Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008355.1 Hibiscus syriacus cultivar Beakdansim tig00111092_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: 983659
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:136208 original size:36 final size:36
Alignment explanation
Indices: 136112--136196 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
136102 TTAAGATACA
* **
136112 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
136148 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
136183 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
136197 TCAACTTTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 7 0.17
36 35 0.83
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:136335 original size:105 final size:102
Alignment explanation
Indices: 136148--136385 Score: 270
Period size: 105 Copynumber: 2.3 Consensus size: 102
136138 TAGAGAAATT
*
136148 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGA-AAACGATCTCAAGTGAGATCAACTTTGTTTAA
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAAATAAACGATCTCAAGTGAGATCAACTTTGTTTAA
* *
136211 TGCGAAACAAATTCGAAATTT-TGATCTCAAAGGGAAAAG
64 TGCGAAACAAATTCAAAATTTGT-ATCTCAAAGGAAAAAG
* *
136250 GTCTCAAGCGAGACGAAATTTGTTTTGAAATAAACAAGAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTGAAATAAAC--G-ATCTCAA-GTGAGATCAACTTTGTTT
* * * *
136314 -TTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
62 AAT-GCGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAAG
* *
136355 GTCTCAAGCGAGACGCAATTTGTTTTAAAAT
1 GTCTCAAGCGAGACGAAATTTGTTTTGAAAT
136386 TTTCAAAATT
Statistics
Matches: 117, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
101 7 0.06
102 22 0.19
103 3 0.03
104 4 0.03
105 80 0.68
106 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (102 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAAATAAACGATCTCAAGTGAGATCAACTTTGTTTAATG
CGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAAG
Found at i:136484 original size:36 final size:37
Alignment explanation
Indices: 136400--136508 Score: 114
Period size: 38 Copynumber: 2.9 Consensus size: 37
136390 AAAATTTGTG
*
136400 GAAAAATGTCTCAAGCGAGACATAATTTG-TTTTAGA
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAGA
* *
136436 GAGAAAGTTGTCTCAAGCGAGATAAAATTTGTTTTTA-A
1 GA-AAA-ATGTCTCAAGCGAGACAAAATTTGTTTTTAGA
* * * *
136474 GAAAACTGTCTCTAGTGAGACGAAACTTTGTTTTT
1 GAAAAATGTCTCAAGCGAGAC-AAAATTTGTTTTT
136509 TTAATAAGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
36 14 0.23
37 18 0.30
38 24 0.39
39 5 0.08
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (37 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAGA
Found at i:136893 original size:12 final size:14
Alignment explanation
Indices: 136844--136897 Score: 76
Period size: 14 Copynumber: 3.9 Consensus size: 14
136834 TTTATGTATC
136844 ATGTATGTATGTGT
1 ATGTATGTATGTGT
136858 ATGTATGTATGTATGT
1 ATGTATGTATG--TGT
136874 ATGTATGTATGTGT
1 ATGTATGTATGTGT
136888 -TG-ATGTATGT
1 ATGTATGTATGT
136898 TTTTCTCGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.21
13 2 0.05
14 14 0.37
16 14 0.37
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (14 bp):
ATGTATGTATGTGT
Found at i:136897 original size:4 final size:4
Alignment explanation
Indices: 136844--136885 Score: 70
Period size: 4 Copynumber: 11.0 Consensus size: 4
136834 TTTATGTATC
136844 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
136886 GTTGATGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
4 34 0.94
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:138099 original size:12 final size:11
Alignment explanation
Indices: 138071--138108 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
138061 TCCTCTTTTG
*
138071 TTCTTTGCTTT
1 TTCTTTGATTT
138082 TTCTTTGATTT
1 TTCTTTGATTT
138093 TTGCTTTGATTT
1 TT-CTTTGATTT
138105 TTCT
1 TTCT
138109 CTTTTCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:138125 original size:12 final size:12
Alignment explanation
Indices: 138066--138112 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
138056 CTTTGTCCTC
138066 TTTTGTTCTTTG-
1 TTTT-TTCTTTGA
*
138078 CTTTTTCTTTGA
1 TTTTTTCTTTGA
*
138090 TTTTTGCTTTGA
1 TTTTTTCTTTGA
138102 TTTTTCTCTTT
1 TTTTT-TCTTT
138113 TCTCTTTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 7 0.24
12 18 0.62
13 4 0.14
ACGTcount: A:0.04, C:0.13, G:0.11, T:0.72
Consensus pattern (12 bp):
TTTTTTCTTTGA
Found at i:138801 original size:20 final size:20
Alignment explanation
Indices: 138773--138814 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
138763 CAAAGAGAGG
*
138773 GAATGTTTCAAGGTCTAAAA
1 GAATATTTCAAGGTCTAAAA
*
138793 GAATATTTCAAGGTCTCAAA
1 GAATATTTCAAGGTCTAAAA
138813 GA
1 GA
138815 GATAGAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (20 bp):
GAATATTTCAAGGTCTAAAA
Found at i:138821 original size:26 final size:25
Alignment explanation
Indices: 138745--138824 Score: 89
Period size: 26 Copynumber: 3.3 Consensus size: 25
138735 TCGAGGTGGA
138745 AAGAATGTTTCAAGGTCTCAAAGAG
1 AAGAATGTTTCAAGGTCTCAAAGAG
*
138770 AGGGAATGTTTCAAGGTCT---A-A-
1 A-AGAATGTTTCAAGGTCTCAAAGAG
*
138791 AAGAATATTTCAAGGTCTCAAAGAG
1 AAGAATGTTTCAAGGTCTCAAAGAG
138816 ATAGAATGT
1 A-AGAATGT
138825 CAAAAATTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
20 15 0.34
21 1 0.02
22 1 0.02
23 2 0.05
24 1 0.02
25 2 0.05
26 22 0.50
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (25 bp):
AAGAATGTTTCAAGGTCTCAAAGAG
Found at i:143060 original size:29 final size:29
Alignment explanation
Indices: 143028--143087 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
143018 TGGTAATAAT
* * *
143028 AAATTAAAGGGCTAAAACAGAAAAATAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
* *
143057 AAATTAAAAGACTAAAATAGCAAAACAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
143086 AA
1 AA
143088 CGTAGGGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.65, C:0.08, G:0.13, T:0.13
Consensus pattern (29 bp):
AAATTAAAAGACTAAAACAGAAAAACAGA
Found at i:144707 original size:3 final size:3
Alignment explanation
Indices: 144688--144740 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
144678 ATGTAAAATG
*
144688 TAA TAT TAA TAA T-A TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
144733 TAA -AA TAA
1 TAA TAA TAA
144741 CGATAAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:145859 original size:2 final size:2
Alignment explanation
Indices: 145852--145888 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
145842 TAGCTTTTGT
145852 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 T
145889 GCTATTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:147269 original size:20 final size:20
Alignment explanation
Indices: 147244--147284 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
147234 TAAATTCAAC
147244 TCCTAATTATTATTTTAATA
1 TCCTAATTATTATTTTAATA
147264 TCCTAATTATTATTTTAATA
1 TCCTAATTATTATTTTAATA
147284 T
1 T
147285 ATTTATGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (20 bp):
TCCTAATTATTATTTTAATA
Found at i:152545 original size:19 final size:19
Alignment explanation
Indices: 152518--152562 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
152508 AAAAATAGTC
152518 AAAATCACAGTTTACCATA
1 AAAATCACAGTTTACCATA
* *
152537 AATATCACAGTTTACTATA
1 AAAATCACAGTTTACCATA
152556 AAAATCA
1 AAAATCA
152563 AATATATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.29
Consensus pattern (19 bp):
AAAATCACAGTTTACCATA
Found at i:154844 original size:16 final size:16
Alignment explanation
Indices: 154825--154865 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
154815 ATTTATAAGT
154825 ATATATATACTTATAC
1 ATATATATACTTATAC
*
154841 ATATGTATACTTATAC
1 ATATATATACTTATAC
*
154857 CTATATATA
1 ATATATATA
154866 TAATTACACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.44
Consensus pattern (16 bp):
ATATATATACTTATAC
Found at i:158101 original size:32 final size:32
Alignment explanation
Indices: 158065--158127 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
158055 AGGCGGGAGG
158065 GGTTATATAGTATATAACTTTAGAGCGGGACT
1 GGTTATATAGTATATAACTTTAGAGCGGGACT
*
158097 GGTTATATAGTATATAACTTTGGAGCGGGAC
1 GGTTATATAGTATATAACTTTAGAGCGGGAC
158128 AGGATTGGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (32 bp):
GGTTATATAGTATATAACTTTAGAGCGGGACT
Found at i:158249 original size:24 final size:24
Alignment explanation
Indices: 158215--158303 Score: 75
Period size: 23 Copynumber: 4.0 Consensus size: 24
158205 AATTTTTATT
158215 ATATATT-ATTTAATTATTATAAA
1 ATATATTAATTTAATTATTATAAA
**
158238 ATATATTAATTTAACCA-TATAAA
1 ATATATTAATTTAATTATTATAAA
* *
158261 ATATAATAA-AT-A-T-TTAT-AA
1 ATATATTAATTTAATTATTATAAA
* *
158280 ATATATTATTTTAATTATTTTAAA
1 ATATATTAATTTAATTATTATAAA
158304 TATTAATATA
Statistics
Matches: 50, Mismatches: 9, Indels: 13
0.69 0.12 0.18
Matches are distributed among these distances:
19 9 0.18
20 4 0.08
21 2 0.04
22 2 0.04
23 24 0.48
24 9 0.18
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATATTAATTTAATTATTATAAA
Found at i:163324 original size:17 final size:18
Alignment explanation
Indices: 163302--163352 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
163292 TCTTGATTTG
163302 TAATTGTAATATTATTA-
1 TAATTGTAATATTATTAT
163319 TAATTGTAATATT-TTAT
1 TAATTGTAATATTATTAT
*
163336 TAAATAGTAATATTATT
1 T-AATTGTAATATTATT
163353 GTAAGTGAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 3 0.10
