Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018643.1 Corchorus olitorius cultivar O-4 contig18676, 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: 42594
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:479 original size:121 final size:127
Alignment explanation
Indices: 343--595 Score: 392
Period size: 121 Copynumber: 2.0 Consensus size: 127
333 CATTGTTTAA
*
343 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C-T-T-TA
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
404 -TGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAA-TTTTAAATAT
66 TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTAAATAT
*
464 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATATC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCC-T-TATC
* *
529 TATTTTATTTTTACCATTTTACTATTTTATTTAAAAAACTTATATATATTAGAATTTTTTAAATA
64 TA-TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAA-TTTTTAAATA
594 T
127 T
595 A
1 A
596 TTTCTTAAAT
Statistics
Matches: 118, Mismatches: 4, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
121 54 0.46
122 1 0.01
125 1 0.01
126 1 0.01
127 2 0.02
129 48 0.41
131 11 0.09
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (127 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTAAATAT
Found at i:617 original size:14 final size:13
Alignment explanation
Indices: 581--619 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
571 TATATATTAG
581 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
594 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
608 AATTTTTTAAAT
1 AATTTTTTAAAT
620 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:1944 original size:12 final size:11
Alignment explanation
Indices: 1900--1952 Score: 56
Period size: 10 Copynumber: 4.8 Consensus size: 11
1890 TCGTGAATAC
1900 CATATAATATAA
1 CATAT-ATATAA
*
1912 TATATATATAA
1 CATATATATAA
1923 CA-ATATATAA
1 CATATATATAA
*
1933 CATATAACATAA
1 CATAT-ATATAA
1945 CATA-ATAT
1 CATATATAT
1953 TAAAGTTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 13 0.37
11 9 0.26
12 13 0.37
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (11 bp):
CATATATATAA
Found at i:5439 original size:50 final size:52
Alignment explanation
Indices: 5379--5488 Score: 154
Period size: 52 Copynumber: 2.2 Consensus size: 52
5369 ATATATTCCC
*
5379 AATTATATTTATTACCCATATTA-AT-CATATATATCAGAGATAATTATGGT
1 AATTATATTTATTAACCATATTATATCCATATATATCAGAGATAATTATGGT
* * * *
5429 GATTATATTTATTAACCATTTTATATCCTTATATATTAGAGATAATTATGGT
1 AATTATATTTATTAACCATATTATATCCATATATATCAGAGATAATTATGGT
5481 AATT-TATT
1 AATTATATT
5489 AGTTATCAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
50 20 0.38
51 6 0.12
52 26 0.50
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.46
Consensus pattern (52 bp):
AATTATATTTATTAACCATATTATATCCATATATATCAGAGATAATTATGGT
Found at i:8965 original size:2 final size:2
Alignment explanation
Indices: 8958--8994 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
8948 CTCGTTAAGA
8958 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 A
8995 GAGTATAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18774 original size:43 final size:43
Alignment explanation
Indices: 18720--18805 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
18710 TGTAAGCGAT
*
18720 TTGAATCTTGTCAACAATCTTTATTAGTGGATAATATGTAAGC
