Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003866.1 Hibiscus syriacus cultivar Beakdansim tig00008319_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: 51723
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:8762 original size:65 final size:65
Alignment explanation
Indices: 8627--8782 Score: 183
Period size: 65 Copynumber: 2.4 Consensus size: 65
8617 TTTTCGTCTT
* * * *
8627 ACTTGAGACAGTTTTC-CTTGAACACAAGTTTAGAAATTGTTTCAATCTAAAGAAAGTTTTTATC
1 ACTTGAGATA-TTTTCTCTTGAATACAAGTTTAGAAATTATTTC-ATCTAAAGAAAATTTTTATC
8691 TC
64 TC
* *
8693 ACTTGAGATATTTTCTCTTGAAATACAA-TTTTGAAATTATTTC-TCTCAAGACAAATTTTTATC
1 ACTTGAGATATTTTCTCTTG-AATACAAGTTTAGAAATTATTTCATCTAAAGA-AAATTTTTATC
8756 TC
64 TC
*
8758 ACTTGGGATATTTTCTCTTGGAATA
1 ACTTGAGATATTTTCTCTT-GAATA
8783 TGATTTTTGA
Statistics
Matches: 79, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
64 7 0.09
65 39 0.49
66 27 0.34
67 6 0.08
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (65 bp):
ACTTGAGATATTTTCTCTTGAATACAAGTTTAGAAATTATTTCATCTAAAGAAAATTTTTATCTC
Found at i:10886 original size:33 final size:33
Alignment explanation
Indices: 10814--10886 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
10804 AATACTAGCT
*
10814 CGCTAACTTTTTATTTTATTGTTCGAACTAACC
1 CGCTAACTTTTTATTTTATTGTCCGAACTAACC
**
10847 TACTAACTTTTTATTTTATTGTCCGAACTAACC
1 CGCTAACTTTTTATTTTATTGTCCGAACTAACC
10880 CGCTAAC
1 CGCTAAC
10887 ACCATTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.42
Consensus pattern (33 bp):
CGCTAACTTTTTATTTTATTGTCCGAACTAACC
Found at i:11114 original size:29 final size:29
Alignment explanation
Indices: 11081--11136 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
11071 CATTTTAGTA
11081 CTTTTATTTTAGCCCCTTT-AGTTTCCAGT
1 CTTTTATTTTAG-CCCTTTCAGTTTCCAGT
*
11110 CTTTTATTTTAGTCCTTTCAGTTTCCA
1 CTTTTATTTTAGCCCTTTCAGTTTCCA
11137 ACTCTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.14, C:0.23, G:0.09, T:0.54
Consensus pattern (29 bp):
CTTTTATTTTAGCCCTTTCAGTTTCCAGT
Found at i:11127 original size:14 final size:14
Alignment explanation
Indices: 11072--11127 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
11062 AGAACTTTAC
*
11072 ATTTTAGTACTTTT
1 ATTTTAGTCCTTTT
* *
11086 ATTTTAGCCCCTTT
1 ATTTTAGTCCTTTT
*
11100 AGTTTCCAGT-CTTTT
1 A-TTT-TAGTCCTTTT
11115 ATTTTAGTCCTTT
1 ATTTTAGTCCTTT
11128 CAGTTTCCAA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
13 3 0.09
14 19 0.59
15 8 0.25
16 2 0.06
ACGTcount: A:0.16, C:0.18, G:0.09, T:0.57
Consensus pattern (14 bp):
ATTTTAGTCCTTTT
Found at i:11144 original size:28 final size:29
Alignment explanation
Indices: 11084--11147 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
11074 TTTAGTACTT
* *
11084 TTATTTTAGCCCCTTTAGTTTCCAGTCTT
1 TTATTTTAGCCCCTTTAGTTTCCAGACTC
*
11113 TTATTTTAG-TCCTTTCAGTTTCCA-ACTC
1 TTATTTTAGCCCCTTT-AGTTTCCAGACTC
11141 TTATTTT
1 TTATTTT
11148 TCTATATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.16, C:0.22, G:0.08, T:0.55
Consensus pattern (29 bp):
TTATTTTAGCCCCTTTAGTTTCCAGACTC
