Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007967.1 Hibiscus syriacus cultivar Beakdansim tig00110402_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: 2476418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:172179 original size:21 final size:20
Alignment explanation
Indices: 172124--172179 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
172114 TTACATTATG
* *
172124 TTTTTATTGAATTTTATTCA
1 TTTTTATTTATTTTTATTCA
172144 TTTTTAATTCT-TTTTTATTGCA
1 TTTTT-ATT-TATTTTTATT-CA
172166 TTTTTATTTATTTT
1 TTTTTATTTATTTT
172180 AAAAAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 6 0.20
21 17 0.57
22 7 0.23
ACGTcount: A:0.20, C:0.05, G:0.04, T:0.71
Consensus pattern (20 bp):
TTTTTATTTATTTTTATTCA
Found at i:176278 original size:21 final size:21
Alignment explanation
Indices: 176252--176296 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
176242 ATTTCTGGGT
* *
176252 AAGGGGAATCGGTACCCATTC
1 AAGGGGAACCGATACCCATTC
*
176273 AAGGGGAACCGATACCCCTTC
1 AAGGGGAACCGATACCCATTC
176294 AAG
1 AAG
176297 CGAATATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AAGGGGAACCGATACCCATTC
Found at i:177228 original size:2 final size:2
Alignment explanation
Indices: 177221--177298 Score: 147
Period size: 2 Copynumber: 39.0 Consensus size: 2
177211 AATCTTGAGG
177221 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
*
177263 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
177299 GAAATGAAAT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:178081 original size:13 final size:13
Alignment explanation
Indices: 178063--178103 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
178053 TCTACGGGCA
178063 CTACGGTGCAATT
1 CTACGGTGCAATT
178076 CTACGG-GC-A--
1 CTACGGTGCAATT
178085 CTACGGTGCAATT
1 CTACGGTGCAATT
178098 CTACGG
1 CTACGG
178104 GCACTTCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.25
10 2 0.08
11 2 0.08
12 2 0.08
13 12 0.50
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:178124 original size:22 final size:22
Alignment explanation
Indices: 178051--178116 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
178041 TAGGGACATC
178051 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
178073 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTACGGTGCA
*
178095 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTACGGTGCA
178117 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.24
Consensus pattern (22 bp):
ATTCTACGGGCACTACGGTGCA
Found at i:189916 original size:21 final size:21
Alignment explanation
Indices: 189883--189922 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
189873 ATACTTCCTG
*
189883 CTCCTCCTCCCCCGCCTCCAC
1 CTCCACCTCCCCCGCCTCCAC
* *
189904 CTCCACCTTCCCCTCCTCC
1 CTCCACCTCCCCCGCCTCC
189923 TGCACCACCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.70, G:0.03, T:0.23
Consensus pattern (21 bp):
CTCCACCTCCCCCGCCTCCAC
Found at i:191266 original size:14 final size:14
Alignment explanation
Indices: 191249--191347 Score: 51
Period size: 14 Copynumber: 7.1 Consensus size: 14
191239 CTCAAATTCA
191249 AAATCTTAAACCCT
1 AAATCTTAAACCCT
*
191263 AAATCCT-AACCCT
1 AAATCTTAAACCCT
* * **
191276 AAAGCATAAATTCT
1 AAATCTTAAACCCT
* *
191290 AAAACTCAAAACCC-
1 AAATCT-TAAACCCT
***
191304 AAA-CTCTAAAATTT
1 AAATCT-TAAACCCT
191318 AAATCTTAAACCCT
1 AAATCTTAAACCCT
* *
191332 AAGTCTTAAACTCT
1 AAATCTTAAACCCT
191346 AA
1 AA
191348 CCCTCAAAGA
Statistics
Matches: 62, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
13 17 0.27
14 39 0.63
15 6 0.10
ACGTcount: A:0.46, C:0.25, G:0.02, T:0.26
Consensus pattern (14 bp):
AAATCTTAAACCCT
Found at i:191512 original size:2 final size:2
Alignment explanation
Indices: 191505--191543 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
191495 GATTATAACT
191505 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 T
191544 CCACTTGCAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:193617 original size:21 final size:21
Alignment explanation
Indices: 193517--193618 Score: 84
Period size: 21 Copynumber: 4.8 Consensus size: 21
193507 GTCAAGAGTC
*
193517 TTATGTGGTTC-TCCGGGACAA
1 TTATGTGG-TCATTCGGGACAA
193538 TTATGTGGTCATTCGGGACAA
1 TTATGTGGTCATTCGGGACAA
* * *
193559 ATATGTGG-CACTTCGGTATAAA
1 TTATGTGGTCA-TTCGGGA-CAA
* *
193581 CCTAAGTGGTCATTCGGGACAA
1 -TTATGTGGTCATTCGGGACAA
193603 TTATGTGG-CACTTCGG
1 TTATGTGGTCA-TTCGG
193619 TGCAAATTAC
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
20 6 0.09
21 41 0.63
22 4 0.06
23 12 0.18
24 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (21 bp):
TTATGTGGTCATTCGGGACAA
Found at i:199190 original size:2 final size:2
Alignment explanation
Indices: 199183--199226 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
199173 CATGTATGTA
199183 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
199225 AT
1 AT
199227 GTGTGATATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:200675 original size:18 final size:18
Alignment explanation
Indices: 200640--200675 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
200630 TCGAGGGATT
* *
200640 ATAGTGGTCTTTCGGGAC
1 ATAGTGGTCCTTCAGGAC
200658 ATAGTGGTCCTTCAGGAC
1 ATAGTGGTCCTTCAGGAC
200676 TTATATTCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (18 bp):
ATAGTGGTCCTTCAGGAC
Found at i:210536 original size:23 final size:23
Alignment explanation
Indices: 210510--210573 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
210500 AGCTCATATA
210510 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
210533 AATTGTACCGTAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
210556 AAATACACCGAAGTGCCA
1 AATTGCACCGAAGTGCCA
210574 TATAAGGTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:213524 original size:23 final size:23
Alignment explanation
Indices: 213461--213529 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
213451 CATTATTATA
213461 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * * *
213484 CGGTACTCCAGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
213507 TGGCACTTCGGTGTAATTATACG
1 TGGCACTACGGTGCAATTCTACG
213530 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.29
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:217134 original size:21 final size:21
Alignment explanation
Indices: 217092--217134 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
217082 TTTTTGGGCT
* *
217092 AGGGGAATCGATACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
217113 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
217134 A
1 A
217135 ACAAACCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:218736 original size:23 final size:23
Alignment explanation
Indices: 218709--218776 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
218699 ATTATTATAT
218709 GGCACTAT-GGTACAATTCTACGC
1 GGCACT-TCGGTACAATTCTACGC
* *
218732 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTACAATTCTACGC
* *
218755 GGCACTTCGGTGCAATTATACG
1 GGCACTTCGGTACAATTCTACG
218777 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 1 0.02
23 40 0.98
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTACAATTCTACGC
Found at i:220732 original size:21 final size:21
Alignment explanation
Indices: 220715--220784 Score: 131
Period size: 21 Copynumber: 3.3 Consensus size: 21
220705 GGGGGGTATT
220715 GATTCCCATTGAATGGGTACC
1 GATTCCCATTGAATGGGTACC
220736 GATTCCCATTGAATGGGTACC
1 GATTCCCATTGAATGGGTACC
*
220757 GATTCTCATTGAATGGGTACC
1 GATTCCCATTGAATGGGTACC
220778 GATTCCC
1 GATTCCC
220785 CTAGCCCAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (21 bp):
GATTCCCATTGAATGGGTACC
Found at i:224337 original size:165 final size:165
Alignment explanation
Indices: 224024--224354 Score: 540
Period size: 165 Copynumber: 2.0 Consensus size: 165
224014 TAATGTAGTT
** *
224024 TGACTGGTTTTATGACGTAGATTTTACCAATGTTTTTAGCCTTTTGGTTGCTTGTAACTTTTTCC
1 TGACTGGTTGGATGACGTAGATTTTACCAATGTTTTAAGCCTTTTGGTTGCTTGTAACTTTTTCC
*
224089 TGAAATTTGATTGTTCTACTATTTTACTTATGATTTTTCCTGAAATCTCGAAAGATTCCTAGCCA
66 TGAAATTTGATTGTTCTACTATTTTACTTATGATTTTTCCTGAAATCTCGAAAGATTACTAGCCA
*
224154 ATGCTTGATCATGGATGGAGAATATAGCTATTTCG
131 ATGCCTGATCATGGATGGAGAATATAGCTATTTCG
* * *
224189 TGACTGGTTGGATGATGTATATTTTACCACTGTTTTAAGCCTTTTGGTTGCTTGTAACTTTTTCC
1 TGACTGGTTGGATGACGTAGATTTTACCAATGTTTTAAGCCTTTTGGTTGCTTGTAACTTTTTCC
*
224254 TGAATTTTGATT-TTACTACTATTTTACTTATGATTTTTTCCTGAAATCTCGAAAGATTACTAGC
66 TGAAATTTGATTGTT-CTACTATTTTACTTATGA-TTTTTCCTGAAATCTCGAAAGATTACTAGC
*
224318 GAATGCCTGATCA-GGATGGAGAATATAGCTATTTCG
129 CAATGCCTGATCATGGATGGAGAATATAGCTATTTCG
224354 T
1 T
224355 ATTTTAACTA
Statistics
Matches: 154, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
164 2 0.01
165 112 0.73
166 40 0.26
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.44
Consensus pattern (165 bp):
TGACTGGTTGGATGACGTAGATTTTACCAATGTTTTAAGCCTTTTGGTTGCTTGTAACTTTTTCC
TGAAATTTGATTGTTCTACTATTTTACTTATGATTTTTCCTGAAATCTCGAAAGATTACTAGCCA
