Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008651.1 Hibiscus syriacus cultivar Beakdansim tig00111641_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: 314694
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 1 of 2
Found at i:14482 original size:20 final size:17
Alignment explanation
Indices: 14443--14485 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
14433 TATACTGCAG
*
14443 ATCATCGATTCAACCCC
1 ATCATCAATTCAACCCC
14460 ATCATCAATTCAACCCC
1 ATCATCAATTCAACCCC
14477 ATCATCAAT
1 ATCATCAAT
14486 GGCCTGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.35, C:0.37, G:0.02, T:0.26
Consensus pattern (17 bp):
ATCATCAATTCAACCCC
Found at i:16043 original size:21 final size:20
Alignment explanation
Indices: 15957--16114 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
15947 AAATGACCAA
**
15957 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
15976 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
15996 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
16016 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
16037 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
16058 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
16078 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
16099 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
16115 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:16143 original size:20 final size:20
Alignment explanation
Indices: 16081--16274 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
16071 CGATTTTCCA
* ** *
16081 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
16101 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
16121 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
16141 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
16161 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
16181 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
16201 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
16221 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
16241 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
16262 AAATCGCAACGCG
1 AAATCGCAACGCG
16275 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:16165 original size:60 final size:60
Alignment explanation
Indices: 16081--16274 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
16071 CGATTTTCCA
* ** * *
16081 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
16141 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
16201 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
16262 AAATCGCAACGCG
1 AAATCGCAACGCG
16275 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:16694 original size:33 final size:33
Alignment explanation
Indices: 16655--16725 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
16645 TTCACTTAGA
* *
16655 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
16688 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
16721 TTTCA
1 TTTCA
16726 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:16831 original size:21 final size:20
Alignment explanation
Indices: 16805--16910 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
16795 TGCAGAAGAG
16805 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
16826 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
16846 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
16867 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
16881 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
16900 TCGCAACGAGA
1 TCGCAACGAGA
16911 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:16849 original size:20 final size:21
Alignment explanation
Indices: 16803--16881 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
16793 TTTGCAGAAG
*
16803 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
16825 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
16844 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
16866 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
16882 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:16862 original size:41 final size:38
Alignment explanation
Indices: 16798--16914 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
16788 TTCAATTTGC
* *
16798 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
16836 AGAATGACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
16877 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
16910 AGAAT
1 AGAAT
16915 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:16887 original size:14 final size:14
Alignment explanation
Indices: 16868--16921 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
16858 AAATGAAAAG
16868 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
16882 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
16901 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
16915 CGCAACG
1 CGCAACG
16922 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:16897 original size:33 final size:33
Alignment explanation
Indices: 16857--16926 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
16847 CGCAACGAGA
16857 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
16890 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
16923 GAAA
1 GAAA
16927 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:16933 original size:33 final size:33
Alignment explanation
Indices: 16863--16937 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
16853 GAGAGAAATG
* **
16863 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
16896 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
16929 AAAATCGCA
1 AAAATCGCA
16938 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:16955 original size:19 final size:19
Alignment explanation
Indices: 16933--17030 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
16923 GAAACCAAAA
*
16933 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
16952 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
16966 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
16985 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
16999 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
17018 TCGCGTTGCGATT
1 TCGCGTTGCGATT
17031 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:16974 original size:14 final size:14
Alignment explanation
Indices: 16955--17044 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
16945 TTTCATTTCG
16955 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
16969 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
16988 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
17002 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
17019 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
17035 CGTTGCGATT
1 CGTTGCGATT
17045 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:16980 original size:33 final size:33
Alignment explanation
Indices: 16938--17052 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
16928 CAAAATCGCA
16938 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
16971 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
17004 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
17037 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
17053 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:18903 original size:93 final size:93
Alignment explanation
Indices: 18744--19217 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
18734 TAGATTGCTT
*
18744 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
18809 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
18837 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
18902 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
18930 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
18995 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
19023 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
19088 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
