Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007558.1 Hibiscus syriacus cultivar Beakdansim tig00021265_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: 93373
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3904 original size:32 final size:33
Alignment explanation
Indices: 3849--3916 Score: 120
Period size: 32 Copynumber: 2.1 Consensus size: 33
3839 TGTTTGTTGT
*
3849 TGTTGTATATGATGTTCCTTGCTACAAGTTTAA
1 TGTTGTATATGATGTTCCCTGCTACAAGTTTAA
3882 TGTTGTATATGA-GTTCCCTGCTACAAGTTTAA
1 TGTTGTATATGATGTTCCCTGCTACAAGTTTAA
3914 TGT
1 TGT
3917 GTTAATGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 22 0.65
33 12 0.35
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (33 bp):
TGTTGTATATGATGTTCCCTGCTACAAGTTTAA
Found at i:7183 original size:20 final size:22
Alignment explanation
Indices: 7158--7205 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
7148 AACGGGTCAT
7158 TTCGGTTCAG-GTTAACTC-AA
1 TTCGGTTCAGAGTTAACTCGAA
7178 TTCGG-TCAGAGTTAACTCGAA
1 TTCGGTTCAGAGTTAACTCGAA
7199 -TCGGTTC
1 TTCGGTTC
7206 TAGGGGGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.16
20 17 0.68
21 4 0.16
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (22 bp):
TTCGGTTCAGAGTTAACTCGAA
Found at i:17239 original size:24 final size:24
Alignment explanation
Indices: 17207--17255 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
17197 GAATTTCTAG
17207 CATTATGATTTGGACTAATAAGGA
1 CATTATGATTTGGACTAATAAGGA
17231 CATTATGATTTGGACTAATAAGGA
1 CATTATGATTTGGACTAATAAGGA
17255 C
1 C
17256 CTGCTTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (24 bp):
CATTATGATTTGGACTAATAAGGA
Found at i:19593 original size:29 final size:29
Alignment explanation
Indices: 19552--19608 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
19542 AAGATTGGGT
*
19552 AAAGTATACAAATGGTCCCTCGACTATTA
1 AAAGTATACAAATGGTCACTCGACTATTA
19581 AAAGTTATA-AAATGGTCACTCGACTATT
1 AAAG-TATACAAATGGTCACTCGACTATT
19609 CATTTATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (29 bp):
AAAGTATACAAATGGTCACTCGACTATTA
Found at i:20689 original size:57 final size:57
Alignment explanation
Indices: 20620--20735 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
20610 GTTGATGATG
20620 ACCGGTGGATAGAGATGGTCAGACGATCGAAAGAATTGATATTTTTCTATCAAAACA
1 ACCGGTGGATAGAGATGGTCAGACGATCGAAAGAATTGATATTTTTCTATCAAAACA
20677 ACCGGTGGATAGAGATGGTCAGACGATCGAAAGAATTGATATTTTTCTATCAAAACA
1 ACCGGTGGATAGAGATGGTCAGACGATCGAAAGAATTGATATTTTTCTATCAAAACA
20734 AC
1 AC
20736 ACGAAAATGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (57 bp):
ACCGGTGGATAGAGATGGTCAGACGATCGAAAGAATTGATATTTTTCTATCAAAACA
Found at i:21299 original size:13 final size:13
Alignment explanation
Indices: 21281--21307 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21271 CATATATAGT
21281 CTTGTACTTACCC
1 CTTGTACTTACCC
21294 CTTGTACTTACCC
1 CTTGTACTTACCC
21307 C
1 C
21308 AAATTAATAA
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:0.15, C:0.41, G:0.07, T:0.37
Consensus pattern (13 bp):
CTTGTACTTACCC
Found at i:21973 original size:19 final size:19
Alignment explanation
Indices: 21940--21987 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
21930 AGGATTGATA
*
21940 TAAAAA-TATTTTAAAATA-
1 TAAAAATTAATTTAAAA-AC
*
21958 TAAATATTAATTTAAAAAC
1 TAAAAATTAATTTAAAAAC
21977 TAAAAATTAAT
1 TAAAAATTAAT
21988 ACAAAAACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAATTAATTTAAAAAC
Found at i:28536 original size:21 final size:20
Alignment explanation
Indices: 28503--28542 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
28493 TTTATTTTAC
28503 TATTTAAACTTAAACATATAT
1 TATTTAAACTTAAA-ATATAT
* *
28524 TATTTTAATTTAAAATATA
1 TATTTAAACTTAAAATATA
28543 CAAAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTTAAACTTAAAATATAT
Found at i:28697 original size:21 final size:21
Alignment explanation
Indices: 28671--28716 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
28661 TTTTAGTGAT
* *
28671 CTTAACGAGCAATGAGTCGAG
1 CTTAACAAGCAACGAGTCGAG
28692 CTTAACAAGCAACGAGTCGAG
1 CTTAACAAGCAACGAGTCGAG
28713 -TTAA
1 CTTAA
28717 GCAGTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (21 bp):
CTTAACAAGCAACGAGTCGAG
Found at i:29741 original size:12 final size:12
Alignment explanation
Indices: 29724--29748 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29714 GCTCGAAACA
29724 CGTAAGAGGCCG
1 CGTAAGAGGCCG
29736 CGTAAGAGGCCG
1 CGTAAGAGGCCG
29748 C
1 C
29749 CTCTGCCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.40, T:0.08
Consensus pattern (12 bp):
CGTAAGAGGCCG
Found at i:34121 original size:11 final size:11
Alignment explanation
Indices: 34105--34150 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
34095 ATAACAAAAT
*
34105 AAATAATATAA
1 AAATAATACAA
34116 AAATAATACAA
1 AAATAATACAA
34127 ATAATAATACAA
1 A-AATAATACAA
*
34139 GAATAATA-AA
1 AAATAATACAA
34149 AA
1 AA
34151 GAAAGAGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 3 0.10
11 18 0.58
12 10 0.32
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (11 bp):
AAATAATACAA
Found at i:34121 original size:23 final size:22
Alignment explanation
Indices: 34095--34190 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 22
34085 GCATATATAT
* *
34095 ATAACAAAATAAATAATATAAAA
1 ATAATAAAAT-AATAATACAAAA
*
34118 ATAATACAAATAATAATACAAGA
1 ATAATA-AAATAATAATACAAAA
* *
34141 ATAATAAAA-AGA-AAGA-GAAA
1 ATAATAAAATA-ATAATACAAAA
*
34161 ATAA-AAAATAATAATA-AAAT
1 ATAATAAAATAATAATACAAAA
34181 ATAA-AAAATA
1 ATAATAAAATA
34191 TACATATAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
19 5 0.08
20 22 0.37
21 4 0.07
22 4 0.07
23 21 0.35
24 4 0.07
