Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000333.1 Hibiscus syriacus cultivar Beakdansim tig00000617_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: 88375
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3393 original size:22 final size:21
Alignment explanation
Indices: 3351--3390 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3341 GAGTTTATTT
*
3351 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3372 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3391 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:17689 original size:19 final size:19
Alignment explanation
Indices: 17665--17716 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
17655 TTGGACCCTT
*
17665 AGTGCATCGGTGCACTAAG
1 AGTGCATCGATGCACTAAG
17684 AGTGCATCGATGCACTAAG
1 AGTGCATCGATGCACTAAG
*
17703 AGTGCACCGATGCA
1 AGTGCATCGATGCA
17717 TCAAGTGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.29, C:0.23, G:0.29, T:0.19
Consensus pattern (19 bp):
AGTGCATCGATGCACTAAG
Found at i:18522 original size:2 final size:2
Alignment explanation
Indices: 18515--18545 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18505 ATCAAACCAA
18515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18546 ATAAGTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18985 original size:21 final size:21
Alignment explanation
Indices: 18960--19003 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
18950 CAAGAGGAGG
*
18960 AGGAGGAGCACG-AGAAGAGCT
1 AGGAGCAGCACGTA-AAGAGCT
*
18981 AGGAGCAGCTCGTAAAGAGCT
1 AGGAGCAGCACGTAAAGAGCT
19002 AG
1 AG
19004 CTCCCGAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.36, C:0.16, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGTAAAGAGCT
Found at i:19979 original size:64 final size:64
Alignment explanation
Indices: 19905--20129 Score: 197
Period size: 64 Copynumber: 3.5 Consensus size: 64
19895 TTGTTTGAAT
* * * * * *
19905 GTGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTATAATAAAGACATTGAATGCAATTC
1 GTGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAA-ACATCGAATGCAA-TC
19969 -
64 G
* * * *
19969 GTGCATCGATGCATAAGTAGTGGATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATCG
1 GTGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCG
* * ** * * * **
20033 GTGCATCGATGTATAAGG-AGTGCATCGATGCATCTCAGCAATAATACAACATCGAATACATTTT
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCG
* *
20097 GTGCACCGATGCATCA-GTAGTGTATCGATGCAT
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCAT
20130 ACCTTCATTA
Statistics
Matches: 130, Mismatches: 27, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
63 3 0.02
64 115 0.88
65 12 0.09
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (64 bp):
GTGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCG
Found at i:20874 original size:31 final size:31
Alignment explanation
Indices: 20785--20864 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
20775 AGGGTCGAGG
20785 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
20816 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
20847 GTTTACCTAGGTTCTTCG
1 GTTTACCTATGTTCTTCG
20865 AGATCTATGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:23548 original size:64 final size:64
Alignment explanation
Indices: 23480--23621 Score: 153
Period size: 64 Copynumber: 2.2 Consensus size: 64
23470 TTGTTTGAAT
* ** * * * *
23480 GTGCACCGATGCATTGGTATTGCATCGATGCA-CTCTTTTATAATAAAGACATCGAATGCAATTC
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAA-ACATCGAATGCAA-TC
23544 -
64 G
* * * *
23544 GTGCATCGATACATAAGTAGTGCATCGATTCATCCCATTAATAGTGAAACATCGAATGCAATCG
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCG
23608 GTGCATCGATGCAT
1 GTGCATCGATGCAT
23622 CTCAGCAATA
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
63 2 0.03
64 52 0.81
65 10 0.16
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCG
Found at i:24493 original size:31 final size:31
Alignment explanation
Indices: 24342--24486 Score: 263
Period size: 31 Copynumber: 4.7 Consensus size: 31
24332 AGGGTCGAGG
24342 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
24373 GTTTACTTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
24404 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
24435 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
24466 GTTTACCTAGGTTCTTCGGGA
1 GTTTACCTATGTTCTTCGGGA
24487 TCTATGGCCT
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 109 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:27937 original size:21 final size:21
Alignment explanation
Indices: 27911--27955 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
27901 GTTTTCTGGG
* *
27911 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
27932 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
27953 CAA
1 CAA
27956 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:28329 original size:18 final size:16
Alignment explanation
Indices: 28308--28347 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
28298 TGATTATACG
28308 TATATGAATGACATGAAT
1 TATATGAATG-CATG-AT
*
28326 TATATGTATGCATGAT
1 TATATGAATGCATGAT
28342 TATATG
1 TATATG
28348 TGTTAACATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 4 0.19
18 9 0.43
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (16 bp):
TATATGAATGCATGAT
Found at i:28345 original size:16 final size:18
Alignment explanation
Indices: 28308--28348 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
28298 TGATTATACG
*
28308 TATATGAATGACATGAAT
1 TATATGTATGACATGAAT
28326 TATATGTATG-CATG-AT
1 TATATGTATGACATGAAT
28342 TATATGT
1 TATATGT
28349 GTTAACATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.41
17 4 0.18
18 9 0.41
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (18 bp):
