Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002421.1 Hibiscus syriacus cultivar Beakdansim tig00004949_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: 129229
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:673 original size:107 final size:107
Alignment explanation
Indices: 487--700 Score: 383
Period size: 107 Copynumber: 2.0 Consensus size: 107
477 ATTGCAGCAG
* *
487 CCCCTATATGTGATGATGTGCCGTCCATGAACCCCAAACGAAGCCATCAGGCACACAGCCAGAGC
1 CCCCTATATGTGATGATGTGCCGTCCATGAACCCCAAACGAAGCCATCAGACACACAACCAGAGC
* *
552 GTGCTTTGCTCAAGAACAGGCAGGGAAAGTCTTTACAGTAAA
66 GTGCTTTGCCCAAGAACAAGCAGGGAAAGTCTTTACAGTAAA
*
594 CCCCTATATGTGATGATGTGCCGTCCATGAACCGCAAACGAAGCCATCAGACACACAACCAGAGC
1 CCCCTATATGTGATGATGTGCCGTCCATGAACCCCAAACGAAGCCATCAGACACACAACCAGAGC
659 GTGCTTTGCCCAAGAACAAGCAGGGAAAGTCTTTACAGTAAA
66 GTGCTTTGCCCAAGAACAAGCAGGGAAAGTCTTTACAGTAAA
701 GTTAGTTGAA
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 102 1.00
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.18
Consensus pattern (107 bp):
CCCCTATATGTGATGATGTGCCGTCCATGAACCCCAAACGAAGCCATCAGACACACAACCAGAGC
GTGCTTTGCCCAAGAACAAGCAGGGAAAGTCTTTACAGTAAA
Found at i:962 original size:18 final size:18
Alignment explanation
Indices: 939--973 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
929 AAAAACGTGT
939 TGTTGCGATAATGAAAAG
1 TGTTGCGATAATGAAAAG
*
957 TGTTGCGATAGTGAAAA
1 TGTTGCGATAATGAAAA
974 ATCCAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (18 bp):
TGTTGCGATAATGAAAAG
Found at i:14122 original size:29 final size:29
Alignment explanation
Indices: 14080--14139 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
14070 ATACAGTGGT
14080 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
14109 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
14138 CT
1 CT
14140 GTGTGTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.13, C:0.32, G:0.37, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:14201 original size:17 final size:16
Alignment explanation
Indices: 14179--14249 Score: 90
Period size: 17 Copynumber: 4.4 Consensus size: 16
14169 ATGCAATCAA
14179 CATGGGACGTGGGAATG
1 CATGGG-CGTGGGAATG
* * *
14196 CATGGGGGAGGGGATG
1 CATGGGCGTGGGAATG
14212 CATGGGACGTGGGAATG
1 CATGGG-CGTGGGAATG
14229 CATGGG-GTGGGAATG
1 CATGGGCGTGGGAATG
14244 CATGGG
1 CATGGG
14250 GGAGGGGATG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
15 15 0.32
16 13 0.28
17 19 0.40
ACGTcount: A:0.21, C:0.10, G:0.52, T:0.17
Consensus pattern (16 bp):
CATGGGCGTGGGAATG
Found at i:14214 original size:16 final size:16
Alignment explanation
Indices: 14189--14255 Score: 82
Period size: 16 Copynumber: 4.2 Consensus size: 16
14179 CATGGGACGT
14189 GGGAATGCATGGGGGA
1 GGGAATGCATGGGGGA
* * *
14205 GGGGATGCATGGGACGT
1 GGGAATGCATGGG-GGA
*
14222 GGGAATGCAT-GGGGT
1 GGGAATGCATGGGGGA
14237 GGGAATGCATGGGGGA
1 GGGAATGCATGGGGGA
14253 GGG
1 GGG
14256 GATGGTGCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
15 12 0.28
16 21 0.49
17 10 0.23
ACGTcount: A:0.21, C:0.07, G:0.57, T:0.15
Consensus pattern (16 bp):
GGGAATGCATGGGGGA
Found at i:14216 original size:33 final size:32
Alignment explanation
Indices: 14179--14249 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 32
14169 ATGCAATCAA
*
14179 CATGGGACGTGGGAATGCATGGGGGAGGGGATG
1 CATGGGACGTGGGAATGCAT-GGGGAGGGAATG
*
14212 CATGGGACGTGGGAATGCATGGGGTGGGAATG
1 CATGGGACGTGGGAATGCATGGGGAGGGAATG
14244 CATGGG
1 CATGGG
14250 GGAGGGGATG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 16 0.44
33 20 0.56
ACGTcount: A:0.21, C:0.10, G:0.52, T:0.17
Consensus pattern (32 bp):
CATGGGACGTGGGAATGCATGGGGAGGGAATG
Found at i:14240 original size:15 final size:15
Alignment explanation
Indices: 14187--14250 Score: 83
Period size: 15 Copynumber: 4.1 Consensus size: 15
14177 AACATGGGAC
