Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002485.1 Hibiscus syriacus cultivar Beakdansim tig00005071_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: 244926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:167356 original size:23 final size:23
Alignment explanation
Indices: 167330--167375 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
167320 CTACCAAAAA
167330 ACAGAGAAAAACGTGTCACAAAG
1 ACAGAGAAAAACGTGTCACAAAG
* *
167353 ACAGAGATAAACGTGTCATAAAG
1 ACAGAGAAAAACGTGTCACAAAG
167376 GCAAAGAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.15, G:0.22, T:0.13
Consensus pattern (23 bp):
ACAGAGAAAAACGTGTCACAAAG
Found at i:168931 original size:20 final size:20
Alignment explanation
Indices: 168908--168960 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
168898 CAGTTTCAAG
* *
168908 AATCGCAACGCTAATATGA-A
1 AATCGCAACGCGAACAT-ATA
168928 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
168948 AATCGCAACGCGA
1 AATCGCAACGCGA
168961 TTCTTACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.43, C:0.25, G:0.17, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:169014 original size:20 final size:20
Alignment explanation
Indices: 168946--169183 Score: 216
Period size: 20 Copynumber: 11.7 Consensus size: 20
168936 CGCGAACATA
* *
168946 TAAATCGCAACGCG-ATTCT
1 TAAATCGCAACGCGTATCCG
* *
168965 TACTATCGCAACGAGTATCCG
1 TA-AATCGCAACGCGTATCCG
168986 TAAAAATCGCAACGCGTATCCG
1 T--AAATCGCAACGCGTATCCG
* * *
169008 TAAATCGTAACGAC-AATACG
1 TAAATCGCAACG-CGTATCCG
169028 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
* * *
169049 TAAATCGCAACGAGAATACG
1 TAAATCGCAACGCGTATCCG
*
169069 TAAATCGCAACGCG-ATTC-
1 TAAATCGCAACGCGTATCCG
* *
169087 TGAATATCGCAACGAGAATCCG
1 T-AA-ATCGCAACGCGTATCCG
169109 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
* *
169130 TAAATCGCAACGAC-AATACG
1 TAAATCGCAACG-CGTATCCG
169150 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
169171 TAAATCGCAACGC
1 TAAATCGCAACGC
169184 AATTTTTAAA
Statistics
Matches: 179, Mismatches: 26, Indels: 27
0.77 0.11 0.12
Matches are distributed among these distances:
18 1 0.01
19 7 0.04
20 94 0.53
21 56 0.31
22 20 0.11
23 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:169043 original size:41 final size:41
Alignment explanation
Indices: 168947--169186 Score: 310
Period size: 41 Copynumber: 5.9 Consensus size: 41
168937 GCGAACATAT
* * * ** *
168947 AAATCGCAACGCG-ATTCTTACTATCGCAACGAGTATCCGTAA
1 AAATCGCAACGCGTATCCGTA-AATCGCAACGACAATACGT-A
*
168989 AAATCGCAACGCGTATCCGTAAATCGTAACGACAATACGTA
1 AAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA
*
169030 AAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-
1 AAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA
* * *
169070 AAATCGCAACGCG-ATTC-TGAATATCGCAACGAGAATCCGTA
1 AAATCGCAACGCGTATCCGT-AA-ATCGCAACGACAATACGTA
169111 AAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA
1 AAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA
169152 AAATCGCAACGCGTATCCGTAAATCGCAACG-CAAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGACAAT
169187 TTTTAAAGCG
Statistics
Matches: 178, Mismatches: 14, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
38 1 0.01
39 5 0.03
40 34 0.19
41 100 0.56
42 32 0.18
43 6 0.03
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (41 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA
Found at i:169118 original size:81 final size:80
Alignment explanation
Indices: 168908--169182 Score: 281
Period size: 81 Copynumber: 3.4 Consensus size: 80
168898 CAGTTTCAAG
* * * * * * * *
168908 AATCGCAACGCTAATATGAAAATCGCAACGCGAA-CATATAAATCGCAACGCG-ATTCTTACTAT
1 AATCGCAACGCGATTCTG-AAATCGCAACGAGAATCGTA-AAATCGCAACGCGTATCCGTA-AAT
* *
168971 CGCAACGAGTATCCGTAAA
63 CGCAACGAGAATACGT-AA
* * *
168990 AATCGCAACGCG-TATCCGTAAATCGTAACGACAATACGTAAAATCGCAACGCGTATCCGTAAAT
1 AATCGCAACGCGAT-TCTG-AAATCGCAACGAGAAT-CGTAAAATCGCAACGCGTATCCGTAAAT
169054 CGCAACGAGAATACGT-A
63 CGCAACGAGAATACGTAA
169071 AATCGCAACGCGATTCTGAATATCGCAACGAGAATCCGTAAAATCGCAACGCGTATCCGTAAATC
1 AATCGCAACGCGATTCTGAA-ATCGCAACGAGAAT-CGTAAAATCGCAACGCGTATCCGTAAATC
*
169136 GCAACGACAATACGTAA
64 GCAACGAGAATACGTAA
*
169153 AATCGCAACGCG-TATCCGTAAATCGCAACG
1 AATCGCAACGCGAT-TCTG-AAATCGCAACG
169183 CAATTTTTAA
Statistics
Matches: 164, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
80 2 0.01
81 72 0.44
82 51 0.31
83 31 0.19
84 8 0.05
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (80 bp):
AATCGCAACGCGATTCTGAAATCGCAACGAGAATCGTAAAATCGCAACGCGTATCCGTAAATCGC
AACGAGAATACGTAA
Found at i:169164 original size:122 final size:123
Alignment explanation
Indices: 168927--169182 Score: 433
Period size: 122 Copynumber: 2.1 Consensus size: 123
168917 GCTAATATGA
* * * * *
168927 AAATCGCAACGCGAACATATAAATCGCAACGCGATTCTTACTATCGCAACGAGTATCCGTAAAAA
1 AAATCGCAACGAGAACACATAAATCGCAACGCGATTCTGAATATCGCAACGAGAATCCGTAAAAA
*
168992 TCGCAACGCGTATCCGTAAATCGTAACGACAATACGTAAAATCGCAACGCGTATCCGT
66 TCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGT
* *
169050 AAATCGCAACGAGAATACGTAAATCGCAACGCGATTCTGAATATCGCAACGAGAATCCGT-AAAA
1 AAATCGCAACGAGAACACATAAATCGCAACGCGATTCTGAATATCGCAACGAGAATCCGTAAAAA
169114 TCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGT
66 TCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGT
169172 AAATCGCAACG
1 AAATCGCAACG
169183 CAATTTTTAA
Statistics
Matches: 125, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
122 72 0.58
123 53 0.42
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.19
Consensus pattern (123 bp):
AAATCGCAACGAGAACACATAAATCGCAACGCGATTCTGAATATCGCAACGAGAATCCGTAAAAA
TCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGT
Found at i:169749 original size:21 final size:21
Alignment explanation
Indices: 169723--169814 Score: 74
Period size: 21 Copynumber: 4.8 Consensus size: 21
169713 TTTGCAGAAG
169723 AATCGCAACGAGAGAAATGAA
1 AATCGCAACGAGAGAAATGAA
***
169744 AATCGCAACGAGAG-AATCTC
1 AATCGCAACGAGAGAAATGAA
*
169764 AA-CGC-A--A-A--AATGAC
1 AATCGCAACGAGAGAAATGAA
*
169778 TATCGCAACGAGAGAAATGAA
1 AATCGCAACGAGAGAAATGAA
*
169799 AATCGCAATGAGAGAA
1 AATCGCAACGAGAGAA
169815 TCGCAACGGG
Statistics
Matches: 55, Mismatches: 9, Indels: 14
0.71 0.12 0.18
Matches are distributed among these distances:
14 5 0.09
15 4 0.07
16 2 0.04
18 2 0.04
19 4 0.07
20 5 0.09
21 33 0.60
ACGTcount: A:0.49, C:0.17, G:0.22, T:0.12
Consensus pattern (21 bp):
AATCGCAACGAGAGAAATGAA
Found at i:169856 original size:19 final size:19
Alignment explanation
Indices: 169834--169898 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
169824 GAAACCAAAA
*
169834 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
169853 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
169867 TCTCGTTGCAATTTTCATT
1 TCGCGTTGCGATTTTCATT
169886 TCGCGTTGCGATT
1 TCGCGTTGCGATT
169899 CTCTCGTTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 9 0.25
16 3 0.08
17 3 0.08
19 21 0.58
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:169875 original size:14 final size:14
Alignment explanation
Indices: 169856--169912 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
169846 TTTCATTTCG
169856 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
169870 CGTTGCAATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
169889 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
169903 CGTTGCGATT