TATATGTATGACATGAAT
Found at i:28805 original size:31 final size:31
Alignment explanation
Indices: 28767--28891 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
28757 AGGGTCGAGG
*
28767 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
28798 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
28829 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
28860 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
28891 G
1 G
28892 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:34872 original size:64 final size:63
Alignment explanation
Indices: 34800--34942 Score: 157
Period size: 64 Copynumber: 2.2 Consensus size: 63
34790 TTAGACCCTT
* *
34800 AGTGCATCGGTGCA-CTAAGAGTGCATCGATGCAACAAGTGCATTCGATG-TTTCA-AAATAGCC
1 AGTGCATCGGTGCAGCT--G-GTGCATCGATGCAACAAATGCATTCCATGTTTTCATAAA-AGCC
*
34862 TG
62 TC
* * *
34864 AGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCCATGTTTTCATAAAATCCTC
1 AGTGCATCGGTGCA--GCTGGTGCATCGATGCAACAAATGCATTCCATGTTTTCATAAAAGCCTC
34929 AGTGCATCGGTGCA
1 AGTGCATCGGTGCA
34943 TGGTATGTGC
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
64 39 0.58
65 23 0.34
66 3 0.04
67 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (63 bp):
AGTGCATCGGTGCAGCTGGTGCATCGATGCAACAAATGCATTCCATGTTTTCATAAAAGCCTC
Found at i:34953 original size:65 final size:64
Alignment explanation
Indices: 34820--34962 Score: 173
Period size: 65 Copynumber: 2.2 Consensus size: 64
34810 TGCACTAAGA
* * * *
34820 GTGCATCGATGCAACAAGTGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCCATGTTTCAAAATAGCCTCAGTGCATCGATGCATGGCTG
* *
34884 GTGCATCGATGCATCAAATGCATTCCATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCCATG-TTTCA-AAATAGCCTCAGTGCATCGATGCATGGCT
*
34947 AT
64 -G
*
34949 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
34963 GGTATGTGCA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
64 27 0.40
65 38 0.56
66 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCCATGTTTCAAAATAGCCTCAGTGCATCGATGCATGGCTG
Found at i:34954 original size:19 final size:19
Alignment explanation
Indices: 34930--34982 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
34920 AAAATCCTCA
34930 GTGCATCGGTGCATGGTAT
1 GTGCATCGGTGCATGGTAT
34949 GTGCATCGGTGCATGGTAT
1 GTGCATCGGTGCATGGTAT
*
34968 GTGCATCGATGCATG
1 GTGCATCGGTGCATG
34983 AAATGCATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.17, C:0.17, G:0.36, T:0.30
Consensus pattern (19 bp):
GTGCATCGGTGCATGGTAT
Found at i:36098 original size:31 final size:31
Alignment explanation
Indices: 36051--36117 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
36041 CAGTTACGTT
*
36051 GGGG-CCATATTGCAAACAAACTAAATGTTA
1 GGGGACCATATTACAAACAAACTAAATGTTA
* *
36081 GGGGACCATATTACAAACAGACTAAATGTTG
1 GGGGACCATATTACAAACAAACTAAATGTTA
36112 GGGGAC
1 GGGGAC
36118 TATGTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.21
Consensus pattern (31 bp):
GGGGACCATATTACAAACAAACTAAATGTTA
Found at i:37193 original size:30 final size:31
Alignment explanation
Indices: 37124--37190 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
37114 TGCAATACAA
* *
37124 TCCCCCAACATTTAATTCGTTTGTAATATGG
1 TCCCCCAACATTTAATTCATTTGCAATATGG
**
37155 TCCCCCAACATTTCGTTCATTTGCAATATGG
1 TCCCCCAACATTTAATTCATTTGCAATATGG
37186 TCCCC
1 TCCCC
37191 AACGTAGCTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.22, C:0.30, G:0.12, T:0.36
Consensus pattern (31 bp):
TCCCCCAACATTTAATTCATTTGCAATATGG
Found at i:41598 original size:18 final size:19
Alignment explanation
Indices: 41563--41604 Score: 68
Period size: 18 Copynumber: 2.2 Consensus size: 19
41553 TGTTAGGAAT
41563 TTAATTAAAATTTTGAAAAA
1 TTAATTAAAA-TTTGAAAAA
41583 TTAATTAAAA-TTGAAAAA
1 TTAATTAAAATTTGAAAAA
41601 TTAA
1 TTAA
41605 ATTATTAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 12 0.55
20 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
TTAATTAAAATTTGAAAAA
Found at i:43064 original size:20 final size:21
Alignment explanation
Indices: 43039--43090 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
43029 TTTTCCCAAT
*
43039 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
43059 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
43080 TCGCAATGCGA
1 TCGCAATGCGA
43091 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:43104 original size:20 final size:20
Alignment explanation
Indices: 43079--43132 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
43069 AATTGGGAAA
43079 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
43099 ATCGCAATGTGATACTTACT
1 ATCGCAATGCGATACTGACT
43119 ATCGCAATGCGATA
1 ATCGCAATGCGATA
43133 ATACAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:43711 original size:19 final size:19
Alignment explanation
Indices: 43687--43736 Score: 75
Period size: 18 Copynumber: 2.7 Consensus size: 19
43677 TAGTTCCGAG
43687 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
43706 AATGAAAATCGC-ACGCGA
1 AATGAAAATCGCAACGCGA
**
43724 AACCAAAATCGCA
1 AATGAAAATCGCA
43737 TTGCGATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 16 0.57
19 12 0.43
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:43754 original size:19 final size:19
Alignment explanation
Indices: 43732--43810 Score: 122
Period size: 19 Copynumber: 4.1 Consensus size: 19
43722 GAAACCAAAA
*
43732 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
43751 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
43770 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
43789 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
43809 TC
1 TC
43811 AACCAAAAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 38 0.69
20 17 0.31
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:43805 original size:39 final size:38
Alignment explanation