14187 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* *
14203 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
14218 ACGTGGGAATGCATGGG
1 --GTGGGAATGCATGGG
14235 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
14250 G
1 G
14251 GAGGGGATGG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
15 19 0.45
16 10 0.24
17 13 0.31
ACGTcount: A:0.20, C:0.08, G:0.55, T:0.17
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:14840 original size:21 final size:21
Alignment explanation
Indices: 14815--14858 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
14805 AATCTAGTTA
14815 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
14836 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
14857 AT
1 AT
14859 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:14868 original size:28 final size:28
Alignment explanation
Indices: 14835--14895 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
14825 TAGTATAAAT
*
14835 TATTAGTTTGTTAGTTTAAGTTA-TATTA
1 TATTAGTTTATTAGTTTAAGTTATTA-TA
14863 TATTAGTTTATTAGTTTAAGTTATTATA
1 TATTAGTTTATTAGTTTAAGTTATTATA
14891 TATTA
1 TATTA
14896 TATAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (28 bp):
TATTAGTTTATTAGTTTAAGTTATTATA
Found at i:15436 original size:19 final size:20
Alignment explanation
Indices: 15393--15436 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
15383 AAATATTGTG
**
15393 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTA-TGTTAA
15414 TTTAAAAATATTT-TGTTAA
1 TTTAAAAATATTTATGTTAA
15433 TTTA
1 TTTA
15437 CATTGTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
21 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTAAAAATATTTATGTTAA
Found at i:15726 original size:26 final size:25
Alignment explanation
Indices: 15697--15755 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
15687 AAATCATATT
*
15697 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
15723 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
15749 ATTATTA
1 ATTATTA
15756 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:18663 original size:26 final size:26
Alignment explanation
Indices: 18637--19101 Score: 407
Period size: 26 Copynumber: 18.6 Consensus size: 26
18627 GATGATTTAG
*
18637 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
18663 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
18689 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
18715 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
18738 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
18761 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
18787 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
18813 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
18839 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
18862 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
18885 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
18911 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
18937 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
18963 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
** * * * * * *
18986 TTTTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
19009 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
19035 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
19061 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* *
19087 AAATGATTTAATAAT
1 TAATGATTTGATAAT
19102 GATTTAAATA
Statistics
Matches: 361, Mismatches: 52, Indels: 52
0.78 0.11 0.11
Matches are distributed among these distances:
21 12 0.03
22 9 0.02
23 34 0.09
24 21 0.06
25 22 0.06
26 259 0.72
27 4 0.01
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:18799 original size:124 final size:124
Alignment explanation
Indices: 18579--19158 Score: 1126
Period size: 124 Copynumber: 4.7 Consensus size: 124
18569 ATGTATTTAT
