Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002113.1 Hibiscus syriacus cultivar Beakdansim tig00004323_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: 66183
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:1574 original size:14 final size:14
Alignment explanation
Indices: 1557--1602 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1547 GGGATTTAGG
*
1557 GTTTAGGGTTTAAA
1 GTTTAGAGTTTAAA
* *
1571 GTTTAGATTTTAAT
1 GTTTAGAGTTTAAA
*
1585 GTTTAGAGTTTATA
1 GTTTAGAGTTTAAA
1599 GTTT
1 GTTT
1603 TGAGGTCCAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (14 bp):
GTTTAGAGTTTAAA
Found at i:1665 original size:21 final size:21
Alignment explanation
Indices: 1641--1689 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1631 TAGGATTTGG
* *
1641 GGTTTAGAGTATGGATTTTAA
1 GGTTTAGAATATGGAGTTTAA
* * *
1662 GGTTTGGAATTTTGAGTTTAA
1 GGTTTAGAATATGGAGTTTAA
1683 GGTTTAG
1 GGTTTAG
1690 GATTTGTGAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (21 bp):
GGTTTAGAATATGGAGTTTAA
Found at i:1702 original size:20 final size:20
Alignment explanation
Indices: 1658--1705 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1648 AGTATGGATT
1658 TTAAGGTTTGGAATTTTGAG
1 TTAAGGTTTGGAATTTTGAG
1678 TTTAAGGTTTAGG-ATTTGTGA-
1 -TTAAGGTTT-GGAATTT-TGAG
1699 TTAAGGT
1 TTAAGGT
1706 AAAGAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 7 0.28
21 13 0.52
22 5 0.20
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (20 bp):
TTAAGGTTTGGAATTTTGAG
Found at i:1945 original size:8 final size:7
Alignment explanation
Indices: 1920--1944 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1910 TCGTATATTA
1920 AAAATTT
1 AAAATTT
1927 AAAATTT
1 AAAATTT
1934 AAAATTT
1 AAAATTT
1941 AAAA
1 AAAA
1945 AGATCTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAAATTT
Found at i:4581 original size:30 final size:30
Alignment explanation
Indices: 4547--4604 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
4537 CATTCAGGCC
4547 GTTTGCTTTACTTGCAGCTT-CTATAATTGT
1 GTTTGCTTTACTTGCAGCTTGC-ATAATTGT
*
4577 GTTTGCTTTGCTTGCAGCTTGCATAATT
1 GTTTGCTTTACTTGCAGCTTGCATAATT
4605 ACAACTAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.16, C:0.17, G:0.19, T:0.48
Consensus pattern (30 bp):
GTTTGCTTTACTTGCAGCTTGCATAATTGT
Found at i:8588 original size:31 final size:31
Alignment explanation
Indices: 8552--8610 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
8542 AACTTAAAAG
* *
8552 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
8583 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
8611 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:8661 original size:22 final size:22
Alignment explanation
Indices: 8635--8677 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
8625 TAATAAATTA
8635 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
8657 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
8678 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:8686 original size:22 final size:22
Alignment explanation
Indices: 8637--8685 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
8627 ATAAATTATT
**
8637 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
8659 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
8682 TAAA
1 TAAA
8686 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:8689 original size:54 final size:54
Alignment explanation
Indices: 8625--9295 Score: 280
Period size: 54 Copynumber: 12.4 Consensus size: 54
8615 ACAACTACAA
*
8625 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* **
8679 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** ** *
8736 TTTTAAAATAAAT-CAATCCATACAAATAAAT-TATTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
8791 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * **
8845 TAATAAATTATTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** **
8902 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
* *
8957 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAA
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * * **
9005 TAAT-AA--A-TT-AAATCAAT-ACATACA-ACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCA-ATCCATATTTTAA-AATAAATCAATCCATAC
** * ** * ** ** * * *
9053 TTTTAAAATAAAT-CAATCCATACAAATAAATTATTTAAAAAAAAAACCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCA-TATTT-TAAAATAAATCAATCCATAC
9110 TAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATAC
* *
9174 -AACTACA--A--T--AATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
9222 TAATAAATTATTT----TAAATAAAT---TATTTTAAAATAAATCAATCCATATTTTA
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA----C
9273 TAATAAATTATTTTAAAATAAAT
1 TAATAAATTA-TTTAAAATAAAT
