Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008653.1 Hibiscus syriacus cultivar Beakdansim tig00111644_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: 1778368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:420332 original size:13 final size:12
Alignment explanation
Indices: 420255--420342 Score: 57
Period size: 13 Copynumber: 7.8 Consensus size: 12
420245 AAATGAGAAA
420255 AAAG-AAAAATG
1 AAAGAAAAAATG
** *
420266 ATGGAAAAAACG
1 AAAGAAAAAATG
*
420278 AAAAGAAAAAAAG
1 -AAAGAAAAAATG
420291 -AAGAAAAAATG
1 AAAGAAAAAATG
420302 ---G--AAAATG
1 AAAGAAAAAATG
*
420309 GAAGAAAAAATG
1 AAAGAAAAAATG
420321 AAAGAGAAAAATG
1 AAAGA-AAAAATG
420334 AAA-AAAAAA
1 AAAGAAAAAA
420343 GAGAAATAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
7 6 0.10
9 1 0.02
10 1 0.02
11 17 0.28
12 17 0.28
13 19 0.31
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.07
Consensus pattern (12 bp):
AAAGAAAAAATG
Found at i:420337 original size:31 final size:30
Alignment explanation
Indices: 420280--420338 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
420270 AAAAAACGAA
420280 AAGAAAAAAAGAAGAAAAAATGGAAAATGG
1 AAGAAAAAAAGAAGAAAAAATGGAAAATGG
* *
420310 AAGAAAAAATGAAAGAGAAAAATGAAAAA
1 AAGAAAAAAAG-AAGA-AAAAATGGAAAA
420339 AAAAGAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 10 0.40
31 4 0.16
32 11 0.44
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (30 bp):
AAGAAAAAAAGAAGAAAAAATGGAAAATGG
Found at i:421865 original size:166 final size:166
Alignment explanation
Indices: 421591--422415 Score: 1246
Period size: 166 Copynumber: 5.0 Consensus size: 166
421581 AATACGTTTG
* * *
421591 ATGAAGATTGTTCGAGTTCTATACTCCCTGAATGAATA-AGGAGCGAACCCGTTTTATGAAGATT
1 ATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGA-GAGCGGACCCGTTTTATGAAGATT
* *
421655 GTTCGAGTTATATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTAAGATTGTTCGAGTTC
65 GTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTC
*
421720 TATACTCTCTGAATGAATAGAGAGCGGACCCGTTTTT
130 TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTT
* * * **
421757 ATGAAGATTGTTCGAGTTTTATACTCTCTGATGGAATAGGGAGCATACCCGTTTTATGAAGATTG
1 ATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTG
*
421822 TTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTAAGATTGTTCGAGTTCT
66 TTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCT
*
421887 ATACTCTCTGAAGGAATATAGAGCGGACCCGTTTTT
131 ATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTT
* *
421923 ATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTAAGATTA
1 ATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTG
*
421988 TTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTTATGAAGATTGTTCGAGTTA
66 TTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCG-TTTTATGAAGATTGTTCGAGTTC
* *
422053 TATACTCTCTGATGGAATAGGGAGCGGACCCG-TTTT
130 TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTT
*
422089 ATAAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTG
1 ATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTG
* * *
422154 TTCGAGTTTTATACTCTCTGATGGAATAGGGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCT
66 TTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCT
*
422219 ATACTCTCTGAAGAAATAGAGAGCGGACCCG-TTTT
131 ATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTT
*
422254 ATTAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTG
1 ATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTG
* * * * * * ** *
422319 TTCGAGTTCTATAATC-CATGAATGAATAGGGAGCAGACACATTTGCTGAAGATTGGTCGAG-TC
66 TTCGAGTTCTATACTCTC-TGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTC
* * * *
422382 TTATACTCCCTGAAGGGATAGGGAGCAGACCCGT
130 -TATACTCTCTGAAGGAATAGAGAGCGGACCCGT
422416 CATTCGAAGA
Statistics
Matches: 606, Mismatches: 48, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
164 3 0.00
165 195 0.32
166 358 0.59
167 50 0.08
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (166 bp):
ATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTG
TTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCT
ATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTT
Found at i:422426 original size:55 final size:55
Alignment explanation
Indices: 421585--422415 Score: 1245
Period size: 55 Copynumber: 15.1 Consensus size: 55
421575 GAAGCAAATA
* * * *
421585 CGTTTGATGAAGATTGTTCGAGTTCTATACTCCCTGAATGAATA-AGGAGCGAACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGA-GAGCGGACC
*
421640 CGTTTTATGAAGATTGTTCGAGTTATATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
* *
421695 CGTTTTATTAAGATTGTTCGAGTTCTATACTCTCTGAATGAATAGAGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
* * * **
421750 CGTTTTTATGAAGATTGTTCGAGTTTTATACTCTCTGATGGAATAGGGAGCATACC
1 CG-TTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
421806 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
* *
421861 CGTTTTATTAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATATAGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
421916 CGTTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CG-TTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
* *
421972 CGTTTTATTAAGATTATTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
* * *
422027 CGTTTTTATGAAGATTGTTCGAGTTATATACTCTCTGATGGAATAGGGAGCGGACC
1 CG-TTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
*
422083 CGTTTTATAAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
* * *
422138 CGTTTTATGAAGATTGTTCGAGTTTTATACTCTCTGATGGAATAGGGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
*
422193 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGAAATAGAGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
*
422248 CGTTTTATTAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
* * * * *
422303 CGTTTTATGAAGATTGTTCGAGTTCTATAATC-CATGAATGAATAGGGAGCAGACA
1 CGTTTTATGAAGATTGTTCGAGTTCTATACTCTC-TGAAGGAATAGAGAGCGGACC
* ** * * * * *
422358 CATTTGCTGAAGATTGGTCGAG-TCTTATACTCCCTGAAGGGATAGGGAGCAGACC
1 CGTTTTATGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACC
422413 CGT
1 CGT
422416 CATTCGAAGA
Statistics
Matches: 709, Mismatches: 60, Indels: 14
0.91 0.08 0.02
Matches are distributed among these distances:
54 3 0.00
55 553 0.78
56 153 0.22
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (55 bp):
CGTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
Found at i:427674 original size:15 final size:15
Alignment explanation
Indices: 427647--427683 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
427637 TGAGACATTA
*
427647 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
*
427662 CCTGCCCCACATCCG
1 CCCGCCCCACATCCG
427677 CCCGCCC
1 CCCGCCC
427684 AGCTAAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.08, C:0.68, G:0.16, T:0.08
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:435690 original size:21 final size:21
Alignment explanation
Indices: 435661--435719 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
435651 ATTCTGACTA
*
435661 TCGCATTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
435682 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
435703 TCGCGTTGCGATTTTCC
1 TCGCGTTGCGATTTTCC
435720 GACTATCGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCAAAT
Found at i:435808 original size:40 final size:40
Alignment explanation
Indices: 435720--435815 Score: 149
Period size: 40 Copynumber: 2.4 Consensus size: 40
435710 GCGATTTTCC
435720 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
* *
435760 GTA-AATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
*
435800 GACTATCGCAACGCGA
1 GACTATCGCAATGCGA
435816 TTCTGACTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
39 1 0.02
40 48 0.96
41 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (40 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
Found at i:435810 original size:20 final size:20
Alignment explanation
Indices: 435724--435800 Score: 136
Period size: 20 Copynumber: 3.9 Consensus size: 20
435714 TTTTCCGACT
435724 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
435744 ATCGCAATGCGAGTATGTAA
1 ATCGCAATGCGAATATGTAA
435764 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
435784 ATCGCAATGCGATTATG
1 ATCGCAATGCGAATATG
435801 ACTATCGCAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:435815 original size:20 final size:20
Alignment explanation
Indices: 435784--435831 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
435774 GAATATGTAA
*
435784 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTATGACT
*
435804 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTATGACT
*
435824 GTCGCAAC
1 ATCGCAAC
435832 ACTGAATTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTATGACT
Found at i:437123 original size:23 final size:22
Alignment explanation
Indices: 437075--437123 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
437065 CCAGAATGTC
*
437075 AAGG-GGGAATCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
437096 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
437119 AAGGA
1 AAGGA
437124 AAATTGTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.14
22 14 0.64
23 5 0.23
ACGTcount: A:0.33, C:0.29, G:0.29, T:0.10
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:438043 original size:103 final size:103
Alignment explanation
Indices: 437818--438035 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