Found at i:11823 original size:23 final size:22
Alignment explanation
Indices: 11772--11825 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
11762 GTTTATTTTA
11772 TTTTACTTTATTTTGCTTATTAT
1 TTTTA-TTTATTTTGCTTATTAT
* *
11795 TATTATTTCATTTTGGTTCATT-T
1 TTTTATTT-ATTTTGCTT-ATTAT
11818 TTTTATTT
1 TTTTATTT
11826 GTTTATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 3 0.12
23 20 0.77
24 3 0.12
ACGTcount: A:0.17, C:0.07, G:0.06, T:0.70
Consensus pattern (22 bp):
TTTTATTTATTTTGCTTATTAT
Found at i:18899 original size:11 final size:11
Alignment explanation
Indices: 18885--18983 Score: 87
Period size: 11 Copynumber: 8.6 Consensus size: 11
18875 AAAAATCAAG
18885 AGCTCGATTGA
1 AGCTCGATTGA
*
18896 AGCTCGAGACTCG-
1 AGCTC--GA-TTGA
18909 AGCTCGATTGA
1 AGCTCGATTGA
18920 AGCTCGATTGA
1 AGCTCGATTGA
18931 AGCTCGATTTTG-
1 AGCTCGA--TTGA
18943 AGCTCGATTTTG-
1 AGCTCGA--TTGA
*
18955 AGCTCGATTCA
1 AGCTCGATTGA
*
18966 AGCTCGATTCA
1 AGCTCGATTGA
18977 AGCTCGA
1 AGCTCGA
18984 ACTCGATTAA
Statistics
Matches: 78, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
10 4 0.05
11 43 0.55
12 19 0.24
13 10 0.13
14 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.28
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:18937 original size:46 final size:45
Alignment explanation
Indices: 18885--18983 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 45
18875 AAAAATCAAG
* *
18885 AGCTCGA-TTGAAGCTCGAGACTCGAGCTCGATTGAAGCTCGATTGA
1 AGCTCGATTTG-AGCTCGA-ACTCGAGCTCGATTCAAGCTCGATTCA
** *
18931 AGCTCGATTTTGAGCTCGATTTTGAGCTCGATTCAAGCTCGATTCA
1 AGCTCGA-TTTGAGCTCGAACTCGAGCTCGATTCAAGCTCGATTCA
18977 AGCTCGA
1 AGCTCGA
18984 ACTCGATTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
46 36 0.78
47 7 0.15
48 3 0.07
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.28
Consensus pattern (45 bp):
AGCTCGATTTGAGCTCGAACTCGAGCTCGATTCAAGCTCGATTCA
Found at i:18948 original size:12 final size:12
Alignment explanation
Indices: 18931--18963 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
18921 GCTCGATTGA
18931 AGCTCGATTTTG
1 AGCTCGATTTTG
18943 AGCTCGATTTTG
1 AGCTCGATTTTG
18955 AGCTCGATT
1 AGCTCGATT
18964 CAAGCTCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (12 bp):
AGCTCGATTTTG
Found at i:18973 original size:35 final size:33
Alignment explanation
Indices: 18884--18983 Score: 112
Period size: 35 Copynumber: 2.9 Consensus size: 33
18874 AAAAAATCAA
**
18884 GAGCTCGATTGAAGCTCGAGACTCGAGCTCGATT
1 GAGCTCGATTGAAGCTCGA-TTTCGAGCTCGATT
*
18918 GAAGCTCGATTGAAGCTCGATTTTGAGCTCGATTTT
1 G-AGCTCGATTGAAGCTCGATTTCGAGCTCGA--TT
* *
18954 GAGCTCGATTCAAGCTCGA-TTCAAGCTCGA
1 GAGCTCGATTGAAGCTCGATTTCGAGCTCGA
18984 ACTCGATTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
34 19 0.33
35 35 0.61
36 3 0.05
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (33 bp):
GAGCTCGATTGAAGCTCGATTTCGAGCTCGATT
Found at i:18990 original size:17 final size:17
Alignment explanation
Indices: 18968--19004 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
18958 TCGATTCAAG
*
