Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007324.1 Hibiscus syriacus cultivar Beakdansim tig00019545_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: 89345
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2926 original size:33 final size:33
Alignment explanation
Indices: 2884--2952 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
2874 GTTGATGAAT
*
2884 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
2917 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
2950 GAA
1 GAA
2953 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:2973 original size:35 final size:36
Alignment explanation
Indices: 2934--3034 Score: 152
Period size: 35 Copynumber: 2.9 Consensus size: 36
2924 GATGTTATTG
2934 GCGTGAT-ATGGTGATGGAATATGGTGATGATATAA
1 GCGTGATAATGGTGATGGAATATGGTGATGATATAA
* *
2969 GCGTGATAATGGTGATGGACTAT-GTGATGATATAG
1 GCGTGATAATGGTGATGGAATATGGTGATGATATAA
* *
3004 GCGTGATAATGGAGATGGATTATGGTGATGA
1 GCGTGATAATGGTGATGGAATATGGTGATGA
3035 AAATAGTATC
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 39 0.65
36 21 0.35
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
GCGTGATAATGGTGATGGAATATGGTGATGATATAA
Found at i:11129 original size:20 final size:21
Alignment explanation
Indices: 11088--11136 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
11078 GTAAAGCTAT
*
11088 TGAGCTAATATAAACATAACA
1 TGAGCTAAAATAAACATAACA
*
11109 TGAGCTAAAAT-AACATGACA
1 TGAGCTAAAATAAACATAACA
11129 TGAGCTAA
1 TGAGCTAA
11137 TGAATGAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (21 bp):
TGAGCTAAAATAAACATAACA
Found at i:11757 original size:17 final size:17
Alignment explanation
Indices: 11716--11758 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
11706 ATTTAAACAT
* *
11716 GTAGTTCATTTAGCTAT
1 GTAGTTCATTTAACTAA
* *
11733 GCACTTCATTTAACTAA
1 GTAGTTCATTTAACTAA
11750 GTAGTTCAT
1 GTAGTTCAT
11759 CGATTAAACT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (17 bp):
GTAGTTCATTTAACTAA
Found at i:11771 original size:17 final size:16
Alignment explanation
Indices: 11751--11816 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 16
11741 TTTAACTAAG
11751 TAGTTCATCGATTAAAC
1 TAGTTCATC-ATTAAAC
*
11768 TAG-T--TCATTGAAC
1 TAGTTCATCATTAAAC
*
11781 TAGTTCATTCATCAAAC
1 TAGTTCA-TCATTAAAC
*
11798 TAGTTCATTTATTAAAC
1 TAGTTCA-TCATTAAAC
11815 TA
1 TA
11817 ACTCTTAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
13 9 0.22
14 3 0.08
16 1 0.03
17 27 0.68
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (16 bp):
TAGTTCATCATTAAAC
Found at i:11783 original size:13 final size:13
Alignment explanation
Indices: 11765--11789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11755 TCATCGATTA
11765 AACTAGTTCATTG
1 AACTAGTTCATTG
11778 AACTAGTTCATT
1 AACTAGTTCATT
11790 CATCAAACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (13 bp):
AACTAGTTCATTG
Found at i:25988 original size:13 final size:13
Alignment explanation
Indices: 25972--26012 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
25962 TTTTTGGCTC
25972 TTTTTTTG--TTT
1 TTTTTTTGCCTTT
25983 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
25996 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
26009 TTTT
1 TTTT
26013 GTTTTTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 8 0.29
13 20 0.71
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (13 bp):
TTTTTTTGCCTTT
Found at i:25998 original size:23 final size:22
Alignment explanation
Indices: 25961--26036 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 22
25951 AAATTTTGGC
* *
25961 TTTTTTGGCTCTTTTTTTGTTT
1 TTTTTTTGCTTTTTTTTTGTTT
25983 TTTTTTTGCCTTTTTTTTTTGCCTTT
1 TTTTTTTG-C-TTTTTTTTTG--TTT
*
26009 TTTTGTTT-TTTGTTTTTTTGTTT
1 TTTT-TTTGCTT-TTTTTTTGTTT
26032 TTTTT
1 TTTTT
26037 GAAAAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
22 8 0.18
23 8 0.18
24 11 0.24
25 8 0.18
26 7 0.16