437808 GTCGAGGGTC
437818 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
* *
437883 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* * *
437921 TATATGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
*
437986 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
438024 TATGTGGTCCTT
1 TATGTGGTCCTT
438036 ATGGACATTA
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:438096 original size:47 final size:47
Alignment explanation
Indices: 438042--438161 Score: 197
Period size: 47 Copynumber: 2.6 Consensus size: 47
438032 CCTTATGGAC
*
438042 ATTATTATATGGCACTACGGTACAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
*
438089 ATTATTATATGGCACTACGGTGCAATTCTACGCGGTACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
* *
438136 ATTA-TATGTGGCACTTCGGTGCAATT
1 ATTATTATATGGCACTACGGTGCAATT
438162 ATATGAGCTG
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
46 20 0.29
47 49 0.71
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
Found at i:438162 original size:23 final size:23
Alignment explanation
Indices: 438042--438166 Score: 115
Period size: 23 Copynumber: 5.3 Consensus size: 23
438032 CCTTATGGAC
* *
438042 ATTATTATATGGCACTACGGTACA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
438066 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
438089 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * * *
438113 ATTCTACGCGGTACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
438136 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
438159 ATTATATG
1 ATTATATG
438167 AGCTGTGGTG
Statistics
Matches: 78, Mismatches: 22, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
23 57 0.73
24 21 0.27
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:442948 original size:22 final size:21
Alignment explanation
Indices: 442906--442948 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
442896 GAATGTCAAG
*
442906 GGGAACCGATACCCCACAGGA
1 GGGAACCGATACCCCAAAGGA
* *
442927 GGGAATCGATTCCCCTAAAGGA
1 GGGAACCGATACCCC-AAAGGA
442949 AAATTGTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.33, C:0.28, G:0.28, T:0.12
Consensus pattern (21 bp):
GGGAACCGATACCCCAAAGGA
Found at i:443825 original size:103 final size:104
Alignment explanation
Indices: 443641--443860 Score: 388
Period size: 103 Copynumber: 2.1 Consensus size: 104
443631 GTCGAGGGTC
*
443641 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
* *
443706 TTGATCCTTGGCATATG-TATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGATATATGATTCTTAAGGAATGA
443744 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
*
443809 TTGATCCCTAGTATATGTATATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATG-ATATATGATTCTTAAGGAATGA
443849 TATGTGGTCCTT
1 TATGTGGTCCTT
443861 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
103 78 0.70
105 33 0.30
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (104 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGATATATGATTCTTAAGGAATGA
Found at i:443921 original size:47 final size:47
Alignment explanation
Indices: 443867--443986 Score: 197
Period size: 47 Copynumber: 2.6 Consensus size: 47
443857 CCTTATGGAC
*
443867 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGTA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCAGTGTA
*
443914 ATTATTATATGGCACTACGGTGTAATTCTACGCGGCACTCCAGTGTA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCAGTGTA
* *
443961 ATTA-TATGTGGCACTTCGGTGCAATT
1 ATTATTATATGGCACTACGGTGCAATT
443987 ATATGAGTTG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 19 0.28
47 49 0.72
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCAGTGTA
Found at i:443987 original size:23 final size:23
Alignment explanation
Indices: 443867--443991 Score: 106
Period size: 23 Copynumber: 5.3 Consensus size: 23
443857 CCTTATGGAC
* *
443867 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGTA
* * * *
443891 ATTCTACGCGGCACTCCGGTGTA
1 ATTATATGTGGCACTACGGTGTA
*
443914 ATTATTATATGGCACTACGGTGTA
1 ATTA-TATGTGGCACTACGGTGTA
* * * * *
443938 ATTCTACGCGGCACTCCAGTGTA
1 ATTATATGTGGCACTACGGTGTA
* *
443961 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGTA
443984 ATTATATG
1 ATTATATG
443992 AGTTGTGGTG
Statistics
Matches: 77, Mismatches: 23, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
23 56 0.73
24 21 0.27
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGTA
Found at i:445279 original size:24 final size:24
Alignment explanation
Indices: 445247--445300 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
445237 GTATTCGAAA
445247 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
445271 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
445295 TTTGAT
1 TTTGAT
445301 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:445519 original size:14 final size:14
Alignment explanation
Indices: 445490--445526 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
445480 AGAAAAAGAA
445490 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
445505 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
445519 GAAGAAAA
1 GAAGAAAA
445527 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:447916 original size:140 final size:140
Alignment explanation
Indices: 447656--447925 Score: 477
Period size: 140 Copynumber: 1.9 Consensus size: 140
447646 AAACGTTGTA
447656 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* * * *
447721 TGATCTGTTCAGTTGTTATAAGTTATTACACATTCATTTGAATATCGCAACGCGAATTTGATTAT
66 TGATATGTTCAGTTATTATAACTTATTACACATTCATTTGAATATCACAACGCGAATTTGATTAT
447786 TATGTGTATT
131 TATGTGTATT
*
447796 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTTAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* *
447861 TGATATGTTCAGTTATTATCACTTATTACACATTCATTTGAATATCACAATGCGAATTTGATTAT
66 TGATATGTTCAGTTATTATAACTTATTACACATTCATTTGAATATCACAACGCGAATTTGATTAT
447926 CGCAACTCAA
Statistics
Matches: 123, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 123 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.44
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTATTATAACTTATTACACATTCATTTGAATATCACAACGCGAATTTGATTAT
TATGTGTATT
Found at i:447970 original size:20 final size:20
Alignment explanation
Indices: 447942--447980 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
447932 TCAACAATCG
* *
447942 CAACGCGAATTTGACTATCT
1 CAACACGAATATGACTATCT
447962 CAACACGAATATGACTATC
1 CAACACGAATATGACTATC
447981 GCAATGCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (20 bp):
CAACACGAATATGACTATCT
Found at i:447981 original size:54 final size:55
Alignment explanation
Indices: 447913--448039 Score: 168
Period size: 54 Copynumber: 2.3 Consensus size: 55
447903 TATCACAATG
* * *
447913 CGAATTTGATTATCGCAACT-CAACAATCGCAACGCGAATTTGACTATCTCAACA
1 CGAATTTGACTATCGCAACTGCAAAAATCGCAACGCGAATTTGACTATCGCAACA
* * * * *
447967 CGAATATGACTATCGCAA-TGCAAAAATCGGAACGTGAATTTGTCTATCGCAACG
1 CGAATTTGACTATCGCAACTGCAAAAATCGCAACGCGAATTTGACTATCGCAACA
448021 CGAATTTGACTATCGCAAC
1 CGAATTTGACTATCGCAAC
448040 GGCTATTTGA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
53 1 0.02
54 61 0.98
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (55 bp):
CGAATTTGACTATCGCAACTGCAAAAATCGCAACGCGAATTTGACTATCGCAACA
Found at i:448020 original size:20 final size:19
Alignment explanation
Indices: 447992--448112 Score: 101
Period size: 20 Copynumber: 6.4 Consensus size: 19
447982 CAATGCAAAA
* *
447992 ATCGGAACGTGAATTTGTCT
1 ATCGCAACG-GAATTTGACT
448012 ATCGCAACGCGAATTTGACT
1 ATCGCAACG-GAATTTGACT
*
448032 ATCGCAACGGCTATTTGACT
1 ATCGCAACGG-AATTTGACT
448052 ATCGCAACGAGAA----A--
1 ATCGCAACG-GAATTTGACT
*
448066 ATCGCAACGCGAATTTGATT
1 ATCGCAACG-GAATTTGACT
*
448086 ATCGCAACGGGTATTTGACT
1 ATCGCAAC-GGAATTTGACT
448106 ATCGCAA
1 ATCGCAA
448113 TGAGAAAATC
Statistics
Matches: 84, Mismatches: 8, Indels: 18
0.76 0.07 0.16
Matches are distributed among these distances:
14 12 0.14
16 1 0.01
18 1 0.01
19 1 0.01
20 67 0.80
21 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (19 bp):
ATCGCAACGGAATTTGACT
Found at i:448029 original size:74 final size:74
Alignment explanation
Indices: 447938--448112 Score: 221
Period size: 74 Copynumber: 2.4 Consensus size: 74
447928 CAACTCAACA
* * *
447938 ATCGCAACGCGAATTTGACTATCTCAACACG-AATATGACTATCGCAATGCA-AAAATCGGAACG
1 ATCGCAACGCGAATTTGACTATCGCAAC-CGCAATATGACTATCGCAACG-AGAAAATCGCAACG
*
448001 TGAATTTG-TCT
64 CGAATTTGAT-T
* * *
448012 ATCGCAACGCGAATTTGACTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATCGCAACGCG
1 ATCGCAACGCGAATTTGACTATCGCAACCGCAATATGACTATCGCAACGAGAAAATCGCAACGCG
448077 AATTTGATT
66 AATTTGATT
* *
448086 ATCGCAACGGGTATTTGACTATCGCAA
1 ATCGCAACGCGAATTTGACTATCGCAA
448113 TGAGAAAATC
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
73 2 0.02
74 86 0.97
75 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACCGCAATATGACTATCGCAACGAGAAAATCGCAACGCG
AATTTGATT
Found at i:448070 original size:54 final size:54
Alignment explanation
Indices: 448012--448148 Score: 220
Period size: 54 Copynumber: 2.5 Consensus size: 54
448002 GAATTTGTCT
448012 ATCGCAACGCGAATTTGACTATCGCAACGGCTATTTGACTATCGCAACGAGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGGCTATTTGACTATCGCAACGAGAAA
* * *
448066 ATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAATGAGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGGCTATTTGACTATCGCAACGAGAAA
* * *
