Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_022796
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: 682498
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:3938 original size:25 final size:25
Alignment explanation
Indices: 3902--3950 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
3892 TTTCCTATAC
3902 CCTCTGTCATAGGCTTATACGATAT
1 CCTCTGTCATAGGCTTATACGATAT
* *
3927 CCTCTGTTATAGGTTTATACGATA
1 CCTCTGTCATAGGCTTATACGATA
3951 CTATACCTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (25 bp):
CCTCTGTCATAGGCTTATACGATAT
Left flanking sequence: Indices 3402 -- 3901
ACAGTCACAAGGAGACGGAAAGGGAAAGGTTGGTATTAGAATCCCTAATCCAATTCATAGGATAT
CTTTAGTTCATATAGAATCAGTCAATATCTAATATCACATATACGTGTCTTTCTTCCATAACGTA
AACCAAGCATGAATCTTAGATGAACTAGGATTCCTCTTCTCTTGAGCTTGTAAAGGAGCTTGGTA
TCGACGAATCACCAATGGGTATTTTCCGCTGGAGATCTGGTGTTGTAGTTCTTGTTAGCTGGGCC
TAGGAGCCAAACCCGAAGCCAAGGTCGAACGCAAGCCCGAAGCGGGCCCTAGGAGCGTAATGAAA
TGAAGCGAACCATAAAGAAAGGAGCTCTGAGCCCCTGCAGTTTCATTGCCAGTTTTTAAGGATAG
ATTCGAATTGCCAGCTCCTTTTATATGAATTTCACAGTCCTAAGGTATTGCGAACCAGTGAAAGT
ATTTGAACCTTTTTCCTTTGCTTTAGGAGTTCGCCTTTCCTATAC
Right flanking sequence: Indices 3951 -- 4450
CTATACCTCCTTTTATAGGCTTATAACTACCTAATGAACTACCTAAGGAACTACCTAAGGAACTA
GCTAACTACCCTATCCTACCTAACTACCTAACTACCTCTTATAACTACCCTATCCTACCTAACTA
CCTTTAGAACTAGCTAACTACCTTTAGAACTACCTAATGATAGTATCGTACTACCTAATGCTAGT
ATAGTAACCCTGTATTAACTACCTAATGAATAGTAACCCTGTCTTATGATTAATAGGAAGATTGT
ATTATACCCTTTAAGGCATGTCTATACCCTCATACCATTACTAGGTACCTTTCCTTGTGTTTATT
TAAGTCAATATAAGGCATATATCTCGTTTATGACATACTGTAATAGTTGATTCGGTATACTCGTA
CTCGTAGCTTTCCTTATACCCTATTCCCTTTAACAAGAGGAATAGTCAGGACGCTAGCTACAGTA
TAGGTACGGCCTATATCCTATTCCTTAGACAGGAATTGTTAGGCC
Found at i:3992 original size:12 final size:12
Alignment explanation
Indices: 3975--4020 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
3965 ATAGGCTTAT
*
3975 AACTACCTAATG
1 AACTACCTAAGG
3987 AACTACCTAAGG
1 AACTACCTAAGG
3999 AACTACCTAAGG
1 AACTACCTAAGG
*
4011 AACTAGCTAA
1 AACTACCTAA
4021 CTACCCTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.43, C:0.24, G:0.13, T:0.20
Consensus pattern (12 bp):
AACTACCTAAGG
Left flanking sequence: Indices 3475 -- 3974
CATATAGAATCAGTCAATATCTAATATCACATATACGTGTCTTTCTTCCATAACGTAAACCAAGC
ATGAATCTTAGATGAACTAGGATTCCTCTTCTCTTGAGCTTGTAAAGGAGCTTGGTATCGACGAA
TCACCAATGGGTATTTTCCGCTGGAGATCTGGTGTTGTAGTTCTTGTTAGCTGGGCCTAGGAGCC
AAACCCGAAGCCAAGGTCGAACGCAAGCCCGAAGCGGGCCCTAGGAGCGTAATGAAATGAAGCGA
ACCATAAAGAAAGGAGCTCTGAGCCCCTGCAGTTTCATTGCCAGTTTTTAAGGATAGATTCGAAT
TGCCAGCTCCTTTTATATGAATTTCACAGTCCTAAGGTATTGCGAACCAGTGAAAGTATTTGAAC
CTTTTTCCTTTGCTTTAGGAGTTCGCCTTTCCTATACCCTCTGTCATAGGCTTATACGATATCCT
CTGTTATAGGTTTATACGATACTATACCTCCTTTTATAGGCTTAT
Right flanking sequence: Indices 4021 -- 4520
CTACCCTATCCTACCTAACTACCTAACTACCTCTTATAACTACCCTATCCTACCTAACTACCTTT
AGAACTAGCTAACTACCTTTAGAACTACCTAATGATAGTATCGTACTACCTAATGCTAGTATAGT
AACCCTGTATTAACTACCTAATGAATAGTAACCCTGTCTTATGATTAATAGGAAGATTGTATTAT
ACCCTTTAAGGCATGTCTATACCCTCATACCATTACTAGGTACCTTTCCTTGTGTTTATTTAAGT
CAATATAAGGCATATATCTCGTTTATGACATACTGTAATAGTTGATTCGGTATACTCGTACTCGT
AGCTTTCCTTATACCCTATTCCCTTTAACAAGAGGAATAGTCAGGACGCTAGCTACAGTATAGGT
ACGGCCTATATCCTATTCCTTAGACAGGAATTGTTAGGCCGGGAAGAGAGACCTATAACCAATCA
GATAGTATCAATGGGTTAGCTACAGGTTATTAACTCTTAGAAAGA
Found at i:4040 original size:18 final size:18
Alignment explanation
Indices: 4017--4082 Score: 64
Period size: 18 Copynumber: 3.5 Consensus size: 18
4007 AAGGAACTAG
4017 CTAACTACCCTATCCTAC
1 CTAACTACCCTATCCTAC
4035 CTAACTA-CCTAACTACCT-C
1 CTAACTACCCT-A-T-CCTAC
*
4054 TTATAACTACCCTATCCTAC
1 --CTAACTACCCTATCCTAC
4074 CTAACTACC
1 CTAACTACC
4083 TTTAGAACTA
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
17 3 0.08
18 16 0.41
19 5 0.13
20 5 0.13
21 7 0.18
22 3 0.08
ACGTcount: A:0.30, C:0.41, G:0.00, T:0.29
Consensus pattern (18 bp):
CTAACTACCCTATCCTAC
Left flanking sequence: Indices 3517 -- 4016
TTCTTCCATAACGTAAACCAAGCATGAATCTTAGATGAACTAGGATTCCTCTTCTCTTGAGCTTG
TAAAGGAGCTTGGTATCGACGAATCACCAATGGGTATTTTCCGCTGGAGATCTGGTGTTGTAGTT
CTTGTTAGCTGGGCCTAGGAGCCAAACCCGAAGCCAAGGTCGAACGCAAGCCCGAAGCGGGCCCT
AGGAGCGTAATGAAATGAAGCGAACCATAAAGAAAGGAGCTCTGAGCCCCTGCAGTTTCATTGCC
AGTTTTTAAGGATAGATTCGAATTGCCAGCTCCTTTTATATGAATTTCACAGTCCTAAGGTATTG
CGAACCAGTGAAAGTATTTGAACCTTTTTCCTTTGCTTTAGGAGTTCGCCTTTCCTATACCCTCT
GTCATAGGCTTATACGATATCCTCTGTTATAGGTTTATACGATACTATACCTCCTTTTATAGGCT
TATAACTACCTAATGAACTACCTAAGGAACTACCTAAGGAACTAG