27 3 0.07
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.82
Consensus pattern (22 bp):
TTTTTTTGCTTTTTTTTTGTTT
Found at i:26033 original size:34 final size:34
Alignment explanation
Indices: 25961--26037 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 34
25951 AAATTTTGGC
*
25961 TTTTTTGGCTCTTTTTTTGTTTTTTTTTTGCCTTT
1 TTTTTTTGCTCTTTTTTTGTTTTTTTTTT-CCTTT
*
25996 TTTTTTTGC-CTTTTTTTGTTTTTTGTTTT-TTTGT
1 TTTTTTTGCTCTTTTTTTGTTTTTT-TTTTCCTT-T
26030 TTTTTTTG
1 TTTTTTTG
26038 AAAAAAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 2 0.05
34 24 0.63
35 12 0.32
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.81
Consensus pattern (34 bp):
TTTTTTTGCTCTTTTTTTGTTTTTTTTTTCCTTT
Found at i:37674 original size:10 final size:10
Alignment explanation
Indices: 37643--37667 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
37633 CTATTTTTTT
37643 AAAAAAACAA
1 AAAAAAACAA
37653 AAAAAAACAA
1 AAAAAAACAA
37663 AAAAA
1 AAAAA
37668 CAAAAAATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:44171 original size:15 final size:15
Alignment explanation
Indices: 44136--44164 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44126 GTGCTTCAAC
44136 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
44150 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
44165 CTTTTTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:44187 original size:27 final size:28
Alignment explanation
Indices: 44157--44218 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
44147 CTTTTCTTTG
** *
44157 CTTTTCTTCTTTTTGAATGC-TGAATTT
1 CTTTTCTTCTTTCGGAATGCTTCAATTT
* *
44184 CTTTTTTTCTTTCGGAGTGCTTCAATTT
1 CTTTTCTTCTTTCGGAATGCTTCAATTT
44212 CTTTTCT
1 CTTTTCT
44219 GATTTTCTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 16 0.57
28 12 0.43
ACGTcount: A:0.11, C:0.18, G:0.11, T:0.60
Consensus pattern (28 bp):
CTTTTCTTCTTTCGGAATGCTTCAATTT
Found at i:46742 original size:13 final size:12
Alignment explanation
Indices: 46724--46765 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
46714 GCTTACTTTC
46724 TCTTTTTGAATTT
1 TCTTTTTG-ATTT
*
46737 TCTTTTT-CTTT
1 TCTTTTTGATTT
46748 TCTTTTCTGATTT
1 TCTTTT-TGATTT
46761 TCTTT
1 TCTTT
46766 CTTTTTGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 1 0.04
13 15 0.60
ACGTcount: A:0.07, C:0.14, G:0.05, T:0.74
Consensus pattern (12 bp):
TCTTTTTGATTT
Found at i:46752 original size:24 final size:25
Alignment explanation
Indices: 46719--46765 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
46709 CCTTGGCTTA
46719 CTTTCTCTTTT-TGAATTTTCTTTTT
1 CTTTCTCTTTTCTG-ATTTTCTTTTT
46744 CTTT-TCTTTTCTGATTTTCTTT
1 CTTTCTCTTTTCTGATTTTCTTT
46766 CTTTTTGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.72
Consensus pattern (25 bp):
CTTTCTCTTTTCTGATTTTCTTTTT
Found at i:47553 original size:19 final size:20
Alignment explanation
Indices: 47512--47562 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
47502 AAAACCCCTT
*
47512 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
47532 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
47551 TGAAGATACATG
1 TGAAAATACATG
47563 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:48438 original size:13 final size:13
Alignment explanation
Indices: 48420--48445 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48410 GTTATAGGCG
48420 TGAAAATGGTGAT
1 TGAAAATGGTGAT
48433 TGAAAATGGTGAT
1 TGAAAATGGTGAT
48446 GAACAGATAG
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:0.31, T:0.31
Consensus pattern (13 bp):
TGAAAATGGTGAT
Found at i:48833 original size:19 final size:20
Alignment explanation
Indices: 48791--48833 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
48781 GAAACCCCTT
*
48791 TGAAAACACATGATTTTAAA
1 TGAAAACACATAATTTTAAA
*
48811 TGAAAATACATAATTTT-AA
1 TGAAAACACATAATTTTAAA
48830 TGAA
1 TGAA
48834 GATAAAGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (20 bp):
