Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006105.1 Hibiscus syriacus cultivar Beakdansim tig00014469_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: 102374
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:4405 original size:24 final size:23
Alignment explanation
Indices: 4362--4406 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
4352 TTTAATTATT
*
4362 TATTATTAGAATTTTTAGTTTAC
1 TATTATTAGAATTTTAAGTTTAC
4385 TATTAATTAGGAA-TTTAAGTTT
1 TATT-ATTA-GAATTTTAAGTTT
4407 TAAATTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 12 0.63
25 3 0.16
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.53
Consensus pattern (23 bp):
TATTATTAGAATTTTAAGTTTAC
Found at i:7653 original size:21 final size:21
Alignment explanation
Indices: 7627--7771 Score: 164
Period size: 21 Copynumber: 6.8 Consensus size: 21
7617 CCATATAGAA
7627 ATGTCCCGAAGGACCACATAT
1 ATGTCCCGAAGGACCACATAT
* *
7648 ATGTCCCGAATGACCACATAGA
1 ATGTCCCGAAGGACCACATA-T
*
7670 ATTGTCCCTAAGGACCACATAT
1 A-TGTCCCGAAGGACCACATAT
* * *
7692 ATGTTCCAAAGGACCAAATAT
1 ATGTCCCGAAGGACCACATAT
*
7713 ATGTCCCGAAGGACCGCATAT
1 ATGTCCCGAAGGACCACATAT
* * * * *
7734 ATATTCCAAAAGATCACATAT
1 ATGTCCCGAAGGACCACATAT
7755 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAGGACCAC
7772 GTAGAACCCT
Statistics
Matches: 99, Mismatches: 23, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
21 80 0.81
22 2 0.02
23 17 0.17
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (21 bp):
ATGTCCCGAAGGACCACATAT
Found at i:7733 original size:42 final size:42
Alignment explanation
Indices: 7627--7771 Score: 182
Period size: 42 Copynumber: 3.4 Consensus size: 42
7617 CCATATAGAA
* * * *
7627 ATGTCCCGAAGGACCACATATATGTCCCGAATGACCACATAGA
1 ATGTCCCGAAGGACCACATATATGTTCCAAAAGACCACATA-T
* * *
7670 ATTGTCCCTAAGGACCACATATATGTTCCAAAGGACCAAATAT
1 A-TGTCCCGAAGGACCACATATATGTTCCAAAAGACCACATAT
* * *
7713 ATGTCCCGAAGGACCGCATATATATTCCAAAAGATCACATAT
1 ATGTCCCGAAGGACCACATATATGTTCCAAAAGACCACATAT
7755 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAGGACCAC
7772 GTAGAACCCT
Statistics
Matches: 88, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
42 51 0.58
43 2 0.02
44 35 0.40
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (42 bp):
ATGTCCCGAAGGACCACATATATGTTCCAAAAGACCACATAT
Found at i:12374 original size:24 final size:24
Alignment explanation
Indices: 12347--12405 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
12337 CACATATATC
*
12347 ATCATTATCATCATCAATATTCTT
1 ATCATTATCATCATCAACATTCTT
12371 ATCATTATCATCATCAACATTCTT
1 ATCATTATCATCATCAACATTCTT
12395 ATCATTATCAT
1 ATCATTATCAT
12406 ATTTTACTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.44
Consensus pattern (24 bp):
ATCATTATCATCATCAACATTCTT
Found at i:12673 original size:23 final size:23
Alignment explanation
Indices: 12647--12722 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
12637 TATCCCGAAG
12647 GACCACATAGAAATGTCCTGAAT
1 GACCACATAGAAATGTCCTGAAT
* * *
12670 GACCACAT--ATATATCCCGAAT
1 GACCACATAGAAATGTCCTGAAT
* * *
12691 GACCAAATAGAATTGTCCCT-AAA
1 GACCACATAGAAATGT-CCTGAAT
12714 GACCACATA
1 GACCACATA
12723 TATGTTCCAA
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
21 17 0.43
23 21 0.52
24 2 0.05
ACGTcount: A:0.41, C:0.25, G:0.13, T:0.21
Consensus pattern (23 bp):
GACCACATAGAAATGTCCTGAAT
Found at i:12692 original size:21 final size:21
Alignment explanation
Indices: 12639--12801 Score: 110
Period size: 21 Copynumber: 7.6 Consensus size: 21
12629 TATAAAATTA
* *
12639 TCCCGAAGGACCACATAGAAATG
1 TCCCGAATGACCACAT--ATATG
* *
12662 TCCTGAATGACCACATATATA
1 TCCCGAATGACCACATATATG
* *
12683 TCCCGAATGACCAAATAGAATTG
1 TCCCGAATGACCACATA-TA-TG
* *
12706 TCCCTAAAGACCACATATATG
1 TCCCGAATGACCACATATATG
* * * *
12727 TTCCAAAAGACCAAATATATG
1 TCCCGAATGACCACATATATG
* *
12748 TCCCGAAGGACCGCATATATG
1 TCCCGAATGACCACATATATG
* * * *
12769 TTCCAAATGATCACATATGTG
1 TCCCGAATGACCACATATATG
* *
12790 TCCTGAAGGACC
1 TCCCGAATGACC
12802 GCGTAGAACC
Statistics
Matches: 107, Mismatches: 31, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
21 76 0.71
22 2 0.02
23 29 0.27
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.23
Consensus pattern (21 bp):
TCCCGAATGACCACATATATG
Found at i:12750 original size:42 final size:44
Alignment explanation
Indices: 12647--12775 Score: 136
Period size: 44 Copynumber: 3.0 Consensus size: 44
12637 TATCCCGAAG
* * * * * * * *
12647 GACCACATAGAAATGTCCTGAATGACCACATATATATCCCGAAT
1 GACCAAATAGAATTGTCCCGAAAGACCACATATATGTTCCAAAA
*
12691 GACCAAATAGAATTGTCCCTAAAGACCACATATATGTTCCAAAA
1 GACCAAATAGAATTGTCCCGAAAGACCACATATATGTTCCAAAA
* * *
12735 GACCAAATA-TA-TGTCCCGAAGGACCGCATATATGTTCCAAA
1 GACCAAATAGAATTGTCCCGAAAGACCACATATATGTTCCAAA
12776 TGATCACATA
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 27 0.38
43 1 0.01
44 44 0.61
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.22
Consensus pattern (44 bp):
GACCAAATAGAATTGTCCCGAAAGACCACATATATGTTCCAAAA
Found at i:21290 original size:18 final size:18
Alignment explanation
Indices: 21258--21292 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21248 AATTAGGAAT
**
21258 TTAAGAGTTTTTATTTTC
1 TTAAGAGTTAGTATTTTC
21276 TTAAGAGTTAGTATTTT
1 TTAAGAGTTAGTATTTT
21293 ATTTTCATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (18 bp):
TTAAGAGTTAGTATTTTC
Found at i:23537 original size:2 final size:2
Alignment explanation
Indices: 23530--23555 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23520 ATTTGTTTCA
23530 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
23556 TCTAATAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28250 original size:20 final size:20
Alignment explanation
Indices: 28225--28268 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
28215 TTCTAATAAC
28225 AACTACGAAAGTAAATGACT
1 AACTACGAAAGTAAATGACT
*
28245 AACTACGAAAGTAAATGATT
1 AACTACGAAAGTAAATGACT
28265 AACT
1 AACT
28269 GTGGTCAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.23
Consensus pattern (20 bp):
