Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002647.1 Hibiscus syriacus cultivar Beakdansim tig00005406_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: 7027529
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 26
Found at i:5840385 original size:49 final size:48
Alignment explanation
Indices: 5840332--5840424 Score: 125
Period size: 49 Copynumber: 1.9 Consensus size: 48
5840322 CAATTTTGAA
*
5840332 AGCTCGA-TTGAAGCTCGAGACTCGAGCTCGATTTGAAGCTCGAGACTCG
1 AGCTCGATTTGAAGCTCG-GACTCGAGCTCGA-TTCAAGCTCGAGACTCG
** *
5840381 AGCTCGATTTGAAGCTCGGTTTTGAGCTCGATTCAAGCTCGAGA
1 AGCTCGATTTGAAGCTCGGACTCGAGCTCGATTCAAGCTCGAGA
5840425 ACAGGTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
48 12 0.31
49 17 0.44
50 10 0.26
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (48 bp):
AGCTCGATTTGAAGCTCGGACTCGAGCTCGATTCAAGCTCGAGACTCG
Found at i:5842179 original size:108 final size:107
Alignment explanation
Indices: 5842048--5842256 Score: 364
Period size: 108 Copynumber: 1.9 Consensus size: 107
5842038 AATAACACTA
*
5842048 TATGTGCAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTGTGTGTGCAAAA
1 TATGTGCAAACTAAGAAATTCATAACAAGTTTATGAATTTCCGTATGGACACTGTGTGTGCAAAA
*
5842113 CTAAGAAATTCATAATAAGTTTATGAATTTCCTTATGGGCAC
66 CTAAGAAATTCATAATAAGATTATGAATTTCCTTATGGGCAC
* *
5842155 TATGTGCAAAACTAAGAAATTCATAACAAGTTTATGAATTTCCGTATGGGCACTGTGTGTGTAAA
1 TATGTGC-AAACTAAGAAATTCATAACAAGTTTATGAATTTCCGTATGGACACTGTGTGTGCAAA
*
5842220 ACTAAGAAATTCATAATGAGATTATGAATTTCCTTAT
65 ACTAAGAAATTCATAATAAGATTATGAATTTCCTTAT
5842257 TGACATTAGG
Statistics
Matches: 96, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
107 7 0.07
108 89 0.93
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (107 bp):
TATGTGCAAACTAAGAAATTCATAACAAGTTTATGAATTTCCGTATGGACACTGTGTGTGCAAAA
CTAAGAAATTCATAATAAGATTATGAATTTCCTTATGGGCAC
Found at i:5842270 original size:55 final size:55
Alignment explanation
Indices: 5842050--5842261 Score: 313
Period size: 55 Copynumber: 3.9 Consensus size: 55
5842040 TAACACTATA
5842050 TGTGC-AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTGTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTGTG
* * *
5842104 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCTTATGGGCAC--TA
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTGTG
* *
5842157 TGTGCAAAACTAAGAAATTCATAACAAGTTTATGAATTTCCGTATGGGCACTGTG
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTGTG
* * * * *
5842212 TGTGTAAAACTAAGAAATTCATAATGAGATTATGAATTTCCTTATTGACA
1 TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACA
5842262 TTAGGTGTGC
Statistics
Matches: 142, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
53 50 0.35
54 5 0.04
55 87 0.61
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (55 bp):
TGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTGTG
Found at i:5842592 original size:45 final size:46
Alignment explanation
Indices: 5842511--5842597 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 46
5842501 GTTAGATGAA
*
5842511 TAACGGTGCATTACTGGCATGAAAGGATGTACTAAAT-AAAATGCC
1 TAACGGTGCATTACTGGCATGAAAGGATGCACTAAATGAAAATGCC
*
5842556 TAACGGTGTATTA-TCGGCATGAAAGGATGC-CATAAATGAAAA
1 TAACGGTGCATTACT-GGCATGAAAGGATGCAC-TAAATGAAAA
5842598 GAATTAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
44 2 0.05
45 31 0.84
46 4 0.11
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (46 bp):
TAACGGTGCATTACTGGCATGAAAGGATGCACTAAATGAAAATGCC
Found at i:5844830 original size:21 final size:18
Alignment explanation
Indices: 5844812--5844849 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
5844802 AAAATAATAC
5844812 TAAAAAAAAAAGTAGTAAT
1 TAAAAAAAAAA-TAGTAAT
*
5844831 TAAACAAAAAATAGTAAT
1 TAAAAAAAAAATAGTAAT
5844849 T
1 T
5844850 CTCCCTCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.24
Consensus pattern (18 bp):
TAAAAAAAAAATAGTAAT
Found at i:5849773 original size:54 final size:54
Alignment explanation
Indices: 5849676--5849990 Score: 373
Period size: 55 Copynumber: 5.8 Consensus size: 54
5849666 CAATGGTATA
* * *
5849676 CACTATGTGTGCAAATCCAAAGAATTCATCATGAGTTGATGAATAACTATACAAG
1 CACTATGTGTGCAAAT-CACATAATTCATCATGAGTTGATGAATAACTGTACAAG
* *
5849731 CACTATGTGTGCAAATC-CATGATATCATCATGAGTTGATGAATAACCGTAC-AG
1 CACTATGTGTGCAAATCACATAAT-TCATCATGAGTTGATGAATAACTGTACAAG
*
5849784 TCACTATGTGTGCAAATCACATAATTCATCTTGAGTTGATGAATAACTGTACAAG
1 -CACTATGTGTGCAAATCACATAATTCATCATGAGTTGATGAATAACTGTACAAG
* * * *
5849839 CACTATGTGTGCAAATCCGCAAAATTTATCATGAGTTGATGAATAACTGTACATG
1 CACTATGTGTGCAAAT-CACATAATTCATCATGAGTTGATGAATAACTGTACAAG
* * ** * * * *
5849894 CACTATATGTTCAAATCGACGGAATTTATCATTAGTTGATGAATAACCGTACAGG
1 CACTATGTGTGCAAATC-ACATAATTCATCATGAGTTGATGAATAACTGTACAAG
* ** *
5849949 CACGATGTGTGCAACCCACATAATTCATCATAAGTTGATGAA
1 CACTATGTGTGCAAATCACATAATTCATCATGAGTTGATGAA
5849991 CTACCGGATA
Statistics
Matches: 224, Mismatches: 30, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
53 5 0.02
54 106 0.47
55 113 0.50
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (54 bp):
CACTATGTGTGCAAATCACATAATTCATCATGAGTTGATGAATAACTGTACAAG
Found at i:5849898 original size:109 final size:108
Alignment explanation
Indices: 5849676--5849990 Score: 386
Period size: 109 Copynumber: 2.9 Consensus size: 108
5849666 CAATGGTATA
* * *
5849676 CACTATGTGTGCAAATCCAAAGAATTCATCATGAGTTGATGAATAACTATACAAGCACTATGTGT
1 CACTATGTGTGCAAAT-CACAGAATTCATCTTGAGTTGATGAATAACTGTACAAGCACTATGTGT
*
5849741 GCAAAT-CCATGATATCATCATGAGTTGATGAATAACCGTACAGT
65 GCAAATCCCATAAT-TCATCATGAGTTGATGAATAACCGTACAGT
*
5849785 CACTATGTGTGCAAATCACATAATTCATCTTGAGTTGATGAATAACTGTACAAGCACTATGTGTG
1 CACTATGTGTGCAAATCACAGAATTCATCTTGAGTTGATGAATAACTGTACAAGCACTATGTGTG
* * *
5849850 CAAATCCGCAAAATTTATCATGAGTTGATGAATAACTGTACA-T
66 CAAATCC-CATAATTCATCATGAGTTGATGAATAACCGTACAGT
* * * * * * *
5849893 GCACTATATGTTCAAATCGACGGAATTTATCATT-AGTTGATGAATAACCGTACAGGCACGATGT
1 -CACTATGTGTGCAAATC-ACAGAATTCATC-TTGAGTTGATGAATAACTGTACAAGCACTATGT
* *
5849957 GTGC-AACCCACATAATTCATCATAAGTTGATGAA
63 GTGCAAATCC-CATAATTCATCATGAGTTGATGAA
5849991 CTACCGGATA
Statistics
Matches: 180, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
108 51 0.28
109 83 0.46
110 44 0.24
111 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (108 bp):
CACTATGTGTGCAAATCACAGAATTCATCTTGAGTTGATGAATAACTGTACAAGCACTATGTGTG
CAAATCCCATAATTCATCATGAGTTGATGAATAACCGTACAGT
Found at i:5855288 original size:21 final size:21
Alignment explanation
Indices: 5855262--5855313 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
5855252 CTAGAATGAG
5855262 AAGTTCCAAAGAATGTATCCA
1 AAGTTCCAAAGAATGTATCCA
*
5855283 AAGTTCCAAAGAATGTATCCG
1 AAGTTCCAAAGAATGTATCCA
5855304 AAGTT-CAAAG
1 AAGTTCCAAAG
5855314 TTTTCTGGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (21 bp):
AAGTTCCAAAGAATGTATCCA
Found at i:5859033 original size:22 final size:22
Alignment explanation
Indices: 5859003--5859069 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 22
5858993 AGTTGAGGGT
5859003 TACATAGGTCCTTCGAGACATA
1 TACATAGGTCCTTCGAGACATA
*
5859025 TACACAGGTCCTTC-AGGACATA
1 TACATAGGTCCTTCGA-GACATA
* *
5859047 TGCATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGAGACATA
5859069 T
1 T
5859070 TTTACATGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 38 0.97
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (22 bp):
TACATAGGTCCTTCGAGACATA
Found at i:5859850 original size:55 final size:55
Alignment explanation
Indices: 5859786--5860154 Score: 416
Period size: 55 Copynumber: 6.8 Consensus size: 55
5859776 CAATGATATA
* * *
5859786 CACTATGTGTGTAAATACACGAAATTCATCATGAGTTGATGAAGAACCGTACAAG
1 CACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACAAG
*
5859841 CACTATGTGTGCAAATCCAC-AGAATTCATCATGAGTTGATGAATAACCGTACATG
1 CACTATGTGTGCAAATCCACGA-AATTCATCATGAGTTGATGAATAACCGTACAAG
* **
5859896 CACTATTTGTGCAAATCCA--AAGATTTCATCATGAGTTGATGAATAACCACACAAG
1 CACTATGTGTGCAAATCCACGAA-A-TTCATCATGAGTTGATGAATAACCGTACAAG
* * *
5859951 AACTA--TGTGCAAATCCAC-AGAATTCATCATGAGTTGATGAATAACTGTACAGG
1 CACTATGTGTGCAAATCCACGA-AATTCATCATGAGTTGATGAATAACCGTACAAG
* * ** * *
5860004 CACTATATGTGAAAATCTGCAAAATTTATCATGAGTTGATGAATAACCGTAC-AG
1 CACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACAAG
* * * *
5860058 ACACTATGTGTACAAATCCACCG-AATTTATCATGAGTTGATGAATAACCGTATAGG
1 -CACTATGTGTGCAAATCCA-CGAAATTCATCATGAGTTGATGAATAACCGTACAAG
* *
5860114 CACGATGTGTGC-AACCCACGAAATTCATCATGAGTTG-TGAA
1 CACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAA
5860155 CTACCATATA
Statistics
Matches: 270, Mismatches: 32, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
53 50 0.19
54 26 0.10
55 191 0.71
56 3 0.01
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (55 bp):
CACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACAAG
Found at i:5859993 original size:108 final size:108
Alignment explanation
Indices: 5859810--5860154 Score: 439
Period size: 108 Copynumber: 3.2 Consensus size: 108
5859800 ATACACGAAA
* *
5859810 TTCATCATGAGTTGATGAAGAACCGTACAAGCACTATGTGTGCAAATCCACAGAATTCATCATGA
1 TTCATCATGAGTTGATGAATAACCGTACAAGAACTA--TGTGCAAATCCACAGAATTCATCATGA
* *
5859875 GTTGATGAATAACCGTACATGCACTATTTGTGCAAATC-CAAAGAT
64 GTTGATGAATAACCGTACAGGCACTATATGTGCAAATCGCAAA-AT
**
5859920 TTCATCATGAGTTGATGAATAACCACACAAGAACTATGTGCAAATCCACAGAATTCATCATGAGT
1 TTCATCATGAGTTGATGAATAACCGTACAAGAACTATGTGCAAATCCACAGAATTCATCATGAGT
* *
5859985 TGATGAATAACTGTACAGGCACTATATGTGAAAATCTGCAAAAT
66 TGATGAATAACCGTACAGGCACTATATGTGCAAATC-GCAAAAT
* *
5860029 TT-ATCATGAGTTGATGAATAACCGTAC-AGACACTATGTGTACAAATCCACCGAATTTATCATG
1 TTCATCATGAGTTGATGAATAACCGTACAAGA-ACTATGTG--CAAATCCACAGAATTCATCATG
* * * ** * *
5860092 AGTTGATGAATAACCGTATAGGCACGATGTGTGCAACCCACGAAA-
63 AGTTGATGAATAACCGTACAGGCACTATATGTGCAAATCGCAAAAT
5860137 TTCATCATGAGTTG-TGAA
1 TTCATCATGAGTTGATGAA
5860155 CTACCATATA
Statistics
Matches: 208, Mismatches: 21, Indels: 14
0.86 0.09 0.06
Matches are distributed among these distances:
107 3 0.01
108 98 0.47
109 19 0.09
110 88 0.42
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (108 bp):
TTCATCATGAGTTGATGAATAACCGTACAAGAACTATGTGCAAATCCACAGAATTCATCATGAGT
TGATGAATAACCGTACAGGCACTATATGTGCAAATCGCAAAAT
Found at i:5860092 original size:163 final size:163
Alignment explanation
Indices: 5859808--5860106 Score: 449
Period size: 163 Copynumber: 1.8 Consensus size: 163
5859798 AAATACACGA
* * *
5859808 AATTCATCATGAGTTGATGAAGAACCGTACAAGCACTATGTGTGCAAATCCACAGAATTCATCAT
