Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018216.1 Corchorus olitorius cultivar O-4 contig18249, 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: 15676
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Found at i:7150 original size:29 final size:30
Alignment explanation
Indices: 7101--7157 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
7091 AAAACCAAAA
7101 TGACCAAAATGCCCCCTGGATACGCAAAGG
1 TGACCAAAATGCCCCCTGGATACGCAAAGG
*
7131 TGACCAAAATGCCCCC-GGATATGCAAA
1 TGACCAAAATGCCCCCTGGATACGCAAA
7158 AATTACCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.35, C:0.30, G:0.21, T:0.14
Consensus pattern (30 bp):
TGACCAAAATGCCCCCTGGATACGCAAAGG
Found at i:7165 original size:29 final size:29
Alignment explanation
Indices: 7097--7471 Score: 317
Period size: 29 Copynumber: 12.8 Consensus size: 29
7087 AAATAAAACC
**
7097 AAAATGACCAAAATGCCCCCTGGATACGCA
1 AAAATGACCAAAATG-CCCCTGGATGTGCA
** * *
7127 AAGGTGACCAAAATGCCCCCGGATATGCA
1 AAAATGACCAAAATGCCCCTGGATGTGCA
* * * *
7156 AAAATTACCATAATGCCCTTGGATATGCA
1 AAAATGACCAAAATGCCCCTGGATGTGCA
* * *
7185 AAAATGACCATAATGTCCCTGGATGTGTA
1 AAAATGACCAAAATGCCCCTGGATGTGCA
* * * *
7214 AATACGACTAAAAATG-CCTTCGGATGTGCA
1 AAAATGAC-CAAAATGCCCCT-GGATGTGCA
* * *
7244 AATACGACCAAAATG-CCTTCGGATGTGCA
1 AAAATGACCAAAATGCCCCT-GGATGTGCA
* * * *
7273 AAAACGATCAAAATGCCCCTGAATTATGCA
1 AAAATGACCAAAATGCCCCTGGA-TGTGCA
*
7303 AAAATGACCAAAATGCCCTTGGATGTGC-
1 AAAATGACCAAAATGCCCCTGGATGTGCA
*
7331 AAAATGACCAAAATGCCCCTAGATGTGCAA
1 AAAATGACCAAAATGCCCCTGGATGTGC-A
* **
7361 AAAATGACCAAAATG-CCCTAGGATATGTG
1 AAAATGACCAAAATGCCCCT-GGATGTGCA
* * * *
7390 AAAATTACCAAAATGCCCTTGGATTTGCG
1 AAAATGACCAAAATGCCCCTGGATGTGCA
* * * * *
7419 TAAATGACCAAAATGCTCCTGAATGTACC
1 AAAATGACCAAAATGCCCCTGGATGTGCA
7448 AAAATGACCAAAATGCCCCTGGAT
1 AAAATGACCAAAATGCCCCTGGAT
7472 TTACAAAAGG
Statistics
Matches: 284, Mismatches: 53, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
28 26 0.09
29 174 0.61
30 84 0.30
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTGGATGTGCA
Found at i:7244 original size:88 final size:86
Alignment explanation
Indices: 7097--7471 Score: 283
Period size: 88 Copynumber: 4.3 Consensus size: 86
7087 AAATAAAACC
* *** * ** * *
7097 AAAATGACCAAAATGCCCCCTGGATACGCAAAGGTGACCAAAATGCCCCCGGATATGCAAAAATT
1 AAAATGACCAAAATG--CCCTGGATATGCAAAAACGACAAAAATGCCTTCGGATGTGCAAAAATG
* *
7162 ACCATAATGCCCTTGGATATGCA
64 ACCAAAATGCCCTTGGATGTGCA
* * * * * *
7185 AAAATGACCATAATGTCCCTGGATGTGTAAATACGACTAAAAATGCCTTCGGATGTGCAAATACG
1 AAAATGACCAAAATG-CCCTGGATATGCAAAAACGAC-AAAAATGCCTTCGGATGTGCAAAAATG
7250 ACCAAAATG-CCTTCGGATGTGCA
64 ACCAAAATGCCCTT-GGATGTGCA
* * * * *
7273 AAAACGATCAAAATGCCCCTGAATTATGCAAAAATGACCAAAATGCCCTT-GGATGTGC-AAAAT
1 AAAATGACCAAAATG-CCCTGGA-TATGCAAAAACGACAAAAATG-CCTTCGGATGTGCAAAAAT
* *
7336 GACCAAAATGCCCCTAGATGTGCAA
63 GACCAAAATGCCCTTGGATGTGC-A
** ** * * **
7361 AAAATGACCAAAATGCCCTAGGATATGTGAAAATTACCAAAATGCCCTT-GGATTTGCGTAAATG