AACTACGAAAGTAAATGACT
Found at i:30532 original size:13 final size:13
Alignment explanation
Indices: 30514--30539 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30504 AATATAATAT
30514 TATTTTTTAAAAA
1 TATTTTTTAAAAA
30527 TATTTTTTAAAAA
1 TATTTTTTAAAAA
30540 AATATAACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATTTTTTAAAAA
Found at i:31101 original size:14 final size:16
Alignment explanation
Indices: 31079--31131 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 16
31069 AATAGTTGTT
31079 ATATTTTTTATAAAT-
1 ATATTTTTTATAAATA
31094 AT-TTTTTTA-AAATA
1 ATATTTTTTATAAATA
31108 ATATTTTTTATTAAAATA
1 ATATTTTTTA-T-AAATA
31126 ATATTT
1 ATATTT
31132 ATATAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
13 4 0.12
14 9 0.27
15 9 0.27
18 11 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTTTTTATAAATA
Found at i:32937 original size:42 final size:42
Alignment explanation
Indices: 32847--32926 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
32837 GTACACGCTC
* *
32847 AGCCCACCAGTTCAGATGCCATCTCCGCAAGGGTATATGTCA
1 AGCCCACCAGTTCAGATGCCATCTCCGCAAGAGTACATGTCA
* * * *
32889 AGCCCACCAGTTCATATGTCATCTCCGCATGATTACAT
1 AGCCCACCAGTTCAGATGCCATCTCCGCAAGAGTACAT
32927 TCCTAGCCCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (42 bp):
AGCCCACCAGTTCAGATGCCATCTCCGCAAGAGTACATGTCA
Found at i:32955 original size:21 final size:21
Alignment explanation
Indices: 32931--32973 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
32921 TTACATTCCT
*
32931 AGCCCACAGGGGTACATACTC
1 AGCCCACAAGGGTACATACTC
*
32952 AGCCCACAAGGTTACATACTC
1 AGCCCACAAGGGTACATACTC
32973 A
1 A
32974 ACCTGTAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.16
Consensus pattern (21 bp):
AGCCCACAAGGGTACATACTC
Found at i:34075 original size:64 final size:64
Alignment explanation
Indices: 33971--34121 Score: 164
Period size: 64 Copynumber: 2.4 Consensus size: 64
33961 AATTAAATTG
* * * *
33971 AACATCGAATGCATTTCATGCATTGATGCACATACGATGCACCG-TGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACATACCATGCACCGATGCACTCAGGATATTT-T-A
34034 A
64 A
* * * *
34035 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATTTTAA
1 AACATCGAATGCATTTGATGCATCGATGCA-CATACCATGCACCGATGCACTCAGGATATTTTAA
* *
34099 AACATCGAAAGCACTTGATGCAT
1 AACATCGAATGCATTTGATGCAT
34122 TGATAAGAGT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
64 59 0.80
65 12 0.16
66 3 0.04
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACATACCATGCACCGATGCACTCAGGATATTTTAA
Found at i:36732 original size:15 final size:15
Alignment explanation
Indices: 36712--36746 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
36702 ATCAAAGGAA
36712 GAAACGAAAAATGAG
1 GAAACGAAAAATGAG
36727 GAAACGAAAAATGAG
1 GAAACGAAAAATGAG
36742 GAAAC
1 GAAAC
36747 TCATGATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.60, C:0.09, G:0.26, T:0.06
Consensus pattern (15 bp):
GAAACGAAAAATGAG
Found at i:38735 original size:24 final size:24
Alignment explanation
Indices: 38703--38781 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
38693 TCTATGCCTA
38703 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
38727 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
38749 -TGCACCGATGCA-CGCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
38771 GTGCATCGATG
1 GTGCATCGATG
38782 TACCTGGTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
20 3 0.07
21 11 0.26
22 1 0.02
23 12 0.28
24 16 0.37
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:39198 original size:2 final size:2
Alignment explanation
Indices: 39191--39248 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
39181 AATTTTTAAA
39191 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
39233 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
39249 GATTTCAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41547 original size:65 final size:64
Alignment explanation
Indices: 41428--41629 Score: 198
Period size: 65 Copynumber: 3.1 Consensus size: 64
41418 TTTTTCAGAG
* ** *
41428 TGATGCACCGATGCACCAATCCATGCATAGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCACCAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGC
41490 ATT
62 ATT
* *
41493 TCATGCATCGATGCA-CATACGATGCACCGATGCACTCAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACCA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCA
41556 TT
63 TT
* * * * * *
41558 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAAAGCACT
1 TGATGCATCGATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
41622 TGATGCAT
1 TGATGCAT
41630 TGATAAGAGT
Statistics
Matches: 115, Mismatches: 14, Indels: 17
0.79 0.10 0.12
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 37 0.32
65 70 0.61
66 5 0.04
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.26
Consensus pattern (64 bp):
TGATGCATCGATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:44907 original size:138 final size:138
Alignment explanation
Indices: 44504--45135 Score: 736
Period size: 140 Copynumber: 4.6 Consensus size: 138
44494 GTGTTATTCC
* * **
44504 GGGGAACATTACACATAATAGTGCAATTATAACATATTCTCTGACAAAAAAATGGAAGGTACACC
1 GGGG-ACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAA-GGAAGGCGCACC
* * * * * *
44569 CCCTAAAACGCGCTTTAGCCACATTGTTGTGTCCCCTCAAATATGAT-AGTTACTAACCTAAATA
64 CCCTGAAACGCGCTTTAACCACATTGTTGCGTCCCCTCAAACATGATAAG-TACTAACATGAATA
*
44633 GTGTCCTGCCG
128 GTGTCCTGCCA
* * *
44644 GGGGACATCACACATAATAAGACAATTATAACATATTCTCTGAC-AAAAAGGGAAGGCG---CCC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGGAAGGCGCACCCC
* * * * * *
44705 CTAAAACGCGCTTTAATCACATTGTTGCGTCCCCTCAAACATGATAGGTATTGATATGAATAGTG
66 CTGAAACGCGCTTTAACCACATTGTTGCGTCCCCTCAAACATGATAAGTACTAACATGAATAGTG
44770 TCCTGCCA
131 TCCTGCCA
** * *
44778 GGATACATCACACATAATAGGGCAATTATAATATATTCTCTGACAAAAAAGGGAAGGCGCACCCC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGGAAGGCGCACCCC
* * *
44843 CTGAAACGCGCTTTAACCACATTGTTACGTCCTCTCAAACATGATAAGTACTGACATGAATAGTG
66 CTGAAACGCGCTTTAACCACATTGTTGCGTCCCCTCAAACATGATAAGTACTAACATGAATAGTG
