Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 15 of 27
Found at i:1958853 original size:2 final size:2
Alignment explanation
Indices: 1958846--1958870 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1958836 ACTTTTATGC
1958846 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 A
1958871 GACAAAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1959835 original size:21 final size:20
Alignment explanation
Indices: 1959807--1959848 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1959797 TACAATAAAT
1959807 TCTTTTATTAATAAATAATA
1 TCTTTTATTAATAAATAATA
* *
1959827 TCTTATTATTTATCAATAATA
1 TCTT-TTATTAATAAATAATA
1959848 T
1 T
1959849 ATAAATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (20 bp):
TCTTTTATTAATAAATAATA
Found at i:1959871 original size:19 final size:19
Alignment explanation
Indices: 1959834--1959871 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1959824 ATATCTTATT
*
1959834 ATTTATCAATAATATATAA
1 ATTTATCAATAATAAATAA
1959853 ATTTATACAATAA-AAATAA
1 ATTTAT-CAATAATAAATAA
1959872 TCAAATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTTATCAATAATAAATAA
Found at i:1961912 original size:2 final size:2
Alignment explanation
Indices: 1961905--1961931 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1961895 ACCCTTGATC
1961905 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1961932 GAATGTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1962851 original size:21 final size:21
Alignment explanation
Indices: 1962827--1962896 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
1962817 TTGGTATAAC
*
1962827 ATTAT-TATAAATATTATCAAA
1 ATTATATATAAA-AATATCAAA
* *
1962848 ATTATGT-TAAAAATATTAAA
1 ATTATATATAAAAATATCAAA
*
1962868 ATTATATATAAAAAAATCAAA
1 ATTATATATAAAAATATCAAA
1962889 ATTATATA
1 ATTATATA
1962897 AAATTTACCC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 13 0.31
21 28 0.67
22 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (21 bp):
ATTATATATAAAAATATCAAA
Found at i:1963803 original size:2 final size:2
Alignment explanation
Indices: 1963796--1963823 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1963786 CAAGTTCAAA
1963796 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1963824 TTAACGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1964440 original size:37 final size:36
Alignment explanation
Indices: 1964399--1964483 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 36
1964389 TAATTTAATA
*
1964399 AATTTAATTTGA-TTTGAAT-TTAAATAATAATATTTAT
1 AATTTAATTT-ATTTTAAATATT-AA-AATAATATTTAT
*
1964436 AATTTAATATTATTTTAAATATTAAAATAATATTTTT
1 AATTTAAT-TTATTTTAAATATTAAAATAATATTTAT
*
1964473 AATTAAATTTA
1 AATTTAATTTA
1964484 AATATAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 3 0.07
37 27 0.64
38 10 0.24
39 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (36 bp):
AATTTAATTTATTTTAAATATTAAAATAATATTTAT
Found at i:1964477 original size:18 final size:18
Alignment explanation
Indices: 1964424--1964479 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 18
1964414 GAATTTAAAT
* *
1964424 AATAATATTTATAATT-T
1 AATAATATTTTTAATTAA
* *
1964441 AATATTATTTTAAATATTAA
1 AATAATATTTT-TA-ATTAA
1964461 AATAATATTTTTAATTAA
1 AATAATATTTTTAATTAA
1964479 A
1 A
1964480 TTTAAATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 9 0.30
18 7 0.23
19 4 0.13
20 10 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATAATATTTTTAATTAA
Found at i:1964530 original size:13 final size:13
Alignment explanation
Indices: 1964512--1964553 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1964502 ATTAATATAA
*
1964512 AAATAATTATTTT
1 AAATAATTAATTT
1964525 AAATAA-TAATTT
1 AAATAATTAATTT
* *
1964537 AAATTATTAAATT
1 AAATAATTAATTT
1964550 AAAT
1 AAAT
1964554 TAAATTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AAATAATTAATTT
Found at i:1965639 original size:18 final size:17
Alignment explanation
Indices: 1965602--1965640 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1965592 AGTTAATAGA
*
1965602 TATTAAATATATTATTT
1 TATTAAATATATTATAT
*
1965619 TATTAAATTTAATTATAT
1 TATTAAATAT-ATTATAT
1965637 TATT
1 TATT
1965641 TTATTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTAAATATATTATAT
Found at i:1966027 original size:22 final size:21
Alignment explanation
Indices: 1966002--1966042 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1965992 TTTTAATTCA
* *
1966002 TTATAAGTAAAATTTTTAAATT
1 TTATAAAT-AAATTTATAAATT
1966024 TTATAAATAAATTTATAAA
1 TTATAAATAAATTTATAAA
1966043 GTCATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TTATAAATAAATTTATAAATT
Found at i:1972774 original size:19 final size:18
Alignment explanation
Indices: 1972725--1972783 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
1972715 AATTTTTATT
1972725 TTATT-ATAA-AAATATAA
1 TTATTAATAATAAA-ATAA
*
1972742 TTATTAATATTAAAATAA
1 TTATTAATAATAAAATAA
*
1972760 TTTTTAAATAATAAAATAGA
1 TTATT-AATAATAAAATA-A
1972780 TTAT
1 TTAT
1972784 CAAGTCGATC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
17 5 0.15
18 11 0.32
19 14 0.41
20 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TTATTAATAATAAAATAA
Found at i:1981653 original size:17 final size:17
Alignment explanation
Indices: 1981631--1981666 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1981621 ATCTGAGCTC
1981631 TAGCCATAACCATAAAT
1 TAGCCATAACCATAAAT
1981648 TAGCCATAACCATAAAT
1 TAGCCATAACCATAAAT
1981665 TA
1 TA
1981667 AGTAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (17 bp):
TAGCCATAACCATAAAT
Found at i:1982566 original size:2 final size:2
Alignment explanation
Indices: 1982559--1982595 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1982549 TCCGTAAAAA
1982559 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1982596 TCCTTTTTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1983025 original size:17 final size:17
Alignment explanation
Indices: 1982990--1983040 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
1982980 ATCGTATGTA
1982990 TATATTATATTTAAA-TT
1 TATA-TATATTTAAATTT
1983007 TATATATATTTAAATTT
1 TATATATATTTAAATTT
* *
1983024 TATA-AAATTAAAATTT
1 TATATATATTTAAATTT
1983040 T
1 T
1983041 TAATTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 21 0.68
17 10 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATATATTTAAATTT
Found at i:1983039 original size:22 final size:22
Alignment explanation
Indices: 1983015--1983058 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1983005 TTTATATATA
1983015 TTTAAATTTTATAAAATTAAAAT
1 TTTAAATTTT-TAAAATTAAAAT
* *
1983038 TTTTAATTTTTAATATTAAAA
1 TTTAAATTTTTAAAATTAAAA
1983059 AATATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTAAATTTTTAAAATTAAAAT
Found at i:1983543 original size:2 final size:2
Alignment explanation
Indices: 1983536--1983565 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1983526 TGGGAGAGTA
1983536 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1983566 TACAATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1983618 original size:18 final size:17
Alignment explanation
Indices: 1983595--1983640 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
1983585 GATGGATAGG
1983595 TAATTTTATTTAGTAAA-A
1 TAATTTTATTT--TAAATA
1983613 TAATTTT-TTTTAAATA
1 TAATTTTATTTTAAATA
1983629 TAATTTTATTTT
1 TAATTTTATTTT
