Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007916.1 Hibiscus syriacus cultivar Beakdansim tig00110319_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: 3725575
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 16
Found at i:212439 original size:20 final size:20
Alignment explanation
Indices: 212394--212433 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
212384 CTGAAACTTT
*
212394 AAATCACAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
212414 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
212434 CTATCGTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.10
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:212514 original size:20 final size:20
Alignment explanation
Indices: 212489--212535 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
212479 GATTATCTCG
212489 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
**
212509 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
212529 TTGCGAT
1 TTGCGAT
212536 TCACTCGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:215180 original size:57 final size:57
Alignment explanation
Indices: 214936--215159 Score: 376
Period size: 57 Copynumber: 3.9 Consensus size: 57
214926 TTCGATTTGC
* ** * * *
214936 GAAATTCGCGTTGCGATAGTTGTATTTACATATATCGGTAATTAGCGTTGCAAATTT
1 GAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
*
214993 GAAAATCGCGTTGCGATAGTACTGTTTATCTATATCGGTAATTAGCGTTGCGAATTT
1 GAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
215050 GAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
1 GAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
*
215107 GAAAATCACGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGA
1 GAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGA
215160 TTTACATATT
Statistics
Matches: 158, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 158 1.00
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (57 bp):
GAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
Found at i:216069 original size:56 final size:55
Alignment explanation
Indices: 215999--216183 Score: 244
Period size: 56 Copynumber: 3.2 Consensus size: 55
215989 TAGGGACCTC
* * *
215999 AAATCGAGTATATCTATCAGTTGTTGCCATTAATAAGCATAAAAATAGTGGTCCCG
1 AAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAACATAAAAATAGAGG-CCCG
*
216055 AAATCGAGTATATCTATAAGTTGTTGCCATTAAGAAACATAAAAATAGAGGCCTCG
1 AAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAACATAAAAATAGAGGCC-CG
* *
216111 AAATCGAGTATATATATATATCAGTTGTTGCCATTAAGAAACATAAAAATAGGGGGCCCG
1 AAATCGAG----TATATCTATCAGTTGTTGCCATTAAGAAACATAAAAATA-GAGGCCCG
*
216171 AAATCGAATATAT
1 AAATCGAGTATAT
216184 ATAGAAAATA
Statistics
Matches: 115, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
55 2 0.02
56 62 0.54
60 46 0.40
61 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (55 bp):
AAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAACATAAAAATAGAGGCCCG
Found at i:216153 original size:60 final size:59
Alignment explanation
Indices: 216007--216186 Score: 242
Period size: 60 Copynumber: 3.1 Consensus size: 59
215997 TCAAATCGAG
* * * *
216007 TATATCTATCAGTTGTTGCCATTAATAAGCATAAAAATAGTGGTCCCGAAATCGAG--TA
1 TATATATATCAGTTGTTGCCATTAAGAAACATAAAAATAGAGG-CCCGAAATCGAGTATA
*
216065 TATCTATA--AGTTGTTGCCATTAAGAAACATAAAAATAGAGGCCTCGAAATCGAGTATA
1 TATATATATCAGTTGTTGCCATTAAGAAACATAAAAATAGAGGCC-CGAAATCGAGTATA
* *
216123 TATATATATCAGTTGTTGCCATTAAGAAACATAAAAATAGGGGGCCCGAAATCGAATATA
1 TATATATATCAGTTGTTGCCATTAAGAAACATAAAAATA-GAGGCCCGAAATCGAGTATA
216183 TATA
1 TATA
216187 GAAAATAGGA
Statistics
Matches: 108, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
55 2 0.02
56 40 0.37
58 15 0.14
60 46 0.43
61 5 0.05
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (59 bp):
TATATATATCAGTTGTTGCCATTAAGAAACATAAAAATAGAGGCCCGAAATCGAGTATA
Found at i:222869 original size:9 final size:9
Alignment explanation
Indices: 222855--222880 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
222845 TATGCTCCCT
222855 TTTCTTTTC
1 TTTCTTTTC
222864 TTTCTTTTC
1 TTTCTTTTC
222873 TTTCTTTT
1 TTTCTTTT
222881 TCCCGCTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:227261 original size:40 final size:40
Alignment explanation
Indices: 227212--227307 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
227202 GCAATTTTCC
* *
227212 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAACGCGAATATGTAAATCACAATGCGAGTAT
* *
227252 GACTATCGCAACGCAAATATGTAAATCACAATGCGATTAT
1 GACTATCGCAACGCGAATATGTAAATCACAATGCGAGTAT
227292 GACTATCGCAACGCGA
1 GACTATCGCAACGCGA
227308 TTCTGGCTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (40 bp):
GACTATCGCAACGCGAATATGTAAATCACAATGCGAGTAT
Found at i:227307 original size:20 final size:20
Alignment explanation
Indices: 227212--227330 Score: 89
Period size: 20 Copynumber: 5.9 Consensus size: 20
227202 GCAATTTTCC
227212 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGAATAT
* *
227232 GTA-AATCGCAATGCGAGTAT
1 G-ACTATCGCAATGCGAATAT
* *
227252 GACTATCGCAACGCAAATAT
1 GACTATCGCAATGCGAATAT
* * *
227272 GTA-AATCACAATGCGATTAT
1 G-ACTATCGCAATGCGAATAT
* * *
227292 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGAATAT
* *
227312 GGCTGTCGCAATGCTGAAT
1 GACTATCGCAATGC-GAAT
227331 TTCAAATTCG
Statistics
Matches: 75, Mismatches: 19, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
19 2 0.03
20 68 0.91
21 5 0.07
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (20 bp):
GACTATCGCAATGCGAATAT
Found at i:228176 original size:24 final size:24
Alignment explanation
Indices: 228142--228188 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
228132 GTATTCGAAA
*
228142 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
*
228166 TTTGATATTGGTCAATACTCGGA
1 TTTGATATTGGTCAATACCCGGA
228189 TTTTTATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:229779 original size:54 final size:54
Alignment explanation
Indices: 229697--229853 Score: 251
Period size: 54 Copynumber: 2.9 Consensus size: 54
229687 GAATATGATT
* * * *
229697 ATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAATATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
*
229751 ATCGCAATGCGAAAATGACTATCGCAACGCAAATTTGACTATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
* *
229805 ATCGCAATGCGAAAATGACTATCGCAACACGAATATGACTATCGCAACG
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACG
229854 CGAATTTAAC
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 95 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (54 bp):
ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
Found at i:229798 original size:74 final size:74
Alignment explanation
Indices: 229677--230005 Score: 328
Period size: 74 Copynumber: 4.5 Consensus size: 74
229667 TCATTTGACT
* * * *
229677 ATCGCAACGCGAATATGATTATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAATATCGC
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAGAATTTGAATATCGC
*
229742 AACGGGATA
66 AACGAGATA
* * * * * *
229751 ATCGCAATGCGAAAATGACTATCGCAACGCAAATTTGACTATCGCAACGGGATAATCGCA-AT-G
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAGA-ATTTGAATATCG
*
229814 CGAA-AATGACT-
65 C-AACGA-GA-TA
* * * * * *
229825 ATCGCAACACGAATATGACTATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATAGC
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAGAATTTGAATATCGC
229890 AACGAGATA
66 AACGAGATA
* * * *
229899 ATCGCAACGCG-AAATGACTATCACAATGCGAATTTGATTATCGCAACGAGAATTTGACTATCGC
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAGAATTTGAATATCGC
*
229963 AACGAGAAA
66 AACGAGATA
* * * *
229972 ATCGCAAAGTG-TATTAGACTATCGCAACGCGAAT
1 ATCGCAACGCGAAAAT-GACTATCGCAACGCGAAT
230006 ATGATGCAGA
Statistics
Matches: 209, Mismatches: 37, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
73 71 0.34
74 130 0.62
75 8 0.04
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (74 bp):
ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGAGAATTTGAATATCGC
AACGAGATA
Found at i:229908 original size:34 final size:34
Alignment explanation
Indices: 229865--229978 Score: 106
Period size: 34 Copynumber: 3.2 Consensus size: 34
229855 GAATTTAACT
229865 ATCGCAACGCGAATTTGACTATAGCAACGAGATA
1 ATCGCAACGCGAATTTGACTATAGCAACGAGATA
* *
229899 ATCGCAACGCGAA-ATGACTATCA-CAATGCGAATTTGATT
1 ATCGCAACGCGAATTTGACTAT-AGCAA--CG-A---GATA
* * *
229938 ATCGCAACGAGAATTTGACTATCGCAACGAGAAA
1 ATCGCAACGCGAATTTGACTATAGCAACGAGATA
229972 ATCGCAA
1 ATCGCAA
229979 AGTGTATTAG
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
33 10 0.16
34 23 0.36
35 2 0.03
36 1 0.02
37 1 0.02
38 2 0.03
39 15 0.23
40 10 0.16
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATAGCAACGAGATA
Found at i:229932 original size:53 final size:54
Alignment explanation
Indices: 229845--229949 Score: 149
Period size: 53 Copynumber: 2.0 Consensus size: 54
229835 GAATATGACT
* *
229845 ATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATAGCAACGAGATA
1 ATCGCAACGCGAATATAACTATCACAACGCGAATTTGACTATAGCAACGAGATA
* * * *
229899 ATCGCAACGCGAA-ATGACTATCACAATGCGAATTTGATTATCGCAACGAGA
1 ATCGCAACGCGAATATAACTATCACAACGCGAATTTGACTATAGCAACGAGA
229950 ATTTGACTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
53 32 0.71
54 13 0.29
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (54 bp):
ATCGCAACGCGAATATAACTATCACAACGCGAATTTGACTATAGCAACGAGATA
Found at i:229970 original size:20 final size:20
Alignment explanation
Indices: 229669--229966 Score: 247
Period size: 20 Copynumber: 15.8 Consensus size: 20
