Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MZ905370
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: 312510
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Found at i:62191 original size:18 final size:18
Alignment explanation
Indices: 62151--62193 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
62141 AGCGCCCTGC
62151 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
62170 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
62187 CATAGTC
1 CATAGTC
62194 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 61651 -- 62150
ACCCCCGAAAGGGCTGCCGTCCGATGGGTACACGAAAGTGACGAAGTTGCTTTGACTACAGAACC
ATGCCTGTCTGTTGGAGCGAATTGGATGATCGGGCCGAGCCCCCTCTTCCCCGTGCTCTCCTTTC
CCTAATATGAACCTCACGTCATCAATTTCTGACTCGGCCTGGCCCGGTCGCCCTACGCGACTGGC
GCTTCAAAAGGCGAAACTCTCGTCGTAGTTTGGCGACCTGACGGGGCTCCCACTTTTTGTTATCT
AAAGGCGAAGACTCAGAAGTGGGCGTCGACTCGGCCCAGCGGGCGAACATGCCGGGCTCCGGCTC
CGCGCACCTGCCCTTTCGAAGCACTTTCTAGTGTGCGCTTTAGTTTTCGAATGTGTTGTTCAGCG
TCACGAGTCTACAAGCCTTTCGTGTTTCAGTGCTCGCCTTCATAATCTTCAGTAGGGGCCGTCTA
GTCTTTTGATTAGAGTAGGGGTCGCGAGAGAGCAGAGCGCCCTGC
Right flanking sequence: Indices 62194 -- 62693
AACAAGGTCACAACTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACAC
GATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAGAAGTGTTATAAGCTTTGA
ATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCGC
ATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGAA
ATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTA
Found at i:81327 original size:33 final size:33
Alignment explanation
Indices: 81285--81352 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
81275 ACAGAGGTGA
* * *
81285 CTAATACAGACGAGGAGAAAGAGAAACCGATAC
1 CTAATACAGACGACGAGAAAAAGAAACCGAAAC
*
81318 CTAATACAGACGACGAGAAAAAGAAAGCGAAAC
1 CTAATACAGACGACGAGAAAAAGAAACCGAAAC
81351 CT
1 CT
81353 CCTTGAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.50, C:0.19, G:0.22, T:0.09
Consensus pattern (33 bp):
CTAATACAGACGACGAGAAAAAGAAACCGAAAC
Left flanking sequence: Indices 80785 -- 81284
TGCCCAGAGGAGGATGCTAGTGAGTTGTTAAGGAACTTCTTGCATTGCACATAGGGAAGGTGCGG
AGCGGTTCTTTATCTTATCATTGCCCTAAGGTAAGGCTTGGAACTGAACTGCAAGTATATAAGAA
AGGATATTGCTAAGAGTTAGCAGTCGAAGGGAGTTTGAACTGTGAAGGAATTACCGGTGCGCACA
GAGAAGGGGGAGAGAATACAGAAAATACGCCCTTGACTATACGGAGGATAAGAAATTAGGCAGGA
CTGATTTCCCTTCTTATCTTATTGTTGAGACAGGAAAGCAGTCAAGCGAGTCGACGCATCTATCA
GCAGTAGGAGTAGGACGTAGCGCATAAGAGGGTCTTAGGAATCGATCTAGATGCCCAGAAGAGGA
TGCTATCGAATGCCCTCTTTGACGGGCTTGTGCAAGAAGCCGATTATTCTACCATCTTTTCCAAT
AGTGCCATTTTATTGATGCTATCGAAGAAGAACCAACAGAGGTGA
Right flanking sequence: Indices 81353 -- 81852
CCTTGAAAGAAGGAAAAATGCCACATCAGTAAGAGAAGTGGGCAAAAAAGCTGCTCTCCTATTTG
