Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 38 of 199
Found at i:11738365 original size:21 final size:21
Alignment explanation
Indices: 11738341--11738384 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
11738331 TTGTTAAAAC
11738341 TAGTTTAAGATAAGTTAGGCT
1 TAGTTTAAGATAAGTTAGGCT
11738362 TAGTTTAAGATAAGTTAGGCT
1 TAGTTTAAGATAAGTTAGGCT
11738383 TA
1 TA
11738385 TTAATGTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.39
Consensus pattern (21 bp):
TAGTTTAAGATAAGTTAGGCT
Found at i:11745849 original size:30 final size:27
Alignment explanation
Indices: 11745786--11745849 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 27
11745776 ATCAGCAATT
11745786 AATTAA-TTTTTATTTTTTTTCTAAAA
1 AATTAATTTTTTATTTTTTTTCTAAAA
* *
11745812 AAATAATTTTTTAATTTTTTAATTTTAAAA
1 AATTAATTTTTT-ATTTTTT--TTCTAAAA
11745842 AATTAATT
1 AATTAATT
11745850 AATTGCTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 5 0.16
27 5 0.16
28 7 0.23
30 14 0.45
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (27 bp):
AATTAATTTTTTATTTTTTTTCTAAAA
Found at i:11747055 original size:15 final size:15
Alignment explanation
Indices: 11747035--11747063 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11747025 TAATAGTAAA
11747035 AATAGATGAATTTTT
1 AATAGATGAATTTTT
11747050 AATAGATGAATTTT
1 AATAGATGAATTTT
11747064 GTTTGTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (15 bp):
AATAGATGAATTTTT
Found at i:11748190 original size:21 final size:21
Alignment explanation
Indices: 11748150--11748190 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11748140 TCAAAAATAG
**
11748150 GCCTTGATTGAGTTTTTTTTT
1 GCCTTGATTGAGTTGATTTTT
*
11748171 GCCTTGATTTAGTTGATTTT
1 GCCTTGATTGAGTTGATTTT
11748191 GATTCTTCAC
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:0.12, C:0.10, G:0.20, T:0.59
Consensus pattern (21 bp):
GCCTTGATTGAGTTGATTTTT
Found at i:11748959 original size:17 final size:16
Alignment explanation
Indices: 11748935--11748973 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
11748925 TAATGAGTGT
11748935 AGAG-AAGAAATGAAAA
1 AGAGAAAGAAA-GAAAA
11748951 AGAGAAAGAAAGAAAA
1 AGAGAAAGAAAGAAAA
11748967 AG-GAAAG
1 AGAGAAAG
11748974 TTCTTTTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.23
16 11 0.50
17 6 0.27
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (16 bp):
AGAGAAAGAAAGAAAA
Found at i:11756545 original size:2 final size:2
Alignment explanation
Indices: 11756538--11756563 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11756528 AAGTTTATGC
11756538 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
11756564 TTGTCTAATT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:11766660 original size:18 final size:20
Alignment explanation
Indices: 11766620--11766663 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
11766610 ACTTTAGCCT
11766620 TTTTTTTATATAAATCTTAA
1 TTTTTTTATATAAATCTTAA
*
11766640 TTTTTTTATCTAAAT-TT-A
1 TTTTTTTATATAAATCTTAA
11766658 TTTTTT
1 TTTTTT
11766664 AAGCTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 2 0.09
20 14 0.61
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTTTATATAAATCTTAA
Found at i:11784694 original size:13 final size:13
Alignment explanation
Indices: 11784676--11784700 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11784666 ATTCTGTCTT
11784676 TCCTTATTTTATG
1 TCCTTATTTTATG
11784689 TCCTTATTTTAT
1 TCCTTATTTTAT
11784701 CTATGTATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.04, T:0.64
Consensus pattern (13 bp):
TCCTTATTTTATG
Found at i:11793548 original size:36 final size:35
Alignment explanation
Indices: 11793454--11793919 Score: 271
Period size: 35 Copynumber: 13.1 Consensus size: 35
11793444 AATTATTTTC
* *
11793454 TTTGAAAACACGAAAAATTTTTAAAACACGAGAATT
1 TTTGAAAACACG-GAAATTTTTAAAACACGAAAATT
* * * *
11793490 TTAG-AGACACGAAAATTCTTAAAAACACGAAAATT
1 TTTGAAAACACGGAAATT-TTTAAAACACGAAAATT
* *
11793525 TTTGAAAACACGGAAATTTTTAAAACATGAGAATTT
1 TTTGAAAACACGGAAATTTTTAAAACACGA-AAATT
* *
11793561 TTTGAAAACATGAAAATTTTTAAAACAC-AAAATTTT
1 TTTGAAAACACGGAAATTTTTAAAACACGAAAA--TT
* *
11793597 TTTGAAAACACGAAAATTTTTAAAACACCG-GAATT
1 TTTGAAAACACGGAAATTTTTAAAACA-CGAAAATT
* * *
11793632 TTTGAAAACA-AGAGGATTTTTGAAACAC-AAAATTTT
1 TTTGAAAACACGGA-AATTTTTAAAACACGAAAA--TT
** * * *
11793668 CTTTGAAAACAC-G--ATTTTTTTATCACCAAAAAT
1 -TTTGAAAACACGGAAATTTTTAAAACACGAAAATT
* * * *
11793701 TTTGAAAACA-TGAAATTTTTTGAAATACTG-GAATT
1 TTTGAAAACACGGAAA-TTTTTAAAACAC-GAAAATT
* * * *
11793736 TTTGAAAAAAC-GAGGATTTTTGAAACACGAAATTTT
1 TTTGAAAACACGGA-AATTTTTAAAACACGAAA-ATT
11793772 TTTGAAAACAC-GAAATTTTTTGAAAGAC-CG-AAATT
1 TTTGAAAACACGGAAA-TTTTT-AAA-ACACGAAAATT
* *
11793807 TTTGAAAACACGGAATTTTTTTCTGAAAACAAGAAAATT
1 TTTGAAAACACGGAA--ATTTT-T-AAAACACGAAAATT
* * *
11793846 TTTG-AAATACGGGAATTTTTGAAAACACGGGAAATTTT
1 TTTGAAAACACGGAAATTTTT-AAAACAC--GAAA-ATT
* * *
11793884 TTTGAAAACGCGAAAATTTTTGAAACAC-AAAATT
1 TTTGAAAACACGGAAATTTTTAAAACACGAAAATT
11793918 TT
1 TT
11793920 GTTTTAAAAA
Statistics
Matches: 340, Mismatches: 54, Indels: 74
0.73 0.12 0.16
Matches are distributed among these distances:
32 11 0.03
33 1 0.00
34 28 0.08
35 121 0.36
36 102 0.30
37 28 0.08
38 28 0.08
39 21 0.06
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (35 bp):
TTTGAAAACACGGAAATTTTTAAAACACGAAAATT
Found at i:11793631 original size:17 final size:18
Alignment explanation
Indices: 11793454--11793919 Score: 317
Period size: 18 Copynumber: 26.1 Consensus size: 18
11793444 AATTATTTTC
11793454 TTTGAAAACACGAAAAATT
1 TTTGAAAACACG-AAAATT
*
11793473 TTT-AAAACACGAGAATT
1 TTTGAAAACACGAAAATT
* *
11793490 TTAG-AGACACGAAAATT
1 TTTGAAAACACGAAAATT
* *
11793507 CTTAAAAACACGAAAATT
1 TTTGAAAACACGAAAATT
*
11793525 TTTGAAAACACGGAAATT
1 TTTGAAAACACGAAAATT
* *
11793543 TTT-AAAACATGAGAATTT
1 TTTGAAAACACGA-AAATT
*
11793561 TTTGAAAACATGAAAATT
1 TTTGAAAACACGAAAATT
11793579 TTT-AAAACAC-AAAATTTT
1 TTTGAAAACACGAAAA--TT
11793597 TTTGAAAACACGAAAATT
1 TTTGAAAACACGAAAATT
*
11793615 TTT-AAAACACCG-GAATT
1 TTTGAAAACA-CGAAAATT
* **
11793632 TTTGAAAACAAGAGGATT
1 TTTGAAAACACGAAAATT
11793650 TTTG-AAACAC-AAAATTTT
1 TTTGAAAACACGAAAA--TT
11793668 CTTTGAAAACACG---ATT
1 -TTTGAAAACACGAAAATT
** * * *
11793684 TTT-TTATCACCAAAAAT
1 TTTGAAAACACGAAAATT
* *
11793701 TTTGAAAACATGAAATTT
1 TTTGAAAACACGAAAATT
* *
11793719 TTTGAAATAC-TG-GAATT
1 TTTGAAA-ACACGAAAATT
* **
11793736 TTTGAAAAAACGAGGATT
1 TTTGAAAACACGAAAATT
*
11793754 TTTG-AAACACGAAATTTT
1 TTTGAAAACACGAAA-ATT
*
11793772 TTTGAAAACACGAAATTT
1 TTTGAAAACACGAAAATT
11793790 TTTGAAAGAC-CG-AAATT
1 TTTGAAA-ACACGAAAATT
**
11793807 TTTGAAAACACGGAATTTTT
1 TTTGAAAACAC-GAA-AATT
*
11793827 TTCTGAAAACAAGAAAATT
1 TT-TGAAAACACGAAAATT
* **
11793846 TTTG-AAATACGGGAATT
1 TTTGAAAACACGAAAATT
*
11793863 TTTGAAAACACGGGAAATTTT
1 TTTGAAAACAC--GAAA-ATT
*
11793884 TTTGAAAACGCGAAAATT
1 TTTGAAAACACGAAAATT
11793902 TTTG-AAACAC-AAAATT
1 TTTGAAAACACGAAAATT
11793918 TT
1 TT
11793920 GTTTTAAAAA
Statistics
Matches: 352, Mismatches: 60, Indels: 73
0.73 0.12 0.15
Matches are distributed among these distances:
14 4 0.01
15 3 0.01
16 19 0.05
17 104 0.30
18 137 0.39
19 46 0.13
20 19 0.05
21 20 0.06
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (18 bp):
TTTGAAAACACGAAAATT
Found at i:11793641 original size:71 final size:72
Alignment explanation
Indices: 11793418--11793919 Score: 310
Period size: 71 Copynumber: 7.0 Consensus size: 72
11793408 GAGAATTTTG
* * **
11793418 TTTT-AAAACACGAAGATTTTTTAAACA-ATTATTTTCTTTGAAAACACGAAAAATTTTTAAAAC
1 TTTTGAAAACACGAAAATTTTTAAAACACAAAATTTTCTTTGAAAACACG-AAAATTTTTAAAAC
11793481 ACGAGAAT
65 ACGAGAAT
* * * *
11793489 TTTAG-AGACACGAAAATTCTTAAAAACACGAAAA--TT-TTTGAAAACACGGAAATTTTTAAAA
1 TTTTGAAAACACGAAAATT-TTTAAAACAC-AAAATTTTCTTTGAAAACACGAAAATTTTTAAAA
*
11793550 CATGAGAATT
64 CACGAGAA-T
*
11793560 TTTTGAAAACATGAAAATTTTTAAAACACAAAATTTT-TTTGAAAACACGAAAATTTTTAAAACA
1 TTTTGAAAACACGAAAATTTTTAAAACACAAAATTTTCTTTGAAAACACGAAAATTTTTAAAACA
11793624 CCG-GAAT
66 -CGAGAAT
* ** * ** *
11793631 TTTTGAAAACAAGAGGATTTTTGAAACACAAAATTTTCTTTGAAAACACG---ATTTTTTTATCA
1 TTTTGAAAACACGAAAATTTTTAAAACACAAAATTTTCTTTGAAAACACGAAAATTTTTAAAACA
* * *
11793693 CCAAAAA
66 CGAGAAT
* * * * ** * ** *
11793700 TTTTGAAAACATGAAATTTTTTGAAATACTGGAA--TT-TTTGAAAAAACGAGGATTTTTGAAAC
1 TTTTGAAAACACGAAAATTTTTAAAACAC-AAAATTTTCTTTGAAAACACGAAAATTTTTAAAAC
11793762 ACGA-AATTT
65 ACGAGAA--T
* * **
11793771 TTTTGAAAACACGAAATTTTTTGAAAGAC-CGAAA--TT-TTTGAAAACACGGAATTTTTTTCTG
1 TTTTGAAAACACGAAAATTTTT-AAA-ACACAAAATTTTCTTTGAAAACAC-GAA-AATTTT-T-
* *
11793832 AAAACAAGAAAAT
60 AAAACACGAGAAT
* ** * * *
11793845 TTTTG-AAATACGGGAATTTTTGAAAACACGGGAAATTTT-TTTGAAAACGCGAAAATTTTTGAA
1 TTTTGAAAACACGAAAATTTTT-AAAACAC--AAAATTTTCTTTGAAAACACGAAAATTTTTAAA
*
11793908 ACAC-AAAAT
63 ACACGAGAAT
11793917 TTT
1 TTT
11793920 GTTTTAAAAA
Statistics
Matches: 345, Mismatches: 57, Indels: 57
0.75 0.12 0.12
Matches are distributed among these distances:
67 11 0.03
68 3 0.01
69 37 0.11
70 36 0.10
71 110 0.32
72 78 0.23
73 28 0.08
74 10 0.03
75 15 0.04
76 5 0.01
77 12 0.03
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (72 bp):
TTTTGAAAACACGAAAATTTTTAAAACACAAAATTTTCTTTGAAAACACGAAAATTTTTAAAACA
CGAGAAT
Found at i:11793751 original size:104 final size:103
Alignment explanation
Indices: 11793596--11793784 Score: 299
Period size: 104 Copynumber: 1.8 Consensus size: 103
11793586 CACAAAATTT
11793596 TTTTGAAAACACGAAAATTTTTAAAACACCGGAATTTTTGAAAACAAGAGGATTTTTGAAACACA
1 TTTTGAAAACACGAAAATTTTTAAAACACCGGAATTTTTGAAAACAAGAGGATTTTTGAAACACA
11793661 AAATTTTCTTTGAAAACACGATTTTTTTATCACCAAAAA
66 AAATTTT-TTTGAAAACACGATTTTTTTATCACCAAAAA
* * * * *
11793700 TTTTGAAAACATGAAATTTTTTGAAATACTGGAATTTTTGAAAA-AACGAGGATTTTTGAAACAC
1 TTTTGAAAACACGAAAATTTTTAAAACACCGGAATTTTTGAAAACAA-GAGGATTTTTGAAACAC
*
11793764 GAAATTTTTTTGAAAACACGA
65 AAAATTTTTTTGAAAACACGA
11793785 AATTTTTTGA
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
103 15 0.19
104 63 0.81
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (103 bp):
TTTTGAAAACACGAAAATTTTTAAAACACCGGAATTTTTGAAAACAAGAGGATTTTTGAAACACA
AAATTTTTTTGAAAACACGATTTTTTTATCACCAAAAA
Found at i:11794037 original size:18 final size:18
Alignment explanation
Indices: 11794009--11794059 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
11793999 TTTTATTATT
11794009 ATTTTTGAAACACGATAA
1 ATTTTTGAAACACGATAA
*
11794027 A-TTTTGAAAACATGA-AA
1 ATTTTTG-AAACACGATAA
