Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004707.1 Hibiscus syriacus cultivar Beakdansim tig00010584_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: 64162
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:125 original size:13 final size:14
Alignment explanation
Indices: 107--146 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
97 CAACGTATTA
*
107 AATAATTATTTT-T
1 AATAATCATTTTAT
120 AATAATCATTTTAT
1 AATAATCATTTTAT
134 AAT-AT-ATTTTAT
1 AATAATCATTTTAT
146 A
1 A
147 TATGACATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 8 0.32
13 13 0.52
14 4 0.16
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
AATAATCATTTTAT
Found at i:2422 original size:26 final size:26
Alignment explanation
Indices: 2392--2441 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
2382 AAAAACAAGG
*
2392 CTTGAAAA-TAAAAGTAAAATGAAAAA
1 CTTGAAAAGTAAAA-TAAAAAGAAAAA
2418 CTTGAAAAGTAAAATAAAAAGAAA
1 CTTGAAAAGTAAAATAAAAAGAAA
2442 GCTTTAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.66, C:0.04, G:0.12, T:0.18
Consensus pattern (26 bp):
CTTGAAAAGTAAAATAAAAAGAAAAA
Found at i:7211 original size:18 final size:18
Alignment explanation
Indices: 7188--7224 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7178 TAGTAACTTT
*
7188 GGCGAAGTCCCCGGTAAC
1 GGCGAAGTCCCCGGCAAC
*
7206 GGCGAAGTCTCCGGCAAC
1 GGCGAAGTCCCCGGCAAC
7224 G
1 G
7225 ATGACAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.32, G:0.35, T:0.11
Consensus pattern (18 bp):
GGCGAAGTCCCCGGCAAC
Found at i:8078 original size:25 final size:26
Alignment explanation
Indices: 8049--8097 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
8039 TAAAACAAGG
* *
8049 CTTGAAAA-TAAACTAAAATGAAAAA
1 CTTGAAAAGTAAAATAAAAAGAAAAA
8074 CTTGAAAAGTAAAATAAAAAGAAA
1 CTTGAAAAGTAAAATAAAAAGAAA
8098 GCTTTAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.18
Consensus pattern (26 bp):
CTTGAAAAGTAAAATAAAAAGAAAAA
Found at i:9080 original size:18 final size:18
Alignment explanation
Indices: 9040--9085 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
9030 ATTTAAAATT
* *
9040 ATTTAT-ATATTTATATT
1 ATTTATAATATATATATG
9057 ATTTTATAATATATATATG
1 A-TTTATAATATATATATG
9076 ATTTATAATA
1 ATTTATAATA
9086 AAAATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 14 0.56
19 10 0.40
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
ATTTATAATATATATATG
Found at i:9934 original size:18 final size:18
Alignment explanation
Indices: 9896--9934 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
9886 AATGGAAATG
*
9896 GCAATAGAAGCAGAAGTA
1 GCAATAGAAGCAGAAGCA
* *
9914 GCAATAGCAGCAGCAGCA
1 GCAATAGAAGCAGAAGCA
9932 GCA
1 GCA
9935 GCTTGTTGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.28, T:0.08
Consensus pattern (18 bp):
GCAATAGAAGCAGAAGCA
Found at i:10133 original size:17 final size:17
Alignment explanation
Indices: 10111--10144 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
10101 CCGCATCTCT
10111 CAGCCACCCACTTCCTC
1 CAGCCACCCACTTCCTC
10128 CAGCCACCCACTTCCTC
1 CAGCCACCCACTTCCTC
10145 TTCCACTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.59, G:0.06, T:0.18
Consensus pattern (17 bp):
CAGCCACCCACTTCCTC
Found at i:14805 original size:6 final size:6
Alignment explanation
Indices: 14794--14818 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
14784 AAGCTTAAGA
14794 TTGAGC TTGAGC TTGAGC TTGAGC T
1 TTGAGC TTGAGC TTGAGC TTGAGC T
14819 CAACTCCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.36
Consensus pattern (6 bp):
TTGAGC
Found at i:15665 original size:20 final size:20
Alignment explanation
Indices: 15640--15690 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 20
15630 CACGAAATGT
15640 AAGATTACCAGT-GAGAATAA
1 AAGATTACCAGTAG-GAATAA
15660 AAGATTACCAGTAGGAATAA
1 AAGATTACCAGTAGGAATAA
15680 AAGATTACCAG
1 AAGATTACCAG
15691 AGAATATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.20
Consensus pattern (20 bp):
AAGATTACCAGTAGGAATAA
Found at i:17094 original size:30 final size:30
Alignment explanation
Indices: 17058--17118 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
17048 TCAGCAGATG
*
17058 TGCATGGAAGCTTGGAGCTCTTGGCGTCTT
1 TGCATGGAAGCTTGGAGCTCTCGGCGTCTT
* *
17088 TGCATGGAAGGTTGGATCTCTCGGCGTCTT
1 TGCATGGAAGCTTGGAGCTCTCGGCGTCTT
17118 T
1 T
17119 AACACAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.13, C:0.20, G:0.33, T:0.34
Consensus pattern (30 bp):
TGCATGGAAGCTTGGAGCTCTCGGCGTCTT
Found at i:18104 original size:174 final size:173
Alignment explanation
Indices: 17815--18175 Score: 641
Period size: 174 Copynumber: 2.1 Consensus size: 173
17805 TTTTAAAGTT
* * * *
17815 TTAGGGACCGTTTTGTAAAATTTGAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGGTAT
1 TTAGGGATCATTTTGTAAAATTTGAGGAATTCAAGGAATAAGAGTAAATTATAAAAAGTTGGTAT
*
17880 ACTATGTTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTTGCAAGAATTTATAAATTTAGG
66 ACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTTGCAAGAATTTATAAATTTAGG
*
17945 GATTAAATTACAAAGTTTGAAAATATTGAGAACCAAATAGTAA
