Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007721.1 Hibiscus syriacus cultivar Beakdansim tig00109957_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: 3738426
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 16
Found at i:18 original size:4 final size:4
Alignment explanation
Indices: 1--1769 Score: 2679
Period size: 4 Copynumber: 447.0 Consensus size: 4
*
1 CATA CAT- CCTA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
48 CATA CATA -ATA CATA CATA CATA CATA CATA CATA CAGA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
95 CATA CATA CATA CATA CATA CATA CATAA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CAT-A CATA CATA CATA CATA CATA
*
144 CATA CATA -ATA CATA CATA CATA CAGA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
191 CATA CATA CATA CATA CATA CATA CATC CATA -ATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
238 CATA CAATA CATA CATA CATA CATA CATA CATA CATA CATA CA-A CATA
1 CATA C-ATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
286 CATA CATA CATA CATA CATA CATA CATA CATA CATC CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
334 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
382 CATA CATA CATA CATA CATA CATA CATA CATA C-TA C-TA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
428 CATA CATA CATA CATA CATA TCCATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA --CATA CATA CATA CATA CATA CATA CATA
478 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
526 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
574 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
622 CATA -ATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
669 CATA -ATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
716 CATA CATA CATA CATA CATA CATA CATA CATA C--A CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
762 CATA CATA CATA CATA CATA CATA CATA CATA C-TA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
809 CATA CATA CATA CATA CATA CATA C-TA CATA CAT- CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
855 CATA CATA CATA CATA CATA CA-A CATA CATA CATA CATA C--A CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
900 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA -ATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
947 C-TA CATA CATA CATA CATA CATA CATA CATA C--A CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
992 CATA CATA CATA CATA CATA CATA CATA CATA CATA -ATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1039 CCTA CATA CATA CATA CATA CAT- CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1086 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * ** *
1134 CATA CATA CATA CATA CATA CATA CATA TATA TATA TAAA TGTTGA -AGTC
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA -CAT-A CA-TA
* ** * * * *
1184 CAT- CAAA CAATA GTTTA -AGTT CGA-A CATA -ATA TATA -TTA AATA
1 CATA CATA C-ATA -CATA CA-TA C-ATA CATA CATA CATA CATA CATA
* ** * * * **
1227 CAT- C-TA C-T- CA-A AATA -ATA -ATA TTGGTT CATA TTATC CATA TTTAA
1 CATA CATA CATA CATA CATA CATA CATA --CATA CATA -CATA CATA CAT-A
* * * * * * * * *
1272 AATA GCATA -AAA CGATT CAGTT TATC CATTA CAAA CCAGTTTC CA-A AATA
1 CATA -CATA CATA C-ATA CA-TA CATA CA-TA CATA -CA---TA CATA CATA
1322 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1370 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1418 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1466 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1514 CATA CATA CATA CA-A CATA TAATA CATA CATA -ATA CATA CATA CATA
1 CATA CATA CATA CATA CATA -CATA CATA CATA CATA CATA CATA CATA
1561 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1609 C-TA CATA CATA CATA CATA CATA -ATA C-TA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1654 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1702 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1750 CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA
1770 TAAATGTTGA
Statistics
Matches: 1642, Mismatches: 59, Indels: 128
0.90 0.03 0.07
Matches are distributed among these distances:
2 8 0.00
3 86 0.05
4 1505 0.92
5 34 0.02
6 7 0.00
7 2 0.00
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:6125 original size:72 final size:72
Alignment explanation
Indices: 6034--6170 Score: 211
Period size: 72 Copynumber: 1.9 Consensus size: 72
6024 AAAATAAATC
* * *
6034 CATAACTAAAATGCATGAAATGATGCATTAAAGCATGAAAGGATGCCATAATTAAAATGCATGAA
1 CATAACTAAAATGCATGAAATGATGAATTAAAGCATGAAAAGATGCCATAACTAAAATGCATGAA
6099 TGAATAT
66 TGAATAT
* * * *
6106 CATATCTAAAATGCATGAAATGATGAATTAAGGCATGAAAAGATTCTATAACTAAAATGCATGAA
1 CATAACTAAAATGCATGAAATGATGAATTAAAGCATGAAAAGATGCCATAACTAAAATGCATGAA
6171 AGGATACATT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 58 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (72 bp):
CATAACTAAAATGCATGAAATGATGAATTAAAGCATGAAAAGATGCCATAACTAAAATGCATGAA
TGAATAT
Found at i:6142 original size:46 final size:46
Alignment explanation
Indices: 6092--6222 Score: 151
Period size: 46 Copynumber: 2.8 Consensus size: 46
6082 TAATTAAAAT
* *
6092 GCATGAATGAATATCATATCTAAAATGCATGAAATGATGA-ATTAAG
1 GCATGAA-GAATATCATAACTAAAATGCATGAAAGGATGACATTAAG
*
6138 GCATGAA-AAGATTCTATAACTAAAATGCATGAAAGGAT-ACATTAAG
1 GCATGAAGAATA-TC-ATAACTAAAATGCATGAAAGGATGACATTAAG
* **
6184 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATG
1 GCATG-AAGAATATCATAACTAAAATGCATGAAAGGATG
6223 TCATATCTAA
Statistics
Matches: 72, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
44 3 0.04
45 3 0.04
46 62 0.86
47 3 0.04
48 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.24
Consensus pattern (46 bp):
GCATGAAGAATATCATAACTAAAATGCATGAAAGGATGACATTAAG
Found at i:6243 original size:118 final size:118
Alignment explanation
Indices: 6035--6327 Score: 442
Period size: 118 Copynumber: 2.5 Consensus size: 118
6025 AAATAAATCC
* * * * *
6035 ATAACTAAAATGCATGAAATGATGCATTAAAGCATGAAAGGATGCCATAATTAAAATGCATGAAT
1 ATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAA
* **
6100 GAATATCATATCTAAAATGCATGAAATGATGAATTAAGGCATGAAAAGATTCT
66 GAATATCATATCTAAAATGCATGAAAGGATGAATTAAGGCATGAAAAGATGAT
6153 ATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAA
1 ATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAA
* * * *
6218 GGATGTCATATCTAAAATGTATGAAAGGATGCATTAAGGCATGAAAAGATGAT
66 GAATATCATATCTAAAATGCATGAAAGGATGAATTAAGGCATGAAAAGATGAT
* * * *
6271 AAAACTAAAATACATGAAAGGATACATTAAGGCATGAAATGATGCCACAACTAAAAT
1 ATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAACTAAAAT
6328 TAACGAATAC
Statistics
Matches: 159, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
118 159 1.00
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (118 bp):
ATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAA
GAATATCATATCTAAAATGCATGAAAGGATGAATTAAGGCATGAAAAGATGAT
Found at i:6290 original size:72 final size:72
Alignment explanation
Indices: 6139--6293 Score: 213
Period size: 72 Copynumber: 2.2 Consensus size: 72
6129 TGAATTAAGG
* * * *
6139 CATGAAAAGATTCTATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAC
1 CATGAAAGGATTCTATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAAGATGACAAAAC
*
6204 TAAAATG
66 TAAAATA
* * * *
6211 CATGAAAGGATGTC-ATATCTAAAATGTATGAAAGGATGCATTAAGGCATGAAAAGATGATAAAA
1 CATGAAAGGAT-TCTATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAAGATGACAAAA
6275 CTAAAATA
65 CTAAAATA
6283 CATGAAAGGAT
1 CATGAAAGGAT
6294 ACATTAAGGC
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
72 71 0.97
73 2 0.03
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.23
Consensus pattern (72 bp):
CATGAAAGGATTCTATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAAGATGACAAAAC
TAAAATA
Found at i:6323 original size:46 final size:46
Alignment explanation
Indices: 6210--6327 Score: 137
Period size: 46 Copynumber: 2.6 Consensus size: 46
6200 TAACTAAAAT
* * * * ** *
6210 GCATGAAAGGATGTCATATCTAAAATGTATGAAAGGATGCATTAAG
1 GCATGAAAAGATGACAAAACTAAAATACATGAAAGGATACATTAAG
*
6256 GCATGAAAAGATGATAAAACTAAAATACATGAAAGGATACATTAAG
1 GCATGAAAAGATGACAAAACTAAAATACATGAAAGGATACATTAAG
* * *
6302 GCATGAAATGATGCCACAACTAAAAT
1 GCATGAAAAGATGACAAAACTAAAAT
6328 TAACGAATAC
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.22
Consensus pattern (46 bp):
GCATGAAAAGATGACAAAACTAAAATACATGAAAGGATACATTAAG
Found at i:13153 original size:46 final size:46
Alignment explanation
Indices: 13086--13381 Score: 423
Period size: 46 Copynumber: 6.4 Consensus size: 46
13076 TAAAATAACT
*
13086 CCATAACTAAAATGCATGAAATGTTGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
* *
13132 CCATAACTAGAATGCATGAAATGATGCATTAAGGCATAAAAGGATG
1 CCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
* * * * *
13178 CCATAACTAAAATACATGAAAGGATGCATTAGGGCATGAAATGATT
1 CCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
* * * *
13224 CCATAACTAAAATGCAGGAAA-GTATTCATTAAGGCATGGAAGGGTG
1 CCATAACTAAAATGCATGAAATG-ATGCATTAAGGCATGAAAGGATG
* * * *
13270 CCAAAACTAAAATTCATGGAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
13316 CCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
*
13362 CCATAACTAAAAGGCATGAA
1 CCATAACTAAAATGCATGAA
13382 TGGATGCCAT
Statistics
Matches: 218, Mismatches: 30, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
45 1 0.00
46 216 0.99
47 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.22
Consensus pattern (46 bp):
CCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
Found at i:13312 original size:20 final size:20
Alignment explanation
Indices: 13284--13362 Score: 77
Period size: 20 Copynumber: 3.6 Consensus size: 20
13274 AACTAAAATT
*
13284 CATGGAAGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
*
13304 CATGAAAGGATGCCATAACTAAAATG
1 CATGAAAGGATG-CAT---T--AAGG
*
13330 CATGAAATGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
13350 CATGAAAGGATGC
1 CATGAAAGGATGC
13363 CATAACTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 26 0.54
21 3 0.06
22 1 0.02
24 1 0.02
25 3 0.06
26 14 0.29
ACGTcount: A:0.41, C:0.13, G:0.27, T:0.20
Consensus pattern (20 bp):
CATGAAAGGATGCATTAAGG
Found at i:13387 original size:72 final size:72
Alignment explanation
Indices: 13300--13460 Score: 259
Period size: 72 Copynumber: 2.2 Consensus size: 72
13290 AGGATGCATT
* * *
13300 AAGGCATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCA
1 AAGGCATGAAAGGATGCCATAACTAAAATACATAAAAGGATGCATTAAGGCATGAAAGGATGCCA
13365 TAACTAA
66 TAACTAA
* *
13372 AAGGCATGAATGGATGCCATAACTAAAATACATAAAAGGATGCATTAAGGCATGAAAGGATGCCG
1 AAGGCATGAAAGGATGCCATAACTAAAATACATAAAAGGATGCATTAAGGCATGAAAGGATGCCA
13437 TAACTAA
66 TAACTAA
* *
13444 AATGCATCAAAGGATGC
1 AAGGCATGAAAGGATGC
13461 ATTAAGTCAT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 81 1.00
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.19