229659 TTACACATTC
229669 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
229689 ATATGATTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
229709 ATATGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
229729 ATTTGAATATCGCAACG-GG
1 ATTTGACTATCGCAACGCGA
*
229748 A--T-A--ATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
** *
229763 AAATGACTATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
*
229783 ATTTGACTATCGCAACG-GG
1 ATTTGACTATCGCAACGCGA
*
229802 A--T-A--ATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
** *
229817 AAATGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
229837 ATATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
229857 ATTTAACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
229877 ATTTGACTATAGCAACGAG-
1 ATTTGACTATCGCAACGCGA
229896 A--T-A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
229911 A-ATGACTATCACAATGCGA
1 ATTTGACTATCGCAACGCGA
* *
229930 ATTTGATTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
229950 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
229967 AGAAAATCGC
Statistics
Matches: 224, Mismatches: 36, Indels: 36
0.76 0.12 0.12
Matches are distributed among these distances:
14 25 0.11
15 5 0.02
16 4 0.02
17 6 0.03
18 2 0.01
19 15 0.07
20 167 0.75
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:230087 original size:36 final size:33
Alignment explanation
Indices: 230047--230125 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 33
230037 TTACATTTCA
230047 ATCAATTAAACAAGCAAAAATAAGAATTATTTACAC
1 ATCAATTAAACAA-C--AAATAAGAATTATTTACAC
230083 ATCAATT--A-AACAAATAAGAATTATTTACAC
1 ATCAATTAAACAACAAATAAGAATTATTTACAC
*
230113 GTCAATTAAACAA
1 ATCAATTAAACAA
230126 ATCAACTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
30 25 0.64
32 2 0.05
33 4 0.10
34 1 0.03
36 7 0.18
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.27
Consensus pattern (33 bp):
ATCAATTAAACAACAAATAAGAATTATTTACAC
Found at i:230100 original size:30 final size:30
Alignment explanation
Indices: 230064--230127 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
230054 AAACAAGCAA
230064 AAATAAGAATTATTTACACATCAATTAAAC
1 AAATAAGAATTATTTACACATCAATTAAAC
*
230094 AAATAAGAATTATTTACACGTCAATTAAAC
1 AAATAAGAATTATTTACACATCAATTAAAC
230124 AAAT
1 AAAT
230128 CAACTCTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATAAGAATTATTTACACATCAATTAAAC
Found at i:231565 original size:21 final size:22
Alignment explanation
Indices: 231541--231617 Score: 65
Period size: 21 Copynumber: 3.7 Consensus size: 22
231531 TGACAGTGGC
231541 CTCTTGAACGG-TGAGAGGGGA
1 CTCTTGAACGGATGAGAGGGGA
* * *
231562 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAACGGATGAGAGGGGA
* *
231583 CTCTTGAAC-GAT-AGGGGAGGC
1 CTCTTGAACGGATGAGAGG-GGA
231604 CTCTTGAAC-GATGA
1 CTCTTGAACGGATGA
231618 CAGGTGAGTC
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 6 0.13
21 38 0.83
22 2 0.04
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (22 bp):
CTCTTGAACGGATGAGAGGGGA
Found at i:231608 original size:42 final size:42
Alignment explanation
Indices: 231529--231621 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
231519 CCTCTTCAAC
* *
231529 GATGACAGTGGCCTCTTGAACGGTGAGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGAGAGGGGACTCTTGAGG
* * * **
231571 GATGATAGGGGCCTCTTGAACGAT-AGGGGAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGATGAGAGG-GGACTCTTGAGG
231613 GATGACAGG
1 GATGACAGG
231622 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 4 0.10
42 38 0.90
ACGTcount: A:0.24, C:0.17, G:0.39, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGAGAGGGGACTCTTGAGG
Found at i:232143 original size:20 final size:20
Alignment explanation
Indices: 232118--232173 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
232108 TCGCAACACG
*
232118 AATGACTATCGCAACGTGAA
1 AATGACTATCGCAACGCGAA
232138 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
232158 AATGACTATCACAACG
1 AATGACTATCGCAACG
232174 AGAGAATCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:232241 original size:20 final size:20
Alignment explanation
Indices: 232216--232283 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
232206 GCGATTCTTT
*
232216 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
* *
232236 CGTTGCAATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
232256 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
232276 CGTTGCGA
1 CGTTGCGA
232284 AAGTGAACTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 3 0.07
20 39 0.93
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:232454 original size:18 final size:18
Alignment explanation
Indices: 232431--232480 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
232421 TTTACTAAGC
232431 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
232449 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
232467 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
232481 TATGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:234263 original size:20 final size:20
Alignment explanation
Indices: 234208--234264 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
234198 TTTGAAACTT
*
234208 AAAATCGCAACACAAAAATG
1 AAAATCGCAACACGAAAATG
234228 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
234248 ACTATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
234265 CAAAAATCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.53, C:0.23, G:0.14, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:234681 original size:22 final size:22
Alignment explanation
Indices: 234655--234729 Score: 114
Period size: 22 Copynumber: 3.4 Consensus size: 22
234645 GAGATAGACG
234655 GATTTCGCCGGAGATGGGGACT
1 GATTTCGCCGGAGATGGGGACT
*
234677 GATTTCGTCGGAGATGGGGACT
1 GATTTCGCCGGAGATGGGGACT
* *
234699 GATTTCGTCGGAGATGGGGACG
1 GATTTCGCCGGAGATGGGGACT
*
234721 GATGTCGCC
1 GATTTCGCC
234730 TTAGAGAGTG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.17, C:0.17, G:0.41, T:0.24
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACT
Found at i:234919 original size:20 final size:20
Alignment explanation
Indices: 234894--234952 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
234884 GCGCTTTGAA
*
234894 AATCGCATTGCGACAGTCAG
1 AATCGCATTGCGATAGTCAG
*
234914 AATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
234934 AATCGCATTGCGATAGTCA
1 AATCGCATTGCGATAGTCA
234953 TACTCATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:234963 original size:20 final size:20
Alignment explanation
Indices: 234921--234998 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
234911 CAGAATCGCG
* * *
234921 TTGCGATAGTCAGAATCGCA
1 TTGCGATAGTCATACTCACA
*
234941 TTGCGATAGTCATACTCATA
1 TTGCGATAGTCATACTCACA
* * * *
234961 TTGCGAT-TTACATATTCGCG
1 TTGCGATAGT-CATACTCACA
234981 TTGCGATAGTCATACTCA
1 TTGCGATAGTCATACTCA
234999 TACTCGCATT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
21 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATACTCACA
Found at i:234965 original size:40 final size:40
Alignment explanation
Indices: 234894--235000 Score: 108
Period size: 40 Copynumber: 2.7 Consensus size: 40
234884 GCGCTTTGAA
* * * ***
234894 AATCGCATTGCGACAGTCAGAATCGCGTTGCGATAGT-CAG
1 AATCGCATTGCGATAGTCATACTCATATTGCGAT-GTACAG
* *
234934 AATCGCATTGCGATAGTCATACTCATATTGCGATTTACAT
1 AATCGCATTGCGATAGTCATACTCATATTGCGATGTACAG
* *
234974 ATTCGCGTTGCGATAGTCATACTCATA
1 AATCGCATTGCGATAGTCATACTCATA
235001 CTCGCATTGC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.02
40 55 0.98
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (40 bp):
AATCGCATTGCGATAGTCATACTCATATTGCGATGTACAG
Found at i:235017 original size:46 final size:46
Alignment explanation
Indices: 234950--235037 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
234940 ATTGCGATAG
* *
234950 TCATACTCATATTGCGATTTACATATTCGCGTTGCGATAGTCATAC
1 TCATACTCACATTGCGATTTACATATTCGCATTGCGATAGTCATAC
* *
234996 TCATACTCGCATTGCGATTTACATATTCGCATTGTGATAGTC
1 TCATACTCACATTGCGATTTACATATTCGCATTGCGATAGTC
235038 GGAAAATCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (46 bp):
TCATACTCACATTGCGATTTACATATTCGCATTGCGATAGTCATAC
Found at i:235025 original size:20 final size:20
Alignment explanation
Indices: 234960--235029 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 20
234950 TCATACTCAT
234960 ATTGCGATTTACATATTCGC
1 ATTGCGATTTACATATTCGC
* *
234980 GTTGCGATAGTCATACTCATACTCGC
1 ATTGCGAT--T--TA--CATATTCGC
235006 ATTGCGATTTACATATTCGC
1 ATTGCGATTTACATATTCGC
235026 ATTG
1 ATTG
235030 TGATAGTCGG
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
20 19 0.47
22 3 0.08
24 3 0.08
26 15 0.38
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.37
Consensus pattern (20 bp):
ATTGCGATTTACATATTCGC
Found at i:236200 original size:21 final size:21
Alignment explanation
Indices: 236161--236200 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
236151 GTTTCCACTC
* * *
236161 TTCTTCTTCCTTTTTCCTCCT
1 TTCTTCCTCCATTTCCCTCCT
236182 TTCTTCCTCCATTTCCCTC
1 TTCTTCCTCCATTTCCCTC
236201 TCAGCAGCTT
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:0.03, C:0.42, G:0.00, T:0.55
Consensus pattern (21 bp):
TTCTTCCTCCATTTCCCTCCT
Found at i:238670 original size:2 final size:2
Alignment explanation
Indices: 238663--238702 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
238653 TTTGAAAGTT
238663 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