1 CGTTGCGATT
169913 TTCATTTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:169886 original size:33 final size:33
Alignment explanation
Indices: 169839--169920 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
169829 CAAAATCGCA
169839 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
169872 TTGCAATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
169905 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
169921 AACCAAAAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:171829 original size:93 final size:94
Alignment explanation
Indices: 171616--171878 Score: 395
Period size: 94 Copynumber: 2.8 Consensus size: 94
171606 TAGATTGCTT
* * *
171616 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGATAGT
*
171681 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 AGTTGTCTTTTGTTTTGTCTTTTGGTTGA
*
171710 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAA-ATAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGATAGT
171774 AGTTGTC-TTTGTTTTGTCTTTTGGTTGAA
66 AGTTGTCTTTTGTTTTGTCTTTTGGTTG-A
* * * * * *
171803 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCCAAATTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGATAGT
*
171868 ATTTGTCTTTT
66 AGTTGTCTTTT
171879 TCTATTGGTT
Statistics
Matches: 153, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
92 20 0.13
93 64 0.42
94 66 0.43
95 3 0.02
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGATAGT
AGTTGTCTTTTGTTTTGTCTTTTGGTTGA
Found at i:171999 original size:19 final size:19
Alignment explanation
Indices: 171943--172048 Score: 124
Period size: 19 Copynumber: 5.4 Consensus size: 19
171933 TAGTTTACTT
* *
171943 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
171963 TCGCAAC-CTGAAAAATGACTA
1 TCGCAACGC-G--AAATGAAAA
171984 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
172003 TCGCAACGAGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
172022 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
172041 TCGCAACG
1 TCGCAACG
172049 ACAAAATCGC
Statistics
Matches: 75, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
19 52 0.69
20 8 0.11
21 11 0.15
22 4 0.05
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:172026 original size:38 final size:38
Alignment explanation
Indices: 171943--172055 Score: 145
Period size: 38 Copynumber: 2.9 Consensus size: 38
171933 TAGTTTACTT
* * **
171943 TCGCAACACGAAACTTAAAATCGCAACCTGAAAAATGACTA
1 TCGCAACGCGAAA-TGAAAATCGCAA-C-GAAAAATGAAAA
*
171984 TCGCAACGCGAAATGAAAATCGCAACGAGAAATGAAAA
1 TCGCAACGCGAAATGAAAATCGCAACGAAAAATGAAAA
172022 TCGCAACGCGAAATGAAAATCGCAACGACAAAAT
1 TCGCAACGCGAAATGAAAATCGCAACGA-AAAAT
172056 CGCAACGCGA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
38 37 0.57
39 5 0.08
40 11 0.17
41 12 0.18
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (38 bp):
TCGCAACGCGAAATGAAAATCGCAACGAAAAATGAAAA
Found at i:172060 original size:33 final size:36
Alignment explanation
Indices: 171983--172067 Score: 122
Period size: 38 Copynumber: 2.4 Consensus size: 36
171973 AAAAATGACT
*
171983 ATCGCAACGCGAAATGAAAATCGCAACGAGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAAC-AG-AATCAAA
172021 ATCGCAACGCGAAATGAAAATCGCAAC-G-A-CAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAGAATCAAA
172054 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
172068 CTATAATCGC
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
33 17 0.37
34 1 0.02
36 1 0.02
38 27 0.59
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.09
Consensus pattern (36 bp):
ATCGCAACGCGAAATGAAAATCGCAACAGAATCAAA
Found at i:172119 original size:33 final size:33
Alignment explanation
Indices: 172077--172170 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
172067 ACTATAATCG
** *
172077 CGTTGCGATTTTGGTTTCGCGTTGCGATTCTAT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTAC
* *
172110 CGTTGCGATTTTCATTTCTCGTTGCGATTCTCC
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTAC
172143 CGTTGCGATTTTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
172171 AGTCATTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.10, C:0.22, G:0.23, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTAC
Found at i:172133 original size:19 final size:19
Alignment explanation
Indices: 172109--172194 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 19
172099 TGCGATTCTA
172109 TCGTTGCGATTTTCATTTC
1 TCGTTGCGATTTTCATTTC
172128 TCGTTGCGA--TTC---TC
1 TCGTTGCGATTTTCATTTC
*
172142 CCGTTGCGATTTTCATTTC
1 TCGTTGCGATTTTCATTTC
* **
172161 GCGTTGCGATAGTCATTTTTC
1 TCGTTGCGATTTTCA--TTTC
*
172182 ACGTTGCGATTTT
1 TCGTTGCGATTTT
172195 AAGTTTCGTG
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
14 10 0.19
16 3 0.06
17 3 0.06
19 23 0.43
21 14 0.26
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.47
Consensus pattern (19 bp):
TCGTTGCGATTTTCATTTC
Found at i:172686 original size:42 final size:42
Alignment explanation
Indices: 172640--172725 Score: 95
Period size: 42 Copynumber: 2.0 Consensus size: 42
172630 ATTGTTGAAA
* * *
172640 AGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAG
1 AGGCCACTATCA-TCATCGAAGAGGT-CCCTCCCACCATTCAAG
* *
172682 AGGCCACTGTCATCATTGAAGAGGTCCCTCCCACCATTCAAG
1 AGGCCACTATCATCATCGAAGAGGTCCCTCCCACCATTCAAG
172724 AG
1 AG
172726 CCCGATTCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
41 4 0.11
42 31 0.84
43 2 0.05
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (42 bp):
AGGCCACTATCATCATCGAAGAGGTCCCTCCCACCATTCAAG
Found at i:174097 original size:14 final size:14
Alignment explanation
Indices: 174078--174113 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
174068 ATTGTTTAAT
174078 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
174092 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
174106 TGATTTGT
1 TGATTTGT
174114 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:174273 original size:14 final size:14
Alignment explanation
Indices: 174236--174280 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
174226 ATGCGAAATG
*
174236 AAAATCGCAACGAG
1 AAAATCGCAACGAA
*
174250 AGAATCGCAACGAA
1 AAAATCGCAACGAA
*
174264 AAAATTGCAACGCAA
1 AAAATCGCAACG-AA
174279 AA
1 AA
174281 CTAAATTCGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 22 0.85
15 4 0.15
ACGTcount: A:0.53, C:0.20, G:0.18, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:174332 original size:33 final size:33
Alignment explanation
Indices: 174290--174384 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 33
174280 ACTAAATTCG
174290 CGTTGCGATTTTAATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTAATTTCGCATTGCGATTCCCT
* *
174323 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTAATTTCGCATTGCGATTCCCT
* * *
174356 CGTTGTGATTGTAATTTCCGCGTTGCGAT
1 CGTTGCGATTTTAATTT-CGCATTGCGAT
174385 AGTCATTAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
33 45 0.82
34 10 0.18
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTAATTTCGCATTGCGATTCCCT
Found at i:174349 original size:19 final size:19
Alignment explanation
Indices: 174286--174351 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
174276 CAAAACTAAA
* *
174286 TTCGCGTTGCGATTTTAAT
1 TTCGCATTGCGATTTTCAT
*
174305 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
174321 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
174338 TTCGCATTGCGATT
1 TTCGCATTGCGATT
174352 CTCTCGTTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