Consensus pattern (72 bp):
AAGGCATGAAAGGATGCCATAACTAAAATACATAAAAGGATGCATTAAGGCATGAAAGGATGCCA
TAACTAA
Found at i:13390 original size:118 final size:117
Alignment explanation
Indices: 13254--13519 Score: 370
Period size: 118 Copynumber: 2.2 Consensus size: 117
13244 AGTATTCATT
* * **
13254 AAGGCATGGAAGGGTGCCAAAACTAAAATTCATGGAAGGATGCATTAAGGCATGAAAGGATGCCA
1 AAGGCAT-GAAGGATGCCATAACTAAAATTCATAAAAGGATGCATTAAGGCATGAAAGGATGCCA
* *
13319 TAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAACTAA
65 TAACTAAAATGCATCAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAA
* *
13372 AAGGCATGAATGGATGCCATAACTAAAATACATAAAAGGATGCATTAAGGCATGAAAGGATGCCG
1 AAGGCATGAA-GGATGCCATAACTAAAATTCATAAAAGGATGCATTAAGGCATGAAAGGATGCCA
* * * *
13437 TAACTAAAATGCATCAAAGGATGCATTAAGTCATGAAATGATGCCTTAATTAA
65 TAACTAAAATGCATCAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAA
* * *
13490 AATGCATAAAAGGATACCATAACTAAAATT
1 AAGGCAT-GAAGGATGCCATAACTAAAATT
13520 AACGAATAAT
Statistics
Matches: 130, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
117 3 0.02
118 125 0.96
119 2 0.02
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (117 bp):
AAGGCATGAAGGATGCCATAACTAAAATTCATAAAAGGATGCATTAAGGCATGAAAGGATGCCAT
AACTAAAATGCATCAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAA
Found at i:13422 original size:46 final size:46
Alignment explanation
Indices: 13372--13504 Score: 187
Period size: 46 Copynumber: 2.9 Consensus size: 46
13362 CCATAACTAA
*
13372 AAGGCATGAATGGATGCCATAACTAAAATACATAAAAGGATGCATT
1 AAGGCATGAATGGATGCCATAACTAAAATGCATAAAAGGATGCATT
* * *
13418 AAGGCATGAAAGGATGCCGTAACTAAAATGCATCAAAGGATGCATT
1 AAGGCATGAATGGATGCCATAACTAAAATGCATAAAAGGATGCATT
* * *
13464 AAGTCATGAAAT-GATGCCTTAATTAAAATGCATAAAAGGAT
1 AAGGCATG-AATGGATGCCATAACTAAAATGCATAAAAGGAT
13505 ACCATAACTA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
46 75 0.97
47 2 0.03
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (46 bp):
AAGGCATGAATGGATGCCATAACTAAAATGCATAAAAGGATGCATT
Found at i:16412 original size:30 final size:30
Alignment explanation
Indices: 16355--16413 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
16345 TTTTTGAATT
* *
16355 GATGAGAATTTAAGAGCTTATTTGAAGTTA
1 GATGAGAATTTAAGAGCATATTAGAAGTTA
* *
16385 GATGTGAATTTAAGAGCATCTTAGAAGTT
1 GATGAGAATTTAAGAGCATATTAGAAGTT
16414 GGAGAGTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.36
Consensus pattern (30 bp):
GATGAGAATTTAAGAGCATATTAGAAGTTA
Found at i:22983 original size:21 final size:20
Alignment explanation
Indices: 22954--22992 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
22944 TAAAAAAAAC
* *
22954 ATTCTTTCCAATATACTCGCT
1 ATTCATTCC-ATAAACTCGCT
22975 ATTCATTCCATAAACTCG
1 ATTCATTCCATAAACTCG
22993 TAAGCTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.28, C:0.28, G:0.05, T:0.38
Consensus pattern (20 bp):
ATTCATTCCATAAACTCGCT
Found at i:24104 original size:30 final size:30
Alignment explanation
Indices: 24064--24134 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
24054 TACAACAATC
* *
24064 CCTCAA-TTTTCTAGAATTTATGAATTGAT
1 CCTCAACTTTTCTAAAATTTATGAAATGAT
*
24093 -CTCCAACTTTTC-AAAATTTATGAAATGGT
1 CCT-CAACTTTTCTAAAATTTATGAAATGAT
24122 CCTCAACTTTTCT
1 CCTCAACTTTTCT
24135 GAAACTTGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
28 2 0.06
29 26 0.74
30 7 0.20
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (30 bp):
CCTCAACTTTTCTAAAATTTATGAAATGAT
Found at i:40902 original size:19 final size:19
Alignment explanation
Indices: 40878--40914 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
40868 TAGGATACCA
40878 TCCACATTCATT-TCATTTT
1 TCCACATT-ATTCTCATTTT
40897 TCCACATTATTCTCATTT
1 TCCACATTATTCTCATTT
40915 GTGCATACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (19 bp):
TCCACATTATTCTCATTTT
Found at i:47142 original size:16 final size:16
Alignment explanation
Indices: 47121--47152 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
47111 GATATAAAAA
*
47121 GAGGTGTAAGGTCTAG
1 GAGGTGTAAGGACTAG
47137 GAGGTGTAAGGACTAG
1 GAGGTGTAAGGACTAG
47153 CAGCTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.06, G:0.44, T:0.22
Consensus pattern (16 bp):
GAGGTGTAAGGACTAG
Found at i:58251 original size:13 final size:13
Alignment explanation
Indices: 58233--58258 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58223 TCTTGGGAAT
58233 AAAAAGAAGAGAG
1 AAAAAGAAGAGAG
58246 AAAAAGAAGAGAG
1 AAAAAGAAGAGAG
58259 TTTGATGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAAAAGAAGAGAG
Found at i:58902 original size:6 final size:6
Alignment explanation
Indices: 58893--58917 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
58883 AGGAGGCCCC
58893 TAACCT TAACCT TAACCT TAACCT T
1 TAACCT TAACCT TAACCT TAACCT T
58918 TGAGGGTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (6 bp):
TAACCT
Found at i:64731 original size:20 final size:20
Alignment explanation
Indices: 64706--64743 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
64696 ATATTTGACC
* *
64706 CTAGGGTTTTGATACTACAT
1 CTAGGGTATCGATACTACAT
64726 CTAGGGTATCGATACTAC
1 CTAGGGTATCGATACTAC
64744 CCACCTCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (20 bp):
CTAGGGTATCGATACTACAT
Found at i:65934 original size:32 final size:32
Alignment explanation
Indices: 65870--65936 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
65860 TAACTAATAT
* * * *
65870 ACAACAGAGTTAGTATTGCATTTAGGTGATGC
1 ACAACAGAGTTAGTATGGCATTCAGATAATGC
65902 ACAACAGAGTTAGTATGGCATTCAGATAATGC
1 ACAACAGAGTTAGTATGGCATTCAGATAATGC
65934 ACA
1 ACA
65937 GTAGATTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (32 bp):
ACAACAGAGTTAGTATGGCATTCAGATAATGC
Found at i:73924 original size:19 final size:19
Alignment explanation
Indices: 73900--73943 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
73890 ACGTAAGCTT
73900 AGTGCAGGCTTAGCACTAC
1 AGTGCAGGCTTAGCACTAC
73919 AGTGCAGGCTTAGCACTAC
1 AGTGCAGGCTTAGCACTAC
73938 AGTGCA
1 AGTGCA
73944 AGTATTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.20
Consensus pattern (19 bp):
AGTGCAGGCTTAGCACTAC
Found at i:74122 original size:33 final size:33
Alignment explanation
Indices: 74078--74149 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
74068 GTAAGTATAT
74078 TGGTAAAATAAGCTTACGAGCTTATGGTATTAAA
1 TGGT-AAATAAGCTTACGAGCTTATGGTATTAAA
*
74112 TGGTAAATAAGCTTACGAGCTTATGGTTTTAAA
1 TGGTAAATAAGCTTACGAGCTTATGGTATTAAA
74145 TGGTA
1 TGGTA
74150 CGTATATTGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 33 0.89
34 4 0.11
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (33 bp):
TGGTAAATAAGCTTACGAGCTTATGGTATTAAA
Found at i:74128 original size:79 final size:79
Alignment explanation
Indices: 74037--74354 Score: 573
Period size: 79 Copynumber: 4.0 Consensus size: 79
74027 GTAACCATGC
* *
74037 AAATAAGTTTACGATCTTATGGTTTTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTATGGTTTTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
74102 TGGTATTAAATGGT
66 TGGTATTAAATGGT
*
74116 AAATAAGCTTACGAGCTTATGGTTTTAAATGGTACGTATATTGGTAAAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTATGGTTTTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
74181 TGGTATTAAATGAT
66 TGGTATTAAATGGT
74195 AAATAAGCTTACGAGCTTATGGTTTTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTATGGTTTTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
74260 TGGTATTAAATGGT
66 TGGTATTAAATGGT
* *
74274 AAATAAGCTTACGAGATTATGGTTTTAAATGGTAAGTATTTTGGTAAAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTATGGTTTTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
74339 TGGTTTTAAATGGT
66 TGGTATTAAATGGT
74353 AA
1 AA
74355 GTATTTTGGT
Statistics
Matches: 230, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 230 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (79 bp):
AAATAAGCTTACGAGCTTATGGTTTTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
TGGTATTAAATGGT
Found at i:74200 original size:33 final size:33
Alignment explanation
Indices: 74162--74225 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
74152 TATATTGGTA
74162 AAATAAGCTTACGAGCTTATGGTATTAAATGAT
1 AAATAAGCTTACGAGCTTATGGTATTAAATGAT
*
74195 AAATAAGCTTACGAGCTTATGGTTTTAAATG
1 AAATAAGCTTACGAGCTTATGGTATTAAATG
74226 GTAAGTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (33 bp):
AAATAAGCTTACGAGCTTATGGTATTAAATGAT
Found at i:74280 original size:33 final size:33
Alignment explanation
Indices: 74236--74308 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
74226 GTAAGTATAT
*
74236 TGGTAAAATAAGCTTACGAGCTTATGGTATTAAA
1 TGGT-AAATAAGCTTACGAGATTATGGTATTAAA
*
74270 TGGTAAATAAGCTTACGAGATTATGGTTTTAAA
1 TGGTAAATAAGCTTACGAGATTATGGTATTAAA
74303 TGGTAA
1 TGGTAA
74309 GTATTTTGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
33 33 0.89
34 4 0.11
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (33 bp):
TGGTAAATAAGCTTACGAGATTATGGTATTAAA
Found at i:74407 original size:46 final size:46
Alignment explanation
Indices: 74270--74387 Score: 211
Period size: 46 Copynumber: 2.6 Consensus size: 46
74260 TGGTATTAAA
*
74270 TGGT-AAATAAGCTTACGAGATTATGGTTTTAAATGGTAAGTATTT
1 TGGTAAAATAAGCTTACGAGCTTATGGTTTTAAATGGTAAGTATTT
74315 TGGTAAAATAAGCTTACGAGCTTATGGTTTTAAATGGTAAGTATTT
1 TGGTAAAATAAGCTTACGAGCTTATGGTTTTAAATGGTAAGTATTT
*
74361 TGGTAAAATAAGCTGACGAGCTTATGG
1 TGGTAAAATAAGCTTACGAGCTTATGG
74388 GATAAATGGT
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
45 4 0.06
46 66 0.94
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (46 bp):
TGGTAAAATAAGCTTACGAGCTTATGGTTTTAAATGGTAAGTATTT
Found at i:77254 original size:27 final size:27
Alignment explanation
Indices: 77245--77341 Score: 76
Period size: 27 Copynumber: 3.6 Consensus size: 27
77235 GAAGAAACAA
*
77245 AAAAAGAAAAGAAAATAGAAAAAAAAG
1 AAAAAGAAAACAAAATAGAAAAAAAAG
* * *
77272 AAAAAGAAAA-AAAA-ACAGAAAATAG
1 AAAAAGAAAACAAAATAGAAAAAAAAG
*
77297 AAAATAGAAAATAGAAAATAGAAAACGAAAAG
1 AAAA-AG-AAA-ACAAAATAGAAAA--AAAAG
77329 -AAAAGAAAA-AAAA
1 AAAAAGAAAACAAAA
77342 GAGAGATAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
25 12 0.21
26 6 0.11
27 17 0.30
28 2 0.04
29 7 0.12
30 6 0.11
31 3 0.05
32 4 0.07
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.05
Consensus pattern (27 bp):
AAAAAGAAAACAAAATAGAAAAAAAAG
Found at i:77264 original size:7 final size:7
Alignment explanation
Indices: 77254--77321 Score: 79
Period size: 7 Copynumber: 9.9 Consensus size: 7
77244 AAAAAAGAAA
77254 AGAAAAT
1 AGAAAAT
*
77261 AGAAAAAAA
1 AG--AAAAT
77270 AGAAAA-
1 AGAAAAT
77276 AGAAAA-
1 AGAAAAT
*
77282 A-AAAAC
1 AGAAAAT
77288 AGAAAAT
1 AGAAAAT
77295 AGAAAAT
1 AGAAAAT
77302 AGAAAAT
1 AGAAAAT
77309 AGAAAAT
1 AGAAAAT
77316 AGAAAA
1 AGAAAA
77322 CGAAAAGAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
5 4 0.07
6 8 0.15
7 37 0.67
9 6 0.11
ACGTcount: A:0.78, C:0.01, G:0.13, T:0.07
