Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_031158
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: 265768
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:7043 original size:24 final size:24
Alignment explanation
Indices: 7011--7057 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
7001 CCATTTCTTC
* *
7011 GGAATTGTCCGCTCATAGCACGAT
1 GGAAGTGTCCGATCATAGCACGAT
*
7035 GGAAGTGTCCGATTATAGCACGA
1 GGAAGTGTCCGATCATAGCACGA
7058 CGCGCTGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (24 bp):
GGAAGTGTCCGATCATAGCACGAT
Left flanking sequence: Indices 6511 -- 7010
AGCCCACTTACTTTAGTTTGACTGAAACAACTTCCTTTCCTGAATCTTAGCTCTTCTCTTTCTTA
TTTATTCTTACTACTAGAACTTTAGAAACCGGTCCGGAAGAAAGAAACCTTAACGTATCCGGGTC
GTACGCCTGGAACAGTCGTACAATTTCGGCGATTCTAAAAAGGAGTATATCCCTCTCCCTTAGTG
TCTTTCCACTTCCCTCGTTCAGGAACAAACACTTCGCCTAATTCTTTTGAATTTCCCCACTAACT
AATTAGCTTACGACCACTGAACAAACTTGGTTGACGAACATAGTTTATGCGCCGCTAATCTAGCG
GCTTGTCGAGCATTTGACAAACTCACACCATCCATTTCAAATAGGATTTGTCCCGTGGACACACG
AGCAATCCAACCCGTAGGATTTCCTTTTCCTCTTCCCATTCTTACTTCTGTAGGTTTCCCGGTAA
TAGGGATATCTGCGAAAACTCTTACCCATATCTTACCATTTCTTC
Right flanking sequence: Indices 7058 -- 7557
CGCGCTGCTTCAATGGCTCGATATGAAAGACGACCAGCTCTACAACTTTTAGTGCCATATCTTCC
AAAACCAAGTTGTGTACCGTCCGGTTTGCAACCCCTACTACATCTGCCTTTACGATATTTACTAT
ATTTCGTACGTTTCGGATATAGCACGTCCCCCTTTTTTTTAACTATATGAAATCCACACTTTGAC
ACCTGAGATTCCGTAACGAGTAGATACTTCCGCAGGAGCATAATCTATTTTCTGGTTAAATACAT
TACGAGATGTTTTTCCATACTTTCCGCATTCAGTTCTAGCTATTTCTGCACCTTTTAATCGACCT
GAACAACATATACGGATCCCCTCCACCCCCTTTTTCATTACTAATGGAATACCCTTCACTATTTT
ACTAAAAATGGAACGAAATGATCTTCTTTTGTTCCTCGGTTGAAAAGGGATGTCTTGAGCAATCG
GAGAAGCACTTTGATAAACAGATTTGATCTTGACTGATTCAATTA
Found at i:23041 original size:18 final size:18
Alignment explanation
Indices: 23018--23052 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
23008 AAGACTAAAA
*
23018 GAAGAATTCGCTCAACAT
1 GAAGAATTAGCTCAACAT
23036 GAAGAATTAGCTCAACA
1 GAAGAATTAGCTCAACA
23053 AACCAAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (18 bp):
GAAGAATTAGCTCAACAT
Left flanking sequence: Indices 22518 -- 23017
AAACTGAATTTTGAAAAAGTTTGGAAAGAAAAGTAGACGGAACGACACCTGTGAACTCGGATAGC
ATTGTGGCATACCTTTTCATCTGAACTAGGCTACTTTCTTTCTTCTCTTATGAAATTTTTAGTTT
CAGATCATTCTTAAAAGAAGCTCTCTCTTATATACGATACCACCAGATGTGCCCCCTCCACCCTC
GTCCAATCTTCCTAAGTGCCAGCCTAGCTTCATAGGAAGCTTAACAATACGTCCAGCTCCTTAAG
