Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_065806
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: 274779
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:93676 original size:54 final size:54
Alignment explanation
Indices: 93612--93719 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
93602 TCCACCTAAC
*
93612 AAATATTTCTCCCATGAAGAAGATTGAGTGTTTGAAATCGAAGGAGATGTCGAG
1 AAATATTTCTCCCACGAAGAAGATTGAGTGTTTGAAATCGAAGGAGATGTCGAG
*
93666 AAATATTTCTCCCACGAAGAAGATTGAGTGTTTGAAATCGAAGGAGGTGTCGAG
1 AAATATTTCTCCCACGAAGAAGATTGAGTGTTTGAAATCGAAGGAGATGTCGAG
93720 CGGGAGTTCG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (54 bp):
AAATATTTCTCCCACGAAGAAGATTGAGTGTTTGAAATCGAAGGAGATGTCGAG
Left flanking sequence: Indices 93112 -- 93611
CTTTATATGTTCTTGATTCCGTGGCATTTGCCGTATTCAGGTCATGTAGCTTTCTCTCTAAAACC
GCAACTTTGAATTCCGCACCCCGGGAAGGGAGCAGGTAATCGCGAATTAATGTGTTTTGCCTTTG
TTCCCAGAACTGGTTTAAATCTAATTGCCCCATTCGATGAAAAATACGTCGCTTTATATCAATAA
TTCGATGGATCTCGTCATCGGAGACATTGTTCGGACCCTGTCGACCCAGAAAAAATCTATTCCTA
ATTACATCTTTGACTGATTCTAGATCTGGTTCCGCTGGCTGAATAGCCGGAAGCGGATTAGCAGC
AGCAGGGTGGGCAGCATTGGGAGCTGCAGGGTGCGGTGCTTCAGCCGCCGCGGGGGACTGGGGCT
GCGCCGGAGCCACGGAAGAGGCATTCTGTGGTCCTCTTCCAGACGGCCCCGCTTCATCCCTGGTT
TCGGGTGGGATGTTGCTTGTTTCGTCTTCCAGCGTTCCACCTAAC
Right flanking sequence: Indices 93720 -- 94219
CGGGAGTTCGACGGTAGCTTTCCGCTCTGAGCGGGCGGAGCGGCACTACTCGCTTCCTCGCCCGG
ATCAGCAAGGGAGCCGTGAGTCCGGTTACTCTCGCTACCATTCGCCCAAGAAAAGGAGTTTGGAA
TCTGACTTGGGCCTGACTCCTCACTATCATCGCAGCCGTAGATGTTTATCCCGTGTGTTGCGAGA
GCCAGACCCACAATAATTTGGATGCATTTCCAAATGACGGCTAAGTCGGTCAAGCTCCCTGCGCC
TGTCTGGTCCGATCGTTTAGGCATAGGCACCACTTTGCAGTAGATCTCTTCTTCCAAGTCCAAGT
CTTTTATCTGAGAATAGAACAGCTCTTCTGTGGAATATACAAGTTCCTCTAGTCTTTTTTTTTCC
CATTCTTTCATATGTTTAACGCGTGCTCACATTCTTTTAAGAAATTTTCTATTTCTATTTTTTTT
TCTTTCGTTAAGGGCCTTTTTAAGTCTTCTAGTAAGTCTGGTTTT
Found at i:201773 original size:17 final size:17
Alignment explanation
Indices: 201731--201773 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
201721 AAGGAAAAAG
*
201731 GATTCCCCG-AACAACG
1 GATTCCCCGAAACAACC
**
201747 GATTTTCCGAAACAACC
1 GATTCCCCGAAACAACC
201764 GATTCCCCGA
1 GATTCCCCGA
