Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_640 ID=scaffold_640-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: 6280
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.28
Warning! 1232 characters in sequence are not A, C, G, or T
Found at i:3945 original size:199 final size:199
Alignment explanation
Indices: 3605--4033 Score: 817
Period size: 199 Copynumber: 2.2 Consensus size: 199
3595 CGAGCTATTC
3605 ACTTTCTCAGGTCTGCTCACACAAGCTGTCAGTCTTTTGTTACTACTCAGTGCTGCACTGTTGCT
1 ACTTTCTCAGGTCTGCTCACACAAGCTGTCAGTCTTTTGTTACTACTCAGTGCTGCACTGTTGCT
3670 TACACAAGCTGTCAGGTATTCGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACC
66 TACACAAGCTGTCAGGTATTCGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACC
3735 AACACCCGAGTTCACATTAATCACAGTTTCGCATCACGACCTACTCACACAAGCTGTCAGTCATT
131 AACACCCGAGTTCACATTAATCACAGTTTCGCATCACGACCTACTCACACAAGCTGTCAGTCATT
3800 CGTT
196 CGTT
3804 ACTTTCTCAGGTCTGCTCACACAAGCTGTCAGTCTTTTGTTACTACTCAGTGCTGCACTGTTGCT
1 ACTTTCTCAGGTCTGCTCACACAAGCTGTCAGTCTTTTGTTACTACTCAGTGCTGCACTGTTGCT
3869 TACACAAGCTGTCAGGTATTCGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACC
66 TACACAAGCTGTCAGGTATTCGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACC
3934 AACACCCGAGTTCACATTAATCACAGTTTCGCATCACGACCTACTCACACAAGCTGTCAGTCATT
131 AACACCCGAGTTCACATTAATCACAGTTTCGCATCACGACCTACTCACACAAGCTGTCAGTCATT
3999 CGTT
196 CGTT
* *
4003 AC-TACTCA-GTGCTGCTCACACAAGCTATCAG
1 ACTTTCTCAGGT-CTGCTCACACAAGCTGTCAG
4034 GTATCCGCAA
Statistics
Matches: 227, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
197 2 0.01
198 24 0.11
199 201 0.89
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (199 bp):
ACTTTCTCAGGTCTGCTCACACAAGCTGTCAGTCTTTTGTTACTACTCAGTGCTGCACTGTTGCT
TACACAAGCTGTCAGGTATTCGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACC
AACACCCGAGTTCACATTAATCACAGTTTCGCATCACGACCTACTCACACAAGCTGTCAGTCATT
CGTT
Found at i:4108 original size:150 final size:154
Alignment explanation
Indices: 3819--4113 Score: 411
Period size: 150 Copynumber: 1.9 Consensus size: 154
3809 CTCAGGTCTG
* * *
3819 CTCACACAAGCTGTCAGTCTTTTGTTACTACTCAGTGCTGCACTGTTGCTTACACAAGCTGTCAG
1 CTCACACAAGCTGTCAGTCATTCGTTACTACTCAGTGCTG-AC--TTGC-TACACAAGCTATCAG
* * *
3884 GTATTCGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAACACCCGAGTTCAC
62 GTATCCGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAACACCAGAGTCCAC
*
3949 ATTAATCACAGTTTCGCATCACGACCTA
127 ATTAATCACAATTTCGCATCACGACCTA
3977 CTCACACAAGCTGTCAGTCATTCGTTACTACTCAGTGCTG-C-T-C-ACACAAGCTATCAGGTAT
1 CTCACACAAGCTGTCAGTCATTCGTTACTACTCAGTGCTGACTTGCTACACAAGCTATCAGGTAT
* * *
4038 CCGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTATGACCAACGCTCAGA-TCCACTTT
66 CCGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAACAC-CAGAGTCCACATT
*
4102 ATTCACAATTTC
130 AATCACAATTTC
4114 ACATAGATCT
Statistics
Matches: 125, Mismatches: 11, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
150 81 0.65
151 3 0.02
152 1 0.01
153 1 0.01
156 1 0.01
158 38 0.30
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.26
Consensus pattern (154 bp):
CTCACACAAGCTGTCAGTCATTCGTTACTACTCAGTGCTGACTTGCTACACAAGCTATCAGGTAT
CCGCAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAACACCAGAGTCCACATTA
ATCACAATTTCGCATCACGACCTA
Done.