448120 ATCGCAAAGCGTATTAGACTATCGCAACG
1 ATCGCAACGCGAATTTGACTATCGCAACG
448149 CGAATTGACT
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 76 1.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACGGCTATTTGACTATCGCAACGAGAAA
Found at i:448163 original size:19 final size:20
Alignment explanation
Indices: 448120--448163 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
448110 CAATGAGAAA
*
448120 ATCGCAAAGCGTATTAGACT
1 ATCGCAAAGCGAATTAGACT
*
448140 ATCGCAACGCGAATT-GACT
1 ATCGCAAAGCGAATTAGACT
*
448159 TTCGC
1 ATCGC
448164 GTTGCGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAAAGCGAATTAGACT
Found at i:448208 original size:20 final size:20
Alignment explanation
Indices: 448153--448210 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
448143 GCAACGCGAA
*
448153 TTGACTTTCGCGTTGCGATT
1 TTGACTTTAGCGTTGCGATT
* * **
448173 TTGTCTTTTGTATTGCGATT
1 TTGACTTTAGCGTTGCGATT
*
448193 TTGAGTTTAGCGTTGCGA
1 TTGACTTTAGCGTTGCGA
448211 AAGTGTACCT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.12, C:0.14, G:0.26, T:0.48
Consensus pattern (20 bp):
TTGACTTTAGCGTTGCGATT
Found at i:449751 original size:21 final size:21
Alignment explanation
Indices: 449699--449739 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
449689 TTGGGAGGGA
*
449699 CCTCTTCAACGATGACATTGG
1 CCTCTTCAACGATGACAGTGG
449720 CCTCTTCAACGATGACAGTG
1 CCTCTTCAACGATGACAGTG
449740 TTCTCTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (21 bp):
CCTCTTCAACGATGACAGTGG
Found at i:450344 original size:20 final size:20
Alignment explanation
Indices: 450319--450374 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
450309 TCGCAACTCG
450319 AATGACTATCGCAACGCCAA
1 AATGACTATCGCAACGCCAA
*
450339 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCCAA
450359 AATGACTATCGCAACG
1 AATGACTATCGCAACG
450375 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.16
Consensus pattern (20 bp):
AATGACTATCGCAACGCCAA
Found at i:450442 original size:20 final size:20
Alignment explanation
Indices: 450417--450480 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
450407 GCGATTCTTT
**
450417 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
450437 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
450457 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
450477 CGTT
1 CGTT
450481 ATGAAAGTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:452411 original size:20 final size:20
Alignment explanation
Indices: 452388--452455 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
452378 TCTGAAACTT
452388 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
452408 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
** * *
452428 ACTATCGCAATACGAAACT-
1 AAAATCGCAACACGAAAATG
452447 AAAATCGCA
1 AAAATCGCA
452456 TTGTGATTCT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 7 0.17
20 33 0.82
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:452868 original size:22 final size:22
Alignment explanation
Indices: 452841--452882 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
452831 GAGATAGACG
*
452841 GATTTCGCCGGAGATGGGGACT
1 GATTTCGCCGAAGATGGGGACT
**
452863 GATTTCTTCGAAGATGGGGA
1 GATTTCGCCGAAGATGGGGA
452883 TGGATGTCGC
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:0.21, C:0.14, G:0.38, T:0.26
Consensus pattern (22 bp):
GATTTCGCCGAAGATGGGGACT
Found at i:453084 original size:20 final size:20
Alignment explanation
Indices: 453059--453165 Score: 126
Period size: 20 Copynumber: 5.3 Consensus size: 20
453049 GAAAATCACT
*
453059 TTGCGATAGTCAGCATCGCA
1 TTGCGATAGTCAGAATCGCA
* *
453079 TTGCGATAGTCAGCATCGCG
1 TTGCGATAGTCAGAATCGCA
* *
453099 TTACGACAGTCAGAATCG-A
1 TTGCGATAGTCAGAATCGCA
*
453118 GTTGCGATAGTCAGAATCGCG
1 -TTGCGATAGTCAGAATCGCA
* *
453139 TTGCGATAGTCATACTCGCA
1 TTGCGATAGTCAGAATCGCA
453159 TTGCGAT
1 TTGCGAT
453166 TTATATATTC
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
20 74 1.00
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:453213 original size:22 final size:22
Alignment explanation
Indices: 453181--453243 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 22
453171 TATTCGCATT
453181 TCGCAATGCGATAGTCAGAAAA
1 TCGCAATGCGATAGTCAGAAAA
* * **
453203 TCGCAACGCGA-ATTTGGAAAA
1 TCGCAATGCGATAGTCAGAAAA
453224 TCGCAATGCGATAGTCAGAA
1 TCGCAATGCGATAGTCAGAA
453244 TCGCGTTGCG
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (22 bp):
TCGCAATGCGATAGTCAGAAAA
Found at i:453262 original size:41 final size:42
Alignment explanation
Indices: 453181--453263 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 42
453171 TATTCGCATT
*
453181 TCGCAATGCGATAGTCAGAAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGATAGTCAG-AAATCGCAACGCGAATCTGGAAAA
***
453224 TCGCAATGCGATAGTCAG-AATCGCGTTGCGAATCTGGAAA
1 TCGCAATGCGATAGTCAGAAATCGCAACGCGAATCTGGAAA
453264 CTGATTTGCG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 18 0.50
43 18 0.50
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.20
Consensus pattern (42 bp):
TCGCAATGCGATAGTCAGAAATCGCAACGCGAATCTGGAAAA
Found at i:462395 original size:20 final size:20
Alignment explanation
Indices: 462370--462502 Score: 221
Period size: 20 Copynumber: 6.7 Consensus size: 20
462360 TTTTCCTAAT
462370 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
462390 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
462410 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
462430 TCACAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
462450 TCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
**
462470 TCGCAATGTAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
462490 TCGCAACGCGAAT
1 TCGCAATGCGAAT
462503 CTGACTATCG
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 104 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:462724 original size:22 final size:22
Alignment explanation
Indices: 462699--462764 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
462689 GGCGACATCC
462699 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
462721 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
462743 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
462765 TTCACGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:463172 original size:20 final size:20
Alignment explanation
Indices: 463132--463201 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
463122 TGCGATTCTT
* **
463132 GCGTTGTGATAGTCAAATTC
1 GCGTTGCGATAGTCATTTTC
463152 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCATTTTC
* ** *
463172 GTGTTGCGATTTTTATTTTC
1 GCGTTGCGATAGTCATTTTC
*
463192 GTGTTGCGAT
1 GCGTTGCGAT
463202 TTAAAGTTTC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.16, C:0.14, G:0.26, T:0.44
Consensus pattern (20 bp):
GCGTTGCGATAGTCATTTTC
Found at i:463202 original size:20 final size:20
Alignment explanation
Indices: 463166--463203 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
463156 TGCGATAGTC
463166 ATTTTCGTGTTGCGATTTTT
1 ATTTTCGTGTTGCGATTTTT
463186 ATTTTCGTGTTGCGATTT
1 ATTTTCGTGTTGCGATTT
463204 AAAGTTTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.21, T:0.58
Consensus pattern (20 bp):
ATTTTCGTGTTGCGATTTTT
Found at i:463211 original size:20 final size:20
Alignment explanation
Indices: 463168--463211 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
463158 CGATAGTCAT
** *
463168 TTTCGTGTTGCGATTTTTAT
1 TTTCGTGTTGCGATTTAAAG
463188 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
463208 TTTC
1 TTTC
463212 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.11, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:465194 original size:20 final size:20
Alignment explanation
Indices: 465169--465225 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
465159 ATTACAACGT
465169 GAAAATGACTATCGCAATGC
1 GAAAATGACTATCGCAATGC
465189 GAAAATGACTATCGCAATGC
1 GAAAATGACTATCGCAATGC
**
465209 GAATTTGACTATCGCAA
1 GAAAATGACTATCGCAA
465226 CGAAAGAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (20 bp):
GAAAATGACTATCGCAATGC
Found at i:465237 original size:34 final size:34
Alignment explanation
Indices: 465092--465246 Score: 125
Period size: 34 Copynumber: 4.4 Consensus size: 34
465082 ATAGTTTACT
* *
465092 ATCGCAATGTGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
** * *
465126 ATCGCAATGCG-AAATGAAAATCGTAAC-AACAAA
1 ATCGCAATGCGAAAATGACTATCGCAACGAA-AGA
** * *
465159 ATTACAACGTGAAAATGACTATCGCAATGCGAAAATGA
1 ATCGCAATGCGAAAATGACTATCGCAA--CG-AAA-GA
**
465197 CTATCGCAATGCGAATTTGACTATCGCAACGAAAGA
1 --ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
465233 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
465247 TGAAAATCGC
Statistics
Matches: 91, Mismatches: 21, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
32 1 0.01
33 22 0.24
34 35 0.38
36 3 0.03
37 4 0.04
38 5 0.05
40 21 0.23
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
Found at i:465298 original size:20 final size:20
Alignment explanation
Indices: 465273--465378 Score: 176
Period size: 20 Copynumber: 5.3 Consensus size: 20
465263 ATTCTCTCGA
**
465273 TGCGATAGTCAAATTCGCAT
1 TGCGATAGTCATTTTCGCAT
465293 TGCGATAGTCATTTTCGCAT
1 TGCGATAGTCATTTTCGCAT
465313 TGCGATAGTCATTTTCGCAT
1 TGCGATAGTCATTTTCGCAT
*
465333 TGCGATAGTCATTTTCGCGT
1 TGCGATAGTCATTTTCGCAT
*
465353 TGCGATAGTCATTTTCGCGT
1 TGCGATAGTCATTTTCGCAT
465373 TGCGAT
1 TGCGAT
465379 TTTAAGTTTC
