Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024601.1 Corchorus olitorius cultivar O-4 contig24634, 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: 7416
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:1864 original size:21 final size:22
Alignment explanation
Indices: 1840--1881 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1830 TTTGCCTCAT
1840 GCATTCATTCAT-CATGCCATG
1 GCATTCATTCATGCATGCCATG
*
1861 GCATTCATTCATGCATTCCAT
1 GCATTCATTCATGCATGCCAT
1882 TAAAACCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.36
Consensus pattern (22 bp):
GCATTCATTCATGCATGCCATG
Found at i:4388 original size:18 final size:19
Alignment explanation
Indices: 4367--4402 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4357 CAATCAATCA
4367 ATCAAAAA-AAAATCAAAG
1 ATCAAAAATAAAATCAAAG
*
4385 ATCAAAAATCAAATCAAA
1 ATCAAAAATAAAATCAAA
4403 TCAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.69, C:0.14, G:0.03, T:0.14
Consensus pattern (19 bp):
ATCAAAAATAAAATCAAAG
Found at i:4722 original size:12 final size:12
Alignment explanation
Indices: 4705--4738 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
4695 CCAAGTGCGC
4705 AAAAAAAAGGAA
1 AAAAAAAAGGAA
4717 AAAAAAAA-GAA
1 AAAAAAAAGGAA
*
4728 AAAAAGAAGGA
1 AAAAAAAAGGA
4739 GAGCTCTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGGAA
Found at i:5087 original size:50 final size:50
Alignment explanation
Indices: 5006--5301 Score: 421
Period size: 50 Copynumber: 5.9 Consensus size: 50
4996 TTACAATAAG
* * *
5006 ATTGCATTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCAAAGTAAA
1 ATTGCTTTCCATTTGTAAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAA
* *
5056 ACTGCTTTCCATTTGTAAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAA
1 ATTGCTTTCCATTTGTAAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAA
* * * * **
5106 ACTGCTTTCCATTTGTAAGTTCAAGATCAAAATTTGCTTTTCAAGGTAGG
1 ATTGCTTTCCATTTGTAAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAA
* * * *
5156 ATTGCATTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAA
1 ATTGCTTTCCATTTGTAAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAA
**
5206 ATTGCTTTCCATTTGTAAGTCCAAGATCAAAATTCGCTTTTCAAAGTAGG
1 ATTGCTTTCCATTTGTAAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAA
* *
5256 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 ATTGCTTTCCATTTGTAAGTCCAAGATCAAAATTCGCTTTTCAAAG
5302 GGCATTTAAG
Statistics
Matches: 221, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 221 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (50 bp):
ATTGCTTTCCATTTGTAAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAA
Found at i:5281 original size:150 final size:150
Alignment explanation
Indices: 5005--5299 Score: 482
Period size: 150 Copynumber: 2.0 Consensus size: 150
4995 TTTACAATAA
*
5005 GATTGCATTCCATTTGTGAGCCCAAGATCAAAATTCGCTTTTCAAAGTAAAACTGCTTTCCATTT
1 GATTGCATTCCATTTATGAGCCCAAGATCAAAATTCGCTTTTCAAAGTAAAACTGCTTTCCATTT
* * *
5070 GTAAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAACTGCTTTCCATTTGTAAGTTCAAGATCA
66 GTAAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAAACTGCATTCCATTTGTAAGTCCAAGATCA
*
5135 AAATTTGCTTTTCAAGGTAG
131 AAATTCGCTTTTCAAGGTAG
** *
5155 GATTGCATTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAAATTGCTTTCCATTT
1 GATTGCATTCCATTTATGAGCCCAAGATCAAAATTCGCTTTTCAAAGTAAAACTGCTTTCCATTT
** * *
5220 GTAAGTCCAAGATCAAAATTCGCTTTTCAAAGTAGGATTGCATTCCATTTGTGAGTCCAAGATCA
66 GTAAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAAACTGCATTCCATTTGTAAGTCCAAGATCA
5285 AAATTCGCTTTTCAA
131 AAATTCGCTTTTCAA
5300 AGGGCATTTA
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
150 133 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.36
Consensus pattern (150 bp):
GATTGCATTCCATTTATGAGCCCAAGATCAAAATTCGCTTTTCAAAGTAAAACTGCTTTCCATTT
GTAAGTCCAAGATCAAAATTCGCTTTTCAAAGTAAAACTGCATTCCATTTGTAAGTCCAAGATCA
AAATTCGCTTTTCAAGGTAG
Found at i:6047 original size:50 final size:50
Alignment explanation
Indices: 5972--6159 Score: 358
Period size: 50 Copynumber: 3.8 Consensus size: 50
5962 CGAATGCATT
5972 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
6022 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
*
6072 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGGGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
*
6122 GGCTTTTCCACAAGCCAAACTCATTTCCATACGAGTCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA
6160 TTTCAAACCT
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 135 1.00
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.26
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
Found at i:6290 original size:52 final size:50
Alignment explanation
Indices: 6216--6425 Score: 357
Period size: 52 Copynumber: 4.1 Consensus size: 50
6206 CATTACCTTT
*
6216 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGATGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
6266 TTTTATAGAATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTA-AG-ATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
6318 TTTTATAGAATTGAGTTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTA-AG-ATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
6370 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCT
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
6420 TTTTAA
1 TTTTAA
6426 TATATTAGAG
Statistics
Matches: 154, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
50 52 0.34
51 4 0.03
52 98 0.64
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:6411 original size:102 final size:102
Alignment explanation
Indices: 6216--6425 Score: 361
Period size: 102 Copynumber: 2.1 Consensus size: 102
6206 CATTACCTTT
*
6216 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGATGGTCCTTTTATAGAATTGAA
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTATAGAATTGAA
6281 TTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
66 TTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
6318 TTTTATAGAATTGAGTTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA-AG-ATTG
1 TTTTA-AG-ATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTATAGAATTG
*
6381 AATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCT
64 AATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
6420 TTTTAA
1 TTTTAA
6426 TATATTAGAG
Statistics
Matches: 103, Mismatches: 3, Indels: 5
0.93 0.03 0.05
Matches are distributed among these distances:
101 1 0.01
102 52 0.50
103 4 0.04
104 46 0.45
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (102 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTATAGAATTGAA
TTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:6450 original size:102 final size:104
Alignment explanation
Indices: 6216--6452 Score: 333
Period size: 102 Copynumber: 2.3 Consensus size: 104
6206 CATTACCTTT
* * * *
6216 TTTTA-AG-ATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGATGGTCCTTTTATAGAATTG
1 TTTTATAGAATTGAGTTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTTTTATAGAATTG
6279 AATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
66 AATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
6318 TTTTATAGAATTGAGTTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA-AG-ATTG
1 TTTTATAGAATTGAGTTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTTTTATAGAATTG
*
6381 AATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCT
66 AATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
6420 TTTTAATA-TATTAGAG-TGGAAGATAATTCAAAG
1 TTTT-ATAGAATT-GAGTTGGAAGACAATTCAAAG
6453 TAATTGATCG
Statistics
Matches: 124, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
102 68 0.55
103 10 0.08
104 46 0.37
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.29
Consensus pattern (104 bp):
TTTTATAGAATTGAGTTGGAAGACAATTCAAAGGATAAGCGGAAGACGGTCCTTTTATAGAATTG
AATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:6858 original size:21 final size:21
Alignment explanation
Indices: 6832--6875 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
6822 TTTTGTCTCT
6832 ATTTCGTTCACCGTAAGTTGC
1 ATTTCGTTCACCGTAAGTTGC
6853 ATTTCGTTCACCGTAAGTTGC
1 ATTTCGTTCACCGTAAGTTGC
6874 AT
1 AT
6876 GGTATTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (21 bp):
ATTTCGTTCACCGTAAGTTGC
Found at i:6967 original size:46 final size:46
Alignment explanation
Indices: 6900--6992 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
6890 TTTTTGATTA
*
6900 AGTCAAATTCTCATGTCCTATTATCACATTAGCCTTTTACTTTAGC
1 AGTCAAATTCTCATGCCCTATTATCACATTAGCCTTTTACTTTAGC
*
6946 AGTCACATTCTCATGCCCTATTATCACATTAGCCTTTTACTTTAGC
1 AGTCAAATTCTCATGCCCTATTATCACATTAGCCTTTTACTTTAGC
6992 A
1 A
6993 TATGAAGTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.40
Consensus pattern (46 bp):
AGTCAAATTCTCATGCCCTATTATCACATTAGCCTTTTACTTTAGC
Done.