17 14 0.47
18 11 0.37
19 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
TAATTGTAATATTATTAT
Found at i:163347 original size:18 final size:19
Alignment explanation
Indices: 163313--163349 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
163303 AATTGTAATA
*
163313 TTATTATAATTGTAATATT
1 TTATTATAATAGTAATATT
163332 TTATTA-AATAGTAATATT
1 TTATTATAATAGTAATATT
163350 ATTGTAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTATTATAATAGTAATATT
Found at i:165148 original size:2 final size:2
Alignment explanation
Indices: 165141--165173 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
165131 TTATCCCAGG
165141 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 T
165174 TGAAATCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:176684 original size:8 final size:7
Alignment explanation
Indices: 176661--176718 Score: 53
Period size: 8 Copynumber: 7.6 Consensus size: 7
176651 CCTTTTTCCT
176661 TTTTTTA
1 TTTTTTA
176668 TTCTTTTA
1 TT-TTTTA
176676 TTTTCTTA
1 TTTT-TTA
176684 TTTTCTATA
1 TTTT-T-TA
176693 TTTTTTA
1 TTTTTTA
*
176700 TATTATTA
1 T-TTTTTA
*
176708 TTTTATA
1 TTTTTTA
176715 TTTT
1 TTTT
176719 GATTTAGGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
7 15 0.34
8 23 0.52
9 6 0.14
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTTA
Found at i:176698 original size:24 final size:22
Alignment explanation
Indices: 176661--176718 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
176651 CCTTTTTCCT
* * *
176661 TTTTTTATTCTTTTATTTTCTTA
1 TTTTATATT-TTTTATATTATTA
176684 TTTTCTATATTTTTTATATTATTA
1 -TTT-TATATTTTTTATATTATTA
176708 TTTTATATTTT
1 TTTTATATTTT
176719 GATTTAGGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 8 0.27
23 3 0.10
24 14 0.47
25 5 0.17
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTATATTTTTTATATTATTA
Found at i:176723 original size:13 final size:13
Alignment explanation
Indices: 176665--176716 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
176655 TTTCCTTTTT
* *
176665 TTATTCTTTTATT
1 TTATTATTTTATA
* *
176678 TTCTTATTTTCTA
1 TTATTATTTTATA
176691 -TATT-TTTTATA
1 TTATTATTTTATA
176702 TTATTATTTTATA
1 TTATTATTTTATA
176715 TT
1 TT
176717 TTGATTTAGG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 6 0.19
12 7 0.23
13 18 0.58
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (13 bp):
TTATTATTTTATA
Found at i:178910 original size:2 final size:2
Alignment explanation
Indices: 178903--178942 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
178893 ACTTTTAAAG
178903 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
178943 GGTCAAGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:184134 original size:3 final size:3
Alignment explanation
Indices: 184122--184238 Score: 211
Period size: 3 Copynumber: 39.7 Consensus size: 3
184112 TAGACATGGA
184122 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
184169 A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
184216 ATT ATT ATT ATC ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT AT
184239 CAGAAAAGAA
Statistics
Matches: 110, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
2 4 0.04
3 106 0.96
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:184851 original size:20 final size:21
Alignment explanation
Indices: 184826--184864 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
184816 TTTAGTCAAG
184826 TAAATTCCTA-TGAATATTCT
1 TAAATTCCTATTGAATATTCT
*
184846 TAAATTCGTATTGAATATT
1 TAAATTCCTATTGAATATT
184865 GTAAAAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (21 bp):
TAAATTCCTATTGAATATTCT
Found at i:184869 original size:20 final size:20
Alignment explanation
Indices: 184825--184869 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
184815 GTTTAGTCAA
184825 GTAAATTCCTATGAATATTC
1 GTAAATTCCTATGAATATTC
* *
184845 TTAAATTCGTATTGAATATT-
1 GTAAATTCCTA-TGAATATTC
184865 GTAAA
1 GTAAA
184870 AGGATATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (20 bp):
GTAAATTCCTATGAATATTC
Found at i:187669 original size:20 final size:20
Alignment explanation
Indices: 187642--187696 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
187632 ATAACCAACG
187642 AATTCGCAACACGAACTCCA
1 AATTCGCAACACGAACTCCA
* **
187662 ATTTCGCAACAC-AGTTTCCA
1 AATTCGCAACACGA-ACTCCA
187682 AATTCGCAACACGAA
1 AATTCGCAACACGAA
187697 TTTGGATTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.38, C:0.31, G:0.11, T:0.20
Consensus pattern (20 bp):
AATTCGCAACACGAACTCCA
Found at i:187870 original size:20 final size:20
Alignment explanation
Indices: 187845--187892 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
187835 CGCGTTTCAA
187845 TTTCGCAATGCGAATTTTAC
1 TTTCGCAATGCGAATTTTAC
187865 TTTCGCAATGCGAATTTTAC
1 TTTCGCAATGCGAATTTTAC
187885 TTTCGCAA
1 TTTCGCAA
187893 CACAAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.40
Consensus pattern (20 bp):
TTTCGCAATGCGAATTTTAC
Found at i:188012 original size:22 final size:22
Alignment explanation
Indices: 187982--188034 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
187972 TCTCACTCTC
*
187982 TCCGACGACATTTGTCCCCATA
1 TCCGACGACATCTGTCCCCATA
*
188004 TCCGGCGACATCTGTCCCCATA
1 TCCGACGACATCTGTCCCCATA
*
188026 TCCGCCGAC
1 TCCGACGAC
188035 CCCCCTCCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.42, G:0.17, T:0.23
Consensus pattern (22 bp):
TCCGACGACATCTGTCCCCATA
Found at i:188392 original size:20 final size:20
Alignment explanation
Indices: 188333--188384 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
188323 TCGAGTTTTG
*
188333 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGAGTTGCGAATTTC
**
188353 ACGTTCGAGTTGCGAATTTC
1 ATTTTCGAGTTGCGAATTTC
188373 ATTTTCGAGTTG
1 ATTTTCGAGTTG
188385 TGATTTTCGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.44
Consensus pattern (20 bp):
ATTTTCGAGTTGCGAATTTC
Found at i:189984 original size:42 final size:42
Alignment explanation
Indices: 189910--190037 Score: 145
Period size: 42 Copynumber: 3.0 Consensus size: 42
189900 CCCCACTTTT
* *
189910 TCATCGAGTCAATTCT-TCACTTCGACACCGAGATCCATCACC
1 TCATCGAGTCGATTCTCT-ACTTTGACACCGAGATCCATCACC
* *
189952 TCATCGAGTCGATTCTCTACTTTGACAACGAGATACATCACC
1 TCATCGAGTCGATTCTCTACTTTGACACCGAGATCCATCACC
* * *
189994 TAATCGAG-CTGATTCTAC-ACCTTGACACCGAGAGCCATCACC
1 TCATCGAGTC-GATTCT-CTACTTTGACACCGAGATCCATCACC
190036 TC
1 TC
190038 TAGCCTACTC
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.01
42 70 0.96
43 2 0.03
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.26
Consensus pattern (42 bp):
TCATCGAGTCGATTCTCTACTTTGACACCGAGATCCATCACC
Found at i:190219 original size:21 final size:21
Alignment explanation
Indices: 190195--190242 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
190185 GTGCCTTATG
*
190195 TGATGAGGTCAGTGTTTTACA
1 TGATGAGATCAGTGTTTTACA
* *
190216 TGATAAGATCGGTGTTTTACA
1 TGATGAGATCAGTGTTTTACA
190237 TGATGA
1 TGATGA
190243 CAATGGTGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (21 bp):
TGATGAGATCAGTGTTTTACA
Found at i:190280 original size:21 final size:20
Alignment explanation
Indices: 190256--190364 Score: 119
Period size: 21 Copynumber: 5.2 Consensus size: 20
190246 TGGTGTATGG
*
190256 CGTGATGAGGTAGGGTCTTTA
1 CGTGATGAGGTAGTG-CTTTA
* *
190277 CGTGGTGAGGTAGCTGTTTTA
1 CGTGATGAGGTAG-TGCTTTA
**
190298 CGTGATGACAATAGTGCTTTA
1 CGTGATGA-GGTAGTGCTTTA
*
190319 CGTGGTGAGGTAGTGCTTTA
1 CGTGATGAGGTAGTGCTTTA
*
190339 CGTGATGAGGTAGGTGCTCTA
1 CGTGATGAGGTA-GTGCTTTA
190360 CGTGA
1 CGTGA
190365 AATTGTTTCA
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
20 21 0.29
21 48 0.66
22 4 0.05
ACGTcount: A:0.19, C:0.12, G:0.36, T:0.33
Consensus pattern (20 bp):
CGTGATGAGGTAGTGCTTTA
Found at i:190295 original size:63 final size:62
Alignment explanation
Indices: 190228--190351 Score: 160
Period size: 63 Copynumber: 2.0 Consensus size: 62
190218 ATAAGATCGG
* * *
190228 TGTTTTACATGATGACAATGGTG-TATGGCGTGATGAGGTAGGGTCTTTACGTGGTGAGGTAGC
1 TGTTTTACATGATGACAATAGTGCT-TGACGTGATGAGGTAGGG-CTTTACGTGATGAGGTAGC
* * * *
190291 TGTTTTACGTGATGACAATAGTGCTTTACGTGGTGAGGTAGTGCTTTACGTGATGAGGTAG
1 TGTTTTACATGATGACAATAGTGCTTGACGTGATGAGGTAGGGCTTTACGTGATGAGGTAG
190352 GTGCTCTACG
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
62 17 0.32
63 35 0.66
64 1 0.02
ACGTcount: A:0.21, C:0.10, G:0.35, T:0.35
Consensus pattern (62 bp):
TGTTTTACATGATGACAATAGTGCTTGACGTGATGAGGTAGGGCTTTACGTGATGAGGTAGC
Found at i:190356 original size:41 final size:42
Alignment explanation
Indices: 190256--190363 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 42
190246 TGGTGTATGG
*
190256 CGTGATGAGGTAGG-GTCTTTACGTGGTGAGGTAGCTGTTTTA
1 CGTGATGAGGTAGGTG-CTTTACGTGGTGAGGTAGCTGCTTTA
**
190298 CGTGATGACAATA-GTGCTTTACGTGGTGAGGTAG-TGCTTTA
1 CGTGATGA-GGTAGGTGCTTTACGTGGTGAGGTAGCTGCTTTA
*
190339 CGTGATGAGGTAGGTGCTCTACGTG
1 CGTGATGAGGTAGGTGCTTTACGTG
190364 AAATTGTTTC
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
40 2 0.04
41 25 0.44
42 27 0.47
43 3 0.05
ACGTcount: A:0.19, C:0.12, G:0.36, T:0.33
Consensus pattern (42 bp):
CGTGATGAGGTAGGTGCTTTACGTGGTGAGGTAGCTGCTTTA
Found at i:190482 original size:4 final size:4
Alignment explanation
Indices: 190473--190518 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
190463 TTTTTCGACA
* * * *
190473 TTAT TTAT TTAT TTAT TTAT TTAC TAAT TTAT ATAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
