Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_065236
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: 277763
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Found at i:815 original size:15 final size:15
Alignment explanation
Indices: 795--824 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
785 TATGTTCTCC
795 CTTAACAGTAACAAG
1 CTTAACAGTAACAAG
810 CTTAACAGTAACAAG
1 CTTAACAGTAACAAG
825 GCCCCGGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (15 bp):
CTTAACAGTAACAAG
Left flanking sequence: Indices 295 -- 794
TCAGGCTGTGCACCAAGCTGAAAGGTCTCAAGCCGGATCTTTAATTCTAAACACTATGGTAGCAT
CAACTCTAAGGTTGCCCAAGCTAGAGAGGACCTTACTAGATTGCAGTTACTCCACTTGCAGGATC
CTTCCAACTCTGACCTAGCTAATGCAGAAAAAGATAGTTTAAAAGTTTTTACTCATTTCACTCTT
ATGGAAGAGGCCTACCTCAAACAGAAGTCCAGAATTCAGTGAGGGGGGGAGTAACACGGGGTTTT
TTCACAAGGTGGTGAGAGCTAGGCAGTCCAAGAACAGATTGTTGAGTGTTTACAATGCCGAGGGG
GATAAGTTTACAGACCATAAAGCTGTTAGTCAAGAGGCTGTCTCCTTTTGCCAGCATCTTTTTGG
TGGCTTTGGAAAAAGAGTTGGTGGCGAGGGATTTTTTATTTCACCTTTTCCCAGGATGCCTTTTG
TCCCTTCCCGTAGAAGCAGAGGAAATGAAAAGAACTATGTTCTCC
Right flanking sequence: Indices 825 -- 1324
GCCCCGGGCCCTGATGGGTATTCTGCCCACTTCTTCAAAAGTGCTTGGGAGATTGTGAGTCAGGA
TGTGATAGAAGCCATAAAGTCTTTCTTTGCTTCAGGCAAGCTTCTAAGGACTCCACTATCATTGT
TTTGGTACCTAAAGTGCCTAATCCTACAGTCATGGGAGATTTTCGGCCGCTGCAATACGATCTAT
AAGTGTATTACCAAGTTGATTGCTAATAGGATCAAAGGCTTGCTTCCCAAGATCATTAGCCCCAC
CCAGTCTGCTTTTGTTGAAGGGAGGAAGATTAAAGAGAATTTCCTTTTGGCTCAGGAACTTCTTA
TAAACTACCACAGGAAGACAGGGAAGCCTCGGTGTGCCATCAAAATGGATTTGAAGAAAGCCTAC
GACTCAGTGCATTGGGATTTCATTCTGGGGATTTTGAAAGCTGTTGACCTTCTTGCCCATCTGAT
TGAATGCATTGTGGCTTGTATCACCACCCCCAAGTTCTCGGTCTC
Found at i:13195 original size:22 final size:22
Alignment explanation
Indices: 13141--13198 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
13131 GAAAGTAAAA
* * *
13141 TAAACGAAGTAAGGTTGCGAAG
1 TAAACAAAGTGAGGTTACGAAG
*
13163 CAAACAAAGTGAGGTTACGAAG
1 TAAACAAAGTGAGGTTACGAAG
13185 TAAACAAAGTGAGG
1 TAAACAAAGTGAGG
13199 AAGTGAATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.45, C:0.10, G:0.29, T:0.16
Consensus pattern (22 bp):
TAAACAAAGTGAGGTTACGAAG
Left flanking sequence: Indices 12641 -- 13140
AGAGGGGTGGTAGATGACTCCGTGGATAGATCTGAAACAACCTAACTTATGACGAGGAACTTCGT
TTCGAGTTTTTCGGCCTTTTTCCACCAACGGATCCCTCTGACTAATATAATGGATCGAAATAAAA
TAATAGTAGTGGCATATTCGTCCCTGTAATCAAAAAAGGTATTGAATAGTATATAGCTCCGCCGG
TGTCTCCGGGTCTTGCCGCCACTCGTGCAAAATAAATCATAAGGGGAAGCGCAAAGCGCGAGCTG
TAGAACAAATCTTTTTTTCGTACCGTGATATATATATATTTTTTCTTTCGTTTCACATAGGGGTT
TTCTTTTTTTTGAGTCGAGAAAAAGGTCGCCGACTGCTACTAAGAACCTAACAGAACTCTCGTTG
AGAGAATCTTGATTTGAGAGAGTCTAGTACGATTGCTCCTATTCAGGATATAGTCTGTTATTTTT
TTTTATATGAAAAAAAAGAGGTTGCGAAGCCGAAGGAAAGTAAAA
Right flanking sequence: Indices 13199 -- 13698
AAGTGAATAGAAGCAGTGAGGTGTAAAGACTGCTAAGGTAGCGAAGCAAAGGTTACGAAGTAAAG
CCGCGGTTTATGATATTTGGCTTGTTGCTAATCAAATGGATGCAGTTCTATATAATTACGTGCCC
AGGACGTGTAATATAGCTGCCCATTTTGTTGCCTCTTATGCTGCCAAATGTGGTTTTCGTTGTAC
TTGGAATAGCTCTATGCCTAGTTGGTTGTGTCATGGCATTGACAATGATGTAAACCTCTCAGTTT
