Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002182.1 Hibiscus syriacus cultivar Beakdansim tig00004445_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: 59198
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:6342 original size:45 final size:47
Alignment explanation
Indices: 6275--6380 Score: 135
Period size: 45 Copynumber: 2.3 Consensus size: 47
6265 CCATGCTTTG
*
6275 TTATTCACAAAAATAAATCCTAACCGCATGATATATAATTTGCATGC-
1 TTATTCA-AAAAATAAATCCTAACCGCATGATATATAATTCGCATGCA
* * *
6322 TTATTCAAAAAATAAA-CCTAACCGTATGATATCTAGTTCGCATGCA
1 TTATTCAAAAAATAAATCCTAACCGCATGATATATAATTCGCATGCA
*
6368 TTTATTCGAAAAA
1 -TTATTCAAAAAA
6381 CAAAATAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
45 25 0.48
46 9 0.17
47 18 0.35
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (47 bp):
TTATTCAAAAAATAAATCCTAACCGCATGATATATAATTCGCATGCA
Found at i:8317 original size:20 final size:18
Alignment explanation
Indices: 8275--8317 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
8265 ATTTGGAGGA
*
8275 CTAAAAACCTAAATTATC
1 CTAAAAACCTAAATTACC
8293 CTAAAAACCTAATATATACC
1 CTAAAAACCTAA-AT-TACC
8313 CTAAA
1 CTAAA
8318 TAAAACAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.55
19 2 0.09
20 8 0.36
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (18 bp):
CTAAAAACCTAAATTACC
Found at i:10992 original size:21 final size:21
Alignment explanation
Indices: 10968--11037 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
10958 AGAGGTTAAG
* *
10968 ACCTTTCGATGAAATGACTTA
1 ACCTTTTGATGAAAAGACTTA
* *
10989 ACCTTTTGATTAAAAGACTTC
1 ACCTTTTGATGAAAAGACTTA
* * *
11010 TCCTTTTGATGAAAGGGCTTA
1 ACCTTTTGATGAAAAGACTTA
*
11031 ACATTTT
1 ACCTTTT
11038 CATTAAAGGA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (21 bp):
ACCTTTTGATGAAAAGACTTA
Found at i:13128 original size:23 final size:23
Alignment explanation
Indices: 13090--13146 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
13080 GAAGCTCAAG
* *
13090 ACTCGATTGAAGCTCGATTTTGA
1 ACTCGATTCAAACTCGATTTTGA
* *
13113 GCTTGATTCAAACTCGATTTTGA
1 ACTCGATTCAAACTCGATTTTGA
13136 ACTCGATTCAA
1 ACTCGATTCAA
13147 GCCCGACTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (23 bp):
ACTCGATTCAAACTCGATTTTGA
Found at i:13948 original size:3 final size:3
Alignment explanation
Indices: 13940--13996 Score: 89
Period size: 3 Copynumber: 19.0 Consensus size: 3
13930 TTTTATTTAT
*
13940 TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA -TA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
13985 TTA TTA TTA TTA
1 TTA TTA TTA TTA
13997 AAAAAGTAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:13966 original size:21 final size:21
Alignment explanation
Indices: 13932--13996 Score: 98
Period size: 21 Copynumber: 3.1 Consensus size: 21
13922 TTTACCCATT
*
13932 TTATTTAT-TTATTATTATTA
1 TTATATATATTATTATTATTA
13952 TTATA-ATTATTATTATTATTA
1 TTATATA-TATTATTATTATTA
13973 TTATATATATTATTATTATTA
1 TTATATATATTATTATTATTA
13994 TTA
1 TTA
13997 AAAAAGTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 1 0.02
20 5 0.12
21 34 0.83
22 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATATATATTATTATTATTA
Found at i:15632 original size:12 final size:12
Alignment explanation
Indices: 15600--15632 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
15590 TATTATAAAA
*
15600 AAATTATAATTT
1 AAATTATTATTT
15612 AAATT-TTATTT
1 AAATTATTATTT
15623 AAATTATTAT
1 AAATTATTAT
15633 AATATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AAATTATTATTT
Found at i:26863 original size:15 final size:14
Alignment explanation
Indices: 26843--26941 Score: 92
Period size: 15 Copynumber: 6.6 Consensus size: 14
26833 ATTATGTTTG
26843 AAGAAAAAAAATGAA
1 AAGAAAAAAAA-GAA
26858 AAGAAAAAAAAGAGA
1 AAGAAAAAAAAGA-A
*
26873 AAGAAAAGAAAAAAATA
1 AAG-AAA-AAAAAGA-A
26890 GAAGAAAAAAAAGAA
