Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007950.1 Hibiscus syriacus cultivar Beakdansim tig00110372_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: 1941792
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:202237 original size:32 final size:32
Alignment explanation
Indices: 202192--202258 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
202182 TGACAAAAAC
* *
202192 TTTTAAGTGATATATCATTTCATTTCAACAAA
1 TTTTAAGTAATATATCACTTCATTTCAACAAA
* * *
202224 TTTTCAGTAATATATTACTTCATTTCAACCAA
1 TTTTAAGTAATATATCACTTCATTTCAACAAA
202256 TTT
1 TTT
202259 AATCTCTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.46
Consensus pattern (32 bp):
TTTTAAGTAATATATCACTTCATTTCAACAAA
Found at i:204371 original size:18 final size:20
Alignment explanation
Indices: 204333--204373 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
204323 TCATAAATTG
204333 AATAATTTTGTTCTAACATT
1 AATAATTTTGTTCTAACATT
*
204353 AATATTTTTGTT-T-ACATT
1 AATAATTTTGTTCTAACATT
204371 AAT
1 AAT
204374 TTAAATCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 1 0.05
20 11 0.55
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (20 bp):
AATAATTTTGTTCTAACATT
Found at i:208927 original size:12 final size:12
Alignment explanation
Indices: 208912--208979 Score: 100
Period size: 12 Copynumber: 5.7 Consensus size: 12
208902 GGTTATTTAA
208912 ACGGGTATTGGG
1 ACGGGTATTGGG
208924 ACGGGTATTGGG
1 ACGGGTATTGGG
*
208936 TCGGGTATTGGG
1 ACGGGTATTGGG
*
208948 CCGGGTATTGGG
1 ACGGGTATTGGG
*
208960 TCGGGTATTGGG
1 ACGGGTATTGGG
*
208972 CCGGGTAT
1 ACGGGTAT
208980 ATATATATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 52 1.00
ACGTcount: A:0.12, C:0.12, G:0.49, T:0.28
Consensus pattern (12 bp):
ACGGGTATTGGG
Found at i:208932 original size:24 final size:24
Alignment explanation
Indices: 208913--208979 Score: 116
Period size: 24 Copynumber: 2.8 Consensus size: 24
208903 GTTATTTAAA
208913 CGGGTATTGGGACGGGTATTGGGT
1 CGGGTATTGGGACGGGTATTGGGT
*
208937 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGACGGGTATTGGGT
*
208961 CGGGTATTGGGCCGGGTAT
1 CGGGTATTGGGACGGGTAT
208980 ATATATATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.10, C:0.12, G:0.49, T:0.28
Consensus pattern (24 bp):
CGGGTATTGGGACGGGTATTGGGT
Found at i:208984 original size:2 final size:2
Alignment explanation
Indices: 208977--209068 Score: 52
Period size: 2 Copynumber: 49.0 Consensus size: 2
208967 TTGGGCCGGG
* * * *
208977 TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
209017 TT TT TA TT TA AA T- TA AA TT TA T- TA -A TA T- 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
209055 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
209069 AATAATTATT
Statistics
Matches: 67, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
1 6 0.09
2 61 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:209119 original size:13 final size:12
Alignment explanation
Indices: 209088--209124 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
209078 TTTTAATATT
*
209088 TATCGGGTCGGG
1 TATCGGGGCGGG
209100 TATCGGGGCGGG
1 TATCGGGGCGGG
209112 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
209125 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:213355 original size:18 final size:18
Alignment explanation
Indices: 213328--213368 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
213318 ACATTCTCAA
* *
213328 TAATCTTATTCCCGCTGG
1 TAATCCTATTCCCACTGG
213346 TAATCCTATTCCCACTGG
1 TAATCCTATTCCCACTGG
213364 TAATC
1 TAATC
213369 TTATATTCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.22, C:0.29, G:0.12, T:0.37
Consensus pattern (18 bp):
TAATCCTATTCCCACTGG
Found at i:216942 original size:21 final size:21
Alignment explanation
Indices: 216918--216958 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
216908 TCCATTCGCA
216918 AAAATGAT-AGATCCCTTTTTC
1 AAAATGATCA-ATCCCTTTTTC
216939 AAAATGATCAATCCCTTTTT
1 AAAATGATCAATCCCTTTTT
216959 GCGAAGGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (21 bp):
AAAATGATCAATCCCTTTTTC
Found at i:217468 original size:17 final size:17
Alignment explanation
Indices: 217442--217476 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
217432 GACATAATTT
*
217442 AAACATTTTTTAATCAA
1 AAACAATTTTTAATCAA
*
217459 AAACAATTTTTCATCAA
1 AAACAATTTTTAATCAA
217476 A
1 A
217477 TCTTTTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (17 bp):
AAACAATTTTTAATCAA
Found at i:219153 original size:20 final size:21
Alignment explanation
Indices: 219102--219153 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
219092 TTAAGTTTCC
* * *
219102 AAGGATCAATCCCTTTGATCA
1 AAGGATCGATCCCCTTGATAA
* *
219123 AAGAATTGATCCCCTTGA-AA
1 AAGGATCGATCCCCTTGATAA
219143 AAGGATCGATC
1 AAGGATCGATC
219154 ACTTGGATTC
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (21 bp):
AAGGATCGATCCCCTTGATAA
Found at i:219207 original size:21 final size:21
Alignment explanation
Indices: 219183--219271 Score: 72
Period size: 21 Copynumber: 4.2 Consensus size: 21
219173 TGGGATCTAT
*
219183 CCCTTTACAAAAAGGATCGAC
1 CCCTTCACAAAAAGGATCGAC
* *
219204 CCCTTCACCAAAAGGATCGAT
1 CCCTTCACAAAAAGGATCGAC
** * *
219225 CCC-TCGATGAAAATGATCGAT
1 CCCTTC-ACAAAAAGGATCGAC
* **
219246 CCCTTCCCTTAAAGGATCGAC
1 CCCTTCACAAAAAGGATCGAC
219267 CCCTT
1 CCCTT
219272 TATTACAACG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
20 2 0.04
21 50 0.93
22 2 0.04
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.22
Consensus pattern (21 bp):
CCCTTCACAAAAAGGATCGAC
Found at i:223475 original size:26 final size:27
Alignment explanation
Indices: 223441--223493 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
223431 TATATTTTAT
* *
223441 AATTATAAA-ATAAATTATATATAAATA
1 AATTATAAAGA-AAATTAAAAATAAATA
223468 AATT-TAAAGAAAATTAAAAATAAATA
1 AATTATAAAGAAAATTAAAAATAAATA
223494 TTAACAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (27 bp):
AATTATAAAGAAAATTAAAAATAAATA
Found at i:224412 original size:30 final size:30
Alignment explanation
Indices: 224376--224441 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
224366 TAAATTGCTT
224376 GGTCGCCATGCAAGCCAAACGACCTGTGCA
1 GGTCGCCATGCAAGCCAAACGACCTGTGCA
*
224406 GGTCGCCATGCAAGCCGAACGACCTGTGCA
1 GGTCGCCATGCAAGCCAAACGACCTGTGCA
*
224436 AGTCGC
1 GGTCGC
224442 TTCTCTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.24, C:0.33, G:0.29, T:0.14
Consensus pattern (30 bp):
GGTCGCCATGCAAGCCAAACGACCTGTGCA
Found at i:230944 original size:28 final size:29
Alignment explanation
Indices: 230901--230956 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
230891 ATTTCAAAAG
*
230901 AATATTATTTTGATAAATA-ATATTATTTA
1 AATATTATTTTAATAAA-AGATATTATTTA
230930 AATATT-TTTTAATAAAAGATATTATTT
1 AATATTATTTTAATAAAAGATATTATTT
230957 TCATAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 1 0.04
28 18 0.72
29 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (29 bp):
AATATTATTTTAATAAAAGATATTATTTA
Found at i:236673 original size:103 final size:106
Alignment explanation
Indices: 236566--236773 Score: 235
Period size: 103 Copynumber: 2.0 Consensus size: 106
236556 GTTTTAAGTC
* * * * * *
236566 CCCCAAATTTTCTCTTATTTTTACAAAATGGTCACTTTTAAGGACCGTTTTTA-TATTTTTCCCA
1 CCCCAAACTTTCTCATATTTTTACAAAATCGTCACTATCAAGGACCGTTTTCATTA-TTTTCCCA
*
236630 TTTAC-G-TGCTTT-ATATTTTGGTAAAATCTCATTCCAGAT
65 TTTACAGATGCTTTGATATTTTGGTAAAATATCATTCCAGAT
* * * * *
236669 CCCCAAACTTTGTCATGTTTTTGCAAAATCGTCACTATCAGGGACTGTTTTCATTATTTTCCCAT
1 CCCCAAACTTTCTCATATTTTTACAAAATCGTCACTATCAAGGACCGTTTTCATTATTTTCCCAT
* *
236734 TTACATGTATGCTTTGTTTTTTTGGTAAAATATCATTCCA
66 TTACA-G-ATGCTTTGATATTTTGGTAAAATATCATTCCA
236774 AGTCATCCTA
Statistics
Matches: 85, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
103 55 0.65
104 2 0.02
105 1 0.01
107 6 0.07
108 21 0.25
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.45
Consensus pattern (106 bp):
CCCCAAACTTTCTCATATTTTTACAAAATCGTCACTATCAAGGACCGTTTTCATTATTTTCCCAT
TTACAGATGCTTTGATATTTTGGTAAAATATCATTCCAGAT
Found at i:237037 original size:12 final size:12
Alignment explanation
Indices: 237020--237081 Score: 81
Period size: 12 Copynumber: 5.1 Consensus size: 12
237010 TGTACTTATG
237020 TTTATTTTATTT
1 TTTATTTTATTT
*
237032 TTTATTTTATGT
1 TTTATTTTATTT
*
237044 TGT-TTTTACTTT
1 TTTATTTTA-TTT
237056 TTTATTTTATTT
1 TTTATTTTATTT
237068 TTTATTGTTATTT
1 TTTATT-TTATTT
237081 T
1 T
237082 AGTTTTTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
11 5 0.12
12 26 0.60
13 12 0.28
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.79
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:237082 original size:31 final size:31
Alignment explanation
Indices: 237024--237088 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
237014 CTTATGTTTA
*
237024 TTTTATTTTTTATTTTATGTTGTTTTTACTT
1 TTTTATTTTTTATTTTATGTTGATTTTACTT
*
237055 TTTTATTTTATT-TTTTATTGTT-ATTTTAGTT
1 TTTTATTTT-TTATTTTA-TGTTGATTTTACTT
237086 TTT
1 TTT
237089 AAAATTAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.14, C:0.02, G:0.06, T:0.78
Consensus pattern (31 bp):
TTTTATTTTTTATTTTATGTTGATTTTACTT
Found at i:238444 original size:29 final size:30
Alignment explanation
Indices: 238411--238471 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
238401 TTTTTATTAT
*
238411 TAAAAAATAA-AAATATAATGGTAGACACC
1 TAAAAAATAATAAATAAAATGGTAGACACC
* * *
238440 TAAAATATAATAGATAAAATGTTAGACACC
1 TAAAAAATAATAAATAAAATGGTAGACACC
238470 TA
1 TA
238472 TATTTAACGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.25
Consensus pattern (30 bp):
TAAAAAATAATAAATAAAATGGTAGACACC
Found at i:242186 original size:4 final size:4
Alignment explanation
Indices: 242179--242209 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
242169 GGTTGGTATT
*
242179 ATGG ATGG ATGG ATGG ATGG ATAG ATGG ATG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATG
242210 AGATTTCTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.45, T:0.26
Consensus pattern (4 bp):
ATGG
Found at i:252628 original size:21 final size:21
Alignment explanation
Indices: 252585--252637 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
252575 TAACTTTTTC
* *
252585 TTTTCTCTTTCTTTGTTCATT
1 TTTTCTCTTTCTATGTTAATT
*
252606 TTTTCTCTTTC-ATGTTAACT
1 TTTTCTCTTTCTATGTTAATT
* *
252626 TTTACTTTTTCT
1 TTTTCTCTTTCT
252638 CTCTCTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.09, C:0.19, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTTCTCTTTCTATGTTAATT
Found at i:254795 original size:11 final size:10
Alignment explanation
Indices: 254779--254807 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
254769 CGTAACAGTT
254779 AAAAAAATAA
1 AAAAAAATAA
254789 AAAAAAATAA
1 AAAAAAATAA
254799 AAAAAAATA
1 AAAAAAATA
254808 TTCAAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:260061 original size:19 final size:20
Alignment explanation
Indices: 260033--260086 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
260023 AGATCCAATC
*
260033 AGAACAAAAAGAGAAAG-GA
1 AGAAAAAAAAGAGAAAGAGA
*
260052 AGAAAAAAAA-ACAAAGAGA
1 AGAAAAAAAAGAGAAAGAGA
*
260071 AAATAAAAAAAGAGAA
1 AGA-AAAAAAAGAGAA
260087 CAAAAACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 5 0.18
19 13 0.46
20 7 0.25
21 3 0.11
ACGTcount: A:0.76, C:0.04, G:0.19, T:0.02
Consensus pattern (20 bp):
AGAAAAAAAAGAGAAAGAGA
Found at i:260067 original size:24 final size:25
Alignment explanation
Indices: 260040--260103 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
260030 ATCAGAACAA
260040 AAAGAGAAAGGAAGAAAAA-AAAAC
