Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_056359
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: 303026
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:16393 original size:20 final size:20
Alignment explanation
Indices: 16368--16409 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
16358 ATTCTCCCTT
*
16368 AACTCTATCTTTCATTTCAG
1 AACTCTATCTTTAATTTCAG
16388 AACTCTATCTTTAATTTCAG
1 AACTCTATCTTTAATTTCAG
16408 AA
1 AA
16410 TGGAATTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.43
Consensus pattern (20 bp):
AACTCTATCTTTAATTTCAG
Left flanking sequence: Indices 15868 -- 16367
AAATATGGCAATATGAGATTCCGATTCCTTCGTAGGCAAGGCGTTCCGATCCGCCAGCGACATTC
CCAACAACTGAAAAAGCCTTCCCTACTATCCTCCTCTCCCATAGGTCGAGTTACTTCATACCAAA
GAGTCGAGTGACAAAGTACGTAAAGTAGTAAACTGCACTAGCTTTATGCCTTAGAAGAGGCAATT
GAAAATTATTCTCCGCCATAGAAGAAATTCATTCGCTAAAGATAGGCTTTCTTGACCCGTCTTTC
TTCTTTATTATCTCCTAAAAGAAACTCCACATCGGTCTGAACTCGCAACGTATAAAAAACTTCTA
TCTTACCCATCTCCCAGCTAAGCTCAAGCCCTTTCTATGAAATTGCGTATATATAGAAAAAGAAA
AATGATTCGTCTTGCTTCTTCACAGGATAGAAAATGAATTGGCAGGAAAGTATTTCGACAAAGAA
AGTACGATCGGTTCATTAATAGTAATAGTAGCGGCATTCTCCCTT
Right flanking sequence: Indices 16410 -- 16909
TGGAATTCTCTGCCAGAGCTGCTGAACTAACAACTCTATTAGAAAGTCGAATTAGCAACTTTTAC
ACAAATTTTCAAATGGATGAGATCGGTCGAGTGGTTTCAGTTGGAGATGGGATTGCACGTGTTTA
TGGATTGAACGAGATTCAAGCTGGGGAAATGGTTGAATTTGCCAGCGGTGTGAAAGGAATAGCGT
TGAATCTTGAGAATGAGAATGTAGGGATTATTGTCTTTGGTAGTGATACCGCTATTAAAGAGGGA
GATCTTGTCAAGCGCACTGGATCTATTGTGGATGTTCCTGCGGGAAAGGCTATGCTAGGGCGTGT
GGTCGACGGGTTGGGAGTACCTATTGATGGAAGAGGGGCTCTAAGCGATCACGAGCGAAGACGTG
TCGAAGTGAAAGCCCCTGGGATTATTGAACGTAAATCTGTGCACGAGCCTATGCAAACAGGGTTA
AAAGCGGTAGATAGCTTGGTTCCTATAGGCCGTGGTCAACGAGAA
Found at i:33353 original size:15 final size:15
Alignment explanation
Indices: 33333--33364 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
33323 ACCCTTTCTT
33333 ATTAGTAAAGAAAAA
1 ATTAGTAAAGAAAAA
33348 ATTAGTAAAGAAAAA
1 ATTAGTAAAGAAAAA
33363 AT
1 AT
33365 GTCCTTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (15 bp):
ATTAGTAAAGAAAAA
Left flanking sequence: Indices 32833 -- 33332
CGGCTCTCGCTCAAACCCAACCTGTGGTGGATCCCGGGGGACAAAGTCAAAGCGTTTGATCCTTT
GCCCCATACTTTGAGATGCTCCTCCCCGCGCAGCGACGCTGCTCGTGATAGGCTTAGCTTTAAGC
CGCTATCGTTCGGTTCGCTCAGGGGGTCTTCCCTTATCTTCCCTAACGTTCAGAGTTGTTCTGGT
TTGAGAAAGAAGCACCGGCCGAGCACCCTGAATGAATAAAAAATGGACAGCAAAGGGAATCAATG
ATTCTTATTCAACTGAGTTGAAGCTAGCAACATGTCGATTACACACCGGAGGTTGGTAAGAACTG
AGGGACAATGCCCCTAACCCAAGTGGGCTTACCAGCGAAGCAACTGGTACTTGATCGGGCGGGGG
ACGGTTTGGTTTCGTGCAACGCCCTCGCAGCAGAAAGAGGCAGTTGTCATTTGAAAGGAAACGCC
CTTTATAGGGTTCCAAACGCACCCTGATAAAAAAAACCCTTTCTT
Right flanking sequence: Indices 33365 -- 33864
GTCCTTATTGAAAACTAAAGCGCTAACGCACCTTATTATTAGTAAAGCAACCTTTCGCCTTTATT
TCATTGATATGATATAAAACAAGCTTACTTACTAATAAAGCGGCAACAAGCACCCTCTTTCTCAA
AGCAAAGTCAACTTTCGCGCTTCTTACTTTAAAAAGATTGCAGCTAGCGCGCTTGACTAAAAAAA
GTAAAGGCTCTTTTCCTTTTTTACGAATCTACAACTCTCTTTACTGAGCGAGACTCCATCCATCT
CCCTTCCCTACTAGTAGGTTATTTTAAATTTTCCATTCTATCATTTGTTTGACAGCTTAAATTAA
ACTAGGCTCCATTTTAGATAGGGTTTCGGTCTTAATCAAGATGGGTCAGGGGCGCGTCGGAACGG
TTGGTGGCTGCTTAGTCTCATCCGAGAGTCTAATTTCTTTGTACTGCTTTTTTCTTTTAAAAAAA
GAAAGAAGGGGGTCGATTTAGACTCCTTCCTTTCCACTGCATAGC
Found at i:54094 original size:16 final size:15
Alignment explanation
Indices: 54069--54102 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
54059 TTTATACTTT
54069 TATTTATACATAATA
1 TATTTATACATAATA
54084 TATTATATACATAATA
1 TATT-TATACATAATA
54100 TAT
1 TAT
54103 AAGATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTTATACATAATA
Left flanking sequence: Indices 53569 -- 54068
TCAGTAGTATAAGTGTTATTGTTAGGAGAATAAGTGTCTACTACAAGGTGCCTAAAGCGCATTTC
TCGAGCTCTAGGAGTGATTCTTCTCCGTTTGTAAAAAAGAGTAAGAGCAGTAAAGTTGACCGAAG
AGATTCTTTTTTGAAGTCAAGATGCTCTAATAACTGGCTAGGGATTCGCATTTCCCTCTAGGTAA
AGTCAAGAAAAAAGCTTATAGTATCTGGCATGCCTAAAAGAGATAGCAGGCATATCTTATCTTCA
ACTTGATTCTATTATAGAAGTGAATTCTCAAGCCTTTAGTGAGTTCCAGCGAGCTAGTTTCAGTC
ACAATAGGAGGGGGTTTAGTTATCTAACGTGCCAGGCTCCTTCCTTTACAACCATTGTAAGTTCC
CTTGAAGGCAGCATGAAAGTGTAAGAAAGAAGAGAAGGTTGAAAGTCTTATCTTATTTAAAGAAA
GAAAAGAAGGTTGAAAGAAGTTAAATTCTTTCTTTTTTATACTTT
Right flanking sequence: Indices 54103 -- 54602
AAGATTAAATAAGATGCTTTTTAGAAAGAAAGTATCTTGAGTCTCTTAATACAGCCCCATAAGGT
TGCAATGATTCGCTCCTCTATCAAGTCTTCAAGCTTTGAAACGAACTTGAGTATGATAAATCTAT
CTTGATAGCTGCTCTTTCCCCGGGGAGGCCTTGGGAATTCCTTGGCGTGATCCAATAGGCTCTTA
CTTCACCTCGAAAGGGAGCTAGTAAGTCGCAAACAGTCTTTCAATTCCTCCTGAAAAGAGGGCTC