AATGAATGAAGTATCTTGATCGTTTAACAAAAAAGGTGGTTTAGTAAATGATGTTAAGGATCTGC
TTCTCGGTATTAAGTTAGTGTTGGAAGACTGAAAAAGATGAGATGCATGGGATGAAAGTGCTCAC
TTACATTCAATTCTATCTGTTAGGCTGCCTCAGAGGCGAAGAATGATAGATGTGTAGATAGAAAA
CATCTTGTATAAGGAGCCACCAGAGAGGGGTTCCAGGTATAAATA
Found at i:25826 original size:20 final size:20
Alignment explanation
Indices: 25801--25840 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
25791 TCAGAACCTA
25801 CCTTTATTTATGGAATATTT
1 CCTTTATTTATGGAATATTT
25821 CCTTTATTTATGGAATATTT
1 CCTTTATTTATGGAATATTT
25841 GAAGAAGCAT
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:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (20 bp):
CCTTTATTTATGGAATATTT
Left flanking sequence: Indices 25301 -- 25800
AAAATCTCCCCAAGTAGGATTTGAACCTACGACCAGTCAGTTAACAGCCGACCGCTCTACCACTG
AGCTACTGAGGAACAACGGATTTAAGGAAGCCGACTCTCGTTCCACCCGAAAAATAAAATGGGTT
CGTCACGGAGAAAAGGTTACGATAGCCCCCGGCCGGAGAGCCTCCAGGACAAGGGGGCGGCGGTC
AACCATCCACTCTCGAGATTCATATTGATCAATCGATCTCCGCGTCCTGCCAGTTCGCTAAGTAG
ACTCACTCTACCGAGGGGCAACAAAGGCTGGAACTATTCCTGCCGGACCTACTTCTCATCCTAGG
AGTTAGCAGGTATGATAGAGTCCCCTCTCTGTCTGTCTCTCCGAGTTTCTACAACTAAGTAGCAC
TTCTGCTATTCAATCATAGAATAGATTCCTGAAAAAGCCCTTTATTATTAGTAAGCTAGCGCGCC
CCCTTCTTTCTCAAAGTCAAGTTTCTCGCTTTCTTTCAGAACCTA
Right flanking sequence: Indices 25841 -- 26340
GAAGAAGCATAGGTTTGGACCCCTATACAAGGGGCTTTTCCCCAACCTATACAAGGTGCTGGTCT
CGATCTCGCTTTCTTTCAGAACCTCTCGATGATTGTTGATTCAACATTGATTTTGTGCGGCCCTC
CATCCGTAATTAGCTATCGGAATTTTTTCCGCCGCGAATCTCATGCCATGCTTCTTGTTTCTCCC
GAGGGCATGGTATGGCTTTGTTCTTGGTGTTGTTTAATAGATGTCGAGTCCCTCTTTTCCCCGTC
CGAGAATCTCCATCTGCTCTAAGTAGGCGAGCTATAATCCCGGTTGGTTGTTCAAAAAACTTTTT
CTCTTTACCCTTTGCATCTTTGCATCTTCATCTTTTCGAAAGCCCAGACCCATTCTTCTGGATCT
TCATTAGTCCTATTTCAGGTGCAAAGCCTCTTCAATAAAGACCTCTTTCTCTCTTTCTCCCCCAT
TTCCTATTTTGTTGATTGAAAGAGGATAAGCGCTATCCATTGAGT
Found at i:41262 original size:22 final size:22
Alignment explanation
Indices: 41237--41280 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
41227 ACTTCGAATT
41237 GAGTAGTTAGTCTTCTTTCTAC
1 GAGTAGTTAGTCTTCTTTCTAC
41259 GAGTAGTTAGTCTTCTTTCTAC
1 GAGTAGTTAGTCTTCTTTCTAC
41281 TCTTTTGTAA
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:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (22 bp):
GAGTAGTTAGTCTTCTTTCTAC
Left flanking sequence: Indices 40737 -- 41236
TACGGAGCAATCAACGAATTACGGCATAATAGAAGATCTACGTAACCCCCTTCAAAAGATGATCT
CTTTTCTTCTTCATTCTCAACAGGAATGCATCAAGAAAACTGCCAGATGCATGAACTCAGAATTT
CTTCGCCGCCCCCTCGTCGTTGGCCCTTCGTTCGTAGTGCTCATTGTATAGTGAGAAAACTCGCC
CCACGAGAAAGCCCTCTTTTACATCCCCTAGACAAAAATGTATAGGAAATGCTACAACCTTCTTT
TGACGACCGGTACAACAAGCTAAAGTGACCTCTACGCGCGACCTGAAAGTTTGTGTTAAGCATAT
AGTTCCTTTTTGTCTTGCGGTGTCCTATCGCTTAGCGACAGAGCCATCTTCTTTTGGGGCAGTGA
GGAGGACAGGAAAATCCCCTACTCCCCCGCTTTCTTTTTTACAACCTCAAACAAAAGAAGCAAAG
AAGGGAAATCTTCGTAAAGGAAGCAAGGGGTGTCGACTTCGAATT
Right flanking sequence: Indices 41281 -- 41780
TCTTTTGTAATCGAAACTAGAATCGAAAGAGCCTCACCCTTTTTTTTATGTATGTGAATTTTCCG
AATCTAGTTCTAAATACTGGACTGATCTTTCTCCGCGGTTCGTTCTATTTTGATAGATAGAGATA
