Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001232.1 Hibiscus syriacus cultivar Beakdansim tig00002426_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: 82487
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4212 original size:38 final size:37
Alignment explanation
Indices: 4140--4219 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 37
4130 TCAATTGTAA
* *
4140 AAAATAAAATAAAAGTTAGCGTTTAGTGGCATAAAAAT
1 AAAATAAAATAAAAGTTAGAGTTTAG-GGAATAAAAAT
*
4178 AAAATAAAATAATAGTTAGTAGTATTA-GGAATAAAAAT
1 AAAATAAAATAAAAGTTAG-AGT-TTAGGGAATAAAAAT
4216 AAAA
1 AAAA
4220 GTCACAAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 32 0.86
39 2 0.05
40 3 0.08
ACGTcount: A:0.57, C:0.03, G:0.14, T:0.26
Consensus pattern (37 bp):
AAAATAAAATAAAAGTTAGAGTTTAGGGAATAAAAAT
Found at i:8272 original size:20 final size:20
Alignment explanation
Indices: 8233--8274 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
8223 AATTATTCTT
8233 ATACCATAAAATAAATAAAA
1 ATACCATAAAATAAATAAAA
*
8253 ATACCTATAATATAAA-AAAA
1 ATACC-ATAAAATAAATAAAA
8273 AT
1 AT
8275 TAAACTATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.24
Consensus pattern (20 bp):
ATACCATAAAATAAATAAAA
Found at i:10731 original size:19 final size:19
Alignment explanation
Indices: 10704--10742 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
10694 CTCATAAAGT
*
10704 TATCTATTTTCATATAAAA
1 TATCAATTTTCATATAAAA
*
10723 TATCAATTTTGATATAAAA
1 TATCAATTTTCATATAAAA
10742 T
1 T
10743 TATAATGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (19 bp):
TATCAATTTTCATATAAAA
Found at i:15164 original size:15 final size:14
Alignment explanation
Indices: 15144--15197 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
15134 CGCTTGCCTG
15144 ACTGAGTCAACTTAC
1 ACTGAGTCAACTT-C
*
15159 ACTGAGTTAAC-TC
1 ACTGAGTCAACTTC
15172 AGCTGAGTCAAC-TC
1 A-CTGAGTCAACTTC
15186 ACT-AGTTCAACT
1 ACTGAG-TCAACT
15198 CGTTGACTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
12 2 0.06
13 9 0.26
14 13 0.38
15 10 0.29
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (14 bp):
ACTGAGTCAACTTC
Found at i:15197 original size:13 final size:14
Alignment explanation
Indices: 15144--15198 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 14
15134 CGCTTGCCTG
15144 ACTGAG-TCAACTTAC
1 ACTGAGTTCAAC-T-C
15159 ACTGAGTT-AACTC
1 ACTGAGTTCAACTC
15172 AGCTGAG-TCAACTC
1 A-CTGAGTTCAACTC
15186 ACT-AGTTCAACTC
1 ACTGAGTTCAACTC
15199 GTTGACTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
12 2 0.06
13 12 0.33
14 12 0.33
15 9 0.25
16 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (14 bp):
ACTGAGTTCAACTC
Found at i:17351 original size:24 final size:24
Alignment explanation
Indices: 17324--17404 Score: 90
Period size: 24 Copynumber: 3.4 Consensus size: 24
17314 ATTTGAATTA
* *
17324 TGTTCTGATACCTGACCTGGATTC
1 TGTTCTGATATCTGATCTGGATTC
* * *
17348 TGTTCTGATTTCTTATATGGATTC
1 TGTTCTGATATCTGATCTGGATTC
* *
17372 TGTTCTGATATCTGATCTGAATTT
1 TGTTCTGATATCTGATCTGGATTC
*
17396 TGTTTTGAT
1 TGTTCTGAT
17405 TTCTAATATC
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.17, C:0.15, G:0.19, T:0.49
Consensus pattern (24 bp):
TGTTCTGATATCTGATCTGGATTC
Found at i:29122 original size:21 final size:21
Alignment explanation
Indices: 29071--29115 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
29061 CTCTTTTGAG
29071 GGTATATCCAGATGATTAGTC
1 GGTATATCCAGATGATTAGTC
29092 GGTATATCCAGATGATTAGTC
1 GGTATATCCAGATGATTAGTC
29113 GGT
1 GGT
29116 TCATCCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (21 bp):
GGTATATCCAGATGATTAGTC
Found at i:46870 original size:12 final size:13
Alignment explanation
Indices: 46855--46884 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
46845 TTAAAAATAT
46855 TAATATTTTTTA-
1 TAATATTTTTTAG
46867 TAATATTTTTTAG
1 TAATATTTTTTAG
46880 TAATA
1 TAATA
46885 CATTAAGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (13 bp):
TAATATTTTTTAG
Found at i:48637 original size:29 final size:29
Alignment explanation
Indices: 48604--48674 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
48594 GGCGACATCG
48604 CGACATGGTAGGTCGCCATGGAGTCCCGA
1 CGACATGGTAGGTCGCCATGGAGTCCCGA
*
48633 CGACATGGTAGGTCGCCATGGAGTCCCTA
1 CGACATGGTAGGTCGCCATGGAGTCCCGA
48662 CGACATGGTAGGT
1 CGACATGGTAGGT
48675 GGTAGGGTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.21, C:0.25, G:0.34, T:0.20
Consensus pattern (29 bp):
CGACATGGTAGGTCGCCATGGAGTCCCGA
Found at i:48685 original size:12 final size:12
Alignment explanation
Indices: 48668--48692 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48658 CCTACGACAT