Indices: 43732--43810 Score: 122
Period size: 39 Copynumber: 2.1 Consensus size: 38
43722 GAAACCAAAA
*
43732 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCATTTCGCGTTGCGATTTTCATT
* *
43770 TCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCATT-TCGCGTTGCGATTTTCATT
43809 TC
1 TC
43811 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 17 0.46
39 20 0.54
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.47
Consensus pattern (38 bp):
TCGCATTGCGATTCTCATTTCGCGTTGCGATTTTCATT
Found at i:46016 original size:42 final size:42
Alignment explanation
Indices: 45896--46070 Score: 190
Period size: 42 Copynumber: 4.2 Consensus size: 42
45886 CCCGACTCGC
* * * *
45896 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
* * * *
45938 CTATCAT-TCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
* * * * *
45979 CTGTCATCCCTCAATAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
* * * *
46021 CTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
46063 CTGTCATC
1 CTGTCATC
46071 GTTGAAGAGG
Statistics
Matches: 104, Mismatches: 28, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
41 33 0.32
42 71 0.68
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
Found at i:46073 original size:21 final size:21
Alignment explanation
Indices: 45965--46085 Score: 57
Period size: 21 Copynumber: 5.8 Consensus size: 21
45955 CCCCTCCCAC
45965 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
** * * *
45986 CCCTCAATAGTCCACT-CCTAT
1 CGTTCAAGAGGCCACTGTC-AT
* * *
46007 CGTTGAAGAGGCCCCTATCATT
1 CGTTCAAGAGGCCACTGTCA-T
* * * * ** *
46029 C-CTCGAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCACTGTCAT
46049 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
* *
46070 CGTTGAAGAGGTCACT
1 CGTTCAAGAGGCCACT
46086 CCCACAATTA
Statistics
Matches: 68, Mismatches: 28, Indels: 8
0.65 0.27 0.08
Matches are distributed among these distances:
20 2 0.03
21 63 0.93
22 3 0.04
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.24
Consensus pattern (21 bp):
CGTTCAAGAGGCCACTGTCAT
Found at i:46087 original size:84 final size:83
Alignment explanation
Indices: 45896--46070 Score: 332
Period size: 83 Copynumber: 2.1 Consensus size: 83
45886 CCCGACTCGC
45896 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCTCGAGAGTCCCCTC
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCTCGAGAGTCCCCTC
45961 CCACCGTTCAAGAGGCCA
66 CCACCGTTCAAGAGGCCA
*
45979 CTGTCATCCCTCAATAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATT-CTCGAGAGTCCCCT
46044 CCCACCGTTCAAGAGGCCA
65 CCCACCGTTCAAGAGGCCA
46063 CTGTCATC
1 CTGTCATC
46071 GTTGAAGAGG
Statistics
Matches: 90, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
83 49 0.54
84 41 0.46
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (83 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCTCGAGAGTCCCCTC
CCACCGTTCAAGAGGCCA
Found at i:46088 original size:42 final size:42
Alignment explanation
Indices: 45896--46090 Score: 162
Period size: 42 Copynumber: 4.7 Consensus size: 42
45886 CCCGACTCGC
* * * * * *
45896 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTGTCATCCTTGAAGAGTCCACTCCCACCGTTCAAGAGGCCA
* * * *
45938 CTATCATTCTCG-AGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCCTTGAAGAGTCCACTCCCACCGTTCAAGAGGCCA
* * * * * * *
45979 CTGTCATCCCTCAATAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTGTCATCCTTGAAGAGTCCACTCCCACCGTTCAAGAGGCCA
* * *
46021 CTATCATTCCTCG-AGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCA-TCCTTGAAGAGTCCACTCCCACCGTTCAAGAGGCCA
*
46063 CTGTCATCGTTGAAGAGGT-CACTCCCAC
1 CTGTCATCCTTGAAGA-GTCCACTCCCAC
46091 AATTAAAGAG
Statistics
Matches: 114, Mismatches: 35, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
41 35 0.31
42 74 0.65
43 5 0.04
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.24
Consensus pattern (42 bp):
CTGTCATCCTTGAAGAGTCCACTCCCACCGTTCAAGAGGCCA
Found at i:46100 original size:84 final size:83
Alignment explanation
Indices: 45896--46100 Score: 279
Period size: 84 Copynumber: 2.5 Consensus size: 83
45886 CCCGACTCGC
* * *
45896 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCTCGAGAGTCCCCTC
1 CTGTCATCCCTCAAGAGTCCACTCCCATCATTAAAGAGGCCCCTATCATTCTCGAGAGTCCCCTC
45961 CCACCGTTCAAGAGGCCA
66 CCACCGTTCAAGAGGCCA
* * * *
45979 CTGTCATCCCTCAATAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCATCATTAAAGAGGCCCCTATCATT-CTCGAGAGTCCCCT
46044 CCCACCGTTCAAGAGGCCA
65 CCCACCGTTCAAGAGGCCA
** *
46063 CTGTCATCGTTGAAGAGGT-CACTCCCA-CAATTAAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCATC-ATTAAAGAG
46101 CCCGATTCAC
Statistics
Matches: 111, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
83 50 0.45
84 59 0.53
85 2 0.02
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.23
Consensus pattern (83 bp):
CTGTCATCCCTCAAGAGTCCACTCCCATCATTAAAGAGGCCCCTATCATTCTCGAGAGTCCCCTC
CCACCGTTCAAGAGGCCA
Found at i:47609 original size:19 final size:19
Alignment explanation
Indices: 47585--47651 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
47575 AAAAAGTACT
*
47585 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
47604 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
47618 ATTGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
47637 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
47652 TAAATTCGCG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 9 0.23
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 24 0.62
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:47660 original size:19 final size:19
Alignment explanation
Indices: 47586--47660 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 19
47576 AAAAGTACTA
* *
47586 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAT
*
47605 TCGCAA--CGAGA-G-AAT
