Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007894.1 Hibiscus syriacus cultivar Beakdansim tig00110279_pilon, 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: 1425917
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:975774 original size:22 final size:22
Alignment explanation
Indices: 975748--975790 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
975738 TAATAAATTA
975748 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
975770 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
975791 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:975799 original size:22 final size:22
Alignment explanation
Indices: 975750--975798 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
975740 ATAAATTATT
**
975750 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
975772 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
975795 TAAA
1 TAAA
975799 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:975871 original size:134 final size:132
Alignment explanation
Indices: 975706--976002 Score: 467
Period size: 134 Copynumber: 2.2 Consensus size: 132
975696 CAATCCATAC
*
975706 AAATAAATTA-TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 AAATAAATTATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
975770 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATACATAC-AACTACAATA
66 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATACATACTAA-TA-AATA
975834 -AT-
129 TATA
* *
975836 AAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCA
1 AAATAAAT---TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
* *
975901 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATTAATCCATACTAATAAAT
63 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATACATACTAATAAAT
*
975966 ATTTA
128 ATATA
975971 AAATAAATTATTTTAAAATAAATCAATCCATA
1 AAATAAATTATTTTAAAATAAATCAATCCATA
976003 TTTTATAATA
Statistics
Matches: 153, Mismatches: 7, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
130 7 0.05
132 24 0.16
133 6 0.04
134 107 0.70
135 9 0.06
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (132 bp):
AAATAAATTATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATACATACTAATAAATATA
TA
Found at i:975879 original size:22 final size:22
Alignment explanation
Indices: 975804--975878 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
975794 ATAAATTATT
* *
975804 TAAAATAAATCAATACATACAA
1 TAAAATAAATCAATCCATATAA
**
975826 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
975852 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
975875 TAAA
1 TAAA
975879 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:975908 original size:22 final size:22
Alignment explanation
Indices: 975882--975924 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
975872 TAATAAATTA
*
975882 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
975904 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
975925 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:975915 original size:54 final size:54
Alignment explanation
Indices: 975833--976013 Score: 236
Period size: 54 Copynumber: 3.5 Consensus size: 54
975823 CAACTACAAT
975833 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
975887 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * * *
975941 AATAAATTAATCCATA--CT--AATAAAT--AT--TTA-AAATAAATTATTTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA-TTTAA
*
975987 AATAAATCAATCCATATTTTATAATAA
1 AATAAATCAATCCATATTTTAAAATAA
976014 TTTATTTTAA
Statistics
Matches: 114, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
45 9 0.08
46 22 0.19
48 3 0.03
50 12 0.11
52 1 0.01
54 67 0.59
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.37
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:975915 original size:170 final size:168
Alignment explanation
Indices: 975546--975902 Score: 630
Period size: 170 Copynumber: 2.1 Consensus size: 168
975536 CAATCCATAT
* *
975546 TTTAAAATAAATCAGTCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
*
975611 TCAATTCATACTAATAAATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCC
66 TCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCC
975676 ATATTTTAAAATAAATCAATCAATCCATACAAATAAATTA
131 ATATTTTAAAAT-AA-CAATCAATCCATACAAATAAATTA
975716 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
975781 TCAATCCATACTAATAAATTATTTAAAATAAATCAATAC-ATACAACTACAATAATAAATCAATC
66 TCAATCCATACTAATAAATTATTTAAAATAAATCAAT-CTATACAACTACAATAATAAATCAATC
*
975845 CATATTTTAAAAT-A-AATCAATCCATACTAATAAATTA
130 CATATTTTAAAATAACAATCAATCCATACAAATAAATTA
975882 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATTCATA
975903 TTTTAAAATA
Statistics
Matches: 182, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
166 43 0.24
168 1 0.01
170 137 0.75
171 1 0.01
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (168 bp):
TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCC
ATATTTTAAAATAACAATCAATCCATACAAATAAATTA
Found at i:975933 original size:22 final size:22
Alignment explanation
Indices: 975884--975932 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
975874 ATAAATTATT
* **
975884 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
975906 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
975929 TAAA
1 TAAA
975933 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:975964 original size:18 final size:18
Alignment explanation
Indices: 975909--975965 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
975899 CATATTTTAA
*
975909 AATAAATCAATCCATACT
1 AATAAATTAATCCATACT
* *
975927 AATAAATT-AT--TTA-A
1 AATAAATTAATCCATACT
975941 AATAAATTAATCCATACT
1 AATAAATTAATCCATACT
975959 AATAAAT
1 AATAAAT
975966 ATTTAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 8 0.27
15 4 0.13
17 4 0.13
18 14 0.47
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAATTAATCCATACT
Found at i:975987 original size:15 final size:15
Alignment explanation
Indices: 975927--976099 Score: 121
Period size: 15 Copynumber: 11.5 Consensus size: 15
975917 AATCCATACT
975927 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
** *
975941 AATAAATTAATCCATACT
1 AATAAATT-AT-TTTA-A
975959 AATAAA-TA-TTTAA
1 AATAAATTATTTTAA
975972 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
975987 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
976009 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
976024 AATAATTTATTTTAT
1 AATAAATTATTTTAA
976039 AATAAATTATTTTAA
1 AATAAATTATTTTAA
976054 AAT--A--A--TTAA
1 AATAAATTATTTTAA
*
976063 AATAAATTATTTTAT
1 AATAAATTATTTTAA
976078 AATAAATTATTTTAA
1 AATAAATTATTTTAA
976093 AATAAAT
1 AATAAAT
976100 AACCTTATTA
Statistics
Matches: 126, Mismatches: 14, Indels: 37
0.71 0.08 0.21
Matches are distributed among these distances:
9 7 0.06
11 2 0.02
13 8 0.06
14 12 0.10
15 70 0.56
16 1 0.01
17 4 0.03
18 8 0.06
19 3 0.02
20 1 0.01
22 10 0.08
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:976074 original size:39 final size:39
Alignment explanation
Indices: 976020--976097 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
976010 ATAATTTATT
*
976020 TTAAAATAATTTATTTTATAATAAATTATTTTAAAATAA
1 TTAAAATAAATTATTTTATAATAAATTATTTTAAAATAA
976059 TTAAAATAAATTATTTTATAATAAATTATTTTAAAATAA
1 TTAAAATAAATTATTTTATAATAAATTATTTTAAAATAA
976098 ATAACCTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (39 bp):
TTAAAATAAATTATTTTATAATAAATTATTTTAAAATAA
Found at i:978010 original size:18 final size:19
Alignment explanation
Indices: 977969--978007 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
977959 TTGGTTCACA
*
977969 GAATGTAAGATTAGCAGTGG
1 GAATGTAAGATTACCAG-GG
977989 GAATGTAAGATTACCAGGG
1 GAATGTAAGATTACCAGGG
978008 AATAGGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.36, C:0.08, G:0.33, T:0.23
Consensus pattern (19 bp):
GAATGTAAGATTACCAGGG
Found at i:978496 original size:21 final size:21
Alignment explanation
Indices: 978472--978578 Score: 92
Period size: 21 Copynumber: 5.2 Consensus size: 21
978462 GCAAATTCGC
978472 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* ** *
978493 GTTGGAAATCACGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
978513 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
978534 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* * *
978554 TTTCCATTTCGCGTTGCTATA
1 GTTGCATTTCGCGTTGCGATA
978575 GTTG
1 GTTG
978579 AAAATCGCAC
Statistics
Matches: 61, Mismatches: 23, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
20 28 0.46
21 33 0.54
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:978529 original size:20 final size:20
Alignment explanation
Indices: 978504--978570 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
