Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008338.1 Hibiscus syriacus cultivar Beakdansim tig00111059_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: 2210178
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 12
Found at i:259932 original size:4 final size:4
Alignment explanation
Indices: 259917--259969 Score: 52
Period size: 4 Copynumber: 12.5 Consensus size: 4
259907 TTTACATTGT
* * *
259917 TTTA TATA TTTA TTTA TTTA TTTA TTTCA TTTT TTTA TTAA TATTA TTATA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA T-TTA TT-TA
259968 TT
1 TT
259970 AAAATTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
4 29 0.73
5 11 0.28
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:259969 original size:27 final size:25
Alignment explanation
Indices: 259925--259983 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 25
259915 GTTTTATATA
* ** *
259925 TTTATTTATTTATTTATTTCATTTT
1 TTTATTAATTTATTTATTAAAATTT
259950 TTTATTAATATTATTATATTAAAATTT
1 TTTATTAAT-TTATT-TATTAAAATTT
259977 TTTATTA
1 TTTATTA
259984 TTCTTTTCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 8 0.29
26 5 0.18
27 15 0.54
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTATTAATTTATTTATTAAAATTT
Found at i:261085 original size:181 final size:182
Alignment explanation
Indices: 260749--261221 Score: 734
Period size: 181 Copynumber: 2.6 Consensus size: 182
260739 AATCCAAATT
* * * **
260749 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * *
260814 AAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
260879 GTGAATTTAAAAGAGAAGCAGTTTTAAAT-CCTATAAAGTGTCGATACTTTTA
131 GTGAATTTAAAAAAGAAGCAGTTTT-AATGCCTATAAAGTGTCGATACTTTAA
* * *
260931 AAAAATGTATCGATCCAAAACGATATACCATGTAAAAATATGATAAAACTGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
260996 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
261060 GTGAATTTAAAAAAGAAGCAGTTTTAGTGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAAAGAAGCAGTTTTAATGCCTATAAAGTGTCGATACTTTAA
* *
261112 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
261177 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
261222 CGTAAGTACG
Statistics
Matches: 266, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
180 2 0.01
181 167 0.63
182 97 0.36
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAAAGAAGCAGTTTTAATGCCTATAAAGTGTCGATACTTTAA
Found at i:261165 original size:20 final size:19
Alignment explanation
Indices: 261142--261188 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
261132 CGATATAACA
261142 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
261162 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
261182 GGTAAAA
1 GGTAAAA
261189 CGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:261193 original size:17 final size:19
Alignment explanation
Indices: 261153--261193 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
261143 GTAAAAATAT
*
261153 GATAAAACCGGTATCAAAAT
1 GATAAAACCGG-ATCAAAAC
261173 GATAAAACCGG-T-AAAAC
1 GATAAAACCGGATCAAAAC
261190 GATA
1 GATA
261194 CCGGATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
20 11 0.55
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (19 bp):
GATAAAACCGGATCAAAAC
Found at i:263448 original size:21 final size:21
Alignment explanation
Indices: 263418--263482 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
263408 AAGACAATCA
*
263418 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
*
263439 AGAGTAGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
263460 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
263481 AG
1 AG
263483 GCATAAGGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.43, C:0.09, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:263558 original size:33 final size:33
Alignment explanation
Indices: 263516--263581 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
263506 AAATAGATGG
*
263516 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
263549 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
263582 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:266376 original size:400 final size:388
Alignment explanation
Indices: 265631--266382 Score: 1209
Period size: 400 Copynumber: 1.9 Consensus size: 388
265621 AATTTACAAT
*
265631 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
265696 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGATACAAGTATACCGGTTAG
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGATACAAGTATACCGGATAG
* *
265761 GTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTTGTCCATAACGAATGGCAA
131 GTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAACGAATGGCAA
* * *
265826 ACAGGGTGCAATAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACATCGAAACC
196 ACAAGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACC
*
265891 CATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
261 CAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
265956 AATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGA
326 AATAGGTATAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGA
*
266019 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATTCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
266084 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGATACAAGTATACC------
266149 ATAAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
125 ----G-G-ATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
* *
266214 AATGAATGGCAAACAAGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
184 AACGAATGGCAAACAAGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
* *
266279 AACATCGAAACCCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTATAAGTATACCG
249 AACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCG
* *
266344 GTTTTATGGGAGAATTGGTATATAAT-ATGTATCGACACT
314 GTTTTATGAGAGAATAGGTATA-AATAATGTATCGACACT
266383 GTTTAATGTT
Statistics
Matches: 332, Mismatches: 19, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
388 119 0.36
398 1 0.00
399 1 0.00
400 208 0.63
401 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (388 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGATACAAGTATACCGGATAG
GTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAACGAATGGCAA
ACAAGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACC
CAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATAGGTATAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGA
Found at i:266401 original size:200 final size:200
Alignment explanation
Indices: 265758--266382 Score: 1090
Period size: 200 Copynumber: 3.1 Consensus size: 200
265748 GTATACCGGT
* * *
265758 TAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTTGTCCATAACGAATGG
1 TAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
* *
265823 CAAACAGGGTGCAATAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACATCGAA
66 CAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAA
265888 ACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
131 ACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
265953 GAGAA
196 GAGAA
265958 TAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
1 TAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
*
266023 CAAACAGGGTGCAACAATAAAGTGTCGATTCATATATAAAAAGTGTCGATCCCATAAACATCGAA
66 CAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAA
* *
266088 ACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTTATAA
131 ACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
266153 GAGAA
196 GAGAA
266158 TAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
1 TAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
* *
266223 CAAACAAGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAA
66 CAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAA
* * * *
266288 ACCCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGG
131 ACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
266353 GAGAA
196 GAGAA
* *
266358 TTGGTATATAAT-ATGTATCGACACT
1 TAGGTCTA-AATAATGTATCGACACT
266383 GTTTAATGTT
Statistics
Matches: 405, Mismatches: 19, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
200 402 0.99
201 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (200 bp):
TAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
CAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAA
ACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
GAGAA
Found at i:269271 original size:180 final size:180
Alignment explanation
Indices: 268824--269309 Score: 766
Period size: 181 Copynumber: 2.7 Consensus size: 180
268814 CAAAGTTTTC
* *
268824 ACACTTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGAAAGAAAAATGTGTCGATACCTTT
1 ACAC-TTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTG
* * *
268889 TCAAAAAGTGTCG--ATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGATAATTTTATA
65 TCAAAAAGTGTCGACATT---TACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTATA
*
268952 ATATAATCGGTAAATATACCGGTTTATGAGCGAATAGGTCTATAACCTATATCG
127 ATATAATCGGTAAATATACCGGTTTATGAGCGAATAGGTCTACAACCTATATCG
*
269006 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCATAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* *
269071 CAAAAAGTGTCGACATTTACACATCAGAACCCAGAA-TATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTATAATAT
*
269135 AA-CGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AATCGG--TAAATATACC-GGTTTATGAGCGAATAGGTCTACAACCTATATCG
269187 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATG-GTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
269251 CAGAAAGTGTCGACATTTACACATCGGAACCCAAGAATTATAATGTAATAGATAATTTT
66 CAAAAAGTGTCGACATTTACACATCGGAACCC-AGAATTATAATGTAATAGATAATTTT
269310 CTATATCGAC
Statistics
Matches: 284, Mismatches: 13, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
178 3 0.01
179 29 0.10
180 68 0.24
181 156 0.55
182 25 0.09
183 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (180 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTATAATAT
AATCGGTAAATATACCGGTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:269413 original size:131 final size:129
Alignment explanation
Indices: 269179--269438 Score: 461
Period size: 131 Copynumber: 2.0 Consensus size: 129