1 TCGCAACGCGAAATGAAAT
*
47620 T-GCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAT
*
47638 TCGCAACGCGAAATTAAAT
1 TCGCAACGCGAAATGAAAT
47657 TCGC
1 TCGC
47661 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
14 4 0.09
15 3 0.07
16 5 0.11
17 5 0.11
18 3 0.07
19 25 0.56
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAT
Found at i:47678 original size:19 final size:19
Alignment explanation
Indices: 47656--47773 Score: 67
Period size: 19 Copynumber: 6.7 Consensus size: 19
47646 CGAAATTAAA
47656 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
47675 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
47690 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
47708 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
47722 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
47741 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
47760 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
47774 AGACATTAAG
Statistics
Matches: 71, Mismatches: 17, Indels: 21
0.65 0.16 0.19
Matches are distributed among these distances:
14 19 0.27
16 3 0.04
17 3 0.04
19 36 0.51
20 10 0.14
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.41
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:47702 original size:33 final size:31
Alignment explanation
Indices: 47659--47753 Score: 136
Period size: 33 Copynumber: 2.9 Consensus size: 31
47649 AATTAAATTC
*
47659 GCGTTGCGATTTTCATTTCGCATTGCGATTCCC
1 GCGTTGCGATTTTCATTTCGCATTGCGATT--A
*
47692 TCGTTGCGATTTTCATTTCGCATTGCGAAATTA
1 GCGTTGCGATTTTCATTTCGCATTGCG--ATTA
47725 GCGTTGCGATTTTCATTTCGCATTGCGAT
1 GCGTTGCGATTTTCATTTCGCATTGCGAT
47754 AGTAATTTCC
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
31 2 0.04
33 52 0.91
35 3 0.05
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.41
Consensus pattern (31 bp):
GCGTTGCGATTTTCATTTCGCATTGCGATTA
Found at i:50052 original size:12 final size:12
Alignment explanation
Indices: 50035--50071 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
50025 TCTTCGGGGA
50035 CTTTTTCTTCTT
1 CTTTTTCTTCTT
50047 CTTTTTCTTCTT
1 CTTTTTCTTCTT
50059 CTTTTTCTTCTT
1 CTTTTTCTTCTT
50071 C
1 C
50072 AGGATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:51106 original size:20 final size:21
Alignment explanation
Indices: 51081--51132 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
51071 TTTTCCTAAT
*
51081 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
51101 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
51122 TCGCAATGCGA
1 TCGCAATGCGA
51133 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:51154 original size:20 final size:20
Alignment explanation
Indices: 51121--51195 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
51111 AATTTGGAAA
* *
51121 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
51141 ATCGCAACGAGATAAT-ACAAAA
1 ATCGCAACGAGATACTGAC---T
*
51163 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
*
51183 TTCGCAACGAGAT
1 ATCGCAACGAGAT
51196 TTTGAAAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
19 2 0.05
20 25 0.58
22 14 0.33
23 2 0.05
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:51207 original size:20 final size:20
Alignment explanation
Indices: 51160--51209 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
51150 AGATAATACA
51160 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
*** *
51180 ACTTTCGCAACGAGATTTTG
1 AAAATCGCAACGAGATTCTG
51200 AAAATCGCAA
1 AAAATCGCAA
51210 TCATCTTCAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:51486 original size:20 final size:20
Alignment explanation
Indices: 51423--51490 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
51413 CAACGGGGAA
51423 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* ** ***
51443 ATCGCCATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
51463 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
51483 ATCGCAAC
1 ATCGCAAC
51491 TAGAAAATCG
Statistics
Matches: 34, Mismatches: 12, Indels: 4
0.68 0.24 0.08
Matches are distributed among these distances:
19 5 0.15
20 24 0.71
21 5 0.15
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:51564 original size:19 final size:19
Alignment explanation
Indices: 51539--51584 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
51529 TTTCTCGTTA
51539 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
*
51558 CGGTTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
51577 CGATTTTC
1 CGATTTTC
51585 TCGTTGCGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.22, G:0.17, T:0.48
Consensus pattern (19 bp):
CGATTTTCATTTCGCATTG
Found at i:51740 original size:14 final size:14
Alignment explanation
Indices: 51721--51757 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
51711 CATCAATTAA
51721 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
51735 ACAAATCATCTTTT
1 ACAAATCAACATTT
51749 ACAAATCAA
1 ACAAATCAA
51758 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:53224 original size:42 final size:42
Alignment explanation
Indices: 53178--53260 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
53168 CTTCAACGAT
* * *
53178 GATAGTGGCCTCTTGAACGGTGGGGGGGGACTCTTGAGGGAG
1 GATAGAGGCCTCTTGAACGATGGGAGGGGACTCTTGAGGGAG
*
53220 GATAGAGGCCTCTTGAACGATTGGAGGGGACTCTTGAGGGA
1 GATAGAGGCCTCTTGAACGATGGGAGGGGACTCTTGAGGGA
53261 TGACAGGTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.20, C:0.14, G:0.43, T:0.22
Consensus pattern (42 bp):
GATAGAGGCCTCTTGAACGATGGGAGGGGACTCTTGAGGGAG
Found at i:53640 original size:20 final size:20
Alignment explanation
Indices: 53625--53693 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
53615 TACGAAACTT
53625 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
**
53645 ACTATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