48668 GGTAGGTGGTAG
1 GGTAGGTGGTAG
48680 GGTAGGTGGTAG
1 GGTAGGTGGTAG
48692 G
1 G
48693 TCGCCATGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.60, T:0.24
Consensus pattern (12 bp):
GGTAGGTGGTAG
Found at i:48771 original size:35 final size:35
Alignment explanation
Indices: 48732--48799 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
48722 TCCTGCATCG
*
48732 CGACCCAGCTTTAACTGTAGCACTCATGCATGCAA
1 CGACCAAGCTTTAACTGTAGCACTCATGCATGCAA
*
48767 CGACCAAGCTTTAACTGTATCACTCATGCATGC
1 CGACCAAGCTTTAACTGTAGCACTCATGCATGC
48800 GTTGCATCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (35 bp):
CGACCAAGCTTTAACTGTAGCACTCATGCATGCAA
Found at i:49257 original size:21 final size:21
Alignment explanation
Indices: 49232--49275 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
49222 AATCTAGTTA
*
49232 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTGGTTAGTATAAATT
* *
49253 ATTAGTTGGTTAGTTTAAGTT
1 ATTAGTTGGTTAGTATAAATT
49274 AT
1 AT
49276 ATATTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (21 bp):
ATTAGTTGGTTAGTATAAATT
Found at i:49697 original size:14 final size:14
Alignment explanation
Indices: 49678--49704 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49668 AGTAATTTAT
49678 TATTTTTTGTTGTC
1 TATTTTTTGTTGTC
49692 TATTTTTTGTTGT
1 TATTTTTTGTTGT
49705 TGTGTATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (14 bp):
TATTTTTTGTTGTC
Found at i:49704 original size:17 final size:17
Alignment explanation
Indices: 49675--49707 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
49665 GTGAGTAATT
49675 TATTATTTTTTGTTGTC
1 TATTATTTTTTGTTGTC
49692 TATT-TTTTGTTGTTGT
1 TATTATTTT-TTGTTGT
49708 GTATGTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.03, G:0.15, T:0.73
Consensus pattern (17 bp):
TATTATTTTTTGTTGTC
Found at i:49843 original size:23 final size:23
Alignment explanation
Indices: 49800--49843 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
49790 TATTGTGTTT
*
49800 AAAAATATTTAGTGTTGTTTAAA
1 AAAAATATTTAGTGTTATTTAAA
* *
49823 AAAAATATTTTGTTTTATTTA
1 AAAAATATTTAGTGTTATTTA
49844 TATTGTATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (23 bp):
AAAAATATTTAGTGTTATTTAAA
Found at i:50102 original size:26 final size:25
Alignment explanation
Indices: 50073--50137 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
50063 AAATCATATT
*
50073 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AATAAATATCAAATC
* *
50099 ATTAGATT-AATAATAATTATTAAATC
1 ATT--ATTAAATAATAAATATCAAATC
50125 ATTATT-AATAATA
1 ATTATTAAATAATA
50138 TTAGTAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 10 0.29
26 18 0.53
27 3 0.09
28 3 0.09
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTATTAAATAATAAATATCAAATC
Found at i:53060 original size:26 final size:26
Alignment explanation
Indices: 53034--53509 Score: 356
Period size: 26 Copynumber: 19.2 Consensus size: 26
53024 GATGATTTAG
*
53034 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
53060 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
53086 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
53112 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
53135 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
53158 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
53184 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
53210 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
53236 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
53259 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
53282 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
53308 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
53334 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
53360 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
53383 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
53406 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
* * *
53432 TAATGATTTTATAATAATTATTAT-G
1 TAATGATTTGATAATAATCATTATAA
* * *
53457 TTATTATTT-AGTAATTAT--TTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
53481 TAATGATTTAATACTAATGATT-TAA
1 TAATGATTTGATAATAATCATTATAA
53506 TAAT
1 TAAT
53510 TATTAATAAT
Statistics
Matches: 361, Mismatches: 60, Indels: 59
0.75 0.12 0.12
Matches are distributed among these distances:
21 12 0.03
22 9 0.02
23 40 0.11
24 34 0.09
25 42 0.12
26 221 0.61
27 3 0.01
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:53196 original size:124 final size:124
Alignment explanation
Indices: 52976--53493 Score: 943
