Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000692.1 Hibiscus syriacus cultivar Beakdansim tig00001349_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: 1095174
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 5
Found at i:207203 original size:20 final size:20
Alignment explanation
Indices: 207178--207289 Score: 109
Period size: 20 Copynumber: 5.5 Consensus size: 20
207168 TTTTCATAAT
207178 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * * *
207198 TCGCAACGCGATTAGGAAAA
1 TCGCAATGCGAATACGTAAA
* * * *
207218 TCACAATACGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
207239 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
207259 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
207279 TCGCAATGCGA
1 TCGCAATGCGA
207290 TTTACATAGC
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
19 3 0.04
20 55 0.72
21 18 0.24
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:207233 original size:21 final size:21
Alignment explanation
Indices: 207208--207251 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
207198 TCGCAACGCG
207208 ATTAGGAAAATCACAATACGA
1 ATTAGGAAAATCACAATACGA
* *
207229 ATTAGGAAAATCGCAATGCGA
1 ATTAGGAAAATCACAATACGA
207250 AT
1 AT
207252 ACGTAAATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (21 bp):
ATTAGGAAAATCACAATACGA
Found at i:207886 original size:19 final size:19
Alignment explanation
Indices: 207864--208056 Score: 93
Period size: 19 Copynumber: 11.1 Consensus size: 19
207854 GAAACCAAAA
*
207864 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
207883 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
207899 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
207916 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
207930 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
207949 TTGCGTTACGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
207963 TCTCGTTGTGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
207982 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
207996 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
208015 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
208035 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
208055 TC
1 TC
208057 AACCAAAAGA
Statistics
Matches: 128, Mismatches: 24, Indels: 44
0.65 0.12 0.22
Matches are distributed among these distances:
14 34 0.27
16 12 0.09
17 13 0.10
19 37 0.29
20 31 0.24
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:207905 original size:14 final size:14
Alignment explanation
Indices: 207886--208007 Score: 55
Period size: 14 Copynumber: 7.6 Consensus size: 14
207876 TTTCATTTCG
*
207886 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
207900 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
207919 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
207933 CGTTGCGATTTTCATTTT
1 CGTTGCGA--TTC--TCT
*
207951 GCGTTACGATTCTCT
1 -CGTTGCGATTCTCT
* *
207966 CGTTGTGATAGTCATTT
1 CGTTGCGAT--TC-TCT
207983 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
207999 CGTTGCGAT
1 CGTTGCGAT
208008 AGTCATTTCC
Statistics
Matches: 82, Mismatches: 11, Indels: 30
0.67 0.09 0.24
Matches are distributed among these distances:
14 32 0.39
15 2 0.02
16 12 0.15
17 12 0.15
18 2 0.02
19 22 0.27
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:207911 original size:33 final size:33
Alignment explanation
Indices: 207869--208031 Score: 236
Period size: 33 Copynumber: 4.9 Consensus size: 33
207859 CAAAATCGCA
*
207869 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
207902 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
207935 TTGCGATTTTCATTTTGCGTTACGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* ** *
207968 TTGTGATAGTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
208001 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATTTTCATTT-CGCGTTGCGATTCTC
208032 ATTATCTCGT
Statistics
Matches: 118, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 104 0.88
34 14 0.12
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:208033 original size:20 final size:20
Alignment explanation
Indices: 207999--208056 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
207989 GCGATTCTCT
**
207999 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
208019 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
208039 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
208057 AACCAAAAGA
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:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:210132 original size:21 final size:21
Alignment explanation
Indices: 210108--210174 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
210098 TCATTCCTCG
210108 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
210129 AGAGGCCACTGTCAACGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
210150 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
210171 AGAG
1 AGAG
210175 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.21, T:0.18
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:210874 original size:20 final size:20
Alignment explanation
Indices: 210851--210906 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
210841 AAACTTACTT
210851 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
210871 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
210891 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
210907 AAATCGCGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 6 0.18
20 27 0.82
ACGTcount: A:0.34, C:0.23, G:0.27, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:210936 original size:19 final size:18
Alignment explanation
Indices: 210912--211034 Score: 99
Period size: 19 Copynumber: 7.3 Consensus size: 18
210902 AATGAAAATC
210912 GCGATTTGTGTTTCGCATT
1 GCGATTT-TGTTTCGCATT
210931 GCGATTTTG--TCG--TT
1 GCGATTTTGTTTCGCATT
*
210945 GCGATTTTCATTTCGCATT
1 GCGATTTT-GTTTCGCATT
210964 GCGATTTTG--TCG--TT
1 GCGATTTTGTTTCGCATT
*
210978 GCGATTTTCATTTCGCATT
1 GCGATTTT-GTTTCGCATT
210997 GCGATTTTG--TCG--TT
1 GCGATTTTGTTTCGCATT
*
211011 GCGATTTTCATTTCGCATT
1 GCGATTTT-GTTTCGCATT
211030 GCGAT
1 GCGAT
211035 AGCCATTTCC
Statistics
Matches: 84, Mismatches: 5, Indels: 30
0.71 0.04 0.25
Matches are distributed among these distances:
14 30 0.36
16 9 0.11
17 9 0.11
18 2 0.02
19 34 0.40
ACGTcount: A:0.12, C:0.18, G:0.23, T:0.47
Consensus pattern (18 bp):
GCGATTTTGTTTCGCATT
Found at i:210946 original size:14 final size:14
Alignment explanation
Indices: 210929--211018 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
210919 GTGTTTCGCA
210929 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
210943 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
210960 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
*
210976 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
210993 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
211009 TTGCGATTTT
1 TTGCGATTTT
211019 CATTTCGCAT
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 22 0.35
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 12 0.19
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:210949 original size:33 final size:33
Alignment explanation
Indices: 210922--211034 Score: 226
Period size: 33 Copynumber: 3.4 Consensus size: 33
210912 GCGATTTGTG
210922 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
210955 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
210988 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
211021 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
211035 AGCCATTTCC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:211053 original size:20 final size:19
Alignment explanation
Indices: 211019--211073 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
211009 TTGCGATTTT
*
211019 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
211038 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
211058 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
211074 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:211235 original size:18 final size:18
Alignment explanation
Indices: 211212--211280 Score: 138
Period size: 18 Copynumber: 3.8 Consensus size: 18
211202 ATTTATTAAG
211212 TAATCTAAGTGAAATGGT
1 TAATCTAAGTGAAATGGT
211230 TAATCTAAGTGAAATGGT
1 TAATCTAAGTGAAATGGT
211248 TAATCTAAGTGAAATGGT
1 TAATCTAAGTGAAATGGT
211266 TAATCTAAGTGAAAT
1 TAATCTAAGTGAAAT
211281 TACGAGTAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (18 bp):
TAATCTAAGTGAAATGGT
Found at i:211673 original size:18 final size:18
Alignment explanation
Indices: 211650--211697 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
211640 CGGGTCGATC
211650 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
211668 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
211686 AGGTGATGGCTC
1 AGGTGATGGCTC
211698 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:213065 original size:20 final size:20
Alignment explanation
Indices: 213017--213075 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
213007 AAAAGTTTCT
* *
213017 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
213037 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
213057 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
213076 AGATAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:213365 original size:22 final size:22
Alignment explanation
Indices: 213338--213380 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
213328 GATGGAGATA
213338 GACGGATTTCGCCGGAGATGGT
1 GACGGATTTCGCCGGAGATGGT
*
213360 GACGGATTTCGTCGGAGATGG
1 GACGGATTTCGCCGGAGATGG
213381 GTGAGAGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.16, G:0.42, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGT
Found at i:213640 original size:20 final size:20
Alignment explanation
Indices: 213574--213632 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
213564 GTATTATCTC
*
213574 GTTGCGAAAGTCAGTATTGA
1 GTTGCGAAAGTCAGTATCGA
* *
213594 GTTGCGAAATTAAGTATCGA
1 GTTGCGAAAGTCAGTATCGA
213614 GTTGCGAAAGTCAGTATCG
1 GTTGCGAAAGTCAGTATCG
213633 CATTGCGATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.29
Consensus pattern (20 bp):
GTTGCGAAAGTCAGTATCGA
Found at i:213667 original size:41 final size:41
Alignment explanation
Indices: 213548--213685 Score: 138
Period size: 41 Copynumber: 3.4 Consensus size: 41
213538 CGCTTTGAAA
* *
213548 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** * * *
213589 ATTG-AGTTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGT
1 ATCGCA-TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* *
213629 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGC
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
213670 A-CTGCGTTGCGATTTT
1 ATC-GCATTGCGATTTT
213686 CCAAATTCGC
Statistics
Matches: 76, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
40 33 0.43
41 43 0.57
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:213702 original size:21 final size:20
Alignment explanation
Indices: 213676--213722 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
213666 CAGCACTGCG
*
213676 TTGCGATTTTCCAAATTCGCA
