Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397265.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_146.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8065533
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 116430 characters in sequence are not A, C, G, or T
File 16 of 18
Found at i:6561104 original size:18 final size:18
Alignment explanation
Indices: 6561081--6561117 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6561071 TAAGTTGCTT
*
6561081 AAAAATAAATTAATTATA
1 AAAAATAAATAAATTATA
*
6561099 AAAAATAACTAAATTATA
1 AAAAATAAATAAATTATA
6561117 A
1 A
6561118 TTAAAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATAAATAAATTATA
Found at i:6562839 original size:17 final size:17
Alignment explanation
Indices: 6562811--6562848 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
6562801 AAGCTTAGCC
*
6562811 AATTTATTTTATTTATG
1 AATTTATTTTATGTATG
6562828 TAATTT-TTTTATGTATG
1 -AATTTATTTTATGTATG
6562845 AATT
1 AATT
6562849 AAATTTATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 10 0.53
18 5 0.26
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (17 bp):
AATTTATTTTATGTATG
Found at i:6563314 original size:17 final size:18
Alignment explanation
Indices: 6563294--6563331 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
6563284 TAAGATATAA
*
6563294 AAAAATCAAAAGTT-TTT
1 AAAAATCAAAAATTATTT
*
6563311 AAAAATTAAAAATTATTT
1 AAAAATCAAAAATTATTT
6563329 AAA
1 AAA
6563332 TAAAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (18 bp):
AAAAATCAAAAATTATTT
Found at i:6563620 original size:2 final size:2
Alignment explanation
Indices: 6563615--6563640 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6563605 TTGTAACACA
6563615 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
6563641 TCCACTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6564162 original size:39 final size:43
Alignment explanation
Indices: 6564085--6564165 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
6564075 CATGTGTTTG
*
6564085 TTATTTAAATTTATTTATGTATTGATAGTATATAATTTTTTAAT
1 TTATTTAAATTTATTTA-GTATTAATAGTATATAATTTTTTAAT
* *
6564129 TTATTT-AATTTATTTA-TATTAATATTA-ATATTTTTTT
1 TTATTTAAATTTATTTAGTATTAATAGTATATAATTTTTT
6564166 CATAATTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 9 0.26
41 9 0.26
43 10 0.29
44 6 0.18
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (43 bp):
TTATTTAAATTTATTTAGTATTAATAGTATATAATTTTTTAAT
Found at i:6564402 original size:22 final size:22
Alignment explanation
Indices: 6564377--6564422 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
6564367 ATAATTTTTT
6564377 ATTTTT-TATTATATTCAATTAA
1 ATTTTTATATT-TATTCAATTAA
* *
6564399 ATTTTTATATTTTTTGAATTAA
1 ATTTTTATATTTATTCAATTAA
6564421 AT
1 AT
6564423 AAGTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTTTTATATTTATTCAATTAA
Found at i:6564693 original size:26 final size:25
Alignment explanation
Indices: 6564663--6564726 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 25
6564653 TATAAGATTT
6564663 ATTTAATTTAAAATAAAAATATAAAA
1 ATTTAATTTAAAATAAAAA-ATAAAA
*
6564689 ATTTAATTGATATAATAAAAAATAAAA
1 ATTTAATT--TAAAATAAAAAATAAAA
6564716 ATTT-ATTTAAA
1 ATTTAATTTAAA
6564727 TTTGTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 3 0.09
26 11 0.32
27 10 0.29
28 10 0.29
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTTAATTTAAAATAAAAAATAAAA
Found at i:6565415 original size:9 final size:9
Alignment explanation
Indices: 6565401--6565425 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
6565391 GTGGAGGTTA
6565401 TTTTTTAAT
1 TTTTTTAAT
6565410 TTTTTTAAT
1 TTTTTTAAT
6565419 TTTTTTA
1 TTTTTTA
6565426 TTATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:6571253 original size:2 final size:2
Alignment explanation
Indices: 6571246--6571273 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6571236 GTAGGTATCC
6571246 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6571274 TCACATTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6582406 original size:21 final size:21
Alignment explanation
Indices: 6582363--6582411 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
6582353 ATTTAAGTAT
6582363 AATA-TTTAAAAAATCTCAAA
1 AATATTTTAAAAAATCTCAAA
6582383 AAT-TTTTAAAAAAT-TCAAATA
1 AATATTTTAAAAAATCTC-AA-A
6582404 AATATTTT
1 AATATTTT
6582412 TTATTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 2 0.08
20 15 0.60
21 4 0.16
22 4 0.16
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (21 bp):
AATATTTTAAAAAATCTCAAA
Found at i:6582465 original size:30 final size:29
Alignment explanation
Indices: 6582405--6582465 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
6582395 ATTCAAATAA
* * * *
6582405 ATATTTTTTATTATATTCAATAAGTTTTT
1 ATATTTTTTATTAAATTAAATAAATATTT
*
6582434 ATATTTTTATTTTAAATTAAATAAATATTT
1 ATATTTTT-TATTAAATTAAATAAATATTT
6582464 AT
1 AT
6582466 TATTAATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (29 bp):
ATATTTTTTATTAAATTAAATAAATATTT
Found at i:6582704 original size:29 final size:28
Alignment explanation
Indices: 6582658--6582730 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 28
6582648 AGTGATATTT
*
6582658 TAAT-AAAAA-TAATTTATTAATAATTAA
1 TAATAAAAAATTAATTTATTAA-AAATAA
*
6582685 TAATAAAAAATTATTTTATTAAAAATAA
1 TAATAAAAAATTAATTTATTAAAAATAA
*
6582713 AAATATAAAAATTTAATT
1 TAATA-AAAAA-TTAATT
6582731 AAATATCATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
27 4 0.11
28 14 0.37
29 15 0.39
30 5 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
TAATAAAAAATTAATTTATTAAAAATAA
Found at i:6584001 original size:2 final size:2
Alignment explanation
Indices: 6583994--6584021 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6583984 AATTCTCCAG
6583994 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6584022 TTCTTTTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6585083 original size:19 final size:18
Alignment explanation
Indices: 6585035--6585088 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 18
6585025 AAGTGTATGA
6585035 TTTTTTTATT-ATAAAAAT
1 TTTTTTTATTAAT-AAAAT
*
6585053 TTTGATTT-TTAATAAAAT
1 TTT-TTTTATTAATAAAAT
6585071 GTTTTTTTATTAA-AAAAT
1 -TTTTTTTATTAATAAAAT
6585089 CTAACATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 18 0.60
19 12 0.40
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (18 bp):
TTTTTTTATTAATAAAAT
Found at i:6605734 original size:20 final size:21
Alignment explanation
Indices: 6605709--6605756 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
6605699 TTTTTTAAGC
*
6605709 TTTTTTTTAAAAAA-ATTTAT
1 TTTTTTTTAAAAAACACTTAT
6605729 TTTTTTTTAAAAAACTACTTAT
1 TTTTTTTTAAAAAAC-ACTTAT
6605751 TTTTTT
1 TTTTTT
6605757 AAAAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 14 0.56
22 11 0.44
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTTTTTAAAAAACACTTAT
Found at i:6624554 original size:20 final size:19
Alignment explanation
Indices: 6624516--6624554 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
6624506 CTGCTAGATT
*
6624516 GAAAGCTCCTGATAAGCTC
1 GAAAGCTCCTGACAAGCTC
*
6624535 GAAAGCTCTTGGACAAGCTC
1 GAAAGCTCCT-GACAAGCTC
6624555 TTTGAGGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.21
Consensus pattern (19 bp):
GAAAGCTCCTGACAAGCTC
Found at i:6637061 original size:28 final size:28
Alignment explanation
Indices: 6637026--6637080 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
6637016 ATTTGAAATT
6637026 TTATTTATATTTGATGTAATGTATTTGC
1 TTATTTATATTTGATGTAATGTATTTGC
* *
6637054 TTATTTATTTTTGATGTAATTTATTTG
1 TTATTTATATTTGATGTAATGTATTTG
6637081 TTTGTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.02, G:0.13, T:0.62
Consensus pattern (28 bp):
TTATTTATATTTGATGTAATGTATTTGC
Found at i:6647222 original size:2 final size:2
Alignment explanation
Indices: 6647217--6647252 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
6647207 TTCTTTTTTG
*
6647217 CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6647253 GTGTTCCGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:6662869 original size:32 final size:32
Alignment explanation
Indices: 6662801--6662870 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
6662791 ACAATTAATG
* **
