Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014603.1 Corchorus olitorius cultivar O-4 contig14636, 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: 38355
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:11248 original size:93 final size:93
Alignment explanation
Indices: 11146--11330 Score: 289
Period size: 93 Copynumber: 2.0 Consensus size: 93
11136 AATTTTTAAT
* * * *
11146 TAAATTAGTAATATCGTAAAAATAATATAGATATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAACAGATATAAGGATATTAGATTTAATTAAATAAAAATAG
*
11211 AGTTTTTAGTTAAGTAAAACTATAAAAG
66 AGTTTTTAGTTAACTAAAACTATAAAAG
* *
11239 TAAAATAGTAAAATGGTAAAAATAAAACAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAACAGATATAAGGATATTAGATTTAATTAAATAAAAATAG
* *
11304 ATTTTTTAGTTGACTAAAACTATAAAA
66 AGTTTTTAGTTAACTAAAACTATAAAA
11331 ATTTAAACAA
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 83 1.00
ACGTcount: A:0.52, C:0.03, G:0.11, T:0.34
Consensus pattern (93 bp):
TAAAATAGTAAAATCGTAAAAATAAAACAGATATAAGGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGTTAACTAAAACTATAAAAG
Found at i:13773 original size:30 final size:30
Alignment explanation
Indices: 13737--13793 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
13727 ATAGAGTTTC
*
13737 TTTTTTTTCTCGGTTCTTATGATATATAGT
1 TTTTTTTTCTCGATTCTTATGATATATAGT
13767 TTTTTTTTCTCGATTCTTATGATATAT
1 TTTTTTTTCTCGATTCTTATGATATAT
13794 GTGAGTATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.61
Consensus pattern (30 bp):
TTTTTTTTCTCGATTCTTATGATATATAGT
Found at i:14071 original size:28 final size:28
Alignment explanation
Indices: 14020--14073 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
14010 TCATGAATTT
** * *
14020 ATAAGACTATAATTTTTTTTTTTGAAAA
1 ATAAGACTATAATCATTCTATTTGAAAA
14048 ATAAGACTATAATCATTCTATTTGAA
1 ATAAGACTATAATCATTCTATTTGAA
14074 CATGAAATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (28 bp):
ATAAGACTATAATCATTCTATTTGAAAA
Found at i:17776 original size:31 final size:31
Alignment explanation
Indices: 17741--17805 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
17731 AAAAACGATT
* * * *
17741 AATTTAGTCCTTGTATTCATAAGATTGAGTC
1 AATTTAATCCATGTACTCACAAGATTGAGTC
*
17772 AATTTAATCCATGTACTCACAAGATTGGGTC
1 AATTTAATCCATGTACTCACAAGATTGAGTC
17803 AAT
1 AAT
17806 CGAGTTCTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (31 bp):
AATTTAATCCATGTACTCACAAGATTGAGTC
Found at i:17874 original size:31 final size:31
Alignment explanation
Indices: 17833--17891 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
17823 TTTACCAATT
* *
17833 AAACTCAATTGACTC-AATCTTGTGAGTATAG
1 AAACTAAATTGAC-CGAATCTTGTAAGTATAG
17864 AAACTAAATTGACCGAATCTTGTAAGTA
1 AAACTAAATTGACCGAATCTTGTAAGTA
17892 CAAGGACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (31 bp):
AAACTAAATTGACCGAATCTTGTAAGTATAG
Found at i:18653 original size:19 final size:19
Alignment explanation
Indices: 18631--18679 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
18621 ACCTAATCCA
18631 ATCTGTACAGTGTAATTTC
1 ATCTGTACAGTGTAATTTC
18650 ATCTGTACAGTGTAATTTC
1 ATCTGTACAGTGTAATTTC
18669 ATCTGTACAGT
1 ATCTGTACAGT
18680 TGCTAAACAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (19 bp):
ATCTGTACAGTGTAATTTC
Found at i:22137 original size:18 final size:18
Alignment explanation
Indices: 22094--22131 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
22084 ATTCTTGGCT
22094 TTACAATTTACATAATAG
1 TTACAATTTACATAATAG
22112 TTACAATTTACATAATAG
1 TTACAATTTACATAATAG
22130 TT
1 TT
22132 TTAATTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (18 bp):
TTACAATTTACATAATAG
Found at i:23049 original size:4 final size:4
Alignment explanation
Indices: 23021--23105 Score: 52
Period size: 4 Copynumber: 21.2 Consensus size: 4
23011 TTGCTAGGAC
* * *
23021 CATA CGTA CATG CATA C--A CACA CATA CATA CCATA CATA CATA CGCATA
