Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold53
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: 5321
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.29
Found at i:467 original size:24 final size:24
Alignment explanation
Indices: 435--489 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
425 GGTTTAGGAA
* *
435 ACTCTGCTACATT-ATATGCATTCT
1 ACTCTGCTAAATTGA-ATGCAGTCT
459 ACTCTGCTAAATTGAATGCAGTCT
1 ACTCTGCTAAATTGAATGCAGTCT
483 ACTCTGC
1 ACTCTGC
490 CCAATACTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.36
Consensus pattern (24 bp):
ACTCTGCTAAATTGAATGCAGTCT
Left flanking sequence: Indices 1 -- 434
AGCCCTGGGTCCCCGTCAGTTGCTAACACTTCCCCGATGGTCGCGTGGCCTGGAGGTTTGAAGTG
GGCAATCTGGCTCCCAGGGTGGGTGCTACGGCACTGCTGAGTCTGTGGTAACGACGTCTGGAGGG
AGCAGTCTAGCTCTCTCTCGCGGAATCAAAGGAACTTGCTCCCAAAGCAGGGGTTAGGGGAGTGT
CTGGTTGCCGGGTTACCCAGCAAGTGTATATAGGTGTAGGCACACTGTACTATTATTCTAGCTGG
GGCCCCCGGGCCAACAACCAGACCGGGTTTATAATTTAAAAATAATATATGCACGAGATGCATTA
GCCTGCATGGCTCTCATGCAAGCTATGCACCTCGTATAATACACAGAATACGAAACCTACGGCAC
CGCCGTTTGTAGACCAGTCACGTGATTGTTTTCAGGTTTAGGAA
Right flanking sequence: Indices 490 -- 989
CCAATACTCTGCAAAATTGCATGCAGTAAACTCTGCCAAATACTCTGCAAAATTGTATGCAGTAA
ACTCTGCCACATACTCTGCAAAATTGTATGCAGTGAACTCTGCCAAATACTCTGCAAAATTGTAT
GCAGTAAACTCTGCAAAATACTCTGCTAGTTTGTATGCAGGCTACTCTGCCAAATACTCTGCAAA
TTTACATGCAGTTTACTCTGCTGAATTTAAGTCTACTCTGCTAAAATGCGCTTATATACAGTTTA
CTCTGCTAATAAATATGTGTACTCTGCTAAATTGTATCTCTGTGCAGTGAACTCTGCTGAAAAGC
GGAATCTCCTCTGCAAAACAGCTTGTGTGCAGTTTTCTCGGAAAATAATCCTTGTGTAGCAGACA
CAGCTCGCAAATAGCTTCACGTGCAGCAATTCTCTCGTAACTCTCTCGTAACTGCCAGTGCTTTC
TCAACGTCGCCCACAGGTCAACACACGACACAACCCCATCAAAAA
Found at i:536 original size:12 final size:12
Alignment explanation
Indices: 519--645 Score: 53
Period size: 12 Copynumber: 10.6 Consensus size: 12
509 CATGCAGTAA
*
519 ACTCTGCCAAAT
1 ACTCTGCAAAAT
531 ACTCTGCAAAAT
1 ACTCTGCAAAAT
** * *
543 TGTATGCAGTAA-
1 ACTCTGCA-AAAT
* *
555 ACTCTGCCACAT
1 ACTCTGCAAAAT
567 ACTCTGCAAAAT
1 ACTCTGCAAAAT
** * **
579 TGTATGCAGTGA-
1 ACTCTGCA-AAAT
*
591 ACTCTGCCAAAT
1 ACTCTGCAAAAT
603 ACTCTGCAAAAT
1 ACTCTGCAAAAT
** * *
615 TGTATGCAGTAA-
1 ACTCTGCA-AAAT
627 ACTCTGCAAAAT
1 ACTCTGCAAAAT
639 ACTCTGC
1 ACTCTGC
646 TAGTTTGTAT
Statistics
Matches: 76, Mismatches: 33, Indels: 12
0.63 0.27 0.10
Matches are distributed among these distances:
11 4 0.05
12 67 0.88
13 5 0.07
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (12 bp):
ACTCTGCAAAAT
Left flanking sequence: Indices 19 -- 518
GTTGCTAACACTTCCCCGATGGTCGCGTGGCCTGGAGGTTTGAAGTGGGCAATCTGGCTCCCAGG
GTGGGTGCTACGGCACTGCTGAGTCTGTGGTAACGACGTCTGGAGGGAGCAGTCTAGCTCTCTCT
CGCGGAATCAAAGGAACTTGCTCCCAAAGCAGGGGTTAGGGGAGTGTCTGGTTGCCGGGTTACCC
AGCAAGTGTATATAGGTGTAGGCACACTGTACTATTATTCTAGCTGGGGCCCCCGGGCCAACAAC