GACAGGAGCTAAGTAAACAGAATACAAAAGGCTTACTCCCATTTCTCTCGACTCAGGAATTCTTT
CATAGAATCCTTTTTGATTGCACTACTTTTTGAAAACAACCGTACGGGAGGCGGAGGCCAAAGGA
GACCCTTTTACCGGTTGGGTGTGTCCTTCCGGAGAAGACATACCCTTAGGAAGCTTACCGCGCTT
TACTCCCGGAAGACAACCCCAGTACAGTAAATCGTGCATAATTGAATACGAAATCTTTTCGCGCT
TTCTTTGTGTCGTACTTCTTGGTCTTTGCCGGAATTCCGGGCCCCGGGGAAAAGCAGAAGAGGAA
GAAGCCAGAAGAATCAAACAAAGAATTCATGAATACAATGAAGCA
Found at i:54132 original size:60 final size:60
Alignment explanation
Indices: 54008--54133 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 60
53998 CTGATCCCTT
* ******
54008 CTTTCCTCATCTTCAGGATCCTGATTGAGGTCAGGAATTAGCGGCGGACGCTGATTCCTT
1 CTTTCCTCATCTTCAGGATCCTGATTGAGGTCAGGAATTAGCGGCGGACGCGGAAAAAGC
* * * *
54068 CTTTCCTCATCTTCAGGATCCTGATTGAGGTCAGGAATTTGTGGCGGTCGGGGAAAAAGC
1 CTTTCCTCATCTTCAGGATCCTGATTGAGGTCAGGAATTAGCGGCGGACGCGGAAAAAGC
54128 CTTTCC
1 CTTTCC
54134 CTCAGAGAGG
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (60 bp):
CTTTCCTCATCTTCAGGATCCTGATTGAGGTCAGGAATTAGCGGCGGACGCGGAAAAAGC
Left flanking sequence: Indices 53508 -- 54007
TAACCCAATAGCAGATTCCGCAGCTGCCACCGTTGGAACCAATGAAGCAAATGATTGACCCATCA
TATCATCCGAAGAAACGGAAAATACCAAAAAGTTCGAATTCACGGCTAATAACATTGATTCAATT
GGCATTGACATAATAGGAATATTTCGTCTATTAAGGAGGATTCCCCGAATACCTAAAATAGAGAT
GATCATAGAAAATGTGAAATATTTGATAAGATCCGTTTCGGAAACGTAGAATGTCAGAGAAATTC
AAATGTTATAACTCCCCCCAGTACGTCAGGAAACCCCAGCTTCTTACAACTTCACATTATTTCCG
CCGCTCTCGGTCCTTTAAATATTGTGGAAGGTTTTTAAAATAGACATAGAACTGGTGAAGCCTCT
TCCGAACGAGGAGGCTTTCACATAGTTTGTCTATTTCTTCGGAAGTAGCTTTTAGCTCCGCCTCA
TATTCGTCGAATAACGACGAAATCCGGCTCCGCCGCTGATCCCTT
Right flanking sequence: Indices 54134 -- 54633
CTCAGAGAGGCAAGTTTCTGAGCCGGATCATCGTTGAGATCCTTTGAGGGGATTCTTGGGCGTGA
CGGCCCGGCCTCGTCTTTCCCTCCGGCTACTTCACCGCCTGACTCGAGTATACCCTTACCCTTTT
CCCCACCTACCCCATCCAAGGGTACCCTTTCCATAAAAGAAAGGAGGTCTTGGATGGAATCAGCG
ATAGTTGATAGCATTCCGAAAAAAAAGAGATCCAAAATAGAGATTATCATACTGAAAAAAAAGTT
CTTCCTTCGCATAATTCCCGTACTTCATTCAATTCACTTCAAGGCTGGTTCTGAACGCCGCGTAA
CATCATCTATTCACTGTTTTGTTTCTGATTGTCTGCCTACCCGAAAGCGAAAAAGGTCTCGGCGA
ATCCAGACTTTCCAATCTTTTACCCTCCCTTTGAAGTTCATTTTTCAGACTATTGCTGAAGAGCT
CTTTATGTGGTCTCACCACCATCTGAAATGGGCGAAACTTCGATT
Found at i:108741 original size:25 final size:25
Alignment explanation
Indices: 108707--108756 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
108697 ACTTTCTCAA
108707 TGGCGAACTTGTGTAGTTGATTAGG
1 TGGCGAACTTGTGTAGTTGATTAGG
108732 TGGCGAACTTGTGTAGTTGATTAGG
1 TGGCGAACTTGTGTAGTTGATTAGG
108757 AGCCGTAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.08, G:0.36, T:0.36
Consensus pattern (25 bp):
TGGCGAACTTGTGTAGTTGATTAGG
Left flanking sequence: Indices 108207 -- 108706
AGAGAGTACGGTTTTGTCAAGCTCATGAACTATTTCATCCGATTCACAATCCATTCCAATCTAAG
TTTGTGGGCTAGTGAGGAAGAAAGGTAACTCAATCTCAGTAGTAGAATAGGGACGAAGTGACTCG
AAGGTAGCTCGACCTGCGGGTGGGGGATGAAAGAGCTAAGTACTGACCAGGCCGGAAAAGAGCAT
TTCAATATCTTTCTAAGGTAAGCTTCTATCAGCATAGATAGACATCAACTTCGATATCTAGACTG
GGATGCAGGAATCTTTGAAAGACTCGCGGGATATTCCATATTCATATTCCATACCGGTCTTTGTC
AGCAAGTTCTGCAGACCTGAACGAACGACAAGAAACTTCCGTAAAAGCGGAATTCTCCCCAAGTA