1 AAAGAGAAAGGAAGAAAAAGAAAAC
** *
260064 AAAGAGAAAATAA-AAAAAGAGAAC
1 AAAGAGAAAGGAAGAAAAAGAAAAC
* *
260088 AAAAACAAAGGAAGAA
1 AAAGAGAAAGGAAGAA
260104 GTGAAGAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
23 5 0.16
24 24 0.77
25 2 0.06
ACGTcount: A:0.75, C:0.05, G:0.19, T:0.02
Consensus pattern (25 bp):
AAAGAGAAAGGAAGAAAAAGAAAAC
Found at i:260073 original size:15 final size:15
Alignment explanation
Indices: 260051--260097 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
260041 AAGAGAAAGG
260051 AAGA-AAAAAAAACA
1 AAGAGAAAAAAAACA
260065 AAGAGAAAATAAAA-A
1 AAGAGAAAA-AAAACA
*
260080 AAGAGAACAAAAACA
1 AAGAGAAAAAAAACA
260095 AAG
1 AAG
260098 GAAGAAGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 8 0.28
15 17 0.59
16 4 0.14
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.02
Consensus pattern (15 bp):
AAGAGAAAAAAAACA
Found at i:261828 original size:64 final size:64
Alignment explanation
Indices: 261747--261940 Score: 334
Period size: 64 Copynumber: 3.0 Consensus size: 64
261737 AAGCTGTCTG
* *
261747 TCAACAAATAACGTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
1 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
*
261811 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTTACAACGAAGGATATTGGAC
1 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
* * *
261875 TCAACAAACAACTTTCCAGATTCATTCAGAGTCAATTTCAACTTCACAATGAATGATATTGGAC
1 TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
261939 TC
1 TC
261941 GAAACAACAC
Statistics
Matches: 123, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 123 1.00
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.29
Consensus pattern (64 bp):
TCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGAC
Found at i:262117 original size:60 final size:62
Alignment explanation
Indices: 261964--262128 Score: 226
Period size: 65 Copynumber: 2.6 Consensus size: 62
261954 TTACTAGAGA
* * * *
261964 TTGGATTTCAACTTCGCAACGAAGGATATCCAACTGAAAGCCAATTTGGTGAAACTTACTCAAAC
1 TTGGATTTCAACTTCACGACGAAAGATATCCAACTCAAAGCCAATTTGGTGAAAC-TA--CAAAC
*
262029 TTGGATTTCAACTTCACGACGAAAGATATCCAACTCAAAGCCAATTTGGTGAAAC-A-ATAC
1 TTGGATTTCAACTTCACGACGAAAGATATCCAACTCAAAGCCAATTTGGTGAAACTACAAAC
* *
262089 TTGGATTTCAACTTCACGACGAATGATATCCAATTCAAAG
1 TTGGATTTCAACTTCACGACGAAAGATATCCAACTCAAAG
262129 TTTAACTTCA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
60 41 0.44
63 1 0.01
65 51 0.55
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (62 bp):
TTGGATTTCAACTTCACGACGAAAGATATCCAACTCAAAGCCAATTTGGTGAAACTACAAAC
Found at i:262224 original size:55 final size:54
Alignment explanation
Indices: 262158--262359 Score: 163
Period size: 55 Copynumber: 3.5 Consensus size: 54
262148 AGCTATCCAC
*
262158 GATTTCAACTTCATGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTG
1 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATG-AACCCTTG
* * * * * *
262213 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCA-CAACGAATGAGCCATCC
1 GATTTCAACTTCACGACGAAGGATAT-C--GT----GC-CCAC--AAGCAGC-AATGAACC--CT
**
262277 AC
53 TG
262279 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGTAACCCTTG
1 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATG-AACCCTTG
* *
262334 GATTTCAACTTCATGACGAAAGATAT
1 GATTTCAACTTCACGACGAAGGATAT
262360 ACAATTCAAA
Statistics
Matches: 113, Mismatches: 19, Indels: 30
0.70 0.12 0.19
Matches are distributed among these distances:
55 50 0.44
56 6 0.05
57 6 0.05
58 4 0.04
59 2 0.02
62 2 0.02
63 4 0.04
64 6 0.05
65 6 0.05
66 27 0.24
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (54 bp):
GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGAACCCTTG
Found at i:262515 original size:124 final size:124
Alignment explanation
Indices: 262089--262678 Score: 818
Period size: 121 Copynumber: 4.8 Consensus size: 124
262079 GAAACAATAC
* * * * * *
262089 TTGGATTTCAACTTCACGACGAATGATATCCAATTCAAAGTTTAACTTCACAATGAAGGAGCTAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCGCAATGAATGAGCCAT
* * * *
262154 CCACGATTTCAACTTCATGACGAAGGATATCGTGCCCACAAGCAGCAATGCAAC-C---C
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGC-ATCCATCTCTAGA
* *
262210 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCGCAATGAATGAGCCAT
* * **
262275 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCA---ATGT-AACCC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCATCCATCTCTA-GA
* * * * * * *
262331 TTGGATTTCAACTTCATGACGAAAGATATACAATTCAAAGCTCAACTTTGTAACGAATGAGCCAA
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCGCAATGAATGAGCCAT
*
262396 CCACGATTTTAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCATCCATCTCTAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCATCCATCTCTAGA
* *
262455 TTAGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCGCAATGAATGAGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCGCAATGAATGAGCCAT
* **
262520 TCACGATTTCAACTTCACGACGAAGGATATATTGCCCACAAGCAGCATCCATCTCTAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCATCCATCTCTAGA
* * *
262579 TTGGATTTCAACTTCACAATGAAGGATATCCAATTCAAAGTTCAACTTCGCAATGAATGAGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCGCAATGAATGAGCCAT
262644 CCACGATTTCAACTTCACGACGAAGGATATCGTGC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGC
262679 TCAGGATTTT
Statistics
Matches: 420, Mismatches: 40, Indels: 15
0.88 0.08 0.03
Matches are distributed among these distances:
117 1 0.00
120 1 0.00
121 209 0.50
124 208 0.50
125 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (124 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCGCAATGAATGAGCCAT
CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCATCCATCTCTAGA
Found at i:266969 original size:26 final size:26
Alignment explanation
Indices: 266930--266982 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
266920 AATAAACATC
* * *
266930 ACCGTAAGATCAATTCAAAGAAAACT
1 ACCGCAAGAGCAATCCAAAGAAAACT
266956 ACCGCAAGAGCAATCCAAAGAAAACT
1 ACCGCAAGAGCAATCCAAAGAAAACT
266982 A
1 A
266983 ACTTTTCAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.51, C:0.23, G:0.13, T:0.13
Consensus pattern (26 bp):
ACCGCAAGAGCAATCCAAAGAAAACT
Found at i:267826 original size:31 final size:31
Alignment explanation
Indices: 267788--267852 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
267778 TCCTTCACAC
267788 ATACGTAGGTGACTTCATCAAGTCTATCTCA
1 ATACGTAGGTGACTTCATCAAGTCTATCTCA
267819 ATACGTAGGTGACTTCATCAAGTCTATCTCA
1 ATACGTAGGTGACTTCATCAAGTCTATCTCA
267850 ATA
1 ATA
267853 TACATCATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (31 bp):
ATACGTAGGTGACTTCATCAAGTCTATCTCA
Found at i:269761 original size:92 final size:92
Alignment explanation
Indices: 269652--269848 Score: 331
Period size: 92 Copynumber: 2.1 Consensus size: 92
269642 ATAATGAAAT
* *
269652 TGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCTTTTTTATAAAAATGATCGAT
1 TGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCATTTTTATAAAAAAGATCGAT
269717 ACTTTCAACATATCAAGTAAATTTTAC
66 ACTTTCAACATATCAAGTAAATTTTAC
* *
269744 TGGTTTTGTCATATTTTTACTTGTTATATTGTAAAGTATCGATCATTTTTATAAAAAAGATCTAT
1 TGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCATTTTTATAAAAAAGATCGAT
* *
269809 ACTTTCAACATATTAGGTAAATTTTAC
66 ACTTTCAACATATCAAGTAAATTTTAC
*
269836 CGGTTTTGTCATA
1 TGGTTTTGTCATA
269849 ATGAAACTGG
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 98 1.00
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (92 bp):
TGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCATTTTTATAAAAAAGATCGAT
ACTTTCAACATATCAAGTAAATTTTAC
Found at i:269939 original size:112 final size:112
Alignment explanation
Indices: 269742--270221 Score: 725
Period size: 112 Copynumber: 4.4 Consensus size: 112
269732 AGTAAATTTT
* * *
269742 ACTGGTTTTGTCATATTTTTACTTGTTATATTGTAAAGTATCGATCATTTTTATAAAAAAGATCT
1 ACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCATTTTTATAAAAAGGATCG
269807 ATACTTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGAA
66 ATACTTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGAA
**
269854 ACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATTAATCATTTTTATAAAAAGGATCG
1 ACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCATTTTTATAAAAAGGATCG
269919 ATACTTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGAA
66 ATACTTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGAA
*
269966 ACTGGTTTTGTCATA-TTTTACTTGTTATATTGTAAAGTATCG-----------AAAAAGGATCG
1 ACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCATTTTTATAAAAAGGATCG
* * *
270019 ATACTTTCAACATATCAGGTAAATTTTACCGATTTTGTCATAATAAA
66 ATACTTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGAA
*
270066 ATTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATACATTTTTATAAAAAGGATC
1 ACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGAT-CATTTTTATAAAAAGGATC
270131 GATACTTTCAACATATTCA-GTAAATTTTACCGGTTTTGTCATAATGAA
65 GATACTTTCAACATATT-AGGTAAATTTTACCGGTTTTGTCATAATGAA
* * *
270179 ACTGATTTTTTTCATATTTGTACCTGTTATATTGTAAAGTATC
1 ACTG-GTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATC
270222 AATACTTTAT
Statistics
Matches: 333, Mismatches: 20, Indels: 28
0.87 0.05 0.07
Matches are distributed among these distances:
100 69 0.21
101 26 0.08
111 24 0.07
112 122 0.37
113 56 0.17
114 36 0.11
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (112 bp):
ACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCATTTTTATAAAAAGGATCG
ATACTTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGAA
Found at i:269943 original size:204 final size:203
Alignment explanation
Indices: 269569--270182 Score: 809
Period size: 204 Copynumber: 3.0 Consensus size: 203
269559 ATAACTTTCA
* *
269569 ATAAAATATCGATACAATTTTAT-AAAAAGTATATATACTTTCAACATATTAGGTAAATTTTACC
1 ATAAAATATCGAT-CATTTTTATAAAAAAG-ATCTATACTTTCAACATATTAGGTAAATTTTACC
* *
269633 AGTTTTGTCATAATGAAATTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCTT
64 GGTTTTGTCATAATGAAATTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCAT
* * * * ***
269698 TTTTATAAAAATGATCGATACTTTCAACATATCAAGTAAATTTTACTGGTTTTGTCATATTTTTA
129 TTTTATAAAAAGGATCGATACTTTCAACATAT-TAGTAAATTTTACCGGTTTTGTCATAATGAAA
* *
269763 CTTGTTATATT
193 CTGGTTATATC
* *
269774 GTAAAGTATCGATCATTTTTATAAAAAAGATCTATACTTTCAACATATTAGGTAAATTTTACCGG
1 ATAAAATATCGATCATTTTTATAAAAAAGATCTATACTTTCAACATATTAGGTAAATTTTACCGG
* **
269839 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATTAATCATTT
66 TTTTGTCATAATGAAATTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCATTT
269904 TTATAAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGAAACT
131 TTATAAAAAGGATCGATACTTTCAACATATTA-GTAAATTTTACCGGTTTTGTCATAATGAAACT
* *
269969 GGTTTTGTC
195 GGTTATATC
*** * * * * *
269978 ATATTTTACTTGTTAT-ATTGTAAAGTATCGAAAAAGGATCGATACTTTCAACATATCAGGTAAA
1 ATAAAATA-TCG--ATCATT-T---TTAT--AAAAAAGATCTATACTTTCAACATATTAGGTAAA
* *
270042 TTTTACCGATTTTGTCATAATAAAATTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTAT
57 TTTTACCGGTTTTGTCATAATGAAATTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTAT
270107 CGATACATTTTTATAAAAAGGATCGATACTTTCAACATATTCAGTAAATTTTACCGGTTTTGTCA
122 CGAT-CATTTTTATAAAAAGGATCGATACTTTCAACATATT-AGTAAATTTTACCGGTTTTGTCA
270172 TAATGAAACTG
185 TAATGAAACTG
270183 ATTTTTTTCA
Statistics
Matches: 362, Mismatches: 34, Indels: 18
0.87 0.08 0.04
Matches are distributed among these distances:
203 1 0.00
204 168 0.46
205 19 0.05
206 3 0.01
207 3 0.01
210 3 0.01
212 95 0.26
213 69 0.19
214 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43
