Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_046466
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: 339352
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:1763 original size:13 final size:13
Alignment explanation
Indices: 1745--1770 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1735 TGGAGCCTTA
1745 CAACTTTATCAGC
1 CAACTTTATCAGC
1758 CAACTTTATCAGC
1 CAACTTTATCAGC
1771 TCAAGCAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (13 bp):
CAACTTTATCAGC
Left flanking sequence: Indices 1245 -- 1744
TTTCTTTATATACACAATTTTCAGTCTAGTTCGCCACAAGGCATGCAAGCAAGGAAGCTAGCCTA
TGTGGAAGAAAGAAAGAAGTAAAGCTGCACGCAATCCACAACCAAAAGAGAAAAGCCACTCACAC
TCACGGGACAAAGACTCTATTCCACAACTCCTGCAAGAGACGATTCGTTGATAACATCTGAAGCC
TATACTAATTAATATAAAGCCTGCTAAGAGGGGCCTTTCGCCGGTTCAAGTAATGGGAGGCCTTT
GCTGGTCAACTATTTTGAGGCCTTACGATTCACTCAATGGCAGAGGGATCTTGCTCGTCAACGTC
CGTTGCCGATCCGGTCATCTATCTCGGAGTCATCAACATCTGCTTTTCTTCGGGACAAGAATGGT
TATATCCTTGAGCTTATCGTACCTGTCGTCCAATCCATTAGCGTTGCCACCAGCCATTACGAAGA
GAGCCTTGGGGCATCCGCTTAAACCCTACTAGGCTTGGAGCCTTA
Right flanking sequence: Indices 1771 -- 2270
TCAAGCAATTTTTACCTTAGACTGAAGCGCATTCACTCACTCATAGGACGACCATCATGTACTTG
TACTCAAGTGACGATGAACACTGAACCTAACAGCCGAGGAGACGATCTCCGGTACCCATGAAGAG
TAGATTACCAATTCTGTCACCGCGTAATATAAAGTGTAGGGGGCTTTTATGATTACACTACTCAC
GAATCTATCTATCCAATTTCTTACTGAACTTGACTTGTCTCCGATTGCCATGCTGCGCTTTTCGC
TCCTTATCCCGTACAGAACGAAGTGAATCTTATTTAAACATTAATTGCTATGGGCCCTCTTATTG
CACTGAATGACGGATCACATGGGGTGGATCCTACTAATGCAATGTTTTCTCCGTGTAGTAAGGCA
TTTTTCACATCTAGCTTGTATAGGGACCACTTCTTTGATGCAGCAATAGCCAGTAAAGTCCTAAT
CTTCACAACTGGACTGAAGTTAAGGTTTCCTCCAAATCTATCCAA
Found at i:118276 original size:17 final size:17
Alignment explanation
Indices: 118250--118284 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
118240 GAGCCTCTTC
*
118250 CAAGACAAGATTATGGG
1 CAAGACAAGATTAGGGG
*
118267 CAAGAGAAGATTAGGGG
1 CAAGACAAGATTAGGGG
118284 C
1 C
118285 TATTCGAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.11, G:0.34, T:0.14
Consensus pattern (17 bp):
CAAGACAAGATTAGGGG
Left flanking sequence: Indices 117750 -- 118249
AGGCGTGGCCCCAGAAGTGCTTTTTCGGAGATAGCGAAAGAAGAGCTTAGCTTAGAAAGTAGTGT
CTCCAAAAGCCGGTCAAACCCGAAGCCCCTCTGGATTAAAAACTTAGCCTTTGAAACCCTCATTC
TCTTATTGTGCAGGCAAAGGCCTTCTTTTCTTCTCGCAACAGACGGTTCGATCAAAGAGTGCAGC