* *
44908 TCCCGCCG
131 TCCTGCCA
* * *
44916 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAAAGGAAAGCACGCC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGAC--AAAAAAAGGAAGGCGCACC
* ** * *
44981 CCTTGAAACGCGCTTTAACCACATTGTTGCGTCTACTCAAACATGATAGGCACTAACATGAATAG
64 CCCTGAAACGCGCTTTAACCACATTGTTGCGTCCCCTCAAACATGATAAGTACTAACATGAATAG
*
45046 TG-CCTCCCTA
129 TGTCCTGCC-A
* ** * * * * **
45056 GGGGACATTACATGTAATAAGGAAATTATAACATATTCTCTGACAAAAGAAAGGAAAGCGCGCAA
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAA-AAAGGAAGGCGCACCC
45121 CCTGAAACGCGCTTT
65 CCTGAAACGCGCTTT
45136 CACGTGAATA
Statistics
Matches: 425, Mismatches: 58, Indels: 19
0.85 0.12 0.04
Matches are distributed among these distances:
134 102 0.24
135 15 0.04
137 6 0.01
138 117 0.28
139 67 0.16
140 118 0.28
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (138 bp):
GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGGAAGGCGCACCCC
CTGAAACGCGCTTTAACCACATTGTTGCGTCCCCTCAAACATGATAAGTACTAACATGAATAGTG
TCCTGCCA
Found at i:48607 original size:30 final size:30
Alignment explanation
Indices: 48571--48639 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
48561 TCAAAAAGTG
48571 TTATTTAGGACATATAAGGTTTAAAGGGTA
1 TTATTTAGGACATATAAGGTTTAAAGGGTA
* * * *
48601 TTATTTAGGGCATATTAGGTTTATAGGGTG
1 TTATTTAGGACATATAAGGTTTAAAGGGTA
*
48631 TTAGTTAGG
1 TTATTTAGG
48640 TCAAATCGCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.29, C:0.03, G:0.28, T:0.41
Consensus pattern (30 bp):
TTATTTAGGACATATAAGGTTTAAAGGGTA
Found at i:50823 original size:11 final size:11
Alignment explanation
Indices: 50807--50832 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
50797 GAGGATGAAG
50807 AGCTGGATCGA
1 AGCTGGATCGA
50818 AGCTGGATCGA
1 AGCTGGATCGA
50829 AGCT
1 AGCT
50833 ATCCCTCTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.19, G:0.35, T:0.19
Consensus pattern (11 bp):
AGCTGGATCGA
Found at i:52743 original size:30 final size:29
Alignment explanation
Indices: 52689--52770 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 29
52679 TTTATTTAAT
* *
52689 GACCAAATTATTAA-TTTGGTAAAGTTTAGT
1 GACCAAAATA-TAACTTTGG-AAAGTTTAGG
*
52719 GATCAAAATATAAACTTTGGAAAGTTTAGG
1 GACCAAAATAT-AACTTTGGAAAGTTTAGG
* *
52749 GACCAAAATGTAATTTTGGAAA
1 GACCAAAATATAACTTTGGAAA
52771 AATTACAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 11 0.25
30 28 0.64
31 5 0.11
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.33
Consensus pattern (29 bp):
GACCAAAATATAACTTTGGAAAGTTTAGG
Found at i:54488 original size:40 final size:40
Alignment explanation
Indices: 54433--54594 Score: 270
Period size: 40 Copynumber: 4.0 Consensus size: 40
54423 TGCAGGTTTA
* *
54433 TAATACACTTTGGTGTATACGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
54473 TAATACACTTCGGTGTATATGGTGGGAACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
54513 TAATACACTTTGGTGTATATGGTGGGGACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
54553 TAATACACTTCGGTGTATATGGTGGACACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
54593 TA
1 TA
54595 GCACTACGGT
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 114 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:55322 original size:22 final size:22
Alignment explanation
Indices: 55278--55333 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
55268 GGTACACTGT
* *
55278 TCACTGTTCACGGGTTTTGTTCA
1 TCACTGTTCA-TGGTATTGTTCA
55301 TCACTGTTCATGGTATTGTTCA
1 TCACTGTTCATGGTATTGTTCA
*
55323 TCACTATTCAT
1 TCACTGTTCAT
55334 AAAAAAATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 20 0.67
23 10 0.33
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (22 bp):
TCACTGTTCATGGTATTGTTCA
Found at i:56822 original size:13 final size:13
Alignment explanation
Indices: 56804--56832 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
56794 TGATATAAGC
56804 AATGGTTGCGATT
1 AATGGTTGCGATT
56817 AATGGTTGCGATT
1 AATGGTTGCGATT
56830 AAT
1 AAT
56833 ATGATGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.38
Consensus pattern (13 bp):
AATGGTTGCGATT
Found at i:57139 original size:2 final size:2
Alignment explanation
Indices: 57132--57181 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
57122 GGTGTTGTAA
57132 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
57174 AT AT AT AT
1 AT AT AT AT
57182 GCGATTGCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57704 original size:16 final size:15
Alignment explanation
Indices: 57680--57741 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 15
57670 TATATAATAT
57680 AAAAAAAGAAACAGA
1 AAAAAAAGAAACAGA
*
57695 AAAAAGAAGAAAAAGA
1 AAAAA-AAGAAACAGA
*
57711 AAAAAATGAAAC--A
1 AAAAAAAGAAACAGA
* *
57724 ATAAAAAGAAAAAGA
1 AAAAAAAGAAACAGA
57739 AAA
1 AAA
57742 CGAAGAAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
13 10 0.27
15 13 0.35
16 14 0.38
ACGTcount: A:0.81, C:0.03, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAAAAAGAAACAGA
Found at i:57749 original size:28 final size:29
Alignment explanation
Indices: 57701--57765 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
57691 CAGAAAAAAG
57701 AAGAAAAAGAAAAAAATGAAACAA-T-AAA
1 AAGAAAAAGAAAAAAATGAAA-AATTGAAA
*
57729 AAGAAAAAGAAAACGAA-GAAAAATTGAAA
1 AAGAAAAAGAAAA-AAATGAAAAATTGAAA
57758 AAGAAAAA
1 AAGAAAAA
57766 AAATGAGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 2 0.06
28 18 0.55
29 13 0.39
ACGTcount: A:0.77, C:0.03, G:0.14, T:0.06
Consensus pattern (29 bp):
AAGAAAAAGAAAAAAATGAAAAATTGAAA
Found at i:62644 original size:843 final size:842
Alignment explanation
Indices: 60030--63391 Score: 6660
Period size: 843 Copynumber: 4.0 Consensus size: 842
60020 CGGTAAAGTG
60030 AAAAACAAATTTGTTCACCTTTGACTATTAAAAGATTACAAGGCTGATATTTAATTGATTTTGAA
1 AAAAACAAATTTGTTCACCTTTGACTATTAAAAGATTACAAGGCTGATATTTAATTGATTTTGAA
60095 GATGATAAGGATATGTATCTTTGTTTTATGGTAATTATGAAGTTATATTAAGGGTATATTGGTAT
66 GATGATAAGGATATGTATCTTTGTTTTATGGTAATTATGAAGTTATATTAAGGGTATATTGGTAT
60160 TTTACAAGTTAATGATTAAATATTATATTAAAAGATGATAAGCATGATATGAATCTAAAATATCA
