Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008256.1 Hibiscus syriacus cultivar Beakdansim tig00110909_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: 250029
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:194961 original size:23 final size:23
Alignment explanation
Indices: 194903--194967 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
194893 AGCTCGTAAT
*
194903 TTGCACCGAAGTGCCACAT-AGT
1 TTGCACCGAAGTGCCACATAAGG
* *
194925 TTACATCGAAGTGCCACATAAGG
1 TTGCACCGAAGTGCCACATAAGG
194948 TTGCACCGAAGTGCCACATA
1 TTGCACCGAAGTGCCACATA
194968 TTTTTCCCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 17 0.46
23 20 0.54
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACATAAGG
Found at i:195627 original size:55 final size:54
Alignment explanation
Indices: 195553--195700 Score: 183
Period size: 55 Copynumber: 2.7 Consensus size: 54
195543 CATTCAAATG
* *
195553 GCAAGGTATCGATACACTCCTTAGTATACCGATACACAAAT-AACATTCGATCTTTT
1 GCAA-GTATCGATACACTCCTCAGTGTACCGATACACAAATGAAC--TCGATCTTTT
* * *
195609 G-ATAGTATCGATGCACTCCTCAGTGTACCGATACATAAATGGAACTCGATGTTTT
1 GCA-AGTATCGATACACTCCTCAGTGTACCGATACACAAAT-GAACTCGATCTTTT
*
195664 GCAGGTATCGATACACTCCTCAGTGTACCGATACACA
1 GCAAGTATCGATACACTCCTCAGTGTACCGATACACA
195701 CTCATATAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
55 74 0.93
56 3 0.04
57 3 0.04
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (54 bp):
GCAAGTATCGATACACTCCTCAGTGTACCGATACACAAATGAACTCGATCTTTT
Found at i:201656 original size:2 final size:2
Alignment explanation
Indices: 201649--201700 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
201639 CTAAAATTTA
201649 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
*
201691 AT AT AC AT AT
1 AT AT AT AT AT
201701 TAAAAGAAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:202065 original size:47 final size:47
Alignment explanation
Indices: 202011--202106 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
202001 AAAACTTAAC
202011 TTGAACCTAAACCTAAACTAAACTAAACAATTCAGTCACATTTGCTT
1 TTGAACCTAAACCTAAACTAAACTAAACAATTCAGTCACATTTGCTT
* **
202058 TTGAACCTAAACCTAAACTAAACTAGACAATTCAGTTGCATTTGCTT
1 TTGAACCTAAACCTAAACTAAACTAAACAATTCAGTCACATTTGCTT
202105 TT
1 TT
202107 TCACTCTCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (47 bp):
TTGAACCTAAACCTAAACTAAACTAAACAATTCAGTCACATTTGCTT
Found at i:203202 original size:22 final size:22
Alignment explanation
Indices: 203174--203228 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
203164 ACATGGCTAC
203174 TACAACCGGGTTCGGGTCAGGT
1 TACAACCGGGTTCGGGTCAGGT
203196 TACAACCGGGTTCGGGTCAGGT
1 TACAACCGGGTTCGGGTCAGGT
* *
203218 TGCGACCGGGT
1 TACAACCGGGT
203229 CTAGGTCGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.16, C:0.24, G:0.38, T:0.22
Consensus pattern (22 bp):
TACAACCGGGTTCGGGTCAGGT
Found at i:203634 original size:53 final size:53
Alignment explanation
Indices: 203553--203776 Score: 306
Period size: 53 Copynumber: 4.2 Consensus size: 53
203543 CTCTTCTTTA
* *
203553 AACAATCTTC-GACCAACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCG
1 AACAATCTTCTG-CCTACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCG
* * *
203606 AACAATCTTCTGCCTACAGGTTCCCTCCCTTTTGCTTCAGGGAGTAGAACTCG
1 AACAATCTTCTGCCTACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCG
* * * *
203659 ATCAATCTTATACCTACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACGCG
1 AACAATCTTCTGCCTACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCG
* ** * *
203712 AACAATCTTATGCCTACGGGTTTTCTCCCTCTTGCTTCAGGAAGTAGAACACG
1 AACAATCTTCTGCCTACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCG
203765 AACAATCTTCTG
1 AACAATCTTCTG
203777 GTGTGATTCA
Statistics
Matches: 152, Mismatches: 18, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
53 151 0.99
54 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (53 bp):
AACAATCTTCTGCCTACGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCG
Found at i:204262 original size:41 final size:42
Alignment explanation
Indices: 204205--204327 Score: 142
Period size: 42 Copynumber: 3.0 Consensus size: 42
204195 TGTCTTATGG
* * * *
204205 ATGACCTGAAGGATTT-ATCATCTTGCTTGAGAGA-TTCACAA
1 ATGACCCGAAGGATTTAATCATCATGCTCGAAAGAGTT-ACAA
**
204246 ATGACCCGAAGGATTTAATCATCATGCTCGAAAGAGTTACTG
1 ATGACCCGAAGGATTTAATCATCATGCTCGAAAGAGTTACAA
* * *
204288 ATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTAC
1 ATGACCCGAAGGATTTAATCATCATGCTCGAAAGAGTTAC
204328 TGATGGATTT
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
41 15 0.21
42 54 0.76
43 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (42 bp):
ATGACCCGAAGGATTTAATCATCATGCTCGAAAGAGTTACAA
Found at i:204277 original size:22 final size:21
Alignment explanation
Indices: 204252--204319 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
204242 ACAAATGACC
204252 CGAAGGATTTAATCATCATGCT
1 CGAAGGATTT-ATCATCATGCT
* * * *
204274 CGAAAGAGTTA-C-TGATGGCC
1 CGAAGGATTTATCATCAT-GCT
204294 CGAAGGATTTCATCATCATGCT
1 CGAAGGATTT-ATCATCATGCT
204316 CGAA
1 CGAA
204320 AGACTTACTG
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 3 0.09
20 11 0.32
21 2 0.06
22 15 0.44
23 3 0.09
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (21 bp):
CGAAGGATTTATCATCATGCT
Found at i:204296 original size:42 final size:42
Alignment explanation
Indices: 204250--204726 Score: 191
Period size: 42 Copynumber: 11.0 Consensus size: 42
204240 TCACAAATGA
*
204250 CCCGAAGGATTTAATCATCATGCTCGAAAGAGTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
*
204292 CCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
*** **** ** * * * ** **
204334 ATTTGCTTCA-TTGCTCTTTA-G-T-G-AAGGCTTACAAATTA
1 -CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * ** *
204372 CTCAAATAATTTAACCATCATGCTTC-AAAGACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGC-TCGAAAGACTTACTGATGG
* * * *
204414 CCTGAAGGATTTCATCATCGTGCTCGAAAGACTTACAGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* ** * ** **
204456 CACTTACTGATGGATTTGCTTCA-CTACT-CTTCAGAGAAGGCTTACAAATTA
1 C-C---C-GAAGGATTT-AATCATC-A-TGC-TC-GA-AAGACTTACTGATGG
* * *
204507 CCCGAATGATTTAACCATCATGCTTGAAAGACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* *
204549 CCCGAAGGATTTCATCATCATGCTCGAAAGACTTACAGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* ** * ** **
204591 CACTTACTGATGGATTTGCTTCA-CTACT-CTTCAGAGAAGGCTTACAAATTA
1 C-C---C-GAAGGATTT-AATCATC-A-TGC-TC-GA-AAGACTTACTGATGG
* *
204642 CCCGAATGATTTAACCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * *
204684 CCCGAAGAATTTCATCATCATGCTCGAAAGACTTACAGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
204726 C
1 C
204727 ACTTACTGAT
Statistics
Matches: 313, Mismatches: 88, Indels: 68
0.67 0.19 0.14
Matches are distributed among these distances:
37 3 0.01
38 15 0.05
39 2 0.01
40 1 0.00
41 4 0.01
42 183 0.58
43 8 0.03
44 5 0.02
45 8 0.03
46 17 0.05
47 20 0.06
48 11 0.04
49 6 0.02
50 6 0.02
51 24 0.08
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (42 bp):
CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
Found at i:204564 original size:135 final size:135
Alignment explanation
Indices: 204322--204775 Score: 766
Period size: 135 Copynumber: 3.4 Consensus size: 135
204312 TGCTCGAAAG
* * * * * * *
204322 ACTTACTGATGGATTTGCTTCATTGCTCTTTAGTGAAGGCTTACAAATTACTCAAATAATTTAAC
1 ACTTACTGATGGATTTGCTTCACTACTCTTCAGAGAAGGCTTACAAATTACCCGAATGATTTAAC
* * *
204387 CATCATGCTTCAAAGACTTACTGATGGCCTGAAGGATTTCATCATCGTGCTCGAAAGACTTACAG
66 CATCATGCTTGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTACAG
204452 ATGGC
131 ATGGC
204457 ACTTACTGATGGATTTGCTTCACTACTCTTCAGAGAAGGCTTACAAATTACCCGAATGATTTAAC
1 ACTTACTGATGGATTTGCTTCACTACTCTTCAGAGAAGGCTTACAAATTACCCGAATGATTTAAC
