Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012977.1 Corchorus olitorius cultivar O-4 contig13010, 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: 23623
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:3048 original size:20 final size:20
Alignment explanation
Indices: 3007--3048 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2997 CTAACCCTAA
*
3007 AACTAGAAGAAAAAAACTAG
1 AACTAGAAGAAAAAAACAAG
* *
3027 AACTAGAAGAGAAAAAGAAG
1 AACTAGAAGAAAAAAACAAG
3047 AA
1 AA
3049 GAGAAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.07, G:0.19, T:0.07
Consensus pattern (20 bp):
AACTAGAAGAAAAAAACAAG
Found at i:3676 original size:19 final size:18
Alignment explanation
Indices: 3643--3678 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3633 TGGAAATAAT
3643 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
3661 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
3679 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:6135 original size:50 final size:50
Alignment explanation
Indices: 6080--6253 Score: 267
Period size: 50 Copynumber: 3.5 Consensus size: 50
6070 ATCCAGAAGG
*
6080 GTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGA
1 GTGAATTGGAAGACAGTTCAAAGGATGAGCGGAAGACGGTCCTTTTAAGA
*
6130 GTGAATTGGAAGACAGTTCAAAGGATGAGCGGAAGACGGTCTTTTTAAGA
1 GTGAATTGGAAGACAGTTCAAAGGATGAGCGGAAGACGGTCCTTTTAAGA
* * *
6180 GTGAATTGGGAGACAGTTCAAAGGATGAGCGGAAGACGGTCCTTTTTATA
1 GTGAATTGGAAGACAGTTCAAAGGATGAGCGGAAGACGGTCCTTTTAAGA
* * *
6230 TTTGAATTGGAAAACAATTCAAAG
1 -GTGAATTGGAAGACAGTTCAAAG
6254 AAGTTGATTG
Statistics
Matches: 113, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 94 0.83
51 19 0.17
ACGTcount: A:0.35, C:0.11, G:0.29, T:0.25
Consensus pattern (50 bp):
GTGAATTGGAAGACAGTTCAAAGGATGAGCGGAAGACGGTCCTTTTAAGA
Found at i:6584 original size:28 final size:28
Alignment explanation
Indices: 6475--6593 Score: 139
Period size: 28 Copynumber: 4.2 Consensus size: 28
6465 ATTTATTTCT
* * *
6475 TATTTTGGTCATTTTGCATGTTCAGCGG
1 TATTTTGGTCATTTTGCATATCCAGGGG
* * * *
6503 CATTTTGGTCATTTTGTATGTCTAGGGG
1 TATTTTGGTCATTTTGCATATCCAGGGG
* *
6531 CATTTTGGTCATTTTGCATATACAGGGG
1 TATTTTGGTCATTTTGCATATCCAGGGG
* *
6559 TATTTTAGTCATTTTGCACATCCAGGGG
1 TATTTTGGTCATTTTGCATATCCAGGGG
6587 TATTTTG
1 TATTTTG
6594 ATCACTTCAA
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 77 1.00
ACGTcount: A:0.18, C:0.13, G:0.24, T:0.45
Consensus pattern (28 bp):
TATTTTGGTCATTTTGCATATCCAGGGG
Found at i:14761 original size:21 final size:21
Alignment explanation
Indices: 14737--14786 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
14727 TGCTAGGAGT
14737 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
14758 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
14779 TCAATGGA
1 TCATTGGA
14787 ATTGCCTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:18569 original size:5 final size:6
Alignment explanation
Indices: 18537--18576 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
18527 AACATTTTAA
* * *
18537 TTTTCT TTCTAT TTTTCT TTTTAT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
18577 AGGGTTTCAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:18569 original size:12 final size:12
Alignment explanation
Indices: 18531--18576 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
18521 TTTACTAACA
*
18531 TTTTAATTTTCT
1 TTTTATTTTTCT
*
18543 TTCTATTTTTCT
1 TTTTATTTTTCT
18555 TTTTATTTTTCT
1 TTTTATTTTTCT
*
18567 TTTTCTTTTT
1 TTTTATTTTT
18577 AGGGTTTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTATTTTTCT
Found at i:18771 original size:16 final size:14
Alignment explanation
Indices: 18738--18777 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 14
18728 TATTTATTTC
18738 CTTTGCATTGTTTTG
1 CTTTG-ATTGTTTTG
18753 CTTTGATTGATTATTG
1 CTTTGATTG-TT-TTG
18769 CTTTGATTG
1 CTTTGATTG
18778 CTTGCCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.17
15 7 0.30
16 12 0.52
ACGTcount: A:0.12, C:0.10, G:0.20, T:0.57
Consensus pattern (14 bp):
CTTTGATTGTTTTG
Found at i:19462 original size:18 final size:18
Alignment explanation
Indices: 19439--19475 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
19429 AAAGGGTAGT
*
19439 TAAAAAAAATTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
*
19457 TAAAAAGAAGTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
19475 T
1 T
19476 GCAAGAGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (18 bp):
TAAAAAAAAGTGTTTTCA
Done.