1 -AAGAAAAAAAAGAA
*
26905 AAGAAAAAAGAGAA
1 AAGAAAAAAAAGAA
* *
26919 GAAGAAGAAAAA-AC
1 -AAGAAAAAAAAGAA
26933 AAGAAAAAA
1 AAGAAAAAA
26942 GAAAAAAAGG
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
13 8 0.11
14 16 0.23
15 25 0.35
16 9 0.13
17 10 0.14
18 3 0.04
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.02
Consensus pattern (14 bp):
AAGAAAAAAAAGAA
Found at i:26866 original size:14 final size:15
Alignment explanation
Indices: 26843--26949 Score: 83
Period size: 17 Copynumber: 6.7 Consensus size: 15
26833 ATTATGTTTG
26843 AAGAAAAAAAATGA-A
1 AAGAAAAAAAA-GAGA
26858 AAGAAAAAAAAGAGA
1 AAGAAAAAAAAGAGA
* *
26873 AAGAAAAGAAAAAAATA
1 AAG-AAA-AAAAAGAGA
26890 GAAGAAAAAAAAGA-A
1 -AAGAAAAAAAAGAGA
*
26905 AAGAAAAAAGAGAAGAA
1 AAGAAAAAAAAG-AG-A
*
26922 GAAGAAAAAACAAGAAAA
1 -AAGAAAAAA-AAG-AGA
26940 AAGAAAAAAA
1 AAGAAAAAAA
26950 GGGGGGTCAA
Statistics
Matches: 77, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
14 13 0.17
15 17 0.22
16 10 0.13
17 20 0.26
18 13 0.17
19 4 0.05
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.02
Consensus pattern (15 bp):
AAGAAAAAAAAGAGA
Found at i:26868 original size:9 final size:9
Alignment explanation
Indices: 26856--26949 Score: 86
Period size: 9 Copynumber: 10.3 Consensus size: 9
26846 AAAAAAAATG
26856 AAAAGAAAA
1 AAAAGAAAA
26865 AAAAGAGAAA
1 AAAAGA-AAA
26875 GAAAAGAAAA
1 -AAAAGAAAA
*
26885 AAATAGAAGA
1 AAA-AGAAAA
*
26895 AAAA-AAAG
1 AAAAGAAAA
26903 AAAAGAAAA
1 AAAAGAAAA
* *
26912 AAGAGAAGA
1 AAAAGAAAA
*
26921 AGAAGAAAA
1 AAAAGAAAA
26930 AACAAG--AA
1 AA-AAGAAAA
26938 AAAAGAAAA
1 AAAAGAAAA
26947 AAA
1 AAA
26950 GGGGGGTCAA
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
7 3 0.04
8 10 0.15
9 32 0.47
10 17 0.25
11 6 0.09
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.01
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:26898 original size:47 final size:46
Alignment explanation
Indices: 26842--26948 Score: 130
Period size: 45 Copynumber: 2.3 Consensus size: 46
26832 TATTATGTTT
*
26842 GAAGAAAAAAAATGAAAAGAAAAAAAAGAGAAAGAA-AAGAAAAAAATA
1 GAAGAAAAAAAAAGAAAAG--AAAAAAGAG-AAGAAGAAGAAAAAAATA
26890 GAAG-AAAAAAAAGAAAAGAAAAAAGAGAAGAAGAAGAAAAAACA-A
1 GAAGAAAAAAAAAGAAAAGAAAAAAGAGAAGAAGAAGAAAAAA-ATA
*
26935 GAAAAAAGAAAAAA
1 GAAGAAA-AAAAAA
26949 AGGGGGGTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
44 5 0.09
45 22 0.42
46 3 0.06
47 19 0.36
48 4 0.08
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.02
Consensus pattern (46 bp):
GAAGAAAAAAAAAGAAAAGAAAAAAGAGAAGAAGAAGAAAAAAATA
Found at i:26914 original size:45 final size:47
Alignment explanation
Indices: 26842--26931 Score: 141
Period size: 45 Copynumber: 1.9 Consensus size: 47
26832 TATTATGTTT
26842 GAAGAAAAAAAATGAAAAGAAAAAAAAGAGAAAGAA-AAGAAAAAAATA
1 GAAGAAAAAAAATGAAAAG-AAAAAAAGAG-AAGAAGAAGAAAAAAATA
26890 GAAGAAAAAAAA-GAAAAG-AAAAAAGAGAAGAAGAAGAAAAAA
1 GAAGAAAAAAAATGAAAAGAAAAAAAGAGAAGAAGAAGAAAAAA
26932 CAAGAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
44 5 0.12
45 18 0.44
47 6 0.15
48 12 0.29
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (47 bp):
GAAGAAAAAAAATGAAAAGAAAAAAAGAGAAGAAGAAGAAAAAAATA
Found at i:26918 original size:26 final size:28
Alignment explanation
Indices: 26867--26943 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
26857 AAAGAAAAAA
*
26867 AAGAGAAAGAAAAGAAAAAAATAGAAGAA-
1 AAGA-AAAGAAAAG-AAAAAAGAGAAGAAG
26896 AA-AAAAGAAAAGAAAAAAGAGAAGAAG
1 AAGAAAAGAAAAGAAAAAAGAGAAGAAG
26923 AAGAAAA-AACAAGAAAAAAGA
1 AAGAAAAGAA-AAGAAAAAAGA
26944 AAAAAAGGGG
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
26 13 0.30
27 13 0.30
28 16 0.36
29 2 0.05
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (28 bp):
AAGAAAAGAAAAGAAAAAAGAGAAGAAG
Found at i:27316 original size:20 final size:22
Alignment explanation
Indices: 27280--27319 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