204522 CATCATGCTTGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTACAG
66 CATCATGCTTGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTACAG
204587 ATGGC
131 ATGGC
204592 ACTTACTGATGGATTTGCTTCACTACTCTTCAGAGAAGGCTTACAAATTACCCGAATGATTTAAC
1 ACTTACTGATGGATTTGCTTCACTACTCTTCAGAGAAGGCTTACAAATTACCCGAATGATTTAAC
* *
204657 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGAATTTCATCATCATGCTCGAAAGACTTACAG
66 CATCATGCTTGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTACAG
204722 ATGGC
131 ATGGC
**
204727 ACTTACTGATGGATTTGCTTCACTTTTCTTC-GATGAAGGCTTACAAATT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCAGA-GAAGGCTTACAAATT
204776 TCCCAAAATC
Statistics
Matches: 304, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
134 2 0.01
135 302 0.99
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (135 bp):
ACTTACTGATGGATTTGCTTCACTACTCTTCAGAGAAGGCTTACAAATTACCCGAATGATTTAAC
CATCATGCTTGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTACAG
ATGGC
Found at i:206517 original size:33 final size:33
Alignment explanation
Indices: 206473--206541 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
206463 CATCACCATA
*
206473 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
206506 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
206539 TTC
1 TTC
206542 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:212155 original size:33 final size:33
Alignment explanation
Indices: 212118--212186 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
212108 CATCACCATA
*
212118 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
212151 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
212184 TTC
1 TTC
212187 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:212700 original size:13 final size:12
Alignment explanation
Indices: 212666--212703 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
212656 TCTGATCTTC
212666 TTTTATCTTC-T
1 TTTTATCTTCAT
*
212677 TTTTGTCTTCAT
1 TTTTATCTTCAT
212689 TTTCTATCTTCAT
1 TTT-TATCTTCAT
212702 TT
1 TT
212704 CAGAGAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 9 0.39
12 4 0.17
13 10 0.43
ACGTcount: A:0.11, C:0.18, G:0.03, T:0.68
Consensus pattern (12 bp):
TTTTATCTTCAT
Found at i:215999 original size:59 final size:59
Alignment explanation
Indices: 215894--216256 Score: 401
Period size: 59 Copynumber: 6.2 Consensus size: 59
215884 TGACACTATA
* * * * *
215894 TGTGCTAAAATAATAAGG-AATCATACTGAATATATGAAATTCCATATAGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATAGAGCACTAAG
* * *
215952 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGTACTAAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATAGAGCACTAAG
* * *
216011 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATAGAGCACTAAG
* * * * * *
216070 TGTGCTAAAATGATAAGGAAATGATATTGAATATATGGATTTCCAGATAGGGCATTATA-
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATAGAGCACTA-AG
* * * * * * *
216129 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGAAAAATCACTAAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATAGAGCACTAAG
* * * * * *
216188 GGTGCTACAAGGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAGGGCACTTCA-
1 TGTGCTAAAATGATAAGGAAATCATACTGAAT-GTATGGATTTCCATATAGAGCAC-TAAG
216247 TGTGCTAAAA
1 TGTGCTAAAA
216257 ATGGTAAATG
Statistics
Matches: 255, Mismatches: 45, Indels: 9
0.83 0.15 0.03
Matches are distributed among these distances:
58 20 0.08
59 232 0.91
60 3 0.01
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.29
Consensus pattern (59 bp):
TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATAGAGCACTAAG
Found at i:216073 original size:118 final size:117
Alignment explanation
Indices: 215887--216256 Score: 451
Period size: 118 Copynumber: 3.1 Consensus size: 117
215877 TACCAAATGA
* * * * *
215887 CACTATATGTGCTAAAATAATAAGGAATCATACTGAATATATGAAATTCCATATAGAGCACTGAG
1 CACTATATGTGCTAAAATGATAAGGAATCATACTGAGTGTATGGATTTCCATATAGAGCACTGAG