18968 CTCGATTCAAGCTCGAA
1 CTCGATTAAAGCTCGAA
18985 CTCGATTAAAGCTCGAA
1 CTCGATTAAAGCTCGAA
19002 CTC
1 CTC
19005 AAACTCGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (17 bp):
CTCGATTAAAGCTCGAA
Found at i:19315 original size:21 final size:21
Alignment explanation
Indices: 19291--19372 Score: 87
Period size: 21 Copynumber: 3.9 Consensus size: 21
19281 CTTAAACCCC
19291 AACACATAAACCCTAAATCTT
1 AACACATAAACCCTAAATCTT
19312 AACACATAAACCCTAAA-CTCT
1 AACACATAAACCCTAAATCT-T
* * *
19333 AA-ACTTTAAACCTTAAATCCT
1 AACAC-ATAAACCCTAAATCTT
* *
19354 ATCACATAAACCCAAAATC
1 AACACATAAACCCTAAATC
19373 CTAAACCCTA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 4 0.08
21 43 0.86
22 3 0.06
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (21 bp):
AACACATAAACCCTAAATCTT
Found at i:19329 original size:42 final size:42
Alignment explanation
Indices: 19283--19366 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
19273 TGGCATAACT
*
19283 TAAACCCCAACAC-ATAAACCCTAAATCTTAACACATAAACCC
1 TAAACCCCAA-ACTATAAACCCTAAATCCTAACACATAAACCC
* * * * *
19325 TAAACTCTAAACTTTAAACCTTAAATCCTATCACATAAACCC
1 TAAACCCCAAACTATAAACCCTAAATCCTAACACATAAACCC
19367 AAAATCCTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.06
42 33 0.94
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (42 bp):
TAAACCCCAAACTATAAACCCTAAATCCTAACACATAAACCC
Found at i:19377 original size:42 final size:42
Alignment explanation
Indices: 19297--19389 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
19287 CCCCAACACA
* * * **
19297 TAAACCCTAAATCTTAACACATAAACCCTAAACTCTAAACTT
1 TAAACCTTAAATCCTAACACATAAACCCAAAACTCTAAACCC
*
19339 TAAACCTTAAATCCTATCACATAAACCCAAAA-TCCTAAACCC
1 TAAACCTTAAATCCTAACACATAAACCCAAAACT-CTAAACCC
19381 TAAACCTTA
1 TAAACCTTA
19390 TCACATAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
41 1 0.02
42 43 0.98
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (42 bp):
TAAACCTTAAATCCTAACACATAAACCCAAAACTCTAAACCC
Found at i:19677 original size:15 final size:14
Alignment explanation
Indices: 19651--19680 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19641 TTTATTCATC
19651 AATAATGTATTTTT
1 AATAATGTATTTTT
*
19665 AATAATGTAATTTT
1 AATAATGTATTTTT
19679 AA
1 AA
19681 AAAATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:20043 original size:30 final size:30
Alignment explanation
Indices: 19973--20053 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 30
19963 AAAAATATAG
* *
19973 TTTTAAATTTTTTTAAATATTTAATTTGAT
1 TTTTAAATTTTTTTAAATATTCAATTTAAT
*
20003 CTTTACAATTTTTTTAGAA-ATTC-ATATTAAT
1 TTTTA-AATTTTTTTA-AATATTCAAT-TTAAT
20034 TTTTAAA--TTTTTAAATATTC
1 TTTTAAATTTTTTTAAATATTC
20054 TTAATTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
27 2 0.05
28 10 0.23
30 8 0.19
31 21 0.49
32 2 0.05
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (30 bp):
TTTTAAATTTTTTTAAATATTCAATTTAAT
Found at i:21169 original size:15 final size:14
Alignment explanation
Indices: 21143--21172 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21133 TTTATTCATC
