Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold10
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 5587
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Found at i:261 original size:144 final size:144
Alignment explanation
Indices: 1--767 Score: 781
Period size: 144 Copynumber: 5.2 Consensus size: 144
* * *
1 TACCTGTGAAGAGTGTACTGAGTACACTTCCACTTGGGAGACTACCGACGAAGACGGCTCGACTG
1 TACCTGTGAGGAGTGCACTGAGTACACTTCCACTTGGGAGACTACCGACGAAGACGGCTCCACTG
* * * *
66 CCACTGACTCTGGTGTGGTGATTGTGACCACTGACGAAGACGGCTCGTTGACGACTCTGACCTCA
66 CCACCGACTCTGGTGTGGTTATTGTGACCACTGACGAAGATGGCTCGTTGACCACTCTGACCTCA
131 GTCATTCCCCGTCC
131 GTCATTCCCCGTCC
* * *
145 TACCTGTGAAGAGTGTACTGAGTACACTTCCACTTGGGAGACTACCGACGAAGACGGCTCGACTG
1 TACCTGTGAGGAGTGCACTGAGTACACTTCCACTTGGGAGACTACCGACGAAGACGGCTCCACTG
* * * * *
210 CCACTGACTCTGGTGTGGTGATTGTGACCACTGATGAAGATGGCTCGTTGACGACTCTGACCTCG
66 CCACCGACTCTGGTGTGGTTATTGTGACCACTGACGAAGATGGCTCGTTGACCACTCTGACCTCA
275 GTCATTCCCCGTCC
131 GTCATTCCCCGTCC
* * * * * *
289 TACTTGTGAGGAGTGCACTGAGCACACTTCGACCTGGGAGACTACGGACGAAGATGGCTCCACTG
1 TACCTGTGAGGAGTGCACTGAGTACACTTCCACTTGGGAGACTACCGACGAAGACGGCTCCACTG
* * * * * *
354 CCACCGACACTGGGGTTGTTATTGTGACCACTGATGAAGATGGCTCGTTGACCACCCTGACCTCG
66 CCACCGACTCTGGTGTGGTTATTGTGACCACTGACGAAGATGGCTCGTTGACCACTCTGACCTCA
* *
419 GTCATTCCTCGCCC
131 GTCATTCCCCGTCC
* * * * ** ** * * * *
433 CACTTGCGAGGAGTGCACCGAGTACACCATT--ACTTATGCCACCACCGATGAAGATGGCTTCAC
1 TACCTGTGAGGAGTGCACTGAGTACA-C-TTCCACTTGGGAGACTACCGACGAAGACGGCTCCAC
* * * * * *
496 TGCCACCGACTCTGGGGTTGTTATTGTGACCACCGACGAGGATGGCTCGTTGACCACTCAGACTT
64 TGCCACCGACTCTGGTGTGGTTATTGTGACCACTGACGAAGATGGCTCGTTGACCACTCTGACCT
* * **
561 CCACGCTTCCTCGGCCGACCAACTC
129 -CA-G--TCAT--TCC--CCGTC-C
*
586 TGACTACTGTGAGGAGTGCACTGAGTACACTTCCACTTGGGAGACTACCGACGAGGACGGCTCCA
1 T-AC--CTGTGAGGAGTGCACTGAGTACACTTCCACTTGGGAGACTACCGACGAAGACGGCTCCA
* * * * * * *
651 CTGCCTCCGACTCTGCGAT-T-GTTACTGTGACCACCGACGAAGACGGCTTGTTAACCTC-CATG
63 CTGCCACCGACTCTG-G-TGTGGTTATTGTGACCACTGACGAAGATGGCTCGTTGACCACTC-TG
*
713 ACCTCAATCATTCCCCGTCC
125 ACCTCAGTCATTCCCCGTCC
*
733 TACCTGTGAGGAGTGCACTGA-TCACACTTCGACTT
1 TACCTGTGAGGAGTGCACTGAGT-ACACTTCCACTT
768 ACACCAACTC
Statistics
Matches: 527, Mismatches: 76, Indels: 40
0.82 0.12 0.06
Matches are distributed among these distances:
143 1 0.00
144 399 0.76
145 2 0.00
146 5 0.01
147 2 0.00
148 6 0.01
150 4 0.01
152 5 0.01
153 1 0.00
154 4 0.01
155 4 0.01
156 92 0.17
157 2 0.00
ACGTcount: A:0.21, C:0.30, G:0.25, T:0.24
Consensus pattern (144 bp):
TACCTGTGAGGAGTGCACTGAGTACACTTCCACTTGGGAGACTACCGACGAAGACGGCTCCACTG
CCACCGACTCTGGTGTGGTTATTGTGACCACTGACGAAGATGGCTCGTTGACCACTCTGACCTCA
GTCATTCCCCGTCC
Left flanking sequence: None
Right flanking sequence: Indices 768 -- 1267
ACACCAACTCCGACGGAGTTGAATCGACTGCCATTGGCTCTGCAGATGTGAATACTGAAGAACAA
GAGTCGTTGACCACTTCAATCTCCCTGTTTTCTGATCTTGAGTGTAAGGAGTGCACTGAATACGC
TAGTACATGGGAGACAATTGAAGAAGATGGCTCGACTTCCACCAGTTCTGGTGCTGTTGTTGTGA
CAAGTGACGAAAATGGTCAATTGGCCACTTCAGTGAAAACCTTCGAAACCTCTACGGAATGCGTT
GATTGCAATGAGTACTCCTCATCCGAGAACCACGGGGATGCCGATGTTCATGCAACTAATTCTGG
TAACACTGATAACACTATCGCAGGAGAAAGCCCCTCGACCACTCTCATTCCTTCACCTGCTCTGG
ACACCGAATGTTCTGAGTGTGACTTTGACTCTACGCTTCGTTCTGAACTGGTTGTATCGCAAGTC
GAAATCAACACCGAGGATGTCTCTCTGTTGCATTTCTCAGAGTCA
Done.