Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold10946.1
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: 3187
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.29
Warning! 54 characters in sequence are not A, C, G, or T
Found at i:825 original size:16 final size:16
Alignment explanation
Indices: 804--836 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
794 ACTCAGAGAG
*
804 GAATCTGTACATATAT
1 GAATCTATACATATAT
820 GAATCTATACATATAT
1 GAATCTATACATATAT
836 G
1 G
837 GTATGACTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (16 bp):
GAATCTATACATATAT
Found at i:1010 original size:28 final size:28
Alignment explanation
Indices: 970--1025 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
960 GATGGTTTCG
970 TTACTTTCCTATGAAAGTAGATTCATCA
1 TTACTTTCCTATGAAAGTAGATTCATCA
998 TTACTTTCCTATGAAAGTAGATTCATCA
1 TTACTTTCCTATGAAAGTAGATTCATCA
1026 AGGTTTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (28 bp):
TTACTTTCCTATGAAAGTAGATTCATCA
Found at i:1986 original size:39 final size:40
Alignment explanation
Indices: 1869--2089 Score: 269
Period size: 39 Copynumber: 5.6 Consensus size: 40
1859 GCTCCTCGTT
* *
1869 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
1909 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
1949 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
1988 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * *
2027 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACCTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATCTCGCA
2068 C-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
2090 AACATCATCC
Statistics
Matches: 164, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
38 2 0.01
39 87 0.53
40 63 0.38
41 12 0.07
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:2046 original size:79 final size:80
Alignment explanation
Indices: 1869--2089 Score: 267
Period size: 79 Copynumber: 2.8 Consensus size: 80
1859 GCTCCTCGTT
* * *
1869 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTC-GGACTTAGCCCGGAAT-TAGTAATCTCGCACAAATGCCTTCGGGACTTAGCCC
*
1932 GGATTTAGTAACTCGCA
64 GGAATTAGTAACTCGCA
*
1949 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGACTTAGCCCGGAATTAGTAATCTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
2012 AATTAGTATCTCGCA
66 AATTAGTAACTCGCA
* * * *
2027 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCACCTAGCAC-AA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGA-CTTAGCCCGGA-ATTAGTAATCTCGCACAAATGCCTTCGGGACTTAGCCC
2089 G
64 G
2090 AACATCATCC
Statistics
Matches: 125, Mismatches: 10, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
78 46 0.37
79 57 0.46
80 22 0.18
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGACTTAGCCCGGAATTAGTAATCTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATTAGTAACTCGCA
Found at i:3026 original size:32 final size:32
Alignment explanation
Indices: 2980--3043 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
2970 CCGAGTGTCA
*
2980 TTTCCATCACATAGCAAGATTTAGACCATGGG
1 TTTCAATCACATAGCAAGATTTAGACCATGGG
3012 TTTCAATCACATAGCAAGATTTAGACCATGGG
1 TTTCAATCACATAGCAAGATTTAGACCATGGG
3044 CTAGGTAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (32 bp):
TTTCAATCACATAGCAAGATTTAGACCATGGG
Done.