1 AATTCATCATGAGTTGATGAAGAACCGTACAAGCACTATATGTGAAAATCCACAAAATTCATCAT
* *
5859873 GAGTTGATGAATAACCGTACATGCACTATTTGTGCAAATCCAAAGATTTCATCATGAGTTGATGA
66 GAGTTGATGAATAACCGTACATGCACTATGTGTACAAATCCAAAGATTTCATCATGAGTTGATGA
5859938 ATAACCACACAAGAACTATGTGCAAATCCACAG
131 ATAACCACACAAGAACTATGTGCAAATCCACAG
* * * ** *
5859971 AATTCATCATGAGTTGATGAATAACTGTACAGGCACTATATGTGAAAATCTGCAAAATTTATCAT
1 AATTCATCATGAGTTGATGAAGAACCGTACAAGCACTATATGTGAAAATCCACAAAATTCATCAT
**
5860036 GAGTTGATGAATAACCGTACA-GACACTATGTGTACAAATCCACCGAATTT-ATCATGAGTTGAT
66 GAGTTGATGAATAACCGTACATG-CACTATGTGTACAAATCCAAAG-ATTTCATCATGAGTTGAT
5860099 GAATAACC
129 GAATAACC
5860107 GTATAGGCAC
Statistics
Matches: 121, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
162 1 0.01
163 116 0.96
164 4 0.03
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.27
Consensus pattern (163 bp):
AATTCATCATGAGTTGATGAAGAACCGTACAAGCACTATATGTGAAAATCCACAAAATTCATCAT
GAGTTGATGAATAACCGTACATGCACTATGTGTACAAATCCAAAGATTTCATCATGAGTTGATGA
ATAACCACACAAGAACTATGTGCAAATCCACAG
Found at i:5860170 original size:163 final size:162
Alignment explanation
Indices: 5859803--5860171 Score: 433
Period size: 163 Copynumber: 2.3 Consensus size: 162
5859793 TGTGTAAATA
* * * * *
5859803 CACGAAATTCATCATGAGTTGATGAAGAACCGTACAAGCACTATGTGTGCAAATCCACAGAATTC
1 CACGAAATTCATCATGAGTTGATGAA-TACCGTACAGGCACTATATGTGAAAATCCACAAAATTC
* *
5859868 ATCATGAGTTGATGAATAACCGTACATGCACTATTTGTGCAAATCCAAAGATTTCATCATGAGTT
65 ATCATGAGTTGATGAATAACCGTACATGCACTATGTGTACAAATCCAAAGATTTCATCATGAGTT
*
5859933 GATGAATAACCACACAAGAACTATGTGCAAATC
130 GATGAATAACCACACAAGAACTATGTGCAAACC
* **
5859966 CAC-AGAATTCATCATGAGTTGATGAATAACTGTACAGGCACTATATGTGAAAATCTGCAAAATT
1 CACGA-AATTCATCATGAGTTGATGAAT-ACCGTACAGGCACTATATGTGAAAATCCACAAAATT
* **
5860030 TATCATGAGTTGATGAATAACCGTACA-GACACTATGTGTACAAATCCACCGAATTT-ATCATGA
64 CATCATGAGTTGATGAATAACCGTACATG-CACTATGTGTACAAATCCAAAG-ATTTCATCATGA
** * * * *
5860093 GTTGATGAATAACCGTATAGGCACGATGTGTGC-AACC
127 GTTGATGAATAACCACACAAGAAC--TATGTGCAAACC
* *
5860130 CACGAAATTCATCATGAGTTG-TGAACTACCATATAGGCACTA
1 CACGAAATTCATCATGAGTTGATGAA-TACCGTACAGGCACTA
5860172 CGTGTGCATC
Statistics
Matches: 175, Mismatches: 23, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
162 2 0.01
163 139 0.79
164 27 0.15
165 7 0.04
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (162 bp):
CACGAAATTCATCATGAGTTGATGAATACCGTACAGGCACTATATGTGAAAATCCACAAAATTCA
TCATGAGTTGATGAATAACCGTACATGCACTATGTGTACAAATCCAAAGATTTCATCATGAGTTG
ATGAATAACCACACAAGAACTATGTGCAAACC
Found at i:5866368 original size:148 final size:149
Alignment explanation
Indices: 5866095--5866380 Score: 364
Period size: 148 Copynumber: 1.9 Consensus size: 149
5866085 AAAACAACAC
* * * *
5866095 TGAGAGGAAGTCATTTACACCTATCTCGATGACATATTGTAAGCTTTTTTCAAAGATTGGTCAAA
1 TGAGAGGAAGTCATTTACACCTATCTCGATGACATATAGGAAGCTTCTTCCAAAGATTGGTCAAA
* ** * * *
5866160 GCACATGTGGTACCTCTAAAGTATGTGAACTAGCTCAAATTATCGTACCCAAAATGGTACAATCA
66 GCACATATGGTACCTCTAAAGTACATGAACGAGCTCAAATCATCGTACCCAAAATAGTACAATCA
5866225 GAATGAAACTTATTAGCAA
131 GAATGAAACTTATTAGCAA
5866244 TGAGAGGAAGTCATTTACACCTATCTCGATGACATATAGCGAA-C-TCTTCCAAAGATTGGTCAA
1 TGAGAGGAAGTCATTTACACCTATCTCGATGACATATAG-GAAGCTTCTTCCAAAGATTGGTCAA
* ** * **
5866307 AGCGCATATGGTACCT-TCAAAGTACATGAACCGA-CTTGAATCGTCGTACCTGAAATAGTACAA
65 AGCACATATGGTACCTCT-AAAGTACATGAA-CGAGCTCAAATCATCGTACCCAAAATAGTACAA
*
5866370 TGAGAATGAAA
128 TCAGAATGAAA
5866381 TTTACGAGCA
Statistics
Matches: 117, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
147 1 0.01
148 73 0.62
149 41 0.35
150 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (149 bp):
TGAGAGGAAGTCATTTACACCTATCTCGATGACATATAGGAAGCTTCTTCCAAAGATTGGTCAAA
GCACATATGGTACCTCTAAAGTACATGAACGAGCTCAAATCATCGTACCCAAAATAGTACAATCA
GAATGAAACTTATTAGCAA
Found at i:5871993 original size:12 final size:12
Alignment explanation
Indices: 5871976--5872000 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5871966 TATATCCGAT
5871976 AGTTCATGGGTC
1 AGTTCATGGGTC
5871988 AGTTCATGGGTC
1 AGTTCATGGGTC
5872000 A
1 A
5872001 ATCCATGCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (12 bp):
AGTTCATGGGTC
Found at i:5882426 original size:3 final size:3
Alignment explanation
Indices: 5882420--5882514 Score: 93
Period size: 3 Copynumber: 31.7 Consensus size: 3
5882410 TAAGAAGAAT
5882420 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* * * * * * * * *
5882468 CAA CAA CAA CAA CAA CAA CAA CAA CAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5882515 TACAAAAAAT
Statistics
Matches: 88, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
2 2 0.02
3 84 0.95
4 2 0.02
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.24
Consensus pattern (3 bp):
TAA
Found at i:5886541 original size:18 final size:18
Alignment explanation
Indices: 5886518--5886563 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
5886508 CGCCGTCCTA
5886518 GTCGTCA-TCGGCAGCCGC
1 GTCGTCACT-GGCAGCCGC
*
5886536 GTCGTCACTGGTAGCCGC
1 GTCGTCACTGGCAGCCGC
*
5886554 GTCATCACTG
1 GTCGTCACTG
5886564 TCTCATGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 24 0.96
19 1 0.04
ACGTcount: A:0.13, C:0.35, G:0.30, T:0.22
Consensus pattern (18 bp):
GTCGTCACTGGCAGCCGC
Found at i:5887687 original size:115 final size:115
Alignment explanation
Indices: 5887480--5887692 Score: 338
Period size: 115 Copynumber: 1.9 Consensus size: 115
5887470 AATATGCGAT
* * *
5887480 GAATCGAGTTAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTATCCCTCATCAGGTGAGTTA
1 GAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCATCAGATGAGTTA
* * *
5887545 TTCTCATTATGAACTCTCTAGTGGAAATGTTGATCCCTCATTCTGTGATG
66 TTCTCATTATGAACTCTCCACTAGAAATGTTGATCCCTCATTCTGTGATG
* *
5887595 GAATCGAGCTAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCCTCATC-GAATGAGTT
1 GAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCATCAG-ATGAGTT
5887659 ATTCTCATTATGAACTCTCCACTAGAAATGTTGA
65 ATTCTCATTATGAACTCTCCACTAGAAATGTTGA
5887693 GCCAAGGTTG
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
114 1 0.01
115 88 0.99
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (115 bp):
GAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCATCAGATGAGTTA
TTCTCATTATGAACTCTCCACTAGAAATGTTGATCCCTCATTCTGTGATG
Found at i:5887760 original size:91 final size:91
Alignment explanation
Indices: 5887600--5887859 Score: 421
Period size: 91 Copynumber: 2.9 Consensus size: 91
5887590 TGATGGAATC
* * * * *
5887600 GAGCTAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCCTCATCGAATGAGTTATTCTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTC
5887665 ATTATGAACTCTCCACTAGAAATGTT
66 ATTATGAACTCTCCACTAGAAATGTT
* *
5887691 GAGCCAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTTATTGGATGAGTTCTTCTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTC
*
5887756 ATTATGAACTCTCCACTGGAAATGTT
66 ATTATGAACTCTCCACTAGAAATGTT
* *
5887782 GATCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTGTCGGATGAGTTCTTCTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTC
*
5887847 ATTATGATCTCTC
66 ATTATGAACTCTC
5887860 TTCACTGGAA
Statistics
Matches: 156, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 156 1.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (91 bp):
GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTC
ATTATGAACTCTCCACTAGAAATGTT
Found at i:5887961 original size:20 final size:20
Alignment explanation
Indices: 5887938--5887998 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
5887928 TTGAACAAGC
5887938 TCTTCTCATTATGAACTTCT
1 TCTTCTCATTATGAACTTCT
* * *
5887958 TCTTCCTC-TTTTGGA-TGTGT
1 TCTT-CTCATTATGAACT-TCT
5887978 TCTTCTCATTATGAAC-TCT
1 TCTTCTCATTATGAACTTCT
5887997 TC
1 TC
5887999 GTTAGAAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 9
0.67 0.13 0.20
Matches are distributed among these distances:
19 8 0.26
20 20 0.65
21 3 0.10
ACGTcount: A:0.15, C:0.25, G:0.10, T:0.51
Consensus pattern (20 bp):
TCTTCTCATTATGAACTTCT
Found at i:5888602 original size:42 final size:42
Alignment explanation
Indices: 5888556--5888636 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
5888546 GGTCTTATGG
* *
5888556 ATGACCCGAAGGATTAAAACATCATGCTCGAAAGACTTATTA
1 ATGACCCAAAGGATTAAAACACCATGCTCGAAAGACTTATTA
* *
5888598 ATGACCCAAAGGATTTAAGCACCATGCTCGAAAGACTTA
1 ATGACCCAAAGGATTAAAACACCATGCTCGAAAGACTTA
5888637 CTGATGGCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (42 bp):
ATGACCCAAAGGATTAAAACACCATGCTCGAAAGACTTATTA
Found at i:5888652 original size:42 final size:42
Alignment explanation
Indices: 5888556--5888652 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
5888546 GGTCTTATGG
* *
5888556 ATGACCCGAAGGATTAAAACATCATGCTCGAAAGACTTATTA
1 ATGACCCGAAGGATTAAAACACCATGCTCGAAAGACTTACTA
* * * *
5888598 ATGACCCAAAGGATTTAAGCACCATGCTCGAAAGACTTACTG
1 ATGACCCGAAGGATTAAAACACCATGCTCGAAAGACTTACTA
* *
5888640 ATGGCTCGAAGGA
1 ATGACCCGAAGGA
5888653 CTTACTATTA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (42 bp):
ATGACCCGAAGGATTAAAACACCATGCTCGAAAGACTTACTA
Found at i:5889177 original size:41 final size:42
Alignment explanation
Indices: 5889120--5889206 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 42
5889110 GCCCGAAGGT
* * * *
5889120 CTTATGGATGACCCGAAGGACTT-ATCATCTTGCTCGAAAGA
1 CTTATAGATGACCCGAAAGACTTAAGCATCATGCTCGAAAGA
*
5889161 CTTATAGATGACCCGAAAGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGACCCGAAAGACTTAAGCATCATGCTCGAAAGA
5889203 CTTA
1 CTTA
5889207 CTGATGGACT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 20 0.50
42 20 0.50
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (42 bp):
CTTATAGATGACCCGAAAGACTTAAGCATCATGCTCGAAAGA
Found at i:5889222 original size:20 final size:20
Alignment explanation
Indices: 5889196--5889248 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
5889186 GCATCATGCT
5889196 CGAAAGACTTACTGATGGAC
1 CGAAAGACTTACTGATGGAC
*
5889216 TGAAAGACTTACTGATGGAC
1 CGAAAGACTTACTGATGGAC
*
5889236 CGAAGGACTTACT
1 CGAAAGACTTACT
5889249 CAACAAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (20 bp):
CGAAAGACTTACTGATGGAC
Found at i:5889379 original size:59 final size:58
Alignment explanation
Indices: 5889300--5889467 Score: 184
Period size: 58 Copynumber: 2.9 Consensus size: 58
5889290 TAATCAAGGT
* *
5889300 ACCCCTAAAAATTAGGCTTAGCTTCATTTTAAAAATT-ATTTTG-AGATAATCATCAAGAA
1 ACCCCTAAAAACTAGGCTTAGCTTC-TTTTAAAAATTCA--TTGAAAATAATCATCAAGAA
* *
5889359 ATCCCTAAAAACTAGGCTTAGCTTCTTTTAAAAATTCATTGAAAATCATCATCAAGAA
