Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397259.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_147.0, 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: 10737078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 75620 characters in sequence are not A, C, G, or T
File 14 of 22
Found at i:5692760 original size:2 final size:2
Alignment explanation
Indices: 5692755--5692781 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5692745 TCTCTCTCTC
5692755 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5692782 TACATAGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5693156 original size:38 final size:38
Alignment explanation
Indices: 5693108--5693185 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
5693098 ATGATTTGAC
* *
5693108 TAAATACAAATCCAAATTC-ATCCAGGACTATGACTTAA
1 TAAATACAAATCCAAATTCAAT-AAGGACTATGACTCAA
* *
5693146 TAAATCCAAATCCATATTCAATAAGGACTATGACTCAA
1 TAAATACAAATCCAAATTCAATAAGGACTATGACTCAA
5693184 TA
1 TA
5693186 GGAAGCCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 33 0.94
39 2 0.06
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.27
Consensus pattern (38 bp):
TAAATACAAATCCAAATTCAATAAGGACTATGACTCAA
Found at i:5694119 original size:27 final size:27
Alignment explanation
Indices: 5694078--5694133 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
5694068 AAATTTTTAA
* * *
5694078 AAAAAAAATTCTTTTTTTTTTAAATAT
1 AAAAAAAATTATTTTTGTTTTAAAAAT
5694105 AAAAAAAATTATTTTTGTTTTAAAAAT
1 AAAAAAAATTATTTTTGTTTTAAAAAT
5694132 AA
1 AA
5694134 CCTCATCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
AAAAAAAATTATTTTTGTTTTAAAAAT
Found at i:5710625 original size:58 final size:57
Alignment explanation
Indices: 5710523--5710637 Score: 185
Period size: 58 Copynumber: 2.0 Consensus size: 57
5710513 TAAGGAGAAA
* *
5710523 AACAAAATTGATACCCAGGTAATGTAGGTAAAATATTAGCACACAGTAATGAGCTAT
1 AACAAAATTGATACCCAGGTAACGTAGGTAAAATATTAGAACACAGTAATGAGCTAT
* *
5710580 AACAAAATTGATACCCAGAGTAACGTAGGTAAAATATTATAACACAGTATTGAGCTAT
1 AACAAAATTGATACCCAG-GTAACGTAGGTAAAATATTAGAACACAGTAATGAGCTAT
5710638 GCCAGTCAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
57 18 0.34
58 35 0.66
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (57 bp):
AACAAAATTGATACCCAGGTAACGTAGGTAAAATATTAGAACACAGTAATGAGCTAT
Found at i:5731792 original size:57 final size:57
Alignment explanation
Indices: 5731726--5731853 Score: 188
Period size: 57 Copynumber: 2.2 Consensus size: 57
5731716 TCTTTGATAG
** *
5731726 CTAGCAACAAAAGTTATCCTT-GAAATACC-AAAAAATGGGAAGAAAAATATTTAGTAA
1 CTAGCAACAAAAGTTAT-CTTCGAAATACCAAAAAAAAAGGAAG-AAAATATTTAATAA
5731783 CTAGCAACAAAAGTTATCTTCGAAATACCAAAAAAAAAGGAAGAAAATATTTAATAA
1 CTAGCAACAAAAGTTATCTTCGAAATACCAAAAAAAAAGGAAGAAAATATTTAATAA
*
5731840 TTAGCAACAAAAGT
1 CTAGCAACAAAAGT
5731854 AATCATTACT
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
56 3 0.05
57 51 0.78
58 11 0.17
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.22
Consensus pattern (57 bp):
CTAGCAACAAAAGTTATCTTCGAAATACCAAAAAAAAAGGAAGAAAATATTTAATAA
Found at i:5734028 original size:36 final size:35
Alignment explanation
Indices: 5733979--5734051 Score: 83
Period size: 36 Copynumber: 2.1 Consensus size: 35
5733969 CATTTATATT
* *
5733979 TTACAATGTAATGTGATTGCAAATAACGTGTGAGA
1 TTACAATGCAATGTAATTGCAAATAACGTGTGAGA
* ** *
5734014 TTACATATGCAATGTAATTGTAGGTAATGTGTGAGA
1 TTACA-ATGCAATGTAATTGCAAATAACGTGTGAGA
5734050 TT
1 TT
5734052 GCATGGAAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
35 5 0.16
36 26 0.84
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (35 bp):
TTACAATGCAATGTAATTGCAAATAACGTGTGAGA
Found at i:5749804 original size:24 final size:23
Alignment explanation
Indices: 5749743--5749804 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
5749733 GAAAATGTGA
* *
5749743 TAAATAAT-AAAAATATCTTTTAT
1 TAAA-AATAAAAAATTTATTTTAT
*
5749766 TAAAATTAAAAAATTTATTTTAT
1 TAAAAATAAAAAATTTATTTTAT
5749789 TAAAAGATAAAAAATT
1 TAAAA-ATAAAAAATT
5749805 CTAAGTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 2 0.06
23 22 0.67
24 9 0.27
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TAAAAATAAAAAATTTATTTTAT
Found at i:5749911 original size:23 final size:22
Alignment explanation
Indices: 5749868--5749911 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
5749858 AAATACAAGC
* **
5749868 ATATTTTTATTATAATTTAATA
1 ATATTTTTATTAAAAGATAATA
5749890 ATATTTTGTATTAAAAGATAAT
1 ATATTTT-TATTAAAAGATAAT
5749912 TAAACCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
ATATTTTTATTAAAAGATAATA
Found at i:5750057 original size:45 final size:45
Alignment explanation
Indices: 5749979--5750085 Score: 123
Period size: 45 Copynumber: 2.4 Consensus size: 45
5749969 ATTAAATTTA
* * *
5749979 AATAATACTAAATAATATTCTTTATTACATTTATTATA-TTCAAAT
1 AATAATATTAAATAATTTTCTTTATAACATTTATTATAGTT-AAAT
** *
5750024 AATAATATTAAATAATTTTCTTTATAATTTTTATTTTAGTTAAAT
1 AATAATATTAAATAATTTTCTTTATAACATTTATTATAGTTAAAT
5750069 AAT-AT-TTAAAT-ATTTTC
1 AATAATATTAAATAATTTTC
5750086 ATTTTCTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
42 6 0.11
43 6 0.11
44 2 0.04
45 39 0.71
46 2 0.04
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (45 bp):
AATAATATTAAATAATTTTCTTTATAACATTTATTATAGTTAAAT
Found at i:5754229 original size:26 final size:26
Alignment explanation
Indices: 5754200--5754257 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
5754190 ATAATTCAAT
5754200 ATATAT-AATTAAAATACATAATAAGA
1 ATATATCAATTAAAA-ACATAATAAGA
* *
5754226 ATATATCATTTAAAAATATAATAAGA
1 ATATATCAATTAAAAACATAATAAGA
*
5754252 ACATAT
1 ATATAT
5754258 TAAAACATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 21 0.75
27 7 0.25
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (26 bp):
ATATATCAATTAAAAACATAATAAGA
Found at i:5754606 original size:14 final size:15
Alignment explanation
Indices: 5754581--5754616 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
5754571 TCTATGTTCC
5754581 TTTTATTCTTTTCAT
1 TTTTATTCTTTTCAT
5754596 TTTTATT-TTTTCAT
1 TTTTATTCTTTTCAT
5754610 TATTTAT
1 T-TTTAT
5754617 CCACTTATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTATTCTTTTCAT
Found at i:5754914 original size:25 final size:25
Alignment explanation
Indices: 5754876--5754984 Score: 105
Period size: 25 Copynumber: 4.3 Consensus size: 25
5754866 TTTTGGTGGA
*
5754876 AAAATTATCCTTAGATTCTGA-AGGT
1 AAAATTATTCTTAGATTCTGATA-GT
* *
5754901 AAAATTATTTTTAGATTTTGATAGT
1 AAAATTATTCTTAGATTCTGATAGT
* **
5754926 AAAATTATTCATCCACTTCTGAT-GAT
1 AAAATTATTCTTAGA-TTCTGATAG-T
* *
5754952 AAAATTATTTTTAGAATCTGATAGT
1 AAAATTATTCTTAGATTCTGATAGT
5754977 AAAATTAT
1 AAAATTAT
5754985 CCATCCACTT
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
25 47 0.70
26 20 0.30
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (25 bp):
AAAATTATTCTTAGATTCTGATAGT
Found at i:5754955 original size:51 final size:51
Alignment explanation
Indices: 5754891--5755020 Score: 172
Period size: 51 Copynumber: 2.5 Consensus size: 51
5754881 TATCCTTAGA
* * * * *
5754891 TTCTGAAGGTAAAATTATTTTTAGATTTTGATAGTAAAATTATTCATCCAC
1 TTCTGATGATAAAATTATTTTTAGAATCTGATAGTAAAATTATCCATCCAC
5754942 TTCTGATGATAAAATTATTTTTAGAATCTGATAGTAAAATTATCCATCCAC
1 TTCTGATGATAAAATTATTTTTAGAATCTGATAGTAAAATTATCCATCCAC
* *
5754993 TTCATGGT-ATTAAAATTATTCTTAGAAT
1 TTC-TGATGA-TAAAATTATTTTTAGAAT
5755021 TAAAATAATA
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
51 50 0.71
52 20 0.29
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (51 bp):
TTCTGATGATAAAATTATTTTTAGAATCTGATAGTAAAATTATCCATCCAC
Found at i:5756915 original size:19 final size:20
Alignment explanation
Indices: 5756893--5756930 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5756883 TTATTAATAC
5756893 TTAAAATAA-ATATTTCATT
1 TTAAAATAATATATTTCATT
*
5756912 TTAAAATAATATGTTTCAT
1 TTAAAATAATATATTTCAT
5756931 AAGATGCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (20 bp):
TTAAAATAATATATTTCATT
Found at i:5759845 original size:42 final size:42
Alignment explanation
Indices: 5759789--5759950 Score: 207
Period size: 42 Copynumber: 3.9 Consensus size: 42
5759779 ATCCAACGGT
* * *
5759789 GAGGCAGCAACTGGAGTTGAGAATGAAATTTTGTCCAAGGAC
1 GAGGCCGCAGCTGGAGTTGAGAACGAAATTTTGTCCAAGGAC
** * * *
5759831 GAGGTTGTAGCTGGAGTTGAGAACGGAATTTTGTCCAAAGAC
1 GAGGCCGCAGCTGGAGTTGAGAACGAAATTTTGTCCAAGGAC
**
5759873 GAGGCCGCAGCTGGAGTTGAGAGTGAAATTTTGTCCAAGGAC
1 GAGGCCGCAGCTGGAGTTGAGAACGAAATTTTGTCCAAGGAC
* * *
5759915 AAGGCCGCAGCTGGAGCTGAGAACGGAATTTTGTCC