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (20 bp):
TGCGATAGTCATTTTCGCAT
Found at i:465959 original size:42 final size:42
Alignment explanation
Indices: 465889--465969 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
465879 TCCCCTATCA
*
465889 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCT
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCACCT
* ** *
465931 TTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
465970 ACATTCTAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 31 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.22
Consensus pattern (42 bp):
TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCACCT
Found at i:467650 original size:45 final size:45
Alignment explanation
Indices: 467594--467698 Score: 126
Period size: 45 Copynumber: 2.3 Consensus size: 45
467584 ATGCATTGGT
**
467594 AGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATTC
1 AGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAA-TC
* *
467640 -GTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATC
1 AGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATC
467684 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
467699 AAGGAGTGCA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
44 2 0.04
45 45 0.87
46 5 0.10
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (45 bp):
AGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATC
Found at i:468102 original size:24 final size:24
Alignment explanation
Indices: 468075--468124 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
468065 ACATGCATAA
*
468075 GATATAT-ATATGTTCATGTGATAT
1 GATATATGATATGAT-ATGTGATAT
*
468099 GATATGTGATATGATATGTGATAT
1 GATATATGATATGATATGTGATAT
468123 GA
1 GA
468125 CCTGTGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.34, C:0.02, G:0.22, T:0.42
Consensus pattern (24 bp):
GATATATGATATGATATGTGATAT
Found at i:468107 original size:12 final size:12
Alignment explanation
Indices: 468090--468136 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
468080 ATATATGTTC
468090 ATGTGATATGAT
1 ATGTGATATGAT
468102 ATGTGATATGAT
1 ATGTGATATGAT
*
468114 ATGTGATATGAC
1 ATGTGATATGAT
*
468126 CTGTGATATGA
1 ATGTGATATGA
468137 GAACATGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (12 bp):
ATGTGATATGAT
Found at i:468194 original size:29 final size:28
Alignment explanation
Indices: 468152--468281 Score: 224
Period size: 28 Copynumber: 4.6 Consensus size: 28
468142 TGATATGAAG
468152 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAG-TACATGATCACAAGAGAAA
468181 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAG-TACATGATCACAAGAGAAA
*
468210 TGACATGAGTACATAATCACAAGAGAAA
1 TGACATGAGTACATGATCACAAGAGAAA
*
468238 TGACATGAGTACATAATCACAAGAGAAA
1 TGACATGAGTACATGATCACAAGAGAAA
468266 TGACATGAGTACATGA
1 TGACATGAGTACATGA
468282 ATATATGAAA
Statistics
Matches: 99, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
28 61 0.62
29 38 0.38
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.18
Consensus pattern (28 bp):
TGACATGAGTACATGATCACAAGAGAAA
Found at i:469622 original size:14 final size:14
Alignment explanation
Indices: 469603--469638 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
469593 ATTGTTTAAT
469603 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
469617 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
469631 TGATTTGT
1 TGATTTGT
469639 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:469832 original size:34 final size:33
Alignment explanation
Indices: 469743--469839 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 33
469733 CAAAACAGAC
* ** *
469743 AATCGCAACGCGGAAATGACTATCACAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
*
469777 AATCACAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
469810 AATCGCAATGCGAAAATGAAAATCGCAACG
1 AATCGCAATGCG-AAATGAAAATCGCAACG
469840 CGAAACTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:469911 original size:33 final size:34
Alignment explanation
Indices: 469854--469949 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
469844 ACTAAATTCG
469854 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
*
469888 CGTTGCGATTTTTA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
** * *
469921 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
469950 AGTCAATTCC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:469946 original size:20 final size:20
Alignment explanation
Indices: 469921--470009 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
469911 GCGATTCTCT
469921 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
469941 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
469961 CGTTACGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
469981 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
470001 CGTTGCGAT
1 CGTTGCGAT
470010 TTCCGTGTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 60 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:472233 original size:14 final size:14
Alignment explanation
Indices: 472214--472240 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
472204 TCCCGTGGCA
472214 TTTTCTTTGGGGAC
1 TTTTCTTTGGGGAC
472228 TTTTCTTTGGGGA
1 TTTTCTTTGGGGA
472241 TTTCTTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.30, T:0.52
Consensus pattern (14 bp):
TTTTCTTTGGGGAC
Found at i:472472 original size:24 final size:24
Alignment explanation
Indices: 472438--472491 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
472428 CTGAAAAATT
472438 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
472462 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
472486 ATCAAA
1 ATCAAA
472492 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:472505 original size:24 final size:24
Alignment explanation
Indices: 472438--472505 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
472428 CTGAAAAATT
* * *
472438 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
472462 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
472486 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
472506 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:473376 original size:20 final size:20
Alignment explanation
Indices: 473332--473379 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
473322 GAAATTCAGT
*
473332 ATTGCGATAGTCAGAATCTC
1 ATTGCGATAGTCAGAATCGC
*
473352 ATTGCGATAGTCAGATTCGC
1 ATTGCGATAGTCAGAATCGC
*
473372 GTTGCGAT
1 ATTGCGAT
473380 TTACGTATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
ATTGCGATAGTCAGAATCGC
Found at i:473389 original size:20 final size:20
Alignment explanation
Indices: 473366--473415 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
473356 CGATAGTCAG
*
473366 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
473386 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
473406 ATTCGCATTG
1 ATTCGCATTG
473416 AAGATTAGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:476510 original size:30 final size:31
Alignment explanation
Indices: 476474--476562 Score: 89
Period size: 30 Copynumber: 3.0 Consensus size: 31
476464 TATAATATAT
476474 AACTTTTAAAAATTATAATTTTAGTCC-CTA
1 AACTTTTAAAAATTATAATTTTAGTCCACTA
* * *
476504 AACTTTTTAAAGTT-TATACTTTAG-CCACTA
1 AACTTTTAAAAATTATA-ATTTTAGTCCACTA
* *
476534 AACTTTCAAAACTTA-AATTTTAGT-CACTA
1 AACTTTTAAAAATTATAATTTTAGTCCACTA
476563 GACAAAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
29 15 0.31
30 33 0.69
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (31 bp):
AACTTTTAAAAATTATAATTTTAGTCCACTA
Found at i:476561 original size:29 final size:29
Alignment explanation
Indices: 476474--476562 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
476464 TATAATATAT
*
476474 AACTTTTAAAAATTATAATTTTAGTCCCTA
1 AACTTTTAAAAATTA-AATTTTAGTCACTA
** * * *
476504 AACTTTTTAAAGTTTATACTTTAGCCACTA
1 AAC-TTTTAAAAATTAAATTTTAGTCACTA
* *
476534 AACTTTCAAAACTTAAATTTTAGTCACTA
1 AACTTTTAAAAATTAAATTTTAGTCACTA
476563 GACAAAATTT
Statistics
Matches: 46, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
29 20 0.43
30 16 0.35
31 10 0.22
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (29 bp):
AACTTTTAAAAATTAAATTTTAGTCACTA
Found at i:487060 original size:15 final size:15
Alignment explanation
Indices: 487040--487076 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
487030 TCGGCCCGTG
487040 ACCATCACCATTGAC
1 ACCATCACCATTGAC
487055 ACCATCACCATTGAC
1 ACCATCACCATTGAC
487070 ACCATCA
1 ACCATCA
487077 AAACTGTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.35, C:0.41, G:0.05, T:0.19
Consensus pattern (15 bp):
ACCATCACCATTGAC
Found at i:492554 original size:2 final size:2
Alignment explanation
Indices: 492547--492605 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
492537 TGATTTTCCC
492547 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
492589 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
492606 GTAAGAGTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:492727 original size:14 final size:15
Alignment explanation
Indices: 492640--492729 Score: 101
Period size: 15 Copynumber: 6.1 Consensus size: 15
492630 AATTGGTTTT
492640 CTGGAAAATGAATTA
1 CTGGAAAATGAATTA
**
492655 CTGGAATTTGAATTA
1 CTGGAAAATGAATTA
* **
492670 TTGGAATTTGAATTA
1 CTGGAAAATGAATTA
492685 CTGGAAAATGAATTA
1 CTGGAAAATGAATTA
**
492700 CTGGAATTTGAATT-
1 CTGGAAAATGAATTA
*
