Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_071385
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: 412026
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Found at i:44228 original size:22 final size:22
Alignment explanation
Indices: 44200--44243 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
44190 TGTCGTCTAG
44200 CGGAGCCTAGAAGAAGGTGACT
1 CGGAGCCTAGAAGAAGGTGACT
44222 CGGAGCCTAGAAGAAGGTGACT
1 CGGAGCCTAGAAGAAGGTGACT
44244 TGCGCAGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.36, T:0.14
Consensus pattern (22 bp):
CGGAGCCTAGAAGAAGGTGACT
Left flanking sequence: Indices 43700 -- 44199
GAAAAGGCCTCTGACTCTAGATAGGGCGTTAGCGCTTTACTAATAGAATAGTTAGGGCTTTTCTT
GCTTGTTTAGTAAAGTCACGCTTTTCATTTTGATAGGAGTAGGTGCTTTTTTGGGCAGGGCACTC
TTCATTCCTTTCTTCAAAACTAATGAATGTCGGGTCGGGGCTTTCTGCCTTGTTATCAAAAAAGG
AGTTGGGTAAAGCAAACTCCCTCCTTGGACGAGCACGGGGCAACGTCAAGTAGAACCGGGTTGCG
TTGCTTGATGCTCCGATCGAAAACAAATCAGTGGGGCCATGCCGGTACGACTGAATATGCGTTAA
AAAGGTCAATCCCTCCCCTACGACACCAAAAAAAACCGGGCCGAACTTATAACTGCCCGCCCGCT
TCCATAGAACAATATCGTGGCAACGTAGACCTAAGTGGTCATATTGGATCCTTGGGAACCATCAC
AAGTAGGGCCGGCCTATATTTGAACGAGAATGCCGTGTCGTCTAG
Right flanking sequence: Indices 44244 -- 44743
TGCGCAGACAGCTGACTCCTTTTCAATAGAAAGGAATAGCCAAACCAACCCAGCTGGATGGTCAA
TCTCAGAGATCAACTCGGCCGGCAAACCGGAGACGGACGACCACGGTCCCGACCTGACCAGCACC
ATAGGTGTACTAATCAAAGAAGCCCCTAAACCTACTTTCTTTTCTTACAAAATCAACCAAGCCTA
ACCGGTCAGGACATCTTGTTGATATTGATTGAGTTTGAGGGACTTTCGCTGACTGAATCCATCCA
TAAACCTAGACCCCGGTAACCTTCGTAACCAAAACGTCACGACAACATCCAAAGGTCACCTTTGG
ATTCTTAAGTAGGGGGGCAAGGAGGAGCACGTAGGAATGCCGACCACTACAGTTGCCACTAGTGG
CTGAGAGAAAGCGAGCAGCACCTTGTATAGGTTGGGCGGAGCTTGAAGAAGCGAGCCCCTATCAG
AGAAAGCCATTGCGCGTTAGCCTAGCTAGCTAACTTCAGCTGGCT
Found at i:76626 original size:15 final size:16
Alignment explanation
Indices: 76606--76638 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
76596 ACAAAGCAAG
*
76606 CTTA-TTGAAATAGCC
1 CTTATTTGAAAAAGCC
76621 CTTATTTGAAAAAGCC
1 CTTATTTGAAAAAGCC
76637 CT
1 CT
76639 ATAGCTGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (16 bp):
CTTATTTGAAAAAGCC
Left flanking sequence: Indices 76106 -- 76605
GAATGACGACTAGGTACTGAGCCCCTCAGCAAACCCTTGCAAGAAAGAAGAGAAGGACACAAGAA
GAACACGCTCCTTCCTGGAGTTGAAAGACTCCAAATTCGAATCACTTGCTACTGGTGCTTTCCAC
CTTCCACCGCTCTAAAGTGTGTTTCGTAAGGGGGTAGGTTGCATTCTATCGTATAGAAAATAAAG
AAGCAAGACGGACAACATAAAGTTAAGCATAAGGTGCTATTATTGGCAAAAAACCTGGTCTTCGC
TCCCTGTCCCTGGATCAACGACTAACGGACGAGGAGAACTCGACGTGAAAGCTTAATGGGCAAGC
GAGACTTCCCTTGGTCTTAAGGGCGTGGAACCCGAAGCGTGAGCGTGAGGTCGCGCCAAAGAGAC
GATCGACAGTGAGGCCTATCATAAAGTAAAAGTGACTTGTTTGGGAGTCAGAGGGACATTGTCGT
GATAATGTGCCTGGGAGTTAAACTGATAAACAACTACAAAGCAAG
Right flanking sequence: Indices 76639 -- 77138
ATAGCTGCTCTACAGTAAGGCCGGCCTGGCCTCTGGGCCGATTCATCATATTCTCGATCGAGATT
