Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009631.1 Hibiscus syriacus cultivar Beakdansim tig00117027_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: 652059
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:160470 original size:2 final size:2
Alignment explanation
Indices: 160463--160510 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
160453 TTAATCTTTA
160463 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
160505 AT AT AT
1 AT AT AT
160511 TCATATAACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:169170 original size:7 final size:7
Alignment explanation
Indices: 169160--169236 Score: 74
Period size: 7 Copynumber: 11.6 Consensus size: 7
169150 ACCCTACACC
169160 CTAAACT
1 CTAAACT
*
169167 CTAATCT
1 CTAAACT
169174 CTAAACT
1 CTAAACT
169181 CTAAACT
1 CTAAACT
169188 CTAAAC-
1 CTAAACT
169194 CTAAAC-
1 CTAAACT
*
169200 CTAAACC
1 CTAAACT
*
169207 CCAAACT
1 CTAAACT
169214 C-AAAC-
1 CTAAACT
*
169219 CATAAACA
1 C-TAAACT
169227 CTAAAC-
1 CTAAACT
169233 CTAA
1 CTAA
169237 GCCCTAAACC
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
5 1 0.02
6 20 0.32
7 40 0.65
8 1 0.02
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACT
Found at i:169186 original size:21 final size:19
Alignment explanation
Indices: 169159--169236 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 19
169149 CACCCTACAC
*
169159 CCTAAACTCTAATCTCTAAA
1 CCTAAACTCTAAAC-CTAAA
169179 CTCTAAACTCTAAACCTAAA
1 C-CTAAACTCTAAACCTAAA
* *
169199 CCTAAACCCCAAA-CTCAAA
1 CCTAAACTCTAAACCT-AAA
*
169218 CCATAAACACTAAACCTAA
1 CC-TAAACTCTAAACCTAA
169237 GCCCTAAACC
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.04
19 15 0.31
20 18 0.37
21 14 0.29
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (19 bp):
CCTAAACTCTAAACCTAAA
Found at i:169242 original size:7 final size:7
Alignment explanation
Indices: 169150--169248 Score: 71
Period size: 7 Copynumber: 14.7 Consensus size: 7
169140 TGTTGATTAC
*
169150 ACCCTAC
1 ACCCTAA
169157 ACCCTAA
1 ACCCTAA
*
169164 ACTCTAA
1 ACCCTAA
* *
169171 TCTCTAA
1 ACCCTAA
*
169178 ACTCTAA
1 ACCCTAA
*
169185 ACTCTAA
1 ACCCTAA
169192 A-CCTAA
1 ACCCTAA
169198 A-CCTAA
1 ACCCTAA
*
169204 ACCCCAA
1 ACCCTAA
*
169211 ACTC-AA
1 ACCCTAA
*
169217 ACCATAA
1 ACCCTAA
*
169224 ACACTAA
1 ACCCTAA
169231 A-CCTAA
1 ACCCTAA
*
169237 GCCCTAA
1 ACCCTAA
169244 ACCCT
1 ACCCT
169249 TAATCTAATC
Statistics
Matches: 75, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
6 19 0.25
7 56 0.75
ACGTcount: A:0.42, C:0.37, G:0.01, T:0.19
Consensus pattern (7 bp):
ACCCTAA
Found at i:169441 original size:162 final size:165
Alignment explanation
Indices: 169102--169464 Score: 463
Period size: 162 Copynumber: 2.2 Consensus size: 165
169092 CGTTGTATAT
*
169102 TACTAAAAGAAAAATAAAAGCTCATTTAATTAACCACATGTTGATTACACCCTACACCCTAAACT
1 TACTAAAAGAAAAATAAAAGCTCATTTAATTAAGCACATGTTGATTA-A--CTACACCCTAAACT
* * * * * *
169167 CTAATCTCTAAACTCTAAACTCTAAACCTAAACCTAAACCCCAAACTCAAACCATAAACACTAAA
63 CTAAACCCTAAACTATAAACTCCAAACCCAAACCTAAACCCCAAACCCAAACCATAAACACTAAA
*
169232 CCTAAGCCCTAAACCCTTAATCTAATCACGTGATAAGG
128 CCTAAGCCCTAAACCCTTAATCTAATCACGTAATAAGG
*
169270 TTCTAAAAGAAAAATAAAAGCTCATTTAATTAAGCACATGTTAGATT-A-TAC-CCCTAAAC-CT
1 TACTAAAAGAAAAATAAAAGCTCATTTAATTAAGCACATGTT-GATTAACTACACCCTAAACTCT
* * *
169331 AAACCCTAAACTATAATCTCCAAACCCAAA-CTCAAA-CCCAAACCCCAAACCATAAGCACTAAG
65 AAACCCTAAACTATAAACTCCAAACCCAAACCT-AAACCCCAAA-CCCAAACCATAAACACTAAA
* * * *
169394 CCTAAGTCCTAAACCCTTAATCTAATTATGTAATAGGG
128 CCTAAGCCCTAAACCCTTAATCTAATCACGTAATAAGG
*
169432 TACTAAAAG-AAAAT-AAAGCTCGTTTAATTAAGC
1 TACTAAAAGAAAAATAAAAGCTCATTTAATTAAGC
169465 TCATTTAATT
Statistics
Matches: 174, Mismatches: 18, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
160 18 0.10
161 13 0.07
162 87 0.50
163 8 0.05
164 3 0.02
167 1 0.01
168 40 0.23
169 4 0.02
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.24
Consensus pattern (165 bp):
TACTAAAAGAAAAATAAAAGCTCATTTAATTAAGCACATGTTGATTAACTACACCCTAAACTCTA
AACCCTAAACTATAAACTCCAAACCCAAACCTAAACCCCAAACCCAAACCATAAACACTAAACCT
AAGCCCTAAACCCTTAATCTAATCACGTAATAAGG
Found at i:169466 original size:14 final size:14
Alignment explanation
Indices: 169447--169476 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
169437 AAAGAAAATA
*
169447 AAGCTCGTTTAATT
1 AAGCTCATTTAATT
169461 AAGCTCATTTAATT
1 AAGCTCATTTAATT
169475 AA
1 AA
169477 ACCATGTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (14 bp):
AAGCTCATTTAATT
Found at i:169530 original size:20 final size:20
Alignment explanation
Indices: 169505--169543 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
169495 CTAAACCCTA
*
169505 AATTATAAACTTTAAACTCT
1 AATTATAAACCTTAAACTCT
169525 AATTATAAACCTTAAACTC
1 AATTATAAACCTTAAACTC
169544 AACCCCAAAA
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:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTATAAACCTTAAACTCT
Found at i:170059 original size:157 final size:158
Alignment explanation
Indices: 169803--170117 Score: 596
Period size: 157 Copynumber: 2.0 Consensus size: 158
169793 AACATAAACA
169803 TTGATTAATGACGAAATCAGAAGATTACAAATATAACAGGTCCTAAAATGCTAATAATTCATTTT
1 TTGATTAATGACGAAATCAGAAGATTACAAATATAACAGGTCCTAAAATGCTAATAATTCATTTT
*
169868 GGTGTTGATTAAAGTTACGTCGTTTTGGTCGTTGGAATATATTGGAA-ATTAGGGTGAAACGCTT
66 GGTGCTGATTAAAGTTACGTCGTTTTGGTCGTTGGAATATATTGGAAGATTAGGGTGAAACGCTT
169932 AACCTAAATCATTTCCTCATCTATCCTC
131 AACCTAAATCATTTCCTCATCTATCCTC
*
169960 TTGATTAATGACGAAATCAGAAGATTACAAATATAACAGGTCCTAAAATGCTAATAATTCGTTTT
1 TTGATTAATGACGAAATCAGAAGATTACAAATATAACAGGTCCTAAAATGCTAATAATTCATTTT
170025 GGTGCTGATTAAAGTTACGTCGTTTTGGTCGTTGGAATATATTGGAAGATTAGGGTGAAACGCTT
66 GGTGCTGATTAAAGTTACGTCGTTTTGGTCGTTGGAATATATTGGAAGATTAGGGTGAAACGCTT
*
170090 AACCTAAATCATTTCCTCATCTCTCCTC
131 AACCTAAATCATTTCCTCATCTATCCTC
170118 AACGAGACAC
Statistics
Matches: 154, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
157 110 0.71
158 44 0.29
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (158 bp):
TTGATTAATGACGAAATCAGAAGATTACAAATATAACAGGTCCTAAAATGCTAATAATTCATTTT
GGTGCTGATTAAAGTTACGTCGTTTTGGTCGTTGGAATATATTGGAAGATTAGGGTGAAACGCTT
AACCTAAATCATTTCCTCATCTATCCTC
Found at i:172177 original size:17 final size:17
Alignment explanation
Indices: 172157--172193 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
172147 AATTCGAGTT
172157 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
172174 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
172191 GAG
1 GAG
172194 CTCAAAATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.27
Consensus pattern (17 bp):
GAGTTCGAGCTTGAATC
Found at i:172304 original size:31 final size:31
Alignment explanation
Indices: 172243--172304 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
172233 GAGTTCGAGC
* * * *
172243 CTTTTGAGTTCGAGTCGAGTTTCAATATTTT
1 CTTTCGAGTTCAAGTCGAGCTTCAAAATTTT
*
172274 CTTTCGAGTTCAAGTCGAGCTTGAAAATTTT
1 CTTTCGAGTTCAAGTCGAGCTTCAAAATTTT
172305 AGGCTAGCGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.44
Consensus pattern (31 bp):
CTTTCGAGTTCAAGTCGAGCTTCAAAATTTT
Found at i:175149 original size:37 final size:37
Alignment explanation
Indices: 175075--175294 Score: 187
Period size: 35 Copynumber: 6.1 Consensus size: 37
175065 TTTTTAAAAC
* * *
175075 TATAAATATAGTTTTAAAAAAAATATTTT-AAAAATATA
1 TATATATATAGTTTT-TAAAACAT-TTTTGAAAAATATA
175113 TATATATA-A-TTTTTAAAATCA-TTTTG-AAAA-ATA
1 TATATATATAGTTTTTAAAA-CATTTTTGAAAAATATA
*
175146 TATATATATAGTTTTTGAAAACATTTTT--AAAA-ACA
1 TATATATATAGTTTTT-AAAACATTTTTGAAAAATATA
*
175181 TATAT-TATAGTTTTGAAAACATTTTTTTGAAAACATATA
1 TATATATATAGTTTTTAAAACA--TTTTTGAAAA-ATATA
* * **
175220 TAT-T-TATAGTTTTTGAAGATATTTTTG-AAACCATA
1 TATATATATAGTTTTT-AAAACATTTTTGAAAAATATA
175255 TATATATATAGTTTTTAAAACCATTTTTGAAAAATATA
1 TATATATATAGTTTTTAAAA-CATTTTTGAAAAATATA
175293 TA
1 TA
175295 ATAGTTTTAA
Statistics
Matches: 150, Mismatches: 15, Indels: 34
0.75 0.08 0.17
Matches are distributed among these distances:
33 17 0.11
34 18 0.12
35 33 0.22
36 20 0.13
37 27 0.18
38 26 0.17
39 9 0.06
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (37 bp):
TATATATATAGTTTTTAAAACATTTTTGAAAAATATA
Found at i:175150 original size:35 final size:35
Alignment explanation
Indices: 175094--175331 Score: 207
Period size: 37 Copynumber: 6.9 Consensus size: 35
175084 AGTTTTAAAA
*
175094 AAAAT-ATTTTAAAAATATATATATATA-A-TTTTT
1 AAAATCATTTTGAAAA-ATATATATATATAGTTTTT
175127 AAAATCATTTTGAAAAATATATATATATAGTTTTT
1 AAAATCATTTTGAAAAATATATATATATAGTTTTT
* * *
175162 GAAAA-CATTTTTAAAAACATATAT-TATAGTTTTG
1 -AAAATCATTTTGAAAAATATATATATATAGTTTTT
*
175196 AAAA-CATTTTTTTGAAAACATATATATTTATAGTTTTT
1 AAAATCA---TTTTGAAAA-ATATATATATATAGTTTTT
* *
