Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003629.1 Hibiscus syriacus cultivar Beakdansim tig00007686_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: 55776
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:10799 original size:10 final size:10
Alignment explanation
Indices: 10784--10813 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
10774 AATAAAATTT
10784 AAGATCGAAC
1 AAGATCGAAC
10794 AAGATCGAAC
1 AAGATCGAAC
10804 AAGATCGAAC
1 AAGATCGAAC
10814 GGTCACCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.50, C:0.20, G:0.20, T:0.10
Consensus pattern (10 bp):
AAGATCGAAC
Found at i:11697 original size:182 final size:182
Alignment explanation
Indices: 11281--12135 Score: 1186
Period size: 182 Copynumber: 4.7 Consensus size: 182
11271 TGTTGGTTTA
* * * *
11281 TGTCGATACTTTATAAAAACTGTATCGATCCACATCAATATAACAGGTAAAAATATGACAAAACC
1 TGTCGATACTTTATAACAA-TGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACC
* * * * *
11346 GGTCTCGAAAAGACAAAACTGGTACAGCG-GTACTGGATATATTGAAAGTGTCGATACTTTAATA
65 GGTCTCTAAAAGACAAAACCGGTATAGAGCG-ACCGGATATATTGAAAGTGTCGATACTTTAATA
*
11410 TAAGTAT---CACTTTGTGAATTTAAAAGAGAAACTGTTTTAGCGCCTATAAAG
129 TAAGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
** * *
11461 TGTCGATGTTTTATAACAATGTATCGTTCCACAACGATATAACAGGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCG
*
11526 GTCTCTAAAAGACAAAACCGGTATAGAGCGATCGGATATATTGAAAGTGTCGATACTTTAATATA
66 GTCTCTAAAAGACAAAACCGGTATAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATA
*
11591 AGTATCGACACTTTGTGAATTTAAAAGAGAAAC-GATTTTAGAGCCTATAAAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAACAG-TTTTAGCGCCTATAAAG
* **
11643 TGTCGATACTTTATAACAATGTATTGATCCACAACGATATAACAAGTAAAAATATGACAAAATTG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCG
* * *
11708 GTCTCTAAATGACAAAATCGGTATAGAGCGACCAGATATATTGAAAGTGTCGATACTTTAATATA
66 GTCTCTAAAAGACAAAACCGGTATAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATA
* *
11773 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATACAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
* * * *
11825 TGTCGATACTTTATAACAATGTATCGATTCTCAACGATATAACAAGTAAAAATATGATAAAATCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCG
* * *
11890 GTCTCTAAAGGACAAAATCGGTATAGAGCGACCGAATATATTGAAAGTGTCGATACTTTAATATA
66 GTCTCTAAAAGACAAAACCGGTATAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATA
* * * * * *
11955 AGTATCGACACTTTGTGAATTTAAAAGATAAGCAGCTTTAGCGTCAATAAAA
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
* * *
12007 TGTCGATACTTTATAAAAATGTATCGATCAATAACGATATAACATA-TAAAAATATGACAAAAAC
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACA-AGTAAAAATATGAC-AAAAC
** * * *
12071 CAATCTC-AAAATGACAAAACCGGTA-AAACGCTACCAGATATATTGAAAGTGTCGATACTTTAA
64 CGGTCTCTAAAA-GACAAAACCGGTATAGA-GCGACCGGATATATTGAAAGTGTCGATACTTTAA
12134 TA
127 TA
12136 AGTATGCGTA
Statistics
Matches: 609, Mismatches: 56, Indels: 17
0.89 0.08 0.02
Matches are distributed among these distances:
179 105 0.17
180 17 0.03
181 1 0.00
182 430 0.71
183 56 0.09
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (182 bp):
TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCG
GTCTCTAAAAGACAAAACCGGTATAGAGCGACCGGATATATTGAAAGTGTCGATACTTTAATATA
AGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
Found at i:14399 original size:17 final size:18
Alignment explanation
Indices: 14377--14412 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
14367 GAAGATTATT
*
14377 GGCAATG-AGGTAGAGGA
1 GGCAATGAAGGCAGAGGA
14394 GGCAATGAAGGCAGAGGA
1 GGCAATGAAGGCAGAGGA
14412 G
1 G
14413 AAGGAAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.36, C:0.08, G:0.47, T:0.08
Consensus pattern (18 bp):
GGCAATGAAGGCAGAGGA
Found at i:14822 original size:199 final size:197
Alignment explanation
Indices: 14433--15012 Score: 659
Period size: 199 Copynumber: 2.9 Consensus size: 197
14423 AGATGGTTGT
* * * *
14433 ATTTGTGTCGATATTTATTGTCCGTAATGAATGCCCAAATGAGGTGCACACATAAAGTGTCGATA
1 ATTTGTGTCGATACTT-TTGTCCATAATGAATG-TCAAACGAGGTGCACACATAAAGTGTCGATA
* * *
14498 CATTTATTAAAAGTATCGATCCCAATAAAATCGAAACTGATAATTATACTGTAATATGTAAATTT
64 CATTTATTAAAAGTATCGAT-CCAA-AAAATCGAAACCGATAATTATAATGTAATAGGTAAATTT
* * **
14563 ACAATGTAACATATATAAATATACCGGTTTTATGAGAAAATAGGTCAGCATAAAGTATCGACACT
127 ACAATGTAACAGATAGAAATATACCGGTTTTATGAGAAAATAGGTCAAAATAAAGTATCGACACT
14628 TGTTAA
192 TGTTAA
* *
14634 ATTTGTGTTGATACATTTTGTCCATAATGAATGTCAAACG-GGTGCACGCATAAAGTGTCGATAC
1 ATTTGTGTCGATAC-TTTTGTCCATAATGAATGTCAAACGAGGTGCACACATAAAGTGTCGATAC
* * *
14698 ATTTATTAAAAGTATCGATCTCAAAAACATCGAAACCGATAATTACAATATGATAGGTAAATTTA
65 ATTTATTAAAAGTATCGATC-CAAAAA-ATCGAAACCGATAATTATAATGTAATAGGTAAATTTA
* * * * *
14763 CAATGTACCCGATAGAAATATACTGGTTTTATGAGAAAATAGGT-ATAAATAATGTATCGATACT
128 CAATGTAACAGATAGAAATATACCGGTTTTATGAGAAAATAGGTCA-AAATAAAGTATCGACACT
*
14827 TTTTAA
192 TGTTAA
* * * * * *
14833 GTTTGTGTCGATGCTTTTTTCCAGAATGAATGTCCAACGAGGTGCACACATAAAGTATCGATACA
1 ATTTGTGTCGATACTTTTGTCCATAATGAATGTCAAACGAGGTGCACACATAAAGTGTCGATACA
** *
14898 TTTCA--AATTGTATCGATCCAAAAAATATCGAAACCGATAATTATAATGTAATAGGTAAATTTG
66 TTT-ATTAAAAGTATCGATCC-AAAAA-ATCGAAACCGATAATTATAATGTAATAGGTAAATTTA
* * * * * * *
14961 TAATTTTACCAG-TATAAATATACCGG-TTTACTTATAAAATAGGTCAATATAA