11794044 ATTTTTGAAACACGAT
1 ATTTTTGAAACACGAT
11794060 TAGTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (18 bp):
ATTTTTGAAACACGATAA
Found at i:11794067 original size:18 final size:17
Alignment explanation
Indices: 11794009--11794059 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
11793999 TTTTATTATT
11794009 ATTTTTGAAACACGATA
1 ATTTTTGAAACACGATA
* * *
11794026 AATTTTGAAAACATGAAA
1 ATTTTTG-AAACACGATA
11794044 ATTTTTGAAACACGAT
1 ATTTTTGAAACACGAT
11794060 TAGTTTTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (17 bp):
ATTTTTGAAACACGATA
Found at i:11794769 original size:29 final size:30
Alignment explanation
Indices: 11794737--11794801 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
11794727 GTAAAAGTGC
*
11794737 AATTT-TAGGAAAATATA-GGGCCTAAATGT
1 AATTTATA-GAAAATATAGGGGCCCAAATGT
* *
11794766 AATTTATAGAAAGTTTAGGGGCCCAAATGT
1 AATTTATAGAAAATATAGGGGCCCAAATGT
11794796 AATTTA
1 AATTTA
11794802 CAAATTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 12 0.39
30 19 0.61
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (30 bp):
AATTTATAGAAAATATAGGGGCCCAAATGT
Found at i:11796187 original size:20 final size:20
Alignment explanation
Indices: 11796154--11796210 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
11796144 ATTTTTTCTT
*
11796154 TATTTAGTTA-TTATTTTGAA
1 TATTTA-TTATTTATTTTAAA
11796174 TATTTATTATTTATTCTTAAA
1 TATTTATTATTTATT-TTAAA
*
11796195 T-TTTTTTATTTTATTT
1 TATTTATTA-TTTATTT
11796211 GTTTTTCTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 3 0.09
20 18 0.56
21 11 0.34
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (20 bp):
TATTTATTATTTATTTTAAA
Found at i:11797951 original size:11 final size:11
Alignment explanation
Indices: 11797931--11798008 Score: 60
Period size: 12 Copynumber: 7.4 Consensus size: 11
11797921 ACAAAAATTA
11797931 AAAAAGTATTTT
1 AAAAA-TATTTT
11797943 AAAAATATTTT
1 AAAAATATTTT
11797954 --AAA-A--TT
1 AAAAATATTTT
* * *
11797960 AAAAAAAATTA
1 AAAAATATTTT
11797971 AAAAAGTATTTT
1 AAAAA-TATTTT
11797983 AAAAA-ATTTT
1 AAAAATATTTT
11797993 AAAAAGTATTTT
1 AAAAA-TATTTT
11798005 AAAA
1 AAAA
11798009 TATAAAAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
6 2 0.04
8 4 0.07
9 4 0.07
10 10 0.19
11 12 0.22
12 22 0.41
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:11797975 original size:40 final size:42
Alignment explanation
Indices: 11797905--11797996 Score: 154
Period size: 40 Copynumber: 2.2 Consensus size: 42
11797895 ACCAAAAATT
11797905 TATTTTAAAAATTAAAACAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAACAAAAATTAAAAAAGTATTTTAAAAA
11797948 TATTTTAAAATT-AAA-AAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAACAAAAATTAAAAAAGTATTTTAAAAA
11797988 -ATTTTAAAA
1 TATTTTAAAA
11797997 AGTATTTTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
39 9 0.18
40 25 0.51
41 3 0.06
42 6 0.12
43 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (42 bp):
TATTTTAAAATTAAAACAAAAATTAAAAAAGTATTTTAAAAA
Found at i:11816716 original size:2 final size:2
Alignment explanation
Indices: 11816709--11816734 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11816699 AAAGAAGAAA
11816709 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
11816735 CAAACGAAGA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11821891 original size:31 final size:31
Alignment explanation
Indices: 11821823--11821892 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
11821813 AACTAATAGC
** *
11821823 TTAGTGACTTAAATAAAAACTTTTGAACAGT
1 TTAGTGACTTAAATAAAAACTTTCAAACAAT
* ** *
11821854 TCAGTGACTTAAATGCAAACTTTCAAATAAT
1 TTAGTGACTTAAATAAAAACTTTCAAACAAT
11821885 TTAGTGAC
1 TTAGTGAC
11821893 CAAATTATAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (31 bp):
TTAGTGACTTAAATAAAAACTTTCAAACAAT
Found at i:11824371 original size:31 final size:31
Alignment explanation
Indices: 11824328--11824456 Score: 115
Period size: 30 Copynumber: 4.2 Consensus size: 31
11824318 AAATAAATAC
*
11824328 AAAAAAATTATTTTAAAAAT-TTAAAAAATTT
1 AAAAAAAGTATTTTAAAAATATTAAAAAA-TT
**
11824359 AAAAAAAGTATTTTAAAAATATTTTAAAATT
1 AAAAAAAGTATTTTAAAAATATTAAAAAATT
* **
11824390 AAAAAAA-T-TTTGAAAAAGTATTTTAAAATT
1 AAAAAAAGTATTTTAAAAA-TATTAAAAAATT
* **
11824420 AAAAAAA-T-TTTGAAAAATTATTTTAAAATT
1 AAAAAAAGTATTTTAAAAA-TATTAAAAAATT
11824450 AAAAAAA
1 AAAAAAA
11824457 TAAAAAATAA
Statistics
Matches: 91, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
29 8 0.09
30 49 0.54
31 28 0.31
32 6 0.07
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (31 bp):
AAAAAAAGTATTTTAAAAATATTAAAAAATT
Found at i:11824395 original size:41 final size:43
Alignment explanation
Indices: 11824330--11824417 Score: 135
Period size: 41 Copynumber: 2.1 Consensus size: 43
11824320 ATAAATACAA
*
11824330 AAAAATTATTTTAAAAATTTAAAAAATTTAAAAAAAGTATTTT
1 AAAAATTATTTTAAAAATTAAAAAAATTTAAAAAAAGTATTTT
**
11824373 AAAAA-TATTTT-AAAATTAAAAAAATTTTGAAAAAGTATTTT
1 AAAAATTATTTTAAAAATTAAAAAAATTTAAAAAAAGTATTTT
11824414 AAAA
1 AAAA
11824418 TTAAAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
41 31 0.74
42 6 0.14
43 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (43 bp):
AAAAATTATTTTAAAAATTAAAAAAATTTAAAAAAAGTATTTT
Found at i:11824412 original size:30 final size:29
Alignment explanation
Indices: 11824352--11824457 Score: 158
Period size: 30 Copynumber: 3.5 Consensus size: 29
11824342 AAAAATTTAA
*
11824352 AAAATTTAAAAAAAGTATTTTAAAAATATTTT
1 AAAA-TTAAAAAAA-T-TTTGAAAAATATTTT
11824384 AAAATTAAAAAAATTTTGAAAAAGTATTTT
1 AAAATTAAAAAAATTTTGAAAAA-TATTTT
11824414 AAAATTAAAAAAATTTTGAAAAATTATTTT
1 AAAATTAAAAAAATTTTGAAAAA-TATTTT
11824444 AAAATTAAAAAAAT
1 AAAATTAAAAAAAT
11824458 AAAAAATAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
29 8 0.11
30 50 0.70
31 9 0.13
32 4 0.06
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (29 bp):
AAAATTAAAAAAATTTTGAAAAATATTTT
Found at i:11824417 original size:12 final size:11
Alignment explanation
Indices: 11824330--11824387 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
11824320 ATAAATACAA
11824330 AAAAATTATTTT
1 AAAAA-TATTTT
11824342 -AAAA-A-TTT
1 AAAAATATTTT
*
11824350 AAAAA-ATTTAA
1 AAAAATATTT-T
11824361 AAAAAGTATTTT
1 AAAAA-TATTTT
11824373 AAAAATATTTT
1 AAAAATATTTT
11824384 AAAA
1 AAAA
11824388 TTAAAAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
8 3 0.08
9 6 0.15
10 2 0.05
11 19 0.49
12 5 0.13
13 4 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:11828089 original size:20 final size:20
Alignment explanation
Indices: 11828064--11828137 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 20
11828054 CGTAAAATGA
11828064 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGTTTTACT
*
11828084 TTTCTGTAAAATG----A--
1 TTTCTGGAAAATGTTTTACT
11828098 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGTTTTACT
* *
11828118 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGTTTTACT
11828138 GGAAAATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
14 12 0.27
16 1 0.02
18 1 0.02
20 30 0.68
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (20 bp):
TTTCTGGAAAATGTTTTACT
Found at i:11828093 original size:34 final size:34
Alignment explanation
Indices: 11828049--11828149 Score: 175
Period size: 34 Copynumber: 2.9 Consensus size: 34
11828039 CAGTGAAATG
*
11828049 TTTTCCGTAAAATGATTTCTGGAAAATGTTTTAC
1 TTTTCTGTAAAATGATTTCTGGAAAATGTTTTAC
11828083 TTTTCTGTAAAATGATTTCTGGAAAATGTTTTAC
1 TTTTCTGTAAAATGATTTCTGGAAAATGTTTTAC
*
11828117 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCTGTAAAATGATTT-CTGGAAAATGTTTT
11828150 CTGGTGTTTG
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
34 51 0.80
35 13 0.20
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.47
Consensus pattern (34 bp):
TTTTCTGTAAAATGATTTCTGGAAAATGTTTTAC
Found at i:11828153 original size:14 final size:15
Alignment explanation
Indices: 11828044--11828153 Score: 57
Period size: 14 Copynumber: 6.9 Consensus size: 15
11828034 ATTGGCAGTG
* *
11828044 AAATG-TTTTCCGTA
1 AAATGATTTTCTGGA
11828058 AAATGA-TTTCTGGA
1 AAATGATTTTCTGGA
*
11828072 AAATGTTTTACTTTTCTGTA
1 AAATG----A-TTTTCTGGA
11828092 AAATGA-TTTCTGGA
1 AAATGATTTTCTGGA
*
11828106 AAATGTTTTACTTTTCTGTA
1 AAATG----A-TTTTCTGGA
*
11828126 AAATGATTTACTGGA
1 AAATGATTTTCTGGA
11828141 AAAT-ATTTTCTGG
1 AAATGATTTTCTGG
11828154 TGTTTGATTG
Statistics
Matches: 75, Mismatches: 8, Indels: 26
0.69 0.07 0.24
Matches are distributed among these distances:
14 36 0.48
15 11 0.15
16 2 0.03
18 2 0.03
20 24 0.32
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (15 bp):
AAATGATTTTCTGGA
Found at i:11828261 original size:20 final size:20
Alignment explanation
Indices: 11828236--11828274 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
11828226 GTTTTTACAT
11828236 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
11828256 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
11828275 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:11830547 original size:11 final size:11
Alignment explanation
Indices: 11830531--11830556 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11830521 AACCATCTGT
11830531 ATATAACCAAA
1 ATATAACCAAA
11830542 ATATAACCAAA
1 ATATAACCAAA
11830553 ATAT
1 ATAT
11830557 CATCCAGCAA
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:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (11 bp):
ATATAACCAAA
Found at i:11830792 original size:25 final size:25
Alignment explanation
Indices: 11830744--11830793 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
11830734 AGAAGAGAAG
*
11830744 ATGAAGAACAGAAGGAGAAAAAGGA
1 ATGAAGAACAGAAGAAGAAAAAGGA
* *
11830769 ATGAAGAACGGAAGAAGAAGAAGGA
1 ATGAAGAACAGAAGAAGAAAAAGGA
11830794 GCCTTACCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.58, C:0.04, G:0.34, T:0.04
Consensus pattern (25 bp):
ATGAAGAACAGAAGAAGAAAAAGGA
Found at i:11830903 original size:24 final size:24
Alignment explanation
Indices: 11830853--11830904 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
11830843 TTTGCAGCCC
* * **
11830853 AAGGGGAAGGGAAAATGGGAGGGG
1 AAGGGAAAGGGAAAAGGGGAGAAG
*
11830877 AAGGGAAAGGGGAAAGGGGAGAAG
1 AAGGGAAAGGGAAAAGGGGAGAAG
11830901 AAGG
1 AAGG
11830905 CATCATTCCG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.56, T:0.02
Consensus pattern (24 bp):
AAGGGAAAGGGAAAAGGGGAGAAG
Found at i:11831303 original size:37 final size:37
Alignment explanation
Indices: 11831253--11831329 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