269169 GGTCTACAAC
269179 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGGTCGAT
1 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGGTCGAT
269244 ACCTTGTCAGAAAGTGTCGACATTTACACATCGGAACCCAAGAATTATAATGTAATAGATAATTT
66 ACCTTGTCAGAAAGTGTCGACATTTACACATCGGAACCC-A-AATTATAATGTAATAGATAATTT
269309 T
129 T
*
269310 CTATATCGACACTTTTTAATATTGTG-CTGTACTTTATGTCCAGAATGGAAGGAAAAAAT-GTCG
1 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAA-G-AAAAATGGTCG
269373 ATACCTTGTCAGAAAGTGTCGACATTTACACATCGGAACCCAAATTATAATGTAATAGATAATTT
64 ATACCTTGTCAGAAAGTGTCGACATTTACACATCGGAACCCAAATTATAATGTAATAGATAATTT
269438 T
129 T
269439 GTAATATAAC
Statistics
Matches: 126, Mismatches: 1, Indels: 6
0.95 0.01 0.05
Matches are distributed among these distances:
129 24 0.19
130 24 0.19
131 72 0.57
132 6 0.05
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (129 bp):
CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGGTCGAT
ACCTTGTCAGAAAGTGTCGACATTTACACATCGGAACCCAAATTATAATGTAATAGATAATTTT
Found at i:273093 original size:21 final size:21
Alignment explanation
Indices: 273068--273119 Score: 77
Period size: 23 Copynumber: 2.4 Consensus size: 21
273058 AAATAGGTCA
273068 ATATAAGCTACATATTACATT
1 ATATAAGCTACATATTACATT
*
273089 ATATAAGCGCTACCTATTACATT
1 ATATAA--GCTACATATTACATT
273112 ATATAAGC
1 ATATAAGC
273120 GCTACCTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 8 0.29
23 20 0.71
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (21 bp):
ATATAAGCTACATATTACATT
Found at i:273106 original size:23 final size:23
Alignment explanation
Indices: 273074--273127 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
273064 GTCAATATAA
*
273074 GCTACATATTACATTATATAAGC
1 GCTACCTATTACATTATATAAGC
273097 GCTACCTATTACATTATATAAGC
1 GCTACCTATTACATTATATAAGC
273120 GCTACCTA
1 GCTACCTA
273128 ATATGTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.33
Consensus pattern (23 bp):
GCTACCTATTACATTATATAAGC
Found at i:273245 original size:23 final size:23
Alignment explanation
Indices: 273172--273236 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
273162 ATACCTATTT
273172 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTATCTATTAC
273195 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTATCTATTAC
*
273218 ATTATATAAGCGTTATCTA
1 ATTATATAAGCGCTATCTA
273237 ATATGTTATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.40
Consensus pattern (23 bp):
ATTATATAAGCGCTATCTATTAC
Found at i:273299 original size:108 final size:109
Alignment explanation
Indices: 273080--273321 Score: 425
Period size: 108 Copynumber: 2.2 Consensus size: 109
273070 ATAAGCTACA
273080 TATTACATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTG
1 TATTACATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTG
273145 ATAATATTTCCCGTTAAATACCTATTTATTATATAAGCGCTATC
66 ATAATATTTCCCGTTAAATACCTATTTATTATATAAGCGCTATC
* * *
273189 TATTACATTATATAAGCGCTATCTATTACATTATATAAGCGTTATCTAATATGTTA-TGTACTTG
1 TATTACATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTG
273253 ATAATATTTCCCGTTAAATA-CTATTTTATTATATAAGCGCTATC
66 ATAATATTTCCCGTTAAATACCTA-TTTATTATATAAGCGCTATC
*
273297 TATTACATTATATAAGCGTTACCTA
1 TATTACATTATATAAGCGCTACCTA
273322 ATATGTTATT
Statistics
Matches: 127, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
107 3 0.02
108 71 0.56
109 53 0.42
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (109 bp):
TATTACATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTG
ATAATATTTCCCGTTAAATACCTATTTATTATATAAGCGCTATC
Found at i:273330 original size:23 final size:23
Alignment explanation
Indices: 273280--273324 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
273270 ATACTATTTT
* *
273280 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
273303 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
273325 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:280190 original size:19 final size:19
Alignment explanation
Indices: 280162--280202 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
280152 GCACGTTAAT
280162 AAATATTAAAA-AATATAA
1 AAATATTAAAAGAATATAA
*
280180 AAATCATTAAAAGACTATAA
1 AAAT-ATTAAAAGAATATAA
280200 AAA
1 AAA
280203 CAATATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
20 9 0.45
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.24
Consensus pattern (19 bp):
AAATATTAAAAGAATATAA
Found at i:285096 original size:20 final size:20
Alignment explanation
Indices: 285071--285327 Score: 228
Period size: 20 Copynumber: 13.8 Consensus size: 20
285061 GAATTTCTCA
* * *
285071 TTGCGATAGTTAAATACCCG
1 TTGCGATAGTCAAATTCGCG
285091 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
*
285111 TTGCGAT--T----TTCTCG
1 TTGCGATAGTCAAATTCGCG
*
285125 TTGCGATAGTCAAA-TAGCCG
1 TTGCGATAGTCAAATTCG-CG
*
285145 TTGCGATAATCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
285165 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
285185 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
*
285205 TTGCGAT--T----TTTGCG
1 TTGCGATAGTCAAATTCGCG
* * *
285219 TTGCGATAGTGATATTCGTG
1 TTGCGATAGTCAAATTCGCG
*
285239 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCG
* *
285259 TTGCGAT--T----TTTGAG
1 TTGCGATAGTCAAATTCGCG
* *
285273 TTTCGATAATCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
285293 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
*
285313 TTGCGATATTCAAAT
1 TTGCGATAGTCAAAT
285328 GAATGTGTAA
Statistics
Matches: 192, Mismatches: 25, Indels: 40
0.75 0.10 0.16
Matches are distributed among these distances:
14 33 0.17
16 3 0.02
18 3 0.02
19 1 0.01
20 150 0.78
21 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:285146 original size:54 final size:54
Alignment explanation
Indices: 285064--285171 Score: 180
Period size: 54 Copynumber: 2.0 Consensus size: 54
285054 GCTTTGTGAA
* *
285064 TTTCTCATTGCGATAGTTAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 TTTCTCATTGCGATAGTCAAATACCCGTTGCGATAATCAAATTCGCGTTGCGAT
* *
285118 TTTCTCGTTGCGATAGTCAAATAGCCGTTGCGATAATCAAATTCGCGTTGCGAT
1 TTTCTCATTGCGATAGTCAAATACCCGTTGCGATAATCAAATTCGCGTTGCGAT
285172 AGTCAAATTC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (54 bp):
TTTCTCATTGCGATAGTCAAATACCCGTTGCGATAATCAAATTCGCGTTGCGAT
Found at i:285178 original size:40 final size:40
Alignment explanation
Indices: 285071--285328 Score: 167
Period size: 34 Copynumber: 6.9 Consensus size: 40
285061 GAATTTCTCA
* * * * *
285071 TTGCGATAGTTAAATACCCGTTGCGATAGTCAAATTCGCG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATGCGCG
*
285111 TTGCGAT--T----TTCTCGTTGCGATAGTCAAATAGC-CG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAAT-GCGCG
*
285145 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATGCGCG
* **
285185 TTGCGATAGTCAAATTCGCGTTGCGAT--T----TTTGCG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATGCGCG
* * * * * *
285219 TTGCGATAGTGATATTCGTGTTGCGATAGTCAAATTCGCA
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATGCGCG
* * * * *
285259 TTGCGAT--T----TTTGAGTTTCGATAATCAAATTCGCG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATGCGCG
* *
285293 TTGCGATAGTCAAATTCGCGTTGCGATATTCAAATG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATG
285329 AATGTGTAAT
Statistics
Matches: 176, Mismatches: 22, Indels: 40
0.74 0.09 0.17
Matches are distributed among these distances:
34 85 0.48
35 1 0.01
36 3 0.02
38 3 0.02
39 1 0.01
40 83 0.47
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (40 bp):
TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATGCGCG
Found at i:285220 original size:54 final size:54
Alignment explanation
Indices: 285162--285319 Score: 253
Period size: 54 Copynumber: 2.9 Consensus size: 54
285152 AATCAAATTC
285162 GCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
* * * *
285216 GCGTTGCGATAGTGATATTCGTGTTGCGATAGTCAAATTCGCATTGCGATTTTT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
* * *
285270 GAGTTTCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
285320 ATTCAAATGA
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 93 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.35
Consensus pattern (54 bp):
GCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
Found at i:285242 original size:94 final size:94
Alignment explanation
Indices: 285069--285265 Score: 281
Period size: 94 Copynumber: 2.1 Consensus size: 94
285059 GTGAATTTCT
*
285069 CATTGCGATAGTTAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAG
1 CATTGCGATAGTCAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAG
285134 TCAAATAGCCGTTGCGATAATCAAATTCG
66 TCAAATAGCCGTTGCGATAATCAAATTCG
* * *
285163 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGCGTTGCGATA
1 CATTGCGATAGTCAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT-CGTTGCGATA
* * * * *
285227 GTGATAT-TCGTGTTGCGATAGTCAAATTCG
65 GTCAAATAGC-CGTTGCGATAATCAAATTCG
285257 CATTGCGAT
1 CATTGCGAT
285266 TTTTGAGTTT
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
93 2 0.02
94 89 0.98
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (94 bp):
CATTGCGATAGTCAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAG
TCAAATAGCCGTTGCGATAATCAAATTCG
Found at i:285294 original size:74 final size:72
Alignment explanation
Indices: 285071--285327 Score: 239
Period size: 74 Copynumber: 3.5 Consensus size: 72
285061 GAATTTCTCA
* * * * *
285071 TTGCGATAGTTAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTC
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TAGTTTCGATA-TC
285136 AAA-TAGCCG
64 AAATTAG-CG
* ** * ** *
285145 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGT-TGC
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTAGTTTCG-ATAT-C
** *
285209 GATTTTTGCG
64 -AAATTAGCG
* * * *
285219 TTGCGATAGTGATATTCGTGTTGCGATAGTCAAATTCGCATTGCGATTTTTGAGTTTCGATAATC
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT-AGTTTCGAT-ATC
*
285284 AAATTCGCG
64 AAATTAGCG
*
285293 TTGCGATAGTCAAATTCGCGTTGCGATATTCAAAT
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAT
285328 GAATGTGTAA
Statistics
Matches: 143, Mismatches: 33, Indels: 14
0.75 0.17 0.07
Matches are distributed among these distances:
72 1 0.01
73 4 0.03
