Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 21 of 125
Found at i:6458706 original size:40 final size:40
Alignment explanation
Indices: 6458644--6458793 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
6458634 CATCTTGCTC
6458644 TTACTACAACTTCAGAGAGATAAAGAATTGCTATCTAACT
1 TTACTACAACTTCAGAGAGATAAAGAATTGCTATCTAACT
* **
6458684 TTACTACAACTTCA-AGAGGATAAGGATTGATGTTTGAAGCTTTATCTTGCT
1 TTACTACAACTTCAGAGA-GATAA--A--GA--ATT---GC--TATCTAACT
* *
6458735 CTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACT
1 -TTACTACAACTTCAGAGAGATAAAGAATTGCTATCTAACT
6458776 TTACTACAACTTCA-AGAG
1 TTACTACAACTTCAGAGAG
6458794 GATAGGGATT
Statistics
Matches: 89, Mismatches: 7, Indels: 29
0.71 0.06 0.23
Matches are distributed among these distances:
39 7 0.08
40 33 0.37
41 6 0.07
42 1 0.01
43 2 0.02
44 2 0.02
46 4 0.04
48 2 0.02
49 2 0.02
50 1 0.01
51 7 0.08
52 19 0.21
53 3 0.03
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (40 bp):
TTACTACAACTTCAGAGAGATAAAGAATTGCTATCTAACT
Found at i:6458758 original size:52 final size:50
Alignment explanation
Indices: 6458684--6459035 Score: 187
Period size: 52 Copynumber: 7.5 Consensus size: 50
6458674 CTATCTAACT
*
6458684 TTACTACAACTTCAAGAGGATAAGGATTGATGTTTGAAGCTTTATCTTGCTC
1 TTACTACAACTTCAAGAGGATAA--ATTGATGCTTGAAGCTTTATCTTGCTC
***
6458736 TTACTACAACTTC-AGAGAGATAAA--GA--CTT---GC--TATCCAACT-
1 TTACTACAACTTCAAGAG-GATAAATTGATGCTTGAAGCTTTATCTTGCTC
* * *
6458776 TTACTACAACTTCAAGAGGATAGGGATTGATGTTTGAAGCTTTATCTTGATC
1 TTACTACAACTTCAAGAGGATA--AATTGATGCTTGAAGCTTTATCTTGCTC
***
6458828 TTACTACAACTTC-AGAGAGATAAA--G--GCTT---GC--TATCCAACT-
1 TTACTACAACTTCAAGAG-GATAAATTGATGCTTGAAGCTTTATCTTGCTC
* *
6458868 TTACTACAACTTCAAAAGGATAAAAATTGATGCTTGAAACTTTATCTTGCTC
1 TTACTACAACTTCAAGAGGAT--AAATTGATGCTTGAAGCTTTATCTTGCTC
***
6458920 TTACTACAACTTC-AGAGAGATAAA--GA--CTT---GC--TATCCAACT-
1 TTACTACAACTTCAAGAG-GATAAATTGATGCTTGAAGCTTTATCTTGCTC
* * * *
6458960 TTACTACAACTTCAAGAGGATAGGAATTGATGTTTGAAACTTCATCTTACTC
1 TTACTACAACTTCAAGAGGATA--AATTGATGCTTGAAGCTTTATCTTGCTC
6459012 TTACTACAACTTCAA-AGAGATAAA
1 TTACTACAACTTCAAGAG-GATAAA
6459036 GACTTGTTAT
Statistics
Matches: 226, Mismatches: 31, Indels: 88
0.66 0.09 0.26
Matches are distributed among these distances:
40 50 0.22
41 28 0.12
42 6 0.03
43 5 0.02
44 5 0.02
46 16 0.07
48 5 0.02
49 4 0.02
50 7 0.03
51 30 0.13
52 70 0.31
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (50 bp):
TTACTACAACTTCAAGAGGATAAATTGATGCTTGAAGCTTTATCTTGCTC
Found at i:6458890 original size:40 final size:40
Alignment explanation
Indices: 6458828--6458977 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
6458818 TATCTTGATC
6458828 TTACTACAACTTCAGAGAGATAAAGGCTTGCTATCCAACT
1 TTACTACAACTTCAGAGAGATAAAGGCTTGCTATCCAACT
* ***
6458868 TTACTACAACTTCA-AAAGGATAAAAATTGATGCTTGAAACTTTATCTTGCT
1 TTACTACAACTTCAGAGA-GAT--AAA--G--GCTTG---C--TATCCAACT
*
6458919 CTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACT
1 -TTACTACAACTTCAGAGAGATAAAGGCTTGCTATCCAACT
6458960 TTACTACAACTTCA-AGAG
1 TTACTACAACTTCAGAGAG
6458978 GATAGGAATT
Statistics
Matches: 87, Mismatches: 9, Indels: 29
0.70 0.07 0.23
Matches are distributed among these distances:
39 6 0.07
40 31 0.36
41 6 0.07
42 3 0.03
43 1 0.01
44 1 0.01
46 9 0.10
48 1 0.01
49 1 0.01
50 3 0.03
51 6 0.07
52 17 0.20
53 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.30
Consensus pattern (40 bp):
TTACTACAACTTCAGAGAGATAAAGGCTTGCTATCCAACT
Found at i:6467887 original size:30 final size:31
Alignment explanation
Indices: 6467851--6467928 Score: 101
Period size: 30 Copynumber: 2.6 Consensus size: 31
6467841 ATTTAGGGGT
*
6467851 AAAATGGTAA-TTTTGGAAGTATC-GAGGTTA
1 AAAATGGTAATTTTTGGAAGTATCAGA-GTCA
*
6467881 AAAATGG-AATTTTTGGAAGTTTCAGAGTCA
1 AAAATGGTAATTTTTGGAAGTATCAGAGTCA
6467911 AAAAT-GTAATTTTTGGAA
1 AAAATGGTAATTTTTGGAA
6467929 ATGTAATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 3 0.07
30 38 0.88
31 2 0.05
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (31 bp):
AAAATGGTAATTTTTGGAAGTATCAGAGTCA
Found at i:6467932 original size:15 final size:15
Alignment explanation
Indices: 6467912--6467942 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6467902 TCAGAGTCAA
6467912 AAATGTAATTTTTGG
1 AAATGTAATTTTTGG
6467927 AAATGTAATTTTTGG
1 AAATGTAATTTTTGG
6467942 A
1 A
6467943 TGTTTCGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.45
Consensus pattern (15 bp):
AAATGTAATTTTTGG
Found at i:6467948 original size:45 final size:45
Alignment explanation
Indices: 6467882--6467973 Score: 141
Period size: 45 Copynumber: 2.0 Consensus size: 45
6467872 TCGAGGTTAA
6467882 AAATGGAATTTTTGGAAGTTTC-AGAGTCAAAAATGTAATTTTTGG
1 AAATGGAATTTTTGGAAGTTTCGAGAGT-AAAAATGTAATTTTTGG
* * *
6467927 AAATGTAATTTTTGGATGTTTCGAGGGTAAAAATGTAATTTTTGG
1 AAATGGAATTTTTGGAAGTTTCGAGAGTAAAAATGTAATTTTTGG
6467972 AA
1 AA
6467974 GTTTTGGGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 39 0.91
46 4 0.09
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (45 bp):
AAATGGAATTTTTGGAAGTTTCGAGAGTAAAAATGTAATTTTTGG
Found at i:6467951 original size:75 final size:75
Alignment explanation
Indices: 6467852--6468002 Score: 214
Period size: 75 Copynumber: 2.0 Consensus size: 75
6467842 TTTAGGGGTA
* *
6467852 AAATGGTAATTTTGGAAGTATCGAGGTTAAAAATGGAATTTTTGGAAGTTTCAGAGTCAAAAATG
1 AAATGGTAATTTTGGAAGTATCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAGAGTCAAAAATA
6467917 TAATTTTTGG
66 TAATTTTTGG
* * * ** *
6467927 AAAT-GTAATTTTTGGATGTTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAAT
1 AAATGGTAA-TTTTGGAAGTATCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAGAGTCAAAAAT
6467991 ATAATTTTTGG
65 ATAATTTTTGG
6468002 A
1 A
6468003 TAATTTAGGG
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
74 4 0.06
75 63 0.94
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (75 bp):
AAATGGTAATTTTGGAAGTATCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAGAGTCAAAAATA
TAATTTTTGG
Found at i:6467961 original size:30 final size:30
Alignment explanation
Indices: 6467927--6468003 Score: 111
Period size: 30 Copynumber: 2.6 Consensus size: 30
6467917 TAATTTTTGG
6467927 AAATGTAATTTTTGGATGTTTCGAGGGT-AA
1 AAATGTAATTTTTGGATGTTTCG-GGGTCAA
* *
6467957 AAATGTAATTTTTGGAAGTTTTGGGGTCAA
1 AAATGTAATTTTTGGATGTTTCGGGGTCAA
*
6467987 AAATATAATTTTTGGAT
1 AAATGTAATTTTTGGAT
6468004 AATTTAGGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 4 0.10
30 38 0.90
ACGTcount: A:0.32, C:0.03, G:0.23, T:0.42
Consensus pattern (30 bp):
AAATGTAATTTTTGGATGTTTCGGGGTCAA
Found at i:6469061 original size:11 final size:11
Alignment explanation
Indices: 6469045--6469111 Score: 57
Period size: 11 Copynumber: 6.0 Consensus size: 11
6469035 TTATAATAAT
6469045 ATTAAATTTAA
1 ATTAAATTTAA
*
6469056 ATTAAATTCAA
1 ATTAAATTTAA
6469067 ACTTAAA-TTAA
1 A-TTAAATTTAA
*
6469078 ATTTAAA-ATACA
1 A-TTAAATTTA-A
*
6469090 TTTAAATTTAA
1 ATTAAATTTAA
*
6469101 AATAAATTTAA
1 ATTAAATTTAA
6469112 TCTTAAAGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
11 37 0.82
12 8 0.18
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:6469062 original size:28 final size:27
Alignment explanation
Indices: 6469023--6469111 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 27
6469013 GGACTTTTGG
6469023 ATTT-AATTAAATTTATAA-TAATATTAA
1 ATTTAAATTAAATTTA-AACTAA-ATTAA
*
6469050 ATTTAAATTAAATTCAAACTTAAATTAA
1 ATTTAAATTAAATTTAAAC-TAAATTAA
* * * *
6469078 ATTTAAAATACATTTAAATTTAAAATAA
1 ATTTAAATTAAATTTAAA-CTAAATTAA
6469106 ATTTAA
1 ATTTAA
6469112 TCTTAAAGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 6 0.12
28 43 0.83
29 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (27 bp):
ATTTAAATTAAATTTAAACTAAATTAA
Found at i:6469078 original size:45 final size:45
Alignment explanation
Indices: 6469027--6469131 Score: 140
Period size: 45 Copynumber: 2.3 Consensus size: 45
6469017 TTTTGGATTT
* *
6469027 AATTAAATTTATAATA-ATATTAAATTTAAATTAAATTCAAACTTA
1 AATTAAATTTAAAATACAT-TTAAATTTAAAATAAATTCAAACTTA
* *
6469072 AATTAAATTTAAAATACATTTAAATTTAAAATAAATTTAATCTTA
1 AATTAAATTTAAAATACATTTAAATTTAAAATAAATTCAAACTTA
* *
6469117 AAGTAAATTAAAAAT
1 AATTAAATTTAAAAT
6469132 GATTTGGGCC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 51 0.96
46 2 0.04
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (45 bp):
AATTAAATTTAAAATACATTTAAATTTAAAATAAATTCAAACTTA
Found at i:6469094 original size:17 final size:17
Alignment explanation
Indices: 6469070--6469125 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
6469060 AATTCAAACT
6469070 TAAA-TTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
6469086 TACATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
6469103 TAAATTT-AATCTTAAAG
1 TAAATTTAAAT-TTAAAA
6469120 TAAATT
1 TAAATT
6469126 AAAAATGATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
16 6 0.17
17 29 0.83
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:6469103 original size:7 final size:6
Alignment explanation
Indices: 6469046--6469111 Score: 59
Period size: 6 Copynumber: 11.7 Consensus size: 6
6469036 TATAATAATA
* * * *
6469046 TTAAAT TTAAA- TTAAAT TCAAAC TTAAA- TTAAAT TTAAA- ATACAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
6469091 TTAAAT TTAAA- ATAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAA
6469112 TCTTAAAGTA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
5 17 0.36
6 30 0.64
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:6470189 original size:24 final size:24
Alignment explanation
Indices: 6470128--6470190 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
6470118 TAAAGTAATA
* *
6470128 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
6470152 AGAGTTTAATTGAACCAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
6470176 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
6470191 GATTATTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:6476867 original size:34 final size:29