TGGCTAAGCCGCATCTTCTGCTTTAGTTTTAGCGCGAGTGCTTGAAAGTGACTGTCCCCCCTTCT
GCGGGAATGAATGAATGGGATAGTGGAAGGCTCTTTCTCTCTTTCTTTACATCCAATCGCTCTGG
CCTGCTATTGAAGGGATCATACTAATGCATTTCCCGAACAAGAAAAGAAGTAGGTCTTCCCCAGT
GCTGCTTTCTGCCTTCTCTTCGTAGTATCCTCCTAAGCCTAGTCCAGCTGTCCTTGTTATTGCCC
CTCCAGTTCTGGTTCCGGTTGCTGTGGGTCCAGTCGAGCCTCTTC
Right flanking sequence: Indices 118285 -- 118784
TATTCGAGTACTTCTTCCTCTCGAGATTGCTTTTCTTGTTATCAAAAGTAAGGGGCAGGATAAGA
AATAGAGAATCCCCCTATCGATCCCTATCGAGCCAGCCCAGGCTAGGAAATCTCCCTTAGTTTAA
TTAGTCTCTCCAACCCGCCTAGTCAAAAGCCCTTTTTTTGAGTTTCACCTGAATATAAAGAGACC
TTCTATTGGGAGGACTAGTCTTTTTGCGTAAGCCGCCTTGCTCTAAGAATCATCTCTTCTCCCCG
CGAGGGAGTAGCCTTTGCCAAAGAAGCGCTAATTACTTGTTGCATTGCCTGCGTTAGGAGATGAG
TGCACTTGAGAAGAATGAGACATGGGAAAAAGAAGTGAAAACTAAAAAGGGGCCAGAACATAAGG
AGGTGGTAGACAATTTAGAGAGCTTGGAGGAAAAGATCAAGACCATCAAGGGTATAGAGAGGCAC
CAAGTTCGCAGAGATCTGCTTCTTCTCAGACATCAAGCTCCCCCA
Found at i:144577 original size:13 final size:13
Alignment explanation
Indices: 144559--144585 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
144549 AACAGCCCTT
144559 TCTATGTTATTAG
1 TCTATGTTATTAG
144572 TCTATGTTATTAG
1 TCTATGTTATTAG
144585 T
1 T
144586 AAAGAGCTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (13 bp):
TCTATGTTATTAG
Left flanking sequence: Indices 144059 -- 144558
TTCCCTGTATTGGTTATGTTCTTCATTTCTCGTCTAGCAGAAACTAATCGAGCTCCGTTTGATCT
CCCAGAAGCGGAAGCTGAATCAGTTGCAGGCTATAATGTAGAATATGCGCGGGATGCGATCCTTA
ATTTAATATAATAGTCCACTGTTGGCGGAAGCCAATGTCCCGGGGTCCCGGGGACTCATTCTGAC
TGAAACAAGGGGTGGGTCTTTACCAACTTAAAAATAGAAGATTTTAGGTAAGCCAAAAAACGTGA
GCGCCCCTACGCGAGCCTTATTGAAAAGGCCCCTTACTATAGAACAAAGCAAGGGATTGAGCTGC
GCGAAAGCCTCCATTACTAATAAAGGGCTGCATCCGTTTTCTTGCTCGTTAGCGCTCCTTAGCAC
AAGCACTAAGTCAGAAACCTACCTTATTGAAAACTCAAGTAAAGCTATATATATGTATTCTATTA
ATGCGCTCAAGCATGCGAAGAAAGCAACAAGCGAGAACAGCCCTT
Right flanking sequence: Indices 144586 -- 145085
AAAGAGCTGTTCTTGCTTGTTTAGTAAAGTCACGCTTTTCATTTTGATAGGAGTAGGTGCTTGCT
GGGGCAGGGCACTCTTCATTCTTCATTCGAAACTAATGAATGTCGGGTCGGGGCTTTCTGCCTTG
TTATCAAAAAGGGAGTTGGGTAAAGCAAACTCCCTCCCTGGACGAGCACGGGGCTTAGTCAAGTA
GAACCGGGTTGCGCTGCTTGATGCTCCGATCGAAAACAAATCAGTGGGGCCATGCCGGTACGACT
GAATATGCGTTAAAAAGGTCAATCCCTCCCCTACGACACCAAAAAAAACCGGGCCGAACTTCTAA
CAGCCCGCCCGCTTCCATAGAACAATATCGTGGCAACGTAGACCTAAGTGGTCATATTGGATCTT