201774 CTCGAGTTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.30, C:0.35, G:0.16, T:0.19
Consensus pattern (17 bp):
GATTCCCCGAAACAACC
Left flanking sequence: Indices 201231 -- 201730
TCACTGCCAGGAGAATTGACTTACCTCCAGACTTTGAGTACTTTCTCCCTTGACCCAACATAAGG
GGGGACTCCTTGACTTTTACACAAAAGCTAAACTAAACAAGGGAAAGAAGGGTAACTCAGTTAGA
GCAACTTTAATTGGATTGGTTGGATCGACATCATCGAAAGCAACCCCAACTATATGGTTTACAAT
TCTCAAGAGAACAGAATGTGCTCAGCTTTGCAACTTCCACTCCTTCTCAATACCTATCCAAAAGA
GAAGCAGGGGCAGAAGCACTCGACTTAATTTAATAGGAGAGGAAAGAGCTGGAGTTGAACTCCCA
ATAGCGTAAGCAAACGATAAAGACATCTACTTAGCCTTCTTTATTGCCTCGAATGGACCGCCCTG
AAGGATACTCTTATTAGATCGTATTCAAATCTGAGGGGACTATTTGAAGATCTCAAGGTTGCGGC
AATCGAACGTAGGCGAAAGACTAGTTCAATTTTGAAAGGAAAAAG
Right flanking sequence: Indices 201774 -- 202273
CTCGAGTTATTCCACCAGACCGGTTTCAGTTTCCACGCCTTTTAGAGAACACTCTTCTGAAAGAC
CGTACAAATGGGGGTGATTCATACATATCTTCCCGCATTCAAGTCAGATAGAACTTTTGGGAAGC
TCCAGAATAGACTCCGTGACGTGATTGAGGATCCTTTTAGGCGAAAGCCCCCTATAGTCACCTAT
TAACATAACAGAAAGATGATGCCTTCGAAATGCGCTAACAATGCTCTAAGGAGCCTTTGAAAAGA
AGGAAAAGTACACCACCCTCTATGTGGGGGAAAATCGAGTATAGAATATGGAAAGTCAAAATCCA
TATGGGGGAAACCCCTAGAAAAATGGGTAAGTAGCGCTTCTCTAAATGATTACTAGTTTCCCATA
GCCGGTCTCTCTCCGCGTTGAGGTCTACATCAGACATAAATGCTTTCCCTGTCTTCCAAGGAAGA
AAATTGGATGAAAAAGAAAGCCTTGCCTATGGGGATAAGTTTTCA
Found at i:236805 original size:15 final size:15
Alignment explanation
Indices: 236782--236811 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
236772 CTGTAGAATG
236782 AAGTCAAGTAAGTAC
1 AAGTCAAGTAAGTAC
*
236797 AAGTTAAGTAAGTAC
1 AAGTCAAGTAAGTAC
236812 TATTTAGTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (15 bp):
AAGTCAAGTAAGTAC
Left flanking sequence: Indices 236282 -- 236781
TAAAATCCTTAACTTAAACCCGCTTTCGAAGAATCAGTTAAATTAGAAGAATTCATCCATTTCTT
AAGAAAAGTGGGCGTCATCGTCATTTGAAGCGTCCAATGGAAAATTGACTATCTAATCAGCGGAA
CGCGGCTTAAAACGATGATTTAAGGGCCTTTCTCGATTTGGAGACTTCGATTGAGATATTCCCCG
AGGGTATGGTACCTTTTCCATTGACTTCTCGACTGCTTCATCGGAGGAAGAATCAGGTGAAGAAA
GCCGGTTTTGTTGGTGAATCACCCTTTCCTTTCCCCTTGGCTTCTCCGCAAAGTTGGATCTGGCT
AAGCCTATTGAAATCTCGCTTACTTGGAACAGAACTATTAAAGCTAACGGCCGCCGCCTTGGAAT
CAGTTCTCCTAACGGCAGGCTCGGAACTAAGGGAACTAGGCGTGGTTGTAAATCCTTGACTCATG