*** *
53665 GCTATCGCAATGCG-AAATG
1 AAAATCGCAACGCGAAAATG
53684 AAAATCGCAA
1 AAAATCGCAA
53694 TGACAAAATC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 12 0.29
20 30 0.71
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:53703 original size:14 final size:14
Alignment explanation
Indices: 53684--53742 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
53674 ATGCGAAATG
53684 AAAATCGCAATGAC
1 AAAATCGCAATGAC
*
53698 AAAATCGCAATGCGAAATG
1 AAAATCGCAAT--G--A-C
*
53717 AAAATCGCAACGAC
1 AAAATCGCAATGAC
53731 AAAATCGCAATG
1 AAAATCGCAATG
53743 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 22 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 10 0.28
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.14
Consensus pattern (14 bp):
AAAATCGCAATGAC
Found at i:53710 original size:33 final size:33
Alignment explanation
Indices: 53668--53757 Score: 164
Period size: 33 Copynumber: 2.8 Consensus size: 33
53658 GAAAATGGCT
*
53668 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
53701 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
53734 ATCGCAATGCGAAATG-AAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCA
53758 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 8 0.14
33 48 0.86
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:53780 original size:19 final size:19
Alignment explanation
Indices: 53753--53834 Score: 95
Period size: 18 Copynumber: 4.6 Consensus size: 19
53743 CGAAATGAAA
53753 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
53772 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
53790 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
53806 TCG--TTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
53823 TCGCATTGCGAT
1 TCGCATTGCGAT
53835 AGCCATTTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 5 0.10
15 3 0.06
16 4 0.08
17 4 0.08
18 20 0.38
19 16 0.31
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:53846 original size:20 final size:20
Alignment explanation
Indices: 53821--53865 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
53811 GCAATTTTCA
*
53821 TTTCGCATTGCGATAGCCAT
1 TTTCGCATTACGATAGCCAT
* * *
53841 TTTCGCGTTATGATAGTCAT
1 TTTCGCATTACGATAGCCAT
53861 TTTCG
1 TTTCG
53866 TGTTGCGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (20 bp):
TTTCGCATTACGATAGCCAT
Found at i:54381 original size:18 final size:18
Alignment explanation
Indices: 54355--54399 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
54345 GTCGATCAGA
*
54355 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
54373 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
54391 TGATGGCTC
1 TGATGGCTC
54400 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:55768 original size:20 final size:20
Alignment explanation
Indices: 55720--55783 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
55710 AATAGTTTCT
** *
55720 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
55740 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
** *
55760 GAATTTGACTATCGCAATGC
1 GAAAATGACTATCGCAACGC
55780 GAAA
1 GAAA
55784 CTAAAATCGC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.44, C:0.20, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:56052 original size:22 final size:22
Alignment explanation
Indices: 56026--56069 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
56016 GATAGAGATA
56026 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
56048 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
56070 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:56343 original size:20 final size:20
Alignment explanation
Indices: 56237--56371 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
56227 CGCTTTGAAA
*
56237 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
56258 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
56278 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
56298 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
56319 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
56339 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
56359 ATCGCATTGCGAT
1 ATCGCATTGCGAT
56372 TTTTCCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:56392 original size:61 final size:61
Alignment explanation
Indices: 56237--56374 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
56227 CGCTTTGAAA
* * * *
56237 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
56298 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
56359 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
56375 TCCAATTTGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:56482 original size:21 final size:21
Alignment explanation
Indices: 56442--56482 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
56432 ACTGTAGACC
** *
56442 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
56463 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
56483 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:60171 original size:20 final size:20
Alignment explanation
Indices: 60143--60213 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 20
60133 ATTTTAATAG
* *
60143 TTATAAAATGATAATTAAAT
1 TTATAAAATAATAATAAAAT
* * *
60163 TTATTAAATTATTATAAAAT
1 TTATAAAATAATAATAAAAT
60183 GTTATAAAATAATAATAAAAT
1 -TTATAAAATAATAATAAAAT
60204 TTAATAAAAT
1 TT-ATAAAAT
60214 TAAGGAACAT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 18 0.43
21 24 0.57
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
TTATAAAATAATAATAAAAT
Found at i:61256 original size:19 final size:19
Alignment explanation
Indices: 61220--61257 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
61210 GAATCATAAA
*
61220 AATTAAAAAATGTATACTT
1 AATTAAAAAATATATACTT
61239 AATTAAAAAA-ATATTACTT
