9 18 0.82
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAATAAAA
Found at i:14810 original size:15 final size:16
Alignment explanation
Indices: 14777--14816 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
14767 TTGCTTTGTT
14777 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
14793 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
14808 TTGCTTTCT
1 TTGTTTTCT
14817 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:15718 original size:17 final size:17
Alignment explanation
Indices: 15696--15729 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
15686 TAAGGATTTT
15696 TCTTAATAATTAATTGA
1 TCTTAATAATTAATTGA
15713 TCTTAATAATTAATTGA
1 TCTTAATAATTAATTGA
15730 AAATTACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (17 bp):
TCTTAATAATTAATTGA
Found at i:17550 original size:15 final size:15
Alignment explanation
Indices: 17530--17560 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17520 TTCAAGAAAA
*
17530 TAATAATTATTTAAT
1 TAATAATTAATTAAT
17545 TAATAATTAATTAAT
1 TAATAATTAATTAAT
17560 T
1 T
17561 TCAGCCCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATAATTAATTAAT
Found at i:19496 original size:22 final size:22
Alignment explanation
Indices: 19447--19497 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
19437 AAATATTACC
**
19447 ATAATTATTTTTGCCAGCCATA
1 ATAATTATTTTTGCCAGAAATA
19469 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGCC-AGAAATA
19492 A-AATTA
1 ATAATTA
19498 GGGAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (22 bp):
ATAATTATTTTTGCCAGAAATA
Found at i:27577 original size:6 final size:6
Alignment explanation
Indices: 27568--27595 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
27558 AATCCTAATA
27568 TTTTTC TTTTTC TTTTTC TTTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTT
27596 ATTACTCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:27996 original size:25 final size:25
Alignment explanation
Indices: 27966--28014 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
27956 AATCTGGAAA
27966 TGAGTCTGCACTAAACGGCGCCGTC
1 TGAGTCTGCACTAAACGGCGCCGTC
*
27991 TGAGTCTGTACTAAACGGCGCCGT
1 TGAGTCTGCACTAAACGGCGCCGT
28015 TTTGGTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.22
Consensus pattern (25 bp):
TGAGTCTGCACTAAACGGCGCCGTC
Done.