1983641 TTTTCAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 4 0.15
16 8 0.31
17 7 0.27
18 7 0.27
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TAATTTTATTTTAAATA
Found at i:1983641 original size:18 final size:17
Alignment explanation
Indices: 1983595--1983641 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
1983585 GATGGATAGG
*
1983595 TAATTTTATTTAGTAAAA
1 TAATTTTATTT-TTAAAA
1983613 TAA-TTT-TTTTTAAATA
1 TAATTTTATTTTTAAA-A
1983629 TAATTTTATTTTT
1 TAATTTTATTTTT
1983642 TTTCAATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 4 0.16
16 7 0.28
17 6 0.24
18 8 0.32
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
TAATTTTATTTTTAAAA
Found at i:1984002 original size:21 final size:21
Alignment explanation
Indices: 1983973--1984015 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1983963 GTATTAAAAA
*
1983973 ATATTTTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
1983994 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
1984015 A
1 A
1984016 AAAAATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:1989498 original size:20 final size:21
Alignment explanation
Indices: 1989475--1989514 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1989465 TTTTATCTAC
*
1989475 TTTTCT-GTGTTTTTAATTTT
1 TTTTCTCGTATTTTTAATTTT
1989495 TTTTCTCGTATTTTTAATTT
1 TTTTCTCGTATTTTTAATTT
1989515 ATATGATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.72
Consensus pattern (21 bp):
TTTTCTCGTATTTTTAATTTT
Found at i:1996760 original size:2 final size:2
Alignment explanation
Indices: 1996753--1996778 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1996743 CTTCGATTGC
1996753 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1996779 TTTATCTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2003361 original size:19 final size:19
Alignment explanation
Indices: 2003339--2003378 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2003329 AAAATATATT
* *
2003339 AATATTAAATTATTTTTTA
1 AATAATAAAATATTTTTTA
2003358 AATAATAAAATATTTTTTA
1 AATAATAAAATATTTTTTA
2003377 AA
1 AA
2003379 ATTTAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATAATAAAATATTTTTTA
Found at i:2003992 original size:32 final size:29
Alignment explanation
Indices: 2003934--2004001 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 29
2003924 TTGAATTTAT
2003934 TTAAAATTATTTTGTTATTTTAAAATAATA
1 TTAAAATTATTTTGTTATTTTAAAATAA-A
*
2003964 TTAAAATT-TTATTTTTATATTTATAAATAAA
1 TTAAAATTATT-TTGTTAT-TTTA-AAATAAA
*
2003995 TTTAAAT
1 TTAAAAT
2004002 AAAATATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 2 0.06
30 14 0.42
31 11 0.33
32 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (29 bp):
TTAAAATTATTTTGTTATTTTAAAATAAA
Found at i:2004036 original size:34 final size:32
Alignment explanation
Indices: 2003976--2004038 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 32
2003966 AAAATTTTAT
2003976 TTTTATATTTATAAATAAATTTAAATAAAATA
1 TTTTATATTTATAAATAAATTTAAATAAAATA
2004008 TTTTAT-TTATATAAATAGTAATTTAAATAAA
1 TTTTATATT-TATAAATA--AATTTAAATAAA
2004039 CTCAAATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 2 0.07
32 14 0.50
34 12 0.43
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (32 bp):
TTTTATATTTATAAATAAATTTAAATAAAATA
Found at i:2004253 original size:28 final size:27
Alignment explanation
Indices: 2004202--2004266 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 27
2004192 TTATATATTT
2004202 ATTT-AAATTTTATTTTAAATAATTTAA
1 ATTTAAAATTTTA-TTTAAATAATTTAA
*
2004229 ATTTAAAATTTTA-TTAACATCAATTTAT
1 ATTTAAAATTTTATTTAA-AT-AATTTAA
2004257 ATTTATAAAT
1 ATTTA-AAAT
2004267 GAATAATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 4 0.12
27 6 0.18
28 19 0.58
29 4 0.12
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTTAAAATTTTATTTAAATAATTTAA
Found at i:2004484 original size:2 final size:2
Alignment explanation
Indices: 2004477--2004514 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2004467 CAAATCCTTG
*
2004477 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2004515 GTTAGTCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2004760 original size:39 final size:42
Alignment explanation
Indices: 2004695--2004794 Score: 113
Period size: 41 Copynumber: 2.5 Consensus size: 42
2004685 ATTACATATA
*
2004695 ATAATTT-AATAATAAAT-ATTTATTTT-AATAATT-TATTAT
1 ATAATTTAAATAA-AAATAATTTATTTTAAAAAATTATATTAT
**
2004734 -TAATTTTTATAACAAATAATTT-TTTTAAAAAATTATATTAT
1 ATAATTTAAATAA-AAATAATTTATTTTAAAAAATTATATTAT
2004775 ATAATTTAAATAAAAATAAT
1 ATAATTTAAATAAAAATAAT
2004795 ATATATTGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
38 6 0.12
39 12 0.24
40 10 0.20
41 13 0.25
42 10 0.20
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (42 bp):
ATAATTTAAATAAAAATAATTTATTTTAAAAAATTATATTAT
Found at i:2005171 original size:22 final size:22
Alignment explanation
Indices: 2005120--2005172 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
2005110 AGCATATTGA
*
2005120 TAAAA-TAAATTTGAATTAATT
1 TAAAATTAAATTTAAATTAATT
* *
2005141 TATAGTTAAATTTAAATTAATT
1 TAAAATTAAATTTAAATTAATT
2005163 TAAAATTAAA
1 TAAAATTAAA
2005173 AATTAAATAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
TAAAATTAAATTTAAATTAATT
Found at i:2005842 original size:16 final size:16
Alignment explanation
Indices: 2005821--2005865 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
2005811 AATTTTTACA
2005821 TATATATTTAAAATAT
1 TATATATTTAAAATAT
2005837 TATATATTT---ATAT
1 TATATATTTAAAATAT
2005850 T-TATATTTAAATATAT
1 TATATATTTAAA-ATAT
2005866 ATTAAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 7 0.28
13 5 0.20
16 13 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATATATTTAAAATAT
Found at i:2005897 original size:12 final size:11
Alignment explanation
Indices: 2005864--2005902 Score: 51
Period size: 12 Copynumber: 3.3 Consensus size: 11
2005854 ATTTAAATAT
2005864 ATATTAAATATAA
1 ATATTAAA-A-AA
2005877 ATATTAAAAAA
1 ATATTAAAAAA
2005888 ATATTTAAAAAA
1 ATA-TTAAAAAA
2005900 ATA
1 ATA
2005903 AAATTTAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 5 0.20
12 12 0.48
13 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATATTAAAAAA
Found at i:2008462 original size:21 final size:21
Alignment explanation
Indices: 2008436--2008476 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2008426 CATAAAAAAT
2008436 TTATTTATAT-TATATTTTTAA
1 TTATTTATATAT-TATTTTTAA
*
2008457 TTATTTTTATATTATTTTTA
1 TTATTTATATATTATTTTTA
2008477 TATAATCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TTATTTATATATTATTTTTAA
Found at i:2008463 original size:10 final size:11
Alignment explanation
Indices: 2008439--2008479 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
2008429 AAAAAATTTA
2008439 TTTATATTATAT
1 TTTATATTAT-T
2008451 TTT-TAATTATT
1 TTTAT-ATTATT
2008462 TTTATATTATT
1 TTTATATTATT
2008473 TTTATAT
1 TTTATAT
2008480 AATCATATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATATTATT
Found at i:2008464 original size:11 final size:12
Alignment explanation
Indices: 2008434--2008479 Score: 53
Period size: 11 Copynumber: 3.9 Consensus size: 12
2008424 ATCATAAAAA
2008434 ATTTATTTATATT
1 ATTT-TTTATATT
2008447 ATATTTTTA-ATT
1 AT-TTTTTATATT
2008459 A-TTTTTATATT
1 ATTTTTTATATT
2008470 A-TTTTTATAT
1 ATTTTTTATAT
2008480 AATCATATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 6 0.19