Right flanking sequence: Indices 4083 -- 4582
TTTAGAACTAGCTAACTACCTTTAGAACTACCTAATGATAGTATCGTACTACCTAATGCTAGTAT
AGTAACCCTGTATTAACTACCTAATGAATAGTAACCCTGTCTTATGATTAATAGGAAGATTGTAT
TATACCCTTTAAGGCATGTCTATACCCTCATACCATTACTAGGTACCTTTCCTTGTGTTTATTTA
AGTCAATATAAGGCATATATCTCGTTTATGACATACTGTAATAGTTGATTCGGTATACTCGTACT
CGTAGCTTTCCTTATACCCTATTCCCTTTAACAAGAGGAATAGTCAGGACGCTAGCTACAGTATA
GGTACGGCCTATATCCTATTCCTTAGACAGGAATTGTTAGGCCGGGAAGAGAGACCTATAACCAA
TCAGATAGTATCAATGGGTTAGCTACAGGTTATTAACTCTTAGAAAGATGAATATAGTCTTATTA
CAAGGTTAGCTACAGGATAGAAGGTGTATTAAGAAATAAGTAGTC
Found at i:4099 original size:20 final size:20
Alignment explanation
Indices: 4070--4117 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
4060 CTACCCTATC
4070 CTACCTAACTACCTTTAGAA
1 CTACCTAACTACCTTTAGAA
*
4090 CTAGCTAACTACCTTTAGAA
1 CTACCTAACTACCTTTAGAA
4110 CTACCTAA
1 CTACCTAA
4118 TGATAGTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.29
Consensus pattern (20 bp):
CTACCTAACTACCTTTAGAA
Left flanking sequence: Indices 3570 -- 4069
CTCTTGAGCTTGTAAAGGAGCTTGGTATCGACGAATCACCAATGGGTATTTTCCGCTGGAGATCT
GGTGTTGTAGTTCTTGTTAGCTGGGCCTAGGAGCCAAACCCGAAGCCAAGGTCGAACGCAAGCCC
GAAGCGGGCCCTAGGAGCGTAATGAAATGAAGCGAACCATAAAGAAAGGAGCTCTGAGCCCCTGC
AGTTTCATTGCCAGTTTTTAAGGATAGATTCGAATTGCCAGCTCCTTTTATATGAATTTCACAGT
CCTAAGGTATTGCGAACCAGTGAAAGTATTTGAACCTTTTTCCTTTGCTTTAGGAGTTCGCCTTT
CCTATACCCTCTGTCATAGGCTTATACGATATCCTCTGTTATAGGTTTATACGATACTATACCTC
CTTTTATAGGCTTATAACTACCTAATGAACTACCTAAGGAACTACCTAAGGAACTAGCTAACTAC
CCTATCCTACCTAACTACCTAACTACCTCTTATAACTACCCTATC
Right flanking sequence: Indices 4118 -- 4617
TGATAGTATCGTACTACCTAATGCTAGTATAGTAACCCTGTATTAACTACCTAATGAATAGTAAC
CCTGTCTTATGATTAATAGGAAGATTGTATTATACCCTTTAAGGCATGTCTATACCCTCATACCA
TTACTAGGTACCTTTCCTTGTGTTTATTTAAGTCAATATAAGGCATATATCTCGTTTATGACATA
CTGTAATAGTTGATTCGGTATACTCGTACTCGTAGCTTTCCTTATACCCTATTCCCTTTAACAAG
AGGAATAGTCAGGACGCTAGCTACAGTATAGGTACGGCCTATATCCTATTCCTTAGACAGGAATT
GTTAGGCCGGGAAGAGAGACCTATAACCAATCAGATAGTATCAATGGGTTAGCTACAGGTTATTA
ACTCTTAGAAAGATGAATATAGTCTTATTACAAGGTTAGCTACAGGATAGAAGGTGTATTAAGAA
ATAAGTAGTCTCATACAAGGAGTAGCTACAGGTTAGAAACTATCT
Found at i:4689 original size:40 final size:40
Alignment explanation
Indices: 4645--4727 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
4635 CTATACTGGT
4645 TTAGATAC-AGGTTAATAACTCCTATATCACATCTGTACTC
1 TTAGA-ACAAGGTTAATAACTCCTATATCACATCTGTACTC
4685 TTAGAACAAGGTTAATAACTCCTATATCACATCTGTACTC
1 TTAGAACAAGGTTAATAACTCCTATATCACATCTGTACTC
4725 TTA
1 TTA
4728 ATGCGAGTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 2 0.05
40 40 0.95
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.35
Consensus pattern (40 bp):
TTAGAACAAGGTTAATAACTCCTATATCACATCTGTACTC
Left flanking sequence: Indices 4145 -- 4644
TATAGTAACCCTGTATTAACTACCTAATGAATAGTAACCCTGTCTTATGATTAATAGGAAGATTG
TATTATACCCTTTAAGGCATGTCTATACCCTCATACCATTACTAGGTACCTTTCCTTGTGTTTAT
TTAAGTCAATATAAGGCATATATCTCGTTTATGACATACTGTAATAGTTGATTCGGTATACTCGT
ACTCGTAGCTTTCCTTATACCCTATTCCCTTTAACAAGAGGAATAGTCAGGACGCTAGCTACAGT
ATAGGTACGGCCTATATCCTATTCCTTAGACAGGAATTGTTAGGCCGGGAAGAGAGACCTATAAC
CAATCAGATAGTATCAATGGGTTAGCTACAGGTTATTAACTCTTAGAAAGATGAATATAGTCTTA
TTACAAGGTTAGCTACAGGATAGAAGGTGTATTAAGAAATAAGTAGTCTCATACAAGGAGTAGCT
ACAGGTTAGAAACTATCTTGACTCTCCTGTACTCTCTATACTGGT
Right flanking sequence: Indices 4728 -- 5227
ATGCGAGTAGCTACAATCAAACTTAGAAGGTGTATTAGCATAAGGTGTATTAGAAAAGGGTTAGC
TAAAGGGTAGAACTCATATAACCTATCAGTACACTTATTAGTACAGTATAGCCGCTAGGTTACCT
CCCCAAGCTAACCATAGCTACAAGAAGAGCTATAGGAGTAGTAGTAGCTACAAGAAGAGCTATAG
GAGTAGTAGTAGCTACAAGAAGATAGGAGTAGTAGTTTATCTTCCTCACTTAAGGACACTATGCT
ACCTTTAACCTATCTTTCAAGTCTTTCAAGTGTTTGTTGTATCAAGATCAGTATGCTACCTTGAT
ATTTCAAGTCTTTGTTTTAGTTCTTTCTATGGCCATGATTAGCTAACAATAACTAGTCCTATCCT
CCTGTAACGTAGGTTACCTTGGGTGAGGTAACAAAGTGGCTATACTGTAGCTCCTACTAAGAGTA
CATATGTATTGGTTCTCTGCTATCTCCTTTCTTTGTGCTATTGTA
Found at i:4908 original size:30 final size:30
Alignment explanation
Indices: 4872--4945 Score: 148
Period size: 30 Copynumber: 2.5 Consensus size: 30
4862 AAGCTAACCA
4872 TAGCTACAAGAAGAGCTATAGGAGTAGTAG
1 TAGCTACAAGAAGAGCTATAGGAGTAGTAG
4902 TAGCTACAAGAAGAGCTATAGGAGTAGTAG
1 TAGCTACAAGAAGAGCTATAGGAGTAGTAG
4932 TAGCTACAAGAAGA
1 TAGCTACAAGAAGA
4946 TAGGAGTAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.42, C:0.11, G:0.28, T:0.19
Consensus pattern (30 bp):
TAGCTACAAGAAGAGCTATAGGAGTAGTAG
Left flanking sequence: Indices 4372 -- 4871