27270 TATTTATTAA
27280 TAAATTCTAAGTTTATTTTCTC
1 TAAATTCTAAGTTTATTTTCTC
27302 TAAATTC-AA-TTTATTTTC
1 TAAATTCTAAGTTTATTTTC
27320 GAAAATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (22 bp):
TAAATTCTAAGTTTATTTTCTC
Found at i:27829 original size:114 final size:114
Alignment explanation
Indices: 27629--28080 Score: 751
Period size: 114 Copynumber: 4.0 Consensus size: 114
27619 GTGCTACGTT
*
27629 CTCATAGTAGGAATATGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGGAATACGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
27694 ATTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTG
66 ATTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTG
*
27743 CTCATAGTAGGAATACGAAGACCCAATAGCATCTTCTGGAAGTGTACTTTGAGTTATCTGATCTG
1 CTCATAGTAGGAATACGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
*
27808 ATTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATTAATTTG
66 ATTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTG
27857 CTCATAGTAGGAATACGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGGAATACGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
27922 ATTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTG
66 ATTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTG
* * * * * *
27971 CTCATAGTAGAAATAAGAAGACCCAATAACATCTTTTGGAAGTTTTCTTTGAGTCATCTGATCTG
1 CTCATAGTAGGAATACGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * * * * * * *
28036 GTTCGGTAGGAACCACAAAACCAATCATTAGAATTAAAAGATGAA
66 ATTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAA
28081 CTGCATGGTC
Statistics
Matches: 319, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 319 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (114 bp):
CTCATAGTAGGAATACGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
ATTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTG
Found at i:29263 original size:228 final size:223
Alignment explanation
Indices: 28767--29329 Score: 783
Period size: 225 Copynumber: 2.5 Consensus size: 223
28757 ACAAAGATTT
* ** * *
28767 AAATCCATCATTCAATGGATCAACAGTACCAGTAGAAGTTCTTAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTCGATGGATCAACTTTTCCAG-AGAAGTTCATAATGAGAAGAACTCATCTGAAG
*
28832 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATG
65 AAGAAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATG
** * *
28897 GATCAACATTGCCAGGTAAAGTTCCTAATGAGAAGAACTCGTCATCTGAAGAAGAAGAAATTCAT
130 GATCAACATCCCCAGGAAAAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGAAGAAATTCAT
*
28962 AATGAGAAGAATTTGTTCAACCTTTTACTC
194 AATGAGAAGAACTTGTTCAACCTTTTACTC
* * *
28992 AAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTCGATGGATCAACTTTTCCAG-AGAAGTTCATAATGAGAAGAACTCATCTGAAG
29057 AAGAAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATG
65 AAGAAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATG
* *
29122 GATCAGCATCCCCAGTGAAAGAGTTCATAATGAGAAGAA-C-TCATCTGAAAAAGGAAGAAGAAG
130 GATCAACATCCCCAG-GAAA-AGTTCATAATGAGAAGAACCGTCATCTG---AA-GAAGAAGAAA
*
29185 TTCATAATGAGAAGAACTTGTTCAA-CTTTTCTCTC
189 TTCATAATGAGAAGAACTTGTTCAACCTTTT-ACTC
* * *
29220 GAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTCGATGGATCAACTTTTCCAGAGA-AGTTCATAATGAGAAGAACTCATCTGAAG
** *
29285 AA-AGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTG
65 AAGA-AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
29330 CATGACTCTA
Statistics
Matches: 302, Mismatches: 27, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
224 7 0.02
225 133 0.44
226 3 0.01
227 27 0.09
228 132 0.44
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (223 bp):
AAATCCATCATTCGATGGATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGAAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGG
ATCAACATCCCCAGGAAAAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGAAGAAATTCATAA
TGAGAAGAACTTGTTCAACCTTTTACTC
Found at i:29343 original size:113 final size:113
Alignment explanation
Indices: 28772--29330 Score: 688
Period size: 113 Copynumber: 4.9 Consensus size: 113
28762 GATTTAAATC
** * * * *
28772 CATCATTCAATGGATCAACAGTACCAGTAG-AAGTTCTTAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTTGATGGATCAACATTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG
*
28836 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
65 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* *
28885 CATCATTTGATGGATCAACATTGCCAG-GTAAAGTTCCTAATGAGAAGAACTCGTCATCTGAAG-
1 CATCATTTGATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGA
* ** *
28948 AAGAAG-A-AA-TTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATC
62 AAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* * *
28997 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAG-AAGA
1 CATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-
*
29061 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
65 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* ** *
29110 CATCATTTGATGGATCAGCATCCCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAA-AAA
1 CATCATTTGATGGATCAACATTTCCAGAG-AA-AGTTCATAATGAGAAGAACTCATCTGAAGAAA
*
29174 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT-CTCTCGAATT
64 -GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCT-T-GAATT
* * * *
29225 CATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
** *
29290 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTGC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
29331 ATGACTCTAT
Statistics
Matches: 389, Mismatches: 38, Indels: 36
0.84 0.08 0.08
Matches are distributed among these distances:
109 13 0.03
110 4 0.01
111 2 0.01
112 80 0.21
113 164 0.42
114 18 0.05
115 97 0.25
116 11 0.03
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
CATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
Found at i:29401 original size:124 final size:119
Alignment explanation
Indices: 29245--29473 Score: 320
Period size: 124 Copynumber: 1.9 Consensus size: 119
29235 TGGATCAACT
* * *
29245 TTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAGAGTTCACAATGAGAAGAACTCATCTGAAG-AAGAAG-A-AA-TTCACAATAAGA
*
29310 AGAGCTTGTTCGACCTTTTGC-ATGACT-CTATCACAGAAGGAGATATATCATCATCAGCA
62 AGAGCTTGTTCAACC-TTTGCTA-GACTAC-ATCACAGAAGGAGATATATCATCATCAGCA
29369 TTTCCAGA-AGAAGTTCACAATGAGAAGAACTCATCTGAAGAAGAAGAAATTCACAATAAGAAGA
1 TTTCCAGAGAG-AGTTCACAATGAGAAGAACTCATCTGAAGAAGAAGAAATTCACAATAAGAAGA
*
29433 GCTTGTTCAACCTTTGCTAGATTACATCACAGAAGGAGATA
65 GCTTGTTCAACCTTTGCTAGACTACATCACAGAAGGAGATA
29474 AATTGTCATC
Statistics
Matches: 97, Mismatches: 5, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
119 24 0.25
120 26 0.27
121 2 0.02
122 1 0.01
123 8 0.08
124 36 0.37
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (119 bp):
TTTCCAGAGAGAGTTCACAATGAGAAGAACTCATCTGAAGAAGAAGAAATTCACAATAAGAAGAG
CTTGTTCAACCTTTGCTAGACTACATCACAGAAGGAGATATATCATCATCAGCA
Found at i:29684 original size:3 final size:3
Alignment explanation
Indices: 29676--29726 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
29666 TTTTATTTAT
*
29676 TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA -TA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
29721 TTA TTA
1 TTA TTA
29727 AAAAAATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:29699 original size:18 final size:17
Alignment explanation
Indices: 29672--29726 Score: 85
Period size: 18 Copynumber: 3.2 Consensus size: 17
29662 CCCATTTTAT
29672 TTAT-TTATTATTATTA
1 TTATATTATTATTATTA
29688 TTATAATTATTATTATTA
1 TTAT-ATTATTATTATTA
29706 TTATATATATTATTATTA
1 TTATAT-TATTATTATTA
29724 TTA
1 TTA
29727 AAAAAATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.11
17 2 0.06
18 30 0.83
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATATTATTATTATTA
Found at i:35613 original size:14 final size:14
Alignment explanation
Indices: 35580--35616 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
35570 ATATTTAATT
35580 ATAAATTTTAAAAA
1 ATAAATTTTAAAAA
35594 ATTAAATTTTAAAAA
1 A-TAAATTTTAAAAA
35609 ATAAATTT
1 ATAAATTT
35617 ATTTCATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAAATTTTAAAAA
Found at i:36814 original size:15 final size:17
Alignment explanation
Indices: 36778--36815 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
36768 CTCCCTTAAA
36778 ATTTTAAATTAGTATAT
1 ATTTTAAATTAGTATAT
36795 ATTTTAAA-TA-TATAT
1 ATTTTAAATTAGTATAT
*
36810 TTTTTA
1 ATTTTA
36816 TTTTCAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 2 0.10
17 8 0.40
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTAGTATAT
Found at i:37166 original size:43 final size:43
Alignment explanation
Indices: 37105--37191 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
37095 TCCCATGGGA
*
37105 TGGGAATCCCACATTCCCATGTTTGGTTGGTCGGGAATCTCAT
1 TGGGAATCCCACAATCCCATGTTTGGTTGGTCGGGAATCTCAT
37148 TGGGAATCCCACAATCCCATGTTTGGTTGGTCGGGAATCTCAT
1 TGGGAATCCCACAATCCCATGTTTGGTTGGTCGGGAATCTCAT
37191 T
1 T
37192 CCCGATAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (43 bp):
TGGGAATCCCACAATCCCATGTTTGGTTGGTCGGGAATCTCAT
Found at i:37572 original size:37 final size:36
Alignment explanation
Indices: 37497--37572 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
37487 TTTTTATATT
*
37497 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
37533 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
37570 TTT
1 TTT
37573 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:38732 original size:18 final size:18
Alignment explanation
Indices: 38711--38746 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38701 GGGTGGTGGA
*
38711 GGTGGGGGAGGTGGAGGT
1 GGTGGGGGAGGAGGAGGT
*
38729 GGTGGTGGAGGAGGAGGT
1 GGTGGGGGAGGAGGAGGT
38747 AATTGTGGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.69, T:0.17
Consensus pattern (18 bp):
GGTGGGGGAGGAGGAGGT
Found at i:40123 original size:8 final size:8
Alignment explanation
Indices: 40102--40140 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
40092 AGATACAATA
40102 AAAATAAAT
1 AAAAT-AAT
*
40111 AAAATATT
1 AAAATAAT
40119 AAAATAAT
1 AAAATAAT
40127 AAAATTAAT
1 AAAA-TAAT
40136 AAAAT
1 AAAAT
40141 TAAAGATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 14 0.52
9 13 0.48
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
AAAATAAT
Found at i:40138 original size:17 final size:17
Alignment explanation
Indices: 40102--40140 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
40092 AGATACAATA
*
40102 AAAATAAATAAAATATT
1 AAAATAAATAAAATAAT
40119 AAAAT-AATAAAATTAAT
1 AAAATAAATAAAA-TAAT
40136 AAAAT
1 AAAAT
40141 TAAAGATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAATAAATAAAATAAT
Found at i:40141 original size:9 final size:9
Alignment explanation
Indices: 40102--40143 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
40092 AGATACAATA
*
40102 AAAATAAAT
1 AAAATTAAT
*
40111 AAAA-TATT
1 AAAATTAAT
40119 AAAA-TAAT
1 AAAATTAAT
40127 AAAATTAAT
1 AAAATTAAT
40136 AAAATTAA
1 AAAATTAA
40144 AGATCAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 13 0.45
9 16 0.55
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAATTAAT
Found at i:41974 original size:83 final size:82
Alignment explanation
Indices: 41717--42323 Score: 777
Period size: 82 Copynumber: 7.4 Consensus size: 82
41707 GATGGAAATA
* * * * * **
41717 TGCTCCACTATACATT-AAGGGAAATCATACTTGATCTGTGTCTCTTTTTCGGGTAAACAGATCA
1 TGCTCCACTATTCATTCAGGGGAGATCAGACTTGATCTGTGCCTCTTTTTCGGGTAGTCAGATCA
41781 ATTTTGGAAGACGTGTC
66 ATTTTGGAAGACGTGTC
* * * * *
41798 TGCTCCACTATTAATTCAGGGAAGATCAAACTTAATCTGTGCCTCTTTTTCAGGTAGTCAGATCA