131 TTTACAAGTTAATGATTAAATATTATATTAAAAGATGATAAGCATGATATGAATCTAAAATATCA
60225 TGCTAAATGTTCATCTTCTCCAGCATCTTCACGTGAGAAAGCTTGAAGGTAAGAAAATATTGTAT
196 TGCTAAATGTTCATCTTCTCCAGCATCTTCACGTGAGAAAGCTTGAAGGTAAGAAAATATTGTAT
60290 TTTCAATTTTTGAGCTAATTCCTTTGGAATTGGAGTTATGTCGTGAGATAGGAAAGTGATCTAAG
261 TTTCAATTTTTGAGCTAATTCCTTTGGAATTGGAGTTATGTCGTGAGATAGGAAAGTGATCTAAG
60355 CGAAAAACGCTAGCATTTGGTACCAATATTGCTTTCTAATCTTGTTGGATTTCAAAGATCCCAAA
326 CGAAAAACGCTAGCATTTGGTACCAATATTGCTTTCTAATCTTGTTGGATTTCAAAGATCCCAAA
60420 TCTAAGGGTTTTTGTTCATATAAGGAATCATGAAATTGATGATTAATTTTGATGATTTAGAGGTT
391 TCTAAGGGTTTTTGTTCATATAAGGAATCATGAAATTGATGATTAATTTTGATGATTTAGAGGTT
60485 GTAGATTCATTTTCAAGCTTGATTGATGATTAGAACATGTTAAATCTTTCTAGAGCTTGTTCTAT
456 GTAGATTCATTTTCAAGCTTGATTGATGATTAGAACATGTTAAATCTTTCTAGAGCTTGTTCTAT
60550 AAATTTTGACCATGAATGGTTTGAGTGAGAAAAATTATGAAAAAA-T-TATATGGGTTGGAAATG
521 AAATTTTGACCATGAATGGTTTGAGTGAGAAAAATTATGAAAAAATTATATATGGGTTGGAAATG
60613 ATGAAGGAAATATTCTACAAGCCTTAGAAAAATATGGGACAATTTTGTAAA-TTTGAAAAGTTGG
586 ATGAAGGAAATATTCTACAAGCCTTAGAAAAATATGGGACAATTTTGTAAATTTTGAAAAGTTGG
60677 GAATCAATTCGTAAATTCTGGAAATTGATGGGTTGTTATGTAAGTGATATATAATTGATGTACTA
651 GAATCAATTCGTAAATTCTGGAAATTGATGGGTTGTTATGTAAGTGATATATAATTGATGTACTA
60742 TGCTGGAAATTGTTGTTTGGAAATTTAAATGAGTGTTATAAGTGAAAAATGACTATTTTGAAAAT
716 TGCTGGAAATTGTTGTTTGGAAATTTAAATGAGTGTTATAAGTGAAAAATGACTATTTTGAAAAT
60807 TTGAAAAGATTGATGATTTAAGTACAACACTTGCATAGTTAGGGTACTTAAATGTAACTTGT
781 TTGAAAAGATTGATGATTTAAGTACAACACTTGCATAGTTAGGGTACTTAAATGTAACTTGT
60869 AAAAACAAATTTGTTCACCTTTGACTATTAAAAGATTACAAGGCTGATATTTAATTGATTTTGAA
1 AAAAACAAATTTGTTCACCTTTGACTATTAAAAGATTACAAGGCTGATATTTAATTGATTTTGAA
*
60934 GATGATAAGGATATGTATCTTTGTTTTATAGTAATTATGAAGTTATATTAAGGGTATATTGGTAT
66 GATGATAAGGATATGTATCTTTGTTTTATGGTAATTATGAAGTTATATTAAGGGTATATTGGTAT
60999 TTTACAAGTTAATGATTAAATATTATATTAAAAGATGATAAGCATGATATGAATCTAAAATATCA
131 TTTACAAGTTAATGATTAAATATTATATTAAAAGATGATAAGCATGATATGAATCTAAAATATCA
61064 TGCTAAATGTTCATCTTCTCCAGCATCTTCACGTGAGAAAGCTTGAAGGTAAGAAAATATTGTAT
196 TGCTAAATGTTCATCTTCTCCAGCATCTTCACGTGAGAAAGCTTGAAGGTAAGAAAATATTGTAT
61129 TTTCAATTTTTGAGCTAATTCCTTTGGAATTGGAGTTATGTCGTGAGATAGGAAAGTGATCTAAG
261 TTTCAATTTTTGAGCTAATTCCTTTGGAATTGGAGTTATGTCGTGAGATAGGAAAGTGATCTAAG
61194 CG-AAAACGCTAGCATTTGGTACCAATATTGCTTTCTAATCTTGTTGGATTTCAAAGATCCCAAA
326 CGAAAAACGCTAGCATTTGGTACCAATATTGCTTTCTAATCTTGTTGGATTTCAAAGATCCCAAA
61258 TCTAAGGGTTTTTGTTCATATAAGGAATCATGAAATTGATGATTAATTTTGATGATTTAGAGGTT
391 TCTAAGGGTTTTTGTTCATATAAGGAATCATGAAATTGATGATTAATTTTGATGATTTAGAGGTT
61323 GTAGATTCATTTTCAAGCTTGATTGATGATTAGAACATGTTAAATCTTTCTAGAGCTTGTTCTAT
456 GTAGATTCATTTTCAAGCTTGATTGATGATTAGAACATGTTAAATCTTTCTAGAGCTTGTTCTAT
61388 AAATTTTGACCATGAATGGTTTGAGTGAGAAAAATTATGAAAAAATTATATATGGGTTGGAAATG
521 AAATTTTGACCATGAATGGTTTGAGTGAGAAAAATTATGAAAAAATTATATATGGGTTGGAAATG
61453 ATGAAGGAAATATTCTACAAGCCTTAGAAAAATATGGGACAATTTTGTAAATTTTGAAAAGTTGG
586 ATGAAGGAAATATTCTACAAGCCTTAGAAAAATATGGGACAATTTTGTAAATTTTGAAAAGTTGG
61518 GAATCAATTCGTAAATTCTGGAAATTGATGGGTTGTTATGTAAGTGATATATAATTGATGTACTA
651 GAATCAATTCGTAAATTCTGGAAATTGATGGGTTGTTATGTAAGTGATATATAATTGATGTACTA
61583 TGCTGGAAATTGTTGTTTGGAAATTTAAATGAGTGTTATAAGTGAAAAATGACTATTTTGAAAAT
716 TGCTGGAAATTGTTGTTTGGAAATTTAAATGAGTGTTATAAGTGAAAAATGACTATTTTGAAAAT
61648 TTGAAAAGATTGATGATTTAAGTACAACACTTGCATAGTTAGGGTACTTAAATGTAACTTGT
781 TTGAAAAGATTGATGATTTAAGTACAACACTTGCATAGTTAGGGTACTTAAATGTAACTTGT
61710 AAAAACAAATTTGTTCACCTTTGACTATTAAAAGATTACAAGGCTGATATTTAATTGATTTTGAA
1 AAAAACAAATTTGTTCACCTTTGACTATTAAAAGATTACAAGGCTGATATTTAATTGATTTTGAA
61775 GATGATAAGGATATGTATCTTTGTTTTATGGTAATTATGAAGTTATATTAAGGGTATATTGGTAT
66 GATGATAAGGATATGTATCTTTGTTTTATGGTAATTATGAAGTTATATTAAGGGTATATTGGTAT
61840 TTTACAAGTTAATGATTAAATATTATATTAAAAGATGATAAGCATGATATGAATCTAAAATATCA
131 TTTACAAGTTAATGATTAAATATTATATTAAAAGATGATAAGCATGATATGAATCTAAAATATCA
61905 TGCTAAATGTTCATCTTCTCCAGCATCTTCACGTGAGAAAGCTTGAAGGTAAGAAAATATTGTAT
196 TGCTAAATGTTCATCTTCTCCAGCATCTTCACGTGAGAAAGCTTGAAGGTAAGAAAATATTGTAT
61970 TTTCAATTTTTGAGCTAATTCCTTTGGAATTGGAGTTATGTCGTGAGATAGGAAAGTGATCTAAG
261 TTTCAATTTTTGAGCTAATTCCTTTGGAATTGGAGTTATGTCGTGAGATAGGAAAGTGATCTAAG
62035 CGAAAAACGCTAGCATTTGGTACCAATATTGCTTTCTAATCTTGTTGGATTTCAAAGATCCCAAA
326 CGAAAAACGCTAGCATTTGGTACCAATATTGCTTTCTAATCTTGTTGGATTTCAAAGATCCCAAA
62100 TCTAAGGGTTTTTGTTCATATAAGGAATCATGAAATTGATGATTAATTTTGATGATTTAGAGGTT
391 TCTAAGGGTTTTTGTTCATATAAGGAATCATGAAATTGATGATTAATTTTGATGATTTAGAGGTT
62165 GTAGATTCATTTTCAAGCTTGATTGATGATTAGAACATGTTAAATCTTTCTAGAGCTTGTTCTAT
456 GTAGATTCATTTTCAAGCTTGATTGATGATTAGAACATGTTAAATCTTTCTAGAGCTTGTTCTAT
62230 AAATTTTGACCATGAATGGTTTGAGTGAGAAAAATTATGAAAAAAATTATATATGGGTTGGAAAT
521 AAATTTTGACCATGAATGGTTTGAGTGAGAAAAATTATG-AAAAAATTATATATGGGTTGGAAAT
*
62295 GATGAAGGAAATATTCTACAAGCCTTAGAAAAACATGGGACAATTTTGTAAATTTTGAAAAGTTG
585 GATGAAGGAAATATTCTACAAGCCTTAGAAAAATATGGGACAATTTTGTAAATTTTGAAAAGTTG
*
62360 GGAATCAATTCATAAATTCTGGAAATTGATGGGTTGTTATGTAAGTGATATATAATTGATGTACT
650 GGAATCAATTCGTAAATTCTGGAAATTGATGGGTTGTTATGTAAGTGATATATAATTGATGTACT
62425 ATGCTGGAAATTGTTGTTTGGAAATTTAAATGAGTGTTATAAGTGAAAAATGACTATTTTGAAAA
715 ATGCTGGAAATTGTTGTTTGGAAATTTAAATGAGTGTTATAAGTGAAAAATGACTATTTTGAAAA
62490 TTTGAAAAGATTGATGATTTAAGTACAACACTTGCATAGTTAGGGTACTTAAATGTAACTTGT
780 TTTGAAAAGATTGATGATTTAAGTACAACACTTGCATAGTTAGGGTACTTAAATGTAACTTGT
62553 AAAAACAAATTTGTTCACCTTTGACTATTAAAAGATTACAAGGCTGATATTTAATTGATTTTGAA
1 AAAAACAAATTTGTTCACCTTTGACTATTAAAAGATTACAAGGCTGATATTTAATTGATTTTGAA
62618 GATGATAAGGATATGTATCTTTGTTTTATGGTAATTATGAAGTTATATTAAGGGTATATTGGTAT
66 GATGATAAGGATATGTATCTTTGTTTTATGGTAATTATGAAGTTATATTAAGGGTATATTGGTAT
62683 TTTACAAGTTAATGATTAAATATTATATTAAAAGATGATAAGCATGATATGAATCTAAAATATCA
131 TTTACAAGTTAATGATTAAATATTATATTAAAAGATGATAAGCATGATATGAATCTAAAATATCA
62748 TGCTAAATGTTCATCTTCTCCAGCATCTTCACGTGAGAAAGCTTGAAGGTAAGAAAATATTGTAT
196 TGCTAAATGTTCATCTTCTCCAGCATCTTCACGTGAGAAAGCTTGAAGGTAAGAAAATATTGTAT
62813 TTTCAATTTTTGAGCTAATTCCTTTGGAATTGGAGTTATGTCGTGAGATAGGAAAGTGATCTAAG