175234 GAAGAT-ATTTTTGAAACCATATATATATATAGTTTTT
1 -AAAATCA-TTTTGAAA-AATATATATATATAGTTTTT
*
175271 AAAACCATTTTTG-AAAA-ATATATA-ATAG-TTTT
1 AAAATCA-TTTTGAAAAATATATATATATAGTTTTT
*
175303 -AAATCATTTTG-AAATTATATA-ATATAGTT
1 AAAATCATTTTGAAAAATATATATATATAGTT
175332 GAAACATATA
Statistics
Matches: 174, Mismatches: 15, Indels: 33
0.78 0.07 0.15
Matches are distributed among these distances:
30 9 0.05
31 14 0.08
32 5 0.03
33 26 0.15
34 26 0.15
35 23 0.13
36 17 0.10
37 41 0.24
38 9 0.05
39 4 0.02
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (35 bp):
AAAATCATTTTGAAAAATATATATATATAGTTTTT
Found at i:175373 original size:49 final size:49
Alignment explanation
Indices: 175281--175382 Score: 111
Period size: 49 Copynumber: 2.0 Consensus size: 49
175271 AAAACCATTT
*
175281 TTGAAAAATATATAATAGTTTTAAATCATTTTGAAATTATATAA-TATAG
1 TTGAAAAATATATAATAGTTTTAAAACATTTTGAAA-TATATAACTATAG
* *
175330 TTGAAACATATA-ATATAGTTTTAAAACGTTTTTGAAA-ACTATAACGTATAG
1 TTGAAAAATATATA-ATAGTTTTAAAAC-ATTTTGAAATA-TATAAC-TATAG
175381 TT
1 TT
175383 TTAAAACATT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
48 2 0.04
49 28 0.62
50 8 0.18
51 7 0.16
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (49 bp):
TTGAAAAATATATAATAGTTTTAAAACATTTTGAAATATATAACTATAG
Found at i:175381 original size:82 final size:84
Alignment explanation
Indices: 175254--175411 Score: 209
Period size: 83 Copynumber: 1.9 Consensus size: 84
175244 TTGAAACCAT
* *
175254 ATATATATATAGTTTTTAAAACCATTTTTGAAAAATATATAATAGTTTTAAATCA-TTTTGAAAT
1 ATATATATATAGTTTTTAAAACCATTTTTGAAAAATATATAATAGTTTTAAAACATTTTTAAAAT
175318 TATATAATATAGTTGAAAC
66 TATATAATATAGTTGAAAC
* *
175337 ATATA-ATATAG-TTTTAAAA-CGTTTTTGAAAACTATA-ACGTATAGTTTTAAAACATTTTTAA
1 ATATATATATAGTTTTTAAAACCATTTTTGAAAAATATATA---ATAGTTTTAAAACATTTTTAA
*
175398 AATTATATAGTATA
63 AATTATATAATATA
175412 TGGTTTTGAA
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
79 1 0.02
80 15 0.23
81 8 0.12
82 19 0.29
83 23 0.35
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (84 bp):
ATATATATATAGTTTTTAAAACCATTTTTGAAAAATATATAATAGTTTTAAAACATTTTTAAAAT
TATATAATATAGTTGAAAC
Found at i:175447 original size:29 final size:28
Alignment explanation
Indices: 175337--175467 Score: 109
Period size: 33 Copynumber: 4.2 Consensus size: 28
175327 TAGTTGAAAC
*
175337 ATATAATATAGTTTTAAAACGTTTTTGAAA
1 ATAT-ATATAGTTTTAAAACATTTTTG-AA
*
175367 ACTATAACGTATAGTTTTAAAACATTTTTAAAA
1 A-TAT-A--TATAGTTTTAAAACATTTTT-GAA
*
175400 TTATATAGTATATGGTTTTGAAAATATTTTTGAA
1 --ATATA-TATA--GTTTT-AAAACATTTTTGAA
*
175434 ATATATATAGTTTTAAAACATTTTTTAA
1 ATATATATAGTTTTAAAACATTTTTGAA
175462 ATATAT
1 ATATAT
175468 TATATAGTTT
Statistics
Matches: 86, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
28 18 0.21
29 5 0.06
30 1 0.01
31 9 0.10
32 10 0.12
33 22 0.26
34 10 0.12
35 11 0.13
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (28 bp):
ATATATATAGTTTTAAAACATTTTTGAA
Found at i:184058 original size:15 final size:15
Alignment explanation
Indices: 184040--184072 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
184030 ATAAATTCAT
*
184040 TTTTTTAAAATTTTA
1 TTTTTAAAAATTTTA
184055 TTTTTAAAAATTTTA
1 TTTTTAAAAATTTTA
184070 TTT
1 TTT
184073 GTATTTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTAAAAATTTTA
Found at i:184191 original size:19 final size:20
Alignment explanation
Indices: 184147--184194 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
184137 ATGAGTTTCG
184147 TCTAATTTT-TTTTGTATTC
1 TCTAATTTTATTTTGTATTC
* * *
184166 ACAAATTTTATTTT-TATTT
1 TCTAATTTTATTTTGTATTC
184185 TCTAATTTTA
1 TCTAATTTTA
184195 AAAAAATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (20 bp):
TCTAATTTTATTTTGTATTC
Found at i:184522 original size:19 final size:19
Alignment explanation
Indices: 184490--184531 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
184480 CCGTCCATCC
184490 AATTGACAACATATTATTA
1 AATTGACAACATATTATTA
* *
184509 AATTGTCAATATATTATTA
1 AATTGACAACATATTATTA
184528 AATT
1 AATT
184532 TTCACATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (19 bp):
AATTGACAACATATTATTA
Found at i:188877 original size:22 final size:21
Alignment explanation
Indices: 188837--188877 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
188827 CAAATGCAGT
188837 AAATAATATTATTTATTAACA
1 AAATAATATTATTTATTAACA
188858 AAATAATTATTACTTT-TTAA
1 AAATAA-TATTA-TTTATTAA
188878 AATATTAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 9 0.50
23 3 0.17
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATAATATTATTTATTAACA
Found at i:188909 original size:14 final size:15
Alignment explanation
Indices: 188890--188921 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
188880 TATTAGAAGA
188890 ATTTATTTT-ATATT
1 ATTTATTTTAATATT
188904 ATTTATTTTAATATT
1 ATTTATTTTAATATT
188919 ATT
1 ATT
188922 ATTAAAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTATTTTAATATT
Found at i:189538 original size:31 final size:30
Alignment explanation
Indices: 189464--189539 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
189454 ACACATGTCA
*
189464 CAATATTATGATTATAATATATATATATTTT
1 CAATATTA-AATTATAATATATATATATTTT
*
189495 CTATCATT-AATTATAATATAATATATATTTT
1 CAAT-ATTAAATTATAATAT-ATATATATTTT
*
189526 GAATATTAAATTAT
1 CAATATTAAATTAT
189540 TTTTAATGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
30 13 0.34
31 22 0.58
32 3 0.08
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (30 bp):
CAATATTAAATTATAATATATATATATTTT
Found at i:191153 original size:44 final size:43
Alignment explanation
Indices: 191066--191154 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 43
191056 AATTATTATA
*
191066 AATTATATTACTTATTATTAAAATAAAAAAATATTATATTATT
1 AATTATATTACTTATTATTAAAATAAAAAAATATTATAATATT
* **
191109 AATTATATTAGTTATTTATTAAAATAATAATGA-ATTATAATATT
1 AATTATATTACTTA-TTATTAAAATAA-AAAAATATTATAATATT
191153 AA
1 AA
191155 AATAAGAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 13 0.32
44 24 0.60
45 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (43 bp):
AATTATATTACTTATTATTAAAATAAAAAAATATTATAATATT
Found at i:191287 original size:28 final size:29
Alignment explanation
Indices: 191249--191314 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 29
191239 TGATTTTATT
191249 AATAATT-TATTATATATTACTAA-AATAA
1 AATAATTATATTATATATTA-TAATAATAA
191277 AAT-ATTATATTATATATTATAATAATAA
1 AATAATTATATTATATATTATAATAATAA
*
191305 TATAATTATA
1 AATAATTATA
191315 ATAATAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
27 6 0.18
28 22 0.65
29 6 0.18
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (29 bp):
AATAATTATATTATATATTATAATAATAA
Found at i:191299 original size:45 final size:46
Alignment explanation
Indices: 191245--191336 Score: 118
Period size: 45 Copynumber: 2.0 Consensus size: 46
191235 ATATTGATTT
* * *
191245 TATTAATAAT-TTATTATATATTACTAA-AATAAAATATTATATTATA
1 TATTAATAATAATAATATA-ATTA-TAATAATAAAATAGTATATTATA
191291 TATT-ATAATAATAATATAATTATAATAATAAAATAGTATATTATA
1 TATTAATAATAATAATATAATTATAATAATAAAATAGTATATTATA
191336 T
1 T
191337 TTTCAAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
44 3 0.07
45 28 0.68
46 10 0.24
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (46 bp):
TATTAATAATAATAATATAATTATAATAATAAAATAGTATATTATA
Found at i:191314 original size:17 final size:18
Alignment explanation
Indices: 191287--191335 Score: 64
Period size: 17 Copynumber: 2.6 Consensus size: 18
191277 AATATTATAT
191287 TATATATTATAATAATAA
1 TATATATTATAATAATAA
191305 TATA-ATTATAATAATAAAA
1 TATATATTATAATAAT--AA
191324 TAGTATATTATA
1 TA-TATATTATA
191336 TTTTCAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 11 0.41
18 4 0.15
19 4 0.15
20 2 0.07
21 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TATATATTATAATAATAA
Found at i:192046 original size:15 final size:15
Alignment explanation
Indices: 192028--192058 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
192018 ATTATATAAA
192028 ATATAATGAATTATT
1 ATATAATGAATTATT
*
192043 ATATTATGAATTATT
1 ATATAATGAATTATT
192058 A
1 A
192059 AATTTTGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
ATATAATGAATTATT
Found at i:192333 original size:18 final size:18
Alignment explanation
Indices: 192310--192345 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
192300 CATCACTATC
192310 AATTTTAGTTTATTTATT
1 AATTTTAGTTTATTTATT
192328 AATTTTAGTTTATTTATT
1 AATTTTAGTTTATTTATT
192346 TATATATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (18 bp):
AATTTTAGTTTATTTATT
Found at i:198640 original size:38 final size:38
Alignment explanation
Indices: 198588--198698 Score: 188
Period size: 38 Copynumber: 2.9 Consensus size: 38
198578 GGCTGCTGGA
*
198588 AACCGGTTTAACCGGTTCTG-ACCGGTTTGACCGGTTTC
1 AACCGGTTTGACCGG-TCTGAACCGGTTTGACCGGTTTC