GGAATTGAACCTACGACCAATCAGTTAACAGCCGACCGCTCTACCACTAAGCTACTTCTAGAAGA
ATGATATGATTAAAGGGGGACTCCAATCGCGGACCACTTTCTCAA
Right flanking sequence: Indices 108757 -- 109256
AGCCGTAGACCGGAGCTACAAAGGGGGATTCCGAGATTGGCATGTGATAGTTGTCCGAATGGCAG
AATCCACTTCAACTGTCTCAAATGAGATAAAGCCCGCTACGAGTCAAAGTGATAAGTTGCACCCC
GTAGTTCTTTGAATTTTTTTCGTCTTTCAATCAGGGAGGATTTTACTTAGTTGTAACAGAAGCAG
ATAGTCATTTCTAACCGTTCGAGAATTAGACGACAGCATCGATAACACTATATCTTATCTGCTGA
GCTGAAGGCCCTTCCCGCGATAGCATAGTAATTCTGACTTTCCAATTGAAAAAAGGGGGACCACT
CTTGCCACATCCTAGTCTTCTAGATCAGTACCGCGCACCTTTTTGATCAGGATAAGCTGATATGG
GATTAGAGGGGCTATCTTAGCCGGGTTCGACTCCTGGGTCCCACCTCTTCCCGGTATGCCCGCTA
GCCAGCGGAATGTTTTTTCGAAAACTATCTTCATGTCCGATCTTC
Found at i:153134 original size:24 final size:28
Alignment explanation
Indices: 153080--153136 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
153070 GGAAGACCGA
153080 TGCATCGTGGTACAGGTCCTCTCTTGCT
1 TGCATCGTGGTACAGGTCCTCTCTTGCT
*
153108 TGCATCGTGGTACAGTTCCTCTCTTGCT
1 TGCATCGTGGTACAGGTCCTCTCTTGCT
153136 T
1 T
153137 CCGCCGGTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.11, C:0.28, G:0.23, T:0.39
Consensus pattern (28 bp):
TGCATCGTGGTACAGGTCCTCTCTTGCT
Left flanking sequence: Indices 152580 -- 153079
AGTCGAACGGTTGTTACCTACTGAAAAACATTGTACCCGCGGCCCCCGTTTTACCAAAGGTTGCC
AATTTCTTATAGATAGAGGATTCTTTCTAATGTTAGAAAAATCTCTTCAGATGCTAAATCTCCAT
TCCCTTTGCAAATCACTTAAACATCTGTCAATAGTAGATATGATAAATGATTTGTCTGGTTTGTA
ATTTAATGGAGTAGCAACCAAGCACAGTCGGAAGGAGATGCTCAACAACTGCATTGCCCCATGCG
GGCATAATGGAATTTTACAATTACAGAAAAGGGCCGTTTACTTACCACGATTTCATCGCCTGGGA
TAGCCAGGAACGCCTTTACAGAGATCGATCTCCACATGCTTAAACTGTGTACTGTCACTCATGGA
TACTTTTCCACAAGCCAAGATGAATCTGGGATGCATCCTACTAAGCATCCCAACACCAAGTCTGC
CGCTGGGTCCCTGCCTTCTCCGCTATCTTTCAAAAGGAAGACCGA
Right flanking sequence: Indices 153137 -- 153636
CCGCCGGTCTTGCCATGATAATCAGGGATTCTCACAGTTTCTATCAGGGATTCTCACACTTTCTT
TCGTGGAGGTTTCGCCTCCTCCCGCCGAAGCTGGAGAGCTGCTCTAAGAGGTATCGAATGGTCTT
ACCAGCTCAGACTTTGTTCGGGACGCTATTCCAAAGCATACTTGTGTCCTGTCATCCTCTTCATT
CTCGAATTCAGATGAATAGTTTGACTGATCTTACCCGGTATAAATATCCTCGCGGCGGAGATTTC
CAATCCGATTGTGGAACGGGTTCTCGCTACCACCACTATCCCTTGTTTCTGTACCCATGGAACAA
CCATTCTTGTAGAATCTCCCATTACTCATAACGATTGTCACTCCTTCTCATCAATTCTCATTGAC
TGACTCAAAAGGGCTTTCTTCCCGTCCTCGAAACGGGTTGGATGAGATATTCCTTTTCTGACCCC
TTCCTGAGGCACTATGGGCTTATAGGACAACTGTTCGCACTTCAA
Found at i:153185 original size:22 final size:22
Alignment explanation
Indices: 153157--153200 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
153147 TGCCATGATA
*
153157 ATCAGGGATTCTCACAGTTTCT
1 ATCAGGGATTCTCACACTTTCT
153179 ATCAGGGATTCTCACACTTTCT
1 ATCAGGGATTCTCACACTTTCT
153201 TTCGTGGAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAGGGATTCTCACACTTTCT
Left flanking sequence: Indices 152657 -- 153156
ATAGAGGATTCTTTCTAATGTTAGAAAAATCTCTTCAGATGCTAAATCTCCATTCCCTTTGCAAA
TCACTTAAACATCTGTCAATAGTAGATATGATAAATGATTTGTCTGGTTTGTAATTTAATGGAGT
AGCAACCAAGCACAGTCGGAAGGAGATGCTCAACAACTGCATTGCCCCATGCGGGCATAATGGAA
TTTTACAATTACAGAAAAGGGCCGTTTACTTACCACGATTTCATCGCCTGGGATAGCCAGGAACG