TGAAAACACATAATTTTAAA
Found at i:50552 original size:8 final size:8
Alignment explanation
Indices: 50539--50600 Score: 67
Period size: 8 Copynumber: 8.0 Consensus size: 8
50529 TATTTTTTTT
50539 CAAAAAAA
1 CAAAAAAA
50547 CAAAAAAA
1 CAAAAAAA
50555 C-AAAAAA
1 CAAAAAAA
*
50562 CAAAAAAGG
1 CAAAAAA-A
50571 C-AAAAAA
1 CAAAAAAA
**
50578 -AAAAAGG
1 CAAAAAAA
50585 CAAAAAAA
1 CAAAAAAA
50593 CAAAAAAA
1 CAAAAAAA
50601 GAGCCAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
7 11 0.25
8 32 0.73
9 1 0.02
ACGTcount: A:0.82, C:0.11, G:0.06, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:50559 original size:6 final size:7
Alignment explanation
Indices: 50541--50599 Score: 57
Period size: 7 Copynumber: 7.9 Consensus size: 7
50531 TTTTTTTTCA
50541 AAAAAAC
1 AAAAAAC
50548 AAAAAAAC
1 -AAAAAAC
50556 AAAAAAC
1 AAAAAAC
50563 AAAAAAGGC
1 AAAAAA--C
50572 AAAAAA-
1 AAAAAAC
*
50578 AAAAAGGC
1 AAAAA-AC
50586 AAAAAAAC
1 -AAAAAAC
50594 AAAAAA
1 AAAAAA
50600 AGAGCCAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
6 5 0.11
7 19 0.43
8 8 0.18
9 12 0.27
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:50566 original size:14 final size:14
Alignment explanation
Indices: 50541--50599 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 14
50531 TTTTTTTTCA
50541 AAAAAACAAAAAAAC
1 AAAAAAC-AAAAAAC
50556 AAAAAACAAAAAAGGC
1 AAAAAACAAAAAA--C
*
50572 AAAAAA-AAAAAGGC
1 AAAAAACAAAAA-AC
50586 AAAAAAACAAAAAA
1 -AAAAAACAAAAAA
50600 AGAGCCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 7 0.19
15 18 0.49
16 12 0.32
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAACAAAAAAC
Found at i:50589 original size:13 final size:14
Alignment explanation
Indices: 50557--50597 Score: 64
Period size: 14 Copynumber: 2.8 Consensus size: 14
50547 CAAAAAAACA
50557 AAAAACAAAAAAGGC
1 AAAAA-AAAAAAGGC
50572 AAAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
50586 AAAAAAACAAAA
1 AAAAAAA-AAAA
50598 AAAGAGCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:50618 original size:20 final size:20
Alignment explanation
Indices: 50574--50611 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
50564 AAAAAGGCAA
*
50574 AAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAC
*
50594 AAAAAAAGAGCCAAAAAA
1 AAAAAAAAAGCCAAAAAA
50612 GCCAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGCCAAAAAAAC
Found at i:56677 original size:16 final size:16
Alignment explanation
Indices: 56656--56688 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
56646 TTCTGCCACC
56656 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
56672 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
56688 T
1 T
56689 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:63054 original size:12 final size:11
Alignment explanation
Indices: 63037--63119 Score: 55
Period size: 11 Copynumber: 7.6 Consensus size: 11
63027 AAATTTTGGC
63037 TTTTTTGGCTCTT
1 TTTTTTGG--CTT
**
63050 TTTTTTGTTTT
1 TTTTTTGGCTT
*
63061 TTTTTTGCCTT
1 TTTTTTGGCTT
*
63072 TTTTTTGCCTT
1 TTTTTTGGCTT
* *
63083 TTTTTTTGC-C
1 TTTTTTGGCTT
*
63093 TTTTTT-GTTT
1 TTTTTTGGCTT
*
63103 TTTTTTTG-TT
1 TTTTTTGGCTT
63113 TTTTTTG
1 TTTTTTG
63120 AAAAAAAATA
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
9 1 0.02
10 20 0.34
11 30 0.52
13 7 0.12
ACGTcount: A:0.00, C:0.10, G:0.11, T:0.80
Consensus pattern (11 bp):
TTTTTTGGCTT
Found at i:63062 original size:11 final size:11
Alignment explanation
Indices: 63048--63118 Score: 74
Period size: 11 Copynumber: 6.5 Consensus size: 11
63038 TTTTTGGCTC
63048 TTTTTTTTGTT
1 TTTTTTTTGTT
**
63059 TTTTTTTTGCC
1 TTTTTTTTGTT
*
63070 TTTTTTTTGCCT
1 TTTTTTTTG-TT
63082 TTTTTTTTG--
1 TTTTTTTTGTT
**
63091 CCTTTTTTGTT
1 TTTTTTTTGTT
63102 TTTTTTTTGTT
1 TTTTTTTTGTT
63113 TTTTTT
1 TTTTTT
63119 GAAAAAAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
9 7 0.14
11 33 0.66