131 GATTAAATTACAAAGTTTAAAAATATTGAGAACCAAATAGTAA
17988 TTAGGGATCATTTTGTAAAATTTGAGGAATTCAAGGAATAAAGAGTAAATTATAAAAAGTTGGTA
1 TTAGGGATCATTTTGTAAAATTTGAGGAATTCAAGGAAT-AAGAGTAAATTATAAAAAGTTGGTA
18053 TACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTTGCAAGAATTTATAAATTTAG
65 TACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTTGCAAGAATTTATAAATTTAG
*
18118 GGATTAAATTACAAAGTTTAAAAATGTTGAGAACCAAATAGTAA
130 GGATTAAATTACAAAGTTTAAAAATATTGAGAACCAAATAGTAA
*
18162 TTAGAGATCATTTT
1 TTAGGGATCATTTT
18176 ATATTTGATG
Statistics
Matches: 179, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
173 36 0.20
174 143 0.80
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (173 bp):
TTAGGGATCATTTTGTAAAATTTGAGGAATTCAAGGAATAAGAGTAAATTATAAAAAGTTGGTAT
ACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTTGCAAGAATTTATAAATTTAGG
GATTAAATTACAAAGTTTAAAAATATTGAGAACCAAATAGTAA
Found at i:18884 original size:28 final size:27
Alignment explanation
Indices: 18852--19245 Score: 222
Period size: 28 Copynumber: 14.4 Consensus size: 27
18842 CTTTATTATT
*
18852 ATTAAATTATTAAAGTTAAATCATTAA
1 ATTAAATCATTAAAGTTAAATCATTAA
* *
18879 AGTTAAATAATTATTA-TTAAATCATTAA
1 A-TTAAATCATTA-AAGTTAAATCATTAA
** * * *
18907 ACCAAGTAATTATTA-TTAAATCATTAA
1 ATTAAATCATTA-AAGTTAAATCATTAA
* *
18934 AGTTAGTAATTATT--A-TTAAATTATTTAA
1 A-TTA--AATCATTAAAGTTAAATCA-TTAA
* * * *
18962 TTTAAATCGTTAAAGTTAAATAATTATT
1 ATTAAATCATTAAAGTTAAATCATTA-A
*
18990 ATTAAATCATT-AATTTAAATCATTAA
1 ATTAAATCATTAAAGTTAAATCATTAA
*
19016 AGTTAAATAATT--A-TTAAATCATTAA
1 A-TTAAATCATTAAAGTTAAATCATTAA
* * * *
19041 ATTTAAATCATTATAGTTAAGTAATTATT
1 A-TTAAATCATTAAAGTTAAATCATTA-A
* *
19070 ATTAAATCATTAAAGTTAAGTCATTATT
1 ATTAAATCATTAAAGTTAAATCATTA-A
* *
19098 ATTAAATTATTAAAGTAAAATCATTAA
1 ATTAAATCATTAAAGTTAAATCATTAA
* * *
19125 AGTTAAGTCATTATTA-TTAAATCATTTAC
1 A-TTAAATCATTA-AAGTTAAATCA-TTAA
* * *
19154 TTTAAATTATT-AAGTTAAATAATT--
1 ATTAAATCATTAAAGTTAAATCATTAA
*
19178 ATTAAATCATTAAAGTTAAAT-AATAA
1 ATTAAATCATTAAAGTTAAATCATTAA
* *
19204 TTATTAAATTATTAAATTTAAATCATTAA
1 --ATTAAATCATTAAAGTTAAATCATTAA
*
19233 ATTTAAATAATTA
1 A-TTAAATCATTA
19246 TTATTAAATA
Statistics
Matches: 292, Mismatches: 49, Indels: 51
0.74 0.12 0.13
Matches are distributed among these distances:
24 11 0.04
25 36 0.12
26 5 0.02
27 71 0.24
28 154 0.53
29 10 0.03
30 5 0.02
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (27 bp):
ATTAAATCATTAAAGTTAAATCATTAA
Found at i:18893 original size:42 final size:41
Alignment explanation
Indices: 18846--19198 Score: 228
Period size: 42 Copynumber: 8.6 Consensus size: 41
18836 GAATATCTTT
* *
18846 ATTATTATTAAATTATTAAAGTTAAATCATTAAAGTTAAATA
1 ATTATTATTAAATAATTAAA-TTAAATCATTAAAGTTAAATC
* ** * * *
18888 ATTATTATTAAATCATTAAACCAAGTAATTATTA-TTAAATC
1 ATTATTATTAAATAATTAAATTAAATCATTA-AAGTTAAATC
* * * * * *
18929 ATTA-AAGTT-AGTAATTATTATTAAATTATTTAATTTAAATC
1 ATTATTA-TTAAATAATTA-AATTAAATCATTAAAGTTAAATC
* * * *
18970 GTTA-AAGTTAAATAATTATTATTAAATCATT-AATTTAAATC
1 ATTATTA-TTAAATAATTA-AATTAAATCATTAAAGTTAAATC
* *
19011 ATTA-AAGTTAAATAATT--ATTAAATCATTAAATTTAAATC
1 ATTATTA-TTAAATAATTAAATTAAATCATTAAAGTTAAATC
* * *
19050 ATTA-TAGTTAAGTAATTATTATTAAATCATTAAAGTTAAGTC
1 ATTATTA-TTAAATAATTA-AATTAAATCATTAAAGTTAAATC
* * *
19092 ATTATTATTAAATTATTAAAGTAAAATCATTAAAGTTAAGTC
1 ATTATTATTAAATAATTAAA-TTAAATCATTAAAGTTAAATC
* ** *
19134 ATTATTATTAAATCATTTACTTTAAATTATT-AAGTTAAAT-
1 ATTATTATTAAAT-AATTAAATTAAATCATTAAAGTTAAATC
*
19174 A--ATTATTAAATCATTAAAGTTAAAT
1 ATTATTATTAAATAATTAAA-TTAAAT
19199 AATAATTATT
Statistics
Matches: 258, Mismatches: 40, Indels: 30
0.79 0.12 0.09
Matches are distributed among these distances:
37 3 0.01
38 27 0.10
39 25 0.10
40 9 0.03
41 76 0.29
42 113 0.44
43 5 0.02
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (41 bp):
ATTATTATTAAATAATTAAATTAAATCATTAAAGTTAAATC
Found at i:18924 original size:27 final size:27
Alignment explanation
Indices: 18867--18954 Score: 122
Period size: 27 Copynumber: 3.2 Consensus size: 27
18857 ATTATTAAAG
* *
18867 TTAAATCATTAAAGTTAAATAATTATTA
1 TTAAATCATTAAA-CTAAGTAATTATTA
*
18895 TTAAATCATTAAACCAAGTAATTATTA
1 TTAAATCATTAAACTAAGTAATTATTA
* *
18922 TTAAATCATTAAAGTTAGTAATTATTA
1 TTAAATCATTAAACTAAGTAATTATTA
18949 TTAAAT
1 TTAAAT
18955 TATTTAATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
27 41 0.76
28 13 0.24
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.42
Consensus pattern (27 bp):
TTAAATCATTAAACTAAGTAATTATTA
Found at i:18981 original size:55 final size:55
Alignment explanation
Indices: 18855--19054 Score: 153
Period size: 55 Copynumber: 3.7 Consensus size: 55
18845 TATTATTATT
*
18855 AAATTATTAAAGTTAAATCATTAAAGTTAAATAATTATTATTAAATCATTAAACC
1 AAATAATTAAAGTTAAATCATTAAAGTTAAATAATTATTATTAAATCATTAAACC
* * * * ***
18910 AAGTAATTATTA-TTAAATCATTAAAGTT-AGTAATTATTATTAAATTATTTAATTT
1 AAATAATTA-AAGTTAAATCATTAAAGTTAAATAATTATTATTAAATCA-TTAAACC
** * * * * **
18965 AAATCGTTAAAGTTAAATAATTATTA-TTAAATCATTAAT-TTAAATCATTAAAGTT
