Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000239.1 Hibiscus syriacus cultivar Beakdansim tig00000413_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: 48278
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2011 original size:59 final size:62
Alignment explanation
Indices: 1898--2017 Score: 167
Period size: 59 Copynumber: 2.0 Consensus size: 62
1888 GTCGAGGGTT
* * *
1898 TACCTATGTTCTACGGAACATATGGACAGTTTTACCTATGTCTTTCGAGACTATGGGCAGTA
1 TACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCTTTCGAGACTATGGACAGTA
*
1960 TACCTATGTTCTAAGG-A-ATATGGACAG-TTTACCTAGGTCTTT-GGGACCTATGGACAGT
1 TACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCTTTCGAGA-CTATGGACAGT
2018 TGCCGAGGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
58 3 0.06
59 24 0.45
60 10 0.19
61 1 0.02
62 15 0.28
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (62 bp):
TACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCTTTCGAGACTATGGACAGTA
Found at i:2014 original size:30 final size:29
Alignment explanation
Indices: 1895--2018 Score: 97
Period size: 29 Copynumber: 4.1 Consensus size: 29
1885 AGAGTCGAGG
** *
1895 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATG-TCTTTGGGAC-TATGGACA
* *
1926 GTTTTACCTATGTCTTTCGAGACTATGGGCA
1 G-TTTACCTATGTCTTT-GGGACTATGGACA
* ** *
1957 GTATACCTATGT-TCTAAGGAATATGGACA
1 GTTTACCTATGTCT-TTGGGACTATGGACA
*
1986 GTTTACCTAGGTCTTTGGGACCTATGGACA
1 GTTTACCTATGTCTTTGGGA-CTATGGACA
2016 GTT
1 GTT
2019 GCCGAGGTTC
Statistics
Matches: 72, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
29 24 0.33
30 23 0.32
31 12 0.17
32 13 0.18
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (29 bp):
GTTTACCTATGTCTTTGGGACTATGGACA
Found at i:2031 original size:30 final size:29
Alignment explanation
Indices: 1978--2072 Score: 100
Period size: 30 Copynumber: 3.2 Consensus size: 29
1968 TTCTAAGGAA
* *
1978 TATGGACAGTTTACCTAGGTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTCTTTGTGACC
* *
2008 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGG-TCTTTGTGACC
* * *
2038 TCTGGATAGTTACCGGGGTCTTTGTGACC
1 TATGGACAGTTACCGAGGTCTTTGTGACC
*
2067 TCTGGA
1 TATGGA
2073 TAGGTCCTTC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
29 23 0.42
30 32 0.58
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (29 bp):
TATGGACAGTTACCGAGGTCTTTGTGACC
Found at i:2065 original size:29 final size:30
Alignment explanation
Indices: 1995--2075 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
1985 AGTTTACCTA
* * * *
1995 GGTCTTTGGGACCTATGGACAGTTGCCGAG
1 GGTCTTTGTGACCTCTGGATAGTTACCGAG
* *
2025 GTTCTTTATGACCTCTGGATAGTTACCG-G
1 GGTCTTTGTGACCTCTGGATAGTTACCGAG
2054 GGTCTTTGTGACCTCTGGATAG
1 GGTCTTTGTGACCTCTGGATAG
2076 GTCCTTCGGG
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 21 0.49
30 22 0.51
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.33
Consensus pattern (30 bp):
GGTCTTTGTGACCTCTGGATAGTTACCGAG
Found at i:4038 original size:14 final size:14
Alignment explanation
Indices: 4019--4054 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4009 AATAAATAGA
*
4019 AAATTAAAGTAATG
1 AAATTAAAGGAATG
*
4033 AAATTAAAGGATTG
1 AAATTAAAGGAATG
4047 AAATTAAA
1 AAATTAAA
4055 TAAAAAAAGT
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:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (14 bp):
AAATTAAAGGAATG
Found at i:6088 original size:40 final size:39
Alignment explanation
Indices: 5953--6106 Score: 175
Period size: 40 Copynumber: 3.8 Consensus size: 39
5943 TCTCTCGGAA
* * * *
5953 ATGTTGACCCAACTCCTT-TGTGATGGTTGACCCAAGGTG
1 ATGTTGATCCAACTCCTTATGTGATGGATGA-GCAAGATG
* *
5992 ATGCTGATCCAACTCCTTATGTGATGGACGAGCAAAATGATG
1 ATGTTGATCCAACTCCTTATGTGATGGATGAGC--AA-GATG
*
6034 ATGTTGATCCAACTCCTTTTGTGATGGATGAGTCAAGATG
1 ATGTTGATCCAACTCCTTATGTGATGGATGAG-CAAGATG
* *
6074 ATGTTGATCTAACTCCTTATGTGATGGACGAGC
1 ATGTTGATCCAACTCCTTATGTGATGGATGAGC
6107 TAATCTTCTC
Statistics
Matches: 98, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
39 18 0.18
40 43 0.44
41 4 0.04
42 32 0.33
43 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (39 bp):
ATGTTGATCCAACTCCTTATGTGATGGATGAGCAAGATG