1 GAGGCCGCAGCTGGAGTTGAGAACGAAATTTTGTCC
5759951 GAAGACAAAA
Statistics
Matches: 101, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 101 1.00
ACGTcount: A:0.28, C:0.16, G:0.33, T:0.22
Consensus pattern (42 bp):
GAGGCCGCAGCTGGAGTTGAGAACGAAATTTTGTCCAAGGAC
Found at i:5759912 original size:84 final size:84
Alignment explanation
Indices: 5759771--5759956 Score: 255
Period size: 84 Copynumber: 2.2 Consensus size: 84
5759761 GGAACTGGAT
* * ** * *
5759771 GGAATTTTATCCAACGGTGAGGCAGCAACTGGAGTTGAGAATGAAATTTTGTCCAAGGACGAGGT
1 GGAATTTTGTCCAAAGACGAGGCAGCAACTGGAGTTGAGAATGAAATTTTGTCCAAGGACAAGGC
* * *
5759836 TGTAGCTGGAGTTGAGAAC
66 CGCAGCTGGAGCTGAGAAC
* * *
5759855 GGAATTTTGTCCAAAGACGAGGCCGCAGCTGGAGTTGAGAGTGAAATTTTGTCCAAGGACAAGGC
1 GGAATTTTGTCCAAAGACGAGGCAGCAACTGGAGTTGAGAATGAAATTTTGTCCAAGGACAAGGC
5759920 CGCAGCTGGAGCTGAGAAC
66 CGCAGCTGGAGCTGAGAAC
*
5759939 GGAATTTTGTCCGAAGAC
1 GGAATTTTGTCCAAAGAC
5759957 AAAACAACTA
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.23
Consensus pattern (84 bp):
GGAATTTTGTCCAAAGACGAGGCAGCAACTGGAGTTGAGAATGAAATTTTGTCCAAGGACAAGGC
CGCAGCTGGAGCTGAGAAC
Found at i:5764073 original size:15 final size:15
Alignment explanation
Indices: 5764032--5764084 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
5764022 ATGATAAGTG
*
5764032 ATTAAAATAATAATA
1 ATTAAAATATTAATA
*
5764047 TTTATAAA-ATTAATA
1 ATTA-AAATATTAATA
5764062 ATTAAAATATTAA-A
1 ATTAAAATATTAATA
5764076 ATCTAAAAT
1 AT-TAAAAT
5764085 TGAATGAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 6 0.19
15 23 0.72
16 3 0.09
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAAAATATTAATA
Found at i:5779061 original size:2 final size:2
Alignment explanation
Indices: 5779054--5779088 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5779044 ATGATAGTGT
5779054 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5779089 GAGACTGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5781042 original size:15 final size:14
Alignment explanation
Indices: 5781022--5781055 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
5781012 TTATAGTGTT
5781022 ATAATTAAAATAATA
1 ATAATTAAAA-AATA
5781037 ATAATTAAAAAATA
1 ATAATTAAAAAATA
*
5781051 TTAAT
1 ATAAT
5781056 ATTAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAATTAAAAAATA
Found at i:5781062 original size:14 final size:15
Alignment explanation
Indices: 5781022--5781065 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
5781012 TTATAGTGTT
*
5781022 ATAATTAAAATAATA
1 ATAATTAAAATATTA
5781037 ATAATTAAAAAATATTA
1 ATAATT--AAAATATTA
5781054 AT-ATTAAAATAT
1 ATAATTAAAATAT
5781066 AAAAGAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 7 0.27
15 6 0.23
16 3 0.12
17 10 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAATTAAAATATTA
Found at i:5781146 original size:90 final size:91
Alignment explanation
Indices: 5781035--5781314 Score: 343
Period size: 91 Copynumber: 3.1 Consensus size: 91
5781025 ATTAAAATAA
* * * *
5781035 TAATAATTAAAAAATATTAATA-TTAAAATATAAAAGAAAATGTTTCTATCATTTCAAGTAATAT
1 TAATAAAT-AAAAATATTAATATTTAAATTATAAAAGAAAATATTTTTATCATTTCAAGTAATAT
*
5781099 CTAAATATTCACATATAAATTATTTTT
65 CTAAATATTCATATATAAATTATTTTT
* * *
5781126 TGATAAATAAAAATATTAATATTTAAATTATAAAAGAAAATATTTTTATTATTTTAAGTAATATC
1 TAATAAATAAAAATATTAATATTTAAATTATAAAAGAAAATATTTTTATCATTTCAAGTAATATC
* * *
5781191 TAAATATTAATATATAAAATACTTTT
66 TAAATATTCATATATAAATTATTTTT
* * * * * *
5781217 TAATAAATAAACATATTAGTATTTAAATTATAGAAG-AATTTTTTTTGA-CTTTTCAAGTAATAT
1 TAATAAATAAAAATATTAATATTTAAATTATAAAAGAAAATATTTTT-ATCATTTCAAGTAATAT
*
5781280 CTAATTATTGC-TATATAAATTATTTTT
65 CTAAATATT-CATATATAAATTATTTTT
5781307 TAATAAAT
1 TAATAAAT
5781315 TTACTTTGGC
Statistics
Matches: 162, Mismatches: 24, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
90 63 0.39
91 99 0.61
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (91 bp):
TAATAAATAAAAATATTAATATTTAAATTATAAAAGAAAATATTTTTATCATTTCAAGTAATATC
TAAATATTCATATATAAATTATTTTT
Found at i:5781414 original size:22 final size:22
Alignment explanation
Indices: 5781384--5781441 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
5781374 CCGATTGAAC
*
5781384 TTTAGAATATTATTT-ATATTAA
1 TTTAAAATA-TATTTAATATTAA
5781406 TTTAAAATATATTTAATATTAA
1 TTTAAAATATATTTAATATTAA
** *
5781428 AATAAAAAATATTT
1 TTTAAAATATATTT
5781442 TTTTTTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 5 0.16
22 26 0.84
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTAAAATATATTTAATATTAA
Found at i:5781418 original size:15 final size:17
Alignment explanation
Indices: 5781398--5781431 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5781388 GAATATTATT
5781398 TATA-TTAAT-TTAAAA
1 TATATTTAATATTAAAA
5781413 TATATTTAATATTAAAA
1 TATATTTAATATTAAAA
5781430 TA
1 TA
5781432 AAAAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 5 0.29
17 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATTTAATATTAAAA
Found at i:5786076 original size:24 final size:23
Alignment explanation
Indices: 5786024--5786077 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
5786014 TGATTAAATA
*
5786024 TTATTTTATTTTTTATTACGTTTT
1 TTATTTTATTTTTAATTAC-TTTT
*
5786048 ATATTTTAATTTTTAATTA-TTTT
1 TTATTTT-ATTTTTAATTACTTTT
5786071 CTTATTT
1 -TTATTT
5786078 GAGTGTCAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 4 0.16
24 11 0.44
25 10 0.40
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (23 bp):
TTATTTTATTTTTAATTACTTTT
Found at i:5786658 original size:2 final size:2
Alignment explanation
Indices: 5786651--5786689 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5786641 ATGATAGTGT
5786651 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5786690 GAGACTGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5786718 original size:13 final size:13
Alignment explanation
Indices: 5786700--5786728 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5786690 GAGACTGAAT
5786700 GAAACTATATAAA
1 GAAACTATATAAA
5786713 GAAACTATATAAA
1 GAAACTATATAAA
5786726 GAA
1 GAA
5786729 TCTCTTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (13 bp):
GAAACTATATAAA
Found at i:5790459 original size:21 final size:20
Alignment explanation
Indices: 5790401--5790456 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
5790391 AAATTTGATG
*
5790401 AATATTAATATTTAACTTAA
1 AATATTAATATTTAATTTAA
* * * *
5790421 AATATAAAAAAATTAATTTCA
1 AATAT-TAATATTTAATTTAA
5790442 AATATTAATATTTAA
1 AATATTAATATTTAA
5790457 ATTATACAAC
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATTAATATTTAATTTAA
Found at i:5795456 original size:42 final size:42
Alignment explanation
Indices: 5795388--5795468 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 42
5795378 TGATAAAAAA
* *
5795388 TAATTTTAAATTACATAATATCATAAATAA-AAATAATAATAG
1 TAATTTTAAATTACAAAAAATCATAAATAATAAA-AATAATAG
*
5795430 TAATTTTAAATTTA-AAAAAATTATAAATAATAAAAATAA
1 TAATTTTAAA-TTACAAAAAATCATAAATAATAAAAATAA
5795469 ATTAAAGATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 28 0.82
43 6 0.18
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.36
Consensus pattern (42 bp):
TAATTTTAAATTACAAAAAATCATAAATAATAAAAATAATAG
Found at i:5795581 original size:18 final size:18
Alignment explanation
Indices: 5795543--5795580 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
5795533 ATTTTTTTTA
*
5795543 TTTAAATAATTTTTAATT
1 TTTAAATAATATTTAATT
5795561 TTTAAA-AATATTTAATT
1 TTTAAATAATATTTAATT
5795578 TTT
1 TTT
5795581 TTAATACCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAAATAATATTTAATT
Found at i:5795581 original size:19 final size:20
Alignment explanation
Indices: 5795538--5795584 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
5795528 AGCAAATTTT
*
5795538 TTTTATTTAAATAATTTTTAA
1 TTTT-TTTAAATAATATTTAA
5795559 --TTTTTAAA-AATATTTAA
1 TTTTTTTAAATAATATTTAA
5795576 TTTTTTTAA
1 TTTTTTTAA
5795585 TACCTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 8 0.35
18 6 0.26
19 9 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTTTAAATAATATTTAA
Found at i:5807961 original size:6 final size:6
Alignment explanation
Indices: 5807950--5807975 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5807940 ATCTTCCTTT
5807950 CCCAAC CCCAAC CCCAAC CCCAAC CC
1 CCCAAC CCCAAC CCCAAC CCCAAC CC
5807976 ACCCCACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.69, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCAAC
Found at i:5813766 original size:29 final size:27
Alignment explanation
Indices: 5813734--5813807 Score: 80
Period size: 29 Copynumber: 2.7 Consensus size: 27