ATGCCTGATCATGGATGGAGAATATAGCTATTTCG
Found at i:228750 original size:275 final size:276
Alignment explanation
Indices: 228250--228778 Score: 801
Period size: 275 Copynumber: 1.9 Consensus size: 276
228240 GAAAATATTT
* * * *
228250 AAAAGTTTAGAAAATCTTTCATGAGGAAATGTTCTATGTCTGCATCTTGGCACTTCTCTGGGTGT
1 AAAAGCTTAGAAAACCTTTCATAAGGAAATGTTCTATGTCTGCATCTTAGCACTTCTCTGGGTGT
* *
228315 TTGCTTCTCTGGTGCAACTTTTGTTTTAATGTTCAAGTGTCTTTGCCTCTTGAGCATATATGATC
66 TTGCTTCTCTGGTGCAACTTTTGTTTTAATGTTCAAGTGTCTTTGCCCCTTGAGCATATATGACC
*
228380 AAATAATATAGATGTCTTGAAGCCTATTCATTGGTGGAACTGTATGCAGGGAATTAGTTCTTGGT
131 AAATAATATAGATGTCTTGAAGCCTATTCATTGGTGGAACTGTATGCAGGAAATTAGTTCTTGGT
* *
228445 TCTAGTTAATTTTGTGTCTCGCACTGATCATTGCATTCATGGGTTCAGAAGACGATAATTTTGTT
196 TCTAGTTAATTTTGTGTCTCGCAATGATCATTGCATTCATGGGTTCAGAAGAAGATAATTTTGTT
228510 GACTCAAAATGGTGAA
261 GACTCAAAATGGTGAA
* * * * *
228526 AAAAGCTTAGAAAACCTTTCATAAGG-AATCGTTGTATGTGTTCATCTTAGCACTTTTCTTGGTG
1 AAAAGCTTAGAAAACCTTTCATAAGGAAAT-GTTCTATGTCTGCATCTTAGCACTTCTCTGGGTG
* * * *
228590 TTTGCTTTTGTGGTGCAGCTTTTGTTTTAATGTTCAAGT-TTTTTGCCCCTTGAGCATATATGAC
65 TTTGCTTCTCTGGTGCAACTTTTGTTTTAATGTTCAAGTGTCTTTGCCCCTTGAGCATATATGAC
* * ** **
228654 CAATTAATATAGATGTGTTGAAGCCTATTTTTTGGTGGAGGTGTATGCAGGAAATTAGTTCTTGG
130 CAAATAATATAGATGTCTTGAAGCCTATTCATTGGTGGAACTGTATGCAGGAAATTAGTTCTTGG
* *
228719 TTCTAGTTAATTTTGTGTTTTGCAATGATCATTGCATTCATGGGTTCAGAAGAAGATAAT
195 TTCTAGTTAATTTTGTGTCTCGCAATGATCATTGCATTCATGGGTTCAGAAGAAGATAAT
228779 GTCTTTAACT
Statistics
Matches: 226, Mismatches: 26, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
275 139 0.62
276 87 0.38
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.40
Consensus pattern (276 bp):
AAAAGCTTAGAAAACCTTTCATAAGGAAATGTTCTATGTCTGCATCTTAGCACTTCTCTGGGTGT
TTGCTTCTCTGGTGCAACTTTTGTTTTAATGTTCAAGTGTCTTTGCCCCTTGAGCATATATGACC
AAATAATATAGATGTCTTGAAGCCTATTCATTGGTGGAACTGTATGCAGGAAATTAGTTCTTGGT
TCTAGTTAATTTTGTGTCTCGCAATGATCATTGCATTCATGGGTTCAGAAGAAGATAATTTTGTT
GACTCAAAATGGTGAA
Found at i:230647 original size:4 final size:4
Alignment explanation
Indices: 230640--230670 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
230630 TATCTGTTTG
230640 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
230671 GTTTTGGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:237093 original size:31 final size:29
Alignment explanation
Indices: 237058--237123 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
237048 GATTTTATGT
*
237058 TAGGGGAGACGAACTTGAACTTTTAAAATTC
1 TAGGGG-G-CGAACTTGAACTTATAAAATTC
* * *
237089 TAGGGGGTGAATTTGAACTTATAAAATTT
1 TAGGGGGCGAACTTGAACTTATAAAATTC
237118 TAGGGG
1 TAGGGG
237124 TGAAAATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 24 0.77
30 1 0.03
31 6 0.19
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.32
Consensus pattern (29 bp):
TAGGGGGCGAACTTGAACTTATAAAATTC
Found at i:237106 original size:29 final size:28
Alignment explanation
Indices: 237072--237127 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
237062 GGAGACGAAC
*
237072 TTGAACTTTTAAAATTCTAGGGGGTGAAT
1 TTGAACTTATAAAATTCTA-GGGGTGAAT
*
237101 TTGAACTTATAAAATTTTAGGGGTGAA
1 TTGAACTTATAAAATTCTAGGGGTGAA
237128 AATAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (28 bp):
TTGAACTTATAAAATTCTAGGGGTGAAT
Found at i:242451 original size:20 final size:20
Alignment explanation
Indices: 242426--242466 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
242416 TTAGTTCTTG
242426 TATTTTGGAGAACTTTGAGA
1 TATTTTGGAGAACTTTGAGA
242446 TATTTTGGAGAACTTTGAGA
1 TATTTTGGAGAACTTTGAGA
242466 T
1 T
242467 TTAGTCCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.41
Consensus pattern (20 bp):
TATTTTGGAGAACTTTGAGA
Found at i:244108 original size:2 final size:2
Alignment explanation
Indices: 244101--244125 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
244091 ATGACATCTA
244101 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
244126 GAGAGAGAGA
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:244130 original size:2 final size:2
Alignment explanation
Indices: 244125--244230 Score: 203
Period size: 2 Copynumber: 53.0 Consensus size: 2
244115 ATATATATAT
244125 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
244167 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
244209 AG AG AG AG AG AG AA AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG
244231 GCAATATTCG
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 102 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:245461 original size:21 final size:21
Alignment explanation
Indices: 245417--245461 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
245407 GATTTTTGGG
* * *
245417 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
245438 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
245459 CAA
1 CAA
245462 ACGAACCAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:247234 original size:103 final size:103
Alignment explanation
Indices: 247014--247226 Score: 390
Period size: 103 Copynumber: 2.1 Consensus size: 103
247004 GGGTCTACGC
247014 GGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
247079 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
*
247117 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
247182 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
247220 GGTCCTT
1 GGTCCTT
247227 ATGGACATTA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:247300 original size:23 final size:23
Alignment explanation
Indices: 247242--247294 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
247232 CATTATTATA
*
247242 TGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
* *
247265 CGGCACTACGGTGTAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
247288 TGGCACT
1 TGGCACT
247295 TTGGTGCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:252304 original size:103 final size:103
Alignment explanation
Indices: 252115--252329 Score: 376
Period size: 103 Copynumber: 2.1 Consensus size: 103
252105 GTCGAGGGTC
* *
252115 TATGCGGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
252180 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
252218 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
252283 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
252321 TATGTGGTC
1 TATGTGGTC
252330 CTTATGGACA
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCATTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:252406 original size:23 final size:23
Alignment explanation
Indices: 252348--252400 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
252338 CATTATTATA
*
252348 TGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
* *
252371 CGGCACTACGGTGTAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
252394 TGGCACT
1 TGGCACT
252401 TTGGTGCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:255139 original size:24 final size:23
Alignment explanation
Indices: 255096--255145 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
255086 ATATTTAATG
*
255096 TTTAATATTCTCGAACATGTTCA
1 TTTAATATTCTCGAACATGTGCA
*
255119 TTTATATATTCGTC-AATATGTGCA
1 TTTA-ATATTC-TCGAACATGTGCA
255143 TTT
1 TTT
255146 GGTGAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 17 0.74
25 2 0.09
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (23 bp):
TTTAATATTCTCGAACATGTGCA
Found at i:259632 original size:24 final size:24
Alignment explanation
Indices: 259600--259654 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
259590 GACTAAATAA
259600 ATAATTTATCATTTTTAATTATAT
1 ATAATTTATCATTTTTAATTATAT
259624 ATAATTTATCATTTTTAATTATAT
1 ATAATTTATCATTTTTAATTATAT
259648 ATAATTT
1 ATAATTT
259655 TATAGTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (24 bp):
ATAATTTATCATTTTTAATTATAT
Found at i:259663 original size:24 final size:24
Alignment explanation
Indices: 259600--259664 Score: 96
Period size: 24 Copynumber: 2.7 Consensus size: 24
259590 GACTAAATAA
*
259600 ATAATTTATCATTTTTAATTATAT
1 ATAATTTATCAGTTTTAATTATAT
*
259624 ATAATTTATCATTTTTAATTATAT
1 ATAATTTATCAGTTTTAATTATAT
259648 ATAATTTTAT-AGTTTTA
1 ATAA-TTTATCAGTTTTA
259665 GTCCTTTAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
24 34 0.87
25 5 0.13
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (24 bp):
ATAATTTATCAGTTTTAATTATAT
Found at i:260277 original size:13 final size:13
Alignment explanation
Indices: 260259--260296 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
260249 CATTTCACAT
*
260259 TTATTTTTTTAAA
1 TTATTTTTTAAAA
260272 TTATTTTTTAAAA
1 TTATTTTTTAAAA
*
260285 ATA-TTTTTAAAA
1 TTATTTTTTAAAA
260297 AACTTTAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATTTTTTAAAA
Found at i:270426 original size:31 final size:31
Alignment explanation
Indices: 270386--270454 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 31
270376 TTTTTTAAAA
270386 AAAATTATTATAAAATGTCTTTAAA-ATTTT
1 AAAATTATTATAAAATGTCTTTAAATATTTT
