Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007891.1 Hibiscus syriacus cultivar Beakdansim tig00110273_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: 893409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:181266 original size:34 final size:36
Alignment explanation
Indices: 181226--181312 Score: 83
Period size: 34 Copynumber: 2.4 Consensus size: 36
181216 ACCGCACTCG
*
181226 AAAAAAGAAA-AAAAAGAAAAAAAGAA-AA--GAAGAA
1 AAAAAAGAAAGAAAAAG-AAGAAAGAAGAAAAGAA-AA
*
181260 AAAAAAGAAAGAAAATGAAGAAAGAAGAAAAGAAAA
1 AAAAAAGAAAGAAAAAGAAGAAAGAAGAAAAGAAAA
*
181296 AAGTGAAAGAAAGAAAA
1 AA--AAAAGAAAGAAAA
181313 GATATATAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
34 18 0.41
35 7 0.16
36 4 0.09
37 3 0.07
38 12 0.27
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.02
Consensus pattern (36 bp):
AAAAAAGAAAGAAAAAGAAGAAAGAAGAAAAGAAAA
Found at i:181305 original size:25 final size:25
Alignment explanation
Indices: 181225--181312 Score: 85
Period size: 25 Copynumber: 3.5 Consensus size: 25
181215 TACCGCACTC
*
181225 GAAA-AAAGAAAAAAAAGAAAAAA-A
1 GAAAGAAAG-AAAAAAAGAAAAAAGT
*
181249 GAAA-AGAAGAAAAAAAAGAAAGAAAAT
1 GAAAGA-AAG-AAAAAAAGAAA-AAAGT
*
181276 G-AAGAAAGAAGAAAAGAAAAAAGT
1 GAAAGAAAGAAAAAAAGAAAAAAGT
181300 GAAAGAAAGAAAA
1 GAAAGAAAGAAAA
181313 GATATATAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
24 10 0.18
25 35 0.64
26 8 0.15
27 2 0.04
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.02
Consensus pattern (25 bp):
GAAAGAAAGAAAAAAAGAAAAAAGT
Found at i:184062 original size:45 final size:44
Alignment explanation
Indices: 184008--184114 Score: 160
Period size: 44 Copynumber: 2.4 Consensus size: 44
183998 ACTCCTTCAT
184008 GAAGAGAAGTCAATCTTTCAGCAATGTCATTCTTGACTTTCTCGG
1 GAAGAGAAGTCAATCTTTCAGCAATG-CATTCTTGACTTTCTCGG
* * * * *
184053 GATGAGAAGTCAATCTTTTAGTATTGCATTCTTGACTTTCTCGT
1 GAAGAGAAGTCAATCTTTCAGCAATGCATTCTTGACTTTCTCGG
184097 GAAGAGAAGTCAATCTTT
1 GAAGAGAAGTCAATCTTT
184115 TAGTATTGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
44 34 0.61
45 22 0.39
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (44 bp):
GAAGAGAAGTCAATCTTTCAGCAATGCATTCTTGACTTTCTCGG
Found at i:184108 original size:89 final size:89
Alignment explanation
Indices: 184004--184293 Score: 264
Period size: 89 Copynumber: 3.2 Consensus size: 89
183994 CCTGACTCCT
* * * *
184004 TCATGAAGAGAAGTCAATCTTTCAGCAATGTCATTCTTGACTTTCTCGGGATGAGAAGTCAATCT
1 TCATGAAGAGAAGTCAATCTTT-AGTATTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCT
184069 TTTAGTATTG-CATTCTTGACTTTC
65 TTTAGTATTGTCATTCTTGACTTTC
* * * * * * *
184093 TCGTGAAGAGAAGTCAATCTTTTAGTATTGTTATTTTTTACGTTCTCATGAAGAAAAGTCAATC-
1 TCATGAAGAGAAGTCAATC-TTTAGTATTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCT
* *
184157 TTTAATGA-TGTTATTCTTGACTTTC
65 TTTAGT-ATTGTCATTCTTGACTTTC
* * * * * * * * *
184182 TTATAAAAAGGAGTCAATCTATTGGTGTTGTCATTCTTGCCTTTCACGTGACGAGAAGTCAATCT
1 TCATGAAGAGAAGTCAATCT-TTAGTATTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCT
* * *
184247 TTTAGTGTTGTCCTTCTTGACTTTT
65 TTTAGTATTGTCATTCTTGACTTTC
* *
184272 TCACGAAGA-AGAGTCAACCTTT
1 TCATGAAGAGA-AGTCAATCTTT
184294 TAGTGGTGAT
Statistics
Matches: 154, Mismatches: 40, Indels: 14
0.74 0.19 0.07
Matches are distributed among these distances:
88 8 0.05
89 111 0.72
90 35 0.23
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (89 bp):
TCATGAAGAGAAGTCAATCTTTAGTATTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTT
TTAGTATTGTCATTCTTGACTTTC
Found at i:184154 original size:45 final size:45
Alignment explanation
Indices: 184004--184297 Score: 272
Period size: 45 Copynumber: 6.6 Consensus size: 45
183994 CCTGACTCCT
* * *
184004 TCATGAAGAGAAGTCAATCTTTCAGCAATGTCATTCTTGACTTTC
1 TCATGAAGAGAAGTCAATCTTTTAGTATTGTCATTCTTGACTTTC
** *
184049 TCGGGATGAGAAGTCAATCTTTTAGTATTG-CATTCTTGACTTTC
1 TCATGAAGAGAAGTCAATCTTTTAGTATTGTCATTCTTGACTTTC
* * * * *
184093 TCGTGAAGAGAAGTCAATCTTTTAGTATTGTTATTTTTTACGTTC
1 TCATGAAGAGAAGTCAATCTTTTAGTATTGTCATTCTTGACTTTC
* * *
184138 TCATGAAGAAAAGTCAATC-TTTAATGA-TGTTATTCTTGACTTTC
1 TCATGAAGAGAAGTCAATCTTTTAGT-ATTGTCATTCTTGACTTTC
* * * * * * * *
184182 TTATAAAAAGGAGTCAATCTATTGGTGTTGTCATTCTTGCCTTTC
1 TCATGAAGAGAAGTCAATCTTTTAGTATTGTCATTCTTGACTTTC
* * * * * *
184227 ACGTGACGAGAAGTCAATCTTTTAGTGTTGTCCTTCTTGACTTTT
1 TCATGAAGAGAAGTCAATCTTTTAGTATTGTCATTCTTGACTTTC
* *
184272 TCACGAAGA-AGAGTCAACCTTTTAGT
1 TCATGAAGAGA-AGTCAATCTTTTAGT
184298 GGTGATATTC
Statistics
Matches: 198, Mismatches: 46, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
44 76 0.38
45 122 0.62
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (45 bp):
TCATGAAGAGAAGTCAATCTTTTAGTATTGTCATTCTTGACTTTC
Found at i:184280 original size:134 final size:134
Alignment explanation
Indices: 184060--184311 Score: 317
Period size: 134 Copynumber: 1.9 Consensus size: 134
184050 CGGGATGAGA
* * *
184060 AGTCAATCTTTTAGTATTGCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTATTGTT
1 AGTCAATCTATTAGTATTGCATTCTTGACTTTCACGTGAAGAGAAGTCAATCTTTTAGTATTGTC
* * * * *
184125 ATTTTTTACGTTCTCATGAAGAAAAGTCAATC-TTTAATGATGTTATTCTTGACTTTCTTATAAA
66 ATTCTTGACGTTCTCACGAAGAAAAGTCAACCTTTTAATGATGATATTCTTGACTTTCTTATAAA
184189 AAGG
131 AAGG
* * * * *
184193 AGTCAATCTATTGGTGTTGTCATTCTTGCCTTTCACGTGACGAGAAGTCAATCTTTTAGTGTTGT
1 AGTCAATCTATTAGTATTG-CATTCTTGACTTTCACGTGAAGAGAAGTCAATCTTTTAGTATTGT
* * * * * *
184258 CCTTCTTGACTTTTTCACGAAGAAGAGTCAACCTTTTAGTGGTGATATTCTTGA
65 CATTCTTGACGTTCTCACGAAGAAAAGTCAACCTTTTAATGATGATATTCTTGA
184312 ATCTCTCGTG
Statistics
Matches: 98, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
133 16 0.16
134 65 0.66
135 17 0.17
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (134 bp):
AGTCAATCTATTAGTATTGCATTCTTGACTTTCACGTGAAGAGAAGTCAATCTTTTAGTATTGTC
ATTCTTGACGTTCTCACGAAGAAAAGTCAACCTTTTAATGATGATATTCTTGACTTTCTTATAAA
AAGG
Found at i:185673 original size:138 final size:136
Alignment explanation
Indices: 185314--185863 Score: 427
Period size: 138 Copynumber: 4.0 Consensus size: 136
185304 CTCCTTTCTT
185314 ACTTAGTCCTTTAATTTATGGA-AACTTTTAATTTGG-CCATCGCTTTTT-CTCGAGG-TTCAAT
1 ACTTAGTCCTTTAATTTA-GGAGAA-TTTTAATTTGGTCC-TCG-TTTTTGCTCGAGGTTTC-AT
* ** * * ** **
185375 TTTATTTATTCAATTCAATAATTGATTAAAATTGAATACGTTAATAATTAGAGAATCCACCTTAG
61 TTTAATTATTTGATT-AATAATTGATTAAAATTGAATAGGTTAATTATTAGAGCCTCCATTTTAG
*
185440 GCTTAATTTCAA
125 GCTTAATCTCAA
* * ** *
185452 ACTTAGTCCTTTAATTTAGGGGAATTTTTATTTTGGTCCTCACTTTTGCTCGAGGTTCCATTTTA
1 ACTTAGTCCTTTAATTTAGGAGAA-TTTTAATTTGGTCCTCGTTTTTGCTCGAGGTTTCATTTTA
* * * * *
185517 ATTTTTTGAATCAATAATTGAATAAAATTGACTAGGTTAATTATTAGAGCCTCAATTTTAGGCTT
65 ATTATTTG-ATTAATAATTGATTAAAATTGAATAGGTTAATTATTAGAGCCTCCATTTTAGGCTT
* *
185582 CATCTCAT
129 AATCTCAA
* * * *
185590 ATTTAGTCCTCTAGTTTAGGAGAATTCTTAATTTGGTCCTCGTTTTTGCTCAAGGTTTCATTTTA
1 ACTTAGTCCTTTAATTTAGGAGAATT-TTAATTTGGTCCTCGTTTTTGCTCGAGGTTTCATTTTA
* * * **
185655 ATTATTTGATTAATTAATTGGTTAAAATTTG-TTAGGTTGA-TATTTAGAGCCTCCATTTTAGTT
65 ATTATTTGATTAA-TAATTGATTAAAA-TTGAATAGGTTAATTA-TTAGAGCCTCCATTTTAGGC
*
185718 TTAATTTC--
127 TTAATCTCAA
* * * * *
185726 ACTTTAGTCCTTTAATTT-GAGATAATTTTTGATTTGGTCCACGATTTTATTCTCGAGGTTCCAT
1 AC-TTAGTCCTTTAATTTAG-GAGAA-TTTTAATTTGGTCCTCG-TTTT-TGCTCGAGGTTTCAT
* * ** * * * * *
185790 TTTGACTATTCAATTTAATAATTTATTAAAAATGATATGGGTTAA-TATTAGAGGCTACATTTTT
61 TTTAATTATTTGA-TTAATAATTGATTAAAATTGA-ATAGGTTAATTATTAGAGCCTCCA-TTTT
*
185854 AGGTTTAATC
123 AGGCTTAATC
185864 CTTTAGAGTC
Statistics
Matches: 328, Mismatches: 66, Indels: 34
0.77 0.15 0.08
Matches are distributed among these distances:
136 2 0.01
137 44 0.13
138 207 0.63
139 51 0.16
140 24 0.07
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (136 bp):
ACTTAGTCCTTTAATTTAGGAGAATTTTAATTTGGTCCTCGTTTTTGCTCGAGGTTTCATTTTAA
TTATTTGATTAATAATTGATTAAAATTGAATAGGTTAATTATTAGAGCCTCCATTTTAGGCTTAA
TCTCAA
Found at i:189199 original size:24 final size:24
Alignment explanation
Indices: 189172--189217 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
189162 GTTAAAGAAT
* *
189172 ACATCTCTTGGTACTTCAAGTGAC
1 ACATCTCTTGGAACATCAAGTGAC
*
189196 ACATCTTTTGGAACATCAAGTG
1 ACATCTCTTGGAACATCAAGTG
189218 GCATAACTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (24 bp):
ACATCTCTTGGAACATCAAGTGAC
Found at i:191381 original size:30 final size:27
Alignment explanation
Indices: 191325--191381 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
191315 TTTCCTTGTT
*
191325 CTTAAATCATTTCATTCTTTTTATTTC
1 CTTAAATCATTTCATTCTTTTAATTTC
*
191352 CTTAAATTATTTCTTATATCTTTTAATTTC
1 CTTAAATCATTTC--AT-TCTTTTAATTTC
191382 TTCTTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.48
29 2 0.08
30 11 0.44
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.60
Consensus pattern (27 bp):
CTTAAATCATTTCATTCTTTTAATTTC
Found at i:196820 original size:14 final size:14
Alignment explanation
Indices: 196787--196820 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
196777 CCGGTCTGAC
*
196787 CCGACCCGACCCTA
1 CCGACCCGACCCGA
*
196801 CTGACCCGACCCGA
1 CCGACCCGACCCGA
196815 CCGACC
1 CCGACC
196821 GTTGATAGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.21, C:0.56, G:0.18, T:0.06
Consensus pattern (14 bp):
CCGACCCGACCCGA
Found at i:203878 original size:9 final size:9
Alignment explanation
Indices: 203864--203907 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
203854 GCTGGAAAAA
203864 CGGTTTGAC
1 CGGTTTGAC
*
203873 CGGTTTTTAAC
1 CGG--TTTGAC
203884 CGGTTATGAC
1 CGGTT-TGAC
203894 CGGTTTGAC
1 CGGTTTGAC
203903 CGGTT
1 CGGTT
203908 CCGATCGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 14 0.47
10 8 0.27
11 8 0.27
ACGTcount: A:0.14, C:0.20, G:0.30, T:0.36
Consensus pattern (9 bp):
CGGTTTGAC
Found at i:217771 original size:19 final size:19
Alignment explanation
Indices: 217733--217778 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
217723 TTCATTAGTG
* *
217733 TTCATACAGTTCGGTACTA
1 TTCATACAATTCGATACTA
217752 -TCATACAATATCGATACTA
1 TTCATACAAT-TCGATACTA
217771 TTCATACA
1 TTCATACA
217779 GTATAATACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.35
19 8 0.35
20 7 0.30
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (19 bp):
TTCATACAATTCGATACTA
Found at i:217787 original size:19 final size:20
Alignment explanation
