Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007824.1 Hibiscus syriacus cultivar Beakdansim tig00110162_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: 895964
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 4
Found at i:223869 original size:17 final size:17
Alignment explanation
Indices: 223844--223877 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
223834 TTGAATATTT
*
223844 TGGAATGTTTGATTTTG
1 TGGAATGTTGGATTTTG
*
223861 TGGATTGTTGGATTTTG
1 TGGAATGTTGGATTTTG
223878 GATTTATGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.32, T:0.53
Consensus pattern (17 bp):
TGGAATGTTGGATTTTG
Found at i:226211 original size:60 final size:60
Alignment explanation
Indices: 226147--226259 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
226137 AAATAATCTC
226147 TCGACTATAT-GATACTACTTTA-TAATGTCTCTT-GACTATTAAAAGTTACAAAACGATCAT
1 TCGACTATATAG-TACTACTTTATTAA-GTC-CTTCGACTATTAAAAGTTACAAAACGATCAT
** *
226207 TCGACTATATAGTGTTGCTTTATTAAGTCCTTCGACTATTAAAAGTTACAAAA
1 TCGACTATATAGTACTACTTTATTAAGTCCTTCGACTATTAAAAGTTACAAAA
226260 TAGTCACCTA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
59 3 0.06
60 40 0.85
61 4 0.09
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (60 bp):
TCGACTATATAGTACTACTTTATTAAGTCCTTCGACTATTAAAAGTTACAAAACGATCAT
Found at i:228326 original size:31 final size:31
Alignment explanation
Indices: 228240--228326 Score: 147
Period size: 31 Copynumber: 2.8 Consensus size: 31
228230 AAAAAATTGA
*
228240 TAAATAAAAATGAAAGTAACCATAACTTAAT
1 TAAATAAAAATGAAAGTAACCATATCTTAAT
*
228271 TAAATAAAAATGAAAGTAATCATATCTTAAT
1 TAAATAAAAATGAAAGTAACCATATCTTAAT
*
228302 TAAATAAAAATGAAAGTGACCATAT
1 TAAATAAAAATGAAAGTAACCATAT
228327 ATTATATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (31 bp):
TAAATAAAAATGAAAGTAACCATATCTTAAT
Found at i:232257 original size:24 final size:23
Alignment explanation
Indices: 232230--232274 Score: 81
Period size: 24 Copynumber: 1.9 Consensus size: 23
232220 CCGATAATAC
232230 AAACTAATTGAAAATTAATTAAAA
1 AAACTAATTGAAAATT-ATTAAAA
232254 AAACTAATTGAAAATTATTAA
1 AAACTAATTGAAAATTATTAA
232275 TACTTGCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (23 bp):
AAACTAATTGAAAATTATTAAAA
Found at i:237029 original size:43 final size:43
Alignment explanation
Indices: 236982--237147 Score: 163
Period size: 43 Copynumber: 3.9 Consensus size: 43
236972 AACGCCGCAA
* * *
236982 TAGGTTTTGATGTTTAGCGGCGTTTTCCCTACAAACGCTACAG
1 TAGGTGTTGATATTTAGCGGCATTTTCCCTACAAACGCTACAG
* **
237025 TAGGTGTTGATATTTAGCGGTATTTTCCCTACAAACGCCGCAG
1 TAGGTGTTGATATTTAGCGGCATTTTCCCTACAAACGCTACAG
* ** * * *
237068 TAGGTGTTGATATTTTGCGGCATTTTTTCAAAAAACGCTACAA
1 TAGGTGTTGATATTTAGCGGCATTTTCCCTACAAACGCTACAG
* * * * *
237111 TATGCGATGATGTTTAGCGGCGTTTCTCCC-ACAAACG
1 TAGGTGTTGATATTTAGCGGCATTT-TCCCTACAAACG
237148 TCGCAGTAGG
Statistics
Matches: 98, Mismatches: 24, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
43 96 0.98
44 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (43 bp):
TAGGTGTTGATATTTAGCGGCATTTTCCCTACAAACGCTACAG
Found at i:237104 original size:86 final size:86
Alignment explanation
Indices: 236971--237158 Score: 207
Period size: 86 Copynumber: 2.2 Consensus size: 86
236961 TTTTAACAAA
* * * * * * * * *
236971 AAACGCCGCAATAGGTTTTGATGTTTAGCGGCGTTTTCCCTACAAACGCTACAGTAGGTGTTGAT
1 AAACGCCGCAGTAGGTGTTGATATTTAGCGGCATTTTCCCAAAAAACGCTACAATAGGCGATGAT
*
237036 ATTTAGCGGTATTT-TCCCTAC
66 ATTTAGCGGCATTTCTCCC-AC
* ** *
237057 AAACGCCGCAGTAGGTGTTGATATTTTGCGGCATTTTTTCAAAAAACGCTACAATATGCGATGAT
1 AAACGCCGCAGTAGGTGTTGATATTTAGCGGCATTTTCCCAAAAAACGCTACAATAGGCGATGAT
* *
237122 GTTTAGCGGCGTTTCTCCCAC
66 ATTTAGCGGCATTTCTCCCAC
*
237143 AAACGTCGCAGTAGGT
1 AAACGCCGCAGTAGGT
237159 TTTCAGATTA
Statistics
Matches: 84, Mismatches: 17, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
86 80 0.95
87 4 0.05
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (86 bp):
AAACGCCGCAGTAGGTGTTGATATTTAGCGGCATTTTCCCAAAAAACGCTACAATAGGCGATGAT
ATTTAGCGGCATTTCTCCCAC
Found at i:237711 original size:21 final size:21
Alignment explanation
Indices: 237687--237735 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
237677 GCTGATATGT
237687 TGCTTCTCTCTGTGCTG-TCGC
1 TGCTTCTCTCTGTGCTGCT-GC
*
237708 TGCTTCACTCTGTGCTGCTGC
1 TGCTTCTCTCTGTGCTGCTGC
237729 TGCTTCT
1 TGCTTCT
237736 TTCTCTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.02, C:0.33, G:0.22, T:0.43
Consensus pattern (21 bp):
TGCTTCTCTCTGTGCTGCTGC
Found at i:245694 original size:41 final size:40
Alignment explanation
Indices: 245575--245760 Score: 147
Period size: 41 Copynumber: 4.5 Consensus size: 40
245565 CGTTTATATT
* * * * * *
245575 AAAAACGCCGCTAATGTACATGACTATGGCGGCATTTATTACC
1 AAAAACGCCACTAAAGTACA-GTCTATAGCGGCGTTT-TCA-C
* * * * * *
245618 AAAAATGCCACTAAATTACATTACTATTGCAGCGTTTTAAC
1 AAAAACGCCACTAAAGTACAGT-CTATAGCGGCGTTTTCAC
*
245659 AAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTCAT
1 AAAAACGCCACTAAAGTAC-AGTCTATAGCGGCGTTTTCAC
** * *
245700 ACGAACGCCACTAAAGTATAAGTCTATAGCGGCGTTTTCAT
1 AAAAACGCCACTAAAGTA-CAGTCTATAGCGGCGTTTTCAC
* *
245741 ACAAACGCCACTAAAATACA
1 AAAAACGCCACTAAAGTACA
245761 AATATTTTGC
Statistics
Matches: 117, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
40 1 0.01
41 85 0.73
42 4 0.03
43 27 0.23
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.25
Consensus pattern (40 bp):
AAAAACGCCACTAAAGTACAGTCTATAGCGGCGTTTTCAC
Found at i:253627 original size:13 final size:13
Alignment explanation
Indices: 253609--253638 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
253599 AGGCATAAAC
253609 CACACAAAAGAGA
1 CACACAAAAGAGA
253622 CACACAAAAGAGA
1 CACACAAAAGAGA
253635 CACA
1 CACA
253639 AAAGGAGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.27, G:0.13, T:0.00
Consensus pattern (13 bp):
CACACAAAAGAGA
Found at i:253637 original size:11 final size:12
Alignment explanation
Indices: 253610--253642 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
253600 GGCATAAACC
253610 ACACAAAAGAGA
1 ACACAAAAGAGA
253622 CACACAAAAGAG-
1 -ACACAAAAGAGA
253634 ACACAAAAG
1 ACACAAAAG
253643 GAGCACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
13 11 0.55
ACGTcount: A:0.64, C:0.21, G:0.15, T:0.00
Consensus pattern (12 bp):
ACACAAAAGAGA
Found at i:260025 original size:20 final size:18
Alignment explanation
Indices: 260002--260040 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
259992 AAATTAAACA
260002 AGAAGAGAAAAAAGAAATTG
1 AGAAGA-AAAAAA-AAATTG
*
260022 AGAAGAAAAATAAAATTG
1 AGAAGAAAAAAAAAATTG
260040 A
1 A
260041 CCAATTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 5 0.28
20 6 0.33
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.13
Consensus pattern (18 bp):
AGAAGAAAAAAAAAATTG
Found at i:267945 original size:61 final size:61
Alignment explanation
Indices: 267857--267989 Score: 248
Period size: 61 Copynumber: 2.2 Consensus size: 61
267847 AGTTGTTTTC
*
267857 TCCTTTTTATCAAGAGAGAATTATCATTGTTTTCTCATTGGTAGATCGAAAGAGGTTGTAAT
1 TCCTATTT-TCAAGAGAGAATTATCATTGTTTTCTCATTGGTAGATCGAAAGAGGTTGTAAT
267919 TCCTATTTTCAAGAGAGAATTATCATTGTTTTCTCATTGGTAGATCGAAAGAGGTTGTAAT
1 TCCTATTTTCAAGAGAGAATTATCATTGTTTTCTCATTGGTAGATCGAAAGAGGTTGTAAT
267980 TCCTATTTTC
1 TCCTATTTTC
267990 TCATAGTGAA
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
61 63 0.90
62 7 0.10
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (61 bp):
TCCTATTTTCAAGAGAGAATTATCATTGTTTTCTCATTGGTAGATCGAAAGAGGTTGTAAT
Found at i:276316 original size:30 final size:30
Alignment explanation
Indices: 276282--276372 Score: 130
Period size: 30 Copynumber: 3.0 Consensus size: 30
276272 AAATTACATC
*
276282 TTAATTAAATAAAAACGAAAGTGATCATAT
1 TTAATTAAATAAAAACGAAAGTGAACATAT
*
276312 TTAATTAAATAAATAAAGAAAGT-AACCATAT
1 TTAATTAAATAAA-AACGAAAGTGAA-CATAT
*
276343 TTAATTAAATAGAAACGAAAGTGAACATAT
1 TTAATTAAATAAAAACGAAAGTGAACATAT
276373 ATTATATTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
30 27 0.50
31 27 0.50
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.29
Consensus pattern (30 bp):
TTAATTAAATAAAAACGAAAGTGAACATAT
Found at i:276342 original size:31 final size:30
Alignment explanation
Indices: 276282--276372 Score: 112
Period size: 31 Copynumber: 3.0 Consensus size: 30
276272 AAATTACATC
* * *
276282 TTAATTAAATAAAAACGAAAGTGATCATAT
1 TTAATTAAATAAAAAAGAAAGTAACCATAT
276312 TTAATTAAATAAATAAAGAAAGTAACCATAT
1 TTAATTAAATAAA-AAAGAAAGTAACCATAT
* *
276343 TTAATTAAATAGAAACGAAAGTGAA-CATAT
1 TTAATTAAATAAAAAAGAAAGT-AACCATAT
276373 ATTATATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
30 26 0.48
31 28 0.52
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.29
Consensus pattern (30 bp):
TTAATTAAATAAAAAAGAAAGTAACCATAT
Found at i:280527 original size:183 final size:183
Alignment explanation
Indices: 280141--280527 Score: 645
Period size: 183 Copynumber: 2.1 Consensus size: 183
280131 ATTAAATTTT
* *
280141 AAATATTAAATATATTATATATAACATATGAGCTCAACCCAAATCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAAAATATGAGCTCAACCCAAACCATTTAAAACCCAATTAATAA
*
280206 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAATTTTT
66 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
*
280271 TATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTAATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
*
280324 AAATATTAAATATATTATATATAAAATATGGGCT-AAGCCCAAACCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAAAATATGAGCTCAA-CCCAAACCATTTAAAACCCAATTAATA
* *
280388 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAATTTTATCTAAAATT
65 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAA-ATTATATAAAATT
280453 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
129 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTT-AATTAAA
* *
280508 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
280528 AATTAGAAAA
Statistics
Matches: 192, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
182 2 0.01
183 123 0.64
184 67 0.35
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAAAATATGAGCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
Found at i:281058 original size:25 final size:25
Alignment explanation
Indices: 281030--281078 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
281020 ACAATTAGAT
281030 TCTAACTTTTGTATTCCTCTTAAAC
1 TCTAACTTTTGTATTCCTCTTAAAC
281055 TCTAACTTTTGTATTCCTCTTAAA
1 TCTAACTTTTGTATTCCTCTTAAA
281079 TTTTCTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.04, T:0.49
Consensus pattern (25 bp):
TCTAACTTTTGTATTCCTCTTAAAC