11831243 ATGTTGAGAA
* *
11831253 AAATGGAAAGCATTGTGTACTTCTGTCTTTCGAAATC
1 AAATGGAAAGCATTGTGCACTTCTGTCTTTCAAAATC
*
11831290 AAATGGAAAGCATTGTGCACTTTTGTCTTTCAAAATC
1 AAATGGAAAGCATTGTGCACTTCTGTCTTTCAAAATC
11831327 AAA
1 AAA
11831330 CTCTGCGTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (37 bp):
AAATGGAAAGCATTGTGCACTTCTGTCTTTCAAAATC
Found at i:11840886 original size:30 final size:31
Alignment explanation
Indices: 11840847--11840906 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
11840837 GGAGGTGAGA
*
11840847 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
11840878 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
11840907 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:11841217 original size:9 final size:9
Alignment explanation
Indices: 11841200--11841229 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
11841190 TCGAGTTGAT
11841200 TCGAATAAC
1 TCGAATAAC
*
11841209 TCGATTAAC
1 TCGAATAAC
11841218 TCGAATAAC
1 TCGAATAAC
11841227 TCG
1 TCG
11841230 CTTCGTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (9 bp):
TCGAATAAC
Found at i:11841792 original size:18 final size:19
Alignment explanation
Indices: 11841769--11841816 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
11841759 CAAATATATG
*
11841769 ATAAAAAG-AAATCAACAA
1 ATAAAAAGTAAATAAACAA
*
11841787 AT-AAAAGTAAATAAATAA
1 ATAAAAAGTAAATAAACAA
*
11841805 ATAAAAATTAAA
1 ATAAAAAGTAAA
11841817 GCACTTAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 5 0.20
18 12 0.48
19 8 0.32
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (19 bp):
ATAAAAAGTAAATAAACAA
Found at i:11842193 original size:3 final size:3
Alignment explanation
Indices: 11842185--11842219 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
11842175 AGTGAAGATG
11842185 ATA ATA ATA A-A TATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA AT
11842220 GTTAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 28 0.93
4 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:11844190 original size:27 final size:27
Alignment explanation
Indices: 11844159--11844363 Score: 252
Period size: 27 Copynumber: 7.6 Consensus size: 27
11844149 ATATTGAGTC
* * *
11844159 CGCACACTCAGTGCTATATCA-TCAACT
1 CGCACACTTAGTGCTACAT-AGTCAAAT
* *
11844186 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
11844213 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
11844241 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
11844268 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
11844295 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
11844322 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
11844349 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
11844364 GTACAATTTA
Statistics
Matches: 156, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
26 1 0.01
27 131 0.84
28 24 0.15
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:11847890 original size:3 final size:3
Alignment explanation
Indices: 11847884--11847939 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
11847874 TTATTATTAT
11847884 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
11847932 TAG TAG TA
1 TAG TAG TA
11847940 TTAATATTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:11848894 original size:40 final size:40
Alignment explanation
Indices: 11848827--11848902 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
11848817 ACAAAAAATC
* *
11848827 GAGCATTAGCGGTGATTTAGCCAAAGCGCTGCTAAAGGTA
1 GAGCATTAGCGGCGATTTAGCCAAAGCGCCGCTAAAGGTA
* *
11848867 GAGCATTAGCGGCGA-TTATCCGGAAGCGCCGCTAAA
1 GAGCATTAGCGGCGATTTAGCC-AAAGCGCCGCTAAA
11848903 AATAGGAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 5 0.16
40 26 0.84
ACGTcount: A:0.29, C:0.21, G:0.30, T:0.20
Consensus pattern (40 bp):
GAGCATTAGCGGCGATTTAGCCAAAGCGCCGCTAAAGGTA
Found at i:11849047 original size:41 final size:41
Alignment explanation
Indices: 11848982--11849196 Score: 243
Period size: 41 Copynumber: 5.2 Consensus size: 41
11848972 TTTTTTAAAC
* * *
11848982 CTTTAGCGGCGTTTTTGTGTAAGCGTCGCTAATGCTCCGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
* **
11849023 CTTTCGCGGCGTTTTTGTGAAAGCGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
* * * ** * *
11849064 CTTTAGCTGTGTTTTTGTCTATGCGTTGCTAATTCTCAGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
* * *
11849105 CTTTAGCAGCGTTTTTGTCTATGCGCCGCTAATGCTCGGGT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
* * *
11849146 CTTTAGCGGCGTTTTTATAC-AAGCGCTGCTAATTCTCGGAT
1 CTTTAGCGGCGTTTTTGT-CTAAGCGCCGCTAATGCTCGGAT
11849187 CTTTAGCGGC
1 CTTTAGCGGC
11849197 ATTTCTAACT
Statistics
Matches: 146, Mismatches: 27, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
41 145 0.99
42 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
Found at i:11849212 original size:41 final size:40
Alignment explanation
Indices: 11848982--11849221 Score: 169
Period size: 41 Copynumber: 5.8 Consensus size: 40
11848972 TTTTTTAAAC
*** * * *
11848982 CTTTAGCGGCGTTTTTGTGTAAGCGTCGCTAATGCTCCGAT
1 CTTTAGCGGCGTTTTTAACT-AGCGCCGCTAATTCTCGGAT
* *
11849023 CTTTCGCGGCGTTTTTGTGAA--AGCGCCGCTAATGCTCGGAT
1 CTTTAGCGGCG-TTTT-T-AACTAGCGCCGCTAATTCTCGGAT
* * ** ** *
11849064 CTTTAGCTGTGTTTTTGTCTATGCGTTGCTAATTCTCAGAT
1 CTTTAGCGGCGTTTTTAACTA-GCGCCGCTAATTCTCGGAT
* ** * *
11849105 CTTTAGCAGCGTTTTTGTCTATGCGCCGCTAATGCTCGGGT
1 CTTTAGCGGCGTTTTTAACTA-GCGCCGCTAATTCTCGGAT
* *
11849146 CTTTAGCGGCGTTTTTATACAAGCGCTGCTAATTCTCGGAT
1 CTTTAGCGGCGTTTTTA-ACTAGCGCCGCTAATTCTCGGAT
* * *
11849187 CTTTAGCGGCATTTCTAACTGAGCGCCACTAATTC
1 CTTTAGCGGCGTTTTTAACT-AGCGCCGCTAATTC
11849222 GCTTGTCTTC
Statistics
Matches: 158, Mismatches: 33, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
39 1 0.01
40 7 0.04
41 143 0.91
42 6 0.04
43 1 0.01
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (40 bp):
CTTTAGCGGCGTTTTTAACTAGCGCCGCTAATTCTCGGAT
Found at i:11849213 original size:82 final size:81
Alignment explanation
Indices: 11849044--11849219 Score: 201
Period size: 82 Copynumber: 2.1 Consensus size: 81
11849034 TTTTTGTGAA
* * * * *
11849044 AGCGCCGCTAATGCTCGGATCTTTAGCTGTGTTTTTGTCTATGCGTTGCTAATTCTCAGATCTTT
1 AGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTATCTAAGCGCTGCTAATTCTCAGATCTTT
* * **
11849109 AGCAGCGTTTTTGTCT
66 AGCAGCATTTCTAACT
* *
11849125 ATGCGCCGCTAATGCTCGGGTCTTTAGCGGCGTTTTTATAC-AAGCGCTGCTAATTCTCGGATCT
1 A-GCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTAT-CTAAGCGCTGCTAATTCTCAGATCT
*
11849189 TTAGCGGCATTTCTAACT
64 TTAGCAGCATTTCTAACT
*
11849207 GAGCGCCACTAAT
1 -AGCGCCGCTAAT
11849220 TCGCTTGTCT
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
81 1 0.01
82 76 0.96
83 2 0.03
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (81 bp):
AGCGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTATCTAAGCGCTGCTAATTCTCAGATCTTT
AGCAGCATTTCTAACT
Found at i:11849219 original size:123 final size:123
Alignment explanation
Indices: 11848982--11849261 Score: 278
Period size: 123 Copynumber: 2.3 Consensus size: 123
11848972 TTTTTTAAAC
* * * * *
11848982 CTTTAGCGGCGTTTTTGTGTAAGCGTCGCTAATGCTCCGATCTTTCGCGGCGTTTTTGTGAAAGC
1 CTTTAGCAGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGATCTTTAGCGGCGTTTTTATGAAAGC
* ** * ** ***
11849047 GCCGCTAATGCTCGGATCTTTAGCTGTGTTTTTGTCTATGCGTTGCTAATTCTCAGAT
66 GCCGCTAATGCTCGGATCTTTAGCGGCATTTCTAACTATGCGCCACTAATTCTCAGAT
* * *
11849105 CTTTAGCAGCGTTTTTGTCTATGCGCCGCTAATGCTCGGGTCTTTAGCGGCGTTTTTAT-ACAAG
1 CTTTAGCAGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGATCTTTAGCGGCGTTTTTATGA-AAG
* * * *
11849169 CGCTGCTAATTCTCGGATCTTTAGCGGCATTTCTAACTGA-GCGCCACTAATTCGCTTG-T
65 CGCCGCTAATGCTCGGATCTTTAGCGGCATTTCTAACT-ATGCGCCACTAATTCTC-AGAT
* * * * *
11849228 CTTCAGCAGCATTTGTATTTAAGCGCCGCTAATG
1 CTTTAGCAGCGTTTTTGTCTAAGCGCCGCTAATG
11849262 TATTTACCTT
Statistics
Matches: 127, Mismatches: 27, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
122 1 0.01
123 124 0.98
124 2 0.02
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.37
Consensus pattern (123 bp):
CTTTAGCAGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGATCTTTAGCGGCGTTTTTATGAAAGC
GCCGCTAATGCTCGGATCTTTAGCGGCATTTCTAACTATGCGCCACTAATTCTCAGAT
Found at i:11849800 original size:15 final size:15
Alignment explanation
Indices: 11849779--11849816 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
11849769 TTTAAGGTTA
11849779 ATTTAGGGGTTAGAG
1 ATTTAGGGGTTAGAG
* *
11849794 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTAGAG
11849809 ATTTAGGG
1 ATTTAGGG
11849817 TTAATTTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTAGAG
Found at i:11850099 original size:14 final size:14
Alignment explanation
Indices: 11850080--11850106 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11850070 ATTTTTTTGA
11850080 TATATATATATGGC
1 TATATATATATGGC
11850094 TATATATATATGG
1 TATATATATATGG
11850107 TTAATTAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (14 bp):
TATATATATATGGC
Found at i:11851219 original size:37 final size:37
Alignment explanation
Indices: 11851149--11851220 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
11851139 AAAATTTGAT
*
11851149 TTTAGGGGTTGGGGGGATTTAGGGTTTAAGGGTTATGC
1 TTTAGGGGTTGAGGGGATTTAGGG-TTAAGGGTTATGC
11851187 TTTAGGGGTT-AGGGGATTTAAGGG-TAATGGGTTA
1 TTTAGGGGTTGAGGGGATTT-AGGGTTAA-GGGTTA
11851221 GGGGGTTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
36 3 0.10
37 14 0.45
38 14 0.45
ACGTcount: A:0.19, C:0.01, G:0.43, T:0.36
Consensus pattern (37 bp):
TTTAGGGGTTGAGGGGATTTAGGGTTAAGGGTTATGC
Found at i:11854272 original size:6 final size:6
Alignment explanation
Indices: 11854263--11854293 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
11854253 TAAAAAATTA
11854263 AAATAT AAATAT AAATAT AAATAT AAGATAT
1 AAATAT AAATAT AAATAT AAATAT AA-ATAT
11854294 TACATAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:11854346 original size:31 final size:31
Alignment explanation
Indices: 11854292--11855133 Score: 714
Period size: 31 Copynumber: 28.8 Consensus size: 31
11854282 AATATAAGAT
*
11854292 ATTACATAACTTACATTAGTTAATATACATAA
1 ATTACATAACTTA-ATTAATTAATATACATAA
*
11854324 ATTACATAACTTAGTTAATTAATAT---T--
1 ATTACATAACTTAATTAATTAATATACATAA
*
11854350 A-TACATAACTTACATTAA-TATTATACAT-A
1 ATTACATAACTTA-ATTAATTAATATACATAA
* *
11854379 ATTACATAACTTAGTTATTTAATAT---T--
1 ATTACATAACTTAATTAATTAATATACATAA
*
11854405 A-TACATAACTTACATTAA-TATTATACATAA