*
215952 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATAT-GGAG
66 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATAGG-G
* *
216004 TACTA-AGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTG
1 CACTATA-TGTGCTAAAATGATAAGG-AATCATACTGAGTGTATGGATTTCCATATAGAGCACTG
* * * *
216068 AGTGTGCTAAAATGATAAGGAAATGATATTGAATATATGGATTTCCAGATAGGG
64 AGTGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATAGGG
* * * * * * *
216122 CATTATATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGAAAAATCACTAA
1 CACTATATGTGCTAAAATGATAA-GGAATCATACTGAGTGTATGGATTTCCATATAGAGCACTGA
* * * *
216187 GGGTGCTACAAGGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAGGG
65 GTGTGCTAAAATGATAAGGAAATCATACTGAAT-GTATGGATTTCCATATAGGG
216240 CACT-TCATGTGCTAAAA
1 CACTAT-ATGTGCTAAAA
216257 ATGGTAAATG
Statistics
Matches: 216, Mismatches: 30, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
116 1 0.00
117 25 0.12
118 185 0.86
119 5 0.02
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (117 bp):
CACTATATGTGCTAAAATGATAAGGAATCATACTGAGTGTATGGATTTCCATATAGAGCACTGAG
TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATAGGG
Found at i:216205 original size:177 final size:176
Alignment explanation
Indices: 215893--216256 Score: 450
Period size: 177 Copynumber: 2.1 Consensus size: 176
215883 ATGACACTAT
* *
215893 ATGTGCTAAAATAATAAGGAATCATACTGAATATATGAAATTCCATATAGAGCACTGAGTGTGCT
1 ATGTGCTAAAATAATAAGGAATCATACTGAATATATGAAATTCCAGATAGAGCACTGAATGTGCT
* ** * * *
215958 AAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGTACTAAGTGTGCTAAAATG
66 AAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAATACTAAGGGTGCTAAAAGG
* *
216023 ATAAGGAAATCATACTGAGT-GTATGGATTTCCATAT-GGAGCAC-TG
131 ATAAGGAAATCATACT-AATAGTATGGATTTCCATATAGG-GCACTTC
* * * * * * *
216068 AGTGTGCTAAAATGATAAGGAAATGATATTGAATATATGGATTTCCAGATAGGGCA-TTATATGT
1 A-TGTGCTAAAATAATAAGG-AATCATACTGAATATATGAAATTCCAGATAGAGCACTGA-ATGT
* * *
216132 GCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGA-AAAATCACTAAGGGTGCTAC
63 GCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAAT-ACTAAGGGTGCTAA
*
216196 AAGGATAAGGAAATCATACTAATAGTATGGATTTTCATATAGGGCACTTC
127 AAGGATAAGGAAATCATACTAATAGTATGGATTTCCATATAGGGCACTTC
216246 ATGTGCTAAAA
1 ATGTGCTAAAA
216257 ATGGTAAATG
Statistics
Matches: 161, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
175 1 0.01
176 23 0.14
177 133 0.83
178 4 0.02
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (176 bp):
ATGTGCTAAAATAATAAGGAATCATACTGAATATATGAAATTCCAGATAGAGCACTGAATGTGCT
AAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAATACTAAGGGTGCTAAAAGG
ATAAGGAAATCATACTAATAGTATGGATTTCCATATAGGGCACTTC
Found at i:216298 original size:60 final size:60
Alignment explanation
Indices: 216207--216376 Score: 243
Period size: 60 Copynumber: 2.8 Consensus size: 60
216197 AGGATAAGGA
* *
216207 AATCATACTAATAGTATGGATTTTC-ATATAGGGCACTTCATGTGCTAAAAATGGTAAATG
1 AATCATACTAATGGTATGGATTCTCGA-ATAGGGCACTTCATGTGCTAAAAATGGTAAATG
* * *
216267 GATCATACTAATGGTATAGATTCTCGAATAGGGCATTTCATGTGCTAAAAATGGTAAATG
1 AATCATACTAATGGTATGGATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTAAATG
* * * *
216327 AATCGTATTAATGGTATGGAATCTCGAATAGGGCACTTCGTGTGCTAAAA
1 AATCATACTAATGGTATGGATTCTCGAATAGGGCACTTCATGTGCTAAAA
216377 TGAGAAGAAA
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 96 0.99
61 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (60 bp):
AATCATACTAATGGTATGGATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTAAATG
Found at i:216628 original size:44 final size:44
Alignment explanation
Indices: 216579--217065 Score: 706
Period size: 44 Copynumber: 11.0 Consensus size: 44
216569 TATGAAATTG
216579 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
216623 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* *