Alignment explanation
Indices: 6476809--6476885 Score: 77
Period size: 34 Copynumber: 2.5 Consensus size: 29
6476799 ATCTAATAAT
6476809 ATAATAAATTATTAATATAATTTATTGTT-
1 ATAATAAATTATTAATATAATTTATT-TTA
*
6476838 TTAATAAATTATTTAATATTTTAATTTTATTTTA
1 ATAATAAATTA-TTAATA---TAA-TTTATTTTA
6476872 ATAATAAATT-TTAA
1 ATAATAAATTATTAA
6476886 AAATAATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
29 10 0.25
30 6 0.15
32 4 0.10
33 5 0.12
34 15 0.38
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (29 bp):
ATAATAAATTATTAATATAATTTATTTTA
Found at i:6476950 original size:14 final size:14
Alignment explanation
Indices: 6476850--6476961 Score: 59
Period size: 13 Copynumber: 8.6 Consensus size: 14
6476840 AATAAATTAT
6476850 TTAATATTTTAAT-
1 TTAATATTTTAATA
6476863 TT--TATTTTAATA
1 TTAATATTTTAATA
* *
6476875 ATAA-ATTTTAAAA
1 TTAATATTTTAATA
*
6476888 ATAATATTTTTAA-A
1 TTAATA-TTTTAATA
6476902 -TAATATTTTTAATA
1 TTAATA-TTTTAATA
* *
6476916 -TATTA-TTGAA-A
1 TTAATATTTTAATA
6476927 --AATA-TTTAATA
1 TTAATATTTTAATA
6476938 TTAATATTTTAATAA
1 TTAATATTTTAAT-A
*
6476953 TAAATATTT
1 TTAATATTT
6476962 ATTACAATTA
Statistics
Matches: 81, Mismatches: 7, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.09
11 11 0.14
12 5 0.06
13 30 0.37
14 13 0.16
15 15 0.19
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (14 bp):
TTAATATTTTAATA
Found at i:6476957 original size:28 final size:28
Alignment explanation
Indices: 6476865--6476962 Score: 86
Period size: 28 Copynumber: 3.8 Consensus size: 28
6476855 ATTTTAATTT
* *
6476865 TATTTTAATAATAAAT-TTTAAAAATAA
1 TATTTTAATAATAAATATTTAATATTAA
*
6476892 TATTTTTA-AAT-AATA-TT--T-TTAA
1 TATTTTAATAATAAATATTTAATATTAA
* *
6476914 TATATTATTGAA-AAATATTTAATATTAA
1 TATTTTAAT-AATAAATATTTAATATTAA
6476942 TATTTTAATAATAAATATTTA
1 TATTTTAATAATAAATATTTA
6476963 TTACAATTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
22 8 0.15
24 6 0.11
25 7 0.13
26 3 0.06
27 10 0.19
28 20 0.37
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (28 bp):
TATTTTAATAATAAATATTTAATATTAA
Found at i:6476960 original size:15 final size:14
Alignment explanation
Indices: 6476865--6476961 Score: 84
Period size: 13 Copynumber: 7.4 Consensus size: 14
6476855 ATTTTAATTT
6476865 TATTTTAATAATAA
1 TATTTTAATAATAA
*
6476879 -ATTTTAAAAATAA
1 TATTTTAATAATAA
*
6476892 TATTTTTA-AATAA
1 TATTTTAATAATAA
6476905 TATTTT--TAAT-A
1 TATTTTAATAATAA
*
6476916 TATTATTGA-AA-AA
1 TATT-TTAATAATAA
*
6476929 TA-TTTAATATTAA
1 TATTTTAATAATAA
6476942 TATTTTAATAATAAA
1 TATTTTAATAAT-AA
6476957 TATTT
1 TATTT
6476962 ATTACAATTA
Statistics
Matches: 68, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
11 8 0.12
12 7 0.10
13 32 0.47
14 14 0.21
15 7 0.10
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (14 bp):
TATTTTAATAATAA
Found at i:6476991 original size:15 final size:15
Alignment explanation
Indices: 6476912--6476991 Score: 58
Period size: 15 Copynumber: 5.2 Consensus size: 15
6476902 TAATATTTTT
*
6476912 AATATATTATTGAA-A
1 AATATATTAAT-AATA
*
6476927 AATAT-TTAAT-ATT
1 AATATATTAATAATA
*
6476940 AATATTTTAATAATA
1 AATATATTAATAATA
*
6476955 AATATTTATTACAATTATA
1 AATA--TATT--AATAATA
6476974 AATATATTAATAATA
1 AATATATTAATAATA
6476989 AAT
1 AAT
6476992 GTTTTGTAGT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
12 1 0.02
13 5 0.10
14 9 0.17
15 20 0.38
17 7 0.13
19 10 0.19
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:6478111 original size:6 final size:6
Alignment explanation
Indices: 6478102--6478160 Score: 59
Period size: 6 Copynumber: 9.8 Consensus size: 6
6478092 TAATTAAGAG
* * *
6478102 TTTAAA TTT-AC TTTAAA TTTAAA TTTACCTA TTTAAA TTT-AC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
6478150 TTTAAA TTTAA
1 TTTAAA TTTAA
6478161 TCAAATTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 8 0.19
6 30 0.70
8 5 0.12
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:6478124 original size:17 final size:17
Alignment explanation
Indices: 6478102--6478159 Score: 86
Period size: 17 Copynumber: 3.6 Consensus size: 17
6478092 TAATTAAGAG
6478102 TTTAAATTTACTTTAAA
1 TTTAAATTTACTTTAAA
*
6478119 TTTAAATTTAC-CT--A
1 TTTAAATTTACTTTAAA
6478133 TTTAAATTTACTTTAAA
1 TTTAAATTTACTTTAAA
6478150 TTTAAATTTA
1 TTTAAATTTA
6478160 ATCAAATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
14 12 0.33
15 1 0.03
16 1 0.03
17 22 0.61
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAATTTACTTTAAA
Found at i:6479282 original size:17 final size:18
Alignment explanation
Indices: 6479250--6479283 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6479240 ATAAAAAAGG
*
6479250 AGAAACAGATTTAAACCA
1 AGAAACAGATTGAAACCA
6479268 AGAAA-AGATTGAAACC
1 AGAAACAGATTGAAACC
6479284 CTTTTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (18 bp):
AGAAACAGATTGAAACCA
Found at i:6479344 original size:8 final size:8
Alignment explanation
Indices: 6479331--6479357 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
6479321 ATTTTGAAAG
6479331 GAATAAAA
1 GAATAAAA
6479339 GAATAAAA
1 GAATAAAA
6479347 GAATAAAA
1 GAATAAAA
6479355 GAA
1 GAA
6479358 AAGGAAGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (8 bp):
GAATAAAA
Found at i:6487788 original size:205 final size:205
Alignment explanation
Indices: 6487435--6488093 Score: 985
Period size: 205 Copynumber: 3.2 Consensus size: 205
6487425 ACATAAACAG
* * * **
6487435 CGAGGCGGTCATCTTCCTGATGAAACAC-AGAGAAGAATACC-AA-C---TCAACGTTCAATGCA
1 CGAGGCGGTCATCTTCCTGATGAGACACTA-AGAAGAAGACCAAATCAAACCAACACTCAATGCA
*
6487494 AGCAAATCTTCGAACCCAGCTTCCTGATGAGACATTGAGAAGCAGGTTGAAGCAATAAAATGGTT
65 AGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTTGAAGCAATAAAATGGTT
* *
6487559 AGCTTTCTGATGAGACACAGAGAAGTGGACCAAATTCATCTTCCTGAGGAGATCCAGAGAAGCGA
130 AGCTTCCTGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGA
6487624 ATTAAAACAAT
195 ATTAAAACAAT
* *
6487635 CGAGGCGGTCATATTCCTGATGAGACACTAAGAAGGAGACCAAATCAAACCAACACTCAATGCAA
1 CGAGGCGGTCATCTTCCTGATGAGACACTAAGAAGAAGACCAAATCAAACCAACACTCAATGCAA
* *
6487700 GCAAATCTTCAAACCCAGCTTCCTGATGAAACACTGAGAAGCAGGTTGAAGCAATAAAATGGTTA
66 GCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTTGAAGCAATAAAATGGTTA
*
6487765 GCTTCCTGATGAGACATAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAA
131 GCTTCCTGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAA
*
6487830 TTAAAACAAG
196 TTAAAACAAT
* * **
6487840 CGAGGCGGTCATCTTCCTGATGAGAAACTGAGAAGAAGACCAAATCAAACCAATGCTCAATGCAA
1 CGAGGCGGTCATCTTCCTGATGAGACACTAAGAAGAAGACCAAATCAAACCAACACTCAATGCAA
* * *
6487905 GCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAATGAAATGGTTA
66 GCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTTGAAGCAATAAAATGGTTA
*
6487970 GCTTCCTGATGAGACACAGAGAAGTGGACTAAATTCGTCTTCCT-AGGGAGATCCAGAGAAGCGA
131 GCTTCCTGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGA-GGAGATCCAGAGAAGCGA
6488034 ATTAAAACAGAT
195 ATTAAAACA-AT
* * *
6488046 -AATTGCGGTCATCTTCCTGATGAGACAC-AGAGAAGAAGACCAGATCAA
1 CGA-GGCGGTCATCTTCCTGATGAGACACTA-AGAAGAAGACCAAATCAA
6488094 TGAAATCAGT
Statistics
Matches: 416, Mismatches: 33, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
200 35 0.08
201 3 0.01
202 1 0.00
204 1 0.00
205 335 0.81
206 41 0.10
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (205 bp):
CGAGGCGGTCATCTTCCTGATGAGACACTAAGAAGAAGACCAAATCAAACCAACACTCAATGCAA
GCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTTGAAGCAATAAAATGGTTA
GCTTCCTGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAA
TTAAAACAAT
Found at i:6488457 original size:6 final size:6
Alignment explanation
Indices: 6488446--6488493 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
6488436 TTAAATTGAT
* *
6488446 TTTAAA TTTAAA TTTACCTA TTTAAA TTT-AC TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
6488494 TCAAATTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 4 0.11
6 26 0.74
8 5 0.14
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:6488487 original size:17 final size:17
Alignment explanation
Indices: 6488435--6488492 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
6488425 TAATTAAGAG
* *
6488435 TTTAAATTGATTTTAAA
1 TTTAAATTTACTTTAAA
*
6488452 TTTAAATTTAC-CT--A
1 TTTAAATTTACTTTAAA
6488466 TTTAAATTTACTTTAAA
1 TTTAAATTTACTTTAAA
6488483 TTTAAATTTA
1 TTTAAATTTA
6488493 ATCAAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 12 0.35
15 1 0.03
16 1 0.03
17 20 0.59
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTACTTTAAA
Found at i:6488523 original size:12 final size:12
Alignment explanation
Indices: 6488500--6488532 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6488490 TTAATCAAAT
6488500 TTAAAA-TAATA
1 TTAAAATTAATA
*
6488511 TTAAACTTAATA
1 TTAAAATTAATA
6488523 TTAAAATTAA
1 TTAAAATTAA
6488533 AAGTCCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (12 bp):
TTAAAATTAATA
Found at i:6490459 original size:58 final size:58
Alignment explanation
Indices: 6490357--6490508 Score: 180
Period size: 58 Copynumber: 2.6 Consensus size: 58
6490347 AAAATTATAC
* * *
6490357 TTTGACTCCCGAACTTCTCAAAAATTAAATTTTAACCCTAAAACTTCCCAAAATTACATT
1 TTTGAC-CTCGAACTTC-CAAAAATTACATTTTAACCCCAAAACTTCCCAAAATTACATT
* * *
6490417 TTTG-CCTCGAAACTTCCAAAAATTACATTTTTACCCCCAAACTTTCCAAAATTACATT
1 TTTGACCTCG-AACTTCCAAAAATTACATTTTAACCCCAAAACTTCCCAAAATTACATT
**
6490475 TTTGACCTCGATTTTACCAAAAATTACTATTTTA
1 TTTGACCTCGAACTT-CCAAAAATTAC-ATTTTA
6490509 TCCTCGAACT
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
58 47 0.59
59 23 0.29
60 9 0.11
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (58 bp):
TTTGACCTCGAACTTCCAAAAATTACATTTTAACCCCAAAACTTCCCAAAATTACATT
Found at i:6490477 original size:29 final size:29
Alignment explanation
Indices: 6490368--6490477 Score: 114
Period size: 29 Copynumber: 3.8 Consensus size: 29
6490358 TTGACTCCCG
* * * *
6490368 AACTTCTCAAAAATTAAATTTTAACCCTAA
1 AACTT-TCCAAAATTACATTTTTACCCCAA