AACAAGAGGAATAGTCAGGACGCTAGCTACAGTATAGGTACGGCCTATATCCTATTCCTTAGACA
GGAATTGTTAGGCCGGGAAGAGAGACCTATAACCAATCAGATAGTATCAATGGGTTAGCTACAGG
TTATTAACTCTTAGAAAGATGAATATAGTCTTATTACAAGGTTAGCTACAGGATAGAAGGTGTAT
TAAGAAATAAGTAGTCTCATACAAGGAGTAGCTACAGGTTAGAAACTATCTTGACTCTCCTGTAC
TCTCTATACTGGTTTAGATACAGGTTAATAACTCCTATATCACATCTGTACTCTTAGAACAAGGT
TAATAACTCCTATATCACATCTGTACTCTTAATGCGAGTAGCTACAATCAAACTTAGAAGGTGTA
TTAGCATAAGGTGTATTAGAAAAGGGTTAGCTAAAGGGTAGAACTCATATAACCTATCAGTACAC
TTATTAGTACAGTATAGCCGCTAGGTTACCTCCCCAAGCTAACCA
Right flanking sequence: Indices 4946 -- 5445
TAGGAGTAGTAGTTTATCTTCCTCACTTAAGGACACTATGCTACCTTTAACCTATCTTTCAAGTC
TTTCAAGTGTTTGTTGTATCAAGATCAGTATGCTACCTTGATATTTCAAGTCTTTGTTTTAGTTC
TTTCTATGGCCATGATTAGCTAACAATAACTAGTCCTATCCTCCTGTAACGTAGGTTACCTTGGG
TGAGGTAACAAAGTGGCTATACTGTAGCTCCTACTAAGAGTACATATGTATTGGTTCTCTGCTAT
CTCCTTTCTTTGTGCTATTGTAGCTCCTTTCTTCTAATACACTACTCCTTTCTACTTGCTACTAT
CTACTAGCTAATACAATACTACTTTCTACTTGCTACTATCTACTAGCTAATACAAGAGTACTTTC
TACTAGCTACTATCTACTAGCTAATACAATACTACTTTCTACTTGCTACTATCTACTTTCTACTT
TCATTACCTTTCTTAGGTTTCTTACACCTTTGTTACCTTCCTTGG
Found at i:5296 original size:39 final size:39
Alignment explanation
Indices: 5239--5392 Score: 263
Period size: 39 Copynumber: 3.9 Consensus size: 39
5229 CTCCTTTCTT
* *
5239 CTAATACACTACTCCTTTCTACTTGCTACTATCTACTAG
1 CTAATACAATACTACTTTCTACTTGCTACTATCTACTAG
5278 CTAATACAATACTACTTTCTACTTGCTACTATCTACTAG
1 CTAATACAATACTACTTTCTACTTGCTACTATCTACTAG
* * *
5317 CTAATACAAGAGTACTTTCTACTAGCTACTATCTACTAG
1 CTAATACAATACTACTTTCTACTTGCTACTATCTACTAG
5356 CTAATACAATACTACTTTCTACTTGCTACTATCTACT
1 CTAATACAATACTACTTTCTACTTGCTACTATCTACT
5393 TTCTACTTTC
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 107 1.00
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.38
Consensus pattern (39 bp):
CTAATACAATACTACTTTCTACTTGCTACTATCTACTAG
Left flanking sequence: Indices 4739 -- 5238
TACAATCAAACTTAGAAGGTGTATTAGCATAAGGTGTATTAGAAAAGGGTTAGCTAAAGGGTAGA
ACTCATATAACCTATCAGTACACTTATTAGTACAGTATAGCCGCTAGGTTACCTCCCCAAGCTAA
CCATAGCTACAAGAAGAGCTATAGGAGTAGTAGTAGCTACAAGAAGAGCTATAGGAGTAGTAGTA
GCTACAAGAAGATAGGAGTAGTAGTTTATCTTCCTCACTTAAGGACACTATGCTACCTTTAACCT
ATCTTTCAAGTCTTTCAAGTGTTTGTTGTATCAAGATCAGTATGCTACCTTGATATTTCAAGTCT
TTGTTTTAGTTCTTTCTATGGCCATGATTAGCTAACAATAACTAGTCCTATCCTCCTGTAACGTA
GGTTACCTTGGGTGAGGTAACAAAGTGGCTATACTGTAGCTCCTACTAAGAGTACATATGTATTG
GTTCTCTGCTATCTCCTTTCTTTGTGCTATTGTAGCTCCTTTCTT
Right flanking sequence: Indices 5393 -- 5892
TTCTACTTTCATTACCTTTCTTAGGTTTCTTACACCTTTGTTACCTTCCTTGGGCTAGTAAGTAT
TTCCATTTTAGGCAAGCAAGCGAGTACCTTTTTATTGACTTTTGCTGCAATAGCCATTGGACTAG
TTAAAAGACTTAGATAACACACCGGGTTTACAGAAACGTAGAGAAAAGAGATTAGACTAGTCATT
GCACTAGTAGCGTCTACGAGCCTCCCGCTTCGGTACCATCTCCTTTTTTACCAGTCGAGCTACCC
TGTCAACCCTTTTCGGTGCTTGCTTCCTAGCTAGAACTCACACAGCGCAAACATAAATTAGAACT
AAGCATAGTCTTATATACCCTCTCTAGCGCACAGAGCAAGAGTAAGCTACTTCACTCGAGAAGAA
GAAATACGCTAACGATCGGCTCAAATAAGGATGCCTCATCTCTTTCCAAGCTAGCTCCGATGCAA
CTGCTATCGAATTTTGGATATCATAGGTAAGAAGGAAGCTGGAGG
Found at i:5379 original size:7 final size:7
Alignment explanation
Indices: 5367--5402 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
5357 TAATACAATA
5367 CTACTTT
1 CTACTTT
*
5374 CTACTTG
1 CTACTTT
*
5381 CTACTAT
1 CTACTTT
5388 CTACTTT
1 CTACTTT
5395 CTACTTT
1 CTACTTT
5402 C
1 C
5403 ATTACCTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.17, C:0.31, G:0.03, T:0.50
Consensus pattern (7 bp):
CTACTTT
Left flanking sequence: Indices 4867 -- 5366
AACCATAGCTACAAGAAGAGCTATAGGAGTAGTAGTAGCTACAAGAAGAGCTATAGGAGTAGTAG
TAGCTACAAGAAGATAGGAGTAGTAGTTTATCTTCCTCACTTAAGGACACTATGCTACCTTTAAC
CTATCTTTCAAGTCTTTCAAGTGTTTGTTGTATCAAGATCAGTATGCTACCTTGATATTTCAAGT
CTTTGTTTTAGTTCTTTCTATGGCCATGATTAGCTAACAATAACTAGTCCTATCCTCCTGTAACG
TAGGTTACCTTGGGTGAGGTAACAAAGTGGCTATACTGTAGCTCCTACTAAGAGTACATATGTAT
TGGTTCTCTGCTATCTCCTTTCTTTGTGCTATTGTAGCTCCTTTCTTCTAATACACTACTCCTTT
CTACTTGCTACTATCTACTAGCTAATACAATACTACTTTCTACTTGCTACTATCTACTAGCTAAT
ACAAGAGTACTTTCTACTAGCTACTATCTACTAGCTAATACAATA
Right flanking sequence: Indices 5403 -- 5902
ATTACCTTTCTTAGGTTTCTTACACCTTTGTTACCTTCCTTGGGCTAGTAAGTATTTCCATTTTA
GGCAAGCAAGCGAGTACCTTTTTATTGACTTTTGCTGCAATAGCCATTGGACTAGTTAAAAGACT
TAGATAACACACCGGGTTTACAGAAACGTAGAGAAAAGAGATTAGACTAGTCATTGCACTAGTAG
CGTCTACGAGCCTCCCGCTTCGGTACCATCTCCTTTTTTACCAGTCGAGCTACCCTGTCAACCCT
TTTCGGTGCTTGCTTCCTAGCTAGAACTCACACAGCGCAAACATAAATTAGAACTAAGCATAGTC
TTATATACCCTCTCTAGCGCACAGAGCAAGAGTAAGCTACTTCACTCGAGAAGAAGAAATACGCT