9296 TATTTTATAA
Statistics
Matches: 466, Mismatches: 89, Indels: 122
0.69 0.13 0.18
Matches are distributed among these distances:
47 26 0.06
48 60 0.13
49 35 0.08
50 15 0.03
51 12 0.03
52 13 0.03
53 1 0.00
54 120 0.26
55 20 0.04
56 39 0.08
57 38 0.08
58 57 0.12
60 1 0.00
61 1 0.00
62 2 0.00
63 3 0.01
64 21 0.05
65 2 0.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:8730 original size:80 final size:80
Alignment explanation
Indices: 8640--9092 Score: 701
Period size: 80 Copynumber: 5.7 Consensus size: 80
8630 AATTATTTAA
*
8640 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
8705 CCATACAACTACAAT
66 CCATACAACTACAAT
*
8720 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *
8785 TCATACTAA-TAAATTATTT
66 CCATAC-AACTACA--A--T
8804 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
*
8869 ATCTATACAACTACAAT
64 ATCCATACAACTACAAT
8886 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
8951 CCATACAACTACAAT
66 CCATACAACTACAAT
*
8966 AATAAATCAATCCATATTTTAAAATAAATCAATCC--A-TAAT--A--A--TAAATTAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
9022 ACATACAACTACAAT
66 CCATACAACTACAAT
*
9037 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAA
9093 AAAAAACCAA
Statistics
Matches: 343, Mismatches: 13, Indels: 34
0.88 0.03 0.09
Matches are distributed among these distances:
71 62 0.18
73 2 0.01
74 3 0.01
75 1 0.00
76 1 0.00
77 4 0.01
78 2 0.01
80 189 0.55
81 2 0.01
82 2 0.01
84 2 0.01
85 2 0.01
86 71 0.21
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.32
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:8766 original size:22 final size:22
Alignment explanation
Indices: 8693--8766 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
8683 AAATTATTTA
*
8693 AAATAAATCAATCCATACAACTACA
1 AAATAAATCAATCCATACAA--A-T
***
8718 ATAATAAATCAATCCATA-TTTT
1 A-AATAAATCAATCCATACAAAT
8740 AAAATAAATCAATCCATACAAAT
1 -AAATAAATCAATCCATACAAAT
8763 AAAT
1 AAAT
8767 TATTTAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
22 20 0.51
23 2 0.05
25 1 0.03
26 16 0.41
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATAAATCAATCCATACAAAT
Found at i:8776 original size:14 final size:14
Alignment explanation
Indices: 8759--8812 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
8749 CAATCCATAC
8759 AAATAAATTATTTA
1 AAATAAATTATTTA
*
8773 AAATAAATCAATTCATA
1 AAATAAAT-TATT--TA
*
8790 CTAATAAATTATTTA
1 -AAATAAATTATTTA
8805 AAATAAAT
1 AAATAAAT
8813 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 5 0.16
17 5 0.16
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:8776 original size:32 final size:32
Alignment explanation
Indices: 8737--9175 Score: 291
Period size: 32 Copynumber: 14.8 Consensus size: 32
8727 CAATCCATAT
8737 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
* *
8769 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
8801 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
8823 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
* * *
8855 TTTAAAATAAATCAATCTATACAACTACA--A
1 TTTAAAATAAATCAATCCATACAAATAAATTA
8885 --T--AATAAATCAATCCAT----AT------
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
8903 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
* *
8935 TTTAAAATAAATCAATCCATACAACTACA--A
1 TTTAAAATAAATCAATCCATACAAATAAATTA
8965 --T--AATAAATCAATCCAT----AT------
1 TTTAAAATAAATCAATCCATACAAATAAATTA
8983 TTTAAAATAAATCAATCCATA-ATAATAAATTA
1 TTTAAAATAAATCAATCCATACA-AATAAATTA
** * * * * *
9015 AAT-CAATACATACAACTACAATAATAAATCAATCCATA
1 TTTAAAATAAAT-CAA-T-CCAT-ACAAATAAAT---TA
9053 TTTTAAAATAAATCAATCCATACAAATAAATTA
1 -TTTAAAATAAATCAATCCATACAAATAAATTA
* * *
9086 TTTAAAAAAAAAACCAATCCATACTAATAAATTA
1 TTT--AAAATAAATCAATCCATACAAATAAATTA
*
9120 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
9152 TTTAAAATAAATCAATCCATACAA
1 TTTAAAATAAATCAATCCATACAA
9176 CTACAATAAT
Statistics
Matches: 326, Mismatches: 31, Indels: 100
0.71 0.07 0.22
Matches are distributed among these distances:
20 2 0.01
22 48 0.15
23 2 0.01
24 1 0.00
26 36 0.11
28 5 0.02
30 3 0.01
31 8 0.02
32 154 0.47
33 3 0.01
34 32 0.10
35 7 0.02
36 9 0.03
37 3 0.01
38 3 0.01
39 4 0.01
40 6 0.02
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACAAATAAATTA
Found at i:8813 original size:166 final size:166
Alignment explanation
Indices: 8625--9140 Score: 803
Period size: 166 Copynumber: 3.2 Consensus size: 166
8615 ACAACTACAA
8625 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
8690 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
*
8755 ATACAAATAAATTATTTAAAATAAATCAATTCATAC
131 ATACAAATAAATTATTTAAAATAAATCAATCCATAC
*
8791 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
*