Consensus pattern (7 bp):
AGAAAAT
Found at i:77299 original size:41 final size:40
Alignment explanation
Indices: 77221--77307 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 40
77211 ATTATATAAG
*
77221 GAAAAAACAGAAATGAAGAAACAAAAAAAGAAAAGAAAATA
1 GAAAAAAAAGAAA-GAAGAAACAAAAAAAGAAAAGAAAATA
77262 GAAAAAAAAGAAA-AAGAAA-AAAAAACAGAAAATAGAAAATA
1 GAAAAAAAAGAAAGAAGAAACAAAAAA-AG-AAA-AGAAAATA
77303 GAAAA
1 GAAAA
77308 TAGAAAATAG
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
38 6 0.14
39 8 0.19
40 3 0.07
41 25 0.60
ACGTcount: A:0.78, C:0.03, G:0.14, T:0.05
Consensus pattern (40 bp):
GAAAAAAAAGAAAGAAGAAACAAAAAAAGAAAAGAAAATA
Found at i:77339 original size:7 final size:7
Alignment explanation
Indices: 77251--77339 Score: 58
Period size: 7 Copynumber: 12.6 Consensus size: 7
77241 ACAAAAAAAG
77251 AAAAGAA
1 AAAAGAA
*
77258 AATAGAA
1 AAAAGAA
*
77265 AAAAAAGA
1 AAAAGA-A
77273 AAAAG-A
1 AAAAGAA
77279 AAAA-AA
1 AAAAGAA
*
77285 AACAGAA
1 AAAAGAA
*
77292 AATAGAA
1 AAAAGAA
*
77299 AATAGAA
1 AAAAGAA
*
77306 AATAGAA
1 AAAAGAA
*
77313 AATAGAA
1 AAAAGAA
77320 AACGAA-AA
1 AA--AAGAA
77328 GAAAAGAA
1 -AAAAGAA
77336 AAAA
1 AAAA
77340 AAGAGAGATA
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
6 9 0.13
7 47 0.69
8 9 0.13
9 3 0.04
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.06
Consensus pattern (7 bp):
AAAAGAA
Found at i:77343 original size:14 final size:14
Alignment explanation
Indices: 77243--77343 Score: 62
Period size: 16 Copynumber: 6.6 Consensus size: 14
77233 ATGAAGAAAC
77243 AAAAAAAGAAAAGA
1 AAAAAAAGAAAAGA
*
77257 AAATAGAAAAAAAAGA
1 AAA-A-AAAGAAAAGA
77273 AAAAGAAA-AAAA-A
1 AAAA-AAAGAAAAGA
*
77286 ACAGAAAATAGAAAATA
1 A-A-AAAA-AGAAAAGA
* *
77303 GAAAATAGAAAATAGA
1 AAAAAAAG-AAA-AGA
77319 AAACGAAAAGAAAAGA
1 AAA--AAAAGAAAAGA
77335 AAAAAAAGA
1 AAAAAAAGA
77344 GAGATAAAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 22
0.71 0.06 0.22
Matches are distributed among these distances:
13 2 0.03
14 18 0.26
15 15 0.21
16 27 0.39
17 4 0.06
18 4 0.06
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (14 bp):
AAAAAAAGAAAAGA
Found at i:90163 original size:31 final size:31
Alignment explanation
Indices: 90128--90186 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
90118 AGTTGTATGC
* *
90128 ATTATTTAAATTTCAGTTTTGTAAAACTAAA
1 ATTATTTAAATTTCAGTATTGCAAAACTAAA
*
90159 ATTATTTAAATTTTAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTGCAAAACT
90187 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTGCAAAACTAAA
Found at i:100163 original size:54 final size:54
Alignment explanation
Indices: 100105--100618 Score: 610
Period size: 54 Copynumber: 9.6 Consensus size: 54
100095 TAAACTCATT
** * *
100105 ATGAATTCTGTGGGTTGCACACATAGTGCTGAAACGGTTATTCATCAACATATG
1 ATGAATTCTGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
** * ** *
100159 ATGAATTCCATGAATTACACACTTAGTGCTAAAATGGTTATTCATCAAC-TCATG
1 ATGAATTCTGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACAT-ATG
* ** * * * *
100213 ATCAATTCCATGAATTGCATAATTACTGCCGAAACCGTTATTCATCAAC-TCATG
1 ATGAATTCTGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACAT-ATG
*
100267 ATAAATTCTGTGAATTGCACACTTAGTGTCC-AAACGGTTATTCATCAACATATG
1 ATGAATTCTGTGAATTGCACACTTAGTG-CCGAAACGGTTATTCATCAACATATG
* * **
100321 ATGAATTCCGTGAATTTCACACTTACCGCCGAAACGGTTATTCATCAAC-TCATG
1 ATGAATTCTGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACAT-ATG
* * * *
100375 CTGAATT-TCATGAATTGCACACTTAGTGCCGAAATGGTTATTCATCAACATAAG
1 ATGAATTCT-GTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
* * * * * *
100429 ATGAATTATGTGAATTGCACACTTAGTACAGACACGATTATTCATCAAC-T-TA
1 ATGAATTCTGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
* **
100481 ATGAATTCTGTGAATTGCACACTTAGTGCCAAAACGGTTATTCATCAACACGTG
1 ATGAATTCTGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
*
100535 ATGAATTCCGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
1 ATGAATTCTGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
100589 ATGAATTCTGTGAATTGCACACTTAGTGCC
1 ATGAATTCTGTGAATTGCACACTTAGTGCC
100619 TATTTGGTAA
Statistics
Matches: 391, Mismatches: 59, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
52 43 0.11
53 5 0.01
54 338 0.86
55 5 0.01
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (54 bp):
ATGAATTCTGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
Found at i:100364 original size:162 final size:162
Alignment explanation
Indices: 100105--100616 Score: 676
Period size: 162 Copynumber: 3.2 Consensus size: 162
100095 TAAACTCATT
** * * *
100105 ATGAATTCTGTGGGTTGCACACATAGTG-CTGAAACGGTTATTCATCAACATATGATGAATTCCA
1 ATGAATTCTGTGAATTGCACACTTAGTGTC-CAAACGGTTATTCATCAACATATGATGAATTCCG
* * * *
100169 TGAATTACACACTTAGTGCTAAAATGGTTATTCATCAACTCATGATCAATTCCATGAATTGCATA
65 TGAATTACACACTTAGTGCCAAAACGGTTATTCATCAACTCATGATGAATTCCATGAATTGCACA
* * *
100234 ATTACTGCCGAAACCGTTATTCATCAAC-TCATG
130 CTTAGTGCCGAAACGGTTATTCATCAACAT-ATG
*
100267 ATAAATTCTGTGAATTGCACACTTAGTGTCCAAACGGTTATTCATCAACATATGATGAATTCCGT
1 ATGAATTCTGTGAATTGCACACTTAGTGTCCAAACGGTTATTCATCAACATATGATGAATTCCGT
* ** * * *
100332 GAATTTCACACTTACCGCCGAAACGGTTATTCATCAACTCATGCTGAATTTCATGAATTGCACAC
66 GAATTACACACTTAGTGCCAAAACGGTTATTCATCAACTCATGATGAATTCCATGAATTGCACAC
* *
100397 TTAGTGCCGAAATGGTTATTCATCAACATAAG
131 TTAGTGCCGAAACGGTTATTCATCAACATATG
* * * * *
100429 ATGAATTATGTGAATTGCACACTTA--GTACAGACACGATTATTCATCAAC-T-TAATGAATTCT
1 ATGAATTCTGTGAATTGCACACTTAGTGTCCA-A-ACGGTTATTCATCAACATATGATGAATTCC
* * * *
100490 GTGAATTGCACACTTAGTGCCAAAACGGTTATTCATCAACACGTGATGAATTCCGTGAATTGCAC
64 GTGAATTACACACTTAGTGCCAAAACGGTTATTCATCAACTCATGATGAATTCCATGAATTGCAC
100555 ACTTAGTGCCGAAACGGTTATTCATCAACATATG
129 ACTTAGTGCCGAAACGGTTATTCATCAACATATG
100589 ATGAATTCTGTGAATTGCACACTTAGTG
1 ATGAATTCTGTGAATTGCACACTTAGTG
100617 CCTATTTGGT
Statistics
Matches: 305, Mismatches: 39, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
160 125 0.41
161 2 0.01
162 176 0.58
163 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (162 bp):
ATGAATTCTGTGAATTGCACACTTAGTGTCCAAACGGTTATTCATCAACATATGATGAATTCCGT
GAATTACACACTTAGTGCCAAAACGGTTATTCATCAACTCATGATGAATTCCATGAATTGCACAC
TTAGTGCCGAAACGGTTATTCATCAACATATG
Found at i:107196 original size:54 final size:54
Alignment explanation
Indices: 107117--107615 Score: 693
Period size: 54 Copynumber: 9.3 Consensus size: 54
107107 TTTTGTGGGA
* * *
107117 TGCACAC--AGTGCCGAAATGGTTATTCATCAACATATAATGAATTACGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* ** *
107169 TGCACACTTAGTGCCAAAACGGTTATTCATCAACCCATGATGAATTTCGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* *
107223 TGCACACTTAGTGTCGAAACGGTTATTCATCAAC-TCATGATGAATTTCGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACAT-ATGATGAATTCCGTGAAT
* **
107277 TGCACACTTAGTGTCGAAACAATTATTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* *
107331 TGCACACTTAGTGCCGAAACAGTTATTCATCAAC-TCATGACGAATTCCGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACAT-ATGATGAATTCCGTGAAT
* * *
107385 TGTACACTTAGTGCTGAAACAGTTATTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
*
107439 TGCACACTTAGTGCCGAAACGGTTATTCATCAAC-TCATGTTGAATTCCGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACAT-ATGATGAATTCCGTGAAT
* * * *
107493 TGCACACTTAGTACCGAAATGGTTATTCATCAACATATGATGAATTTCGTGAAC
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
* * * *
107547 TGCACACTTAGTGCCAAAATGGTTTTTCATCAACATATGATGAATTCTGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
*
107601 TGCACACTTAATGCC
1 TGCACACTTAGTGCC
107616 TATTGTGTAA
Statistics
Matches: 405, Mismatches: 34, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
52 7 0.02
53 2 0.00
54 393 0.97
55 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGAAT
Found at i:107689 original size:15 final size:15
Alignment explanation
Indices: 107669--107700 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
107659 TGACTAGTAT
107669 AACATATAGTTACAC
1 AACATATAGTTACAC
107684 AACATATAGTTACAC
1 AACATATAGTTACAC
107699 AA
1 AA
107701 TTAAATGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (15 bp):
AACATATAGTTACAC
Found at i:120057 original size:31 final size:33
Alignment explanation
Indices: 120022--120095 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
120012 AAAGTCAAAT
* *
120022 AAAAGCAACGA-A-AAAAGAAAAAAAAAAGACA
1 AAAAGCAAAGACATAAAAGAAAAAAAAAAGAAA
* *
120053 AAAAGCAAAGACATAAAAGAATAAAAAGAGAAA
1 AAAAGCAAAGACATAAAAGAAAAAAAAAAGAAA
120086 AAAAGACAAA
1 AAAAG-CAAA
120096 AAACACATGC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 10 0.28
32 1 0.03
33 21 0.58
34 4 0.11
ACGTcount: A:0.76, C:0.08, G:0.14, T:0.03
Consensus pattern (33 bp):
AAAAGCAAAGACATAAAAGAAAAAAAAAAGAAA
Found at i:122041 original size:16 final size:16
Alignment explanation
Indices: 122000--122040 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
121990 TTTTTTATCA
122000 GGGGTAAAAATTTGCT
1 GGGGTAAAAATTTGCT
122016 GGGGTAAAAATTTGCT
1 GGGGTAAAAATTTGCT
122032 GGGG-AAAAA
1 GGGGTAAAAA
122041 AGAAATTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.37, C:0.05, G:0.34, T:0.24
Consensus pattern (16 bp):
GGGGTAAAAATTTGCT
Found at i:122386 original size:12 final size:12
Alignment explanation
Indices: 122364--122396 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
122354 ACTCATAAAA
122364 TTAAC-TCCATC
1 TTAACATCCATC
122375 TTAACATCCATC
1 TTAACATCCATC
*
122387 ATAACATCCA
1 TTAACATCCA
122397 AGATAGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (12 bp):
TTAACATCCATC
Found at i:122568 original size:37 final size:37
Alignment explanation
Indices: 122527--122619 Score: 134
Period size: 37 Copynumber: 2.5 Consensus size: 37
122517 CGTCTAGCTG
* *
122527 GAGACAATTTTTCTTAAAAACCAATTTTGTCTCTCTT
1 GAGACAATTTTTCTTAAAAACAAATTTTATCTCTCTT
*
122564 GAGAC-AGTTTTCTCTAAAAACAAATTTTATCTCTCTT
1 GAGACAATTTTTCT-TAAAAACAAATTTTATCTCTCTT
*
122601 GAGACAATTTCTCTTAAAA
1 GAGACAATTTTTCTTAAAA
122620 TAATTTTTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
36 7 0.14
37 36 0.73
38 6 0.12
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (37 bp):
GAGACAATTTTTCTTAAAAACAAATTTTATCTCTCTT
Found at i:122628 original size:36 final size:36
Alignment explanation
Indices: 122527--122648 Score: 115
Period size: 37 Copynumber: 3.3 Consensus size: 36
122517 CGTCTAGCTG
* *
122527 GAGACA-ATTTTTCTTAAAAACCAATTTTGTCTCTCTT
1 GAGACAGATTTCTCTTAAAAA--AATTTTATCTCTCTT
* *
122564 GAGACAGTTTTCTCTAAAAACAAATTTTATCTCTCTT
1 GAGACAGATTTCTCTTAAAA-AAATTTTATCTCTCTT
*
122601 GAGACA-ATTTCTCTTAAAATAATTTTTATCT-TGCTT
1 GAGACAGATTTCTCTTAAAA-AAATTTTATCTCT-CTT
* *
122637 GATACATATTTC
1 GAGACAGATTTC
122649 CTTTGAGATA
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
35 1 0.01
36 29 0.40
37 31 0.43
38 10 0.14
39 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.43
Consensus pattern (36 bp):
