Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011879.1 Corchorus olitorius cultivar O-4 contig11912, 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: 24724
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:1743 original size:11 final size:12
Alignment explanation
Indices: 1718--1742 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1708 AGTGTATCTC
1718 TTCCTTTTTTTT
1 TTCCTTTTTTTT
1730 TTCCTTTTTTTT
1 TTCCTTTTTTTT
1742 T
1 T
1743 CTTAGGGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTCCTTTTTTTT
Found at i:9230 original size:3 final size:3
Alignment explanation
Indices: 9222--9256 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
9212 TTACCAAAAT
9222 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
9257 AATAAAAAAA
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:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:9369 original size:41 final size:42
Alignment explanation
Indices: 9281--9391 Score: 163
Period size: 41 Copynumber: 2.7 Consensus size: 42
9271 AGAAACAGGC
*
9281 CGCTTGGGCCAACCAAGCTG-GCGGCCCAGGCGCCTGGACCAG
1 CGCTTGGGCCAGCCAAGC-GCGCGGCCCAGGCGCCTGGACCAG
* *
9323 CGCTTGGGCCAGCCAGGCGCGCGGCCCA-GTGCCTGGACCAG
1 CGCTTGGGCCAGCCAAGCGCGCGGCCCAGGCGCCTGGACCAG
*
9364 CGCTTGGGCTAGCCAAGCGCGCGGCCCA
1 CGCTTGGGCCAGCCAAGCGCGCGGCCCA
9392 AGCTTTGGGG
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 39 0.62
42 24 0.38
ACGTcount: A:0.14, C:0.39, G:0.37, T:0.10
Consensus pattern (42 bp):
CGCTTGGGCCAGCCAAGCGCGCGGCCCAGGCGCCTGGACCAG
Found at i:15780 original size:30 final size:31
Alignment explanation
Indices: 15708--15782 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 31
15698 TTGCTTATTT
* *
15708 TATCTTTC-AATTG-TTGATTTGAATTGCCA
1 TATCTTGCTAATTGATTGATTTGAATTGCAA
15737 TATCTTGCT-ATTGATTGA-TTGAATTGCAA
1 TATCTTGCTAATTGATTGATTTGAATTGCAA
*
15766 TTAT-TTGTTAATTGATT
1 -TATCTTGCTAATTGATT
15783 AATAGATTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 25 0.64
30 14 0.36
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.51
Consensus pattern (31 bp):
TATCTTGCTAATTGATTGATTTGAATTGCAA
Found at i:19415 original size:13 final size:13
Alignment explanation
Indices: 19397--19421 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19387 GTTATCAAAT
19397 TTACAGTAATTAG
1 TTACAGTAATTAG
19410 TTACAGTAATTA
1 TTACAGTAATTA
19422 TCAAATTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
TTACAGTAATTAG
Found at i:19725 original size:37 final size:37
Alignment explanation
Indices: 19671--19743 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
19661 TTTACAATAC
19671 TTAATTACTCAAAAAGCTATAACAGTTATGAAAAAAG
1 TTAATTACTCAAAAAGCTATAACAGTTATGAAAAAAG
* *
19708 TTAATTACTCAATAAGCTATAACGGTTATGAAAAAA
1 TTAATTACTCAAAAAGCTATAACAGTTATGAAAAAA
19744 ATTATATATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (37 bp):
TTAATTACTCAAAAAGCTATAACAGTTATGAAAAAAG
Found at i:20347 original size:70 final size:70
Alignment explanation
Indices: 20234--20378 Score: 272
Period size: 70 Copynumber: 2.1 Consensus size: 70
20224 TAACTCCGAA
* *
20234 ACACAACATATGAGTATTGCTTACACAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
1 ACACAACATATGAGCATTGATTACACAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
20299 GTTCT
66 GTTCT
20304 ACACAACATATGAGCATTGATTACACAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
1 ACACAACATATGAGCATTGATTACACAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
20369 GTTCT
66 GTTCT
20374 ACACA
1 ACACA
20379 CAAACATGCA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (70 bp):
ACACAACATATGAGCATTGATTACACAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
GTTCT
Found at i:20786 original size:22 final size:22
Alignment explanation
Indices: 20761--20902 Score: 104
Period size: 22 Copynumber: 6.7 Consensus size: 22