Indices: 217747--217795 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
217737 TACAGTTCGG
*
217747 TACTA-TCATACAATATCGA
1 TACTATTCATACAATATCAA
*
217766 TACTATTCATACAGTAT-AA
1 TACTATTCATACAATATCAA
217785 TACTATTCATA
1 TACTATTCATA
217796 AAAAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.37
Consensus pattern (20 bp):
TACTATTCATACAATATCAA
Found at i:218054 original size:18 final size:18
Alignment explanation
Indices: 218007--218064 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
217997 ATGTTTAATG
*
218007 AAAAAGATACTAATTGTTT
1 AAAAAGATACAAATTG-TT
*
218026 ACAAAAGGATACCAATTGTT
1 A-AAAA-GATACAAATTGTT
218046 AAAAAGATACAAATTGTT
1 AAAAAGATACAAATTGTT
218064 A
1 A
218065 CCAATTGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 13 0.37
19 5 0.14
20 7 0.20
21 10 0.29
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (18 bp):
AAAAAGATACAAATTGTT
Found at i:238382 original size:14 final size:14
Alignment explanation
Indices: 238363--238392 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
238353 AAATAATACC
238363 ACCCATTTGAATAA
1 ACCCATTTGAATAA
238377 ACCCATTTGAATAA
1 ACCCATTTGAATAA
238391 AC
1 AC
238393 ATTTAAGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (14 bp):
ACCCATTTGAATAA
Found at i:240192 original size:17 final size:17
Alignment explanation
Indices: 240170--240214 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
240160 TATTGAATTG
240170 GATTCCAATTCATGACA
1 GATTCCAATTCATGACA
**
240187 GATTCCAATTTTTGACA
1 GATTCCAATTCATGACA
240204 GATTCCAATTC
1 GATTCCAATTC
240215 CTTCATAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (17 bp):
GATTCCAATTCATGACA
Found at i:240226 original size:18 final size:18
Alignment explanation
Indices: 240203--240239 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
240193 AATTTTTGAC
*
240203 AGATTCCAATTCCTTCAT
1 AGATTCCAATTCCCTCAT
240221 AGATTCCAATTCCCTCAT
1 AGATTCCAATTCCCTCAT
240239 A
1 A
240240 AACATTGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (18 bp):
AGATTCCAATTCCCTCAT
Found at i:242286 original size:42 final size:41
Alignment explanation
Indices: 242191--242294 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 41
242181 CGAAGGTCTT
*
242191 ATAGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGACTG
1 ATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTG
* * *
242232 ATAGATGACCCGAAGGATTTAATCAT-TATGCTCGAAACG-CTT
1 ATAGATGGCCCGAAGGACTT-ATCATCT-TGCTCGAAA-GACTG
242274 ACT-GATGGCCCGAAGGACTTA
1 A-TAGATGGCCCGAAGGACTTA
242295 CTAAGTAAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
41 20 0.38
42 31 0.58
43 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (41 bp):
ATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTG
Found at i:242697 original size:228 final size:228
Alignment explanation
Indices: 242166--243240 Score: 959
Period size: 228 Copynumber: 4.6 Consensus size: 228
242156 TTTGAGAATT
* * *
242166 TGAAAATATCATACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCT-AAAGAC
1 TGAAAACATCCTACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCT-TGAAAGGC
* * * *
242230 TGATAGATGACCCGAAGGATTTAATCATTATGCTCGAAACGCTTACTGATGGCCCGAAGGACTTA
65 TTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAACACTTACTGATGGCCCGAAGGACTTA
* * * *
242295 CTAAGTAAGAAACTTTCGAAA-CTGTTTTCTTACTTTTCAAAAAATTTCATTTTC-AAAAAGATT
130 CCAAGTAAGAAACTTTGGAAATC-GCTTTCTTAC-TTT------A---CATTTTCTAAAAACA-T
* * * * *
242358 TAAATGAGAATCTTTGCAAATCACTTTCTCATTTTTCAAAATCACG
183 TAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTCATG
* * *
242404 TGAAAATATCCTACCCGATGGTCTTAGAGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGGCT
1 TGAAAACATCCTACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGGCT
* * * *
242469 TACAAATGACCCGAAGGATTTAATCATCATTCTCGAAATACTTATTGATGGCCCGAAGGACTTAC
66 TACAGATGACCCGAAGGATTTAATCATCATGCTCGAAACACTTACTGATGGCCCGAAGGACTTAC
* *
242534 CAAGTAAGAAACTTTGGAAATCGCTTTCTTTCTTTACATTTTCTAAAAACATTAAATGATAAACT
131 CAAGTAAGAAACTTTGGAAATCGCTTTCTTACTTTACATTTTCTAAAAACATTAAATGAGAAACT
*
242599 TTGAAAATCGCTTTCTTATTTTTCAAATTCATG
196 TTGAAAATCGCTTTCTCATTTTTCAAATTCATG
* * * *
242632 TGAAAACATCTTTCTCGAAGGTCTTATAGATGGCCC-AATGAACTTATCATCTTGCTTGAAAGGC
1 TGAAAACATCCTACCCGAAGGTCTTATAGATGGCCCGAA-GGACTTATCATCTTGCTTGAAAGGC
* * * * *
242696 TTACAGGTGGCCTGAAGGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTA
65 TTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAACACTTACTGATGGCCCGAAGGACTTA
* *
242761 CTC-AGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCATTTTCT-AAAACATTAAATGAGAAA
130 C-CAAGTAAGAAACTTTGGAAATCGCTTTCTTACTTTACATTTTCTAAAAACATTAAATGAGAAA
*
242824 CTTTGAAAATTGCTTTCTCATTTTTCAAATTCATG
194 CTTTGAAAATCGCTTTCTCATTTTTCAAATTCATG
* * * * ** * *
242859 TGAAAACATCCTGCCCGAATGTCTTATAGATGGCACGAAGGTCTTAT-AGATGGCCTG-AAGGAC
1 TGAAAACATCCTACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGG-C
** ** * * * * * **
242922 TTATCATCTTG-CTCAAAATGCTTACAGATGATCTGAATGATTTAATCATCATGCTCGAAATACT
65 TTA-CA-GATGAC-CCGAAGGATT-TA-ATCATC---ATGCTCGAA--A-CA--CT-----TA--
* * * * * * *
242986 TACTGATGTCCCAAATGAATTACTAAGTAAGAAACTTTGGAAATCGATTTCTTTTCAAAAATTT-
110 --CTGATGGCCCGAAGGACTTACCAAGTAAGAAACTTTGGAAATCGCTTTC--TT----ACTTTA
* * * * **
243050 CATCTTCTGAAAATATTTAAATGAGAAACTTTGAAAATCGCTTTCT-AATTTTCAAATGAATG
167 CATTTTCTAAAAACA-TTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTCAAATTCATG
* * * *
243112 TGAAAACATTCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTT-CTTCGAAAGGC
1 TGAAAACATCCTACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTT-GAAAGGC
* * *
243176 TTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCGAATGACTTA
65 TTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAACACTTACTGATGGCCCGAAGGACTTA
243241 ACTTCTTCGG
Statistics
Matches: 687, Mismatches: 108, Indels: 89
0.78 0.12 0.10
Matches are distributed among these distances:
225 4 0.01
226 10 0.01
227 92 0.13
228 208 0.30
229 8 0.01
230 5 0.01
231 1 0.00
233 22 0.03
235 1 0.00
236 1 0.00
237 6 0.01
238 144 0.21
239 1 0.00
242 2 0.00
243 2 0.00
244 1 0.00
245 1 0.00
247 47 0.07
249 2 0.00
250 5 0.01
251 1 0.00
252 15 0.02
253 68 0.10
254 36 0.05
255 4 0.01
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (228 bp):
TGAAAACATCCTACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGGCT
TACAGATGACCCGAAGGATTTAATCATCATGCTCGAAACACTTACTGATGGCCCGAAGGACTTAC
CAAGTAAGAAACTTTGGAAATCGCTTTCTTACTTTACATTTTCTAAAAACATTAAATGAGAAACT
TTGAAAATCGCTTTCTCATTTTTCAAATTCATG
Found at i:242902 original size:20 final size:19
Alignment explanation
Indices: 242873--242925 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
242863 AACATCCTGC
*
242873 CCGAATGTCTTATAGATGG
1 CCGAAGGTCTTATAGATGG
242892 CACGAAGGTCTTATAGATGG
1 C-CGAAGGTCTTATAGATGG
*
242912 CCTGAAGGACTTAT
1 CC-GAAGGTCTTAT
242926 CATCTTGCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (19 bp):
CCGAAGGTCTTATAGATGG
Found at i:242951 original size:41 final size:42
Alignment explanation
Indices: 242901--242993 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 42
242891 GCACGAAGGT
* * * *
242901 CTTATAGATGGCCTGAAGGACTT-ATCATCTTGCTCAAAATG
1 CTTACAGATGACCTGAAGGACTTAATCATCATGCTCAAAATA
* * * *
242942 CTTACAGATGATCTGAATGATTTAATCATCATGCTCGAAATA
1 CTTACAGATGACCTGAAGGACTTAATCATCATGCTCAAAATA
*
242984 CTTACTGATG
1 CTTACAGATG
242994 TCCCAAATGA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 18 0.43
42 24 0.57
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Consensus pattern (42 bp):
CTTACAGATGACCTGAAGGACTTAATCATCATGCTCAAAATA
Found at i:243190 original size:41 final size:42
Alignment explanation
Indices: 243140--243240 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 42
243130 AGGTCTTATG
* *
243140 GATGGCCCGAAGGACTTATCATC-TTCTTCGAAAGGCTTAC-A
1 GATGGCCCGAAGGACTTATCATCATGC-TCGAAAGACTTACTA
* *
243181 GATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTA
1 GATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGACTTACTA
*
243224 -ATGGCCCGAATGACTTA
1 GATGGCCCGAAGGACTTA
243241 ACTTCTTCGG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
41 16 0.32
42 31 0.62
43 3 0.06
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (42 bp):
GATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTTACTA
Found at i:248100 original size:19 final size:19
Alignment explanation
Indices: 248078--248130 Score: 88
Period size: 19 Copynumber: 2.7 Consensus size: 19
248068 AAATACATGC
*
248078 AATGCAAATGCAAATGCTA
1 AATGCAAATGCAAATACTA
248097 AATGCAAATGCAAATACTA
1 AATGCAAATGCAAATACTA
248116 AATGCAAAATGCAAA
1 AATGC-AAATGCAAA
248131 ATGCAAAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 23 0.72
20 9 0.28
ACGTcount: A:0.53, C:0.15, G:0.13, T:0.19
Consensus pattern (19 bp):
AATGCAAATGCAAATACTA
Found at i:248138 original size:7 final size:6
Alignment explanation
Indices: 248074--248137 Score: 76
Period size: 6 Copynumber: 10.2 Consensus size: 6
248064 AAATAAATAC
*
248074 ATGC-A ATGCAA ATGCAA ATGCTAA ATGCAA ATGCAA ATACTAA ATGCAAA
1 ATGCAA ATGCAA ATGCAA ATGC-AA ATGCAA ATGCAA ATGC-AA ATGC-AA
248124 ATGCAAA ATGCAA A
1 ATGC-AA ATGCAA A
248138 AGGTTTCATT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
5 4 0.08
6 25 0.47
7 24 0.45
ACGTcount: A:0.52, C:0.16, G:0.14, T:0.19
Consensus pattern (6 bp):
ATGCAA
Found at i:253707 original size:13 final size:13
Alignment explanation
Indices: 253691--253715 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
253681 CATCATCTTT
253691 ATCGCAACCATTA
1 ATCGCAACCATTA
253704 ATCGCAACCATT
1 ATCGCAACCATT
253716 GCTGATATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.32, G:0.08, T:0.24
Consensus pattern (13 bp):
ATCGCAACCATTA
Found at i:263604 original size:16 final size:19
Alignment explanation
Indices: 263582--263627 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 19
263572 AAACATATAA
263582 TTAATAATAACCT-T-AAC
1 TTAATAATAACCTATAAAC
*
263599 -TAATAATAATCTATAAAC
1 TTAATAATAACCTATAAAC
263617 TTAATAATAAC
1 TTAATAATAAC
263628 AAAAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 11 0.46
17 1 0.04
18 3 0.12
19 9 0.38
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (19 bp):
TTAATAATAACCTATAAAC
Found at i:269130 original size:33 final size:31
Alignment explanation