1 TTGAATCTTGTCAACAATCTTTAGTAGTGGATAATATGTAAGC
18763 TTGAATCTTGTCAACAATCTTTAGTAGTGGATAATATGTAAGC
1 TTGAATCTTGTCAACAATCTTTAGTAGTGGATAATATGTAAGC
18806 ATCATTGTCG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (43 bp):
TTGAATCTTGTCAACAATCTTTAGTAGTGGATAATATGTAAGC
Found at i:18834 original size:59 final size:60
Alignment explanation
Indices: 18763--18880 Score: 193
Period size: 59 Copynumber: 2.0 Consensus size: 60
18753 ATATGTAAGC
*
18763 TTGAATCTTGTCAACAATCTTTAGTAGTGGATAATATGT-AAGCATCATTGTCGGTTGTT
1 TTGAATCTTGTCAACAATCTTTAGTAGTGGATAATATATAAAGCATCATTGTCGGTTGTT
* * *
18822 TTGAATCTTGTCAACAATCTTTATTAGTGGATGATATATAAAGCATCATTGTTGGTTGT
1 TTGAATCTTGTCAACAATCTTTAGTAGTGGATAATATATAAAGCATCATTGTCGGTTGT
18881 CAGCCATCTA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
59 36 0.67
60 18 0.33
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (60 bp):
TTGAATCTTGTCAACAATCTTTAGTAGTGGATAATATATAAAGCATCATTGTCGGTTGTT
Found at i:19966 original size:21 final size:21
Alignment explanation
Indices: 19940--20007 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
19930 TAGTTGTCTA
19940 AATTTGAGATTTCCTTGGATT
1 AATTTGAGATTTCCTTGGATT
* * ** *
19961 AATTT--GATTGCTTTGTCTA
1 AATTTGAGATTTCCTTGGATT
19980 AATTTGAGATTTCCTTGGATT
1 AATTTGAGATTTCCTTGGATT
20001 AATTTGA
1 AATTTGA
20008 TTGCTTTGTC
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
19 14 0.40
21 21 0.60
ACGTcount: A:0.25, C:0.09, G:0.18, T:0.49
Consensus pattern (21 bp):
AATTTGAGATTTCCTTGGATT
Found at i:19978 original size:40 final size:40
Alignment explanation
Indices: 19933--20017 Score: 170
Period size: 40 Copynumber: 2.1 Consensus size: 40
19923 CGGTTCATAG
19933 TTGTCTAAATTTGAGATTTCCTTGGATTAATTTGATTGCT
1 TTGTCTAAATTTGAGATTTCCTTGGATTAATTTGATTGCT
19973 TTGTCTAAATTTGAGATTTCCTTGGATTAATTTGATTGCT
1 TTGTCTAAATTTGAGATTTCCTTGGATTAATTTGATTGCT
20013 TTGTC
1 TTGTC
20018 ATGTTAAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.51
Consensus pattern (40 bp):
TTGTCTAAATTTGAGATTTCCTTGGATTAATTTGATTGCT
Found at i:25775 original size:28 final size:28
Alignment explanation
Indices: 25743--25810 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
25733 TAATAACGCC
* *
25743 AAAAAAAAAGAGTTAATAATTTTTTTTT
1 AAAAAAAAAGACTTAATAATTTTTTATT
* * *
25771 GAAAAACAAGTCTTAATAATTTTTTATT
1 AAAAAAAAAGACTTAATAATTTTTTATT
25799 AAAAAACAAAGA
1 AAAAAA-AAAGA
25811 AATCATTTCA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
28 28 0.90
29 3 0.10
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.35
Consensus pattern (28 bp):
AAAAAAAAAGACTTAATAATTTTTTATT
Found at i:37614 original size:82 final size:82
Alignment explanation
Indices: 37477--37636 Score: 275
Period size: 82 Copynumber: 2.0 Consensus size: 82
37467 TTGAATTATC
* *
37477 TTTGAACAATCATTTGAAGTTTTAAATCTCAGTAACGGATTATGTATTTAATATTAAAAAATGGA
1 TTTGAACAATCATTTGAAGTTTTAAATCTCAGAAACGGATTATGTATTTAATATTAAAAAATAGA
37542 GAATTATACAATACACT
66 GAATTATACAATACACT
* * *
37559 TTTGAACAATTATTTGAAGTTTTAAATCTCAGAAATGGATTGTGTATTTAATATTAAAAAATAGA
1 TTTGAACAATCATTTGAAGTTTTAAATCTCAGAAACGGATTATGTATTTAATATTAAAAAATAGA
37624 GAATTATACAATA
66 GAATTATACAATA
37637 TGTTGTCAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.38
Consensus pattern (82 bp):
TTTGAACAATCATTTGAAGTTTTAAATCTCAGAAACGGATTATGTATTTAATATTAAAAAATAGA
GAATTATACAATACACT
Done.