GAGACAGATTTCTCTTAAAAAAATTTTATCTCTCTT
Found at i:123006 original size:68 final size:68
Alignment explanation
Indices: 122926--123059 Score: 232
Period size: 68 Copynumber: 2.0 Consensus size: 68
122916 GTTTCTCGTG
* * *
122926 AAACATAAAAACATTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAATTTTTCT
1 AAACATAAAAACATTGAGATTGTTTACCTTGAAACAAATTTTGTCTCGCTTGAGATAATTTCTCT
122991 TAA
66 TAA
*
122994 AAACATAAAAACATTGAGATTGTTTACCTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTCTCT
1 AAACATAAAAACATTGAGATTGTTTACCTTGAAACAAATTTTGTCTCGCTTGAGATAATTTCTCT
123059 T
66 T
123060 GAAACAAATT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (68 bp):
AAACATAAAAACATTGAGATTGTTTACCTTGAAACAAATTTTGTCTCGCTTGAGATAATTTCTCT
TAA
Found at i:123352 original size:137 final size:135
Alignment explanation
Indices: 123106--123470 Score: 447
Period size: 137 Copynumber: 2.7 Consensus size: 135
123096 GCATAGAAAT
* * *
123106 CGTGTCATCCACGGACCAGATCTCATCATCACGTAGGAGTCGTGTCATCCTTAGATAGCCAAACT
1 CGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAGTCGT-T-ATCCTTAGATAGCTAAACT
* * * *
123171 TCCTCATCACGTAGGAACTGTGTTATCTCCATTATCCCTAAAGATGGCTAGACATCCTCATCACG
64 TCCTCATCGCGTAGGAACTATATTATCTCCATTATCCCTAAAGATGGCCAGACATCCTCATCACG
123236 TAGGA-A
129 TAGGACA
* *
123242 CCGTGTCATCCACCGATCAGATCTCCTCATCACGTAGGAGTCGTTTTATCCTTAGATAGCTATAC
1 -CGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAGTCG--TTATCCTTAGATAGCTAAAC
* * * *
123307 TTCCTCATCGCGTATGAA-TCATATTATCTCTATTATCCCTAAAGATGGCCAGGCGTCCTCATCA
63 TTCCTCATCGCGTAGGAACT-ATATTATCTCCATTATCCCTAAAGATGGCCAGACATCCTCATCA
*
123371 TGTAGGACA
127 CGTAGGACA
* * *
123380 TGTGTCATCCACCGACCAGATCTCCTCATCATGTAGGCA-TC---ATCCTTAGATAGCTAGACTT
1 CGTGTCATCCACCGACCAGATCTCCTCATCACGTAGG-AGTCGTTATCCTTAGATAGCTAAACTT
*
123441 CCTCATCGCGTAGGAACCA-AGTTATCTCCA
65 CCTCATCGCGTAGGAACTATA-TTATCTCCA
123471 AATTTACCTA
Statistics
Matches: 200, Mismatches: 21, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
131 1 0.00
132 43 0.22
136 1 0.00
137 151 0.75
138 3 0.01
139 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (135 bp):
CGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAGTCGTTATCCTTAGATAGCTAAACTTC
CTCATCGCGTAGGAACTATATTATCTCCATTATCCCTAAAGATGGCCAGACATCCTCATCACGTA
GGACA
Found at i:127628 original size:21 final size:20
Alignment explanation
Indices: 127599--127647 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
127589 TGGAGTATTC
* * *
127599 AATGCTGAAATTTAATTATAG
1 AATGTTGAAATTTAAGT-CAG
*
127620 AATGTTGAATTTTAAGTCAG
1 AATGTTGAAATTTAAGTCAG
127640 AATGTTGA
1 AATGTTGA
127648 TTTGAGGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (20 bp):
AATGTTGAAATTTAAGTCAG
Found at i:129523 original size:3 final size:3
Alignment explanation
Indices: 129515--129563 Score: 73
Period size: 3 Copynumber: 16.0 Consensus size: 3
129505 TTTCATTAAA
129515 ATT ATT ATT ATT ATT -TCT ATT ATT ATT ATT ATAT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT AT-T ATT ATT ATT ATT
129561 ATT
1 ATT
129564 TTTAAATAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.02
3 38 0.88
4 4 0.09
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:131234 original size:137 final size:138
Alignment explanation
Indices: 130978--131340 Score: 382
Period size: 137 Copynumber: 2.6 Consensus size: 138
130968 GATAACAATG
* * *
130978 TTTATTTATTTTTAAATATTAAGAAAGGGTC-GTCTTAAAGCAACTGGATGTCCATTTTCTGATA
1 TTTATTTATTTTTTAATATTAAGAAA-AGACAGTCTTAAAGCAACTGGATGTCCATTTTCTGATA
* * **
131042 -TTTTAATTAAATAAACATTTTACTTTTATAAATTATATATATATATATATATATTA-T-AAATG
65 TTTTTAAATAAATAAATATCCTACTTTTATAAATTATATATATATATATATATATTATTAAAATG
131104 TTTTATTAATA
130 TTTTA--AATA
* *
131115 TTTATTTATTTTTTAATATTAAGAAATGACAGTCTTAAAACAACTGGATGTCCATTTTCTGATAT
1 TTTATTTATTTTTTAATATTAAGAAAAGACAGTCTTAAAGCAACTGGATGTCCATTTTCTGATAT
* * *
131180 TTTTAAATAAATAAATATCCTATTTTTA-AAATTATATAT-TAATCTATTATTATTATTTTTAGA
66 TTTTAAATAAATAAATATCCTACTTTTATAAATTATATATAT-ATATA-TA-TA-TATTATT---
*
131243 AAAATGTTTTAATTA
124 AAAATGTTTTAAATA
* ** * * *
131258 TTTATTTATTTTTTAATAATAAGAAAAGAGCTA-TCTTAAAGCCCCTAGAAG-CCCTTTTCTGAT
1 TTTATTTATTTTTTAATATTAAGAAAAGA-C-AGTCTTAAAGCAACTGGATGTCCATTTTCTGAT
*
131321 ATTTCTAAATAAATAAATAT
64 ATTTTTAAATAAATAAATAT
131341 TTTATTTAAA
Statistics
Matches: 192, Mismatches: 21, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
136 3 0.02
137 72 0.38
138 25 0.13
139 2 0.01
140 4 0.02
141 1 0.01
143 60 0.31
144 14 0.07
145 11 0.06
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.46
Consensus pattern (138 bp):
TTTATTTATTTTTTAATATTAAGAAAAGACAGTCTTAAAGCAACTGGATGTCCATTTTCTGATAT
TTTTAAATAAATAAATATCCTACTTTTATAAATTATATATATATATATATATATTATTAAAATGT
TTTAAATA
Found at i:137146 original size:18 final size:18
Alignment explanation
Indices: 137120--137209 Score: 71
Period size: 18 Copynumber: 5.1 Consensus size: 18
137110 CCAGCAAAGA
137120 AAGAAGAAAAAAAAGATG
1 AAGAAGAAAAAAAAGATG
*
137138 AAGATGAAAAAAAAGATG
1 AAGAAGAAAAAAAAGATG
*
137156 AA-AA-AAGAAAAATGA-G
1 AAGAAGAA-AAAAAAGATG
* **
137172 AAAAAAGAAAAAGAAAGGGG
1 -AAGAAGAAAAA-AAAGATG
*
137192 AAAAAG-AAAAAAAGATG
1 AAGAAGAAAAAAAAGATG
137209 A
1 A
137210 GAAATTGAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
16 3 0.05
17 16 0.27
18 28 0.47
19 11 0.19
20 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (18 bp):
AAGAAGAAAAAAAAGATG
Found at i:137166 original size:16 final size:16
Alignment explanation
Indices: 137129--137185 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 16
137119 AAAGAAGAAA
137129 AAAAAGATGAAGATGAAA-
1 AAAAAGATGAA-A--AAAG
137147 AAAAAGATGAAAAAAG
1 AAAAAGATGAAAAAAG
137163 AAAAATGA-GAAAAAAG
1 AAAAA-GATGAAAAAAG
137179 AAAAAGA
1 AAAAAGA
137186 AAGGGGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
15 5 0.14
16 18 0.49
17 3 0.08
18 11 0.30
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (16 bp):
AAAAAGATGAAAAAAG
Found at i:137188 original size:26 final size:26
Alignment explanation
Indices: 137117--137206 Score: 76
Period size: 26 Copynumber: 3.4 Consensus size: 26
137107 CATCCAGCAA
* *
137117 AGAAAGAAGAAAAAAAAGATGAAGATG
1 AGAAAAAAGAAAAAAAAGA-GAAAATG
* *
137144 AAAAAAAAGATGAAAAAAGA-AAAATG
1 AGAAAAAAGA-AAAAAAAGAGAAAATG
* *
137170 AGAAAAAAGAAAAAGAAAGGGGAAAAAG
1 AGAAAAAAGAAAAA-AAA-GAGAAAATG
137198 A-AAAAAAGA
1 AGAAAAAAGA
137207 TGAGAAATTG
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
25 3 0.06
26 17 0.33
27 17 0.33
28 14 0.27
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.04
Consensus pattern (26 bp):
AGAAAAAAGAAAAAAAAGAGAAAATG
Found at i:141263 original size:22 final size:22
Alignment explanation
Indices: 141238--141314 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
141228 ATCTACACTT
141238 TTCAAAGATGATAGACTCTTTC
1 TTCAAAGATGATAGACTCTTTC
* * *
141260 TTCAAAGATGATAGTCTATCTC
1 TTCAAAGATGATAGACTCTTTC
* *
141282 TTTAAAGATGATAGATTCTCTT-
1 TTCAAAGATGATAGACTCT-TTC
141304 TTCAAAGATGA
1 TTCAAAGATGA
141315 AAGCTTTATT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 44 0.98
23 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGACTCTTTC
Found at i:142046 original size:45 final size:45
Alignment explanation
Indices: 141979--142552 Score: 1004
Period size: 45 Copynumber: 12.8 Consensus size: 45
141969 CTATTTCCCA
* * *
141979 CATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAACCTTCCGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
142024 CATCTGTAAGTCCTTCATTGCATGATGTTTTCAAAACCTTCCGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
142069 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
142114 TATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
142159 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
142204 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
142249 CATCTGTAAGTCCTCCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
142294 CATCTGTAAGTCCTTCAGTGCAAGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
142339 CATCTATAAGTCCTTCAGTGCACGATGTTTTAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
142384 CATCTGTAAGTCCTTCAGTGCACGATGTTTTTAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
142429 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
142474 CATTTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
142519 CATATGTAAGCCCTTCAGTGCATGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAA
142553 CATTTCCATC
Statistics
Matches: 509, Mismatches: 20, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 509 1.00
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (45 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:142689 original size:3 final size:3
Alignment explanation
Indices: 142681--142733 Score: 81
Period size: 3 Copynumber: 17.3 Consensus size: 3
142671 TTTCATTAAA
142681 ATT ATT ATT ATT ATT -TCT ATT ATT ATT ATT ATGT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT AT-T ATT ATT ATT ATT
142727 ATT ATT A
1 ATT ATT A
142734 AATAAATATT
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.02
3 42 0.89
4 4 0.09
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:144266 original size:2 final size:2
Alignment explanation
Indices: 144259--144305 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
144249 ATTTATAAAT
144259 TA 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 TA
144301 T- TA TA
1 TA TA TA
144306 AATGTTTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:149130 original size:21 final size:21
Alignment explanation
Indices: 149106--149167 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
149096 GAGTTATTAA
149106 TATGGATTTCAAGTTGATTGT
1 TATGGATTTCAAGTTGATTGT
149127 TATGGATTTCAAGTTTG-TTGT
1 TATGGATTTCAAG-TTGATTGT
* * *
149148 TATGAATGTCAAGTTTATTG
1 TATGGATTTCAAGTTGATTG
149168 GATAATGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 2 0.06
21 31 0.86
22 3 0.08
ACGTcount: A:0.24, C:0.05, G:0.23, T:0.48
Consensus pattern (21 bp):
TATGGATTTCAAGTTGATTGT
Found at i:149597 original size:84 final size:84
Alignment explanation
Indices: 149499--149677 Score: 358
Period size: 84 Copynumber: 2.1 Consensus size: 84
149489 AAAAGATATA
149499 TAGCGGCGTTTCTTAACAAAGCATCTAAATATTATAACCTTTAGTCGTATTTGTAGAAAAAACGC
1 TAGCGGCGTTTCTTAACAAAGCATCTAAATATTATAACCTTTAGTCGTATTTGTAGAAAAAACGC
149564 CGCTAAAAATATAAACTTT
66 CGCTAAAAATATAAACTTT
149583 TAGCGGCGTTTCTTAACAAAGCATCTAAATATTATAACCTTTAGTCGTATTTGTAGAAAAAACGC
1 TAGCGGCGTTTCTTAACAAAGCATCTAAATATTATAACCTTTAGTCGTATTTGTAGAAAAAACGC
149648 CGCTAAAAATATAAACTTT
66 CGCTAAAAATATAAACTTT
149667 TAGCGGCGTTT
1 TAGCGGCGTTT
149678 GTTGACGACA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 95 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (84 bp):
TAGCGGCGTTTCTTAACAAAGCATCTAAATATTATAACCTTTAGTCGTATTTGTAGAAAAAACGC
CGCTAAAAATATAAACTTT
Found at i:149626 original size:41 final size:41
Alignment explanation
Indices: 149499--149626 Score: 125