GAATGAATACTTGGGCTTGGCCTGGAGTTAGGCTGAGATGCCTGGGCTAGACCCTGAAATCGCCG
TCCACAGGCTTAATATCAAACCAGATGCTAAGCCCATCAAGCAAGCACAACGACGCTTTCATCCA
CTCCTCATGAAGAAGATTGAGAAAAAAGTAAAATGAAGTATGAAGGTAAACGGAAGACCATAGAT
GATGGAATGATGAATGAATGGAAAAACGAAATAAAAAGACTAAAA
Right flanking sequence: Indices 23053 -- 23552
AACCAAAGAAGAATCCATATCACAGAATCACCCTTGGAAGGGTGAGAAACCACCACCTAATAAAG
ACTGAATAAAAAGAGAAAAGGGATCCCGATAACCAACCATAGGAAGAGTTCATTCATATTGGAAG
TCCGGTGCGGGCGTTAAGACTTACTTTACTAACGTTCGGTACCCATATAAAGAGGGGTACCTACA
CTCTCAGTCAGTACTAGAAGGAGGTACCTTCTTCCGAGGAAACAAGGTCTTATTCATATCCTAAG
TACCCGAGCGAGGGTCGGATAGCACGAGGTAAGTAGTTATGTTGCTAATCCTAAATAAAAATCGA
AGACCAAGAGGTTCACTTACAACCAATTGGTCACTTCACTGCTTTCAGTAGCTTAAGGAGTTGTA
AAAGGGTAGTCCTTGTTGTTATCATTCGTTATTACTTCCACCAGGGAAGTCACTCACTTGAAGAG
GGCCCCAACCCTTGTTTGCTGAGCAGAGGTGAGAGGAAGCAGATA
Found at i:27470 original size:42 final size:42
Alignment explanation
Indices: 27407--27507 Score: 184
Period size: 42 Copynumber: 2.4 Consensus size: 42
27397 TGCTTCGGAA
27407 CTGGCGCCAGAACTGCTGCCCAGTACAGATGTCCATCCTTGG
1 CTGGCGCCAGAACTGCTGCCCAGTACAGATGTCCATCCTTGG
* *
27449 TTGTCGCCAGAACTGCTGCCCAGTACAGATGTCCATCCTTGG
1 CTGGCGCCAGAACTGCTGCCCAGTACAGATGTCCATCCTTGG
27491 CTGGCGCCAGAACTGCT
1 CTGGCGCCAGAACTGCT
27508 TCCCCACTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.19, C:0.33, G:0.26, T:0.23
Consensus pattern (42 bp):
CTGGCGCCAGAACTGCTGCCCAGTACAGATGTCCATCCTTGG
Left flanking sequence: Indices 26907 -- 27406
CCAAAAAGAAAGAAGAGAAGGAATGGGGGGTTGGCGCCGTTTAACGGATTGCTTGCTTACCAAGC
GATCCTGGCCTCTCCTGGCCGAACTCGCCAAAAAAATAACAATAGAAGAGATCTATTTACCAGAA
TCGCTTCGTTTTATACGGTAAATAGAGATCCCTCATTAGGTTTGGCTCTCTTTCTAAACGAAGGA
TCCATTCCCGAATGTCGGGGATCGCTTCGTTTTCCACCTCGAGATCGTTCCGGATTATGGAGGCG
CCCGCTTCAAGAAAAGAAGCGTTATCTCGGGATTGTCTCCAGACTGGGAGATCGCGCTCACAATA
ATGCCGGAGTTGGTCGGAAACTAGCCTATGAAGGCGTCTCAGAAGATCTCCCCTCTCCCCCTCTT
CTTGAAGGAATGGGATTAACGGAGCCGGCGGATTCCCTACATGGGTATCTTGTGCCGGGGGGCTA
GGATTCGAAGGGACAGGATGTGGATTATTGACACTTGCTTCGGAA
Right flanking sequence: Indices 27508 -- 28007
TCCCCACTCCCCTCCAGCCGGAGCCATCATGTTCTCCGGATAAAAGATTGGTAAAAATGGGCCCC
CCCACCCCAATTGCTTAAAGAGGTACAGGATCGATTTTCTGACAAGCATGGATTGAACTCTTTCA
AAAAAGAAATTCAAATCCAACCCCAGAAAACAAAATAAAAAGTAGTAAATAATAATAATAATAAA
AACGAATATTACCTGTCTTACCGAAATCGGATTTCCCTTGCGTGCCATATGCGCTTAGACTTCAC
TTTTTCCCCCTTTTTCTTCCCCGTCCAATATTTGTTCTCGTGTAAAAGCAAACTCTCCAAATTTA
TGACCAACCTCCACCGTACGTACCTTTCGCTGCTCTTATACTCCCTGGCACTCGTGTCGCCATAC