270416 AAAATATATTATAAAATGTCTTTAAATTATTTT
1 AAAAT-TATTATAAAATGTCTTTAAA-TATTTT
270449 AAAATT
1 AAAATT
270455 TTAAAATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
30 5 0.14
31 20 0.56
32 1 0.03
33 10 0.28
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (31 bp):
AAAATTATTATAAAATGTCTTTAAATATTTT
Found at i:270451 original size:21 final size:20
Alignment explanation
Indices: 270405--270478 Score: 82
Period size: 18 Copynumber: 3.8 Consensus size: 20
270395 ATAAAATGTC
270405 TTTAAAATTTTAAAATATAT
1 TTTAAAATTTTAAAATATAT
* *
270425 TATAAAATGTCTTTAAAT-TAT
1 TTTAAAAT-T-TTAAAATATAT
270446 TTTAAAATTTTAAAATA-A-
1 TTTAAAATTTTAAAATATAT
*
270464 TTTAAATTTTTAAAA
1 TTTAAAATTTTAAAA
270479 AGAAGTGAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
18 14 0.30
19 7 0.15
20 8 0.17
21 11 0.24
22 6 0.13
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (20 bp):
TTTAAAATTTTAAAATATAT
Found at i:273096 original size:12 final size:12
Alignment explanation
Indices: 273077--273109 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
273067 ATAAATAAAT
273077 AAAT-AAAAAGA
1 AAATGAAAAAGA
*
273088 AAATGAAAATGA
1 AAATGAAAAAGA
273100 AAATGAAAAA
1 AAATGAAAAA
273110 AATATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (12 bp):
AAATGAAAAAGA
Found at i:273121 original size:7 final size:7
Alignment explanation
Indices: 273111--273144 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
273101 AATGAAAAAA
273111 ATATAAT
1 ATATAAT
273118 ATATAAT
1 ATATAAT
*
273125 ACTATACT
1 A-TATAAT
273133 ATATAAT
1 ATATAAT
273140 ATATA
1 ATATA
273145 TAAATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (7 bp):
ATATAAT
Found at i:273167 original size:26 final size:26
Alignment explanation
Indices: 273138--273253 Score: 85
Period size: 26 Copynumber: 4.5 Consensus size: 26
273128 ATACTATATA
* * *
273138 ATATATATAAATATTTTTTTAAAACT
1 ATATATATATATATATTTTAAAAACT
273164 ATATA-ATATATA-ATTTTAAAAACT
1 ATATATATATATATATTTTAAAAACT
* * *
273188 ATATATTATATATATGTTTTCAAAATT
1 ATATA-TATATATATATTTTAAAAACT
* * * * * *
273215 TTATA-AAAAATTATATATTATATACT
1 ATATATATATA-TATATTTTAAAAACT
273241 ATATATATATATA
1 ATATATATATATA
273254 CTAAATAAAA
Statistics
Matches: 67, Mismatches: 18, Indels: 10
0.71 0.19 0.11
Matches are distributed among these distances:
24 15 0.22
25 9 0.13
26 27 0.40
27 16 0.24
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (26 bp):
ATATATATATATATATTTTAAAAACT
Found at i:273197 original size:24 final size:24
Alignment explanation
Indices: 273141--273199 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
273131 CTATATAATA
* *
273141 TATATAA-ATAT-TTTTTTAAAAC
1 TATATAATATATAATTTTAAAAAC
273163 TATATAATATATAATTTTAAAAAC
1 TATATAATATATAATTTTAAAAAC
*
273187 TATATATTATATA
1 TATATAATATATA
273200 TATGTTTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 7 0.22
23 4 0.12
24 21 0.66
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (24 bp):
TATATAATATATAATTTTAAAAAC
Found at i:277476 original size:26 final size:26
Alignment explanation
Indices: 277427--277478 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
277417 ATGATGAGTG
**
277427 ATTATCATATATTTCTTCATAAATAA
1 ATTATCATATATTTCACCATAAATAA
277453 ATTATCATATATTTTCACCA-AAATAA
1 ATTATCATATA-TTTCACCATAAATAA
277479 TAAATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.42
Consensus pattern (26 bp):
ATTATCATATATTTCACCATAAATAA
Found at i:277486 original size:4 final size:4
Alignment explanation
Indices: 277473--277507 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
277463 ATTTTCACCA
*
277473 AAAT -AAT AAAT AAAT AATT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
277508 TTTACTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:280706 original size:18 final size:19
Alignment explanation
Indices: 280669--280706 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
280659 ATTGTATTCG
* *
280669 ATTTTTTTTGTTTGTTTTA
1 ATTTCTTTTGTTTCTTTTA
280688 ATTTCTTTT-TTTCTTTTA
1 ATTTCTTTTGTTTCTTTTA
280706 A
1 A
280707 CATATTGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.76
Consensus pattern (19 bp):
ATTTCTTTTGTTTCTTTTA
Found at i:281798 original size:79 final size:79
Alignment explanation
Indices: 281703--281855 Score: 225
Period size: 79 Copynumber: 1.9 Consensus size: 79
281693 CATTGCTTTA
*
281703 AAGTGTGAACACACGAGCCACACCAATGGCTGGTGTTAAGACATTAATCTAGGATATATAATGCA
1 AAGTGTGAACACACGAGCCACACCAATGGCTGGAGTTAAGACATTAATCTAGGATATATAATGCA
281768 TGAATCTAGCAATG
66 TGAATCTAGCAATG
* ** * * * * *
281782 AAGTGTGAATACACGAGCCACATTAATGGCTGGAGTTAAGGCATTATTTTAGGCTGTATAATGCA
1 AAGTGTGAACACACGAGCCACACCAATGGCTGGAGTTAAGACATTAATCTAGGATATATAATGCA
281847 TGAATCTAG
66 TGAATCTAG
281856 GTGTATATTA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 65 1.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.27
Consensus pattern (79 bp):
AAGTGTGAACACACGAGCCACACCAATGGCTGGAGTTAAGACATTAATCTAGGATATATAATGCA
TGAATCTAGCAATG
Found at i:299365 original size:21 final size:21
Alignment explanation
Indices: 299339--299388 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
299329 GTTCTCGATG
299339 TTCTGCCCGACTTCCTTCGTC
1 TTCTGCCCGACTTCCTTCGTC
* *
299360 TTCTGCCCGGCTTCCTTGGTC
1 TTCTGCCCGACTTCCTTCGTC
299381 TTCTGCCC
1 TTCTGCCC
299389 TGCATACCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.02, C:0.42, G:0.18, T:0.38
Consensus pattern (21 bp):
TTCTGCCCGACTTCCTTCGTC
Found at i:300635 original size:9 final size:9
Alignment explanation
Indices: 300585--300635 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
300575 ATATTTAATT
*
300585 TTTTGTATA
1 TTTTATATA
*
300594 ATTTATATA
1 TTTTATATA
*
300603 TTTTTATTAAA
1 -TTTTA-TATA
300614 TTTTATA-A
1 TTTTATATA
300622 TTTTATATA
1 TTTTATATA
300631 TTTTA
1 TTTTA
300636 AACATCATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 8 0.23
9 15 0.43
10 9 0.26
11 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTATATA
Found at i:301496 original size:11 final size:11
Alignment explanation
Indices: 301470--301502 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
301460 CATTAACTTT
301470 TTAAATT-TTA
1 TTAAATTATTA
*
301480 TAAAATTATTA
1 TTAAATTATTA
301491 TTAAATTATTA
1 TTAAATTATTA
301502 T
1 T
301503 AAAACGACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTAAATTATTA
Found at i:301927 original size:19 final size:20
Alignment explanation
Indices: 301890--301927 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
301880 AAACAACTTG
*
301890 GGTCAAATGGGTCGAGTCAT
1 GGTCAAATGAGTCGAGTCAT
301910 GGTCAAATGAGT-GAGTCA
1 GGTCAAATGAGTCGAGTCA
301928 AATCAGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (20 bp):
GGTCAAATGAGTCGAGTCAT
Found at i:303703 original size:183 final size:183
Alignment explanation
Indices: 303395--304455 Score: 1978
Period size: 183 Copynumber: 5.8 Consensus size: 183
303385 TATTTTATAC
*
303395 AAATTATTTAATTTCACACTGCTAGAATTTTATAATTACGTACTCTTAAATTTTTAATATAATTT
1 AAATTATTTAATTTCACACTGCTAGAATTTTATAAGTACGTACTCTTAAATTTTTAATATAATTT
*
303460 CTTAAATTTATCCTCGTAACATAAATTCTAACGTCTGTCATCGCAATCAACCTATAAAAGGAGTA
66 CTTAAGTTTATCCTCGTAACATAAATTCTAACGTCTGTCATCGCAATCAACCTATAAAAGGAGTA
303525 TAAGGGTTACTATCATCCTACACACTGTCATCCTACCATCCCAAAGCAACCAT
131 TAAGGGTTACTATCATCCTACACACTGTCATCCTACCATCCCAAAGCAACCAT
303578 AAATTATTTAATTTCACACTGCTAGAATTTTATAAGTACGTACTCTTAAATTTTTAATATAATTT
1 AAATTATTTAATTTCACACTGCTAGAATTTTATAAGTACGTACTCTTAAATTTTTAATATAATTT
* *
303643 CTTAAGTTTTTCCTCGTAACATAAATTCTAACGTCTGTCATTGCAATCAACCTATAAAAGGAGTA
66 CTTAAGTTTATCCTCGTAACATAAATTCTAACGTCTGTCATCGCAATCAACCTATAAAAGGAGTA
303708 TAAGGGTTACTATCATCCTACACACTGTCATCCTACCATCCCAAAGCAACCAT
131 TAAGGGTTACTATCATCCTACACACTGTCATCCTACCATCCCAAAGCAACCAT
*
303761 AAATTATTTAATTTCACACTACTAGAATTTTATAAGTACGTACTCTTAAATTTTTAATATAATTT
1 AAATTATTTAATTTCACACTGCTAGAATTTTATAAGTACGTACTCTTAAATTTTTAATATAATTT
* *
303826 CTTAAGTTTTTCCTCGTAACATAAATTCTAACGTCTGTCATTGCAATCAACCTATAAAAGGAGTA
66 CTTAAGTTTATCCTCGTAACATAAATTCTAACGTCTGTCATCGCAATCAACCTATAAAAGGAGTA
303891 TAAGGGTTACTATCATCCTACACACTGTCATCCTACCATCCCAAAGCAACCAT
131 TAAGGGTTACTATCATCCTACACACTGTCATCCTACCATCCCAAAGCAACCAT
** *
303944 AAATTATTTAATTTCACACAACTAGAATTTTATAATTACGTACTCTTAAATTTTTAATATAATTT
1 AAATTATTTAATTTCACACTGCTAGAATTTTATAAGTACGTACTCTTAAATTTTTAATATAATTT
* *
304009 CTTAAGTTTATCCTCGTAACATAAATTTTAACGTTTGTCATCGCAATCAACCTATAAAAGGAGTA
66 CTTAAGTTTATCCTCGTAACATAAATTCTAACGTCTGTCATCGCAATCAACCTATAAAAGGAGTA
304074 TAAGGGTTACTATCATCCTACACACTGTCATCCTACCATCCCAAAGCAACCAT
131 TAAGGGTTACTATCATCCTACACACTGTCATCCTACCATCCCAAAGCAACCAT
304127 AAATTATTTAATTTCACACTGCTAGAATTTTATAAGTACGTACTCTTAAATTTTTAATATAATTT
1 AAATTATTTAATTTCACACTGCTAGAATTTTATAAGTACGTACTCTTAAATTTTTAATATAATTT
*
304192 CTTAAGTTTATCCTCGTAACATAAATTCTAACGTCTGTTATCGCAATCAACCTATAAAAGGAGTA
66 CTTAAGTTTATCCTCGTAACATAAATTCTAACGTCTGTCATCGCAATCAACCTATAAAAGGAGTA
*
304257 TAAGGGTTACTATCATCCTACGCACTGTCATCCTACCATCCCAAAGCAACCAT