Period size: 41 Copynumber: 3.1 Consensus size: 41
149489 AAAAGATATA
149499 TAGCGGCGTTTCTTAACAAAGCATCTAAATATTATAACCTT
1 TAGCGGCGTTTCTTAACAAAGCATCTAAATATTATAACCTT
** * * * ** * *
149540 TAGTC-GTATTTGTAGAAAAAACGCCGCTAAA-AATATAAACTTT
1 TAG-CGGCGTTTCT-TAACAAA-GCATCTAAATATTAT-AACCTT
149583 TAGCGGCGTTTCTTAACAAAGCATCTAAATATTATAACCTT
1 TAGCGGCGTTTCTTAACAAAGCATCTAAATATTATAACCTT
149624 TAG
1 TAG
149627 TCGTATTTGT
Statistics
Matches: 63, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
41 23 0.37
42 20 0.32
43 20 0.32
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (41 bp):
TAGCGGCGTTTCTTAACAAAGCATCTAAATATTATAACCTT
Found at i:160461 original size:19 final size:19
Alignment explanation
Indices: 160429--160486 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
160419 ACTATTAATG
* *
160429 AATAGAATGTAATGCGAAA
1 AATAAAATGCAATGCGAAA
** *
160448 GGTAAAATGCAATGTGAAA
1 AATAAAATGCAATGCGAAA
160467 AATAAAATGCAGATGC-AAA
1 AATAAAATGCA-ATGCGAAA
160486 A
1 A
160487 TGCAAGGTGT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 27 0.90
20 3 0.10
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.19
Consensus pattern (19 bp):
AATAAAATGCAATGCGAAA
Found at i:162861 original size:21 final size:21
Alignment explanation
Indices: 162837--162889 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
162827 ATTCTGACTA
*
162837 TCGCATTGTGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
162858 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
162879 TCGCAATGCGA
1 TCGCATTGCGA
162890 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:162908 original size:20 final size:20
Alignment explanation
Indices: 162879--163149 Score: 240
Period size: 20 Copynumber: 13.2 Consensus size: 20
162869 TTTTCCTAAT
*
162879 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
162899 TCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
162919 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* * * *
162939 TCACAATGTGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
162960 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
162980 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
163001 TCGCCGCAATGCGATTACGTAAA
1 T---CGCAATGCGAATACGTAAA
* *
163024 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
163045 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
163065 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* * *
163086 TCGTAATGTGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
163106 TCGCATTGCGATTTACGT-AA
1 TCGCAATGCGA-ATACGTAAA
* *
163126 TCGCATTGCGATTTACGT-AA
1 TCGCAATGCGA-ATACGTAAA
163146 TCGC
1 TCGC
163150 TTTTCGATTT
Statistics
Matches: 206, Mismatches: 37, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
20 129 0.63
21 60 0.29
23 7 0.03
24 10 0.05
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:162909 original size:41 final size:41
Alignment explanation
Indices: 162858--163364 Score: 364
Period size: 41 Copynumber: 12.3 Consensus size: 41
162848 TTTCCCAAAT
* * *
162858 TCGCGTTGCGATTTTCCTAATTCGCAATGCGAATATGTAAA
1 TCGCATTGCGATTTTCCTAATTCGCAATGCGATTACGTAAA
* * * * * *
162899 TCGTAATGCGA-ATACGTAAATCGCAATGCGATTACGTAAA
1 TCGCATTGCGATTTTCCTAATTCGCAATGCGATTACGTAAA
* * * * **** *
162939 TCACAATGTGAATTAGGAAAATCGCAATGCGATTACGTAAA
1 TCGCATTGCGATTTTCCTAATTCGCAATGCGATTACGTAAA
* ***** *
162980 TCGCAATGCGAATTAGGAAAATCGCCGCAATGCGATTACGTAAA
1 TCGCATTGCG-ATTTTCCTAAT--TCGCAATGCGATTACGTAAA
* * **** *
163024 TCGCAATGCGAATTAGGAAAATCGCAATGCGATTACGTAAA
1 TCGCATTGCGATTTTCCTAATTCGCAATGCGATTACGTAAA
* * **** * * *
163065 TCGCAATGCGAATTAGGAAAATCGTAATGTGATTACGTAAA
1 TCGCATTGCGATTTTCCTAATTCGCAATGCGATTACGTAAA
* * *
163106 TCGCATTGCGATTTACGTAA-TCGCATTGCGATTTACGT-AA
1 TCGCATTGCGATTTTCCTAATTCGCAATGCGA-TTACGTAAA
* *
163146 TCGCTTTTCGATTTTCCTAATTCGCAATGCGATTTACGT-AA
1 TCGCATTGCGATTTTCCTAATTCGCAATGCGA-TTACGTAAA
*
163187 TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT-AA
1 TCGCATTGCGATTTTCCTAATTCGCAATGCGA-TTACGTAAA
* * *
163228 TCGCATTGCAATTTTCATAATTCGCATTGCGATTTACGT-AA
1 TCGCATTGCGATTTTCCTAATTCGCAATGCGA-TTACGTAAA
* * *
163269 TCGCATTGCTATTTTGCTAATTCGCATTGCGATTTACGT-AA
1 TCGCATTGCGATTTTCCTAATTCGCAATGCGA-TTACGTAAA
* **
163310 TCGCATTGCGATTTTCCTAATTCGCACTTTGATTTACGT-AA
1 TCGCATTGCGATTTTCCTAATTCGCAATGCGA-TTACGTAAA
*
163351 TCGCATTGCAATTT
1 TCGCATTGCGATTT
163365 AGTAAATCGC
Statistics
Matches: 403, Mismatches: 57, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
40 57 0.14
41 305 0.76
42 6 0.01
43 6 0.01
44 29 0.07
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCTAATTCGCAATGCGATTACGTAAA
Found at i:163037 original size:85 final size:82
Alignment explanation
Indices: 162879--163149 Score: 359
Period size: 85 Copynumber: 3.3 Consensus size: 82
162869 TTTTCCTAAT
* * * * * *
162879 TCGCAATGCGAATATGTAAATCGTAATGCGAA-TACGTAAATCGCAATGCGATTACGTAAATCAC
1 TCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATTACGTAAATCGC
*
162943 AATGTGAATTAGGAAAA
66 AATGCGAATTAGGAAAA
162960 TCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCCGCAATGCGATTACGTAAAT
1 TCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAAT---CGCAATGCGATTACGTAAAT
163025 CGCAATGCGAATTAGGAAAA
63 CGCAATGCGAATTAGGAAAA
* *
163045 TCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGTAATGTGATTACGTAAATCGC
1 TCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATTACGTAAATCGC
* * * *
163110 ATTGCGATTTACG-TAA
66 AATGCGAATTAGGAAAA
*
163126 TCGCATTGCGATTTACGT-AATCGC
1 TCGCAATGCGA-TTACGTAAATCGC
163150 TTTTCGATTT
Statistics
Matches: 171, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
81 47 0.27
82 44 0.26
85 80 0.47
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.25
Consensus pattern (82 bp):
TCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATTACGTAAATCGC
AATGCGAATTAGGAAAA
Found at i:163266 original size:123 final size:122
Alignment explanation
Indices: 163097--163365 Score: 423
Period size: 123 Copynumber: 2.2 Consensus size: 122
163087 CGTAATGTGA
* * * *
163097 TTACGTAAATCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCTTTTCGATTTTC
1 TTACGT-AATCGCATTGCAATTTACATAATCGCATTGCGATTTACGTAATCGCATTGCGATTTTC
163162 CTAATTCGCAATGCGATTTACGTAATCGCATTGCGATTTTCCTAATTCGCA-TTGCGAT
65 CTAATTCGCAATGCGATTTACGTAATCGCATTGCGATTTTCCTAATTCGCACTT-CGAT
* * *
163220 TTACGTAATCGCATTGCAATTTTCATAATTCGCATTGCGATTTACGTAATCGCATTGCTATTTTG
1 TTACGTAATCGCATTGCAATTTACATAA-TCGCATTGCGATTTACGTAATCGCATTGCGATTTTC
* *
163285 CTAATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAATTCGCACTTTGAT
65 CTAATTCGCAATGCGATTTACGTAATCGCATTGCGATTTTCCTAATTCGCACTTCGAT
163343 TTACGTAATCGCATTGCAATTTA
1 TTACGTAATCGCATTGCAATTTA
163366 GTAAATCGCA
Statistics
Matches: 134, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
122 19 0.14
123 113 0.84
124 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (122 bp):
TTACGTAATCGCATTGCAATTTACATAATCGCATTGCGATTTACGTAATCGCATTGCGATTTTCC
TAATTCGCAATGCGATTTACGTAATCGCATTGCGATTTTCCTAATTCGCACTTCGAT
Found at i:165405 original size:20 final size:19
Alignment explanation
Indices: 165377--165431 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
165367 CAATCATCTT
*
165377 AATGTCTATCGCAACGCGAA
1 AATGACTATCGCAACGCG-A
*
165397 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
165416 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
165432 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:165446 original size:33 final size:33
Alignment explanation
Indices: 165404--165530 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
165394 GAAAATGACT
165404 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
165437 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
165470 ATCACAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
165503 ATTGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
165531 CGAATTTAGT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:165460 original size:19 final size:19
Alignment explanation
Indices: 165384--165495 Score: 91
Period size: 19 Copynumber: 6.4 Consensus size: 19
165374 CTTAATGTCT
* **
165384 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCG-AAATGAAA
165404 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
165423 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
165437 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
165456 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
165470 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
165489 ATCGCAA
1 ATCGCAA
165496 CGAGGGAATT
Statistics
Matches: 73, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
14 19 0.26
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 32 0.44
20 10 0.14
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:165533 original size:19 final size:18
Alignment explanation
Indices: 165384--165534 Score: 83
Period size: 19 Copynumber: 8.7 Consensus size: 18
165374 CTTAATGTCT
**
165384 ATCGCAACGCGAAAATGACT
1 ATCGCAA-GCG-AAATGAAA
165404 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
165423 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
165437 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
165456 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
*
165470 ATCACAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
165489 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
*
165503 ATTGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
165522 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
165535 TTTAGTTTCG
Statistics
Matches: 100, Mismatches: 15, Indels: 33
0.68 0.10 0.22
Matches are distributed among these distances:
14 25 0.25
15 5 0.05
16 6 0.06
17 6 0.06
18 5 0.05
19 43 0.43
20 10 0.10
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:165712 original size:14 final size:14
Alignment explanation
Indices: 165693--165729 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
165683 CATCAATTAA
165693 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
165707 ACAAATCATCTTTT
1 ACAAATCAACTTTT
165721 ACAAATCAA
1 ACAAATCAA
165730 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:167104 original size:21 final size:20
Alignment explanation
Indices: 167080--167140 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
167070 GTGAATCGGG
*
167080 CTCTTGAATGGTGAGAGGGAC
1 CTCTTGAACGGTGAGAGGG-C
* * *
167101 CTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGAGAG-GGC
*
167122 CTCTTGAACGGTGGGAGGG
1 CTCTTGAACGGTGAGAGGG
167141 GACTCTCGAG
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (20 bp):
CTCTTGAACGGTGAGAGGGC
Found at i:167639 original size:19 final size:19
Alignment explanation
Indices: 167599--167667 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
167589 TCTGGAACTT
*
167599 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
167620 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