TGGGCGTATATGCATCTTTCTCATAATTCAATTCTGCGGACTGCGAGGTGACCTTCGGAGAGGCC
TATAAGAACCTAGACAGCAAATAAATGTAGGAGCGGACGGAACGAAACTACATCTGATGTCGCCC
GCTATCAAGCGATCAAGTCAGTGGTGTTAAAGTCAGGTGTTCCAGAGGGGCTAATGGTTTTCCCC
AGTCAGAAGCATTTTGTGAACTAACACTCTGCACAAAGGTCTCCACCCTGTGAAGCTCATTCATG
TGGTAGAGGAATGAGAGCTTTTCTAAATCCCCGGGGGGCCAGCCGAAGATGAAAGGTCCGCGGAT
CAACCTCAGCAGGTTTGGTTCCAGTTTGTTTGGAGGGAGTCCCACCAATGGGGCAGGGGGCGCGA
TAGTGCCCTTTATTCCGGGTGACCTGGATAGAGCACTTTTGATCA
Found at i:92461 original size:21 final size:20
Alignment explanation
Indices: 92437--92482 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
92427 TAAAGCTTAT
*
92437 GAGAAAGACGAATCCCTATA
1 GAGAAAGAAGAATCCCTATA
92457 GGAGAAAGAAGAATCCCTATA
1 -GAGAAAGAAGAATCCCTATA
92478 GAGAA
1 GAGAA
92483 GTATATGCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.48, C:0.15, G:0.24, T:0.13
Consensus pattern (20 bp):
GAGAAAGAAGAATCCCTATA
Left flanking sequence: Indices 91937 -- 92436
GAAAAAGGAATCAATATAGTGATAATTTGATTCTTCGTCGCCGTAGTAAATAGGGGAAAAATGGA
ATTTCGTTCTTCGTCTTTACAAATGAAAAAATAGGAGCAATTAATCGTGACACGTTCACTAAAAA
AAAACCCTTTTGTAGCTAATCCTTTATTAAGAAAAATCGAAAAGCTTAATACAATGATGGAAAAA
GAAATAATAGTAACTTGGTCGCGGGCATCTACCATTATACCTACAATGATTGGGCACACTATTGC
CATTCATAATGGTAGAGAGCATTTGCCGATTTATATAACAGATCGTATGGTCGGTCATAAATTGG
GCGAATTTTCACCTACTAGCAGTTTCCGCGGACATGCAAAAAACGATAATAGATCTCAGCGTTAA
GTTAAAAAAAAAAAAGAATATTAATTTGAATTAAATTAATATCGATAATATTAATATCGAGAATG
AATGATGATTAGTCCTCATTATCTTTAAGAGGAGATAAAGCTTAT
Right flanking sequence: Indices 92483 -- 92982
GTATATGCCTTAGGTCAATATATCTCACTATCTGCTCACAAGTCGCGAAGAGTAATTGATCAGAT
ACGTGGATGCTCTTACGAACAAATCCTTATGATACTTGAACTTATGCCTTATCGAGTGTGTTATC
CAATTATAAAATTGATTTATTCTGCAGCAGCAAATGCTAGCCACAATTGGGATTTCAATAAAACA
AGTTTAGTTATTAGTCAAACTGAAGTTAGCAAGGGTACTACTGTAAAAAAACTAAAACCTCGAGC
TCGGGGGCGGGGTTATCCAATAAAAAGAACCACTTGCCATATAAGAATTGTGTTGCAAGATACTT
CTTGGTATGAGTATGACGAAACTAAAGAATATCTTTTATGCTTCAAAAAGATGACTGAAAAAAAG
AAAAAGAAGCACCAAGATATGACGTATTCTTCGACGTATAATAATGGGGGATTATGGGACAAAAA
ATAAATCCACTCGGTTTCAGACTTGGTACAACCCAAAGTCATCAT
Found at i:96770 original size:22 final size:22
Alignment explanation
Indices: 96742--96787 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
96732 TTGAAAATAG
* *
96742 ACTCTCTAACAAGCATAAGGTA
1 ACTCTCTAACAAACATAAAGTA
96764 ACTCTCTAACAAACATAAAGTA
1 ACTCTCTAACAAACATAAAGTA
96786 AC
1 AC
96788 CAATACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.46, C:0.24, G:0.09, T:0.22
Consensus pattern (22 bp):
ACTCTCTAACAAACATAAAGTA
Left flanking sequence: Indices 96242 -- 96741
ATTCTTTCTACTTCTCAAGGGATAATGACAGACCGAGAGGCTCGACTGGAAGGAATTGGCGGAGA
AATTTTGTGTTATATATGGTAATCCTTCTAATATTTGAATTGTCACCAGAATTGACTATTTGGCA
AAAGAAAAAAAGACGGGTTAATTACTCGTAACTTATTTGATACTTCGAGAGGTTTTAACTAAAAT
GAAAAAATGGATTCCTAATTCATAAGAACAAGGATTCGAATGATTAGGATTAGGTGCTTTTTTTT
