Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MW477237
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: 82926
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Found at i:10855 original size:12 final size:12
Alignment explanation
Indices: 10838--10862 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10828 TCCGGCTTAT
10838 TATATATACTTC
1 TATATATACTTC
10850 TATATATACTTC
1 TATATATACTTC
10862 T
1 T
10863 TCTATTAGAA
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:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATATACTTC
Left flanking sequence: Indices 10338 -- 10837
GCTTGGAAGCAACCTGCTATCTATCGATAGGCGAGAACAGACTGCTATTGGCTGCTTCGCCTATC
TATTCTATTATGGCCGACTTGGAGACATCAGAGGAAGACCACCATCTCTATCTGGGTACGATCAT
AGCTCCATTCGTTGAACCTTGGGGATAACCATTAGCATTGAGGTCAATCACCGCACCACCTCTAT
CATACAATACATACGACATTACACGACGCGAGAGTGCATGGTCAATACACACCTAAAGCGCCTAC
GTTCCGCTTGCAGCCAATACAACCACAACCTAACTTGCACGAGATTCAACAACCGAAGCTACTGA
CTGGTAGTCCCGAGGGGACGACATCCCCCTATAATAGTTAGCAGTACTGAACAAGCGAGTCATCG
GTCCGGGGAAAGAAAAGGACCGCCTTTGAAAAAAAAGAAGGAACTCGCTTAACTCGCTAGGCCTT
CGGAACAAAGGCTATTCTGTTCATGCTTCAGACGATCCGGCTTAT
Right flanking sequence: Indices 10863 -- 11362
TCTATTAGAAAGGCGAACCTATAGGCCTGTTTAGCGCGTTTCTAAAGTAAACCTCCGGTTACCTT
TGTCAACGCTACTAAGGACCGGGTGAAGAATGAAAAACGTCCGCTAACGCCCACGGGAGAAGATC
TTTTTTAGATCAGCAACGAATGTCTTGTATCTATGAAGAAAGATTTATCCCCGGGTTCAGACCCT
GAGTGCCATACCTTGCTGAAGGCGATTCACGAGAGAATCGCGCACAGTTCCCTTTGACCGAGATG
TGAATGCCCGTGATCTGCTCGGTATAGTGATGGATTTCATGGCCGACGTCTAACCGGCACGAATA
CGCCGACATGAAACGAGTTCCCCGCGGAGCATTTTTTCTTTTTCTTATCAATGAATAGATCTCTT
TACTTGTATGACTTAGATGTCTCGTATTTCTCGAAAAAGTGATTCTATTTATGGGATTTGGTATG
ATACTTATGAGATCGATGAGATTGATATTCAAATATTTCTTCTTA
Found at i:53342 original size:21 final size:21
Alignment explanation
Indices: 53316--53370 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
53306 TCTGACGCTT
53316 CGCTCGATTATTGTCCTATTC
1 CGCTCGATTATTGTCCTATTC
53337 CGCTCGATTATTGTCCTATTC
1 CGCTCGATTATTGTCCTATTC
53358 CGCTCGATTATTG
1 CGCTCGATTATTG
53371 CGCCCTTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.15, C:0.27, G:0.16, T:0.42
Consensus pattern (21 bp):
CGCTCGATTATTGTCCTATTC
Left flanking sequence: Indices 52816 -- 53315