AAAGGGCATTCATTTCTAGTTTTAAAAGGGGTTTTCGGCTCTATTCTATTCAAAAAAAAAGACTA
AGCGAGATTTCGAGAAGTGGTGTCTGTAGCCTGTTGATCGGCTTTCTCCTATCTGTTCTGAAGAA
AAGTTCTAGAAAAGGGGTGGGCGTGATCGTCTTCTAACTCTTCTCTTATCCTATCCGCTCTTGAA
AGAGAAAAGAGCCATTGGTCAACCAAGCACAGCACAAAAGGAACT
Found at i:110394 original size:15 final size:15
Alignment explanation
Indices: 110374--110405 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
110364 ATTCTTGCTC
110374 AGAGGGAGAATATAA
1 AGAGGGAGAATATAA
110389 AGAGGGAGAATATAA
1 AGAGGGAGAATATAA
110404 AG
1 AG
110406 GGGGCGACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.34, T:0.12
Consensus pattern (15 bp):
AGAGGGAGAATATAA
Left flanking sequence: Indices 109874 -- 110373
CCAGAATCGAACTGGGCATAGGCGGATCGAAGCCTATCTCTTCCAAAAAAAAGAGTCGCTTTTTG
GTAACGCAGTTCGGTTGGCAAGTTAAGCCTCCCTACGTCTGCGATCCGGTAGACCACCGTAAAAA
AAAGTTAAGAAGGATGTTGCCAGTCCCAGTTTTGAATACGGCGGTGCAATTCTCTAGACCAGTAG
GCCTTCTTACCGAAACTACTTACGTTGTCGTGAATACGCATTAATTCCTCGACCGTCATTGGTCG
CTTTTGACTTATTCCCTTCCCACCAGGGAATAAGTGTTCCCGAATTAAGGGATTCTCCGGATCCC
ACGGATCCCTGGGGTAAAGCTCCCTCAGCCTTTGTATAATGGAACTTTTTATGAGAAACGGGTCC
GGAGCCGGTGCTGGCGCCTGCGGAAGCGCCTCTTGAGCCACCGGCTGTTGTTGTTCAATAGAAGC
GCCCCCCGGAGAAAATAATTGTCTTAGCACTTCGAATTCTTGCTC
Right flanking sequence: Indices 110406 -- 110905
GGGGCGACTCAACGGGGGCAGGATTGGGTTCAGATGGACCAGCTTCCTCCACCGGTCCAGCGACT
GGATTAGCGCGAGGACCAGGCTGATTAACCTCAACGGACTGCTCCCTTGGGAGATTAGGAGCCTC
TCCTCCTTGCGGCTGTTCGACCTCGTTTGGGGCCGGTAGGGCTTGAGGCCCAGTAGTCTGATCTA
CTTCTTCTTCATTGGAAAAATTGAGATACTTTGTCCAACTGCCGGAGCTTGAAGATTCCTCTGTC
GTAGAATTCGCATTAGGCCCAGTGGGTGGCATCATATGATGCCAGAATTCCTGCGCCAAAAAAAG
AGTAACCAAAAAACCAACGGCCGTAGCCATACTCGGAGAGTATCCCATTTTAAATAAGAGACTAG
AGAGGGCCCGACGCCCCATAGAGAACCCAACCTTAGAAAGTAAGGCGGGAAACATTTCCAAAACC
CCAGTGCAGAGACAAAGAATATACACAATCAAAAGGAGAGTGAAA
Found at i:124017 original size:15 final size:15
Alignment explanation
Indices: 123994--124038 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
123984 TGCAAAAACC
123994 AAAACAGAAAAAGAA
1 AAAACAGAAAAAGAA
*
124009 AGAGA-AGAAAAAGAA
1 A-AAACAGAAAAAGAA
124024 AAAACAGAAAAAGAA
1 AAAACAGAAAAAGAA
124039 GGGTCCCGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 2 0.08
15 22 0.85
16 2 0.08
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAACAGAAAAAGAA
Left flanking sequence: Indices 123494 -- 123993
GAGGCTTATTTGGAGTACATTTTTCCCTTGCCAGCTCTAGCTAAAGACTTGGTCAATGCTGAATG
GTTTGAGTCACAGTACCAGGATATGTCTCGGACAAAGCAGGTCAAGGTTGAATCGAATTTTCGAA
TTGATTGGCATACCTTAGATATAATGAAAAAAGAATACCTAATAAACCTTGGAATTCAAGTGAAT
ACAAAAAGGGAGGCTGTGTTTGATGAGAACAATATTTGGGTAGACACAAAACCTAAACATGTAAT
AGACTTCGGCGGGCAAGAAAGCTCTATTCTAGAAATTCTAGATAGAGAATTGAAGATTATGAAGC
ATGAAAATGCTCTCATTAAAGAACAGTTAGACAATAAAGATAGAGAATATGCTAGTCTGGAAGAA
GAAGTTGCTAAACTGCGGGAAGAGATTCAATCGAATACTCAGCTTCCTGAAGATACTGAATCACC
AACGCTATTAGAGGTCACAAAACCTACTCTGTACATGCAAAAACC
Right flanking sequence: Indices 124039 -- 124538
GGGTCCCGGCTAAGAAATAGCAGCAGTGGAAATCACAAGATGCCGACGCCTCGAAGCTGGATTTC
TACTTCCCTACGCCAGATCTATTAGTTGGACTAGATGAGGAAAGATAAGTCGTAAGATAAAAGCC
TCAAAGGTCTTCCTTTCAAAAAAGGGTCCATTTCATCATGATCGCGGTAGCCCACGATGACTTTC
GCTAAGAAAACAGCTCCACTAAAAGACAGAACTCTCGCTCAAGAAGGGAAGGCAGCTTAGCGTCT
TTACTAGTGTCTGGGGTATTCCTATGGGAAAGATCTTGACTTTCTTTAAAAAGAAAGGTATCCCA
ATAGCGTAGAAAGTACTACTTCCGACTTTCATGATCGAGTTCTGTGTACTGATTCTCATTGAGAT
TGGGATAGTGTTCCGTGTACTAAGGTACAAGACAAGAATTTCTTTTCGTTAGATAGTCTGTTTGT
CGTTATGTCTGTCCTACGATCTATCTTCCCTAGAGAGAAGTTTAT
Found at i:128380 original size:32 final size:30
Alignment explanation
Indices: 128320--128381 Score: 72
Period size: 32 Copynumber: 2.0 Consensus size: 30
128310 CAATGGCACT
*
128320 CCAACTGGCTAAGAAGTAGGGCTTTCCAAC
1 CCAACTGGCTAAGAAGTAAGGCTTTCCAAC
*
128350 CCAACTGGCTTTAAGAGGTAAGG-TTCTCCAAC
1 CCAACTGGC--TAAGAAGTAAGGCTT-TCCAAC
128382 TGGCATTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 9 0.33
31 2 0.07
32 16 0.59
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (30 bp):
CCAACTGGCTAAGAAGTAAGGCTTTCCAAC
Left flanking sequence: Indices 127820 -- 128319
ACTAGCTCGGCTCGCATGGACCAACATCGCAAGGCAGGCATCGAAAAAATTCTCCAACTGGATGT
GCGCACCTTACCACTATATATCAAACCGTCGGTCGAGAAGGAGAAGAGATTAGCAATGGCTGTAA
CAATAAATAACAAAAAAGGATACTTCCATTGCCTGTAAGATAATTTCCAAGAGGAGGAATTTTTC
TGCATCGAAGAAAAAAAAACTCCCAAGAGCTGGACTATCAGGGCTTGCACTGACCGGACTGGATG
AAACTGGGTATATCCCAATGGCTTTTGAAATGGGACTATTGGCAATCTTTTTAGCAACTACTAAA
GGGGAATATCTGGAAATGCCACTACAGGGACGACTACGAAGAAGGCTCTCCCACTAAGACTGGTG
GCTCCCCGGGTGAAGCACTAGAACTAGAGGAGCGCTTCCTTATACTCTCAATAAATGCATGTTCT
TAGCTTACCAATTACACTAGATACCTCTGAATTAGCAATGGCACT