Found at i:6089 original size:82 final size:81
Alignment explanation
Indices: 5953--6106 Score: 236
Period size: 82 Copynumber: 1.9 Consensus size: 81
5943 TCTCTCGGAA
* *
5953 ATGTTGACCCAACTCCTTTGTGATGGTTGACCCAAGGTGATGCTGATCCAACTCCTTATGTGATG
1 ATGTTGACCCAACTCCTTTGTGATGGATGACCCAAGATGATGCTGATCCAACTCCTTATGTGATG
6018 GACGAGCAAAATGATG
66 GACGAGCAAAATGATG
* ** * *
6034 ATGTTGATCCAACTCCTTTTGTGATGGATGAGTCAAGATGATGTTGATCTAACTCCTTATGTGAT
1 ATGTTGACCCAACTCC-TTTGTGATGGATGACCCAAGATGATGCTGATCCAACTCCTTATGTGAT
6099 GGACGAGC
65 GGACGAGC
6107 TAATCTTCTC
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
81 15 0.23
82 50 0.77
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (81 bp):
ATGTTGACCCAACTCCTTTGTGATGGATGACCCAAGATGATGCTGATCCAACTCCTTATGTGATG
GACGAGCAAAATGATG
Found at i:9084 original size:57 final size:54
Alignment explanation
Indices: 9023--9160 Score: 156
Period size: 54 Copynumber: 2.5 Consensus size: 54
9013 TAAATTTGGA
* **
9023 TTCTTCAAAAATTCATTT-ATGGTTATCATCAAGAAACCCCTAAAAATTAGGCTCAGC
1 TTCTTCAAAAATTCATTTGA-AG--A-CATCAAGAAACCCCTAAAAACCAGGCTCAGC
* *
9080 TTCTTTAAAAATTCATTTGAAGACATCAAGAAACCCCTAAAAACCAGGCTTAGC
1 TTCTTCAAAAATTCATTTGAAGACATCAAGAAACCCCTAAAAACCAGGCTCAGC
*
9134 TTCTTTC-AAAA-TCATTTGAGGACATCA
1 TTC-TTCAAAAATTCATTTGAAGACATCA
9161 TATTATTTGG
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
53 15 0.21
54 35 0.49
55 3 0.04
57 18 0.25
58 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (54 bp):
TTCTTCAAAAATTCATTTGAAGACATCAAGAAACCCCTAAAAACCAGGCTCAGC
Found at i:9129 original size:54 final size:53
Alignment explanation
Indices: 9049--9160 Score: 170
Period size: 54 Copynumber: 2.1 Consensus size: 53
9039 TTATGGTTAT
**
9049 CATCAAGAAACCCCTAAAAATTAGGCTCAGCTTCTTTAAAAATTCATTTGAAGA
1 CATCAAGAAACCCCTAAAAACCAGGCTCAGCTTCTTTAAAAA-TCATTTGAAGA
* * *
9103 CATCAAGAAACCCCTAAAAACCAGGCTTAGCTTCTTTCAAAATCATTTGAGGA
1 CATCAAGAAACCCCTAAAAACCAGGCTCAGCTTCTTTAAAAATCATTTGAAGA
9156 CATCA
1 CATCA
9161 TATTATTTGG
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 15 0.28
54 38 0.72
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (53 bp):
CATCAAGAAACCCCTAAAAACCAGGCTCAGCTTCTTTAAAAATCATTTGAAGA
Found at i:11772 original size:54 final size:54
Alignment explanation
Indices: 11687--11919 Score: 276
Period size: 54 Copynumber: 4.4 Consensus size: 54
11677 CTATGTGTAC
*
11687 TATAGGCACTAAGTGTGCAACCCAC-AGAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACGA-AATTCATAATATGTTGATGAACGACCG
* * * * **
11741 TATAGGCACTATGTATGCAACCCACGAAATTCATAATGTGTTTATGAATAACC-
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTGATGAACGACCG
* * * * *
11794 -ATAGGCGCTAAGTGTGCAACACACGGAATTCATCATATGTTGATGAACGACCA
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTGATGAACGACCG
* *
11847 TATCA-GCACTAAGTGTGCTACCCACGAAATTCATAATATGTTTATGAACGACCG
1 TAT-AGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTGATGAACGACCG
* *
11901 TATCGGCACTACGTGTGCA
1 TATAGGCACTAAGTGTGCA
11920 TCTCAAAGAA
Statistics
Matches: 147, Mismatches: 27, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
52 42 0.29
54 103 0.70
55 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTGATGAACGACCG
Found at i:11873 original size:106 final size:106
Alignment explanation
Indices: 11688--11894 Score: 326
Period size: 106 Copynumber: 2.0 Consensus size: 106
11678 TATGTGTACT
* * *
11688 ATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCGTATAGGCACTAT
1 ATAGGCACTAAGTGTGCAACACACAGAATTCATCATATGTTGATGAACGACCATATAGGCACTAA
*
11753 GTATGCAACCCACGAAATTCATAATGTGTTTATGAATAACC
66 GTATGCAACCCACGAAATTCATAATATGTTTATGAATAACC
* *
11794 ATAGGCGCTAAGTGTGCAACACACGGAATTCATCATATGTTGATGAACGACCATATCA-GCACTA
1 ATAGGCACTAAGTGTGCAACACACAGAATTCATCATATGTTGATGAACGACCATAT-AGGCACTA
* *
11858 AGTGTGCTACCCACGAAATTCATAATATGTTTATGAA
65 AGTATGCAACCCACGAAATTCATAATATGTTTATGAA
11895 CGACCGTATC
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
106 91 0.99
107 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (106 bp):
ATAGGCACTAAGTGTGCAACACACAGAATTCATCATATGTTGATGAACGACCATATAGGCACTAA
GTATGCAACCCACGAAATTCATAATATGTTTATGAATAACC
Found at i:15448 original size:23 final size:23
Alignment explanation
