Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021780.1 Corchorus olitorius cultivar O-4 contig21813, 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: 26437
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:3061 original size:25 final size:25
Alignment explanation
Indices: 3027--3078 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
3017 ATAATTGGCC
3027 ATAGACTAGAGAAATCAGTGAAGGA
1 ATAGACTAGAGAAATCAGTGAAGGA
3052 ATAGACTAGAGAAATCAGTGAAGGA
1 ATAGACTAGAGAAATCAGTGAAGGA
3077 AT
1 AT
3079 TTATTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.08, G:0.27, T:0.17
Consensus pattern (25 bp):
ATAGACTAGAGAAATCAGTGAAGGA
Found at i:12005 original size:7 final size:7
Alignment explanation
Indices: 11995--12022 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
11985 GAATGAAGAA
11995 GAAGAGG
1 GAAGAGG
12002 GAAGAGG
1 GAAGAGG
12009 GAAGAGG
1 GAAGAGG
12016 GAAGAGG
1 GAAGAGG
12023 CAGAGGAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (7 bp):
GAAGAGG
Found at i:14418 original size:31 final size:31
Alignment explanation
Indices: 14380--14441 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
14370 GAGTTTTGTA
*
14380 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
*
14411 AAACTTTTGAATCGCCTATCATATCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
14442 TTTTCGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATCATACCCTTATT
Found at i:14614 original size:92 final size:93
Alignment explanation
Indices: 14478--14646 Score: 295
Period size: 92 Copynumber: 1.8 Consensus size: 93
14468 TTCTTTAAAT
*
14478 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
14543 TTTTATTTTTACCATTTTGCTATTTTAC
66 TTTTATTTTTACCATTTTGCTATTTTAC
* *
14571 TTTTATAGTTTTACTCAACT-AAAACTCTATTTTTATTTGATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
*
14635 TTTTGTTTTTAC
66 TTTTATTTTTAC
14647 GATATTACTA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 53 0.74
93 19 0.26
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.53
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATTTTGCTATTTTAC
Found at i:14686 original size:92 final size:92
Alignment explanation
Indices: 14492--14678 Score: 230
Period size: 92 Copynumber: 2.0 Consensus size: 92
14482 ATAGTTTTAG
14492 TCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTTTTACCA
1 TCAACT-AAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTTTTACCA
* * * * ** * ** *
14557 TTTTGCTATTTTACTTTTATAGTTTTAC
65 TATTACTAATTTAATTAAAAAGTTAGAA
* * * *
14585 TCAACTAAAACTCTATTTTTATTTGATTAAATCTAATATCCTTATACCTATTTTGTTTTTACGAT
1 TCAACTAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTTTTACCAT
14650 ATTACTAATTTAATTAAAAAGATTAGAA
66 ATTACTAATTTAATTAAAAAG-TTAGAA
14678 T
1 T
14679 TTTTAAAAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
92 69 0.87
93 10 0.13
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (92 bp):
TCAACTAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTTTTACCAT
ATTACTAATTTAATTAAAAAGTTAGAA
Found at i:16505 original size:24 final size:24
Alignment explanation
Indices: 16473--16604 Score: 78
Period size: 24 Copynumber: 5.7 Consensus size: 24
16463 TATATTTTAT
*
16473 TATAAATATTAAATATATTTAAAA
1 TATATATATTAAATATATTTAAAA
*
16497 TATATATATTATATATA-TT---A
1 TATATATATTAAATATATTTAAAA
* * * **
16517 TATAT-TAGTAATTAGTTTTTATTA
1 TATATATATTAAATA-TATTTAAAA
** *
16541 TATATATA-TAAATATATATTTTAT
1 TATATATATTAAATATAT-TTAAAA
* * *
16565 TATAAATATTAAATACATTTAAGA
1 TATATATATTAAATATATTTAAAA
*
16589 TATATATATTATATAT
1 TATATATATTAAATAT
16605 TATATATTAG
Statistics
Matches: 80, Mismatches: 20, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
19 6 0.08
20 7 0.09
21 2 0.03
23 4 0.05
24 51 0.64
25 10 0.12
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (24 bp):