5813724 ACTAATAGTC
*
5813734 ATAAAAATTTATTTAACT-TAAATAAAA
1 ATAAAAATTTATTTAAATGT-AATAAAA
*
5813761 ATATAAATATTTCA-TGAAATGTAATAAAA
1 ATA-AAA-ATTT-ATTTAAATGTAATAAAA
5813790 ATAAAAATTTATTTAAAT
1 ATAAAAATTTATTTAAAT
5813808 TTCTTCAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
26 1 0.03
27 12 0.31
28 6 0.15
29 18 0.46
30 2 0.05
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (27 bp):
ATAAAAATTTATTTAAATGTAATAAAA
Found at i:5814534 original size:22 final size:24
Alignment explanation
Indices: 5814508--5814552 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
5814498 TATGATTATT
*
5814508 AAATATATATATT-TTAA-ATTTA
1 AAATATAAATATTATTAATATTTA
5814530 AAATATAAATATTATTAATATTT
1 AAATATAAATATTATTAATATTT
5814553 GATTTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 4 0.20
24 4 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AAATATAAATATTATTAATATTTA
Found at i:5814889 original size:13 final size:13
Alignment explanation
Indices: 5814871--5814901 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5814861 GATTTGCGGC
*
5814871 AAAACATAAACTG
1 AAAACACAAACTG
5814884 AAAACACAAACTG
1 AAAACACAAACTG
5814897 AAAAC
1 AAAAC
5814902 CAGACCGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.65, C:0.19, G:0.06, T:0.10
Consensus pattern (13 bp):
AAAACACAAACTG
Found at i:5824255 original size:27 final size:26
Alignment explanation
Indices: 5824197--5824247 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
5824187 TGAGTTAAAT
5824197 TTTTAATTTTTAATTATAATTTAGTTA
1 TTTTAATTTTT-ATTATAATTTAGTTA
5824224 TTTTAATTGTTT-TTATAA-TTAGTT
1 TTTTAATT-TTTATTATAATTTAGTT
5824248 TAATTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 6 0.26
26 6 0.26
27 8 0.35
28 3 0.13
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (26 bp):
TTTTAATTTTTATTATAATTTAGTTA
Found at i:5825721 original size:16 final size:16
Alignment explanation
Indices: 5825700--5825732 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5825690 AAATTCAGAG
5825700 TTAGGCTCGCTATTTT
1 TTAGGCTCGCTATTTT
5825716 TTAGGCTCGCTATTTT
1 TTAGGCTCGCTATTTT
5825732 T
1 T
5825733 GGTTGATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.18, G:0.18, T:0.52
Consensus pattern (16 bp):
TTAGGCTCGCTATTTT
Found at i:5845660 original size:16 final size:16
Alignment explanation
Indices: 5845639--5845669 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5845629 ATGTTTATCT
5845639 TATTAAATTATTAATA
1 TATTAAATTATTAATA
*
5845655 TATTAAATTTTTAAT
1 TATTAAATTATTAAT
5845670 GAAAGTGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTAAATTATTAATA
Found at i:5846013 original size:20 final size:21
Alignment explanation
Indices: 5845956--5846058 Score: 75
Period size: 23 Copynumber: 4.6 Consensus size: 21
5845946 TAATTAAAAT
5845956 TATTAATATTTTAATAATAATAA
1 TATTAA-ATTTTAA-AATAATAA
*
5845979 TATTAAATTAT-AAATAA-AA
1 TATTAAATTTTAAAATAATAA
* *
5845998 TATTAGATTTTAAAATATTAA
1 TATTAAATTTTAAAATAATAA
* *
5846019 TGATTAAAATATAATAAAATATTAA
1 T-ATT-AAAT-T-TTAAAATAATAA
5846044 TATTTAAATTATTAA
1 TA-TTAAATT-TTAA
5846059 TTATTAAAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
19 11 0.17
20 10 0.15
21 4 0.06
22 7 0.11
23 14 0.21
24 6 0.09
25 14 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TATTAAATTTTAAAATAATAA
Found at i:5846050 original size:40 final size:39
Alignment explanation
Indices: 5845942--5846092 Score: 153
Period size: 40 Copynumber: 3.7 Consensus size: 39
5845932 TTAAATTTGG
*
5845942 AAATTAATTAAAATTATTAATATTTTAATAATAATAATATTA
1 AAATTAATTAAAA-TATTAATA-TTTAA-AATATTAATATTA
* *
5845984 AATTATAAATAAAATATTAGAT-TTTAAAATATTAATGATTA
1 AAAT-TAATTAAAATATTA-ATATTTAAAATATTAAT-ATTA
*
5846025 AAATATAA-TAAAATATTAATATTTAAATTATTAATTATTA
1 AAAT-TAATTAAAATATTAATATTTAAAATATTAA-TATTA
*
5846065 AAAGCTTAATTAAATTATTAATATTTAA
1 AAA--TTAATTAAAATATTAATATTTAA
5846093 TATTTAAAAA
Statistics
Matches: 95, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
39 2 0.02
40 37 0.39
41 20 0.21
42 26 0.27
43 10 0.11
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.44
Consensus pattern (39 bp):
AAATTAATTAAAATATTAATATTTAAAATATTAATATTA
Found at i:5846092 original size:15 final size:15
Alignment explanation
Indices: 5845949--5846092 Score: 68
Period size: 15 Copynumber: 10.3 Consensus size: 15
5845939 TGGAAATTAA
5845949 TTAAAATTATTAATATT
1 TTAAAA-TATTAATA-T
*
5845966 TTAATAATAATAATA-
1 TTAA-AATATTAATAT
*
5845981 TTAAATTA-TAA-A-
1 TTAAAATATTAATAT
5845993 -TAAAATATTAGAT-T
1 TTAAAATATTA-ATAT
5846007 TTAAAATATTAATGA-
1 TTAAAATATTAAT-AT
5846022 TTAAAATA-T-A-A-
1 TTAAAATATTAATAT
5846033 -TAAAATATTAATAT
1 TTAAAATATTAATAT
*
5846047 TTAAATTATTAAT-T
1 TTAAAATATTAATAT
**
5846061 ATTAAAAGCTT-A-A-
1 -TTAAAATATTAATAT
*
5846074 TTAAATTATTAATAT
1 TTAAAATATTAATAT
5846089 TTAA
1 TTAA
5846093 TATTTAAAAA
Statistics
Matches: 99, Mismatches: 10, Indels: 38
0.67 0.07 0.26
Matches are distributed among these distances:
10 7 0.07
11 8 0.08
12 11 0.11
13 7 0.07
14 9 0.09
15 44 0.44
17 11 0.11
18 2 0.02
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (15 bp):
TTAAAATATTAATAT
Found at i:5846441 original size:19 final size:19
Alignment explanation
Indices: 5846401--5846442 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5846391 ATAATCACTA
*
5846401 TAAAAAAAGCAATTAATGT
1 TAAAAAAAGCAAATAATGT
*
5846420 TAAAAAAGGACAAATAAT-T
1 TAAAAAAAG-CAAATAATGT
5846439 TAAA
1 TAAA
5846443 TCCAACCTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (19 bp):
TAAAAAAAGCAAATAATGT
Found at i:5863539 original size:25 final size:25
Alignment explanation
Indices: 5863511--5863560 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
5863501 AATTACATGG
5863511 CTTTTACTTT-GTGGTTATTTAGTTT
1 CTTTTA-TTTGGTGGTTATTTAGTTT
*
5863536 CTTTTATTTGGTGGTTATTTGGTTT
1 CTTTTATTTGGTGGTTATTTAGTTT
5863561 TTCACGTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.10, C:0.06, G:0.20, T:0.64
Consensus pattern (25 bp):
CTTTTATTTGGTGGTTATTTAGTTT
Found at i:5865131 original size:25 final size:25
Alignment explanation
Indices: 5865103--5865153 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
5865093 TAATTACATG
5865103 TCTTTTACTTGGTGGTTATTTAGTT
1 TCTTTTACTTGGTGGTTATTTAGTT
* *
5865128 TCTTTTATTTGGTGGTTATTTGGTT
1 TCTTTTACTTGGTGGTTATTTAGTT
5865153 T
1 T
5865154 TTCATGTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.10, C:0.06, G:0.22, T:0.63
Consensus pattern (25 bp):
TCTTTTACTTGGTGGTTATTTAGTT
Found at i:5866348 original size:32 final size:27
Alignment explanation
Indices: 5866288--5866341 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
5866278 AATTATAGGA
*
5866288 ATCACCATGGTTATAGGGATTTTATTT
1 ATCACCATAGTTATAGGGATTTTATTT
5866315 ATCACCATAGTTATAGGGATTTTATTT
1 ATCACCATAGTTATAGGGATTTTATTT
5866342 TCTTTATTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (27 bp):
ATCACCATAGTTATAGGGATTTTATTT
Found at i:5870761 original size:13 final size:13
Alignment explanation
Indices: 5870720--5870762 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
5870710 TTGCCCATAG
5870720 AAAGTATTGAGGAA
1 AAAGT-TTGAGGAA
* *
5870734 AAATTTTGTAAGAA
1 AAAGTTTG-AGGAA
5870748 AAAGTTTGAGGAA
1 AAAGTTTGAGGAA
5870761 AA
1 AA
5870763 GCAACAACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (13 bp):
AAAGTTTGAGGAA
Found at i:5878905 original size:18 final size:18
Alignment explanation
Indices: 5878882--5878918 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5878872 CATTACATCA
5878882 ACTTTTAATGGTAATGTG
1 ACTTTTAATGGTAATGTG
5878900 ACTTTTAATGGTAATGTG
1 ACTTTTAATGGTAATGTG
5878918 A
1 A
5878919 TTAATTTTGC
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:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (18 bp):
ACTTTTAATGGTAATGTG
Found at i:5879032 original size:51 final size:51
Alignment explanation
Indices: 5878967--5879068 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
5878957 TCATTAAATC
5878967 GATTGGTTTATTATTCACATTGTAAGAAATATGAATAACTTATTTCATGTT
1 GATTGGTTTATTATTCACATTGTAAGAAATATGAATAACTTATTTCATGTT
5879018 GATTGGTTTATTATTCACATTGTAAGAAATATGAATAACTTATTTCATGTT
1 GATTGGTTTATTATTCACATTGTAAGAAATATGAATAACTTATTTCATGTT
5879069 AACTGTCCGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (51 bp):
GATTGGTTTATTATTCACATTGTAAGAAATATGAATAACTTATTTCATGTT
Found at i:5889697 original size:22 final size:22
Alignment explanation
Indices: 5889663--5889706 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5889653 GTCATTTCTA
* *
5889663 GTTTATGTAATTTTGAAGTCAT
1 GTTTAAGTAATTTCGAAGTCAT