216667 TGAAATAATAGTAAGTATATTGGTAAAATAAGATTACGAGCTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
216711 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACAAGCTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
216755 TGAAATTATAGTAAGTATATTGGTAAAATTAGCTTACGAGCTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* * * * *
216799 TGGAGTAATTGTAAGTATATTGGTAAAATAAGCTTACGTGCTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* * *
216843 TGAAATTATAGTAAGTATATTAGTGAAATAAGCTTACGAACTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* * *
216887 TGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* * * * *
216931 TGGAATAATGGTAAGTATATTAGTAAAATAAGCTTACGATCTTA
1 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* *
216975 TGGAATAAT-GCTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 TGAAATTATAG-TAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* * * * *
217019 GGGATTTAATGGTAAGTATATTGGTAAATTAAGCTTACGAGCTTA
1 TGAAATT-ATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
217064 TG
1 TG
217066 GATTAAATGG
Statistics
Matches: 404, Mismatches: 36, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
43 1 0.00
44 367 0.91
45 35 0.09
46 1 0.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.34
Consensus pattern (44 bp):
TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
Found at i:216695 original size:23 final size:23
Alignment explanation
Indices: 216669--216741 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
216659 CGAGCTTATG
216669 AAATAATAGTAAGTATATTGGTA
1 AAATAATAGTAAGTATATTGGTA
* * * ** * *
216692 AAATAAGATTACG-AGCTT-ATG
1 AAATAATAGTAAGTATATTGGTA
*
216713 AAATTATAGTAAGTATATTGGTA
1 AAATAATAGTAAGTATATTGGTA
216736 AAATAA
1 AAATAA
216742 GCTTACAAGC
Statistics
Matches: 32, Mismatches: 16, Indels: 4
0.62 0.31 0.08
Matches are distributed among these distances:
21 10 0.31
22 6 0.19
23 16 0.50
ACGTcount: A:0.48, C:0.03, G:0.16, T:0.33
Consensus pattern (23 bp):
AAATAATAGTAAGTATATTGGTA
Found at i:222699 original size:58 final size:59
Alignment explanation
Indices: 222615--223077 Score: 244
Period size: 59 Copynumber: 7.9 Consensus size: 59
222605 ATCATTTGAA
* * *
222615 TGTATGAATTTCCATATAGAGCACTGAGTGTGCTAAAATGATAAGGAAATCATACTGAG
1 TGTATGGATTTCCAGATAGGGCACTGAGTGTGCTAAAATGATAAGGAAATCATACTGAG
* * *
222674 TGTATGGATTTTCATG-T-GGGCACTGAGTGTGCTAAAATGATAAGGAAATCATATTGAA
1 TGTATGGATTTCCA-GATAGGGCACTGAGTGTGCTAAAATGATAAGGAAATCATACTGAG
* * * * *
222732 TATATGGATTTCCAGATAGGGCA-TTATATGTGCTAAAATGGTAAGGGAATCATACTGAG
1 TGTATGGATTTCCAGATAGGGCACTGA-GTGTGCTAAAATGATAAGGAAATCATACTGAG
* *** * * * * *
222791 TGTATGGATTTCTAGA-AAATCACTAAGGGTTCTACAAGGATAAGGAAATCATACT-A-
1 TGTATGGATTTCCAGATAGGGCACTGAGTGTGCTAAAATGATAAGGAAATCATACTGAG
* * * * * * *
222847 TAGTATGAATTTTCATATAGGGCACT-ACATGTGCTAAAAATGGTAAAGG-GATCATACT-AA
1 T-GTATGGATTTCCAGATAGGGCACTGA-GTGTGCT-AAAATGAT-AAGGAAATCATACTGAG
* * * * * * *
222907 TGGTATGGATTCTCGA-ATAGGGC-TTCA-TGTGCTAAAAATGGTTAAAGG-AATTATA-TTAA
1 T-GTATGGATT-TCCAGATAGGGCACTGAGTGTGCT-AAAAT-GAT-AAGGAAATCATACTGAG
* * ** * * *
222966 TGGTATGTATTCTCGA-ATAGGGCACTTCGTGTGCTAAAATGAGAAGAAAATCATA-TTA-
1 T-GTATGGATT-TCCAGATAGGGCACTGAGTGTGCTAAAATGATAAGGAAATCATACTGAG
* * * * * *
223024 AGTAT-GATATTCCAAATAGAGCACTGAGAGTGCTAATATTATAAGGAAAT-ATAC
1 TGTATGGAT-TTCCAGATAGGGCACTGAGTGTGCTAAAATGATAAGGAAATCATAC
223078 GAATTATATA
Statistics
Matches: 315, Mismatches: 68, Indels: 44
0.74 0.16 0.10
Matches are distributed among these distances:
56 9 0.03
57 46 0.15
58 103 0.33
59 122 0.39
60 27 0.09
61 8 0.03
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (59 bp):
TGTATGGATTTCCAGATAGGGCACTGAGTGTGCTAAAATGATAAGGAAATCATACTGAG
Found at i:222833 original size:117 final size:116
Alignment explanation
Indices: 222616--222917 Score: 301
Period size: 117 Copynumber: 2.6 Consensus size: 116
222606 TCATTTGAAT
* * * * *
