Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002840.1 Hibiscus syriacus cultivar Beakdansim tig00005846_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: 246210
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:144412 original size:2 final size:2
Alignment explanation
Indices: 144405--144443 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
144395 TTTTGAAAAT
144405 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
144444 TAAAAATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:145307 original size:60 final size:61
Alignment explanation
Indices: 145205--145369 Score: 151
Period size: 60 Copynumber: 2.8 Consensus size: 61
145195 TGCATTATAT
* * *** *
145205 ATCCCC-AAACTATGAGA-CTCATTCTAAATTAATTTTTAAACTTTTAAACA-TTCTAATTTT
1 ATCCCCAAAACTATGA-ATATCATTCTAAATTAGTCCCTAAACTTTTAAACATTTC-AATTTC
* * * * * * *
145265 AT-CTCAAAACTATGACTATTATTTTAAATTAGTCCTTGAAC-TTTGAACATTTCAATTTC
1 ATCCCCAAAACTATGAATATCATTCTAAATTAGTCCCTAAACTTTTAAACATTTCAATTTC
*
145324 ATCCCCCAAACTATGAATATCATTCTAAATTAGTCCCTAAACTTTT
1 ATCCCCAAAACTATGAATATCATTCTAAATTAGTCCCTAAACTTTT
145370 GCATCTTTAG
Statistics
Matches: 82, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
59 16 0.20
60 63 0.77
61 3 0.04
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (61 bp):
ATCCCCAAAACTATGAATATCATTCTAAATTAGTCCCTAAACTTTTAAACATTTCAATTTC
Found at i:152218 original size:17 final size:16
Alignment explanation
Indices: 152191--152222 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
152181 GAAGCCATTG
152191 ATCAACAACAAGAAAC
1 ATCAACAACAAGAAAC
152207 ATCAAGCAACAAGAAA
1 ATCAA-CAACAAGAAA
152223 TCATAGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.62, C:0.22, G:0.09, T:0.06
Consensus pattern (16 bp):
ATCAACAACAAGAAAC
Found at i:152237 original size:18 final size:17
Alignment explanation
Indices: 152197--152238 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
152187 ATTGATCAAC
*
152197 AACAAGAAACATCAAGC
1 AACAAGAAACATCAAGA
152214 AACAAGAAATCAT-AGAGA
1 AACAAGAAA-CATCA-AGA
152232 AACAAGA
1 AACAAGA
152239 GAGAAAGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.62, C:0.17, G:0.14, T:0.07
Consensus pattern (17 bp):
AACAAGAAACATCAAGA
Found at i:154088 original size:20 final size:21
Alignment explanation
Indices: 154055--154094 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
154045 TTTTAACGTA
**
154055 ATTGATATTCATTTT-AAACC
1 ATTGATATAAATTTTCAAACC
154075 ATTGATATAAATTTTCAAAC
1 ATTGATATAAATTTTCAAAC
154095 AATTTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTGATATAAATTTTCAAACC
Found at i:157484 original size:21 final size:21
Alignment explanation
Indices: 157458--157497 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
157448 CCCCCTTTGA
*
157458 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
157479 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
157498 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:159233 original size:15 final size:16
Alignment explanation
Indices: 159194--159235 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
159184 GTTTCAACAT
* *
159194 TTTTTGAATTGTTTGA
1 TTTTTGGATTGTTGGA
159210 TTTTGTGGATTGTTGGA
1 TTTT-TGGATTGTTGGA
159227 -TTTTGGATT
1 TTTTTGGATT
159236 TATGAATGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 7 0.30
17 10 0.43
ACGTcount: A:0.14, C:0.00, G:0.26, T:0.60
Consensus pattern (16 bp):
TTTTTGGATTGTTGGA
Found at i:160189 original size:17 final size:16
Alignment explanation
Indices: 160162--160193 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
160152 GAAGCCATTG
160162 ATCAACAACAAGAAAC
1 ATCAACAACAAGAAAC
160178 ATCAAGCAACAAGAAA
1 ATCAA-CAACAAGAAA
160194 TCATAGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.62, C:0.22, G:0.09, T:0.06
Consensus pattern (16 bp):
ATCAACAACAAGAAAC
Found at i:160208 original size:18 final size:17
Alignment explanation
Indices: 160168--160209 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
160158 ATTGATCAAC
*
160168 AACAAGAAACATCAAGC
1 AACAAGAAACATCAAGA
160185 AACAAGAAATCAT-AGAGA
1 AACAAGAAA-CATCA-AGA
160203 AACAAGA
1 AACAAGA
160210 GAGAAAGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.62, C:0.17, G:0.14, T:0.07
Consensus pattern (17 bp):
AACAAGAAACATCAAGA
Found at i:166057 original size:2 final size:2
Alignment explanation
Indices: 166050--166076 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
166040 TCGAGTTATT
166050 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