*
198626 AACCGGTTTGACCGGTCTGAACTGGTTTGACCGGTTTC
1 AACCGGTTTGACCGGTCTGAACCGGTTTGACCGGTTTC
198664 AACCGGTTTGACCGGTCTGAACCGGTTTGACCGGT
1 AACCGGTTTGACCGGTCTGAACCGGTTTGACCGGT
198699 CTGACCCGAC
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
37 4 0.06
38 65 0.94
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.30
Consensus pattern (38 bp):
AACCGGTTTGACCGGTCTGAACCGGTTTGACCGGTTTC
Found at i:198699 original size:19 final size:19
Alignment explanation
Indices: 198588--198702 Score: 160
Period size: 19 Copynumber: 6.1 Consensus size: 19
198578 GGCTGCTGGA
*
198588 AACCGGTTTAACCGGTTCTG
1 AACCGGTTTGACCGG-TCTG
* *
198608 -ACCGGTTTGACCGGTTTC
1 AACCGGTTTGACCGGTCTG
198626 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
* * *
198645 AACTGGTTTGACCGGTTTC
1 AACCGGTTTGACCGGTCTG
198664 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
198683 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
198702 A
1 A
198703 CCCGACCCGA
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
18 2 0.02
19 81 0.98
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.30
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:198715 original size:38 final size:38
Alignment explanation
Indices: 198598--198715 Score: 103
Period size: 38 Copynumber: 3.1 Consensus size: 38
198588 AACCGGTTTA
* ****
198598 ACCGGTTCTG-ACCGGTTTGACCGGTTTCAACCGGTTTG
1 ACCGG-TCTGAACCGGTTTGACCGGTCTCAACCGACCCG
* * ****
198636 ACCGGTCTGAACTGGTTTGACCGGTTTCAACCGGTTTG
1 ACCGGTCTGAACCGGTTTGACCGGTCTCAACCGACCCG
* *
198674 ACCGGTCTGAACCGGTTTGACCGGTCTGACCCGACCCG
1 ACCGGTCTGAACCGGTTTGACCGGTCTCAACCGACCCG
198712 ACCG
1 ACCG
198716 TTGACCCGAC
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
37 4 0.06
38 66 0.94
ACGTcount: A:0.15, C:0.30, G:0.29, T:0.26
Consensus pattern (38 bp):
ACCGGTCTGAACCGGTTTGACCGGTCTCAACCGACCCG
Found at i:198715 original size:57 final size:57
Alignment explanation
Indices: 198608--198715 Score: 144
Period size: 57 Copynumber: 1.9 Consensus size: 57
198598 ACCGGTTCTG
* * ****
198608 ACCGGTTTGACCGGTTTCAACCGGTTTGACCGGTCTGAACTGGTTTGACCGGTTTCA
1 ACCGGTTTGACCGGTCTCAACCGGTTTGACCGGTCTGAACCGACCCGACCGGTTTCA
* *
198665 ACCGGTTTGACCGGTCTGAACCGGTTTGACCGGTCTGACCCGACCCGACCG
1 ACCGGTTTGACCGGTCTCAACCGGTTTGACCGGTCTGAACCGACCCGACCG
198716 TTGACCCGAC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 43 1.00
ACGTcount: A:0.16, C:0.30, G:0.29, T:0.26
Consensus pattern (57 bp):
ACCGGTTTGACCGGTCTCAACCGGTTTGACCGGTCTGAACCGACCCGACCGGTTTCA
Found at i:198722 original size:17 final size:17
Alignment explanation
Indices: 198700--198732 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
198690 TTGACCGGTC
198700 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
198717 TGACCCGACCCGACCG
1 TGACCCGACCCGACCG
198733 GACCGTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.48, G:0.24, T:0.09
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:198727 original size:22 final size:22
Alignment explanation
Indices: 198701--198765 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
198691 TGACCGGTCT
*
198701 GACCCGACCCGACCGTTGACCC
1 GACCCGACCGGACCGTTGACCC
198723 GACCCGACCGGACCGTTGACCC
1 GACCCGACCGGACCGTTGACCC
198745 GACCCGACCGGACCGTTGACC
1 GACCCGACCGGACCGTTGACC
198766 GTTGACTTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.18, C:0.46, G:0.26, T:0.09
Consensus pattern (22 bp):
GACCCGACCGGACCGTTGACCC
Found at i:205966 original size:10 final size:9
Alignment explanation
Indices: 205931--206029 Score: 72
Period size: 10 Copynumber: 10.3 Consensus size: 9
205921 GCTGCTGGAA
*
205931 ACCGGTTTA
1 ACCGGTTTG
*
205940 ACCGGTTTTCA
1 ACCGG-TTT-G
205951 ACCGGTTCTG
1 ACCGGTT-TG
205961 ACCGGTTTG
1 ACCGGTTTG
*
205970 ACCGGTTTCA
1 ACCGGTTT-G
*
205980 ACCGGTTCG
1 ACCGGTTTG
*
205989 AATCGGTTTG
1 -ACCGGTTTG
*
205999 ACCGGTCTG
1 ACCGGTTTG
*
206008 AACCGATTTG
1 -ACCGGTTTG
*
206018 ACCGGTCTG
1 ACCGGTTTG
206027 ACC
1 ACC
206030 CGACCCAACC
Statistics
Matches: 72, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
9 32 0.44
10 33 0.46
11 7 0.10
ACGTcount: A:0.17, C:0.27, G:0.26, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:205975 original size:19 final size:19
Alignment explanation
Indices: 205932--206029 Score: 69
Period size: 19 Copynumber: 5.1 Consensus size: 19
205922 CTGCTGGAAA
* * *
205932 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
205952 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
205971 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
*
205991 TCGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
*
206010 CCGATTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
206028 CC
1 CC
206030 CGACCCAACC
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
18 6 0.09
19 38 0.58
20 14 0.21
21 8 0.12
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:205995 original size:29 final size:29
Alignment explanation
Indices: 205931--206029 Score: 112
Period size: 29 Copynumber: 3.4 Consensus size: 29
205921 GCTGCTGGAA
*
205931 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTCTG
205961 ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 ACCGGTTTGACCGGTTTCAACCGGTTCTG
* * * *
205989 AATCGGTTTGACCGGTCTGAACCGATT-TG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCTG
*
206018 ACCGGTCTGACC
1 ACCGGTTTGACC
206030 CGACCCAACC
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
28 11 0.18
29 36 0.60
30 13 0.22
ACGTcount: A:0.17, C:0.27, G:0.26, T:0.29
Consensus pattern (29 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:206080 original size:17 final size:17
Alignment explanation
Indices: 206025--206080 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
206015 TTGACCGGTC
**
206025 TGACCCGACCCAACCGT
1 TGACCCGACCGGACCGT
206042 TGACCCGACCGTTGACC--
1 TGACCCGACCG--GACCGT
*
206059 CGACCCGACCGGACCGT
1 TGACCCGACCGGACCGT
206076 TGACC
1 TGACC
206081 GTTGACTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 4 0.13
17 24 0.77
19 3 0.10
ACGTcount: A:0.20, C:0.45, G:0.23, T:0.12
Consensus pattern (17 bp):
TGACCCGACCGGACCGT
Found at i:206081 original size:12 final size:12
Alignment explanation
Indices: 206031--206080 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
206021 GGTCTGACCC
*
206031 GACCCAACCGTT
1 GACCCGACCGTT
206043 GACCCGACCGTT
1 GACCCGACCGTT
*
206055 GACCCGACC--C
1 GACCCGACCGTT
*
206065 GACCGGACCGTT
1 GACCCGACCGTT
206077 GACC
1 GACC
206081 GTTGACTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 8 0.25
12 24 0.75
ACGTcount: A:0.20, C:0.44, G:0.24, T:0.12
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:211291 original size:2 final size:2
Alignment explanation
Indices: 211286--211334 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
211276 TTAAAAAACT
211286 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
211328 TA TA TA T
1 TA TA TA T
211335 TAAAAACATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 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):
TA
Found at i:214842 original size:26 final size:26
Alignment explanation
Indices: 214813--214872 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
214803 TGAACGTTTG
214813 TCATTTAACTTAATTAATTTTTTAAT
1 TCATTTAACTTAATTAATTTTTTAAT
*
214839 TCATTTAACTTAATTGATTTTTTAAT
1 TCATTTAACTTAATTAATTTTTTAAT
*
214865 TCGTTTAA
1 TCATTTAA
214873 TGGGAAATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (26 bp):
TCATTTAACTTAATTAATTTTTTAAT
Found at i:214851 original size:14 final size:14
Alignment explanation
Indices: 214813--214858 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
214803 TGAACGTTTG
214813 TCATTTAACTTAAT
1 TCATTTAACTTAAT
* *
214827 TAATTT--TTTAAT
1 TCATTTAACTTAAT
214839 TCATTTAACTTAAT
1 TCATTTAACTTAAT
*
214853 TGATTT
1 TCATTT
214859 TTTAATTCGT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
12 10 0.40
14 15 0.60
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.57
Consensus pattern (14 bp):
TCATTTAACTTAAT
Found at i:215418 original size:21 final size:21
Alignment explanation
Indices: 215392--215435 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
215382 CGAATTTGGG
*
215392 GTATTACAAATACATCCATCA
1 GTATTACAAATACAACCATCA
215413 GTATTACAAATACAACCATCA
1 GTATTACAAATACAACCATCA
215434 GT
1 GT
215436 TGTCGCCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (21 bp):
GTATTACAAATACAACCATCA
Found at i:216535 original size:2 final size:2
Alignment explanation
Indices: 216528--216579 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
216518 ATTTAAAGTA
216528 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
216570 AT AT AT AT AT
1 AT AT AT AT AT
216580 GATCCAATTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:217723 original size:14 final size:14