238703 AACAATTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:253957 original size:24 final size:23
Alignment explanation
Indices: 253917--253966 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
253907 ATAAATCTAG
*
253917 TTTTTTAATTTGATTATTTTAAT
1 TTTTTTAATTTGATTATATTAAT
*
253940 TTTTTATAATTT-AGTTATATTACT
1 TTTTT-TAATTTGA-TTATATTAAT
253964 TTT
1 TTT
253967 ATATTGTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (23 bp):
TTTTTTAATTTGATTATATTAAT
Found at i:269072 original size:62 final size:62
Alignment explanation
Indices: 268975--269098 Score: 232
Period size: 62 Copynumber: 2.0 Consensus size: 62
268965 AGGAAATTAG
268975 TCAAGGGAGTTGAAGTTGGCGCGGGAAAAGCTCCGGAAAGAGGGCTGGGAAATCG-TAGATCC
1 TCAAGGGAGTTGAAGTTGGCGCGGGAAAAGCTCCGGAAAGAGGGCT-GGAAATCGATAGATCC
269037 TCAAGGGAGTTGAAGTTGGCGCGGGAAAAGCTCCGGAAAGAGGGCTGGAAATCGATAGATCC
1 TCAAGGGAGTTGAAGTTGGCGCGGGAAAAGCTCCGGAAAGAGGGCTGGAAATCGATAGATCC
269099 ATGGGGGAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
61 8 0.13
62 53 0.87
ACGTcount: A:0.30, C:0.16, G:0.38, T:0.16
Consensus pattern (62 bp):
TCAAGGGAGTTGAAGTTGGCGCGGGAAAAGCTCCGGAAAGAGGGCTGGAAATCGATAGATCC
Found at i:271633 original size:2 final size:2
Alignment explanation
Indices: 271621--271688 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
271611 TTAAAAATAG
*
271621 AT AT GT 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
*
271663 AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
271689 TCACATGTGC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
AT
Found at i:273295 original size:45 final size:48
Alignment explanation
Indices: 273228--273325 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 48
273218 TTTATTTTTG
273228 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCT-GTTAGG-TTTA
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATG-TGGTTAGGATTTA
* *
273275 TTTTTCGAA-CAA-GCATGCGAATTAGATATCATGTGGTTAGGATTTA
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGTGGTTAGGATTTA
273321 TTTTT
1 TTTTT
273326 GTGAATAACA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
44 1 0.02
45 26 0.55
46 11 0.23
47 9 0.19
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (48 bp):
TTTTTCGAATAAATGCATGCGAACTAGATATCATGTGGTTAGGATTTA
Found at i:274752 original size:42 final size:41
Alignment explanation
Indices: 274678--274766 Score: 162
Period size: 42 Copynumber: 2.2 Consensus size: 41
274668 TTTGTGAATT
274678 AAAG-TTGGGTTATGATTCTAGGTGATACTTAAGCTTAAGG
1 AAAGCTTGGGTTATGATTCTAGGTGATACTTAAGCTTAAGG
274718 AAAGCTTGGGTTATGATTCTTAGGTGATACTTAAGCTTAAGG
1 AAAGCTTGGGTTATGATTC-TAGGTGATACTTAAGCTTAAGG
274760 AAAGCTT
1 AAAGCTT
274767 AAGTTATCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 4 0.09
41 14 0.30
42 29 0.62
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (41 bp):
AAAGCTTGGGTTATGATTCTAGGTGATACTTAAGCTTAAGG
Found at i:276243 original size:103 final size:103
Alignment explanation
Indices: 276059--276276 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
276049 GTCGAGGGTT
276059 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
276124 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
* *
276162 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
276227 TTGATCCCTAGTATATGTATATGATTATTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
276265 TATGTGGTCCTT
1 TATGTGGTCCTT
276277 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
Found at i:276326 original size:23 final size:23
Alignment explanation
Indices: 276293--276355 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
276283 ATTATTATAT
*
276293 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACAC
* *
276316 GGCACTCCGGTGCAATTCTACAT
1 GGCACTACGGTGCAATTCTACAC
*
276339 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
276356 ATATGAGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACAC
Found at i:285872 original size:23 final size:23
Alignment explanation
Indices: 285841--285909 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
285831 CACCACAGCT
* *
285841 CGTATAATTGTACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
285864 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
285887 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
285910 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:293323 original size:29 final size:30
Alignment explanation
Indices: 293279--293341 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
293269 GAAGGACCTA
*
293279 TCCAGAGGTCACAAAG-ACCCCGGTAACTG
1 TCCAGAGGTCACAAAGAACCCCGATAACTG
* *
293308 TCCAGAGGTCATAAAGAACCTCGATAACTG
1 TCCAGAGGTCACAAAGAACCCCGATAACTG
293338 TCCA
1 TCCA
293342 TATATCCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.33, C:0.29, G:0.21, T:0.17
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGATAACTG
Found at i:293371 original size:31 final size:31
Alignment explanation
Indices: 293333--293428 Score: 133
Period size: 31 Copynumber: 3.1 Consensus size: 31
293323 GAACCTCGAT
293333 AACTGTCCATATATCCC-AACGAACCTAGGTA
1 AACTGTCCATATATCCCGAA-GAACCTAGGTA
*
293364 AACTGTCCATAGATCCCGAAGAACCTAGGTA
1 AACTGTCCATATATCCCGAAGAACCTAGGTA
* *
293395 AACTGTCCATATATCTCGAA-AGACATAGGTA
1 AACTGTCCATATATCCCGAAGA-ACCTAGGTA
293426 AAC
1 AAC
293429 CCTCGACTCT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
30 1 0.02
31 56 0.95
32 2 0.03
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.22
Consensus pattern (31 bp):
AACTGTCCATATATCCCGAAGAACCTAGGTA
Found at i:294068 original size:16 final size:16
Alignment explanation
Indices: 294047--294087 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
294037 CATATCAATA
294047 ACACATATACTCATGC
1 ACACATATACTCATGC
294063 ACACATATACTCATGC
1 ACACATATACTCATGC
294079 ACACATATA
1 ACACATATA
294088 AATCATAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.41, C:0.29, G:0.05, T:0.24
Consensus pattern (16 bp):
ACACATATACTCATGC
Found at i:294466 original size:62 final size:62
Alignment explanation
Indices: 294333--294471 Score: 151
Period size: 63 Copynumber: 2.2 Consensus size: 62
294323 TCTTTAACAT
* * *
294333 GTGCATCGATGCACTACCCATGCATCGATCGACAAATTACCTTCGATGTTTTCATTTTAAGG
1 GTGCATCGATGCACTACCCATGCATCGATCGACAAATTACATTCGATGTTTTCATTTAAAGA
* * *
294395 GATGCATCGATGCACT-CCTTATGCATCGAT-G-CACATTTGCATTCGATGTTTTTTC-TTTAAA
1 G-TGCATCGATGCACTACC-CATGCATCGATCGACA-AATTACATTCGATG--TTTTCATTTAAA
294456 GA
61 GA
294458 GTGCATCGATGCAC
1 GTGCATCGATGCAC
294472 ATTCATTGCA
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
61 2 0.03
62 28 0.42
63 31 0.47
64 5 0.08
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (62 bp):
GTGCATCGATGCACTACCCATGCATCGATCGACAAATTACATTCGATGTTTTCATTTAAAGA
Found at i:297390 original size:30 final size:30
Alignment explanation
Indices: 297327--297428 Score: 143
Period size: 30 Copynumber: 3.4 Consensus size: 30
297317 CCCGAAGGAC
* * * *
297327 CTATCCATAGGTCACAAAG-ACCCCGGTAA
1 CTATCCAGAGGTCATAAAGAACCTCGGCAA
297356 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAGAGGTCATAAAGAACCTCGGCAA
297386 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAGAGGTCATAAAGAACCTCGGCAA
* *
297416 CTTTCCATAGGTC
1 CTATCCAGAGGTC
297429 CCGAAAAACC
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
29 17 0.26
30 49 0.74
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGAACCTCGGCAA
Found at i:297439 original size:30 final size:30
Alignment explanation
Indices: 297327--297470 Score: 96
Period size: 30 Copynumber: 4.8 Consensus size: 30
297317 CCCGAAGGAC
* * * *
297327 CTATCCATAGGTCAC-AAAGACCCCGGTAA
1 CTATCCATAGGTCCCGAAAAACCTCGGCAA
* **
297356 CTATCCAGAGGT-CATAAAGAACCTCGGCAA
1 CTATCCATAGGTCCCGAAA-AACCTCGGCAA
* **
297386 CTATCCAGAGGT-CATAAAGAACCTCGGCAA
1 CTATCCATAGGTCCCGAAA-AACCTCGGCAA
* * *
297416 CTTTCCATAGGTCCCGAAAAACCTAGGTAAA
1 CTATCCATAGGTCCCGAAAAACCTCGG-CAA
* * *
297447 CTGTCTATAGGTCCCGAAGAACCT
1 CTATCCATAGGTCCCGAAAAACCT
297471 AGGTAAACTG
Statistics
Matches: 96, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
29 14 0.15
30 55 0.57
31 27 0.28
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
CTATCCATAGGTCCCGAAAAACCTCGGCAA
Found at i:297458 original size:31 final size:31
Alignment explanation
Indices: 297414--297509 Score: 120
Period size: 31 Copynumber: 3.1 Consensus size: 31
297404 GAACCTCGGC
*
297414 AACTTTCCATAGGTCCCGAAAAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAAAACCTAGGTA
* *
297445 AACTGTCTATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAAAACCTAGGTA
* * * * *
297476 AACTGTCCATATGTCTCTAAAGACATAGGTA
1 AACTGTCCATAGGTCCCGAAAAACCTAGGTA
297507 AAC
1 AAC
297510 CCTCGACTCT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAAAACCTAGGTA
Found at i:298596 original size:64 final size:63
Alignment explanation
Indices: 298528--298648 Score: 147
Period size: 64 Copynumber: 1.9 Consensus size: 63
298518 TGCACTACCC
*
298528 ATGCATCGATACACAAATTACCTTCGATGTTTTCATT-TTAAAAG-GATGCATCGATGCATTCTT
1 ATGCATCGATACACAAATTACATTCGATG-TTTC-TTCTTAAAAGAG-TGCATCGATGCATTCTT
298591 T
63 T
* * * * *
298592 ATGCATCGATGCACCATTTGCATTCGATGTTTCTTCTTTAAAGAGTGCATCGATGCA
1 ATGCATCGATACACAAATTACATTCGATGTTTCTTCTTAAAAGAGTGCATCGATGCA
298649 CATTCAATGT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
62 2 0.04
63 22 0.45
64 25 0.51
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (63 bp):
ATGCATCGATACACAAATTACATTCGATGTTTCTTCTTAAAAGAGTGCATCGATGCATTCTTT
Found at i:300475 original size:8 final size:8
Alignment explanation