Indices: 15415--15466 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
15405 CGTCATTATC
* *
15415 TATACGGTGAGTGTTGCCATGCT
1 TATACGATGAGCGTTGCCATGCT
15438 TATACGATGAGCGTTGCCATGCT
1 TATACGATGAGCGTTGCCATGCT
15461 TATACG
1 TATACG
15467 GATCATAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (23 bp):
TATACGATGAGCGTTGCCATGCT
Found at i:19886 original size:144 final size:144
Alignment explanation
Indices: 19729--20008 Score: 411
Period size: 144 Copynumber: 1.9 Consensus size: 144
19719 AATAAAACAA
* * *
19729 ATTTATATTCTAAACCACAAAAACAAACAATACTCAAATCACCA-TTTGAGGTAAAAACTAAAAA
1 ATTTACATACTAAACCACAAAAACAAACAATACTCAAATCACCACTTGGA-GTAAAAACT-AAAA
* * * *
19793 AATACAAATTTA-ATACTAAAATTTGAAAACAAACAATACCCAAATCCCCATTTGGAGTAAAAAC
64 AACACAAATTTACATACTAAAATATGAAAACAAACAACACCCAAATCACCATTTGGAGTAAAAAC
19857 TAAAAAAAAAATACAC
129 TAAAAAAAAAATACAC
* **
19873 ATTTACATACTAAACTATGAAAACAAACAATACTCAAATCACCACTTGGAGTAAAAACTAAAAAA
1 ATTTACATACTAAACCACAAAAACAAACAATACTCAAATCACCACTTGGAGTAAAAACTAAAAAA
* *
19938 CACAAATTTACATACTAAACTATGAAAACAAACAACACCCAAATTACCATTTGGAGTAAAAACTA
66 CACAAATTTACATACTAAAATATGAAAACAAACAACACCCAAATCACCATTTGGAGTAAAAACTA
*
20003 AGAAAA
131 AAAAAA
20009 TAAGGGAAAT
Statistics
Matches: 121, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
143 15 0.12
144 102 0.84
145 4 0.03
ACGTcount: A:0.54, C:0.19, G:0.06, T:0.21
Consensus pattern (144 bp):
ATTTACATACTAAACCACAAAAACAAACAATACTCAAATCACCACTTGGAGTAAAAACTAAAAAA
CACAAATTTACATACTAAAATATGAAAACAAACAACACCCAAATCACCATTTGGAGTAAAAACTA
AAAAAAAAATACAC
Found at i:19895 original size:74 final size:71
Alignment explanation
Indices: 19725--20010 Score: 371
Period size: 70 Copynumber: 4.0 Consensus size: 71
19715 AATTAATAAA
* * * ** *
19725 ACAAATTTATATTCTAAACCACAAAAACAAACAATACTCAAATCACCATTT-GAGGTAAAAACTA
1 ACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGA-GTAAAAACTA
19789 AAAAAAT
65 AAAAAAT
* * *
19796 ACAAATTTA-ATACTAAAATTTGAAAACAAACAATACCCAAATCCCCATTTGGAGTAAAAACTAA
1 ACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGAGTAAAAACT--
19860 AAAAAAAAT
64 -AAAAAAAT
* * *
19869 ACACATTTACATACTAAACTATGAAAACAAACAATACTCAAATCACCACTTGGAGTAAAAACT-A
1 ACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGAGTAAAAACTAA
*
19933 AAAAAC
66 AAAAAT
* *
19939 ACAAATTTACATACTAAACTATGAAAACAAACAACACCCAAATTACCATTTGGAGTAAAAACTAA
1 ACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGAGTAAAAACTAA
*
20004 GAAAAT
66 AAAAAT
20010 A
1 A
20011 AGGGAAATTT
Statistics
Matches: 187, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
70 106 0.57
71 17 0.09
73 16 0.09
74 48 0.26
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.21
Consensus pattern (71 bp):
ACAAATTTACATACTAAACTATGAAAACAAACAATACCCAAATCACCATTTGGAGTAAAAACTAA
AAAAAT
Found at i:22098 original size:18 final size:18
Alignment explanation
Indices: 22059--22116 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
22049 TGTACTTGTG
* *
22059 TATATTTATTCAT-TTGTG
1 TATATTTATT-ATATTTTA
22077 TATATTTATTATATTTTA
1 TATATTTATTATATTTTA
22095 TATAATTATATTATA-TTTA
1 TAT-ATT-TATTATATTTTA
22114 TAT
1 TAT
22117 GCTTGAAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 2 0.06
18 16 0.46
19 10 0.29
20 7 0.20
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (18 bp):
TATATTTATTATATTTTA
Found at i:23771 original size:21 final size:21
Alignment explanation
Indices: 23745--23784 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
23735 TTCGCAACAC
23745 GAATTTGGAATTCACAACATA
1 GAATTTGGAATTCACAACATA
*
23766 GAATTTGGAATTCGCAACA
1 GAATTTGGAATTCACAACA
23785 CATAAGCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
GAATTTGGAATTCACAACATA
Found at i:23961 original size:20 final size:20
Alignment explanation
Indices: 23796--23987 Score: 67
Period size: 20 Copynumber: 9.5 Consensus size: 20
23786 ATAAGCCAAA
* *
23796 TTCGCAACTCGAATTTGACGAT
1 TTCGCAACACGAATTTTA--AT
* *
23818 TTCGCAACACTAATTTCT-TT
1 TTCGCAACACGAATTT-TAAT
* *
23838 TTCGTAACAC-AATTTTTAAA
1 TTCGCAACACGAA-TTTTAAT
* *
23858 TTCGCAACAAGATTTTCTAAT
1 TTCGCAACACGAATTT-TAAT
* **
23879 TT-GCAA-AGCGCATTTCGAT
1 TTCGCAACA-CGAATTTTAAT
* ***
23898 TTCACAATGTGAATTTT-AT
