Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MZ951176
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: 185591
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:12582 original size:18 final size:18
Alignment explanation
Indices: 12559--12597 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
12549 ACCAATATCA
12559 TTCCCATCTATACCTTCT
1 TTCCCATCTATACCTTCT
12577 TTCCCATCTATACCTTCT
1 TTCCCATCTATACCTTCT
12595 TTC
1 TTC
12598 TAATTTAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.46
Consensus pattern (18 bp):
TTCCCATCTATACCTTCT
Left flanking sequence: Indices 12059 -- 12558
CATTTCACCTCCCTTCTGGCGGAAAGCCCTTTCCAGATGGAGTAAGTAGTCCATGGAACGTTCAG
AATGTGGCTCGACTAAAAGGTTTACGGAGATGCGTACCCTTTAGGTAGGTAGGTAGGTAGGGGGA
GGTTCTTTCTGATGCTCGACCGTAGGGTACGAGCTCCATACTTGGAGCGAGAGGTCACGAGTAAG
GCTGCCCCTATTGCCTTTCTTTTTTGGTTTTGAAAACGGATCCCCATCCCGGGTGTGATGATGTC
AGGAAAGGGCCACGTCATCTAGAAGTCTGTCTACTTGATTTGATGAGTGAGGAATAAAAACCTTA
GCTAAAGGAAGCCTTAAGGCAACAAGAGGATAGGGTCACCTTTACCCCAGTATGCGAATCCAAGT
CAGACGATTGAGTCTCAGAGTCAGTTAAGAGAAAGCGAAGGAAAGGAAAACTTGGAAACATCCAC
TGACGGAATCTAACATAACACATCCATTTTGTTTGACCAATATCA
Right flanking sequence: Indices 12598 -- 13097
TAATTTAGCAGCCTTCTCGGATCAGAAACGGAGCAAAAGAGGTGCAGGAATCAAAGTGAAGTTAT
TCACCTTATTGTGGCTTAAAGTTTCTGAAGAGAAGAAAAGAGCACTGACTTTGACACCGGCAAGA
GAGGAAGGAAAGCGGTTTTCGGGTAGTTGCTAAGAGAGAATAGTCCGTGCGCCCTTTGAGAGAGG
AAAGACAGGAGGGCAGACGGTTGAATCATGAAGATTGTAAAGTGGCTGGATTACAAAGAAGTAGA
TCCGGGGAAGCGACCGGAACAATCGATATGAGAAGGAATGACCCGTCGGGTTGGGTCTTTCTCGA
TATGCTATCTCACAGCATTCAATCTTTCGACGTTGGTGAAAGACCGTCCGTCCAGATGAAAGTAT
GTCTACCTCCCTCCTTCTTGAACGTAATAAAGATGCTAATGAGCTGGCGCACTGAAAGACAGATT
ATGGAAGGGAATCGAGAGTACAGTTCATTCAAATAATGAATTCAC
Found at i:46266 original size:20 final size:20
Alignment explanation
Indices: 46230--46268 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
46220 AAGCTACTGG
46230 TTCTGTTCTGTCATACTCTA
1 TTCTGTTCTGTCATACTCTA
*
46250 TTCTAGTTCTTTC-TACTCT
1 TTCT-GTTCTGTCATACTCT
46269 CGAGTTACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.13, C:0.26, G:0.08, T:0.54
Consensus pattern (20 bp):
TTCTGTTCTGTCATACTCTA
Left flanking sequence: Indices 45730 -- 46229
ACTTTCTCTCCGGGCCAGTCCTAAAAGCCCATCAAATTACGCCTTTCCCTTCCCTCAAGAGCTAA
ATCGACTGCGGATCTTAGCAGCATCGCTTATTCCTCCATCTTCTTAAATAGAAATAGCATCGGAG
TCGTTCACTATTCTCTTTCTCGCTTTCTAGGTTTCGAAAGAGAATTAAGCAGAAGTGATCAACGA
AGACCTAAAAGCAGTTATATAAAGCACTGCTGCCATTTCCTTTGCTATCTTTCAGTCCTAAAGTG
AAAGTCAATCAAGAGGGTAAAGTAAACTCGATCTATCTTTCCGCCCGAACTTCTCACCTGGTATG
TCCTGTATGCCCTACCAGGGGAATCCTGGAGTTACTGAAGGATATTCTGATTCAAGCTCTGAACA
AAAGCTCATTCTTTTCTCTATTGTACCCTCATCGGCATCTCCTTACGCTGATTCAATAGCAGCTG
GATTGTGAACAAGAGCTGAAACACGTGAAAGCTCAAAGCTACTGG
Right flanking sequence: Indices 46269 -- 46768
CGAGTTACCTTTCGAGCAGACTCAGAAAAAGAAGAAGCCCACGAAGCGGTAGCAGCTACTTCTTC
TGCTTCTTCGGTTGTTGCCACCTAATTAGCTACGATCAATGAAAATATCGTAATATAAGAAAGCT
GTGCCACGAACAGCGCTTTGCCCCTTCTATATAAGCTGCACTACGCCGAATGATAAAGATTTCCT
GCTCCCATCTATTTGTTGTGGGGCATCCCATGCTTTCTGTTGGTCAACAACCAACAAGCAAACCT
TATCTATTGTTTACTCGTACAGGCTTGACGGAGTTAAGCGGAATCCTTTTTCTCAAATATCATGC
CTCAACTGGATAAATTTACTTATTTTACACAATTCTTCTGGTTATGCCTTTTCTTCTTTACTTTC
