Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MZ240733
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: 151252
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Found at i:21174 original size:18 final size:18
Alignment explanation
Indices: 21151--21187 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
21141 CCTAGGGTAA
*
21151 GGTCCACCCCATGGATCG
1 GGTCCACCCCACGGATCG
*
21169 GGTCCACCTCACGGATCG
1 GGTCCACCCCACGGATCG
21187 G
1 G
21188 AGTTGCTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.16, C:0.38, G:0.30, T:0.16
Consensus pattern (18 bp):
GGTCCACCCCACGGATCG
Left flanking sequence: Indices 20651 -- 21150
GGGTGGGTCACTACTTCTGTTACTTGTTCGTTTTTCTTGGAATCCGTGAAATTCTATGCGCCGGA
ACGGAATTGACTGCGGAGCTATATAGAAGGCACTAATGGGTATTAGGGCCAAGCAATTTAAAGGA
AGCTTTTTCGGACTTCAAGGGCGTGTGAGAGGACCCCTTTTCAGTTCCAAACCGGTACCAAGGAA
GCGGGCACTACACTAAAAGGTATAGGTGTTCCTACCCAAATTACCTATCCACTGACTATAACAAT
ATGTTCTATATGTGTCTGTAGCTTAGCGCAACAAAAAACATAATCAAACTCTTTTAGTAATAGGC
CCGCCTATTGCTACTAAGAACACCTTTCGGGGGGAATATAATAAACCTGTGTGAAACCCCAGCAA
GCTTCAAGAAAACAGGGTTAATGAATACATATCAAAAGGTCCAATTAAATAAAACATCATGAACA
ACTATACCTTAATAGTAGGTAGACTAGGAGTATATCCTAGGGTAA
Right flanking sequence: Indices 21188 -- 21687
AGTTGCTTACCTTATAAAGCAGTTATTACGAGAGTATACTACCCTAAAGGGGTATCATGCATTTC
AAGTTAGTGTAGGGTCCAGCCCTAATCTAATATAGGCTCTTCTGTTAGTAATTCGGCGAGTCGTA
GGATTCATTCTGAAAAAAGAAGTCCAAGGGAGGCCCTAATCAAGCCTTTTTTCCGACGCTATACT
AGCCTTAATATAATATAATTTTTAGTATTTAATAATCCATTTATTCTTAGAAATTGGAGTCGTTT
AATGGATATGCAGGGTTCTGAGCTATTCTATAATCTATATACGGGGTCGCTCCTAGCGGAAAACG
AGTGGAGCCATACGCTCGATCCTGTGATTATGTGATTATATCGTTAGAGGTCCTGCGTGTATTAT
ACCGCTATGCTTACAATATGGATTCAGACTACATTAAGTTCACCATAGGTTTAGTGGTTGAAACC
TCCTCCGGTATATATAGATTAACCGTTGGAAAGGCTATTCCCTTG
Found at i:34809 original size:8 final size:8
Alignment explanation
Indices: 34790--34852 Score: 76
Period size: 8 Copynumber: 7.9 Consensus size: 8
34780 GTCTACTACA
34790 TATATAAAT
1 TATAT-AAT
34799 TATATAAT
1 TATATAAT
34807 TATATAA-
1 TATATAAT
34814 TATATAAAT
1 TATAT-AAT
34823 TATATAA-
1 TATATAAT
*
34830 AATATAAT
1 TATATAAT
*
34838 AATATAAT
1 TATATAAT
34846 TATATAA
1 TATATAA
34853 ATAGTATATC
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
7 11 0.22
8 28 0.57
9 10 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