6662801 ATGTAATTTGAATGTTTAAAACAAAAATAATG
1 ATGTAATTTGAATGGTTAAAACAAAAATAAAA
6662833 ATGTAATTTGAA-GGTTAAAAGCCAAAAA-AAAA
1 ATGTAATTTGAATGGTTAAAA--CAAAAATAAAA
6662865 ATGTAA
1 ATGTAA
6662871 ACAAATAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 7 0.21
32 20 0.61
33 6 0.18
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (32 bp):
ATGTAATTTGAATGGTTAAAACAAAAATAAAA
Found at i:6669906 original size:27 final size:27
Alignment explanation
Indices: 6669847--6669907 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
6669837 GCTTGGTTAG
*
6669847 GCTGCGGTGGAGGGTATTGTGTCGGCT
1 GCTGCTGTGGAGGGTATTGTGTCGGCT
*
6669874 GCTGCTGTGG-GGGATATTGTGTTGGCT
1 GCTGCTGTGGAGGG-TATTGTGTCGGCT
6669901 GCTGCTG
1 GCTGCTG
6669908 AGCTGGTGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 3 0.10
27 28 0.90
ACGTcount: A:0.07, C:0.15, G:0.46, T:0.33
Consensus pattern (27 bp):
GCTGCTGTGGAGGGTATTGTGTCGGCT
Found at i:6669920 original size:21 final size:21
Alignment explanation
Indices: 6669896--6669949 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
6669886 GATATTGTGT
*
6669896 TGGCTGCTGCTGAGCTGGTGG
1 TGGCTGCTGCTGAGATGGTGG
6669917 TGGCTGCTGCTGAGATGGTGG
1 TGGCTGCTGCTGAGATGGTGG
6669938 TGGCTGCTGCTG
1 TGGCTGCTGCTG
6669950 TGGCTGGAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.06, C:0.19, G:0.46, T:0.30
Consensus pattern (21 bp):
TGGCTGCTGCTGAGATGGTGG
Found at i:6671865 original size:14 final size:13
Alignment explanation
Indices: 6671834--6671879 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 13
6671824 AATATATAAG
6671834 TAAATAGAATAGAAA
1 TAAATA-AATA-AAA
6671849 TAAATAAATAAATA
1 TAAATAAATAAA-A
6671863 TAAAT-AATAAAA
1 TAAATAAATAAAA
6671875 TAAAT
1 TAAAT
6671880 TGATAGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.20
13 8 0.27
14 10 0.33
15 6 0.20
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:6671867 original size:18 final size:18
Alignment explanation
Indices: 6671829--6671879 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
6671819 TTTAGAATAT
*
6671829 ATAAGTAAATAGAATAGAA
1 ATAAATAAATA-AATAGAA
*
6671848 ATAAATAAATAAATATAA
1 ATAAATAAATAAATAGAA
6671866 AT-AATAAAATAAAT
1 ATAAAT-AAATAAAT
6671880 TGATAGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.10
18 16 0.55
19 10 0.34
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAATAAATAAATAGAA
Found at i:6677515 original size:12 final size:13
Alignment explanation
Indices: 6677498--6677526 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6677488 TGTTGGTTGG
6677498 TTTAAAAAAA-AT
1 TTTAAAAAAATAT
6677510 TTTAAAAAAATAT
1 TTTAAAAAAATAT
6677523 TTTA
1 TTTA
6677527 GACATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTTAAAAAAATAT
Found at i:6679876 original size:2 final size:2
Alignment explanation
Indices: 6679869--6679898 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6679859 CAGGTGGATG
6679869 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6679899 GTATCCATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6682938 original size:14 final size:14
Alignment explanation
Indices: 6682902--6682939 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
6682892 GTTGAAGAAA
*
6682902 ATATAAAACAATTT
1 ATATAAAAAAATTT
6682916 ATATGAAAAAAATTT
1 ATAT-AAAAAAATTT
6682931 ATATAAAAA
1 ATATAAAAA
6682940 TATACAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (14 bp):
ATATAAAAAAATTT
Found at i:6692487 original size:15 final size:15
Alignment explanation
Indices: 6692467--6692497 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6692457 AACTGACTAA
6692467 TTCAATTAATTCAGT
1 TTCAATTAATTCAGT
*
6692482 TTCAATTAATTGAGT
1 TTCAATTAATTCAGT
6692497 T
1 T
6692498 AAATCAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (15 bp):
TTCAATTAATTCAGT
Found at i:6693078 original size:18 final size:17
Alignment explanation
Indices: 6693050--6693109 Score: 79
Period size: 18 Copynumber: 3.5 Consensus size: 17
6693040 ACTATAGTAA
*
6693050 TATAGTATAACTTATAT
1 TATAATATAACTTATAT
6693067 TACTAATATAACTTATAT
1 TA-TAATATAACTTATAT
6693085 TAATAAT-TAAC-TATAT
1 T-ATAATATAACTTATAT
6693101 TATAATATA
1 TATAATATA
6693110 TAGCAATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
15 5 0.13
16 8 0.21
17 6 0.15
18 19 0.49
19 1 0.03
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (17 bp):
TATAATATAACTTATAT
Found at i:6693265 original size:21 final size:21
Alignment explanation
Indices: 6693241--6693313 Score: 60
Period size: 25 Copynumber: 3.3 Consensus size: 21
6693231 ACTTATATAT
6693241 TATATAAGT-ATATATTAACTA
1 TATATAAGTAATATATTAA-TA
*
6693262 TATA-CAGTAATATATTAATA
1 TATATAAGTAATATATTAATA
*
6693282 TACTATATGCAATAATATATTAATA
1 TA-TATA---AGTAATATATTAATA
6693307 TACTATA
1 TA-TATA
6693314 CATAGTATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
20 7 0.16
21 15 0.35
25 21 0.49
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (21 bp):
TATATAAGTAATATATTAATA
Found at i:6693297 original size:25 final size:25
Alignment explanation
Indices: 6693258--6693313 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
6693248 GTATATATTA
*
6693258 ACTATATACAGTAATATATTAATAT
1 ACTATATACAATAATATATTAATAT
*
6693283 ACTATATGCAATAATATATTAATAT
1 ACTATATACAATAATATATTAATAT
6693308 ACTATA
1 ACTATA
6693314 CATAGTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (25 bp):
ACTATATACAATAATATATTAATAT
Found at i:6693347 original size:24 final size:23
Alignment explanation
Indices: 6693293--6693352 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 23
6693283 ACTATATGCA
* *
6693293 ATAATATA-TTAATATACTATAC
1 ATAATATACTTAATACACAATAC
6693315 ATAGTATATATCTTAATACACAATAC
1 ATA--ATATA-CTTAATACACAATAC
6693341 ATAATATACTTA
1 ATAATATACTTA
6693353 TTATCACACT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 3 0.09
23 4 0.12
24 10 0.31
26 15 0.47
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (23 bp):
ATAATATACTTAATACACAATAC
Found at i:6693360 original size:24 final size:24
Alignment explanation
Indices: 6693263--6693360 Score: 71
Period size: 25 Copynumber: 4.0 Consensus size: 24
6693253 TATTAACTAT
6693263 ATACAGTAATATA-TTAATAT-ACTA
1 ATACA-TAATATACTTAATATCAC-A
* *
6693287 TATGCAATAATATA-TTAATAT-ACT
1 -ATAC-ATAATATACTTAATATCACA
6693311 ATACATAGTATATATCTTAATA-CACA
1 ATACATA--ATATA-CTTAATATCACA
*
6693337 ATACATAATATACTTATTATCACA
1 ATACATAATATACTTAATATCACA
6693361 CTAATTAATC
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
22 3 0.05
23 9 0.15
24 14 0.23
25 19 0.31
26 16 0.26
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (24 bp):
ATACATAATATACTTAATATCACA
Found at i:6704760 original size:42 final size:42
Alignment explanation
Indices: 6704696--6704778 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
6704686 CTGCCAAGAG
* *
6704696 GTCAAATTGTCCAACCTAATAGAAAATAATATACATGTAAAA
1 GTCAAATTGTCCAACCTAATAGAAAATAAGATAAATGTAAAA
* ** *
6704738 GTCAGATTGTCCAATTTAATAGAAAATTAGATAAATGTAAA
1 GTCAAATTGTCCAACCTAATAGAAAATAAGATAAATGTAAA
6704779 GAATCAGTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (42 bp):
GTCAAATTGTCCAACCTAATAGAAAATAAGATAAATGTAAAA
Found at i:6709702 original size:60 final size:60
Alignment explanation
Indices: 6709603--6709721 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
6709593 AAAAGTTGTA
* * *
6709603 CTAATTTAAATTGTAGGATTATAGGTGTAGCATTCCATTTTTAAATGATTACTTTTATTC
1 CTAAATTAAATTATAGGATTATAGGTATAGCATTCCATTTTTAAATGATTACTTTTATTC
*
6709663 CTAAATTAAATTATAGGATTATAGGTATAGCATTTCATTTTTAAATGATTACTTTTATT
1 CTAAATTAAATTATAGGATTATAGGTATAGCATTCCATTTTTAAATGATTACTTTTATT
6709722 TTTAATTTCT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (60 bp):
CTAAATTAAATTATAGGATTATAGGTATAGCATTCCATTTTTAAATGATTACTTTTATTC
Found at i:6709938 original size:25 final size:25
Alignment explanation
Indices: 6709922--6709969 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
6709912 AATTTATAAT
6709922 AATTAATTAATTATTAATTATAAAA
1 AATTAATTAATTATTAATTATAAAA
*
6709947 AATTATTTAA-T-TTAA-TATAAAA
1 AATTAATTAATTATTAATTATAAAA
6709969 A
1 A
6709970 TATAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 4 0.18
24 1 0.05
25 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AATTAATTAATTATTAATTATAAAA