74 129 0.90
75 8 0.06
76 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (72 bp):
TTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTAGTTTCGATATCAA
ATTAGCG
Found at i:285556 original size:140 final size:140
Alignment explanation
Indices: 285299--285567 Score: 502
Period size: 140 Copynumber: 1.9 Consensus size: 140
285289 CGCGTTGCGA
*
285299 TAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCAT
1 TAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCAT
285364 AGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAA
66 AGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAA
285429 ATACACATAT
131 ATACACATAT
* *
285439 TAGTTAAATTCGCGTTGCGATATTCTAATGAATGTGTAATAAGTGATAACAACTGAACAGATCAT
1 TAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCAT
*
285504 AGTAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 AGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
285568 TACAACGTTT
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 125 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (140 bp):
TAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCAT
AGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAA
ATACACATAT
Found at i:285650 original size:18 final size:18
Alignment explanation
Indices: 285627--285661 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
285617 AAGCCGGTTG
285627 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
285645 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
285662 GCCTATTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.06, G:0.23, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:288841 original size:20 final size:20
Alignment explanation
Indices: 288795--288841 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
288785 AAATTCAGTG
* *
288795 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
288815 TTGCGATAGTCAGAATCGCA
1 TTGCGATAGTCAGAATCGCA
288835 TTGCGAT
1 TTGCGAT
288842 TTACATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:288859 original size:40 final size:40
Alignment explanation
Indices: 288810--288906 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 40
288800 ACAGTCAGAA
*
288810 TCGCGTTGCGATAGT-CAGAATCGCATTGCGATTTACATAT
1 TCGCATTGCGAT-GTACAGAATCGCATTGCGATTTACATAT
* * * *
288850 TCGCATTGCGATTTACATATTCGGATTGCGATTTACATAT
1 TCGCATTGCGATGTACAGAATCGCATTGCGATTTACATAT
* *
288890 TCGCATTACGATTTACA
1 TCGCATTGCGATGTACA
288907 TATTCGAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
39 1 0.02
40 49 0.98
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (40 bp):
TCGCATTGCGATGTACAGAATCGCATTGCGATTTACATAT
Found at i:288907 original size:40 final size:40
Alignment explanation
Indices: 288834--288921 Score: 149
Period size: 40 Copynumber: 2.2 Consensus size: 40
288824 TCAGAATCGC
* *
288834 ATTGCGATTTACATATTCGCATTGCGATTTACATATTCGG
1 ATTGCGATTTACATATTCGCATTACGATTTACATATTCGA
288874 ATTGCGATTTACATATTCGCATTACGATTTACATATTCGA
1 ATTGCGATTTACATATTCGCATTACGATTTACATATTCGA
*
288914 ATCGCGAT
1 ATTGCGAT
288922 AGTCGGAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (40 bp):
ATTGCGATTTACATATTCGCATTACGATTTACATATTCGA
Found at i:288921 original size:20 final size:20
Alignment explanation
Indices: 288830--288912 Score: 148
Period size: 20 Copynumber: 4.2 Consensus size: 20
288820 ATAGTCAGAA
288830 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
288850 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
288870 TCGGATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
288890 TCGCATTACGATTTACATAT
1 TCGCATTGCGATTTACATAT
288910 TCG
1 TCG
288913 AATCGCGATA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:289298 original size:2 final size:2
Alignment explanation
Indices: 289291--289408 Score: 236
Period size: 2 Copynumber: 59.0 Consensus size: 2
289281 CAAACTCCCT
289291 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
289333 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
289375 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
289409 CTCCTAATTC
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 116 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:289485 original size:2 final size:2
Alignment explanation
Indices: 289478--289515 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
289468 TGATCTATTT
289478 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
289516 CTCCTAATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:289495 original size:107 final size:107
Alignment explanation
Indices: 289371--289585 Score: 430
Period size: 107 Copynumber: 2.0 Consensus size: 107
289361 TCTCTCTCTC
289371 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCTCCTAATTCCTATTGAGGTAAAGAAT
1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCTCCTAATTCCTATTGAGGTAAAGAAT
289436 TTAATTCTAGCTAGTGTTTTCATGTAATCACTTGATCTATTT
66 TTAATTCTAGCTAGTGTTTTCATGTAATCACTTGATCTATTT
289478 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCTCCTAATTCCTATTGAGGTAAAGAAT
1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCTCCTAATTCCTATTGAGGTAAAGAAT
289543 TTAATTCTAGCTAGTGTTTTCATGTAATCACTTGATCTATTT
66 TTAATTCTAGCTAGTGTTTTCATGTAATCACTTGATCTATTT
289585 T
1 T
289586 TCAAACGACC
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 108 1.00
ACGTcount: A:0.18, C:0.28, G:0.08, T:0.46
Consensus pattern (107 bp):
TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCTCCTAATTCCTATTGAGGTAAAGAAT
TTAATTCTAGCTAGTGTTTTCATGTAATCACTTGATCTATTT
Found at i:290804 original size:32 final size:31
Alignment explanation
Indices: 290759--290858 Score: 103
Period size: 32 Copynumber: 3.2 Consensus size: 31
290749 ATTGAAATTG
* *
290759 AAAA-CAATCCGAACTGAAATTAACCCAAATC
1 AAAAGCAATTCGAACCGAAATTAACCCAAA-C
* *
290790 AAAAGCAATTCGAACCGAAATTAATCCGAAC
1 AAAAGCAATTCGAACCGAAATTAACCCAAAC
* * *
290821 TTAAAGCAACTCGAACCAAAATTAACCCAAACC
1 -AAAAGCAATTCGAACCGAAATTAACCCAAA-C
290854 AAAAG
1 AAAAG
290859 AAACCCGAAC
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
31 5 0.09
32 50 0.89
33 1 0.02
ACGTcount: A:0.51, C:0.25, G:0.09, T:0.15
Consensus pattern (31 bp):
AAAAGCAATTCGAACCGAAATTAACCCAAAC
Found at i:290853 original size:16 final size:16
Alignment explanation
Indices: 290834--290872 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
290824 AAGCAACTCG
**
290834 AACCAAAATTAACCCA
1 AACCAAAAGAAACCCA
*
290850 AACCAAAAGAAACCCG
1 AACCAAAAGAAACCCA
290866 AACCAAA
1 AACCAAA
290873 TTTTAACCCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.59, C:0.31, G:0.05, T:0.05
Consensus pattern (16 bp):
AACCAAAAGAAACCCA
Found at i:290868 original size:32 final size:32
Alignment explanation
Indices: 290775--290881 Score: 115
Period size: 32 Copynumber: 3.3 Consensus size: 32
290765 ATCCGAACTG
* * *
290775 AAATTAACCCAAATCAAAAGCAATTCGAACCG
1 AAATTAACCCAAACCAAAAGCAACTCGAACCA
* * **
290807 AAATTAATCCGAACTTAAAGCAACTCGAACCA
1 AAATTAACCCAAACCAAAAGCAACTCGAACCA
* *
290839 AAATTAACCCAAACCAAAAGAAACCCGAACCA
1 AAATTAACCCAAACCAAAAGCAACTCGAACCA
*
290871 AATTTTAACCC
1 AA-ATTAACCC
290882 GACCCGAAAA
Statistics
Matches: 60, Mismatches: 14, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
32 53 0.88
33 7 0.12
ACGTcount: A:0.50, C:0.27, G:0.07, T:0.16
Consensus pattern (32 bp):
AAATTAACCCAAACCAAAAGCAACTCGAACCA
Found at i:291177 original size:18 final size:18
Alignment explanation
Indices: 291150--291184 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
291140 CCACCTTTGA
*
291150 TAATACTTTAATGATTTC
1 TAATAATTTAATGATTTC
291168 TAATAATTTAATGATTT
1 TAATAATTTAATGATTT
291185 AATATCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (18 bp):
TAATAATTTAATGATTTC
Found at i:293878 original size:5 final size:5
Alignment explanation
Indices: 293871--293912 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
293861 CGCCGTCCGT
* * *
293871 CTCGT CTCGG CTCGG CTCGG CTCGG CACGG CACGG CTCGG CT
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CT
293913 TGGCGTCGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.05, C:0.40, G:0.36, T:0.19
Consensus pattern (5 bp):
CTCGG
Found at i:295027 original size:54 final size:53
Alignment explanation
Indices: 294921--295363 Score: 165
Period size: 54 Copynumber: 8.5 Consensus size: 53
294911 ATAGGAACAC
* * *
294921 AAATTTCTAA-GATCAAGTAATCTCTAGTGTTCCCTTGTCATAGAGGAGTAGAGCA
1 AAATTT-TAAGGA-CAAGTAAGCTCTAGTGTT-CATTTTCATAGAGGAGTAGAGCA
* * * * *
294976 AACTTTTAAGGCCAATTAAGCTCTAGTGTTCATTTTACATAGAGGAATAGAGTA
1 AAATTTTAAGGACAAGTAAGCTCTAGTGTTCATTTT-CATAGAGGAGTAGAGCA
** * **
295030 AAATTTTAA-GATGAGTAAGTTCTAGCATTCATTTGTCATAGAGGAGTAGAGCA
1 AAATTTTAAGGACAAGTAAGCTCTAGTGTTCATTT-TCATAGAGGAGTAGAGCA
* * * *
295083 AATTTTTAA-GACTGAGTAAGCTCTA------A---GC--A-AGGAGTAGAGAA
1 AAATTTTAAGGAC-AAGTAAGCTCTAGTGTTCATTTTCATAGAGGAGTAGAGCA
* * * * * * *
295124 AATTTTTAA-GACCCAGTAAGATCTAGCGTTCCTTTGTTATGGAGGAGTAGAGCA
1 AAATTTTAAGGA-CAAGTAAGCTCTAGTGTTCATTT-TCATAGAGGAGTAGAGCA
* * * * ** * * * * *
295178 TATTTTTAA-GACTTAGTAAGTTCTAGCATTCCTTTGTAATGGAAGAGTAGAGTA
1 AAATTTTAAGGAC-AAGTAAGCTCTAGTGTTCATTT-TCATAGAGGAGTAGAGCA
* * * * * *
295232 AATTTTTAA-GACCGAGTAAGCTCTGGTGTTCCTTTATCATCGAGGAGCAGAGCA
1 AAATTTTAAGGA-CAAGTAAGCTCTAGTGTTCATTT-TCATAGAGGAGTAGAGCA
* * * * * *
295286 AATTTTTAA-GACTGAGTAAGCTCTAGTGCTCCTTTGTTATGGAGGAGTAGAGC-
1 AAATTTTAAGGAC-AAGTAAGCTCTAGTGTTCATTT-TCATAGAGGAGTAGAGCA
*
295339 AAATTTCTAA-GAC-AGTAAGTTCTAG
1 AAATTT-TAAGGACAAGTAAGCTCTAG
295364 CATTCCTTCA
Statistics
Matches: 309, Mismatches: 57, Indels: 47
0.75 0.14 0.11
Matches are distributed among these distances:
41 32 0.10
42 2 0.01
44 1 0.00
48 1 0.00
52 11 0.04
53 54 0.17
54 201 0.65
55 7 0.02
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (53 bp):
AAATTTTAAGGACAAGTAAGCTCTAGTGTTCATTTTCATAGAGGAGTAGAGCA
Found at i:295074 original size:53 final size:54
Alignment explanation
Indices: 294959--295107 Score: 167
Period size: 53 Copynumber: 2.8 Consensus size: 54
294949 GTTCCCTTGT
* * * ** * **
294959 CATAGAGGAGTAGAGCAAACTTTTAAGGCCAATTAAGCTCTAGTGTTCATTTTA
1 CATAGAGGAATAGAGCAAAATTTTAAGACTGAGTAAGCTCTAGCATTCATTTTA
* *
295013 CATAGAGGAATAGAGTAAAATTTTAAGA-TGAGTAAGTTCTAGCATTCATTTGT-