18579 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
18644 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
18703 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
18768 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
18827 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
18892 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
*
18951 TAATCATTATAAAAATGATTTAATAATGATTTAAATTTTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
19016 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
19075 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* *
19140 TTTATAATAATTATT-TAGT
66 TTGATAATAATCATTATAGT
19159 TATTATTTAG
Statistics
Matches: 452, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
123 4 0.01
124 448 0.99
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:18817 original size:150 final size:145
Alignment explanation
Indices: 18634--19101 Score: 436
Period size: 150 Copynumber: 3.3 Consensus size: 145
18624 TTTGATGATT
* *
18634 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-ATAATAATCATTATAAAAATGA-TT-
* * *
18699 GTAATAATCATTATAAAAATGATTTAAT-A-ATGATTTA-AAT-ATTTAATGATTTGATGATT-T
63 -TAATAATCATT-T--AAAT-ATTTAATGATATGATTTAGAATGATTTAAT-A-ATAATCATTAT
18759 AGTAATGATTTGATAATAATCATTA
121 AGTAATGATTTGATAATAATCATTA
18784 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTA-TAATAATCATTATAAAAATGATTTA
* *
18849 ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAA
65 ATAATCATTTAAATATTTAATGA--T-ATGATTTAG-AATGATTTAATAATAATCATTATAGTAA
18914 TGATTTGATAATAATCATTA
126 TGATTTGATAATAATCATTA
* * *
18934 TAATAATGATTT-AGTAATAATCATTATAAAAATGA-TT-TAATAATGATT-T--AAAT--TTT-
1 TAGTAATGATTTGA-TAATAATCATTATAATAATGATTTATAATAATCATTATAAAAATGATTTA
* *
18990 -T-A--A--T---GA-TT--TG--ATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGA
65 ATAATCATTTAAATATTTAATGATATGATTTAG-AATGATTTAATAATAATCATTATAGTAATGA
19041 TTTGATAATAATCATTA
129 TTTGATAATAATCATTA
* *
19058 TAATAATGATTT-AGTAATAATCATTATAAAAATGATTTAATAAT
1 TAGTAATGATTTGA-TAATAATCATTATAATAATGATTT-ATAAT
19102 GATTTAAATA
Statistics
Matches: 293, Mismatches: 11, Indels: 51
0.83 0.03 0.14
Matches are distributed among these distances:
124 93 0.32
125 2 0.01
127 4 0.01
129 2 0.01
131 2 0.01
132 1 0.00
135 1 0.00
137 1 0.00
139 1 0.00
140 1 0.00
142 3 0.01
143 7 0.02
144 9 0.03
146 2 0.01
147 20 0.07
148 8 0.03
149 12 0.04
150 118 0.40
151 6 0.02
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (145 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTATAATAATCATTATAAAAATGATTTAA
TAATCATTTAAATATTTAATGATATGATTTAGAATGATTTAATAATAATCATTATAGTAATGATT
TGATAATAATCATTA
Found at i:19012 original size:19 final size:19
Alignment explanation
Indices: 18965--19020 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
18955 CATTATAAAA
18965 ATGATTTAATAATGATTT-
1 ATGATTTAATAATGATTTG
* *
18983 A-AATTT-TTAATGATTTG
1 ATGATTTAATAATGATTTG
*
19000 ATGATTTAGTAATGATTTG
1 ATGATTTAATAATGATTTG
19019 AT
1 AT
19021 AATAATCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 9 0.29
17 5 0.16
18 5 0.16
19 12 0.39
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (19 bp):
ATGATTTAATAATGATTTG
Found at i:19338 original size:25 final size:24
Alignment explanation
Indices: 19304--19386 Score: 89
Period size: 24 Copynumber: 3.3 Consensus size: 24
19294 GATTTATTGT
19304 TAATATTTAATTATTTGATACTAG
1 TAATATTTAATTATTTGATACTAG
* *
19328 TAATGATTTAAAATAGTTGATTTACTA-
1 TAAT-ATTT-AATTATTTGA--TACTAG
19355 -AATATTTAATTATTTGATACTAG
1 TAATATTTAATTATTTGATACTAG
19378 TAATGATTT
1 TAAT-ATTT
19387 GATACTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
22 5 0.10
24 15 0.31
25 12 0.25
26 11 0.23
28 5 0.10
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.48
Consensus pattern (24 bp):
TAATATTTAATTATTTGATACTAG
Found at i:19386 original size:17 final size:17