* *
5889685 GTTTAAGTTATTTCGAATTCAT
1 GTTTAAGTAATTTCGAAGTCAT
5889707 ACAGTTTTAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.50
Consensus pattern (22 bp):
GTTTAAGTAATTTCGAAGTCAT
Found at i:5891881 original size:2 final size:2
Alignment explanation
Indices: 5891868--5891898 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5891858 TTTTTGAGGC
*
5891868 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5891899 GTGGTGAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5901493 original size:18 final size:18
Alignment explanation
Indices: 5901463--5901499 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5901453 AGTGGATTTA
5901463 TAGTGCAATAAACACGAT
1 TAGTGCAATAAACACGAT
5901481 TAGTGACAA-AAACACGAT
1 TAGTG-CAATAAACACGAT
5901499 T
1 T
5901500 TTTCAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (18 bp):
TAGTGCAATAAACACGAT
Found at i:5923729 original size:4 final size:4
Alignment explanation
Indices: 5923720--5923744 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5923710 GGTCGTTGGA
5923720 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
5923745 GGTGCCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:5924946 original size:56 final size:56
Alignment explanation
Indices: 5924884--5924996 Score: 190
Period size: 56 Copynumber: 2.0 Consensus size: 56
5924874 AATATAGTAT
* *
5924884 TTAAGTTAAAGTATAGATGAACTTGGTGGCAACACTTGATTGGAGGACATGTTGGG
1 TTAAGTTAAAGCATAGATGAACTTGGTGGCAACACTTGATTGGAGGACATGTGGGG
* *
5924940 TTAAGTTGAAGCATAGATGAACTTGGTGGCCACACTTGATTGGAGGACATGTGGGG
1 TTAAGTTAAAGCATAGATGAACTTGGTGGCAACACTTGATTGGAGGACATGTGGGG
5924996 T
1 T
5924997 CTTTTGGTCA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.28, C:0.11, G:0.32, T:0.29
Consensus pattern (56 bp):
TTAAGTTAAAGCATAGATGAACTTGGTGGCAACACTTGATTGGAGGACATGTGGGG
Found at i:5926554 original size:13 final size:13
Alignment explanation
Indices: 5926538--5926605 Score: 58
Period size: 13 Copynumber: 5.5 Consensus size: 13
5926528 CTGATAATTC
5926538 TATTTTATAAAAT
1 TATTTTATAAAAT
*
5926551 TA-TTT-T-AATT
1 TATTTTATAAAAT
5926561 CTATTTTATAAAAT
1 -TATTTTATAAAAT
*
5926575 TA-TTT-T-AATT
1 TATTTTATAAAAT
5926585 CTATTTTATAAAAT
1 -TATTTTATAAAAT
5926599 TATTTTA
1 TATTTTA
5926606 ATTCAATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 16
0.68 0.06 0.25
Matches are distributed among these distances:
10 6 0.14
11 6 0.14
12 12 0.28
13 13 0.30
14 6 0.14
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (13 bp):
TATTTTATAAAAT
Found at i:5926561 original size:24 final size:24
Alignment explanation
Indices: 5926532--5926615 Score: 159
Period size: 24 Copynumber: 3.5 Consensus size: 24
5926522 GGGGAGCTGA
5926532 TAATTCTATTTTATAAAATTATTT
1 TAATTCTATTTTATAAAATTATTT
5926556 TAATTCTATTTTATAAAATTATTT
1 TAATTCTATTTTATAAAATTATTT
5926580 TAATTCTATTTTATAAAATTATTT
1 TAATTCTATTTTATAAAATTATTT
*
5926604 TAATTCAATTTT
1 TAATTCTATTTT
5926616 GTTATTAAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (24 bp):
TAATTCTATTTTATAAAATTATTT
Found at i:5927813 original size:16 final size:16
Alignment explanation
Indices: 5927792--5927825 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5927782 TAAATTGTTT
*
5927792 TAATTTTAGTACTTAG
1 TAATTTTAGTACTAAG
5927808 TAATTTTAGTACTAAG
1 TAATTTTAGTACTAAG
5927824 TA
1 TA
5927826 TATTGATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (16 bp):
TAATTTTAGTACTAAG
Found at i:5929726 original size:16 final size:15
Alignment explanation
Indices: 5929705--5929747 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
5929695 TTAGTCATTG
5929705 TTAGTTATTTTTATAA
1 TTAGTTATTTTTA-AA
*
5929721 TTAGTTTATTTTTAAG
1 TTAG-TTATTTTTAAA
*
5929737 TGAGTTATTTT
1 TTAGTTATTTT
5929748 AATTTTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 8 0.33
17 9 0.38
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.63
Consensus pattern (15 bp):
TTAGTTATTTTTAAA
Found at i:5931627 original size:15 final size:15
Alignment explanation
Indices: 5931597--5931663 Score: 80
Period size: 15 Copynumber: 4.4 Consensus size: 15
5931587 CGTTTGGTAC
*
5931597 ATTACAATGCAATGTG
1 ATTACAA-GTAATGTG
*
5931613 ATTACAGGTAATGTG
1 ATTACAAGTAATGTG
*
5931628 ATTGCAAGTAATGTG
1 ATTACAAGTAATGTG
* *
5931643 ATTGCAAGCAATGTG
1 ATTACAAGTAATGTG
5931658 ATTACA
1 ATTACA
5931664 GAGAAAATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
15 39 0.87
16 6 0.13
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.31
Consensus pattern (15 bp):
ATTACAAGTAATGTG
Found at i:5931911 original size:20 final size:22
Alignment explanation
Indices: 5931883--5932062 Score: 116
Period size: 21 Copynumber: 8.5 Consensus size: 22
5931873 TCATATATTT
5931883 TATTTT-TATTTATTATTATAA
1 TATTTTATATTTATTATTATAA
5931904 TATTTTATATTTATT-TT-TAA
1 TATTTTATATTTATTATTATAA
* *
5931924 TATATTATATTTTATTATTAATTTA
1 TATTTTATA-TTTATTATT-A-TAA
** * *
5931949 TATAATATCATTTCTTA-AAT-A
1 TATTTTAT-ATTTATTATTATAA
* * **
5931970 TATTTT-TA-ATATCATATATTT
1 TATTTTATATTTATTAT-TATAA
5931991 TATTTT-TA-TTATTATTATAA
1 TATTTTATATTTATTATTATAA
5932011 TATTTTATATTTATT-TT-TAA
1 TATTTTATATTTATTATTATAA
5932031 TATATTTATATTTA-TATTATTAA
1 TAT-TTTATATTTATTATTA-TAA
5932054 T-TTTTATAT
1 TATTTTATAT
5932063 AATATCATAT
Statistics
Matches: 127, Mismatches: 16, Indels: 32
0.73 0.09 0.18
Matches are distributed among these distances:
18 3 0.02
19 1 0.01
20 30 0.24
21 55 0.43
22 17 0.13
23 5 0.04
25 15 0.12
26 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTTATATTTATTATTATAA
Found at i:5931948 original size:32 final size:32
Alignment explanation
Indices: 5931876--5932088 Score: 86
Period size: 32 Copynumber: 6.4 Consensus size: 32
5931866 TTTCATATCA
*
5931876 TATATTTTATTTTTATTTATTATTATAATATTT
1 TATA-TTTATTTTTATATATTATTATAATATTT
**
5931909 TATATTTATTTTTAATATATTA-TATTTTATTAT
1 TATATTTATTTTT-ATATATTATTATAATATT-T
* * * *
5931942 TA-ATTTA-TATAATATCATTTCTTAAATATATTTT
1 TATATTTATTTTTATAT-A-TTATTATA-ATA-TTT
* *
5931976 TAATATCATATATTTTATTTTTATTATTATTATAATATTT
1 T-ATAT--T-TA--TT-TTTATATA-TTATTATAATATTT
5932016 TATATTTATTTTTA-ATA-TATT-T-ATATTT
1 TATATTTATTTTTATATATTATTATAATATTT
* *
5932044 ATATTATTAATTTTTATATA--A-TATCATATTT
1 -TA-TATTTATTTTTATATATTATTATAATATTT
* *
5932075 TAAATATATTTTTA
1 TATATTTATTTTTA
5932089 ATGTCATATA
Statistics
Matches: 137, Mismatches: 22, Indels: 46
0.67 0.11 0.22
Matches are distributed among these distances:
28 6 0.04
29 13 0.09
30 23 0.17
31 12 0.09
32 25 0.18
33 19 0.14
34 6 0.04
35 3 0.02
36 4 0.03
37 1 0.01
38 1 0.01
39 6 0.04
40 4 0.03
41 3 0.02
42 7 0.05
43 4 0.03
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (32 bp):
TATATTTATTTTTATATATTATTATAATATTT
Found at i:5931975 original size:108 final size:109
Alignment explanation
Indices: 5931807--5932139 Score: 539
Period size: 108 Copynumber: 3.0 Consensus size: 109
5931797 AAAATATAAG
* *
5931807 TTTAATATATTTATATTTTTTATTATTATTTTTATATAATATCATTTCTTAAATATATTTTTCAT
1 TTTAATATATTTATA--TTTTATTATTA-ATTTATATAATATCATTTCTTAAATATATTTTTAAT
5931872 ATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATT
63 ATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATT
5931919 TTTAATATA-TTATATTTTATTATTAATTTATATAATATCATTTCTTAAATATATTTTTAATATC
1 TTTAATATATTTATATTTTATTATTAATTTATATAATATCATTTCTTAAATATATTTTTAATATC
5931983 ATATATTTTATTTTTA-TTATTATTATAATATTTTATATTTATT
66 ATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATT
5932026 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTTAA
1 TTTAATATATTTATATTT-TATTATTAA--TTTATATAATATCAT-TTCTTAAATATATTTTTAA
*
5932090 TGTCATATATTTTATTTTTATTTATTATTATAAT-TTTGTATATTTATT
62 TATCATATATTTTATTTTTATTTATTATTATAATATTT-TATATTTATT
5932138 TT
1 TT
5932140 CATTTCTTTA
Statistics
Matches: 211, Mismatches: 3, Indels: 14
0.93 0.01 0.06
Matches are distributed among these distances:
107 36 0.17
108 61 0.29
109 20 0.09
111 58 0.27
112 36 0.17
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (109 bp):
TTTAATATATTTATATTTTATTATTAATTTATATAATATCATTTCTTAAATATATTTTTAATATC
ATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATT
Found at i:5932047 original size:75 final size:77
Alignment explanation
Indices: 5931870--5932054 Score: 182
Period size: 80 Copynumber: 2.4 Consensus size: 77
5931860 TATATTTTTC
* * * * *
5931870 ATATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATTTTTAATATATTATATT
1 ATATAATATATTTTATTTATATTT-TTAATATAATATTTTATATTTATTATTAATATATAATATT
5931935 TTATTATTAATTT
65 TTATTATTAATTT
** *
5931948 ATATAATATCATTTCTTAAATATATTTTTAATATCATATATTTTATTTTTATTATT-AT-TATAA