1 ACCCCTAAAAACTAGGCTTAGCTTCTTTTAAAAATTCATTGAAAATAATCATCAAGAA
* * * *
5889417 ACCCCTAAAAA-TCAGGTTTAGTTTC-TTTAAAATTTCTTTTGAAAAT-ATCAT
1 ACCCCTAAAAACT-AGGCTTAGCTTCTTTTAAAAATTC-ATTGAAAATAATCAT
5889468 GATGTTTGGG
Statistics
Matches: 96, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
57 19 0.20
58 53 0.55
59 24 0.25
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (58 bp):
ACCCCTAAAAACTAGGCTTAGCTTCTTTTAAAAATTCATTGAAAATAATCATCAAGAA
Found at i:5894607 original size:15 final size:16
Alignment explanation
Indices: 5894584--5894617 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5894574 AAACATAAAC
5894584 TCAAAAAAAGGCA-TG
1 TCAAAAAAAGGCATTG
*
5894599 TCAACAAAAGGCATTG
1 TCAAAAAAAGGCATTG
5894615 TCA
1 TCA
5894618 CGAAGGTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (16 bp):
TCAAAAAAAGGCATTG
Found at i:5900760 original size:13 final size:15
Alignment explanation
Indices: 5900739--5900774 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 15
5900729 CCAAATGCAA
5900739 AGATGCAAAAATG-G
1 AGATGCAAAAATGCG
5900753 AG-TGC-AAAATGCG
1 AGATGCAAAAATGCG
5900766 AGATGCAAA
1 AGATGCAAA
5900775 TGCAACAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 6 0.32
13 6 0.32
14 5 0.26
15 2 0.11
ACGTcount: A:0.47, C:0.11, G:0.28, T:0.14
Consensus pattern (15 bp):
AGATGCAAAAATGCG
Found at i:5900762 original size:28 final size:28
Alignment explanation
Indices: 5900704--5900774 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
5900694 TATATATACT
* * *
5900704 AATGCACAA-ATGCAAAAATGTAATTCCA
1 AATGCA-AAGATGCAAAAATGGAATGCAA
*
5900732 AATGCAAAGATGCAAAAATGGAGTGCAA
1 AATGCAAAGATGCAAAAATGGAATGCAA
*
5900760 AATGC-GAGATGCAAA
1 AATGCAAAGATGCAAA
5900775 TGCAACAAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 11 0.30
28 26 0.70
ACGTcount: A:0.49, C:0.14, G:0.20, T:0.17
Consensus pattern (28 bp):
AATGCAAAGATGCAAAAATGGAATGCAA
Found at i:5911525 original size:19 final size:19
Alignment explanation
Indices: 5911513--5911552 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
5911503 ATAAATAAAT
5911513 AAGAAA-AAAATAAAATAA
1 AAGAAATAAAATAAAATAA
5911531 AAGAAATAAAATAAACATAA
1 AAGAAATAAAATAAA-ATAA
5911551 AA
1 AA
5911553 TAAGGACCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.30
19 8 0.40
20 6 0.30
ACGTcount: A:0.80, C:0.03, G:0.05, T:0.12
Consensus pattern (19 bp):
AAGAAATAAAATAAAATAA
Found at i:5911529 original size:5 final size:5
Alignment explanation
Indices: 5911501--5911555 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
5911491 TTAAAACAAT
* *
5911501 AAAT- AAAT- AAATA AGAAAA AAATA AAATA AAA-G AAATA AAATA AACATA
1 AAATA AAATA AAATA A-AATA AAATA AAATA AAATA AAATA AAATA AA-ATA
5911550 AAATA A
1 AAATA A
5911556 GGACCTAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
4 11 0.26
5 23 0.53
6 9 0.21
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (5 bp):
AAATA
Found at i:5911537 original size:25 final size:24
Alignment explanation
Indices: 5911493--5911555 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
5911483 TTAAAAAATT
* *
5911493 AAAACAAT-AAAT-AAATAAATAA
1 AAAAAAATAAAATAAAAGAAATAA
5911515 GAAAAAAATAAAATAAAAGAAATAA
1 -AAAAAAATAAAATAAAAGAAATAA
*
5911540 AATAAACATAAAATAA
1 AA-AAAAATAAAATAA
5911556 GGACCTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.21
24 6 0.18
25 21 0.62
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (24 bp):
AAAAAAATAAAATAAAAGAAATAA
Found at i:5911539 original size:14 final size:13
Alignment explanation
Indices: 5911487--5911545 Score: 52
Period size: 14 Copynumber: 4.6 Consensus size: 13
5911477 TTATTTTTAA
*
5911487 AAAATTAAAACAAT
1 AAAA-TAAAAAAAT
*
5911501 -AAATAAATAAAT
1 AAAATAAAAAAAT
*
5911513 --AAGAAAAAAAT
1 AAAATAAAAAAAT
5911524 AAAATAAAAGAAAT
1 AAAATAAAA-AAAT
5911538 AAAATAAA
1 AAAATAAA
5911546 CATAAAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
11 9 0.24
12 7 0.19
13 9 0.24
14 12 0.32
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:5913410 original size:14 final size:16
Alignment explanation
Indices: 5913381--5913412 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
5913371 GATCCTTGAA
5913381 TTTTGTCATGTTAAAG
1 TTTTGTCATGTTAAAG
5913397 TTTT-TCAT-TTAAAG
1 TTTTGTCATGTTAAAG
5913411 TT
1 TT
5913413 GATGTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.25, C:0.06, G:0.12, T:0.56
Consensus pattern (16 bp):
TTTTGTCATGTTAAAG
Found at i:5939978 original size:23 final size:23
Alignment explanation
Indices: 5939942--5939986 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5939932 AATTAACGAA
* *
5939942 TTTATTTTTCTTTTATCTTTATC
1 TTTATTCTTATTTTATCTTTATC
*
5939965 TTTATTCTTATTTTATTTTTAT
1 TTTATTCTTATTTTATCTTTAT
5939987 TTTTTTATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTATTCTTATTTTATCTTTATC
Found at i:5939979 original size:17 final size:18
Alignment explanation
Indices: 5939954--5939987 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5939944 TATTTTTCTT
5939954 TTATCTTTATCTTTATTC
1 TTATCTTTATCTTTATTC
*
5939972 TTAT-TTTATTTTTATT
1 TTATCTTTATCTTTATT
5939988 TTTTTATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATCTTTATCTTTATTC
Found at i:5951549 original size:22 final size:22
Alignment explanation
Indices: 5951498--5951601 Score: 111
Period size: 22 Copynumber: 4.7 Consensus size: 22
5951488 TACTCCCATC
* * * *
5951498 AGTGCTAAGGCACTTTAGTATT
1 AGTGCAAATGCACTTTAATACT
* **
5951520 AGTACAAATGCACTTCCATA-T
1 AGTGCAAATGCACTTTAATACT
5951541 CAGTGCAAATGCACTTTAATACT
1 -AGTGCAAATGCACTTTAATACT
*
5951564 AGTGCCAATGCACTTTAATACT
1 AGTGCAAATGCACTTTAATACT
*
5951586 AGTGCCAATGCACTTT
1 AGTGCAAATGCACTTT
5951602 CGTTAGTAGT
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
21 1 0.01
22 68 0.97
23 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (22 bp):
AGTGCAAATGCACTTTAATACT
Found at i:5955397 original size:3 final size:3
Alignment explanation
Indices: 5955389--5955447 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
5955379 TTTTCGTCCC
5955389 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5955437 ATT ATT ATT AT
1 ATT ATT ATT AT
5955448 AAACACATTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5957921 original size:2 final size:2
Alignment explanation
Indices: 5957910--5957956 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
5957900 TAAAGGAGAT
5957910 TA TA -A 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
5957951 TA TA TA
1 TA TA TA
5957957 ATAAAGTTGA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5962779 original size:134 final size:135
Alignment explanation
Indices: 5962495--5963128 Score: 714
Period size: 134 Copynumber: 4.7 Consensus size: 135
5962485 TAATTTGCAT
* * * * *
5962495 ATTTGATATTCCATGAGTGACAGTGGAACAAGTCTGCCTCAATTCAATCTTTCCTGAGTGATA-A
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCC-CGATTCAATCTTCCCTGAGTGACAGA
* * * * *
5962559 CGGAATGGAT-AACAT-CCTCAGATCTGATATTCCC-TCCAGAAGAAGCGTAACATATCCCTCTC
65 -GGAATGGATCAACATCCCTCAGATCTGATATTCCCTTCTAGAAAAAGCGGAACAGATCACTCTC
5962621 TTCCAAG
129 TTCCAAG
* * * *
5962628 ATTTGATATACCATGAGTGACAGTGGAACAAGTCTGCACCGATTCAATATTCCCTGAGTGACAGA
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGC-CCGATTCAATCTTCCCTGAGTGACAGA
* * * * *
5962693 GGAATAGATCAAC-TCCCTCATATCTGATATTCCCTTC-AGAAAAAGCGGAATAGATCATTTTCT
65 GGAATGGATCAACATCCCTCAGATCTGATATTCCCTTCTAGAAAAAGCGGAACAGATCACTCTCT
5962756 TCCAAG
130 TCCAAG
* * ** * * *
5962762 ATTTGATATTCCCTGAGTGACAGCAGAATAAGTCTGTCTGGATTCAATCATCCTTGAGTGACAGT
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTG-CCCGATTCAATCTTCCCTGAGTGACAGA
* * * *
5962827 GGAATGGCTCAACATCCC-CAGATCTGATATTTCC-TCTAGAAAAAGCAGAACAGATCCCTCTCT
65 GGAATGGATCAACATCCCTCAGATCTGATATTCCCTTCTAGAAAAAGCGGAACAGATCACTCTCT
5962890 TCCAAG
130 TCCAAG
** * * * * **
5962896 ATTTTTTATTCCCTGAGTAACAGCGGAACAAGACTGCCCAATTCAATCTTCCCTAAGTGACAGCT
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCGATTCAATCTTCCCTGAGTGACAGAG
* * * *
5962961 GAATGGATCAACATCCCT-AGATCTGATATTCCC-TCTAGAAGAAGTGTAACATATCACTCTCTT
66 GAATGGATCAACATCCCTCAGATCTGATATTCCCTTCTAGAAAAAGCGGAACAGATCACTCTCTT
*
5963024 TCAAG
131 CCAAG
* * * *
5963029 ATTTGATATTCCCTGAGTGATAGCGGAACAAGTCTACCCTGATTCAATCTTCTCTGAGTGACAGC
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCC-GATTCAATCTTCCCTGAGTGACAGA
*
5963094 GGAATGGATCAACATCCC-CAGATCTAATATTCCCT
65 GGAATGGATCAACATCCCTCAGATCTGATATTCCCT
5963129 GAGTGACAGC
Statistics
Matches: 421, Mismatches: 68, Indels: 22
0.82 0.13 0.04
Matches are distributed among these distances:
133 179 0.43
134 235 0.56
135 7 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (135 bp):
ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCGATTCAATCTTCCCTGAGTGACAGAG
GAATGGATCAACATCCCTCAGATCTGATATTCCCTTCTAGAAAAAGCGGAACAGATCACTCTCTT
CCAAG
Found at i:5962972 original size:267 final size:266
Alignment explanation
Indices: 5962495--5963128 Score: 767
Period size: 267 Copynumber: 2.4 Consensus size: 266
5962485 TAATTTGCAT
* * * * *
5962495 ATTTGATATTCCATGAGTGACAGTGGAACAAGTCTGCCTCAATTCAATCTTTCC-TGAGTGATAA
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCT-GATTCAATC--TCCTTGAGTGACAG
* * *
5962559 CGGAATGGAT-AACATCCTCAGATCTGATATTCCCTCCAGAAGAAGCGTAACATATCCCTCTCTT
63 CGGAATGGATCAACATCCCCAGATCTGATATTCCCTCCAGAAAAAGCGTAACAGATCCCTCTCTT
* * * * *
5962623 CCAAGATTTGATATACCATGAGTGACAGTGGAACAAGTCTGCACCGATTCAATATTCCCTGAGTG
128 CCAAGATTTGATATACCATGAGTAACAGCGGAACAAGACTGCACCAATTCAATATTCCCTAAGTG
* * *
5962688 ACAGAGGAATAGATCAAC-TCCCTCATATCTGATATTCCCT-TCAGAAAAAGCGGAATAGATCAT
193 ACAGAGGAATAGATCAACATCCCT-AGATCTGATATTCCCTCT-AGAAAAAGCGGAACAGATCAC
*
5962751 TTTCTTCCAAG
256 TCTCTTCCAAG
* * * *
5962762 ATTTGATATTCCCTGAGTGACAGCAGAATAAGTCTGTCTGGATTCAATCATCCTTGAGTGACAGT
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCT-GATTCAATC-TCCTTGAGTGACAGC
* * *
5962827 GGAATGGCTCAACATCCCCAGATCTGATATTTCCTCTAGAAAAAGCAG-AACAGATCCCTCTCTT
64 GGAATGGATCAACATCCCCAGATCTGATATTCCCTCCAGAAAAAGC-GTAACAGATCCCTCTCTT
** * * *
5962891 CCAAGATTTTTTATTCCCTGAGTAACAGCGGAACAAGACTGC-CCAATTCAATCTTCCCTAAGTG
128 CCAAGATTTGATATACCATGAGTAACAGCGGAACAAGACTGCACCAATTCAATATTCCCTAAGTG
** * * * * *
5962955 ACAGCTGAATGGATCAACATCCCTAGATCTGATATTCCCTCTAGAAGAAGTGTAACATATCACTC
193 ACAGAGGAATAGATCAACATCCCTAGATCTGATATTCCCTCTAGAAAAAGCGGAACAGATCACTC
*
5963020 TCTTTCAAG
258 TCTTCCAAG
* * *
5963029 ATTTGATATTCCCTGAGTGATAGCGGAACAAGTCTACCCTGATTCAATCTTCTCTGAGTGACAGC
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCT-GCCTGATTCAATCTCCT-TGAGTGACAGC
*