19116 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
19181 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
19209 AGTAAATTT
1 AGTAAATTT
19218 ATCCATTCAA
Statistics
Matches: 378, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 378 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:19301 original size:19 final size:19
Alignment explanation
Indices: 19261--19389 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
19251 TAGTTTACTT
* *
19261 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
19281 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
19300 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
19319 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
19333 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
19352 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
19366 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
19385 TCGCA
1 TCGCA
19390 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:19340 original size:33 final size:32
Alignment explanation
Indices: 19297--19389 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
19287 CGCGAAACCA
**
19297 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
19329 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
19362 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
19390 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:19387 original size:52 final size:52
Alignment explanation
Indices: 19261--19389 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
19251 TAGTTTACTT
**
19261 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
19313 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
19366 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
19390 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:19407 original size:19 final size:19
Alignment explanation
Indices: 19385--19519 Score: 146
Period size: 19 Copynumber: 7.6 Consensus size: 19
19375 GAAACCAAAA
*
19385 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
19404 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
19420 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
19437 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
19453 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
19470 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
19489 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
19509 TCGTGTTGCGA
1 TCGCGTTGCGA
19520 AAGTAAACTA
Statistics
Matches: 99, Mismatches: 6, Indels: 21
0.79 0.05 0.17
Matches are distributed among these distances:
14 16 0.16
16 12 0.12
17 12 0.12
19 47 0.47
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:19426 original size:14 final size:14
Alignment explanation
Indices: 19407--19463 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
19397 TTTCATTTCG
19407 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
19421 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
19438 CGCGTTGCGATTCTTT
1 --CGTTGCGATTCTTT
19454 CGTTGCGATT
1 CGTTGCGATT
19464 TTCATTTCGC
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
16 6 0.16
17 6 0.16
19 8 0.21
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:19432 original size:33 final size:33
Alignment explanation
Indices: 19390--19482 Score: 186
Period size: 33 Copynumber: 2.8 Consensus size: 33
19380 CAAAATCGCA
19390 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
19423 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
19456 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
19483 TTGGTTTCGC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:21430 original size:14 final size:14
Alignment explanation
Indices: 21411--21446 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
21401 ATTGTTTAAT
21411 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
21425 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
21439 TGATTTGT
1 TGATTTGT
21447 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:21577 original size:19 final size:19
Alignment explanation
Indices: 21553--21650 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
21543 AAAATTGACT
21553 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
21572 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
21591 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
21605 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
21624 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
21644 ATCGCAA
1 ATCGCAA
21651 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:21682 original size:53 final size:53
Alignment explanation
Indices: 21553--21669 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
21543 AAAATTGACT
21553 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
21605 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
21658 ATCGCAATGCGA
1 ATCGCAATGCGA
21670 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:24216 original size:24 final size:24
Alignment explanation
Indices: 24182--24228 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
24172 CTGAAACATC
24182 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
24206 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
24229 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:24937 original size:20 final size:20
Alignment explanation
Indices: 24909--25158 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
24899 AAATTTCAGT
* * *
24909 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
24929 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
24949 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
24969 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
24989 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
25009 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
25029 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
25049 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
*
25069 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
25089 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
25109 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
25129 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
25149 GTTGCGATTT
1 GTTGCGATTT
25159 TGGAAAATCG
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:25175 original size:21 final size:21
Alignment explanation
Indices: 25145--25227 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
25135 ATTTTCATAT
*
25145 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
25166 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
25187 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
25208 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
25228 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:25218 original size:42 final size:43
Alignment explanation
Indices: 25125--25223 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
25115 ATTTATGTGT
* *
25125 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
25166 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
25208 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
25224 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:37830 original size:19 final size:19
Alignment explanation
Indices: 37806--37844 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
37796 AACTTTTGAA
*
37806 TTTAAAAGTATCGATACTT
1 TTTAAAAATATCGATACTT
*
37825 TTTAAAAATATTGATACTT
1 TTTAAAAATATCGATACTT
37844 T
1 T
37845 ATAATCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (19 bp):
TTTAAAAATATCGATACTT
Found at i:38087 original size:78 final size:75
Alignment explanation
Indices: 38000--38276 Score: 253
Period size: 77 Copynumber: 3.7 Consensus size: 75
37990 TGCGCAATCC
* *
38000 TTTTAATTAATAAAAATATTAACATTTCATATCGTAACCTATTTTGTTAGTCAAACATGGCATTC
1 TTTT-ATTAATAAAAATATTAACATTTCATATCGCAACCTATTTT-TTAGT-AAACATGACATTC
*
38065 TTGGGTGTAACATA
63 TTGGGTGCAAC-TA
* * * * *
