Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3678
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: 9597
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Found at i:730 original size:26 final size:26
Alignment explanation
Indices: 700--750 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
690 CCACTGAATC
*
700 GGGGAATCAGCACTTAGCAACCCCCG
1 GGGGAATCAGCACATAGCAACCCCCG
726 GGGGAATCAGCACATAGCAACCCCC
1 GGGGAATCAGCACATAGCAACCCCC
751 TTTCATTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.25, T:0.10
Consensus pattern (26 bp):
GGGGAATCAGCACATAGCAACCCCCG
Found at i:841 original size:101 final size:104
Alignment explanation
Indices: 668--930 Score: 375
Period size: 105 Copynumber: 2.6 Consensus size: 104
658 TAACCGTTAT
*
668 TGGTGGATCTCGCACTTAGCAACCAC--TGAATCGGGGAATCAGCACT-TAGCAACCCC-CGGGG
1 TGGTGGATATCGCACTTAGC-ACCACAATGAATCGGGGAATCAGCACTCTAGCAACCCCTCGGGG
729 GAATCAGCACATAGCAACCCCCTT-T-CATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTATACATTTCAAAGATA
767 TGGTGGATATCGCACTTAGCACCACAATGAA-CGGGGGAATCAGCACTCTAGCAACCCCTC-GGG
1 TGGTGGATATCGCACTTAGCACCACAATGAATC-GGGGAATCAGCACTCTAGCAACCCCTCGGGG
830 GAATCAGCACATAGCAACCCCCTTAATCACATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTT-AT-ACATTTCAAAGATA
* *
872 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACAC-AGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCA-CAATGAATCGGGGAATCAGCACTCTAGCAACCCCT
931 TTATATACAA
Statistics
Matches: 149, Mismatches: 3, Indels: 18
0.88 0.02 0.11
Matches are distributed among these distances:
98 5 0.03
99 20 0.13
100 18 0.12
101 37 0.25
102 1 0.01
103 1 0.01
105 44 0.30
106 22 0.15
107 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.18
Consensus pattern (104 bp):
TGGTGGATATCGCACTTAGCACCACAATGAATCGGGGAATCAGCACTCTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTATACATTTCAAAGATA
Found at i:852 original size:27 final size:27
Alignment explanation
Indices: 800--850 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
790 ACAATGAACG
*
800 GGGGAATCAGCACTCTAGCAACCCCTC
1 GGGGAATCAGCACTATAGCAACCCCTC
827 GGGGAATCAGCAC-ATAGCAACCCC
1 GGGGAATCAGCACTATAGCAACCCC
851 CTTAATCACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (27 bp):
GGGGAATCAGCACTATAGCAACCCCTC
Found at i:1089 original size:8 final size:10
Alignment explanation
Indices: 1061--1090 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1051 CAAATAAATC
*
1061 TCAACATATA
1 TCAAAATATA
1071 TCAAAATATA
1 TCAAAATATA
1081 TCAAAATATA
1 TCAAAATATA
1091 CATTAAGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (10 bp):
TCAAAATATA
Found at i:8303 original size:26 final size:26
Alignment explanation
Indices: 8273--8323 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
8263 ACCAATGAAC
*
8273 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
8299 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
8324 CTTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:8367 original size:103 final size:101
Alignment explanation
Indices: 8139--8401 Score: 404
Period size: 103 Copynumber: 2.6 Consensus size: 101
8129 TAACCGTTAT
* *
8139 TGGTGGATCTCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
8204 AATCAGCACATAGCAACCCCCTTTATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTATTTCAAAGATA
*
8240 TGGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTC-GGG
1 TGGTGGATCA-CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
8303 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTT---ATTTCAAAGATA
* * * **
8343 TGGTGGATCACGCACATAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
8402 TTTATATACA
Statistics
Matches: 148, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
100 28 0.19
101 56 0.38
103 63 0.43
104 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.19
Consensus pattern (101 bp):
TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTATTTCAAAGATA
Found at i:8761 original size:29 final size:29
Alignment explanation
Indices: 8728--8791 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
8718 TAATCCACCA
8728 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
8757 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
8787 CCCAA
1 CCCAA
8792 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:8765 original size:30 final size:30
Alignment explanation
Indices: 8735--8791 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
8725 CCACCCAACT
8735 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
8764 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
8792 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Done.