TATATATATTAAATATATTTAAAA
Found at i:16617 original size:90 final size:92
Alignment explanation
Indices: 16459--16639 Score: 314
Period size: 92 Copynumber: 2.0 Consensus size: 92
16449 CGAGAACTCG
*
16459 AATATATATTTTATTATAAATATTAAATATATTTAAAATATATATATTATATATATTATATATTA
1 AATATATATTTTATTATAAATATTAAATACATTTAAAATATATATATTATATATATTATATATTA
16524 GTAAT-TAGTTTTTATTATATATATATA
66 GTAATCT-GTTTTTATTATATATATATA
*
16551 AATATATATTTTATTATAAATATTAAATACATTTAAGATATATATA-T-TATATATTATATATTA
1 AATATATATTTTATTATAAATATTAAATACATTTAAAATATATATATTATATATATTATATATTA
16614 GTAATCTGTTTTTATTATATATATAT
66 GTAATCTGTTTTTATTATATATATAT
16640 TAAAAATAAT
Statistics
Matches: 86, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
90 40 0.47
91 2 0.02
92 44 0.51
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (92 bp):
AATATATATTTTATTATAAATATTAAATACATTTAAAATATATATATTATATATATTATATATTA
GTAATCTGTTTTTATTATATATATATA
Found at i:17737 original size:14 final size:14
Alignment explanation
Indices: 17718--17746 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17708 ACATCTCTCT
17718 TTACATGAACAAAA
1 TTACATGAACAAAA
17732 TTACATGAACAAAA
1 TTACATGAACAAAA
17746 T
1 T
17747 AATAGACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.24
Consensus pattern (14 bp):
TTACATGAACAAAA
Found at i:17876 original size:32 final size:33
Alignment explanation
Indices: 17839--17925 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 33
17829 CATACTATTC
* *
17839 AAAAGAAAATTAGTTA-TATTGTTCA-ACAAAAA
1 AAAAGAAAATTAATTATTA-TATTCACACAAAAA
*
17871 AAAAGAAAATTAATTATTATATTCACCCAAAAA
1 AAAAGAAAATTAATTATTATATTCACACAAAAA
17904 AAAAGAAAATTAATTATTATAT
1 AAAAGAAAATTAATTATTATAT
17926 ACTAATTTTC
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
32 20 0.40
33 30 0.60
ACGTcount: A:0.57, C:0.07, G:0.06, T:0.30
Consensus pattern (33 bp):
AAAAGAAAATTAATTATTATATTCACACAAAAA
Found at i:19311 original size:13 final size:13
Alignment explanation
Indices: 19293--19317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19283 GTAATACTGC
19293 ACTAAATGTTTGG
1 ACTAAATGTTTGG
19306 ACTAAATGTTTG
1 ACTAAATGTTTG
19318 CTAGAATTGT
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:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
ACTAAATGTTTGG
Found at i:22355 original size:60 final size:60
Alignment explanation
Indices: 22227--22414 Score: 277
Period size: 60 Copynumber: 3.0 Consensus size: 60
22217 GCATGAGATC
*
22227 AAGGAGTTTTAATCAAAATATTGGAAGCTAGCGCTTCGCCGCAGACTTGTTCCTTTATATCGGGT
1 AAGGAGTTTTAATCAAAATATCGGAAGCTA--G---CGCCGCAGACTTGTTCCTTTATATCGGGT
22292 AAGGAGTTTTAATCAAAATATCGGAAGCTAGCGCCGCAGACTTGTTCCTTTATATCGGGT
1 AAGGAGTTTTAATCAAAATATCGGAAGCTAGCGCCGCAGACTTGTTCCTTTATATCGGGT
22352 AAGGAGTTTTAATCAAAATATCGGAAGCTAGCGCTTCACCGCAGACTTGTTCCTTTATATCGG
1 AAGGAGTTTTAATCAAAATATCGGAAGCTAGCG-----CCGCAGACTTGTTCCTTTATATCGG
22415 ATTTGGGAAA
Statistics
Matches: 117, Mismatches: 1, Indels: 10
0.91 0.01 0.08
Matches are distributed among these distances:
60 62 0.53
63 1 0.01
65 54 0.46
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (60 bp):
AAGGAGTTTTAATCAAAATATCGGAAGCTAGCGCCGCAGACTTGTTCCTTTATATCGGGT
Found at i:24063 original size:46 final size:46
Alignment explanation
Indices: 23996--24090 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
23986 GAGCGCAAAT
23996 AAGAACAAACAAACGTTAACAATTGAGACTCCAATTAAATCAATTC
1 AAGAACAAACAAACGTTAACAATTGAGACTCCAATTAAATCAATTC
24042 AAGAACAAACAAACGTTAACAATTGAGACTCCAATTAAATCAATTC
1 AAGAACAAACAAACGTTAACAATTGAGACTCCAATTAAATCAATTC
24088 AAG
1 AAG
24091 GAACCTTACT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.51, C:0.19, G:0.09, T:0.21
Consensus pattern (46 bp):
AAGAACAAACAAACGTTAACAATTGAGACTCCAATTAAATCAATTC
Done.