* * * *
6490398 AACTTCCCAAAATTACATTTTTGCCTCGA
1 AACTTTCCAAAATTACATTTTTACCCCAA
*
6490427 AAC-TTCCAAAAATTACATTTTTACCCCCA
1 AACTTTCC-AAAATTACATTTTTACCCCAA
6490456 AACTTTCCAAAATTACATTTTT
1 AACTTTCCAAAATTACATTTTT
6490478 GACCTCGATT
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
28 3 0.05
29 54 0.82
30 9 0.14
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (29 bp):
AACTTTCCAAAATTACATTTTTACCCCAA
Found at i:6490498 original size:59 final size:59
Alignment explanation
Indices: 6490375--6490713 Score: 257
Period size: 59 Copynumber: 5.7 Consensus size: 59
6490365 CCGAACTTCT
* * * * * **
6490375 CAAAAATTAAATTTTAACCCTAAAACTTCCCAAAATTACATTTTTG-CCTCGAAACTT-C
1 CAAAAATTACATTTTTACCCTCAAACTTTCTAAAATTACATTTTTGACCTCG-ATTTTAC
* *
6490433 CAAAAATTACATTTTTACCCCCAAACTTTCCAAAATTACATTTTTGACCTCGATTTTAC
1 CAAAAATTACATTTTTACCCTCAAACTTTCTAAAATTACATTTTTGACCTCGATTTTAC
* * * * *
6490492 CAAAAATTAC-TATTTTATCCTCGAACTTTTTAAAACT-CTATTTTTTACC-CTGATTTTAC
1 CAAAAATTACAT-TTTTACCCTCAAACTTTCTAAAATTAC-ATTTTTGACCTC-GATTTTAC
* * ** * ** * *
6490551 CCAAAATTACCA-CTTTACCCTTGAACTTTCTAAAATTCCATTTTAAACCTTGATTTCAC
1 CAAAAATTA-CATTTTTACCCTCAAACTTTCTAAAATTACATTTTTGACCTCGATTTTAC
** * *
6490610 CAAAAAATTACCA-TTTTACCC-CTAAACTTTCTAAAATTTTATTTTTGACCCCGATTTTCC
1 C-AAAAATTA-CATTTTTACCCTC-AAACTTTCTAAAATTACATTTTTGACCTCGATTTTAC
**
6490670 CAAAAATTAC-TATTTTACCCTCAAA-AGTCTAAAATTACTATTTT
1 CAAAAATTACAT-TTTTACCCTCAAACTTTCTAAAATTAC-ATTTT
6490714 GCCCCCGAGT
Statistics
Matches: 226, Mismatches: 40, Indels: 29
0.77 0.14 0.10
Matches are distributed among these distances:
58 57 0.25
59 120 0.53
60 49 0.22
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.39
Consensus pattern (59 bp):
CAAAAATTACATTTTTACCCTCAAACTTTCTAAAATTACATTTTTGACCTCGATTTTAC
Found at i:6490500 original size:30 final size:29
Alignment explanation
Indices: 6490401--6490507 Score: 103
Period size: 29 Copynumber: 3.6 Consensus size: 29
6490391 ACCCTAAAAC
* *
6490401 TTCCCAAAATTACATTTTTG-CCTCGAAAC
1 TTCCAAAAATTACATTTTTGACCTCG-AAT
* *
6490430 TTCCAAAAATTACATTTTT-ACCCCCAAACT
1 TTCCAAAAATTACATTTTTGA-CCTCGAA-T
*
6490460 TTCC-AAAATTACATTTTTGACCTCGATT
1 TTCCAAAAATTACATTTTTGACCTCGAAT
6490488 TTACCAAAAATTACTATTTT
1 TT-CCAAAAATTAC-ATTTT
6490508 ATCCTCGAAC
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
28 3 0.05
29 40 0.62
30 16 0.25
31 5 0.08
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (29 bp):
TTCCAAAAATTACATTTTTGACCTCGAAT
Found at i:6490585 original size:29 final size:29
Alignment explanation
Indices: 6490553--6490647 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 29
6490543 GATTTTACCC
*
6490553 AAAATTACCACTTTACCCTTGAACTTTCT
1 AAAATTACCATTTTACCCTTGAACTTTCT
* *
6490582 AAAATT-CCATTTTAAACCTTG-A-TTTCACCAA
1 AAAATTACCATTTT-ACCCTTGAACTTT---C-T
* *
6490613 AAAATTACCATTTTACCCCTAAACTTTCT
1 AAAATTACCATTTTACCCTTGAACTTTCT
6490642 AAAATT
1 AAAATT
6490648 TTATTTTTGA
Statistics
Matches: 51, Mismatches: 7, Indels: 16
0.69 0.09 0.22
Matches are distributed among these distances:
27 3 0.06
28 7 0.14
29 18 0.35
30 2 0.04
31 10 0.20
32 8 0.16
33 3 0.06
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTTGAACTTTCT
Found at i:6491726 original size:87 final size:87
Alignment explanation
Indices: 6491580--6491814 Score: 335
Period size: 87 Copynumber: 2.7 Consensus size: 87
6491570 TGGTTTTAAC
* ** * *
6491580 AGCAATTATGTTAGATAGTACTGAATCGCAATTCACATCAGAAACATTTCAAGTGTGATTGGATG
1 AGCAATTATGTTAGATAGTACTGAATTGTGATTCACATCAAAAACATTTCAAGTGTGATTGGATA
6491645 CAAAGACACAATTTCAACATCA
66 CAAAGACACAATTTCAACATCA
6491667 AGCAATTATGTTAGATAGTACTGAATTGTGATTCACATCAAAAACATTTCAAGTGTGATTGGATA
1 AGCAATTATGTTAGATAGTACTGAATTGTGATTCACATCAAAAACATTTCAAGTGTGATTGGATA
* * *
6491732 CTAAGACACGATTTCAGCATCA
66 CAAAGACACAATTTCAACATCA
* * * *
6491754 AACAATTATATTAGGTAGTACTGAATTGTGATTCACATAAAAAAAAACATTTCAAGTGTGA
1 AGCAATTATGTTAGATAGTACTGAATTGTGATTCACAT---CAAAAACATTTCAAGTGTGA
6491815 AGTTCCAACA
Statistics
Matches: 133, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
87 114 0.86
90 19 0.14
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (87 bp):
AGCAATTATGTTAGATAGTACTGAATTGTGATTCACATCAAAAACATTTCAAGTGTGATTGGATA
CAAAGACACAATTTCAACATCA
Found at i:6494319 original size:62 final size:62
Alignment explanation
Indices: 6494222--6494345 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
6494212 GCAAAACGGA
6494222 ATGTGTTGGAGAAGATTCATAACGAGTGGGAGAAATCATATAATGATTTGTGACAATGGTGT
1 ATGTGTTGGAGAAGATTCATAACGAGTGGGAGAAATCATATAATGATTTGTGACAATGGTGT
6494284 ATGTGTTGGAGAAGATTCATAACGAGTGGGAGAAATCATATAATGATTTGTGACAATGGTGT
1 ATGTGTTGGAGAAGATTCATAACGAGTGGGAGAAATCATATAATGATTTGTGACAATGGTGT
6494346 CAGGTATTGG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (62 bp):
ATGTGTTGGAGAAGATTCATAACGAGTGGGAGAAATCATATAATGATTTGTGACAATGGTGT
Found at i:6498620 original size:39 final size:40
Alignment explanation
Indices: 6498541--6498620 Score: 92
Period size: 39 Copynumber: 2.0 Consensus size: 40
6498531 TGTTTTGGTG
* * * *
6498541 TTATTTTTTTTACTATTTTTTGCTGTTTTGGTGTTATTTT
1 TTATTGTTTTGACTATTTTTTACTGTTTTGGTGCTATTTT
*
6498581 TTATTGTTTTGACT-TTTTTTACTG-TTTGGATGCTGTTTT
1 TTATTGTTTTGACTATTTTTTACTGTTTTGG-TGCTATTTT
6498620 T
1 T
6498621 GCTATTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
38 5 0.15
39 17 0.50
40 12 0.35
ACGTcount: A:0.10, C:0.06, G:0.15, T:0.69
Consensus pattern (40 bp):
TTATTGTTTTGACTATTTTTTACTGTTTTGGTGCTATTTT
Found at i:6498643 original size:12 final size:12
Alignment explanation
Indices: 6498628--6498676 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
6498618 TTTGCTATTA
6498628 TTTTTGTTGCTG
1 TTTTTGTTGCTG
* *
6498640 TTTTTGTTACTA
1 TTTTTGTTGCTG
6498652 TTTTTG-T--TG
1 TTTTTGTTGCTG
*
6498661 TTTTTGTTGTTG
1 TTTTTGTTGCTG
6498673 TTTT
1 TTTT
6498677 GCTGTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 7 0.23
10 1 0.03
11 1 0.03
12 22 0.71
ACGTcount: A:0.04, C:0.04, G:0.18, T:0.73
Consensus pattern (12 bp):
TTTTTGTTGCTG
Found at i:6498664 original size:21 final size:23
Alignment explanation
Indices: 6498613--6498668 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 23
6498603 TGTTTGGATG
* *
6498613 CTGTTTTTGCTATTATTTTTGTT
1 CTGTTTTTGTTACTATTTTTGTT
6498636 GCTGTTTTTGTTACTATTTTTG-T
1 -CTGTTTTTGTTACTATTTTTGTT
6498659 -TGTTTTTGTT
1 CTGTTTTTGTT
6498669 GTTGTTTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 10 0.33
23 1 0.03
24 19 0.63
ACGTcount: A:0.07, C:0.07, G:0.16, T:0.70
Consensus pattern (23 bp):
CTGTTTTTGTTACTATTTTTGTT
Found at i:6498671 original size:24 final size:24
Alignment explanation
Indices: 6498611--6498660 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
6498601 ACTGTTTGGA
* *
6498611 TGCTGTTTTTGCTATTATTTTTGT
1 TGCTGTTTTTGTTACTATTTTTGT
6498635 TGCTGTTTTTGTTACTATTTTTGT
1 TGCTGTTTTTGTTACTATTTTTGT
6498659 TG
1 TG
6498661 TTTTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.08, G:0.18, T:0.66
Consensus pattern (24 bp):
TGCTGTTTTTGTTACTATTTTTGT
Found at i:6498688 original size:24 final size:24
Alignment explanation
Indices: 6498656--6498718 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 24
6498646 TTACTATTTT
*
6498656 TGTTGTTTTTGTTGTTGTTTTG-C
1 TGTTATTTTTGTTGTTGTTTTGAC
* *
6498679 TGTTATTTTTGCTGTTGTTTTGAT
1 TGTTATTTTTGTTGTTGTTTTGAC
6498703 TGTTATTTTTGTTGTT
1 TGTTATTTTTGTTGTT
6498719 TGGATGTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
23 20 0.57
24 15 0.43
ACGTcount: A:0.05, C:0.03, G:0.22, T:0.70
Consensus pattern (24 bp):
TGTTATTTTTGTTGTTGTTTTGAC
Found at i:6499938 original size:29 final size:30
Alignment explanation
Indices: 6499906--6500219 Score: 211
Period size: 29 Copynumber: 10.7 Consensus size: 30
6499896 TATGGATATC
* * *
6499906 CGGGGGCAAAATGGTAATTTT-GGTGTAAT
1 CGGGGGTAAAATGGTAATTTTAGATGAAAT
* * * *
6499935 CGGGGTTTAAAATGG-AATTTTAAAAG-ATT
1 CGGGG-GTAAAATGGTAATTTTAGATGAAAT
*
6499964 CGGGGGTAAAATGGTAATTTTCGATGAAAT
1 CGGGGGTAAAATGGTAATTTTAGATGAAAT
* * * *
6499994 CGGGGTTAAAAATGG-AATTTTAAAAG-ATT
1 CGGGGGT-AAAATGGTAATTTTAGATGAAAT
* *
6500023 CGGGGGTAAAATGGTAATTTTTGGTGAAAT
1 CGGGGGTAAAATGGTAATTTTAGATGAAAT
* * **
6500053 CGGGGTTAAAAATGG-AATTTTAGAAG-CTT
1 CGGGGGT-AAAATGGTAATTTTAGATGAAAT
* * *
6500082 C-GGGGCAAAATGGTAATTTTCGGTGAAAT
1 CGGGGGTAAAATGGTAATTTTAGATGAAAT
* * * *
6500111 CGGGGTTAAAAATGG-AATTTTAAAAG-ATT
1 CGGGGGT-AAAATGGTAATTTTAGATGAAAT
* * *
6500140 CGAGGGTAAAATGGTAATTTTTGGTGAAAT
1 CGGGGGTAAAATGGTAATTTTAGATGAAAT
* * * *
6500170 CGGGGTTAAAAATGG-AATTTTAAAAG-AGT
1 CGGGGGT-AAAATGGTAATTTTAGATGAAAT
6500199 CGGGGGTAAAATGGTAATTTT
1 CGGGGGTAAAATGGTAATTTT
6500220 TGGAAAGTTT
Statistics
Matches: 212, Mismatches: 57, Indels: 32
0.70 0.19 0.11
Matches are distributed among these distances:
27 7 0.03
28 40 0.19
29 73 0.34
30 64 0.30
31 28 0.13
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (30 bp):
CGGGGGTAAAATGGTAATTTTAGATGAAAT
Found at i:6500062 original size:117 final size:118
Alignment explanation
Indices: 6499906--6500219 Score: 533
Period size: 117 Copynumber: 2.7 Consensus size: 118
6499896 TATGGATATC
* * *
6499906 CGGGGGCAAAATGGTAA-TTTTGGTGTAATCGGGGTTTAAAATGGAATTTTAAAAGATTCGGGGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGG
6499970 TAAAATGGTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
66 TAAAATGGTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
6500023 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTC-GGGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGG
* *
6500087 CAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
66 TAAAATGGTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
6500140 CGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGAGTCGGGGG
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGG
6500205 TAAAATGGTAATTTT
66 TAAAATGGTAATTTT
6500220 TGGAAAGTTT
Statistics
Matches: 183, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
117 127 0.69