1 TTCGCAACACGAATTTTAAT
*
23917 TTGCGCAACTCG-ATTTTCGAA-
1 TT-CGCAACACGAATTTT--AAT
23938 TTCGCAACACGAATTTTAAT
1 TTCGCAACACGAATTTTAAT
* *
23958 TTCGCAAAAC-AACTTTTATT
1 TTCGCAACACGAA-TTTTAAT
*
23978 TTTGCAACAC
1 TTCGCAACAC
23988 AAATGTTTTG
Statistics
Matches: 125, Mismatches: 30, Indels: 32
0.67 0.16 0.17
Matches are distributed among these distances:
19 21 0.17
20 76 0.61
21 13 0.10
22 15 0.12
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (20 bp):
TTCGCAACACGAATTTTAAT
Found at i:24961 original size:24 final size:24
Alignment explanation
Indices: 24908--24954 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
24898 GTATTTGAAA
24908 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
*
24932 TTTGATCTTGGTCAATACTCGGA
1 TTTGATCTTGGTCAATACCCGGA
24955 TATTGATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:27244 original size:18 final size:18
Alignment explanation
Indices: 27210--27245 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
27200 AAGCAAAGGG
**
27210 AAATCAAAATCGTAATCA
1 AAATCAAAATCCCAATCA
27228 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
27246 CAACCGCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:27709 original size:20 final size:20
Alignment explanation
Indices: 27685--27741 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
27675 TTCGATATTA
27685 AAATTCGCAACTCGAAAAT-
1 AAATTCGCAACTCGAAAATG
*
27704 ATAATTCACAACTCGAAAATG
1 A-AATTCGCAACTCGAAAATG
* *
27725 AACTTTGCAACTCGAAA
1 AAATTCGCAACTCGAAA
27742 TTGATTTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.23
Consensus pattern (20 bp):
AAATTCGCAACTCGAAAATG
Found at i:27816 original size:20 final size:20
Alignment explanation
Indices: 27791--27829 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
27781 TCGAGTTGCG
*
27791 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGAGTTGCGAATTTC
27811 ATTTTCGAGTTGCGAATTT
1 ATTTTCGAGTTGCGAATTT
27830 GAATATCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.49
Consensus pattern (20 bp):
ATTTTCGAGTTGCGAATTTC
Found at i:27835 original size:54 final size:54
Alignment explanation
Indices: 27753--27870 Score: 175
Period size: 54 Copynumber: 2.2 Consensus size: 54
27743 TGATTTCAAT
* *
27753 TTTCATTTTCGCATTGTGAATTTAAATATCGAGTTGCGATTTTCGTGTTGCGAA
1 TTTCATTTTCGCATTGCGAATTTAAATATCAAGTTGCGATTTTCGTGTTGCGAA
* *
27807 TTTCATTTTCG-AGTTGCGAATTTGAATATCAAGTTGCGATTTTTGTGTTGCGAA
1 TTTCATTTTCGCA-TTGCGAATTTAAATATCAAGTTGCGATTTTCGTGTTGCGAA
*
27861 TTTGATTTTC
1 TTTCATTTTC
27871 TTAAAGGTAG
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
53 1 0.02
54 57 0.98
ACGTcount: A:0.21, C:0.12, G:0.20, T:0.47
Consensus pattern (54 bp):
TTTCATTTTCGCATTGCGAATTTAAATATCAAGTTGCGATTTTCGTGTTGCGAA
Found at i:27841 original size:20 final size:20
Alignment explanation
Indices: 27799--27845 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
27789 CGATTTTCGT
* * *
27799 GTTGCGAATTTCATTTTCGA
1 GTTGCGAATTTCAATATCAA
*
27819 GTTGCGAATTTGAATATCAA
1 GTTGCGAATTTCAATATCAA
27839 GTTGCGA
1 GTTGCGA
27846 TTTTTGTGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTCAATATCAA
Found at i:29754 original size:20 final size:21
Alignment explanation
Indices: 29727--29822 Score: 133
Period size: 21 Copynumber: 4.6 Consensus size: 21
29717 TGGAATGTGG
*
29727 ATCTTGAACGATGGGAGGTG-
1 ATCTTGAACGATGGGAGGGGC
*
29747 ATCATGAACGATGGGAGGGG-
1 ATCTTGAACGATGGGAGGGGC
29767 ACTCTTGAACGATGGGAGGGGC
1 A-TCTTGAACGATGGGAGGGGC
*
29789 CTCTTGAACGATGGGAGGGGC
1 ATCTTGAACGATGGGAGGGGC
*
29810 CTCTTGAACGATG
1 ATCTTGAACGATG
29823 AGAGATGAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
20 19 0.27
21 51 0.73
ACGTcount: A:0.24, C:0.16, G:0.40, T:0.21
Consensus pattern (21 bp):
ATCTTGAACGATGGGAGGGGC
Found at i:29785 original size:41 final size:42
Alignment explanation
Indices: 29728--29875 Score: 158
Period size: 42 Copynumber: 3.6 Consensus size: 42
29718 GGAATGTGGA
29728 TCTTGAACGATGGGAGGTG-ATCATGAACGATGGGAGGGGAC
1 TCTTGAACGATGGGAGGTGAATCATGAACGATGGGAGGGGAC
* ** * *
29769 TCTTGAACGATGGGAGGGGCCTCTTGAACGATGGGAGGGGCC
1 TCTTGAACGATGGGAGGTGAATCATGAACGATGGGAGGGGAC
* * * *
29811 TCTTGAACGATGAGAGATGAATCATGAACAAT-GGAGGTGGAT