978494 TTGGAAATCA
978504 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* ** **
978524 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGAT-TTTCCATTTCG
978545 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
978565 CGTTGC
1 CGTTGC
978571 TATAGTTGAA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 21 0.58
21 15 0.42
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:978585 original size:41 final size:41
Alignment explanation
Indices: 978476--978586 Score: 195
Period size: 41 Copynumber: 2.7 Consensus size: 41
978466 ATTCGCGTTG
* *
978476 CATTTCGCGTTGCGATAGTTGGAAATCACGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
978517 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
978558 CATTTCGCGTTGCTATAGTTGAAAATCGC
1 CATTTCGCGTTGCGATAGTTGAAAATCGC
978587 ACCATTTCGC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:978660 original size:19 final size:19
Alignment explanation
Indices: 978636--978701 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
978626 GTCTACAATG
978636 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
978655 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
*
978676 GTTGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
978696 TCGTTG
1 TCGTTG
978702 TGATAGTTAA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
19 15 0.44
20 5 0.15
21 5 0.15
22 9 0.26
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:978671 original size:40 final size:41
Alignment explanation
Indices: 978596--978708 Score: 149
Period size: 41 Copynumber: 2.8 Consensus size: 41
978586 CACCATTTCG
* *
978596 CGTTGCAATTTTCC-ATTTCGCATTGCGATAGTCTACA-ATGT
1 CGTTGCGATTTTCCAAATTCG--TTGCGATAGTCTACAGATGT
*
978637 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGATGT
* *
978678 TGTTGCGATTTTCCAAATTCGTTGTGATAGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGT
978709 TAAAAAAAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
40 15 0.23
41 45 0.69
42 5 0.08
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGATGT
Found at i:978701 original size:22 final size:22
Alignment explanation
Indices: 978638--978702 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 22
978628 CTACAATGTC
978638 GTTGCGATTTTCCAAATTC---
1 GTTGCGATTTTCCAAATTCGTT
** * *
978657 GTTGCGATAGTCTACAGTT-GTT
1 GTTGCGATTTTCCA-AATTCGTT
978679 GTTGCGATTTTCCAAATTCGTT
1 GTTGCGATTTTCCAAATTCGTT
978701 GT
1 GT
978703 GATAGTTAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
19 11 0.33
20 3 0.09
21 3 0.09
22 16 0.48
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.43
Consensus pattern (22 bp):
GTTGCGATTTTCCAAATTCGTT
Found at i:978796 original size:6 final size:6
Alignment explanation
Indices: 978785--978820 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
978775 GACACGTATT
978785 ACCACG ACCACG ACCACG ACCACG ACCACG A-CACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
978821 GACGAGACGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.36, C:0.47, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:979314 original size:6 final size:6
Alignment explanation
Indices: 979305--979348 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
979295 CGCCGCCGCC
979305 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
979349 AATACGTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.34
Consensus pattern (6 bp):
GTCGTG
Found at i:979530 original size:20 final size:20
Alignment explanation
Indices: 979505--979749 Score: 127
Period size: 20 Copynumber: 12.4 Consensus size: 20
979495 ATTTTCAACT
979505 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
*
979525 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
*
979545 ATCGCAACGCG-A-T----T
1 ATCGCAACGCGAACTGGAAA
* *
979559 TTCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAA-CTGGAAA
* **
979578 ATCGCAACGAC-AACTATAGACT
1 ATCGCAACG-CGAAC--TGGAAA
*
979600 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAA-CTGGAAA
* **
979619 ATTGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAACTG--GAAA
979641 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
*
979661 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
* * ** ** *
979681 ATCGTAACGTGATTTTCAACT
1 ATCGCAACGCGAACTGGAA-A
**
979702 ATCGCAACGCGAACTAAAAA
1 ATCGCAACGCGAACTGGAAA
*
979722 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
979742 ATCGCAAC
1 ATCGCAAC
979750 ACGATTTTCA
Statistics
Matches: 166, Mismatches: 38, Indels: 42
0.67 0.15 0.17
Matches are distributed among these distances:
12 2 0.01
13 1 0.01
14 6 0.04
15 1 0.01
18 1 0.01
19 17 0.10
20 93 0.56
21 18 0.11
22 27 0.16
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAACTGGAAA
Found at i:979584 original size:19 final size:19
Alignment explanation
Indices: 979560--979628 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
979550 AACGCGATTT
979560 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
979579 TCGCAACGACAACTATAGACTA
1 TCGCAACG--AA-TTTGGAAAA
979601 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
*
979620 TTGCAACGA
1 TCGCAACGA
979629 CAACTGTAGA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 21 0.55
20 2 0.05
21 2 0.05
22 13 0.34
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:979606 original size:22 final size:22
Alignment explanation
Indices: 979578--979649 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
979568 AATTTGGAAA
979578 ATCGCAACGACAACTATAGACT
1 ATCGCAACGACAACTATAGACT
* * **
979600 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTATAGACT
* *
979619 ATTGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTATAGACT
979641 ATCGCAACG
1 ATCGCAACG
979650 CGAACTGGAA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 12 0.32
20 2 0.05
21 2 0.05
22 21 0.57
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTATAGACT
Found at i:979617 original size:41 final size:41
Alignment explanation
Indices: 979560--979669 Score: 168
Period size: 41 Copynumber: 2.7 Consensus size: 41
979550 AACGCGATTT
979560 TCGCAACGAATTTGGAAAATCGCAACGACAACTATAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTATAGACTA
* *
979601 TCGCAACGAATTTGGAAAATTGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTATAGACTA
*
979642 TCGCAACGCGAA-CTGGAAAATCGCAACG
1 TCGCAA--CGAATTTGGAAAATCGCAACG
979670 CGAAATGGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
41 45 0.71
42 14 0.22
43 4 0.06
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (41 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTATAGACTA
Found at i:979645 original size:116 final size:115
Alignment explanation
Indices: 979440--979672 Score: 328
Period size: 116 Copynumber: 2.0 Consensus size: 115
979430 TCACAAACGA
* * *
979440 ATTTTCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACACGATTTTCAACT
1 ATTTTCGCAACGAATTTGGAAAATCGCAACGACAACTATAGACTATCGCAACAC-ATTTGCAACA
979505 ATCGCAACGCGAACTGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCG
65 ATCGCAACGCGAACTGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCG
*
979556 ATTTTCGCAACGAATTTGGAAAATCGCAACGACAACTATAGACTATCGCAACGA-ATTTGGAA-A
1 ATTTTCGCAACGAATTTGGAAAATCGCAACGACAACTATAGACTATCGCAAC-ACATTTGCAACA
* ** *
979619 ATTGCAACGAC-AACTGTAGACTATCGCAACGCGAACTGGAAAATCGCAACGCG
65 ATCGCAACG-CGAACTG--GAAAATCGCAACGCGAAATGGAAAATCGCAACGCG
979672 A
1 A
979673 AATGGAAAAT
Statistics
Matches: 105, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
114 13 0.12
115 7 0.07
116 84 0.80
117 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (115 bp):
ATTTTCGCAACGAATTTGGAAAATCGCAACGACAACTATAGACTATCGCAACACATTTGCAACAA
TCGCAACGCGAACTGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCG
Found at i:979703 original size:61 final size:61
Alignment explanation
Indices: 979638--979775 Score: 222
Period size: 61 Copynumber: 2.3 Consensus size: 61
979628 ACAACTGTAG
** * **
979638 ACTATCGCAACGCGAACTGGAAAATCGCAACGCGAAATGGAAAATCGTAACGTGATTTTCA
1 ACTATCGCAACGCGAACTAAAAAATCGCAACGCGAAATGGAAAATCGCAACACGATTTTCA
979699 ACTATCGCAACGCGAACTAAAAAATCGCAACGCGAAATGGAAAATCGCAACACGATTTTCA
1 ACTATCGCAACGCGAACTAAAAAATCGCAACGCGAAATGGAAAATCGCAACACGATTTTCA
*
979760 ATTATCGCAACGCGAA
1 ACTATCGCAACGCGAA
979776 ATGCAACGCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 71 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.18
Consensus pattern (61 bp):
ACTATCGCAACGCGAACTAAAAAATCGCAACGCGAAATGGAAAATCGCAACACGATTTTCA
Found at i:986003 original size:16 final size:15
Alignment explanation
Indices: 985977--986011 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
985967 TAAATAAAAA
*
985977 TAAAATGCATAAATT
1 TAAAATGCATAAAGT
985992 TAAAAGTGCATAAAGT
1 TAAAA-TGCATAAAGT
986008 TAAA
1 TAAA