118 56 0.31
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (118 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGG
TAAAATGGTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
Found at i:6500220 original size:59 final size:59
Alignment explanation
Indices: 6499906--6500222 Score: 521
Period size: 59 Copynumber: 5.4 Consensus size: 59
6499896 TATGGATATC
* * *
6499906 CGGGGGCAAAATGGTAA-TTTTGGTGTAATCGGGGTTTAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
6499964 CGGGGGTAAAATGGTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
6500023 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
6500082 C-GGGGCAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
6500140 CGAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGAGT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
6500199 CGGGGGTAAAATGGTAATTTTTGG
1 CGGGGGTAAAATGGTAATTTTTGG
6500223 AAAGTTTTGG
Statistics
Matches: 239, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
58 70 0.29
59 169 0.71
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
Found at i:6500246 original size:30 final size:30
Alignment explanation
Indices: 6500201--6500283 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
6500191 AAAAGAGTCG
*
6500201 GGGGT-AAAATGGTAATTTTTGGAAAGTTTT
1 GGGGTCAAAAT-GTAATTTTTGGAAAGCTTT
* *
6500231 GGGGTCAAAATGTAATTTTAGAAAAGCTTT
1 GGGGTCAAAATGTAATTTTTGGAAAGCTTT
6500261 GGGGTCAAAATGTAATTTTTGGA
1 GGGGTCAAAATGTAATTTTTGGA
6500284 CAATTTAGGG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 42 0.89
31 5 0.11
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.36
Consensus pattern (30 bp):
GGGGTCAAAATGTAATTTTTGGAAAGCTTT
Found at i:6500250 original size:176 final size:176
Alignment explanation
Indices: 6499908--6500279 Score: 565
Period size: 176 Copynumber: 2.1 Consensus size: 176
6499898 TGGATATCCG
* * *
6499908 GGGGCAAAATGGTAATTTTGGTGTAATCGGGGTTTAAAATGGAATTTTAAAAGATTCGGGGGTAA
1 GGGGCAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGAGGGTAA
*
6499973 AATGGTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATGGT
66 AATGGTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAAAAGAGTCGGGGGTAAAATGGT
6500038 AATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAG-AAGCTTC
131 AATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGCTTC
6500083 GGGGCAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGAGGGTA
1 GGGGCAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGAGGGTA
* *
6500148 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGAGTCGGGGGTAAAATGG
65 AAATGGTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAAAAGAGTCGGGGGTAAAATGG
* * * *
6500213 TAATTTTT-G-GAAAGTTTTGGGG-TCAAAATGTAATTTTAGAAAAGCTTT
130 TAATTTTTGGTGAAA---TCGGGGTTAAAAATGGAATTTTAG-AAAGCTTC
6500261 GGGGTCAAAAT-GTAATTTT
1 GGGG-CAAAATGGTAATTTT
6500280 TGGACAATTT
Statistics
Matches: 180, Mismatches: 10, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
174 4 0.02
175 20 0.11
176 127 0.71
177 5 0.03
178 18 0.10
179 6 0.03
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (176 bp):
GGGGCAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGAGGGTAA
AATGGTAATTTTCGATGAAATCGGGGTTAAAAATGGAATTTTAAAAGAGTCGGGGGTAAAATGGT
AATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGCTTC
Found at i:6502167 original size:17 final size:16
Alignment explanation
Indices: 6502147--6502220 Score: 89
Period size: 17 Copynumber: 4.6 Consensus size: 16
6502137 AATTTTTATT
*
6502147 TAAATTTAAATTCAAA
1 TAAATTTAAATTTAAA
*
6502163 GTAAATTTAAA--TAAT
1 -TAAATTTAAATTTAAA
6502178 TAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
6502195 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
*
6502211 TAAAATTAAA
1 TAAATTTAAA
6502221 AATCAATTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
14 10 0.20
15 2 0.04
16 13 0.26
17 25 0.50
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:6502173 original size:6 final size:6
Alignment explanation
Indices: 6502144--6502211 Score: 77
Period size: 6 Copynumber: 11.3 Consensus size: 6
6502134 CTTAATTTTT
* *
6502144 ATTTAA ATTTAA ATTCAA A-GTAA ATTTAA ATAATTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA ATTTAA ATTTAA
*
6502193 A-ATAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
6502212 AAAATTAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
5 7 0.13
6 39 0.75
8 6 0.12
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:6502181 original size:31 final size:31
Alignment explanation
Indices: 6502146--6502205 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
6502136 TAATTTTTAT
*
6502146 TTAAATTTAAATTCAAAGTAAATTTAAATAA
1 TTAAATTTAAATTCAAAATAAATTTAAATAA
*
6502177 TTAAATTTAAATTTAAAATAAATTTAAAT
1 TTAAATTTAAATTCAAAATAAATTTAAAT
6502206 TTAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (31 bp):
TTAAATTTAAATTCAAAATAAATTTAAATAA
Found at i:6503085 original size:20 final size:20
Alignment explanation
Indices: 6503060--6503118 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
6503050 AAAACAGTAG
*
6503060 CAAAAATAACAGCAAAATAA
1 CAAAAATAACAGCAAAAAAA
**
6503080 CAAAAATAACTCCAAAAAAA
1 CAAAAATAACAGCAAAAAAA
*
6503100 CAACCAA-AACAGCAAAAAA
1 CAA-AAATAACAGCAAAAAA
6503119 TATTAGAAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.69, C:0.20, G:0.03, T:0.07
Consensus pattern (20 bp):
CAAAAATAACAGCAAAAAAA
Found at i:6504230 original size:84 final size:82
Alignment explanation
Indices: 6504080--6504242 Score: 240
Period size: 84 Copynumber: 2.0 Consensus size: 82
6504070 TAAAAGATGC
*
6504080 AAATATAATTTTATCATGTATTAATTTATAATTTTATTATTTTTAAAGAGATTAAATAGAACATT
1 AAATATAATTTTATCATGTATTAATTTATAATTTTATTATTTTTAAAGAGATTAAATAGAA-AAT
6504145 TTTCATATTTAAGGGGTCA
65 TTTCAT-TTTAAGGGGTCA
* *
6504164 AAATATAATTTTATCATAG-ATTAATTTGTAATTTTATTATTTTTAGAGAGATTAAACTA-AAAA
1 AAATATAATTTTATCAT-GTATTAATTTATAATTTTATTATTTTTAAAGAGATTAAA-TAGAAAA
*
6504227 TTTTCATTTTTAGGGG
64 TTTTCATTTTAAGGGG
6504243 AACCAAGGCC
Statistics
Matches: 73, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
82 8 0.11
83 8 0.11
84 54 0.74
85 3 0.04
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (82 bp):
AAATATAATTTTATCATGTATTAATTTATAATTTTATTATTTTTAAAGAGATTAAATAGAAAATT
TTCATTTTAAGGGGTCA
Found at i:6510794 original size:21 final size:20
Alignment explanation
Indices: 6510749--6510797 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
6510739 AACTAAAAAT
*
6510749 AAAAAATATTAACTTCTATTT
1 AAAAAATATTAAC-TCTATTA
6510770 AAAAAATATTAGA-TCATATTA
1 AAAAAATATTA-ACTC-TATTA
6510791 AAAAAAT
1 AAAAAAT
6510798 GTAACAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 22 0.88
22 1 0.04
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAAAATATTAACTCTATTA
Found at i:6517374 original size:17 final size:17
Alignment explanation
Indices: 6517352--6517390 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
6517342 AGGTGAAGAA
* *
6517352 CTTGTTGGTTGAGAGTT
1 CTTGTTGGTAGAGAATT
*
6517369 CTTGTTTGTAGAGAATT
1 CTTGTTGGTAGAGAATT
6517386 CTTGT
1 CTTGT
6517391 CAATGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.08, G:0.28, T:0.49
Consensus pattern (17 bp):
CTTGTTGGTAGAGAATT
Found at i:6520503 original size:17 final size:18
Alignment explanation
Indices: 6520471--6520505 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6520461 TCTTTAACTT
6520471 ATTTTTCATGGAATTTAA
1 ATTTTTCATGGAATTTAA
6520489 ATTTTTCATGG-ATTTAA
1 ATTTTTCATGGAATTTAA
6520506 TATTGTTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.51
Consensus pattern (18 bp):
ATTTTTCATGGAATTTAA
Found at i:6525611 original size:20 final size:21
Alignment explanation
Indices: 6525572--6525626 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
6525562 AGTCTTCAAG
*
6525572 GTATCAGTAGAAGT-GAAGTT
1 GTATCGGTAGAAGTCGAAGTT
6525592 GTATCGGTAGAAGTCG-AGTT
1 GTATCGGTAGAAGTCGAAGTT
* * *
6525612 CTACCGATAGAAGTC
1 GTATCGGTAGAAGTC
6525627 TCACTGGAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (21 bp):
GTATCGGTAGAAGTCGAAGTT
Found at i:6528725 original size:20 final size:20
Alignment explanation
Indices: 6528700--6528739 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6528690 AGTCTTCAAG
6528700 GTATCGGTAAAAGTGGAGTT
1 GTATCGGTAAAAGTGGAGTT
* *
6528720 GTATCGGTAGAAGTTGAGTT
1 GTATCGGTAAAAGTGGAGTT
6528740 CTACCAGTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.35, T:0.33
Consensus pattern (20 bp):
GTATCGGTAAAAGTGGAGTT
Found at i:6533977 original size:13 final size:13
Alignment explanation
Indices: 6533959--6533985 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6533949 GTCTAACCTT
6533959 TTAAAAAATTTAA
1 TTAAAAAATTTAA
6533972 TTAAAAAATTTAA
1 TTAAAAAATTTAA
6533985 T
1 T
6533986 AAGTAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAAAAATTTAA
Found at i:6543195 original size:21 final size:21
Alignment explanation
Indices: 6543156--6543196 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6543146 AAGAAATAAC
**
6543156 TTTGTTAATTATTGTATCAAG
1 TTTGTTAATTATTCCATCAAG
6543177 TTTGTTAATTATTCCATCAA
1 TTTGTTAATTATTCCATCAA
6543197 TCTTGGTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (21 bp):
TTTGTTAATTATTCCATCAAG
Found at i:6546346 original size:49 final size:49
Alignment explanation
Indices: 6546268--6546417 Score: 185
Period size: 49 Copynumber: 3.0 Consensus size: 49
6546258 ATCGCATTGC
* * *
6546268 AACTTGGGCTCCTAGTTCATGGTGGTTATACGGTCACGAGTTCAAGTAT
1 AACTAGGGCTCCTAGTTCACGGTGATTATACGGTCACGAGTTCAAGTAT
*
6546317 AACTAGGGCTCCTAGTTCACGGTGATTATACGGTCACGGGTTTCAAGTAT
1 AACTAGGGCTCCTAGTTCACGGTGATTATACGGTCACGAG-TTCAAGTAT
* * * * * *
6546367 AACTAGGGCTCCCAGTTGACGAT-AGTTATGCAGTCATGAGTTCAAGTAT
1 AACTAGGGCTCCTAGTTCACGGTGA-TTATACGGTCACGAGTTCAAGTAT
6546416 AA
1 AA
6546418 TTCGAGCTCC
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
49 48 0.55
50 40 0.45
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (49 bp):
AACTAGGGCTCCTAGTTCACGGTGATTATACGGTCACGAGTTCAAGTAT