1 AATTAAAAAATATA-TACTT
61258 TTTTGTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (19 bp):
AATTAAAAAATATATACTT
Found at i:63808 original size:183 final size:184
Alignment explanation
Indices: 63497--63883 Score: 656
Period size: 183 Copynumber: 2.1 Consensus size: 184
63487 AATTATAATT
* * *
63497 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
*
63561 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* * *
63626 GGATTTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCCATATGTTA
131 GGATCTTAAATTATTAATTGAGTTTTAAATGATTTGGG-TTGAGCCCATATGTTA
63680 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATATATAA
*
63744 TTATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65 TTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
63808 TGGATCTTAAATTATTAATTGAGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
130 TGGATCTTAAATTATTAATTGAGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
63863 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
63884 AATATTTAAT
Statistics
Matches: 193, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
182 2 0.01
183 125 0.65
184 66 0.34
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
GGATCTTAAATTATTAATTGAGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
Found at i:64093 original size:5 final size:5
Alignment explanation
Indices: 64074--64122 Score: 64
Period size: 5 Copynumber: 10.0 Consensus size: 5
64064 TACCTGCAAC
* * *
64074 AAAAT AAAA- AAAAT ATAAT AAAAT AAAAT TATAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
64123 TATATAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
4 4 0.11
5 33 0.89
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:64115 original size:20 final size:20
Alignment explanation
Indices: 64090--64131 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
64080 AAAAAAATAT
64090 AATAAAATAAAATTATATAA
1 AATAAAATAAAATTATATAA
64110 AATAAAATAAAATTATATAA
1 AATAAAATAAAATTATATAA
64130 AA
1 AA
64132 AATTAACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AATAAAATAAAATTATATAA
Found at i:64129 original size:10 final size:10
Alignment explanation
Indices: 64096--64131 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
64086 ATATAATAAA
64096 ATAAAATTAT
1 ATAAAATTAT
* *
64106 ATAAAATAAA
1 ATAAAATTAT
64116 ATAAAATTAT
1 ATAAAATTAT
64126 ATAAAA
1 ATAAAA
64132 AATTAACTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
ATAAAATTAT
Found at i:65609 original size:249 final size:250
Alignment explanation
Indices: 65098--65842 Score: 1392
Period size: 249 Copynumber: 3.0 Consensus size: 250
65088 GAATTTCCCC
* *
65098 CGTTTTGGGATTATGTTTGTTGGCTCGGATGTTTGTGAGGTGCGGTTAAGTTCTGATTTTTGA-T
1 CGTTTTGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATT
65162 -TGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCTCGTTT
66 GTGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCTCGTTT
*
65226 TGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGCGGTTAAGTTCTGATTTTTGA-T-TGTG
131 TGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATTGTGTG
65289 TCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
196 TCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
65344 CGTTTTGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATT
1 CGTTTTGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATT
65409 GTGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCTCGTTT
66 GTGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCTCGTTT
*
65474 TGGGATTGTG-TTGTTGGCTCGGATGTTTGTGAGGTATGGTTAAGTTCTGATTTTTGATTGTGTG
131 TGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATTGTGTG
65538 TCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
196 TCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
65593 CGTTTTGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATT
1 CGTTTTGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATT
65658 GTGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCTCGTTT
66 GTGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCTCGTTT
65723 TGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATTGTGTG
131 TGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATTGTGTG
* * *
65788 TCCAAGTGTAAACTTGACAATGGCATGATGTATTCTTTTTCCTCCATTTAAGTCT
196 TCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
65843 AGGAGATTTT
Statistics
Matches: 486, Mismatches: 8, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
246 61 0.13
247 46 0.09
248 75 0.15
249 199 0.41
250 105 0.22
ACGTcount: A:0.17, C:0.12, G:0.27, T:0.44
Consensus pattern (250 bp):
CGTTTTGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATT
GTGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCTCGTTT
TGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATTGTGTG
TCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
Found at i:65706 original size:125 final size:125
Alignment explanation
Indices: 65098--65842 Score: 1392
Period size: 125 Copynumber: 6.0 Consensus size: 125
65088 GAATTTCCCC
* *
65098 CGTTTTGGGATTATGTTTGTTGGCTCGGATGTTTGTGAGGTGCGGTTAAGTTCTGATTTTTGA-T
1 CGTTTTGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATT
65162 -TGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
66 GTGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
*
65221 CGTTTTGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGCGGTTAAGTTCTGATTTTTGA-T
1 CGTTTTGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATT
65285 -TGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
66 GTGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
65344 CGTTTTGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATT
1 CGTTTTGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATT
65409 GTGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