AACGATCGGCTCAAATAAGGATGCCTCATCTCTTTCCAAGCTAGCTCCGATGCAACTGCTATCGA
ATTTTGGATATCATAGGTAAGAAGGAAGCTGGAGGAACAATCATA
Found at i:31352 original size:22 final size:21
Alignment explanation
Indices: 31310--31353 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
31300 CATCACATCT
*
31310 GTTGCCTTCCTTGGGCTTCTA
1 GTTGCCTTCCGTGGGCTTCTA
*
31331 GTTGCCTCTCCGTGTGCTTCTA
1 GTTGCCT-TCCGTGGGCTTCTA
31353 G
1 G
31354 CTTCCATCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.05, C:0.30, G:0.25, T:0.41
Consensus pattern (21 bp):
GTTGCCTTCCGTGGGCTTCTA
Left flanking sequence: Indices 30810 -- 31309
GGCTTTCGACCTAGCCCTTATTGTTGAAAGGTCCTATCCTGCTGCCGAACCCTTGATCAGATAAA
TAACCGCTAACTAAGGAAATGGATCCTTCGACTATTTCCGAAGGCTATTCCAATCGACGAATCTT
CTGATGCTGATGTGAAATAAAGCCCCAACCTTTCTAACCGCTGCCCGGCGCTGCTAATTCATAAG
CCCGCTTCGAACTAATCTGCTTCGTCTACGTCGTTGCAACTGCTTTGCCTTTCCACTACTGCTGG
TCCATCCTATACCGAAAATTCAAAGTGAAAAGACCAGTTAAATGCTATAGTTGGGGAGAAAAAAA
GCCTTAAGGTCAAATAAAATGAGTTTGAAGTCCTTATTTTGCGCTTTCCGATCGCATCTTCCTGA
CGCTTGTGCTTAGTCTAACCCTTTAGGCTTTTTAGGAGCAGGACTTGTTCAAAAGCCCGGAACCA
GCTTTGGGGTCCTCTCCTGCACTGACTCCTGAAACCATCACATCT
Right flanking sequence: Indices 31354 -- 31853
CTTCCATCTCACTTCGTAACCCTACTCGTATGCTTGGCTTTCAGAGTAACTCCTCAACCACTTCA
CTTACTTTATTGCCCTCAACCCTTTCTCGTACCTCTATTTCATATTGAAACAGAATGGTTTCATG
TTCTTTCATCGATTGGTTATTCTTCTCCCTTTGTCTCTCTTTTTCCAATTTTGGTCTCGATTAGT
TTACAAGATTGAATGGCCACTGAATTCCATCCAGCCTCGATTCGATTGTTTTCCAAGAATGTTGA
GCCGGGTATGTAAGCCATGTATCTGGGAAGAACTAAAATGAAAAGTGAAAGGAGGGGCTTTCGGT
TCTTTGCACCCTCTTTTTTTGGCTTACTTTTCACCACGCGGGGCGGCTATCCGCATGTGTCCTAA
AGTGACGTCCATTTTTTTGTAATGAGTATACTAGAGAGAAAGGGTTTGGAATTCGACCTCCCCTT
ATACGCTCTTAAAAGAGGTCATGGCATTCCGAAAAGGGATGAAGA
Found at i:109379 original size:21 final size:22
Alignment explanation
Indices: 109353--109407 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
109343 ACGCGCAAGC
*
109353 TAGTTCTAATGGTGGAGAAG-G
1 TAGTTCTAATGATGGAGAAGAG
109374 TAGTTCTAATGATGGAGAAGAG
1 TAGTTCTAATGATGGAGAAGAG
109396 -AGTTCTAATGAT
1 TAGTTCTAATGAT
109408 AGAAATACTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.33, C:0.05, G:0.31, T:0.31
Consensus pattern (22 bp):
TAGTTCTAATGATGGAGAAGAG
Left flanking sequence: Indices 108853 -- 109352
TAGAGCGCAGGTGCGGGCTAAATAAATCAATGGACAGTCTTGGTCCTATTTCAAATACCGGTGAA
ATGAGAATAGAAAAGATAGAACTCAAAATAGGGGGGTCGTGACGATTCTAGTTACAGTAATGTTG
ATCGTTTATTCGGCGTCAAAGACATTCGGAATTTCATCCCTGGTTAAGGATAGTATATTGAAAAT
CCATTTTTTGAGATTGACAACACTGAATGAACTAGAAAATTTTTATAGTTATCGGAATTCTAGTT
ATCTGCATAATGAATCTACGAGTGAAGATACCTACTATAATAACGATACTCAATATAGTTGGAAT
AATCATATTATATTAATAGTTGCATTAACAGTTATCTTCGGTCTGAATTCCAATTATTCGCTGGA
ATTGATCTCGATACTTGCAGTGCTAGTTACATTTATAGGGCCATTTGTCGTGAAAATCCAAATAA
TGGGGAAACAGAGGGTTCGGCGGGTATACGAACCTACGCGCAAGC
Right flanking sequence: Indices 109408 -- 109907
AGAAATACTGGAAATACTGTAGGGCACCCGGCGTGGGTTGTATGTAAGAATTGTCAGGAACCCAA
TTTGCGTACCTTTTTAAAAGACAACAGGAATATTTCTTACTCCTGTGAAAAGGATGTGAATGAGG
GAGACGGTATTCAAAATCGTCCTAATGATTTTGGTCATTTGTGGGTTGTATGTGAGAATTGTGAC
GAATTAAATTATAAGAGACTTTTAAGAAAAAGACTGAATATTTGTGAATCCTGTTCATGGCATTT
GAAAATGAATAGTCCAGATAGACTAGATCTTTCGATCGATCCGGATACTTGGGGTGCTATGGACG
AAGACATGGTCTCTATAGATCCCATTTCATTTCTTGAATTCATTTCAAATTCAGGGGATAAAATG
AAAACGAAAATGAATACGAGAATGCGAATACAAATTTTATAAAGATCGTCTTGATGCTTATCAAA
CAAAGACGGGATTACCCGACGCTATTCAAACAGGCATAGGCGAAC
Found at i:129342 original size:12 final size:12
Alignment explanation
Indices: 129327--129351 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
129317 AAGGTTTGAC
129327 TCAATTACTTCA
1 TCAATTACTTCA
129339 TCAATTACTTCA
1 TCAATTACTTCA
129351 T
1 T
129352 AAGGACTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (12 bp):
TCAATTACTTCA
Left flanking sequence: Indices 128827 -- 129326
CTAGGATTTCTATATCGACTTTCATTCACTCCCCACTTGAAAGTCATTGTTAGGTAAAGCATCTC
TAGCGGGCGCAATTAGTTAATCTTCTTAGTCGCTCGGAGAAAGGTAGCGAAATACGAGTACTCAA
TTCAGATTCGATATCTGGGCTTTCTTCTGTTGGAGTGAATCCCTTGCTTGGTCTCTTGCGGCTCC
TCATCCCTTCTTCCTGGTTCAATTGGATGTTTCAGCAGCATCATAAGGAGGAATTGCCTCAAGCC
ATTCCACTAGCTTGTTTGCTGGTGTAGCAGATATGGGTTAGACAGGTCGGGGATAGGAGGATCGG
CTTTATGCTGGTTTTCCTTCACCAAAGAATTACAATTGTTTAGCCCAAGTCTCCTATTGGGAATC
ACCAGAAGGCGTTGCAGGCCTTTCGTCGGTGAAGTCAGATCTAGTGTCAATTAGTGCCAATCCAG
CCAACTCAGATGTCGGACTCGATTTCGCTGGTTTCAAGGTTTGAC
Right flanking sequence: Indices 129352 -- 129851
AAGGACTTAGTCCATAAGAAAGATGGATTTTTGAATAAGAAATACAACAAAAAGAGTCTAAGTCC
TAGGGATTTGGAGTGTTTTAAGCTCATCTAATCCTGTTGGAGTTCTTCTACCTGGGAAGGCTAAC