Found at i:6546459 original size:49 final size:49
Alignment explanation
Indices: 6546307--6546462 Score: 127
Period size: 49 Copynumber: 3.2 Consensus size: 49
6546297 ACGGTCACGA
* * * * * * * *
6546307 GTTCAAGTATAACTAGGGCTCCTAGTTCACGGT-GATTATACGGTCACGG
1 GTTCAAGTATAACTAGAGCTCCCAATTGACGATAG-TTATGCAGTCACAG
* * *
6546356 GTTTCAAGTATAACTAGGGCTCCCAGTTGACGATAGTTATGCAGTCA-TG
1 G-TTCAAGTATAACTAGAGCTCCCAATTGACGATAGTTATGCAGTCACAG
* * * * *
6546405 AGTTCAAGTATAATTCGAGCTCCCAATTGGCGGTGGTTATGCAGTCACAG
1 -GTTCAAGTATAACTAGAGCTCCCAATTGACGATAGTTATGCAGTCACAG
6546455 GTTCAAGT
1 GTTCAAGT
6546463 TTCATGTCAC
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
49 48 0.54
50 40 0.45
51 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (49 bp):
GTTCAAGTATAACTAGAGCTCCCAATTGACGATAGTTATGCAGTCACAG
Found at i:6548246 original size:235 final size:235
Alignment explanation
Indices: 6547810--6548334 Score: 861
Period size: 235 Copynumber: 2.2 Consensus size: 235
6547800 TTAACCTTTG
* *
6547810 ACATGGTCAAGGGGTGGTAAGACTGATAATGAGGAGGAAGAGGTGACGAGGGAGATGGTGAAAAT
1 ACATGGTGAAGGGGTGGTAAGACTGATAATGAGGAGGAGGAGGTGACGAGGGAGATGGTGAAAAT
* * *
6547875 GGAGAGATGGCAGTGGAGACTTGGAGTAGGCGTAAAATGGGGTGGAGGTGATGATGGCACGAGGG
66 GGAGACAGGGCAGTGGAGACTTGGAGTAGGCGTAAAATGGAGTGGAGGTGATGATGGCACGAGGG
* * *
6547940 TGGGTATGGGGAGGGTTGTGCCCGGAAGACGGTGGAGATGAAGAAGATCGAAGAGATGTGTAGGG
131 TGGGTATGGGGAGGGTTGTGCCCGGAAGACGGTCGAGATGAAGAAGATCGAAGAGATGCGTAGGA
**
6548005 CTACATCTACACCCATACGGTTGTACTGGATACTTGCTTA
196 CTACATCTACACCCATACGACTGTACTGGATACTTGCTTA
* * *
6548045 ATATGGTGATGGGTTGGTAAGACTGATAATGAGGAGGAGGAGGTGACGAGGGAGATGGTGAAAAT
1 ACATGGTGAAGGGGTGGTAAGACTGATAATGAGGAGGAGGAGGTGACGAGGGAGATGGTGAAAAT
* * * *
6548110 GGAGACAGGGCGGTGGAGACTTGTAGTAGGCGTAAAGTGGAGTGGAGGTGGTGATGGCACGAGGG
66 GGAGACAGGGCAGTGGAGACTTGGAGTAGGCGTAAAATGGAGTGGAGGTGATGATGGCACGAGGG
* *
6548175 TGGGTATGGGGAGGGTTGTGCCCGGAAGACGTTCGAGATGAAGGAGATCGAAGAGATGCGTAGGA
131 TGGGTATGGGGAGGGTTGTGCCCGGAAGACGGTCGAGATGAAGAAGATCGAAGAGATGCGTAGGA
*
6548240 CTACATCTACACCCATACGACTGTACTGGATACTTGTTTA
196 CTACATCTACACCCATACGACTGTACTGGATACTTGCTTA
*
6548280 ACATGGTGAAGGGGTGGTAAGACTGATAATGAGGAGGAGAAGGTGACGAGGGAGA
1 ACATGGTGAAGGGGTGGTAAGACTGATAATGAGGAGGAGGAGGTGACGAGGGAGA
6548335 GCGTGAGGGT
Statistics
Matches: 266, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
235 266 1.00
ACGTcount: A:0.29, C:0.10, G:0.41, T:0.20
Consensus pattern (235 bp):
ACATGGTGAAGGGGTGGTAAGACTGATAATGAGGAGGAGGAGGTGACGAGGGAGATGGTGAAAAT
GGAGACAGGGCAGTGGAGACTTGGAGTAGGCGTAAAATGGAGTGGAGGTGATGATGGCACGAGGG
TGGGTATGGGGAGGGTTGTGCCCGGAAGACGGTCGAGATGAAGAAGATCGAAGAGATGCGTAGGA
CTACATCTACACCCATACGACTGTACTGGATACTTGCTTA
Found at i:6549001 original size:8 final size:9
Alignment explanation
Indices: 6548980--6549010 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
6548970 ACACTTGTTT
6548980 TTTTTATTA
1 TTTTTATTA
6548989 TTTTTATTA
1 TTTTTATTA
6548998 TTTTTATATA
1 TTTTTAT-TA
6549008 TTT
1 TTT
6549011 AAAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTATTA
Found at i:6549145 original size:27 final size:27
Alignment explanation
Indices: 6549107--6549162 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
6549097 AATACCTGAT
*
6549107 ACCAGTGGAGGAACACCAAGTGGCGGC
1 ACCAATGGAGGAACACCAAGTGGCGGC
* *
6549134 ACCAATGGAGGAATATCAAGTGGCGGC
1 ACCAATGGAGGAACACCAAGTGGCGGC
6549161 AC
1 AC
6549163 TAAGGGGTGT
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:0.32, C:0.23, G:0.34, T:0.11
Consensus pattern (27 bp):
ACCAATGGAGGAACACCAAGTGGCGGC
Found at i:6549362 original size:9 final size:9
Alignment explanation
Indices: 6549348--6549373 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
6549338 AAGAAAGAAA
6549348 GAAGAAGGT
1 GAAGAAGGT
6549357 GAAGAAGGT
1 GAAGAAGGT
6549366 GAAGAAGG
1 GAAGAAGG
6549374 AGAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.46, T:0.08
Consensus pattern (9 bp):
GAAGAAGGT
Found at i:6549764 original size:20 final size:21
Alignment explanation
Indices: 6549723--6549765 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
6549713 TAATTTACTT
6549723 TAATTTAATTTTGTTAGTTAG
1 TAATTTAATTTTGTTAGTTAG
*
6549744 TAATTTTATTTTGTT-GTTAG
1 TAATTTAATTTTGTTAGTTAG
6549764 TA
1 TA
6549766 GTAGTAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (21 bp):
TAATTTAATTTTGTTAGTTAG
Found at i:6549981 original size:94 final size:93
Alignment explanation
Indices: 6549736--6550184 Score: 649
Period size: 94 Copynumber: 4.8 Consensus size: 93
6549726 TTTAATTTTG
* *
6549736 TTAGTTAGTAATTTTATTTTGTTGTTA--GTAGTAGTAAGTAAAAAATATTATTCATATTTATTG
1 TTAGTTAGTAATTTTATTTTGTTGTTAGTGTAGTAGTAAGTAAAAAACATTGTTCATATTTATTG
***
6549799 ATTTAAAATTTAATAATGTTT-AAATTT
66 ATTTAAAATTTAATAATGTTTAAAAAAA
*
6549826 TGCTAGTTAGTAACTTTATTTTGTTGTTA--GTAGTAGTAAGTAAAAAACATTGTTCATATTTAT
1 T--TAGTTAGTAATTTTATTTTGTTGTTAGTGTAGTAGTAAGTAAAAAACATTGTTCATATTTAT
6549889 TGATTTAAAATTTAATAATGTTTAAAAAAA
64 TGATTTAAAATTTAATAATGTTTAAAAAAA
* *
6549919 ATAGTTAGTAATTTTATTTTGTTGTTAGTTGTAGTAGTAAGTAAAAAACATTGTTTATATTTATT
1 TTAGTTAGTAATTTTATTTTGTTGTTAG-TGTAGTAGTAAGTAAAAAACATTGTTCATATTTATT
*
6549984 GATTTAAAATTTGATAATGTTTAAAAAAA
65 GATTTAAAATTTAATAATGTTTAAAAAAA
* *
6550013 TTAATTAGTAATTTTATATTGTTGTTAGTAGTAGCAGTAGTAAGT-AAAAACATTGTTCATATTT
1 TTAGTTAGTAATTTTATTTTGTTGTTAGT-GT---AGTAGTAAGTAAAAAACATTGTTCATATTT
6550077 ATTGATTTAAAATTTAATAATGTTTAAAAAAA
62 ATTGATTTAAAATTTAATAATGTTTAAAAAAA
* *
6550109 TTAGTTAGTAATTTTATTTTATTGTTAGTAAGTAGTAGTAAGTAAAAAATATTGTTCATATTTAT
1 TTAGTTAGTAATTTTATTTTGTTGTTAGT--GTAGTAGTAAGTAAAAAACATTGTTCATATTTAT
6550174 TGATTTTAAAA
64 TGA-TTTAAAA
6550185 AATAATATAA
Statistics
Matches: 327, Mismatches: 19, Indels: 20
0.89 0.05 0.05
Matches are distributed among these distances:
90 1 0.00
91 25 0.08
92 80 0.24
93 4 0.01
94 99 0.30
95 23 0.07
96 82 0.25
97 13 0.04
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (93 bp):
TTAGTTAGTAATTTTATTTTGTTGTTAGTGTAGTAGTAAGTAAAAAACATTGTTCATATTTATTG
ATTTAAAATTTAATAATGTTTAAAAAAA
Found at i:6550012 original size:47 final size:47
Alignment explanation
Indices: 6549867--6550012 Score: 106
Period size: 47 Copynumber: 3.1 Consensus size: 47
6549857 AGTAGTAAGT
* *
6549867 AAAAAACATTGTTCATATTTATTGATTTAAAATTTAATAATGTTTAA
1 AAAAAACATTGTTAATATTTATTGATTTAAAATTTGATAATGTTTAA
* * *** * *
6549914 AAAAAATAGTTAG-TAAT-TTTATT-TTGTTGTTAGTTG-T-A-GTAGTAA
1 AAAAAACA-TT-GTTAATATTTATTGAT-TTAAAATTTGATAATGT-TTAA
*
6549959 GTAAAAAACATTGTTTATATTTATTGATTTAAAATTTGATAATGTTTAA
1 --AAAAAACATTGTTAATATTTATTGATTTAAAATTTGATAATGTTTAA
6550008 AAAAA
1 AAAAA
6550013 TTAATTAGTA
Statistics
Matches: 70, Mismatches: 17, Indels: 24
0.63 0.15 0.22
Matches are distributed among these distances:
44 2 0.03
45 5 0.07
46 7 0.10
47 42 0.60
48 7 0.10
49 5 0.07
50 2 0.03
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (47 bp):
AAAAAACATTGTTAATATTTATTGATTTAAAATTTGATAATGTTTAA
Found at i:6550029 original size:47 final size:47
Alignment explanation
Indices: 6549884--6550029 Score: 104
Period size: 47 Copynumber: 3.1 Consensus size: 47
6549874 ATTGTTCATA
* * *
6549884 TTTATTGATTTAAAATTTAATAATGTTTAAAAAAAATAGTTAGTAAT
1 TTTATTGATTTAAAATTTGATAATGTTTAAAAAAATTAATTAGTAAT
* *** * * * **
6549931 TTTATT-TTGTTGTTAGTTG-TAGTAGTAAGTAAAAAACATTGTTTA-T-A-
1 TTTATTGAT-TTAAAATTTGATAAT-GT--TTAAAAAA-ATTAATTAGTAAT
6549978 TTTATTGATTTAAAATTTGATAATGTTTAAAAAAATTAATTAGTAAT
1 TTTATTGATTTAAAATTTGATAATGTTTAAAAAAATTAATTAGTAAT
6550025 TTTAT
1 TTTAT
6550030 ATTGTTGTTA
Statistics
Matches: 69, Mismatches: 20, Indels: 20
0.63 0.18 0.18
Matches are distributed among these distances:
44 6 0.09
45 8 0.12
46 5 0.07
47 32 0.46
48 5 0.07
49 8 0.12
50 5 0.07
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.48
Consensus pattern (47 bp):
TTTATTGATTTAAAATTTGATAATGTTTAAAAAAATTAATTAGTAAT
Found at i:6550108 original size:190 final size:184
Alignment explanation
Indices: 6549737--6550184 Score: 659
Period size: 190 Copynumber: 2.4 Consensus size: 184
6549727 TTAATTTTGT
*
6549737 TAGTTAGTAATTTTATTTTGTTGTTA--GTAGTAGTAAGTAAAAAATATTATTCATATTTATTGA
1 TAGTTAGTAATTTTATTTTGTTGTTAGTGTAGTAGTAAGTAAAAAATATTGTTCATATTTATTGA
*** * * *
6549800 TTTAAAATTTAATAATGTTTAAATTTTGCTAGTTAGTAACTTTATTTTGTTGTTAGTAGTAGTAA
66 TTTAAAATTTAATAATGTTTAAAAAAT-CTAATTAGTAACTTTATATTGTTGTTAGTAGTAGCAA
6549865 GTAAAAAACATTGTTCATATTTATTGATTTAAAATTTAATAATGTTTAAAAAAAA
130 GTAAAAAACATTGTTCATATTTATTGATTTAAAATTTAATAATGTTTAAAAAAAA
* *
6549920 TAGTTAGTAATTTTATTTTGTTGTTAGTTGTAGTAGTAAGTAAAAAACATTGTTTATATTTATTG
1 TAGTTAGTAATTTTATTTTGTTGTTAG-TGTAGTAGTAAGTAAAAAATATTGTTCATATTTATTG
* *
6549985 ATTTAAAATTTGATAATGTTTAAAAAAAT-TAATTAGTAATTTTATATTGTTGTTAGTAGTAGCA
65 ATTTAAAATTTAATAATGTTT-AAAAAATCTAATTAGTAACTTTATATTGTTGTTAGTAGTAGCA
*
6550049 GTAGTAAGTAAAAACATTGTTCATATTTATTGATTTAAAATTTAATAATGTTTAAAAAAAT
129 --AGT-A--AAAAACATTGTTCATATTTATTGATTTAAAATTTAATAATGTTTAAAAAAAA
*
6550110 TAGTTAGTAATTTTATTTTATTGTTAGTAAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATT
1 TAGTTAGTAATTTTATTTTGTTGTTAGT--GTAGTAGTAAGTAAAAAATATTGTTCATATTTATT
6550175 GATTTTAAAA
64 GA-TTTAAAA
6550185 AATAATATAA
Statistics
Matches: 238, Mismatches: 15, Indels: 15
0.89 0.06 0.06
Matches are distributed among these distances:
183 26 0.11
185 31 0.13
186 53 0.22
187 7 0.03
188 1 0.00
189 1 0.00
190 77 0.32
191 35 0.15
192 7 0.03
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (184 bp):
TAGTTAGTAATTTTATTTTGTTGTTAGTGTAGTAGTAAGTAAAAAATATTGTTCATATTTATTGA
TTTAAAATTTAATAATGTTTAAAAAATCTAATTAGTAACTTTATATTGTTGTTAGTAGTAGCAAG
TAAAAAACATTGTTCATATTTATTGATTTAAAATTTAATAATGTTTAAAAAAAA
Found at i:6550420 original size:16 final size:16
Alignment explanation
Indices: 6550375--6550424 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
6550365 TAAATCTAGC
6550375 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
*
6550391 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