190519 TTAGAGGCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:191995 original size:24 final size:24
Alignment explanation
Indices: 191968--192014 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
191958 CAAAATCTGA
191968 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
191992 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
192015 AATACTAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:192943 original size:20 final size:19
Alignment explanation
Indices: 192918--192969 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 19
192908 CCCAAAACAT
192918 TTGTGTTGCGAAATTAAAA
1 TTGTGTTGCGAAATTAAAA
192937 CTTGTGTTGCGAAATTAAAA
1 -TTGTGTTGCGAAATTAAAA
192957 TGTGTGTTGCGAA
1 T-TGTGTTGCGAA
192970 TTCGAAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.37
Consensus pattern (19 bp):
TTGTGTTGCGAAATTAAAA
Found at i:193106 original size:22 final size:21
Alignment explanation
Indices: 193072--193112 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
193062 TTGCGAAAAA
* *
193072 CAAATTTGTGTTGCGAAATTGT
1 CAAATTCGAGTTGC-AAATTGT
193094 CAAATTCGAGTTGCAAATT
1 CAAATTCGAGTTGCAAATT
193113 TGACTTCTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (21 bp):
CAAATTCGAGTTGCAAATTGT
Found at i:197096 original size:24 final size:24
Alignment explanation
Indices: 197069--197119 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
197059 AACATATATA
* *
197069 TCAAAAATCAAATCATAGTTCATG
1 TCAAAAATCAAATCATAATCCATG
**
197093 TCAAGTATCAAATCATAATCCATG
1 TCAAAAATCAAATCATAATCCATG
197117 TCA
1 TCA
197120 TGTATCATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (24 bp):
TCAAAAATCAAATCATAATCCATG
Found at i:197124 original size:24 final size:24
Alignment explanation
Indices: 197075--197126 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
197065 TATATCAAAA
* *
197075 ATCAAATCATAGTTCATGTCAAGT
1 ATCAAATCATAATCCATGTCAAGT
*
197099 ATCAAATCATAATCCATGTCATGT
1 ATCAAATCATAATCCATGTCAAGT
197123 ATCA
1 ATCA
197127 TAACAGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (24 bp):
ATCAAATCATAATCCATGTCAAGT
Found at i:199627 original size:18 final size:18
Alignment explanation
Indices: 199582--199643 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
199572 CACCGGTCAA
199582 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
* * *
199600 TGGGTAGGGTCAACGAGT
1 CGGGTCGGGTCAACGGGT
* *
199618 CGAGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
199636 CGGGTCGG
1 CGGGTCGG
199644 TTGGAACCGG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.16, C:0.18, G:0.48, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:205498 original size:31 final size:31
Alignment explanation
Indices: 205463--205534 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
205453 GTTAGCGACT
* * *
205463 ATTTTCTAACGGTTAGATAAATCTAATGATA
1 ATTTTATAACAGTTAGATAAATCTAATGAAA
*
205494 ATTTTATAACAGTTCGATAAATCTAATGAAA
1 ATTTTATAACAGTTAGATAAATCTAATGAAA
*
205525 ATTTTGTAAC
1 ATTTTATAAC
205535 TTTTGAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (31 bp):
ATTTTATAACAGTTAGATAAATCTAATGAAA
Found at i:207225 original size:21 final size:23
Alignment explanation
Indices: 207201--207244 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
207191 TACGGTTTTT
*
207201 TAATATTT-T-TGCCTTTATGAC
1 TAATATTTCTCTGCCTGTATGAC
*
207222 TAATTTTTCTCTGCCTGTATGAC
1 TAATATTTCTCTGCCTGTATGAC
207245 ACATTTTCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 1 0.05
23 11 0.58
ACGTcount: A:0.20, C:0.18, G:0.11, T:0.50
Consensus pattern (23 bp):
TAATATTTCTCTGCCTGTATGAC
Found at i:210779 original size:33 final size:35
Alignment explanation
Indices: 210706--210792 Score: 151
Period size: 35 Copynumber: 2.5 Consensus size: 35
210696 CCTGAACCCA
210706 AAAATATTATATATATAATTAATATAAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAAATAT
*
210741 AAAATATTATATATATAATTAATAT-AAAATATAT
1 AAAATATTATATATATAATTAATATAAAAAAATAT
210775 -AAATATTATATATATAAT
1 AAAATATTATATATATAAT
210793 CGGGAGGGGA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 18 0.35
34 8 0.16
35 25 0.49
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (35 bp):
AAAATATTATATATATAATTAATATAAAAAAATAT
Found at i:211165 original size:19 final size:19
Alignment explanation
Indices: 211133--211170 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
211123 TCGTGTAAGC
*
211133 TTAACAGAATTTATACTTTT
1 TTAACAGAAATTATA-TTTT
211153 TTAA-AGAAATTATATTTT
1 TTAACAGAAATTATATTTT
211171 GGGTGAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (19 bp):
TTAACAGAAATTATATTTT
Found at i:211251 original size:59 final size:60
Alignment explanation
Indices: 211179--211305 Score: 148
Period size: 59 Copynumber: 2.1 Consensus size: 60
211169 TTGGGTGAAG
* * **
211179 TACAGAAATGGTCCCTCGGTGATAGGGTATTGTTTTATTAAATC-CTCAACTATTAAAAGT
1 TACA-AAATGGTCCCTCGATCATAGAATATTGTTTTATTAAATCTCTCAACTATTAAAAGT
* * * * * *
211239 TACAAAATGGTCCTTCGATCATAGAATGTTGTTTTGTTAAGTCTTTCGACTATTAAAAGT
1 TACAAAATGGTCCCTCGATCATAGAATATTGTTTTATTAAATCTCTCAACTATTAAAAGT
211299 TACAAAA
1 TACAAAA
211306 ATCACCTGAC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 31 0.55
60 25 0.45
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (60 bp):
TACAAAATGGTCCCTCGATCATAGAATATTGTTTTATTAAATCTCTCAACTATTAAAAGT
Found at i:212720 original size:29 final size:30
Alignment explanation
Indices: 212661--212726 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
212651 TCTGAGATGA
*
212661 TAAACGGGGACGGGGAAAAACCGAATTTTT
1 TAAACGGGGACGGAGAAAAACCGAATTTTT
* * *
212691 TAAATGGGGATGGAGAAAAACCGTATTTTT
1 TAAACGGGGACGGAGAAAAACCGAATTTTT
212721 TAAACG
1 TAAACG
212727 ATGATGGGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.11, G:0.27, T:0.24
Consensus pattern (30 bp):
TAAACGGGGACGGAGAAAAACCGAATTTTT
Found at i:212827 original size:2 final size:2
Alignment explanation
Indices: 212820--212852 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
212810 ATTTAAATTA
212820 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
212853 AAGGAGATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:213629 original size:22 final size:22
Alignment explanation
Indices: 213601--213676 Score: 152
Period size: 22 Copynumber: 3.5 Consensus size: 22
213591 GTTGATTCAA
213601 TTTTGACAATCAAACAATATTG
1 TTTTGACAATCAAACAATATTG
213623 TTTTGACAATCAAACAATATTG
1 TTTTGACAATCAAACAATATTG
213645 TTTTGACAATCAAACAATATTG
1 TTTTGACAATCAAACAATATTG
213667 TTTTGACAAT
1 TTTTGACAAT
213677 TTAAACTTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTTGACAATCAAACAATATTG
Found at i:214825 original size:22 final size:22
Alignment explanation
Indices: 214800--214850 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
214790 CACCACAGCT
*
214800 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
214822 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
214844 CGTAGAA
1 CGTAGAA
214851 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:214851 original size:22 final size:22
Alignment explanation
Indices: 214808--214852 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
214798 CTCGTATAAA
214808 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
214830 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
214852 T
1 T
214853 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:215113 original size:30 final size:31
Alignment explanation
Indices: 215072--215131 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
215062 TAGCCATAGT
*
215072 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
215102 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
215132 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:215188 original size:29 final size:29
Alignment explanation
Indices: 215146--215217 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
215136 TTTTCTGCAT
**
215146 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
215175 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
215204 ATTCATGTCATGTA
1 ATTCATGTCATGTA
215218 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:215664 original size:67 final size:67
Alignment explanation
Indices: 215519--215669 Score: 191
Period size: 68 Copynumber: 2.2 Consensus size: 67
215509 TTTTCTCATG
* * *
215519 GGGGAATCGGTTCCCCCCCCTGGGGTATCGGTTCCCCTATAGCATTCTGGAATTTCTTATACGAT
1 GGGGTATCGGTT-CCCCCCCTGGGGTATCGATTCCCCTATAGCATTCTGGAAATTCTTATACGAT
*
215584 GAG
65 GAA
*
215587 GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCTTA-CATTCTGGAAATTCATT-T-CG
1 GGGGTATCGGTTCCCCCCCT-GGGGTATCGATTCCCCT-ATAGCATTCTGGAAATTC-TTATACG
*
215649 TTGAA
63 ATGAA
215654 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
215670 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
67 29 0.39
68 41 0.55
69 4 0.05
ACGTcount: A:0.16, C:0.27, G:0.26, T:0.30
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCCTGGGGTATCGATTCCCCTATAGCATTCTGGAAATTCTTATACGATG
AA
Found at i:215679 original size:21 final size:21
Alignment explanation
Indices: 215649--215690 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
215639 ATTCATTTCG
* *
215649 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
215670 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
215691 CAACCCAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:221738 original size:22 final size:22
Alignment explanation
Indices: 221713--221763 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
221703 CACCACAGCT
*
