Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005062.1 Corchorus capsularis cultivar CVL-1 contig05080, 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: 14124
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:2813 original size:22 final size:22
Alignment explanation
Indices: 2771--2813 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2761 ATAATTATGT
*
2771 TATTAAAATTTCATAGAGTGGC
1 TATTAAAATTTCATACAGTGGC
*
2793 TATTAAAATTTCATACTGTGG
1 TATTAAAATTTCATACAGTGG
2814 TTTTCAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (22 bp):
TATTAAAATTTCATACAGTGGC
Found at i:3013 original size:22 final size:21
Alignment explanation
Indices: 2978--3061 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 21
2968 ATAATATGGT
*
2978 GGTTATCGAAATTTCATAGGAA
1 GGTTATC-AAATTTCATAGAAA
* * *
3000 TGTTATCAACATTTAATCA-TAA
1 GGTTATCAA-ATTTCAT-AGAAA
*
3022 GGTTATTAAGATTTCATAGAAA
1 GGTTATCAA-ATTTCATAGAAA
3044 GGTTATCAAAATTTCATA
1 GGTTATC-AAATTTCATA
3062 CAGAGGCTAT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
21 3 0.06
22 43 0.88
23 3 0.06
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (21 bp):
GGTTATCAAATTTCATAGAAA
Found at i:3231 original size:51 final size:49
Alignment explanation
Indices: 3148--3246 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 49
3138 TAGGGTCCGT
* *
3148 TTATTAAAATTTCATAGTGAGATTATCAAATTTCGTGGTGTGGTTATCAAG
1 TTATCAAAATTTCATAGTGAGATTATCAAATTTCAT--TGTGGTTATCAAG
*
3199 TTATCAAAATTT-ATATTGCAG-TTATCACAATTTCATTGTGGTTATCAA
1 TTATCAAAATTTCATAGTG-AGATTATCA-AATTTCATTGTGGTTATCAA
3247 ATTTTAAAGG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
49 12 0.28
50 11 0.26
51 20 0.47
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.42
Consensus pattern (49 bp):
TTATCAAAATTTCATAGTGAGATTATCAAATTTCATTGTGGTTATCAAG
Found at i:3907 original size:31 final size:31
Alignment explanation
Indices: 3869--3946 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
3859 GACATCCGAT
3869 GTGGCATGCCACGTGTACCAAAAAATGCCAC
1 GTGGCATGCCACGTGTACCAAAAAATGCCAC
*
3900 GTGGCATGCCACGTGTACCAAATAATGCCAC
1 GTGGCATGCCACGTGTACCAAAAAATGCCAC
**
3931 GTGGCACACCACGTGT
1 GTGGCATGCCACGTGT
3947 CAAAAATACC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.18
Consensus pattern (31 bp):
GTGGCATGCCACGTGTACCAAAAAATGCCAC
Found at i:3954 original size:31 final size:31
Alignment explanation
Indices: 3877--3954 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
3867 ATGTGGCATG
* **
3877 CCACGTGTACCAAAA-AATGCCACGTGGCATG
1 CCACGTGT-CAAAAATAATGCCACGTGGCACA
*
3908 CCACGTGT-ACCAAATAATGCCACGTGGCACA
1 CCACGTGTCA-AAAATAATGCCACGTGGCACA
3939 CCACGTGTCAAAAATA
1 CCACGTGTCAAAAATA
3955 CCATGTGCCA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 3 0.08
31 35 0.90
32 1 0.03
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (31 bp):
CCACGTGTCAAAAATAATGCCACGTGGCACA
Found at i:5793 original size:18 final size:17
Alignment explanation
Indices: 5770--5817 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 17
5760 TATATATTAT
5770 TTATTTATT-TTGAACTCA
1 TTATTTATTATTGAA-T-A
5788 TTATTTATTATTGAATA
1 TTATTTATTATTGAATA
5805 TATATTTATTATT
1 T-TATTTATTATT
5818 TATTTAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 2 0.07
18 21 0.75
19 5 0.18
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (17 bp):
TTATTTATTATTGAATA
Found at i:5815 original size:25 final size:26
Alignment explanation
Indices: 5787--5840 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
5777 TTTTGAACTC
*
5787 ATTATTTA-TTATTGAATATATATT-T
1 ATTATTTATTTAAT-AATATATATTAT
5812 ATTATTTATTTAATAATATATATTAT
1 ATTATTTATTTAATAATATATATTAT
5838 ATT
1 ATT
5841 TAAGATAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (26 bp):
ATTATTTATTTAATAATATATATTAT
Found at i:5816 original size:21 final size:20
Alignment explanation
Indices: 5792--5837 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
5782 AACTCATTAT
*
5792 TTATTATTGAATATATATTTA
1 TTATTATTGAATA-ATATATA
*
5813 TTATTTATTTAATAATATATA
1 TTA-TTATTGAATAATATATA
5834 TTAT
1 TTAT
5838 ATTTAAGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 1 0.05
21 12 0.55
22 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTATTATTGAATAATATATA
Found at i:6251 original size:2 final size:2
Alignment explanation
Indices: 6244--6268 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6234 ACCCAGTTAC
6244 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6269 TCTTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14101 original size:13 final size:14
Alignment explanation
Indices: 14080--14124 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
14070 AAAATAATAA
14080 ATATA-AATTATAT
1 ATATATAATTATAT
14093 AT-TATAATTATAT
1 ATATATAATTATAT
*
14106 ATATATACTT-TAT
1 ATATATAATTATAT
14119 ATATAT
1 ATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 2 0.07
13 21 0.72
14 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATATAATTATAT
Found at i:14108 original size:15 final size:16
Alignment explanation
Indices: 14088--14124 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
14078 AAATATAAAT
14088 TATATATTATA-ATTA
1 TATATATTATACATTA
*
14103 TATATA-TATACTTTA
1 TATATATTATACATTA
14118 TATATAT
1 TATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATATTATACATTA
Done.