Found at i:281119 original size:18 final size:19
Alignment explanation
Indices: 281082--281119 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
281072 TCTTAAATTT
* *
281082 TCTATTATTTTATTATAAA
1 TCTAATATTTTATAATAAA
281101 TCTAATATTTT-TAATAAA
1 TCTAATATTTTATAATAAA
281119 T
1 T
281120 TATCAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TCTAATATTTTATAATAAA
Found at i:281230 original size:32 final size:33
Alignment explanation
Indices: 281194--281267 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
281184 ATTTCAATAT
* * *
281194 GTTCGGGTTGTTTTCAG-GTCGGGTT-AAATTTG
1 GTTCGGGTTGCTTTC-GTATCGGATTAAAATTTG
*
281226 GTTCGAGTTGCTTTCGTATCGGATTAAAATTTG
1 GTTCGGGTTGCTTTCGTATCGGATTAAAATTTG
281259 GTTCGGGTT
1 GTTCGGGTT
281268 AATTTAGGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 1 0.03
32 19 0.54
33 15 0.43
ACGTcount: A:0.15, C:0.11, G:0.31, T:0.43
Consensus pattern (33 bp):
GTTCGGGTTGCTTTCGTATCGGATTAAAATTTG
Found at i:281299 original size:16 final size:16
Alignment explanation
Indices: 281263--281315 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
281253 AATTTGGTTC
*
281263 GGGTTAATTTAGGTGC
1 GGGTTAATTTAGGTGT
*
281279 AGGTTAATTTAGGTGT
1 GGGTTAATTTAGGTGT
* * *
281295 GGGTTACTTTCGGTTT
1 GGGTTAATTTAGGTGT
281311 GGGTT
1 GGGTT
281316 GCTTTTGGCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.15, C:0.06, G:0.36, T:0.43
Consensus pattern (16 bp):
GGGTTAATTTAGGTGT
Found at i:282366 original size:64 final size:64
Alignment explanation
Indices: 282293--282430 Score: 179
Period size: 64 Copynumber: 2.2 Consensus size: 64
282283 CGGATCCTGA
*
282293 CAGGTCAGGTAAAATCGGATACAGGTCA-AGTCAGGTAAATTTGACATCAGATCCAGATCGGGTT
1 CAGGTCAGGTAAAATCAG-TACAGGTCATAGTCAGGTAAATTTGACATCAGATCCAGATCGGGTT
* * * ** **
282357 CAGGTCAGGTTAAATCAGTTCAGGTTATTTTCAGGTTGATTTGACATCAGATCCAGATCGGGTT
1 CAGGTCAGGTAAAATCAGTACAGGTCATAGTCAGGTAAATTTGACATCAGATCCAGATCGGGTT
*
282421 CAGATCAGGT
1 CAGGTCAGGT
282431 CATTTTCAGT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 7 0.11
64 57 0.89
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (64 bp):
CAGGTCAGGTAAAATCAGTACAGGTCATAGTCAGGTAAATTTGACATCAGATCCAGATCGGGTT
Found at i:283001 original size:215 final size:211
Alignment explanation
Indices: 282751--283552 Score: 1166
Period size: 215 Copynumber: 3.8 Consensus size: 211
282741 ATTTAAGAAT
282751 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACA---A-GAG
*
282816 GGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAATACTAAATTATAC
62 GGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * * *
282881 TCATTTAAAAAGTTATGGGCCAATTAAAAATATAATTAAGTAATAAGTATGGATCAATTTCATAT
127 CCATTTAAAAAGTTATGGGCCAATTAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCAGAT
282946 GCAAATAAAATTTGGAGGAC
192 GCAAATAAAATTTGGAGGAC
*
282966 TAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACA---A-GAG
* *
283031 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
62 GGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* *
283096 CCATTTAAAAAGTTATGGGTCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
127 CCATTTAAAAAGTTATGGGCCAA-TTAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCAGA
283161 TGCAAATAAAATTTGGAGGAC
191 TGCAAATAAAATTTGGAGGAC
*
283182 TAAATTGAACAAATATG---TTACAAATAAAAATTTAAATATATTAAACAACACA-AA-AGGGAT
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACAAGAGGGAT
* * * * *
283242 TAAATCGAAATAATTTTAAATTTTGAGTTTAAAATTAATAC-AAAAAGTACTAAATTATACCCAT
66 CAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCAT
* * *
283306 TTAAAAAGTTATGGGCCAATT-----TAAAAAT-AGAAATAAGTATGGGTCAATTTCAGGTGCAA
131 TTAAAAAGTTATGGGCCAATTAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCAGATGCAA
*
283365 ATAAAATTTGGTGGAC
196 ATAAAATTTGGAGGAC
* *
283381 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAA-AA-ACACAAAAGGGAT
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACAAGAGGGAT
* * * *
283444 CATATCAAAATAATTTTAAATTTTGAGGTTGAAATT-ATACAAAAATGTACTAAATTATACTCAT
66 CAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCAT
*
283508 TTAAAAAGTTATGGGCCAATTAATAAATATAAATAAATAATAAGT
131 TTAAAAAGTTATGGGCCAATTAA-AAATATAAATAAGTAATAAGT
283553 TAAGAAAAAA
Statistics
Matches: 541, Mismatches: 32, Indels: 34
0.89 0.05 0.06
Matches are distributed among these distances:
199 61 0.11
200 9 0.02
201 8 0.01
202 107 0.20
205 2 0.00
206 41 0.08
207 42 0.08
208 6 0.01
209 9 0.02
212 1 0.00
213 33 0.06
215 147 0.27
216 75 0.14
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (211 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACAAGAGGGAT
CAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCAT
TTAAAAAGTTATGGGCCAATTAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCAGATGCAA
ATAAAATTTGGAGGAC
Found at i:283580 original size:2 final size:2
Alignment explanation
Indices: 283575--283661 Score: 54
Period size: 2 Copynumber: 43.0 Consensus size: 2
283565 AAAACAACGA
* * *
283575 AT AT AT AT AT AT AT AT AT A- AT AT AA ACT AT AT AGT TT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT
* * * *
283618 A- AT GT AT AT GT AT -T AT AT AT AT AA ACT AT AT AGT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT
283660 AT
1 AT
283662 TATGTATAAA
Statistics
Matches: 64, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
1 3 0.05
2 57 0.89
3 4 0.06
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:283607 original size:20 final size:21
Alignment explanation
Indices: 283582--283649 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 21
283572 CGAATATATA
283582 TATATATATATA-ATATAAAC
1 TATATATATATACATATAAAC
**
283602 TATATAGT-T-TACATATAATG
1 TATATA-TATATACATATAAAC
* *
283622 TATATGTATTATATATATAAAC
1 TATATATA-TATACATATAAAC
283644 TATATA
1 TATATA
283650 GTTTATATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
19 3 0.08
20 18 0.50
21 2 0.06
22 13 0.36
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (21 bp):
TATATATATATACATATAAAC
Found at i:283640 original size:42 final size:45
Alignment explanation
Indices: 283578--283669 Score: 136
Period size: 42 Copynumber: 2.1 Consensus size: 45
283568 ACAACGAATA
283578 TATATATATATATATAATATAAACTATATAGTTTACATATA-ATG
1 TATATATATATATATAATATAAACTATATAGTTTACATATATATG
* *
283622 TATATGTAT-TATAT-ATATAAACTATATAGTTTATATATATTATG
1 TATATATATATATATAATATAAACTATATAGTTTACATATA-TATG
283666 TATA
1 TATA
283670 AAGTATAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
42 24 0.55
43 5 0.11
44 15 0.34
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (45 bp):
TATATATATATATATAATATAAACTATATAGTTTACATATATATG
Found at i:283669 original size:22 final size:21
Alignment explanation
Indices: 283602--283669 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 21
283592 TAATATAAAC
*
283602 TATATAGTTTACATATA-ATG
1 TATATAGTTTATATATATATG
**
283622 TATAT-GTATTATATATATAAAC
1 TATATAGT-TTATATATAT-ATG
283644 TATATAGTTTATATATATTATG
1 TATATAGTTTATATATA-TATG
283666 TATA
1 TATA
283670 AAGTATAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
19 2 0.05
20 13 0.34
22 20 0.53
23 3 0.08
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (21 bp):
TATATAGTTTATATATATATG
Found at i:283769 original size:11 final size:11
Alignment explanation
Indices: 283755--283792 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
283745 ACTACATAGT
283755 TTATATATAAA
1 TTATATATAAA
*
283766 TTATATATGAA
1 TTATATATAAA
283777 TTATATATAAA
1 TTATATATAAA
*
283788 CTATA
1 TTATA
283793 CAATTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (11 bp):
TTATATATAAA
Found at i:283922 original size:21 final size:20
Alignment explanation
Indices: 283897--283936 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
283887 TAGTATATAT
283897 GGTTTAGGGTTTAATATTTAG
1 GGTTTAGGGTTT-ATATTTAG
283918 GGTTTAGGGTTTATATTTA
1 GGTTTAGGGTTTATATTTA
283937 TATAAACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.50
Consensus pattern (20 bp):
GGTTTAGGGTTTATATTTAG
Found at i:283969 original size:20 final size:20
Alignment explanation
Indices: 283944--283981 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
283934 TTATATAAAC
283944 TATATACTATAATTTATATT
1 TATATACTATAATTTATATT
*
283964 TATATACTATATTTTATA
1 TATATACTATAATTTATA
283982 CTATTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATACTATAATTTATATT
Found at i:283981 original size:27 final size:27
Alignment explanation
Indices: 283927--284014 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
283917 GGGTTTAGGG
**
283927 TTTATATTTATATAAACTATATACTATAA
1 TTTATATTTATAT--ACTATATTTTATAA
*
283956 TTTATATTTATATACTATATTTTATAC
1 TTTATATTTATATACTATATTTTATAA
* *
283983 TATT-TATTTA-A-ACTATAGTTTA-CA
1 T-TTATATTTATATACTATATTTTATAA
284007 TTTATATT
1 TTTATATT
284015 CAATATATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
23 2 0.04
24 5 0.10
25 10 0.20
26 1 0.02
27 18 0.35
28 2 0.04
29 13 0.25
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.55
Consensus pattern (27 bp):
TTTATATTTATATACTATATTTTATAA
Found at i:284054 original size:2 final size:2
Alignment explanation
Indices: 284047--284195 Score: 52
Period size: 2 Copynumber: 70.0 Consensus size: 2
284037 ACATATGAAC
* * * *
284047 TA TA TA TA TA AA CTA TA TA GTT TA CA TA TA TCC TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA T-A TA TA TA TA TA
* * *
284090 TA TA CTA TA GT- TGA TA TT TA TA TA CTA TA TA -A TT TA CA TA TGA
1 TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA TA T-A
** * * *
284133 CC TA TA AA TA TA TA CTA TA GTT TA TA TT TA TA TA CTA TA TA T-
1 TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA -TA TA TA TA
*
284175 TA TA TA TA TA AA CTA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA
284196 CTATGTAGTA
Statistics
Matches: 106, Mismatches: 26, Indels: 30
0.65 0.16 0.19
Matches are distributed among these distances:
1 3 0.03
2 87 0.82
3 16 0.15
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:284054 original size:33 final size:32
Alignment explanation
Indices: 283978--284120 Score: 123
Period size: 33 Copynumber: 4.3 Consensus size: 32
283968 TACTATATTT
* * *
283978 TATACTATTTATTTA-AACTATAGTTTACATT
1 TATACTATATATATATAACTATAGTTTACATA
*
284009 TATATTCA-ATATATATGAACTATAGTTTACATA
1 TATACT-ATATATATAT-AACTATAGTTTACATA
284042 TGA-ACTATATATATA-AACTATATAGTTTACATA
1 T-ATACTATATATATATAAC--TATAGTTTACATA
* **
284075 TATCCTATATATATATATACTATAGTTGATATTTA
1 TATACTATATATATATA-ACTATAGTT--TACATA
284110 TATACTATATA
1 TATACTATATA
284121 ATTTACATAT
Statistics
