Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g00008.P4
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: 6963
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Found at i:1894 original size:224 final size:224
Alignment explanation
Indices: 1424--2029 Score: 1069
Period size: 223 Copynumber: 2.8 Consensus size: 224
1414 TTCAGATTTA
1424 TGCTTATATTCGTCTTTTTAAATCTTGTGATGTCGTCATTTTTTTGATAGTTTATCGCCTGTTAT
1 TGCTTATATTCGTCTTTTTAAATCTTGTGATGTCGTCATTTTTTTGATAGTTTATCGCCTGTTAT
1489 GTGTTTTATTTTTTTTTTGTCGGTTGTTTGTTTCCCTCTATAATCTGTATTGAGGGACATTTTCT
66 GTGTTTTATTTTTTTTTTGTCGGTTGTTTGTTTCCCTCTATAATCTGTATTGAGGGACATTTTCT
*
1554 TGCAAATC-TTTGAGTCCTATTTATGAGATTTTATAGCGAAGATATGTTTCTAGCAACTATATAA
131 TGCAAATCTTTTGAGTCCTATTTATGAGATTTTATAGCGAAGATATGTTTCTAACAACTATATAA
1618 GTATCTACCCTAAAACCCTTATGAAACAC
196 GTATCTACCCTAAAACCCTTATGAAACAC
*
1647 TGCTTATATTCGTCTTTTTAAATCTTGTGATGTCGTCATTTTTTTGATAGTTTATCGCCTGATAT
1 TGCTTATATTCGTCTTTTTAAATCTTGTGATGTCGTCATTTTTTTGATAGTTTATCGCCTGTTAT
1712 GTGTTTTATTTTTTTTTTGTCGGTTGTTTGTTTCCCTCTATAATCTGTATTGAGGGACATTTTCT
66 GTGTTTTATTTTTTTTTTGTCGGTTGTTTGTTTCCCTCTATAATCTGTATTGAGGGACATTTTCT
1777 TGCAAATCTTTTGAGTCCTATTTATGAGATTTTATAGCGAAGATATGTTTCTAACAACTATATAA
131 TGCAAATCTTTTGAGTCCTATTTATGAGATTTTATAGCGAAGATATGTTTCTAACAACTATATAA
1842 GTATCTACCCTAAAACCCTTATGAAACAC
196 GTATCTACCCTAAAACCCTTATGAAACAC
*
1871 TGCTTATATTCGTCTTCTTAAATCTTGTGATGTCTGTCATTTTTTTGATAGTTTATCGCCTGTTA
1 TGCTTATATTCGTCTTTTTAAATCTTGTGATGTC-GTCATTTTTTTGATAGTTTATCGCCTGTTA
1936 TGTGTTTTA---TTTTTTT-T-GGTTGTTTGTTT-CC-C-----TCTGTATTGAGGGACATTTTC
65 TGTGTTTTATTTTTTTTTTGTCGGTTGTTTGTTTCCCTCTATAATCTGTATTGAGGGACATTTTC
*
1989 TTGAAAAT-TTTTGAGTCCTATTTATGAGATTTTATAGCGAA
130 TTGCAAATCTTTTGAGTCCTATTTATGAGATTTTATAGCGAA
2030 AACCCTAACT
Statistics
Matches: 376, Mismatches: 5, Indels: 15
0.95 0.01 0.04
Matches are distributed among these distances:
212 33 0.09
213 28 0.07
218 1 0.00
219 2 0.01
220 12 0.03
221 1 0.00
222 7 0.02
223 137 0.36
224 117 0.31
225 38 0.10
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.48
Consensus pattern (224 bp):
TGCTTATATTCGTCTTTTTAAATCTTGTGATGTCGTCATTTTTTTGATAGTTTATCGCCTGTTAT
GTGTTTTATTTTTTTTTTGTCGGTTGTTTGTTTCCCTCTATAATCTGTATTGAGGGACATTTTCT
TGCAAATCTTTTGAGTCCTATTTATGAGATTTTATAGCGAAGATATGTTTCTAACAACTATATAA
GTATCTACCCTAAAACCCTTATGAAACAC
Found at i:2555 original size:16 final size:16
Alignment explanation
Indices: 2534--2571 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2524 TTCTGGATAG
2534 GGATATCCC-ATTCGAA
1 GGATATCCCGATTCG-A
*
2550 GGATATCCCGGTTCGA
1 GGATATCCCGATTCGA
2566 GGATAT
1 GGATAT
2572 TCTAAGTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (16 bp):
GGATATCCCGATTCGA
Found at i:4627 original size:20 final size:22
Alignment explanation
Indices: 4587--4631 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
4577 AGGGATATTT
4587 AGGTTTGGGGCCTAAGGGTTTG
1 AGGTTTGGGGCCTAAGGGTTTG
*
4609 AGGTTTGGGG-CT-TGGGTTTG
1 AGGTTTGGGGCCTAAGGGTTTG
4629 AGG
1 AGG
4632 CTTAAGGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.45
21 2 0.09
22 10 0.45
ACGTcount: A:0.11, C:0.07, G:0.49, T:0.33
Consensus pattern (22 bp):
AGGTTTGGGGCCTAAGGGTTTG
Found at i:4781 original size:105 final size:105
Alignment explanation
Indices: 4599--4809 Score: 332
Period size: 105 Copynumber: 2.0 Consensus size: 105
4589 GTTTGGGGCC
* * * * *
4599 TAAGGGTTTGAGGTTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGTTGGTGTTTTTGG
1 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGCTGGTATTTTTGA
* *
4664 GCTTTCTTTTAAGTGTTTGTGGCTGTGGACTTCTTAGGTT
66 GCTTTCGTTTAAGTGTTTGGGGCTGTGGACTTCTTAGGTT
* *
4704 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGTGGCTTAAGTTTTACGGTTGGGCTGGTATTTTTGA
1 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGCTGGTATTTTTGA
*
4769 GCTTTCGTTTAAGTGTTTGGGGCTGTGGATTTCTTAGGTT
66 GCTTTCGTTTAAGTGTTTGGGGCTGTGGACTTCTTAGGTT
4809 T
1 T
4810 TGGTTACTGG
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 96 1.00
ACGTcount: A:0.11, C:0.08, G:0.36, T:0.45
Consensus pattern (105 bp):
TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGCTGGTATTTTTGA
GCTTTCGTTTAAGTGTTTGGGGCTGTGGACTTCTTAGGTT
Found at i:6385 original size:66 final size:66
Alignment explanation
Indices: 6303--6437 Score: 225
Period size: 66 Copynumber: 2.0 Consensus size: 66
6293 AAGTATTGAT
* *
6303 AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACGCCTAC
1 AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACACCAAC
6368 C
66 C
* * *
6369 AGGCACTAGATTTGAAGCCAAACTATGTGCGTGCTTGGGCAAACATGGGTATCAGTTACACCAAC
1 AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACACCAAC
6434 C
66 C
6435 AGG
1 AGG
6438 GTATGTATGA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21
Consensus pattern (66 bp):
AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACACCAAC
C
Done.