492714 CTGAAAAATGAATTA
1 CTGGAAAATGAATTA
492729 C
1 C
492730 ATTTTTTTCA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 11 0.17
15 52 0.83
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (15 bp):
CTGGAAAATGAATTA
Found at i:492820 original size:23 final size:22
Alignment explanation
Indices: 492793--492875 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 22
492783 ATACAATAAA
492793 TAATATTATTTATTATAAAACTT
1 TAATATTATTTATTATAAAA-TT
*
492816 TAATATTA-TTATTTTAAAATAT
1 TAATATTATTTATTATAAAAT-T
* * **
492838 TAAAATAATTTATT-TATTATT
1 TAATATTATTTATTATAAAATT
*
492859 AAATATTATTT-TTATAA
1 TAATATTATTTATTATAA
492876 TTTTATTAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.04
21 12 0.25
22 21 0.44
23 13 0.27
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (22 bp):
TAATATTATTTATTATAAAATT
Found at i:493019 original size:23 final size:23
Alignment explanation
Indices: 492970--493020 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
492960 GTGTTATATT
**
492970 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
492993 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
493016 ATATT
1 ATATT
493021 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:493032 original size:19 final size:19
Alignment explanation
Indices: 493008--493078 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
492998 TTAAATATCT
*
493008 TTATTAAAATATTATTAGA
1 TTATTAAAATATTATTAAA
* * *
493027 TTATTATATTAATATTAAA
1 TTATTAAAATATTATTAAA
* *
493046 TATATAAATAATATTATT-CA
1 T-TATTAA-AATATTATTAAA
493066 TTATTAAATATAT
1 TTATTAAA-ATAT
493079 AAAAAATTTA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
18 1 0.03
19 25 0.64
20 6 0.15
21 7 0.18
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAAAATATTATTAAA
Found at i:493045 original size:30 final size:30
Alignment explanation
Indices: 493009--493203 Score: 106
Period size: 30 Copynumber: 6.4 Consensus size: 30
492999 TAAATATCTT
*
493009 TATTAAAATATTATTAGATTATTATATTAA
1 TATTAAAATATTATTATATTATTATATTAA
* *
493039 TATTAAATATATAAATAATATTATTCATTATTAAA
1 TATTAAA-ATAT-TATTATATTATT-A-TATT-AA
*
493074 TATATAAAAAATTTATTATA-TATT-TATTAA
1 TAT-TAAAATA-TTATTATATTATTATATTAA
* *
493104 AATAAAAATA-TATTATATTA-TATTATT-A
1 TATTAAAATATTATTATATTATTA-TATTAA
* * * *
493132 TAATATAAT-TGATTATTTTA-T-TA-TAA
1 TATTAAAATATTATTATATTATTATATTAA
493158 TATTAAAAATATAATATTATATTATTATA--AA
1 TATT-AAAATAT--TATTATATTATTATATTAA
493189 TATTAATAAATATTA
1 TATT-A-AAATATTA
493204 ATAAATATTT
Statistics
Matches: 127, Mismatches: 19, Indels: 38
0.69 0.10 0.21
Matches are distributed among these distances:
25 1 0.01
26 6 0.05
27 12 0.09
28 18 0.14
29 9 0.07
30 21 0.17
31 17 0.13
32 17 0.13
33 1 0.01
34 8 0.06
35 12 0.09
36 5 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
TATTAAAATATTATTATATTATTATATTAA
Found at i:493059 original size:24 final size:26
Alignment explanation
Indices: 493032--493203 Score: 88
Period size: 28 Copynumber: 6.2 Consensus size: 26
493022 TTAGATTATT
493032 ATATTA-A-TATTAAATATATAAATA
1 ATATTATATTATTAAATATATAAATA
*
493056 ATATTATTCATTATTAAATATATAAAAA
1 ATATTA-T-ATTATTAAATATATAAATA
*
493084 ATTTATTATATATTTATTAAA-ATAAAAAT-
1 A--TA-T-TATA-TTATTAAATATATAAATA
*
493113 ATATTATATTA-T-ATTATTATAATATA
1 ATATTATATTATTAAATA-TATAA-ATA
* *
493139 ATTGATTATTTTATTATAATATTAAAAATATA
1 A-T-ATTATATTATTA-AATA-T-ATAA-ATA
*
493171 ATATTATATTATTATAA-ATATTAATAA
1 ATATTATATTATTA-AATATATAAAT-A
493198 ATATTA
1 ATATTA
493204 ATAAATATTT
Statistics
Matches: 117, Mismatches: 11, Indels: 37
0.71 0.07 0.22
Matches are distributed among these distances:
22 1 0.01
23 2 0.02
24 13 0.11
25 6 0.05
26 4 0.03
27 13 0.11
28 26 0.22
29 3 0.03
30 23 0.20
31 16 0.14
32 10 0.09
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.48
Consensus pattern (26 bp):
ATATTATATTATTAAATATATAAATA
Found at i:493216 original size:22 final size:23
Alignment explanation
Indices: 493145--493227 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 23
493135 TATAATTGAT
*
493145 TATTTTATTATAATATTAA-AAA
1 TATTTTAATATAATATTAATAAA
** * *
493167 TATAATATTATATTATT-ATAAA
1 TATTTTAATATAATATTAATAAA
493189 TA--TTAATA-AATATTAATAAA
1 TATTTTAATATAATATTAATAAA
493209 TATTTTAATAATTAATATT
1 TATTTTAAT-A-TAATATT
493228 TTGATGAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
19 5 0.10
20 11 0.23
21 1 0.02
22 24 0.50
23 1 0.02
25 6 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTTTAATATAATATTAATAAA
Found at i:493219 original size:12 final size:10
Alignment explanation
Indices: 493156--493212 Score: 64
Period size: 10 Copynumber: 5.6 Consensus size: 10
493146 ATTTTATTAT
493156 AATATTAA-A
1 AATATTAATA
493165 AATA-TAATA
1 AATATTAATA
*
493174 TTATATTATTATA
1 -AATATTA--ATA
493187 AATATTAATA
1 AATATTAATA
493197 AATATTAATA
1 AATATTAATA
493207 AATATT
1 AATATT
493213 TTAATAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
8 3 0.07
9 5 0.12
10 22 0.54
11 2 0.05
12 6 0.15
13 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AATATTAATA
Found at i:494662 original size:121 final size:121
Alignment explanation
Indices: 494448--494692 Score: 481
Period size: 121 Copynumber: 2.0 Consensus size: 121
494438 AACCAAACAT
*
494448 TAAAATGGTTCTAAATTGTTATTTCATACCATTTTTAATATAAATCTGATAAAGTAACCCAACGA
1 TAAAATGGTTCTAAATTGCTATTTCATACCATTTTTAATATAAATCTGATAAAGTAACCCAACGA
494513 ATATAATGTGCATGCTACTAATAAGTCAAAGTTAGTCTAGAACTTATATTTTGATA
66 ATATAATGTGCATGCTACTAATAAGTCAAAGTTAGTCTAGAACTTATATTTTGATA
494569 TAAAATGGTTCTAAATTGCTATTTCATACCATTTTTAATATAAATCTGATAAAGTAACCCAACGA
1 TAAAATGGTTCTAAATTGCTATTTCATACCATTTTTAATATAAATCTGATAAAGTAACCCAACGA
494634 ATATAATGTGCATGCTACTAATAAGTCAAAGTTAGTCTAGAACTTATATTTTGATA
66 ATATAATGTGCATGCTACTAATAAGTCAAAGTTAGTCTAGAACTTATATTTTGATA
494690 TAA
1 TAA
494693 CAAATAAGAA
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 123 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (121 bp):
TAAAATGGTTCTAAATTGCTATTTCATACCATTTTTAATATAAATCTGATAAAGTAACCCAACGA
ATATAATGTGCATGCTACTAATAAGTCAAAGTTAGTCTAGAACTTATATTTTGATA
Found at i:496300 original size:64 final size:66
Alignment explanation
Indices: 496141--496300 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 66
496131 TAATAAATTG
* *
496141 AACATCGAATGCATTTCATGCATCAATGCA-CATACCATGCATCGATACACTCAGGGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATACACTCAGGCTTTTATGA
496205 A
66 A
* * *
496206 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACTCAGGCTATTT-TG
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATACACTCAGGCT-TTTATG
496269 -A
65 AA
*
496270 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
496301 TCTTAGTGCA
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
64 31 0.36
65 51 0.59
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (66 bp):
AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATACACTCAGGCTTTTATGA
A
Found at i:496316 original size:64 final size:63
Alignment explanation
Indices: 496141--496320 Score: 197
Period size: 65 Copynumber: 2.8 Consensus size: 63
496131 TAATAAATTG
* * *
496141 AACATCGAATGCATTTCATGCATCAATGCACATACCA-TGCATCGATACACTCAGGGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCAC-T--CAGTGCATCGATGCACTCAGGCTTTTATGA
496205 A
63 A
*
496206 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCAGGCTATTT-TG
1 AACATCGAATGCATTTCATGCATCGATGCACTCAG---TGCATCGATGCACTCAGGCT-TTTATG
496269 -A
62 AA
* *
496270 AACATCGAATGCATTTTATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACTC--AGTGCATCGATGCACT
496321 AAGGGTCCAA
Statistics
Matches: 101, Mismatches: 6, Indels: 17
0.81 0.05 0.14
Matches are distributed among these distances:
61 2 0.02
64 44 0.44
65 50 0.50
66 3 0.03
67 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCAGTGCATCGATGCACTCAGGCTTTTATGAA
Found at i:496391 original size:53 final size:53
Alignment explanation
Indices: 496307--496425 Score: 229
Period size: 53 Copynumber: 2.2 Consensus size: 53
496297 GCACTCTTAG
496307 TGCACCGATGCACTAAGGGTCCAACGATCAAAATATTTGAATTTTACACTTGA
1 TGCACCGATGCACTAAGGGTCCAACGATCAAAATATTTGAATTTTACACTTGA
*
496360 TGCACCGATGCACTAAGGGTCCAACGGTCAAAATATTTGAATTTTACACTTGA
1 TGCACCGATGCACTAAGGGTCCAACGATCAAAATATTTGAATTTTACACTTGA
496413 TGCACCGATGCAC
1 TGCACCGATGCAC
496426 CTAGTGTATG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 65 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (53 bp):
TGCACCGATGCACTAAGGGTCCAACGATCAAAATATTTGAATTTTACACTTGA
Found at i:497613 original size:18 final size:18
Alignment explanation
Indices: 497587--497658 Score: 99
Period size: 18 Copynumber: 4.0 Consensus size: 18
497577 TTATTAATCT
497587 ACGTCTGATAACTGTAAA
1 ACGTCTGATAACTGTAAA
* *
497605 ACATCTGATAACTGAAAA
1 ACGTCTGATAACTGTAAA
*
497623 ACGTCCGATAACTGTAAA
1 ACGTCTGATAACTGTAAA
* *
497641 ATGTCTAATAACTGTAAA
1 ACGTCTGATAACTGTAAA
497659 CATTTAGAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (18 bp):
ACGTCTGATAACTGTAAA
Found at i:500403 original size:16 final size:16
Alignment explanation
Indices: 500382--500416 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
500372 TTTTCAAATT
*
500382 TAATTTTGTTTTATTA
1 TAATTTTATTTTATTA
500398 TAATTTTATTTTATTA
1 TAATTTTATTTTATTA
500414 TAA
1 TAA
500417 GAACACGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
TAATTTTATTTTATTA
Found at i:502262 original size:2 final size:2
Alignment explanation
