Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_243 ID=scaffold_243-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: 9032
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:1868 original size:24 final size:25
Alignment explanation
Indices: 1820--1868 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1810 GTCTCTTTTT
* * *
1820 TTGCATTCATCTGCATTACATTTCA
1 TTGCATTCATATGCATTAAACTTCA
1845 TTGCA-TCATATGCATTAAACTTCA
1 TTGCATTCATATGCATTAAACTTCA
1869 CGAAAAAACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (25 bp):
TTGCATTCATATGCATTAAACTTCA
Found at i:4734 original size:19 final size:18
Alignment explanation
Indices: 4710--4765 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 18
4700 CACTTCACTT
4710 GAAAAAAAAGAAACAAGAA
1 GAAAAAAAAGAAA-AAGAA
4729 GAAAAAGAAA-AGAAAAGAA
1 GAAAAA-AAAGA-AAAAGAA
4748 GAACGAAAAAAGAAAAAG
1 GAA--AAAAAAGAAAAAG
4766 CAGAGGCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
19 15 0.47
20 13 0.41
21 4 0.12
ACGTcount: A:0.77, C:0.04, G:0.20, T:0.00
Consensus pattern (18 bp):
GAAAAAAAAGAAAAAGAA
Found at i:5678 original size:24 final size:24
Alignment explanation
Indices: 5646--5702 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
5636 ATGTCCCAAA
*
5646 ATTACAGTGGATTGAACCTTGAAG
1 ATTACAGTGGATTAAACCTTGAAG
* *
5670 ATTATAGTGGATTAAACTTTGAAG
1 ATTACAGTGGATTAAACCTTGAAG
5694 ATTACAGTG
1 ATTACAGTG
5703 TGGGAAATCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (24 bp):
ATTACAGTGGATTAAACCTTGAAG
Found at i:6107 original size:45 final size:45
Alignment explanation
Indices: 5988--6375 Score: 360
Period size: 44 Copynumber: 8.7 Consensus size: 45
5978 AAGATAGCGA
* *
5988 ATCTTGCCTTCCTATACTGACAGCGAAGCAGA-TCGAAGACACCAG
1 ATCTTGCCTTCCTGTACTGACAGCGAAGCAGACT-GAAGATACCAG
* * * * * **
6033 -CCTTACCTT-CTCATACTGGCAGCGGAGCAGACTGAAGATAGTAG
1 ATCTTGCCTTCCT-GTACTGACAGCGAAGCAGACTGAAGATACCAG
* * *
6077 ATCTTGCCTTCCTGTACTAACAGCAAAGCAGA-TCGAAGACACCAG
1 ATCTTGCCTTCCTGTACTGACAGCGAAGCAGACT-GAAGATACCAG
* * * * * * * *
6122 -CCTTGCTTTTCTGTACTGACAGTGGAGCAGACTGAATATAGCAA
1 ATCTTGCCTTCCTGTACTGACAGCGAAGCAGACTGAAGATACCAG
* *
6166 ATCTTGCCTTCCTGTACTAACAGCGAAACAGA-TCGAAGATACCAG
1 ATCTTGCCTTCCTGTACTGACAGCGAAGCAGACT-GAAGATACCAG
* * * * *
6211 -CCTTGCCTTCCTGTACTGACAACGGAGCAGACTAAAGATAACAG
1 ATCTTGCCTTCCTGTACTGACAGCGAAGCAGACTGAAGATACCAG
* * *
6255 ATCTTGCCTTCCTGTACTGACAGCGAAGTAGATTGAAGACACCAG
1 ATCTTGCCTTCCTGTACTGACAGCGAAGCAGACTGAAGATACCAG
* * * * *
6300 -CCTTGCCTTCCTGTACTGACAGTGAAGCATACTGAAGATAGCGG
1 ATCTTGCCTTCCTGTACTGACAGCGAAGCAGACTGAAGATACCAG
*
6344 ATCTTGCCTTCCTGTACTGACGGCGAAGCAGA
1 ATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
6376 TTAAACCCAC
Statistics
Matches: 267, Mismatches: 65, Indels: 22
0.75 0.18 0.06
Matches are distributed among these distances:
43 2 0.01
44 136 0.51
45 127 0.48
46 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (45 bp):
ATCTTGCCTTCCTGTACTGACAGCGAAGCAGACTGAAGATACCAG
Found at i:6377 original size:89 final size:89
Alignment explanation
Indices: 5976--6376 Score: 545
Period size: 89 Copynumber: 4.5 Consensus size: 89
5966 AAAAGATCAA
* *
5976 TGAAGATAGC-GAATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGACACCAGCCTTACC
1 TGAAGATAGCAG-ATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCC
* *
6040 TT-CTCATACTGGCAGCGGAGCAGAC
65 TTCCT-GTACTGACAGCGGAGCAGAC
* * * *