Indices: 300457--300583 Score: 50
Period size: 8 Copynumber: 15.5 Consensus size: 8
300447 TTTCGCCTGA
300457 AAAAGAAAT
1 AAAA-AAAT
300466 AAAAAAAT
1 AAAAAAAT
*
300474 AAAAATA-
1 AAAAAAAT
300481 AAAAAAAT
1 AAAAAAAT
*
300489 GAAAAAGA-
1 -AAAAAAAT
*
300497 AGAAAAAT
1 AAAAAAAT
*
300505 GAAAAAAT
1 AAAAAAAT
* *
300513 GAAACAAT
1 AAAAAAAT
300521 GAAATAAAA-
1 -AAA-AAAAT
*
300530 AGAAAAAT
1 AAAAAAAT
300538 GAAAAAAA-
1 -AAAAAAAT
*
300546 ATGAAAAAT
1 A-AAAAAAT
*
300555 -GAAAAAT
1 AAAAAAAT
300562 GAAAAAAA-
1 -AAAAAAAT
300570 AGAGAAAAAT
1 A-A-AAAAAT
300580 AAAA
1 AAAA
300584 GGGGTTCAAG
Statistics
Matches: 90, Mismatches: 14, Indels: 29
0.68 0.11 0.22
Matches are distributed among these distances:
7 24 0.27
8 33 0.37
9 29 0.32
10 4 0.04
ACGTcount: A:0.78, C:0.01, G:0.11, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:300484 original size:7 final size:8
Alignment explanation
Indices: 300482--300568 Score: 74
Period size: 8 Copynumber: 10.8 Consensus size: 8
300472 ATAAAAATAA
300482 AAAAAATG
1 AAAAAATG
*
300490 AAAAAGAAG
1 AAAAA-ATG
300499 -AAAAATG
1 AAAAAATG
300506 AAAAAATG
1 AAAAAATG
*
300514 AAACAATG
1 AAAAAATG
*
300522 AAATAAA-A
1 AAA-AAATG
300530 AGAAAAATG
1 A-AAAAATG
300539 AAAAAAAATG
1 --AAAAAATG
300549 -AAAAATG
1 AAAAAATG
300556 -AAAAATG
1 AAAAAATG
300563 AAAAAA
1 AAAAAA
300569 AAGAGAAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
7 16 0.25
8 35 0.54
9 6 0.09
10 7 0.11
11 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.13, T:0.10
Consensus pattern (8 bp):
AAAAAATG
Found at i:300487 original size:16 final size:16
Alignment explanation
Indices: 300468--300560 Score: 73
Period size: 17 Copynumber: 5.7 Consensus size: 16
300458 AAAGAAATAA
*
300468 AAAAATAAAAATAAA-
1 AAAAATAAAAAAAAAG
* *
300483 AAAAATGAAAAAGAAG
1 AAAAATAAAAAAAAAG
* *
300499 AAAAAT-GAAAAAATG
1 AAAAATAAAAAAAAAG
*
300514 AAACAATGAAATAAAAAG
1 AAA-AAT-AAAAAAAAAG
*
300532 AAAAATGAAAAAAAATG
1 AAAAAT-AAAAAAAAAG
300549 AAAAATGAAAAA
1 AAAAAT-AAAAA
300561 TGAAAAAAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
15 21 0.33
16 9 0.14
17 24 0.38
18 9 0.14
ACGTcount: A:0.77, C:0.01, G:0.11, T:0.11
Consensus pattern (16 bp):
AAAAATAAAAAAAAAG
Found at i:300493 original size:24 final size:25
Alignment explanation
Indices: 300456--300583 Score: 101
Period size: 24 Copynumber: 5.2 Consensus size: 25
300446 ATTTCGCCTG
300456 AAAAAGAAAT-AAAAAAAT-AAAAAT
1 AAAAA-AAATGAAAAAAATGAAAAAT
300480 AAAAAAAATGAAAAAGAA-GAAAAAT
1 AAAAAAAATGAAAAA-AATGAAAAAT
* *
300505 -GAAAAAATG-AAACAATGAAATAA-
1 AAAAAAAATGAAAAAAATGAAA-AAT
300528 AAAGAAAAATGAAAAAAAATGAAAAAT
1 AAA-AAAAATG-AAAAAAATGAAAAAT
* *
300555 --GAAAAATGAAAAAAAAGAGAAAAAT
1 AAAAAAAATG-AAAAAAA-TGAAAAAT
300580 AAAA
1 AAAA
300584 GGGGTTCAAG
Statistics
Matches: 84, Mismatches: 7, Indels: 23
0.74 0.06 0.20
Matches are distributed among these distances:
22 2 0.02
23 11 0.13
24 36 0.43
25 22 0.26
26 2 0.02
27 11 0.13
ACGTcount: A:0.78, C:0.01, G:0.11, T:0.10
Consensus pattern (25 bp):
AAAAAAAATGAAAAAAATGAAAAAT
Found at i:300569 original size:16 final size:16
Alignment explanation
Indices: 300483--300560 Score: 97
Period size: 17 Copynumber: 4.8 Consensus size: 16
300473 TAAAAATAAA
300483 AAAAATGAAAAAGAA-G
1 AAAAATGAAAAA-AATG
300499 AAAAATG-AAAAAATG
1 AAAAATGAAAAAAATG
*
300514 AAACAATGAAATAAAAAG
1 AAA-AATGAAA-AAAATG
300532 AAAAATGAAAAAAAATG
1 AAAAATG-AAAAAAATG
300549 AAAAATGAAAAA
1 AAAAATGAAAAA
300561 TGAAAAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
14 2 0.04
15 8 0.15
16 16 0.29
17 18 0.33
18 11 0.20
ACGTcount: A:0.76, C:0.01, G:0.13, T:0.10
Consensus pattern (16 bp):
AAAAATGAAAAAAATG
Found at i:300644 original size:45 final size:43
Alignment explanation
Indices: 300581--300664 Score: 114
Period size: 45 Copynumber: 1.9 Consensus size: 43
300571 GAGAAAAATA
*
300581 AAAGGGGTTCAAGATGAAAACCCGGAAAAGGCGTCTTGAAACC
1 AAAGGGGTTCAAGATGAAAACCCGGAAAAGGCGACTTGAAACC
* * *
300624 AAAGGAGGTCTCAAGTTGAAAACTCGGAAAGGGCGACTTGA
1 AAAGG-GGT-TCAAGATGAAAACCCGGAAAAGGCGACTTGA
300665 GTTTTGTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 5 0.14
44 3 0.09
45 27 0.77
ACGTcount: A:0.38, C:0.17, G:0.30, T:0.15
Consensus pattern (43 bp):
AAAGGGGTTCAAGATGAAAACCCGGAAAAGGCGACTTGAAACC
Found at i:302013 original size:55 final size:55
Alignment explanation
Indices: 301938--302321 Score: 324
Period size: 55 Copynumber: 7.0 Consensus size: 55
301928 AGTGAAATAA
* * * ** *
301938 ACACATTTGTTGAAGATTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
1 ACACGTTTATTGAAGATTGTTCGAGTTTTATACTCCCTGAAGGAATAGGGAGCGG
* * * * **
301993 ACACGTTTATTGAAGATTGTTTGAGTTCTATACTCTCTGAAGGAATAGAGAGCAT
1 ACACGTTTATTGAAGATTGTTCGAGTTTTATACTCCCTGAAGGAATAGGGAGCGG
* * *
302048 ACACGTTTCTTGAAGATTGTTTGAGTTTTATACTCCCTGAACGAATAGGGAGCGG
1 ACACGTTTATTGAAGATTGTTCGAGTTTTATACTCCCTGAAGGAATAGGGAGCGG
* * * *
302103 AC-CTGTTTATTGAAAATTGTTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAG
1 ACAC-GTTTATTGAAGATTGTTCGAGTTTTATACTCCCTGAAGGAATAGGGAGCGG
** * * * *
302158 ACACGTTTGCTGAAGATAGTTCGAGTTTTGTACTCCCTGAAGAAATAGGGAGCGA
1 ACACGTTTATTGAAGATTGTTCGAGTTTTATACTCCCTGAAGGAATAGGGAGCGG
* * * * * * * * * * * * *
302213 ACCCCTTTTTTAGAAGATTATTCAAGTTCTGTACTTCCTAAAGGTATATGGAGTGA
1 ACACGTTTATT-GAAGATTGTTCGAGTTTTATACTCCCTGAAGGAATAGGGAGCGG
* * * * *
302269 AC-CTGTTTGTCGAATG-TTTTTCGAGTCTTATACTCCTTGAAGGAATAGGGAGC
1 ACAC-GTTTATTGAA-GATTGTTCGAGTTTTATACTCCCTGAAGGAATAGGGAGC
302322 ATGCTTGTCT
Statistics
Matches: 266, Mismatches: 58, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
54 1 0.00
55 223 0.84
56 42 0.16
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (55 bp):
ACACGTTTATTGAAGATTGTTCGAGTTTTATACTCCCTGAAGGAATAGGGAGCGG
Found at i:304395 original size:2 final size:2
Alignment explanation
Indices: 304388--304415 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
304378 TTAAAAATAG
304388 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
304416 TCACTTGTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:314389 original size:35 final size:35
Alignment explanation
Indices: 314341--314409 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
314331 GCTGGAGGTT
*
314341 GATTACAGATTGCTTATGCTTATGTCATTGATTTC
1 GATTACAGATTGCTTATGCTTATATCATTGATTTC
* *
314376 GATTACTGGTTGCTTATGCTTATATCATTGATTT
1 GATTACAGATTGCTTATGCTTATATCATTGATTT
314410 TGCAGAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (35 bp):
GATTACAGATTGCTTATGCTTATATCATTGATTTC
Found at i:317188 original size:16 final size:17
Alignment explanation
Indices: 317156--317188 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
317146 TCCAGCTACA
*
317156 CCATTTTGATCCGAAAC
1 CCATTTTGATCCAAAAC
317173 CCATTTT-ATCCAAAAC
1 CCATTTTGATCCAAAAC
317189 TTTAAAGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.30
Consensus pattern (17 bp):
CCATTTTGATCCAAAAC
Found at i:334186 original size:38 final size:37
Alignment explanation
Indices: 334094--334186 Score: 100
Period size: 38 Copynumber: 2.5 Consensus size: 37
334084 TCGTGCCGGG
*
334094 TATATATATTTA-AATTAAATATATAAATATTATATA
1 TATATATATATATAATTAAATATATAAATATTATATA
* * * *
334130 TATATTTCA-ATTTAAATTAAATTTATTAATATTATATA
1 TATATAT-ATATAT-AATTAAATATATAAATATTATATA
334168 TATATATATATAATAATTA
1 TATATATATAT-ATAATTA
334187 TTTGTAATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
36 7 0.16
37 2 0.04
38 35 0.78
39 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (37 bp):
TATATATATATATAATTAAATATATAAATATTATATA
Found at i:334284 original size:35 final size:35
Alignment explanation
Indices: 334254--334323 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
334244 GTCCCCGTTG
* *
334254 CGTCCCTGTTTAACATAAACGGTTTTTCCCCATCT
1 CGTCCCCGTTTAACATAAACGATTTTTCCCCATCT
*
334289 CGTCCCCGTTTAGCATAAACGATTTTT-CCCATCT
1 CGTCCCCGTTTAACATAAACGATTTTTCCCCATCT
334323 C
1 C
334324 TATTTAATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 8 0.25
35 24 0.75
ACGTcount: A:0.20, C:0.33, G:0.11, T:0.36
Consensus pattern (35 bp):
CGTCCCCGTTTAACATAAACGATTTTTCCCCATCT
Found at i:339394 original size:21 final size:19
Alignment explanation
Indices: 339356--339394 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
339346 TTTGAAAGCA
*
339356 AAAATGAGTTTTGAAAATC
1 AAAATGAATTTTGAAAATC
339375 AAAATGAAATTTTGGAAAAT
1 AAAATG-AATTTT-GAAAAT
339395 GATTTAGAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.51, C:0.03, G:0.15, T:0.31
Consensus pattern (19 bp):
AAAATGAATTTTGAAAATC
Found at i:340988 original size:21 final size:22
Alignment explanation
Indices: 340949--340989 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
340939 TTAAATATTA
**
340949 CAAAAGTAGTATCGGTACTCAT
1 CAAAAGTAGTATCAATACTCAT
340971 CAAAAG-AGTATCAATACTC
1 CAAAAGTAGTATCAATACTC
340990 CCTGTCCTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (22 bp):
CAAAAGTAGTATCAATACTCAT
Found at i:354232 original size:23 final size:23
Alignment explanation
Indices: 354206--354289 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
354196 CTCGTATAAC
*
354206 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGGAGTGCCACGTAGAAT
* *
354229 TGCATCGGAGTGCCGCGTAGAAT
1 TGCACCGGAGTGCCACGTAGAAT
*
354252 TGCACCGGAGTGCCGCGTAGAAT
1 TGCACCGGAGTGCCACGTAGAAT
*
354275 TGCACCGTAGTGCCA
1 TGCACCGGAGTGCCA
354290 TATAATAATG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.24, C:0.26, G:0.31, T:0.19
Consensus pattern (23 bp):
TGCACCGGAGTGCCACGTAGAAT