38079 TTTTATTAATAAAAATATTAAAATTCCATATCGCAACCTATTTCTTAGTGAACCATGACATT-AT
1 TTTTATTAATAAAAATATTAACATTTCATATCGCAACCTATTTTTTAGT-AAACATGACATTCTT
* *
38143 --CTGCAACCCA
65 GGGTGCAA-CTA
* *
38153 TTTTATT-A-AAAAATATTAACA-TTCTAGATCGCAACCTATTTTTTAGTAAATCATGACAATCT
1 TTTTATTAATAAAAATATTAACATTTC-ATATCGCAACCTATTTTTTAGTAAA-CATGACATTCT
*
38215 TGGGCGCAACTCA
64 TGGGTGCAACT-A
* * * * *
38228 TTTTATAAATAAAAACATTAACA-TTCTATATCACAATCTATTTCTTAGT
1 TTTTATTAATAAAAATATTAACATTTC-ATATCGCAACCTATTTTTTAGT
38277 GAATCATTAC
Statistics
Matches: 162, Mismatches: 27, Indels: 20
0.78 0.13 0.10
Matches are distributed among these distances:
71 4 0.02
72 40 0.25
73 2 0.01
74 13 0.08
75 12 0.07
76 2 0.01
77 49 0.30
78 36 0.22
79 4 0.02
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.38
Consensus pattern (75 bp):
TTTTATTAATAAAAATATTAACATTTCATATCGCAACCTATTTTTTAGTAAACATGACATTCTTG
GGTGCAACTA
Found at i:39069 original size:30 final size:30
Alignment explanation
Indices: 39033--39096 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
39023 GAAGGACCTG
* *
39033 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
39063 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
39093 TCCA
1 TCCA
39097 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:39883 original size:64 final size:64
Alignment explanation
Indices: 39770--39935 Score: 203
Period size: 64 Copynumber: 2.6 Consensus size: 64
39760 TCTTTCAATG
* * * *
39770 AATGTATGCATCGATGCACTTCTTGTGCATCGGTGCATAAAATGCATTCGATGTTTT-TATTT-
1 AATGCATGCATCGATGCACTCCTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTA
* *
39832 AATGGGGATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATT
1 AAT--GCATGCATCGATGCACTCCTTGTGCATCGATGCATAAAATCC-ATTCGATGTTTTCTATT
39896 TA
63 TA
* * *
39898 AATTCATGCATCGATGCACTGCATGTGCATCGATGCAT
1 AATGCATGCATCGATGCACTCCTTGTGCATCGATGCAT
39936 CTTAAACAAT
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
62 3 0.03
63 5 0.06
64 73 0.82
65 5 0.06
66 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.36
Consensus pattern (64 bp):
AATGCATGCATCGATGCACTCCTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTA
Found at i:40942 original size:77 final size:77
Alignment explanation
Indices: 40737--40976 Score: 263
Period size: 77 Copynumber: 3.1 Consensus size: 77
40727 TGTTGGACGT
* * * * * *
40737 AACCCATTTCATTAATAAAAAATATTAACATTCCAGATAGCATCCTATCTCTTAGTGAACCATGC
1 AACCTATTTAATTAAT-AAAAATATTAACATTCCAGATCGCAACCTATTTCTTAGTGAACCATGA
**
40802 CATGCTTAGGCGC
65 CATTTTTAGGCGC
** * * *
40815 AA-CTCATTTAATT-A-CCAAATATTAACA-TCCTAGATCACAACTTATTTCTTAGTAAACCATG
1 AACCT-ATTTAATTAATAAAAATATTAACATTCC-AGATCGCAACCTATTTCTTAGTGAACCATG
*
40876 ACATTTTTTGGCGC
64 ACATTTTTAGGCGC
* *
40890 AACCTATTTTATTAATAAAAATATTAACATTCCATATCGCAACCTATTTCTTAGTGAACCATGAC
1 AACCTATTTAATTAATAAAAATATTAACATTCCAGATCGCAACCTATTTCTTAGTGAACCATGAC
40955 ATTTTTAGGCGC
66 ATTTTTAGGCGC
*
40967 ATCCGTATTT
1 AACC-TATTT
40977 CTTATATATA
Statistics
Matches: 132, Mismatches: 23, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
74 3 0.02
75 54 0.41
76 3 0.02
77 55 0.42
78 17 0.13
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.35
Consensus pattern (77 bp):
AACCTATTTAATTAATAAAAATATTAACATTCCAGATCGCAACCTATTTCTTAGTGAACCATGAC
ATTTTTAGGCGC
Found at i:52117 original size:35 final size:35
Alignment explanation
Indices: 52071--52139 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
52061 TTTCACTTAA
52071 GGAAAATGTTTAATTAGTAGTAGATGGTAAAATAC
1 GGAAAATGTTTAATTAGTAGTAGATGGTAAAATAC
*
52106 GGAAAATGTTTAATTCGTAGTAGATGGTAAAATA
1 GGAAAATGTTTAATTAGTAGTAGATGGTAAAATA
52140 TCCATAAGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.32
Consensus pattern (35 bp):
GGAAAATGTTTAATTAGTAGTAGATGGTAAAATAC
Found at i:53491 original size:31 final size:30
Alignment explanation
Indices: 53430--53491 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
53420 GACCAAATTG
* **
53430 AATTTATTTTCTGAGTTGGGGGCTACATTA
1 AATTTATTTTCTAAGTTAAGGGCTACATTA
*
53460 AATTTATTTTCTAAGTTAAAGGGCTATATTA
1 AATTTATTTTCTAAGTT-AAGGGCTACATTA
53491 A
1 A
53492 TAGAAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.44
Consensus pattern (30 bp):
AATTTATTTTCTAAGTTAAGGGCTACATTA
Found at i:70259 original size:37 final size:37
Alignment explanation
Indices: 70209--70283 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
70199 GACGACATGA
*
70209 ACCACCCCTATAATATAACTCTCTAATGTCCAATCTG
1 ACCACCCCTATAATAGAACTCTCTAATGTCCAATCTG
*
70246 ACCACCCCTATAATAGAACTCTGTAATGTCCAATCTG
1 ACCACCCCTATAATAGAACTCTCTAATGTCCAATCTG
70283 A
1 A
70284 ACTAATCGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.28
Consensus pattern (37 bp):
ACCACCCCTATAATAGAACTCTCTAATGTCCAATCTG
Found at i:71211 original size:24 final size:24
Alignment explanation
Indices: 71184--71233 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
71174 TGACAGTACC
71184 CCTCCCCTTAATTAAAATCCCTAA
1 CCTCCCCTTAATTAAAATCCCTAA
* *
71208 CCTCCCTTTAATTGAAATCCCTAA
1 CCTCCCCTTAATTAAAATCCCTAA
71232 CC
1 CC
71234 CTATTTCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.30, C:0.38, G:0.02, T:0.30
Consensus pattern (24 bp):
CCTCCCCTTAATTAAAATCCCTAA
Found at i:74078 original size:24 final size:24
Alignment explanation
Indices: 74051--74100 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
74041 TGGCAGTACC
74051 CCTCCCCTTAATTAAAATCCCTAA
1 CCTCCCCTTAATTAAAATCCCTAA
* * *
74075 CCTCTCTTTAATTGAAATCCCTAA
1 CCTCCCCTTAATTAAAATCCCTAA
74099 CC
1 CC
74101 CTATTTCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.32
Consensus pattern (24 bp):
CCTCCCCTTAATTAAAATCCCTAA
Found at i:76773 original size:14 final size:14
Alignment explanation
Indices: 76754--76801 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
76744 AGTACACTTC
76754 AAACCAAGTAACAT
1 AAACCAAGTAACAT
76768 AAACC-A-TAAACAT
1 AAACCAAGT-AACAT
76781 AAAACCAAGTAACAT
1 -AAACCAAGTAACAT
76796 AAACCA
1 AAACCA
76802 TAAACATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 1 0.03
13 6 0.20
14 16 0.53
15 6 0.20
16 1 0.03
ACGTcount: A:0.60, C:0.23, G:0.04, T:0.12
Consensus pattern (14 bp):
AAACCAAGTAACAT
Found at i:76794 original size:28 final size:28
Alignment explanation
Indices: 76754--76817 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
76744 AGTACACTTC
76754 AAACCAAGTAACATAAACCATAAACATA
1 AAACCAAGTAACATAAACCATAAACATA
76782 AAACCAAGTAACATAAACCATAAACATA
1 AAACCAAGTAACATAAACCATAAACATA
76810 AAACCAAG
1 AAACCAAG
76818 CATCCAAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.61, C:0.22, G:0.05, T:0.12
Consensus pattern (28 bp):
AAACCAAGTAACATAAACCATAAACATA
Found at i:80113 original size:18 final size:17
Alignment explanation
Indices: 80071--80104 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
80061 ACTATAATTA
80071 TAAAATA-TTTTTTTGT
1 TAAAATATTTTTTTTGT
80087 TAAAATATTTTTTTTGT
1 TAAAATATTTTTTTTGT
80104 T
1 T
80105 GAATCTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TAAAATATTTTTTTTGT
Found at i:85882 original size:89 final size:90
Alignment explanation
Indices: 85775--85956 Score: 357
Period size: 89 Copynumber: 2.0 Consensus size: 90
85765 CGGGGTGTGG
85775 AACAACAAAAACACCGTCACCACTGAACAAAGAAACATCTAGTTTATCGTTGGCAACATAGCTTT
1 AACAACAAAAACACCGTCACCACTGAACAAAGAAACATCTAGTTTATCGTTGGCAACATAGCTTT
85840 GGTCCACCACAGGTCCACTTGCAGA
66 GGTCCACCACAGGTCCACTTGCAGA
85865 AACAAC-AAAACACCGTCACCACTGAACAAAGAAACATCTAGTTTATCGTTGGCAACATAGCTTT
1 AACAACAAAAACACCGTCACCACTGAACAAAGAAACATCTAGTTTATCGTTGGCAACATAGCTTT
85929 GGTCCACCACAGGTCCACTTGCAGA
66 GGTCCACCACAGGTCCACTTGCAGA
85954 AAC
1 AAC
85957 TAGGGAGTCC
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
89 86 0.93
90 6 0.07
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (90 bp):
AACAACAAAAACACCGTCACCACTGAACAAAGAAACATCTAGTTTATCGTTGGCAACATAGCTTT
GGTCCACCACAGGTCCACTTGCAGA
Found at i:97041 original size:64 final size:64
Alignment explanation
Indices: 96969--97189 Score: 231