66 GTGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
*
65469 CGTTTTGGGATTGTG-TTGTTGGCTCGGATGTTTGTGAGGTATGGTTAAGTTCTGATTTTTGATT
1 CGTTTTGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATT
65533 GTGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
66 GTGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
65593 CGTTTTGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATT
1 CGTTTTGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATT
65658 GTGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
66 GTGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
65718 CGTTTTGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATT
1 CGTTTTGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATT
* * *
65783 GTGTGTCCAAGTGTAAACTTGACAATGGCATGATGTATTCTTTTTCCTCCATTTAAGTCT
66 GTGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
65843 AGGAGATTTT
Statistics
Matches: 612, Mismatches: 7, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
123 184 0.30
124 124 0.20
125 304 0.50
ACGTcount: A:0.17, C:0.12, G:0.27, T:0.44
Consensus pattern (125 bp):
CGTTTTGGGATTGTGTTTGTTGGCTCGGATGTTTGTGAGGTGTGGTTAAGTTCTGATTTTTGATT
GTGTGTCCAAGTGTAAACTTGACAATGGCAAGATGTATTCTTTTTCCTTCATTTAGGTCT
Found at i:69582 original size:15 final size:15
Alignment explanation
Indices: 69562--69597 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
69552 ATGGGGGACT
69562 TGGTGGTGGAGGCGG
1 TGGTGGTGGAGGCGG
* *
69577 TGGTGGTGGGGGTGG
1 TGGTGGTGGAGGCGG
69592 TGGTGG
1 TGGTGG
69598 GGGCTCACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.03, C:0.03, G:0.69, T:0.25
Consensus pattern (15 bp):
TGGTGGTGGAGGCGG
Found at i:69595 original size:12 final size:12
Alignment explanation
Indices: 69563--69600 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
69553 TGGGGGACTT
* *
69563 GGTGGTGGAGGC
1 GGTGGTGGTGGG
69575 GGTGGTGGTGGG
1 GGTGGTGGTGGG
69587 GGTGGTGGTGGG
1 GGTGGTGGTGGG
69599 GG
1 GG
69601 CTCACATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.03, C:0.03, G:0.74, T:0.21
Consensus pattern (12 bp):
GGTGGTGGTGGG
Found at i:76002 original size:29 final size:29
Alignment explanation
Indices: 75926--76005 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
75916 ATTCTACAGT
*
75926 GACCAAAGAGGTCGCCATACACGCCCAAC
1 GACCAAAGAGGTCGCCATGCACGCCCAAC
75955 GACCAAAGAGGTCGCCATGCACGCCCAAC
1 GACCAAAGAGGTCGCCATGCACGCCCAAC
*
75984 GACCAAGGAGGTCGCCATGCAC
1 GACCAAAGAGGTCGCCATGCAC
76006 TCGGGGCGAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.31, C:0.36, G:0.25, T:0.07
Consensus pattern (29 bp):
GACCAAAGAGGTCGCCATGCACGCCCAAC
Found at i:76400 original size:21 final size:21
Alignment explanation
Indices: 76342--76433 Score: 103
Period size: 21 Copynumber: 4.3 Consensus size: 21
76332 CTATCACTCA
*
76342 TGCATGCGTTGCATCCATAGC
1 TGCATGCGTTGCATCCGTAGC
* * **
76363 TGGAAGATTCCTGCATCCGTAGC
1 TGCATGCGT--TGCATCCGTAGC
*
76386 TACATGCGTTGCATCCGTAGC
1 TGCATGCGTTGCATCCGTAGC
*
76407 TGCATGCGTTGCATCCATAGC
1 TGCATGCGTTGCATCCGTAGC
76428 TGCATG
1 TGCATG
76434 ATTGCAGCTT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
21 42 0.74
23 15 0.26
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (21 bp):
TGCATGCGTTGCATCCGTAGC
Found at i:76832 original size:21 final size:21
Alignment explanation
Indices: 76807--76846 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
76797 TAGTTAATTA
76807 GTTTGTTAGTATAAATTATTT
1 GTTTGTTAGTATAAATTATTT
* *
76828 GTTTGTTAGTTTAAGTTAT
1 GTTTGTTAGTATAAATTAT
76847 ATATTATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.57
Consensus pattern (21 bp):
GTTTGTTAGTATAAATTATTT
Found at i:77383 original size:18 final size:16
Alignment explanation
Indices: 77346--77376 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
77336 AGATAATTCA
77346 TGTTAAAAAAATATTG
1 TGTTAAAAAAATATTG
*
77362 TGTTTAAAAAATATT
1 TGTTAAAAAAATATT
77377 TAGTGTTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
TGTTAAAAAAATATTG
Found at i:77411 original size:22 final size:23
Alignment explanation
Indices: 77367--77411 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
77357 TATTGTGTTT
**
77367 AAAAAATATTTAGTGTTGTTTTA
1 AAAAAATATTTAGTGTTAATTTA
*
77390 AAAAAATATTTTGT-TTAATTTA
1 AAAAAATATTTAGTGTTAATTTA
77412 TATTGTATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (23 bp):
AAAAAATATTTAGTGTTAATTTA
Found at i:79147 original size:23 final size:21
Alignment explanation
Indices: 79116--79168 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
79106 GATTTGATAC
* *
79116 TAATGATTTACTATTATTATT
1 TAATTATTTACTATTAATATT
*
79137 AATAATTATTTATTATTAATATT
1 --TAATTATTTACTATTAATATT
79160 TAATTATTT
1 TAATTATTT
79169 GATACTAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 9 0.33
23 18 0.67
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TAATTATTTACTATTAATATT
Found at i:79151 original size:17 final size:17
Alignment explanation
Indices: 79128--79167 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
79118 ATGATTTACT
79128 ATTATTATTAATAATTA
1 ATTATTATTAATAATTA
* *
79145 TTTATTATTAATATTTA
1 ATTATTATTAATAATTA
79162 ATTATT
1 ATTATT
79168 TGATACTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTATTATTAATAATTA
Found at i:79173 original size:58 final size:56
Alignment explanation
Indices: 79038--79186 Score: 203
Period size: 54 Copynumber: 2.7 Consensus size: 56
79028 GAAGCTGACG
*
79038 TATTAATATTTAATTATTTGATACTAATGATTTAAAAGTAATTTATTAATGATTTT
1 TATTAATATTTAATTATTTGATACTAATGATTTAAAAGTAATTTAATAATGATTTT
* ** * * *
79094 TA--AATATTTAATGATTTGATACTAATGATTTACTATTATTATTAATAATTATTTAT
1 TATTAATATTTAATTATTTGATACTAATGATTTAAAAGTAAT-TTAATAATGATTT-T
79150 TATTAATATTTAATTATTTGATACTAATGATTTAAAA
1 TATTAATATTTAATTATTTGATACTAATGATTTAAAA