Right flanking sequence: Indices 128382 -- 128881
TGGCATTGGGACGATAGGAGGTGTTACGAAAAGGGCCCTATACCCTATTGGATCGCTTGAAGAAG
GGGAATGGGAAACCTTAATCTTACCCCGGGCAGAGACTGCAACTAGATAGCTTGAAACTGTCCGA
GACCGATAGCAAAGCAAAGAAACTCCATCTGTAAAAAAAAAACTTTAACTCACTTTCCATGGGTA
AGGTTCTAGTTTCACATTCTTTTAATTAAAAGTATTCCCTTAACCCTAACCTTGAGTCTCACACT
CTGTGAAGTGCCTCTCTGGTATTGGGAGAACAAAAAGCCCCTCAGCTCGCTTGGATCGGGGGGAG
CTTACTTCACTTGTTTTCTTTAAGTCACTTGCCAGGAGGGAAAGCGGATTCTCTTCTCGGGTAAG
CGATGGTGTCCTTATAACAGGCACATACGATTCTCACTCTATATGTGGCATGTCCCGATGGTACT
TTCACATGAAACGGAAAGTGTTAAGTTTCGATTCTCGTGGACCAT
Found at i:138884 original size:6 final size:6
Alignment explanation
Indices: 138873--138909 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
138863 GATTTATGTT
138873 TGACTA TGACTA TGACTA TGACTA TGACTA TGACTA T
1 TGACTA TGACTA TGACTA TGACTA TGACTA TGACTA T
138910 AAGGAGAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (6 bp):
TGACTA
Left flanking sequence: Indices 138373 -- 138872
TAAACTTCATTATTTGTATATTTTTCAAAGACTATGCATACTGTATGGAGTCGATCACCATTCCA
GAAAGCTCTATTAATCAAGATGATTTATTTGCCGATCTTGACAGACAAAACCTTCTTAAAGAGAC
TAAAAGGATGTTAAAGGCGCATGACGATGTAGGCCTTCTTATTCGTGAATTGAGGATAGAAGAAA
GGATGATGAGACCGGGGCAGTTTCAACTTGAAAAAATGAGTGAAATTTTAGAGCAAAAATATTGT
GAAAACAGTCATATGAATATGATTGATATGGATGAAGATATTAAAGAAAAAAGAATAAACAGTTT
CTATTACAAGGATTCAAAAACTATTTTTAACGAAATGAGGGCACAGGGGGAAACAGAAGCTCAAT
TACGCAGGGAATGGCAAGGGCGCAGCTGATATGAATTCATTAATTAAACTATCATTTATTTTTTA
CTTTCCTAGAGGACCCCCCATTTTGAAATGCTATTGATTTATGTT
Right flanking sequence: Indices 138910 -- 139409
AAGGAGAAGTTTCTAGGTTTAAAGAAAAACTGATTTATGCCAAAAAAAAAGACAAACTTTCCTCG
TGTTAGCTCAACTGGAACTGGGGTAAAAAATTTCAATTCAATAGCTCCATGTTATGCTGCTGCAA
GACCCGGTTCCTGTCGAGTATGATACAGCTGGGCATGAAAGCTTTTTTATGAAGGCATGCTAAAT
ATGATGGGTTGGGACTGCATCTTAGTACGATGAGATGAGTTGGATGTGGAATGTACAACACAACG
ATGAGTTCGACTATCACTAGTGTTGTACGAACGAACGAAGTGCTATATCCATGGGTACGGATAGT
AGATATACTGGTAAAAATGTTGATTATTACCATTATGACTTATCCCCCGACTGAGCTATTGATCC
CTAGCCCGTGCCAGATCTGAGCACCTAATTCAGCTATTGATGTCTTCACCATACTGAATAGCTCT
CCGCTCTACTCTACCAGATTAGCGTGGCGGTAGTAGCTCCATAGT
Found at i:145528 original size:15 final size:16
Alignment explanation
Indices: 145493--145529 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
145483 GACTTTCTTC
145493 ATAGATAGAAGAAATG
1 ATAGATAGAAGAAATG
145509 ATAGATAGACA-AAA-G
1 ATAGATAGA-AGAAATG
145524 ATAGAT
1 ATAGAT
145530 GAACGAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.35
16 12 0.60
17 1 0.05
ACGTcount: A:0.57, C:0.03, G:0.22, T:0.19
Consensus pattern (16 bp):
ATAGATAGAAGAAATG
Left flanking sequence: Indices 144993 -- 145492
TCTCCGAAAGCTTTTTCCTTCCCCCGCCGCATCTCCCCTCCTTCGTCGAGCCTTTCCTTTAATGG
TTGGGGGAAGCATTCCCTTATCTGAACTTGGCGGGCATTCTTTCCAGGCTTATTCAAATAGGGGA
GTTTGGTTTGAACATAGGCTCAAACATGATTTGAAGGTCCTAGCTACGCCATGCGTTCAATACAA
AATCTGGAAAGCTGCAGGGATGACAAAAAGAGGGCCCTTTCCTGTGTTGCACTGAAAAAAGAAGG
ACCTAAGAGAAAACACTCTTCTCTTTGGTTTCTTCCTCCCGCGCCCGCCGACGCCCGGCCCGCGT
TAGAGGGGAAGATTTGCAAAGCGAGAACAGAGGGAGGGAGAGCAGCATCTTATCGCGAGAACTTC
CAGATCAGAAAAGCATTCGGAACGGGCTCCGCGTTCATTTCGTTGGCAGAAACGATCCAATCCAT
TCGGGGCTTCGGGGAACCCAAAAACAAAGTCGAAAGACTTTCTTC
Right flanking sequence: Indices 145530 -- 146029
GAACGAGATATCTTTTTTTTTTCTCTAAACAAAAAGAGGAATAGAATAGACATCCGTCTATGTAT
CCTTTCTTCCGATTTTTTTTTATATCGTTATATCTGCTCTCTATAAATTGAGAGAAAAAGAGCAG
CTTTATCCAAAACCCTATATCGAACATCAATTCCTATCTATTGATAGGAAGATCTTCGTCAAATA
CCCGACTTTGCCTTTTTTTTTAGGAAAAACTCATATCCAAGGCAGCTTACCACAAGCACCCCACC
CCATACGACTAGTTTGGGGGGCTGTTCGCCTTTTGAATCAAACAAAGTAAGTAGTAGGGGCTTCA
TACTACTTTCATTCATTCTAAAGGAAACCGAAGAACCAACCTTTAGTCAATAGGAGCCCTACTTC
CCTCTTTTCGACCAAAAAACTTCAATTCAAGCGCAAACCAATTTCTTTCTTAGTCACCGGGCTCC
GCGCACCTTTGGTACTTCAGTAGGGCGAGCTGTTTGATAGTGACT
Found at i:148089 original size:15 final size:15
Alignment explanation
Indices: 148069--148097 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
148059 GAATTAGGGG
148069 AAGCTTTGCTTCAAC
1 AAGCTTTGCTTCAAC
148084 AAGCTTTGCTTCAA
1 AAGCTTTGCTTCAA
148098 ACAATGGGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (15 bp):
AAGCTTTGCTTCAAC
Left flanking sequence: Indices 147569 -- 148068
TCTTTTTCTATCGGGCAAAGTAAGATAAAAAAACTGTCGTGACGCTGACTGAATCCACTTCAACA
TCCATTCCACTCCTTCATCCTTAAACCCGGTCACTCTCGTTCCCGCAACTTGGTAGTTTTGTTAC
TCTTTATGTTGACAAAGTGAACAGGGGCGGAATCAAAGTAGGCGACGCGAATCTTTCAATCGGAT
ACCAATTGCTTGGATGCGTTTGAAAGCCAAGAGATGACTTGAAGAATCAATTCTTTCTAGGTTTG
TCTTGTGTCTCCGAAACAAATGGTCCATTTATTGATGGGCGAACGACGGGGATTGAACCCGCGCG
TGGTGGATTCACAATCCACTGCCTTGATCCACTTGGCTACATCCGCCCCTACCCCCCACCCGCAC