CCTTTACAGAGATCGATCTCCACATGCTTAAACTGTGTACTGTCACTCATGGATACTTTTCCACA
AGCCAAGATGAATCTGGGATGCATCCTACTAAGCATCCCAACACCAAGTCTGCCGCTGGGTCCCT
GCCTTCTCCGCTATCTTTCAAAAGGAAGACCGATGCATCGTGGTACAGGTCCTCTCTTGCTTGCA
TCGTGGTACAGTTCCTCTCTTGCTTCCGCCGGTCTTGCCATGATA
Right flanking sequence: Indices 153201 -- 153700
TTCGTGGAGGTTTCGCCTCCTCCCGCCGAAGCTGGAGAGCTGCTCTAAGAGGTATCGAATGGTCT
TACCAGCTCAGACTTTGTTCGGGACGCTATTCCAAAGCATACTTGTGTCCTGTCATCCTCTTCAT
TCTCGAATTCAGATGAATAGTTTGACTGATCTTACCCGGTATAAATATCCTCGCGGCGGAGATTT
CCAATCCGATTGTGGAACGGGTTCTCGCTACCACCACTATCCCTTGTTTCTGTACCCATGGAACA
ACCATTCTTGTAGAATCTCCCATTACTCATAACGATTGTCACTCCTTCTCATCAATTCTCATTGA
CTGACTCAAAAGGGCTTTCTTCCCGTCCTCGAAACGGGTTGGATGAGATATTCCTTTTCTGACCC
CTTCCTGAGGCACTATGGGCTTATAGGACAACTGTTCGCACTTCAACAGGGTGCACACCTGGTGT
ACGGTTCAGAAGCTACCTTTGGAGGTCCAGCTGCCATCTCTAAGG
Found at i:170983 original size:18 final size:18
Alignment explanation
Indices: 170943--170985 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
170933 ACCGCCCTGC
170943 CATAGTCGCGAGTCTGTTT
1 CATAGTCGCGAG-CTGTTT
170962 -ATAGTCGCGA-CTGTTGT
1 CATAGTCGCGAGCTGTT-T
170979 CATAGTC
1 CATAGTC
170986 AACAAGGTTG
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 170443 -- 170942
CCTTGAATTTTTTTCAAGTGTCAGTAGCGGAACGTTCTGTCAATCGGGGAAGGTTTTTGGTGACA
ACACCTGGAGATATCAGAAGTGAGAATGCTGACATGAGTAACGATAAATCCTGTGAAAAACACGA
TCGCCTGCCAGTGGAAGGCTTTCTGCGTTCAGTCAATCTACGCAGAGTGAATCGGTCCCTAAGGA
ACCCCCGAAAGGGCTGCCGTCCGATGGGTACACGAAAGTGACGAAGTTGCTTTGACTACAGAACC
ATGCCTGTCTGTTGGAGCGAATTGAATGATCGGGCCGAGGGCAGCCCCCTCTTCCCCTCACTCTC
CTTTCCCTAATATGAACCTTGAGTCATCAAAGCCTTTCTGACTCGGCCTGGCCCGGGCGCCCTAC
GCGACTGGCGCTTCAAAAGGCGAAACTCTCGTCGTAGTTTGGCGACCTAAGGGGCCTTTACTCTT
TTGATTAGAGTAGGGGTCGCGAGAGAGCAGAGCGTACCGCCCTGC
Right flanking sequence: Indices 170986 -- 171485
AACAAGGTTGAAACTTCCAGGAAAAAACTTCGAATTGGGAGGGCGATCCTCCCGGTGAACTGACC
GTACCCCAAACCGACACAGGTGAACAAGTAGAGTATACTAGGGCGCTTGAGAGAACCATGTCGAA
GGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCCTATCTTTTGATTAGGAA
AGCGGCACATACCAGGGGGTAGCGACTGTTTATTAAAAACACAGGACTCTGCTAAGTGGTAACAC
GATGTATAGAGTCTGACACCTGCCCGGTGCTGGAAGGTCGGAAGGAGAAGTGTTATAAGCTTTGA
ATGGAAGCCCCGGTAAACGGCGGCAGTAACTCTAACTGTCCTAAGGTAGCGAAATTCCTTGTCGC
ATAAGTAGCGACCTGCACGAATGGTGTAACGACTGCCCCGCTGTCTCCGACATGGACCCGGTGAA
ATTGAATTCTCCGTGAAGATGCGGAGTACCAACGGCTAGACGGTA
Found at i:196726 original size:13 final size:13
Alignment explanation
Indices: 196708--196733 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
196698 AACAGGCAAT
196708 GCATTCTATCAAA
1 GCATTCTATCAAA
196721 GCATTCTATCAAA
1 GCATTCTATCAAA
196734 ACATAGCCAT
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:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
GCATTCTATCAAA
Left flanking sequence: Indices 196208 -- 196707
GTCAAGCCTAGAGCACACAGAAATGGGCAACTTGCCTGTCGATATTAGGAGAACATAAGATATTC
TATTTCTCAAAGCGCCCTGAAACCATGCAAAAAGGGGCGGGGCAACTACTCTTTCTAAAGGAGGG
GAATGCAAAGGATGGATCTTTGTATCGGATGCTACTGGTAGCTAAGCATTTGGATCTGCTACTCG
GATTGCAAGTAGTGAAAAAAACTGGTGGTTCTTCAACTGAATCACAAATAGAAATTGGTAGAACT