Found at i:6709970 original size:21 final size:24
Alignment explanation
Indices: 6709910--6709970 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
6709900 TATTATCATT
*
6709910 TTAATTTATAATAATTAATTAATTA
1 TTAA-TTATAAAAATTAATTAATTA
*
6709935 TTAATTATAAAAAATTATTTAA-T-
1 TTAATTAT-AAAAATTAATTAATTA
6709958 TTAA-TATAAAAAT
1 TTAATTATAAAAAT
6709971 ATAAAATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 6 0.18
22 3 0.09
23 4 0.12
24 5 0.15
25 15 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTAATTATAAAAATTAATTAATTA
Found at i:6709978 original size:20 final size:18
Alignment explanation
Indices: 6709955--6710027 Score: 58
Period size: 20 Copynumber: 3.8 Consensus size: 18
6709945 AAAATTATTT
6709955 AATTTAATATAAAAATATAA
1 AATTTAAT-TAAAAATAT-A
*
6709975 AATTTAATTGAAAGA-ATA
1 AATTTAATT-AAAAATATA
* *
6709993 AATATAATAAAAAATCATGA
1 AATTTAATTAAAAAT-AT-A
*
6710013 AATTAAATTAAAAAT
1 AATTTAATTAAAAAT
6710028 TTTCAAATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
17 4 0.10
18 8 0.19
19 5 0.12
20 25 0.60
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (18 bp):
AATTTAATTAAAAATATA
Found at i:6713880 original size:25 final size:27
Alignment explanation
Indices: 6713852--6713903 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
6713842 ATTAATTAAA
*
6713852 TTATATAATA-TT-TTTTATTTTATTT
1 TTATAAAATATTTGTTTTATTTTATTT
6713877 TTATAAAATATTTGTTTTATTTTATTT
1 TTATAAAATATTTGTTTTATTTTATTT
6713904 CATTCTATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.38
26 2 0.08
27 13 0.54
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (27 bp):
TTATAAAATATTTGTTTTATTTTATTT
Found at i:6716229 original size:23 final size:22
Alignment explanation
Indices: 6716179--6716235 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
6716169 AATAAATAAT
6716179 AAAATAATATTAAAATTATATA
1 AAAATAATATTAAAATTATATA
* *
6716201 ATAATAATTTTAAAAATTA-ATTA
1 AAAATAATATT-AAAATTATA-TA
*
6716224 AAAATAAAATTA
1 AAAATAATATTA
6716236 TCTTTTCACT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
22 11 0.39
23 17 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATAATATTAAAATTATATA
Found at i:6731072 original size:23 final size:20
Alignment explanation
Indices: 6731044--6731088 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
6731034 AAAATTATTT
6731044 AATTTAAAATAAAGATATATAAA
1 AATTT-AAATAAAG-TA-ATAAA
*
6731067 AATTTAATTAAAGTAATAAA
1 AATTTAAATAAAGTAATAAA
6731087 AA
1 AA
6731089 AGAATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 2 0.10
22 7 0.33
23 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (20 bp):
AATTTAAATAAAGTAATAAA
Found at i:6738875 original size:30 final size:31
Alignment explanation
Indices: 6738813--6738882 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
6738803 ATTTGTGTAG
*
6738813 CAAAATTAAAAGAATAAAAACTTTTTGGATA
1 CAAAATTAAAAGAATAAAAACTTTTTGAATA
*
6738844 C-AAATTAAAAG-ATGAGAAA-TTTTGTGAATA
1 CAAAATTAAAAGAAT-AAAAACTTTT-TGAATA
6738874 CAAAATTAA
1 CAAAATTAA
6738883 TTGTATTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 6 0.18
30 20 0.59
31 8 0.24
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (31 bp):
CAAAATTAAAAGAATAAAAACTTTTTGAATA
Found at i:6749671 original size:22 final size:22
Alignment explanation
Indices: 6749634--6749680 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
6749624 TCATTATAAA
*
6749634 AATCGATTTTTCTTATAAATATG
1 AATCGATTTTTATTATAAAT-TG
*
6749657 AATCGA-TTTTATTATATATTG
1 AATCGATTTTTATTATAAATTG
6749678 AAT
1 AAT
6749681 TATATCGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 11 0.50
23 6 0.27
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (22 bp):
AATCGATTTTTATTATAAATTG
Found at i:6750597 original size:4 final size:4
Alignment explanation
Indices: 6750588--6750624 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
6750578 AAATAAACGG
6750588 TATT TATT TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT T
6750625 TCTCATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:6755569 original size:22 final size:23
Alignment explanation
Indices: 6755535--6755578 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
6755525 AAAGCTCCCC
*
6755535 AACAGAAATAGAGG-TGATGGTTA
1 AACAGAAAGAGAGGATG-TGGTTA
6755558 AACA-AAAGAGAGGATGTGGTT
1 AACAGAAAGAGAGGATGTGGTT
6755579 CAAAACCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.43, C:0.05, G:0.32, T:0.20
Consensus pattern (23 bp):
AACAGAAAGAGAGGATGTGGTTA
Found at i:6756413 original size:11 final size:12
Alignment explanation
Indices: 6756383--6756428 Score: 53
Period size: 11 Copynumber: 4.0 Consensus size: 12
6756373 TAAAATTTTA
6756383 TAAT-TAATTAT
1 TAATATAATTAT
*
6756394 TAATTTAATT-T
1 TAATATAATTAT
6756405 TAATATAATATAT
1 TAATATAAT-TAT
6756418 TAATAT-ATTAT
1 TAATATAATTAT
6756429 AATTAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 16 0.52
12 8 0.26
13 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TAATATAATTAT
Found at i:6756431 original size:18 final size:18
Alignment explanation
Indices: 6756408--6756447 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
6756398 TTAATTTTAA
*
6756408 TATAATATATTAATAT-AT
1 TATAAT-TAATAATATAAT
6756426 TATAATTAATAATATAAT
1 TATAATTAATAATATAAT
6756444 TATA
1 TATA
6756448 TAATATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATAATTAATAATATAAT
Found at i:6760213 original size:55 final size:55
Alignment explanation
Indices: 6760126--6760240 Score: 194
Period size: 55 Copynumber: 2.1 Consensus size: 55
6760116 TGTATCATGC
* *
6760126 CAAATATGAGATCAAGTGACACCTGATCTCCATATGGATACCGTACGCATTTGCT
1 CAAATATGAGATCAAGTGACACCTGATATCCATATGGATACCATACGCATTTGCT
* *
6760181 CAAATATGAGGTCAAGTGACACGTGATATCCATATGGATACCATACGCATTTGCT
1 CAAATATGAGATCAAGTGACACCTGATATCCATATGGATACCATACGCATTTGCT
6760236 CAAAT
1 CAAAT
6760241 GCCTTACAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (55 bp):
CAAATATGAGATCAAGTGACACCTGATATCCATATGGATACCATACGCATTTGCT
Found at i:6760491 original size:18 final size:20
Alignment explanation
Indices: 6760455--6760492 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6760445 TAATACTTAA
*
6760455 AAAAAAATTATGAATTATTT
1 AAAAAAATTATGAAATATTT
6760475 AAAAAAATT-T-AAATATTT
1 AAAAAAATTATGAAATATTT
6760493 TTTATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
AAAAAAATTATGAAATATTT
Found at i:6760540 original size:26 final size:29
Alignment explanation
Indices: 6760483--6760541 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
6760473 TTAAAAAAAT
* *
6760483 TTAAATATTTTTTATTTTTATAATATTTAA
1 TTAAATATTTTATATTTTTAT-ATATTAAA
6760513 TTAAAT-TTTTATATTTTTAT-T-TTAAA
1 TTAAATATTTTATATTTTTATATATTAAA
6760539 TTA
1 TTA
6760542 GATAAACTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 7 0.26
27 1 0.04
29 13 0.48
30 6 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (29 bp):
TTAAATATTTTATATTTTTATATATTAAA
Found at i:6766982 original size:29 final size:29
Alignment explanation
Indices: 6766927--6766981 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
6766917 CCGTTTATTA
* *
6766927 TAAATATTTATTTAATTAAAAATAAAATG
1 TAAATATTTAATTAAATAAAAATAAAATG
*
6766956 TAAATATTTAATTAAAT-ATAATAAAA
1 TAAATATTTAATTAAATAAAAATAAAA
6766982 AATAAGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
TAAATATTTAATTAAATAAAAATAAAATG
Found at i:6774417 original size:2 final size:2
Alignment explanation
Indices: 6774399--6774449 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
6774389 TGCATCTGAT
* * * *
6774399 TA TA CA TA TA TA CA TA TA TA TA CA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6774441 TA TA TA TA T
1 TA TA TA TA T
6774450 TGTCAAATCT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:6779556 original size:24 final size:25
Alignment explanation
Indices: 6779523--6779577 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
6779513 TAAATATCCG
6779523 TTTATATTTAA-GCATCTAAGATATT
1 TTTATATTTAATG-ATCTAAGATATT
*
6779548 TTTA-ATTTAATTGATTTAAGATATT
1 TTTATATTTAA-TGATCTAAGATATT
6779573 TTTAT
1 TTTAT
6779578 CACTATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
24 6 0.23
25 19 0.73
26 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.55
Consensus pattern (25 bp):
TTTATATTTAATGATCTAAGATATT