1 ATTACATAACTTA-ATTAATTAATATACATAA
*
11854435 ATTACATAACTTAGTTAATTAATAT---T--
1 ATTACATAACTTAATTAATTAATATACATAA
*
11854461 A-TACATAACTTACATTAA-TATTATACATAA
1 ATTACATAACTTA-ATTAATTAATATACATAA
*
11854491 ATTACATAACTTAATTAGTTAATATACATAA
1 ATTACATAACTTAATTAATTAATATACATAA
* *
11854522 ATTACATAACATACATTAA-TATTATACATAA
1 ATTACATAACTTA-ATTAATTAATATACATAA
* *
11854553 ATTACATAACTTAGTTATTTAATAT---T--
1 ATTACATAACTTAATTAATTAATATACATAA
*
11854579 A-TACATAACTTACATTAA-TATTATACATAA
1 ATTACATAACTTA-ATTAATTAATATACATAA
*
11854609 ATTACATAACTTAATTAGTTAATATACATAA
1 ATTACATAACTTAATTAATTAATATACATAA
* *
11854640 ATTACATAACATAATTAGTTAATATACATAA
1 ATTACATAACTTAATTAATTAATATACATAA
* *
11854671 ATTACATAACATAATTAGTTAATATACATAA
1 ATTACATAACTTAATTAATTAATATACATAA
*
11854702 ATTACATAACTTAATTAGTTAATATACATAA
1 ATTACATAACTTAATTAATTAATATACATAA
* *
11854733 ATTACATAACTTAATTAGTTATTATACATAA
1 ATTACATAACTTAATTAATTAATATACATAA
*
11854764 ATTACATAACTTAATTAGTTAATTATACATAA
1 ATTACATAACTTAATTAATTAA-TATACATAA
* * *
11854796 ATTACATAACATACATTAA-TATTATACAGAA
1 ATTACATAACTTA-ATTAATTAATATACATAA
* *
11854827 ATTACATAACTTAGTTATTTAATAT---T--
1 ATTACATAACTTAATTAATTAATATACATAA
* *
11854853 A-TACATAACTTAGTTATTTAATAT---T--
1 ATTACATAACTTAATTAATTAATATACATAA
*
11854878 A-TACATAACTTACATTAA-TATTATACATAA
1 ATTACATAACTTA-ATTAATTAATATACATAA
*
11854908 ATTACATAACTTAGTTAATTAATAT---T--
1 ATTACATAACTTAATTAATTAATATACATAA
*
11854934 A-TACATAACTTACATTAA-TATTATACATAA
1 ATTACATAACTTA-ATTAATTAATATACATAA
* * *
11854964 ATTACATAACATACATTAA-TATTATACAGAA
1 ATTACATAACTTA-ATTAATTAATATACATAA
* * *
11854995 ATTACATAACTTAGTTATTTAATAT--AT-T
1 ATTACATAACTTAATTAATTAATATACATAA
*
11855023 A-TACATAACTTACATTAA-TATTATACATAA
1 ATTACATAACTTA-ATTAATTAATATACATAA
* *
11855053 ATTACATAACTTAGTTATTTAATAT---T--
1 ATTACATAACTTAATTAATTAATATACATAA
*
11855079 A-TACATAACTTACATTAA-TATTATACATAA
1 ATTACATAACTTA-ATTAATTAATATACATAA
* *
11855109 ATTACATAACTTAGTTATTTAATAT
1 ATTACATAACTTAATTAATTAATAT
11855134 TATACATAAC
Statistics
Matches: 675, Mismatches: 69, Indels: 133
0.77 0.08 0.15
Matches are distributed among these distances:
25 137 0.20
26 31 0.05
27 17 0.03
28 16 0.02
29 7 0.01
30 54 0.08
31 369 0.55
32 40 0.06
33 4 0.01
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (31 bp):
ATTACATAACTTAATTAATTAATATACATAA
Found at i:11854369 original size:22 final size:21
Alignment explanation
Indices: 11854341--11854385 Score: 81
Period size: 22 Copynumber: 2.1 Consensus size: 21
11854331 AACTTAGTTA
11854341 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAA-TTAC
11854363 ATTAATATTATACATAATTAC
1 ATTAATATTATACATAATTAC
11854384 AT
1 AT
11854386 AACTTAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTAATATTATACATAATTAC
Found at i:11854422 original size:22 final size:22
Alignment explanation
Indices: 11854397--11854441 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
11854387 ACTTAGTTAT
*
11854397 TTAATATTATACATAACTTACA
1 TTAATATTATACATAAATTACA
11854419 TTAATATTATACATAAATTACA
1 TTAATATTATACATAAATTACA
11854441 T
1 T
11854442 AACTTAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAATATTATACATAAATTACA
Found at i:11854472 original size:25 final size:25
Alignment explanation
Indices: 11854326--11854434 Score: 107
Period size: 25 Copynumber: 4.3 Consensus size: 25
11854316 ATACATAAAT
11854326 TACATAACTTAGTTAATTAATATTA
1 TACATAACTTAGTTAATTAATATTA
* * *
11854351 TACATAACTTACATTAATATTATACATAA
1 TACATAACTTA-GTT-A-ATTA-ATATTA
*
11854380 TTACATAACTTAGTTATTTAATATTA
1 -TACATAACTTAGTTAATTAATATTA
*
11854406 TACATAACTTA---CATTAATATTA
1 TACATAACTTAGTTAATTAATATTA
11854428 TACATAA
1 TACATAA
11854435 ATTACATAAC
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
22 16 0.23
25 22 0.31
26 6 0.09
27 4 0.06
28 5 0.07
29 6 0.09
30 11 0.16
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (25 bp):
TACATAACTTAGTTAATTAATATTA
Found at i:11854480 original size:22 final size:22
Alignment explanation
Indices: 11854452--11854559 Score: 88
Period size: 22 Copynumber: 5.1 Consensus size: 22
11854442 AACTTAGTTA
*
11854452 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAAATTAC
11854474 ATTAATATTATACATAAATTAC
1 ATTAATATTATACATAAATTAC
* * *
11854496 A-TAACT-TAATTA-GTTAATATAC
1 ATTAA-TATTA-TACATAAAT-TAC
11854518 A-TAA-A-T-TACATAACA-TAC
1 ATTAATATTATACATAA-ATTAC
11854536 ATTAATATTATACATAAATTAC
1 ATTAATATTATACATAAATTAC
11854558 AT
1 AT
11854560 AACTTAGTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 22
0.70 0.07 0.23
Matches are distributed among these distances:
18 6 0.09
19 5 0.07
20 2 0.03
21 11 0.16
22 44 0.65
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (22 bp):
ATTAATATTATACATAAATTAC
Found at i:11854599 original size:22 final size:22
Alignment explanation
Indices: 11854571--11854615 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
11854561 ACTTAGTTAT
*
11854571 TTAATATTATACATAACTTACA
1 TTAATATTATACATAAATTACA
11854593 TTAATATTATACATAAATTACA
1 TTAATATTATACATAAATTACA
11854615 T
1 T
11854616 AACTTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAATATTATACATAAATTACA
Found at i:11854898 original size:22 final size:22
Alignment explanation
Indices: 11854845--11854914 Score: 95
Period size: 22 Copynumber: 3.0 Consensus size: 22
11854835 ACTTAGTTAT
*
11854845 TTAATATTATACATAACTTAGTTA
1 TTAATATTATACATAACTTA--CA
11854869 TTTAATATTATACATAACTTACA
1 -TTAATATTATACATAACTTACA
*
11854892 TTAATATTATACATAAATTACA
1 TTAATATTATACATAACTTACA
11854914 T
1 T
11854915 AACTTAGTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
22 22 0.51
23 1 0.02
25 20 0.47
ACGTcount: A:0.44, C:0.10, G:0.01, T:0.44
Consensus pattern (22 bp):
TTAATATTATACATAACTTACA
Found at i:11854945 original size:25 final size:25
Alignment explanation
Indices: 11854829--11854907 Score: 128
Period size: 25 Copynumber: 3.3 Consensus size: 25
11854819 ATACAGAAAT
11854829 TACATAACTTAGTTATTTAATATTA
1 TACATAACTTAGTTATTTAATATTA
11854854 TACATAACTTAGTTATTTAATATTA
1 TACATAACTTAGTTATTTAATATTA
*
11854879 TACATAACTTA--CA-TTAATATTA
1 TACATAACTTAGTTATTTAATATTA
11854901 TACATAA
1 TACATAA
11854908 ATTACATAAC
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
22 16 0.30
23 1 0.02
25 36 0.68
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (25 bp):
TACATAACTTAGTTATTTAATATTA
Found at i:11854953 original size:22 final size:22
Alignment explanation
Indices: 11854925--11855059 Score: 86
Period size: 22 Copynumber: 6.1 Consensus size: 22
11854915 AACTTAGTTA
11854925 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAACTTAC
*
11854947 ATTAATATTATACATAAATTAC
1 ATTAATATTATACATAACTTAC
* * *
11854969 A-TAACATACATTA-AT-ATTATAC
1 ATTAATAT-TA-TACATAACT-TAC
* *
11854991 A-GAA-A-T-TACATAACTTAGTT
1 ATTAATATTATACATAACTTA--C
11855011 ATTTAATATATTATACATAACTTAC
1 A-TT-A-ATATTATACATAACTTAC
*
11855036 ATTAATATTATACATAAATTAC
1 ATTAATATTATACATAACTTAC
11855058 AT
1 AT
11855060 AACTTAGTTA
Statistics
Matches: 88, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
17 2 0.02
18 4 0.05
19 2 0.02
20 1 0.01
21 8 0.09
22 50 0.57
23 4 0.05
24 3 0.03
25 2 0.02
26 1 0.01
27 11 0.12
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.40
Consensus pattern (22 bp):
ATTAATATTATACATAACTTAC
Found at i:11855099 original size:22 final size:22
Alignment explanation
Indices: 11855071--11855115 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
11855061 ACTTAGTTAT
*
11855071 TTAATATTATACATAACTTACA
1 TTAATATTATACATAAATTACA
11855093 TTAATATTATACATAAATTACA
1 TTAATATTATACATAAATTACA
11855115 T
1 T
11855116 AACTTAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAATATTATACATAAATTACA
Found at i:11855104 original size:56 final size:57
Alignment explanation
Indices: 11854609--11855148 Score: 461
Period size: 56 Copynumber: 9.3 Consensus size: 57
11854599 TTATACATAA
* * * * *
11854609 ATTACATAACTTA-ATTAGTTAATATACATAAATTACATAACATAATTAGTTAATATACAT
1 ATTACATAACTTACATTA-ATATTATACATAAATTACATAACTTAGTTATTTAATAT---T
* * * * *
11854669 AAATTACATAACATA-ATTAGTTAATATACATAAATTACATAACTTAATTAGTTAATATACAT
1 --ATTACATAACTTACATTA-ATATTATACATAAATTACATAACTTAGTTATTTAATAT---T
* * *
11854731 AAATTACATAACTTA-ATTAGTTATTATACATAAATTACATAACTTAATTAGTTAATTATACAT
1 --ATTACATAACTTACATTA-ATATTATACATAAATTACATAACTTAGTTATTTAA-TAT---T
* *
11854794 AAATTACATAACATACATTAATATTATACAGAAATTACATAACTTAGTTATTTAATATT
1 --ATTACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTATTTAATATT
* * *
11854853 A-TACATAACTTAGTTATTTAATATTATACATAACTTACATTAA--TA-TTA--TACATA-A
1 ATTACATAACTTA--CA-TTAATATTATACATAAATTACA-TAACTTAGTTATTTA-ATATT
* * *
11854908 ATTACATAACTTAGTTAATTAATATTATACATAACTTACATTAA--TA-TTA--TACATA-A
1 ATTACATAACTTA---CATTAATATTATACATAAATTACA-TAACTTAGTTATTTA-ATATT
* *
11854964 ATTACATAACATACATTAATATTATACAGAAATTACATAACTTAGTTATTTAATA-T
1 ATTACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTATTTAATATT
11855020 ATTATACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTATTTAATATT
1 A-T-TACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTATTTAATATT
11855079 A-TACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTATTTAATATT
1 ATTACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTATTTAATATT
11855135 A-TACATAACTTACA
1 ATTACATAACTTACA
11855149 ACTTACATAA
Statistics
Matches: 438, Mismatches: 23, Indels: 40
0.87 0.05 0.08
Matches are distributed among these distances:
52 3 0.01
53 21 0.05
54 2 0.00
55 6 0.01
56 147 0.34
57 9 0.02
58 54 0.12
59 23 0.05
60 3 0.01
62 114 0.26
63 52 0.12
64 4 0.01
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.40
Consensus pattern (57 bp):
ATTACATAACTTACATTAATATTATACATAAATTACATAACTTAGTTATTTAATATT
Found at i:11855160 original size:9 final size:9
Alignment explanation
Indices: 11855136--11855237 Score: 53
Period size: 9 Copynumber: 12.3 Consensus size: 9
11855126 TTTAATATTA
11855136 TACATAACT
1 TACATAACT
11855145 TAC--AACT
1 TACATAACT
11855152 TACATAACT
1 TACATAACT
**
11855161 TACATATTTT
1 TACATA-ACT
*
11855171 TA-ATTA-T
1 TACATAACT
* *
11855178 T-CGTAAAT
1 TACATAACT
11855186 TACATAACT
1 TACATAACT
*
11855195 TACATAATT
1 TACATAACT
*
11855204 TTCATAA--
1 TACATAACT
*
11855211 TAAATAACT
1 TACATAACT
11855220 TACATAA--
1 TACATAACT
11855227 -ACATAACT
1 TACATAACT
11855235 TAC
1 TAC
11855238 GTAGCTTAAT
Statistics
Matches: 69, Mismatches: 13, Indels: 22
0.66 0.12 0.21
Matches are distributed among these distances:
6 6 0.09
7 16 0.23
8 2 0.03