1 AAATAATTAAAGTTAAATCATTA-AAGTTAAATAATTATTATTAAATCATTAAA-CC
* *
19020 AAATAATT--A-TTAAATCATTAAATTTAAATCATTAT
1 AAATAATTAAAGTTAAATCATTAAAGTTAAATAATTAT
19055 AGTTAAGTAA
Statistics
Matches: 114, Mismatches: 24, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
51 1 0.01
52 21 0.18
53 1 0.01
54 22 0.19
55 60 0.53
56 9 0.08
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (55 bp):
AAATAATTAAAGTTAAATCATTAAAGTTAAATAATTATTATTAAATCATTAAACC
Found at i:19191 original size:8 final size:7
Alignment explanation
Indices: 19177--19256 Score: 60
Period size: 8 Copynumber: 11.4 Consensus size: 7
19167 GTTAAATAAT
19177 TATTAAA
1 TATTAAA
19184 TCATTAAA
1 T-ATTAAA
*
19192 -GTTAAA
1 TATTAAA
* *
19198 TAATAAT
1 TATTAAA
19205 TATTAAA
1 TATTAAA
19212 TTATTAAA
1 -TATTAAA
19220 T-TTAAA
1 TATTAAA
19226 TCATTAAA
1 T-ATTAAA
19234 T-TTAAA
1 TATTAAA
*
19240 TAATT-AT
1 T-ATTAAA
19247 TATTAAA
1 TATTAAA
19254 TAT
1 TAT
19257 ATACTCGAGT
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
6 20 0.35
7 16 0.28
8 21 0.37
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (7 bp):
TATTAAA
Found at i:19255 original size:14 final size:14
Alignment explanation
Indices: 18853--19246 Score: 171
Period size: 14 Copynumber: 28.9 Consensus size: 14
18843 TTTATTATTA
* *
18853 TTAAATTATTAAAG
1 TTAAATCATTATAG
*
18867 TTAAATCATTAAAG
1 TTAAATCATTATAG
*
18881 TTAAATAATTATTA-
1 TTAAATCATTA-TAG
*
18895 TTAAATCATTA-AA
1 TTAAATCATTATAG
** * *
18908 CCAAGTAATTATTA-
1 TTAAATCATTA-TAG
*
18922 TTAAATCATTAAAG
1 TTAAATCATTATAG
* *
18936 TT-AGTAATTATTA-
1 TTAAATCATTA-TAG
* *
18949 TTAAATTATT-TAAT
1 TTAAATCATTAT-AG
* *
18963 TTAAATCGTTAAAG
1 TTAAATCATTATAG
*
18977 TTAAATAATTATTA-
1 TTAAATCATTA-TAG
*
18991 TTAAATCATTA-AT
1 TTAAATCATTATAG
*
19004 TTAAATCATTAAAG
1 TTAAATCATTATAG
*
19018 TTAAAT-AAT-TA-
1 TTAAATCATTATAG
* *
19029 TTAAATCATTAAAT
1 TTAAATCATTATAG
19043 TTAAATCATTATAG
1 TTAAATCATTATAG
* *
19057 TTAAGTAATTATTA-
1 TTAAATCATTA-TAG
*
19071 TTAAATCATTAAAG
1 TTAAATCATTATAG
*
19085 TTAAGTCATTATTA-
1 TTAAATCATTA-TAG
* *
19099 TTAAATTATTAAAG
1 TTAAATCATTATAG
* *
19113 TAAAATCATTAAAG
1 TTAAATCATTATAG
*
19127 TTAAGTCATTATTA-
1 TTAAATCATTA-TAG
*
19141 TTAAATCATT-TACT
1 TTAAATCATTATA-G
*
19155 TTAAATTATTA-AG
1 TTAAATCATTATAG
*
19168 TTAAAT-AAT-TA-
1 TTAAATCATTATAG
*
19179 TTAAATCATTAAAG
1 TTAAATCATTATAG
* *
19193 TTAAATAATAATTA-
1 TTAAATCATTA-TAG
* * *
19207 TTAAATTATTAAAT
1 TTAAATCATTATAG
* *
19221 TTAAATCATTAAAT
1 TTAAATCATTATAG
*
19235 TTAAATAATTAT
1 TTAAATCATTAT
19247 TATTAAATAT
Statistics
Matches: 287, Mismatches: 63, Indels: 60
0.70 0.15 0.15
Matches are distributed among these distances:
11 12 0.04
12 13 0.05
13 41 0.14
14 213 0.74
15 8 0.03
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (14 bp):
TTAAATCATTATAG
Found at i:19284 original size:108 final size:105
Alignment explanation
Indices: 18963--19284 Score: 305
Period size: 108 Copynumber: 3.0 Consensus size: 105
18953 ATTATTTAAT
* *
18963 TTAAATCGTTAAAGTTAAATAATTATTATTAAATCATT-AATTTAAATCATTAAAGTTAAATAAT
1 TTAAATCATTAAAGTTAAATAATTATTATTAAATTATTAAATTTAAATCATTAAAGTTAAATAAT
* * *
19027 TATTAAATCATTAAATTTA-AATCATTATAGTTAA-GTAAT-T-ATTA
66 TA-T---T-ATTAAATATATACTCA--ATAATTAATG-AATATAATTA
* * * * * *
19071 TTAAATCATTAAAGTTAAGTCATTATTATTAAATTATTAAAGTAAAATCATTAAAGTTAAGTCAT
1 TTAAATCATTAAAGTTAAATAATTATTATTAAATTATTAAATTTAAATCATTAAAGTTAAATAAT
* * * *
19136 TATTATTAAATCATTTACTTTAAATTATTAAGTTAA-ATAATTA
66 TATTATTAAAT-ATATAC--TCAATAATTAA-TGAATATAATTA
* *
19179 TTAAATCATTAAAGTTAAATAATAATTATTAAATTATTAAATTTAAATCATTAAATTTAAATAAT
1 TTAAATCATTAAAGTTAAATAATTATTATTAAATTATTAAATTTAAATCATTAAAGTTAAATAAT
*
19244 TATTATTAAATATATACTCGAGTAATTGAATCGAATATAAT
66 TATTATTAAATATATACTC-AATAATT-AAT-GAATATAAT
19285 ATACAAATTT
Statistics
Matches: 173, Mismatches: 28, Indels: 26
0.76 0.12 0.11
Matches are distributed among these distances:
104 7 0.04
105 3 0.02
106 13 0.08
107 12 0.07
108 114 0.66
109 24 0.14
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (105 bp):
TTAAATCATTAAAGTTAAATAATTATTATTAAATTATTAAATTTAAATCATTAAAGTTAAATAAT
TATTATTAAATATATACTCAATAATTAATGAATATAATTA
Found at i:22536 original size:17 final size:17
Alignment explanation
Indices: 22508--22552 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
22498 AAAATAGAAA
22508 CATCGAATGCAATTAGTG
1 CATCG-ATGCAATTAGTG
22526 CATCGATGCAATTAGTG
1 CATCGATGCAATTAGTG
22543 CATCGATGCA
1 CATCGATGCA
22553 TCCCAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 22 0.81
18 5 0.19
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (17 bp):
CATCGATGCAATTAGTG
Found at i:23795 original size:31 final size:31
Alignment explanation
Indices: 23708--23834 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
23698 AGAGTCGAGG
23708 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
23739 GAATTACCTATG-TCTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
* *
23771 GTATACCTATGTTCTAAGGAACATATGGAAA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * *