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.20
Consensus pattern (22 bp):
ATAATAAAATAATAATACAAAA
Found at i:34130 original size:20 final size:19
Alignment explanation
Indices: 34093--34262 Score: 77
Period size: 22 Copynumber: 8.6 Consensus size: 19
34083 ACGCATATAT
*
34093 ATATAACAA-AAT-AAATA
1 ATATAAAAATAATAAAATA
34110 ATATAAAAATAATACAAATA
1 ATATAAAAATAATA-AAATA
34130 ATAATACAAGAATAATAAAA-A
1 AT-ATA-AA-AATAATAAAATA
* *
34151 GAAAGAGAAAATAA-AAAATA
1 -ATATA-AAAATAATAAAATA
34171 ATA-ATAAAAT-ATAAAA-A
1 ATATA-AAAATAATAAAATA
* *
34188 ATATACATATAATATAAATA
1 ATATAAAAATAATA-AAATA
* **
34208 AGTAGAATAAA-AGGAAAATA
1 A-TATAA-AAATAATAAAATA
34228 ATAGTAAAAATAATAATAAATA
1 ATA-TAAAAATAAT-A-AAATA
*
34250 ATAGTAATAATAA
1 ATA-TAAAAATAA
34263 AAATGCAAAG
Statistics
Matches: 117, Mismatches: 17, Indels: 33
0.70 0.10 0.20
Matches are distributed among these distances:
17 16 0.14
18 17 0.15
19 14 0.12
20 24 0.21
21 14 0.12
22 25 0.21
23 7 0.06
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (19 bp):
ATATAAAAATAATAAAATA
Found at i:34134 original size:12 final size:12
Alignment explanation
Indices: 34101--34138 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
34091 ATATATAACA
*
34101 AAATAAATAATAT
1 AAAT-AATAATAC
34114 AAA-AATAATAC
1 AAATAATAATAC
34125 AAATAATAATAC
1 AAATAATAATAC
34137 AA
1 AA
34139 GAATAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 10 0.43
12 10 0.43
13 3 0.13
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAATAATAC
Found at i:34867 original size:37 final size:37
Alignment explanation
Indices: 34826--34922 Score: 151
Period size: 37 Copynumber: 2.6 Consensus size: 37
34816 GGATCCTATC
*
34826 TTTAGGAGTTTAAATCATAGTAGAATTCTATCATATT
1 TTTAGGAGTTTAAATCCTAGTAGAATTCTATCATATT
*
34863 TTTAGGAGTTTAAATCCTA-TCAAAATTCTATCATATT
1 TTTAGGAGTTTAAATCCTAGT-AGAATTCTATCATATT
*
34900 TTTAGGAGTTTGAATCCTAGTAG
1 TTTAGGAGTTTAAATCCTAGTAG
34923 GACGAAAATG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
36 1 0.02
37 52 0.96
38 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTAAATCCTAGTAGAATTCTATCATATT
Found at i:35977 original size:106 final size:105
Alignment explanation
Indices: 35653--36179 Score: 660
Period size: 106 Copynumber: 5.0 Consensus size: 105
35643 GCATTGTTCT
* * ** *
35653 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGAT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
* *
35717 ACCAGACGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAG-CGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
*
35759 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTGTTGACAA
1 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * * *
35818 TCAGTCG-CCTCTTCGTCGTGAAGTTGAGCTTGTGTTGCCTT
66 CCAG-CGTCC-CTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
* * * *
35859 GAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
35924 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGC-GTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
* * * *
35965 GAGTCCAGTATCCTTCGATGTGAAGTTTAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * *
36030 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTATG
66 CCAGC-GTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
* *
36071 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTG-GAAAATTG-TTGTTGACA
1 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAATTGTTTGTTGACA
* *
36134 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
65 ACCAG-CGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
36176 GAGT
1 GAGT
36180 GGCACGATAT
Statistics
Matches: 370, Mismatches: 39, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
99 2 0.01
100 79 0.21
101 3 0.01
102 5 0.01
104 3 0.01
105 52 0.14
106 223 0.60
107 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
CCAGCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
Found at i:37463 original size:2 final size:2
Alignment explanation
Indices: 37456--37520 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
37446 GATAATTACA
37456 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
37498 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
37521 GTAACAATAC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37924 original size:11 final size:11
Alignment explanation
Indices: 37908--37953 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
37898 ATAACAAAAT
*
37908 AAATAATATAA
1 AAATAATACAA
37919 AAATAATACAA
1 AAATAATACAA
37930 ATAATAATACAA
1 A-AATAATACAA
*
37942 GAATAATA-AA
1 AAATAATACAA
37952 AA
1 AA
37954 GAAAGAGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 3 0.10
11 18 0.58
12 10 0.32
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (11 bp):
AAATAATACAA
Found at i:37924 original size:23 final size:22
Alignment explanation
Indices: 37898--38015 Score: 65
Period size: 20 Copynumber: 5.5 Consensus size: 22
37888 ATATATATAT
* *
37898 ATAACAAAATAAATAATATAAAA
1 ATAATAAAAT-AATAATACAAAA
*
37921 ATAATACAAATAATAATACAAGA
1 ATAATA-AAATAATAATACAAAA
* *
37944 ATAATAAAA-AGA-AAGA-GAAA
1 ATAATAAAATA-ATAATACAAAA
37964 ATAA-AAAAT-ATAATA-ATAAA
1 ATAATAAAATAATAATACA-AAA
* *
37984 AT-ATAAAA-AAT-ATACATAT
1 ATAATAAAATAATAATACAAAA
38003 ATAATATAAATAA
1 ATAATA-AAATAA
38016 GTAGAATAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 23
0.69 0.09 0.21
Matches are distributed among these distances:
18 1 0.01
19 14 0.19
20 21 0.28
21 7 0.09
22 6 0.08
23 21 0.28
24 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (22 bp):
ATAATAAAATAATAATACAAAA
Found at i:37937 original size:12 final size:12
Alignment explanation