Period size: 64 Copynumber: 3.5 Consensus size: 64
96959 TTGAAGGTGT
* ** *
96969 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AAT-ATATACATCGAATGCAATTCGT
1 ATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATGA-A-ACATCGAATGCAATTAGT
97031 GC
63 GC
*
97033 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTAGTGC
* * **
97097 ATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAAT-ACAACATCGAATGCCTTTTA-T
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATGA-AACATCGAATG-CAATTAGT
97159 GC
63 GC
* *
97161 ACCGATGCATCA-GTAGTGCATCAATGCAT
1 ATCGATGCAT-AGGTAGTGCATCGATGCAT
97190 AATTTCATTG
Statistics
Matches: 136, Mismatches: 14, Indels: 14
0.83 0.09 0.09
Matches are distributed among these distances:
63 3 0.02
64 120 0.88
65 12 0.09
66 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTAGTGC
Found at i:97970 original size:32 final size:31
Alignment explanation
Indices: 97934--98051 Score: 123
Period size: 32 Copynumber: 3.7 Consensus size: 31
97924 GTTCTACGGA
97934 ACATATGGACAAAATTACCTATGTCTTTCGAG
1 ACATATGGACAAAA-TACCTATGTCTTTCGAG
** *
97966 ACATATGGACAGTATACCTATGT-TCTACG-G
1 ACATATGGACAAAATACCTATGTCT-TTCGAG
* * *
97996 AACATATGGATAGAATTACTTATGTCTTTCGAG
1 -ACATATGGACA-AAATACCTATGTCTTTCGAG
*
98029 ACATATGGACAATATACCTATGT
1 ACATATGGACAAAATACCTATGT
98052 TCTAAGGAAC
Statistics
Matches: 68, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
30 2 0.03
31 31 0.46
32 33 0.49
33 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (31 bp):
ACATATGGACAAAATACCTATGTCTTTCGAG
Found at i:97987 original size:31 final size:31
Alignment explanation
Indices: 97934--98077 Score: 123
Period size: 31 Copynumber: 4.6 Consensus size: 31
97924 GTTCTACGGA
** *
97934 ACATATGGACAAAATTACCTATGTCTTTCGAG
1 ACATATGGACAGTA-TACCTATGTCTTACGAG
97966 ACATATGGACAGTATACCTATGT-TCTACG-G
1 ACATATGGACAGTATACCTATGTCT-TACGAG
* * * *
97996 AACATATGGATAGAATTACTTATGTCTTTCGAG
1 -ACATATGGACAGTA-TACCTATGTCTTACGAG
* * *
98029 ACATATGGACAATATACCTATGTTCTAAGGA-
1 ACATATGGACAGTATACCTATG-TCTTACGAG
*
98060 ACATATGGACAGTTTACC
1 ACATATGGACAGTATACC
98078 GGGGATGTTA
Statistics
Matches: 90, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
30 2 0.02
31 47 0.52
32 39 0.43
33 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (31 bp):
ACATATGGACAGTATACCTATGTCTTACGAG
Found at i:97993 original size:63 final size:63
Alignment explanation
Indices: 97914--98070 Score: 260
Period size: 63 Copynumber: 2.5 Consensus size: 63
97904 AGAGTCGATG
*
97914 GTATACATATGTTCTACGGAACATATGGACAAAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAAAATTACCTATGTCTTTCGAGACATATGGACA
* * *
97977 GTATACCTATGTTCTACGGAACATATGGATAGAATTACTTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAAAATTACCTATGTCTTTCGAGACATATGGACA
* *
98040 ATATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
98071 GTTTACCGGG
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 87 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAAAATTACCTATGTCTTTCGAGACATATGGACA
Found at i:99619 original size:22 final size:21
Alignment explanation
Indices: 99586--99629 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
99576 ACTTAATTGC
*
99586 AAAAAGAAAAAAAGATTTAAA
1 AAAAAGAAAAAAAGAATTAAA
* *
99607 AAAAAGCATAAAAATAATTAAA
1 AAAAAG-AAAAAAAGAATTAAA
99629 A
1 A
99630 TATGGTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (21 bp):
AAAAAGAAAAAAAGAATTAAA
Found at i:101043 original size:10 final size:10
Alignment explanation
Indices: 101028--101070 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
101018 GGGTCTCCAA
101028 CGTTTATGTT
1 CGTTTATGTT
101038 CGTTTATGTT
1 CGTTTATGTT
101048 CG----TGTT
1 CGTTTATGTT
101054 CGTTTATGTT
1 CGTTTATGTT
101064 CGTTTAT
1 CGTTTAT
101071 TTATTAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
6 6 0.21
10 23 0.79
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:101055 original size:16 final size:16
Alignment explanation
Indices: 101034--101066 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
101024 CCAACGTTTA
101034 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
101050 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
101066 T
1 T
101067 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:106646 original size:13 final size:14
Alignment explanation
Indices: 106608--106659 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
106598 CCTTAAATCC
106608 TAAATCCTAAATCC-
1 TAAATCCTAAA-CCT
106622 TAAATCCTAAACCT
1 TAAATCCTAAACCT
*
106636 TAAAT-CTAAACAT
1 TAAATCCTAAACCT
*
106649 TAAATCTTAAA
1 TAAATCCTAAA
106660 ATCCAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 14 0.41
14 20 0.59
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAATCCTAAACCT
Found at i:106659 original size:7 final size:7
Alignment explanation
Indices: 106585--106645 Score: 74
Period size: 7 Copynumber: 8.9 Consensus size: 7
106575 AAACCCAAAC
106585 CCTAAAT
1 CCTAAAT
*
106592 TCTAAA-
1 CCTAAAT
106598 CCTTAAAT
1 CC-TAAAT
106606 CCTAAAT
1 CCTAAAT
106613 CCTAAAT
1 CCTAAAT
106620 CCTAAAT
1 CCTAAAT
106627 CCTAAA-
1 CCTAAAT
106633 CCTTAAAT
1 CC-TAAAT
106641 -CTAAA
1 CCTAAA
106646 CATTAAATCT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
6 7 0.15
7 39 0.81
8 2 0.04
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (7 bp):
CCTAAAT
Found at i:108933 original size:3 final size:3
Alignment explanation
Indices: 108925--108965 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
108915 TGTTCACATT
108925 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
108966 CAACATTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:110968 original size:15 final size:15
Alignment explanation
Indices: 110948--110977 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
110938 GAAGACTAAC
110948 TTTATTTTAATTTAA
1 TTTATTTTAATTTAA
*
110963 TTTATTTTTATTTAA
1 TTTATTTTAATTTAA
110978 CAAAGCAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATTTTAATTTAA
Found at i:111073 original size:16 final size:16
Alignment explanation
Indices: 111049--111079 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
111039 CATAATGGTG
111049 ACACATGACACCATTA
1 ACACATGACACCATTA
*
111065 ACACGTGACACCATT
1 ACACATGACACCATT
111080 CGATAAGAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.32, G:0.10, T:0.19
Consensus pattern (16 bp):
ACACATGACACCATTA
Found at i:111842 original size:20 final size:21
Alignment explanation
Indices: 111817--111855 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
111807 CAGTATAATG
111817 ATATTAT-ATTATTAAAATAC
1 ATATTATAATTATTAAAATAC
*
111837 ATATTATAATTTTTAAAAT
1 ATATTATAATTATTAAAAT
111856 TTATTTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (21 bp):
ATATTATAATTATTAAAATAC
Found at i:125679 original size:23 final size:22
Alignment explanation
Indices: 125647--125692 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
125637 GGTAAACTAA
*
125647 TAAAAAAAAATTAACGTTTTTT
1 TAAAAAAAAATTAACATTTTTT
125669 TAAAAATAAAATTAACATTTTTT
1 TAAAAA-AAAATTAACATTTTTT
125692 T
1 T
125693 CTTCCCCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAAAAAAATTAACATTTTTT
Found at i:125689 original size:22 final size:22
Alignment explanation
Indices: 125647--125691 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
125637 GGTAAACTAA
*
125647 TAAAAAAAAATTAACGTTTTTT
1 TAAAAAAAAATTAACGATTTTT
125669 TAAAAATAAAATTAAC-ATTTTT
1 TAAAAA-AAAATTAACGATTTTT
125691 T
1 T
125692 TCTTCCCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAAAAAAAATTAACGATTTTT
Found at i:129205 original size:2 final size:2
Alignment explanation
Indices: 129198--129237 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
129188 CAAAACACAA
* *
129198 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
129238 TATGTGTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:136612 original size:22 final size:22
Alignment explanation
Indices: 136582--136654 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