14 6 0.17
16 6 0.17
17 5 0.14
19 19 0.53
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:174430 original size:20 final size:20
Alignment explanation
Indices: 174369--174430 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
174359 TGTGATTGTA
*
174369 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGTGTTGCGATAGTC
**
174389 A-TTAAGATGATTGCGA-ACGTC
1 ATTTCCG-TG-TTGCGATA-GTC
174410 ATTTCCGTGTTGCGATAGTC
1 ATTTCCGTGTTGCGATAGTC
174430 A
1 A
174431 AATGAATGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
19 3 0.09
20 13 0.41
21 13 0.41
22 3 0.09
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (20 bp):
ATTTCCGTGTTGCGATAGTC
Found at i:176932 original size:24 final size:24
Alignment explanation
Indices: 176898--176951 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
176888 CTGAAACATC
176898 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
176922 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
176946 ATCAAA
1 ATCAAA
176952 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:176965 original size:24 final size:24
Alignment explanation
Indices: 176898--176965 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
176888 CTGAAACATC
* * *
176898 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
176922 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
176946 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
176966 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:177098 original size:12 final size:12
Alignment explanation
Indices: 177077--177110 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
177067 GGTTGTAGGT
*
177077 TTTGAGATTGTG
1 TTTGATATTGTG
177089 TTTGATATTGTG
1 TTTGATATTGTG
*
177101 TTTGGTATTG
1 TTTGATATTG
177111 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:177797 original size:20 final size:20
Alignment explanation
Indices: 177772--178124 Score: 265
Period size: 20 Copynumber: 17.4 Consensus size: 20
177762 AAATTTCAGT
177772 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTCTC
* *
177792 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCTC
* *
177812 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCTC
177832 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTCTC
177852 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTCTC
177872 GTTGCGATTTTAC-GTATTCTC
1 GTTGCGA-TTTACAG-ATTCTC
** * *
177893 GTTGCGATTTATGGATACGC
1 GTTGCGATTTACAGATTCTC
* * *
177913 ATTACGATTAAC-GTATTCTC
1 GTTGCGATTTACAG-ATTCTC
* *
177933 GTTGCGATAATT--AGAATCGC
1 GTTGCGAT--TTACAGATTCTC
177953 GTTGCGATTTAC-GTATTCTC
1 GTTGCGATTTACAG-ATTCTC
* * *
177973 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACAGATTCTC
* *
177993 GTTGCGATTTTACATATTGTC
1 GTTGCGA-TTTACAGATTCTC
* *
178014 GTTGCGATTTACGGATAT-GC
1 GTTGCGATTTACAGAT-TCTC
* *
178034 GTTGCGATTTTTACGGATACTC
1 GTTGCGA--TTTACAGATTCTC
* *
178056 GTTGCGATAGTT--AGAATCGC
1 GTTGCGAT--TTACAGATTCTC
* *
178076 GTTGCGATTTATATG-TTCGC
1 GTTGCGATTTACA-GATTCTC
* * *
178096 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACAGATTCTC
178116 GTTGCGATT
1 GTTGCGATT
178125 CTGGAAAATC
Statistics
Matches: 271, Mismatches: 40, Indels: 44
0.76 0.11 0.12
Matches are distributed among these distances:
18 4 0.01
19 2 0.01
20 207 0.76
21 38 0.14
22 20 0.07
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCTC
Found at i:177956 original size:121 final size:122
Alignment explanation
Indices: 177831--178124 Score: 387
Period size: 121 Copynumber: 2.4 Consensus size: 122
177821 TACGGATTAT
* *
177831 CGTTGCGATTTACAGATTCTCGTTGCGATTTACAGATTCTCGTTGCGATTTTACGTATTCTCGTT
1 CGTTGCGATTTACAGATTCTCGTTGCGATTTACAGATTCGCGTTGCGATTTTACATATTCTCGTT
* * *
177896 GCGATTTATGGATACGCATTACGA-TTAACGTATTCTCGTTGCGATAATTAGAATCG
66 GCGATTTACGGATACGCATTACGATTTAACGGATACTCGTTGCGATAATTAGAATCG
* * *
177952 CGTTGCGATTTAC-GTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACATATTGTCGT
1 CGTTGCGATTTACAG-ATTCTCGTTGCGATTTACAGATTCGCGTTGCGATTTTACATATTCTCGT
* * * * *
178016 TGCGATTTACGGATATGCGTTGCGATTTTTACGGATACTCGTTGCGATAGTTAGAATCG
65 TGCGATTTACGGATACGCATTACGA-TTTAACGGATACTCGTTGCGATAATTAGAATCG
* * * *
178075 CGTTGCGATTTATATG-TTCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACA-GATTCTCGTTGCGATTTACAGATTCGCGTTGCGATT
178125 CTGGAAAATC
Statistics
Matches: 149, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
120 1 0.01
121 78 0.52
123 69 0.46
125 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (122 bp):
CGTTGCGATTTACAGATTCTCGTTGCGATTTACAGATTCGCGTTGCGATTTTACATATTCTCGTT
GCGATTTACGGATACGCATTACGATTTAACGGATACTCGTTGCGATAATTAGAATCG
Found at i:181679 original size:2 final size:2
Alignment explanation
Indices: 181672--181707 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
181662 ATTGGAAATG
181672 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
181708 TTGGATCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:186163 original size:2 final size:2
Alignment explanation
Indices: 186156--186196 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
186146 CTAGAAATGG
186156 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
186197 GACTGAATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:194301 original size:3 final size:3
Alignment explanation
Indices: 194293--194354 Score: 72
Period size: 3 Copynumber: 20.3 Consensus size: 3
194283 ATATATATAT
* * *
194293 ATA ATA ATA ATA ATA ATA ATA ATA ATA TTTA GTA ATA ATA A-A TTTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA -ATA
194339 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
194355 AATTTAAATG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
2 1 0.02
3 47 0.92
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:195531 original size:76 final size:76
Alignment explanation
Indices: 194481--195504 Score: 1942
Period size: 76 Copynumber: 13.5 Consensus size: 76
194471 GATGGAAATG
* * *
194481 TTTGAAAACATCATGCAC-GAAAGGGCTTATAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTG-AAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
194545 TCCCGAAGGCTT
65 TCCCGAAGGCTT
* *
194557 TTTGGAAACATCATGCACTGAAGGACTTACAAATGACCCGAAGGCTTTGAAAACATCAAAAAACT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
194622 CCCGAAGGCTT
66 CCCGAAGGCTT
194633 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
194698 CCCGAAGGCTT
66 CCCGAAGGCTT
*
194709 TTTGGAAACATCATGCACTGAAGGACTTACAAATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
194774 CCCGAAGGCTT
66 CCCGAAGGCTT
*
194785 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
194850 CCCGAAGGCTT
66 CCCGAAGGCTT
*
194861 TTTGGAAACATCATGCACTGAAGGACTTACAAATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
194926 CCCGAAGGCTT
66 CCCGAAGGCTT
194937 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
195002 CCCGAAGGCTT
66 CCCGAAGGCTT
195013 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
195078 CCCGAAGGCTT
66 CCCGAAGGCTT
195089 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
195154 CCCGAAGGCTT
66 CCCGAAGGCTT
195165 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
195230 CCCGAAGGCTT
66 CCCGAAGGCTT
195241 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
195306 CCCGAAGGCTT
66 CCCGAAGGCTT
*
195317 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAGAGA
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAA-AGC
195382 TCCCGAAGGCTT
65 TCCCGAAGGCTT