21143 AATAATGTATTTTT
1 AATAATGTATTTTT
*
21157 AATAATGTAATTTT
1 AATAATGTATTTTT
21171 AA
1 AA
21173 AAAATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:21535 original size:30 final size:30
Alignment explanation
Indices: 21465--21545 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 30
21455 AAAAATATAG
* *
21465 TTTTAAATTTTTTTAAATATTTAATTTGAT
1 TTTTAAATTTTTTTAAATATTCAATTTAAT
*
21495 CTTTACAATTTTTTTAGAA-ATTC-ATATTAAT
1 TTTTA-AATTTTTTTA-AATATTCAAT-TTAAT
21526 TTTTAAA--TTTTTAAATATTC
1 TTTTAAATTTTTTTAAATATTC
21546 TTAATTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
27 2 0.05
28 10 0.23
30 8 0.19
31 21 0.49
32 2 0.05
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (30 bp):
TTTTAAATTTTTTTAAATATTCAATTTAAT
Found at i:26599 original size:58 final size:59
Alignment explanation
Indices: 26500--26644 Score: 179
Period size: 59 Copynumber: 2.4 Consensus size: 59
26490 TAAAAAAGGT
* * *
26500 AAAG-TACATAAATGGTCTCTCGATTATAGAGTGTTGTTTTGTTGACTCCC-CGACTATTA
1 AAAGTTACA-AAATGGTCTCT-GACTATAGAGCGTTATTTTGTTGACTCCCTCGACTATTA
* *
26559 AAGGTTACAAAATGGTCTCTGACTATA-AGGCGTTATTTTGTTGAGTCCCTCGACTATTA
1 AAAGTTACAAAATGGTCTCTGACTATAGA-GCGTTATTTTGTTGACTCCCTCGACTATTA
*
26618 AAAGTTACAAAATGGTCATCCGACTAT
1 AAAGTTACAAAATGGTC-TCTGACTAT
26645 TCATATGTTC
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
57 1 0.01
58 23 0.31
59 39 0.52
60 12 0.16
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (59 bp):
AAAGTTACAAAATGGTCTCTGACTATAGAGCGTTATTTTGTTGACTCCCTCGACTATTA
Found at i:26765 original size:29 final size:30
Alignment explanation
Indices: 26715--26789 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 30
26705 TTTTTGTCTA
***
26715 GTGACTAAAATGTAAGTTTTG-AAAGTTTG
1 GTGACTAAAATGTAAACATTGAAAAGTTTG
*
26744 GTGACTAAAGTGTAAACATTGAAAAGTTTAG
1 GTGACTAAAATGTAAACATTGAAAAGTTT-G
*
26775 G-GATTGAAAATGTAA
1 GTGACT-AAAATGTAA
26790 TTTTTAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
29 17 0.46
30 10 0.27
31 10 0.27
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (30 bp):
GTGACTAAAATGTAAACATTGAAAAGTTTG
Found at i:28814 original size:131 final size:131
Alignment explanation
Indices: 28578--28823 Score: 298
Period size: 131 Copynumber: 1.9 Consensus size: 131
28568 GGGAAAAAAG
* * *
28578 AAATATTTAATTATCTTCCATCGAGAAGAAACGACCTCTCATGCCTTGAAGCAGTCATTCCTTAA
1 AAATATCTAATTATCTTCCATCGAGAAGAAACGACCTCTCATGCCTTAAAGCAGTCATTCATTAA
* * * *
28643 TCCAATCAAAATAAAGAAATATTATTATTCCCTTCTAAAATTAAATATTAATCCGAGAGAAAATG
66 TCCAATCAAAATAAAGAAATATTACTATTCCATCCCAAAATTAAATATTAATCCGAGAGAAAATG
28708 A
131 A
* * * * *
28709 AAATATCTAATTAT-TTCCAATCGAGAATAAATGGCCTCTCATGCCTTAAAGCGGTCATTTATTA
1 AAATATCTAATTATCTTCC-ATCGAGAAGAAACGACCTCTCATGCCTTAAAGCAGTCATTCATTA
* * * ** *
28773 CTCGAATCGAAA-CGAGAAGATATTACTATTTCATCCCAAAATTAAATATTA
65 ATCCAATCAAAATAAAGAA-ATATTACTATTCCATCCCAAAATTAAATATTA
28824 TTTTGAATGT
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
130 8 0.08
131 87 0.92
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (131 bp):