GGTTGAAAATAAAATAAATGTCGTGGGTTGCGCCGCTGTAGAATG
Right flanking sequence: Indices 236812 -- 237311
TATTTAGTGGCCGGGAAAAAGGAAAGCAAGCAGGAAAGCCTTAACGTTCTTCCCTCTTATGGTCA
CTGCCATTCTGCTCAACACTTTAGTCCACCAGCCGCGGAGGGCATCCCTTCTCAGCTTTCCTTTG
ACAAGGGGCTTCGGTAAATCACTCCCGTCTGTGTTCGCTAGGATTACTTTCCCACCAAAAAGTTT
TCTTTATTACCTACGGCTTCTATTGTTCGGAGCCCATTTTCTACTTTCATATGTGTGTTTTGGCC
TTTCATATTCTTTTTCTTCTTTTGCCCGCTGGGGTGGAAACTGGTCTTGTCAATGAATTCTACTA
AGAAGAGTAAGGAAAAGAGGAAGCCGAGTGAAGGGCTTGATCGGTGTCACTACCCCGCTTCCGCT
TCCCAACGCCAGAAGTGTGTTTTTCCTAACGAGCCTAGCTGCCATTTCAGAGGATGGCACCTGTT
TTTCTCTTTCTTTCGTAAGCTGTTATAGTTTCAACTTCTTTCCAA
Found at i:271472 original size:19 final size:20
Alignment explanation
Indices: 271436--271473 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
271426 AAAAGAATAA
**
271436 AAGTAAAAAGGTGATGATGC
1 AAGTAAAAAGCCGATGATGC
271456 AAGTAAAAAGCCG-TGATG
1 AAGTAAAAAGCCGATGATG
271474 GGATTGGAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.45, C:0.08, G:0.29, T:0.18
Consensus pattern (20 bp):
AAGTAAAAAGCCGATGATGC
Left flanking sequence: Indices 270936 -- 271435
CTGCCCGGAGCGCGCCTCCCATAGAGGCAAGTGAATTTGGTGAGCCGTATGATGGGCAACTATCT
CCTGCGGTTCGGAGAGGACTCAGCTGTTAGTTAGTATCCCCTTACTTTCGGGGTGGACCCTTTCA
CTCTATTTTATTATATACGCTTAGCGAAAAGAATGTTTTTTGATACACCTAGGACATGGATTCTA
TATGAACCAATGGATCGTGACAAGTCGTTACTACTAGCAATGACTTCCTCTTTCATTACTTCATT
CTTTCCATATCCCTCTCCTTTGTTCTCAGTTACTCGTCAAATGGCACTCAGTTCATATCTTTAAG
TTCGATCATCGACAAGGTTCAAAGAAAGGGTGGGGTTCCTTATGCCGGTTCCCCCAGCATTCCAA
GACCACTTACGGTAAGCTTTGTCTTTCGCTGACGCTCCTATCAGAGGTATGAAGTAACTCGACTG
AAAGGAGAGGATGGATGGAATTGAGTACAGCCAACAAAAGAATAA
Right flanking sequence: Indices 271474 -- 271973
GGATTGGAGAAGGTAATGAAAGAAAGCAATTGACTATATACGCGACATTGGTTCAAGCCAAAAAT
GTGTTGTATTATTCCTTGGTCCAAAAAAAGAAAAAAGAAAACAATCCAAATTTAGGGCTGTGCCT
TTGTATCTGGTAACTAACACATTCTTCTACGGTTGAGACATAATTGAATAATGGAAGAAGTAGTA
ATAGCCATAAACTCGTCTACCAACTGAAAGCAAGTCCCCAACTATAATTCCAAAAAAGCCTCTCA
TTTTGAGAAAAGGATCTAGATCTCTATACTAAATAAGCCTAAATCGTCCGATATGCTCTATGGTG
GACTGATTCTCAGTGCCCGAAAAGGTGGAGAAGTCAGTCAGTACAGTCCGTCCCCGCCGGCATGA
AGGCCATTTCCCTCTCTGAGTCTCCCTCTAAGTCTTAAATCACTTCTCCTGAAGTCTTCCTTGAT
CCACTAGCTCTATCTCCTAGATGTAGGGACGCAAGAGAAGTAGGA
Done.