1 ATATAATAT-A-TT-TTATTTATATTTTTAATAT-A-ATATTTTATATTTATTATTAATATATAA
*
5932011 TATTTTA-TATTTATTT
61 TATTTTATTATTAATTT
*
5932027 -T-TAATATATTTATATTTATATTATTAAT
1 ATATAATATATTT-TATTTATATTTTTAAT
5932055 TTTTATATAA
Statistics
Matches: 89, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
74 1 0.01
75 15 0.17
76 1 0.01
77 6 0.07
78 9 0.10
79 9 0.10
80 19 0.21
81 12 0.13
82 17 0.19
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (77 bp):
ATATAATATATTTTATTTATATTTTTAATATAATATTTTATATTTATTATTAATATATAATATTT
TATTATTAATTT
Found at i:5932061 original size:15 final size:14
Alignment explanation
Indices: 5931820--5932255 Score: 96
Period size: 14 Copynumber: 31.4 Consensus size: 14
5931810 AATATATTTA
5931820 TATTTTT-TATTAT
1 TATTTTTATATTAT
5931833 TATTTTTATATAATAT
1 TATTTTTATAT--TAT
* *
5931849 CATTTCTTA-AATA-
1 TATTT-TTATATTAT
*
5931862 TATTTTTCATATCA-
1 TATTTTT-ATATTAT
5931876 TATATTTTAT-TT-T
1 TAT-TTTTATATTAT
*
5931889 TATTTAT-TATTAT
1 TATTTTTATATTAT
*
5931902 AATATTTTATA-T-T
1 TAT-TTTTATATTAT
5931915 TATTTTTA-ATATAT
1 TATTTTTATAT-TAT
*
5931929 TATATTT-TATTAT
1 TATTTTTATATTAT
* *
5931942 TAATTTATATAATAT
1 T-ATTTTTATATTAT
* *
5931957 CATTTCTTA-AATA-
1 TATTT-TTATATTAT
*
5931970 TATTTTTAATATCA-
1 TATTTTT-ATATTAT
5931984 TATATTTTAT-TT-T
1 TAT-TTTTATATTAT
*
5931997 TA-TTAT-TATTAT
1 TATTTTTATATTAT
*
5932009 AATATTTTATA-T-T
1 TAT-TTTTATATTAT
5932022 TATTTTTA-ATATATT
1 TATTTTTATAT-TA-T
*
5932037 TATATTTATATTAT
1 TATTTTTATATTAT
5932051 TAATTTTTATATAATAT
1 T-ATTTTTATAT--TAT
* *
5932068 CATATTTTA-AATA-
1 TAT-TTTTATATTAT
5932081 TATTTTTA-ATGTCA-
1 TATTTTTATAT-T-AT
5932095 TATATTTTAT-TT-T
1 TAT-TTTTATATTAT
*
5932108 TATTTAT-TATTAT
1 TATTTTTATATTAT
*
5932121 AATTTTGTATATTTAT
1 TATTTT-TATA-TTAT
* *
5932137 T-TTCATTTCT-TTAA
1 TATT--TTTATATTAT
5932151 TATATTTTATATTA-
1 TAT-TTTTATATTAT
*
5932165 TATATTTTATTTTAAT
1 TAT-TTTTATATT-AT
*
5932181 T-TGTTTTATCTATAT
1 TAT-TTTTATAT-TAT
* **
5932196 TATATAAATATTA-
1 TATTTTTATATTAT
5932209 -ATTTTTATATT-T
1 TATTTTTATATTAT
*
5932221 TATTTTTATAATTTT
1 TATTTTTAT-ATTAT
*
5932236 TATTCTTATATTAT
1 TATTTTTATATTAT
5932250 ATATTT
1 -TATTT
5932256 ATTTTAATTA
Statistics
Matches: 312, Mismatches: 50, Indels: 120
0.65 0.10 0.25
Matches are distributed among these distances:
10 1 0.00
11 9 0.03
12 40 0.13
13 58 0.19
14 87 0.28
15 81 0.26
16 23 0.07
17 13 0.04
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.64
Consensus pattern (14 bp):
TATTTTTATATTAT
Found at i:5932096 original size:111 final size:111
Alignment explanation
Indices: 5931807--5932139 Score: 554
Period size: 111 Copynumber: 3.0 Consensus size: 111
5931797 AAAATATAAG
*
5931807 TTTAATATATTTATATTTT-TTATTATTATTTTTATATAATATCATTTCTTAAATATATTTTTCA
1 TTTAATATATTTATATTTTATTATTA--ATTTTTATATAATATCATTTCTTAAATATATTTTTAA
5931871 TATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATT
64 TATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATT
5931919 TTTAATATA-TTATATTTTATTATTAA--TTTATATAATATCATTTCTTAAATATATTTTTAATA
1 TTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATA
5931981 TCATATATTTTATTTTTA-TTATTATTATAATATTTTATATTTATT
66 TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATT
5932026 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTTAA
1 TTTAATATATTTATATTT-TATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTAA
*
5932090 TGTCATATATTTTATTTTTATTTATTATTATAAT-TTTGTATATTTATT
64 TATCATATATTTTATTTTTATTTATTATTATAATATTT-TATATTTATT
5932138 TT
1 TT
5932140 CATTTCTTTA
Statistics
Matches: 211, Mismatches: 2, Indels: 16
0.92 0.01 0.07
Matches are distributed among these distances:
107 36 0.17
108 61 0.29
109 9 0.04
110 1 0.00
111 62 0.29
112 42 0.20
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (111 bp):
TTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATA
TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATT
Found at i:5932111 original size:27 final size:26
Alignment explanation
Indices: 5931818--5932139 Score: 190
Period size: 27 Copynumber: 11.8 Consensus size: 26
5931808 TTAATATATT
* *
5931818 TATATTTTTTATTATTATTTTT-ATA
1 TATATATTTTATTTTTATTTTTAATA
** * *
5931843 TAATATCATTTCTTAAATATATTTTTCATA
1 T-ATAT-A-TT-TTATTTTTATTTTTAATA
*
5931873 TCATATATTTTATTTTTATTTATTATTA
1 T-ATATATTTTATTTTTATTT-TTAATA
*
5931901 TA-ATATTTTATATTTATTTTTAATA
1 TATATATTTTATTTTTATTTTTAATA
*
5931926 TATTATATTTTATTATTAATTTATATAATA
1 TA-TATATTTTATT-TTTATTT-T-TAATA
* ** *
5931956 TCAT-T-TCTTAAATATATTTTTAATA
1 T-ATATATTTTATTTTTATTTTTAATA
* *
5931981 TCATATATTTTATTTTTATTATTATTA
1 T-ATATATTTTATTTTTATTTTTAATA
*
5932008 TA-ATATTTTATATTTATTTTTAATA
1 TATATATTTTATTTTTATTTTTAATA
*
5932033 TATTTATATTTATATTATTAATTTTTATATAA
1 TA--TATATTT-TATT-TTTATTTTTA-AT-A
** * *
5932065 TATCATATTTTAAATATATTTTTAATG
1 TAT-ATATTTTATTTTTATTTTTAATA
*
5932092 TCATATATTTTATTTTTATTTATTATTA
1 T-ATATATTTTATTTTTATTT-TTAATA
*
5932120 TA-AT-TTTGTATATTTATTTT
1 TATATATTT-TATTTTTATTTT
5932140 CATTTCTTTA
Statistics
Matches: 230, Mismatches: 42, Indels: 50
0.71 0.13 0.16
Matches are distributed among these distances:
25 43 0.19
26 35 0.15
27 55 0.24
28 34 0.15
29 24 0.10
30 27 0.12
31 9 0.04
32 3 0.01
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (26 bp):
TATATATTTTATTTTTATTTTTAATA
Found at i:5932158 original size:32 final size:31
Alignment explanation
Indices: 5932094--5932176 Score: 78
Period size: 32 Copynumber: 2.5 Consensus size: 31
5932084 TTTTAATGTC
*
5932094 ATATATTTTATTTTTATTTATTATTATAATTTT
1 ATATA-TTTA-TTTTATTTATTAATATAATTTT
* *
5932127 GTATATTTATTTTCATTTCTTTAATAT-ATTTT
1 ATATATTTATTTT-ATTT-ATTAATATAATTTT
*
5932159 ATATTATATATTTTATTT
1 ATA-TATTTATTTTATTT
5932177 TAATTTGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
31 4 0.10
32 19 0.45
33 19 0.45
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.67
Consensus pattern (31 bp):
ATATATTTATTTTATTTATTAATATAATTTT
Found at i:5932176 original size:38 final size:37
Alignment explanation
Indices: 5932128--5932213 Score: 93
Period size: 38 Copynumber: 2.3 Consensus size: 37
5932118 TATAATTTTG
* *
5932128 TATATTTATTTTCATTTCTTTAATATATTTTATATTA
1 TATATTTATTTTAATTTCTTTAATATATATTATATTA
* * *
5932165 TATATTTTATTTTAATTTGTTTTATCTATATTATA-TA
1 TATA-TTTATTTTAATTTCTTTAATATATATTATATTA
* *
5932202 AATATTAATTTT
1 TATATTTATTTT
5932214 TATATTTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
36 7 0.17
37 9 0.22
38 25 0.61
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (37 bp):
TATATTTATTTTAATTTCTTTAATATATATTATATTA
Found at i:5932195 original size:40 final size:41
Alignment explanation
Indices: 5932112--5932264 Score: 106
Period size: 40 Copynumber: 3.7 Consensus size: 41
5932102 TATTTTTATT
* * *
5932112 TATTATTATAATTTTGTATATTTATTTTCATTTCTT-TAA--TA
1 TATTATTAT-ATTATATAT-TTTATTTTAATTT-TTATAATCTA
*
5932153 TATT-TTATATTATATATTTTATTTTAATTTGTT-TTATCTA
1 TATTATTATATTATATATTTTATTTTAATTT-TTATAATCTA
* * *
5932193 TATTATATAAATATTA-AT-TTTTATATTTTATTTTTATAATTTT
1 TATTAT-T--ATATTATATATTTTAT-TTTAATTTTTATAATCTA
*
5932236 TATTCTTATATTATATA-TTTATTTTAATT
1 TATTATTATATTATATATTTTATTTTAATT
5932265 ATAATATTAT
Statistics
Matches: 91, Mismatches: 11, Indels: 21
0.74 0.09 0.17
Matches are distributed among these distances:
38 16 0.18
39 7 0.08
40 22 0.24
41 12 0.13
42 10 0.11
43 18 0.20
44 6 0.07
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (41 bp):
TATTATTATATTATATATTTTATTTTAATTTTTATAATCTA
Found at i:5932207 original size:51 final size:53
Alignment explanation
Indices: 5932152--5932272 Score: 128
Period size: 49 Copynumber: 2.4 Consensus size: 53
5932142 TTTCTTTAAT
*
5932152 ATATTTTATATTATATATTTTATTTTAAT-TTGTTTTA-TC-TATATTATATAA
1 ATATTTTATATTATATATTTTATTTTAATAAT-TTTTATTCTTATATTATATAA
* * * *
5932203 ATA-TTAAT-TTTTATATTTTATTTTTATAATTTTTATTCTTATATTATATAT
1 ATATTTTATATTATATATTTTATTTTAATAATTTTTATTCTTATATTATATAA
*
5932254 TTATTTTA-ATTATAATATT
1 ATATTTTATATTAT-ATATT
5932273 ATAAAATATT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
49 22 0.39
50 7 0.12
51 16 0.29
52 6 0.11
53 5 0.09
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (53 bp):
ATATTTTATATTATATATTTTATTTTAATAATTTTTATTCTTATATTATATAA
Found at i:5932227 original size:13 final size:13
Alignment explanation
Indices: 5932209--5932257 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
5932199 ATAAATATTA
5932209 ATTTTTATATTTT
1 ATTTTTATATTTT
5932222 ATTTTTATAATTTTT
1 ATTTTTAT-A-TTTT
* *
5932237 ATTCTTATATTAT
1 ATTTTTATATTTT
*
5932250 ATATTTAT
1 ATTTTTAT