131 TAAGGGTTACTATCATCCTACACACTGTCATCCTACCATCCCAAAGCAACCAT
304310 AAATTATTTAATTTCACACTGCTAGAATTTTATAAGTACGTACTCTTAAATTTTTAATATAATTT
1 AAATTATTTAATTTCACACTGCTAGAATTTTATAAGTACGTACTCTTAAATTTTTAATATAATTT
* *
304375 CTTAAGTTTTTCCTCGTAACATAAATTCTAACGTCTGTCATTGCAATCAACCTATAAAAGGAGTA
66 CTTAAGTTTATCCTCGTAACATAAATTCTAACGTCTGTCATCGCAATCAACCTATAAAAGGAGTA
304440 TAAGGGTTACTATCAT
131 TAAGGGTTACTATCAT
304456 GCATGGCCCT
Statistics
Matches: 857, Mismatches: 21, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
183 857 1.00
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (183 bp):
AAATTATTTAATTTCACACTGCTAGAATTTTATAAGTACGTACTCTTAAATTTTTAATATAATTT
CTTAAGTTTATCCTCGTAACATAAATTCTAACGTCTGTCATCGCAATCAACCTATAAAAGGAGTA
TAAGGGTTACTATCATCCTACACACTGTCATCCTACCATCCCAAAGCAACCAT
Found at i:308733 original size:21 final size:21
Alignment explanation
Indices: 308691--308736 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
308681 CGATAAAAAA
* * *
308691 TTTTATCTAAAATATTATTAT
1 TTTTATCTAAAACATCAATAT
308712 TTTTATCTAAAACATCAATAT
1 TTTTATCTAAAACATCAATAT
308733 TTTT
1 TTTT
308737 TAATATTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTTATCTAAAACATCAATAT
Found at i:309733 original size:34 final size:37
Alignment explanation
Indices: 309686--309787 Score: 140
Period size: 34 Copynumber: 2.8 Consensus size: 37
309676 TTTCGTCCTG
309686 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
* * *
309721 -TAGGATTTAAACTCCTAAAAAAAAGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
309756 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
309788 GTTCTACTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
33 1 0.02
34 26 0.46
35 3 0.05
37 25 0.45
38 1 0.02
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:310283 original size:13 final size:13
Alignment explanation
Indices: 310267--310293 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
310257 ATATTTTTAT
310267 TATTATATATATA
1 TATTATATATATA
310280 TATTATATATATA
1 TATTATATATATA
310293 T
1 T
310294 TCTTTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTATATATATA
Found at i:310366 original size:25 final size:24
Alignment explanation
Indices: 310338--310385 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
310328 ATATATAATA
310338 TTACTT-TACTATTTTTTTTCTTATC
1 TTACTTAT-CTATTTTTTTT-TTATC
*
310363 TTACTTATTTATTTTTTTTTTAT
1 TTACTTATCTATTTTTTTTTTAT
310386 TTTTTCCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 16 0.76
26 1 0.05
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (24 bp):
TTACTTATCTATTTTTTTTTTATC
Found at i:313882 original size:7 final size:7
Alignment explanation
Indices: 313870--313938 Score: 52
Period size: 8 Copynumber: 9.3 Consensus size: 7
313860 TCCAATCAAG
313870 AAGAAAA
1 AAGAAAA
313877 AAGAAAA
1 AAGAAAA
*
313884 TAAG-CAA
1 -AAGAAAA
*
313891 AA-AACA
1 AAGAAAA
313897 AAGAAAA
1 AAGAAAA
313904 AAGAGAAA
1 AAGA-AAA
313912 CAAGAACAA
1 -AAGAA-AA
313921 AAGGAAAA
1 AA-GAAAA
313929 AAGGAAAA
1 AA-GAAAA
313937 AA
1 AA
313939 CAAGAATCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
6 5 0.10
7 16 0.31
8 21 0.41
9 9 0.18
ACGTcount: A:0.77, C:0.06, G:0.16, T:0.01
Consensus pattern (7 bp):
AAGAAAA
Found at i:313927 original size:16 final size:17
Alignment explanation
Indices: 313892--313965 Score: 66
Period size: 16 Copynumber: 4.4 Consensus size: 17
313882 AATAAGCAAA
313892 AAACAAAGAAAAAAGAG
1 AAACAAAGAAAAAAGAG
313909 AAAC-AAGAACAAAAG-G
1 AAACAAAGAA-AAAAGAG
*
313925 AAA-AAAGGAAAAAACAAG
1 AAACAAA-GAAAAAA-GAG
* *
313943 AATCAAA-AAGAAAGAG
1 AAACAAAGAAAAAAGAG
313959 AAACAAA
1 AAACAAA
313966 AAGCACATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
16 23 0.50
17 17 0.37
18 3 0.07
19 3 0.07
ACGTcount: A:0.74, C:0.08, G:0.16, T:0.01
Consensus pattern (17 bp):
AAACAAAGAAAAAAGAG
Found at i:313930 original size:27 final size:27
Alignment explanation
Indices: 313863--313955 Score: 88
Period size: 27 Copynumber: 3.5 Consensus size: 27
313853 GCAAAGATCC
*
313863 AATCAAGAAGAAAAAAGAAAATAAGCAA-
1 AATCAAAAAGAAAAAAGAAAA-AA-CAAG
*
313891 AA--AACAAAGAAAAAAG-AGAAACAAG
1 AATCAA-AAAGAAAAAAGAAAAAACAAG
*
313916 AA-CAAAAGGAAAAAAGGAAAAAACAAG
1 AATCAAAAAGAAAAAA-GAAAAAACAAG
313943 AATCAAAAAGAAA
1 AATCAAAAAGAAA
313956 GAGAAACAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
24 3 0.06
25 13 0.24
26 7 0.13
27 20 0.37
28 11 0.20
ACGTcount: A:0.74, C:0.08, G:0.15, T:0.03
Consensus pattern (27 bp):
AATCAAAAAGAAAAAAGAAAAAACAAG
Found at i:314606 original size:22 final size:22
Alignment explanation
Indices: 314575--314629 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
314565 GCTATCCCAT
*
314575 CAAACATTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
314597 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
314619 CAAACCTTTGA
1 CAAACCTTTGA
314630 CCAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:315505 original size:36 final size:36
Alignment explanation
Indices: 315458--315716 Score: 246
Period size: 36 Copynumber: 7.3 Consensus size: 36
315448 ATTGAAAACA
*
315458 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
* *
315494 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAA-TAAATTTCGTCTCTCTTGAGACAG
*
315531 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
* * * *
315567 TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACA-G
* * *
315596 TTTTCTTTGAAATAAATTTCGTCTCCCTTGAGACAG
1 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
** * * * *
315632 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTTAGACAG
1 TTTCCCTT-GAAATAAATTTCGTCTCTCTTGAGACAG
* * * *
315669 TTTCTCTTAAAACAAATTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
315705 TTTCCCTTGAAA
1 TTTCCCTTGAAA
315717 CAAAATCTTT
Statistics
Matches: 180, Mismatches: 32, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.01
29 18 0.10
30 2 0.01
35 1 0.01
36 92 0.51
37 65 0.36
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
Found at i:315577 original size:73 final size:73
Alignment explanation
Indices: 315458--315727 Score: 306
Period size: 73 Copynumber: 3.8 Consensus size: 73
315448 ATTGAAAACA
*
315458 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCTCT
1 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCT
315523 TGAGACAG
66 TGAGACAG
* *
315531 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA-------TAT-T
1 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCT
*
315588 TGA-ATATG
66 TGAGACA-G
* * * ** * * *
315596 TTTTCTTTGAAATAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCT
*
315661 TTAGACAG
66 TGAGACAG
* * * *
315669 TTTCTCTTAAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTG
1 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT-TTTG
315728 AATTTATTTC
Statistics
Matches: 158, Mismatches: 28, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
64 2 0.01
65 49 0.31
66 2 0.01
72 2 0.01
73 97 0.61
74 6 0.04
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (73 bp):
TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCT
TGAGACAG
Found at i:315579 original size:138 final size:137
Alignment explanation
Indices: 315399--315783 Score: 491
Period size: 138 Copynumber: 2.8 Consensus size: 137
315389 GATTGCTTTT
* * * *
315399 TTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCC
1 TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAACATTGAATATATTTCCC
* * *
315464 TTGAAATAAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGAC
65 TTGAAATAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGAC
315529 AGTTTCCC
130 AGTTTCCC
* * * * * *
315537 TTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
1 TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACA-TTGAATATATTTCCC
* * * * *
315602 TTGAAATAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTTAGAC
65 TTGAAATAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGAC
*
315667 AGTTTCTC
130 AGTTTCCC
* * * *
315675 TTAAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCC
1 TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA-CATTGAATATATTTCCC
* * * * *
315740 CTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
65 TTGAAATAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACA
315784 CAAAATCTTC
Statistics
Matches: 208, Mismatches: 37, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
137 4 0.02
138 204 0.98
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (137 bp):
TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACATTGAATATATTTCCCT
TGAAATAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACA
GTTTCCC
Found at i:315606 original size:102 final size:102
Alignment explanation
Indices: 315500--315684 Score: 264
Period size: 102 Copynumber: 1.8 Consensus size: 102
315490 ATAGTTTCCC
* *
315500 TTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCTTGAGA
1 TTGAAA-AAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCTTGAGA
*
315564 CAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
65 CAGTTTCCCTTAAAACAAAATATTTGAATATGTTTTCT
* ** * * *
315602 TTGAAATAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTTAGAC
1 TTGAAAAAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCTTGAGAC
*
315667 AGTTTCTCTTAAAACAAA
66 AGTTTCCCTTAAAACAAA
315685 TTTCGTCTAT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
101 27 0.38
102 45 0.62
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (102 bp):
TTGAAAAAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCTTGAGAC
AGTTTCCCTTAAAACAAAATATTTGAATATGTTTTCT
Found at i:315764 original size:65 final size:65
Alignment explanation
Indices: 315676--315852 Score: 228
Period size: 65 Copynumber: 2.7 Consensus size: 65
315666 CAGTTTCTCT
* ** * **
315676 TAAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCC
1 TAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCC
*
315741 TAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCC
1 TAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCC
*
315806 CT
64 CC
* * *
315808 TAAAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 TAAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
315853 CAGATATCTT
Statistics
Matches: 97, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
65 33 0.34
66 6 0.06
67 31 0.32
68 27 0.28
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.36
Consensus pattern (65 bp):
TAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCC
Found at i:316689 original size:105 final size:106
Alignment explanation
Indices: 316492--316912 Score: 605
Period size: 105 Copynumber: 4.0 Consensus size: 106
316482 GTGGCACTCG
* * * *
316492 AGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCCCAATTT
316557 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC
* * *
316598 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCTAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCCCAATTT
* *
316662 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC
** * *
316703 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATCT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCCCAATTT
316767 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC-TC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC
** * * **
316807 GAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCCCGGTT
1 -AGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCCCAATT
* * * *
316872 CCAGAGCCAATTTCAACTTCACGACGGAGGATATTAGACTT
65 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTT
316913 GGAACAATGT
Statistics
Matches: 284, Mismatches: 28, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
104 1 0.00
105 193 0.68
106 89 0.31
107 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (106 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC
Found at i:317503 original size:34 final size:37
Alignment explanation
Indices: 317459--317560 Score: 167
Period size: 34 Copynumber: 2.8 Consensus size: 37
317449 TTTCGTCCTG
317459 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
317494 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
317529 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
317561 GTTATACTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
33 1 0.02
34 29 0.47
35 3 0.05
37 28 0.45
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:317544 original size:37 final size:36
Alignment explanation
Indices: 317457--317594 Score: 174
Period size: 37 Copynumber: 3.8 Consensus size: 36
317447 TTTTTCGTCC
317457 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAATT
317493 T--TAGGATTCAAACTCCTAAAAATAGGATA-ACATTT
1 TGCTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TT
*
317528 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * * *
317564 ATACTAAGATTTAAATTCCTAAAGATAGGAT
1 -TGCTAGGATTCAAACTCCTAAAAATAGGAT
317595 CCACAAGCAT
Statistics
Matches: 90, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 1 0.01
34 29 0.32
35 3 0.03
36 3 0.03
37 53 0.59
38 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (36 bp):
TGCTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:317988 original size:18 final size:17
Alignment explanation
Indices: 317949--317992 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
317939 ATTATATGGA
317949 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
317965 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
317983 TATTATTATT
1 TATTATTATT
317993 ATATGTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 8 0.33
18 13 0.54
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:318713 original size:2 final size:2
Alignment explanation
Indices: 318706--318748 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
318696 ATTCAAAACC
*
318706 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
318748 A
1 A
318749 GGTCTTTAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 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):
AT
Found at i:320120 original size:43 final size:43
Alignment explanation
Indices: 320067--320152 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
320057 CTCTGCAACA
320067 AGAGATCAATTGCATAATCCATCAAGCATTATAGTTTCTCACT
1 AGAGATCAATTGCATAATCCATCAAGCATTATAGTTTCTCACT
320110 AGAGATCAATTGCATAATCCATCAAGCATTATAGTTTCTCACT
1 AGAGATCAATTGCATAATCCATCAAGCATTATAGTTTCTCACT
320153 GTGAAGTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (43 bp):
AGAGATCAATTGCATAATCCATCAAGCATTATAGTTTCTCACT
Found at i:325635 original size:21 final size:21
Alignment explanation
Indices: 325611--325651 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
325601 ATTATAATGT
*
325611 TGATGTGATAATTTACGATAC
1 TGATATGATAATTTACGATAC
*
325632 TGATATTATAATTTACGATA
1 TGATATGATAATTTACGATA
325652 GATGACGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (21 bp):
TGATATGATAATTTACGATAC
Found at i:326213 original size:2 final size:2
Alignment explanation
Indices: 326206--326252 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
326196 TTACTCGTCC
326206 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
326248 AT AT A
1 AT AT A
326253 ATTTCTCACT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:328081 original size:332 final size:331
Alignment explanation
Indices: 327288--328264 Score: 1519
Period size: 330 Copynumber: 2.9 Consensus size: 331
327278 CTGTTAGAAC
* * * * * *
327288 TTAGAATGCAAACCAATTCGATTCTGCC-GGATGTTTGAATAGATATATCTTAGATTAGTGCTGA
1 TTAGAATGCAAACCGATTCTATTTTGCCAGCA-GCTTGAATAGATATATCTTAGATTAGTGCTCA
* * *
327352 GGAAAAGCATTGTTGGTCTGCTATAGTTTATATAGATTCTTTTGTTTTAAAGCTAATCTTGTGTG
65 GGAAAACCATTGTTGGTCTGCTATAGTGTATATAGATGCTTTTGTTTTAAAGCTAATCTTGTGTG
*
327417 TGTTTGATTACGGTGCATAGGAGAACCCTAAAGATTTTTGGTTGAAAACAAGCCCTTAAATAAAG
130 TGTTTGATTACGATGCATAGGAGAACCCTAAAGATTTTTGGTTGAAAACAAGCCCTTAAATAAAG
*
327482 TGTCGATATGTATCTTCGATTTAAAGCCAATCTTGTGTGCATGCATTTGTGTGAGTGATTATAAG
195 TGTCGATATGTATCTTCGATTTAAAGCCAATCTTGTGTGCATGCA-TTGTGTGAGTGATTATAAA
*
327547 CTTATAATGCTAAGAAATTGTATGCTCGACCTTTGATCCGAAATCTTATTTGTCTTTTATGAGAT
259 CTTATAATGCTAAGAAATTGTATGCTTGACCTTTGATCCGAAATCTTATTTGTCTTTTATGAGAT
327612 AAATAGTG
324 AAATAGTG
327620 TTAGAATGCAAACCGATTCTATTTTGCCAGCAGCTTGAATAGATATATCTTAGATTAGTGCTCAG
1 TTAGAATGCAAACCGATTCTATTTTGCCAGCAGCTTGAATAGATATATCTTAGATTAGTGCTCAG
327685 GAAAACCATTGTTGGTCTGCTATAGTGTATATAGATGCTTTTGTTTTAAAGCTAATCTTGTGTGT
66 GAAAACCATTGTTGGTCTGCTATAGTGTATATAGATGCTTTTGTTTTAAAGCTAATCTTGTGTGT
327750 GTTTGATTACGATGCATAGGAGAACCCTAAAGATTTTTGGTTGAAAACAAGCCCTTAAATAAAGT
131 GTTTGATTACGATGCATAGGAGAACCCTAAAGATTTTTGGTTGAAAACAAGCCCTTAAATAAAGT
*
327815 GTCGATATGTATCTTCGATTTAAAGCCAATCTTGTATGCATGCATT-TGTGAGTGATTATAAACT
196 GTCGATATGTATCTTCGATTTAAAGCCAATCTTGTGTGCATGCATTGTGTGAGTGATTATAAACT
*
327879 TATAATGCTAAGAAATTGTATACTTGACCTTTGATCCGAAATCTTATTTGTCTTTTATGAGATAA
261 TATAATGCTAAGAAATTGTATGCTTGACCTTTGATCCGAAATCTTATTTGTCTTTTATGAGATAA
327944 ATAGTG
326 ATAGTG
*
327950 TTAGAATGCAAACTGATTCTATTTTGCCAGCAGCTTGAATAGATATATCTTAGATTAGTGCTCAG
1 TTAGAATGCAAACCGATTCTATTTTGCCAGCAGCTTGAATAGATATATCTTAGATTAGTGCTCAG
*
328015 GAAAACCATTGTTGGTCTGCTATAGTGTATATAGATGCTTTTGATTTAAAGCTAATCTTGTGTGT
66 GAAAACCATTGTTGGTCTGCTATAGTGTATATAGATGCTTTTGTTTTAAAGCTAATCTTGTGTGT
* * * * *
328080 GTTTGATTAC-AGTGCTTAGAAGAACCCTAAAGATTTTAGGTTGGAAACGAGCCCTTAGATGAAG
131 GTTTGATTACGA-TGCATAGGAGAACCCTAAAGATTTTTGGTTGAAAACAAGCCCTT--A--AA-
* * * *
328144 TGTCTATATGTGTGTCTATATGTGTCTTCGATTTAAAGCCAATCTTGTGTGCATGTATGTGTGTG
190 ----TA-A--AGTGTCGATATGTATCTTCGATTTAAAGCCAATCTTGTGTGCATGCAT-TGTGTG
* * * *
328209 AGTGATTATGAACTTATAATGCTAAGAATATTGTACGCTTTACTTTTGATCCGAAA
247 AGTGATTATAAACTTATAATGCTAAGAA-ATTGTATGCTTGACCTTTGATCCGAAA
328265 CCTGATTGTT
Statistics
Matches: 597, Mismatches: 31, Indels: 21
0.92 0.05 0.03
Matches are distributed among these distances:
329 1 0.00
330 263 0.44
331 2 0.00
332 226 0.38
333 2 0.00
334 2 0.00
339 2 0.00
340 1 0.00