221713 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
221735 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
221757 CGTAGAA
1 CGTAGAA
221764 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:221764 original size:22 final size:22
Alignment explanation
Indices: 221721--221765 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
221711 CTCGTATAAA
221721 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
221743 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
221765 T
1 T
221766 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:222026 original size:30 final size:31
Alignment explanation
Indices: 221985--222044 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
221975 TAGCCATAGT
*
221985 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
222015 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
222045 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:222118 original size:27 final size:28
Alignment explanation
Indices: 222059--222137 Score: 97
Period size: 27 Copynumber: 2.8 Consensus size: 28
222049 TTTTCTGCAT
**
222059 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATA-ATATAATACAA
*
222088 ATTCATGTCATGTAAT-ATTTAATACAA
1 ATTCATGTCATGTAATAATATAATACAA
222115 ATTCATGTCATGTATCATAATAT
1 ATTCATGTCATGTA--ATAATAT
222138 GGAATGTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
27 22 0.51
29 18 0.42
30 3 0.07
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (28 bp):
ATTCATGTCATGTAATAATATAATACAA
Found at i:222589 original size:21 final size:21
Alignment explanation
Indices: 222559--222600 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
222549 ATTCATTTCG
* *
222559 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
222580 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
222601 CAACCCAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:222590 original size:67 final size:67
Alignment explanation
Indices: 222431--222579 Score: 189
Period size: 67 Copynumber: 2.2 Consensus size: 67
222421 TTTTCTCATG
* * *
222431 GGGGAATCGGTTTCCCCCCT-GGGGTATCGGTTCCCCTATAGCATTCTGGAATTTCTTATACGAT
1 GGGGTATCGG-TTCCCCCCTGGGGGTATCGATTCCCCTATAGCATTCTGGAAATTCTTATACGAT
*
222495 GAG
65 GAA
* *
222498 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTTA-CATTCTGGAAATTCATT-T-CGT
1 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCT-ATAGCATTCTGGAAATTC-TTATACGA
222560 TGAA
64 TGAA
222564 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
222580 TTGAATGGGT
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
66 30 0.41
67 39 0.53
68 4 0.05
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.32
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTATAGCATTCTGGAAATTCTTATACGATG
AA
Found at i:224946 original size:25 final size:25
Alignment explanation
Indices: 224918--224978 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
224908 ATTTTATATA
224918 TATTAACTTAAAAAAAATATTTT-T
1 TATTAACTTAAAAAAAATATTTTAT
** *
224942 GTATTAACTTATTAAATATATTTTAT
1 -TATTAACTTAAAAAAAATATTTTAT
224968 TATTAACTTAA
1 TATTAACTTAA
224979 TTTAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (25 bp):
TATTAACTTAAAAAAAATATTTTAT
Found at i:226296 original size:22 final size:23
Alignment explanation
Indices: 226253--226295 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
226243 GGCCCGAACC
226253 CGACCCGATAAATAACTTAAAACT
1 CGACCCGA-AAATAACTTAAAACT
226277 CGACCCG-AAATAA-TTAAAA
1 CGACCCGAAAATAACTTAAAA
226296 AATATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
24 7 0.37
ACGTcount: A:0.49, C:0.23, G:0.09, T:0.19
Consensus pattern (23 bp):
CGACCCGAAAATAACTTAAAACT
Found at i:234475 original size:3 final size:3
Alignment explanation
Indices: 234467--234526 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
234457 AACTCTAAAA
234467 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
234515 TAT TAT TAT TAT
1 TAT TAT TAT TAT
234527 CAGATCACAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:236608 original size:2 final size:2
Alignment explanation
Indices: 236601--236625 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
236591 CTGAAACGTG
236601 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
236626 ATGTTTCAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:249867 original size:38 final size:37
Alignment explanation
Indices: 249765--249994 Score: 197
Period size: 38 Copynumber: 6.2 Consensus size: 37
249755 TGAAACTACG
* * *
249765 TATATAATATATAGTTTTTAATA-GTTTT-TAAAAT-
1 TATATAATATATAGTTTTTAAAACATTTTAGAAAATA
*
249799 TATATAATATATAGTTTTAAAAAAAACATTTTAGAAAATA
1 TATATAATATATAGTTTT---TAAAACATTTTAGAAAATA
* *
249839 TATATAATATATAATTTTTAAAATCATTTGA-AAAACT-
1 TATATAATATATAGTTTTTAAAA-CATTTTAGAAAA-TA
* *
249876 TATATATATATATAGTTTTTGAAAACATTTTTGAAAACA
1 TATATA-ATATATAGTTTTT-AAAACATTTTAGAAAATA
* *
249915 TATAT-AT-TATAGTTTTGAAAACATTTT-GAAAACA
1 TATATAATATATAGTTTTTAAAACATTTTAGAAAATA
* * * * *
249949 TTTATATTATATAGTTTTTAAAACGTTTTGGGAAAATT
1 TATATAATATATAGTTTTTAAAACATTTT-AGAAAATA
249987 TATATAAT
1 TATATAAT
249995 CTTTTTTGAA
Statistics
Matches: 160, Mismatches: 20, Indels: 28
0.77 0.10 0.13
Matches are distributed among these distances:
34 29 0.18
35 11 0.07
36 27 0.17
37 19 0.12
38 39 0.24
39 18 0.11
40 17 0.11
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (37 bp):
TATATAATATATAGTTTTTAAAACATTTTAGAAAATA
Found at i:249931 original size:35 final size:36
Alignment explanation
Indices: 249747--250045 Score: 166
Period size: 36 Copynumber: 8.0 Consensus size: 36
249737 TTATATATAT
* * *
249747 ACATATTTTGAAACTACGTATATAATATATAGTTTTTAAT
1 ACAT-TTTTGAAA--ACATATAT-ATATATAGTTTTGAAA
* * *
249787 A-GTTTTT-AAAATTATATA-ATATATAGTTTTAAAAAAA
1 ACATTTTTGAAAA-CATATATATATATAGTTTT---GAAA
* * * *
249824 ACATTTTAGAAAATATATATAATATATAATTTTTAAA
1 ACATTTTTGAAAACATATAT-ATATATAGTTTTGAAA
249861 ATCA--TTTGAAAAACTTATATATATATATAGTTTTTGAAA
1 A-CATTTTTG-AAAAC--ATATATATATATAG-TTTTGAAA
249900 ACATTTTTGAAAACATATATAT-TATAGTTTTGAAA
1 ACATTTTTGAAAACATATATATATATAGTTTTGAAA
* *
249935 ACA-TTTTGAAAACATTTATATTATATAGTTTTTAAA
1 ACATTTTTGAAAACATATATA-TATATAGTTTTGAAA
* * * * **
249971 ACGTTTTGGGAAA-ATTTATATA-ATCTTTTTTGAAA
1 ACATTTTTGAAAACATATATATATAT-AGTTTTGAAA
* * * *
250006 ACATGTTGGAAAACATTCGTATATTATATAGTTTTAAAA
1 ACATTTTTGAAAACA-T-ATATA-TATATAGTTTTGAAA
250045 A
1 A
250046 AAAAAAAAAC
Statistics
Matches: 207, Mismatches: 28, Indels: 49
0.73 0.10 0.17
Matches are distributed among these distances:
34 30 0.14
35 32 0.15
36 34 0.16
37 30 0.14
38 29 0.14
39 34 0.16
40 18 0.09
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (36 bp):
ACATTTTTGAAAACATATATATATATAGTTTTGAAA
Found at i:249943 original size:11 final size:11
Alignment explanation
Indices: 249927--249951 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
249917 TATATTATAG
249927 TTTTGAAAACA
1 TTTTGAAAACA
249938 TTTTGAAAACA
1 TTTTGAAAACA
249949 TTT
1 TTT
249952 ATATTATATA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:249972 original size:36 final size:36
Alignment explanation
Indices: 249821--250045 Score: 185
Period size: 36 Copynumber: 6.1 Consensus size: 36
249811 AGTTTTAAAA
* * * *
249821 AAAACATTTTAGAAAATATATATAATATATAATTTTT
1 AAAACATTTT-GAAAACATTTATATTATATAGTTTTT
249858 AAAATCA-TTTGAAAA-ACTTATATATATATATAGTTTTT
1 AAAA-CATTTTGAAAACA-TT-TATAT-TATATAGTTTTT
* *
249896 GAAAACATTTTTGAAAACATATATA-T-TATAGTTTTG
1 -AAAACA-TTTTGAAAACATTTATATTATATAGTTTTT
249932 AAAACATTTTGAAAACATTTATATTATATAGTTTTT
1 AAAACATTTTGAAAACATTTATATTATATAGTTTTT
* * **
249968 AAAACGTTTTGGGAAA-ATTTATA-TA-ATCTTTTTT
1 AAAACATTTT-GAAAACATTTATATTATATAGTTTTT
* *
250002 GAAAACATGTTGGAAAACATTCGTATATTATATAGTTTTA
1 -AAAACAT-TTTGAAAACATT--TATATTATATAGTTTTT
250042 AAAA
1 AAAA
250046 AAAAAAAAAC
Statistics
Matches: 153, Mismatches: 17, Indels: 34
0.75 0.08 0.17
Matches are distributed among these distances:
34 23 0.15
35 20 0.13
36 45 0.29
37 16 0.10
38 19 0.12
39 14 0.09
40 15 0.10
41 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (36 bp):
AAAACATTTTGAAAACATTTATATTATATAGTTTTT
Found at i:249991 original size:72 final size:72
Alignment explanation
Indices: 249797--250045 Score: 227
Period size: 74 Copynumber: 3.3 Consensus size: 72
249787 AGTTTTTAAA
* * * *
249797 ATTATATAATATATAGTTTTAAAAAAAACATTTTAGAAAATATATATAATATATAATTTTTAAAA
1 ATTATATATTATATAGTTTT---TAAAACATTTTGGAAAATATATAT-AT-TATAATTTTGAAAA
249862 TCA-TTTGAAAA-
61 -CATTTTGAAAAC
* * *
249873 ACTTATATATATATATAGTTTTTGAAAACATTTTTGAAAACATATATATTATAGTTTTGAAAACA
1 A-TTATATAT-TATATAGTTTTT-AAAACATTTTGGAAAATATATATATTATAATTTTGAAAACA
249938 TTTTGAAAAC
63 TTTTGAAAAC
* * * * *
249948 ATT-TATATTATATAGTTTTTAAAACGTTTTGGGAAAATTTATATAATCT-TTTTTGAAAACATG
1 ATTATATATTATATAGTTTTTAAAACATTTT-GGAAAATATATATATTATAATTTTGAAAACAT-
*
250011 TTGGAAAAC
64 TTTGAAAAC
* *
250020 ATTCGTATATTATATAGTTTTAAAAA
1 ATT-ATATATTATATAGTTTTTAAAA
250046 AAAAAAAAAC
Statistics
Matches: 149, Mismatches: 15, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
71 21 0.14
72 36 0.24
73 7 0.05
74 42 0.28
75 3 0.02
76 22 0.15
77 7 0.05
78 11 0.07
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (72 bp):
ATTATATATTATATAGTTTTTAAAACATTTTGGAAAATATATATATTATAATTTTGAAAACATTT
TGAAAAC
Found at i:250017 original size:34 final size:34
Alignment explanation
Indices: 249821--250018 Score: 130
Period size: 35 Copynumber: 5.5 Consensus size: 34
249811 AGTTTTAAAA
* * *