AGGTTTCAGTCTCTATCTACGATCAGATCCTTTCTTTCGGAACCCCCATATGACCGCTATCAAAG
AGAATCCTATACTATAGTTGCATTGTTGTGCTTTGGAATTAGGGG
Right flanking sequence: Indices 148098 -- 148597
ACAATGGGCGATTTGACTTCACTTTACTTAAGATTAAAGATCGGGGTTGGGTTGGTCATCATGTC
TGATTCCCCTCTATCTAATCCCCCCGAACCGTGCTTACCTTGCGTTATAAGCGTCTTAGAGTAGA
GCTAGGTAATGCTAATTGCTAATTAAAGAGCAATAGCCCGTGCCGATCCGCTAGTTCTGTAAGAT
TAGTAGAATTCCTTATTCTTCGGGGCTAAATCCTTCTTCTTCTTGTACCAAAGCATTCCTTTATG
GGTGAATTGGATTGATCTTCTTTACTGTGAGACTAAAGAGTGAAGGCCTCTCAACTTCAATCTAA
GCCCGATCTCGTCTTTTTCCTCTTTTATTCCCTATTTTATAGAGTGTCCGCTTCGCTCTTTGATA
CTAAGCCCCAGTCAAGGCCTTTTTCTTTCCTCTTAATGCGCCCAACGGTCATGGAAGACCTTTGA
GTTCGTCGTTCTCATTCCCTGTCGTCTTATAGTTCTTCAGTCCTC
Found at i:178877 original size:18 final size:18
Alignment explanation
Indices: 178854--178889 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
178844 GGATGAGACT
178854 TTCGTATACTTCTTTTAG
1 TTCGTATACTTCTTTTAG
*
178872 TTCGTATACTTTTTTTAG
1 TTCGTATACTTCTTTTAG
178890 GGTTAGGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.14, G:0.11, T:0.58
Consensus pattern (18 bp):
TTCGTATACTTCTTTTAG
Left flanking sequence: Indices 178354 -- 178853
ATGAATCAGTCTTCGCTTTAGCTATGGGAAATTCTCTTAAGCAATTCAGTCAGCTCTGAACTCAA
TGATTGCAAGTCCAAGATCAGCTGTTCAATGAAACTCTGCCTTGAATTTAAAGAAGGGCATGAAG
GGATCGAACTCTGGCTTTTCGGGCATCCCCGGTTTGGAATTCCTAGCCTTTCTAGTGGCATAGAA
AATCTGTCTTAGACCCCTTATCAATATGTAACACTTTAGGGAAAAAATGGAATCTTTTTCCCGCC
CTACGAAGCACCAGGTATCAGGGTCAATTCACCTTGATATTCTCCTGGGAAATAATACACCAAGG
CCCCGTCTCACCCGAGGATGACTTCTACTTATCAGTATTAATGCTATACTAATTAGTCTTACTAC
AGGGTGAGAATGGTAGGGACAACAGGAACGGTGCTTCAAATCATACCCATCCTTGGGTTTTTAAC
ATAAAATACTATGTATGCATTCGATTCGCACAAAAGGATGAGACT
Right flanking sequence: Indices 178890 -- 179389
GGTTAGGAGGTTTCATAATGGAGAGTATAATGAATGGGTTAATGATCAAATTTCTTTTTTTAATC
GTTCTAAGGATGTTTTCTTACCCGGTGAAGAATTGAATTCCTTTTACGAGTGTCTTGATAAAATT
TATGATAAATTAGTCGAAGATAAAATAATTGACCCTGAGTTATTGCCTGAGTCCGCGCTCCATTT
AATTAAAGAGCGTATTCTATCACCCTCGGGTCACTTCACTCGACTAAGGGTCGTAGCGAAAGAAT
TCCTCCTTCAATTCAAGAGCTAATCAGTCTTGCTTTGGCCAAGAAAGCTCTTCCCTCATCACTCT
TCTATTGACTATTGGGATAAGAAACATCCAATTCCATGCCTCTCGAATAGAGTTGACCTATTATT
AACATTTTCTGAAAGAAGTCCTTATTTAAAAATGAAAAAAGCTAAGAGCAAAAAGCATGCATAGC
ATAGAGATTGCTCGAAGATCCAAGTAAAAACCTGCTGCGCAATAC
Found at i:181607 original size:19 final size:19
Alignment explanation
Indices: 181580--181625 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
181570 CCCAAGAATT
*
181580 TTTTATAAATCCTATCCCG
1 TTTTCTAAATCCTATCCCG
181599 TTTTCTAAATCCTATCCCG
1 TTTTCTAAATCCTATCCCG
181618 TTTTCTAA
1 TTTTCTAA
181626 TGATTTCAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.26, G:0.04, T:0.46
Consensus pattern (19 bp):
TTTTCTAAATCCTATCCCG
Left flanking sequence: Indices 181080 -- 181579
AACAGTACAGCCACTCCTACTTGACTTTCCCGTCGGTTGAGCCACTCCCATTCCTCTCGCTTTCA
GCGGACAGACCGATCAATGAGTACGTGTGACACCAACTTTTTCATCTCTACGCCTCTCCCTTCCA
CCCTCCCTTAGTAGTGGCCCTTTTCAAGCAAAAAACACGGGGTTGGGCGACCTCTTGCCTCTATT
TCCAACTGGCGAAGGGCAGGTTGGGAGCTAGGAAGAATAGGAATAGGAGCAAAGAGACTCTTGCA
GAAATAGTGCTATAATTTCAATAGCTTTAGTATTAGTAGCGGTAGTAGCCTTAATAGCATTGATA
GACTTCCTTTATAGGTATAGAAAGGAGAAAAACCAGTATGGAGCCAGCGTCGGTCAAGTATAGCA
TGTAAACGAGGATTGGTACGAAGGCTATCTCTACATTAGTCATCTGAGTCCCGCTAGGAATTGAG
TTATTGATTTTAAAATCCCGGCAGGAATAAAAAAACCCAAGAATT
Right flanking sequence: Indices 181626 -- 182125
TGATTTCAGCAAGAACACTTTCCGGTCAGGCCTTACTATAACCAACCTCACAGATCCCTTTTACA
CCGATGTATCATACTCCCTCGACCAGGTCATCATAAGAAAATACTGCAAAATCTTTCCGAAGTGA
GAGAAGGAGGGAAGGCGCGCTACAACTAACATAATAGCCAACTGAAAAATGCTAGCTAGCTAGGC
TAGCGCGCAATGGCTTTCTCTGAGAGGGGCGTAGCGCTTTTCATTTTGATAGGAGTTTTTGCTTG
CTGCTCGCTTGCTCTCAGCCACTTGTGGCTTAAGTAGTGGTCGGCATTCCTACGTGCTCTTCCTT
GCCGACCACTACTTAAGAATCCAAAAGTCACCTTTTGATGTTGTCGTGACGCTTTGGTTATGAAG
GTTACGGGGGTCTGGGTTTTTGGATGAATTCAGTCAGCGAAAGTCCCTCAAACTCAATCAATATC
AACAACATGTCGTGACCGGTTAGGCTTGGTTGATTTTGTCAGAAA
Found at i:214030 original size:24 final size:24
Alignment explanation
Indices: 214003--214050 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
213993 AACAGAACAC
214003 TTAGAAATAAATGTGAACAAAAAG
1 TTAGAAATAAATGTGAACAAAAAG
214027 TTAGAAATAAATGTGAACAAAAAG
1 TTAGAAATAAATGTGAACAAAAAG
214051 AAGAAAGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.58, C:0.04, G:0.17, T:0.21
Consensus pattern (24 bp):
TTAGAAATAAATGTGAACAAAAAG
Left flanking sequence: Indices 213503 -- 214002
CACATTTCCATTATGTACTTTCTATGGGAGCCGTTTTTGCTTTATTTGCAGGATTTCACTATTGG
GTGGGTAAAATCTTTGGTCGGACATACCCTGAAACTTTAGGTCAAATCCATTTTTGGATCACTTC