6550405 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
6550421 TAAT
1 TAAT
6550425 ACCCCCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 3 0.11
14 8 0.29
15 2 0.07
16 12 0.43
17 3 0.11
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:6550491 original size:30 final size:30
Alignment explanation
Indices: 6550457--6550558 Score: 82
Period size: 30 Copynumber: 3.4 Consensus size: 30
6550447 AAATGGTACA
6550457 AAATAAATATTTATTTTGTACCATTTTGGT
1 AAATAAATATTTATTTTGTACCATTTTGGT
** * * * *
6550487 AAAT-AAT-GGTGTGTGGATACTATTTTGGT
1 AAATAAATATTTATTTTG-TACCATTTTGGT
* * * *
6550516 ATATAAAAATATATTTTGTACCATTTTAGT
1 AAATAAATATTTATTTTGTACCATTTTGGT
6550546 AAATAACATATTT
1 AAATAA-ATATTT
6550559 TTGGTATTTA
Statistics
Matches: 50, Mismatches: 18, Indels: 7
0.67 0.24 0.09
Matches are distributed among these distances:
28 4 0.08
29 17 0.34
30 21 0.42
31 8 0.16
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (30 bp):
AAATAAATATTTATTTTGTACCATTTTGGT
Found at i:6552298 original size:12 final size:12
Alignment explanation
Indices: 6552283--6552322 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
6552273 CTAGAGCAAC
6552283 AAGAAGAGGAGG
1 AAGAAGAGGAGG
*
6552295 AAGAAAAGGAGG
1 AAGAAGAGGAGG
*
6552307 AGGAAGAGGAGG
1 AAGAAGAGGAGG
6552319 AAGA
1 AAGA
6552323 GGCGTTGGAT
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:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (12 bp):
AAGAAGAGGAGG
Found at i:6555695 original size:13 final size:13
Alignment explanation
Indices: 6555677--6555703 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6555667 TTTCCTTCTT
6555677 CTTTCTTTCTTTC
1 CTTTCTTTCTTTC
6555690 CTTTCTTTCTTTC
1 CTTTCTTTCTTTC
6555703 C
1 C
6555704 CGTTTATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (13 bp):
CTTTCTTTCTTTC
Found at i:6563532 original size:21 final size:22
Alignment explanation
Indices: 6563499--6563548 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
6563489 TTTAATGAAA
*
6563499 TTATTAGTATATA-TTTTTATT
1 TTATTAGTATATACTTTATATT
6563520 TTATT-GTATTATACTTTATATT
1 TTATTAGTA-TATACTTTATATT
*
6563542 TTTTTAG
1 TTATTAG
6563549 AAGGGGTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 3 0.12
21 9 0.38
22 11 0.46
23 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (22 bp):
TTATTAGTATATACTTTATATT
Found at i:6570082 original size:27 final size:26
Alignment explanation
Indices: 6570041--6570096 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
6570031 TTTTAATTAG
*
6570041 ATATTTTTCATTAAT-TAATTAGTTAA
1 ATATTTTTCATTAATAT-ATTACTTAA
*
6570067 ATATTATTTTATTAATATATTACTTAA
1 ATATT-TTTCATTAATATATTACTTAA
6570094 ATA
1 ATA
6570097 ATAATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 5 0.19
27 20 0.77
28 1 0.04
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (26 bp):
ATATTTTTCATTAATATATTACTTAA
Found at i:6570469 original size:3 final size:3
Alignment explanation
Indices: 6570461--6570508 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
6570451 CTACTTCTTA
6570461 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6570509 TTTACACTCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:6575220 original size:15 final size:15
Alignment explanation
Indices: 6575200--6575236 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
6575190 CTTCTGCAAG
6575200 AAGAAAGGGCACATT
1 AAGAAAGGGCACATT
6575215 AAGAAAGGGCACATT
1 AAGAAAGGGCACATT
6575230 AAGAAAG
1 AAGAAAG
6575237 AGTGCTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.11, G:0.27, T:0.11
Consensus pattern (15 bp):
AAGAAAGGGCACATT
Found at i:6577181 original size:17 final size:17
Alignment explanation
Indices: 6577159--6577195 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
6577149 AGGCGGAGAA
* *
6577159 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
6577176 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
6577193 CTT
1 CTT
6577196 ATCAAGGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.14, G:0.24, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:6580351 original size:23 final size:23
Alignment explanation
Indices: 6580325--6580374 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
6580315 GATTATTTAC
6580325 ACTTGAGTCACAAAAATTTTCAT
1 ACTTGAGTCACAAAAATTTTCAT
*
6580348 ACTTGAGTCACAAAAATTTTCGT
1 ACTTGAGTCACAAAAATTTTCAT
6580371 ACTT
1 ACTT
6580375 TTACAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (23 bp):
ACTTGAGTCACAAAAATTTTCAT
Found at i:6587407 original size:140 final size:142
Alignment explanation
Indices: 6587088--6587517 Score: 747
Period size: 140 Copynumber: 3.0 Consensus size: 142
6587078 CGGATGTCAA
*
6587088 ACAGGTGAGTTTTGGGGTAGGGCATATTAATATATATACGGCGGACAAAGGCTCCAGGTGGTCGA
1 ACAGGTGAGTTTTGGGGTAGGGCATATTAACATATATACGGCGGACAAAGGCTCCAGGTGGTCGA
*
6587153 GTACAGAGACAAAGACGAAGAGCGAGGTGGGCGGGCGGGCGGGGGGTTACATTCGGAGGGCAGTG
66 GTCCAGAGACAAAGACGAAGAGCGA---GGGCGGGCGGGCGGGGGGTTACATTCGGAGGGCAGTG
6587218 TCCTGTCGTGGAGTT
128 TCCTGTCGTGGAGTT
6587233 ACAGGTGAGTTTTGGGGTAGGGCATATTAACATATATACGGCGGACAAAGGCTCCAGGTGGTCGA
1 ACAGGTGAGTTTTGGGGTAGGGCATATTAACATATATACGGCGGACAAAGGCTCCAGGTGGTCGA
*
6587298 GTCCAGAGACAAAGACGAAGAACGA-GGCGGGCGGGC-GGGGGTTACATTCGGAGGGCAGTGTCC
66 GTCCAGAGACAAAGACGAAGAGCGAGGGCGGGCGGGCGGGGGGTTACATTCGGAGGGCAGTGTCC
6587361 TGTCGTGGAGTT
131 TGTCGTGGAGTT
*
6587373 ACAGGTGAGTTTTGGGGTAGGGCATATTAACATATATACGGCGGACAAAGGTTCCAGGTGGTCGA
1 ACAGGTGAGTTTTGGGGTAGGGCATATTAACATATATACGGCGGACAAAGGCTCCAGGTGGTCGA
*
6587438 GTCCAGAGACAAAGACGAAGAGCGAGGTGGGCGGGCGGGCGGGGGGTTACATTCGGAGGGCAGTT
66 GTCCAGAGACAAAGACGAAGAGCGA---GGGCGGGCGGGCGGGGGGTTACATTCGGAGGGCAGTG
6587503 TCCTGTCGTGGAGTT
128 TCCTGTCGTGGAGTT
6587518 TCGATATCCA
Statistics
Matches: 274, Mismatches: 6, Indels: 10
0.94 0.02 0.03
Matches are distributed among these distances:
140 127 0.46
141 11 0.04
144 11 0.04
145 125 0.46
ACGTcount: A:0.24, C:0.16, G:0.40, T:0.20
Consensus pattern (142 bp):
ACAGGTGAGTTTTGGGGTAGGGCATATTAACATATATACGGCGGACAAAGGCTCCAGGTGGTCGA
GTCCAGAGACAAAGACGAAGAGCGAGGGCGGGCGGGCGGGGGGTTACATTCGGAGGGCAGTGTCC
TGTCGTGGAGTT
Found at i:6591161 original size:16 final size:16
Alignment explanation
Indices: 6591140--6591172 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6591130 GACCATGGTC
6591140 TTTCAAGTTTA-TTTTT
1 TTTCAA-TTTAGTTTTT
6591156 TTTCAATTTAGTTTTT
1 TTTCAATTTAGTTTTT
6591172 T
1 T
6591173 ATAAATTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (16 bp):
TTTCAATTTAGTTTTT
Found at i:6591170 original size:15 final size:16
Alignment explanation
Indices: 6591140--6591172 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
6591130 GACCATGGTC
*
6591140 TTTCAAGTTTATTTTT
1 TTTCAAGTTTAGTTTT
6591156 TTTCAA-TTTAGTTTT
1 TTTCAAGTTTAGTTTT
6591171 TT
1 TT
6591173 ATAAATTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (16 bp):
TTTCAAGTTTAGTTTT
Found at i:6591751 original size:18 final size:18
Alignment explanation
Indices: 6591728--6591763 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6591718 TAAACGAATC
*
6591728 GAGTTATTCGAGTTAACT
1 GAGTTATTCGAGTCAACT
6591746 GAGTTATTCGAGTCAACT
1 GAGTTATTCGAGTCAACT
6591764 CAATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (18 bp):
GAGTTATTCGAGTCAACT
Found at i:6591908 original size:29 final size:29
Alignment explanation
Indices: 6591876--6591934 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
6591866 ACTTTTTTAC
*
6591876 TTTTCCCTCAAAACTTTTACT-TCTTCTCA
1 TTTTCCC-CAAAACTTTTACTCTCCTCTCA
*
6591905 TTTTCCCCCAAACTTTTACTCTCCTCTCA
1 TTTTCCCCAAAACTTTTACTCTCCTCTCA
6591934 T
1 T
6591935 CCCACTCCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.19, C:0.36, G:0.00, T:0.46
Consensus pattern (29 bp):
TTTTCCCCAAAACTTTTACTCTCCTCTCA
Found at i:6592109 original size:29 final size:29
Alignment explanation
Indices: 6592054--6592111 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
6592044 ATTTTCCCCC
*
6592054 AAAACTTTTATTCCCTCCCACTTTCCACCT
1 AAAACTTTTACTCCCTCCCAC-TTCCACCT
*
6592084 AAAACTTTTACTCCTCTCTCA-TTCCACC
1 AAAACTTTTACTCC-CTCCCACTTCCACC
6592112 CCCCATTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 13 0.52
31 5 0.20
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (29 bp):
AAAACTTTTACTCCCTCCCACTTCCACCT
Found at i:6600036 original size:81 final size:81
Alignment explanation
Indices: 6599901--6600063 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
6599891 TGATGGAGGC
6599901 TTGAATCACGATACCCACTAGAGTCTACAGCCACCAGTTAAAAGTTGAACCGCTAATGCTAATGC
1 TTGAATCACGATACCCACTAGAGTCTACAGCCACCAGTTAAAAGTTGAACCGCTAATGCTAATGC
6599966 CAGAACATCATAAAAA
66 CAGAACATCATAAAAA
6599982 TTGAATCACGATACCCACTAGAGTCTACAGCCACCAGTTAAAAGTTGAACCGCTAATGCTAATGC
1 TTGAATCACGATACCCACTAGAGTCTACAGCCACCAGTTAAAAGTTGAACCGCTAATGCTAATGC
6600047 CAGAACATCATAAAAA
66 CAGAACATCATAAAAA
6600063 T
1 T
6600064 AGATAGAGTA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.39, C:0.25, G:0.15, T:0.21
Consensus pattern (81 bp):
TTGAATCACGATACCCACTAGAGTCTACAGCCACCAGTTAAAAGTTGAACCGCTAATGCTAATGC
CAGAACATCATAAAAA
Found at i:6601722 original size:3 final size:3
Alignment explanation
Indices: 6601714--6601738 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6601704 CTCGATTGAA
6601714 GCG GCG GCG GCG GCG GCG GCG GCG G
1 GCG GCG GCG GCG GCG GCG GCG GCG G
6601739 AGAAAGCAGT
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:0.00, C:0.32, G:0.68, T:0.00
Consensus pattern (3 bp):
GCG
Found at i:6608561 original size:26 final size:28
Alignment explanation
Indices: 6608520--6608574 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
6608510 TTCAGTTCAG
*
6608520 TTTGATTTTCGATTTTTTATATTAATTT
1 TTTGATTTTCGATTTTTTAAATTAATTT
*
6608548 TTTG-TTTT-GATTTTTTAAATTTATTT
1 TTTGATTTTCGATTTTTTAAATTAATTT
6608574 T
1 T
6608575 GATAAAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 17 0.68
27 4 0.16
28 4 0.16
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.71
Consensus pattern (28 bp):