CCCCCCGCGGCATTTCCATCGGACGGGAAAGGCTAGCAGATCTTTTCTTCGTAAGGGGCTCGATA
TGTCCCTGACTCTTTACTAAACCTAGGCCCACCCTTTCTTTGAAC
Found at i:40472 original size:21 final size:21
Alignment explanation
Indices: 40442--40485 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
40432 CTTTCTGCTG
40442 CAGATACAGAACAAGAAGATT
1 CAGATACAGAACAAGAAGATT
*
40463 CAGATGCAGAACAAGAAGATT
1 CAGATACAGAACAAGAAGATT
40484 CA
1 CA
40486 AGGGGAAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.16, G:0.20, T:0.14
Consensus pattern (21 bp):
CAGATACAGAACAAGAAGATT
Left flanking sequence: Indices 39942 -- 40441
TGAGAAATACAAGTCGCCTAGCGCGGGGGGGTGAATGTCCAATCCCTCAAGAGGAGACGGGACGT
CCGAATTAACAAATTGGCGCGACCATGCGTCGATAGCCTCCTCAAACCATTCACTTTGTTCTTTC
TTTTGATTCAAGTCCTTCAAAATGGCACGCAAAGTAGAGGGATCCGATGATTCGCCGTGGACCCA
CTGGCCCAAAACATAGCGTGCCTCCCCGTCCAACTGGAAGCCAGTCTCTTCTGCAATGCTCGCCA
CTTTCTCTTCGATTCTTCCCTGGGCCGAACAGACTTCTCTTTCGGTGTAAGGAGAAAGAGTCGAA
TAAATACTAGACATCTCAGATGACGAGTCAGAATCGGGGGATGAGGGAACACCAATATTATGATA
GGACGAAGGTATCTCCGCAGTCTTGGGCGGAGATGGAGATAACGGAGGGCACTCTACATCTCTAA
GCAAAGGGCTTACGCTCTCCTCCTCAAAGGAGTTTCTTTCTGCTG
Right flanking sequence: Indices 40486 -- 40985
AGGGGAAGGGTTTGTTCGTATATCCATTTAAGCGAGCGAAATTTCTGCACTTTCATTTGCTTTGA
AACTTTTCTTTGGCTGCTCTGCTCCCCCCAAAAAAAGAAGAGAGACTTGTTCTTGCTCACGGAAA
TCGCCGGTTGGGTTTACCAAGAAAAACATGGGAATAATTGGACGTAACATTCTTTAACCGCTTAT
TTACGATATTTCGAGTTGGATGAAAACAGCGCTCAGAAAACTGCGGACCTGTATAGGGCGACCCC
CTATAAAAAAGGGAGAGAGCGCCTCAAGGGTATCTCCTATTTTTTTTCTCTAGAAAAGAGTGAAA
GTAGGGGCTATTGCGGCCCTCGCTCTCAAGACTGTCGAAGATAGCAAGGAGACTTTTCAATGAGC
CCCAGGGTCCAAAATGAATTGGTTTTGTAGAAGAACACATTCTTCTGTGGAAGAAAGTCGTATCT
GGGCTCCACTCAGCAAGAACTCATTATCATTCTCTGGAAGCTTAG
Found at i:42509 original size:30 final size:30
Alignment explanation
Indices: 42473--42529 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
42463 ACCACTATAA
*
42473 AAATCATTATCAGAATCA-CTATCAGAATCC
1 AAATCATTATCAAAATCATC-ATCAGAATCC
42503 AAATCATTATCAAAATCATCATCAGAA
1 AAATCATTATCAAAATCATCATCAGAA
42530 ACCTTAACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.47, C:0.21, G:0.05, T:0.26
Consensus pattern (30 bp):
AAATCATTATCAAAATCATCATCAGAATCC
Left flanking sequence: Indices 41973 -- 42472
TATTCGGGCCTATTAGAGCAGGATCCACTTTTTTGGGAATATTGGTCGAAGCAATAAAAAGAATA
TTTCCAGTGTAACCTTTTTCCAAATCCCCTCTTTCCCCGGAGAAATTGTCCATTAATAGAGTGGA
CCAACCCCATTTTTCATAATCCCCGGAGAGATTGTTCGCTAATATACCAAGAGATAAGGAATTCG