Consensus pattern (203 bp):
ATAAAATATCGATCATTTTTATAAAAAAGATCTATACTTTCAACATATTAGGTAAATTTTACCGG
TTTTGTCATAATGAAATTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCATTT
TTATAAAAAGGATCGATACTTTCAACATATTAGTAAATTTTACCGGTTTTGTCATAATGAAACTG
GTTATATC
Found at i:270081 original size:100 final size:101
Alignment explanation
Indices: 269907--270221 Score: 418
Period size: 100 Copynumber: 3.0 Consensus size: 101
269897 ATCATTTTTA
*
269907 TAAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGGT
1 TAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGGT
*
269972 TTTGTCATATTTTACTTGTTATATTGTAAAGTATCG
66 TTTGTCATATTTTACCTGTTATATTGTAAAGTATCG
* * *
270008 -AAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGATTTTGTCATAATAAAATTGGT
1 TAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGGT
270072 TTTGTCATATTTTTACCTGTTATATTGTAAAGTATCG
66 TTTGTCATA-TTTTACCTGTTATATTGTAAAGTATCG
270109 ATACATTTTTATAAAAAGGATCGATACTTTCAACATATTCA-GTAAATTTTACCGGTTTTGTCAT
1 -----------TAAAAAGGATCGATACTTTCAACATA-TCAGGTAAATTTTACCGGTTTTGTCAT
* *
270173 AATGAAACTGATTTTTTTCATATTTGTACCTGTTATATTGTAAAGTATC
54 AATGAAACTG-GTTTTGTCATATTT-TACCTGTTATATTGTAAAGTATC
270222 AATACTTTAT
Statistics
Matches: 188, Mismatches: 10, Indels: 19
0.87 0.05 0.09
Matches are distributed among these distances:
100 69 0.37
101 26 0.14
113 58 0.31
114 35 0.19
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.42
Consensus pattern (101 bp):
TAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGGT
TTTGTCATATTTTACCTGTTATATTGTAAAGTATCG
Found at i:270154 original size:113 final size:114
Alignment explanation
Indices: 270008--270226 Score: 352
Period size: 113 Copynumber: 1.9 Consensus size: 114
269998 TAAAGTATCG
*
270008 AAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGATTTTGTCATAATAAAATTG-GT
1 AAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGATTTTGTCATAATAAAACTGAGT
* *
270072 TTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATACATTTTTAT
66 TTTGTCATATTTGTACCTGTTATATTGTAAAGTATCAATACATTTTTAT
* * *
270121 AAAAAGGATCGATACTTTCAACATATTCA-GTAAATTTTACCGGTTTTGTCATAATGAAACTGAT
1 AAAAAGGATCGATACTTTCAACATA-TCAGGTAAATTTTACCGATTTTGTCATAATAAAACTGAG
*
270185 TTTTTTCATATTTGTACCTGTTATATTGTAAAGTATCAATAC
65 TTTTGTCATATTTGTACCTGTTATATTGTAAAGTATCAATAC
270227 TTTATAGGCG
Statistics
Matches: 97, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
113 55 0.57
114 42 0.43
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (114 bp):
AAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGATTTTGTCATAATAAAACTGAGT
TTTGTCATATTTGTACCTGTTATATTGTAAAGTATCAATACATTTTTAT
Found at i:270510 original size:22 final size:23
Alignment explanation
Indices: 270474--270522 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
270464 ACATATTTTA
*
270474 TTATATAAGCACTACCTATTACG
1 TTATATAAGCACTACCTAATACG
* *
270497 TTATA-AAGCGCTACCTAATATG
1 TTATATAAGCACTACCTAATACG
270519 TTAT
1 TTAT
270523 TGTGTTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (23 bp):
TTATATAAGCACTACCTAATACG
Found at i:270585 original size:23 final size:23
Alignment explanation
Indices: 270559--270609 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
270549 AACATATTTT
* *
270559 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGATACCTAATAC
*
270582 ATTATATAAGCGATACCTAATAT
1 ATTATATAAGCGATACCTAATAC
270605 ATTAT
1 ATTAT
270610 TGTGCTTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (23 bp):
ATTATATAAGCGATACCTAATAC
Found at i:270633 original size:87 final size:87
Alignment explanation
Indices: 270458--270715 Score: 419
Period size: 87 Copynumber: 3.0 Consensus size: 87
270448 ACAAATTAAA
* * * *
270458 TAATTAACATATTTTATTATATAAGCACTACCTATTACGTTATA-AAGCGCTACCTAATATGTTA
1 TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATATTA
270522 TTGTGTTTGATAATGTTTCTAG
66 TTGTGTTTGATAATGTTTCTAG
270544 TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATATTA
1 TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATATTA
*
270609 TTGTGCTTGATAATGTTTCTAG
66 TTGTGTTTGATAATGTTTCTAG
* * * *
270631 TAATTAACCTATTTTATTATATAAACGCTACTTATTACATTATATAAGCGGTACCTAATATATTA
1 TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATATTA
*
270696 TTGTGTTTGATAATATTTCT
66 TTGTGTTTGATAATGTTTCT
270716 GATTAAATAA
Statistics
Matches: 160, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
86 42 0.26
87 118 0.74
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (87 bp):
TAATTAACATATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATATTA
TTGTGTTTGATAATGTTTCTAG
Found at i:270695 original size:23 final size:23
Alignment explanation
Indices: 270645--270696 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
270635 TAACCTATTT
* *
270645 TATTATATAAACGCTACTTATTA
1 TATTATATAAACGCTACCTAATA
* * *
270668 CATTATATAAGCGGTACCTAATA
1 TATTATATAAACGCTACCTAATA
270691 TATTAT
1 TATTAT
270697 TGTGTTTGAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (23 bp):
TATTATATAAACGCTACCTAATA
Found at i:271966 original size:3 final size:3
Alignment explanation
Indices: 271960--271985 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
271950 CACTGTTGAA
271960 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
271986 AGCTTCAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:272805 original size:6 final size:6
Alignment explanation
Indices: 272794--272828 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
272784 GAAGAAGACC
*
272794 TCCCAT TTCCAT TCCCAT TCCCAT TCCCAT ATCCC
1 TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT -TCCC
272829 CTGCTTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 22 0.85
7 4 0.15
ACGTcount: A:0.17, C:0.49, G:0.00, T:0.34
Consensus pattern (6 bp):
TCCCAT
Found at i:274432 original size:108 final size:107
Alignment explanation
Indices: 274293--274554 Score: 305
Period size: 108 Copynumber: 2.4 Consensus size: 107
274283 ATATGGGTCC
* * * * *
274293 TTAGAAATTCGACAATAAC-AAATATGTTAATTACTTAATTTGTTATTAATATCATCGACATATT
1 TTAGAAA-TCCACGATAACAAAATATGTTAATTATTTATTTTGTTATTAATATCATCAACATATT
*
274357 AGGTAGCGCCTAAAATATTA-TCAAAGTTTAAGA-TAATGAGAAA
65 AAGTAGCGCCTAAAATATTACT-AAAGTTTAA-ACTAATGAGAAA
* * *
274400 TTAGAAATCCAACGATAACAAAATAGGTTAATTATTTATTTTATTATTAATATTATCAACATATT
1 TTAGAAATCC-ACGATAACAAAATATGTTAATTATTTATTTTGTTATTAATATCATCAACATATT
* * * * **
274465 AAGTAGCGTCTAAAATGTTACTAAAGTTTAAACTGATGGGGCA
65 AAGTAGCGCCTAAAATATTACTAAAGTTTAAACTAATGAGAAA
* *
274508 TTCGAAATCTCACGATAACAAAATATGTTAATTTTTTATTTTGTTAT
1 TTAGAAATC-CACGATAACAAAATATGTTAATTATTTATTTTGTTAT
274555 AAAAGAATAT
Statistics
Matches: 131, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
106 2 0.02
107 15 0.11
108 112 0.85
109 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (107 bp):
TTAGAAATCCACGATAACAAAATATGTTAATTATTTATTTTGTTATTAATATCATCAACATATTA
AGTAGCGCCTAAAATATTACTAAAGTTTAAACTAATGAGAAA
Found at i:275008 original size:154 final size:155
Alignment explanation
Indices: 274733--275026 Score: 380
Period size: 154 Copynumber: 1.9 Consensus size: 155
274723 GCAAATATCA
* * *
274733 ATACTTTTATAGTAAATATAGATACATTATTATTATTAATACTTTAGAGTAACCATACTTTTAGA
1 ATACATTTAGAGTAAATATAGATACATTATTATTA-TAATA-TTTAGAGCAACCATACTTTTAGA
* *
274798 GTAAGTATTCATACTTTCGAATTTAAAAAAAATATTTCAAACAGTTAAGTTGTATATATTTTATC
64 GTAAATATTCATACTTTCGAATTTAAAAAAAATATTTCAAACAGTTAAGTTATATATATTTTATC
274863 ATTTACATTACTGTCGAAACAATATTC
129 ATTTACATTACTGTCGAAACAATATTC
* * * *
274890 ATACATTTAGAGTAAGTATGGATACATTATTATTA-ACT-TTTAGAGCATA-CATATTTTTAGAG
1 ATACATTTAGAGTAAATATAGATACATTATTATTATAATATTTAGAGCA-ACCATACTTTTAGAG
* *** *
274952 TAAATATTCATACTTTCGATTTTTTTTAAAAATGTTTCAAAC-GATTAAGTTATATATATTTTAT
65 TAAATATTCATACTTTCGA-ATTTAAAAAAAATATTTCAAACAG-TTAAGTTATATATATTTTAT
*
275016 CGTTTACATTA
128 CATTTACATTA
275027 TTATTAACAT
Statistics
Matches: 119, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
153 39 0.33
154 47 0.39
155 2 0.02
157 31 0.26
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (155 bp):
ATACATTTAGAGTAAATATAGATACATTATTATTATAATATTTAGAGCAACCATACTTTTAGAGT
AAATATTCATACTTTCGAATTTAAAAAAAATATTTCAAACAGTTAAGTTATATATATTTTATCAT
TTACATTACTGTCGAAACAATATTC
Found at i:275126 original size:22 final size:23
Alignment explanation
Indices: 275064--275127 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
275054 TAATTTAGCG
* * *
275064 TAATAGGTAGTGCTTATTTAATG
1 TAATAGGTAGCGCATATTTAATC
* * * *
275087 TAGTAGGTAACACCTATTTAA-C
1 TAATAGGTAGCGCATATTTAATC
275109 TAATAGGTAGCGCATATTT
1 TAATAGGTAGCGCATATTT
275128 TATTTTACCG
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
22 15 0.48
23 16 0.52
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.38
Consensus pattern (23 bp):
TAATAGGTAGCGCATATTTAATC
Found at i:275195 original size:75 final size:75
Alignment explanation
Indices: 275103--275433 Score: 425
Period size: 75 Copynumber: 4.4 Consensus size: 75
275093 GTAACACCTA
* * * *
275103 TTTAAC-TAATAGGTAGCGCATATTTTATTTTACCGTTTACATTATTATTAACATGTAAACAAAC
1 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
** *
275167 TTGTAGCTAG
66 CGGTAGGTAG
* * *
275177 TTTAACATAATATGTAGCGCCTATTTTATTTTACCGTTTATATTATTAGTAACCTTTAAACAAAT
1 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
275242 CGGTAGGTAG
66 CGGTAGGTAG
** **
275252 TTTAATGTAATAGGTAATGCCTATTTTATTTTA-CGTTTACATTATTAGTAACCTTTAAACAAAC
1 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
* *
275316 CGGTAAGTAT
66 CGGTAGGTAG
* * * * *
275326 TTTAACGTAATAAGTAGCACCTATTTTATTTTACCGTTTACATTATTAATAA-TTTTCAAACAAA
1 TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTT-AAACAAA
275390 CCGGTAGGTAG
65 CCGGTAGGTAG
**
275401 TTTAACATAATAGGTAGTACCTATTTTATTTTA
1 TTTAACATAATAGGTAGCGCCTATTTTATTTTA
275434 ACCGGTTAAG
Statistics
Matches: 223, Mismatches: 31, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
74 74 0.33
75 149 0.67
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (75 bp):
TTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAAC
CGGTAGGTAG
Found at i:275311 original size:149 final size:150
Alignment explanation
Indices: 275103--275433 Score: 445
Period size: 149 Copynumber: 2.2 Consensus size: 150
275093 GTAACACCTA
* * *
275103 TTTAAC-TAATAGGTAGCGCATATTTTATTTTACCGTTTACATTATTATTAACATGTAAACAAAC
1 TTTAACATAATAGGTAGTGCCTATTTTATTTTACCGTTTACATTATTAGTAACATGTAAACAAAC
** * * * *
275167 TTGT-AGCTAGTTTAACATAATATGTAGCGCCTATTTTATTTTACCGTTTATATTATTAGTAACC
66 CGGTAAG-TAGTTTAACATAATAAGTAGCACCTATTTTATTTTACCGTTTACATTATTAATAA-C
*
275231 TTT-AAACAAATCGGTAGGTAG
129 TTTCAAACAAACCGGTAGGTAG
** * * *
275252 TTTAATGTAATAGGTAATGCCTATTTTATTTTA-CGTTTACATTATTAGTAACCTTTAAACAAAC
1 TTTAACATAATAGGTAGTGCCTATTTTATTTTACCGTTTACATTATTAGTAACATGTAAACAAAC
* * *
275316 CGGTAAGTATTTTAACGTAATAAGTAGCACCTATTTTATTTTACCGTTTACATTATTAATAATTT
66 CGGTAAGTAGTTTAACATAATAAGTAGCACCTATTTTATTTTACCGTTTACATTATTAATAACTT
275381 TCAAACAAACCGGTAGGTAG
131 TCAAACAAACCGGTAGGTAG
*
275401 TTTAACATAATAGGTAGTACCTATTTTATTTTA
1 TTTAACATAATAGGTAGTGCCTATTTTATTTTA
275434 ACCGGTTAAG
Statistics
Matches: 158, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
148 3 0.02
149 130 0.82
150 25 0.16
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (150 bp):
TTTAACATAATAGGTAGTGCCTATTTTATTTTACCGTTTACATTATTAGTAACATGTAAACAAAC
CGGTAAGTAGTTTAACATAATAAGTAGCACCTATTTTATTTTACCGTTTACATTATTAATAACTT
TCAAACAAACCGGTAGGTAG
Found at i:276421 original size:21 final size:21
Alignment explanation
Indices: 276306--276421 Score: 78
Period size: 21 Copynumber: 5.6 Consensus size: 21