9 42 0.61
10 3 0.04
ACGTcount: A:0.44, C:0.17, G:0.01, T:0.38
Consensus pattern (9 bp):
TACATAACT
Found at i:11855168 original size:34 final size:33
Alignment explanation
Indices: 11855093--11855168 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 33
11855083 ATAACTTACA
* * *
11855093 TTAATATTATACATAAATTACATAACTTAGTTAT
1 TTAATATTATACATAAATTACA-AACTTAATAAC
*
11855127 TTAATATTATACATAACTTAC-AACTTACATAAC
1 TTAATATTATACATAAATTACAAACTTA-ATAAC
11855160 TTACATATT
1 TTA-ATATT
11855169 TTTAATTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
32 6 0.17
33 5 0.14
34 25 0.69
ACGTcount: A:0.43, C:0.13, G:0.01, T:0.42
Consensus pattern (33 bp):
TTAATATTATACATAAATTACAAACTTAATAAC
Found at i:11855177 original size:41 final size:42
Alignment explanation
Indices: 11855115--11855201 Score: 88
Period size: 41 Copynumber: 2.1 Consensus size: 42
11855105 ATAAATTACA
** *
11855115 TAACTTAGTTATTTAATATTATACATAACTTAC-AACTTACA
1 TAACTTACATATTTAATATTATACATAAATTACAAACTTACA
* * *
11855156 TAACTTACATATTT-TTAATTATTCGTAAATTACATAACTTACA
1 TAACTTACATATTTAAT-ATTATACATAAATTACA-AACTTACA
11855199 TAA
1 TAA
11855202 TTTTCATAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
40 1 0.03
41 25 0.68
43 11 0.30
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (42 bp):
TAACTTACATATTTAATATTATACATAAATTACAAACTTACA
Found at i:11855223 original size:34 final size:34
Alignment explanation
Indices: 11855148--11855226 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
11855138 CATAACTTAC
* * ***
11855148 AACTTACATAACTTACATATTTTTAATTATTCGT
1 AACTTACATAACTTACATAATTTTAATAATAAAT
* *
11855182 AAATTACATAACTTACATAATTTTCATAATAAAT
1 AACTTACATAACTTACATAATTTTAATAATAAAT
11855216 AACTTACATAA
1 AACTTACATAA
11855227 ACATAACTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.41
Consensus pattern (34 bp):
AACTTACATAACTTACATAATTTTAATAATAAAT
Found at i:11860742 original size:66 final size:66
Alignment explanation
Indices: 11860659--11860785 Score: 204
Period size: 66 Copynumber: 1.9 Consensus size: 66
11860649 GAGGCAACAT
11860659 CGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAACTGAAAGCAGATGCAG
1 CGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCAGC-AGCAACTGAAAGCAGATGCAG
11860722 TAG
64 TAG
* *
11860725 CGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAGCTTAAAGCAGATGC
1 CGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTGAAAGCAGATGC
11860786 GACAGCAAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
65 1 0.02
66 51 0.89
67 5 0.09
ACGTcount: A:0.41, C:0.18, G:0.26, T:0.15
Consensus pattern (66 bp):
CGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTGAAAGCAGATGCAGTA
G
Found at i:11860797 original size:66 final size:66
Alignment explanation
Indices: 11860661--11860805 Score: 197
Period size: 66 Copynumber: 2.2 Consensus size: 66
11860651 GGCAACATCG
*
11860661 AGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTGAAAGCAGATGCAGTAGC
1 AGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTGAAAGCAGATGCAGCAGC
*
11860726 G
66 A
* *
11860727 AGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCAGC-AGCAGCTTAAAGCAGATGC-GAC
1 AGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAACTGAAAGCAGATGCAG-C
11860789 AGCA
63 AGCA
*
11860793 AGAGAAGCAGAGG
1 AGAGAAGCTGAGG
11860806 CAGCAGCGAG
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
65 2 0.03
66 64 0.90
67 5 0.07
ACGTcount: A:0.42, C:0.17, G:0.28, T:0.13
Consensus pattern (66 bp):
AGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTGAAAGCAGATGCAGCAGC
A
Found at i:11860801 original size:21 final size:21
Alignment explanation
Indices: 11860788--11860848 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
11860778 GCAGATGCGA
11860788 CAGCAAGAGAAGCAGAGGCAG
1 CAGCAAGAGAAGCAGAGGCAG
* * * *
11860809 CAGCGAGAGAAGTACAGGCTG
1 CAGCAAGAGAAGCAGAGGCAG
* *
11860830 CAGCGAGGGAAGCAGAGGC
1 CAGCAAGAGAAGCAGAGGC
11860849 TAAAACGAGG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.20, G:0.41, T:0.03
Consensus pattern (21 bp):
CAGCAAGAGAAGCAGAGGCAG
Found at i:11860849 original size:21 final size:21
Alignment explanation
Indices: 11860796--11860888 Score: 107
Period size: 21 Copynumber: 4.4 Consensus size: 21
11860786 GACAGCAAGA
* *
11860796 GAAGCAGAGGC-AGCAGCGAGA
1 GAAGCAGAGGCTA-AAGCGAGG
* * **
11860817 GAAGTACAGGCTGCAGCGAGG
1 GAAGCAGAGGCTAAAGCGAGG
*
11860838 GAAGCAGAGGCTAAAACGAGG
1 GAAGCAGAGGCTAAAGCGAGG
11860859 GAAGCAGAGGCTAAAGCGAGG
1 GAAGCAGAGGCTAAAGCGAGG
11860880 GAAGCAGAG
1 GAAGCAGAG
11860889 CAGCGTCAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.38, C:0.16, G:0.42, T:0.04
Consensus pattern (21 bp):
GAAGCAGAGGCTAAAGCGAGG
Found at i:11861367 original size:42 final size:43
Alignment explanation
Indices: 11861245--11861596 Score: 199
Period size: 43 Copynumber: 8.2 Consensus size: 43
11861235 TGGTGGCCTT
* * ** * *
11861245 TTTAGTGGCGTTTTTGGTTAAAGCGTCGCTAAAGATAAAGGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCAAGGTC
* * *
11861288 TTTAGCGGCGTTTGTGGAAAAAGCACCACTAAAGATCATGGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCAAGGTC
* *
11861331 TTTAGCGGCGTTTGT-GAGAAAGCGCCGCTACAGATC-AGAGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCAAG-GTC
* * *
11861373 TATT-GCAGTGTTT-TAGGGGAAAA-CGCCGCTAAAGA--ATAGGTC
1 T-TTAGCGGCGTTTGT--GGAAAAAGCGCCGCTAAAGATCA-AGGTC
* * **
11861415 TTTAGTGGCATTTGTGGTCAAAGCGCCGCTAAAGA--ATAGGTTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCA-AGG-TC
* * * *
11861458 TTTAGTGGCGTTTGTGGTATAAA-CGCCGCTATAGATCAGGGTC
1 TTTAGCGGCGTTTGTGG-AAAAAGCGCCGCTAAAGATCAAGGTC
* * * * * ** *
11861501 TATT-GCGGCCTTT-TAGATAAAAACGCTGCTAAAGACCCTGATC
1 T-TTAGCGGCGTTTGTGGA-AAAAGCGCCGCTAAAGATCAAGGTC
* * ** *
11861544 TTTAGCGGCGCTTCTCCCAAAAA-CGCCGCTAAAGATCAGGGTC
1 TTTAGCGGCGTTTGT-GGAAAAAGCGCCGCTAAAGATCAAGGTC
11861587 TTTAGCGGCG
1 TTTAGCGGCG
11861597 CTTCCACTAA
Statistics
Matches: 240, Mismatches: 49, Indels: 40
0.73 0.15 0.12
Matches are distributed among these distances:
41 10 0.04
42 61 0.25
43 151 0.63
44 16 0.07
45 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCAAGGTC
Found at i:11861526 original size:128 final size:128
Alignment explanation
Indices: 11861271--11861535 Score: 304
Period size: 128 Copynumber: 2.1 Consensus size: 128
11861261 GTTAAAGCGT
*
11861271 CGCTAAAGATAAAGGTCTTTAGCGGCGTTTGTGGAAAAAGCACCACTAAAGATCATGGTCTTTAG
1 CGCTAAAGATAAAGGTCTTTAGCGGCATTTGTGGAAAAAGCACCACTAAAGATCATGGTCTTTAG
* ** * *
11861336 CGGCGTTTGTGAGAAAGCGCCGCTACAGATCAGAGTCTATTGCAGTGTTTTAGGGGAAAACGC
66 CGGCGTTTGTGAGAAAACGCCGCTACAGATCAGAGTCTATTGCAGCCTTTTAGAGAAAAACGC
* * ** * *
11861399 CGCTAAAGA-ATAGGTCTTTAGTGGCATTTGTGGTCAAAGCGCCGCTAAAGA--ATAGGTTCTTT
1 CGCTAAAGATAAAGGTCTTTAGCGGCATTTGTGGAAAAAGCACCACTAAAGATCAT-GG-TCTTT
* * * * *
11861461 AGTGGCGTTTGTG-GTATAAACGCCGCTATAGATCAGGGTCTATTGCGGCCTTTTAGATAAAAAC
64 AGCGGCGTTTGTGAG-A-AAACGCCGCTACAGATCAGAGTCTATTGCAGCCTTTTAGAGAAAAAC
11861525 GC
127 GC
*
11861527 TGCTAAAGA
1 CGCTAAAGA
11861536 CCCTGATCTT
Statistics
Matches: 115, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
125 2 0.02
126 3 0.03
127 53 0.46
128 57 0.50
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (128 bp):
CGCTAAAGATAAAGGTCTTTAGCGGCATTTGTGGAAAAAGCACCACTAAAGATCATGGTCTTTAG
CGGCGTTTGTGAGAAAACGCCGCTACAGATCAGAGTCTATTGCAGCCTTTTAGAGAAAAACGC
Found at i:11861597 original size:43 final size:43
Alignment explanation
Indices: 11861478--11861619 Score: 137
Period size: 43 Copynumber: 3.3 Consensus size: 43
11861468 TTTGTGGTAT
* * * *
11861478 AAACGCCGCTATAGATCAGGGTCTATT-GCGGC-CTTTTAGATAA
1 AAACGCCGCTAAAGATCAGGGTCT-TTAGCGGCGCTTCT-CACAA
* * ** * *
11861521 AAACGCTGCTAAAGACCCTGATCTTTAGCGGCGCTTCTCCCAA
1 AAACGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTCTCACAA
*
11861564 AAACGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTC-CACTA
1 AAACGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTCTCACAA
*
11861606 AAGCGCCGCTAAAG
1 AAACGCCGCTAAAG
11861620 GTCTTACTCT
Statistics
Matches: 79, Mismatches: 18, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
42 18 0.23
43 57 0.72
44 4 0.05
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTCTCACAA
Found at i:11861806 original size:22 final size:22
Alignment explanation
Indices: 11861778--11861820 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
11861768 CTGCGGCTCT
*
11861778 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
11861800 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
11861821 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:11873948 original size:15 final size:15
Alignment explanation
Indices: 11873920--11873961 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
11873910 GTTTCGTCTC
* *
11873920 TTCTATTCTGTTTCTT
1 TTCT-TTCTTTTTCTA
11873936 TTCTTTCTTTTTCTA
1 TTCTTTCTTTTTCTA
11873951 TTCTTTCTTTT
1 TTCTTTCTTTT
11873962 GTTTTATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.74
Consensus pattern (15 bp):
TTCTTTCTTTTTCTA
Found at i:11873983 original size:5 final size:5
Alignment explanation
Indices: 11873970--11874041 Score: 62
Period size: 5 Copynumber: 14.4 Consensus size: 5
11873960 TTGTTTTATG
11873970 TATATA TATAA TATAA TATAA TAT-A T-TAA TAATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
11874018 CATAA TCATTAC TATAA TATAA TA
1 TATAA T-A-TAA TATAA TATAA TA
11874042 ATATTTTTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 34 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (5 bp):
TATAA
Found at i:11873995 original size:19 final size:19
Alignment explanation
Indices: 11873971--11874013 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
11873961 TGTTTTATGT
11873971 ATATATATAAT-ATAATATA
1 ATATAT-TAATAATAATATA
11873990 ATATATTAATAATAATATA
1 ATATATTAATAATAATATA
11874009 ATATA
1 ATATA
11874014 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATTAATAATAATATA
Found at i:11874023 original size:24 final size:25
Alignment explanation
Indices: 11873977--11874042 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
11873967 ATGTATATAT
* *
11873977 ATAATATAATATAATATATTAAT-A
1 ATAATATAATATAATAAAATAATCA
11874001 ATAATATAATATAA-AAACATAATCA
1 ATAATATAATATAATAAA-ATAATCA
* *
11874026 TTACTATAATATAATAA
1 ATAATATAATATAATAA
11874043 TATTTTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.06
24 18 0.51
25 13 0.37
26 2 0.06
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (25 bp):
ATAATATAATATAATAAAATAATCA
