Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_27 ID=scaffold_27-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: 91966
ACGTcount: A:0.20, C:0.10, G:0.11, T:0.20
Warning! 36573 characters in sequence are not A, C, G, or T
Found at i:3502 original size:26 final size:26
Alignment explanation
Indices: 3468--3519 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
3458 AATAAAAGAA
*
3468 AACATTCAACATTTCAGTTTAATTAG
1 AACATTCAACATTTCAGTCTAATTAG
*
3494 AACATTCAATATTTCAGTCTAATTAG
1 AACATTCAACATTTCAGTCTAATTAG
3520 CATTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (26 bp):
AACATTCAACATTTCAGTCTAATTAG
Found at i:9857 original size:26 final size:26
Alignment explanation
Indices: 9823--9874 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
9813 AATAAAAGAA
*
9823 AACATTCAACATTTCAGTTTAATTAG
1 AACATTCAACATTTCAGTCTAATTAG
*
9849 AACATTCAATATTTCAGTCTAATTAG
1 AACATTCAACATTTCAGTCTAATTAG
9875 CATTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (26 bp):
AACATTCAACATTTCAGTCTAATTAG
Found at i:11976 original size:26 final size:26
Alignment explanation
Indices: 11942--11993 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
11932 AATAAAAGAA
*
11942 AACATTCAACATTTCAGTTTAATTAG
1 AACATTCAACATTTCAGTCTAATTAG
*
11968 AACATTCAATATTTCAGTCTAATTAG
1 AACATTCAACATTTCAGTCTAATTAG
11994 CATTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (26 bp):
AACATTCAACATTTCAGTCTAATTAG
Found at i:38677 original size:50 final size:50
Alignment explanation
Indices: 38534--38775 Score: 191
Period size: 50 Copynumber: 4.7 Consensus size: 50
38524 GGTAAAGAGA
* *
38534 TCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCATCGAGGTTATGAGAAG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA-C-T-GA-G--ATGAGAAG
* * * * *
38590 TCTCACGTAAGACCATGTCAGGGACATGCCGTTGGCACTGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAAG
* * * * *
38640 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAAG
* * * * * * * *
38690 TCCCATGTAAGACCATATCTGGGATATGACATTGGCAGT-ACAAGA-AACA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAA-G
*** *
38739 TCCTGTGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
38776 TGTTATTATC
Statistics
Matches: 151, Mismatches: 34, Indels: 9
0.78 0.18 0.05
Matches are distributed among these distances:
48 2 0.01
49 35 0.23
50 78 0.52
52 1 0.01
53 2 0.01
54 1 0.01
55 1 0.01
56 31 0.21
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAAG
Found at i:58212 original size:26 final size:26
Alignment explanation
Indices: 58183--58232 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
58173 TAAAAGCAAA
* *
58183 CATTCAATATTTTAGTTTAATTAGAC
1 CATTCAATATATCAGTTTAATTAGAC
58209 CATTCAATATATCAGTTTAATTAG
1 CATTCAATATATCAGTTTAATTAG
58233 CATGAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (26 bp):
CATTCAATATATCAGTTTAATTAGAC
Found at i:60313 original size:26 final size:26
Alignment explanation
Indices: 60284--60335 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
60274 AATAAAAGAA
* *
60284 AACATTCAATATTTTAGTTTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
60310 AACATTCAATATTTCAGTCTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
60336 CATTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (26 bp):
AACATTCAATATTTCAGTCTAATTAG
Found at i:72380 original size:26 final size:26
Alignment explanation
Indices: 72351--72402 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
72341 AATAAAAGAA
*
72351 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
72377 AACATTCAATATTTCAGTCTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
72403 CATTGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (26 bp):
AACATTCAATATTTCAGTCTAATTAG
Found at i:74604 original size:24 final size:25
Alignment explanation
Indices: 74576--74622 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
74566 TCCGACCCAG
*
74576 TTTTAGTGGAATATG-AATGGAAGC
1 TTTTAGTGGAATAAGTAATGGAAGC
*
74600 TTTTAGTGGGATAAGTAATGGAA
1 TTTTAGTGGAATAAGTAATGGAA
74623 CTTGGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (25 bp):
TTTTAGTGGAATAAGTAATGGAAGC
Found at i:76020 original size:26 final size:26
Alignment explanation
Indices: 75986--76037 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
75976 AATAAAAGAA
*
75986 AACATTCTATATTTCAGTTTAATTAG
1 AACATTCTATATTTCAGTCTAATTAG
76012 AACATTCTATATTTCAGTCTAATTAG
1 AACATTCTATATTTCAGTCTAATTAG
76038 CACTAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (26 bp):
AACATTCTATATTTCAGTCTAATTAG
Found at i:78123 original size:26 final size:26
Alignment explanation
Indices: 78094--78145 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
78084 AATAAAAGAA
* *
78094 AACATTGAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
*
78120 AACATTCTATATTTCAGTCTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
78146 CATTAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (26 bp):
AACATTCAATATTTCAGTCTAATTAG
Found at i:81178 original size:26 final size:26
Alignment explanation
Indices: 81149--81198 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
81139 AATAAAAGAA
*
81149 AACATTCAATATTTTAGTTTAATTTG
1 AACATTCAATATTTCAGTTTAATTTG
81175 AACATTCAATATTTCAGTTTAATT
1 AACATTCAATATTTCAGTTTAATT
81199 AGCATTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (26 bp):
AACATTCAATATTTCAGTTTAATTTG
Found at i:88599 original size:26 final size:26
Alignment explanation
Indices: 88570--88621 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
88560 AATAAAAGAA
*
88570 AACATTCAATATTTCAGTTTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
88596 AACATTCAATATTTCAGTCTAATTAG
1 AACATTCAATATTTCAGTCTAATTAG
88622 CATTGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (26 bp):
AACATTCAATATTTCAGTCTAATTAG
Found at i:90754 original size:24 final size:25
Alignment explanation
Indices: 90726--90772 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
90716 TCTGACCCAG
*
90726 TTTTAGTGGAATATG-AATGGAAGC
1 TTTTAGTGGAATAAGTAATGGAAGC
*
90750 TTTTAGTGGGATAAGTAATGGAA
1 TTTTAGTGGAATAAGTAATGGAA
90773 CTTGGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (25 bp):
TTTTAGTGGAATAAGTAATGGAAGC
Done.