AACCATCAGCCTTTCTTTGATGAAAATACAATTCGAGGTTCGGGTTTCAAATTTCCAGAGATTGA
TTTTCTTCCACTAAGTAGATTCAGAATTCAGTTTAGGAATGACAACTATGAAAATAAGGGCCTCC
GTTCGTAAAATTTGTGATAAATGCCGATTGATCCGTAGGAGAGGACGAATTATAGTAATTTGTTC
CAATCCGAGACATAAACAAAGACAAGGATAATCTTTTGAAAATAG
Right flanking sequence: Indices 96788 -- 97287
CAATACAAAAATAGGATCTGTTTTGACATGAAATGGATATATCCATATACCTCTAATTTCTCATT
ATAAGATGATAAAGTAAAGTATGGCAAAATCTATACCAAGAACTGGTTCCCAGAGAAATGCCCGA
ATTGGGTCACGTAAGAATATACACCGAATACCAAAGGGTGTTATTCATGTTCAAGCAAGTTTCAA
CAATACCATTGTGACTATTACAGATGTCCGAGGTCGAGTAATTTCGTGGGCCTCCGCCGGTACTT
GTGGATTCAAAGGTACACGAAGAGGGACGCCATTTGCTGCTCAAACCGCCGCAGGCAAGGCTATT
CGTACAGTCATAGATCAAGGGATGCAACGAGCAGAAGTGATGATCAAAGGGCCCGGTCTCGGTAG
AGATGCAGCATTACGAGCTCTTCGAAGAAGTGGTATACTATTAAGTTTCGTACGTGATGTAACCC
CTATGCCCCATAATGGCTGTAGTCCCCCTAAGAAAAGACGTGTAT
Found at i:120878 original size:13 final size:13
Alignment explanation
Indices: 120860--120885 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
120850 TGCCCTCCCT
120860 CTCTATCTATCCA
1 CTCTATCTATCCA
120873 CTCTATCTATCCA
1 CTCTATCTATCCA
120886 AGGGATGGAA
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:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (13 bp):
CTCTATCTATCCA
Left flanking sequence: Indices 120360 -- 120859
GAACGTCGTGAGACAGTTCGGTCCATATCCGGTGTGGGCGTTAGAGCATTGAGAGGACCTTTCCC
TAGTACGAGAGGACCGGGAAGGACGCACCTCTGGTGTACCAGTTATCGTGCCCACGGTAAACGCT
GGGTAGCCAAGTGCGGAGCGGATAACTGCTGAAAGCATCTAAGTAGTAAGCCCACCCCAAGATGA
GTGCTCTCCTATTCTGACTTCCCCGGAGCCCCCGGTAGCACAGCCGAGACAGCGACGGGTTCTCT
GCCCCTGCGGGGATGGAGCGACAGAAGTTTTGAGAATTCAAGAGAAGAAGGTCACGGCGAGACGA
GCCGTTTCTCATTACGATAGGTGTCAAGTGGAAGTGCAGTAATGTATGCAGCTGAGGCATCCTAA
CAGACCGGTAGACTTGAACCTTGTTCCTACATGACCCGATCAATTCGATCAGGCATTCGCCATCT
ATTTTCATTGTTCAACATGAAAAAACCAAAAGATCTGCCCTCCCT
Right flanking sequence: Indices 120886 -- 121385
AGGGATGGAAGGGCAGAGGCCTTTGGTGTCCCCTCCAGGCAAGAATTGGGTGGGGCCTCACAATC
ACTAGTCAATATGTTTTTCTCTCATGCCTTTCTTCGTTCATGGTTCGATATTCTGGTGTCCTAGG
CGTAGAGGAACCACACCAATCCATCCCGAACTTGGTGGTTAAACTCTACTGCGGTGACGATGCGG
TAGTATATATAAGGGATCAATAGCTGATACCACTCCTCCCTCTTGCTCATTATTCTACCTTTGAA
TTACTTTCTATCGCGGAATATATTGCTCTTACAGATCCTGCTGTTAAATCAGCTGTTATTATACT
TCTATTAGCATTAGCTTTTTCATAATAAATCTTTTTCCTTAGCCGATTAAAGCCTTACTAAAGGC
TCCTTCCTAGAACAATGAACTCGGGAAATTCAAAAAGAAGATTCGCCAGGATGGACGAACGAAGT
AACTCGACCCGAGTCAAAGACTGTTTACGAGATATAGGCTCGACC
Found at i:166956 original size:15 final size:16
Alignment explanation
Indices: 166938--166970 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
166928 AAGTCAGCCA
166938 AAAAG-AAAGACCACC
1 AAAAGTAAAGACCACC
*
166953 AAAAGTAACGACCACC
1 AAAAGTAAAGACCACC
166969 AA
1 AA
166971 GATACGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.58, C:0.27, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAAGTAAAGACCACC
Left flanking sequence: Indices 166438 -- 166937
