Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_063517
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: 350377
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Found at i:168172 original size:27 final size:27
Alignment explanation
Indices: 168134--168196 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
168124 GCGCTTTTTA
* *
168134 GCTTTCGACCACGTATGCGGCGAAATG
1 GCTTTCGACCACGTACGCGGCGAAATC
168161 GCTTTCGACCACGTACGCGGCGAAATC
1 GCTTTCGACCACGTACGCGGCGAAATC
*
168188 GCGTTCGAC
1 GCTTTCGAC
168197 AGCAGGCGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.21, C:0.30, G:0.29, T:0.21
Consensus pattern (27 bp):
GCTTTCGACCACGTACGCGGCGAAATC
Left flanking sequence: Indices 167634 -- 168133
AAAGAGCAGCTTCAAGATCTACTCTTTAATCTTTAAAGGGGGAGAAGTTTCACCAAGGTTTTCGT
AAAATGAGGTGACTAATCAGAAGTTCAAGAAGTCGCTCTAGCTGCTCTTACTCTACCACAAAGAG
GCCATCTTGTTTGAATTGAAGTGCAAAGCCATGACTACTCTATTCCTAGAGACCTATGTACAGAT
GAAAACACGGACTCTCGATCATCTGTTCTACCTCTCTAAAAGGATGATACTTGTATTCTAGCTAT
CCGCATTCATAGAGATCCGGATCGATCCATGTGTTTTGGTATGATATATATAGATTCTTATATCC
GAAGAGATGCGAATCCGTATTAATTATACCTAGGAAGTCAAGGCGAAAGGATAGCTGCTAATAGG
ACCGCCTAAGAAAACACTCAGTGAAATCTGACACCCAGTCAGACTGAACCAAGAGGTAAAGGCTG
ACCAACTACCTAATACTACGCAGGCTCATCAAACAGCGCTTTTTA
Right flanking sequence: Indices 168197 -- 168696
AGCAGGCGCAGGTGCGGGCGGGCGCAGACGCGGCAGTCCCTCTGGTGGGGGTTGGGGAGCCTTTC
ACTCCCGTTTTCCATAAGGTGGACTCAAAGTGAAAGCCGAGGCTTTCACCCGAGAGAATCTTTTT
TACCAATAGCGAATGGAAGTATTGGGTCATAAGAGCCGACTCCCCATGCAAGAGCATGTTGGATA
TGACCACGCCGTAGATTAACACCCAATGCTCTTCTATGAGCCATTTAACGAACTCGAGTATAGGC
TGCAATTGAGGCATGATTGATTGACTGTAAATGCTTCCCTCCCGACAGCTGAACTCCGTCAAGCC
TCTAGAGTGTAATATAGTAACGTTTTCTGTTCTTGGTTGTTGACCAAAGAAAGACATGGGAAATA
TGTACCCGGGGAAGCGCCCTGGAAGCTACCTTCTCCCCTGGTGCGGAACGAAATCATAAATAAGC
TCTACCGTGGACTATCTGTGGGCCGTCGGTGCTCGCACTCAATGG
Found at i:174579 original size:11 final size:11
Alignment explanation
Indices: 174563--174591 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
174553 ACCTAGCCCT
174563 TCCTTCTATTA
1 TCCTTCTATTA
174574 TCCTTCTATTA
1 TCCTTCTATTA
174585 TCCTTCT
1 TCCTTCT
174592 CACTAGCAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.14, C:0.31, G:0.00, T:0.55