Found at i:354430 original size:103 final size:103
Alignment explanation
Indices: 354305--354522 Score: 393
Period size: 103 Copynumber: 2.1 Consensus size: 103
354295 TAATGTCCAT
*
354305 AAGGACCACATATCATTCCTTAAGAATCATATACATATACT-AGGGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATAT-CTCAAGGATCAAGTATGTGTCTCACC
354369 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
354408 AAGGACCACATATCATTCCTTAAGAATCATATACATATGTCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATCTCAAGGATCAAGTATGTGTCTCACCA
*
354473 GACTTCACACATGTTTCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
354511 AAGGACCACATA
1 AAGGACCACATA
354523 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
102 1 0.01
103 110 0.99
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATCTCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:359491 original size:23 final size:23
Alignment explanation
Indices: 359465--359548 Score: 107
Period size: 23 Copynumber: 3.7 Consensus size: 23
359455 CACCACAGCT
*
359465 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
359488 CGTAGAATAGCA-CTAGAGTGCCG
1 CGTAGAATTGCACCGA-AGTGCCA
*
359511 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
359534 CGTAGAATTGCACCG
1 CGTAGAATTGCACCG
359549 TAGTACCATA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
22 2 0.04
23 48 0.94
24 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.19
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:359743 original size:103 final size:103
Alignment explanation
Indices: 359575--359789 Score: 378
Period size: 103 Copynumber: 2.1 Consensus size: 103
359565 TGTCCATAAG
*
359575 GACCACATATCATTCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACAAGAGATCAAGTATGTGTCTCACCAGAC
359640 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
* *
359678 GACCACATATTATTCCTTAAGAATCATATACATATGCCAAG-GATCAAGTATGTGTCTCACCAGA
1 GACCACATATCATTCCTTAAGAATCATATACATAT-ACAAGAGATCAAGTATGTGTCTCACCAGA
*
359742 CTTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
65 CTTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
359781 GACCACATA
1 GACCACATA
359790 GACCCTCGAC
Statistics
Matches: 107, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
103 104 0.97
104 3 0.03
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.27
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACAAGAGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
Found at i:362601 original size:15 final size:16
Alignment explanation
Indices: 362581--362614 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
362571 GATATATATT
*
362581 TTTAAATT-ATTAATA
1 TTTAAATTGAATAATA
362596 TTTAAATTGAATAATA
1 TTTAAATTGAATAATA
362612 TTT
1 TTT
362615 TTATTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAAATTGAATAATA
Found at i:362923 original size:11 final size:11
Alignment explanation
Indices: 362864--362930 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 11
362854 TAGTTGTATT
362864 ATATAATTTTTA
1 ATAT-ATTTTTA
362876 ATATA-TTTTA
1 ATATATTTTTA
362886 A-A-ATTTTATA
1 ATATATTTT-TA
***
362896 AT-TATCAATA
1 ATATATTTTTA
*
362906 ATGTATTTTTA
1 ATATATTTTTA
362917 ATATATTTTTA
1 ATATATTTTTA
362928 ATA
1 ATA
362931 ATGTAATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
8 1 0.02
9 4 0.09
10 13 0.30
11 21 0.49
12 4 0.09
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (11 bp):
ATATATTTTTA
Found at i:365940 original size:117 final size:117
Alignment explanation
Indices: 365797--366035 Score: 338
Period size: 117 Copynumber: 2.0 Consensus size: 117
365787 AATTACTCCA
* * ** *
365797 CTAATCCTTAATTTTCTTAGACTTCACAATTTGAATTTTAAAATTCACCTTATATTCAATTTAAT
1 CTAATCCTTAAGTTTCTTAGACTTCACAATTTGAAATCCAAAATTCACCTTATATACAATTTAAT
* *
365862 CTCTATC-TACATCGATATTTAAAATGTAAACAAGTTAAAGGAAAA-GGAGAAC
66 CTCTA-CATACACCAATATTTAAAATGTAAACAAGTTAAA-GAAAACGGAGAAC
* *
365914 CTAATCCTTAAGTTTCTTAGGCTTCACAATTTGAAATCCAAAATTCACCTTATGTACAATTTAAT
1 CTAATCCTTAAGTTTCTTAGACTTCACAATTTGAAATCCAAAATTCACCTTATATACAATTTAAT
* * *
365979 CTTTACATTCACCAATATTTAACATGTAAACAAGTTAAAGAAAACGGAGAAC
66 CTCTACATACACCAATATTTAAAATGTAAACAAGTTAAAGAAAACGGAGAAC
366031 CTAAT
1 CTAAT
366036 AGACGAGTTT
Statistics
Matches: 108, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
116 6 0.06
117 102 0.94
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (117 bp):
CTAATCCTTAAGTTTCTTAGACTTCACAATTTGAAATCCAAAATTCACCTTATATACAATTTAAT
CTCTACATACACCAATATTTAAAATGTAAACAAGTTAAAGAAAACGGAGAAC
Found at i:369879 original size:15 final size:17
Alignment explanation
Indices: 369842--369882 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
369832 AATTTTCTTA
369842 TTTATTT-TTTAACATG
1 TTTATTTATTTAACATG
369858 TTTATTTATTTAA-ATG
1 TTTATTTATTTAACATG
369874 -TTATTTATT
1 TTTATTTATT
369883 ATTGCTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.38
16 10 0.42
17 5 0.21
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (17 bp):
TTTATTTATTTAACATG
Found at i:375181 original size:2 final size:2
Alignment explanation
Indices: 375176--375208 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
375166 TCTCTCTCTT
375176 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 T
375209 TCAATTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:381193 original size:21 final size:21
Alignment explanation
Indices: 381167--381240 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
381157 AATTTGGAAA
381167 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
381188 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
*
381207 ATCGTAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
381228 ATCGCAATGCGAA
1 ATCGCAACGCGAA
381241 TATGTAAATC
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 14 0.35
21 26 0.65
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:381193 original size:40 final size:40
Alignment explanation
Indices: 381148--381234 Score: 156
Period size: 40 Copynumber: 2.2 Consensus size: 40
381138 ATATATATAA
381148 ATCGCAACAAATTTGGAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACAAATTTGGAAAATCGCAACGCGAACTTCGACT
* *
381188 ATCGCAACGAATTTGGAAAATCGTAACGCGAACTTCGACT
1 ATCGCAACAAATTTGGAAAATCGCAACGCGAACTTCGACT
381228 ATCGCAA
1 ATCGCAA
381235 TGCGAATATG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (40 bp):
ATCGCAACAAATTTGGAAAATCGCAACGCGAACTTCGACT
Found at i:381210 original size:19 final size:19
Alignment explanation
Indices: 381146--381215 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
381136 ATATATATAT
*
381146 AAATCGCAACAAATTTGGA
1 AAATCGCAACGAATTTGGA
* *
381165 AAATCGCAACGCGAACTTCGA
1 AAATCGCAA--CGAATTTGGA
**
381186 CTATCGCAACGAATTTGGA
1 AAATCGCAACGAATTTGGA
*
381205 AAATCGTAACG
1 AAATCGCAACG
381216 CGAACTTCGA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
19 25 0.64
21 14 0.36
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (19 bp):
AAATCGCAACGAATTTGGA
Found at i:384523 original size:185 final size:188
Alignment explanation
Indices: 384211--384583 Score: 725
Period size: 185 Copynumber: 2.0 Consensus size: 188
384201 GGGATCTCAA
384211 TTACCTTCTTTACTTAACTTTCTAATCAATTCCCTCCCTTAAAGCTTGGTTAACTTTCTAATCAG
1 TTACCTTCTTTACTTAACTTTCTAATCAATTCCCTCCCTTAAAGCTTGGTTAACTTTCTAATCAG
384276 TTTTTTTTTTTTAAATTTTGATCCACGCATTAAATTGTAACTATCTAAATCAA-TTTTTTTTTTA
66 TTTTTTTTTTTTAAATTTTGATCCACGCATTAAATTGTAACTATCTAAATCAATTTTTTTTTTTA
384340 ATTTTGT-AAAAAA-ATCTTATATCTAAGTTAATAATCCAAACCGGTAAAATTTAGTT
131 ATTTTGTAAAAAAATATCTTATATCTAAGTTAATAATCCAAACCGGTAAAATTTAGTT
384396 TTACCTTCTTTACTTAACTTTCTAATCAATTCCCTCCCTTAAAGCTTGGTTAACTTTCTAATCAG
1 TTACCTTCTTTACTTAACTTTCTAATCAATTCCCTCCCTTAAAGCTTGGTTAACTTTCTAATCAG
384461 TTTTTTTTTTTTAAATTTTGATCCACGCATTAAATTGTAACTATCTAAATCAATTTTTTTTTTTA
66 TTTTTTTTTTTTAAATTTTGATCCACGCATTAAATTGTAACTATCTAAATCAATTTTTTTTTTTA
384526 ATTTTGTAAAAAAATATCTTATATCTAAGTTAATAATCCAAACCGGTAAAATTTAGTT
131 ATTTTGTAAAAAAATATCTTATATCTAAGTTAATAATCCAAACCGGTAAAATTTAGTT
384584 CAAACTTTTG
Statistics
Matches: 185, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
185 118 0.64
186 18 0.10
187 6 0.03
188 43 0.23
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.46
Consensus pattern (188 bp):
TTACCTTCTTTACTTAACTTTCTAATCAATTCCCTCCCTTAAAGCTTGGTTAACTTTCTAATCAG
TTTTTTTTTTTTAAATTTTGATCCACGCATTAAATTGTAACTATCTAAATCAATTTTTTTTTTTA
ATTTTGTAAAAAAATATCTTATATCTAAGTTAATAATCCAAACCGGTAAAATTTAGTT
Found at i:386276 original size:29 final size:29
Alignment explanation
Indices: 386244--386307 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
386234 TTCAACATTG
*
386244 AATTTTTTAAA-G-TTATAAAATAATTATT
1 AATTTTTCAAATGATTA-AAAATAATTATT
*
386272 AAATTTATCAAATGATTAAAAATAATTATT
1 -AATTTTTCAAATGATTAAAAATAATTATT
386302 AATTTT
1 AATTTT
386308 CATCAAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 14 0.47
30 13 0.43
31 3 0.10
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (29 bp):
AATTTTTCAAATGATTAAAAATAATTATT
Found at i:386279 original size:20 final size:20
Alignment explanation
Indices: 386250--386289 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
386240 ATTGAATTTT
386250 TTAAAGTTATAAAATAATTA
1 TTAAAGTTATAAAATAATTA
* * *
386270 TTAAATTTATCAAATGATTA
1 TTAAAGTTATAAAATAATTA
386290 AAAATAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (20 bp):
TTAAAGTTATAAAATAATTA
Found at i:386296 original size:30 final size:31
Alignment explanation
Indices: 386260--386320 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
386250 TTAAAGTTAT
386260 AAAATAATTATTAAATTT-ATCAAATGATTA