TTTCGGGGTTAATCCGACCTTCTTTCCCATGCATTTCTTAGGGCTTTCGGGTATGCCACGTCGCA
TTCCAGATTATCCAGATGCTTACGCTGGATGGAATGCCCTTAGCAGTTTTGGCTCTTATATATCC
GTAATTGGGATTTGTCGTTTCTTCGTGGTCGTAACAATCACTTCAAGCAGTGGAAATAACAAAAG
ATGTGCTCCAAGTCCTTGGGCTGTTGAACAGAATTCAACCACACTGGAATGGATGGTACAAAGTC
CTCCAGCTTTTCATACTTTTGGAGAACTTCCAGCTATCAAGGAGACGAAAAGCTATGTTAAGTAA
AAGAAGAAAAGGTTGCCGACTGCTACTAAGAACCTAACAGAACAC
Right flanking sequence: Indices 214051 -- 214550
AAGAAAGAGGGAACTCCTATTGGTGAGAGTCTTCCTATTGAGGCAAGATCCTTCAATGTAGAGAC
TCCTTCTTTGAATAAAAGGCCTTATAATGTGGGCATATCTGGTTCAAATTTGGATCCAATTTCAT
TTAATATGGAGCAGTCCATATTGAGGTTCGAACCATGGATCTACGGATCTCAACTTCACTCACAA
AGGTGTAGAAAGGGAGCTCGGGTAAGAAGCTTCACCTGGGTGAGGAGATGAATGGTAGGGGCAGA
GGACCTGCTAATAAATACTCTTCAGACCCGGGCCGAGGGCCGACCACTCGCTCCATGACTCAAGC
GGGCGACCGGGGCTCTTCTGAACCTAGATCCTCACTTCAATCTTTGTCTCCATGAAAGTTCTAGC
CTGGCCGAGGCCTTGGGAGGAAAAATGTGAGAGAATTGTTGATAGAGCATATTTACTCTAACAAG
GTGGATATTGCTTTTTTTCCTGGAAAGCTGTGCATACATCTTTCA
Found at i:214055 original size:23 final size:24
Alignment explanation
Indices: 214005--214056 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
213995 CAGAACACTT
*
214005 AGAAATAAATGTGAACAAAAAGTT
1 AGAAATAAATGTGAACAAAAAGTA
214029 AGAAATAAATGTGAACAAAAAG-A
1 AGAAATAAATGTGAACAAAAAGTA
214052 AGAAA
1 AGAAA
214057 GAGGGAACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.63, C:0.04, G:0.17, T:0.15
Consensus pattern (24 bp):
AGAAATAAATGTGAACAAAAAGTA
Left flanking sequence: Indices 213505 -- 214004
CATTTCCATTATGTACTTTCTATGGGAGCCGTTTTTGCTTTATTTGCAGGATTTCACTATTGGGT
GGGTAAAATCTTTGGTCGGACATACCCTGAAACTTTAGGTCAAATCCATTTTTGGATCACTTCTT
TCGGGGTTAATCCGACCTTCTTTCCCATGCATTTCTTAGGGCTTTCGGGTATGCCACGTCGCATT
CCAGATTATCCAGATGCTTACGCTGGATGGAATGCCCTTAGCAGTTTTGGCTCTTATATATCCGT
AATTGGGATTTGTCGTTTCTTCGTGGTCGTAACAATCACTTCAAGCAGTGGAAATAACAAAAGAT
GTGCTCCAAGTCCTTGGGCTGTTGAACAGAATTCAACCACACTGGAATGGATGGTACAAAGTCCT
CCAGCTTTTCATACTTTTGGAGAACTTCCAGCTATCAAGGAGACGAAAAGCTATGTTAAGTAAAA
GAAGAAAAGGTTGCCGACTGCTACTAAGAACCTAACAGAACACTT
Right flanking sequence: Indices 214057 -- 214556
GAGGGAACTCCTATTGGTGAGAGTCTTCCTATTGAGGCAAGATCCTTCAATGTAGAGACTCCTTC
TTTGAATAAAAGGCCTTATAATGTGGGCATATCTGGTTCAAATTTGGATCCAATTTCATTTAATA
TGGAGCAGTCCATATTGAGGTTCGAACCATGGATCTACGGATCTCAACTTCACTCACAAAGGTGT
AGAAAGGGAGCTCGGGTAAGAAGCTTCACCTGGGTGAGGAGATGAATGGTAGGGGCAGAGGACCT
GCTAATAAATACTCTTCAGACCCGGGCCGAGGGCCGACCACTCGCTCCATGACTCAAGCGGGCGA
CCGGGGCTCTTCTGAACCTAGATCCTCACTTCAATCTTTGTCTCCATGAAAGTTCTAGCCTGGCC
GAGGCCTTGGGAGGAAAAATGTGAGAGAATTGTTGATAGAGCATATTTACTCTAACAAGGTGGAT
ATTGCTTTTTTTCCTGGAAAGCTGTGCATACATCTTTCAAGCTTA
Found at i:219889 original size:69 final size:70
Alignment explanation
Indices: 219788--219919 Score: 196
Period size: 69 Copynumber: 1.9 Consensus size: 70
219778 AAAAGGCATA
* *
219788 ACTGACTTTTCCCTTCATAATTGGCATTTTCAAATTCATTTATTTCATTTTACCGGGATTTTTCG
1 ACTGACTTTTCCCTTAATAATTGGCATTTTCAAATTCATTTATTTCAATTTACCGGGATTTTTCG
219853 TTGTC
66 TTGTC
* * *
219858 ACTGACTTTTCGC-TAATAAATT-GCATTTTCAAATTCATTTATTTCAATTTCCCGGGTTTTTT
1 ACTGACTTTTCCCTTAAT-AATTGGCATTTTCAAATTCATTTATTTCAATTTACCGGGATTTTT
219920 GGCATAACAG
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
69 40 0.71
70 16 0.29
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (70 bp):
ACTGACTTTTCCCTTAATAATTGGCATTTTCAAATTCATTTATTTCAATTTACCGGGATTTTTCG
TTGTC
Left flanking sequence: Indices 219288 -- 219787
TTGAAGTCCGTCCTCTAAACGCCGCAGTTCTTGAATCTGAACTAGAATGATACAAGATGAAACCT
TCTAGCACTGATAGCGCTATCAGTCTCAATCTAGGAGGGGAAACAACCAGTAAAGATACATCTAT
AGTAACTCTCACATTAAGATGATCATACATTAACCATTCCGTCCCGACTAAGCCGTTCAGTATCG
ACCCAGCAGTCCCAACCTAGCAGTCCCAGCATTCCAGTCTAGCCCTTCCAGTCTGGGTATGGAAG
TCAGTGCTCTATCGCCCCCGCTCTTTCGACCAAGCCTATAAGCTTGAATCTCATGATAGTTCTGA
TGTAAGTGTGAAAGAACGCATATATAAGCGTATATTGAGATTCGGTATCATAAGCGACTATAGAG
GGATCAATACTAGTTTGGACTATCCACTCAGATATTGGGACTTACATCCCTTAATGCGCTTGAAG
TTCTAGATGGTGACATTAGTGCGTTTTCCCGGGAAAAAAGGCATA
Right flanking sequence: Indices 219920 -- 220419
GGCATAACAGAGATTTCCGCTCTAAAGTGGCATTTTCAAATGACATGATTTCATTTTACCGGGAA
AAATTGCTGACTTTCGATGGAACACTAACCCAATCAGTCTAATTTAAAGCATCAGTCGCCAAAGA
CACCTCTCCTTGAAGTCGAGCGTACGTCCTAACTTCCCTCTCGCTTCGCTCACGCCCGCTAAAGG
CCCTCTCCTGTAAGTCGATCATATGGACATATTTCCAGTCAGTATGGAAGGGGCCCCATAAGATT
CAACCTTAACGCACTGAAAGCTAGTTTCTTATATGCCTTCTTTCACACTATCATATATTCGCTTT
TTCCAATGGATTCTAGATTACTGGAATCCTAACTCTCATGAGCCTCCGTATCTACCTTATTGAAC
TTCAAGCGCCTTAAGGGTCTAGCAAGAAGTTACAATCTAGGAGGAGAGGGGCCCCAATATAGGAG
CATAAACAACTAGTATACGCACCATGTCTGTCCTCCCGCTTCGAT