ACTCAGTCATATGCAGATCATGAATGTTTGGAATCCATATTATGCAAGGATACATTGCTTTTGCT
AATTCGAATTGAAGGTTGATAAAAAAAGGGTCTCTGTGTTCCGGTTCTAGCAGATCCACAGCCTC
ATTTATCACCTTTTCAAACTCCTGCTCCGCCTCAAGGGCACGGGCGATAGCGATCTCGTAAACCA
CATCAGTAACGTCAATACCACAAATCTCTTCAATTTCCTTACTATCATCAATATCGTCAATCATA
TCAAGATAAACATCGTCTTCTTCGTCAATATTGCCACCACTATAA
Right flanking sequence: Indices 42530 -- 43029
ACCTTAACCAGGTCCCGGTTCCGAAATACTGTAACGAAAGGAACATAGGAGTTTGTTGCTAGGTA
TTTGACCAAATAGGATCGTCCAGTTTTTATAGAACCTATCACTAAAATACCCCTAGAAGGGGATA
GGGGTAAGCGGAGCGAAAAGGGTAGGTTAGGAGATGGGTAATGAAAACGATTCGAGGTTTGTATT
GTCTGATAATAAGCAAGGAATATCCGTCTTTCCGCTAAACAGAGTGTATTGAACTCATAATTCAG
TAGATACTTTTTATGAATGTAAATGAAGTTTCGTAAGTAAATTACTCCCGGCTCTTCATTCATTA
GAGAACCAGAGTCAGTATTTGATAAATGATCACTCTGAGTCAGACTCAATAGAATTTTATCAATC
CTTTTTTCTGTCGTTAAGTTAGCTCACTTCACAAACCCAAAGCGTCAAACTCACCTCGGTTTAGC
AATTACACGTACAGTCCAGGAGTTGCAGAAGGGATATCAGGATCT
Found at i:74993 original size:21 final size:21
Alignment explanation
Indices: 74969--75009 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
74959 TAGCTTTCGA
*
74969 TTCCTTAGAATCAAGCTCAAT
1 TTCCTTACAATCAAGCTCAAT
74990 TTCCTTACAATCAAGCTCAA
1 TTCCTTACAATCAAGCTCAA
75010 GCTGGACCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (21 bp):
TTCCTTACAATCAAGCTCAAT
Left flanking sequence: Indices 74469 -- 74968
GATTCCAACATACTCAGTTTGAACAGTCTCCACGTCTCGAAATGAATTCGGATTCGCTCAGTAAG
CTAGTTCTGGAGTCAATCAATCCGGATGAGACAAGACTAAAGCGTTCACTAGATGTTCAATCGAT
CGTGATAGAATCCTGGTTACGAGGGGATCGCTCCATCCATAGGTCAGTAATTGTGTCATAGAGAG
TCATTCGATCACTCGAGAGTACATTCAATGCTACGACCCATTTATAAGGAGCAATCGAAAAATCC
AGAATTCCTTAGACATATAAAGAAAAAGATGGGCTTTTGCGTTCTAAATAGAAGTGAAGATTCAA
GTTGGTTCAATGAGGGACTATTTGGCTTATTCTCGTTCTGCCTTATTTATTTATTCTTTTTGTTT
ATTATTTGAACTAGATTCATTTTTTCTTTCATTTATTTTTCTCTTTTGCATTGGTTTTTTAACAA
CAGTGGCTTAGGGGTAGGGATAGATGGTCTTCGCTTAGCTTTCGA
Right flanking sequence: Indices 75010 -- 75509
GCTGGACCGAAGACTCCTTTGAAATCAACGTTCTCCTTGAATCTTCGCTGTAGAAAGGTAGAAAG
GCTTGCTGGCGGTGCGGATGAGGCAATCCCCTATGTTAGGAGCAATTCATGCGAGCTCTGTTTTA
GCTAGTTTCTTTGCGGAGCCAGAGACCTGGTGGGGGTATGTGAAAGATTTGGTACATGCCTTGGG
CAGACTTTCTTCTTCTATTTATTGGATATTGTCCCTTGGAGAAATGGGATTCTCTTTAGTCCCTG
CCAATCTCGGTGGGACTTCTTTCTCTGATGGCCCCCTCATTTCGTCCTCCTGCTCGCTAGCAGTC
GCCTTTTCTTTGGAAGGGCGAAGTGTCTCAGTCTTCTCACCAATATCTGTCAGAGTGCTGATCCC
TTCTTGTGCTTCGTGCTTTGCCTCGTCTAACTAGGATAAGTGGCTAAGGGGCATAGCATGAATAC
CAGGAGTTTGCGGGCAGTTAGAGTCCAGTGGTCAACCTCTCCCCT