8856 TTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
*
8921 ATACTAATAAATTATTTAAAATAAATCAATCCATAC
131 ATACAAATAAATTATTTAAAATAAATCAATCCATAC
*
8957 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAA-TC---C--AT-AA-TA
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTA
* * *
9007 -ATAAATTAAATCAATACATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
65 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
* *
9071 CATACAAATAAATTATTTAAAAAAAAAACCAATCCATAC
130 CATACAAATAAATTATTT--AAAATAAATCAATCCATAC
9110 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
9141 CTAATAAATT
Statistics
Matches: 326, Mismatches: 14, Indels: 27
0.89 0.04 0.07
Matches are distributed among these distances:
151 77 0.24
152 2 0.01
153 22 0.07
154 4 0.01
155 1 0.00
156 1 0.00
157 1 0.00
159 17 0.05
160 32 0.10
162 1 0.00
164 1 0.00
165 2 0.01
166 165 0.51
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (166 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
ATACAAATAAATTATTTAAAATAAATCAATCCATAC
Found at i:8827 original size:22 final size:22
Alignment explanation
Indices: 8801--8843 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
8791 TAATAAATTA
8801 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
8823 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
8844 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:8852 original size:22 final size:22
Alignment explanation
Indices: 8803--8851 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
8793 ATAAATTATT
**
8803 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
8825 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
8848 TAAA
1 TAAA
8852 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:8932 original size:22 final size:22
Alignment explanation
Indices: 8857--8931 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
8847 ATAAATTATT
* *
8857 TAAAATAAATCAATCTATACAA
1 TAAAATAAATCAATCCATATAA
**
8879 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
8905 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
8928 TAAA
1 TAAA
8932 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:8991 original size:22 final size:22
Alignment explanation
Indices: 8933--9074 Score: 115
Period size: 22 Copynumber: 6.1 Consensus size: 22
8923 ACTAATAAAT
8933 TATT-TAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
* *
8954 TACAACTACAATAATAAATCAATCCA
1 T---ATTATAA-AATAAATCAATCCA
*
8980 TATTTTAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
* * *
9002 TAATAATAAATTAAATCAATACA
1 T-ATTATAAAATAAATCAATCCA
* *
9025 TACAACTACAATAATAAATCAATCCA
1 T---ATTATAA-AATAAATCAATCCA
*
9051 TATTTTAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
9073 TA
1 TA
9075 CAAATAAATT
Statistics
Matches: 95, Mismatches: 17, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
21 1 0.01
22 31 0.33
23 26 0.27
24 2 0.02
25 7 0.07
26 28 0.29
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (22 bp):
TATTATAAAATAAATCAATCCA
Found at i:9206 original size:48 final size:46
Alignment explanation
Indices: 9143--9353 Score: 177
Period size: 47 Copynumber: 4.5 Consensus size: 46
9133 AATCCATACT
9143 AATAAATTA-TTTAAAATAAATCAATCCATAC-AACTACAA-TA-ATA
1 AATAAATTATTTTAAAATAAATCAATCCATACTAA-TA-AATTATATA
* *
9187 AATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTTA
1 AAT-AA-AT-TATTTTAAAATAAATCAATCCATACTAATAAATTA-TATA
* *
9237 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATA----CTAATAAATTA-TAT-A
* * * *
9289 AATAAATTATTTTATAATAAAT-TAT--TTA-TAATAAATTATTTA
1 AATAAATTATTTTAAAATAAATCAATCCATACTAATAAATTATATA
9331 TAATAAATTATTTTAAAATAAAT
1 -AATAAATTATTTTAAAATAAAT
9354 TATTTTATAA
Statistics
Matches: 145, Mismatches: 8, Indels: 29
0.80 0.04 0.16
Matches are distributed among these distances:
42 1 0.01
43 24 0.17
44 13 0.09
45 2 0.01
46 1 0.01
47 28 0.19
48 27 0.19
49 6 0.04
50 5 0.03
51 16 0.11
52 22 0.15
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (46 bp):
AATAAATTATTTTAAAATAAATCAATCCATACTAATAAATTATATA
Found at i:9208 original size:22 final size:22
Alignment explanation
Indices: 9183--9280 Score: 79
Period size: 22 Copynumber: 4.3 Consensus size: 22
9173 CAACTACAAT
*
9183 AATAAATCAATCTATATTTTAA
1 AATAAATCAATCCATATTTTAA
**
9205 AATAAATCAATCCATACTAATAA
1 AATAAATCAATCCATA-TTTTAA
* ** * **
9228 ATTATTTTAAATAAATTATTTTAA
1 AATA-AATCAATCCA-TATTTTAA
*
9252 AATAAATCAATCCATATTTTAT
1 AATAAATCAATCCATATTTTAA
9274 AATAAAT
1 AATAAAT
9281 TATTTTAAAA
Statistics
Matches: 55, Mismatches: 18, Indels: 6
0.70 0.23 0.08
Matches are distributed among these distances:
22 29 0.53
23 12 0.22
24 12 0.22
25 2 0.04
