Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: C10375
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, 409
Length: 682
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Found at i:370 original size:29 final size:29
Alignment explanation
Indices: 338--395 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
328 TATAAGTTAG
*
338 TATACTTAT-TATATAAGTATATATATATA
1 TATACTTATAT-TATAAATATATATATATA
*
367 TATATTTATATTATAAATATATATATATA
1 TATACTTATATTATAAATATATATATATA
396 AATATATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
TATACTTATATTATAAATATATATATATA
Left flanking sequence: Indices 1 -- 337
ATATTTAAAACTGTATCATAAATAGCTAATACTGCTACTCCTCATCTTGTTCATCCTAAATAACT
TTTATTTAATAAAATTGAAATACCATAAATTAATGATACTACAATAATTAAATAAATTACATAAT
TTGTTAAACTTAATGTTAAAATATTATTTATTGTAAATAATGGTTTGATCTCAAATTGATCTAAT
GGTGAAAAAATCATTTTGTTTATATTTATTTATTTTTATTTACTTATATATATATTTTTTCCTTT
TATTTTATATGGAAATATTTATATATTAGTTTATAATTTATAATTCTAACTTATTTATATATAAT
TTTATAAGTTAG
Right flanking sequence: Indices 396 -- 682
AATATATTTCTTTTAGATATATATTTATAATTTAACAATAATAGTTCTAGCTAATAATAATCTTA
AAATATTTGGTAATAAAATTGTTGAAACAAAGTAAATTAAGAAACCTAAAGCTAAAATACCAAAA
GTTAATAAATTTAAAAAGTAAAAAGGTACTAATTGAGGCATTATAATTATAATAATTATTTGATA
AAAATATATATATATATAAATTATATATATATATTAAAATATATAAAATATATCAGATCGGGAGG
ACTCGAACCCCCAGTACCCTACACCCA
Found at i:419 original size:2 final size:2
Alignment explanation
Indices: 355--402 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
345 ATTATATAAG
* *
355 TA TA TA TA TA TA TA TA TT TA TA T- TA TA AA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
396 AA TA TA T
1 TA TA TA T
403 TTCTTTTAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Left flanking sequence: Indices 1 -- 354
ATATTTAAAACTGTATCATAAATAGCTAATACTGCTACTCCTCATCTTGTTCATCCTAAATAACT
TTTATTTAATAAAATTGAAATACCATAAATTAATGATACTACAATAATTAAATAAATTACATAAT
TTGTTAAACTTAATGTTAAAATATTATTTATTGTAAATAATGGTTTGATCTCAAATTGATCTAAT
GGTGAAAAAATCATTTTGTTTATATTTATTTATTTTTATTTACTTATATATATATTTTTTCCTTT
TATTTTATATGGAAATATTTATATATTAGTTTATAATTTATAATTCTAACTTATTTATATATAAT
TTTATAAGTTAGTATACTTATTATATAAG
Right flanking sequence: Indices 403 -- 682
TTCTTTTAGATATATATTTATAATTTAACAATAATAGTTCTAGCTAATAATAATCTTAAAATATT
TGGTAATAAAATTGTTGAAACAAAGTAAATTAAGAAACCTAAAGCTAAAATACCAAAAGTTAATA
AATTTAAAAAGTAAAAAGGTACTAATTGAGGCATTATAATTATAATAATTATTTGATAAAAATAT
ATATATATATAAATTATATATATATATTAAAATATATAAAATATATCAGATCGGGAGGACTCGAA
CCCCCAGTACCCTACACCCA
Found at i:617 original size:9 final size:9
Alignment explanation
Indices: 591--643 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
581 TTATTTGATA
591 AAAATATAT
1 AAAATATAT
*
600 -ATATATAT
1 AAAATATAT
*
608 AAATTATAT
1 AAAATATAT
*
617 -ATATATATT
1 AAAATATA-T
626 AAAATATAT
1 AAAATATAT
635 AAAATATAT
1 AAAATATAT
644 CAGATCGGGA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
8 12 0.34
9 17 0.49