CAGACCGGGTTTATAATTTAAAAATAATATATGCACGAGATGCATTAGCCTGCATGGCTCTCATG
CAAGCTATGCACCTCGTATAATACACAGAATACGAAACCTACGGCACCGCCGTTTGTAGACCAGT
CACGTGATTGTTTTCAGGTTTAGGAAACTCTGCTACATTATATGCATTCTACTCTGCTAAATTGA
ATGCAGTCTACTCTGCCCAATACTCTGCAAAATTGCATGCAGTAA
Right flanking sequence: Indices 646 -- 1145
TAGTTTGTATGCAGGCTACTCTGCCAAATACTCTGCAAATTTACATGCAGTTTACTCTGCTGAAT
TTAAGTCTACTCTGCTAAAATGCGCTTATATACAGTTTACTCTGCTAATAAATATGTGTACTCTG
CTAAATTGTATCTCTGTGCAGTGAACTCTGCTGAAAAGCGGAATCTCCTCTGCAAAACAGCTTGT
GTGCAGTTTTCTCGGAAAATAATCCTTGTGTAGCAGACACAGCTCGCAAATAGCTTCACGTGCAG
CAATTCTCTCGTAACTCTCTCGTAACTGCCAGTGCTTTCTCAACGTCGCCCACAGGTCAACACAC
GACACAACCCCATCAAAAAGGCCTGATATGGGCTTTCCATGGCATTGCTGGTGTTTCTGATTGGC
TCTAGCTGGCATGGAGCCTTCAGCTGGCTTGTTGCGGTCATTTTGATTGAGCCAAAACGTGTTAG
TCATTGGATGGCTTGTGAAATCCGGAACAAAGGCGATCGACGGCT
Found at i:705 original size:36 final size:36
Alignment explanation
Indices: 458--684 Score: 319
Period size: 36 Copynumber: 6.3 Consensus size: 36
448 ATATGCATTC
* * ** *
458 TACTCTGCTAAATTGAATGCAGTCTACTCTGCCCAA
1 TACTCTGCAAAATTGTATGCAGTAAACTCTGCCAAA
*
494 TACTCTGCAAAATTGCATGCAGTAAACTCTGCCAAA
1 TACTCTGCAAAATTGTATGCAGTAAACTCTGCCAAA
*
530 TACTCTGCAAAATTGTATGCAGTAAACTCTGCCACA
1 TACTCTGCAAAATTGTATGCAGTAAACTCTGCCAAA
*
566 TACTCTGCAAAATTGTATGCAGTGAACTCTGCCAAA
1 TACTCTGCAAAATTGTATGCAGTAAACTCTGCCAAA
*
602 TACTCTGCAAAATTGTATGCAGTAAACTCTGCAAAA
1 TACTCTGCAAAATTGTATGCAGTAAACTCTGCCAAA
* ** ***
638 TACTCTGCTAGTTTGTATGCAGGCTACTCTGCCAAA
1 TACTCTGCAAAATTGTATGCAGTAAACTCTGCCAAA
674 TACTCTGCAAA
1 TACTCTGCAAA
685 TTTACATGCA
Statistics
Matches: 171, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 171 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (36 bp):
TACTCTGCAAAATTGTATGCAGTAAACTCTGCCAAA
Left flanking sequence: Indices 1 -- 457
AGCCCTGGGTCCCCGTCAGTTGCTAACACTTCCCCGATGGTCGCGTGGCCTGGAGGTTTGAAGTG
GGCAATCTGGCTCCCAGGGTGGGTGCTACGGCACTGCTGAGTCTGTGGTAACGACGTCTGGAGGG
AGCAGTCTAGCTCTCTCTCGCGGAATCAAAGGAACTTGCTCCCAAAGCAGGGGTTAGGGGAGTGT
CTGGTTGCCGGGTTACCCAGCAAGTGTATATAGGTGTAGGCACACTGTACTATTATTCTAGCTGG
GGCCCCCGGGCCAACAACCAGACCGGGTTTATAATTTAAAAATAATATATGCACGAGATGCATTA
GCCTGCATGGCTCTCATGCAAGCTATGCACCTCGTATAATACACAGAATACGAAACCTACGGCAC
CGCCGTTTGTAGACCAGTCACGTGATTGTTTTCAGGTTTAGGAAACTCTGCTACATTATATGCAT
TC
Right flanking sequence: Indices 685 -- 1184
TTTACATGCAGTTTACTCTGCTGAATTTAAGTCTACTCTGCTAAAATGCGCTTATATACAGTTTA
CTCTGCTAATAAATATGTGTACTCTGCTAAATTGTATCTCTGTGCAGTGAACTCTGCTGAAAAGC
GGAATCTCCTCTGCAAAACAGCTTGTGTGCAGTTTTCTCGGAAAATAATCCTTGTGTAGCAGACA
CAGCTCGCAAATAGCTTCACGTGCAGCAATTCTCTCGTAACTCTCTCGTAACTGCCAGTGCTTTC
TCAACGTCGCCCACAGGTCAACACACGACACAACCCCATCAAAAAGGCCTGATATGGGCTTTCCA
TGGCATTGCTGGTGTTTCTGATTGGCTCTAGCTGGCATGGAGCCTTCAGCTGGCTTGTTGCGGTC
ATTTTGATTGAGCCAAAACGTGTTAGTCATTGGATGGCTTGTGAAATCCGGAACAAAGGCGATCG
ACGGCTTTAGAAGCCGTCGATTCGGCTGGCCTGGTTGGCAGCAAC
Done.