276296 GCGAAATAAA
*
276306 AATCGCAATGCGA-TCTCCAG
1 AATCGCAATGCGATTTTCCAG
* *
276326 AATCGCAAAT-C-AGTTCCCAG
1 AATCGC-AATGCGATTTTCCAG
* * **
276346 AATCGCAACGCGATTATGAAG
1 AATCGCAATGCGATTTTCCAG
** *
276367 AATCGCAATGCGATAGTACA-
1 AATCGCAATGCGATTTTCCAG
*
276387 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAATGCGATTTTCCAG
*
276409 AATCGCAACGCGA
1 AATCGCAATGCGA
276422 ACATATAAAT
Statistics
Matches: 71, Mismatches: 19, Indels: 11
0.70 0.19 0.11
Matches are distributed among these distances:
19 3 0.04
20 21 0.30
21 45 0.63
22 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (21 bp):
AATCGCAATGCGATTTTCCAG
Found at i:276473 original size:41 final size:41
Alignment explanation
Indices: 276428--276581 Score: 213
Period size: 41 Copynumber: 3.8 Consensus size: 41
276418 GCGAACATAT
* * *
276428 AAATCGCAACGCG-ATTC-TAACTATCGCAACGAGTATCCGTA
1 AAATCGCAACGCGTATCCGTAA--ATCGCAACGAGAATACGTA
* *
276469 AAATCGCAACGCGTATCCGTAAATCGCAATGACAATACGTA
1 AAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
*
276510 AAATCTCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
1 AAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
*
276551 AAATCGCAACGCGTATCCATAAATCGCAACG
1 AAATCGCAACGCGTATCCGTAAATCGCAACG
276582 CGATTTTTAA
Statistics
Matches: 101, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
41 95 0.94
42 3 0.03
43 3 0.03
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (41 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
Found at i:276476 original size:21 final size:20
Alignment explanation
Indices: 276450--276581 Score: 138
Period size: 21 Copynumber: 6.5 Consensus size: 20
276440 GATTCTAACT
276450 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGT-AA
*
276471 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* ** *
276491 ATCGCAATGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
* *
276512 ATCTCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* *
276532 ATCGCAACGAGAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
* *
276553 ATCGCAACGCGTATCCATAA
1 ATCGCAACGAGTATCCGTAA
276573 ATCGCAACG
1 ATCGCAACG
276582 CGATTTTTAA
Statistics
Matches: 89, Mismatches: 20, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
20 42 0.47
21 47 0.53
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:276494 original size:20 final size:20
Alignment explanation
Indices: 276427--276583 Score: 149
Period size: 20 Copynumber: 7.7 Consensus size: 20
276417 CGCGAACATA
*
276427 TAAATCGCAACGCG-ATTC-
1 TAAATCGCAACGCGTATCCG
*
276445 TAACTATCGCAACGAGTATCCG
1 TAA--ATCGCAACGCGTATCCG
276467 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
* * *
276488 TAAATCGCAATGAC-AATACG
1 TAAATCGCAACG-CGTATCCG
*
276508 TAAAATCTCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
* * *
276529 TAAATCGCAACGAGAATACG
1 TAAATCGCAACGCGTATCCG
*
276549 TAAAATCGCAACGCGTATCCA
1 T-AAATCGCAACGCGTATCCG
276570 TAAATCGCAACGCG
1 TAAATCGCAACGCG
276584 ATTTTTAAAG
Statistics
Matches: 112, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
18 3 0.03
20 55 0.49
21 51 0.46
22 1 0.01
23 2 0.02
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:277199 original size:40 final size:40
Alignment explanation
Indices: 277141--277265 Score: 140
Period size: 40 Copynumber: 3.3 Consensus size: 40
277131 TTCTAAACTT
**
277141 AAAATCGCAACATAAAAATGAAAATCGCAACATGA-AAATG
1 AAAATCGCAACACGAAAATGAAAATCGCAACA-GAGAAATG
**
277181 AAAATCGCAACACGAAAATGACTATCGCAACGAGAGAAATG
1 AAAATCGCAACACGAAAATGAAAATCGCAAC-AGAGAAATG
277222 AAAATCGC-A-ACG---A-GAAAATCGCAAC-GAGAAATG
1 AAAATCGCAACACGAAAATGAAAATCGCAACAGAGAAATG
277255 AAAATCGCAAC
1 AAAATCGCAAC
277266 GAGAGAATCG
Statistics
Matches: 75, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
33 16 0.21
34 1 0.01
35 10 0.13
36 1 0.01
39 3 0.04
40 30 0.40
41 14 0.19
ACGTcount: A:0.53, C:0.18, G:0.17, T:0.12
Consensus pattern (40 bp):
AAAATCGCAACACGAAAATGAAAATCGCAACAGAGAAATG
Found at i:277222 original size:21 final size:20
Alignment explanation
Indices: 277141--277269 Score: 125
Period size: 20 Copynumber: 6.8 Consensus size: 20
277131 TTCTAAACTT
*
277141 AAAATCGCAAC-ATAAAAATG
1 AAAATCGCAACGA-GAAAATG
277161 AAAATCGCAAC-ATGAAAATG
1 AAAATCGCAACGA-GAAAATG
277181 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGA-GAAAATG
**
277201 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGA-AAATG
277222 AAAATCGCAAC--G---A-G
1 AAAATCGCAACGAGAAAATG
277236 AAAATCGCAACGAG-AAATG
1 AAAATCGCAACGAGAAAATG
277255 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
277270 GAATCGCAAC
Statistics
Matches: 95, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
14 12 0.13
15 1 0.01
16 1 0.01
18 1 0.01
19 16 0.17
20 49 0.52
21 15 0.16
ACGTcount: A:0.53, C:0.18, G:0.18, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGAGAAAATG
Found at i:277240 original size:14 final size:14
Alignment explanation
Indices: 277221--277285 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 14
277211 CGAGAGAAAT
277221 GAAAATCGCAACGA
1 GAAAATCGCAACGA
277235 GAAAATCGCAACGAGAAA
1 GAAAATCGCAAC--G--A
277253 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
277268 GAGAATCGCAACGC
1 GAAAATCGCAACGA
277282 GAAA
1 GAAA
277286 TGAAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
14 27 0.63
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 12 0.28
ACGTcount: A:0.49, C:0.20, G:0.23, T:0.08
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:277256 original size:33 final size:33
Alignment explanation
Indices: 277160--277297 Score: 152
Period size: 33 Copynumber: 3.9 Consensus size: 33
277150 ACATAAAAAT
277160 GAAAATCGCAAC-ATGAAAATGAAAATCGCAACACGA
1 GAAAATCGCAACGA-G-AAATGAAAATCGC-A-ACGA
*
277196 AAATGACTATCGCAACGAGAGAAATGAAAATCGCAACGA
1 GAA--A--ATCGCAAC--GAGAAATGAAAATCGCAACGA
277235 GAAAATCGCAACGAGAAATGAAAATCGCAACGA
1 GAAAATCGCAACGAGAAATGAAAATCGCAACGA
* *
277268 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAAAATCGCAACGAGAAATGAAAATCGCAA
277298 TGCGATTTTG
Statistics
Matches: 91, Mismatches: 4, Indels: 17
0.81 0.04 0.15
Matches are distributed among these distances:
33 49 0.54
35 8 0.09
36 2 0.02
37 1 0.01
38 1 0.01
39 6 0.07
40 9 0.10
41 13 0.14
42 1 0.01
43 1 0.01
ACGTcount: A:0.50, C:0.19, G:0.20, T:0.11
Consensus pattern (33 bp):
GAAAATCGCAACGAGAAATGAAAATCGCAACGA
Found at i:277351 original size:33 final size:33
Alignment explanation
Indices: 277298--277380 Score: 130
Period size: 33 Copynumber: 2.5 Consensus size: 33
277288 AAAATCGCAA
** *
277298 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCTCGTTGCGATTATCTCGT
*
277331 TGCGATTTTCATTTCTCGTTGCGATTTTCTCGT
1 TGCGATTTTCATTTCTCGTTGCGATTATCTCGT
277364 TGCGATTTTCATTTCTC
1 TGCGATTTTCATTTCTC
277381 TCATTGCGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.49
Consensus pattern (33 bp):
TGCGATTTTCATTTCTCGTTGCGATTATCTCGT
Found at i:277371 original size:14 final size:14
Alignment explanation
Indices: 277309--277373 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 14
277299 GCGATTTTGG
*
277309 TTTCGCGTTGCGAT
1 TTTCTCGTTGCGAT
*
277323 TATCTCGTTGCGATTTT
1 TTTCTCGTTGCGA---T
277340 CATTTCTCGTTGCGAT
1 --TTTCTCGTTGCGAT
277356 TTTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
277370 TTTC
1 TTTC
277374 ATTTCTCTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
14 29 0.67
16 1 0.02
17 1 0.02
19 12 0.28
ACGTcount: A:0.09, C:0.22, G:0.20, T:0.49
Consensus pattern (14 bp):
TTTCTCGTTGCGAT
Found at i:277407 original size:20 final size:21
Alignment explanation
Indices: 277356--277439 Score: 79
Period size: 20 Copynumber: 4.2 Consensus size: 21
277346 TCGTTGCGAT
**
277356 TTTCTCG--TTGCGATTTTCA
1 TTTCTCGCATTGCGATAGTCA
*
277375 TTTCTCTCATTGCGATAGTCA
1 TTTCTCGCATTGCGATAGTCA
277396 TTT-TCGCATTGCGATAGTCA
1 TTTCTCGCATTGCGATAGTCA
**
277416 TTCTCTCG--TTGCGATTTTCA
1 TT-TCTCGCATTGCGATAGTCA
277436 TTTC
1 TTTC
277440 AACCAAAAGA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
19 8 0.15
20 30 0.55
21 14 0.25
22 3 0.05
ACGTcount: A:0.14, C:0.23, G:0.15, T:0.48
Consensus pattern (21 bp):
TTTCTCGCATTGCGATAGTCA
Found at i:279332 original size:94 final size:93
Alignment explanation
Indices: 279110--279488 Score: 634
Period size: 94 Copynumber: 4.1 Consensus size: 93
279100 TAGATTGCTT
* * *
279110 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAATTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
279175 ATTTGTCTTTTGTTTTGTCTTTTGGTT-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
*
279203 AGTAAATTTATTCGGTTGCTGACAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
279268 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
279297 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
279362 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * *
279391 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
279456 ATTTGTCTTTGTTTTGTCTTTTGATTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
279484 AGTAA
1 AGTAA
279489 TGCAATCCAT
Statistics
Matches: 273, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
92 18 0.07
93 74 0.27
94 181 0.66
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:279598 original size:19 final size:19
Alignment explanation
Indices: 279552--279623 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
279542 CACGAAACTT
*
279552 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAAC--GAGAAATG
**
279573 ACTATCGCAACGAGAAATG
1 AAAATCGCAACGAGAAATG
* * **
279592 AAAATCGCAATGCGAAACC
1 AAAATCGCAACGAGAAATG
279611 AAAATCGCAACGA
1 AAAATCGCAACGA
279624 CAAAATCGCA
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
19 31 0.77
21 9 0.22
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGAGAAATG
Found at i:279627 original size:14 final size:14
Alignment explanation
Indices: 279610--279636 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
279600 AATGCGAAAC
279610 CAAAATCGCAACGA
1 CAAAATCGCAACGA
279624 CAAAATCGCAACG
1 CAAAATCGCAACG
279637 CGAAACCAAA
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:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAAATCGCAACGA
Found at i:279634 original size:33 final size:33
Alignment explanation
Indices: 279592--279655 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
279582 ACGAGAAATG
*
279592 AAAATCGCAATGCGAAACCAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAC
*
279625 AAAATCGCAACGCGAAACCAAAATTGCAACG
1 AAAATCGCAACGCGAAACCAAAATCGCAACG
279656 CGAAACTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.48, C:0.27, G:0.16, T:0.09
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:279648 original size:19 final size:19
Alignment explanation
Indices: 279576--279661 Score: 92
Period size: 19 Copynumber: 4.8 Consensus size: 19
279566 AAAAATGACT
* **
279576 ATCGCAACGAGAAATGAAA
1 ATCGCAACGCGAAACCAAA
*
279595 ATCGCAATGCGAAACCAAA
1 ATCGCAACGCGAAACCAAA
279614 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAACCAAA
279628 ATCGCAACGCGAAACCAAA
1 ATCGCAACGCGAAACCAAA
*
279647 ATTGCAACGCGAAAC
1 ATCGCAACGCGAAAC
279662 TATAATCGCG
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
14 11 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 40 0.70
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (19 bp):
ATCGCAACGCGAAACCAAA
Found at i:279736 original size:20 final size:20
Alignment explanation
Indices: 279711--279797 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
279701 GATTATCTCG
**
279711 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