261 TTTCAATTTTTGAGCTAATTCCTTTGGAATTGGAGTTATGTCGTGAGATAGGAAAGTGATCTAAG
62878 CGAAAAACGCTAGCATTTGGTACCAATATTGCTTTCTAATCTTGTTGGATTTCAAAGATCCCAAA
326 CGAAAAACGCTAGCATTTGGTACCAATATTGCTTTCTAATCTTGTTGGATTTCAAAGATCCCAAA
62943 TCTAAGGGTTTTTGTTCATATAAGGAATCATGAAATTGATGATTAATTTTGATGATTTAGAGGTT
391 TCTAAGGGTTTTTGTTCATATAAGGAATCATGAAATTGATGATTAATTTTGATGATTTAGAGGTT
63008 GTAGATTCATTTTCAAGCTTGATTGATGATTAGAACATGTTAAATCTTTCTAGAGCTTGTTCTAT
456 GTAGATTCATTTTCAAGCTTGATTGATGATTAGAACATGTTAAATCTTTCTAGAGCTTGTTCTAT
63073 AAATTTTGACCATGAATGGTTTGAGTGAGAAAAATTATGAAAAAATTATATATGGGTTGGAAATG
521 AAATTTTGACCATGAATGGTTTGAGTGAGAAAAATTATGAAAAAATTATATATGGGTTGGAAATG
63138 ATGAAGGAAATATTCTACAAGCCTTAGAAAAATATGGGACAATTTTGTAAATTTTGAAAAGTTGG
586 ATGAAGGAAATATTCTACAAGCCTTAGAAAAATATGGGACAATTTTGTAAATTTTGAAAAGTTGG
63203 GAATCAATTCGTAAATTCTGGAAATTGATGGGTTGTTATGTAAGTGATATATAATTGATGTACTA
651 GAATCAATTCGTAAATTCTGGAAATTGATGGGTTGTTATGTAAGTGATATATAATTGATGTACTA
63268 TGCTGGAAATTGTTGTTTGGAAATTTAAATGAGTGTTATAAGTGAAAAATGACTATTTTGAAAAT
716 TGCTGGAAATTGTTGTTTGGAAATTTAAATGAGTGTTATAAGTGAAAAATGACTATTTTGAAAAT
63333 TTGAAAAGATTGATGATTTAAGTACAACACTTGCATAGTTAGGGTACTTAAATGTAACT
781 TTGAAAAGATTGATGATTTAAGTACAACACTTGCATAGTTAGGGTACTTAAATGTAACT
63392 ATGCCATTGT
Statistics
Matches: 2512, Mismatches: 6, Indels: 7
0.99 0.00 0.00
Matches are distributed among these distances:
838 237 0.09
839 327 0.13
840 68 0.03
841 531 0.21
842 509 0.20
843 840 0.33
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (842 bp):
AAAAACAAATTTGTTCACCTTTGACTATTAAAAGATTACAAGGCTGATATTTAATTGATTTTGAA
GATGATAAGGATATGTATCTTTGTTTTATGGTAATTATGAAGTTATATTAAGGGTATATTGGTAT
TTTACAAGTTAATGATTAAATATTATATTAAAAGATGATAAGCATGATATGAATCTAAAATATCA
TGCTAAATGTTCATCTTCTCCAGCATCTTCACGTGAGAAAGCTTGAAGGTAAGAAAATATTGTAT
TTTCAATTTTTGAGCTAATTCCTTTGGAATTGGAGTTATGTCGTGAGATAGGAAAGTGATCTAAG
CGAAAAACGCTAGCATTTGGTACCAATATTGCTTTCTAATCTTGTTGGATTTCAAAGATCCCAAA
TCTAAGGGTTTTTGTTCATATAAGGAATCATGAAATTGATGATTAATTTTGATGATTTAGAGGTT
GTAGATTCATTTTCAAGCTTGATTGATGATTAGAACATGTTAAATCTTTCTAGAGCTTGTTCTAT
AAATTTTGACCATGAATGGTTTGAGTGAGAAAAATTATGAAAAAATTATATATGGGTTGGAAATG
ATGAAGGAAATATTCTACAAGCCTTAGAAAAATATGGGACAATTTTGTAAATTTTGAAAAGTTGG
GAATCAATTCGTAAATTCTGGAAATTGATGGGTTGTTATGTAAGTGATATATAATTGATGTACTA
TGCTGGAAATTGTTGTTTGGAAATTTAAATGAGTGTTATAAGTGAAAAATGACTATTTTGAAAAT
TTGAAAAGATTGATGATTTAAGTACAACACTTGCATAGTTAGGGTACTTAAATGTAACTTGT
Found at i:64116 original size:40 final size:40
Alignment explanation
Indices: 64061--64222 Score: 270
Period size: 40 Copynumber: 4.0 Consensus size: 40
64051 TGCAAGTTTA
64061 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
* *
64101 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATTTG
1 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
*
64141 TAATACACTTTGGTGTATATGGTGGGCACAACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
* * *
64181 TAATACACTTCGGTGTATATGGTGGACACGACCTTATATG
1 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
64221 TA
1 TA
64223 GCACTACGGT
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 113 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
Found at i:64802 original size:18 final size:18
Alignment explanation
Indices: 64779--64817 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
64769 TTATGATTTT
64779 TGTAGCGCGTCGATGGAC
1 TGTAGCGCGTCGATGGAC
* *
64797 TGTAGCGCGTTGATGTAC
1 TGTAGCGCGTCGATGGAC
64815 TGT
1 TGT
64818 TGCAGTGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.36, T:0.31
Consensus pattern (18 bp):
TGTAGCGCGTCGATGGAC
Found at i:65182 original size:39 final size:39
Alignment explanation
Indices: 65139--65230 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 39
65129 AGTGTTAAAC
65139 TAACATTCTAAATTCCTAATTTCTTAAAA-ATTTTCACCA-
1 TAACATTCTAAATTCCTAATTTCTTAAAATA-TTTCA-CAT
* * *
65178 TAACATTCTAAATTCTTAATTTGTTAAATTATTTCACAT
1 TAACATTCTAAATTCCTAATTTCTTAAAATATTTCACAT
*
65217 TAACATTATAAATT
1 TAACATTCTAAATT
65231 ATTTTTTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
38 2 0.04
39 44 0.94
40 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.01, T:0.45
Consensus pattern (39 bp):
TAACATTCTAAATTCCTAATTTCTTAAAATATTTCACAT
Found at i:65552 original size:30 final size:30
Alignment explanation
Indices: 65495--65554 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
65485 ACACGGGCTG
***
65495 AAATTTTGATACCCGAAAATTTTGGGTACC
1 AAATTTTGATACCCGAAAATCACGGGTACC
65525 AAATTTTGGATACCCGAAAA-CACGGGTACC
1 AAATTTT-GATACCCGAAAATCACGGGTACC
65555 TGGTTTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (30 bp):
AAATTTTGATACCCGAAAATCACGGGTACC
Found at i:70234 original size:16 final size:15
Alignment explanation
Indices: 70196--70240 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
70186 GCCCTAAATT
70196 GAAAAAAATGAAAAAA
1 GAAAAAAA-GAAAAAA
70212 GAGAAAAAAGAACAAAA
1 GA-AAAAAAGAA-AAAA
*
70229 GAAAAAGAGAAA
1 GAAAAAAAGAAA
70241 GAACAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 1 0.04
16 13 0.50
17 12 0.46
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (15 bp):
GAAAAAAAGAAAAAA
Found at i:71115 original size:146 final size:146
Alignment explanation
Indices: 70851--71140 Score: 535
Period size: 146 Copynumber: 2.0 Consensus size: 146
70841 TCAAGATTCC
*
70851 AGACATATTTTAGCTAGAGTCAATTTCAACTGCACAGTAAAGGATATTGGACTCAAGACAACACA
1 AGACAGATTTTAGCTAGAGTCAATTTCAACTGCACAGTAAAGGATATTGGACTCAAGACAACACA
* * *
70916 AGTTCAACTTCAAAATGAAGGGACGGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAAT
66 AGTTCAACTTCAAAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAAT
70981 TTCAACTTCACATCAA
131 TTCAACTTCACATCAA
70997 AGACAGATTTTAGCTAGAGTCAATTTCAACTGCACAGTAAAGGATATTGGACTCAAGACAACACA
1 AGACAGATTTTAGCTAGAGTCAATTTCAACTGCACAGTAAAGGATATTGGACTCAAGACAACACA
*
71062 AGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAAT
66 AGTTCAACTTCAAAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAAT
71127 TTCAACTTCACATC
131 TTCAACTTCACATC
71141 GAAGGATGTT
Statistics
Matches: 139, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