Matches: 91, Mismatches: 9, Indels: 20
0.76 0.08 0.17
Matches are distributed among these distances:
31 13 0.14
32 3 0.03
33 57 0.63
34 2 0.02
35 16 0.18
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (32 bp):
TATACTATATATATATAACTATAGTTTACATA
Found at i:284164 original size:20 final size:20
Alignment explanation
Indices: 284135--284194 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
284125 ACATATGACC
*
284135 TATAAATATATACTATAGT-T
1 TATATATATATACTATA-TAT
*
284155 TATATTTATATACTATATAT
1 TATATATATATACTATATAT
*
284175 TATATATATAAACTATATAT
1 TATATATATATACTATATAT
284195 ACTATGTAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.03
20 34 0.97
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (20 bp):
TATATATATATACTATATAT
Found at i:284167 original size:53 final size:55
Alignment explanation
Indices: 284047--284195 Score: 189
Period size: 53 Copynumber: 2.7 Consensus size: 55
284037 ACATATGAAC
* * *
284047 TATATATATAAACTATATAGTTTACATATATCCTATATATATATATACTATAGTT
1 TATATTTATATACTATATAATTTACATATATCCTATATATATATATACTATAGTT
*
284102 GATATTTATATACTATATAATTTACATATGA-CCTATA-A-ATATATACTATAGTT
1 TATATTTATATACTATATAATTTACATAT-ATCCTATATATATATATACTATAGTT
* **
284155 TATATTTATATACTATAT-ATTATATATATAAACTATATATA
1 TATATTTATATACTATATAATT-TACATATATCCTATATATA
284196 CTATGTAGTA
Statistics
Matches: 82, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
52 4 0.05
53 43 0.52
54 2 0.02
55 32 0.39
56 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (55 bp):
TATATTTATATACTATATAATTTACATATATCCTATATATATATATACTATAGTT
Found at i:284301 original size:18 final size:18
Alignment explanation
Indices: 284271--284492 Score: 158
Period size: 18 Copynumber: 12.4 Consensus size: 18
284261 ATTATGTAGT
284271 CTAT-TAGTATATATAAA
1 CTATATAGTATATATAAA
* *
284288 CTATATAATATATATAGA
1 CTATATAGTATATATAAA
*
284306 CTATATGGTATATATAAA
1 CTATATAGTATATATAAA
* * * *
284324 TTATACATTATATAT-AG
1 CTATATAGTATATATAAA
*
284341 TTCAT-TAGTATATATAAA
1 CT-ATATAGTATATATAAA
*
284359 CTATATAGTACATATAAA
1 CTATATAGTATATATAAA
*
284377 CTATATA-T-TATAT-AG
1 CTATATAGTATATATAAA
* *
284392 TTCAT-TAGTATATATAAC
1 CT-ATATAGTATATATAAA
284410 CTATATAGTATATGATATATA
1 CTATATAGTATAT-ATA-A-A
* *
284431 C-AAACTA-TATATTATATA
1 CTATA-TAGTATA-TATAAA
*
284449 GT-TCATTAGTATATATAAA
1 CTAT-A-TAGTATATATAAA
284468 CTATATAGTATATATAAA
1 CTATATAGTATATATAAA
284486 CTATATA
1 CTATATA
284493 TTAATTTATT
Statistics
Matches: 159, Mismatches: 28, Indels: 35
0.72 0.13 0.16
Matches are distributed among these distances:
15 4 0.03
16 7 0.04
17 25 0.16
18 91 0.57
19 13 0.08
20 15 0.09
21 4 0.03
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.41
Consensus pattern (18 bp):
CTATATAGTATATATAAA
Found at i:284353 original size:51 final size:52
Alignment explanation
Indices: 284297--284495 Score: 224
Period size: 58 Copynumber: 3.7 Consensus size: 52
284287 ACTATATAAT
* * *
284297 ATATATAGACTATATGGTATATATAAATTATACATTATATATAGTTCATTAG
1 ATATATAAACTATATAGTATATATAAACTATACATTATATATAGTTCATTAG
* *
284349 TATATATAAACTATATAGTACATATAAACTATATA-T-TATATAGTTCATTAG
1 -ATATATAAACTATATAGTATATATAAACTATACATTATATATAGTTCATTAG
* *
284400 TATATATAACCTATATAGTATATGATATATAC-AAACTATATATTATATAGTTCATTAG
1 -ATATATAAACTATATAGTATAT-ATA-A-ACTATAC-AT-TA-TATATAGTTCATTAG
*
284458 TATATATAAACTATATAGTATATATAAACTATATATTA
1 -ATATATAAACTATATAGTATATATAAACTATACATTA
284496 ATTTATTAAT
Statistics
Matches: 125, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
51 36 0.29
52 4 0.03
53 32 0.26
54 5 0.04
55 4 0.03
56 4 0.03
57 3 0.02
58 37 0.30
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.42
Consensus pattern (52 bp):
ATATATAAACTATATAGTATATATAAACTATACATTATATATAGTTCATTAG
Found at i:284407 original size:33 final size:33
Alignment explanation
Indices: 284364--284481 Score: 135
Period size: 33 Copynumber: 3.8 Consensus size: 33
284354 ATAAACTATA
* *
284364 TAGTACATATAAACTATATATTATATAGTTCAT
1 TAGTATATATAAACTATATAGTATATAGTTCAT
*
284397 TAGTATATATAACCTATATAGTATAT-G-----
1 TAGTATATATAAACTATATAGTATATAGTTCAT
* *
284424 -A-TATATACAAACTATATATTATATAGTTCAT
1 TAGTATATATAAACTATATAGTATATAGTTCAT
284455 TAGTATATATAAACTATATAGTATATA
1 TAGTATATATAAACTATATAGTATATA
284482 TAAACTATAT
Statistics
Matches: 69, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
25 20 0.29
26 2 0.03
32 2 0.03
33 45 0.65
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.42
Consensus pattern (33 bp):
TAGTATATATAAACTATATAGTATATAGTTCAT
Found at i:284470 original size:109 final size:112
Alignment explanation
Indices: 284289--284525 Score: 323
Period size: 109 Copynumber: 2.2 Consensus size: 112
284279 ATATATAAAC
* * * *
284289 TATATAATATATATAGACTATATGGTATATATAAATTATACATTATATATAGTTCATTAGTATAT
1 TATATAACATATATAGA-TATATGATATATACAAACTATACATTATATATAGTTCATTAGTATAT
284354 ATAAACTATATAGTACATATAAACTATATATTATATAGTTCATTAGTA
65 ATAAACTATATAGTACATATAAACTATATATTATATAGTTCATTAGTA
* *
284402 TATATAACCTATATAG-TATATGATATATACAAACTATATA-T-TATATAGTTCATTAGTATATA
1 TATATAACATATATAGATATATGATATATACAAACTATACATTATATATAGTTCATTAGTATATA
*
284464 TAAACTATATAGTATATATAAACTATATATTA-AT--TT-ATTA--A
66 TAAACTATATAGTACATATAAACTATATATTATATAGTTCATTAGTA
*
284505 TATA-AACATATATATATATAT
1 TATATAACATATATAGATATAT
284526 TAATTGAAAG
Statistics
Matches: 114, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
102 9 0.08
103 10 0.09
105 4 0.04
106 2 0.02
108 2 0.02
109 52 0.46
110 1 0.01
111 20 0.18
113 14 0.12
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (112 bp):
TATATAACATATATAGATATATGATATATACAAACTATACATTATATATAGTTCATTAGTATATA
TAAACTATATAGTACATATAAACTATATATTATATAGTTCATTAGTA
Found at i:284525 original size:18 final size:18
Alignment explanation
Indices: 284278--284525 Score: 72
Period size: 18 Copynumber: 13.4 Consensus size: 18
284268 AGTCTATTAG
284278 TATATATAAAC-TATATAA
1 TATATATAAACATATAT-A
* *
284296 TATATATAGAC-TATATGG
1 TATATATAAACATATAT-A
* *
284314 TATATATAAA-TTATACA
1 TATATATAAACATATATA
** *
284331 TTATATATAGTTCAT-TA-G
1 -TATATATA-AACATATATA
284349 TATATATAAAC-TATATA
1 TATATATAAACATATATA
*
284366 GTACATATAAAC-TATATA
1 -TATATATAAACATATATA
** *
284384 T-TATATAGTTCAT-TA-G
1 TATATATA-AACATATATA
*
284400 TATATATAACCTATATAGTA
1 TATATATAAAC-ATATA-TA
* *
284420 TATGATATATACAAACTATA
1 TAT-ATATAAACATA-TATA
** *
284440 TATTATATAGTTCAT-TA-G
1 TA-TATATA-AACATATATA
284458 TATATATAAAC-TATATA
1 TATATATAAACATATATA
284475 GTATATATAAACTATATATTAA
1 -TATATATAAAC-ATATA-T-A
284497 TTTATTAATATAAACATATATA
1 --TA-T-ATATAAACATATATA
284519 TATATAT
1 TATATAT
284526 TAATTGAAAG
Statistics
Matches: 171, Mismatches: 31, Indels: 56
0.66 0.12 0.22
Matches are distributed among these distances:
15 2 0.01
16 13 0.08
17 26 0.15
18 72 0.42
19 5 0.03
20 21 0.12
21 13 0.08
22 2 0.01
23 3 0.02
24 6 0.04
25 8 0.05
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.42
Consensus pattern (18 bp):
TATATATAAACATATATA
Found at i:284526 original size:24 final size:24
Alignment explanation
Indices: 284479--284529 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
284469 TATATAGTAT
*
284479 ATATAAACTATATATTAATTTATTA
1 ATATAAACTATATATT-ATATATTA
284504 ATATAAAC-ATATATATATATATTA
1 ATATAAACTATATAT-TATATATTA
284528 AT
1 AT
284530 TGAAAGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (24 bp):
ATATAAACTATATATTATATATTA
Found at i:284639 original size:61 final size:61
Alignment explanation
Indices: 284558--284687 Score: 172
Period size: 61 Copynumber: 2.1 Consensus size: 61
284548 TATAAGGATC
* * * * * *
284558 AAATTGAACAAATTTTAAATATGAAGTTTAAATTAATAAATTATAA-CATTAAATTTTGATT
1 AAATTGAAAAAAGTTAAAATATGAAGCTTAAATTAATAAATTA-AATCATTAAATTTGGACT
* *
284619 AAATTGAAAAAAGTTAAAATATGAAGCTTAAATTAATATATTAAATTATTAAATTTGGACT
1 AAATTGAAAAAAGTTAAAATATGAAGCTTAAATTAATAAATTAAATCATTAAATTTGGACT
284680 AAATTGAA
1 AAATTGAA
284688 TACATTTCCC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 2 0.03
61 58 0.97
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (61 bp):
AAATTGAAAAAAGTTAAAATATGAAGCTTAAATTAATAAATTAAATCATTAAATTTGGACT
Found at i:287357 original size:14 final size:14
Alignment explanation
Indices: 287338--287364 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
287328 ATCTAATATA
287338 ATTTTAAAATTTTT
1 ATTTTAAAATTTTT
287352 ATTTTAAAATTTT
1 ATTTTAAAATTTT
287365 AAGTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTTAAAATTTTT
Found at i:287515 original size:13 final size:13
Alignment explanation
Indices: 287496--287533 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
287486 TAATTTAGTG
287496 ATTATAAATAA-A
1 ATTATAAATAAGA
287508 ATTTATAATATAAGA
1 A-TTATAA-ATAAGA
287523 ATTATAAATAA
1 ATTATAAATAA
287534 TATATGGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:287533 original size:18 final size:18
Alignment explanation
Indices: 287512--287601 Score: 65
Period size: 18 Copynumber: 4.8 Consensus size: 18
287502 AATAAAATTT
*
287512 ATAATATAAGAATTATAA
1 ATAATATAAAAATTATAA
** *
287530 ATAATATATGGAATTAGAA
1 ATAATATA-AAAATTATAA
* *
287549 TTAATATAAAAATCA-AA
1 ATAATATAAAAATTATAA
*
287566 TTTATAATATACAAATTATAA
1 ---ATAATATAAAAATTATAA
*
287587 TTAATATAAAAATTA
1 ATAATATAAAAATTA
287602 AATTTCAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
17 2 0.04
18 25 0.45
19 15 0.27
20 12 0.21
21 2 0.04
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (18 bp):
ATAATATAAAAATTATAA
Found at i:287545 original size:19 final size:18
Alignment explanation
Indices: 287512--287557 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
287502 AATAAAATTT
*
287512 ATAATATAAGAATTATAA
1 ATAATATAAGAATTAGAA
*
287530 ATAATATATGGAATTAGAA
1 ATAATATA-AGAATTAGAA
*
287549 TTAATATAA
1 ATAATATAA
287558 AAATCAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.35
Consensus pattern (18 bp):
ATAATATAAGAATTAGAA
Found at i:287575 original size:20 final size:19
Alignment explanation
Indices: 287549--287606 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 19
287539 GGAATTAGAA
*
287549 TTAATATAAAAATCAAATT
1 TTAATATAAAAATTAAATT
*
287568 TATAATATACAAATTATAA--
1 T-TAATATAAAAATTA-AATT
287587 TTAATATAAAAATTAAATT
1 TTAATATAAAAATTAAATT
287606 T
1 T
287607 CAAAAAGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 2 0.06
18 13 0.41
19 3 0.09
20 12 0.38
21 2 0.06
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAATATAAAAATTAAATT
Found at i:289310 original size:19 final size:22
Alignment explanation
Indices: 289282--289324 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 22
289272 TTCTATTTAG
289282 ATAAACTATT-AT-TTTTA-AA