Indices: 37904--37941 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
37894 ATATATAACA
*
37904 AAATAAATAATAT
1 AAAT-AATAATAC
37917 AAA-AATAATAC
1 AAATAATAATAC
37928 AAATAATAATAC
1 AAATAATAATAC
37940 AA
1 AA
37942 GAATAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 10 0.43
12 10 0.43
13 3 0.13
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAATAATAC
Found at i:37983 original size:15 final size:15
Alignment explanation
Indices: 37905--38076 Score: 67
Period size: 15 Copynumber: 11.5 Consensus size: 15
37895 TATATAACAA
* *
37905 AATAAATAATATAAA
1 AATAAAAAATATAAT
*
37920 AATAATACAA-ATAAT
1 AATAA-AAAATATAAT
* *
37935 AATACAAGA-ATAAT
1 AATAAAAAATATAAT
* *
37949 AA-AAAGAAAGAGAA-
1 AATAAA-AAATATAAT
37963 AATAAAAAATATAAT
1 AATAAAAAATATAAT
* *
37978 AATAAAATATA-AAA
1 AATAAAAAATATAAT
* *
37992 AATATACATATATAAT
1 AATA-AAAAATATAAT
* *
38008 -ATAAATAAGTAGAAT
1 AATAAA-AAATATAAT
38023 AA-AAGGAAAATATAAT
1 AATAA--AAAATATAAT
*
38039 AGT--AAAA-ATAAT
1 AATAAAAAATATAAT
38051 AATAAATATAATAGTAAT
1 AATAAA-A-AATA-TAAT
38069 AATAAAAA
1 AATAAAAA
38077 TGCAAAGAAA
Statistics
Matches: 117, Mismatches: 22, Indels: 35
0.67 0.13 0.20
Matches are distributed among these distances:
12 7 0.06
13 6 0.05
14 27 0.23
15 47 0.40
16 17 0.15
17 3 0.03
18 10 0.09
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.24
Consensus pattern (15 bp):
AATAAAAAATATAAT
Found at i:37992 original size:22 final size:22
Alignment explanation
Indices: 37964--38012 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
37954 GAAAGAGAAA
37964 ATAAAAAATATA-ATAATAAAAT
1 ATAAAAAATATACAT-ATAAAAT
*
37986 ATAAAAAATATACATATATAAT
1 ATAAAAAATATACATATAAAAT
38008 ATAAA
1 ATAAA
38013 TAAGTAGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
ATAAAAAATATACATATAAAAT
Found at i:38097 original size:61 final size:59
Alignment explanation
Indices: 37904--38102 Score: 149
Period size: 62 Copynumber: 3.2 Consensus size: 59
37894 ATATATAACA
*
37904 AAATAAATAATATAAAAATAATACAAATAATAATACA-AG-AATAATAAAAAGAAAGAGAAAAT
1 AAATATATAATATAAAAATAATA-AAA-AAT-ATA-ATAGTAATAATAAAAAGAAA-AGAAAAT
* * * *
37966 AAAAAATATAATA-ATAAAAT-ATAAAAAATATACATATATAAT-ATAAATAAGTAGAATAAAAG
1 -AAATATATAATATA-AAAATAATAAAAAATATA-ATA-GTAATAATAAA-AAG-AAAAGAAAA-
*
38028 G
59 T
* *
38029 AAA-ATATAATAGTAAAAATAATAATAAATATAATAGTAATAATAAAAATGCAAAGAAAAT
1 AAATATATAATA-TAAAAATAATAAAAAATATAATAGTAATAATAAAAA-GAAAAGAAAAT
38089 AAATATATATATAT
1 AAATATATA-ATAT
38103 GGGTAATAAC
Statistics
Matches: 110, Mismatches: 12, Indels: 30
0.72 0.08 0.20
Matches are distributed among these distances:
59 5 0.05
60 7 0.06
61 34 0.31
62 35 0.32
63 29 0.26
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (59 bp):
AAATATATAATATAAAAATAATAAAAAATATAATAGTAATAATAAAAAGAAAAGAAAAT
Found at i:38675 original size:37 final size:37
Alignment explanation
Indices: 38634--38730 Score: 151
Period size: 37 Copynumber: 2.6 Consensus size: 37
38624 GGATCCTATC
*
38634 TTTAGGAGTTTAAATCATAGTAGAATTCTATCATATT
1 TTTAGGAGTTTAAATCCTAGTAGAATTCTATCATATT
*
38671 TTTAGGAGTTTAAATCCTA-TCAAAATTCTATCATATT
1 TTTAGGAGTTTAAATCCTAGT-AGAATTCTATCATATT
*
38708 TTTAGGAGTTTGAATCCTAGTAG
1 TTTAGGAGTTTAAATCCTAGTAG
38731 GACGAAAATG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
36 1 0.02
37 52 0.96
38 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTAAATCCTAGTAGAATTCTATCATATT
Found at i:39785 original size:106 final size:105
Alignment explanation
Indices: 39461--39987 Score: 660
Period size: 106 Copynumber: 5.0 Consensus size: 105
39451 GCATTGTTCT
* * ** *
39461 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGAT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
* *
39525 ACCAGACGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAG-CGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
*
39567 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTGTTGACAA
1 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * * *
39626 TCAGTCG-CCTCTTCGTCGTGAAGTTGAGCTTGTGTTGCCTT
66 CCAG-CGTCC-CTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
* * * *
39667 GAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
39732 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGC-GTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
* * * *
39773 GAGTCCAGTATCCTTCGATGTGAAGTTTAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * *
39838 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTATG
66 CCAGC-GTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
* *
39879 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTG-GAAAATTG-TTGTTGACA
1 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAATTGTTTGTTGACA
* *
39942 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
65 ACCAG-CGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
39984 GAGT
1 GAGT
39988 GGCACGATAT
Statistics
Matches: 370, Mismatches: 39, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
99 2 0.01
100 79 0.21
101 3 0.01
102 5 0.01
104 3 0.01
105 52 0.14
106 223 0.60
107 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
CCAGCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
Found at i:40825 original size:22 final size:22
Alignment explanation
Indices: 40799--40852 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
40789 ATGTTTGGTC
40799 AAAGGTTTGACATTTGATGCTA
1 AAAGGTTTGACATTTGATGCTA
* *
40821 AAAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGACATTTGATGCTA
40843 AAAGGTTTGA
1 AAAGGTTTGA
40853 TGGGGTAGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (22 bp):
AAAGGTTTGACATTTGATGCTA
Found at i:41489 original size:11 final size:11
Alignment explanation