986012 TAAAATACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (15 bp):
TAAAATGCATAAAGT
Found at i:986185 original size:5 final size:5
Alignment explanation
Indices: 986175--986211 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
986165 AAATATATAT
986175 AAATA AAATA AAATA AAATA AAAT- AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
986212 AAGTTAGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:986212 original size:15 final size:14
Alignment explanation
Indices: 986165--986211 Score: 67
Period size: 14 Copynumber: 3.2 Consensus size: 14
986155 TAATTCAAAC
*
986165 AAATATATATAAATA
1 AAATAAATA-AAATA
986180 AAATAAAATAAAATA
1 AAAT-AAATAAAATA
986195 AAATAAATAAAATA
1 AAATAAATAAAATA
986209 AAA
1 AAA
986212 AAGTTAGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 13 0.43
15 13 0.43
16 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATAAATAAAATA
Found at i:986321 original size:135 final size:135
Alignment explanation
Indices: 986072--986315 Score: 321
Period size: 135 Copynumber: 1.8 Consensus size: 135
986062 GGTGAGTAGT
* * * *
986072 TAAAAAAGTTAGCGGTTAAAAGAGTCTGAACCATAATAATGTGAATCATACATCGGATCTGGTCA
1 TAAAAAAGTTAGCGGTTAAAAGAGTCCGAACCATAATAACGTGAATCATACATCGAATCGGGTCA
* * *
986137 CCACAAGGTCGAATCGAATAATTCAAACAAATATATATAAATAAAATAAAATAAAATAAAATAAA
66 CCACAAGGTCGAATCAAATAATTCAAACAAAAATAGATAAATAAAATAAAATAAAATAAAATAAA
986202 TAAAA
131 TAAAA
* ** * *
986207 TAAAAAAGTTAGTGGTTAGCAGAGTCCGAACTATAATAACGTGGATCATATC-TCGAATCGGGTC
1 TAAAAAAGTTAGCGGTTAAAAGAGTCCGAACCATAATAACGTGAATCATA-CATCGAATCGGGTC
* *
986271 ACTACAAGGTCGAATCAAAT-ATTAGAAACAAGAAATAGATAAATA
65 ACCACAAGGTCGAATCAAATAATT-CAAACAA-AAATAGATAAATA
986316 GATAAACAAT
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
134 3 0.03
135 77 0.84
136 12 0.13
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.24
Consensus pattern (135 bp):
TAAAAAAGTTAGCGGTTAAAAGAGTCCGAACCATAATAACGTGAATCATACATCGAATCGGGTCA
CCACAAGGTCGAATCAAATAATTCAAACAAAAATAGATAAATAAAATAAAATAAAATAAAATAAA
TAAAA
Found at i:986349 original size:135 final size:136
Alignment explanation
Indices: 986200--986450 Score: 328
Period size: 135 Copynumber: 1.8 Consensus size: 136
986190 AAATAAAATA
* * * * * **
986200 AATAAAATAAAAAAGTTAGTGGTTAGCAGAGTCCGAACTATAATAACGTGGATCATA-TCTCGAA
1 AATAAAAT-AAAAAGTCAATAGTTAACAGAGTCCGAACCATAATAACGCAGATCATATTCT-GAA
* * *
986264 TCGGGTCACTACAAGGTCGAATCAAATATTAGAAACAA-GAAATAGATAAATAGATAAACAATGG
64 TCGGATCACCACAAGGTCGAATCAAATATTAGAAACAATG-AATAAATAAATAGATAAACAATGG
986328 TTACAGTGC
128 TTACAGTGC
* * *
986337 AATAAAAT-AAAAGTCAATAGTTAACAGATTCCGAACCATAATAATGCAGATCATATTCTGGATC
1 AATAAAATAAAAAGTCAATAGTTAACAGAGTCCGAACCATAATAACGCAGATCATATTCTGAATC
*
986401 GGATCACCACAAGGTCGAATCGAATATTAGAAACAATGAATAAATAAATA
66 GGATCACCACAAGGTCGAATCAAATATTAGAAACAATGAATAAATAAATA
986451 ACAGTGCAAT
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
135 86 0.88
136 4 0.04
137 8 0.08
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.24
Consensus pattern (136 bp):
AATAAAATAAAAAGTCAATAGTTAACAGAGTCCGAACCATAATAACGCAGATCATATTCTGAATC
GGATCACCACAAGGTCGAATCAAATATTAGAAACAATGAATAAATAAATAGATAAACAATGGTTA
CAGTGC
Found at i:994277 original size:28 final size:29
Alignment explanation
Indices: 994237--994298 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
994227 AAAATATTAA
*
994237 AATATATTTTAATATT-TATAAT-AATAT
1 AATATATTTTAATATTATAAAATCAATAT
994264 AATATTATTTTAATATTATAAAATCAATAT
1 AATA-TATTTTAATATTATAAAATCAATAT
994294 -ATATA
1 AATATA
994299 AATAAGATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 4 0.13
28 14 0.45
29 8 0.26
30 5 0.16
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
AATATATTTTAATATTATAAAATCAATAT
Found at i:994282 original size:27 final size:26
Alignment explanation
Indices: 994223--994297 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
994213 AAAATATAAT
* *
994223 TATTAAAATATTAAAATATATTTTAA
1 TATTATAATAATAAAATATATTTTAA
*
994249 TATTTATAATAATATAATATTATTTTAA
1 TA-TTATAATAATAAAATA-TATTTTAA
*
994277 TATTATAA-AATCAATATATAT
1 TATTATAATAAT-AAAATATAT
994298 AAATAAGATA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
26 8 0.20
27 23 0.56
28 10 0.24
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (26 bp):
TATTATAATAATAAAATATATTTTAA
Found at i:994326 original size:29 final size:29
Alignment explanation
Indices: 994292--994382 Score: 82
Period size: 29 Copynumber: 3.1 Consensus size: 29
994282 TAAAATCAAT
*
994292 ATATATAAATAAGATATTTATTTATTTAATA
1 ATATAT-AATAA-ATATTTATATATTTAATA
* *
994323 ATATATAATAATTTTTTATATATTTAATA
1 ATATATAATAAATATTTATATATTTAATA
*
994352 ATGA-AT-AT-ATTATTTATATATTTTAA-A
1 AT-ATATAATAAATATTTATATA-TTTAATA
994379 ATAT
1 ATAT
994383 TTTCGTAAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
26 1 0.02
27 14 0.26
28 7 0.13
29 19 0.36
30 6 0.11
31 6 0.11
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
ATATATAATAAATATTTATATATTTAATA
Found at i:994381 original size:23 final size:25
Alignment explanation
Indices: 994329--994382 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 25
994319 AATAATATAT
*
994329 AATA-ATTTTTTATATATTTAATAATG
1 AATATATTATTTATATATTT-ATAA-G
994355 AATATATTATTTATATATTT-TAA-
1 AATATATTATTTATATATTTATAAG
994378 AATAT
1 AATAT
994383 TTTCGTAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 5 0.19
25 3 0.12
26 4 0.15
27 14 0.54
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
AATATATTATTTATATATTTATAAG
Found at i:994758 original size:20 final size:20
Alignment explanation
Indices: 994701--994750 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
994691 TTTCCAGATG
* *
994701 TTTTCCATAAATGTAATTCA
1 TTTTCCAGAAATATAATTCA
994721 TTTTCCAGAAATATAATTCA
1 TTTTCCAGAAATATAATTCA
994741 TTTTCCAGAA
1 TTTTCCAGAA
994751 TTCAAATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (20 bp):
TTTTCCAGAAATATAATTCA
Found at i:994785 original size:30 final size:30
Alignment explanation
Indices: 994734--994814 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
994724 TCCAGAAATA
994734 TAATTCATTTTCCAG-AATTCAAATTTCAG
1 TAATTCATTTTCCAGTAATTCAAATTTCAG
994763 TAATTCATTTTCCAGTAATTCAAATTTCAG
1 TAATTCATTTTCCAGTAATTCAAATTTCAG
**
994793 TAATTCAAATTCCAGTAATTCA
1 TAATTCATTTTCCAGTAATTCA
994815 TTTTCCGGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 15 0.31
30 34 0.69
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.41
Consensus pattern (30 bp):
TAATTCATTTTCCAGTAATTCAAATTTCAG
Found at i:994820 original size:15 final size:15
Alignment explanation
Indices: 994734--994820 Score: 99
Period size: 15 Copynumber: 5.9 Consensus size: 15
994724 TCCAGAAATA
*
994734 TAATTCATTTTCCAG
1 TAATTCAATTTCCAG
994749 -AATTCAAATTT-CAG
1 TAATTC-AATTTCCAG
*
994763 TAATTCATTTTCCAG
1 TAATTCAATTTCCAG
994778 TAATTCAAATTT-CAG
1 TAATTC-AATTTCCAG
*
994793 TAATTCAAATTCCAG
1 TAATTCAATTTCCAG
*
994808 TAATTCATTTTCC
1 TAATTCAATTTCC
994821 GGAAAACCAA
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
14 16 0.26
15 41 0.67
16 4 0.07
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (15 bp):
TAATTCAATTTCCAG
Found at i:996075 original size:10 final size:10
Alignment explanation
Indices: 996070--996109 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
996060 ATTAATTAAT
996070 ATTAATATTA
1 ATTAATATTA
996080 ATTAATATTA
1 ATTAATATTA
996090 ATTAATATT-
1 ATTAATATTA
*
996099 ATTCATATTA
1 ATTAATATTA
996109 A
1 A
996110 AATTTTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
9 8 0.29
10 20 0.71
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (10 bp):
ATTAATATTA
Found at i:996099 original size:16 final size:16
Alignment explanation
Indices: 996060--996091 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
996050 ATATGTTCGA
996060 ATTAATTAATATTAAT
1 ATTAATTAATATTAAT
996076 ATTAATTAATATTAAT
1 ATTAATTAATATTAAT
996092 TAATATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAATTAATATTAAT
Found at i:1007873 original size:60 final size:59
Alignment explanation
Indices: 1007800--1007941 Score: 203
Period size: 60 Copynumber: 2.4 Consensus size: 59
1007790 TCAAAAAAAG
* * * * *
1007800 AATAGTCGGGGGACTCAACAAAACAATGTCATATAGTTAGAGTATCATTTTGCAACTTTT
1 AATAGTC-GGGGACTTAACAAAACAATGGCACATAGTCAGAGTACCATTTTGCAACTTTT
*
1007860 AATAGTCGAGGGACTTAACAAAACAATGGCACATAGTCAGAGTACCATTTTGTAACTTTT
1 AATAGTCG-GGGACTTAACAAAACAATGGCACATAGTCAGAGTACCATTTTGCAACTTTT
1007920 AATAGTCGGGAGACTTAACAAA
1 AATAGTCGGG-GACTTAACAAA
1007942 GTAACACCCT
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
59 3 0.04
60 71 0.96
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (59 bp):
AATAGTCGGGGACTTAACAAAACAATGGCACATAGTCAGAGTACCATTTTGCAACTTTT
Found at i:1010875 original size:6 final size:6