Alignment explanation
Indices: 19361--19393 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19351 ACTAAATATT
*
19361 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
19378 TAATGATTTGATACTA
1 TAATGATTTGATACTA
19394 AAAATCATTG
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:21565 original size:15 final size:14
Alignment explanation
Indices: 21542--21572 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
21532 TACAACACTA
21542 AACTTTAATATAAT
1 AACTTTAATATAAT
21556 AACTTATAATATAAT
1 AACTT-TAATATAAT
21571 AA
1 AA
21573 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:21580 original size:16 final size:16
Alignment explanation
Indices: 21547--21593 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
21537 CACTAAACTT
*
21547 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
21562 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
21578 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
21594 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:21825 original size:45 final size:45
Alignment explanation
Indices: 21748--21880 Score: 136
Period size: 45 Copynumber: 3.0 Consensus size: 45
21738 TCAACAAACA
*
21748 AATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 AATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAAATAATTTTTT
* *
21796 TATATAACTAACTATTAACAAAACAAACTAATT-AATTATTTTTT
1 AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
21840 AACTAT-A-TAACTA-T--C-AAACATATACTAATTAAATAATTTTT
1 AA-TATAACTAACTATTAACAAAACA-A-ACTAATTAAATAATTTTT
21881 AATTTATGTA
Statistics
Matches: 76, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
39 5 0.07
40 2 0.03
41 7 0.09
42 10 0.13
43 6 0.08
44 12 0.16
45 16 0.21
46 5 0.07
47 6 0.08
48 7 0.09
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (45 bp):
AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
Found at i:21908 original size:41 final size:40
Alignment explanation
Indices: 21820--21908 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
21810 TTAACAAAAC
* *
21820 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
21861 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
21902 AAACTAA
1 AAACTAA
21909 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:22073 original size:21 final size:21
Alignment explanation
Indices: 22043--22095 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
22033 CCCTTTCTTC
*
22043 TTCTTACTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
22064 TTCTTTCTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCCCT
22085 TTCTTTCTTTC
1 TTCTTTCTTTC
22096 TCGGCTGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (21 bp):
TTCTTTCTTTCCTTTCTCCCT
Found at i:22086 original size:17 final size:16
Alignment explanation
Indices: 22066--22097 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
22056 TTCTCCCTTT
22066 CTTTCTTTCCTTTCTCC
1 CTTTCTTT-CTTTCTCC
22083 CTTTCTTTCTTTCTC
1 CTTTCTTTCTTTCTC
22098 GGCTGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTCTTTCTTTCTCC
Found at i:22130 original size:23 final size:23
Alignment explanation
Indices: 22100--22145 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
22090 TCTTTCTCGG
22100 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
22123 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
22146 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.39, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTCTTCTCCCTTTCTT
Found at i:22186 original size:25 final size:25
Alignment explanation
Indices: 22158--22209 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
22148 TTTCTTTTAT
22158 AACCGGCTGCCTCAATTATTTCACC
1 AACCGGCTGCCTCAATTATTTCACC
22183 AACCGGCTGCCTCAATTATTTCACC
1 AACCGGCTGCCTCAATTATTTCACC
22208 AA
1 AA
22210 TAATTGTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.35, G:0.12, T:0.27
