Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: MZ240735
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: 97771
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:43535 original size:24 final size:25
Alignment explanation
Indices: 43508--43557 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
43498 ACCATAACCA
43508 AACTTGAAGCT-GTAGTTACGGATT
1 AACTTGAAGCTAGTAGTTACGGATT
*
43532 AACTTGACGCTGCAGTAGTTACGGAT
1 AACTTGAAGCT--AGTAGTTACGGAT
43558 CTGGCTAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
27 12 0.55
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (25 bp):
AACTTGAAGCTAGTAGTTACGGATT
Left flanking sequence: Indices 43008 -- 43507
GGACCTAGGGCGTGAAATCGCTCCTAAAAAGAATTTATCTCAGGGCAAACTCAAAATTCATTTAA
CTAACCGGGTATTCACTTCTACTAGTCTCGCCTACAACGGATTCAATAGCAGTGGATCTTGTTAA
GACCGCGTCTTCCTTCAACAGCGGGGATAAGAGAAGAGCTAATGCTCTTACTATAGCACCAACCA
AAAGCAGATTCTCGGCATCTCAGAGCACAAGCTAAAGCTTCCCTTGCTTTCGGGCGATTCCTCTT
TGAGCCCGGCCACTCTTTTCATTTACTATCGAGAACTGGATTCGTGAAAATAGAGGATCTCCACT
TGACTTATAGCTGCGTAAGAAAAGCTAGTCAAAGGAGCTGGAAGAGATCCCGCCTCAGATGTACT
CGAGGGATGATGAATCCCCTTTTTTGAGGAACTGAGCAACAAAAGGGGCCATGAGAACTACATTT
TGGTCTGATACCAAAACAATTTTTTTTCCATCATTACCATAACCA
Right flanking sequence: Indices 43558 -- 44057
CTGGCTAGGTTATGTGCTCGTCCCTTCTCTGGGATATCAATTTTAATGGCGGGCTCGACTATGGA
AAAAAATGAATTAATTTTGTTTGAAAGTAACAAAAAGAAGGAATTTCTGCTTTGTAAGAGGGATT
GAGGGACCCAGTCACACTAGCTCAGGCGCAGTACCAGCAGATGCATAAGATGGAGAGGTGCCCCA
TTGATTTAAGACGTAGGTTTAGAATGCCCCACTAATTGATCAAGGGCTCAAGGCAGTGGTAGAGG
TATAGGGCTTGCCCATCATAGGTCGTATTAACCCTATAATAAGTCTAAGCCAGTCCAGCTCTTTT
TTTTAATAATCCCGAACTTCCTATCCTCCTTTCTTTCTAATGAACTTACGTAGATAGATAGCTAT
TCGATATCAATATCTCCTGCTGTAATGACTAGGGGTTATCCTCAACTAGTTTCAAAGTTATGCTA
AGGGGAATTATTGGCATGGTAGAAGGGATTGAGAGCCCTAGAAAG
Found at i:45857 original size:20 final size:20
Alignment explanation
Indices: 45818--45856 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
45808 TCCTTTCTTT
*
45818 TTATTATTTATATTTATATA
1 TTATTATTTATATATATATA
45838 TTATTATTT-TA-ATATATA
1 TTATTATTTATATATATATA
45856 T
1 T
45857 AAATAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTATTTATATATATATA
Left flanking sequence: Indices 45318 -- 45817