166077 TAATTTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:174808 original size:13 final size:13
Alignment explanation
Indices: 174790--174839 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
174780 ATGGGGCCTG
174790 AAAAAATAAAAAT
1 AAAAAATAAAAAT
*
174803 AAAAAATAATAAT
1 AAAAAATAAAAAT
*
174816 AATAAATAATAATAT
1 AAAAAATAA-AA-AT
174831 AATAAAATA
1 AA-AAAATA
174840 TTTTTATAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 20 0.67
14 1 0.03
15 4 0.13
16 5 0.17
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:174819 original size:16 final size:16
Alignment explanation
Indices: 174790--174837 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
174780 ATGGGGCCTG
*
174790 AAAA-AATAAAAATAA
1 AAAATAATAATAATAA
174805 AAAATAATAATAATAA
1 AAAATAATAATAATAA
*
174821 ATAATAAT-ATAATAA
1 AAAATAATAATAATAA
174836 AA
1 AA
174838 TATTTTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATAATAATAATAA
Found at i:174823 original size:10 final size:11
Alignment explanation
Indices: 174808--174840 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
174798 AAAATAAAAA
174808 ATAATAATAAT
1 ATAATAATAAT
174819 A-AATAATAAT
1 ATAATAATAAT
174829 ATAATAA-AAT
1 ATAATAATAAT
174839 AT
1 AT
174841 TTTTATAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 15 0.71
11 6 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:175057 original size:32 final size:32
Alignment explanation
Indices: 175021--175094 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
175011 ATCCTTTGTC
*
175021 GTGAAGTTGAAATCGTGGATGACTCATTCGTT
1 GTGAAGTTGAAATCGTGGATGACCCATTCGTT
*
175053 GTGAAGTTGAAATCGTGGATGACCCCTTCGTT
1 GTGAAGTTGAAATCGTGGATGACCCATTCGTT
*
175085 GTAAAGTTGA
1 GTGAAGTTGA
175095 GCCTTGAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (32 bp):
GTGAAGTTGAAATCGTGGATGACCCATTCGTT
Found at i:182684 original size:18 final size:17
Alignment explanation
Indices: 182657--182700 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
182647 ATTATCTATG
*
182657 TCCCGTAGGACCACTACA
1 TCCCGAAGGA-CACTACA
182675 TCCCGAAGG--ACTACA
1 TCCCGAAGGACACTACA
182690 TCCCGAAGGAC
1 TCCCGAAGGAC
182701 TATTATACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 15 0.65
18 8 0.35
ACGTcount: A:0.30, C:0.36, G:0.20, T:0.14
Consensus pattern (17 bp):
TCCCGAAGGACACTACA
Found at i:182689 original size:15 final size:15
Alignment explanation
Indices: 182669--182702 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
182659 CCGTAGGACC
182669 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
182684 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
182699 ACTA
1 ACTA
182703 TTATACCCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:182851 original size:23 final size:26
Alignment explanation
Indices: 182814--182882 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
182804 TTTTCTTGTG
182814 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
182838 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
182863 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
182883 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:182864 original size:12 final size:12
Alignment explanation
Indices: 182847--182882 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
182837 TATCATGTTC
182847 TCATATCACATG
1 TCATATCACATG
*
182859 TCATATCACATA
1 TCATATCACATG
182871 TCATATCACATG
1 TCATATCACATG
182883 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:184377 original size:120 final size:120
Alignment explanation
Indices: 184164--184596 Score: 605
Period size: 120 Copynumber: 3.6 Consensus size: 120
184154 TTGTGGGCAC
* * * * *
184164 GATATCCTCCATCGTGGAGTTAAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGAATT
* * *
184229 GGATATCCTTCATCGTGAAGTTGAAATCCAAGTATTGTATGTTGCTGGTGAACAT
66 GGATATCATTCATCGTGAAGTTAAAATCCAAGTATTATATGTTGCTGGTGAACAT
* *
184284 GATATCCTTCGTCGTGAAGTTGTAATCGTGGATGGCCTCTTCGTCGTGAAGTTGAGCCTTGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGAATT
* ** * * ** **
184349 GGATATCATTCGTCGTGAAGTTAAAATCCAAGGGTTACATTGCTGCTTTTGGGCAT
66 GGATATCATTCATCGTGAAGTTAAAATCCAAGTATTATA-TGTTGCTGGTGAACAT
* * *
184405 GATATCCTTCGTCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTTGTGATGTTGAGCCTTGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGAATT
* *
184470 GGATATCTTTCATCGTGAAGTTAAAATCCAAGTATTATATGTTGCTGGTGAACAC
66 GGATATCATTCATCGTGAAGTTAAAATCCAAGTATTATATGTTGCTGGTGAACAT
* * *