23802 GTTTACCTAGGTTCTTCGGAACCTATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
23833 GT
1 GT
23835 TGCCAAGGAT
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
31 52 0.66
32 27 0.34
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:23876 original size:30 final size:30
Alignment explanation
Indices: 23822--23890 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
23812 GTTCTTCGGA
* *
23822 ACCTATGGACAGTTGCCAAGGATCTTTATG
1 ACCTCTGGACAGTTACCAAGGATCTTTATG
* *
23852 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGACAGTTACCAAGGATCTTTATG
23882 ACCTCTGGA
1 ACCTCTGGA
23891 AAGGTCCTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (30 bp):
ACCTCTGGACAGTTACCAAGGATCTTTATG
Found at i:26390 original size:6 final size:6
Alignment explanation
Indices: 26379--26404 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
26369 CTGTTGCGTA
26379 GAAGCT GAAGCT GAAGCT GAAGCT GA
1 GAAGCT GAAGCT GAAGCT GAAGCT GA
26405 GCAATTAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.35, T:0.15
Consensus pattern (6 bp):
GAAGCT
Found at i:29859 original size:33 final size:33
Alignment explanation
Indices: 29815--29886 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
29805 TTGCAAGGTG
*
29815 GCCTCAACCCTCAGTGCACCCTGATGTGTGCTA
1 GCCTCAACCCTCAGTGCACCCCGATGTGTGCTA
* *
29848 GCCTCAGCCCTCAGTGCACCCCGATGTGTGCTG
1 GCCTCAACCCTCAGTGCACCCCGATGTGTGCTA
29881 GCCTCA
1 GCCTCA
29887 CCACTAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.15, C:0.39, G:0.24, T:0.22
Consensus pattern (33 bp):
GCCTCAACCCTCAGTGCACCCCGATGTGTGCTA
Found at i:30034 original size:10 final size:10
Alignment explanation
Indices: 30019--30043 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
30009 CAGCGGTATC
30019 GACCCTAGGT
1 GACCCTAGGT
30029 GACCCTAGGT
1 GACCCTAGGT
30039 GACCC
1 GACCC
30044 CTGGTATGTG
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:0.20, C:0.36, G:0.28, T:0.16
Consensus pattern (10 bp):
GACCCTAGGT
Found at i:32353 original size:27 final size:26
Alignment explanation
Indices: 32314--32379 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
32304 ATGAAGAAAG
*
32314 CAAAGATAAAATAATA-AGTAAAAAAA
1 CAAAAATAAAATAATATA-TAAAAAAA
32340 CAAATAATAAAAT-ATATATAAAAAAA
1 CAAA-AATAAAATAATATATAAAAAAA
* *
32366 GAAAAAGAAAATAA
1 CAAAAATAAAATAA
32380 ATTAAACAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 7 0.21
26 19 0.56
27 8 0.24
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (26 bp):
CAAAAATAAAATAATATATAAAAAAA
Found at i:32452 original size:35 final size:34
Alignment explanation
Indices: 32376--32470 Score: 84
Period size: 35 Copynumber: 2.6 Consensus size: 34
32366 GAAAAAGAAA
*
32376 ATAAATTAAACAAAATAATAATAACAAAGTACGAATAAT
1 ATAAATT-AA-AAAAT-A-AATAAAAAAGTAC-AATAAT
*
32415 ATATATATAAAAAATAAATAAAAAAGTA-AATATAT
1 ATAAAT-TAAAAAATAAATAAAAAAGTACAATA-AT
*
32450 ATAAATTAATAAATTAAATAA
1 ATAAATTAA-AAAATAAATAA
32471 CGAAAAGAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
34 7 0.14
35 17 0.35
36 11 0.22
37 1 0.02
38 5 0.10
39 7 0.14
40 1 0.02
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (34 bp):
ATAAATTAAAAAATAAATAAAAAAGTACAATAAT
Found at i:32532 original size:2 final size:2
Alignment explanation
Indices: 32525--32575 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
32515 GATAATTACA
*
32525 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32567 AT AT AT AT A
1 AT AT AT AT A
32576 GTAACAATAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:32998 original size:12 final size:11
Alignment explanation
Indices: 32971--33010 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
32961 TAACAAAATA
*
32971 AATAATATAA-
1 AATAATACAAG
32981 AATAATACAAG
1 AATAATACAAG
32992 TAATAATACAAG
1 -AATAATACAAG
33004 AATAATA
1 AATAATA
33011 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.33
11 7 0.26
12 11 0.41
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (11 bp):
AATAATACAAG
Found at i:33050 original size:21 final size:21
Alignment explanation
Indices: 33026--33071 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
33016 AAAGAGAAAG
33026 TAAAAATATA-ATAATAAAATA
1 TAAAAATATACAT-ATAAAATA
*
33047 TAAAAATATACATATATAATA
1 TAAAAATATACATATAAAATA
33068 TAAA
1 TAAA
33072 TAGTAGAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAAATATACATATAAAATA
Found at i:33099 original size:23 final size:22
Alignment explanation
Indices: 33064--33131 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 22
33054 ATACATATAT
*
33064 AATATAAATAGTAGAATAAAAGGA
1 AATAT-AATAGTAAAATAAAA-GA
*
33088 AATATAATAGTAAAATAATAATA
1 AATATAATAGTAAAATAA-AAGA
33111 AATATAATAGTAATAATAAAA
1 AATATAATAGTAA-AATAAAA
33132 ATGCAAAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 28 0.70
24 12 0.30
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (22 bp):
AATATAATAGTAAAATAAAAGA
Found at i:33149 original size:58 final size:56
Alignment explanation
Indices: 33004--33151 Score: 142
Period size: 58 Copynumber: 2.5 Consensus size: 56
32994 ATAATACAAG