Alignment explanation
Indices: 1010865--1010898 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1010855 CATCCACCAT
* *
1010865 CTCTCT CTCTCC CTCTCC CTCTCC CTCTCT CTCT
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCT
1010899 GTCTTACCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (6 bp):
CTCTCC
Found at i:1010886 original size:12 final size:12
Alignment explanation
Indices: 1010865--1010898 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1010855 CATCCACCAT
1010865 CTCTCTCTCTCC
1 CTCTCTCTCTCC
*
1010877 CTCTCCCTCTCC
1 CTCTCTCTCTCC
1010889 CTCTCTCTCT
1 CTCTCTCTCT
1010899 GTCTTACCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (12 bp):
CTCTCTCTCTCC
Found at i:1021780 original size:31 final size:31
Alignment explanation
Indices: 1021738--1021819 Score: 123
Period size: 31 Copynumber: 2.7 Consensus size: 31
1021728 AAACCACAAC
*
1021738 CACC-AAAATGCAACTTTATGAAGCTACATG
1 CACCTAAAATGCAACTATATGAAGCTACATG
1021768 CACCTAAAATGCAACTATATGAAGCTACATG
1 CACCTAAAATGCAACTATATGAAGCTACATG
* *
1021799 TACCTAAAATG-ACCTATATGA
1 CACCTAAAATGCAACTATATGA
1021820 GCCTTTAGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
30 13 0.27
31 35 0.73
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.24
Consensus pattern (31 bp):
CACCTAAAATGCAACTATATGAAGCTACATG
Found at i:1027158 original size:17 final size:17
Alignment explanation
Indices: 1027136--1027191 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
1027126 GACTCTGGTG
1027136 TTTCTGATGAAGTGAAC
1 TTTCTGATGAAGTGAAC
**
1027153 TTTCTGAT--TTTGAA-
1 TTTCTGATGAAGTGAAC
**
1027167 AATCTGATGAAGTGAAC
1 TTTCTGATGAAGTGAAC
1027184 TTTCTGAT
1 TTTCTGAT
1027192 TTAGAAATTG
Statistics
Matches: 28, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
14 6 0.21
15 4 0.14
16 4 0.14
17 14 0.50
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.41
Consensus pattern (17 bp):
TTTCTGATGAAGTGAAC
Found at i:1027176 original size:31 final size:30
Alignment explanation
Indices: 1027138--1027205 Score: 111
Period size: 31 Copynumber: 2.3 Consensus size: 30
1027128 CTCTGGTGTT
*
1027138 TCTGATGAAGTGAACTTTCTGATTTTGAAAA
1 TCTGATGAAGTGAACTTTCTGATTTAG-AAA
1027169 TCTGATGAAGTGAACTTTCTGATTTAGAAA
1 TCTGATGAAGTGAACTTTCTGATTTAGAAA
1027199 T-TGATGA
1 TCTGATGA
1027206 GATAAGGTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 6 0.17
30 4 0.11
31 26 0.72
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (30 bp):
TCTGATGAAGTGAACTTTCTGATTTAGAAA
Found at i:1027276 original size:18 final size:18
Alignment explanation
Indices: 1027253--1027298 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1027243 AAAAGTTGTT
*
1027253 ATTAAATAAAAG-ATATGA
1 ATTAAATAAAAGAAAAT-A
*
1027271 ATTAAATAATAGAAAATA
1 ATTAAATAAAAGAAAATA
1027289 ATTAAATAAA
1 ATTAAATAAA
1027299 TAAATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (18 bp):
ATTAAATAAAAGAAAATA
Found at i:1028063 original size:20 final size:20
Alignment explanation
Indices: 1028035--1028076 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1028025 AAAAATAATG
* *
1028035 AAAAGATAATTCTTAAAAAT
1 AAAAAATAATTCCTAAAAAT
*
1028055 AAAAAATAATTCCTAAAGAT
1 AAAAAATAATTCCTAAAAAT
1028075 AA
1 AA
1028077 TTCTTATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (20 bp):
AAAAAATAATTCCTAAAAAT
Found at i:1028124 original size:3 final size:3
Alignment explanation
Indices: 1028109--1028153 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
1028099 CGTTTTTTGG
*
1028109 ATT ATT GTT ATT ATT ATT ATT ATT -TAT ATT ATT ATT ATTT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT A-TT ATT AT
1028154 AAATTAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 1 0.03
3 32 0.86
4 4 0.11
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1028145 original size:15 final size:15
Alignment explanation
Indices: 1028120--1028150 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1028110 TTATTGTTAT
1028120 TATTATTATTATTTA
1 TATTATTATTATTTA
1028135 TATTATTATTATTTA
1 TATTATTATTATTTA
1028150 T
1 T
1028151 TATAAATTAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTATTATTATTTA
Found at i:1029332 original size:30 final size:29
Alignment explanation
Indices: 1029279--1029461 Score: 176
Period size: 29 Copynumber: 6.3 Consensus size: 29
1029269 AAATTCACAT
*
1029279 TTAACATTAAAAATATA-TTTATTTTTACC
1 TTAAC-TTAAAAATATATTTTATTTTTATC
* *
1029308 TTAACTTATTAAATATATTTTATTTTTATT
1 TTAACTTA-AAAATATATTTTATTTTTATC
* * *
1029338 TTAACTTAAACAATATA-TTTAGTCTTATT
1 TTAACTTAAA-AATATATTTTATTTTTATC
* *
1029367 TTAACTTAAAAATATATTTTAATCTTATC
1 TTAACTTAAAAATATATTTTATTTTTATC
*
1029396 TTAGCTT-AAAA-ATATTTTATTTTTATC
1 TTAACTTAAAAATATATTTTATTTTTATC
* * * *
1029423 TTAACCTATGAAATATATTTTACTTTTATT
1 TTAACTTA-AAAATATATTTTATTTTTATC
*
1029453 TTAATTTAA
1 TTAACTTAA
1029462 GATGTCTTTT
Statistics
Matches: 128, Mismatches: 19, Indels: 14
0.80 0.12 0.09
Matches are distributed among these distances:
27 19 0.15
28 13 0.10
29 52 0.41
30 44 0.34
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (29 bp):
TTAACTTAAAAATATATTTTATTTTTATC
Found at i:1029511 original size:30 final size:28
Alignment explanation
Indices: 1029475--1029600 Score: 92
Period size: 30 Copynumber: 4.2 Consensus size: 28
1029465 GTCTTTTTAA
*
1029475 AAGTTAATATAAGAAGACAATATATTTTTT
1 AAGTTAA-ATAA-AAGAAAATATATTTTTT
** *
1029505 AAGTTAAA-AAGATTAAAATATATATTTT
1 AAGTTAAATAA-AAGAAAATATATTTTTT
* * **
1029533 AAATTAAAATAAAATCAAAATATATTTAAT
1 AAGTT-AAATAAAA-GAAAATATATTTTTT
*
1029563 AAGTTAAGATAAAAGCAATATATATTTTTT
1 AAGTTAA-ATAAAAG-AAAATATATTTTTT
1029593 AATGTTAA
1 AA-GTTAA
1029601 GATGTGAATT
Statistics
Matches: 75, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
28 20 0.27
29 7 0.09
30 43 0.57
31 5 0.07
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (28 bp):
AAGTTAAATAAAAGAAAATATATTTTTT
Found at i:1029516 original size:28 final size:28
Alignment explanation
Indices: 1029475--1029541 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
1029465 GTCTTTTTAA
* *
1029475 AAGTTAATATAAGAAGACAATATATTTTTT
1 AAGTTAA-A-AAGAAGAAAATATATATTTT
**
1029505 AAGTTAAAAAGATTAAAATATATATTTT
1 AAGTTAAAAAGAAGAAAATATATATTTT
*
1029533 AAATTAAAA
1 AAGTTAAAA
1029542 TAAAATCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 24 0.75
29 1 0.03
30 7 0.22
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.37
Consensus pattern (28 bp):
AAGTTAAAAAGAAGAAAATATATATTTT
Found at i:1038184 original size:21 final size:21
Alignment explanation
Indices: 1038160--1038200 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1038150 AATTCTAAAA
**
1038160 ATTAAAAGGTCAATTTGAAAT
1 ATTAAAAGACCAATTTGAAAT
*
1038181 ATTAAATGACCAATTTGAAA
1 ATTAAAAGACCAATTTGAAA
1038201 ATTTAGTGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (21 bp):
ATTAAAAGACCAATTTGAAAT
Found at i:1039855 original size:36 final size:36
Alignment explanation
Indices: 1039808--1039880 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1039798 TTTTATTTTG
*
1039808 ACTTATTATAACAGTTGAGTAAAGTTCCACTTATGT
1 ACTTATTATAACAGTTGAGTAAAGCTCCACTTATGT
1039844 ACTTATTATAACAGTTGAGTAAAGCTCCACTTATGT
1 ACTTATTATAACAGTTGAGTAAAGCTCCACTTATGT
1039880 A
1 A
1039881 TGAGATTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (36 bp):
ACTTATTATAACAGTTGAGTAAAGCTCCACTTATGT
Found at i:1040565 original size:23 final size:25
Alignment explanation
Indices: 1040514--1040577 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 25
1040504 CCATGCATTG
* *
1040514 ATGTTGATGTATCGATA-AGCTCGA
1 ATGTGGATGTATCGGTACAGCTCGA
1040538 A-GTGGATGTATCGGTACA-CTC-A
1 ATGTGGATGTATCGGTACAGCTCGA
* *
1040560 ATGTGGTTGTATCAGTAC
1 ATGTGGATGTATCGGTAC
1040578 CTAATCTGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
22 2 0.06
23 30 0.88
24 2 0.06
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.33
Consensus pattern (25 bp):
ATGTGGATGTATCGGTACAGCTCGA
Found at i:1042377 original size:22 final size:23
Alignment explanation
Indices: 1042363--1042409 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1042353 ATTAATATTG
1042363 TATTTT-AAATAAATTAGAATTA
1 TATTTTCAAATAAATTAGAATTA
* *
1042385 TATTTTCAACTAAATTATAATTA
1 TATTTTCAAATAAATTAGAATTA
1042408 TA
1 TA
1042410 CTTAGAGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (23 bp):
TATTTTCAAATAAATTAGAATTA
Found at i:1044651 original size:22 final size:24
Alignment explanation
Indices: 1044621--1044683 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
1044611 TATAAAAATT
*
1044621 AATATAATTAAT-ATTGTATTTT-A
1 AATA-AATTAATAATTATATTTTCA
1044644 AATAAATT-ATAATTATATTTTCA
1 AATAAATTAATAATTATATTTTCA
*
1044667 ACTAAATT-ATAATTATA
1 AATAAATTAATAATTATA