TGGGAACCATCACAAGTGCGGCCGGCCTATCTTTAAACGAGAATGCCGTGTCGTCCAGCGGAGCC
TAGAAGAAGGTGACTCGCGCAGACAGCTGACTCCTTCTTTTCAAT
Found at i:282425 original size:10 final size:10
Alignment explanation
Indices: 282410--282434 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
282400 TCTCGCCCAT
282410 AAGATAAGAG
1 AAGATAAGAG
282420 AAGATAAGAG
1 AAGATAAGAG
282430 AAGAT
1 AAGAT
282435 TGACCATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (10 bp):
AAGATAAGAG
Left flanking sequence: Indices 281910 -- 282409
TAACTACGATCTGTCTTCGGTGTTGATATGATCTTTCTATCAAGAAAAGATCGGGAATTGCCGCT
AGGCTTTTCTTTTAGCTCTCACTCATCCCGGGCGATTCTTATTATTTTTTTCTTTGTCACTAAGG
AAGGAGTAGTTGTGGCTTTTGACCAAGAGAACGAGCTAGACAGAAAAGGTACCACCGAAAGAAGG
TCGACCTCACCCCCTTTGGTAAACCGAAGCAGAGAAAGAGGAAGAAGCAAAGCTAGGCCATTCGA
TTAGGGATGTTCTCACCTATGCGTACTCTCTTGAATAAGGAATCTAAAAAAGAACCTTATTCTTT
TTCGCATCTCCCAAGTTCGAATGCTTTTATGCTGTTAAAAGAAATCGAATACCATTCGTGACCCA
ATTCAAAAACGGAGTGACTGAAGACCTCCTCCCCCTTTCCCGCCTATCCCTCCCGCAAGAGAGGA
CTCGTTCTGGCTTTAAAGAGCCTCTTTTTTAGCAGTCTCGCCCAT
Right flanking sequence: Indices 282435 -- 282934
TGACCATCTCTTCTTCCAAGCTTCTTTCTGCTTCTTCTCGGCGTAACGAAAGAACTAGATGAGGA
GAGGCCTCCGGTTTCAAATCCCTACCCTACGCCTTACGAGGGCGCCCTAGCCAGATTCACTCCCA
AGGGTCAATCAAGCCTTTTCAACTAGTTCAAATAGTCGTCACAGTCTTCGTTCCTGCTTTCAACG
AGACTTTCTTAGCTGCATCAGCTTGTAAAACTCTCTCTCCTTCACCAGGAAAGGGAGAGCGGACA
AAGTACCAGACGATTTGGGTTGGGTAAGAAGAGCGTACGATAAGAGTAAGCAGACGATGTCGATA
GAAGACGATTCGTGGGATCTTATCTTCCTCAAAGTCAAAGAAAGAGAAAAATGAGCTAAAGAAGG
TATGCCCAGCCCATGGAATTAGATGTCGAATGAGTACGATTTCGAGCATAAAGAGAGAAGAAAAA
GGAACTTTTTAGCAAGAATCTAGGTTTAGCAAGATAGCTGCCAGA
Found at i:295509 original size:12 final size:12
Alignment explanation
Indices: 295492--295516 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
295482 CGGACCCCTT
295492 ACGAGTGAGCAG
1 ACGAGTGAGCAG
295504 ACGAGTGAGCAG
1 ACGAGTGAGCAG
295516 A
1 A
295517 AAAGGGAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.40, T:0.08
Consensus pattern (12 bp):
ACGAGTGAGCAG
Left flanking sequence: Indices 294992 -- 295491
TGCTCATGGGCAGCTTATCTCTAATTGGATTTCCTTTTCTAACTGGATTTTATTCCAAAGATGTG
ATATTAGAGCTCGCTTACACTAAGTATACCATCAGTGGGAATTTTGCTTTCTGGTTGGGAAGTGT
CTCTGTCCTTTTCACTTCTTATTACTCTTTTCGTTCACTTTTTCTAACATTTCTAGTACCAACTA