TTTGATTTTCGATTTTTTAAATTAATTT
Found at i:6609171 original size:30 final size:30
Alignment explanation
Indices: 6609135--6609194 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
6609125 ATGGGAGTTT
6609135 GAGTACGTTACCTTCTTATTTATAGATTAA
1 GAGTACGTTACCTTCTTATTTATAGATTAA
* *
6609165 GAGTACGTTACCTTCTTGTTTATGGATTAA
1 GAGTACGTTACCTTCTTATTTATAGATTAA
6609195 AGAAGAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (30 bp):
GAGTACGTTACCTTCTTATTTATAGATTAA
Found at i:6610267 original size:16 final size:16
Alignment explanation
Indices: 6610246--6610277 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6610236 AATTAGGTAC
6610246 TAAATTAAAAAAAAAT
1 TAAATTAAAAAAAAAT
*
6610262 TAAATTAATAAAAAAT
1 TAAATTAAAAAAAAAT
6610278 ATCAAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAATTAAAAAAAAAT
Found at i:6610289 original size:16 final size:16
Alignment explanation
Indices: 6610247--6610318 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 16
6610237 ATTAGGTACT
* * *
6610247 AAATTAAAAAAAAATT
1 AAATTTAAAAAATATC
6610263 AAATTAATAAAAAATATC
1 AAATT--TAAAAAATATC
*
6610281 AAATTT---AAATATT
1 AAATTTAAAAAATATC
*
6610294 AAATTAAAAAAATATC
1 AAATTTAAAAAATATC
*
6610310 AATTTTAAA
1 AAATTTAAA
6610319 TACGAAATTA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
13 11 0.26
16 19 0.44
18 13 0.30
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTTAAAAAATATC
Found at i:6610319 original size:29 final size:31
Alignment explanation
Indices: 6610260--6610320 Score: 99
Period size: 29 Copynumber: 2.0 Consensus size: 31
6610250 TTAAAAAAAA
6610260 ATTAAATTAATAAAAAATATCAAATTTAAAT
1 ATTAAATTAATAAAAAATATCAAATTTAAAT
*
6610291 ATTAAATT-A-AAAAAATATCAATTTTAAAT
1 ATTAAATTAATAAAAAATATCAAATTTAAAT
6610320 A
1 A
6610321 CGAAATTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 20 0.69
30 1 0.03
31 8 0.28
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (31 bp):
ATTAAATTAATAAAAAATATCAAATTTAAAT
Found at i:6610326 original size:29 final size:29
Alignment explanation
Indices: 6610271--6610328 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
6610261 TTAAATTAAT
**
6610271 AAAAAATATCAAATTTAAATATTAAATTA
1 AAAAAATATCAAATTTAAATACGAAATTA
*
6610300 AAAAAATATCAATTTTAAATACGAAATTA
1 AAAAAATATCAAATTTAAATACGAAATTA
6610329 TATCATAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAAAATATCAAATTTAAATACGAAATTA
Found at i:6623747 original size:34 final size:34
Alignment explanation
Indices: 6623701--6623765 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
6623691 AAAAATTATA
6623701 TTTAATACAATAAAATATTTATTATATTTATTTT
1 TTTAATACAATAAAATATTTATTATATTTATTTT
* *
6623735 TTTAATATAATAAAATATTTATTCTATTTAT
1 TTTAATACAATAAAATATTTATTATATTTAT
6623766 GGTTGTGTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (34 bp):
TTTAATACAATAAAATATTTATTATATTTATTTT
Found at i:6623755 original size:17 final size:17
Alignment explanation
Indices: 6623698--6623755 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
6623688 TTTAAAAATT
*
6623698 ATATTTAATACAATAAA
1 ATATTTAATATAATAAA
* * * *
6623715 ATATTTATTATATTTAT
1 ATATTTAATATAATAAA
* *
6623732 TTTTTTAATATAATAAA
1 ATATTTAATATAATAAA
6623749 ATATTTA
1 ATATTTA
6623756 TTCTATTTAT
Statistics
Matches: 28, Mismatches: 13, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATTTAATATAATAAA
Found at i:6627018 original size:15 final size:15
Alignment explanation
Indices: 6626998--6627041 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
6626988 TCACGAGTTT
6626998 GGGTCGATTCGAGTC
1 GGGTCGATTCGAGTC
*
6627013 GGGTCGATTTG-GATC
1 GGGTCGATTCGAG-TC
*
6627028 GGGTCGGTTCGAGT
1 GGGTCGATTCGAGT
6627042 TCACACACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.11, C:0.16, G:0.43, T:0.30
Consensus pattern (15 bp):
GGGTCGATTCGAGTC
Found at i:6627758 original size:19 final size:18
Alignment explanation
Indices: 6627736--6627780 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
6627726 CTCACATTAC
6627736 TAATTAGTCCTCAAAATCG
1 TAATTAGTCC-CAAAATCG
* *
6627755 TAATTTTGTCCCAAAATCT
1 TAA-TTAGTCCCAAAATCG
6627774 TAATTAG
1 TAATTAG
6627781 AGTTCAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 3 0.14
19 13 0.59
20 6 0.27
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.38
Consensus pattern (18 bp):
TAATTAGTCCCAAAATCG
Found at i:6631958 original size:16 final size:15
Alignment explanation
Indices: 6631932--6631963 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
6631922 CACTTCTTAA
6631932 AATAAAATAAATAAT
1 AATAAAATAAATAAT
6631947 AATAATAATAAATAAT
1 AATAA-AATAAATAAT
6631963 A
1 A
6631964 CAATAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AATAAAATAAATAAT
Found at i:6636523 original size:6 final size:6
Alignment explanation
Indices: 6636512--6636561 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
6636502 ATTTAGGATA
* *
6636512 ATATTT ATATTT -TATTT TTATTT A-ATTT ATATTT ATCTTTTT ATATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT A--TATTT ATATTT
6636560 AT
1 AT
6636562 CTTTTAAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
5 10 0.27
6 22 0.59
8 5 0.14
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (6 bp):
ATATTT
Found at i:6636556 original size:14 final size:14
Alignment explanation
Indices: 6636537--6636566 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6636527 TTTTATTTAA
6636537 TTTATATTTATCTT
1 TTTATATTTATCTT
6636551 TTTATATTTATCTT
1 TTTATATTTATCTT
6636565 TT
1 TT
6636567 AAAGTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATATTTATCTT
Found at i:6638646 original size:27 final size:27
Alignment explanation
Indices: 6638591--6638675 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
6638581 GAACCTTGAC
* **
6638591 CCTAAACATCAAACCTTAAATCTTGAAT
1 CCTAAA-ATCAAACCCTAAATCTCAAAT
*
6638619 CCTAAAATCAAACCCTAAGTCTCAAAT
1 CCTAAAATCAAACCCTAAATCTCAAAT
* * * *
6638646 CATAAACTCTAAACCTTAAA-CACAAAT
1 CCTAAAATC-AAACCCTAAATCTCAAAT
6638673 CCT
1 CCT
6638676 GAATCTTGAA
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
27 32 0.70
28 14 0.30
ACGTcount: A:0.45, C:0.28, G:0.02, T:0.25
Consensus pattern (27 bp):
CCTAAAATCAAACCCTAAATCTCAAAT
Found at i:6640276 original size:166 final size:169
Alignment explanation
Indices: 6639994--6640315 Score: 399
Period size: 166 Copynumber: 1.9 Consensus size: 169
6639984 GGGAGTAGAA
* *
6639994 TTTTGAGGGAAAGTAAATAGGGAGAGTAAAATTTTGGAGGTGAAATATTCAAAAAAAAATTGGGA
1 TTTTGAGGGAAAATAAATAGGGAGAGTAAAATTTTGGAGGTAAAATATT---AAAAAAATTGGG-
* *
6640059 AGGGAGAATGGGTTTGAGTAGATGGAGGGTTGGATGGGAAGGGAATAAAAGTTTTAGGGAAAAGT
62 AGGGAAAATGGGTTTGAGTAGATGGAGAGTTGGATGGGAAGGGAATAAAAGTTTTAGGGAAAAGT
*
6640124 GAGAGAGAGTAAAAGTTTTGGGAGAAAATAATGAGTTTTGAGAG
127 GAGAAAGAGTAAAAGTTTTGGG-GAAAATAATGAGTTTTGAGAG
* *
6640168 TTTTGGGGGAAAATAAAT-GGGGGAGTAAAATTTTGGAGAG-AAAATATT-AAAAAATT-GG-GG
1 TTTTGAGGGAAAATAAATAGGGAGAGTAAAATTTTGGAG-GTAAAATATTAAAAAAATTGGGAGG
* * * *
6640228 GAAAATGGGTTTGGGGTAGATGG-GAG-TGAGATGGG-AGAGGAGTAAAAGTTTTGGGGGAAAGT
65 GAAAATGGGTTT-GAGTAGATGGAGAGTTG-GATGGGAAG-GGAATAAAAGTTTTAGGGAAAAGT
*
6640290 GGGAAAGAGTAAAAGTTTTGGGGAAA
127 GAGAAAGAGTAAAAGTTTTGGGGAAA
6640316 GTAAAATGGT
Statistics
Matches: 132, Mismatches: 12, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
165 8 0.06
166 62 0.47
167 9 0.07
168 2 0.02
169 8 0.06
173 26 0.20
174 17 0.13
ACGTcount: A:0.39, C:0.00, G:0.37, T:0.24
Consensus pattern (169 bp):
TTTTGAGGGAAAATAAATAGGGAGAGTAAAATTTTGGAGGTAAAATATTAAAAAAATTGGGAGGG
AAAATGGGTTTGAGTAGATGGAGAGTTGGATGGGAAGGGAATAAAAGTTTTAGGGAAAAGTGAGA
AAGAGTAAAAGTTTTGGGGAAAATAATGAGTTTTGAGAG
Found at i:6640420 original size:24 final size:24
Alignment explanation
Indices: 6640393--6640447 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
6640383 TATTCCAGTT
6640393 ATTCGAATTCGAAAACTCAACTTA
1 ATTCGAATTCGAAAACTCAACTTA
6640417 ATTCGAATTCGAAAACTCAACTTA
1 ATTCGAATTCGAAAACTCAACTTA
6640441 ATTCGAA
1 ATTCGAA
6640448 CTCAAAATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (24 bp):
ATTCGAATTCGAAAACTCAACTTA
Found at i:6643708 original size:36 final size:36
Alignment explanation
Indices: 6643664--6643737 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
6643654 GTAACAAAAT
* *
6643664 TAATAATAAAACAAG-AATTATACAATATTCAAATAA
1 TAATAATAAAA-AAGTAATTACACAATAATCAAATAA
* *
6643700 TAATAATAAAATAGTAATTACATAATAATCAAATAA
1 TAATAATAAAAAAGTAATTACACAATAATCAAATAA
6643736 TA
1 TA
6643738 GCAAAACAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 2 0.06
36 31 0.94
ACGTcount: A:0.61, C:0.07, G:0.03, T:0.30
Consensus pattern (36 bp):
TAATAATAAAAAAGTAATTACACAATAATCAAATAA
Found at i:6655540 original size:30 final size:30
Alignment explanation
Indices: 6655506--6655575 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
6655496 TAATTTATAT
* *
6655506 TTTTATCATTTTT-AAAGGATTAAATTAAAA
1 TTTTATCATTTTTGAAAGG-TCAAAGTAAAA
* * *
6655536 TTTTATTATTTTTGGAAGGTCAAAGTATAA
1 TTTTATCATTTTTGAAAGGTCAAAGTAAAA
6655566 TTTTATCATT
1 TTTTATCATT
6655576 ACTAATTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 29 0.88
31 4 0.12
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.50
Consensus pattern (30 bp):
TTTTATCATTTTTGAAAGGTCAAAGTAAAA
Found at i:6656016 original size:22 final size:22
Alignment explanation
Indices: 6655988--6656038 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
6655978 GGTTAAAGCG
6655988 TAAATTTATCATTATGTTGACT
1 TAAATTTATCATTATGTTGACT
*
6656010 TAAATTTATGATTATGTTGACT
1 TAAATTTATCATTATGTTGACT
6656032 TAAATTT
1 TAAATTT
6656039 TTTATTTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (22 bp):
TAAATTTATCATTATGTTGACT
Found at i:6657518 original size:18 final size:18
Alignment explanation
Indices: 6657480--6657526 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
6657470 GATATCTGAA
*
6657480 TTTGGTAATTTATATTTT
1 TTTGGTAATTTAAATTTT
6657498 TTTGGT-ATTTAAATTTT
1 TTTGGTAATTTAAATTTT
*
6657515 TTTTG-AATTTAA
1 TTTGGTAATTTAA