342 43 0.07
343 1 0.00
344 31 0.05
345 23 0.04
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.37
Consensus pattern (331 bp):
TTAGAATGCAAACCGATTCTATTTTGCCAGCAGCTTGAATAGATATATCTTAGATTAGTGCTCAG
GAAAACCATTGTTGGTCTGCTATAGTGTATATAGATGCTTTTGTTTTAAAGCTAATCTTGTGTGT
GTTTGATTACGATGCATAGGAGAACCCTAAAGATTTTTGGTTGAAAACAAGCCCTTAAATAAAGT
GTCGATATGTATCTTCGATTTAAAGCCAATCTTGTGTGCATGCATTGTGTGAGTGATTATAAACT
TATAATGCTAAGAAATTGTATGCTTGACCTTTGATCCGAAATCTTATTTGTCTTTTATGAGATAA
ATAGTG
Found at i:328160 original size:12 final size:12
Alignment explanation
Indices: 328143--328168 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
328133 CTTAGATGAA
328143 GTGTCTATATGT
1 GTGTCTATATGT
328155 GTGTCTATATGT
1 GTGTCTATATGT
328167 GT
1 GT
328169 CTTCGATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.27, T:0.50
Consensus pattern (12 bp):
GTGTCTATATGT
Found at i:329084 original size:26 final size:27
Alignment explanation
Indices: 329045--329139 Score: 97
Period size: 26 Copynumber: 3.5 Consensus size: 27
329035 CCATGACCAA
* *
329045 TTTCTTATCTCCATCAAGATTCTTTGC
1 TTTCTCATCTCCATCAAGCTTCTTTGC
*
329072 TTTCTCAT-TCCATCAAGCTTCTAAAT-C
1 TTTCTCATCTCCATCAAGCTTCT--TTGC
* *
329099 TTTTCTTATCCCCATCAAGCTTCTTTGC
1 -TTTCTCATCTCCATCAAGCTTCTTTGC
329127 TTTCTCAT-TCCAT
1 TTTCTCATCTCCAT
329140 GACCAATTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
26 17 0.31
27 16 0.29
28 9 0.16
29 13 0.24
ACGTcount: A:0.19, C:0.29, G:0.05, T:0.46
Consensus pattern (27 bp):
TTTCTCATCTCCATCAAGCTTCTTTGC
Found at i:331175 original size:78 final size:76
Alignment explanation
Indices: 331070--331224 Score: 238
Period size: 78 Copynumber: 2.0 Consensus size: 76
331060 AGTTTTGTTC
* * *
331070 GAATAAAATGAGCCAAAGATTGAGTTTTTTTCTCAGAACTCAAGCTTGAAGATGGCTCGAAACAG
1 GAATAAAATGAGCCAAAGATTGAGTTTTTTTCTCAGAACCCAAGCCTGAAGATGGCTCAAAACAG
331135 ATAAAAAACAA
66 ATAAAAAACAA
* *
331146 GAATAAAATGAGCCCGAAGATTTGAGTTTTTTTCTCGGAACCCAAGCCTGAAGATGGCTCAAAAC
1 GAATAAAATGAG-CCAAAGA-TTGAGTTTTTTTCTCAGAACCCAAGCCTGAAGATGGCTCAAAAC
*
331211 AGATCAAAAACAA
64 AGATAAAAAACAA
331224 G
1 G
331225 GGGAAAGGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
76 12 0.17
77 6 0.08
78 53 0.75
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (76 bp):
GAATAAAATGAGCCAAAGATTGAGTTTTTTTCTCAGAACCCAAGCCTGAAGATGGCTCAAAACAG
ATAAAAAACAA
Found at i:331962 original size:113 final size:113
Alignment explanation
Indices: 331759--331977 Score: 341
Period size: 113 Copynumber: 1.9 Consensus size: 113
331749 CACACATATG
* * * * *
331759 AACATAAAGAACTTGCAAATCCGGCTATCGTGACGAGACTGGCGAAGAATGTAATACAATTAGGG
1 AACAGAAAGAACTCGCAAATCCGACTATCGTGACAAGACTGGCAAAGAATGTAATACAATTAGGG
* *
331824 ATGGGCAAGGGATTCGAACCCGACGAGTTCCGACCCGACCCGACAATA
66 ATGGGCAAGAGATTCGAACCCGACGAGTTCCGACCCAACCCGACAATA
*
331872 AACAGAAAGAACTCGCAAATCCGACTATCGTGTCAAGACTGGCAAAGAATGTAATACAATTAGGG
1 AACAGAAAGAACTCGCAAATCCGACTATCGTGACAAGACTGGCAAAGAATGTAATACAATTAGGG
*
331937 ATGGGCATGAGA-TCTGAACCCGACGAGTTCCGACCCAACCC
66 ATGGGCAAGAGATTC-GAACCCGACGAGTTCCGACCCAACCC
331978 AACATTTTTT
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
112 2 0.02
113 94 0.98
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (113 bp):
AACAGAAAGAACTCGCAAATCCGACTATCGTGACAAGACTGGCAAAGAATGTAATACAATTAGGG
ATGGGCAAGAGATTCGAACCCGACGAGTTCCGACCCAACCCGACAATA
Found at i:334105 original size:16 final size:16
Alignment explanation
Indices: 334084--334135 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
334074 AAAAATAAAT
*
334084 TTAAAAGTTAGAGTGA
1 TTAAAAGTTAGAGTAA
*
334100 TTAAAA-TAAGAGTAA
1 TTAAAAGTTAGAGTAA
*
334115 TTGTAAAGTTA-AGTAA
1 TT-AAAAGTTAGAGTAA
334131 TTAAA
1 TTAAA
334136 TTAAATTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 11 0.38
16 16 0.55
17 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (16 bp):
TTAAAAGTTAGAGTAA
Found at i:340134 original size:37 final size:37
Alignment explanation
Indices: 340058--340134 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
340048 TTTTATATTT
*
340058 TTTAATTTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTTGTAAAAAAATTATATAAATATTATCAA
*
340095 TTTAATTTTT-TAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTTGTAAA-AAAATTATATAAATATTAT-CAA
340132 TTT
1 TTT
340135 GTAATATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 17 0.47
37 19 0.53
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTAATTTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:342933 original size:21 final size:22
Alignment explanation
Indices: 342907--342970 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
342897 TAAATATTAA
*
342907 AATATTTATAATATAT-TTATT
1 AATATTTATAATATATAATATT
*
342928 AATATTTCTAATAATATAATATT
1 AATATTTATAAT-ATATAATATT
*
342951 -ATATTTTTAATATTATAATA
1 AATATTTATAATA-TATAATA
342971 AAATAATCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 12 0.32
22 21 0.57
23 4 0.11
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
AATATTTATAATATATAATATT
Found at i:342953 original size:8 final size:8
Alignment explanation
Indices: 342892--343002 Score: 52
Period size: 8 Copynumber: 13.6 Consensus size: 8
342882 TTTTAATCAA
342892 AATATTA-
1 AATATTAT
*
342899 AATATTAA
1 AATATTAT
342907 AATATTTAT
1 AATA-TTAT
342916 AATATATTTATT
1 -A-ATA-TTA-T
*
342928 AATATTTCT
1 AATA-TTAT
*
342937 AATAATAT
1 AATATTAT
342945 AATATTAT
1 AATATTAT
*
342953 -AT-TTTT
1 AATATTAT
342959 AATATTAT
1 AATATTAT
**
342967 AATAAAAT
1 AATATTAT
342975 AATCA--AT
1 AAT-ATTAT
*
342982 TATATTAT
1 AATATTAT
*
342990 AATAATAT
1 AATATTAT
342998 AATAT
1 AATAT
343003 AAGATATTAT
Statistics
Matches: 81, Mismatches: 13, Indels: 19
0.72 0.12 0.17
Matches are distributed among these distances:
6 4 0.05
7 15 0.19
8 37 0.46
9 9 0.11
10 7 0.09
11 8 0.10
12 1 0.01
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (8 bp):
AATATTAT
Found at i:342954 original size:22 final size:23
Alignment explanation
Indices: 342914--342970 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
342904 TAAAATATTT
*
342914 ATAATATATTTATTAATATTTCTA
1 ATAATATA-ATATTAATATTTCTA
*
342938 ATAATATAATATT-ATATTTTTA
1 ATAATATAATATTAATATTTCTA
*
342960 ATATTATAATA
1 ATAATATAATA
342971 AAATAATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 18 0.60
23 4 0.13
24 8 0.27
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATAATATAATATTAATATTTCTA
Found at i:343009 original size:23 final size:23
Alignment explanation
Indices: 342960--343013 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
342950 TATATTTTTA
**
342960 ATATTATAATAAAATAATCAATT
1 ATATTATAATAAAATAATCAAAG
*
342983 ATATTATAATAATATAAT-ATAAG
1 ATATTATAATAAAATAATCA-AAG
343006 ATATTATA
1 ATATTATA
343014 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATTATAATAAAATAATCAAAG
Found at i:343140 original size:53 final size:53
Alignment explanation
Indices: 343024--343129 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 53
343014 TTTTTATTTT
* * *
343024 AATAATATATAATAAATTATTAATAAAATTTATATTATTTATTAATTTCATAGA
1 AATAATA-ATATTAAATTATTAATAAAATTAATATTATTTATTAATTTAATAGA
343078 AATAATAATATTAAATTATTAATAATGAA-TAATATTATTTA-TATATTTAATA
1 AATAATAATATTAAATTATTAATAA--AATTAATATTATTTATTA-ATTTAATA
343130 TTAATCTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
53 19 0.41
54 25 0.54
55 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (53 bp):
AATAATAATATTAAATTATTAATAAAATTAATATTATTTATTAATTTAATAGA
Found at i:343175 original size:23 final size:23
Alignment explanation
Indices: 343155--343199 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
343145 AATAATATTT
343155 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
343178 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
343200 ATATAACACT
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:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:343331 original size:27 final size:26
Alignment explanation
Indices: 343301--343377 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 26
343291 ATTATAAAAA
343301 TAATATTTAATAATAAATAAATTATTT
1 TAATATTT-ATAATAAATAAATTATTT
* *
343328 TAATATTT-TAA-AAAT-AATAATAT
1 TAATATTTATAATAAATAAATTATTT
*
343351 TAA-ATTTTATGATAAATAATATTATTT
1 TAATA-TTTATAATAAATAA-ATTATTT
343378 ATTGTATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
22 1 0.03
23 12 0.30
24 6 0.15
25 7 0.17
26 1 0.03
27 13 0.32
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (26 bp):
TAATATTTATAATAAATAAATTATTT
Found at i:345772 original size:2 final size:2
Alignment explanation
Indices: 345765--345789 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
345755 CCTGATTTAT
345765 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 T
345790 TATTTTTATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:345923 original size:39 final size:38
Alignment explanation
Indices: 345815--345926 Score: 102
Period size: 39 Copynumber: 2.9 Consensus size: 38
345805 TTAAATGTTT
