Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 31 of 100
Found at i:5737092 original size:15 final size:15
Alignment explanation
Indices: 5737068--5737111 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
5737058 AGAAATGTTA
*
5737068 GAGAAGGCTAGAAAG
1 GAGAAAGCTAGAAAG
*
5737083 GAGAAAGCTAAAAAAG
1 GAGAAAGCT-AGAAAG
*
5737099 GAGAAAGATAGAA
1 GAGAAAGCTAGAA
5737112 TAATCCTGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.57, C:0.05, G:0.32, T:0.07
Consensus pattern (15 bp):
GAGAAAGCTAGAAAG
Found at i:5741995 original size:8 final size:8
Alignment explanation
Indices: 5741982--5742038 Score: 64
Period size: 8 Copynumber: 6.9 Consensus size: 8
5741972 CTATGCTTAA
5741982 GAAAAAAT
1 GAAAAAAT
5741990 GAAAAAAT
1 GAAAAAAT
5741998 GAAAAAAAAAT
1 G---AAAAAAT
5742009 GGAAAAAAT
1 -GAAAAAAT
5742018 GAAAAAAT
1 GAAAAAAT
5742026 -AAAAAAT
1 GAAAAAAT
5742033 -AAAAAA
1 GAAAAAA
5742039 AAAAAAGTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
7 13 0.29
8 17 0.38
9 7 0.16
11 7 0.16
12 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
GAAAAAAT
Found at i:5742013 original size:20 final size:19
Alignment explanation
Indices: 5741983--5742024 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
5741973 TATGCTTAAG
5741983 AAAAAATGAAAAAATGAAA
1 AAAAAATGAAAAAATGAAA
5742002 AAAAAATGGAAAAAATGAAA
1 AAAAAAT-GAAAAAATGAAA
5742022 AAA
1 AAA
5742025 TAAAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (19 bp):
AAAAAATGAAAAAATGAAA
Found at i:5742042 original size:28 final size:28
Alignment explanation
Indices: 5741983--5742044 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
5741973 TATGCTTAAG
***
5741983 AAAAAATGAAAAAATGAAAAAAAAATGG
1 AAAAAATGAAAAAATGAAAAAAAAAAAA
5742011 AAAAAATGAAAAAAT-AAAAAATAAAAAA
1 AAAAAATGAAAAAATGAAAAAA-AAAAAA
5742039 AAAAAA
1 AAAAAA
5742045 GTAAATGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 6 0.20
28 24 0.80
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (28 bp):
AAAAAATGAAAAAATGAAAAAAAAAAAA
Found at i:5742044 original size:14 final size:14
Alignment explanation
Indices: 5742011--5742049 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
5742001 AAAAAAATGG
*
5742011 AAAAAATGAAAAAAT
1 AAAAAAT-AAAAAAA
5742026 AAAAAATAAAAAAA
1 AAAAAATAAAAAAA
*
5742040 AAAAAGTAAA
1 AAAAAATAAA
5742050 TGAAAAAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (14 bp):
AAAAAATAAAAAAA
Found at i:5743103 original size:41 final size:41
Alignment explanation
Indices: 5743058--5743484 Score: 481
Period size: 40 Copynumber: 10.1 Consensus size: 41
5743048 ATGATTGTCA
*
5743058 AGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
5743099 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
5743140 AAGAGCAATTTAC-TTTCAAAGTC---GTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
*
5743177 AGGAGCAATTTACTTTCCAAAGTCGCGTCCAAAGTCGCTGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAA-----GT-C---GT-G--GTGCCTCTGTTTAG
5743230 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
5743271 AGGAGCAATTTAC-TTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
5743311 AGGAGCAATTTAC-TTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * *
5743351 AGGAGCAATTTATTTTTTCAAAGTCGTTGAGCCTCTGTTTAG