Found at i:6780073 original size:17 final size:17
Alignment explanation
Indices: 6780048--6780085 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
6780038 TAAAGGGTAA
6780048 TATTAAAAAAATT-ATAT
1 TATT-AAAAAATTGATAT
*
6780065 TATTGAAAAATTGATAT
1 TATTAAAAAATTGATAT
6780082 TATT
1 TATT
6780086 TCGAGACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (17 bp):
TATTAAAAAATTGATAT
Found at i:6780075 original size:16 final size:17
Alignment explanation
Indices: 6780054--6780085 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6780044 GTAATATTAA
6780054 AAAAATT-ATATTATTG
1 AAAAATTGATATTATTG
6780070 AAAAATTGATATTATT
1 AAAAATTGATATTATT
6780086 TCGAGACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
AAAAATTGATATTATTG
Found at i:6783945 original size:96 final size:96
Alignment explanation
Indices: 6783781--6783970 Score: 317
Period size: 96 Copynumber: 2.0 Consensus size: 96
6783771 TTCAAGACCC
*
6783781 AAGTGGAACAGGAAAAGTTCATAAAAACATAAAGCATAAGTTTCAGAAACCAAGACATAGAATGC
1 AAGTGGAACAGGAAAAGTTCATAAAAACATAAAGCATAAGTTTCAGAAACCAAGACATAGAACGC
6783846 TAACAATTAAGGATTTGTTTGGTTGTTACCG
66 TAACAATTAAGGATTTGTTTGGTTGTTACCG
* * * * *
6783877 AAGTGGAACAGGAAAATTTCATAAGAACATAGAGCATAAGTTTCGGAAACCAAGACATAGAGCGC
1 AAGTGGAACAGGAAAAGTTCATAAAAACATAAAGCATAAGTTTCAGAAACCAAGACATAGAACGC
*
6783942 TAACAATTTAGGATTTGTTTGGTTGTTAC
66 TAACAATTAAGGATTTGTTTGGTTGTTAC
6783971 TTTGTTTACT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 87 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.26
Consensus pattern (96 bp):
AAGTGGAACAGGAAAAGTTCATAAAAACATAAAGCATAAGTTTCAGAAACCAAGACATAGAACGC
TAACAATTAAGGATTTGTTTGGTTGTTACCG
Found at i:6788661 original size:20 final size:21
Alignment explanation
Indices: 6788620--6788676 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
6788610 TTGATTTCAC
* * *
6788620 TTAAATACAAGGAAATT-TTT
1 TTAAATATAATGAAATTAATT
6788640 TTAAATAT-ATGAAATTAATT
1 TTAAATATAATGAAATTAATT
**
6788660 TTTCATATAATGAAATT
1 TTAAATATAATGAAATT
6788677 TATCAAGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 7 0.23
20 15 0.50
21 8 0.27
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.44
Consensus pattern (21 bp):
TTAAATATAATGAAATTAATT
Found at i:6790480 original size:31 final size:29
Alignment explanation
Indices: 6790411--6790488 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
6790401 NNNNNNNNNT
*
6790411 AATATCCACAATAGCTAAACAAGATATAA
1 AATATCCATAATAGCTAAACAAGATATAA
* *
6790440 AGTATCCATAGAT-GCTAAGCAAGATATATTA
1 AATATCCATA-ATAGCTAAACAAGATATA--A
*
6790471 AATATCCATAATAACTAA
1 AATATCCATAATAGCTAA
6790489 CACATAATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 22 0.55
30 4 0.10
31 14 0.35
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (29 bp):
AATATCCATAATAGCTAAACAAGATATAA
Found at i:6791703 original size:28 final size:28
Alignment explanation
Indices: 6791671--6791744 Score: 148
Period size: 28 Copynumber: 2.6 Consensus size: 28
6791661 ACCTAGGAAA
6791671 TTTGATTTGAGAGATGTCTAAAGGGAGC
1 TTTGATTTGAGAGATGTCTAAAGGGAGC
6791699 TTTGATTTGAGAGATGTCTAAAGGGAGC
1 TTTGATTTGAGAGATGTCTAAAGGGAGC
6791727 TTTGATTTGAGAGATGTC
1 TTTGATTTGAGAGATGTC
6791745 GTGATGAAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.27, C:0.07, G:0.31, T:0.35
Consensus pattern (28 bp):
TTTGATTTGAGAGATGTCTAAAGGGAGC
Found at i:6794628 original size:4 final size:4
Alignment explanation
Indices: 6794619--6794644 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
6794609 CATTGAATAT
6794619 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
6794645 GTCATGAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:6802100 original size:13 final size:14
Alignment explanation
Indices: 6802077--6802105 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6802067 GGGGACTCAT
6802077 TTTGTTATTAATTA
1 TTTGTTATTAATTA
6802091 TTTG-TATTAATTA
1 TTTGTTATTAATTA
6802104 TT
1 TT
6802106 AAATTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTGTTATTAATTA
Found at i:6802302 original size:3 final size:3
Alignment explanation
Indices: 6802294--6802319 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6802284 TGTTAAATTA
6802294 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
6802320 AGTGTGGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6802988 original size:36 final size:38
Alignment explanation
Indices: 6802903--6802988 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 38
6802893 TTTGATGAAT
*
6802903 ATTAATATTTAACTTAAAATATTAACAAAATTAAAAAT
1 ATTAATATTTAACTTAAAATATTAACAAAATTAAAAAC
****
6802941 ATTAATATTTAACTTAAAAT-TTTTTTAAATT-AAAAC
1 ATTAATATTTAACTTAAAATATTAACAAAATTAAAAAC
6802977 ATTAATATTTAA
1 ATTAATATTTAA
6802989 ATTATTCAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 16 0.37
37 7 0.16
38 20 0.47
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (38 bp):
ATTAATATTTAACTTAAAATATTAACAAAATTAAAAAC
Found at i:6808524 original size:22 final size:18
Alignment explanation
Indices: 6808480--6808516 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
6808470 TCTCTGCTAT
6808480 CATATGCATAAATAAGAA
1 CATATGCATAAATAAGAA
6808498 CATATGCATAAATAAGAA
1 CATATGCATAAATAAGAA
6808516 C
1 C
6808517 GAGAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.22
Consensus pattern (18 bp):
CATATGCATAAATAAGAA
Found at i:6808923 original size:13 final size:13
Alignment explanation
Indices: 6808905--6808929 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6808895 GTTTTGGACT
6808905 AATTAAAAAATTC
1 AATTAAAAAATTC
6808918 AATTAAAAAATT
1 AATTAAAAAATT
6808930 TGGTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AATTAAAAAATTC
Found at i:6809339 original size:12 final size:12
Alignment explanation
Indices: 6809308--6809347 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
6809298 TTCTTCCAAA
*
6809308 CATACATACATA
1 CATACATACATG
6809320 CATACATACATG
1 CATACATACATG
* *
6809332 CATGCATATATG
1 CATACATACATG
6809344 CATA
1 CATA
6809348 TATGGAACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (12 bp):
CATACATACATG
Found at i:6810003 original size:15 final size:15
Alignment explanation
Indices: 6809985--6810013 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6809975 TTTTTTAATT
6809985 TTATTTTTTAAAAAA
1 TTATTTTTTAAAAAA
6810000 TTATTTTTTAAAAA
1 TTATTTTTTAAAAA
6810014 TATTTATTTA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATTTTTTAAAAAA
Found at i:6810023 original size:14 final size:14
Alignment explanation
Indices: 6809985--6810023 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
6809975 TTTTTTAATT
6809985 TTATTTTTTAAAAAA
1 TTATTTTTT-AAAAA
6810000 TTATTTTTTAAAAA
1 TTATTTTTTAAAAA
6810014 -TATTTATTTA
1 TTATTT-TTTA
6810024 GTTTGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.22
14 9 0.39
15 9 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTTTTAAAAA
Found at i:6811398 original size:42 final size:41
Alignment explanation
Indices: 6811351--6811434 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 41
6811341 TATACATTTT
* ** *
6811351 TAATGTGTAATTATTTGTGTATATTTATATATATGTAATGTA
1 TAATGTGTAATTATTTATGTATACATATATATATAT-ATGTA
6811393 TAATGTGTAATTATTTATGTATACATATATATATATATGTA
1 TAATGTGTAATTATTTATGTATACATATATATATATATGTA
6811434 T
1 T
6811435 GTACGGACGT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
41 6 0.16
42 32 0.84
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.51
Consensus pattern (41 bp):
TAATGTGTAATTATTTATGTATACATATATATATATATGTA
Found at i:6811403 original size:14 final size:13
Alignment explanation
Indices: 6811351--6811406 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 13
6811341 TATACATTTT
6811351 TAATGTGTAATTA
1 TAATGTGTAATTA
*
6811364 T-TTGTGTATATTTA
1 TAATGTGTA-A-TTA
*
6811378 TATATATGTAATGTA
1 TA-ATGTGTAAT-TA
6811393 TAATGTGTAATTA
1 TAATGTGTAATTA
6811406 T
1 T
6811407 TTATGTATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
12 6 0.18
13 5 0.15
14 13 0.38
15 5 0.15
16 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (13 bp):
TAATGTGTAATTA
Found at i:6819834 original size:1 final size:1
Alignment explanation
Indices: 6819830--6819898 Score: 138
Period size: 1 Copynumber: 69.0 Consensus size: 1
6819820 CTCCCCCTCA