33004 AATAATAAAAA-GAAAGAGAAAGTAAAAATATAATAATAAAATATAAAAATATACATAT
1 AATAATAAAAATGAAAGA-AAAGT--AAATATAATAATAAAATATAAAAATATACATAT
* * * *
33062 -ATAATATAAATAGTAGAATAAAAGGAAATATAATAGTAAAATAATAATAAATATA-ATAGT
1 AATAATAAAAAT-G-A-AAGAAAAGTAAATATAATAATAAAAT-ATAA-AAATATACATA-T
33122 AATAATAAAAATGCAAAGAAAA-TAAATATA
1 AATAATAAAAATG-AAAGAAAAGTAAATATA
33152 TATATATATG
Statistics
Matches: 74, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
57 9 0.12
58 23 0.31
59 14 0.19
60 15 0.20
61 13 0.18
ACGTcount: A:0.66, C:0.01, G:0.08, T:0.24
Consensus pattern (56 bp):
AATAATAAAAATGAAAGAAAAGTAAATATAATAATAAAATATAAAAATATACATAT
Found at i:33725 original size:37 final size:37
Alignment explanation
Indices: 33684--33788 Score: 165
Period size: 37 Copynumber: 2.8 Consensus size: 37
33674 GTGCTTGTGG
* * *
33684 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* *
33721 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
33758 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
33789 GACGAAAAGG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:34837 original size:106 final size:106
Alignment explanation
Indices: 34518--35455 Score: 1307
Period size: 106 Copynumber: 8.9 Consensus size: 106
34508 AGCATTGTTC
* * * ** *
34518 TGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* * *
34583 ACCAGAC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCT
66 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
34624 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA---GGAAA-T-TTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* * * * * *
34683 ATCAACCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
34724 TGGGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
*
34789 ACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
34830 TGAGTCCAATATCCTACGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* * *
34895 ACCAGCAGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * * * *
34936 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTATTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
35001 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
35042 TGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTTTGAAATTGGGAAAATATTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
35107 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAC-TTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG-CGTTGTCT
* * ** * * *
35148 GGAGTCCAATATCATTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
*
35213 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
35254 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* *
35319 ACCACCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
35360 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAACTGTTTATTGATA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
35425 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
35456 CCACTCTCGA
Statistics
Matches: 747, Mismatches: 76, Indels: 18
0.89 0.09 0.02
Matches are distributed among these distances:
99 1 0.00
100 79 0.11
101 3 0.00
102 5 0.01
104 4 0.01
105 4 0.01
106 650 0.87
107 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:35975 original size:18 final size:17
Alignment explanation
Indices: 35948--35981 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
35938 CTTTATTTTC
35948 AAAATTTTGAAAATATG
1 AAAATTTTGAAAATATG
35965 AAAAGTTTTGAAAATAT
1 AAAA-TTTTGAAAATAT
35982 TGTCCCTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (17 bp):
AAAATTTTGAAAATATG
Found at i:36194 original size:22 final size:22
Alignment explanation
Indices: 36168--36244 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
36158 TTGTGTTTGG
36168 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* *
36190 TCAAAGGTTTGACATGTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
36212 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
36234 TCAACGGTTTG
1 TCAAAGGTTTG
36245 ATAGGGTAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:36878 original size:14 final size:14
Alignment explanation
Indices: 36861--36914 Score: 67
Period size: 14 Copynumber: 3.8 Consensus size: 14
36851 TTCTTTTTGA
36861 TTTTTGTTTTTTCT
1 TTTTTGTTTTTTCT
36875 TTTTT-TTTTCTTCT
1 TTTTTGTTTT-TTCT
36889 TTTTTGCTTCTTTTC-
1 TTTTTG-TT-TTTTCT
36904 TTTTTGTTTTT
1 TTTTTGTTTTT
36915 GCCCTTTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 7 0.19
14 16 0.44
15 6 0.17
16 5 0.14
17 2 0.06
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (14 bp):
TTTTTGTTTTTTCT
Found at i:36883 original size:11 final size:11
Alignment explanation
Indices: 36862--36914 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
36852 TCTTTTTGAT
36862 TTTTGTTTTTTC
1 TTTT-TTTTTTC
36874 TTTTTTTTTTC
1 TTTTTTTTTTC
36885 TTCTTTTTTGCTTC
1 TT-TTTTTT--TTC
* *
36899 TTTTCTTTTTG
1 TTTTTTTTTTC
36910 TTTTT
1 TTTTT
36915 GCCCTTTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
11 15 0.43
12 10 0.29
13 5 0.14
14 5 0.14