1 CATAGAGGAATAGAGCAAAATTTTAAGACTGAGTAAGCTCTAGCATTCATTT-TA
* *
295066 CATAGAGGAGTAGAGCAAATTTTTAAGACTGAGTAAGCTCTA
1 CATAGAGGAATAGAGCAAAATTTTAAGACTGAGTAAGCTCTA
295108 AGCAAGGAGT
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
53 42 0.53
54 37 0.47
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (54 bp):
CATAGAGGAATAGAGCAAAATTTTAAGACTGAGTAAGCTCTAGCATTCATTTTA
Found at i:295142 original size:41 final size:41
Alignment explanation
Indices: 295071--295148 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
295061 TTTGTCATAG
* ** *
295071 AGGAGTAGAGCAAATTTTTAAGACTGAGTAAGCTCTAAGCA
1 AGGAGTAGAGAAAATTTTTAAGACCCAGTAAGATCTAAGCA
295112 AGGAGTAGAGAAAATTTTTAAGACCCAGTAAGATCTA
1 AGGAGTAGAGAAAATTTTTAAGACCCAGTAAGATCTA
295149 GCGTTCCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24
Consensus pattern (41 bp):
AGGAGTAGAGAAAATTTTTAAGACCCAGTAAGATCTAAGCA
Found at i:295437 original size:54 final size:54
Alignment explanation
Indices: 295112--295654 Score: 458
Period size: 54 Copynumber: 10.2 Consensus size: 54
295102 GCTCTAAGCA
* * ** *
295112 AGGAGTAGAGAAAATTTTTAAGACCCAGTAAGATCTAGCGTTCCTTTGTTATGG
1 AGGAGTAGAGCAAATTTCTAAGACTGAGTAAGCTCTAGCGTTCCTTTGTTATGG
* * * * * *
295166 AGGAGTAGAGCATATTTTTAAGACTTAGTAAGTTCTAGCATTCCTTTGTAATGG
1 AGGAGTAGAGCAAATTTCTAAGACTGAGTAAGCTCTAGCGTTCCTTTGTTATGG
* * * * * * * * *
295220 AAGAGTAGAGTAAATTTTTAAGACCGAGTAAGCTCTGGTGTTCCTTTATCATCG
1 AGGAGTAGAGCAAATTTCTAAGACTGAGTAAGCTCTAGCGTTCCTTTGTTATGG
* * * *
295274 AGGAGCAGAGCAAATTTTTAAGACTGAGTAAGCTCTAGTGCTCCTTTGTTATGG
1 AGGAGTAGAGCAAATTTCTAAGACTGAGTAAGCTCTAGCGTTCCTTTGTTATGG
* * *
295328 AGGAGTAGAGCAAATTTCTAAGAC--AGTAAGTTCTAGCATTCC--T-TCATGG
1 AGGAGTAGAGCAAATTTCTAAGACTGAGTAAGCTCTAGCGTTCCTTTGTTATGG
* * * * *
295377 AGGAGTAAAGTAGATTTCTAAGATTGAGTAAGCTCCAGCGTTCCTTTGTTATGG
1 AGGAGTAGAGCAAATTTCTAAGACTGAGTAAGCTCTAGCGTTCCTTTGTTATGG
* * * * * * * *
295431 ATGAGTATAGCAAATTTATAGGATTGAGTAAGCTTTAGCGTTCCTTTGTCATGT
1 AGGAGTAGAGCAAATTTCTAAGACTGAGTAAGCTCTAGCGTTCCTTTGTTATGG
* * * * * *
295485 A-GAGTATAACATATTTCTATA-ACT-AGGTAAGCTCTAGCATTCATTTGTTTTGG
1 AGGAGTAGAGCAAATTTCTA-AGACTGA-GTAAGCTCTAGCGTTCCTTTGTTATGG
* * * *
295538 AGGAGTGGAGC-AGTTTCTAAGACTAAGTAAGCTCTAGCGTCCCTTTGTTATGG
1 AGGAGTAGAGCAAATTTCTAAGACTGAGTAAGCTCTAGCGTTCCTTTGTTATGG
** * * * * * *
295591 AGGAGTAGAAAAAAATTT-TAAGACTGAGCAAACTCTAGCATTCTTTTATTATGA
1 AGGAGTAG-AGCAAATTTCTAAGACTGAGTAAGCTCTAGCGTTCCTTTGTTATGG
*
295645 AGAAGTAGAG
1 AGGAGTAGAG
295655 TACATTATTC
Statistics
Matches: 390, Mismatches: 87, Indels: 25
0.78 0.17 0.05
Matches are distributed among these distances:
49 25 0.06
50 1 0.00
51 15 0.04
52 16 0.04
53 80 0.21
54 249 0.64
55 4 0.01
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (54 bp):
AGGAGTAGAGCAAATTTCTAAGACTGAGTAAGCTCTAGCGTTCCTTTGTTATGG
Found at i:297021 original size:11 final size:10
Alignment explanation
Indices: 296997--297038 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
296987 ATTATGGTCT
296997 TAATTTTT-A
1 TAATTTTTAA
297006 TAATTTGTTAA
1 TAATTT-TTAA
297017 TAATTTTTAA
1 TAATTTTTAA
297027 TAATTTATTAA
1 TAATTT-TTAA
297038 T
1 T
297039 TGATTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.20
10 12 0.40
11 12 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:298671 original size:6 final size:6
Alignment explanation
Indices: 298660--298685 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
298650 ATCGATTGGC
298660 GGTGGA GGTGGA GGTGGA GGTGGA GG
1 GGTGGA GGTGGA GGTGGA GGTGGA GG
298686 AGGCGGGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.69, T:0.15
Consensus pattern (6 bp):
GGTGGA
Found at i:310924 original size:33 final size:33
Alignment explanation
Indices: 310887--310951 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
310877 TGTGCTACCA
* *
310887 TGAGTAATATCGGTATTGTTGTGTATTTTTAAT
1 TGAGTAATATCAGTATTGTTGTCTATTTTTAAT
310920 TGAGTAATATCAGTATTGTTGTCTATTTTTAA
1 TGAGTAATATCAGTATTGTTGTCTATTTTTAA
310952 GCTTTTAGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.51
Consensus pattern (33 bp):
TGAGTAATATCAGTATTGTTGTCTATTTTTAAT
Found at i:312530 original size:20 final size:20
Alignment explanation
Indices: 312505--312545 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
312495 TGATCAAAAC
* *
312505 ATGAGTAATTTAAAAGTATA
1 ATGAGTAAATTAAAAGAATA
312525 ATGAGTAAATTAAAAGAATA
1 ATGAGTAAATTAAAAGAATA
312545 A
1 A
312546 AAAATACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (20 bp):
ATGAGTAAATTAAAAGAATA
Found at i:319016 original size:2 final size:2
Alignment explanation
Indices: 319009--319035 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
318999 AATCAAAGTA
319009 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
319036 AGTATGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:319134 original size:25 final size:26
Alignment explanation
Indices: 319086--319135 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
319076 ATGAAGCATA
**
319086 ATTTATATGATATGTTATAAGTTATT
1 ATTTATATGATATGAAATAAGTTATT
*
319112 ATTTATAT-ATATGAAATATGTTAT
1 ATTTATATGATATGAAATAAGTTAT
319136 GAAGCAATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (26 bp):
ATTTATATGATATGAAATAAGTTATT
Found at i:319218 original size:15 final size:15
Alignment explanation
Indices: 319198--319227 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
319188 GTGAATGATA
*
319198 TGATAAGAAGCTATG
1 TGATAAGAAGATATG
319213 TGATAAGAAGATATG
1 TGATAAGAAGATATG
319228 GGTTTATGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.03, G:0.27, T:0.27
Consensus pattern (15 bp):
TGATAAGAAGATATG
Found at i:319514 original size:30 final size:30
Alignment explanation
Indices: 319478--319534 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
319468 CATTGATAGT
*
319478 TTACCTATGTCCTTAGGGACATATGGACAG
1 TTACCTATGTCCTTAGGAACATATGGACAG
* *
319508 TTACCTATGTTCTTCGGAACATATGGA
1 TTACCTATGTCCTTAGGAACATATGGA
319535 TAGTGGTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (30 bp):
TTACCTATGTCCTTAGGAACATATGGACAG
Found at i:319569 original size:22 final size:23
Alignment explanation
Indices: 319519--319577 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
319509 TACCTATGTT
* *
319519 CTTCGGAACATATGGATAGTGGTC
1 CTTCGGGACATATGCATAG-GGTC
*
319543 ATTCGGGACATATGCATA-GGTC
1 CTTCGGGACATATGCATAGGGTC
319565 CTTCGGGACATAT
1 CTTCGGGACATAT
319578 TTCACATGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 16 0.52
24 15 0.48
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (23 bp):
CTTCGGGACATATGCATAGGGTC
Found at i:323837 original size:20 final size:21
Alignment explanation
Indices: 323796--323842 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
323786 CAGATTGTCT
*
323796 AGGGGGTACAGATTCCCTCCC
1 AGGGGGAACAGATTCCCTCCC
323817 AGGGGGAACAGATTCCC-CCC
1 AGGGGGAACAGATTCCCTCCC
323837 AGGGGG
1 AGGGGG
323843 TATTGATTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.21, C:0.30, G:0.36, T:0.13
Consensus pattern (21 bp):
AGGGGGAACAGATTCCCTCCC
Found at i:323850 original size:20 final size:20
Alignment explanation
Indices: 323796--323854 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
323786 CAGATTGTCT
323796 AGGGGGTACAGATTCCCTCCC
1 AGGGGGTACAGATTCCC-CCC
*
323817 AGGGGGAACAGATTCCCCCC
1 AGGGGGTACAGATTCCCCCC
**
323837 AGGGGGTATTGATTCCCC
1 AGGGGGTACAGATTCCCC
323855 GGGAACAGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.20, C:0.31, G:0.31, T:0.19
Consensus pattern (20 bp):
AGGGGGTACAGATTCCCCCC
Found at i:323867 original size:15 final size:15
Alignment explanation
Indices: 323847--323902 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
323837 AGGGGGTATT
323847 GATTCCCCGGGAACA
1 GATTCCCCGGGAACA
*
323862 GATTCCTCCAGGGGTATC-
1 GATTCC-CC--GGG-AACA
*
323880 GATTCCCCGGGTACA
1 GATTCCCCGGGAACA
323895 GATTCCCC
1 GATTCCCC
323903 CTGTATGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 1 0.03
15 17 0.52
16 2 0.06
17 2 0.06
18 9 0.27
19 2 0.06
ACGTcount: A:0.20, C:0.34, G:0.25, T:0.21
Consensus pattern (15 bp):
GATTCCCCGGGAACA
Found at i:323884 original size:33 final size:34
Alignment explanation
Indices: 323820--323903 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 34
323810 CCCTCCCAGG
*
323820 GGGAACAGATTCCCCCCAGGGGGTATTGATTCCCC
1 GGGAACAGATT-CCCCCAGGGGGTATCGATTCCCC
*
323855 GGGAACAGATTCCTCCA-GGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCAGGGGGTATCGATTCCCC
*
323888 GGGTACAGATTCCCCC
1 GGGAACAGATTCCCCC
323904 TGTATGGTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 29 0.64
34 5 0.11
35 11 0.24
ACGTcount: A:0.20, C:0.32, G:0.27, T:0.20
Consensus pattern (34 bp):
GGGAACAGATTCCCCCAGGGGGTATCGATTCCCC
Found at i:324040 original size:21 final size:21
Alignment explanation
Indices: 324016--324057 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
324006 ATTTGAATAT
**
324016 TATGAAGGGGTATTGATTCCC
1 TATGAAGGGGTACCGATTCCC
324037 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
324058 CCCATTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:324379 original size:34 final size:32
Alignment explanation
Indices: 324340--324409 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
324330 TTTTGTAAAG
*
324340 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
324374 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
324406 GGGA
1 GGGA
324410 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:325421 original size:3 final size:3
Alignment explanation
Indices: 325400--325440 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
325390 TGAAGAAAGG
* *
325400 GAA G-A GAA GAA AAA TAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
325441 TGAGGATGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:327441 original size:19 final size:19
Alignment explanation
Indices: 327388--327461 Score: 77
Period size: 20 Copynumber: 4.1 Consensus size: 19
327378 ATCAGATTGT
327388 CCAGGGGTACAGATTCCCC
1 CCAGGGGTACAGATTCCCC
* *
327407 CAAGGGGGAACAGATTCCCC
1 CCA-GGGGTACAGATTCCCC
327427 CCAGGGGTATC-GATT--CC
1 CCAGGGGTA-CAGATTCCCC
327444 CC--GGGTACAGATTCCCC
1 CCAGGGGTACAGATTCCCC
327461 C
1 C
327462 TGCATGGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
14 1 0.02
15 9 0.20
17 7 0.15
