Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019654.1 Corchorus olitorius cultivar O-4 contig19687, 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: 50564
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:2026 original size:31 final size:31
Alignment explanation
Indices: 1964--2027 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
1954 CGGAAAAAAA
* **
1964 AAAATGTAACGTGACAATGCCACGTTGGACC
1 AAAATGTAACGTGACAAGGCCACGTCAGACC
*
1995 AAAATG-ACACGTGGCAAGGCCACGTCAGACC
1 AAAATGTA-ACGTGACAAGGCCACGTCAGACC
2026 AA
1 AA
2028 GGCGCTGATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.14
Consensus pattern (31 bp):
AAAATGTAACGTGACAAGGCCACGTCAGACC
Found at i:13463 original size:17 final size:17
Alignment explanation
Indices: 13438--13518 Score: 81
Period size: 17 Copynumber: 5.2 Consensus size: 17
13428 AGTATTTACT
13438 ATTTAGGCTTAATCATC
1 ATTTAGGCTTAATCATC
*
13455 ATTTGGGCTT-A-C-T-
1 ATTTAGGCTTAATCATC
13468 ATTTAGGCTTAATCATC
1 ATTTAGGCTTAATCATC
13485 ATTT-GGACTT-A-C-T-
1 ATTTAGG-CTTAATCATC
13498 ATTTAGGCTTAATCATC
1 ATTTAGGCTTAATCATC
13515 ATTT
1 ATTT
13519 GGACTTACTA
Statistics
Matches: 52, Mismatches: 2, Indels: 20
0.70 0.03 0.27
Matches are distributed among these distances:
13 16 0.31
14 6 0.12
15 4 0.08
16 6 0.12
17 20 0.38
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (17 bp):
ATTTAGGCTTAATCATC
Found at i:13469 original size:30 final size:30
Alignment explanation
Indices: 13433--13540 Score: 207
Period size: 30 Copynumber: 3.6 Consensus size: 30
13423 CTTTTAGTAT
*
13433 TTACTATTTAGGCTTAATCATCATTTGGGC
1 TTACTATTTAGGCTTAATCATCATTTGGAC
13463 TTACTATTTAGGCTTAATCATCATTTGGAC
1 TTACTATTTAGGCTTAATCATCATTTGGAC
13493 TTACTATTTAGGCTTAATCATCATTTGGAC
1 TTACTATTTAGGCTTAATCATCATTTGGAC
13523 TTACTATTTAGGCTTAAT
1 TTACTATTTAGGCTTAAT
13541 ACTAGCAACA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 77 1.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (30 bp):
TTACTATTTAGGCTTAATCATCATTTGGAC
Found at i:13476 original size:13 final size:13
Alignment explanation
Indices: 13433--13538 Score: 63
Period size: 13 Copynumber: 7.2 Consensus size: 13
13423 CTTTTAGTAT
13433 TTACTATTTAGGC
1 TTACTATTTAGGC
*
13446 TTAATCATCATTTGGGC
1 TT-A-C-T-ATTTAGGC
13463 TTACTATTTAGGC
1 TTACTATTTAGGC
13476 TTAATCATCATTT-GGAC
1 TT-A-C-T-ATTTAGG-C
13493 TTACTATTTAGGC
1 TTACTATTTAGGC
13506 TTAATCATCATTT-GGAC
1 TT-A-C-T-ATTTAGG-C
13523 TTACTATTTAGGC
1 TTACTATTTAGGC
13536 TTA
1 TTA
13539 ATACTAGCAA
Statistics
Matches: 75, Mismatches: 2, Indels: 32
0.69 0.02 0.29
Matches are distributed among these distances:
13 26 0.35
14 10 0.13
15 6 0.08
16 10 0.13
17 23 0.31
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.44
Consensus pattern (13 bp):
TTACTATTTAGGC
Found at i:17972 original size:30 final size:32
Alignment explanation
Indices: 17899--17977 Score: 108
Period size: 30 Copynumber: 2.5 Consensus size: 32
17889 CGGCGTCCGT
17899 CGTGACACGCCACGTGTACAAAAAAAGTGACA
1 CGTGACACGCCACGTGTACAAAAAAAGTGACA
* *
17931 TGTGACACGCCACGTGTAC-CAAAAAG-GACA
1 CGTGACACGCCACGTGTACAAAAAAAGTGACA
* *
17961 CGTGGCACGCCATGTGT
1 CGTGACACGCCACGTGT