AACCATTGCTGGATATTTCTCAAAAGCCTTAGTCTCTTTTCCTTCAAACTCCCTTGTATAACTTT
CGATTTGAATCTGTAATTCATATAAATTCAATCTTTATCCGTTTTACAATCATAATAACCATCTT
TTAACATTTTTAAAAAAATTCTTATTATGAGCCTTAGTTTTCCATTTTTTAGATTTCATATGCAT
CTCAACTTTATTTAGGAATATATTCATGAACTTGTCATACATTAAACATCTTACAGCATCCTTAT
CTTTCATCTCACTACTCTTTTTACCCACTTCTATACCGGTCCCTTCTTTTATCCCATCATGTAGC
TGGAAATAAGCCAGTAAAAGACAACTAGAAGCAAGTGGGGGTACGTAAACGAGGACGGATCACAG
TGTTTTTGTACTGGTCAGCTTTGAGGTGTCGAGTGATGGATTGTTCTATCTCTTATGAAAGGGGC
CTTGGTGCCTTATTATTAGAGAAAGGGGAGTACTATCTGACGCTT
Right flanking sequence: Indices 53371 -- 53870
CGCCCTTTTCTTTAGGGCCGGGGACGGGGTTAAGCCGCGTGTCGATTATTGCGCCCTTTTCTTTA
GGGCCGGGGACGGGATTAAGCCGCGTGGCGATACCCGCGAAAAACAAAACATAGGAACTTCAACT
ATTGAGATAATTATTTTAGTTGGTGGGCCCTTCGTACTCAAATCCGAACAGGGAAAGGACAATTT
TTCAGCGCACTCAAAGATAGTGTGTATGGGGGTTAAATATTCATGAAAAACCATTATGTTATGAA
ATGATCCATGTTACGGAACTAAGACGCCCTATTATATTACAAATACGAATATAATAAAGAAGAGG
GTTACTAATAAGAAGAAAGAGTTAAGGGTCTCCAACGCCTATAAATAGAAGCTTCTTTCAGTCTC
TATTTGGCAAAGGGTCGGCAAGAAAGTGAGTAGCCATGGATCCCAATCCCAATGGAATTGACAGA
CTGTCTCTTATTTCAAATCAAATAGCGCAGGTGGAGGAAGCAAAG
Found at i:53437 original size:51 final size:51
Alignment explanation
Indices: 53361--53467 Score: 196
Period size: 51 Copynumber: 2.1 Consensus size: 51
53351 CCTATTCCGC
*
53361 TCGATTATTGCGCCCTTTTCTTTAGGGCCGGGGACGGGGTTAAGCCGCGTG
1 TCGATTATTGCGCCCTTTTCTTTAGGGCCGGGGACGGGATTAAGCCGCGTG
53412 TCGATTATTGCGCCCTTTTCTTTAGGGCCGGGGACGGGATTAAGCCGCGTG
1 TCGATTATTGCGCCCTTTTCTTTAGGGCCGGGGACGGGATTAAGCCGCGTG
*
53463 GCGAT
1 TCGAT
53468 ACCCGCGAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (51 bp):
TCGATTATTGCGCCCTTTTCTTTAGGGCCGGGGACGGGATTAAGCCGCGTG
Left flanking sequence: Indices 52861 -- 53360
AAACTCCCTTGTATAACTTTCGATTTGAATCTGTAATTCATATAAATTCAATCTTTATCCGTTTT
ACAATCATAATAACCATCTTTTAACATTTTTAAAAAAATTCTTATTATGAGCCTTAGTTTTCCAT
TTTTTAGATTTCATATGCATCTCAACTTTATTTAGGAATATATTCATGAACTTGTCATACATTAA
ACATCTTACAGCATCCTTATCTTTCATCTCACTACTCTTTTTACCCACTTCTATACCGGTCCCTT
CTTTTATCCCATCATGTAGCTGGAAATAAGCCAGTAAAAGACAACTAGAAGCAAGTGGGGGTACG
TAAACGAGGACGGATCACAGTGTTTTTGTACTGGTCAGCTTTGAGGTGTCGAGTGATGGATTGTT
CTATCTCTTATGAAAGGGGCCTTGGTGCCTTATTATTAGAGAAAGGGGAGTACTATCTGACGCTT