AAATATCTAATTATCTTCCATCGAGAAGAAACGACCTCTCATGCCTTAAAGCAGTCATTCATTAA
TCCAATCAAAATAAAGAAATATTACTATTCCATCCCAAAATTAAATATTAATCCGAGAGAAAATG
A
Found at i:30973 original size:13 final size:13
Alignment explanation
Indices: 30955--31000 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
30945 AAACAAAAAA
30955 AAATAATAATAAT
1 AAATAATAATAAT
*
30968 AAATAATTATAAT
1 AAATAATAATAAT
* *
30981 TATTAATAATAAT
1 AAATAATAATAAT
30994 AATATAA
1 AA-ATAA
31001 AAACATCATG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 23 0.88
14 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:32019 original size:41 final size:41
Alignment explanation
Indices: 31959--32066 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 41
31949 ACATGAAGGT
* * *
31959 CTTATGGATGGCCCAAAGGACTTA-TCATCTTGCTCGAAAGA
1 CTTAT-GATGACCCAAAGGACTTACTCATCATGCTCAAAAGA
* *
32000 CTTATAGATGACCCGAAGGATTTACTCATCATGCTCAAAAGA
1 CTTAT-GATGACCCAAAGGACTTACTCATCATGCTCAAAAGA
*
32042 CTTACTGATGACCCAAATGACTTAC
1 CTTA-TGATGACCCAAAGGACTTAC
32067 CAATTTTGGA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
41 20 0.36
42 35 0.62
43 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (41 bp):
CTTATGATGACCCAAAGGACTTACTCATCATGCTCAAAAGA
Found at i:32279 original size:42 final size:41
Alignment explanation
Indices: 32187--32309 Score: 115
Period size: 42 Copynumber: 3.0 Consensus size: 41
32177 TATGTGAAAA
* * *
32187 CATCATGCACG-AAGGTCTTATGGATGGCTCGAAGAACTTAT
1 CATCATGCTCGAAAGG-CTTATAGATGACTCGAAGAACTTAT
* * * *
32228 CATCTTGCTCGAAAGGCTTATAGATGACTTGAAGGATTTACT
1 CATCATGCTCGAAAGGCTTATAGATGACTCGAAGAACTTA-T
* * *
32270 CATCATGCTCGAAAGACTTA-ATGATGGCTCGAAGGACTTA
1 CATCATGCTCGAAAGGCTTATA-GATGACTCGAAGAACTTA
32310 CCAATTTTGG
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
41 29 0.43
42 38 0.57
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (41 bp):
CATCATGCTCGAAAGGCTTATAGATGACTCGAAGAACTTAT
Found at i:32287 original size:244 final size:244
Alignment explanation
Indices: 31264--32797 Score: 2110
Period size: 244 Copynumber: 6.3 Consensus size: 244
31254 ATCTTACCCG
* * * * * * *
31264 AAGGTCTTATAGATGACCCGAAGGACTTA-TCATCTTGCTTGAACGACTAACAGATGGCCTGAAG
1 AAGG-CTTATAGATGACCCGAAGGATTTACTCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
* * * *
31328 GA-TGTACTAATTTTGGAAGTAGTTTACTAGGTAAGAAACTTTGCAAATTGTTTTCTTACTTTTC
65 GACT-TACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATCGTTTTCTTACTTTTC
* * *
31392 AAAAACTTCAATTTTCAGATTTAAATGAGAAATTTTTCTCATTTTTCGAAAAACATGTGAAAACA
129 AAAAACTTTAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTTGAAAAACATGTGAAAACA
* ** *
31457 TCCTGCCCGAAGGTCTTATGGATGTCTGGAAGGACTTATCAACTTGCTCGA
194 TCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGA
* * *
31508 AAGGCTTATAGATGACCCAAATGATTTACTCATCATGCTCGAAAGACTTACTGATGTCCCGAAGG
1 AAGGCTTATAGATGACCCGAAGGATTTACTCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* *
31573 ACTTACCAATTTTGGGAATAGTTTACTAGGTAAGAAACTTTTG-AAATCGCTTTCTTACTTTTCA
66 ACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAAC-TTTGAAAATCGTTTTCTTACTTTTCA