Consensus pattern (11 bp):
TCCTTCTATTA
Left flanking sequence: Indices 174063 -- 174562
AATGATGGCTGGAGAACTTTTCGTATCGTACAGAGGCTCCCGGCGATTGAGTGAGGGGGTCGATC
TTTCAGTCAAAGCGGCGGCACAAGTAGATGCAACCTTATGAAAATGAGGCTGCCTTCGCCTATGG
TACTACCGTAGCTACCAGATTCAAAGATGGGATACTTTTCGAATCTGCCATAAGGGAAACGCGGA
TGAAAGAACACTTTAAGAGGAAAGACTTTGAGTGGGCCAGTGAGCGGTGAATCTTAGGAGATTGA
AGATTGAGAAAGCTTTCTCGAGCAGGTAGAATTAGCAACTATATATAAAAGAAATAGAAAGTCAA
ACTCACCTATTAGGTAGTTAATGAAAGCTTCTACGCCCGAGAAGGAAAAGGCCCGCACGAAGCCA
AGCGCCAGCCACTAACTGATCGACTGACTGACTTGGGCTACCTTTAACCCTCTCCTCTGACCGCT
TGCTTTCTGGCCTTGCTCGCTTCCTTCACCGACAGACCTAGCCCT
Right flanking sequence: Indices 174592 -- 175091
CACTAGCAGGTGTGTAAATTCAACTTCTTGATCCCTCAGAAAGTCAACTCAGAAGTACTACTTAC
TCCTACTCTTCTTCTACTTATGTAATTCCTCAACAGGGTGGATTCTGCCTCTCCTAACTATGAGA
GATCGGAAAGGTTAGGTCAACCTATCACCTAGCTGTGGATTCGATAGCTGCTGATTCTAGCGCAT
GAAGCGATTCGGCGCCCCTTCTTATTCACTAGCAGCAAAGAGGGCAAGATCAGATATGTCTATTT
CTCCCACGAGTGCAGTCTCAGTCTAAAGAGATAAGCAGGAAGTTTAGGAGGTGTCACCGTCAATA
ACTCTGTATTGCACGGCTTGCATTAGGTTTTCTCTTTGCCGGAACAGATAAAACTAAAGGTTCTT
AGTTAGAGAAGGAAGTAGTCCTTGTCAGAGACTAGTACTTTTTTTTGAATCTTTGGAAAAGGTAG
GAACGGGTTATTTCGACTCGGAAGTTCTGATTGATTAGCGAGTAT
Found at i:333162 original size:7 final size:7
Alignment explanation
Indices: 333150--333174 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
333140 GCTCACTCCC
333150 TATATAG
1 TATATAG
333157 TATATAG
1 TATATAG
333164 TATATAG
1 TATATAG
333171 TATA
1 TATA
333175 GGACCAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (7 bp):
TATATAG
Left flanking sequence: Indices 332650 -- 333149
GGATAGATGGCTTTCAGGTCTTGACTCTGAGAACTCTACACTCACACCAAGATCACATCGGCTTG
CAACAAGGCCAATCATTGAAAGTCAATCGGGATTGATACCGCTATGAGGTATACATCAAATTTGC
ATCTAATCAACAAATCCATTAGCAATAAAAGTGGATTTTTGGTCTCGGTGGATACGAAGAGAATT
CATTTTTTGTATGAAGTGGATAAGCCCCAGGCTGTCAGCAGGCTCTTAAAAATACGGTGCAATAA
TAGGGATTGTTGTCCCTTCTTGGATGATTCTTTCTGCTCGGATGAGGCGTTGATTACTTATTCCA
TAAAGCTGGCCAGCGGCCATCCTCTCTTGGCAAGATCCGAGCTCTCTTCTCTTATTTAATGCTTT
GCACCTTTAAAACAAAGTCAAAGAGACTCTTTTTGCTAATATAGGAACTAGAGCTTCCCTTACTT
ATTTTAGAGCGTTCGTGCCCCTTGCGAAATGGTTCGCTCACTCCC
