Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MZ951174
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: 336205
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Found at i:34222 original size:20 final size:20
Alignment explanation
Indices: 34197--34234 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34187 GTTGTCGCAA
* *
34197 CCCTTGTCTTGGCGTTCTTC
1 CCCTTGGCTTAGCGTTCTTC
34217 CCCTTGGCTTAGCGTTCT
1 CCCTTGGCTTAGCGTTCT
34235 GCCACACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.34, G:0.21, T:0.42
Consensus pattern (20 bp):
CCCTTGGCTTAGCGTTCTTC
Left flanking sequence: Indices 33697 -- 34196
CATTAAATCGACTCGTGTCTTGAAAGAAGAATCGAATAAATCTGAGACCCAAAAAGTTAAGACGT
CGGCCAGACCTTTGTCAGGCGTTTTGCGCAAGTGCTGGTGTTTCACTTTGGTGAATAAGACACCT
CCTGGAGTTGGATGCTTGGATAAGATCCTTTGAGCCCGGTGAGCGGGGGTCATTCACCTTTCTGG
GTATCAACAAATAATACAAAAAGAATTTCTGTGCAAGCCAATTAATTTGTTCCATACCCAAGAAA
GTATTATCCCACTTATGCTTATGCCATTCTATATGAACCTTGCGATTCAACAATTGGAAGTTATT
AACACAAAAAACCCTCTTATATATAATACTCATGTATTGATTTTATTTCGTTCTGCAACACAAAG
AATTAGCATTCTTTCTCATATTATATAACATATTTCTTTTTTTTTTTTTTTTAATCCGAGTAAAA
CCCTGGCTTTCCCTGAGGTTATTAATAAGATTTCAGTTGTCGCAA
Right flanking sequence: Indices 34235 -- 34734
GCCACACAAAGATCAGAGTAAAACCCTGAGCTCAGGTGTGGCACCCCACCCCACCCTATTTGGCG
TTCTGCCTCACAAAGATCTGAGTGAAACCCTGAGCTTATTAATACGATTTCAGGTGTCGCTACCC
TGGACCATCAGTCTCAGTCTGATTTAGACTTAACACCTGCTATGAGAGGTTTTCGGACACTATAT
CCATAAAACATACAGCAGGAGACCGGCATTTAATAGAGCTTTGTTCCTTTTAAGGTCTCTATCCG
TGGATTGAATAGAGCTTTGTTCCTGTGAAGGTCATTCTCTATCTAAGGATTTCCTAAGTGTATTA
AGCTTAGTGCCATTACCCAAAGACTTCATAATCCCTCCAGCATAGCATAGCCAGATTCATATAAT
CCCTCCAGCATAGCATAGCCAGAGAACGACATTAGTTTTACTCTAAAGGTGATCATAATGGTATG
TGTACTTTTTTCCTCATTTTGATCTATTGTCATTTATTTGATCAG
Found at i:52627 original size:18 final size:18
Alignment explanation
Indices: 52587--52629 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
52577 AGCGCCCTGC
52587 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
52606 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
52623 CATAGTC
1 CATAGTC
52630 AACAAGGTCA
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 52087 -- 52586
ACCCCCGAAAGGGCTGCCGTCCGATGGGTACACGAAAGTGACGAAGTTGCTTTGACTACAGAACC
ATGCCTGTCTGTTGGAGCGAATTGGATGATCGGGCCGAGCCCCCTCTTCCCCGTGCTCTCCTTTC
CCTAATATGAACCTCACGTCATCAATTTCTGACTCGGCCTGGCCCGGTCGCCCTACGCGACTGGC
GCTTCAAAAGGCGAAACTCTCGTCGTAGTTTGGCGACCTGACGGGGCTCCCACTTTTTGTTATCT
AAAGGCGAAGACTCAGAAGTGGGCGTCGACTCGGCCCAGCGGGCGAACATGCCGGGCTCCGGCTC
CGCGCACCTGCCCTTTCGAAGCACTTTCTAGTGTGCGCTTTAGTTTTCGAATGTGTTGTTCAGCG
TCACGAGTCTACAAGCCTTTCGTGTTTCAGTGCTCGCCTTCATAATCTTCAGTAGGGGCCGTCTA
GTCTTTTGATTAGAGTAGGGGTCGCGAGAGAGCAGAGCGCCCTGC
Right flanking sequence: Indices 52630 -- 53129
AACAAGGTCACAACTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATAGCCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACA
CGATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAGAAGTGTTATAAGCTTTG
AATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCG
CATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGA
AATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGT
Found at i:71621 original size:33 final size:33
Alignment explanation
Indices: 71579--71646 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
71569 ACAGAGGTGA
* *
71579 CTAATACAGACGACGAGAAAGAGAAACCGATAC
1 CTAATACAGACGACGAGAAAAAGAAACCGAAAC
71612 CTAATACAGACGACGAGAAAAAGAAACCGAAAC
1 CTAATACAGACGACGAGAAAAAGAAACCGAAAC
71645 CT
1 CT
71647 CCTTGAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.50, C:0.22, G:0.19, T:0.09
Consensus pattern (33 bp):
CTAATACAGACGACGAGAAAAAGAAACCGAAAC
Left flanking sequence: Indices 71079 -- 71578
TGCCCAGAGGAGGATGCTAGTGAGTTGTTAAGGAACTTCTTGCATTGCACATAGGGAAGGTGCGG
AGCGGTTCTTTATCTTATCATTGCCCTAAGGTAAGGCTTGGAACTGAACTGCAAGTATATAAGAA
AGGATATTGCTAAGAGTTAGCAGTCGAAGGGAGTTTGAACTGTGAAGGAATTACCGGTGCGCACA
GAGAAGGGGGAGAGAATACAGAAAATACGCCCTTGACTATACGGAGGATAAGAAATTAGGCAGGA
CTGATTTCCCTTCTTATCTTATTGTTGAGACAGGAAAGCAGTCAAGCGAGTCGACGCATCTATCA
GCAGTAGGAGTAGGACGTAGCGCATAAGAGGGTCTTAGGAATCGATCTAGATGCCCAGAAGAGGA
TGCTATCGAATGCCCTCTTTGACGGGCTTGTGCAAGAAGCCGATTATTCTACCATCTTTTCCAAT
AGTGCCATTTTATTGATGCTATCGAAGAAGAACCAACAGAGGTGA
Right flanking sequence: Indices 71647 -- 72146
CCTTGAAAGAAGGAAAAATGCCACATCAGTAAGAGAAGTGGGCAAAAAAGCTGCTCTCCTATTTG
GACCACCTTCCACCCTGTCTCCCTCTCCATACATACAGAACCGTAGTTTATGGTCTCTTGTGTTT
ACAGCCCATTCTTCACCTTTCCTATAGCCAGCAAATCAAGGAGATACGGCTTAAAAGCCTACGCG
CGTCAGGTTGTTCGGCTTCGGCCCTTCCTACACGTGACTACACGGAATTCACTTTACTTTACGGT
ACGGAACTAGATATGAATTTCATCCTCTGTTGGCGAGATCAGAGGCAACGGTGGCAGCAGCTGTG
GATTCTGTTGATTCTTCATCTCCTCGCTTGACGCTCTCTTCAATTGCAGATCCTGAACCTTCGGT
CAAGTTGCTTTTCTATCCTGAACTTTCGGCTAAAGTGGCTTCCTCCTCTCTTCTCTTGAACTTTC
GTTCAAGTGGCTTCCTGTAGGGGCCTTTGAACGGGCCTTGGTGGG
Found at i:153028 original size:13 final size:13
Alignment explanation
Indices: 153010--153035 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
153000 TAAGGAAGGC
153010 CTTGCCTTATTAG
1 CTTGCCTTATTAG
153023 CTTGCCTTATTAG
1 CTTGCCTTATTAG
153036 AGAGATATAG
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:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
CTTGCCTTATTAG
Left flanking sequence: Indices 152510 -- 153009
CTCAGACTCGCAGAAGACAAGTGAAAAGTATCTCGAGGTTTCTCCGCTTCTTGTTTCAAAATATC
GCAAAAATTCAGCGCTCTAAAAAAAAGGCCGGAAGGCCCCAGGACCCCCACCCCACGGCCCCTAT
GCCAAAGCAGTTGAGTGCAAGGAGGTCAGAGCAGAGGAGCTTCCCGGGTAGCAAGCTAGTTAGGA
GAGAATTCACCTATGGATTATTAAGTAGGTAGGAAAGCACGATAGGAGGCATGTCTCAGGCCTAG
GTGACAGCGGAGAACTTTAGAGGTAGGCTGGAAGGAAAGAGAAAGGCTAGGAGCTAGGCTAAATA