Indices: 41468--41517 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
41458 TCTTTTTGAT
41468 TTTTGTTCTTTC
1 TTTT-TTCTTTC
41480 TTTTTTCTTT-
1 TTTTTTCTTTC
41490 TGTTTTT-TTTC
1 T-TTTTTCTTTC
41501 TTTTTTGC-TTC
1 TTTTTT-CTTTC
41512 TTTTTT
1 TTTTTT
41518 TTTGTCCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.26
11 21 0.62
12 4 0.12
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:41500 original size:21 final size:20
Alignment explanation
Indices: 41454--41520 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
41444 TTTTTGTTCC
** *
41454 TTTTTCTTTTTGATTTTTGT
1 TTTTTCTTTTTTCTTTTTTT
*
41474 TCTTTCTTTTTTCTTTTGTTT
1 TTTTTCTTTTTTCTTTT-TTT
41495 TTTTTCTTTTTTGCTTCTTTTT
1 TTTTTCTTTTTT-CTT-TTTTT
41517 TTTT
1 TTTT
41521 GTCCTTTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
20 14 0.36
21 13 0.33
22 10 0.26
23 2 0.05
ACGTcount: A:0.01, C:0.10, G:0.06, T:0.82
Consensus pattern (20 bp):
TTTTTCTTTTTTCTTTTTTT
Found at i:41506 original size:22 final size:22
Alignment explanation
Indices: 41467--41534 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 22
41457 TTCTTTTTGA
41467 TTTTTGTTCTTTC-TTTTTTCTT-
1 TTTTT-TT-TTTCTTTTTTTCTTC
*
41489 TTGTTTTTTTTCTTTTTTGCTTC
1 TT-TTTTTTTTCTTTTTTTCTTC
41512 TTTTTTTTTGTCCTTTTTGTTCT
1 TTTTTTTTT-T-CTTTTT-TTCT
41535 GATTGATTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
21 4 0.11
22 19 0.50
23 6 0.16
24 6 0.16
25 3 0.08
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.79
Consensus pattern (22 bp):
TTTTTTTTTTCTTTTTTTCTTC
Found at i:41529 original size:25 final size:24
Alignment explanation
Indices: 41454--41529 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 24
41444 TTTTTGTTCC
41454 TTTTTCTTTTTGATTTTTGTTCTTTCT
1 TTTTTC-TTTTG-TTTTTGTTCTTT-T
*
41481 TTTTTCTTTTGTTTTTTTTCTTTT
1 TTTTTCTTTTGTTTTTGTTCTTTT
* *
41505 TTGCTTCTTTT-TTTTTGTCCTTTT
1 TT-TTTCTTTTGTTTTTGTTCTTTT
41529 T
1 T
41530 GTTCTGATTG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
24 15 0.34
25 18 0.41
26 5 0.11
27 6 0.14
ACGTcount: A:0.01, C:0.12, G:0.07, T:0.80
Consensus pattern (24 bp):
TTTTTCTTTTGTTTTTGTTCTTTT
Found at i:44990 original size:20 final size:20
Alignment explanation
Indices: 44965--45007 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
44955 CCGAGTTCTC
* *
44965 CTTGCCGGTGCTCCCTTGGG
1 CTTGCCGGTGCCCCCTTGAG
44985 CTTGCCGGTGCCCCCTTGAG
1 CTTGCCGGTGCCCCCTTGAG
45005 CTT
1 CTT
45008 TCCAGACCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.02, C:0.37, G:0.30, T:0.30
Consensus pattern (20 bp):
CTTGCCGGTGCCCCCTTGAG
Found at i:45776 original size:20 final size:19
Alignment explanation
Indices: 45718--45777 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
45708 AAAAGAAAAC
**
45718 AAAT-TAAGTAAAATGATA
1 AAATATAAGTAAAAAAATA
*
45736 AAATA-AAGGAAACAAAGATA
1 AAATATAAGTAAA-AAA-ATA
45756 AAATAGTAAGTAAAAAAATA
1 AAATA-TAAGTAAAAAAATA
45776 AA
1 AA
45778 TAATAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 10 0.30
19 1 0.03
20 13 0.39
21 3 0.09
22 6 0.18
ACGTcount: A:0.68, C:0.02, G:0.12, T:0.18
Consensus pattern (19 bp):
AAATATAAGTAAAAAAATA
Found at i:45785 original size:14 final size:14
Alignment explanation
Indices: 45768--45832 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 14
45758 ATAGTAAGTA
45768 AAAAAATAAATAAT
1 AAAAAATAAATAAT
* *
45782 AAAATATATATAAT
1 AAAAAATAAATAAT
* * *
45796 AAAGAA-AAAGAAA
1 AAAAAATAAATAAT
45809 AAGAAAATAAATAA-
1 AA-AAAATAAATAAT
*
45823 AACAAATAAA
1 AAAAAATAAA
45833 CAAAATAATA
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
13 13 0.33
14 21 0.54
15 5 0.13
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.17
Consensus pattern (14 bp):
AAAAAATAAATAAT
Found at i:46362 original size:2 final size:2
Alignment explanation
Indices: 46355--46398 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
46345 AACATACGTG
46355 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46397 TA
1 TA
46399 CAAAAAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46418 original size:11 final size:11
Alignment explanation
Indices: 46402--46449 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
46392 ATATATACAA
*
46402 AAAAATAATAT
1 AAAAATAATAC
46413 AAAAATAATAC
1 AAAAATAATAC
*
46424 AAGTAATAATAC
1 AA-AAATAATAC
*
46436 AAGAATAATA-
1 AAAAATAATAC
46446 AAAA
1 AAAA
46450 GAAAGAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 3 0.09
11 19 0.59
12 10 0.31
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (11 bp):
AAAAATAATAC
Found at i:46431 original size:12 final size:11
Alignment explanation
Indices: 46405--46445 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
46395 TATACAAAAA
* *
46405 AATAATATAAA
1 AATAATACAAG
46416 AATAATACAAG
1 AATAATACAAG
46427 TAATAATACAAG
1 -AATAATACAAG
46439 AATAATA
1 AATAATA
46446 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:46483 original size:16 final size:15
Alignment explanation
Indices: 46459--46545 Score: 52
Period size: 16 Copynumber: 5.5 Consensus size: 15
46449 AGAAAGAGAA
46459 AATAAAAAATATAAT
1 AATAAAAAATATAAT
*
46474 AATAATAAAATATAAA
1 AATAA-AAAATATAAT
* *
46490 AAGTATACATATATAAT
1 AA-TA-AAAAATATAAT
* *
46507 -ATAAATAAGTAGAAT
1 AATAAA-AAATATAAT
46522 AA-AAGGAAAATATAAT
1 AATAA--AAAATATAAT
*
46538 AGTAAAAA
1 AATAAAAA
46546 TAATAATATA
Statistics
Matches: 53, Mismatches: 11, Indels: 16
0.66 0.14 0.20
Matches are distributed among these distances:
14 1 0.02
15 18 0.34
16 21 0.40
17 12 0.23
18 1 0.02
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (15 bp):
AATAAAAAATATAAT
Found at i:46545 original size:20 final size:20
Alignment explanation