128 CAA-TGTAACAGATAGAAATATACCGGTTTTA-TGAGAAAATAGGTCAAAATAA
15013 GCGCTACTTA
Statistics
Matches: 324, Mismatches: 45, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
197 5 0.02
198 106 0.33
199 178 0.55
200 6 0.02
201 27 0.08
202 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (197 bp):
ATTTGTGTCGATACTTTTGTCCATAATGAATGTCAAACGAGGTGCACACATAAAGTGTCGATACA
TTTATTAAAAGTATCGATCCAAAAAATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAA
TGTAACAGATAGAAATATACCGGTTTTATGAGAAAATAGGTCAAAATAAAGTATCGACACTTGTT
AA
Found at i:15103 original size:87 final size:87
Alignment explanation
Indices: 15007--15169 Score: 317
Period size: 87 Copynumber: 1.9 Consensus size: 87
14997 AAATAGGTCA
*
15007 ATATAAGCGCTACTTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
15072 CCGGTTAAATGTCTATTTTATT
66 CCGGTTAAATGTCTATTTTATT
15094 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
15159 CCGGTTAAATG
66 CCGGTTAAATG
15170 ATATAACATA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 75 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATGTCTATTTTATT
Found at i:15141 original size:23 final size:23
Alignment explanation
Indices: 15091--15135 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
15081 TGTCTATTTT
*
15091 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
15114 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
15136 TGTTATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:15538 original size:161 final size:161
Alignment explanation
Indices: 15266--15587 Score: 608
Period size: 161 Copynumber: 2.0 Consensus size: 161
15256 CATACAGTAG
* * *
15266 GAAACAATTTGAGTTTATTTTGTTGTAGTTTTAGGGTTTAATGTACAATTTAATCTTTTAATTAT
1 GAAACAATTTGAGTTCATTTTGCTGTAGTTTTAGGGTTTAATGTACAATTTAATATTTTAATTAT
15331 ATCATTTAATCACTTTGATATTTAAATATGTTTATAAAATAATATTTAAAGTTTTATTTCAATAA
66 ATCATTTAATCACTTTGATATTTAAATATGTTTATAAAATAATATTTAAAGTTTTATTTCAATAA
15396 TCGATTTATTATTAAAAAATTAATAATACAC
131 TCGATTTATTATTAAAAAATTAATAATACAC
*
15427 GAAACAGTTTGAGTTCATTTTGCTGTAGTTTTAGGGTTTAATGTACAATTTAATATTTTAATTAT
1 GAAACAATTTGAGTTCATTTTGCTGTAGTTTTAGGGTTTAATGTACAATTTAATATTTTAATTAT
15492 ATCATTTAATCACTTTGATATTTAAATATGTTTATAAAATAATATTTAAAGTTTTATTTCAATAA
66 ATCATTTAATCACTTTGATATTTAAATATGTTTATAAAATAATATTTAAAGTTTTATTTCAATAA
15557 TCGATTTATTATTAAAAAATTAATAATACAC
131 TCGATTTATTATTAAAAAATTAATAATACAC
15588 AACTAAAGAT
Statistics
Matches: 157, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
161 157 1.00
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (161 bp):
GAAACAATTTGAGTTCATTTTGCTGTAGTTTTAGGGTTTAATGTACAATTTAATATTTTAATTAT
ATCATTTAATCACTTTGATATTTAAATATGTTTATAAAATAATATTTAAAGTTTTATTTCAATAA
TCGATTTATTATTAAAAAATTAATAATACAC
Found at i:21070 original size:20 final size:20
Alignment explanation
Indices: 21045--21096 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
21035 GATTTTCCAG
* *
21045 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
*
21065 AATCGCAACCCGAACACATA
1 AATCGCAACGCGAACACATA
21085 AATCGCAACGCG
1 AATCGCAACGCG
21097 TATCCGTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.42, C:0.29, G:0.17, T:0.12
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:21106 original size:20 final size:20
Alignment explanation
Indices: 21083--21237 Score: 222
Period size: 20 Copynumber: 7.7 Consensus size: 20
21073 CCCGAACACA
21083 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
21103 TAAACCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
21123 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
21143 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
21163 TAAATCGCAACGCGTGTCCG
1 TAAATCGCAACGCGTATCCG
* *
21183 TAAATCGCAACGAC-AATACG
1 TAAATCGCAACG-CGTATCCG
*
21203 TAAAATCGCAACGCATATCCG
1 T-AAATCGCAACGCGTATCCG
21224 TAAATCGCAACGCG
1 TAAATCGCAACGCG
21238 ATTTTTAAAG
Statistics
Matches: 119, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
20 102 0.86
21 17 0.14
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.19
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:21112 original size:40 final size:40
Alignment explanation
Indices: 21045--21237 Score: 203
Period size: 40 Copynumber: 4.8 Consensus size: 40
21035 GATTTTCCAG
* ** * * *
21045 AATCGCAACGCGAATATGAAAATCGCAACCCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTAAC-CGTA
* * *
21085 AATCGCAACGCGTATCCGTAAACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCGTA
* *
21125 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCGTA
* *
21165 AATCGCAACGCGTGTCCGTAAATCGCAACGAC--AATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGTAA-CCGT-A
*
21206 AATCGCAACGCATATCCGTAAATCGCAACGCG
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG
21238 ATTTTTAAAG
Statistics
Matches: 130, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.01
40 97 0.75
41 32 0.25
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCGTA
Found at i:21133 original size:60 final size:60
Alignment explanation
Indices: 21045--21237 Score: 219
Period size: 60 Copynumber: 3.2 Consensus size: 60
21035 GATTTTCCAG
* ** * * *
21045 AATCGCAACGCGAATATGAAAATCGCAACCCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACACGAACACGTAAATCGCAACGCGTATCCGTA
* * * * *
21105 AACCGCAACGTGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACACG-AACACGTAAATCGCAACGCGTATCCGTA