146 139 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (146 bp):
AGACAGATTTTAGCTAGAGTCAATTTCAACTGCACAGTAAAGGATATTGGACTCAAGACAACACA
AGTTCAACTTCAAAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAAT
TTCAACTTCACATCAA
Found at i:71346 original size:95 final size:99
Alignment explanation
Indices: 71031--71719 Score: 549
Period size: 106 Copynumber: 6.8 Consensus size: 99
71021 TTCAACTGCA
* *
71031 CAGTAAAGGATATTGGACTCA-AGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTG
1 CAGTGAAGGATATTGGACT-AGAGACGACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTG
71095 TCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTT
65 TCAACAAACAATTTCCCAATTTCAGAGCC----TCAAC-T
* * * * *
71135 CACATCGAAGGATGTTGGACTCG-G--G--ACAA-CT-AA--GCACAACGAAGGGACGACTGGTT
1 CA-GT-GAAGGATATTGGACTAGAGACGACACAAGTTCAACTTCACAACGAAGGGACGACTGGTT
71191 GTCAACAAACAATTTCCCAATTTCAGAGTCACTTTCAACTT
64 GTCAACAAACAATTTCCCAATTTCAGAG-C-C--TCAAC-T
* * *
71232 CACAGCGAAGGATATTGGACTTAG-GACAACACAAGTTCAACTTCACAACGAAGGGATGACTGGT
1 --CAGTGAAGGATATTGGAC-TAGAGACGACACAAGTTCAACTTCACAACGAAGGGACGACTGGT
*
71296 TGTCAACAAACAATCTCCCAATTTCAGAG-C-CAA-T
63 TGTCAACAAACAATTTCCCAATTTCAGAGCCTCAACT
*
71330 -AGTGAAGGATATTGGACTAGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGT
1 CAGTGAAGGATATTGGACTAGAGACGACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGT
* * * *
71394 CAACAAACAATTTCCTAATTTTAGGGTCAATTTCAACTT
66 CAACAAACAATTTCCCAATTTCAGAG-C---CTCAAC-T
* * * * * *
71433 CACATCGAAGGATATTGAACTCGAGAC--CACAAGTTTAACTTCACAACAAAGGGACGGCTGGTT
1 CA-GT-GAAGGATATTGGACTAGAGACGACACAAGTTCAACTTCACAACGAAGGGACGACTGGTT
* *
71496 GTCAACAAATAATTTCCCAATTTCATAGCCAATTTCAACTT
64 GTCAACAAACAATTTCCCAATTTCAGAGCC----TCAAC-T
* *
71537 CACAGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACG---GGTT
1 --CAGTGAAGGATATTGGACTAGAGACGACACAAGTTCAACTTCACAACGAAGGGACGACTGGTT
* * *
71599 GTCAACAAACAATTTCCCAATTTCAGGGTCAATTTTAACTT
64 GTCAACAAACAATTTCCCAATTTCAGAG-C---CTCAAC-T
* * * * **
71640 CACATCGAAGGATATTAGACTCA-AGAC-AGCACAAGCTCAACTTCACAACGAAGGGGCGGTTGG
1 CA-GT-GAAGGATATTGGACT-AGAGACGA-CACAAGTTCAACTTCACAACGAAGGGACGACTGG
*
71703 CTGTCAACAAACAATTT
62 TTGTCAACAAACAATTT
71720 TTGAGTTCCA
Statistics
Matches: 485, Mismatches: 53, Indels: 92
0.77 0.08 0.15
Matches are distributed among these distances:
94 3 0.01
95 78 0.16
97 72 0.15
98 5 0.01
99 5 0.01
100 4 0.01
101 9 0.02
102 5 0.01
103 84 0.17
104 90 0.19
105 3 0.01
106 127 0.26
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (99 bp):
CAGTGAAGGATATTGGACTAGAGACGACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGT
CAACAAACAATTTCCCAATTTCAGAGCCTCAACT
Found at i:71588 original size:305 final size:295
Alignment explanation
Indices: 71036--71748 Score: 881
Period size: 298 Copynumber: 2.3 Consensus size: 295
71026 CTGCACAGTA
71036 AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACA
1 AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACA
* * *
71101 AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATGTTGGACTCGGGACAACT
66 AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGAACTCGGCACAACT
* * *
71166 AAGCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGTCACTTTCAACT
131 AAGCACAACAAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACT
* *
71231 TCACAGCGAAGGATATTGGACTTAGGACAACACAAGTTCAACTTCACAACGAAGGGATGACTGGT
196 TCACAGCGAAGGATATTGGACTGAGGACAACACAAGTTCAACTTCACAACGAA-GG--GACGGGT
71296 TGTCAACAAACAATCTCCCAATTTCAGAGCCAATAGTG
258 TGTCAACAAACAATCTCCCAATTTCAGAGCCAATAGTG
* *
71334 AAGGATATTGGACT-AGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC
1 AAGGATATTGGACTCA-AGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAAC
* * * *
71398 AAACAATTTCCTAATTTTAGGGTCAATTTCAACTTCACATCGAAGGATATTGAACTCGAGACCAC
65 AAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGAACTCG-G--CAC
* * * * *
71463 AAGTTTAACTTCACAACAAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTCATAGCCAA
127 AA--CTAA--GCACAACAAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAA
*
71528 TTTCAACTTCACAGCGAAGGATATTGGACTCGA-GACGACACAAGTTCAACTTCACAACGAAGGG
188 TTTCAACTTCACAGCGAAGGATATTGGACT-GAGGACAACACAAGTTCAACTTCACAACGAAGGG
* * * *
71592 ACGGGTTGTCAACAAACAATTTCCCAATTTCAGGGTCAATTTTAACTTCACATCG
252 ACGGGTTGTCAACAAACAATCTCCCAATTTCAGAG-C-----CAA--T-A-GT-G
* * * * ** *
71647 AAGGATATTAGACTCAAGACAGCACAAGCTCAACTTCACAACGAAGGGGCGGTTGGCTGTCAACA
1 AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACA
*** * *
71712 AACAATTTTTGAGTTCCAGAGCCAATTTCAACTTCAC
66 AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCAC
71749 GGTGGAGGAT
Statistics
Matches: 355, Mismatches: 39, Indels: 27
0.84 0.09 0.06
Matches are distributed among these distances:
297 1 0.00
298 112 0.32
299 1 0.00
301 4 0.01
302 33 0.09
303 4 0.01
304 2 0.01
305 105 0.30
306 1 0.00
308 2 0.01
310 1 0.00
311 1 0.00
312 1 0.00
313 86 0.24
314 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (295 bp):
AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACA
AACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGAACTCGGCACAACT
AAGCACAACAAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACT
TCACAGCGAAGGATATTGGACTGAGGACAACACAAGTTCAACTTCACAACGAAGGGACGGGTTGT
CAACAAACAATCTCCCAATTTCAGAGCCAATAGTG
Found at i:71639 original size:103 final size:104
Alignment explanation
Indices: 71333--71719 Score: 546
Period size: 104 Copynumber: 3.7 Consensus size: 104
71323 AGCCAATAGT
*
71333 GAAGGATATTGGACTAGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC
1 GAAGGATATTGGACTCGAGAC-ACACAAGTTCAACTTCACAACGAAGGGACGG-TGGTTGTCAAC
* *
71398 AAACAATTTCCTAATTTTAGGGTCAATTTCAACTTCACATC
64 AAACAATTTCCCAATTTCAGGGTCAATTTCAACTTCACATC
* * *
71439 GAAGGATATTGAACTCGAGAC-CACAAGTTTAACTTCACAACAAAGGGACGGCTGGTTGTCAACA
1 GAAGGATATTGGACTCGAGACACACAAGTTCAACTTCACAACGAAGGGACGG-TGGTTGTCAACA
* ** * *
71503 AATAATTTCCCAATTTCATAGCCAATTTCAACTTCACAGC
65 AACAATTTCCCAATTTCAGGGTCAATTTCAACTTCACATC
71543 GAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGAC-G-GGTTGTCAACA