Found at i:219953 original size:69 final size:69
Alignment explanation
Indices: 219804--219983 Score: 168
Period size: 69 Copynumber: 2.6 Consensus size: 69
219794 TTTTCCCTTC
* * *** * * * *
219804 ATAATTGGCATTTTCAAATTCATTTATTTCATTTTACCGGGATTTTTCGTTGTCACTGACTTTTC
1 ATAAATGGCATTTTCAAATTCATTTATTTCAATTTACCGGGATTTTTCGGCATAACAGAATTTCC
219869 GCTA
66 GCTA
* * *
219873 ATAAATTGCATTTTCAAATTCATTTATTTCAATTTCCCGGG-TTTTTTGGCATAACAGAGATTTC
1 ATAAATGGCATTTTCAAATTCATTTATTTCAATTTACCGGGATTTTTCGGCATAACAGA-ATTTC
219937 CGCT-
65 CGCTA
* * * *
219941 CTAAAGTGGCATTTTCAAATGACA-TGATTTCATTTTACCGGGA
1 ATAAA-TGGCATTTTCAAAT-TCATTTATTTCAATTTACCGGGA
219984 AAAATTGCTG
Statistics
Matches: 89, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
68 15 0.17
69 72 0.81
70 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (69 bp):
ATAAATGGCATTTTCAAATTCATTTATTTCAATTTACCGGGATTTTTCGGCATAACAGAATTTCC
GCTA
Left flanking sequence: Indices 219304 -- 219803
AAACGCCGCAGTTCTTGAATCTGAACTAGAATGATACAAGATGAAACCTTCTAGCACTGATAGCG
CTATCAGTCTCAATCTAGGAGGGGAAACAACCAGTAAAGATACATCTATAGTAACTCTCACATTA
AGATGATCATACATTAACCATTCCGTCCCGACTAAGCCGTTCAGTATCGACCCAGCAGTCCCAAC
CTAGCAGTCCCAGCATTCCAGTCTAGCCCTTCCAGTCTGGGTATGGAAGTCAGTGCTCTATCGCC
CCCGCTCTTTCGACCAAGCCTATAAGCTTGAATCTCATGATAGTTCTGATGTAAGTGTGAAAGAA
CGCATATATAAGCGTATATTGAGATTCGGTATCATAAGCGACTATAGAGGGATCAATACTAGTTT
GGACTATCCACTCAGATATTGGGACTTACATCCCTTAATGCGCTTGAAGTTCTAGATGGTGACAT
TAGTGCGTTTTCCCGGGAAAAAAGGCATAACTGACTTTTCCCTTC
Right flanking sequence: Indices 219984 -- 220483
AAAATTGCTGACTTTCGATGGAACACTAACCCAATCAGTCTAATTTAAAGCATCAGTCGCCAAAG
ACACCTCTCCTTGAAGTCGAGCGTACGTCCTAACTTCCCTCTCGCTTCGCTCACGCCCGCTAAAG
GCCCTCTCCTGTAAGTCGATCATATGGACATATTTCCAGTCAGTATGGAAGGGGCCCCATAAGAT
TCAACCTTAACGCACTGAAAGCTAGTTTCTTATATGCCTTCTTTCACACTATCATATATTCGCTT
TTTCCAATGGATTCTAGATTACTGGAATCCTAACTCTCATGAGCCTCCGTATCTACCTTATTGAA
CTTCAAGCGCCTTAAGGGTCTAGCAAGAAGTTACAATCTAGGAGGAGAGGGGCCCCAATATAGGA
GCATAAACAACTAGTATACGCACCATGTCTGTCCTCCCGCTTCGATATTCATTCTACTTAAACAT
CAATATCAGTCCCTATCATCCATATTCACCCTTTCAAACCCTCAA
Found at i:225149 original size:18 final size:19
Alignment explanation
Indices: 225128--225170 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
225118 CAACCTTGTT
225128 GACTATGACAACA-A-TCGC
1 GACTATGA-AACAGACTCGC
225146 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGACTCGC
225164 GACTATG
1 GACTATG
225171 GCAGGGCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.18
17 2 0.09
18 16 0.73
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (19 bp):
GACTATGAAACAGACTCGC
Left flanking sequence: Indices 224628 -- 225127
TACCGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGA
GACAGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTAC
CTTAGGACAGTTATAGTTACTGCCGCCGTTTACCGGGGCTTCCATTCAAAGCAACTAACACTTCT
CCTTCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGT
CCTGTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGA
GAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAG
CGCCCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGAT
CGCCCTCCCAATTCGAAGTTTTTTCCTGGAAGTTTCAACCTTGTT
Right flanking sequence: Indices 225171 -- 225670
GCAGGGCGGTACGCTCTGCTCTCTCGCGACCCCTACTCTAATCAAAAGACTAAAGGCCCCTACTG
AAGATTAAAAAGGCGAGCACTGAAATGAGAAAGGCTTGTAGACTCGTGACACATTCTAAAACTAA
AGCGCACACTAGAAAAGTGCTTCGAAAGGTGTCAGCAGGTGCGCAGAGCCGGAACCCGGCATGTT
CGCCCGCTGGGCCGAGTGTTCGCCCACTGAAGAGTCTTCGCCTTTACTTGACTTTAAAAGTGTCC
GCCCCTTAGGTCGCCAAACTACGACGAGAGTTTCGCCTTTTGAAGCGCCAGTCGCGTAGGGCTTT
AGGGCCAGGCCGAGTCAGAAAGGCTTTGATGACTCAAGGGGCGCAGCGTTAGGGAAAGGAGAGTG
AGGGGAAGAGGGGGCAGTCCTCGGCCCGATCATCCAATTCGCTCCAACAGACAGGCATGGTTCTG
TAGTCAAAGCAACTTCGTCACTTTCGTGTACCCATCGGACGGCAG
Found at i:255989 original size:13 final size:13
Alignment explanation
Indices: 255971--255996 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
255961 CCCCTGTCAT
255971 CATTATCCAAGCC
1 CATTATCCAAGCC
255984 CATTATCCAAGCC
1 CATTATCCAAGCC
255997 AAGGGCTCCT
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:0.31, C:0.38, G:0.08, T:0.23
Consensus pattern (13 bp):
CATTATCCAAGCC
Left flanking sequence: Indices 255471 -- 255970
ACGCATGAATAAAGCTGTCAAGCATTGAATTCAGGAAGGTTTTCGGGAAGATGTGAAAGTTACTC
TTTGAGAATGCCTTACTTCATCCGCAGCAAGAGAAGTAGCTCTTTTCGCCTTATCTGCTCTTATC
AGACTGACCCCTGTTGATGCGGAATAAGAGATGGAGCTCTTTTGCGGGATAACCGCCGCTAGCTC
ACATTAGCAAGGATGGATGAAGAAAGATTGTTTGCTGCAGAAGAAGACGTTGATCGAGAATCAAA
GAAAGAAACCTGGAAATTGGACTTCCAAGCCCACTTCCTACACTAATAGATAGGCCTCGGCCAAA
GAAGGTGGCTCTGTCACTAAGCAGGCCGGCAGAGAGGGCACTTTATGCCTAAACATGACAAGAAA
