Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024087.1 Corchorus olitorius cultivar O-4 contig24120, 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: 38955
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:3611 original size:2 final size:2
Alignment explanation
Indices: 3606--3640 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3596 TATATATATA
*
3606 TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3641 AAGTTAGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (2 bp):
TG
Found at i:3845 original size:43 final size:42
Alignment explanation
Indices: 3713--4026 Score: 266
Period size: 43 Copynumber: 7.5 Consensus size: 42
3703 AAAATGCGTC
* * *
3713 TGTGTTTGAGGACTTTGAGATAGAGGTGCCTTTGTGTTATAAA
1 TGTGTTTGAGGACTTTTAGATAGA-ATGCCTCTGTGTTATAAA
* *
3756 TGTGTTTGGGGAC-TTTAG-TACGGATGCCTCTGTGTTATAAA
1 TGTGTTTGAGGACTTTTAGATA-GAATGCCTCTGTGTTATAAA
* * *
3797 TGTGTTTGAGGACTTTTAGAGAGAATTGCCCCTGTGTTATAAT
1 TGTGTTTGAGGACTTTTAGATAGAA-TGCCTCTGTGTTATAAA
* * * *
3840 TGTGTTTGGGGACTTTGATATAG-ATGCCTCTATGTTATAAA
1 TGTGTTTGAGGACTTTTAGATAGAATGCCTCTGTGTTATAAA
* * * * *
3881 TGTGTTTTAGGAC-TTTGGAAAAGAATTGCC-CATGTGCTATAAT
1 TGTGTTTGAGGACTTTTAG-ATAGAA-TGCCTC-TGTGTTATAAA
* * *
3924 TGTGTTTG-GAGACTTTGATATAG-ATGTCTCTGTGTTATAAA
1 TGTGTTTGAG-GACTTTTAGATAGAATGCCTCTGTGTTATAAA
* * *
3965 TGTGTTTGAGGAC-TTTGGAATAGAGGTGCCCCTGTGTTATAAA
1 TGTGTTTGAGGACTTTTAG-ATAGA-ATGCCTCTGTGTTATAAA
* *
4008 TGTGTTTGGGGACGTTTAG
1 TGTGTTTGAGGACTTTTAG
4027 TTATTGGATA
Statistics
Matches: 213, Mismatches: 42, Indels: 31
0.74 0.15 0.11
Matches are distributed among these distances:
40 4 0.02
41 85 0.40
42 19 0.09
43 99 0.46
44 6 0.03
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.39
Consensus pattern (42 bp):
TGTGTTTGAGGACTTTTAGATAGAATGCCTCTGTGTTATAAA
Found at i:3854 original size:84 final size:84
Alignment explanation
Indices: 3713--4020 Score: 388
Period size: 84 Copynumber: 3.7 Consensus size: 84
3703 AAAATGCGTC
* **
3713 TGTGTTTGAGGACTTT-GAGATAGAGGTGCCTTTGTGTTATAAATGTGTTTGGGGACTTT-AGTA
1 TGTGTTTGAGGACTTTAGA-ATAGAAGTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGA-TA
**
3776 CGGATGCCTCTGTGTTATAAA
64 TAGATGCCTCTGTGTTATAAA
* * *
3797 TGTGTTTGAGGACTTTTAG-AGAGAATTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTGATAT
1 TGTGTTTGAGGAC-TTTAGAATAGAAGTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGATAT
*
3861 AGATGCCTCTATGTTATAAA
65 AGATGCCTCTGTGTTATAAA
* * * * * * * *
3881 TGTGTTTTAGGACTTTGGAAAAGAATTGCCCATGTGCTATAATTGTGTTTGGAGACTTTGATATA
1 TGTGTTTGAGGACTTTAGAATAGAAGTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGATATA
*
3946 GATGTCTCTGTGTTATAAA
66 GATGCCTCTGTGTTATAAA
* *
3965 TGTGTTTGAGGACTTTGGAATAGAGGTGCCCCTGTGTTATAAATGTGTTTGGGGAC
1 TGTGTTTGAGGACTTTAGAATAGAAGTGCCCCTGTGTTATAAATGTGTTTGGGGAC
4021 GTTTAGTTAT
Statistics
Matches: 195, Mismatches: 25, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
83 4 0.02
84 186 0.95
85 4 0.02
86 1 0.01
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.39
Consensus pattern (84 bp):
TGTGTTTGAGGACTTTAGAATAGAAGTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGATATA
GATGCCTCTGTGTTATAAA
Found at i:8358 original size:19 final size:18
Alignment explanation
Indices: 8334--8369 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8324 TGAAAACTTA
8334 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
8353 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
8370 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:9908 original size:6 final size:6
Alignment explanation
Indices: 9899--9926 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
9889 GAGATTGTGA
9899 TTTCTT TTTCTT TTTCTT TTTCTT TTTC
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTC
9927 AATTTGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:31564 original size:103 final size:103
Alignment explanation
Indices: 31385--31591 Score: 396
Period size: 103 Copynumber: 2.0 Consensus size: 103
31375 ATTGAAAATG
* *
31385 GTGTCGAGATCACAATGATTTGTGTTGTATTTTTTAATGGAAACCGTAACACCCTTCAAGAAATC
1 GTGTCGAGATCACAATGATTTGTGTTGTATTTTTTAATGGAAACCGTAACACCCTCCAAAAAATC
31450 ACCACCGTATAAGTCGAAAAAATGTCCACTTAAATATC
66 ACCACCGTATAAGTCGAAAAAATGTCCACTTAAATATC
31488 GTGTCGAGATCACAATGATTTGTGTTGTATTTTTTAATGGAAACCGTAACACCCTCCAAAAAATC
1 GTGTCGAGATCACAATGATTTGTGTTGTATTTTTTAATGGAAACCGTAACACCCTCCAAAAAATC
31553 ACCACCGTATAAGTCGAAAAAATGTCCACTTAAATATC
66 ACCACCGTATAAGTCGAAAAAATGTCCACTTAAATATC
31591 G
1 G
31592 ATCGCTCCGT
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (103 bp):
GTGTCGAGATCACAATGATTTGTGTTGTATTTTTTAATGGAAACCGTAACACCCTCCAAAAAATC
ACCACCGTATAAGTCGAAAAAATGTCCACTTAAATATC
Done.