184525 GATATCCTTCGTCGTGAAGTTGAAATCGTTGATGGCCCCTTCATCATGAAGTTGAGCCTTGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGAATT
184590 GGGATAT
66 -GGATAT
184597 TGTTGAGTTA
Statistics
Matches: 270, Mismatches: 41, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
120 159 0.59
121 111 0.41
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (120 bp):
GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGAATT
GGATATCATTCATCGTGAAGTTAAAATCCAAGTATTATATGTTGCTGGTGAACAT
Found at i:184587 original size:241 final size:242
Alignment explanation
Indices: 184146--184596 Score: 751
Period size: 241 Copynumber: 1.9 Consensus size: 242
184136 TTACATTTGT
184146 ATTGCTACTTGTGGGCACGATATCCTCCATCGTGGAGTTAAAATCGTGGATGGCCCCTTCGTTGT
1 ATTGCTACTTGTGGGCACGATATCCTCCATCGTGGAGTTAAAATCGTGGATGGCCCCTTCGTTGT
* *
184211 GAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAGTATTGTATGTTGCTG
66 GAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTAAAATCCAAGTATTATATGTTGCTG
* * * * *
184276 GTGAACATGATATCCTTCGTCGTGAAGTTGTAATCGTGGATGGCCTCTTCGTCGTGAAGTTGAGC
131 GTGAACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCATCATGAAGTTGAGC
184341 CTTGAATT-GGATATCATTCGTCGTGAAGTTAAAATCCAAGGGTTAC
196 CTTGAATTGGGATATCATTCGTCGTGAAGTTAAAATCCAAGGGTTAC
* * * * * *
184387 ATTGCTGCTTTTGGGCATGATATCCTTCGTCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTTGT
1 ATTGCTACTTGTGGGCACGATATCCTCCATCGTGGAGTTAAAATCGTGGATGGCCCCTTCGTTGT
* *
184452 GATGTTGAGCCTTGAATTGGATATCTTTCATCGTGAAGTTAAAATCCAAGTATTATATGTTGCTG
66 GAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTAAAATCCAAGTATTATATGTTGCTG
*
184517 GTGAACACGATATCCTTCGTCGTGAAGTTGAAATCGTTGATGGCCCCTTCATCATGAAGTTGAGC
131 GTGAACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCATCATGAAGTTGAGC
184582 CTTGAATTGGGATAT
196 CTTGAATTGGGATAT
184597 TGTTGAGTTA
Statistics
Matches: 193, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
241 187 0.97
242 6 0.03
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (242 bp):
ATTGCTACTTGTGGGCACGATATCCTCCATCGTGGAGTTAAAATCGTGGATGGCCCCTTCGTTGT
GAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTAAAATCCAAGTATTATATGTTGCTG
GTGAACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCATCATGAAGTTGAGC
CTTGAATTGGGATATCATTCGTCGTGAAGTTAAAATCCAAGGGTTAC
Found at i:185382 original size:76 final size:77
Alignment explanation
Indices: 185294--185485 Score: 275
Period size: 75 Copynumber: 2.5 Consensus size: 77
185284 CCGTTGTACA
* * *
185294 AGGGGGGAATCGGTACCCCCT-TGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
** *
185358 ACAAAACTGTTT
66 ACAAAACCATTC
*
185370 AGGGGGGAATCGGTTCCTCCTAT--GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
* *
185433 GCCAAACCATTC
66 ACAAAACCATTC
185445 A-GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCT
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCT
185486 ATGAGCAATT
Statistics
Matches: 104, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
74 21 0.20
75 46 0.44
76 36 0.35
77 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.23
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
ACAAAACCATTC
Found at i:188098 original size:21 final size:21
Alignment explanation
Indices: 188072--188111 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
188062 CAGAACCTCA
*
188072 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
188093 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
188112 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:188133 original size:22 final size:23
Alignment explanation
Indices: 188094--188154 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
188084 TTCCCCTGTG
188094 GGGGGAATCGGTTCCCCTTCA-AA
1 GGGGGAATCGGTT-CCCTTCAGAA
*
188117 GGGGGAATCGGTTCCC-TCAGGA
1 GGGGGAATCGGTTCCCTTCAGAA
*
188139 GGGGG-ATCGATTCCCT
1 GGGGGAATCGGTTCCCT
188155 CTGCACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 12 0.35
22 9 0.26
23 13 0.38
ACGTcount: A:0.18, C:0.25, G:0.36, T:0.21
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCTTCAGAA
Found at i:188147 original size:21 final size:21
Alignment explanation
Indices: 188094--188155 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
188084 TTCCCCTGTG
188094 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
188117 GGGGGAATCGGTTCCCTCAGGA
1 GGGGGAATCGGTTCCCTCA-AA
*
188139 GGGGG-ATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
188156 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.39
22 9 0.25