1 ATAAACTATTGATATTTTATAA
*
289301 ATAAATTATTGATATTTTATAA
1 ATAAACTATTGATATTTTATAA
289323 AT
1 AT
289325 TTAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 5 0.25
22 4 0.20
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
ATAAACTATTGATATTTTATAA
Found at i:298138 original size:31 final size:31
Alignment explanation
Indices: 298096--298272 Score: 246
Period size: 31 Copynumber: 5.7 Consensus size: 31
298086 CGACAAATAG
* *
298096 CTTAATTGAATGTATTTAAACAATTGAGTGA
1 CTTAATTGAATATATTTAAATAATTGAGTGA
* * *
298127 CTTGATTGAATGTATTTAAATAGTTGAGTGA
1 CTTAATTGAATATATTTAAATAATTGAGTGA
* * *
298158 CTTGATTGAATGTATTTAAATAGTTGAGTGA
1 CTTAATTGAATATATTTAAATAATTGAGTGA
* *
298189 TTTAATTGAATATATTTAAATAATCGAGTGA
1 CTTAATTGAATATATTTAAATAATTGAGTGA
* *
298220 TTTAATTGAATATATTTAAATAATCGAGTGA
1 CTTAATTGAATATATTTAAATAATTGAGTGA
298251 CTTAATTGAATATATTTAAATA
1 CTTAATTGAATATATTTAAATA
298273 GTCGAGTGTT
Statistics
Matches: 137, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 137 1.00
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (31 bp):
CTTAATTGAATATATTTAAATAATTGAGTGA
Found at i:298171 original size:62 final size:62
Alignment explanation
Indices: 298096--298280 Score: 271
Period size: 62 Copynumber: 3.0 Consensus size: 62
298086 CGACAAATAG
* * * *
298096 CTTAATTGAATGTATTTAAACAATTGAGTGACTTGATTGAATGTATTTAAATAGTTGAGTGA
1 CTTAATTGAATGTATTTAAATAATTGAGTGACTTAATTGAATATATTTAAATAGTCGAGTGA
* * * *
298158 CTTGATTGAATGTATTTAAATAGTTGAGTGATTTAATTGAATATATTTAAATAATCGAGTGA
1 CTTAATTGAATGTATTTAAATAATTGAGTGACTTAATTGAATATATTTAAATAGTCGAGTGA
* * *
298220 TTTAATTGAATATATTTAAATAATCGAGTGACTTAATTGAATATATTTAAATAGTCGAGTG
1 CTTAATTGAATGTATTTAAATAATTGAGTGACTTAATTGAATATATTTAAATAGTCGAGTG
298281 TTATAGAATT
Statistics
Matches: 108, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 108 1.00
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.41
Consensus pattern (62 bp):
CTTAATTGAATGTATTTAAATAATTGAGTGACTTAATTGAATATATTTAAATAGTCGAGTGA
Found at i:308984 original size:36 final size:36
Alignment explanation
Indices: 308944--309020 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
308934 CACTCCCAGC
* *
308944 GAGATGACTGGTATTGGAAGGCTGAAGCACAATATA
1 GAGATGACTGGCATCGGAAGGCTGAAGCACAATATA
* *
308980 GAGATGACTGGCATCGGAAGGCTGAAGGACAATATG
1 GAGATGACTGGCATCGGAAGGCTGAAGCACAATATA
309016 GAGAT
1 GAGAT
309021 CAAGGAACGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.12, G:0.34, T:0.19
Consensus pattern (36 bp):
GAGATGACTGGCATCGGAAGGCTGAAGCACAATATA
Found at i:310434 original size:31 final size:31
Alignment explanation
Indices: 310395--310466 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
310385 GTCTCAAAAT
310395 TAACAAATTGATCACTAATATTATCAATTTA
1 TAACAAATTGATCACTAATATTATCAATTTA
* * * * * *
310426 TAATAAATTAATCATTGATTTTATCAATTTG
1 TAACAAATTGATCACTAATATTATCAATTTA
310457 TAACAAATTG
1 TAACAAATTG
310467 GTAACTCTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.42
Consensus pattern (31 bp):
TAACAAATTGATCACTAATATTATCAATTTA
Found at i:312920 original size:23 final size:23
Alignment explanation
Indices: 312894--312938 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
312884 CACCACAACT
*
312894 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
312917 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
312939 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:313156 original size:149 final size:149
Alignment explanation
Indices: 312906--313220 Score: 569
Period size: 149 Copynumber: 2.1 Consensus size: 149
312896 TATAATTGCA
312906 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
312970 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
* * *
313035 CCACATAATATATATATATC
130 CCAAAGAATATACATATATC
313055 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
313120 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
313185 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
*
313204 TCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
313221 CCCTCGACTC
Statistics
Matches: 160, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 1 0.01
149 159 0.99
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:313466 original size:53 final size:53
Alignment explanation
Indices: 313409--313521 Score: 226
Period size: 53 Copynumber: 2.1 Consensus size: 53
313399 TTTCCATATA
313409 AATCACACGTCACATATATCATGTTTTCATATAATTTCTATCATTTCTCACCC
1 AATCACACGTCACATATATCATGTTTTCATATAATTTCTATCATTTCTCACCC
313462 AATCACACGTCACATATATCATGTTTTCATATAATTTCTATCATTTCTCACCC
1 AATCACACGTCACATATATCATGTTTTCATATAATTTCTATCATTTCTCACCC
313515 AATCACA
1 AATCACA
313522 TTTATTCATG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 60 1.00
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.38
Consensus pattern (53 bp):
AATCACACGTCACATATATCATGTTTTCATATAATTTCTATCATTTCTCACCC
Found at i:314761 original size:21 final size:21
Alignment explanation
Indices: 314737--314781 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
314727 TTTTGTTCGT
* *
314737 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
314758 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
314779 TTG
1 TTG
314782 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:319214 original size:28 final size:30
Alignment explanation
Indices: 319149--319210 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
319139 ATGAAATTAT
*
319149 TAAAATTCCAAAAAAACACCTTAAATTCCA
1 TAAAATTTCAAAAAAACACCTTAAATTCCA
*
319179 TAAAATTTC-AAAAAACTCC-TAAATTCC-
1 TAAAATTTCAAAAAAACACCTTAAATTCCA
319206 TAAAA
1 TAAAA
319211 ATTTAGGGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 5 0.17
28 8 0.27
29 9 0.30
30 8 0.27
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (30 bp):
TAAAATTTCAAAAAAACACCTTAAATTCCA
Found at i:326767 original size:12 final size:12
Alignment explanation
Indices: 326752--326777 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
326742 TTTTTACTTG
326752 TATTTTAATGAT
1 TATTTTAATGAT
326764 TATTTTAATGAT
1 TATTTTAATGAT
326776 TA
1 TA
326778 AAAAATGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (12 bp):
TATTTTAATGAT
Found at i:329324 original size:18 final size:18
Alignment explanation
Indices: 329301--329357 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 18
329291 ACATGTGTGT
*
329301 TATAGTTGAAAATATATG
1 TATAGTTTAAAATATATG
329319 TATAGTTTTAAAATATA--
1 TATAG-TTTAAAATATATG
* *
329336 TATATTTTAAAAAATATG
1 TATAGTTTAAAATATATG
329354 TATA
1 TATA
329358 TAAATATAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 10 0.30
17 4 0.12
18 9 0.27
19 10 0.30
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (18 bp):
TATAGTTTAAAATATATG
Found at i:329333 original size:19 final size:18
Alignment explanation
Indices: 329309--329358 Score: 68
Period size: 16 Copynumber: 2.8 Consensus size: 18
329299 GTTATAGTTG
329309 AAAATATATGTATAGTTTT
1 AAAATATATGTATA-TTTT
329328 AAAATATA--TATATTTT
1 AAAATATATGTATATTTT
*
329344 AAAAAATATGTATAT
1 AAAATATATGTATAT
329359 AAATATAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 11 0.39
17 4 0.14
18 5 0.18
19 8 0.29
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
AAAATATATGTATATTTT
Found at i:329358 original size:18 final size:18
Alignment explanation
Indices: 329309--329358 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
329299 GTTATAGTTG
*
329309 AAAATATATGTATAGTTTT
1 AAAAAATATGTATA-TTTT
*
329328 --AAAATATATATATTTT
1 AAAAAATATGTATATTTT
329344 AAAAAATATGTATAT
1 AAAAAATATGTATAT
329359 AAATATAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 4 0.15
17 10 0.38
18 12 0.46
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
AAAAAATATGTATATTTT
Found at i:339073 original size:15 final size:15
Alignment explanation
Indices: 339053--339104 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
339043 GGGTATCGGA
339053 TACCCGATTACCGGG
1 TACCCGATTACCGGG
** *
339068 TACCCGCAAAATCCGGA
1 TACCCG-ATTA-CCGGG
339085 TACCCGATTACCGGG
1 TACCCGATTACCGGG
339100 TACCC
1 TACCC
339105 ATAACATCCG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 15 0.52
16 4 0.14
17 10 0.34
ACGTcount: A:0.25, C:0.37, G:0.21, T:0.17
Consensus pattern (15 bp):
TACCCGATTACCGGG
Found at i:339114 original size:32 final size:32
Alignment explanation
Indices: 339049--339115 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
339039 AATCGGGTAT
*
339049 CGGATACCCGATTACCGGGTACCCGCAAAATC
1 CGGATACCCGATTACCGGGTACCCACAAAATC
* *
339081 CGGATACCCGATTACCGGGTACCCATAACATC
1 CGGATACCCGATTACCGGGTACCCACAAAATC
339113 CGG
1 CGG
339116 GTCGAGACAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.27, C:0.34, G:0.22, T:0.16
Consensus pattern (32 bp):
CGGATACCCGATTACCGGGTACCCACAAAATC
Found at i:340217 original size:2 final size:2
Alignment explanation
Indices: 340210--340265 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
340200 ATTTTATACA
340210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
340252 AT A- AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT
340266 TATTCATTCA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:341399 original size:3 final size:3
Alignment explanation
Indices: 341387--341434 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
341377 TTTTTACTTT
341387 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
341434 T
1 T
341435 ATGTATATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:344017 original size:18 final size:17
Alignment explanation
Indices: 343994--344036 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
343984 TAAGGCAAAG
343994 AAGATGGAAGAGAAGATC
1 AAGAT-GAAGAGAAGATC
*
344012 AAGATG-ATAGAAGATC
1 AAGATGAAGAGAAGATC
344028 -AGATGAAGA
1 AAGATGAAGA
344037 TGGTCCAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 5 0.23
16 11 0.50
17 1 0.05
18 5 0.23
ACGTcount: A:0.51, C:0.05, G:0.30, T:0.14
Consensus pattern (17 bp):
AAGATGAAGAGAAGATC
Found at i:348276 original size:36 final size:36
Alignment explanation
Indices: 348216--348332 Score: 162
Period size: 36 Copynumber: 3.2 Consensus size: 36
348206 TAATTTACTC
* *
348216 AAAACAAAGTTTTGTCACTTTTGAGACAGTTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
* *
348253 AAAACAAATTTTGTCTCTCTTGAGACATTTTCTTTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* *
348289 AAAACAAATTTTGTCTCTCTTGAGACAGTCTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
348325 GAAACAAA
1 AAAACAAA
348333 ATCTTTGAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
36 63 0.89
37 8 0.11