11 13 0.42
12 4 0.13
13 6 0.19
14 2 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTTTTATATT
Found at i:2008648 original size:30 final size:30
Alignment explanation
Indices: 2008612--2008668 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
2008602 ATCATCATAT
* *
2008612 ATAAATGACGGTATGTCGGCAAGAGATTAC
1 ATAAATGACGGCATGTCGACAAGAGATTAC
2008642 ATAAATGACGGCATGTCGACAAGAGAT
1 ATAAATGACGGCATGTCGACAAGAGAT
2008669 GTGATGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.21
Consensus pattern (30 bp):
ATAAATGACGGCATGTCGACAAGAGATTAC
Found at i:2009666 original size:17 final size:18
Alignment explanation
Indices: 2009631--2009676 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
2009621 ATAATATATT
*
2009631 AAATAAA-AATATAATAA
1 AAATAAATAAAATAATAA
*
2009648 AAATACATAAAATAA-AA
1 AAATAAATAAAATAATAA
*
2009665 AATTAAATAAAA
1 AAATAAATAAAA
2009677 AACGAGGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (18 bp):
AAATAAATAAAATAATAA
Found at i:2010211 original size:28 final size:28
Alignment explanation
Indices: 2010159--2010218 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
2010149 TGTTTATATA
* *
2010159 TATTTTCATAATATTTAATATTTAAATT
1 TATTTTCATAATATTTAATAATTAAAAT
2010187 TATTTT-A-AATATTTTAATTAATTAAAAT
1 TATTTTCATAATA-TTTAA-TAATTAAAAT
2010215 TATT
1 TATT
2010219 ATATAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.14
27 6 0.21
28 18 0.64
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (28 bp):
TATTTTCATAATATTTAATAATTAAAAT
Found at i:2010300 original size:16 final size:16
Alignment explanation
Indices: 2010279--2010323 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
2010269 AAAATTATAA
*
2010279 AATAAACTAAAAAATT
1 AATAAAATAAAAAATT
*
2010295 AATAAAAATGAAAAATT
1 AAT-AAAATAAAAAATT
2010312 AATAAAAATAAA
1 AAT-AAAATAAA
2010324 TATTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 3 0.12
17 22 0.88
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (16 bp):
AATAAAATAAAAAATT
Found at i:2010310 original size:17 final size:17
Alignment explanation
Indices: 2010288--2010320 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2010278 AAATAAACTA
2010288 AAAAATTAATAAAAATG
1 AAAAATTAATAAAAATG
2010305 AAAAATTAATAAAAAT
1 AAAAATTAATAAAAAT
2010321 AAATATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAAATTAATAAAAATG
Found at i:2010808 original size:22 final size:23
Alignment explanation
Indices: 2010770--2010823 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
2010760 AAAATTTATA
* * *
2010770 TTTTTA-TTAATATATTTTTACT
1 TTTTTATTTAATAGATTTTAAAT
2010792 TTTTTATTTAAT-GATTTTAAAT
1 TTTTTATTTAATAGATTTTAAAT
*
2010814 TATTTATTTA
1 TTTTTATTTA
2010824 TTTAATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTATTTAATAGATTTTAAAT
Found at i:2010866 original size:21 final size:20
Alignment explanation
Indices: 2010828--2010876 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
2010818 TATTTATTTA
* *
2010828 ATATAATAAATTATTATATGT
1 ATATAAT-AATTAATATATAT
2010849 ATATAATAATTAA-ATATAT
1 ATATAATAATTAATATATAT
2010868 ATAATAATA
1 AT-ATAATA
2010877 TTTGTTAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.28
20 11 0.44
21 7 0.28
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATATAATAATTAATATATAT
Found at i:2016356 original size:7 final size:7
Alignment explanation
Indices: 2016344--2016384 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
2016334 GTGCCGCCCA
2016344 AGGAAGT
1 AGGAAGT
2016351 AGGAAGT
1 AGGAAGT
2016358 AGGAAGT
1 AGGAAGT
2016365 AGGAAGT
1 AGGAAGT
2016372 AGGAAGT
1 AGGAAGT
2016379 AGGAAG
1 AGGAAG
2016385 AGGGAAAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (7 bp):
AGGAAGT
Found at i:2016586 original size:16 final size:16
Alignment explanation
Indices: 2016545--2016586 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2016535 GGCTTAAAAA
2016545 TTAAAAAAA-TTAAAT
1 TTAAAAAAATTTAAAT
***
2016560 TTAATTCAATTTAAAT
1 TTAAAAAAATTTAAAT
2016576 TTAAAAAAATT
1 TTAAAAAAATT
2016587 AACTTAAATT
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAAAAAATTTAAAT
Found at i:2016996 original size:15 final size:16
Alignment explanation
Indices: 2016969--2017004 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
2016959 AATTAAAAAT
2016969 AAATTTAAATATTAAA
1 AAATTTAAATATTAAA
2016985 AAATTT-AATATTAAA
1 AAATTTAAATATTAAA
*
2017000 TAATT
1 AAATT
2017005 ACTAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATTTAAATATTAAA
Found at i:2017994 original size:16 final size:17
Alignment explanation
Indices: 2017969--2018003 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2017959 ATAAATATTG
2017969 TAATAGATTTAA-AATT
1 TAATAGATTTAATAATT
*
2017985 TAATATATTTAATAATT
1 TAATAGATTTAATAATT
2018002 TA
1 TA
2018004 TATTATATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TAATAGATTTAATAATT
Found at i:2019556 original size:17 final size:16
Alignment explanation
Indices: 2019534--2019567 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2019524 ATTTAAAATA
*
2019534 TTAATATTATATATTTT
1 TTAATATCATAT-TTTT
2019551 TTAATATCATATTTTT
1 TTAATATCATATTTTT
2019567 T
1 T
2019568 ATATTATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTAATATCATATTTTT
Found at i:2023885 original size:34 final size:34
Alignment explanation
Indices: 2023838--2024031 Score: 178
Period size: 34 Copynumber: 5.7 Consensus size: 34
2023828 GTGGTTTGTT
* *
2023838 ATTATTGACTAAATGAGAGATTTGATAGTATATC
1 ATTATTGATTAAATGAGAGATTTGATAGTTTATC
* * * *
2023872 ATTGTTGATTAAATG-GATGATTTGGTAATTTATT
1 ATTATTGATTAAATGAGA-GATTTGATAGTTTATC
* *
2023906 ATTATCGATTAAATGAGAGATTTGATAGTTT-GC
1 ATTATTGATTAAATGAGAGATTTGATAGTTTATC
* * * **
2023939 TATTATTGATTAAATGGGTGATTT-AGTGGTTTGCC
1 -ATTATTGATTAAATGAGAGATTTGA-TAGTTTATC
* *
2023974 ATTATTGACTAAATGAGAGATTTGATAGTTTACC
1 ATTATTGATTAAATGAGAGATTTGATAGTTTATC
* * *
2024008 ATTGTTGATTAAATGGGTGATTTG
1 ATTATTGATTAAATGAGAGATTTG
2024032 GTAATTTTTA
Statistics
Matches: 128, Mismatches: 26, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
33 3 0.02
34 121 0.95
35 4 0.03
ACGTcount: A:0.31, C:0.05, G:0.22, T:0.43
Consensus pattern (34 bp):
ATTATTGATTAAATGAGAGATTTGATAGTTTATC
Found at i:2023930 original size:68 final size:66
Alignment explanation
Indices: 2023836--2024042 Score: 263
Period size: 68 Copynumber: 3.1 Consensus size: 66
2023826 TTGTGGTTTG
*
2023836 TTATTATTGACTAAATGAGAGATTTGATAGTATATCATTGTTGATTAAATGGATGATTTGGTAAT
1 TTATTATTGACTAAATGAGAGATTTGATAGT-TATCATTGTTGATTAAATGGGTGATTTGGTAAT
2023901 TT
65 TT
* * * * *
2023903 ATTATTATCGATTAAATGAGAGATTTGATAGTT-TGCTATTATTGATTAAATGGGTGATTTAGTG
1 -TTATTATTGACTAAATGAGAGATTTGATAGTTAT-C-ATTGTTGATTAAATGGGTGATTTGGTA
*
2023967 GTTT
63 ATTT
** *
2023971 GCCATTATTGACTAAATGAGAGATTTGATAGTTTACCATTGTTGATTAAATGGGTGATTTGGTAA
1 -TTATTATTGACTAAATGAGAGATTTGATAG-TTATCATTGTTGATTAAATGGGTGATTTGGTAA
2024036 TTT
64 TTT
2024039 TTAT
1 TTAT
2024043 CAAATCTTTG
Statistics
Matches: 116, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
66 1 0.01
67 4 0.03
68 108 0.93
69 3 0.03
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.44
Consensus pattern (66 bp):
TTATTATTGACTAAATGAGAGATTTGATAGTTATCATTGTTGATTAAATGGGTGATTTGGTAATT
T
Found at i:2028520 original size:34 final size:33
Alignment explanation
Indices: 2028470--2028686 Score: 238