Indices: 502255--502341 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
502245 ATACTTCTAC
502255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
502297 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
502339 TA T
1 TA T
502342 CACAATAAAT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:504735 original size:6 final size:6
Alignment explanation
Indices: 504724--504824 Score: 188
Period size: 6 Copynumber: 17.2 Consensus size: 6
504714 ACTGATTATA
504724 TATATT TATATT TATATT TATATT TATATT TATA-T T-TATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
504770 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
504818 TATATT T
1 TATATT T
504825 GAAAGTTGTA
Statistics
Matches: 93, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
4 2 0.02
5 4 0.04
6 87 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:508403 original size:37 final size:36
Alignment explanation
Indices: 508362--508431 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 36
508352 TAAGACACAA
* * *
508362 CTATTAACCTCAAATTAATCTAATTAAAAGAATTACT
1 CTATTAAACTCAAACTAATCTAACTAAAA-AATTACT
508399 CTATTAAACTCAAACTAATCTAACTAAAAAATT
1 CTATTAAACTCAAACTAATCTAACTAAAAAATT
508432 TACAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 4 0.13
37 26 0.87
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.33
Consensus pattern (36 bp):
CTATTAAACTCAAACTAATCTAACTAAAAAATTACT
Found at i:508629 original size:12 final size:12
Alignment explanation
Indices: 508612--508637 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
508602 GAAATAATTT
508612 TATTAAATATAA
1 TATTAAATATAA
508624 TATTAAATATAA
1 TATTAAATATAA
508636 TA
1 TA
508638 ATTTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TATTAAATATAA
Found at i:509182 original size:26 final size:28
Alignment explanation
Indices: 509153--509208 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
509143 TTGACTTATT
*
509153 ATGATTGATATTT-TTTTAAA-A-AATAA
1 ATGATTAAT-TTTATTTTAAATATAATAA
509179 ATGATTAATTTTATTTTAAATATAATAA
1 ATGATTAATTTTATTTTAAATATAATAA
509207 AT
1 AT
509209 AATTCAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 3 0.12
26 15 0.58
27 1 0.04
28 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (28 bp):
ATGATTAATTTTATTTTAAATATAATAA
Found at i:517353 original size:18 final size:17
Alignment explanation
Indices: 517332--517369 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
517322 GTTTTTAGCA
517332 TTTTCAAATATAAATACT
1 TTTTCAAATATAAATA-T
*
517350 TTTTTAAATATAAATAT
1 TTTTCAAATATAAATAT
517367 TTT
1 TTT
517370 GAAACTAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTCAAATATAAATAT
Found at i:521896 original size:25 final size:25
Alignment explanation
Indices: 521868--521934 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
521858 GCAAAAAAGA
* *
521868 AGACAAGTAAATGTGAAAAGCTATG
1 AGACAAGAAAATGTGAAAAGATATG
*
521893 AGACACGAAAATGTGAAAAGATATG
1 AGACAAGAAAATGTGAAAAGATATG
*
521918 AGACATGAAAATGTGAA
1 AGACAAGAAAATGTGAA
521935 TTTCATGGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (25 bp):
AGACAAGAAAATGTGAAAAGATATG
Found at i:522839 original size:18 final size:18
Alignment explanation
Indices: 522818--522860 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
522808 TTTATGTAAA
*
522818 AGAATTTCTTTATAGAAT
1 AGAAGTTCTTTATAGAAT
*
522836 AGAAGTTCTTTTTAGAAT
1 AGAAGTTCTTTATAGAAT
522854 AGAAGTT
1 AGAAGTT
522861 TTAAATTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (18 bp):
AGAAGTTCTTTATAGAAT
Found at i:531892 original size:16 final size:16
Alignment explanation
Indices: 531871--531903 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
531861 TAAATGCCTC
531871 GTTCTATTTTCTTACA
1 GTTCTATTTTCTTACA
531887 GTTCTATTTTCTTACA
1 GTTCTATTTTCTTACA
531903 G
1 G
531904 AAGGTCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.55
Consensus pattern (16 bp):
GTTCTATTTTCTTACA
Found at i:532265 original size:2 final size:2
Alignment explanation
Indices: 532258--532285 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
532248 CTACAGCAAG
532258 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
532286 AAACAATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:537062 original size:15 final size:16
Alignment explanation
Indices: 537042--537071 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
537032 ATATGGTAAC
537042 AAATTTT-GTAACTAA
1 AAATTTTAGTAACTAA
537057 AAATTTTAGTAACTA
1 AAATTTTAGTAACTA
537072 TGATAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (16 bp):
AAATTTTAGTAACTAA
Found at i:543243 original size:32 final size:32
Alignment explanation
Indices: 543197--543261 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
543187 TCGAGCAATA
*
543197 TATTCGCAGCTTTGACATCCCGATGATTTATC
1 TATTCGCAGCTTTGACATCCCGATGAATTATC
*
543229 TATTTGCAGCTTTGACATCCCGATGAATTATC
1 TATTCGCAGCTTTGACATCCCGATGAATTATC
543261 T
1 T
543262 TTGGATCGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (32 bp):
TATTCGCAGCTTTGACATCCCGATGAATTATC
Found at i:549664 original size:18 final size:20
Alignment explanation
Indices: 549643--549687 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
549633 TAAACTATAT
549643 ATGAAAATTTAT-ATG-AAA
1 ATGAAAATTTATAATGTAAA
549661 ATG-AAA-TTATAATGTAAA
1 ATGAAAATTTATAATGTAAA
*
549679 CTGAAAATT
1 ATGAAAATT
549688 GAGGAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
16 4 0.18
17 6 0.27
18 8 0.36
19 3 0.14
20 1 0.05
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.33
Consensus pattern (20 bp):
ATGAAAATTTATAATGTAAA
Found at i:554565 original size:26 final size:26
Alignment explanation
Indices: 554516--554566 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
554506 GTTTTGAAAT
*
554516 TTTTTGAAAACATATATAATATATAG
1 TTTTTGAAAACATATATAAAATATAG
* *
554542 TTTTTGAAAACATTTTTAAAATATA
1 TTTTTGAAAACATATATAAAATATA
554567 TATATAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (26 bp):
TTTTTGAAAACATATATAAAATATAG
Found at i:554577 original size:37 final size:38
Alignment explanation
Indices: 554386--554734 Score: 214
Period size: 36 Copynumber: 9.2 Consensus size: 38
554376 TAAATATTTT
* *
554386 TATAGTTTTGGAAAACAGTTTTTGAAAACATATA-ATAATA
1 TATAGTTTTTGAAAACA-TTTTT-AAAATATATATAT-ATA
* * *
554426 TATACTTTTTTAAAAAATCGGTTTTTAAAA-ATATATAT-TA
1 TATA-GTTTTT-GAAAA-C-ATTTTTAAAATATATATATATA
* *
554466 TATAG-TTTTGAAAACGGTTTTCGAAAATAT-T-TAT-TA
1 TATAGTTTTTGAAAAC-ATTTT-TAAAATATATATATATA
* *
554502 TATAG-TTTTG-AAA-TTTTTTGAAAACATATATA-ATA
1 TATAGTTTTTGAAAACATTTTT-AAAATATATATATATA
554537 TATAGTTTTTGAAAACATTTTTAAAATATATATATAATA
1 TATAGTTTTTGAAAACATTTTTAAAATATATATAT-ATA
* * *
554576 TATAGTTTTTAAAAATATTTTGAAAATATATATAATATATA
1 TATAGTTTTTGAAAACATTTT-TAAA-ATATAT-ATATATA
* * *
554617 TATAGTTTTGGAAAATATTTTT-GAA-A-ATATAT-TA
1 TATAGTTTTTGAAAACATTTTTAAAATATATATATATA
** * *
554651 TATAGTTTTAAAAAAACAAATTTTGAAA-ATATATAT-TA
1 TATAGTTTT-TGAAAAC-ATTTTTAAAATATATATATATA
* * *
554689 TA-GGTTTTTGAAAACATTTTTTAAAAAACATATA-ATA
1 TATAGTTTTTGAAAACA-TTTTTAAAATATATATATATA
554726 TATAGTTTT
1 TATAGTTTT
554735 AAAAAATAAT
Statistics
Matches: 251, Mismatches: 31, Indels: 56
0.74 0.09 0.17
Matches are distributed among these distances:
33 10 0.04
34 12 0.05
35 21 0.08
36 46 0.18
37 42 0.17
38 27 0.11
39 23 0.09
40 13 0.05
41 37 0.15
42 14 0.06
43 6 0.02
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (38 bp):
TATAGTTTTTGAAAACATTTTTAAAATATATATATATA
Found at i:554621 original size:151 final size:143
Alignment explanation
Indices: 554371--554747 Score: 356
Period size: 151 Copynumber: 2.5 Consensus size: 143
554361 ATAGGTTAAT
* * * *
554371 TTTTGTAAATAT-TTTTATAGTTTTGGAAAACAGTTTTTGAAAACATATA-ATAATATATACTTT
1 TTTTGAAAATATATATTATAGTTTTTGAAAACAGTTTTT-AAAA-ATATATATAATATATA-GTT
** *
554434 TTTAAAAA-ATCGGTTTTTAAAAATATATATTATATAGTTTT-GAAAACGGTTTTCGAAAATATT
63 TTTAAAAATAT---TTTGAAAAAATATATATTATATAGTTTTGGAAAA-GATTTTCGAAAATA--
* **
554497 TATTATATAGTTTT-GAA-ATT
122 TATTATATAGTTTTAAAACAAA
554517 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA-TTTTTAAAATATATATATAATATATAG
1 TTTTG-AAA-ATATAT-AT-TATAGTTTTTGAAAACAGTTTTTAAAA-ATATATATAATATATAG
* *
554581 TTTTTAAAAATATTTTGAAAATATATATAATATATATATAGTTTTGGAAAATATTTTTGAAAATA
61 TTTTTAAAAATATTTTGAAAA-A-ATAT-ATAT-TATATAGTTTTGGAAAAGATTTTCGAAAATA
554646 TATTATATAGTTTTAAAAAAACAAA
122 TATTATATAGTTTT---AAAACAAA
* *
554671 TTTTGAAAATATATATTATAGGTTTTTGAAAACATTTTTTAAAAA-ACATATAATATATAGTTTT
1 TTTTGAAAATATATATTATA-GTTTTTGAAAACAGTTTTTAAAAATATATATAATATATAGTTTT
*
554735 AAAAAATAATTTT
65 TAAAAAT-ATTTT
554748 TATTTTCGTT
Statistics
Matches: 196, Mismatches: 15, Indels: 35
0.80 0.06 0.14
Matches are distributed among these distances:
146 5 0.03
147 8 0.04
148 5 0.03
149 38 0.19
150 50 0.26
151 59 0.30
152 20 0.10
153 5 0.03
154 6 0.03
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (143 bp):
TTTTGAAAATATATATTATAGTTTTTGAAAACAGTTTTTAAAAATATATATAATATATAGTTTTT
AAAAATATTTTGAAAAAATATATATTATATAGTTTTGGAAAAGATTTTCGAAAATATATTATATA
GTTTTAAAACAAA
Found at i:554685 original size:80 final size:80
Alignment explanation
Indices: 554529--554747 Score: 205
Period size: 75 Copynumber: 2.8 Consensus size: 80
554519 TTGAAAACAT
* * *
554529 ATATAATATATAGTTTTTGAAAACATTTTTAAAATATATATATAATATATAGTTTTTAAAAATAT
1 ATATAATATATAGTTTTGGAAAACATTTTTAAAATATATATAT-ATATATAGTTTTAAAAAAAAT
554594 TTTGAAAATATATATA
65 TTTGAAAATATATATA
* *