AAAGATGTTGCTTTACACTTTCTTTCCGTTCCTCCCCATCCCCCTAGACGCTACGGGAAGTTAAT
GCAAGTCGATAGGTCCACTCTTTGACTTCGCATAGCCCCTGTCAT
Right flanking sequence: Indices 255997 -- 256496
AAGGGCTCCTCTTTCATTAACAAAAAGTCTATAAAGCTTCATTGACTGTCTTTCCTCTTTGATAG
TGAACCGCTAGATACAATCTTTCAAGCTGAGGATTTAGCCTTTCATTCCAGAAGCTTCCCAAGTT
AAAAGGAGTGCAGGTCAAGCGAATGACTCGGCTTACCATAACTAACATAAGGGGTCAGTCAAGTG
AAGATATTTCTCTCTTCCACCCGCTGGCTTTGTAGTGGAAAACCGTGGCCCGAGGGCTTTCTCTG
GAAAAATGCTATCTCACAACTTCAAAATATATGAATGAGTGCTTTCTTCTTCAAGAGGGTTAATT
ACTTAATAAGAGTGAACGAAAGGCGCTTGCTTAACGCCCTAGGTTTTCTTCAATGAGAGCGCCCA
ATGATTGGTGATAAAGAAAGGGGGGAAAAGAAGGGCACAAAATACCCGGTGAATACGGCTTCTTA
CCTTAGCCTTGTATGCTTCCTTCGGGAAATCGATCCATCTGCCCT
Found at i:258988 original size:18 final size:18
Alignment explanation
Indices: 258967--259023 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
258957 GTCACGGTCG
258967 ATATCGTCACTCA-CATCA
1 ATATCGTCACT-AGCATCA
258985 ATATCGTCACTAGCATCA
1 ATATCGTCACTAGCATCA
*
259003 ATATCGTCACTATCATCA
1 ATATCGTCACTAGCATCA
259021 ATA
1 ATA
259024 AGAAAACCCT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
17 1 0.03
18 36 0.97
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (18 bp):
ATATCGTCACTAGCATCA
Left flanking sequence: Indices 258467 -- 258966
TACTAATCGATAGGGCCTCATTGGTAAGTGCTACAAGATCTCGTACATTGGAACCCATGGTTATG
GACCCGAATCCATTAGTATGGAACATTTTCTTTTCCAAGTGAAATCCCCTAGTATATGAAAGAGT
GAAAAAGTACTTTCGTTGTTGTGGAATAAGAAGCCTTCGTATCTTAATGCATGTATTTAATTTAT
TCGGAGCTATTAGAGCGGGATCCACTTTTTGGGGAATATGAGTCGAAGCAATAACAAGAATATTT
CTAGTGGAACATCTTTCACAATCCCTGGAGAGATAGTTCACTAATAGACCGAGGGATAAGTAATT
CGACTCATTCACATCCAGATCATGAATGTTTGGAATCCATATTATGCAAGGAGACATTGCTTTTG
CTAATTCGAATTGAAGGGTGATATAAAATCGGTCTATTTCCGGCATCATATCCATAGTTAGCGCA
TTCATCCTAGTTAGAAGCTCCAGCTCCGTATCAAGGTCACGGTCG
Right flanking sequence: Indices 259024 -- 259523
AGAAAACCCTTAGGCTTGTTATCCAGGAACTTGTTCAGAAATACTGTAATGAAAGGAACATAGGA
GTTTGTCGCTAGGTATTTGACCAAATAGGATCGTCCAGTTCCTATAGAACCTATCACTAAAATAC
CCCTAGAGGGGGATAGGGCTAAGCGGCGGAGCGAAAAGGGTTTTCCATGAGATGGGAAATGAAAA
CTATTCGCCCCACACGAGGTTTGTGAATAAGTGATTGTCTGATAATGAGCAAGGAATATCCGTCT
TTCTGCTAAACAGGGTGTATTGAACTCATAATTCATTAGATACTTTTTATGAATGTCAACTAAGT
ATCGTAAGTAAATTGCTCCTGGCTCTTCAATCATTTGATAACCAGAGTCATTCTTTGATAAATGA
TCACTATGAGTCAGACTCAATAGAATTTGATCAATCCTTTTTTCTGTCGTTAAGGTGGAGAACTG
AACCAAGAATTCTCTTTCTTTATCATCAATCGAATCACTGTTCGC
Found at i:261411 original size:21 final size:21
Alignment explanation
Indices: 261385--261474 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
261375 ACTCACAAAG
* * *
261385 AAAAAAGGAAGTGAGTTAGAC
1 AAAAAAAGAAGTAACTTAGAC
* *
261406 AAAAAAAGAAGAAACTTGGAC
1 AAAAAAAGAAGTAACTTAGAC
*
261427 AAAAAAAGAAGTAACTTGGAC
1 AAAAAAAGAAGTAACTTAGAC
*
261448 AAAAAGAAAGGAAGTGACTTAGAC
1 -AAAA-AAA-GAAGTAACTTAGAC
261472 AAA
1 AAA
261475 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
21 36 0.62
22 4 0.07
23 6 0.10
24 12 0.21
ACGTcount: A:0.58, C:0.08, G:0.22, T:0.12
Consensus pattern (21 bp):
AAAAAAAGAAGTAACTTAGAC
Left flanking sequence: Indices 260885 -- 261384
ATTGTCCATACGTAAAATCATAATTCTTGATACGGGCCTTTTCCACATAAAAAGGGAATCTTTTG
TTACAATAGAAACAGAAGTGATGTAGATTATTCAAGAATCGAAGTCGATTTGCTTTATAAAAAGA
AGATATCAATGAACTTCTATGAAATGGTTTCAGGGGATTCAGCCAATTGTCTTGATCGTGGGATA
TCATTGAGAAATAGGAATCCGTGTTATCAAAAGATTTCTTATTTCTAGTATGGAATGAGTCAATC
ATCCACTTTAGTATCTTATTATTGAACAAAAATAGTGATATTGTTCCTCCATTGATCAAAAATTT
CGATTTTTGGGAAGTATCATGATCATCCAATAAGAAGGGTTTCAATTTTTTCAAATGAACGATTT
GAAGACCTATTGGTTCTAACAGCTGATTGCAGAGTTGATCATTCGAACCTTTCAATTCATAGATA
TGAATCTCGGACCGATGAATGGGGATATTCCCGAAACTCACAAAG
Right flanking sequence: Indices 261475 -- 261974
TCTTTTTTGTCGATAACCTCAGACCAATCAATCGAATATTGATTAATACGTAATCGATCGAACAC
TACTTGAAAAAGAAAACGGCTCTTCTGCTCAGAAATGAAATGTTCCAAATGTTCCTGGAAATTCT
TGCTCCCATTAGACCATTTGTATCTATATGCATTAGGATCCCAATTCATGGATCTCTCGGTTCGA
GAAAGAAAAAAAAGAGGATCGAACCATTTCTTCTGACTCAGTTTCAAATTCGATAAATGTTGGTT
GATCGTATATTTCATTATAGTTCTATGATTCAGAGTATCATTTCCTATTTGATCCCTTTGAATTC
CATATTCGAAGTTGCGATCGGATCTATTCATTAAAAAGAATTGATTCAATACATTTCTTATGTAC
CCATAGGTGCTATATTGGATTTGAATCAGATTTCGGATCAATCCATATTGATTGACTGCCTCCAT
TATGTTGTTGCTAGCAAATACCACTCTTTTTTGTTTTGGATCTTC
Found at i:263814 original size:9 final size:9
Alignment explanation
Indices: 263800--263836 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
263790 CTTTCGATTG
263800 TTAATACGA
1 TTAATACGA
263809 TTAATACGA
1 TTAATACGA
263818 TTAATACGA
1 TTAATACGA
263827 TTAATACGA
1 TTAATACGA
263836 T
1 T