Period size: 34 Copynumber: 6.4 Consensus size: 33
2028460 GTTTACCATT
*
2028470 GATTTGGTGGTTTGCCATTATTGATTAAATGAGA
1 GATTTGGTAGTTTGCCATTATTGATTAAATG-GA
* *
2028504 GATTTGGTAGTATGCCATTGTTGATTAAATGGA
1 GATTTGGTAGTTTGCCATTATTGATTAAATGGA
* * * *
2028537 TGATTTGGTGGTTTACAATTATTGACTAAATGGGA
1 -GATTTGGTAGTTTGCCATTATTGATTAAAT-GGA
* *
2028572 GATTTGGTAGTTTGTCATTGTTGATTAAATCGGTA
1 GATTTGGTAGTTTGCCATTATTGATTAAAT-GG-A
* * **
2028607 -ATTTGGTGGTTTGCCATTGTTGACAAAATGGGA
1 GATTTGGTAGTTTGCCATTATTGATTAAAT-GGA
2028640 GATTTGGTAGTTTGCCATTATTGATTAAATGGA
1 GATTTGGTAGTTTGCCATTATTGATTAAATGGA
*
2028673 TGATTTGGTGGTTT
1 -GATTTGGTAGTTT
2028687 TTACCAAACC
Statistics
Matches: 152, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
33 6 0.04
34 142 0.93
35 4 0.03
ACGTcount: A:0.25, C:0.06, G:0.27, T:0.42
Consensus pattern (33 bp):
GATTTGGTAGTTTGCCATTATTGATTAAATGGA
Found at i:2028578 original size:68 final size:68
Alignment explanation
Indices: 2028469--2028686 Score: 330
Period size: 68 Copynumber: 3.2 Consensus size: 68
2028459 AGTTTACCAT
* * *
2028469 TGATTTGGTGGTTTGCCATTATTGATTAAATGAGAGATTTGGTAGTATGCCATTGTTGATTAAAT
1 TGATTTGGTGGTTTGCCATTATTGACTAAATGGGAGATTTGGTAGTTTGCCATTGTTGATTAAAT
2028534 GGA
66 GGA
* * *
2028537 TGATTTGGTGGTTTACAATTATTGACTAAATGGGAGATTTGGTAGTTTGTCATTGTTGATTAAAT
1 TGATTTGGTGGTTTGCCATTATTGACTAAATGGGAGATTTGGTAGTTTGCCATTGTTGATTAAAT
2028602 CGG-
66 -GGA
* * * *
2028605 TAATTTGGTGGTTTGCCATTGTTGACAAAATGGGAGATTTGGTAGTTTGCCATTATTGATTAAAT
1 TGATTTGGTGGTTTGCCATTATTGACTAAATGGGAGATTTGGTAGTTTGCCATTGTTGATTAAAT
2028670 GGA
66 GGA
2028673 TGATTTGGTGGTTT
1 TGATTTGGTGGTTT
2028687 TTACCAAACC
Statistics
Matches: 134, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
67 2 0.01
68 130 0.97
69 2 0.01
ACGTcount: A:0.25, C:0.06, G:0.27, T:0.42
Consensus pattern (68 bp):
TGATTTGGTGGTTTGCCATTATTGACTAAATGGGAGATTTGGTAGTTTGCCATTGTTGATTAAAT
GGA
Found at i:2028646 original size:102 final size:102
Alignment explanation
Indices: 2028469--2028686 Score: 273
Period size: 102 Copynumber: 2.1 Consensus size: 102
2028459 AGTTTACCAT
**
2028469 TGATTTGGTGGTTTGCCATTATTGATTAAATGAGAGATTTGGTAGTATGCCATTGTTGATTAAAT
1 TGATTTGGTGGTTTGCCATTATTGATTAAATGAGAGATTTGGTAGTATGCCATTGTTGACAAAAT
*
2028534 GGATGATTTGGTGGTTTACAATTATTGACTAAATGGGA
66 GGATGATTTGGTAGTTTACAATTATTGACTAAAT-GGA
* * * * *
2028572 -GATTTGGTAGTTTGTCATTGTTGATTAAATCG-GTA-ATTTGGTGGTTTGCCATTGTTGACAAA
1 TGATTTGGTGGTTTGCCATTATTGATTAAAT-GAG-AGATTTGGTAGTATGCCATTGTTGACAAA
* * *
2028634 ATGGGA-GATTTGGTAGTTTGCCATTATTGATTAAATGGA
64 AT-GGATGATTTGGTAGTTTACAATTATTGACTAAATGGA
2028673 TGATTTGGTGGTTT
1 TGATTTGGTGGTTT
2028687 TTACCAAACC
Statistics
Matches: 99, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
101 3 0.03
102 91 0.92
103 5 0.05
ACGTcount: A:0.25, C:0.06, G:0.27, T:0.42
Consensus pattern (102 bp):
TGATTTGGTGGTTTGCCATTATTGATTAAATGAGAGATTTGGTAGTATGCCATTGTTGACAAAAT
GGATGATTTGGTAGTTTACAATTATTGACTAAATGGA
Found at i:2033058 original size:13 final size:13
Alignment explanation
Indices: 2033036--2033068 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2033026 TATTTAAATT
*
2033036 TATTATATATAAA
1 TATTAAATATAAA
2033049 TATTAAATATAAA
1 TATTAAATATAAA
2033062 TATTAAA
1 TATTAAA
2033069 AAAAAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TATTAAATATAAA
Found at i:2033733 original size:20 final size:22
Alignment explanation
Indices: 2033684--2033730 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
2033674 GGTGGATTGA
2033684 ATTAATTGATTAATTAAAATTTT
1 ATTAATTGATTAATT-AAATTTT
*
2033707 ATTAATTGAATTAATTAATTTTT
1 ATTAATTG-ATTAATTAAATTTT
2033730 A
1 A
2033731 ATTTTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
ATTAATTGATTAATTAAATTTT
Found at i:2035201 original size:9 final size:9
Alignment explanation
Indices: 2035187--2035217 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2035177 TTCAAGGTTG
2035187 AAGATATTT
1 AAGATATTT
2035196 AAGATATTT
1 AAGATATTT
*
2035205 AAGACATTT
1 AAGATATTT
2035214 AAGA
1 AAGA
2035218 AGATTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.48, C:0.03, G:0.13, T:0.35
Consensus pattern (9 bp):
AAGATATTT
Found at i:2035231 original size:21 final size:18
Alignment explanation
Indices: 2035187--2035225 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2035177 TTCAAGGTTG
* *
2035187 AAGATATTTAAGATATTT
1 AAGACATTTAAGAGATTT
2035205 AAGACATTTAAGAAGATTT
1 AAGACATTTAAG-AGATTT
2035224 AA
1 AA
2035226 ATGACAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (18 bp):
AAGACATTTAAGAGATTT
Found at i:2038813 original size:3 final size:3
Alignment explanation
Indices: 2038805--2038850 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
2038795 TAAAAAGTAA
2038805 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2038851 ACTTTTGTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2040661 original size:14 final size:14
Alignment explanation
Indices: 2040629--2040655 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2040619 TCCAATTAAT
2040629 TAATTACTTAAAAA
1 TAATTACTTAAAAA
2040643 TAATTACTTAAAA
1 TAATTACTTAAAA
2040656 TAAATTGGTG
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:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATTACTTAAAAA
Found at i:2041467 original size:16 final size:16
Alignment explanation
Indices: 2041448--2041486 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2041438 ATTCAAAATT
*
2041448 TTTTAAATTTAAGTTA
1 TTTTAAATTTAAGTAA
*
2041464 TTTTGAATTTAAGTAA
1 TTTTAAATTTAAGTAA
2041480 TTTTAAA
1 TTTTAAA
2041487 CTCAATCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (16 bp):
TTTTAAATTTAAGTAA
Found at i:2042844 original size:7 final size:7
Alignment explanation
Indices: 2042832--2042882 Score: 68
Period size: 7 Copynumber: 7.3 Consensus size: 7
2042822 AATATATAAA
2042832 AAATTTT
1 AAATTTT
2042839 AAATTTT
1 AAATTTT
**
2042846 AAA-TAA
1 AAATTTT
2042852 AAATTTT
1 AAATTTT
2042859 AAATTTT
1 AAATTTT
2042866 AAATTTT
1 AAATTTT
2042873 AAATTATT
1 AAATT-TT
2042881 AA
1 AA
2042883 TTATATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
6 4 0.11
7 30 0.79
8 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (7 bp):
AAATTTT
Found at i:2042855 original size:20 final size:20
Alignment explanation
Indices: 2042830--2042869 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2042820 TTAATATATA
2042830 AAAAATTTTAAATTTTAAAT
1 AAAAATTTTAAATTTTAAAT
2042850 AAAAATTTTAAATTTTAAAT
1 AAAAATTTTAAATTTTAAAT
2042870 TTTAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAAATTTTAAATTTTAAAT
Found at i:2042893 original size:34 final size:35
Alignment explanation
Indices: 2042832--2042932 Score: 109
Period size: 34 Copynumber: 2.9 Consensus size: 35
2042822 AATATATAAA
* * **
2042832 AAATTTTAAATT-TTAAATAAAAATTTTAAATTTT
1 AAATTTTAAATTATTAAATTAAATTTTTAAAAATT
*
2042866 AAATTTTAAATTATT-AATTATATTTTTAAAAATT
1 AAATTTTAAATTATTAAATTAAATTTTTAAAAATT
* *
2042900 ATA-TTTAAATTAATTAAATTAAATTTATAAAAA
1 AAATTTTAAATT-ATTAAATTAAATTTTTAAAAA
2042933 AAATAAAAAC
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
33 8 0.14
34 31 0.55
35 17 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
AAATTTTAAATTATTAAATTAAATTTTTAAAAATT
Found at i:2042920 original size:20 final size:20
Alignment explanation
Indices: 2042870--2042926 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 20