6657527 TTGATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 20 0.77
18 6 0.23
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.64
Consensus pattern (18 bp):
TTTGGTAATTTAAATTTT
Found at i:6660106 original size:15 final size:14
Alignment explanation
Indices: 6660086--6660115 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6660076 AACTTTACGT
6660086 AATAAAATAAAAAAA
1 AATAAAA-AAAAAAA
6660101 AATAAAAAAAAAAA
1 AATAAAAAAAAAAA
6660115 A
1 A
6660116 TTGAAGGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (14 bp):
AATAAAAAAAAAAA
Found at i:6661935 original size:16 final size:16
Alignment explanation
Indices: 6661916--6661971 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
6661906 TCATAATTGG
6661916 TTCATAATTTATGAAA
1 TTCATAATTTATGAAA
*
6661932 TTCATAATTTCA-GAGA
1 TTCATAATTT-ATGAAA
*
6661948 CT-A-AATTTATGAAA
1 TTCATAATTTATGAAA
6661962 TTCATAATTT
1 TTCATAATTT
6661972 CAGAGACTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 1 0.03
14 9 0.28
15 2 0.06
16 19 0.59
17 1 0.03
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (16 bp):
TTCATAATTTATGAAA
Found at i:6661957 original size:30 final size:30
Alignment explanation
Indices: 6661921--6661995 Score: 150
Period size: 30 Copynumber: 2.5 Consensus size: 30
6661911 ATTGGTTCAT
6661921 AATTTATGAAATTCATAATTTCAGAGACTA
1 AATTTATGAAATTCATAATTTCAGAGACTA
6661951 AATTTATGAAATTCATAATTTCAGAGACTA
1 AATTTATGAAATTCATAATTTCAGAGACTA
6661981 AATTTATGAAATTCA
1 AATTTATGAAATTCA
6661996 ATTTCGAAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (30 bp):
AATTTATGAAATTCATAATTTCAGAGACTA
Found at i:6668970 original size:23 final size:22
Alignment explanation
Indices: 6668922--6668971 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
6668912 ACATTGTACT
* * **
6668922 ATTTTACAATACAATTTGCAGT
1 ATTTTACAATACAACTCGCAAA
6668944 ATTTTCACAATACAACTCGCAAA
1 ATTTT-ACAATACAACTCGCAAA
6668967 ATTTT
1 ATTTT
6668972 GCTGTACAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (22 bp):
ATTTTACAATACAACTCGCAAA
Found at i:6672204 original size:10 final size:10
Alignment explanation
Indices: 6672189--6672213 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6672179 GGAGTTCAAC
6672189 GCAGACAGTT
1 GCAGACAGTT
6672199 GCAGACAGTT
1 GCAGACAGTT
6672209 GCAGA
1 GCAGA
6672214 AGTAAAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.20, G:0.32, T:0.16
Consensus pattern (10 bp):
GCAGACAGTT
Found at i:6681720 original size:18 final size:18
Alignment explanation
Indices: 6681697--6681734 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
6681687 TTTTTAGGTT
6681697 ATTATATT-TATTATTATA
1 ATTATATTATATTA-TATA
6681715 ATTATATTATATTATATA
1 ATTATATTATATTATATA
6681733 AT
1 AT
6681735 ACATATATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTATATTATATTATATA
Found at i:6681741 original size:16 final size:17
Alignment explanation
Indices: 6681722--6681758 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
6681712 ATAATTATAT
*
6681722 TATATTATATA-ATACA
1 TATATTACATATATACA
6681738 TATA-TACATATATACA
1 TATATTACATATATACA
6681754 TATAT
1 TATAT
6681759 GCGTGAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (17 bp):
TATATTACATATATACA
Found at i:6681746 original size:8 final size:8
Alignment explanation
Indices: 6681728--6681758 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
6681718 ATATTATATT
6681728 ATATAATAC
1 ATAT-ATAC
6681737 ATATATAC
1 ATATATAC
6681745 ATATATAC
1 ATATATAC
6681753 ATATAT
1 ATATAT
6681759 GCGTGAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:6685064 original size:21 final size:21
Alignment explanation
Indices: 6685021--6685064 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
6685011 AAGGTTTGAA
*
6685021 TTTAGGGTTTAAAGTTCATGG
1 TTTAGGGTTTAAAGTTCAGGG
* * *
6685042 TTTATGGTTTCAAGTTTAGGG
1 TTTAGGGTTTAAAGTTCAGGG
6685063 TT
1 TT
6685065 GGGGTTCATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.05, G:0.27, T:0.48
Consensus pattern (21 bp):
TTTAGGGTTTAAAGTTCAGGG
Found at i:6688404 original size:2 final size:2
Alignment explanation
Indices: 6688397--6688423 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6688387 TACGAGGTAG
6688397 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6688424 CCCCTTTTAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6688746 original size:49 final size:49
Alignment explanation
Indices: 6688674--6688775 Score: 195
Period size: 49 Copynumber: 2.1 Consensus size: 49
6688664 CTTTGATCTT
*
6688674 CATAGTCTATATATATATATATGGTTGATCGACTGTATGTTATTAGTTG
1 CATAGTCTATATATATATATATGGTTGATCAACTGTATGTTATTAGTTG
6688723 CATAGTCTATATATATATATATGGTTGATCAACTGTATGTTATTAGTTG
1 CATAGTCTATATATATATATATGGTTGATCAACTGTATGTTATTAGTTG
6688772 CATA
1 CATA
6688776 TATATAGACA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (49 bp):
CATAGTCTATATATATATATATGGTTGATCAACTGTATGTTATTAGTTG
Found at i:6693118 original size:28 final size:28
Alignment explanation
Indices: 6693085--6693369 Score: 126
Period size: 29 Copynumber: 9.8 Consensus size: 28
6693075 TTTGGATACC
*
6693085 CGAGGGCAAAATGGTAATTTTGGTGAAAT
1 CGAGGGTAAAATGG-AATTTTGGTGAAAT
6693114 C-AGGGTTAAAATGGAATTTT-G-GAAAGTT
1 CGAGGG-TAAAATGGAATTTTGGTGAAA--T
*
6693142 CGGGGGTAAAATGGCAATTTTGGTGAAAT
1 CGAGGGTAAAATGG-AATTTTGGTGAAAT
* *
6693171 CG-GGGTTAAAAATAGAATTTT--TGAGAGT
1 CGAGGG-T-AAAATGGAATTTTGGTGA-AAT
** *
6693199 TTAGGGGTAAAATGGTAATTTTTGGTAAAAT
1 CGA-GGGTAAAATGG-AA-TTTTGGTGAAAT
* **
6693230 C-AGGGTTAAAAATGGAATTTTGAT-AGTT
1 CGAGGG-T-AAAATGGAATTTTGGTGAAAT
* *
6693258 TGGGGGTAAAATGGTAATTTTTGGTGAAAT
1 CGAGGGTAAAATGG-AA-TTTTGGTGAAAT
* *
6693288 CAAGGTTAAAAATGGAATTTT--T-AATAGT
1 CGAGGGT-AAAATGGAATTTTGGTGAA-A-T
** *
6693316 TTAGGGGTAAAATGGTAATTTTTGGTGAAAC
1 CGA-GGGTAAAATGG-AA-TTTTGGTGAAAT
6693347 CG-GGGTTAAAAATGGAATTTTGG
1 CGAGGG-T-AAAATGGAATTTTGG
6693370 AAAGTTTAGG
Statistics
Matches: 195, Mismatches: 28, Indels: 66
0.67 0.10 0.23
Matches are distributed among these distances:
26 6 0.03
27 13 0.07
28 45 0.23
29 66 0.34
30 32 0.16
31 27 0.14
32 4 0.02
33 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (28 bp):
CGAGGGTAAAATGGAATTTTGGTGAAAT
Found at i:6693124 original size:58 final size:59
Alignment explanation
Indices: 6693050--6693397 Score: 372
Period size: 59 Copynumber: 6.0 Consensus size: 59
6693040 GAAGAAACGA
* * ** *
6693050 TGAAATC-GGGATTAAAAACGAGACTTTTGGATA-CCCGAGGGCAAAATGGTAA-TTTTGG
1 TGAAATCAGGG-TTAAAAATG-GAATTTTGGATAGTTCGAGGGTAAAATGGTAATTTTTGG
* * *
6693108 TGAAATCAGGGTT-AAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGCAA-TTTTGG
1 TGAAATCAGGGTTAAAAATGGAATTTTGGATAGTTCGAGGGTAAAATGGTAATTTTTGG
* * * * *
6693165 TGAAATCGGGGTTAAAAATAGAATTTTTGAGAGTT-TAGGGGTAAAATGGTAATTTTTGG
1 TGAAATCAGGGTTAAAAATGGAATTTTGGATAGTTCGA-GGGTAAAATGGTAATTTTTGG
* * *
6693224 TAAAATCAGGGTTAAAAATGGAATTTT-GATAGTTTGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCAGGGTTAAAAATGGAATTTTGGATAGTTCGAGGGTAAAATGGTAATTTTTGG
* ** *
6693282 TGAAATCAAGGTTAAAAATGGAATTTTTAATAGTT-TAGGGGTAAAATGGTAATTTTTGG
1 TGAAATCAGGGTTAAAAATGGAATTTTGGATAGTTCGA-GGGTAAAATGGTAATTTTTGG
* * * *
6693341 TGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTT-TAGGGGTAAAATGGTAATTTTT
1 TGAAATCAGGGTTAAAAATGGAATTTTGGATAGTTCGA-GGGTAAAATGGTAATTTTT
6693398 CTGAAATTTT
Statistics
Matches: 250, Mismatches: 32, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
56 10 0.04
57 37 0.15
58 92 0.37
59 111 0.44
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (59 bp):
TGAAATCAGGGTTAAAAATGGAATTTTGGATAGTTCGAGGGTAAAATGGTAATTTTTGG
Found at i:6693236 original size:59 final size:59
Alignment explanation
Indices: 6693092--6693397 Score: 442
Period size: 59 Copynumber: 5.3 Consensus size: 59
6693082 ACCCGAGGGC
* **
6693092 AAAATGGTAA-TTTTGGTGAAATCAGGGTT-AAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTTGAAAGTTTAGGGGT
* * * *
6693149 AAAATGGCAA-TTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTGAGAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTTGAAAGTTTAGGGGT
* * *
6693207 AAAATGGTAATTTTTGGTAAAATCAGGGTTAAAAATGGAA-TTTTGATAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTTGAAAGTTTAGGGGT
*
6693265 AAAATGGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTT-AATAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTTGAA-AGTTTAGGGGT
* * *
6693324 AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTTGAAAGTTTAGGGGT
6693383 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
6693398 CTGAAATTTT
Statistics
Matches: 223, Mismatches: 21, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
57 27 0.12
58 87 0.39
59 107 0.48
60 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.35
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTTGAAAGTTTAGGGGT
Found at i:6693306 original size:117 final size:118
Alignment explanation
Indices: 6693092--6693397 Score: 476
Period size: 117 Copynumber: 2.6 Consensus size: 118
6693082 ACCCGAGGGC
*
6693092 AAAATGGTAA-TTTTGGTGAAATCAGGGTT-AAAATGGAATTTTGGAAAGTTCGGGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATG
* ** *
6693155 GCAA-TTTTGGTGAAATCGGGGTTAAAAATAGAATTTTTGAGAGTTTAGGGGT
66 GTAATTTTTGGTGAAATCAAGGTTAAAAATAGAATTTTTAAGAGTTTAGGGGT
* *
6693207 AAAATGGTAATTTTTGGTAAAATCAGGGTTAAAAATGGAATTTT-GATAGTTTGGGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATG
* *
6693271 GTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTTAATAGTTTAGGGGT
66 GTAATTTTTGGTGAAATCAAGGTTAAAAATAGAATTTTTAAGAGTTTAGGGGT
* * *
6693324 AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATG
6693389 GTAATTTTT
66 GTAATTTTT
6693398 CTGAAATTTT
Statistics
Matches: 173, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
115 10 0.06
116 39 0.23
117 97 0.56
118 27 0.16
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.35
Consensus pattern (118 bp):
AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATG
GTAATTTTTGGTGAAATCAAGGTTAAAAATAGAATTTTTAAGAGTTTAGGGGT
Done.