AATAATAGATGGATATTTATTTCCATGATATTTTATTTATATGGTGGAATACTAGAATTAAGATT
TTTTTGAGGACTCCTAACGCGGCTTTCCCTTTCGACTGGCATTCACTCCTCCAACACCAACTGAT
TCAATGTCACTTGGGATCGGATCCTTCCTAAATGCATTTCCACTGGAGCAGGGTTCTTTCCCTCC
GAAATCTATGATTCTTGGCTACTTGATTAGGCATTTCCATCTCTCAAACTAGAAAGCGCTTTAGC
TTAGGAAAGCTCCTTACTTCTTTTTATACCGCGAGTGACGAACTATAGCCATTCGCGGTCACCGC
TGCCCTACTTGACTTTTTTATTAAACCTCACCCATCGAGCCCCAT
Found at i:151095 original size:24 final size:24
Alignment explanation
Indices: 151054--151101 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
151044 TTCGGATTCC
*
151054 TTACTTCGGGCTGATGAGGATGAG
1 TTACTTCGGGCTCATGAGGATGAG
* *
151078 TTACTTCGGGCTCCTGAGGGTGAG
1 TTACTTCGGGCTCATGAGGATGAG
151102 GAATTCTTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.17, G:0.38, T:0.29
Consensus pattern (24 bp):
TTACTTCGGGCTCATGAGGATGAG
Left flanking sequence: Indices 150554 -- 151053
TCGTTGCCTTGGGTACGAATGTGATAGCTTTCTCTAGACACCATGGAAAAGATCACTGACGAGCT
CAATCTCTAAGTGTGAAATTTCCTCCTAGGGTCAACAATTCTCATTTCTTAGTTACAATAAATCT
CAAGGAAGTGATCCTTGAGCCACTCATCTGAGCCAGCGGATTCCTATTCTGCTGTGCCGGTGCGC
AAAGCAAGCACGCTTAGACTGCGATGTGCAATCTTTGGTCTGCCTATCATTGTCCATTAAGGGTC
CGCTAGGCAAGAGGACCACTACTGGGATTATTTAACTACTAACTGATGACCAGGGTGTCTGCTTT
TTCCACTACACTGACCTGTTGAGAAGATAGCTGCAGGAAAAAGAAAAGAAGTAGAGTTAGGTTGT
GTTTTAGTGTGTAAGCATCTCTTTCCTCGGTCGATTCGTCTGCTCATTCAGCCTATGATTCTTAT
CCTTCCGAAAAGTCTTATGAAAGGGGAGATAGGCATTCGGATTCC
Right flanking sequence: Indices 151102 -- 151601
GAATTCTTCCCTGAAGCCGTTGATCCAGTTCGATAATTACCACCATCAGATGATGACCCAGAAGT
CCAAATCCGTTATTTTGACCTTGACCTGCCTCTTTCCCCAATGGGCACAAGATGCTACAAACTAT
CATACACGGGCCACTCAAGAGTTCATATCCAATCTGGACTTCTACTTTAGGCAACTCCTAAGTGC
AGAGATTCTCTACCGAATCGAACTCAAGCTCCTAGCTAAAGACCACCTGAAAGAGGAGCGGATCG
GAATTTGGCCTGATAATGACGCTTTTCCTTGACGAGCTCATCTAAAAAGTATAGGAAGACATACG
AAAGGAAGAATGTAGAACTGCAAGAAGTCACTTCCAAGGATACGGATTGCGAGACTCCCGGAAAG
ACATAGAGATACATTCGCGCGGCTACAAGAGAGTTCTTTAACTGTGTCAACCTGCTTAATGAATG
GTTTGGGGCTTTCGTTGACAGTCCCCTATGAAGACTTCATCCGTC
Found at i:163281 original size:21 final size:21
Alignment explanation
Indices: 163256--163306 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
163246 AAGGGGTAAA
* * *
163256 TAAAGGAAAAGGAATAGAGAG
1 TAAAGGAAAAGCAAAAGAAAG
*
163277 TAAAGGAGAAGCAAAAGAAAG
1 TAAAGGAAAAGCAAAAGAAAG
163298 -AAAGGAAAA
1 TAAAGGAAAA
163307 AGGTAAACTG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.63, C:0.02, G:0.29, T:0.06
Consensus pattern (21 bp):
TAAAGGAAAAGCAAAAGAAAG
Left flanking sequence: Indices 162756 -- 163255
GCAGTAGGAAGGGCGGGAGAGCCTATTGAACCGGGATAGAGAACTAGAGCTTTTCGCAGAATCAG
GAAATTTTTCAAGAGCATTAGAAAGTGTATTATGACTCATGGTTTCAATTGAAATGAAATCAGAC
ATCTTCTTATTCATCAACACTGAGTTCCAAACATGACGTTTGCCTCTATATTGAACCTTCAGCAG
GAACACTTGAAAGAGTCTTCACTGAAGCGAAGAATTGGTATCAACTCAAGTTTCTTTCTGATGCT
TCAAGCGGCCTAGTAGCGAAAGTTATCAATTCCTTTCAATCTTTGAATTTCACTTTTTGCGTTTT
ATATAGATGAAAAATCTATCTACTCGATTTCCCTTCGGAGCGACCAGTTGAAATTGAACAAATTG
CATCTCATATAGTGCCAACCTCAAACTAGGAAAGTCTTACCACTTTAACCATCCCTACTAGAAAC
GAATGCACTCCTAGGGGTGGGTATCTCGTACAAGAAAGGGGTAAA
Right flanking sequence: Indices 163307 -- 163806
AGGTAAACTGTAGAATACTACTTTAGGGCATACCTACCATACTTCTTTATTACACTCTTCCAATA
AAGGAAAGAAGCTACTAGCTACAGCTTTAGTACTTCCTTAAGCGCTCGGAACCCTTACCCAAGGT
TTCCATCGCTCCCTAGAAGAGATATTTAGGAAATCATAAACCTACTCCTTCCAGTAAGAAGATTC
GTTTTAGGTTGATAACCGTTGCTGGAATTGAGACTAGCTGCACTTGATCTTTCTTTTCCTGCTTT
CCGTAGCTACTGCCGCCTAGTTTGGTGTTTAGGAGTGGGAGTCTTTTCTAAAGAGTGATCATTCA
AAGATTATCGAGGTTTGCAAAGTCTAAAACTTCAGCATGTTGGATGCACCCAGTTAACCAAAAGG
CGAATATTCTATCTATTTTCTTTTCCACTTCTGCCTGGCTGACTGAATAAAGAAATGGAACCATA
GCTAAGACTGATCGATGAGCCTTCTTCCATCAAGAAAGAAAAGCC
Found at i:180765 original size:12 final size:12
Alignment explanation
Indices: 180748--180772 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
180738 AGGGAAGGCT
180748 AGTCAATCCATC
1 AGTCAATCCATC
180760 AGTCAATCCATC
1 AGTCAATCCATC
180772 A
1 A
180773 ATATTAGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.32, G:0.08, T:0.24
Consensus pattern (12 bp):
AGTCAATCCATC
Left flanking sequence: Indices 180248 -- 180747
GAAGGAAAAAACTACCACCCACTTCATGTAATCTTTCTCCAACTAACTCGCAAGGGCTTAAAGCC
AGATTTTTCGAGCGCTTAGACGGGAACTCTATCTTCTCCTGCGTCTATGAACTCATTTCTTGCAA
CAAAGAGAAGCGAGATTAGACTTACTAAGATACTAGGTTCCCCTGATCACATACAGCACATACTT
TGTATGCCCAAAAAAGAGGACTCAAACTGGATCAATGGCAGGTTCAAAAATGAACTTTTTCAAAT
AAAAGCCTGCTTACCTTTTTTATCCAATTGTATCGCATGGACTCTATGGGTACCTTTTTCGGATC
GGTTGTACCTTACCTATAGGTAAATCATTCCTGGAAGGAAAGAAATGGATTAGAAACTAGGCTCT