1044684 CTTAGAGTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.06
22 13 0.36
23 21 0.58
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (24 bp):
AATAAATTAATAATTATATTTTCA
Found at i:1044674 original size:23 final size:22
Alignment explanation
Indices: 1044637--1044683 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
1044627 ATTAATATTG
1044637 TATTTTAAATAAATTATAATTA
1 TATTTTAAATAAATTATAATTA
*
1044659 TATTTTCAACTAAATTATAATTA
1 TATTTT-AAATAAATTATAATTA
1044682 TA
1 TA
1044684 CTTAGAGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTTTAAATAAATTATAATTA
Found at i:1045218 original size:15 final size:15
Alignment explanation
Indices: 1045192--1045230 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
1045182 AGAGGACTAT
1045192 ATTTATTTTTAATTTA
1 ATTTA-TTTTAATTTA
1045208 ATTTATTTTAATTTA
1 ATTTATTTTAATTTA
*
1045223 ATATATTT
1 ATTTATTT
1045231 ATTTTCCACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTATTTTAATTTA
Found at i:1049470 original size:36 final size:36
Alignment explanation
Indices: 1049404--1049475 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
1049394 AATATCTACC
1049404 AAACTTTACCAAACTTTGAAAAAACATTTTTCAAAG
1 AAACTTTACCAAACTTTGAAAAAACATTTTTCAAAG
1049440 AAACATTTACCAAACTTTG-AAAAACATTTTTCAAAG
1 AAAC-TTTACCAAACTTTGAAAAAACATTTTTCAAAG
1049476 TTGGTTGCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 21 0.60
37 14 0.40
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.31
Consensus pattern (36 bp):
AAACTTTACCAAACTTTGAAAAAACATTTTTCAAAG
Found at i:1051252 original size:20 final size:20
Alignment explanation
Indices: 1051219--1051256 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1051209 TATGCTCGGA
1051219 GGGAACCGATTTCCCCCCAG
1 GGGAACCGATTTCCCCCCAG
1051239 GGGATACCGA-TTCCCCCC
1 GGGA-ACCGATTTCCCCCC
1051257 TTGTATAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.18, C:0.42, G:0.24, T:0.16
Consensus pattern (20 bp):
GGGAACCGATTTCCCCCCAG
Found at i:1057029 original size:20 final size:20
Alignment explanation
Indices: 1057000--1057037 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1056990 AGTATACTCG
1057000 GAGGGAACCGATTCCCCCCA
1 GAGGGAACCGATTCCCCCCA
*
1057020 GAGGGTACCGATTCCCCC
1 GAGGGAACCGATTCCCCC
1057038 TTGTATAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.39, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCCA
Found at i:1079250 original size:21 final size:21
Alignment explanation
Indices: 1079224--1079270 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1079214 GCACAAGGAG
1079224 TATCGGTACTACTATGAACAA
1 TATCGGTACTACTATGAACAA
* *
1079245 TATCGGTACTGCTATGAACAG
1 TATCGGTACTACTATGAACAA
1079266 TATCG
1 TATCG
1079271 ATACAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (21 bp):
TATCGGTACTACTATGAACAA
Found at i:1080506 original size:33 final size:33
Alignment explanation
Indices: 1080461--1080528 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
1080451 AAAAAACACA
*
1080461 ATATATGATCACTTTCATATTTATTTAATTAAG
1 ATATATGATCACTTTCATATTTATTTAACTAAG
* * *
1080494 ATATATGGTCACTTTCATTTTTATTTGACTAAG
1 ATATATGATCACTTTCATATTTATTTAACTAAG
1080527 AT
1 AT
1080529 GTTGTCACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.49
Consensus pattern (33 bp):
ATATATGATCACTTTCATATTTATTTAACTAAG
Found at i:1081920 original size:20 final size:20
Alignment explanation
Indices: 1081884--1081921 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1081874 ATCTTATTCC
**
1081884 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1081904 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1081922 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1082137 original size:28 final size:29
Alignment explanation
Indices: 1082071--1082137 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
1082061 GTTACCACAT
1082071 ATTATTGACGTGATATTATACATATATTCA
1 ATTATTGACGTGATATTATACA-ATATTCA
**
1082101 ATTCCTGACGTGATACTT-TAC-ATATTCA
1 ATTATTGACGTGATA-TTATACAATATTCA
1082129 ATTATTGAC
1 ATTATTGAC
1082138 CGGTATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 14 0.44
30 16 0.50
31 2 0.06
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (29 bp):
ATTATTGACGTGATATTATACAATATTCA
Found at i:1083788 original size:19 final size:19
Alignment explanation
Indices: 1083764--1083801 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1083754 AATGTTAGCG
* *
1083764 AAAATAATGTTTTTAATAA
1 AAAATAATATTTTAAATAA
1083783 AAAATAATATTTTAAATAA
1 AAAATAATATTTTAAATAA
1083802 CATTTTACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
AAAATAATATTTTAAATAA
Found at i:1087117 original size:13 final size:13
Alignment explanation
Indices: 1087096--1087138 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1087086 ATCAAGTGTC
*
1087096 AATGACTAAGAAA
1 AATGTCTAAGAAA
1087109 AATGTCTAAGAAA
1 AATGTCTAAGAAA
* *
1087122 AATTATGTAAGAAA
1 AA-TGTCTAAGAAA
1087136 AAT
1 AAT
1087139 TTTGAATAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.58, C:0.05, G:0.14, T:0.23
Consensus pattern (13 bp):
AATGTCTAAGAAA
Found at i:1087132 original size:14 final size:14
Alignment explanation
Indices: 1087101--1087139 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1087091 GTGTCAATGA
*
1087101 CTAAGAAAAA-TGT
1 CTAAGAAAAATTAT
1087114 CTAAGAAAAATTAT
1 CTAAGAAAAATTAT
*
1087128 GTAAGAAAAATT
1 CTAAGAAAAATT
1087140 TTGAATAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.56, C:0.05, G:0.13, T:0.26
Consensus pattern (14 bp):
CTAAGAAAAATTAT
Found at i:1096077 original size:79 final size:79
Alignment explanation
Indices: 1095931--1096090 Score: 187
Period size: 79 Copynumber: 2.0 Consensus size: 79
1095921 TATAAAAAAT
* * ** *
1095931 AACATTTTAGGTAGTGTCCAATATTAACATTTCCGGTAGAAAAAATAATGTTTTAGGTAACGGTT
1 AACATTTTAGGTAGCGTCCAATATTAACATTTCCGGTAGAAAAAATAATATTTTAAATAACAGTT
*
1095996 TATCGGAAATGTTA
66 TATCGAAAATGTTA
* * * * ** *
1096010 AACATTTTAGGTGGCG-CCTAATTTTAACATTTTCGGTAGAAATAATAATATTTTAAATAGTATT
1 AACATTTTAGGTAGCGTCC-AATATTAACATTTCCGGTAGAAAAAATAATATTTTAAATAACAGT
1096074 TTATCGAAAATGTTA
65 TTATCGAAAATGTTA
1096089 AA
1 AA
1096091 AAAATAATAA
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 2 0.03
79 65 0.97
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (79 bp):
AACATTTTAGGTAGCGTCCAATATTAACATTTCCGGTAGAAAAAATAATATTTTAAATAACAGTT
TATCGAAAATGTTA
Found at i:1096833 original size:14 final size:14
Alignment explanation
Indices: 1096814--1096840 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1096804 CCCACTCTGG
1096814 AAATCATTTACTAA
1 AAATCATTTACTAA
1096828 AAATCATTTACTA
1 AAATCATTTACTA
1096841 TATAAGTCCA
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:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATCATTTACTAA
Found at i:1098278 original size:15 final size:15
Alignment explanation
Indices: 1098258--1098345 Score: 88
Period size: 15 Copynumber: 5.6 Consensus size: 15
1098248 AACCGGGTAT
1098258 CGGGTACCCAATTAC
1 CGGGTACCCAATTAC
*
1098273 CGGGTACCCGCAA-AATC
1 CGGGTA-CC-CAATTA-C
1098290 CGGGTACCCAATTAC
1 CGGGTACCCAATTAC
**
1098305 CGGGTACCCACAAAATC
1 CGGGTACCCA-ATTA-C
*
1098322 CGGGTACCCGATTAC
1 CGGGTACCCAATTAC
1098337 CGGGTACCC
1 CGGGTACCC
1098346 GTAACATCCG
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
15 30 0.50
16 10 0.17
17 20 0.33
ACGTcount: A:0.26, C:0.35, G:0.23, T:0.16
Consensus pattern (15 bp):
CGGGTACCCAATTAC
Found at i:1098294 original size:17 final size:17
Alignment explanation
Indices: 1098272--1098358 Score: 76
Period size: 17 Copynumber: 5.4 Consensus size: 17
1098262 TACCCAATTA
1098272 CCGGGTACCCGCAAAAT
1 CCGGGTACCCGCAAAAT
*
1098289 CCGGGTA-CC-C-AATT
1 CCGGGTACCCGCAAAAT
*
1098303 ACCGGGTACCCACAAAAT
1 -CCGGGTACCCGCAAAAT
**
1098321 CCGGGTACCCG-ATTA-
1 CCGGGTACCCGCAAAAT
* *
1098336 CCGGGTACCCGTAACAT
1 CCGGGTACCCGCAAAAT
1098353 CCGGGT
1 CCGGGT
1098359 CGGGACACGG
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
14 3 0.05
15 19 0.33
16 8 0.14
17 24 0.42
18 3 0.05
ACGTcount: A:0.25, C:0.34, G:0.24, T:0.16
Consensus pattern (17 bp):
CCGGGTACCCGCAAAAT
Found at i:1098299 original size:32 final size:32
Alignment explanation
Indices: 1098258--1098358 Score: 166
Period size: 32 Copynumber: 3.2 Consensus size: 32
1098248 AACCGGGTAT
1098258 CGGGTACCCAATTACCGGGTACCCGCAAAATC
1 CGGGTACCCAATTACCGGGTACCCGCAAAATC
*
1098290 CGGGTACCCAATTACCGGGTACCCACAAAATC
1 CGGGTACCCAATTACCGGGTACCCGCAAAATC
* * *
1098322 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCAATTACCGGGTACCCGCAAAATC
1098354 CGGGT
1 CGGGT
1098359 CGGGACACGG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.26, C:0.34, G:0.24, T:0.17
Consensus pattern (32 bp):
CGGGTACCCAATTACCGGGTACCCGCAAAATC
