Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6489.1
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: 11376
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:1940 original size:30 final size:30
Alignment explanation
Indices: 1906--2002 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
1896 TAAACTAAAA
*
1906 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
1936 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
1966 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
1995 ATGAGCTA
1 -TGAGCTA
2003 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:7129 original size:108 final size:108
Alignment explanation
Indices: 6940--7156 Score: 425
Period size: 108 Copynumber: 2.0 Consensus size: 108
6930 ATGGGTAAAA
6940 TTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCC
1 TTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCC
*
7005 AAATGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGG
66 AAATGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGG
7048 TTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCC
1 TTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCC
7113 AAATGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGG
66 AAATGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGG
7156 T
1 T
7157 CAAATGCTTC
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (108 bp):
TTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCC
AAATGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGG
Found at i:7142 original size:45 final size:45
Alignment explanation
Indices: 7071--7201 Score: 208
Period size: 45 Copynumber: 2.9 Consensus size: 45
7061 TCGGCCATGG
* * * *
7071 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
*
7116 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
*
7161 TGCTTCCTCAAATTCTTCTATGAATTATGCATGATGTTGGC
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGC
7202 AGCCAAATTC
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
Found at i:7257 original size:104 final size:104
Alignment explanation
Indices: 7116--7304 Score: 324
Period size: 104 Copynumber: 1.8 Consensus size: 104
7106 GTTGGCCAAA
* * *
7116 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCTA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
7181 TGAATTATGCATGATGTTGGCAGCCAAATTCGGCCATGG
66 TGAATTATGCATGATGTTGGCAGCCAAATTCGGCCATGG
* * *
7220 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
7285 TGAATTATGCATGATGTTGG
66 TGAATTATGCATGATGTTGG
7305 TCAAATGCTT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
104 79 1.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (104 bp):
TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
TGAATTATGCATGATGTTGGCAGCCAAATTCGGCCATGG
Found at i:7267 original size:149 final size:149
Alignment explanation
Indices: 6963--7348 Score: 664
Period size: 149 Copynumber: 2.6 Consensus size: 149
6953 TCGGCCATGG
* * * * * *
6963 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAATGCTTCCTTAAATTCTTCCA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCA
7028 TGAATTATGCATGATGTTGGTTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTTCCTTA
66 TGAATTATGCATGA---T-GTTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTTCCTTA
7093 AATTATGCATGATGTTGGCCAAA
127 AATTATGCATGATGTTGGCCAAA
*
7116 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCTA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCA
*
7181 TGAATTATGCATGATGTTGGCAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTTCCTTAAATT
66 TGAATTATGCATGATGTTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTTCCTTAAATT
7246 ATGCATGATGTTGGCCAAA
131 ATGCATGATGTTGGCCAAA
7265 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCA
7330 TGAATTATGCATGATGTTG
66 TGAATTATGCATGATGTTG
7349 TCCACCTCTT
Statistics
Matches: 224, Mismatches: 9, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
149 151 0.67
150 1 0.00
153 72 0.32
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (149 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAATGCTTCCTCAAATTCTTCCA
TGAATTATGCATGATGTTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTTCCTTAAATT
ATGCATGATGTTGGCCAAA
Found at i:7291 original size:45 final size:45
Alignment explanation
Indices: 7220--7348 Score: 213
Period size: 45 Copynumber: 2.9 Consensus size: 45
7210 TCGGCCATGG
* * * *
7220 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
*
7265 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
7310 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
7349 TCCACCTCTT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.40
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
Found at i:8727 original size:30 final size:30
Alignment explanation
Indices: 8671--8727 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
8661 TGGGCTCAAA
* **
8671 TCAAGAAAATCAAGATTCACTTTCTTGTTT
1 TCAAGAAAATCAAGAATCACAATCTTGTTT
8701 TCAAGAAAATCAAGAAATCA-AATCTTG
1 TCAAGAAAATCAAG-AATCACAATCTTG
8728 GCCCAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (30 bp):
TCAAGAAAATCAAGAATCACAATCTTGTTT
Found at i:10228 original size:9 final size:9
Alignment explanation
Indices: 10214--10248 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
10204 CAAAAAAATC
10214 AGTCAAAAA
1 AGTCAAAAA
10223 AGTCAAAAA
1 AGTCAAAAA
*
10232 AATCAAAAA
1 AGTCAAAAA
*
10241 AGACAAAA
1 AGTCAAAA
10249 TTCAATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.71, C:0.11, G:0.09, T:0.09
Consensus pattern (9 bp):
AGTCAAAAA
Done.