2042860 AATTTTAAAT
2042870 TTTAAATT-ATT-AATTATA
1 TTTAAATTAATTAAATTATA
2042888 TTT---TTAA--AAATTATA
1 TTTAAATTAATTAAATTATA
*
2042903 TTTAAATTAATTAAATTAAA
1 TTTAAATTAATTAAATTATA
2042923 TTTA
1 TTTA
2042927 TAAAAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
15 12 0.39
16 1 0.03
18 7 0.23
20 11 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAAATTAATTAAATTATA
Found at i:2044776 original size:195 final size:195
Alignment explanation
Indices: 2044444--2044827 Score: 552
Period size: 195 Copynumber: 2.0 Consensus size: 195
2044434 TATATTTATA
* * * * *
2044444 ATATAATCGTATAATTTGACATAAATAGATAAATATATGAAAATTTATATAAAATAAAACATTAA
1 ATATAATCATATAATCTGACATAAATAGACAAATATATCAAAATTTATATAAAACAAAACATTAA
* * * * * * *
2044509 CATATAAAAAATTTATACAAATATATAATATATTGAATAGGATTATGATACGAAAAAGTAATACG
66 CATATAAAAAATTTATACAAATATATAATACATTGAATACGATTATAACACAAAAAAGTAACACA
*
2044574 AACATGATAACAAATGTAACAAAATTGAGAGTTATTTGAATACTGTCAATTAGACCGAACAACTT
131 AACATGATAACAAATGTAACAAAATTGAGAATTATTTGAATACTGTCAATTAGACCGAACAACTT
* * *
2044639 ATATAATCATATAATCTGACATAAATAGACAAATGTGTCAAAATTTATATAAAACAAAATATTAA
1 ATATAATCATATAATCTGACATAAATAGACAAATATATCAAAATTTATATAAAACAAAACATTAA
* * * * * *
2044704 CATGTTAGAAATTTATATAAATATATAATACATTGAATACGATTATAACATAAAAAAGTAACATA
66 CATATAAAAAATTTATACAAATATATAATACATTGAATACGATTATAACACAAAAAAGTAACACA
* *
2044769 AACATGATTACAAATGTAACAAAATTGAGAATTATTTGAATACTGTTAATTAGACCGAA
131 AACATGATAACAAATGTAACAAAATTGAGAATTATTTGAATACTGTCAATTAGACCGAA
2044828 TAATTTTGAA
Statistics
Matches: 165, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
195 165 1.00
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.31
Consensus pattern (195 bp):
ATATAATCATATAATCTGACATAAATAGACAAATATATCAAAATTTATATAAAACAAAACATTAA
CATATAAAAAATTTATACAAATATATAATACATTGAATACGATTATAACACAAAAAAGTAACACA
AACATGATAACAAATGTAACAAAATTGAGAATTATTTGAATACTGTCAATTAGACCGAACAACTT
Found at i:2048472 original size:80 final size:80
Alignment explanation
Indices: 2048330--2048481 Score: 241
Period size: 80 Copynumber: 1.9 Consensus size: 80
2048320 GTGTTGGTTC
* *
2048330 TATGTTGGTGTCCTCCCTAAATATGCAGCATAATGTTGCATGTGGCCTTATGGGATTAAGCCATG
1 TATGTTGGTGTCCTCCCTAAATATGCAGCATAATGTTGCATGTGACCTTATGAGATTAAGCCATG
2048395 AAAGGCTTGGAGCTA
66 AAAGGCTTGGAGCTA
* * * * *
2048410 TATGTTGGTGTCCTCCCTAGATGTGCAGCATAATGTTGTATGTGACCTTGTGAGATTGAGCCATG
1 TATGTTGGTGTCCTCCCTAAATATGCAGCATAATGTTGCATGTGACCTTATGAGATTAAGCCATG
2048475 AAAGGCT
66 AAAGGCT
2048482 ATCGAGTAGA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (80 bp):
TATGTTGGTGTCCTCCCTAAATATGCAGCATAATGTTGCATGTGACCTTATGAGATTAAGCCATG
AAAGGCTTGGAGCTA
Found at i:2049142 original size:23 final size:24
Alignment explanation
Indices: 2049098--2049148 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
2049088 TTAGATAGAC
2049098 AATAATAAAAAAAGAATAAAAA-A
1 AATAATAAAAAAAGAATAAAAATA
**
2049121 AATAATAATTAAAGAA-AGAAAATA
1 AATAATAAAAAAAGAATA-AAAATA
2049145 AATA
1 AATA
2049149 TGTATCTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.04
23 18 0.75
24 5 0.21
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (24 bp):
AATAATAAAAAAAGAATAAAAATA
Found at i:2050414 original size:17 final size:18
Alignment explanation
Indices: 2050367--2050411 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
2050357 TTTAATTCGG
2050367 TTTTAA-ATAAATCTTATT
1 TTTTAATATAAAT-TTATT
*
2050385 TTTT-AT-TCAATTTATT
1 TTTTAATATAAATTTATT
2050401 TTTTAATATAA
1 TTTTAATATAA
2050412 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
16 9 0.41
17 7 0.32
18 6 0.27
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTAATATAAATTTATT
Found at i:2059678 original size:17 final size:18
Alignment explanation
Indices: 2059638--2059679 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2059628 ATTTATTACG
*
2059638 TATTAAAATTTTAAATTA
1 TATTAATATTTTAAATTA
2059656 -ATTTAATATTTT-AATTA
1 TA-TTAATATTTTAAATTA
2059673 TATTAAT
1 TATTAAT
2059680 TATAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTAATATTTTAAATTA
Found at i:2059706 original size:30 final size:31
Alignment explanation
Indices: 2059661--2059721 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
2059651 AATTAATTTA
*
2059661 ATATTTTAATTATA-TTAATTA-TAAAAAAT
1 ATATTTTAATTATATTTAATGATTAAAAAAT
*
2059690 ATATTTTTATTAATATTTAATGATTAAAAAAT
1 ATATTTTAATT-ATATTTAATGATTAAAAAAT
2059722 TTTATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 10 0.37
30 3 0.11
31 6 0.22
32 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (31 bp):
ATATTTTAATTATATTTAATGATTAAAAAAT
Found at i:2059751 original size:27 final size:28
Alignment explanation
Indices: 2059648--2059755 Score: 73
Period size: 29 Copynumber: 3.9 Consensus size: 28
2059638 TATTAAAATT
* *
2059648 TTAAATTAATTTAATA-TTTTAATT-ATA
1 TTAAA-TAATTAAATATTTTTTATTAATA
*
2059675 TTAATTATAA-AAAATATATTTTTATTAATA
1 TTAA--ATAATTAAATAT-TTTTTATTAATA
* * * *
2059705 TTTAATGATTAAAAAATTTTATATTAA-A
1 TTAAATAATT-AAATATTTTTTATTAATA
2059733 -TAAATAATTAAATATTTTTTATT
1 TTAAATAATTAAATATTTTTTATT
2059756 TATTCAAGAT
Statistics
Matches: 62, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
26 12 0.19
27 15 0.24
28 7 0.11
29 17 0.27
30 11 0.18
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (28 bp):
TTAAATAATTAAATATTTTTTATTAATA
Found at i:2061186 original size:31 final size:31
Alignment explanation
Indices: 2061121--2061188 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
2061111 TTTTATTTAT
* * *
2061121 TATTAATAGAGTTTTTATATTTTATAAGTGA
1 TATTAATAAAGTTTATATATTTTATAAATGA
2061152 TATTAATAAAGTTATATATATTTT-TAAAAT-A
1 TATTAATAAAGTT-TATATATTTTAT-AAATGA
2061183 TATTAA
1 TATTAA
2061189 AAAATAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 20 0.62
32 12 0.38
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (31 bp):
TATTAATAAAGTTTATATATTTTATAAATGA
Found at i:2061203 original size:24 final size:24
Alignment explanation
Indices: 2061176--2061234 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
2061166 TATATATTTT
*
2061176 TAAAAT-ATATTAAAAAATAAAAAA
1 TAAAATAAT-TTAAAAAAGAAAAAA
* *
2061200 TAAAATAATTTTAAAAAGAAAATA
1 TAAAATAATTTAAAAAAGAAAAAA
2061224 TAAAATAATTT
1 TAAAATAATTT
2061235 TTTATTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 29 0.94
25 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (24 bp):
TAAAATAATTTAAAAAAGAAAAAA
Found at i:2061235 original size:24 final size:24
Alignment explanation
Indices: 2061188--2061235 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
2061178 AAATATATTA
*
2061188 AAAAATAAAAAATAAAATAATTTT
1 AAAAAGAAAAAATAAAATAATTTT
*
2061212 AAAAAGAAAATATAAAATAATTTT
1 AAAAAGAAAAAATAAAATAATTTT
2061236 TTATTTTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAAAGAAAAAATAAAATAATTTT
Found at i:2062660 original size:21 final size:19
Alignment explanation
Indices: 2062636--2062679 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
2062626 TACAAGTATA
2062636 ATAATAAAAAATAATTAAAAT
1 ATAATAAAAAATAA--AAAAT
* *
2062657 ATAATATAATATAAAAAAT
1 ATAATAAAAAATAAAAAAT
2062676 ATAA
1 ATAA
2062680 ATGTGATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
21 12 0.57
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAATAAAAAATAAAAAAT
Found at i:2062674 original size:19 final size:18
Alignment explanation
Indices: 2062652--2062709 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