GACCACCTTCCACCCTGTCTCCCTCTCCATACATACAGAACCGTAGTTTATGGTCTCTTGTGTTT
ACAGCCCATTCTTCACCTTTCCTATAGCCAGCAAATCAAGGAGATACGGCTTAAAAGCCTACGCG
CGTCAGGTTGTTCGGCTTCGGCCCTTCCTACACGTGACTACACGGAATTCACTTTACTTTACGGT
ACGGAACTAGATATGAATTTCATCCTCTGTTGGCGAGATCAGAGGCAACGGTGGCAGCAGCTGTG
GATTCTGTTGATTCTTCATCTCCTCGCTTGACGCTCTCTTCAATTGCAGATCCTGAACCTTCGGT
CAAGTTGCTTTTCTATCCTGAACTTTCGGCTAAAGTGGCTTCCTCCTCTCTTCTCTTGAACTTTC
GTTCAAGTGGCTTCCTGTAGGGGCCTTTGAACGGGCCTTGGTGGG
Found at i:159668 original size:18 final size:17
Alignment explanation
Indices: 159641--159677 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
159631 TCCCAGCTCC
*
159641 TGCCTTGCTTGCTTTCTT
1 TGCCTGGCTTGC-TTCTT
159659 TGCCTGGCTTGCTTCTT
1 TGCCTGGCTTGCTTCTT
159676 TG
1 TG
159678 TGTTTCATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.00, C:0.27, G:0.22, T:0.51
Consensus pattern (17 bp):
TGCCTGGCTTGCTTCTT
Left flanking sequence: Indices 159141 -- 159640
CCCAGGGTTGACTCCCTTCACTAGTCAACGAAGTGCATCTACGGATGTAGGCACATTCTTGCTTG
ATCATTTGCTCTCACTAGACCGCCCTAGAGTACGATACTGGTTCGCCATAGGTTCGAAGGGCTGT
CTCTTGTGTGCGATGGTTGGGTATGAATGGAGCTTGCTCGGTAGAAAGGAGAGTAACCTTTGGGT
AATATAATATAATTTACTCATTCCTTCATAATGAAATATTCTACTCTTTTCTTTCTCCGTGGATT
ACTTGAGGATTGATCTGTTGTTGGATCCGTTGATGGATCGACCCTCCCTAACCACCCTATTTTTG
AGCACAGGCAGGTTTGAAGTGAAGGGATAGAATCCTGTACGTAGAAGGCTGAACCCATAACTCGT
GATTCGTAGCTTACAACCTATCCTTTCTCATCTTTGCTTACCGCTTCGCCCCCTTGCTCAAGTAT
GAGTCCTAAAGGTAAGGCAAGAAAGAGATTCTCAATCCCAGCTCC
Right flanking sequence: Indices 159678 -- 160177
TGTTTCATAGTGACTAATCTACCTATTCCTATGCTGGCAGGGGACTCAAGGTTGGCAGGGTTGTC
TCTAGGGTTGGGAATGAGACTATGAAACTCTTTCCTTTCCCGCCGGTAAGCAAGCAAGTCAAAAC
GCTAACACTGATGAGCTTGCTCTAATGAAACTACTAACACTCAGACTAGGGACAGGGGCTCAGAC
CCTGTTGCCTAGAAGAAGGAGATTCTATTTAGTTAGTCGGGTCTTAACAAGGAGCTAATGGATGC
ACTAACATATCGCCCCGTGTCCTAATAGTTATCTTACTACTGGAGTTAGATTGACTCCTTGGGTC
GGGCACCAAGGGAAGGATTAGTTCATATCCTAAACACCTATCGATTGTGTTAGTGAGTAAGTAAT
CACCCCCCGTGTATCCTTATAGAGTTCAGTTTAGTGCTTCTTACTGGTTGGGGTGGAGTCTAGCT
ACTACTACACGAGTCCCACACACCACTCCACAGCTCTAGGCTTTC
Found at i:168579 original size:13 final size:13
Alignment explanation
Indices: 168561--168586 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
168551 TAAGGAAGGC
168561 CTTGCCTTATTAG
1 CTTGCCTTATTAG
168574 CTTGCCTTATTAG
1 CTTGCCTTATTAG
168587 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 168061 -- 168560
CTCAGACTCGCAGAAGACAAGTGAAAAGTATCTCGAGGTTTCTCCGCTTCTTGTTTCAAAATATC
GCAAAAATTCAGCGCTCTAAAAAAAAGGCCGGAAGGCCCCAGGACCCCCACCCCACGGCCCCTAT
GCCAAAGCAGTTGAGTGCAAGGAGGTCAGAGCAGAGGAGCTTCCCGGGTAGCAAGCTAGTTAGGA
GAGAATTCACCTATGGATTATTAAGTAGGTAGGAAAGCACGATAGGAGGCATGTCTCAGGCCTAG
