Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_141 ID=scaffold_141-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: 11260
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.31
Warning! 158 characters in sequence are not A, C, G, or T
Found at i:3740 original size:44 final size:45
Alignment explanation
Indices: 3677--3810 Score: 107
Period size: 44 Copynumber: 3.0 Consensus size: 45
3667 GATCTACTAT
*
3677 ATTGTAA-CTTCAGAGAGATAAGATCCT-TTATTTTAATCTGCTCC
1 ATTGTAATCTCCAG-GAGATAAGATCCTATTATTTTAATCTGCTCC
* * * *
3721 ATTGTAATCTCCAGGAGATAGGAT--TACTAGCTTCAATCTGCTCC
1 ATTGTAATCTCCAGGAGATAAGATCCTATTA-TTTTAATCTGCTCC
** * * * *
3765 GCTGTAATCTCAAGGAGATAAGA-CCTGTTATCTTTAACCAGCTCC
1 ATTGTAATCTCCAGGAGATAAGATCCTATTAT-TTTAATCTGCTCC
3810 A
1 A
3811 CTGCAACCGA
Statistics
Matches: 68, Mismatches: 16, Indels: 11
0.72 0.17 0.12
Matches are distributed among these distances:
42 1 0.01
43 2 0.03
44 47 0.69
45 18 0.26
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (45 bp):
ATTGTAATCTCCAGGAGATAAGATCCTATTATTTTAATCTGCTCC
Found at i:3887 original size:87 final size:87
Alignment explanation
Indices: 3784--4193 Score: 678
Period size: 87 Copynumber: 4.7 Consensus size: 87
3774 TCAAGGAGAT
* *
3784 AAGACCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
*
3849 TTCGCTGTTAATGCAAGAAGGC
66 TTCGCTGTTAATGCAGGAAGGC
* * *
3871 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGTAAGGCTTTATTTTCGATCTAC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
3936 TTCGCTGTTAATGCAGGAAGGC
66 TTCGCTGTTAATGCAGGAAGGC
* *
3958 AAGATCTGCTATCTTTAACCAGCT-CACTGCAACCGATGGAGGCAAGGCTTTGTTTTTGATCTGT
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
* *
4022 TTTGTTGTTAATGCAGGAAGGC
66 TTCGCTGTTAATGCAGGAAGGC
*
4044 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTTGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
* * * *
4109 TTTGTTGTCAATGCGGGAAGGC
66 TTCGCTGTTAATGCAGGAAGGC
4131 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCT
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCT
4194 TCACTGATCT
Statistics
Matches: 305, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
86 79 0.26
87 226 0.74
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (87 bp):
AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
TTCGCTGTTAATGCAGGAAGGC
Found at i:4083 original size:173 final size:174
Alignment explanation
Indices: 3784--4193 Score: 678
Period size: 173 Copynumber: 2.4 Consensus size: 174
3774 TCAAGGAGAT
* *
3784 AAGACCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
3849 TTCGCTGTTAATGCAAGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGG
66 TTCGCTGTTAATGCAAGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGG
* *
3914 TAAGGCTTTATTTTCGATCTACTTCGCTGTTAATGCAGGAAGGC
131 CAAGGCTTTATTTTCGATCTACTTCGCTGTCAATGCAGGAAGGC
* *
3958 AAGATCTGCTATCTTTAACCAGCT-CACTGCAACCGATGGAGGCAAGGCTTTGTTTTTGATCTGT
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
* * *
4022 TTTGTTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGG
66 TTCGCTGTTAATGCAAGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGG
* * * * * *
4087 CAAGGCTTTGTTTTTGATCTGCTTTGTTGTCAATGCGGGAAGGC
131 CAAGGCTTTATTTTCGATCTACTTCGCTGTCAATGCAGGAAGGC
4131 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCT
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCT
4194 TCACTGATCT
Statistics
Matches: 219, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
173 160 0.73
174 59 0.27
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (174 bp):
AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
TTCGCTGTTAATGCAAGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGG
CAAGGCTTTATTTTCGATCTACTTCGCTGTCAATGCAGGAAGGC
Found at i:5394 original size:7 final size:7
Alignment explanation
Indices: 5382--5433 Score: 72
Period size: 7 Copynumber: 7.7 Consensus size: 7
5372 AGCCTCTCCT
5382 TTTTTCA
1 TTTTTCA
5389 TTTTTCA
1 TTTTTCA
5396 -TTTTCA
1 TTTTTCA
*
5402 ATTTTCA
1 TTTTTCA
5409 TTTTTCA
1 TTTTTCA
*
5416 -TTCTCA
1 TTTTTCA
5422 TTTTTCA
1 TTTTTCA
5429 TTTTT
1 TTTTT
5434 TTGACTCAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
6 11 0.28
7 29 0.73
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTTTCA
Found at i:5401 original size:13 final size:13
Alignment explanation
Indices: 5382--5432 Score: 68
Period size: 13 Copynumber: 3.8 Consensus size: 13
5372 AGCCTCTCCT
5382 TTTTTCATTTTTCA
1 TTTTTCA-TTTTCA
5396 -TTTTCAATTTTCA
1 TTTTTC-ATTTTCA
*
5409 TTTTTCATTCTCA
1 TTTTTCATTTTCA
5422 TTTTTCATTTT
1 TTTTTCATTTT
5433 TTTGACTCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 27 0.82
14 6 0.18
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTCATTTTCA
Found at i:5408 original size:20 final size:20
Alignment explanation
Indices: 5383--5433 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
5373 GCCTCTCCTT
*
5383 TTTTCATTTTTCATTTTCAA
1 TTTTCATTTTTCATTCTCAA
*
5403 TTTTCATTTTTCATTCTCAT
1 TTTTCATTTTTCATTCTCAA
5423 TTTTCATTTTT
1 TTTTCATTTTT
5434 TTGACTCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTCATTTTTCATTCTCAA
Found at i:6291 original size:15 final size:16
Alignment explanation
Indices: 6271--6305 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
6261 TCTCCTTTTC
*
6271 TTTTTTCTTTTC-CTT
1 TTTTTTCTTCTCTCTT
6286 TTTTTTCTTCTCTCTT
1 TTTTTTCTTCTCTCTT
6302 TTTT
1 TTTT
6306 CATTTTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTCTTCTCTCTT
Found at i:7074 original size:39 final size:39
Alignment explanation
Indices: 7030--7109 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
7020 GTATAAATTC
* * *
7030 ATGAATAATTATTTGTATCATATGATTATGAATGAATGA
1 ATGAATAATAATTTGTACCATATGATTATGAACGAATGA
7069 ATGAATAATAATTTGTACCATATGATTATGAACGAATGA
1 ATGAATAATAATTTGTACCATATGATTATGAACGAATGA
7108 AT
1 AT
7110 AATGAATGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (39 bp):
ATGAATAATAATTTGTACCATATGATTATGAACGAATGA
Done.