Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014788.1 Corchorus olitorius cultivar O-4 contig14821, 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: 44245
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:47 original size:3 final size:3
Alignment explanation
Indices: 41--67 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
31 AGAAGAGGTG
41 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
68 AAAGGGCCGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2348 original size:14 final size:15
Alignment explanation
Indices: 2329--2357 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2319 GACGATCTGG
2329 ATTTTAT-AACTGTT
1 ATTTTATGAACTGTT
2343 ATTTTATGAACTGTT
1 ATTTTATGAACTGTT
2358 TTGGTTGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (15 bp):
ATTTTATGAACTGTT
Found at i:5467 original size:13 final size:13
Alignment explanation
Indices: 5449--5474 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5439 AAAATTTTAA
5449 CAACCAAAAAAAT
1 CAACCAAAAAAAT
5462 CAACCAAAAAAAT
1 CAACCAAAAAAAT
5475 TAAAGATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.23, G:0.00, T:0.08
Consensus pattern (13 bp):
CAACCAAAAAAAT
Found at i:27013 original size:106 final size:103
Alignment explanation
Indices: 26742--27038 Score: 364
Period size: 106 Copynumber: 2.8 Consensus size: 103
26732 TAAATATATT
* *
26742 TTATTATAGAGTTTTAGAAATAAAATATAAAACTAATTCACTATGTTTAGCCTCAAATT-AAA-T
1 TTATTATAGGGTTTTAGAAATAAAATATAAAACTAATTCACTAAGTTTAG-CTCAAATTAAAATT
* * * * **
26805 TTAATATTATTATAAGGTTAAATTACAAATTAATATTTA
65 TTAATTTTATTTTAAGGGTAAATTACAAATTAAAACCTA
* * *
26844 TTATTATAGGGTTTTAGAGATAAAATACAAAACTAATTTCACTAAGTTTAGCCCTAAATTAAAAT
1 TTATTATAGGGTTTTAGAAATAAAATATAAAACTAA-TTCACTAAGTTTAGCTC-AAATTAAAAT
26909 TTTAATTTTATTTTAAGGGTAAATTACATAATTAACAACCTA
64 TTTAATTTTATTTTAAGGGTAAATTACA-AATTAA-AACCTA
* * * *
26951 TTGTTATAGGGTTTTAGAAATAAAATATATAATTAATTCACTAAATTTAGTCTCAAATTAAAATT
1 TTATTATAGGGTTTTAGAAATAAAATATAAAACTAATTCACTAAGTTTAG-CTCAAATTAAAATT
** *
27016 AAAATTTTATTTTAAGAGTAAAT
65 TTAATTTTATTTTAAGGGTAAAT
27039 GCCAAAATTG
Statistics
Matches: 167, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
102 35 0.21
103 18 0.11
104 3 0.02
105 25 0.15
106 50 0.30
107 36 0.22
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.40
Consensus pattern (103 bp):
TTATTATAGGGTTTTAGAAATAAAATATAAAACTAATTCACTAAGTTTAGCTCAAATTAAAATTT
TAATTTTATTTTAAGGGTAAATTACAAATTAAAACCTA
Found at i:28041 original size:2 final size:2
Alignment explanation
Indices: 28036--28062 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28026 AGAAAGTAGA
28036 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28063 ATAAAGCCTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29442 original size:42 final size:42
Alignment explanation
Indices: 29379--29800 Score: 409
Period size: 42 Copynumber: 10.0 Consensus size: 42
29369 TGGGGGTGAC
* *
29379 GAAGGTTTTGGTGGTTTTCCTGGTGGCGAAGAGTAAGGTGGT
1 GAAGATTTCGGTGGTTTTCCTGGTGGCGAAGAGTAAGGTGGT
* *
29421 GAAGATTTCGGGGGTTTTCCTGGTGGCGAAGAGTAGGGTGGT
1 GAAGATTTCGGTGGTTTTCCTGGTGGCGAAGAGTAAGGTGGT
* *
29463 GAAGATTTTGGGGGTTTTCCTGGTGGCGAAGAGTAAGGTGGT
1 GAAGATTTCGGTGGTTTTCCTGGTGGCGAAGAGTAAGGTGGT
* *
29505 GAAGATTTTGGTGGTTTTCCTGGTGGCGAAGAGTAGGGTGGT
1 GAAGATTTCGGTGGTTTTCCTGGTGGCGAAGAGTAAGGTGGT
* *
29547 GAAGATTTGGGTGGTTTTCCTGGCGGCGAAGAGTAAGGTGGT
1 GAAGATTTCGGTGGTTTTCCTGGTGGCGAAGAGTAAGGTGGT
* * * * *
29589 GAAGCTTTAGGTGGTTTT-GTGGGAGGGGAAGAGTAAGGTGGT
1 GAAGATTTCGGTGGTTTTCCT-GGTGGCGAAGAGTAAGGTGGT
* * * ** * * **
29631 GAGGCTTTTGGTGGTTTTGTTGGCGGTGAAGAGTGGGGTGGT
1 GAAGATTTCGGTGGTTTTCCTGGTGGCGAAGAGTAAGGTGGT
* * * * *
29673 GAAGCTTTAGGTGGTTTT-GTGGGAGGGGAAGAGTAAGGTGGT
1 GAAGATTTCGGTGGTTTTCCT-GGTGGCGAAGAGTAAGGTGGT
* * ** * * * * *
29715 GACGCTTTCGGTGGTTTTGTTGGCGGTGAGGAGTGAGGCGGT
1 GAAGATTTCGGTGGTTTTCCTGGTGGCGAAGAGTAAGGTGGT
* * * * *
29757 GAAGGTTTCGGTGGTTTT-GTGGGAGGGGAAGAGTGAGGTGGT