17978 TAAAAGGCCA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 18 0.43
31 6 0.14
32 18 0.43
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.15
Consensus pattern (32 bp):
CGTGACACGCCACGTGTACAAAAAAAGTGACA
Found at i:20190 original size:31 final size:31
Alignment explanation
Indices: 20155--20315 Score: 171
Period size: 31 Copynumber: 5.2 Consensus size: 31
20145 GGTATCCGAC
*
20155 GTGGCATGCCATGTGTATCAAAAAGCGACAT
1 GTGGCATGCCATGTGTACCAAAAAGCGACAT
*
20186 GTGGCATGCCATGTGTACCAAAAAGCGACAC
1 GTGGCATGCCATGTGTACCAAAAAGCGACAT
**
20217 GTGGCATGCCACATGTACCAAAAAGCGACAT
1 GTGGCATGCCATGTGTACCAAAAAGCGACAT
* * * ** * *
20248 GCGACACGCCACATGTATC-AAAAGTGACAT
1 GTGGCATGCCATGTGTACCAAAAAGCGACAT
** * * *
20278 GTATCACGCCATGTGTACCAAAAAGTGACAC
1 GTGGCATGCCATGTGTACCAAAAAGCGACAT
20309 GTGGCAT
1 GTGGCAT
20316 ACCACGACGC
Statistics
Matches: 109, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
30 23 0.21
31 86 0.79
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.19
Consensus pattern (31 bp):
GTGGCATGCCATGTGTACCAAAAAGCGACAT
Found at i:20508 original size:15 final size:16
Alignment explanation
Indices: 20488--20529 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
20478 GGACAGAGAA
*
20488 CTCTGTTTTCC-TTAT
1 CTCTGTTTTCCATCAT
20503 CTCTGTTTTTCCATCAT
1 CTCTG-TTTTCCATCAT
20520 CTCTGTTTTC
1 CTCTGTTTTC
20530 TTTTCCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 11 0.46
17 8 0.33
ACGTcount: A:0.07, C:0.29, G:0.07, T:0.57
Consensus pattern (16 bp):
CTCTGTTTTCCATCAT
Found at i:20523 original size:17 final size:16
Alignment explanation
Indices: 20488--20528 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
20478 GGACAGAGAA
*
20488 CTCTG-TTTTCCTTAT
1 CTCTGTTTTTCCTCAT
20503 CTCTGTTTTTCCATCAT
1 CTCTGTTTTTCC-TCAT
20520 CTCTGTTTT
1 CTCTGTTTT
20529 CTTTTCCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.22
16 6 0.26
17 12 0.52
ACGTcount: A:0.07, C:0.27, G:0.07, T:0.59
Consensus pattern (16 bp):
CTCTGTTTTTCCTCAT
Found at i:39816 original size:3 final size:3
Alignment explanation
Indices: 39808--39842 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
39798 CTGTCCTGCA
39808 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
39843 AGAAAGAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:40860 original size:18 final size:18
Alignment explanation
Indices: 40829--40868 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40819 TGGTAATTAG
* *
40829 CTTTCCCTCTCTTTTTCT
1 CTTTCCCTCCCTTTTTAT
*
40847 CTTTCTCTCCCTTTTTAT
1 CTTTCCCTCCCTTTTTAT
40865 CTTT
1 CTTT
40869 TTTTTGGGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.62
Consensus pattern (18 bp):
CTTTCCCTCCCTTTTTAT
Found at i:48761 original size:37 final size:37
Alignment explanation
Indices: 48706--48776 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
48696 TGCAAAAAGA
48706 ACTTATAATGATACTTACGGATCACCCATCAACAAGG
1 ACTTATAATGATACTTACGGATCACCCATCAACAAGG
* *
48743 ACTTATAATGATATTTACGGATCATCCATCAACA
1 ACTTATAATGATACTTACGGATCACCCATCAACA
48777 GGAACTGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.28
Consensus pattern (37 bp):
ACTTATAATGATACTTACGGATCACCCATCAACAAGG
Done.