1 AAAATAATTATTAAATTTCATCAAATGATTA
* *
386290 AAAATAATTATTAATTTTCATCAAATTATTA
1 AAAATAATTATTAAATTTCATCAAATGATTA
386321 TAACGTCACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (31 bp):
AAAATAATTATTAAATTTCATCAAATGATTA
Found at i:393750 original size:2 final size:2
Alignment explanation
Indices: 393743--393787 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
393733 ACTATATGTT
393743 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
393784 TA TA
1 TA TA
393788 AATAATCCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:398545 original size:23 final size:23
Alignment explanation
Indices: 398512--398574 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
398502 ATTATTATAT
398512 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
398535 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
398558 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
398575 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:404749 original size:64 final size:63
Alignment explanation
Indices: 404664--404805 Score: 187
Period size: 64 Copynumber: 2.2 Consensus size: 63
404654 TTGTTTAAGG
* * *
404664 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGCAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * * *
404728 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGCAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
404792 TGCATCGATGCATA
1 TGCATCGATGCATA
404806 CCTCCATTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
64 62 0.90
65 6 0.09
66 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCATAAGCAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:405429 original size:23 final size:23
Alignment explanation
Indices: 405403--405463 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
405393 TATGGAACTA
405403 CGGTGCAATTCTATGCGGCACTC
1 CGGTGCAATTCTATGCGGCACTC
* * *
405426 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTATGCGGCACTC
* *
405449 AGGTGCAATTATATG
1 CGGTGCAATTCTATG
405464 AGCTGTGGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (23 bp):
CGGTGCAATTCTATGCGGCACTC
Found at i:411312 original size:60 final size:60
Alignment explanation
Indices: 411214--411333 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
411204 AGAGGAATAA
411214 CGAATGAGTGAAGAGGATATGAGGAGAGAGAAAAGAGGGTTA-AGGATTATGGAGAGCAAT
1 CGAATGAGTGAAGAGGATATGAGGAGAGAGAAAAGAGGGTTAGA-GATTATGGAGAGCAAT
* *
411274 CGAATGAGTGAAGAGGA-ATTG-GGAAGAGAGGAACGAGGGTTAGAGATTATGGAGAGCAAT
1 CGAATGAGTGAAGAGGATA-TGAGG-AGAGAGAAAAGAGGGTTAGAGATTATGGAGAGCAAT
411334 TTGGGAATTG
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
59 3 0.05
60 51 0.93
61 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.39, T:0.17
Consensus pattern (60 bp):
CGAATGAGTGAAGAGGATATGAGGAGAGAGAAAAGAGGGTTAGAGATTATGGAGAGCAAT
Found at i:412270 original size:59 final size:59
Alignment explanation
Indices: 412153--412270 Score: 155
Period size: 59 Copynumber: 2.0 Consensus size: 59
412143 TGTGAGACTT
* * * * * * *
412153 TATATTTTAAATTAGGTTTATAATATTACACAATATAATCTCACGTTGTATAAGATTTG
1 TATATTTAAAATCAGATTTAAAATATTACACAATATAATCTCACATTATATAAAATTTG
* *
412212 TATATTTAAAATCAGATTTAAAATGTTACACAATATAATCTCACATTATGTAAAATTTG
1 TATATTTAAAATCAGATTTAAAATATTACACAATATAATCTCACATTATATAAAATTTG
412271 AACCCCTCTA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (59 bp):
TATATTTAAAATCAGATTTAAAATATTACACAATATAATCTCACATTATATAAAATTTG
Found at i:414204 original size:12 final size:12
Alignment explanation
Indices: 414187--414211 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
414177 TGAGGAGCAA
414187 AAAATAAATTTT
1 AAAATAAATTTT
414199 AAAATAAATTTT
1 AAAATAAATTTT
414211 A
1 A
414212 TTTTTAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATAAATTTT
Found at i:415433 original size:17 final size:17
Alignment explanation
Indices: 415394--415475 Score: 119
Period size: 17 Copynumber: 4.8 Consensus size: 17
415384 TGTTTTTTAG
* *
415394 GGAATTGGAATCTATGAA
1 GGAATTGGAATCTGT-CA
*
415412 GGAATTAGAATCTGTCA
1 GGAATTGGAATCTGTCA
415429 GGAATTGGAATCTGTCA
1 GGAATTGGAATCTGTCA
415446 GGAATTGGAATCTGTCA
1 GGAATTGGAATCTGTCA
*
415463 GGAATTGAAATCT
1 GGAATTGGAATCT
415476 AATTTCATAT
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
17 46 0.78
18 13 0.22
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (17 bp):
GGAATTGGAATCTGTCA
Found at i:415937 original size:32 final size:33
Alignment explanation
Indices: 415868--415944 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
415858 CCCGAACCTG
*
415868 ACCCGACCCAACCCGAATATCACACTTAAAAAA
1 ACCCGACCCGACCCGAATATCACACTTAAAAAA
415901 ACCCGACCCGACCCGAATATCACACTT-AAAAA
1 ACCCGACCCGACCCGAATATCACACTTAAAAAA
415933 ACCCGA-CCGACC
1 ACCCGACCCGACC
415945 TGAACAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
31 6 0.14
32 11 0.26
33 26 0.60
ACGTcount: A:0.40, C:0.40, G:0.09, T:0.10
Consensus pattern (33 bp):
ACCCGACCCGACCCGAATATCACACTTAAAAAA
Found at i:422059 original size:2 final size:2
Alignment explanation
Indices: 422052--422084 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
422042 AACATTAATC
422052 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
422085 AAATTATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:423193 original size:58 final size:58
Alignment explanation
Indices: 423120--423240 Score: 158
Period size: 58 Copynumber: 2.1 Consensus size: 58
423110 ACCGAGTGAT
* * *
423120 CATTTTTTAACTTTTAATAGTTGGG-GAACTCAACAAAATAACGTCC-TATAATCAGGGAC
1 CATTTTATAACTTTTAATAGTTGGGAG-ACTCAACAAAAT-A-GCCCTTATAATAAGGGAC
*
423179 CATTTTATAA-TTTTAATAGTTGGGAGACTCAACAAAGTAGCCCTTATAATAAGGGAC
1 CATTTTATAACTTTTAATAGTTGGGAGACTCAACAAAATAGCCCTTATAATAAGGGAC
423236 CATTT
1 CATTT
423241 GTGTACTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
56 3 0.05
57 18 0.32
58 25 0.45
59 10 0.18
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (58 bp):
CATTTTATAACTTTTAATAGTTGGGAGACTCAACAAAATAGCCCTTATAATAAGGGAC
Found at i:423236 original size:57 final size:59
Alignment explanation
Indices: 423120--423240 Score: 160
Period size: 57 Copynumber: 2.1 Consensus size: 59
423110 ACCGAGTGAT
* * *
423120 CATTTTTTAACTTTTAATAGTTGGGGAACTCAACAAAATAACGTCCTATAATCAGGGAC
1 CATTTTATAACTTTTAATAGTTGGGGAACTCAACAAAATAACGCCCTATAATAAGGGAC
*
423179 CATTTTATAA-TTTTAATAGTT-GGGAGACTCAACAAAGT-A-GCCCTTATAATAAGGGAC
1 CATTTTATAACTTTTAATAGTTGGGGA-ACTCAACAAAATAACGCCC-TATAATAAGGGAC
423236 CATTT
1 CATTT
423241 GTGTACTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
56 3 0.05
57 22 0.39
58 22 0.39
59 9 0.16
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (59 bp):
CATTTTATAACTTTTAATAGTTGGGGAACTCAACAAAATAACGCCCTATAATAAGGGAC
Found at i:423343 original size:16 final size:16
Alignment explanation
Indices: 423322--423352 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
423312 ATACACCAAA
423322 AAATAATTAATAAAAC
1 AAATAATTAATAAAAC
423338 AAATAATTAATAAAA
1 AAATAATTAATAAAA
423353 AAAAAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAATTAATAAAAC
Found at i:423740 original size:57 final size:57
Alignment explanation
Indices: 423647--423762 Score: 142
Period size: 57 Copynumber: 2.0 Consensus size: 57
423637 CATCTCCAAT
** * * * *
423647 TTTTATGATTAAATTATACTTTAAATCTTTATTAATTTTAAAATTAATTAAGTTAAG
1 TTTTATGATTAAATTATACTTTAAATCACTACTAATTTTAAAATCAATGAAATTAAG
* * * *
423704 TTTTATGATTATATTATACTTTGAGTCACTCCTAATTTTAAAATCAATGAAATTAAG
1 TTTTATGATTAAATTATACTTTAAATCACTACTAATTTTAAAATCAATGAAATTAAG
423761 TT
1 TT
423763 ATCGAGATCC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (57 bp):
TTTTATGATTAAATTATACTTTAAATCACTACTAATTTTAAAATCAATGAAATTAAG
Found at i:425295 original size:2 final size:2
Alignment explanation
Indices: 425283--425314 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
425273 TAAGATATTC
*
425283 AT AT AT TT 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
425315 TCATTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:432243 original size:12 final size:13
Alignment explanation
Indices: 432226--432262 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
432216 GTTAATTATT
*
432226 TTTATTCTTTT-A
1 TTTATTATTTTCA
432238 TTTATTATTTTCA
1 TTTATTATTTTCA
432251 TTT-TTATTTTCA
1 TTTATTATTTTCA
432263 CTTACATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTATTATTTTCA
Found at i:433170 original size:3 final size:3
Alignment explanation
Indices: 433162--433190 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
433152 TTTGCATTTT
433162 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
433191 TTCATTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:434331 original size:33 final size:33
Alignment explanation
Indices: 434289--434363 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
434279 AATGTAATAT
434289 ATGTTCAAAAGGCTTTGAACCGATTGATAATGA
1 ATGTTCAAAAGGCTTTGAACCGATTGATAATGA
434322 ATGTTCAAAAGGCTTTGAACCGATTGATAATGA
1 ATGTTCAAAAGGCTTTGAACCGATTGATAATGA
*
434355 ACGTTCAAA
1 ATGTTCAAA
434364 CGCCTTTGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (33 bp):
ATGTTCAAAAGGCTTTGAACCGATTGATAATGA
Found at i:443650 original size:2 final size:2
Alignment explanation
Indices: 443643--443676 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
443633 TATGTATAGG
443643 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
443677 GTTTGGATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:448313 original size:23 final size:23
Alignment explanation
