Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015072.1 Corchorus olitorius cultivar O-4 contig15105, 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: 14996
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:6000 original size:33 final size:31
Alignment explanation
Indices: 5934--6001 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 31
5924 TTTTTAGTGA
* *
5934 TTCATTATAATTCCTTTAAAAAAAAGTAATT
1 TTCATTATAATGCCTTTAAAAAAAACTAATT
* *
5965 TTCATTATAATAGCACTTTTAAAAAAACTAGTT
1 TTCATTATAAT-GC-CTTTAAAAAAAACTAATT
5998 TTCA
1 TTCA
6002 CTTCCACGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 11 0.35
32 1 0.03
33 19 0.61
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (31 bp):
TTCATTATAATGCCTTTAAAAAAAACTAATT
Found at i:6831 original size:16 final size:16
Alignment explanation
Indices: 6810--6841 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6800 CAAAAAAACT
6810 CAAAACCCGAATGACC
1 CAAAACCCGAATGACC
*
6826 CAAAACCCGAGTGACC
1 CAAAACCCGAATGACC
6842 TGAGGCCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.38, G:0.16, T:0.06
Consensus pattern (16 bp):
CAAAACCCGAATGACC
Found at i:7614 original size:93 final size:94
Alignment explanation
Indices: 7494--7664 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 94
7484 TAGTAATATC
* *
7494 GTAAAAGAGAAAATAGGTATAAGGATATTAGATTTAATAAAATAAAAATAGAGTTTTTAGTTGAG
1 GTAAAAGAGAAAATAGGTATAAAGATATTAGATTTAATAAAATAAAAATAGAGTTTTTAGTTGAC
7559 TAAAACTATAAAAGTAAAATACTAAAATG
66 TAAAACTATAAAAGTAAAATACTAAAATG
* * *
7588 GTAAAA-ATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAC
1 GTAAAAGAGAAAATAGGTATAAAGATATTAGATTTAATAAAATAAAAATAGAGTTTTTAGTTGAC
7652 TAAAACTATAAAA
66 TAAAACTATAAAA
7665 ATTTAAACAA
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
93 66 0.92
94 6 0.08
ACGTcount: A:0.53, C:0.02, G:0.13, T:0.31
Consensus pattern (94 bp):
GTAAAAGAGAAAATAGGTATAAAGATATTAGATTTAATAAAATAAAAATAGAGTTTTTAGTTGAC
TAAAACTATAAAAGTAAAATACTAAAATG
Found at i:8741 original size:11 final size:11
Alignment explanation
Indices: 8717--8751 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
8707 TTGACAGCAT
8717 AACAAAAACAA
1 AACAAAAACAA
* *
8728 AACGAAAACGA
1 AACAAAAACAA
8739 AACAAAAACAA
1 AACAAAAACAA
8750 AA
1 AA
8752 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:10349 original size:2 final size:2
Alignment explanation
Indices: 10342--10394 Score: 61
Period size: 2 Copynumber: 25.5 Consensus size: 2
10332 CATGATCTGC
* * *
10342 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TG GA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
10385 TGA TA TA TA T
1 T-A TA TA TA T
10395 GATCTATAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
2 40 0.93
3 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.47
Consensus pattern (2 bp):
TA
Found at i:10365 original size:16 final size:16
Alignment explanation
Indices: 10344--10392 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 16
10334 TGATCTGCTA
10344 TATATATATATATATG
1 TATATATATATATATG
10360 TATATATATATATATG
1 TATATATATATATATG
*
10376 GAGTATATATGATATAT
1 TA-TATATAT-ATATAT
10393 ATGATCTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 17 0.57
17 7 0.23
18 6 0.20
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (16 bp):
TATATATATATATATG
Found at i:10395 original size:20 final size:19
Alignment explanation
Indices: 10342--10402 Score: 81
Period size: 18 Copynumber: 3.2 Consensus size: 19
10332 CATGATCTGC
10342 TATATATATATATAT-ATG
1 TATATATATATATATGATG
10360 TATATATATATATATGGA-G
1 TATATATATATATAT-GATG
*
10379 TATATATGATATATATGATC
1 TATATAT-ATATATATGATG
10399 TATA
1 TATA
10403 GTTATAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
18 15 0.39
19 10 0.26
20 13 0.34
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.46
Consensus pattern (19 bp):
TATATATATATATATGATG
Found at i:12537 original size:19 final size:20
Alignment explanation
Indices: 12487--12542 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
12477 GCTGCTCTAA
*
12487 TAATCTCATCTGTACAATACC
1 TAATATCATCTGTACAATA-C
* * *
12508 TAATTTTATCTGTACAAT-G
1 TAATATCATCTGTACAATAC
12527 TAATATCATCTGTACA
1 TAATATCATCTGTACA
12543 GTATCTAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 14 0.47
21 16 0.53
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (20 bp):
TAATATCATCTGTACAATAC
Done.