1 AAAATGACCAAAATGCCCT-GGATATGCAAAAACGACAAAAATG-CCTTCGGATGTGCAAAAATG
* * *
7425 ACCAAAATGCTCC-TGAATGTACC
64 ACCAAAATGC-CCTTGGATGTGCA
7448 AAAATGACCAAAATGCCCCTGGAT
1 AAAATGACCAAAATG-CCCTGGAT
7472 TTACAAAAGG
Statistics
Matches: 234, Mismatches: 43, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
87 92 0.39
88 126 0.54
89 16 0.07
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (86 bp):
AAAATGACCAAAATGCCCTGGATATGCAAAAACGACAAAAATGCCTTCGGATGTGCAAAAATGAC
CAAAATGCCCTTGGATGTGCA
Found at i:7904 original size:58 final size:58
Alignment explanation
Indices: 7738--8039 Score: 523
Period size: 58 Copynumber: 5.2 Consensus size: 58
7728 CTCGACCAAA
* *
7738 ATAAGATTTTGAATTGAAAACTCTCTAGCAGAGACCTCGAACAGGATTTTAAAAACAAG
1 ATAAGATTTTAAATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTT-AAAACAAG
* *
7797 ATGAGATTTTAAATTGAAAAACTCTCTAGCAGAGACCTCGAACAGGATTTTAAAACAAG
1 ATAAGATTTTAAATTG-AAAACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAG
*
7856 ATAAGATTTTAAATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACTAG
1 ATAAGATTTTAAATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAG
*
7914 ATAAGATTTTAAATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTAAAAGAAG
1 ATAAGATTTTAAATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAG
*
7972 ATAAGATTTTAAATTGAAAACTTTCTAACAGAGACCTCGAACAGGATTTTAAAACAAG
1 ATAAGATTTTAAATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAG
8030 ATAAGATTTT
1 ATAAGATTTT
8040 GTTTTAAACT
Statistics
Matches: 233, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
58 162 0.70
59 37 0.16
60 34 0.15
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.27
Consensus pattern (58 bp):
ATAAGATTTTAAATTGAAAACTCTCTAACAGAGACCTCGAACAGGATTTTAAAACAAG
Found at i:8932 original size:32 final size:32
Alignment explanation
Indices: 8896--8967 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 32
8886 TTATCTTCTT
*
8896 TTTTTTTTGACCTCTCTCTGTTTTAGG-CCAAG
1 TTTTTTTTGACCTCTCTCTATTTTAGGTCC-AG
* *
8928 TTTTTTTCGACCTCTTTCTATTTTAGGTCCAG
1 TTTTTTTTGACCTCTCTCTATTTTAGGTCCAG
8960 TTTTTTTT
1 TTTTTTTT
8968 TTTAGCTCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.11, C:0.19, G:0.12, T:0.57
Consensus pattern (32 bp):
TTTTTTTTGACCTCTCTCTATTTTAGGTCCAG
Found at i:13067 original size:15 final size:16
Alignment explanation
Indices: 13047--13076 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13037 TGTAAGTTTA
13047 TCAAAAG-TCAATTTT
1 TCAAAAGATCAATTTT
13062 TCAAAAGATCAATTT
1 TCAAAAGATCAATTT
13077 GAATTCACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (16 bp):
TCAAAAGATCAATTTT
Found at i:14004 original size:11 final size:11
Alignment explanation
Indices: 13988--14012 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13978 GGGGAATAAT
13988 CAATCCAAAAA
1 CAATCCAAAAA
13999 CAATCCAAAAA
1 CAATCCAAAAA
14010 CAA
1 CAA
14013 ACAATTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.28, G:0.00, T:0.08
Consensus pattern (11 bp):
CAATCCAAAAA
Done.