195394 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
195459 CCCGAAGGCTT
66 CCCGAAGGCTT
195470 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
195505 TGGGAAATAG
Statistics
Matches: 931, Mismatches: 15, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
76 855 0.92
77 76 0.08
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:198738 original size:83 final size:83
Alignment explanation
Indices: 198598--199276 Score: 1200
Period size: 83 Copynumber: 8.2 Consensus size: 83
198588 CTTATTTCTA
* * * * *
198598 CTATGAGCAAATTCATCTTCCAAATTCAATGACTGGTTCTGTCC-AACCAGATTAGATAACTCAA
1 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTG-CCAAACCAGATCAGATAACTCAA
198662 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
198681 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
198746 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * * *
198764 CTATGAGCACATTAATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
198829 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
198847 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
198912 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
198930 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
198995 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * * *
199013 CTATGAGCACATTAATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
199078 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
199096 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
199161 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
199179 CTATGAACAAATTCATCTTCT-AATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
199243 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
199261 CTATGAGCACATTCAT
1 CTATGAACAAATTCAT
199277 TTGTTCCATT
Statistics
Matches: 572, Mismatches: 23, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
82 77 0.13
83 495 0.87
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (83 bp):
CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:206186 original size:17 final size:17
Alignment explanation
Indices: 206161--206209 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
206151 TTAATACCTG
206161 AATAATAATAAAAAAAC
1 AATAATAATAAAAAAAC
* * *
206178 AATATTAATATAAAAAT
1 AATAATAATAAAAAAAC
206195 AATAAATAATAAAAA
1 AAT-AATAATAAAAA
206210 TTTGAAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (17 bp):
AATAATAATAAAAAAAC
Found at i:206220 original size:20 final size:19
Alignment explanation
Indices: 206183--206246 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
206173 AAAACAATAT
206183 TAATATAAAAA-T-AATAAA
1 TAAT-TAAAAATTAAATAAA
206201 TAA-TAAAAATTTGAAATAAAA
1 TAATTAAAAA-TT-AAAT-AAA
*
206222 GAATTAAAAATTAAATAAA
1 TAATTAAAAATTAAATAAA
206241 TGAATT
1 T-AATT
206247 TTTAATTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
16 6 0.16
18 4 0.11
19 3 0.08
20 11 0.30
21 7 0.19
22 6 0.16
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
TAATTAAAAATTAAATAAA
Found at i:208230 original size:3 final size:3
Alignment explanation
Indices: 208222--208283 Score: 72
Period size: 3 Copynumber: 20.3 Consensus size: 3
208212 ATATATATAT
* * *
208222 ATA ATA ATA ATA ATA ATA ATA ATA ATA TTTA GTA ATA ATA A-A TTTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA -ATA
208268 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
208284 AATTTAAATG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
2 1 0.02
3 47 0.92
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:210951 original size:2 final size:2
Alignment explanation
Indices: 210944--210969 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
210934 CTGTAAGTTT
210944 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
210970 ATTACATGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:213137 original size:16 final size:16
Alignment explanation
Indices: 213113--213152 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
213103 TGATATTACA
* *
213113 TGACATGTTTTCAACC
1 TGACCTGTTATCAACC
*
213129 TGACCTGTTATGAACC
1 TGACCTGTTATCAACC
213145 TGACCTGT
1 TGACCTGT
213153 AATTGACTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (16 bp):
TGACCTGTTATCAACC
Found at i:213390 original size:38 final size:38
Alignment explanation
Indices: 213318--213401 Score: 97
Period size: 38 Copynumber: 2.3 Consensus size: 38
213308 TTAATTTTTG
213318 AAATTTAGTTTTAATATTAATTATAATTTATATATTAT
1 AAATTTAGTTTTAATATTAATTATAATTTATATATTAT
*
213356 AAATTT-GATTTTTATATTAATTCA-AATTCT-TATA-T-T
1 AAATTTAG-TTTTAATATTAATT-ATAATT-TATATATTAT
213392 AAATTTAGTT
1 AAATTTAGTT
213402 ATTGTCTTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
36 9 0.22
37 3 0.07
38 27 0.66
39 2 0.05
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (38 bp):
AAATTTAGTTTTAATATTAATTATAATTTATATATTAT
Found at i:213983 original size:23 final size:23
Alignment explanation
Indices: 213953--214000 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
213943 AACAACCGAA
*
213953 AAGCATCACTGTATCAATTCAGC
1 AAGCATCACTGCATCAATTCAGC
*
213976 AAGCATCATTGCATCAATTCAGC
1 AAGCATCACTGCATCAATTCAGC
213999 AA
1 AA
214001 ACAACATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (23 bp):
AAGCATCACTGCATCAATTCAGC
Found at i:214422 original size:42 final size:41
Alignment explanation
Indices: 214375--214476 Score: 150
Period size: 42 Copynumber: 2.4 Consensus size: 41
214365 CCAAATGCTG
*
214375 CAATAGAGTGTTAATGTAGCGACGTTTATACCACAAATGTCA
1 CAATAGAGTGTAAAT-TAGCGACGTTTATACCACAAATGTCA
* *
214417 TAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAATGTCA
1 CAATAGAGT-GTAAATTAGCGACGTTTATACCACAAATGTCA
214459 CAATAGAGTGGTAAATTA
1 CAATAGAGT-GTAAATTA
214477 ATAGCGTTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (41 bp):
CAATAGAGTGTAAATTAGCGACGTTTATACCACAAATGTCA
Found at i:214484 original size:42 final size:42
Alignment explanation
Indices: 214397--214488 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
214387 AATGTAGCGA
* * *
214397 CGTTTATACCACAAATGTCATAATAGAGTGGTAAATTAGCGG
1 CGTTTATACCACAAATGTCACAATAGAGTGGTAAATTAACAG
*
214439 CGTTTATACCACAAATGTCACAATAGAGTGGTAAATTAATAG
1 CGTTTATACCACAAATGTCACAATAGAGTGGTAAATTAACAG
214481 CGTTTATA
1 CGTTTATA
214489 TCTAAAACGC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.30
Consensus pattern (42 bp):
CGTTTATACCACAAATGTCACAATAGAGTGGTAAATTAACAG
Found at i:216438 original size:81 final size:81
Alignment explanation
Indices: 216330--216487 Score: 262
Period size: 81 Copynumber: 2.0 Consensus size: 81
216320 GCTTTAACAA
* *
216330 CGTCGCTGCCCGGTACTCAACTACTGCTGCTCGTCGCCGCTTGAAGCCGTCGTTCCTGCTGCTGC
1 CGTCGCTGCCCGGTACTCAACTACTGCTGCTCGTCGCCGCTTGAAGCCGTCATTCCTGCTGCTAC
216395 TCATCATCACCTACAC
66 TCATCATCACCTACAC
* * *
216411 CGTCGCTGCCCGGTACTCAATTGCTGCTGCTCGTCGCCGCTTGAAGCCGTCATTCTTGCTGCTAC
1 CGTCGCTGCCCGGTACTCAACTACTGCTGCTCGTCGCCGCTTGAAGCCGTCATTCCTGCTGCTAC
*
216476 TCGTCATCACCT
66 TCATCATCACCT
216488 CCATCGTTAC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 71 1.00
ACGTcount: A:0.13, C:0.38, G:0.22, T:0.28
Consensus pattern (81 bp):
CGTCGCTGCCCGGTACTCAACTACTGCTGCTCGTCGCCGCTTGAAGCCGTCATTCCTGCTGCTAC
TCATCATCACCTACAC
Found at i:222542 original size:44 final size:43
Alignment explanation
Indices: 222492--222587 Score: 131
Period size: 43 Copynumber: 2.2 Consensus size: 43
222482 CAGAATTTTA
222492 GCGGCGTTTACAT-AAAAAAACGCCACTAAATCTCAACACCTATT
1 GCGGCGTTT--ATGAAAAAAACGCCACTAAATCTCAACACCTATT