1 TGCTCCACTATTCATTCAGGGGAGATCAGACTTGATCTGTGCCTCTTTTTCGGGTAGTCAGATCA
* * *
41863 ATTTTGAAAGATGTGTA
66 ATTTTGGAAGACGTGTC
* * * * * *
41880 TGCCCCGCTATTCATTCAGGGGAGATAAAACTTGATATGTGCCTCTTTTTTTGGGTAGTCAGATC
1 TGCTCCACTATTCATTCAGGGGAGATCAGACTTGATCTGTGCCTC-TTTTTCGGGTAGTCAGATC
41945 AATTTTGGAAGACGTGTC
65 AATTTTGGAAGACGTGTC
* * *
41963 TGCTCCACTATTCATTCAGGGGAGATTAGACTTGAGCTGTGCCTCTTTTTTCGGGTAGTCAAATC
1 TGCTCCACTATTCATTCAGGGGAGATCAGACTTGATCTGTGCCTC-TTTTTCGGGTAGTCAGATC
*
42028 AATTTTGGAAGACGAGTC
65 AATTTTGGAAGACGTGTC
* * *
42046 TTCTCCACTATTCATTCAGGGGAGATCATG-CTTGATCTGTGCCTCTTTTTTGAGTAGTCAGATC
1 TGCTCCACTATTCATTCAGGGGAGATCA-GACTTGATCTGTGCCTCTTTTTCGGGTAGTCAGATC
*
42110 AATTTTGGAAGATGTGTC
65 AATTTTGGAAGACGTGTC
* * * * * * *
42128 TACTCCTCTATTCATTCAAGGGAGATTAGACTTGATTTGTACATCTTTTTCGGGTAGTCAGATCA
1 TGCTCCACTATTCATTCAGGGGAGATCAGACTTGATCTGTGCCTCTTTTTCGGGTAGTCAGATCA
*
42193 ATTTTGGAAGACGGGTC
66 ATTTTGGAAGACGTGTC
* * * **
42210 TGCTCCACTATTCATTCAGAGGAGATTAGACTTGATCTATGCCTCTTTTTCAAGTAGTCAGATCA
1 TGCTCCACTATTCATTCAGGGGAGATCAGACTTGATCTGTGCCTCTTTTTCGGGTAGTCAGATCA
*
42275 ATTTTGGAAGACGAGTC
66 ATTTTGGAAGACGTGTC
*
42292 TGCTCCACTATTCATTCAGGGGAGATTAGACT
1 TGCTCCACTATTCATTCAGGGGAGATCAGACT
42324 CGAGATTGAT
Statistics
Matches: 456, Mismatches: 66, Indels: 7
0.86 0.12 0.01
Matches are distributed among these distances:
81 15 0.03
82 294 0.64
83 146 0.32
84 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.35
Consensus pattern (82 bp):
TGCTCCACTATTCATTCAGGGGAGATCAGACTTGATCTGTGCCTCTTTTTCGGGTAGTCAGATCA
ATTTTGGAAGACGTGTC
Found at i:42414 original size:90 final size:89
Alignment explanation
Indices: 42290--43121 Score: 914
Period size: 90 Copynumber: 9.4 Consensus size: 89
42280 GGAAGACGAG
* * * *
42290 TCTGCTCCACTATTCATTCAGGGGAGATTAGACTCGAGATTGATTTGCTTCACTACTCTTTCAAG
1 TCTGCTCCACTACTCTTTC-GGGGAGATCAGACTCGAGATTGATTTGCTTCACTACTCTTTCATG
42355 AAGGCCAATATCTGAAATAAGAAGAA
65 AAGGCCAA-ATCTGAAATAAGAAGAA
** * * * * * **
42381 TCTATTCCACTACTCTCTCGGGGAGATCAGACTCGAGATTAATTTTCTTTAATACTCTTTTGTGA
1 TCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTGCTTCACTACTCTTTCATGA
* *
42446 AGGACAACATCTGAAATGAGAAGAA
66 AGGCCAA-ATCTGAAATAAGAAGAA
* * * *
42471 TCTGTTCCACTACTCTTTCAGGGAGATCAGACTCGAGATTTATTTGCTTCACTGCTCTTTCATGA
1 TCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTGCTTCACTACTCTTTCATGA
*
42536 AGGCCAAATATGAAATAAGAAGAA
66 AGGCCAAATCTGAAATAAGAAGAA
* * * * *
42560 TCTGCTCCTCTACTCTTCCGGGGAGATCGGACTCAAGATTGATTTGCTTCACTAATCTTTCATGA
1 TCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTGCTTCACTACTCTTTCATGA
* * *
42625 AGGACAACATCTGAAATGAGAAAAA
66 AGGCCAA-ATCTGAAATAAGAAGAA
** * *
42650 TCTATTCCACTACTCTTTCGGGGAGATCAGACTTGAGATTGATTTGCTTCACTACTCTTTCGTGA
1 TCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTGCTTCACTACTCTTTCATGA
* * *
42715 AGGCCTACATATGATATAAGAAGAA
66 AGGCC-AAATCTGAAATAAGAAGAA
* * * *
42740 TCTGCTCCTCTACTTTTTCGGGGAGATCAGACTCAAGAATGATTTGCTTCACTACTCTTTCATGA
1 TCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTGCTTCACTACTCTTTCATGA
*
42805 AGGCCAACATCTGAAATGAGAAGAA
66 AGGCCAA-ATCTGAAATAAGAAGAA
* *
42830 TCTGTTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTGCTTCATTACTCTTTCATGA
1 TCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTGCTTCACTACTCTTTCATGA
*
42895 AAGCCAAATCTGAAATAAGAAGAA
66 AGGCCAAATCTGAAATAAGAAGAA
* * * * *
42919 TCTGCTCCTCTACT-TTTCCAGGGAGATCAGACTCGAGATTGATTTGATTCGCTGCT-TCTTCA-
1 TCTGCTCCACTACTCTTT-CGGGGAGATCAGACTCGAGATTGATTTGCTTCACTACTCT-TTCAT
* * *
42981 GAAAGACTAAATCTGAAATAAAAAG-A
64 G-AAGGCCAAATCTGAAATAAGAAGAA
* * * * * * *
43007 -CT-CT--ACT-CT-TCT-GAGGAGATCATACTCGAGATTGATTTGATTCGCTGCT-TCTTCAGG
1 TCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTGCTTCACTACTCT-TTCATG
* *
43064 AAGACCAAATATGAAATAAGAAGAA
65 AAGGCCAAATCTGAAATAAGAAGAA
* * * *
43089 TATGCTCCTCTACTCTTCCGGGGATATCAGACT