249821 AAAACATTTTAGAAAATATATATAATATATAATTTTT
1 AAAACATTTTGGAAAATTTATATAATAT-T--TTTTG
*
249858 AAAATCA-TTTGAAAAACTTATATATATATATAGTTTTTG
1 AAAA-CATTTTGGAAAA-TT-TATATA-ATAT--TTTTTG
* ** * *
249897 AAAACATTTTTGAAAACATATATATTATAGTTTTG
1 AAAACATTTTGGAAAATTTATATAATAT-TTTTTG
* *
249932 AAAACATTTTGAAAACATTTATATTATATAGTTTTT-
1 AAAACATTTTGGAAA-ATTTATA-TA-ATATTTTTTG
* *
249968 AAAACGTTTTGGGAAAATTTATATAATCTTTTTTG
1 AAAACATTTT-GGAAAATTTATATAATATTTTTTG
*
250003 AAAACATGTTGGAAAA
1 AAAACATTTTGGAAAA
250019 CATTCGTATA
Statistics
Matches: 125, Mismatches: 25, Indels: 25
0.71 0.14 0.14
Matches are distributed among these distances:
34 13 0.10
35 28 0.22
36 24 0.19
37 27 0.22
38 7 0.06
39 21 0.17
40 4 0.03
41 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (34 bp):
AAAACATTTTGGAAAATTTATATAATATTTTTTG
Found at i:250115 original size:3 final size:3
Alignment explanation
Indices: 250107--250138 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
250097 TGTATATATA
250107 TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT T
250139 TTTCATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:250126 original size:16 final size:16
Alignment explanation
Indices: 250107--250139 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
250097 TGTATATATA
250107 TATTATTATTATTATT
1 TATTATTATTATTATT
250123 TATTATTATTATTATT
1 TATTATTATTATTATT
250139 T
1 T
250140 TTCATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTATTATTATTATT
Found at i:253069 original size:19 final size:19
Alignment explanation
Indices: 253045--253090 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
253035 ATTTAGACAT
253045 TTTGCATTTCGTTATTTTC
1 TTTGCATTTCGTTATTTTC
*
253064 TTTGCATTTTGTTATTTTC
1 TTTGCATTTCGTTATTTTC
*
253083 TTTACATT
1 TTTGCATT
253091 CACATTAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.09, T:0.65
Consensus pattern (19 bp):
TTTGCATTTCGTTATTTTC
Found at i:256857 original size:245 final size:241
Alignment explanation
Indices: 256425--257307 Score: 927
Period size: 245 Copynumber: 3.6 Consensus size: 241
256415 TAAACAAACT
* * * * * * *
256425 ATTTGCAGCT-TAGCTCAAGGCCAGAAGGGCTATCTGCCACCAAGACCTTCGAGTTCGACTACGC
1 ATTTGCAG-TATAGCTTAAGTCGAGAAGGGCTATCTGCCA--AAGACCCTCAAGTTCGATTACAC
* *
256489 TCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG-C-CAAAGACC
63 TCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCACAAAGACC
** *
256552 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGG
128 CTTGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGG
*
256617 TTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAAAGGCATATC
193 TTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAAAGGCACATC
* * **
256666 ATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACGTTCA
1 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCA
** * * *
256731 GCTTTGAAGGCACATCATTTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGAC
66 GC-TCCAAGGCACATCA-TTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCC-AC-AAAGAC
* *
256796 CCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGG
127 CCTTGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGG
256861 GTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
192 GTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCA-----AAGGCACATC
* * * *
256916 ATTTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTAC
1 A-TTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCTCAAGTTCGATTAC
* * * * * * * *
256981 ACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAA
61 ACTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCA-CAAA
* * * * * * * * * *
257046 GACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGAATAGCTTAAGTCCAGA
124 GACCCTTGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGA
* * * *
257110 AGGGCTATCTGCCCACC-AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATC
189 AGGGTTATCTG-TCACCAAAGACCTTTGAGTTCGACT--A--C-GCTCAAAGGCACATC
* ** * * *
257168 ATTTGCAGTATAGGTTAAGTCGAGAATAGCTATCTGCCAAAGACCCCCAAGTTTGATTACATTCA
1 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCA
* * * *
257233 GCTTCGAGGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C-TAAAGA-CCT
66 GC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCACAAAGACCCT
257295 TCGAGTTCGATTA
130 T-GAGTTCGATTA
257308 TATTCAACTT
Statistics
Matches: 541, Mismatches: 74, Indels: 51
0.81 0.11 0.08
Matches are distributed among these distances:
239 25 0.05
240 12 0.02
241 65 0.12
242 1 0.00
243 3 0.01
244 16 0.03
245 106 0.20
246 1 0.00
247 62 0.11
248 3 0.01
250 11 0.02
251 60 0.11
252 66 0.12
253 34 0.06
254 38 0.07
255 33 0.06
256 1 0.00
257 4 0.01
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (241 bp):
ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCA
GCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCACAAAGACCCTT
GAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
TCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAAAGGCACATC
Found at i:256924 original size:169 final size:163
Alignment explanation
Indices: 256447--257363 Score: 816
Period size: 169 Copynumber: 5.6 Consensus size: 163
256437 GCTCAAGGCC
* * * * *
256447 AGAAGGGCTATCTGCCACCAAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGTTATCTGCCACAAAGACCCTT-GAGTTCGACTACACTCAGCTTCAAGGCATATCATTT
* * * * * * *
256511 GCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTT
65 ACAGAATAACTCAAGGCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGCTCAGCTT
* * * * * * *
256576 CGAGGGCACATCATTTACAGCATAACTCAAGGCT
130 CCAAGGCACATCATTTGCAGTATAACTTAAGTCA
* * *
256610 AGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCA-----AAGGCATATCATTT
1 AGAAGGGTTATCTGCCA-CAAAGACCCTTGAGTTCGACTACACTCAGCTTCAAGGCATATCATTT
* * * * * *
256670 GCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACGTTCAGCTT
65 ACAGAATAACTCAAGGCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGCTCAGCTT
**
256735 TGAAGGCACATCATTTTGCAGTATAACTTAAGTCA
130 CCAAGGCACATCA-TTTGCAGTATAACTTAAGTCA
* *
256770 AGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCAT
1 AGAAGGGTTATCTGCC-AC-AAAGACCCTTGAGTTCGACTACACTCAGCTTCAA-GGCATATCAT
* * * * *
256835 TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTC
63 TTACAGAATAACTCAAGGCGAGAAGGGCTATCTG---CCAAAGACCCTCGAGTTCGACTACGCTC
256900 AGC-TCCAAGGCACATCATTTTGCAGTATAACTTAAGTCA
125 AGCTTCCAAGGCACATCA-TTTGCAGTATAACTTAAGTCA
* *
256939 AGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCAT
1 AGAAGGGTTATCTGCC-AC-AAAGACCCTTGAGTTCGACTACACTCAGCTTCAA-GGCATATCAT
* * * * *
257004 TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTC
63 TTACAGAATAACTCAAGGCGAGAAGGGCTATCTG---CCAAAGACCCTCGAGTTCGACTACGCTC
* * *
257069 AGC-TCCAAGGCACATCATTTGCAGAATAGCTTAAGTCC
125 AGCTTCCAAGGCACATCATTTGCAGTATAACTTAAGTCA
* * * *
257107 AGAAGGGCTATCTGCCCACCAAGA-CCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTG-CCACAAAGACCCTT-GAGTTCGACTACACTCAGCTTCAAGGCATATCATT
* * ** * * ** * * * * **
257171 TGCAGTATAGGTTAAGTCGAGAATAGCTATCTGCCAAAGACCCCCAAGTTTGATTACATTCAGCT
64 TACAGAATAACTCAAGGCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGCTCAGCT
* * * * *
257236 TCGAGGGCACATCATTTGCAGCATAGCTTAAGTCG
129 TCCAAGGCACATCATTTGCAGTATAACTTAAGTCA
* * * * * * *
257271 AGAAGGGCTATCTG-C-TAAAGA-CCTTCGAGTTCGATTATATTCAACTT-AGAGGCAAATCAAG
1 AGAAGGGTTATCTGCCACAAAGACCCTT-GAGTTCGACTACACTCAGCTTCA-AGGCATATC-A-
* * * *
257332 CTTACAGAATAGCCCAAGGCAAGAAGGGCTAT
62 TTTACAGAATAACTCAAGGCGAGAAGGGCTAT
257364 TTGTCAATAA
Statistics
Matches: 652, Mismatches: 82, Indels: 40
0.84 0.11 0.05
Matches are distributed among these distances:
159 86 0.13
160 33 0.05
161 57 0.09
162 2 0.00
163 60 0.09
164 67 0.10
165 3 0.00
166 39 0.06
167 62 0.10
168 33 0.05
169 183 0.28
170 27 0.04
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (163 bp):
AGAAGGGTTATCTGCCACAAAGACCCTTGAGTTCGACTACACTCAGCTTCAAGGCATATCATTTA
CAGAATAACTCAAGGCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGCTCAGCTTC
CAAGGCACATCATTTGCAGTATAACTTAAGTCA
Found at i:257357 original size:414 final size:411
Alignment explanation
Indices: 256438--257359 Score: 1078
Period size: 414 Copynumber: 2.2 Consensus size: 411
256428 TGCAGCTTAG
* * *
256438 CTCAAGGCCAGAAGGGCTATCTG-CCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCGAGAAGGGCTATCTGACCA--AAGACCTTCGAGTTCGACTACACTCAACTCCAAGGC
* * * * ** * * * ***
256502 ACATCA-TTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCCCGAGTTCG
64 AAATCAGCTTACAGAATAACCCAAGGCAAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCG
*
256562 ATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA
129 ATTACACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA
* *
256627 CCAAAGACCTTTGAGTTCGACTACGCTCAAAGGCATATCATTTGCAGAATAGCTTAAGTCGAGAA
194 CCAAAGACCTTTGAGTTCGACTACGCTCAAAGGCACATCATTTGCAGAATAGCTTAAGTCCAGAA
* ** **
256692 GGGCTATCTGCCAAAGACCCTCGAGTTCGATTACGTTCAGCTTTGAAGGCACATCATTTTGCAGT
259 GGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTTGCAGT
* * **
256757 ATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTC
324 ATAACTTAAGTCAAGAAGAGCTATCTGCC-ACTAAAGACCCCCAAGTTCGATTACACTCAGCTTC
*
256822 AAGGGCATATCATTTACAGCATAA
388 AAGGGCACATCATTTACAGCATAA
* * * * *
256846 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCGAGAAGGGCTATCTG--ACCAAAGACCTTCGAGTTCGACTACACTCAACTCCAAGGC
* ** * * ** *
256911 ACATCATTTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCG
64 AAATCAGCTTACAGAATAACCCAAGGCAAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCG
*
256976 ATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA
129 ATTACACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA
257041 CCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTC
194 CCAAAGACCTTTGAGTTCGACTACGCTCA-----AAGGCACATCATTTGCAGAATAGCTTAAGTC
*
257106 CAGAAGGGCTATCTGCCCACCAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCA-
254 CAGAAGGGCTATCTG-CCA--AAGACCCTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCAT
** * * * *
257169 TTTGCAGTATAGGTTAAGTCGAGAATAGCTATCTG-C-C-AAAGACCCCCAAGTTTGATTACATT
316 TTTGCAGTATAACTTAAGTCAAGAAGAGCTATCTGCCACTAAAGACCCCCAAGTTCGATTACACT
* * *
257231 CAGCTTCGAGGGCACATCATTTGCAGCATAG
381 CAGCTTCAAGGGCACATCATTTACAGCATAA
* * * * * * *
257262 CTTAAGTCGAGAAGGGCTATCTG-CTAAAGACCTTCGAGTTCGATTATATTCAACT-TAGAGGCA
1 CTCAAGGCGAGAAGGGCTATCTGACCAAAGACCTTCGAGTTCGACTACACTCAACTCCA-AGGCA
*
257325 AATCAAGCTTACAGAATAGCCCAAGGCAAGAAGGG
65 AATC-AGCTTACAGAATAACCCAAGGCAAGAAGGG
257360 CTATTTGTCA
Statistics
Matches: 441, Mismatches: 55, Indels: 30
0.84 0.10 0.06
Matches are distributed among these distances:
408 21 0.05
409 41 0.09
410 31 0.07
411 4 0.01
412 1 0.00
413 34 0.08
414 128 0.29
416 67 0.15
417 1 0.00
419 45 0.10
420 32 0.07
421 12 0.03
422 24 0.05
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (411 bp):
CTCAAGGCGAGAAGGGCTATCTGACCAAAGACCTTCGAGTTCGACTACACTCAACTCCAAGGCAA
ATCAGCTTACAGAATAACCCAAGGCAAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGAT
TACACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC
AAAGACCTTTGAGTTCGACTACGCTCAAAGGCACATCATTTGCAGAATAGCTTAAGTCCAGAAGG
GCTATCTGCCAAAGACCCTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTTGCAGTAT
AACTTAAGTCAAGAAGAGCTATCTGCCACTAAAGACCCCCAAGTTCGATTACACTCAGCTTCAAG
GGCACATCATTTACAGCATAA
Found at i:258051 original size:74 final size:73
Alignment explanation
Indices: 257959--258163 Score: 197
Period size: 74 Copynumber: 2.8 Consensus size: 73
257949 TGAAACTACG
* **
257959 TATATAATATATAGTTTTT-AAT-AGTTTTTAAAA-TTATATAATATATAGTTTTAAAAAAAACA
1 TATATAATATATAATTTTTAAATCA-TTTGAAAAACTTATAT-ATATATAGTTTT--AAAAAACA
*
258021 TTTTAGAAAATA
62 TTTTAGAAAACA
**
258033 TATATAATATATAATTTTTAAAATCATTTGAAAAACTTATATATATATAGTTTTTGAAAACATTT
1 TATATAATATATAATTTTT-AAATCATTTGAAAAACTTATATATATATAGTTTTAAAAAACATTT
*
258098 TTGAAAACA
65 TAGAAAACA
* * * * *
258107 TATAT-AT-TATAGTTTTGAAAACATTTTGAAAACATTTATAT-TATATAGTTTTTAAAA
1 TATATAATATATAATTTTTAAATCA-TTTGAAAA-ACTTATATATATATAGTTTTAAAAA
258164 CGTTTTGGGA
Statistics
Matches: 113, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
71 5 0.04
72 31 0.27
73 9 0.08
74 39 0.35
76 22 0.19
77 7 0.06
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (73 bp):
TATATAATATATAATTTTTAAATCATTTGAAAAACTTATATATATATAGTTTTAAAAAACATTTT
AGAAAACA
Found at i:258066 original size:36 final size:36
Alignment explanation
Indices: 257945--258170 Score: 203
Period size: 36 Copynumber: 6.2 Consensus size: 36
257935 ATATATACAT
* *
257945 ATTTTGAAACTACGTATATAATATATAGTTTTTAATA-
1 ATTTTGAAA--ACATATATAATATATAGTTTTTAAAAC
* * * *
257982 GTTTTTAAAA-TTATATAATATATAGTTTTAAAAAAAAC
1 ATTTTGAAAACATATATAATATATAGTTTT---TAAAAC
* *
258020 ATTTTAGAAAATATATATAATATATAATTTTTAAAATC
1 ATTTT-GAAAACATATATAATATATAGTTTTTAAAA-C
*
258058 A-TTTGAAAAACTTATAT-ATATATAGTTTTTGAAAAC
1 ATTTTG-AAAACATATATAATATATAGTTTTT-AAAAC
*
258094 ATTTTTGAAAACATATAT-AT-TATAGTTTTGAAAAC
1 A-TTTTGAAAACATATATAATATATAGTTTTTAAAAC
* *
258129 ATTTTGAAAACATTTATATTATATAGTTTTTAAAAC
1 ATTTTGAAAACATATATAATATATAGTTTTTAAAAC
*
258165 GTTTTG
1 ATTTTG
258171 GGAAAATTTA
Statistics
Matches: 157, Mismatches: 19, Indels: 27
0.77 0.09 0.13
Matches are distributed among these distances:
34 33 0.21
35 8 0.05
36 43 0.27
37 42 0.27
38 10 0.06
39 4 0.03
40 17 0.11
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (36 bp):
ATTTTGAAAACATATATAATATATAGTTTTTAAAAC
Found at i:258135 original size:11 final size:11
Alignment explanation
Indices: 258119--258143 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
258109 TATATTATAG
258119 TTTTGAAAACA
1 TTTTGAAAACA
258130 TTTTGAAAACA
1 TTTTGAAAACA
258141 TTT
1 TTT
258144 ATATTATATA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:258159 original size:72 final size:70
Alignment explanation
Indices: 258015--258237 Score: 216
Period size: 72 Copynumber: 3.1 Consensus size: 70
258005 AGTTTTAAAA
* *
258015 AAAACATTTTAGAAAATATATATAATATATAATTTTTAAAATCA-TTTGAAAA-ACTTATATATA
1 AAAACATTTTAGAAAA-ATATAT-AT-TATAATTTTGAAAA-CATTTTGAAAACATTTATAT-TA
258078 TATAGTTTTT
61 TATAGTTTTT
* *
258088 GAAAACATTTTTGAAAACATATATATTATAGTTTTGAAAACATTTTGAAAACATTTATATTATAT
1 -AAAACATTTTAGAAAA-ATATATATTATAATTTTGAAAACATTTTGAAAACATTTATATTATAT
258153 AGTTTTT
64 AGTTTTT
* * * * * ** *
258160 AAAACGTTTTGGGAAAATTTATATAATCTTTTTTGAAAACATGTTGGAAAACATTCGTATATTAT
1 AAAACATTTTAGAAAAATATATATTAT-AATTTTGAAAACAT-TTTGAAAACATT--TATATTAT
*
258225 ATAGTTTTA
62 ATAGTTTTT
258234 AAAA
1 AAAA
258238 AAAAAAACAT
Statistics
Matches: 129, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
70 9 0.07
71 27 0.21
72 43 0.33
73 9 0.07
74 41 0.32
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (70 bp):
AAAACATTTTAGAAAAATATATATTATAATTTTGAAAACATTTTGAAAACATTTATATTATATAG
TTTTT
Found at i:258180 original size:36 final size:35
Alignment explanation
Indices: 257961--258237 Score: 179
Period size: 36 Copynumber: 7.6 Consensus size: 35
257951 AAACTACGTA
* * * * * *
257961 TATAATATATAGTTTTTAATA-GTTTTTAAAATTA
1 TATATTATATAGTTTTTAAAACATTTTGAAAAATT
* * *
257995 TATAATATATAGTTTTAAAAAAAACATTTTAGAAAATATA
1 TATATTATATAGTTTT---TAAAACATTTT-GAAAA-ATT
* * *
258035 TATAATATATAATTTTTAAAATCA-TTTGAAAAACT
1 TATATTATATAGTTTTTAAAA-CATTTTGAAAAATT
*
258070 TATATATATATAGTTTTTGAAAACATTTTTGAAAACATA
1 TATAT-TATATAGTTTTT-AAAACA-TTTTGAAAA-ATT
*
258109 TATA-T-TATAGTTTTGAAAACATTTTGAAAACATT
1 TATATTATATAGTTTTTAAAACATTTTGAAAA-ATT
* *
258143 TATATTATATAGTTTTTAAAACGTTTTGGGAAAATT
1 TATATTATATAGTTTTTAAAACATTTT-GAAAAATT
** *
258179 TATA-TA-ATCTTTTTTGAAAACATGTTGGAAAACATT
1 TATATTATATAGTTTTT-AAAACAT-TTTGAAAA-ATT
*
258215 CGTATATTATATAGTTTTAAAAA
1 --TATATTATATAGTTTTTAAAA
258238 AAAAAAACAT
Statistics
Matches: 195, Mismatches: 26, Indels: 39
0.75 0.10 0.15
Matches are distributed among these distances:
34 39 0.20
35 24 0.12
36 57 0.29
37 19 0.10
38 18 0.09
39 15 0.08
40 23 0.12
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (35 bp):
TATATTATATAGTTTTTAAAACATTTTGAAAAATT
Found at i:258194 original size:71 final size:71
Alignment explanation
Indices: 258015--258237 Score: 220
Period size: 74 Copynumber: 3.1 Consensus size: 71
258005 AGTTTTAAAA
* * *
258015 AAAACATTTTAGAAAATATATATAATATATAATTTTT-AAAATCA-TTTGAAAA-ACTTATATAT
1 AAAACATTTTGGAAAACATATAT-ATA-AT-ATTTTTGAAAA-CATTTTGAAAACATTTATAT-T
258077 ATATAGTTTTT
61 ATATAGTTTTT
* * *
258088 GAAAACATTTTTGAAAACATATATATTATAGTTTTGAAAACATTTTGAAAACATTTATATTATAT
1 -AAAACATTTTGGAAAACATATATATAATATTTTTGAAAACATTTTGAAAACATTTATATTATAT
258153 AGTTTTT
65 AGTTTTT
* * * * *
258160 AAAACGTTTTGGGAAA-ATTTATATAATCTTTTTTGAAAACATGTTGGAAAACATTCGTATATTA
1 AAAACATTTTGGAAAACATATATATAAT-ATTTTTGAAAACAT-TTTGAAAACATT--TATATTA
*
258224 TATAGTTTTA
62 TATAGTTTTT
258234 AAAA
1 AAAA
258238 AAAAAAACAT
Statistics
Matches: 128, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
70 9 0.07
71 32 0.25
72 37 0.29
73 9 0.07
74 41 0.32
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (71 bp):
AAAACATTTTGGAAAACATATATATAATATTTTTGAAAACATTTTGAAAACATTTATATTATATA
GTTTTT
Found at i:258209 original size:34 final size:34
Alignment explanation
Indices: 258015--258210 Score: 135
Period size: 37 Copynumber: 5.5 Consensus size: 34
258005 AGTTTTAAAA
* * *
258015 AAAACATTTTAGAAAATATATATAATATATAATTTTT
1 AAAACATTTTGGAAAATTTATATAATAT-T--TTTTG
* *
258052 AAAATCA-TTTGAAAAACTTATATATATATAGTTTTTG
1 AAAA-CATTTTGGAAAA-TT-TATATA-ATATTTTTTG
* ** * *
258089 AAAACATTTTTGAAAACATATATATTATAGTTTTG
1 AAAACATTTTGGAAAATTTATATAATAT-TTTTTG
* *
258124 AAAACATTTTGAAAACATTTATATTATATAGTTTTT-
1 AAAACATTTTGGAAA-ATTTATA-TA-ATATTTTTTG
* *
258160 AAAACGTTTTGGGAAAATTTATATAATCTTTTTTG
1 AAAACATTTT-GGAAAATTTATATAATATTTTTTG
*
258195 AAAACATGTTGGAAAA
1 AAAACATTTTGGAAAA
258211 CATTCGTATA
Statistics
Matches: 123, Mismatches: 25, Indels: 25
0.71 0.14 0.14
Matches are distributed among these distances:
34 15 0.12
35 34 0.28
36 23 0.19
37 36 0.29
38 5 0.04
39 7 0.06
40 3 0.02
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (34 bp):
AAAACATTTTGGAAAATTTATATAATATTTTTTG
Found at i:258305 original size:3 final size:3
Alignment explanation
Indices: 258297--258328 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
258287 TGTATATATA
258297 TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT T
258329 TTTCATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:258316 original size:16 final size:16
Alignment explanation
Indices: 258297--258329 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
258287 TGTATATATA
258297 TATTATTATTATTATT
1 TATTATTATTATTATT
258313 TATTATTATTATTATT
1 TATTATTATTATTATT
258329 T
1 T
258330 TTCATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTATTATTATTATT
Found at i:260036 original size:30 final size:30
Alignment explanation
Indices: 259996--260054 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
259986 GAATCTTATA
*