1 TTGCGA-TTTACAAATTCGCA
**
213697 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACAAATTCGCA
213717 TTGCGA
1 TTGCGA
213723 ATTGGGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACAAATTCGCA
Found at i:213764 original size:21 final size:22
Alignment explanation
Indices: 213712--213764 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
213702 ATTTACTTAT
213712 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
213733 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
213754 TCGCATTGCGA
1 TCGCATTGCGA
213765 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:226380 original size:16 final size:17
Alignment explanation
Indices: 226351--226382 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
226341 AACTGAGCCA
226351 TTTATTATATTTTCACC
1 TTTATTATATTTTCACC
226368 TTTATTA-ATTTTCAC
1 TTTATTATATTTTCAC
226383 ATACCCTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATTATATTTTCACC
Found at i:226731 original size:20 final size:17
Alignment explanation
Indices: 226690--226738 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 17
226680 TTTATTCTTG
*
226690 TATTGTTCCTTTTTCCA
1 TATTGTTCTTTTTTCCA
226707 TATTGTTACTTTTTTCCTTA
1 TATTGTT-CTTTTTTCC--A
226727 TATTGTTCTTTT
1 TATTGTTCTTTT
226739 CACTACATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 7 0.25
18 8 0.29
19 5 0.18
20 8 0.29
ACGTcount: A:0.12, C:0.16, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTGTTCTTTTTTCCA
Found at i:226786 original size:17 final size:17
Alignment explanation
Indices: 226764--226847 Score: 98
Period size: 17 Copynumber: 4.9 Consensus size: 17
226754 TTTATTGTTA
226764 TATATCTTTTACTGTAC
1 TATATCTTTTACTGTAC
* *
226781 TTTATCTTTCAC-GATAC
1 TATATCTTTTACTG-TAC
*
226798 TATATCTTTTAATGTAC
1 TATATCTTTTACTGTAC
*
226815 TATATCTTTTACTGTAA
1 TATATCTTTTACTGTAC
* *
226832 TGTATCTTTTTCTGTA
1 TATATCTTTTACTGTA
226848 TTATTTCTCT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
16 1 0.02
17 54 0.96
18 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.07, T:0.54
Consensus pattern (17 bp):
TATATCTTTTACTGTAC
Found at i:227142 original size:24 final size:24
Alignment explanation
Indices: 227071--227248 Score: 114
Period size: 24 Copynumber: 7.5 Consensus size: 24
227061 ACCCAATGGT
* *
227071 ACTAATACAGGAGTGCACAA-AGC
1 ACTAATACAAGAGTGCACAATTGC
* *** *
227094 ACTTAATACATGAGTGTGTATTTGC
1 AC-TAATACAAGAGTGCACAATTGC
*
227119 ACTAATACAGGAGTGCACAATTGC
1 ACTAATACAAGAGTGCACAATTGC
* * *
227143 ACT-ATACAAGAGTGTA-TATTCAC
1 ACTAATACAAGAGTGCACAATT-GC
* * *
227166 ACTAATATAAGAGTGCTCAATTGT
1 ACTAATACAAGAGTGCACAATTGC
* * *
227190 ATTAATTCAAGAGTGCACGAA-GGC
1 ACTAATACAAGAGTGCAC-AATTGC
* * *
227214 ACTAATACAGGAGTGCACAAATGT
1 ACTAATACAAGAGTGCACAATTGC
227238 ACTAAT-CAAGA
1 ACTAATACAAGA
227249 TTAATATATA
Statistics
Matches: 115, Mismatches: 33, Indels: 14
0.71 0.20 0.09
Matches are distributed among these distances:
22 3 0.03
23 23 0.20
24 80 0.70
25 9 0.08
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (24 bp):
ACTAATACAAGAGTGCACAATTGC
Found at i:227169 original size:47 final size:49
Alignment explanation
Indices: 227071--227204 Score: 150
Period size: 47 Copynumber: 2.8 Consensus size: 49
227061 ACCCAATGGT
* * * **
227071 ACTAATACAGGAGTGCACAA-AGCACTTAATACATGAGTGTGTATTTGC
1 ACTAATACAGGAGTGCACAATTGCACTTAATACAAGAGTGTATATTCAC
227119 ACTAATACAGGAGTGCACAATTGCAC-T-ATACAAGAGTGTATATTCAC
1 ACTAATACAGGAGTGCACAATTGCACTTAATACAAGAGTGTATATTCAC
* * * * *
227166 ACTAATATAAGAGTGCTCAATTGTA-TTAATTCAAGAGTG
1 ACTAATACAGGAGTGCACAATTGCACTTAATACAAGAGTG
227205 CACGAAGGCA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
47 38 0.52
48 31 0.42
49 4 0.05
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (49 bp):
ACTAATACAGGAGTGCACAATTGCACTTAATACAAGAGTGTATATTCAC
Found at i:233326 original size:40 final size:40
Alignment explanation
Indices: 233246--233329 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
233236 TTCTTAGGCA
* **
233246 CAACCTATTTTATTAATAAAAATATTAGTATTACAAATCG
1 CAACCTACTTTATTAATAAAAATATTAACATTACAAATCG
* * *
233286 CAACCTACTTTATTAATGAAAATATTAACATTATATATCG
1 CAACCTACTTTATTAATAAAAATATTAACATTACAAATCG
233326 CAAC
1 CAAC
233330 GTATTTCTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (40 bp):
CAACCTACTTTATTAATAAAAATATTAACATTACAAATCG
Found at i:236913 original size:183 final size:187
Alignment explanation
Indices: 236604--236973 Score: 712
Period size: 183 Copynumber: 2.0 Consensus size: 187
236594 GATTTATCGA
236604 ATTTATCGAATATCAAATCAAGCACGAATCAAATTATTTTCAAGTCAATTAAAACATTGTTAATC
1 ATTTATCGAATATCAAATCAAGCACGAATCAAATTATTTTCAAGTCAATTAAAACATTGTTAATC
236669 TCGAGATTGACTCGTTCGACTATATTATAGCCCGTAGTGCGTAAACGTTGGTCGAATTTCATGGA
66 TCGAGATTGACTCGTTCGACTATATTATAGCCCGTAGTGCGTAAACGTTGGTCGAATTTCATGGA
236734 AACAGTGAAAACAGATGAAAGTAC-AAGCATGT-TTG-TCTTGTTTTGCTATATTTT
131 AACAGTGAAAACAGATGAAAGTACAAAGCATGTATTGTTCTTGTTTTGCTATATTTT
236788 ATTTATCGAATATCAAATCAAGCACGAATCAAATTA-TTTCAAGTCAATTAAAACATTGTTAATC
1 ATTTATCGAATATCAAATCAAGCACGAATCAAATTATTTTCAAGTCAATTAAAACATTGTTAATC
236852 TCGAGATTGACTCGTTCGACTATATTATAGCCCGTAGTGCGTAAACGTTGGTCGAATTTCATGGA
66 TCGAGATTGACTCGTTCGACTATATTATAGCCCGTAGTGCGTAAACGTTGGTCGAATTTCATGGA
236917 AACAGTGAAAACAGATGAAAGTACAAAGCATGTATTGTTCTTGTTTTGCTATATTTT
131 AACAGTGAAAACAGATGAAAGTACAAAGCATGTATTGTTCTTGTTTTGCTATATTTT
236974 GATACCAATC
Statistics
Matches: 183, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
183 117 0.64
184 44 0.24
185 3 0.02
186 19 0.10
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (187 bp):
ATTTATCGAATATCAAATCAAGCACGAATCAAATTATTTTCAAGTCAATTAAAACATTGTTAATC
TCGAGATTGACTCGTTCGACTATATTATAGCCCGTAGTGCGTAAACGTTGGTCGAATTTCATGGA
AACAGTGAAAACAGATGAAAGTACAAAGCATGTATTGTTCTTGTTTTGCTATATTTT
Found at i:239015 original size:6 final size:6
Alignment explanation
Indices: 239006--239031 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
238996 TAGAAATAAG
239006 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
239032 AAGGTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:240931 original size:20 final size:20
Alignment explanation
Indices: 240908--240948 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
240898 CGAAATATAT
*
240908 AAAATAAAATATAAATTTTA
1 AAAATAAAATACAAATTTTA
**
240928 AAAATATTATACAAATTTTA
1 AAAATAAAATACAAATTTTA
240948 A
1 A
240949 TATTTTAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATAAAATACAAATTTTA
Found at i:241523 original size:19 final size:17
Alignment explanation
Indices: 241501--241549 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
241491 CACAATTCAT
241501 ATTTAATAAATAATTATAA
1 ATTTAATAAA-AATTA-AA
*
241520 ATTTAAGAAAAATTAAA
1 ATTTAATAAAAATTAAA
*
241537 TTATTAATAAAAA
1 AT-TTAATAAAAA
241550 ATAATTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 14 0.54
19 9 0.35
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
ATTTAATAAAAATTAAA
Found at i:241551 original size:19 final size:21
Alignment explanation
Indices: 241527--241575 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 21
241517 TAAATTTAAG
241527 AAAAATTAAATT-ATTA-ATA
1 AAAAATTAAATTAATTATATA
*
241546 AAAAA-TAATTTAATTATATA
1 AAAAATTAAATTAATTATATA
*
241566 AAAATTTAAA
1 AAAAATTAAA
241576 AAATATCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 5 0.21
19 9 0.38
20 7 0.29
21 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAATTAAATTAATTATATA
Found at i:241560 original size:22 final size:20
Alignment explanation
Indices: 241530--241569 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
241520 ATTTAAGAAA
241530 AATTAAATTATTAATAAAAAAT
1 AATTAAATTA-T-ATAAAAAAT
*
241552 AATTTAATTATATAAAAA
1 AATTAAATTATATAAAAA
241570 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 1 0.06
22 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTAAATTATATAAAAAAT
Found at i:249389 original size:29 final size:31
Alignment explanation
Indices: 249356--249416 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
249346 TTTAAAAAAA
*
249356 ATTATTAACAAGTAATAT-A-ATTAAATATT
1 ATTATAAACAAGTAATATAACATTAAATATT
* *
249385 ATTATAAACAAGTCATGTAACATTAAATATT
1 ATTATAAACAAGTAATATAACATTAAATATT
249416 A
1 A
249417 GATGAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 15 0.56
30 1 0.04
31 11 0.41
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.38
Consensus pattern (31 bp):
ATTATAAACAAGTAATATAACATTAAATATT
Found at i:250202 original size:16 final size:15
Alignment explanation
Indices: 250174--250212 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
250164 ATAATTATTT
250174 AAAAAATTAAATAAA
1 AAAAAATTAAATAAA
*
250189 AAAAATATTTAATAAA
1 AAAAA-ATTAAATAAA
*
250205 AAATAATT
1 AAAAAATT
250213 TTTTATATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAAAATTAAATAAA
Found at i:264887 original size:80 final size:81
Alignment explanation
Indices: 264757--264913 Score: 244
Period size: 80 Copynumber: 2.0 Consensus size: 81
264747 TACTAACAAG
* * * *
264757 GAAAGTCACGTCCCAGGGGATGCATTTTTCTATTATTATTCAGAGAATCTCTAGATTATAATAGT
1 GAAAGACACGTCCCAGGGGAAGCATTTTTCCATTATTATTCAGAAAATCTCTAGATTATAATAGT
264822 GATCCATCCCATAAAT
66 GATCCATCCCATAAAT
* * *
264838 GAAAGACACGTTCCAGGGGAAGCA-TTTTCCATTATTATTTAGAAAATCTCTGGATTATAATAGT
1 GAAAGACACGTCCCAGGGGAAGCATTTTTCCATTATTATTCAGAAAATCTCTAGATTATAATAGT
264902 GATCCATCCCAT
66 GATCCATCCCAT
264914 CCGAAATAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
80 48 0.70
81 21 0.30
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (81 bp):
GAAAGACACGTCCCAGGGGAAGCATTTTTCCATTATTATTCAGAAAATCTCTAGATTATAATAGT
GATCCATCCCATAAAT
Found at i:264971 original size:83 final size:80
Alignment explanation
Indices: 264769--264972 Score: 230
Period size: 80 Copynumber: 2.5 Consensus size: 80
264759 AAGTCACGTC
* * *
264769 CCAGGGGATGCATTTTTCTATTATTATTCAGAGAATCTCTAGATTATAATAGTGATCCATCCCAT
1 CCAGGGGAAGCA-TTTTCCATTATTATTCAGAAAATCTCTAGATTATAATAGTGATCCATCCCAT
* *
264834 AAATGAAAGACACGTT
65 AAATAAAAGACACATT
* *
264850 CCAGGGGAAGCATTTTCCATTATTATTTAGAAAATCTCTGGATTATAATAGTGATCCATCCCATC
1 CCAGGGGAAGCATTTTCCATTATTATTCAGAAAATCTCTAGATTATAATAGTGATCCATCCCAT-
**
264915 CGAAATAAAAGACTTATT
65 --AAATAAAAGACACATT
** ** *
264933 -TTGGGAGAAGTGTTTTCCATTATTATTCAAAAAATCTCTA
1 CCAGGG-GAAGCATTTTCCATTATTATTCAGAAAATCTCTA
264973 CCATGTTAGA
Statistics
Matches: 103, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
80 48 0.47
81 11 0.11
82 3 0.03
83 41 0.40
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (80 bp):
CCAGGGGAAGCATTTTCCATTATTATTCAGAAAATCTCTAGATTATAATAGTGATCCATCCCATA
AATAAAAGACACATT
Found at i:264994 original size:83 final size:82
Alignment explanation
Indices: 264857--265224 Score: 348
Period size: 83 Copynumber: 4.4 Consensus size: 82
264847 GTTCCAGGGG
* * * * * * * *
264857 AAGCATTTTCCATTATTATTTAGAAAATCTCTG-GATTATAATAGTGATCCATCCCATCCGAAAT
1 AAGCGTTTTCCATTATTATTCAGAAAATCTCTGCCA-TGTCAGAGTGTTTCATCCCATCCGAAAT
*
264921 -AAAAGACTTATTTTGGGA
65 GAAAAGACGT-TTTTGGGA
* * * *
264939 GAAGTGTTTTCCATTATTATTCAAAAAATCTCTACCATGTTAGAGTG-TTCTATCCCATCCGAAA
1 -AAGCGTTTTCCATTATTATTCAGAAAATCTCTGCCATGTCAGAGTGTTTC-ATCCCATCCGAAA
* *
265003 TGAAAGGCAC-ATTTTGAGGA
64 TGAAAAG-ACGTTTTTG-GGA