Consensus pattern (25 bp):
AACCGGCTGCCTCAATTATTTCACC
Found at i:22399 original size:13 final size:13
Alignment explanation
Indices: 22381--22412 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
22371 GGCTGCATGT
22381 GAATGGATGATGG
1 GAATGGATGATGG
22394 GAATGGATGATGG
1 GAATGGATGATGG
22407 GAATGG
1 GAATGG
22413 CGCCGGGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.47, T:0.22
Consensus pattern (13 bp):
GAATGGATGATGG
Found at i:22544 original size:58 final size:58
Alignment explanation
Indices: 22413--22550 Score: 215
Period size: 58 Copynumber: 2.4 Consensus size: 58
22403 ATGGGAATGG
* *
22413 CGCCGGGACTACATGGCGACCTACAAGGTCGCCGGGACCACATGGCGACCTACAAGGT
1 CGCCAGGACCACATGGCGACCTACAAGGTCGCCGGGACCACATGGCGACCTACAAGGT
*
22471 CGCCGGGACCACATGGCGACCTACAAGGTCGCCGGGACCACATGGCGACCTACAAGGT
1 CGCCAGGACCACATGGCGACCTACAAGGTCGCCGGGACCACATGGCGACCTACAAGGT
**
22529 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-AGGACCACATGGCGACCT
22551 CTCTATTCCA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
58 73 0.97
59 2 0.03
ACGTcount: A:0.22, C:0.34, G:0.31, T:0.12
Consensus pattern (58 bp):
CGCCAGGACCACATGGCGACCTACAAGGTCGCCGGGACCACATGGCGACCTACAAGGT
Found at i:22550 original size:29 final size:29
Alignment explanation
Indices: 22413--22532 Score: 231
Period size: 29 Copynumber: 4.1 Consensus size: 29
22403 ATGGGAATGG
*
22413 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACCACATGGCGACCTACAAGGT
22442 CGCCGGGACCACATGGCGACCTACAAGGT
1 CGCCGGGACCACATGGCGACCTACAAGGT
22471 CGCCGGGACCACATGGCGACCTACAAGGT
1 CGCCGGGACCACATGGCGACCTACAAGGT
22500 CGCCGGGACCACATGGCGACCTACAAGGT
1 CGCCGGGACCACATGGCGACCTACAAGGT
22529 CGCC
1 CGCC
22533 TAGGCTGCAT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 90 1.00
ACGTcount: A:0.23, C:0.35, G:0.31, T:0.11
Consensus pattern (29 bp):
CGCCGGGACCACATGGCGACCTACAAGGT
Found at i:22598 original size:17 final size:17
Alignment explanation
Indices: 22598--22657 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 17
22588 CGCTCGTATG
22598 GCTCGCATGGGGAGAAC
1 GCTCGCATGGGGAGAAC
* *****
22615 GCTCGTATGGCTCCTAC
1 GCTCGCATGGGGAGAAC
22632 -CTCGCATGGGGAGAAC
1 GCTCGCATGGGGAGAAC
*
22648 GCTCGTATGG
1 GCTCGCATGG
22658 CTCGCATGGG
Statistics
Matches: 29, Mismatches: 13, Indels: 2
0.66 0.30 0.05
Matches are distributed among these distances:
16 10 0.34
17 19 0.66
ACGTcount: A:0.18, C:0.27, G:0.35, T:0.20
Consensus pattern (17 bp):
GCTCGCATGGGGAGAAC
Found at i:22609 original size:26 final size:26
Alignment explanation
Indices: 22573--22686 Score: 165
Period size: 26 Copynumber: 4.1 Consensus size: 26
22563 GCATGCACAC
22573 CTCGCATGGGGAGAACGCTCGTATGG
1 CTCGCATGGGGAGAACGCTCGTATGG
22599 CTCGCATGGGGAGAACGCTCGTATGG
1 CTCGCATGGGGAGAACGCTCGTATGG
22625 CTCCTACCTCGCATGGGGAGAACGCTCGTATGG
1 -------CTCGCATGGGGAGAACGCTCGTATGG
22658 CTCGCATGGGGAGAACGCTCGTATGG
1 CTCGCATGGGGAGAACGCTCGTATGG
22684 CTC
1 CTC
22687 CTATGCATGG
Statistics
Matches: 81, Mismatches: 0, Indels: 14
0.85 0.00 0.15
Matches are distributed among these distances:
26 55 0.68
33 26 0.32
ACGTcount: A:0.18, C:0.26, G:0.35, T:0.20
Consensus pattern (26 bp):
CTCGCATGGGGAGAACGCTCGTATGG
Found at i:22641 original size:33 final size:32
Alignment explanation
Indices: 22573--22738 Score: 157
Period size: 26 Copynumber: 5.5 Consensus size: 32
22563 GCATGCACAC
22573 CTCGCATGGGGAGAACGCTCGTATGG------
1 CTCGCATGGGGAGAACGCTCGTATGGCTCCTA
22599 CTCGCATGGGGAGAACGCTCGTATGGCTCCTA
1 CTCGCATGGGGAGAACGCTCGTATGGCTCCTA
22631 CCTCGCATGGGGAGAACGCTCGTATGG------
1 -CTCGCATGGGGAGAACGCTCGTATGGCTCCTA
22658 CTCGCATGGGGAGAACGCTCGTATGGCTCCTA
1 CTCGCATGGGGAGAACGCTCGTATGGCTCCTA
*
22690 -T-GCATGGGGAGAACCATTGGCTCGTATGGCTCGTA
1 CTCGCATGGGGAGAA-C----GCTCGTATGGCTCCTA
22725 -T-GCATGGGGAGAAC
1 CTCGCATGGGGAGAAC
22739 CATTGGCTCG
Statistics