12 10 0.20
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:63074 original size:23 final size:23
Alignment explanation
Indices: 63037--63109 Score: 87
Period size: 22 Copynumber: 3.2 Consensus size: 23
63027 AAATTTTGGC
*
63037 TTTTTTGGCTCTTTTTTTTGTTTT
1 TTTTTTGCCT-TTTTTTTTGTTTT
*
63061 TTTTTTGCC-TTTTTTTTGCCTTT
1 TTTTTTGCCTTTTTTTTTG-TTTT
*
63084 TTTTTTGCCTTTTTTGTT-TTTT
1 TTTTTTGCCTTTTTTTTTGTTTT
63106 TTTT
1 TTTT
63110 GTTTTTTTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
22 16 0.37
23 12 0.28
24 15 0.35
ACGTcount: A:0.00, C:0.11, G:0.10, T:0.79
Consensus pattern (23 bp):
TTTTTTGCCTTTTTTTTTGTTTT
Found at i:65978 original size:16 final size:16
Alignment explanation
Indices: 65957--65989 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
65947 TTCTGCCACC
*
65957 TATGTTAGAATGCAAA
1 TATGTTAGAATACAAA
65973 TATGTTAGAATACAAA
1 TATGTTAGAATACAAA
65989 T
1 T
65990 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATACAAA
Found at i:70400 original size:11 final size:11
Alignment explanation
Indices: 70384--70414 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
70374 GTGGAATATG
70384 GTAAATAAACA
1 GTAAATAAACA
70395 GTAAATAAACA
1 GTAAATAAACA
*
70406 GCAAATAAA
1 GTAAATAAA
70415 ATGAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.16
Consensus pattern (11 bp):
GTAAATAAACA
Found at i:74236 original size:18 final size:17
Alignment explanation
Indices: 74215--74264 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
74205 TTGAAATTTC
74215 TTTTTTCTTTTCTGAATT
1 TTTTTTCTTTT-TGAATT
**
74233 TTTTATTCTTTTTGTCTT
1 TTTT-TTCTTTTTGAATT
74251 TTTCTTTCTTTTTG
1 TTT-TTTCTTTTTG
74265 CACTCCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.06, C:0.12, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTTTCTTTTTGAATT
Found at i:81347 original size:90 final size:90
Alignment explanation
Indices: 81194--81369 Score: 307
Period size: 90 Copynumber: 2.0 Consensus size: 90
81184 TAACACATCA
*
81194 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAAATAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAAATAATTAAATCTATAT
* *
81259 TTCATTAATTGAAATTTAATAATCC
66 TTAATTAATTGAAATTAAATAATCC
* *
81284 TTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAAATAATTAAATCTATAT
81349 TTAATTAATTGAAATTAAATA
66 TTAATTAATTGAAATTAAATA
81370 TTCGTGATTA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (90 bp):
TTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAAATAATTAAATCTATAT
TTAATTAATTGAAATTAAATAATCC
Found at i:82374 original size:33 final size:33
Alignment explanation
Indices: 82334--82402 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
82324 TATTACAATC
82334 ATCATATGATTGGTCTTTGGGCATACTCTAACA
1 ATCATATGATTGGTCTTTGGGCATACTCTAACA
*
82367 ATCATATGATTGGTCTTTGGGCATACTTTAACA
1 ATCATATGATTGGTCTTTGGGCATACTCTAACA
82400 ATC
1 ATC
82403 TCCCACTAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (33 bp):
ATCATATGATTGGTCTTTGGGCATACTCTAACA
Found at i:88275 original size:24 final size:24
Alignment explanation
Indices: 88246--88314 Score: 120
Period size: 24 Copynumber: 2.8 Consensus size: 24
88236 AAAGAAATTG
88246 AAGCACTCAAAAGAAGAAAATTTC
1 AAGCACTCAAAAGAAGAAAATTTC
*
88270 AAGCACTCAAAAAAAGAAAATTTC
1 AAGCACTCAAAAGAAGAAAATTTC
88294 AAGCACTCAAAAAGAAGAAAA
1 AAGCACTC-AAAAGAAGAAAA
88315 AGAAAAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
24 31 0.74
25 11 0.26
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.13
Consensus pattern (24 bp):
AAGCACTCAAAAGAAGAAAATTTC
Found at i:88322 original size:14 final size:14
Alignment explanation
Indices: 88303--88335 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
88293 CAAGCACTCA
88303 AAAAGAAGAA-AAAG
1 AAAAGAA-AAGAAAG
88317 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
88331 AAAAG
1 AAAAG
88336 TTGAAAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Done.