279731 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
279751 TTGCTATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
279771 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
279791 TTGCGAT
1 TTGCGAT
279798 TTTAAGTTTC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:280322 original size:18 final size:19
Alignment explanation
Indices: 280283--280324 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
280273 CTCACATGTC
280283 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
280304 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
280322 ATC
1 ATC
280325 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:280378 original size:42 final size:41
Alignment explanation
Indices: 280279--280383 Score: 102
Period size: 42 Copynumber: 2.5 Consensus size: 41
280269 CCGACTCACA
* * *
280279 TGTCATCGTTCAAGAGGCCTCCCCTATCGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGTCC-CCCCTACCGTTCAAGAGGCCAC
* ** * *
280321 TATCATCCCTCAAGAGTCCCCTCCTACCGTTTAATAGGCCAC
1 TGTCATCGTTCAAGAGTCCCC-CCTACCGTTCAAGAGGCCAC
*
280363 TGTCATCGTTGAAGAGGTCCC
1 TGTCATCGTTCAAGA-GTCCC
280384 TCCCAATATT
Statistics
Matches: 49, Mismatches: 12, Indels: 3
0.77 0.19 0.05
Matches are distributed among these distances:
41 2 0.04
42 42 0.86
43 5 0.10
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.26
Consensus pattern (41 bp):
TGTCATCGTTCAAGAGTCCCCCCTACCGTTCAAGAGGCCAC
Found at i:281779 original size:14 final size:14
Alignment explanation
Indices: 281730--281779 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
281720 TTATTATTTT
*
281730 TTGA-TTGTTTAA-
1 TTGATTTGTTAAAG
*
281742 TTGATTTGTAAAAG
1 TTGATTTGTTAAAG
* *
281756 ATGATTTGTTAATG
1 TTGATTTGTTAAAG
281770 TTGATTTGTT
1 TTGATTTGTT
281780 TAATTGATGT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
12 4 0.13
13 6 0.20
14 20 0.67
ACGTcount: A:0.26, C:0.00, G:0.20, T:0.54
Consensus pattern (14 bp):
TTGATTTGTTAAAG
Found at i:281900 original size:19 final size:19
Alignment explanation
Indices: 281876--281938 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 19
281866 ATGCAAAACA
281876 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
** *
281895 GAAAATAACAA--CG-AGT
1 GAAAATCGCAATGCGAAAT
281911 G--AATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
281928 GATAATCGCAA
1 GAAAATCGCAA
281939 CGAGTGAATC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
14 6 0.18
16 5 0.15
17 5 0.15
19 17 0.52
ACGTcount: A:0.48, C:0.16, G:0.21, T:0.16
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:281968 original size:33 final size:32
Alignment explanation
Indices: 281879--281970 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 32
281869 CAAAACAGAA
**
281879 AATCGCAATGCGAAATGAAAATAACAACGAGTG
1 AATCGCAATGCGAAATG-AAATCGCAACGAGTG
281912 AATCGCAATGCGAAATGATAATCGCAACGAGTG
1 AATCGCAATGCGAAATGA-AATCGCAACGAGTG
*
281945 AATCGTAATGCGAAAATGAAATCGCA
1 AATCGCAATGCG-AAATGAAATCGCA
281971 TCGCGTTGCG
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
32 1 0.02
33 47 0.87
34 6 0.11
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.17
Consensus pattern (32 bp):
AATCGCAATGCGAAATGAAATCGCAACGAGTG
Found at i:282017 original size:19 final size:20
Alignment explanation
Indices: 281993--282032 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
281983 AGTCAATTGC
281993 CAATT-CGCATTGCGATAGT
1 CAATTCCGCATTGCGATAGT
282012 CAATTCCGCATTGCGATAGT
1 CAATTCCGCATTGCGATAGT
282032 C
1 C
282033 TTAGGGGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (20 bp):
CAATTCCGCATTGCGATAGT
Found at i:282576 original size:40 final size:40
Alignment explanation
Indices: 282487--282581 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
282477 TTGTGATAGT
* *
282487 CAGAATCTCGTTGCGATTTACAGATTCGCATTGCGATTTA
1 CAGAATCGCATTGCGATTTACAGATTCGCATTGCGATTTA
*
282527 CAGATTCGCATTGCGATTTAC-GTATTCGCATTGCGATTTA
1 CAGAATCGCATTGCGATTTACAG-ATTCGCATTGCGATTTA
*
282567 C-GTAATCGCAATGCG
1 CAG-AATCGCATTGCG
282582 TATCCGTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.04
40 46 0.96
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (40 bp):
CAGAATCGCATTGCGATTTACAGATTCGCATTGCGATTTA
Found at i:282581 original size:20 final size:20
Alignment explanation
Indices: 282497--282567 Score: 126
Period size: 20 Copynumber: 3.5 Consensus size: 20
282487 CAGAATCTCG
282497 TTGCGATTTACAGATTCGCA
1 TTGCGATTTACAGATTCGCA
282517 TTGCGATTTACAGATTCGCA
1 TTGCGATTTACAGATTCGCA
282537 TTGCGATTTAC-GTATTCGCA
1 TTGCGATTTACAG-ATTCGCA
282557 TTGCGATTTAC
1 TTGCGATTTAC
282568 GTAATCGCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
19 1 0.02
20 49 0.98
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACAGATTCGCA
Found at i:282596 original size:40 final size:40
Alignment explanation
Indices: 282512--282596 Score: 93
Period size: 40 Copynumber: 2.1 Consensus size: 40
282502 ATTTACAGAT
* * * *
282512 TCGCATTGCGATTTACAGATTCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACAGAATCGCAATGCGATATACGTAA
*
282552 TCGCATTGCGATTTAC-GTAATCGCAATGCG-TATCCGTAAA
1 TCGCATTGCGATTTACAG-AATCGCAATGCGATATACGT-AA
282592 TCGCA
1 TCGCA
282597 ACGACAATAC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
39 6 0.16
40 32 0.84
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (40 bp):
TCGCATTGCGATTTACAGAATCGCAATGCGATATACGTAA
Found at i:282718 original size:20 final size:20
Alignment explanation
Indices: 282694--282887 Score: 167
Period size: 20 Copynumber: 9.6 Consensus size: 20
282684 TACCGGAGAT
282694 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
282714 TGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
282734 TGTCGTTGCGATTTACGGGTA
1 CG-CGTTGCGATTTACGGATA
** *
282755 CGTATTGCGATTTACGTATA
1 CGCGTTGCGATTTACGGATA
* *
282775 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
282795 CTCGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
282815 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
282835 TGTCGTTGCGATTTACTGATA
1 CG-CGTTGCGATTTACGGATA
* *
282856 CGCATTGCAATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
* *
282877 CTCATTGCGAT
1 CGCGTTGCGAT
282888 AGTCATAATC
Statistics
Matches: 139, Mismatches: 28, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
20 88 0.63
21 51 0.37
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:282781 original size:40 final size:40
Alignment explanation
Indices: 282694--282877 Score: 160
Period size: 41 Copynumber: 4.5 Consensus size: 40
282684 TACCGGAGAT
* *
282694 CGCGTTGCGATTTACGGATATGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGATTTACGGATACGTGTTGCGA-TTTACGTATA
* * *
282734 TGTCGTTGCGATTTACGGGTACGTATTGCGATTTACGTATA
1 CG-CGTTGCGATTTACGGATACGTGTTGCGATTTACGTATA
* * * *
282775 CGCGTTGCGATTTACGTATTC-TCGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGT-GTTGCGATTTACGTATA
* *
282815 CGCGTTGCGATTTTACGTAT-TGTCGTTGCGATTTAC-TGATA
1 CGCGTTGCGA-TTTACGGATACGT-GTTGCGATTTACGT-ATA
* *
282856 CGCATTGCAATTTTACGGATAC
1 CGCGTTGCGA-TTTACGGATAC
282878 TCATTGCGAT
Statistics
Matches: 118, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
39 1 0.01
40 50 0.42
41 67 0.57
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (40 bp):
CGCGTTGCGATTTACGGATACGTGTTGCGATTTACGTATA
Found at i:282814 original size:101 final size:102
Alignment explanation
Indices: 282696--282887 Score: 296
Period size: 101 Copynumber: 1.9 Consensus size: 102
282686 CCGGAGATCG
* * *
282696 CGTTGCGATTTACGGATATGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGGTACGTATT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
* * *
282761 GCGA-TTTACGTATACGCGTTGCGATTTACGTATTCT
66 GCAATTTTACGGATACGCATTGCGATTTACGTATTCT
* *
282797 CGTTGTGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACTGATACGCATT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
*
282862 GCAATTTTACGGATACTCATTGCGAT
66 GCAATTTTACGGATACGCATTGCGAT
282888 AGTCATAATC
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
101 63 0.78
102 18 0.22
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.39
Consensus pattern (102 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
GCAATTTTACGGATACGCATTGCGATTTACGTATTCT
Found at i:283051 original size:20 final size:19
Alignment explanation
Indices: 282998--283051 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
282988 ATTCTTCATA
282998 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* ** *
283017 AACTGATTTGTGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
283038 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
283052 TTTATTTCGC
Statistics
Matches: 25, Mismatches: 8, Indels: 3
0.69 0.22 0.08
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.35
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:288180 original size:18 final size:17
Alignment explanation
Indices: 288166--288202 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
288156 TTATATATCA
288166 TTTTA-AATAATTATAT
1 TTTTACAATAATTATAT
288182 TTTTACAATAA-TATCAT
1 TTTTACAATAATTAT-AT
288199 TTTT
1 TTTT
288203 CACCTCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTACAATAATTATAT
Found at i:288193 original size:17 final size:16
Alignment explanation
Indices: 288160--288202 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
288150 TTAAAGTTAT
288160 ATATCA-TTTTAAATA
1 ATATCATTTTTAAATA
288175 ATTAT-ATTTTTACAATA
1 A-TATCATTTTTA-AATA
288192 ATATCATTTTT
1 ATATCATTTTT
288203 CACCTCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 2 0.08
16 11 0.46
17 11 0.46
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATCATTTTTAAATA
Found at i:288800 original size:2 final size:2
Alignment explanation
Indices: 288793--288833 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
288783 TAAATGGCAT
288793 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
288834 TACGTGTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:294041 original size:118 final size:117
Alignment explanation
Indices: 293800--294032 Score: 292
Period size: 118 Copynumber: 2.0 Consensus size: 117
293790 AAAAAATATT
* *
293800 AATTAATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCAAGGT
1 AATTAATATA-ATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCAAGGT
* * *
293865 GCCTTAAGACAGTTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAAC
65 GCCTTAAGACAGTCCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAAC
** * *
293918 AATTAATATAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCTAGT
1 AATTAATATAATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCAAGG
** * * *
293983 TGTTTTAAGACCG-CCCTTTCTT-AATATTGAAAAATAAATACAT-ATTAAAA
64 TGCCTTAAGACAGTCCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAA
294033 TAGGATTAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
116 7 0.07
117 24 0.24
118 50 0.51
119 18 0.18
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (117 bp):
AATTAATATAATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCAAGGTG
CCTTAAGACAGTCCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAAC
Found at i:294131 original size:3 final size:3
Alignment explanation
Indices: 294123--294149 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
294113 TTTATGGCTA
294123 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
294150 TAAAAGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:295334 original size:16 final size:16
Alignment explanation
Indices: 295310--295345 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
