Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MT075726
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: 78009
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:34130 original size:15 final size:15
Alignment explanation
Indices: 34110--34139 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34100 GTGTTTGCAC
*
34110 CTTGTATTTTGAATG
1 CTTGTAGTTTGAATG
34125 CTTGTAGTTTGAATG
1 CTTGTAGTTTGAATG
34140 TTTGAATTGA
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:0.20, C:0.07, G:0.23, T:0.50
Consensus pattern (15 bp):
CTTGTAGTTTGAATG
Left flanking sequence: Indices 33610 -- 34109
AGATTGGCATACGATGATTATGGCAGGCATAATCCAAGCATGGTCCATGTTCACCAAACCCGATG
AAGAAGCTCCAGCTCAGAAAGAGCAAGCGAAACGGGGGGCTACAGATTGACAGCCCAGGGAAAAG
CAAACCCCAGTTCAGCTGAATCAGACTAAAGAAGATGCGCGGAAAGTCTTGACCAAAGACGAGCT
GAAAGCAATCAAAGAACAGGTAAAGGCTGCGCTAAACCTCAACTACTAGATAACAGTCTAAGAAG
AAGCAGAAGAAAGGTTGGAGAGGAGTTAACCCTACACATCCTCCGTCACCTTGGAAACCTCCACC
GGAGAAGCCCACCTAAAGACTGACCAGAGGTCCCTAAGTATTATATAAGCAGGGGTGGGAAGTGG
GGATGCACTGCGAAGGAAGCGTGGTAGCACAACAAAAGCATGGGTAAAGCACAGGGCAGGTTCAG
CCGGTGCAGCTAACGAGCTAATCGAAGAGCTCTTGGTGTTTGCAC
Right flanking sequence: Indices 34140 -- 34639
TTTGAATTGACTAGTCAAGTAATAGGTACCGGACAACACCCTATAGAGGTAAGAAAGATGTATCC
CCTCTATCTCTACTCTAAAGGGGCTTACGCACTTCGATTCGCTCTGTATGCACCAAAATCCAATC
ATTGTGTATACAGCTGTGGTGGCTCCTTTCATTTATTTCATTTAGAGTTGTTTAAAACGAAAGTC
AAGGCTCTTCCACTTCTATTTACTTTACTATATATGCTGTTCGACTGAACTCATTCTCGTTTTGG
CTCCGCCTTCATGAAATTCCAAGACCAAAAAAATTCTTCGATCTCAATTTCGGGCGTATGGAATT
TTTTCATCTCTAGTACTGAAGATAGAAGGGGAATCCATCTTTGTTTTTGGCTCGCAATAAAGCTA
GGGTCCTGATCGAGAAAGTACTAGTCCTATCTATCCACCTCTCCAGACACAATATCTTGAGTACC
TATGATGGTGACCACATCTGCTGGCATGTGATGTTTGGACATAGA
Found at i:74708 original size:21 final size:21
Alignment explanation
Indices: 74669--74710 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
74659 AGTTAGCTAG
*
74669 TAGTTAGTCAGTTACTACAGC
1 TAGTTAGTCAGCTACTACAGC
* *
74690 TAGTTAGTTAGCTAGTACAGC
1 TAGTTAGTCAGCTACTACAGC
74711 AAGTATAGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (21 bp):
TAGTTAGTCAGCTACTACAGC
Left flanking sequence: Indices 74169 -- 74668
ACAGGTTTTGACACGGCAGTTTCTGCTTCTGCTTTCCTTTCAAGGTCTCGACCTCATAGTGATGT
TTCTGGCAAGTCTTTACCATCTTTCTGGGTAGCTGATTCTGTTTCTGTAAAGATAGAGATAGAAC
TAGTTGAACAAGCGAGTGAGTCTCCTCTATCCTTAGAGTCAGGACAGAACCTTGCTTTATAGCTT
TCTAAAGCTGATTCTCTATCCGCTTAAGCAGGTTTCGGAGTCTAAGCAGGGAAAGAGTGCTAAGC
TCGTGGGACGGGAGTAGTTTCAGTAATCGGAACAAGAACAGGATGGGATACAGCTGTTTCAGCTT