Found at i:80916 original size:12 final size:12
Alignment explanation
Indices: 80899--80939 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
80889 GGGAATAACA
*
80899 ACCGGTTGCGGT
1 ACCGGTTGAGGT
80911 ACCGGTTGAGGT
1 ACCGGTTGAGGT
80923 ACCGGTTGAGGT
1 ACCGGTTGAGGT
80935 ACCGG
1 ACCGG
80940 CGCCGCTTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.15, C:0.22, G:0.41, T:0.22
Consensus pattern (12 bp):
ACCGGTTGAGGT
Left flanking sequence: Indices 80399 -- 80898
CTCCCACTTGAGTTATCTTAGCCTACCCCCTTCCCATGCTGCTTGCCAACGACAACTGGTACTTT
CGGGTCATCCCCTTCCCCTCTACCCCCTTTCGGTTCTGGCAAATACCCAAACTATGATATCATCT
TCGTTCTAAAAGGATATCATAGTTTTGGATTGCTCGAAGAATCCGGCGATAGGGAACGCTTTGTC
GGGTTCCCCGTTCCATTATCTGAGTCACGTACGACTGGTAGGTTCTAGGACTCAATAGTTCCCCT
TGCGGGCAGTGAATATACCCGCGAATTTCTCGAAATCGAGCCATAATGGAATTCGGATGAAATCC
ATCGGCCACCAAAGCCGCCTCTATATGGCGCTCTACTACGACTTGTGTGTCAATTATGGATACCA
GTCGTTGTGGGTCCCAATTCCCCCCGAGATTCAGGAGAGAATACCTTTGATAAAGAAGGGCCGCT
CGCATATCATCGGGGATAAGAGGGTGGGCCAATTGGGGAATAACA
Right flanking sequence: Indices 80940 -- 81439
CGCCGCTTCGGGTGGAGTAAGTGGTTCTTCCGGCAATTGCACTGGACTTTGTGGGGGAGAGAAAG
CGTTTAAACCCTCGCAATGGGCAGCTTCAACGCACCCTATCACAAGCCCAACGAGAGGAGAGTTC
CTTATCACTTCGGAAAACAGAGAAATGCATTCTTTCCAGTTAGGCCGAAGTGTTTGGCCTTTCCT
TCTCCGCGCCCGCTCACGCTTCGCTGACCTATCGCGTGGTAAACGCTTCGCTGACCTATCGCGTG
GTAAAAAAAAGAAAAATAAAGTACGAAAGAATAGTAAACAGAGCACACCGCAGAAAGATTCTAAA
TATGAGAAGCCCCCCTTGTATTTGAGAAGAAGGAAATGAATAAAGAAAACGAAACGTAATAAAGC
GTTTCTAGCTCTAGTTTCGGATGAGCTTCTCCCAATTCTGTCTAGTAATAGAATAGGGCGGTTTG
CTCTGACCAAGACTCCCCTTTTTGCTCCGTCCGCGGAGCGTATGA
Found at i:81180 original size:27 final size:27
Alignment explanation
Indices: 81150--81204 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
81140 GCGCCCGCTC
81150 ACGCTTCGCTGACCTATCGCGTGGTAA
1 ACGCTTCGCTGACCTATCGCGTGGTAA
81177 ACGCTTCGCTGACCTATCGCGTGGTAA
1 ACGCTTCGCTGACCTATCGCGTGGTAA
81204 A
1 A
81205 AAAAAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.25
Consensus pattern (27 bp):
ACGCTTCGCTGACCTATCGCGTGGTAA
Left flanking sequence: Indices 80650 -- 81149
AGTTCCCCTTGCGGGCAGTGAATATACCCGCGAATTTCTCGAAATCGAGCCATAATGGAATTCGG
ATGAAATCCATCGGCCACCAAAGCCGCCTCTATATGGCGCTCTACTACGACTTGTGTGTCAATTA
TGGATACCAGTCGTTGTGGGTCCCAATTCCCCCCGAGATTCAGGAGAGAATACCTTTGATAAAGA
AGGGCCGCTCGCATATCATCGGGGATAAGAGGGTGGGCCAATTGGGGAATAACAACCGGTTGCGG
TACCGGTTGAGGTACCGGTTGAGGTACCGGCGCCGCTTCGGGTGGAGTAAGTGGTTCTTCCGGCA