GACCCCCGTTGAAGCAATTCCCTCCGCTCCCGATGAATGAGTCACTACAGACTGAAGATGTAGCT
AGCAGGTCCTTGCTTCTCCACTGTTCTGGCTAATCCATGAGATCAGGGCTACCCGCCGTAGCAGT
GAATCCTGACCATGAAGAAAGGTAGTTCCACAAGCCCTTTCTCTTTACGTAACGTAATTTCGGGG
TTGGTAGTTAGCTGCGCAGCAACCAATCCACCTAACGGGAATCAATCAATCCTAAATAGAGTCCC
AAGAACGAGGAGAAAGAATTAAGATTTTTTTCTATTCTTTTTCTTTTTTTAGTAATAATGTAAAA
ATTCCGTTTGTAGGAACAGAGAAAAGAGAACCAGATCTATTCTATACCCGATAAGTACCAATACG
CAATGGGGAGTTGACCCGATTTTATATGAGCGAATGCATAGGGATTTGTTCATCATTCAAAGTAC
CTATTCGTAAGAATTTTACTCTATCTGTTTTGTCTTCCTTTCTTT
Right flanking sequence: Indices 45857 -- 46356
AAATAATAATATATAAATATAAACTTATCGAATAAACTTATCGAATCCATGCATAAAATATTATA
AAAGTTATTATTATTAAGACAATAAATTTTTTCTTACGTTTTCACATCAAAGTGAAATAGAGTAC
TTAATTTTTTCTGTCAAAAAATGCCTATTGGTGTTCCATAAGTCCCTTTTCGATATCCTGGGCAA
CAGGGTTCCATTTGGATTGACATATAGTGCGACTTGTCAGATATATTGGGTCATACGGGATTCCC
CCGTTCTCTCTCCCGATTGAGATATCCTCTGTTTCGCCCAAGAAAGATTGATTAAATCATCCAAA
AATTGATTAAATCATCCAAAATTTGGAGCGTGAAGTGCAATGAAGTCTAATTAGATCTATGCTTT
TGAGGTACTCAGATTTATTATATATATTAGAATAATTTATGGTTGGCTTATTTGGACCAAAAAAA
TGAAGTATCCAGGCTACGTTTAGAAGAACCCAATTGGTAATATAT
Found at i:45891 original size:13 final size:13
Alignment explanation
Indices: 45875--45902 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
45865 ATATATAAAT
45875 ATAAACTTATCGA
1 ATAAACTTATCGA
45888 ATAAACTTATCGA
1 ATAAACTTATCGA
45901 AT
1 AT
45903 CCATGCATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.32
Consensus pattern (13 bp):
ATAAACTTATCGA
Left flanking sequence: Indices 45375 -- 45874
ATGTAGCTAGCAGGTCCTTGCTTCTCCACTGTTCTGGCTAATCCATGAGATCAGGGCTACCCGCC
GTAGCAGTGAATCCTGACCATGAAGAAAGGTAGTTCCACAAGCCCTTTCTCTTTACGTAACGTAA
TTTCGGGGTTGGTAGTTAGCTGCGCAGCAACCAATCCACCTAACGGGAATCAATCAATCCTAAAT
AGAGTCCCAAGAACGAGGAGAAAGAATTAAGATTTTTTTCTATTCTTTTTCTTTTTTTAGTAATA
ATGTAAAAATTCCGTTTGTAGGAACAGAGAAAAGAGAACCAGATCTATTCTATACCCGATAAGTA
CCAATACGCAATGGGGAGTTGACCCGATTTTATATGAGCGAATGCATAGGGATTTGTTCATCATT
CAAAGTACCTATTCGTAAGAATTTTACTCTATCTGTTTTGTCTTCCTTTCTTTTTATTATTTATA
TTTATATATTATTATTTTAATATATATAAATAATAATATATAAAT
Right flanking sequence: Indices 45903 -- 46402
CCATGCATAAAATATTATAAAAGTTATTATTATTAAGACAATAAATTTTTTCTTACGTTTTCACA
TCAAAGTGAAATAGAGTACTTAATTTTTTCTGTCAAAAAATGCCTATTGGTGTTCCATAAGTCCC