Found at i:1098415 original size:15 final size:15
Alignment explanation
Indices: 1098395--1098435 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1098385 CCCGGAAGTT
1098395 TCGGGTACCCGAAAA
1 TCGGGTACCCGAAAA
*
1098410 TCGGGTA-CCAAAAA
1 TCGGGTACCCGAAAA
1098424 TCCGGGTACCCG
1 T-CGGGTACCCG
1098436 GATTTGCACA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 7 0.32
15 13 0.59
16 2 0.09
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.15
Consensus pattern (15 bp):
TCGGGTACCCGAAAA
Found at i:1099692 original size:14 final size:14
Alignment explanation
Indices: 1099673--1099701 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1099663 CCTTGGACAA
1099673 TATGTTTATACAGC
1 TATGTTTATACAGC
1099687 TATGTTTATACAGC
1 TATGTTTATACAGC
1099701 T
1 T
1099702 CAAGTGCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (14 bp):
TATGTTTATACAGC
Found at i:1100575 original size:30 final size:30
Alignment explanation
Indices: 1100527--1100583 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1100517 AAATTTTCGT
* *
1100527 TCTTGAAATTTTATAAGTTTAAATTCATCC
1 TCTTGAAATTTTAAAAGTTCAAATTCATCC
1100557 TCTT-AAATTTTAAAAAGTTCAAATTCA
1 TCTTGAAATTTT-AAAAGTTCAAATTCA
1100584 CCCCTAACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (30 bp):
TCTTGAAATTTTAAAAGTTCAAATTCATCC
Found at i:1101226 original size:20 final size:20
Alignment explanation
Indices: 1101201--1101238 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1101191 TTTGGTTCAC
*
1101201 GGAATATAAGATTATCAGTG
1 GGAATAAAAGATTATCAGTG
1101221 GGAATAAAAGATTATCAG
1 GGAATAAAAGATTATCAG
1101239 GGAATAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26
Consensus pattern (20 bp):
GGAATAAAAGATTATCAGTG
Found at i:1101241 original size:18 final size:19
Alignment explanation
Indices: 1101201--1101244 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1101191 TTTGGTTCAC
*
1101201 GGAATATAAGATTATCAGTG
1 GGAATAAAAGATTATCAG-G
1101221 GGAATAAAAGATTATCA-G
1 GGAATAAAAGATTATCAGG
1101239 GGAATA
1 GGAATA
1101245 GAATTATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.45, C:0.05, G:0.25, T:0.25
Consensus pattern (19 bp):
GGAATAAAAGATTATCAGG
Found at i:1101434 original size:2 final size:2
Alignment explanation
Indices: 1101423--1101458 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1101413 AAATTAAATT
1101423 TA TA -A 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 T
1101459 TTACAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1103382 original size:20 final size:20
Alignment explanation
Indices: 1103357--1103394 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1103347 TTTGGTTCAC
1103357 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
1103377 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
1103395 GGAATATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:1104253 original size:21 final size:22
Alignment explanation
Indices: 1104207--1104259 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
1104197 TTTTGATATG
*
1104207 TTTTAATATAGTTTTTGTTTTA
1 TTTTAGTATAGTTTTTGTTTTA
1104229 TTTTAGTATAGTTTTTGTTTT-
1 TTTTAGTATAGTTTTTGTTTTA
1104250 TTTTAGTATA
1 TTTTAGTATA
1104260 TGTCGTTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (22 bp):
TTTTAGTATAGTTTTTGTTTTA
Found at i:1105609 original size:38 final size:38
Alignment explanation
Indices: 1105521--1105609 Score: 126
Period size: 38 Copynumber: 2.3 Consensus size: 38
1105511 TATTATATAT
1105521 ATATATATATATATATAATATTAATAAATTTAATTTAA
1 ATATATATATATATATAATATTAATAAATTTAATTTAA
* * * *
1105559 AT-TAAAAAATATATATAATATTTATATATTTAATTTAA
1 ATAT-ATATATATATATAATATTAATAAATTTAATTTAA
1105597 ATATATATATATA
1 ATATATATATATA
1105610 CCCGACCCGA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
37 1 0.02
38 41 0.95
39 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (38 bp):
ATATATATATATATATAATATTAATAAATTTAATTTAA
Found at i:1111411 original size:21 final size:20
Alignment explanation
Indices: 1111383--1111421 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
1111373 GTAGTCTTTC
1111383 AGGAAAAGGATCGATCCCTT
1 AGGAAAAGGATCGATCCCTT
1111403 AGGAGAAAGGATCGATCCC
1 AGGA-AAAGGATCGATCCC
1111422 AAAGTTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.21, G:0.28, T:0.15
Consensus pattern (20 bp):
AGGAAAAGGATCGATCCCTT
Found at i:1112005 original size:181 final size:179
Alignment explanation
Indices: 1111688--1112048 Score: 695
Period size: 181 Copynumber: 2.0 Consensus size: 179
1111678 GAGTGATCAC
1111688 TTCTTAAACACACTTAATTACATAATGGAACTCTCAATTGTATGTTACTGATTGGTACATAAGTT
1 TTCTTAAACACACTTAATTACATAATGGAACTCTCAATTGTATGTTACTGATTGGTACATAAGTT
1111753 TTACATATTTATGTTTAGGTTCTTAATCTTGTATGATCAATTGAGTGATTGTCTGATATCCTATA
66 TTACATATTTATGTTTAGGTTCTTAATCTTGTATGATCAATTGAGTGATTGTCTGATATCCTATA
1111818 GGTATAAAATTTTGCATGTTGTTTCCTTATAAAAATGTTTAACATGTGG
131 GGTATAAAATTTTGCATGTTGTTTCCTTATAAAAATGTTTAACATGTGG
1111867 TTCTTAATTACACACTTAATTACATAATGGAACTCTCAATTGTATGTTACTGATTGGTACATAAG
1 TTCTTAA--ACACACTTAATTACATAATGGAACTCTCAATTGTATGTTACTGATTGGTACATAAG
1111932 TTTTACATATTTATGTTTAGGTTCTTAATCTTGTATGATCAATTGAGTGATTGTCTGATATCCTA
64 TTTTACATATTTATGTTTAGGTTCTTAATCTTGTATGATCAATTGAGTGATTGTCTGATATCCTA
*
1111997 TTGGTATAAAATTTTGCATGTTGTTTCCTTATAAAAATGTTTAACATGTGG
129 TAGGTATAAAATTTTGCATGTTGTTTCCTTATAAAAATGTTTAACATGTGG
1112048 T
1 T
1112049 AACCTTAATT
Statistics
Matches: 179, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
179 7 0.04
181 172 0.96
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.44
Consensus pattern (179 bp):
TTCTTAAACACACTTAATTACATAATGGAACTCTCAATTGTATGTTACTGATTGGTACATAAGTT
TTACATATTTATGTTTAGGTTCTTAATCTTGTATGATCAATTGAGTGATTGTCTGATATCCTATA
GGTATAAAATTTTGCATGTTGTTTCCTTATAAAAATGTTTAACATGTGG
Found at i:1113546 original size:20 final size:21
Alignment explanation
Indices: 1113497--1113558 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
1113487 AACATAATGT
*
1113497 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
*
1113518 CTAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
* *
1113539 CCA-TGGGTATCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
1113559 TGTCTAACGG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.16, C:0.39, G:0.26, T:0.19
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:1114859 original size:19 final size:20
Alignment explanation
Indices: 1114835--1114882 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
1114825 AACGATTTTC
*
1114835 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
*
1114854 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1114874 TTTTGAAAA
1 TTTTGAAAA
1114883 AGAAATTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1116296 original size:20 final size:20
Alignment explanation
Indices: 1116271--1116331 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
1116261 ATCATATTGT
1116271 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
* *
1116291 CCAGGGAGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
1116311 CCAGGGGGTACTGATTCCCC
1 CCAGGGGGTACAGATTCCCC
1116331 C
1 C
1116332 TGTCTAACGG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.21, C:0.36, G:0.28, T:0.15
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:1123441 original size:31 final size:30
Alignment explanation
Indices: 1123368--1123456 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 30
1123358 CCTAAACCCA
**
1123368 TTTAATATTTAAACTATTAATTTTATTTGT
1 TTTAATATTTAAACTATTAATTTTATTCAT
* * *
1123398 TTTAATACTTAAATTATTAATTTTGGTTCAT
1 TTTAATATTTAAACTATTAATTTT-ATTCAT
* * *
1123429 TTTAGTATTTAAACT-TTTATTTTTTTCA
1 TTTAATATTTAAACTATTAATTTTATTCA
1123457 AAATTATACC
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 4 0.08
30 29 0.60
31 15 0.31
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (30 bp):
TTTAATATTTAAACTATTAATTTTATTCAT
Found at i:1123497 original size:30 final size:31
Alignment explanation
Indices: 1123376--1123499 Score: 89
Period size: 30 Copynumber: 4.1 Consensus size: 31
1123366 CATTTAATAT
* * *
1123376 TTAAACTATTAATTTTATTT-GTTTTAATA-C
1 TTAAACT-TTAATTTTGTTTCATTTTAGTACC
* * *
1123406 TTAAATTATTAATTTTGGTTCATTTTAGTA-T
1 TTAAACT-TTAATTTTGTTTCATTTTAGTACC
* **
1123437 TTAAACTTTTATTTT-TTTCAAAATTA-TACC
1 TTAAACTTTAATTTTGTTTC-ATTTTAGTACC
*
1123467 TTACA-TTTAATTTTGTTTCATTTTAGTACC
1 TTAAACTTTAATTTTGTTTCATTTTAGTACC
1123497 TTA
1 TTA
1123500 TCGTTAAACA
Statistics
Matches: 73, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
29 17 0.23
30 43 0.59
31 13 0.18
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (31 bp):
TTAAACTTTAATTTTGTTTCATTTTAGTACC
Found at i:1136944 original size:55 final size:54
Alignment explanation
Indices: 1136886--1137592 Score: 431