222616 GTATGAATTTCCATATAGAGCACTGA-GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATG
1 GTATGAATTTCCAGATAGGGCACT-ACATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATG
*** * * * *
222680 GATTTTCATGTGGGCACTGAGTGTGCTAAAATGATAAGGAAATCATATTGAATA
65 GATTTTCATGAAAGCACTAAGGGTGCTAAAAGGATAAGGAAATCATACT--ATA
* * *
222734 -TATGGATTTCCAGATAGGGCATTATATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGG
1 GTATGAATTTCCAGATAGGGCACTACATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGG
* * *
222798 A-TTTC-TAGAAAATCACTAAGGGTTCTACAAGGATAAGGAAATCATACTATA
66 ATTTTCAT-G-AAAGCACTAAGGGTGCTAAAAGGATAAGGAAATCATACTATA
* * *
222849 GTATGAATTTTCATATAGGGCACTACATGTGCTAAAAATGGTAAAGGG-ATCATACT-AATGGTA
1 GTATGAATTTCCAGATAGGGCACTACATGTGCT-AAAATGGT-AAGGGAATCATACTGAGT-GTA
222912 TGGATT
63 TGGATT
222918 CTCGAATAGG
Statistics
Matches: 153, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
115 4 0.03
116 35 0.23
117 108 0.71
118 6 0.04
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (116 bp):
GTATGAATTTCCAGATAGGGCACTACATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGG
ATTTTCATGAAAGCACTAAGGGTGCTAAAAGGATAAGGAAATCATACTATA
Found at i:225771 original size:60 final size:60
Alignment explanation
Indices: 225689--225863 Score: 235
Period size: 60 Copynumber: 2.9 Consensus size: 60
225679 CTACAAGGAT
* * *
225689 AAGGAAATCATACTAATAGTATGAATTTTC-ATATAGGGCACTACATGTGCTAAAAATGGTA
1 AAGG-AATCATACTAATGGTATGAATTCTCGA-ATAGGGCACTTCATGTGCTAAAAATGGTA
* *
225750 AAGGGATCATACTAATGGTATGGATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTA
1 AAGGAATCATACTAATGGTATGAATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTA
* * * * *
225810 AAGGAATTATATTAATGATATGTATTCTCGAATAGGGCACTTCGTGTGCTAAAA
1 AAGGAATCATACTAATGGTATGAATTCTCGAATAGGGCACTTCATGTGCTAAAA
225864 TGAGAAGAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
60 97 0.95
61 5 0.05
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (60 bp):
AAGGAATCATACTAATGGTATGAATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTA
Found at i:225896 original size:60 final size:60
Alignment explanation
Indices: 225721--225909 Score: 208
Period size: 60 Copynumber: 3.2 Consensus size: 60
225711 GAATTTTCAT
* ** * * *
225721 ATAGGGCACTACATGTGCTAAAAATGGTAAAGGGATCATACTAATGGTATGGATTCTCGA
1 ATAGGGCACTTCATGTGCTAAAAATGGTAAAGAAATCATATTAATGATATGTATTCTCGA
* *
225781 ATAGGGCACTTCATGTGCTAAAAATGGTAAAGGAATTATATTAATGATATGTATTCTCGA
1 ATAGGGCACTTCATGTGCTAAAAATGGTAAAGAAATCATATTAATGATATGTATTCTCGA
* *
225841 ATAGGGCACTTCGTGTGCT-AAAAT-G-AGAAGAAAATCATATTAA-GTATATGATATTC-CAA
1 ATAGGGCACTTCATGTGCTAAAAATGGTA-AAG-AAATCATATTAATG-ATATG-TATTCTCGA
*
225900 ATAGAGCACT
1 ATAGGGCACT
225910 GAGAGTGCTA
Statistics
Matches: 114, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
57 1 0.01
58 5 0.04
59 31 0.27
60 77 0.68
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (60 bp):
ATAGGGCACTTCATGTGCTAAAAATGGTAAAGAAATCATATTAATGATATGTATTCTCGA
Found at i:225903 original size:59 final size:60
Alignment explanation
Indices: 225692--225909 Score: 205
Period size: 60 Copynumber: 3.6 Consensus size: 60
225682 CAAGGATAAG
* * * * *
225692 GAAATCATACTAAT-AGTATGAATTTTCATATAGGGCACTACATGTGCTAAAAATGGTAAA
1 GAAATCATATTAATGA-TATGTATTCTCAAATAGGGCACTTCATGTGCTAAAAATGGTAAA
** * * * *
225752 GGGATCATACTAATGGTATGGATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTAAA
1 GAAATCATATTAATGATATGTATTCTCAAATAGGGCACTTCATGTGCTAAAAATGGTAAA
* * * *
225812 GGAATTATATTAATGATATGTATTCTCGAATAGGGCACTTCGTGTGCT-AAAAT-G-AGAA
1 GAAATCATATTAATGATATGTATTCTCAAATAGGGCACTTCATGTGCTAAAAATGGTA-AA
*
225870 GAAAATCATATTAA-GTATATGATATTC-CAAATAGAGCACT
1 G-AAATCATATTAATG-ATATG-TATTCTCAAATAGGGCACT
225910 GAGAGTGCTA
Statistics
Matches: 135, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
57 1 0.01
58 5 0.04
59 31 0.23
60 98 0.73
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (60 bp):