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:36892 original size:20 final size:20
Alignment explanation
Indices: 36847--36883 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
36837 TTTTTTGTCC
36847 CTTTTTCTTTTTGATTTTTGT
1 CTTTTTCTTTTT-ATTTTTGT
36868 -TTTTTCTTTTT-TTTTT
1 CTTTTTCTTTTTATTTTT
36884 CTTCTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.31
20 11 0.69
ACGTcount: A:0.03, C:0.08, G:0.05, T:0.84
Consensus pattern (20 bp):
CTTTTTCTTTTTATTTTTGT
Found at i:38189 original size:14 final size:15
Alignment explanation
Indices: 38172--38200 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38162 TACATGATAT
38172 GCATA-AACATAAGA
1 GCATATAACATAAGA
38186 GCATATAACATAAGA
1 GCATATAACATAAGA
38201 TATGTGATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.17
Consensus pattern (15 bp):
GCATATAACATAAGA
Found at i:38463 original size:15 final size:15
Alignment explanation
Indices: 38445--38477 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
38435 CGAGGGTTCT
38445 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
38460 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
38475 GTA
1 GTA
38478 ATGGTCCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.24, G:0.33, T:0.27
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:38512 original size:22 final size:19
Alignment explanation
Indices: 38462--38514 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
38452 TTCGGGACGT
*
38462 AGTCCTTCGGGACGTAATG
1 AGTCCTTCGGGACATAATG
*
38481 -GTCCTACGGGACATATATAG
1 AGTCCTTCGGGACATA-AT-G
38501 CAGTCCTTCGGGAC
1 -AGTCCTTCGGGAC
38515 GAATACTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 13 0.48
19 2 0.07
20 1 0.04
22 11 0.41
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (19 bp):
AGTCCTTCGGGACATAATG
Found at i:44340 original size:14 final size:15
Alignment explanation
Indices: 44323--44351 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44313 TATATGATAT
44323 GCATA-AACATAAGA
1 GCATATAACATAAGA
44337 GCATATAACATAAGA
1 GCATATAACATAAGA
44352 TATGTGATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.17
Consensus pattern (15 bp):
GCATATAACATAAGA
Found at i:44625 original size:14 final size:15
Alignment explanation
Indices: 44595--44626 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
44585 CAAGGGTTCT
44595 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
44610 GTAGTCCTTC-GGAC
1 GTAGTCCTTCGGGAC
44624 GTA
1 GTA
44627 ATGGTCCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.16, C:0.25, G:0.31, T:0.28
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:44658 original size:19 final size:18
Alignment explanation
Indices: 44611--44659 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
44601 CTTCGGGACG
*
44611 TAGTCCTTC-GGACGTAA
1 TAGTCCTTCGGGACATAA
* *
44628 TGGTCCTACGGGACATATA
1 TAGTCCTTCGGGACATA-A
44647 TAGTCCTTCGGGA
1 TAGTCCTTCGGGA
44660 TGAATACTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (18 bp):
TAGTCCTTCGGGACATAA
Found at i:49713 original size:12 final size:12
Alignment explanation
Indices: 49691--49760 Score: 61
Period size: 12 Copynumber: 5.5 Consensus size: 12
49681 GAAAGCAAAG
*
49691 ATAAAATAATAA
1 ATAAAAAAATAA
*
49703 GTAAAAAAATAA
1 ATAAAAAAATAA
*
49715 ATAATAAAATATAT
1 ATAA-AAAA-ATAA
49729 ATAAAAAAGA-AA
1 ATAAAAAA-ATAA
49741 ATAAAAGAAAATAA
1 AT-AAA-AAAATAA
49755 ATAAAA
1 ATAAAA
49761 CAAAATAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
12 17 0.36
13 16 0.34
14 14 0.30
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (12 bp):
ATAAAAAAATAA
Found at i:49713 original size:15 final size:15
Alignment explanation
Indices: 49693--49774 Score: 56
Period size: 14 Copynumber: 5.9 Consensus size: 15
49683 AAGCAAAGAT
49693 AAAAT-AATAAGTAAA
1 AAAATAAATAA-TAAA
49708 AAAATAAATAAT---
1 AAAATAAATAATAAA
*
49720 AAAATATAT-ATAAA
1 AAAATAAATAATAAA
*
49734 AAAGA-AAATAA-AAG
1 AAA-ATAAATAATAAA
*
49748 AAAATAAATAA-AAC
1 AAAATAAATAATAAA
49762 AAAAT-AATAATAA
1 AAAATAAATAATAA
49775 CAAAGTACGA
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
11 2 0.04
12 8 0.15
13 6 0.11
14 26 0.47
15 8 0.15
16 5 0.09
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.20
Consensus pattern (15 bp):
AAAATAAATAATAAA
Found at i:49723 original size:14 final size:13
Alignment explanation
Indices: 49705--49768 Score: 67
Period size: 14 Copynumber: 4.8 Consensus size: 13
49695 AATAATAAGT
49705 AAAAAAATAAATA
1 AAAAAAATAAATA
* *
49718 ATAAAATATATATA
1 A-AAAAAATAAATA
*
49732 AAAAAGA-AAATA
1 AAAAAAATAAATA
49744 AAAGAAAATAAATA
1 AAA-AAAATAAATA
49758 AAACAAAATAA
1 AAA-AAAATAA
49769 TAATAACAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
12 7 0.17
13 9 0.21
14 26 0.62
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (13 bp):
AAAAAAATAAATA
Found at i:49742 original size:26 final size:25
Alignment explanation
Indices: 49691--49774 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 25
49681 GAAAGCAAAG
49691 ATAAAATA-ATAAGTAAAAAAATAAATA
1 ATAAAATATAT-A-TAAAAAAA-AAATA
49718 ATAAAATATATATAAAAAAGAAAATA