5932258 TTTAATTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 17 0.57
14 2 0.07
15 11 0.37
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTTATATTTT
Found at i:5932252 original size:22 final size:22
Alignment explanation
Indices: 5932207--5932252 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5932197 ATATAAATAT
* *
5932207 TAATTTTTATATTTTATTTTTA
1 TAATTTTTATATCTTATTTATA
5932229 TAATTTTTAT-TCTTATATTATA
1 TAATTTTTATATCTTAT-TTATA
5932251 TA
1 TA
5932253 TTTATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TAATTTTTATATCTTATTTATA
Found at i:5942360 original size:22 final size:22
Alignment explanation
Indices: 5942306--5942360 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
5942296 AAAAGTATAT
* *
5942306 TTATTTTATTTAAATTAACTTA
1 TTATTTAATTTAAATTAACTGA
*
5942328 TTATTTTATTTAAATTAA-TGA
1 TTATTTAATTTAAATTAACTGA
*
5942349 TTGTATTAATTT
1 TTAT-TTAATTT
5942361 CGTTAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 5 0.17
22 24 0.83
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (22 bp):
TTATTTAATTTAAATTAACTGA
Found at i:5944466 original size:30 final size:31
Alignment explanation
Indices: 5944408--5944466 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
5944398 GTGAATTTTG
*
5944408 ATTTCTTTTTCTTCTGCCTTATTCACTTCTA
1 ATTTCTTTTTCTTCTGCCTTATTAACTTCTA
* *
5944439 ATTTC-TTTTCTTCTGTCTTGTTAACTTC
1 ATTTCTTTTTCTTCTGCCTTATTAACTTC
5944467 CTACTTGTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.12, C:0.24, G:0.05, T:0.59
Consensus pattern (31 bp):
ATTTCTTTTTCTTCTGCCTTATTAACTTCTA
Found at i:5951605 original size:29 final size:29
Alignment explanation
Indices: 5951573--5951631 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
5951563 TCTCACTCAA
*
5951573 TTTTAAATTTTTGTTTCCATT-TATATTAT
1 TTTTAAATTTTTATTTCCATTCTAT-TTAT
* * *
5951602 TTTTTATTTTTTATTTCTATTCTATTTAT
1 TTTTAAATTTTTATTTCCATTCTATTTAT
5951631 T
1 T
5951632 CATATATGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (29 bp):
TTTTAAATTTTTATTTCCATTCTATTTAT
Found at i:5963099 original size:35 final size:35
Alignment explanation
Indices: 5963053--5963134 Score: 146
Period size: 35 Copynumber: 2.3 Consensus size: 35
5963043 AATTGTGACA
*
5963053 ATTACCTCCACTGCTTACAAAAGAAATAACAAAAT
1 ATTACCCCCACTGCTTACAAAAGAAATAACAAAAT
*
5963088 ATTACCCCCACTGCTTACAAAAGAAATAGCAAAAT
1 ATTACCCCCACTGCTTACAAAAGAAATAACAAAAT
5963123 ATTACCCCCACT
1 ATTACCCCCACT
5963135 TAGTGGGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.44, C:0.28, G:0.06, T:0.22
Consensus pattern (35 bp):
ATTACCCCCACTGCTTACAAAAGAAATAACAAAAT
Found at i:5963398 original size:4 final size:4
Alignment explanation
Indices: 5963391--5963416 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5963381 CTTCATTCAT
5963391 TCAC TCAC TCAC TCAC TCAC TCAC TC
1 TCAC TCAC TCAC TCAC TCAC TCAC TC
5963417 CCTCCCTTCA
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:0.50, G:0.00, T:0.27
Consensus pattern (4 bp):
TCAC
Found at i:5967840 original size:35 final size:35
Alignment explanation
Indices: 5967794--5967867 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
5967784 TGAGCTCGAT
5967794 AATTCTTATTTGGATAAAGATTAATGAAGTAAAAC
1 AATTCTTATTTGGATAAAGATTAATGAAGTAAAAC
5967829 AATTCTTATTTGGATAAAGATTAATGAAGTAAAAC
1 AATTCTTATTTGGATAAAGATTAATGAAGTAAAAC
5967864 AATT
1 AATT
5967868 AACCTTTAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (35 bp):
AATTCTTATTTGGATAAAGATTAATGAAGTAAAAC
Found at i:5989012 original size:17 final size:16
Alignment explanation
Indices: 5988973--5989015 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
5988963 AAAAAAATAA
5988973 AAATTTTAA-AATTAT
1 AAATTTTAATAATTAT
*
5988988 -AGTTTTAATAATTAAT
1 AAATTTTAATAATT-AT
5989004 AAATTTTAATAA
1 AAATTTTAATAA
5989016 ATATTACATC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 7 0.30
15 4 0.17
16 2 0.09
17 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
AAATTTTAATAATTAT
Found at i:5989310 original size:10 final size:11
Alignment explanation
Indices: 5989291--5989318 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5989281 AATATAATTG
5989291 ATTAAAAAAAT
1 ATTAAAAAAAT
5989302 ATTAAAAAAAT
1 ATTAAAAAAAT
5989313 ATTAAA
1 ATTAAA
5989319 TATTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
ATTAAAAAAAT
Found at i:5992394 original size:12 final size:13
Alignment explanation
Indices: 5992372--5992406 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
5992362 TGTTTGTTTT
5992372 TAAATTAAATTAA
1 TAAATTAAATTAA
5992385 TAAA-TAAATTAA
1 TAAATTAAATTAA
*
5992397 CAAATTAAAT
1 TAAATTAAAT
5992407 AACTTTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (13 bp):
TAAATTAAATTAA
Found at i:5994316 original size:2 final size:2
Alignment explanation
Indices: 5994309--5994342 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5994299 CATTAAACGC
5994309 AT AT 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 AT AT
5994343 CAGCATTCAT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5994499 original size:20 final size:22
Alignment explanation
Indices: 5994474--5994522 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
5994464 AAGATTTGAA
* *
5994474 TTTAAATAT-TTGAAAAAGT-T
1 TTTAAATATATTCAAAAAATAT
5994494 TTTAAAT-TATTCAAAAAATAT
1 TTTAAATATATTCAAAAAATAT
5994515 TTTAAATA
1 TTTAAATA
5994523 AGTTTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 15 0.62
21 8 0.33
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (22 bp):
TTTAAATATATTCAAAAAATAT
Found at i:6001279 original size:32 final size:32
Alignment explanation
Indices: 6001240--6001304 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
6001230 TCCAATGCTA
6001240 TTGTTATCGACATTAACTGTCTTTACTATTGT
1 TTGTTATCGACATTAACTGTCTTTACTATTGT
6001272 TTGTTATCGACATTAACTGTCTTTACTATTGT
1 TTGTTATCGACATTAACTGTCTTTACTATTGT
6001304 T
1 T
6001305 GACCCCTTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.15, G:0.12, T:0.51
Consensus pattern (32 bp):
TTGTTATCGACATTAACTGTCTTTACTATTGT
Found at i:6009838 original size:15 final size:15
Alignment explanation
Indices: 6009804--6009838 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6009794 AATTACAATT
*
6009804 ATATATATACTTTTA
1 ATATATATACTTTAA
*
6009819 GTATATATACTTTAA
1 ATATATATACTTTAA
6009834 ATATA
1 ATATA
6009839 AATATATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (15 bp):
ATATATATACTTTAA
Found at i:6011394 original size:15 final size:16
Alignment explanation
Indices: 6011361--6011393 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6011351 ATAATTTTTT
*
6011361 AATTTTTAAAAATAAA
1 AATTCTTAAAAATAAA
6011377 AATTCTTAAAAATAAA
1 AATTCTTAAAAATAAA
6011393 A
1 A
6011394 TCCACATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTCTTAAAAATAAA
Found at i:6011571 original size:13 final size:15
Alignment explanation
Indices: 6011542--6011572 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
6011532 GAATATAATT
6011542 AAAAATATAAATAAA
1 AAAAATATAAATAAA
6011557 AAAAAT-TAAATAAA
1 AAAAATATAAATAAA
6011571 AA
1 AA
6011573 TTTTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAAATATAAATAAA
Found at i:6011771 original size:24 final size:24
Alignment explanation
Indices: 6011724--6011773 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
6011714 TATTAATTAT
* *
6011724 TTAATAAAAAAATATTTTAAAAAA
1 TTAATAAAAAAATAATATAAAAAA
*
6011748 TTAATAAAAAAATAATATATAAAA
1 TTAATAAAAAAATAATATAAAAAA
6011772 TT
1 TT
6011774 TCAAAAATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
TTAATAAAAAAATAATATAAAAAA
Found at i:6014260 original size:14 final size:12
Alignment explanation
Indices: 6014231--6014268 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 12
6014221 GAGGGGAAAG
6014231 AGAAA-AAAAAA
1 AGAAAGAAAAAA
6014242 AGAAAGAAAAAGA
1 AGAAAGAAAAA-A
6014255 AGGAAAGAAAAAA
1 A-GAAAGAAAAAA
6014268 A
1 A
6014269 ATAAAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.21
12 5 0.21
13 4 0.17
14 10 0.42
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAAAA
Found at i:6030798 original size:14 final size:14
Alignment explanation
Indices: 6030779--6030806 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6030769 GTCTTGCTCT
6030779 TATGGATCATCTCC
1 TATGGATCATCTCC
6030793 TATGGATCATCTCC
1 TATGGATCATCTCC
6030807 ACTTCATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.36
Consensus pattern (14 bp):
TATGGATCATCTCC
Found at i:6035207 original size:2 final size:2
Alignment explanation
Indices: 6035200--6035225 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6035190 TATTAATTAT
