Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_81 ID=scaffold_81-JGI_221_v2.0
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: 15908
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.27
Warning! 416 characters in sequence are not A, C, G, or T
Found at i:2701 original size:108 final size:109
Alignment explanation
Indices: 2512--2817 Score: 485
Period size: 108 Copynumber: 2.8 Consensus size: 109
2502 TTTCTAATTG
*
2512 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* * **
2577 CGTTTAACCAAATGGCTTAATATCCTTT-TAAATTTTTAAAATA
66 CGTTTAACCAAATGGCTTAATATCCTTTCAAAAATTACAAAATA
2620 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
2685 CGTTCAACCAAATGGCTTAATATCCTTTCCAAAAATTACAAAATA
66 CGTTTAACCAAATGGCTTAATATCCTTT-CAAAAATTACAAAATA
* *
2730 AGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACATGCCCTAAGGTGCTGGGTATCGA--TTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
**
2792 CGTTTAACCAAATGGCCAAATATCCT
66 CGTTTAACCAAATGGCTTAATATCCT
2818 CTGGAATTTT
Statistics
Matches: 185, Mismatches: 11, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
107 28 0.15
108 91 0.49
109 26 0.14
110 40 0.22
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (109 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTTAACCAAATGGCTTAATATCCTTTCAAAAATTACAAAATA
Found at i:14171 original size:41 final size:41
Alignment explanation
Indices: 14064--14662 Score: 381
Period size: 41 Copynumber: 13.8 Consensus size: 41
14054 ATTATACAGG
* * *
14064 TCTTATCTCCCTGAGGTTACAGTGGAATAGACCGAAGACTTTCAGGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATC---G-C-ATCA-GA
* * *
14111 TCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGCATCAGA
* * *
14152 TCTTATCTCCCTGAGGTTACAGTGGAATAGACCGAAGACTTTCAGGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATC---G-C-ATCA-GA
* * * *
14199 TCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGCATCAGA
* *
14240 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATC---G-C-ATCAGA
* * * * *
14286 TCTTATCTCCCTAAGGTTACAGCGGAGCAGATCGAAGACAGGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGCA-TCA-GA
* * * * * *
14329 TCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGCACCAGG
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGCATCAGA
* *
14370 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATC---G-C-ATCAGA
* * * *
14416 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACAGGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGCA-TCA-GA
* * * * *
14459 TCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGG
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGCATCAGA
* *
14500 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATC---G-C-ATCAGA
* * * ** *** *
14546 TCCTATCTCCCTGAAGTTACAGCGGAGCGGATTAAAATAAAAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGA-TCGCAT--CAGA
* * ** *
14590 TCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGTATCCA-A
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGCAT-CAGA
* *
14631 TCTTATCTTCCTGAGGTTACAGTGGAGCAGAT
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGAT
14663 TGAAGCCGAT
Statistics
Matches: 426, Mismatches: 98, Indels: 62
0.73 0.17 0.11
Matches are distributed among these distances:
41 146 0.34
42 16 0.04
43 69 0.16
44 35 0.08
45 4 0.01
46 98 0.23
47 58 0.14
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (41 bp):
TCTTATCTCCCTGAGGTTACAGTGGAGTAGATCGCATCAGA
Found at i:14213 original size:88 final size:88
Alignment explanation
Indices: 14064--14567 Score: 602
Period size: 88 Copynumber: 5.8 Consensus size: 88