6819830 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
6819895 CCCC
1 CCCC
6819899 AAAAAAAAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:6828975 original size:2 final size:2
Alignment explanation
Indices: 6828968--6829001 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6828958 CTCCCCTTTC
6828968 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6829002 TCCGTTTGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:6830708 original size:14 final size:14
Alignment explanation
Indices: 6830689--6830715 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6830679 TATTATAGTT
6830689 GCAATTTCTGAATC
1 GCAATTTCTGAATC
6830703 GCAATTTCTGAAT
1 GCAATTTCTGAAT
6830716 ACAAAACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (14 bp):
GCAATTTCTGAATC
Found at i:6840127 original size:48 final size:47
Alignment explanation
Indices: 6840056--6840151 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 47
6840046 TATATTTACC
6840056 AAAAGATTGTTTGGGAAAATGGTGAAAGAAAGGAAAAAAAGTTTAAAT
1 AAAAGATTGTTTGGGAAAATGGTGAAAGAAAGG-AAAAAAGTTTAAAT
*
6840104 AAAAGATTGTTTGGGAAAATGGTGCAAGAAAGGAAAAAAGTTTAAAT
1 AAAAGATTGTTTGGGAAAATGGTGAAAGAAAGGAAAAAAGTTTAAAT
6840151 A
1 A
6840152 TAGCATTCCA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 15 0.32
48 32 0.68
ACGTcount: A:0.51, C:0.01, G:0.25, T:0.23
Consensus pattern (47 bp):
AAAAGATTGTTTGGGAAAATGGTGAAAGAAAGGAAAAAAGTTTAAAT
Found at i:6844867 original size:19 final size:19
Alignment explanation
Indices: 6844830--6844873 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
6844820 CCACCATCAA
* *
6844830 TTTTGATGAATAATCTTTT
1 TTTTTATGAATAATATTTT
*
6844849 TTTTTATGAATATTATTTT
1 TTTTTATGAATAATATTTT
*
6844868 ATTTTA
1 TTTTTA
6844874 AAATTATCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (19 bp):
TTTTTATGAATAATATTTT
Found at i:6851910 original size:53 final size:53
Alignment explanation
Indices: 6851830--6851935 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
6851820 TTACTCTTAG
*
6851830 GGCATATGGCAAATCTGGCAGTTTAATTAATTAGCTACATCTTTATAGCAACA
1 GGCATATGGCAAATCTGGCAGTTTAATTAATTAGCAACATCTTTATAGCAACA
6851883 GGCATATGGCAAATCTGGCAGTTTAATTAATTAGCAACATCTTTATAGCAACA
1 GGCATATGGCAAATCTGGCAGTTTAATTAATTAGCAACATCTTTATAGCAACA
6851936 TAGGTTAGAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (53 bp):
GGCATATGGCAAATCTGGCAGTTTAATTAATTAGCAACATCTTTATAGCAACA
Found at i:6857612 original size:2 final size:2
Alignment explanation
Indices: 6857605--6857638 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6857595 AACATGGTAG
6857605 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6857639 TCTGTTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6862415 original size:25 final size:25
Alignment explanation
Indices: 6862387--6862467 Score: 79
Period size: 25 Copynumber: 3.6 Consensus size: 25
6862377 AAAATTTTGA
6862387 TTAAGCCTTTTAATGTAACTATTGC
1 TTAAGCCTTTTAATGTAACTATTGC
**
6862412 TTAAGCC---TAAT-TAAAAATT--
1 TTAAGCCTTTTAATGTAACTATTGC
*
6862431 TT--GCTTTTTAATGTAACTATTGC
1 TTAAGCCTTTTAATGTAACTATTGC
6862454 TTAAGCCTTTTAAT
1 TTAAGCCTTTTAAT
6862468 CTTCAATTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
17 2 0.05
19 2 0.05
20 4 0.10
21 12 0.29
22 4 0.10
23 2 0.05
25 16 0.38
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.46
Consensus pattern (25 bp):
TTAAGCCTTTTAATGTAACTATTGC
Found at i:6868848 original size:18 final size:18
Alignment explanation
Indices: 6868815--6868849 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6868805 CTTTCGTTTC
*
6868815 TTTTCCTTATCTTTCTTT
1 TTTTCCTTATCCTTCTTT
*
6868833 TTTTCCTTGTCCTTCTT
1 TTTTCCTTATCCTTCTT
6868850 CTTCTTCTCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.26, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTCCTTATCCTTCTTT
Found at i:6880446 original size:63 final size:63
Alignment explanation
Indices: 6880295--6880483 Score: 265
Period size: 63 Copynumber: 3.0 Consensus size: 63
6880285 GAAGAAACAA
* *
6880295 AAGACAACAATTTTGGGTTCCCTTGGTCATCTCTGACTCCCACTTGAAAC-CATTTGATTGTT
1 AAGACAACAATTTTGTGTTCCCTTGGTCATCTCTAACTCCCACTTGAAACACATTTGATTGTT
* * * ** *
6880357 ACA-AAAAGAATTTTGTGTTCCATTGGTTGTCTCTAACTCCCACTTAAAACACATTTGATTGTT
1 A-AGACAACAATTTTGTGTTCCCTTGGTCATCTCTAACTCCCACTTGAAACACATTTGATTGTT
* *
6880420 AAGACAACAATTTTGTGCTCCCTTGGTCATCTCTAACTCCCACTTGAAACACATTTAATTGTT
1 AAGACAACAATTTTGTGTTCCCTTGGTCATCTCTAACTCCCACTTGAAACACATTTGATTGTT
6880483 A
1 A
6880484 TTTTTGCCAC
Statistics
Matches: 108, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
62 41 0.38
63 67 0.62
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (63 bp):
AAGACAACAATTTTGTGTTCCCTTGGTCATCTCTAACTCCCACTTGAAACACATTTGATTGTT
Found at i:6881975 original size:29 final size:29
Alignment explanation
Indices: 6881940--6882006 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
6881930 GCACTAACAC
6881940 ATCTTTTCTTTCTTTGACAAGCAACAGAT
1 ATCTTTTCTTTCTTTGACAAGCAACAGAT
*
6881969 ATCTTTTCTTTTTTTGACAAGCAACAGAT
1 ATCTTTTCTTTCTTTGACAAGCAACAGAT
6881998 ATCTTTTCT
1 ATCTTTTCT
6882007 GCTAAAGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.46
Consensus pattern (29 bp):
ATCTTTTCTTTCTTTGACAAGCAACAGAT
Found at i:6883287 original size:32 final size:32
Alignment explanation
Indices: 6883242--6883309 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
6883232 TGTGTGTCCT
6883242 TACA-AGTGATAATTTCATTTTGAGAAAACAC
1 TACAGAGTGATAATTTCATTTTGAGAAAACAC
6883273 TACAGAGTGATAATTTCATTTTGAGAAAACAC
1 TACAGAGTGATAATTTCATTTTGAGAAAACAC
6883305 TACAG
1 TACAG
6883310 CAGGATTAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 4 0.11
32 32 0.89
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (32 bp):
TACAGAGTGATAATTTCATTTTGAGAAAACAC
Found at i:6892661 original size:27 final size:27
Alignment explanation
Indices: 6892560--6892661 Score: 73
Period size: 27 Copynumber: 3.7 Consensus size: 27
6892550 AAAAAAAATC
* * * *
6892560 ATATTGAAAATATAATTGTTACACTTA
1 ATATTGAAAATTTAGTTATTACACATA
* * *
6892587 ATATTGAAAATTTAGTTATTATATATC
1 ATATTGAAAATTTAGTTATTACACATA
** *
6892614 ACGTTGAAAAATGTAAG-TATTACACACT-
1 ATATTG-AAAAT-TTAGTTATTACACA-TA
6892642 ATATTGAAAATTTAGTTATT
1 ATATTGAAAATTTAGTTATT
6892662 GCACGTCATA
Statistics
Matches: 56, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
26 3 0.05
27 33 0.59
28 16 0.29
29 4 0.07
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (27 bp):
ATATTGAAAATTTAGTTATTACACATA
Found at i:6892679 original size:55 final size:55
Alignment explanation
Indices: 6892587--6892690 Score: 127
Period size: 55 Copynumber: 1.9 Consensus size: 55
6892577 GTTACACTTA
* * * * *
6892587 ATATTGAAAATTTAGTTATTATATATCACGTTGAAAAATGTAAGTATTACACACT
1 ATATTGAAAATTTAGTTATTACACATCACATTAAAAAATATAAGTATTACACACT
* * * *
6892642 ATATTGAAAATTTAGTTATTGCACGTCATATTAAAAAATATAATTATTA
1 ATATTGAAAATTTAGTTATTACACATCACATTAAAAAATATAAGTATTA
6892691 TATATTATGT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 40 1.00
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (55 bp):
ATATTGAAAATTTAGTTATTACACATCACATTAAAAAATATAAGTATTACACACT
Found at i:6892707 original size:55 final size:56
Alignment explanation
Indices: 6892648--6892792 Score: 157
Period size: 55 Copynumber: 2.6 Consensus size: 56
6892638 CACTATATTG
* * *
6892648 AAAATTTAGTTATTGCACGTCATATTAAAAAATATAATTATTATATATTATGTT-A
1 AAAATTTAATTATTACACGTCATATTAAAAAATATAATTATTACATATTATGTTAA
* ** * * * *
6892703 AAAATTTAATTGTTACATTTCATGTTAAAAAATTTAATTGTTACATGTTATGTTAA
1 AAAATTTAATTATTACACGTCATATTAAAAAATATAATTATTACATATTATGTTAA
* * *
6892759 AAAATTTAATTGTTACACGTTATAATGAAAAAAT
1 AAAATTTAATTATTACACGTCAT-ATTAAAAAAT
6892793 TGTTATACAC
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
55 44 0.60
56 21 0.29
57 8 0.11
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (56 bp):
AAAATTTAATTATTACACGTCATATTAAAAAATATAATTATTACATATTATGTTAA
Found at i:6892713 original size:27 final size:27
Alignment explanation
Indices: 6892672--6892775 Score: 147
Period size: 28 Copynumber: 3.8 Consensus size: 27
6892662 GCACGTCATA
* * *
6892672 TTAAAAAATATAATTATTATATATTATG
1 TTAAAAAATTTAATTGTTACAT-TTATG
6892700 TT-AAAAATTTAATTGTTACATTTCATG
1 TTAAAAAATTTAATTGTTACATTT-ATG
6892727 TTAAAAAATTTAATTGTTACATGTTATG