* * *
222536 GCGGCGTTTATGATAAAAATGCCGCTAAATCTCAACACCTATT
1 GCGGCGTTTATGAAAAAAACGCCACTAAATCTCAACACCTATT
*
222579 GCGACGTTT
1 GCGGCGTTT
222588 GTAAGACAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
42 2 0.04
43 36 0.77
44 9 0.19
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (43 bp):
GCGGCGTTTATGAAAAAAACGCCACTAAATCTCAACACCTATT
Found at i:222604 original size:43 final size:42
Alignment explanation
Indices: 222517--222641 Score: 126
Period size: 43 Copynumber: 2.9 Consensus size: 42
222507 AAAAACGCCA
* * **
222517 CTAAATCTCAACACCTATTGCGGCGTTTATGATAA-AAATGCCG
1 CTAAATCTCAACACCTATTGCGACGTTTGT-A-AACAAACACCG
222560 CTAAATCTCAACACCTATTGCGACGTTTGTAAGACAAACACCG
1 CTAAATCTCAACACCTATTGCGACGTTTGTAA-ACAAACACCG
* ** * *
222603 CTAAATATCAGTACCTATTACAACGTTTGTTAAACAAAC
1 CTAAATCTCAACACCTATTGCGACGTTTG-TAAACAAAC
222642 GCCCCTATAT
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.01
42 2 0.03
43 64 0.91
44 3 0.04
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (42 bp):
CTAAATCTCAACACCTATTGCGACGTTTGTAAACAAACACCG
Found at i:222654 original size:43 final size:43
Alignment explanation
Indices: 222572--222664 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 43
222562 AAATCTCAAC
* * *
222572 ACCTATTGCGACGTTTGTAAGACAAACACCGCTAAATATCAGT
1 ACCTATTACAACGTTTGTAAGACAAACACCCCTAAATATCAGT
* * *
222615 ACCTATTACAACGTTTGTTAA-ACAAACGCCCCTATATATCATT
1 ACCTATTACAACGTTTG-TAAGACAAACACCCCTAAATATCAGT
222658 ACCTATT
1 ACCTATT
222665 GCGGCATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 40 0.93
44 3 0.07
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (43 bp):
ACCTATTACAACGTTTGTAAGACAAACACCCCTAAATATCAGT
Found at i:222908 original size:20 final size:20
Alignment explanation
Indices: 222883--222940 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
222873 AACCCTTACA
*
222883 AATATCAAGCAGAATCAAAC
1 AATATCAAACAGAATCAAAC
*
222903 AATATCAAATAGAAGT-AAAC
1 AATATCAAACAGAA-TCAAAC
*
222923 AATATAAAACAGAATCAA
1 AATATCAAACAGAATCAA
222941 GCATAATCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.60, C:0.14, G:0.09, T:0.17
Consensus pattern (20 bp):
AATATCAAACAGAATCAAAC
Found at i:225566 original size:47 final size:47
Alignment explanation
Indices: 225485--225574 Score: 117
Period size: 47 Copynumber: 1.9 Consensus size: 47
225475 AAGGGTTAGA
* * * * * *
225485 GTTATAAAAGATGAACAGAGACAGAAGATGAAGAGGCTTGGTTTGGG
1 GTTAGAAAAGATGAACAAAAACAGAAAATAAAGAGGCTAGGTTTGGG
*
225532 GTTAGAAAAGATGAACAAAAATAGAAAATAAAGAGGCTAGGTT
1 GTTAGAAAAGATGAACAAAAACAGAAAATAAAGAGGCTAGGTT
225575 AGGGTTTGGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 36 1.00
ACGTcount: A:0.46, C:0.06, G:0.29, T:0.20
Consensus pattern (47 bp):
GTTAGAAAAGATGAACAAAAACAGAAAATAAAGAGGCTAGGTTTGGG
Found at i:225622 original size:53 final size:53
Alignment explanation
Indices: 225524--225633 Score: 130
Period size: 53 Copynumber: 2.1 Consensus size: 53
225514 GAAGAGGCTT
* * *
225524 GGTTTGGGGTTAGAAAAGATGAACAAAAATAGAAAATAAAGAGGCTAGGTTAG
1 GGTTTGGGATTAGAAAAGATGAACAAAAACAGAAAATAAAGAGGCTAGATTAG
* ** * * * *
225577 GGTTTGGGATTAGAAAGGATGAACAAAGGCAGAAAGTGAATAGGCTCGATTAG
1 GGTTTGGGATTAGAAAAGATGAACAAAAACAGAAAATAAAGAGGCTAGATTAG
225630 GGTT
1 GGTT
225634 CAGGTTCAGA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.40, C:0.05, G:0.33, T:0.22
Consensus pattern (53 bp):
GGTTTGGGATTAGAAAAGATGAACAAAAACAGAAAATAAAGAGGCTAGATTAG
Found at i:225653 original size:6 final size:6
Alignment explanation
Indices: 225644--225762 Score: 85
Period size: 6 Copynumber: 19.8 Consensus size: 6
225634 CAGGTTCAGA
* * * * * *
225644 TTTGGG TTTGGG TTTGGT TTTGGA TTTGAG TTTAGG TTCGGA TTTGGG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
* * * * * ** *
225692 TTTGGG TTCGGG TTCGGG TTTGGT TTTAGG TTTAGG TTCAGG TTTAGG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
* * *
225740 TTCGTG TTTGGG CTTGGG TTTGG
1 TTTGGG TTTGGG TTTGGG TTTGG
225763 TGATAACTTC
Statistics
Matches: 88, Mismatches: 25, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 88 1.00
ACGTcount: A:0.07, C:0.05, G:0.40, T:0.48
Consensus pattern (6 bp):
TTTGGG
Found at i:227551 original size:12 final size:12
Alignment explanation
Indices: 227534--227577 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
227524 CAAGCAATCA
*
227534 TTTGGGTTCAAG
1 TTTGGGTTCTAG
*
227546 TTTGGGTTCTGG
1 TTTGGGTTCTAG
227558 TTTGGGTTCTAG
1 TTTGGGTTCTAG
227570 TTTGGGTT
1 TTTGGGTT
227578 AGGATTAGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.07, C:0.07, G:0.36, T:0.50
Consensus pattern (12 bp):
TTTGGGTTCTAG
Found at i:227588 original size:24 final size:24
Alignment explanation
Indices: 227537--227589 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
227527 GCAATCATTT
* *
227537 GGGTTCAAGTTTGGGTTCTGGTTT
1 GGGTTCAAGTTTGGGTTCAGGTTA
*
227561 GGGTTCTAGTTTGGGTT-AGGATTA
1 GGGTTCAAGTTTGGGTTCAGG-TTA
227585 GGGTT
1 GGGTT
227590 AGAGAAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.11, C:0.06, G:0.40, T:0.43
Consensus pattern (24 bp):
GGGTTCAAGTTTGGGTTCAGGTTA
Found at i:228297 original size:59 final size:60
Alignment explanation
Indices: 228231--228365 Score: 218
Period size: 59 Copynumber: 2.2 Consensus size: 60
228221 TCCTAGTTTT
228231 AAATTTGTTCAATTTAGCCCAAATTTAATGATGCAATGTATTAATTTAAGCTTC-ATTTA
1 AAATTTGTTCAATTTAGCCCAAATTTAATGATGCAATGTATTAATTTAAGCTTCAATTTA
* * * *
228290 AAATTTGTTCAATTTAGTCCAAATTTAATGTTGCAATTTATTAATTTTAGCTTCATATTTA
1 AAATTTGTTCAATTTAGCCCAAATTTAATGATGCAATGTATTAATTTAAGCTTCA-ATTTA
228351 AAATTTGTTCAATTT
1 AAATTTGTTCAATTT
228366 GATCCTTATA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 50 0.71
61 20 0.29
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (60 bp):
AAATTTGTTCAATTTAGCCCAAATTTAATGATGCAATGTATTAATTTAAGCTTCAATTTA
Found at i:228458 original size:2 final size:2
Alignment explanation
Indices: 228453--228493 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
228443 ACTAATGATT
228453 TA TA TA CTA 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
228494 GTTCATATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:228519 original size:18 final size:18
Alignment explanation
Indices: 228462--228539 Score: 81
Period size: 18 Copynumber: 4.3 Consensus size: 18
228452 TTATATACTA
*
228462 TATATATATA-TATATA-
1 TATATATAAACTATATAG
*
228478 TATATATATA-TATATAG
1 TATATATAAACTATATAG
*
228495 TTCATATGTAAACTATATAG
1 -T-ATATATAAACTATATAG
228515 TATATATAAACTATATAG
1 TATATATAAACTATATAG
228533 TAGTATA
1 TA-TATA
228540 CTGTATAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
16 16 0.30
18 19 0.35
19 12 0.22
20 7 0.13
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (18 bp):
TATATATAAACTATATAG
Found at i:228752 original size:20 final size:19
Alignment explanation
Indices: 228719--228779 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
228709 ATATAGTTTT
*
228719 TATATAGT-TCATATGTAAA
1 TATATAGTAT-ATATATAAA
* *
228738 CTATATAGTATATATTTATA
1 -TATATAGTATATATATAAA
228758 TATATA-TATATATATAAA
1 TATATAGTATATATATAAA
228776 TATA
1 TATA
228780 ACTATACTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 14 0.39
19 6 0.17
20 15 0.42
21 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (19 bp):
TATATAGTATATATATAAA
Found at i:228767 original size:18 final size:18
Alignment explanation
Indices: 228739--228850 Score: 63
Period size: 18 Copynumber: 6.1 Consensus size: 18