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:348406 original size:36 final size:36
Alignment explanation
Indices: 348357--348469 Score: 154
Period size: 36 Copynumber: 3.1 Consensus size: 36
348347 TTTCCTTGAT
*
348357 ACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAA
1 ACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTAAA
* * *
348393 ACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAA
1 ACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTAAA
* * * *
348429 ACAAATTTTGTCTCGCTTGAGATAGTTTCCTTTGAA
1 ACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTAAA
348465 ACAAA
1 ACAAA
348470 ATATTTGAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (36 bp):
ACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTAAA
Found at i:348482 original size:137 final size:136
Alignment explanation
Indices: 348236--348799 Score: 800
Period size: 137 Copynumber: 4.2 Consensus size: 136
348226 TTTGTCACTT
* *
348236 TTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTTTTAAAACAAATTTT
1 TTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAA-AAATTTT
* *
348301 GTCTCTCTTGAGACAGTCTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTGATACAAATTTC
65 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTGAAACAAATTTC
348366 GTCTCCC
130 GTCTCCC
348373 TTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATTTT
1 TTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAA-AAATTTT
* * * * *
348438 GTCTCGCTTGAGATAGTTTCCTTTGAAACAAAATATTTGAATCTGTTTTCTTTGAAACAAATTTC
65 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTGAAACAAATTTC
*
348503 ATCTCCC
130 GTCTCCC
* *
348510 TTGAGACAGTTTCTTTTAAAATAATTTTTGTCTCTCTTGAGACATTTTCTCTTAAAAAAA---T-
1 TTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAAAAATTTTG
* * *
348571 TATCTCTTGAGACAATTTCCCTTGAAACAAAAATCTTTGAATCTGTTTTCCTTGAAAAAAATTTC
66 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAAATCTTTGAATCTGTTTTCCTTGAAACAAATTTC
348636 GTCTCCC
130 GTCTCCC
* * *
348643 TTGAGACATTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACGTTTTCTCTT--AAGAATTTTG
1 TTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAAAAATTTTG
* * * * * * *
348706 TCTATCTTGAGATATTTTCCCTTGAAACAAAATCTTTGAATCTAG-TTCCCTTTAAACAAGTTTT
66 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCT-GTTTTCCTTGAAACAAATTTC
348770 GTCTCCC
130 GTCTCCC
* *
348777 TTGAGACAGTTTCTCTTGAAACA
1 TTGAGACAGTTTCTTTTAAAACA
348800 CAAAATCTTT
Statistics
Matches: 383, Mismatches: 38, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
131 4 0.01
132 23 0.06
133 89 0.23
134 57 0.15
135 25 0.07
136 3 0.01
137 182 0.48
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (136 bp):
TTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAAAAATTTTG
TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTGAAACAAATTTCG
TCTCCC
Found at i:348580 original size:31 final size:32
Alignment explanation
Indices: 348542--348697 Score: 92
Period size: 36 Copynumber: 4.7 Consensus size: 32
348532 AATTTTTGTC
348542 TCTCTTGAGACATTTTCTCTTAAAAAAA-TTA
1 TCTCTTGAGACATTTTCTCTTAAAAAAATTTA
* *
348573 TCTCTTGAGACAATTTCCCTTGAAACAAAA---A
1 TCTCTTGAGACATTTTCTCTT-AAA-AAAATTTA
* *
348604 TCT-TTGA-ATCTGTTTTC-CTTGAAAAAAATTTCG
1 TCTCTTGAGA-C-ATTTTCTCTT-AAAAAAATTT-A
* *
348637 TCTCCCTTGAGACATTTTCTTTTAAAACAAATTTTGTC
1 TCT--CTTGAGACATTTTCTCTTAAAA-AAA--TT-TA
*
348675 TCTCTTGAGACGTTTTCTCTTAA
1 TCTCTTGAGACATTTTCTCTTAA
348698 GAATTTTGTC
Statistics
Matches: 98, Mismatches: 10, Indels: 29
0.72 0.07 0.21
Matches are distributed among these distances:
29 5 0.05
30 12 0.12
31 27 0.28
32 3 0.03
33 7 0.07
35 9 0.09
36 28 0.29
37 1 0.01
38 5 0.05
39 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (32 bp):
TCTCTTGAGACATTTTCTCTTAAAAAAATTTA
Found at i:348685 original size:36 final size:35
Alignment explanation
Indices: 348359--348571 Score: 111
Period size: 36 Copynumber: 6.1 Consensus size: 35
348349 TCCTTGATAC
* *
348359 AAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAA
1 AAATTTCATCTCCCTTGAGACATTTTCTTTTAAAA
** * *
348394 CAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAA
1 -AAATTTCATCTCCCTTGAGACATTTTCTTTTAAAA
** * * * *
348430 CAAATTTTGTCTCGCTTGAGATAGTTTCCTTTGAAACA
1 -AAATTTCATCTCCCTTGAGACA-TTTTCTTTTAAA-A
* * *
348468 AAA--T-A--T---TTGA-ATCTGTTTTCTTTGAAAC
1 AAATTTCATCTCCCTTGAGA-C-ATTTTCTTTTAAAA
*
348496 AAATTTCATCTCCCTTGAGACAGTTTCTTTTAAAA
1 AAATTTCATCTCCCTTGAGACATTTTCTTTTAAAA
* ** * *
348531 TAATTTTTGTCTCTCTTGAGACATTTTCTCTTAAAA
1 -AAATTTCATCTCCCTTGAGACATTTTCTTTTAAAA
348567 AAATT
1 AAATT
348572 ATCTCTTGAG
Statistics
Matches: 138, Mismatches: 25, Indels: 29
0.72 0.13 0.15
Matches are distributed among these distances:
28 4 0.03
29 15 0.11
30 1 0.01
31 1 0.01
32 1 0.01
33 1 0.01
35 15 0.11
36 86 0.62
37 13 0.09
38 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.43
Consensus pattern (35 bp):
AAATTTCATCTCCCTTGAGACATTTTCTTTTAAAA
Found at i:348691 original size:36 final size:35
Alignment explanation
Indices: 348615--348717 Score: 111
Period size: 36 Copynumber: 3.0 Consensus size: 35
348605 CTTTGAATCT
* * * *
348615 GTTTTCCTTGAAAAAAATTTCGTCTCCCTTGAGAC
1 GTTTTCTTTTAAAAAAATTTTGTCTCTCTTGAGAC
*
348650 ATTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGAC
1 GTTTTCTTTTAAAA-AAATTTTGTCTCTCTTGAGAC
* * *
348686 GTTTTCTCTT--AAGAATTTTGTCTATCTTGAGA
1 GTTTTCTTTTAAAAAAATTTTGTCTCTCTTGAGA
348718 TATTTTCCCT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
33 18 0.31
34 2 0.03
35 11 0.19
36 27 0.47
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (35 bp):
GTTTTCTTTTAAAAAAATTTTGTCTCTCTTGAGAC
Found at i:348795 original size:65 final size:66
Alignment explanation
Indices: 348699--348865 Score: 183
Period size: 67 Copynumber: 2.5 Consensus size: 66
348689 TTCTCTTAAG
* * * * * *
348699 AATTTTGTCTATCTTGAGATATTTTCCCTTGAAACAAAATCTTTGAATCTAGTTCCCTTTAAA-C
1 AATTTTGTCTACCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATCTAGTTCCCTTAAAATA
348763 A
66 A
* * * *
348764 AGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTTGAATTTATTTCCCTTAAAA
1 AATTTTGTCTACCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTTGAATCTAGTTCCCTTAAAA
348829 TAA
64 TAA
* * * *
348832 AATTTTGTTTACATTGAGACCGTTTCTCATGAAA
1 AATTTTGTCTACCTTGAGACAGTTTCTCTTGAAA
348866 TAACAAATAT
Statistics
Matches: 83, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
65 25 0.30
66 3 0.04
67 29 0.35
68 26 0.31
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.41
Consensus pattern (66 bp):
AATTTTGTCTACCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAATCTAGTTCCCTTAAAATA
A
Found at i:348865 original size:68 final size:68
Alignment explanation
Indices: 348731--348881 Score: 178
Period size: 68 Copynumber: 2.2 Consensus size: 68
348721 TTTCCCTTGA
* * * * * *
348731 AACAAAATCTTTGAATCTAGTTCCCTTTAAACAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 AACAAAATCTTTGAATCTAGTTCCCTTAAAAAAAATTTTGTCTACATTGAGACAGTTTCTCATGA
348796 AA-
66 AAT
* * * * *
348798 CACAAAATCTTTGAATTTATTTCCCTTAAAATAAAATTTTGTTTACATTGAGACCGTTTCTCATG
1 AACAAAATCTTTGAATCTAGTTCCCTTAAAA-AAAATTTTGTCTACATTGAGACAGTTTCTCATG
348863 AAAT
65 AAAT
348867 AACAAATATCTTTGA
1 AACAAA-ATCTTTGA
348882 GATCGTTTCC
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
67 27 0.39
68 29 0.42
69 5 0.07
70 8 0.12
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (68 bp):
AACAAAATCTTTGAATCTAGTTCCCTTAAAAAAAATTTTGTCTACATTGAGACAGTTTCTCATGA
AAT
Found at i:349626 original size:2 final size:2
Alignment explanation
Indices: 349614--349680 Score: 95
Period size: 2 Copynumber: 35.0 Consensus size: 2
349604 ATTTTATACA
*
349614 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
349656 AT TT AT AT -T AT AT A- AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
349681 TATTCATTCA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
1 3 0.05
2 55 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:355059 original size:17 final size:18
Alignment explanation
Indices: 355022--355060 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
355012 ATCTTTTGTA
355022 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
355040 TTTAATTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
355057 TTTA
1 TTTA
355061 CTTATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:355563 original size:23 final size:23
Alignment explanation
Indices: 355535--355585 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
355525 AGGGATCGCA
355535 CAGGGTTCCTGGACTACTTTGCG
1 CAGGGTTCCTGGACTACTTTGCG
*
355558 CAGGGTTCCTGGACTACTTTGTG
1 CAGGGTTCCTGGACTACTTTGCG
355581 CAGGG
1 CAGGG
355586 AAAATCTAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.14, C:0.24, G:0.33, T:0.29
Consensus pattern (23 bp):
CAGGGTTCCTGGACTACTTTGCG
Found at i:361534 original size:81 final size:79
Alignment explanation
Indices: 361418--361580 Score: 188
Period size: 80 Copynumber: 2.0 Consensus size: 79
361408 AAATACTGCC
* *
361418 GATTTTATTATTATTATTTTAATATTTTTGGTAAAAAAATTA-TTAAAAAATTATTATTTTTA-T
1 GATTTTATTATTATTATTTTAATATATCTGGT-AAAAAATTACTTAAAAAATTATT-TTTTTACT
* *
361481 CGATTTTGTTATTATTA
64 -AATTTTATTATTATTA
* * * *
361498 GATTTTTTTATCTATT-TTATTAATATATCTGTTAAAAAGTTACTTAAAATATTATTTTTTTACT
1 GATTTTATTAT-TATTATT-TTAATATATCTGGTAAAAAATTACTTAAAAAATTATTTTTTTACT
361562 AATTTTATTATTATTA
64 AATTTTATTATTATTA
361578 GAT
1 GAT
361581 ACTTTACCGA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
80 43 0.61
81 28 0.39
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (79 bp):
GATTTTATTATTATTATTTTAATATATCTGGTAAAAAATTACTTAAAAAATTATTTTTTTACTAA
TTTTATTATTATTA
Found at i:362697 original size:168 final size:168
Alignment explanation
Indices: 362419--362752 Score: 668
Period size: 168 Copynumber: 2.0 Consensus size: 168
362409 TGAAGCAGAT
362419 GACTTTGGGAAGTTTTAGGTTTGGTGCAGATTCAGTTGATGTTAGAATTGAAGCATGTCTTAAAT
1 GACTTTGGGAAGTTTTAGGTTTGGTGCAGATTCAGTTGATGTTAGAATTGAAGCATGTCTTAAAT
362484 TTTACACGAAAGAGAACATTGTAGAAATTTAAGAGATGCGTAGAGAGTACGAAGAGAGGATGGTG
66 TTTACACGAAAGAGAACATTGTAGAAATTTAAGAGATGCGTAGAGAGTACGAAGAGAGGATGGTG
362549 AAGATGGAAGAGAAATTGTTTTCTTCTACACTTTAAGA
131 AAGATGGAAGAGAAATTGTTTTCTTCTACACTTTAAGA
362587 GACTTTGGGAAGTTTTAGGTTTGGTGCAGATTCAGTTGATGTTAGAATTGAAGCATGTCTTAAAT
1 GACTTTGGGAAGTTTTAGGTTTGGTGCAGATTCAGTTGATGTTAGAATTGAAGCATGTCTTAAAT
362652 TTTACACGAAAGAGAACATTGTAGAAATTTAAGAGATGCGTAGAGAGTACGAAGAGAGGATGGTG
66 TTTACACGAAAGAGAACATTGTAGAAATTTAAGAGATGCGTAGAGAGTACGAAGAGAGGATGGTG
362717 AAGATGGAAGAGAAATTGTTTTCTTCTACACTTTAA
131 AAGATGGAAGAGAAATTGTTTTCTTCTACACTTTAA
