Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5379.1
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: 25179
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Warning! 511 characters in sequence are not A, C, G, or T
Found at i:5741 original size:15 final size:15
Alignment explanation
Indices: 5700--5767 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
5690 TAGCACCGGT
* *
5700 ATACCACTGTTCACA
1 ATACCAATGTTCATA
* **
5715 ATATCACCGTTCATA
1 ATACCAATGTTCATA
5730 ATACCAATGTTCATA
1 ATACCAATGTTCATA
* *
5745 TTACCAATATTCATA
1 ATACCAATGTTCATA
5760 ATACCAAT
1 ATACCAAT
5768 ACCACCCTAC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.32
Consensus pattern (15 bp):
ATACCAATGTTCATA
Found at i:5871 original size:92 final size:92
Alignment explanation
Indices: 5759--5941 Score: 285
Period size: 92 Copynumber: 2.0 Consensus size: 92
5749 CAATATTCAT
** *
5759 AATACCAATACCACCCTACTTTTAGCACAGAGTCTTATCACGACCCGATTGCCTAGGCCATCTCA
1 AATACCAATACCACCCTACTTTTAGCACAGAGTCCGATCACGACCCGATCGCCTAGGCCATCTCA
* *
5824 TTAGAGACATCAACCACCATTACAATC
66 TTAGAGACATCAACCACAATCACAATC
* * * *
5851 AATACCAATACCACCGTACTTTTAGCACGGAGTCCGATCATGACCCGATCGGCTAGGCCATCTCA
1 AATACCAATACCACCCTACTTTTAGCACAGAGTCCGATCACGACCCGATCGCCTAGGCCATCTCA
5916 TTAGAGACATCAACCACAATCACAAT
66 TTAGAGACATCAACCACAATCACAAT
5942 TTCAATTACA
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
92 82 1.00
ACGTcount: A:0.33, C:0.32, G:0.13, T:0.22
Consensus pattern (92 bp):
AATACCAATACCACCCTACTTTTAGCACAGAGTCCGATCACGACCCGATCGCCTAGGCCATCTCA
TTAGAGACATCAACCACAATCACAATC
Found at i:9419 original size:46 final size:45
Alignment explanation
Indices: 9359--9486 Score: 145
Period size: 46 Copynumber: 2.8 Consensus size: 45
9349 TGGATATTAT
* *
9359 ATTTGGGATAGAGTTCCCTTAGCATGGAGTTGACC-TATATATTCAC
1 ATTTGGGATGGAGTTCCC-TAGCATGGAGTTG-CCTTATATATTCAA
* *
9405 ATTTGGGATGGAGTT-CCTAGGGCATGGAGTTGCCTTATTTATTGAA
1 ATTTGGGATGGAGTTCCCTA--GCATGGAGTTGCCTTATATATTCAA
9451 ATTTGGGATGGAGTTCCC-AGGGCATGGAGTTGCCTT
1 ATTTGGGATGGAGTTCCCTA--GCATGGAGTTGCCTT
9487 CTTTCATTTA
Statistics
Matches: 74, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
44 2 0.03
45 4 0.05
46 66 0.89
47 2 0.03
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (45 bp):
ATTTGGGATGGAGTTCCCTAGCATGGAGTTGCCTTATATATTCAA
Found at i:17533 original size:16 final size:15
Alignment explanation
Indices: 17508--17538 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
17498 ATATTATATT
17508 TGGGATGGAGTTGCC
1 TGGGATGGAGTTGCC
17523 TGGGCATGGAGTTGCC
1 TGGG-ATGGAGTTGCC
17539 ATATATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.13, C:0.16, G:0.45, T:0.26
Consensus pattern (15 bp):
TGGGATGGAGTTGCC
Found at i:17574 original size:46 final size:46
Alignment explanation
Indices: 17505--17676 Score: 184
Period size: 46 Copynumber: 3.7 Consensus size: 46
17495 TGGATATTAT
* * * * *
17505 ATTTGGGATGGAGTTGCCTGGGCATGGAGTTGCCATATATATTCAC
1 ATTTGGGATGGAGTTCCCAGGGCATGGAGTTGCCATATTTATTTAA
* * * * *
17551 ATTTGGGATGGTGTTCCCAGGGCATGAAGTTTCCTTATTTATTTAT
1 ATTTGGGATGGAGTTCCCAGGGCATGGAGTTGCCATATTTATTTAA
* * * * *
17597 ATTAGGGATGGACTTACTAGGGCATGGAATTG-CATTATTTATTTAA
1 ATTTGGGATGGAGTTCCCAGGGCATGGAGTTGCCA-TATTTATTTAA
*
17643 ATTTGGGATGGAGTTCCCAGGGCATGGTGTTGCC
1 ATTTGGGATGGAGTTCCCAGGGCATGGAGTTGCC
17677 TTCTTTCATT
Statistics
Matches: 99, Mismatches: 25, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
45 1 0.01
46 97 0.98
47 1 0.01
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.36
Consensus pattern (46 bp):
ATTTGGGATGGAGTTCCCAGGGCATGGAGTTGCCATATTTATTTAA
Found at i:17659 original size:92 final size:93
Alignment explanation
Indices: 17501--17691 Score: 235
Period size: 92 Copynumber: 2.1 Consensus size: 93
17491 GCATTGGATA
* * * * * *
17501 TTATATTTGGGATGGAGTTGCCTGGGCATGGAGTTGCCATATATATTCACATTTGGGATGGTGTT
1 TTATATTAGGGATGGACTTGACTGGGCATGGAATTGCCATATATATTCAAATTTGGGATGGAGTT
*
17566 CCCAGGGCATGAAGTTTCCTTATTT-AT
66 CCCAGGGCATGAAGTTGCCTTATTTCAT
* *
17593 TTATATTAGGGATGGACTT-ACTAGGGCATGGAATTG-CATTATTTATTTAAATTTGGGATGGAG
1 TTATATTAGGGATGGACTTGACT-GGGCATGGAATTGCCA-TATATATTCAAATTTGGGATGGAG
** *
17656 TTCCCAGGGCATGGTGTTGCCTTCTTTCAT
64 TTCCCAGGGCATGAAGTTGCCTTATTTCAT
17686 TTATAT
1 TTATAT
17692 CTAGAATAGA
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
91 4 0.05
92 72 0.86
93 8 0.10
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.39
Consensus pattern (93 bp):
TTATATTAGGGATGGACTTGACTGGGCATGGAATTGCCATATATATTCAAATTTGGGATGGAGTT
CCCAGGGCATGAAGTTGCCTTATTTCAT
Done.