1 GAAGGATATTGGACTCGAGAC-ACACAAGTTCAACTTCACAACGAAGGGACGGTGGTTGTCAACA
*
71606 AACAATTTCCCAATTTCAGGGTCAATTTTAACTTCACATC
65 AACAATTTCCCAATTTCAGGGTCAATTTCAACTTCACATC
* * * * *
71646 GAAGGATATTAGACTCAAGACAGCACAAGCTCAACTTCACAACGAAGGGGCGGTTGGCTGTCAAC
1 GAAGGATATTGGACTCGAGACA-CACAAGTTCAACTTCACAACGAAGGGACGG-TGGTTGTCAAC
71711 AAACAATTT
64 AAACAATTT
71720 TTGAGTTCCA
Statistics
Matches: 250, Mismatches: 25, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
102 1 0.00
103 90 0.36
104 95 0.38
105 1 0.00
106 63 0.25
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (104 bp):
GAAGGATATTGGACTCGAGACACACAAGTTCAACTTCACAACGAAGGGACGGTGGTTGTCAACAA
ACAATTTCCCAATTTCAGGGTCAATTTCAACTTCACATC
Found at i:72297 original size:35 final size:35
Alignment explanation
Indices: 72251--72322 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
72241 ACCAAAAAGA
72251 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
*
72286 AGAGTTGGATTAGGACTCGAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
72321 AG
1 AG
72323 GGTTTTTAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:73167 original size:41 final size:39
Alignment explanation
Indices: 73122--73198 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 39
73112 AGGGCCCATT
* *
73122 TTTTTGTTTTATTTCTAACTAAAGTCTCTCCCACTTTCCTC
1 TTTTTGTCTTATTTCTAACTAAAG-C-CCCCCACTTTCCTC
*
73163 TTTTTGTCTTATTTCTGACTAAAGCCCCCCACTTTC
1 TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTC
73199 GGTGAAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 10 0.30
40 1 0.03
41 22 0.67
ACGTcount: A:0.17, C:0.29, G:0.06, T:0.48
Consensus pattern (39 bp):
TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTCCTC
Found at i:73377 original size:9 final size:9
Alignment explanation
Indices: 73365--73407 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
73355 CCTTATCTTA
73365 TTTATTTAT
1 TTTATTTAT
73374 TTTATTTAT
1 TTTATTTAT
*
73383 TTTATTTTT
1 TTTATTTAT
*
73392 TTCTTTTTAT
1 TT-TATTTAT
73402 TTTATT
1 TTTATT
73408 CTCTTTATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 22 0.76
10 7 0.24
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTAT
Found at i:73388 original size:14 final size:14
Alignment explanation
Indices: 73357--73431 Score: 66
Period size: 14 Copynumber: 5.4 Consensus size: 14
73347 ATTTTTTTCC
*
73357 TTATCTTATTTA-T
1 TTATTTTATTTATT
73370 TTATTTTATTTATT
1 TTATTTTATTTATT
*
73384 TTATTTT-TTTCTTT
1 TTATTTTATTT-ATT
*
73398 TTATTTTATTCT-CT
1 TTATTTTATT-TATT
* *
73412 TTATCTTATTTGTT
1 TTATTTTATTTATT
73426 TTATTT
1 TTATTT
73432 GCCTTGTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
13 15 0.29
14 33 0.65
15 2 0.04
16 1 0.02
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.76
Consensus pattern (14 bp):
TTATTTTATTTATT
Found at i:74853 original size:90 final size:90
Alignment explanation
Indices: 74682--74853 Score: 229
Period size: 90 Copynumber: 1.9 Consensus size: 90
74672 CGCAAACATA
* * * * *
74682 AACACATAAGTTGATGTAGGAATCATGATGCAGCTGAGGGGCTACATCTCGGAGCTCACACACCC
1 AACACACAAGTTAAAGTAGGAATCATGATGCAACTGAGGGGCTACATCTCGAAGCTCACACACCC
*
74747 CTCTAGCCTACTTGTACTACTATAC
66 CTCTAGCCTACCTGTACTACTATAC
* * * *
74772 AACACACAAGTTAAAGTAGGCATCATGGTGTAACTGAGGGGCTACATCTCGAAGCTCATACACCC
1 AACACACAAGTTAAAGTAGGAATCATGATGCAACTGAGGGGCTACATCTCGAAGCTCACACACCC
*
74837 TTCTATG-CTACCTGTAC
66 CTCTA-GCCTACCTGTAC
74854 CCATGTCTAA
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
90 69 0.99
91 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (90 bp):
AACACACAAGTTAAAGTAGGAATCATGATGCAACTGAGGGGCTACATCTCGAAGCTCACACACCC
CTCTAGCCTACCTGTACTACTATAC
Found at i:84049 original size:13 final size:13
Alignment explanation
Indices: 84031--84058 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
84021 TGATATAAGC
84031 AATGGTTGCGATT
1 AATGGTTGCGATT
84044 AATGGTTGCGATT
1 AATGGTTGCGATT
84057 AA
1 AA
84059 GATGATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (13 bp):
AATGGTTGCGATT
Found at i:84375 original size:2 final size:2
Alignment explanation
Indices: 84368--84425 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
84358 GGTGTTGTAA
84368 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
84410 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
84426 GCGATTGCAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84953 original size:15 final size:14
Alignment explanation
Indices: 84935--85036 Score: 69
Period size: 15 Copynumber: 6.5 Consensus size: 14
84925 TATATAATAT
84935 AAAAAAAGAAACAAA
1 AAAAAAAGAAA-AAA
*
84950 AAAAGAAAAAAAGAAA
1 AAAA-AAAGAAA-AAA
84966 ATAGAAAAAGAAAAAA
1 A-A-AAAAAGAAAAAA
*
84982 AAATGAAAGAATAAAA
1 AAA-AAAAGAA-AAAA
*
84998 AGAAAAAGAAAACGAA
1 AAAAAAAGAAAA--AA
*
85014 GAAAAATAGAAAAAGA
1 -AAAAAAAGAAAAA-A
85030 AAAAAAA
1 AAAAAAA
85037 TGAGAGATGA
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
14 3 0.04
15 24 0.35
16 23 0.33
17 17 0.25
18 2 0.03
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.04
Consensus pattern (14 bp):
AAAAAAAGAAAAAA
Found at i:84961 original size:21 final size:21
Alignment explanation
Indices: 84935--85033 Score: 73
Period size: 21 Copynumber: 4.6 Consensus size: 21
84925 TATATAATAT
84935 AAAAAAAGAAACAA-AAAAAG-
1 AAAAAAAGAAA-AAGAAAAAGA
84955 AAAAAAAGAAAATAGAAAAAGA
1 AAAAAAAGAAAA-AGAAAAAGA
*
84977 AAAAAAA-ATGAAAGAATAAA-A
1 AAAAAAAGA-AAAAGAA-AAAGA
* *
84998 AGAAAAAGAAAACGAAGAAA-A
1 AAAAAAAGAAAAAGAA-AAAGA
85019 ATAGAAAAAGAAAAA
1 A-A-AAAAAGAAAAA
85034 AAATGAGAGA
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
19 1 0.02
20 12 0.19
21 28 0.44
22 13 0.20
23 10 0.16
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.04
Consensus pattern (21 bp):
AAAAAAAGAAAAAGAAAAAGA
Found at i:84966 original size:6 final size:6
Alignment explanation
Indices: 84937--85033 Score: 83
Period size: 6 Copynumber: 15.8 Consensus size: 6
84927 TATAATATAA
*
84937 AAAAAG AAACAA- AAAAAG AAAAAAAG AAAATAG AAAAAG AAAAA- AAAATG
1 AAAAAG AAA-AAG AAAAAG --AAAAAG AAAA-AG AAAAAG AAAAAG AAAAAG
* * * *