19 11 0.24
20 18 0.39
ACGTcount: A:0.22, C:0.35, G:0.27, T:0.16
Consensus pattern (19 bp):
CCAGGGGTACAGATTCCCC
Found at i:327601 original size:21 final size:21
Alignment explanation
Indices: 327575--327616 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
327565 ATTTGAATAT
*
327575 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
327596 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
327617 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:328528 original size:22 final size:22
Alignment explanation
Indices: 328503--328546 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
328493 TGTATGATAG
328503 AGATCTAT-GGAGCCATATGAAA
1 AGAT-TATAGGAGCCATATGAAA
**
328525 AGATTATAGGAGTTATATGAAA
1 AGATTATAGGAGCCATATGAAA
328547 TTGAATTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (22 bp):
AGATTATAGGAGCCATATGAAA
Found at i:328604 original size:2 final size:2
Alignment explanation
Indices: 328597--328621 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
328587 AATCAAAGTA
328597 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
328622 AGTATGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:328804 original size:15 final size:15
Alignment explanation
Indices: 328784--328813 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
328774 GTTAATGATA
*
328784 TGATAAGAAGCTATG
1 TGATAAGAAGATATG
328799 TGATAAGAAGATATG
1 TGATAAGAAGATATG
328814 AGTTTATGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.03, G:0.27, T:0.27
Consensus pattern (15 bp):
TGATAAGAAGATATG
Found at i:329099 original size:30 final size:30
Alignment explanation
Indices: 329031--329119 Score: 106
Period size: 30 Copynumber: 2.9 Consensus size: 30
329021 AGAGTCGAGG
* * * *
329031 GTTACCTATGTCTTTCGAGACATATGAATA
1 GTTACCTATGTCCTTCGGGACATATGGACA
*
329061 GTTTACCTATGTCCTTAGGGACATATGGACA
1 G-TTACCTATGTCCTTCGGGACATATGGACA
* *
329092 GTTACCTATGTTCTTCGGAACATATGGA
1 GTTACCTATGTCCTTCGGGACATATGGA
329120 TAGTGGTCCT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
30 25 0.50
31 25 0.50
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (30 bp):
GTTACCTATGTCCTTCGGGACATATGGACA
Found at i:329139 original size:24 final size:22
Alignment explanation
Indices: 329104--329162 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
329094 TACCTATGTT
* *
329104 CTTCGGAACATATGGATAGTGGTC
1 CTTCGGGACATATGCATA--GGTC
*
329128 CTTCGGGCCATATGCATAGGTC
1 CTTCGGGACATATGCATAGGTC
329150 CTTCGGGACATAT
1 CTTCGGGACATAT
329163 TTCACATGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 16 0.52
24 15 0.48
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (22 bp):
CTTCGGGACATATGCATAGGTC
Found at i:329961 original size:29 final size:28
Alignment explanation
Indices: 329909--329974 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 28
329899 TAATTTTCTC
*
329909 TTTATTTTTGTTTTAACTTTTAAT-TATT
1 TTTATTTTTGTCTTAACTTTTAATATA-T
*
329937 TTTATTTTTGTCTTAATTTATTAATATAT
1 TTTATTTTTGTCTTAACTT-TTAATATAT
329966 TTTATTTTT
1 TTTATTTTT
329975 ATTTTAATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 17 0.50
29 15 0.44
30 2 0.06
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (28 bp):
TTTATTTTTGTCTTAACTTTTAATATAT
Found at i:329981 original size:29 final size:29
Alignment explanation
Indices: 329909--330006 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 29
329899 TAATTTTCTC
* *
329909 TTTATTTTTGTTTTAACTT-TTAAT-TATT
1 TTTATTTTTATTTTAATTTATTAATATA-T
* *
329937 TTTATTTTTGTCTTAATTTATTAATATAT
1 TTTATTTTTATTTTAATTTATTAATATAT
* **
329966 TTTATTTTTATTTTAATGTAAAAAATATAT
1 TTTATTTTTATTTTAAT-TTATTAATATAT
*
329996 TTTATCTTTAT
1 TTTATTTTTAT
330007 AATCACTTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 17 0.29
29 21 0.36
30 21 0.36
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (29 bp):
TTTATTTTTATTTTAATTTATTAATATAT
Found at i:330154 original size:59 final size:59
Alignment explanation
Indices: 329962--330168 Score: 167
Period size: 59 Copynumber: 3.5 Consensus size: 59
329952 ATTTATTAAT
* * *
329962 ATATTTTATTTTTATTTT-AATGTAAAAA-ATAT-AT-TTTATCTTTATAATCACTTAAAA
1 ATATTTTATTCTTATTTTAAAT-TAAAAATATATAATATTTAT-TTTATATTTACTTAAAA
*** * * * * *
330019 ATATTTT-TAAATATCTTAACTT-GAAATATTTAAATATTTTATTATTA-ATTTAATATAAAACA
1 ATATTTTATTCTTATTTTAAATTAAAAATATAT-AATA-TTTATT-TTATATTTACT-T-AAA-A
* *
330081 TATATTTTACTCTTATTTTAAATTAAAAATGTATAATATTTATTTTATATTTACTTAAAA
1 -ATATTTTATTCTTATTTTAAATTAAAAATATATAATATTTATTTTATATTTACTTAAAA
330141 ATATTTTATTCTTATTTTAAATTAAAAA
1 ATATTTTATTCTTATTTTAAATTAAAAA
330169 AAATTTTAAA
Statistics
Matches: 115, Mismatches: 21, Indels: 26
0.71 0.13 0.16
Matches are distributed among these distances:
55 3 0.03
56 10 0.09
57 9 0.08
58 2 0.02
59 32 0.28
60 10 0.09
61 6 0.05
62 5 0.04
63 19 0.17
64 13 0.11
65 6 0.05
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.52
Consensus pattern (59 bp):
ATATTTTATTCTTATTTTAAATTAAAAATATATAATATTTATTTTATATTTACTTAAAA
Found at i:330165 original size:27 final size:25
Alignment explanation
Indices: 330115--330168 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
330105 AAAAATGTAT
*
330115 AATATTTATTTTATATTTACTTAAA
1 AATATTTATTTTATATTTAATTAAA
330140 AATATTTTATTCTTAT-TTTAAATTAAA
1 AATA-TTTATT-TTATATTT-AATTAAA
330167 AA
1 AA
330169 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 4 0.16
26 9 0.36
27 12 0.48
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
AATATTTATTTTATATTTAATTAAA
Found at i:330176 original size:17 final size:19
Alignment explanation
Indices: 330154--330197 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
330144 TTTTATTCTT
330154 ATTTTAAATTAA-AA-AAA
1 ATTTTAAATTAATAATAAA
330171 ATTTTAAATTAATAATAAA
1 ATTTTAAATTAATAATAAA
330190 ATATTTAA
1 AT-TTTAA
330198 TATATTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.50
18 2 0.08
19 5 0.21
20 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTTAAATTAATAATAAA
Found at i:330258 original size:2 final size:2
Alignment explanation
Indices: 330251--330279 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
330241 GATGATAAAG
330251 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
330280 CATTAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:330320 original size:30 final size:30
Alignment explanation
Indices: 330284--330350 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 30
330274 TATATACATT
*
330284 AAAATAAAAAATATTTAATAAATTAAGACA
1 AAAATAAAAAATATTTAATAAATTAAAACA
* *
330314 AAAAT-AAAAATATTTAATAAGTTAAAATA
1 AAAATAAAAAATATTTAATAAATTAAAACA
330343 AAAATAAA
1 AAAATAAA
330351 GATTATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 26 0.79
30 7 0.21
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (30 bp):
AAAATAAAAAATATTTAATAAATTAAAACA
Found at i:334702 original size:2 final size:2
Alignment explanation
Indices: 334695--334756 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
334685 TTCATATGTG
334695 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
334737 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
334757 CAGACAGACT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:335543 original size:22 final size:23
Alignment explanation
Indices: 335517--335565 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 23
335507 CTGAATATCA
335517 TCGGCAGCTATTTTCCTCCGG-G
1 TCGGCAGCTATTTTCCTCCGGAG
335539 TCGGCAGCTATTTTCCTCCGGAG
1 TCGGCAGCTATTTTCCTCCGGAG
335562 TCGG
1 TCGG
335566 AAACGACGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.10, C:0.31, G:0.29, T:0.31
Consensus pattern (23 bp):
TCGGCAGCTATTTTCCTCCGGAG
Found at i:341380 original size:24 final size:23
Alignment explanation
Indices: 341338--341383 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
341328 AGTTTAAAGA
*
341338 AATTTTAAGATTATTTTTAATTT
1 AATTTTAAGATTATATTTAATTT
*
341361 AATTTTCAAGCTTATATTTAATT
1 AATTTT-AAGATTATATTTAATT
341384 CAACCATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (23 bp):
AATTTTAAGATTATATTTAATTT
Found at i:343611 original size:25 final size:25
Alignment explanation
Indices: 343575--343636 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
343565 TATACTCGTC
*
343575 CATCTTCCAGAAGGCGCGCTGAGTA
1 CATCTTCTAGAAGGCGCGCTGAGTA
343600 CATCTTCTAGAAGGCGCGCTGAGTA
1 CATCTTCTAGAAGGCGCGCTGAGTA
*
343625 TATCTTCTAGAA
1 CATCTTCTAGAA
343637 ACCGCCGCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (25 bp):
CATCTTCTAGAAGGCGCGCTGAGTA
Found at i:349259 original size:13 final size:13
Alignment explanation
Indices: 349243--349287 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
349233 CTCAATGCGC
349243 GTCATAAATGTGA
1 GTCATAAATGTGA
* *
349256 GTCATAAATATGT
1 GTCATAAATGTGA
*
349269 GTCATAAATGTGC
1 GTCATAAATGTGA
349282 GTCATA
1 GTCATA
349288 GATTTATGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (13 bp):
GTCATAAATGTGA
Found at i:349260 original size:85 final size:85
Alignment explanation
Indices: 349107--349264 Score: 192
Period size: 85 Copynumber: 1.9 Consensus size: 85
349097 ACGGCACATG
* * * * * *
349107 AATGTATGTCATCTTTTTTAATGACGTGTGCTTCAATTACACGCAATGTAAGTCATACATGCGTG
1 AATGTATGTCATCTTTTTTAATGACGGGGGCTTCAATGACACGCAATGCAAGTCATAAATGCGAG
349172 TCATAAATTTATGACACGCA
66 TCATAAATTTATGACACGCA
* * * ** *
349192 AATGTGTGTCATCTTTATTT-ATGACGGGGGCTTCAATGACGCTCAATGCGCGTCATAAATGTGA
1 AATGTATGTCATCTTT-TTTAATGACGGGGGCTTCAATGACACGCAATGCAAGTCATAAATGCGA
349256 GTCATAAAT
65 GTCATAAAT
349265 ATGTGTCATA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
85 57 0.95
86 3 0.05
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (85 bp):
AATGTATGTCATCTTTTTTAATGACGGGGGCTTCAATGACACGCAATGCAAGTCATAAATGCGAG
TCATAAATTTATGACACGCA
Found at i:364197 original size:30 final size:32
Alignment explanation
Indices: 364163--364235 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 32
364153 ATAGTTTTTA
364163 TATTTTTTATT-AAT-ATAATTATATAAATAT
1 TATTTTTTATTAAATAATAATTATATAAATAT
* *
364193 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTTTATT-AAATAATAATTATATAAATAT
364226 TATTTATTTA
1 TATTT-TTTA
364236 AATTTATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 11 0.30
32 3 0.08
33 19 0.51