295300 AGCGACTGGT
* *
295310 TGGACCATCTGGCAGC
1 TGGAACATCTGGAAGC
295326 TGGAACATCTGGAAGC
1 TGGAACATCTGGAAGC
295342 TGGA
1 TGGA
295346 GAGGCGGCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.22, G:0.33, T:0.19
Consensus pattern (16 bp):
TGGAACATCTGGAAGC
Found at i:295595 original size:3 final size:3
Alignment explanation
Indices: 295589--295641 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
295579 ATTATTTATT
* *
295589 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
295633 TAA TAA TAA
1 TAA TAA TAA
295642 ATAAAACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:295611 original size:19 final size:18
Alignment explanation
Indices: 295589--295644 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
295579 ATTATTTATT
295589 TAATAATAATAATATAATA
1 TAATAATAATAATA-AATA
* *
295608 TAATAATAATATTAAAACA
1 TAATAATAATAAT-AAATA
*
295627 AAATAATAATAATAAATA
1 TAATAATAATAATAAATA
295645 AAACAAATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 4 0.13
19 26 0.84
20 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TAATAATAATAATAAATA
Found at i:295614 original size:22 final size:21
Alignment explanation
Indices: 295567--295645 Score: 74
Period size: 22 Copynumber: 3.8 Consensus size: 21
295557 TGTAAAAATG
* * *
295567 TAATAATAATAAATTATTTATT
1 TAATAATAATAAATAATATA-A
295589 TAATAATAATAATATAATATAA
1 TAATAATAATAA-ATAATATAA
*
295611 TAATAATATTAAA-ACA-A-AA
1 TAATAATAATAAATA-ATATAA
295630 TAATAATAATAAATAA
1 TAATAATAATAAATAA
295646 AACAAATGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
19 15 0.31
20 3 0.06
21 2 0.04
22 23 0.47
23 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATAATAATAAATAATATAA
Found at i:295652 original size:22 final size:22
Alignment explanation
Indices: 295589--295652 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
295579 ATTATTTATT
* *
295589 TAATAAT-AATAATATAATATAA
1 TAATAATAAATAAAACAA-ATAA
*
295611 TAATAATA-TTAAAACAAAATAA
1 TAATAATAAATAAAAC-AAATAA
295633 TAATAATAAATAAAACAAAT
1 TAATAATAAATAAAACAAAT
295653 GAAATAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 27 0.77
23 8 0.23
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAATAAATAAAACAAATAA
Found at i:296138 original size:113 final size:113
Alignment explanation
Indices: 295993--296751 Score: 1048
Period size: 113 Copynumber: 6.8 Consensus size: 113
295983 ATAGAGTCAT
* * *
295993 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
296058 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAATGCTGATCCATCGAGTGATGAATTCAA
* * * *
296106 ACAAAAGGTTGAACAAATTCTTTTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * **
296171 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAATGCTGATCCATCGAGTGATGAATTCAA
* *
296219 GTAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
296284 ATTATGAACTCTAC-CTGGTAATGCTGATCCATCGAATGATGAATTCAA
66 ATTATGAACT-TTCTCTGGAAATGCTGATCCATCGAGTGATGAATTCAA
* * * *
296332 GCGAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTATTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * **
296397 ATTATGAACTTTAC-CTGGCAATGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTT-CTCTGGAAATGCTGATCCATCGAGTGATGAATTCAA
* * *
296445 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCCTCTTCCTTTTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
296510 ATTATGAACTTTCTCTGGCAATGCTAATCCATCGGGTGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAATGCTGATCCATCGAGTGATGAATTCAA
296558 GCAAAA-GTTGAACAAG---TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
296619 ATTATGAACTTTCTCTGGCAATGCTAATCAATCGGGTGATGAATTAAA
66 ATTATGAACTTTCTCTGGAAATGCTGATCCATCGAGTGATGAATTCAA
* * * *
296667 GCAAAATGTTGAAGAAGTTCTTCTAATTATGAACTTTTTCTTCC-TCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
296731 ATTATGAACTCT-TCTGGAAAT
66 ATTATGAACTTTCTCTGGAAAT
296752 ATTGAAAACA
Statistics
Matches: 577, Mismatches: 62, Indels: 16
0.88 0.09 0.02
Matches are distributed among these distances:
109 94 0.16
110 9 0.02
111 8 0.01
112 43 0.07
113 421 0.73
114 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAATGCTGATCCATCGAGTGATGAATTCAA
Found at i:296938 original size:76 final size:73
Alignment explanation
Indices: 296801--296976 Score: 237
Period size: 76 Copynumber: 2.4 Consensus size: 73
296791 GAGGTCTTAT
* *
296801 CATCTTGCACTGTAGGGCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGGCTTACAGATGACCCTGAGGCTTTAACATCAAAAAGCTCCCGAAGGCTT
296866 TTTGAAAA
66 TTTGAAAA
* * *
296874 CATCATGCA-TGTAGGTCTTACATATGACCCTGAGGGTTTTGAAAACATCAAAAAGCTCCCGAAG
1 CATCATGCACTGTAGGGCTTACAGATGACCCTGA-GGCTTT---AACATCAAAAAGCTCCCGAAG
296938 GCTTTTTGAAAA
62 GCTTTTTGAAAA
* * *
296950 CATCCTGCACTGCAGGGCTTACGGATG
1 CATCATGCACTGTAGGGCTTACAGATG
296977 TTGGAAATAG
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
72 22 0.25
73 13 0.15
76 40 0.45
77 13 0.15
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (73 bp):
CATCATGCACTGTAGGGCTTACAGATGACCCTGAGGCTTTAACATCAAAAAGCTCCCGAAGGCTT
TTTGAAAA
Found at i:304652 original size:12 final size:13
Alignment explanation
Indices: 304628--304656 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
304618 AAAATGAAAA
304628 AAATGCTAAATGT
1 AAATGCTAAATGT
304641 AAATGC-AAATGT
1 AAATGCTAAATGT
304653 AAAT
1 AAAT
304657 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (13 bp):
AAATGCTAAATGT
Found at i:304748 original size:14 final size:14
Alignment explanation
Indices: 304729--304767 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
304719 GCAAAGATTC
304729 CAAATGTAAATATG
1 CAAATGTAAATATG
*
304743 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
304757 TAAATGTAAAT
1 CAAATGTAAAT
304768 TATTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.54, C:0.05, G:0.13, T:0.28
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:306936 original size:29 final size:30
Alignment explanation
Indices: 306890--306947 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
306880 ATTTCAAAAT
306890 TATAATTATGAAAAAAAATATTAATTTATA
1 TATAATTATGAAAAAAAATATTAATTTATA
* * *
306920 TATATTTAT-AAATAAAATATTTATTTAT
1 TATAATTATGAAAAAAAATATTAATTTAT
306948 TTAGAAATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
TATAATTATGAAAAAAAATATTAATTTATA
Found at i:308717 original size:3 final size:3
Alignment explanation
Indices: 308711--308763 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
308701 ATTATTTATT
* *
308711 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
308755 TAA TAA TAA
1 TAA TAA TAA
308764 ATAAAACACA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:308733 original size:19 final size:18
Alignment explanation
Indices: 308711--308766 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
308701 ATTATTTATT
308711 TAATAATAATAATATAATA
1 TAATAATAATAATA-AATA
* *
308730 TAATAATAATATTAAAACA
1 TAATAATAATAAT-AAATA
*
308749 AAATAATAATAATAAATA
1 TAATAATAATAATAAATA
308767 AAACACATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 4 0.13
19 26 0.84
20 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TAATAATAATAATAAATA
Found at i:308736 original size:22 final size:21
Alignment explanation
Indices: 308689--308767 Score: 74
Period size: 22 Copynumber: 3.8 Consensus size: 21
308679 TGTAAAAATG
* * *
308689 TAATAATAATAAATTATTTATT
1 TAATAATAATAAATAATATA-A
308711 TAATAATAATAATATAATATAA
1 TAATAATAATAA-ATAATATAA
*
308733 TAATAATATTAAA-ACA-A-AA
1 TAATAATAATAAATA-ATATAA
308752 TAATAATAATAAATAA
1 TAATAATAATAAATAA
308768 AACACATGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
19 15 0.31
20 3 0.06
21 2 0.04
22 23 0.47
23 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATAATAATAAATAATATAA
Found at i:310444 original size:23 final size:23
Alignment explanation
Indices: 310397--310444 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
310387 AATAACATAT
**
310397 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
*
310420 TAGGTAGCTCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
310443 TA
1 TA
310445 TGCATTTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:310520 original size:87 final size:86
Alignment explanation
Indices: 310356--310522 Score: 298
Period size: 87 Copynumber: 1.9 Consensus size: 86
310346 CGATTATGTT
310356 ATATCATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAAT
1 ATATCATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAAT
* * *
310421 AGGTAGCTCTTATATAATAAA
66 AGATAACGCTTATATAATAAA
310442 ATATGCATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAA
1 ATAT-CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAA
310507 TAGATAACGCTTATAT
65 TAGATAACGCTTATAT
310523 TGACCTATTT
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
86 4 0.05
87 73 0.95
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (86 bp):
ATATCATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAAT
AGATAACGCTTATATAATAAA
Found at i:310871 original size:200 final size:198
Alignment explanation
Indices: 310523--311046 Score: 662
Period size: 201 Copynumber: 2.6 Consensus size: 198
310513 ACGCTTATAT
* *
310523 TGACCTATTTTCTAAGT-AAACCAGTATATTTATATCGGTAACATTGCAAATTTACCTATTACAT
1 TGACCTATTTTCTAA-TAAAACCGGTATATTTATATCGGT-ACATTGTAAATTTACCTATTACAT
* * ** *
310587 TATAATTATCGGTTTCAATTTTTTTTGATCGATACAATTT--TAAATGTATCGACACTTTATGCA
64 TATAATTATCGGTTTCGATGTTTTGAGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCA
* * *
310650 TGCACCTCGTTGGGCATTCATTCTGGA-AAAAAGTATCGACACAAACTTAAAAAGTGTTGATACA
128 TGCACCTCGTTGGACATTCATTATGGACAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACA
*
310714 TTAT-T
193 TTATGC
* * * *
310719 TAGACCTATTTTCTCATAAAACCGGTATATTTCTGTCGGGTACATTGTAAATTTACCTATCACAT
1 T-GACCTATTTTCTAATAAAACCGGTATATTTATATC-GGTACATTGTAAATTTACCTATTACAT
* * * *
310784 TGTAATTATCAGTTTTCGATGTTTGTGAGATTGATACTTTTAATAAATGTATCGACACTTTATGT
64 TATAATTATC-GGTTTCGATGTTT-TGAGATCGATACTTTTAATAAATGTATCGACACTTTATGC
* * * *
310849 GTGCACCTCGTTTGACATTCATTATGGACAAAAAGTATCGACACAAATTTAAATAGTGTCGATAC
127 ATGCACCTCGTTGGACATTCATTATGGACAAAAAGTATCGACACAAACTTAAAAAGTGTCGATAC
* *
310914 TTTGTGC
192 ATTATGC
* *
310921 TGACCTATTTTCTTATAAAACCGGTATATTTATATCAGTTACATTGTAAATTTACCTATTACATT
1 TGACCTATTTTCTAATAAAACCGGTATATTTATATC-GGTACATTGTAAATTTACCTATTACATT
* * *
310986 ATAATTATCGGTTTCGATGTTATTGGGATCGATACTTTTAATAAATGTATCAAAACTTTAT
65 ATAATTATCGGTTTCGATGTT-TTGAGATCGATACTTTTAATAAATGTATCGACACTTTAT
311047 ATTCTGGACA
Statistics
Matches: 281, Mismatches: 37, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
196 2 0.01
197 60 0.21
198 16 0.06
199 9 0.03
200 90 0.32
201 103 0.37
202 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.40
Consensus pattern (198 bp):
TGACCTATTTTCTAATAAAACCGGTATATTTATATCGGTACATTGTAAATTTACCTATTACATTA
TAATTATCGGTTTCGATGTTTTGAGATCGATACTTTTAATAAATGTATCGACACTTTATGCATGC
ACCTCGTTGGACATTCATTATGGACAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTA
TGC
Found at i:311170 original size:177 final size:178
Alignment explanation
Indices: 310873--311213 Score: 497
Period size: 177 Copynumber: 1.9 Consensus size: 178
310863 ACATTCATTA
* * ** * *
310873 TGGACAAAAAGTATCGACACAAATTTAAATAGTGTCGATACTTTGTGCTGACCTATTTTCTTATA
1 TGGACAAAAAGTATCGACACAAATTCAAAAAGTGTCGATAAATTATGCTGACCTATTTTCTAATA
*
310938 AAACCGGTATATTTATATCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
66 AAACCGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
311003 TGTTATTGGGATCGATACTTTTA-ATAAATGTATCAAAACTTTATATTC
131 TGTTATTGGGATCGATACTTTTAGA-AAATGTATCAAAACTTTATATTC
* * * *