1 ATAAAATATATATAAAAAA-AAAATA
* *
49744 A-AAGAAAATAAATAAAACAAAATAATA
1 ATAA-AATATATATAAAA-AAAA-AATA
49771 ATAA
1 ATAA
49775 CAAAGTACGA
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
25 2 0.04
26 26 0.53
27 17 0.35
28 4 0.08
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (25 bp):
ATAAAATATATATAAAAAAAAAATA
Found at i:49797 original size:69 final size:70
Alignment explanation
Indices: 49693--49829 Score: 163
Period size: 69 Copynumber: 2.0 Consensus size: 70
49683 AAGCAAAGAT
*
49693 AAAATAATAAGTAAAAAAATAAATAATAAAATATATATAAAAAAGAAA-ATAAAAGAAAATAAAT
1 AAAATAATAAGTAAAAAAATAAATAATAAAATATATATAAAAAAGAAATAAAAAAGAAAATAAAT
49757 AAAAC
66 AAAAC
* * * * * * *
49762 AAAATAATAA-TAACAAAGTACGAATAAT-ATATATATATATAAAATAAATAAAAAAGTAAATAT
1 AAAATAATAAGTAAAAAAATA--AATAATAAAATATATATAAAAAAGAAATAAAAAAGAAAATAA
49825 ATAAA
64 ATAAA
49830 TTAATAAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
68 8 0.14
69 27 0.47
70 22 0.39
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (70 bp):
AAAATAATAAGTAAAAAAATAAATAATAAAATATATATAAAAAAGAAATAAAAAAGAAAATAAAT
AAAAC
Found at i:50179 original size:2 final size:2
Alignment explanation
Indices: 50068--50160 Score: 177
Period size: 2 Copynumber: 46.5 Consensus size: 2
50058 CTTGTGTAGA
*
50068 AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50110 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50152 AT AT AT AT A
1 AT AT AT AT A
50161 ATAGTAAAAT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50393 original size:12 final size:11
Alignment explanation
Indices: 50365--50405 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
50355 ATAACAAATA
* *
50365 AATAATATAAA
1 AATAATACAAG
50376 AATAATACAAG
1 AATAATACAAG
50387 TAATAATACAAG
1 -AATAATACAAG
50399 AATAATA
1 AATAATA
50406 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:51115 original size:37 final size:37
Alignment explanation
Indices: 51074--51178 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
51064 GTGCTTGTGG
* * *
51074 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
51111 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
51148 ATCATATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
51179 GACGAAAAGG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:55203 original size:20 final size:20
Alignment explanation
Indices: 55178--55247 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
55168 GCGATTTTCT
*
55178 AAATTCGCAACGCGATAGTC
1 AAATTCGCAACGCGAAAGTC
*
55198 AAATTCTCAACGCGAAAGTC
1 AAATTCGCAACGCGAAAGTC
* **
55218 AAATTCGCAAC-TGAATTTC
1 AAATTCGCAACGCGAAAGTC
55237 AAATTCGCAAC
1 AAATTCGCAAC
55248 TGAATTTCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 16 0.36
20 28 0.64
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.23
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGTC
Found at i:55240 original size:19 final size:19
Alignment explanation
Indices: 55216--55263 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
55206 AACGCGAAAG
55216 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
55235 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
55254 TCAAATTCGC
1 TCAAATTCGC
55264 GACAGGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.31
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:55643 original size:15 final size:15
Alignment explanation
Indices: 55589--55647 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
55579 TTGATTTTCC
55589 GGAAAATGAATTACT
1 GGAAAATGAATTACT
* **
55604 AGAATTTGAATTACT
1 GGAAAATGAATTACT
*
55619 -GAAATTTGAATTACT
1 GGAAA-ATGAATTACT
55634 GGAAAATGAATTAC
1 GGAAAATGAATTAC
55648 ATTTATGGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 3 0.08
15 30 0.81
16 4 0.11
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (15 bp):
GGAAAATGAATTACT
Found at i:55658 original size:20 final size:20
Alignment explanation
Indices: 55633--55679 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
55623 TTTGAATTAC
55633 TGGAAAATGAATTACATTTA
1 TGGAAAATGAATTACATTTA
*
55653 TGGAAAATGAATTACATTTC
1 TGGAAAATGAATTACATTTA
55673 TGGAAAA
1 TGGAAAA
55680 CATCTGGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (20 bp):
TGGAAAATGAATTACATTTA
Found at i:56027 original size:26 final size:25
Alignment explanation
Indices: 55996--56144 Score: 103
Period size: 25 Copynumber: 5.9 Consensus size: 25
55986 CTTTACTAAA
*
55996 ATATTATTTAAATATATAAATATTAT
1 ATATTA-TTAAATATAAAAATATTAT
56022 -TCATTATTAAATATAAAAATTATTAT
1 AT-ATTATTAAATATAAAAA-TATTAT
*
56048 ATATTATTAAA-ATAAAAATATAAT
1 ATATTATTAAATATAAAAATATTAT
* * * * *
56072 ATCTTATATTATTATAATAAT-TGAT
1 ATATTAT-TAAATATAAAAATATTAT
*
56097 -TATTATTAAA-CTAAAAATAATGT-T
1 ATATTATTAAATATAAAAAT-AT-TAT
* *
56121 ATATTATAAAATAATAAATATATT
1 ATATTATTAAAT-ATAAAAATATT
56145 TTAAATATTT
Statistics
Matches: 96, Mismatches: 16, Indels: 23
0.71 0.12 0.17
Matches are distributed among these distances:
22 6 0.06
23 2 0.02
24 18 0.19
25 35 0.36
26 28 0.29
27 7 0.07
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (25 bp):
