Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MZ951175
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: 280841
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:23224 original size:21 final size:21
Alignment explanation
Indices: 23165--23216 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
23155 GCCAATACCC
* * * *
23165 GCAATCAAGTCATACTCAACA
1 GCAATCAAGTTAAAATCACCA
23186 GCAATCAAGTTAAAATCACCA
1 GCAATCAAGTTAAAATCACCA
23207 GCAATCAAGT
1 GCAATCAAGT
23217 AAGCATCAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.19
Consensus pattern (21 bp):
GCAATCAAGTTAAAATCACCA
Left flanking sequence: Indices 22665 -- 23164
AGGGTCCTCTTGGAAATCCTGCTCCTTCTACGGCTGCTAGTATCCTTGTTCTTCTACTCGCAGGC
AGGGCTGCTCTTGCTATTGTTGCTAGGATCCTCTTATCCTATTGGTTGCTAGTCCCGGGCTTCTA
GGACAAAGTGTAAAGAGAAGAGTTAGAGTTCTTCCTCTTTCTCCCCTATCACTTAAAGGGAGATG
GCCTAATTTCTATTCTATCTATGGATCGAGAATAATCGTCAGTTTGAGGCCTGTCTTTGAACATA
AGGCATGAGAATCCTTCTCAGCGGAGTCTCTGTGTGTTGAGATCGAGGGTAGTTTGATTCTGGGA
ACCGAGCCGGCTTCGGCCAACGAATGAAGTTCTTTAGTAGGTTATCCGGGCATAGTTGAGTTAGG
AGCGAGGGAGTTCCATTTACTAGCAATATCCTCTTATTCTCGGGAAAGGGCAGTTCCAGCTAGGG
CTAGAGGACAGTCACATTCCTATTAGTAGGTTGAGGCCAATACCC
Right flanking sequence: Indices 23217 -- 23716
AAGCATCAACTGCTTTACCGTATAACAGTTCCTTGAGCAGATGTGATTGCAAATCTTCTACTACC
AAAGAATCTCTATCCGTCTTCCTTCCAACTAGCACAGAGCCTATACGCACTGAGGAGAATTGCTA
TGACCTAGCAGACCTGCACTAGCAAGACCTCTTTGCATCCGTTAGAGTAAAACCCTTGGCTTGGC
GTTCTGCCCCTTTTCGGTATGGTCCTTTCATTCAGGCCTTTCCTTATGCACCGATGGTTTCATGA
TTCCTTGAAAAAAAAAATGTTTGCGAGCGTCAAAGCACCTAACCATACCTACTACACCATGCACT
CCGCCGGTAAGCAGCCCGGACATGAAAGAAAGTGCATTTGGAAGCATATGTGTGCCACTTTGGCA
CGAGATTTCAGCTCTACTTTGACTTTCATGGTTCCACTGTTCGTCGAGATCCCTTGAGTGCTACT
AAATGTAGAGAAAGACATTCATAGCTTGAACCTTCTGGTCACTTC
Found at i:77824 original size:17 final size:17
Alignment explanation
Indices: 77802--77846 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
77792 TGGGGAAGAA
*
77802 AGGAAATCTGTCTTTAT
1 AGGAAATCTGTATTTAT
* *
77819 AGGAAATTTATATTTAT
1 AGGAAATCTGTATTTAT
*
77836 AGGGAATCTGT
1 AGGAAATCTGT
77847 GCTTACTAAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (17 bp):
AGGAAATCTGTATTTAT
Left flanking sequence: Indices 77302 -- 77801
CTCCCTGTCAGCTCCCTTCAACCATACATATATCTTAAATCTAGCTGGGTGCATGCAGACGTTTG
CGGACATCACCTATGGTGAATTTCCCGAAGCACATCTCGTTGGATGGATGTCGTTGCCGCGAAGT
GAGCTGGGCCACCTTCTGAGCGGAAGTGCCTTTGTAGCCTAGATCGTGCTCAGCTGGATAGGTTC
