Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022129.1 Corchorus olitorius cultivar O-4 contig22162, 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: 21026
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Found at i:1465 original size:28 final size:28
Alignment explanation
Indices: 1432--1495 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
1422 GTTTTAATTA
1432 CATTAGAAAAGAAGGGTCTTTAGGATTC
1 CATTAGAAAAGAAGGGTCTTTAGGATTC
*
1460 CATTAGAAAAGAAGGGTTTTTAGGATTC
1 CATTAGAAAAGAAGGGTCTTTAGGATTC
1488 CATT-GAAA
1 CATTAGAAA
1496 TGATGTCACA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 4 0.11
28 31 0.89
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (28 bp):
CATTAGAAAAGAAGGGTCTTTAGGATTC
Found at i:1857 original size:15 final size:15
Alignment explanation
Indices: 1837--1868 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1827 TAATAAGAAA
*
1837 ATAATAATTATTTTT
1 ATAATAATTATTATT
1852 ATAATAATTATTATT
1 ATAATAATTATTATT
1867 AT
1 AT
1869 TCAATATGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATAATAATTATTATT
Found at i:4095 original size:15 final size:15
Alignment explanation
Indices: 4075--4109 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
4065 GATCTTGGAT
*
4075 GTTTGAGTCAGTTTA
1 GTTTGAGTCAGTTGA
4090 GTTTGAGTCAGTTGA
1 GTTTGAGTCAGTTGA
4105 GTTTG
1 GTTTG
4110 TTGAGTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.06, G:0.31, T:0.46
Consensus pattern (15 bp):
GTTTGAGTCAGTTGA
Found at i:6225 original size:21 final size:21
Alignment explanation
Indices: 6185--6230 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 21
6175 TTGTTTATGT
6185 CTTAGGAGTAGTCATAATGTAA
1 CTTAGGAGTAGT-ATAATGTAA
6207 CTTAGGAGTAG-ATTAATGTAA
1 CTTAGGAGTAGTA-TAATGTAA
6228 CTT
1 CTT
6231 TTAGATTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 1 0.04
21 11 0.48
22 11 0.48
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.35
Consensus pattern (21 bp):
CTTAGGAGTAGTATAATGTAA
Found at i:6978 original size:30 final size:30
Alignment explanation
Indices: 6944--7006 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
6934 CTTGTGATTC
6944 ATGAAGACATTATTTAAAC-TTGGGGGCAAG
1 ATGAAGACATT-TTTAAACTTTGGGGGCAAG
* *
6974 ATGAAGGCATTTTTCAACTTTGGGGGCAAG
1 ATGAAGACATTTTTAAACTTTGGGGGCAAG
7004 ATG
1 ATG
7007 TAGCCATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.29
Consensus pattern (30 bp):
ATGAAGACATTTTTAAACTTTGGGGGCAAG
Found at i:15646 original size:37 final size:37
Alignment explanation
Indices: 15596--15903 Score: 296
Period size: 37 Copynumber: 8.3 Consensus size: 37
15586 GATTTCTAAA
* * *
15596 GAGAGCTCTGTGGTAAAGAGGGTGCTGCTGCAGTAAG
1 GAGAGCTCTGCGGTAAAGAGGGTGCTACCGCAGTAAG
* * * **
15633 GAGAGCTCTGTGGTGAATAGGGTGCCGCCGCAGTAAG
1 GAGAGCTCTGCGGTAAAGAGGGTGCTACCGCAGTAAG
* * * * *
15670 CAGAGCTCAGCGGTAAAGAGGGTGTTATCGCAATAAG
1 GAGAGCTCTGCGGTAAAGAGGGTGCTACCGCAGTAAG
* * *
15707 AAGAGCTATGCGGTAAAGAGGGT-CGTACCGCGGTAAG
1 GAGAGCTCTGCGGTAAAGAGGGTGC-TACCGCAGTAAG
* * * *
15744 GGGAGCTTTGCGTTAAAGAGGGTGCTACCGCGGTAAG
1 GAGAGCTCTGCGGTAAAGAGGGTGCTACCGCAGTAAG
** ** *
15781 TTGAGCTCTATGGTAAAGAGGGTGCTACCGCGGTAAG
1 GAGAGCTCTGCGGTAAAGAGGGTGCTACCGCAGTAAG
* **
15818 GAGAGCTCTGCGTTAAAGAGGGTGCTACCGTGGTAAG
1 GAGAGCTCTGCGGTAAAGAGGGTGCTACCGCAGTAAG
* * * *
15855 GGGAGCTCTGCAGTAAATAGGGGGCTACCG-AGGTAAG
1 GAGAGCTCTGCGGTAAAGAGGGTGCTACCGCA-GTAAG
15892 GAGAGCTCTGCG
1 GAGAGCTCTGCG
15904 ATGAGGAAGG
Statistics
Matches: 223, Mismatches: 45, Indels: 6
0.81 0.16 0.02
Matches are distributed among these distances:
37 222 1.00
38 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.38, T:0.20
Consensus pattern (37 bp):
GAGAGCTCTGCGGTAAAGAGGGTGCTACCGCAGTAAG
Found at i:15995 original size:30 final size:30
Alignment explanation
Indices: 15938--16001 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
15928 GATTTTCTGT
* * **
15938 AAAGTGTTTGGTAAAGCGAGTGTTGCGGCA
1 AAAGTGTTTCGCAAAGCGAGTCCTGCGGCA
* *
15968 AAAGTGTTTCGCAAAGTGAGTCCTGCGGTA
1 AAAGTGTTTCGCAAAGCGAGTCCTGCGGCA
15998 AAAG
1 AAAG
16002 GGGTGCTACT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.12, G:0.33, T:0.25
Consensus pattern (30 bp):
AAAGTGTTTCGCAAAGCGAGTCCTGCGGCA
Done.