TATATAAT
Left flanking sequence: Indices 34290 -- 34789
CGTGAACTTAACTTGGTGATTATGTTCACCCCCGGTCTAGCTATCGGAAAAGGATGCCGGACCTT
CTTCTGGAAGCGGGAAGGTTAGTCACCGCATTGACTCGAATGATCTAGCCAATCATTTCTCCCAG
TAGGCTATTATTCATCACTCTTCGCTTTACCGCCCCGTGGGTTTCGGCTTAGTTAGGAAGAAAGA
ATTGTTAACAAGTCTATGAGCTTCTTCTATGGCATGCCGCCTTTCCTACTACCGCAGAAGCCGCG
TTATATGTTAAGTTAATAAGAAGCCGTTGCTTGTTTGCTTAAAAGCTTAAAAATGAAGACTAATA
CAGGAGTTTCGTGGAAAATAAAAAAGCCCTTTATCGGCGATGACTTAAGCCTCTTTCTTATTCTT
ATAGGGCGTTTAAAGAGCGTGACTCTTTACTTTAGTTTAATACATTTTCACTTAATTAGTTAAGC
CCATTTGATTCAATTCATGAATTAGCCCACTATGAGTCTACTACA
Right flanking sequence: Indices 34853 -- 35352
ATAGTATATCATTCGTGTCTTTGTTACGGCGAAACCGAATAAAAAGAAGAAAATTAGAATTTAAT
TTTAGGCTGTACACCTAATTTTCCTGGGATTGTAGTTCAATCGGTTAGAGCACCGCCCTGTCAAG
GCGGAAGCTGCGGGTTCGAGCCCCGTCAGTCCCGACGGATTAAATAAATATATCAATTCATCTCT
CCATTTTCTGTGAAAAGGGGGACGGGGAGCATAATTTCATTCTCAACGGGGGATCTCTTTTTTTC
CTTTTTCGCTTCGCATTTCCACAAAAAAGGGATTTTTTCATTACTTCAACTAGTACCGATTGATG
GGAGAGAGACATATGTGGATTAGTACAATTATTGGCATATTCAGGATTCCAAGAGAGACTGGGTC
TGGTTTTTTGACCCGATCCATGTATGTAATGGAATAGAGTACCATATGTTTCTCGGGAGCACATA
CACAAATGGAATTCGTTTCTTGTACGATACAAAATAAATTTAACT
Found at i:34821 original size:24 final size:23
Alignment explanation
Indices: 34789--34853 Score: 96
Period size: 23 Copynumber: 2.8 Consensus size: 23
34779 AGTCTACTAC
*
34789 ATATATAAATTATATAATTATATA
1 ATATATAAATTATATAA-AATATA
34813 ATATATAAATTATATAAAATATA
1 ATATATAAATTATATAAAATATA
34836 ATA-ATATAATTATATAAA
1 ATATATA-AATTATATAAA
34854 TAGTATATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
22 3 0.08
23 19 0.49
24 17 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATATATAAATTATATAAAATATA
Left flanking sequence: Indices 34289 -- 34788
TCGTGAACTTAACTTGGTGATTATGTTCACCCCCGGTCTAGCTATCGGAAAAGGATGCCGGACCT
TCTTCTGGAAGCGGGAAGGTTAGTCACCGCATTGACTCGAATGATCTAGCCAATCATTTCTCCCA
GTAGGCTATTATTCATCACTCTTCGCTTTACCGCCCCGTGGGTTTCGGCTTAGTTAGGAAGAAAG
AATTGTTAACAAGTCTATGAGCTTCTTCTATGGCATGCCGCCTTTCCTACTACCGCAGAAGCCGC
GTTATATGTTAAGTTAATAAGAAGCCGTTGCTTGTTTGCTTAAAAGCTTAAAAATGAAGACTAAT
ACAGGAGTTTCGTGGAAAATAAAAAAGCCCTTTATCGGCGATGACTTAAGCCTCTTTCTTATTCT
TATAGGGCGTTTAAAGAGCGTGACTCTTTACTTTAGTTTAATACATTTTCACTTAATTAGTTAAG
CCCATTTGATTCAATTCATGAATTAGCCCACTATGAGTCTACTAC