2062642 AAAAATAATT
2062652 AAAATATAATATAATATAA
1 AAAATATAATAT-ATATAA
*
2062671 AAAATATAA-ATGTGATATA
1 AAAATATAATATAT-ATA-A
2062690 AAAATATAA-ATATATAA
1 AAAATATAATATATATAA
2062707 AAA
1 AAA
2062710 TCTATTTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 5 0.14
18 8 0.23
19 22 0.63
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAATATAATATATATAA
Found at i:2062690 original size:20 final size:19
Alignment explanation
Indices: 2062632--2062703 Score: 71
Period size: 19 Copynumber: 3.9 Consensus size: 19
2062622 ATTGTACAAG
* *
2062632 TATAATAATA-AAAAATAA
1 TATAAAAATATAAATATAA
2062650 T-T-AAAATAT-AATATAA
1 TATAAAAATATAAATATAA
* *
2062666 TATAAAAAATATAAATGTGA
1 TAT-AAAAATATAAATATAA
2062686 TATAAAAATATAAATATA
1 TATAAAAATATAAATATA
2062704 TAAAAATCTA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
16 12 0.28
17 2 0.05
18 1 0.02
19 20 0.47
20 8 0.19
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TATAAAAATATAAATATAA
Found at i:2062728 original size:33 final size:32
Alignment explanation
Indices: 2062691--2062773 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 32
2062681 TGTGATATAA
*
2062691 AAATATAAATATATAAAAATCTATTTATAATAT
1 AAATATAAATATATAAAAATCTATATA-AATAT
* * *
2062724 AAATATTAATATATTAAAATTTATATAAATAT
1 AAATATAAATATATAAAAATCTATATAAATAT
*
2062756 ACATATTAAATATTATAA
1 AAATA-TAAATA-TATAA
2062774 TTATCAGATT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
32 9 0.22
33 28 0.68
34 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (32 bp):
AAATATAAATATATAAAAATCTATATAAATAT
Found at i:2063355 original size:102 final size:102
Alignment explanation
Indices: 2063243--2063457 Score: 414
Period size: 102 Copynumber: 2.1 Consensus size: 102
2063233 TAGAAATTGG
*
2063243 TAATAATTAATAAATAATAAAGTTTACCATTTCATTAATCCTTGAATTTCTCTCACACCTTCTAC
1 TAATAATTAATAAATAATAAACTTTACCATTTCATTAATCCTTGAATTTCTCTCACACCTTCTAC
2063308 CATTATGCAATTACTCTCCTCTTCCATAAAGTAATAA
66 CATTATGCAATTACTCTCCTCTTCCATAAAGTAATAA
2063345 TAATAATTAATAAATAATAAACTTTACCATTTCATTAATCCTTGAATTTCTCTCACACCTTCTAC
1 TAATAATTAATAAATAATAAACTTTACCATTTCATTAATCCTTGAATTTCTCTCACACCTTCTAC
2063410 CATTATGCAATTACTCTCCTCTTCCATAAAGTAATAA
66 CATTATGCAATTACTCTCCTCTTCCATAAAGTAATAA
2063447 TAATAA-TAATA
1 TAATAATTAATA
2063458 TAATTAAAAT
Statistics
Matches: 112, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
101 5 0.04
102 107 0.96
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (102 bp):
TAATAATTAATAAATAATAAACTTTACCATTTCATTAATCCTTGAATTTCTCTCACACCTTCTAC
CATTATGCAATTACTCTCCTCTTCCATAAAGTAATAA
Found at i:2063767 original size:23 final size:22
Alignment explanation
Indices: 2063740--2063782 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2063730 ACGAATGTTT
2063740 TAATTTTACATTTTTTTTTATAA
1 TAATTTT-CATTTTTTTTTATAA
**
2063763 TAATTTTTTTTTTTTTTTAT
1 TAATTTTCATTTTTTTTTAT
2063783 TTGTTCGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
TAATTTTCATTTTTTTTTATAA
Found at i:2068083 original size:23 final size:23
Alignment explanation
Indices: 2068049--2068098 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
2068039 AACTTGTTTG
*
2068049 AAAGGCTGGCATCAGACTAACCT
1 AAAGGCTAGCATCAGACTAACCT
2068072 AAAGGCTAGCATCAGACTAACCT
1 AAAGGCTAGCATCAGACTAACCT
2068095 AAAG
1 AAAG
2068099 ACGAGCCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (23 bp):
AAAGGCTAGCATCAGACTAACCT
Found at i:2068250 original size:23 final size:23
Alignment explanation
Indices: 2068218--2068274 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
2068208 AATACAATGA
*
2068218 ATATTATATATTAAATATATTATT
1 ATATT-TATATTAAATATATTAAT
* *
2068242 ATATTTATATTTAATATTTTAAT
1 ATATTTATATTAAATATATTAAT
2068265 ATATTTATAT
1 ATATTTATAT
2068275 AATTAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 25 0.83
24 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATATTTATATTAAATATATTAAT
Found at i:2068280 original size:17 final size:17
Alignment explanation
Indices: 2068218--2068281 Score: 64
Period size: 16 Copynumber: 4.0 Consensus size: 17
2068208 AATACAATGA
*
2068218 ATATT-ATATATTAAAT
1 ATATTAATATATTTAAT
*
2068234 ATATTATTATATTT-AT
1 ATATTAATATATTTAAT
2068250 AT-TTAATAT-TTTAAT
1 ATATTAATATATTTAAT
* *
2068265 ATATTTATATAATTAAT
1 ATATTAATATATTTAAT
2068282 TTAAAAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 3 0.08
15 10 0.26
16 15 0.38
17 11 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATTAATATATTTAAT
Found at i:2068283 original size:23 final size:23
Alignment explanation
Indices: 2068241--2068308 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 23
2068231 AATATATTAT
*
2068241 TATATTTATAT--TTAATATTTTAA
1 TATATTTATATAATT-A-ATTTAAA
2068264 TATATTTATATAATTAATTTAAA
1 TATATTTATATAATTAATTTAAA
* * *
2068287 AATATATATAAAATATAATTTA
1 TATATTTATATAAT-TAATTTA
2068309 TATAAATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 28 0.74
24 8 0.21
25 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATATTTATATAATTAATTTAAA
Found at i:2073129 original size:36 final size:36
Alignment explanation
Indices: 2073059--2073129 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
2073049 ATAAAAAATA
* * *
2073059 ATAATAAAATTTAAATTCAATAATTATTTTATATAT
1 ATAATAAAATATAAATTCAATAATCATTTGATATAT
*
2073095 ATAATAAAATATAAATTACAA-CATCATTTGATATA
1 ATAATAAAATATAAATT-CAATAATCATTTGATATA
2073130 ATTTTTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 27 0.90
37 3 0.10
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (36 bp):
ATAATAAAATATAAATTCAATAATCATTTGATATAT
Found at i:2079256 original size:15 final size:15
Alignment explanation
Indices: 2079236--2079272 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
2079226 CTGACTCTTT
*
2079236 TATTATTTTTCAGTA
1 TATTATTTTTCAATA
*
2079251 TATTATTTTTTAATA
1 TATTATTTTTCAATA
2079266 TATTATT
1 TATTATT
2079273 AATTATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (15 bp):
TATTATTTTTCAATA
Found at i:2079338 original size:16 final size:17
Alignment explanation
Indices: 2079317--2079348 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2079307 TACTTAAATT
2079317 TTAAAA-AAAATAATGG
1 TTAAAACAAAATAATGG
2079333 TTAAAACAAAATAATG
1 TTAAAACAAAATAATG
2079349 TACTGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.25
Consensus pattern (17 bp):
TTAAAACAAAATAATGG
Found at i:2079571 original size:22 final size:23
Alignment explanation
Indices: 2079546--2079602 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
2079536 CAGATCACTT
2079546 ATTTATATTTATTTTT-AATTTA
1 ATTTATATTTATTTTTAAATTTA
*
2079568 ATTTA-ATATGATTTTTAAATTTA
1 ATTTATAT-TTATTTTTAAATTTA
*
2079591 TTTTATTATTTA
1 ATTTA-TATTTA
2079603 AAAATATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 2 0.07
22 12 0.43
23 10 0.36
24 2 0.07
25 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
ATTTATATTTATTTTTAAATTTA
Found at i:2080225 original size:14 final size:14
Alignment explanation
Indices: 2080206--2080233 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2080196 ACGATTATTG
2080206 CATGACGTAATAAT
1 CATGACGTAATAAT
2080220 CATGACGTAATAAT
1 CATGACGTAATAAT
2080234 AATTTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
CATGACGTAATAAT
Found at i:2080466 original size:2 final size:2
Alignment explanation