* * * * * *
265023 AAGCGTTTTTCTTTATTATTCAGAGAATCTATGTCATGTCAGAGTGTTTCATCCCATCTGAAATG
1 AAGCGTTTTCCATTATTATTCAGAAAATCTCTGCCATGTCAGAGTGTTTCATCCCATCCGAAATG
* **
265088 AAATGCACGTTTCAGGGA
66 AAAAG-ACGTTTTTGGGA
** * * *
265106 AAATGTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTATTTCATCCCATCCGAAATG
1 AAGCGTTTTCCATTATTATTCAGAAAATCTCTGCCATGTCAGAGTGTTTCATCCCATCCGAAATG
* *
265171 AAATACACGTTTTGGGGA
66 AAA-AGACGTTTTTGGGA
*
265189 AAGCGATTTCCATTATTATTCAGAAAATCTCTGCCA
1 AAGCGTTTTCCATTATTATTCAGAAAATCTCTGCCA
265225 CTTTATATAA
Statistics
Matches: 234, Mismatches: 43, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
82 2 0.01
83 216 0.92
84 14 0.06
85 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (82 bp):
AAGCGTTTTCCATTATTATTCAGAAAATCTCTGCCATGTCAGAGTGTTTCATCCCATCCGAAATG
AAAAGACGTTTTTGGGA
Found at i:265078 original size:166 final size:166
Alignment explanation
Indices: 264906--265218 Score: 398
Period size: 166 Copynumber: 1.9 Consensus size: 166
264896 AATAGTGATC
* ** *
264906 CATCCCATCCGAAAT-AAAAG-ACTTATTTTGGGAGAAGTGTTTTCCATTATTATTCAAAAAATC
1 CATCCCATCCGAAATGAAAAGCACGT-TTCAGGGA-AAATGTTTTCCATTATTATTCAAAAAATC
* * * * *
264969 TCTACCATGTTAGAGT-GTTCTATCCCATCCGAAATGAAAGGCACATTTTGAGGAAAGCGTTTTT
64 TCTACCATGTCAGAGTATTTC-ATCCCATCCGAAATGAAAGACACATTTTGAGGAAAGCGATTTC
* *
265033 CTTTATTATTCAGAGAATCTATGTCATGTCAGAGTGTTT
128 CATTATTATTCAGAAAATCTATGTCATGTCAGAGTGTTT
* * * *
265072 CATCCCATCTGAAATGAAATGCACGTTTCAGGGAAAATGTTTTCCATTATTATTCAGAGAATCTC
1 CATCCCATCCGAAATGAAAAGCACGTTTCAGGGAAAATGTTTTCCATTATTATTCAAAAAATCTC
* * * * *
265137 TGCCATGTCATAGTATTTCATCCCATCCGAAATGAAATACACGTTTTGGGGAAAGCGATTTCCAT
66 TACCATGTCAGAGTATTTCATCCCATCCGAAATGAAAGACACATTTTGAGGAAAGCGATTTCCAT
265202 TATTATTCAGAAAATCT
131 TATTATTCAGAAAATCT
265219 CTGCCACTTT
Statistics
Matches: 124, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
166 108 0.87
167 13 0.10
168 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (166 bp):
CATCCCATCCGAAATGAAAAGCACGTTTCAGGGAAAATGTTTTCCATTATTATTCAAAAAATCTC
TACCATGTCAGAGTATTTCATCCCATCCGAAATGAAAGACACATTTTGAGGAAAGCGATTTCCAT
TATTATTCAGAAAATCTATGTCATGTCAGAGTGTTT
Found at i:269739 original size:21 final size:21
Alignment explanation
Indices: 269687--269747 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
269677 ATTTCTTTAA
269687 TATTAATAAATA-AATAAATAT
1 TATTAA-AAATATAATAAATAT
* * *
269708 TAATAAGAATATAATAAATTT
1 TATTAAAAATATAATAAATAT
*
269729 TCTTAAAAATAATAA-AAAT
1 TATTAAAAAT-ATAATAAAT
269748 GAAGTAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 4 0.12
21 24 0.75
22 4 0.12
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
TATTAAAAATATAATAAATAT
Found at i:270157 original size:18 final size:18
Alignment explanation
Indices: 270108--270162 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
270098 CATTTATTTG
270108 ATATTAAAAATAA-ATAA
1 ATATTAAAAATAATATAA
* *
270125 ATATTAAGAAGAATAT-A
1 ATATTAAAAATAATATAA
*
270142 ATAATTAAAAATAATAAAA
1 AT-ATTAAAAATAATATAA
270161 AT
1 AT
270163 GAAGTAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 14 0.47
18 13 0.43
19 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
ATATTAAAAATAATATAA
Found at i:270176 original size:35 final size:35
Alignment explanation
Indices: 270110--270174 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 35
270100 TTTATTTGAT
* *
270110 ATTAAAAATAAATAAATATTAAGAAGAATATAATA
1 ATTAAAAATAAATAAAAATGAAGAAGAATATAATA
*
270145 ATTAAAAAT-AATAAAAATGAAGTA-AATATA
1 ATTAAAAATAAATAAAAATGAAGAAGAATATA
270175 TATATTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 6 0.22
34 12 0.44
35 9 0.33
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (35 bp):
ATTAAAAATAAATAAAAATGAAGAAGAATATAATA
Found at i:271630 original size:3 final size:3
Alignment explanation
Indices: 271624--271676 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
271614 TATTTATTAT
* *
271624 TAA TAA T-A TAA TAA T-A TAA TAA TAA TAA TAC TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
271670 TAA TAA T
1 TAA TAA T
271677 TTTTAAAATG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:272049 original size:45 final size:45
Alignment explanation
Indices: 271999--272167 Score: 248
Period size: 45 Copynumber: 3.8 Consensus size: 45
271989 AACTATAGGT
* * * * *
271999 CTTACAAATGATCCGGAGGTTTTAAAAATATCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
* *
272044 CTTACAGATGACCCGAAGCTTTTGAAAACATCATGCACTGAAGGA
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
* *
272089 CTTATAGATGACCTGAAGGTTTTGAAAACATCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
*
272134 CTTACAGATGACCCGAAGGCTTTGAAAACATCAT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCAT
272168 AAAGCTCCTG
Statistics
Matches: 110, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 110 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (45 bp):
CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
Found at i:272191 original size:31 final size:31
Alignment explanation
Indices: 272145--272229 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 31
272135 TTACAGATGA
272145 CCCGAAGGC--TTTGAAAACATCATAAAGCT
1 CCCGAAGGCTTTTTGAAAACATCATAAAGCT
* * * *
272174 CCTGGAGGCTTTTTGAAAATATCAAAAAGCT
1 CCCGAAGGCTTTTTGAAAACATCATAAAGCT
*
272205 CCCGAATGCTTTTTGAAAACATCAT
1 CCCGAAGGCTTTTTGAAAACATCAT
272230 GTACTGTAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 7 0.16
31 38 0.84
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (31 bp):
CCCGAAGGCTTTTTGAAAACATCATAAAGCT
Found at i:272271 original size:45 final size:45
Alignment explanation
Indices: 272215--272363 Score: 235
Period size: 45 Copynumber: 3.3 Consensus size: 45
272205 CCCGAATGCT
* *
272215 TTTTGAAAACATCATGTACTGTAGGTCTTATGGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGTAGGTCTTATAGATGACCCGAAGG
*
272260 TTTTGAAAACATCATGCACTATAGGTCTTATAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGTAGGTCTTATAGATGACCCGAAGG
* * *
272305 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGTAGGTCTTATAGATGACCCGAAGG
*
272350 CTTTGAAAACATCA
1 TTTTGAAAACATCA
272364 AAAAGCTCCC
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 96 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGTAGGTCTTATAGATGACCCGAAGG
Found at i:272385 original size:197 final size:197
Alignment explanation
Indices: 272018--272389 Score: 611
Period size: 197 Copynumber: 1.9 Consensus size: 197
272008 GATCCGGAGG
*
272018 TTTTAAAAATATCATGCACTGAAGGGCTTACAGATGACCCGAAGCTTTTGAAAACATCATGCACT
1 TTTTAAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGCTTTTGAAAACATCATGCACT
*
272083 GAAGGACTTATAGATGACCTGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
66 GAAGGACTTATAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
* * *
272148 GAAGGCTTTGAAAACATCATAAAGCTCCTGGAGGCTTTTTGAAAATATCAAAAAGCTCCCGAATG
131 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAATATCAAAAAGCTCCCGAATG
272213 CT
196 CT
* * * * ** *
272215 TTTTGAAAACATCATGTACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACT
1 TTTTAAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGCTTTTGAAAACATCATGCACT
*
272280 -ATAGGTCTTATAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACC
66 GA-AGGACTTATAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACC
272344 CGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
130 CGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
272390 CATCCTGCAC
Statistics
Matches: 161, Mismatches: 13, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
196 1 0.01
197 160 0.99
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (197 bp):
TTTTAAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGCTTTTGAAAACATCATGCACT
GAAGGACTTATAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAATATCAAAAAGCTCCCGAATG
CT
Found at i:272421 original size:76 final size:74
Alignment explanation
Indices: 272297--272439 Score: 205
Period size: 76 Copynumber: 1.9 Consensus size: 74
272287 TTATAGATGA
*
272297 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACAT
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATAACCCGAAGGCTTTGAAAACAT
272362 CAAAAAGCT
66 CAAAAAGCT
* * * ** *
272371 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATAACCCGAAGGTTTTGAAAAC
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATAACCCGAAGGCTTTGAAAAC
272436 ATCA
64 ATCA
272440 TGCACTGTAG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
74 8 0.13
76 52 0.87
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.24
Consensus pattern (74 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATAACCCGAAGGCTTTGAAAACAT
CAAAAAGCT
Found at i:272421 original size:121 final size:121
Alignment explanation
Indices: 272252--273431 Score: 979
Period size: 121 Copynumber: 9.9 Consensus size: 121
272242 TTATGGATGA
* * *
272252 CCCGAAGG--TTTTGAAAACATCATGCACTATAGGTCTTATAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
* *
272315 ATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
66 ATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
272371 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATAACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
* * * * *
272436 ATCATGCACTGTAGGACTTACATATGACCTGGAGGCTTT--AAATATCAAAAAGCT
66 ATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
* *
272490 CCCGAAGACTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCAAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
*
272555 ATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCT
66 ATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
* *
272611 CCCGAAGGCTTTTTAAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAT
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
* * * * *
272676 ATCATGCACTGTATGTCTTACATATAACCCGAAGGTTTTGAAAACATC---ATGC-
66 ATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
* * *** ** * * *** * * * *
272728 ACTGAAGGGCTTACAGATGAC--CC-GAAGGCTTTGAAAAC--AT-CATGTA-CTGTAGGTCTT-
1 CCCGAA-GGCTTTTTGAAAACATCCTGCA--CTGT-AGGTCTTATGGATG-ACCCGAAGGTTTTG
*** * * * * * ** * ** * * * *
272785 -ATGGATGA--C-CCGAAGGTTTTGA-A-A--ACATC-ATACACTGT-AAGTC-TTACAGATG-A
61 AAAACATCATGCACTGTAGGTCTT-ACAGATGAC-CCGA-AGGCTTTGAAAACATCA-AAAAGCT
* * * ** *
272838 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
* * * * * * *** * * *** ** *
272901 ATCAAAAAGCTCCCGAAGGATTTTTGA-AAAT-ATTTTGCA--CTGT-AGGTCTTATGGATAA-C
66 ATC---ATGC-ACTGTAGG--TCTT-ACAGATGA-CCCGAAGGCTTTGAAAAC--ATCAAAAAGC
272960 T
121 T
* * * **
272961 --CGAAGG--TTTTGAAAACATCATGCACTGTAAGACTTACAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
* *
273022 ATCATGCACTGAAGGACTTACAGATG-CCCAGAAGGCTTTGAAAACATCAAAAAGCT
66 ATCATGCACTGTAGGTCTTACAGATGACCC-GAAGGCTTTGAAAACATCAAAAAGCT
* *
273078 CCCGTAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATAACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
* * * *
273143 ATCATGCATTGTAGGACTTACAGATGACCCGAAGGCTTT--AAATATCAAAGAGCT
66 ATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
* *
273197 CCCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
* * *
273262 ATCATGCACTGTAGGTCTAACAGATGACCCGAAGGCTTTGAAAATATCAAAAAACT
66 ATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