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.35, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:193969 original size:21 final size:22
Alignment explanation
Indices: 193908--193964 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
193898 CGTTGTACAA
*
193908 GGGGGGAATCGGTACCCCCTTG
1 GGGGGGAATCGGTACCCCTTTG
193930 GGGGGGAATCGGTACCCCTTTG
1 GGGGGGAATCGGTACCCCTTTG
193952 GGGGGGAATCGGT
1 GGGGGGAATCGGT
193965 TCCCTCCGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.14, C:0.21, G:0.46, T:0.19
Consensus pattern (22 bp):
GGGGGGAATCGGTACCCCTTTG
Found at i:194058 original size:75 final size:76
Alignment explanation
Indices: 193930--194138 Score: 278
Period size: 75 Copynumber: 2.8 Consensus size: 76
193920 TACCCCCTTG
* * *
193930 GGGGGGAATCGGTACC-CCTTTGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
1 GGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAA
** *
193994 CAAAACTGTTTA
65 CAAAACCATTCA
* *
194006 GGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGC
1 GGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAAC
*
194070 CAAACCATTCA
66 AAAACCATTCA
** *
194081 GGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTATGAGCAATCTGGAATT
1 GGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
194139 TTTGGCTTTG
Statistics
Matches: 117, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
75 68 0.58
76 15 0.13
77 34 0.29
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (76 bp):
GGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAAC
AAAACCATTCA
Found at i:194580 original size:120 final size:121
Alignment explanation
Indices: 194373--194836 Score: 601
Period size: 120 Copynumber: 3.9 Consensus size: 121
194363 ACAGATATTC
* * * * ** * *
194373 TTCGTCGTGAAGTTAAAATCCAAGGGTTGCATTGAAGCTTGTGGGCACGATGTCCTCCGTCGTGG
1 TTCGTCGTGAAGTTGAAATCCAAGGATTGCATTGATGCTGGTGAACACGATATCCTCCGTCGTGA
*
194438 AGTTGAAATCGTGGATGGCCCCTTCGTCATGAAGTTGAGGCTCGAATTGGATATCA
66 AGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGGCTCGAATTGGATATCA
* * * *
194494 TTCGTCGTGAAGTTGAAATCCAAGTATTGTA-TGTTGCTGGTGAACACGATATCCTTCGTCGTGA
1 TTCGTCGTGAAGTTGAAATCCAAGGATTGCATTGATGCTGGTGAACACGATATCCTCCGTCGTGA
* * *
194558 AGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGAATTGGATATCC
66 AGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGGCTCGAATTGGATATCA
* * * * * *
194614 TTCGTCGTAAAGTTTAAATCCAAGGGTTGCATTGATGCTTGTGGGA-ACGATGTCCTCCGTCGTG
1 TTCGTCGTGAAGTTGAAATCCAAGGATTGCATTGATGCTGGT-GAACACGATATCCTCCGTCGTG
* *
194678 GAGTTGAAATCGTGGATGACCCCTTCGTCGTGAAGTTGAGGCTCGAATTGGATATCA
65 AAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGGCTCGAATTGGATATCA
* * * * * * *
194735 TTCGTCATGAAGTTGAAATGCAAGTATTGTA-TGTTGTTGGTGAACACGATATCCTTCGTCGTGA
1 TTCGTCGTGAAGTTGAAATCCAAGGATTGCATTGATGCTGGTGAACACGATATCCTCCGTCGTGA
**
194799 AGTTGAAATTATGGATGGCCCCTTCGTCGTGAAGTTGA
66 AGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGA
194837 AATCCAAGAG
Statistics
Matches: 292, Mismatches: 48, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
119 2 0.01
120 161 0.55
121 127 0.43
122 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (121 bp):
TTCGTCGTGAAGTTGAAATCCAAGGATTGCATTGATGCTGGTGAACACGATATCCTCCGTCGTGA
AGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGGCTCGAATTGGATATCA
Found at i:194795 original size:241 final size:241
Alignment explanation
Indices: 194366--194836 Score: 834
Period size: 241 Copynumber: 2.0 Consensus size: 241
194356 TGTTTCAACA
* * *
194366 GATATTCTTCGTCGTGAAGTTAAAATCCAAGGGTTGCATTGAAGCTTGTGGGCACGATGTCCTCC
1 GATATCCTTCGTCGTAAAGTTAAAATCCAAGGGTTGCATTGAAGCTTGTGGGAACGATGTCCTCC
*
194431 GTCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTCATGAAGTTGAGGCTCGAATTGGATATCATT
66 GTCGTGGAGTTGAAATCGTGGATGACCCCTTCGTCATGAAGTTGAGGCTCGAATTGGATATCATT
*
194496 CGTCGTGAAGTTGAAATCCAAGTATTGTATGTTGCTGGTGAACACGATATCCTTCGTCGTGAAGT
131 CGTCATGAAGTTGAAATCCAAGTATTGTATGTTGCTGGTGAACACGATATCCTTCGTCGTGAAGT
*
194561 TGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGAATTG
196 TGAAATCATGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGAATTG
* *
194607 GATATCCTTCGTCGTAAAGTTTAAATCCAAGGGTTGCATTGATGCTTGTGGGAACGATGTCCTCC
1 GATATCCTTCGTCGTAAAGTTAAAATCCAAGGGTTGCATTGAAGCTTGTGGGAACGATGTCCTCC
*
194672 GTCGTGGAGTTGAAATCGTGGATGACCCCTTCGTCGTGAAGTTGAGGCTCGAATTGGATATCATT
66 GTCGTGGAGTTGAAATCGTGGATGACCCCTTCGTCATGAAGTTGAGGCTCGAATTGGATATCATT
* *
194737 CGTCATGAAGTTGAAATGCAAGTATTGTATGTTGTTGGTGAACACGATATCCTTCGTCGTGAAGT
131 CGTCATGAAGTTGAAATCCAAGTATTGTATGTTGCTGGTGAACACGATATCCTTCGTCGTGAAGT