14054 ATTATACAGG
* *
14064 TCTTATCTCCCTGAGGTTACAGTGGAATAGACCGAAGACTTTCAGGATCTTATCTCTCTGAAGTT
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGGATCTTATCTCCCTGAAGTT
14129 ACAGTAGAGTAGATCGCATCAGA
66 ACAGTAGAGTAGATCGCATCAGA
* *
14152 TCTTATCTCCCTGAGGTTACAGTGGAATAGACCGAAGACTTTCAGGATCTTATCTCTCTGAAGTT
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGGATCTTATCTCCCTGAAGTT
*
14217 ACAGTAGAGTAGATCGCATCAGG
66 ACAGTAGAGTAGATCGCATCAGA
14240 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCA-GATCTTATCTCCCT-AAGGT
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGGATCTTATCTCCCTGAA-GT
** * * *
14303 TACAGCGGAGCAGATCGAAGACAGGA
65 TACAGTAGAGTAGATCGCA-TCA-GA
* * * * * * *
14329 TCTTATCTCTCTGAAGTTATAGTAGAGTAGATCG--CAC---CAGG-TCTTATCTCCCTGAGGTT
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGGATCTTATCTCCCTGAAGTT
* * *
14388 ACAGTGGAGTAGACCGAAGACTTTCAGA
66 ACAGTAGAGTAGATC---G-C-ATCAGA
* * * *
14416 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGA----CAGGATCTTATCTCTCTGAAGTT
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGGATCTTATCTCCCTGAAGTT
* *
14477 ACAGTAGAGTAGATCGCACCAGG
66 ACAGTAGAGTAGATCGCATCAGA
*
14500 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCA-GATCCTATCTCCCTGAAGTT
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGGATCTTATCTCCCTGAAGTT
14564 ACAG
66 ACAG
14568 CGGAGCGGAT
Statistics
Matches: 358, Mismatches: 41, Indels: 35
0.82 0.09 0.08
Matches are distributed among these distances:
84 67 0.19
85 3 0.01
86 3 0.01
87 85 0.24
88 140 0.39
89 60 0.17
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (88 bp):
TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCAGGATCTTATCTCCCTGAAGTT
ACAGTAGAGTAGATCGCATCAGA
Found at i:14358 original size:130 final size:130
Alignment explanation
Indices: 14147--14657 Score: 774
Period size: 130 Copynumber: 3.9 Consensus size: 130
14137 GTAGATCGCA
* * ** *
14147 TCAGATCTTATCTCCCTGAGGTTACAGTGGAATAGACCGAAGACTTTCAGGATCTTATCTCTCTG
1 TCAGATCTTATCTCCCTAAGGTTACAGCGGAGCAGATCGAAGA----CAGGATCTTATCTCTCTG
*
14212 AAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAG
62 AAGTTACAGTAGAGTAGATCGCACCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAG
14277 ACTT
127 ACTT
14281 TCAGATCTTATCTCCCTAAGGTTACAGCGGAGCAGATCGAAGACAGGATCTTATCTCTCTGAAGT
1 TCAGATCTTATCTCCCTAAGGTTACAGCGGAGCAGATCGAAGACAGGATCTTATCTCTCTGAAGT
*
14346 TATAGTAGAGTAGATCGCACCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTT
66 TACAGTAGAGTAGATCGCACCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTT
*
14411 TCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACAGGATCTTATCTCTCTGAAGT
1 TCAGATCTTATCTCCCTAAGGTTACAGCGGAGCAGATCGAAGACAGGATCTTATCTCTCTGAAGT
14476 TACAGTAGAGTAGATCGCACCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTT
66 TACAGTAGAGTAGATCGCACCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTT
* * ** * * *
14541 TCAGATCCTATCTCCCTGAA-GTTACAGCGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAA
1 TCAGATCTTATCTCCCT-AAGGTTACAGCGGAGCAGA-TCGAAGACAGGATCTTATCTCTCTGAA
* * * *
14605 GTTACAGCAGAGTAGATCGTATCCA-ATCTTATCTTCCTGAGGTTACAGTGGAG
64 GTTACAGTAGAGTAGATCGCA-CCAGGTCTTATCTCCCTGAGGTTACAGTGGAG
14658 CAGATTGAAG
Statistics
Matches: 353, Mismatches: 21, Indels: 9
0.92 0.05 0.02
Matches are distributed among these distances:
130 244 0.69
131 68 0.19
132 3 0.01
134 38 0.11
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (130 bp):
TCAGATCTTATCTCCCTAAGGTTACAGCGGAGCAGATCGAAGACAGGATCTTATCTCTCTGAAGT
TACAGTAGAGTAGATCGCACCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTT
Done.