TTAAATGGCTCGATAGAATTTTGGTAGAGAAGGGCTGGCTAAGAAGCACTTTTTTGATAGAGTAG
CTGGCTCAATATGGAGATCTTAGGCAAGATTACAAAGGGAAGGCT
Right flanking sequence: Indices 180773 -- 181272
ATATTAGTGAGAGTCTTAGGAACCATATGTTATATGGCCTATTAAGGTAAAATGAAGGCGGATCA
GATAACCTTGTGAGCTTTAGTCTAACATTAGACTATGGAAAGTACAAGTTACACTAGTGCTACCC
TTCCAAACGACAAGCATAAGAACTAGCCGTCTAAAGCACTACTTTACTTATACTACTTATATACT
TAGTCTTAGTACTAAGCTGGGAAGCGGTCCAGAGTCAAGACCTTCTAGCATTAAATAAAGTTCCA
TCAGGAAGGAAAAAGGAGTTATGGAGCACTCTCATCCACAAGCTTATAGGTAACTGGCCTTTAAA
TGGATGCCCATTAGTCTGGAAATGGAATCAAAGACGCTTACCTCAAAAGGGCTAGACGAAAAGAT
GAAGGAGAATAGACGAAGGATAGTTGACGAACTAAAGAAAAAGATTGAGCATAACTTATAGGTCT
TGGATTCGGAATAGGAAGGGCTATTTTCATCCTTTGTTGGTTTGA
Found at i:201895 original size:18 final size:19
Alignment explanation
Indices: 201869--201905 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
201859 TTCTGGGCTT
*
201869 TGATGTTATTA-TTATTAA
1 TGATATTATTATTTATTAA
201887 TGATATTATTATTTATTAA
1 TGATATTATTATTTATTAA
201906 ATATTAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TGATATTATTATTTATTAA
Left flanking sequence: Indices 201369 -- 201868
TTTCTTAGGGCAAAGGGCGCTCCATCCTCCTAACTCCTTCCACTTCTCCCAGGGGCAGGGACTAC
GGCTTGACCTTCGGGGAAGAAGTCCGCGGGACCCCTCCTTGACGGGCGCCTAGATAGTGAAAGGT
TATCCCTTTGCAACGCTGGAAGCTAAGCAAAGTCAGGAAGCTGGCTGACTACGCTCGAGCAGAGC
TCAGGAGCGAGCAAGACTATCTTGGTGAATGCAATAAGAACCGGCTGCTCGCCGCAGCAGAGTGC
TTTGCCCATGCTGCTATCCGCCGCCGAAGCGCTCAAGGGATTCGTGCTTGAATGTCGAGATCAGG
TTGTGACAGCGGAACAAGGGCAAATCTATTTGTGGTGGAATAAACTCAAATATATCAAAAATTTG
GATTGATTGCTCCGATACAAGAGATCGACCCCAGTATGGTGGGTGCCAGCAACTTTCACTTGTTA
GGAGTCAAAAAAGAGCTCTTTGTATAGGTTGGGTTTTCTGGGCTT
Right flanking sequence: Indices 201906 -- 202405
ATATTAAATGAAAAGTGATAAAGGATTTTCATCTTTTGCTGGATTGTTGGTCCGCAGCCCCGCCC
TATAGAATGAATAAGGAGAGGCTTATCGATGACCGAGCCACTCTTCCGACGCGGCCTTACCTCAC
CCCCCTTGTCACTTAAAGGTCGAAGTCGGAGATTTGAAGGAATTTGAAACTATCAGAAATTACTC
ATAGTAGAGTCTAAGGTAGGTTTGGGTATAGCAGGACTTGAACCTGCGACCATTAGGTTAAAAGC
CCAATGCTCTACCAACTGAGCTATACACCCAAAATAAGATGTAGTAGTAAATAAGGATTGGTGCG
GAAAAGAGGGCTTCTTCTCATCATATTAAAGGAGCGCGGCTCTGTATAAGGCTCGTACTGCAAAG
CAAGCGTAAGGGCGCGCGTTAGCACTCCTGCAAGAAAACGACCTAGCTAACCCTTATTTATTAAA
AACTAAAAGGCGTTAAGCGTATGAGCGCTCAAGCACCCAACCGTT
Found at i:244571 original size:12 final size:12
Alignment explanation
Indices: 244554--244579 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
244544 GACTCATTTC
244554 ATTATGAAAAGT
1 ATTATGAAAAGT
244566 ATTATGAAAAGT
1 ATTATGAAAAGT
244578 AT
1 AT
244580 CCTCAAGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (12 bp):
ATTATGAAAAGT
Left flanking sequence: Indices 244054 -- 244553
GGAAGCTTGCTGGAGGTGATTGTGATTTCCATTTTACCATACCGACAAGAGAGAGAGATCTTATA
GGCGCCTAAGAAATGAAATATCATATTTAAGGTTTCGACTCCTATTTGCTAAGGATTCAGACTAT
AAAGAACTTCTTTGAGGAGTCCCTCTATCCCAGTGATGATAGTCCAATAGCTTGATCATCTTCAT
CTACGGATTCCACTCCCTTTGAAACTGACTTTGCTACTGAGTTGATCGAATCCTAATCTTCAATC
TTCAATTGAAACTGCAACTCCCTATTCTGACTCTGACGCTACTTACTATTCTCTATTCTTTCGAA
TCTGAGTCCTTTTCTACTACTAAACCTTAAAGCACCGCTGGAATGAACAAGTCCAGTCCGATGTA
AAGCAAGAAATCAGTCTTCAATGCCAGGAAAAAGGATAGCAACTTATCTTAATGTTTAAGTGCCC
ATTAGGGATTGATAAATGAGCTAGTTCCGGGAGATGACTCATTTC
Right flanking sequence: Indices 244580 -- 245079
CCTCAAGGTCACCGCCTTAACCCTCCTGCTAGGATCAGGATCCAGCTTCTGATCTGCCTTAATCC
GTGGATTCCCCGCAGCAGGATTCATTCTTCTTTTTTTTTGAGTGTGCCATTGTTTTTTGTTCCCT
ATTGGATGTCGAAATGGATTCCAAGGGACTATGAATTGATGCTCTCTTCCTCTTTCCCCCCTTTT
TCCCATGAAGCATTAGCATTGGGAAGAGGTCATGCTATCAGCCATAAAGCTAAGAATCATAAGAA
ATGCCCACATGATGGTTTACCTTCTTTACTTAAGATCCCATGTCTTAGTTAGCTGGGCATATCTT
TTTCATGTTCCCGAAATGAATTAGTGTCTTTTGATTAGCTTTCACATTTTGGCAATTCGTGAAAT
CTTGCCTTTTCTGTTTTTGAAGAAAGGTTCACAGAATAGCAAATTGCAATAAGAATAAGATAAGG
GAGAAGTGCTCGATCTATAGAAATTCTTAATTACATAAGAAATTA
Found at i:321927 original size:25 final size:25
Alignment explanation
Indices: 321873--321927 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
321863 CTACATAACA
** *
321873 CTTT-AAGAGATAGGAGTAGCTACC
1 CTTTAAAGAGATAAAAGGAGCTACC
321897 CTTTTAAAGAGATAAAAGGAGCTACC
1 C-TTTAAAGAGATAAAAGGAGCTACC
321923 CTTTA
1 CTTTA
321928 CCTGCACCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 7 0.27
26 18 0.69
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (25 bp):
CTTTAAAGAGATAAAAGGAGCTACC
Left flanking sequence: Indices 321373 -- 321872
TATAACTCGGTAAAAAGCCTTAACCTCATTCTTTTCCTTGAGGTCGAAATTGTGACACTGTCTCC
GGACTGTCAACCTTCGGTATAAGAGTAAGAAGACTTTCATTCATAATTCAAGGAAGGAGAGAAAA
