Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g00008.P21
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: 10519
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
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:2623 original size:52 final size:52
Alignment explanation
Indices: 2540--2641 Score: 150
Period size: 52 Copynumber: 2.0 Consensus size: 52
2530 AATTTTGCTT
** ** *
2540 CATGCATCTGTAAGTGAAATGTGTGTGTATATATATTCTTTTGATATATTTG
1 CATGCATCCATAAGTGAAATGTGCATCTATATATATTCTTTTGATATATTTG
*
2592 CATGCATCCATAAGTGAAATTTGCATCTATATATATTCTTTTGATATATT
1 CATGCATCCATAAGTGAAATGTGCATCTATATATATTCTTTTGATATATT
2642 CTTTCTATCT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (52 bp):
CATGCATCCATAAGTGAAATGTGCATCTATATATATTCTTTTGATATATTTG
Found at i:2623 original size:114 final size:114
Alignment explanation
Indices: 2412--2628 Score: 380
Period size: 116 Copynumber: 1.9 Consensus size: 114
2402 GCACATTTCA
* *
2412 TATAAATTTTGCTTCCTGCATCTGTAAGTGAAATGTGTGTTTATATATTCTTTTTATATATTTGC
1 TATAAATTTTGCTTCATGCATCTGTAAGTGAAATGTGTGTTTATATATTCTTTTGATATATTTGC
2477 ATGCATCCATAAGTGAAATTTGCAAGTATATATATTTATTTCTATCTGT
66 ATGCATCCATAAGTGAAATTTGCAAGTATATATATTTATTTCTATCTGT
2526 TATAAATTTTGCTTCATGCATCTGTAAGTGAAATGTGTGTGTATATATATTCTTTTGATATATTT
1 TATAAATTTTGCTTCATGCATCTGTAAGTGAAATGTGTGT-T-TATATATTCTTTTGATATATTT
**
2591 GCATGCATCCATAAGTGAAATTTGCATCTATATATATT
64 GCATGCATCCATAAGTGAAATTTGCAAGTATATATATT
2629 CTTTTGATAT
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
114 39 0.40
115 1 0.01
116 57 0.59
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (114 bp):
TATAAATTTTGCTTCATGCATCTGTAAGTGAAATGTGTGTTTATATATTCTTTTGATATATTTGC
ATGCATCCATAAGTGAAATTTGCAAGTATATATATTTATTTCTATCTGT
Found at i:5450 original size:224 final size:224
Alignment explanation
Indices: 4980--5585 Score: 1069
Period size: 223 Copynumber: 2.8 Consensus size: 224
4970 TTCAGATTTA
4980 TGCTTATATTCGTCTTTTTAAATCTTGTGATGTCGTCATTTTTTTGATAGTTTATCGCCTGTTAT
1 TGCTTATATTCGTCTTTTTAAATCTTGTGATGTCGTCATTTTTTTGATAGTTTATCGCCTGTTAT
5045 GTGTTTTATTTTTTTTTTGTCGGTTGTTTGTTTCCCTCTATAATCTGTATTGAGGGACATTTTCT
66 GTGTTTTATTTTTTTTTTGTCGGTTGTTTGTTTCCCTCTATAATCTGTATTGAGGGACATTTTCT
*
5110 TGCAAATC-TTTGAGTCCTATTTATGAGATTTTATAGCGAAGATATGTTTCTAGCAACTATATAA
131 TGCAAATCTTTTGAGTCCTATTTATGAGATTTTATAGCGAAGATATGTTTCTAACAACTATATAA
5174 GTATCTACCCTAAAACCCTTATGAAACAC
196 GTATCTACCCTAAAACCCTTATGAAACAC
*
5203 TGCTTATATTCGTCTTTTTAAATCTTGTGATGTCGTCATTTTTTTGATAGTTTATCGCCTGATAT
1 TGCTTATATTCGTCTTTTTAAATCTTGTGATGTCGTCATTTTTTTGATAGTTTATCGCCTGTTAT
5268 GTGTTTTATTTTTTTTTTGTCGGTTGTTTGTTTCCCTCTATAATCTGTATTGAGGGACATTTTCT
66 GTGTTTTATTTTTTTTTTGTCGGTTGTTTGTTTCCCTCTATAATCTGTATTGAGGGACATTTTCT