Found at i:11876177 original size:42 final size:41
Alignment explanation
Indices: 11876085--11876313 Score: 289
Period size: 42 Copynumber: 5.5 Consensus size: 41
11876075 TGATTCAGTA
* * *
11876085 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTTT
1 CACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGAATTGTTT
*
11876126 CACCGGCATTAAGCCTGCTAGACGTAAAGTTTGATATTGTTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGA-ATTGTTT
* *
11876168 CACCAGCATTAAGCCTGCTAGACGTAAAGTCTGAAATTATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTG-AATTGTTT
* * * * *
11876210 CACCGGCATTAAGCTTGCTAGACATATAGTCTGAAATGTCT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTGTTT
*
11876251 CACCGACATTAAGCCTGCTAGACGTAAAGTCTGATATTGTTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGA-ATTGTTT
* *
11876293 CACTGGCAATAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
11876314 GCGCTAAGCC
Statistics
Matches: 161, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
40 2 0.01
41 63 0.39
42 95 0.59
43 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTGTTT
Found at i:11876202 original size:83 final size:82
Alignment explanation
Indices: 11876096--11876313 Score: 285
Period size: 83 Copynumber: 2.6 Consensus size: 82
11876086 ACCGGCACTT
* * * *
11876096 AGCCTGCTAGACATATAGTCTGAAATGTTTCACCGGCATTAAGCCTGCTAGACGTAAAGTTTGAT
1 AGCCTGCTAGACGTAAAGTCTGAAATGTTTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGA-
* *
11876161 ATTGTTTCACC-AGCATTA
65 AATGTCTCACCGA-CATTA
* * *
11876179 AGCCTGCTAGACGTAAAGTCTGAAATTATTTCACCGGCATTAAGCTTGCTAGACATATAGTCTGA
1 AGCCTGCTAGACGTAAAGTCTGAAA-TGTTTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGA
11876244 AATGTCTCACCGACATTA
65 AATGTCTCACCGACATTA
* * *
11876262 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACTGGCAATAAGCCTGCTAG
1 AGCCTGCTAGACGTAAAGTCTGA-AATGTTTCACCGGCATTAAGCCTGCTAG
11876314 GCGCTAAGCC
Statistics
Matches: 118, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
83 82 0.69
84 36 0.31
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (82 bp):
AGCCTGCTAGACGTAAAGTCTGAAATGTTTCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAA
ATGTCTCACCGACATTA
Found at i:11876327 original size:125 final size:126
Alignment explanation
Indices: 11876042--11876329 Score: 397
Period size: 125 Copynumber: 2.3 Consensus size: 126
11876032 TTTAAACAGA
* * *
11876042 TTCACTGGCACTTAGCCTGCTAGGCTTAAAGCCTG--ATTCAGTACACCGGCACTTAGCCTGCTA
1 TTCACTGGCAATAAGCCTGCTAGGCGTAAAGCCTGAAATTCAGTACACCGGCACTTAGCCTGCTA
* * *
11876105 GACATATAGTCTGAAATGTTTCACCGGCATTAAGCCTGCTAGACGTAAAGTTTGATATTGT
66 GACATATAGTCTGAAATGTCTCACCGACATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
** * * * * * *
11876166 TTCACCAGCATTAAGCCTGCTAGACGTAAAGTCTGAAATT-ATTTCACCGGCA-TTAAGCTTGCT
1 TTCACTGGCAATAAGCCTGCTAGGCGTAAAGCCTGAAATTCAGTACACCGGCACTT-AGCCTGCT
11876229 AGACATATAGTCTGAAATGTCTCACCGACATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
65 AGACATATAGTCTGAAATGTCTCACCGACATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
11876291 TTCACTGGCAATAAGCCTGCTAGGCGCT-AAGCCTGAAAT
1 TTCACTGGCAATAAGCCTGCTAGGCG-TAAAGCCTGAAAT
11876330 CTCAATTTCA
Statistics
Matches: 142, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
124 30 0.21
125 108 0.76
126 4 0.03
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (126 bp):
TTCACTGGCAATAAGCCTGCTAGGCGTAAAGCCTGAAATTCAGTACACCGGCACTTAGCCTGCTA
GACATATAGTCTGAAATGTCTCACCGACATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
Found at i:11880131 original size:4 final size:4
Alignment explanation
Indices: 11880122--11880181 Score: 111
Period size: 4 Copynumber: 15.0 Consensus size: 4
11880112 CTCAGCAAAA
*
11880122 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
11880170 ATAC ATAC ATAC
1 ATAC ATAC ATAC
11880182 TGATTTGATA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:11882122 original size:6 final size:6
Alignment explanation
Indices: 11882092--11882139 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
11882082 ATAAAAATGA
* * * *
11882092 TTGAG- TTGAGT TTGAAT TTGGGT TTCAGT TTGAGT TTGAGT TCGAGT
1 TTGAGT TTGAGT TTGAGT TTGAGT TTGAGT TTGAGT TTGAGT TTGAGT
11882139 T
1 T
11882140 CGGTTTCTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.17, C:0.04, G:0.31, T:0.48
Consensus pattern (6 bp):
TTGAGT
Found at i:11889141 original size:57 final size:57
Alignment explanation
Indices: 11889027--11889168 Score: 223
Period size: 57 Copynumber: 2.5 Consensus size: 57
11889017 TAAACTTTGC
* * * *
11889027 AATTAATCCTATATTGAGACTTGAAC-TTTTTGTTCAAGTTAGCCCCTAAACTTGTT
1 AATTATTCCCATATTGAGGCTTGAACTTTTTTGTTCAAGTTAGCCCCTAAACTAGTT
* *
11889083 AATTATTCCCATATTGAGGCTTAAACTTTTTTGTTCAAGTTAGCCCCTGAACTAGTT
1 AATTATTCCCATATTGAGGCTTGAACTTTTTTGTTCAAGTTAGCCCCTAAACTAGTT
11889140 AATTATTCCCATATTGAGGCTTGAACTTT
1 AATTATTCCCATATTGAGGCTTGAACTTT
11889169 AGAGTTTTCA
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
56 22 0.28
57 56 0.72
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.41
Consensus pattern (57 bp):
AATTATTCCCATATTGAGGCTTGAACTTTTTTGTTCAAGTTAGCCCCTAAACTAGTT
Found at i:11897182 original size:30 final size:30
Alignment explanation
Indices: 11897148--11897218 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
11897138 TAGTACATGG
*
11897148 TAAAATTATATTTTAAT-TTTCAAAAAATAA
1 TAAAATTATAATTTAATATTT-AAAAAATAA
* * *
11897178 TAAAATTTTAATTTAATATTTTAAAAATTA
1 TAAAATTATAATTTAATATTTAAAAAATAA
*
11897208 TAAAAATATAA
1 TAAAATTATAA
11897219 ACTAATCTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 31 0.91
31 3 0.09
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (30 bp):
TAAAATTATAATTTAATATTTAAAAAATAA
Found at i:11898984 original size:22 final size:22
Alignment explanation
Indices: 11898959--11899000 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
11898949 CCTCACTGCT
*
11898959 TTGCTGCAATTTCATTATTACG
1 TTGCTACAATTTCATTATTACG
* *
11898981 TTGCTACTATTTTATTATTA
1 TTGCTACAATTTCATTATTA
11899001 TTGTTTTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.52
Consensus pattern (22 bp):
TTGCTACAATTTCATTATTACG
Found at i:11906946 original size:19 final size:19
Alignment explanation
Indices: 11906922--11906961 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
11906912 TCTGGTTTCG
11906922 TTCTCCCGTTCGTTCTCCC
1 TTCTCCCGTTCGTTCTCCC
*
11906941 TTCTCCCTTTCGTTCTCCC
1 TTCTCCCGTTCGTTCTCCC
11906960 TT
1 TT
11906962 GATTTGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.00, C:0.45, G:0.07, T:0.47
Consensus pattern (19 bp):
TTCTCCCGTTCGTTCTCCC
Found at i:11909637 original size:41 final size:41
Alignment explanation
Indices: 11909592--11909682 Score: 128
Period size: 41 Copynumber: 2.2 Consensus size: 41
11909582 GCTTAGAACT
* *
11909592 TAGCAGGCTTATTGCCGGTGAAACACTTCAGACAAAATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAAACAAAATGTC
* * * *
11909633 TAGCAGGCTTAATGCCGGTGAAATATTTCAAACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAAACAAAATGTC
11909674 TAGCAGGCT
1 TAGCAGGCT
11909683 AAGTGCCAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAACACTTCAAACAAAATGTC
Found at i:11910819 original size:13 final size:13
Alignment explanation
Indices: 11910801--11910827 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11910791 TGGTTCATGT
11910801 TTTTAAGTATCTG
1 TTTTAAGTATCTG
11910814 TTTTAAGTATCTG
1 TTTTAAGTATCTG
11910827 T
1 T
11910828 CTTACCTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (13 bp):
TTTTAAGTATCTG
Found at i:11912122 original size:14 final size:15
Alignment explanation
Indices: 11912100--11912176 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
11912090 CAATCAAACA
11912100 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
11912114 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
11912129 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
11912149 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
11912163 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
11912177 AATGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:11912141 original size:20 final size:20
Alignment explanation
Indices: 11912116--11912155 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11912106 AATATTTTCC
*
11912116 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
11912136 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
11912156 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:11912161 original size:34 final size:35
Alignment explanation
Indices: 11912104--11912170 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
11912094 CAAACACCAG
*
11912104 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
11912139 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
11912171 CATTTTAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:11915083 original size:22 final size:23
Alignment explanation
Indices: 11915057--11915100 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
11915047 GTGATGAGGT
**
11915057 TATCTTGTGAATATGTT-AAATC
1 TATCTTGAAAATATGTTGAAATC
11915079 TATCTTGAAAATATGTTGAAAT
1 TATCTTGAAAATATGTTGAAAT
11915101 GGATTGGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (23 bp):
TATCTTGAAAATATGTTGAAATC
Found at i:11916281 original size:87 final size:84
Alignment explanation
Indices: 11916139--11916297 Score: 189
Period size: 87 Copynumber: 1.8 Consensus size: 84
11916129 TATATATATA
* *
11916139 TTATAAAATATATGTCGAGATTATAAAATATATGGATGCATGTACATAGTTTTAAAATGATAAAA
1 TTATAAAATATATGTCGAGATTATAAAACATACGGATGCATGTA-ATAGTTTTAAAATGAT-AAA
11916204 CATAAAAAAATACATTTAGGAT
64 -ATAAAAAAATACATTTAGGAT
* * *
11916226 TTATAAAATATATGTAC-AGATTATAAGAACGTACGTG-TGCATGT-ATATTTCTTAAAATTATA
1 TTATAAAATATATGT-CGAGATTATAA-AACATACG-GATGCATGTAATAGTT-TTAAAATGATA
11916288 AAATAAAAAA
62 AAATAAAAAA
11916298 GACGTATGTA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
85 8 0.13
86 8 0.13
87 33 0.52
88 13 0.21
89 1 0.02
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (84 bp):
TTATAAAATATATGTCGAGATTATAAAACATACGGATGCATGTAATAGTTTTAAAATGATAAAAT
AAAAAAATACATTTAGGAT
Found at i:11918987 original size:17 final size:17
Alignment explanation
Indices: 11918945--11918990 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
11918935 CAACTAGTCC
* *
11918945 AATTAAAAATTATTAAG
1 AATTAAAAAATAATAAG
*
11918962 AATTCAAAAAATAATAAT
1 AATT-AAAAAATAATAAG
11918980 AATTAAAAAAT
1 AATTAAAAAAT
11918991 CTGGTTCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
