Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013169.1 Corchorus olitorius cultivar O-4 contig13202, 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: 15557
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:1453 original size:76 final size:76
Alignment explanation
Indices: 1316--1465 Score: 171
Period size: 76 Copynumber: 2.0 Consensus size: 76
1306 ACAAGGACCC
* * * *
1316 CGACTCCACCTGGGTGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGTGCCCACATGGTTACCTTGAGCACCCATGTGGTTTACCTGAGAACCCAGAT
1381 GGGCAGTGTTA
66 GGGCAGTGTTA
* * **
1392 CGACTCCAGCTGGGTGCCCACATGGTTTATC-TGAAG-ACCCATGT-GTTTCACCTGATCACCCA
1 CGACTCCACCTGGGTGCCCACATGG-TTACCTTG-AGCACCCATGTGGTTT-ACCTGAGAACCCA
*
1454 GATGGGCTGTGT
63 GATGGGCAGTGT
1466 CTTAGCTCAT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
75 4 0.06
76 53 0.85
77 5 0.08
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (76 bp):
CGACTCCACCTGGGTGCCCACATGGTTACCTTGAGCACCCATGTGGTTTACCTGAGAACCCAGAT
GGGCAGTGTTA
Found at i:2407 original size:15 final size:16
Alignment explanation
Indices: 2383--2422 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
2373 AGAGGTTGAA
*
2383 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
2398 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
2414 AGAAAACAA
1 AGAAAACAA
2423 AACAAAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:6053 original size:2 final size:2
Alignment explanation
Indices: 6048--6092 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
6038 ACACATGATA
* *
6048 AT AT AT AT AT AT AT AT AT AT AG GT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6089 AT AT
1 AT AT
6093 TAACCCACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10462 original size:23 final size:23
Alignment explanation
Indices: 10432--10478 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
10422 AATCTCAACC
10432 CTGCATGTGTAGTCTGTTAAACT
1 CTGCATGTGTAGTCTGTTAAACT
10455 CTGCATGTGTAGTCTGTTAAACT
1 CTGCATGTGTAGTCTGTTAAACT
10478 C
1 C
10479 CATTGACAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (23 bp):
CTGCATGTGTAGTCTGTTAAACT
Found at i:10762 original size:52 final size:52
Alignment explanation
Indices: 10705--10808 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
10695 AAGAAAAAGA
10705 TGGCTTAATGTCCAATTTGCACCCTGAATTATCAGTGAATGGACAATTTTGC
1 TGGCTTAATGTCCAATTTGCACCCTGAATTATCAGTGAATGGACAATTTTGC
10757 TGGCTTAATGTCCAATTTGCACCCTGAATTATCAGTGAATGGACAATTTTGC
1 TGGCTTAATGTCCAATTTGCACCCTGAATTATCAGTGAATGGACAATTTTGC
10809 ACCATAAACT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (52 bp):
TGGCTTAATGTCCAATTTGCACCCTGAATTATCAGTGAATGGACAATTTTGC
Found at i:10861 original size:30 final size:29
Alignment explanation
Indices: 10804--10871 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
10794 AATGGACAAT
* *
10804 TTTGCACCATAAACTTTAATTTTGGATAA
1 TTTGCACCCTAAACTTTAATTTCGGATAA
10833 TTTGCACCCTAAACTATT-ATTTACGGATAA
1 TTTGCACCCTAAACT-TTAATTT-CGGATAA
*
10863 TATGCACCC
1 TTTGCACCC
10872 AATTGGACGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 18 0.53
30 16 0.47
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (29 bp):
TTTGCACCCTAAACTTTAATTTCGGATAA
Found at i:11033 original size:29 final size:29
Alignment explanation
Indices: 10987--11042 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
10977 TATTGTCTGT
* *
10987 AAATTATAGTTTATGGTGCAAATTGTCCA
1 AAATTAAAGTTTAGGGTGCAAATTGTCCA
*
11016 AAATTAAAGTTTCGGGTGCAAATTGTC
1 AAATTAAAGTTTAGGGTGCAAATTGTC
11043 AATTAGTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.36
Consensus pattern (29 bp):
AAATTAAAGTTTAGGGTGCAAATTGTCCA
Found at i:12347 original size:8 final size:8
Alignment explanation
Indices: 12334--12373 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
12324 TTATCGATTC
12334 TTTTTCAT
1 TTTTTCAT
*
12342 TTTTTCCT
1 TTTTTCAT
* *
12350 TTCTTCTT
1 TTTTTCAT
12358 TTTTTCAT
1 TTTTTCAT
12366 TTTTTCAT
1 TTTTTCAT
12374 CAACTTTGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTCAT
Done.