362753 TGAATGCTCA
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
168 166 1.00
ACGTcount: A:0.34, C:0.08, G:0.27, T:0.31
Consensus pattern (168 bp):
GACTTTGGGAAGTTTTAGGTTTGGTGCAGATTCAGTTGATGTTAGAATTGAAGCATGTCTTAAAT
TTTACACGAAAGAGAACATTGTAGAAATTTAAGAGATGCGTAGAGAGTACGAAGAGAGGATGGTG
AAGATGGAAGAGAAATTGTTTTCTTCTACACTTTAAGA
Found at i:368129 original size:6 final size:6
Alignment explanation
Indices: 368118--368158 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
368108 TCTAAACAAG
368118 ACAGCA ACAGCA ACAGCA ACAGCA ACAGCA ACAGCA ACAGC
1 ACAGCA ACAGCA ACAGCA ACAGCA ACAGCA ACAGCA ACAGC
368159 TGAGTAGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.49, C:0.34, G:0.17, T:0.00
Consensus pattern (6 bp):
ACAGCA
Found at i:379372 original size:9 final size:10
Alignment explanation
Indices: 379349--379374 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
379339 TACGGAATTT
379349 TTTTTTAATA
1 TTTTTTAATA
379359 TTTTTTAATA
1 TTTTTTAATA
379369 TTTTTT
1 TTTTTT
379375 TTTAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTAATA
Found at i:379494 original size:31 final size:30
Alignment explanation
Indices: 379452--379521 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
379442 GTTAACATCG
*
379452 AGGCACCTAAAGTGGTAACATTTGTAACGT
1 AGGCACCTAAAGTGGTAACATTTGTAACCT
* * *
379482 CAGGCACGTAAAGTTGTAACGTTTGTAACCT
1 -AGGCACCTAAAGTGGTAACATTTGTAACCT
379513 AGGCACCTA
1 AGGCACCTA
379522 GATGGACTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 8 0.24
31 26 0.76
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (30 bp):
AGGCACCTAAAGTGGTAACATTTGTAACCT
Found at i:393161 original size:3 final size:3
Alignment explanation
Indices: 393155--393204 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
393145 GTCATCATCA
** * * *
393155 TCG TCG TCG TTA TCA TCG TCG TTG TCG TCG TCG TCG TCA TCG TCG TCG
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG
393203 TC
1 TC
393205 CTGAGCAGGT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.06, C:0.30, G:0.26, T:0.38
Consensus pattern (3 bp):
TCG
Found at i:393171 original size:18 final size:18
Alignment explanation
Indices: 393148--393182 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
393138 TCTCGCTGTC
393148 ATCATCATCGTCGTCGTT
1 ATCATCATCGTCGTCGTT
* *
393166 ATCATCGTCGTTGTCGT
1 ATCATCATCGTCGTCGT
393183 CGTCGTCGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (18 bp):
ATCATCATCGTCGTCGTT
Found at i:393201 original size:12 final size:12
Alignment explanation
Indices: 393152--393204 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
393142 GCTGTCATCA
393152 TCATCGTCGTCG
1 TCATCGTCGTCG
*
393164 TTATCATCGTCGTTG
1 ---TCATCGTCGTCG
*
393179 TCGTCGTCGTCG
1 TCATCGTCGTCG
393191 TCATCGTCGTCG
1 TCATCGTCGTCG
393203 TC
1 TC
393205 CTGAGCAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
12 23 0.68
15 11 0.32
ACGTcount: A:0.08, C:0.30, G:0.25, T:0.38
Consensus pattern (12 bp):
TCATCGTCGTCG
Found at i:396181 original size:32 final size:32
Alignment explanation
Indices: 396145--396219 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
396135 CAATAGCAAC
*
396145 AGATAAAAAACAACAACAAAATCAAACAATGA
1 AGATAAAAAACAACAACAAAATCAAACAAAGA
** *
396177 AGATAGTAAATAACAACAAAATCAAACAAAGA
1 AGATAAAAAACAACAACAAAATCAAACAAAGA
*
396209 AGCAAAAAAAA
1 AG-ATAAAAAA
396220 AAAAATTGAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
32 30 0.86
33 5 0.14
ACGTcount: A:0.69, C:0.13, G:0.08, T:0.09
Consensus pattern (32 bp):
AGATAAAAAACAACAACAAAATCAAACAAAGA
Found at i:413503 original size:11 final size:11
Alignment explanation
Indices: 413487--413515 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
413477 TGTGTAAGGT
413487 ATGGGCACGAG
1 ATGGGCACGAG
413498 ATGGGCACGAG
1 ATGGGCACGAG
413509 ATGGGCA
1 ATGGGCA
413516 GGTGGAGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.45, T:0.10
Consensus pattern (11 bp):
ATGGGCACGAG
Found at i:419481 original size:3 final size:3
Alignment explanation
Indices: 419473--419523 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
419463 ATGCATATTA
419473 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
419520 AAT A
1 AAT A
419524 TAAAACTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:419807 original size:40 final size:41
Alignment explanation
Indices: 419688--419943 Score: 124
Period size: 40 Copynumber: 6.0 Consensus size: 41
419678 GTTGGTTGCT
* * *
419688 GGGGACGACACTGCTCATACGTGATGAAGAGGTCTGGTTGTCTA
1 GGGGATGACACGGCTCATACGTGATGAAGAGATCT-G--GTCTA
* * * * *
419732 AGGG-TGACACGGTTCCTACGTGATGAGGAAATCTGGTC-A
1 GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGTCTA
*
419771 GGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTA
1 GGGGATGACACGGCTCATACGTGATGAAGAGATCTGG---TC--TA
* * * * * * * * *
419817 GGAATGGTGATAACTCGGTTCCTACGCGATGAGGACAGCTGATTATCTA
1 -G---GG-GATGACACGGCTCATACGTGATGAAGAGATCTG---GTCTA
* * * *
419866 TGGG-TGACATGGCTCCTACATGATGAAGAGATCTGGTC-A
1 GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGTCTA
* *
419905 GGGGATGACACGGCTCATACGTGATGAATAGTTCTGGTC
1 GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGTC
419944 ATTTTTAGAA
Statistics
Matches: 155, Mismatches: 41, Indels: 36
0.67 0.18 0.16
Matches are distributed among these distances:
39 8 0.05
40 61 0.39
42 1 0.01
43 47 0.30
44 4 0.03
45 2 0.01
46 1 0.01
47 1 0.01
49 2 0.01
50 2 0.01
51 26 0.17
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (41 bp):
GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGTCTA
Found at i:419951 original size:134 final size:134
Alignment explanation
Indices: 419705--420065 Score: 456
Period size: 134 Copynumber: 2.7 Consensus size: 134
419695 ACACTGCTCA
* * * * * * * *
419705 TACGTGATGAAGAGGTCTGGTTGTCTAAGGGTGACACGGTTCCTACGTGATGAGGAAATCTGGTC
1 TACGCGATGAGGACGTCTGATTATCTAAGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTC
* * *
419770 AGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAATG-GTGATAACTCG
66 AGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTA-GAAAGAGCGATAACACG
419834 GTTCC
130 GTTCC
* * *
419839 TACGCGATGAGGACAG-CTGATTATCTATGGGTGACATGGCTCCTACATGATGAAGAGATCTGGT
1 TACGCGATGAGGAC-GTCTGATTATCTAAGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGT
* * *
419903 CAGGGGATGACACGGCTCATACGTGATGAATAGTTCTGGTCATTTTTAGAAAGAGCGATAACACG
65 CAGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGAAAGAGCGATAACACG
419968 GTTCC
130 GTTCC
* * * * * *
419973 TACGTGATGAGGACGTCTGGTTATCTAGGGGTAACACGACTCCTACGCGATGAAGAGATCTGGTC
1 TACGCGATGAGGACGTCTGATTATCTAAGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTC
* * *
420038 AAGGGATGACACTGCTCCTACGTGATGA
66 AGGGGATGACACGGCTCATACGTGATGA
420066 GGACAGCTGG
Statistics
Matches: 196, Mismatches: 28, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
133 5 0.03
134 190 0.97
135 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (134 bp):
TACGCGATGAGGACGTCTGATTATCTAAGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTC
AGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGAAAGAGCGATAACACGG
TTCC
Found at i:420134 original size:28 final size:28
Alignment explanation
Indices: 420094--420173 Score: 108
Period size: 28 Copynumber: 2.9 Consensus size: 28
420084 AGTGATTATG
** *
420094 GTTTCAAGGGAAACCGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
420122 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
*
420150 GTTTCAAGAA-AAACATACTCAAAG
1 GTTTCAA-AAGAAACAGACTCAAAG
420174 GTGATGTGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
28 45 0.96
29 2 0.04
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACTCAAAGATTT
Found at i:420187 original size:31 final size:28
Alignment explanation
Indices: 420094--420190 Score: 97
Period size: 28 Copynumber: 3.4 Consensus size: 28
420084 AGTGATTATG
** * *
420094 GTTTCAAGGGAAACCGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATGT
*
420122 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATGT
*
420150 GTTTCAAGAA-AAACATACTCAAAGGTGATGT
1 GTTTCAA-AAGAAACAGACTCAAA---GATGT
420181 GTTTCAAAAG
1 GTTTCAAAAG
420191 TAACTGTCTC
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
28 44 0.75
29 2 0.03
30 2 0.03
31 11 0.19
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACTCAAAGATGT
Found at i:420357 original size:32 final size:34
Alignment explanation
Indices: 420310--420442 Score: 101
Period size: 38 Copynumber: 3.8 Consensus size: 34
420300 CAAAGATCGG
*
420310 TGTTTCGAGAGAAACAAACTCAAAGATG-T-TTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGTTGTTT
* * *
420342 TGTTTCAAGAAAAACACACTCAAAGTTTTTGTTTGTTT
1 TGTTTCAAGAGAAACAAACTCAAAG---ATG-TTGTTT
* **
420380 TGTTTCAAGGGAAACAAACTCAAAGATGGTAAATTT
1 TGTTTCAAGAGAAACAAACTCAAAGAT-GT-TGTTT
* *
420416 TGTTTTCAA-AGACACAAACTTAAAGAT
1 TG-TTTCAAGAGAAACAAACTCAAAGAT
420443 TTTTTCTCAA
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
32 22 0.28
35 4 0.05
36 21 0.27
37 7 0.09
38 25 0.32
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (34 bp):
TGTTTCAAGAGAAACAAACTCAAAGATGTTGTTT
Found at i:420635 original size:66 final size:67
Alignment explanation
Indices: 420524--420680 Score: 212
Period size: 66 Copynumber: 2.4 Consensus size: 67
420514 CGTTTTAAGT
* * *
420524 GAGACGAAATTTG-TTTCAAATGAAACAATCTCAAAGGTTGGTTTTTCATTAAAAATTATCTCAA
1 GAGACAAAATTTGTTTTCAAATGAAACAATCTCAAAGGTTGATTTTTCATTAAAAACTATCTCAA
420588 GA
66 GA
* * * *
420590 GAGACAAAATTTGTTTTCAAAT-AAACAATCTCAGAGGTTGATTTTTTATTAGAAACTGTCTCAA
1 GAGACAAAATTTGTTTTCAAATGAAACAATCTCAAAGGTTGATTTTTCATTAAAAACTATCTCAA
420654 GA
66 GA
* *
420656 GAGATAAAATTTGTTTTTAAA-GAAA
1 GAGACAAAATTTGTTTTCAAATGAAA
420681 TAGACTCAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
66 72 0.90
67 8 0.10
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (67 bp):
GAGACAAAATTTGTTTTCAAATGAAACAATCTCAAAGGTTGATTTTTCATTAAAAACTATCTCAA
GA
Found at i:420710 original size:66 final size:64
Alignment explanation
Indices: 420582--420892 Score: 205
Period size: 66 Copynumber: 4.8 Consensus size: 64
420572 TTAAAAATTA
* * * **
420582 TCTCAAGAGAGACAAAATTTGTTTTCAAATAAACA-ATCTCAGAGGTTGATTTTTTATTAGAAAC
1 TCTCAAGAGAGACAAAATTTGTTTTCAAAGAAACAGA-CTCA-AAGAT-ATTTTTTAAAAGAAAC
420646 TG
63 TG
* * * * *
420648 TCTCAAGAGAGATAAAATTTGTTTTTAAAGAAATAGACTCAAAGATGATTTTGTTAAGAGAAACA
1 TCTCAAGAGAGACAAAATTTGTTTTCAAAGAAACAGACTCAAAGAT-ATTTT-TTAAAAGAAACT
*
420713 A
64 G
* * * *
420714 ACTCAA-AG-G------TTTTTTTTAAAAAAAGAACAGACTCAAAGAT-TTGTTTTAAAAGAAAC
1 TCTCAAGAGAGACAAAATTTGTTTT-CAAAGA-AACAGACTCAAAGATATT-TTTTAAAAGAAAC