* * **
345815 ATTTATAATTTTCAAATTATTTCACTTTAACATTATAA
1 ATTTTTAATTTTTAAATTATTTCACAATAACATTATAA
* * * *
345853 ATTCTTAATTTCTTAAAATT-TGTT-ACCATAACGTTTTAA
1 ATTTTTAATTT-TT-AAATTAT-TTCACAATAACATTATAA
345892 ATTTTTAATTTATTAAATTATTTCACAATAACATT
1 ATTTTTAATTT-TTAAATTATTTCACAATAACATT
345927 CGAAACTATT
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
38 16 0.28
39 35 0.60
40 7 0.12
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (38 bp):
ATTTTTAATTTTTAAATTATTTCACAATAACATTATAA
Found at i:345994 original size:17 final size:18
Alignment explanation
Indices: 345974--346007 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
345964 ACATTTGAAA
345974 TTTAATT-ATATTTTTTT
1 TTTAATTAATATTTTTTT
*
345991 TTTATTTAATATTTTTT
1 TTTAATTAATATTTTTT
346008 CAATTATGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTAATTAATATTTTTTT
Found at i:356587 original size:14 final size:14
Alignment explanation
Indices: 356536--356588 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
356526 AAACAATTGT
*
356536 AATAATTAAATAGA
1 AATAATTAAATACA
356550 AAT-ATTAAATACA
1 AATAATTAAATACA
* *
356563 AA-AGTTAAAATTCA
1 AATAATT-AAATACA
356577 AATAATTAAATA
1 AATAATTAAATA
356589 ATAACAACAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 13 0.42
14 15 0.48
15 3 0.10
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (14 bp):
AATAATTAAATACA
Found at i:358411 original size:80 final size:80
Alignment explanation
Indices: 358274--358432 Score: 282
Period size: 80 Copynumber: 2.0 Consensus size: 80
358264 GATATTCGAT
* *
358274 CACCGTTGAAATTAGGCGTGATACCTCCAAGATACTCCTCGCACAAGGAATGTCAATTACCATCT
1 CACCGTTGAAATTAGGCGTGATACCTCCAAGATACTCATCGCACAAGGAATGCCAATTACCATCT
*
358339 GCCACACCAGAAATC
66 GCCACACCAAAAATC
358354 CACCGTTGAAATTAGGCGTGATACCTCCAAGATACTCATCGCACAAGGAATGCCAATTACCATCT
1 CACCGTTGAAATTAGGCGTGATACCTCCAAGATACTCATCGCACAAGGAATGCCAATTACCATCT
*
358419 GTCACACCAAAAAT
66 GCCACACCAAAAAT
358433 AACATCCCCA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (80 bp):
CACCGTTGAAATTAGGCGTGATACCTCCAAGATACTCATCGCACAAGGAATGCCAATTACCATCT
GCCACACCAAAAATC
Found at i:358917 original size:23 final size:24
Alignment explanation
Indices: 358875--358919 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
358865 TTACAAAAAG
358875 TAATAAGAAAATTAATAAATTAAA
1 TAATAAGAAAATTAATAAATTAAA
*
358899 TAATAATAAAA-TAATAAATTA
1 TAATAAGAAAATTAATAAATTA
358920 TTAAATGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (24 bp):
TAATAAGAAAATTAATAAATTAAA
Found at i:365427 original size:75 final size:75
Alignment explanation
Indices: 365304--365455 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
365294 GGCTTTTGTG
365304 TGCTTCATCCCGATACAGAACGCAGTCGAATTGGTTCGAAACACTAATATCATCTCTTGATTTGC
1 TGCTTCATCCCGATACAGAACGCAGTCGAATTGGTTCGAAACACTAATATCATCTCTTGATTTGC
365369 TTGGAGAGAT
66 TTGGAGAGAT
365379 TGCTTCATCCCGATACAGAACGCAGTCGAATTGGTTCGAAACACTAATATCATCTCTTGATTTGC
1 TGCTTCATCCCGATACAGAACGCAGTCGAATTGGTTCGAAACACTAATATCATCTCTTGATTTGC
365444 TTGGAGAGAT
66 TTGGAGAGAT
365454 TG
1 TG
365456 TTTCCTTTCA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (75 bp):
TGCTTCATCCCGATACAGAACGCAGTCGAATTGGTTCGAAACACTAATATCATCTCTTGATTTGC
TTGGAGAGAT
Found at i:366807 original size:21 final size:21
Alignment explanation
Indices: 366759--366810 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
366749 TAACCATGCG
* *
366759 GTGGTGCCATCTGAATCGGCA
1 GTGGTGGCATCTGAATCGACA
* *
366780 GTTGTGGCATCTGAATCGACT
1 GTGGTGGCATCTGAATCGACA
366801 GTGGTGGCAT
1 GTGGTGGCAT
366811 TTGCGGGTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.35, T:0.29
Consensus pattern (21 bp):
GTGGTGGCATCTGAATCGACA
Found at i:370443 original size:30 final size:30
Alignment explanation
Indices: 370408--370465 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
370398 AAAATCTACA
* *
370408 TTGATTAGTACACTGTATATTTGGCATATG
1 TTGATTAGTACACTGGATATTTGACATATG
370438 TTGATTAGTACACTGGATATTTGACATA
1 TTGATTAGTACACTGGATATTTGACATA
370466 CGGTATTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.41
Consensus pattern (30 bp):
TTGATTAGTACACTGGATATTTGACATATG
Found at i:377873 original size:24 final size:24
Alignment explanation
Indices: 377841--377926 Score: 77
Period size: 24 Copynumber: 3.6 Consensus size: 24
377831 CATTTAAATG
377841 ATAAACGAACACAAATGAACGAAC
1 ATAAACGAACACAAATGAACGAAC
** *
377865 ATAAACG-A-ACGGATGTAATTGAAC
1 ATAAACGAACACAAATG-AA-CGAAC
* *
377889 ATAAACGAACACAAACGAACGATC
1 ATAAACGAACACAAATGAACGAAC
* *
377913 GTAAACAAACACAA
1 ATAAACGAACACAA
377927 TAAATGAACA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
22 5 0.10
23 3 0.06
24 33 0.69
25 3 0.06
26 4 0.08
ACGTcount: A:0.55, C:0.20, G:0.14, T:0.12
Consensus pattern (24 bp):
ATAAACGAACACAAATGAACGAAC
Found at i:381069 original size:16 final size:18
Alignment explanation
Indices: 381036--381072 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
381026 TAAATCACTA
381036 TTTTAAGTATCTGAAATT
1 TTTTAAGTATCTGAAATT
381054 TTTTAA-TATCTG-AATT
1 TTTTAAGTATCTGAAATT
381070 TTT
1 TTT
381073 AGATCCGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 6 0.32
18 6 0.32
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (18 bp):
TTTTAAGTATCTGAAATT
Found at i:381338 original size:21 final size:21
Alignment explanation
Indices: 381294--381339 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
381284 CCATATCTCG
**
381294 ATCATAATTTTAAATTACTGT
1 ATCATAATTTTAAATTACAAT
*
381315 ATCATAATTTTAAATTGCAAT
1 ATCATAATTTTAAATTACAAT
381336 ATCA
1 ATCA
381340 ATATAAGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.43
Consensus pattern (21 bp):
ATCATAATTTTAAATTACAAT
Found at i:382617 original size:21 final size:22
Alignment explanation
Indices: 382578--382630 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
382568 AGGGTTTTAA
* *
382578 GTTAGGATTTAGGGCTTAAG-T
1 GTTAGGGTTTAGAGCTTAAGAT
*
382599 GTTAGGGTTTAGAGTTTAAGAT
1 GTTAGGGTTTAGAGCTTAAGAT
382621 -TTAGGGTTTA
1 GTTAGGGTTTA
382631 AGTGTTATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.25, C:0.02, G:0.32, T:0.42
Consensus pattern (22 bp):
GTTAGGGTTTAGAGCTTAAGAT
Found at i:382623 original size:14 final size:14
Alignment explanation
Indices: 382606--382652 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
382596 AGTGTTAGGG
382606 TTTAGAGTTTAAGA
1 TTTAGAGTTTAAGA
*
382620 TTTAGGGTTTAAG-
1 TTTAGAGTTTAAGA
*
382633 TGTTATAGTTTAAGA
1 T-TTAGAGTTTAAGA
382648 TTTAG
1 TTTAG
382653 GATTTTAACC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (14 bp):
TTTAGAGTTTAAGA
Found at i:382644 original size:35 final size:35
Alignment explanation
Indices: 382583--382657 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
382573 TTTAAGTTAG
*
382583 GATTTAGGGCTTAAGTGTTAGGGTTT-AGAGTTTAA
1 GATTTAGGGCTTAAGTGTTAGAGTTTAAGA-TTTAA
* * *
382618 GATTTAGGGTTTAAGTGTTATAGTTTAAGATTTAG
1 GATTTAGGGCTTAAGTGTTAGAGTTTAAGATTTAA
382653 GATTT
1 GATTT
382658 TAACCTAGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 32 0.91
36 3 0.09
ACGTcount: A:0.27, C:0.01, G:0.28, T:0.44
Consensus pattern (35 bp):
GATTTAGGGCTTAAGTGTTAGAGTTTAAGATTTAA
Found at i:384006 original size:4 final size:4
Alignment explanation
Indices: 383997--384021 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
383987 AATCTCAATA
383997 TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG T
384022 CTTTCATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:384114 original size:98 final size:100
Alignment explanation
Indices: 383914--384119 Score: 290
Period size: 98 Copynumber: 2.1 Consensus size: 100
383904 GTATGCATGC
* * * * * *
383914 ATGTATGTCTTTCATTGTTTGGTAAGGTGTTTTGGAGTCGGTTGTGTAGTTTTGATTTTTTTATG
1 ATGTATGTCTTTCATTATTTGGTAAGGTGTCTTGGAATCGGTTGTGTAGTTTCGACTTTTTGATG
* * *
383979 CTAATATGAATCTCAATATATGTATGTATGTATGT
66 CTAATATGAATCTCAAGATATGTATGAATGTAGGT
* *
384014 ATGTATGTCTTTCATTATTTGGTAAGGTG-CTTGGAATTGGTTTTGTAG-TTCGACTTTTTGATG
1 ATGTATGTCTTTCATTATTTGGTAAGGTGTCTTGGAATCGGTTGTGTAGTTTCGACTTTTTGATG
*
384077 CTAATATGAATCTCAAGATATGTATGAATTTAGGT
66 CTAATATGAATCTCAAGATATGTATGAATGTAGGT
384112 ATGTATGT
1 ATGTATGT
384120 ATGCATGCAT
Statistics
Matches: 94, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
98 51 0.54
99 15 0.16
100 28 0.30
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.48
Consensus pattern (100 bp):
ATGTATGTCTTTCATTATTTGGTAAGGTGTCTTGGAATCGGTTGTGTAGTTTCGACTTTTTGATG
CTAATATGAATCTCAAGATATGTATGAATGTAGGT
Found at i:386567 original size:23 final size:23
Alignment explanation
Indices: 386541--386586 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
386531 CTATTAATAA
386541 TTTTAATAATATAATATTATATT
1 TTTTAATAATATAATATTATATT
* *
386564 TTTTAGTATTATAATATTATATT
1 TTTTAATAATATAATATTATATT
386587 AAATTATACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTTAATAATATAATATTATATT
Found at i:386599 original size:23 final size:23
Alignment explanation