228729 ATATGTAAAC
228739 TATATAGTATATATTTATA
1 TATATA-TATATATTTATA
* *
228758 TATATATATATATATAAA
1 TATATATATATATTTATA
*
228776 TATA-ACTATACTA-GTATA
1 TATATA-TATA-TATTTATA
* *
228794 TATAAAAACTATATTTATA
1 TATATATA-TATATTTATA
*
228813 GT-T-TATATATA-GTATA
1 -TATATATATATATTTATA
*
228829 TACTATATAAATAGTTTATA
1 TA-TATATATATA-TTTATA
228849 TA
1 TA
228851 GTTCATTAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
15 1 0.01
16 4 0.06
17 6 0.08
18 37 0.52
19 16 0.23
20 7 0.10
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (18 bp):
TATATATATATATTTATA
Found at i:228850 original size:2 final size:2
Alignment explanation
Indices: 228739--228837 Score: 65
Period size: 2 Copynumber: 46.0 Consensus size: 2
228729 ATATGTAAAC
* *
228739 TA TA TA GTA TA TA TT TA TA TA TA TA TA TA TA TA TA AA TA TA -A
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
228781 CTA TA CTA GTA TA TA TA AA AA CTA TA TT TA TA GTT TA TA TA TA GTA
1 -TA TA -TA -TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA -TA
228827 TA TA CTA TA TA
1 TA TA -TA TA TA
228838 AATAGTTTAT
Statistics
Matches: 78, Mismatches: 11, Indels: 16
0.74 0.10 0.15
Matches are distributed among these distances:
1 1 0.01
2 64 0.82
3 13 0.17
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:228863 original size:64 final size:61
Alignment explanation
Indices: 228676--228872 Score: 153
Period size: 64 Copynumber: 3.2 Consensus size: 61
228666 TATAAATATC
* * * **
228676 AACTATATAAACTATAATTTATATAGT-T-TATATATAT-AGTTTTTATATAGTTCAT-ATGTA
1 AACTATATATA-TAT-ATTTATATA-TATATATATATATAAATATTTATATAGTTCATAATAAA
*
228736 AACTATATAGTATATATTTATATATATATATATATATAAATATAACTATACTAG-T-ATATATAA
1 AACTATATA-TATATATTTATATATATATATATATATAAATAT--TTATA-TAGTTCATA-ATAA
228799 A
61 A
228800 AACTATAT-T-TATAGTTTATATATAGTATATACTATATAAATAGTTTATATAGTTCAT--TAAT
1 AACTATATATATATA-TTTATATATA-TATATA-TATATAAATA-TTTATATAGTTCATAATAA-
228861 A
61 A
228862 AACTATATATA
1 AACTATATATA
228873 GTTCATAAGT
Statistics
Matches: 112, Mismatches: 7, Indels: 32
0.74 0.05 0.21
Matches are distributed among these distances:
58 1 0.01
59 10 0.09
60 21 0.19
61 11 0.10
62 25 0.22
63 17 0.15
64 26 0.23
65 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (61 bp):
AACTATATATATATATTTATATATATATATATATATAAATATTTATATAGTTCATAATAAA
Found at i:228870 original size:22 final size:22
Alignment explanation
Indices: 228845--228892 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
228835 ATAAATAGTT
228845 TATATAGTTCATTAA-TAAACTA
1 TATATAGTTCA-TAAGTAAACTA
228867 TATATAGTTCATAAGTAAACTA
1 TATATAGTTCATAAGTAAACTA
228889 TATA
1 TATA
228893 GTTTATATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (22 bp):
TATATAGTTCATAAGTAAACTA
Found at i:228967 original size:33 final size:33
Alignment explanation
Indices: 228887--228955 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 33
228877 ATAAGTAAAC
* *
228887 TATATAGTTTATATAGCTTATATATATATAGTT
1 TATATGGTATATATAGCTTATATATATATAGTT
*
228920 TATATGGTACATATAG-TT-TATATATATAGTT
1 TATATGGTATATATAGCTTATATATATATAGTT
228951 TATAT
1 TATAT
228956 ATGTAGTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 18 0.55
32 2 0.06
33 13 0.39
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (33 bp):
TATATGGTATATATAGCTTATATATATATAGTT
Found at i:228969 original size:15 final size:15
Alignment explanation
Indices: 228739--228982 Score: 77
Period size: 15 Copynumber: 15.9 Consensus size: 15
228729 ATATGTAAAC
*
228739 TATATAGTATATATT
1 TATATAGTATATATA
228754 TATATA-TATATATA
1 TATATAGTATATATA
*
228768 TATATA-AATATA-A
1 TATATAGTATATATA
228781 CTATACTAGTATATATAAA
1 -TATA-TAGTATATAT--A
* * *
228800 AACTATATTTATAGTTTA
1 TA-TATA-GTATA-TATA
228818 TATATAGTATATACTA
1 TATATAGTATATA-TA
228834 TATAAATAGT-T-TATA
1 TAT--ATAGTATATATA
* *
228849 TAGT-TCATTAATAAACTA
1 TA-TAT-AGT-ATATA-TA
228867 TATATAGT-TCATA-A
1 TATATAGTAT-ATATA
* *
228881 GTA-A-ACTATATAGTT
1 -TATATAGTATATA-TA
228896 TATATAGCT-TATATA
1 TATATAG-TATATATA
*
228911 TATATAGTTTATATGGTA
1 TATATAG--TATAT-ATA
*
228929 CATATAGT-T-TATA
1 TATATAGTATATATA
228942 TATATAGT-T-TATA
1 TATATAGTATATATA
*
228955 TATGTAGTATATATA
1 TATATAGTATATATA
*
228970 TACATAGTATATA
1 TATATAGTATATA
228983 GTTCTTACGT
Statistics
Matches: 172, Mismatches: 25, Indels: 64
0.66 0.10 0.25
Matches are distributed among these distances:
13 28 0.16
14 31 0.18
15 41 0.24
16 27 0.16
17 13 0.08
18 23 0.13
19 7 0.04
20 2 0.01
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (15 bp):
TATATAGTATATATA
Found at i:228980 original size:13 final size:13
Alignment explanation
Indices: 228695--228982 Score: 81
Period size: 13 Copynumber: 22.0 Consensus size: 13
228685 AACTATAATT
*
228695 TATATAGTTTATA
1 TATATAGTATATA
*
228708 TATATAGT-T-TT
1 TATATAGTATATA
228719 TATATAGT-TCATA
1 TATATAGTAT-ATA
* * *
228732 TGTAAACTATATA
1 TATATAGTATATA
*
228745 GTATATA-TTTATA
1 -TATATAGTATATA
228758 TATATA-TATATA
1 TATATAGTATATA
*
228770 TATA-AATATA-A
1 TATATAGTATATA
228781 CTATACTAGTATATA
1 -TATA-TAGTATATA
* * *
228796 TAAAAACTATAT-
1 TATATAGTATATA
228808 T-TATAGT-T-TA
1 TATATAGTATATA
228818 TATATAGTATATA
1 TATATAGTATATA
* *
228831 CTATATA-AATAGTT
1 -TATATAGTATA-TA
228845 TATATAGT-TCAT-
1 TATATAGTAT-ATA
* *
228857 TAATAAACTATATA
1 T-ATATAGTATATA
228871 TAGTTCATAAGTA-A-A
1 TA--T-AT-AGTATATA
*
228886 CTATATAGTTTATA
1 -TATATAGTATATA
228900 TAGCTTATA-TATATA
1 TA---TATAGTATATA
* *
228915 TAGTTTA-TATGGTA
1 TA-TATAGTAT-ATA
* *
228929 CATATAGTTTATA
1 TATATAGTATATA
*
228942 TATATAGTTTATA
1 TATATAGTATATA
*
228955 TATGTAGTATATA
1 TATATAGTATATA
228968 TATACATAGTATATA
1 TAT--ATAGTATATA
228983 GTTCTTACGT
Statistics
Matches: 205, Mismatches: 36, Indels: 66
0.67 0.12 0.21
Matches are distributed among these distances:
9 1 0.00
10 2 0.01
11 21 0.10
12 30 0.15
13 91 0.44
14 30 0.15
15 19 0.09
16 8 0.04
17 3 0.01
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.46
Consensus pattern (13 bp):
TATATAGTATATA
Found at i:229032 original size:9 final size:9
Alignment explanation
Indices: 228887--228943 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
228877 ATAAGTAAAC
228887 TATATAGTT
1 TATATAGTT
*
228896 TATATAGCT
1 TATATAGTT
228905 TATATA---
1 TATATAGTT
228911 TATATAGTT
1 TATATAGTT
* *
228920 TATATGGTA
1 TATATAGTT
*
228929 CATATAGTT
1 TATATAGTT
228938 TATATA
1 TATATA
228944 TATAGTTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
6 6 0.16
9 32 0.84
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.49
Consensus pattern (9 bp):
TATATAGTT
Found at i:229092 original size:110 final size:107
Alignment explanation
Indices: 228868--229126 Score: 276
Period size: 110 Copynumber: 2.4 Consensus size: 107
228858 AATAAACTAT
*
228868 ATATAGTTCATAAGTAAACTATATAGTTTATATAGCTTATATATATATAGTTTATATGGTACATA
1 ATATAGTTCATAAGTAAACTATATAGTTTATATAG-TT-TATATATATAGTTCATATGGTACATA
* * * * *
228933 TAGTTTATATATATAGTTTATATATGTAGTATATATATACATAGT
64 AACTTTATATATATAGTTTACATATGTA-TATATAGATACATAGC
* *
228978 ATATAGTTCTTACGTAAACTATATAGTTTATATAGTTTATATATATAGTTCATAT-GTAAACTAC
1 ATATAGTTCATAAGTAAACTATATAGTTTATATAGTTTATATATATAGTTCATATGGT--AC-A-
*
229042 TAAACTATATATATTATATAGTTTACATA-GT-T-TATAGATAGTATA-C
62 TAAACT-T-TATA-TATATAGTTTACATATGTATATATAGATA-CATAGC
* * *
229088 ATATAGTTCATATGTAAACTATATAGTATATATTGTTTA
1 ATATAGTTCATAAGTAAACTATATAGTTTATATAGTTTA
229127 CATGTAACAC
Statistics