1 TTAAAAAATTTAATTGTTACAT-TTATG
6892755 TTAAAAAATTTAATTGTTACA
1 TTAAAAAATTTAATTGTTACA
6892776 CGTTATAATG
Statistics
Matches: 70, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
26 2 0.03
27 21 0.30
28 45 0.64
29 2 0.03
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (27 bp):
TTAAAAAATTTAATTGTTACATTTATG
Found at i:6892780 original size:28 final size:28
Alignment explanation
Indices: 6892648--6892781 Score: 137
Period size: 28 Copynumber: 4.8 Consensus size: 28
6892638 CACTATATTG
* * * * *
6892648 AAAATTTAGTTATTGCACGTCATATTAA
1 AAAATTTAATTGTTACACGTTATGTTAA
* * * **
6892676 AAAATATAATTATTATATATTATGTT-A
1 AAAATTTAATTGTTACACGTTATGTTAA
*
6892703 AAAATTTAATTGTTACA-TTTCATGTTAA
1 AAAATTTAATTGTTACACGTT-ATGTTAA
*
6892731 AAAATTTAATTGTTACATGTTATGTTAA
1 AAAATTTAATTGTTACACGTTATGTTAA
6892759 AAAATTTAATTGTTACACGTTAT
1 AAAATTTAATTGTTACACGTTAT
6892782 AATGAAAAAA
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
26 2 0.02
27 20 0.22
28 65 0.73
29 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (28 bp):
AAAATTTAATTGTTACACGTTATGTTAA
Found at i:6894004 original size:20 final size:20
Alignment explanation
Indices: 6893972--6894011 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6893962 ATAAAATTTT
6893972 ATTTAAATATTA-TTAAATA
1 ATTTAAATATTATTTAAATA
*
6893991 ATTTAAAATTTTATTTAAATA
1 ATTT-AAATATTATTTAAATA
6894012 GTATACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 7 0.39
21 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTAAATATTATTTAAATA
Found at i:6908568 original size:18 final size:19
Alignment explanation
Indices: 6908547--6908586 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
6908537 TAAAATATTA
6908547 ATAATTATA-TAAATAAAT
1 ATAATTATATTAAATAAAT
*
6908565 ATAATTATATTTAATAAAT
1 ATAATTATATTAAATAAAT
6908584 ATA
1 ATA
6908587 TAACACGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAATTATATTAAATAAAT
Found at i:6908587 original size:31 final size:29
Alignment explanation
Indices: 6908530--6908589 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
6908520 TCACTGTTAC
*
6908530 ATAAATATAAAATATTAATAATTATATAA
1 ATAAATATAAAATATTAATAAATATATAA
*
6908559 ATAAATATAATTATATTTAATAAATATATAA
1 ATAAATATAA-AATA-TTAATAAATATATAA
6908590 CACGATATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 3 0.11
31 14 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
ATAAATATAAAATATTAATAAATATATAA
Found at i:6909290 original size:19 final size:20
Alignment explanation
Indices: 6909258--6909296 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
6909248 ACATAACATT
*
6909258 TAAAAATTCATAAATTATTTA
1 TAAAAATT-ATAAATAATTTA
6909279 TAAAAATT-TAAATAATTT
1 TAAAAATTATAAATAATTT
6909297 TTTATATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAAAATTATAAATAATTTA
Found at i:6909367 original size:30 final size:30
Alignment explanation
Indices: 6909321--6909392 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
6909311 ATATTTAATA
* * *
6909321 AAATATTTATATTTTTACTTTAGATAAAAT
1 AAATTTTTATAATTTTACTTTAAATAAAAT
* *
6909351 AAATTTTTATAATTTTATTTTAAATTAAAT
1 AAATTTTTATAATTTTACTTTAAATAAAAT
6909381 AAATTTTTATAA
1 AAATTTTTATAA
6909393 CTAATAATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (30 bp):
AAATTTTTATAATTTTACTTTAAATAAAAT
Found at i:6909500 original size:22 final size:24
Alignment explanation
Indices: 6909473--6909523 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
6909463 ACGAACATAA
*
6909473 AATAATAAGTAAT-AATT-TTATT
1 AATAATAAGTAATCAATTGTTAAT
*
6909495 AATAATAATTAATCAATTGTTAAT
1 AATAATAAGTAATCAATTGTTAAT
6909519 AATAA
1 AATAA
6909524 AAACTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 12 0.48
23 4 0.16
24 9 0.36
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (24 bp):
AATAATAAGTAATCAATTGTTAAT
Found at i:6910207 original size:20 final size:21
Alignment explanation
Indices: 6910179--6910262 Score: 97
Period size: 20 Copynumber: 4.2 Consensus size: 21
6910169 ATAATGTTAT
*
6910179 AATTAAAATAAAAAATATTAA
1 AATTAAAATATAAAATATTAA
*
6910200 AA-TAAAATATATAATA-TAA
1 AATTAAAATATAAAATATTAA
*
6910219 AATTAAAA-ATTAAAAT-TAAA
1 AATTAAAATA-TAAAATATTAA
6910239 AATTAAAAT-TAAAATATTAA
1 AATTAAAATATAAAATATTAA
6910259 AATT
1 AATT
6910263 TATATAACAT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
19 12 0.23
20 39 0.74
21 2 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AATTAAAATATAAAATATTAA
Found at i:6910218 original size:14 final size:14
Alignment explanation
Indices: 6910185--6910309 Score: 55
Period size: 13 Copynumber: 8.6 Consensus size: 14
6910175 TTATAATTAA
*
6910185 AATAAAAAATAT-T
1 AATATAAAATATAT
*
6910198 AAAATAAAATATAT
1 AATATAAAATATAT
6910212 AATATAAAAT-TA-
1 AATATAAAATATAT
*
6910224 AAAATTAAAAT-TA-
1 AATA-TAAAATATAT
* *
6910237 AAAATTAAAAT-TAA
1 AATA-TAAAATATAT
6910251 AATATTAAAATTTATAT
1 AATA-TAAAA--TATAT
*
6910268 AACATAAGTAAAATAAATT
1 -A-AT-A-TAAAATATA-T
*
6910287 AAAATAAAATATAT
1 AATATAAAATATAT
6910301 AATATAAAA
1 AATATAAAA
6910310 AATTATATTA
Statistics
Matches: 91, Mismatches: 11, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
12 3 0.03
13 33 0.36
14 28 0.31
15 8 0.09
16 2 0.02
17 3 0.03
18 5 0.05
19 3 0.03
20 6 0.07
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (14 bp):
AATATAAAATATAT
Found at i:6910343 original size:19 final size:19
Alignment explanation
Indices: 6910282--6910344 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
6910272 TAAGTAAAAT
* *
6910282 AAATTAAAATAAAATATAT
1 AAATAAAAATAAAATATAG
* * *
6910301 AATATAAAAAATTATATTAAAG
1 AA-AT-AAAAA-TAAAATATAG
6910323 AAATAAAAATAAAATATAG
1 AAATAAAAATAAAATATAG
6910342 AAA
1 AAA
6910345 ATTATAATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 12 0.36
20 7 0.21
21 6 0.18
22 8 0.24
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (19 bp):
AAATAAAAATAAAATATAG
Found at i:6910346 original size:20 final size:19
Alignment explanation
Indices: 6910190--6910369 Score: 80
Period size: 20 Copynumber: 8.9 Consensus size: 19
6910180 ATTAAAATAA
*
6910190 AAAATATTAAAATAAAATAT
1 AAAATATAAAAATAAAA-AT
* *
6910210 ATAATATAAAATTAAAAATT
1 AAAATATAAAAATAAAAA-T
*
6910230 AAAAT-TAAAAATTAAAATT
1 AAAATATAAAAA-TAAAAAT
*
6910249 AAAATATTAAAATTTATATAACAT
1 AAAATA-TAAAA---ATA-AAAAT
* * *
6910273 -AAGTAAAATAAATTAAAAT
1 AAAATATAA-AAATAAAAAT
*
6910292 AAAATATATAATATAAAAA-
1 AAAATATA-AAAATAAAAAT
**
6910311 ATTATATTAAAGAAATAAAAAT
1 AAAATA-T-AA-AAATAAAAAT
* *
6910333 AAAATATAGAAAATTATAAT
1 AAAATATA-AAAATAAAAAT
6910353 AATAA-ATAAAAATAAAA
1 AA-AATATAAAAATAAAA
6910370 TATATGACAT
Statistics
Matches: 118, Mismatches: 25, Indels: 35
0.66 0.14 0.20
Matches are distributed among these distances:
19 27 0.23
20 54 0.46
21 19 0.16
22 6 0.05
23 8 0.07
24 4 0.03
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATATAAAAATAAAAAT
Found at i:6910365 original size:33 final size:34
Alignment explanation
Indices: 6910288--6910373 Score: 120
Period size: 33 Copynumber: 2.5 Consensus size: 34
6910278 AAATAAATTA
* *
6910288 AAATAAAATATATAATATAAAAAATTATATTAAAG
1 AAATAAAA-ATAAAATATAAAAAATTATAATAAAG
* *
6910323 AAATAAAAATAAAATATAGAAAATTATAAT-AAT
1 AAATAAAAATAAAATATAAAAAATTATAATAAAG
6910356 AAATAAAAATAAAATATA
1 AAATAAAAATAAAATATA
6910374 TGACATTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
33 20 0.43
34 19 0.40
35 8 0.17
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (34 bp):
AAATAAAAATAAAATATAAAAAATTATAATAAAG
Found at i:6910365 original size:84 final size:85
Alignment explanation
Indices: 6910175--6910368 Score: 204
Period size: 84 Copynumber: 2.3 Consensus size: 85
6910165 TTTTATAATG
* *
6910175 TTATAATTA-AAATAAAAA-ATATTAAAATAAAATATATAATATAAAATTAAAAATTAAAATTAA
1 TTATAATAATAAATAAAAATAAATTAAAATAAAATATATAATAT--AA-TAAAAATTAAAATTAA
* * *
6910238 AAATTAAAATTAAAATATTAAAA
63 AAAATAAAAATAAAATATGAAAA
* *
6910261 TT-TATATAACATAAGT-AAAATAAATTAAAATAAAATATATAATAT-A-AAAAATT-ATATTAA
1 TTATA-AT-A-ATAAATAAAAATAAATTAAAATAAAATATATAATATAATAAAAATTAAAATTAA
6910321 AGAAATAAAAATAAAATATAGAAAA
63 A-AAATAAAAATAAAATAT-GAAAA
6910346 TTATAATAATAAATAAAAATAAA
1 TTATAATAATAAATAAAAATAAA
6910369 ATATATGACA
Statistics
Matches: 91, Mismatches: 8, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