311051 TGGACAATAAGTATCGACACAAATTCAAAAAGTGTCGATAAATTATGTTGACTTGTTTTCTAAT-
1 TGGACAAAAAGTATCGACACAAATTCAAAAAGTGTCGATAAATTATGCTGACCTATTTTCTAATA
* * * * *
311115 TAACCGGTATATTTATACCGGTTACATTGTTAATTTACCTATTATATTATAATTATTGGTTTCGA
66 AAACCGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
* *
311180 TGTTTTTGGGGTCGATACTTTTAGAAAATGTATC
131 TGTTATTGGGATCGATACTTTTAGAAAATGTATC
311214 GACACCTATT
Statistics
Matches: 144, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
177 89 0.62
178 55 0.38
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (178 bp):
TGGACAAAAAGTATCGACACAAATTCAAAAAGTGTCGATAAATTATGCTGACCTATTTTCTAATA
AAACCGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
TGTTATTGGGATCGATACTTTTAGAAAATGTATCAAAACTTTATATTC
Found at i:311959 original size:23 final size:23
Alignment explanation
Indices: 311912--311961 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
311902 AATAACATAT
* **
311912 TAGGTATCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
*
311935 TAGGTAGCTCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
311958 TAGG
1 TAGG
311962 CATTTAACCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:312035 original size:87 final size:87
Alignment explanation
Indices: 311875--312037 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
311865 TATGTTATAT
* *
311875 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTATCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGAT
* *
311940 AGCTCTTATATAATAAAATAGG
66 AACGCTTATATAATAAAATAGG
311962 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGAT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGAT
312027 AACGCTTATAT
66 AACGCTTATAT
312038 TGACCTATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGAT
AACGCTTATATAATAAAATAGG
Found at i:312464 original size:200 final size:196
Alignment explanation
Indices: 312038--312561 Score: 676
Period size: 200 Copynumber: 2.6 Consensus size: 196
312028 ACGCTTATAT
*
312038 TGACCTATTTTCTAAGT-AAACCGGTATATTTATATCGGTAACATTGCAAATTTACCTATTACAT
1 TGACCTATTTTCTAA-TAAAACCGGTATATTTATATCGGT-ACATTGTAAATTTACCTATTACAT
* ** *
312102 TATAATTATCGGTTTCGATTTTTTTTTGATTGATACAATTT--TAAATGTATCGACACTTTATGC
64 TATAATTATCGGTTTCGA-TGTTTTGAGATTGATAC-TTTTAATAAATGTATCGACACTTTATGC
* * *
312165 ATGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAAAGTGTTGATACA
127 ATGCACCTCGTTGGACATTCATTATGGAAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACA
*
312230 TTATT
192 TTATC
* * * *
312235 TAGACCTATTTTCTCATAAAACCGGTATATTTCTGTCGGGTACATTGTAAATTTACCTATCACAT
1 T-GACCTATTTTCTAATAAAACCGGTATATTTATATC-GGTACATTGTAAATTTACCTATTACAT
* * **
312300 TGTAATTATCAGTTTCGATGTTTGTGAGATTGATACTTTTAATAAATGTATCGACACTTTATGTG
64 TATAATTATCGGTTTCGATGTTT-TGAGATTGATACTTTTAATAAATGTATCGACACTTTATGCA
* * * *
312365 TGCACCTCGTTTGACATTCATTATGGACAAAAAGTATCGACACAAATTTAAATAGTGTCGATACT
128 TGCACCTCGTTGGACATTCATTATGGA-AAAAAGTATCGACACAAACTTAAAAAGTGTCGATACA
*
312430 TTGTGC
192 TTAT-C
* *
312436 TGACCTATTTTCTTATAAAACCGGTATATTTATATCAGTTACATTGTAAATTTACCTATTACATT
1 TGACCTATTTTCTAATAAAACCGGTATATTTATATC-GGTACATTGTAAATTTACCTATTACATT
* * * *
312501 ATAATTATCGGTTTCGATGTTATTGGGATCGATACTTTTAATAAATGTATCAAAACTTTAT
65 ATAATTATCGGTTTCGATGTT-TTGAGATTGATACTTTTAATAAATGTATCGACACTTTAT
312562 ATTCTGGACA
Statistics
Matches: 284, Mismatches: 34, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
197 9 0.03
198 78 0.27
199 48 0.17
200 147 0.52
201 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (196 bp):
TGACCTATTTTCTAATAAAACCGGTATATTTATATCGGTACATTGTAAATTTACCTATTACATTA
TAATTATCGGTTTCGATGTTTTGAGATTGATACTTTTAATAAATGTATCGACACTTTATGCATGC
ACCTCGTTGGACATTCATTATGGAAAAAAGTATCGACACAAACTTAAAAAGTGTCGATACATTAT
C
Found at i:312685 original size:177 final size:178
Alignment explanation
Indices: 312388--312728 Score: 497
Period size: 177 Copynumber: 1.9 Consensus size: 178
312378 ACATTCATTA
* * ** * *
312388 TGGACAAAAAGTATCGACACAAATTTAAATAGTGTCGATACTTTGTGCTGACCTATTTTCTTATA
1 TGGACAAAAAGTATCGACACAAATTCAAAAAGTGTCGATAAATTATGCTGACCTATTTTCTAATA
*
312453 AAACCGGTATATTTATATCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
66 AAACCGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
312518 TGTTATTGGGATCGATACTTTTA-ATAAATGTATCAAAACTTTATATTC
131 TGTTATTGGGATCGATACTTTTAGA-AAATGTATCAAAACTTTATATTC
* * * *
312566 TGGACAATAAGTATCGACACAAATTCAAAAAGTGTCGATAAATTATGTTGACTTGTTTTCTAAT-
1 TGGACAAAAAGTATCGACACAAATTCAAAAAGTGTCGATAAATTATGCTGACCTATTTTCTAATA
* * * * *
312630 TAACCGGTATATTTATACCGGTTACATTGTTAATTTACCTATTATATTATAATTATTGGTTTCGA
66 AAACCGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
* *
312695 TGTTTTTGGGGTCGATACTTTTAGAAAATGTATC
131 TGTTATTGGGATCGATACTTTTAGAAAATGTATC
312729 GACACCTATT
Statistics
Matches: 144, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
177 89 0.62
178 55 0.38
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (178 bp):
TGGACAAAAAGTATCGACACAAATTCAAAAAGTGTCGATAAATTATGCTGACCTATTTTCTAATA
AAACCGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
TGTTATTGGGATCGATACTTTTAGAAAATGTATCAAAACTTTATATTC
Found at i:313464 original size:23 final size:23
Alignment explanation
Indices: 313417--313466 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
313407 AATAACATAT
**
313417 TAGGTAGTGCTTATATAATGTAA
1 TAGGTAGTGCTTATATAATAAAA
313440 TAGGTAGCT-CTTATATAATAAAA
1 TAGGTAG-TGCTTATATAATAAAA
313463 TAGG
1 TAGG
313467 CATTTAACCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (23 bp):
TAGGTAGTGCTTATATAATAAAA
Found at i:313540 original size:87 final size:87
Alignment explanation
Indices: 313380--313542 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
313370 TATGTTATAT
* *
313380 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGTGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGAT
* *
313445 AGCTCTTATATAATAAAATAGG
66 AACACTTATATAATAAAATAGG
313467 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGAT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGAT
313532 AACACTTATAT
66 AACACTTATAT
313543 TGACCTATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGAT
AACACTTATATAATAAAATAGG
Found at i:313983 original size:194 final size:194
Alignment explanation
Indices: 313543--314059 Score: 641
Period size: 194 Copynumber: 2.6 Consensus size: 194
313533 ACACTTATAT
* *
313543 TGACCTATTTTCTAAGT-AAACCGGTATATTTATATCGGTAACATTGCAAATTTACCTATTACAT
1 TGACCTATTTTCTAA-TAAAACCGGTATATTTATATCGGTTACATTGTAAATTTACCTATTACAT
* ** *
313607 TATAATTATCGGTTTCGATTTTTTTTGATCGATACAATTT--TAAATGTATCGACACTTTATGCA
65 TATAATTATCGGTTTCGATGTTTTGAGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCA
* * *
313670 TGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAAAGTGTTGATACAT
129 TGCACCTCGTTGGACATTCATTATGGAAAAAAGTATCGACACAAACTTAAAAA--G-TAATACAT
*
313735 TATT
191 TATC
* * * * *
313739 TAGACCTATTTTCTCATAAAACCGGTATATTTCTGTCGGGTACATTGTAAATTTACCTATCACAT
1 T-GACCTATTTTCTAATAAAACCGGTATATTTATATCGGTTACATTGTAAATTTACCTATTACAT
* * * **
313804 TGTAATTATCAGTTTCGATGTTTGTGAGATTGATACTTTTAATAAATGTATCGACACTTTATGTG
65 TATAATTATCGGTTTCGATGTTT-TGAGATCGATACTTTTAATAAATGTATCGACACTTTATGCA
* * * *
313869 TGCACCTCGTTTGACATTCATTATGGACAAAAAGTATCGACACAAA-TT-TAAA-TAATACTTTG
129 TGCACCTCGTTGGACATTCATTATGGA-AAAAAGTATCGACACAAACTTAAAAAGTAATACATTA
313931 TGC
193 T-C
* *
313934 TGACCTATTTTCTTATAAAACCGGTATATTTATATCAGTTACATTGTAAATTTACCTATTACATT
1 TGACCTATTTTCTAATAAAACCGGTATATTTATATCGGTTACATTGTAAATTTACCTATTACATT
* * *
313999 ATAATTATCGGTTTCGATGTTATTGGGATCGATACTTTTAATAAATGTATCAAAACTTTAT
66 ATAATTATCGGTTTCGATGTT-TTGAGATCGATACTTTTAATAAATGTATCGACACTTTAT
314060 ATTCTGGACA
Statistics
Matches: 277, Mismatches: 36, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
194 119 0.43
195 2 0.01
196 2 0.01
197 77 0.28
198 12 0.04
199 47 0.17
200 18 0.06
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.40
Consensus pattern (194 bp):
TGACCTATTTTCTAATAAAACCGGTATATTTATATCGGTTACATTGTAAATTTACCTATTACATT
ATAATTATCGGTTTCGATGTTTTGAGATCGATACTTTTAATAAATGTATCGACACTTTATGCATG
CACCTCGTTGGACATTCATTATGGAAAAAAGTATCGACACAAACTTAAAAAGTAATACATTATC
Found at i:315472 original size:34 final size:32
Alignment explanation
Indices: 315412--315481 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
315402 CCTTGCAAAC
*
315412 TCCCTAGTTTTTCCGGGATAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
* *
315444 TCCCTAGCTTTTACACGGGATTAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
315478 TCCC
1 TCCC
315482 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:319018 original size:200 final size:199
Alignment explanation
Indices: 318651--319419 Score: 890
Period size: 200 Copynumber: 3.8 Consensus size: 199
318641 ACGTAATTTT
* * *
318651 AAAATGTATCGACACAAATTT-AAAAGTGTTGATACACTATGTTAACTTATTTTCTCATAAAACC
1 AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTT-ACCTATTTTCTCATAAAACC
* *
318715 GGTATATTTATACCGATTATATTGTAAATTTACCTATTACATTATAATTTTCAGTTTCGATGTTT
65 GGTATATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTT
* * * *
318780 TTTGGATCGATATTTTTTATGAATGTATCGATACTTTATGCGTGCACCCCGTTTTGCATTCATTA
130 TTTGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCCGTTTAGCATTCATTA
318845 TGGAC
195 TGGAC
* * * *
318850 AAAATGTATTGACACAAATCTAAAAAGTGTCGATACATTATGTTCACCTATTTTCTTAAAAAACC
1 AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTT-ACCTATTTTCTCATAAAACC
* * *
318915 GGTATACTTATACCGATTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATG-TT
65 GGTATATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTT
* * * *
318979 TTTGAGATCGATACTTTTTAAAAATGTATCGACACTTTATGTGTGCACACCGTTTGGCATTCATT
130 TTTG-GATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCCGTTTAGCATTCATT
319044 ATGGAC
194 ATGGAC
* * * *
319050 AAAATGTATCAACACAAATTTAAACAGTGTCAATACATTATGTATACCTATTTTCTCATAAAACA
1 AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGT-TACCTATTTTCTCATAAAACC
* * * * * *
319115 TGTATATTTATATCGGTTACATTGTATATTTACCTATTATATTATAA-TATTCAGTTTTGATGTT
65 GGTATATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATTA-TCAGTTTCGATGTT
* * * * * * *
319179 TTTTGGATCGATA-TAATTT-TAAATGTATCGACACTTTTATGCATGAAGCTCGTTGAGCA--AA
129 TTTTGGATCGATACT-TTTTATAAATGTATCGACAC-TTTATGCGTGCACCCCGTTTAGCATTCA
***
319240 GGCTCGGAC
192 TTAT-GGAC
* * * * * * *
319249 AAAAAGTATC-AGCACAAATTTAAAAGGTGTCGATACTTTATGCTGACATATTTGCTCATAAAAT
1 AAAATGTATCGA-CACAAATTTAAAAAGTGTCGATACATTATG-TTACCTATTTTCTCATAAAAC
* * * * * *
319313 CGGTATATTTATACCGGTCACATTGTAAATTTACCTATTACATTATAATTTTCGGTTT-AATTGC
64 CGGTATATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGA-TGT
319377 TTTTTGGATCGATACTTTTTTATAAATGTATCGACACTTTATG
128 TTTTTGGATCGATAC-TTTTTATAAATGTATCGACACTTTATG
319420 TGAAACTTTA
Statistics
Matches: 484, Mismatches: 71, Indels: 29
0.83 0.12 0.05
Matches are distributed among these distances:
198 4 0.01
199 161 0.33
200 296 0.61
201 23 0.05
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (199 bp):
AAAATGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTACCTATTTTCTCATAAAACCG
GTATATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTT
TTGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCCGTTTAGCATTCATTAT
GGAC
Found at i:319389 original size:399 final size:398
Alignment explanation
Indices: 318651--319421 Score: 998
Period size: 399 Copynumber: 1.9 Consensus size: 398
318641 ACGTAATTTT
* ** * *
318651 AAAATGTATCGACACAAATTTAAAAGTGTTGATACACTATGTTAACTTATTTTCTCATAAAACCG
1 AAAATGTATCAACACAAATTTAAAAGTGTCAATACACTATGTTAACCTATTTTCTCATAAAACAG
* *