Matches: 128, Mismatches: 13, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
107 2 0.02
108 17 0.13
109 4 0.03
110 76 0.59
111 8 0.06
112 1 0.01
113 6 0.05
114 14 0.11
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (107 bp):
ATATAGTTCATAAGTAAACTATATAGTTTATATAGTTTATATATATAGTTCATATGGTACATAAA
CTTTATATATATAGTTTACATATGTATATATAGATACATAGC
Found at i:229726 original size:54 final size:54
Alignment explanation
Indices: 229668--230139 Score: 714
Period size: 54 Copynumber: 8.8 Consensus size: 54
229658 ATTAAGTGAT
** * *
229668 TTGCACACCCAGTACCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
* * ** *
229722 TTGCACAAATAGTGCCAATACGAAAATTCATAAACAAATTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
* *
229776 TTGCACACATAGTGCCAATACAGAAATTCATAAATTCATTATGAA-TTCTTAAG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
* *
229829 TTGCACACATAGTGTCAATACAGAAATTCATAAACTCATTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
* * *
229883 TTACACACATAGTGCCAATACGGAAATTCATAAACTCATTATGGATTTATTAAG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
*
229937 TTGCACACATAGTGCTAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
*
229991 TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
* * *
230045 TTGCACACATAGTGCCAATATGGAAATACATAAACTCATTATAAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
* *
230099 TTGCACACATAGTGCCAATTA-GAAAATTTATAAACTCATTA
1 TTGCACACATAGTGCCAA-TACGGAAATTCATAAACTCATTA
230140 AGCAACATGC
Statistics
Matches: 381, Mismatches: 35, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
53 50 0.13
54 329 0.86
55 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (54 bp):
TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
Found at i:240093 original size:54 final size:54
Alignment explanation
Indices: 240031--240475 Score: 698
Period size: 54 Copynumber: 8.2 Consensus size: 54
240021 GGGGTATACA
*
240031 CATAAACTCATTATGAATATT-TTAGGTTGCACACATAGTGCCAATACAGAAATT
1 CATAAACTCATTATGAAT-TTCTTAAGTTGCACACATAGTGCCAATACAGAAATT
* *
240085 CATAAACTCATTATGAA-TTCTTAAGTAGCACACATAGTGTCAATACAGAAATT
1 CATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACAGAAATT
*
240138 CATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGGAAATT
1 CATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACAGAAATT
*
240192 CATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATAC-GAAAACT
1 CATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACAG-AAATT
* *
240246 CATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAAAAACT
1 CATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATAC-AGAAATT
* *
240301 CATAAACTCATTATGAATTTCTTAAGTTGCACAGATAGTGCTAATACAGAAATT
1 CATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACAGAAATT
* **
240355 CATAAACTCTTTATGAATTTCTTAAGTTGCACACATAGTGCCAATATGGAAATT
1 CATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACAGAAATT
* *
240409 CATAAACTCATTATAAATTTCTTAAGTTGCACACATAGTGCCAATACGGAAATT
1 CATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACAGAAATT
* *
240463 AATAAACTTATTA
1 CATAAACTCATTA
240476 AGCAGCATGC
Statistics
Matches: 364, Mismatches: 22, Indels: 10
0.92 0.06 0.03
Matches are distributed among these distances:
52 2 0.01
53 48 0.13
54 264 0.73
55 50 0.14
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.32
Consensus pattern (54 bp):
CATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACAGAAATT
Found at i:240371 original size:163 final size:163
Alignment explanation
Indices: 240031--240456 Score: 689
Period size: 163 Copynumber: 2.6 Consensus size: 163
240021 GGGGTATACA
*
240031 CATAAACTCATTATGAATATT-TTAGGTTGCACACATAGTGCCAATAC-AGAAATTCATAAACTC
1 CATAAACTCATTATGAAT-TTCTTAAGTTGCACACATAGTGCCAATACGA-AAATTCATAAACTC
* * * *
240094 ATTATGAA-TTCTTAAGTAGCACACATAGTGTCAATAC-AGAAATTCATAAACTCATTATGAATT
64 ATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAAAAACTCATAAACTCATTATGAATT
*
240157 TCTTAAGTTGCACACATAGTGCCAATACGGAAATT
129 TCTTAAGTTGCACACATAGTGCCAATACAGAAATT
*
240192 CATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAAAACTCATAAACTCAT
1 CATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAAAATTCATAAACTCAT
240257 TATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAAAAACTCATAAACTCATTATGAATTTC
66 TATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAAAAACTCATAAACTCATTATGAATTTC
* *
240322 TTAAGTTGCACAGATAGTGCTAATACAGAAATT
131 TTAAGTTGCACACATAGTGCCAATACAGAAATT
* * *
240355 CATAAACTCTTTATGAATTTCTTAAGTTGCACACATAGTGCCAATATGGAAATTCATAAACTCAT
1 CATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAAAATTCATAAACTCAT
*
240420 TATAAATTTCTTAAGTTGCACACATAGTGCCAATACG
66 TATGAATTTCTTAAGTTGCACACATAGTGCCAATACG
240457 GAAATTAATA
Statistics
Matches: 247, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
160 2 0.01
161 64 0.26
162 28 0.11
163 153 0.62
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.31
Consensus pattern (163 bp):
CATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAAAATTCATAAACTCAT
TATGAATTTCTTAAGTTGCACACATAGTGCCAATACGAAAAACTCATAAACTCATTATGAATTTC
TTAAGTTGCACACATAGTGCCAATACAGAAATT
Found at i:240408 original size:217 final size:215
Alignment explanation
Indices: 240031--240475 Score: 732
Period size: 217 Copynumber: 2.1 Consensus size: 215
240021 GGGGTATACA
* * *
240031 CATAAACTCATTATGAATATTTTAGGTTGCACACATAGTGCCAATACAGAAATTCATAAACTCAT
1 CATAAACTCATTATGAATATTTTAAGTTGCACACATAGTGCCAATACAAAAACTCATAAACTCAT
240096 TATGAATTCTTAAGTAGCACACATAGTGTCAATACAGAAATTCATAAACTCATTATGAATTTCTT
66 TATGAATTCTTAAGTAGCACACATAGTGTCAATACAGAAATTCATAAACTCATTATGAATTTCTT
*
240161 AAGTTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACAC
131 AAGTTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATAAATTTCTTAAGTTGCACAC
240226 ATAGTGCCAATACGAAAACT
196 ATAGTGCCAATACGAAAACT
240246 CATAAACTCATTATGAAT-TTCTTAAGTTGCACACATAGTGCCAATACGAAAAACTCATAAACTC
1 CATAAACTCATTATGAATATT-TTAAGTTGCACACATAGTGCCAATAC-AAAAACTCATAAACTC
* * *
240310 ATTATGAATTTCTTAAGTTGCACAGATAGTG-CTAATACAGAAATTCATAAACTCTTTATGAATT
64 ATTATGAA-TTCTTAAGTAGCACACATAGTGTC-AATACAGAAATTCATAAACTCATTATGAATT
*
240374 TCTTAAGTTGCACACATAGTGCCAATATGGAAATTCATAAACTCATTATAAATTTCTTAAGTTGC
127 TCTTAAGTTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATAAATTTCTTAAGTTGC
* *
240439 ACACATAGTGCCAATACGGAAATT
192 ACACATAGTGCCAATACGAAAACT
* *
240463 AATAAACTTATTA
1 CATAAACTCATTA
240476 AGCAGCATGC
Statistics
Matches: 214, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
214 2 0.01
215 43 0.20
216 23 0.11
217 146 0.68
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.32
Consensus pattern (215 bp):
CATAAACTCATTATGAATATTTTAAGTTGCACACATAGTGCCAATACAAAAACTCATAAACTCAT
TATGAATTCTTAAGTAGCACACATAGTGTCAATACAGAAATTCATAAACTCATTATGAATTTCTT
AAGTTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATAAATTTCTTAAGTTGCACAC
ATAGTGCCAATACGAAAACT
Found at i:240913 original size:19 final size:19
Alignment explanation
Indices: 240889--240926 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
240879 ATCGATACTT
* *
240889 TTATATTATGGTATCGATA
1 TTATATTATAGTATAGATA
240908 TTATATTATAGTATAGATA
1 TTATATTATAGTATAGATA
240927 CCATTTCTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (19 bp):
TTATATTATAGTATAGATA
Found at i:241865 original size:18 final size:18
Alignment explanation
Indices: 241842--242225 Score: 87
Period size: 18 Copynumber: 20.3 Consensus size: 18
241832 TATATACTAC
*
241842 TATATACTATATAGTTTA