5333 TGCAAATCTTTTGAGTCCTATTTATGAGATTTTATAGCGAAGATATGTTTCTAACAACTATATAA
131 TGCAAATCTTTTGAGTCCTATTTATGAGATTTTATAGCGAAGATATGTTTCTAACAACTATATAA
5398 GTATCTACCCTAAAACCCTTATGAAACAC
196 GTATCTACCCTAAAACCCTTATGAAACAC
*
5427 TGCTTATATTCGTCTTCTTAAATCTTGTGATGTCTGTCATTTTTTTGATAGTTTATCGCCTGTTA
1 TGCTTATATTCGTCTTTTTAAATCTTGTGATGTC-GTCATTTTTTTGATAGTTTATCGCCTGTTA
5492 TGTGTTTTA---TTTTTTT-T-GGTTGTTTGTTT-CC-C-----TCTGTATTGAGGGACATTTTC
65 TGTGTTTTATTTTTTTTTTGTCGGTTGTTTGTTTCCCTCTATAATCTGTATTGAGGGACATTTTC
*
5545 TTGAAAAT-TTTTGAGTCCTATTTATGAGATTTTATAGCGAA
130 TTGCAAATCTTTTGAGTCCTATTTATGAGATTTTATAGCGAA
5586 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:6111 original size:16 final size:16
Alignment explanation
Indices: 6090--6127 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6080 TTCTGGATAG
6090 GGATATCCC-ATTCGAA
1 GGATATCCCGATTCG-A
*
6106 GGATATCCCGGTTCGA
1 GGATATCCCGATTCGA
6122 GGATAT
1 GGATAT
6128 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:8183 original size:20 final size:22
Alignment explanation
Indices: 8143--8187 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
8133 AGGGATATTT
8143 AGGTTTGGGGCCTAAGGGTTTG
1 AGGTTTGGGGCCTAAGGGTTTG
*
8165 AGGTTTGGGG-CT-TGGGTTTG
1 AGGTTTGGGGCCTAAGGGTTTG
8185 AGG
1 AGG
8188 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:8337 original size:105 final size:105
Alignment explanation
Indices: 8155--8365 Score: 332
Period size: 105 Copynumber: 2.0 Consensus size: 105
8145 GTTTGGGGCC
* * * * *
8155 TAAGGGTTTGAGGTTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGTTGGTGTTTTTGG
1 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGCTGGTATTTTTGA
* *
8220 GCTTTCTTTTAAGTGTTTGTGGCTGTGGACTTCTTAGGTT
66 GCTTTCGTTTAAGTGTTTGGGGCTGTGGACTTCTTAGGTT
* *
8260 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGTGGCTTAAGTTTTACGGTTGGGCTGGTATTTTTGA
1 TAAGGGTTTGAAGCTTGGGGCTTGGGTTTGAGGCTTAAGGTTTACGGTTGGGCTGGTATTTTTGA
*
8325 GCTTTCGTTTAAGTGTTTGGGGCTGTGGATTTCTTAGGTT
66 GCTTTCGTTTAAGTGTTTGGGGCTGTGGACTTCTTAGGTT
8365 T
1 T
8366 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:9941 original size:66 final size:66
Alignment explanation
Indices: 9859--9993 Score: 225
Period size: 66 Copynumber: 2.0 Consensus size: 66
9849 AAGTATTGAT
* *
9859 AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACGCCTAC
1 AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACACCAAC
9924 C
66 C
* * *
9925 AGGCACTAGATTTGAAGCCAAACTATGTGCGTGCTTGGGCAAACATGGGTATCAGTTACACCAAC
1 AGGCACTAGATTTGAAGCCAAACTACGTGCATGCTTGGGCAAACACGGGTATCAGTTACACCAAC
9990 C
66 C
9991 AGG
1 AGG
9994 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.