Indices: 46521--46562 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
46511 ATAAGTAGAA
*
46521 TAAAAGGAA-AATATAATAG
1 TAAAAAGAATAATATAATAG
*
46540 TAAAAATAATAATATAATAG
1 TAAAAAGAATAATATAATAG
46560 TAA
1 TAA
46563 TAATAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (20 bp):
TAAAAAGAATAATATAATAG
Found at i:46567 original size:20 final size:20
Alignment explanation
Indices: 46530--46568 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
46520 ATAAAAGGAA
46530 AATATAATAGTAAAAATAAT
1 AATATAATAGTAAAAATAAT
*
46550 AATATAATAGTAATAATAA
1 AATATAATAGTAAAAATAA
46569 AATGCAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
AATATAATAGTAAAAATAAT
Found at i:47164 original size:37 final size:37
Alignment explanation
Indices: 47123--47228 Score: 131
Period size: 37 Copynumber: 2.8 Consensus size: 37
47113 GTGCTTGTGG
* * *
47123 ATCATATCTTTAGGAATTTAAATCATAGTAGAACTCT
1 ATCATATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * *
47160 ATCATATTTTTAGGAGTTTAAATCCTATTAAAATTCT
1 ATCATATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* *
47197 ATCTTATTTTTTAGGAGTTTGAATCCTAGTAG
1 ATCATA-TTTTTAGGAGTTTAAATCCTAGTAG
47229 GACGAAAAGG
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
37 36 0.62
38 22 0.38
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.43
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:52640 original size:46 final size:46
Alignment explanation
Indices: 52590--52682 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
52580 CTAATTACAG
52590 TTAATGTATTCTAATAGAGAGGAAATAATAAGGTGGAGGATAGTTA
1 TTAATGTATTCTAATAGAGAGGAAATAATAAGGTGGAGGATAGTTA
52636 TTAATGTATTCTAATAGAGAGGAAATAATAAGGTGGAGGATAGTTA
1 TTAATGTATTCTAATAGAGAGGAAATAATAAGGTGGAGGATAGTTA
52682 T
1 T
52683 CCCTTTTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.41, C:0.02, G:0.26, T:0.31
Consensus pattern (46 bp):
TTAATGTATTCTAATAGAGAGGAAATAATAAGGTGGAGGATAGTTA
Found at i:52820 original size:24 final size:25
Alignment explanation
Indices: 52788--52838 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
52778 CAAATCCAAT
52788 TCGATCCAAAAAA-ATAACCGAAAA
1 TCGATCCAAAAAACATAACCGAAAA
52812 TCGATCCAAAAAACCGATAACCGAAAA
1 TCGATCCAAAAAA-C-ATAACCGAAAA
52839 AAACCGAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 13 0.54
27 11 0.46
ACGTcount: A:0.55, C:0.24, G:0.10, T:0.12
Consensus pattern (25 bp):
TCGATCCAAAAAACATAACCGAAAA
Found at i:52841 original size:17 final size:16
Alignment explanation
Indices: 52819--52851 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
52809 AAATCGATCC
52819 AAAAAACCGATAACCGA
1 AAAAAACCGA-AACCGA
52836 AAAAAACCGAAACCGA
1 AAAAAACCGAAACCGA
52852 TTTAGTGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.61, C:0.24, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAAAACCGAAACCGA
Found at i:55601 original size:3 final size:3
Alignment explanation
Indices: 55593--55619 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
55583 GTAGGTGTTC
55593 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
55620 TGACAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:57889 original size:22 final size:21
Alignment explanation
Indices: 57864--57955 Score: 89
Period size: 22 Copynumber: 4.3 Consensus size: 21
57854 AAAATGTTAA
*
57864 AAAAATAATATATATAATTTAT
1 AAAAATAAAATAT-TAATTTAT
* *
57886 AAAAGTAAAATATTTA-TT-T
1 AAAAATAAAATATTAATTTAT
*
57905 AAAAATAATATATATAATTTAT
1 AAAAATAAAATAT-TAATTTAT
* *
57927 AAAAGTAAAATATTTATTTATT
1 AAAAATAAAATATTAATTTA-T
57949 AAAAATA
1 AAAAATA
57956 TCAGAAAATG
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
19 12 0.21
20 4 0.07
21 10 0.18
22 30 0.54
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAAATAAAATATTAATTTAT
Found at i:57897 original size:24 final size:24
Alignment explanation
Indices: 57870--57939 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
57860 TTAAAAAAAT
57870 AATATATATAATTTATAAAAGTAA
1 AATATATATAATTTATAAAAGTAA
57894 AATAT-T-T-ATTTA-AAAA-T--
1 AATATATATAATTTATAAAAGTAA
57911 AATATATATAATTTATAAAAGTAA
1 AATATATATAATTTATAAAAGTAA
57935 AATAT
1 AATAT
57940 TTATTTATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
17 5 0.13
18 1 0.03
19 2 0.05
20 9 0.23
21 9 0.23
22 2 0.05
23 1 0.03
24 10 0.26
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (24 bp):
AATATATATAATTTATAAAAGTAA
Found at i:57902 original size:17 final size:17
Alignment explanation
Indices: 57880--57943 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
57870 AATATATATA
57880 ATTTATAAAAGTAAAAT
1 ATTTATAAAAGTAAAAT
*
57897 ATTTATTTAAAAATAATATATAT
1 ATTTA--TAAAAGT-A-A-A-AT
57920 AATTTATAAAAGTAAAAT
1 -ATTTATAAAAGTAAAAT
57938 ATTTAT
1 ATTTAT
57944 TTATTAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
17 11 0.29
18 2 0.05
19 7 0.18
20 2 0.05
21 2 0.05
22 7 0.18
23 2 0.05
24 5 0.13
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
ATTTATAAAAGTAAAAT
Found at i:57904 original size:21 final size:21
Alignment explanation
Indices: 57880--57952 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
57870 AATATATATA
57880 ATTTATAAAAGTAAAATATTT
1 ATTTATAAAAGTAAAATATTT
* *
57901 ATTTA-AAAA-TAATATATATA
1 ATTTATAAAAGTAAAATAT-TT
57921 ATTTATAAAAGTAAAATATTT
1 ATTTATAAAAGTAAAATATTT
57942 ATTTATTAAAA
1 ATTTA-TAAAA
57953 ATATCAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 7 0.16
20 10 0.23
21 15 0.34
22 12 0.27
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
ATTTATAAAAGTAAAATATTT
Found at i:57956 original size:41 final size:41
Alignment explanation
Indices: 57864--57946 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
57854 AAAATGTTAA