* *
273318 CCCGAAGGCTTTCTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAATGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
* * *
273383 ATCATGCACTGTAGGTCTTACAGATGACCCAAAGGTTTTGAAAATATCA
66 ATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCA
273432 TGCACTGAAG
Statistics
Matches: 862, Mismatches: 142, Indels: 112
0.77 0.13 0.10
Matches are distributed among these distances:
106 1 0.00
107 13 0.02
108 6 0.01
109 6 0.01
110 27 0.03
111 2 0.00
112 3 0.00
113 4 0.00
114 1 0.00
115 21 0.02
116 10 0.01
117 19 0.02
118 18 0.02
119 241 0.28
121 480 0.56
122 4 0.00
123 5 0.01
124 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (121 bp):
CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
ATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
Found at i:272564 original size:45 final size:45
Alignment explanation
Indices: 272500--272603 Score: 154
Period size: 45 Copynumber: 2.3 Consensus size: 45
272490 CCCGAAGACT
* **
272500 TTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCAAAGG
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCAAAGG
*
272545 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCAAAGG
* *
272590 CTTTAAAAACATCA
1 TTTTGAAAACATCA
272604 AAAAGCTCCC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCAAAGG
Found at i:272564 original size:240 final size:247
Alignment explanation
Indices: 272251--272859 Score: 835
Period size: 240 Copynumber: 2.5 Consensus size: 247
272241 CTTATGGATG
* * *
272251 ACCCGAAG-GTTTTGAAAACATCATGCACTATAGGTCTTATAGATGACCCGAAGGTTTTGAAAAC
1 ACCCGAAGACTTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
*
272315 ATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
66 ATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
272380 TTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATAACCCGAAGGTTTTGAAAACATCATGCAC
131 TTTTTAAAAACATCCTGCACTGTAGGTCTTATGGATAACCCGAAGGTTTTGAAAACATCATGCAC
* * * *
272445 TGTAGGACTTACATATGACCTGGAGGCTTT-AA-AT-AT-CA-AA-A-AGCT
196 TGTAGGACTTACATATAACCCGAAGGCTTTAAACATCATGCACAAGACAGAT
* *
272490 -CCCGAAGACTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCAAAGGTTTTGAAAA
1 ACCCGAAGAC-TTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAA
* *
272554 CATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGG
65 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGG
* *
272619 CTTTTTAAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAATATCATGCA
130 CTTTTTAAAAACATCCTGCACTGTAGGTCTTATGGATAACCCGAAGGTTTTGAAAACATCATGCA
* * *
272684 CTGTATGTCTTACATATAACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGAT
195 CTGTAGGACTTACATATAACCCGAAGGCTTT--AAACATCATGCAC--AA--G---ACAGAT
* *
272746 GACCCGAAGGC-TTTGAAAACATCATGTACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAA
1 -ACCCGAAGACTTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAA
* *
272810 CATCATACACTGTAA-GTCTTACAGATGACCCGAAGGTTTTGAAAACATCA
65 CATCATGCACTG-AAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCA
272860 TGCACTGAAG
Statistics
Matches: 323, Mismatches: 26, Indels: 25
0.86 0.07 0.07
Matches are distributed among these distances:
238 7 0.02
240 199 0.62
243 2 0.01
244 2 0.01
245 2 0.01
246 2 0.01
249 2 0.01
255 1 0.00
256 97 0.30
257 1 0.00
258 8 0.02
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (247 bp):
ACCCGAAGACTTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
ATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
TTTTTAAAAACATCCTGCACTGTAGGTCTTATGGATAACCCGAAGGTTTTGAAAACATCATGCAC
TGTAGGACTTACATATAACCCGAAGGCTTTAAACATCATGCACAAGACAGAT
Found at i:272687 original size:45 final size:45
Alignment explanation
Indices: 272611--272904 Score: 399
Period size: 45 Copynumber: 6.5 Consensus size: 45
272601 TCAAAAAGCT
* * **
272611 CCCGAAGGCTTTTTAAAAACATCCTGCACTGTAGGTCTTATGGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
* * * *
272658 CCCGAAGGTTTTGAAAATATCATGCACTGTATGTCTTACATATAA
1 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
* *
272703 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
* * **
272748 CCCGAAGGCTTTGAAAACATCATGTACTGTAGGTCTTATGGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
* *
272793 CCCGAAGGTTTTGAAAACATCATACACTGTAAGTCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
* *
272838 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
*
272883 CCCGAAGGCTTTGAAAACATCA
1 CCCGAAGGTTTTGAAAACATCA
272905 AAAAGCTCCC
Statistics
Matches: 216, Mismatches: 31, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
45 208 0.96
47 8 0.04
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
Found at i:272985 original size:45 final size:45
Alignment explanation
Indices: 272912--273070 Score: 176
Period size: 45 Copynumber: 3.5 Consensus size: 45
272902 TCAAAAAGCT
* ** * **
272912 CCCGAAGGATTTTTGAAAATATTTTGCACTGTAGGTCTTATGGATAA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGTAGGACTTACAGATAA
* * *
272959 CTCGAAGGTTTTGAAAACATCATGCACTGTAAGACTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATAA
* *
273004 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGAT-G
1 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATAA
*
273048 CCCAGAAGGCTTTGAAAACATCA
1 CCC-GAAGGTTTTGAAAACATCA
273071 AAAAGCTCCC
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
44 3 0.03
45 87 0.90
47 7 0.07
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATAA
Found at i:273031 original size:166 final size:166
Alignment explanation
Indices: 272757--273177 Score: 700
Period size: 166 Copynumber: 2.5 Consensus size: 166
272747 ACCCGAAGGC
* * * *
272757 TTTGAAAACATCATGTACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATACACTG
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATAACCCGAAGGTTTTGAAAACATCATGCACTG
* *
272822 TAAGTCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC-
66 TAAGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATG-CCCA
272886 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGATT
130 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGATT
* ** *
272923 TTTGAAAATATTTTGCACTGTAGGTCTTATGGATAACTCGAAGGTTTTGAAAACATCATGCACTG
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATAACCCGAAGGTTTTGAAAACATCATGCACTG
272988 TAAGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGCCCAG
66 TAAGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGCCCAG
* *
273053 AAGGCTTTGAAAACATCAAAAAGCTCCCGTAGGCTT
131 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGATT
*
273089 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATAACCCGAAGGTTTTGAAAACATCATGCATTG
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATAACCCGAAGGTTTTGAAAACATCATGCACTG
*
273154 TAGGACTTACAGATGACCCGAAGG
66 TAAGACTTACAGATGACCCGAAGG
273178 CTTTAAATAT
Statistics
Matches: 237, Mismatches: 17, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
165 3 0.01
166 234 0.99
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (166 bp):
TTTGAAAACATCCTGCACTGTAGGTCTTATGGATAACCCGAAGGTTTTGAAAACATCATGCACTG
TAAGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGCCCAG
AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGATT
Found at i:273156 original size:45 final size:45
Alignment explanation
Indices: 273088--273177 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
273078 CCCGTAGGCT
* * **
273088 TTTTGAAAACATCCTGCACTGTAGGTCTTATGGATAACCCGAAGG
1 TTTTGAAAACATCATGCACTGTAGGACTTACAGATAACCCGAAGG
* *
273133 TTTTGAAAACATCATGCATTGTAGGACTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGTAGGACTTACAGATAACCCGAAGG
273178 CTTTAAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGTAGGACTTACAGATAACCCGAAGG
Found at i:273271 original size:45 final size:45
Alignment explanation
Indices: 273207--273310 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 45
273197 CCCAAAGGCT
* **
273207 TTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGTAGGTCTAACAGATGACCCGAAGG
273252 TTTTGAAAACATCATGCACTGTAGGTCTAACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGTAGGTCTAACAGATGACCCGAAGG
* *
273297 CTTTGAAAATATCA
1 TTTTGAAAACATCA
273311 AAAAACTCCC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGTAGGTCTAACAGATGACCCGAAGG
Found at i:273381 original size:76 final size:74
Alignment explanation
Indices: 273244--273386 Score: 205
Period size: 76 Copynumber: 1.9 Consensus size: 74
273234 TTATGGATGA
*
273244 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTAACAGATGACCCGAAGGCTTTGAAAATAT
1 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTAACAGATGACCCGAAGGCTTTGAAAACAT
273309 CAAAAAACT
66 CAAAAAACT
* * ** * *
273318 CCCGAAGGCTTTCTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAATGTTTTGAAAAC
1 CCCGAAGG-TTT-TGAAAACATCATGCACTGTAGGTCTAACAGATGACCCGAAGGCTTTGAAAAC
273383 ATCA
64 ATCA
273387 TGCACTGTAG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
74 8 0.13
75 3 0.05
76 49 0.82
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (74 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTAACAGATGACCCGAAGGCTTTGAAAACAT
CAAAAAACT
Found at i:273384 original size:45 final size:45
Alignment explanation
Indices: 273318--273476 Score: 219
Period size: 45 Copynumber: 3.5 Consensus size: 45
273308 TCAAAAAACT
* **
273318 CCCGAAGGCTTTCTGAAAACATCCTGCACTGTAGGTCTTATGGATGA
1 CCCGAAGG-TTT-TGAAAACATCATGCACTGTAGGTCTTACAGATGA
*
273365 CCCGAATGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
* * * *
273410 CCCAAAGGTTTTGAAAATATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
*
273455 CCCGAAGGCTTTGAAAACATCA
1 CCCGAAGGTTTTGAAAACATCA
273477 AAAAGCTCCC
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
45 90 0.90
46 3 0.03
47 7 0.07
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
Found at i:273420 original size:166 final size:166
Alignment explanation
Indices: 273207--273583 Score: 628
Period size: 166 Copynumber: 2.3 Consensus size: 166
273197 CCCAAAGGCT
**
273207 TTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACT
* * *
273272 GTAGGTCTAACAGATGACCCGAAGGCTTTGAAAATATCAAAAAACTCCCGAAGGCTTTCTGAAAA
66 GAAGGGCTAACAGATGACCCGAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTCTGAAAA
*
273337 CATCCTGCACTGTAGGTCTTATGGATGACCCGAATG
131 CATCCTGCACTGTAGGTCTTATGGATGACCCGAAGG
* *
273373 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCAAAGGTTTTGAAAATATCATGCACT
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACT
* * *
273438 GAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
66 GAAGGGCTAACAGATGACCCGAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTCTGAAAA
*
273503 TATCCTGCACTGTAGGTCTTATGGATGACCCGAAGG
131 CATCCTGCACTGTAGGTCTTATGGATGACCCGAAGG
* *
273539 TTTTGAAAACATCATACACTGTAGGACTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGG
273584 CTTTAAATAT
Statistics
Matches: 196, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
166 196 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (166 bp):
TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACT
GAAGGGCTAACAGATGACCCGAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTCTGAAAA
CATCCTGCACTGTAGGTCTTATGGATGACCCGAAGG
Found at i:273490 original size:240 final size:241
Alignment explanation