318716 GTATATTTATACCGATTATATTGTAAATTTACCTATTACATTATAATTTTCAGTTTCGATGTTTT
66 GTATATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATATTCAGTTTCGATGTTTT
* * * * ** * **
318781 TTGGATCGATATTTTTTATGAATGTATCGATACTTTATGCGTGCACCCCGTTTTGCATTCATTAT
131 TTGGATCGATATATTTTA-GAATGTATCGACACTTTATGCATGAACCCCGTTGAGCA-TAAGGAT
* * * * * *
318846 GGACAAAATGTATTGACACAAATCTAAAAAGTGTCGATACATTATGTTCACCTATTTTCTTAAAA
194 GGACAAAAAGTATAGACACAAATCTAAAAAGTGTCGATACATTATGCTCACATATTTGCTCAAAA
* * *
318911 AACCGGTATACTTATACCGATTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGAT
259 AACCGGTATACTTATACCGATCACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAAT
318976 GTTTTTGAGATCGATAC-TTTTTAAAAATGTATCGACACTTTATGTGTGCACACCGTTTGGCATT
324 GTTTTTGAGATCGATACTTTTTTAAAAATGTATCGACACTTTATGTGTGCACACCGTTTGGCATT
319040 CATTATGGAC
389 CATTATGGAC
*
319050 AAAATGTATCAACACAAATTTAAACAGTGTCAATACATTATG-TATACCTATTTTCTCATAAAAC
1 AAAATGTATCAACACAAATTTAAA-AGTGTCAATACACTATGTTA-ACCTATTTTCTCATAAAAC
* * * * * *
319114 ATGTATATTTATATCGGTTACATTGTATATTTACCTATTATATTATAATATTCAGTTTTGATGTT
64 AGGTATATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATATTCAGTTTCGATGTT
* *
319179 TTTTGGATCGATATAATTTTA-AATGTATCGACACTTTTATGCATGAAGCTCGTTGAGCA-AAGG
129 TTTTGGATCGATAT-ATTTTAGAATGTATCGACAC-TTTATGCATGAACCCCGTTGAGCATAAGG
* * * * *
319242 CTCGGACAAAAAGTATCAG-CACAAATTTAAAAGGTGTCGATACTTTATGCTGACATATTTGCTC
192 AT-GGACAAAAAGTAT-AGACACAAATCTAAAAAGTGTCGATACATTATGCTCACATATTTGCTC
* * * * *
319306 ATAAAATCGGTATATTTATACCGGTCACATTGTAAATTTACCTATTACATTATAATTTTCGGTTT
255 AAAAAACCGGTATACTTATACCGATCACATTGTAAATTTACCTATTACATTATAATTATCGGTTT
*
319371 -AATTGCTTTTTG-GATCGATACTTTTTTATAAATGTATCGACACTTTATGTG
320 CAA-TG-TTTTTGAGATCGATACTTTTTTAAAAATGTATCGACACTTTATGTG
319422 AAACTTTAAG
Statistics
Matches: 318, Mismatches: 45, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
398 3 0.01
399 155 0.49
400 155 0.49
401 5 0.02
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (398 bp):
AAAATGTATCAACACAAATTTAAAAGTGTCAATACACTATGTTAACCTATTTTCTCATAAAACAG
GTATATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATATTCAGTTTCGATGTTTT
TTGGATCGATATATTTTAGAATGTATCGACACTTTATGCATGAACCCCGTTGAGCATAAGGATGG
ACAAAAAGTATAGACACAAATCTAAAAAGTGTCGATACATTATGCTCACATATTTGCTCAAAAAA
CCGGTATACTTATACCGATCACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAATGT
TTTTGAGATCGATACTTTTTTAAAAATGTATCGACACTTTATGTGTGCACACCGTTTGGCATTCA
TTATGGAC
Found at i:319678 original size:18 final size:18
Alignment explanation
Indices: 319655--319691 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
319645 CGAAATTTAT
319655 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
319673 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
319691 A
1 A
319692 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:321034 original size:12 final size:12
Alignment explanation
Indices: 321013--321044 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
321003 GATCATCATA
321013 ATCATCATCTTC
1 ATCATCATCTTC
321025 ATCATCATCTTC
1 ATCATCATCTTC
*
321037 ATCTTCAT
1 ATCATCAT
321045 TGGCCTCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:322863 original size:200 final size:200
Alignment explanation
Indices: 322520--323668 Score: 1432
Period size: 200 Copynumber: 5.8 Consensus size: 200
322510 TTTTAAAATG
* * * * * *
322520 GTATCGACACAAATTT-AACAATTGTCGATACTTTATGCT-GACATATTTTCTCATAAAACCGAT
1 GTATCGACACAAATTTCAA-AAGTGTCGATACATTATG-TAGACCTATTCTCACATAAAACCGGT
** * * ** * *
322583 ATATTTATACCGGTTACATTGGAAATTTACGTATTTTATTATAATTATTGGTTTCGATGTTTTTG
64 ATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTG
* * * * * *
322648 GGATCGACACTTTTTAAAAATGTATCGACACTTAATGGGTGCACCCTTTTTGGCATTCCTTCTGG
129 GGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGG
*
322713 ATAAAAA
194 ACAAAAA
* * * * *
322720 GTATCGACACAAATTCCAGAAGTGTCGATACATTTTCTAGACCTATTCTCTCATAAAACCGGTAT
1 GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* * *
322785 ATTTATACCGGTTACATTGA-AACATTACCTATTAAATTATAATCATGGGTTTCGATGTTTCTGG
66 ATTTATACCGGTTACATT-ACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
* *
322849 GATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCATTTTTTTGGGCATTTATTCT
130 GATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCA---TTTTGGGCATTCATTCT
*
322914 GGACAAAAT
192 GGACAAAAA
* *
322923 GTATCGACACATAA-TTAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCAGTA
1 GTATCGACACA-AATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTA
* * *
322987 TATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGG-TTCGATGTCTCTGG
65 TATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
* * *
323051 GATCGACACTTTTTAAAAATGTTTCGACACTTTATGCGTTCACCATTTTGGGCATTCATTCTGGA
130 GATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGA
323116 CAAAAA
195 CAAAAA
* * *
323122 GTATCGACACCAATTTCAAATGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGATAT
1 GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* *
323187 ATTTATATCGGTTACATTACAAAATTACCTATTACATTTTAATTATGGGTTTCGA----TC---G
66 ATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
* * * * * *
323245 A-C---ACTTTTAAAAAATGTATCGATACTTTATGGGTGCACCCTTTTGGGCATTCCTTCCGGAC
131 ATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGAC
323306 AAACAA
196 AAA-AA
* * * * *
323312 -TATCGACACAAATTCCAGAAGTGTTGATACATTATGTAGACCTATTCTCTCATAAAATCGGTAT
1 GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* * ** * *
323376 AGTTATACCAGTTACATTGTAAATTTACCTATTACGTTATAATTATGGGTTTCGATGTTTCTGGG
66 ATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
* * * * *
323441 ATCGATACTTTTTATAAATGTATCGACACTTTATGCTTTCACCATTTTGGGCATTTATTCTGGAT
131 ATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGAC
323506 AAAAA
196 AAAAA
* * *
323511 GTATCGACACCAATTTCAAAAGTGTCAATACATTATGTAGATCTATTCTCACATAAAACCGGTAT
1 GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
* * * *
323576 ATTTATACCGGTTATATTACAAAATTACCTATTATATTATAATTATAGGTTTCGATGTTTTTGGG
66 ATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
*
323641 ATCGATACTTTTTATAAATGTATCGACA
131 ATCGATACTTTTTAAAAATGTATCGACA
323669 TATCTTCTTA
Statistics
Matches: 817, Mismatches: 109, Indels: 46
0.84 0.11 0.05
Matches are distributed among these distances:
189 157 0.19
190 2 0.00
192 1 0.00
193 4 0.00
196 4 0.00
197 1 0.00
198 2 0.00
199 129 0.16
200 341 0.42
201 1 0.00
202 55 0.07
203 118 0.14
204 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (200 bp):
GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTAT
ATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
ATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGAC
AAAAA
Found at i:324045 original size:19 final size:19
Alignment explanation
Indices: 324021--324069 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
324011 TTACATTCAC
324021 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
324040 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
324059 ATACAAAATTA
1 ATACAAAATTA
324070 ACTCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:326164 original size:29 final size:30
Alignment explanation
Indices: 326094--326153 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
326084 CAATTTAAGG
326094 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
*
326125 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
326154 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:326259 original size:21 final size:21
Alignment explanation
Indices: 326233--326309 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
326223 AGGGTGTCAA
326233 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
326254 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
* * *
326275 AGTGTATCCATGCA-TCATGC
1 AGTGCATCCATGCACCCCTGC
326295 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
326310 TCAAACACCG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
20 17 0.34
21 33 0.66
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:328875 original size:29 final size:31
Alignment explanation
Indices: 328817--328877 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
328807 TTTTGATATA
328817 ACAAAATGGTTTTTGGACTTGAATTGAATTT
1 ACAAAATGGTTTTTGGACTTGAATTGAATTT
*
328848 ACAAAAT-GTTTTTGGACTT-AATTTAATTT
1 ACAAAATGGTTTTTGGACTTGAATTGAATTT
328877 A
1 A
328878 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 10 0.34
30 12 0.41
31 7 0.24
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (31 bp):
ACAAAATGGTTTTTGGACTTGAATTGAATTT
Found at i:328983 original size:21 final size:21
Alignment explanation
Indices: 328957--329054 Score: 153
Period size: 21 Copynumber: 4.7 Consensus size: 21
328947 AGGGTGTCAA
328957 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
328978 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
328999 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
* *
329020 AGTGCATCCATGCA-TCATGC
1 AGTGCATCCATGCACCCCTGC
329040 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
329055 TCAAACACTG
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
20 18 0.25
21 55 0.75
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:329018 original size:42 final size:41
Alignment explanation
Indices: 328957--329054 Score: 169
Period size: 42 Copynumber: 2.4 Consensus size: 41
328947 AGGGTGTCAA
*
328957 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCAT-CATGC
*
328999 AGTGCATCCATGCATCCCTGCAGTGCATCCATGCATCATGC
1 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCATCATGC
329040 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
329055 TCAAACACTG
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 18 0.34
42 35 0.66
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.22
Consensus pattern (41 bp):
AGTGCATCCATGCACCCCTGCAGTGCATCCATGCATCATGC
Found at i:329513 original size:34 final size:32
Alignment explanation
Indices: 329474--329543 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
329464 TTTTGTAAAG
* *
329474 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
329508 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
329540 GGGA
1 GGGA
329544 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:337173 original size:149 final size:148
Alignment explanation
Indices: 336860--337162 Score: 489
Period size: 149 Copynumber: 2.0 Consensus size: 148
336850 GAGTCGAGGG
* * * * *
336860 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAAGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* *
336925 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
* *
336990 ATGGCACTATGGTGCAAT
131 AGGGCACTACGGTGCAAT
* *
337008 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
337073 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
337138 TAGGGCATTACGGTGCAAT
130 TAGGGCACTACGGTGCAAT
337157 TCTACG
1 TCTACG
337163 TGGCACTTCG
Statistics
Matches: 142, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
148 49 0.35
149 93 0.65
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
AGGGCACTACGGTGCAAT
Found at i:337383 original size:21 final size:21
Alignment explanation
Indices: 337359--337419 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
337349 ATAAATAATT
*
337359 TGATGATAATGATAGA-GATAA
1 TGATAATAAT-ATAGATGATAA
*
337380 TGATAATAATATATATGATAA
1 TGATAATAATATAGATGATAA
* * *
337401 TGCTAAGAAAATAGATGAT
1 TGATAATAATATAGATGAT
337420 GATATATGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.49, C:0.02, G:0.18, T:0.31
Consensus pattern (21 bp):
TGATAATAATATAGATGATAA
Done.