* *
167639 AAAATCGCAACGCAAAACG
1 AAAATCGCAACGCGAAATG
167658 AAAATCGCAA
1 AAAATCGCAA
167668 TGATAGAATC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 30 0.73
21 11 0.27
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:167737 original size:20 final size:20
Alignment explanation
Indices: 167712--167749 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
167702 CGCGATTATA
167712 GTTTCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTG
167732 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
167750 CATTCTCTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.16, G:0.29, T:0.50
Consensus pattern (20 bp):
GTTTCGCGTTGCGATTTTTG
Found at i:168016 original size:94 final size:94
Alignment explanation
Indices: 167882--168235 Score: 549
Period size: 94 Copynumber: 3.8 Consensus size: 94
167872 CAACCAAAAG
* * * *
167882 ACAAA-ACAAAGACTAACTTCAGAGTATTAAAGAATACACAGTTTAGCAGAATTGGCAGCAAACG
1 ACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAATCG
167946 AACAAATTTACTTTCAACCAAAAGACAAA
66 AACAAATTTACTTTCAACCAAAAGACAAA
* *
167975 ACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGTAGCAGTCG
1 ACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAATCG
168040 AACAAATTTACTTTCAACCAAAAGACAAA
66 AACAAATTTACTTTCAACCAAAAGACAAA
*
168069 ACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGTAATCG
1 ACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAATCG
*
168134 AATAAATTTAC-TTCAACCAAAAGACAAA
66 AACAAATTTACTTTCAACCAAAAGACAAA
* * *
168162 ACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGTTTAGCAGTATTGGCAGCAACC
1 AC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAATC
*
168223 GAATAAATTTACT
65 GAACAAATTTACT
168236 AAGCAATCTA
Statistics
Matches: 244, Mismatches: 14, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
90 39 0.16
93 24 0.10
94 181 0.74
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (94 bp):
ACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAATCG
AACAAATTTACTTTCAACCAAAAGACAAA
Found at i:170019 original size:19 final size:19
Alignment explanation
Indices: 169933--170038 Score: 105
Period size: 19 Copynumber: 5.7 Consensus size: 19
169923 TTGGTTGAAT
*
169933 TGAAAATCGCAACGAGAGAA
1 TGAAAATCGCAACGCGA-AA
169953 TGAAAATCGCAACGCGGAAA
1 TGAAAATCGCAACGC-GAAA
**
169973 TGACTATCGCAA--CG--A
1 TGAAAATCGCAACGCGAAA
* *
169988 -GAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGCGAAA
170006 TGAAAATCGCAACGCGAAA
1 TGAAAATCGCAACGCGAAA
*
170025 TGAAAATGGCAACG
1 TGAAAATCGCAACG
170039 AGAGAATCGC
Statistics
Matches: 71, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
14 8 0.11
15 1 0.01
16 2 0.03
17 1 0.01
18 2 0.03
19 29 0.41
20 26 0.37
21 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (19 bp):
TGAAAATCGCAACGCGAAA
Found at i:170043 original size:52 final size:53
Alignment explanation
Indices: 169937--170069 Score: 187
Period size: 52 Copynumber: 2.5 Consensus size: 53
169927 TTGAATTGAA
* **
169937 AATCGCAACGAGAGAATGAAAATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGCGGAAATGAAAATCGCAACGAGAG
* *
169991 AATCGTAACGCGAAATGAAAATCGCAACGC-GAAATGAAAATGGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGCGGAAATGAAAATCGCAACGAGAG
**
170043 AATCGCAACGCGAAACCAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
170070 TAGTCATTTC
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
52 43 0.61
53 17 0.24
54 11 0.15
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (53 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGGAAATGAAAATCGCAACGAGAG
Found at i:170704 original size:20 final size:20
Alignment explanation
Indices: 170652--170723 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
170642 GCTATGTAAA
**
170652 TCGCATTGCGATAGTCAG-AT
1 TCGCATTGCGATTTTC-GTAT
170672 TCGCATTGCGATTTTCGTAT
1 TCGCATTGCGATTTTCGTAT
*
170692 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCGT-AT
*
170713 TCGCAATGCGA
1 TCGCATTGCGA
170724 ATACGTAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
19 1 0.02
20 33 0.72
21 12 0.26
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTTCGTAT
Found at i:170737 original size:41 final size:40
Alignment explanation
Indices: 170713--170867 Score: 166
Period size: 41 Copynumber: 3.8 Consensus size: 40
170703 TTTTCCTAAT
*
170713 TCGCAATGCGAATACGTAAATCGCAATGCAATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAA
* * * *
170753 TCGCAATGCGAATTATGAAAATCGCAACGCGAATACGTAAA
1 TCGCAATGCGAA-TACGTAAATCGCAATGCGATTACGTAAA
* * * *
170794 TCGCAACGCGAATACGTAAATCGCAACGCGAATTAGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCG-ATTACGTAAA
* ** *
170835 TCGCAACGCGAATTTGGGAAATCGCAATGCGAT
1 TCGCAATGCGAA-TACGTAAATCGCAATGCGAT
170868 AGTCAGAATC
Statistics
Matches: 97, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
40 28 0.29
41 55 0.57
42 14 0.14
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAA
Found at i:170757 original size:61 final size:61
Alignment explanation
Indices: 170713--170847 Score: 200
Period size: 61 Copynumber: 2.2 Consensus size: 61
170703 TTTTCCTAAT
* * *
170713 TCGCAATGCGAATACGTAAATCGCAATGC-AATTACGTAAATCGCAATGCGAATTATGAAAA
1 TCGCAACGCGAATACGTAAATCGCAACGCGAA-TACGTAAATCGCAATGCGAATTATCAAAA
* **
170774 TCGCAACGCGAATACGTAAATCGCAACGCGAATACGTAAATCGCAACGCGAATTAGGAAAA
1 TCGCAACGCGAATACGTAAATCGCAACGCGAATACGTAAATCGCAATGCGAATTATCAAAA
170835 TCGCAACGCGAAT
1 TCGCAACGCGAAT
170848 TTGGGAAATC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 67 0.97
62 2 0.03
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (61 bp):
TCGCAACGCGAATACGTAAATCGCAACGCGAATACGTAAATCGCAATGCGAATTATCAAAA
Found at i:170774 original size:21 final size:21
Alignment explanation
Indices: 170713--170866 Score: 181
Period size: 20 Copynumber: 7.5 Consensus size: 21
170703 TTTTCCTAAT
*
170713 TCGCAATGCGAA-TACGTAAA
1 TCGCAACGCGAATTACGTAAA
*
170733 TCGCAATGC-AATTACGTAAA
1 TCGCAACGCGAATTACGTAAA
* * *
170753 TCGCAATGCGAATTATGAAAA
1 TCGCAACGCGAATTACGTAAA
170774 TCGCAACGCGAA-TACGTAAA
1 TCGCAACGCGAATTACGTAAA
170794 TCGCAACGCGAA-TACGTAAA
1 TCGCAACGCGAATTACGTAAA
* *
170814 TCGCAACGCGAATTAGGAAAA
1 TCGCAACGCGAATTACGTAAA
** *
170835 TCGCAACGCGAATTTGGGAAA
1 TCGCAACGCGAATTACGTAAA
*
170856 TCGCAATGCGA
1 TCGCAACGCGA
170867 TAGTCAGAAT
Statistics
Matches: 121, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
19 2 0.02
20 64 0.53
21 55 0.45
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAATTACGTAAA
Found at i:172676 original size:31 final size:31
Alignment explanation
Indices: 172620--172712 Score: 127
Period size: 31 Copynumber: 3.0 Consensus size: 31
172610 TTAACGTCCG
*
172620 GACACCT-AAATTGTAACAAAGAAAACATTA
1 GACACCTAAAATTATAACAAAGAAAACATTA
172650 GACACCTAAAATTATAACGAAA-AAAACATTA
1 GACACCTAAAATTATAAC-AAAGAAAACATTA
* * *
172681 GACACCTAAAATGACAACAAAGAAAACTTTA
1 GACACCTAAAATTATAACAAAGAAAACATTA
172712 G
1 G
172713 GTATCAAGAT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
30 10 0.18
31 43 0.77
32 3 0.05
ACGTcount: A:0.55, C:0.17, G:0.10, T:0.18
Consensus pattern (31 bp):
GACACCTAAAATTATAACAAAGAAAACATTA
Found at i:176146 original size:33 final size:33
Alignment explanation
Indices: 176104--176171 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
176094 ATCCGCTTTC
176104 GACTTGGAGAAAATTGAAATTACATTTTAAAAT
1 GACTTGGAGAAAATTGAAATTACATTTTAAAAT
176137 GACTTGGAGAAAATTGAAATTACATTTTAAAAT
1 GACTTGGAGAAAATTGAAATTACATTTTAAAAT
176170 GA
1 GA
176172 TAAATAATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (33 bp):
GACTTGGAGAAAATTGAAATTACATTTTAAAAT
Found at i:176984 original size:80 final size:80
Alignment explanation
Indices: 176849--176998 Score: 273
Period size: 80 Copynumber: 1.9 Consensus size: 80
176839 AAATGACGCA
* *
176849 ATATGACCTAAAAATAGAGTTTAAATAATAAAAATTGGGTAAACTACATAGTTGGTCACTAATGT
1 ATATGACCTAAAAATAGAGTTTAAATAATAAAAATTGGGTAAACTACACACTTGGTCACTAATGT
176914 TTGGGATAGTTTTTG
66 TTGGGATAGTTTTTG
*
176929 ATATGACCTAAAAATAGAGTTTAAATAATAATAATTGGGTAAACTACACACTTGGTCACTAATGT
1 ATATGACCTAAAAATAGAGTTTAAATAATAAAAATTGGGTAAACTACACACTTGGTCACTAATGT
176994 TTGGG
66 TTGGG
176999 GTAATTTTCA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.33
Consensus pattern (80 bp):
ATATGACCTAAAAATAGAGTTTAAATAATAAAAATTGGGTAAACTACACACTTGGTCACTAATGT
TTGGGATAGTTTTTG
Found at i:186205 original size:13 final size:13
Alignment explanation
Indices: 186187--186211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
186177 AGCCATTAGT
186187 TTCATAATTAATA
1 TTCATAATTAATA
186200 TTCATAATTAAT
1 TTCATAATTAAT
186212 GTGATATTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCATAATTAATA
Found at i:186681 original size:12 final size:12
Alignment explanation
Indices: 186664--186692 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
186654 TTGTTGTGCT
186664 TGCTCCTCGGGC
1 TGCTCCTCGGGC
186676 TGCTCCTCGGGC
1 TGCTCCTCGGGC
186688 TGCTC
1 TGCTC
186693 AGGCTCATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.41, G:0.31, T:0.28
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:192092 original size:20 final size:21
Alignment explanation
Indices: 192054--192093 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
192044 GAAGCTTTAA
* *
192054 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACCTTTGAT
192075 GATCATC-ATTTACCTTTGA
1 GATCATCAATTTACCTTTGA
192094 AAGTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACCTTTGAT
Found at i:198484 original size:54 final size:54
Alignment explanation
Indices: 198409--198528 Score: 161
Period size: 54 Copynumber: 2.2 Consensus size: 54
198399 ATGTAAGGTA
* *
198409 CATGTATTGCAC-CAAAGTGCCAAAATGGAAATTCAAAAACTCATTATGAATTC
1 CATGTATTGCACACAAAGTGCCAAAATGGAAATTCAAAAACACATTATGAATAC
* * ** *
198462 CATGAATTGCACACATAGTGCCAAAATGGTCATTCATAAACACATTATGAATAC
1 CATGTATTGCACACAAAGTGCCAAAATGGAAATTCAAAAACACATTATGAATAC
*
198516 CATGTGTTGCACA
1 CATGTATTGCACA
198529 TTTAATGTCA
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
53 11 0.19
54 46 0.81
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (54 bp):
CATGTATTGCACACAAAGTGCCAAAATGGAAATTCAAAAACACATTATGAATAC
Found at i:200837 original size:24 final size:23
Alignment explanation
Indices: 200804--200848 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
200794 TCCTAATTTA
200804 ATAAATAATA-TACAAATTAAAAT
1 ATAAATAATACTA-AAATTAAAAT
200827 ATAAACTAATACTAAAATTAAA
1 ATAAA-TAATACTAAAATTAAA
200849 TAAATAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 5 0.25
24 13 0.65
25 2 0.10
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (23 bp):
ATAAATAATACTAAAATTAAAAT
Found at i:201185 original size:23 final size:23
Alignment explanation
Indices: 201155--201210 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
201145 AAGAGGGGAG
201155 GGGAGACGGATGGTAATCAATGT
1 GGGAGACGGATGGTAATCAATGT
201178 GGGAGACGGATGGTAATCAATGT