34 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (32 bp):
TATTTTTTATTAAATAATAATTATATAAATAT
Found at i:364219 original size:27 final size:30
Alignment explanation
Indices: 364163--364260 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
364153 ATAGTTTTTA
*
364163 TATTTTTTATTAATATAATTATATAAATAT
1 TATTTTTTATTAAAATAATTATATAAATAT
* *
364193 TATTTTTTATTAAAATAA-TATTTATATAAT
1 TATTTTTTATTAAAATAATTATATAAAT-AT
* * *
364223 TATTATTTATTTAAAT--TTAT-TAATTAAT
1 TATTTTTTATTAAAATAATTATATAAAT-AT
364251 TATTTTTTAT
1 TATTTTTTAT
364261 GCTAATTATA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
28 15 0.26
29 10 0.17
30 33 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TATTTTTTATTAAAATAATTATATAAATAT
Found at i:364242 original size:25 final size:24
Alignment explanation
Indices: 364212--364259 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
364202 TTAAAATAAT
364212 ATTTATATAATT-ATTATTTATTTAA
1 ATTTAT-TAATTAATTATTT-TTTAA
364237 ATTTATTAATTAATTATTTTTTA
1 ATTTATTAATTAATTATTTTTTA
364260 TGCTAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTATTAATTAATTATTTTTTAA
Found at i:364417 original size:17 final size:17
Alignment explanation
Indices: 364397--364435 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
364387 TATTATTTTT
* *
364397 AATTTAAATTTATTATG
1 AATTTAAATTAATTATA
*
364414 AATTTATATTAATTATA
1 AATTTAAATTAATTATA
364431 AATTT
1 AATTT
364436 TTATAATGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
AATTTAAATTAATTATA
Found at i:373112 original size:15 final size:16
Alignment explanation
Indices: 373092--373130 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
373082 GATTACTTCA
373092 GAATGATTAAG-CGTT
1 GAATGATTAAGACGTT
* *
373107 GAATGATTCAGATGTT
1 GAATGATTAAGACGTT
373123 GAATGATT
1 GAATGATT
373131 CAGAGGTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (16 bp):
GAATGATTAAGACGTT
Found at i:373125 original size:16 final size:16
Alignment explanation
Indices: 373104--373134 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
373094 ATGATTAAGC
373104 GTTGAATGATTCAGAT
1 GTTGAATGATTCAGAT
373120 GTTGAATGATTCAGA
1 GTTGAATGATTCAGA
373135 GGTTCTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (16 bp):
GTTGAATGATTCAGAT
Found at i:373581 original size:51 final size:51
Alignment explanation
Indices: 373522--373684 Score: 140
Period size: 51 Copynumber: 3.3 Consensus size: 51
373512 GATACAGTAA
373522 AGCGCGCCCCCTGAAACGCGCTATATGCTGAGTTG-GCGCCACGTGGGGTAT
1 AGCGCGCCCCCTGAAACGCGCTATATGCTGAG-TGAGCGCCACGTGGGGTAT
* * * *
373573 AGCGCGCCCCCT-ACACCACGCTATATGCTGACATGAGCGCAACGT-GGGTAT
1 AGCGCGCCCCCTGA-AACGCGCTATATGCTGA-GTGAGCGCCACGTGGGGTAT
* * * * * * * * *
373624 A--GCGCCCTCTGCATCGCGCTATACG-TGTGTGTGTGACACGTGGGATAT
1 AGCGCGCCCCCTGAAACGCGCTATATGCTGAGTGAGCGCCACGTGGGGTAT
373672 AGCGCGCCCCCTG
1 AGCGCGCCCCCTG
373685 CACCGTGCTA
Statistics
Matches: 88, Mismatches: 17, Indels: 15
0.73 0.14 0.12
Matches are distributed among these distances:
47 8 0.09
48 8 0.09
49 18 0.20
50 10 0.11
51 36 0.41
52 8 0.09
ACGTcount: A:0.18, C:0.31, G:0.30, T:0.20
Consensus pattern (51 bp):
AGCGCGCCCCCTGAAACGCGCTATATGCTGAGTGAGCGCCACGTGGGGTAT
Found at i:375252 original size:633 final size:633
Alignment explanation
Indices: 373644--375550 Score: 3589
Period size: 635 Copynumber: 3.0 Consensus size: 633
373634 GCATCGCGCT
373644 ATACGTGTGTGTGTGACACGTGGGATATAGCGCGCCCCCTGCACCGTGCTATACCACACAATTAT
1 ATACGTGTGTGTGTGACACGTGGGATATAGCGCGCCCCCTGCACCGTGCTATACCACACAATTAT
373709 ATATAACGCGCTATATCATACAATCAGAAAGTTCTTTACTTTTTCTTTTCGTTTGTTATCATCCA
66 ATATAACGCGCTATATCATACAATCAGAAAGTTCTTTACTTTTTCTTTTCGTTTGTTATCATCCA
373774 ATTGTATTTTAGATAATATTCTTTAACAATAATAGGATAAATCTCATAAATGGTACACAATTGCT
131 ATTGTATTTTAGATAATATTCTTTAACAATAATAGGATAAATCTCATAAATGGTACACAATTGCT
373839 ATTGGAATTGCAAATAATGAGGCGATTTTGCTTTTGTACTTTCTAACATTGTGTAATGGATTATG
196 ATTGGAATTGCAAATAATGAGGCGATTTTGCTTTTGTACTTTCTAACATTGTGTAATGGATTATG
373904 GTTTAGACTAGATTGCTAAGACACATTTTAAGATTAATTAATTTTTCAATGGCAGGTCATAAGAA
261 GTTTAGACTAGATTGCTAAGACACATTTTAAGATTAATTAATTTTTCAATGGCAGGTCATAAGAA
373969 TATATAACGCGTCATCTTGATCAGTCGTGATCATTTCAAATTCACCTTGCAAAAAAAACGAAAAT
326 TATATAACGCGTCATCTTGATCAGTCGTGATCATTTCAAATTCACCTTGCAAAAAAAACGAAAAT
*
374034 AATAGGCAAGCGATCGAAAACTACCAAAAACAAAAAGAAATGTCATAAAAACAAATATAAACATG
391 AACAGGCAAGCGATCGAAAACTACCAAAAACAAAAA-AAATGTCATAAAAACAAATATAAACATG
374099 TCACAAAGGCAAAGATAATTGTGTCTCAAAAATAAAATTATTTTTATTAAAAAACTAAAAAGAAA
455 TCACAAAGGCAAAGATAATTGTGTCTCAAAAATAAAATTATTTTTATTAAAAAACTAAAAAGAAA
*
374164 AAGAAAAACTAACAGTCGATAACTAACATTAAAATCGATGCCGTCGCGGATTAACCAAAATCAAA
520 AAGAAAAACTAACCGTCGATAACTAACATTAAAATCGATGCCGTCGCGGATTAACCAAAATCAAA
374229 AAAGAAAAAATTGATTTGATCTATAGAAAATAACACAAATTATAAAAAAA
585 AAAGAAAAAATTGATTTGATCTATAGAAAATAACACAAATTAT-AAAAAA
*
374279 ATACGTGTGTGTGTGACACGTGGGATATAGCGCGTCCCCTGCACCGTGCTATACCACACAATTAT
1 ATACGTGTGTGTGTGACACGTGGGATATAGCGCGCCCCCTGCACCGTGCTATACCACACAATTAT
*
374344 ATATAACGCGCTATATCATACAATCAGAAAGTTCTCTACTTTTTCTTTTCGTTTGTTATCATCCA
66 ATATAACGCGCTATATCATACAATCAGAAAGTTCTTTACTTTTTCTTTTCGTTTGTTATCATCCA
374409 ATTGTATTTTAGATAATATTCTTTAACAATAATAGGATAAATCTCATAAATGGTACACAATTGCT
131 ATTGTATTTTAGATAATATTCTTTAACAATAATAGGATAAATCTCATAAATGGTACACAATTGCT
374474 ATTGGAATTGCAAATAATGAGGCGATTTTGCTTTTGTACTTTCTAACATTGTGTAATGGATTATG
196 ATTGGAATTGCAAATAATGAGGCGATTTTGCTTTTGTACTTTCTAACATTGTGTAATGGATTATG
374539 GTTTAGACTAGATTGCTAAGACACATTTTAAGATTAATTAATTTTTCAATGGCAGGTCATAAGAA
261 GTTTAGACTAGATTGCTAAGACACATTTTAAGATTAATTAATTTTTCAATGGCAGGTCATAAGAA
374604 TATATAACGCGTCATCTTGATCAGTCGTGATCATTTCAAATTCACCTTGCAAAAAAAACGAAAAT
326 TATATAACGCGTCATCTTGATCAGTCGTGATCATTTCAAATTCACCTTGCAAAAAAAACGAAAAT
374669 AACAGGCAAGCGATCGAAAACTACCAAAAACAAAAAAAATGTCATAAAAACAAATATAAACATGT
391 AACAGGCAAGCGATCGAAAACTACCAAAAACAAAAAAAATGTCATAAAAACAAATATAAACATGT
374734 CACAAAGGCAAAGATAATTGTGTCTCAAAAATAAAATTATTTTTATTAAAAAACTAAAAAGAAAA
456 CACAAAGGCAAAGATAATTGTGTCTCAAAAATAAAATTATTTTTATTAAAAAACTAAAAAGAAAA
374799 AGAAAAACTAACCGTCGATAACTAACATTAAAATCGATGCCGTCGCGGATTAACCAAAATCAAAA
521 AGAAAAACTAACCGTCGATAACTAACATTAAAATCGATGCCGTCGCGGATTAACCAAAATCAAAA
374864 AAGAAAAAATTGATTTGATCTATAGAAAATAACACAAATTATAAAAAA
586 AAGAAAAAATTGATTTGATCTATAGAAAATAACACAAATTATAAAAAA
374912 ATACGTGTGTGTGTGACACGTGGGATATAGCGCGCCCCCTGCACCGTGCTATACCACACAATTAT
1 ATACGTGTGTGTGTGACACGTGGGATATAGCGCGCCCCCTGCACCGTGCTATACCACACAATTAT
374977 ATATAACGCGCTATATCATACAATCAGAAAGTTCTTTACTTTTTCTTTTCGTTTGTTATCATCCA
66 ATATAACGCGCTATATCATACAATCAGAAAGTTCTTTACTTTTTCTTTTCGTTTGTTATCATCCA
* *
375042 ATTGTATTTTAGATAATATTCTTTAACAATAATAAGATAAATCTCATAAATGGTACACAATTACT
131 ATTGTATTTTAGATAATATTCTTTAACAATAATAGGATAAATCTCATAAATGGTACACAATTGCT
375107 ATTGGAATTGCAAATAATGAGGCGATTTTGCTTTTGTACTTTCTAACATTGTGTAATGGATTATG
196 ATTGGAATTGCAAATAATGAGGCGATTTTGCTTTTGTACTTTCTAACATTGTGTAATGGATTATG
* * *
375172 GTTTAGACTATATTGCTAAGGCACATTTTAAGATTAATCAATTTTTCAATGGCAGGTCATAAGAA
261 GTTTAGACTAGATTGCTAAGACACATTTTAAGATTAATTAATTTTTCAATGGCAGGTCATAAGAA
* *
375237 TATATAACACGTCATCTTGATCAGTCGTGATCATTTCAAATTCACCTTGCAAAAAAAAAACAAAA
326 TATATAACGCGTCATCTTGATCAGTCGTGATCATTTCAAATTCACCTTGC--AAAAAAAACGAAA
375302 ATAACAGGCAAGCGATCGAAAACTACCAAAAACAAAAAAAAATGTCATAAAAACAAATATAAACA
389 ATAACAGGCAAGCGATCGAAAACTACCAAAAAC-AAAAAAAATGTCATAAAAACAAATATAAACA
* * * *
375367 TGTCACAAAGACAAAGATAAATGTGTCTCAAAAATAAAATTATTTTTATTGAAAAACTAAAAATA
453 TGTCACAAAGGCAAAGATAATTGTGTCTCAAAAATAAAATTATTTTTATTAAAAAACTAAAAAGA
* * *
375432 AAAAGAAAAACTAACCGTCGATAACTAACATTAAAATCGATGCCGCCGCAGATTAAACAAAATCA
518 AAAAGAAAAACTAACCGTCGATAACTAACATTAAAATCGATGCCGTCGCGGATTAACCAAAATCA
* *
375497 AAAAATAAAAAATTGATTTGATCTATAGAAAATGACACAAATTATAAAAAA
583 AAAAAGAAAAAATTGATTTGATCTATAGAAAATAACACAAATTATAAAAAA
375548 ATA
1 ATA
375551 ATATTTTCCT
Statistics
Matches: 1247, Mismatches: 22, Indels: 5
0.98 0.02 0.00
Matches are distributed among these distances:
633 373 0.30
634 200 0.16
635 468 0.38
636 206 0.17
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (633 bp):
ATACGTGTGTGTGTGACACGTGGGATATAGCGCGCCCCCTGCACCGTGCTATACCACACAATTAT
ATATAACGCGCTATATCATACAATCAGAAAGTTCTTTACTTTTTCTTTTCGTTTGTTATCATCCA
ATTGTATTTTAGATAATATTCTTTAACAATAATAGGATAAATCTCATAAATGGTACACAATTGCT
ATTGGAATTGCAAATAATGAGGCGATTTTGCTTTTGTACTTTCTAACATTGTGTAATGGATTATG
GTTTAGACTAGATTGCTAAGACACATTTTAAGATTAATTAATTTTTCAATGGCAGGTCATAAGAA
TATATAACGCGTCATCTTGATCAGTCGTGATCATTTCAAATTCACCTTGCAAAAAAAACGAAAAT
AACAGGCAAGCGATCGAAAACTACCAAAAACAAAAAAAATGTCATAAAAACAAATATAAACATGT
CACAAAGGCAAAGATAATTGTGTCTCAAAAATAAAATTATTTTTATTAAAAAACTAAAAAGAAAA
AGAAAAACTAACCGTCGATAACTAACATTAAAATCGATGCCGTCGCGGATTAACCAAAATCAAAA
AAGAAAAAATTGATTTGATCTATAGAAAATAACACAAATTATAAAAAA
Found at i:375393 original size:23 final size:23
Alignment explanation
Indices: 375328--375387 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
375318 CGAAAACTAC
*
375328 CAAAAACAAA-A-AAAAATGTCA
1 CAAAAACAAAGATAAACATGTCA
* *
375349 TAAAAACAAATATAAACATGTCA
1 CAAAAACAAAGATAAACATGTCA
*
375372 CAAAGACAAAGATAAA
1 CAAAAACAAAGATAAA
375388 TGTGTCTCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 9 0.28
22 1 0.03
23 22 0.69
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (23 bp):
CAAAAACAAAGATAAACATGTCA
Found at i:376114 original size:51 final size:49
Alignment explanation
Indices: 376014--376118 Score: 122
Period size: 51 Copynumber: 2.1 Consensus size: 49
376004 CACACACAAG
* * * **
376014 TATAGCGCGGTGCAGGGGGCGCTATAGCCACGTGACGCCCATGTCAGCA
1 TATAGCGCAGTGCAGGGGGCGCTATACCCACGTAACGCCCAACTCAGCA
*
376063 TATAGCGCAGTGCAGGGGGCGCGCTATACCCCACGTAACG-CTAACTCAGCA
1 TATAGCGCAGTGCA-GGGG-GCGCTATA-CCCACGTAACGCCCAACTCAGCA
376114 TATAG
1 TATAG
376119 TATGTTTCAG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
49 13 0.28
50 4 0.09
51 21 0.45
52 9 0.19
ACGTcount: A:0.24, C:0.29, G:0.30, T:0.17
Consensus pattern (49 bp):
TATAGCGCAGTGCAGGGGGCGCTATACCCACGTAACGCCCAACTCAGCA
Found at i:376196 original size:29 final size:29
Alignment explanation
Indices: 376164--376228 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
376154 TTTGATCGGG
*
376164 AAATATAGTTTAA-CAGATGTTAGATCAGA-
1 AAATATAGTATAATC-GATGTTAGATC-GAT
376193 AAATATAGTATAATCGATGTTAGATCGAT
1 AAATATAGTATAATCGATGTTAGATCGAT