6035200 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
6035226 ATGGTGTCTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6040998 original size:44 final size:44
Alignment explanation
Indices: 6040940--6041023 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
6040930 ATCAATACCA
6040940 TATATATAAAGGAATGAACAATATAATAATCAAGATTCATACTG
1 TATATATAAAGGAATGAACAATATAATAATCAAGATTCATACTG
* *
6040984 TATATATAAGGGAATGAACAATGTAATAATCAAGATTCAT
1 TATATATAAAGGAATGAACAATATAATAATCAAGATTCAT
6041024 TTAATAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (44 bp):
TATATATAAAGGAATGAACAATATAATAATCAAGATTCATACTG
Found at i:6065164 original size:24 final size:24
Alignment explanation
Indices: 6065137--6065184 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
6065127 AATGCCAGAG
*
6065137 ATGCCTTTCCTCTATTTAATGAAT
1 ATGCCTTTCCTATATTTAATGAAT
6065161 ATGCCTTTCCTATATTTAATGAAT
1 ATGCCTTTCCTATATTTAATGAAT
6065185 TTTTACGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.46
Consensus pattern (24 bp):
ATGCCTTTCCTATATTTAATGAAT
Found at i:6065249 original size:2 final size:2
Alignment explanation
Indices: 6065242--6065274 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
6065232 TTGTAAATAG
*
6065242 CA CA CA CA CA CA CA CA CA CA CA CA CA CA TA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
6065275 TACTATTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.48, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:6096143 original size:19 final size:19
Alignment explanation
Indices: 6096119--6096155 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6096109 TAAACTAACT
6096119 TTTTAAGAAATAATAATAA
1 TTTTAAGAAATAATAATAA
* *
6096138 TTTTAATATATAATAATA
1 TTTTAAGAAATAATAATA
6096156 TCTTAATCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
TTTTAAGAAATAATAATAA
Found at i:6098173 original size:2 final size:2
Alignment explanation
Indices: 6098166--6098195 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6098156 ATGGTACATG
*
6098166 AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6098196 TGGGTACATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6102611 original size:18 final size:17
Alignment explanation
Indices: 6102562--6102607 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
6102552 AAGCCTACCA
6102562 GGATAACCAGCT--GGT
1 GGATAACCAGCTGCGGT
* *
6102577 GGATATCCACCATGCGGT
1 GGATAACCAGC-TGCGGT
6102595 GGATAACCAGCTG
1 GGATAACCAGCTG
6102608 GCGGATACGC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
15 9 0.38
16 1 0.04
17 2 0.08
18 12 0.50
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (17 bp):
GGATAACCAGCTGCGGT
Found at i:6102613 original size:15 final size:15
Alignment explanation
Indices: 6102562--6102614 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
6102552 AAGCCTACCA
6102562 GGATAACCAGCTGGT
1 GGATAACCAGCTGGT
6102577 GGATATCCACCATGC-GGT
1 GGATA---ACCA-GCTGGT
*
6102595 GGATAACCAGCTGGC
1 GGATAACCAGCTGGT
6102610 GGATA
1 GGATA
6102615 CGCCGCTGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
14 2 0.06
15 16 0.50
18 12 0.38
19 2 0.06
ACGTcount: A:0.26, C:0.23, G:0.32, T:0.19
Consensus pattern (15 bp):
GGATAACCAGCTGGT
Found at i:6102649 original size:18 final size:18
Alignment explanation
Indices: 6102622--6102720 Score: 105
Period size: 18 Copynumber: 5.7 Consensus size: 18
6102612 ATACGCCGCT
* * *
6102622 GGAGGGTATCCTCCTGGG
1 GGAGGATATCCACCTGGA
*
6102640 GGAGGATATCCA---GCA
1 GGAGGATATCCACCTGGA
* * *
6102655 GGTGGATATCCGCCAGGA
1 GGAGGATATCCACCTGGA
6102673 GGAGGATATCCACCTGGA
1 GGAGGATATCCACCTGGA
6102691 GGAGGATATCCACCTGGA
1 GGAGGATATCCACCTGGA
*
6102709 GGAGGGTATCCA
1 GGAGGATATCCA
6102721 GCAGGTGGGT
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
15 11 0.16
18 56 0.84
ACGTcount: A:0.24, C:0.21, G:0.37, T:0.17
Consensus pattern (18 bp):
GGAGGATATCCACCTGGA
Found at i:6119857 original size:17 final size:17
Alignment explanation
Indices: 6119835--6119875 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
6119825 AAAGCTCTTA
*
6119835 AAAAAAATAACTTTTTT
1 AAAAAAATAAATTTTTT
6119852 AAAAAAATAAATTTTTT
1 AAAAAAATAAATTTTTT
6119869 AAAAAAA
1 AAAAAAA
6119876 GAGCTTTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAAAAATAAATTTTTT
Found at i:6120058 original size:14 final size:14
Alignment explanation
Indices: 6120039--6120065 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6120029 CCAAAATTAT
6120039 AACTTATAAAAAAG
1 AACTTATAAAAAAG
6120053 AACTTATAAAAAA
1 AACTTATAAAAAA
6120066 AAATTTACCA
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:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (14 bp):
AACTTATAAAAAAG
Found at i:6120576 original size:16 final size:17
Alignment explanation
Indices: 6120555--6120589 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
6120545 TGATCATAGG
*
6120555 TACTTCTTTA-TACTTA
1 TACTTCTTGATTACTTA
6120571 TACTTCTTGATTACTTA
1 TACTTCTTGATTACTTA
6120588 TA
1 TA
6120590 GTATACGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.26, C:0.17, G:0.03, T:0.54
Consensus pattern (17 bp):
TACTTCTTGATTACTTA
Found at i:6127429 original size:15 final size:16
Alignment explanation
Indices: 6127409--6127447 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
6127399 AAAAAATAAA
6127409 ATAAAATTA-TAATTT
1 ATAAAATTAGTAATTT
6127424 ATAAAA-TAGTAATTT
1 ATAAAATTAGTAATTT
6127439 ATAAAATTA
1 ATAAAATTA
6127448 ATGAAGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
ATAAAATTAGTAATTT
Found at i:6128421 original size:2 final size:2
Alignment explanation
Indices: 6128414--6128446 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6128404 ATTTTAATTT
6128414 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6128447 TCTAGCTGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6138965 original size:18 final size:18
Alignment explanation
Indices: 6138942--6138978 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
6138932 TTAATATGTT
6138942 AAAGGTGGATTAATGATC
1 AAAGGTGGATTAATGATC
*
6138960 AAAGGTTGATTAATGATC
1 AAAGGTGGATTAATGATC
6138978 A
1 A
6138979 TTAGTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.24, T:0.30
Consensus pattern (18 bp):
AAAGGTGGATTAATGATC
Found at i:6139861 original size:3 final size:3
Alignment explanation
Indices: 6139842--6139927 Score: 100
Period size: 3 Copynumber: 28.3 Consensus size: 3
6139832 GGACTTGGAG
* * * *
6139842 AGA AAA AGA AGGA AGA AGA AGG AGA AGA AGA AGA GGA AGA GGA AGA
1 AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * *
6139888 GGA AGA TGA AGA AGA AGA AGA AGA AGG AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
6139928 AATAATGAAG
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
3 65 0.96
4 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:6139937 original size:24 final size:23
Alignment explanation
Indices: 6139854--6139952 Score: 76
Period size: 24 Copynumber: 4.0 Consensus size: 23
6139844 AAAAAGAAGG
*
6139854 AAGAAGAAGG-AGAAGAAGAAGAGG
1 AAGAAGAAGGCA-AAGAAGAAGA-A
* *
6139878 AAGAGGAAGAGGAAGATGAAGAAGAA
1 AAGAAGAAG-GCAA-A-GAAGAAGAA
6139904 GAAGAAGAAGG-AGAAGAAGAAGAA
1 -AAGAAGAAGGCA-AAGAAGAAGAA
*
6139928 AATAATGAAGGCAAAGAAGAAGAA
1 AAGAA-GAAGGCAAAGAAGAAGAA
6139952 A
1 A
6139953 GGACTAAGCT
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
23 4 0.06
24 34 0.54
25 5 0.08
26 4 0.06
27 16 0.25
ACGTcount: A:0.61, C:0.01, G:0.35, T:0.03
Consensus pattern (23 bp):
AAGAAGAAGGCAAAGAAGAAGAA
Found at i:6139949 original size:12 final size:11
Alignment explanation
Indices: 6139843--6139953 Score: 68
Period size: 12 Copynumber: 9.5 Consensus size: 11
6139833 GACTTGGAGA
6139843 GAAA-AAGAAG
1 GAAAGAAGAAG
6139853 G-AAGAAGAAG
1 GAAAGAAGAAG
6139863 GAGAAGAAGAAGAG
1 GA-AAGAAG-A-AG
6139877 GAAGAGGAAG-AG
1 GAA-A-GAAGAAG
6139889 GAAGATGAAGAAG
1 GAA-A-GAAGAAG
*
6139902 AAGAAGAAGAAG
1 GA-AAGAAGAAG
6139914 GAGAAGAAGAAG
1 GA-AAGAAGAAG
* *
6139926 AAAATAATGAAG
1 GAAAGAA-GAAG
6139938 GCAAAGAAGAA-
1 G-AAAGAAGAAG
6139949 GAAAG
1 GAAAG
6139954 GACTAAGCTC
Statistics
Matches: 83, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
9 2 0.02
10 12 0.14
11 5 0.06
12 43 0.52
13 11 0.13
14 6 0.07
15 4 0.05
ACGTcount: A:0.60, C:0.01, G:0.36, T:0.03
Consensus pattern (11 bp):
GAAAGAAGAAG
Found at i:6154034 original size:26 final size:26
Alignment explanation
Indices: 6154005--6154058 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
6153995 TTTTATAACC
6154005 TTTAATTAAAAAAAATTTATATATTT
1 TTTAATTAAAAAAAATTTATATATTT