1 GAAGATTTCGGTGGTTTTCCT-GGTGGCGAAGAGTAAGGTGGT
29799 GA
1 GA
29801 TCCATTGTAG
Statistics
Matches: 330, Mismatches: 45, Indels: 10
0.86 0.12 0.03
Matches are distributed among these distances:
41 3 0.01
42 325 0.98
43 2 0.01
ACGTcount: A:0.17, C:0.06, G:0.46, T:0.31
Consensus pattern (42 bp):
GAAGATTTCGGTGGTTTTCCTGGTGGCGAAGAGTAAGGTGGT
Found at i:29472 original size:84 final size:84
Alignment explanation
Indices: 29379--29800 Score: 461
Period size: 84 Copynumber: 5.0 Consensus size: 84
29369 TGGGGGTGAC
* * * *
29379 GAAGGTTTTGGTGGTTTTCCTGGTGGCGAAGAGTAAGGTGGTGAAGATTTCGGGGGTTTTCCT-G
1 GAAGATTTTGGTGGTTTTCCTGGCGGCGAAGAGTAAGGTGGTGAAGATTTAGGTGGTTTT-CTGG
* *
29443 GTGGCGAAGAGTAGGGTGGT
65 GAGGCGAAGAGTAAGGTGGT
* * *
29463 GAAGATTTTGGGGGTTTTCCTGGTGGCGAAGAGTAAGGTGGTGAAGATTTTGGTGGTTTTCCT-G
1 GAAGATTTTGGTGGTTTTCCTGGCGGCGAAGAGTAAGGTGGTGAAGATTTAGGTGGTTTT-CTGG
* *
29527 GTGGCGAAGAGTAGGGTGGT
65 GAGGCGAAGAGTAAGGTGGT
* * *
29547 GAAGATTTGGGTGGTTTTCCTGGCGGCGAAGAGTAAGGTGGTGAAGCTTTAGGTGGTTTTGTGGG
1 GAAGATTTTGGTGGTTTTCCTGGCGGCGAAGAGTAAGGTGGTGAAGATTTAGGTGGTTTTCTGGG
*
29612 AGGGGAAGAGTAAGGTGGT
66 AGGCGAAGAGTAAGGTGGT
* * ** * ** * *
29631 GAGGCTTTTGGTGGTTTTGTTGGCGGTGAAGAGTGGGGTGGTGAAGCTTTAGGTGGTTTTGTGGG
1 GAAGATTTTGGTGGTTTTCCTGGCGGCGAAGAGTAAGGTGGTGAAGATTTAGGTGGTTTTCTGGG
*
29696 AGGGGAAGAGTAAGGTGGT
66 AGGCGAAGAGTAAGGTGGT
* * * ** * * * * * * *
29715 GACGCTTTCGGTGGTTTTGTTGGCGGTGAGGAGTGAGGCGGTGAAGGTTTCGGTGGTTTTGTGGG
1 GAAGATTTTGGTGGTTTTCCTGGCGGCGAAGAGTAAGGTGGTGAAGATTTAGGTGGTTTTCTGGG
* *
29780 AGGGGAAGAGTGAGGTGGT
66 AGGCGAAGAGTAAGGTGGT
29799 GA
1 GA
29801 TCCATTGTAG
Statistics
Matches: 308, Mismatches: 29, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
83 1 0.00
84 307 1.00
ACGTcount: A:0.17, C:0.06, G:0.46, T:0.31
Consensus pattern (84 bp):
GAAGATTTTGGTGGTTTTCCTGGCGGCGAAGAGTAAGGTGGTGAAGATTTAGGTGGTTTTCTGGG
AGGCGAAGAGTAAGGTGGT
Found at i:30583 original size:2 final size:2
Alignment explanation
Indices: 30576--30614 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
30566 GTATCTATTA
30576 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30615 AACAATCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33602 original size:15 final size:16
Alignment explanation
Indices: 33582--33616 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
33572 TTTTATTATT
33582 AAAAAAAATTA-AATA
1 AAAAAAAATTATAATA
*
33597 AAAAAATATTATAATA
1 AAAAAAAATTATAATA
33613 AAAA
1 AAAA
33617 TATTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAAAAATTATAATA
Found at i:33612 original size:16 final size:14
Alignment explanation
Indices: 33581--33616 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 14
33571 TTTTTATTAT
33581 TAAAAAAAATTAAA
1 TAAAAAAAATTAAA
33595 TAAAAAAATATTATAA
1 TAAAAAAA-ATTA-AA
33611 TAAAAA
1 TAAAAA
33617 TATTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 4 0.20
16 8 0.40
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAAAAAAATTAAA
Found at i:37319 original size:5 final size:5
Alignment explanation
Indices: 37282--37316 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
37272 TATAGTCCTC
*
37282 TCTTT TCTTT TCTTT CCTTT TCTTT TCTTT T-TTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
37317 TTTCTCGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TCTTT
Found at i:38879 original size:41 final size:41
Alignment explanation
Indices: 38816--38897 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
38806 ACTTGACTCT
* *
38816 CCTAATAATTAAGGAAATAAATTAAATTC-AGATTTAGCCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAAG-TTTAGCCCC
*
38857 CCTAATAATTAAGGTAAGAAATTAAATCCAAGTTTAGCCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAAGTTTAGCCCC
38898 TAGTTACAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 35 0.95
42 2 0.05
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.28
Consensus pattern (41 bp):
CCTAATAATTAAGGAAAGAAATTAAATCCAAGTTTAGCCCC
Done.