ATTGCACTGGACTTTGTGGGGGAGAGAAAGCGTTTAAACCCTCGCAATGGGCAGCTTCAACGCAC
CCTATCACAAGCCCAACGAGAGGAGAGTTCCTTATCACTTCGGAAAACAGAGAAATGCATTCTTT
CCAGTTAGGCCGAAGTGTTTGGCCTTTCCTTCTCCGCGCCCGCTC
Right flanking sequence: Indices 81205 -- 81704
AAAAAGAAAAATAAAGTACGAAAGAATAGTAAACAGAGCACACCGCAGAAAGATTCTAAATATGA
GAAGCCCCCCTTGTATTTGAGAAGAAGGAAATGAATAAAGAAAACGAAACGTAATAAAGCGTTTC
TAGCTCTAGTTTCGGATGAGCTTCTCCCAATTCTGTCTAGTAATAGAATAGGGCGGTTTGCTCTG
ACCAAGACTCCCCTTTTTGCTCCGTCCGCGGAGCGTATGAATTTCCAGAAATGTAGATAGAACAA
AAGAGGGAATGAAGGGATAGGAATAGGAATTATAGTACCATTGGAAAAAGGGGCACCCGTGGGAA
CATCTCTACTGACGAACAATTTCAATAGTACGGGTGCGGCCGTGCCACGAGGCACGACCAGGAAA
GTAATGATAAATGCCAAGTTATGTAGTAGTACCATATGTTTCATATCTGTTTCAATATTCAATAT
CTATCTCGTTCTCTTGTAGTTCCGCTTCTTGCAAAAAAAATGAAG
Found at i:86285 original size:21 final size:21
Alignment explanation
Indices: 86261--86304 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
86251 ATAAGGGAGT
*
86261 TCATTCGTAGTATAAGTTCTA
1 TCATTCGTAGTATAAGGTCTA
*
86282 TCATTCGTTGTATAAGGTCTA
1 TCATTCGTAGTATAAGGTCTA
86303 TC
1 TC
86305 TCGTTCAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (21 bp):
TCATTCGTAGTATAAGGTCTA
Left flanking sequence: Indices 85761 -- 86260
TAGGATACAGGCTTTTACGATGATCGATCTTCCTCGCTTCTGGGTGTTCCACCGCAGCCCCGCTG
TTCGTGCTCACCCCCATCAGGCTAGCTATCAGGTCTTCAGACAAATGAAGCGGCTCATTCGAGTG
ACATCCTAAATAATAAATTCGAATATATATTCTTGTTATCTCATATTTACCGTACTCCTCCCCCT
TCAACCTCACATAGTGATCCACTAAACTATAGACTGGCAGATCTTGACCCCCCTCTCTAAATGTG
ATAGCATTACATATTGTAAAGGGTACTCGCCCGGCTGGTATTTGCATCACATAATGAATAGTAAA
TTTACCAAAATCTGCATTTATAGGGTATGCGTACTTGATTAGTAGGTACATAATGATTGAGGCTA
TCTGTGCACAGTTCCCGCACATCAATGATTGGCCTGAGAGATCCGCTGTAGCAATTCTCAGCCCC
GGATAGGGATCTTTACAAGATTCATCCCAAGTTGTATAAGGGAGT
Right flanking sequence: Indices 86305 -- 86804
TCGTTCAGTCTTTATCCTTGCCATGGTGATATATCTTCTTCCAACTCTATCTTTCCACTCCAAAG
TCCCAGTTCGCACATTAATCGACCATGTACCGGGTCGCACTCGGTATGAGTATGAGATTTGCATG
ATTTTATTTTAATCTTTTAAGGGGCCCCCCGCTCGTTGGGAGACAAACCCTAAAGAAGGGGATAA
ATGTCTATATACTTTTTCTCGAAAGACTCCGGATCCCGATAAGAATTGAAGATGGTGCCAAGATG
TATGACCTTTCCTTCCCTTATGAAAAGAGCACGGCCAATCGAAGACCTTCCCTTCGGGCATAGGT
CAAGTAATCTTAATCGCCTCGGGCTGAGTTGCTTTCCTATAAACATATTCTTTACTCCTGCGCGA
GTACCATATAGCAGTCTTCTTTCAAGCCAGTTCAAAAAGAAGTTCAGTCCTCTTAGCGCTTCCCT
TAGCAATCCCTTGCTGCTAGTGTAGCAATAGTCAAGTGAGATAAG
Found at i:136967 original size:21 final size:21
Alignment explanation
Indices: 136941--136984 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