GAAATCATATTAATGATATGTATTCTCAAATAGGGCACTTCATGTGCTAAAAATGGTAAA
Found at i:226077 original size:43 final size:43
Alignment explanation
Indices: 226016--226243 Score: 377
Period size: 43 Copynumber: 5.3 Consensus size: 43
226006 CAGTGATGCA
*
226016 AATTATAGTAAGTCTATTGGTAAAATAAGCTTACGAGCTTATG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* *
226059 AATTATAGTGAGTATATTGGAAAAATAAGCTTACGAGCTTATG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
226102 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 -AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
226146 AATTATAGTAAGTATATTGGT-AAATAAGCTTACGAGCTTATG
1 AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
*
226188 AAATTACAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 -AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT-G
*
226233 AATAATAGTAA
1 AATTATAGTAA
226244 ATAAGCTTAC
Statistics
Matches: 173, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
42 21 0.12
43 81 0.47
44 70 0.40
45 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (43 bp):
AATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
Found at i:226161 original size:87 final size:86
Alignment explanation
Indices: 226015--226243 Score: 395
Period size: 87 Copynumber: 2.6 Consensus size: 86
226005 TCAGTGATGC
* *
226015 AAATTATAGTAAGTCTATTGGTAAAATAAGCTTACGAGCTTATGAATTATAGTGAGTATATTGGA
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAATTATAGTAAGTATATTGG-
226080 AAAATAAGCTTACGAGCTTATG
65 AAAATAAGCTTACGAGCTTATG
*
226102 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAATTATAGTAAGTATATTGGT
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAATTATAGTAAGTATATTGGA
226167 AAATAAGCTTACGAGCTTATG
66 AAATAAGCTTACGAGCTTATG
* *
226188 AAATTACAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATAGTAA
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT-GAATTATAGTAA
226244 ATAAGCTTAC
Statistics
Matches: 136, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
86 63 0.46
87 73 0.54
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (86 bp):
AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAATTATAGTAAGTATATTGGA
AAATAAGCTTACGAGCTTATG
Found at i:226263 original size:30 final size:31
Alignment explanation
Indices: 226211--226273 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
226201 TATATTGGTA
226211 AAATAAGCTTACGAGCTTATGGAATAATAGT
1 AAATAAGCTTACGAGCTTATGGAATAATAGT
*
226242 AAATAAGCTTACGAG-TTATGGAATAATGGT
1 AAATAAGCTTACGAGCTTATGGAATAATAGT
226272 AA
1 AA
226274 GTATATTGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.29
Consensus pattern (31 bp):
AAATAAGCTTACGAGCTTATGGAATAATAGT
Found at i:226281 original size:74 final size:75
Alignment explanation
Indices: 226165--226303 Score: 226
Period size: 74 Copynumber: 1.9 Consensus size: 75
226155 AAGTATATTG
* *
226165 GTAAATAAGCTTACGAGCTTATGAAATTACAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 GTAAATAAGCTTACGAGCTTATGAAATAACAGTAAGTATATTGGTAAAATAAGCTTACGACCTTA
226230 TGGAATAATA
66 TGGAATAATA
* **
226240 GTAAATAAGCTTACGAG-TTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGACCTTA
1 GTAAATAAGCTTACGAGCTTATGAAATAACAGTAAGTATATTGGTAAAATAAGCTTACGACCTTA
226304 GGGATTTAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
74 42 0.71
75 17 0.29
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.31
Consensus pattern (75 bp):
GTAAATAAGCTTACGAGCTTATGAAATAACAGTAAGTATATTGGTAAAATAAGCTTACGACCTTA
TGGAATAATA
Found at i:226323 original size:45 final size:44
Alignment explanation
Indices: 226242--226371 Score: 163
Period size: 45 Copynumber: 2.9 Consensus size: 44
226232 GAATAATAGT
* *
226242 AAATAAGCTTACGAGTTATGGA-ATAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGACTTATGGATTTAATGGTAAGTATATTGGTA
*
226285 AAATAAGCTTACGACCTTAGGGATTTAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGA-CTTATGGATTTAATGGTAAGTATATTGGTA
* * * * *