* * * *
6154031 TTTATTTTAAATAAATTTTTATATTT
1 TTTAATTAAAAAAAATTTATATATTT
6154057 TT
1 TT
6154059 ATTTTAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTAATTAAAAAAAATTTATATATTT
Found at i:6154072 original size:26 final size:26
Alignment explanation
Indices: 6154017--6154065 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
6154007 TAATTAAAAA
6154017 AAATTTATATATTTTTTATTTTAAAT
1 AAATTTATATATTTTTTATTTTAAAT
*
6154043 AAATTTTTATA-TTTTTATTTTAA
1 AAATTTATATATTTTTTATTTTAA
6154066 GTTAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
AAATTTATATATTTTTTATTTTAAAT
Found at i:6158416 original size:348 final size:355
Alignment explanation
Indices: 6157799--6158472 Score: 855
Period size: 348 Copynumber: 1.9 Consensus size: 355
6157789 GTATATATAC
* ** * *
6157799 TAAAAGTATTTTAATATATTATATATAATAGTAATTATATTTTTTATAAATGAACTCATTGTATA
1 TAAAAGCATTTTAATATATTATATATAATAGTAATTATATTCCTTATAAATGAACTCAATATATA
* * *
6157864 TAAAGTATATATACTAAAAGACATTATAGGTCAATTAATAATCATAATTTTCTTAATTAATTTAA
66 TAAAGTATATATACTAAAAGACATTACAGGTCAATTAATAATCATAAGTTTCATAATTAATTTAA
*
6157929 TTAACTATATGAGTTTATCCTTAATTATATGAAATTAAAAAAAATAACTAAGTTTCAAAATTATT
131 TTAACTATATGAGTTTATCCTTAATTATAT--AATTAAAAAAAATAACTAAGTTTCAAAACTATT
* * * * *
6157994 GTAATCTCATAACTTCGCTTTAGATTTATATGTTATAAGTTTATACAAACAAAGGTATATATATT
194 CTAATCTCACAACTTCGCTTTAAATTTATATATTATAAGTTTATACAAACAAAGATATATATATT
*
6158059 ATAATTTTATGAGTTATAATTTTTGTAATGTTAACACAAAAT-AGAAAGTAAATAT-ATTTATAT
259 ATAATTTTATAAGTTATAA-TTTTGTAATGTTAACA-AAAATCA-AAAGTAAATATGA-TTATAT
6158122 TTAAATACGTATATATATATATACACACACACACAT
320 TTAAATACGTATATATATATATACACACACACACAT
6158158 TAAAAGCATTTT-A-ATA-TATATATAATAG-AATTATATTCCTTATAAATGAA-TCAATATA-A
1 TAAAAGCATTTTAATATATTATATATAATAGTAATTATATTCCTTATAAATGAACTCAATATATA
* * *
6158217 TAAAGTA-ATA-ATTAAAAGATA-TACAGGT-AATTAATAATTAT-AGTTTCATAATTAATTTAA
66 TAAAGTATATATACTAAAAGACATTACAGGTCAATTAATAATCATAAGTTTCATAATTAATTTAA
* * * * *
6158277 TTAACTATGTAGGGTTTGTCCTTAA-TATAT-A-TAAAAAAGAA-AA-TAAGTTTTACAACTATT
131 TTAACTATAT-GAGTTTATCCTTAATTATATAATTAAAAAA-AATAACTAAGTTTCAAAACTATT
* *
6158337 CTAATCTCACAACTTCTC-TTAAATTTATATATTATAAGTTTATATAAACAAAGTATATATATTA
194 CTAATCTCACAACTTCGCTTTAAATTTATATATTATAAGTTTATACAAACAAAG---ATATA-TA
*
6158401 TAATTAATAATTTTATAAGTTATAATTTTGTAATGTTAACATAAATCAAAAGTAAATATGATTAT
255 T-ATT-ATAATTTTATAAGTTATAATTTTGTAATGTTAACAAAAATCAAAAGTAAATATGATTAT
6158466 ATTTAAA
318 ATTTAAA
6158473 GTATTATATA
Statistics
Matches: 279, Mismatches: 26, Indels: 33
0.83 0.08 0.10
Matches are distributed among these distances:
342 32 0.11
343 29 0.10
344 9 0.03
345 7 0.03
346 29 0.10
347 21 0.08
348 49 0.18
349 24 0.09
350 6 0.02
351 9 0.03
352 3 0.01
353 8 0.03
354 6 0.02
355 20 0.07
356 12 0.04
357 3 0.01
358 1 0.00
359 11 0.04
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (355 bp):
TAAAAGCATTTTAATATATTATATATAATAGTAATTATATTCCTTATAAATGAACTCAATATATA
TAAAGTATATATACTAAAAGACATTACAGGTCAATTAATAATCATAAGTTTCATAATTAATTTAA
TTAACTATATGAGTTTATCCTTAATTATATAATTAAAAAAAATAACTAAGTTTCAAAACTATTCT
AATCTCACAACTTCGCTTTAAATTTATATATTATAAGTTTATACAAACAAAGATATATATATTAT
AATTTTATAAGTTATAATTTTGTAATGTTAACAAAAATCAAAAGTAAATATGATTATATTTAAAT
ACGTATATATATATATACACACACACACAT
Found at i:6171177 original size:125 final size:122
Alignment explanation
Indices: 6171019--6171243 Score: 351
Period size: 125 Copynumber: 1.8 Consensus size: 122
6171009 TAAAATCAAG
* * * *
6171019 AAAACATACATCTAGATCTAGAGTAGAATAATCTAAGAGGGTAACTATTTCATGAAAAACAGTGA
1 AAAACATACATCTAGATCAAGAGTAGAAAAATCTAAAAGGGTAACTATTTCATGAAAAACAATGA
* *
6171084 GAAAAAGTTAAGTTGAAGAATAAATTCATGGAGTAATAATATCTGCAGAGCTACCCTTAC
66 G---AAGTGAAGCTGAAGAATAAATTCATGGAGTAATAATATCTGCAGAGCTACCCTTAC
* *
6171144 AAAACATACATCTAGCTCAAGAGTAGAAAAATCTAAAAGGGTAACTATTTCATGACAAACAATGA
1 AAAACATACATCTAGATCAAGAGTAGAAAAATCTAAAAGGGTAACTATTTCATGAAAAACAATGA
6171209 GAAGTGAAGCTGAAGAATAAATTCATGGAGTAATA
66 GAAGTGAAGCTGAAGAATAAATTCATGGAGTAATA
6171244 CCTGTGGAGC
Statistics
Matches: 92, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
122 32 0.35
125 60 0.65
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (122 bp):
AAAACATACATCTAGATCAAGAGTAGAAAAATCTAAAAGGGTAACTATTTCATGAAAAACAATGA
GAAGTGAAGCTGAAGAATAAATTCATGGAGTAATAATATCTGCAGAGCTACCCTTAC
Found at i:6181046 original size:5 final size:5
Alignment explanation
Indices: 6181036--6181062 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
6181026 TCCTTTACCT
6181036 TCTTC TCTTC TCTTC TCTTC TCTTC TC
1 TCTTC TCTTC TCTTC TCTTC TCTTC TC
6181063 AAAGTGTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (5 bp):
TCTTC
Found at i:6197995 original size:3 final size:3
Alignment explanation
Indices: 6197987--6198017 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
6197977 AGTTGGACAA
*
6197987 AAT AAT AAT ATT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
6198018 TTGTAATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:6208434 original size:2 final size:2
Alignment explanation
Indices: 6208427--6208452 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6208417 ATGGAAACAC
6208427 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
6208453 GGGAAGGGGC
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6209384 original size:31 final size:27
Alignment explanation
Indices: 6209312--6209388 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 27
6209302 TTATTAAAAA
6209312 AAATTAAATAATTTTTTATTTTTTATT
1 AAATTAAATAATTTTTTATTTTTTATT
* *
6209339 ACATTCAAATAATTTTTTATAATTTTATTTT
1 AAATT-AAATAATTTTTTAT--TTTT-TATT
*
6209370 AAATTAAATAAATTTTTAT
1 AAATTAAATAATTTTTTAT
6209389 GACTAATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 4 0.10
28 14 0.33
30 17 0.40
31 7 0.17
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (27 bp):
AAATTAAATAATTTTTTATTTTTTATT
Found at i:6216926 original size:2 final size:2
Alignment explanation
Indices: 6216919--6216965 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
6216909 GGAATATAAT
* **
6216919 TA TA TA TA TA CA TA TA TA TA CC TA TA 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
6216961 TA TA T
1 TA TA T
6216966 GATTGAGCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6218613 original size:17 final size:17
Alignment explanation
Indices: 6218559--6218613 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
6218549 AGAGGATTCC
*
6218559 ATTTTTGGTCTCTCTTT
1 ATTTTTGATCTCTCTTT
* *
6218576 CTTTTTGAT-TCTTTTT
1 ATTTTTGATCTCTCTTT
*
6218592 AATTTTTGATCTCTCTGT
1 -ATTTTTGATCTCTCTTT
6218610 ATTT
1 ATTT
6218614 AACCCATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
16 6 0.20
17 19 0.63
18 5 0.17
ACGTcount: A:0.11, C:0.15, G:0.09, T:0.65
Consensus pattern (17 bp):
ATTTTTGATCTCTCTTT
Found at i:6219847 original size:3 final size:3
Alignment explanation
Indices: 6219827--6219873 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
6219817 GCGTGTGGGG
* * * *
6219827 GAT GAT GAG GAC GGT GAT GAT CAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
6219874 ATCTATGGAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.32, C:0.04, G:0.36, T:0.28
Consensus pattern (3 bp):
GAT
Found at i:6220906 original size:15 final size:15
Alignment explanation
Indices: 6220886--6220914 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6220876 GAGCCAATCA
6220886 TCTGTGGATGTTGAG
1 TCTGTGGATGTTGAG
6220901 TCTGTGGATGTTGA
1 TCTGTGGATGTTGA
6220915 TGAAGCTGAG
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:0.14, C:0.07, G:0.38, T:0.41
Consensus pattern (15 bp):
TCTGTGGATGTTGAG
Found at i:6230385 original size:18 final size:17
Alignment explanation
Indices: 6230367--6230424 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
6230357 AAAGATGAAT
6230367 TTATATTATTAATTAAA
1 TTATATTATTAATTAAA
*
6230384 TTA-A-T-TT-ATGAAA
1 TTATATTATTAATTAAA
*
6230397 TTATAATTATTAATTAAT
1 TTAT-ATTATTAATTAAA
*
6230415 TTATAATATT
1 TTATATTATT
6230425 TTTTAATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
13 8 0.25
14 2 0.06
15 2 0.06
16 2 0.06
17 10 0.31
18 8 0.25
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
TTATATTATTAATTAAA
Found at i:6230454 original size:24 final size:24
Alignment explanation
Indices: 6230414--6230460 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
6230404 TATTAATTAA
*
6230414 TTTATAATATTTTTTAATATATAT
1 TTTATAATATTTGTTAATATATAT
*
6230438 TTTAT-ATATTGTGTTAATTTATA
1 TTTATAATATT-TGTTAATATATA
6230461 AGAAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (24 bp):
TTTATAATATTTGTTAATATATAT
Done.