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Found at i:9242 original size:14 final size:15
Alignment explanation
Indices: 9222--9383 Score: 204
Period size: 15 Copynumber: 10.5 Consensus size: 15
9212 CAATCCATAC
9222 TAATAAATTATTTTA
1 TAATAAATTATTTTA
9237 -AATAAATTATTTTAAAA
1 TAATAAATTATTTT---A
*
9254 TAAATCAATCCATATTTTA
1 T-AATAAAT---TATTTTA
9273 TAATAAATTATTTTA
1 TAATAAATTATTTTA
*
9288 AAATAAATTATTTTA
1 TAATAAATTATTTTA
9303 TAATAAATTA-TTTA
1 TAATAAATTATTTTA
9317 TAATAAATTA-TTTA
1 TAATAAATTATTTTA
9331 TAATAAATTATTTTA
1 TAATAAATTATTTTA
*
9346 AAATAAATTATTTTA
1 TAATAAATTATTTTA
9361 TAATAAATTATTTTA
1 TAATAAATTATTTTA
*
9376 AAATAAAT
1 TAATAAAT
9384 AACCTTATTA
Statistics
Matches: 131, Mismatches: 7, Indels: 18
0.84 0.04 0.12
Matches are distributed among these distances:
14 41 0.31
15 69 0.53
17 1 0.01
18 6 0.05
19 8 0.06
22 6 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATAAATTATTTTA
Found at i:9396 original size:58 final size:57
Alignment explanation
Indices: 9270--9406 Score: 197
Period size: 58 Copynumber: 2.4 Consensus size: 57
9260 AATCCATATT
* * *
9270 TTATAATAAATTATTTTAAAATAAATTATTTTATAATAAATTATTTATAATAAATTAT
1 TTAT-ATAAATTATTTTAAAATAAATTATTTTATAATAAATTATTTAAAATAAATAAC
9328 TTATAATAAATTATTTTAAAATAAATTATTTTATAATAAATTATTTTAAAATAAATAACC
1 TTAT-ATAAATTATTTTAAAATAAATTATTTTATAATAAATTA-TTTAAAATAAATAA-C
9388 TTAT-TAAATTA-TTTAAAAT
1 TTATATAAATTATTTTAAAAT
9407 TATTTTAATA
Statistics
Matches: 74, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
57 8 0.11
58 50 0.68
59 12 0.16
60 4 0.05
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.48
Consensus pattern (57 bp):
TTATATAAATTATTTTAAAATAAATTATTTTATAATAAATTATTTAAAATAAATAAC
Found at i:11078 original size:19 final size:19
Alignment explanation
Indices: 11051--11095 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
11041 AAATGCAATT
*
11051 AGTGTATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
11070 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
11089 AGTGCAT
1 AGTGCAT
11096 TGATCCACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.24
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:11335 original size:24 final size:20
Alignment explanation
Indices: 11308--11365 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
11298 GCATGGGTAG
11308 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
11332 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
11352 TGTATCGATGCACT
1 TGCATCGATGCACT
11366 TCAAGGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:11840 original size:75 final size:75
Alignment explanation
Indices: 11678--11867 Score: 245
Period size: 75 Copynumber: 2.5 Consensus size: 75
11668 CAATTCAAAG
* * * * *
11678 CCAAAAATTCCAGATTGCTCAGAGGGAATCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGA
1 CCAAGAATTCCAGAATGCTCAGAGGGAACCGATT-CCCCCATAGGAGGAACCAATTCCCCCCTAA
**
11743 ATGGTTTGGCT
65 ACAGTTTGGCT
* * *
11754 CCGAGATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCAATTCCCCCCTAAA
1 CCAAGAATTCCAGAATGCTCAGAGGGAACCGATTCCCCCATAGGAGGAACCAATTCCCCCCTAAA
* *
11819 CAGTTTTGTT
66 CAGTTTGGCT
* *
11829 CCAAGAATTCCAGTATGCTCAGAGGGAACCGATCCCCCC
1 CCAAGAATTCCAGAATGCTCAGAGGGAACCGATTCCCCC
11868 CAAGGGGGTA
Statistics
Matches: 97, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
75 69 0.71
76 28 0.29
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.21
Consensus pattern (75 bp):
CCAAGAATTCCAGAATGCTCAGAGGGAACCGATTCCCCCATAGGAGGAACCAATTCCCCCCTAAA
CAGTTTGGCT
Found at i:14894 original size:21 final size:22
Alignment explanation
Indices: 14851--14904 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 22
14841 TTAGGCACAT
* *
14851 AAAATTAATACAATTTTTCTAA
1 AAAATTAATACAATTATTATAA
*
14873 AAAATT-ATATAATTATTATAA
1 AAAATTAATACAATTATTATAA
14894 ACATAATTAAT
1 A-A-AATTAAT
14905 TTTAGAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 13 0.50
22 7 0.27
23 4 0.15
24 2 0.08
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATTAATACAATTATTATAA
Found at i:15091 original size:21 final size:21
Alignment explanation
Indices: 15062--15101 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
15052 CAGATACCAA
*
15062 ATGTAAGACATGTTTTCATAC
1 ATGTAAGACATGCTTTCATAC
*
15083 ATGTTAGACATGCTTTCAT
1 ATGTAAGACATGCTTTCAT
15102 CTACATTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (21 bp):
ATGTAAGACATGCTTTCATAC
Found at i:17023 original size:31 final size:32
Alignment explanation
Indices: 16988--17057 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
16978 ATAATTGTAG
*
16988 TGTAGAAACATGCGTTAC-TTCTGTGTATAAT
1 TGTAGAAACATGCGGTACTTTCTGTGTATAAT
17019 TGTAGAAACATGCGGTACTTTCTGTGTATAAT
1 TGTAGAAACATGCGGTACTTTCTGTGTATAAT
17051 TGTAGAA