* * ***
31637 AAAACTTCAATTTTCAAATTTAAATGAG-TTGTTTTCTCATTTTTTGAAAAACATGTGAAAACAT
130 AAAACTTTAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTTGAAAAACATGTGAAAACAT
* *
31701 CCTGCCCGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTTGA
195 CCTGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGA
* * *
31751 ATGGCTTATAGATAACCTGAAGGATTTACTCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTATAGATGACCCGAAGGATTTACTCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* *
31816 ACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGTTTTCTTACTGTT-AA
66 ACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATCGTTTTCTTACTTTTCAA
* * **
31880 AAATTTTCAATTTTCAGATTTAAATGAGAAACTATTCTCATTTTTCAAAAAAACATGTGAAAACA
131 AAACTTT-AATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTT-TGAAAAACATGTGAAAACA
* * ** *
31945 CCCTACATGAAGGTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGA
194 TCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGA
* * * * *
31996 AAGACTTATAGATGACCCGAAGGATTTACTCATCATGCTCAAAAGACTTACTGATGACCCAAATG
1 AAGGCTTATAGATGACCCGAAGGATTTACTCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* *
32061 ACTTACCAATTTTGGAAATAGTTTAATAGGTAAGAAACTTTGAAAATCATTTTCTTACTTTTCAA
66 ACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATCGTTTTCTTACTTTTCAA
* * *
32126 AAACTTTAATTTTCAGATTTAAATGAGAAACGTTTCTCGTTTTTTGAAAAATATGTGAAAACATC
131 AAACTTTAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTTGAAAAACATGTGAAAACATC
* * * *
32191 ATGCACGAAGGTCTTATGGATGGCTCGAAGAACTTATCATCTTGCTCGA
196 CTGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGA
** * *
32240 AAGGCTTATAGATGACTTGAAGGATTTACTCATCATGCTCGAAAGACTTAATGATGGCTCGAAGG
1 AAGGCTTATAGATGACCCGAAGGATTTACTCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
*
32305 ACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATCATTTTCTTACTTTTCAA
66 ACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATCGTTTTCTTACTTTTCAA
* * *
32370 AAACTTTAATTTTCAGTTTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACTTGTGAAAACATC
131 AAACTTTAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTTGAAAAACATGTGAAAACATC
* * * * * * *
32435 TTGCTCGAAGGTCTTATGGATGTCCCGAATGACTTATCATTTTTCTCCA
196 CTGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGA
*
32484 AAGGCTTATAGATGACCCAAAGGATTTACTCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTATAGATGACCCGAAGGATTTACTCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* * *
32549 ACTTACCAATTTTGGAAAGAGTTT-CTAGGTAAGAAACTTTGGAAATCGTTTCCTTACTTTTCAA
66 ACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATCGTTTTCTTACTTTTCAA
* *
32613 AAA-TTTCAATTTTCAGATTTAAATGGGAAATTTTTCTCATTTTTTGAAAAACATGTGAAAACAT
131 AAACTTT-AATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTTGAAAAACATGTGAAAACAT
* * * * * ** *
32677 CATGCCCGAAGGTATTATGGGTGGCCCGAATGACTTATCATATTATTCAA
195 CCTGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGA
* * * * * * * *
32727 AAGACTTACAGATGACCCGAAGAATTTAATCATCATGCTCGAAAAATTTATTGATGGCCCAAAGG