1 GGGAGACGGATGGTAATCAATGT
*
201201 GAGAGACGGA
1 GGGAGACGGA
201211 CTGTTGTGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.32, C:0.09, G:0.41, T:0.18
Consensus pattern (23 bp):
GGGAGACGGATGGTAATCAATGT
Found at i:204925 original size:77 final size:76
Alignment explanation
Indices: 204781--204930 Score: 178
Period size: 76 Copynumber: 2.0 Consensus size: 76
204771 ATTTTCTCTG
* * *
204781 TTACACTTTTAAGTGCTTATCATTAAAAAAACTATTAAGTGAAACGTCTCACGTCCATATTTTTA
1 TTACACTTTTAAGTGCTTATCATTAAAAAAACTATTAAGTGAAACATCTCACATCCAGATTTTT-
204846 AAAAATAATCCT
65 AAAAATAATCCT
* * * * * *
204858 TTACACTTTTAAGTG-TCTATCGTTAAAAAATC-GTTAAGTGACACATGTCACATCCAGGTTTTC
1 TTACACTTTTAAGTGCT-TATCATTAAAAAAACTATTAAGTGAAACATCTCACATCCAGATTTT-
204921 TAAAAATAAT
64 TAAAAATAAT
204931 TTTAAAAATA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
76 33 0.53
77 29 0.47
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (76 bp):
TTACACTTTTAAGTGCTTATCATTAAAAAAACTATTAAGTGAAACATCTCACATCCAGATTTTTA
AAAATAATCCT
Found at i:204970 original size:21 final size:20
Alignment explanation
Indices: 204934--204981 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
204924 AAATAATTTT
204934 AAAAATATTCTATTTTTTAA
1 AAAAATATTCTATTTTTTAA
* *
204954 AAAAATATTTTATTTTTTTA
1 AAAAATATTCTATTTTTTAA
204974 AAAAATAT
1 AAAAATAT
204982 AGACGTGGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAAATATTCTATTTTTTAA
Found at i:205637 original size:51 final size:51
Alignment explanation
Indices: 205561--205664 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
205551 AATTGGTTTT
205561 CACTAATCTAGGCTTTAGGGCATAGATCTCATAAGTATAAGGTCACCTTTC
1 CACTAATCTAGGCTTTAGGGCATAGATCTCATAAGTATAAGGTCACCTTTC
*
205612 CACTAATCTAGGCTTTTGGGCATAGATCTCATAAGTATAAGGTCACCTTTC
1 CACTAATCTAGGCTTTAGGGCATAGATCTCATAAGTATAAGGTCACCTTTC
205663 CA
1 CA
205665 ATTTATTCTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (51 bp):
CACTAATCTAGGCTTTAGGGCATAGATCTCATAAGTATAAGGTCACCTTTC
Found at i:209439 original size:26 final size:24
Alignment explanation
Indices: 209410--209457 Score: 78
Period size: 26 Copynumber: 1.9 Consensus size: 24
209400 ATGCACTATT
209410 TTTTATTTTATGTTTATTTGATTATG
1 TTTTATTTTAT-TTTATTT-ATTATG
209436 TTTTATTTTATTTTATTTATTA
1 TTTTATTTTATTTTATTTATTA
209458 ACCATTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 4 0.18
25 7 0.32
26 11 0.50
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (24 bp):
TTTTATTTTATTTTATTTATTATG
Found at i:209476 original size:5 final size:5
Alignment explanation
Indices: 209410--209453 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
209400 ATGCACTATT
* * *
209410 TTTTA TTTTA TGTTTA TTTGA TTATG TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
209454 ATTAACCATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:209962 original size:20 final size:21
Alignment explanation
Indices: 209924--209962 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
209914 CAGCCCTTTA
209924 ATTTTATTAGTTTAATTTACT
1 ATTTTATTAGTTTAATTTACT
* *
209945 ATTTT-TTATTTTATTTTA
1 ATTTTATTAGTTTAATTTA
209963 ACCCTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (21 bp):
ATTTTATTAGTTTAATTTACT
Found at i:222755 original size:14 final size:13
Alignment explanation
Indices: 222731--222772 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
222721 TTAAGTGAGA
222731 CAATTTTAAAAAT
1 CAATTTTAAAAAT
222744 CAATTCTTAAAAA-
1 CAATT-TTAAAAAT
* *
222757 AAATTATAAAAAT
1 CAATTTTAAAAAT
222770 CAA
1 CAA
222773 AATGGACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 6 0.25
13 11 0.46
14 7 0.29
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (13 bp):
CAATTTTAAAAAT
Found at i:223066 original size:21 final size:21
Alignment explanation
Indices: 223040--223091 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
223030 AATTAAGTAT
223040 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
223061 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
223082 AAATG-ATTTT
1 AAATGAATTTT
223092 CTAAGTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 5 0.16
21 26 0.84
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:223470 original size:64 final size:65
Alignment explanation
Indices: 223315--223474 Score: 236
Period size: 65 Copynumber: 2.5 Consensus size: 65
223305 GAATAAATTG
* *
223315 AACATTGAATGCATTTTATGCATCGATACACATACCATGCATCGATGCACTCAAGATTTTATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAAGATTTTATGAA
* * *
223380 AACATCGAATGCATTTTTTGCATCGATGCACA-AGCCATGCATCGATGCACTCAGGCTATTT-T-
1 AACATCGAATGCATTTTATGCATCGATGCACATA-CCATGCATCGATGCACTCAAGAT-TTTATG
223442 AA
64 AA
223444 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
223475 TCTTAGTGCA
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
64 33 0.38
65 51 0.59
66 3 0.03
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAAGATTTTATGAA
Found at i:223714 original size:10 final size:10
Alignment explanation
Indices: 223699--223723 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
223689 GCCATTGATC
223699 AACAACAAGA
1 AACAACAAGA
223709 AACAACAAGA
1 AACAACAAGA
223719 AACAA
1 AACAA
223724 AATCAAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.20, G:0.08, T:0.00
Consensus pattern (10 bp):
AACAACAAGA
Found at i:231954 original size:65 final size:64
Alignment explanation
Indices: 231885--232043 Score: 234
Period size: 65 Copynumber: 2.5 Consensus size: 64
231875 TAATAAATTG
* *
231885 AACATCGAATGTATTTTATGCATCGATGCACATA-CCATGCATCGATGCACTCAGG-TTTTTATG
1 AACATCGAATGCATTTTATGCATCGATGCACA-AGCCATGCATCGATGCACTCAGGCTATTT-T-
231948 AA
63 AA
*
231950 AACATCGAATACATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTAA
1 AACATCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTAA
*
232014 AATATCGAA-GCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
232044 TCAGGTTTTT
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
63 20 0.23
64 11 0.13
65 52 0.60
66 4 0.05
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTAA
Found at i:232035 original size:44 final size:46
Alignment explanation
Indices: 231986--232089 Score: 151
Period size: 44 Copynumber: 2.3 Consensus size: 46
231976 TGCACAAGCC
* *
231986 ATGCATCGATGCACTCAGGCTATTT-T-AAAATATCGAA-GCATTTT
1 ATGCATCGATGCACTCAGG-TATTTATGAAAACATCGAATACATTTT
*
232030 ATGCATCGATGCACTCAGGTTTTTATGAAAACATCGAATACATTTT
1 ATGCATCGATGCACTCAGGTATTTATGAAAACATCGAATACATTTT
232076 ATGCATCGATGCAC
1 ATGCATCGATGCAC
232090 AAGCCATGCA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
43 4 0.07
44 20 0.37
45 10 0.19
46 20 0.37
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (46 bp):
ATGCATCGATGCACTCAGGTATTTATGAAAACATCGAATACATTTT
Found at i:232052 original size:109 final size:109
Alignment explanation
Indices: 231921--232131 Score: 413
Period size: 109 Copynumber: 1.9 Consensus size: 109
231911 TGCACATACC
231921 ATGCATCGATGCACTCAGGTTTTTATGAAAACATCGAATACATTTTATGCATCGATGCACAAGCC
1 ATGCATCGATGCACTCAGGTTTTTATGAAAACATCGAATACATTTTATGCATCGATGCACAAGCC
*
231986 ATGCATCGATGCACTCAGGCTATTTTAAAATATCGAAGCATTTT
66 ATGCATCGATGCACTCAAGCTATTTTAAAATATCGAAGCATTTT
232030 ATGCATCGATGCACTCAGGTTTTTATGAAAACATCGAATACATTTTATGCATCGATGCACAAGCC
1 ATGCATCGATGCACTCAGGTTTTTATGAAAACATCGAATACATTTTATGCATCGATGCACAAGCC
232095 ATGCATCGATGCACTCAAGCTATTTTAAAATATCGAA
66 ATGCATCGATGCACTCAAGCTATTTTAAAATATCGAA
232132 TGCACCAGAC
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 101 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (109 bp):
ATGCATCGATGCACTCAGGTTTTTATGAAAACATCGAATACATTTTATGCATCGATGCACAAGCC
ATGCATCGATGCACTCAAGCTATTTTAAAATATCGAAGCATTTT
Found at i:233439 original size:37 final size:37
Alignment explanation
Indices: 233389--233463 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
233379 TGATCAAGGC
233389 ATACATTTATAGCTTTAGTATTTTAATTTGTTTAATA
1 ATACATTTATAGCTTTAGTATTTTAATTTGTTTAATA
233426 ATACATTTATAGCTTTAGTATTTTAATTTGTTTAATA
1 ATACATTTATAGCTTTAGTATTTTAATTTGTTTAATA
233463 A
1 A
233464 ATTTTGGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.53
Consensus pattern (37 bp):
ATACATTTATAGCTTTAGTATTTTAATTTGTTTAATA
Found at i:234362 original size:2 final size:2
Alignment explanation
Indices: 234357--234414 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
234347 TATGTGTGTG
234357 TA 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 TA
234399 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
234415 GTTTTTCAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:243804 original size:17 final size:18
Alignment explanation
Indices: 243782--243818 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
243772 TCTATGCATG
243782 TTTATTTCTT-TA-TTTAT
1 TTTATTT-TTATATTTTAT
243799 TTTATTTTTATATTTTAT
1 TTTATTTTTATATTTTAT
243817 TT
1 TT
243819 AATCTTAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.11
17 9 0.50
18 7 0.39
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTATTTTTATATTTTAT
Found at i:247685 original size:53 final size:53
Alignment explanation
Indices: 247605--247711 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
247595 AAGCATGTCG
247605 CAAAGTTGCAACAAGCACATCCACCAGCTTGAAGAAAGTAAACCTCTAACCAA
1 CAAAGTTGCAACAAGCACATCCACCAGCTTGAAGAAAGTAAACCTCTAACCAA
*
247658 CAAAGTTGCAACAAGCACATCCACCAGCTTGAAGAAAGTAAACCTCTAATCAA
1 CAAAGTTGCAACAAGCACATCCACCAGCTTGAAGAAAGTAAACCTCTAACCAA
247711 C
1 C
247712 CTAGAACTTG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.43, C:0.28, G:0.13, T:0.16
Consensus pattern (53 bp):
CAAAGTTGCAACAAGCACATCCACCAGCTTGAAGAAAGTAAACCTCTAACCAA
Found at i:251743 original size:9 final size:9
Alignment explanation
Indices: 251729--251783 Score: 64
Period size: 9 Copynumber: 6.6 Consensus size: 9
251719 AAATGGAAAT
*
251729 CATTCTTTG
1 CATTCTTTA
251738 CATTCTTTA
1 CATTCTTTA
251747 CATTCTTTA
1 CATTCTTTA
251756 CA-T-TTTA
1 CATTCTTTA
*
251763 CATTCATT-
1 CATTCTTTA
251771 -ATTCTTTA
1 CATTCTTTA
251779 CATTC
1 CATTC
251784 ATTTTATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
7 12 0.31
8 2 0.05
9 25 0.64
ACGTcount: A:0.22, C:0.22, G:0.02, T:0.55
Consensus pattern (9 bp):
CATTCTTTA
Found at i:251764 original size:16 final size:18
Alignment explanation
Indices: 251729--251783 Score: 64
Period size: 16 Copynumber: 3.3 Consensus size: 18
251719 AAATGGAAAT
*
251729 CATTCTTTGCATTCTTTA
1 CATTCTTTACATTCTTTA
251747 CATTCTTTACA-T-TTTA
1 CATTCTTTACATTCTTTA
*
251763 CATTCATT--ATTCTTTA
1 CATTCTTTACATTCTTTA
251779 CATTC
1 CATTC
251784 ATTTTATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 1 0.03
15 1 0.03
16 20 0.61
17 1 0.03
18 10 0.30
ACGTcount: A:0.22, C:0.22, G:0.02, T:0.55
Consensus pattern (18 bp):
CATTCTTTACATTCTTTA
Found at i:255003 original size:19 final size:19
Alignment explanation
Indices: 254959--255003 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
254949 TGCTTTTATG
* *