GTGACAGCGGAGAACTTTAGAGGTAGGCTGGAAGGAAAGAGAAAGGCTAGGAGCTAGGCTAAATA
CGGAAGTCAATTCGTCTTTCGTCTGTATTGTGATCCCATGCCAGGACGAAGAAATCAAAGGATTT
ATAGTCATGCTCATGGAAGTATTGACTGGTTTAACGCTCATACCAATACGGCAGAGCATTTTTTC
TTAACTATTGAAAAAGCTCTTGATTTTTTCGGTTTTAAGGAAGGC
Right flanking sequence: Indices 168587 -- 169086
AGAGATATAGCCACCATAGACTAGCTCGTCCGTAGGGCTATGATCAGGCCATGCGGTCTAGAGAT
CTAGTTGACGCTTGGAAGAAACGGATATCCTTTCGAGAGAGAACGTGGCCATCCCGACCTGGAAG
GACTTTTATACTTCCTGCTTTGAGTGGGCCAGAAGCCAGAAAGACAGATCAGTTCGTTTGCAACA
GATCTTGGAAGAAAATCAACAGAAAGAAGGTTGAGTGATAGACGAGGGGTTGTTTTCAGATGACG
AAGTATTCGTCAGCGATAGGGCTTCGCGCCTGAGAACAAAAAAAATTAAGGAAAAAAAAAGGCTT
ACAGAGGATTTCCAATAAGAAAAGGAAGAAGACCCCCATAGAACTCAAAGCGGAGGGGCTCTTCC
TCAGAATGACGATGTGTGAGTTGCTTTTGTGAGGGGATAAAAGAGGTATGAAGAAAGTTGGCCAA
GGTCATAAGGTAAGGCCAAAGGTATTGGTGCATCTTTTTCTAGAA
Found at i:211289 original size:22 final size:22
Alignment explanation
Indices: 211250--211292 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
211240 CTTCATCCGA
*
211250 ATAAGGAAGAGACAGGTACAAT
1 ATAAGGAAGAAACAGGTACAAT
* *
211272 ATAAGGAATAAACTGGTACAA
1 ATAAGGAAGAAACAGGTACAA
211293 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 210750 -- 211249
GTGAAACAAAGGAATGCTCCGTCAATTAAGTATTACCGGGGCCCCTTCTCCCTTATTCGCTCCTA
GGAATTAAGGGGAATAGGGCGCCTCGATTCAGTAGTTACAGGCCCGGGGCCTATATCTAGATTAG
AGGAATTAAATCGAGGAAGAAAAGGGAGCTGCGGATAAGGACAAGTCCGATCAGAACTACTACAC
AACCTTCAATGACTCTAACAAAAAACCTTGATGAATTAGATTAGAAAGGAAAGAAAGAGAAAAGG
AAGAAGAAAAGAAATTATCCTAAGGAAATGAAACTAATAACAAATAGGATAATAGAGAGAAAGAA
CAACTTAAAGCTCATAGCATGCTAGCCGCCCTAGCTACTAGAGCGCTTAGCTAACAGCTCTTGGC
TCAGAAAGAATAGCTCCTAGGGCGAAAATCATTTTATAAATTACCCGCTCAATCAGATAGGACGA
CCTACTCCTTAGTTGAACCGGACTTTGCCACTCACCTTCATCCGA
Right flanking sequence: Indices 211293 -- 211792
GGAGTCCAGCTGAACCACCCAGATCCGCTTCTTTCATCAAGCAACACAGCCTAGTCTAACCCGAG
CCCGAGTTCGTATTGGTAAATTTCGGGTCAGCAGGCAAAGGAAAGGGAACACCCACGTTCTACTT
TAATTAAGAGGTTTGTGGTACAGTACTCTTCCCATGTTAAACTGCCCTGCCTTTCTAAAGCTAAA
GGCCTGGTACATCTTTTTTTTTGAAACCTATTCTCGACCCGTATTCCTACCCCACCCACCGCTCT
TCCTTTGAGGCAAAAGTCTCTCTTATTCGACCAGAAGAGCCTTCTTCTTCATTTCACCTATGGAC
TTTTTCCACGTAGCAACTTCCATACTGCACGAAGTCTTCTTCGGGAATGGCTTACCGCTCCGTGG
GAATTGGATTGAGTTGTCGTGACGATACCTTTCTTAGTGGAAAGCAAAGGTGTGGAATAGCGCTA
GCTAACAAGTAAACGAACATGGGAATAGATCTGATACCCCTTAGG
Found at i:233244 original size:25 final size:25
Alignment explanation
Indices: 233199--233246 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
233189 GAAGCGAGAC
*
233199 TCGACTGTTAAGGACCCAGAGGGGA
1 TCGACTGTTAAGGACACAGAGGGGA
* *
233224 TCGACTGTTAAGGAGAGAGAGGG
1 TCGACTGTTAAGGACACAGAGGG
233247 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 232699 -- 233198