83 12 0.13
84 31 0.34
85 10 0.11
86 7 0.08
88 5 0.05
89 26 0.29
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.31
Consensus pattern (85 bp):
TTATAATAATAAATAAAAATAAATTAAAATAAAATATATAATATAATAAAAATTAAAATTAAAAA
ATAAAAATAAAATATGAAAA
Found at i:6910369 original size:89 final size:88
Alignment explanation
Indices: 6910182--6910371 Score: 205
Period size: 89 Copynumber: 2.1 Consensus size: 88
6910172 ATGTTATAAT
*
6910182 TAAAATAAAA-AATATTAAAATAAAATATATAATATAAAATTAAAAATTAAAATTAAAAATTAAA
1 TAAAATAAAATAATATTAAAATAAAATATATAATAT--AA-TAAAAATTAAAATTAAAAAATAAA
* *
6910246 ATTAAAATATTAAAATTTATATAACA
63 AATAAAATATGAAAATTTATATAACA
* *
6910272 T-AAGTAAAATAA-ATTAAAATAAAATATATAATAT-A-AAAAATT-ATATTAAAGAAATAAAAA
1 TAAAATAAAATAATATTAAAATAAAATATATAATATAATAAAAATTAAAATTAAA-AAATAAAAA
6910332 TAAAATATAGAAAATTATAATAATAA-A
65 TAAAATAT-GAAAATT-T-AT-ATAACA
6910359 TAAAAATAAAATA
1 T-AAAATAAAATA
6910372 TATGACATTA
Statistics
Matches: 86, Mismatches: 6, Indels: 17
0.79 0.06 0.16
Matches are distributed among these distances:
83 7 0.08
84 22 0.26
85 6 0.07
86 2 0.02
87 4 0.05
88 4 0.05
89 38 0.44
90 3 0.03
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.30
Consensus pattern (88 bp):
TAAAATAAAATAATATTAAAATAAAATATATAATATAATAAAAATTAAAATTAAAAAATAAAAAT
AAAATATGAAAATTTATATAACA
Found at i:6910617 original size:15 final size:15
Alignment explanation
Indices: 6910597--6910632 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
6910587 CCCTAAAATG
*
6910597 ACATTACTTGCAATC
1 ACATTACCTGCAATC
6910612 ACATTACCTGCAATC
1 ACATTACCTGCAATC
6910627 ACATTA
1 ACATTA
6910633 TATTATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.31
Consensus pattern (15 bp):
ACATTACCTGCAATC
Found at i:6913256 original size:2 final size:2
Alignment explanation
Indices: 6913251--6913287 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6913241 GTGTGTGTGT
6913251 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6913288 TTCTTCTGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6917160 original size:14 final size:16
Alignment explanation
Indices: 6917138--6917170 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
6917128 GATTTTAATT
6917138 ATAT-TTTTTCA-ATA
1 ATATGTTTTTCACATA
6917152 ATATGTTTTTCACATA
1 ATATGTTTTTCACATA
6917168 ATA
1 ATA
6917171 AAATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 7 0.41
16 6 0.35
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (16 bp):
ATATGTTTTTCACATA
Found at i:6923666 original size:158 final size:159
Alignment explanation
Indices: 6923353--6923651 Score: 381
Period size: 158 Copynumber: 1.9 Consensus size: 159
6923343 CCGGGATGTC
* *
6923353 GATTACTAAGGTGCCTTCCCAAATTGCCTTCACAATAAAGGGAGATCATCAGATGAATGAGATAA
1 GATTACTAAGGTGACTTCCCAAATTGCCTTCACAATAAAGGGAGATCATCAGATGAATGAGAGAA
* * *
6923418 TTACAATGAGTGGTAATATTATCAAAGACTCAAACATGCCATAAGCTTTCTAAAAGCTACATCCA
66 TTACAATGAGTGGCAATATTATCAAAGACTCAAACATGCCATAAACTTGCTAAAAGCTACATCCA
6923483 TTGACTCAAACCATGGTAAACAGCCACCT
131 TTGACTCAAACCATGGTAAACAGCCACCT
* * * * *
6923512 GATTACTAAGGTGACTTCCC-AATTGCCTTCATGAA-GAAGGGGGATCATTAGATGGATGAGAGA
1 GATTACTAAGGTGACTTCCCAAATTGCCTTCA-CAATAAAGGGAGATCATCAGATGAATGAGAGA
** * * * * *
6923575 ATTGTAATGAGTGGCCCA-ATTATCATAGGCTCAAACATGGCATAAACTTGCTAAATA-CTGCAT
65 ATTACAATGAGTGG-CAATATTATCAAAGACTCAAACATGCCATAAACTTGCTAAA-AGCTACAT
*
6923638 GCATTGACTCAAAC
128 CCATTGACTCAAAC
6923652 TGTGGTAAGA
Statistics
Matches: 119, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
158 96 0.81
159 23 0.19
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (159 bp):
GATTACTAAGGTGACTTCCCAAATTGCCTTCACAATAAAGGGAGATCATCAGATGAATGAGAGAA
TTACAATGAGTGGCAATATTATCAAAGACTCAAACATGCCATAAACTTGCTAAAAGCTACATCCA
TTGACTCAAACCATGGTAAACAGCCACCT
Found at i:6930507 original size:6 final size:6
Alignment explanation
Indices: 6930463--6930504 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
6930453 ACCTTTCTGA
* *
6930463 TCCCTT TCCC-C T-CCTC TCCCTC TCCCTC TCCCTC TCTCTC TC
1 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TC
6930505 TCTAGAGTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 2 0.06
5 3 0.09
6 27 0.84
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
TCCCTC
Found at i:6931729 original size:24 final size:23
Alignment explanation
Indices: 6931702--6931749 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
6931692 TAACATGTTC
6931702 ATTAAAA-TAACTGAATAATAATAA
1 ATTAAAACTAA-T-AATAATAATAA
6931726 ATTAAAACTTAATAATAATAATAA
1 ATTAAAAC-TAATAATAATAATAA
6931750 TAATCATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 18 0.82
25 1 0.05
26 3 0.14
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (23 bp):
ATTAAAACTAATAATAATAATAA
Found at i:6932192 original size:24 final size:25
Alignment explanation
Indices: 6932166--6932230 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 25
6932156 CAATTGTTGT
***
6932166 TTTTTTTTTTTTCTGATT-TTTATT
1 TTTTTTTTTTTTAAAATTCTTTATT
**
6932190 TTTCATTTTTTTAAAATTCTTTATT
1 TTTTTTTTTTTTAAAATTCTTTATT
6932215 TTCTTTTCTTTTTTAA
1 TT-TTTT-TTTTTTAA
6932231 TTACAATCTT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
24 13 0.42
25 8 0.26
26 2 0.06
27 8 0.26
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (25 bp):
TTTTTTTTTTTTAAAATTCTTTATT
Found at i:6940415 original size:39 final size:39
Alignment explanation
Indices: 6940339--6940520 Score: 188
Period size: 39 Copynumber: 4.7 Consensus size: 39
6940329 GATTGATACA
* * *
6940339 AATGTAGAGTT-TAGGGTGCTAGCACCTGAAGGTGGCAGC
1 AATGTGGAGTTCT-GGGAGCTAGCACTTGAAGGTGGCAGC
* *
6940378 ACTGTGTG-GTTCTGGGAGCTAGCACTTGAAGGAGGCAGC
1 AATGTG-GAGTTCTGGGAGCTAGCACTTGAAGGTGGCAGC
* * * *
6940417 ATTGTGGAGTTCTGGGCGCTAGCACTTGAAGGTGGAAAC
1 AATGTGGAGTTCTGGGAGCTAGCACTTGAAGGTGGCAGC
* * * *
6940456 AATATGGAATTCTGGGAGCTAGCACTTGAAGATGGAAGC
1 AATGTGGAGTTCTGGGAGCTAGCACTTGAAGGTGGCAGC
* **
6940495 AATGTAGAGTTGAGGGAGCTAGCACT
1 AATGTGGAGTTCTGGGAGCTAGCACT
6940521 AGGTGGCAGT
Statistics
Matches: 119, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 116 0.97
40 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.24
Consensus pattern (39 bp):
AATGTGGAGTTCTGGGAGCTAGCACTTGAAGGTGGCAGC
Found at i:6942012 original size:17 final size:17
Alignment explanation
Indices: 6941990--6942024 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6941980 ACTGCAAAAG
6941990 GAAGAAAGGAA-GGGGAA
1 GAAGAAA-GAATGGGGAA
6942007 GAAGAAAGAATGGGGAA
1 GAAGAAAGAATGGGGAA
6942024 G
1 G
6942025 CAAAACGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.03
Consensus pattern (17 bp):
GAAGAAAGAATGGGGAA
Found at i:6954175 original size:3 final size:3
Alignment explanation
Indices: 6954167--6954191 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6954157 AGAGTTCCTT
6954167 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
6954192 CGTTGCTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:6959679 original size:35 final size:35
Alignment explanation
Indices: 6959611--6959679 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
6959601 AAAGTATTCA
* * * *
6959611 TTATTATAATTTAATAATATTTTTTAATTTTATTT
1 TTATTAAAAATTAATAATATTTATTAATATTATTT
6959646 TTATTAAAAATTAATAATATATTATTAA-ATTATT
1 TTATTAAAAATTAATAATAT-TTATTAATATTATT
6959680 AATATGATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 23 0.79
36 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (35 bp):
TTATTAAAAATTAATAATATTTATTAATATTATTT
Found at i:6959793 original size:21 final size:20
Alignment explanation
Indices: 6959767--6959812 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
6959757 TCATTAAAAA
6959767 TTTAAA-CATTAATAATATAT
1 TTTAAATCATTAAT-ATATAT
*
6959787 TATTAAATTATTAATATATAT
1 T-TTAAATCATTAATATATAT
6959808 TTTAA
1 TTTAA
6959813 TTTTAATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 5 0.22
21 12 0.52
22 6 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAAATCATTAATATATAT
Found at i:6959814 original size:19 final size:22
Alignment explanation
Indices: 6959774--6959819 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
6959764 AAATTTAAAC
6959774 ATTAATAATATATTATTAAATT
1 ATTAATAATATATTATTAAATT
6959796 ATTAAT-ATATATT-TT-AATT
1 ATTAATAATATATTATTAAATT
6959815 -TTAAT