226330 TATTAAGCTTTCGAGCTTATGGATTAAATGGTATGTATATTG
1 AAATAAGCTTACGA-CTTATGGATTTAATGGTAAGTATATTG
226372 ATAAGAAACT
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
43 14 0.19
44 6 0.08
45 55 0.73
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (44 bp):
AAATAAGCTTACGACTTATGGATTTAATGGTAAGTATATTGGTA
Found at i:238455 original size:47 final size:47
Alignment explanation
Indices: 238381--238476 Score: 147
Period size: 47 Copynumber: 2.0 Consensus size: 47
238371 AAAACTTAAC
* * *
238381 TTGAAACTAAACCTAAACTAAACTAAACAATTCAGCCGCATTTGCTT
1 TTGAAACTAAACCTAAAATAAAATAAACAATTCAGCCACATTTGCTT
* *
238428 TTGAACCTAAACCTAAAATAAAATAAACAATTCAGCCACATTTTCTT
1 TTGAAACTAAACCTAAAATAAAATAAACAATTCAGCCACATTTGCTT
238475 TT
1 TT
238477 TCACTCTCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.30
Consensus pattern (47 bp):
TTGAAACTAAACCTAAAATAAAATAAACAATTCAGCCACATTTGCTT
Found at i:239560 original size:22 final size:22
Alignment explanation
Indices: 239531--239599 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
239521 AGACATGGTT
*
239531 TTGCAACCGGGTTCGGGTTAGG
1 TTGCAACCGGGTTCGGGTCAGG
* *
239553 TTGTAACCAGGTTCGGGTCAGG
1 TTGCAACCGGGTTCGGGTCAGG
*
239575 TTGCAACCGGG-TCTGGGTCGGG
1 TTGCAACCGGGTTC-GGGTCAGG
239597 TTG
1 TTG
239600 GGTCGTAACC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
21 2 0.05
22 38 0.95
ACGTcount: A:0.13, C:0.19, G:0.41, T:0.28
Consensus pattern (22 bp):
TTGCAACCGGGTTCGGGTCAGG
Found at i:241217 original size:54 final size:55
Alignment explanation
Indices: 241141--241266 Score: 139
Period size: 55 Copynumber: 2.3 Consensus size: 55
241131 TACCTTCACA
* *
241141 TGTACCAACAC-CTAAATTACATTCAAAATGGCAAGGGTATC-ATACACTCCTCAG
1 TGTACCAATACAC-AAATAACATTCAAAATGGCAAGGGTATCAATACACTCCTCAG
* * ** ****
241195 TGTACCGATACACAAATAACATTCGATGTTTTGAGGGTATCAATACACTCCTCAG
1 TGTACCAATACACAAATAACATTCAAAATGGCAAGGGTATCAATACACTCCTCAG
241250 TGTACCAATACACAAAT
1 TGTACCAATACACAAAT
241267 GGAATTCGAT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
54 29 0.49
55 30 0.51
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (55 bp):
TGTACCAATACACAAATAACATTCAAAATGGCAAGGGTATCAATACACTCCTCAG
Found at i:241254 original size:55 final size:53
Alignment explanation
Indices: 241174--241318 Score: 193
Period size: 55 Copynumber: 2.7 Consensus size: 53
241164 CAAAATGGCA
241174 AGGGTATCATACACTCCTCAGTGTACCGATACACAAAT-AACATTCGATGTTTT
1 AGGGTATCATACACTCCTCAGTGTACCGATACACAAATGAA-ATTCGATGTTTT
* *
241227 GAGGGTATCAATACACTCCTCAGTGTACCAATACACAAATGGAATTCGATGTTTT
1 -AGGGTATC-ATACACTCCTCAGTGTACCGATACACAAATGAAATTCGATGTTTT
* * *
241282 ACGGGTATCGATACACTCTTTAGTGTACTGATACACA
1 A-GGGTATC-ATACACTCCTCAGTGTACCGATACACA
241319 CCCATACAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
54 9 0.11
55 71 0.88
56 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (53 bp):
AGGGTATCATACACTCCTCAGTGTACCGATACACAAATGAAATTCGATGTTTT
Found at i:246068 original size:25 final size:25
Alignment explanation
Indices: 246014--246068 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
246004 ACAAATGGGG
**
246014 CTGATCGGATACCTTGATTTCTTGG
1 CTGATCGGATACCTTGATTTCTTAC
*
246039 ATGATCGGATACCTTGATTTCTTAC
1 CTGATCGGATACCTTGATTTCTTAC
246064 CTGAT
1 CTGAT
246069 TTGTATCTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (25 bp):
CTGATCGGATACCTTGATTTCTTAC
Found at i:247825 original size:27 final size:27
Alignment explanation
Indices: 247794--247861 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
247784 TCTATTTACA
247794 AAATCACATCTCTATAGGAATGGTAAC
1 AAATCACATCTCTATAGGAATGGTAAC
*
247821 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCACATCTCTATAGGAATGGTAAC
247848 AAAT--CATCTCTATA
1 AAATCACATCTCTATA
247862 ATTCCTACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 9 0.23
27 30 0.77
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (27 bp):
AAATCACATCTCTATAGGAATGGTAAC
Done.