1 TCTTGAACGATGGGAGGTGAATCATGAACGATGGGAGG-GGAC
* * *
29853 TC-TGAACAATGGTAGGTGGATCA
1 TCTTGAACGATGGGAGGTGAATCA
29876 GGCTTCTTCT
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
41 39 0.45
42 48 0.55
ACGTcount: A:0.28, C:0.14, G:0.37, T:0.22
Consensus pattern (42 bp):
TCTTGAACGATGGGAGGTGAATCATGAACGATGGGAGGGGAC
Found at i:29860 original size:20 final size:21
Alignment explanation
Indices: 29835--29873 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
29825 AGATGAATCA
29835 TGAACAATGG-AGGTGGATTC
1 TGAACAATGGTAGGTGGATTC
29855 TGAACAATGGTAGGTGGAT
1 TGAACAATGGTAGGTGGAT
29874 CAGGCTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.31, C:0.08, G:0.36, T:0.26
Consensus pattern (21 bp):
TGAACAATGGTAGGTGGATTC
Found at i:30181 original size:21 final size:21
Alignment explanation
Indices: 30157--30355 Score: 131
Period size: 21 Copynumber: 9.5 Consensus size: 21
30147 TGAAACAATC
*
30157 TCACGTAGAGCACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
* * *
30178 TCACGTAAAGCAGCTACGTAA
1 TCACGTAAAGCACCTACCTCA
* **
30199 CCACGTAAAGCACCGT-TGTCA
1 TCACGTAAAGCACC-TACCTCA
** *
30220 TCACGTAAAATAGCTACCTCA
1 TCACGTAAAGCACCTACCTCA
30241 TCACGTAAAG-ACCATACCTCA
1 TCACGTAAAGCACC-TACCTCA
** * **
30262 TCACGCCATGCACC-ATTTTCA
1 TCACGTAAAGCACCTA-CCTCA
*
30283 TCACGTAAAACA-CTGACCTCA
1 TCACGTAAAGCACCT-ACCTCA
*
30304 TCATGTAAAGCA-CTGACCTCA
1 TCACGTAAAGCACCT-ACCTCA
* *
30325 TCACGTAAAACACCTAACTCA
1 TCACGTAAAGCACCTACCTCA
30346 TC-CTGTAAAG
1 TCAC-GTAAAG
30356 GTGGAGAATA
Statistics
Matches: 136, Mismatches: 33, Indels: 18
0.73 0.18 0.10
Matches are distributed among these distances:
20 6 0.04
21 123 0.90
22 7 0.05
ACGTcount: A:0.34, C:0.32, G:0.13, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGCACCTACCTCA
Found at i:30275 original size:63 final size:63
Alignment explanation
Indices: 30172--30329 Score: 162
Period size: 63 Copynumber: 2.5 Consensus size: 63
30162 TAGAGCACCT
* * * ** * * *
30172 ACCTCATCACGTAAAGCAGCT-ACGTAACCACGTAAAGCACCGTTGTCATCACGTAAAATAGCT-
1 ACCTCATCACGTAAAGCA-CTGACCTCATCACGCCATGCACCATTGTCATCACGTAAAACA-CTG
*
30235 ACCTCATCACGTAAAG-ACCAT-ACCTCATCACGCCATGCACCATTTTCATCACGTAAAACACTG
1 ACCTCATCACGTAAAGCA-C-TGACCTCATCACGCCATGCACCATTGTCATCACGTAAAACACTG
*
30298 ACCTCATCATGTAAAGCACTGACCTCATCACG
1 ACCTCATCACGTAAAGCACTGACCTCATCACG
30330 TAAAACACCT
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
62 5 0.06
63 74 0.93
64 1 0.01
ACGTcount: A:0.34, C:0.32, G:0.13, T:0.22
Consensus pattern (63 bp):
ACCTCATCACGTAAAGCACTGACCTCATCACGCCATGCACCATTGTCATCACGTAAAACACTG
Found at i:30549 original size:42 final size:42
Alignment explanation
Indices: 30447--30591 Score: 188
Period size: 42 Copynumber: 3.5 Consensus size: 42
30437 GTGATGGAAT
*
30447 AGGTGATGGATCTCGGTGTCGAGGTGTAGAGTCGGCT--A-G
1 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGGCTCGATG
*
30486 AGGTGATGGCTCTCGGTGTCGAGGTGTAGAATCGGCTCGATG
1 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGGCTCGATG
* * * * **
30528 AGGTGATGGATCTTGGAGTCGAAGTGGAGAATCTACTCGATG
1 AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGGCTCGATG
*
30570 AGGTGATGGATCACGGTGTCGA
1 AGGTGATGGATCTCGGTGTCGA
30592 AGTGGATAAT
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
39 35 0.38
41 1 0.01
42 55 0.60
ACGTcount: A:0.21, C:0.14, G:0.40, T:0.26
Consensus pattern (42 bp):
AGGTGATGGATCTCGGTGTCGAGGTGTAGAATCGGCTCGATG
Found at i:30603 original size:42 final size:41
Alignment explanation
Indices: 30447--30612 Score: 167
Period size: 42 Copynumber: 4.0 Consensus size: 41
30437 GTGATGGAAT
* * * *
30447 AGGTGATGGATCTCGGTGTCGAGGTGTAGAGTCGGCT--A-G
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATC-TCTCGATG
* * * *
30486 AGGTGATGGCTCTCGGTGTCGAGGTGTAGAATCGGCTCGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATC-TCTCGATG
* *
30528 AGGTGATGGATCTTGGAGTCGAAGTGGAGAATCTACTCGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCT-CTCGATG
* *
30570 AGGTGATGGATCACGGTGTCGAAGTGGATAATCTCGTCGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCTC-TCGATG
30612 A
1 A
30613 AAAAGTGAGG
Statistics
Matches: 110, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
39 35 0.32