554610 ATAT-ATATATAGTTTTGGAAAATATTTTT-GAA-A-ATATAT-TATATAGTTTTAAAAAAACAA
1 ATATAATATATAGTTTTGGAAAACATTTTTAAAATATATATATATATATAGTTTT--AAAAA-AA
554670 ATTTTG--AA-A-ATAT-
63 ATTTTGAAAATATATATA
* * * *
554683 ATAT--TATA-GGTTTTTGAAAACATTTTTTAAAAAACATATA-ATATATAGTTTTAAAAAATAA
1 ATATAATATATAGTTTTGGAAAACA-TTTTTAAAATATATATATATATATAGTTTTAAAAAA-AA
554744 TTTT
64 TTTT
554748 TATTTTCGTT
Statistics
Matches: 120, Mismatches: 9, Indels: 26
0.77 0.06 0.17
Matches are distributed among these distances:
71 11 0.09
72 10 0.08
73 17 0.14
74 5 0.04
75 28 0.23
76 2 0.02
77 10 0.08
78 8 0.07
79 2 0.02
80 23 0.19
81 4 0.03
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.44
Consensus pattern (80 bp):
ATATAATATATAGTTTTGGAAAACATTTTTAAAATATATATATATATATAGTTTTAAAAAAAATT
TTGAAAATATATATA
Found at i:554747 original size:39 final size:37
Alignment explanation
Indices: 554386--554749 Score: 190
Period size: 39 Copynumber: 9.6 Consensus size: 37
554376 TAAATATTTT
* * * *
554386 TATAGTTTTGGAAAACAGTTTTTGAAAACATATAATAATA
1 TATAGTTTT-TAAAAAAATTTTT-AAAAAATAT-ATAATA
* * * *
554426 TATACTTTTTTAAAAAATCGGTTTTTAAAAATATATATTA
1 TATAGTTTTTAAAAAAAT---TTTTAAAAAATATATAATA
* *** ** * *
554466 TATAG-TTTTGAAAACGGTTTTCGAAAATATTTATTA
1 TATAGTTTTTAAAAAAATTTTTAAAAAATATATAATA
* * *
554502 TATAG-TTTT--GAAATTTTTTGAAAACATATATAATA
1 TATAGTTTTTAAAAAAATTTTT-AAAAAATATATAATA
* *
554537 TATAGTTTTTGAAAACATTTTTAAAATATATATATAATA
1 TATAGTTTTTAAAAAAATTTTTAAAA-A-ATATATAATA
* *
554576 TATAGTTTTTAAAAATATTTTGAAAATATATATAATATATA
1 TATAGTTTTTAAAAAAATTTTTAAAA-A-ATAT-ATA-ATA
** * *
554617 TATAGTTTTGGAAAATATTTTT-GAAAATATAT--TA
1 TATAGTTTTTAAAAAAATTTTTAAAAAATATATAATA
* * *
554651 TATAGTTTTAAAAAAACAAATTTT-GAAAATATAT-AT-
1 TATAGTTTT-TAAAAA-AATTTTTAAAAAATATATAATA
* * *
554687 TATAGGTTTTTGAAAACATTTTTTAAAAAACATATAATA
1 TATA-GTTTTT-AAAAAAATTTTTAAAAAATATATAATA
*
554726 TATAGTTTTAAAAAATAATTTTTA
1 TATAGTTTTTAAAAA-AATTTTTA
554750 TTTTCGTTTC
Statistics
Matches: 255, Mismatches: 49, Indels: 42
0.74 0.14 0.12
Matches are distributed among these distances:
34 17 0.07
35 19 0.07
36 53 0.21
37 28 0.11
38 25 0.10
39 58 0.23
40 22 0.09
41 29 0.11
42 4 0.02
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (37 bp):
TATAGTTTTTAAAAAAATTTTTAAAAAATATATAATA
Found at i:555785 original size:16 final size:16
Alignment explanation
Indices: 555759--555791 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
555749 AATTTTTTAA
555759 ATTTTTATTATGTTTTT
1 ATTTTTATTAT-TTTTT
555776 ATTTTT-TTATTTTTT
1 ATTTTTATTATTTTTT
555791 A
1 A
555792 AATTATATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 4 0.25
17 6 0.38
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (16 bp):
ATTTTTATTATTTTTT
Found at i:560217 original size:2 final size:2
Alignment explanation
Indices: 560210--560241 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
560200 TCTGTTATTA
560210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
560242 TCACCTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:561642 original size:2 final size:2
Alignment explanation
Indices: 561635--561676 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
561625 AAACCAATAA
561635 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
561677 TCTTTGCTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:562731 original size:3 final size:3
Alignment explanation
Indices: 562704--562748 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
562694 AAAAAATATA
*
562704 TAT TA- TAT TAT GTAT TAT GTAT TAT TAT TAT TTT TAT TAT TAT TA
1 TAT TAT TAT TAT -TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TA
562749 ATAGAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 29 0.78
4 6 0.16
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:565729 original size:27 final size:28
Alignment explanation
Indices: 565681--565733 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
565671 ACATGTACTA
* *
565681 ACTAATTTCTTTTCTTTTGTTTGTGTAC
1 ACTAATTTCATTTATTTTGTTTGTGTAC
565709 ACTAATTT-ATTTATTTTGTTTGTGT
1 ACTAATTTCATTTATTTTGTTTGTGT
565734 CATTTTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.62
Consensus pattern (28 bp):
ACTAATTTCATTTATTTTGTTTGTGTAC
Found at i:567267 original size:36 final size:36
Alignment explanation
Indices: 567227--567303 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
567217 ATTTTAATTC
567227 ACATCTTTACATTTTTATGTTTATAGTTTCAATCTT
1 ACATCTTTACATTTTTATGTTTATAGTTTCAATCTT
*
567263 ACATCTTTGCATTTTTATGTTTATAGTTTCAATCTT
1 ACATCTTTACATTTTTATGTTTATAGTTTCAATCTT
567299 ACATC
1 ACATC
567304 ATGCATTTGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (36 bp):
ACATCTTTACATTTTTATGTTTATAGTTTCAATCTT
Found at i:569581 original size:8 final size:9
Alignment explanation
Indices: 569563--569595 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
569553 TGCTCAAAGG
569563 AAAAAGAAA
1 AAAAAGAAA
569572 AAAAAGAAA
1 AAAAAGAAA
569581 AAAAAGAAA
1 AAAAAGAAA
569590 AAAAAG
1 AAAAAG
569596 GATTAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:570064 original size:1 final size:1
Alignment explanation
Indices: 570060--570161 Score: 51
Period size: 1 Copynumber: 102.0 Consensus size: 1
570050 AAATGAAAGG
* * * * * * * * * * * *
570060 AAAAAAAGAAAAGAAAAGAAAAGAAAAAAGAAAGAAAGAAAAAGAAAAGAAAAGAAATAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
570125 ATAAAAGAAATAAAAGAAAAAAGAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
570162 GAAATGAAAT
Statistics
Matches: 67, Mismatches: 34, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (1 bp):
A
Found at i:570065 original size:13 final size:13
Alignment explanation
Indices: 570041--570158 Score: 90
Period size: 14 Copynumber: 9.2 Consensus size: 13
570031 CTCATCCATC
570041 AAAGAAAAAAAATGA
1 AAAG-AAAAAAA-GA
*
570056 AAGGAAAAAAAGA
1 AAAGAAAAAAAGA
570069 AAAG---AAAAGA
1 AAAGAAAAAAAGA
570079 AAAG-AAAAAAG-
1 AAAGAAAAAAAGA
570090 AAAGAAAGAAAAAGA
1 AAAG-AA-AAAAAGA
*
570105 AAAGAAAAGAAATA
1 AAAGAAAA-AAAGA
570119 AAAGAAATAAAAG-
1 AAAGAAA-AAAAGA
* *
570132 AAATAAAAGAA-A
1 AAAGAAAAAAAGA
570144 AAAGAAAAAAA-A
1 AAAGAAAAAAAGA
570156 AAA
1 AAA
570159 AAAGAAATGA
Statistics
Matches: 86, Mismatches: 8, Indels: 21
0.75 0.07 0.18
Matches are distributed among these distances:
10 10 0.12
11 4 0.05
12 21 0.24
13 14 0.16
14 29 0.34
15 8 0.09
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.03
Consensus pattern (13 bp):
AAAGAAAAAAAGA
Found at i:570071 original size:5 final size:5
Alignment explanation
Indices: 570041--570170 Score: 94
Period size: 5 Copynumber: 26.4 Consensus size: 5
570031 CTCATCCATC
* *
570041 AAAGA AAA-A AAATG- AAAGG AAA-A AAAGA AAAGA AAAGA AAAGA AAAAA
1 AAAGA AAAGA AAA-GA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
* *
570089 GAAAG- AAAGAA AAAGA AAAGA AAAG- AAATA AAAG- AAATA AAAGA AATA-A
1 -AAAGA AAAG-A AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA-AGA
* * * *
570138 AAGAAA AAAGA AAAAA AAAAA AAAGA AATGA AA
1 AA-AGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
570171 TTGAATCAAG
Statistics
Matches: 102, Mismatches: 12, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
4 18 0.18
5 73 0.72
6 11 0.11
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:570123 original size:9 final size:8
Alignment explanation
Indices: 570041--570165 Score: 109
Period size: 8 Copynumber: 15.9 Consensus size: 8
570031 CTCATCCATC
570041 AAAGAAAA
1 AAAGAAAA
**
570049 AAA-ATGA
1 AAAGAAAA
*
570056 AAGGAAAA
1 AAAGAAAA
570064 AAAGAAAA
1 AAAGAAAA
* *
570072 GAA-AAGA
1 AAAGAAAA
570079 AAAG-AAA
1 AAAGAAAA
*
570086 AAAGAAAG
1 AAAGAAAA
570094 AAAGAAAA
1 AAAGAAAA
*
570102 AGAA-AAGA
1 A-AAGAAAA
570110 AAAGAAATA
1 AAAGAAA-A
570119 AAAGAAATA
1 AAAGAAA-A
570128 AAAGAAATA
1 AAAGAAA-A
570137 AAAG-AAA
1 AAAGAAAA
570144 AAAGAAAA
1 AAAGAAAA
570152 AAA-AAAA
1 AAAGAAAA
570159 AAAGAAA
1 AAAGAAA
570166 TGAAATTGAA
Statistics
Matches: 95, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
7 29 0.31
8 41 0.43
9 25 0.26
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (8 bp):
AAAGAAAA
Found at i:570156 original size:54 final size:50
Alignment explanation
Indices: 570047--570170 Score: 109
Period size: 45 Copynumber: 2.6 Consensus size: 50
570037 CATCAAAGAA
* *
570047 AAAAAATGAAAG-GAAAAAAAGAAAAGAAAAGAAA-AGAA-AAAAG-AAAG
1 AAAAAA-GAAAGAAAAAAAAAGAAAAGAAAAGAAATAAAAGAAAAGAAAAG
* * * *
570094 AAAGAA-AAAGAAAAGAAAAG-AAATAAAAGAAATAAAAG-AAATAAAAG
1 AAAAAAGAAAGAAAAAAAAAGAAAAGAAAAGAAATAAAAGAAAAGAAAAG
* *
570141 AAAAAAGAAAAAAAAAAAAAAGAAATGAAA
1 AAAAAAG-AAAGAAAAAAAAAGAAAAGAAA
570171 TTGAATCAAG
Statistics
Matches: 59, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
45 15 0.25
46 13 0.22
47 14 0.24
49 12 0.20
50 5 0.08
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (50 bp):
AAAAAAGAAAGAAAAAAAAAGAAAAGAAAAGAAATAAAAGAAAAGAAAAG
Found at i:570171 original size:54 final size:55
Alignment explanation
Indices: 570045--570171 Score: 154
Period size: 54 Copynumber: 2.3 Consensus size: 55
570035 TCCATCAAAG
* * *
570045 AAAAAAAATGAAAGGAAA-AAAAGAAAAGAAAAGAAAAGAAAAAAGAAAGAAAGA
1 AAAAAAAAAGAAAAGAAATAAAAGAAAAGAAAAGAAAAGAAAAAAGAAAGAAAAA
* *
570099 AAAAGAAAAGAAAAGAAATAAAAG-AAATAAAAGAAATA-AAAGAAA-AAAGAAAAA
1 AAAAAAAAAGAAAAGAAATAAAAGAAAAGAAAAGAAA-AGAAA-AAAGAAAGAAAAA
*
570153 AAAAAAAAAGAAATGAAAT
1 AAAAAAAAAGAAAAGAAAT
570172 TGAATCAAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