TTTTCGATATCCTGGGCAACAGGGTTCCATTTGGATTGACATATAGTGCGACTTGTCAGATATAT
TGGGTCATACGGGATTCCCCCGTTCTCTCTCCCGATTGAGATATCCTCTGTTTCGCCCAAGAAAG
ATTGATTAAATCATCCAAAAATTGATTAAATCATCCAAAATTTGGAGCGTGAAGTGCAATGAAGT
CTAATTAGATCTATGCTTTTGAGGTACTCAGATTTATTATATATATTAGAATAATTTATGGTTGG
CTTATTTGGACCAAAAAAATGAAGTATCCAGGCTACGTTTAGAAGAACCCAATTGGTAATATATC
TATTACTACTTGTATCATATTCTCTTTATGATTATGAAGTAGGAA
Found at i:46180 original size:23 final size:21
Alignment explanation
Indices: 46154--46202 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
46144 TCTGTTTCGC
46154 CCAAGAAAGATTGATTAAATCAT
1 CCAA-AAA-ATTGATTAAATCAT
46177 CC-AAAAATTGATTAAATCAT
1 CCAAAAAATTGATTAAATCAT
46197 CCAAAA
1 CCAAAA
46203 TTTGGAGCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 16 0.64
21 6 0.24
22 1 0.04
23 2 0.08
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.24
Consensus pattern (21 bp):
CCAAAAAATTGATTAAATCAT
Left flanking sequence: Indices 45654 -- 46153
AGGAACAGAGAAAAGAGAACCAGATCTATTCTATACCCGATAAGTACCAATACGCAATGGGGAGT
TGACCCGATTTTATATGAGCGAATGCATAGGGATTTGTTCATCATTCAAAGTACCTATTCGTAAG
AATTTTACTCTATCTGTTTTGTCTTCCTTTCTTTTTATTATTTATATTTATATATTATTATTTTA
ATATATATAAATAATAATATATAAATATAAACTTATCGAATAAACTTATCGAATCCATGCATAAA
ATATTATAAAAGTTATTATTATTAAGACAATAAATTTTTTCTTACGTTTTCACATCAAAGTGAAA
TAGAGTACTTAATTTTTTCTGTCAAAAAATGCCTATTGGTGTTCCATAAGTCCCTTTTCGATATC
CTGGGCAACAGGGTTCCATTTGGATTGACATATAGTGCGACTTGTCAGATATATTGGGTCATACG
GGATTCCCCCGTTCTCTCTCCCGATTGAGATATCCTCTGTTTCGC
Right flanking sequence: Indices 46203 -- 46702
TTTGGAGCGTGAAGTGCAATGAAGTCTAATTAGATCTATGCTTTTGAGGTACTCAGATTTATTAT
ATATATTAGAATAATTTATGGTTGGCTTATTTGGACCAAAAAAATGAAGTATCCAGGCTACGTTT
AGAAGAACCCAATTGGTAATATATCTATTACTACTTGTATCATATTCTCTTTATGATTATGAAGT
AGGAAGAATTTCAAACTGCCTCAATCAAATAAGAATAATAGAATAATAATATAATTAATGAATAT
GTCAAATATTTGGCAGAAGACGTGAAATGAATTAAATAACAAAAAGAAGTTGTAACAAAAAGACG
CAGTATTGGGGCATTTGCTCTATATGTGCAAATATAAATCGGGCAAATTGTTTTCATGCGTGCTG
GTGTTCGTGGTCTGTTGGTTTTTCTGTTTCTGGATCTAATCAACTATGTCTTCTAGTCTGAGAAC
TCTTTGAAAGTGGGATTCCCCCTTTACTTTATAATAATTATATAT
Found at i:46204 original size:19 final size:20
Alignment explanation
Indices: 46163--46202 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