Period size: 124 Copynumber: 4.2 Consensus size: 124
52966 ATGTATTTAT
52976 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
53041 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
53100 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
53165 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
53224 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
53289 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
53348 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* * * * * *
53413 TTGATAATAATCATTATAATAATGATTTTATAATAATTATTAT-GTTATTATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
* *
53471 TTAT--TTATAATAATGATTTAATA
1 TAATCATTATAAAAATGATTTAATA
53494 CTAATGATTT
Statistics
Matches: 386, Mismatches: 8, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
121 18 0.05
123 15 0.04
124 353 0.91
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:53214 original size:150 final size:145
Alignment explanation
Indices: 53031--53374 Score: 412
Period size: 150 Copynumber: 2.3 Consensus size: 145
53021 TTTGATGATT
* *
53031 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-ATAATAATCATTATAAAAATGA-TT-
* * *
53096 GTAATAATCATTATAAAAATGATTTAAT-A-ATGATTTA-AAT-ATTTAATGATTTGATGATT-T
63 -TAATAATCATT-T--AAAT-ATTTAATGATATGATTTAGAATGATTTAAT-A-ATAATCATTAT
53156 AGTAATGATTTGATAATAATCATTA
121 AGTAATGATTTGATAATAATCATTA
53181 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTA-TAATAATCATTATAAAAATGATTTA
* *
53246 ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAA
65 ATAATCATTTAAATATTTAATGA--T-ATGATTTAG-AATGATTTAATAATAATCATTATAGTAA
53311 TGATTTGATAATAATCATTA
126 TGATTTGATAATAATCATTA
* *
53331 TAATAATGATTT-AGTAATAATCATTATAAAAATGATTTAATAAT
1 TAGTAATGATTTGA-TAATAATCATTATAATAATGATTT-ATAAT
53375 GATTTAAATA
Statistics
Matches: 173, Mismatches: 9, Indels: 24
0.84 0.04 0.12
Matches are distributed among these distances:
143 7 0.04
144 5 0.03
146 1 0.01
147 10 0.06
148 8 0.05
149 10 0.06
150 125 0.72
151 7 0.04
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (145 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTATAATAATCATTATAAAAATGATTTAA
TAATCATTTAAATATTTAATGATATGATTTAGAATGATTTAATAATAATCATTATAGTAATGATT
TGATAATAATCATTA
Found at i:53500 original size:14 final size:14
Alignment explanation
Indices: 53468--53509 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
53458 TATTATTTAG
*
53468 TAATTATTT-ATAA
1 TAATGATTTAATAA
*
53481 TAATGATTTAATAC
1 TAATGATTTAATAA
53495 TAATGATTTAATAA
1 TAATGATTTAATAA
53509 T
1 T
53510 TATTAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:53739 original size:17 final size:17
Alignment explanation
Indices: 53714--53746 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53704 ACTAAATATT
*
53714 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
53731 TAATGATTTGATACTA
1 TAATGATTTGATACTA
53747 AACATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:55919 original size:15 final size:14
Alignment explanation
Indices: 55896--55926 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
55886 TACAACACTA
55896 AACTTTAATATAAT
1 AACTTTAATATAAT
55910 AACTTATAATATAAT
1 AACTT-TAATATAAT
55925 AA
1 AA
55927 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:55934 original size:16 final size:16
Alignment explanation
Indices: 55901--55947 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
55891 CACTAAACTT
*
55901 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
55916 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
55932 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
55948 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:56062 original size:32 final size:33
Alignment explanation
Indices: 55988--56068 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
55978 CCAAACCCTT
*
55988 AAAC-AACTAATAAAATATTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTATATAACTA
56020 AAACTAACTAATAAACTATTTTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTTTTT-A-TATAACTA
*
56053 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
56069 TACTAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
32 15 0.34
33 22 0.50
34 2 0.05
35 5 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.38
Consensus pattern (33 bp):
AAACTAACTAATAAACTATTTTTTATATAACTA
Found at i:56199 original size:45 final size:48
Alignment explanation
Indices: 56109--56199 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 48
56099 CAACAAACAA
56109 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
1 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
*