Right flanking sequence: Indices 34854 -- 35353
TAGTATATCATTCGTGTCTTTGTTACGGCGAAACCGAATAAAAAGAAGAAAATTAGAATTTAATT
TTAGGCTGTACACCTAATTTTCCTGGGATTGTAGTTCAATCGGTTAGAGCACCGCCCTGTCAAGG
CGGAAGCTGCGGGTTCGAGCCCCGTCAGTCCCGACGGATTAAATAAATATATCAATTCATCTCTC
CATTTTCTGTGAAAAGGGGGACGGGGAGCATAATTTCATTCTCAACGGGGGATCTCTTTTTTTCC
TTTTTCGCTTCGCATTTCCACAAAAAAGGGATTTTTTCATTACTTCAACTAGTACCGATTGATGG
GAGAGAGACATATGTGGATTAGTACAATTATTGGCATATTCAGGATTCCAAGAGAGACTGGGTCT
GGTTTTTTGACCCGATCCATGTATGTAATGGAATAGAGTACCATATGTTTCTCGGGAGCACATAC
ACAAATGGAATTCGTTTCTTGTACGATACAAAATAAATTTAACTA
Found at i:55635 original size:21 final size:21
Alignment explanation
Indices: 55595--55636 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
55585 GGTTGGTATG
**
55595 CACCATACTCTATTTTCGTAA
1 CACCATACTCTATTCGCGTAA
55616 CACCATACTCTATTCGCGTAA
1 CACCATACTCTATTCGCGTAA
55637 GATGATACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.33
Consensus pattern (21 bp):
CACCATACTCTATTCGCGTAA
Left flanking sequence: Indices 55095 -- 55594
GTATTTTCCTTCCTATTTGAGTTCTTCATTTCCCCATTCCCCCCTACATGACTTTCTCGAACCCG
TCTAAGTAATGTGCGCAGTACAAAGTTTTGGTTGGCTCATTCGAACTAAGTATCTTCCAAATAAA
TGTTAGAATTCCACTGAATGCTTTTTTGTTAGCCTATCCTATCAAAAATTCTCTAAATAAGACCT
GGTTCATCTAGAGCAGAACGTACAATTCTGGAATATAAGTCAAAATTATTTTCTTATCATTCAAT
GAGCGTCTTGTATTTCATAAAAATGCGGGGCAACGTAATCCTTACGTAAGGGCCATCCTATCCAA
CTTTCAGGCATTAAGATACGTTTCAAGCGCGGATGATTATCATAAGAAATTCCCAGCATATCATA
AGACTCTCGTTCTTGAAAATCCGCACTTTTCCAAATCCAGAAAACAGAGGGAATTCGAGGATTAT
TCCTTGAGGAAAATACTTTTATGCATACCTCTTCCGGTTGGTATG
Right flanking sequence: Indices 55637 -- 56136
GATGATACACACTAGCTAACAGTCCGCCAGGTGCTACATCATAGGCGCATTGAGAGCGTAGATAA
TTGTAACCATATACATATAAAATGATCGCAACGGAATACCAATCCTCGGGCTTGATTTGTAAAGT
CTCTATTCCTTGGTAATCAAAGCCCAAAGATCTATGAATTATCCCATGCTTGACTAGCCAACCAG
ACAAACAACTCTGCATCTTTTTTCTCTCTCCTTCATTTTGATTTGTATAAGTATTTCTTGCGATG
AAATTGATGAAGATTTACCTACTATTTTTTATTCTGTACAAAAGAATCCTGCCTAATTCCCTAAT
TCGTGGGAAGATACTGAATTTTTGTATGTGAAAAGCGTTTCCGTCTCAGTAGGAATCTCTGAAGT
AGATGGTGGTTGAGAAATGAATCTTTGATCAAAATTTCCAGTATGAATACTGCGTCCAACACGAA
ACTTGTGATTGGTAGTAAAACACCGATTCGCTCGTGAAGACTTAA
Found at i:61870 original size:21 final size:20
Alignment explanation
Indices: 61829--61870 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
61819 TATTAAGTAG
*