57864 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
57905 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
57946 A
1 A
57947 TTAAAAATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (41 bp):
AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
Found at i:59430 original size:3 final size:3
Alignment explanation
Indices: 59424--59475 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
59414 AATATTTTAT
*
59424 TAA TAA TAA TAA TAA CAA TAA TAA TAA TATA TAA T-A TAAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA T-AA TAA TAA
59469 TAA TAA T
1 TAA TAA T
59476 CAAATGAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 4 0.09
3 34 0.79
4 5 0.12
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:59998 original size:113 final size:113
Alignment explanation
Indices: 59786--60478 Score: 761
Period size: 113 Copynumber: 6.1 Consensus size: 113
59776 ATCTCCTTCT
59786 GTGATAGAA-TCAAAC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCA
1 GTGAT-GAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* ** **
59848 GATAAGTTCTTCTCATTGCGAACTTTCTCTGGAAAAGTTGATCCATTGA
65 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAA
* * *
59897 GTAATGAATTCAAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAG
1 GTGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
**
59962 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATACTAATCTATCTCTTTCT
66 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGAT-C----C-A--TC---AA
* ** * * *
60021 GTGAT-AGAGTCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCA
1 GTGATGA-ATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
*
60085 GATGAGTTCTTCTCATTATGAACTTTATCTGGAAAAGTTGATCCATCAA
65 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAA
** * * *
60134 GTGATGAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCTTCTTCAG
1 GTGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * * * *
60199 ATGAGTTCTTCTCATTATGAACTTTAC-CTGGCAATGCTAATCCATCGA
66 ATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAAGTTGATCCATCAA
* * * *
60247 GTGATGAATT-AAAGCAAAAGGTTAAACAAGTTCTTCTCGTTATGAACTTATTCTTCATTCTTCA
1 GTGATGAATTCAAA-CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* * *
60311 GACGAGTTCTTCTCATTATGAACTCTAC-CTGGAAATGTTGATCCATCAA
65 GATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTTGATCCATCAA
* * * * * * *
60360 GTGATGGATTCGAGCGAAATGTTGAACAAATTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAG
1 GTGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * * * * *
60425 ATGAGTTCTTCTTATTATGAACTCTATCTGGCAATGTTGATCTATCAA
66 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAA
*
60473 GCGATG
1 GTGATG
60479 GATTTGAATC
Statistics
Matches: 492, Mismatches: 69, Indels: 40
0.82 0.11 0.07
Matches are distributed among these distances:
110 3 0.01
111 10 0.02
112 40 0.08
113 332 0.67
114 4 0.01
116 2 0.00
118 2 0.00
119 2 0.00
121 1 0.00
123 2 0.00
124 94 0.19
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
GTGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAA
Found at i:60154 original size:237 final size:235
Alignment explanation
Indices: 59710--60468 Score: 927
Period size: 226 Copynumber: 3.3 Consensus size: 235
59700 GTTGAACAAA
* * * * *
59710 TTCTTC-TCCTTTTTCAGATGAATTCTTCTCATTATGAAC-TCCTTCTGGAAATGTTGATTCTGA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC-TCTGGAAAAGTTGA-TCTAA
*
59773 TCTATCTCCTTCTGTGATAGAATCAAAC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTT
64 TCTATCT-CTTCTGTGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTT
* ** * ** *
59837 CTTCC-TCTTCAGATAAGTTCTTCTCATTGCGAACTTTCTCTGGAAAAGTTGATCCATTGAGTAA
128 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTGGAAAAGTTGATCCATCAAGTGA
* * * *
59901 TGAATTCAAACAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
193 TGAATTCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
*
59944 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATACTAAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGAT-CTAAT
* * * * *
60009 CTATCTCTTTCTGTGATAGAGTCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTA
65 CTATCTC-TTCTGTGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
60074 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTGGAAAAGTTGATCCATCAAGTGAT
129 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTGGAAAAGTTGATCCATCAAGTGAT
*
60139 GAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
194 GAATTCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
60181 TTCTTCTCCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CTGG-CAA--TG--CTAAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAAGTTGATCTAAT
* ** * * * *
60240 CCA--TC--GAGTGAT-GAATTAAAGCAAAAGGTTAAACAAGTTCTTCTCGTTATGAACTTATTC
65 CTATCTCTTCTGTGATAGAA-TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
* * * * *
60300 TTCATTCTTCAGACGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGAT
129 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTGGAAAAGTTGATCCATCAAGTGAT
* * *
60365 GGATTCGAGCGAAATGTTGAACAAATTCTTCTCATTATGAAC
194 GAATTCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * * * * *
60407 TTCCTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCTATCTGGCAATGTTGATCTA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCTA
60469 TCAAGCGATG
Statistics
Matches: 456, Mismatches: 55, Indels: 31
0.84 0.10 0.06
Matches are distributed among these distances:
225 2 0.00
226 182 0.40
227 1 0.00
229 4 0.01
231 10 0.02
234 10 0.02
235 69 0.15
236 42 0.09
237 135 0.30
238 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (235 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCTAATC
TATCTCTTCTGTGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
CCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTGGAAAAGTTGATCCATCAAGTGATGA
ATTCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
Found at i:61338 original size:54 final size:54
Alignment explanation
Indices: 61247--61350 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
61237 TATTGGTTCT
* * * * *
61247 TAAAACACTTGACAACACATTCATTATTTCTTGTGGCTTCTGCTCAGATGCTTG
1 TAAAACACTTGAAAACACATTCATCATCTCATATGGCTTCTGCTCAGATGCTTG
* *
61301 TAAAACATTTGAAAACACATTCATCATCTCATATGGCTTCTTCTCAGATG
1 TAAAACACTTGAAAACACATTCATCATCTCATATGGCTTCTGCTCAGATG
61351 TTTGGTCAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (54 bp):
TAAAACACTTGAAAACACATTCATCATCTCATATGGCTTCTGCTCAGATGCTTG
Found at i:65491 original size:9 final size:9
Alignment explanation
Indices: 65477--65524 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
65467 TCAATTTTTC
65477 TTTTTCTTT
1 TTTTTCTTT
65486 TTTTTCTTT
1 TTTTTCTTT
65495 TTTTTC--T
1 TTTTTCTTT
*
65502 TTTTCCTTT
1 TTTTTCTTT
65511 TTTTTCTTT
1 TTTTTCTTT
65520 TTTTT
1 TTTTT
65525 TCAAGTATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 6 0.17
9 29 0.83
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:65503 original size:24 final size:25
Alignment explanation
Indices: 65471--65524 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
65461 CTTGGTTCAA
65471 TTTTTCTTTTT-CTTTTTTTTCTTT
1 TTTTTCTTTTTCCTTTTTTTTCTTT
65495 TTTTTCTTTTTCCTTTTTTTTCTTT
1 TTTTTCTTTTTCCTTTTTTTTCTTT
65520 TTTTT
1 TTTTT
65525 TCAAGTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 11 0.38
25 18 0.62
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (25 bp):
TTTTTCTTTTTCCTTTTTTTTCTTT
Found at i:67317 original size:91 final size:91
Alignment explanation
Indices: 67162--67345 Score: 296
Period size: 91 Copynumber: 2.0 Consensus size: 91
67152 CAGGTGTTTG
* * * **
67162 AGGTTTCTTCAAGGTTACATCTTTCCCATTCATTTTTAAACCTATGGGCCAGTCTTGAATTACCT
1 AGGTTTCTTCAAGGTTACATCTTTCCCATTCATTTTTAAACATATGGGCCAATATCAAATTACCT
*
67227 CTCCTTTTATTTCTTTCTCATTTTTT
66 CTCCTTTTATTTCATTCTCATTTTTT
*
67253 AGGTTTCTTCAGGGTTACATCTTTCCCATTCATTTTTAAACATATGGGCCAATATCAAATTACCT
1 AGGTTTCTTCAAGGTTACATCTTTCCCATTCATTTTTAAACATATGGGCCAATATCAAATTACCT
*
67318 CTCCTTTTATTTCATTCTTATTTTTT
66 CTCCTTTTATTTCATTCTCATTTTTT
67344 AG
1 AG
67346 CATCAGAGAA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.21, C:0.22, G:0.10, T:0.47
Consensus pattern (91 bp):
AGGTTTCTTCAAGGTTACATCTTTCCCATTCATTTTTAAACATATGGGCCAATATCAAATTACCT
CTCCTTTTATTTCATTCTCATTTTTT
Found at i:68359 original size:20 final size:20
Alignment explanation
Indices: 68331--68369 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
68321 GCCAAGATGC
* *
68331 AAATGCAAAAATGAAAATGT
1 AAATACAAAAATAAAAATGT
*
68351 AAATACAAACATAAAAATG
1 AAATACAAAAATAAAAATG
68370 AAAAAATGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.08, G:0.10, T:0.18
Consensus pattern (20 bp):
AAATACAAAAATAAAAATGT
Found at i:68480 original size:15 final size:14
Alignment explanation
Indices: 68447--68484 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
68437 ATAAAAGTAT
68447 AAATGCAAAATGAA
1 AAATGCAAAATGAA
*
68461 AAATGCAAAGATGCA
1 AAATGCAAA-ATGAA
68476 AAATGCAAA
1 AAATGCAAA
68485 TGCATGTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.61, C:0.11, G:0.16, T:0.13
Consensus pattern (14 bp):
AAATGCAAAATGAA
Found at i:68481 original size:7 final size:7
Alignment explanation
Indices: 68447--68488 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
68437 ATAAAAGTAT
68447 AAATGCA
1 AAATGCA
*
68454 AAATGAA
1 AAATGCA
68461 AAATGCA
1 AAATGCA
68468 AAGATGCA
1 AA-ATGCA
68476 AAATGC-
1 AAATGCA
68482 AAATGCA
1 AAATGCA
68489 TGTATGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 6 0.19
7 18 0.58
8 7 0.23
ACGTcount: A:0.57, C:0.12, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:71259 original size:22 final size:21
Alignment explanation
Indices: 71234--71325 Score: 89
Period size: 22 Copynumber: 4.3 Consensus size: 21
71224 AAAACGTTAA
*
71234 AAAAATAATATATATAATTTAT
1 AAAAATAAAATAT-TAATTTAT
* *
71256 AAAATTAAAATATTTA-TT-T
1 AAAAATAAAATATTAATTTAT
*
71275 AAAAATAATATATATAATTTAT
1 AAAAATAAAATAT-TAATTTAT
* *
71297 AAAAGTAAAATATTTATTTATT
1 AAAAATAAAATATTAATTTA-T
71319 AAAAATA
1 AAAAATA
71326 TCAGAAAATG
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
19 12 0.21
20 4 0.07
21 10 0.18
22 30 0.54
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (21 bp):
AAAAATAAAATATTAATTTAT
Found at i:71264 original size:30 final size:29
Alignment explanation
Indices: 71203--71265 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
71193 TCTTAATATT
71203 AAAAAATAAATAAATATTAATAAAACGTTA
1 AAAAAATAAATAAATATTAATAAAAC-TTA
* *
71233 AAAAAATAATATATATAATTTATAAAA-TTA
1 AAAAAATAA-ATAAAT-ATTAATAAAACTTA
71263 AAA
1 AAA
71266 TATTTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 15 0.52
31 5 0.17
32 9 0.31
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (29 bp):
AAAAAATAAATAAATATTAATAAAACTTA
Found at i:71267 original size:24 final size:23
Alignment explanation
Indices: 71231--71309 Score: 80
Period size: 24 Copynumber: 3.6 Consensus size: 23
71221 AATAAAACGT
*
71231 TAAAAAAATAATATATATAATTTA
1 TAAAATAA-AATATATATAATTTA
71255 TAAAATTAAAATAT-T-T-ATTTA
1 TAAAA-TAAAATATATATAATTTA
71276 -AAAAT--AATATATATAATTTA
1 TAAAATAAAATATATATAATTTA
71296 TAAAAGTAAAATAT
1 TAAAA-TAAAATAT
71310 TTATTTATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
17 5 0.11
18 1 0.02
19 2 0.04
20 9 0.20
21 9 0.20
22 2 0.04
23 1 0.02
24 15 0.33
