Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016658.1 Corchorus olitorius cultivar O-4 contig16691, 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: 23057
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--30 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1 TAC
4 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
31 TTGGCCAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:438 original size:17 final size:17
Alignment explanation
Indices: 416--455 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
406 AAATTGAATA
**
416 TTTTTATTTTAATGTAT
1 TTTTTATTAAAATGTAT
*
433 TTTTTATTAAAATTTAT
1 TTTTTATTAAAATGTAT
450 TTTTTA
1 TTTTTA
456 ATAATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTTTATTAAAATGTAT
Found at i:1772 original size:16 final size:16
Alignment explanation
Indices: 1751--1789 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1741 TTAATTATTA
**
1751 AAAAATAAATTTTAAT
1 AAAAATAAATTAAAAT
*
1767 AAAAATACATTAAAAT
1 AAAAATAAATTAAAAT
1783 AAAAATA
1 AAAAATA
1790 TTTAATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAATAAATTAAAAT
Found at i:3806 original size:2 final size:2
Alignment explanation
Indices: 3788--3831 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
3778 AACAGCTACC
3788 TA TA T- TA TA TCA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3829 TA T
1 TA T
3832 GGTATTTGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.05
2 35 0.90
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3818 original size:21 final size:20
Alignment explanation
Indices: 3788--3831 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
3778 AACAGCTACC
*
3788 TATATTATATCATATATATA
1 TATATTATATAATATATATA
3808 TATATATATATAATATATATA
1 TATAT-TATATAATATATATA
3829 TAT
1 TAT
3832 GGTATTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TATATTATATAATATATATA
Found at i:4284 original size:4 final size:4
Alignment explanation
Indices: 4275--4301 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4265 TTCTAGTCTT
4275 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
4302 TTTTTTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:5004 original size:15 final size:16
Alignment explanation
Indices: 4981--5019 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
4971 TCGATTAAAT
4981 TTCGGGTC-ATTTGGG
1 TTCGGGTCAATTTGGG
* *
4996 TTTGGGTCAATTTTGG
1 TTCGGGTCAATTTGGG
5012 TTCGGGTC
1 TTCGGGTC
5020 TTTTTCAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.08, C:0.13, G:0.36, T:0.44
Consensus pattern (16 bp):
TTCGGGTCAATTTGGG
Found at i:15319 original size:31 final size:31
Alignment explanation
Indices: 15242--15319 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
15232 ACTGGGCAAA
*
15242 ATGCTCAATTTGGGGCCAAACATTTTCCGTG
1 ATGCTCAATTTGGGGCCAAACATTTTCCGGG
* * * *
15273 ATACTCGATTTGGGGCCAAACGTTTTCGGGG
1 ATGCTCAATTTGGGGCCAAACATTTTCCGGG
* *
15304 TTGCTCAATTCGGGGC
1 ATGCTCAATTTGGGGC
15320 TTTTTCTGAC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (31 bp):
ATGCTCAATTTGGGGCCAAACATTTTCCGGG
Found at i:16473 original size:21 final size:20
Alignment explanation
Indices: 16447--16485 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