ACGACTGATGAGTCAACTCGGTCAAGTACTGCAACTTTTCTTAGGCGCTGAGCTATGCATGGACG
CCTATCGAGCCGCCGTTGGCGCCTGATTATGATCCCCTCCACGATATATATATCTATATATAATA
TCTCTTTGCCTTTGCATAGTATACGGGTCGGGAGGTAAAACCTTTCTAAAAAACCAAAAAGACTA
GAGCACATCTTTCGTGAGAGAGGGATGCTAAGAACAACAGGCAAT
Right flanking sequence: Indices 196734 -- 197233
ACATAGCCATTTCTCGTAACATAAACAGGAACGCCTCCTCGAAACAACAGGGATGCTTTCTAGGA
CTGGTTCAATAGGTGCTCTGGCTGGGTCAACTACTGAGCTGAATCAACAACTTACATTAGCTTAG
ATGCAGCTGTATCCGCCCACTGGGTCAATTGGATCTGATTCAATCCGCCTTTGACGCTGATCCAC
TGGATGCTGCCTCCCTTTGCTACTTTTTTCTGGGTCGACTAAAATGGGTGAAGCTTCTGCCTTCC
CGGCTTCTGCTCTACCCGCCTCTGACTCGGCCTTTTCTGTTGAAACGAATGCTGTAGAGATGGTG
GTGCCTTTGCTTGCTCTGCCCCTTTTTCTGGTGGGCTGCTGCTTCCACTGATTAATCGGGTCTTC
AACCACTGCTTCTGCTGCCTCCATCTGAACTCTAGCTGGCTCTAGATCAATAGAATAAACTGCAA
CTGGGGGACTGATACTGATGCTTTTGGTTCCGAGCGCTCCGGATT
Found at i:197708 original size:15 final size:15
Alignment explanation
Indices: 197688--197717 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
197678 ATCCGACAAG
*
197688 CTCATTCGGTCACAC
1 CTCATTCGCTCACAC
197703 CTCATTCGCTCACAC
1 CTCATTCGCTCACAC
197718 ACAATATGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.43, G:0.10, T:0.27
Consensus pattern (15 bp):
CTCATTCGCTCACAC
Left flanking sequence: Indices 197188 -- 197687
ACTGGGGGACTGATACTGATGCTTTTGGTTCCGAGCGCTCCGGATTGGTTCTTAAACCACCTATG
TCTCTATGGCCTCTGCTTCTTTAGTAGGAAGAAGTGCCCCTTCATTTTTTTTATCAGCCGGAAGT
GGAACAATGGCAGATTTCGGAACTGAGAGTAACTTAATAGAATGAATGCCGATTTTAGGAACATG
TGAAATTGTTGGAACGCCCAAACATGAAACTCCCCACTTCTTGTTCCCGCCCAACCCGCTTTATT
ATCTTTCTCCTTCTCCTGGAAAAGTTCATTTCTTGATTCAATTTGTCTTATTGGCGCCCTTCTCT
CTTGAAAGAGGAGTTCATTTTGTGAATGGCCAGTTTCAAATGTCTTTGTGCGTGCCGTAGGCGAT
CCAGTTGGTGCTTAGTCTGTCGACTCTATCTCAACAAAGGAAGAATCGTTCGTTCCGCTTCTTTT
TTCGTAAATAGACTCAGTCCCCTGAGAAGCGGCGGATCCGACAAG
Right flanking sequence: Indices 197718 -- 198217
ACAATATGCATAGATAAATGAATCGATCTTTGTGAAAGTGCGATTCTAACTTTCACAAAGGGAGT
GAATAATTTCACTGGCTTACTTTAGTTCTTTTTTCAATCGAGATTGGATGGGTGTTCAGTGCCGT
GGCTACAAGATCGAAAAGAATTCCATTTCCTGTGAGATGCCAAAAGATTCCCATGTCTTTCTTGG
TTGGACCAACCCAACCGGCGATTTCTTACAAGTCTTTTTTCTTTTTTAGAGCAAGAAGCGGAACT
ACAAGTGAATCTTAATCATTATGTATAACCAATTCATTTTCAAATATAGTTGGGAGACTTTACCT
AAGAAATGGGTCAAAAAAATGGAAAGATCGGAACATGGGAATAGATCTGATACCAATACGGACTA
CCCATTTCAATTATTGTGCTTTCTTAAATTGCATACCTATACAAGGGTTCAAGTTTTGATCGATA
TTTGCGGAGTTGATTATCCTTCTCGAAAACGAAGATTTGAAGTGG
Found at i:205832 original size:18 final size:19
Alignment explanation
Indices: 205798--205833 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
205788 GAAAGAAGAA
*
205798 TGCACCAAAATGCAGGTGC
1 TGCACCAAAACGCAGGTGC
205817 TGCACC-AAACGCAGGTG
1 TGCACCAAAACGCAGGTG
205834 GTTGTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.14
Consensus pattern (19 bp):
TGCACCAAAACGCAGGTGC
Left flanking sequence: Indices 205298 -- 205797
AATCCTTTTTCCTTCTCGCGAAGCACGGGAGCGCCTAGCGCCCAGAGGAGCAAAACTCTTTTTCC
TTTCAGGGTAAAGCGGCGCATAAAAAAGGGCTAGCCCGTCAAAAGTCCGGTTCCTTCGCGAAGGA
AGTTCAGAATCAACAAGGGTTCGTAGAACGAAGGGAGTGTACAACTGGCGGTGTACAACACCACC