CTCAGCATACAGAAGACTGGGATAAGCACTTGACAGAAGAAGACAGGGAAGGGCACTTCACGCCA
ATGAAAAGATAAAATGGATAATCTATATGTTAGTAGCAAGAAGAGGCCAGGCTATGCCTACTAGC
TAGCACCAGCCCTCCCTGTCCTTTTATTAAAGTTCAATCTCTTATCATCTTATCATAAAGCCTTT
AACTGGGTGTGTGAATATGGATATGGTTCGATGAGCTCAGATTGTGGATAGACTTAAGTGCTGTC
TGATCTTAGCATCTCTTTCCCTCTCCTCCCAAGAAAGATAGCTGTTATAGTAGTTCTTATCGATA
GTAGCCGCTTGGCCCCCTCCCCAAGGGGTCCTGCGCTACATAACA
Right flanking sequence: Indices 321928 -- 322427
CCTGCACCTTAAGGCGCTTGGATCCCTTACCAAATATTAAGGAAGATAAGACTTTTTAGTTGATC
CTGGGGCCTCAGGCGCCGGCCAGGCTCACACTTAGACTGTATTGGCTTCGGATACCTACCAGGGT
ATCCTCAGCTATAGGATTAACTACTTTGACTGTCCTTTAAGCGTTTGGTACCCATTCCCAAGGGT
ACCTACACTTGCCTTAAGGATACTTAAGGGAAATACAATCCCTACCAAGATAGGAAAGAAGGGTA
GTTCTTCTAATTGCTAGTCCTTACCCCTACTGCCTTCCCTTCCTCAAAGACTTACTGAATAGGGT
TCGCTCTTCTCTCGATGTTCATTGGCCTCTTTCGCCTGTAGCTGCGAACTCAACTGTCTGCTTGG
TCTGTCTTTTGCCAAGTTCAGTTCTTTTCCACAGTGGGTCAGTTCATTTCTGTTATTATACGATT
CTAACTCCGTCTGGCATCTGCCCTTGGTCCCAGACCGTGATCCCT
Found at i:410571 original size:10 final size:10
Alignment explanation
Indices: 410556--410583 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
410546 CTTTCCCTTG
410556 GCTTTCAGCT
1 GCTTTCAGCT
410566 GCTTTCAGCT
1 GCTTTCAGCT
410576 GCTTTCAG
1 GCTTTCAG
410584 GCCCGACAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.29, G:0.21, T:0.39
Consensus pattern (10 bp):
GCTTTCAGCT
Left flanking sequence: Indices 410056 -- 410555
GGCCGGGGGACCAGACCCACAAAAACAAGCAATTCTGCGTTGTCAACGATCTCTTTTCAAGGTTC
CTACACCTGTTAATTCCTATTTCAGTGATCATCATTCGAAACAGGCGCCTAAGCAGAGGGTTCGG
GCTCAGCTGACTCGGGAAATAGAACTCCGGGAGAACTTTAGAATCGCACAGTTGCTTGGGACATG
TCTGCTACGTCTCCAGCTTTCTCCGGGCGAGCTCCGTGCGTGAGCAGCGACTAAGCTTAATCCAA
TCTTTCTTAACATTGTACGCGCCCATCAAATATTACTATTACGTTGCGCTATCGAAGTCTAAATG
ACCTGATGGAATTTATTCTTATTAGGGTATTCTCTCATTCCCTTCCGTCAACTAGCGCACGTAGG
CCTTTTTGTCGTATCGCTTATCGTAGTGTACTTGTTATATGTTTGCTTATCCTGGTTCAAAGCTG
CATATTACGATTCACGTCTGTCTGTTTTTTTTCAGCTTTCCCTTG
Right flanking sequence: Indices 410584 -- 411083
GCCCGACAGCTTCCATACCATACGGAAGCAGGAAGGAGCTGGGAATAACTATCAGAAGGGAGAAA
GAACCAAGATCCTCTCGGAGTGGCGGTTTAGGCGCTGTCCTTTTCCGAAAAGATAGATAGAGATG
GAAGTTGTAAATTCGGTACAGTTGTTTAAGCTCCCTACGATTTGATCAACGCCATTGGTCTAAGT
CCAATTGGCCTATCCGCTCCCTTAAGACAAGAAAGACTTAGGGCGCCCCACAGCAAGCAGCCCTT
ATTTACAACTACGGACCAATCCAGAACAATTAAGGAATACCGAAGAGAGAGCAGAAGCTAACGCC
GGCCTTCCCTACCTCTGATATTGTTAGTGGATAATGAAATTGCAAACTGGAGAAAGGGGTATCAG
TAGAGCCAACGGAGGGAAAAACGGAAGGGCGCGCTAGCGCACACTTAGGTTCAATGTAGTTCCGT
CACAGCCAGCTTGGGCAACGTAGAGTTAAGCCGTTGCGCGCTAGC
Found at i:479005 original size:14 final size:15
Alignment explanation
Indices: 478982--479014 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
478972 TAAACTTGCC
478982 ATTTTATCTTT-TTG
1 ATTTTATCTTTATTG
*
478996 ATTTTGTCTTTATTG
1 ATTTTATCTTTATTG
479011 ATTT
1 ATTT
479015 ATATACTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.15, C:0.06, G:0.09, T:0.70
Consensus pattern (15 bp):
ATTTTATCTTTATTG
Left flanking sequence: Indices 478482 -- 478981
GAAGACTGCGTTAGTTGTAAAAGATGTGAATCCGCCTGTCCAACGGATTGATTGAGTGTTCGGGT
TGATTTAGGGGCTGAAACAACTCGCAGTACAGTATGGGTCTAGCTTATTGATACGTTCCAATAAA
CTATACTTGATTCAGTAGAATTTTATCTAAGAATCAAAAAATCACGCTCTGTAGGATTTGAACCT
ACGACATTGGGTTTTGGAGACCCACGTTCTACCGAACTGAACTAAGAGCGCTTTCTTATCACAGT
AGATACGACTGTAAAGAAAAAGGATTGATTCTTTTTGTACCCCCACTTGCATGTAGAATAGTATC
ATAAAATTTAAATATGTCTGTCCAAGGGGATTTGAACCCATGAAATTGGGTACCCAAAACTAAGG
CGCTACCAAGCTGCGCTACATCCCTTTCAATAGGTCTACAGTGTCATTGTAGAGAATCCCAGCCC
TGTTTTCCGCCACATCGTTATTTCCTCCATCAATATAAACTTGCC
Right flanking sequence: Indices 479015 -- 479514
ATATACTCATCATCCCGCCGCTCCTACCAACGCTTACTTACTTATGAGCAAAACGGGTTCTAAAT
AATCAGCCCTTTGAATAAAATAAGCGAGGCTTTCCCGATAGAAAGATTTGCATGAGACAGAGATC
CCAATTCCGTGTATCCGGTTAAGCAAGCCCTGCCCGCCAGTTTCCACCCAGACAAAAAAAAGGTG
AGCGCCTAGCGCGAAAGGTTGCTTTACTAAAAGGCCGTTAAGGATTGAGCTTTAGAAAGCCGTTG
CGCTAATGAGCAAGAAAGGACGTTAGCCTTTGATTGCTTATTACTAATAAGATATAAGGGACTTT
TTCAGCGTACTCTGCTATAAGCGGACCGTTAGCAGGGTGCCGCGGTTTGTGGGCTTGAAGGACCT
AGCGCCGTGACAAGTGGTATCAGAGCCAAAGGTTGGGGCAAGCCATGGCTAGTAGGAAGAACGCG
TAGGCTAGTGCCGTCGAAGAGGATCGACGGGAGCAGACTCGTGAT
Found at i:559716 original size:28 final size:28
Alignment explanation
Indices: 559684--559744 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
559674 GAGGTGAGTC
559684 GAGGGGAAAAGCAGCTCGACCACAGGGA
1 GAGGGGAAAAGCAGCTCGACCACAGGGA
*
559712 GAGGGTAAAAGCAGCTCGACCACAGGGA
1 GAGGGGAAAAGCAGCTCGACCACAGGGA
559740 GAGGG
1 GAGGG