259996 CTTTGAAAAATTTATTAACCTAAAGAAACG
1 CTTTGAAAAATTTATTAACCTAAAAAAACG
*
260026 CTTTTAAAAATTTATTAACCTAAAAAAAC
1 CTTTGAAAAATTTATTAACCTAAAAAAAC
260055 ACGTGTGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (30 bp):
CTTTGAAAAATTTATTAACCTAAAAAAACG
Found at i:264618 original size:13 final size:13
Alignment explanation
Indices: 264582--264635 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
264572 TTAGTGCTCG
*
264582 TTTGATTAACTGA
1 TTTGATTAATTGA
*
264595 TTTAATTAATTGA
1 TTTGATTAATTGA
* *
264608 TTTGATAAATTAA
1 TTTGATTAATTGA
* *
264621 TTCGATTGATTGA
1 TTTGATTAATTGA
264634 TT
1 TT
264636 ATATAAAATT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (13 bp):
TTTGATTAATTGA
Found at i:266380 original size:24 final size:25
Alignment explanation
Indices: 266353--266401 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
266343 TTATTTTTTA
*
266353 TTAATTTAATATTAAT-AAAATATT
1 TTAATATAATATTAATCAAAATATT
* *
266377 TTAATATCATTTTAATCAAAATATT
1 TTAATATAATATTAATCAAAATATT
266402 AATTATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (25 bp):
TTAATATAATATTAATCAAAATATT
Found at i:266436 original size:21 final size:23
Alignment explanation
Indices: 266394--266437 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
266384 CATTTTAATC
266394 AAAATATTAATTATTAAATATTT
1 AAAATATTAATTATTAAATATTT
*
266417 AAAATA-TATTTATT-AATATTT
1 AAAATATTAATTATTAAATATTT
266438 CTAATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 7 0.35
23 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AAAATATTAATTATTAAATATTT
Found at i:266447 original size:22 final size:23
Alignment explanation
Indices: 266403--266470 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 23
266393 CAAAATATTA
*
266403 ATTATTAAATATTTAAAAT-ATAT
1 ATTATT-AATATTTATAATAATAT
*
266426 -TTATTAATATTTCTAATAATAT
1 ATTATTAATATTTATAATAATAT
* * *
266448 AATATT-ATATTTTTAATATTAT
1 ATTATTAATATTTATAATAATAT
266470 A
1 A
266471 ATAAAATAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
21 10 0.26
22 24 0.63
23 4 0.11
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTATTAATATTTATAATAATAT
Found at i:266471 original size:22 final size:23
Alignment explanation
Indices: 266427--266473 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
266417 AAAATATATT
266427 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
266450 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
266472 TA
1 TA
266474 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:266487 original size:32 final size:32
Alignment explanation
Indices: 266421--266500 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
266411 ATATTTAAAA
* *
266421 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
266453 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
*
266485 TATATTATAATAATAT
1 TATATT-TATTAATAT
266501 AAGATATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 13 0.32
31 6 0.15
32 15 0.38
33 1 0.03
34 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:267687 original size:28 final size:31
Alignment explanation
Indices: 267656--267719 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 31
267646 TTATGTTAGG
*
267656 AGGGGCG-AAT-TTGAACTTTTAAAATT-TT
1 AGGGGCGTAATCTTGAACTTATAAAATTCTT
*
267684 AGGGG-GTGATCTTGAACTTATAAAATTCTT
1 AGGGGCGTAATCTTGAACTTATAAAATTCTT
*
267714 GGGGGC
1 AGGGGC
267720 AAAAACATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 1 0.03
28 7 0.24
29 15 0.52
30 6 0.21
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.34
Consensus pattern (31 bp):
AGGGGCGTAATCTTGAACTTATAAAATTCTT
Found at i:268080 original size:22 final size:22
Alignment explanation
Indices: 268039--268082 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
268029 TTAAAACTTT
**
268039 TTAAAAAAATTAAAGGTTTAAA
1 TTAAAAAAATTAAAAATTTAAA
268061 TTAAAAAAATTAAAAATTTAAA
1 TTAAAAAAATTAAAAATTTAAA
268083 GAGCTCAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (22 bp):
TTAAAAAAATTAAAAATTTAAA
Found at i:275399 original size:175 final size:176
Alignment explanation
Indices: 275095--275455 Score: 489
Period size: 175 Copynumber: 2.1 Consensus size: 176
275085 ACGACGGAGG
* ** *
275095 ATATATCGACATTGACAACATCCTCGTACCCATCATTCACCATCTCTTCACTAAAAACTGCAGAA
1 ATATATCGACATCGACAACATCCTCCCACCCATCATTCACCATATCTTCACTAAAAACTGCAGAA
* * * * *
275160 AAAGTGGAGATTTGTTACCTAAAAAACGAGAGATCTGAGAAAGGGTATGGCTATATTCAGGGACG
66 AAAGTGGAGATTTGTTACATAAAAAACGAGAGATCAGAGAAAGCGTATGACTAGATTCAGGGACG
* * * *
275225 AACTT--AGAATTTTATGCTAGTA-CTAGAAACGTATTGTCAATAGAAA
131 AA-TTCAAG-ATTTTATGCTAG-AGCTAAAAACATATTATCAACAGAAA
* *
275271 ATATATCGGCATCGACAACATCC-CCCACCCATCGTTCACCATATCTTCACTAAAAAACTGCAGA
1 ATATATCGACATCGACAACATCCTCCCACCCATCATTCACCATATCTTCACT-AAAAACTGCAGA
*
275335 AAAAGTGGAGATTTGTTACAT-AAAAACGAGAGATCAGAGAAAGCGTATGACTAGATTGAGGGAC
65 AAAAGTGGAGATTTGTTACATAAAAAACGAGAGATCAGAGAAAGCGTATGACTAGATTCAGGGAC
*
275399 GGATTCAAGATTTTATGCTAGAGCTAAAAACATATTATCAACAGAAA
130 GAATTCAAGATTTTATGCTAGAGCTAAAAACATATTATCAACAGAAA
*
275446 ATACATCGAC
1 ATATATCGAC
275456 GCTAACAACA
Statistics
Matches: 162, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
174 3 0.02
175 104 0.64
176 55 0.34
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (176 bp):
ATATATCGACATCGACAACATCCTCCCACCCATCATTCACCATATCTTCACTAAAAACTGCAGAA
AAAGTGGAGATTTGTTACATAAAAAACGAGAGATCAGAGAAAGCGTATGACTAGATTCAGGGACG
AATTCAAGATTTTATGCTAGAGCTAAAAACATATTATCAACAGAAA
Found at i:275466 original size:175 final size:175
Alignment explanation
Indices: 275122--275555 Score: 465
Period size: 175 Copynumber: 2.6 Consensus size: 175
275112 ACATCCTCGT
* *
275122 ACCCATCATTCACCATCTCTTCACTAAAAACTGCAGAAAAAGTGGAGATTTGTTACCTAAAAAAC
1 ACCCATCATTCACCATATCTTCACTAAAAACTGCAGAAAAAGTGGAGATTTGTTACATAAAAAAC
* * * * *
275187 GAGAGATCTGAGAAAGGGTATGGCTATATTCAGGGACGAACTTAGAATTTTATGCTAGTACTAGA
66 GAGAGATCAGAGAAAGCGTATGACTAGATTCAGGGACGAACTTAGAATTTTATGCTAGTACTAAA
* * * * *
275252 AACGTATTGTCAATAGAAAATATATCGGCATCGACAACATCCCCC
131 AACATATTATCAACAGAAAATACATCGGCATCAACAACATCCCCC
*
275297 ACCCATCGTTCACCATATCTTCACTAAAAAACTGCAGAAAAAGTGGAGATTTGTTACAT-AAAAA
1 ACCCATCATTCACCATATCTTCACT-AAAAACTGCAGAAAAAGTGGAGATTTGTTACATAAAAAA
* *
275361 CGAGAGATCAGAGAAAGCGTATGACTAGATTGAGGGACGGA-TTCA-AGATTTTATGCTAG-AGC
65 CGAGAGATCAGAGAAAGCGTATGACTAGATTCAGGGACGAACTT-AGA-ATTTTATGCTAGTA-C
*
275423 TAAAAACATATTATCAACAGAAAATACATC-G-A-C-GCTAACA------
127 TAAAAACATATTATCAACAGAAAATACATCGGCATCAAC-AACATCCCCC
* * * *
275463 A--CATCATTCATCATCTCTTCCCTAAAAA-TGCAGAAAACA-TGGAGATTTGTTGCAT-AAAAA
1 ACCCATCATTCACCATATCTTCACTAAAAACTGCAGAAAA-AGTGGAGATTTGTTACATAAAAAA
* * * *
275523 TGAGAGATCACAGAAAGGGTATGTCTAGATTCA
65 CGAGAGATCAGAGAAAGCGTATGACTAGATTCA
275556 CGCGGGATTC
Statistics
Matches: 228, Mismatches: 25, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
162 57 0.25
163 6 0.03
164 18 0.08
166 1 0.00
171 1 0.00
172 5 0.02
173 1 0.00
174 5 0.02
175 102 0.45
176 32 0.14
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (175 bp):
ACCCATCATTCACCATATCTTCACTAAAAACTGCAGAAAAAGTGGAGATTTGTTACATAAAAAAC
GAGAGATCAGAGAAAGCGTATGACTAGATTCAGGGACGAACTTAGAATTTTATGCTAGTACTAAA
AACATATTATCAACAGAAAATACATCGGCATCAACAACATCCCCC
Found at i:276003 original size:3 final size:3
Alignment explanation
Indices: 275995--276029 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
275985 GGCCATGTTT
*
275995 ATC ATC ATC ATC ATC ATC AT- ATC ATC ATC AAC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
276030 TGCTACAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.37, C:0.31, G:0.00, T:0.31
Consensus pattern (3 bp):
ATC
Found at i:277863 original size:16 final size:16
Alignment explanation
Indices: 277842--277872 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
277832 GTTGAATGTA
277842 GGCACATTAAATGCTG
1 GGCACATTAAATGCTG
277858 GGCACATTAAATGCT
1 GGCACATTAAATGCT
277873 AGGTTGCTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (16 bp):
GGCACATTAAATGCTG
Found at i:281445 original size:20 final size:21
Alignment explanation
Indices: 281417--281460 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
281407 CCACATAAGA
*
281417 TTTATATTTAATAAAATAAAT
1 TTTATATTTAAAAAAATAAAT
*
281438 TTTA-ATTTAAAAAAATCAAT
1 TTTATATTTAAAAAAATAAAT
281458 TTT
1 TTT
281461 TAAGAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTATATTTAAAAAAATAAAT
Found at i:282779 original size:2 final size:2
Alignment explanation
Indices: 282772--282803 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
282762 CCCCATGCAT
282772 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
282804 GACACACGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:284680 original size:6 final size:6
Alignment explanation
Indices: 284672--284712 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
284662 CCTCAAAATG
* *
284672 CATATG CATATG CATATA CATATA CATATA CATATA CATAT
1 CATATA CATATA CATATA CATATA CATATA CATATA CATAT
284713 TTGGTAATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (6 bp):
CATATA
Found at i:287271 original size:18 final size:18
Alignment explanation
Indices: 287244--287284 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
287234 CAATATTGTC
*
287244 ACCCTAAGTATCGATACT
1 ACCCTTAGTATCGATACT
*
287262 ACCCTTAGTATTGATACT
1 ACCCTTAGTATCGATACT
287280 -CCCTT
1 ACCCTT
287285 CCCAAATCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34
Consensus pattern (18 bp):
ACCCTTAGTATCGATACT