ACTTTTTTCTTCGTAACGAGGGAGAGATAGAATGGAGTTCTTCACGAAGTTCGAGACAAAGGAAT
AAAAAATCGTTTCTTTATGGCCTCCTCGTTTTGAGACATTATGGCTTTGGGGTCGACCCCGGTAA
CAAAGAAGGAATCCATAAAAACTTGGGATCCGACACCATGATAAAATACTACCCTCATGATTAGA
CCATGTCCCTGAGATTTGATAAAAGAAAGGTGCATTAGCGGTTAATACGTTGTAATTGGATAAGT
TATTAGGAATATGACGGAACGAAAGACCAAGGAAAGAAAGAAGAA
Right flanking sequence: Indices 205834 -- 206333
GTTGTTTCTTGTTGTAAGTGAATGCAATGAAAAGACCCGGAAATAACGAATAATGAAACAATTCA
TATATTGACATTTCGTGCTCATTTCATAATTGCTGCTTTGTTATTCCCATCATCCGGTAACCATA
AGATGATCCACAAGAAAGGTGGCAGGATTCGAACCTATGGCCGGCCCGCCCCTGACCCGCTGGGT
TAGGTGGCCGGGTTAGCACCCCTCGTCGCCTCTGTACCCAAAACAGATGCGCTGCGCTACCCAGG
GCGTAACCTTGTCACCTCTACCCCTCTTCTGGTTATGCCATTACCAATCGCGGGTAACCCCCGGG
CCGGCCGCCCCTGACCTAATAAGAACGATTATCCTATTGACTAAAGAAGAAGCAGCTTACTTACT
TCTCGAGCGATAGTTCCACGATCCCGACAAGAGATTTTGAGGATGTCACGCCTGAGTGTCGAAGA
CCCTTACGCCGAGAAGGCCGGTGGACCATAAGATAGAGCTGGAAC
Found at i:210456 original size:39 final size:39
Alignment explanation
Indices: 210399--210477 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
210389 CCCATCCTTC
* *
210399 AATATCATGATTGGGTCGACCAGGCCAGATCATGAGTGA
1 AATATCATGATCGAGTCGACCAGGCCAGATCATGAGTGA
210438 AATATCATGATCGAGTCGACCAGGCCAGATCATGAGTGA
1 AATATCATGATCGAGTCGACCAGGCCAGATCATGAGTGA
210477 A
1 A
210478 TAGAAAATCG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.22
Consensus pattern (39 bp):
AATATCATGATCGAGTCGACCAGGCCAGATCATGAGTGA
Left flanking sequence: Indices 209899 -- 210398
GTAACACTGGAGAAGGTCATTTTTGGAGGGGTCGGAAGAACGGGTTTAAAAGAAATATATATATA
TTATATTAGCTTGGTTTTTATGCAAAAAAGACAAAACGGGATTGGATTTCCACTCAGAAGGAAGG
TTAGATACCTTTGACAGGGTTGTATTTTTGGGATGGTGTTCAAACTCCCGAAATGAACCATTACA
GCTGGCGTCGACCAGCTTTGCGATACGGACGGACACGAAGAAGAACGCAGGCAGCGGAAATGCAA
AAGAGAAGAGCAAAGATTCCCGACCCTTATTGACTCAACCACAAATCTGTTGAATGAAGGTAGCT
TGCTTACTCTCAGCCACTAGTTAGAAGGAAATCCCTTTACTTTCTTTCAGAACCTTATGCAGTAC
AGAAAGCAAGTGAGGCGGGCTAAGATTCCATTCGAAGTAAGGTAACAAGATTCGATGTTGCACCA
CCTTCAACTCGATCCGGAGTTTTTCGAGAAAAGGTCCCATCCTTC
Right flanking sequence: Indices 210478 -- 210977
TAGAAAATCGAAAACGTACATAGCTGTTCCAGCCGAAATACTTGGAATAATTCTACCACTTCTAC
TAGGAGTAGCCTTTTTAGTGCTAGCTGAACGTAAAGTAATGGCTTTTGTGCAACGTCGAAAGGGT
CCTGATGTAGTGGGAGCGTTCGGATTGTTACAACCTCTAGCGGATGGTTTGAAATTGATTCTAAA
AGAACCTATTTCACCAAGTAGTGCTAATTTCTCCCTTTTTAGAATGGCTCCAGTGACTACATTTA
TGTTAAGTCTGGTTGCTCGGGCCGTTGTACCTTTTGATTATGGTATGGTATTGTCAGATTCGAAC
ATAGGGCTACTTTATTTGTTTGCCATATCTTCGCTAGGTGTTTATGGAATTATTATAGCAGGTTG
GTCTAGTAATTAGGGGGCGGCCGTTCGGTCGCCTATGATACTAGGACCAATAGGTCAAAAATGGG
TTTGTGCCGCAGGTGTTGAACGATCTACTCTACACAGGTGTGGGC
Found at i:221614 original size:22 final size:22
Alignment explanation
Indices: 221589--221662 Score: 130
Period size: 22 Copynumber: 3.4 Consensus size: 22
221579 AAAGTCAAAG
221589 AAGTGAGGTTGCGAAGCAAACA
1 AAGTGAGGTTGCGAAGCAAACA
221611 AAGTGAGGTTGCGAAGCAAACA
1 AAGTGAGGTTGCGAAGCAAACA
* *
221633 AAGTGAGGTTACGAAGTAAACA
1 AAGTGAGGTTGCGAAGCAAACA
221655 AAGTGAGG
1 AAGTGAGG
221663 GGCCGAAGGC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.42, C:0.11, G:0.32, T:0.15