Matches: 121, Mismatches: 1, Indels: 28
0.81 0.01 0.19
Matches are distributed among these distances:
26 52 0.43
30 12 0.10
31 2 0.02
33 26 0.21
34 1 0.01
35 28 0.23
ACGTcount: A:0.20, C:0.24, G:0.35, T:0.21
Consensus pattern (32 bp):
CTCGCATGGGGAGAACGCTCGTATGGCTCCTA
Found at i:22642 original size:59 final size:59
Alignment explanation
Indices: 22571--22703 Score: 245
Period size: 59 Copynumber: 2.3 Consensus size: 59
22561 CTGCATGCAC
22571 ACCTCGCATGGGGAGAACGCTCGTATGGCTCGCATGGGGAGAACGCTCGTATGGCTCCT
1 ACCTCGCATGGGGAGAACGCTCGTATGGCTCGCATGGGGAGAACGCTCGTATGGCTCCT
22630 ACCTCGCATGGGGAGAACGCTCGTATGGCTCGCATGGGGAGAACGCTCGTATGGCTCCT
1 ACCTCGCATGGGGAGAACGCTCGTATGGCTCGCATGGGGAGAACGCTCGTATGGCTCCT
22689 A--T-GCATGGGGAGAAC
1 ACCTCGCATGGGGAGAAC
22704 CATTGGCTCG
Statistics
Matches: 74, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
56 13 0.18
57 1 0.01
59 60 0.81
ACGTcount: A:0.20, C:0.26, G:0.35, T:0.20
Consensus pattern (59 bp):
ACCTCGCATGGGGAGAACGCTCGTATGGCTCGCATGGGGAGAACGCTCGTATGGCTCCT
Found at i:22720 original size:35 final size:35
Alignment explanation
Indices: 22674--22761 Score: 167
Period size: 35 Copynumber: 2.5 Consensus size: 35
22664 TGGGGAGAAC
*
22674 GCTCGTATGGCTCCTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
22709 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
22744 GCTCGTATGGCTCGTATG
1 GCTCGTATGGCTCGTATG
22762 TCACCCCGTA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.18, C:0.22, G:0.33, T:0.27
Consensus pattern (35 bp):
GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
Found at i:22773 original size:12 final size:12
Alignment explanation
Indices: 22756--22797 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
22746 TCGTATGGCT
22756 CGTATGTCACCC
1 CGTATGTCACCC
*
22768 CGTATGTCAACC
1 CGTATGTCACCC
22780 CGTATGTCACCC
1 CGTATGTCACCC
22792 CGTATG
1 CGTATG
22798 GCCACCTCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.26
Consensus pattern (12 bp):
CGTATGTCACCC
Found at i:22840 original size:30 final size:32
Alignment explanation
Indices: 22806--22871 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 32
22796 TGGCCACCTC
22806 GCATGGGGAGAA-C-GCTCGTATGGCTCGTAT
1 GCATGGGGAGAACCTGCTCGTATGGCTCGTAT
22836 GCATGGGGAGAACCATTGGCTCGTATGGCTCGTAT
1 GCATGGGGAGAACC--T-GCTCGTATGGCTCGTAT
22871 G
1 G
22872 TCAACCCGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
30 12 0.39
31 1 0.03
35 18 0.58
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.24
Consensus pattern (32 bp):
GCATGGGGAGAACCTGCTCGTATGGCTCGTAT
Found at i:22926 original size:29 final size:29
Alignment explanation
Indices: 22884--22965 Score: 164
Period size: 29 Copynumber: 2.8 Consensus size: 29
22874 AACCCGTATG
22884 TCGCCTGGATTGCATGGCGTCCTACAAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
22913 TCGCCTGGATTGCATGGCGTCCTACAAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
22942 TCGCCTGGATTGCATGGCGTCCTA
1 TCGCCTGGATTGCATGGCGTCCTA
22966 TGATCACTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (29 bp):
TCGCCTGGATTGCATGGCGTCCTACAAGA
Found at i:26857 original size:23 final size:23
Alignment explanation
Indices: 26804--26868 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
26794 CTAAATGACC
* * *
26804 GAAAAACATGCCACAAAGACAGA
1 GAAAAACGTGTCAAAAAGACAGA
*
26827 GAAAAACGTGTCATAAAGACAGA
1 GAAAAACGTGTCAAAAAGACAGA
* *
26850 GATAAACGTTTCAAAAAGA
1 GAAAAACGTGTCAAAAAGA
26869 TATAATTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.54, C:0.15, G:0.18, T:0.12
Consensus pattern (23 bp):
GAAAAACGTGTCAAAAAGACAGA
Found at i:28492 original size:2 final size:2
Alignment explanation
Indices: 28487--28551 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
28477 ACACACACAC
28487 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
28529 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