Indices: 269084--269168 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 31
269074 TTTTTAGTTG
*
269084 ATAAAAATGAAAAAAGAAAACA-AT-GAATGAAA
1 ATAAAAATAAAAAAAGAAAA-ATATAG-AT-AAA
269116 ATGAAAAATAAAAAAAGAAAAATATAGATAAA
1 AT-AAAAATAAAAAAAGAAAAATATAGATAAA
*
269148 ATAAAAATAAGAACAAGAAAA
1 ATAAAAATAA-AAAAAGAAAA
269169 TAAGTGATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
31 8 0.17
32 17 0.36
33 21 0.45
34 1 0.02
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (31 bp):
ATAAAAATAAAAAAAGAAAAATATAGATAAA
Found at i:269171 original size:25 final size:25
Alignment explanation
Indices: 269120--269171 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
269110 ATGAAAATGA
* *
269120 AAAATAAAAAAAGAAAAATATAGAT
1 AAAATAAAAAAAGAAAAAGATAAAT
*
269145 AAAATAAAAATAAGAACAAGA-AAAT
1 AAAATAAAAA-AAGAAAAAGATAAAT
269170 AA
1 AA
269172 GTGATGAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.13
Consensus pattern (25 bp):
AAAATAAAAAAAGAAAAAGATAAAT
Found at i:288729 original size:31 final size:31
Alignment explanation
Indices: 288694--288760 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
288684 ATACTTTTCG
*
288694 TACATATTAATATGTGTGTATACATATTAAA
1 TACATATTAATATATGTGTATACATATTAAA
288725 TACATATTAATATATGTGTATACATATTAAA
1 TACATATTAATATATGTGTATACATATTAAA
288756 TACAT
1 TACAT
288761 TTTCATCCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.42
Consensus pattern (31 bp):
TACATATTAATATATGTGTATACATATTAAA
Found at i:288960 original size:87 final size:87
Alignment explanation
Indices: 288813--288985 Score: 276
Period size: 87 Copynumber: 2.0 Consensus size: 87
288803 TTAATTTGTT
* * *
288813 GAACAAGCTTTGTGCCCTGTATGTATATTATATAATATATAAGAGTGAAAATATCATATCATTTT
1 GAACAAGCTTTGTGCCCTGTACGTATATTATATAATATACAAGAGTGAAAATATCATATCACTTT
288878 AA-TTATTATTTTCTAAAATTC
66 AATTTATTATTTTCTAAAATTC
* * *
288899 GAACAAGCTTTGTGCCTTGTACGTATATTTATATAATATACAAGAGTGCAAATATCCTATCACTT
1 GAACAAGCTTTGTGCCCTGTACGTATA-TTATATAATATACAAGAGTGAAAATATCATATCACTT
288964 TAATTTATTATTTTCTAAAATT
65 TAATTTATTATTTTCTAAAATT
288986 AAATACTTGT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
86 25 0.32
87 36 0.46
88 18 0.23
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (87 bp):
GAACAAGCTTTGTGCCCTGTACGTATATTATATAATATACAAGAGTGAAAATATCATATCACTTT
AATTTATTATTTTCTAAAATTC
Found at i:291190 original size:19 final size:20
Alignment explanation
Indices: 291152--291192 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
291142 GAAACCCCTT
291152 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
*
291172 TGAAAATACATTA-TTTTAA
1 TGAAAATACATGATTTTTAA
291191 TG
1 TG
291193 TAGATAATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:292164 original size:21 final size:22
Alignment explanation
Indices: 292114--292164 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
292104 TGCTGTCATT
292114 ATATGTAAATGATATGCAAAAC
1 ATATGTAAATGATATGCAAAAC
*
292136 ATA-ATAAATGA-AT-CTAAAAC
1 ATATGTAAATGATATGC-AAAAC
292156 ATATGTAAA
1 ATATGTAAA
292165 CATAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 10 0.40
21 11 0.44
22 3 0.12
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (22 bp):
ATATGTAAATGATATGCAAAAC
Found at i:293663 original size:25 final size:25
Alignment explanation
Indices: 293629--293704 Score: 152
Period size: 25 Copynumber: 3.0 Consensus size: 25
293619 GAATAGGAAA
293629 AGGAAGTAGTAATAGTTTATATATC
1 AGGAAGTAGTAATAGTTTATATATC
293654 AGGAAGTAGTAATAGTTTATATATC
1 AGGAAGTAGTAATAGTTTATATATC
293679 AGGAAGTAGTAATAGTTTATATATC
1 AGGAAGTAGTAATAGTTTATATATC
293704 A
1 A
293705 TTCTTTTTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.36
Consensus pattern (25 bp):
AGGAAGTAGTAATAGTTTATATATC
Found at i:296080 original size:23 final size:23
Alignment explanation
Indices: 296037--296084 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
296027 TTTTTCAGTG
*
296037 TTATAATAATATATTTAATTATA
1 TTATAATAATATATATAATTATA
296060 TTATAATAATATATGAT-ATTATA
1 TTATAATAATATAT-ATAATTATA
296083 TT
1 TT
296085 CTTATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATAATAATATATATAATTATA
Found at i:306451 original size:85 final size:85
Alignment explanation
Indices: 306303--306478 Score: 214
Period size: 85 Copynumber: 2.1 Consensus size: 85
306293 ATACAATCAC
* * * *
306303 GACACAAGAATGTGTGTCATCTTTTTTAATGACGTGTGCTTCAATGACACGCAATGTAAGTCATA
1 GACACAAGAATGTGTGTCATCTTATTTAATGACGAGGGCTTCAATGACAAGCAATGTAAGTCATA
* ** *
306368 CATGCGTGTCATAAATTTGT
66 AATGCACGTCATAAATTTAT
*
306388 GACACATA-AATGTGTGTCATCTTCATTT-ATGACGAGGGCTTCAATGACAAGCAATG-AGCGTC
1 GACACA-AGAATGTGTGTCATCTT-ATTTAATGACGAGGGCTTCAATGACAAGCAATGTA-AGTC
*
306450 ATAAATGCACGTCATAGATTTAT
63 ATAAATGCACGTCATAAATTTAT
306473 GACACA
1 GACACA
306479 CAATTGCGCG
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
84 1 0.01
85 73 0.94
86 4 0.05
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (85 bp):
GACACAAGAATGTGTGTCATCTTATTTAATGACGAGGGCTTCAATGACAAGCAATGTAAGTCATA
AATGCACGTCATAAATTTAT
Found at i:307425 original size:12 final size:12
Alignment explanation
Indices: 307408--307442 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
307398 ATTCATTCAT
307408 CATATTTTTCTC
1 CATATTTTTCTC
307420 CATATTTTTCTC
1 CATATTTTTCTC
307432 CATATTTTTCT
1 CATATTTTTCT
307443 TACACGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (12 bp):
CATATTTTTCTC
Found at i:310000 original size:12 final size:12
Alignment explanation
Indices: 309977--310023 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
309967 AAATCTAATT
309977 TAAAAAATAACAA
1 TAAAAAA-AACAA
309990 TAAAAAAAACAA
1 TAAAAAAAACAA
* *
310002 TGAAAACAAC-A
1 TAAAAAAAACAA
*
310013 TAAAATAAACA
1 TAAAAAAAACA
310024 TAAGTACAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 8 0.29
12 13 0.46
13 7 0.25
ACGTcount: A:0.74, C:0.11, G:0.02, T:0.13
Consensus pattern (12 bp):
TAAAAAAAACAA
Found at i:311750 original size:13 final size:13
Alignment explanation
Indices: 311732--311757 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
311722 TAAATATTAA
311732 ATAATATAATAAT
1 ATAATATAATAAT
311745 ATAATATAATAAT
1 ATAATATAATAAT
311758 CTGAAAAAAA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATATAATAAT
Found at i:312904 original size:15 final size:16
Alignment explanation
Indices: 312884--312914 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
312874 CACCAAAAAT
312884 TTCATCCAT-ATCCGC
1 TTCATCCATCATCCGC
312899 TTCATCCATCATCCGC
1 TTCATCCATCATCCGC
312915 GGGTGGAGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.19, C:0.42, G:0.06, T:0.32
Consensus pattern (16 bp):
TTCATCCATCATCCGC
Found at i:313365 original size:20 final size:22
Alignment explanation
Indices: 313332--313375 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
313322 TATTTTTTTA
313332 ATATATATATATGGATGAATGG
1 ATATATATATATGGATGAATGG
* *
313354 ATATAT-TA-ATGGGTGGATGG
1 ATATATATATATGGATGAATGG
313374 AT
1 AT
313376 GCTGCGGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 2 0.10
22 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (22 bp):
ATATATATATATGGATGAATGG
Found at i:314485 original size:60 final size:57
Alignment explanation
Indices: 314387--314526 Score: 156
Period size: 60 Copynumber: 2.4 Consensus size: 57
314377 AAAGGGAAAG
* * *
314387 TACACAAATGATCCCTTGACTATATGACGATGCTTTGTTGAGTCTCCCGACTACTAAAAAT
1 TACA-AAATGATCCCTCGACTATAAGACGATGCTTTGTTCAGTC-CCCGA--ACTAAAAAT
* * * *
314448 TACAAAATGATCCCTCGACTATAAGGCGTTGCTTTGTTCAGTCCCCGAATTAAAAGT
1 TACAAAATGATCCCTCGACTATAAGACGATGCTTTGTTCAGTCCCCGAACTAAAAAT
*
314505 TACAAAATGGTCACC-CGACTAT
1 TACAAAATGATC-CCTCGACTAT
314527 TTATATGTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
57 25 0.36
58 2 0.03
59 5 0.07
60 34 0.49
61 4 0.06
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (57 bp):
TACAAAATGATCCCTCGACTATAAGACGATGCTTTGTTCAGTCCCCGAACTAAAAAT
Found at i:329745 original size:2 final size:2
Alignment explanation
Indices: 329738--329771 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
329728 ATTTAATCAA
*
329738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
329772 GACTAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:331174 original size:3 final size:3
Alignment explanation
Indices: 331168--331220 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
331158 TTTTTATTAT
* *
331168 TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA AAA TAA TAA -AA CGAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
331212 TAA TAA TAA
1 TAA TAA TAA
331221 ATAAATAACA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.09
3 38 0.86
4 2 0.05
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:331589 original size:123 final size:123
Alignment explanation
Indices: 331351--331975 Score: 816
Period size: 123 Copynumber: 5.1 Consensus size: 123
331341 TTGATTAAGA
* * * *
331351 TGGAAATGTTGATGCTGATCTATCTCCTTCTGCGAT-GAGTCGAGC-TAAGGTTGAACAAGTTCT
1 TGGAAATGTTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCT
* * *
331414 TCAGA-TATGAACTTATTCATCCTCTTTAGATGAGTTCTTCTTATTACGAACTCCTTC
66 TCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTC
* *
331471 TGGAAATGTTGATGTTGCTCTATCTCCTTCTACGATAGAGTCGAGCAAAGGGTTGAATAAGTTCT
1 TGGAAATGTTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCT
* * * *
331536 CCAGATTATGAACTTCTTCTTCATATTCAGATGAGTTCTTCTTATTACAAACTCCTTC
66 TCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTC
** * * * * *
331594 TGGAAACATTAATACTT-CTCTATCTCCTTCTGCAATAGAATCAAGCAAAAGGTTGAATAAGTTC
1 TGGAAATGTTGAT-GTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTC
*
331658 TTCAGATTATGAACTTCTTCTTCCTCTTCAGAAGAGTTCTTCTTATTACGAACTCCTTC
65 TTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTC
* * * *
331717 TGGAAATGTTGAT-TATGCTCTATCTCATTTTGTGATAGAATCGAGCAAAAGGTTGAATAAGTTC
1 TGGAAATGTTGATGT-TGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTC
* * * *
331781 TTCATATTATGAACTTATTCTTCCTCTTTAGATGAGTTCTTCTTATTATGAACTCCTGT-
65 TTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCT-TC
* * * *
331840 TGGAAATGTTGATGCTT-ATTTATCTCCTTTTGCAATAGAGTCGAGCAAAAGGTTGAATAAGTTC
1 TGGAAATGTTGATG-TTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTC
* * **
331904 TTTAGATTATGAACTTCGTT-TTCCTCTTCAGATGAGTTCTTCTTATTGCGAACTTTTTC
65 TTCAGATTATGAACTTC-TTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTC
331963 TGGAAATGTTGAT
1 TGGAAATGTTGAT
331976 CCATCGAGTG
Statistics
Matches: 440, Mismatches: 54, Indels: 19
0.86 0.11 0.04
Matches are distributed among these distances:
120 33 0.08
121 10 0.02
122 21 0.05
123 369 0.84
124 6 0.01
125 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (123 bp):
TGGAAATGTTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGTTCT
TCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTC
Found at i:341406 original size:117 final size:117
Alignment explanation
Indices: 341198--341412 Score: 308
Period size: 117 Copynumber: 1.8 Consensus size: 117
341188 TAATTGAAGG
* * *
341198 GTTCATAATGAGAAGAACTCATCCGAACAGGGAGAATAAGTTCATAATGAGAAGAACTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCCGAACAGGGAGAAGAAGTTCATAATAAGAAGAACTTATTCAA
* * *
341263 CCTTTGTTCGATTCCATCACAGAAGGAGGTGGATCAACATTTTCAGTGGAGA
66 CATTAGCTCGATTCCATCACAGAAGGAGGTGGATCAACATTTTCAGTGGAGA
*
341315 GTTCATAATGAGAAGAACTCATTC-AACGAGGGAGAAGAAGTTCATAATAAGAA-AGACTTATTC
1 GTTCATAATGAGAAGAACTCATCCGAAC-AGGGAGAAGAAGTTCATAATAAGAAGA-ACTTATTC
* * *
341378 AATATTAGCTCGATTCCATCACATAAGGAGTTGGA
64 AACATTAGCTCGATTCCATCACAGAAGGAGGTGGA
341413 ACGATATCAA
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
116 4 0.05
117 82 0.95
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (117 bp):
GTTCATAATGAGAAGAACTCATCCGAACAGGGAGAAGAAGTTCATAATAAGAAGAACTTATTCAA
CATTAGCTCGATTCCATCACAGAAGGAGGTGGATCAACATTTTCAGTGGAGA
Found at i:341869 original size:3 final size:3
Alignment explanation
Indices: 341861--341907 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
341851 TATTACCTTA
* *
341861 TAT TAT TAT TAT AAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
341908 CAAACCCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:344981 original size:21 final size:21
Alignment explanation
Indices: 344928--345003 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
344918 TGTGGAGTCA
* *
344928 TAGCTAGCTATGTAGTGTAGT
1 TAGCTAGCTAGGTAGTGTAGG
*
344949 TAACTA-CTTAGGTAGCT-TAGG
1 TAGCTAGC-TAGGTAG-TGTAGG
*
344970 TAGCTAGCTAGGCAGTGTAGG
1 TAGCTAGCTAGGTAGTGTAGG
344991 TAGCTAGCTAGGT
1 TAGCTAGCTAGGT
345004 TATTGACACT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
20 2 0.04
21 41 0.91
22 2 0.04
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.32
Consensus pattern (21 bp):
TAGCTAGCTAGGTAGTGTAGG
Found at i:351042 original size:18 final size:18
Alignment explanation
Indices: 351019--351053 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
351009 TCCCAGACTC
*
351019 TGGTTGAATCAACACTGG
1 TGGTTGAATCAAAACTGG
351037 TGGTTGAATCAAAACTG
1 TGGTTGAATCAAAACTG
351054 CCTTTAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (18 bp):
TGGTTGAATCAAAACTGG
Found at i:355657 original size:29 final size:27
Alignment explanation
Indices: 355625--355690 Score: 69
Period size: 30 Copynumber: 2.3 Consensus size: 27
355615 ACTAATACAC
355625 TTTTAAAAATATTTACGAAAATAACACCTT
1 TTTTAAAAATATTTA-GAAAATAACA--TT
* * *
355655 TTTTAAGAATATTTATAAAATATCATT
1 TTTTAAAAATATTTAGAAAATAACATT
*
355682 TTTAAAAAA
1 TTTTAAAAA
355691 ATAGCACACT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 9 0.29
29 8 0.26
30 14 0.45
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (27 bp):
TTTTAAAAATATTTAGAAAATAACATT
Found at i:355720 original size:29 final size:29
Alignment explanation
Indices: 355688--355778 Score: 121
Period size: 29 Copynumber: 3.1 Consensus size: 29
355678 CATTTTTAAA
* *
355688 AAAATAGCACACTTTTAAAATTATTTATG
1 AAAATAGCACACTTTTAAAAATATTTACG
*
355717 AAAATAACAC-CATTTTAAAAATATTTACG
1 AAAATAGCACAC-TTTTAAAAATATTTACG
* *
355746 AAAATAGCACAATTTCAAAAATATTTACG
1 AAAATAGCACACTTTTAAAAATATTTACG
355775 AAAA
1 AAAA
355779 CAACACCGGG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
28 1 0.02
29 53 0.98
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (29 bp):
AAAATAGCACACTTTTAAAAATATTTACG
Found at i:355768 original size:75 final size:75
Alignment explanation
Indices: 355621--355766 Score: 186
Period size: 75 Copynumber: 1.9 Consensus size: 75
355611 CAAAACTAAT
* * * * **
355621 ACACTTTTAAAAATATTTACGAAAATAACACCTTTTTTAAGAATATTTATAAAATATCATTTTTA
1 ACACTTTTAAAAATATTTACGAAAATAACACCTATTTTAAAAATATTTAGAAAATAGCAAATTTA
355686 AAAAAATAGC
66 AAAAAATAGC
* *
355696 ACACTTTTAAAATTATTTATGAAAATAACACC-ATTTTAAAAATATTTACGAAAATAGCACAATT
1 ACACTTTTAAAAATATTTACGAAAATAACACCTATTTTAAAAATATTTA-GAAAATAGCA-AATT
*
355760 TCAAAAA
64 TAAAAAA
355767 TATTTACGAA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
74 14 0.23
75 38 0.63
76 8 0.13
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35
Consensus pattern (75 bp):
ACACTTTTAAAAATATTTACGAAAATAACACCTATTTTAAAAATATTTAGAAAATAGCAAATTTA
AAAAAATAGC
Found at i:359749 original size:24 final size:24
Alignment explanation
Indices: 359722--359773 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
359712 ATTAGGATTT
* *
359722 TTTAATGTTTGTAGGTTGAAGTGG
1 TTTAAGGTTTGTAGGTTAAAGTGG
* *
359746 TTTAGGGTTTTTAGGTTAAAGTGG
1 TTTAAGGTTTGTAGGTTAAAGTGG
359770 TTTA
1 TTTA
359774 GGGGGTTGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (24 bp):
TTTAAGGTTTGTAGGTTAAAGTGG
Found at i:359774 original size:24 final size:24
Alignment explanation
Indices: 359728--359776 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
359718 ATTTTTTAAT
*
359728 GTTTGTAGGTTGAAGTGGTTTAGG
1 GTTTGTAGGTTAAAGTGGTTTAGG
*
359752 GTTTTTAGGTTAAAGTGGTTTAGG
1 GTTTGTAGGTTAAAGTGGTTTAGG
359776 G
1 G
359777 GGTTGATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.39, T:0.43
Consensus pattern (24 bp):
GTTTGTAGGTTAAAGTGGTTTAGG
Found at i:369374 original size:34 final size:31
Alignment explanation
Indices: 369332--369403 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 31
369322 GTACAAAAAG
*
369332 AAAGAAAAGACA-AAAAGAAGAAGAAAATTCAGAA
1 AAAGAAAAGA-AGAAAAGAAAAAG-AAATTC--AA
369366 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
1 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
369397 AAAGAAA
1 AAAGAAA
369404 GTAAGCCAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 9 0.25
33 7 0.19
34 20 0.56
ACGTcount: A:0.74, C:0.04, G:0.17, T:0.06
Consensus pattern (31 bp):
AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
Found at i:375373 original size:20 final size:20
Alignment explanation
Indices: 375335--375373 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
375325 GACGATCTGA
*
375335 CATCTAAACATAGTCAAAAT
1 CATCTAAACATAGTAAAAAT
375355 CATCT-AACATTAGTAAAAA
1 CATCTAAACA-TAGTAAAAA
375374 GTAACTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26
Consensus pattern (20 bp):
CATCTAAACATAGTAAAAAT
Found at i:382532 original size:27 final size:26
Alignment explanation
Indices: 382502--382616 Score: 114
Period size: 25 Copynumber: 4.5 Consensus size: 26
382492 GAAAATACAT
*
382502 TACATGGAAATATTGGAAACAAGCACA
1 TACATTGAAATATTGGAAA-AAGCACA
*
382529 TACATTGAAATATTGGAAAATAAG-A-T
1 TACATTGAAATATTGG-AAA-AAGCACA
382555 TACATTGAAATATT--ATAAAAGCACA
1 TACATTGAAATATTGGA-AAAAGCACA
* *
382580 TACATTAAAATATTAGAAAAA-CACA
1 TACATTGAAATATTGGAAAAAGCACA
*
382605 TACATTGTAATA
1 TACATTGAAATA
382617 ATATAAAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
23 4 0.05
24 3 0.04
25 27 0.36
26 18 0.24
27 17 0.23
28 6 0.08
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.27
Consensus pattern (26 bp):
TACATTGAAATATTGGAAAAAGCACA
Found at i:382565 original size:26 final size:26
Alignment explanation
Indices: 382486--382568 Score: 89
Period size: 27 Copynumber: 3.2 Consensus size: 26
382476 TCCTTGAAAT
* * *
382486 ATATTAGAAAAT-ACATTACATGGAA
1 ATATTGGAAAATAAGATTACATTGAA
* *
382511 ATATTGG-AAACAAGCACATACATTGAA
1 ATATTGGAAAATAAG-A-TTACATTGAA
382538 ATATTGGAAAATAAGATTACATTGAA
1 ATATTGGAAAATAAGATTACATTGAA
382564 ATATT
1 ATATT
382569 ATAAAAGCAC
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
24 3 0.06
25 7 0.15
26 15 0.32
27 16 0.34
28 6 0.13
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.29
Consensus pattern (26 bp):
ATATTGGAAAATAAGATTACATTGAA
Found at i:382574 original size:26 final size:24
Alignment explanation
Indices: 382486--382626 Score: 111
Period size: 25 Copynumber: 5.5 Consensus size: 24
382476 TCCTTGAAAT
* *
382486 ATATTAGAAAATACATTACATGGAA
1 ATATTAGAAAAAACA-TACATTGAA
*
382511 ATATTGGAAACAAGCACATACATTGAA
1 ATATTAGAAA-AA--ACATACATTGAA
* *
382538 ATATTGGAAAATAAGATTACATTGAA
1 ATATTAGAAAA-AACA-TACATTGAA
* * *
382564 ATATTATAAAAGCACATACATTAAA
1 ATATTAGAAAA-AACATACATTGAA
*
382589 ATATTAGAAAAACACATACATTGTA
1 ATATTAGAAAAA-ACATACATTGAA
* *
382614 ATAATATAAAAAA
1 ATATTAGAAAAAA
382627 AATTACATAA
Statistics
Matches: 94, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
24 1 0.01
25 49 0.52
26 22 0.23
27 19 0.20
28 3 0.03
ACGTcount: A:0.54, C:0.09, G:0.10, T:0.27
Consensus pattern (24 bp):
ATATTAGAAAAAACATACATTGAA
Found at i:382591 original size:51 final size:51
Alignment explanation
Indices: 382486--382624 Score: 160
Period size: 51 Copynumber: 2.7 Consensus size: 51
382476 TCCTTGAAAT
* *
382486 ATATTAGAAAAT-ACATTACATGGAAATATTGGA-AACAAGCACATACATTGAA
1 ATATTAGAAAATAACATTACATTGAAATATT--ATAA-AAGCACATACATTAAA
* *
382538 ATATTGGAAAATAAGATTACATTGAAATATTATAAAAGCACATACATTAAA
1 ATATTAGAAAATAACATTACATTGAAATATTATAAAAGCACATACATTAAA
* *
382589 ATATTAGAAAA-ACACA-TACATTGTAATAATATAAAA
1 ATATTAGAAAATA-ACATTACATTGAAATATTATAAAA
382625 AAAATTACAT
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
50 19 0.25
51 28 0.37
52 13 0.17
53 16 0.21
ACGTcount: A:0.53, C:0.09, G:0.10, T:0.27
Consensus pattern (51 bp):
ATATTAGAAAATAACATTACATTGAAATATTATAAAAGCACATACATTAAA
Found at i:385549 original size:8 final size:8
Alignment explanation
Indices: 385538--385600 Score: 58
Period size: 8 Copynumber: 8.0 Consensus size: 8
385528 AATGGATAAA
385538 TTTGAGAG
1 TTTGAGAG
*
385546 TTTGAGAA
1 TTTGAGAG
385554 TTTGAGAG
1 TTTGAGAG
*
385562 ATTGAGAG
1 TTTGAGAG
385570 TTTGA-AGG
1 TTTGAGA-G
* *
385578 TGTAAGAG
1 TTTGAGAG
*
385586 TTTGA-AA
1 TTTGAGAG
385593 TTTGAGAG
1 TTTGAGAG
385601 CATACATCAA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
7 7 0.17
8 34 0.81
9 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.33, T:0.35
Consensus pattern (8 bp):
TTTGAGAG
Found at i:386285 original size:341 final size:335