Found at i:287847 original size:16 final size:16
Alignment explanation
Indices: 287828--287874 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
287818 CGGAGAGGAA
287828 AAGAAGATGAGAAATG
1 AAGAAGATGAGAAATG
287844 AAGAAGATGAGAAATG
1 AAGAAGATGAGAAATG
*
287860 AAGAAGATGACAAAT
1 AAGAAGATGAGAAAT
287875 TGCTCTTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.28, T:0.13
Consensus pattern (16 bp):
AAGAAGATGAGAAATG
Found at i:289734 original size:2 final size:2
Alignment explanation
Indices: 289686--289722 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
289676 CATTTAAATA
289686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
289723 ACTTTTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:290008 original size:23 final size:24
Alignment explanation
Indices: 289982--290032 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
289972 TATATGTCAT
*
289982 TGTGACATGT-TTTTCTATGCTCG
1 TGTGACAAGTGTTTTCTATGCTCG
*
290005 TGTGACAAGTGTTTTCTATGCTCT
1 TGTGACAAGTGTTTTCTATGCTCG
290029 TGTG
1 TGTG
290033 GTATGATCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.14, C:0.16, G:0.24, T:0.47
Consensus pattern (24 bp):
TGTGACAAGTGTTTTCTATGCTCG
Found at i:293117 original size:238 final size:234
Alignment explanation
Indices: 292693--293144 Score: 604
Period size: 238 Copynumber: 1.9 Consensus size: 234
292683 TGAACGTGTT
* * * *
292693 TAGGTGCCGATGAGGAACTTCGATGCGCCCCTTCGGTGCCTCTTGAAGCCTGGGGGCACAGAACC
1 TAGGTGCCGATGAGGAACATCGAGGCGCCCCTTCGGTGCCTCTTGAAGCCTCGGGGAACAGAACC
* * *
292758 TTTAAGGGCGTCTCGATTTTTCGACTGAAAAATCGAATATCCGGGAAGAGTTCGATCATCTAAAT
66 TTTAAGGGCGTCTCGATTTTTCGACGGAAAAACCGAATATCCGGGAAGAGTTCAATCATCTAAAT
* * *
292823 GATAGGCTTGTGTGATGTTTTACATCAACAATGTTATGCAGGCTATGGTAAAACAGACTATATAT
131 GATAGACTTGTGTAATGTTTTACAT-----ATGTTATACAGGCTATGGTAAAACAGACTATATAT
292888 GCATAGGTTAGGATATAGGCTATGGATTGCAAACCAGACCAAAG
191 GCATAGGTTAGGATATAGGCTATGGATTGCAAACCAGACCAAAG
* * * * *
292932 TAGGTGCTGCTGAGGAACATCGAGGTGCCCCTTCGGTGCTTCTTGAATCCTCGGGGAACA-ATAC
1 TAGGTGCCGATGAGGAACATCGAGGCGCCCCTTCGGTGCCTCTTGAAGCCTCGGGGAACAGA-AC
* *
292996 CTTTAAGGGTGTCTC-ATTTTTCGACGGAAAAACCGAATATCCGGGAAGAGTTCAATCATCTTAA
65 CTTTAAGGGCGTCTCGATTTTTCGACGGAAAAACCGAATATCCGGGAAGAGTTCAATCATCTAAA
* *
293060 TGATAATTTCTGACTTGTGTAATGTTTTACAT-TGTTATACAGGCTGTGGTGAAACAGACTATAT
130 TGAT-A-----GACTTGTGTAATGTTTTACATATGTTATACAGGCTATGGTAAAACAGACTATAT
293124 ATGCATAGGTTAGGATATAGG
189 ATGCATAGGTTAGGATATAGG
293145 TTAAACCTTT
Statistics
Matches: 187, Mismatches: 19, Indels: 15
0.85 0.09 0.07
Matches are distributed among these distances:
238 100 0.53
239 68 0.36
244 19 0.10
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (234 bp):
TAGGTGCCGATGAGGAACATCGAGGCGCCCCTTCGGTGCCTCTTGAAGCCTCGGGGAACAGAACC
TTTAAGGGCGTCTCGATTTTTCGACGGAAAAACCGAATATCCGGGAAGAGTTCAATCATCTAAAT
GATAGACTTGTGTAATGTTTTACATATGTTATACAGGCTATGGTAAAACAGACTATATATGCATA
GGTTAGGATATAGGCTATGGATTGCAAACCAGACCAAAG
Found at i:293295 original size:156 final size:155
Alignment explanation
Indices: 292994--293300 Score: 510
Period size: 156 Copynumber: 2.0 Consensus size: 155
292984 GGGGAACAAT
292994 ACCTTTAAGGGTGTCTCATTTTTCGACGGAAAAACCGAATATCCGGGAAGAGTTCAATCATCTTA
1 ACCTTTAAGGGTGTCTCATTTTTCGACGGAAAAACCGAATATCCGGGAAGAGTTCAATCATCTTA
* *
293059 ATGATAATTTCTGACTTGTGTAATGTTTTACATTGTTATACAGGCTGTGGTGAAACAGACTATAT
66 ATGATAATTTCTGACTTGTGTAATGTTTTACATTGTTATACAGGCTATGGTGAAACAGACTAGAT
293124 ATGCATAGGTTAGGATATAGGTTAA
131 ATGCATAGGTTAGGATATAGGTTAA
* *
293149 ACCTTTAAGGGTGTCTCGATTTTTTGACGGAAAAACCGAATATCCGGGAAGAGTTCGATCATCTT
1 ACCTTTAAGGGTGTCTC-ATTTTTCGACGGAAAAACCGAATATCCGGGAAGAGTTCAATCATCTT
* *
293214 AATGATAATTTTTGACTTGTGTGATGTTTTACCA-TGTTATACAGGCTATGGT-AGAACAGACTA
65 AATGATAATTTCTGACTTGTGTAATGTTTTA-CATTGTTATACAGGCTATGGTGA-AACAGACTA
*
293277 GGTATGCATAGGTTAGGATATAGG
128 GATATGCATAGGTTAGGATATAGG
293301 CTATGTAGTT
Statistics
Matches: 142, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
155 18 0.13
156 122 0.86
157 2 0.01
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (155 bp):
ACCTTTAAGGGTGTCTCATTTTTCGACGGAAAAACCGAATATCCGGGAAGAGTTCAATCATCTTA
ATGATAATTTCTGACTTGTGTAATGTTTTACATTGTTATACAGGCTATGGTGAAACAGACTAGAT
ATGCATAGGTTAGGATATAGGTTAA
Found at i:294641 original size:17 final size:17
Alignment explanation
Indices: 294619--294656 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
294609 CATCTTGCTG
294619 AGTTCGAGTAATCGATC
1 AGTTCGAGTAATCGATC
294636 AGTTCGAGTAATCGATC
1 AGTTCGAGTAATCGATC
294653 AGTT
1 AGTT
294657 TGAGCTGCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.32
Consensus pattern (17 bp):
AGTTCGAGTAATCGATC
Found at i:309122 original size:21 final size:21
Alignment explanation
Indices: 309096--309138 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
309086 TTTCTGGGTT
* *
309096 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
309117 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
309138 A
1 A
309139 CGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:309198 original size:66 final size:67
Alignment explanation
Indices: 309118--309268 Score: 191
Period size: 67 Copynumber: 2.3 Consensus size: 67
309108 ACCCATTCAA
* * *
309118 GGGGAACCGATACCCCTTCAACG-A-AATGAATTTCCAGAATGCAAGAGGGGAATCGATACCCCC
1 GGGGAACCGATACCCCCTCAACGTATAA-GAAATTCCAGAATGCAAGAGGGGAACCGATA-CCCC
309181 A-GG
64 AGGG
* * *
309184 GGGGAACCGATACCCCCTCATCGTATAAGAAATTCCAGAATGCTATAGGGGAACCGATACCCCAG
1 GGGGAACCGATACCCCCTCAACGTATAAGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCA-
309249 GGG
65 GGG
*
309252 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
309269 ATGAGAAAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
66 26 0.35
67 28 0.38
68 20 0.27
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGTATAAGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCAG
GG
Found at i:309604 original size:29 final size:29
Alignment explanation
Indices: 309570--309639 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
309560 CATATTATGA
**
309570 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
* *
309599 TACATGACATAAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
309628 TACATGACATGA
1 TACATGACATGA
309640 TTATGCAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:309697 original size:30 final size:31
Alignment explanation
Indices: 309655--309714 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
309645 CAGAAAAGTT
*
309655 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
309686 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
309715 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:309994 original size:23 final size:22
Alignment explanation
Indices: 309934--310001 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
309924 TTATGGACAA
309934 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
309956 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
309978 AATTCTACGGGGCACTTCGGTGC
1 AATTCTAC-GGGCACTTCGGTGC
310001 A
1 A
310002 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 30 0.67
23 15 0.33
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.26
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:316193 original size:66 final size:67
Alignment explanation
Indices: 316063--316211 Score: 196
Period size: 67 Copynumber: 2.2 Consensus size: 67
316053 ACCCATTCAA
* * *
316063 GGGAACCGATACCCCTTCAACGAAATGAATTTCCAGAATGCAAGAGGGGAATCGATACCCCCA-G
1 GGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCCAGG
316127 GG
66 GG
* * *
316129 GGGAACCGATACCCCCTCATCGTATAA-GAAATTCCAGAATGCTATAGGGGAACCGATA-CCCCA
1 GGGAACCGATACCCCCTCAACG-A-AATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCCA
316192 GGGG
64 GGGG
*
316196 GGGAACCGATTCCCCC
1 GGGAACCGATACCCCC
316212 ATGAGAAAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
66 25 0.34
67 46 0.63
68 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.15
Consensus pattern (67 bp):
GGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCCAGG
GG
Found at i:316544 original size:28 final size:29
Alignment explanation
Indices: 316512--316580 Score: 104
Period size: 28 Copynumber: 2.4 Consensus size: 29
316502 CATATTATGA
**
316512 TACATGACATGAATTTGTATTA-ATGTAT
1 TACATGACATGAATTCATATTATATGTAT
*
316540 TACATGACATAAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTATATGTAT
316569 TACATGACATGA
1 TACATGACATGA
316581 TTATGCAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 19 0.53
29 17 0.47
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTATATGTAT
Found at i:316638 original size:30 final size:31
Alignment explanation
Indices: 316596--316655 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
316586 CAGAAAAGTT
*
316596 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
316627 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
316656 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:316933 original size:23 final size:22
Alignment explanation
Indices: 316875--316940 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 22
316865 TTATGGACAA
316875 AATTCTAC-GGCACTTC-GTGC
1 AATTCTACGGGCACTTCGGTGC
316895 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
316917 AATTCTACGGGGCACTTCGGTGC
1 AATTCTAC-GGGCACTTCGGTGC
316940 A
1 A
316941 TTTATACGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
20 8 0.19
21 8 0.19
22 12 0.28
23 15 0.35
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Done.