AAAACAGCCTTGAATCAAGCTCTCTCTCAGAGGGAGTATAACCGATTACTCGAGTTCGAGAATAG
GGATCTTCAGATCCGGGAGGGGAAACATAATTGTTTTTCTCTCTTTCAACAAGTTCTTTCTAAGC
ATCCTGCCTTGGCCGAAAAGGCCTGCTACAAGCCCCAAGAAGCCTTTTTTTTTAGACTTCTTTAA
CGAGAAGCGGGACGAGCTGGACACTCGCCTAGAGTGGAGCCCAGAAGCAAGAGACCAAAGATAAA
TCCTTTATAAAGTTGGTCAAGATATCCGAAACCGAGGACCCAACTCTATCTATATAAAAGAAATC
CTCGGATATCCTACTAACGAGTAAGGGATTGGAATGGAAGCCTGCGGAAGAGAGAAGGTGAAGCA
GCTCCCTGGGCTTGGCTTACAAGCCTTGTTGTTTTGGACTCGGGAAGCCCCGAAGTTTGCGCAGT
GAATGCTGCTGGATGCTTCTGATCAATAGGAAGAGAAGTCAGCCA
Right flanking sequence: Indices 166971 -- 167470
GATACGCATAGTGATTCGATCTTTTGATCACCCATTTTTTGAAAACCATTTGTGGGGGCTTCCGC
CTTACACACGGAAGATTGGATTGCCTGAATCACGAGTAAACTATACTGTCTTACGATCACCTCAT
ATTGATAAAAAGTCCAGAGAACAATTTGAAATGGAAATCAAGAAAAAATTTCTGGTCATAAAAAC
AGAAAGGCATGAATTGCGCAAGAAGTTCTTTCGGTTAAAACGCCGTGCGACTCGGAGGACATAAG
ACTTCTTTTCTTGGTCAAGCCAAAAAGATTTCCGACAGGATGCTCCTACCCCACCGTGCCTGGCC
CTTTACCTTACCTTAAGAAGAAAGAGGGGGTATGAAGCGTGGGAAAGACTGCCATAAGTGTATGA
TAAACAGGTAACCAACAGTCTTGGAGTGGCGGCAAAACTCTTGATTGATCAACGCGAGTGAACTG
TGCTTAGACGCTTCGTCAAACCGCACCGATCTACAAGAAGAGCTG
Found at i:249539 original size:24 final size:24
Alignment explanation
Indices: 249512--249559 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
249502 TCGATTTTGG
249512 TTCTCAATAGAGGGGAATTAGTAA
1 TTCTCAATAGAGGGGAATTAGTAA
* *
249536 TTCTCTATTGAGGGGAATTAGTAA
1 TTCTCAATAGAGGGGAATTAGTAA
249560 ATGCCATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.33
Consensus pattern (24 bp):
TTCTCAATAGAGGGGAATTAGTAA
Left flanking sequence: Indices 249012 -- 249511
ACTACTGGAACTCAAAGCGGGGTAAACATTGCATGAGGGACCACAAGACAAAATAAATGGAAAGC
GTACCTTACGTTGGATGGAGAGACGGACAAAGAGAAAAAGAAGAACCAATGTTTCCAGTCGAAGA
GGCGGGCGCATATAGCTTATTCTAAGTATATTATGAAACAGGTTACCCGGACCTATAAATAGCCC
ACGGACGTTTTCAACCCAATCAATCTTTTTGAAGCCTTCACTTCACCGTTGAGCGCTTAGTCCCG
CCAGAAGGAAATTATAAACTTCTTACCAACGCGGATTAGTTCTTAAGACTGCTCCGCTCACTAGG
ATACCGTCTTACGCGGTACCCGGTCTCAGACCGGACAGAACAAAACTACTCTCTAGCTCCTTCTA
TAGCTAATCGAGGAGAAGTTCTCTAGACATCCCTGGTTGTTACCGTTTTAGGAAGTCAACTCTTG
CCACTCCTACCTCTGGTTATCAGGCCAAAATAACCTCGATTTTGG
Right flanking sequence: Indices 249560 -- 250059
ATGCCATAAGATCCCGTGCTATCGGAGATCTAGGCACAAGCTCCCATCCATACTAAGTCTTAGCC
TCTTCTCCATACAAAAAAAAGGGTGTTAAGCCAAGCCCGTGGTCGACTTCAACGAAATTCGTTAC
ATTGCCCCTACTGAATATGACTATTCGGTGAGTGCTGTGATCAGGGATGTCCAGTGGAACTTTAA
TGATATTGTTACTTCAATACCCGCTGCTCTCCAGGAGAGAATTCGGGGAGTACATCTTAAACTCT
ATAGCCGGGGTCATGATACTCTTCGATGGTTTGGTTCTTCCTCTGGGATAAAAAAGAGATAGAGG
CGGAGCACTTAGAAGAGCTCAAGGAGTGCTTAGGCGTCTGTCGCACGACTTGCCGCTGGTCAAAG
AATCTTTCACTTCCCTTCGGGGACCGGCCATAACCTTGCTTTCAGTCCCCTTTAAGCAAGTCCTC
ATCGTCGTCTTAGTCACTTTCAGACGAACTAGTCTTCTATCTTAA
Found at i:285770 original size:24 final size:24
Alignment explanation
Indices: 285738--285853 Score: 144