Alignment explanation
Indices: 385646--386721 Score: 1085
Period size: 341 Copynumber: 3.2 Consensus size: 335
385636 CTAGTCAAGA
* ** * * * *
385646 AACTATTCATATCAACCAATAATATGTTTGATGGGATGATATAGTCTGACATGGTAAAGATTCTT
1 AACTATTCACATCAACCCCTAATATGTTTGATGGGATGAGACAATATGACATGGTAAAGATTCTT
* * * * * *
385711 TGAAAAATGTGAAAGCGCTTCTTGTGGGGCACGCCTTCCCTTTTCGTTATAGTTTATATGCATTC
66 TGAAAAAGGTGAAAGCGCTTCTTGTGAGACAC-CCTTCCCTTTTCGATAGAGTTTCTATGCATTC
* * * * *
385776 TTCAGTTAACAATTGGAAGTTATG-GTGTCCCCATTCGAGGGGAACTATTCACATCAACCTCTAA
130 TTCAGTTAATAATAGGTAGTTATGTGT-TCCCAATT--A-GGGAACTATTCAAATCAACC-CTAA
* * * *
385840 AATTTTTGATGGGATGTGACAGTATGACAT-ACAGAGATTCTCT-AAAAACGGTAAAAGAGCTTC
190 TA-TTTTGATGGGATGAGACAGTATGACATGGCAGAGATTCTCTGAAAAA-GGTAAAAGCGCTTC
* * * *
385903 TTGTGGGATGTGCCTTCCCTTTTCGTTAGAGTTTCTTTGCATTGTTCATTTAATAATAGGCAAAT
253 TTGGGGGATGTGTCTTCCCTTTTCGTTAGAGTTTATTTGCATTCTTCATTTAATAATAGG-AAAT
385968 ATGGTGTTCCCAGTTGAGG
317 ATGGTGTTCCCAGTTGAGG
* * *
385987 AACTATTCACATCAACCCCTAATATGTTTAATGGGATGAGACAATATGACATGGAAAAGATTCTA
1 AACTATTCACATCAACCCCTAATATGTTTGATGGGATGAGACAATATGACATGGTAAAGATTCTT
* * * **
386052 TGAAAAAGGTGAAAGCGCTTCTTGTGAGACACATCTTTCCTTTTCGACAGAGTTTCTCGGCATTC
66 TGAAAAAGGTGAAAGCGCTTCTTGTGAGACAC-CCTTCCCTTTTCGATAGAGTTTCTATGCATTC
* *
386117 TTTAGTTAATAATAGGTAGTTATAGTGTTCCCAATTTGGGAACTATTCAAATCAACTCCTAATAT
130 TTCAGTTAATAATAGGTAGTTAT-GTGTTCCCAATTAGGGAACTATTCAAATCAAC-CCTAATAT
* * * *
386182 TTTGAATGGGGTGAGA-ATTTATGACATGGCAGAGATTCTGTGAAAAAGGTGAAAGCGCTTCTTG
193 TTTG-ATGGGATGAGACA-GTATGACATGGCAGAGATTCTCTGAAAAAGGTAAAAGCGCTTCTTG
* * * * * * *
386246 GGGGATGTGTCTTCCCTTTTTTGTCATAATTGT-TTTGCATTCATCATTTTATAATAGGTAGCA-
256 GGGGATGTGTCTTCCC-TTTTCGTTAGAGTT-TATTTGCATTCTTCATTTAATAATAGG-A-AAT
* *
386309 ATGGTGTTCCCAATCGAGG
317 ATGGTGTTCCCAGTTGAGG
* * *** * * * *
386328 AACTATTCAAATCAACCCCTAATATGTTTGCTATTATTAGATAGTATGACATGGTAGAGATTCTT
1 AACTATTCACATCAACCCCTAATATGTTTGATGGGATGAGACAATATGACATGGTAAAGATTCTT
** * * *
386393 TG-AAAAGGTGAAAATGCTTCTTAT-AGGACGCGCATTCCCTTTTC-ATTAGAGTTTCTATGCAT
66 TGAAAAAGGTGAAAGCGCTTCTTGTGA-GACAC-CCTTCCCTTTTCGA-TAGAGTTTCTATGCAT
* * * * * * * ***
386455 TCTTCAATTAATAATAGGTTGCTATGATGTTCCCAGTAAGAGAACTATTTAGGCCAACCCCTAAT
128 TCTTCAGTTAATAATAGGTAGTTATG-TGTTCCCAATTAGGGAACTATTCAAATCAA-CCCTAAT
* * *
386520 ATGTTTGATGGGATGAGACAGTATGACATGGAAAAGATTCTCTGAAAAAGGTAAAATCGCTTCTT
191 AT-TTTGATGGGATGAGACAGTATGACATGGCAGAGATTCTCTGAAAAAGGTAAAAGCGCTTCTT
* * * *
386585 -GGGGACGCGTCTTCCCTTTTCGTTAGAGTTTATCTGCATTCTTCAATTAATAATAGGAAACTAT
255 GGGGGATGTGTCTTCCCTTTTCGTTAGAGTTTATTTGCATTCTTCATTTAATAATAGGAAA-TAT
* * *
386649 TGTGTTCCTAG-TCAGGG
319 GGTGTTCCCAGTTGA-GG
*
386666 AACTATTCACATCAACCCCTAATATTTTTGATGGGATGAGACAATATGACATGGTA
1 AACTATTCACATCAACCCCTAATATGTTTGATGGGATGAGACAATATGACATGGTA
386722 GATATTCTCT
Statistics
Matches: 598, Mismatches: 117, Indels: 43
0.79 0.15 0.06
Matches are distributed among these distances:
336 1 0.00
337 3 0.01
338 96 0.16
339 57 0.10
340 186 0.31
341 243 0.41
342 10 0.02
343 2 0.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (335 bp):
AACTATTCACATCAACCCCTAATATGTTTGATGGGATGAGACAATATGACATGGTAAAGATTCTT
TGAAAAAGGTGAAAGCGCTTCTTGTGAGACACCCTTCCCTTTTCGATAGAGTTTCTATGCATTCT
TCAGTTAATAATAGGTAGTTATGTGTTCCCAATTAGGGAACTATTCAAATCAACCCTAATATTTT
GATGGGATGAGACAGTATGACATGGCAGAGATTCTCTGAAAAAGGTAAAAGCGCTTCTTGGGGGA
TGTGTCTTCCCTTTTCGTTAGAGTTTATTTGCATTCTTCATTTAATAATAGGAAATATGGTGTTC
CCAGTTGAGG
Found at i:386731 original size:169 final size:170
Alignment explanation
Indices: 385631--386731 Score: 984
Period size: 169 Copynumber: 6.5 Consensus size: 170
385621 GCAGAAATGA
* * * * ** * * *
385631 TGTTCCTAGTCAAGAAACTATTCATATCAACCAATAATATGTTTGATGGGATGATATAGTCTGAC
1 TGTTCCCAGTCAGGGAACTATTCACATCAACCCCTAATATGTTTGATGGGATGAGACAGTATGAC
* * * * * * * *
385696 ATGGTAAAGATTCTTTGAAAAATGTGAAAGCGCTTCTTGTGGGGCACGCCTTCCCTTTTCGTTAT
66 ATGGTAGAGATTCTCTGAAAAAGGTAAAAGCGCTTCTTGTGGGACGCGTCTTCCCTTTTCGTTAG
* * * * *
385761 AGTTTATATGCATTCTTCAGTTAACAATTGGAAGTTATGG
131 AGTTTCTATGCATTCTTCAATTAATAATAGGAAGCTATGG
* * * * * *
385801 TGTCCCCATTCGAGGGGAACTATTCACATCAACCTCTAAAATTTTTGATGGGATGTGACAGTATG
1 TGTTCCCAGTC-A-GGGAACTATTCACATCAACCCCTAATATGTTTGATGGGATGAGACAGTATG
** * * * *
385866 ACAT-ACAGAGATTCTCT-AAAAACGGTAAAAGAGCTTCTTGTGGGATGTGCCTTCCCTTTTCGT
64 ACATGGTAGAGATTCTCTGAAAAA-GGTAAAAGCGCTTCTTGTGGGACGCGTCTTCCCTTTTCGT
* * * *
385929 TAGAGTTTCTTTGCATTGTTCATTTAATAATAGGCAA-ATATGG
128 TAGAGTTTCTATGCATTCTTCAATTAATAATAGG-AAGCTATGG
* * *
385972 TGTTCCCAGT-TGAGGAACTATTCACATCAACCCCTAATATGTTTAATGGGATGAGACAATATGA
1 TGTTCCCAGTCAG-GGAACTATTCACATCAACCCCTAATATGTTTGATGGGATGAGACAGTATGA
* * * * * * * * **
386036 CATGGAAAAGATTCTATGAAAAAGGTGAAAGCGCTTCTTGTGAGACACATCTTTCCTTTTCGACA
65 CATGGTAGAGATTCTCTGAAAAAGGTAAAAGCGCTTCTTGTGGGACGCGTCTTCCCTTTTCGTTA
** * * * * *
386101 GAGTTTCTCGGCATTCTTTAGTTAATAATAGGTAGTTATAG
130 GAGTTTCTATGCATTCTTCAATTAATAATAGGAAGCTATGG
* ** * * * *
386142 TGTTCCCAATTTGGGAACTATTCAAATCAACTCCTAATAT-TTTGAATGGGGTGAGA-ATTTATG
1 TGTTCCCAGTCAGGGAACTATTCACATCAACCCCTAATATGTTTG-ATGGGATGAGACA-GTATG
* * * * * * *
386205 ACATGGCAGAGATTCTGTGAAAAAGGTGAAAGCGCTTCTTGGGGGATGTGTCTTCCCTTTTTTGT
64 ACATGGTAGAGATTCTCTGAAAAAGGTAAAAGCGCTTCTTGTGGGACGCGTCTTCCC-TTTTCGT
* * * * * * * * *
386270 CATAATTGT-TTTGCATTCATCATTTTATAATAGGTAGCAATGG
128 TAGAGTT-TCTATGCATTCTTCAATTAATAATAGGAAGCTATGG
* * * *** * *
386313 TGTTCCCAATC-GAGGAACTATTCAAATCAACCCCTAATATGTTTGCTATTATTAGATAGTATGA
1 TGTTCCCAGTCAG-GGAACTATTCACATCAACCCCTAATATGTTTGATGGGATGAGACAGTATGA
* * * * *
386377 CATGGTAGAGATTCTTTG-AAAAGGTGAAAA-TGCTTCTTATAGGACGCG-CATTCCCTTTTCAT
65 CATGGTAGAGATTCTCTGAAAAAGGT-AAAAGCGCTTCTTGTGGGACGCGTC-TTCCCTTTTCGT
** *
386439 TAGAGTTTCTATGCATTCTTCAATTAATAATAGGTTGCTATGA
128 TAGAGTTTCTATGCATTCTTCAATTAATAATAGGAAGCTATGG
* * * ***
386482 TGTTCCCAGTAAGAGAACTATTTAGGCCAACCCCTAATATGTTTGATGGGATGAGACAGTATGAC
1 TGTTCCCAGTCAGGGAACTATTCACATCAACCCCTAATATGTTTGATGGGATGAGACAGTATGAC
* * *
386547 ATGGAAAAGATTCTCTGAAAAAGGTAAAATCGCTTCTTG-GGGACGCGTCTTCCCTTTTCGTTAG
66 ATGGTAGAGATTCTCTGAAAAAGGTAAAAGCGCTTCTTGTGGGACGCGTCTTCCCTTTTCGTTAG
* * * *
386611 AGTTTATCTGCATTCTTCAATTAATAATAGGAAACTATTG
131 AGTTTCTATGCATTCTTCAATTAATAATAGGAAGCTATGG
* * *
386651 TGTTCCTAGTCAGGGAACTATTCACATCAACCCCTAATATTTTTGATGGGATGAGACAATATGAC
1 TGTTCCCAGTCAGGGAACTATTCACATCAACCCCTAATATGTTTGATGGGATGAGACAGTATGAC
*
386716 ATGGTAGATATTCTCT
66 ATGGTAGAGATTCTCT
386732 CTTCACATCA
Statistics
Matches: 745, Mismatches: 163, Indels: 47
0.78 0.17 0.05
Matches are distributed among these distances:
168 2 0.00
169 281 0.38
170 220 0.30
171 190 0.26
172 52 0.07
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (170 bp):
TGTTCCCAGTCAGGGAACTATTCACATCAACCCCTAATATGTTTGATGGGATGAGACAGTATGAC
ATGGTAGAGATTCTCTGAAAAAGGTAAAAGCGCTTCTTGTGGGACGCGTCTTCCCTTTTCGTTAG
AGTTTCTATGCATTCTTCAATTAATAATAGGAAGCTATGG
Found at i:387605 original size:18 final size:18
Alignment explanation
Indices: 387568--387652 Score: 80
Period size: 18 Copynumber: 4.7 Consensus size: 18
387558 GCAATTTGAG
* * *
387568 TTTGAATTTTAATGTCAA
1 TTTGAATTTGAATATGAA
*
387586 TTTTAATTTGAATATGAA
1 TTTGAATTTGAATATGAA
*
387604 TTTGAATTTGTATATGAA
1 TTTGAATTTGAATATGAA
* * * *
387622 TTTGGATTTGGATTTCAA
1 TTTGAATTTGAATATGAA
*
387640 TTTCAATTTGAAT
1 TTTGAATTTGAAT
387653 TTACATTTTC
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.32, C:0.04, G:0.14, T:0.51
Consensus pattern (18 bp):
TTTGAATTTGAATATGAA
Found at i:387654 original size:18 final size:18
Alignment explanation
Indices: 387572--387672 Score: 69
Period size: 18 Copynumber: 5.6 Consensus size: 18
387562 TTTGAGTTTG
* * *
387572 AATTTTAATGTCAATTTT
1 AATTTGAATTTCAATTTC
* * *
387590 AATTTGAATATGAATTTG
1 AATTTGAATTTCAATTTC
* * * *
387608 AATTTGTATATGAATTTG
1 AATTTGAATTTCAATTTC
* *
387626 GATTTGGATTTCAATTTC
1 AATTTGAATTTCAATTTC
*
387644 AATTTGAATTTACATTTTC
1 AATTTGAATTT-CAATTTC
387663 -ATTTGAATTT
1 AATTTGAATTT
387673 TTTTAGCTCA
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
18 63 0.91
19 6 0.09
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (18 bp):
AATTTGAATTTCAATTTC
Found at i:387673 original size:12 final size:12
Alignment explanation
Indices: 387568--387673 Score: 72
Period size: 12 Copynumber: 8.8 Consensus size: 12
387558 GCAATTTGAG
387568 TTTGAATTTTAA
1 TTTGAATTTTAA
* *
387580 TGTCAATTTTAA
1 TTTGAATTTTAA
* *
387592 TTTGAATATGAA
1 TTTGAATTTTAA
387604 TTTGAATTTGT-A
1 TTTGAATTT-TAA
* **
387616 TATGAATTTGGA
1 TTTGAATTTTAA
* *
387628 TTTGGATTTCAA
1 TTTGAATTTTAA
* *
387640 TTTCAATTTGAA
1 TTTGAATTTTAA
*
387652 TTT-ACATTTTCA
1 TTTGA-ATTTTAA
387664 TTTGAATTTT
1 TTTGAATTTT
387674 TTTAGCTCAT
Statistics
Matches: 71, Mismatches: 19, Indels: 8
0.72 0.19 0.08
Matches are distributed among these distances:
11 1 0.01
12 69 0.97
13 1 0.01
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (12 bp):
TTTGAATTTTAA
Found at i:391079 original size:35 final size:34
Alignment explanation
Indices: 391039--391162 Score: 158
Period size: 35 Copynumber: 3.6 Consensus size: 34
391029 ATCAAAAAAA
* *
391039 TTGATTAAAGTAGAAGGGAAGGAAGCATCACACT
1 TTGATTCAAGTAGAACGGAAGGAAGCATCACACT
* * *
391073 TCTGATTCAAGTAGAACGGAATGAGGCATCGCACT
1 T-TGATTCAAGTAGAACGGAAGGAAGCATCACACT
*
391108 TTCGATTCAAGTCGAACGGAAGGAAGCATCACACT
1 TT-GATTCAAGTAGAACGGAAGGAAGCATCACACT
*
391143 TTCGATTCAACTAGAACGGA
1 TT-GATTCAAGTAGAACGGA
391163 TGGTTTACTA
Statistics
Matches: 77, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
34 2 0.03
35 75 0.97
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (34 bp):
TTGATTCAAGTAGAACGGAAGGAAGCATCACACT
Found at i:391292 original size:19 final size:19
Alignment explanation
Indices: 391268--391304 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
391258 TATTGGAATA
*
391268 TGCATTCTAGAATATGCAG
1 TGCATTCTAGAACATGCAG
391287 TGCATTCTAGAACATGCA
1 TGCATTCTAGAACATGCA
391305 CTGCTAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (19 bp):
TGCATTCTAGAACATGCAG
Found at i:391898 original size:146 final size:146
Alignment explanation
Indices: 391634--391930 Score: 585
Period size: 146 Copynumber: 2.0 Consensus size: 146
391624 GACATTTCTA
391634 TTGATATTTTAGATTTCTTTATATGCTTGAATTCATCTGCTTTAATCCATTGTTGATAGCTTTTA
1 TTGATATTTTAGATTTCTTTATATGCTTGAATTCATCTGCTTTAATCCATTGTTGATAGCTTTTA