136572 TTACGGCAAC
* *
136582 ATCCGTCCCCATCTCTGACGAA
1 ATCCGTCCCCATCTCCGACAAA
* *
136604 ATCCATCCCCATCTCCGGCAAA
1 ATCCGTCCCCATCTCCGACAAA
*
136626 ATCCGTCCCCATCTCCGGCAAA
1 ATCCGTCCCCATCTCCGACAAA
136648 ATCCGTC
1 ATCCGTC
136655 TATCTCCATC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.23, C:0.44, G:0.12, T:0.21
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACAAA
Found at i:136968 original size:19 final size:20
Alignment explanation
Indices: 136944--136985 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
136934 TTCATTCAAG
136944 TTTCA-TTTCGCGTTGCGAT
1 TTTCATTTTCGCGTTGCGAT
136963 TTTCATTTTCGCGTTGCGAT
1 TTTCATTTTCGCGTTGCGAT
136983 TTT
1 TTT
136986 AAGTTTCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.10, C:0.19, G:0.19, T:0.52
Consensus pattern (20 bp):
TTTCATTTTCGCGTTGCGAT
Found at i:136992 original size:20 final size:20
Alignment explanation
Indices: 136949--136992 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
136939 TCAAGTTTCA
* *
136949 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTAAG
136969 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
136989 TTTC
1 TTTC
136993 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:139005 original size:21 final size:21
Alignment explanation
Indices: 138975--139080 Score: 67
Period size: 21 Copynumber: 5.0 Consensus size: 21
138965 GAAGCACCTG
*
138975 TCATCGTTCAAGAGGCCTCTCC
1 TCATCATTCAAGAGGCC-CTCC
* *
138997 T-ATCATTCAAGATGACCCT-A
1 TCATCATTCAAGA-GGCCCTCC
139017 TCATCATTCAAGAGGCCACTCC
1 TCATCATTCAAGAGGCC-CTCC
* * * *
139039 -CACCGTTCAAGAAGCCC-CTG
1 TCATCATTCAAGAGGCCCTC-C
*
139059 TCATCGTTCAAGAGGTCCCTCC
1 TCATCATTCAAGAGG-CCCTCC
139081 CACCGTTCGA
Statistics
Matches: 64, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
19 1 0.02
20 5 0.08
21 50 0.78
22 7 0.11
23 1 0.02
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.25
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCCTCC
Found at i:139085 original size:42 final size:42
Alignment explanation
Indices: 138965--139096 Score: 151
Period size: 42 Copynumber: 3.2 Consensus size: 42
138955 GAAGAAGCCC
* * * * *
138965 GAAGCACCTGTCATCGTTCAAGAGGCCTCTCCTATCATTCAA
1 GAAGCCCCTGTCATCGTTCAAGAGGCCACTCCCACCGTTCAA
* * * *
139007 GATGACCCTATCATCATTCAAGAGGCCACTCCCACCGTTCAA
1 GAAGCCCCTGTCATCGTTCAAGAGGCCACTCCCACCGTTCAA
*
139049 GAAGCCCCTGTCATCGTTCAAGAGGTCC-CTCCCACCGTTCGA
1 GAAGCCCCTGTCATCGTTCAAGAGG-CCACTCCCACCGTTCAA
139091 G-AGCCC
1 GAAGCCC
139097 GATTCACATG
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
41 5 0.07
42 68 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (42 bp):
GAAGCCCCTGTCATCGTTCAAGAGGCCACTCCCACCGTTCAA
Found at i:139087 original size:21 final size:20
Alignment explanation
Indices: 139023--139093 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
139013 CCTATCATCA
139023 TTCAAGAGGCCACTCCCACCG
1 TTCAAGAGGCC-CTCCCACCG
* ** *
139044 TTCAAGAAGCCCCTGTCATCG
1 TTCAAG-AGGCCCTCCCACCG
139065 TTCAAGAGGTCCCTCCCACCG
1 TTCAAGAGG-CCCTCCCACCG
*
139086 TTCGAGAG
1 TTCAAGAG
139094 CCCGATTCAC
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.05
21 33 0.85
22 4 0.10
ACGTcount: A:0.23, C:0.37, G:0.21, T:0.20
Consensus pattern (20 bp):
TTCAAGAGGCCCTCCCACCG
Found at i:140328 original size:64 final size:64
Alignment explanation
Indices: 140250--140398 Score: 253
Period size: 64 Copynumber: 2.3 Consensus size: 64
140240 AAATTGATGT
140250 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
* * ***
140314 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
140378 ATTTGTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
140399 GTTTTAAATT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 80 1.00
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
Found at i:140520 original size:20 final size:20
Alignment explanation
Indices: 140491--140597 Score: 70
Period size: 20 Copynumber: 5.3 Consensus size: 20
140481 CGTTGCGATG
* *
140491 GTTGCTAAAGTCAAATTCGC
1 GTTGCGAAAGCCAAATTCGC
140511 GTTGCGAAAGCCAAATTCGC
1 GTTGCGAAAGCCAAATTCGC
*** * *
140531 AACGTGAAAGCCAAATTTGC
1 GTTGCGAAAGCCAAATTCGC
*** *
140551 AACGTGAAAGCCAAATTCGC
1 GTTGCGAAAGCCAAATTCGC
*** * *
140571 AACGCGAAAGTCAACTTCGC
1 GTTGCGAAAGCCAAATTCGC
140591 GTTGCGA
1 GTTGCGA
140598 TTTTCACGTT
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 73 1.00
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (20 bp):
GTTGCGAAAGCCAAATTCGC
Found at i:143160 original size:24 final size:24
Alignment explanation
Indices: 143126--143179 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
143116 CTGAAACATC
143126 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
143150 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
143174 ATCAAA
1 ATCAAA
143180 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:143193 original size:24 final size:24
Alignment explanation
Indices: 143126--143193 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
143116 CTGAAACATC
* * *
143126 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
143150 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
143174 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
143194 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:144138 original size:20 final size:20
Alignment explanation
Indices: 144114--144262 Score: 94
Period size: 20 Copynumber: 7.4 Consensus size: 20
144104 ACTAAAACCT
*
144114 GTTGCGAAATTAAAATTCGT
1 GTTGCGAAATTAAAATTCGA
144134 GTTGCG-AATTCGAAAA-TCGA
1 GTTGCGAAATT--AAAATTCGA
* *
144154 GTTGCTACAA-TAAAATTCGC
1 GTTGCGA-AATTAAAATTCGA
144174 GTTGCG-AATTCAGAAA-TCGA
1 GTTGCGAAATT-A-AAATTCGA
* *
144194 GTTGCGAATTTAAAATTCAGT
1 GTTGCGAAATTAAAATTC-GA
* * *
144215 GTTGCGAATTTGGAAACT-GA
1 GTTGCGAAATT-AAAATTCGA
* * *
144235 GTTGCGAAATTAGAGTTCGG
1 GTTGCGAAATTAAAATTCGA
144255 GTTGCGAA
1 GTTGCGAA
144263 TTCGAGATCG
Statistics
Matches: 100, Mismatches: 16, Indels: 26
0.70 0.11 0.18
Matches are distributed among these distances:
18 2 0.02
19 14 0.14
20 55 0.55
21 23 0.23
22 6 0.06
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (20 bp):
GTTGCGAAATTAAAATTCGA
Found at i:144158 original size:40 final size:40
Alignment explanation
Indices: 144114--144267 Score: 179
Period size: 40 Copynumber: 3.8 Consensus size: 40
144104 ACTAAAACCT
144114 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
* *
144154 GTTGCTACAA-TAAAATTCGCGTTGCGAATTC-AGAAATCGA
1 GTTGCGA-AATTAAAATTCGTGTTGCGAATTCGA-AAATCGA
* * *
144194 GTTGCGAATTTAAAATTCAGTGTTGCGAATTTGGAAA-CTGA
1 GTTGCGAAATTAAAATTC-GTGTTGCGAATTCGAAAATC-GA
* * *
144235 GTTGCGAAATTAGAGTTCGGGTTGCGAATTCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGA
144268 GATCGCATTA
Statistics
Matches: 95, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
39 2 0.02
40 60 0.63
41 33 0.35
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.31
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
Found at i:144259 original size:81 final size:80
Alignment explanation
Indices: 144114--144265 Score: 200
Period size: 81 Copynumber: 1.9 Consensus size: 80
144104 ACTAAAACCT
*
144114 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGAGTTGCTACAATAAAATTCGCGTTGC
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGACAATAAAATTCGCGTTGC
144179 GAATTCAGAAATCGA
66 GAATTCAGAAATCGA
* * * * * *
144194 GTTGCGAATTTAAAATTCAGTGTTGCGAATTTGGAAA-CTGAGTTGCGA-AATTAGAGTTCGGGT
1 GTTGCGAAATTAAAATTC-GTGTTGCGAATTCGAAAATC-GAGTTGCGACAA-TAAAATTCGCGT
144257 TGCGAATTC
63 TGCGAATTC
144266 GAGATCGCAT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
80 20 0.32
81 42 0.68
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (80 bp):
GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGACAATAAAATTCGCGTTGC
GAATTCAGAAATCGA
Found at i:148157 original size:16 final size:16
Alignment explanation
Indices: 148136--148168 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