Period size: 24 Copynumber: 4.8 Consensus size: 24
285728 CCAACTCTAT
** *
285738 ACAATACAAAGCCTAAGAAGAAAG
1 ACAATACAAAGGATAAGAAGAAGG
285762 ACAATACAAAGGATAAGAAGAAGG
1 ACAATACAAAGGATAAGAAGAAGG
* *
285786 GCAATACCAAGGATAAGAAGAAGG
1 ACAATACAAAGGATAAGAAGAAGG
* *
285810 GCAATACCAAGGATAAGAAGAAGG
1 ACAATACAAAGGATAAGAAGAAGG
*
285834 ATAATA-ACAAGGATAAGAAG
1 ACAATACA-AAGGATAAGAAG
285854 GACCACGACA
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
24 83 1.00
ACGTcount: A:0.55, C:0.11, G:0.24, T:0.09
Consensus pattern (24 bp):
ACAATACAAAGGATAAGAAGAAGG
Left flanking sequence: Indices 285238 -- 285737
GCTAAGCCTATGCCTCAGCTCTGGGAACCGGAAGGAACTGAGCGCCCCGGCGGAGAAATTCAATT
TAGAATAAGAATAAAAATGGAAGCCTAAGCCTTCACATTAGAAACTTCAAAATTCTCAGTTGGAG
AATCGTTTTTACAGGGTGGGCATGGTGTTGGCAGAATGGAAATATAAAACTACTAAATGACTTAG
TCTTGCCTTCTAATAGATGTTCTGTCTTTCATTATTAACATCCAATCCCATGCTAATAAGAAAAA
CGAGCGATTGCTAGTCAGCTTTCATTTTTTGAAATAGTGTTTGTTTGGTAGGGGCTGAGGCTCAG
AAGGCTTTCCAACTTGCTTCAATTAGGGAATAGCGCAGATGGATCAATCACGCGGTTCTGGAGCG
TCCTCCAACTTGCTTTCCGCTCCCCTTCACTTTCAACGCTGGACGGGAAGGCCTGGCATTGTGGA
GCTGTGAAGATGATAATACCTTTATTATCAATATACCAACTCTAT
Right flanking sequence: Indices 285854 -- 286353
GACCACGACAATAGCTCTCCCGATAGACCCAAACCAGATGAATAAAAGAAAAGAAGGCAACCAGG
AGAAGGAGCTAAGAAAGATAATGCAGGAGAAAGATAATGAGAAGATGAATAAAAGAAAAGAAAGA
TAATGAGAAGGGCCCTCCCCTTATCTCCCAACTCTCCGGTTCAACCGTTAGACCGGTCCATTTTA
ACACCATAATCTCCTCGTTGACACGATCACCTAAGATAACCAGACACACCAAATCCTAAGCACTA
ATCATACGATTTCTCATTACAGATGAATTATACTTTCAGGTCTTTCCCATTGTAGATGCCAATAT
ATATTCCAATATAGCTTTCCTTGCCAAGGTCTAAGATCCCTCCTTCTAGATTATTGTTTAGCTGT
CATTATTCTCAAAGTATTCTTTCATTTTTTTGGCTATCTGGTCTTTCGGCATCGTGGATATGGAT
TCATCCACATGTGGTTTTTCTTCTTTCGAAAAGAAGTGAATAACC
Found at i:285833 original size:12 final size:12
Alignment explanation
Indices: 285770--285853 Score: 60
Period size: 12 Copynumber: 7.0 Consensus size: 12
285760 AGACAATACA
285770 AAGGATAAGAAG
1 AAGGATAAGAAG
** * **
285782 AAGGGCAATACC
1 AAGGATAAGAAG
285794 AAGGATAAGAAG
1 AAGGATAAGAAG
** * **
285806 AAGGGCAATACC
1 AAGGATAAGAAG
285818 AAGGATAAGAAG
1 AAGGATAAGAAG
* *
285830 AAGGATAATAAC
1 AAGGATAAGAAG
285842 AAGGATAAGAAG
1 AAGGATAAGAAG
285854 GACCACGACA
Statistics
Matches: 48, Mismatches: 24, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
12 48 1.00
ACGTcount: A:0.54, C:0.08, G:0.29, T:0.10
Consensus pattern (12 bp):
AAGGATAAGAAG
Left flanking sequence: Indices 285270 -- 285769
AGGAACTGAGCGCCCCGGCGGAGAAATTCAATTTAGAATAAGAATAAAAATGGAAGCCTAAGCCT
TCACATTAGAAACTTCAAAATTCTCAGTTGGAGAATCGTTTTTACAGGGTGGGCATGGTGTTGGC
AGAATGGAAATATAAAACTACTAAATGACTTAGTCTTGCCTTCTAATAGATGTTCTGTCTTTCAT
TATTAACATCCAATCCCATGCTAATAAGAAAAACGAGCGATTGCTAGTCAGCTTTCATTTTTTGA
AATAGTGTTTGTTTGGTAGGGGCTGAGGCTCAGAAGGCTTTCCAACTTGCTTCAATTAGGGAATA
GCGCAGATGGATCAATCACGCGGTTCTGGAGCGTCCTCCAACTTGCTTTCCGCTCCCCTTCACTT