Indices: 2080459--2080487 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2080449 TCTATTTATA
2080459 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2080488 TTGGTAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2080649 original size:13 final size:13
Alignment explanation
Indices: 2080631--2080656 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2080621 CATATCATCT
2080631 TGTCACTGGCAGC
1 TGTCACTGGCAGC
2080644 TGTCACTGGCAGC
1 TGTCACTGGCAGC
2080657 ACTCTGCAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
TGTCACTGGCAGC
Found at i:2081031 original size:22 final size:21
Alignment explanation
Indices: 2080987--2081031 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2080977 TTTAATAATT
* *
2080987 TTATTTTATCTTATAAAATAA
1 TTATTTTATATTATAAAACAA
*
2081008 TTATTTTATATTAATAAACCAA
1 TTATTTTATATT-ATAAAACAA
2081030 TT
1 TT
2081032 TATCACTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATTTTATATTATAAAACAA
Found at i:2087398 original size:15 final size:15
Alignment explanation
Indices: 2087362--2087392 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2087352 TTTTATAAAT
2087362 AAAAT-AAAAATTTA
1 AAAATAAAAAATTTA
2087376 AAAATAAAAAATTTA
1 AAAATAAAAAATTTA
2087391 AA
1 AA
2087393 TTTAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATAAAAAATTTA
Found at i:2087443 original size:23 final size:24
Alignment explanation
Indices: 2087412--2087456 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
2087402 ATTAAATATT
2087412 ATTATAATTATATAAA-TTAATTAA
1 ATTATAATTATA-AAATTTAATTAA
2087436 ATTA-AATTATAAAATTTAATT
1 ATTATAATTATAAAATTTAATT
2087457 TTTTACAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 3 0.15
23 13 0.65
24 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTATAATTATAAAATTTAATTAA
Found at i:2087546 original size:30 final size:30
Alignment explanation
Indices: 2087510--2087569 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2087500 CGACAAAATC
* *
2087510 TTTTTTTATTTATAATTTTA-TTAAATTAAT
1 TTTTTTTAATTA-AATTTTATTTAAAATAAT
*
2087540 TTTTTTTAATTAATTTTTATTTAAAATAAT
1 TTTTTTTAATTAAATTTTATTTAAAATAAT
2087570 ATCAATCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (30 bp):
TTTTTTTAATTAAATTTTATTTAAAATAAT
Found at i:2087557 original size:14 final size:14
Alignment explanation
Indices: 2087522--2087563 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
2087512 TTTTTATTTA
* *
2087522 TAATTTTATTAAAT
1 TAATTTTTTTTAAT
2087536 TAATTTTTTTTAAT
1 TAATTTTTTTTAAT
2087550 TAATTTTTATTTAA
1 TAATTTTT-TTTAA
2087564 AATAATATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TAATTTTTTTTAAT
Found at i:2089319 original size:18 final size:17
Alignment explanation
Indices: 2089296--2089341 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
2089286 CTTAAAATAC
2089296 AATTTATATTTATTTATT
1 AATTTATATTTATTTA-T
*
2089314 AATTTATTTTTTATTTAT
1 AATTTA-TATTTATTTAT
2089332 AATTTA-ATTT
1 AATTTATATTT
2089342 TACATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 3 0.12
18 13 0.52
19 9 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
AATTTATATTTATTTAT
Found at i:2089328 original size:19 final size:19
Alignment explanation
Indices: 2089304--2089342 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2089294 ACAATTTATA
2089304 TTTATTTATTAATTT-ATTT
1 TTTATTTA-TAATTTAATTT
2089323 TTTATTTATAATTTAATTT
1 TTTATTTATAATTTAATTT
2089342 T
1 T
2089343 ACATAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTATTTATAATTTAATTT
Found at i:2089342 original size:18 final size:19
Alignment explanation
Indices: 2089304--2089342 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
2089294 ACAATTTATA
*
2089304 TTTATTTATTAATTTATTT
1 TTTATTTATTAATTTAATT
2089323 TTTATTTA-TAATTTAATT
1 TTTATTTATTAATTTAATT
2089341 TT
1 TT
2089343 ACATAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTATTTATTAATTTAATT
Found at i:2090927 original size:21 final size:22
Alignment explanation
Indices: 2090888--2090929 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2090878 CAATCATTAT
**
2090888 AAAATAAAAAAATTTTAAAATA
1 AAAATAAAAAAATAATAAAATA
2090910 AAAAT-AAAAAATAATAAAAT
1 AAAATAAAAAAATAATAAAAT
2090930 TATTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAATAAAAAAATAATAAAATA
Found at i:2092014 original size:2 final size:2
Alignment explanation
Indices: 2092007--2092032 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2091997 ACTTCTTGGT
2092007 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2092033 AAATAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2092734 original size:2 final size:2
Alignment explanation
Indices: 2092723--2092783 Score: 67
Period size: 2 Copynumber: 32.5 Consensus size: 2
2092713 GTTGTTGAAC
*
2092723 AT AT -T AT AT AT AT A- AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2092763 AT TT AT AT AC AT A- AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
2092784 CATAATATCT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
1 4 0.08
2 45 0.92
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2092754 original size:12 final size:12
Alignment explanation
Indices: 2092727--2092791 Score: 64
Period size: 12 Copynumber: 5.6 Consensus size: 12
2092717 TTGAACATAT
2092727 TATATATATA-A
1 TATATATATACA
* *
2092738 TATATACATATA
1 TATATATATACA
*
2092750 TATATATATATA
1 TATATATATACA
*
2092762 TATTTATATACA
1 TATATATATACA
2092774 TA-ATATTATACA
1 TATATA-TATACA
2092786 TA-ATAT
1 TATATAT
2092792 CTCAGTCTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
11 12 0.26
12 35 0.74
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (12 bp):
TATATATATACA
Found at i:2094449 original size:2 final size:2
Alignment explanation
Indices: 2094442--2094472 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2094432 TTTCAAAAAC
2094442 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2094473 CATTAACTCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2095848 original size:20 final size:19
Alignment explanation
Indices: 2095816--2095858 Score: 52
Period size: 22 Copynumber: 2.2 Consensus size: 19
2095806 TTTTAAAAAA
2095816 TAAAAAAATTAAT-TTTTT
1 TAAAAAAATTAATATTTTT
2095834 TAAAAAATATGTAATAATTTTT
1 TAAAAAA-AT-TAAT-ATTTTT
2095856 TAA
1 TAA
2095859 TTTTACTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 7 0.33
19 2 0.10
20 4 0.19
22 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TAAAAAAATTAATATTTTT
Found at i:2096726 original size:1 final size:1
Alignment explanation
Indices: 2096720--2096744 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2096710 ACTATTAACA
2096720 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
2096745 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:2099691 original size:46 final size:46
Alignment explanation
Indices: 2099619--2099710 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
2099609 AGCATTCATA
*
2099619 AATTGATTAAGGAAACAACATACCTGTTCTTCTTTGTCAGTGTATG
1 AATTGATTAAGGAAACAACATACCTGTTCTTCATTGTCAGTGTATG
* * *
2099665 AATTGATTAATGAAACAACATGCCTGTTCTTCATTGTGAGTGTATG
1 AATTGATTAAGGAAACAACATACCTGTTCTTCATTGTCAGTGTATG
2099711 TTACTTCCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.37
Consensus pattern (46 bp):
AATTGATTAAGGAAACAACATACCTGTTCTTCATTGTCAGTGTATG
Found at i:2100300 original size:2 final size:2
Alignment explanation
Indices: 2100289--2100357 Score: 84