136931 CCCTTCCCCT
136941 TGAATCTTCTTGTTCTGCATC
1 TGAATCTTCTTGTTCTGCATC
*
136962 TGAATCTTCTTGTTCTGTATC
1 TGAATCTTCTTGTTCTGCATC
136983 TG
1 TG
136985 CAGCAGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.20, G:0.16, T:0.50
Consensus pattern (21 bp):
TGAATCTTCTTGTTCTGCATC
Left flanking sequence: Indices 136441 -- 136940
TACTTCCTTCACTAATGCAGTCTATTTCGCTTCTTTATTACCTAATAAAGTCAGTTCTCTTCTTT
TGCAACCAAAAATAACATATAAGTAAGCCTTCTTGCTACTAACCCGCACCTACTCATAAGCATCT
TACCCGTGGGAACTGAACCCTCTAAAAGACCCATTCATTCACGACGACCTCCCACTCGAAGTGAT
CATCCCTTCCTTACGCGTGGCAATCCAGAGCTCGCTCACCGAGGATCAGAACGCAGTCTGACGGC
TGTCCGAATTGGAAGCTCTCGAGACGCAGCTCGTATGACAGACAAGGGCTTTCGACAAAAAGGTT
CAGGTCTTTTTTTAGTCTATTCCTTAGACTCCCATGCTTTACATTGGTCAAGAACCAAGCACATT
TCCGACAAGTCTCCCTGGGGTGAGCAGAGCAGCCAAAGAAAAGTTTCAAAGCAAATGAAAGTGCA
GAAATTTCGCTCGCTTAAAGGGATATACGAACAAACCCTTCCCCT
Right flanking sequence: Indices 136985 -- 137484
CAGCAGAAAGAAACTCCTTTGAGGAGGAGAGCGTAAGCCCTTTGCTTAGAGATGTAGAGTGCCCT
CCGTTATCTCCATCTCCGCCCAAGACTGCGGAGATACCTTCGTCCTATCGTAATATTGGTGTTCC
CTCATCCCCCGATTCTGAAACCGAAGAAGAGTGGGTTCTCCTAAGTAGTTGGAGGCGTCTTCTTT
GAACTCAAAAACAATTTCACTTGAATGAAACCACTTATATGAGTGAATCCTATCAACTAGACTCT
TATCGAAATTTCGTAGTATAGAAAGAGAAAGAGATTCGTCTTGCTTATTTGCTTGATCATTGAGT
TGAGTGCGGGGTAAATGCTTTTGACTGAACCTCCCATTGCTCTCTCCGATAGCATGCAGCTGATA
ATGGAGACAGATATCTAGAAAGTGTTCAGTGAGGGAACAAGCAACGGCGCAGCTAGCGCGTTAGC
CGCGCATCCGTTTTCTTGCAGAAGTGCTCACGCGCGCCCTTACGT
Found at i:149870 original size:60 final size:60
Alignment explanation
Indices: 149771--149889 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
149761 CGCTAGGCGA
* *
149771 ACCAAGGAAGACGCTTCGCGTCACATTACTCACGCACAACGGCTTCATATTCACTATATAT
1 ACCAAGGAAGACGCTTCGAGTCACATTACTCACGCACAACGGCTTCATATTAAC-ATATAT
** *
149832 ACCAAGGAAGACGCTT-GAGTCTTATTACTCACGCACAACGGCTTCTTATTAACATATA
1 ACCAAGGAAGACGCTTCGAGTCACATTACTCACGCACAACGGCTTCATATTAACATATA
149890 GCGTCTGTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 5 0.09
60 32 0.60
61 16 0.30
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (60 bp):
ACCAAGGAAGACGCTTCGAGTCACATTACTCACGCACAACGGCTTCATATTAACATATAT
Left flanking sequence: Indices 149271 -- 149770
ATTGCGCTCCCTAGACCACTACCATGTAGTTAGGTAGGGACAATCAATCCGTAGTGACGGGAATC
TAGGAATGAATGGGGATCCCTATCAATATAAAAAGAATATCTAATTAGAGGTTTCTCCCTTTCTC
TCACTCAATAGATCTATCTGGTCTGATACGGCACAGTACAATACGAGACGATGGAATGAAATGGG