CGGAAGTCAATTCGTCTTTCGTCTGTATTGTGATCCCATGCCAGGACGAAGAAATCAAAGGATTT
ATAGTCATGCTCATGGAAGTATTGACTGGTTTAACGCTCATACCAATACGGCAGAGCATTTTTTC
TTAACTATTGAAAAAGCTCTTGATTTTTTCGGTTTTAAGGAAGGC
Right flanking sequence: Indices 153036 -- 153535
AGAGATATAGCCACCATAGACTAGCTCGTCCGTAGGGCTATGATCAGGCCATGCGGTCTAGAGAT
CTAGTTGACGCTTGGAAGAAACGGATATCCTTTCGAGAGAGAACGTGGCCATCCCGACCTGGAAG
GACTTTTATACTTCCTGCTTTGAGTGGGCCAGAAGCCAGAAAGACAGATCAGTTCGTTTGCAACA
GATCTTGGAAGAAAATCAACAGAAAGAAGGTTGAGTGATAGACGAGGGGTTGTTTTCAGATGACG
AAGTATTCGTCAGCGATAGGGCTTCGCGCCTGAGAACAAAAAAAATGAAGGAAAAAAAAAGGCTT
ACAGAGGATTTCCAATAAGAAAAGGAAGAAGACCCCCATAGAACTCAAAGCGGAGGGGCTCTTCC
TCAGAATGACGATGTGTGAGTTGCTTTTGTGAGGGGATAAAAGAGGTATGAAGAAAGTTGGCCAA
GGTCATAAGGTAAGGCCAAAGGTATTGGTGCATCTTTTTCTAGAA
Found at i:195734 original size:22 final size:22
Alignment explanation
Indices: 195695--195737 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
195685 CTTCATCCGA
*
195695 ATAAGGAAGAGACAGGTACAAT
1 ATAAGGAAGAAACAGGTACAAT
* *
195717 ATAAGGAATAAACTGGTACAA
1 ATAAGGAAGAAACAGGTACAA
195738 GGAGTCCAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.09, G:0.23, T:0.16
Consensus pattern (22 bp):
ATAAGGAAGAAACAGGTACAAT
Left flanking sequence: Indices 195195 -- 195694
GTGAAACAAAGGAATGCTCCGTCAATTAAGTATTACCGGGGCCCCTTCTCCCTTATTCGCTCCTA
GGAATTAAGGGGAATAGGGCGCCTCGATTCAGTAGTTACAGGCCCGGGGCCTATATCTAGATTAG
AGGAATTAAATCGAGGAAGAAAAGGGAGCTGCGGATAAGGACAAGTCCGATCAGAACTACTACAC
AACCTTCAATGACTCTAACAAAAAACCTTGATGAATTAGATTAGAAAGGAAAGAAAGAGAAAAGG
AAGAAGAAAAGAAATTATCCTAAGGAAATGAAACTAATAACAAATAGGATAATAGAGAGAAAGAA
CAACTTAAAGCTCATAGCATGCTAGCCGCCCTAGCTACTAGAGCGCTTAGCTAACAGCTCTTGGC
TCAGAAAGAATAGCTCCTAGGGCGAAAATTCTTTTATAAATTACCCGCTCAATCAGATAGGACGA
CCTACTCCTTAGTTGAACCGGACTTTGCCACTCACCTTCATCCGA
Right flanking sequence: Indices 195738 -- 196237
GGAGTCCAGCTGAACCACCCAGATCCGCTTCTTTCATCAAGCAACACAGCCTAGTCTAACCCGAG
CCCGAGTTCGTATTGGTAAATTTCGGGTCAGCAGGCAAAGGAAAGGGAACACCCACGTTCTACTT
TAATTAAGAGGTTTGTGGTACAGTACTCTTCCCATGTTAAACTGCCCTGCCTTTCTAAAGCTAAA
GGCCTGGTACATCTTTTTTTTTGAAACCTATTCTCGACCCGTATTCCTACCCCACCCACCGCTCT
TCCTTTGAGGCAAAAGTCTCTCTTATTCGACCAGAAGAGCCTTCTTCTTCATTTCACCTATGGAC
TTTTTCCACGTAGCAACTTCCATACTGCACGAAGTCTTCTTCGGGAATGGCTTACCGCTCCGTGG
GAATTGGATTGAGTCCCGCGCGCTCCTGAAATGGGGGCTCTTTCCTCGGTGCGAAGGATCAAACC
CTACGCCCACTGCCCTTGTTCCAAGATCTCACTTCATTCACGTAT
Found at i:202818 original size:19 final size:19
Alignment explanation
Indices: 202785--202823 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
202775 GAAGAAAGCG
** *
202785 TAAAAAAGAGCTTCCTCTA
1 TAAAAAAGAAATTCCCCTA
202804 TAAAAAAGAAATTCCCCTA
1 TAAAAAAGAAATTCCCCTA
202823 T
1 T
202824 CACCCGAGGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.26
Consensus pattern (19 bp):