1 TCTGCTCCACTACTCTTTCGGGGAGATCAGACT
43122 TTCTTTATGA
Statistics
Matches: 623, Mismatches: 103, Indels: 32
0.82 0.14 0.04
Matches are distributed among these distances:
81 60 0.10
82 2 0.00
83 5 0.01
84 4 0.01
86 4 0.01
87 4 0.01
88 7 0.01
89 173 0.28
90 349 0.56
91 15 0.02
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (89 bp):
TCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTGCTTCACTACTCTTTCATGA
AGGCCAAATCTGAAATAAGAAGAA
Found at i:42789 original size:269 final size:268
Alignment explanation
Indices: 42290--43121 Score: 995
Period size: 269 Copynumber: 3.1 Consensus size: 268
42280 GGAAGACGAG
* * * *
42290 TCTGCTCCACTATTCATTCAGGGGAGATTAGACTCGAGATTGATTTGCTTCACTACTCTTTCAAG
1 TCTGCTCCACTACTC-TTCCGGGGAGATCAGACTCGAGATTGATTTGCTTCACTACTCTTTCATG
*
42355 AAGGCCAATATCTGAAATAAGAAGAATCTATTCCACTACTCTCTCGGGGAGATCAGACTCGAGAT
65 AAGGCCAA-ATCTGAAATAAGAAGAATCTATTCCACTACTCTTTCGGGGAGATCAGACTCGAGAT
* * * * * * * *
42420 TAATTTTCTTTAATACTCTTTTGTGAAGGACAACATCTGAAATGAGAAGAATCTGTTCCACTACT
129 TGATTTGCTTCACTACTCTTTCGTGAAGGACTACATCTGAAATAAGAAGAATCTGCTCCACTACT
* * *
42485 CTTTCAGGGAGATCAGACTCGAGATTTATTTGCTTCACTGCTCTTTCATGAAGGCCAAATATGAA
194 TTTTCGGGGAGATCAGACTCGAGATTGATTTGCTTCACTGCTCTTTCATGAAGGCCAAATATGAA
42550 ATAAGAAGAA
259 ATAAGAAGAA
* * * *
42560 TCTGCTCCTCTACTCTTCCGGGGAGATCGGACTCAAGATTGATTTGCTTCACTAATCTTTCATGA
1 TCTGCTCCACTACTCTTCCGGGGAGATCAGACTCGAGATTGATTTGCTTCACTACTCTTTCATGA
* * * *
42625 AGGACAACATCTGAAATGAGAAAAATCTATTCCACTACTCTTTCGGGGAGATCAGACTTGAGATT
66 AGGCCAA-ATCTGAAATAAGAAGAATCTATTCCACTACTCTTTCGGGGAGATCAGACTCGAGATT
* * * *
42690 GATTTGCTTCACTACTCTTTCGTGAAGGCCTACATATGATATAAGAAGAATCTGCTCCTCTACTT
130 GATTTGCTTCACTACTCTTTCGTGAAGGACTACATCTGAAATAAGAAGAATCTGCTCCACTACTT
* * * *
42755 TTTCGGGGAGATCAGACTCAAGAATGATTTGCTTCACTACTCTTTCATGAAGGCCAACATCTGAA
195 TTTCGGGGAGATCAGACTCGAGATTGATTTGCTTCACTGCTCTTTCATGAAGGCCAA-ATATGAA
*
42820 ATGAGAAGAA
259 ATAAGAAGAA
* * *
42830 TCTGTTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTGCTTCATTACTCTTTCATGA
1 TCTGCTCCACTACTCTTCCGGGGAGATCAGACTCGAGATTGATTTGCTTCACTACTCTTTCATGA
* ** * *
42895 AAGCCAAATCTGAAATAAGAAGAATCTGCTCCTCTACT-TTTCCAGGGAGATCAGACTCGAGATT
66 AGGCCAAATCTGAAATAAGAAGAATCTATTCCACTACTCTTT-CGGGGAGATCAGACTCGAGATT
* * * * * * *
42959 GATTTGATTCGCTGCT-TCTTC-AGAAAGACTAAATCTGAAATAAAAAG-A-CT-CT--ACT-C-
130 GATTTGCTTCACTACTCT-TTCGTGAAGGACTACATCTGAAATAAGAAGAATCTGCTCCACTACT
* * * * * * *
43015 TTCT-GAGGAGATCATACTCGAGATTGATTTGATTCGCTGCT-TCTTCAGGAAGACCAAATATGA
194 TTTTCGGGGAGATCAGACTCGAGATTGATTTGCTTCACTGCTCT-TTCATGAAGGCCAAATATGA
43078 AATAAGAAGAA
258 AATAAGAAGAA
* * *
43089 TATGCTCCTCTACTCTTCCGGGGATATCAGACT
1 TCTGCTCCACTACTCTTCCGGGGAGATCAGACT
43122 TTCTTTATGA
Statistics
Matches: 480, Mismatches: 78, Indels: 19
0.83 0.14 0.03
Matches are distributed among these distances:
259 44 0.09
260 42 0.09
261 3 0.01
262 1 0.00
263 2 0.00
265 2 0.00
266 2 0.00
267 1 0.00
268 23 0.05
269 269 0.56
270 91 0.19
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (268 bp):
TCTGCTCCACTACTCTTCCGGGGAGATCAGACTCGAGATTGATTTGCTTCACTACTCTTTCATGA
AGGCCAAATCTGAAATAAGAAGAATCTATTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTG
ATTTGCTTCACTACTCTTTCGTGAAGGACTACATCTGAAATAAGAAGAATCTGCTCCACTACTTT
TTCGGGGAGATCAGACTCGAGATTGATTTGCTTCACTGCTCTTTCATGAAGGCCAAATATGAAAT
AAGAAGAA
Found at i:43279 original size:62 final size:62
Alignment explanation
Indices: 43201--43740 Score: 665
Period size: 62 Copynumber: 8.6 Consensus size: 62
43191 ATGAATATCA
* * * *
43201 AATAAGAAAAGTTGACTTCTCTTCACGAGGAAATCAAGGATTGACTCTACTGGGGAGTCATG
1 AATAACAAAGGTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGG
* *
43263 AATAATAAAGGTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGTGGAGTCAGG
1 AATAACAAAGGTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGG
* * * * *