AATTAAAAAATAATAAG
Found at i:11920535 original size:16 final size:16
Alignment explanation
Indices: 11920514--11920557 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
11920504 TGGATTTAGA
11920514 TCATTTCAAGTTTCGG
1 TCATTTCAAGTTTCGG
* *
11920530 TCATTTTAAGTTTGGG
1 TCATTTCAAGTTTCGG
*
11920546 TCAATTCAAGTT
1 TCATTTCAAGTT
11920558 CAAGTTGGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (16 bp):
TCATTTCAAGTTTCGG
Found at i:11927923 original size:14 final size:13
Alignment explanation
Indices: 11927904--11927955 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
11927894 GTTTATTAAA
11927904 TTATTTGAAATTTT
1 TTATTT-AAATTTT
* **
11927918 TTATTTAAGTTAA
1 TTATTTAAATTTT
11927931 TTATTTAAAATTTT
1 TTATTT-AAATTTT
11927945 TTATTTAAATT
1 TTATTTAAATT
11927956 ATTGGATTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 15 0.48
14 16 0.52
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (13 bp):
TTATTTAAATTTT
Found at i:11927955 original size:23 final size:23
Alignment explanation
Indices: 11927895--11927958 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 23
11927885 TTACAAAATG
*
11927895 TTTA-TTAAATTATTTGAAATTT
1 TTTATTTAAATTATTTAAAATTT
11927917 TTTATTTAAGTTAATTATTTAAAATTT
1 TTTATTT-A---AATTATTTAAAATTT
11927944 TTTATTTAAATTATT
1 TTTATTTAAATTATT
11927959 GGATTAACTT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
22 4 0.11
23 9 0.25
24 1 0.03
26 1 0.03
27 21 0.58
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (23 bp):
TTTATTTAAATTATTTAAAATTT
Found at i:11927965 original size:27 final size:27
Alignment explanation
Indices: 11927902--11927956 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
11927892 ATGTTTATTA
* *
11927902 AATTATTTGAAATTTTTTATTTAAGTT
1 AATTATTTAAAATTTTTTATTTAAATT
11927929 AATTATTTAAAATTTTTTATTTAAATT
1 AATTATTTAAAATTTTTTATTTAAATT
11927956 A
1 A
11927957 TTGGATTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (27 bp):
AATTATTTAAAATTTTTTATTTAAATT
Found at i:11940520 original size:57 final size:57
Alignment explanation
Indices: 11940440--11940604 Score: 303
Period size: 57 Copynumber: 2.9 Consensus size: 57
11940430 TGATTCAAAG
* *
11940440 CAAAGCATACCATTACACTGCTGGGCATGATAGCATCCCATATTAAATTCAATGTTT
1 CAAAGCACACCATTACACAGCTGGGCATGATAGCATCCCATATTAAATTCAATGTTT
11940497 CAAAGCACACCATTACACAGCTGGGCATGATAGCATCCCATATTAAATTCAATGTTT
1 CAAAGCACACCATTACACAGCTGGGCATGATAGCATCCCATATTAAATTCAATGTTT
*
11940554 CAAAGCACACCATTACACAGCTGGGCATGATAGCATCCCATACTAAATTCA
1 CAAAGCACACCATTACACAGCTGGGCATGATAGCATCCCATATTAAATTCA
11940605 CTGATAACAT
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 105 1.00
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.25
Consensus pattern (57 bp):
CAAAGCACACCATTACACAGCTGGGCATGATAGCATCCCATATTAAATTCAATGTTT
Found at i:11943335 original size:29 final size:29
Alignment explanation
Indices: 11943288--11943347 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
11943278 CAGCTTAAAT
* **
11943288 ATATTTAAAAAATTTAAAT-TATAGTATTC
1 ATATATAAAAAATAAAAATATATA-TATTC
11943317 ATATATAAAAAATAAAAATATATATATTC
1 ATATATAAAAAATAAAAATATATATATTC
11943346 AT
1 AT
11943348 GTTTGGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (29 bp):
ATATATAAAAAATAAAAATATATATATTC
Found at i:11946407 original size:27 final size:27
Alignment explanation
Indices: 11946377--11946428 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
11946367 TTTACATTAT
11946377 TAAAATTAACACAACTT-TTTTTACAAA
1 TAAAATTAACACAA-TTCTTTTTACAAA
*
11946404 TAAAATTAGCACAATTCTTTTTACA
1 TAAAATTAACACAATTCTTTTTACA
11946429 TCAAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.38
Consensus pattern (27 bp):
TAAAATTAACACAATTCTTTTTACAAA
Found at i:11946434 original size:26 final size:26
Alignment explanation
Indices: 11946377--11946436 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
11946367 TTTACATTAT
11946377 TAAAATTAACACAACTTTTTTTACAAA
1 TAAAATTAACACAACTTTTTTTAC-AA
*
11946404 TAAAATTAGCACAA-TTCTTTTTAC-A
1 TAAAATTAACACAACTT-TTTTTACAA
11946429 TCAAAATT
1 T-AAAATT
11946437 TTTAACTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 2 0.07
26 8 0.27
27 20 0.67
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (26 bp):
TAAAATTAACACAACTTTTTTTACAA
Found at i:11947017 original size:15 final size:16
Alignment explanation
Indices: 11946997--11947029 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11946987 TCGAAAAGTC
*
11946997 AATTTTG-AGATTCAA
1 AATTTTGAAGATCCAA
11947012 AATTTTGAAGATCCAA
1 AATTTTGAAGATCCAA
11947028 AA
1 AA
11947030 AATACATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.33
Consensus pattern (16 bp):
AATTTTGAAGATCCAA
Found at i:11948601 original size:20 final size:21
Alignment explanation
Indices: 11948565--11948603 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
11948555 TAATAATTGT
11948565 AAAAGAAAATAAAGGAAGAGG
1 AAAAGAAAATAAAGGAAGAGG
11948586 AAAA-AAAA-AAAGGGAAGA
1 AAAAGAAAATAAA-GGAAGA
11948604 AAAGATCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 10 0.59
21 4 0.24
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.03
Consensus pattern (21 bp):
AAAAGAAAATAAAGGAAGAGG
Found at i:11952768 original size:29 final size:29
Alignment explanation
Indices: 11952721--11952780 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
11952711 CAGCTTAAAT
* **
11952721 ATATTTAAAAAATTTAAAT-TATAGTATTC
1 ATATATAAAAAATAAAAATATATA-TATTC
11952750 ATATATAAAAAATAAAAATATATATATTC
1 ATATATAAAAAATAAAAATATATATATTC
11952779 AT
1 AT
11952781 GTTTGGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (29 bp):
ATATATAAAAAATAAAAATATATATATTC
Found at i:11956005 original size:24 final size:24
Alignment explanation
Indices: 11955969--11956016 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
11955959 CTAATAAATG
*
11955969 TAAATATAAATTAT-ACTTATTTT
1 TAAATATAAATTATCACATATTTT
*
11955992 TAAATTTATAATTATCACATATTTT
1 TAAATATA-AATTATCACATATTTT
11956017 ATTTTACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (24 bp):
TAAATATAAATTATCACATATTTT
Found at i:11958659 original size:15 final size:16
Alignment explanation
Indices: 11958614--11958660 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
11958604 ATTTTTTTGT
11958614 TAGTATAAATTCAAAA
1 TAGTATAAATTCAAAA
**
11958630 TA-TATAGTCTTCAAAA
1 TAGTATA-AATTCAAAA
11958646 -AGTATAAATTCAAAA
1 TAGTATAAATTCAAAA
11958661 GGGTATCTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (16 bp):
TAGTATAAATTCAAAA
Found at i:11961587 original size:21 final size:23
Alignment explanation
Indices: 11961552--11961593 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
11961542 TTATAAATTT
11961552 TTTATAATATTAT-AAATAAAAA
1 TTTATAATATTATAAAATAAAAA
*
11961574 TTTA-AATTTTATAAAATAAA
1 TTTATAATATTATAAAATAAA
11961594 CTATAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTATAATATTATAAAATAAAAA
Found at i:11963458 original size:75 final size:75
Alignment explanation
Indices: 11963335--11963481 Score: 276
Period size: 75 Copynumber: 2.0 Consensus size: 75
11963325 ACAATCCATG
* *
11963335 TTACATTCCAAATTACTTAGATTCAATTATGGCTTTGATCCCTCTGCAATGCTCATGTTTAGGAT
1 TTACATTCCAAATTACTTAGATCCAATTATGGCTTTGATCCCTCTGCAATGCTCATATTTAGGAT
11963400 TTAGTTCTTA
66 TTAGTTCTTA
11963410 TTACATTCCAAATTACTTAGATCCAATTATGGCTTTGATCCCTCTGCAATGCTCATATTTAGGAT
1 TTACATTCCAAATTACTTAGATCCAATTATGGCTTTGATCCCTCTGCAATGCTCATATTTAGGAT
11963475 TTAGTTC
66 TTAGTTC
11963482 ATATAATTTG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (75 bp):
TTACATTCCAAATTACTTAGATCCAATTATGGCTTTGATCCCTCTGCAATGCTCATATTTAGGAT
TTAGTTCTTA
Found at i:11966972 original size:22 final size:22
Alignment explanation
Indices: 11966938--11966984 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
11966928 TGACAATACT
11966938 ATAATGAATACAATAAT-AAGAA
1 ATAATGAATACAATAATGAA-AA
11966960 ATAAT-AATAACAATAATGAAAA
1 ATAATGAAT-ACAATAATGAAAA
11966982 ATA
1 ATA
11966985 TTAAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 3 0.13
22 18 0.78
23 2 0.09
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.23
Consensus pattern (22 bp):
ATAATGAATACAATAATGAAAA
Found at i:11968867 original size:44 final size:44
Alignment explanation
Indices: 11968795--11968966 Score: 127
Period size: 44 Copynumber: 3.8 Consensus size: 44
11968785 GATTTGTTTG
* * *
11968795 TTGTAGTTTCAATTCGAC-CCACTACAACTTTAGGGGTATAAGAT
1 TTGTAGCTTCAATTTG-CTCCACAACAACTTTAGGGGTATAAGAT
*** *
11968839 TTGTAGCTTCAATTTGCTCCATTGCAACTTTAAGGAG-ATAAGAT
1 TTGTAGCTTCAATTTGCTCCACAACAACTTT-AGGGGTATAAGAT
* * *
11968883 TCGCTATAG-TAAAATCAATTCGATCCACAACAACTTTAGGGGTATAAGAT
1 T---TGTAGCT----TCAATTTGCTCCACAACAACTTTAGGGGTATAAGAT
* *
11968933 TTGTAGCTTCAATTTGCT-CACTACAACTTCAGGG
1 TTGTAGCTTCAATTTGCTCCACAACAACTTTAGGG
11968967 AGAAAAGATT
Statistics
Matches: 100, Mismatches: 17, Indels: 23
0.71 0.12 0.16
Matches are distributed among these distances:
43 15 0.15
44 41 0.41
45 4 0.04
46 1 0.01
47 8 0.08
48 1 0.01
49 4 0.04
50 26 0.26
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (44 bp):
TTGTAGCTTCAATTTGCTCCACAACAACTTTAGGGGTATAAGAT
Found at i:11968933 original size:94 final size:94
Alignment explanation
Indices: 11968757--11969258 Score: 483
Period size: 94 Copynumber: 5.3 Consensus size: 94
11968747 CAATTTCATC
* * * * * * * ** *
11968757 TTGCTCCATTGCAACTTCAAGGAGATAAGATTTGTTTGTTGTAGTTTCAATTCGACCCACTACAA
1 TTGCTCCACTGCAACTTTAGGGAGATAAGATTCG-CTATAGTAGAATCAATCCGACCCACTACAA
11968822 CTTTAGGGGTATAAGATTTGTAGCTTCAAT
65 CTTTAGGGGTATAAGATTTGTAGCTTCAAT
* * * * * *
11968852 TTGCTCCATTGCAACTTTAAGGAGATAAGATTCGCTATAGTAAAATCAATTCGATCCACAACAAC
1 TTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATAGTAGAATCAATCCGACCCACTACAAC
11968917 TTTAGGGGTATAAGATTTGTAGCTTCAAT
66 TTTAGGGGTATAAGATTTGTAGCTTCAAT
* * * * *
11968946 TTGCT-CACTACAACTTCAGGGAGAAAAGATTCTCTATAGTAGAATCAATCCGACCCACTGCAAC
1 TTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATAGTAGAATCAATCCGACCCACTACAAC
*
11969010 -TTAGGGGAATAAGATTTTGTAGCTTCAAT
66 TTTAGGGGTATAAGA-TTTGTAGCTTCAAT
* * * * *
11969039 ATGCTCCAATGCAA-TTTCAGGGAGATAAGATTCGCTAT-GATAGATTCAATCCAACCCACTGCA
1 TTGCTCCACTGCAACTTT-AGGGAGATAAGATTCGCTATAG-TAGAATCAATCCGACCCACTACA
* * ** *
11969102 ACTTCAAGGGTATGGGATTTGTAGTTTCAAT
64 ACTTTAGGGGTATAAGATTTGTAGCTTCAAT
* * ** ** * * *
11969133 TTGCTCCACTACAACTTTAGGGACATAAGATTCATTATAGTAGTTTCATTCCGACCTACTGCAAC
1 TTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATAGTAGAATCAATCCGACCCACTACAAC