263837 ATATAAGGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (9 bp):
TTAATACGA
Left flanking sequence: Indices 263300 -- 263799
TTTCGAATAGCTGTCCCGAATTCAAGTTGATTATGTTTCGACCCTTCCTCGGAGAAAGACGATCA
AACAATTCCCAATCAGGGTCCTTGCGGATTGGATCATCCATATAATATACAAAAAGAAACTCCAG
ATATTTGATATCTTTCTCTTTGAATGAGATCTCAATTCCAGCGACAGTTTCATTAGATATCTTAC
AACTAGAATCCCTCTTTTTTCCGATCCAGTTCCTCCACCACCGCGAACCCCAGTTAGATTCAGAC
ATGATACACTTTTTAGTTATTGGGAGAACCCGAGTACTCTCTTTCGGATCCAGGAAACAGCTCTC
AGAGATCTTTTTTCCTTTTGGAAGATACAGGAGCGAAACAATCAACCTATTGATATTGGAAGACC
CAAAGGATTCTTCCAATGTATCATTTCTGGGTCCAATGGAATTCATAGGTATAGGAAGAAGCCCC
GTCAAATAGAGATTTTTTCTTTTTCTTTCGACCAGCTTTCGATTG
Right flanking sequence: Indices 263837 -- 264336
ATATAAGGACCACTACTACAAATAGTACTACTACAAATAGTACTACACCCTTGATCGTGAAATAT
CGATTGCTTGTTGACCTCTGTGAATTGCGTGAAAGTAGGATACTCCAAATTCGGGAATCCAAGAG
TTTTATAAAACGTTCTTGATGGAAAAAAATGTGAATGAAAGATCCCACTGAATTGAATTGAGTCC
ATGAATCTAAGAAATAGTGAGAATTCTTGATCTCTCTCAATATCTCTCTCAATTCGAAAATCCAG
GATTTGACTTGATGTCCTTTCATTGATTCCTCCGAAATTGGATTGATTTATCCTCCAAATTTTAT
TTCAATTGGAATTTGGTTATTCAGCCATGGACGCAAAGAGACTCAGCGAGTGAACTAGTGGCTCC
ACACCTTTTCGAACTTCTCTTTCTTCCGTTAAAGGAGATTCTAGAAAAGATAGAATAGGAAGACG
TGTTTCCAGAACAAAGAAGATACGGGTTGAGAAGGAGGAGTTAGC
Found at i:263868 original size:15 final size:15
Alignment explanation
Indices: 263848--263882 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
263838 TATAAGGACC
263848 ACTACTACAAATAGT
1 ACTACTACAAATAGT
263863 ACTACTACAAATAGT
1 ACTACTACAAATAGT
263878 ACTAC
1 ACTAC
263883 ACCCTTGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.26
Consensus pattern (15 bp):
ACTACTACAAATAGT
Left flanking sequence: Indices 263348 -- 263847
TCGGAGAAAGACGATCAAACAATTCCCAATCAGGGTCCTTGCGGATTGGATCATCCATATAATAT
ACAAAAAGAAACTCCAGATATTTGATATCTTTCTCTTTGAATGAGATCTCAATTCCAGCGACAGT
TTCATTAGATATCTTACAACTAGAATCCCTCTTTTTTCCGATCCAGTTCCTCCACCACCGCGAAC
CCCAGTTAGATTCAGACATGATACACTTTTTAGTTATTGGGAGAACCCGAGTACTCTCTTTCGGA
TCCAGGAAACAGCTCTCAGAGATCTTTTTTCCTTTTGGAAGATACAGGAGCGAAACAATCAACCT
ATTGATATTGGAAGACCCAAAGGATTCTTCCAATGTATCATTTCTGGGTCCAATGGAATTCATAG
GTATAGGAAGAAGCCCCGTCAAATAGAGATTTTTTCTTTTTCTTTCGACCAGCTTTCGATTGTTA
ATACGATTAATACGATTAATACGATTAATACGATATATAAGGACC
Right flanking sequence: Indices 263883 -- 264382
ACCCTTGATCGTGAAATATCGATTGCTTGTTGACCTCTGTGAATTGCGTGAAAGTAGGATACTCC
AAATTCGGGAATCCAAGAGTTTTATAAAACGTTCTTGATGGAAAAAAATGTGAATGAAAGATCCC
ACTGAATTGAATTGAGTCCATGAATCTAAGAAATAGTGAGAATTCTTGATCTCTCTCAATATCTC
TCTCAATTCGAAAATCCAGGATTTGACTTGATGTCCTTTCATTGATTCCTCCGAAATTGGATTGA
TTTATCCTCCAAATTTTATTTCAATTGGAATTTGGTTATTCAGCCATGGACGCAAAGAGACTCAG
CGAGTGAACTAGTGGCTCCACACCTTTTCGAACTTCTCTTTCTTCCGTTAAAGGAGATTCTAGAA
AAGATAGAATAGGAAGACGTGTTTCCAGAACAAAGAAGATACGGGTTGAGAAGGAGGAGTTAGCA
AAGTTAGACAAGATTGGAATGGGCATAGGAAGATGTATTGATGTA
Found at i:273917 original size:43 final size:43
Alignment explanation
Indices: 273864--273956 Score: 177
Period size: 43 Copynumber: 2.2 Consensus size: 43
273854 CTTGTTGTTT
*
273864 TTTTTTTTCTTTTTTTGATGAGTTGATCTCATCTCTTTATGTA
1 TTTTCTTTCTTTTTTTGATGAGTTGATCTCATCTCTTTATGTA
273907 TTTTCTTTCTTTTTTTGATGAGTTGATCTCATCTCTTTATGTA
1 TTTTCTTTCTTTTTTTGATGAGTTGATCTCATCTCTTTATGTA
273950 TTTTCTT
1 TTTTCTT
273957 AGTATATACT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.13, C:0.13, G:0.11, T:0.63
Consensus pattern (43 bp):
TTTTCTTTCTTTTTTTGATGAGTTGATCTCATCTCTTTATGTA
Left flanking sequence: Indices 273364 -- 273863
GGAAGCAGTGAGTGGAGATTCCCCTGCGGAGAGCCGGATGAGGGGAGACCTTCACGTCCGGTTCG
GAGGGCGGGGATATCCCGACCCTACTATCATTATGCCTTTGCAATCTTACTTGGTTCAACTCTAT
TTGTGACCTTTTCTCGTATGTGGGACTCTCTATCTTCTTGGGTAGATAATCGATCGTCTTTCATT
TTGATAGTGAGTACTTTTATTAATAATAAGTCAAGTCAAGAATAATAATCGAACTGGAGGAGCGA
AGCTGACTCGACCGGACGGGAGAGGAGCGGAAAGCCAGGATCGCTTGGTAAGCAAGCAGGTTTTT
CTTCCAGTTCTTTCTCTTCTTTCTTTTTGATTGAAGATACTATAGTAGATTGGAAAGTTTTCCAG
GTCAGCTTTCTTTCGTTCGTTCTCGGTGCGCTCGTTCAGGATGGTTTTTTTTACTGTTATGTAAA
TGTTCCTTTTTTCTTTTTTTACTTAGTTGGTTTTCCTTGTTGTTT
Right flanking sequence: Indices 273957 -- 274456
AGTATATACTTTTCCATATGAAAGTAAGAAACCTAATTTTTTGGCCCCGCCGACCTGCTTTCGGT
TATTTCCTGGAGTGCCAAACCTGTAGACCAATAATCCATGTTCCTAGTGGGCCAAGTGGAAGCAA
TCAACAGGCTATTCATTAGTTTGAGTTTTTGGAATTCCAAGGGAACACAGCGCTTACTCTCTTTA
AGCGCAAATTCAACGATCAATAGTAGTTTCCCGGTGGAAAGGTTACTTCAAAGACCTAACTAACT
AATTGGGTTAGAAACCGCAGGAGCAGCTTTCCCATCCCTAGTAGTATCCGCTGTCCCTATACCAT
TTCGAAGAAAGAGTGGGCCCCTACCCTCAAAAAAAAAGTAGCACCTGCTTTTGGATAATAAACCT
CTCTTGCCACGGTTTTAGGAACGGAAAGAAGAACCGTACCGTACAACCCCTTGTATATCGATTGG
AAAGAAGCAGCTGCAAATGCTATCAGTGGTTCTTCCTTCCTATCT
Done.