Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017912.1 Corchorus olitorius cultivar O-4 contig17945, 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: 11623
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Found at i:1406 original size:27 final size:27
Alignment explanation
Indices: 1331--1407 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 27
1321 ATGTGAACTT
* *
1331 AAAATGACCAAAATGCCCCTGAATGTA
1 AAAATGACCAAAATGCCCCTGGACGTA
* *
1358 AAAATGTCCAAAATGCCCCTGGACGTG
1 AAAATGACCAAAATGCCCCTGGACGTA
**
1385 AAAATGACTTAAATGCCCCTGGA
1 AAAATGACCAAAATGCCCCTGGA
1408 TTTTTGAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.19
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGGACGTA
Found at i:1926 original size:50 final size:50
Alignment explanation
Indices: 1851--2464 Score: 1027
Period size: 50 Copynumber: 12.3 Consensus size: 50
1841 ACTCGGTTTA
** * * *
1851 TGGAAAAGCCCATGTTGATAATTGACCCGTATGGAAACGAGTTTGGCTTT
1 TGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
* *
1901 TGGAAAAGCCTGTGCTGATAATTGACTCGTATGGAAACGAGTTTGGCTTG
1 TGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
*
1951 TGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTG
1 TGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
* *
2001 TGGAAAAGCCGGTGTTGATAATTGACTCGTATGGAAACGAGTTTGGCTTG
1 TGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
*
2051 TGGAAAAGCCGGTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
1 TGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
*
2101 TGGAAATA-CCTGGGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
1 TGGAAA-AGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
* *
2151 TGGAAATA-CCTGGGTTGATAATTGACTCGTACGGAAACGAGTTCGGCTTG
1 TGGAAA-AGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
*
2201 TGGAAAAGCCGGTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
1 TGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
*
2251 TGGAAAAG-CTGGTGTTGATAATTGACTCATATGGAAACGAGTTCGGCTTG
1 TGGAAAAGCCT-GTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
*
2301 TGGAAAAGCTTGTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
1 TGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
2351 TGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
1 TGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
2401 TGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
1 TGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
2451 TGGAAAAGCCTGTG
1 TGGAAAAGCCTGTG
2465 CATTCGGATG
Statistics
Matches: 541, Mismatches: 19, Indels: 8
0.95 0.03 0.01
Matches are distributed among these distances:
49 2 0.00
50 537 0.99
51 2 0.00
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (50 bp):
TGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTCGGCTTG
Found at i:3036 original size:50 final size:50
Alignment explanation
Indices: 2982--3133 Score: 252
Period size: 50 Copynumber: 3.0 Consensus size: 50
2972 CTTAAATGCC
* * *
2982 CTTTGAAAAGCGAATTCTGATCTTGGACTCACAAATGGAATGCAATCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
3032 CTTTGAAAAGC-AATTTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
1 CTTTGAAAAGCGAA-TTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
*
3082 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
3132 CT
1 CT
3134 GTAAAACTTC
Statistics
Matches: 96, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
49 2 0.02
50 92 0.96
51 2 0.02
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
Found at i:3435 original size:20 final size:20
Alignment explanation
Indices: 3405--3448 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3395 CTAGAACTTC
*
3405 TTTTCTTCATTCTTC-TTTT
1 TTTTCTTCATTCATCATTTT
3424 TTTTCATTCATTCATCATTTT
1 TTTTC-TTCATTCATCATTTT
3445 TTTT
1 TTTT
3449 GGCACTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 9 0.41
21 8 0.36
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTCTTCATTCATCATTTT
Found at i:3768 original size:15 final size:15
Alignment explanation
Indices: 3748--3778 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3738 TTTGATTTGA
3748 TTTGATTTTTTTTAT
1 TTTGATTTTTTTTAT
3763 TTTGATTTTTTTTAT
1 TTTGATTTTTTTTAT
3778 T
1 T
3779 GACTTTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.06, T:0.81
Consensus pattern (15 bp):
TTTGATTTTTTTTAT
Found at i:3803 original size:19 final size:19
Alignment explanation
Indices: 3739--3799 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
3729 TCCTTTGATT
*
3739 TTGA-TTTGATTTGATTTTT
1 TTGACTTTGATTTGA-TTTA
* * **
3758 TTTATTTTGATTTTTTTTA
1 TTGACTTTGATTTGATTTA
3777 TTGACTTTGATTTGATTT-
1 TTGACTTTGATTTGATTTA
3795 TTGAC
1 TTGAC
3800 CTTTTTTTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
18 5 0.15
19 20 0.61
20 8 0.24
ACGTcount: A:0.16, C:0.03, G:0.13, T:0.67
Consensus pattern (19 bp):
TTGACTTTGATTTGATTTA
Found at i:6201 original size:21 final size:22
Alignment explanation
Indices: 6166--6207 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
6156 TAGGGTTTTA
*
6166 ATGGGATGCATGAATGAATGCC
1 ATGGCATGCATGAATGAATGCC
6188 ATGGCATG-ATGAATGAATGC
1 ATGGCATGCATGAATGAATGC
6208 ATGAGGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.33, C:0.12, G:0.31, T:0.24
Consensus pattern (22 bp):
ATGGCATGCATGAATGAATGCC
Found at i:8987 original size:27 final size:26
Alignment explanation
Indices: 8942--8992 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
8932 ACAAAACCTT
** *
8942 TTACCATTTTATTTTTTTCTAAAAAC
1 TTACCATTTTATTAATTTCCAAAAAC
8968 TTACCAATTTTATTAATTTCCAAAA
1 TTACC-ATTTTATTAATTTCCAAAA
8993 TCTTCTTTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (26 bp):
TTACCATTTTATTAATTTCCAAAAAC
Done.