56157 ATATAAC-TAACTA-TTAAC-AA-AACAAACTAATT-AATTATTTTTT
1 ATATAACTTAACTATTTAACTAACAA-AAACTAATTAAATAATTTTTT
56200 AACTATATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
44 12 0.29
45 11 0.27
46 5 0.12
47 6 0.15
48 7 0.17
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (48 bp):
ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTT
Found at i:56268 original size:41 final size:40
Alignment explanation
Indices: 56180--56268 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
56170 TTAACAAAAC
* *
56180 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
56221 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
56262 AAACTAA
1 AAACTAA
56269 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:56333 original size:16 final size:18
Alignment explanation
Indices: 56304--56342 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
56294 ACTAATTAAC
*
56304 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
56322 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
56338 ATTTA
1 ATTTA
56343 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:56636 original size:50 final size:49
Alignment explanation
Indices: 56573--56670 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 49
56563 CAATAGCTGT
56573 AGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCTTGGCATGCATGC
1 AGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCTTGGC-TGCATGC
56623 AGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCTTGGCTGCATG
1 AGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCTTGGCTGCATG
56671 TGCATGCATG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 6 0.12
50 42 0.88
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.18
Consensus pattern (49 bp):
AGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCTTGGCTGCATGC
Found at i:56747 original size:29 final size:29
Alignment explanation
Indices: 56705--56799 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
56695 GTGACGCCGG
56705 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
56734 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
** *
56763 GGCGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
56792 GGCGACCT
1 GGCGACCT
56800 CTCCATTGGC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.23, C:0.33, G:0.31, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCGGGACTACAT
Found at i:56828 original size:32 final size:32
Alignment explanation
Indices: 56786--56864 Score: 149
Period size: 32 Copynumber: 2.5 Consensus size: 32
56776 GTCGCCCAGA
56786 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
*
56818 TTGCATGGCGACCTCTCCATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
56850 CTGCATGGCGACCTC
1 CTGCATGGCGACCTC
56865 ACCTCGTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.10, C:0.34, G:0.28, T:0.28
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
Found at i:57000 original size:29 final size:29
Alignment explanation
Indices: 56958--57017 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
56948 CTCCCGTATG
*
56958 TCGCCTGGATTGCATGGCGTCCTACAAGA
1 TCGCCTGGATTGCATGACGTCCTACAAGA
*
56987 TCGCCTGGATTGCATGACGTCCTACGAGA
1 TCGCCTGGATTGCATGACGTCCTACAAGA
57016 TC
1 TC
57018 ACTGTAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.20, C:0.28, G:0.27, T:0.25
Consensus pattern (29 bp):
TCGCCTGGATTGCATGACGTCCTACAAGA
Found at i:63832 original size:18 final size:18
Alignment explanation
Indices: 63809--63845 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
63799 GACAATTGCG
*
63809 TGTTAATATACCATTTCC
1 TGTTAATATACAATTTCC
63827 TGTTAATATACAATTTCC
1 TGTTAATATACAATTTCC
63845 T
1 T
63846 CAACAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (18 bp):
TGTTAATATACAATTTCC
Found at i:66558 original size:15 final size:15
Alignment explanation
Indices: 66518--66560 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
66508 CGATCATCTT
*
66518 CAACTACTGCACCAA
1 CAACTACTCCACCAA
*
66533 CAACTGCTCCACCAA
1 CAACTACTCCACCAA
*
66548 CAACTATTCCACC
1 CAACTACTCCACC
66561 TCTATATCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.35, C:0.44, G:0.05, T:0.16
Consensus pattern (15 bp):
CAACTACTCCACCAA
Found at i:66868 original size:32 final size:32
Alignment explanation
Indices: 66822--66882 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
66812 ACATGTTCTG
66822 CATATTTTAAATAGAATGTCTAGTTGAAACTA
1 CATATTTTAAATAGAATGTCTAGTTGAAACTA
*
66854 CATATTTTATATAGAATGTCTAGTTGAAA
1 CATATTTTAAATAGAATGTCTAGTTGAAA
66883 TTTTCTATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (32 bp):