1 AAGGCTTATAGATGACCCGAAGGATTTACTCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
32792 ACTTAC
66 ACTTAC
32798 TGAGTAAGAA
Statistics
Matches: 1148, Mismatches: 133, Indels: 19
0.88 0.10 0.01
Matches are distributed among these distances:
242 14 0.01
243 425 0.37
244 486 0.42
245 215 0.19
246 8 0.01
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (244 bp):
AAGGCTTATAGATGACCCGAAGGATTTACTCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
ACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATCGTTTTCTTACTTTTCAA
AAACTTTAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTTGAAAAACATGTGAAAACATC
CTGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGA
Found at i:42853 original size:23 final size:23
Alignment explanation
Indices: 42827--42872 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
42817 GCTTAGTAGT
*
42827 TGGGCCGAGTGTTGAG-TTGTAAA
1 TGGGCCCAGT-TTGAGTTTGTAAA
*
42850 TGGGCCCAGTTTGGGTTTGTAAA
1 TGGGCCCAGTTTGAGTTTGTAAA
42873 GCCTGAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.20, C:0.11, G:0.37, T:0.33
Consensus pattern (23 bp):
TGGGCCCAGTTTGAGTTTGTAAA
Found at i:42893 original size:3 final size:3
Alignment explanation
Indices: 42885--42935 Score: 75
Period size: 3 Copynumber: 16.3 Consensus size: 3
42875 CTGAAAACAA
*
42885 AAT AAT AAT AAT AAT AAAT AAT TAT AATT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT
42932 AAT A
1 AAT A
42936 TAAAAACGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:44078 original size:12 final size:12
Alignment explanation
Indices: 44053--44122 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
44043 ACGGAGATAT
* *
44053 CAGAAATCAAAA
1 CAGAATTCAGAA
44065 CAGAATTCAGAA
1 CAGAATTCAGAA
44077 CA-AATATCAGAA
1 CAGAAT-TCAGAA
* * * *
44089 TAAAATCCAGAT
1 CAGAATTCAGAA
* *
44101 CAGAAATCAAAA
1 CAGAATTCAGAA
44113 CAGAATTCAG
1 CAGAATTCAG
44123 GTCATATATC
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
11 3 0.07
12 37 0.86
13 3 0.07
ACGTcount: A:0.56, C:0.17, G:0.11, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:44085 original size:24 final size:24
Alignment explanation
Indices: 44058--44145 Score: 79
Period size: 24 Copynumber: 3.7 Consensus size: 24
44048 GATATCAGAA
* *
44058 ATCAAAACAGAATTCAGAACAAAT
1 ATCAAAACAAAATTCAGATCAAAT
* * *
44082 ATCAGAATAAAATCCAGATCAGAA-
1 ATCAAAACAAAATTCAGATCA-AAT
* * *
44106 ATCAAAACAGAATTCAGGTCATAT
1 ATCAAAACAAAATTCAGATCAAAT
*
44130 ATCATAACAAAATTCA
1 ATCAAAACAAAATTCA
44146 AGTCGGAAAT
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
23 1 0.02
24 46 0.94
25 2 0.04
ACGTcount: A:0.53, C:0.17, G:0.09, T:0.20
Consensus pattern (24 bp):
ATCAAAACAAAATTCAGATCAAAT
Found at i:44132 original size:48 final size:48
Alignment explanation
Indices: 44051--44142 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
44041 AAACGGAGAT
*
44051 ATCAGAAATCAAAACAGAATTCAGAACAAATATCAGAATAAAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGAACAAATATCAGAACAAAATCCAG
** * *
44099 ATCAGAAATCAAAACAGAATTCAGGTCATATATCATAACAAAAT