* * *
21165 AATCGCAACGCGTGTCCGTAAATCGCAACGAC-AATACGTAAAATCGCAACGCATATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAAC-ACGAACACGT-AAATCGCAACGCGTATCCGTA
21226 AATCGCAACGCG
1 AATCGCAACGCG
21238 ATTTTTAAAG
Statistics
Matches: 111, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
59 1 0.01
60 76 0.68
61 34 0.31
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACACGAACACGTAAATCGCAACGCGTATCCGTA
Found at i:21635 original size:14 final size:14
Alignment explanation
Indices: 21616--21672 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
21606 TTTCATTTCG
21616 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
21630 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
*
21649 CGTTGCTATTCTCT
1 CGTTGCGATTCTCT
21663 CGTTGCGATT
1 CGTTGCGATT
21673 TTCAAGTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 9 0.26
ACGTcount: A:0.09, C:0.26, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:21647 original size:33 final size:32
Alignment explanation
Indices: 21604--21673 Score: 122
Period size: 33 Copynumber: 2.2 Consensus size: 32
21594 ATTTCACTTA
21604 GATTTCATTTCGCGTTGCGATTCTCTCGTTGC
1 GATTTCATTTCGCGTTGCGATTCTCTCGTTGC
*
21636 GATTTCCATTTCGCGTTGCTATTCTCTCGTTGC
1 GATTT-CATTTCGCGTTGCGATTCTCTCGTTGC
21669 GATTT
1 GATTT
21674 TCAAGTTAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 5 0.14
33 31 0.86
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (32 bp):
GATTTCATTTCGCGTTGCGATTCTCTCGTTGC
Found at i:21654 original size:19 final size:18
Alignment explanation
Indices: 21604--21654 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 18
21594 ATTTCACTTA
21604 GATTTCATTTCGCGTTGC
1 GATTTCATTTCGCGTTGC
*
21622 GA-TTC---TCTCGTTGC
1 GATTTCATTTCGCGTTGC
21636 GATTTCCATTTCGCGTTGC
1 GATTT-CATTTCGCGTTGC
21655 TATTCTCTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
14 10 0.38
15 2 0.08
16 1 0.04
17 3 0.12
18 2 0.08
19 8 0.31
ACGTcount: A:0.10, C:0.25, G:0.22, T:0.43
Consensus pattern (18 bp):
GATTTCATTTCGCGTTGC
Found at i:21782 original size:21 final size:21
Alignment explanation
Indices: 21756--21832 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
21746 TGCAGAAGAG
21756 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
21777 TCGCAACGCGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
*
21797 TCTGCAACGAGATAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
21819 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
21833 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.19
21 29 0.62
22 9 0.19
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:21836 original size:14 final size:14
Alignment explanation
Indices: 21817--21873 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
21807 GATAAATGAA
21817 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
21831 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
21850 AATCGCAACGAGAG
1 AATCGCAACGAGAG
21864 AATCGCAACG
1 AATCGCAACG
21874 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:21848 original size:33 final size:33
Alignment explanation
Indices: 21810--21889 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
21800 GCAACGAGAT
21810 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
21843 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
21876 AAACCAAAATCGCA
1 AAATGAAAATCGCA
21890 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:21926 original size:14 final size:14
Alignment explanation
Indices: 21907--21963 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
21897 TTTCATTTCG
21907 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
21921 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
21940 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
21954 CGTTGCGATT
1 CGTTGCGATT
21964 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:21932 original size:33 final size:33
Alignment explanation
Indices: 21890--22012 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
21880 CAAAATCGCA
21890 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
21923 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
21956 TTGCGATTTTCATTTCTCTCGTTGCGATAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTTGC----G--ATTCTCTCG
21997 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
22013 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 8 0.10
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:21974 original size:21 final size:21
Alignment explanation
Indices: 21948--22012 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
21938 CGCGTTGCGA
21948 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
21969 TTCTCTCGTTGCGATAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
21989 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
22010 TTC
1 TTC
22013 AACCAAAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 18 0.46
21 21 0.54
ACGTcount: A:0.11, C:0.25, G:0.15, T:0.49
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:23970 original size:19 final size:19
Alignment explanation
Indices: 23930--24050 Score: 144
Period size: 19 Copynumber: 6.6 Consensus size: 19
23920 TAGTTTACTT
* *
23930 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