TCAACGCTGGACGGGAAGGCCTGGCATTGTGGAGCTGTGAAGATGATAATACCTTTATTATCAAT
ATACCAACTCTATACAATACAAAGCCTAAGAAGAAAGACAATACA
Right flanking sequence: Indices 285854 -- 286353
GACCACGACAATAGCTCTCCCGATAGACCCAAACCAGATGAATAAAAGAAAAGAAGGCAACCAGG
AGAAGGAGCTAAGAAAGATAATGCAGGAGAAAGATAATGAGAAGATGAATAAAAGAAAAGAAAGA
TAATGAGAAGGGCCCTCCCCTTATCTCCCAACTCTCCGGTTCAACCGTTAGACCGGTCCATTTTA
ACACCATAATCTCCTCGTTGACACGATCACCTAAGATAACCAGACACACCAAATCCTAAGCACTA
ATCATACGATTTCTCATTACAGATGAATTATACTTTCAGGTCTTTCCCATTGTAGATGCCAATAT
ATATTCCAATATAGCTTTCCTTGCCAAGGTCTAAGATCCCTCCTTCTAGATTATTGTTTAGCTGT
CATTATTCTCAAAGTATTCTTTCATTTTTTTGGCTATCTGGTCTTTCGGCATCGTGGATATGGAT
TCATCCACATGTGGTTTTTCTTCTTTCGAAAAGAAGTGAATAACC
Found at i:292785 original size:18 final size:19
Alignment explanation
Indices: 292759--292794 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
292749 GCCTCAACAG
292759 CAGAGCTAGATGC-AGATA
1 CAGAGCTAGATGCGAGATA
*
292777 CAGATCTAGATGCGAGAT
1 CAGAGCTAGATGCGAGAT
292795 GATCCCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (19 bp):
CAGAGCTAGATGCGAGATA
Left flanking sequence: Indices 292259 -- 292758
GTACAGCTTTCGATCAAGATGTTCTCGCCTCCCCAGTTCGGGCTCTTGCTCGAATCGGAACCTTT
ATGCGTTAGTAGGCTTTCGACTCAATCTAATAGCCCGGGCGCCAATAAAAGAGAAAGTTTTCGCA
TAGGCTCATCATCTGATGCAGAACCGATGCGAGAGGGATAATAAAGATGGGAGAAGCGGGGATTG
AACGCTTTCAAGAACTAGTGGAAATGAACGCCACCCTTGGTAGTTTTCAAACAAATTCCATCTTG
GGCCAAGCGTTGCCAGCCGGTAATAGTCGAAGGCAAAAAAAGACTTTTTTTGTTGGAATGAAATA
AGGGCGAGAAGGAAGAGAAGAAGGATGAGTAGTTGCCTAGCCGAGGAACTTGAGGCCGACATTCA
GAGTGCGGTCCTGAAGTTCAAGACGGCGCCTAAAACTAGTGTCGGTCATAGAGAGGCATTGATTT
TTCAATGAAAGAAAGCCCATCTCTTCTTCCCTCCCGCCTCAACAG
Right flanking sequence: Indices 292795 -- 293294
GATCCCGAACCTATTTCATAACCACCATACATCACCAATCACATTCCACATCCCACTTCAAGCTT
TTCGATTCCCCGGGTAGCCTCCTCTAGAAAGGCATTCCAGCTTCAGAGGCAGGTGAGCCGGGGTC
AGGAAGGACTTTGACTGCTGGGATGGGATCGGATCCAACTCGCAGCACTCCACCCCGAAGGTGAG
TCTTCGGGGCAGTAGATATAGGAACTCCTATCTGTAGGGCGGGATTTCAAGACAGAGATTCACTA
CTCCATCTGGAAAGGGCTTTACCTCGTGGGGAAAGAGAAGAACCCTTATTTATTGTTAGGTAAGG
CCAGAAGGGAGTCATAAATCAATAGAAAAAAGACCTTCCCCTGAACAGGTCGAGAGAGATGAACT
CGCACCCCATTTATTTGACTTCCTTCGAACCGAAACCCCCAACTAGAGATAGAATTCCAGAACCT
AAACAACTCAGTTGAGAGCTCCGTGACCGGTTCAAGGGAAGGGTG
Found at i:334471 original size:23 final size:23
Alignment explanation
Indices: 334445--334488 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
334435 GTATAGAGAG
334445 ATCCCCTAGATATACAGATAGTT
1 ATCCCCTAGATATACAGATAGTT
334468 ATCCCCTAGATATACAGATAG
1 ATCCCCTAGATATACAGATAG
334489 AATAAATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (23 bp):
ATCCCCTAGATATACAGATAGTT
Left flanking sequence: Indices 333945 -- 334444
GGTGAACAAGGCCCTAGCTTCTAGAGTTCGCTGCTTTTCCCAGGCCTGATAAGGGCTCGCCTTTG
TTTGATATGTTCATTCAGTACCAATACAAACAACAACTACACCAAAGTGAAAGTGGAAGGCCCAC