28552 GCTGGCTTGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44677 original size:11 final size:11
Alignment explanation
Indices: 44663--44692 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
44653 AAAGTATACA
44663 GAAGCAGAAGT
1 GAAGCAGAAGT
44674 GAAGCAGAAGT
1 GAAGCAGAAGT
44685 GAAGCAGA
1 GAAGCAGA
44693 GAGAGTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.10, G:0.37, T:0.07
Consensus pattern (11 bp):
GAAGCAGAAGT
Found at i:53006 original size:2 final size:2
Alignment explanation
Indices: 52995--53034 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
52985 TACATGACAA
52995 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
53035 ATTTTGTCGG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:62548 original size:43 final size:43
Alignment explanation
Indices: 62500--62590 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
62490 ATTTATCGCT
62500 ATTTGTAAAGAAGAGTTAAAGAGTCTAAACTTTGAATGGTTTA
1 ATTTGTAAAGAAGAGTTAAAGAGTCTAAACTTTGAATGGTTTA
*
62543 ATTTGTAAAGAAGAGTTTAAGAGTCTAAACTTTGAATGGTTTA
1 ATTTGTAAAGAAGAGTTAAAGAGTCTAAACTTTGAATGGTTTA
62586 ATTTG
1 ATTTG
62591 ACAGCCTTCG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.37
Consensus pattern (43 bp):
ATTTGTAAAGAAGAGTTAAAGAGTCTAAACTTTGAATGGTTTA
Found at i:64606 original size:4 final size:4
Alignment explanation
Indices: 64599--64893 Score: 590
Period size: 4 Copynumber: 73.8 Consensus size: 4
64589 ACACACACAC
64599 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
64647 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
64695 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
64743 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
64791 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
64839 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
64887 ACAT ACA
1 ACAT ACA
64894 CATATATATA
Statistics
Matches: 291, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 291 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:64902 original size:2 final size:2
Alignment explanation
Indices: 64895--64928 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
64885 ATACATACAC
64895 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
64929 TCGAGTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69298 original size:54 final size:52
Alignment explanation
Indices: 69215--69315 Score: 139
Period size: 54 Copynumber: 1.9 Consensus size: 52
69205 AGATGGTAGC
*
69215 AAGTTCTGGAATATCATATCGTAAACACAAAGAATCAAGTAAAACAAGCAACAT
1 AAGTTCTGGAATATCATATCGTAAACACAAACAATCAAG-AAAA-AAGCAACAT
** * *
69269 AAGTTCTGGAATATCATATTTTGATCACAAACAATCAAGAAAAAAGC
1 AAGTTCTGGAATATCATATCGTAAACACAAACAATCAAGAAAAAAGC
69316 GACAAACATA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 4 0.10
53 4 0.10
54 34 0.81
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.23
Consensus pattern (52 bp):
AAGTTCTGGAATATCATATCGTAAACACAAACAATCAAGAAAAAAGCAACAT
Found at i:78360 original size:31 final size:31
Alignment explanation
Indices: 78303--78366 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
78293 TAGTATATGC
**
78303 TATGTATCAAAATTGATGACTTGATATATAT
1 TATGTATCAAAATTGATGACACGATATATAT
*
78334 TATGTATCCAAAA-TGATGGCACGATATATAT
1 TATGTAT-CAAAATTGATGACACGATATATAT
78365 TA
1 TA
78367 CATCCATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 24 0.83
32 5 0.17
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (31 bp):
TATGTATCAAAATTGATGACACGATATATAT
Found at i:78408 original size:26 final size:25
Alignment explanation
Indices: 78379--78437 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
78369 TCCATAAAAA
78379 TATTATATTTTTTATGAAATTAATAT
1 TATTATA-TTTTTATGAAATTAATAT
*
78405 TATTAGTATTTTTATGATATTAATAT
1 TATTA-TATTTTTATGAAATTAATAT
78431 TATTATA
1 TATTATA
78438 ATATTATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 2 0.06