Alignment explanation
Indices: 217686--217760 Score: 50
Period size: 14 Copynumber: 5.4 Consensus size: 14
217676 ACCTTAAATT
*
217686 GTTAAATATTTATA
1 GTTAAATATATATA
217700 -TTAAAAATATATATA
1 GTT--AAATATATATA
217715 GTTAAATAT-T-TA
1 GTTAAATATATATA
* *
217727 TTTGAAAATATATATG
1 GTT--AAATATATATA
*
217743 GTTAAATATTTATA
1 GTTAAATATATATA
217757 -TTAA
1 GTTAA
217761 TAAAGTATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 15
0.70 0.09 0.22
Matches are distributed among these distances:
12 4 0.08
13 7 0.15
14 21 0.44
15 11 0.23
16 5 0.10
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
GTTAAATATATATA
Found at i:217746 original size:28 final size:29
Alignment explanation
Indices: 217686--217775 Score: 137
Period size: 28 Copynumber: 3.1 Consensus size: 29
217676 ACCTTAAATT
*
217686 GTTAAATATTTATATTAAAAATATATATA
1 GTTAAATATTTATATTAAAAATATATATG
*
217715 GTTAAATATTTAT-TTGAAAATATATATG
1 GTTAAATATTTATATTAAAAATATATATG
217743 GTTAAATATTTATATTAATAAAGTATATATG
1 GTTAAATATTTATATTAA-AAA-TATATATG
217774 GT
1 GT
217776 AAGTGTAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
28 26 0.47
29 16 0.29
30 3 0.05
31 10 0.18
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (29 bp):
GTTAAATATTTATATTAAAAATATATATG
Found at i:218807 original size:24 final size:24
Alignment explanation
Indices: 218771--218830 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
218761 AAGGCGAAAG
*
218771 CACCGCCGCCTATGGAAACACCTC
1 CACCACCGCCTATGGAAACACCTC
* *
218795 CACCACCGTCTATGGAAACATCTC
1 CACCACCGCCTATGGAAACACCTC
* *
218819 CATCACTGCCTA
1 CACCACCGCCTA
218831 CCAAAACATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.27, C:0.42, G:0.13, T:0.18
Consensus pattern (24 bp):
CACCACCGCCTATGGAAACACCTC
Found at i:224045 original size:60 final size:59
Alignment explanation
Indices: 223938--224050 Score: 129
Period size: 60 Copynumber: 1.9 Consensus size: 59
223928 AGTTCAAACA
* * * * * * *
223938 TTCAAAAGTTTGAGATCAATTTAGAATGAGAGTTATAGTTTGAGGATGGAATTAAAATT
1 TTCAAAAGTTTGAAATCAATTTAGAATGAAAGATAAAATATGAGGATGAAATTAAAATT
*
223997 TTCAAAAGTTT-AAATGCAAATTTAGAATGAAAGATAAAATATGGGGATGAAATT
1 TTCAAAAGTTTGAAAT-C-AATTTAGAATGAAAGATAAAATATGAGGATGAAATT
224051 GCAGCACTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
58 3 0.07
59 12 0.27
60 29 0.66
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (59 bp):
TTCAAAAGTTTGAAATCAATTTAGAATGAAAGATAAAATATGAGGATGAAATTAAAATT
Found at i:240714 original size:19 final size:20
Alignment explanation
Indices: 240677--240714 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
240667 ATCTAGATAT
*
240677 TATTCAAATAAAAATAAATC
1 TATTCAAATAAAAACAAATC
*
240697 TATT-AAATATAAACAAAT
1 TATTCAAATAAAAACAAAT
240715 ATCCAATTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (20 bp):
TATTCAAATAAAAACAAATC
Found at i:241716 original size:3 final size:3
Alignment explanation
Indices: 241708--241741 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
241698 AGAGTGTGTG
241708 AGA AGA AGA AGAA AGA AGGA AGA AGA AGA AGA AG
1 AGA AGA AGA AG-A AGA A-GA AGA AGA AGA AGA AG
241742 CTGCCAGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:255642 original size:17 final size:18
Alignment explanation
Indices: 255616--255655 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
255606 ATTATATGGA
255616 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
255632 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
255650 TATTAT
1 TATTAT
255656 ATATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:260226 original size:183 final size:183
Alignment explanation
Indices: 259913--260449 Score: 932
Period size: 183 Copynumber: 2.9 Consensus size: 183
259903 ATTAAATCCG
* * *
259913 TAAAACTGAGCTATTCCATTAAGGCAATTGGTTATAGAAGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
259978 ATAGATTATGTTCAAACTATGACACTTCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
260043 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
*
260096 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGTCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* *
260161 ATAGATTATGTTCAAACTATGACACTGCTCGGATACTTGCCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
260226 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
*
260279 TAAAGATGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** *
260344 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
* *
260408 TTTGTCAGGTCAAAGACTTTGTGATAAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
260450 TAAACCTGAT
Statistics
Matches: 335, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
182 1 0.00
183 334 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:261670 original size:36 final size:36
Alignment explanation
Indices: 261637--261773 Score: 98
Period size: 36 Copynumber: 3.7 Consensus size: 36
261627 GTCTCACTTG
261637 AGACTGTTTTTCTCAAAAGAAGATTTATTTCACTCA
1 AGACTGTTTTTCTCAAAAGAAGATTTATTTCACTCA
* * * * * **
261673 AGA-TCGTTTTTCTTAAAACAAGATTTGTCTCGCTTG
1 AGACT-GTTTTTCTCAAAAGAAGATTTATTTCACTCA
* * *
261709 AGACCGTTTTCACTCGAAAGAAGGCATTTCATTTCACTCA
1 AGACTGTTTT-TCTCAAAAGAA-G-ATTT-ATTTCACTCA
* **
261749 AGGCTGTTTTT-TTTAAAGAAGATTT
1 AGACTGTTTTTCTCAAAAGAAGATTT
261774 TATCTTGCTT
Statistics
Matches: 73, Mismatches: 22, Indels: 12
0.68 0.21 0.11
Matches are distributed among these distances:
35 1 0.01
36 39 0.53
37 8 0.11
38 8 0.11
39 4 0.05
40 13 0.18
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (36 bp):
AGACTGTTTTTCTCAAAAGAAGATTTATTTCACTCA
Found at i:261685 original size:72 final size:76
Alignment explanation
Indices: 261589--261750 Score: 192
Period size: 72 Copynumber: 2.2 Consensus size: 76
261579 ATGCAGATGA
* * * * * *
261589 TTATCTCACTCAA-ATTTGTTTTTCTTAAAATATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGATTCGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
261651 AAAAGAA-G-AT
65 AAAAGAAGGCAT
* *
261661 TTATTTCACTCAAGA-TCGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCG
1 TTATTTCACTCAAGATTCGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCA
261725 AAAGAAGGCAT
66 AAAGAAGGCAT
261736 TTCATTTCACTCAAG
1 TT-ATTTCACTCAAG
261751 GCTGTTTTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
71 1 0.01
72 48 0.63
73 10 0.13
74 1 0.01
75 4 0.05
76 12 0.16
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (76 bp):
TTATTTCACTCAAGATTCGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCA
AAAGAAGGCAT
Found at i:261765 original size:76 final size:72
Alignment explanation
Indices: 261589--261787 Score: 181
Period size: 72 Copynumber: 2.7 Consensus size: 72
261579 ATGCAGATGA
* * * * * * *
261589 TTATCTCACTCAA-ATTTGTTTTTCTTAAA-ATATACTTTGTCTCACTTGAGACTGTTTTTCTCA
1 TTATTTCACTCAAGA-TCGTTTTTCTTAAACA-AGATTTTGTCTCGCTTGAGACCGTTTTACTCA
261652 AAAGAAGAT
64 AAAGAAGAT
*
261661 TTATTTCACTCAAGATCGTTTTTCTTAAAACAAGA-TTTGTCTCGCTTGAGACCGTTTTCACTCG
1 TTATTTCACTCAAGATCGTTTTTCTT-AAACAAGATTTTGTCTCGCTTGAGACCGTTTT-ACTCA
261725 AAAGAAGGCAT
64 AAAGAA-G-AT
* * * * *
261736 TTCATTTCACTCAAG-GCTGTTTTTTTTAAAGAAGATTTTATCTTGCTTGAGA
1 TT-ATTTCACTCAAGATC-GTTTTTCTTAAACAAGATTTTGTCTCGCTTGAGA
261788 TAGTTTCCCT
Statistics
Matches: 106, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
72 43 0.41
73 15 0.14
74 2 0.02
75 12 0.11
76 34 0.32
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (72 bp):
TTATTTCACTCAAGATCGTTTTTCTTAAACAAGATTTTGTCTCGCTTGAGACCGTTTTACTCAAA
AGAAGAT
Found at i:261824 original size:39 final size:39
Alignment explanation
Indices: 261781--261933 Score: 110
Period size: 39 Copynumber: 3.6 Consensus size: 39
261771 TTTTATCTTG
*
261781 CTTGAGATAGTTTCCCTCAAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCAAAACAGAAAATTTTGTCTCC
* * *
261820 CTTGAGACAGTTTCTCTTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTC
1 CTTGAGACAGTTTC-CCTCAAAACA--------G-AA--AATTTTGTCTC-C
* *
261872 C-TGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCAAAACAGAAAATTTTGTCTCC
* *
261910 CTTGAGACAGTTTCTCTTAAAACA
1 CTTGAGACAGTTTCCCTCAAAACA
261934 TAAACATTGA
Statistics
Matches: 87, Mismatches: 13, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
38 2 0.02
39 41 0.47
40 8 0.09
41 2 0.02
42 1 0.01
48 1 0.01
49 2 0.02
50 7 0.08
51 21 0.24
52 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (39 bp):
CTTGAGACAGTTTCCCTCAAAACAGAAAATTTTGTCTCC
Found at i:262019 original size:107 final size:104
Alignment explanation
Indices: 261836--262156 Score: 481
Period size: 107 Copynumber: 3.1 Consensus size: 104
261826 ACAGTTTCTC
*
261836 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCC-TGAGATAGTTTCCCTCGAAACAGAAAA
1 TTGAAAACATTTCCCTTGAAA-TGATTTTTTCTCTCCTTGAGATAGTTTCCCTCGAAACAGAAAA