Right flanking sequence: Indices 333175 -- 333674
GGACCAAAGAAAGAAGAACATGCATATCTTTTTGAAGGATGGTGCGAAGATTGGGCGAACGATCG
ACAAAGCTGATTAGCTCTTCTGCTCTGTATCCAGGTGAGCTTCCTGACAGGCTCAACGTAGTTCG
GTTCACGAGGTGGAACGAGACATCTGGCTGCTCAATGAGGAAGGCCTCGACGGTCGTTCCCTGTT
CGACGTTCGATTGATTGGGGCCAGGCCATATGATGACACTTGGTCTGGTCCATTAGCGCTACATA
GCCCCATCCCACCAGCAGCGAGAACTGCTATCGAGAAGTTCGTTCCTCCAGCGGATCTCTTTGCT
TCCCCTGGGGGGCGGCCCTTCATAAATGATTTTTTTAATTATTCTGGATGGGAGGTATGCCCGTA
TGCTTGGCGAGGTCAAACAACAAATCATTTCCACCCCGCACTCTTTAAGGCTCCTTAAGGAGTGG
CATCTGACTTGATTCGCCTGCCTTGTCTTTCCAAATACCAAGATC
Found at i:342021 original size:15 final size:15
Alignment explanation
Indices: 342001--342030 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
341991 AGATCCGCTG
*
342001 CTAGTCTTTGCTTCA
1 CTAGTCCTTGCTTCA
342016 CTAGTCCTTGCTTCA
1 CTAGTCCTTGCTTCA
342031 GTTGGTCTAC
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:0.13, C:0.30, G:0.13, T:0.43
Consensus pattern (15 bp):
CTAGTCCTTGCTTCA
Left flanking sequence: Indices 341501 -- 342000
ATCCCGGGAGAAAGCAAGTTCAGTTAGCCCTTAGGCAGAAAGCCTTGAAGGAAAGATTCATTGGA
TGGTTCATTCCAGTCCAGTCTTCAGTCAGTCAAGTCATGGAATTGGCAGAAGTTCCCCCTTCCCC
GGAAATTCATTTTGAATTAAGCAATTCAGTCAGCTCTGAATCTGAATTCAATGATTGCAAGTCCA
AGTCCATCCAAGATCAGCTGTTCAATGAAACTCTGCCTTTAAGGCATGAAGCTGTGGGATGGGAT
CGAACTCCGGCTTTTCGGGTAGCTAACTCTCCGGTTTGGAATTCCTAGCCTGATGCTTTATAGTG
GCATAGAAAATCTGTTTTAGATCCCGAATCTACTGCCTTAGGAAAGGAAAGAGTCAACAGTAAGA
TCAATGTCGGAGAATCCGCTCTTGCCTTAGCTTAGGATGAGTTCATAGGCACAGTACAGGTTACG
TAGTCAGAGTGAACAAGATCCGATGTTCCAGATCCAGATCCGCTG
Right flanking sequence: Indices 342031 -- 342530
GTTGGTCTACCCACTGTTTGCAAGATCCAATATTATGCTTAACGCTCTCGAACACCATAGCGAAG
AAAGGGATTCTCCTCCACTTCTTTACCTACCTTACTTGACTACATTAATCAACTTAAGAATTATT
ACTGTTTTAGAAAAAACTTCTATTGAACGCTAGTCTTTCTCTTGTGAACGACTCCGCTGCAAAAA
GAGTAAGCGCTCTTTTCAATATCCGGTGTGTTCCTTTCCTTAGCCGGAGCAGTGAGCGAGTCTAC
CGAAAGCCAGTGTCCGGCTGGATTCCATCTGCTTCCTTCCCTCGATGGGTCTATACTTGGCTAAA
GTATGTAGCCTGGTATGCTAAGCTATCCCCCGAACCTGATATTTCCATTCAATGCTGGTTTGAGT
GCCCTTTAGTCTGTCTCGGAAGCACCTAAGGAAAGGGATGAAGCCATTATGAATCGTTAAACGTG
ATTTTATCAGTAAGAAGATAAAGTGCTGGCTATGAGACTCTATTT
Done.