148126 ACTTTCATGA
148136 TGTAATAGTTGAATAT
1 TGTAATAGTTGAATAT
148152 TGTAATAGTTGAATAT
1 TGTAATAGTTGAATAT
148168 T
1 T
148169 CTAAAGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (16 bp):
TGTAATAGTTGAATAT
Found at i:180130 original size:33 final size:33
Alignment explanation
Indices: 180088--180154 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
180078 AGGATGATTA
180088 TCATTCTCTTTGAGTTATACATATATTTAATTC
1 TCATTCTCTTTGAGTTATACATATATTTAATTC
**
180121 TCATTCTCTTTGAGTTATAGTTATATTTAATTC
1 TCATTCTCTTTGAGTTATACATATATTTAATTC
180154 T
1 T
180155 TCGTTGTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.07, T:0.54
Consensus pattern (33 bp):
TCATTCTCTTTGAGTTATACATATATTTAATTC
Found at i:183386 original size:13 final size:13
Alignment explanation
Indices: 183368--183394 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
183358 AATTATAGAA
183368 GGCCAAATACCTT
1 GGCCAAATACCTT
183381 GGCCAAATACCTT
1 GGCCAAATACCTT
183394 G
1 G
183395 CGGTCAGGAA
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:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (13 bp):
GGCCAAATACCTT
Found at i:187244 original size:2 final size:2
Alignment explanation
Indices: 187239--187286 Score: 64
Period size: 2 Copynumber: 24.5 Consensus size: 2
187229 TTTTAATGAT
*
187239 TA TA TA TA TCA AA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
187280 TA TA TA T
1 TA TA TA T
187287 TACAATTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 2 0.05
2 38 0.93
3 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:188723 original size:12 final size:12
Alignment explanation
Indices: 188706--188730 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
188696 CGTCATCCTT
188706 TGCATTTGCATC
1 TGCATTTGCATC
188718 TGCATTTGCATC
1 TGCATTTGCATC
188730 T
1 T
188731 TCACCCCTTT
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:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (12 bp):
TGCATTTGCATC
Found at i:191790 original size:12 final size:12
Alignment explanation
Indices: 191773--191818 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
191763 CCTCGTTATG
191773 TTCTTCTTCATC
1 TTCTTCTTCATC
*
191785 TTCTTCATCATC
1 TTCTTCTTCATC
* *
191797 TTCTTCGTCCTC
1 TTCTTCTTCATC
191809 TTCTTCTTCA
1 TTCTTCTTCA
191819 ATAGCGAGGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.09, C:0.35, G:0.02, T:0.54
Consensus pattern (12 bp):
TTCTTCTTCATC
Found at i:194327 original size:2 final size:2
Alignment explanation
Indices: 194320--194349 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
194310 TGAGAAAGAC
*
194320 AG AG AG AG AC AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
194350 GTACCATCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:194329 original size:10 final size:10
Alignment explanation
Indices: 194311--194348 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
194301 ACTACAAGCT
*
194311 GAGAAAGACA
1 GAGAGAGACA
194321 GAGAGAGACA
1 GAGAGAGACA
*
194331 GAGAGAGAGA
1 GAGAGAGACA
194341 GAGAGAGA
1 GAGAGAGA
194349 GGTACCATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.53, C:0.05, G:0.42, T:0.00
Consensus pattern (10 bp):
GAGAGAGACA
Found at i:200086 original size:73 final size:70
Alignment explanation
Indices: 199966--200099 Score: 187
Period size: 73 Copynumber: 1.9 Consensus size: 70
199956 ACACGTCCAC
** * *
199966 CCTGAAATTTAAATTTTTTATTAGTTATTTATTTTATTAATTATGTCCACTCTGAAAATTTTCGT
1 CCTGAAATTTAAATTTTTTATTAGTTATTTATTTTACGAATGATGTCCACCCTG-AAATTTTCGT
200031 GTCTAT
65 GTCTAT
* *
200037 CCTGAAATTTAAGTTTTTGTTATTAGTTATTTATTTTACGAATGGTGTCCACCCTGAAATTTT
1 CCTGAAATTTAA-ATTTT-TTATTAGTTATTTATTTTACGAATGATGTCCACCCTGAAATTTT
200100 ATTTGTACTC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
71 12 0.22
72 11 0.20
73 32 0.58
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.50
Consensus pattern (70 bp):
CCTGAAATTTAAATTTTTTATTAGTTATTTATTTTACGAATGATGTCCACCCTGAAATTTTCGTG
TCTAT
Found at i:203260 original size:26 final size:26
Alignment explanation
Indices: 203202--203263 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 26
203192 CACAAATAAT
*
203202 AAATAAATGAACACGAACAATTTTAA
1 AAATAAATAAACACGAACAATTTTAA
*
203228 AAA-AAATAAACATGAACACA-TTTAA
1 AAATAAATAAACACGAACA-ATTTTAA
203253 AAATAAATAAA
1 AAATAAATAAA
203264 AGAATATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 21 0.66
26 11 0.34
ACGTcount: A:0.65, C:0.10, G:0.05, T:0.21
Consensus pattern (26 bp):
AAATAAATAAACACGAACAATTTTAA
Found at i:205043 original size:13 final size:13
Alignment explanation
Indices: 205025--205052 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
205015 ATTTTATCAC
205025 ATTAAAATAAAAA
1 ATTAAAATAAAAA
205038 ATTAAAATAAAAA
1 ATTAAAATAAAAA
205051 AT
1 AT
205053 ATTTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
ATTAAAATAAAAA
Found at i:208979 original size:23 final size:23
Alignment explanation
Indices: 208952--209026 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
208942 TAAACGAATG
208952 TGTTCGTGAATGTTAAATAAACA
1 TGTTCGTGAATGTTAAATAAACA
* * * *
208975 CGTTCGTGAACGCTAAATGAACA
1 TGTTCGTGAATGTTAAATAAACA
* * *
208998 TGTTTGTGAATATATAAACAAACA
1 TGTTCGTGAATGT-TAAATAAACA
209022 TGTTC
1 TGTTC
209027 ACAAATAATA
Statistics
Matches: 39, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
23 27 0.69
24 12 0.31
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (23 bp):
TGTTCGTGAATGTTAAATAAACA
Found at i:209068 original size:25 final size:25
Alignment explanation
Indices: 209040--209089 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
209030 AATAATAAAT
*
209040 AAATGAACACGAACA-ATTTTAAAAA
1 AAATAAACACGAACACA-TTTAAAAA
*
209065 AAATAAACATGAACACATTTAAAAA
1 AAATAAACACGAACACATTTAAAAA
209090 TAAACAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.20
Consensus pattern (25 bp):
AAATAAACACGAACACATTTAAAAA
Found at i:220553 original size:20 final size:20
Alignment explanation
Indices: 220497--220560 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
220487 CAAATATGGC
*
220497 GGATGAGTGT-TATATACAG
1 GGATGAGTGTGTATATATAG
* *
220516 AGACGAGTGTGTATATATAG
1 GGATGAGTGTGTATATATAG
220536 GGATGAGTGTGTATATATAG
1 GGATGAGTGTGTATATATAG
220556 GGATG
1 GGATG
220561 CGCACGGTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 8 0.21
20 31 0.79
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.31
Consensus pattern (20 bp):
GGATGAGTGTGTATATATAG
Found at i:221639 original size:22 final size:24
Alignment explanation
Indices: 221614--221657 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
221604 TCCATAGCCT
*
221614 TTAAAAAATTATT-T-AAAAATTG
1 TTAAAAAAATATTATGAAAAATTG
221636 TTAAAAAAATATTATGAAAAAT
1 TTAAAAAAATATTATGAAAAAT
221658 AATGTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 1 0.05
24 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (24 bp):
TTAAAAAAATATTATGAAAAATTG
Found at i:222114 original size:24 final size:23
Alignment explanation
Indices: 222078--222122 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
222068 TATTGTTTAC
*
222078 TTTTTATAATTTAACCTTTTAAT
1 TTTTTATAATTTAACATTTTAAT
*
222101 TTTTTTTAATTTTAACATTTTA
1 TTTTTATAA-TTTAACATTTTA
222123 TCATTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTTATAATTTAACATTTTAAT
Found at i:222193 original size:44 final size:45
Alignment explanation
Indices: 222096--222193 Score: 103
Period size: 43 Copynumber: 2.2 Consensus size: 45
222086 ATTTAACCTT
* * ** *
222096 TTAATTTTTTTTAATTTTAACATTTTATCATTATAATCGAGGTCT
1 TTAATTTTTTGTAATTTTAACATTTTATCATTAGAATCGAGACCC
* *
222141 TTAA-TTTTTGTAATTTT-AC-TTGTTATCTTTAGAATGGAGACCC
1 TTAATTTTTTGTAATTTTAACATT-TTATCATTAGAATCGAGACCC
222184 TTAATTTTTT
1 TTAATTTTTT
222194 TCAATCCTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
42 2 0.05
43 21 0.48
44 17 0.39
45 4 0.09
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (45 bp):
TTAATTTTTTGTAATTTTAACATTTTATCATTAGAATCGAGACCC