23950 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
23969 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
23988 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
24002 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
24021 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
24040 TCGCATCGCGA
1 TCGCAACGCGA
24051 TTTTCATTTC
Statistics
Matches: 88, Mismatches: 8, Indels: 11
0.82 0.07 0.10
Matches are distributed among these distances:
14 9 0.10
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 60 0.68
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:24069 original size:19 final size:19
Alignment explanation
Indices: 24047--24212 Score: 145
Period size: 19 Copynumber: 9.2 Consensus size: 19
24037 AAATCGCATC
24047 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
*
24066 GCGA--TTC---TCCCGTT
1 GCGATTTTCATTTCGCGTT
*
24080 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCGTT
*
24099 GCGA--TTC-TGT--CGTT
1 GCGATTTTCATTTCGCGTT
*
24113 GCGATTTTCATTTTGCGTT
1 GCGATTTTCATTTCGCGTT
**
24132 GCGATTTTGGTTTCGCGTT
1 GCGATTTTCATTTCGCGTT
** *
24151 GCGATTTTGGTTTCTCGTT
1 GCGATTTTCATTTCGCGTT
*
24170 GCGATTCTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
* *
24189 GCGATTTTAAGTTTCGTGTT
1 GCGATTTTCA-TTTCGCGTT
24209 GCGA
1 GCGA
24213 AAGTAAACTA
Statistics
Matches: 119, Mismatches: 17, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
14 17 0.14
16 8 0.07
17 8 0.07
19 74 0.62
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:24089 original size:33 final size:33
Alignment explanation
Indices: 24047--24137 Score: 146
Period size: 33 Copynumber: 2.8 Consensus size: 33
24037 AAATCGCATC
24047 GCGATTTTCATTTCGCGTTGCGATTCTCCCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCCCGTT
* **
24080 GCGATTTTCATTTCGCATTGCGATTCTGTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCCCGTT
*
24113 GCGATTTTCATTTTGCGTTGCGATT
1 GCGATTTTCATTTCGCGTTGCGATT
24138 TTGGTTTCGC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.45
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCCCGTT
Found at i:24151 original size:38 final size:37
Alignment explanation
Indices: 24047--24196 Score: 138
Period size: 33 Copynumber: 4.2 Consensus size: 37
24037 AAATCGCATC
* *
24047 GCGATTTTCATTTCGCGTTGCGATTC----TCCCGTT
1 GCGATTTTCATTTTGCGTTGCGATTCTGTTTCGCGTT
* *
24080 GCGATTTTCATTTCGCATTGCGATTCTG--T--CGTT
1 GCGATTTTCATTTTGCGTTGCGATTCTGTTTCGCGTT
*
24113 GCGATTTTCATTTTGCGTTGCGATTTTGGTTTCGCGTT
1 GCGATTTTCATTTTGCGTTGCGATTCT-GTTTCGCGTT
** *
24151 GCGATTTTGGTTTCT-CGTTGCGATTCTCATTTCGCGTT
1 GCGATTTTCATTT-TGCGTTGCGATTCT-GTTTCGCGTT
24189 GCGATTTT
1 GCGATTTT
24197 AAGTTTCGTG
Statistics
Matches: 100, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
33 53 0.53
34 1 0.01
35 1 0.01
36 1 0.01
38 43 0.43
39 1 0.01
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (37 bp):
GCGATTTTCATTTTGCGTTGCGATTCTGTTTCGCGTT
Found at i:26700 original size:12 final size:12
Alignment explanation
Indices: 26683--26707 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26673 TCTTCGGGGA
26683 CTTTTTCTTCTT
1 CTTTTTCTTCTT
26695 CTTTTTCTTCTT
1 CTTTTTCTTCTT
26707 C
1 C
26708 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:27648 original size:20 final size:20
Alignment explanation
Indices: 27620--27848 Score: 253
Period size: 20 Copynumber: 11.4 Consensus size: 20
27610 AAATTTTAGT
* * *
27620 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
27640 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
27660 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
27680 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
27700 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
27720 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
27740 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
27760 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
27780 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
27800 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
27820 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
27840 GTTGCGATT
1 GTTGCGATT
27849 CTGGAAAATC
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 184 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:28534 original size:18 final size:18
Alignment explanation
Indices: 28513--28547 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28503 TGATTATGTT
28513 ATATAAATAAAAATAAAA
1 ATATAAATAAAAATAAAA
*
28531 ATATAAATATAAATAAA
1 ATATAAATAAAAATAAA
28548 TCTGCTGATG
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
ATATAAATAAAAATAAAA
Found at i:28538 original size:12 final size:12
Alignment explanation
Indices: 28513--28547 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
28503 TGATTATGTT
28513 ATATAAATAAAA
1 ATATAAATAAAA
* *
28525 ATAAAAATATAA
1 ATATAAATAAAA
28537 ATATAAATAAA
1 ATATAAATAAA
28548 TCTGCTGATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
ATATAAATAAAA
Found at i:30475 original size:183 final size:186
Alignment explanation
Indices: 30126--30501 Score: 616
Period size: 183 Copynumber: 2.0 Consensus size: 186
30116 ATATAAATTA
*
30126 AATATTTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATAAATAATTATAAAATAAAAA
1 AATATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATAAATAATTATAAAATAAAAA
*
30191 ATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTATTAGATCTTAAATTA
66 ATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTATTAGATATTAAATTA
* *
30256 TTAATTGGGTTTTAAATGATTTGAGCTTAGCCCATATGTTATATAT-AATATATTT
131 TTAATTAGGTTTTAAATGATTTGAGCTTAACCCATATGTTATATATAAATATATTT
* *
30311 AATATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAA
1 AATATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATAAATAATTATAAAATAAAAA
* * *
30375 ATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATATTAAATTA
66 ATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTATTAGATATTAAATTA
* *
30439 TTAATTAGGTTTTTAATGATTTG-GGTTGAACCCATATGTTATATATAAATATATTT
131 TTAATTAGGTTTTAAATGATTTGAGCTT-AACCCATATGTTATATATAAATATATTT
30495 AATATTT
1 AATATTT
30502 AAAATTTAAT
Statistics
Matches: 178, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
182 3 0.02
183 91 0.51
184 70 0.39
185 14 0.08
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (186 bp):
AATATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATAAATAATTATAAAATAAAAA
ATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTATTAGATATTAAATTA
TTAATTAGGTTTTAAATGATTTGAGCTTAACCCATATGTTATATATAAATATATTT
Found at i:30844 original size:20 final size:20
Alignment explanation
Indices: 30819--30858 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
30809 TAGTTGTATA
*
30819 CTATTCTTATCTCATTAACG
1 CTATTCTTATCTCATCAACG
*
30839 CTATTCTTGTCTCATCAACG
1 CTATTCTTATCTCATCAACG
30859 ATGAAGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.28, G:0.07, T:0.42
Consensus pattern (20 bp):
CTATTCTTATCTCATCAACG
Found at i:31494 original size:182 final size:180
Alignment explanation
Indices: 31248--31734 Score: 559
Period size: 182 Copynumber: 2.7 Consensus size: 180
31238 ATACAAATGA
* * * * * *
31248 AAAATGTATCGCTCTATAGCAATATAACAGGTAAAAATATAATAAAACCGGTTTC-ATTATGATA
1 AAAATGTATCGATCCATAGCAATATAACAGGT-AAAATATGACAAAACCGGTCTCGA-AATGATA
* * *
31312 AAATCGGTAAACCGCTACTGAATATATCGAAAGTATCGAT-TAGATTTAA-ATAAGTATCGACAC
64 AAACCGGTAAACAGCTACCGAATATATCGAAAGTATCGATAT-G--TTAATATAAGTATCGACAC
* *
31375 -TTTGGAATTTAAAATAGAAGAAGTAATAAAGCATATAAAGTGTTGATACTTTAT
126 TTTTGGAATTTAAAAGAGAAGAAGTAATAAAGCATATAAAGTGTCGATACTTTAT
* * * *
31429 GAAAACGTATCGATCCATAACAATATAACAGGTATAAGTATGACAAAACCGGTCACGAAATGATA
1 -AAAATGTATCGATCCATAGCAATATAACAGGTA-AAATATGACAAAACCGGTCTCGAAATGATA
* * * *
31494 AAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATATGTTAATATAAGTATCGACACTTT
64 AAACCGGTAAACAGCTACCGAATATATCGAAAGTATCGATATGTTAATATAAGTATCGACACTTT
* * ** *
31559 TTGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAT
129 TGGAATTTAAAAGAGAAGAAGTAATAAAGCATATAAAGTGTCGATACTTTAT
*
31611 ACAAATGTATCGATCCATAGCAATATAACAGGTAAGAATATGACAAAACAGGTCTCGAAATGATA
1 A-AAATGTATCGATCCATAGCAATATAACAGGTAA-AATATGACAAAACCGGTCTCGAAATGATA
* * * * * * ** *
31676 AAACCAGTAAAAAGCTATCGGATATATTGAAAGTGTCGATAAATTAATATAAGTGTCGA
64 AAACCGGTAAACAGCTACCGAATATATCGAAAGTATCGATATGTTAATATAAGTATCGA
31735 TAAATTAATA
Statistics
Matches: 263, Mismatches: 35, Indels: 14
0.84 0.11 0.04
Matches are distributed among these distances:
180 4 0.02
181 17 0.06
182 240 0.91
183 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.28
Consensus pattern (180 bp):
AAAATGTATCGATCCATAGCAATATAACAGGTAAAATATGACAAAACCGGTCTCGAAATGATAAA
ACCGGTAAACAGCTACCGAATATATCGAAAGTATCGATATGTTAATATAAGTATCGACACTTTTG
GAATTTAAAAGAGAAGAAGTAATAAAGCATATAAAGTGTCGATACTTTAT
Found at i:31731 original size:20 final size:20
Alignment explanation
Indices: 31706--31754 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
31696 GATATATTGA
31706 AAGTGTCGATAAATTAATAT
1 AAGTGTCGATAAATTAATAT
31726 AAGTGTCGATAAATTAATAT
1 AAGTGTCGATAAATTAATAT
*
31746 AAGTATCGA
1 AAGTGTCGA
31755 CACTTTCGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
AAGTGTCGATAAATTAATAT
Found at i:31805 original size:202 final size:202
Alignment explanation
Indices: 31524--31915 Score: 565
Period size: 202 Copynumber: 1.9 Consensus size: 202
31514 GATATATTGA
** *
31524 AAGTGTCGATATGTTAATATAAGTATCGACACTTTTTGAATTTAAAAGAGAAGAAGTTATAGCGC
1 AAGTGTCGATAAATTAATATAAGTATCGACACTTTGTGAATTTAAAAGAGAAGAAGTTATAGCGC
* * * * *
31589 CTATAAAGTGTCGATACTTTAT-ACAAATGTATCGATCCATAGCAATATAACAGGTAAGAATATG
66 ATAAAAAATGTCGATACTTTATGA-AAATGTATCGATCCATAACAATATAACAGGTAAAAATATG
* *
31653 ACAAAA-CAGGTCTCGAAATGATAAAACCAGTAAAAAGCTATCGGATATATTGAAAGTGTCGATA
130 ACAAAATC-GGTATCGAAATGATAAAACCAGTAAAAAGCTACCGGATATATTGAAAGTGTCGATA
31717 AATTAATAT
194 AATTAATAT
*
31726 AAGTGTCGATAAATTAATATAAGTATCGACACTTTCGT-AATTTAAAAGAGAATAAGTTATAGCG
1 AAGTGTCGATAAATTAATATAAGTATCGACACTTT-GTGAATTTAAAAGAGAAGAAGTTATAGCG
* *
31790 CATAAAAAATGTCGATACTTTATGAAAATGTATCGATCCATAACAATATAATATGTAAAAATATG
65 CATAAAAAATGTCGATACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATG
* * ** * *
31855 ACAAAATCGGTATCGAAATGATAAAATCGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCG
130 ACAAAATCGGTATCGAAATGATAAAACCAGTAAAAAGCTACCGGATATATTGAAAGTGTCG
31916 GTACTTTAAT
Statistics
Matches: 168, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
202 165 0.98
203 3 0.02
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (202 bp):
AAGTGTCGATAAATTAATATAAGTATCGACACTTTGTGAATTTAAAAGAGAAGAAGTTATAGCGC
ATAAAAAATGTCGATACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA
CAAAATCGGTATCGAAATGATAAAACCAGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAA
TTAATAT
Found at i:33810 original size:22 final size:22
Alignment explanation
Indices: 33760--33814 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
33750 AATGTTTTTG
33760 TTTT-TTATATAAAATGATGGTA
1 TTTTATTATATAAAATGAT-GTA
*
33782 TAGTTATTATATAAAATGAT-TAA
1 T-TTTATTATATAAAATGATGT-A
33805 TTTTATTATA
1 TTTTATTATA
33815 AATTCAGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 10 0.36
23 4 0.14
24 14 0.50
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TTTTATTATATAAAATGATGTA
Found at i:34800 original size:17 final size:17
Alignment explanation
Indices: 34778--34813 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
34768 TTTAAATATT
34778 TCATGAAAAGATATTAA
1 TCATGAAAAGATATTAA
34795 TCATGAAAAGATATTAA
1 TCATGAAAAGATATTAA
34812 TC
1 TC
34814 CTAATGATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (17 bp):
TCATGAAAAGATATTAA
Found at i:36025 original size:19 final size:19
Alignment explanation
Indices: 35979--36027 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
35969 AATGTAGGGT
* *
35979 TAATTTTGAATAAGATTTT
1 TAATTTTGTATAAGATTTA
*
35998 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
36017 TAATTTTGTAT
1 TAATTTTGTAT
36028 GTGAATGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:36833 original size:198 final size:198
Alignment explanation
Indices: 36360--37321 Score: 1561
Period size: 198 Copynumber: 4.9 Consensus size: 198
36350 TGGTAAACAT
*
36360 ATGTGTCGATACATTTATAAAAAGTATCGATCCTAAAAACATCGAGACCCATAATTATAATGTAA
1 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
* *
36425 TAGGTAAATTATGAATCTAACCGATCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAG
66 TAGGTAAATTATGAATCTAACCGGTCTAAATACACCAGTTTATGAGAAAACAGGTGTACATAAAG
*
36490 CATCGACACTTGTTGAATTTGTGTCGATA-----TGTCCAGAATGATTTCCTTACCAA-GTGCAT
131 TATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGGT-CA-
**
36549 GGA-A
194 CCATA
36553 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
1 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
*
36618 TAGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAG
66 TAGGTAAATTATGAATCTAACCGGTCTAAATACACCAGTTTATGAGAAAACAGGTGTACATAAAG
*
36683 TATCGACACTTGTTGAATTTATGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAA-GTGCAT
131 TATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGGT-CA-
**
36747 GGA-A
194 CCATA
* * *
36751 ATGTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATTGAGACTCATAATTATAATGTAA
1 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
*
36816 TAGGTAAATTATGAATCTAACCGGTCTAAATACACCA-TTTGATGAGAAAACATGTGTACATAAA
66 TAGGTAAATTATGAATCTAACCGGTCTAAATACACCAGTTT-ATGAGAAAACAGGTGTACATAAA
*
36880 GTATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCTAGAATGATTTCCTTACCAAGGTCAC
130 GTATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCAC
36945 CATA
195 CATA
36949 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
1 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
* * *
37014 TAGGTAAATTATCAATCTAACCGGTCTAAATATACCAGTTTATGAGAAAATAGGTGTACATAAAG
66 TAGGTAAATTATGAATCTAACCGGTCTAAATACACCAGTTTATGAGAAAACAGGTGTACATAAAG
* *
37079 TATCGACACTTGTTTAATTTGTGTCGATACTTTGTGTCCAAAATGATTTCCTTACCAAGGTCACC
131 TATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACC
37144 ATA
196 ATA
*
37147 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAA
1 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
* *
37212 TAGGTAAATTATGAATCTAACCGGTCTAAATACACAAGTTTATGATAAAACAGGTGTACATAAAG
66 TAGGTAAATTATGAATCTAACCGGTCTAAATACACCAGTTTATGAGAAAACAGGTGTACATAAAG
*
37277 TATCGACACTCT-TTGAATTTGTATCGATACGTTT-TGTCCAGAATG
131 TATCGACACT-TGTTGAATTTGTGTCGATAC-TTTGTGTCCAGAATG
37322 TAAATGGTCA
Statistics
Matches: 726, Mismatches: 32, Indels: 17
0.94 0.04 0.02
Matches are distributed among these distances:
193 155 0.21
197 4 0.01
198 558 0.77
199 9 0.01
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (198 bp):
ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
TAGGTAAATTATGAATCTAACCGGTCTAAATACACCAGTTTATGAGAAAACAGGTGTACATAAAG
TATCGACACTTGTTGAATTTGTGTCGATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACC
ATA
Found at i:37481 original size:199 final size:200
Alignment explanation
Indices: 36360--37510 Score: 911
Period size: 198 Copynumber: 5.8 Consensus size: 200
36350 TGGTAAACAT
* * *
36360 ATGTGTCGATACATTTATAAAAAGTATCGATCCTAAAAACATCGAGACCCATAATTATAATGTAA
1 ATGTGTCGATACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAA
* * * ** * *
36425 TAGGTAAATTATGAATCTAACCGATCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAG
66 TAGGTAAATTATGAATATAACCGGTATAAATACACAAGTTTATGATAAAACAGGTGCACATAAAG
* * * * ** ** * ** * *
36490 CATCGACAC-TTGTTGAATTTGTGTCGAT--A---TGTCCAGAATG-ATTTCCTTACCAAGTGCA
131 TATCGACACATT-TTAAATTTATATCGATACATTTTGTCCAGAATGTAAATGGTCAAAAATTTCA
***
36548 -TGGAA
195 CAAAAA
* *
36553 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
1 ATGTGTCGATACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAA
* * ** * *
36618 TAGGTAAATTATGAATCTAACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAG
66 TAGGTAAATTATGAATATAACCGGTATAAATACACAAGTTTATGATAAAACAGGTGCACATAAAG