TTACTCTTACTTACGGATCGAAATAACAAAAGAAAGAACTAGAGCCCTGCTGTTCTAAAGCACAA
GTAAGGGCTTTTTTGTTCTACCAGAGAGAGTCTATTCTCACACTGAATCAATCATTCGAAGGGTC
GGGGAAGGAAGCGATGATCGGTCTATCCCATTAAGCGTAATCCCGTTAGCCAATGAAAGGACTAC
CTTTCTTGGACTGTGAGCGACGACACCAGATCAGAGCTAAGCGAGAAACGAGAAGCTGCGGTGAA
TCAATCAGTATTAGCTAAGGCAAGCATTCTAATTCTGGGGAAGAA
Right flanking sequence: Indices 77847 -- 78346
GCTTACTAAGCCTTTGTTTGAAGGACCGGTCTGAAAGTGCAAGACTAGCTGGACCCGGACTGACT
AATCGCTAAGAGCTCGTCCCGAGAGAACTCTCAGTACGGCATTCAGTAAGAAGTTAGCCAAGTTC
TGTTAGCCGTTACGTTAGGGTGACTCGAGAAAGTTTGAAAGGGAATTCCGATAGCCCTTAAGCTT
CAAGCTATCCGGCTTCAAGCCGTGAAGGAGGAATCCGAGTTACATCCTCTTAAAATAAGGAAGAT
CGTTCATCAGCGCTTTCAGTAACTAAGAGTCAATCAGGTGCGTAATCAAGCTCATCTCATTACTT
AGGATCTCACTCTCTCAATCTCCTATCTGGATTCTTTGCTTAGTCAGAGTTGAATCTTATAATAA
GGACAAGAAAGACTGGCATTCAGGTAAGGCATGATTCGGAAGATAGTGAATCTCTCCTTACTTGA
CTCTAGAAAGCTCTTTCTTTGCAAGTGGCAAGCAAGACTATGGTT
Found at i:277023 original size:24 final size:24
Alignment explanation
Indices: 276996--277043 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
276986 AACTTGCAAA
*
276996 CATAACCAGGCAGTGAGGGATCTT
1 CATAACCAGGCAGTGAGGAATCTT
* *
277020 CATACCCAGGCGGTGAGGAATCTT
1 CATAACCAGGCAGTGAGGAATCTT
277044 AAGGGAAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (24 bp):
CATAACCAGGCAGTGAGGAATCTT
Left flanking sequence: Indices 276496 -- 276995
AAGGCCAAATCAGGTCTTGTAATATACTGCAGGGCTCCAACGATGCTTCTGTACAGAGATGGATT
ATGAAATGGAGTAGAAGAGACTGCAGCAGAGGACTGATTTTAAAGTTAATTGGAGAAGAGCAGGG
CTTACAATTCAGCATAGCAGCTCTCTGGAGGAGATCCAACGCATATTTTTGCTGTGTTAAAAAAA
GTCCACGATCATTCTTGTCTTGAGTACCTCAATGCCAAGAAAATAGTTCAAGTTCCCGAGGTTCT
TTATAGCAAACTGAGCACTTAATTCAGTGATTAGAGTGGAGATATAAGAGGTATCACTGCCAGTT
ATAATAATATCATCCACATAAACCGCAAGAATTGTAGTTCGCAAACTGTTAGTTTGAATAAATAA
CGAGGAATCACTACGGCTCATAAGAAAGCCTTTACTGATTAAAAAAAACTTATCATACCAAGCGC
GTGATGCCTGTTTAAGACCATACAATGCTTTCTGCAACTTGCAAA
Right flanking sequence: Indices 277044 -- 277543
AAGGGAAGGGGTTGGTAGTGAAGGGAAGTCCAGGGCTGTGTCTGATCAGCTTACTGGGAGAATTC
CAGGCGAGGGAGTATTGGTAAGGTTATGGAGGAAAGAGGAAATAGGATTTTGGGCATCTCTCGTT
GCTTCGGATGTTTATGAGAAAGAAGCTTCTCACAGATATTGACTTTTAGATAGATACCAGCATAG
TATCTTAATTAGCAGTTTCTTGAACTTGGTTGCACTCGTAAAGCAGCTTAAGAGAGCAACGAAAG
ACGGAGCGGTGATATTTCCTGACTAGCAAGTGGAGGATCATTCCAGGCTCTAATTCAGTCTCTGA
TGGCGTAGCTGATGTGTCATGCTAGGAAGCTGAGCTAGGGCATTTCTTCTTTCGGTTTAAGTGTT
CTAAGAAGTGAAAACCCTCCTCTCCGCTTCTGGCAGCATAGAAGGAAGCTTGGGGGAAAGGTCTA
AGTGCAAGCATTGAGTCAAACTGATTCAGGTATAGCAATGTAGTT
Done.