Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018758.1 Corchorus olitorius cultivar O-4 contig18791, 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: 34671
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1853 original size:38 final size:36
Alignment explanation
Indices: 1785--1894 Score: 202
Period size: 36 Copynumber: 3.0 Consensus size: 36
1775 GTTAGGCATG
1785 TGTTAAACGTGTAGTGTAACATCTACTCGTGTTATC
1 TGTTAAACGTGTAGTGTAACATCTACTCGTGTTATC
1821 TGTTAAACGTGTAGTGTAAAACATCTACTCGTGTTATC
1 TGTTAAACGTGTAGTGT--AACATCTACTCGTGTTATC
1859 TGTTAAACGTGTAGTGTAACATCTACTCGTGTTATC
1 TGTTAAACGTGTAGTGTAACATCTACTCGTGTTATC
1895 GTATAAATCA
Statistics
Matches: 72, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
36 36 0.50
38 36 0.50
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.38
Consensus pattern (36 bp):
TGTTAAACGTGTAGTGTAACATCTACTCGTGTTATC
Found at i:12386 original size:30 final size:30
Alignment explanation
Indices: 12319--12386 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
12309 TTGCTAAGCT
*
12319 CCTTTGGAGAGTTCAGAAAAACCCAAATAA
1 CCTTTGGGGAGTTCAGAAAAACCCAAATAA
12349 CCTTTGGGGAGTTCAGAAAAACCCAAATAA
1 CCTTTGGGGAGTTCAGAAAAACCCAAATAA
12379 CCTTTGGG
1 CCTTTGGG
12387 TCAAAGCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (30 bp):
CCTTTGGGGAGTTCAGAAAAACCCAAATAA
Found at i:15502 original size:51 final size:52
Alignment explanation
Indices: 15401--15502 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 52
15391 GTTCATCAAA
* **
15401 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGTTT
1 TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
* *
15453 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TTCTCCTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGTT
15503 CTTCATTCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 2 0.05
51 36 0.84
52 5 0.12
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (52 bp):
TTCTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTT
Found at i:16168 original size:28 final size:28
Alignment explanation
Indices: 16116--16169 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
16106 TATCGAAATC
*** *
16116 AAGAAGCAAACTTAAATTCTCTAAAAAA
1 AAGAAGCAAACTTAAAAAATATAAAAAA
16144 AAGAAGCAAACTTAAAAAATATAAAA
1 AAGAAGCAAACTTAAAAAATATAAAA
16170 TCATATATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.63, C:0.11, G:0.07, T:0.19
Consensus pattern (28 bp):
AAGAAGCAAACTTAAAAAATATAAAAAA
Found at i:20675 original size:25 final size:24
Alignment explanation
Indices: 20641--20688 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
20631 AAATCACTCC
20641 TTTTTTTTTTCCGTTTCATGACAGA
1 TTTTTTTTTT-CGTTTCATGACAGA
*
20666 TTTTTTTTTTGGTTTCATGACAG
1 TTTTTTTTTTCGTTTCATGACAG
20689 TTGACACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (24 bp):
TTTTTTTTTTCGTTTCATGACAGA
Found at i:22714 original size:16 final size:16
Alignment explanation
Indices: 22677--22723 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
22667 GTTTGGCATC
*
22677 GTTTTCGTTTTTCTGTTT
1 GTTTT-GTTTTTGT-TTT
22695 -TTTTGTTTTTGTTTT
1 GTTTTGTTTTTGTTTT
22710 GTTTTGTTTTTGTT
1 GTTTTGTTTTTGTT
22724 GTGCTGTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 3 0.11
16 20 0.74
17 4 0.15
ACGTcount: A:0.00, C:0.04, G:0.17, T:0.79
Consensus pattern (16 bp):
GTTTTGTTTTTGTTTT
Found at i:23669 original size:27 final size:30
Alignment explanation
Indices: 23597--23669 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 30
23587 TTAATGCCCT
*
23597 TTTTGCCCCCTGAACTTGTACGATTTTGACG
1 TTTTGCCCCCTGAACTTGTAC-ATTTGGACG
* * *
23628 TTTTG-CCCATAAACTT-TA-ATTTGGATG
1 TTTTGCCCCCTGAACTTGTACATTTGGACG
23655 -TTTGCCCCCTGAACT
1 TTTTGCCCCCTGAACT
23670 CGCAATTTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
26 4 0.11
27 15 0.43
29 2 0.06
30 9 0.26
31 5 0.14
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.40
Consensus pattern (30 bp):
TTTTGCCCCCTGAACTTGTACATTTGGACG
Found at i:25285 original size:22 final size:22
Alignment explanation
Indices: 25240--25286 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
25230 TTTTTAAACA
* **
25240 TTTTTAGTAACCTTATAAGTTT
1 TTTTTAATAACCTTATAAAATT
*
25262 TTTTTAATAATCTTATAAAATT
1 TTTTTAATAACCTTATAAAATT
25284 TTT
1 TTT
25287 AACACTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (22 bp):
TTTTTAATAACCTTATAAAATT
Found at i:27429 original size:2 final size:2
Alignment explanation
Indices: 27422--27453 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
27412 TAATTGAGTG
27422 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27454 CTTCTTGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:28617 original size:23 final size:23
Alignment explanation
Indices: 28567--28614 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
28557 CTGAAAGCCC
*
28567 ATTG-AATTCCAAATGCCATGCA
1 ATTGCAATTCCAAATGCAATGCA
28589 ATTGCAATTCCAAATGCAAATGCA
1 ATTGCAATTCCAAATGC-AATGCA
28613 AT
1 AT
28615 GCATAATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.17
23 12 0.52
24 7 0.30
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (23 bp):
ATTGCAATTCCAAATGCAATGCA
Found at i:28722 original size:7 final size:7
Alignment explanation
Indices: 28710--28748 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
28700 TGCAACTGCA
28710 TTTCTCC
1 TTTCTCC
28717 TTTCTCC
1 TTTCTCC
*
28724 TTTCCCC
1 TTTCTCC
28731 TTTC-CC
1 TTTCTCC
28737 TTTC-CC
1 TTTCTCC
28743 TTTCTC
1 TTTCTC
28749 TTGATCAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (7 bp):
TTTCTCC
Done.