5963094 GGAATGGATCAACATCCCCAGATCTAATATTCCCT
64 GGAATGGATCAACATCCCCAGATCTGATATTCCCT
5963129 GAGTGACAGC
Statistics
Matches: 311, Mismatches: 49, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
266 6 0.02
267 214 0.69
268 90 0.29
269 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (266 bp):
ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCTGATTCAATCTCCTTGAGTGACAGCGG
AATGGATCAACATCCCCAGATCTGATATTCCCTCCAGAAAAAGCGTAACAGATCCCTCTCTTCCA
AGATTTGATATACCATGAGTAACAGCGGAACAAGACTGCACCAATTCAATATTCCCTAAGTGACA
GAGGAATAGATCAACATCCCTAGATCTGATATTCCCTCTAGAAAAAGCGGAACAGATCACTCTCT
TCCAAG
Found at i:5963284 original size:3 final size:3
Alignment explanation
Indices: 5963276--5963321 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
5963266 TTTACGTACA
5963276 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5963322 CATTTTTCTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5977037 original size:12 final size:12
Alignment explanation
Indices: 5977020--5977061 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
5977010 TGTAGTGGTC
5977020 ATTAAAAAATAA
1 ATTAAAAAATAA
*
5977032 ATTAAAAGAAAAA
1 ATTAAAA-AATAA
*
5977045 ATTAAAAAATAT
1 ATTAAAAAATAA
5977057 ATTAA
1 ATTAA
5977062 TATTAGGGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (12 bp):
ATTAAAAAATAA
Found at i:5977048 original size:13 final size:12
Alignment explanation
Indices: 5977020--5977053 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
5977010 TGTAGTGGTC
*
5977020 ATTAAAAAATAA
1 ATTAAAAAAAAA
5977032 ATTAAAAGAAAAA
1 ATTAAAA-AAAAA
5977045 ATTAAAAAA
1 ATTAAAAAA
5977054 TATATTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (12 bp):
ATTAAAAAAAAA
Found at i:5985256 original size:15 final size:15
Alignment explanation
Indices: 5985238--5985267 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5985228 CCACGGTGCT
5985238 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
5985253 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
5985268 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:5995436 original size:49 final size:49
Alignment explanation
Indices: 5995342--5995436 Score: 122
Period size: 49 Copynumber: 1.9 Consensus size: 49
5995332 AAGTCCAACA
* * * *
5995342 AATTTAACAAAATAAAGTAAGTATTAAATGATAAATAATAAAAAATTAC
1 AATTTAACAAAATAAAGTAAATATCAAATGATAAAAAAAAAAAAATTAC
5995391 AATTTAACAAAATAAAGTAAATA-CAAAT-ATAATAAAAAAACAAAAT
1 AATTTAACAAAATAAAGTAAATATCAAATGATAA-AAAAAAA-AAAAT
5995437 CTATCGATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 4 0.10
48 9 0.22
49 27 0.68
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.25
Consensus pattern (49 bp):
AATTTAACAAAATAAAGTAAATATCAAATGATAAAAAAAAAAAAATTAC
Found at i:5997659 original size:17 final size:18
Alignment explanation
Indices: 5997616--5997656 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
5997606 AATTTATATT
5997616 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
5997633 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
5997651 ATTAAA
1 AGTAAA
5997657 TACAGAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:5997905 original size:50 final size:50
Alignment explanation
Indices: 5997826--5997976 Score: 125
Period size: 50 Copynumber: 3.0 Consensus size: 50
5997816 TGCACCGTGT
* **
5997826 TATACCCCACGTGTCAGATAAAT-AG-GTATAGCGCGGAGCAGGGGGCGCGC
1 TATACCCCACGTGAC-GCCAAATCAGCGTATAGCGCGG-GCAGGGGGCGCGC
* * *
5997876 TATA-GCCACGTGTAAC-CC-AATCAGCGTATAGCACGGTGCA-GGGGCGTGC
1 TATACCCCACGTG--ACGCCAAATCAGCGTATAGCGCGG-GCAGGGGGCGCGC
* * *
5997925 TATACCCCACGTGACGCCAAATCAGCATATAACGCGGGTTAGGGGGCGCGC
1 TATACCCCACGTGACGCCAAATCAGCGTATAGCGCGGG-CAGGGGGCGCGC
5997976 T
1 T
5997977 TTATTGCTAC
Statistics
Matches: 79, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
48 5 0.06
49 24 0.30
50 40 0.51
51 10 0.13
ACGTcount: A:0.25, C:0.26, G:0.31, T:0.17
Consensus pattern (50 bp):
TATACCCCACGTGACGCCAAATCAGCGTATAGCGCGGGCAGGGGGCGCGC
Found at i:5998588 original size:20 final size:20
Alignment explanation
Indices: 5998563--5998609 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5998553 AGCTTTTAAT
*
5998563 ATTTTATAAGTTTTAACA-AA
1 ATTTTATAA-TGTTAACATAA
*
5998583 ATTTTATAATGTTAATATAA
1 ATTTTATAATGTTAACATAA
5998603 ATTTTAT
1 ATTTTAT
5998610 TATTTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (20 bp):
ATTTTATAATGTTAACATAA
Found at i:5998620 original size:21 final size:20
Alignment explanation
Indices: 5998563--5998620 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
5998553 AGCTTTTAAT
*
5998563 ATTTTA-TAAGTTTTAACAAA
1 ATTTTATTAA-TTTTAATAAA
*
5998583 ATTTTA-TAATGTTAATATAA
1 ATTTTATTAATTTTAATA-AA
*
5998603 ATTTTATTATTTTTAATA
1 ATTTTATTAATTTTAATA
5998621 GAAGTAGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 6 0.19
20 17 0.53
21 9 0.28
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (20 bp):
ATTTTATTAATTTTAATAAA
Found at i:5999129 original size:22 final size:22
Alignment explanation
Indices: 5999077--5999135 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
5999067 TAAACGACTA
*
5999077 AAAACGTGCCAAAAGACAAAAG
1 AAAACGTGTCAAAAGACAAAAG
* * *
5999099 AAAATGTGTCATAAAGAC-ATAT
1 AAAACGTGTCA-AAAGACAAAAG
5999121 AAAACGTGTCAAAAG
1 AAAACGTGTCAAAAG
5999136 GCAGAACGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 4 0.13
22 21 0.68
23 6 0.19
ACGTcount: A:0.54, C:0.14, G:0.17, T:0.15
Consensus pattern (22 bp):
AAAACGTGTCAAAAGACAAAAG
Found at i:6000105 original size:24 final size:23
Alignment explanation
Indices: 6000077--6000142 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
6000067 TCATGTAATG
*
6000077 TTTTTTTTACATTATATGCATTT
1 TTTTTTTTACATTATATACATTT
* * *
6000100 TCTTTTTTACTTTAGTATATATTT
1 TTTTTTTTACATTA-TATACATTT
*
6000124 TTATTTTTTAGATTATATA
1 TT-TTTTTTACATTATATA
6000143 TATATATATA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
23 12 0.35
24 12 0.35
25 10 0.29
ACGTcount: A:0.24, C:0.06, G:0.05, T:0.65
Consensus pattern (23 bp):
TTTTTTTTACATTATATACATTT
Found at i:6000143 original size:24 final size:24
Alignment explanation
Indices: 6000079--6000145 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 24
6000069 ATGTAATGTT
** *
6000079 TTTTTTACATTATATGCA-TTTTC
1 TTTTTTACATTATATATATTTTTA
*
6000102 TTTTTTACTTTAGTATATATTTTTA
1 TTTTTTACATTA-TATATATTTTTA
*
6000127 TTTTTTAGATTATATATAT
1 TTTTTTACATTATATATAT
6000146 ATATATATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
23 11 0.31
24 11 0.31
25 14 0.39
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.64
Consensus pattern (24 bp):
TTTTTTACATTATATATATTTTTA
Found at i:6000193 original size:2 final size:2
Alignment explanation
Indices: 6000186--6000234 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
6000176 TATTAATTTT
* * *
6000186 TA TA TA TA TA TA TA TT TA CTA TT TT TA T- 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
6000228 TA TA TA T
1 TA TA TA T
6000235 TATTTTTACT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:6000241 original size:30 final size:30
Alignment explanation
Indices: 6000186--6000242 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
6000176 TATTAATTTT
*
6000186 TATATATATATATATTTACTATTTTTATTA
1 TATATATATATATATATACTATTTTTATTA
*
6000216 TATATATATATATATATATTATTTTTA
1 TATATATATATATATATACTATTTTTA
6000243 CTTTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (30 bp):
TATATATATATATATATACTATTTTTATTA
Found at i:6000251 original size:14 final size:14
Alignment explanation
Indices: 6000234--6000282 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
6000224 TATATATATA
*
6000234 TTATTTTTACTTTT
1 TTATTATTACTTTT
*
6000248 TTATTATTATTTTT
1 TTATTATTACTTTT
6000262 TTATTATT--TTTT
1 TTATTATTACTTTT
6000274 TTATATATT
1 TTAT-TATT
6000283 TTTTCTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
12 8 0.25
13 4 0.12
14 20 0.62
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (14 bp):
TTATTATTACTTTT
Found at i:6000263 original size:23 final size:23
Alignment explanation
Indices: 6000232--6000354 Score: 73
Period size: 21 Copynumber: 5.5 Consensus size: 23
6000222 TATATATATA
*
6000232 TATTATTTTTACTTTTTTATTAT
1 TATTTTTTTTACTTTTTTATTAT
6000255 TATTTTTTTATTA-TTTTTT-TTA-
1 TA-TTTTTT-TTACTTTTTTATTAT
* * *
6000277 TATATTTTTT-CTTCTTT-TTCT
1 TATTTTTTTTACTTTTTTATTAT
*
6000298 TCTTTTTTTTA-TTTTTTA-TATT
1 TATTTTTTTTACTTTTTTATTA-T
** *
6000320 TATTTTACTTACTATTTTATCT-T
1 TATTTTTTTTACTTTTTTAT-TAT
6000343 TACTTTTTTTTA
1 TA-TTTTTTTTA
6000355 TCTTATCTTT
Statistics
Matches: 75, Mismatches: 14, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
20 9 0.12
21 19 0.25
22 11 0.15
23 14 0.19
24 18 0.24
25 4 0.05
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (23 bp):
TATTTTTTTTACTTTTTTATTAT
Found at i:6000265 original size:11 final size:11
Alignment explanation
Indices: 6000232--6000286 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 11
6000222 TATATATATA
6000232 TATTATTTTTACT
1 TATT-TTTTTA-T
*
6000245 T-TTTTATTAT
1 TATTTTTTTAT
6000255 TATTTTTTTAT
1 TATTTTTTTAT
6000266 TATTTTTTTTAT
1 TA-TTTTTTTAT
6000278 ATATTTTTT
1 -TATTTTTT
6000287 CTTCTTTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
10 2 0.05
11 15 0.41
12 17 0.46
13 3 0.08
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (11 bp):
TATTTTTTTAT
Found at i:6000277 original size:9 final size:9
Alignment explanation
Indices: 6000244--6000326 Score: 51
Period size: 9 Copynumber: 8.8 Consensus size: 9
6000234 TTATTTTTAC
6000244 TTTTTTATT
1 TTTTTTATT
* *
6000253 ATTATT-TT
1 TTTTTTATT
*
6000261 TTTATTATT
1 TTTTTTATT
6000270 TTTTTTATAT
1 TTTTTTAT-T
*
6000280 ATTTTTTCTTCT
1 -TTTTTT-AT-T
*
6000292 TTTTCTTCTT
1 TTTT-TTATT
6000302 TTTTTTATT
1 TTTTTTATT
*
6000311 TTTTATATT
1 TTTTTTATT
*
6000320 TATTTTA
1 TTTTTTA
6000327 CTTACTATTT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
8 7 0.12
9 30 0.52
10 6 0.10
11 11 0.19
12 4 0.07
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTATT
Found at i:6000285 original size:14 final size:13
Alignment explanation
Indices: 6000244--6000314 Score: 63
Period size: 14 Copynumber: 5.2 Consensus size: 13
6000234 TTATTTTTAC
6000244 TTTTTTATTATTAT
1 TTTTTTATTATT-T
6000258 TTTTTTATTA-TT
1 TTTTTTATTATTT
6000270 TTTTTTATATATTT
1 TTTTTTAT-TATTT
* * *
6000284 TTTCTTCTTTTTCT
1 TTTTTTATTATT-T
*
6000298 TCTTTTTTTTATTT
1 T-TTTTTATTATTT
6000312 TTT
1 TTT
6000315 ATATTTATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
12 9 0.19
13 8 0.17
14 22 0.47
15 8 0.17
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTATTATTT
Found at i:6000314 original size:11 final size:11
Alignment explanation
Indices: 6000237--6000325 Score: 63
Period size: 11 Copynumber: 7.9 Consensus size: 11
6000227 ATATATATTA
*
6000237 TTTTTACTTTT
1 TTTTTATTTTT
* *
6000248 TTATTATTATT
1 TTTTTATTTTT
6000259 TTTTTATTATTT
1 TTTTTATT-TTT
* *
6000271 TTTTTATATAT
1 TTTTTATTTTT
* *
6000282 TTTTTCTTCTT
1 TTTTTATTTTT
* *
6000293 TTTCT-TCTTT
1 TTTTTATTTTT
6000303 TTTTTATTTTT
1 TTTTTATTTTT
6000314 TATATTTATTTT
1 T-T-TTTATTTT
6000326 ACTTACTATT
Statistics
Matches: 58, Mismatches: 16, Indels: 6
0.73 0.20 0.08
Matches are distributed among these distances:
10 7 0.12
11 33 0.57
12 10 0.17
13 8 0.14
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTATTTTT
Found at i:6000370 original size:16 final size:16
Alignment explanation
Indices: 6000316--6000370 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
6000306 TTATTTTTTA
*
6000316 TATTTAT-TTTACTTAC
1 TATTTATCTTTACTT-T
6000332 TATTTTATCTTTACTTT
1 TA-TTTATCTTTACTTT
*
6000349 TTTTTATC-TTATCTTT
1 TATTTATCTTTA-CTTT
6000365 TATTTA
1 TATTTA
6000371 ATTTGTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.09
16 17 0.52
17 6 0.18
18 7 0.21
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTATCTTTACTTT
Found at i:6003498 original size:16 final size:14
Alignment explanation
Indices: 6003470--6003518 Score: 75
Period size: 13 Copynumber: 3.6 Consensus size: 14
6003460 AAAAAGAGAA
6003470 AAAGAGAAAAAAAC
1 AAAGAGAAAAAAAC
*
6003484 AAAGAGAAAATAA-
1 AAAGAGAAAAAAAC
6003497 AAAGAGAAAAAAAC
1 AAAGAGAAAAAAAC
6003511 AAAG-GAAA
1 AAAGAGAAA
6003519 TTGAAGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
13 16 0.50
14 16 0.50
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.02
Consensus pattern (14 bp):
AAAGAGAAAAAAAC
Found at i:6003498 original size:27 final size:26
Alignment explanation
Indices: 6003468--6003518 Score: 93
Period size: 27 Copynumber: 1.9 Consensus size: 26
6003458 GCAAAAAGAG
6003468 AAAAAGAGAAAAAAACAAAGAGAAAAT
1 AAAAAGAGAAAAAAACAAAG-GAAAAT
6003495 AAAAAGAGAAAAAAACAAAGGAAA
1 AAAAAGAGAAAAAAACAAAGGAAA
6003519 TTGAAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.02
Consensus pattern (26 bp):
AAAAAGAGAAAAAAACAAAGGAAAAT
Found at i:6003706 original size:69 final size:69
Alignment explanation
Indices: 6003595--6003728 Score: 241
Period size: 69 Copynumber: 1.9 Consensus size: 69
6003585 CAAACTATGA
*
6003595 GATTGATCAAGCAAAATCATTTCTGAATCACTGAACCACTTCACTCGAAGATCATAGAGCATCAA
1 GATTGATCAAGCAAAATCATTTCTGAATCACTAAACCACTTCACTCGAAGATCATAGAGCATCAA
6003660 ATGG
66 ATGG
* *
6003664 GATTGATCAAGCACAATCATTTCTGAATCACTAAATCACTTCACTCGAAGATCATAGAGCATCAA
1 GATTGATCAAGCAAAATCATTTCTGAATCACTAAACCACTTCACTCGAAGATCATAGAGCATCAA
6003729 GAGAGAGACA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (69 bp):
GATTGATCAAGCAAAATCATTTCTGAATCACTAAACCACTTCACTCGAAGATCATAGAGCATCAA
ATGG
Found at i:6004701 original size:32 final size:32
Alignment explanation
Indices: 6004660--6004754 Score: 136
Period size: 32 Copynumber: 2.9 Consensus size: 32
6004650 TTAGGGCATC
6004660 TTTGAAGATTCAACATCAAATGTTGGGGCATTT
1 TTTG-AGATTCAACATCAAATGTTGGGGCATTT
* * *
6004693 TTTTAGATTTAACACCAAATGTTGGGGCATTT
1 TTTGAGATTCAACATCAAATGTTGGGGCATTT
* *
6004725 TTTGAGATTCAACATCGAATATTGGGGCAT
1 TTTGAGATTCAACATCAAATGTTGGGGCAT
6004755 CTTTGGGAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
32 51 0.94
33 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATGTTGGGGCATTT
Found at i:6005665 original size:106 final size:105
Alignment explanation
Indices: 6005318--6005671 Score: 413
Period size: 106 Copynumber: 3.3 Consensus size: 105
6005308 GCCACCTGCG
* * * *
6005318 ATTTCAACTCCACGACGGAGGATATTGTGCCACTCGAAACAACATAAGTTCAACTCCACAATGAA
1 ATTTCAACTTCACGAC-GAGGATATTG-G--ACTCGAGACAACAAAAGTTCAACTTCACAATGAA
* *
6005383 GGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCA
62 GGGACGGCTGGTTGTCAACAAACAATTTCCTAATTTCAGAGCCA
* * *
6005427 AATTCAACTTCACAACGAAGGATATTAGACTCGAGACAACAAAAGTTCAACTTCACAATGAAGGG
1 ATTTCAACTTCACGACG-AGGATATTGGACTCGAGACAACAAAAGTTCAACTTCACAATGAAGGG
*
6005492 ACGGCTGGTTGTCAACAAACAATTTCCTAATTTCGGAGCCA
65 ACGGCTGGTTGTCAACAAACAATTTCCTAATTTCAGAGCCA
* * * * * *
6005533 ATTTCAACTTCAC-AGCAAAGGATATTGGACTCGAGACAGCACAAGCTCAACTTCACAGTAAAGG
1 ATTTCAACTTCACGA-C-GAGGATATTGGACTCGAGACAACAAAAGTTCAACTTCACAATGAAGG
* * * * * *
6005597 GGCGACTGGCTGTCAACAAACAATTTCTTAGTTCCAGAGCCA
64 GACGGCTGGTTGTCAACAAACAATTTCCTAATTTCAGAGCCA
* *
6005639 ATTTTAACTTCACGACTGAGGATATTGAACTCG
1 ATTTCAACTTCACGAC-GAGGATATTGGACTCG
6005672 GAACAATACA
Statistics
Matches: 212, Mismatches: 29, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
105 1 0.00
106 187 0.88
107 1 0.00
108 2 0.01
109 21 0.10
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (105 bp):
ATTTCAACTTCACGACGAGGATATTGGACTCGAGACAACAAAAGTTCAACTTCACAATGAAGGGA
CGGCTGGTTGTCAACAAACAATTTCCTAATTTCAGAGCCA
Found at i:6006012 original size:65 final size:65
Alignment explanation
Indices: 6005900--6006057 Score: 194
Period size: 65 Copynumber: 2.4 Consensus size: 65
6005890 TTTTGGAACT
6005900 AAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAAC-ATTTCCCTTGAAA
1 AAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTG-AAACTATTTCCCTTGAAA
*
6005964 T
65 C
* * * * * * * *
6005965 GAATTTTGTATCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTGAATCTGTTTCCCTTGAAA
1 AAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAA-CATTGAAACTATTTCCCTTGAAA
6006029 C
65 C
*
6006030 AAATTTTGTCTCCCTTGAGACATTTTCT
1 AAATTTTGTCTCCCTTGAGACAATTTCT
6006058 TTTGGAACTA
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
64 6 0.08
65 71 0.92
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (65 bp):
AAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAACTATTTCCCTTGAAAC
Found at i:6006085 original size:102 final size:102
Alignment explanation
Indices: 6005968--6006151 Score: 271
Period size: 102 Copynumber: 1.8 Consensus size: 102
6005958 TTGAAATGAA
* * ** *
6005968 TTTTGTATCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTGAATCTGTTTCCCTTGAAACAA
1 TTTTGTATCTCTTGAGATAGTTTCTATTGAAACATAAA-CATTGAAAATATTTCCCTTGAAACAA
6006032 ATTTTGTCTCCCTTGAGACATTTTCTTTTGGAACTAAG
65 ATTTTGTCTCCCTTGAGACATTTTCTTTTGGAACTAAG
* **
6006070 TTTTGTCTCTCTTGAGATAGTTTCTATTGAAACATAAACATTGAAAATATTTCCCTTGAAATGAA
1 TTTTGTATCTCTTGAGATAGTTTCTATTGAAACATAAACATTGAAAATATTTCCCTTGAAACAAA
*
6006135 TTTTGTCTCTCTTGAGA
66 TTTTGTCTCCCTTGAGA
6006152 TAGTTTCTCT
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
102 69 0.96
103 3 0.04
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (102 bp):
TTTTGTATCTCTTGAGATAGTTTCTATTGAAACATAAACATTGAAAATATTTCCCTTGAAACAAA
TTTTGTCTCCCTTGAGACATTTTCTTTTGGAACTAAG
Found at i:6006102 original size:167 final size:167
Alignment explanation
Indices: 6005826--6006337 Score: 853
Period size: 167 Copynumber: 3.1 Consensus size: 167
6005816 CCAAGACTCC
* * * * * *
6005826 CTTGAAACAAAATATTTAAATCTGTTTTCATTGAAACTAATTTCGTCTCCCTTGAGACATTTTCT
1 CTTGAAACAAAATCTTTGAATCTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACATTTTCT
* * * *
6005891 TTTGGAACTAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACATTTC
66 TTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTC
*
6005956 CCTTGAAATGAATTTTGTATCTCTTGAGATAGTTTCT
131 CCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCT
6005993 CTTGAAACAAAATCTTTGAATCTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACATTTTCT
1 CTTGAAACAAAATCTTTGAATCTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACATTTTCT
* *
6006058 TTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTATTGAAACATAAACATTGAAAATATTTC
66 TTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTC
6006123 CCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCT
131 CCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCT
* *
6006160 CTTGAAATAAAATCTTTGAATTTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACATTTTCT
1 CTTGAAACAAAATCTTTGAATCTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACATTTTCT
*
6006225 TTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACAGTTC
66 TTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTC
* * *
6006290 CCTTGAGATGAATTTTGTCTCTCTTGAGATAGGTTCC
131 CCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCT
6006327 CTTGAAACAAA
1 CTTGAAACAAA
6006338 TTTTTGTCTC
Statistics
Matches: 323, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
167 323 1.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (167 bp):
CTTGAAACAAAATCTTTGAATCTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACATTTTCT
TTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTC
CCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCT
Found at i:6006224 original size:65 final size:65
Alignment explanation
Indices: 6006070--6006216 Score: 197
Period size: 65 Copynumber: 2.3 Consensus size: 65
6006060 TGGAACTAAG
**
6006070 TTTTGTCTCTCTTGAGATAGTTTCTATTGAAACATAAACATTGAAAATATTTCCCTTGAAATGAA
1 TTTTGTCTCTCTTGAGATAGTTTCTATTGAAACATAAACATTGAAAATATTTCCCTTGAAACAAA
* * * ** *
6006135 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAATA-AAATCTTTGAATTTGTTTCCCTTGAAACAA
1 TTTTGTCTCTCTTGAGATAGTTTCTATTGAAACATAAA-CATTGAAAATATTTCCCTTGAAACAA
6006199 A
65 A
*
6006200 TTTTGTCTCCCTTGAGA
1 TTTTGTCTCTCTTGAGA
6006217 CATTTTCTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
64 3 0.04
65 69 0.96
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (65 bp):
TTTTGTCTCTCTTGAGATAGTTTCTATTGAAACATAAACATTGAAAATATTTCCCTTGAAACAAA
Found at i:6006281 original size:102 final size:102
Alignment explanation
Indices: 6006119--6006505 Score: 406
Period size: 102 Copynumber: 3.8 Consensus size: 102
6006109 ATTGAAAATA
** * * * *
6006119 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAATA-AAATCTTTG-AATT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAA-CATTGAAAAT
* * *
6006182 TGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAT
65 AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAG
** * * * *
6006220 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAT
* ** *
6006285 AG-TTCCCTTGAGATGAATTTTGTCTCTCTTGAGATAG
65 AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAG
* * * *
6006322 GTTCCCTTGAAACAAATTTTTGTCTCCCTTGAGAGATTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAA-TTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAT
* ** * *
6006387 A-TTTCCCTTAAAATGAATTTTGTC-ACTTATGAGATAG