1 TGTAGAA
17058 GCATATGTGC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 17 0.46
32 20 0.54
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.37
Consensus pattern (32 bp):
TGTAGAAACATGCGGTACTTTCTGTGTATAAT
Found at i:25365 original size:156 final size:156
Alignment explanation
Indices: 25130--25477 Score: 449
Period size: 156 Copynumber: 2.2 Consensus size: 156
25120 TGAGCATGTG
*
25130 GTTCAAATTTGGTAAAAAAATGACTTAAAATAAATCACAAATTGAAAGAATAAAGAGATTATAAA
1 GTTCAAATTT-G-ATAAAAATGACTTAAAATAAATCACAAATTGAAAGAATAAAGAGATTATAAA
25195 AAATTGAAAGACTAAATT-AAAAATAAAAAAATTGTTATCAAAAA-ATAGGAATTAAAAGTACAC
64 AAATTGAAAGACTAAATTAAAAAATAAAAAAATTGTTATCAAAAAGA-A-GAATTAAAAGTACAC
* *
25258 ATATACTCTAATATGGTTTA-AAAGCATGTA
127 ATATACTCTAATATAGTTTAGAAA-CATATA
* * *
25288 GCTT-AAATTTGATAAAAATGACTTAAAATAAATGACGAATTTAATA-AAT-AAGAAGATTATAA
1 G-TTCAAATTTGATAAAAATGACTTAAAATAAATCACAAATTGAA-AGAATAAAG-AGATTATAA
25350 AAAATTG-AAGAACTAAATTAAAAAATAAAAAAATTGTTATCAAAAAGAAGAATTAAAAGTACAC
63 AAAATTGAAAG-ACTAAATTAAAAAATAAAAAAATTGTTATCAAAAAGAAGAATTAAAAGTACAC
* * * * *
25414 ATGTATTCTACTATAGTTTAGGAATATATA
127 ATATACTCTAATATAGTTTAGAAACATATA
25444 GTTCAAATTTGATAAATAATAGACTTAAAATAAA
1 GTTCAAATTTGATAAA-AAT-GACTTAAAATAAA
25478 GAAGGAATTG
Statistics
Matches: 169, Mismatches: 11, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
155 8 0.05
156 104 0.62
157 34 0.20
158 21 0.12
159 2 0.01
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (156 bp):
GTTCAAATTTGATAAAAATGACTTAAAATAAATCACAAATTGAAAGAATAAAGAGATTATAAAAA
ATTGAAAGACTAAATTAAAAAATAAAAAAATTGTTATCAAAAAGAAGAATTAAAAGTACACATAT
ACTCTAATATAGTTTAGAAACATATA
Found at i:33996 original size:18 final size:18
Alignment explanation
Indices: 33923--34002 Score: 54
Period size: 18 Copynumber: 4.2 Consensus size: 18
33913 ATATTTGAAA
* *
33923 ATTTAATATAAATATTAT
1 ATTTAATATTAATTTTAT
* *
33941 AATTAATATTTATTAATTAT
1 ATTTAATATTAATT--TTAT
* *
33961 GTATTCATATTTAA-TTTAT
1 AT-TTAATA-TTAATTTTAT
33980 ATTTAATATTAATTTTACT
1 ATTTAATATTAATTTTA-T
33999 ATTT
1 ATTT
34003 TTAAACTCGA
Statistics
Matches: 46, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
17 4 0.09
18 19 0.41
19 10 0.22
20 4 0.09
21 6 0.13
22 3 0.07
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (18 bp):
ATTTAATATTAATTTTAT
Found at i:37216 original size:15 final size:16
Alignment explanation
Indices: 37198--37231 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
37188 AATGAAAATA
37198 ATGAAAATATT-TTTT
1 ATGAAAATATTCTTTT
37213 ATGAAAATATTCTTTT
1 ATGAAAATATTCTTTT
37229 ATG
1 ATG
37232 TTTTCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (16 bp):
ATGAAAATATTCTTTT
Found at i:47810 original size:29 final size:29
Alignment explanation
Indices: 47767--47879 Score: 165
Period size: 29 Copynumber: 3.9 Consensus size: 29
47757 TATGTGATAT
47767 GAGAACATGACATGAGCTACATGAACACAA
1 GAGAA-ATGACATGAGCTACATGAACACAA
* *
47797 GAGAAATGAAATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGAACACAA
* *
47826 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGAACACAA
*
47855 GATAAATGACATGAG-TACATGAACA
1 GAGAAATGACATGAGCTACATGAACA
47880 TATGAAATAT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
28 9 0.12
29 62 0.82
30 5 0.07
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGAACACAA
Found at i:53562 original size:20 final size:20
Alignment explanation
Indices: 53537--53577 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
53527 AGGAAGAAGG
53537 AATGGAAGGACAATAGAGTA
1 AATGGAAGGACAATAGAGTA
53557 AATGGAAGGACAATAGAGTA
1 AATGGAAGGACAATAGAGTA
53577 A
1 A
53578 TTGCAAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.29, T:0.15
Consensus pattern (20 bp):
AATGGAAGGACAATAGAGTA
Found at i:53585 original size:20 final size:20
Alignment explanation
Indices: 53537--53586 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
53527 AGGAAGAAGG
*
53537 AATGGAAGGACAATAGAGTA
1 AATGCAAGGACAATAGAGTA
*
53557 AATGGAAGGACAATAGAGTA
1 AATGCAAGGACAATAGAGTA
*
53577 ATTGCAAGGA
1 AATGCAAGGA
53587 AAAATAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.48, C:0.06, G:0.30, T:0.16
Consensus pattern (20 bp):
AATGCAAGGACAATAGAGTA
Found at i:54315 original size:45 final size:46
Alignment explanation
Indices: 54229--54334 Score: 112
Period size: 45 Copynumber: 2.3 Consensus size: 46
54219 GATGTACTGG
** *
54229 TAGTGCATCGATGCACTCTTTTAAAATAAAAAGATCAAATGCA-AT
1 TAGTGCATCGATGCACTCCATTAAAATAAAAACATCAAATGCATAT
* *
54274 TAGTGCATCGATGCA-TCCCATTAATAAT-AAAACATCGAATGCATTT
1 TAGTGCATCGATGCACT-CCATTAA-AATAAAAACATCAAATGCATAT
*
54320 TA-TGCACCGATGCAC
1 TAGTGCATCGATGCAC
54335 AAGTAGTGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