CATATTTTAAATAGAATGTCTAGTTGAAACTA
Found at i:71327 original size:106 final size:106
Alignment explanation
Indices: 71142--71561 Score: 678
Period size: 106 Copynumber: 4.0 Consensus size: 106
71132 TATTGTTCCA
* * * *
71142 AGTCCAATATCCTTCGCTGTGAATTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* *
71207 CAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTAG
* *
71248 AGTCCAATATCCTTCGATGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
*
71313 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTAG
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTAG
**
71354 AGTCCAATGCCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* * *
71419 TAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTAG
* * * *
71460 AGTCCAATATCCTTCGCTGTGAAGTTAAAATTAGCTCTGAAATTGGGAAGTTATTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
71525 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGT
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGT
71562 TTCGGGTGGC
Statistics
Matches: 291, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 291 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTAG
Found at i:72118 original size:12 final size:12
Alignment explanation
Indices: 72101--72125 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
72091 GAGCTGAGTG
72101 TAACGGTTCAGA
1 TAACGGTTCAGA
72113 TAACGGTTCAGA
1 TAACGGTTCAGA
72125 T
1 T
72126 GATGCTTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (12 bp):
TAACGGTTCAGA
Found at i:73027 original size:18 final size:18
Alignment explanation
Indices: 73000--73035 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
72990 TGTTGAATCC
* *
73000 CCAAAGATACCCTAATAT
1 CCAAAAATACCCCAATAT
73018 CCAAAAATACCCCAATAT
1 CCAAAAATACCCCAATAT
73036 TTGATGTTGA
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:0.47, C:0.31, G:0.03, T:0.19
Consensus pattern (18 bp):
CCAAAAATACCCCAATAT
Found at i:77567 original size:6 final size:6
Alignment explanation
Indices: 77558--77604 Score: 58
Period size: 6 Copynumber: 7.3 Consensus size: 6
77548 AACAGTTAGT
*
77558 AAAATA AAAATA AATAATA ATAAATA AAAATA ATAATAA AAAATA AA
1 AAAATA AAAATA AA-AATA A-AAATA AAAATA AAAAT-A AAAATA AA
77605 TGGCAAGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
6 20 0.56
7 15 0.42
8 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:77574 original size:10 final size:10
Alignment explanation
Indices: 77559--77604 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
77549 ACAGTTAGTA
77559 AAATAAAAAT
1 AAATAAAAAT
*
77569 AAATAATAAT
1 AAATAAAAAT
77579 AAATAAAAAT
1 AAATAAAAAT
77589 -AATAATAAA-
1 AAATAA-AAAT
77598 AAATAAA
1 AAATAAA
77605 TGGCAAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 6 0.19
10 26 0.81
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:77581 original size:16 final size:16
Alignment explanation
Indices: 77560--77605 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 16
77550 CAGTTAGTAA
77560 AATAAAAATAAATAAT
1 AATAAAAATAAATAAT
77576 AATAAATAA-AAATAAT
1 AATAAA-AATAAATAAT
77592 AATAAAAAATAAAT
1 AAT-AAAAATAAAT
77606 GGCAAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AATAAAAATAAATAAT
Found at i:77600 original size:13 final size:13
Alignment explanation
Indices: 77558--77603 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
77548 AACAGTTAGT
*
77558 AAAATAAAAATAA
1 AAAATAATAATAA
*
77571 ATAATAATAA-ATA
1 AAAATAATAATA-A
77584 AAAATAATAATAA
1 AAAATAATAATAA
77597 AAAATAA
1 AAAATAA
77604 ATGGCAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 1 0.04
13 26 0.93
14 1 0.04
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAATAATAATAA
Found at i:81803 original size:19 final size:18
Alignment explanation
Indices: 81756--81796 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
81746 TGATTAAATA
81756 TTTAATAAAATTTTATTT
1 TTTAATAAAATTTTATTT
81774 TTTAAATTAAAATATTTATTT
1 TTT-AA-TAAAAT-TTTATTT
81795 TT
1 TT
81797 ACATAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.15
19 2 0.10
20 6 0.30
21 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAATAAAATTTTATTT
Found at i:81808 original size:24 final size:21
Alignment explanation
Indices: 81761--81811 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 21
81751 AAATATTTAA
*
81761 TAAAAT-TTTATTTTTTAAAT
1 TAAAATATTTATTTTTTAAAC
81781 TAAAATATTTATTTTTACATAAAC
1 TAAAATATTTATTTTT---TAAAC
81805 TAAAATA
1 TAAAATA
81812 CTATTAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.23
21 9 0.35
24 11 0.42
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAAATATTTATTTTTTAAAC
Done.