TATATAAAAATATGCAATGATGGAGATGGAGTACTTGGGATCAGCCGAATTCTAAAACTACGGAA
CCAACTCCTTTCACAACGGAGAAAGAAGATCTGGAGCAAGGACCC
Found at i:110013 original size:19 final size:19
Alignment explanation
Indices: 109978--110016 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
109968 GAGCAAGCCC
*
109978 AAACAGAAGCAACAAGAAA
1 AAACAGAAGCAAAAAGAAA
109997 AAACA-AAGCAAGAAAGAAA
1 AAACAGAAGCAA-AAAGAAA
110016 A
1 A
110017 CAGCTCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.72, C:0.13, G:0.15, T:0.00
Consensus pattern (19 bp):
AAACAGAAGCAAAAAGAAA
Left flanking sequence: Indices 109478 -- 109977
TTCACTGGTCGGAGGCTAAGAGCTTTCTTTGACTCTGAGTCATATGGGATGGGTCCCTACTCTCA
CTATGGCATAGTGGCCCAACGGTTCCTATGAAAGTCATAGCCGGACCTACTCTCCTCTCGCCGAT
GGTTTGAGAGTTGCGTTGGCGTGACGCTAATCTACTGATATTCGAGTGCTTGAGTTTCACTCATG
TAGAGATAACGAAGGGAAAGGGCATTTGAGGGAGAGCCCAACCCAAGGGAAGGGGCAAAGAAAGG
ACCTGAGCACATTGACATCGAAGAAAAGGCCAATGAAAATAGGGAAAGTCCTATTCAAGCCGCTT
TACCGACGAGGTTAAAGAGCGGTAGCCCCTCCTTCGAGCAAGCAAGCGGCACTAAAAGCAGGATG
AAAGCAAGCAAGGAGTGTAAGCCACTTGCCCGATAGGGTAAGGAGCGGAGACCCTTCCTTCATTC
ATTAAGTTTAGGGATTTGAGTCAGGGATAACAGAGGAGCAAGCCC
Right flanking sequence: Indices 110017 -- 110516
CAGCTCTTTGTCTTACTGTGCCCGAGGAAGGGAAGAAAGAAGATGACAGACAAAGCACAACGGAG
GAATGAACTTCAAGCATGGAGGGGGAAAGTAACGGCACTCAAAGCTGTCTTCCATCAACCAAGCA
TGAAACAGAAGCCATGGACTAAGATGACTGGACAGGAGCGATAAGCAGCTATCAGCCACTCGAAC
CAAGTTAGAGGTTTTTTTCATGAGAGTCTTTCTAACATTCTTCACCTGAACCCGGGAACAGCTTT
GACTTAGATACTCTATTGTCAGATAGTTGAATGGCACCGGGAATGGATTAGGGAGCAAAGGAGAT
TAGGGAAAGTCCTCTGAAAGCCCTTTTTCCAACTGAGAGGGGCAGGAGAAGGATAGAAAGGTAGT
TTCCTCCAGCAAGAGGGATGACTTCTTCCTTTCCGCAAATAACAAGCGCTTTTCTTCGCCACATC
GCGTATAACGGGAATCGAACCCCCCTGCTGCTGGCGGGCGGATGG
Found at i:168272 original size:11 final size:11
Alignment explanation
Indices: 168256--168285 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
168246 GACAAAGAGA
168256 AAGGAAAAGGG
1 AAGGAAAAGGG
168267 AAGGAAAAGGG
1 AAGGAAAAGGG
168278 AAGGAAAA
1 AAGGAAAA
168286 TACTGATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (11 bp):
AAGGAAAAGGG
Left flanking sequence: Indices 167756 -- 168255
GGACACTAGCTACCCTTTTCTAGATTTGTGGCGGGAGGCAGGAAACTCCGTCTATACCACAGACG
AGACCCGGGAGTCATAGTTCCAATAGCGAAGGAATTAGAACTATTGGCGGCCGCGAAGGATACGG
AACGTTTAGGCTAATGGTACTACTAGTCAACTACACTAGCGGACTATTTATGCGCTGACTGAACT
TGCTTCGTAGACAAGGTTCGTTCCGTAGCACGCTTCGGGCGAAGCCGGGGCCCGATTCCCTTGAC
CCCAAAATCTAGTTTTTATTCAAATCCCGACTCAACCCCTCACCCTGCCTGCACCACAACCACTA
TTACCCCTTACCAACCACCTCCCGTCTACAATCTTGATAAAGTCTCTTGGGAGAAAAGATACAGA
GAAGAGAGAAAGGGAAGATTGTGATGAGATTGGGAACATGACTCGCTCTGGCAGATGTTTTAAGC
CAGACAACCTGAAAACAGATGGAAATAAAGAAAAAGACAAAGAGA
Right flanking sequence: Indices 168286 -- 168785
TACTGATGCTTTTCTCAAGGAAATCCAGAGGTCGGAATAGAATGCGGCTGAACAGTTTAGCAAAG
CCCCTGCCCAAATTTCGATCTTAGGTCTTCTTTTAACTTCAGAGTGAGAATAAATGATGGAAAAA
TTTCGGAATGCACATGTCACCCCAGACATTTCACCCAAGAGATTGGCCAGGTTAGTGGGACAGAT
TTTGGCTCAGCTTCAACCTCATGAGAGGTGATTGCACCAGTAGCAAAAGAGATCTCAGGATAAAG
AGGTACCATATCATATGTGTAACGAAAACGGACATGACACAGCAAGTTGCTAGTATAACTTGTTC
GCACAGGGGTCTGAAAGCTTTTCAGTCAAGACTGGTCGGGGCTCTGGAGAGGAAGAATCTACATC
GATCACGATGCGAGCAACAAGGTAATGGTGTCCGAAAGACAGATCTCATCACAGCACTTGCTTTC
CCTAAACTATCTATCTTTAGAAGAGCAAAACTTCAAGAGGGAATT
Done.