61829 ATTTAATATTATTATTTATA
1 ATTTAATATTATAATTTATA
61849 ATTTAAGTATT-TAATTTGATA
1 ATTTAA-TATTATAATTT-ATA
61870 A
1 A
61871 ATATCGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
ATTTAATATTATAATTTATA
Left flanking sequence: Indices 61329 -- 61828
AAGCGTATATCTTACCAGGAAAGCAATTCTTCCATCTTGAAGTCCTAATAGAATTTCGTAATCGT
TCCCAGTAACCATAATTTTGGATAGACGAATACGCCCTTCTTCTTTGATTTATCTGTGTTTGAAA
TGTCATGCACTTTCTCTGCAACTTCAAGTCAATCAACTCCTTGCTCTGCCACTTCCTATCAACCA
AATGCTTTCTCTTCCACTTAGATGAAACCAAATACTTTCTCTGACCTATTAATCCATTTATCTTA
CTATACAGCCTTCGACGCATAATGCTATCAATCTCTCTCCTAGTGTGAAATCCTCCCCTTTTGTT
AATCGCTGGGAGCGCTGAGCGATACCCTCCTATTTTATTGTTCGCTCGGAAGGTGATGCGATTCA
TTGTGCTAAAAGTCATGATATTCTTATACTTATACAATTCTTGGGGAGCTATTTTCCCCTAAAGA
GAGCCAAGTTATACTTGTTAAATTAAAAATAATAATATTAAGTAG
Right flanking sequence: Indices 61871 -- 62370
ATATCGTATATAAGGATAAGACTACATCCATATCAGAAATGAAATTCAAGCTCTGATAGTCGATC
GAGTAATCTGCGCCCAGTAGAGCTTAGCCAAGAGTAGACCGAAATGGTCTCGCGAAGCCGGTCCC
CGCGTGATGAAGATCCTTGATGAGCTTGATTTCTTGAAAGATTGGGTTAGTGTTCAGTGTGCTCA
AAGTCAATCTTAAATTTTCATTGTACAAGAAGCAAGGGGAGACGAAGTCTTCTTACTCACGCACA
ACGGCTTATAAATACGATATAGCGGATTCCTTGGTTCTTAAATTTTCATTGTACCTTGATAGTCC
GGGAGGCTTAACTAAACAACAACAAAGAAAATTTAAATAAGATATTTTTTTGTGCTAATCTAATA
GAAGTCAAGGCCGAACGTAGGTGCTACACCGAGATTTAATAGCATACCATACATTATGGTAATCC
CTAGGTTTCAGTCCTTCCAGCCTTTGTGGATCTAGTAGGGGCTTA
Found at i:76340 original size:17 final size:17
Alignment explanation
Indices: 76297--76342 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
76287 GCAGTAAATG
*
76297 GAATAAACTAAGCAAGA
1 GAATAAACTAACCAAGA
*
76314 G-ATCAACTAACCAAGA
1 GAATAAACTAACCAAGA
*
76330 GAATGAACTAACC
1 GAATAAACTAACC
76343 CCAAGGGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.52, C:0.20, G:0.15, T:0.13
Consensus pattern (17 bp):
GAATAAACTAACCAAGA
Left flanking sequence: Indices 75797 -- 76296
GAACTAAAGGAATGTCTCTAAGCAGCCAAGGCCAAGAGCAAGCAGGAGTGGTCCTATCTGCCTAG
AAGGATTCGATAAAGAGAATGTGAGTGGGCGGGGGATCAATGGACACAGAAAGAGAAGAGCAAAA
GGAGCAGAAGGCACAAAGTTTTTTATGTGAAATCAAGGAGCAGCAGGTTACACTTTTACACTTTC
CCGAAGAGAGCTCAAAGCAATAAGATGAAAGATGGGATGAGATGCTAGCCTTAGCGCAGAAGATC
AATCATTGAGCCTTAGGCCACTACCGAGCAGCAATGGAGGATCATAACACTTGAGAGATGATCCC
TACTTGAAAAGGCGGAGACATCTTGTTGCGAGAAATCGAGTTTAAAAAGCCCATTTATCAATCAC