1 ATTAAT
6959820 TTCCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.21
19 4 0.17
20 2 0.08
21 7 0.29
22 6 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTAATAATATATTATTAAATT
Found at i:6966745 original size:21 final size:21
Alignment explanation
Indices: 6966721--6966760 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6966711 TTTTTTTATA
*
6966721 TATATTTATGAGATAATATTT
1 TATATTTAAGAGATAATATTT
*
6966742 TATATTTAAGTGATAATAT
1 TATATTTAAGAGATAATAT
6966761 ATAAATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (21 bp):
TATATTTAAGAGATAATATTT
Found at i:6974758 original size:97 final size:99
Alignment explanation
Indices: 6974656--6974842 Score: 247
Period size: 99 Copynumber: 1.9 Consensus size: 99
6974646 TAACCCAAAT
*
6974656 TTATTCATGAATTGTTTGACGAACATACT-A-C-ATTTACATCTT-TAAAATTAATAACAAATAA
1 TTATTCATGAATTGTTTGACGAACATACTAATCTATTTAAAT-TTCT-AAATTAATAACAAATAA
*
6974717 ATTTATTCATGAACATAAATAAACTAAGCACAGAAC
64 ATTTATTCATAAACATAAATAAACTAAGCACAGAAC
* * * *
6974753 TTATTCGTGAGTTGTTTGACGAACATACTAATCTATTTAAATTTCTAAATTAATAATAAATGAAT
1 TTATTCATGAATTGTTTGACGAACATACTAATCTATTTAAATTTCTAAATTAATAACAAATAAAT
* * *
6974818 TTGTTTATAAACATAAATGAACTAA
66 TTATTCATAAACATAAATAAACTAA
6974843 ATACAATTGT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
97 27 0.35
98 1 0.01
99 41 0.53
100 8 0.10
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (99 bp):
TTATTCATGAATTGTTTGACGAACATACTAATCTATTTAAATTTCTAAATTAATAACAAATAAAT
TTATTCATAAACATAAATAAACTAAGCACAGAAC
Found at i:6983111 original size:180 final size:180
Alignment explanation
Indices: 6982800--6983319 Score: 487
Period size: 193 Copynumber: 2.9 Consensus size: 180
6982790 TATTTCATCT
* * * * * *
6982800 TACATCAACACCACGTCAGTACCACAAGGCATAAAATGATTGATCACACATGTTGACACATTATA
1 TACATCAACACCACGTCAGTACCACGAGACATAAAATAATTAATAACATATGTTGACACATTATA
* * * * * * *
6982865 CTAGATGAC--G----TG-ATCATTTCACCTTATTATTTTATATTACGTGACACTAACGTAACAT
66 ATAAATGACATGATAATGTAGCATTTCATCTTATTATTTTATATTACATGACACTAATGTAATAT
*
6982923 GTTGACACATTATAATAGATGATGACATGGTCATATAGTATTTCACCTTA
131 GTTGACACATTATAATAGATGATGACATGGTCATATAGCATTTCACCTTA
* * * * * * *
6982973 TACATCAACACGACGTCTGTACCACGAGATATAAAATGATTAATGACATATGTTGATATATTATA
1 TACATCAACACCACGTCAGTACCACGAGACATAAAATAATTAATAACATATGTTGACACATTATA
* * *
6983038 ATAAATGACATGATTATGTAGCATTTCATCTTATTATTTTATATTACATGACATTAATATAATAT
66 ATAAATGACATGATAATGTAGCATTTCATCTTATTATTTTATATTACATGACACTAATGTAATAT
* *
6983103 GTTGACACATTATAATAGATGATATTGTGGTATGATGATATGGTCATGTAGCATTTCACCTTA
131 GTTGACACA-T-T-AT--A--ATA-----G-ATGATGACATGGTCATATAGCATTTCACCTTA
** * * *
6983166 TACATCAACACCTGGTCAGTACCTCGAGGCATAAAATAATTGATAACATATGTTGACACATTATA
1 TACATCAACACCACGTCAGTACCACGAGACATAAAATAATTAATAACATATGTTGACACATTATA
* * * * * * * * *
6983231 ATAAATGATATGATAATGTAGCGTTTTATTTTATTGTTTTATAATATATGATACTGATGTAATAT
66 ATAAATGACATGATAATGTAGCATTTCATCTTATTATTTTATATTACATGACACTAATGTAATAT
* * *
6983296 ATTAACATATTATAATAGATGATG
131 GTTGACACATTATAATAGATGATG
6983320 GTATAGTATG
Statistics
Matches: 278, Mismatches: 49, Indels: 33
0.77 0.14 0.09
Matches are distributed among these distances:
173 62 0.22
175 1 0.00
179 2 0.01
180 54 0.19
181 2 0.01
182 1 0.00
183 2 0.01
185 1 0.00
186 3 0.01
187 3 0.01
188 1 0.00
190 2 0.01
191 1 0.00
192 2 0.01
193 141 0.51
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (180 bp):
TACATCAACACCACGTCAGTACCACGAGACATAAAATAATTAATAACATATGTTGACACATTATA
ATAAATGACATGATAATGTAGCATTTCATCTTATTATTTTATATTACATGACACTAATGTAATAT
GTTGACACATTATAATAGATGATGACATGGTCATATAGCATTTCACCTTA
Found at i:6983400 original size:193 final size:193
Alignment explanation
Indices: 6982937--6983402 Score: 540
Period size: 193 Copynumber: 2.4 Consensus size: 193
6982927 ACACATTATA
* *
6982937 ATAG-ATGATGACATGGTCATATAGTATTTCACCTTATACATCAAC-ACGACGTCTGTACCACGA
1 ATAGTATGATGACATGGTCATATAGCATTTCACCTTATACATCAACAAC-ACGTCAGTACCACGA
* * * * * *
6983000 GATATAAAATGATTAATGACATATGTTGATATATTATAATAAATGACATGATTATGTAGCATTTC
65 GATATAAAATAATTGATAACATATGTTGACACATTATAATAAATGACATGATAATGTAGCATTTC
* * * * *
6983065 ATCTTATTATTTTATATTACATGACATTAATATAATATGTTGACACATTATAATAGATGATATT
130 ATCTTATTATTTTATAATACATGACACTAATATAATATATTAACACATTATAATAGATGATAGT
* * * * * ** *
6983129 GTGGTATGATGATATGGTCATGTAGCATTTCACCTTATACATCAACACCTGGTCAGTACCTCGAG
1 ATAGTATGATGACATGGTCATATAGCATTTCACCTTATACATCAACAACACGTCAGTACCACGAG
** * * *
6983194 GCATAAAATAATTGATAACATATGTTGACACATTATAATAAATGATATGATAATGTAGCGTTTTA
66 ATATAAAATAATTGATAACATATGTTGACACATTATAATAAATGACATGATAATGTAGCATTTCA
* * * * * * * *
6983259 TTTTATTGTTTTATAATATATGATACTGATGTAATATATTAACATATTATAATAGATGATGGT
131 TCTTATTATTTTATAATACATGACACTAATATAATATATTAACACATTATAATAGATGATAGT
* * * * * * *
6983322 ATAGTATGATGACATGATCATATAACATTTCACTTTATATATTAACAACACATCAGTATCACGAG
1 ATAGTATGATGACATGGTCATATAGCATTTCACCTTATACATCAACAACACGTCAGTACCACGAG
6983387 ATATAAAATAATTGAT
66 ATATAAAATAATTGAT
6983403 GATAATTAAT
Statistics
Matches: 221, Mismatches: 51, Indels: 3
0.80 0.19 0.01
Matches are distributed among these distances:
192 2 0.01
193 218 0.99
194 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.37
Consensus pattern (193 bp):
ATAGTATGATGACATGGTCATATAGCATTTCACCTTATACATCAACAACACGTCAGTACCACGAG
ATATAAAATAATTGATAACATATGTTGACACATTATAATAAATGACATGATAATGTAGCATTTCA
TCTTATTATTTTATAATACATGACACTAATATAATATATTAACACATTATAATAGATGATAGT
Found at i:6991175 original size:16 final size:16
Alignment explanation
Indices: 6991139--6991185 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
6991129 CACACACAAC
* *
6991139 AGGAAATAAAGGAAGGA
1 AGGAAAGAAA-GAAAGA
6991156 AGGAAAGAAAGAAAGA
1 AGGAAAGAAAGAAAGA
*
6991172 AGGACAGAAAGAAA
1 AGGAAAGAAAGAAA
6991186 AGTTGAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.64, C:0.02, G:0.32, T:0.02
Consensus pattern (16 bp):
AGGAAAGAAAGAAAGA
Found at i:6993152 original size:27 final size:27
Alignment explanation
Indices: 6993110--6993282 Score: 136
Period size: 27 Copynumber: 6.4 Consensus size: 27
6993100 GTCCTCCTGA
*
6993110 GATGGTGCTTGTACACTTATTGCAGGG
1 GATGGTGCTTGTACACATATTGCAGGG
*
6993137 GATGGTGCTTGCACACATATTGCAGGG
1 GATGGTGCTTGTACACATATTGCAGGG
* * * ** *** *
6993164 GCTGGTGCCTG-AGAGGGTCCAGCAGGA
1 GATGGTGCTTGTACA-CATATTGCAGGG
*
6993191 GATGGCGCTTGTACACATATTGCAGGG
1 GATGGTGCTTGTACACATATTGCAGGG
* * * * *
6993218 GCTGGTGCTTG-AGAC-TGTCCAGCAGGA
1 GATGGTGCTTGTACACATAT--TGCAGGG
6993245 GATGGTGCTTGTACACATATTGCAGGG
1 GATGGTGCTTGTACACATATTGCAGGG
*
6993272 GGTGGTGCTTG
1 GATGGTGCTTG
6993283 AAAGGGTCCA
Statistics
Matches: 107, Mismatches: 33, Indels: 12
0.70 0.22 0.08
Matches are distributed among these distances:
25 2 0.02
26 5 0.05
27 93 0.87
28 5 0.05
29 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.37, T:0.26
Consensus pattern (27 bp):
GATGGTGCTTGTACACATATTGCAGGG
Found at i:6993195 original size:54 final size:54
Alignment explanation
Indices: 6993131--6993299 Score: 257
Period size: 54 Copynumber: 3.1 Consensus size: 54
6993121 TACACTTATT
* * *
6993131 GCAGGGGATGGTGCTTGCACACATATTGCAGGGGCTGGTGCCTGAGAGGGTCCA
1 GCAGGAGATGGTGCTTGTACACATATTGCAGGGGCTGGTGCTTGAGAGGGTCCA
* **
6993185 GCAGGAGATGGCGCTTGTACACATATTGCAGGGGCTGGTGCTTGAGACTGTCCA
1 GCAGGAGATGGTGCTTGTACACATATTGCAGGGGCTGGTGCTTGAGAGGGTCCA
* *
6993239 GCAGGAGATGGTGCTTGTACACATATTGCAGGGGGTGGTGCTTGAAAGGGTCCA
1 GCAGGAGATGGTGCTTGTACACATATTGCAGGGGCTGGTGCTTGAGAGGGTCCA
*
6993293 GTAGGAG
1 GCAGGAG
6993300 CTGCTTCTGA
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 103 1.00
ACGTcount: A:0.21, C:0.18, G:0.39, T:0.22
Consensus pattern (54 bp):
GCAGGAGATGGTGCTTGTACACATATTGCAGGGGCTGGTGCTTGAGAGGGTCCA
Found at i:6996777 original size:33 final size:32
Alignment explanation
Indices: 6996730--6996805 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 32
6996720 GGAACCCAAT
*
6996730 CGTTATCGTATCATCTCATCAGGACGCTATCG
1 CGTTTTCGTATCATCTCATCAGGACGCTATCG
* *
6996762 CGTTTGTCGTATCATCTCATCAGGACTCTATTG
1 CGTTT-TCGTATCATCTCATCAGGACGCTATCG
6996795 CGTTTTCGTAT
1 CGTTTTCGTAT
6996806 TATCCTGTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 10 0.25
33 30 0.75
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.38
Consensus pattern (32 bp):
CGTTTTCGTATCATCTCATCAGGACGCTATCG
Done.