Consensus pattern (22 bp):
AAGTGAGGTTGCGAAGCAAACA
Left flanking sequence: Indices 221089 -- 221588
TTTGATTGAGTATGATTGGCATTCATCTTCAGCACCTCTTCTGTTGGTCTCCCACTTCGCTGTGT
TCAGTGTAAAGACGGGCCAAGTGCCCTTATAGCATAGTTCCTGAATAAGAAGCCGATGGGGTGTC
CCCTAGAATGGCAGTTCCTGGGCAACTGACCTGGGCATTGATTGGAGCCTGCGTTGTTGTTCAGC
ACACTTTCAGTGCCTACTTCGTAGCCTCTCTGCAAGTTAATTATTTTCTCTTGCTTGAGACAATC
CCGAGATCATGGGCCGATCAATGCCTTGGATGTTATACGTAGCTCGCCTTTATTCACTTCTTTAT
GTCATTTATGATTTCTACCCTAGATCAATGAGCAGCTTTGCATCATATTCTAATAAAGGGGCTTT
GGAATCAACTCCCATATTCGAAGTTGCGATCGGATCATACATCTATAGATGGATGGGGCCGTGCC
ACTTCTTGTTGCAAGAGATGAACAAAAACGGTTAAAAAGTCAAAG
Right flanking sequence: Indices 221663 -- 222162
GGCCGAAGGCGAAGAAGTGAAGTGGCAAAGAGGTCACATTAGAGAGAGCCTGAGTCCTTATGCTG
TACCTGCCTTGCTTACTGAAGGATCGTGGCGTATGTGTGTTGACAGCCGCGCCATCAACAAGATC
ATGGTTTTCCGATCCCTCGTTTAGATGACCTGCTGGATCAATTAAGTGGTGCTACAGTTTTTAGC
AAGCTGGATTTGCAGAGCGGGTACCGCCGGATTCGAATTAGAGAAGGCTACGAAGTAGGCAGTGA
AGAGGGAGTGGGGAAGACGGCCTTCAAAACCCGCCTATATGAGTGGCCGGTCATGCCTTTTGGCC
CGCGCGCTTTTATGAGAGTGATGAACGAGATGCTTCGACCATTTATTGGAATTTTTCTGGTGGTG
TACTTTGATGACATCCTAATTTTTAGTTCGAGTCCAGAATTGCACTTAGAGCACTTGAGGCACTG
AGCATAGTGAAGTGGAGCAGTGAAGAGAAAAGATAATTTTTATGC
Found at i:221681 original size:44 final size:43
Alignment explanation
Indices: 221584--221682 Score: 119
Period size: 44 Copynumber: 2.3 Consensus size: 43
221574 GTTAAAAAGT
* *
221584 CAAAGAAGTGAGGTTGCGAAGCAAACAAAGTGAGGTTGCGAAG
1 CAAAGAAGTGAGGTTACGAAGCAAACAAAGTGAGGTGGCGAAG
* *
221627 CAAACAAAGTGAGGTTACGAAGTAAACAAAGTGAGG-GGCCGAAGG
1 CAAA-GAAGTGAGGTTACGAAGCAAACAAAGTGAGGTGG-CGAA-G
*
221672 CGAAGAAGTGA
1 CAAAGAAGTGA
221683 AGTGGCAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
43 5 0.11
44 38 0.81
45 4 0.09
ACGTcount: A:0.41, C:0.12, G:0.34, T:0.12
Consensus pattern (43 bp):
CAAAGAAGTGAGGTTACGAAGCAAACAAAGTGAGGTGGCGAAG
Left flanking sequence: Indices 221084 -- 221583
CTTCTTTTGATTGAGTATGATTGGCATTCATCTTCAGCACCTCTTCTGTTGGTCTCCCACTTCGC
TGTGTTCAGTGTAAAGACGGGCCAAGTGCCCTTATAGCATAGTTCCTGAATAAGAAGCCGATGGG
GTGTCCCCTAGAATGGCAGTTCCTGGGCAACTGACCTGGGCATTGATTGGAGCCTGCGTTGTTGT
TCAGCACACTTTCAGTGCCTACTTCGTAGCCTCTCTGCAAGTTAATTATTTTCTCTTGCTTGAGA
CAATCCCGAGATCATGGGCCGATCAATGCCTTGGATGTTATACGTAGCTCGCCTTTATTCACTTC
TTTATGTCATTTATGATTTCTACCCTAGATCAATGAGCAGCTTTGCATCATATTCTAATAAAGGG
GCTTTGGAATCAACTCCCATATTCGAAGTTGCGATCGGATCATACATCTATAGATGGATGGGGCC
GTGCCACTTCTTGTTGCAAGAGATGAACAAAAACGGTTAAAAAGT
Right flanking sequence: Indices 221683 -- 222182
AGTGGCAAAGAGGTCACATTAGAGAGAGCCTGAGTCCTTATGCTGTACCTGCCTTGCTTACTGAA
GGATCGTGGCGTATGTGTGTTGACAGCCGCGCCATCAACAAGATCATGGTTTTCCGATCCCTCGT
TTAGATGACCTGCTGGATCAATTAAGTGGTGCTACAGTTTTTAGCAAGCTGGATTTGCAGAGCGG
GTACCGCCGGATTCGAATTAGAGAAGGCTACGAAGTAGGCAGTGAAGAGGGAGTGGGGAAGACGG
CCTTCAAAACCCGCCTATATGAGTGGCCGGTCATGCCTTTTGGCCCGCGCGCTTTTATGAGAGTG
ATGAACGAGATGCTTCGACCATTTATTGGAATTTTTCTGGTGGTGTACTTTGATGACATCCTAAT
TTTTAGTTCGAGTCCAGAATTGCACTTAGAGCACTTGAGGCACTGAGCATAGTGAAGTGGAGCAG
TGAAGAGAAAAGATAATTTTTATGCAGCAGCCAAGAAGTGTTTTT
Done.