25 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (23 bp):
TAAAATAAAATATATATAATTTA
Found at i:71274 original size:21 final size:20
Alignment explanation
Indices: 71235--71322 Score: 88
Period size: 21 Copynumber: 4.2 Consensus size: 20
71225 AAACGTTAAA
* *
71235 AAAATAATATATATAATTTAT
1 AAAATAAAATAT-TTATTTAT
71256 AAAATTAAAATATTTATTTA-
1 AAAA-TAAAATATTTATTTAT
* *
71276 AAAATAATATATATAATTTAT
1 AAAATAAAATAT-TTATTTAT
71297 AAAAGTAAAATATTTATTTATT
1 AAAA-TAAAATATTTATTTA-T
71319 AAAA
1 AAAA
71323 ATATCAGAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
19 7 0.12
20 10 0.18
21 20 0.36
22 19 0.34
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (20 bp):
AAAATAAAATATTTATTTAT
Found at i:71326 original size:41 final size:41
Alignment explanation
Indices: 71234--71316 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
71224 AAAACGTTAA
*
71234 AAAAATAATATATATAATTTATAAAATTAAAATATTTATTT
1 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
71275 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
1 AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
71316 A
1 A
71317 TTAAAAATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (41 bp):
AAAAATAATATATATAATTTATAAAAGTAAAATATTTATTT
Found at i:71457 original size:4 final size:4
Alignment explanation
Indices: 71448--71472 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
71438 AATAGGATCA
71448 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
71473 TTATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:72068 original size:16 final size:17
Alignment explanation
Indices: 72032--72078 Score: 73
Period size: 16 Copynumber: 2.9 Consensus size: 17
72022 CATGCCATTA
72032 TTCTCATT-TC-CTCTC
1 TTCTCATTCTCTCTCTC
72047 TTCTCATTCTCTCTCT-
1 TTCTCATTCTCTCTCTC
72063 TTCTCATTCTCTCTCT
1 TTCTCATTCTCTCTCT
72079 AACTAAGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.27
16 18 0.60
17 4 0.13
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.55
Consensus pattern (17 bp):
TTCTCATTCTCTCTCTC
Found at i:72844 original size:9 final size:9
Alignment explanation
Indices: 72830--72911 Score: 57
Period size: 9 Copynumber: 8.8 Consensus size: 9
72820 AATAATATTT
72830 TAATAATAA
1 TAATAATAA
72839 TAATAATAA
1 TAATAATAA
72848 TATATAAT-A
1 TA-ATAATAA
72857 TAAATATATAA
1 T-AATA-ATAA
72868 T-ATAAATATA
1 TAAT-AATA-A
72878 TAAT-ATAAA
1 TAATAAT-AA
72887 TATATAAT-A
1 TA-ATAATAA
72896 TAAATAAT-A
1 T-AATAATAA
72905 TAATAAT
1 TAATAAT
72912 CAAATGAAGA
Statistics
Matches: 62, Mismatches: 0, Indels: 23
0.73 0.00 0.27
Matches are distributed among these distances:
8 6 0.10
9 35 0.56
10 15 0.24
11 6 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
TAATAATAA
Found at i:72856 original size:13 final size:13
Alignment explanation
Indices: 72834--72909 Score: 120
Period size: 13 Copynumber: 5.8 Consensus size: 13
72824 ATATTTTAAT
72834 AATA-ATAATA-A
1 AATATATAATATA
72845 TAATATATAATATA
1 -AATATATAATATA
72859 AATATATAATATA
1 AATATATAATATA
72872 AATATATAATATA
1 AATATATAATATA
72885 AATATATAATATA
1 AATATATAATATA
72898 AATAATATAATA
1 AAT-ATATAATA
72910 ATCAAATGAA
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.07
13 48 0.79
14 9 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATATAATATA
Found at i:74739 original size:36 final size:36
Alignment explanation
Indices: 74686--74767 Score: 146
Period size: 36 Copynumber: 2.3 Consensus size: 36
74676 TCGTGAGTTT
*
74686 TCGAGTCGAGTCTAGCTTCAATTTAGAGTTTTTGAG
1 TCGAGTCGAGTCGAGCTTCAATTTAGAGTTTTTGAG
*
74722 TTGAGTCGAGTCGAGCTTCAATTTAGAGTTTTTGAG
1 TCGAGTCGAGTCGAGCTTCAATTTAGAGTTTTTGAG
74758 TCGAGTCGAG
1 TCGAGTCGAG
74768 CTCAACAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.37
Consensus pattern (36 bp):
TCGAGTCGAGTCGAGCTTCAATTTAGAGTTTTTGAG
Found at i:76660 original size:40 final size:40
Alignment explanation
Indices: 76606--76699 Score: 170
Period size: 40 Copynumber: 2.4 Consensus size: 40
76596 TTGTAACTCT
* *
76606 TAATAATTGAAGGATTTAACAATGACCATTCAAAAATTTA
1 TAATAGTTGAAGGATTTAACAATAACCATTCAAAAATTTA
76646 TAATAGTTGAAGGATTTAACAATAACCATTCAAAAATTTA
1 TAATAGTTGAAGGATTTAACAATAACCATTCAAAAATTTA
76686 TAATAGTTGAAGGA
1 TAATAGTTGAAGGA
76700 CTTGTTGATG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.32
Consensus pattern (40 bp):
TAATAGTTGAAGGATTTAACAATAACCATTCAAAAATTTA
Found at i:82546 original size:29 final size:30
Alignment explanation
Indices: 82484--82551 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
82474 CCCCCTAGGA
* * *
82484 GGTTGTTGCTGGTTTTTTGAGGCTTGTATT
1 GGTTGTAGCTGGATGTTTGAGGCTTGTATT
*
82514 GGTTGTAGCTGGATGTTT-AGGTTTGTATT
1 GGTTGTAGCTGGATGTTTGAGGCTTGTATT
82543 GGTTGTAGC
1 GGTTGTAGC
82552 AGTGAGTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.10, C:0.06, G:0.35, T:0.49
Consensus pattern (30 bp):
GGTTGTAGCTGGATGTTTGAGGCTTGTATT
Found at i:85309 original size:17 final size:18
Alignment explanation
Indices: 85280--85318 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
85270 AAATTTCATA
85280 ATAC-CAAATAGGTACCG
1 ATACTCAAATAGGTACCG
85297 ATACTCAAA-AGGTACCG
1 ATACTCAAATAGGTACCG
85314 ATACT
1 ATACT
85319 ACTTTACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (18 bp):
ATACTCAAATAGGTACCG
Found at i:89647 original size:31 final size:31
Alignment explanation
Indices: 89609--89667 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
89599 AGTTGTATGG
*
89609 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAGTATTGCAAAACTAAA
89640 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTGCAAAACT
89668 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTGCAAAACTAAA
Done.