420770 TG
63 TG
* * *
420772 TCTAAAGAGAGACAAAAATTGTTTT-AAGAGAAACA-AGCTCAAAGATTTTTTTTCTCAAAAGAA
1 TCTCAAGAGAGACAAAATTTGTTTTCAA-AGAAACAGA-CTCAAAGA-TATTTTT-T-AAAAGAA
* *
420835 ATTC
61 ACTG
* * *
420839 TCTCAAGAGAGACAAAATTTTGTTTCCAAAGAAATAGACTCAAAGATTTTTTTT
1 TCTCAAGAGAGACAAAA-TTTGTTTTCAAAGAAACAGACTCAAAGATATTTTTT
420893 TTCAAAAGAA
Statistics
Matches: 194, Mismatches: 29, Indels: 44
0.73 0.11 0.16
Matches are distributed among these distances:
58 23 0.12
59 8 0.04
60 15 0.08
63 1 0.01
64 15 0.08
65 17 0.09
66 59 0.30
67 33 0.17
68 20 0.10
69 3 0.02
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32
Consensus pattern (64 bp):
TCTCAAGAGAGACAAAATTTGTTTTCAAAGAAACAGACTCAAAGATATTTTTTAAAAGAAACTG
Found at i:420886 original size:68 final size:66
Alignment explanation
Indices: 420739--420904 Score: 196
Period size: 68 Copynumber: 2.5 Consensus size: 66
420729 TTAAAAAAAG
* * *
420739 AACAGACTCAAAGA-TTTGTTTT-AAAAGAAACTGTCTAAAGAGAGACAAAAATTGTTTTAAGAG
1 AACAGACTCAAAGATTTTTTTTTCAAAAGAAACTCTCTAAAGAGAGACAAAAATTGTTTCAAGAG
420802 A
66 A
* * *
420803 AACA-AGCTCAAAGATTTTTTTTCTCAAAAGAAATTCTCTCAAGAGAGACAAAATTTTGTTTCCA
1 AACAGA-CTCAAAGATTTTTTTT-TCAAAAGAAACTCTCTAAAGAGAGACAAAA-ATTGTTT-CA
420867 A-AGA
62 AGAGA
*
420871 AATAGACTCAAAGATTTTTTTTTTCAAAAGAAAC
1 AACAGACTCAAAGA-TTTTTTTTTCAAAAGAAAC
420905 GACTTAAAGA
Statistics
Matches: 86, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
63 1 0.01
64 12 0.14
65 6 0.07
66 1 0.01
67 25 0.29
68 30 0.35
69 11 0.13
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (66 bp):
AACAGACTCAAAGATTTTTTTTTCAAAAGAAACTCTCTAAAGAGAGACAAAAATTGTTTCAAGAG
A
Found at i:420916 original size:30 final size:31
Alignment explanation
Indices: 420856--420921 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
420846 AGAGACAAAA
* *
420856 TTTTGTTTCCAAAGAAATAGACTCAAAGATT
1 TTTTTTTTCAAAAGAAATAGACTCAAAGATT
* *
420887 TTTTTTTTCAAAAGAAA-CGACTTAAAGATT
1 TTTTTTTTCAAAAGAAATAGACTCAAAGATT
420917 TTTTT
1 TTTTT
420922 CACGAAATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (31 bp):
TTTTTTTTCAAAAGAAATAGACTCAAAGATT
Found at i:420980 original size:60 final size:62
Alignment explanation
Indices: 420891--421040 Score: 211
Period size: 61 Copynumber: 2.5 Consensus size: 62
420881 AAGATTTTTT
* * *
420891 TTTTCAAAAGAAAC-GACTTAAAGATTTTTTTCACGAAATTGTC-TCA-AGAGACAAAACTTTG
1 TTTT-AAAAGAAACAGACTCAAAGA-TTTTTTCACGAAATTGTCTTAAGAGAGACAAAACTTTA
420952 TTTTAAAAGAAACAGACTCAAAGA-TTTTTCACGAAATTGTCTTAAGAGAGACAAAACTTTA
1 TTTTAAAAGAAACAGACTCAAAGATTTTTTCACGAAATTGTCTTAAGAGAGACAAAACTTTA
*
421013 TTTCAAAAGAAACA-ACTCAAAGATTTTT
1 TTTTAAAAGAAACAGACTCAAAGATTTTT
421041 ACTCAAAAGG
Statistics
Matches: 81, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
59 17 0.21
60 20 0.25
61 44 0.54
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (62 bp):
TTTTAAAAGAAACAGACTCAAAGATTTTTTCACGAAATTGTCTTAAGAGAGACAAAACTTTA
Found at i:421046 original size:28 final size:28
Alignment explanation
Indices: 421013--421081 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
421003 CAAAACTTTA
421013 TTTCAAAAGAAACA-ACTCAAAGATTT-
1 TTTCAAAAGAAACAGACTCAAAGATTTG
*
421039 TTACTCAAAAGGAACAGACTCAAAGATTTG
1 TT--TCAAAAGAAACAGACTCAAAGATTTG
421069 TTTCAAAAGAAAC
1 TTTCAAAAGAAAC
421082 TATCTCAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
26 2 0.05
28 21 0.57
29 12 0.32
30 2 0.05
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.25
Consensus pattern (28 bp):
TTTCAAAAGAAACAGACTCAAAGATTTG
Found at i:421387 original size:36 final size:35
Alignment explanation
Indices: 421307--421442 Score: 188
Period size: 36 Copynumber: 3.9 Consensus size: 35
421297 GTATTATGAG
* *
421307 GGAAAATGTCTCAAGTGAGACGAAATTTG-TTTT-
1 GGAAATTGTCTCAAGTGAGACAAAATTTGTTTTTA
*
421340 -GAAATTGTCTCAAATGAGACAAAATTTGTTTTTAA
1 GGAAATTGTCTCAAGTGAGACAAAATTTGTTTTT-A
*
421375 GGAAATTGTCTCAAGTGAGACAAAATTTATTTTTA
1 GGAAATTGTCTCAAGTGAGACAAAATTTGTTTTTA
*
421410 GAGAAATTGTCTCAAGCGAGACAAAATTTGTTT
1 G-GAAATTGTCTCAAGTGAGACAAAATTTGTTT
421443 ATGAGAAAAC
Statistics
Matches: 91, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
32 25 0.27
33 4 0.04
35 2 0.02
36 60 0.66
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.35
Consensus pattern (35 bp):
GGAAATTGTCTCAAGTGAGACAAAATTTGTTTTTA
Found at i:421439 original size:72 final size:68
Alignment explanation
Indices: 421307--421616 Score: 208
Period size: 72 Copynumber: 4.5 Consensus size: 68
421297 GTATTATGAG
* *
421307 GGAAAATGTCTCAAGTGAGACGAAATTTGTTTTGAAATTGTCTCAAATGAGACAAAATTTGTTTT
1 GGAAAATGTCTCAAGTGAGACAAAATTTGTTTTGAAATTGTCTCAAACGAGACAAAATTTGTTTT
421372 TAA
66 TAA
* * *
421375 GGAAATTGTCTCAAGTGAGACAAAATTTATTTTTAGAGAAATTGTCTCAAGCGAGACAAAATTTG
1 GGAAAATGTCTCAAGTGAGACAAAATTT-GTTTT---GAAATTGTCTCAAACGAGACAAAATTTG
* *
421440 TTTATGA
62 TTTTTAA
* ** * * * * *
421447 -GAAAACGATCTCAAGTGAGATTAACTTT-ATTT--AA-TG--TGAAAC-AAATTCGAAATTTGT
1 GGAAAATG-TCTCAAGTGAGACAAAATTTGTTTTGAAATTGTCTCAAACGAGA--CAAAATTTGT
*
421504 ATTTCAAA
63 -TTT-TAA
* * *
421512 GGAAAAATGTCTCATGTGAGACGAAATTTGTTTTTCAAGAAATTGTCTCAAATGAGACAAAATTT
1 GG-AAAATGTCTCAAGTGAGACAAAATTTG-TTTT---GAAATTGTCTCAAACGAGACAAAATTT
*
421577 GATTTT-A
61 GTTTTTAA
* * *
421584 -GAAAACTGTCTCAAGCGAGACAAGATTTTTTTT
1 GGAAAA-TGTCTCAAGTGAGACAAAATTTGTTTT
421617 TCAAAAGAAG
Statistics
Matches: 182, Mismatches: 37, Indels: 44
0.69 0.14 0.17
Matches are distributed among these distances:
61 2 0.01
62 4 0.02
63 9 0.05
64 4 0.02
65 3 0.02
66 17 0.09
67 5 0.03
68 29 0.16
69 4 0.02
70 11 0.06
71 24 0.13
72 49 0.27
73 2 0.01
74 5 0.03
75 8 0.04
76 4 0.02
77 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (68 bp):
GGAAAATGTCTCAAGTGAGACAAAATTTGTTTTGAAATTGTCTCAAACGAGACAAAATTTGTTTT
TAA
Found at i:421459 original size:36 final size:35
Alignment explanation
Indices: 421291--421466 Score: 187
Period size: 36 Copynumber: 4.9 Consensus size: 35
421281 AACAACTTTG
* *
421291 AAATTTGTATTATGAGGGAAAATGTCTCAAGTGAGACG
1 AAATTTGT-TTATGA--GAAATTGTCTCAAGTGAGACA
*
421329 AAATTTGTTT-T--GAAATTGTCTCAAATGAGACA
1 AAATTTGTTTATGAGAAATTGTCTCAAGTGAGACA
* *
421361 AAATTTGTTTTTAAGGAAATTGTCTCAAGTGAGACA
1 AAATTTGTTTATGA-GAAATTGTCTCAAGTGAGACA
* * *
421397 AAATTTATTTTTAGAGAAATTGTCTCAAGCGAGACA
1 AAATTTGTTTAT-GAGAAATTGTCTCAAGTGAGACA
**
421433 AAATTTGTTTATGAGAAAACGATCTCAAGTGAGA
1 AAATTTGTTTATGAGAAATTG-TCTCAAGTGAGA
421467 TTAACTTTAT
Statistics
Matches: 120, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
32 28 0.23
33 1 0.01
35 7 0.06
36 73 0.61
37 3 0.03
38 8 0.07
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (35 bp):
AAATTTGTTTATGAGAAATTGTCTCAAGTGAGACA
Found at i:421568 original size:36 final size:37
Alignment explanation
Indices: 421494--421642 Score: 119
Period size: 36 Copynumber: 4.0 Consensus size: 37
421484 GAAACAAATT
* *
421494 CGAAATTTGTATTTCAAAGGAAAAATGTCTCATGTGAGA
1 CGAAATTTGTTTTTC-AA-GAAAAATGTCTCAAGTGAGA
* *
421533 CGAAATTTGTTTTTCAAG-AAATTGTCTCAAATGAGA
1 CGAAATTTGTTTTTCAAGAAAAATGTCTCAAGTGAGA
* * * *
421569 CAAAATTTGATTTT--AGAAAACTGTCTCAAGCGAGA
1 CGAAATTTGTTTTTCAAGAAAAATGTCTCAAGTGAGA
* * *
421604 C-AAGATTTTTTTTTCAA-AAGAAGATGTCTCTAGCGAGA
1 CGAA-ATTTGTTTTTCAAGAA-AA-ATGTCTCAAGTGAGA
421642 C
1 C
421643 AACATTTTGT
Statistics
Matches: 91, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
34 4 0.04
35 24 0.26
36 29 0.32
37 4 0.04
38 16 0.18
39 14 0.15
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (37 bp):
CGAAATTTGTTTTTCAAGAAAAATGTCTCAAGTGAGA
Found at i:421965 original size:4 final size:4
Alignment explanation
Indices: 421965--422023 Score: 86
Period size: 4 Copynumber: 14.8 Consensus size: 4
421955 TGCATGTATG
421965 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGCATA TGT-
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG--TA TGTA
422014 TG-A TGTA TGT
1 TGTA TGTA TGT
422024 TTTTCTCGAT
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
3 4 0.08
4 43 0.84
6 4 0.08
ACGTcount: A:0.24, C:0.02, G:0.25, T:0.49
Consensus pattern (4 bp):
TGTA
Found at i:423197 original size:23 final size:22
Alignment explanation
Indices: 423171--423228 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 22
423161 TCCTCTTTTG
*
423171 TTCTTTGCTTTTTCTTTGCTATT
1 TTCTTTGCTTTTTCTTTCCT-TT
423194 TTCTTTG--TTTT-TTTCCTTT
1 TTCTTTGCTTTTTCTTTCCTTT
*
423213 TTCTTT-CTATTTCTTT
1 TTCTTTGCTTTTTCTTT
423229 TCTCTTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
19 8 0.27
20 8 0.27
21 7 0.23
23 7 0.23
ACGTcount: A:0.03, C:0.17, G:0.05, T:0.74
Consensus pattern (22 bp):
TTCTTTGCTTTTTCTTTCCTTT
Found at i:423201 original size:30 final size:28
Alignment explanation
Indices: 423167--423244 Score: 86
Period size: 31 Copynumber: 2.7 Consensus size: 28
423157 TTTGTCCTCT
423167 TTTGTTCTTTGCTTTTTCTTTGCTATTTTC
1 TTTGTTCTTTGCTTTTTCTTT-CTA-TTTC
* *
423197 TTTGTTTTTTTCCTTTTTCTTTCTATTTC
1 TTTG-TTCTTTGCTTTTTCTTTCTATTTC
*
423226 TTT-TCTCTTTGTTTTTTCT
1 TTTGT-TCTTTGCTTTTTCT
423245 CTTTTTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
27 1 0.02
28 11 0.27
29 7 0.17
30 7 0.17
31 15 0.37
ACGTcount: A:0.03, C:0.17, G:0.06, T:0.74
Consensus pattern (28 bp):
TTTGTTCTTTGCTTTTTCTTTCTATTTC
Found at i:423240 original size:11 final size:11
Alignment explanation
Indices: 423171--423228 Score: 61
Period size: 10 Copynumber: 5.5 Consensus size: 11
423161 TCCTCTTTTG
423171 TTCTTTGCTTT
1 TTCTTTGCTTT
423182 TTCTTTGCTATT
1 TTCTTTGCT-TT
423194 TTCTTTG--TT
1 TTCTTTGCTTT
*
423203 TT-TTTCCTTT
1 TTCTTTGCTTT
*
423213 TTCTTT-CTAT
1 TTCTTTGCTTT
423223 TTCTTT
1 TTCTTT
423229 TCTCTTTGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
8 3 0.07
9 4 0.10
10 13 0.32
11 12 0.29
12 9 0.22
ACGTcount: A:0.03, C:0.17, G:0.05, T:0.74
Consensus pattern (11 bp):
TTCTTTGCTTT
Found at i:423244 original size:13 final size:12
Alignment explanation
Indices: 423192--423252 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 12
423182 TTCTTTGCTA
423192 TTTTCT-TTGTTT
1 TTTTCTCTT-TTT
423204 TTTTC-CTTTTT
1 TTTTCTCTTTTT
* * *
423215 CTTTCT-ATTTC
1 TTTTCTCTTTTT
423226 TTTTCTCTTTGTT
1 TTTTCTCTTT-TT
423239 TTTTCTCTTTTT
1 TTTTCTCTTTTT
423251 TT
1 TT
423253 ATTGGATCTT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
11 15 0.38
12 13 0.33
13 11 0.28
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTTCTCTTTTT
Found at i:423861 original size:20 final size:20
Alignment explanation
Indices: 423836--423876 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
423826 AAATAAAGGC
423836 AATGTTTCAAGGTCTCAAAG