261900 TTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACATAAACA
65 TTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACATAAACA
261940 TTGAAAACATTTCCCTTGAAATGATTTTTTTTCTCTCTCTTGAGATAGTTTCCCTCGAAACAGAA
1 TTGAAAACATTTCCCTTGAAATGA--TTTTTTCTCTC-CTTGAGATAGTTTCCCTCGAAACAGAA
* *
262005 AATTTTATCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
63 AATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACATAAACA
* * *
262047 TTGAAAACATTTCCCTTGAAATGAATTTTATCTC-GCTTGAGATAGTTTCCCTTGAAAC-G--AA
1 TTGAAAACATTTCCCTTGAAATG-ATTTTTTCTCTCCTTGAGATAGTTTCCCTCGAAACAGAAAA
** *
262108 TTTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
65 TTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACATAAACA
262148 TTGAAAACA
1 TTGAAAACA
262157 ATTTAACGAA
Statistics
Matches: 202, Mismatches: 10, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
101 47 0.23
103 3 0.01
104 43 0.21
105 11 0.05
106 9 0.04
107 88 0.44
108 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGATTTTTTCTCTCCTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTAAAACATAAACA
Found at i:262103 original size:36 final size:36
Alignment explanation
Indices: 262056--262131 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
262046 ATTGAAAACA
* * *
262056 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
262092 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
262128 TTTC
1 TTTC
262132 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:262531 original size:105 final size:105
Alignment explanation
Indices: 262331--262961 Score: 957
Period size: 105 Copynumber: 6.0 Consensus size: 105
262321 ATATCGTGAC
* * * * * *
262331 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
262396 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
262437 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
262502 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
262542 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
262607 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
262647 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
262712 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
262752 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGATCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
262813 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * *
262852 ACTCGAGACAACACAAGTTCAACTTCACAACGAAAGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
** * * * *
262917 GGTTCCAGAGTCAATTTCAACTTCACGACGGAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
262958 ACTC
1 ACTC
262962 GGAACAATGC
Statistics
Matches: 490, Mismatches: 29, Indels: 12
0.92 0.05 0.02
Matches are distributed among these distances:
100 80 0.16
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 311 0.63
106 86 0.18
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:263598 original size:37 final size:37
Alignment explanation
Indices: 263504--263608 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
263494 CATTTTCATC
*
263504 CTACTAGGATTCAAACTCCTAAAAATATGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
263541 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
263578 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
263609 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:264003 original size:18 final size:17
Alignment explanation
Indices: 263964--264006 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
263954 ATTATATGGA
263964 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
263980 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
263998 TATTATTAT
1 TATTATTAT
264007 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:266348 original size:23 final size:23
Alignment explanation
Indices: 266320--266375 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
266310 ATAACTGCTC
266320 CTAACAGCTTCCTAACTACACAA
1 CTAACAGCTTCCTAACTACACAA
266343 CTAACAGCTTCCTAACTACACAA
1 CTAACAGCTTCCTAACTACACAA
*
266366 CTAACTGCTT
1 CTAACAGCTT
266376 ACATCAGCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.36, C:0.34, G:0.05, T:0.25
Consensus pattern (23 bp):
CTAACAGCTTCCTAACTACACAA
Found at i:266683 original size:19 final size:18
Alignment explanation
Indices: 266655--266707 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
266645 ATATTATTCT
266655 CTAAAAATTATAATTTAA
1 CTAAAAATTATAATTTAA
* *
266673 CTAAAATATTATTATAT-A
1 CTAAAA-ATTATAATTTAA
266691 -TAAAAAATTATAATTTA
1 CT-AAAAATTATAATTTA
266708 CATCCCACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 9 0.32
18 11 0.39
19 8 0.29
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
CTAAAAATTATAATTTAA
Found at i:267105 original size:2 final size:2
Alignment explanation
Indices: 267098--267150 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
267088 CTTTTGAGTT
267098 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
267140 TA TA TA TA TA T
1 TA TA TA TA TA T
267151 GAAGAGTTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:273743 original size:3 final size:3
Alignment explanation
Indices: 273735--273771 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
273725 TTCAAAGCTT
273735 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
273772 GTACCCTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:273922 original size:22 final size:21
Alignment explanation
Indices: 273892--273932 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
273882 TATTTAAATT
*
273892 ATAATATTTATTAATTAAAAAA
1 ATAAAATTT-TTAATTAAAAAA
*
273914 ATAAAATTTTTATTTAAAA
1 ATAAAATTTTTAATTAAAA
273933 TTAATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAAAATTTTTAATTAAAAAA
Found at i:278234 original size:32 final size:33
Alignment explanation
Indices: 278172--278245 Score: 116
Period size: 32 Copynumber: 2.3 Consensus size: 33
278162 AAACCCGAAC
*
278172 CCGACCCGAATATCACACTTAAAAAAACCTGA-
1 CCGACCCGAATATCAAACTTAAAAAAACCTGAT
278204 CCTGACCCGAATATCAAACTT-AAAAAACCTGAT
1 CC-GACCCGAATATCAAACTTAAAAAAACCTGAT
278237 CCGACCCGA
1 CCGACCCGA
278246 TTTTTTTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
32 20 0.51
33 19 0.49
ACGTcount: A:0.41, C:0.32, G:0.11, T:0.16
Consensus pattern (33 bp):
CCGACCCGAATATCAAACTTAAAAAAACCTGAT
Found at i:278300 original size:32 final size:34
Alignment explanation
Indices: 278245--278310 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 34
278235 ATCCGACCCG
* *
278245 ATTTTTTTAAAAAAATCCGACCCG-ATCCCAAAAT
1 ATTTTTTT-AAAAAATCCAACCCGAATACCAAAAT
*
278279 ATTTTTTT-AAAATTCCAACCCGAATACCAAAA
1 ATTTTTTTAAAAAATCCAACCCGAATACCAAAA
278311 GATTGATGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 12 0.43
33 8 0.29
34 8 0.29
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (34 bp):
ATTTTTTTAAAAAATCCAACCCGAATACCAAAAT
Found at i:278779 original size:21 final size:21
Alignment explanation
Indices: 278754--278797 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
278744 GAAAATATTA
*
278754 AAAAATATTAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
278775 AAAAATAATAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
278796 AA
1 AA
278798 TTTTTACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAAT
Found at i:279077 original size:12 final size:11
Alignment explanation
Indices: 279044--279068 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
279034 CCACATCGAA
279044 TTAATTAATTT
1 TTAATTAATTT
279055 TTAATTAATTT
1 TTAATTAATTT
279066 TTA
1 TTA
279069 GTTAGATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTAATTAATTT
Found at i:284571 original size:72 final size:72
Alignment explanation
Indices: 284454--284598 Score: 281
Period size: 72 Copynumber: 2.0 Consensus size: 72
284444 CGTAGTATTC
*
284454 AATATTCGTGATTATTTCTGAATTCCATGAATTTGTTTGGATGCTTATTTAGTGGTGAATTAGAA
1 AATATTCGTGATTATTTCTGAATTCCATGAATTTGTTTGGATGCTTATTTAGTAGTGAATTAGAA
284519 ATTCCGA
66 ATTCCGA
284526 AATATTCGTGATTATTTCTGAATTCCATGAATTTGTTTGGATGCTTATTTAGTAGTGAATTAGAA
1 AATATTCGTGATTATTTCTGAATTCCATGAATTTGTTTGGATGCTTATTTAGTAGTGAATTAGAA
284591 ATTCCGA
66 ATTCCGA
284598 A
1 A
284599 GGAATTTATG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.43
Consensus pattern (72 bp):
AATATTCGTGATTATTTCTGAATTCCATGAATTTGTTTGGATGCTTATTTAGTAGTGAATTAGAA
ATTCCGA
Found at i:289127 original size:23 final size:23
Alignment explanation
Indices: 289083--289127 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
289073 TCTATCTTTG
* **
289083 TGACATGTTTTTCTTTGTTCTTA
1 TGACATATTTTTCTTTACTCTTA
*
289106 TGACATATTTTTTTTTACTCTT
1 TGACATATTTTTCTTTACTCTT
289128 GTGGCTTGTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.16, C:0.13, G:0.09, T:0.62
Consensus pattern (23 bp):
TGACATATTTTTCTTTACTCTTA
Found at i:297118 original size:2 final size:2