254959 TATTTTATACGATAAATCG
1 TATTTTGTACGATAAATCA
254978 TATTTTGTACGATAAATCA
1 TATTTTGTACGATAAATCA
254997 TATTTTG
1 TATTTTG
255004 ATATTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (19 bp):
TATTTTGTACGATAAATCA
Found at i:257309 original size:12 final size:12
Alignment explanation
Indices: 256841--257308 Score: 612
Period size: 12 Copynumber: 38.8 Consensus size: 12
256831 ACATACATAT
* *
256841 ACATACACATAC
1 ACATGCACATGC
* *
256853 ACATACACATAC
1 ACATGCACATGC
* *
256865 ACATACACATAC
1 ACATGCACATGC
* *
256877 ACATACACATAC
1 ACATGCACATGC
256889 ACATACGCACATGC
1 ACAT--GCACATGC
256903 ACATGCACATGC
1 ACATGCACATGC
256915 ACATGCACATGC
1 ACATGCACATGC
256927 ACATGCACATGC
1 ACATGCACATGC
256939 ACATGCACATGC
1 ACATGCACATGC
256951 ACATGCACATGC
1 ACATGCACATGC
256963 ACATGCACATGC
1 ACATGCACATGC
256975 ACATGCACATGC
1 ACATGCACATGC
256987 ACATGCACATGC
1 ACATGCACATGC
256999 ACATGCACATGC
1 ACATGCACATGC
257011 ACATGCACATGC
1 ACATGCACATGC
257023 ACATGCACATGC
1 ACATGCACATGC
257035 ACATGCACATGC
1 ACATGCACATGC
257047 ACATGCACATGC
1 ACATGCACATGC
257059 ACATGCACATGC
1 ACATGCACATGC
*
257071 ACATGCGCATGC
1 ACATGCACATGC
*
257083 ACATGCGCATGC
1 ACATGCACATGC
*
257095 ACATGCGCATGC
1 ACATGCACATGC
*
257107 ACATGCGCATGC
1 ACATGCACATGC
*
257119 ACATGCGCATGC
1 ACATGCACATGC
*
257131 ACATGCGCATGC
1 ACATGCACATGC
*
257143 ACATGCGCATGC
1 ACATGCACATGC
*
257155 ACATGCGCATGC
1 ACATGCACATGC
*
257167 ACATGCGCATGC
1 ACATGCACATGC
*
257179 ACATGCGCATGC
1 ACATGCACATGC
*
257191 ACATGCGCATGC
1 ACATGCACATGC
*
257203 ACATGCGCATGC
1 ACATGCACATGC
*
257215 ACATGCACATAC
1 ACATGCACATGC
* *
257227 ACATACACATAC
1 ACATGCACATGC
* *
257239 ACATACACATAC
1 ACATGCACATGC
* *
257251 ACATACACATAC
1 ACATGCACATGC
* *
257263 ACATACACATAC
1 ACATGCACATGC
* *
257275 ACATACACATAC
1 ACATGCACATGC
* *
257287 ACATACACATAC
1 ACATGCACATGC
*
257299 ACATACACAT
1 ACATGCACAT
257309 ATACATATCA
Statistics
Matches: 448, Mismatches: 6, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
12 438 0.98
14 10 0.02
ACGTcount: A:0.36, C:0.33, G:0.14, T:0.17
Consensus pattern (12 bp):
ACATGCACATGC
Found at i:257316 original size:6 final size:6
Alignment explanation
Indices: 256835--257315 Score: 332
Period size: 6 Copynumber: 79.8 Consensus size: 6
256825 TACAAAACAT
*
256835 ACATAT ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * * * * *
256883 ACATAC ACATACGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC
1 ACATAC ACATA--C ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * * * * * * *
256933 ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * * * * * * *
256981 ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * * * * * * *
257029 ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC ACATGC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * * * * * * * * * * *
257077 GCATGC ACATGC GCATGC ACATGC GCATGC ACATGC GCATGC ACATGC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * * * * * * * * * * *
257125 GCATGC ACATGC GCATGC ACATGC GCATGC ACATGC GCATGC ACATGC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * * * * * * * * * * *
257173 GCATGC ACATGC GCATGC ACATGC GCATGC ACATGC GCATGC ACATGC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
257221 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
*
257269 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAT ACATA
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATA
257316 TCATACCAAA
Statistics
Matches: 445, Mismatches: 28, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
6 440 0.99
8 5 0.01
ACGTcount: A:0.36, C:0.33, G:0.14, T:0.17
Consensus pattern (6 bp):
ACATAC
Found at i:257610 original size:23 final size:24
Alignment explanation
Indices: 257576--257630 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
257566 CACCATAGCT
*
257576 CGTATAAA-TGCACCAAAGTGCCA
1 CGTAGAAATTGCACCAAAGTGCCA
** *
257599 CGTA-AAATTGCACTGAAGTGCCG
1 CGTAGAAATTGCACCAAAGTGCCA
257622 CGTAGAAAT
1 CGTAGAAAT
257631 GTACCGTAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.11
23 20 0.74
24 4 0.15
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (24 bp):
CGTAGAAATTGCACCAAAGTGCCA
Found at i:259886 original size:2 final size:2
Alignment explanation
Indices: 259879--259921 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
259869 TCCTAAGACT
259879 TA 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 TA
259921 T
1 T
259922 TATTTATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:261962 original size:87 final size:87
Alignment explanation
Indices: 261863--262030 Score: 300
Period size: 87 Copynumber: 1.9 Consensus size: 87
261853 TTAATTTTAA
*
261863 AAAAAAATTATGAAAATAGCACCATTTTGAAATTAATTACCAAAATAGCACCATTTTCAAAATAA
1 AAAAAAATTATGAAAATAGCACCATTTTGAAAATAATTACCAAAATAGCACCATTTTCAAAATAA
261928 TTACTAAAATATCATCTCTTTT
66 TTACTAAAATATCATCTCTTTT
* * *
261950 AAAAAAATTATGAAAATAGCACCATTTTTAAAATAATTACCAAAATATCATCATTTTCAAAATAA
1 AAAAAAATTATGAAAATAGCACCATTTTGAAAATAATTACCAAAATAGCACCATTTTCAAAATAA
262015 TTACTAAAATATCATC
66 TTACTAAAATATCATC
262031 CGATCAACGG
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 77 1.00
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (87 bp):
AAAAAAATTATGAAAATAGCACCATTTTGAAAATAATTACCAAAATAGCACCATTTTCAAAATAA
TTACTAAAATATCATCTCTTTT
Found at i:262030 original size:29 final size:29
Alignment explanation
Indices: 261875--262025 Score: 173
Period size: 29 Copynumber: 5.2 Consensus size: 29
261865 AAAAATTATG
* * *
261875 AAAATAGCACCATTTTGAAATTAATTACC
1 AAAATAGCACCATTTTCAAAATAATTACT
261904 AAAATAGCACCATTTTCAAAATAATTACT
1 AAAATAGCACCATTTTCAAAATAATTACT
* *
261933 AAAATATCATCTC-TTTT-AAAAAAATTA-T
1 AAAATAGCA-C-CATTTTCAAAATAATTACT
* *
261961 GAAAATAGCACCATTTTTAAAATAATTACC
1 -AAAATAGCACCATTTTCAAAATAATTACT
* *
261991 AAAATATCATCATTTTCAAAATAATTACT
1 AAAATAGCACCATTTTCAAAATAATTACT
262020 AAAATA
1 AAAATA
262026 TCATCCGATC
Statistics
Matches: 104, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
27 1 0.01
28 6 0.06
29 91 0.88
30 5 0.05
31 1 0.01
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATAGCACCATTTTCAAAATAATTACT
Found at i:264379 original size:26 final size:26
Alignment explanation
Indices: 264340--264400 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
264330 TGTTGACGAA
*
264340 TAAGGCTCTGAGATCTGATATCGTCT
1 TAAGGCTCAGAGATCTGATATCGTCT
*
264366 TACGGCTCAGAGATCTGATATCGTCT
1 TAAGGCTCAGAGATCTGATATCGTCT
264392 TAAGGCTCA
1 TAAGGCTCA
264401 AGGCGTCTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (26 bp):
TAAGGCTCAGAGATCTGATATCGTCT
Found at i:269261 original size:29 final size:28
Alignment explanation
Indices: 269211--269411 Score: 208
Period size: 29 Copynumber: 7.0 Consensus size: 28
269201 AACTAATTTT
* *
269211 TTTTAAAAACAATTACGAAAAATAGCACCA
1 TTTT-AAAATAATTAC-AAAAATATCACCA
*
269241 TTTTAAAATTAATTACAAAAATAGCACCA
1 TTTTAAAA-TAATTACAAAAATATCACCA
* *
269270 TTTTAAAAATAATTACTAAAATATCACCC
1 TTTT-AAAATAATTACAAAAATATCACCA
* * *
269299 TTTTAAAA-AATTACGAAATTATCACTCTT
1 TTTTAAAATAATTACAAAAATATCAC-C-A
* *
269328 TTTTAAAA-AATTACAAAAATAACACTA
1 TTTTAAAATAATTACAAAAATATCACCA
*
269355 TTTTTAAAATAATTACCAAAATATCACCA
1 -TTTTAAAATAATTACAAAAATATCACCA
*
269384 TTTTCAAAATAATTACTAAAATATCACC
1 TTTT-AAAATAATTACAAAAATATCACC
269412 TGGTCAACGG
Statistics
Matches: 148, Mismatches: 16, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
27 15 0.10
28 17 0.11
29 102 0.69
30 14 0.09
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (28 bp):
TTTTAAAATAATTACAAAAATATCACCA
Found at i:269347 original size:85 final size:88
Alignment explanation
Indices: 269211--269410 Score: 248
Period size: 85 Copynumber: 2.3 Consensus size: 88
269201 AACTAATTTT
* * * * *
269211 TTTTAAAAACAATTACGAAAAATAGCAC-C-ATTTTAAAATTAATTACAAAAATAGCACCATTTT
1 TTTTCAAAATAATTACG-AAAATATCACTCTTTTTTAAAA-TAATTACAAAAATAACACCATTTT
* *
269274 AAAAATAATTACTAAAATATCACCC
64 AAAAATAATTACCAAAATATCACCA
* * *
269299 TTTT-AAAA-AATTACGAAATTATCACTCTTTTTTAAAA-AATTACAAAAATAACACTATTTTTA
1 TTTTCAAAATAATTACGAAAATATCACTCTTTTTTAAAATAATTACAAAAATAACACCATTTTAA
269361 AAATAATTACCAAAATATCACCA
66 AAATAATTACCAAAATATCACCA
*
269384 TTTTCAAAATAATTACTAAAATATCAC
1 TTTTCAAAATAATTACGAAAATATCAC
269411 CTGGTCAACG
Statistics
Matches: 98, Mismatches: 10, Indels: 9
0.84 0.09 0.08
Matches are distributed among these distances:
85 55 0.56
86 12 0.12
87 27 0.28
88 4 0.04
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (88 bp):
TTTTCAAAATAATTACGAAAATATCACTCTTTTTTAAAATAATTACAAAAATAACACCATTTTAA
AAATAATTACCAAAATATCACCA
Found at i:270371 original size:28 final size:28
Alignment explanation
Indices: 270340--270394 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
270330 AAATAAACTT
*
270340 AGTT-AGTGACCAAATTATAAAATTTTAA
1 AGTTAAGTGACCAAAATAT-AAATTTTAA
270368 AGTTAAGTGACCAAAATATAAATTTTA
1 AGTTAAGTGACCAAAATATAAATTTTA
270395 GAAAAGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (28 bp):
AGTTAAGTGACCAAAATATAAATTTTAA
Found at i:270411 original size:31 final size:29
Alignment explanation
Indices: 270342--270415 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 29
270332 ATAAACTTAG
*
270342 TTAGTGACCAAATTATAAAATTTTAAAGT
1 TTAGTGACCAAAATATAAAATTTTAAAGT
*
270371 TAAGTGACCAAAATAT-AAATTTTAGAAAAGT
1 TTAGTGACCAAAATATAAAATTTT---AAAGT
*
270402 TTAGGGACCAAAAT
1 TTAGTGACCAAAAT
270416 GGTAATTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 7 0.18
29 14 0.37
31 17 0.45
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (29 bp):
TTAGTGACCAAAATATAAAATTTTAAAGT
Found at i:273049 original size:3 final size:3
Alignment explanation
Indices: 273041--273069 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
273031 TTAATGAATG
273041 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
273070 AAATATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:276056 original size:19 final size:19
Alignment explanation
Indices: 276010--276057 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
276000 AAAGAGAGAT
*
276010 AAAGAGAAAGAATATAAAA
1 AAAGAGAAAGAAAATAAAA
*
276029 AAAGAAGAAA-AAAATAAGAG
1 AAAG-AGAAAGAAAATAA-AA
276049 AAAGAGAAA
1 AAAGAGAAA
276058 TGAACAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (19 bp):
AAAGAGAAAGAAAATAAAA
Found at i:277438 original size:44 final size:44
Alignment explanation
Indices: 277397--277488 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
277387 TTTGATCAGT
* *
277397 ATCACACTTT-TTGGCTCTTCCATCGCATAAGGAGTTGGATCAAC
1 ATCACA-TTTCTTAGCTCGTCCATCGCATAAGGAGTTGGATCAAC
* * *
277441 ATTATATTTCTTAGCTCGTCCATCGCATAGGGAGTTGGATCAAC
1 ATCACATTTCTTAGCTCGTCCATCGCATAAGGAGTTGGATCAAC
277485 ATCA
1 ATCA
277489 TTTTCCTTGG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 3 0.07
44 38 0.93
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (44 bp):
ATCACATTTCTTAGCTCGTCCATCGCATAAGGAGTTGGATCAAC
Done.