84987 AAAGAAT AAAAAG AAAAAG AAAACG AAGAA- AAATAG AAAAAG AAAAA
1 AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
85034 AAATGAGAGA
Statistics
Matches: 73, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
5 9 0.12
6 46 0.63
7 12 0.16
8 6 0.08
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:85008 original size:36 final size:36
Alignment explanation
Indices: 84951--85019 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
84941 AGAAACAAAA
84951 AAAGAAAAAAAGAAAATAGAAAAAGAAAAAAAAATG
1 AAAGAAAAAAAGAAAATAGAAAAAGAAAAAAAAATG
* *
84987 AAAGAATAAAAAGAAAA-AGAAAACGAAGAAAAA
1 AAAGAA-AAAAAGAAAATAGAAAAAGAAAAAAAA
85020 TAGAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 20 0.67
37 10 0.33
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.04
Consensus pattern (36 bp):
AAAGAAAAAAAGAAAATAGAAAAAGAAAAAAAAATG
Found at i:85016 original size:52 final size:54
Alignment explanation
Indices: 84949--85053 Score: 155
Period size: 52 Copynumber: 2.0 Consensus size: 54
84939 AAAGAAACAA
84949 AAAAAGAAAAAAAG-AAAATAGAAAAAGAAAAAAAAATGA-A-A-GAATAAAAAG
1 AAAAAGAAAAAAAGAAAAATAGAAAAAG-AAAAAAAATGAGAGATGAATAAAAAG
*
85000 AAAAAGAAAACGAAGAAAAATAGAAAAAGAAAAAAAATGAGAGATGAATAAAAA
1 AAAAAGAAAA-AAAGAAAAATAGAAAAAGAAAAAAAATGAGAGATGAATAAAAA
85054 AGGAGAAAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
51 10 0.21
52 14 0.29
53 14 0.29
54 1 0.02
55 9 0.19
ACGTcount: A:0.77, C:0.01, G:0.15, T:0.07
Consensus pattern (54 bp):
AAAAAGAAAAAAAGAAAAATAGAAAAAGAAAAAAAATGAGAGATGAATAAAAAG
Found at i:88519 original size:40 final size:40
Alignment explanation
Indices: 88464--88625 Score: 288
Period size: 40 Copynumber: 4.0 Consensus size: 40
88454 TGCAAGTTTA
88464 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
88504 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATTTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
88544 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
88584 TAATACACTTCGGTGTATATGGTGGACACGACCTTATATG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
88624 TA
1 TA
88626 GCACTACGGT
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 116 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:88823 original size:45 final size:46
Alignment explanation
Indices: 88733--88841 Score: 143
Period size: 45 Copynumber: 2.4 Consensus size: 46
88723 AGCATGCAAG
* *
88733 TAAGCTTACGAGCTTAT-GGAATATTGGCAAGTATATGGGTAAAAA
1 TAAGCTTACGAGCTTATGGGAATAATGACAAGTATATGGGTAAAAA
* * *
88778 TAAGCTTACGAGCTTATGGGACA-AATGATAAGTATTTTGGT-AAAA
1 TAAGCTTACGAGCTTATGGGA-ATAATGACAAGTATATGGGTAAAAA
88823 TAAGCTTACGAGCTTATGG
1 TAAGCTTACGAGCTTATGG
88842 TTAATAAATG
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
45 40 0.70
46 16 0.28
47 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (46 bp):
TAAGCTTACGAGCTTATGGGAATAATGACAAGTATATGGGTAAAAA
Found at i:89586 original size:39 final size:39
Alignment explanation
Indices: 89543--89634 Score: 125
Period size: 39 Copynumber: 2.4 Consensus size: 39
89533 GGTGTTAAAC
89543 TAACATTCTAAATTCCTAATTTCTTAAAATT-TTTCACCA-
1 TAACATTCTAAATTCCTAATTTCTT-AAATTATTTCA-CAT
* *
89582 TAACATTCTAAATTCTTAATTTGTTAAATTATTTCACAT
1 TAACATTCTAAATTCCTAATTTCTTAAATTATTTCACAT
*
89621 TAACATTATAAATT
1 TAACATTCTAAATT
89635 ATTTTTTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
38 7 0.15
39 41 0.85
ACGTcount: A:0.38, C:0.15, G:0.01, T:0.46
Consensus pattern (39 bp):
TAACATTCTAAATTCCTAATTTCTTAAATTATTTCACAT
Found at i:89955 original size:30 final size:30
Alignment explanation
Indices: 89898--89957 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
89888 ACACGGGCTG
***
89898 AAATTTTGATACCCGAAAATTTTGGGTACC
1 AAATTTTGATACCCGAAAATCACGGGTACC
89928 AAATTTTGGATACCCGAAAA-CACGGGTACC
1 AAATTTT-GATACCCGAAAATCACGGGTACC
89958 TGGTTTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (30 bp):
AAATTTTGATACCCGAAAATCACGGGTACC
Found at i:95385 original size:3 final size:3
Alignment explanation
Indices: 95377--95419 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
95367 TCGGGTCTTG
*
95377 TAA TAA TAA TAA TAA TAA TAA TATA TTA TAAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA TA
95420 TATTATATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 32 0.89
4 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:95411 original size:23 final size:25
Alignment explanation
Indices: 95381--95431 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
95371 GTCTTGTAAT
*
95381 AATAATAATAATAATAATATATTATA
1 AATAATAATAAT-ATATTATATTATA
95407 AATAATAATAATATATTATATTATA
1 AATAATAATAATATATTATATTATA
95432 TATGTATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATAATAATAATATATTATATTATA
Found at i:95412 original size:20 final size:20
Alignment explanation
Indices: 95387--95426 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
95377 TAATAATAAT
95387 AATAATAATAATATATTATA
1 AATAATAATAATATATTATA
95407 AATAATAATAATATATTATA
1 AATAATAATAATATATTATA
95427 TTATATATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAATAATAATATATTATA
Found at i:95662 original size:36 final size:36
Alignment explanation
Indices: 95615--95706 Score: 175
Period size: 36 Copynumber: 2.6 Consensus size: 36
95605 TCTAATCTTG
95615 CTTCACTACTCTTCCGTGAAGGTTGAAAATGACTAA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATGACTAA
*
95651 CTTCACTACTCTTCCGTGAAGGTTGAAAATGACTGA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATGACTAA
95687 CTTCACTACTCTTCCGTGAA
1 CTTCACTACTCTTCCGTGAA
95707 ACTCAGATTC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (36 bp):
CTTCACTACTCTTCCGTGAAGGTTGAAAATGACTAA
Found at i:95837 original size:20 final size:20
Alignment explanation
Indices: 95814--95873 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
95804 ACCCAAATAA
* *
95814 TTTACAAATTACCCAGAGGT
1 TTTACAAATGACCCGGAGGT
* *
95834 TTTACAAATGGCCTGGAGGT
1 TTTACAAATGACCCGGAGGT
95854 TTTACAAATGACCCGGAGGT
1 TTTACAAATGACCCGGAGGT
95874 CTAAAATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (20 bp):
TTTACAAATGACCCGGAGGT
Done.