*
194802 TGAAATTATGGATGGCCCCTTCGTCGTGAAGTTGA
196 TGAAATCATGGATGGCCCCTTCGTCGTGAAGTTGA
194837 AATCCAAGAG
Statistics
Matches: 218, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
241 218 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.32
Consensus pattern (241 bp):
GATATCCTTCGTCGTAAAGTTAAAATCCAAGGGTTGCATTGAAGCTTGTGGGAACGATGTCCTCC
GTCGTGGAGTTGAAATCGTGGATGACCCCTTCGTCATGAAGTTGAGGCTCGAATTGGATATCATT
CGTCATGAAGTTGAAATCCAAGTATTGTATGTTGCTGGTGAACACGATATCCTTCGTCGTGAAGT
TGAAATCATGGATGGCCCCTTCGTCGTGAAGTTGAGCCTTGAATTG
Found at i:194851 original size:86 final size:87
Alignment explanation
Indices: 194733--194923 Score: 219
Period size: 87 Copynumber: 2.2 Consensus size: 87
194723 AATTGGATAT
* * *
194733 CATTCGTCATGAAGTTGAAATGCAAGTATTGTA-TGTTG-TTGGTGAACACGATATCCT-TCGTC
1 CATTCGTCGTGAAGTTGAAATCCAAGTATTGTATTGCTGCTT-GTGAACACGATATCCTCT-GTC
* * *
194795 GTGAAGTTGAAATTATGGATGGCC
64 ATGAAGTTGAAATCATAGATGGCC
* ** *
194819 CCTTCGTCGTGAAGTTGAAATCCAAG-AGTTGTATTGCTGCTTGTGGGCACGATGTCCTCTGTCA
1 CATTCGTCGTGAAGTTGAAATCCAAGTA-TTGTATTGCTGCTTGTGAACACGATATCCTCTGTCA
* *
194883 TGGAGTTGAAATCGTAGATGGCC
65 TGAAGTTGAAATCATAGATGGCC
194906 CATTCGTCGTGAAGTTGA
1 CATTCGTCGTGAAGTTGA
194924 GCCTCGAATT
Statistics
Matches: 88, Mismatches: 13, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
85 1 0.01
86 28 0.32
87 56 0.64
88 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (87 bp):
CATTCGTCGTGAAGTTGAAATCCAAGTATTGTATTGCTGCTTGTGAACACGATATCCTCTGTCAT
GAAGTTGAAATCATAGATGGCC
Found at i:194862 original size:207 final size:208
Alignment explanation
Indices: 194612--195044 Score: 591
Period size: 207 Copynumber: 2.1 Consensus size: 208
194602 AATTGGATAT
* * *
194612 CCTTCGTCGTAAAGTTTAAATCCAAGGGTTGCATTGATGCTTGTGGGAACGATGTCCTCCGTCGT
1 CCTTCGTCGTAAAGTTGAAATCCAAGAGTTGCATTGATGCTTGTGGGAACGATGTCCTCCGTCAT
* * * *
194677 GGAGTTGAAATCGTGGATGACCCCTTCGTCGTGAAGTTGAGGCTCGAATTGGATATCATTCGTCA
66 GGAGTTGAAATCGTAGATGACCCATTCGTCGTGAAGTTGAGCCTCGAATTAGATATCATTCGTCA
* * * * * *
194742 TGAAGTTGAAATGCAAGTATTGTA-TGTTGT-TGGTGAACACGATATCCTTCGTCGTGAAGTTGA
131 TGAAGTTGAAATCCAAGGATTGCATTGTT-TCTGATGAACACGATATCCTCCATCGTGAAGTTGA
*
194805 AATTATGGATGGCC
195 AATTATGGATAGCC
* * * * *
194819 CCTTCGTCGTGAAGTTGAAATCCAAGAGTTGTATTGCTGCTTGTGGGCACGATGTCCTCTGTCAT
1 CCTTCGTCGTAAAGTTGAAATCCAAGAGTTGCATTGATGCTTGTGGGAACGATGTCCTCCGTCAT
* * *
194884 GGAGTTGAAATCGTAGATGGCCCATTCGTCGTGAAGTTGAGCCTCGAATTAGATATCCTTCGTCG
66 GGAGTTGAAATCGTAGATGACCCATTCGTCGTGAAGTTGAGCCTCGAATTAGATATCATTCGTCA
* * **
194949 TGAAGTTGAAATCCAAGGGTTGCATTGTTTCTTATGGGCACGATATCCTCCATCGTGAAGTTGAA
131 TGAAGTTGAAATCCAAGGATTGCATTGTTTCTGATGAACACGATATCCTCCATCGTGAAGTTGAA
*
195014 ATTGTGGATAGCC
196 ATTATGGATAGCC
*
195027 CCTTCGTTGTAAAGTTGA
1 CCTTCGTCGTAAAGTTGA
195045 GCCTTGAATT
Statistics
Matches: 195, Mismatches: 29, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
207 136 0.70
208 59 0.30
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (208 bp):
CCTTCGTCGTAAAGTTGAAATCCAAGAGTTGCATTGATGCTTGTGGGAACGATGTCCTCCGTCAT
GGAGTTGAAATCGTAGATGACCCATTCGTCGTGAAGTTGAGCCTCGAATTAGATATCATTCGTCA
TGAAGTTGAAATCCAAGGATTGCATTGTTTCTGATGAACACGATATCCTCCATCGTGAAGTTGAA
ATTATGGATAGCC
Found at i:195011 original size:121 final size:121
Alignment explanation
Indices: 194819--195085 Score: 363
Period size: 121 Copynumber: 2.2 Consensus size: 121
194809 ATGGATGGCC
* * * **
194819 CCTTCGTCGTGAAGTTGAAATCCAAGAGTTGTATTGCTGCTTGTGGGCACGATGTCCTCTGTCAT
1 CCTTCGTCGTGAAGTTGAAATCCAAGAGTTGCATTGCTGCTTATGGGCACGATATCCTCCATCAT
* * *
194884 GGAGTTGAAATCGTAGATGGCCCATTCGTCGTGAAGTTGAGCCTCGAATTAGATAT
66 GAAGTTGAAATCGTAGATAGCCCATTCGTCGTAAAGTTGAGCCTCGAATTAGATAT
* * * *
194940 CCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGTTTCTTATGGGCACGATATCCTCCATCGT
1 CCTTCGTCGTGAAGTTGAAATCCAAGAGTTGCATTGCTGCTTATGGGCACGATATCCTCCATCAT
* * * * * *
195005 GAAGTTGAAATTGTGGATAGCCCCTTCGTTGTAAAGTTGAGCCTTGAATTGGATAT
66 GAAGTTGAAATCGTAGATAGCCCATTCGTCGTAAAGTTGAGCCTCGAATTAGATAT
*
195061 CATTCGTCGTGAAGTTGAAATCCAA
1 CCTTCGTCGTGAAGTTGAAATCCAA
195086 ATATAAGAAT
Statistics
Matches: 127, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
121 127 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (121 bp):
CCTTCGTCGTGAAGTTGAAATCCAAGAGTTGCATTGCTGCTTATGGGCACGATATCCTCCATCAT
GAAGTTGAAATCGTAGATAGCCCATTCGTCGTAAAGTTGAGCCTCGAATTAGATAT
Found at i:195220 original size:64 final size:64
Alignment explanation
Indices: 195114--195277 Score: 256