TATAGAAGCTAGAAGTAGCCTAGAGTAGTCGGCCCGTAATGCCTCCCGTCATTTGCTTGCCTCCT
TCCTTCCAGCTCAGAATGCTTAGCCTCCAGCGCTAAGTAGATCTTTTAGGCTGGGCTTCGTCCCG
GAAGCTACCGCTTGGTAGACAGCTCCGCTTCCTCGTCTTCCTTCTGGCAAAGCTTCAACAACTTT
GCTTGCTTCTCTCGCGCTTGCTTGCCCGAAGGCAACAAGTCCTTTTCGCTAGGTCCAAAAGCTTC
CGTGTCAAAGCAAAAGATCTGATCCAACCCGCATATTGAGCGCAGCTGATTTGCGCCTAGGACTA
GGTGATCATCTCATGCCATAAAACATTTTTTTTTTGTATAGAGAG
Right flanking sequence: Indices 334489 -- 334988
AATAAATGTTCATGGATAAACAGACATTCCATTGATTCGTCAGTTTTGGGGCTGAAAAAGCTCGT
CGATCCAAATGAATCATTCTTCTGGTCTCTATTCGCCCCCTCGCCCCGAAACTGACCCACAGCAC
AGCGCCCATTCGCTTCGCGCGCGGGAAGGCAACGAAGTTCAGTTCATGAGACCGCAGCGCGGAGT
GGAGCAGCCGCGACACGAAGTTCCTTACCAACGCTGGATATCGCTGGTGCCACCTAAACGGTAGT
TAGGCGGTGGATGTGTGACGTTTGGAGTTGTCGTTCGTGCACCTGTCCCCAATGGAAGAATGAGT
GATCCGTTCCCCTGCAGATCATGGCCTTCCCACTCGGTCCCCGATGGCCAGCGGGGGATTCGGTA
TAGCTGCTCACGGTCGTTTGCGCTGCGCGTTCCCGCTGGACTGGACACGTGTTAGCTGTAGGAAG
TATGGTTCCGAAAGTGACTTCGGTTCGCCAGTTCAGGCTCAACTC
Found at i:382095 original size:18 final size:18
Alignment explanation
Indices: 382074--382118 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
382064 AAGGTCACGA
382074 TCAATATCGTCACTATCC
1 TCAATATCGTCACTATCC
382092 TCAATATCGTCACTATCC
1 TCAATATCGTCACTATCC
382110 TCAATATCG
1 TCAATATCG
382119 ATATCATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.33
Consensus pattern (18 bp):
TCAATATCGTCACTATCC
Left flanking sequence: Indices 381574 -- 382073
TAATCGATAGGGCCTCATTGGTAAGTGCTACAAGATCTCGTACATTGGAACCCATGGTTATGGAC
CTGAATTCATTAGTATGGAACATTTTCTTTTTCTTTTCCAAGTGAAATCCCCTAGTATACGAAAG
GGTGAAAAAGCGCTTTCGTTGTTGTGGAATAAGAAGCCTTCGTATCTTAATGCATGTATTTAATT
TATTCGGAGCTATTAGAGCGGGATCCACTTTTTTGGGAATATGAGTCGAAGCAATAACAAGAATA
TTTTGAGTGGAACATCTTTCACAATCCCTGGAGAGATCGTTCGCTAATAGACCGAGGGATAAGTA
ATTCGACTCATTCACATCCAGATCATGAATGTTTGGAATCCCTATTATGCAAGGAGACATTGCTT
TTGCTAATTCGAATTGAAGGGTGATATAAAATCGGTCTATTTCCGGCATCATATCCATAGTTAGC
GCATTCATCCTAGTTAGAAGCTCCAGCTCCGTATCAAGGTCACGA
Right flanking sequence: Indices 382119 -- 382618
ATATCATCAATAAGAAAACCTTTAGGCTTGTTATCCAGGAACTTGTTCAGAAATACTGTAATGAA
AGGAACATAGGAGTTTGCCGCTAGGTATTTGACCAAATAGGATCGTCCAGTTCCTATAGAACCTA
TCACTAAAATACCCCTAGAGGGGGATAGGGCTAAGCGGAGCGAAAAGGGTTTTCCATGAGATGGG
AAATGAAAACTATTAGCCCCACACGAGTTTTGTGAATAAGTGATTGTCTGATAATGAGCAAGGAA
TATCCGCCTTTCTGCTAAACAGAATGTATTGAACTCATAATTCATTAGATACTTTTTATGAATGT
CAACTAAGTATCGTAAGTAAATTGCTCCCGGTTGTTCAATCATTTGATAACCAGAGTCATTCTTT
GATAAATGATCACTATGAGTCAAACTCAATAGAATTTGATCAATCCTTTTTTCTGTCGTTAAGGT
GGAAAATTGAACCAAGAATTCTCTTTCTTTATCATCAATCGAATC
Found at i:382099 original size:9 final size:9
Alignment explanation
Indices: 382074--382117 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
382064 AAGGTCACGA
*
382074 TCAATATCG
1 TCAATATCC
*
382083 TCACTATCC
1 TCAATATCC
*
382092 TCAATATCG
1 TCAATATCC
*
382101 TCACTATCC
1 TCAATATCC
382110 TCAATATC