* * *
11969198 TTCAAGGGTAT-AGAAATTGTAGCTTCAAT
66 TTTAGGGGTATAAG-ATTTGTAGCTTCAAT
* * * * *
11969227 ATGATCCACCGCAACTTTAGGGATATAGGATT
1 TTGCTCCACTGCAACTTTAGGGAGATAAGATT
11969259 TGTATCTTCA
Statistics
Matches: 344, Mismatches: 55, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
92 13 0.04
93 70 0.20
94 216 0.63
95 45 0.13
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (94 bp):
TTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATAGTAGAATCAATCCGACCCACTACAAC
TTTAGGGGTATAAGATTTGTAGCTTCAAT
Found at i:11969124 original size:187 final size:187
Alignment explanation
Indices: 11968803--11969245 Score: 518
Period size: 187 Copynumber: 2.4 Consensus size: 187
11968793 TGTTGTAGTT
* * * *
11968803 TCAATTCGACCCACTACAACTTTAGGGGTATAAGATTTGTAGCTTCAATTTGCTCCATTGCAACT
1 TCAATCCGACCCACTGCAAC-TTAGGGGTATAAGATTTGTAGCTTCAATATGCTCCAATGCAACT
* * * * *
11968868 TTAAGGAGATAAGATTCGCTATAGTAAAATCAATTCGATCCACAACAACTTTAGGGGTATAAGAT
65 TTAAGGAGATAAGATTCGCTATAGTAAAATCAATCCAACCCACAACAACTTCAAGGGTATAAGAT
*
11968933 TTGTAGCTTCAATTTGCT-CACTACAACTTCAGGGAGAAAAGATTC-TCTATAGTAGAA
130 TTGTAGCTTCAATTTGCTCCACTACAACTTCAGGGACAAAAGATTCAT-TATAGTAGAA
*
11968990 TCAATCCGACCCACTGCAACTTAGGGGAATAAGATTTTGTAGCTTCAATATGCTCCAATGCAA-T
1 TCAATCCGACCCACTGCAACTTAGGGGTATAAGA-TTTGTAGCTTCAATATGCTCCAATGCAACT
* * * ** **
11969054 TTCAGGGAGATAAGATTCGCTAT-GATAGATTCAATCCAACCCACTGCAACTTCAAGGGTATGGG
65 TT-AAGGAGATAAGATTCGCTATAG-TAAAATCAATCCAACCCACAACAACTTCAAGGGTATAAG
* * * **
11969118 ATTTGTAGTTTCAATTTGCTCCACTACAACTTTAGGGACATAAGATTCATTATAGTAGTT
128 ATTTGTAGCTTCAATTTGCTCCACTACAACTTCAGGGACAAAAGATTCATTATAGTAGAA
* * * * * **
11969178 TCATTCCGACCTACTGCAACTTCAAGGGTAT-AGAAATTGTAGCTTCAATATGATCCACCGCAAC
1 TCAATCCGACCCACTGCAACTT-AGGGGTATAAG-ATTTGTAGCTTCAATATGCTCCAATGCAAC
11969242 TTTA
64 TTTA
11969246 GGGATATAGG
Statistics
Matches: 217, Mismatches: 31, Indels: 15
0.83 0.12 0.06
Matches are distributed among these distances:
186 17 0.08
187 110 0.51
188 79 0.36
189 11 0.05
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (187 bp):
TCAATCCGACCCACTGCAACTTAGGGGTATAAGATTTGTAGCTTCAATATGCTCCAATGCAACTT
TAAGGAGATAAGATTCGCTATAGTAAAATCAATCCAACCCACAACAACTTCAAGGGTATAAGATT
TGTAGCTTCAATTTGCTCCACTACAACTTCAGGGACAAAAGATTCATTATAGTAGAA
Found at i:11974833 original size:280 final size:280
Alignment explanation
Indices: 11974332--11974891 Score: 1102
Period size: 280 Copynumber: 2.0 Consensus size: 280
11974322 AATGGAGCAT
11974332 CTCTTCTTTGTAATCTATTCGGGTGACCTCTAAAGGTTTGATATGGTAATACCTACGGTAGGTTC
1 CTCTTCTTTGTAATCTATTCGGGTGACCTCTAAAGGTTTGATATGGTAATACCTACGGTAGGTTC
*
11974397 TTAGGGCTCACCACATGCGGTTTGGTTCTAAAGTAAGGGTATCTAAACCAACAGATTCCTCAATC
66 TTAGGGCTCACCACATGCGGTTTGGTTCTAAAGTAAGGGTACCTAAACCAACAGATTCCTCAATC
11974462 CTCACCCATTATAGCCTCATACGGAAAAAGTTTAGTTCAGGGGAACACATTTCCCTATGTCTATA
131 CTCACCCATTATAGCCTCATACGGAAAAAGTTTAGTTCAGGGGAACACATTTCCCTATGTCTATA
*
11974527 TGGAGGTGAAGACCTCACGAAAACATAGGTACGGATGTATCCCGAAAGCGATCCACTATTCTATA
196 TGGAGGTGAAGACCTCACGAAAACATAGGTACGGATGTATCCCGAAAGCGATCCACTATCCTATA
11974592 CGGAGGTGAAGACCTCACAA
261 CGGAGGTGAAGACCTCACAA
11974612 CTCTTCTTTGTAATCTATTCGGGTGACCTCTAAAGGTTTGATATGGTAATACCTACGGTAGGTTC
1 CTCTTCTTTGTAATCTATTCGGGTGACCTCTAAAGGTTTGATATGGTAATACCTACGGTAGGTTC
11974677 TTAGGGCTCACCACATGCGGTTTGGTTCTAAAGTAAGGGTACCTAAACCAACAGATTCCTCAATC
66 TTAGGGCTCACCACATGCGGTTTGGTTCTAAAGTAAGGGTACCTAAACCAACAGATTCCTCAATC
11974742 CTCACCCATTATAGCCTCATACGGAAAAAGTTTAGTTCAGGGGAACACATTTCCCTATGTCTATA
131 CTCACCCATTATAGCCTCATACGGAAAAAGTTTAGTTCAGGGGAACACATTTCCCTATGTCTATA
11974807 TGGAGGTGAAGACCTCACGAAAACATAGGTACGGATGTATCCCGAAAGCGATCCACTATCCTATA
196 TGGAGGTGAAGACCTCACGAAAACATAGGTACGGATGTATCCCGAAAGCGATCCACTATCCTATA
11974872 CGGAGGTGAAGACCTCACAA
261 CGGAGGTGAAGACCTCACAA
11974892 AGGAATAGCT
Statistics
Matches: 278, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
280 278 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (280 bp):
CTCTTCTTTGTAATCTATTCGGGTGACCTCTAAAGGTTTGATATGGTAATACCTACGGTAGGTTC
TTAGGGCTCACCACATGCGGTTTGGTTCTAAAGTAAGGGTACCTAAACCAACAGATTCCTCAATC
CTCACCCATTATAGCCTCATACGGAAAAAGTTTAGTTCAGGGGAACACATTTCCCTATGTCTATA
TGGAGGTGAAGACCTCACGAAAACATAGGTACGGATGTATCCCGAAAGCGATCCACTATCCTATA
CGGAGGTGAAGACCTCACAA
Found at i:11976461 original size:12 final size:12
Alignment explanation
Indices: 11976446--11976478 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
11976436 CTCCTTTATT
11976446 TATCATTTTTTG
1 TATCATTTTTTG
*
11976458 TATCATTTTTTT
1 TATCATTTTTTG
11976470 TA-CATTTTT
1 TATCATTTTT
11976479 AACTATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.18, C:0.09, G:0.03, T:0.70
Consensus pattern (12 bp):
TATCATTTTTTG
Found at i:11977147 original size:3 final size:3
Alignment explanation
Indices: 11977139--11977205 Score: 62
Period size: 3 Copynumber: 22.3 Consensus size: 3
11977129 TATTTTAATG
** * * * *
11977139 TTA TTA TTA TTA TTA TCC TTA CTA TTA TTA TTA GTA TTA TTA CTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
11977187 TTA TTA TTA CTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA T
11977206 ATTTACACTT
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.09, G:0.01, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:11977176 original size:12 final size:12
Alignment explanation
Indices: 11977139--11977205 Score: 71
Period size: 12 Copynumber: 5.6 Consensus size: 12
11977129 TATTTTAATG
*
11977139 TTATTATTATTA
1 TTATTATTACTA
**
11977151 TTATCCTTACTA
1 TTATTATTACTA
*
11977163 TTATTATTAGTA
1 TTATTATTACTA
* *
11977175 TTATTACTAATA
1 TTATTATTACTA
11977187 TTATTATTACTA
1 TTATTATTACTA
*
11977199 TCATTAT
1 TTATTAT
11977206 ATTTACACTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.33, C:0.09, G:0.01, T:0.57
Consensus pattern (12 bp):
TTATTATTACTA
Found at i:11977630 original size:27 final size:25
Alignment explanation
Indices: 11977583--11977638 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
11977573 TGTAAATACT
*
11977583 TATATTTTTTATATCTTATAATTTA
1 TATATTTTTCATATCTTATAATTTA
* *
11977608 TATATATTTTCATATTTTCATAATTTT
1 TATAT-TTTTCATATCTT-ATAATTTA
11977635 TATA
1 TATA
11977639 CATATATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 5 0.19
26 10 0.38
27 11 0.42
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (25 bp):
TATATTTTTCATATCTTATAATTTA
Found at i:11980333 original size:99 final size:99
Alignment explanation
Indices: 11980162--11980538 Score: 479
Period size: 99 Copynumber: 3.6 Consensus size: 99
11980152 GGAAATTCGA
* * * *
11980162 GGAAATGTGCCCTAATGTGCTGGGTTTCGATTTTTCTTGTTCAACCAAATAGCTAAGTATCCTTT
1 GGAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTT
*
11980227 TAAAAATTTCAAAATGAGGCACTGTTTTGCGTTT
66 TAAAAATTTCAAAATGAGGCAATGTTTTGCGTTT
* *
11980261 GGAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTT
1 GGAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTT
11980326 TAAAAATTTCAAAATGAGGCAATGTTTTGCGTTT
66 TAAAAATTTCAAAATGAGGCAATGTTTTGCGTTT
11980360 GGAAATTCGAGGAAATGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAGCCA
1 GGAAA--C--------GTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAGCCA
* *
11980425 AATATCCTTTCAAAAATTTCAAAATAAGGCAATGTTTTGCGTTT
56 AATATCCTTTTAAAAATTTCAAAATGAGGCAATGTTTTGCGTTT
*
11980469 GAAAATTCGAGGAACGTGCCCTAATGTGCTGGGTTTCGA--TTTCTTGTTCAACCAAATAGCCAA
1 G-------GA--AACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAGCCAA
11980532 ATATCCT
57 ATATCCT
11980539 CTTGAATTTT
Statistics
Matches: 251, Mismatches: 8, Indels: 31
0.87 0.03 0.11
Matches are distributed among these distances:
99 101 0.40
101 1 0.00
106 30 0.12
108 24 0.10
109 90 0.36
116 3 0.01
118 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (99 bp):
GGAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTT
TAAAAATTTCAAAATGAGGCAATGTTTTGCGTTT
Found at i:11980455 original size:109 final size:109
Alignment explanation
Indices: 11980261--11980538 Score: 472
Period size: 109 Copynumber: 2.6 Consensus size: 109
11980251 TTTTGCGTTT
* *
11980261 GGAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAGCTAAGTATCCTTT
1 GGAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTT
* * *
11980326 TAAAAATTTCAAAATGAGGCAATGTTTTGCGTTTGGAAATTCGA
66 CAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGA
*
11980370 GGAAATGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTT
1 GGAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTT
11980435 CAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGA
66 CAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGA
*
11980479 GG-AACGTGCCCTAATGTGCTGGGTTTCGA--TTTCTTGTTCAACCAAATAGCCAAATATCCT
1 GGAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAGCCAAATATCCT
11980539 CTTGAATTTT
Statistics
Matches: 161, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
106 30 0.19
108 26 0.16
109 105 0.65
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (109 bp):
GGAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAGCCAAATATCCTTT
CAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGA
Found at i:11981093 original size:3 final size:3
Alignment explanation
Indices: 11981085--11981135 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
11981075 TGACTATAAC
* * * *
11981085 ATA ATA ATA ACA ATA ATA ATT ATA ATA ATT ATT ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11981133 ATA
1 ATA
11981136 TCTAATGACA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:11983145 original size:19 final size:19
Alignment explanation
Indices: 11983121--11983158 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
11983111 AGCAATAATT
11983121 TTTTTGACTTT-TTTTATTC
1 TTTTTG-CTTTCTTTTATTC
*
11983140 TTTTTGTTTTCTTTTATTC
1 TTTTTGCTTTCTTTTATTC
11983159 AAAATAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.08, C:0.11, G:0.05, T:0.76
Consensus pattern (19 bp):
TTTTTGCTTTCTTTTATTC
Found at i:11988233 original size:31 final size:29
Alignment explanation
Indices: 11988195--11988271 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
11988185 TTAACGGCTC
*
11988195 AGTGACTAAAATGTTACATCATAATAACATA
1 AGTGACTAAAATGTAACAT-ATAA-AACATA
* * * *
11988226 AGTGACTACAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACATATAAAACATA
*
11988255 AGTGACTGAAATGTAAC
1 AGTGACTAAAATGTAAC
11988272 CTGAACCAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 20 0.53
30 2 0.05
31 16 0.42
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (29 bp):
AGTGACTAAAATGTAACATATAAAACATA
Done.