Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g00008.P12
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: 8680
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Found at i:1788 original size:26 final size:26
Alignment explanation
Indices: 1752--1811 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
1742 GCTAAGGTGG
1752 TGCATATTAGTCAGTCCATGGATCAA
1 TGCATATTAGTCAGTCCATGGATCAA
* *
1778 TGCATATTAGTTAGTCCTTGGATCAA
1 TGCATATTAGTCAGTCCATGGATCAA
*
1804 TGCGTATT
1 TGCATATT
1812 CGGTTTTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (26 bp):
TGCATATTAGTCAGTCCATGGATCAA
Found at i:3611 original size:224 final size:224
Alignment explanation
Indices: 3141--3746 Score: 1069
Period size: 223 Copynumber: 2.8 Consensus size: 224
3131 TTCAGATTTA
3141 TGCTTATATTCGTCTTTTTAAATCTTGTGATGTCGTCATTTTTTTGATAGTTTATCGCCTGTTAT
1 TGCTTATATTCGTCTTTTTAAATCTTGTGATGTCGTCATTTTTTTGATAGTTTATCGCCTGTTAT
3206 GTGTTTTATTTTTTTTTTGTCGGTTGTTTGTTTCCCTCTATAATCTGTATTGAGGGACATTTTCT
66 GTGTTTTATTTTTTTTTTGTCGGTTGTTTGTTTCCCTCTATAATCTGTATTGAGGGACATTTTCT
*
3271 TGCAAATC-TTTGAGTCCTATTTATGAGATTTTATAGCGAAGATATGTTTCTAGCAACTATATAA
131 TGCAAATCTTTTGAGTCCTATTTATGAGATTTTATAGCGAAGATATGTTTCTAACAACTATATAA
3335 GTATCTACCCTAAAACCCTTATGAAACAC
196 GTATCTACCCTAAAACCCTTATGAAACAC
*
3364 TGCTTATATTCGTCTTTTTAAATCTTGTGATGTCGTCATTTTTTTGATAGTTTATCGCCTGATAT
1 TGCTTATATTCGTCTTTTTAAATCTTGTGATGTCGTCATTTTTTTGATAGTTTATCGCCTGTTAT
3429 GTGTTTTATTTTTTTTTTGTCGGTTGTTTGTTTCCCTCTATAATCTGTATTGAGGGACATTTTCT
66 GTGTTTTATTTTTTTTTTGTCGGTTGTTTGTTTCCCTCTATAATCTGTATTGAGGGACATTTTCT
3494 TGCAAATCTTTTGAGTCCTATTTATGAGATTTTATAGCGAAGATATGTTTCTAACAACTATATAA
131 TGCAAATCTTTTGAGTCCTATTTATGAGATTTTATAGCGAAGATATGTTTCTAACAACTATATAA
3559 GTATCTACCCTAAAACCCTTATGAAACAC
196 GTATCTACCCTAAAACCCTTATGAAACAC
*
3588 TGCTTATATTCGTCTTCTTAAATCTTGTGATGTCTGTCATTTTTTTGATAGTTTATCGCCTGTTA
1 TGCTTATATTCGTCTTTTTAAATCTTGTGATGTC-GTCATTTTTTTGATAGTTTATCGCCTGTTA
3653 TGTGTTTTA---TTTTTTT-T-GGTTGTTTGTTT-CC-C-----TCTGTATTGAGGGACATTTTC
65 TGTGTTTTATTTTTTTTTTGTCGGTTGTTTGTTTCCCTCTATAATCTGTATTGAGGGACATTTTC
*
3706 TTGAAAAT-TTTTGAGTCCTATTTATGAGATTTTATAGCGAA
130 TTGCAAATCTTTTGAGTCCTATTTATGAGATTTTATAGCGAA
3747 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:4272 original size:16 final size:16
Alignment explanation
Indices: 4251--4288 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4241 TTCTGGATAG
4251 GGATATCCC-ATTCGAA
1 GGATATCCCGATTCG-A
*
4267 GGATATCCCGGTTCGA
1 GGATATCCCGATTCGA
4283 GGATAT
1 GGATAT
4289 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:6344 original size:20 final size:22
Alignment explanation
Indices: 6304--6348 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
6294 AGGGATATTT
6304 AGGTTTGGGGCCTAAGGGTTTG
1 AGGTTTGGGGCCTAAGGGTTTG
*
6326 AGGTTTGGGG-CT-TGGGTTTG
1 AGGTTTGGGGCCTAAGGGTTTG
6346 AGG
1 AGG
6349 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:6498 original size:105 final size:105
Alignment explanation
Indices: 6316--6526 Score: 332
Period size: 105 Copynumber: 2.0 Consensus size: 105
6306 GTTTGGGGCC
* * * * *
6316 TAAGGGTTTGAGGTTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGTTGGTGTTTTTGG
1 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGCTGGTATTTTTGA
* *
6381 GCTTTCTTTTAAGTGTTTGTGGCTGTGGACTTCTTAGGTT
66 GCTTTCGTTTAAGTGTTTGGGGCTGTGGACTTCTTAGGTT
* *
6421 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGTGGCTTAAGTTTTACGGTTGGGCTGGTATTTTTGA
1 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGCTGGTATTTTTGA
*
6486 GCTTTCGTTTAAGTGTTTGGGGCTGTGGATTTCTTAGGTT
66 GCTTTCGTTTAAGTGTTTGGGGCTGTGGACTTCTTAGGTT
6526 T
1 T
6527 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:8102 original size:66 final size:66
Alignment explanation
Indices: 8020--8154 Score: 225
Period size: 66 Copynumber: 2.0 Consensus size: 66
8010 AAGTATTGAT
* *
8020 AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACGCCTAC
1 AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACACCAAC
8085 C
66 C
* * *
8086 AGGCACTAGATTTGAAGCCAAACTATGTGCGTGCTTGGGCAAACATGGGTATCAGTTACACCAAC
1 AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACACCAAC
8151 C
66 C
8152 AGG
1 AGG
8155 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.