Indices: 273004--273792 Score: 705
Period size: 240 Copynumber: 3.3 Consensus size: 241
272994 TTACAGATGA
* *
273004 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATG-CCCAGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCC-GAAGGCTTTGAAAAC
* * *
273067 ATCAAAAAGCTCCCGTAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATAACCCGAAG
65 ATCAAAAAACTCCCGTAGGCTTTCTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAG
* * * *
273132 GTTTTGAAAACATCATGCATTGTAGGACTTACAGATGACCCGAAGGCTTT--AAATATCAAAG-A
130 GTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAATATC-ATGCA
* * *** * * ** *** * ** * *
273194 GCTCCCAAAGGCTTTTTGAAAACATC--ATGCACTGTAGGTC-TTATGGATG-A
194 -CT--GAAGGGCTTACAGATAAC-TCGAAGGCTTTG-AAAACATCA-AAAAGCT
* *
273244 CCCGAAGG-TTTTGAAAACATCATGCACTGTAGGTCTAACAGATGACCCGAAGGCTTTGAAAATA
1 CCCGAAGGCTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACA
* *
273308 TCAAAAAACTCCCGAAGGCTTTCTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAATG
66 TCAAAAAACTCCCGTAGGCTTTCTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGG
*
273373 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCAAAGGTTTTGAAAATATCATGCACT
131 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAATATCATGCACT
* *
273438 GAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
196 GAAGGGCTTACAGATAACTCGAAGGCTTTGAAAACATCAAAAAGCT
* * ** *
273484 CCCGAAGGCTTTTTGAAAATATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGC-TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAC
* * * * ** * * ** * * ** * *
273549 ATC-ATACACT---GTAGGACTTACAGATGAC--CC-GAAGGCTTTAAATATCA-AAAAGCTCCC
65 ATCAAAAAACTCCCGTAGG-CTTTCTGAAAACATCCTGCA--CTGTAGGTCTTATGGATG-ACCC
*** *
273606 GAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTGTGGATGACCCGAAGGTTTTGAAAACATC
126 GAAGG--TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAATATC
* * *
273671 ATGCACTGTAGGTCTTACAGATTACTCGAAGGCTTTGAAAACATCAAAAAGCT
189 ATGCACTGAAGGGCTTACAGATAACTCGAAGGCTTTGAAAACATCAAAAAGCT
* * ** * *
273724 CCCGAAGGCTTTTTGAAAACATCCTGCACTCTAGGTCTTATGGATGACCCAAAGGTTTTGAAAAC
1 CCCGAAGGC-TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAC
273789 ATCA
65 ATCA
273793 TGCACTGTAG
Statistics
Matches: 462, Mismatches: 70, Indels: 33
0.82 0.12 0.06
Matches are distributed among these distances:
236 2 0.00
237 4 0.01
238 19 0.04
239 23 0.05
240 343 0.74
241 12 0.03
242 59 0.13
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (241 bp):
CCCGAAGGCTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACA
TCAAAAAACTCCCGTAGGCTTTCTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGG
TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAATATCATGCACT
GAAGGGCTTACAGATAACTCGAAGGCTTTGAAAACATCAAAAAGCT
Found at i:273498 original size:121 final size:121
Alignment explanation
Indices: 273373--273866 Score: 789
Period size: 121 Copynumber: 4.1 Consensus size: 121
273363 GACCCGAATG
** *
273373 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCAAAGGTTTTGAAAATATCATGCACT
1 TTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCAAAGGTTTTGAAAACATCATGCACT
* *
273438 GAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
66 GTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
* * * *
273494 TTTTGAAAATATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATACACT
1 TTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCAAAGGTTTTGAAAACATCATGCACT
*
273559 GTAGGACTTACAGATGACCCGAAGGCTTT--AAATATCAAAAAGCTCCCGAAGGCT
66 GTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
* *
273613 TTTTGAAAACATCATGCACTGTAGGTCTTGTGGATGACCCGAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCAAAGGTTTTGAAAACATCATGCACT
* * *
273678 GTAGGTCTTACAGATTACTCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
66 GTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
* *
273734 TTTTGAAAACATCCTGCACTCTAGGTCTTATGGATGACCCAAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCAAAGGTTTTGAAAACATCATGCACT
**
273799 GTAGGACTTACAGATGAATCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC-
66 GTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
273854 -TTTGAAAACATCA
1 TTTTGAAAACATCA
273867 AAAAGCTCCC
Statistics
Matches: 345, Mismatches: 26, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
119 123 0.36
121 222 0.64
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (121 bp):
TTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCAAAGGTTTTGAAAACATCATGCACT
GTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
Found at i:273535 original size:47 final size:47
Alignment explanation
Indices: 273484--273587 Score: 140
Period size: 45 Copynumber: 2.3 Consensus size: 47
273474 TCAAAAAGCT
* * * * **
273484 CCCGAAGGCTTTTTGAAAATATCCTGCACTGTAGGTCTTATGGATGA
1 CCCGAAGGCTTTTTGAAAACATCATACACTGTAGGACTTACAGATGA
273531 CCCGAAGG--TTTTGAAAACATCATACACTGTAGGACTTACAGATGA
1 CCCGAAGGCTTTTTGAAAACATCATACACTGTAGGACTTACAGATGA
273576 CCCGAAGGCTTT
1 CCCGAAGGCTTT
273588 AAATATCAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
45 39 0.80
47 10 0.20
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (47 bp):
CCCGAAGGCTTTTTGAAAACATCATACACTGTAGGACTTACAGATGA
Found at i:273553 original size:406 final size:403
Alignment explanation
Indices: 272801--273964 Score: 1742
Period size: 406 Copynumber: 2.9 Consensus size: 403
272791 GACCCGAAGG
* * **
272801 TTTTGAAAACATCATACACTGTAAGTCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACT
* * *
272866 GAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGATTTTTGAAAA
66 GTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
* ** * * *
272931 TATTTTGCACTGTAGGTCTTATGGATAACTCGAAGGTTTTGAAAACATCATGCACTGTAAGACTT
131 CATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTT
272996 ACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGCCCAGAAGGCTTT
196 ACAGATGACCCGAAGGTTTTGAAAA-ATCATGCACTGAAGG-CTTACAGATGCCC-GAAGGCTTT
*
273061 GAAAACATCAAAAAGCTCCCGTAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATAAC
258 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATAAC
*
273126 CCGAAGGTTTTGAAAACATCATGCATTGTAGGACTTACAGATGACCCGAAGGCTTTAAATATCAA
323 CCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTAAATATCAA
*
273191 AGAGCTCCCAAAGGCT
388 AAAGCTCCCAAAGGCT
273207 TTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACT
* * * *
273272 GTAGGTCTAACAGATGACCCGAAGGCTTTGAAAATATCAAAAAACTCCCGAAGGCTTTCTGAAAA
66 GTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
* *
273337 CATCCTGCACTGTAGGTCTTATGGATGACCCGAATGTTTTGAAAACATCATGCACTGTAGGTCTT
131 CATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTT
*
273402 ACAGATGACCCAAAGGTTTTGAAAATATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTT
196 ACAGATGACCCGAAGGTTTTGAAAA-ATCATGCACTGAA-GGCTTACAGATG-CCCGAAGGCTTT
* *
273467 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAATATCCTGCACTGTAGGTCTTATGGATGAC
258 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATAAC
*
273532 CCGAAGGTTTTGAAAACATCATACACTGTAGGACTTACAGATGACCCGAAGGCTTTAAATATCAA
323 CCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTAAATATCAA
*
273597 AAAGCTCCCGAAGGCT
388 AAAGCTCCCAAAGGCT
*
273613 TTTTGAAAACATCATGCACTGTAGGTCTTGTGGATGACCCGAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACT
* *
273678 GTAGGTCTTACAGATTACTCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
66 GTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
* *
273743 CATCCTGCACTCTAGGTCTTATGGATGACCCAAAGGTTTTGAAAACATCATGCACTGTAGGACTT
131 CATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTT
** * *
273808 ACAGATGAATCGAAGGCTTTG-AAAA-CAT-CA---AA-----A-AGCT-CCCGAAGGCTTTGAA
196 ACAGATGACCCGAAGGTTTTGAAAAATCATGCACTGAAGGCTTACAGATGCCCGAAGGCTTTGAA
* * * * ** * **
273860 AACATCAAAAAGCTCCCGAAGGATTTTTGAAAACATCATGCACTGAAGGGCTTACAGATTACCTA
261 AACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATAACCCG
* * * *
273925 AAGGCTTTGAAAACATCCTGCACTGAAGGTCTTACAGATG
326 AAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATG
273965 TGAGAAATAG
Statistics
Matches: 697, Mismatches: 59, Indels: 20
0.90 0.08 0.03
Matches are distributed among these distances:
390 105 0.15
392 3 0.00
393 1 0.00
399 2 0.00
402 2 0.00
403 3 0.00
404 1 0.00
405 3 0.00
406 572 0.82
407 5 0.01
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (403 bp):
TTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACT
GTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
CATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTT
ACAGATGACCCGAAGGTTTTGAAAAATCATGCACTGAAGGCTTACAGATGCCCGAAGGCTTTGAA
AACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATAACCCG
AAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTAAATATCAAAAA
GCTCCCAAAGGCT
Found at i:273669 original size:45 final size:45
Alignment explanation
Indices: 273603--273716 Score: 156
Period size: 45 Copynumber: 2.5 Consensus size: 45
273593 TCAAAAAGCT
***
273603 CCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTGTGGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
*
273650 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATTA
1 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
* *
273695 CTCGAAGGCTTTGAAAACATCA
1 CCCGAAGGTTTTGAAAACATCA
273717 AAAAGCTCCC
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 53 0.87
47 8 0.13
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
Found at i:273784 original size:76 final size:74
Alignment explanation
Indices: 273650--273792 Score: 196
Period size: 76 Copynumber: 1.9 Consensus size: 74
273640 TTGTGGATGA
* * * *
273650 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATTACTCGAAGGCTTTGAAAACAT
1 CCCGAAGGTTTTGAAAACATCATGCACTCTAGGTCTTACAGATGACCCAAAGGCTTTGAAAACAT
273715 CAAAAAGCT
66 CAAAAAGCT
* ** *
273724 CCCGAAGGCTTTTTGAAAACATCCTGCACTCTAGGTCTTATGGATGACCCAAAGGTTTTGAAAAC
1 CCCGAAGG--TTTTGAAAACATCATGCACTCTAGGTCTTACAGATGACCCAAAGGCTTTGAAAAC
273789 ATCA
64 ATCA
273793 TGCACTGTAG
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
74 8 0.14
76 51 0.86
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (74 bp):
CCCGAAGGTTTTGAAAACATCATGCACTCTAGGTCTTACAGATGACCCAAAGGCTTTGAAAACAT
CAAAAAGCT
Found at i:273798 original size:45 final size:45
Alignment explanation
Indices: 273734--273837 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 45
273724 CCCGAAGGCT
* * ** *
273734 TTTTGAAAACATCCTGCACTCTAGGTCTTATGGATGACCCAAAGG
1 TTTTGAAAACATCATGCACTCTAGGACTTACAGATGAACCAAAGG
* * *
273779 TTTTGAAAACATCATGCACTGTAGGACTTACAGATGAATCGAAGG
1 TTTTGAAAACATCATGCACTCTAGGACTTACAGATGAACCAAAGG
*
273824 CTTTGAAAACATCA
1 TTTTGAAAACATCA
273838 AAAAGCTCCC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTCTAGGACTTACAGATGAACCAAAGG
Found at i:273801 original size:240 final size:240
Alignment explanation
Indices: 273365--273866 Score: 812
Period size: 240 Copynumber: 2.1 Consensus size: 240
273355 TTATGGATGA
* *
273365 CCCGAATG-TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCAAAGGTTTTGAAAATA
1 CCCGAAGGCTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCAAAGGTTTTGAAAACA
273429 TCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