376222 AAATATA
1 AAATATA
376229 CCGATCACCG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
28 2 0.06
29 30 0.91
30 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.32
Consensus pattern (29 bp):
AAATATAGTATAATCGATGTTAGATCGAT
Found at i:380150 original size:27 final size:29
Alignment explanation
Indices: 380091--380194 Score: 155
Period size: 29 Copynumber: 3.7 Consensus size: 29
380081 CAACGTAGGT
*
380091 CGCCATGCACGCCCGGCGTCCT-TATAGGT
1 CGCCATGCACGCCCGGCGTCCTATA-AGGA
380120 CGCCATGCACG-CC-GCGTCCTATAAGGA
1 CGCCATGCACGCCCGGCGTCCTATAAGGA
380147 CGCCATGCACGCCCGGCGTCCTATAAGGA
1 CGCCATGCACGCCCGGCGTCCTATAAGGA
380176 CGCCATGCAC-CCC-GCGTCC
1 CGCCATGCACGCCCGGCGTCC
380195 ATCATTATTT
Statistics
Matches: 71, Mismatches: 1, Indels: 8
0.89 0.01 0.10
Matches are distributed among these distances:
27 27 0.38
28 9 0.13
29 35 0.49
ACGTcount: A:0.17, C:0.41, G:0.26, T:0.15
Consensus pattern (29 bp):
CGCCATGCACGCCCGGCGTCCTATAAGGA
Found at i:380418 original size:29 final size:29
Alignment explanation
Indices: 380379--380449 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
380369 CCGGCGATCG
380379 CGACATGGTAGGTCGCCATGGAGTCCCGA
1 CGACATGGTAGGTCGCCATGGAGTCCCGA
*
380408 CGACATGGTAGGTCGCCATGGAGTCCCTA
1 CGACATGGTAGGTCGCCATGGAGTCCCGA
380437 CGACATGGTAGGT
1 CGACATGGTAGGT
380450 GGTAGGGTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.21, C:0.25, G:0.34, T:0.20
Consensus pattern (29 bp):
CGACATGGTAGGTCGCCATGGAGTCCCGA
Found at i:380460 original size:12 final size:12
Alignment explanation
Indices: 380443--380467 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
380433 CCTACGACAT
380443 GGTAGGTGGTAG
1 GGTAGGTGGTAG
380455 GGTAGGTGGTAG
1 GGTAGGTGGTAG
380467 G
1 G
380468 TCGCCATGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.60, T:0.24
Consensus pattern (12 bp):
GGTAGGTGGTAG
Found at i:380545 original size:35 final size:35
Alignment explanation
Indices: 380506--380573 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
380496 TCCTGCATCG
*
380506 CGACCCAGCTTTAACTGTAGCACTCATGCATGCAA
1 CGACCAAGCTTTAACTGTAGCACTCATGCATGCAA
*
380541 CGACCAAGCTTTAACTGTATCACTCATGCATGC
1 CGACCAAGCTTTAACTGTAGCACTCATGCATGC
380574 GTTGCATCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (35 bp):
CGACCAAGCTTTAACTGTAGCACTCATGCATGCAA
Found at i:381039 original size:20 final size:20
Alignment explanation
Indices: 380993--381039 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
380983 ACTAAAATCT
380993 AGTTAATTAGTTGTTAGTATA
1 AGTT-ATTAGTTGTTAGTATA
* *
381014 AATTATTAGTTGGTT-GTTTA
1 AGTTATTAGTT-GTTAGTATA
381034 AGTTAT
1 AGTTAT
381040 ATTATATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (20 bp):
AGTTATTAGTTGTTAGTATA
Found at i:381440 original size:14 final size:14
Alignment explanation
Indices: 381421--381447 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
381411 AGTAATTTAT
381421 TATTTTTTGTTGTC
1 TATTTTTTGTTGTC
381435 TATTTTTTGTTGT
1 TATTTTTTGTTGT
381448 TGTGTATGTG
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:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (14 bp):
TATTTTTTGTTGTC
Found at i:381447 original size:17 final size:17
Alignment explanation
Indices: 381418--381450 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
381408 GTGAGTAATT
381418 TATTATTTTTTGTTGTC
1 TATTATTTTTTGTTGTC
381435 TATT-TTTTGTTGTTGT
1 TATTATTTT-TTGTTGT
381451 GTATGTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.03, G:0.15, T:0.73
Consensus pattern (17 bp):
TATTATTTTTTGTTGTC
Found at i:381574 original size:17 final size:17
Alignment explanation
Indices: 381514--381577 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 17
381504 GCGAGATAAT
381514 TTTTGTTTAAAAAAAATA
1 TTTTGTTT-AAAAAAATA
* *
381532 TTGTGTTTAAAAATATTTA
1 TTTTGTTTAAAAA-A-ATA
*
381551 GTGTTGTTTAAAAAAATA
1 -TTTTGTTTAAAAAAATA
381569 TTTTGTTTA
1 TTTTGTTTA
381578 TTTATATTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
17 13 0.35
18 10 0.27
19 3 0.08
20 11 0.30
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (17 bp):
TTTTGTTTAAAAAAATA
Found at i:381581 original size:21 final size:22
Alignment explanation
Indices: 381540--381581 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
381530 TATTGTGTTT
*
381540 AAAAATATTTAGTGTTGTTTAA
1 AAAAATATTTAGTGTTATTTAA
*
381562 AAAAATATTTTGT-TTATTTA
1 AAAAATATTTAGTGTTATTTA
381582 TATTGTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (22 bp):
AAAAATATTTAGTGTTATTTAA
Found at i:381834 original size:26 final size:25
Alignment explanation
Indices: 381805--381869 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
381795 AAATCATATT
*
381805 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AATAAATATCAAATC
* *
381831 ATTAGATT-AATAATAATTATTAAATC
1 ATT--ATTAAATAATAAATATCAAATC
381857 ATTATT-AATAATA
1 ATTATTAAATAATA
381870 TTAGTAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 10 0.29
26 18 0.53
27 3 0.09
28 3 0.09
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTATTAAATAATAAATATCAAATC
Found at i:382961 original size:146 final size:147
Alignment explanation
Indices: 382697--382989 Score: 579
Period size: 146 Copynumber: 2.0 Consensus size: 147
382687 TGTGATGTCC
382697 ATGTGCAGAGTCCAACCAGAAAACCCTATACGCAAAGTGTGTAAAATATGGCCCAGAGTGCAAGT
1 ATGTGCAGAGTCCAACCAGAAAACCCTATACGCAAAGTGTGTAAAATATGGCCCAGAGTGCAAGT
382762 GGAAGATCAGAGTGTCAAAAAATCAAAGGCACGATGTTTGGGTCATCACGAGGTAC-ATGGTTCG
66 GGAAGATCAGAGTGTCAAAAAATCAAAGGCACGATGTTTGGGTCATCACGAGGTACAATGGTTCG
382826 CACACATGTTTGCGAAA
131 CACACATGTTTGCGAAA
382843 ATGTGCAGAGTCCAACCAGAAAACCCTATACGCAAAGTGTGTAAAATATGGCCCAGAGTGCAAGT
1 ATGTGCAGAGTCCAACCAGAAAACCCTATACGCAAAGTGTGTAAAATATGGCCCAGAGTGCAAGT
382908 GGAAGATCAGAGTGTCAAAAAATCAAAGGCACGATGTTTGGGTCATCACGAGGTACAATGGTTCG
66 GGAAGATCAGAGTGTCAAAAAATCAAAGGCACGATGTTTGGGTCATCACGAGGTACAATGGTTCG
382973 CACACATGTTTGCGAAA
131 CACACATGTTTGCGAAA
382990 CTCCATCGAA
Statistics
Matches: 146, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
146 121 0.83
147 25 0.17
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.20
Consensus pattern (147 bp):
ATGTGCAGAGTCCAACCAGAAAACCCTATACGCAAAGTGTGTAAAATATGGCCCAGAGTGCAAGT
GGAAGATCAGAGTGTCAAAAAATCAAAGGCACGATGTTTGGGTCATCACGAGGTACAATGGTTCG
CACACATGTTTGCGAAA
Found at i:384741 original size:12 final size:12
Alignment explanation
Indices: 384724--384924 Score: 103
Period size: 12 Copynumber: 16.5 Consensus size: 12
384714 TAATGATTTG
384724 AATAATCATTAT
1 AATAATCATTAT
* *
384736 AGTAATGATTTGAT
1 AATAATCA-TT-AT
384750 AATAATCATTAT
1 AATAATCATTAT
*
384762 AATAATGATTAGT
1 AATAATCATTA-T
384775 AATAATCATTAT
1 AATAATCATTAT
* *
384787 AAAAATGATT-T
1 AATAATCATTAT
*
384798 AATAATGATT-T
1 AATAATCATTAT
384809 -A-AAT-ATT-T
1 AATAATCATTAT
* * *
384817 AATGATTTGATGATT
1 AAT-A-ATCATTA-T
* *
384832 AGTAATGATTTGAT
1 AATAATCA-TT-AT
384846 AATAATCATTAT
1 AATAATCATTAT
* *
384858 AGTAATGATTTGAT
1 AATAATCA-TT-AT
384872 AATAATCATTAT
1 AATAATCATTAT
* *
384884 AATAATGATTTAG
1 AATAATCA-TTAT
384897 AATAATCATTAT
1 AATAATCATTAT
*
384909 AA-AATGATT-T
1 AATAATCATTAT
384919 AATAAT
1 AATAAT
384925 GATTTAAATA
Statistics
Matches: 148, Mismatches: 25, Indels: 33
0.72 0.12 0.16
Matches are distributed among these distances:
8 4 0.03
9 4 0.03
10 4 0.03
11 21 0.14
12 50 0.34
13 36 0.24
14 25 0.17
15 4 0.03
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (12 bp):
AATAATCATTAT
Found at i:384760 original size:26 final size:26
Alignment explanation
Indices: 384711--385120 Score: 243
Period size: 26 Copynumber: 17.0 Consensus size: 26
384701 TGATTTGATT
384711 TAGTAATGATTTG--AATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
384735 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
384761 TAATAATGATTAG-TAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
** *
384786 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
384808 TA--AAT-ATTTAATGATTTGATGA-T-
1 TAGTAATGATTTGAT-A-ATAATCATTA
384831 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
384857 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
384883 TAATAATGATTT-AGAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
384908 TA-AAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
384929 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
384953 TAGTAATGATTTGATAATAAT-A-T-
1 TAGTAATGATTTGATAATAATCATTA
384976 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
385002 TAATAATGA---G-TAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
385024 -A-AAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * *
385044 TA--AAT-ATTT-ATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
385067 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* * *
385093 TAATAATGATTTTTATAATAATTATTA
1 TAGTAATGA-TTTGATAATAATCATTA
385120 T
1 T
385121 GTTATATTTA
Statistics
Matches: 318, Mismatches: 32, Indels: 69
0.76 0.08 0.16
Matches are distributed among these distances:
19 3 0.01
20 20 0.06
21 15 0.05
22 26 0.08
23 49 0.15
24 39 0.12
25 52 0.16
26 90 0.28
27 24 0.08
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:384901 original size:122 final size:122
Alignment explanation
Indices: 384659--385120 Score: 756
Period size: 122 Copynumber: 3.9 Consensus size: 122
384649 AGGTATTTAT
384659 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGA-TT--TGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
384721 TTG--AATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTAG-AA
384777 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGA-TTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
384841 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGA-TTAGAA
384899 TAATCATTAT-AAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
*
384963 TTGATAATAAT-A-T-TAGTAATGATTTGATAATAATCATTATAATAATGAGT--AA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTAGAA
385015 TAATCA-T-TAAAAATGATTTAATAATGATTTAAATATTT-ATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* * *
385077 TTGATAATAATCATTATAATAATGATTTTTATAATAATTATTAT
66 TTGATAATAATCATTATAGTAATGA-TTTGATAATAATCATTAT
385121 GTTATATTTA
Statistics
Matches: 328, Mismatches: 4, Indels: 24
0.92 0.01 0.07