41 2 0.02
42 73 0.66
ACGTcount: A:0.22, C:0.14, G:0.39, T:0.26
Consensus pattern (41 bp):
AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCTCTCGATG
Found at i:32073 original size:13 final size:13
Alignment explanation
Indices: 32049--32101 Score: 76
Period size: 13 Copynumber: 4.2 Consensus size: 13
32039 TTTAGTAATT
32049 TTAAGATTTTGAAA
1 TTAAG-TTTTGAAA
32063 TTAAGTTTTGAAA
1 TTAAGTTTTGAAA
32076 TT---TTTTGAAA
1 TTAAGTTTTGAAA
32086 TTAAGTTTTGAAA
1 TTAAGTTTTGAAA
32099 TTA
1 TTA
32102 CTCCCCCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
10 10 0.28
13 21 0.58
14 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTTTTGAAA
Found at i:32085 original size:23 final size:23
Alignment explanation
Indices: 32055--32100 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
32045 AATTTTAAGA
32055 TTTTGAAATTAAGTTTTGAAATT
1 TTTTGAAATTAAGTTTTGAAATT
32078 TTTTGAAATTAAGTTTTGAAATT
1 TTTTGAAATTAAGTTTTGAAATT
32101 ACTCCCCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (23 bp):
TTTTGAAATTAAGTTTTGAAATT
Found at i:34000 original size:21 final size:21
Alignment explanation
Indices: 33966--34023 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
33956 CAGAACCCAT
* *
33966 GGGGTATCGATTCCCTC-AAG
1 GGGGAATCGGTTCCCTCAAAG
*
33986 GAGGGAATCGGTTCCAATCAAAG
1 G-GGGAATCGGTTCC-CTCAAAG
34009 GGGGAATCGGTTCCC
1 GGGGAATCGGTTCCC
34024 CTTCAAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 11 0.35
22 15 0.48
23 4 0.13
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGAATCGGTTCCCTCAAAG
Found at i:37991 original size:117 final size:117
Alignment explanation
Indices: 37771--37992 Score: 288
Period size: 117 Copynumber: 1.9 Consensus size: 117
37761 TTTTCAAATC
*
37771 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAAATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAAATTT
* *
37836 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
* * * * *
37888 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTT-TCTCAACAT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAAAAT
* * **
37951 TTCATTTTGATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
64 TTCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
37993 ATTATTTTTA
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
116 2 0.02
117 84 0.93
118 4 0.04
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.47
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAAATTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:40731 original size:15 final size:15
Alignment explanation
Indices: 40713--40745 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
40703 CTTGAAACTT
40713 AAATTCGCAACACGA
1 AAATTCGCAACACGA
*
40728 AAA-TCGCAACTCGA
1 AAATTCGCAACACGA
40742 AAAT
1 AAAT
40746 GAAATTTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
14 13 0.81
15 3 0.19
ACGTcount: A:0.48, C:0.24, G:0.12, T:0.15
Consensus pattern (15 bp):
AAATTCGCAACACGA
Found at i:40804 original size:60 final size:60
Alignment explanation
Indices: 40731--40845 Score: 180
Period size: 60 Copynumber: 1.9 Consensus size: 60
40721 AACACGAAAA
40731 TCGCAACTCGAAAATGAAATT-TGCAAGTCAAATTTTGAATTCGCAA-GTCGAATTTTGAAT
1 TCGCAACTCGAAAATGAAATTCT-CAAGTCAAATTTTGAATTCGCAACG-CGAATTTTGAAT
**
40791 TCGCAACTCGAAAATGAAATTCTCAAGTTGAATTTTGAATTCGCAACGCGAATTT
1 TCGCAACTCGAAAATGAAATTCTCAAGTCAAATTTTGAATTCGCAACGCGAATTT
40846 CTTTTTCGAG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
60 49 0.96
61 2 0.04
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (60 bp):
TCGCAACTCGAAAATGAAATTCTCAAGTCAAATTTTGAATTCGCAACGCGAATTTTGAAT
Found at i:40843 original size:20 final size:20
Alignment explanation
Indices: 40748--40845 Score: 101
Period size: 20 Copynumber: 4.9 Consensus size: 20
40738 TCGAAAATGA
* *
40748 AATTTGCAAGTCAAATTTTG
1 AATTCGCAAGTCGAATTTTG
40768 AATTCGCAAGTCGAATTTTG
1 AATTCGCAAGTCGAATTTTG
* **
40788 AATTCGCAACTCGAA-AATG
1 AATTCGCAAGTCGAATTTTG
* *
40807 AAATTCTCAAGTTGAATTTTG
1 -AATTCGCAAGTCGAATTTTG
40828 AATTCGCAACG-CGAATTT
1 AATTCGCAA-GTCGAATTT
40846 CTTTTTCGAG
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
19 2 0.03
20 58 0.92
21 3 0.05