391699 GATGAGAAATGCTTGAATTTCCTTATTCTCTCATGATTTTCACCTTCTTGGAAGTAGAGATCTGT
66 GATGAGAAATGCTTGAATTTCCTTATTCTCTCATGATTTTCACCTTCTTGGAAGTAGAGATCTGT
391764 CGCGTGAAATTGCCTC
131 CGCGTGAAATTGCCTC
391780 TTGATATTTTAGATTTCTTTATATGCTTGAATTCATCTGCTTTAATCCATTGTTGATAGCTTTTA
1 TTGATATTTTAGATTTCTTTATATGCTTGAATTCATCTGCTTTAATCCATTGTTGATAGCTTTTA
*
391845 GATGAGAAATGCTTGAATTTCCTTATTCTCTCGTGATTTTCACCTTCTTGGAAGTAGAGATCTGT
66 GATGAGAAATGCTTGAATTTCCTTATTCTCTCATGATTTTCACCTTCTTGGAAGTAGAGATCTGT
391910 CGCGTGAAATTGCCTC
131 CGCGTGAAATTGCCTC
391926 TTGAT
1 TTGAT
391931 TAACTTGCTT
Statistics
Matches: 150, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
146 150 1.00
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.44
Consensus pattern (146 bp):
TTGATATTTTAGATTTCTTTATATGCTTGAATTCATCTGCTTTAATCCATTGTTGATAGCTTTTA
GATGAGAAATGCTTGAATTTCCTTATTCTCTCATGATTTTCACCTTCTTGGAAGTAGAGATCTGT
CGCGTGAAATTGCCTC
Found at i:395032 original size:45 final size:47
Alignment explanation
Indices: 394939--395030 Score: 114
Period size: 50 Copynumber: 1.9 Consensus size: 47
394929 ACTAGATTTA
* * *
394939 TTATTTTATTAGGAATTAAGATCGAGTTAAAACATTATTCTTTGTTTATT
1 TTATTTTATTAGGAATTAAGATAGAATCAAAACATTATTC--T-TTTATT
*
394989 TTATTTTATTAGGAATTAGGATAGAATCAAAACATTA-TCTTT
1 TTATTTTATTAGGAATTAAGATAGAATCAAAACATTATTCTTT
395031 ATCCATTAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
46 2 0.05
47 1 0.03
49 2 0.05
50 33 0.87
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.47
Consensus pattern (47 bp):
TTATTTTATTAGGAATTAAGATAGAATCAAAACATTATTCTTTTATT
Found at i:401784 original size:26 final size:26
Alignment explanation
Indices: 401755--401804 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
401745 TTCTGTAAAA
401755 GAAATGAAACCATAATTAGTACTATT
1 GAAATGAAACCATAATTAGTACTATT
401781 GAAATGAAACCATAATTAGTACTA
1 GAAATGAAACCATAATTAGTACTA
401805 ATTCCAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (26 bp):
GAAATGAAACCATAATTAGTACTATT
Found at i:401816 original size:26 final size:26
Alignment explanation
Indices: 401756--401820 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
401746 TCTGTAAAAG
*
401756 AAATGAAACCATAATTAGTACTATTG
1 AAATGAAACCATAATTAGTACTATTC
401782 AAATGAAACCATAATTAGTACTAATTC
1 AAATGAAACCATAATTAGTACT-ATTC
*
401809 CAAT-AAA-CATAA
1 AAATGAAACCATAA
401821 GATTAATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
25 5 0.14
26 25 0.69
27 6 0.17
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.28
Consensus pattern (26 bp):
AAATGAAACCATAATTAGTACTATTC
Found at i:406074 original size:22 final size:21
Alignment explanation
Indices: 406049--406093 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
406039 AAAAATGGAA
*
406049 AATAACAAAACACGTAAAAAAT
1 AATAACAAAACA-ATAAAAAAT
* *
406071 AATAATAAAATAATAAAAAAT
1 AATAACAAAACAATAAAAAAT
406092 AA
1 AA
406094 ACAAAATGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (21 bp):
AATAACAAAACAATAAAAAAT
Found at i:406092 original size:10 final size:10
Alignment explanation
Indices: 406063--406108 Score: 58
Period size: 11 Copynumber: 4.5 Consensus size: 10
406053 ACAAAACACG
406063 TAAAAAATAA
1 TAAAAAATAA
406073 TAATAAAATAA
1 TAA-AAAATAA
406084 TAAAAAATAA
1 TAAAAAATAA
*
406094 -ACAAAATGAA
1 TAAAAAAT-AA
406104 TAAAA
1 TAAAA
406109 TGTTAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 6 0.19
10 12 0.39
11 13 0.42
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (10 bp):
TAAAAAATAA
Found at i:406094 original size:28 final size:28
Alignment explanation
Indices: 406063--406124 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
406053 ACAAAACACG
406063 TAAAAAATAAT-AATAAAATAATAAAAAA
1 TAAAAAA-AATGAATAAAATAATAAAAAA
* **
406091 TAAACAAAATGAATAAAATGTTAAAAAA
1 TAAAAAAAATGAATAAAATAATAAAAAA
*
406119 CAAAAA
1 TAAAAA
406125 CACATATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 3 0.11
28 25 0.89
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.19
Consensus pattern (28 bp):
TAAAAAAAATGAATAAAATAATAAAAAA
Found at i:406476 original size:2 final size:2
Alignment explanation
Indices: 406469--406529 Score: 90
Period size: 2 Copynumber: 31.0 Consensus size: 2
406459 TACATACATT
406469 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
*
406511 -A TGA TA TA -A GA TA TA TA TA
1 TA T-A TA TA TA TA TA TA TA TA
406530 ATGAAAATAA
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
1 2 0.04
2 51 0.93
3 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:406542 original size:25 final size:25
Alignment explanation
Indices: 406469--406544 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 25
406459 TACATACATT
* *
406469 TATATATATATATATATATATATATATA
1 TATATATATATA-AAATA-ATATA-AGA
* *
406497 TATATATATATATAATGATATAAGA
1 TATATATATATAAAATAATATAAGA
406522 TATATATA-ATGAAAATAATATAA
1 TATATATATAT-AAAATAATATAA
406545 TATAAATAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
24 2 0.05
25 20 0.49
26 5 0.12
27 2 0.05
28 12 0.29
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
TATATATATATAAAATAATATAAGA
Found at i:406547 original size:19 final size:19
Alignment explanation
Indices: 406480--406549 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
406470 ATATATATAT
*
406480 ATATATATATATAT-ATATA
1 ATATATATATA-ATGAAATA
*
406499 TATATATATATAATGATATA
1 -ATATATATATAATGAAATA
*
406519 AGATATATATAATGAAAATA
1 ATATATATATAATG-AAATA
406539 ATATA-ATATAA
1 ATATATATATAA
406550 ATAAAAAAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
19 21 0.47
20 24 0.53
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
ATATATATATAATGAAATA
Found at i:406553 original size:14 final size:15
Alignment explanation
Indices: 406472--406552 Score: 76
Period size: 16 Copynumber: 5.2 Consensus size: 15
406462 ATACATTTAT
*
406472 ATATATATATATATAT
1 ATATATATA-ATATAA
*
406488 ATATATATATATATAT
1 ATATATATA-ATATAA
*
406504 ATATATAATGATATAA
1 ATATAT-ATAATATAA
406520 GATATATATAATGA-AA
1 -ATATATATAAT-ATAA
406536 ATA-ATATAATATAA
1 ATATATATAATATAA
406550 ATA
1 ATA
406553 AAAAAAGAGG
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
13 1 0.02
14 12 0.21
15 3 0.05
16 33 0.57
17 9 0.16
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (15 bp):
ATATATATAATATAA
Found at i:409025 original size:65 final size:66
Alignment explanation
Indices: 408852--409039 Score: 220
Period size: 65 Copynumber: 2.8 Consensus size: 66
408842 TCTCAAAGAT
* * * *
408852 ATTTGTTGTTTCATGA-AAACGGTCTCAAGGGAAACAAAATTTTGTTTTAAGAGAAATAAATTTG
1 ATTT-TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTTAAGAGAAATAAATTTC
408916 AAG
64 AAG
* * *
408919 ATTTTATGTTTCAAGAGAAACTGTCTCCAGGGAGACAAAATTTGTTTTAGGGGAAATAAA-TTCA
1 ATTTT-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGAGAAATAAATTTCA
408983 A-
65 AG
* * * *
408984 ATATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACTAAATTTGTTTCAAGAGAAA
1 AT-TTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGAGAAA
409040 CTGTCTCAAG
Statistics
Matches: 104, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
65 45 0.43
66 8 0.08
67 31 0.30
68 20 0.19
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.33
Consensus pattern (66 bp):
ATTTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGAGAAATAAATTTCAA
G
Found at i:409035 original size:36 final size:36
Alignment explanation
Indices: 408988--409213 Score: 186
Period size: 36 Copynumber: 6.4 Consensus size: 36
408978 ATTCAAATAT
*
408988 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACTAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACTAAA
*
409024 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACTAAA
* * * *
409060 CTTAGTTCCAAAAGAAACTGTCTCAATG-GAGA-TGAAT
1 -TTTGTTTCAAGAGAAACTGTCTCAA-GAGAGACT-AAA
* * *
409097 TTTTTTTCAA-ATAAAACATAT-TC---A-A-A-T-AA
1 TTTGTTTCAAGA-GAAAC-TGTCTCAAGAGAGACTAAA
* * *
409126 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACTAAA
* *
409162 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACTAAA
* *
409198 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGAGAAA
409214 TGTTTTCAAT
Statistics
Matches: 153, Mismatches: 22, Indels: 30
0.75 0.11 0.15
Matches are distributed among these distances:
28 2 0.01
29 15 0.10
31 2 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 1 0.01
36 98 0.64
37 30 0.20
38 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACTAAA
Found at i:409248 original size:101 final size:101
Alignment explanation
Indices: 409022--409273 Score: 283
Period size: 101 Copynumber: 2.5 Consensus size: 101
409012 AGAGAGACTA
* *
409022 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAT
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAAAGAAACTGTCTCAAT
* * * *
409087 GGAGATGAATTTTTTTTCAAATAAAACATATTCAAAT
65 GGAGACGAAATTTATTTCAAAGAAAACATATTCAAAT
* * **
409124 AATTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAA-G
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAAACTGTCTCAATG
* * ** *
409188 AGAGACGAAATTTATTTCAAGGGAAATGTTTTC-AAT
66 -GAGACGAAATTTATTTCAAAGAAAACATATTCAAAT
** * **
409224 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGATGAAATTTGTTTCAAA
1 AATT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAA
409274 TAAAACATAT
Statistics
Matches: 125, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
100 6 0.05
101 83 0.66
102 36 0.29
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.31
Consensus pattern (101 bp):
AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAAACTGTCTCAATG
GAGACGAAATTTATTTCAAAGAAAACATATTCAAAT
Found at i:409300 original size:65 final size:64
Alignment explanation
Indices: 409160--409309 Score: 158
Period size: 65 Copynumber: 2.3 Consensus size: 64
409150 AGAGAGACAA
* * * ** *
409160 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAAT
1 AATTTATTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTATTTCAAAGAAAACATATTCAAT
* * * * * *
409224 -GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGATGAAATTTGTTTCAAATAAAACATATTCAA
1 AATTTA--TTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTATTTCAAAGAAAACATATTC-A
409288 AT
63 AT
409290 AATTTATTTCAAGGGAAACT
1 AATTTATTTCAAGGGAAACT
409310 TGGAAATTGT
Statistics
Matches: 68, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
63 3 0.04
65 58 0.85
66 3 0.04
67 4 0.06
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (64 bp):
AATTTATTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTATTTCAAAGAAAACATATTCAAT
Found at i:410175 original size:32 final size:32
Alignment explanation
Indices: 410139--410232 Score: 109
Period size: 31 Copynumber: 2.9 Consensus size: 32
410129 ATTCCCAAAG
* * *
410139 ATGCCCCAATATTCGATGTTGAATCTCAAAAA
1 ATGCCCCAACATTTGATGTTAAATCTCAAAAA
***
410171 ATGCCAGGACATTTGATGTTAAATCT-AAAAA
1 ATGCCCCAACATTTGATGTTAAATCTCAAAAA
*
410202 ATGTCCCAACATTTGATGTTAAATCTTCAAA
1 ATGCCCCAACATTTGATGTTAAATC-TCAAA
410233 GATGCCCTCA
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
31 26 0.52
32 21 0.42
33 3 0.06
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (32 bp):
ATGCCCCAACATTTGATGTTAAATCTCAAAAA
Found at i:411268 original size:69 final size:69
Alignment explanation
Indices: 411155--411289 Score: 227
Period size: 69 Copynumber: 2.0 Consensus size: 69
411145 CTCTCTCTTG
411155 ATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATCTCA
1 ATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATCTCA
411220 TTTT
66 TTTT
* **
411224 ATGCTCTATGATCTTTGAGTGAAGTGATTCAGTGATTC-GAAAATGATTGTTTTTGATCAATCTC
1 ATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAG-AAATGATTGTGCTTGATCAATCTC
411288 AT
65 AT
411290 AGTTTGAATC
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
68 1 0.02
69 61 0.98
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (69 bp):
ATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATCTCA
TTTT
Found at i:411400 original size:25 final size:23
Alignment explanation
Indices: 411361--411413 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 23
411351 TTTTTCTTCA
411361 ATTTTCCTTTGTTTTTTCTCTTTTT
1 ATTTTCC--TGTTTTTTCTCTTTTT
411386 ATTTTCTCT-TTTTTTCTCTTTTT
1 ATTTTC-CTGTTTTTTCTCTTTTT
*
411409 GTTTT
1 ATTTT
411414 GATTGAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 18 0.69
24 1 0.04
25 6 0.23
26 1 0.04
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.77
Consensus pattern (23 bp):
ATTTTCCTGTTTTTTCTCTTTTT
Found at i:411413 original size:13 final size:12
Alignment explanation
Indices: 411362--411413 Score: 56
Period size: 13 Copynumber: 4.3 Consensus size: 12
411352 TTTTCTTCAA
411362 TTTTC-CTTTGTT
1 TTTTCTCTTT-TT
411374 TTTTCTCTTTTT
1 TTTTCTCTTTTT
411386 ATTTTCTC--TTT
1 -TTTTCTCTTTTT
411397 TTTTCTCTTTTT
1 TTTTCTCTTTTT
411409 GTTTT
1 -TTTT
411414 GATTGAATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
10 7 0.20
11 3 0.09
12 10 0.29
13 15 0.43
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (12 bp):
TTTTCTCTTTTT
Found at i:415902 original size:22 final size:21
Alignment explanation
Indices: 415877--415917 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
415867 AAAAATGGAA
415877 AATAACAAAACACATAAAAAAT
1 AATAACAAAACA-ATAAAAAAT
* *
415899 AATAATAAAATAATAAAAA
1 AATAACAAAACAATAAAAA
415918 TAAACAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (21 bp):
AATAACAAAACAATAAAAAAT
Found at i:415908 original size:11 final size:10
Alignment explanation
Indices: 415890--415935 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 10
415880 AACAAAACAC
415890 ATAAAAAATA
1 ATAAAAAATA
415900 ATAATAAAATA
1 ATAA-AAAATA
415911 AT-AAAAATA
1 ATAAAAAATA
*
415920 A-ACAAAATGA
1 ATAAAAAAT-A
415930 ATAAAA
1 ATAAAA
415936 TATTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
9 12 0.40
10 7 0.23
11 11 0.37
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (10 bp):
ATAAAAAATA
Found at i:415920 original size:27 final size:27
Alignment explanation
Indices: 415890--415944 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
415880 AACAAAACAC
415890 ATAAAAAATAAT-AATAAAATAATAAAA
1 ATAAAAAA-AATGAATAAAATAATAAAA
* *
415917 ATAAACAAAATGAATAAAATATTAAAA
1 ATAAAAAAAATGAATAAAATAATAAAA
415944 A
1 A
415945 AAGACACAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (27 bp):
ATAAAAAAAATGAATAAAATAATAAAA
Found at i:416144 original size:8 final size:8
Alignment explanation
Indices: 416133--416171 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
416123 AAATAATAAA
416133 AAAAATAT
1 AAAAATAT
416141 AAAAATAT
1 AAAAATAT
416149 AATAAATA-
1 AA-AAATAT
*
416157 AATAATAT
1 AAAAATAT
416165 AAAAATA
1 AAAAATA
416172 GAATATTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 4 0.15
8 18 0.67
9 5 0.19
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAAATAT
Found at i:416167 original size:24 final size:22
Alignment explanation
Indices: 416125--416176 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 22
416115 TATTAAGAAA
416125 ATAATAAAAAAAATATAAAAAT
1 ATAATAAAAAAAATATAAAAAT
416147 ATAATAAATAAATAATATAAAAAT
1 ATAATAAA-AAA-AATATAAAAAT
*
416171 AGAATA
1 ATAATA
416177 TTAAGAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 8 0.30
23 3 0.11
24 16 0.59
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (22 bp):
ATAATAAAAAAAATATAAAAAT
Found at i:416203 original size:2 final size:2
Alignment explanation
Indices: 416198--416323 Score: 229
Period size: 2 Copynumber: 64.0 Consensus size: 2
416188 TATAAAAACG
416198 TA TA TA TA TA TA TA TA TA TA TA TA -A 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
416239 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
*
416281 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A GA 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
416322 TA
1 TA
416324 ATGAAAATAA
Statistics
Matches: 121, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
1 2 0.02
2 119 0.98
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:424276 original size:20 final size:21
Alignment explanation
Indices: 424236--424277 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
424226 CATTACAAAA
*
424236 ACATGTACACAAAACACAGGC
1 ACATGTACACAAAACAAAGGC
*
424257 ACATGT-CACAAAATAAAGGC
1 ACATGTACACAAAACAAAGGC
424277 A
1 A
424278 ATCTAGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.50, C:0.24, G:0.14, T:0.12
Consensus pattern (21 bp):
ACATGTACACAAAACAAAGGC
Found at i:425478 original size:21 final size:22
Alignment explanation
Indices: 425453--425493 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
425443 AATTGACTTT
*
425453 TTGGTGAAAGTCAAA-TTAATA
1 TTGGTCAAAGTCAAAGTTAATA
*
425474 TTGGTCAAGGTCAAAGTTAA
1 TTGGTCAAAGTCAAAGTTAA
425494 CATGTTAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (22 bp):
TTGGTCAAAGTCAAAGTTAATA
Found at i:426277 original size:30 final size:30
Alignment explanation
Indices: 426241--426298 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
426231 TTTCATGGGG
426241 GATCAATCCTTTGCAAAACAGTAAGTTTGA
1 GATCAATCCTTTGCAAAACAGTAAGTTTGA
* *
426271 GATCAATCCTTTGTAAAATAGTAAGTTT
1 GATCAATCCTTTGCAAAACAGTAAGTTT
426299 AGGATTGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (30 bp):
GATCAATCCTTTGCAAAACAGTAAGTTTGA
Found at i:428507 original size:16 final size:16
Alignment explanation
Indices: 428453--428508 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 16
428443 TGATATGAGT
* *
428453 TATGTGGTA-ATGATA
1 TATGTGTTACATGATC
*
428468 TATGTTTTACATGCTATAC
1 TATGTGTTACATG--AT-C
428487 TATGTGTTACATGATC
1 TATGTGTTACATGATC
428503 TATGTG
1 TATGTG
428509 AACTGGTATC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
15 7 0.21
16 10 0.30
17 2 0.06
18 2 0.06
19 12 0.36
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.45
Consensus pattern (16 bp):
TATGTGTTACATGATC
Found at i:428972 original size:21 final size:21
Alignment explanation
Indices: 428948--429050 Score: 125
Period size: 21 Copynumber: 4.8 Consensus size: 21
428938 TTGAAGGTTC
*
428948 TATGCGGTCCTTCGGGACATA
1 TATGTGGTCCTTCGGGACATA
* *
428969 TATGTGGTCCTTCGTGACAATTC
1 TATGTGGTCCTTCGGGAC-A-TA
** *
428992 TACATAGTCCTTCGGGACATA
1 TATGTGGTCCTTCGGGACATA
*
429013 TATGTGATCCTTCGGGACATA
1 TATGTGGTCCTTCGGGACATA
429034 TATGTGGTCCTTCGGGA
1 TATGTGGTCCTTCGGGA
429051 TATTCTATAT
Statistics
Matches: 67, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
21 50 0.75
22 2 0.03
23 15 0.22
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.33
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACATA
Found at i:438169 original size:17 final size:17
Alignment explanation
Indices: 438147--438186 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
438137 CCTAGGTGAC
438147 GAAGGTGGGAGTTTTAG
1 GAAGGTGGGAGTTTTAG
438164 GAAGGTGGGAGTTTTAG
1 GAAGGTGGGAGTTTTAG
438181 GAAGGT
1 GAAGGT
438187 ATTAGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.25, C:0.00, G:0.47, T:0.28
Consensus pattern (17 bp):
GAAGGTGGGAGTTTTAG
Found at i:450084 original size:3 final size:3
Alignment explanation
Indices: 450078--450116 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
450068 TATTTTTTAT
*
450078 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
450117 AAGAAAATGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:450790 original size:112 final size:112
Alignment explanation
Indices: 450606--450937 Score: 488
Period size: 112 Copynumber: 3.0 Consensus size: 112
450596 AGAGTGAAGC
* *
450606 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTACT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
*
450671 ATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGA
66 ATGAACTTTCTCTGGAAATGTTGATCCATCGAGTGATGAATTCAAGA
* * * *
450718 AAAAGGCTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
* * * *
450783 ATCAACTTTATCTGGAAATGTTGATCCATCAAGTGATGAATTCGAGA
66 ATGAACTTTCTCTGGAAATGTTGATCCATCGAGTGATGAATTCAAGA
*
450830 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCAT
* * * *
450895 TATGAACTCTAC-CTGG-CATGTTGATCCATTGAGTGATGGATTC
65 TATGAACT-TTCTCTGGAAATGTTGATCCATCGAGTGATGAATTC
450938 GAATCTTTTC
Statistics
Matches: 195, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
112 162 0.83
113 32 0.16
114 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (112 bp):
AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAATGTTGATCCATCGAGTGATGAATTCAAGA
Found at i:451322 original size:22 final size:22
Alignment explanation
Indices: 451297--451353 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
451287 AATAAAGCTT
451297 TCATCTTTGAAA-AGAGAATCTA
1 TCATCTTT-AAAGAGAGAATCTA
451319 TCATCTTTAAAGAGAGAATCTA
1 TCATCTTTAAAGAGAGAATCTA
*
451341 TTATCTTTAAAGA
1 TCATCTTTAAAGA
451354 ATGTAGATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