65 AGTTTCCCTTGAAACAAATTTTGTCTCCCT-TGAGATAG
* ** *
6006424 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGACGCATAAACTTTGAAAATA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAATA
*
6006489 GTTTCCTTTGAAACAAA
66 GTTTCCCTTGAAACAAA
6006506 ATCTTTGAAT
Statistics
Matches: 238, Mismatches: 41, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
101 55 0.23
102 177 0.74
103 6 0.03
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (102 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAATA
GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAG
Found at i:6006368 original size:37 final size:37
Alignment explanation
Indices: 6006302--6006372 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
6006292 TTGAGATGAA
* *
6006302 TTTTGTCTCTCTTGAGATAGGTTCCCTTGAAACAAAT
1 TTTTGTCTCCCTTGAGAGAGGTTCCCTTGAAACAAAT
** *
6006339 TTTTGTCTCCCTTGAGAGATTTTCTCTTGAAACA
1 TTTTGTCTCCCTTGAGAGAGGTTCCCTTGAAACA
6006373 TAAACATTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGAGAGGTTCCCTTGAAACAAAT
Found at i:6006611 original size:36 final size:36
Alignment explanation
Indices: 6006569--6006637 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
6006559 TTTTGGAAGT
*
6006569 TTTTGTCTCTCTTAAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTAAGACAGTTTCCCTTGAAACAAA
*
6006605 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 TTTTGTCTCTCTTAAGACAGTTTCCCTTGAAAC
6006638 TTCAATCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (36 bp):
TTTTGTCTCTCTTAAGACAGTTTCCCTTGAAACAAA
Found at i:6006694 original size:33 final size:32
Alignment explanation
Indices: 6006644--6006736 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 32
6006634 AAACTTCAAT
6006644 CTTTGAATACAGTTTCTCTTGAAACACAAAAAAC
1 CTTTGAA-A-AGTTTCTCTTGAAACACAAAAAAC
* *
6006678 CTTTGAAGTAGTTTCTCTTGAAACAAAAAAAAC
1 CTTTGAA-AAGTTTCTCTTGAAACACAAAAAAC
6006711 CTTTGAAAATGTTTCTCTTGAAACAC
1 CTTTGAAAA-GTTTCTCTTGAAACAC
6006737 CAAACCCTCG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
32 1 0.02
33 45 0.85
34 7 0.13
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (32 bp):
CTTTGAAAAGTTTCTCTTGAAACACAAAAAAC
Found at i:6007977 original size:4 final size:4
Alignment explanation
Indices: 6007927--6008065 Score: 78
Period size: 4 Copynumber: 35.8 Consensus size: 4
6007917 TATTATCATC
* * * * *
6007927 TTTA TTAA TTTA TATA TATA TATA TTTA -CTA TTT- TTTA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
6007972 TTTA TTTCA TATA TATA TATTA -TT- TTTA CTTT- TTTA -TTA TTT- TTTA
1 TTTA TTT-A TTTA TTTA T-TTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA
* * * * *
6008018 TTTA TTTTT TTTA TTTA TATA TATA TATA TATA TTTA TTTA TTTA TTT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
6008066 TACATACTAT
Statistics
Matches: 111, Mismatches: 12, Indels: 24
0.76 0.08 0.16
Matches are distributed among these distances:
3 21 0.19
4 79 0.71
5 11 0.10
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:6007977 original size:11 final size:11
Alignment explanation
Indices: 6007961--6008027 Score: 57
Period size: 11 Copynumber: 5.9 Consensus size: 11
6007951 TTTACTATTT
6007961 TTTATTTTTTA
1 TTTATTTTTTA
*
6007972 TTTATTTCATATA
1 TTTATTT--TTTA
* *
6007985 TATATATTATT-
1 TTTAT-TTTTTA
6007996 TTTACTTTTTTA
1 TTTA-TTTTTTA
6008008 -TTATTTTTTA
1 TTTATTTTTTA
6008018 TTTATTTTTT
1 TTTATTTTTT
6008028 TTATTTATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
10 7 0.16
11 26 0.59
12 2 0.05
13 7 0.16
14 2 0.05
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:6007984 original size:42 final size:42
Alignment explanation
Indices: 6007892--6008024 Score: 162
Period size: 44 Copynumber: 3.0 Consensus size: 42
6007882 TTTTTTTAGA
* *
6007892 TTATATATATATATATATTA-TTTTTTATTATCATCTTTATTAAT
1 TTATATATATATATAT-TTACTTTTTTATTAT--TTTTTATTTAT
*
6007936 TTATATATATATATATTTACTATTTT-TTATTTTTTATTTAT
1 TTATATATATATATATTTACTTTTTTATTATTTTTTATTTAT
6007977 TTCATATATATATATTATTTTTACTTTTTTATTATTTTTTATTTAT
1 TT-ATATATATATA-TA--TTTACTTTTTTATTATTTTTTATTTAT
6008023 TT
1 TT
6008025 TTTTTATTTA
Statistics
Matches: 79, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
41 11 0.14
42 11 0.14
43 9 0.11
44 21 0.27
45 10 0.13
46 17 0.22
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (42 bp):
TTATATATATATATATTTACTTTTTTATTATTTTTTATTTAT
Found at i:6008037 original size:46 final size:46
Alignment explanation
Indices: 6007893--6008065 Score: 165
Period size: 46 Copynumber: 3.8 Consensus size: 46
6007883 TTTTTTAGAT
* * ** * *
6007893 TATATATATATATATATTATTTTTTATTATCATCTTTA-TTAATTTA
1 TATATATATATATTTACTATTTTTTATT-TTTTATTTATTTCATTTA
*
6007939 TATATATATATATTTACTATTTTTTATTTTTTATTTATTTCATATA
1 TATATATATATATTTACTATTTTTTATTTTTTATTTATTTCATTTA
* * **
6007985 TATATAT-TATTTTTACTTTTTTATTATTTTTTATTTATTTTTTTTA
1 TATATATATATATTTACTATTTT-TTATTTTTTATTTATTTCATTTA
* * *
6008031 TTTATATATATATATA-TA-TATTTATTTATTTATTT
1 TATATATATATATTTACTATTTTTTATTT-TTTATTT
6008066 TACATACTAT
Statistics
Matches: 106, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
44 6 0.06
45 28 0.26
46 66 0.62
47 6 0.06
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (46 bp):
TATATATATATATTTACTATTTTTTATTTTTTATTTATTTCATTTA
Found at i:6008067 original size:60 final size:53
Alignment explanation
Indices: 6007951--6008062 Score: 147
Period size: 55 Copynumber: 2.1 Consensus size: 53
6007941 TATATATATA
6007951 TTTACTATTTTTTATTTTTTATTTATTTCATATATATATATTATTTTTACTTT
1 TTTACTATTTTTTATTTTTTATTTATTTCATATATATATATTATTTTTACTTT
* * *
6008004 TTTATTATTTTTTATTTATTTTTTTTATTT-ATATATATATATATATATTTA-TTT
1 TTTACTATTTTTTA-TT-TTTTATTTATTTCATATATATATAT-TATTTTTACTTT
6008058 ATTTA
1 -TTTA
6008063 TTTTACATAC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
53 13 0.25
54 17 0.33
55 22 0.42
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.71
Consensus pattern (53 bp):
TTTACTATTTTTTATTTTTTATTTATTTCATATATATATATTATTTTTACTTT
Found at i:6008077 original size:64 final size:59
Alignment explanation
Indices: 6007943--6008100 Score: 142
Period size: 64 Copynumber: 2.5 Consensus size: 59
6007933 AATTTATATA
*
6007943 TATA-TATATTTACTATTTTTTATTTTTTATTTATTTCATATATATATATTATTTTTACTTT
1 TATACTAT-TTTA-TATTTATT-TTTTTTATTTATTTCATATATATATATTATTTTTACTTT
* * *
6008004 TTTATTATTTTTTATTTATTTTTTTTATTTATATAT-ATATATATATATTTATTTATTTA-TTT
1 TATACTATTTTATATTTATTTTTTTTATTTAT-T-TCATATATATATA-TTA-TT-TTTACTTT
* *
6008066 TACATACTATTTTATCTTTATTTTCTTTATCTTAT
1 T--ATACTATTTTATATTTATTTTTTTTAT-TTAT
6008101 CTTTTATTTA
Statistics
Matches: 80, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
59 12 0.15
60 19 0.24
61 10 0.12
62 9 0.11
63 4 0.05
64 22 0.28
65 4 0.05
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (59 bp):
TATACTATTTTATATTTATTTTTTTTATTTATTTCATATATATATATTATTTTTACTTT
Found at i:6008124 original size:26 final size:27
Alignment explanation
Indices: 6008095--6008158 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
6008085 ATTTTCTTTA
*
6008095 TCTTATCTTTTATTTAATTTGTTT-TT
1 TCTTATCTTTTATTTAATTTATTTATT
*
6008121 TCTTCAT-TTTAATTTAATTTATTTATT
1 TCTT-ATCTTTTATTTAATTTATTTATT
*
6008148 TCTTACCTTTT
1 TCTTATCTTTT
6008159 TATCTAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
26 20 0.65
27 11 0.35
ACGTcount: A:0.19, C:0.11, G:0.02, T:0.69
Consensus pattern (27 bp):
TCTTATCTTTTATTTAATTTATTTATT
Found at i:6015656 original size:69 final size:69
Alignment explanation
Indices: 6015576--6015705 Score: 242
Period size: 69 Copynumber: 1.9 Consensus size: 69
6015566 ATAAAAATAA
* *
6015576 TTTTTAAATAATATTATAATATATAATAATACAAGCAACATAAATATCTAAAAACTAAAAATATA
1 TTTTTAAATAATATTATAATATATAATAATACAAGAAACATAAATATCTAAAAAATAAAAATATA
6015641 ATTT
66 ATTT
6015645 TTTTTAAATAATATTATAATATATAATAATACAAGAAACATAAATATCTAAAAAATAAAAA
1 TTTTTAAATAATATTATAATATATAATAATACAAGAAACATAAATATCTAAAAAATAAAAA
6015706 CATACTTTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (69 bp):
TTTTTAAATAATATTATAATATATAATAATACAAGAAACATAAATATCTAAAAAATAAAAATATA
ATTT
Found at i:6017413 original size:96 final size:96
Alignment explanation
Indices: 6017304--6017593 Score: 445
Period size: 96 Copynumber: 3.0 Consensus size: 96
6017294 AATCGATCAT
* * * *
6017304 AATGACAATGTTGATGATGCTGATCCAACTCCGTATGTGATGGATAAGCCAAGTATTGGTGCTGT
1 AATGACAATGTTGATGATGCTGATCCAACTCCGTATGCGATGGATGAGCCAAGCATTGGTCCTGT
* *
6017369 TCCAACTCTGTATGTGATGGAATCGAGCTAG
66 TCCAACTCCGTATGTGATGGAATCGAGCAAG
* * * **
6017400 AATGACGATGTTGATTATGCTGATCCAACTCCATATGCGATGGATGAGCCAAGCATTGGTTTTGT
1 AATGACAATGTTGATGATGCTGATCCAACTCCGTATGCGATGGATGAGCCAAGCATTGGTCCTGT
* * *
6017465 TCCAACTCCATATTTGATGGAATCAAGCAAG
66 TCCAACTCCGTATGTGATGGAATCGAGCAAG
*
6017496 AATGACAATGTTGATGATGTTGATCCAACTCCGTATGCGATGGATGAGCCAAGCATTGGTCCTGT
1 AATGACAATGTTGATGATGCTGATCCAACTCCGTATGCGATGGATGAGCCAAGCATTGGTCCTGT
6017561 TCCAACTCCGTATGTGATGGAATCGAGCAAG
66 TCCAACTCCGTATGTGATGGAATCGAGCAAG
6017592 AA
1 AA
6017594 GTTAAATAAG
Statistics
Matches: 172, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 172 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (96 bp):
AATGACAATGTTGATGATGCTGATCCAACTCCGTATGCGATGGATGAGCCAAGCATTGGTCCTGT
TCCAACTCCGTATGTGATGGAATCGAGCAAG
Found at i:6018117 original size:66 final size:66
Alignment explanation
Indices: 6017941--6018110 Score: 202
Period size: 66 Copynumber: 2.6 Consensus size: 66
6017931 AATTTGTTTG
* * *
6017941 AAGAGAAACTATCTCAAGTGAGATAAAATTTGTTTCGAGGGAAACAGATTCAAAGATTGACGTTT
1 AAGAGAAACTATCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTGACGCTT
6018006 C
66 C
* * * * *
6018007 AAGGGAAATTGTCTCAA-AGGAGATAAAATTCGTTTCAAGGGAAAC-GATCTCAAAGATTTG-TG
1 AAGAGAAACTATCTCAAGA-GAGATAAAATTTGTTTCAAGGGAAACAGAT-TCAAAGA-TTGACG
6018069 CTTC
63 CTTC
* *
6018073 AAGAGAAACTATCTCAAGAGAGACAAACTTTGTTTCAA
1 AAGAGAAACTATCTCAAGAGAGATAAAATTTGTTTCAA
6018111 AAGAAACATA
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
65 3 0.03
66 79 0.92
67 4 0.05
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (66 bp):
AAGAGAAACTATCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTGACGCTT
C
Found at i:6018361 original size:20 final size:19
Alignment explanation
Indices: 6018333--6018405 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 19
6018323 TCATCTTGCT
6018333 CGAAAGACTTATAGATGGCC
1 CGAAAGACTTAT-GATGGCC
* * *
6018353 CGAAGGACTTATGTATCATGCT
1 CGAAAGACTTATG-AT--GGCC
*
6018375 CGAAAGACTTATTGAGGGCC
1 CGAAAGACTTA-TGATGGCC
*
6018395 CGAAGGACTTA
1 CGAAAGACTTA
6018406 CTCACCAAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