46153 CCCAAGAAAG
46163 ATTGATTAAATCATCCAAAA
1 ATTGATTAAATCATCCAAAA
46183 ATTGATTAAATCATCCAAAA
1 ATTGATTAAATCATCCAAAA
46203 TTTGGAGCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (20 bp):
ATTGATTAAATCATCCAAAA
Left flanking sequence: Indices 45663 -- 46162
GAAAAGAGAACCAGATCTATTCTATACCCGATAAGTACCAATACGCAATGGGGAGTTGACCCGAT
TTTATATGAGCGAATGCATAGGGATTTGTTCATCATTCAAAGTACCTATTCGTAAGAATTTTACT
CTATCTGTTTTGTCTTCCTTTCTTTTTATTATTTATATTTATATATTATTATTTTAATATATATA
AATAATAATATATAAATATAAACTTATCGAATAAACTTATCGAATCCATGCATAAAATATTATAA
AAGTTATTATTATTAAGACAATAAATTTTTTCTTACGTTTTCACATCAAAGTGAAATAGAGTACT
TAATTTTTTCTGTCAAAAAATGCCTATTGGTGTTCCATAAGTCCCTTTTCGATATCCTGGGCAAC
AGGGTTCCATTTGGATTGACATATAGTGCGACTTGTCAGATATATTGGGTCATACGGGATTCCCC
CGTTCTCTCTCCCGATTGAGATATCCTCTGTTTCGCCCAAGAAAG
Right flanking sequence: Indices 46203 -- 46702
TTTGGAGCGTGAAGTGCAATGAAGTCTAATTAGATCTATGCTTTTGAGGTACTCAGATTTATTAT
ATATATTAGAATAATTTATGGTTGGCTTATTTGGACCAAAAAAATGAAGTATCCAGGCTACGTTT
AGAAGAACCCAATTGGTAATATATCTATTACTACTTGTATCATATTCTCTTTATGATTATGAAGT
AGGAAGAATTTCAAACTGCCTCAATCAAATAAGAATAATAGAATAATAATATAATTAATGAATAT
GTCAAATATTTGGCAGAAGACGTGAAATGAATTAAATAACAAAAAGAAGTTGTAACAAAAAGACG
CAGTATTGGGGCATTTGCTCTATATGTGCAAATATAAATCGGGCAAATTGTTTTCATGCGTGCTG
GTGTTCGTGGTCTGTTGGTTTTTCTGTTTCTGGATCTAATCAACTATGTCTTCTAGTCTGAGAAC
TCTTTGAAAGTGGGATTCCCCCTTTACTTTATAATAATTATATAT
Found at i:59422 original size:18 final size:18
Alignment explanation
Indices: 59391--59430 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
59381 GCTGATATCG
59391 ATATTGATGATAGTGACA
1 ATATTGATGATAGTGACA
* * *
59409 ATATTTATGCTAGTGACG
1 ATATTGATGATAGTGACA
59427 ATAT
1 ATAT
59431 CGATCGTGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (18 bp):
ATATTGATGATAGTGACA
Left flanking sequence: Indices 58891 -- 59390
CCAACTAACTTGATCGATTCAGTGCTTGGATTAGGTCCGGGTAGAGAAGAGGTAAGGGCGGTAGG
CTTTTCACTTTAGCCGTTGTTATTAAAGGCCTTTTTCAAGCTTTTTTGAGCCCCTCTCCCTTTGG
TCGAGCTGCTTTTCGCCCCTCTTTCTTTCTAGTTAGGGAGGCAGTAGATGAAAGCCTATTCAGTA
AACTCTTTCAGCTTCCGCTTCTTAATCTGGATGGCGGCTTTCGTTGGAGAAGAGAGTGTTTCAGT
TACGGTTTAGGGCTAGTTAGTTACTATACGTTCGTGAAAGCAGACAGGCGCTTGACGAAAGAAAA
GCCTTTTCGCTCCGCTTAGCCTTATCCCCCTCTAGGGGTATTTTAGTGATAGGTTCTATAGGAAC