Matches are distributed among these distances:
114 36 0.11
115 31 0.09
116 9 0.03
117 8 0.02
118 62 0.19
119 37 0.11
120 15 0.05
121 46 0.14
122 80 0.24
123 4 0.01
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (122 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTAGAA
Found at i:385120 original size:12 final size:12
Alignment explanation
Indices: 385083--385182 Score: 61
Period size: 12 Copynumber: 8.9 Consensus size: 12
385073 TGATTTGATA
* *
385083 ATAATCATTATA
1 ATAATAATTATT
* *
385095 ATAATGATTTTT
1 ATAATAATTATT
385107 ATAATAATTATT
1 ATAATAATTATT
* *
385119 AT-GTTA-TATT
1 ATAATAATTATT
*
385129 -TAGTAATTATT
1 ATAATAATTATT
*
385140 -T-ATAATGATT
1 ATAATAATTATT
* *
385150 -TAATACTAATT
1 ATAATAATTATT
385161 -TAATAATTATT
1 ATAATAATTATT
385172 ATAATAATTAT
1 ATAATAATTAT
385183 AGAATACTAA
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
9 1 0.01
10 15 0.21
11 23 0.33
12 31 0.44
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (12 bp):
ATAATAATTATT
Found at i:387647 original size:31 final size:33
Alignment explanation
Indices: 387569--387647 Score: 105
Period size: 31 Copynumber: 2.5 Consensus size: 33
387559 ACCAAACCCT
*
387569 TAAAC-AACTAATAAA--ATTTTTTTATATAAC
1 TAAACTAACTAATAAACTATTTTTTCATATAAC
387599 TAAACTAACTAATAAACTATTTTTTCATATAA-
1 TAAACTAACTAATAAACTATTTTTTCATATAAC
*
387631 TATACT-ACTAATAAACT
1 TAAACTAACTAATAAACT
387648 TGCTAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
30 5 0.11
31 21 0.48
32 5 0.11
33 13 0.30
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (33 bp):
TAAACTAACTAATAAACTATTTTTTCATATAAC
Found at i:388188 original size:49 final size:49
Alignment explanation
Indices: 388133--388229 Score: 178
Period size: 50 Copynumber: 2.0 Consensus size: 49
388123 CAATAGCTGT
388133 AGGCATGCAGC-GGGAGCAGGAGCACGTGAAGTTATCTTGGCATGCATGC
1 AGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCTTGGC-TGCATGC
388182 AGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCTTGGCTGCATG
1 AGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCTTGGCTGCATG
388230 TGCATGTATG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 17 0.36
50 30 0.64
ACGTcount: A:0.24, C:0.20, G:0.38, T:0.19
Consensus pattern (49 bp):
AGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCTTGGCTGCATGC
Found at i:388306 original size:29 final size:29
Alignment explanation
Indices: 388264--388329 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
388254 GTGACGCCGG
**
388264 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCCAGACTACAT
*
388293 GGCGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCCAGACTACAT
388322 GGCGACCT
1 GGCGACCT
388330 CTCATGGCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.23, C:0.33, G:0.30, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCCAGACTACAT
Found at i:388353 original size:30 final size:32
Alignment explanation
Indices: 388316--388392 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 32
388306 GTCGCCCAGA
388316 CTGCATGGCGACCTCT-CA-TGGCTGGCTCCT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCCT
* *
388346 TTGCATGGCGACCTCTCCATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCCT
388378 CTGCATGGCGACCTC
1 CTGCATGGCGACCTC
388393 ACCTCGTATA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
30 15 0.36
31 2 0.05
32 25 0.60
ACGTcount: A:0.10, C:0.35, G:0.27, T:0.27
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCCT
Found at i:388525 original size:29 final size:29
Alignment explanation
Indices: 388483--388542 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
388473 CTCCCGTATG
388483 TCGCCTGAATTGCATGGCGTCCTACAAGA
1 TCGCCTGAATTGCATGGCGTCCTACAAGA
* *
388512 TCGCCTGGATTGCATGGCGTCCTACGAGA
1 TCGCCTGAATTGCATGGCGTCCTACAAGA
388541 TC
1 TC
388543 ACTGTAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.20, C:0.28, G:0.27, T:0.25
Consensus pattern (29 bp):
TCGCCTGAATTGCATGGCGTCCTACAAGA
Found at i:389269 original size:17 final size:17
Alignment explanation
Indices: 389249--389290 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
389239 ATAAAAAGTG
389249 AATAATAA-ATAAACAAA
1 AATAATAATATAAAC-AA
*
389266 AATAA-AATATTAACAA
1 AATAATAATATAAACAA
389282 AATAATAAT
1 AATAATAAT
389291 GAGACAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (17 bp):
AATAATAATATAAACAA
Found at i:391147 original size:29 final size:29
Alignment explanation
Indices: 391114--391187 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 29
391104 TTTAAAATAA
* *
391114 TTACCAGAATAGTACCAAAACCGAATTAT
1 TTACCAGAATAGCACCAAAACCAAATTAT
* * *
391143 TTACCAAAATAGCATCAAAATCAAATTAT
1 TTACCAGAATAGCACCAAAACCAAATTAT
391172 TTACCAGAATAGCACC
1 TTACCAGAATAGCACC
391188 GGTCAACGGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.46, C:0.22, G:0.08, T:0.24
Consensus pattern (29 bp):
TTACCAGAATAGCACCAAAACCAAATTAT
Found at i:397810 original size:29 final size:29
Alignment explanation
Indices: 397740--397810 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
397730 TTTAAAATAA
*
397740 TTACCAGAATAGAACCAAAACCGAATTAT
1 TTACCAGAATAGCACCAAAACCGAATTAT
*
397769 TTACCAGAATAGCACCAAAACTGAATTAT
1 TTACCAGAATAGCACCAAAACCGAATTAT
397798 TTACCAGAATAGC
1 TTACCAGAATAGC
397811 GCCGGTCAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (29 bp):
TTACCAGAATAGCACCAAAACCGAATTAT
Found at i:399310 original size:42 final size:42
Alignment explanation
Indices: 399197--399312 Score: 178
Period size: 42 Copynumber: 2.8 Consensus size: 42
399187 CCCGAATTCT
* *
399197 CGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTAGTTTTCCGGAAAATGTTTTCC
* * *
399239 GGTGTTTGTTTCATGTAATTTGTTTTCCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTAGTTTTCCGGAAAATGTTTTCC
*
399281 CGTGTTTGTTTTACGTAATTAGTTTTCCGGAA
1 CGTGTTTGTTTCACGTAATTAGTTTTCCGGAA
399313 TGTAATTCAT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.18, C:0.15, G:0.20, T:0.47
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTAGTTTTCCGGAAAATGTTTTCC
Found at i:399589 original size:29 final size:28
Alignment explanation
Indices: 399556--399625 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 28
399546 TAATCATTAT
399556 ATATAATAATAAGATATATTTT-TAT-TTTA
1 ATATAATAATAA-A-AT-TTTTATATATTTA
399585 ATATATATAATAAAATTTTTATATATTTA
1 ATATA-ATAATAAAATTTTTATATATTTA
399614 ATATGAATAATA
1 ATAT-AATAATA
399626 TTATTTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
27 4 0.11
28 5 0.14
29 20 0.54
30 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (28 bp):
ATATAATAATAAAATTTTTATATATTTA
Found at i:399602 original size:20 final size:20
Alignment explanation
Indices: 399579--399616 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
399569 ATATATTTTT
399579 ATTTTAATATATATAATAAA
1 ATTTTAATATATATAATAAA
* *
399599 ATTTTTATATATTTAATA
1 ATTTTAATATATATAATA
399617 TGAATAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTTAATATATATAATAAA
Found at i:399617 original size:25 final size:26
Alignment explanation
Indices: 399589--399647 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
399579 ATTTTAATAT
399589 ATATAATAAAATT-TTTATATATTTA
1 ATATAATAAAATTATTTATATATTTA
* *
399614 ATATGAATAATATTATTTATATGTTTA
1 ATAT-AATAAAATTATTTATATATTTA
399641 A-ATAATA
1 ATATAATA
399648 GTTTAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 8 0.27
26 10 0.33
27 12 0.40
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (26 bp):
ATATAATAAAATTATTTATATATTTA
Found at i:399767 original size:28 final size:28
Alignment explanation
Indices: 399721--399791 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 28
399711 TTAATAAATA
* *
399721 ATTAATAATT-TATAATATT-TTA-TTTC
1 ATTAATAATTATA-AAAATTATTATTTTT
399747 ATTAA-AA-TATACAAAATTATTATTTTT
1 ATTAATAATTATA-AAAATTATTATTTTT
399774 ATTAATAATTATAAAAAT
1 ATTAATAATTATAAAAAT
399792 AATATTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
24 1 0.03
25 9 0.24
26 8 0.22
27 8 0.22
28 7 0.19
29 4 0.11
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (28 bp):
ATTAATAATTATAAAAATTATTATTTTT
Found at i:399789 original size:27 final size:27
Alignment explanation
Indices: 399721--399798 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
399711 TTAATAAATA
*
399721 ATTAATAATTTATAATATT-TTA-TTTC
1 ATTAATAA-TTATAAAATTATTATTTTC
* *
399747 ATTAA-AATATACAAAATTATTATTTTT
1 ATTAATAAT-TATAAAATTATTATTTTC
* *
399774 ATTAATAATTATAAAAATAATATTT
1 ATTAATAATTATAAAATTATTATTT
399799 AATAATTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
24 1 0.02
25 9 0.21
26 8 0.19
27 21 0.50
28 3 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (27 bp):
ATTAATAATTATAAAATTATTATTTTC
Found at i:399799 original size:25 final size:27
Alignment explanation
Indices: 399771--399823 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
399761 AATTATTATT
*
399771 TTTATTAATAATT-ATA-AAAATAATA
1 TTTAATAATAATTAATATAAAATAATA
*
399796 TTTAATAATTATTAATATTAAAATAATA
1 TTTAATAATAATTAATA-TAAAATAATA
399824 ATATTAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 11 0.48
26 3 0.13
28 9 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TTTAATAATAATTAATATAAAATAATA
Found at i:401423 original size:21 final size:21
Alignment explanation
Indices: 401399--401442 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
401389 CATACATAAA
*
401399 ATAAAAATATTAAATCCAAAG
1 ATAAAAATATTAAACCCAAAG
401420 ATAAAAATATTAAACCCAAAG
1 ATAAAAATATTAAACCCAAAG
401441 AT
1 AT
401443 TCAAAGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.23
Consensus pattern (21 bp):
ATAAAAATATTAAACCCAAAG
Found at i:401718 original size:22 final size:23
Alignment explanation
Indices: 401705--401787 Score: 62
Period size: 23 Copynumber: 3.6 Consensus size: 23
401695 AATCATAAAG
*
401705 AAAGTTTCACAAAAGCATAGAAA
1 AAAGTGTCACAAAAGCATAGAAA
** * *
401728 AAAGTGTCACAAGTGTAGAGAAA
1 AAAGTGTCACAAAAGCATAGAAA
* *
401751 AAAGTG-CTACAAGAA-TAAAGAAA
1 AAAGTGTC-ACAA-AAGCATAGAAA
*
401774 AACGTGTCACAAAA
1 AAAGTGTCACAAAA
401788 ATATAAATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
22 3 0.06
23 44 0.92
24 1 0.02
ACGTcount: A:0.54, C:0.12, G:0.18, T:0.16
Consensus pattern (23 bp):
AAAGTGTCACAAAAGCATAGAAA
Done.