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (20 bp):
AATTCGCAAGTCGAATTTTG
Found at i:40861 original size:20 final size:20
Alignment explanation
Indices: 40838--40906 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
40828 AATTCGCAAC
40838 GCGAATTTCTTTTTCGAGTT
1 GCGAATTTCTTTTTCGAGTT
*
40858 GCGATTTTCATTTTT-GAGTT
1 GCGAATTTC-TTTTTCGAGTT
** *
40878 GCGAATTTCAATTTCAAGTT
1 GCGAATTTCTTTTTCGAGTT
*
40898 GCGATTTTC
1 GCGAATTTC
40907 GTGTGGCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 3 0.07
20 33 0.80
21 5 0.12
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.48
Consensus pattern (20 bp):
GCGAATTTCTTTTTCGAGTT
Found at i:40916 original size:34 final size:33
Alignment explanation
Indices: 40878--40962 Score: 109
Period size: 33 Copynumber: 2.5 Consensus size: 33
40868 TTTTTGAGTT
*
40878 GCGAATTTCAATTTCAAGTTGCGATTTTCGTGTG
1 GCGAATTTCAATTTCAAGTTGAGA-TTTCGTGTG
* * *
40912 GCGAATTTCATTTTCGAGTTGAGATTTCGTGTT
1 GCGAATTTCAATTTCAAGTTGAGATTTCGTGTG
40945 GCGAATTT-AAGTTTCAAG
1 GCGAATTTCAA-TTTCAAG
40963 AATAAACTAC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 1 0.02
33 22 0.50
34 21 0.48
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.41
Consensus pattern (33 bp):
GCGAATTTCAATTTCAAGTTGAGATTTCGTGTG
Found at i:40949 original size:33 final size:34
Alignment explanation
Indices: 40875--40962 Score: 117
Period size: 34 Copynumber: 2.6 Consensus size: 34
40865 TCATTTTTGA
*
40875 GTTGCGAATTTCAATTTCAAGTTGCGATTTTCGT
1 GTTGCGAATTTCAATTTCAAGTTGAGATTTTCGT
* * *
40909 GTGGCGAATTTCATTTTCGAGTTGAGA-TTTCGT
1 GTTGCGAATTTCAATTTCAAGTTGAGATTTTCGT
40942 GTTGCGAATTT-AAGTTTCAAG
1 GTTGCGAATTTCAA-TTTCAAG
40963 AATAAACTAC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
32 1 0.02
33 22 0.48
34 23 0.50
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.42
Consensus pattern (34 bp):
GTTGCGAATTTCAATTTCAAGTTGAGATTTTCGT
Found at i:41334 original size:22 final size:22
Alignment explanation
Indices: 41309--41363 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
41299 ATGGAGGAGG
* * *
41309 GTCGTCAGATATGGGGACGGAT
1 GTCGCCAGAGATGGAGACGGAT
*
41331 GTCGCCAGAGATGGAGATGGAT
1 GTCGCCAGAGATGGAGACGGAT
41353 GTCGCCAGAGA
1 GTCGCCAGAGA
41364 GAGTGAGAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.40, T:0.18
Consensus pattern (22 bp):
GTCGCCAGAGATGGAGACGGAT
Found at i:41499 original size:39 final size:39
Alignment explanation
Indices: 41445--41554 Score: 105
Period size: 39 Copynumber: 2.8 Consensus size: 39
41435 ATTTACATTT
* ** * *
41445 GTGTTGCAAAAATAAAGCT-GTTTTGGAAAATTAAAATTC
1 GTGTTGCGAAAATAAA-CTCGCGTTGCAAAATTAAAAATC
* *
41484 GTGTTGCGAAAATAAATTCGCGTTGCAAATTTAAAAATC
1 GTGTTGCGAAAATAAACTCGCGTTGCAAAATTAAAAATC
* * *
41523 GTGTTGCGAAAAAAAAACTCGTGTTGCGAAAT
1 GTGTTGCG-AAAATAAACTCGCGTTGCAAAAT
41555 CGTCAAATTC
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
38 1 0.02
39 38 0.67
40 18 0.32
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (39 bp):
GTGTTGCGAAAATAAACTCGCGTTGCAAAATTAAAAATC
Found at i:41539 original size:20 final size:20
Alignment explanation
Indices: 41477--41553 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
41467 TTGGAAAATT
41477 AAAATTCGTGTTGCG-AAAA
1 AAAATTCGTGTTGCGAAAAA
* * *
41496 TAAATTCGCGTTGC-AAATTTA
1 AAAATTCGTGTTGCGAAA--AA
41517 AAAA-TCGTGTTGCGAAAAA
1 AAAATTCGTGTTGCGAAAAA
*
41536 AAAACTCGTGTTGCGAAA
1 AAAATTCGTGTTGCGAAA
41554 TCGTCAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
19 19 0.40
20 21 0.45
21 7 0.15
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (20 bp):
AAAATTCGTGTTGCGAAAAA
Found at i:44587 original size:31 final size:30
Alignment explanation
Indices: 44528--44603 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 30
44518 TTTAAATAGT
*
44528 TATTATATTTTATATTAATATATTTATATAAA
1 TATTAT-TTTT-TATTAAAATATTTATATAAA
*
44560 TATTATTTTTTATTAAAATAATTTATATAAT
1 TATTATTTTTTATTAAAAT-ATTTATATAAA
44591 TATTATTTATTTA
1 TATTATTT-TTTA
44604 GAATTATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 8 0.20
31 22 0.55
32 10 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TATTATTTTTTATTAAAATATTTATATAAA
Found at i:44795 original size:27 final size:27
Alignment explanation