Alignment explanation
Indices: 297111--297153 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
297101 AATCTGCAAC
297111 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
297153 A
1 A
297154 ATAATGAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:299955 original size:23 final size:23
Alignment explanation
Indices: 299928--299979 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
299918 AAAAAGCGAA
* *
299928 AAACATATCATAAAGACAGAGAT
1 AAACATATCACAAAAACAGAGAT
* * *
299951 AAACATGTCACAAAAACATATAT
1 AAACATATCACAAAAACAGAGAT
299974 AAACAT
1 AAACAT
299980 GCAACACAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.58, C:0.15, G:0.08, T:0.19
Consensus pattern (23 bp):
AAACATATCACAAAAACAGAGAT
Found at i:300324 original size:28 final size:28
Alignment explanation
Indices: 300293--300346 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
300283 TTGATAAAAA
* *
300293 AATTTATTCTATATAAATTG-TCGAATTC
1 AATTTATT-TATACAAACTGCTCGAATTC
300321 AATTTATTTATACAAACTGCTCGAAT
1 AATTTATTTATACAAACTGCTCGAAT
300347 GACCATTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (28 bp):
AATTTATTTATACAAACTGCTCGAATTC
Found at i:301618 original size:22 final size:22
Alignment explanation
Indices: 301590--301633 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
301580 AAAGCATGTG
301590 TATTTTTGCATTAGAAACTTAC
1 TATTTTTGCATTAGAAACTTAC
301612 TATTTTTGCATTAGAAACTTAC
1 TATTTTTGCATTAGAAACTTAC
301634 CAGGTCAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (22 bp):
TATTTTTGCATTAGAAACTTAC
Found at i:307678 original size:21 final size:21
Alignment explanation
Indices: 307648--307695 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
307638 TAATTTTCAA
*
307648 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
307669 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
307690 ACATTG
1 ACATTG
307696 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:312317 original size:21 final size:21
Alignment explanation
Indices: 312287--312334 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
312277 TAATTTTCAA
*
312287 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
312308 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
312329 ACATTG
1 ACATTG
312335 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:313414 original size:37 final size:37
Alignment explanation
Indices: 313364--313474 Score: 204
Period size: 37 Copynumber: 3.0 Consensus size: 37
313354 AGAAACCATC
*
313364 TTTAAGAGATTCTCTAGCATCGATAATACACCTCCAA
1 TTTAAGAGATTCTCTAGCAACGATAATACACCTCCAA
*
313401 TTTAAGAGATTCTCTAGCAACAATAATACACCTCCAA
1 TTTAAGAGATTCTCTAGCAACGATAATACACCTCCAA
313438 TTTAAGAGATTCTCTAGCAACGATAATACACCTCCAA
1 TTTAAGAGATTCTCTAGCAACGATAATACACCTCCAA
313475 GCAAATGAAG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 71 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (37 bp):
TTTAAGAGATTCTCTAGCAACGATAATACACCTCCAA
Found at i:318708 original size:2 final size:2
Alignment explanation
Indices: 318703--318771 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
318693 ATTCGAAAAC
318703 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
318745 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
318772 CAGGGCGGAG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:319305 original size:30 final size:32
Alignment explanation
Indices: 319269--319344 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 32
319259 TGATTGTCAC
*
319269 TGACATGATAA-ATCTTATATATTCAAA-TGA
1 TGACATGATAACATATTATATATTCAAAGTGA
* *
319299 TGACATGA-AACATATTATATGTTTAAAGTGA
1 TGACATGATAACATATTATATATTCAAAGTGA
*
319330 AGACATGAT-ACATAT
1 TGACATGATAACATAT
319345 CATGTGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 2 0.05
30 21 0.54
31 16 0.41
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.34
Consensus pattern (32 bp):
TGACATGATAACATATTATATATTCAAAGTGA
Found at i:320816 original size:3 final size:3
Alignment explanation
Indices: 320808--320837 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
320798 AACTATATAA
320808 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
320838 TCATGCAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:323585 original size:2 final size:2
Alignment explanation
Indices: 323578--323615 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
323568 AACTAAACAA
323578 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
323616 CATTTTGGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:324631 original size:17 final size:18
Alignment explanation
Indices: 324609--324655 Score: 78
Period size: 18 Copynumber: 2.6 Consensus size: 18
324599 CCATAATAAA
324609 AAATATTAAAAAGAAA-T
1 AAATATTAAAAAGAAATT
324626 AAATATTAGAAAAGAAATT
1 AAATATTA-AAAAGAAATT
324645 AAATATTAAAA
1 AAATATTAAAA
324656 GCATGTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.29
18 11 0.39
19 9 0.32
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (18 bp):
AAATATTAAAAAGAAATT
Found at i:324716 original size:30 final size:30
Alignment explanation
Indices: 324665--324747 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
324655 AGCATGTTTG
*
324665 TAATAACAAATATTGAAAAAAATTTAGCCCA
1 TAATAACAAATATT-AAAAAAATTGAGCCCA
* * **
324696 TAATAATAATTATTAAAAAAATTGAGCCTT
1 TAATAACAAATATTAAAAAAATTGAGCCCA
324726 TAATAACAAATATTAGAAAAAA
1 TAATAACAAATATTA-AAAAAA
324748 AATATTGACA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 26 0.59
31 18 0.41
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.29
Consensus pattern (30 bp):
TAATAACAAATATTAAAAAAATTGAGCCCA
Found at i:325308 original size:37 final size:37
Alignment explanation
Indices: 325261--325337 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
325251 TGTTTCTTAG
325261 TATAATCTTAAATTCTGAATGTTAACTATTTTAATCT
1 TATAATCTTAAATTCTGAATGTTAACTATTTTAATCT
325298 TATAATCTTAAATTCTGAATGTTAACTATTTTAATCT
1 TATAATCTTAAATTCTGAATGTTAACTATTTTAATCT
325335 TAT
1 TAT
325338 CTTAACTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.49
Consensus pattern (37 bp):
TATAATCTTAAATTCTGAATGTTAACTATTTTAATCT
Found at i:325366 original size:30 final size:29
Alignment explanation
Indices: 325332--325600 Score: 160
Period size: 30 Copynumber: 9.2 Consensus size: 29
325322 ACTATTTTAA
*
325332 TCTTATCTTAACTTATAAAATGTATTTTGT
1 TCTTATCTTAACTTATAAAATATATTTT-T
*
325362 TCTTACCTTAACTTA-AAAATATATTTATT
1 TCTTATCTTAACTTATAAAATATATTT-TT
* * * *
325391 T-TTATCTTAACTTGTTACATATATTATAT
1 TCTTATCTTAACTTATAAAATATATT-TTT
* * * *
325420 TCTTAACTTAAATTATTAAATATATTATAT
1 TCTTATCTTAACTTATAAAATATATT-TTT
* * *
325450 TCTTACCTTAAATTATTAAATATTATTTATT
1 TCTTATCTTAACTTATAAAATA-TATTT-TT
*
325481 T-TTATCTTAACTTA-AAAATATA-TATT
1 TCTTATCTTAACTTATAAAATATATTTTT
**
325507 T-TTAGT-TTAGTTTA-AAAATGTATATTTTAT
1 TCTTA-TCTTAACTTATAAAA--TATATTTT-T
* * ***
325537 TCTTATTTTAAGTTGGGAAATATATTTTAT
1 TCTTATCTTAACTTATAAAATATATTTT-T
* *
325567 TTTTATCTTAAC-TATAAAAAATATTTTT
1 TCTTATCTTAACTTATAAAATATATTTTT
325595 ATCTTA
1 -TCTTA
325601 ATTTTAAAAT
Statistics
Matches: 192, Mismatches: 32, Indels: 31
0.75 0.13 0.12
Matches are distributed among these distances:
26 16 0.08
27 2 0.01
28 18 0.09
29 44 0.23
30 95 0.49
31 14 0.07
32 3 0.02
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.53
Consensus pattern (29 bp):
TCTTATCTTAACTTATAAAATATATTTTT
Found at i:325490 original size:60 final size:58
Alignment explanation
Indices: 325327--325503 Score: 158
Period size: 58 Copynumber: 3.0 Consensus size: 58
325317 TGTTAACTAT
* * * * * * * * *
325327 TTTAATCTTATCTTAACTTATAAAATGTATTTTGTTCTTACCTTAACTTAAAAATATA
1 TTTATTCTTACCTTAAATTATTAAATATATTATATTCTTAACTTAAATTAAAAATATA
* * * * * *
325385 TTTATTTTTATCTTAACTTGTTACATATATTATATTCTTAACTTAAATTATTAAATATA
1 TTTATTCTTACCTTAAATTATTAAATATATTATATTCTTAACTTAAATTA-AAAATATA
* * *
325444 TTATATTCTTACCTTAAATTATTAAATATTATT-TATTTTTATCTTAACTTAAAAATATA
1 TT-TATTCTTACCTTAAATTATTAAATA-TATTATATTCTTAACTTAAATTAAAAATATA
325503 T
1 T
325504 ATTTTTAGTT
Statistics
Matches: 96, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
58 40 0.42
59 17 0.18
60 35 0.36
61 4 0.04
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.52
Consensus pattern (58 bp):
TTTATTCTTACCTTAAATTATTAAATATATTATATTCTTAACTTAAATTAAAAATATA
Found at i:326272 original size:31 final size:31
Alignment explanation
Indices: 326207--326285 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
326197 TAGTCTACCC
*
326207 TAATAAATATTAGAAAAAAATTGAACCTACAA
1 TAATAAATATTA-AAAAAAATTAAACCTACAA
* * **
326239 TAATAAATATTAAAAAAATTTAAACTTTTAA
1 TAATAAATATTAAAAAAAATTAAACCTACAA
*
326270 TAACAAATATTAAAAA
1 TAATAAATATTAAAAA
326286 TAATCGGGCC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 29 0.71
32 12 0.29