26 27 0.87
27 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (25 bp):
TATTATATTTTTATGAAATTAATAT
Found at i:78431 original size:17 final size:17
Alignment explanation
Indices: 78405--78443 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
78395 AAATTAATAT
* * *
78405 TATTAGTATTTTTATGA
1 TATTAATATTATTATAA
78422 TATTAATATTATTATAA
1 TATTAATATTATTATAA
78439 TATTA
1 TATTA
78444 TTAATAAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
TATTAATATTATTATAA
Found at i:96553 original size:29 final size:30
Alignment explanation
Indices: 96518--96574 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
96508 AGGGTAAACT
*
96518 ATAAATATA-TATTATTTA-TAAGAATTAAA
1 ATAAATATATTATAATTTATTAA-AATTAAA
96547 ATAAATATATTATAATTTATTAAAATTA
1 ATAAATATATTATAATTTATTAAAATTA
96575 TGATCAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 9 0.36
30 13 0.52
31 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (30 bp):
ATAAATATATTATAATTTATTAAAATTAAA
Found at i:101670 original size:31 final size:32
Alignment explanation
Indices: 101598--101671 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 32
101588 TGAAATATTA
*
101598 ATAAATTTAA-CGACCTTTTTATAACAGTCTG
1 ATAAATTTAATCGACCATTTTATAACAGTCTG
* *
101629 GTAAAATTTAATC-ACCATTTTATATCAG-CTCG
1 AT-AAATTTAATCGACCATTTTATAACAGTCT-G
101661 ATAAATTTAAT
1 ATAAATTTAAT
101672 AATCGTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
31 12 0.33
32 23 0.64
33 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (32 bp):
ATAAATTTAATCGACCATTTTATAACAGTCTG
Found at i:115769 original size:18 final size:19
Alignment explanation
Indices: 115727--115771 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
115717 TTTGGTTCAC
*
115727 GGAATATAAGATTATCAGTG
1 GGAATATAAGATTACCAG-G
*
115747 GGAATGTAAGATTACCA-G
1 GGAATATAAGATTACCAGG
115765 GGAATAT
1 GGAATAT
115772 GATTACTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.27
Consensus pattern (19 bp):
GGAATATAAGATTACCAGG
Found at i:117239 original size:66 final size:66
Alignment explanation
Indices: 117151--117355 Score: 347
Period size: 66 Copynumber: 3.1 Consensus size: 66
117141 ACCTTTGCCG
* * * * *
117151 CCGACGCTCACATGAGTGCCACCTCCTCGCTTTCCTTTCCCGGTGTTCACTCCAATTCCGCCCTT
1 CCGACGTTCACATGGGTGCCACCCCCTGGCTTTCCTTTCCCGGTGTTCACTCCAACTCCGCCCTT
117216 T
66 T
*
117217 CCAACGTTCACATGGGTGCCACCCCCTGGCTTTCCTTTCCCGGTGTTCACTCCAACTCCGCCCTT
1 CCGACGTTCACATGGGTGCCACCCCCTGGCTTTCCTTTCCCGGTGTTCACTCCAACTCCGCCCTT
117282 T
66 T
*
117283 CCGACGTTTACATGGGTGCCACCCCCTGGCTTTCCTTTCCCGGTGTTCACTCCAACTCCGCCCTT
1 CCGACGTTCACATGGGTGCCACCCCCTGGCTTTCCTTTCCCGGTGTTCACTCCAACTCCGCCCTT
117348 T
66 T
117349 CCGACGT
1 CCGACGT
117356 CCACGGAAGT
Statistics
Matches: 131, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 131 1.00
ACGTcount: A:0.12, C:0.42, G:0.17, T:0.29
Consensus pattern (66 bp):
CCGACGTTCACATGGGTGCCACCCCCTGGCTTTCCTTTCCCGGTGTTCACTCCAACTCCGCCCTT
T
Found at i:121144 original size:23 final size:24
Alignment explanation
Indices: 121092--121145 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
121082 CGTTAAACGA
* *
121092 ACATGTTCGTGAACATATAAATGG
1 ACATGTTCATGAACATATAAAAGG
121116 ACATGTTCATGAACAT-TAAAAGG
1 ACATGTTCATGAACATATAAAAGG
*
121139 ATATGTT
1 ACATGTT
121146 AACAAATAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (24 bp):
ACATGTTCATGAACATATAAAAGG
Found at i:125236 original size:21 final size:21
Alignment explanation
Indices: 125222--125268 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
125212 ACTTGACTTC
125222 CATAACAACAAACTTGAAATT
1 CATAACAACAAACTTGAAATT
* *
125243 CATAACAACAAACTTAAAATC
1 CATAACAACAAACTTGAAATT
125264 CATAA
1 CATAA
125269 TAATAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.55, C:0.21, G:0.02, T:0.21
Consensus pattern (21 bp):
CATAACAACAAACTTGAAATT
Done.