66 TCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
* * *
273494 TTTTGAAAATATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATACACT
131 TTTTGAAAACATCCTGCACTCTAGGTCTTATGGATGACCCAAAGGTTTTGAAAACATCATACACT
* *
273559 GTAGGACTTACAGATGACCCGAAGGCTTT-AAATATCAAAAAGCT
196 GTAGGACTTACAGATGAACCGAAGGCTTTAAAACATCAAAAAGCT
*** *
273603 CCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTGTGGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGC-TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCAAAGGTTTTGAAAAC
* * * *
273668 ATCATGCACTGTAGGTCTTACAGATTACTCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
65 ATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
273733 TTTTTGAAAACATCCTGCACTCTAGGTCTTATGGATGACCCAAAGGTTTTGAAAACATCATGCAC
130 TTTTTGAAAACATCCTGCACTCTAGGTCTTATGGATGACCCAAAGGTTTTGAAAACATCATACAC
*
273798 TGTAGGACTTACAGATGAATCGAAGGCTTTGAAAACATCAAAAAGCT
195 TGTAGGACTTACAGATGAACCGAAGGCTTT-AAAACATCAAAAAGCT
273845 CCCGAAGGC-TTTGAAAACATCA
1 CCCGAAGGCTTTTGAAAACATCA
273867 AAAAGCTCCC
Statistics
Matches: 243, Mismatches: 17, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
238 7 0.03
240 213 0.88
242 23 0.09
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (240 bp):
CCCGAAGGCTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCAAAGGTTTTGAAAACA
TCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
TTTTGAAAACATCCTGCACTCTAGGTCTTATGGATGACCCAAAGGTTTTGAAAACATCATACACT
GTAGGACTTACAGATGAACCGAAGGCTTTAAAACATCAAAAAGCT
Found at i:273892 original size:31 final size:29
Alignment explanation
Indices: 273818--273897 Score: 133
Period size: 29 Copynumber: 2.7 Consensus size: 29
273808 ACAGATGAAT
273818 CGAAGGCTTTGAAAACATCAAAAAGCTCC
1 CGAAGGCTTTGAAAACATCAAAAAGCTCC
273847 CGAAGGCTTTGAAAACATCAAAAAGCTCC
1 CGAAGGCTTTGAAAACATCAAAAAGCTCC
*
273876 CGAAGGATTTTTGAAAACATCA
1 CGAAGG--CTTTGAAAACATCA
273898 TGCACTGAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 35 0.73
31 13 0.27
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.20
Consensus pattern (29 bp):
CGAAGGCTTTGAAAACATCAAAAAGCTCC
Found at i:274675 original size:22 final size:23
Alignment explanation
Indices: 274638--274704 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 23
274628 TAGAAATCCA
* *
274638 ATAAAGCTTTCATCTTTGAAGAG
1 ATAAATCTATCATCTTTGAAGAG
* *
274661 A-GAATCTATCATCTTTGAA-AA
1 ATAAATCTATCATCTTTGAAGAG
274682 ATAAATCTATCATCTTTGAAGAG
1 ATAAATCTATCATCTTTGAAGAG
274705 TGTAGATGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (23 bp):
ATAAATCTATCATCTTTGAAGAG
Found at i:275163 original size:55 final size:55
Alignment explanation
Indices: 275073--275176 Score: 154
Period size: 55 Copynumber: 1.9 Consensus size: 55
275063 CACTGATTCA
* *
275073 TAAAACATTTGATAATAAATTCATTATTTCCTGTGGCTTCTGCACAGATGTTCCG
1 TAAAACATTTGACAATAAATTCATCATTTCCTGTGGCTTCTGCACAGATGTTCCG
* ** *
275128 TAAAACATTTGACAATACATTCATCATTTTTTGTGGCTTCTGCCCAGAT
1 TAAAACATTTGACAATAAATTCATCATTTCCTGTGGCTTCTGCACAGAT
275177 TTCTCATCAG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 43 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (55 bp):
TAAAACATTTGACAATAAATTCATCATTTCCTGTGGCTTCTGCACAGATGTTCCG
Found at i:277908 original size:124 final size:123
Alignment explanation
Indices: 277688--277943 Score: 424
Period size: 124 Copynumber: 2.1 Consensus size: 123
277678 GACATTAGCC
* *
277688 TTTATTGGACTAATTAAAGGGTTCAGATCATCACAATGTCTTTGATTTGACAATCACAGTGGAGC
1 TTTATTAGACTAATTAAAGGGTTCAGATCATCACAATGTCTTTGACTTGACAATCACAGTGGAGC
* *
277753 AAACACCAAACTGCCAAATACCCTATCAAGGTCATGCTTTGAATATATGATTTCTTTTT
66 AAACACCAAACTGCCAAATACCCGATCAAGGTCATGCTTTGAATATATGATTT-TATTT
277812 TTTATTAGACTAATTAAAGGGTTCA-ACTCATCACAATGTCTTTGACTTGACAATCACAGTGGAG
1 TTTATTAGACTAATTAAAGGGTTCAGA-TCATCACAATGTCTTTGACTTGACAATCACAGTGGAG
* *
277876 CAAACACCGAACTGCCAAATACCCGATCAAGGTCATGCTTTGAATATATGGTTTTATTT
65 CAAACACCAAACTGCCAAATACCCGATCAAGGTCATGCTTTGAATATATGATTTTATTT
*
277935 TTCATTAGA
1 TTTATTAGA
277944 GAACTTGTTA
Statistics
Matches: 124, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
123 13 0.10
124 111 0.90
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (123 bp):
TTTATTAGACTAATTAAAGGGTTCAGATCATCACAATGTCTTTGACTTGACAATCACAGTGGAGC
AAACACCAAACTGCCAAATACCCGATCAAGGTCATGCTTTGAATATATGATTTTATTT
Found at i:280042 original size:27 final size:26
Alignment explanation
Indices: 280000--280050 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
279990 TGCAAATATA
280000 AAATGAAAATATAAAAATACAAATAC
1 AAATGAAAATATAAAAATACAAATAC
*
280026 AAATGCAAACATA-AAAAATGCAAAT
1 AAATG-AAA-ATATAAAAATACAAAT
280051 GTAATGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 5 0.23
27 14 0.64
28 3 0.14
ACGTcount: A:0.67, C:0.10, G:0.06, T:0.18
Consensus pattern (26 bp):
AAATGAAAATATAAAAATACAAATAC
Found at i:280044 original size:21 final size:20
Alignment explanation
Indices: 280020--280075 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
280010 ATAAAAATAC
280020 AAATACAAATGCAAACATAAA
1 AAATACAAATGCAAACA-AAA
* * **
280041 AAATGCAAATGTAATGAAAA
1 AAATACAAATGCAAACAAAA
*
280061 AAATACGAATGCAAA
1 AAATACAAATGCAAA
280076 ATGCAAATGC
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.16
Consensus pattern (20 bp):
AAATACAAATGCAAACAAAA
Found at i:282436 original size:8 final size:8
Alignment explanation
Indices: 282393--282459 Score: 52
Period size: 8 Copynumber: 8.8 Consensus size: 8
282383 ATAAATTAAT
282393 ATATAAAA
1 ATATAAAA
282401 A-ATAAAAA
1 ATAT-AAAA
*
282409 ATATAAAC
1 ATATAAAA
*
282417 AT-T-AAT
1 ATATAAAA
*
282423 ATATAAGA
1 ATATAAAA
282431 ATATAAAA
1 ATATAAAA
*
282439 ATAAAAAA
1 ATATAAAA
282447 ATA-AAAA
1 ATATAAAA
*
282454 AAATAA
1 ATATAA
282460 TTGAAGGAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
6 4 0.09
7 10 0.21
8 31 0.66
9 2 0.04
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (8 bp):
ATATAAAA
Found at i:283521 original size:18 final size:18
Alignment explanation
Indices: 283472--283526 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
283462 CATTTCTTTG
283472 ATATTAAAAAT-ATATAA
1 ATATTAAAAATAATATAA
* *
283489 ATATTAAGAAGAATAT-A
1 ATATTAAAAATAATATAA
*
283506 ATAATTAAAAATAATAAAA
1 AT-ATTAAAAATAATATAA
283525 AT
1 AT
283527 GAAGTATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 12 0.40
18 15 0.50
19 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (18 bp):
ATATTAAAAATAATATAA
Found at i:283538 original size:2 final size:2
Alignment explanation
Indices: 283531--283564 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
283521 AAAAATGAAG
*
283531 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
283565 AATAAGATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:284916 original size:3 final size:3
Alignment explanation
Indices: 284896--284941 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
284886 AATTATTTAT
* * *
284896 TAA TAA TGA TAC TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
284942 TTTTAAAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:285006 original size:30 final size:30
Alignment explanation
Indices: 284970--285031 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
284960 GGTGTCTACA
284970 CTAATACTATAACATGTAGTGCAATGCACC
1 CTAATACTATAACATGTAGTGCAATGCACC
285000 CTAATACTATAACATGTAGTGCAATGCACC
1 CTAATACTATAACATGTAGTGCAATGCACC
285030 CT
1 CT
285032 TTTTCACAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.27
Consensus pattern (30 bp):
CTAATACTATAACATGTAGTGCAATGCACC
Found at i:285179 original size:22 final size:22
Alignment explanation
Indices: 285149--285190 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
285139 GTGGCATATG
* * *
285149 AAATTTATCCCTAAGGACCTCT
1 AAATATATCCCGAAAGACCTCT
285171 AAATATATCCCGAAAGACCT
1 AAATATATCCCGAAAGACCT
285191 ATGAGTATGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.26
Consensus pattern (22 bp):
AAATATATCCCGAAAGACCTCT
Found at i:285447 original size:26 final size:26
Alignment explanation
Indices: 285411--285472 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
285401 TTGAATATAT
285411 TCATATGTCATATAACATGTATTGAA
1 TCATATGTCATATAACATGTATTGAA
285437 TCATATGTCATATAACATGTATTGAA
1 TCATATGTCATATAACATGTATTGAA
285463 TCATATGTCA
1 TCATATGTCA
285473 AAATATATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (26 bp):
TCATATGTCATATAACATGTATTGAA
Found at i:287216 original size:7 final size:7
Alignment explanation
Indices: 287204--287229 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
287194 TTCCCTATAG
287204 CCATGCC
1 CCATGCC
287211 CCATGCC
1 CCATGCC
287218 CCATGCC
1 CCATGCC
287225 CCATG
1 CCATG
287230 AAATAATCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.54, G:0.15, T:0.15
Consensus pattern (7 bp):
CCATGCC
Found at i:287373 original size:15 final size:14
Alignment explanation
Indices: 287340--287383 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
287330 TTCTTTTATC
*
287340 ATATTTAGAA-ATA
1 ATATTAAGAATATA
287353 ATATTAAGAATATA
1 ATATTAAGAATATA
287367 TATATTAAGAATATA
1 -ATATTAAGAATATA
287382 AT
1 AT
287384 TTTTAATGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 9 0.32
14 5 0.18
15 14 0.50
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (14 bp):
ATATTAAGAATATA
Found at i:288565 original size:82 final size:83
Alignment explanation
Indices: 288470--288628 Score: 257
Period size: 84 Copynumber: 1.9 Consensus size: 83
288460 TATTATGATA
* * * *
288470 AAATTAT-ATTTTTTTACTCGCATATCATAGATTCATATTTATATTCATAACTTTATATCGCAGA
1 AAATTATAATTTTTTTACTCACATATCATAGATTCATATTTATATTCATAACTATATATCACACA
288534 CATATCTTATTTCTTATG
66 CATATCTTATTTCTTATG
*
288552 AAATTATAATTTTTTTTACTCACATATCTTAGATTCATATTTATATTCATAACTATATATCACAC
1 AAATTATAA-TTTTTTTACTCACATATCATAGATTCATATTTATATTCATAACTATATATCACAC
288617 ACATATCTTATT
65 ACATATCTTATT
288629 CGCATACATT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
82 7 0.10
83 1 0.01
84 62 0.89
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.47
Consensus pattern (83 bp):
AAATTATAATTTTTTTACTCACATATCATAGATTCATATTTATATTCATAACTATATATCACACA
CATATCTTATTTCTTATG
Found at i:288622 original size:44 final size:44
Alignment explanation
Indices: 288490--288626 Score: 138
Period size: 44 Copynumber: 3.2 Consensus size: 44
288480 TTTTTACTCG
* * *
288490 CATATCATAGATTCATATTTATATTCATAACTTTATATCGCAGA
1 CATATCTTAGATTCATATTTATATTCATAACTTTATATCACACA
* * * * * * * *
288534 CATATCTTA-TTTCTTA-TGAAATT-ATAA-TTTTTTTTACTCA
1 CATATCTTAGATTCATATTTATATTCATAACTTTATATCACACA
*
288574 CATATCTTAGATTCATATTTATATTCATAACTATATATCACACA
1 CATATCTTAGATTCATATTTATATTCATAACTTTATATCACACA
288618 CATATCTTA
1 CATATCTTA
288627 TTCGCATACA
Statistics
Matches: 69, Mismatches: 20, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
40 16 0.23
41 9 0.13
42 10 0.14
43 9 0.13
44 25 0.36
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.45
Consensus pattern (44 bp):
CATATCTTAGATTCATATTTATATTCATAACTTTATATCACACA
Found at i:289104 original size:20 final size:20
Alignment explanation
Indices: 289063--289127 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
289053 AACTTTCCAA
289063 ATTCATAA-TTTA-TTTC-G
1 ATTCATAACTTTACTTTCAG
* *
289080 TATTCGTAGCTTTACTTTCAG
1 -ATTCATAACTTTACTTTCAG