Period size: 51 Copynumber: 13.6 Consensus size: 54
1136876 TGACGAGCCT
**
1136886 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATAAAACGTGTTT
1 GCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCA-AAAACGTGTCC
* * * * *
1136941 GCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATC-TTCA-AAAACGTGTCC
* * *
1136997 GCTCTCTCTTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCAAAAAACAG-GTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTC-AAAAAC-GTGTCC
* * * *
1137052 GCTCCCTATTCTTTCAGGGAGTATAGGACT----CAATCTTCAACGAAC-TAGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-AAACGT-GTCC
* * *
1137103 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAACTTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-AAACGTGTCC
* * *
1137154 GCTCCCTATTCCTTCAGAGAGTATATGACT----CAATCTTCAATGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-AAACGTGTCC
* * * * *
1137205 GCTCTCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-AAACGTGTCC
* * * *
1137256 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-AAACGTGTCC
* * * *
1137307 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-AAACGTGTCC
* * * * *
1137358 ACTCCCTATTCATTCAGAGAGTATATGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-AAACGTGTCC
* * * * *
1137409 ACTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAATGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-AAACGTGTCC
* * * * * * *
1137460 GCTCTCTATTCATTCAGAGATTATAGGACT----CAATCTTCAACGAACTTATCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-AAACGTGTCC
* * * *
1137511 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-AAACGTGTCC
** *
1137562 GCTCCCTATTCAATCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTC
1137593 AATCTTCAAC
Statistics
Matches: 596, Mismatches: 45, Indels: 25
0.89 0.07 0.04
Matches are distributed among these distances:
50 2 0.00
51 475 0.80
52 1 0.00
55 70 0.12
56 48 0.08
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (54 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAAAAACGTGTCC
Found at i:1137108 original size:51 final size:51
Alignment explanation
Indices: 1136993--1137608 Score: 962
Period size: 51 Copynumber: 12.0 Consensus size: 51
1136983 AATAAAACGG
* * * * ** **
1136993 GTCCGCTCTCTCTTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAAAAAACAG
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAACGAACTT
* * *
1137048 GTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCAATCTTCAACGAACTA
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
* *
1137099 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
* * * *
1137150 GTCTGCTCCCTATTCCTTCAGAGAGTATATGACTCAATCTTCAATGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
1137201 GTCCGCTCTCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1137252 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1137303 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
* *
1137354 GTCCACTCCCTATTCATTCAGAGAGTATATGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
* *
1137405 GTCCACTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
* *
1137456 GTCCGCTCTCTATTCATTCAGAGATTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
1137507 ATCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
1137558 GTCCGCTCCCTATTCAATCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1137609 ATTTGCTTCA
Statistics
Matches: 525, Mismatches: 36, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
51 495 0.94
55 30 0.06
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (51 bp):
GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:1137498 original size:27 final size:27
Alignment explanation
Indices: 1137468--1137549 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
1137458 CCGCTCTCTA
1137468 TTCATTCAGAGATTATAGGACTCAATC
1 TTCATTCAGAGATTATAGGACTCAATC
* ** ** *
1137495 TTCA-AC-GA-ACTTATCCG-CTCCCTA
1 TTCATTCAGAGA-TTATAGGACTCAATC
*
1137519 TTCATTCAGAGAGTATAGGACTCAATC
1 TTCATTCAGAGATTATAGGACTCAATC
1137546 TTCA
1 TTCA
1137550 ACGAACTTGT
Statistics
Matches: 37, Mismatches: 13, Indels: 10
0.62 0.22 0.17
Matches are distributed among these distances:
24 9 0.24
25 8 0.22
26 7 0.19
27 13 0.35
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.32
Consensus pattern (27 bp):
TTCATTCAGAGATTATAGGACTCAATC
Found at i:1138761 original size:17 final size:18
Alignment explanation
Indices: 1138739--1138813 Score: 57
Period size: 17 Copynumber: 4.2 Consensus size: 18
1138729 CCTCCTTTTA
1138739 TTTCTCTTTTT-TTCATT
1 TTTCTCTTTTTATTCATT
*
1138756 TTTCTCTTTTTATT-TTT
1 TTTCTCTTTTTATTCATT
* * *
1138773 TTTCCATTTTTTCTCTTCTTT
1 TTT-C-TCTTTT-TATTCATT
*
1138794 TTTTTCTTTTT-TTCATT
1 TTTCTCTTTTTATTCATT
1138811 TTT
1 TTT
1138814 TTTTCGTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
17 24 0.51
18 4 0.09
19 10 0.21
20 3 0.06
21 6 0.13
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTCTCTTTTTATTCATT
Found at i:1138782 original size:24 final size:24
Alignment explanation
Indices: 1138745--1138799 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
1138735 TTTATTTCTC
*
1138745 TTTTTTT-CATTTTTCTCTTTTTAT
1 TTTTTTTCCATTTTTCTC-TCTTAT
*
1138769 TTTTTTTCCATTTTT-TCTCTTCT
1 TTTTTTTCCATTTTTCTCTCTTAT
1138792 TTTTTTTC
1 TTTTTTTC
1138800 TTTTTTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 12 0.43
24 9 0.32
25 7 0.25
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTTTTCCATTTTTCTCTCTTAT
Found at i:1138783 original size:26 final size:23
Alignment explanation
Indices: 1138745--1138798 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 23
1138735 TTTATTTCTC
*
1138745 TTTTTTTCATTTTTCTCTTTTTAT
1 TTTTTTTCATTTTTCTCTTCTT-T
1138769 TTTTTTTCCATTTTTTCTCTTCTTT
1 TTTTTTT-CA-TTTTTCTCTTCTTT
1138794 TTTTT
1 TTTTT
1138799 CTTTTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 7 0.26
25 8 0.30
26 12 0.44
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTTTCATTTTTCTCTTCTTT
Found at i:1138832 original size:23 final size:20
Alignment explanation
Indices: 1138754--1138849 Score: 81
Period size: 19 Copynumber: 4.7 Consensus size: 20
1138744 CTTTTTTTCA
*
1138754 TTTTTCTCTTTT-T-ATTTT
1 TTTTTCTTTTTTCTCATTTT
* *
1138772 TTTTCCATTTTTTCTCTTCTTT
1 TTTTTC-TTTTTTCTCAT-TTT
1138794 TTTTTCTTTTTT-TCATTTT
1 TTTTTCTTTTTTCTCATTTT
**
1138813 TTTTTCGTTTTTTCCATCATCAT
1 TTTTTC-TTTTTT-C-TCATTTT
1138836 TTTTTCTTTTTTCT
1 TTTTTCTTTTTTCT
1138850 TCTTTTCTCT
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
18 5 0.08
19 14 0.22
20 11 0.17
21 8 0.13
22 14 0.22
23 11 0.17
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.76
Consensus pattern (20 bp):
TTTTTCTTTTTTCTCATTTT
Found at i:1138839 original size:42 final size:40
Alignment explanation
Indices: 1138754--1138847 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 40
1138744 CTTTTTTTCA
* * *
1138754 TTTTTCTCTTTTTATTTTTTTTCCATTTTTTCTCTTCTTT
1 TTTTTCTTTTTTTATTTTTTTTCCATTTTTTCTCATCTAT
* *
1138794 TTTTTCTTTTTTTCATTTTTTTTTCGTTTTTTC-CATCATCAT
1 TTTTTCTTTTTTT-ATTTTTTTTCCATTTTTTCTCATC-T-AT
1138836 TTTTTCTTTTTT
1 TTTTTCTTTTTT
1138848 CTTCTTTTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 15 0.33
41 18 0.39
42 13 0.28
ACGTcount: A:0.06, C:0.16, G:0.01, T:0.77
Consensus pattern (40 bp):
TTTTTCTTTTTTTATTTTTTTTCCATTTTTTCTCATCTAT
Found at i:1158087 original size:2 final size:2
Alignment explanation
Indices: 1158080--1158168 Score: 178
Period size: 2 Copynumber: 44.5 Consensus size: 2
1158070 AACCCTAGAA
1158080 AT AT AT AT 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 AT AT AT AT
1158122 AT AT AT AT 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 AT AT AT AT
1158164 AT AT A
1 AT AT A
1158169 GCAGGGGAGT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1159446 original size:60 final size:60
Alignment explanation
Indices: 1159353--1159471 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
1159343 CATTTATTTT
* ** ** * * * *
1159353 AAATTAGTCCTTAAACTTTTAATTATTTTAATTTCATCCCTAAACTATGACTTTCATTCC
1 AAATTAGTCCTTAAACTTCTAAACATTCCAATTTAACCCCTAAACTATGAATCTCATTCC
*
1159413 AAATTAGTCCTTATACTTCTAAACATTCCAATTTAACCCCTAAACTATGAATCTCATTC
1 AAATTAGTCCTTAAACTTCTAAACATTCCAATTTAACCCCTAAACTATGAATCTCATTC
1159472 TAATTTTGTC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (60 bp):
AAATTAGTCCTTAAACTTCTAAACATTCCAATTTAACCCCTAAACTATGAATCTCATTCC
Found at i:1159514 original size:60 final size:60
Alignment explanation
Indices: 1159353--1159516 Score: 143
Period size: 60 Copynumber: 2.7 Consensus size: 60
1159343 CATTTATTTT
* * ** ** * *
1159353 AAATTAGTCCTTAAACTTTTAATTATTTTAATTTCATCCCTAAACTATGACTTTCATTCC
1 AAATTAGTCCCTAAACTTCTAAACATTCCAATTTCATCCCTAAACTATGAATCTCATTCC