1 TATATACTATATAATTTA
*
241860 TATATAATTCATATAAAATTTA
1 TATAT-A--C-TATATAATTTA
*
241882 TATAAACTATATAATTTA
1 TATATACTATATAATTTA
241900 TAT-TA--A-A-AATTATA
1 TATATACTATATAATT-TA
* *
241914 CAATATAC-A-ATAATATAA
1 -TATATACTATATAAT-TTA
* *
241932 TATAAACTATATAGTTTA
1 TATATACTATATAATTTA
*
241950 TACATATA-TATATATATATA
1 T--ATATACTATATA-ATTTA
*
241970 TATATA-TATACACACTTTA
1 TATATACTATATA-A-TTTA
* *
241989 TATACAGTATATAATAATATA
1 TATATACTATATAAT--T-TA
* * *
242010 AATATAAATATATAGTTTA
1 TATAT-ACTATATAATTTA
*
242029 TATATAATATATATACTTTA
1 TATATACTATATA-A-TTTA
* * *
242049 TATAAAACTATTTAGTTTATA
1 TAT-ATACTATATA-ATT-TA
*
242070 TATATATTATTATATAGTTTA
1 TATATACTA-TATA-A-TTTA
*
242091 TATATA-TATTATAATTATT
1 TATATACTA-TATAATT-TA
* ** *
242110 TCAAAGTTTTATATAGTTTA
1 T-ATA-TACTATATAATTTA
*
242130 TAT-TA--ATATAGTTTA
1 TATATACTATATAATTTA
* * *
242145 TACATAATATATAGTTTA
1 TATATACTATATAATTTA
*
242163 TATATAC-ACTATATAGTTA
1 TATATACTA-TATA-ATTTA
*
242182 TATAATA-TATATACTTTA
1 TAT-ATACTATATAATTTA
*
242200 TATATAAACTATATAGTTTA
1 TATAT--ACTATATAATTTA
242220 TATATA
1 TATATA
242226 GTTTATAAAC
Statistics
Matches: 275, Mismatches: 50, Indels: 82
0.68 0.12 0.20
Matches are distributed among these distances:
13 4 0.01
14 3 0.01
15 15 0.05
16 4 0.01
17 12 0.04
18 74 0.27
19 43 0.16
20 58 0.21
21 37 0.13
22 25 0.09
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (18 bp):
TATATACTATATAATTTA
Found at i:241958 original size:2 final size:2
Alignment explanation
Indices: 241926--242103 Score: 84
Period size: 2 Copynumber: 88.5 Consensus size: 2
241916 ATATACAATA
* * *
241926 AT AT A- AT AT AA ACT AT AT AGT TT AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * * * *
241969 AT AT AT AT AT AC AC ACT TT AT AT AC AGT AT AT A- AT A- AT AT AA
1 AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * *
242011 AT AT AA AT AT AT AGT TT AT AT AT A- AT AT AT AT ACT TT AT AT A-
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * *
242053 AA ACT AT TT AGT TT AT AT AT AT AT -T AT -T AT AT AGT TT AT AT
1 AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
242094 AT AT AT -T AT A
1 AT AT AT AT AT A
242104 ATTATTTCAA
Statistics
Matches: 132, Mismatches: 27, Indels: 34
0.68 0.14 0.18
Matches are distributed among these distances:
1 8 0.06
2 116 0.88
3 8 0.06
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:242031 original size:11 final size:11
Alignment explanation
Indices: 242017--242232 Score: 59
Period size: 11 Copynumber: 21.3 Consensus size: 11
242007 ATAAATATAA
242017 ATATATAGTTT
1 ATATATAGTTT
*
242028 ATATATA--AT
1 ATATATAGTTT
*
242037 ATATATACTTT
1 ATATATAGTTT
***
242048 ATATA-AAACT
1 ATATATAGTTT
242058 AT-T-TAGTTT
1 ATATATAGTTT
242067 ATATATA-TATT
1 ATATATAGT-TT
242078 ATTATATAGTTT
1 A-TATATAGTTT
242090 ATATATA-TATT
1 ATATATAGT-TT
242101 ATA-ATTA-TTT
1 ATATA-TAGTTT
*
242111 -CA-A-AGTTT
1 ATATATAGTTT
242119 -TATATAGTTT
1 ATATATAGTTT
* *
242129 ATAT-TAATAT
1 ATATATAGTTT
* ** *
242139 AGTTTATACATA
1 A-TATATAGTTT
242151 ATATATAGTTT
1 ATATATAGTTT
*
242162 ATATATA---C
1 ATATATAGTTT
242170 ACTATATAG-TT
1 A-TATATAGTTT
242181 ATATA-A---T
1 ATATATAGTTT
*
242188 ATATATACTTT
1 ATATATAGTTT
*
242199 ATATATA---A
1 ATATATAGTTT
242207 ACTATATAGTTT
1 A-TATATAGTTT
242219 ATATATAGTTT
1 ATATATAGTTT
242230 ATA
1 ATA
242233 AACGTATCTC
Statistics
Matches: 153, Mismatches: 25, Indels: 54
0.66 0.11 0.23
Matches are distributed among these distances:
7 7 0.05
8 7 0.05
9 29 0.19
10 24 0.16
11 72 0.47
12 13 0.08
13 1 0.01
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.50
Consensus pattern (11 bp):
ATATATAGTTT
Found at i:242031 original size:23 final size:23
Alignment explanation
Indices: 242005--242099 Score: 71
Period size: 23 Copynumber: 4.4 Consensus size: 23
241995 GTATATAATA
242005 ATATAAATATAAATATATAGTTT
1 ATATAAATATAAATATATAGTTT
* *
242028 ATAT--ATA-ATATATATACTTT
1 ATATAAATATAAATATATAGTTT
242048 ATATAAA-ACT--AT-T-TAGTTT
1 ATATAAATA-TAAATATATAGTTT
* * *
242067 ATATATATATTATTATATAGTTT
1 ATATAAATATAAATATATAGTTT
*
242090 ATATATATAT
1 ATATAAATAT
242100 TATAATTATT
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
19 12 0.21
20 17 0.29
21 7 0.12
22 2 0.03
23 20 0.34
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (23 bp):
ATATAAATATAAATATATAGTTT
Found at i:242175 original size:20 final size:18
Alignment explanation
Indices: 241939--242225 Score: 138
Period size: 20 Copynumber: 14.9 Consensus size: 18
241929 TAATATAAAC
241939 TATATAGTTTATACATATATA
1 TATATAGTTTAT--ATATA-A
*
241960 TATATA-TATATATATATA
1 TATATAGTTTATATATA-A
* * * *
241978 TACACACTTTATATACAGTA
1 TATATAGTTTATATATA--A
* * *
241998 TATAATAATATAAATATAAA
1 TAT-ATAGTTTATATAT-AA
242018 TATATAGTTTATATATAATA
1 TATATAGTTTATATAT-A-A
* *
242038 TATATACTTTATATAAAA
1 TATATAGTTTATATATAA
*
242056 CTATTTAGTTTATATATATATTA
1 -TATATAG-TT-TATATATA--A
242079 TTATATAGTTTATATAT-A
1 -TATATAGTTTATATATAA
* * * **
242097 TATTATAATTATTTCAAAGTTT
1 TA-TATAGTT-TAT-ATA-TAA
242119 TATATAGTTTATAT-T-A
1 TATATAGTTTATATATAA
*
242135 -ATATAGTTTATACATAA
1 TATATAGTTTATATATAA
242152 TATATAGTTTATATATACA
1 TATATAGTTTATATATA-A
242171 CTATATAG-TTATATA-ATA
1 -TATATAGTTTATATATA-A
*
242189 TATATACTTTATATATAAA
1 TATATAGTTTATATAT-AA
242208 CTATATAGTTTATATATA
1 -TATATAGTTTATATATA
242226 GTTTATAAAC
Statistics
Matches: 208, Mismatches: 34, Indels: 50
0.71 0.12 0.17
Matches are distributed among these distances:
15 12 0.06
16 1 0.00
17 10 0.05
18 43 0.21
19 39 0.19
20 56 0.27
21 35 0.17
22 5 0.02
23 7 0.03
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.48
Consensus pattern (18 bp):
TATATAGTTTATATATAA
Found at i:242177 original size:13 final size:13
Alignment explanation
Indices: 242143--242214 Score: 55
Period size: 13 Copynumber: 5.8 Consensus size: 13
242133 TAATATAGTT
242143 TATAC-ATA-ATA
1 TATACTATATATA
* *
242154 TATAGTTTATATA
1 TATACTATATATA
*
242167 TACACTATATAGT-
1 TATACTATATA-TA
242180 TATA-TA-ATATA
1 TATACTATATATA
*
242191 TATACTTTATATA
1 TATACTATATATA
*
242204 TAAACTATATA
1 TATACTATATA
242215 GTTTATATAT
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
10 1 0.02
11 11 0.24
12 5 0.11
13 28 0.61
14 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (13 bp):
TATACTATATATA
Found at i:242190 original size:15 final size:16
Alignment explanation
Indices: 242119--242192 Score: 71
Period size: 15 Copynumber: 4.4 Consensus size: 16
242109 TTCAAAGTTT
*
242119 TATATAGTTTATATTA
1 TATATAGTTTATATAA
242135 -ATATAGTTTATACATAA
1 TATATAGTTTAT--ATAA
242152 TATATAGTTTATATATACA
1 TATATAG-TT-TATATA-A
242171 CTATATAG-TTATATAA
1 -TATATAGTTTATATAA
242187 TATATA
1 TATATA
242193 TACTTTATAT
Statistics
Matches: 50, Mismatches: 1, Indels: 15
0.76 0.02 0.23
Matches are distributed among these distances:
15 17 0.34
16 1 0.02
17 9 0.18
18 10 0.20
19 3 0.06
20 10 0.20
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.47
Consensus pattern (16 bp):
TATATAGTTTATATAA
Found at i:243911 original size:21 final size:20
Alignment explanation
Indices: 243886--243925 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
243876 CTCCACATTA
243886 GTATCAATACTTCTTCATTCG
1 GTATCAATA-TTCTTCATTCG
* *
243907 GTATCGATATTGTTCATTC
1 GTATCAATATTCTTCATTC
243926 TATTCATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.23, C:0.20, G:0.12, T:0.45
Consensus pattern (20 bp):
GTATCAATATTCTTCATTCG
Done.