TAAAAAAGAAATTCCCCTA
Left flanking sequence: Indices 202285 -- 202784
AGTGATTGTTAAAAAGCTTCCTTTAACAATTAGATTAGGATCGGAGAAGTAAGCCAAGTCAAGTC
AAGGAAGATGCCCACTACTTATATAATAATAAATTTCCAGCCTCTAAACTAAAGGCTTTGAGCAA
GAAAAGGGATTGATATAGAGCATCGTGCTGATCGATGCGCGAAATACCCGGTTTTATAGTAAAAA
GATCTGCTAGCTATGGAGAAAGTATCCCGTCGACCTTCCTTCGATGACATCTCTGGACCAAGGTT
CCGGGCGTAGAATCCGCGTTAGTATCTGAAATGGATCAGTAGTCTCTCACAGAGTCCTCTCTTAC
GCTTAAGGCATCAAAAATAGAAACGAATCTGAGCTGGCTTTCAAGAAGGTATGTATAGCAGTAAG
ACTCGTAGGCGGACTAAGAGCTCTTGTCTTAGGCTGTTCTCAAATCCACACTTTCGGAATAGAAT
GGCTTGTTTTCAAGGTAACTAGAAATTGCATAAGAGAAGAAAGCG
Right flanking sequence: Indices 202824 -- 203323
CACCCGAGGGAACTCACTTAATCCTCATCTCTTGAACTCACTGAAACCAAGCCAATGGAGATTGG
CGGGTAAGATGCTGGAAATAGACTTCGCCGAATCCCTTTTCATTACATCCAACCGTCTGCTACTT
CTGCTACCGCAGCCCTTGCGACTTGATTGGTCCCCTTCCACTTCCCCCATTGTCAACTCGCTTGC
CCCGGCGTGAAGAACTCTCTCACGGAAGTGACTTCGACCAAGCATCTCGATTCAACTACAAGCCT
GCTATTCACTCGCTTTCGACGTTTCAAGTCGGATCTTGCCTTCACTCCTAAAGGAAGAAAACCTC
ACCTCAGAGCTTCACAAGAGCAGTCGAAAGAGCAAACTGATTCAACTTGAGCTATTCTTATTATT
GTGACAAGATCTGGAATTGCCTCTACGCTTTTTTCCTTTGCAACTTGCTACTAATGTCATACCGC
ATTCAGTCTAATTGGCCCAGCTCTCCTCTTTTCTTTGGTCAAGCC
Found at i:237667 original size:25 final size:25
Alignment explanation
Indices: 237622--237669 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
237612 GAAGCGAGAC
*
237622 TCGACTGTTAAGGACCCAGAGGGGA
1 TCGACTGTTAAGGACACAGAGGGGA
* *
237647 TCGACTGTTAAGGAGAGAGAGGG
1 TCGACTGTTAAGGACACAGAGGG
237670 AAGCACAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.15, G:0.40, T:0.17
Consensus pattern (25 bp):
TCGACTGTTAAGGACACAGAGGGGA
Left flanking sequence: Indices 237122 -- 237621
GCATTCGCTGCATCTGACAGGGACGATTTCAGATAGGTAGGTTAGGTTGCTCGTTGTGGTTGCCC
GGACCTCGATCTAGATCCAAGATAAACCAAAAGCATGGGTCGTGGTCGGCAGAATCCTATATATC
TGCCGGGGCTTGGGCTTGACTTCTTTCTTCATGAATGATTTTGGAGAAGCCTGCCTCGAGAGAGA
CATATGGCATATCTGACTGCCTGATTGGCGAGCAGCTGTCCTCATTCATAAGTCCAAAGAACTAG
CAACCAAACTGGTGGCAAGCAGGAGAGTGACCAGGCCTGATACTGATTGAAACGTTTATTTAATT
GGAAGCCGTTCAGATAGCCCTAATTAGTTTTAATTAGTTTAGTGAATGTTGAGCTGTCATATCTA
GCTGCCATATATGTAAACATGCCCTAAAAGTAAAGGGATCATATTTCCTTTAGTAACCACTTTTA
CCCATCCGCTCTTCTCCTGACCGATTGGAGGAAGGGAAGCGAGAC
Right flanking sequence: Indices 237670 -- 238169
AAGCACAAGGTTGGTGACCCGGGGGAAAGCGAATGCAGATCTCACGCAAAGTGAAATCTCAAGAT
TCAGATTGGGTTTGTGTTCGGTGTGGAGTAGATAGGGCTATTCCTTAGCAAGGCTATTCAGTAAA
GGCGAGAAGGGATCTATAGCAAGGGCAGCCCGGGTCTACCCAAAGAAAGGCAGAGTTGAGGAAGA
TAGATCAAACAGCCTTAGCGCTTTAGCTTGAACTGTAACCTTACCCTCGCTACTGACCTGTCGCT
TGGCCCGAAAGACTGGAACTAGAAGTTCCTAGAAGTCAACTGTGCCTAGACCTCAATCAATACGC
TTACTGAGAGTACCGGTACCAGAACAAGAACAAGGATTTCTCTTTGGTCAAAGCCGCCGCACTTG
AACCGTAACCAGCTAATGCATCGCCTTCTATCTGCATTTCTAAGACCAGTCCCTTATTCCGCTAA
CCAATTAGGTTGGTTCATCAGGTGCCAAGGCATCTCTTTCTCCCA
Done.