Period size: 64 Copynumber: 2.6 Consensus size: 64
195104 CTTCGAGTTC
* * *
195114 AATATCCTTCGTTGTGAAATTGAAATTGACTCTGAATAAAACTAGAAAGTTGTTTGTTGAGTCT
1 AATATCCTTCGTTGTGAAGTTGAAATTGACTTTAAATAAAACTAGAAAGTTGTTTGTTGAGTCT
* *
195178 AATATCCTTCGTTGTGAAGTTGAAATTGACTTTAAATGAAACTGGAAAGTTGTTTGTTGAGTCT
1 AATATCCTTCGTTGTGAAGTTGAAATTGACTTTAAATAAAACTAGAAAGTTGTTTGTTGAGTCT
***
195242 AATATCCTTCACCGTGAAGTTGAAATTGACTTTAAA
1 AATATCCTTCGTTGTGAAGTTGAAATTGACTTTAAA
195278 AGCTGCAAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 92 1.00
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (64 bp):
AATATCCTTCGTTGTGAAGTTGAAATTGACTTTAAATAAAACTAGAAAGTTGTTTGTTGAGTCT
Found at i:195651 original size:24 final size:25
Alignment explanation
Indices: 195604--195667 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
195594 AAAGGAATCA
195604 ATAGCTCTTTACAACTTTCAGAGTT
1 ATAGCTCTTTACAACTTTCAGAGTT
*
195629 ATAGCTCTTTAC-AGTTTCAGAGTT
1 ATAGCTCTTTACAACTTTCAGAGTT
195653 ATAGCTCTTTGACAA
1 ATAGCTCTTT-ACAA
195668 ATGTTCAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
24 21 0.58
25 14 0.39
26 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (25 bp):
ATAGCTCTTTACAACTTTCAGAGTT
Found at i:196195 original size:95 final size:95
Alignment explanation
Indices: 196011--196262 Score: 357
Period size: 95 Copynumber: 2.6 Consensus size: 95
196001 TCAATAAAAC
* * *
196011 CGGGGCGTTT-ACCTAATTTCTCTAGAGGGACAACTTAA--TATCATTGTATAGGTATTATAATC
1 CGGGGCGTTTAACC-AATTGCTCTAGAGGGACAACTCAAGCT-TTATTG--TA--TATTATAATC
196073 ACCTTTATCAGGCTAACTGAATATTATCCATAAAGA
60 ACCTTTATCAGGCTAACTGAATATTATCCATAAAGA
196109 CGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTT
1 CGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTT
* * *
196174 ATCAGGCTAGCTGAATCTTATCCATAAAGC
66 ATCAGGCTAACTGAATATTATCCATAAAGA
*
196204 CGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATATATAAT
1 CGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-TATAAT
196263 ATTATAATAT
Statistics
Matches: 143, Mismatches: 7, Indels: 10
0.89 0.04 0.06
Matches are distributed among these distances:
95 94 0.66
96 6 0.04
97 2 0.01
98 32 0.22
99 8 0.06
100 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (95 bp):
CGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTATAATCACCTTT
ATCAGGCTAACTGAATATTATCCATAAAGA
Found at i:196820 original size:3 final size:3
Alignment explanation
Indices: 196812--196853 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
196802 TTTATTTCAT
*
196812 TTA TTA TTA TTA TT- TTG TT- TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
196854 AATAATTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.17
3 30 0.83
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:198664 original size:2 final size:2
Alignment explanation
Indices: 198657--198686 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
198647 TGTTATTTAA
198657 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
198687 TCTTTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:199230 original size:26 final size:27
Alignment explanation
Indices: 199178--199235 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
199168 TAATTATTTC
*
199178 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
199206 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
199232 TTTT
1 TTTT
199236 ATTAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:204032 original size:23 final size:23
Alignment explanation
Indices: 203984--204031 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
203974 TTCATCCAGC
*
203984 AAACAAAGAAGAAGGAAAAAAGA
1 AAACAAAAAAGAAGGAAAAAAGA
* *
204007 AAACAAAAAAG-ATGAAAAAGGA
1 AAACAAAAAAGAAGGAAAAAAGA
204029 AAA
1 AAA
204032 ATGAGAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.02
Consensus pattern (23 bp):
AAACAAAAAAGAAGGAAAAAAGA
Found at i:209749 original size:113 final size:113
Alignment explanation
Indices: 209174--209736 Score: 871
Period size: 113 Copynumber: 5.0 Consensus size: 113
209164 TAACAATGAT
* * *
209174 TCAAATCCATCAC--AATGGATCAACATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
209237 AGAAAGAAGAAGAAGTTCAAAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* **
209285 TCTAATCCATCACTTGATGGATCGGCTTTTCCAGA-AAGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTG
209349 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* * *
209398 TCAAATCCATCACTTGATGGATCAAATTTTTCAGAGAAAGTTTATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
209463 AGAAGGAAGAAGAATTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* *
209511 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* ** * *
209576 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
** * * *
209624 TTGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
209689 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
209737 ATGATTCTAT
Statistics
Matches: 413, Mismatches: 35, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
111 12 0.03
112 2 0.00
113 397 0.96
114 2 0.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
Found at i:210075 original size:3 final size:3
Alignment explanation
Indices: 210058--210113 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
210048 TTTATTTCAT
*
210058 TTA TT- TTA TTTA TTA TTA TTA TT- TTG TT- TTA TTA TTA -TA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
210100 -TA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA
210114 AATAATTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
2 10 0.22
3 32 0.71
4 3 0.07
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:210107 original size:13 final size:13
Alignment explanation
Indices: 210058--210113 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
210048 TTTATTTCAT
*
210058 TTATTTTATT-TA
1 TTATATTATTATA
* *
210070 TTATTATTATTTTG
1 TTA-TATTATTATA
*
210084 TTTTATTATTATA
1 TTATATTATTATA
210097 TTATATTATTAATA
1 TTATATTATT-ATA
210111 TTA
1 TTA
210114 AATAATTAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
12 3 0.09
13 23 0.66
14 9 0.26
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TTATATTATTATA
Found at i:218423 original size:23 final size:22
Alignment explanation
Indices: 218368--218450 Score: 96
Period size: 23 Copynumber: 3.6 Consensus size: 22
218358 ATCATTATAA
218368 AAATAT-TTATTTATTTAATTTTT
1 AAATATATTATTTATTT-A-TTTT
*
218391 AAAATCATATGATTTATTTATTTT
1 -AAAT-ATATTATTTATTTATTTT
*
218415 AAATAATATTAATTATTTATTTT
1 AAAT-ATATTATTTATTTATTTT
218438 AAATATATTATTT
1 AAATATATTATTT
218451 TTAAATTATC
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
22 8 0.15
23 24 0.46
24 8 0.15
25 3 0.06
26 9 0.17
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (22 bp):
AAATATATTATTTATTTATTTT
Found at i:218447 original size:18 final size:18
Alignment explanation
Indices: 218426--218483 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 18
218416 AATAATATTA
218426 ATTATTTATTTTAAATAT
1 ATTATTTATTTTAAATAT
218444 ATTA--T-TTTTAAAT-T
1 ATTATTTATTTTAAATAT
*
218458 ATCTATTAAATTTTAAATAAT
1 AT-TATT-TATTTTAAAT-AT
218479 ATTAT
1 ATTAT
218484 ATGGGACCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
14 3 0.09
15 10 0.31
16 1 0.03
18 4 0.12
19 8 0.25
20 3 0.09
21 3 0.09
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTATTTATTTTAAATAT
Found at i:218608 original size:21 final size:21
Alignment explanation
Indices: 218582--218650 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
218572 ATTATTTCAA
218582 ATAAATAATTAATATAATTTT
1 ATAAATAATTAATATAATTTT
* *
218603 ATAAATTAAATAA-ATACTTTT
1 ATAAA-TAATTAATATAATTTT
* * *
218624 ATAATATTATAAATATACTTTTT
1 ATAA-ATAATTAATATA-ATTTT
218647 ATAA
1 ATAA
218651 TGATTTCATA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 20 0.53
22 10 0.26
23 8 0.21
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (21 bp):
ATAAATAATTAATATAATTTT
Found at i:218618 original size:23 final size:21
Alignment explanation
Indices: 218591--218669 Score: 56
Period size: 22 Copynumber: 3.6 Consensus size: 21
218581 AATAAATAAT
218591 TAATATAATTTTATAA-ATTA
1 TAATATAATTTTATAATATTA
*
218611 -AATAAATACTTTTATAATATTA
1 TAAT--ATAATTTTATAATATTA
*
218633 TAAATATACTTTTTATAATGATT-
1 T-AATATA-ATTTTATAAT-ATTA
*
218656 TCATATAAATTTTA
1 TAATAT-AATTTTA
218670 AAAAAAATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
19 3 0.06
21 11 0.23
22 16 0.34
23 11 0.23
24 6 0.13
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (21 bp):
TAATATAATTTTATAATATTA
Found at i:218633 original size:29 final size:30
Alignment explanation
Indices: 218580--218637 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
218570 ATATTATTTC
*
218580 AAATAAATAATTAATATAATTTTATAAATT
1 AAATAAATAATTAATATAATATTATAAATT
* *
218610 AAATAAATACTT-TTATAATATTATAAAT
1 AAATAAATAATTAATATAATATTATAAAT
218638 ATACTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (30 bp):
AAATAAATAATTAATATAATATTATAAATT
Found at i:220336 original size:5 final size:5
Alignment explanation