21 3 0.09
22 30 0.91
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATCTTTAAAGAGAGAATCTA
Found at i:452020 original size:18 final size:18
Alignment explanation
Indices: 451997--452034 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
451987 TATATGAAAG
451997 AATAAATTGAATTTCAAA
1 AATAAATTGAATTTCAAA
*
452015 AATAAATTGAATTTTAAA
1 AATAAATTGAATTTCAAA
452033 AA
1 AA
452035 GATAAACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (18 bp):
AATAAATTGAATTTCAAA
Found at i:452421 original size:19 final size:16
Alignment explanation
Indices: 452388--452430 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
452378 TCATTTCTAT
452388 ATTTTTTTCTTTCATC
1 ATTTTTTTCTTTCATC
452404 ATTTTTTTCTTTCATC
1 ATTTTTTTCTTTCATC
452420 ATTTTTTTCTT
1 ATTTTTTTCTT
452431 CAAGCATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTTTTCTTTCATC
Found at i:459712 original size:15 final size:15
Alignment explanation
Indices: 459692--459723 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
459682 TGCAATGAAT
*
459692 AATGAATGTATGCAA
1 AATGAATGTATACAA
459707 AATGAATGTATACAA
1 AATGAATGTATACAA
459722 AA
1 AA
459724 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (15 bp):
AATGAATGTATACAA
Found at i:461195 original size:165 final size:165
Alignment explanation
Indices: 460916--461244 Score: 586
Period size: 165 Copynumber: 2.0 Consensus size: 165
460906 AACATAGCTA
* * *
460916 TATTTCATCGCATTTGTTCTAGCTCTTTCGAACAACCCTCTCTTTCTGCTTCAAACTCAGCTTTT
1 TATTTCATCGCATTTCTTATAGCTCTTTCGAACAACCCTCTCTTTCTGCTTCAAACTCACCTTTT
* *
460981 AGGATTTCAATCTCTGATGGAACTACCCGAATGCGATCTTCCATAGAGATATCCTCATTTTGGTT
66 AGGATTTCAATATCTGATGGAACTACCCGAATGCGATCTTCCATAGAGATATCCTCATTTTGGTC
*
461046 TGGTAGAGGAATATTTTCATTTTTCCTGACAGATT
131 TGGTAGAGGAATATTTTCATTTTTCCTAACAGATT
* *
461081 TATTTCGTCGCATTTCTTATAGCTCTTTCGACCAACCCTCTCTTTCTGCTTCAAACTCACCTTTT
1 TATTTCATCGCATTTCTTATAGCTCTTTCGAACAACCCTCTCTTTCTGCTTCAAACTCACCTTTT
461146 AGGATTTCAATATCTGATGGAACTACCCGAATGCGATCTTCCATAGAGATATCCTCATTTTGGTC
66 AGGATTTCAATATCTGATGGAACTACCCGAATGCGATCTTCCATAGAGATATCCTCATTTTGGTC
461211 TGGTAGAGGAATATTTTCATTTTTCCTAACAGAT
131 TGGTAGAGGAATATTTTCATTTTTCCTAACAGAT
461245 CTCCATTCCT
Statistics
Matches: 156, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
165 156 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (165 bp):
TATTTCATCGCATTTCTTATAGCTCTTTCGAACAACCCTCTCTTTCTGCTTCAAACTCACCTTTT
AGGATTTCAATATCTGATGGAACTACCCGAATGCGATCTTCCATAGAGATATCCTCATTTTGGTC
TGGTAGAGGAATATTTTCATTTTTCCTAACAGATT
Found at i:464537 original size:18 final size:20
Alignment explanation
Indices: 464510--464560 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
464500 TACTTAAATT
*
464510 GTATCAATACTCAGGG-T-A
1 GTATCGATACTCAGGGATAA
464528 GTATCGATACTACAGGGATAA
1 GTATCGATACT-CAGGGATAA
464549 GTATCGATACTC
1 GTATCGATACTC
464561 TTGTGTGAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 10 0.34
19 5 0.17
20 2 0.07
21 12 0.41
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (20 bp):
GTATCGATACTCAGGGATAA
Found at i:465983 original size:50 final size:50
Alignment explanation
Indices: 465923--466019 Score: 133
Period size: 50 Copynumber: 1.9 Consensus size: 50
465913 CATGAAGAAA
*
465923 TTGGCACCAAGATGAACCAA-CACAACACCATTCGGCCATGGAAGATGACT
1 TTGGCACCAAGATGAA-CAAGCACAACACCATTCGGCCAAGGAAGATGACT
* * * *
465973 TTGGCGCCAAGATGAACAAGCATATCACCATTCGGCCAAGGGAGATG
1 TTGGCACCAAGATGAACAAGCACAACACCATTCGGCCAAGGAAGATG
466020 CATCTTCATC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
49 3 0.07
50 38 0.93
ACGTcount: A:0.34, C:0.26, G:0.24, T:0.16
Consensus pattern (50 bp):
TTGGCACCAAGATGAACAAGCACAACACCATTCGGCCAAGGAAGATGACT
Found at i:470595 original size:22 final size:22
Alignment explanation
Indices: 470564--470626 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
470554 CGGGTTTGAG
*
470564 ATACACCATCATCACCATCTTA
1 ATACAACATCATCACCATCTTA
470586 ATACAACATCATCACCATCTTA
1 ATACAACATCATCACCATCTTA
* *
470608 ATACAAAATCAACACCATC
1 ATACAACATCATCACCATC
470627 AACCATCTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (22 bp):
ATACAACATCATCACCATCTTA
Found at i:470773 original size:34 final size:34
Alignment explanation
Indices: 470730--470797 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
470720 ATTTCGTATT
470730 TCTTTGCTAATACTATCTTCTATCATCTTTGTTG
1 TCTTTGCTAATACTATCTTCTATCATCTTTGTTG
470764 TCTTTGCTAATACTATCTTCTATCATCTTTGTTG
1 TCTTTGCTAATACTATCTTCTATCATCTTTGTTG
470798 CAGCCATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.18, C:0.21, G:0.09, T:0.53
Consensus pattern (34 bp):
TCTTTGCTAATACTATCTTCTATCATCTTTGTTG
Found at i:473774 original size:25 final size:24
Alignment explanation
Indices: 473737--473785 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
473727 GTTTAAGGGC
**
473737 TTATTTATTTTTAAAATAATAAAAT
1 TTATTTAAATTTAAAAT-ATAAAAT
473762 TTATTTAAATTTAAAATATAAAAT
1 TTATTTAAATTTAAAATATAAAAT
473786 ATCCATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTATTTAAATTTAAAATATAAAAT
Found at i:473821 original size:21 final size:22
Alignment explanation
Indices: 473795--473844 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
473785 TATCCATATT
473795 TAAAAAAGTAAA-TATCAAAAA
1 TAAAAAAGTAAATTATCAAAAA
* *
473816 T-AAAAATTAAATTATTAAAAA
1 TAAAAAAGTAAATTATCAAAAA
473837 TAATAAAA
1 TAA-AAAA
473845 ATATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 9 0.38
21 10 0.42
22 1 0.04
23 4 0.17
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
TAAAAAAGTAAATTATCAAAAA
Found at i:473826 original size:20 final size:21
Alignment explanation
Indices: 473797--473839 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
473787 TCCATATTTA
473797 AAAAAGTAAA-TATCAAAAAT
1 AAAAAGTAAATTATCAAAAAT
* *
473817 AAAAATTAAATTATTAAAAAT
1 AAAAAGTAAATTATCAAAAAT
473838 AA
1 AA
473840 TAAAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAAAGTAAATTATCAAAAAT
Found at i:473851 original size:20 final size:20
Alignment explanation
Indices: 473824--473887 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
473814 AATAAAAATT
473824 AAAT-TATTAAAAATAATAA
1 AAATATATTAAAAATAATAA
* *
473843 AAATATATTAAACAT-A-CA
1 AAATATATTAAAAATAATAA
*
473861 AAA-ACATTAATAAA-AATAA
1 AAATATATTAA-AAATAATAA
473880 AAATATAT
1 AAATATAT
473888 CTCAAGTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
17 6 0.18
18 7 0.21
19 9 0.26
20 12 0.35
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATATATTAAAAATAATAA
Found at i:474116 original size:13 final size:14
Alignment explanation
Indices: 474096--474128 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
474086 CAATTTACCC
*
474096 ATAAAATAATAATA
1 ATAAAATAAAAATA
474110 A-AAAATAAAAATA
1 ATAAAATAAAAATA
474123 ATAAAA
1 ATAAAA
474129 AAAGGGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAAAATAAAAATA
Found at i:476704 original size:19 final size:21
Alignment explanation
Indices: 476679--476732 Score: 87
Period size: 19 Copynumber: 2.7 Consensus size: 21
476669 CATTAGCATA
476679 TATACATTGTACATTA-ATGG
1 TATACATTGTACATTACATGG
476699 -ATACATTGTACATTACATGG
1 TATACATTGTACATTACATGG
476719 TATAC-TTGTACATT
1 TATACATTGTACATT
476733 GTACTTTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.47
20 13 0.41
21 4 0.12
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (21 bp):
TATACATTGTACATTACATGG
Found at i:477400 original size:15 final size:16
Alignment explanation
Indices: 477382--477411 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
477372 AAGAGGGGAA
477382 AAGA-AAAAAAAAGAT
1 AAGAGAAAAAAAAGAT
477397 AAGAGAAAAAAAAGA
1 AAGAGAAAAAAAAGA
477412 AAGCAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (16 bp):
AAGAGAAAAAAAAGAT
Found at i:477409 original size:26 final size:25
Alignment explanation
Indices: 477380--477493 Score: 90
Period size: 22 Copynumber: 4.5 Consensus size: 25
477370 AAAAGAGGGG
477380 AAAAGAAAAAAAAAGATAAGAGAAAA
1 AAAAGAAAAAAAAAGAT-AGAGAAAA
**
477406 AAAAGAAAGCAAAAGATAGAG---A
1 AAAAGAAAAAAAAAGATAGAGAAAA
** * *
477428 AAAAGAAAGCAAAAGATGGAGGAAA
1 AAAAGAAAAAAAAAGATAGAGAAAA
* *
477453 AAAAGAAAAATAAAGAAAGAAAGAAGAA
1 AAAAGAAAAAAAAAGATAG--AGAA-AA
*
477481 AAAAGAAATAAAA
1 AAAAGAAAAAAAA
477494 GAAAAAAATA
Statistics
Matches: 71, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
22 21 0.30
25 19 0.27
26 15 0.21
27 3 0.04
28 13 0.18
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (25 bp):
AAAAGAAAAAAAAAGATAGAGAAAA
Found at i:477468 original size:47 final size:46
Alignment explanation
Indices: 477380--477501 Score: 124
Period size: 46 Copynumber: 2.6 Consensus size: 46
477370 AAAAGAGGGG
*
477380 AAAAGAAAAAAAAAGATAAGAGAAAAAAAAGAAAGCAAAAGATAGAGA
1 AAAAGAAAAAAAAAGATAAGAGAAAAAAAAGAAAGAAAAAGA-A-AGA
** * *
477428 AAAAGAAAGCAAAAGAT-GGAGGAAAAAAAGAAA-AATAAAGAAAGA
1 AAAAGAAAAAAAAAGATAAGAGAAAAAAAAGAAAGAA-AAAGAAAGA
* *
477473 AAGAAGAAAAAAGAA-ATAAAAGAAAAAAA
1 AA-AAGAAAAAAAAAGATAAGAGAAAAAAA
477502 TAAGAAGAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
45 7 0.12
46 19 0.32
47 19 0.32
48 15 0.25
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (46 bp):
AAAAGAAAAAAAAAGATAAGAGAAAAAAAAGAAAGAAAAAGAAAGA
Found at i:477475 original size:18 final size:17
Alignment explanation
Indices: 477449--477501 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 17
477439 AAAGATGGAG
477449 GAAAAAAAGAAAAATAAA
1 GAAAAAAAGAAAAA-AAA
*
477467 GAAAGAAAGAAGAAAAAA
1 GAAAAAAAGAA-AAAAAA
477485 GAAATAAAAGAAAAAAA
1 GAAA-AAAAGAAAAAAA
477502 TAAGAAGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 22 0.71
19 9 0.29
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (17 bp):
GAAAAAAAGAAAAAAAA
Found at i:477494 original size:27 final size:29
Alignment explanation
Indices: 477451--477525 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 29
477441 AGATGGAGGA
* *
477451 AAAAAAGAAAAATAAAG-AAAGA-AAGAAG
1 AAAAAAGAAATA-AAAGAAAAAATAAGAAG
477479 AAAAAAGAAATAAAAGAAAAAAATAAGAAG
1 AAAAAAGAAATAAAAG-AAAAAATAAGAAG
477509 AATAAGAAGAAATAAAA
1 AA-AA-AAGAAATAAAA
477526 TAGATCAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
27 4 0.10
28 11 0.28
29 4 0.10
30 8 0.20
31 2 0.05
32 11 0.28
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.07
Consensus pattern (29 bp):
AAAAAAGAAATAAAAGAAAAAATAAGAAG
Done.