6065 TGAAGATAGTAGATCTTGCCTTCCTGTACTAACAGCAAAGCAGATCGAAGACACCAGCCTTGCTT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
6130 TTCTGTACTGACAGTGGAGCAGAC
66 TCCTGTACTGACAGCGGAGCAGAC
* * * * *
6154 TGAATATAGCAAATCTTGCCTTCCTGTACTAACAGCGAAACAGATCGAAGATACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
6219 TCCTGTACTGACAACGGAGCAGAC
66 TCCTGTACTGACAGCGGAGCAGAC
* * * *
6243 TAAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGTAGATTGAAGACACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
6308 TCCTGTACTGACAGTGAAGCATAC
66 TCCTGTACTGACAGCGGAGCAGAC
* *
6332 TGAAGATAGCGGATCTTGCCTTCCTGTACTGACGGCGAAGCAGAT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGAT
6377 TAAACCCACA
Statistics
Matches: 273, Mismatches: 37, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
89 270 0.99
90 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.23
Consensus pattern (89 bp):
TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
TCCTGTACTGACAGCGGAGCAGAC
Found at i:6531 original size:130 final size:128
Alignment explanation
Indices: 6386--6682 Score: 420
Period size: 130 Copynumber: 2.3 Consensus size: 128
6376 TTAAACCCAC
*
6386 AGATCTTATCTCTCTGAAGTTTCAGTAGAGCAGATTGCATCCAGTCTTATCTCCCTGAAGTTGCA
1 AGATCTTATCTCTCTGAAGTTTCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCA
* *
6451 GTGGAGCAGACAGAAGAAACCAATCCTA-CGTCGCTAAAGTTGCAGTGGAGC-AGATTAAAAAAA
66 GCGGAGCAGACAGAAGAAACCAATCCTATCGTC-CTAAAGTTGCAGTGAAGCGA-ATT--AAAAA
6514 AT
127 AT
6516 AGATCTTATCTCTCTGAAGTTGT-AGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGC
1 AGATCTTATCTCTCTGAAGTT-TCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGC
** * * *
6580 AGCGGAGCAGATTGAAGAAACCAATCCTATCTTCCTGAAGTTGCAGTGAAGCGAATTAAAATAT
65 AGCGGAGCAGACAGAAGAAACCAATCCTATCGTCCTAAAGTTGCAGTGAAGCGAATTAAAAAAT
* * * *
6644 GGATCTTATCTCTTTGAAGTTGCAGTAGAGCAGACCGCA
1 AGATCTTATCTCTCTGAAGTTTCAGTAGAGCAGATCGCA
6683 CCAAATTTTA
Statistics
Matches: 151, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
128 40 0.26
130 106 0.70
131 5 0.03
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (128 bp):
AGATCTTATCTCTCTGAAGTTTCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCA
GCGGAGCAGACAGAAGAAACCAATCCTATCGTCCTAAAGTTGCAGTGAAGCGAATTAAAAAAT
Found at i:6723 original size:128 final size:129
Alignment explanation
Indices: 6368--6806 Score: 327
Period size: 130 Copynumber: 3.4 Consensus size: 129
6358 TACTGACGGC
*** * * ** *
6368 GAAGCAGATTAAACCCACAGATCTTATCTCTCTGAAGTTTCAGTAGAGCAGATTGCATCCAGTCT
1 GAAGCAGATTAAAAAAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGACCGCATCCAATCT
* * *** * **
6433 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTACGTCGCTAAAGTTGCAGT
66 TATCTCCCTAAAGATGCAGCAAAACAGATTGAAGAAACCAATCCTACGTCGCTAAAGTTGCAGT
* * * *
6497 GGAGCAGATTAAAAAAAATAGATCTTATCTCTCTGAAGTTGTAGTAGAGCAGATCGCATCCAGTC
1 GAAGCAGATT-AAAAAAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGACCGCATCCAATC
* * ** * * *
6562 TTATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGAAACCAATCCTATCTTC-CTGAAGTTGCAG
65 TTATCTCCCTAAAGATGCAGCAAAACAGATTGAAGAAACCAATCCTA-CGTCGCTAAAGTTGCAG
6626 T
129 T
* * *
6627 GAAGC-GAATT-AAAATATGGATCTTATCTCTTTGAAGTTGCAGTAGAGCAGACCGCA-CCAAAT
1 GAAGCAG-ATTAAAAAAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGACCGCATCC-AAT
* * * * * ** ** *
6689 TTTATTTTCTTAAAGATGCAGTAAAACA-AGTTGAAGCTA-CAAGTTTTATC-TCACTAAAGTTG
64 CTTATCTCCCTAAAGATGCAGCAAAACAGA-TTGAAGAAACCAA-TCCTA-CGTCGCTAAAGTTG
*
6751 TAGT