Indices: 386550--386602 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
386540 ATTTTAATAA
** *
386550 TATAATATTATATTTTTTAGTAT
1 TATAATATTATATTAATTAGTAC
386573 TATAATATTATATTAAATTA-TAC
1 TATAATATTATATT-AATTAGTAC
386596 TATAATA
1 TATAATA
386603 ATAAATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TATAATATTATATTAATTAGTAC
Found at i:386986 original size:23 final size:22
Alignment explanation
Indices: 386956--387010 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
386946 TGCATGTGTT
*
386956 GCACGTTTTCATCTGCCTTTATG
1 GCACGTTTTCATATGCCTTT-TG
* *
386979 GCACGTTTTCTTATGTCTTTTG
1 GCACGTTTTCATATGCCTTTTG
*
387001 GCATGTTTTC
1 GCACGTTTTC
387011 GGTTTTTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 11 0.39
23 17 0.61
ACGTcount: A:0.11, C:0.22, G:0.18, T:0.49
Consensus pattern (22 bp):
GCACGTTTTCATATGCCTTTTG
Found at i:387025 original size:26 final size:27
Alignment explanation
Indices: 386995--387052 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
386985 TTTCTTATGT
* * *
386995 CTTTTGGCATGTTTTCGGTT-TTTTAC
1 CTTTTGACATATTTTCGGTTCTTTGAC
*
387021 CTTTTGACATATTTTTGGTTCTTTGAC
1 CTTTTGACATATTTTCGGTTCTTTGAC
387048 CTTTT
1 CTTTT
387053 TTATTTATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.10, C:0.16, G:0.16, T:0.59
Consensus pattern (27 bp):
CTTTTGACATATTTTCGGTTCTTTGAC
Found at i:387425 original size:13 final size:13
Alignment explanation
Indices: 387407--387432 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
387397 TTAATTTACG
387407 ATTTTGATTGTAA
1 ATTTTGATTGTAA
387420 ATTTTGATTGTAA
1 ATTTTGATTGTAA
387433 TTTGAGATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
ATTTTGATTGTAA
Found at i:390231 original size:20 final size:18
Alignment explanation
Indices: 390206--390256 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
390196 AATCTATTAT
390206 TTTTAATAAATAATAAATA
1 TTTTAATAAATAAT-AATA
*
390225 TTATTAAT-AATAATATTA
1 TT-TTAATAAATAATAATA
390243 TTTTAATACAATAA
1 TTTTAATA-AATAA
390257 AACCCAATCC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 5 0.18
18 5 0.18
19 13 0.46
20 5 0.18
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTTAATAAATAATAATA
Found at i:390241 original size:15 final size:16
Alignment explanation
Indices: 390214--390244 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
390204 ATTTTTAATA
390214 AATAATAAATATTATT
1 AATAATAAATATTATT
390230 AATAAT-AATATTATT
1 AATAATAAATATTATT
390245 TTAATACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATAATAAATATTATT
Found at i:390671 original size:42 final size:42
Alignment explanation
Indices: 390615--390714 Score: 155
Period size: 42 Copynumber: 2.4 Consensus size: 42
390605 CTAGAACTTC
* *
390615 CTTCCCATTTGAAAACTTCACATTCGAAAACACGCGCTAGAA
1 CTTCCCGTTTGAAAACTTCACATTCGAAAACACGCGCCAGAA
* *
390657 CTTCCCGTTTGAAAACTTCCCATTTGAAAACACGCGCCAGAA
1 CTTCCCGTTTGAAAACTTCACATTCGAAAACACGCGCCAGAA
*
390699 CTTCCCGTTTAAAAAC
1 CTTCCCGTTTGAAAAC
390715 GAAACGAGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.25
Consensus pattern (42 bp):
CTTCCCGTTTGAAAACTTCACATTCGAAAACACGCGCCAGAA
Found at i:390675 original size:15 final size:15
Alignment explanation
Indices: 390655--390687 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
390645 CACGCGCTAG
*
390655 AACTTCCCGTTTGAA
1 AACTTCCCATTTGAA
390670 AACTTCCCATTTGAA
1 AACTTCCCATTTGAA
390685 AAC
1 AAC
390688 ACGCGCCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.27, G:0.09, T:0.30
Consensus pattern (15 bp):
AACTTCCCATTTGAA
Found at i:392998 original size:90 final size:92
Alignment explanation
Indices: 392822--393002 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 92
392812 GCATGCATGC
* * * * *
392822 ATGTATGTCTTTCATTGTTTGGTAAGGTGTTTTGGAGTCGGTTGTGTAGTTTTGATTTTTTGATG
1 ATGTATGTCTTTCATTATTTGGTAAGGTGTCTTGGAATCGGTTGTGTAGTTTCGACTTTTTGATG
*
392887 CTAATATGAATCTCAATATATGTATGT
66 CTAATATGAATCTCAAGATATGTATGT
* *
392914 ATGTATGTCTTTCATTATTTGGTAAGGTG-CTTGGAATTGGTTTTGTAG-TTCGACTTTTTGATG
1 ATGTATGTCTTTCATTATTTGGTAAGGTGTCTTGGAATCGGTTGTGTAGTTTCGACTTTTTGATG
392977 CTAATATGAATCTCAAGATATGTATG
66 CTAATATGAATCTCAAGATATGTATG
393003 AATTTAGGTA
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
90 38 0.47
91 15 0.19
92 28 0.35
ACGTcount: A:0.22, C:0.08, G:0.23, T:0.47
Consensus pattern (92 bp):
ATGTATGTCTTTCATTATTTGGTAAGGTGTCTTGGAATCGGTTGTGTAGTTTCGACTTTTTGATG
CTAATATGAATCTCAAGATATGTATGT
Found at i:395694 original size:18 final size:18
Alignment explanation
Indices: 395671--395706 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
395661 CGACCCGTTT
395671 ACCCGACCAGTTGACCCG
1 ACCCGACCAGTTGACCCG
*
395689 ACCCGACCCGTTGACCCG
1 ACCCGACCAGTTGACCCG
395707 TTGACCCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.47, G:0.22, T:0.11
Consensus pattern (18 bp):
ACCCGACCAGTTGACCCG
Found at i:395704 original size:8 final size:8
Alignment explanation
Indices: 395693--395718 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
395683 GACCCGACCC
395693 GACCCGTT
1 GACCCGTT
395701 GACCCGTT
1 GACCCGTT
395709 GACCCGTT
1 GACCCGTT
395717 GA
1 GA
395719 TCGGCGTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.35, G:0.27, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:395706 original size:13 final size:13
Alignment explanation
Indices: 395658--395693 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
395648 ACCGGTCATA
*
395658 ACCCGACCCGTTT
1 ACCCGACCCGTTG
*
395671 ACCCGACCAGTTG
1 ACCCGACCCGTTG
395684 ACCCGACCCG
1 ACCCGACCCG
395694 ACCCGTTGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.47, G:0.19, T:0.14
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:397684 original size:24 final size:24
Alignment explanation
Indices: 397657--397724 Score: 111
Period size: 24 Copynumber: 2.8 Consensus size: 24
397647 TTCGATTTGA
*
397657 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
397681 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
397705 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
397725 TTGAATTATG
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
23 1 0.02
24 39 0.95
25 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:397710 original size:12 final size:12
Alignment explanation
Indices: 397673--397711 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
397663 ATCTGATACT
397673 TGACATGGATTC
1 TGACATGGATTC
*
397685 TGATAT-GATATC
1 TGACATGGAT-TC
397697 TGACATGGATTC
1 TGACATGGATTC
397709 TGA
1 TGA
397712 TATGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:397904 original size:43 final size:43
Alignment explanation
Indices: 397843--397937 Score: 172
Period size: 43 Copynumber: 2.2 Consensus size: 43
397833 GGGCCTTACT
*
397843 TGGTGTGTTGGTGGGTGTACGGTTCTGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTACGGTTCTGGGAAACCTACACATTA
*
397886 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTACGGTTCTGGGAAACCTACACATTA
397929 TGGTGTGTT
1 TGGTGTGTT
397938 CGGTTGGAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.16, C:0.12, G:0.37, T:0.36
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTACGGTTCTGGGAAACCTACACATTA
Found at i:399227 original size:23 final size:23
Alignment explanation
Indices: 399201--399246 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
399191 CTATTAATAA
*
399201 TTTTAATAATATAATATTATATT
1 TTTTAATAATATAATAATATATT
* *
399224 TTTTAGTATTATAATAATATATT
1 TTTTAATAATATAATAATATATT
399247 AAATTATACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTAATAATATAATAATATATT
Found at i:399275 original size:23 final size:23
Alignment explanation
Indices: 399233--399277 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
399223 TTTTTAGTAT
*
399233 TATAATAATATATTAAATTATAC
1 TATAATAATATAATAAATTATAC
399256 TATAATAATA-AATAATATTATA
1 TATAATAATATAATAA-ATTATA
399278 TTTTTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TATAATAATATAATAAATTATAC
Found at i:399364 original size:26 final size:24
Alignment explanation
Indices: 399335--399404 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 24
399325 AATTTCATAA
*
399335 AATAATATTATTAAATTTATATATTT
1 AATAATATTATTAAATATA-ATA-TT
*
399361 AATAATATTTTTTAGAATATAATATT
1 AATAATA-TTATTA-AATATAATATT
*
399387 GATGAATATTATTAAATA
1 AAT-AATATTATTAAATA
399405 AATTATCTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
25 4 0.11
26 16 0.43
27 12 0.32
28 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
AATAATATTATTAAATATAATATT
Found at i:400005 original size:25 final size:25
Alignment explanation
Indices: 399977--400030 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
399967 TTGTATCATC
*
399977 TTTATTCAAGTTTCTTGGTTAAATT
1 TTTATTCAAGTTTCTTGATTAAATT
400002 TTTATTCAAGTTTCTTGATTAAATT
1 TTTATTCAAGTTTCTTGATTAAATT
400027 TTTA
1 TTTA
400031 ATCTTTTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.26, C:0.07, G:0.09, T:0.57
Consensus pattern (25 bp):
TTTATTCAAGTTTCTTGATTAAATT
Done.