44 1 0.02
45 44 0.86
46 6 0.12
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (46 bp):
TAGTGCATCGATGCACTCCATTAAAATAAAAACATCAAATGCATAT
Found at i:54769 original size:29 final size:29
Alignment explanation
Indices: 54730--54839 Score: 195
Period size: 29 Copynumber: 3.8 Consensus size: 29
54720 TATGTGATAT
54730 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
54760 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
54789 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
54818 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
54840 ATATATGAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
28 7 0.09
29 66 0.85
30 5 0.06
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:54942 original size:15 final size:15
Alignment explanation
Indices: 54924--54957 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
54914 GAGGGTATAA
54924 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
54939 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
54954 TAGT
1 TAGT
54958 GGTCCTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:56199 original size:127 final size:127
Alignment explanation
Indices: 55972--56321 Score: 637
Period size: 127 Copynumber: 2.7 Consensus size: 127
55962 ACTATTCACA
* *
55972 TGAAGGCTCATTCCCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCC-GGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
56037 TTATATCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
65 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
56100 TGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
1 TGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
56165 TATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* *
56227 TGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCTCTA
1 TGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
56292 TTATGTCACTCATGTCCCTCGGGGACACTA
65 TTATGTCACTCATGTCCCTCGGGGACACTA
56322 GATGGATTGT
Statistics
Matches: 216, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
127 130 0.60
128 86 0.40
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (127 bp):
TGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
TATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:56795 original size:35 final size:35
Alignment explanation
Indices: 56725--56824 Score: 118
Period size: 35 Copynumber: 3.0 Consensus size: 35
56715 AAATTTAATG
* *
56725 TTAAATTTTGAATACTATAA---TTTATTTTAAAT
1 TTAAATTTCGAATAATATAATTTTTTATTTTAAAT
* * *
56757 TTAAATTTCGAATAATATTATTTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTTTTATTTTAAAT
*
56792 TTAAATTTCGAATAATATAA-TTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTTTTATTTTAAA
56825 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
32 17 0.30
34 10 0.18
35 29 0.52
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (35 bp):
TTAAATTTCGAATAATATAATTTTTTATTTTAAAT
Found at i:57409 original size:42 final size:42
Alignment explanation
Indices: 57346--57454 Score: 164
Period size: 42 Copynumber: 2.6 Consensus size: 42
57336 TATGGTATAA
* * * *
57346 AACCCTACGGGCTAGGCATGTAACCTGGTGAGCTAGGAATGT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGAGCTAGGAATGT
* *
57388 AACCCTGTGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGAGCTAGGAATGT
57430 AACCCTGCGGGCTCGGAATGTAACC
1 AACCCTGCGGGCTCGGAATGTAACC
57455 CTGCGGAGAT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.20
Consensus pattern (42 bp):
AACCCTGCGGGCTCGGAATGTAACCTGGCGAGCTAGGAATGT
Found at i:57455 original size:21 final size:21
Alignment explanation
Indices: 57346--57460 Score: 137
Period size: 21 Copynumber: 5.5 Consensus size: 21
57336 TATGGTATAA
* *
57346 AACCCTACGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
57367 AA-CCTG-GTGAGCTAGGAATGT
1 AACCCTGCG-G-GCTAGGAATGT
* *
57388 AACCCTGTGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
57409 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
57430 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
57451 AACCCTGCGG
1 AACCCTGCGG
57461 AGATGGCATA
Statistics
Matches: 82, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.01
20 7 0.09
21 65 0.79
22 8 0.10
23 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.33, T:0.20
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:57490 original size:21 final size:21
Alignment explanation
Indices: 57464--57511 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
57454 CCTGCGGAGA
*
57464 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAACTGGAGGGCT
*
57485 TGGCATATGAAGTGGAGGGCT
1 TGGCATATGAACTGGAGGGCT
*
57506 GGGCAT
1 TGGCAT
57512 GTACCCCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.42, T:0.25
