Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_204 ID=scaffold_204-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: 9365
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:4373 original size:37 final size:35
Alignment explanation
Indices: 4313--4423 Score: 86
Period size: 37 Copynumber: 3.1 Consensus size: 35
4303 ATTCAATAAA
4313 AAAAATCAAAAA-CAAAA-ACAAAAAAGAAGAAAAAT
1 AAAAAT-AAAAATCAAAACA-AAAAAAGAAGAAAAAT
* * *
4348 AAAAATCAAAGTCAAACGCAAAAAAAGAA-AAATCAAT
1 AAAAATAAAAATCAAA-ACAAAAAAAGAAGAAA--AAT
* * *
4385 CAAAATAAAAATCAAAATAAAAAAA-AGAGAAAAAG
1 AAAAATAAAAATCAAAACAAAAAAAGA-AGAAAAAT
4420 AAAA
1 AAAA
4424 TGAGAGGCCA
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
34 3 0.05
35 19 0.32
36 17 0.29
37 20 0.34
ACGTcount: A:0.76, C:0.09, G:0.07, T:0.08
Consensus pattern (35 bp):
AAAAATAAAAATCAAAACAAAAAAAGAAGAAAAAT
Found at i:4399 original size:12 final size:12
Alignment explanation
Indices: 4382--4407 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4372 AAGAAAAATC
4382 AATCAAAATAAA
1 AATCAAAATAAA
4394 AATCAAAATAAA
1 AATCAAAATAAA
4406 AA
1 AA
4408 AAAGAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
AATCAAAATAAA
Found at i:5318 original size:13 final size:13
Alignment explanation
Indices: 5300--5329 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5290 GAAAAGTGAA
*
5300 AAAATGAAAATGG
1 AAAATGAAAAAGG
5313 AAAATGAAAAAGG
1 AAAATGAAAAAGG
5326 AAAA
1 AAAA
5330 AGTAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (13 bp):
AAAATGAAAAAGG
Found at i:6883 original size:88 final size:87
Alignment explanation
Indices: 6596--7084 Score: 583
Period size: 88 Copynumber: 5.6 Consensus size: 87
6586 TAAAAAACAA
* * *
6596 AGCCTTGTCTCCCTCGGTTACAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCGCTGA
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGC-ATGA
*
6661 TAGCGAAGCAGATCGAAGATACC
65 TAGTGAAGCAGATCGAAGATACC
* * * *
6684 AGCCTTGCCTCCCTCGATTGCAGTGGAGCAAGTTAAAGATAGCGGATCTTGCCTCCCTAAGCA-G
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCT--GCATG
* *
6748 -TAGTGGAGCAGATCGAAAATACC
64 ATAGTGAAGCAGATCGAAGATACC
* *
6771 AACCTTGCATCCCTCGGTTGCAGTGGAGCAGAG-TAAAGATAGCAGATCTTGCCTTCCTGCGATG
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAG-GTTAAAGATAGCAGATCTTGCCTTCCTGC-ATG
* *
6835 ACAGTGAAGCAGATCGAAGATATC
64 ATAGTGAAGCAGATCGAAGATACC
* * *
6859 ACCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCGGATCTTGCCTCCCTAAGCA-G
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCT--GCATG
*
6923 -TAGTGGAGCAGATCGAAGATACC
64 ATAGTGAAGCAGATCGAAGATACC
* * *
6946 AGCCTTGCCTCCCTCGGTTGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGCCTTTCTGCACTGA
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCA-TGA
* * * * * *
7011 CAGCGAAGCGGATTGAAGACACA
65 TAGTGAAGCAGATCGAAGATACC
* * * * *
7034 AGCCTTGCCTCCCTCGGTTGTAGTGAAACAGATTGAAGATAGCAGATCTTG
1 AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTG
7085 TCTCCCTAAG
Statistics
Matches: 344, Mismatches: 45, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
85 5 0.01
86 1 0.00
87 145 0.42
88 188 0.55
89 1 0.00
90 4 0.01
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (87 bp):
AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCATGAT
AGTGAAGCAGATCGAAGATACC
Found at i:6896 original size:175 final size:174
Alignment explanation
Indices: 6605--7117 Score: 751
Period size: 175 Copynumber: 2.9 Consensus size: 174
6595 AAGCCTTGTC
* * *
6605 TCCCTCGGTTACAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCGCTGATAGCGAAGC
1 TCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCGATGACAGCGAAGC
* *
6670 AGATCGAAGATACCAGCCTTGCCTCCCTCGATTGCAGTGGAGCAAGTTAAAGATAGCGGATCTTG
66 AGATCGAAGATA-CAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCGGATCTTG
6735 CCTCCCTAAGCAGTAGTGGAGCAGATCGAAAATACCAACCTTGCA
130 CCTCCCTAAGCAGTAGTGGAGCAGATCGAAAATACCAACCTTGCA
*
6780 TCCCTCGGTTGCAGTGGAGCAGAG-TAAAGATAGCAGATCTTGCCTTCCTGCGATGACAGTGAAG
1 TCCCTCGGTTGCAGTGGAGCAG-GTTAAAGATAGCAGATCTTGCCTTCCTGCGATGACAGCGAAG
*
6844 CAGATCGAAGATATCACCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCGGATCTT
65 CAGATCGAAGATA-CAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCGGATCTT
* * *
6909 GCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATACCAGCCTTGCC
129 GCCTCCCTAAGCAGTAGTGGAGCAGATCGAAAATACCAACCTTGCA
* * *
6955 TCCCTCGGTTGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGCCTTTCTGC-ACTGACAGCGAAG
1 TCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCGA-TGACAGCGAAG
* * * * * * * * *
7019 CGGATTGAAGACACAAGCCTTGCCTCCCTCGGTTGTAGTGAAACAGATTGAAGATAGCAGATCTT
65 CAGATCGAAGATAC-AGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCGGATCTT
* *
7084 GTCTCCCTAAGCAGTAGCGGAGCAGATCGAAAAT
129 GCCTCCCTAAGCAGTAGTGGAGCAGATCGAAAAT
7118 GGTAAATCTT
Statistics
Matches: 306, Mismatches: 28, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
174 3 0.01
175 302 0.99
176 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (174 bp):
TCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCAGATCTTGCCTTCCTGCGATGACAGCGAAGC
AGATCGAAGATACAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTAAAGATAGCGGATCTTGC
CTCCCTAAGCAGTAGTGGAGCAGATCGAAAATACCAACCTTGCA
Found at i:7192 original size:44 final size:43
Alignment explanation
Indices: 7122--7234 Score: 129
Period size: 44 Copynumber: 2.6 Consensus size: 43
7112 GAAAATGGTA
* * * *
7122 AATCTTATCTCTCTGAGGTTGCAGTGGAGTA-GATTGAAGCCGAT
1 AATCTTATCTCTCTGAAGTTGTAGTGGAG-AGGATTAAAG-CAAT
* * *
7166 AATCCTATCTCCCTGAAGTTGTAGTGGAGAGGATTAAAGTAAT
1 AATCTTATCTCTCTGAAGTTGTAGTGGAGAGGATTAAAGCAAT
7209 AGATCTTATCTCTCTGAAGTTGTAGT
1 A-ATCTTATCTCTCTGAAGTTGTAGT
7235 AGAACAGATC
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
43 4 0.07
44 54 0.93
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (43 bp):
AATCTTATCTCTCTGAAGTTGTAGTGGAGAGGATTAAAGCAAT
Found at i:8599 original size:17 final size:17
Alignment explanation
Indices: 8573--8610 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
8563 AATCCAGTTC
*
8573 TTTTATCTCTT-TTTGA
1 TTTTATCTCTTATTTCA
8589 TTTTAATCTCTTATTTCA
1 TTTT-ATCTCTTATTTCA
8607 TTTT
1 TTTT
8611 TGTTTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 7 0.37
18 8 0.42
ACGTcount: A:0.16, C:0.13, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTATCTCTTATTTCA
Done.