Found at i:222335 original size:42 final size:42
Alignment explanation
Indices: 222279--222390 Score: 127
Period size: 43 Copynumber: 2.6 Consensus size: 42
222269 CCTGCTTTTA
* *
222279 TCAATCTCACTTTTTATCTTTATAATTTAGGTCTCTAAATATT
1 TCAATCTCACTTTTTATCTTTATAATTTAGGCCCCT-AATATT
* * * *
222322 TCAATCTCATTTTTTA-CTCATATAATTTAGGCCCCTATTTTT
1 TCAATCTCACTTTTTATCT-TTATAATTTAGGCCCCTAATATT
* *
222364 TCAATCTCACTTTTTACCTTTAAAATT
1 TCAATCTCACTTTTTATCTTTATAATT
222391 GACCCACTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
42 27 0.47
43 31 0.53
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.50
Consensus pattern (42 bp):
TCAATCTCACTTTTTATCTTTATAATTTAGGCCCCTAATATT
Found at i:224452 original size:18 final size:18
Alignment explanation
Indices: 224431--224465 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
224421 ATGAATGTTT
* *
224431 TATTTATTTATTTTTTAG
1 TATTAATTTATATTTTAG
224449 TATTAATTTATATTTTA
1 TATTAATTTATATTTTA
224466 ATTTGGATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TATTAATTTATATTTTAG
Found at i:231397 original size:20 final size:20
Alignment explanation
Indices: 231359--231402 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
231349 AACCTTGAAA
* *
231359 TTTTATAAAATTTATAGTTT
1 TTTTATAAAATTCAAAGTTT
231379 CTTTT-TAAAATTCAAAGTTT
1 -TTTTATAAAATTCAAAGTTT
231399 TTTT
1 TTTT
231403 CTTTTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTATAAAATTCAAAGTTT
Found at i:233952 original size:13 final size:14
Alignment explanation
Indices: 233919--233954 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
233909 AAAATGAATT
*
233919 ACATTTTCTGAAAA
1 ACATTTTATGAAAA
233933 ACATTTTATGAAAA
1 ACATTTTATGAAAA
*
233947 ACTTTTTA
1 ACATTTTA
233955 CGATGTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.42
Consensus pattern (14 bp):
ACATTTTATGAAAA
Found at i:234095 original size:27 final size:27
Alignment explanation
Indices: 234065--234116 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
234055 TCATAAAACT
*
234065 TAATATTA-TTATTTTTAAAATATTAAA
1 TAAT-TTATTTATTATTAAAATATTAAA
234092 TAATTTATTTATTATTAAAATATTA
1 TAATTTATTTATTATTAAAATATTA
234117 TATTTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TAATTTATTTATTATTAAAATATTAAA
Found at i:234107 original size:19 final size:20
Alignment explanation
Indices: 234085--234123 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
234075 ATTTTTAAAA
234085 TATT-AAATAATT-TATTTAT
1 TATTAAAAT-ATTATATTTAT
234104 TATTAAAATATTATATTTAT
1 TATTAAAATATTATATTTAT
234124 AAATTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTAAAATATTATATTTAT
Found at i:234120 original size:20 final size:19
Alignment explanation
Indices: 234085--234123 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
234075 ATTTTTAAAA
234085 TATTAAATAATTTATTTAT
1 TATTAAATAATTTATTTAT
234104 TATTAAA-ATATTATATTTAT
1 TATTAAATA-ATT-TATTTAT
234124 AAATTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.06
19 10 0.56
20 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTAAATAATTTATTTAT
Found at i:234138 original size:28 final size:29
Alignment explanation
Indices: 234098--234177 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 29
234088 TAAATAATTT
* *
234098 ATTTATTATTAAAATATTATATTTATA-A
1 ATTTATTAATAAAATATTATATTGATATA
234126 ATTTATTAATAAAAATATTAATATTGATATA
1 ATTTATTAAT-AAAATATT-ATATTGATATA
*
234157 TTTTATTGAAATAAAATATTA
1 ATTTATT--AATAAAATATTA
234178 AAAAATATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 9 0.20
29 8 0.18
30 8 0.18
31 8 0.18
32 8 0.18
33 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
ATTTATTAATAAAATATTATATTGATATA
Found at i:234175 original size:32 final size:29
Alignment explanation
Indices: 234098--234178 Score: 92
Period size: 32 Copynumber: 2.7 Consensus size: 29
234088 TAAATAATTT
* *
234098 ATTTATTATTAAAATATT-ATATTTATAA
1 ATTTATTAATAAAATATTAATATTGATAA
234126 ATTTATTAATAAAAATATTAATATTGATATA
1 ATTTATTAAT-AAAATATTAATATTGATA-A
*
234157 TTTTATTGAAATAAAATATTAA
1 ATTTATT--AATAAAATATTAA
234179 AAAATATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
28 9 0.20
29 8 0.18
30 8 0.18
31 7 0.16
32 10 0.22
33 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
ATTTATTAATAAAATATTAATATTGATAA
Found at i:234262 original size:23 final size:23
Alignment explanation
Indices: 234218--234290 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
234208 AATGTTATAT
*
234218 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAA
* * *
234241 TATATTTTAAATATCTTTATTAA
1 TATATTTTAAAAATATTAATTAA
* * * *
234264 AATATTTTTAGATTATTATATTAA
1 TATATTTTAAAAATATTA-ATTAA
234288 TAT
1 TAT
234291 TAAATATATA
Statistics
Matches: 37, Mismatches: 12, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
23 30 0.81
24 7 0.19
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAA
Found at i:234476 original size:22 final size:23
Alignment explanation
Indices: 234448--234494 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
234438 TTGATTATTT
234448 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
234470 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
234493 TA
1 TA
234495 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:234499 original size:22 final size:22
Alignment explanation
Indices: 234456--234499 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
234446 TTTATTATAA
*
234456 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
234478 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
234500 ATTTTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:239468 original size:19 final size:19
Alignment explanation
Indices: 239429--239493 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
239419 ATTTTTAGAC
* * *
239429 TCATAACTTACTGTCAGAT
1 TCATAACTTATTTTCAAAT
*
239448 TCATAACTTATTTTTAAAT
1 TCATAACTTATTTTCAAAT
* *
239467 TCATAGCTTGTTTTCAAAT
1 TCATAACTTATTTTCAAAT
*
239486 TCACAACT
1 TCATAACT
239494 CAATGTATAT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.43
Consensus pattern (19 bp):
TCATAACTTATTTTCAAAT
Found at i:245316 original size:17 final size:17
Alignment explanation
Indices: 245296--245328 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
245286 GGCTGGTAAT
245296 CACTGGTTAGGGTTTAC
1 CACTGGTTAGGGTTTAC
245313 CACTGGTTAGGGTTTA
1 CACTGGTTAGGGTTTA
245329 TATCTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.15, G:0.30, T:0.36
Consensus pattern (17 bp):
CACTGGTTAGGGTTTAC
Found at i:245563 original size:39 final size:38
Alignment explanation
Indices: 245482--245565 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 38
245472 TAATCATGGA
*
245482 TAGATGTGCTGCATTTAACATCAGGATAATGCATTGAAT
1 TAGACGTGCTGCATTTAACATCAGGATAATGCATTG-AT
*
245521 TAGACGTGCTGCATTTAACAGT-AGGATTAAATGCGTTG-T
1 TAGACGTGCTGCATTTAACA-TCAGGA-T-AATGCATTGAT
245560 TAGACG
1 TAGACG
245566 AGGAACTAGC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
39 30 0.75
40 2 0.05
41 8 0.20
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (38 bp):
TAGACGTGCTGCATTTAACATCAGGATAATGCATTGAT
Found at i:246832 original size:23 final size:24
Alignment explanation
Indices: 246791--246838 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
246781 TTTAACACAA
246791 TTTTAATAAATATTGTGTTTAATTT
1 TTTTAATAAATATTGTGTTT-ATTT
*
246816 TTTTGATAAA-ATT-TGTTTATTT
1 TTTTAATAAATATTGTGTTTATTT
246838 T
1 T
246839 GATATTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 5 0.23
24 3 0.14
25 9 0.41
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.62
Consensus pattern (24 bp):
TTTTAATAAATATTGTGTTTATTT
Found at i:250379 original size:22 final size:22
Alignment explanation
Indices: 250360--250401 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
250350 TACCAAAATA
**
250360 ATTATCTGTTTATAATAAAAGT
1 ATTATCTAATTATAATAAAAGT
*
250382 ATTGTCTAATTATAATAAAA
1 ATTATCTAATTATAATAAAA
250402 ATTATATAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (22 bp):