54 54 0.86
55 9 0.14
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (55 bp):
AAAAAAAAAGAAAAGAAATAAAAGAAAAGAAAAGAAAAGAAAAAAGAAAGAAAAA
Found at i:573193 original size:43 final size:43
Alignment explanation
Indices: 572960--573181 Score: 304
Period size: 43 Copynumber: 5.2 Consensus size: 43
572950 CATGATTTTC
** *
572960 AGGGG-TTCTTTGATGACAAGCTTGAGAAACCATCGTGGTATGT
1 AGGGGTTTC-TTGATGACAAGCTTGAGGGACCATCGTGATATGT
* * *
573003 AGGGGTTTCTTGATGATAAGCTTGAAGGACCATCGTTATATGT
1 AGGGGTTTCTTGATGACAAGCTTGAGGGACCATCGTGATATGT
* * *
573046 AGGGGTTTCTTGATGATAAGCTTGAAGGACCATCATGATATGT
1 AGGGGTTTCTTGATGACAAGCTTGAGGGACCATCGTGATATGT
**
573089 AGGGG-TTCTTTGATGACAAGCTTGAGAAACCATCGTGATATGT
1 AGGGGTTTC-TTGATGACAAGCTTGAGGGACCATCGTGATATGT
*
573132 AGGGGTTTCTTGATGACAAGTTTGAGGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGACAAGCTTGAGGGACCATCGTGATATGT
573175 AGGGGTT
1 AGGGGTT
573182 CTTTGGTGAC
Statistics
Matches: 160, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
42 3 0.02
43 151 0.94
44 6 0.04
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.32
Consensus pattern (43 bp):
AGGGGTTTCTTGATGACAAGCTTGAGGGACCATCGTGATATGT
Found at i:573444 original size:91 final size:90
Alignment explanation
Indices: 573195--573594 Score: 539
Period size: 91 Copynumber: 4.4 Consensus size: 90
573185 TGGTGACAAT
* * *
573195 TAAGAAACTGAGCCTTTGGGGGTTTCTTGATTTTTAAGTCCTTTGGGCCATCCATAAGACCTTTA
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCA
573260 GTGCAGGATGTTTTCAAATGAGATC
66 GTGCAGGATGTTTTCAAATGAGATC
* * * * *
573285 TAAGAAATTGAACATTCGGGGGTTTCTTTATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTTA
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCA
*
573350 GTGCATGATGTTTTCAAATGAGATC
66 GTGCAGGATGTTTTCAAATGAGATC
* * * * **
573375 TAAGAAACTGAGCCTTCGAGGTTTTTTTGATTTTTTAAGTCATTCGGGCCATCTGTAAGACCTTC
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGA-TTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
573440 AGTGCAGGATGTTTTCAAATGAGATC
65 AGTGCAGGATGTTTTCAAATGAGATC
* * ***
573466 TAAGAAACTGAGCATTCGGGGGTTTCTTGATTTTTTAATTCCTTCGGGCCATCCATAAGACCCAA
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGA-TTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
*** *
573531 ACAACAGGATGTTTTCAAATGAGATTT
65 AGTGCAGGATGTTTTCAAATGAGA-TC
* *
573558 TAAGAAACTAAGCCTTCAGGGGTTTCTTGATTTTTAA
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAA
573595 ATCATTCAGG
Statistics
Matches: 271, Mismatches: 37, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
90 106 0.39
91 137 0.51
92 28 0.10
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (90 bp):
TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCA
GTGCAGGATGTTTTCAAATGAGATC
Found at i:573905 original size:15 final size:15
Alignment explanation
Indices: 573893--573922 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
573883 TATATTATAT
573893 TATGTATTATTATTA
1 TATGTATTATTATTA
*
573908 TATTTATTATTATTA
1 TATGTATTATTATTA
573923 ATAGAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
TATGTATTATTATTA
Found at i:573908 original size:18 final size:18
Alignment explanation
Indices: 573885--573922 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
573875 AAAAAATATA
573885 TATTATA-TTATGTATTAT
1 TATTATATTTAT-TATTAT
573903 TATTATATTTATTATTAT
1 TATTATATTTATTATTAT
573921 TA
1 TA
573923 ATAGAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TATTATATTTATTATTAT
Found at i:573914 original size:12 final size:13
Alignment explanation
Indices: 573881--573920 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
573871 GATTAAAAAA
573881 TATATATTA-TAT
1 TATATATTATTAT
*
573893 TATGTATTATTAT
1 TATATATTATTAT
573906 TATAT-TTATTAT
1 TATATATTATTAT
573918 TAT
1 TAT
573921 TAATAGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 18 0.72
13 7 0.28
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
TATATATTATTAT
Found at i:573932 original size:18 final size:19
Alignment explanation
Indices: 573891--573932 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
573881 TATATATTAT
* *
573891 ATTATGTATTATTATTATA
1 ATTATGTATTATTAATAGA
*
573910 TTTAT-TATTATTAATAGA
1 ATTATGTATTATTAATAGA
573928 ATTAT
1 ATTAT
573933 AATACATGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
ATTATGTATTATTAATAGA
Found at i:581390 original size:38 final size:38
Alignment explanation
Indices: 581348--581422 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
581338 ATATAAAAGT
581348 AAGAATCTAATTGTAAGATTGAAAACAATAATAAATAA
1 AAGAATCTAATTGTAAGATTGAAAACAATAATAAATAA
*
581386 AAGAATCTAATTGTAAGATTGAAAATAATAATAAATA
1 AAGAATCTAATTGTAAGATTGAAAACAATAATAAATA
581423 GTTTATTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.28
Consensus pattern (38 bp):
AAGAATCTAATTGTAAGATTGAAAACAATAATAAATAA
Found at i:581578 original size:11 final size:11
Alignment explanation
Indices: 581562--581621 Score: 70
Period size: 11 Copynumber: 5.6 Consensus size: 11
581552 ACTTAACAAA
581562 TAAAATTATTT
1 TAAAATTATTT
**
581573 TAAAATT-TAA
1 TAAAATTATTT
581583 TAAAATTATTT
1 TAAAATTATTT
**
581594 TAAAATT-TAA
1 TAAAATTATTT
581604 TAAAATTATTT
1 TAAAATTATTT
581615 TAAAATT
1 TAAAATT
581622 TAATAAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 16 0.41
11 23 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:581584 original size:21 final size:21
Alignment explanation
Indices: 581560--581629 Score: 140
Period size: 21 Copynumber: 3.3 Consensus size: 21
581550 AAACTTAACA
581560 AATAAAATTATTTTAAAATTT
1 AATAAAATTATTTTAAAATTT
581581 AATAAAATTATTTTAAAATTT
1 AATAAAATTATTTTAAAATTT
581602 AATAAAATTATTTTAAAATTT
1 AATAAAATTATTTTAAAATTT
581623 AATAAAA
1 AATAAAA
581630 AATTTAAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATAAAATTATTTTAAAATTT
Found at i:581588 original size:10 final size:10
Alignment explanation
Indices: 581573--581629 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
581563 AAAATTATTT
581573 TAAAATTTAA
1 TAAAATTTAA
**
581583 TAAAATTATTT
1 TAAAATT-TAA
581594 TAAAATTTAA
1 TAAAATTTAA
**
581604 TAAAATTATTT
1 TAAAATT-TAA
581615 TAAAATTTAA
1 TAAAATTTAA
581625 TAAAA
1 TAAAA
581630 AATTTAAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 21 0.57
11 16 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TAAAATTTAA
Found at i:582522 original size:13 final size:13
Alignment explanation
Indices: 582504--582545 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
582494 CATCAAATAA
*
582504 GTCAAAAAATGTT
1 GTCAAAAAATGAT
582517 GTCAAAAAATGAT
1 GTCAAAAAATGAT
582530 GT-AAAAAATGAT
1 GTCAAAAAATGAT
582542 GTCA
1 GTCA
582546 TTTAAACCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (13 bp):
GTCAAAAAATGAT
Found at i:585970 original size:3 final size:3
Alignment explanation
Indices: 585962--585995 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
585952 TTTGAATATG
585962 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
585996 TTTCAAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:594358 original size:114 final size:114
Alignment explanation
Indices: 594158--594385 Score: 429
Period size: 114 Copynumber: 2.0 Consensus size: 114
594148 GTGCCACGTT
*
594158 CTCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTG
*
594223 GTTTGGTATGAACCCCAAAACCAATTATTGGATTTGAAAGATGAATTTG
66 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
*
594272 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTG
594337 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
594386 ATAATAGTCT
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 111 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTG
GTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
Found at i:597682 original size:113 final size:113
Alignment explanation
Indices: 597469--598142 Score: 829
Period size: 113 Copynumber: 5.9 Consensus size: 113
597459 TAGCAAAGAT
* * *
597469 TCAAATCCATCAC--AATGGATCAAGATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
597532 AGAAGGAATAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
597580 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
597645 AGAAGGAAGAAGAAATTCATAATGAGAAGAGCATGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
597693 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATATTGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
597758 AGAAGGAATAAGAAGTTCATAATGAGAAGAA-TCTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACT-TGTTCAACCTTTTGC
** * * * *
597806 TTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
* * * *
597870 AAGAAGGAAGAATAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * ** *
597919 TCGAATTCATCACTCGATGGATTAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
1 TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
597984 AGAA-GAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * ** *
598031 TTAACTCTATCACAGAAGGATATAGATCAACATCAACATTTCCAGATAAAGTTCATAATGAGAAG
1 TCAAATCCATCAC-------T-T-GAT--GGATCAACATTTCCAGAGAAAGTTCATAATGAGAAG
*
598096 AACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
55 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
598143 TGACTTTAGC
Statistics
Matches: 489, Mismatches: 56, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
111 13 0.03
112 46 0.09
113 349 0.71
114 2 0.00
119 1 0.00
121 3 0.01
122 1 0.00
123 74 0.15
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Done.