ATTTTCAGGCACACCAGTCAAAGAGCCATCGGACCCATGAAAGTCCCCTTTTTTTACTAATATAC
AAGGCCTTTGCCGGGATGTCTTTCTCAAAAGAGGGGCAGTAAATG
Right flanking sequence: Indices 76343 -- 76842
CCAAGGGATGATCTCGGATTGAAATCCAAGGCATGGTCCCATTGAAAGCCCAGGGAATAATTCCT
AAAACAGAAAAAAAAATAGGATTTAAATAAAGTCCAAGGGGGTATGATCCCAATAAAGATAGGAT
GGATTGTCAGTAATTTTGGACGAAGCAGCGGGCATACCAGAAATGGATTGTCAGGAATGGTAGAT
GGAGCAAGAACTAGCATGAAATACGAACAACCCTGAATTCACTTTTCACTCTATGTGATATTTAA
TATCCGCTCACTTTGAACTTGAGAAAGAACTTGCCTCTCACTCTAGGAAGAAAAGCCTTGCACCT
TGCGCTGAGAAAGGCAAAGCTTACCTTCTTTCAAAGGTCTTCCCCGCCTCTACCGCTGGTGAGAT
CTCTGCTTGAAAGACCTTAATCATTCTTTTTTTGGATCGTTTTGAGGGCTGTTCTAGATGGATGC
ACCACAAGACCTCTCGCGGATGCTTACCTAAGCTACGGAACTAAA
Found at i:90865 original size:37 final size:37
Alignment explanation
Indices: 90814--90887 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
90804 ATGGCTTCCC
90814 TTCAAAGCCGAAATTTAACTTTACAAGTGGGTCCCAT
1 TTCAAAGCCGAAATTTAACTTTACAAGTGGGTCCCAT
* *
90851 TTCAAAGTCTAAATTTAACTTTACAAGTGGGTCCCAT
1 TTCAAAGCCGAAATTTAACTTTACAAGTGGGTCCCAT
90888 GGATGAGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (37 bp):
TTCAAAGCCGAAATTTAACTTTACAAGTGGGTCCCAT
Left flanking sequence: Indices 90314 -- 90813
GGTGCGGAAAAACCAAAATCGAGATGAATGGAAGATGCCTATGGAACTCGGTCAGGAGAGGTTTA
TCCTTTGCCTCAATGATGGCCTTTTTGATCTCATTCTCTGATCGATTTTCATTCAACCAACTATC
TTTTTGAAGCAGATAGTGAACAGTGCTTATTCTATAGATACTGTAAAAGCAAACTCATGGTTTTT
CCTACAAAGATGAAAAAGCGAAAACTGGTGGATCTTACTCTTAGCCTTTCCTGCTTTACTGCTTG
GAGGAAGAGAATCAGCTGTTACAGACCCGGCTGTGAAAGAAGGCAAGTCTGCTGACTTGGCTTTT
GAAGGACAACTTCCCAGTTAATGTACGAACAGGGGACTAGAAGAAAGAAGCCAACAATCCTATGC
TAAAGGAAGAAAAAACGTATATCTTGATCTTAAGTATGAAAGGGGCCCCCTAATGCCCATATTAG
CGAAATCTGACTTAATAGGAACTTCACTTGCCTCTATGGCTTCCC
Right flanking sequence: Indices 90888 -- 91387
GGATGAGAAGAATACAATTTAGGAGTCCCTTGGATAAGAAATTAAAATAAATCCGTAAAAAGCTT
AAAGACCAAGAAAACTCCTGCGCGGCTAACGCTAGCTTATACTATTCTAAGCTTTCGCGTCAGCC
CTTGCTTGGAATTCGGATAAGCAAAGGAGAGTACGAATTAGAGCCTCACATTGCATCACAACTGC
GCACTTCCCCATATTAAAATCTCACCTTCCAGCAGCTCCATAAATTCCTAGGGATCGTAATCAAT
TAAATGTAATACTTTATTTAATTAAAGGAAGATCGATCTTTCTTCTTCAAGCTCATGAAAAAGAA
GAATCCTCTAGCATGGACAGATGACCACAGAGCAAGAGAGCAGGGGTGAAAAAGCTTGAATCTTT
GGCACATAACTTGCCACCAATCAATCTTCCGTACCAAAGGTCAAAAAATCTTGCAGACTGAAGAG
ACTATTAATAAAAATGCTATCATAAACAAGACGACAGAGGAAGCA
Done.