19 1 0.02
20 25 0.61
22 13 0.32
23 2 0.05
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (19 bp):
CGAAAGACTTATGATGGCC
Found at i:6018383 original size:22 final size:20
Alignment explanation
Indices: 6018314--6018386 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
6018304 GGATGACCTA
*
6018314 AAAGACTTATCATCTTGCTCG
1 AAAGACTTATGATC-TGCTCG
* *
6018335 AAAGACTTATAGAT-GGCCCG
1 AAAGACTTAT-GATCTGCTCG
*
6018355 AAGGACTTATGTATCATGCTCG
1 AAAGACTTATG-ATC-TGCTCG
6018377 AAAGACTTAT
1 AAAGACTTAT
6018387 TGAGGGCCCG
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
19 1 0.02
20 15 0.37
21 10 0.24
22 15 0.37
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (20 bp):
AAAGACTTATGATCTGCTCG
Found at i:6018793 original size:43 final size:43
Alignment explanation
Indices: 6018446--6018789 Score: 464
Period size: 43 Copynumber: 8.0 Consensus size: 43
6018436 AGTTTCTTAG
* * *
6018446 TTGTCATCAAGGAACCCCTATATATCACGTTGGTCCCTCTAA--
1 TTGTTATCAAGGAACCCCTACATATCACGATGGTCCCTC-AAGC
* *
6018488 -TGATCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGC
1 TTG-TTATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
* * *
6018531 TTATCATC-AGCGAACCCCTACATATCATGATGGTCCCTCAAGC
1 TTGTTATCAAG-GAACCCCTACATATCACGATGGTCCCTCAAGC
*
6018574 TTGTTATCAAGGAACCCCTACATATCACGATGCTCCCTCAAGC
1 TTGTTATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
* * *
6018617 TTGTTGTCAAGGAACCCTTACATATCAAGATGGTCCCTCAAGC
1 TTGTTATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
* *
6018660 TTGTTATCAAGGAACCCCTACATATCACGATGGTCCTTCAAGA
1 TTGTTATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
* * *
6018703 TTGTCATCAAGGAACCCCTACATATCACGATGGTCTCTTAAGC
1 TTGTTATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
*
6018746 TTGTTATCAAGGAA-CCCTACATATAACGATGGTCCCTCAAGC
1 TTGTTATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
6018788 TT
1 TT
6018790 TGTTTCTTAT
Statistics
Matches: 270, Mismatches: 26, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
41 4 0.01
42 64 0.24
43 199 0.74
44 3 0.01
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (43 bp):
TTGTTATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
Found at i:6020741 original size:15 final size:17
Alignment explanation
Indices: 6020721--6020757 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
6020711 AATCTGTCTA
6020721 TTTTC-TTCTT-TCTTT
1 TTTTCTTTCTTATCTTT
*
6020736 TTTTCTTTTTTATCTTT
1 TTTTCTTTCTTATCTTT
6020753 TTTTC
1 TTTTC
6020758 CTGTTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 4 0.21
17 10 0.53
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTCTTTCTTATCTTT
Found at i:6020751 original size:9 final size:8
Alignment explanation
Indices: 6020729--6020777 Score: 62
Period size: 9 Copynumber: 5.6 Consensus size: 8
6020719 TATTTTCTTC
6020729 TTTCTTTT
1 TTTCTTTT
6020737 TTTCTTTT
1 TTTCTTTT
6020745 TTATCTTTT
1 TT-TCTTTT
6020754 TTTCCTGTTT
1 TTT-CT-TTT
6020764 TTTCTGTTT
1 TTTCT-TTT
6020773 TTTCT
1 TTTCT
6020778 ATATATTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
8 11 0.29
9 21 0.55
10 6 0.16
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.80
Consensus pattern (8 bp):
TTTCTTTT
Found at i:6031447 original size:27 final size:27
Alignment explanation
Indices: 6031417--6031469 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
6031407 ATGAAAAATG
6031417 ACACAAACAAAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAAATAAGTTAGTAT
*
6031444 ACACAAACAAAAGAAATTAGTTAGTA
1 ACACAAACAAAAGAAATAAGTTAGTA
6031470 CATGTAAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.19
Consensus pattern (27 bp):
ACACAAACAAAAGAAATAAGTTAGTAT
Found at i:6035447 original size:3 final size:3
Alignment explanation
Indices: 6035441--6035465 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6035431 AAGCAACGTG
6035441 CAA CAA CAA CAA CAA CAA CAA CAA C
1 CAA CAA CAA CAA CAA CAA CAA CAA C
6035466 CGAAATACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.36, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:6042083 original size:33 final size:33
Alignment explanation
Indices: 6042041--6042108 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
6042031 TTGTAAAGGA
*
6042041 GAAAGGTTCTAGCTTAGT-CCATGAAAAGCTAGG
1 GAAAGGTTCTAGCTTA-TCCCATGAAAAACTAGG
* *
6042074 GAAAGGTTCTAGTTTATCCCGTGAAAAACTAGG
1 GAAAGGTTCTAGCTTATCCCATGAAAAACTAGG
6042107 GA
1 GA
6042109 GTTGTAAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 1 0.03
33 30 0.97
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (33 bp):
GAAAGGTTCTAGCTTATCCCATGAAAAACTAGG
Found at i:6045015 original size:20 final size:19
Alignment explanation
Indices: 6044987--6045076 Score: 69
Period size: 20 Copynumber: 4.8 Consensus size: 19
6044977 AGGGGGTCAA
* *
6044987 AGTGAATCCATGTACCCTGC
1 AGTGAATCCATGCA-CATGC
*
6045007 AGTGCATCCATGCACATGC
1 AGTGAATCCATGCACATGC
*
6045026 AGTGTATCCATGCAC-T--
1 AGTGAATCCATGCACATGC
* *
6045042 AGTGCATCAATGCACCATGC
1 AGTGAATCCATGCA-CATGC
**
6045062 AGTTCATCCATGCAC
1 AGTGAATCCATGCAC
6045077 TCAAACACTG
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
16 12 0.21
17 1 0.02
18 2 0.03
19 19 0.33
20 24 0.41
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (19 bp):
AGTGAATCCATGCACATGC
Found at i:6045028 original size:19 final size:19
Alignment explanation
Indices: 6045004--6045076 Score: 89
Period size: 19 Copynumber: 3.9 Consensus size: 19
6044994 CCATGTACCC
6045004 TGCAGTGCATCCATGCACA
1 TGCAGTGCATCCATGCACA
*
6045023 TGCAGTGTATCCATGCAC-
1 TGCAGTGCATCCATGCACA
*
6045041 T--AGTGCATCAATGCACCA
1 TGCAGTGCATCCATGCA-CA
*
6045059 TGCAGTTCATCCATGCAC
1 TGCAGTGCATCCATGCAC
6045077 TCAAACACTG
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
16 12 0.27
17 1 0.02
18 2 0.04
19 18 0.40
20 12 0.27
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (19 bp):
TGCAGTGCATCCATGCACA
Found at i:6045048 original size:35 final size:36
Alignment explanation
Indices: 6045007--6045077 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
6044997 TGTACCCTGC
*
6045007 AGTGCATCCATGCA-CATGCAGTGT-ATCCATGCACT
1 AGTGCATCAATGCACCATGCAGT-TCATCCATGCACT
6045042 AGTGCATCAATGCACCATGCAGTTCATCCATGCACT
1 AGTGCATCAATGCACCATGCAGTTCATCCATGCACT
6045078 CAAACACTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 14 0.42
36 19 0.58
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (36 bp):
AGTGCATCAATGCACCATGCAGTTCATCCATGCACT
Found at i:6050562 original size:15 final size:16
Alignment explanation
Indices: 6050538--6050570 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
6050528 ATTTAGGTTG
6050538 AAAATATTTTAAATAT
1 AAAATATTTTAAATAT
*
6050554 AAAAT-TTTTAAGTAT
1 AAAATATTTTAAATAT
6050569 AA
1 AA
6050571 TTAGTAGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
AAAATATTTTAAATAT
Found at i:6057374 original size:22 final size:22
Alignment explanation
Indices: 6057348--6057430 Score: 73
Period size: 23 Copynumber: 3.8 Consensus size: 22
6057338 TTAGTGCAGA
6057348 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* * *
6057370 GGGAACCGATTTCCCCTTTGAAG
1 GGGAATCGA-TACCCCCTTGAAG
* *
6057393 GGGAA-CTGATTCCCCC--CACAG
1 GGGAATC-GATACCCCCTTGA-AG
6057414 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
6057431 GAGGGTTCTA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.02
21 15 0.30
22 16 0.32
23 18 0.36
ACGTcount: A:0.24, C:0.31, G:0.25, T:0.19
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:6057390 original size:23 final size:23
Alignment explanation
Indices: 6057359--6057409 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
6057349 GGAATCGATA
*
6057359 CCCCCTTGAAGGGGAACCGATTT
1 CCCCCTTGAAGGGGAACCGATTC
* *
6057382 CCCCTTTGAAGGGGAACTGATTC
1 CCCCCTTGAAGGGGAACCGATTC
6057405 CCCCC
1 CCCCC
6057410 ACAGGGGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.20, C:0.35, G:0.24, T:0.22
Consensus pattern (23 bp):
CCCCCTTGAAGGGGAACCGATTC
Found at i:6059048 original size:18 final size:18
Alignment explanation
Indices: 6059013--6059053 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
6059003 AGAATAGCAC
*
6059013 GAGGAACAAGCTCCACCA
1 GAGGAACAAGCACCACCA
*
6059031 GAGGAACAAGCACGACCA
1 GAGGAACAAGCACCACCA
*
6059049 AAGGA
1 GAGGA
6059054 TCAAATGCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.27, G:0.27, T:0.02
Consensus pattern (18 bp):
GAGGAACAAGCACCACCA
Found at i:6068323 original size:16 final size:17
Alignment explanation
Indices: 6068299--6068338 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
6068289 ATATATAAAC
*
6068299 TATAATATAAATTATAT
1 TATAATATAAACTATAT
6068316 TA-AATATAAACTATAT
1 TATAATATAAACTATAT
6068332 TATAATA
1 TATAATA
6068339 GTCCATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TATAATATAAACTATAT
Found at i:6068358 original size:27 final size:29
Alignment explanation
Indices: 6068322--6068376 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 29
6068312 ATATTAAATA
*
6068322 TAAACTATATTATA-A-TAGTCCATATAT
1 TAAACCATATTATATAGTAGTCCATATAT
6068349 TAAACCATATTATATATGTAGTCCATAT
1 TAAACCATATTATATA-GTAGTCCATAT
6068377 TAAATAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 13 0.54
28 1 0.04
30 10 0.42
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (29 bp):
TAAACCATATTATATAGTAGTCCATATAT
Found at i:6069438 original size:53 final size:53
Alignment explanation
Indices: 6069310--6069443 Score: 155
Period size: 53 Copynumber: 2.5 Consensus size: 53
6069300 TAATCATCCC
* * * **
6069310 CTAAGAAATTAGGAAAGTCTAAGTCTTTCATTTATGGATGAAGATGTATGATG
1 CTAAGAAATTAGGAAAATGTGAGTCTTTCATTTATGGATGAAGATGTATGAAA
* * * *
6069363 CTAAGAAACTA-GAAAGACGTGAGTTTTTCATTTATGGATGATGATGTATGCAAA
1 CTAAGAAATTAGGAAA-ATGTGAGTCTTTCATTTATGGATGAAGATGTATG-AAA
6069417 C-AAGAAATTAGGAAAATGTGAGTCTTT
1 CTAAGAAATTAGGAAAATGTGAGTCTTT
6069444 GACCTCATTT
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
52 4 0.06
53 56 0.85
54 6 0.09
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.32
Consensus pattern (53 bp):
CTAAGAAATTAGGAAAATGTGAGTCTTTCATTTATGGATGAAGATGTATGAAA
Found at i:6077028 original size:111 final size:110
Alignment explanation
Indices: 6076833--6077060 Score: 300
Period size: 111 Copynumber: 2.1 Consensus size: 110
6076823 GTTGTAGGTT
*
6076833 CATTTCGACATACTTTGTGTATAATAGTATCGATCGATTTTCTTTAATGCACAACGGTGCATTTT
1 CATTTCGACATACTTCGTGTATAATAGTATCGATCGATTTTCTTTAATGCACAACGGTGCATTTT
* **
6076898 CGGTATAAAAGGTACCACCCATGGTATTCATAATCAGGTGAATTAC
66 CGGCATAAAAGGTACCACCCATAATATTCA-AATCAGGTGAATTAC
