Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1085
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: 2874
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.29
Warning! 518 characters in sequence are not A, C, G, or T
Found at i:1341 original size:518 final size:516
Alignment explanation
Indices: 1--1456 Score: 2468
Period size: 516 Copynumber: 2.8 Consensus size: 516
1 CATTTTATATAAAAAGCCATTAAATCTACAATTATATA-A-TTAATATATATATGCAAAAACACA
1 CATTTTATATAAAAAGCCATTAAATCTACAATTATATATATTTAATATATATA--CAAAAACACA
* * * *
64 ATTCAAATATAATACGAAAATGTAGTAACTTCCATATGAACTTACCTAGAAAATGGCAAGTAGAA
64 ATTAAAATATAACACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAA
* * * * *
129 CGTTTCAGGCACTAATCATCACAGATTGCTATATAATGATCCGATACTGTTCACTGGAGCCGTCG
129 AGTTTCAGGCACTAATCATCACAGATTGCTATATAATGATCCGATACTGCTCAGTCGAGCTGTCG
* ** * * *
194 AGAATCCATAAGTTCCGCTGGATCTCAACCATCGAAGAAATCTCTAATCACGATTCTCATTTTTC
194 AGAATCCATAATTTGTGCTGGATCTTAACCATCGAATAAATCTCTAATCACGATTCCCATTTTTC
* * *
259 TTTTTTATAACCGTAATCACTTTCTATTCTTATCTAAACCATTTGTTAAATTCATACAGGTTCTT
259 CTTTTTATAACCATAATCACTTTCCATTCTTATCTAAACCATTTGTTAAATTCATACAGGTTCTT
* *
324 TTACCGATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAAAAA
324 TTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAA
389 TTCTCTATACATTTTAAATTTGCAACATCATCATAAACATGCTATCCAACAACATACCATTCCCA
389 TTCTCTATACATTTTAAATTTGCAACATCATCATAAACATGCTATCCAACAACATACCATTCCCA
* * *
454 TATCCATTAAATGTCATGAATCTCTTCATATTTATCAAGCAGTTCTTATTTTACGATTTGATC
454 CATCCATTAAACGTCATGAATCTCTTCATATTTATCAAGCAGTTCTCATTTTACGATTTGATC
*
517 CATTTTATATAAAAAGCCATTAAATCTACAATTATATATCTTTAATATATATACAAAAACACAAT
1 CATTTTATATAAAAAGCCATTAAATCTACAATTATATATATTTAATATATATACAAAAACACAAT
* * *
582 TAAAATATAACACAAAAATGCAGCAACTTCCATATGAGCTTACCTAGAAAATGGCAACTAGAAAG
66 TAAAATATAACACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAAAG
* * * *
647 TTTCAGGGACTAATCAGCACAGATTTCTATATAATGATCCGATACTGCTCAGTCGAGCTGTCGAC
131 TTTCAGGCACTAATCATCACAGATTGCTATATAATGATCCGATACTGCTCAGTCGAGCTGTCGAG
*
712 AATCCACAATTTGTGCTGGATCTTAACCATCGAATAAATCTCTAATCACGATTCCCATTTTTCCT
196 AATCCATAATTTGTGCTGGATCTTAACCATCGAATAAATCTCTAATCACGATTCCCATTTTTCCT
777 TTTTATAACCATAATCACTTTCCATTCTTATCTAAACCATTTGTTAAATTCATACAGGTTCTTTT
261 TTTTATAACCATAATCACTTTCCATTCTTATCTAAACCATTTGTTAAATTCATACAGGTTCTTTT
842 ACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAATT
326 ACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAATT
* * *
907 CTCTATACATTTTAAATTTGCAACATCATCATATACATGCT-TACCAACAACATTCCATTCTCAC
391 CTCTATACATTTTAAATTTGCAACATCATCATAAACATGCTAT-CCAACAACATACCATTCCCAC
* * * *
971 ATCCATTCAACGTCATGAATCTCTTCATATTTATCAAGTATTTCTCATTTTACGTTTTGATC
455 ATCCATTAAACGTCATGAATCTCTTCATATTTATCAAGCAGTTCTCATTTTACGATTTGATC
1033 CATTTTATATAAAAAGCCATTAAATCTACAATTATATATATATTTAATATATATACAAAAACACA
1 CATTTTATATAAAAAGCCATTAAATCTACAA-T-TATATATATTTAATATATATACAAAAACACA
*
1098 ATTAAAATATAACACGAAAATGCAGTAACTTCCATATGAACCTACCTAGAAAATGGCAACTAGAA
64 ATTAAAATATAACACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAA
*
1163 AGTTTCAGGCACTAATCATCACAAATTGCTATATAATGATCCGATACTGCTCAGTCGAGCTGTCG
129 AGTTTCAGGCACTAATCATCACAGATTGCTATATAATGATCCGATACTGCTCAGTCGAGCTGTCG
1228 AGAATCCATAATTTGTGCTGGATCTTAACCATCGAATAAATCTCTAATCACGATTCCCATTTTTC
194 AGAATCCATAATTTGTGCTGGATCTTAACCATCGAATAAATCTCTAATCACGATTCCCATTTTTC
*
1293 CTTTTTATAACCATAATCACTTTCCATTCTTATCTAAACCATTTGTTAAATTCATACAGGTTATT
259 CTTTTTATAACCATAATCACTTTCCATTCTTATCTAAACCATTTGTTAAATTCATACAGGTTCTT
1358 TTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAA
324 TTACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAA
1423 TTCTCTATACATTTTAAATTTGCAACATCATCAT
389 TTCTCTATACATTTTAAATTTGCAACATCATCAT
1457 NNNNNNNNNN
Statistics
Matches: 884, Mismatches: 51, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
515 1 0.00
516 492 0.56
517 1 0.00
518 390 0.44
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.36
Consensus pattern (516 bp):
CATTTTATATAAAAAGCCATTAAATCTACAATTATATATATTTAATATATATACAAAAACACAAT
TAAAATATAACACGAAAATGCAGTAACTTCCATATGAACTTACCTAGAAAATGGCAACTAGAAAG
TTTCAGGCACTAATCATCACAGATTGCTATATAATGATCCGATACTGCTCAGTCGAGCTGTCGAG
AATCCATAATTTGTGCTGGATCTTAACCATCGAATAAATCTCTAATCACGATTCCCATTTTTCCT
TTTTATAACCATAATCACTTTCCATTCTTATCTAAACCATTTGTTAAATTCATACAGGTTCTTTT
ACCAATTTCGTATCATTTCAAACTCTTTAATTGTATACACACATTAGTTATTTTGAATAACAATT
CTCTATACATTTTAAATTTGCAACATCATCATAAACATGCTATCCAACAACATACCATTCCCACA
TCCATTAAACGTCATGAATCTCTTCATATTTATCAAGCAGTTCTCATTTTACGATTTGATC
Done.