79187 TAGTCGAATT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
54 33 0.42
55 11 0.14
56 5 0.06
58 30 0.38
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (56 bp):
TATTAATATTTAATTATTTGATACTAATGATTTAAAAGTAATTTAATAATGATTTT
Found at i:81511 original size:22 final size:22
Alignment explanation
Indices: 81486--81534 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
81476 ACAACTAATA
*
81486 AACTATTCTTTAATATAACT-TT
1 AACTATTCTCTAATATAA-TGTT
81508 AACTATTCTCTAATATAATGTT
1 AACTATTCTCTAATATAATGTT
81530 AACTA
1 AACTA
81535 ATAAACTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (22 bp):
AACTATTCTCTAATATAATGTT
Found at i:81512 original size:30 final size:29
Alignment explanation
Indices: 81478--81603 Score: 99
Period size: 30 Copynumber: 4.4 Consensus size: 29
81468 TCCCTTATAC
81478 AACTAATAAACTATTCTTT-A-AT-A--T
1 AACTAATAAACTATTCTTTAATATAATTT
* *
81502 AACT--TTAACTATTCTCTAATATAATGTT
1 AACTAATAAACTATTCTTTAATATAAT-TT
*
81530 AACTAATAAACTATTCTTTAATATAACTTA
1 AACTAATAAACTATTCTTTAATATAA-TTT
81560 AACTAATAAA-TGATT-TTTAATTATAATTT
1 AACTAATAAACT-ATTCTTTAA-TATAATTT
*
81589 ACTACTAAAAAACTA
1 A--ACTAATAAACTA
81604 ATTAACTAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 21
0.74 0.06 0.19
Matches are distributed among these distances:
22 11 0.14
23 1 0.01
24 6 0.07
25 1 0.01
28 5 0.06
29 9 0.11
30 37 0.46
31 10 0.12
32 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (29 bp):
AACTAATAAACTATTCTTTAATATAATTT
Found at i:81808 original size:21 final size:21
Alignment explanation
Indices: 81784--81823 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
81774 TTTATATATG
81784 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
81805 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
81824 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:81904 original size:18 final size:18
Alignment explanation
Indices: 81851--81905 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
81841 TTGTTTTACC
*
81851 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
81869 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
81881 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
81898 CTAATTTA
1 CTAATTTA
81906 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:81961 original size:28 final size:29
Alignment explanation
Indices: 81906--81962 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
81896 AACTAATTTA
* *
81906 AATAATTATTCTTTTATATAACTTAAACT
1 AATAACTATTCTTTTATATAACTAAAACT
81935 AATAACTATT-TTTTATTATAA-TAAAACT
1 AATAACTATTCTTTTA-TATAACTAAAACT
81963 TAAACTACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (29 bp):
AATAACTATTCTTTTATATAACTAAAACT
Found at i:81967 original size:34 final size:36
Alignment explanation
Indices: 81920--81996 Score: 97
Period size: 34 Copynumber: 2.2 Consensus size: 36
81910 ATTATTCTTT
* *
81920 TATATAACTTAAACTA-AT-AACT-ATTTTTTATTA
1 TATAAAACTTAAACTACATAAACTAATTTTTTATAA
81953 TAATAAAACTTAAACTACTATAAACTAATTTTTTATAA
1 T-ATAAAACTTAAACTAC-ATAAACTAATTTTTTATAA
81991 TATAAA
1 TATAAA
81997 TTCAACAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
33 1 0.03
34 14 0.38
36 2 0.05
37 9 0.24
38 11 0.30
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (36 bp):
TATAAAACTTAAACTACATAAACTAATTTTTTATAA
Found at i:82044 original size:25 final size:28
Alignment explanation
Indices: 82016--82077 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
82006 CAAATATAAC
*
82016 TTAACTATTA-ACTAACT-ACA-ACTAA
1 TTAAATATTAGACTAACTAACACACTAA
82041 TTAAATATTAGACTAACTAACACACTAA
1 TTAAATATTAGACTAACTAACACACTAA
*
82069 TTAATTATT
1 TTAAATATT
82078 TTTTAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 9 0.28
26 7 0.22
27 3 0.09
28 13 0.41
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (28 bp):
TTAAATATTAGACTAACTAACACACTAA
Found at i:82513 original size:29 final size:28
Alignment explanation
Indices: 82481--82564 Score: 114
Period size: 29 Copynumber: 2.9 Consensus size: 28
82471 GAAGGCATAG
*
82481 GTCGTTGGGATCCCTTGGCGACCTACAAT
1 GTCGATGGGATCCC-TGGCGACCTACAAT
82510 GTCGATGGGATGCCCTGGCGACCTACAAT
1 GTCGATGGGAT-CCCTGGCGACCTACAAT
* *
82539 GTCGCTGGGATTCCCTGGCAACCTAC
1 GTCGATGGGA-TCCCTGGCGACCTAC
82565 CCACGTTGCC
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.18, C:0.30, G:0.29, T:0.24
Consensus pattern (28 bp):
GTCGATGGGATCCCTGGCGACCTACAAT
Found at i:82679 original size:29 final size:29
Alignment explanation
Indices: 82645--82733 Score: 160
Period size: 29 Copynumber: 3.1 Consensus size: 29
82635 CATGCAGAGA
82645 CTCCAAGCTCGCCCGGATGCCATGGCGAC
1 CTCCAAGCTCGCCCGGATGCCATGGCGAC
* *
82674 CTCCAAGCTCGCCTGGATGCCATGACGAC
1 CTCCAAGCTCGCCCGGATGCCATGGCGAC
82703 CTCCAAGCTCGCCCGGATGCCATGGCGAC
1 CTCCAAGCTCGCCCGGATGCCATGGCGAC
82732 CT
1 CT
82734 ACGGTAACAC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.18, C:0.40, G:0.26, T:0.16
Consensus pattern (29 bp):
CTCCAAGCTCGCCCGGATGCCATGGCGAC
Found at i:85005 original size:21 final size:22
Alignment explanation
Indices: 84973--85016 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
84963 CAACTCGTAG
*
84973 CGTAGAATGTCCCGAAGGACCA
1 CGTAGAATGTCCCAAAGGACCA
84995 CGTAG-ATGTCCCAAAGGACCA
1 CGTAGAATGTCCCAAAGGACCA
85016 C
1 C
85017 ATATAACACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.32, C:0.30, G:0.25, T:0.14
Consensus pattern (22 bp):
CGTAGAATGTCCCAAAGGACCA
Found at i:85877 original size:24 final size:20
Alignment explanation
Indices: 85828--85885 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
85818 TTCTCATTGA
*
85828 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
85848 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
85871 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
85886 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Done.