Period size: 2 Copynumber: 34.0 Consensus size: 2
2100279 TGTGAGAGAT
* * * *
2100289 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA CA CA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2100331 TA TG TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA
2100358 GACGTTAGTT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
2 58 0.97
3 2 0.03
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2102866 original size:22 final size:21
Alignment explanation
Indices: 2102820--2102878 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
2102810 AATTATAATT
* *
2102820 TTTATAAAATTAAAATTAAATA
1 TTTAT-AAATTTAATTTAAATA
2102842 TTT-TAATATTTAATTTAAATAA
1 TTTATAA-ATTTAATTTAAAT-A
2102864 TTTATAAATTTAATT
1 TTTATAAATTTAATT
2102879 AATTTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 12 0.38
22 15 0.47
23 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTATAAATTTAATTTAAATA
Found at i:2102983 original size:25 final size:26
Alignment explanation
Indices: 2102936--2103011 Score: 74
Period size: 25 Copynumber: 3.1 Consensus size: 26
2102926 TCATTTTAAT
* *
2102936 AATAAATAATCAAATTTA-AAATTA-A
1 AATAAA-AATTAAATTTATAATTTATA
2102961 ATATAAAAATTAAATTTATAATTTATA
1 A-ATAAAAATTAAATTTATAATTTATA
2102988 AAT-AAAA-TAAATTTAT--TTTATA
1 AATAAAAATTAAATTTATAATTTATA
2103010 AA
1 AA
2103012 ATTTAAATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
22 8 0.17
24 9 0.20
25 15 0.33
26 12 0.26
27 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (26 bp):
AATAAAAATTAAATTTATAATTTATA
Found at i:2103003 original size:24 final size:23
Alignment explanation
Indices: 2102966--2103011 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
2102956 ATTAAATATA
2102966 AAAATTAAATTTATAATTTATAAAT
1 AAAATTAAATTTAT--TTTATAAAT
2102991 AAAA-TAAATTTATTTTATAAA
1 AAAATTAAATTTATTTTATAAA
2103012 ATTTAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.38
24 9 0.43
25 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAATTAAATTTATTTTATAAAT
Found at i:2103018 original size:29 final size:28
Alignment explanation
Indices: 2102952--2103021 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
2102942 TAATCAAATT
*
2102952 TAAAA-TTAAATATAAAAATTAAATTTA
1 TAAAATTTAAATAAAAAAATTAAATTTA
* * *
2102979 T-AATTTATAAATAAAATAAATTTATTTTA
1 TAAAATT-TAAATAAAA-AAATTAAATTTA
2103008 TAAAATTTAAATAA
1 TAAAATTTAAATAA
2103022 TTTAATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.06
27 2 0.06
28 8 0.24
29 18 0.53
30 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
TAAAATTTAAATAAAAAAATTAAATTTA
Found at i:2103614 original size:2 final size:2
Alignment explanation
Indices: 2103607--2103658 Score: 95
Period size: 2 Copynumber: 25.5 Consensus size: 2
2103597 GGTTAAATTT
2103607 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2103649 TA TA TCA TA T
1 TA TA T-A TA T
2103659 GTCAAATGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 47 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2105689 original size:16 final size:16
Alignment explanation
Indices: 2105668--2105716 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
2105658 ATAAATTTAT
2105668 TAAATTTTATATAATA
1 TAAATTTTATATAATA
2105684 TAAATTATTA-ATAA-A
1 TAAATT-TTATATAATA
*
2105699 TTAAAATTTATATAATA
1 -TAAATTTTATATAATA
2105716 T
1 T
2105717 TTAATATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
15 4 0.14
16 20 0.71
17 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATTTTATATAATA
Found at i:2105709 original size:32 final size:33
Alignment explanation
Indices: 2105643--2105716 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 33
2105633 ATAATATAAA
** *
2105643 ATATAATATAAATATATAAATTTATTAAATTTT
1 ATATAATATAAATATATAAATAAATTAAAATTT
*
2105676 ATATAATATAAAT-TATTAATAAATTAAAATTT
1 ATATAATATAAATATATAAATAAATTAAAATTT
2105708 ATATAATAT
1 ATATAATAT
2105717 TTAATATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 24 0.65
33 13 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
ATATAATATAAATATATAAATAAATTAAAATTT
Found at i:2107542 original size:24 final size:24
Alignment explanation
Indices: 2107515--2107560 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2107505 AATAATTTTA
2107515 TAAATAAAATATA-ATATAAATTAT
1 TAAATAAAATATATAT-TAAATTAT
*
2107539 TAAATATAATATATATTAAATT
1 TAAATAAAATATATATTAAATT
2107561 TTATATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TAAATAAAATATATATTAAATTAT
Found at i:2107557 original size:16 final size:15
Alignment explanation
Indices: 2107527--2107582 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 15
2107517 AATAAAATAT
2107527 AATATAA-ATTATTA
1 AATATAATATTATTA
2107541 AATATAATATATATTA
1 AATATAATAT-TATTA
* * *
2107557 AATTTTATATTAATTG
1 AATATAATATT-ATTA
*
2107573 TATATAATAT
1 AATATAATAT
2107583 ATATAATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
14 7 0.21
15 3 0.09
16 23 0.70
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
AATATAATATTATTA
Found at i:2107600 original size:18 final size:18
Alignment explanation
Indices: 2107579--2107629 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
2107569 ATTGTATATA
2107579 ATATATATAATATTTATT
1 ATATATATAATATTTATT
* * *
2107597 ATATTTTTAATATTAATT
1 ATATATATAATATTTATT
*
2107615 A-ATTATATTATATTT
1 ATA-TATATAATATTT
2107630 GTGATCGAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATATATATAATATTTATT
Found at i:2108059 original size:16 final size:16
Alignment explanation
Indices: 2108028--2108070 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
2108018 TATTATGATC
* *
2108028 TAATTTATTAATAATA
1 TAATTTAATAAAAATA
2108044 TAATTTAATAAAAATA
1 TAATTTAATAAAAATA
2108060 -AACTTTAATAA
1 TAA-TTTAATAA
2108071 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 2 0.08
16 22 0.92
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATTTAATAAAAATA
Found at i:2110244 original size:22 final size:21
Alignment explanation
Indices: 2110216--2110276 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
2110206 TAATATATAT
2110216 ATATATATGTATAAGGTAAAAA
1 ATATATAT-TATAAGGTAAAAA
** *
2110238 ATATATATTATAATATTAAAA
1 ATATATATTATAAGGTAAAAA
*
2110259 ATA-ATATAAATAAGGTAA
1 ATATATAT-TATAAGGTAA
2110277 GAAACATGGA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 4 0.13
21 19 0.61
22 8 0.26
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.34
Consensus pattern (21 bp):
ATATATATTATAAGGTAAAAA
Found at i:2116375 original size:21 final size:21
Alignment explanation
Indices: 2116335--2116375 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2116325 AAAATTTTAA
* * *
2116335 AAAATAATTTTTTATCTTTTG
1 AAAATAATTATTGATATTTTG
2116356 AAAATAATTATTGATATTTT
1 AAAATAATTATTGATATTTT
2116376 TAATTTTTAT
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:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (21 bp):
AAAATAATTATTGATATTTTG
Found at i:2116823 original size:20 final size:21
Alignment explanation
Indices: 2116780--2116826 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
2116770 GAATAGTAAG
2116780 AAAATTTTATTTATTTAAATTT
1 AAAATTTTATTTATTT-AATTT
2116802 AAAATTTTGATTTA-TT-ATTT
1 AAAATTTT-ATTTATTTAATTT
2116822 AAAAT
1 AAAAT
2116827 ATATTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.38
22 10 0.42
23 5 0.21
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
AAAATTTTATTTATTTAATTT
Done.