ATTCATTCGGGCGAGACATCTTACGATGTCATGATGCGCCCATTCCTATGGCCATTCCTTTAATA
CTTCTGGCTCTCGGGAGTCTCTTTGTAGGATACTTGGCCAAAGTGTGACCCGTTAGCCCATAAGT
AAGTACTGTGACGAAGCGGCTGTTGCTCACCCGACACGATCGTACGAGGTCACAATTCACCCAAC
ACGATCATCCGGGGTGAACAAGAATTGGGGATCGGATGCGGGCGAAATTCCCGCCAATGGCTGAG
ATGTTCAGTCGACTCCCTCCCCCTTTGTGGGGGTCCGGACCCCTT
Right flanking sequence: Indices 295517 -- 296016
AAAGGGAGGAGGAAAGAGGCCCTGGCGAACCGTCATAATTAGTAAACAAGTGTAAGCTTCGCTGC
CCGACAGTATGGAGTACTGACCACACCGAGGGACAGGCCCTGAAGCGAAGGACAGGAACGAGCGG
AATCAATGTGTTCCAATTTCTGGCCTTGCACCGACCATCTAATGGACCATGGACTAAACGGCCAC
TGCCTGAAAGGACTATGCCCCGTGGACCGCCGCCCCCCCCACAAGGTACATCTCGCGCCTATGGG
CCGCTATAACTATCCAAGAAGACACTCGAAACTGGAAGGATAAACAAACCCACCCGGTGGACTGC
CGAGCTACAAGTCCCACGACACAGGAGCGGGATTCTCTAAAAAGCCAAGGTCGCGGGTGGCCAAG
AGGGCCCACTTGGAGACTTGGGATCTCAGCAGGAAATGCGAAGGTTGCTTAAAGCCGGCCGGCCG
ATAGGCGAAAGAGAATCAACTAGTTTAGTTCTGATCTGAGTAGGC
Found at i:328353 original size:18 final size:18
Alignment explanation
Indices: 328313--328355 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
328303 ACCGCCCTGC
328313 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
328332 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
328349 CATAGTC
1 CATAGTC
328356 AACAAGGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (18 bp):
CATAGTCGCGAGCTGTTT
Left flanking sequence: Indices 327813 -- 328312
TCAAGTGATTCACCGAAGCGACGAGACCTTGAAAGTTGCTTTTTCAAGTGTCAGTAGCGGGACGT
TCTGTCAATCGGGGAAGGTTTTTGGTGACAACACCTGGAGATATCAGAAGTGAGAATGCTGACAT
GAGTAACGAGAAATCCTGTGAAAAACACGATCGCCTGCCAGTGGAAGGCTTTCTGCGTTCAGTCA
ATCTACGCAGAGTGAATCGGTCCCTAAGGAAGCCCCGAAAGGGCTGCCGTCCGATGGGTACACGA
AAGTGACGAAGTTGCTTTGACTACAGAACCATGCCTGTCTGTTGGAGTTAATTGGATGATCGGGC
CGAGGGCTGCCCCCTCTTCCCCTCACTCTCCTTTCCCTAAGATGAACCTTGAGTCATCAAAGCCT
TTCTGACTCGGCCTGGCCCGGTCGCCCTACGCGACTGGCGCTTCAAAAGGTAGTTGACTTGCTTA
CTCGTTAGAGTAGGGGTCGCGAGAGAGCAGAGCGTACCGCCCTGC
Right flanking sequence: Indices 328356 -- 328855
AACAAGGTTGAAACTTCCAGGAAAAAACTTCGAAATGGGAGGGCGATCCTCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACAC
GATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAGAAGTGTTATAAGCTTTGA
ATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCGC
ATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGAA
ATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTA
Done.