Indices: 220326--220360 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
220316 ACTACGTCAA
* *
220326 TCGAT TCGAT TTGAT TCGAT TTGAT TCGAT TCGAT
1 TCGAT TCGAT TCGAT TCGAT TCGAT TCGAT TCGAT
220361 CCAATTAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (5 bp):
TCGAT
Found at i:220343 original size:10 final size:10
Alignment explanation
Indices: 220328--220356 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
220318 TACGTCAATC
220328 GATTCGATTT
1 GATTCGATTT
220338 GATTCGATTT
1 GATTCGATTT
220348 GATTCGATT
1 GATTCGATT
220357 CGATCCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.48
Consensus pattern (10 bp):
GATTCGATTT
Found at i:220585 original size:5 final size:5
Alignment explanation
Indices: 220577--220602 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
220567 TAAAATTTAG
220577 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
220603 ATTGTAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:222459 original size:20 final size:20
Alignment explanation
Indices: 222434--222472 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
222424 AAAATGAAAC
*
222434 GGGTATCGATATTTTAGGTT
1 GGGTATCGATATTGTAGGTT
222454 GGGTATCGATATTGTAGGT
1 GGGTATCGATATTGTAGGT
222473 AAGATATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.05, G:0.33, T:0.41
Consensus pattern (20 bp):
GGGTATCGATATTGTAGGTT
Found at i:222480 original size:20 final size:20
Alignment explanation
Indices: 222437--222484 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
222427 ATGAAACGGG
* ** *
222437 TATCGATATTTTAGGTTGGG
1 TATCGATATTGTAGGTAAGA
222457 TATCGATATTGTAGGTAAGA
1 TATCGATATTGTAGGTAAGA
222477 TATCGATA
1 TATCGATA
222485 CTCGCAGGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.06, G:0.25, T:0.40
Consensus pattern (20 bp):
TATCGATATTGTAGGTAAGA
Found at i:230903 original size:21 final size:21
Alignment explanation
Indices: 230879--230947 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
230869 TTCTTCATCA
*
230879 TCTTCTCTTCCTCTTCCTTCT
1 TCTTCTCTTCCTCCTCCTTCT
230900 TCTTCTCTTCCTCCTCCTTC-
1 TCTTCTCTTCCTCCTCCTTCT
*
230920 TCTCCTCCTT-CTCCTCC-TCTT
1 TCTTCT-CTTCCTCCTCCTTC-T
230941 TCTTCTC
1 TCTTCTC
230948 ATTTTCCTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.05
20 13 0.31
21 27 0.64
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (21 bp):
TCTTCTCTTCCTCCTCCTTCT
Found at i:230907 original size:15 final size:15
Alignment explanation
Indices: 230880--230961 Score: 62
Period size: 15 Copynumber: 5.5 Consensus size: 15
230870 TCTTCATCAT
230880 CTTC-TCTTCCTCTTC
1 CTTCTTCTT-CTCTTC
230895 CTTCTTCTTCTCTTC
1 CTTCTTCTTCTCTTC
* *
230910 CTCCTCCTTCTC-TC
1 CTTCTTCTTCTCTTC
* * *
230924 CTCCTTCTCCTCCTC
1 CTTCTTCTTCTCTTC
* *
230939 TTTCTTC-TCATTTTC
1 CTTCTTCTTC-TCTTC
230954 CTTCTTCT
1 CTTCTTCT
230962 CATTCTCCTC
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
14 13 0.25
15 36 0.68
16 4 0.08
ACGTcount: A:0.01, C:0.45, G:0.00, T:0.54
Consensus pattern (15 bp):
CTTCTTCTTCTCTTC
Found at i:230924 original size:11 final size:11
Alignment explanation
Indices: 230893--230943 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
230883 CTCTTCCTCT
*
230893 TCCTTCT-TCT
1 TCCTTCTCTCC
230903 TCTCTTC-CTCC
1 TC-CTTCTCTCC
230914 TCCTTCTCTCC
1 TCCTTCTCTCC
230925 TCCTTCTCCTCC
1 TCCTTCT-CTCC
*
230937 TCTTTCT
1 TCCTTCT
230944 TCTCATTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 6 0.17
11 19 0.54
12 10 0.29
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (11 bp):
TCCTTCTCTCC
Found at i:230962 original size:15 final size:15
Alignment explanation
Indices: 230920--230970 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
230910 CTCCTCCTTC
* *
230920 TCTCCTCCTTCTCCT
1 TCTCCTTCTTCTCAT
* *
230935 CCTCTTTCTTCTCAT
1 TCTCCTTCTTCTCAT
*
230950 TTTCCTTCTTCTCAT
1 TCTCCTTCTTCTCAT
230965 TCTCCT
1 TCTCCT
230971 CTAAGTGCTT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.04, C:0.43, G:0.00, T:0.53
Consensus pattern (15 bp):
TCTCCTTCTTCTCAT
Found at i:242282 original size:25 final size:25
Alignment explanation
Indices: 242247--242315 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
242237 CGATGTAGCG
* *
242247 TGGCTCAGCTCGACTCGGTGCGGCT
1 TGGCTCGGCTCAACTCGGTGCGGCT
242272 TGGCTCGGCTCAACTCGGTGCGGCT
1 TGGCTCGGCTCAACTCGGTGCGGCT
242297 TGGCTCGGCTCAACTCGGT
1 TGGCTCGGCTCAACTCGGT
242316 CTGGTCCAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.09, C:0.32, G:0.35, T:0.25
Consensus pattern (25 bp):
TGGCTCGGCTCAACTCGGTGCGGCT
Done.