Indices: 448281--448341 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
448271 TCTTATATGC
*
448281 CACTTCGGTGCATTTTTACGCGG
1 CACTTCGGTGCATTTCTACGCGG
* * *
448304 CACTTAGGTGCAATTCTACGTGG
1 CACTTCGGTGCATTTCTACGCGG
448327 CACTTCGGTGCATTT
1 CACTTCGGTGCATTT
448342 ATAAGAGCTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.34
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGCGG
Found at i:448712 original size:2 final size:2
Alignment explanation
Indices: 448705--448749 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
448695 TATGTATAGG
*
448705 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
448746 AT AT
1 AT AT
448750 TTATGTTTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:448721 original size:19 final size:19
Alignment explanation
Indices: 448706--448749 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
448696 ATGTATAGGA
*
448706 TATATATATATATATATAT
1 TATATATATATATATAGAT
*
448725 TATATATATATATATATAT
1 TATATATATATATATAGAT
448744 T-TATAT
1 TATATAT
448750 TTATGTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATATATATATATATAGAT
Found at i:452476 original size:72 final size:72
Alignment explanation
Indices: 452359--452504 Score: 292
Period size: 72 Copynumber: 2.0 Consensus size: 72
452349 AGGAAATTTT
452359 TTCTGATGTGGAAGATCAGCCTAAGCCGCAACCATAGAGCATACTAAAATAAACCAAGAGCGTTG
1 TTCTGATGTGGAAGATCAGCCTAAGCCGCAACCATAGAGCATACTAAAATAAACCAAGAGCGTTG
452424 ATACCAA
66 ATACCAA
452431 TTCTGATGTGGAAGATCAGCCTAAGCCGCAACCATAGAGCATACTAAAATAAACCAAGAGCGTTG
1 TTCTGATGTGGAAGATCAGCCTAAGCCGCAACCATAGAGCATACTAAAATAAACCAAGAGCGTTG
452496 ATACCAA
66 ATACCAA
452503 TT
1 TT
452505 GTTATGGAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (72 bp):
TTCTGATGTGGAAGATCAGCCTAAGCCGCAACCATAGAGCATACTAAAATAAACCAAGAGCGTTG
ATACCAA
Found at i:453162 original size:24 final size:24
Alignment explanation
Indices: 453134--453186 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
453124 AAGTTGGCTC
453134 GATTTAAATTAGAGCTCAACTCAA
1 GATTTAAATTAGAGCTCAACTCAA
* *
453158 GATTTAAATTAGAGCTCGACTTAA
1 GATTTAAATTAGAGCTCAACTCAA
453182 GATTT
1 GATTT
453187 TAACGAGTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (24 bp):
GATTTAAATTAGAGCTCAACTCAA
Found at i:453693 original size:20 final size:19
Alignment explanation
Indices: 453668--453713 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
453658 TTTTTGTTGA
453668 TATTAAACTGTACATAGTAT
1 TATTAAACTGTACATA-TAT
* *
453688 TATTAAATTTTACATATAT
1 TATTAAACTGTACATATAT
*
453707 TTTTAAA
1 TATTAAA
453714 AACAAAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (19 bp):
TATTAAACTGTACATATAT
Found at i:453838 original size:3 final size:3
Alignment explanation
Indices: 453825--453913 Score: 164
Period size: 3 Copynumber: 30.3 Consensus size: 3
453815 AATCAGAAAT
453825 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
453872 ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
453914 CACCATAATT
Statistics
Matches: 84, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.05
3 80 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:454858 original size:26 final size:28
Alignment explanation
Indices: 454815--454870 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
454805 GTTTATATAA
454815 TTTTTAAGTTTAAAACCT-AAATAATTT
1 TTTTTAAGTTTAAAACCTAAAATAATTT
* *
454842 TTTTTAA-TTTGATACCTAAAATAATTT
1 TTTTTAAGTTTAAAACCTAAAATAATTT
454869 TT
1 TT
454871 CGAGCTTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.52
Consensus pattern (28 bp):
TTTTTAAGTTTAAAACCTAAAATAATTT
Found at i:456199 original size:53 final size:53
Alignment explanation
Indices: 456119--456225 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
456109 TCAAACTCAA
456119 GGGCAGAGCATCTGCGTGGTGGGAACAGTTGCGACGTTCACGAGAAAGACATG
1 GGGCAGAGCATCTGCGTGGTGGGAACAGTTGCGACGTTCACGAGAAAGACATG
456172 GGGCAGAGCATCTGCGTGGTGGGAACAGTTGCGACGTTCACGAGAAAGACATG
1 GGGCAGAGCATCTGCGTGGTGGGAACAGTTGCGACGTTCACGAGAAAGACATG
456225 G
1 G
456226 CAAGGCCAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.26, C:0.19, G:0.38, T:0.17
Consensus pattern (53 bp):
GGGCAGAGCATCTGCGTGGTGGGAACAGTTGCGACGTTCACGAGAAAGACATG
Found at i:468206 original size:19 final size:18
Alignment explanation
Indices: 468184--468225 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
468174 GAAATTTGGC
468184 TTTTTGTTTGTTGGTTTT
1 TTTTTGTTTGTTGGTTTT
* *
468202 TTTTTGTTTTTTTGTTTT
1 TTTTTGTTTGTTGGTTTT
468220 TTTTTG
1 TTTTTG
468226 AAAAAATAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (18 bp):
TTTTTGTTTGTTGGTTTT
Found at i:469201 original size:322 final size:313
Alignment explanation
Indices: 468528--469159 Score: 976
Period size: 322 Copynumber: 2.0 Consensus size: 313
468518 TAGGTTTCTT
*
468528 CAAGGCAATAAGATTAGAATAAATAAACAAAAGAT----AAA--GAAAAGAAAATAAATAGATAA
1 CAAGGCAAAAAGATTAG-ATAAATAAACAAAAGATAAAGAAATTGAAAAGAAAATAAATAGATAA
*
468587 ATAGAATCAAAAGATCTCCCTTACGAAGGTGGATGGTAAAGAGATTGATGGTGAATGGATTTGTG
65 AAAGAATCAAAAGATCTCCCTTACGAAGGTGGATGGTAAAGAGATTGATGGTGAATGGATTTGTG
468652 GAAAATAGATGATAAGTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCATAAATG
130 GAAAATAGATGATAAGTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCATAAATG
468717 GCTCTAACCAACCCTCCTAGTCGCGATGAAAAGGCAAATTGGAGTGTGAAGATTAATCTCCCTCA
195 GCTCTAACCAACCCTCCTAGTCGCGATGAAAAGGCAAATTGGAGTGTGAAGATTAATCTCCCTCA
* *** ** **
468782 CAAGAACTTGAAAGAACTCCAGGAGAAGAAGCTTCGAAGTCTTTAGGGTTTCTT
260 CAAGAACTTGAAAGAACTCCAGGAGAAGAAGCTTCGAAGGCACAAGGAATTCAG
* *
468836 CAAGGCAATAAGATTAGAATAAAATAAACAAAAGATAAAGAAATTGAAAATAAAATAAGATAAGA
1 CAAGGCAAAAAGATTAG-AT-AAATAAACAAAAGATAAAGAAATTGAAAAGAAAATAA-AT-AGA
468901 TAAAAAGAAATC-AAAGATCTCCCTTACGAAGGTGGATGGTAAAGATGATTGATGGTGCAGATGG
62 TAAAAAG-AATCAAAAGATCTCCCTTACGAAGGTGGATGGTAAAGA-GATTGATGGTG-A-ATGG
468965 ATTTGTGGAAAAATAGATGGATAAGTGTCCTATCGAA-CCTCCTAGTCGCAATGAAAAGGCAAAC
123 ATTTGTGG-AAAATAGAT-GATAAGTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGCAAAC
469029 TCGATAAATGGCTCTAACCAACCCTCCTAGTCGCGATGAAAAGGCAAATTGGAGTGTGAAGATTA
186 TC-ATAAATGGCTCTAACCAACCCTCCTAGTCGCGATGAAAAGGCAAATTGGAGTGTGAAGATTA
469094 ATCTCCCTCACAAGAACTTGAAAGAACTCCAGGAGAAGAAGCTTCGAAGGCACAAGGCAATT-AG
250 ATCTCCCTCACAAGAACTTGAAAGAACTCCAGGAGAAGAAGCTTCGAAGGCACAAGG-AATTCAG
469158 CA
1 CA
469160 CTTGCAAAAA
Statistics
Matches: 297, Mismatches: 10, Indels: 20
0.91 0.03 0.06
Matches are distributed among these distances:
308 20 0.07
309 15 0.05
313 3 0.01
315 12 0.04
316 2 0.01
317 42 0.14
318 15 0.05
319 1 0.00
320 12 0.04
321 38 0.13
322 135 0.45
323 2 0.01
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.22
Consensus pattern (313 bp):
CAAGGCAAAAAGATTAGATAAATAAACAAAAGATAAAGAAATTGAAAAGAAAATAAATAGATAAA
AAGAATCAAAAGATCTCCCTTACGAAGGTGGATGGTAAAGAGATTGATGGTGAATGGATTTGTGG
AAAATAGATGATAAGTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGCAAACTCATAAATGG
CTCTAACCAACCCTCCTAGTCGCGATGAAAAGGCAAATTGGAGTGTGAAGATTAATCTCCCTCAC
AAGAACTTGAAAGAACTCCAGGAGAAGAAGCTTCGAAGGCACAAGGAATTCAG
Found at i:475528 original size:2 final size:2
Alignment explanation
Indices: 475512--475563 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
475502 AAATACATTA
*
475512 AT AT TT AT A- 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
475553 AT AT AT AT AT A
1 AT AT AT AT AT A
475564 AATAAGATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:475656 original size:10 final size:10
Alignment explanation
Indices: 475633--475663 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
475623 CTCCTTTCTT
475633 AATATTAA-A
1 AATATTAATA
475642 AATATTAATA
1 AATATTAATA
475652 AATATTAATA
1 AATATTAATA
475662 AA
1 AA
475664 ACATTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AATATTAATA
Found at i:475907 original size:27 final size:28
Alignment explanation
Indices: 475874--475945 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 28
475864 TAATATTTAA
475874 AAATAAATAA-ATATTATTAATTTATAAATTT
1 AAATAAATAATATA-TATTAA--TAT-AATTT
* *
475905 AAACAAATAATATATATTAATATAATTA
1 AAATAAATAATATATATTAATATAATTT
475933 AAATAAAATAATA
1 AAAT-AAATAATA
475946 ATTAAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 7 0.19
29 11 0.31
31 15 0.42
32 3 0.08
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (28 bp):
AAATAAATAATATATATTAATATAATTT
Found at i:476309 original size:2 final size:2
Alignment explanation
Indices: 476302--476351 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
476292 ATTTAACCTA
476302 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
476344 AT AT AT AT
1 AT AT AT AT
476352 TAGATATGCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:477353 original size:3 final size:3
Alignment explanation
Indices: 477338--477422 Score: 68
Period size: 3 Copynumber: 28.0 Consensus size: 3
477328 GTAATAGTAT
* *
477338 TAA TAA TAT TAA TAA TAA TAA TAA GTAA T-A TAA TTAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA -TAA TAA TAA TAA
* * *
477384 TAA -AG TAA TAAA TAA -ATA TAA TAA TGA TAA TAA AAA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
477423 AAACCAAATG
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
2 4 0.06
3 51 0.78
4 10 0.15
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:477373 original size:25 final size:25
Alignment explanation
Indices: 477338--477408 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 25
477328 GTAATAGTAT
477338 TAATAATATTAATAATAATAAT-AAG
1 TAATAA-ATTAATAATAATAATAAAG
*
477363 TAATATAATTAAAAATAATAATAAAG
1 TAATA-AATTAATAATAATAATAAAG