*
289101 ATTCATAACTTTACTTTCAT
1 ATTCATAACTTTACTTTCAG
289121 ATTCATA
1 ATTCATA
289128 GTCCAATGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 6 0.15
19 4 0.10
20 28 0.72
21 1 0.03
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (20 bp):
ATTCATAACTTTACTTTCAG
Found at i:290918 original size:19 final size:20
Alignment explanation
Indices: 290894--290931 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
290884 TAAAATGATC
*
290894 CAATTTC-ACATTCTAACAG
1 CAATTTCAACACTCTAACAG
290913 CAATTTCAACACTCTAACA
1 CAATTTCAACACTCTAACA
290932 TTAATTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.39, C:0.29, G:0.03, T:0.29
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAG
Found at i:295306 original size:20 final size:20
Alignment explanation
Indices: 295254--295328 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
295244 TAGATTCAGA
*
295254 ACTTTCCAAATTCATA-ATTT
1 ACTTT-CAAATTCATAGCTTT
* *
295274 A-TTTTAGATTCATAGCTTT
1 ACTTTCAAATTCATAGCTTT
*
295293 ACTTTCAAATTCATAACTTT
1 ACTTTCAAATTCATAGCTTT
* *
295313 AATTTCAGATTCATAG
1 ACTTTCAAATTCATAG
295329 TCCAATGTAT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
18 8 0.18
19 7 0.16
20 29 0.66
ACGTcount: A:0.33, C:0.16, G:0.05, T:0.45
Consensus pattern (20 bp):
ACTTTCAAATTCATAGCTTT
Found at i:297155 original size:20 final size:20
Alignment explanation
Indices: 297123--297188 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
297113 CAAAATGATC
297123 CAATTTC-ACATTCTAACAT
1 CAATTTCAACATTCTAACAT
297142 CAATTTCAACATTCTAACAT
1 CAATTTCAACATTCTAACAT
*
297162 CAATTTCAACACTCTAACAT
1 CAATTTCAACATTCTAACAT
*
297182 TAATTTC
1 CAATTTC
297189 CAGCATAGTA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 7 0.16
20 37 0.84
ACGTcount: A:0.38, C:0.26, G:0.00, T:0.36
Consensus pattern (20 bp):
CAATTTCAACATTCTAACAT
Found at i:299066 original size:14 final size:14
Alignment explanation
Indices: 299047--299074 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
299037 AATTACCATC
299047 ACTTTATTTTATAT
1 ACTTTATTTTATAT
299061 ACTTTATTTTATAT
1 ACTTTATTTTATAT
299075 TTGTATACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (14 bp):
ACTTTATTTTATAT
Found at i:307670 original size:27 final size:26
Alignment explanation
Indices: 307640--307706 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 26
307630 ATGTAGTATC
*
307640 TAATTTTTAAAAA-TAGAAATAAACAAA
1 TAATTATTAAAAACTA-AAATAAAC-AA
*
307667 TAATTATTAAATAACTAAATTAAACAA
1 TAATTATTAAA-AACTAAAATAAACAA
307694 TAATTATTAAAAA
1 TAATTATTAAAAA
307707 AATCATTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
26 2 0.06
27 23 0.64
28 9 0.25
29 2 0.06
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.33
Consensus pattern (26 bp):
TAATTATTAAAAACTAAAATAAACAA
Found at i:308813 original size:28 final size:28
Alignment explanation
Indices: 308781--308840 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
308771 ATGGTGATTT
308781 CCACGACATAAAAGACATGTTACGTTGG
1 CCACGACATAAAAGACATGTTACGTTGG
308809 CCACGACATAAAAGACATGTTACGTTGG
1 CCACGACATAAAAGACATGTTACGTTGG
308837 CCAC
1 CCAC
308841 CTTTACTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (28 bp):
CCACGACATAAAAGACATGTTACGTTGG
Found at i:310512 original size:5 final size:5
Alignment explanation
Indices: 310499--310616 Score: 110
Period size: 5 Copynumber: 23.6 Consensus size: 5
310489 ATCAACATAT
* * * * * *
310499 ATAAC ATAAT ATAAC ATAAC ATAGC ATAAC ATAGC ATAGC ATAGC ATAGC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * * * * * * *
310549 ATAGC ATAAC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
310599 ATAAC ATAAC ATAAC ATA
1 ATAAC ATAAC ATAAC ATA
310617 CAAACATCAT
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 105 1.00
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.21
Consensus pattern (5 bp):
ATAAC
Found at i:310519 original size:15 final size:15
Alignment explanation
Indices: 310509--310616 Score: 153
Period size: 15 Copynumber: 7.2 Consensus size: 15
310499 ATAACATAAT
*
310509 ATAACATAACATAGC
1 ATAACATAGCATAGC
310524 ATAACATAGCATAGC
1 ATAACATAGCATAGC
*
310539 ATAGCATAGCATAGC
1 ATAACATAGCATAGC
310554 ATAACATAGCATAGC
1 ATAACATAGCATAGC
*
310569 ATAGCATAGCATAGC
1 ATAACATAGCATAGC
* *
310584 ATAGCATAGCATAAC
1 ATAACATAGCATAGC
* *
310599 ATAACATAACATAAC
1 ATAACATAGCATAGC
310614 ATA
1 ATA
310617 CAAACATCAT
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 86 1.00
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.20
Consensus pattern (15 bp):
ATAACATAGCATAGC
Found at i:310528 original size:10 final size:10
Alignment explanation
Indices: 310503--310616 Score: 147
Period size: 10 Copynumber: 11.4 Consensus size: 10
310493 ACATATATAA
* *
310503 CATAATATAA
1 CATAACATAG
310513 CATAACATAG
1 CATAACATAG
310523 CATAACATAG
1 CATAACATAG
*
310533 CATAGCATAG
1 CATAACATAG
*
310543 CATAGCATAG
1 CATAACATAG
310553 CATAACATAG
1 CATAACATAG
*
310563 CATAGCATAG
1 CATAACATAG
*
310573 CATAGCATAG
1 CATAACATAG
*
310583 CATAGCATAG
1 CATAACATAG
*
310593 CATAACATAA
1 CATAACATAG
*
310603 CATAACATAA
1 CATAACATAG
310613 CATA
1 CATA
310617 CAAACATCAT
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 97 1.00
ACGTcount: A:0.48, C:0.19, G:0.11, T:0.21
Consensus pattern (10 bp):
CATAACATAG
Found at i:317222 original size:19 final size:21
Alignment explanation
Indices: 317185--317227 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
317175 TCATTTCTTG
*
317185 AAAGGGATCGATCCTTTTG-A
1 AAAGAGATCGATCCTTTTGCA
*
317205 AAAGAGATCGATTC-TTTGCA
1 AAAGAGATCGATCCTTTTGCA
317225 AAA
1 AAA
317228 CAGAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (21 bp):
AAAGAGATCGATCCTTTTGCA
Found at i:317993 original size:36 final size:37
Alignment explanation
Indices: 317946--318017 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 37
317936 ACCATGTTAT
*
317946 AATTGTATCCTCATTAAAAAAATATAA-TATTTTTTA
1 AATTGTATCCTCACTAAAAAAATATAATTATTTTTTA
*
317982 AATTGTATCCTCACTATAAAAATATAATTATTTTTT
1 AATTGTATCCTCACTAAAAAAATATAATTATTTTTT
318018 TATAAAAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 25 0.76
37 8 0.24
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.46
Consensus pattern (37 bp):
AATTGTATCCTCACTAAAAAAATATAATTATTTTTTA
Found at i:318458 original size:40 final size:40
Alignment explanation
Indices: 318364--318458 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
318354 GTTCGTGAAC
* *
318364 AAACGAACATGAACAAAATTTTGTATTTGTTTAATTAAAT
1 AAACAAACAAGAACAAAATTTTGTATTTGTTTAATTAAAT
* * * *
318404 GAACAAATACGAACAAGATTTTGTATTTGTTTAATTAAAT
1 AAACAAACAAGAACAAAATTTTGTATTTGTTTAATTAAAT
318444 AAACAAACAAGAACA
1 AAACAAACAAGAACA
318459 GATGGCTCGT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (40 bp):
AAACAAACAAGAACAAAATTTTGTATTTGTTTAATTAAAT
Found at i:318519 original size:14 final size:14
Alignment explanation
Indices: 318500--318543 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
318490 CGTTCGGTAA
*
318500 TATGTTCATTCATT
1 TATGTTCGTTCATT
318514 TATGTTCGTTCATT
1 TATGTTCGTTCATT
*
318528 TATATTCGTTCATT
1 TATGTTCGTTCATT
318542 TA
1 TA
318544 CGTTTAGCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.20, C:0.14, G:0.09, T:0.57
Consensus pattern (14 bp):
TATGTTCGTTCATT
Found at i:318760 original size:40 final size:42
Alignment explanation
Indices: 318685--318768 Score: 145
Period size: 40 Copynumber: 2.0 Consensus size: 42
318675 TAATATAATC
*
318685 TTAAAATTGTTAGGAAATTAAAAAAATCTATTTTCATTTATG
1 TTAAAATTGTTAAGAAATTAAAAAAATCTATTTTCATTTATG
318727 TTAAAATTGTTAAGAAA-T-AAAAAATCTATTTTCATTTATG
1 TTAAAATTGTTAAGAAATTAAAAAAATCTATTTTCATTTATG
318767 TT
1 TT
318769 CATTTACGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 24 0.59
41 1 0.02
42 16 0.39
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (42 bp):
TTAAAATTGTTAAGAAATTAAAAAAATCTATTTTCATTTATG
Found at i:320685 original size:177 final size:180
Alignment explanation
Indices: 320356--320714 Score: 622
Period size: 182 Copynumber: 2.0 Consensus size: 180
320346 ATGGATTAAT
320356 AATTCACGTTAAAATAAAATAGTAAATTTTTAGAAAAATTGAAACCTTGGGATCAAAGAATTTTT
1 AATTCACGTTAAAATAAAATAGTAAATTTTTAGAAAAATTGAAACCTTGGGATCAAAGAATTTTT
320421 GAAAGAAGAAACAAAAATTAAATTATATATTACGATGCGAGTGAATTTTAATAACATGATATATA
66 GAAAGAAGAAACAAAAATTAAATTATATATTA--A-GCGAGTGAATTTTAATAACATGATATATA
320486 TAATATACATTTTAATATATG-AAAAC-AGTTCAAGCTGATAATAAGGGTTGTG
128 TAATATACATTTTAATATATGAAAAACAAGTTCAAGCTGATAATAA-GGTTGTG
320538 AATTCACGTTAAAATAAAATAGTAAATTTTTAGAAAAATTGAAACCTTGGGATCAAAGAATTTTT
1 AATTCACGTTAAAATAAAATAGTAAATTTTTAGAAAAATTGAAACCTTGGGATCAAAGAATTTTT
320603 GAAAGAAGAAACAAAAATTAAATTATATATT-A-CGAGTGAATTTTAATAACATG--ATATATAA
66 GAAAGAAGAAACAAAAATTAAATTATATATTAAGCGAGTGAATTTTAATAACATGATATATATAA
320664 TATAACATTTTTAATATATGAAAAACAAGTTCAAGCTGATAATAAGGTTGT
131 TAT-ACA-TTTTAATATATGAAAAACAAGTTCAAGCTGATAATAAGGTTGT
320715 TTGTGATATT
Statistics
Matches: 173, Mismatches: 0, Indels: 12
0.94 0.00 0.06
Matches are distributed among these distances:
175 11 0.06
176 3 0.02
177 33 0.19
178 11 0.06
179 19 0.11
182 96 0.55
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (180 bp):
AATTCACGTTAAAATAAAATAGTAAATTTTTAGAAAAATTGAAACCTTGGGATCAAAGAATTTTT
GAAAGAAGAAACAAAAATTAAATTATATATTAAGCGAGTGAATTTTAATAACATGATATATATAA
TATACATTTTAATATATGAAAAACAAGTTCAAGCTGATAATAAGGTTGTG
Found at i:323779 original size:24 final size:20
Alignment explanation
Indices: 323731--323779 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
323721 TATCATTATC
323731 TTTTATTTAGAAATTAGCTA
1 TTTTATTTAGAAATTAGCTA
323751 TTTTATTTAGAAATTAGCTA
1 TTTTATTTAGAAATTAGCTA
323771 TTTTATTTA
1 TTTTATTTA
323780 CTTAAAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (20 bp):
TTTTATTTAGAAATTAGCTA
Found at i:336220 original size:19 final size:20
Alignment explanation
Indices: 336196--336653 Score: 202
Period size: 20 Copynumber: 22.6 Consensus size: 20
336186 AATGACCAAT
* *
336196 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
336215 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
336235 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
336255 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
336275 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
336295 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
336316 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
336339 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
336359 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
336379 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
336399 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
336419 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
336439 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
336459 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
336479 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
336499 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
336519 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
336539 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
336559 ATAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
336579 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