* * ** ** * ** * *
36683 TATCGACAC-TTGTTGAATTTATGTCGATAC-TTTGTGTCCAGAATG-ATTTCCTTACCAAGTGC
131 TATCGACACATT-TTAAATTTATATCGATACATTT-TGTCCAGAATGTAAATGGTCAAAAATTTC
***
36745 A-TGGAA
194 ACAAAAA
* * * * *
36751 ATGTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATTGAGACTCATAATTATAATGTAA
1 ATGTGTCGATACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAA
* * * * * *
36816 TAGGTAAATTATGAATCTAACCGGTCTAAATACACCA-TTTGATGAGAAAACATGTGTACATAAA
66 TAGGTAAATTATGAATATAACCGGTATAAATACACAAGTTT-ATGATAAAACAGGTGCACATAAA
* * * * ** ** * ** **
36880 GTATCGACAC-TTGTTGAATTTGTGTCGATAC-TTTGTGTCTAGAATG-ATTTCCTTACCAAGGT
130 GTATCGACACATT-TTAAATTTATATCGATACATTT-TGTCCAGAATGTAAATGGTCAAAAATTT
* *
36942 CAC-CATA
193 CACAAAAA
* *
36949 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAA
1 ATGTGTCGATACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAA
* * * * * * * *
37014 TAGGTAAATTATCAATCTAACCGGTCTAAATATACCAGTTTATGAGAAAATAGGTGTACATAAAG
66 TAGGTAAATTATGAATATAACCGGTATAAATACACAAGTTTATGATAAAACAGGTGCACATAAAG
* * * * ** ** * ** **
37079 TATCGACAC-TTGTTTAATTTGTGTCGATAC-TTTGTGTCCAAAATG-ATTTCCTTACCAAGGTC
131 TATCGACACATT-TTAAATTTATATCGATACATTT-TGTCCAGAATGTAAATGGTCAAAAATTTC
* *
37141 AC-CATA
194 ACAAAAA
*
37147 ATGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAA
1 ATGTGTCGATACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAA
* * *
37212 TAGGTAAATTATGAATCTAACCGGTCTAAATACACAAGTTTATGATAAAACAGGTGTACATAAAG
66 TAGGTAAATTATGAATATAACCGGTATAAATACACAAGTTTATGATAAAACAGGTGCACATAAAG
* * *
37277 TATCGACAC-TCTTTGAATTTGTATCGATACGTTTTGTCCAGAATGTAAATGGTCAAAAATTTCA
131 TATCGACACAT-TTTAAATTTATATCGATACATTTTGTCCAGAATGTAAATGGTCAAAAATTTCA
37341 CAAAAA
195 CAAAAA
* **
37347 ATGTGTCGATACATTTATAAAAAGTATCAAT-CCTAAAACAAT-GAAATTCATAATT-TGAATGT
1 ATGTGTCGATACATTTATAAAAAGTATCAATCCCAAAAAC-ATCGAAACCCATAATTAT-AATGT
* * * * * *
37409 AATAGGT-CATTTTGCAATATAACCGGTATAAATATACCTA-TTTAAT-TTTAAACAGGT-CACC
64 AATAGGTAAATTATG-AATATAACCGGTATAAATACA-CAAGTTT-ATGATAAAACAGGTGCA-C
* *
37470 ATAATGTATCGACACATTTTAAATTTATGTCGATACATTTT
125 ATAAAGTATCGACACATTTTAAATTTATATCGATACATTTT
37511 TAAATTACTC
Statistics
Matches: 874, Mismatches: 64, Indels: 34
0.90 0.07 0.03
Matches are distributed among these distances:
193 154 0.18
197 3 0.00
198 566 0.65
199 112 0.13
200 39 0.04
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (200 bp):
ATGTGTCGATACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAA
TAGGTAAATTATGAATATAACCGGTATAAATACACAAGTTTATGATAAAACAGGTGCACATAAAG
TATCGACACATTTTAAATTTATATCGATACATTTTGTCCAGAATGTAAATGGTCAAAAATTTCAC
AAAAA
Found at i:37817 original size:15 final size:15
Alignment explanation
Indices: 37797--37848 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
37787 AGAATCGGGG
*
37797 CTCTTCTCAACCCAT
1 CTCTTCTCAACCCAC
37812 CTCTTCTCAACCCAC
1 CTCTTCTCAACCCAC
*
37827 CTCTTCTCAACCCAG
1 CTCTTCTCAACCCAC
37842 CTCTTCT
1 CTCTTCT
37849 GAGGAAGTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.17, C:0.48, G:0.02, T:0.33
Consensus pattern (15 bp):
CTCTTCTCAACCCAC
Found at i:41687 original size:22 final size:21
Alignment explanation
Indices: 41661--41706 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
41651 AAAAGAAAGG
*
41661 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
41683 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
41704 TAT
1 TAT
41707 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:41793 original size:200 final size:200
Alignment explanation
Indices: 41135--42504 Score: 1824
Period size: 200 Copynumber: 6.8 Consensus size: 200
41125 GTGCATGAAC
* * * * * *
41135 AAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAATATCGAGACCCATAATTATAATGCA
1 AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
* *
41200 ATAGGTAAAATAACAATGTAACCGGTCTAAATATACCGATT-TATAAGAAAAG--AGGTATACAT
66 ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTAT-TAA-AAAAGAAAGGTATACAT
* * * * **
41262 AAAGTATCGACACTTTATACATTTGTGTCGATACTTTGTGTCCATAATGTATTTTCCAACCAAAA
129 AATGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTT----CC-AAA
41327 CAAGTTCACAAA
189 CAAGTTCACAAA
* * * * * * *
41339 TAAGTGTCTATACATTTATATCAAGTGTCGATCCCAGAAACATCGAAACCCGTAACTATAATGTA
1 AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
* * * ** * * * * * *
41404 ATAGGTCACTTTACAATGTAACCATTTTAAATTTACCGGCTT-TATGAGAAA-ATAGGTCTACA-
66 ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGG-TTAT-TAAAAAAGAAAGGTATACAT
* * * * * **
41466 ATATGTATCGACACTTTATTCATTTGTGTCGATACATGT-TGTCCAGAATGTA-TTTCCAAACCA
129 A-ATGTATCGATACTTTATACATTTGTGTCGACAC-TTTATGTCCATAATAAATTTTCCAAA-CA
*
41529 AGTGCACGAAA
191 AGTTCAC-AAA
*
41540 AAAGTGTCGGTACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
1 AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
*
41605 ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGATTATTAAAAAAGAAAGGTATACATAA
66 ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAA
41670 TGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTC
131 TGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTC
41735 ACAAA
196 ACAAA
* * *
41740 AAAGTGTCGATACATTTATACCAAGTGTAGATCCCAAAAACATCGAAACACATAATTATAATATA
1 AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
* *