*
477389 TAATAAATAAAT-ATAATAAT
1 TAATAAATTAATAATAATAAT
477409 GATAATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
24 8 0.20
25 24 0.59
26 9 0.22
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (25 bp):
TAATAAATTAATAATAATAATAAAG
Found at i:478358 original size:445 final size:445
Alignment explanation
Indices: 477521--478418 Score: 1744
Period size: 445 Copynumber: 2.0 Consensus size: 445
477511 TAAGTTTTTT
477521 TCATT-TGACTTCACTTGATTAGGATGGAAATGTTGAACAAGTTCTTCTCTGGGATTAGTTCTTA
1 TCATTATGACTTCACTTGATTAGGATGGAAATGTTGAACAAGTTCTTCTCTGGGATTAGTTCTTA
477585 TTATTATGAACTCTTTCATTTTTCCACTGGGGATGATAATCTATCTTTTTCTGTGATAAGATCTA
66 TTATTATGAACTCTTTCATTTTTCCACTGGGGATGATAATCTATCTTTTTCTGTGATAAGATCTA
*
477650 GCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTATTCTCATTA
131 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTATTCTCATTA
477715 TGAACTCTTCTGGAAATGTTGACCTTCAAAAGAGGTATTGTTGATTCAACTTTAATATGTGATGA
196 TGAACTCTTCTGGAAATGTTGACCTTCAAAAGAGGTATTGTTGATTCAACTTTAATATGTGATGA
*
477780 ATCAAATTAAGGTTGAACATGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTT
261 ATCAAATTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTT
*
477845 CTCATTATGAACACTTCTGGAAATGTTGATGTTGGTCTATCTCCTTCTGTGATAGAGTCATACAA
326 CTCATTATGAACACTTCTGGAAATGTTGATATTGGTCTATCTCCTTCTGTGATAGAGTCATACAA
477910 AATGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCTTTAGATGAGTTCTTC
391 AATGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCTTTAGATGAGTTCTTC
*
477965 TCATTATGACTTCACTTGATTAGGATGGAAATGTTGAACAAGTTCTTCTCTGGGATTAGTTCTTC
1 TCATTATGACTTCACTTGATTAGGATGGAAATGTTGAACAAGTTCTTCTCTGGGATTAGTTCTTA
478030 TTATTATGAACTCTTTCATTTTTCCACTGGGGATGATAATCTATCTTTTTCTGTGATAAGATCTA
66 TTATTATGAACTCTTTCATTTTTCCACTGGGGATGATAATCTATCTTTTTCTGTGATAAGATCTA
478095 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTATTCTCATTA
131 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTATTCTCATTA
478160 TGAACTCTTCTGGAAATGTTGACCTTCAAAAGAGGTATTGTTGATTCAACTTTAATATGTGATGA
196 TGAACTCTTCTGGAAATGTTGACCTTCAAAAGAGGTATTGTTGATTCAACTTTAATATGTGATGA
478225 ATCAAATTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTT
261 ATCAAATTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTT
*
478290 CTCATTATGAACACTTCTGGAAATGTTGATATTGGTCTATCTCCTTCTGTGATAGAGTCATGCAA
326 CTCATTATGAACACTTCTGGAAATGTTGATATTGGTCTATCTCCTTCTGTGATAGAGTCATACAA
478355 AATGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCTTTAGATGAGTTCTTC
391 AATGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCTTTAGATGAGTTCTTC
478410 TCATTATGA
1 TCATTATGA
478419 ACTCTTCTGG
Statistics
Matches: 448, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
444 5 0.01
445 443 0.99
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.41
Consensus pattern (445 bp):
TCATTATGACTTCACTTGATTAGGATGGAAATGTTGAACAAGTTCTTCTCTGGGATTAGTTCTTA
TTATTATGAACTCTTTCATTTTTCCACTGGGGATGATAATCTATCTTTTTCTGTGATAAGATCTA
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTATTCTCATTA
TGAACTCTTCTGGAAATGTTGACCTTCAAAAGAGGTATTGTTGATTCAACTTTAATATGTGATGA
ATCAAATTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTT
CTCATTATGAACACTTCTGGAAATGTTGATATTGGTCTATCTCCTTCTGTGATAGAGTCATACAA
AATGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCTTTAGATGAGTTCTTC
Found at i:478463 original size:85 final size:85
Alignment explanation
Indices: 478363--478533 Score: 324
Period size: 85 Copynumber: 2.0 Consensus size: 85
478353 AAAATGTTGA
*
478363 ACAAGCTCTTCTCATTATGAACTTCTTATTCTTTAGATGAGTTCTTCTCATTATGAACTCTTCTG
1 ACAAGCTCTTCTCATTATGAACTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTG
478428 GAAATATTGACCTTCAAAAG
66 GAAATATTGACCTTCAAAAG
*
478448 ACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTG
1 ACAAGCTCTTCTCATTATGAACTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTG
478513 GAAATATTGACCTTCAAAAG
66 GAAATATTGACCTTCAAAAG
478533 A
1 A
478534 GGTATTGTTG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (85 bp):
ACAAGCTCTTCTCATTATGAACTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTG
GAAATATTGACCTTCAAAAG
Found at i:478498 original size:341 final size:344
Alignment explanation
Indices: 478107--478776 Score: 1186
Period size: 341 Copynumber: 2.0 Consensus size: 344
478097 AAAAGGTTGA
478107 ACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTATTCTCATTATGAACTCTTCTG
1 ACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTATTCTCATTATGAACTCTTCTG
*
478172 GAAATGTTGACCTTCAAAAGAGGTATTGTTGATTCAACTTTAATATGTGATGAATCAAATTAAGG
66 GAAATATTGACCTTCAAAAGAGGTATTGTTGATTCAACTTTAATATGTGATGAATCAAATTAAGG
*
478237 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
131 TTGAACAAGTTCTTCTCATTATGAACTTCTTATCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
* * * * *
478302 ACTTCTGGAAATGTTGAT-ATTGGTCTATCTCCTTCTGTGATAGAGTCATGCAAAATGTTGAACA
196 ACTTCTGGAAATGTTGATGA-TGATATATCTCCTTCTGTGATAGAATCACGCAAAAGGTTGAACA
* * *
478366 AGCTCTTCTCATTATGAACTTC-T-T-ATTCTTTAGATGAGTTCTTCTCATTATGAACTCTTCTG
260 AGCTCTTCACATTATGAACTTCTTCTCATTCTTCAGATGAGTTCTTCTCATTATGAACTATTCTG
478428 GAAATATTGACCTTCAAAAG
325 GAAATATTGACCTTCAAAAG
*
478448 ACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTG
1 ACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTATTCTCATTATGAACTCTTCTG
478513 GAAATATTGACCTTCAAAAGAGGTATTGTTGATTCAACTTTAATATGTGATGAATCAAATTAAGG
66 GAAATATTGACCTTCAAAAGAGGTATTGTTGATTCAACTTTAATATGTGATGAATCAAATTAAGG
478578 TTGAACAAGTTCTTCTCATTATGAACTTCTTATCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
131 TTGAACAAGTTCTTCTCATTATGAACTTCTTATCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
478643 ACTTCTGGAAATGTTGATGATGATATATCTCCTTCTGTGATAGAATCACGCAAAAGGTTGAACAA
196 ACTTCTGGAAATGTTGATGATGATATATCTCCTTCTGTGATAGAATCACGCAAAAGGTTGAACAA
* *
478708 GCTCTTCACATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATTTTGG
261 GCTCTTCACATTATGAACTTCTTCTCATTCTTCAGATGAGTTCTTCTCATTATGAACTATTCTGG
478773 AAAT
326 AAAT
478777 TGATCCATCG
Statistics
Matches: 312, Mismatches: 13, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
341 270 0.87
342 2 0.01
343 1 0.00
344 39 0.12
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (344 bp):
ACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTATTCTCATTATGAACTCTTCTG
GAAATATTGACCTTCAAAAGAGGTATTGTTGATTCAACTTTAATATGTGATGAATCAAATTAAGG
TTGAACAAGTTCTTCTCATTATGAACTTCTTATCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
ACTTCTGGAAATGTTGATGATGATATATCTCCTTCTGTGATAGAATCACGCAAAAGGTTGAACAA
GCTCTTCACATTATGAACTTCTTCTCATTCTTCAGATGAGTTCTTCTCATTATGAACTATTCTGG
AAATATTGACCTTCAAAAG
Found at i:479096 original size:22 final size:22
Alignment explanation
Indices: 479071--479155 Score: 134
Period size: 22 Copynumber: 3.9 Consensus size: 22
479061 AAATCCAATA
* * *
479071 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAGAGAG
479093 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
*
479115 AATCTATCATCTTTGGAGAGAG
1 AATCTATCATCTTTGAAGAGAG
479137 AATCTATCATCTTTGAAGA
1 AATCTATCATCTTTGAAGA
479156 ATGTATCATT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:479162 original size:18 final size:18
Alignment explanation
Indices: 479135--479178 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
479125 CTTTGGAGAG
*
479135 AGAATCTATCATCTTTGA
1 AGAATGTATCATCTTTGA
*
479153 AGAATGTATCATTTTTGA
1 AGAATGTATCATCTTTGA
479171 AGAATGTA
1 AGAATGTA
479179 GATGTAGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (18 bp):
AGAATGTATCATCTTTGA
Found at i:480010 original size:20 final size:19
Alignment explanation
Indices: 479965--480019 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 19
479955 ATGTTTATAT
*
479965 AAAATAATAAATTGAATTTC
1 AAAA-AATAAATTGGATTTC
479985 -AAAAATAAATTGGATTTC
1 AAAAAATAAATTGGATTTC
480003 GAAAAAATAAACTTGGA
1 -AAAAAATAAA-TTGGA
480020 ATATATTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 14 0.45
19 3 0.10
20 9 0.29
21 5 0.16
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.29
Consensus pattern (19 bp):
AAAAAATAAATTGGATTTC
Found at i:491771 original size:31 final size:31
Alignment explanation
Indices: 491698--491891 Score: 209
Period size: 31 Copynumber: 6.2 Consensus size: 31
491688 GGAGTCGAGG
491698 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * *
491729 GAATTACCTATGTTTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTCTACGGA-ACATATGGACA
491761 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
491792 GAATTACCTATG-TCTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
*
491824 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * *
491855 GTTTACCTAGGTTC-ATCGGAACCTATAGACA
1 GTATACCTATGTTCTA-CGGAACATATGGACA
491886 GT-TACC
1 GTATACC
491892 GAGGATCTTT
Statistics
Matches: 138, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
30 5 0.04
31 79 0.57
32 54 0.39
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:491797 original size:63 final size:63
Alignment explanation
Indices: 491698--491863 Score: 298
Period size: 63 Copynumber: 2.7 Consensus size: 63
491688 GGAGTCGAGG
*
491698 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTTTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
491761 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* *
491824 GTATACCTATGTTCTAAGGAACATATGGACAG-TTTACCTA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTA
491864 GGTTCATCGG
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 7 0.07
63 93 0.93
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
Done.