Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021279.1 Corchorus olitorius cultivar O-4 contig21312, 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: 23870
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:7525 original size:22 final size:22
Alignment explanation
Indices: 7506--7549 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
7496 AAGTATAATA
7506 AATAGCTAGGACTGAAATAAGT
1 AATAGCTAGGACTGAAATAAGT
7528 AATAGCTAGGACTGAAATAAGT
1 AATAGCTAGGACTGAAATAAGT
7550 TAAGATAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (22 bp):
AATAGCTAGGACTGAAATAAGT
Found at i:12005 original size:15 final size:16
Alignment explanation
Indices: 11951--12024 Score: 57
Period size: 15 Copynumber: 4.7 Consensus size: 16
11941 TTTCGGGATT
11951 TTCTTCTCTGCTCTTGGC
1 TTCTTCTCTGC-C-TGGC
* *
11969 TTCTTCTCGGCCGGAGC
1 TTCTTCTCTGCCTG-GC
11986 -T-TTCTCTGCC-GGC
1 TTCTTCTCTGCCTGGC
* *
11999 TTCTTCTCCG-CTGGT
1 TTCTTCTCTGCCTGGC
12014 TTCTTCTCTGC
1 TTCTTCTCTGC
12025 TGCCTTTGGC
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
13 2 0.04
14 3 0.07
15 25 0.56
16 2 0.04
17 3 0.07
18 10 0.22
ACGTcount: A:0.01, C:0.35, G:0.20, T:0.43
Consensus pattern (16 bp):
TTCTTCTCTGCCTGGC
Found at i:18821 original size:60 final size:60
Alignment explanation
Indices: 18768--18905 Score: 197
Period size: 60 Copynumber: 2.3 Consensus size: 60
18758 AATGTTTGTT
*
18768 AAAATGTTCAAATAAGGGTCCAATCTTTTAATTCGGCCAAATAAGGGCTTAATGTTATGG
1 AAAATGCTCAAATAAGGGTCCAATCTTTTAATTCGGCCAAATAAGGGCTTAATGTTATGG
*** * * *
18828 AAAATGCTCAAATAAGGGTCTGGTCTTTTAATTTGGCCAAATAAGGG-TCTAATATTATCG
1 AAAATGCTCAAATAAGGGTCCAATCTTTTAATTCGGCCAAATAAGGGCT-TAATGTTATGG
18888 AAAATGCTCAAATAAGGG
1 AAAATGCTCAAATAAGGG
18906 CATGTCGTCA
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
59 1 0.01
60 69 0.99
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.30
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGGTCCAATCTTTTAATTCGGCCAAATAAGGGCTTAATGTTATGG
Found at i:18903 original size:31 final size:30
Alignment explanation
Indices: 18738--18905 Score: 89
Period size: 31 Copynumber: 5.6 Consensus size: 30
18728 GGGAAAGGTT
* *
18738 AAATGCTCAAATAAGGATCTAATGTT-TGTTA
1 AAATGCTCAAATAAGGGTCTAATATTATG--A
* * * *
18769 AAATGTTCAAATAAGGGTCCAATCTT-T-T
1 AAATGCTCAAATAAGGGTCTAATATTATGA
* *
18797 AATTCGGC-CAAATAAGGG-CTTAATGTTATGGA
1 AAAT--GCTCAAATAAGGGTC-TAATATTAT-GA
** * *
18829 AAATGCTCAAATAAGGGTCTGGTCTT-TTA
1 AAATGCTCAAATAAGGGTCTAATATTATGA
**
18858 ATTTGGC-CAAATAAGGGTCTAATATTATCGA
1 AAAT-GCTCAAATAAGGGTCTAATATTAT-GA
18889 AAATGCTCAAATAAGGG
1 AAATGCTCAAATAAGGG
18906 CATGTCGTCA
Statistics
Matches: 102, Mismatches: 23, Indels: 24
0.68 0.15 0.16
Matches are distributed among these distances:
28 4 0.04
29 34 0.33
30 10 0.10
31 50 0.49
32 4 0.04
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (30 bp):
AAATGCTCAAATAAGGGTCTAATATTATGA
Found at i:19041 original size:60 final size:60
Alignment explanation
Indices: 18945--19109 Score: 204
Period size: 60 Copynumber: 2.8 Consensus size: 60
18935 ATTTTTGATG
* * * *
18945 TCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGA
1 TCAGGCCCTTATTTGAGCATTTTGACAAACATTAGGCCCTTATTTGACCAAATTAAAAAA
* * * * *
19005 TCGGGCCCTTATTTGAACATTTTGACAAACATTAGGCTCTTATTTGATCAGATTAAAAAA
1 TCAGGCCCTTATTTGAGCATTTTGACAAACATTAGGCCCTTATTTGACCAAATTAAAAAA
* * * **
19065 TCAAGCCCTTATCTGAGCATTTTAACAAACATTAAACCCTTATTT
1 TCAGGCCCTTATTTGAGCATTTTGACAAACATTAGGCCCTTATTT
19110 AAGCAATTAG
Statistics
Matches: 88, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 88 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (60 bp):
TCAGGCCCTTATTTGAGCATTTTGACAAACATTAGGCCCTTATTTGACCAAATTAAAAAA
Found at i:20323 original size:18 final size:20
Alignment explanation
Indices: 20297--20333 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
20287 TTAATACATT
20297 ACTTATATA-ATTG-TCAAA
1 ACTTATATACATTGATCAAA
*
20315 ACTTGTATACATTGATCAA
1 ACTTATATACATTGATCAA
20334 TCATTCGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 4 0.25
20 4 0.25
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38
Consensus pattern (20 bp):
ACTTATATACATTGATCAAA
Found at i:20537 original size:21 final size:22
Alignment explanation
Indices: 20468--20549 Score: 103
Period size: 22 Copynumber: 3.8 Consensus size: 22
20458 TGAATAGTTT
*
20468 TATGAAATTTTGATAACTATCC
1 TATGAAATTTTGATAATTATCC
* * *
20490 TATTAAATTTTGATAATCATGC
1 TATGAAATTTTGATAATTATCC
20512 TATGAAATTTTGATAATTA-CC
1 TATGAAATTTTGATAATTATCC
* *
20533 TATGAGATTTTGTTAAT
1 TATGAAATTTTGATAAT
20550 CTCCCTATAA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
21 16 0.31
22 35 0.69
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (22 bp):
TATGAAATTTTGATAATTATCC
Found at i:20565 original size:22 final size:22
Alignment explanation
Indices: 20540--20588 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
20530 ACCTATGAGA
20540 TTTTGTTAATCTCCCTATAATT
1 TTTTGTTAATCTCCCTATAATT
20562 TTTTGTTAATCTCCCTATAATT
1 TTTTGTTAATCTCCCTATAATT
20584 TTTTG
1 TTTTG
20589 ATACTATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.06, T:0.57
Consensus pattern (22 bp):
TTTTGTTAATCTCCCTATAATT
Found at i:23545 original size:2 final size:2
Alignment explanation
Indices: 23540--23580 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
23530 ATATATATGG
*
23540 AC AC AC AC AC AC AC AC AC AC AC AC AT AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
23581 TACATACATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:23585 original size:4 final size:4
Alignment explanation
Indices: 23562--23870 Score: 591
Period size: 4 Copynumber: 77.2 Consensus size: 4
23552 ACACACACAC
* * *
23562 ACAT ACAC ACAC ACAC ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23610 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23658 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23706 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23754 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23802 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
23850 ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT A
Statistics
Matches: 303, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 303 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Done.