* * * * *
1159413 AAATTAGTCCTTATACTTCTAAACATTCCAATTTAACCCCTAAACTATGAATCTCATTCT
1 AAATTAGTCCCTAAACTTCTAAACATTCCAATTTCATCCCTAAACTATGAATCTCATTCC
* * * *
1159473 AATTTTGTCCCTAAACCTT-TAAATC-TTTCATTTTCATCCCTAAA
1 AAATTAGTCCCTAAA-CTTCTAAA-CATTCCAATTTCATCCCTAAA
1159517 GTCATCCAAA
Statistics
Matches: 83, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
60 79 0.95
61 4 0.05
ACGTcount: A:0.32, C:0.23, G:0.03, T:0.41
Consensus pattern (60 bp):
AAATTAGTCCCTAAACTTCTAAACATTCCAATTTCATCCCTAAACTATGAATCTCATTCC
Found at i:1161582 original size:2 final size:2
Alignment explanation
Indices: 1161575--1161606 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1161565 TAGGTGATCA
1161575 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
1161607 GATTTTTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1162952 original size:20 final size:20
Alignment explanation
Indices: 1162916--1162953 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1162906 ATCCTATTCC
**
1162916 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1162936 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1162954 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1166644 original size:17 final size:18
Alignment explanation
Indices: 1166603--1166646 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
1166593 CCATACTTGA
1166603 TTAAATATTTTATAAACT
1 TTAAATATTTTATAAACT
* *
1166621 TT-TATATTTTTTAAA-T
1 TTAAATATTTTATAAACT
1166637 TTAAATATTT
1 TTAAATATTT
1166647 ATTTTTACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 3 0.14
17 17 0.77
18 2 0.09
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAAATATTTTATAAACT
Found at i:1167848 original size:23 final size:23
Alignment explanation
Indices: 1167822--1167866 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1167812 CATGTTAATA
*
1167822 AAAAGAATACTTATAATTTAAAT
1 AAAAGAATAATTATAATTTAAAT
** *
1167845 AAAATCATAATTATCATTTAAA
1 AAAAGAATAATTATAATTTAAA
1167867 GACAAAAATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (23 bp):
AAAAGAATAATTATAATTTAAAT
Found at i:1170679 original size:25 final size:24
Alignment explanation
Indices: 1170651--1170700 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1170641 TTGATACTGC
*
1170651 CAGTTCAACTTCTAGCATGCAGGGA
1 CAGTT-AACTTCCAGCATGCAGGGA
*
1170676 CAGTTGACTTCCAGCATGCAGGGA
1 CAGTTAACTTCCAGCATGCAGGGA
1170700 C
1 C
1170701 CGATTTCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (24 bp):
CAGTTAACTTCCAGCATGCAGGGA
Found at i:1178879 original size:19 final size:19
Alignment explanation
Indices: 1178832--1178884 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
1178822 ACCCGACCCG
* *
1178832 TTGACTGTTGACTTTTCTC
1 TTGACAGTTGACTTTTCTA
* *
1178851 TTGGCCGTTGACTTTTCTA
1 TTGACAGTTGACTTTTCTA
*
1178870 TTGATAGTTGA-TTTT
1 TTGACAGTTGACTTTT
1178885 TTTGTTGATC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.13, C:0.15, G:0.19, T:0.53
Consensus pattern (19 bp):
TTGACAGTTGACTTTTCTA
Found at i:1178961 original size:20 final size:20
Alignment explanation
Indices: 1178936--1178976 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1178926 TTTTCGACCA
*
1178936 TTGATCGTTGACTTTGACTT
1 TTGATCGTTAACTTTGACTT
*
1178956 TTGATCGTTAATTTTGACTT
1 TTGATCGTTAACTTTGACTT
1178976 T
1 T
1178977 GACCAATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.54
Consensus pattern (20 bp):
TTGATCGTTAACTTTGACTT
Found at i:1179613 original size:29 final size:30
Alignment explanation
Indices: 1179581--1179637 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1179571 TTTTTCATGG
*
1179581 GATTA-TATCCCCATAC-TGATTCTGCATAA
1 GATTATTATCCCAAT-CTTGATTCTGCATAA
*
1179610 GATTATTATTCCAATCTTGATTCTGCAT
1 GATTATTATCCCAATCTTGATTCTGCAT
1179638 GTAATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (30 bp):
GATTATTATCCCAATCTTGATTCTGCATAA
Found at i:1184590 original size:20 final size:22
Alignment explanation
Indices: 1184546--1184593 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1184536 TAATAATTAA
*
1184546 GAATATATGAAATAAGCTATGT
1 GAATATATGAAATAAGCTATAT
*
1184568 GAATATATGAAATGA-C-ATAT
1 GAATATATGAAATAAGCTATAT
1184588 GAATAT
1 GAATAT
1184594 GCAATACGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.38
21 1 0.04
22 14 0.58
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.31
Consensus pattern (22 bp):
GAATATATGAAATAAGCTATAT
Found at i:1186098 original size:19 final size:19
Alignment explanation
Indices: 1186057--1186104 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1186047 CCTGTTGACT
* ** *
1186057 GTTGACTTTTCTCTTGGTT
1 GTTGACTTTTCTATTAATA
1186076 GTTGACTTTTCTATTAATA
1 GTTGACTTTTCTATTAATA
1186095 GTTGACTTTT
1 GTTGACTTTT
1186105 TTGTTGATCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.15, C:0.12, G:0.17, T:0.56
Consensus pattern (19 bp):
GTTGACTTTTCTATTAATA
Found at i:1186812 original size:29 final size:29
Alignment explanation
Indices: 1186779--1186863 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
1186769 ATACATTCCC
* * *
1186779 GATTCTTCATGGGATTGTATCCCCATCCT
1 GATTCTTCATGAGATTATATTCCCATCCT
* * * *
1186808 GATTCTGCATAAGATTATATTCCAATCTT
1 GATTCTTCATGAGATTATATTCCCATCCT
*
1186837 GATTCTTCATGTGATTATATTCCCATC
1 GATTCTTCATGAGATTATATTCCCATC
1186864 ATGTTTATGC
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (29 bp):
GATTCTTCATGAGATTATATTCCCATCCT
Found at i:1186876 original size:29 final size:29
Alignment explanation
Indices: 1186820--1186876 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
1186810 TTCTGCATAA
* * *
1186820 GATTATATTCCAATCTTGATTCTTCATGT
1 GATTATATTCCAATCATGATTATGCATGT
* *
1186849 GATTATATTCCCATCATGTTTATGCATG
1 GATTATATTCCAATCATGATTATGCATG
1186877 GAATCCTCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.46
Consensus pattern (29 bp):
GATTATATTCCAATCATGATTATGCATGT
Found at i:1190645 original size:19 final size:19
Alignment explanation
Indices: 1190623--1190699 Score: 111
Period size: 19 Copynumber: 4.1 Consensus size: 19
1190613 TTTGAATCAA
*
1190623 AACTTATTTCCAGATTCAT
1 AACTTATTTTCAGATTCAT
*
1190642 AACTTATTTTCAGACTCAT
1 AACTTATTTTCAGATTCAT
1190661 AACTTATTATT-AGATTCAT
1 AACTTATT-TTCAGATTCAT
*
1190680 AACTTATTTTCAAATTCAT
1 AACTTATTTTCAGATTCAT
1190699 A
1 A
1190700 GCCCAATGCA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
18 2 0.04
19 48 0.92
20 2 0.04
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.44
Consensus pattern (19 bp):
AACTTATTTTCAGATTCAT
Found at i:1190649 original size:38 final size:38
Alignment explanation
Indices: 1190598--1190691 Score: 109
Period size: 38 Copynumber: 2.5 Consensus size: 38
1190588 TACTTCCACA
* * **
1190598 ATTCAAAATTTATTTTTTGAATCAAAACTTATT-TCCAG
1 ATTCATAACTTATTTTCAGAATCAAAACTTATTAT-CAG
* * *
1190636 ATTCATAACTTATTTTCAGACTCATAACTTATTATTAG
1 ATTCATAACTTATTTTCAGAATCAAAACTTATTATCAG
1190674 ATTCATAACTTATTTTCA
1 ATTCATAACTTATTTTCA
1190692 AATTCATAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 47 0.98
39 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (38 bp):
ATTCATAACTTATTTTCAGAATCAAAACTTATTATCAG
Found at i:1192168 original size:26 final size:26
Alignment explanation
Indices: 1192145--1192194 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1192135 ATTGAATAGA
*
1192145 ATTAATATAATAAAAAATTAAATAAT
1 ATTAATATAATAAAAAATAAAATAAT
*
1192171 ATTAATATAATAATAAATAAAATA
1 ATTAATATAATAAAAAATAAAATA
1192195 TTTTTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (26 bp):
ATTAATATAATAAAAAATAAAATAAT
Found at i:1194404 original size:21 final size:21
Alignment explanation
Indices: 1194380--1194419 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1194370 ATGTTTAAAT
*
1194380 AAATTGAAAGTTTAGGTACCA
1 AAATTGAAACTTTAGGTACCA
*
1194401 AAATTGATACTTTAGGTAC
1 AAATTGAAACTTTAGGTAC
1194420 TAAACATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (21 bp):
AAATTGAAACTTTAGGTACCA
Found at i:1198276 original size:3 final size:3
Alignment explanation
Indices: 1198268--1198345 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
1198258 GATAGGTTGT
1198268 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1198316 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1198346 ACCAAGAAAG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1199446 original size:22 final size:20
Alignment explanation
Indices: 1199409--1199451 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
1199399 TTCATCTTAA
*
1199409 ATTTATAAAAAAATTACTTT
1 ATTTATAAAAAAATTAATTT
*
1199429 ATTTATTAAAAACTATTAATTT
1 ATTTA-TAAAAA-AATTAATTT
1199451 A
1 A
1199452 AGATTTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 8 0.42
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTATAAAAAAATTAATTT
Done.