559745 CGTGCCGGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.34, C:0.20, G:0.41, T:0.05
Consensus pattern (28 bp):
GAGGGGAAAAGCAGCTCGACCACAGGGA
Left flanking sequence: Indices 559184 -- 559683
TGCATAAAAACGCCGGGACGCAGGCTCACTAAGAGGGAAGCCCAACGAATGTCAGATGCAAAGCC
CCGCACCTCATTAAGATCATATTGGCATACTCTCCCAAAAAAAAAAGAGCAGACCCCATTGAAGA
CGAGAGTGAGGTACAACAAGGCCAGGCCATTTCTGTCCACCGCCCTTCTCACGGAGCCGTACGTG
GACGTTACCGCTCATACAGCTCCCAGCCAGCAAACTCTTTTCCTTCCTCTACAAGGAATGGAAGT
GTGGATGAATCGACATCAAGCTTCTTTTTAGCAATAACATGATATCACAAAAACCTACTTATCCT
GCCACTTCAGCACCTTGTGATCTTTGAGAAGATCATTAGAAGCCCTCTCCGTTAATGTTTTTGTA
GATTCCAAAAAGGATCAGGACGAGAATGAATCCGGGAATCCAGGACATACTCATCCTGGAGTGGA
GCTTCTCCTCTGGGAAGGGGTTTTTTATAGAGAGAGAGGTGAGTC
Right flanking sequence: Indices 559745 -- 560244
CGTGCCGGCAAGCTTGACCGATTTCTCGGAGTCGGAGGATCATCTGATGACCCTGAACAAGAAGG
AGCTGCTCTCGATGTGAGATCAGCAAAGAGGAATTTGATGCCCCAGAGCAGCAGCCCCCGGATAA
GCCTTAAAAAAACACACACAACGGACCGGACACAAACAAAAGAAAGAAGAAAAGGGCCACGATCC
TATCTTCGTTTTCGCCCTGCCCCGATGATGCGCTCCTAGGTCGCGGAGCTACATACCAGAAAAAG
AAAAAGACTCTATCTGAAAAGAGAATCGTTGGTTTGCCCGAACGTGGGAAATACGAGATCTAGGC
AAGCCGCTACATGTTCTCCCCCTGCCCTTGAACGATAGAAGAACTACTTATCTTCTCTTAGGTAG
GGGTCGATCGGTTCGCATCTTATGGTCAATCAATAGGTCCGCGGATCTATTCTTCTATACGATAA
ATCGCCATCTCGTAGCACCAACCACCACGACACCGATTTTCCGAC
Found at i:637507 original size:20 final size:21
Alignment explanation
Indices: 637482--637521 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
637472 ACCTGTGTGC
*
637482 AAGAGA-TTCTCAAAACAGGG
1 AAGAGAGTTCCCAAAACAGGG
637502 AAGAGAGTTTCCCAAAACAG
1 AAGAGAG-TTCCCAAAACAG
637522 CTTACAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (21 bp):
AAGAGAGTTCCCAAAACAGGG
Left flanking sequence: Indices 636982 -- 637481
CACTGATTGATACAGATACAGCTCCTATCGTACAAGACCACGATAATCTACGTCGGAGAGATGAA
AGTCTCTTTCGATTTGGATTCCAGTGGAAATGTTACGATATGCTCAGAGATTCTAGGTATGTAAT
GCCTGGGATCCTTGGCACAGGCAGAAACGATTCAAACAACAAGTGGTTGCTTGGAGGTTTCGCTT
TCCTTCCTTATCTGGGTCTGGAACAACCTCGAGCAGGGGTTGGAATTCTTATTCATACTAGGTCT
GTTGATCTATATGGTAAGATTCAAAACAATATTAGTACTTTTTAGATTTTGTCTCCGGAGAGTTG
TTCTGTGCCACAAAGCGAGTTCGGGCTCGGGTAGTCAAGTCACCCTAAGTCAGTACCAGTGGATT
CTACTTTCAATCCCATACATAAGAAAAGGTTTGGAACAGTGAGTCGATAAGCTCATTTGGCCACA
CTAAGGTCTCGATCCTCCTACCTTTGGCCAAAACTACCTGTGTGC
Right flanking sequence: Indices 637522 -- 638021
CTTACAATAGACTGATGATGAGTGGTATGAACTAAAGATATCATCCCCTTCCACCTTCAAAAGGG
ATACCTCTTGGAGCCCGCGTCTTGGATTCTTGAGATGGAACTCTTTCACAAACCGATGGCTCGCT
TAAATCCTTTCTGAGTGACTGGCTTGACTTTAGGGCTATATGATATTTCCAAGCGTTGGAGTCGT
GACTTCGAGCTGGGGTTAGGAGAACTCTTCCAATTTGACACCAACATATCATATGGTTGCCCATG
AATCTAGGTACCAATTAGGATCATATTCTTGCTAGGAAAGGTGCATTGCAGCAAAGGACCGGGGA
GCTTTAAAACACCTGGATATGAGTGATCAGACCGATGCTAGCATTTGATTTGATAACTTACCCTT
CCCACCAACCTGTGTTATCTAGTGCGGTCTTGCTAAAGCTAAAGTCCTCTCGACTTTCAATTGAG
GATAGGAAATGGAGATATAGGCAAGAACTCGTCTTCCTGGGCTAA
Found at i:666486 original size:17 final size:17
Alignment explanation
Indices: 666444--666486 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
666434 AAGGAAAAAG
*
666444 GATTCCCCG-AACAACG
1 GATTCCCCGAAACAACC
**
666460 GATTTTCCGAAACAACC
1 GATTCCCCGAAACAACC
666477 GATTCCCCGA
1 GATTCCCCGA
666487 CTCGAGTTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.30, C:0.35, G:0.16, T:0.19
Consensus pattern (17 bp):
GATTCCCCGAAACAACC
Left flanking sequence: Indices 665944 -- 666443
AGCTATTTACGTGTAGGTCTATAGTAGTAGCAACGGAGACACATGAAGACGGAGGGTACCACTAT
CATGTAGGTGTCTTAAATGAGAATGCGTCCAGATAGTGGTGCTTTAAACAAATAAGGGCGCTCTT
CCCCGGGGAGGCAGATCATTGTCAAAGTACACAAAGGATGGGGAATCATCTGCCGATATATACCT
AAAATGGAAAAAAAGAAAGTGGTATGGGGCGAATACAGCCTTAAGCAGATATTGGAAATTGGAGA
TGCAAGTGCGAAAGACCAAGCTATTCCATACAAGCCAGAAAAGACAGGAGGAGCCCTTGTTATTC
CGAAAGTCATGAAGTACGACGAATGGTATGATGCCCTCGAAGATCCCGCCCTGAAGGATACTCTT
ATTAGATCGTATTCAAATCTGAGGGTCCGAAGGAGTTGAAGATCTCAAGGTTGCAAAATTCCGGC
AATCGAACGTAGGCGAAAGACTAGTTCAATTTTGAAAGGAAAAAG
Right flanking sequence: Indices 666487 -- 666986
CTCGAGTTATTCCACCAGACAACAGCGGTTTCAGTTTCCACGCCTTTTAGAGAACACTCTTATGA
AAGACCGTACAAATGGGGGTGATTCATACATATCTTCCCGCGTTCAAGTCAGATAGAACTTTTGG
GAAGCTCCAGAATAGACTCCGTGACGTGATTGAGGATCCTTTTAGGCGAAAGCCCCCTATAGTCA
CCTATTAACATAACAGAAAGATGATGCCTTCGAAATGCGCTAACAATGCTCTAAGGAGCTGGAAT
TTATTTTCAAAGAAGGAAAACACCCTCTATGTGATTCTTTAGGGGGAAAATCGAGTATAGAATAT
GGAAAGTAAAAATCCATATATATCCTAGGGGGAAACCCCTAGAAAAAAATGGGTAAGTAGCGCTT
CTCTAAATTCTTACTACTTTCCCATAGCCGGTCTCTCTCCGCGTTGAGGTCTACATCAGACATAA
ATTCTTAGGTCATTCTCATGACTCATCGAGAGTGATGATGATAGA
Done.