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (31 bp):
TAATAAATATTAAAAAAAATTAAACCTACAA
Found at i:326575 original size:13 final size:13
Alignment explanation
Indices: 326557--326582 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
326547 AAATTATTAC
326557 TTTTAATAATTTA
1 TTTTAATAATTTA
326570 TTTTAATAATTTA
1 TTTTAATAATTTA
326583 AAAATAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTAATAATTTA
Found at i:327130 original size:28 final size:30
Alignment explanation
Indices: 327065--327143 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 30
327055 AATAAATACA
* * *
327065 AAAATTTACATAATATTTTATATTAAGAGAT
1 AAAATTT-TATAATATTTTAAAATAAGAGAT
327096 -AAA-TTTATAATATTTTAAAATAA-A-AT
1 AAAATTTTATAATATTTTAAAATAAGAGAT
327122 AAAATTTTA-AAT-TTTTAAAATA
1 AAAATTTTATAATATTTTAAAATA
327144 TAAAATATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
26 12 0.28
27 7 0.16
28 19 0.44
29 2 0.05
30 3 0.07
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (30 bp):
AAAATTTTATAATATTTTAAAATAAGAGAT
Found at i:327147 original size:7 final size:7
Alignment explanation
Indices: 327137--327191 Score: 69
Period size: 7 Copynumber: 8.1 Consensus size: 7
327127 TTTAAATTTT
327137 TAAAATA
1 TAAAATA
327144 TAAAATA
1 TAAAATA
327151 TAAAATA
1 TAAAATA
327158 TAAAA-A
1 TAAAATA
*
327164 TAAATTA
1 TAAAATA
*
327171 T-TAATA
1 TAAAATA
*
327177 GAAAATA
1 TAAAATA
327184 TAAAATA
1 TAAAATA
327191 T
1 T
327192 TTGAAGTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
6 8 0.20
7 32 0.80
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (7 bp):
TAAAATA
Found at i:327168 original size:26 final size:26
Alignment explanation
Indices: 327137--327188 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
327127 TTTAAATTTT
* *
327137 TAAAATATAAAATATAAAATATAAAAA
1 TAAATTAT-AAATAGAAAATATAAAAA
*
327164 TAAATTATTAATAGAAAATATAAAA
1 TAAATTATAAATAGAAAATATAAAA
327189 TATTTGAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (26 bp):
TAAATTATAAATAGAAAATATAAAAA
Found at i:328152 original size:19 final size:20
Alignment explanation
Indices: 328128--328202 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
328118 AAATGATCAA
328128 CAAATTCGCAACGCGATCT-
1 CAAATTCGCAACGCGATCTC
* *
328147 CAAATTCGCAACGTGAACTC
1 CAAATTCGCAACGCGATCTC
* * *
328167 CAATTTCGCAAC-CCAGTTTC
1 CAAATTCGCAACGCGA-TCTC
328187 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
328203 ATACGTGAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 18 0.41
20 24 0.55
21 2 0.05
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGATCTC
Found at i:328176 original size:20 final size:19
Alignment explanation
Indices: 328128--328178 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
328118 AAATGATCAA
*
328128 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACGCGAACT
*
328147 CAAATTCGCAACGTGAACT
1 CAAATTCGCAACGCGAACT
*
328166 CCAATTTCGCAAC
1 -CAAATTCGCAAC
328179 CCAGTTTCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (19 bp):
CAAATTCGCAACGCGAACT
Found at i:328235 original size:20 final size:20
Alignment explanation
Indices: 328212--328289 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
328202 AATACGTGAA
328212 TCGCAACAAAGAAGTCAAAT
1 TCGCAACAAAGAAGTCAAAT
* *
328232 TCGCAAC--TGAATATCAAAT
1 TCGCAACAAAGAA-GTCAAAT
*
328251 TCGCAACACAA-AAGTTAAAT
1 TCGCAACA-AAGAAGTCAAAT
*
328271 TCGCAACACAGAAGTCAAA
1 TCGCAACAAAGAAGTCAAA
328290 GCGCGTTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
18 3 0.07
19 14 0.30
20 27 0.59
21 2 0.04
ACGTcount: A:0.47, C:0.22, G:0.13, T:0.18
Consensus pattern (20 bp):
TCGCAACAAAGAAGTCAAAT
Found at i:328911 original size:20 final size:20
Alignment explanation
Indices: 328834--328907 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
328824 TCACGTTGCG
328834 ATTTTCG-AGTTGCGATTTTC
1 ATTTTCGCA-TTGCGATTTTC
328854 ATTTTCGCATTGCGATTTTC
1 ATTTTCGCATTGCGATTTTC
*
328874 ATTTTCGCGTTGCGATTTTC
1 ATTTTCGCATTGCGATTTTC
328894 A-TTTCGCATTGCGA
1 ATTTTCGCATTGCGA
328908 ATTTAAGTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
19 12 0.24
20 38 0.75
21 1 0.02
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47
Consensus pattern (20 bp):
ATTTTCGCATTGCGATTTTC
Found at i:330863 original size:4 final size:4
Alignment explanation
Indices: 330854--330895 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
330844 TTTTTTGGCA
* * *
330854 TTAT TTAT TTAT TTAT TTAC TTAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
330896 TCAGCGATCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:331067 original size:21 final size:21
Alignment explanation
Indices: 331041--331157 Score: 105
Period size: 21 Copynumber: 5.6 Consensus size: 21
331031 TGCACCTGTC
*
331041 ATCGTTCAAGAGGCGCATCCT
1 ATCGTTCAAGAGGCCCATCCT
*
331062 ATCGTTCAAGAGGCCCCT-CT
1 ATCGTTCAAGAGGCCCATCCT
* *
331082 CATCGTTCAAAAGGCCCATCCC
1 -ATCGTTCAAGAGGCCCATCCT
* **
331104 ACCGTTCAAGAGGCCC-TTGT
1 ATCGTTCAAGAGGCCCATCCT
*
331124 CATCGTTCAAGAGGTCCC-TCCC
1 -ATCGTTCAAGAGG-CCCATCCT
*
331146 ACCGTTCAAGAG
1 ATCGTTCAAGAG
331158 CCCGATTCAC
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
20 3 0.04
21 69 0.90
22 5 0.06
ACGTcount: A:0.23, C:0.34, G:0.21, T:0.22
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCATCCT
Found at i:331086 original size:42 final size:42
Alignment explanation
Indices: 331039--331157 Score: 168
Period size: 42 Copynumber: 2.8 Consensus size: 42
331029 GATGCACCTG
* * *
331039 TCATCGTTCAAGAGGCGCATCCTATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCATCCCACCGTTCAAGAGGCCCCTC
* * *
331081 TCATCGTTCAAAAGGCCCATCCCACCGTTCAAGAGGCCCTTG
1 TCATCGTTCAAGAGGCCCATCCCACCGTTCAAGAGGCCCCTC
331123 TCATCGTTCAAGAGGTCCC-TCCCACCGTTCAAGAG
1 TCATCGTTCAAGAGG-CCCATCCCACCGTTCAAGAG
331158 CCCGATTCAC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 66 0.96
43 3 0.04
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCATCCCACCGTTCAAGAGGCCCCTC
Found at i:332645 original size:64 final size:64
Alignment explanation
Indices: 332530--332687 Score: 273
Period size: 64 Copynumber: 2.5 Consensus size: 64
332520 TTAATTGAAT
*
332530 TTTACATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATTAGAATTATTTTTTGCTTG
1 TTTA-ATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
*
332595 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGCA-TAAATAAGAATTATTTTTTGCTTG
1 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATG-AGGAAATAAGAATTATTTTTTGCTTG
332659 TTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTAATTGATTTGTAAAAGTTGATTTGTT
332688 GTTTATTTAA
Statistics
Matches: 90, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
64 85 0.94
65 5 0.06
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.51
Consensus pattern (64 bp):
TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
Found at i:332808 original size:20 final size:20
Alignment explanation
Indices: 332784--332877 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
332774 TTTTTTCGTT
* *
332784 GTGATAGTCAAATTCGCAAT
1 GTGAAAGTCAAATTCGCAAC
*
332804 GTGATAGTCAAATTCGCAAC
1 GTGAAAGTCAAATTCGCAAC
* *
332824 GTTAAAGTCAAATGCGCAAC
1 GTGAAAGTCAAATTCGCAAC
* *
332844 GTTAAAGTCAAATTCACAAC
1 GTGAAAGTCAAATTCGCAAC
*
332864 GCGAAAGTCAAATT
1 GTGAAAGTCAAATT
332878 TGCATTGCGA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (20 bp):
GTGAAAGTCAAATTCGCAAC
Found at i:333239 original size:18 final size:18
Alignment explanation
Indices: 333216--333251 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
333206 AAGCCGGTTG
*
333216 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
333234 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
333252 CCTTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:335568 original size:24 final size:24
Alignment explanation
Indices: 335510--335569 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
335500 CTAAAACATC
*
335510 ATCAAAATCCGAGTATTTACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
335534 ATCCAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
335558 ATCAAATTCCGA
1 ATCAAAATCCGA
335570 ATACTGACTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:336338 original size:14 final size:15
Alignment explanation
Indices: 336302--336339 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
336292 GAAATCATTG
336302 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
336317 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
336332 AAAAATTA
1 AAAAATTA
336340 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:336540 original size:20 final size:19
Alignment explanation
Indices: 336496--336587 Score: 87
Period size: 19 Copynumber: 4.7 Consensus size: 19
336486 ACTAAAACCT
* *
336496 GTTGCGAAATT-AAATTCA
1 GTTGCGAATTTGAAAATCA