16437 CTGCCCCCAC
16447 CTCATC-TAGATCCATCTCCTT
1 CTCATCATA-ATCCA-CTCCTT
16468 CTCATCATAATCCACTCC
1 CTCATCATAATCCACTCC
16486 ACTATATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 11 0.65
22 2 0.12
ACGTcount: A:0.23, C:0.41, G:0.03, T:0.33
Consensus pattern (20 bp):
CTCATCATAATCCACTCCTT
Found at i:19021 original size:226 final size:225
Alignment explanation
Indices: 18599--19281 Score: 1029
Period size: 225 Copynumber: 3.0 Consensus size: 225
18589 TCTATATATA
* * * * *
18599 TGTATACTAATTATAAAGCTAAGTCCTGAGTTTGTGTCACGAGTTGACTTGGATATAAACTCAGT
1 TGTATACTAATTATAAAGCCAAGTCCTGAGTTTGTGTCACGAGTTGACTCGAACACAAACTCAGT
* *
18664 TTTTAAAAATTCAAAATAAAATAAAAACTACCCATTTTAAATAAAACTACTCATTATAGGATAAA
66 TTTTAAAAATTCAAAACAAAATAAAAACTACCCATTTTAAATAAAACTACTCATTAGAGGATAAA
* * *
18729 TATAAGAATTTATATTTTATTTATATCATTTTAAAAAAACTACCCATTT-AAAAAAACTGGCAAA
131 TATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAACTACCCATTTAAAAAAAACTGCCAAA
*
18793 AACTACTCACGTAGTGAGTGCCCAGTGTCT
196 AACTACTCACGTAGTGAGTGCCCTGTGTCT
* *
18823 TGTCTATACTAATTATAAAGCGAAGTTCTGAGTTTGTGTCACGAGTTGACTCGAACACAAACTCA
1 TG--TATACTAATTATAAAGCCAAGTCCTGAGTTTGTGTCACGAGTTGACTCGAACACAAACTCA
18888 G-TTTTAAAAATTCAAAACAAAATAAAAACTACCCATTTTAAATAAAACTACTCATTAGAGGATA
64 GTTTTTAAAAATTCAAAACAAAATAAAAACTACCCATTTTAAATAAAACTACTCATTAGAGGATA
* *
18952 AATATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAACAACTCATTTAAAAAAAACTGCCA
129 AATATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAACTACCCATTTAAAAAAAACTGCCA
19017 AAAACTACTCACGTAGTGAGTGCCCTGTGTCT
194 AAAACTACTCACGTAGTGAGTGCCCTGTGTCT
19049 TG--T--TAATTATAAAGCCAAGTCCTGAGTTTGTGTCACGAGTTGACTCGAACACAAACTCAGT
1 TGTATACTAATTATAAAGCCAAGTCCTGAGTTTGTGTCACGAGTTGACTCGAACACAAACTCAG-
* * * *
19110 TTTTTAAAAGTTCAAAACAAAATAAAAACTACCCACTTTAAATAATACTACTCATTAGAGGATGA
65 TTTTTAAAAATTCAAAACAAAATAAAAACTACCCATTTTAAATAAAACTACTCATTAGAGGATAA
*
19175 ATATAAGTATTTAAATTTTATTTAATATCATTTTTTAAAAAA-TACCCATTTAACAAAAAAAAAC
130 ATATAAGTATTTAAATTTTATTT-ATATCA-TTTTAAAAAAACTACCCATTT----AAAAAAAAC
* *
19239 TACAAAAAACTACTCACGTAGTGAGTGCCCTGTGTCT
189 TGCCAAAAACTACTCACGTAGTGAGTGCCCTGTGTCT
*
19276 TATATA
1 TGTATA
19282 TATATATGCG
Statistics
Matches: 419, Mismatches: 26, Indels: 22
0.90 0.06 0.05
Matches are distributed among these distances:
220 55 0.13
222 84 0.20
223 13 0.03
224 12 0.03
225 108 0.26
226 101 0.24
227 45 0.11
229 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.32
Consensus pattern (225 bp):
TGTATACTAATTATAAAGCCAAGTCCTGAGTTTGTGTCACGAGTTGACTCGAACACAAACTCAGT
TTTTAAAAATTCAAAACAAAATAAAAACTACCCATTTTAAATAAAACTACTCATTAGAGGATAAA
TATAAGTATTTAAATTTTATTTATATCATTTTAAAAAAACTACCCATTTAAAAAAAACTGCCAAA
AACTACTCACGTAGTGAGTGCCCTGTGTCT
Found at i:22527 original size:31 final size:31
Alignment explanation
Indices: 22492--22562 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
22482 TGTTTTTAGA
* *
22492 CTCAAATTGAGCAATTTTTGAAATGTGTAGG
1 CTCAAATTGAGCAACTTTTGAAAGGTGTAGG
* *
22523 CTCAAATTGAGCAACTTTTGAAAGGTTTAGT
1 CTCAAATTGAGCAACTTTTGAAAGGTGTAGG
22554 CTCAAATTG
1 CTCAAATTG
22563 GTAATTTGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (31 bp):
CTCAAATTGAGCAACTTTTGAAAGGTGTAGG
Done.