20751 CATAATGATG
*
20761 TGAAAATTTGATAACATCATTA
1 TGAAAATTTGATAACCTCATTA
*
20783 TGAAATTTTGATAA-C-C--TA
1 TGAAAATTTGATAACCTCATTA
* * *
20801 TGAAAATTTGATAAACACACTA
1 TGAAAATTTGATAACCTCATTA
* * * *
20823 TCAAATTTTGATAACCTCAGTG
1 TGAAAATTTGATAACCTCATTA
*
20845 TG-AAA-TTG-TAACCGCATTA
1 TGAAAATTTGATAACCTCATTA
20864 TGAAAATTTTGATAACCTC-TTCA
1 TGAAAA-TTTGATAACCTCATT-A
20887 T-AAAATTTTGATAACC
1 TGAAAA-TTTGATAACC
20903 ACACCATGAA
Statistics
Matches: 96, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
18 15 0.16
19 11 0.11
20 8 0.08
21 2 0.02
22 52 0.54
23 8 0.08
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCATTA
Found at i:20804 original size:18 final size:18
Alignment explanation
Indices: 20781--20839 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
20771 ATAACATCAT
20781 TATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
*
20799 TATGAAAATTTGATAAACACAC
1 TATGAAATTTTGAT--A-AC-C
*
20821 TATCAAATTTTGATAACC
1 TATGAAATTTTGATAACC
20839 T
1 T
20840 CAGTGTGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
18 15 0.44
19 2 0.06
20 2 0.06
21 2 0.06
22 13 0.38
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (18 bp):
TATGAAATTTTGATAACC
Found at i:20811 original size:40 final size:41
Alignment explanation
Indices: 20760--20882 Score: 137
Period size: 40 Copynumber: 3.0 Consensus size: 41
20750 TCATAATGAT
20760 GTGAAAATTTGATAACATCATTATGAAATTTTGATAACCT-A
1 GTGAAAATTTGATAACA-CATTATGAAATTTTGATAACCTCA
* *
20801 -TGAAAATTTGATAAACACACTATCAAATTTTGATAACCTCA
1 GTGAAAATTTGAT-AACACATTATGAAATTTTGATAACCTCA
* *
20842 GTGTGAAA-TTG-TAACCGCATTATGAAAATTTTGATAACCTC
1 GTG-AAAATTTGATAA-CACATTATG-AAATTTTGATAACCTC
20883 TTCATAAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
40 34 0.49
41 12 0.17
42 21 0.30
43 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (41 bp):
GTGAAAATTTGATAACACATTATGAAATTTTGATAACCTCA
Found at i:21017 original size:22 final size:22
Alignment explanation
Indices: 20962--21260 Score: 134
Period size: 22 Copynumber: 13.3 Consensus size: 22
20952 CTCTTTATTT
* *
20962 AATTTTGATAACATCTCC-ATAA
1 AATTTTGATAACCT-TCCTATGA
20984 AATTGTTG-TAACCTTCCTATGA
1 AATT-TTGATAACCTTCCTATGA
* * *
21006 AATTTTGTTAACCTCCCTAGGA
1 AATTTTGATAACCTTCCTATGA
* *
21028 TACTTTGATAACCTCCCTCCCTATGA
1 AATTTTGATAACCT---T-CCTATGA
* *
21054 AATTTTGATAAGC-ACACTAT-A
1 AATTTTGATAACCTTC-CTATGA
* *
21075 AATTTTGATAACCTTCGTATAAA
1 AATTTTGATAACCTTCCTAT-GA
* *
21098 AATTTTGTTAATGACAC-T-CTAAGA
1 AATTTTG---ATAAC-CTTCCTATGA
** *
21122 AATTTTGATAACCTTTTTATAA
1 AATTTTGATAACCTTCCTATGA
* * * *
21144 AATTTTGGTAA-CGTCTATATGG
1 AATTTTGATAACCTTC-CTATGA
*
21166 AATTTTGATAA-CTACACTATGA
1 AATTTTGATAACCTTC-CTATGA
**
21188 CGTTTTGATAACC-TCCATATGA
1 AATTTTGATAACCTTCC-TATGA
*
21210 AATTTT-AGTAACC-ACACTATGA
1 AATTTTGA-TAACCTTC-CTATGA
* *
21232 AAATTTGATAACCTTCCTATGT
1 AATTTTGATAACCTTCCTATGA
21254 AATTTTG
1 AATTTTG
21261 GTTTGATTGA
Statistics
Matches: 207, Mismatches: 46, Indels: 48
0.69 0.15 0.16
Matches are distributed among these distances:
20 1 0.00
21 32 0.15
22 127 0.61
23 15 0.07
24 8 0.04
25 2 0.01
26 21 0.10
27 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (22 bp):
AATTTTGATAACCTTCCTATGA
Found at i:22987 original size:27 final size:27
Alignment explanation
Indices: 22951--23024 Score: 69
Period size: 28 Copynumber: 2.7 Consensus size: 27
22941 TCCGGCATTT
* *
22951 AAGGACAAAACTGTAATTTAGTTAACC
1 AAGGGCAAAACTGTAATTTAGCTAACC
* * *
22978 AGGGGTAAAA-TGGTAATTTTAGCTGACC
1 AAGGGCAAAACT-GTAA-TTTAGCTAACC
*
23006 AAGGGCAAAACAGTAATTT
1 AAGGGCAAAACTGTAATTT
23025 TGACATCTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
26 1 0.03
27 14 0.39
28 21 0.58
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.26
Consensus pattern (27 bp):
AAGGGCAAAACTGTAATTTAGCTAACC
Done.