Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017186.1 Corchorus olitorius cultivar O-4 contig17219, 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: 32798
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:7379 original size:12 final size:12
Alignment explanation
Indices: 7362--7387 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
7352 TTTCGTAAAC
7362 TCTTCCATTGAA
1 TCTTCCATTGAA
7374 TCTTCCATTGAA
1 TCTTCCATTGAA
7386 TC
1 TC
7388 GGTAAACTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.08, T:0.42
Consensus pattern (12 bp):
TCTTCCATTGAA
Found at i:7867 original size:37 final size:38
Alignment explanation
Indices: 7812--7890 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 38
7802 TTTATATACT
* *
7812 TGATCAACATACATGTCTTTTCATATAGACATAACTTTA
1 TGATCAACA-ACATGTCTTTCCAAATAGACATAACTTTA
7851 TGATCAAC-ACATGTCTTTCCAAATAGACATAACTTTA
1 TGATCAACAACATGTCTTTCCAAATAGACATAACTTTA
7888 TGA
1 TGA
7891 ATAATCATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 30 0.79
39 8 0.21
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (38 bp):
TGATCAACAACATGTCTTTCCAAATAGACATAACTTTA
Found at i:9627 original size:26 final size:25
Alignment explanation
Indices: 9589--9640 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
9579 TTTCTTACAA
9589 AAATAATAGAAATAAACATTAGATAT
1 AAATAATAGAAATAAAC-TTAGATAT
* * * *
9615 AAATCATATAAATGAACTTATATAT
1 AAATAATAGAAATAAACTTAGATAT
9640 A
1 A
9641 TCTCATTGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (25 bp):
AAATAATAGAAATAAACTTAGATAT
Found at i:10827 original size:37 final size:38
Alignment explanation
Indices: 10772--10848 Score: 111
Period size: 37 Copynumber: 2.0 Consensus size: 38
10762 TTTATATACT
* *
10772 TGATCAACATACATGTCTTTTCATATAGACACAACTTTA
1 TGATCAACA-ACATGTCTTTCCAAATAGACACAACTTTA
*
10811 TGATCAAC-ACATGTCTTTCCAAATAGACATAACTTTA
1 TGATCAACAACATGTCTTTCCAAATAGACACAACTTTA
10848 T
1 T
10849 AAATAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
37 27 0.77
39 8 0.23
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (38 bp):
TGATCAACAACATGTCTTTCCAAATAGACACAACTTTA
Found at i:14967 original size:16 final size:15
Alignment explanation
Indices: 14930--15035 Score: 104
Period size: 16 Copynumber: 6.7 Consensus size: 15
14920 GTTAGGGTAC
14930 TTCGGGTTCGGGTTT
1 TTCGGGTTCGGGTTT
* *
14945 TTTGGGTTCGGCTATT
1 TTCGGGTTCGGGT-TT
*
14961 TTCGGGTTCGGGTTAA
1 TTCGGGTTCGGGTT-T
* *
14977 ATCGGGTTCGGATATT
1 TTCGGGTTCGGGT-TT
*
14993 TTCGGGCTCGGGTTAT
1 TTCGGGTTCGGGTT-T
*
15009 GTCGGGTTCGGGTATT
1 TTCGGGTTCGGGT-TT
15025 TTCGGGTTCGG
1 TTCGGGTTCGG
15036 TCTCGGGTAG
Statistics
Matches: 72, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
15 13 0.18
16 57 0.79
17 2 0.03
ACGTcount: A:0.08, C:0.14, G:0.38, T:0.41
Consensus pattern (15 bp):
TTCGGGTTCGGGTTT
Found at i:14993 original size:32 final size:32
Alignment explanation
Indices: 14930--15035 Score: 142
Period size: 32 Copynumber: 3.3 Consensus size: 32
14920 GTTAGGGTAC
* * *
14930 TTCGGGTTCGGGTT-TTTTGGGTTCGGCTATT
1 TTCGGGTTCGGGTTATATCGGGTTCGGATATT
*
14961 TTCGGGTTCGGGTTAAATCGGGTTCGGATATT
1 TTCGGGTTCGGGTTATATCGGGTTCGGATATT
* * *
14993 TTCGGGCTCGGGTTATGTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTTATATCGGGTTCGGATATT
15025 TTCGGGTTCGG
1 TTCGGGTTCGG
15036 TCTCGGGTAG
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
31 14 0.22
32 51 0.78
ACGTcount: A:0.08, C:0.14, G:0.38, T:0.41
Consensus pattern (32 bp):
TTCGGGTTCGGGTTATATCGGGTTCGGATATT
Found at i:15064 original size:23 final size:22
Alignment explanation
Indices: 15009--15065 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
14999 CTCGGGTTAT
**
15009 GTCGGGTTCGGGTATTTTCGGG
1 GTCGGGTTCGGGTAAATTCGGG
*
15031 TTC-GGTCTCGGGTAGAATTCGGG
1 GTCGGGT-TCGGGTA-AATTCGGG
15054 GTCGGGTTCGGG
1 GTCGGGTTCGGG
15066 GTCGGCTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 3 0.11
22 9 0.32
23 13 0.46
24 3 0.11
ACGTcount: A:0.07, C:0.16, G:0.46, T:0.32
Consensus pattern (22 bp):
GTCGGGTTCGGGTAAATTCGGG
Found at i:15221 original size:13 final size:12
Alignment explanation
Indices: 15198--15244 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
