Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016250.1 Corchorus olitorius cultivar O-4 contig16283, 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: 31936
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:326 original size:25 final size:25
Alignment explanation
Indices: 298--488 Score: 217
Period size: 25 Copynumber: 7.6 Consensus size: 25
288 CGCTCATGTT
*
298 CTTGTGTTTGGAAAACGAGCCTGTG
1 CTTGCGTTTGGAAAACGAGCCTGTG
*
323 CTTGCGTTTGGAAAACGAACCTGTG
1 CTTGCGTTTGGAAAACGAGCCTGTG
**
348 CTTGCGTTTGGAAAACGAATCTGTG
1 CTTGCGTTTGGAAAACGAGCCTGTG
* *
373 CTTGCGTTTGGCAAGCGAGCCT-TAG
1 CTTGCGTTTGGAAAACGAGCCTGT-G
* *
398 CTTGCGTTTAGAAAACGAACCT-TAG
1 CTTGCGTTTGGAAAACGAGCCTGT-G
*
423 CTTGCGTTTAGCAAAA-GAGCCTGTG
1 CTTGCGTTT-GGAAAACGAGCCTGTG
* *
448 CTTGCGTTTAGCAAACGAGCCTGTG
1 CTTGCGTTTGGAAAACGAGCCTGTG
* *
473 CTTGTGTTTAGAAAAC
1 CTTGCGTTTGGAAAAC
489 ACATAGGCTA
Statistics
Matches: 143, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
24 4 0.03
25 134 0.94
26 5 0.03
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (25 bp):
CTTGCGTTTGGAAAACGAGCCTGTG
Found at i:412 original size:75 final size:75
Alignment explanation
Indices: 298--488 Score: 253
Period size: 75 Copynumber: 2.5 Consensus size: 75
288 CGCTCATGTT
* * * *
298 CTTGTGTTTGGAAAACGAGCCTGTGCTTGCGTTTGGAAAACGAACCTGT-GCTTGCGTTT-GGAA
1 CTTGCGTTTGGCAAACGAGCCTGTGCTTGCGTTTAGAAAACGAACCT-TAGCTTGCGTTTAGCAA
*
361 AACGAATCTGTG
65 AA-GAACCTGTG
*
373 CTTGCGTTTGGCAAGCGAGCCT-TAGCTTGCGTTTAGAAAACGAACCTTAGCTTGCGTTTAGCAA
1 CTTGCGTTTGGCAAACGAGCCTGT-GCTTGCGTTTAGAAAACGAACCTTAGCTTGCGTTTAGCAA
*
437 AAGAGCCTGTG
65 AAGAACCTGTG
* *
448 CTTGCGTTTAGCAAACGAGCCTGTGCTTGTGTTTAGAAAAC
1 CTTGCGTTTGGCAAACGAGCCTGTGCTTGCGTTTAGAAAAC
489 ACATAGGCTA
Statistics
Matches: 102, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
74 2 0.02
75 94 0.92
76 6 0.06
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (75 bp):
CTTGCGTTTGGCAAACGAGCCTGTGCTTGCGTTTAGAAAACGAACCTTAGCTTGCGTTTAGCAAA
AGAACCTGTG
Found at i:768 original size:16 final size:16
Alignment explanation
Indices: 747--779 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
737 TTTTTTGAAA
*
747 AATAATACTTTCTTGT
1 AATAATACTATCTTGT
763 AATAATACTATCTTGT
1 AATAATACTATCTTGT
779 A
1 A
780 GTATCATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (16 bp):
AATAATACTATCTTGT
Found at i:24122 original size:11 final size:11
Alignment explanation
Indices: 24098--24145 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
24088 TTGACAGCGC
24098 AACAAAAACAA
1 AACAAAAACAA
* *
24109 AACGAAAACGA
1 AACAAAAACAA
24120 AACAAAAACAAA
1 AACAAAAAC-AA
24132 AACAAAAAACAA
1 AAC-AAAAACAA
24144 AA
1 AA
24146 ATGATGCCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
11 17 0.55
12 8 0.26
13 6 0.19
ACGTcount: A:0.79, C:0.17, G:0.04, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:24139 original size:7 final size:6
Alignment explanation
Indices: 24098--24146 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
24088 TTGACAGCGC
* *
24098 AACAAA AAC-AA AACGAA AAC-GA AACAAA AACAAA AACAAAA AACAAA
1 AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AAC-AAA AACAAA
24145 AA
1 AA
24147 TGATGCCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 9 0.24
6 23 0.61
7 6 0.16
ACGTcount: A:0.80, C:0.16, G:0.04, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:27285 original size:3 final size:3
Alignment explanation
Indices: 27277--27319 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
27267 ATTTACTATA
27277 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
27320 TTAAAATACC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:28776 original size:21 final size:21
Alignment explanation
Indices: 28752--28804 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 21
28742 TCCACTTCCC
28752 CTACTTCTGCTCCTCGCGCCA
1 CTACTTCTGCTCCTCGCGCCA
28773 CTACTTCTCCTGCTCCTCGCGCCA
1 CTAC-T-T-CTGCTCCTCGCGCCA
28797 CTACTTCT
1 CTACTTCT
28805 TCAAGTGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.21
22 2 0.07
23 2 0.07
24 19 0.66
ACGTcount: A:0.09, C:0.47, G:0.11, T:0.32
Consensus pattern (21 bp):
CTACTTCTGCTCCTCGCGCCA
Found at i:28789 original size:24 final size:24
Alignment explanation
Indices: 28758--28804 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
28748 TCCCCTACTT
28758 CTGCTCCTCGCGCCACTACTTCTC
1 CTGCTCCTCGCGCCACTACTTCTC
28782 CTGCTCCTCGCGCCACTACTTCT
1 CTGCTCCTCGCGCCACTACTTCT
28805 TCAAGTGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.09, C:0.49, G:0.13, T:0.30
Consensus pattern (24 bp):
CTGCTCCTCGCGCCACTACTTCTC
Found at i:28964 original size:36 final size:36
Alignment explanation
Indices: 28904--28977 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
28894 TGCTGCGTTG
* * *
28904 AGAGTTCTTCCTTCAATTCTTGGTACTG-TTCCTGCT
1 AGAGTTCTCCCTCCAATTCCTGGTACTGCTT-CTGCT
*
28940 AGAGTTCTCCCTCCAGTTCCTGGTACTGCTTCTGCT
1 AGAGTTCTCCCTCCAATTCCTGGTACTGCTTCTGCT
28976 AG
1 AG
28978 TAGTACTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 31 0.94
37 2 0.06
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.39
Consensus pattern (36 bp):
AGAGTTCTCCCTCCAATTCCTGGTACTGCTTCTGCT
Found at i:30001 original size:14 final size:14
Alignment explanation
Indices: 29961--30003 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
29951 CCTCTAGCGT
* **
29961 CGCGAATACCATAT
1 CGCGAGTACCATGC
29975 CGCGAGTACCATGC
1 CGCGAGTACCATGC
29989 CGCGAGTACCATGC
1 CGCGAGTACCATGC
30003 C
1 C
30004 TTTGCGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.26, C:0.35, G:0.23, T:0.16
Consensus pattern (14 bp):
CGCGAGTACCATGC
Done.