1 CATA CATA CATA CATA CATA CATA CATA CATA -CATA CATA CATA --CATA
** *
23070 TGTA CATA CCATA CATA CATA C--A CATA CAGA CATA C
1 CATA CATA -CATA CATA CATA CATA CATA CATA CATA C
23106 GTGCATACGT
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
2 4 0.06
4 46 0.74
5 8 0.13
6 4 0.06
ACGTcount: A:0.44, C:0.29, G:0.06, T:0.21
Consensus pattern (4 bp):
CATA
Found at i:23058 original size:27 final size:27
Alignment explanation
Indices: 23027--23105 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
23017 GGACCATACG
* *
23027 TACATGCATACACACACATACATACCA
1 TACATACATACACATACATACATACCA
* **
23054 TACATACATACGCATATGTACATACCA
1 TACATACATACACATACATACATACCA
*
23081 TACATACATACACATACAGACATAC
1 TACATACATACACATACATACATAC
23106 GTGCATACGT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.44, C:0.29, G:0.05, T:0.22
Consensus pattern (27 bp):
TACATACATACACATACATACATACCA
Found at i:24199 original size:96 final size:96
Alignment explanation
Indices: 24035--24228 Score: 361
Period size: 96 Copynumber: 2.0 Consensus size: 96
24025 CTGGTTGTGA
*
24035 GATTACGAGTCCTAAGAAATCACACCCTAATTATGAGGCTATGAACTCGATCCCTTCTTAACGCC
1 GATTACGAGTCCTAAGAAATCACACCCTAATTATGAGACTATGAACTCGATCCCTTCTTAACGCC
24100 TTGAAGTTGTTAGGAATCGAACCTTAATTAT
66 TTGAAGTTGTTAGGAATCGAACCTTAATTAT
* *
24131 GATTACGAGTCCTAAGGAATCACACCCTGATTATGAGACTATGAACTCGATCCCTTCTTAACGCC
1 GATTACGAGTCCTAAGAAATCACACCCTAATTATGAGACTATGAACTCGATCCCTTCTTAACGCC
24196 TTGAAGTTGTTAGGAATCGAACCTTAATTAT
66 TTGAAGTTGTTAGGAATCGAACCTTAATTAT
24227 GA
1 GA
24229 AAACTAAGAG
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (96 bp):
GATTACGAGTCCTAAGAAATCACACCCTAATTATGAGACTATGAACTCGATCCCTTCTTAACGCC
TTGAAGTTGTTAGGAATCGAACCTTAATTAT
Found at i:24486 original size:19 final size:19
Alignment explanation
Indices: 24462--24501 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
24452 TTACTCTATT
24462 TATTGATCAACAACAATAA
1 TATTGATCAACAACAATAA
24481 TATTGATCAACAACAATAA
1 TATTGATCAACAACAATAA
24500 TA
1 TA
24502 GTAACATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.28
Consensus pattern (19 bp):
TATTGATCAACAACAATAA
Found at i:27696 original size:29 final size:29
Alignment explanation
Indices: 27661--27716 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
27651 ATGTGGAACA
* * *
27661 AAAATAAAACATTAGGGTGCAAAGTGATC
1 AAAATAAAAAAATAGAGTGCAAAGTGATC
27690 AAAATAAAAAAATAGAGTGCAAAGTGA
1 AAAATAAAAAAATAGAGTGCAAAGTGA
27717 CAGTTCGTAT
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:0.55, C:0.07, G:0.20, T:0.18
Consensus pattern (29 bp):
AAAATAAAAAAATAGAGTGCAAAGTGATC
Found at i:28312 original size:56 final size:56
Alignment explanation
Indices: 28238--28352 Score: 221
Period size: 56 Copynumber: 2.1 Consensus size: 56
28228 CCTTTTGCAA
*
28238 CCAATTCCAAATATAATTCCTAATCGGCTTAATCTTTATGGTTTTAATTTAAAAAG
1 CCAATTCCAAATATAATTCATAATCGGCTTAATCTTTATGGTTTTAATTTAAAAAG
28294 CCAATTCCAAATATAATTCATAATCGGCTTAATCTTTATGGTTTTAATTTAAAAAG
1 CCAATTCCAAATATAATTCATAATCGGCTTAATCTTTATGGTTTTAATTTAAAAAG
28350 CCA
1 CCA
28353 TTGGATTAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.38
Consensus pattern (56 bp):
CCAATTCCAAATATAATTCATAATCGGCTTAATCTTTATGGTTTTAATTTAAAAAG
Found at i:38244 original size:2 final size:2
Alignment explanation
Indices: 38237--38355 Score: 222
Period size: 2 Copynumber: 59.5 Consensus size: 2
38227 ATCACAAAGT
38237 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
38279 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GTA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G-A GA GA GA
38322 GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
Statistics
Matches: 115, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 112 0.97
3 2 0.02
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.01
Consensus pattern (2 bp):
GA
Done.