* * *
6076944 CATTTCGACATACTTCGTGTATGAA-AGTTATCGATCGATTTTGC-TT-ATGTATAATGGTGCAT
1 CATTTCGACATACTTCGTGTAT-AATAG-TATCGATCGATTTT-CTTTAATGCACAACGGTGCAT
* ** *
6077006 TTTTGGCATAAAAGGTGTCACCCATAATATTCAAATTAGGTGAATTAC
63 TTTCGGCATAAAAGGTACCACCCATAATATTCAAATCAGGTGAATTAC
6077054 CATTTCG
1 CATTTCG
6077061 GAACTTCGGT
Statistics
Matches: 103, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
110 21 0.20
111 63 0.61
112 18 0.17
113 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (110 bp):
CATTTCGACATACTTCGTGTATAATAGTATCGATCGATTTTCTTTAATGCACAACGGTGCATTTT
CGGCATAAAAGGTACCACCCATAATATTCAAATCAGGTGAATTAC
Found at i:6083239 original size:111 final size:111
Alignment explanation
Indices: 6083116--6083344 Score: 354
Period size: 111 Copynumber: 2.1 Consensus size: 111
6083106 GTTATAGGTG
* * * *
6083116 CATTTCGACATACTTTGTGTATG-ATAG-TATCGATCGATTTTGTTTAATGCATAACGGTGGATT
1 CATTTCGACATACTTCGTGTATGAAT-GTTATCGATCGATTTTGCTTAATGCATAACGATGCATT
*
6083179 TTCGGCATAAAAGGTGCCACCCACGGTATTCATAATGAGGTGAATTAC
65 TT-GGCATAAAAGGTGCCACCCACGGTATTCATAATAAGGTGAATTAC
**
6083227 CATTTCGACATACTTCGTGTATGAATGTTATCGATCGATTTTGCTTAATGCATAATTATGCATTT
1 CATTTCGACATACTTCGTGTATGAATGTTATCGATCGATTTTGCTTAATGCATAACGATGCATTT
*
6083292 TGGCATAAAAGGTGCCACCCATGGTATTCATAATAAGGTGAATTAC
66 TGGCATAAAAGGTGCCACCCACGGTATTCATAATAAGGTGAATTAC
6083338 CATTTCG
1 CATTTCG
6083345 GCACTTCGGT
Statistics
Matches: 108, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
111 73 0.68
112 35 0.32
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (111 bp):
CATTTCGACATACTTCGTGTATGAATGTTATCGATCGATTTTGCTTAATGCATAACGATGCATTT
TGGCATAAAAGGTGCCACCCACGGTATTCATAATAAGGTGAATTAC
Found at i:6092096 original size:38 final size:38
Alignment explanation
Indices: 6092045--6092122 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
6092035 GAAGCTTCAT
6092045 TTCAAGATTTAAACATCAAGCTAGTGTATTTTTAATCC
1 TTCAAGATTTAAACATCAAGCTAGTGTATTTTTAATCC
6092083 TTCAAGATTTAAACATCAAGCTAGTGTATTTTTAATCC
1 TTCAAGATTTAAACATCAAGCTAGTGTATTTTTAATCC
6092121 TT
1 TT
6092123 TAGACTGTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (38 bp):
TTCAAGATTTAAACATCAAGCTAGTGTATTTTTAATCC
Found at i:6093709 original size:27 final size:27
Alignment explanation
Indices: 6093671--6093733 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
6093661 ATTAAGGTTA
6093671 GAGACCCTTTAGAGGTGTACCCATGGT
1 GAGACCCTTTAGAGGTGTACCCATGGT
6093698 GAGACCCTTTAGAGGTGTACCCATGGT
1 GAGACCCTTTAGAGGTGTACCCATGGT
6093725 GAGACCCTT
1 GAGACCCTT
6093734 AGTAGAGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (27 bp):
GAGACCCTTTAGAGGTGTACCCATGGT
Found at i:6094560 original size:31 final size:31
Alignment explanation
Indices: 6094525--6094626 Score: 159
Period size: 31 Copynumber: 3.3 Consensus size: 31
6094515 ATTGGAACTA
6094525 GGGGACCACGACTGGATGGCTCATATGGACG
1 GGGGACCACGACTGGATGGCTCATATGGACG
*
6094556 GGGGACCACGACAGGATGGCTCATATGGACG
1 GGGGACCACGACTGGATGGCTCATATGGACG
* ** *
6094587 GGGGACCACGGCTGGATGGCTCACGTAGACG
1 GGGGACCACGACTGGATGGCTCATATGGACG
6094618 GGGGACCAC
1 GGGGACCAC
6094627 TGCTAGCATG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.23, C:0.25, G:0.40, T:0.13
Consensus pattern (31 bp):
GGGGACCACGACTGGATGGCTCATATGGACG
Found at i:6095019 original size:2 final size:2
Alignment explanation
Indices: 6095012--6095049 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6095002 TTAGGCGTAA
6095012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6095050 TGATTTATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6103455 original size:17 final size:17
Alignment explanation
Indices: 6103419--6103484 Score: 87
Period size: 18 Copynumber: 3.8 Consensus size: 17
6103409 TGATGATGGA
6103419 TTTCAGTTATCAGATGAT
1 TTTCAGTTATCAGAT-AT
6103437 TTTCAGTTATCAGATAT
1 TTTCAGTTATCAGATAT
* * *
6103454 TTACAGATATAAGATAT
1 TTTCAGTTATCAGATAT
6103471 TTTACAGTTATCAG
1 TTT-CAGTTATCAG
6103485 CCATAGATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
17 18 0.44
18 23 0.56
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (17 bp):
TTTCAGTTATCAGATAT
Found at i:6116722 original size:19 final size:19
Alignment explanation
Indices: 6116695--6116733 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
6116685 TTAGTTTGAA
* * *
6116695 TAGGTTTTAGTATTTTATT
1 TAGGATTTAGAATATTATT
6116714 TAGGATTTAGAATATTATT
1 TAGGATTTAGAATATTATT
6116733 T
1 T
6116734 TAATTATTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.56
Consensus pattern (19 bp):
TAGGATTTAGAATATTATT
Found at i:6116790 original size:73 final size:75
Alignment explanation
Indices: 6116623--6116795 Score: 201
Period size: 73 Copynumber: 2.3 Consensus size: 75
6116613 GTATTTTAGT
* * * *
6116623 TTTTAGTATTTTAATTATGTTTTAGGATATTAGTTTTATATTTTATCTTTGTTTTAGATATTTTA
1 TTTTAGTATTTTAATTAGGATTTAGAATATTAGTTTTATATTTTATCTATGTTTTAGATATTTTA
* * *
6116688 GTTTGAATAGG
66 GCTTAAACA-G
* *
6116699 TTTTAGTATTTTATTTAGGATTTAGAATATTA-TTTTA-ATTATTA-CTAT-TTTTAGGTATTTT
1 TTTTAGTATTTTAATTAGGATTTAGAATATTAGTTTTATATT-TTATCTATGTTTTAGATATTTT
6116760 AGCTTAAACAG
65 AGCTTAAACAG
*
6116771 TTTTAAGTGTTTTAATTAGGATTTA
1 TTTT-AGTATTTTAATTAGGATTTA
6116796 AGATGTTTTA
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
72 5 0.06
73 37 0.44
74 6 0.07
75 8 0.10
76 28 0.33
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (75 bp):
TTTTAGTATTTTAATTAGGATTTAGAATATTAGTTTTATATTTTATCTATGTTTTAGATATTTTA
GCTTAAACAG
Found at i:6119016 original size:92 final size:92
Alignment explanation
Indices: 6118854--6119044 Score: 373
Period size: 92 Copynumber: 2.1 Consensus size: 92
6118844 ACCCAAACTC
*
6118854 TAGCTATGCGGCAAATCAAAGGCCAACTTATCAACCAAAACCTCCTCAACAGAAAATGCAAAAAT
1 TAGCAATGCGGCAAATCAAAGGCCAACTTATCAACCAAAACCTCCTCAACAGAAAATGCAAAAAT
6118919 CATCATTGGAGGAACTCATAGGAAAGT
66 CATCATTGGAGGAACTCATAGGAAAGT
6118946 TAGCAATGCGGCAAATCAAAGGCCAACTTATCAACCAAAACCTCCTCAACAGAAAATGCAAAAAT
1 TAGCAATGCGGCAAATCAAAGGCCAACTTATCAACCAAAACCTCCTCAACAGAAAATGCAAAAAT
6119011 CATCATTGGAGGAACTCATAGGAAAGT
66 CATCATTGGAGGAACTCATAGGAAAGT
6119038 TAGCAAT
1 TAGCAAT
6119045 CTCACAAGAA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 98 1.00
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (92 bp):
TAGCAATGCGGCAAATCAAAGGCCAACTTATCAACCAAAACCTCCTCAACAGAAAATGCAAAAAT
CATCATTGGAGGAACTCATAGGAAAGT
Found at i:6123178 original size:5 final size:5
Alignment explanation
Indices: 6123168--6123259 Score: 53
Period size: 5 Copynumber: 17.8 Consensus size: 5
6123158 TCGTTCTATT
* * **
6123168 TTTTA TTTTA TTTCA TTTCA TTTTTA TTTTA TTTT- TTAGCAAA TTTTA
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TT---TTA TTTTA
* * * *
6123216 TTTTCA TTATA -ATTA TTTTA TTTTA ATTAA TTTTA TTTTA TTTT
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
6123260 TCTCTAAACA
Statistics
Matches: 66, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
4 4 0.06
5 52 0.79
6 8 0.12
8 2 0.03
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (5 bp):
TTTTA
Found at i:6123235 original size:20 final size:20
Alignment explanation
Indices: 6123210--6123259 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
6123200 TTTTTAGCAA
*
6123210 ATTTTATTTTCATT-ATAATT
1 ATTTTATTTTAATTAAT-ATT
*
6123230 ATTTTATTTTAATTAATTTT
1 ATTTTATTTTAATTAATATT
6123250 ATTTTATTTT
1 ATTTTATTTT
6123260 TCTCTAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTTATTTTAATTAATATT
Found at i:6123253 original size:15 final size:14
Alignment explanation
Indices: 6123213--6123255 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
6123203 TTAGCAAATT
*
6123213 TTATTTTCATTATAA
1 TTATTTT-ATTTTAA
6123228 TTATTTTATTTTAA
1 TTATTTTATTTTAA
6123242 TTAATTTTATTTTA
1 TT-ATTTTATTTTA
6123256 TTTTTCTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTTTATTTTAA
Found at i:6125101 original size:74 final size:74
Alignment explanation
Indices: 6124935--6125107 Score: 215
Period size: 75 Copynumber: 2.3 Consensus size: 74
6124925 GTAATTTAGT
* * * * * * *
6124935 TTTTAGTATTTTAATTAAGCTTTAGGATATTTTTTTATATTTTATCTTTGTTTTATATATTTTAG
1 TTTTAGTATTTTAATTAGGATTTAGAATATTATTTTAAATATTATCTTTGTTTTAGATATTTTAG
6125000 TTTAAATAGG
66 TTTAAATA-G
*
6125010 TTTTAGTATTTTAATTAGGATTTAGAATATTATTTTAAATATTAT-TATT-TTTTAGGTATTTTA
1 TTTTAGTATTTTAATTAGGATTTAGAATATTATTTTAAATATTATCT-TTGTTTTAGATATTTTA
6125073 GTTTAAATAG
65 GTTTAAATAG
* *
6125083 TTTTAAGTGTTTTAATTAGGGTTTA
1 TTTT-AGTATTTTAATTAGGATTTA
6125108 ATATGTTTTA
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
73 5 0.06
74 40 0.47
75 41 0.48
ACGTcount: A:0.29, C:0.01, G:0.12, T:0.58
Consensus pattern (74 bp):
TTTTAGTATTTTAATTAGGATTTAGAATATTATTTTAAATATTATCTTTGTTTTAGATATTTTAG
TTTAAATAG
Found at i:6125233 original size:11 final size:12
Alignment explanation
Indices: 6125205--6125234 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6125195 AAAATCTTCT
6125205 TTTTCTCTCTAG
1 TTTTCTCTCTAG
6125217 TTTTCTCTCTA-
1 TTTTCTCTCTAG
6125228 TTTTCTC
1 TTTTCTC
6125235 ATACTCCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.07, C:0.27, G:0.03, T:0.63
Consensus pattern (12 bp):
TTTTCTCTCTAG
Found at i:6125730 original size:17 final size:17
Alignment explanation
Indices: 6125705--6125738 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6125695 CTTTATCTCA
*
6125705 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
6125722 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
6125739 TTATCTCATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:6125851 original size:24 final size:23
Alignment explanation
Indices: 6125806--6125851 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
6125796 TTAAAATCAA
* *
6125806 TATTTTTTTTATTTTCCCTTTTT
1 TATTTTTTTTATTCTACCTTTTT
*
6125829 TATTTTATTTTATTCTACGTTTT
1 TATTTT-TTTTATTCTACCTTTT
6125852 CAATTTCATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74
Consensus pattern (23 bp):
TATTTTTTTTATTCTACCTTTTT
Found at i:6129896 original size:56 final size:56
Alignment explanation
Indices: 6129810--6129922 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
6129800 TAAACTACGT
*
6129810 ATTTGATCATCCAACTATTCACGGGATTTCATTTTGGTCACCTATTTATCTTTTTA
1 ATTTGATCATCCAACTATTCACGGGATTTCATTTTGGTCACCTAATTATCTTTTTA
6129866 ATTTGATCATCCAACTATTCACGGGATTTCATTTTGGTCACCTAATTATCTTTTTA
1 ATTTGATCATCCAACTATTCACGGGATTTCATTTTGGTCACCTAATTATCTTTTTA
6129922 A
1 A
6129923 ACCATACCTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.45
Consensus pattern (56 bp):
ATTTGATCATCCAACTATTCACGGGATTTCATTTTGGTCACCTAATTATCTTTTTA
Done.