10 6 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AAAATATAT
Left flanking sequence: Indices 91 -- 590
TAAATTAATGATACTACAATAATTAAATAAATTACATAATTTGTTAAACTTAATGTTAAAATATT
ATTTATTGTAAATAATGGTTTGATCTCAAATTGATCTAATGGTGAAAAAATCATTTTGTTTATAT
TTATTTATTTTTATTTACTTATATATATATTTTTTCCTTTTATTTTATATGGAAATATTTATATA
TTAGTTTATAATTTATAATTCTAACTTATTTATATATAATTTTATAAGTTAGTATACTTATTATA
TAAGTATATATATATATATATTTATATTATAAATATATATATATAAATATATTTCTTTTAGATAT
ATATTTATAATTTAACAATAATAGTTCTAGCTAATAATAATCTTAAAATATTTGGTAATAAAATT
GTTGAAACAAAGTAAATTAAGAAACCTAAAGCTAAAATACCAAAAGTTAATAAATTTAAAAAGTA
AAAAGGTACTAATTGAGGCATTATAATTATAATAATTATTTGATA
Right flanking sequence: Indices 644 -- 682
CAGATCGGGAGGACTCGAACCCCCAGTACCCTACACCCA
Found at i:641 original size:17 final size:18
Alignment explanation
Indices: 591--643 Score: 65
Period size: 17 Copynumber: 3.0 Consensus size: 18
581 TTATTTGATA
591 AAAATATAT-ATATATAT
1 AAAATATATAATATATAT
*
608 AAATTATAT-ATATATATT
1 AAAATATATAATATATA-T
*
626 AAAATATATAAAATATAT
1 AAAATATATAATATATAT
644 CAGATCGGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.48
18 10 0.32
19 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATATATAATATATAT
Left flanking sequence: Indices 91 -- 590
TAAATTAATGATACTACAATAATTAAATAAATTACATAATTTGTTAAACTTAATGTTAAAATATT
ATTTATTGTAAATAATGGTTTGATCTCAAATTGATCTAATGGTGAAAAAATCATTTTGTTTATAT
TTATTTATTTTTATTTACTTATATATATATTTTTTCCTTTTATTTTATATGGAAATATTTATATA
TTAGTTTATAATTTATAATTCTAACTTATTTATATATAATTTTATAAGTTAGTATACTTATTATA
TAAGTATATATATATATATATTTATATTATAAATATATATATATAAATATATTTCTTTTAGATAT
ATATTTATAATTTAACAATAATAGTTCTAGCTAATAATAATCTTAAAATATTTGGTAATAAAATT
GTTGAAACAAAGTAAATTAAGAAACCTAAAGCTAAAATACCAAAAGTTAATAAATTTAAAAAGTA
AAAAGGTACTAATTGAGGCATTATAATTATAATAATTATTTGATA
Right flanking sequence: Indices 644 -- 682
CAGATCGGGAGGACTCGAACCCCCAGTACCCTACACCCA
Found at i:643 original size:19 final size:18
Alignment explanation
Indices: 591--635 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 18
581 TTATTTGATA
591 AAAATATATATATATA-T
1 AAAATATATATATATATT
*
608 AAATTATATATATATATT
1 AAAATATATATATATATT
626 AAAATATATA
1 AAAATATATA
636 AAATATATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATATATATATATATT
Left flanking sequence: Indices 91 -- 590
TAAATTAATGATACTACAATAATTAAATAAATTACATAATTTGTTAAACTTAATGTTAAAATATT
ATTTATTGTAAATAATGGTTTGATCTCAAATTGATCTAATGGTGAAAAAATCATTTTGTTTATAT
TTATTTATTTTTATTTACTTATATATATATTTTTTCCTTTTATTTTATATGGAAATATTTATATA
TTAGTTTATAATTTATAATTCTAACTTATTTATATATAATTTTATAAGTTAGTATACTTATTATA
TAAGTATATATATATATATATTTATATTATAAATATATATATATAAATATATTTCTTTTAGATAT
ATATTTATAATTTAACAATAATAGTTCTAGCTAATAATAATCTTAAAATATTTGGTAATAAAATT
GTTGAAACAAAGTAAATTAAGAAACCTAAAGCTAAAATACCAAAAGTTAATAAATTTAAAAAGTA
AAAAGGTACTAATTGAGGCATTATAATTATAATAATTATTTGATA
Right flanking sequence: Indices 636 -- 682
AAATATATCAGATCGGGAGGACTCGAACCCCCAGTACCCTACACCCA
Done.