Indices: 44743--44806 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
44733 TTAATATTTA
*
44743 AATTTAT-TTTATTTTAAAGTTATTAT
1 AATTTATATTAATTTTAAAGTTATTAT
* *
44769 GAATTTATATTAATTTT-AATTTTTTAT
1 -AATTTATATTAATTTTAAAGTTATTAT
*
44796 AATATATATTA
1 AATTTATATTA
44807 TTTAGGATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 10 0.31
27 15 0.47
28 7 0.22
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (27 bp):
AATTTATATTAATTTTAAAGTTATTAT
Found at i:46370 original size:20 final size:21
Alignment explanation
Indices: 46345--46458 Score: 119
Period size: 21 Copynumber: 5.5 Consensus size: 21
46335 TATGCCATCT
*
46345 CCGCAGGGTTACATT-CGAGA
1 CCGCAGGGTTACATTCCGAGC
*
46365 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
46386 CCGCCA-GGTTACATTCCGAGC
1 CCG-CAGGGTTACATTCCGAGC
* *
46407 CCGCAGGGTTACATTCCTAAC
1 CCGCAGGGTTACATTCCGAGC
* *
46428 CCGCCA-AGTTACATGT-CTAGC
1 CCG-CAGGGTTACAT-TCCGAGC
46449 CCGCAGGGTT
1 CCGCAGGGTT
46459 TTATACCATA
Statistics
Matches: 80, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
20 19 0.24
21 56 0.70
22 5 0.06
ACGTcount: A:0.21, C:0.32, G:0.25, T:0.22
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:46416 original size:42 final size:41
Alignment explanation
Indices: 46351--46458 Score: 162
Period size: 42 Copynumber: 2.6 Consensus size: 41
46341 ATCTCCGCAG
* *
46351 GGTTACATTCGAGACCGCAGGGTTACATTCCTAGCCCGCCA
1 GGTTACATTCGAGCCCGCAGGGTTACATTCCTAACCCGCCA
46392 GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAACCCGCCA
1 GGTTACATT-CGAGCCCGCAGGGTTACATTCCTAACCCGCCA
* *
46434 AGTTACATGTCTAGCCCGCAGGGTT
1 GGTTACAT-TCGAGCCCGCAGGGTT
46459 TTATACCATA
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
41 9 0.15
42 51 0.84
43 1 0.02
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.23
Consensus pattern (41 bp):
GGTTACATTCGAGCCCGCAGGGTTACATTCCTAACCCGCCA
Found at i:46996 original size:31 final size:32
Alignment explanation
Indices: 46960--47061 Score: 127
Period size: 34 Copynumber: 3.2 Consensus size: 32
46950 TGATAATATT
*
46960 TTAAAATACAAATATATTA-TCAAAATTTAAAA
1 TTAAAATA-AAATATATTATTCGAAATTTAAAA
*
46992 TAAAAATAAAA-ATATTATTCGAAATTTAAAA
1 TTAAAATAAAATATATTATTCGAAATTTAAAA
* *
47023 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATA-AAA-TATATTATTCGAAATTTAAAA
47057 TTAAA
1 TTAAA
47062 TTTCAACTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
30 6 0.10
31 22 0.36
32 10 0.16
34 23 0.38
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (32 bp):
TTAAAATAAAATATATTATTCGAAATTTAAAA
Found at i:47005 original size:32 final size:33
Alignment explanation
Indices: 46962--47054 Score: 111
Period size: 31 Copynumber: 2.9 Consensus size: 33
46952 ATAATATTTT
* *
46962 AAAATACAAATATATTA-TCAAAATTTAAAATA
1 AAAATAAAAATATATTATTCGAAATTTAAAATA
*
46994 AAAAT-AAAA-ATATTATTCGAAATTTAAAATT
1 AAAATAAAAATATATTATTCGAAATTTAAAATA
* *
47025 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATA-AAAATATATTATTCGAAATTTAA
47055 CATTAAATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
30 6 0.12
31 21 0.40
32 5 0.10
33 3 0.06
34 17 0.33
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.34
Consensus pattern (33 bp):
AAAATAAAAATATATTATTCGAAATTTAAAATA
Found at i:47685 original size:128 final size:128
Alignment explanation
Indices: 47457--47817 Score: 659
Period size: 128 Copynumber: 2.8 Consensus size: 128
47447 ACAATCCATC
*
47457 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
47522 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCTTGAGAAATAATAGGTACTCATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTCATATGAA
47585 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
47650 GGAAGACGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTCATATGAA
* *
47713 CAGTGACCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
47778 GGAAGGCGCGCCCCCGTGAACGCGCCTTCAAGTCCCCTGA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGA
47818 TAACATATTC
Statistics
Matches: 225, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 225 1.00
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (128 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTCATATGAA
Done.