GCATTCGCTGCATCTGACAGGGACGATTTCAGATAGGTAGGTTAGGTTGCTCGTTGTGGTTGCCC
GGACCTCGATCTAGATCCAAGATAAACCAAAAGCATGGGTCGTGGTCGGCAGAATCATATATATC
TGCCGGGGCTTGGGCTTGACTTCTTTCTTCATGAATGATTTTGGAGAAGCCTGCCTCGAGAGAGA
CATATGGCATATCTGACTGCCTGATTGGCGAGCAGCTGTCCTCATTCATAAGTCCAAAGAACTAG
CAACCAAACTGGTGGCAAGCAGGAGAGTGACCAGGCCTGATACTGATTGAAACGTTTATTTAATT
GGAAGCCGTTCAGATAGCCCTAATTAGTTTTAATTAGTTTAGTGAATGTTGAGCTGTCATATCTA
GCTGCCATATATGTAAACATGCCCTAAAAGTAAAGGGATCATATTTCCTTTAGTAACCACTTTTA
CCCATCCGCTCTTCTCCTGACCGATTGGAGGAAGGGAAGCGAGAC
Right flanking sequence: Indices 233247 -- 233746
AAGCACAAGGTTGGTGACCCGGGGGAAAGCGAATGCAGATCTCACGCAAAGTGAAATCTCAAGAT
TCAGATTGGGTTTGTGTTCGGTGTGGAGTAGATAGGGCTATTCCTTAGCAAGGCTATTCAGTAAA
GGCGAGAAGGGATCTATAGCAAGGGCAGCCCGGGTCTACCCAAAGAAAGGCAGAGTTGAGGAAGA
TAGATCAAACAGCCTTAGCGCTTTAGCTTGAACTGTAACCTTACCCTCGCTACTGACCTGTCGCT
TGGCCCGAAAGACTGGAACTAGAAGTTCCTAGAAGTCAACTGTGCCTAGACCTCAATCAATACGC
TTACTGAGAGTACCGGTACCAGAACAAGAACAAGGATTTCTCTTTGGTCAAAGCCGCCGCACTTG
AACCGTAACCAGCTAATGCATCGCCTTCTATCTGCATTTCTAAGACCAGTCCCTTATTCCGCTAA
CCAATTAGGTTGGTTCATCAGGTGCCAAGGCATCTCTTTCTCCCA
Found at i:255572 original size:16 final size:16
Alignment explanation
Indices: 255551--255586 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
255541 GATAGAGATC
255551 TATATCTATCGATAGA
1 TATATCTATCGATAGA
255567 TATATCTATCGATAGA
1 TATATCTATCGATAGA
255583 TATA
1 TATA
255587 GATAGAGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (16 bp):
TATATCTATCGATAGA
Left flanking sequence: Indices 255051 -- 255550
AGAACCGTCGGTTACCTTTTGAATCAAAGTACAAGCCGAGTACTACGACTACAGGGGGGGGGAGC
TTTGCTTCGTAGACAGCTTCGCTTCCTCGTCGCTTCTTTCTGGCGACTAGCTTCGTGAGTAGGTG
GCTTGGTAAGCAACAAGCTACCCTCAGCATCGGTAAAATCCCTATCAAAAAAAAAAGAGGCCAGA
ATGGTGGGGAAGGGGGCCCTCCCTACTTCAATGGAAAGGGGGGCCGTTTCACAGCCGTTCCTCTA
CAACTACCTTTCGCCCAACATGATCACAAACGAAGACAGAGAATTGCAGGAGGACGAAATGAACC
ATGTCCTGATCGGAACGATTGAAGAAAGAAAGAAAATGGTGGCCCCTTTCGCCCAGGGGACATCG
TCGGAGAACAATGTCGGGGACAGGGTGAGAACCTTCCTTCCGTTGGTTACGCCTTTTAAGTGTCG
GTTCTTCCATATTTAGATATGGAGATAGATCCAGAGATAGAGATC
Right flanking sequence: Indices 255587 -- 256086
GATAGAGATCTGGTTTCAAGATCTATGAACACGAGAGACCCCTAAATATCCATTTGAAAAAAGAG
ATGAATAAATGGGTAGGGCGGAGCCAGCGGAAGGAAGGTCGCCGTTAGCGCCCCTGCAATCTTTC
TAAAGTAAGAAGCGCGAAACGTCGACTTCACGAAAGAAGGGCCTTCCATTAGATATTAGAATATT
AGTAAAGGCGCGTTAGCCTATCTATAGAAAGGGGCTTCTTCAAATATCCCATAAATAAAGCAGGG
GCTTCTCATGTAGTTTTTAGGGGTGCGTAGGCGCGACGGCCCCCTGGGGCTAGCGCGCAATGACT
TTCTCTGATAGGGGCTCGCTTCTTCGACGCTCCGCTTGCTGCTTTTCATTTTGATAGGAGTAGTA
GGTGCTTGCTGCTCGCTTGCTGTCTACTAAACGAGCCTTCACTGCCCGCCCGGCCCCTCTCTTTA
ATCTTAAAAGTGAAGTCAAATCAATGAAGTGAACAGCCCAACCTC
Done.