*
336514 TGTTGCGAATTCGAAAATCGA
1 -GTTGCGAATTTGAAAATC-A
*
336535 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAAATCA
* *
336554 GTTGCGAATTTGAAATTTA
1 GTTGCGAATTTGAAAATCA
336573 GTGTTGCGAATTTGA
1 --GTTGCGAATTTGA
336588 CTTATGTGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
19 28 0.44
20 21 0.33
21 14 0.22
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.36
Consensus pattern (19 bp):
GTTGCGAATTTGAAAATCA
Found at i:336579 original size:40 final size:40
Alignment explanation
Indices: 336495--336587 Score: 118
Period size: 39 Copynumber: 2.4 Consensus size: 40
336485 AACTAAAACC
* *
336495 TGTTGCGAAATT-AAATTCATGTTGCGAATTCGAAAATCG
1 TGTTGCGAATTTGAAATTCATGTTGCGAATTCGAAAATAG
* * *
336534 AGTTGCGAATTTGAAATTCA-GTTGCGAATTTGAAATTTAG
1 TGTTGCGAATTTGAAATTCATGTTGCGAATTCGAAA-ATAG
336574 TGTTGCGAATTTGA
1 TGTTGCGAATTTGA
336588 CTTATGTGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 24 0.52
40 22 0.48
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.37
Consensus pattern (40 bp):
TGTTGCGAATTTGAAATTCATGTTGCGAATTCGAAAATAG
Found at i:336618 original size:19 final size:21
Alignment explanation
Indices: 336495--336620 Score: 99
Period size: 20 Copynumber: 6.4 Consensus size: 21
336485 AACTAAAACC
* *
336495 TGTTGCGAAATT-AAATTC-A
1 TGTTGCGAATTTGAAATTCTG
* *
336514 TGTTGCGAATTCGAAAATC-G
1 TGTTGCGAATTTGAAATTCTG
*
336534 AGTTGCGAATTTGAAATTC--
1 TGTTGCGAATTTGAAATTCTG
*
336553 AGTTGCGAATTTGAAATT-TAG
1 TGTTGCGAATTTGAAATTCT-G
* *
336574 TGTTGCGAATTTG-ACTTATG
1 TGTTGCGAATTTGAAATTCTG
*
336594 TGTTGCGAATTTG-ACTTCT-
1 TGTTGCGAATTTGAAATTCTG
336613 TGTTGCGA
1 TGTTGCGA
336621 TTTTCTAAAT
Statistics
Matches: 92, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
19 36 0.39
20 43 0.47
21 13 0.14
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (21 bp):
TGTTGCGAATTTGAAATTCTG
Found at i:336640 original size:21 final size:21
Alignment explanation
Indices: 336614--336664 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
336604 TTGACTTCTT
*
336614 GTTGCGATTTTCTAAATTCGA
1 GTTGCGATTTTCCAAATTCGA
*
336635 GTTGCGATTTTCCAAATTCGC
1 GTTGCGATTTTCCAAATTCGA
336656 GTTGCGATT
1 GTTGCGATT
336665 AACATATTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.41
Consensus pattern (21 bp):
GTTGCGATTTTCCAAATTCGA
Found at i:337123 original size:121 final size:121
Alignment explanation
Indices: 336916--337134 Score: 366
Period size: 121 Copynumber: 1.8 Consensus size: 121
336906 CACTAAAATC
**
336916 TGATTGTAAATATATGATTCTTCGATGACAAGAACAAATATTGATATAGTACTATATTAATTAAT
1 TGATTGTAAATATATGATTCTTCGATGACAAGAACAAATATTGATATAACACTATATTAATTAAT
* * *
336981 ATATAAATAATACTACATCACATTGAAACAATACTATTGTTGCCCACCTTAAAACG
66 ACATAAACAATACTACATCACATTAAAACAATACTATTGTTGCCCACCTTAAAACG
* * *
337037 TGATTGTAAATATATGATTCTTCGATGACTAGAATAAATATTTATATAACACTATATTAATTAAT
1 TGATTGTAAATATATGATTCTTCGATGACAAGAACAAATATTGATATAACACTATATTAATTAAT
337102 ACATAAACAATACTACATCACATTAAAACAATA
66 ACATAAACAATACTACATCACATTAAAACAATA
337135 GTGTTGTCTA
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 90 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.34
Consensus pattern (121 bp):
TGATTGTAAATATATGATTCTTCGATGACAAGAACAAATATTGATATAACACTATATTAATTAAT
ACATAAACAATACTACATCACATTAAAACAATACTATTGTTGCCCACCTTAAAACG
Found at i:337341 original size:2 final size:2
Alignment explanation
Indices: 337300--337328 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
337290 GCCTAACATC
337300 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 T
337329 GAAAAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:338278 original size:3 final size:3
Alignment explanation
Indices: 338265--338331 Score: 77
Period size: 3 Copynumber: 22.7 Consensus size: 3
338255 AAGACCCTTT
* *
338265 TTA TT- TTA TTA TTA TTA TTTA TTA ATA TTA TTGA -TA TAA TTA -TA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TT-A TTA TTA TTA TTA
338309 TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
338332 TATTTTCACA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
2 5 0.09
3 46 0.84
4 4 0.07
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:339096 original size:33 final size:33
Alignment explanation
Indices: 339055--339305 Score: 295
Period size: 33 Copynumber: 7.4 Consensus size: 33
339045 ATTTCAGCCT
* *
339055 TAACATTTTATTTTGTGGTTCATACTAACATAC
1 TAACATTTTATTTTATTGTTCATACTAACATAC
* * * *
339088 AAACATTTTATTTTATTATTCGTATTAACATAC
1 TAACATTTTATTTTATTGTTCATACTAACATAC
**
339121 TAACATTTTATTTTATTGTTTGTACTAACATAC
1 TAACATTTTATTTTATTGTTCATACTAACATAC
339154 TAACATTTTATTTTATTGTTCATACTAACATAC
1 TAACATTTTATTTTATTGTTCATACTAACATAC
*
339187 TAATATTTTATTTTATTGTTCATACTAACATAC
1 TAACATTTTATTTTATTGTTCATACTAACATAC
* * *
339220 TAATATTTTATTTTATTGTTCATGCTAACTTAC
1 TAACATTTTATTTTATTGTTCATACTAACATAC
* * * *
339253 TAATATTCTAACTTTTATTTTGTTGTTTATATTAACTTAC
1 T-A-A--C--A-TTTTATTTTATTGTTCATACTAACATAC
339293 TAACATTTTATTT
1 TAACATTTTATTT
339306 ATTTGCTCAA
Statistics
Matches: 191, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
33 159 0.83
34 2 0.01
35 1 0.01
36 1 0.01
38 1 0.01
39 2 0.01
40 25 0.13
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.52
Consensus pattern (33 bp):
TAACATTTTATTTTATTGTTCATACTAACATAC
Found at i:339558 original size:28 final size:28
Alignment explanation
Indices: 339505--339558 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
339495 ATTTTTATGT
* * *
339505 TCCTTTAATTTCCTGCATTTTGTTTTAG
1 TCCTTTAATTTCCAGCATCTTATTTTAG
339533 TCCTTTAATATTCCAGCA-CTTATTTT
1 TCCTTTAAT-TTCCAGCATCTTATTTT
339559 TCTGTGTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 15 0.68
29 7 0.32
ACGTcount: A:0.19, C:0.20, G:0.07, T:0.54
Consensus pattern (28 bp):
TCCTTTAATTTCCAGCATCTTATTTTAG
Found at i:341594 original size:2 final size:2
Alignment explanation
Indices: 341589--341650 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
341579 ATTTCCAACA
341589 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
341631 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
341651 TTTGTTTCCT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:343303 original size:14 final size:15
Alignment explanation
Indices: 343284--343312 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
343274 CAATTTAAAA
343284 TGAGGAT-TATGGTT
1 TGAGGATGTATGGTT
343298 TGAGGATGTATGGTT
1 TGAGGATGTATGGTT
343313 GAATTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (15 bp):
TGAGGATGTATGGTT
Found at i:344785 original size:43 final size:43
Alignment explanation
Indices: 344738--344824 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
344728 TTAATTAGAA
344738 TTACTTCTTAAACTCAATAATAAGTTTATTATAGACTAAAATT
1 TTACTTCTTAAACTCAATAATAAGTTTATTATAGACTAAAATT
* * *
344781 TTACTTCTTAAATTCAATAATGAGTTTATTATAGATTAAAATT
1 TTACTTCTTAAACTCAATAATAAGTTTATTATAGACTAAAATT
344824 T
1 T
344825 ATTGAGTGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (43 bp):
TTACTTCTTAAACTCAATAATAAGTTTATTATAGACTAAAATT
Found at i:347293 original size:2 final size:2
Alignment explanation
Indices: 347286--347329 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
347276 TCTTTAATTC
* * * *
347286 TA TA TA TA TA TA TA TA TA TA TA TT TC GA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
347328 TA
1 TA
347330 ATTATTGTCC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:352269 original size:14 final size:15
Alignment explanation
Indices: 352250--352279 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
352240 AGCATTTTTG
352250 TTAATT-ATATAATT
1 TTAATTGATATAATT
352264 TTAATTGATATAATT
1 TTAATTGATATAATT
352279 T
1 T
352280 AAATAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TTAATTGATATAATT
Found at i:356581 original size:32 final size:31
Alignment explanation
Indices: 356541--356632 Score: 139
Period size: 32 Copynumber: 2.9 Consensus size: 31
356531 TAAATTTCTG
* *
356541 TAAGTTTAAGGACTATTTTATACTAATTTGA
1 TAAGTTTAAAGACTATTTTATAATAATTTGA
*
356572 TAAGTTTTAAAGACTATTTTGTAATAATTTGA
1 TAAG-TTTAAAGACTATTTTATAATAATTTGA
*
356604 TAAGTTTAATGACTATTTTATAATAATTT
1 TAAGTTTAAAGACTATTTTATAATAATTT
356633 AATGATCATT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 27 0.49
32 28 0.51
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (31 bp):
TAAGTTTAAAGACTATTTTATAATAATTTGA
Found at i:356636 original size:22 final size:23
Alignment explanation
Indices: 356603--356649 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
356593 TAATAATTTG
356603 ATAAGTTTAATGA-CTATTTTATA
1 ATAAGTTTAATGATC-ATTTTATA
356626 ATAA-TTTAATGATCATTTTATA
1 ATAAGTTTAATGATCATTTTATA
356648 AT
1 AT
356650 TTTTTGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.49
Consensus pattern (23 bp):
ATAAGTTTAATGATCATTTTATA
Done.