CTGCTTGAACTGCGAGTTCTGTCGAAAGGAAGGACAGAGAACGAATCATCCGGAAAGTTAAGCCT
TCTGCTTGAAAGTAAGTCATCGGAAGTAAAGATAGAACTAGCAGTCGGGATTCTCCCATAATCAA
GGACAAAAGCGCCCTTCCATTACTAAGAAGTTATTAGTTAGCTAG
Right flanking sequence: Indices 74711 -- 75210
AAGTATAGCTAGTATAGTATAGTTAGTAGTGGAGAGGGGGGAAAGAAAGCAAAACAACAGGTCAA
AGAAGCAGCGATGGGTTCGCAAACAAAGGTCAGGAAGAAAAGGCCTCTCTCATCCCTTGCAGCTA
ACTAATGGCAGCCCCTTTCTTGCTCCTGTTTACCGTATTATTACTCTTCAACTAGAGGATTGGTT
AGACCGATTGGCCGGTTGAGCAAGAGAAATACAAGGCTTTGGCCGGAGGTTCAATTCTTGACTTA
GATCAGGGATCGGGTCACAGACCATCAAAAGAAAGGAAAGGCTACTCTTTAGCCGCAGGGTCGCC
ATCAAGACATCAAATGCAAGGAAAGCAGCCCATCTTCCGGAGAGCTACTGGGTCCCATCGACAGC
AGGAAATGAACTACTTGGCTGCAGGGTCCCGTTCCTCTGGTCGTTTCTGCGACTTGCCACTCTGC
CTTTGCAGGAGACTAGGGAGTTCATGACCAGTCCACTCGCTAGGC
Found at i:75725 original size:20 final size:20
Alignment explanation
Indices: 75700--75765 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
75690 ACTTCGTTTC
75700 TTTTTGTCCAAGTCACTTCT
1 TTTTTGTCCAAGTCACTTCT
**
75720 TTTTTGTCCAAGTTGCTT-T
1 TTTTTGTCCAAGTCACTTCT
* *
75739 TCTTTTGTCGAACTCACTTCCT
1 T-TTTTGTCCAAGTCACTT-CT
75761 TTTTT
1 TTTTT
75766 CTGTGTGAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
19 2 0.05
20 29 0.78
21 4 0.11
22 2 0.05
ACGTcount: A:0.12, C:0.23, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTTGTCCAAGTCACTTCT
Left flanking sequence: Indices 75200 -- 75699
ACTCGCTAGGCCTCTTCCCCTGGGGCTCGGGTCCAAGGAAACCAACATATTGGGCGACAGAGGGT
GTACTTTTTCTTAGGAGAAGGAGTTGTTCGAACGCGTGAATACACCGGACCAGCCGTGGAGTACA
TGGTCCACCCGAGGAGTGCAGGCAAGCTGTCCAAAGAGTTCTGAGTTATGAGTTCTGCGTCCATG
CCGTTAAGAAGAGTCTTTTTCCTCCCGTTTGAACGAACAAAGCAGCTTTTCTGCGAAAGGAAAGC
TTTACGTCTCCTTCCTTTCAACCAAAAGAAGAGGAAAACTACGAACAAGATCCACTGACAAAGCT
TTCGAAGAAAAGGTATAATTGTCAGCTTTCGCCTCCTCTTCCTCGGCTTTCTGCCCCTCGTTTCT
GAGCAGAAGAGCCGTTTTCAAATAGTGTTCGATCGATTACGTATTAATCAATATTTGATTGATTG
GTCTGAGGTTATCGACAAAAAGATTTGTCTAAGCCACTTCGTTTC
Right flanking sequence: Indices 75766 -- 76265
CTGTGTGAGTTTCGGGAATATCCCCATTCATAGGTCCGAGATCTACATCTATGAATTGAAAGGTC
CGAATGATCAACTCTGCAATCAGTTGTTAGAATCAATAGGTCTTCAAATTGTTCATTTGAAAAAA
TGGAAACCCTTCTTATTGGATGATCATGATACTTCCCGAAAATCGAAATTCTTGATCAATGGAGG
AACGCCCTTTTTGTTCAATAAGATACCAAAGTGGATGATTGACTCATTCCATACTAGAAATAATC
GCAGGAAATCCTTTGATAACGCGGATTCCTATTTCTCAATGATATTCCACAATCAAGACAATTGG
CTGAATCCCGTGAAACCATTTCATAGAAGTTCATTGATATCTTCTTTTTATAAAGCAAATCGACT
TCGATTCTTGAATAATCCACATCACTTCTGCTTCTACTGTAACACAAGATTCCCCTTTTCTGTTT
CTGTAGAAAAGGCCCGTATCAATAATTATGATTTTACGTATGGAC
Done.