TGGACGATCCTATTTGGTCAAATACCTAGCGACAAACTCCTATGTTCCTTTCATTACGGTATTTC
TGAACAAGTTCCTGGATAAGAAGCCTAAATTTATTGCTGATATCG
Right flanking sequence: Indices 59431 -- 59930
CGATCGTGACCTTGATACGGAGCTGGAACTGCTAACTTGGATGAATGCGCTAACTATGGATATGG
AGATGATGGCAGAAATAGACCGATTGTCTATCACCCTTCAATTCGAATTTGCAAGAGCAATGTCT
CATTGCATAATATGGATCCCATGATCCGGATGTGAATGCTCCACGGAGAAAGGGTTCACCGAGGC
CCTAGACGAGGGAGATATTGGCTTTGTTGGCGAAAGTTAAGCTTAACGGTTGGATCGAGTAGCAG
GTCTCAGTTAATTGAGAAGACGGAAACTACAGACGGTGAAAGGGAAGACCAAGATAAAAAAGACC
CAAAGCTATTAATTCGATGATACGGGAACGACCACGGTTTCATCATTCCACAGGGAGCCCCGCCT
AAAGTGTATTGGTTCTGGTTCTCACACTGTTTCCCATTCGGGAATTGAGTCTTTCATCGCGAGGT
AGGCTTTCGTATCACCGATAGGTCTTTCGCTCCTGTTATTGGTTC
Found at i:71361 original size:11 final size:11
Alignment explanation
Indices: 71336--71366 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
71326 TCTAGGAATA
71336 TCTACTGTA-T
1 TCTACTGTAGT
71346 TCTACTGTAGT
1 TCTACTGTAGT
71357 TCTACTGTAG
1 TCTACTGTAG
71367 CATCCTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.45
Consensus pattern (11 bp):
TCTACTGTAGT
Left flanking sequence: Indices 70836 -- 71335
TACAGATGCTGATTGGGCAGGATGCCCCTGGGATAGGAGGTAAACTTCAGGGTATTGTGTTCTTT
TTGGTGGAAACTTAATCTCATGGAAAAGTAAGAAACAAGATGTGGTAGCACGATCAAGTGCAGAA
GCAGAATATCGGTCAATGGCCCTTGGAACATGTGAGTTAATATGGTAGAAACACCTTCTCAGTGA
ATTGAAGTTCTGCAAGTTAGGCCCTTTGAAATTAATATGTGACAATCAGGCAGCTTTGCATATTG
CCTCTAACCCAGTCTTCCATGAAAGAACAAAACATATTGAGGTTGATTGTCACTTTGTTCGAGAA
AAGGTTGCCTCTGGAGAACTAATTACCTCTTTTGTTGGTTCGAATGATCAACTAGCAGATATTTT
CAAAAAATCTCTTAGGATTGACTATATATGTAACAAGCTTGGAGCCTATAATATATACGCTCCAG
CTTGAGGGGGAGTGTTGAGTTGAGAATGTAAAATATCTAGGAATA
Right flanking sequence: Indices 71367 -- 71866
CATCCTTGGGCTCCAAGTATTTCCCCCTGTATAAATATGTCTCTTGTTATCCCTTTTGAGATCAG
ATAATAGAAACCTTCTTTTTCTTCCTAAATATTCTCTTACTCAACAGCTACTAAGAACCTCACAG
AAGCATCTTTCTTTTTTCTTTTTCAAGAGCCTTTTTAGCCTCTTTCGATCGTCTTGGTCGTGGGA
GGATCAACACCAAGATTGATCTTCGTTAAAGCCTACAAAATAAAGTCTCAAGCGAAGTAGGAGTT
CCATGTTCGTAAACAAGGTGTTTTTGAACGAGTATTGGCATTTGGCACCGGCAACACAGGCAATC
TATGATAAACTGCAACTAGAACTATTTTAGGGCGTAACGTTTTAGTTGTTCCCTCTCCTTTCAGT
CGAGCTCTATTAACATAGACCCTCTCCTTCGGTTCTGTCTCCTGGTTGTGAATAACCCACTAACT
TGCTTGGTCAGGTCTTCCTTTTATGTGAGTAGAGTAGGCGGAGAC
Done.