Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 199 of 199
Found at i:58264365 original size:121 final size:121
Alignment explanation
Indices: 58264151--58264392 Score: 475
Period size: 121 Copynumber: 2.0 Consensus size: 121
58264141 AAAAAACTAA
58264151 TAGTTCACATTCTAGTCTAGCTTTTATGGTTAGAAATCATGCTGAAATAAAAAGAGGAAAAGCTA
1 TAGTTCACATTCTAGTCTAGCTTTTATGGTTAGAAATCATGCTGAAATAAAAAGAGGAAAAGCTA
*
58264216 GAATAGTTATTAACTATAAAAGATTAAATCAAAATTTTATTTTTTATGGATATTTT
66 GAATAGTTATTAACTATAAAAGATTAAATCAAAATTTTATTTTTGATGGATATTTT
58264272 TAGTTCACATTCTAGTCTAGCTTTTATGGTTAGAAATCATGCTGAAATAAAAAGAGGAAAAGCTA
1 TAGTTCACATTCTAGTCTAGCTTTTATGGTTAGAAATCATGCTGAAATAAAAAGAGGAAAAGCTA
58264337 GAATAGTTATTAACTATAAAAGATTAAATCAAAATTTTATTTTTGATGGATATTTT
66 GAATAGTTATTAACTATAAAAGATTAAATCAAAATTTTATTTTTGATGGATATTTT
58264393 ATTACAAGAA
Statistics
Matches: 120, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 120 1.00
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (121 bp):
TAGTTCACATTCTAGTCTAGCTTTTATGGTTAGAAATCATGCTGAAATAAAAAGAGGAAAAGCTA
GAATAGTTATTAACTATAAAAGATTAAATCAAAATTTTATTTTTGATGGATATTTT
Found at i:58266307 original size:33 final size:35
Alignment explanation
Indices: 58266270--58266366 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
58266260 ATGGTTATAT
58266270 TTAAATATTTAAAATATAATTTATATATT-C-TAA
1 TTAAATATTTAAAATATAATTTATATATTGCTTAA
* *
58266303 TTAAAT-TTTATAA-ATAATTAATATTTATTGCTTAA
1 TTAAATATTTAAAATATAATT--TATATATTGCTTAA
*
58266338 --AAATATTTAAAATTTATAATTCATATATT
1 TTAAATATTTAAAA--TATAATTTATATATT
58266367 AAAATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 6 0.12
32 6 0.12
33 17 0.33
34 7 0.14
35 9 0.18
37 6 0.12
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTTATATATTGCTTAA
Found at i:58266566 original size:13 final size:13
Alignment explanation
Indices: 58266547--58266608 Score: 70
Period size: 13 Copynumber: 4.8 Consensus size: 13
58266537 TAAACTAAAA
58266547 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
58266560 TTCTCAAAATCAC
1 TTTTCAAAAGCAC
* *
58266573 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
**
58266586 TTTTCAAAAATAC
1 TTTTCAAAAGCAC
58266599 TTTTCAAAAG
1 TTTTCAAAAG
58266609 TAATGAAGAA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:58267344 original size:21 final size:21
Alignment explanation
Indices: 58267315--58267362 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
58267305 ATATTGGCAT
*
58267315 ATGATATTGAAAATATCCAGG
1 ATGACATTGAAAATATCCAGG
58267336 ATGACATTGAAAATATCCAGG
1 ATGACATTGAAAATATCCAGG
58267357 ATGACA
1 ATGACA
58267363 GAGATGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (21 bp):
ATGACATTGAAAATATCCAGG
Found at i:58267694 original size:18 final size:18
Alignment explanation
Indices: 58267659--58267696 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
58267649 GAGTTGATCC
*
58267659 AAATAACTCGATTAATTT
1 AAATAACTCGACTAATTT
58267677 AAATAACTCGAACT-ATTT
1 AAATAACTCG-ACTAATTT
58267695 AA
1 AA
58267697 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.34
Consensus pattern (18 bp):
AAATAACTCGACTAATTT
Found at i:58270359 original size:3 final size:3
Alignment explanation
Indices: 58270351--58270383 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
58270341 AAGCATAATT
58270351 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
58270384 GCTTACAGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:58276965 original size:15 final size:15
Alignment explanation
Indices: 58276945--58276973 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
58276935 AAATAAGTCC
58276945 AATTTATTAAAAAGA
1 AATTTATTAAAAAGA
58276960 AATTTATTAAAAAG
1 AATTTATTAAAAAG
58276974 TTAGAAGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (15 bp):
AATTTATTAAAAAGA
Found at i:58291076 original size:91 final size:91
Alignment explanation
Indices: 58290906--58291125 Score: 250
Period size: 91 Copynumber: 2.4 Consensus size: 91
58290896 TAAGCAGGAA
* * * ** * *
58290906 AATTACAAAAATTATTATTTATTATATTGTATTTTTGGGCACTTAGTCTTGAGTATAGTGTTGCA
1 AATTATAAAAATTATTATTTATTTTATTTTATTTTTGGAAACTTAGTCTCGAGTATAGTGCTGCA
58290971 AAAATATTTTTTTTATTTTCT-GAAAT
66 AAAATATTTTTTTTATTTT-TAGAAAT
58290997 AATTATAAAAATTATTATTTATTTTATTTTATTTTTGGAAACTTGAGT-TCGAGTATAGTGCTG-
1 AATTATAAAAATTATTATTTATTTTATTTTATTTTTGGAAACTT-AGTCTCGAGTATAGTGCTGC
* * * *
58291060 TAAATTTTTTTATTTTATTTTTAGGAAT
65 AAAAATATTTT-TTTTATTTTTAGAAAT
* * *
58291088 AACTATAAAAATTATTATTT-TTTATACTTCATTTTTGG
1 AATTATAAAAATTATTATTTATTT-TATTTTATTTTTGG
58291126 TGCAATTTGG
Statistics
Matches: 111, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
90 12 0.11
91 96 0.86
92 3 0.03
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.52
Consensus pattern (91 bp):
AATTATAAAAATTATTATTTATTTTATTTTATTTTTGGAAACTTAGTCTCGAGTATAGTGCTGCA
AAAATATTTTTTTTATTTTTAGAAAT
Found at i:58316072 original size:10 final size:10
Alignment explanation
Indices: 58316038--58316072 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
58316028 GTTGTCTGCC
58316038 AAATATATAA
1 AAATATATAA
*
58316048 AAAAATATTAA
1 AAATATA-TAA
58316059 AAATATATAA
1 AAATATATAA
58316069 AAAT
1 AAAT
58316073 CATAGAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAATATATAA
Found at i:58320442 original size:21 final size:21
Alignment explanation
Indices: 58320418--58320459 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
58320408 AGAATTTCCC
58320418 CTGTCCGGGTCAG-TTGTTTTA
1 CTGTCCGGGTCAGATT-TTTTA
*
58320439 CTGTCCGGTTCAGATTTTTTA
1 CTGTCCGGGTCAGATTTTTTA
58320460 TGCTTCTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.45
Consensus pattern (21 bp):
CTGTCCGGGTCAGATTTTTTA
Done.