126 CAGT
* * * ** *
6755 TAAGCAGGTTAAAGATACCA-ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGA
1 GAAGCAGATTAAA-AAAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA
6807 TTGAAGCTAC
Statistics
Matches: 255, Mismatches: 45, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
127 8 0.03
128 90 0.35
129 43 0.17
130 111 0.44
131 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (129 bp):
GAAGCAGATTAAAAAAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGACCGCATCCAATCT
TATCTCCCTAAAGATGCAGCAAAACAGATTGAAGAAACCAATCCTACGTCGCTAAAGTTGCAGT
Found at i:6805 original size:44 final size:44
Alignment explanation
Indices: 6388--7032 Score: 174
Period size: 44 Copynumber: 14.7 Consensus size: 44
6378 AAACCCACAG
* * *
6388 ATCTTATCTCTCTGAAGTTTCAGTAGAGCAGATT---GCAT-CCA
1 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTAAAG-ATACCA
* * ** *
6429 GTCTTATCTCCCTGAAGTTGCAGTGGAGCA-GACAGAAGAAACCA
1 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTA-AAGATACCA
* * * * * * **
6473 ATCCTA-CGTCGCTAAAGTTGCAGTGGAGCAGATTAAAAAAAATA
1 ATCTTATC-TCTCTGAAGTTGCAGTGGAGCAGGTTAAAGATACCA
* * **
6517 GATCTTATCTCTCTGAAGTTGTAGTAGAGCA-G--ATCGCAT-CCA
1 -ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTAAAG-ATACCA
* * * * * *
6559 GTCTTATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGAAACCA
1 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTAAAGATACCA
* * * ***
6603 ATCCTATCT-TCCTGAAGTTGCAGTGAAGC-GAATTAAA-ATATGG
1 ATCTTATCTCT-CTGAAGTTGCAGTGGAGCAG-GTTAAAGATACCA
* * ** *
6646 ATCTTATCTCTTTGAAGTTGCAGTAGAGCA-G--ACCG-CACCAA
1 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTAAAGATACC-A
* * * * ** * * * *
6687 ATTTTAT-TTTCTTAAAGATGCAGTAAAACAAGTTGAAGCTA-CA
1 ATCTTATCTCTC-TGAAGTTGCAGTGGAGCAGGTTAAAGATACCA
* * * * **
6730 AGTTTTATCTCACTAAAGTTGTAGTTAAGCAGGTTAAAGATACCA
1 A-TCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTAAAGATACCA
* * * *
6775 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGCTACTA
1 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTAAAGATACCA
* *
6819 ATCCTATCTC-CTTGAAGTTGCAGTGGAGC-GGATTAAAACGAT--GA
1 ATCTTATCTCTC-TGAAGTTGCAGTGGAGCAGG-TT-AAA-GATACCA
* ** * * ** *
6863 ATCTTATAC-CTCTGAAATTGCAGTAGGTCGAATTAGATCTTATCATATCAA
1 ATCTTAT-CTCTCTGAAGTTGCAGT--G--G-AGCAGGT-TAAAGATA-CCA
* * * * *
6914 ACCTTATCTCCCTAAAGTTGCAATGGAGCAGGTTGAAGATA-CA
1 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTAAAGATACCA
* * *
6957 AGTCTTATCT-TCCAGACGTTGCAGTGGAGCAGGTTGAAGATA-CA
1 A-TCTTATCTCT-CTGAAGTTGCAGTGGAGCAGGTTAAAGATACCA
* * *
7001 AGTCTTATCTCCCTAAAGTTGTAGTGGAGCAG
1 A-TCTTATCTCTCTGAAGTTGCAGTGGAGCAG
7033 ACTAAAACCA
Statistics
Matches: 428, Mismatches: 128, Indels: 93
0.66 0.20 0.14
Matches are distributed among these distances:
40 4 0.01
41 71 0.17
42 3 0.01
43 36 0.08
44 238 0.56
45 39 0.09
46 8 0.02
47 1 0.00
48 3 0.01
49 4 0.01
50 3 0.01
51 18 0.04
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (44 bp):
ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTAAAGATACCA
Found at i:8578 original size:24 final size:24
Alignment explanation
Indices: 8529--8579 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
8519 TTAGATTTAT
* * *
8529 TATTATTTATTTCAAGTTTATATA
1 TATTATTCATTTCAAATATATATA
*
8553 TATTATTCATTTCAAATATATGTA
1 TATTATTCATTTCAAATATATATA
8577 TAT
1 TAT
8580 ACCTTACCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (24 bp):
TATTATTCATTTCAAATATATATA
Done.