41805 ATAGGTAACATTACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAATGGTATACATAA
66 ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAA
41870 TGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTC
131 TGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTC
*
41935 ACGAA
196 ACAAA
41940 AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
1 AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
*
42005 ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAATGGTATACATAA
66 ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAA
*
42070 TGTATCAATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTC
131 TGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTC
*
42135 ACGAA
196 ACAAA
* * *
42140 AAAGTGTCGATACATTTATAACAAGTGTTGATCCCAAAAACATCAAAACACATAATTTTAATGTA
1 AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
* *
42205 ATAGGTAACATAACAATGTAACCGGTCTAAATATATCGGTTATTAAAAAAGAAAGGTATACGTAA
66 ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAA
*
42270 TGTATCGATACTTTATACATTTATGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTC
131 TGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTC
*
42335 ACGAA
196 ACAAA
* * * * * *
42340 AAAGTGTTGATACATTTAGAAAAAGTGTCGATCCTAAAAACATCGAAACTCGTAATTATAATGTA
1 AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
* * * * * * * * * *
42405 ATAGGTCACTTTACAATGTAACCAGTTTAAATTTTCCGGTT-TTATGAGAAA-ATAGGTCTACAT
66 ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTA--AAAAAGAAAGGTATACAT
* * * * *
42468 AATGTATCGACACTTTTTAAATTAGTGTCGATACTTT
129 AATGTATCGATACTTTATACATTTGTGTCGACACTTT
42505 TTAAAATTAC
Statistics
Matches: 1048, Mismatches: 104, Indels: 32
0.89 0.09 0.03
Matches are distributed among these distances:
199 6 0.01
200 730 0.70
201 153 0.15
202 9 0.01
204 91 0.09
205 57 0.05
206 2 0.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (200 bp):
AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTA
ATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTATACATAA
TGTATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTC
ACAAA
Found at i:41887 original size:22 final size:21
Alignment explanation
Indices: 41861--41906 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
41851 AAAAGAATGG
*
41861 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
41883 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
41904 TAT
1 TAT
41907 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:46010 original size:199 final size:196
Alignment explanation
Indices: 45646--46168 Score: 566
Period size: 199 Copynumber: 2.6 Consensus size: 196
45636 TTAGATTTTA
* * ** *
45646 TGTCGACACATTTATAACAAGTATCGATCCCAAAATCAAAGAGACCGATAATTATAATGTAATAG
1 TGTCGATACATTT-TAAAAAGTATCGATCCCAAAA-CATCGAAACCGATAATTATAATGTAATAG
* * * * *
45711 GTAAATTTCCATTGTAACCGG-TAGAAATATACTGGGTTCATGAGAGAATATGTCAACATAAAGT
64 GTAAATTTACAATGTAACCGGTTA-AAATATAC-CGGTTAATGAGAGAATAGGTCAACATAAAGT
* * * * * * *
45775 ATCGACATTTTTTTAATTTGTGTCGATACATTTTTCCAAAATTAATG-GCAAACGAGGTGTACGC
127 ATCGACACTCTTTAAATATGTGTCGATACATTTTTCCAAAA-TAAAGCACAAACGAGGTGCACGC
45839 ATAAAG
191 ATAAAG
* * *
45845 TGTCGATACATTTGTAAAAAGTATCGATCCTCAAAACATCGAAATCGATAATTATTATGTAACAG
1 TGTCGATACATTT-TAAAAAGTATCGATCC-CAAAACATCGAAACCGATAATTATAATGTAATA-
* * * *
45910 GGTAAATTTACAATGTAACCGGTTAAAATATACCGGTTAATTAGCA-AATAGGTCTACATTATGT
63 GGTAAATTTACAATGTAACCGGTTAAAATATACCGGTTAATGAG-AGAATAGGTCAACATAAAGT
* *
45974 ATCGACACTCTTTAAATATGTGTCGATACTTTTTTCCAAAATAAAGCACAAACGAGTTGCACGCA
127 ATCGACACTCTTTAAATATGTGTCGATACATTTTTCCAAAATAAAGCACAAACGAGGTGCACGCA
46039 TAAAG
192 TAAAG
* ** * *
46044 TGTCGATACATTTCAAATTGTATCGATCCCGAAAACATCGAAACCAATATTTATAATGTAATAGG
1 TGTCGATACATTTTAAAAAGTATCGATCCC-AAAACATCGAAACCGATAATTATAATGTAATAGG
* * * * * * * * *
46109 TCAATTTATAATGTAATCGGTTTAAATTTATCGGTTTTATGAGAAAATAGGTCAATATAA
65 TAAATTTACAATGTAACCGGTTAAAATATACCGG-TTAATGAGAGAATAGGTCAACATAA
46169 GCGCTACCTA
Statistics
Matches: 270, Mismatches: 46, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
197 32 0.12
198 62 0.23
199 140 0.52
200 34 0.13
201 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.32
Consensus pattern (196 bp):
TGTCGATACATTTTAAAAAGTATCGATCCCAAAACATCGAAACCGATAATTATAATGTAATAGGT
AAATTTACAATGTAACCGGTTAAAATATACCGGTTAATGAGAGAATAGGTCAACATAAAGTATCG
ACACTCTTTAAATATGTGTCGATACATTTTTCCAAAATAAAGCACAAACGAGGTGCACGCATAAA
G
Found at i:46139 original size:22 final size:20
Alignment explanation
Indices: 46092--46139 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
46082 CGAAACCAAT
*
46092 ATTTATAATGTAATAGGTCA
1 ATTTATAATGTAATAGGTAA
*
46112 ATTTATAATGTAATCGGTTTAA
1 ATTTATAATGTAATAGG--TAA
46134 ATTTAT
1 ATTTAT
46140 CGGTTTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 16 0.67
22 8 0.33
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (20 bp):
ATTTATAATGTAATAGGTAA
Found at i:46284 original size:23 final size:23
Alignment explanation
Indices: 46237--46284 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
46227 TCCGGTTAAA
** **
46237 TACCTATTTTATTATATAATTGC
1 TACCTATTACATTATATAAGCGC
46260 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAGCGC
46283 TA
1 TA
46285 TCTAATATGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (23 bp):
TACCTATTACATTATATAAGCGC
Done.