ATAGAAGGTAGAGGGCTGCCTGCGACGCCCAAAAGCGATGATTCACTTGTCCCCTTGTCCATAGG
GACCTCGTGGCATACAACCGAAACGACTCCCGCTAGATAGCCGCCCCTTTCTCTCTTTTTACAGC
CTCGTGGACGGACGAAAGAAGGGAAGTTACAGAACGGGGCAGCCAAGGCTCGCGCAGTAGACAGC
AAGCAGCAAGCAACAGCTTCTCAGCCCCCTCACCTTTCTATTAGTCAAGTTTATAAGCGGTGAAC
AAATAAAAAAGGCAAGCAACGCTTTATAATAGAGGCGCTAGGCGA
Right flanking sequence: Indices 149890 -- 150389
GCGTCTGTAGCGTTAGAAGCCGTTGCTTGTTCGGTAGGGTAATAGTTGCTTGAAGCCGTTGCTTG
TTCACCCCTTTTAATAATAAGGTAAGCTTTGAAGCTGGCTGCTCTGCTATACTATACTAGTTGTA
GGGCGCTAGCGCTTGACTAATATAATAGAAAGTAAAGGGACTCTATTATGATCTTACGAATCTAA
AGATCTAAAAATTGAAGAACGAGCTCTTTTGCTCGCCCCTATCTCTAATGGGGCGTAAGCATTTC
ACTCGCTAGGGGATGGGATTCATTCACTTGCATTTCTGCTAGCACTACAAAAAGCTCCGGTCTTA
ACGCCCTTACTACTGCTGTGCAGCCTTTCCTCGGGTTCGTAGAGTCGGGTTTCCCGTTTACCCAC
AACGGAGGAGCCGCCCCCACCAGGCAGGCGGCCACGGGTCATAACGCATTCTTCGCACAACAAAT
CCACTTTGAAGTTGACTTATTCGCTCGGCCAATCGTCGGAATGTG
Found at i:229892 original size:17 final size:17
Alignment explanation
Indices: 229870--229905 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
229860 AACATTGAAT
*
229870 AAAAATATGAAAATAAA
1 AAAAATAGGAAAATAAA
229887 AAAAATAGGAAAATAAA
1 AAAAATAGGAAAATAAA
229904 AA
1 AA
229906 TACCGCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (17 bp):
AAAAATAGGAAAATAAA
Left flanking sequence: Indices 229370 -- 229869
GTCCCCATTTGAATTCCTTATATGTAGAGAAATATCTTGTTGGATAACTTACATAATCTTTATTA
CAAATCCTTTGTGTATCTTGGTCTTCCTACCCATCCACTCGTTTTTGAAATCTCCCGTTATGGAA
ATACATCTAGGATATATAGATAGTAAAAACTCCATACAGTTGATCTTTGAAACCCGCTTCCGGCT
ATGATGACTAATCCACCAAGCTTGGGGGTAAAAAGCAAACATAATAAAACTTTTTTATGTTTGCT
TTTTTAACTTTATTCTTGTACATAGGAAAGAAGACTTAATCGTTGTACTGCCAAATTCGAAGCCG
CTTTTTTTTCACTTATATAACTATCTAGTTTCCTTTATCATCCCCAAGTACCCAATACTCTAGAA
GAACTACGAACACAAAAAAATATGTATATAAAAAAAAGAATAAATCACCCTAAAGATCTGAAAAG
TTAGAAACTTAGAAGGATTATTCTTATAAAAGAAAAACATTGAAT
Right flanking sequence: Indices 229906 -- 230405
TACCGCATATATAGCATCCATAGAAAAAAAAAGAGAGATAAACATAAGAAATATTACTAGAAATA
TTACTCAAAAATGATAATGATAGAGAATTACTTTTCTTTTATCTTTTAAAGTGTTTTTTTTGCTT
CGCTTATTACTAGCGAAGCAAGAAATTGCATTGTGGGTGCAAAAAGAAAAAATTGATTTCTAGTT
AGCATATTTATAGTTATCATAATTTTATTGAACTTCGGGTTTTAAGAGGAAATTAATAGTTGTTC
GATCTCACAAGTCAAAACTACCAAAACGCATAGAGCTTTTTTATACCTGATCGAATCACACGCAG
AGAAATTGATAATACACATAAAGCTAAGGGTATTTCATAACTAATTGATTGAGCAGCTGCCCGTA
GACCACCTAAAAAGGAATATTTATTATTTGATCCATATCCGGACATAAGAAGTCCAACGGGAGCA
ATACTTGAAGCGGCGATCCAGAAAAAAACCCCAATACTAAGATCG
Done.