15188 AAGTTTATTG
15198 ATAATATATAAT
1 ATAATATATAAT
15210 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
15223 ATAACAT-TATT
1 ATAATATATAAT
15234 ATCAATATATA
1 AT-AATATATA
15245 TAAAGATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:15533 original size:31 final size:32
Alignment explanation
Indices: 15498--15569 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 32
15488 TAAATTATTG
*
15498 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAACAAATGAAAGTC-TTAAATTAAA
***
15529 CAAA-TAATTGAAATGAAAGTCTTAAATTAAA
1 CAAATTAAAACAAATGAAAGTCTTAAATTAAA
15560 CAAATTAAAA
1 CAAATTAAAA
15570 GCTGATAGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
30 7 0.22
31 21 0.66
32 4 0.12
ACGTcount: A:0.60, C:0.08, G:0.06, T:0.26
Consensus pattern (32 bp):
CAAATTAAAACAAATGAAAGTCTTAAATTAAA
Found at i:16646 original size:75 final size:75
Alignment explanation
Indices: 16548--16720 Score: 179
Period size: 75 Copynumber: 2.3 Consensus size: 75
16538 CAATAACATT
* * * * * *
16548 TTCAAAATATTGCCTATCGTCATTGGGAAGCTCAAAA-TTAGAATTCGAAACA-ACATCCTGATT
1 TTCAAGATGTTGCCTATCATCATTAGGAAGCTCAAAATTTA-AATTCGAAACAGA-AACCTGATA
* *
16611 AGGAGAATCAGC
64 AAGAGAATCAAC
* * *
16623 TTCAAGATGTTGCCTATCATCATTATGATGCTCAAAATTTAAATTCGAATCAGAAACCTGATAAA
1 TTCAAGATGTTGCCTATCATCATTAGGAAGCTCAAAATTTAAATTCGAAACAGAAACCTGATAAA
*
16688 GTGAATCAAC
66 GAGAATCAAC
* **
16698 TTCAAGTTGTTGCAAATCATCAT
1 TTCAAGATGTTGCCTATCATCAT
16721 CAGAAAACTT
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
75 77 0.95
76 4 0.05
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (75 bp):
TTCAAGATGTTGCCTATCATCATTAGGAAGCTCAAAATTTAAATTCGAAACAGAAACCTGATAAA
GAGAATCAAC
Found at i:16743 original size:75 final size:75
Alignment explanation
Indices: 16659--16833 Score: 165
Period size: 75 Copynumber: 2.3 Consensus size: 75
16649 GATGCTCAAA
* *
16659 ATTTAAATTCGAATCAGAAACCTGATAAAGTGAATCAACTTCAAG-TTGTTG-CAAATCATCATC
1 ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAACTTCAAGATT-TTGCCAAA-CACCATC
*
16722 AGAAAACTTAGT
64 AGAAAACTCAGT
* ** ** * * * * *
16734 ATTTGAATTCAAAAGAGGCATCTGGTCAGGTGAATCAACTTCAAGATTTTGCCTAACACCATCAG
1 ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAACTTCAAGATTTTGCCAAACACCATCAG
* *
16799 CAAACTCATT
66 AAAACTCAGT
* *
16809 ATTTGAATTCGAATTAGCAACCTGA
1 ATTTGAATTCGAATCAGAAACCTGA
16834 GAAGGAGAAT
Statistics
Matches: 76, Mismatches: 22, Indels: 4
0.75 0.22 0.04
Matches are distributed among these distances:
75 71 0.93
76 5 0.07
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (75 bp):
ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAACTTCAAGATTTTGCCAAACACCATCAG
AAAACTCAGT
Found at i:18324 original size:23 final size:23
Alignment explanation
Indices: 18291--18342 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
18281 TTCAAATTAT
*
18291 TTCGGGTTCGGGCTCAGGTCGAG
1 TTCGGGCTCGGGCTCAGGTCGAG
* * *
18314 TTCGGGCTCGGTCTCGGGTCGGG
1 TTCGGGCTCGGGCTCAGGTCGAG
18337 TTCGGG
1 TTCGGG
18343 TATTTTCGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.04, C:0.23, G:0.46, T:0.27
Consensus pattern (23 bp):
TTCGGGCTCGGGCTCAGGTCGAG
Found at i:18357 original size:16 final size:16
Alignment explanation
Indices: 18332--18368 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
18322 CGGTCTCGGG
* *
18332 TCGGGTTCGGGTATTT
1 TCGGGCTCGGGTAATT
18348 TCGGGCTCGGGTAATT
1 TCGGGCTCGGGTAATT
18364 TCGGG
1 TCGGG
18369 TTCAGGTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.08, C:0.16, G:0.41, T:0.35
Consensus pattern (16 bp):
TCGGGCTCGGGTAATT
Found at i:24257 original size:54 final size:54
Alignment explanation
Indices: 24135--24258 Score: 221
Period size: 54 Copynumber: 2.3 Consensus size: 54
24125 GTGCCGCCTC
*
24135 CTTTGTTGCTTTCTACAAGCAGGGAGGTATCTCCTGAAACAACATATGCATCTT
1 CTTTGTTGCTTTCTGCAAGCAGGGAGGTATCTCCTGAAACAACATATGCATCTT
* *
24189 CTTTGTTTCTTTCTGCAAGCAGGGAGGTATCTCTTGAAACAACATATGCATCTT
1 CTTTGTTGCTTTCTGCAAGCAGGGAGGTATCTCCTGAAACAACATATGCATCTT
24243 CTTTGTTGCTTTCTGC
1 CTTTGTTGCTTTCTGC
24259 GCCACTTTCA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (54 bp):
CTTTGTTGCTTTCTGCAAGCAGGGAGGTATCTCCTGAAACAACATATGCATCTT
Done.