1 AATGTTTCAAGGTCTCAAAG
*
423856 AATGTTTCAAGGTCTTAAAG
1 AATGTTTCAAGGTCTCAAAG
423876 A
1 A
423877 GAGTGAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
AATGTTTCAAGGTCTCAAAG
Found at i:432225 original size:241 final size:241
Alignment explanation
Indices: 431797--432277 Score: 854
Period size: 241 Copynumber: 2.0 Consensus size: 241
431787 GAAGAGCCTT
*
431797 AGTAAATATATCAACCAGTTGGTCATTTGTGCTGCAATAGAGCAAAGAAACTTCACCATTCTTCT
1 AGTAAATATATCAACCAGTTGGTCATTTGTGCTGCAATAGAGCAAAGAAACTTCACCATTCTTAT
*
431862 AGACTTCTTTAAGAAAATAAAGTTTAATGTTAAAGTGTTTGGTCTTTCCATGAAAGACTGGATTA
66 AGACTTCTCTAAGAAAATAAAGTTTAATGTTAAAGTGTTTGGTCTTTCCATGAAAGACTGGATTA
* * * *
431927 TTGGAGATTGCAATGGCATCTTGGTTATCCACAAACACTTCTTTGCTCCTTCTTTGTTCCAAGTA
131 TTGGAGATTGCAATAGCAGCTTGGTTATCCACAAACACTTCTGTGCTCCTCCTTTGTTCCAAGTA
431992 TAAATCATTCAAAATCTTCCTCAACCATAAGGCTTGATTTACAACC
196 TAAATCATTCAAAATCTTCCTCAACCATAAGGCTTGATTTACAACC
** *
432038 AGTAAATATATCAGTCAGTTGGTCATTTGTGCTGCAGTAGAGCAAAGAAACTTCACCATTCTTAT
1 AGTAAATATATCAACCAGTTGGTCATTTGTGCTGCAATAGAGCAAAGAAACTTCACCATTCTTAT
*
432103 GGACTTCTCTAAGAAAATAAAGTTTAATGTTAAAGTGTTTGGTCTTTCCATGAAAGACTGGATTA
66 AGACTTCTCTAAGAAAATAAAGTTTAATGTTAAAGTGTTTGGTCTTTCCATGAAAGACTGGATTA
* *
432168 TTGGAGATTGCAATAGTAGCTTGGTTATCCACAAACACTTCTGTGTTCCTCCTTTGTTCCAAGTA
131 TTGGAGATTGCAATAGCAGCTTGGTTATCCACAAACACTTCTGTGCTCCTCCTTTGTTCCAAGTA
432233 TAAATCATTCAAAATCTTCCTCAACCATAAGGCTTGATTTACAAC
196 TAAATCATTCAAAATCTTCCTCAACCATAAGGCTTGATTTACAAC
432278 TACTGTAGCA
Statistics
Matches: 228, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
241 228 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (241 bp):
AGTAAATATATCAACCAGTTGGTCATTTGTGCTGCAATAGAGCAAAGAAACTTCACCATTCTTAT
AGACTTCTCTAAGAAAATAAAGTTTAATGTTAAAGTGTTTGGTCTTTCCATGAAAGACTGGATTA
TTGGAGATTGCAATAGCAGCTTGGTTATCCACAAACACTTCTGTGCTCCTCCTTTGTTCCAAGTA
TAAATCATTCAAAATCTTCCTCAACCATAAGGCTTGATTTACAACC
Found at i:433079 original size:21 final size:21
Alignment explanation
Indices: 433041--433080 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
433031 TGCCCGTGGA
*
433041 GCCTATTTTAAGCCGTACAAG
1 GCCTATTTTAAGCAGTACAAG
433062 GCCT-TTTTAAGCAAGTACA
1 GCCTATTTTAAGC-AGTACA
433081 CCTTATTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (21 bp):
GCCTATTTTAAGCAGTACAAG
Found at i:436661 original size:76 final size:76
Alignment explanation
Indices: 436534--436687 Score: 281
Period size: 76 Copynumber: 2.0 Consensus size: 76
436524 ATTTCTCATC
*
436534 AAGAAGATATTGTGTGTTTCAGAACTAGCAATCAAGTACTCTGTTTCGGCCATATGAAAGCTAAG
1 AAGAAGATATTGTGTGTTTCAGAACTAGCAACCAAGTACTCTGTTTCGGCCATATGAAAGCTAAG
*
436599 CAATTATGAAG
66 CAAATATGAAG
*
436610 AAGAAGATATTGTGTGTTTCAGAACTAGCAACCAAGTACTCTGTTTTGGCCATATGAAAGCTAAG
1 AAGAAGATATTGTGTGTTTCAGAACTAGCAACCAAGTACTCTGTTTCGGCCATATGAAAGCTAAG
436675 CAAATATGAAG
66 CAAATATGAAG
436686 AA
1 AA
436688 AAAGCGTTGA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (76 bp):
AAGAAGATATTGTGTGTTTCAGAACTAGCAACCAAGTACTCTGTTTCGGCCATATGAAAGCTAAG
CAAATATGAAG
Found at i:451364 original size:17 final size:18
Alignment explanation
Indices: 451329--451370 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
451319 TGTTGAATGC
451329 TTGTTTTAGGTTGCGTTG
1 TTGTTTTAGGTTGCGTTG
* *
451347 TT-TTTTAGGTTTCTTTG
1 TTGTTTTAGGTTGCGTTG
451364 TTGTTTT
1 TTGTTTT
451371 GGCATGGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.05, C:0.05, G:0.24, T:0.67
Consensus pattern (18 bp):
TTGTTTTAGGTTGCGTTG
Found at i:457455 original size:177 final size:176
Alignment explanation
Indices: 457139--457471 Score: 542
Period size: 177 Copynumber: 1.9 Consensus size: 176
457129 TGTCAAACGA
* * *
457139 CTTTCTGCTTTCAATGGAGCATAATATTCTGAAGTTTGAGTTAAATTCAATAAAAAAATCTTGAC
1 CTTTCTGCTTTCAATGGAACATAATATTCTGAAATTTGAGTTAAATTCAATAAAAAAATCTAGAC
* *
457204 AGGCCATAAAACCAATGCTAGATGAAGAAAAAGTTGACTGTAATATAAGGAGCTAATTGGAGAAA
66 AGGCCATAAAACCAATGCTAGATGAAGAAAAAGTTGACTGAAATATAAGGAGCTAATTGAAGAAA
* *
457269 CTGTAATGTTACAGTTTACGTTAATGTTACAGTTTATGTCAATAGG
131 CTATAATGTTACAGTTTAAGTTAATGTTACAGTTTATGTCAATAGG
*
457315 CTTTCTGCTTTCAATGGAATATAATATTCTGAAATTTGAGTTAAATTCAATAAATAAAAATCTAG
1 CTTTCTGCTTTCAATGGAACATAATATTCTGAAATTTGAGTTAAATTCAAT-AA-AAAAATCTAG
* * *
457380 GCA-GCCATAAAACCAATGCTAGATGAAGCAAAAGTTGACTGAAATATAAGGAGCTAATTGAAGT
64 ACAGGCCATAAAACCAATGCTAGATGAAGAAAAAGTTGACTGAAATATAAGGAGCTAATTGAAGA
457444 AACTATAATGTTACAGTTTAAGTTAATG
129 AACTATAATGTTACAGTTTAAGTTAATG
457472 CATAGCAACA
Statistics
Matches: 144, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
176 48 0.33
177 85 0.59
178 11 0.08
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (176 bp):
CTTTCTGCTTTCAATGGAACATAATATTCTGAAATTTGAGTTAAATTCAATAAAAAAATCTAGAC
AGGCCATAAAACCAATGCTAGATGAAGAAAAAGTTGACTGAAATATAAGGAGCTAATTGAAGAAA
CTATAATGTTACAGTTTAAGTTAATGTTACAGTTTATGTCAATAGG
Found at i:460367 original size:27 final size:27
Alignment explanation
Indices: 460335--460404 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
460325 GTTCAACCGG
*
460335 TTTAGATTGAACCGAACTAAACAACGA
1 TTTAGATTAAACCGAACTAAACAACGA
460362 TTTAGATTAAACCGAACTAAACAACGA
1 TTTAGATTAAACCGAACTAAACAACGA
*
460389 TTCTCGATTAAACCGA
1 TT-TAGATTAAACCGA
460405 TCAATCCGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 28 0.70
28 12 0.30
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (27 bp):
TTTAGATTAAACCGAACTAAACAACGA
Found at i:466397 original size:23 final size:23
Alignment explanation
Indices: 466363--466425 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
466353 CATCTTATAT
*
466363 GGCACTTCGGTGTATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
466386 GGCACTTAGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
466409 GGCACTTCGGTGCATTT
1 GGCACTTCGGTGCATTT
466426 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:467404 original size:149 final size:149
Alignment explanation
Indices: 467134--467432 Score: 598
Period size: 149 Copynumber: 2.0 Consensus size: 149
467124 TAAACCGCTT
467134 TTACTTTAATGAAAGTTTTAAATTTGCTTTGAATTTTGTCAAGAGTCAAAGTTTGAAAAGTCAAT
1 TTACTTTAATGAAAGTTTTAAATTTGCTTTGAATTTTGTCAAGAGTCAAAGTTTGAAAAGTCAAT
467199 ATGACACCTCAGACTCGTATCTGGGTTGGGTACGGGTTGGGGGTGTTACATTTAATGGTATCAGA
66 ATGACACCTCAGACTCGTATCTGGGTTGGGTACGGGTTGGGGGTGTTACATTTAATGGTATCAGA
467264 GGTAAGGTTTAGTCGATTC
131 GGTAAGGTTTAGTCGATTC
467283 TTACTTTAATGAAAGTTTTAAATTTGCTTTGAATTTTGTCAAGAGTCAAAGTTTGAAAAGTCAAT
1 TTACTTTAATGAAAGTTTTAAATTTGCTTTGAATTTTGTCAAGAGTCAAAGTTTGAAAAGTCAAT
467348 ATGACACCTCAGACTCGTATCTGGGTTGGGTACGGGTTGGGGGTGTTACATTTAATGGTATCAGA
66 ATGACACCTCAGACTCGTATCTGGGTTGGGTACGGGTTGGGGGTGTTACATTTAATGGTATCAGA
467413 GGTAAGGTTTAGTCGATTC
131 GGTAAGGTTTAGTCGATTC
467432 T
1 T
467433 CGGCGTAAAA
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.36
Consensus pattern (149 bp):
TTACTTTAATGAAAGTTTTAAATTTGCTTTGAATTTTGTCAAGAGTCAAAGTTTGAAAAGTCAAT
ATGACACCTCAGACTCGTATCTGGGTTGGGTACGGGTTGGGGGTGTTACATTTAATGGTATCAGA
GGTAAGGTTTAGTCGATTC
Found at i:469129 original size:236 final size:236
Alignment explanation
Indices: 468716--469190 Score: 878
Period size: 236 Copynumber: 2.0 Consensus size: 236
468706 TCAACTGGAG
*
468716 GAGGGTGATGGAGGAGGATCTCTCTCACTGTGGCCAGGTACGGATGTACATGACTCTATAGGGGA
1 GAGGGTGATGAAGGAGGATCTCTCTCACTGTGGCCAGGTACGGATGTACATGACTCTATAGGGGA
468781 GTTATTGCACACCCATTATTTTGAGAAAATGTTAAATTTAATTTAGTTTGTTAATGAGAACAGAA
66 GTTATTGCACACCCATTATTTTGAGAAAATGTTAAATTTAATTTAGTTTGTTAATGAGAACAGAA
** *
468846 AAAATAAGAAAATTTGTACACCCAAATTGTTGATCTTCCCTGTTTTTACCATGAATTTGGATTTG
131 AAAATAAGAAAATTTACACACCCAAATTGTTGATCTTCCCTGTTTTTACCATGAAATTGGATTTG
*
468911 AATACTCGTTATGCGTTTGTGTATAGCTTTTCATGTAATTA
196 AATACTCGTTATGCGTTCGTGTATAGCTTTTCATGTAATTA
*
468952 GAGGGTGATGAAGGAGGATCTCTCTCACTGTGGCCAGGTACGGATGTACATGGCTCTATAGGGGA
1 GAGGGTGATGAAGGAGGATCTCTCTCACTGTGGCCAGGTACGGATGTACATGACTCTATAGGGGA
469017 GTTATTGCACACCCATTATTTTGAGAAAATGTTAAATTTAATTTAGTTTGTTAATGAGAACAGAA
66 GTTATTGCACACCCATTATTTTGAGAAAATGTTAAATTTAATTTAGTTTGTTAATGAGAACAGAA
469082 AAAATAAGAAAATTTACACACCCAAATTGTTGATCTTCCCTGTTTTTACCATGAAATTGGATTTG
131 AAAATAAGAAAATTTACACACCCAAATTGTTGATCTTCCCTGTTTTTACCATGAAATTGGATTTG
* *
469147 AATACTCGTTATGCGTTCGTGTATAGTTTTTCATGTCATTA
196 AATACTCGTTATGCGTTCGTGTATAGCTTTTCATGTAATTA
469188 GAG
1 GAG
469191 TATGATTTGC
Statistics
Matches: 231, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
236 231 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (236 bp):
GAGGGTGATGAAGGAGGATCTCTCTCACTGTGGCCAGGTACGGATGTACATGACTCTATAGGGGA
GTTATTGCACACCCATTATTTTGAGAAAATGTTAAATTTAATTTAGTTTGTTAATGAGAACAGAA
AAAATAAGAAAATTTACACACCCAAATTGTTGATCTTCCCTGTTTTTACCATGAAATTGGATTTG
AATACTCGTTATGCGTTCGTGTATAGCTTTTCATGTAATTA
Found at i:469477 original size:2 final size:2
Alignment explanation
Indices: 469466--469513 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
469456 TAATGACTTC
469466 TA TA -A 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
469507 TA T- TA TA
1 TA TA TA TA
469514 ATTTTTCAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:469927 original size:26 final size:26
Alignment explanation
Indices: 469898--469980 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
469888 ATATTTACAC
469898 TTATAAATGAATCATATCAATTTAAA
1 TTATAAATGAATCATATCAATTTAAA
* * **
469924 TTAT-AATAAATCCAAAAAAATATT--A
1 TTATAAATGAAT-CATATCAAT-TTAAA
* *
469949 TTATATATGAATTATATCAATTTAAA
1 TTATAAATGAATCATATCAATTTAAA
*
469975 CTATAA
1 TTATAA
469981 TAAAAATAAA
Statistics
Matches: 40, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (26 bp):
TTATAAATGAATCATATCAATTTAAA
Found at i:469992 original size:51 final size:52
Alignment explanation
Indices: 469898--469997 Score: 139
Period size: 51 Copynumber: 1.9 Consensus size: 52
469888 ATATTTACAC
* **
469898 TTATAAATGAATCATATCAATTTAAATTATAATAAATCCAAAAA-AATATTA
1 TTATAAATGAATCATATCAATTTAAACTATAATAAAAACAAAAATAATATTA
* * *
469949 TTATATATGAATTATATCAATTTAAACTATAATAAAAATAAAAATAATA
1 TTATAAATGAATCATATCAATTTAAACTATAATAAAAACAAAAATAATA
469998 AAAATAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 38 0.90
52 4 0.10
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (52 bp):
TTATAAATGAATCATATCAATTTAAACTATAATAAAAACAAAAATAATATTA
Found at i:469995 original size:15 final size:15
Alignment explanation
Indices: 469977--470009 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
469967 AATTTAAACT
469977 ATAATAAAAATAAAA
1 ATAATAAAAATAAAA
469992 ATAATAAAAATAAAA
1 ATAATAAAAATAAAA
470007 ATA
1 ATA
470010 TAATTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
ATAATAAAAATAAAA
Done.