1 ATCAGAAATCAAAACAGAATTCAGAACAAATATCAGAACAAAAT
44143 TCAAGTCGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.54, C:0.16, G:0.10, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGAACAAATATCAGAACAAAATCCAG
Found at i:44155 original size:48 final size:48
Alignment explanation
Indices: 44051--44157 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 48
44041 AAACGGAGAT
* *
44051 ATCAGAAATCAAAACAGAATTCAGAACAAATATCAGAATAAAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGAACAAATATCAGAACAAAATCAAG
** * *
44099 ATCAGAAATCAAAACAGAATTCAGGTCATATATCATAACAAAATTCAAG
1 ATCAGAAATCAAAACAGAATTCAGAACAAATATCAGAACAAAA-TCAAG
*
44148 -TCGGAAATCA
1 ATCAGAAATCA
44158 GATAAAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 47 0.92
49 4 0.08
ACGTcount: A:0.52, C:0.17, G:0.11, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGAACAAATATCAGAACAAAATCAAG
Found at i:44157 original size:24 final size:24
Alignment explanation
Indices: 44052--44157 Score: 65
Period size: 24 Copynumber: 4.4 Consensus size: 24
44042 AACGGAGATA
*
44052 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAAAACAAAATTCAAG
* * * *
44075 AACA-AATATCAGAATAAAA-TCCAG
1 -TCAGAA-ATCAAAACAAAATTCAAG
* *
44099 ATCAGAAATCAAAACAGAATTCAGG
1 -TCAGAAATCAAAACAAAATTCAAG
* * *
44124 TCATATATCATAACAAAATTCAAG
1 TCAGAAATCAAAACAAAATTCAAG
*
44148 TCGGAAATCA
1 TCAGAAATCA
44158 GATAAAATAT
Statistics
Matches: 60, Mismatches: 18, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
23 4 0.07
24 51 0.85
25 5 0.08
ACGTcount: A:0.52, C:0.17, G:0.11, T:0.20
Consensus pattern (24 bp):
TCAGAAATCAAAACAAAATTCAAG
Found at i:46639 original size:13 final size:13
Alignment explanation
Indices: 46621--46650 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
46611 GGTCAACGCC
46621 GGTCAACGGGTCG
1 GGTCAACGGGTCG
46634 GGTCAACGGGTCG
1 GGTCAACGGGTCG
46647 GGTC
1 GGTC
46651 GGGTCGGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:49909 original size:3 final size:3
Alignment explanation
Indices: 49901--49985 Score: 170
Period size: 3 Copynumber: 28.3 Consensus size: 3
49891 TTTATTGAAA
49901 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
49949 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
49986 TGAGACAAAA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:50599 original size:13 final size:13
Alignment explanation
Indices: 50581--50606 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50571 ACTTACTCTA
50581 AAGTATGGATATT
1 AAGTATGGATATT
50594 AAGTATGGATATT
1 AAGTATGGATATT
50607 TATAGAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
AAGTATGGATATT
Found at i:50796 original size:15 final size:15
Alignment explanation
Indices: 50776--50805 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
50766 AATAGGTGAT
50776 ACCTATTACATTAAA
1 ACCTATTACATTAAA
50791 ACCTATTACATTAAA
1 ACCTATTACATTAAA
50806 CTACCTCCTA
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:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (15 bp):
ACCTATTACATTAAA
Done.