Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_159 ID=scaffold_159-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: 10480
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.33
Found at i:3633 original size:13 final size:13
Alignment explanation
Indices: 3615--3640 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3605 TTGTTTTCAG
3615 GTCATTTTCATTT
1 GTCATTTTCATTT
3628 GTCATTTTCATTT
1 GTCATTTTCATTT
3641 TGGAGAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (13 bp):
GTCATTTTCATTT
Found at i:3688 original size:51 final size:51
Alignment explanation
Indices: 3620--3740 Score: 165
Period size: 51 Copynumber: 2.4 Consensus size: 51
3610 TTCAGGTCAT
*
3620 TTTCATTTGT-CATTTTCATTTTGGAGAAAACCATAATCATTTG-AAAATGA
1 TTTCATTTCTCCATTTTCATTTTGGAGAAAACCATAATCA-TTGCAAAATGA
* * *
3670 TTTCATTTCTCCATTTTCATTTTGGAGAAAATCATAATCATTGCCAAATGT
1 TTTCATTTCTCCATTTTCATTTTGGAGAAAACCATAATCATTGCAAAATGA
*
3721 TTTATATTTCTCCATTTTCA
1 TTT-CATTTCTCCATTTTCA
3741 CCATTCAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
50 12 0.19
51 36 0.57
52 15 0.24
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.45
Consensus pattern (51 bp):
TTTCATTTCTCCATTTTCATTTTGGAGAAAACCATAATCATTGCAAAATGA
Found at i:3755 original size:32 final size:32
Alignment explanation
Indices: 3714--3777 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
3704 TAATCATTGC
3714 CAAATGTTTTATATTTCTCCATTTTCACCATT
1 CAAATGTTTTATATTTCTCCATTTTCACCATT
3746 CAAATGTTTTATATTTCTCCATTTTCACCATT
1 CAAATGTTTTATATTTCTCCATTTTCACCATT
3778 TCTATTCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.03, T:0.50
Consensus pattern (32 bp):
CAAATGTTTTATATTTCTCCATTTTCACCATT
Found at i:4856 original size:17 final size:17
Alignment explanation
Indices: 4834--4866 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4824 ATAATCAATG
*
4834 AATTTGTTTTATTAACT
1 AATTTGTTCTATTAACT
4851 AATTTGTTCTATTAAC
1 AATTTGTTCTATTAAC
4867 CCTTGTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (17 bp):
AATTTGTTCTATTAACT
Found at i:7402 original size:64 final size:63
Alignment explanation
Indices: 7304--7425 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 63
7294 CATGAAGAGA
* * * * * * *
7304 CATATATCGGGACGCTCATAAGAGTTGCGGTATGTCCGCAATACATGCAGGATCAATATCGAT
1 CATATAACAGGACGCTCAAAAGAGCTGCGGTATGTCCACAACACATACAGGATCAATATCGAT
7367 CATATAACAGGACGCTCACAAAGAGCTGCGGTATGTCCACAACACATACAGGATCAATA
1 CATATAACAGGACGCTCA-AAAGAGCTGCGGTATGTCCACAACACATACAGGATCAATA
7426 CAGATCGGGA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 16 0.31
64 35 0.69
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (63 bp):
CATATAACAGGACGCTCAAAAGAGCTGCGGTATGTCCACAACACATACAGGATCAATATCGAT
Found at i:9099 original size:11 final size:11
Alignment explanation
Indices: 9083--9140 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
9073 TTATATAAGA
*
9083 AATAAAATTAT
1 AATAAAATAAT
9094 AATAAAATAAT
1 AATAAAATAAT
*
9105 AATAAAATATCT
1 AATAAAATA-AT
* *
9117 CATTAAAATATT
1 -AATAAAATAAT
9129 AATAAAATAAT
1 AATAAAATAAT
9140 A
1 A
9141 TTGATCTTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 29 0.74
12 2 0.05
13 8 0.21
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
AATAAAATAAT
Done.