ATTATCTAATTATAATAAAAGT
Found at i:250565 original size:130 final size:125
Alignment explanation
Indices: 250388--250620 Score: 294
Period size: 126 Copynumber: 1.8 Consensus size: 125
250378 AAGTATTGTC
* *
250388 TAATTATAATAAAAATTATATAAGATATTCAGTTGTATCAAAG-AAAAA-AAGCCGAAATGTCTA
1 TAATTATAATAAAAATAATATAAGATATTCAATTGTATCAAAGAAAAAATAAG--G---TGTCTA
*
250451 ATTACACTACAAAAGTTATCTAATTATAATAAAAATATTATCATGTACAAAAGTACTAGGTAGCG
61 ATTACACTA-AAAAGATATCTAATTATAATAAAAATATTATCATGTACAAAAGTACTAGGTAGCG
250516 A
125 A
*
250517 TAATTATAATAGAAAATAATATTAA-ATACTT-AATTGTATCAAAGAAAAAATAAGGTGTTTAAT
1 TAATTATAATA-AAAATAATA-TAAGATA-TTCAATTGTATCAAAGAAAAAATAAGGTGTCTAAT
** *
250580 TGGATTAAAAAGATATCTAATTATAATAAAAATATTATCAT
63 TACACTAAAAAGATATCTAATTATAATAAAAATATTATCAT
250621 AATATATATA
Statistics
Matches: 92, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
126 33 0.36
127 11 0.12
129 11 0.12
130 24 0.26
131 10 0.11
132 3 0.03
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (125 bp):
TAATTATAATAAAAATAATATAAGATATTCAATTGTATCAAAGAAAAAATAAGGTGTCTAATTAC
ACTAAAAAGATATCTAATTATAATAAAAATATTATCATGTACAAAAGTACTAGGTAGCGA
Found at i:250618 original size:22 final size:23
Alignment explanation
Indices: 250585--250628 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
250575 TTAATTGGAT
250585 TAAAAAGATATC-TAAT-TATAA
1 TAAAAAGATATCATAATATATAA
*
250606 TAAAAATATTATCATAATATATA
1 TAAAAAGA-TATCATAATATATA
250629 TATATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 4 0.21
24 4 0.21
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (23 bp):
TAAAAAGATATCATAATATATAA
Found at i:252220 original size:182 final size:183
Alignment explanation
Indices: 251913--252278 Score: 725
Period size: 182 Copynumber: 2.0 Consensus size: 183
251903 TAACTTTTTT
251913 GCTCTTTTTCTGCCATGTATTATAGTGTCCCCTAATTTACTCCTACCCTGTAATATCTTTATCAG
1 GCTCTTTTTCTGCCATGTATTATAGTGTCCCCTAATTTACTCCTACCCTGTAATATCTTTATCAG
251978 TGTACTATCTATAGTTTAGTCGCATGCATATCCTTTAATGATTTTTCATTTTGACTACATAATTA
66 TGTACTATCTATAGTTTAGTCGCATGCATATCCTTTAATGATTTTTCATTTTGACTACATAATTA
252043 ATTATATGCGCTTCCAGGATGAGATTCTGTGCAATGCTGTTCGACG-TTTAAA
131 ATTATATGCGCTTCCAGGATGAGATTCTGTGCAATGCTGTTCGACGTTTTAAA
252095 GCTCTTTTTCTGCCATGTATTATAGTGTCCCCTAATTTACTCCTACCCTGTAATATCTTTATCAG
1 GCTCTTTTTCTGCCATGTATTATAGTGTCCCCTAATTTACTCCTACCCTGTAATATCTTTATCAG
252160 TGTACTATCTATAGTTTAGTCGCATGCATATCCTTTAATGATTTTTCATTTTGACTACATAATTA
66 TGTACTATCTATAGTTTAGTCGCATGCATATCCTTTAATGATTTTTCATTTTGACTACATAATTA
252225 ATTATATGCGCTTCCAGGATGAGATTCTGTGCAATGCTGTTCGACGTTTTAAA
131 ATTATATGCGCTTCCAGGATGAGATTCTGTGCAATGCTGTTCGACGTTTTAAA
252278 G
1 G
252279 GAAAAAAATT
Statistics
Matches: 183, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
182 176 0.96
183 7 0.04
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (183 bp):
GCTCTTTTTCTGCCATGTATTATAGTGTCCCCTAATTTACTCCTACCCTGTAATATCTTTATCAG
TGTACTATCTATAGTTTAGTCGCATGCATATCCTTTAATGATTTTTCATTTTGACTACATAATTA
ATTATATGCGCTTCCAGGATGAGATTCTGTGCAATGCTGTTCGACGTTTTAAA
Found at i:257889 original size:19 final size:19
Alignment explanation
Indices: 257865--257931 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
257855 TAATTTAATT
257865 TTTATTTTTAATAAAATAA
1 TTTATTTTTAATAAAATAA
* * *
257884 TTTATTTGTATTAACATAA
1 TTTATTTTTAATAAAATAA
*
257903 TTAAATTGTTTTAATAAAATAA
1 TT-TA-T-TTTTAATAAAATAA
*
257925 ATTATTT
1 TTTATTT
257932 GTATTAAATA
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
19 20 0.56
20 2 0.06
21 2 0.06
22 12 0.33
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (19 bp):
TTTATTTTTAATAAAATAA
Found at i:257933 original size:22 final size:22
Alignment explanation
Indices: 257872--257938 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 22
257862 ATTTTTATTT
*
257872 TTAATAAAATAATTTATTTGTA
1 TTAATAAAATAAATTATTTGTA
* * * *
257894 TTAACATAATTAA--A-TTGTT
1 TTAATAAAATAAATTATTTGTA
257913 TTAATAAAATAAATTATTTGTA
1 TTAATAAAATAAATTATTTGTA
257935 TTAA
1 TTAA
257939 ATAACTTACC
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
19 14 0.42
20 1 0.03
21 1 0.03
22 17 0.52
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (22 bp):
TTAATAAAATAAATTATTTGTA
Found at i:258571 original size:15 final size:16
Alignment explanation
Indices: 258551--258582 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
258541 AAAATACAAC
258551 ATTCCC-AGTAATCTT
1 ATTCCCTAGTAATCTT
258566 ATTCCCTAGTAATCTT
1 ATTCCCTAGTAATCTT
258582 A
1 A
258583 CATTCTCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.41
Consensus pattern (16 bp):
ATTCCCTAGTAATCTT
Found at i:276366 original size:36 final size:36
Alignment explanation
Indices: 276324--276399 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
276314 TTATAGCTAA
*
276324 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
276360 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
276396 AAAA
1 AAAA
276400 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:280896 original size:15 final size:15
Alignment explanation
Indices: 280878--280907 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
280868 CCACGGTGCT
280878 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
280893 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
280908 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:281372 original size:36 final size:36
Alignment explanation
Indices: 281330--281405 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
281320 GTTATAGCTA
*
281330 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
281366 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
281402 AAAA
1 AAAA
281406 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:287719 original size:23 final size:23
Alignment explanation
Indices: 287693--287740 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
287683 ATAAAGTACA
*
287693 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
287716 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
287739 AT
1 AT
287741 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:288525 original size:23 final size:23
Alignment explanation
Indices: 288499--288561 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
288489 ATATAACCAC
288499 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
288522 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
288545 TACCTATTACATCATAT
1 TACCTATTACATTATAT
288562 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:289020 original size:39 final size:39
Alignment explanation
Indices: 288966--289052 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
288956 TCAAGTTGTA
*
288966 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
289005 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
289044 GATTTTGAT
1 GATTTTGAT
289053 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:289332 original size:18 final size:18
Alignment explanation
Indices: 289309--289345 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
289299 CGAAATATAT
289309 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
289327 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
289345 A
1 A
289346 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:289768 original size:25 final size:25
Alignment explanation
Indices: 289734--289784 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
289724 TTTTTCCAAA
*
289734 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
289759 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
289784 T
1 T
289785 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:290078 original size:21 final size:22
Alignment explanation
Indices: 290053--290104 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
290043 ACACTTTACA
*
290053 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
290076 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
290099 ATATAA
1 ATATAA
290105 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Done.