CGCTCGATTATTGTCCTATTCCGCTCGATTATTGTCCTATTCCGC
Right flanking sequence: Indices 53468 -- 53967
ACCCGCGAAAAACAAAACATAGGAACTTCAACTATTGAGATAATTATTTTAGTTGGTGGGCCCTT
CGTACTCAAATCCGAACAGGGAAAGGACAATTTTTCAGCGCACTCAAAGATAGTGTGTATGGGGG
TTAAATATTCATGAAAAACCATTATGTTATGAAATGATCCATGTTACGGAACTAAGACGCCCTAT
TATATTACAAATACGAATATAATAAAGAAGAGGGTTACTAATAAGAAGAAAGAGTTAAGGGTCTC
CAACGCCTATAAATAGAAGCTTCTTTCAGTCTCTATTTGGCAAAGGGTCGGCAAGAAAGTGAGTA
GCCATGGATCCCAATCCCAATGGAATTGACAGACTGTCTCTTATTTCAAATCAAATAGCGCAGGT
GGAGGAAGCAAAGCTCTACTGGGAGCAAAGGCTGGGGCTATTCTGGGAGCATCCGCCTGCTCTCG
ATCCTGAGGTGATAGGACAAGCAATGCAGCAAATCCGGGACCGCA
Found at i:78909 original size:33 final size:33
Alignment explanation
Indices: 78872--78937 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
78862 CTTTTTCATA
78872 CTACCCAGCTAAGAGATTCGGTTGTTTAACCTG
1 CTACCCAGCTAAGAGATTCGGTTGTTTAACCTG
78905 CTACCCAGCTAAGAGATTCGGTTGTTTAACCTG
1 CTACCCAGCTAAGAGATTCGGTTGTTTAACCTG
78938 AGGCAATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (33 bp):
CTACCCAGCTAAGAGATTCGGTTGTTTAACCTG
Left flanking sequence: Indices 78372 -- 78871
CGTTAAATAACCTCTTTCCCGTTACTTCGTAACCCTTTCTATCCAGCTAACCGCAGGAGATATGC
CAGACTTCTATTATAAGTAAACTGCCTTTATCTAATTCTCTTCAGGTAAGCCCTGGCCAACATGG
GGCTTTAGGAGCCACCGAGCAGTTGTCAGATAAATTTTTGTTTGTATGCTGTGTTTTTGAGCCTG
TATGGTTGCTCGCGAGTTGGGAGCAGGAGACCGCCTTTAAGAGAAAGAAGGTCTACTGGCCCGGT
ACGGTGTGGTTTTGTTGGATTTCTCCCTTTCACTGGCCCGATCCTGAAAGACTCCCCCATAAAAG
AGAAGGTTATCCGCTTATCCGCTGTTTAAGCTCGAAATCTGAACTTTCACAACCACCGACAGGAA
GACAAGTCAGTCAGTATGGGATCAAAAAAAGCCTTTTTTAGGTGTATGCTCCTACACCAGTTACT
ACAACAGCCAATATACTTTTTGATGGATTTTTGTTCTTTTTCATA
Right flanking sequence: Indices 78938 -- 79437
AGGCAATGAAATTGATCTCGAAAGCTTTAGTCTTTCACCCCCTAGAGAAAATCTCTATGACTCTT
AGGAAGGGCAAGAAAGATTCGTTTGAGACATAAAAAGCAAGAATGAATAGCAAGGTGCGGAGCGG
CAGTCTTAATGGCAAGGAATGAATAGAAGCCAATTCGCCTTTAAGCTAATTACCCGGATAAAAAG
AGTATGTTTGAAGGAATTATGTAACTAGAAGGGAGGAGTTCATACCTGGAAAACTCAGACATGCA
AAGAGCATGCCTACTGTAAATAAGCTCTTCCTAAACATAAGCTCTACTTTCTCTCTCTTGCGGTT
GCATCTTGTCTAGCAGGCTCGGATGCCCTATTTTTAGGCTGCTAGGTAAGGTGGATCATAGGATC
TGTCGTTGGCTGCCCGTGTTACCAGTCCTATAGTCCTATAGGGGTGGAGATGTGGCCACCTTCGA
ACTAGCCTTTTCTTCAGAAGTTTCAAGGCGGAAAGAATGAATTGG
Done.