1 AGGAGCAATTTA-CTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * * * *
5743393 AGGAGCTATTTATGTTTCTCAAAGTCGTTGAGCCTCTGATTAG
1 AGGAGCAATTTA-CTTT-TCAAAGTCGTGGTGCCTCTGTTTAG
* * * * * *
5743436 AGAAGGC-ATTTATGTTTCTCAAAGTCGTTGAGCCTCTGCTTAA
1 AGGA-GCAATTTA-CTTT-TCAAAGTCGTGGTGCCTCTGTTTAG
5743479 AGGAGC
1 AGGAGC
5743485 TTTAATAAAA
Statistics
Matches: 349, Mismatches: 17, Indels: 39
0.86 0.04 0.10
Matches are distributed among these distances:
37 26 0.07
38 6 0.02
40 88 0.25
41 78 0.22
42 42 0.12
43 67 0.19
44 5 0.01
47 1 0.00
48 2 0.01
53 34 0.10
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:5743176 original size:37 final size:39
Alignment explanation
Indices: 5743058--5743201 Score: 220
Period size: 41 Copynumber: 3.6 Consensus size: 39
5743048 ATGATTGTCA
*
5743058 AGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTC--GGTGCCTCTGTTTAG
5743099 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTC--GGTGCCTCTGTTTAG
*
5743140 AAGAGCAATTTACTTT-CAAAGTC-GTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGGTGCCTCTGTTTAG
5743177 AGGAGCAATTTACTTTCCAAAGTCG
1 AGGAGCAATTTACTTTCCAAAGTCG
5743202 CGTCCAAAGT
Statistics
Matches: 97, Mismatches: 4, Indels: 6
0.91 0.04 0.06
Matches are distributed among these distances:
37 29 0.30
38 7 0.07
40 7 0.07
41 54 0.56
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.34
Consensus pattern (39 bp):
AGGAGCAATTTACTTTCCAAAGTCGGTGCCTCTGTTTAG
Found at i:5743684 original size:5 final size:5
Alignment explanation
Indices: 5743662--5743712 Score: 50
Period size: 5 Copynumber: 9.6 Consensus size: 5
5743652 CCAATTTGGC
*
5743662 TTTTA TTTTGTA TTTTA TATTA TTTTA TTTTTA TTTTA TATTT- TTTTA
1 TTTTA -TTT-TA TTTTA TTTTA TTTTA -TTTTA TTTTA T-TTTA TTTTA
5743710 TTT
1 TTT
5743713 CTTTTGTATC
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
4 3 0.08
5 20 0.51
6 14 0.36
7 2 0.05
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:5743698 original size:21 final size:22
Alignment explanation
Indices: 5743662--5743712 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 22
5743652 CCAATTTGGC
5743662 TTTTATTTTGTATTTTATATTA
1 TTTTATTTTGTATTTTATATTA
*
5743684 TTTTATTTT-TATTTTATATTT
1 TTTTATTTTGTATTTTATATTA
5743705 TTTTATTT
1 TTTTATTT
5743713 CTTTTGTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTATTTTGTATTTTATATTA
Found at i:5743741 original size:4 final size:4
Alignment explanation
Indices: 5743691--5743929 Score: 83
Period size: 4 Copynumber: 61.2 Consensus size: 4
5743681 TTATTTTATT
* * * * *
5743691 TTTA TTT- TATA TTTT TTTA TTTC TTT- TGTA TCTTA TGTA TTTA -TTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA
* * * * * *
5743737 TTTA TTTA TTTA -TTA TTACTA TGTA TTAA TATA TGTA TATC TTTA TTTA
1 TTTA TTTA TTTA TTTA TT--TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * * *
5743786 TTTA TTTA TTTT TTCTC TGTTA -ATA TTTA TATA TGTA TTTTA TTTA TCTA
1 TTTA TTTA TTTA TT-TA T-TTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA
* * * *
5743836 GTTA TATA TTTA TATA TATTA -TAA TTTA TTTA -TTA -TTA -TTA -TTA
1 TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * *
5743880 TTTA TTTA TCTG TATA TTT- TTTA TTTA TCTTA -TTA -TTA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA
*
5743925 ATTA T
1 TTTA T