336602 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
336622 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
*
336642 AGAATCGCAACG
1 AAAATCGCAACG
336654 TTGAAAATAA
Statistics
Matches: 384, Mismatches: 43, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.04
20 324 0.84
21 14 0.04
23 29 0.08
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:336366 original size:20 final size:20
Alignment explanation
Indices: 336341--336651 Score: 507
Period size: 20 Copynumber: 15.4 Consensus size: 20
336331 TTTAGAAGAA
336341 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
336361 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
336381 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
336401 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
336421 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
336441 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
336461 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
336481 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
336501 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
336521 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
* *
336541 AATCGCAATGCGATTTATAT
1 AATCGCAATGCGATTGATAG
*
336561 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGATAG
* *
336581 AGTCGCAACGCGATTTAGA-AG
1 AATCGCAATGCGA-TT-GATAG
* *
336602 AAAATCGCAATGCGACTGAGAG
1 --AATCGCAATGCGATTGATAG
*
336624 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGATAG
336644 AATCGCAA
1 AATCGCAA
336652 CGTTGAAAAT
Statistics
Matches: 273, Mismatches: 13, Indels: 10
0.92 0.04 0.03
Matches are distributed among these distances:
20 251 0.92
21 6 0.02
22 5 0.02
23 11 0.04
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (20 bp):
AATCGCAATGCGATTGATAG
Found at i:336772 original size:6 final size:6
Alignment explanation
Indices: 336761--336807 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
336751 GACACGTATT
336761 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCAC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCAC
336808 AATACAACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.34, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:354359 original size:29 final size:29
Alignment explanation
Indices: 354326--354386 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
354316 TTAACTCGAT
354326 ATATTATAATTATATTATT-ATAATATACA
1 ATATTATAATTATATT-TTAATAATATACA
* * *
354355 ATATTATACTTTTATTTTAATAATATATA
1 ATATTATAATTATATTTTAATAATATACA
354384 ATA
1 ATA
354387 AATTAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (29 bp):
ATATTATAATTATATTTTAATAATATACA
Found at i:354505 original size:22 final size:23
Alignment explanation
Indices: 354480--354531 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
354470 AAATATAATA
354480 TAATATTT-TAATATTA-TATTTT
1 TAATATTTATAATATTATTA-TTT
354502 TAATAATTTAATAATATTATTATTT
1 TAAT-ATTT-ATAATATTATTATTT
354527 TAATA
1 TAATA
354532 AGTAATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
22 4 0.15
23 4 0.15
24 1 0.04
25 15 0.58
26 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TAATATTTATAATATTATTATTT
Found at i:354528 original size:39 final size:36
Alignment explanation
Indices: 354474--354570 Score: 97
Period size: 39 Copynumber: 2.6 Consensus size: 36
354464 TCCTTAAAAT
* * * *
354474 ATAATA-TAATATTTTAATATTATATTTTTAATAATTTA
1 ATAATATTATTATTTTAATAGTA-ATTATT-AT-ATTAA
354512 ATAATATTATTATTTTAATAAGTAATTATTATATTAA
1 ATAATATTATTATTTTAAT-AGTAATTATTATATTAA
354549 ATAATATATTATTATTTTAATA
1 AT-A-ATATTATTATTTTAATA
354571 AATAATTAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
37 6 0.12
38 10 0.20
39 32 0.63
40 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (36 bp):
ATAATATTATTATTTTAATAGTAATTATTATATTAA
Found at i:354559 original size:20 final size:19
Alignment explanation
Indices: 354510--354571 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
354500 TTTAATAATT
*
354510 TAATAATATTATTATTTTAA
1 TAAT-ATATTATTATTTAAA
354530 TAAGTA-ATTATTATATTAAA
1 TAA-TATATTATTAT-TTAAA
*
354550 TAATATATTATTATTTTAA
1 TAATATATTATTATTTAAA
354569 TAA
1 TAA
354572 ATAATTAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 17 0.46
20 19 0.51
21 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATATATTATTATTTAAA
Found at i:354578 original size:16 final size:17
Alignment explanation
Indices: 354508--354578 Score: 63
Period size: 19 Copynumber: 3.9 Consensus size: 17
354498 TTTTTAATAA
*
354508 TTTAATAATATTATTAT
1 TTTAATAATATAATTAT
*
354525 TTTAATAAGTAATTATTAT
1 TTTAATAA-T-ATAATTAT
*
354544 ATTAAATAATATATTATTAT
1 -TTTAATAATATA--ATTAT
354564 TTTAATAA-ATAATTA
1 TTTAATAATATAATTA
354579 ACATAATTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
16 4 0.09
17 8 0.17
18 6 0.13
19 16 0.35
20 12 0.26
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (17 bp):
TTTAATAATATAATTAT
Found at i:354592 original size:39 final size:39
Alignment explanation
Indices: 354510--354612 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 39
354500 TTTAATAATT
* **
354510 TAATAATATTATTATTTTAATAAGTAATTATTATATTAAA
1 TAAT-ATATTATTATTTTAATAAATAATTAACATATTAAA
*
354550 TAATATATTATTATTTTAATAAATAATTAACATAATT-TA
1 TAATATATTATTATTTTAATAAATAATTAACAT-ATTAAA
354589 TAATA-ATT-TTATTTTAATGAAATA
1 TAATATATTATTATTTTAAT-AAATA
354613 TAATAATCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
37 10 0.18
38 8 0.14
39 32 0.56
40 7 0.12
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (39 bp):
TAATATATTATTATTTTAATAAATAATTAACATATTAAA
Found at i:354677 original size:15 final size:14
Alignment explanation
Indices: 354659--354690 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
354649 ATATTATTTT
354659 AATAATATTAACATA
1 AATAATATTAA-ATA
354674 AATAATATTAAATA
1 AATAATATTAAATA
354688 AAT
1 AAT
354691 TATTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
AATAATATTAAATA
Found at i:354725 original size:21 final size:21
Alignment explanation
Indices: 354699--354745 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
354689 ATTATTATAA
*
354699 TATTTTAAAAATAAATACTAT
1 TATTTTAAAAATAAATAATAT
***
354720 TATTTTGTTAATAAATAATAT
1 TATTTTAAAAATAAATAATAT
354741 TATTT
1 TATTT
354746 ATTGTATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TATTTTAAAAATAAATAATAT
Found at i:355694 original size:104 final size:105
Alignment explanation
Indices: 355520--355716 Score: 335
Period size: 104 Copynumber: 1.9 Consensus size: 105
355510 TAAATATATG
*
355520 ATTGATATTTTATTTAAGATAATTAAAAATATTTATATTTACTTTATTTCTTTTCTAAGCAATCA
1 ATTGATATTTTATTTAAGATAATTAAAAATATTTATATTTACTTTATTTCTTTTCTAAACAATCA
*
355585 CTAATATCTACATTTGATTATTAGATCTAATAAATACTTT
66 CTAATATCTACATTTGATTATAAGATCTAATAAATACTTT
*
355625 ATTGATATTTTATTT-AGATAATTAAACATATTTATATTTACTTTATTT-TTTTCTAATACAATC
1 ATTGATATTTTATTTAAGATAATTAAAAATATTTATATTTACTTTATTTCTTTTCTAA-ACAATC
*
355688 ATTAATATCTACATTTGATTATAAGATCT
65 ACTAATATCTACATTTGATTATAAGATCT
355717 TAAAGATAAT
Statistics
Matches: 87, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
103 8 0.09
104 64 0.74
105 15 0.17
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.50
Consensus pattern (105 bp):
ATTGATATTTTATTTAAGATAATTAAAAATATTTATATTTACTTTATTTCTTTTCTAAACAATCA
CTAATATCTACATTTGATTATAAGATCTAATAAATACTTT
Found at i:357466 original size:18 final size:18
Alignment explanation
Indices: 357443--357477 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
357433 ACTGAATATT
*
357443 TGTCCCGAAGGACCACTA
1 TGTCCCAAAGGACCACTA
357461 TGTCCCAAAGGACCACT
1 TGTCCCAAAGGACCACT
357478 GATAATCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:363566 original size:18 final size:18
Alignment explanation
Indices: 363543--363595 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
363533 ACTGAATATT
363543 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
*
363561 TGTCCCGAAGGACCACTA
1 TGTCCCGAATGACCACTA
363579 TGTCCCGAATGACCACT
1 TGTCCCGAATGACCACT
363596 GATAATCCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.26, C:0.34, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:364868 original size:15 final size:14
Alignment explanation
Indices: 364838--364871 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
364828 TATACCATCC
364838 AAGTA-AATTTATA
1 AAGTATAATTTATA
364851 AAGTATAATTTAATA
1 AAGTATAATTT-ATA
364866 AAGTAT
1 AAGTAT
364872 TACTCAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 5 0.26
15 9 0.47
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (14 bp):
AAGTATAATTTATA
Found at i:364972 original size:32 final size:33
Alignment explanation
Indices: 364936--364997 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 33
364926 TAACATGGAT
*
364936 TATTTGTAGGTAATTTTA-TTTAATTTATTTTA
1 TATTTGTAGGTAAATTTATTTTAATTTATTTTA
364968 TATTTGTAGGTAAATTTATTTTAATTTATT
1 TATTTGTAGGTAAATTTATTTTAATTTATT
364998 AAAATTAGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (33 bp):
TATTTGTAGGTAAATTTATTTTAATTTATTTTA
Found at i:365507 original size:24 final size:24
Alignment explanation
Indices: 365480--365541 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
365470 GTTCGTGAAC
*
365480 GTTCGGTTATGTTCGTACGGTTAT
1 GTTCGTTTATGTTCGTACGGTTAT
*
365504 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTACGGTTAT
365528 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
365542 ATTCATTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.10, C:0.13, G:0.26, T:0.52
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTACGGTTAT
Found at i:365534 original size:14 final size:14
Alignment explanation
Indices: 365479--365534 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
365469 CGTTCGTGAA
365479 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
365493 CGTACGGTTATGTT
1 CGTTCGGTTATGTT
365507 CG-T---TTATGTT
1 CGTTCGGTTATGTT
365517 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
365531 CGTT
1 CGTT
365535 TATGTTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
14 26 0.72
ACGTcount: A:0.09, C:0.14, G:0.27, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:365551 original size:24 final size:24
Alignment explanation
Indices: 365480--365554 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
365470 GTTCGTGAAC
* * * *
365480 GTTCGGTTATGTTCGTACGGTTAT
1 GTTCGTTTATGTTCATTCAGTTAT
* *
365504 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCATTCAGTTAT
*
365528 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCATTCAGTTAT
365552 GTT
1 GTT
365555 TAACCCAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.12, C:0.12, G:0.23, T:0.53
Consensus pattern (24 bp):
GTTCGTTTATGTTCATTCAGTTAT
Found at i:366659 original size:16 final size:16
Alignment explanation
Indices: 366628--366686 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
366618 GGGTATCCAA
*
366628 CGTTTATGTTCGTGTT
1 CGTTTATGTTCATGTT
* *
366644 CATTTATATTCATGTT
1 CGTTTATGTTCATGTT
366660 CGTTTATGTTCATGTT
1 CGTTTATGTTCATGTT
366676 CGTTTATGTTC
1 CGTTTATGTTC
366687 GTTTATTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.14, C:0.14, G:0.17, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCATGTT
Done.