Consensus pattern (21 bp):
TGGCATATGAACTGGAGGGCT
Found at i:59078 original size:17 final size:17
Alignment explanation
Indices: 59041--59094 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
59031 CCATTATAAA
* *
59041 AAATT-AAAATTAATAT
1 AAATTAAAAATAAATTT
* * *
59057 AAATTCATAATAACTTT
1 AAATTAAAAATAAATTT
59074 AAATTAAAAATAAATTT
1 AAATTAAAAATAAATTT
59091 AAAT
1 AAAT
59095 ATTAACATTA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 5 0.17
17 25 0.83
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTAAAAATAAATTT
Found at i:59288 original size:33 final size:30
Alignment explanation
Indices: 59237--59315 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 30
59227 TTAATAATTC
*
59237 TAAATAAATAATAATTATATACATATTATTTTAA
1 TAAA-AAATAATAATTATAT--A-ATTATATTAA
*
59271 TAAAAAATAATATTTATATAATTATATTAA
1 TAAAAAATAATAATTATATAATTATATTAA
59301 TATAAAATATAATAA
1 TA-AAAA-ATAATAA
59316 CTTTTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 11 0.28
31 5 0.12
32 6 0.15
33 14 0.35
34 4 0.10
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (30 bp):
TAAAAAATAATAATTATATAATTATATTAA
Found at i:59295 original size:30 final size:32
Alignment explanation
Indices: 59237--59314 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 32
59227 TTAATAATTC
*
59237 TAAATAAATAATAATTATATACATATTATTTTAA
1 TAAA-AAATAAT-ATTATATACATATTATATTAA
*
59271 TAAAAAATAATATT-TATATA-ATTATATTAA
1 TAAAAAATAATATTATATACATATTATATTAA
59301 TATAAAATATAATA
1 TA-AAAA-ATAATA
59315 ACTTTTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
30 11 0.28
31 9 0.22
32 9 0.22
33 7 0.17
34 4 0.10
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (32 bp):
TAAAAAATAATATTATATACATATTATATTAA
Found at i:60026 original size:41 final size:40
Alignment explanation
Indices: 59972--60081 Score: 175
Period size: 41 Copynumber: 2.7 Consensus size: 40
59962 ATTCACGTTG
* *
59972 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
1 CATTTCGCGTTGCGATAGTTG-AAATCGCGTTGCGATTTTC
*
60013 CATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTT-GAAATCGCGTTGCGATTTTC
60054 CATTTCGCGTTGCGATAGTTGAAATCGC
1 CATTTCGCGTTGCGATAGTTGAAATCGC
60082 AACGCGATCT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
40 7 0.11
41 56 0.88
42 1 0.02
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.36
Consensus pattern (40 bp):
CATTTCGCGTTGCGATAGTTGAAATCGCGTTGCGATTTTC
Found at i:60068 original size:20 final size:20
Alignment explanation
Indices: 59997--60069 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
59987 TAGTTGAAAA
*
59997 TCGCGTTGCGTTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
60017 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCGAT-TTTCCATT
60038 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
60058 TCGCGTTGCGAT
1 TCGCGTTGCGAT
60070 AGTTGAAATC
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.11, C:0.22, G:0.27, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:60081 original size:20 final size:21
Alignment explanation
Indices: 59976--60081 Score: 67
Period size: 20 Copynumber: 5.2 Consensus size: 21
59966 ACGTTGCATT
*
59976 TCGCATTGCGATAGTT-GAAAA
1 TCGCGTTGCGATAGTTCG-AAA
** * **
59997 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATAGTTCGAAA
* *
60017 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCGATAGTTCGAAA
* * **
60038 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTCGAAA
60058 TCGCGTTGCGATAGTT-GAAA
1 TCGCGTTGCGATAGTTCGAAA
60078 TCGC
1 TCGC
60082 AACGCGATCT
Statistics
Matches: 61, Mismatches: 21, Indels: 7
0.69 0.24 0.08
Matches are distributed among these distances:
20 34 0.56
21 27 0.44
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTCGAAA
Found at i:60164 original size:20 final size:20
Alignment explanation
Indices: 60139--60231 Score: 125
Period size: 20 Copynumber: 4.6 Consensus size: 20
60129 TAGTTGAAAA
*
60139 TCGCGTTACGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
60159 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
60180 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
60200 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
60220 TCGCGTTGCGAT
1 TCGCGTTGCGAT
60232 AGTCTACAGT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
19 4 0.06
20 43 0.68
21 12 0.19
22 4 0.06
ACGTcount: A:0.13, C:0.25, G:0.23, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:60184 original size:41 final size:41
Alignment explanation
Indices: 60114--60211 Score: 153
Period size: 41 Copynumber: 2.4 Consensus size: 41
60104 ATTCGTGTTG
60114 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTC
* * *
60155 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTACGATTTTC
60196 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
60212 TTTCCATTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
41 52 0.98
42 1 0.02
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTC
Found at i:60192 original size:142 final size:141
Alignment explanation
Indices: 59944--60211 Score: 432
Period size: 142 Copynumber: 1.9 Consensus size: 141
59934 AATTCGCATT
* *
59944 GCGATCTCCACTATCGCAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTT
1 GCGATCTCCACTATCGCAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTACGAT
**
60009 TTTCCATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTT
66 TTTCCATTTCGCGTTGCGATAGTTACAGATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTT
60074 GAAATCGCAAC
131 GAAATCGCAAC
** *
60085 GCGATCTCCA-TCATCGCAAATTCGTGTTGCATTTCGCGTTGCGATAGTTGAAAATCGCGTTACG
1 GCGATCTCCACT-ATCGC-AATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTACG
60149 ATTTTCCATTTCGCGTTGCGATAGTCTACAG-TCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
64 ATTTTCCATTTCGCGTTGCGATAGT-TACAGATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
60212 TTTCCATTTC
Statistics
Matches: 117, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
140 1 0.01
141 15 0.13
142 98 0.84
143 3 0.03
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (141 bp):
GCGATCTCCACTATCGCAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTACGAT
TTTCCATTTCGCGTTGCGATAGTTACAGATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTT
GAAATCGCAAC
Found at i:60217 original size:61 final size:61
Alignment explanation
Indices: 60139--60258 Score: 222
Period size: 61 Copynumber: 2.0 Consensus size: 61
60129 TAGTTGAAAA
*
60139 TCGCGTTACGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATT
1 TCGCGTTACGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGAGTTGCGATTTTCCATT
*
60200 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGAGTTGCGATTTTCCA
1 TCGCGTTACGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGAGTTGCGATTTTCCA
60259 AATTCGTTGC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (61 bp):
TCGCGTTACGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGAGTTGCGATTTTCCATT
Found at i:60506 original size:6 final size:6
Alignment explanation
Indices: 60470--60545 Score: 117
Period size: 6 Copynumber: 13.5 Consensus size: 6
60460 TCTCGTCTCG
60470 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
60513 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
60546 AATACGTGTC
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 25 0.36
6 45 0.64
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:60747 original size:41 final size:41
Alignment explanation
Indices: 60695--60952 Score: 439
Period size: 41 Copynumber: 6.3 Consensus size: 41
60685 ACTGTATACT
* * *
60695 ATCGCAACGCGATTTTCA-ACTATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGACTGT-AGACTATCGCAACGCGAAATGGAAA
* *
60736 ATCGCAACGCGATTTTCA-ACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGACTGT-AGACTATCGCAACGCGAAATGGAAA
60777 ATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAA
60818 ATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAA
60859 ATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAA
60900 ATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAA
60941 ATCGCAACGCGA
1 ATCGCAACGCGA
60953 AATGGAAAAT
Statistics
Matches: 213, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
40 1 0.00
41 212 1.00
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (41 bp):
ATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAA
Found at i:61624 original size:17 final size:18
Alignment explanation
Indices: 61597--61637 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
61587 AATTTATTAA
*
61597 ATATTTTATTTTTGAATT
1 ATATTTAATTTTTGAATT
*
61615 A-ATTTAATTTTTTAATT
1 ATATTTAATTTTTGAATT
61632 ATATTT
1 ATATTT
61638 CATACATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
ATATTTAATTTTTGAATT
Found at i:64101 original size:50 final size:49
Alignment explanation
Indices: 64042--64168 Score: 139
Period size: 51 Copynumber: 2.5 Consensus size: 49
64032 AGCAGTAAAG
* * * *
64042 CGCGCCCCCTGAATCGCGCTATATGCTGATTTGCG-CCACGTGGAGTATAA
1 CGCGCCCCCTG-ATCGCGCTATACGCTGA-CTGAGTACACGTGGAGTATAA
* * *
64092 CGCGCCCCCTGTACCGCGCTATACGCTGACTGAGTTACACGTGGGGTATAG
1 CGCGCCCCCTG-ATCGCGCTATACGCTGACTGAG-TACACGTGGAGTATAA
64143 CGCGCCCCCTGATCCGCGCTATACGC
1 CGCGCCCCCTGAT-CGCGCTATACGC
64169 CATGTAGGGG
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
49 3 0.05
50 27 0.42
51 35 0.54
ACGTcount: A:0.17, C:0.35, G:0.27, T:0.21
Consensus pattern (49 bp):
CGCGCCCCCTGATCGCGCTATACGCTGACTGAGTACACGTGGAGTATAA
Done.