ATATTATTAAATATAAAAATATTAT
Found at i:56715 original size:39 final size:39
Alignment explanation
Indices: 56671--56753 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
56661 GATGCTCATC
* *
56671 AAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAAATCA
1 AAATCCAAAGATCATATGGTGCCAAGCAAAAGAAAATCA
* *
56710 AAATCCAAATATCATATGGTTCCAAGCAAAAGAAAATCA
1 AAATCCAAAGATCATATGGTGCCAAGCAAAAGAAAATCA
56749 AAATC
1 AAATC
56754 TACAACTTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.49, C:0.19, G:0.13, T:0.18
Consensus pattern (39 bp):
AAATCCAAAGATCATATGGTGCCAAGCAAAAGAAAATCA
Found at i:57184 original size:60 final size:62
Alignment explanation
Indices: 57049--57185 Score: 181
Period size: 63 Copynumber: 2.2 Consensus size: 62
57039 TTTTAAAAAC
57049 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATTCTTATTTACAAATCAAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAA-CAAAAAAATTCTTATTTACAAATCAAATTA
* * * ** *
57112 AACAAATCAACTTTTACAAATCAATTAATCAA-AAATAAA-TCTTATTTCCTCATC-AATTGT
1 AACAAATCAACTTTTACAAATCAATTAAACAACAAAAAAATTCTTATTTACAAATCAAATT-A
57172 AACAAATCAACTTT
1 AACAAATCAACTTT
57186 CAATGTAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
59 4 0.06
60 26 0.39
61 6 0.09
63 31 0.46
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.31
Consensus pattern (62 bp):
AACAAATCAACTTTTACAAATCAATTAAACAACAAAAAAATTCTTATTTACAAATCAAATTA
Found at i:58556 original size:21 final size:20
Alignment explanation
Indices: 58532--58627 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 20
58522 GGCGGGACCA
*
58532 CTTGAACGATGACAGGGGCCT
1 CTTGAATGATGA-AGGGGCCT
* * *
58553 CTTGAACGGTGGAAGGGGCTT
1 CTTGAATGAT-GAAGGGGCCT
58574 CTTCG-ATGATGATAGGGGCCT
1 CTT-GAATGATGA-AGGGGCCT
58595 CTTGAATGAT-ATGAGGGGCCT
1 CTTGAATGATGA--AGGGGCCT
58616 CTTGAATGATGA
1 CTTGAATGATGA
58628 TAGGTGCATC
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
20 4 0.06
21 55 0.87
22 4 0.06
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (20 bp):
CTTGAATGATGAAGGGGCCT
Found at i:58612 original size:42 final size:42
Alignment explanation
Indices: 58532--58631 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
58522 GGCGGGACCA
* * * *
58532 CTTGAACGATGACAGGGGCCTCTTGAACGGTGGAAGGGGCTT
1 CTTGAATGATGATAGGGGCCTCTTGAACGATGGAAGGGGCCT
* *
58574 CTTCG-ATGATGATAGGGGCCTCTTGAATGATATG-AGGGGCCT
1 CTT-GAATGATGATAGGGGCCTCTTGAACGAT-GGAAGGGGCCT
58616 CTTGAATGATGATAGG
1 CTTGAATGATGATAGG
58632 TGCATCGGGC
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
41 1 0.02
42 46 0.94
43 2 0.04
ACGTcount: A:0.23, C:0.16, G:0.35, T:0.26
Consensus pattern (42 bp):
CTTGAATGATGATAGGGGCCTCTTGAACGATGGAAGGGGCCT
Found at i:59074 original size:21 final size:21
Alignment explanation
Indices: 59025--59074 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
59015 ACCATTATCT
59025 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGTACCGACCTCA
* *
59046 TGATGTAAAGTACCGACCTCA
1 TCACGTAAAGTACCGACCTCA
59067 TCACGTAA
1 TCACGTAA
59075 TTCCCCTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGTACCGACCTCA
Found at i:60778 original size:20 final size:20
Alignment explanation
Indices: 60762--60816 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
60752 TCTGAAACTT
60762 AAATTCGCAACGCGAAAATGA
1 AAATTCGCAACGCGAAAAT-A
*
60783 AAA-TCGCAACGCAAAAATGA
1 AAATTCGCAACGCGAAAAT-A
60803 AAATT-GCAACGCGA
1 AAATTCGCAACGCGA
60817 TTTTAGTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 27 0.87
21 4 0.13
ACGTcount: A:0.49, C:0.20, G:0.18, T:0.13
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATA
Found at i:60873 original size:20 final size:20
Alignment explanation
Indices: 60813--60875 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
60803 AAATTGCAAC
*
60813 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
60832 GAGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
60852 GCGATTTTCATTTTTGCGTT
1 GCGATTTTCATTTTCGCGTT
60872 GCGA
1 GCGA
60876 ATTTGGTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 7 0.18
20 32 0.82
ACGTcount: A:0.13, C:0.16, G:0.24, T:0.48
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:61183 original size:22 final size:22
Alignment explanation
Indices: 61126--61183 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
61116 TCTGAGAGAT
61126 GGAGAT-A-GACGGATTTCGTC
1 GGAGATGAGGACGGATTTCGTC
* * * *
61146 AGAAATGGGGATGGATTTCGTC
1 GGAGATGAGGACGGATTTCGTC
61168 GGAGATGAGGACGGAT
1 GGAGATGAGGACGGAT
61184 ATCGCCGTAG
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 4 0.14
22 24 0.86
ACGTcount: A:0.28, C:0.10, G:0.40, T:0.22
Consensus pattern (22 bp):
GGAGATGAGGACGGATTTCGTC
Found at i:61902 original size:18 final size:19
Alignment explanation
Indices: 61867--61904 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
61857 CACGGAATGT
61867 AAGATTATCAGTGGGAATAA
1 AAGATTATCAG-GGGAATAA
61887 AAGATTATCA-GGGAATAA
1 AAGATTATCAGGGGAATAA
61905 GATTACAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGGGAATAA
Done.