43325 AATAATAAAGTTTGACTTCTCTTTATGAGAAAGTCAAGGATTGACTCTACT-GGGAGTCAGG
1 AATAACAAAGGTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGG
* * **
43386 AATAACAAAGGTTGACTTCTCTTCACGAGGAAGTCAAAGATTGACTCTATTAAGGAGTCAGG
1 AATAACAAAGGTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGG
* * * * * * *
43448 AATAACAAAGGTTGTCTTCTCTTCATGAGAAAGTCAAGGATTAACTCATCTTCATGAAGAAGTCA
1 AATAACAAAGGTTGACTTCTCTTCACGAGGAAGTCAAGGATTGA--C-TCTAC-TG-GGGAGTC-
43513 AGG
60 AGG
* ** * * * *
43516 -ATAACAAAGATTGACTTCTCTTCATTAGAAAGTCAAGGATTGACTATACTGAGGAGTCAAG
1 AATAACAAAGGTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGG
* * *
43577 AATAACAAAGTTTGAGTTCTCTTCACGAGGAAGTCAAGGATTGACTCTA-AGAGGGAGTCAGG
1 AATAACAAAGGTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTG-GGGAGTCAGG
* *
43639 AATAACAAAGGTTGACTTCTCTTCACAAGGAAGTCAAGGATTGACTCTATTGGGGAGTCAGG
1 AATAACAAAGGTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGG
*
43701 AATAATC-AAGGTTGACTTCTCTTCATGAGGAAGTCAAGGA
1 AATAA-CAAAGGTTGACTTCTCTTCACGAGGAAGTCAAGGA
43741 ATAGAAAACA
Statistics
Matches: 417, Mismatches: 50, Indels: 22
0.85 0.10 0.04
Matches are distributed among these distances:
61 56 0.13
62 300 0.72
63 4 0.01
64 4 0.01
65 4 0.01
66 1 0.00
67 45 0.11
68 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.27
Consensus pattern (62 bp):
AATAACAAAGGTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCAGG
Found at i:43722 original size:253 final size:252
Alignment explanation
Indices: 43264--43740 Score: 740
Period size: 253 Copynumber: 1.9 Consensus size: 252
43254 GGAGTCATGA
* * * * * *
43264 ATAATAAAGGTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCTACTGTGGAGTCAGGAATA
1 ATAACAAAGATTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTATACTGAGGAGTCAAGAATA
* * * *
43329 ATAAAGTTTGACTTCTCTTTATGAGAAAGTCAAGGATTGACTCTACTGGGAGTCAGGAATAACAA
66 ACAAAGTTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTCTACAGGGAGTCAGGAATAACAA
*
43394 AGGTTGACTTCTCTTCACGAGGAAGTCAAAGATTGACTCTATTAAGGAGTCAGGAATAACAAAGG
131 AGGTTGACTTCTCTTCACAAGGAAGTCAAAGATTGACTCTATTAAGGAGTCAGGAATAACAAAGG
*
43459 TTGTCTTCTCTTCATGAGAAAGTCAAGGATTAACTCATCTTCATGAAGAAGTCAAGG
196 TTGACTTCTCTTCATGAGAAAGTCAAGGATTAACTCATCTTCATGAAGAAGTCAAGG
**
43516 ATAACAAAGATTGACTTCTCTTCATTAGAAAGTCAAGGATTGACTATACTGAGGAGTCAAGAATA
1 ATAACAAAGATTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTATACTGAGGAGTCAAGAATA
* * *
43581 ACAAAGTTTGAGTTCTCTTCACGAGGAAGTCAAGGATTGACTCTAAGAGGGAGTCAGGAATAACA
66 ACAAAGTTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTCT-ACAGGGAGTCAGGAATAACA
* **
43646 AAGGTTGACTTCTCTTCACAAGGAAGTCAAGGATTGACTCTATTGGGGAGTCAGGAATAATC-AA
130 AAGGTTGACTTCTCTTCACAAGGAAGTCAAAGATTGACTCTATTAAGGAGTCAGGAATAA-CAAA
*
43710 GGTTGACTTCTCTTCATGAGGAAGTCAAGGA
194 GGTTGACTTCTCTTCATGAGAAAGTCAAGGA
43741 ATAGAAAACA
Statistics
Matches: 202, Mismatches: 21, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
252 96 0.48
253 105 0.52
254 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.27
Consensus pattern (252 bp):
ATAACAAAGATTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTATACTGAGGAGTCAAGAATA
ACAAAGTTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTCTACAGGGAGTCAGGAATAACAA
AGGTTGACTTCTCTTCACAAGGAAGTCAAAGATTGACTCTATTAAGGAGTCAGGAATAACAAAGG
TTGACTTCTCTTCATGAGAAAGTCAAGGATTAACTCATCTTCATGAAGAAGTCAAGG
Found at i:58067 original size:18 final size:20
Alignment explanation
Indices: 58040--58086 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
58030 TAAAGGAGTA
*
58040 CCAACAGCTCCAA-AAAT-C
1 CCAACGGCTCCAAGAAATCC
* *
58058 CCAACGGCTCTAAGACATCC
1 CCAACGGCTCCAAGAAATCC
58078 CCAACGGCT
1 CCAACGGCT
58087 AGAAATGGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 11 0.46
19 3 0.12
20 10 0.42
ACGTcount: A:0.34, C:0.40, G:0.13, T:0.13
Consensus pattern (20 bp):
CCAACGGCTCCAAGAAATCC
Done.