1 TCAATATC
382118 GATATCATCA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.30, C:0.32, G:0.05, T:0.34
Consensus pattern (9 bp):
TCAATATCC
Left flanking sequence: Indices 381574 -- 382073
TAATCGATAGGGCCTCATTGGTAAGTGCTACAAGATCTCGTACATTGGAACCCATGGTTATGGAC
CTGAATTCATTAGTATGGAACATTTTCTTTTTCTTTTCCAAGTGAAATCCCCTAGTATACGAAAG
GGTGAAAAAGCGCTTTCGTTGTTGTGGAATAAGAAGCCTTCGTATCTTAATGCATGTATTTAATT
TATTCGGAGCTATTAGAGCGGGATCCACTTTTTTGGGAATATGAGTCGAAGCAATAACAAGAATA
TTTTGAGTGGAACATCTTTCACAATCCCTGGAGAGATCGTTCGCTAATAGACCGAGGGATAAGTA
ATTCGACTCATTCACATCCAGATCATGAATGTTTGGAATCCCTATTATGCAAGGAGACATTGCTT
TTGCTAATTCGAATTGAAGGGTGATATAAAATCGGTCTATTTCCGGCATCATATCCATAGTTAGC
GCATTCATCCTAGTTAGAAGCTCCAGCTCCGTATCAAGGTCACGA
Right flanking sequence: Indices 382118 -- 382617
GATATCATCAATAAGAAAACCTTTAGGCTTGTTATCCAGGAACTTGTTCAGAAATACTGTAATGA
AAGGAACATAGGAGTTTGCCGCTAGGTATTTGACCAAATAGGATCGTCCAGTTCCTATAGAACCT
ATCACTAAAATACCCCTAGAGGGGGATAGGGCTAAGCGGAGCGAAAAGGGTTTTCCATGAGATGG
GAAATGAAAACTATTAGCCCCACACGAGTTTTGTGAATAAGTGATTGTCTGATAATGAGCAAGGA
ATATCCGCCTTTCTGCTAAACAGAATGTATTGAACTCATAATTCATTAGATACTTTTTATGAATG
TCAACTAAGTATCGTAAGTAAATTGCTCCCGGTTGTTCAATCATTTGATAACCAGAGTCATTCTT
TGATAAATGATCACTATGAGTCAAACTCAATAGAATTTGATCAATCCTTTTTTCTGTCGTTAAGG
TGGAAAATTGAACCAAGAATTCTCTTTCTTTATCATCAATCGAAT
Found at i:406992 original size:19 final size:19
Alignment explanation
Indices: 406968--407005 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
406958 TATAAACGCG
406968 ATTTATCTTTCTTTCTTTA
1 ATTTATCTTTCTTTCTTTA
406987 ATTTATCTTTCTTTCTTTA
1 ATTTATCTTTCTTTCTTTA
407006 TAAGGGTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTATCTTTCTTTCTTTA
Left flanking sequence: Indices 406468 -- 406967
GGGTTTTTCCTTAACCTCTGAAAGGAGAACAACTGCAGCGGAGATTCAAAAAAGACTAGCTTTTT
CTCTACCATATAAATAAGGGAAATTCCACCCCGGAAACCATTTTCTCAAGAGTGAGCAGCTGAGA
GTAATGGCATACTTTCCTTTCTCCCTATCTTAGGATTGAGACCCTGGGGTGACTGAATTCGCTTT
TCCTGTGCCCTTTGAAAGCCTTTTATTAGATAGGCAGCGATATAGGGGAGAGGGGAAGGAAAAAG
CAGAGACAGGTTGCCAACCTGAGCCAGGGGTGCGGCTTGAGTGAGGTCGATCCAAGACGGACGGA
AGGAAAAAGAGGCTCACTCGGTTTCTTCTCATACGTAATTAAAAGTGATTTTGGGAATAGGTCGG
CAGAGGGACCGGTGGAGAGAATATGTAAAAAGAAGGGCTTTCTGTCGCATTTTCTTTTTGTAGGC
CCTAACAATCGTATGGAGTCTGTATTATATATATATATAAACGCG
Right flanking sequence: Indices 407006 -- 407505
TAAGGGTGCTGCCTTAGTCCTTGAGCTTTGAGAAAGTCCCTTGTTCGGATAAGATTCTGAAAATA
CCTGATGATATCTTGTTCTCTGAGCTGACAAGAACAGCAGCAAGCGAAGGCTACATAGATTTTAT
TAAAGACAGGAGGGGAAAGCGGAAAGGTTTTGTTTCTTTACCGTTTTTGCCATTATGTGTTCTAA
AGTGAACTTCTTTTTCCAGAGCCTTAGCCTTTGAGGGGGCTAATGAGAAAGCCGCATAGGCCTCG
AGTATGAGTATTATCAAAACAATAATCCTTTGCAAAAAATTGGATTACGCTATCGTGACCCAAAG
ATAAAAGACCCCTAAACGGGAAAAAGGGAACTTCTCCCCATCTCTCTTCAAACTGACCTTATTCA
TTAAGGTTAGCACCTTCCTCAAATTCAGGAGAGCTATGCCGCACTCTCAAATCCACTCATAAAAG
CATAGCGAGAGATATAGCAGCTTCTGATAAGATATCCCCGGAGAT
Done.