5743930 CTGTTAATTT
Statistics
Matches: 173, Mismatches: 44, Indels: 36
0.68 0.17 0.14
Matches are distributed among these distances:
3 38 0.22
4 117 0.68
5 14 0.08
6 4 0.02
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:5743845 original size:33 final size:29
Alignment explanation
Indices: 5743780--5743852 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
5743770 TGTATATCTT
* * *
5743780 TATTTATTTATTTATTTTTTCTCTGTTAA
1 TATTTATATATGTATTTTTTATCTGTTAA
5743809 TATTTATATATGTATTTTATTTATCTAGTTATA
1 TATTTATATATGTA-TTT-TTTATCT-GTTA-A
5743842 TATTTATATAT
1 TATTTATATAT
5743853 ATTATAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 12 0.32
30 3 0.08
31 6 0.16
32 4 0.11
33 12 0.32
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.64
Consensus pattern (29 bp):
TATTTATATATGTATTTTTTATCTGTTAA
Found at i:5743885 original size:16 final size:17
Alignment explanation
Indices: 5743809--5743884 Score: 68
Period size: 17 Copynumber: 4.4 Consensus size: 17
5743799 TCTCTGTTAA
5743809 TATTTATATATGTATT-T
1 TATTTATATAT-TATTAT
*
5743826 TATTTATCTAGTTATATAT
1 TATTTATATA-TTAT-TAT
* *
5743845 T-TATATATATTATAATT
1 TATTTATATATTATTA-T
5743862 TATTTAT-TATTATTAT
1 TATTTATATATTATTAT
5743878 TATTTAT
1 TATTTAT
5743885 TTATCTGTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
16 9 0.19
17 25 0.52
18 12 0.25
19 2 0.04
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (17 bp):
TATTTATATATTATTAT
Found at i:5743907 original size:23 final size:22
Alignment explanation
Indices: 5743860--5743947 Score: 82
Period size: 22 Copynumber: 4.3 Consensus size: 22
5743850 TATATTATAA
*
5743860 TTTATTTA--TTATTATTATTA
1 TTTATTTATCTTATTATTATTT
*
5743880 TTTATTTATC-T-GTA-TATTT
1 TTTATTTATCTTATTATTATTT
5743899 TTTATTTATCTTATTATTATTT
1 TTTATTTATCTTATTATTATTT
* *
5743921 TTTAATTATCTGT-TAATT-TTT
1 TTTATTTATCT-TATTATTATTT
5743942 TTTATT
1 TTTATT
5743948 ATTTTTTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
19 14 0.25
20 11 0.20
21 11 0.20
22 19 0.34
23 1 0.02
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTATTTATCTTATTATTATTT
Found at i:5743930 original size:41 final size:39
Alignment explanation
Indices: 5743860--5743947 Score: 117
Period size: 41 Copynumber: 2.3 Consensus size: 39
5743850 TATATTATAA
* *
5743860 TTTATTTA-TTATTATTATTATTTATTTATCTGTATATTT
1 TTTATTTATTTATTATTATTATTTAATTATCTGT-TAATT
*
5743899 TTTATTTATCTTATTATTATTTTTTAATTATCTGTTAATT
1 TTTATTTAT-TTATTATTATTATTTAATTATCTGTTAATT
5743939 TTT-TTTATT
1 TTTATTTATT
5743948 ATTTTTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
38 1 0.02
39 13 0.30
40 7 0.16
41 23 0.52
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.70
Consensus pattern (39 bp):
TTTATTTATTTATTATTATTATTTAATTATCTGTTAATT
Found at i:5743941 original size:19 final size:20
Alignment explanation
Indices: 5743860--5743942 Score: 82
Period size: 19 Copynumber: 4.2 Consensus size: 20
5743850 TATATTATAA
* *
5743860 TTTATTTAT-TATTATTATTA
1 TTTATTTATCTGTTA-TATTT
5743880 TTTATTTATCTG-TATATTT
1 TTTATTTATCTGTTATATTT
*
5743899 TTTATTTATCTTATTATTATTT
1 TTTATTTATC-TGTTA-TATTT
*
5743921 TTTAATTATCTGTTA-ATTT
1 TTTATTTATCTGTTATATTT
5743940 TTT
1 TTT
5743943 TTATTATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
19 21 0.39
20 12 0.22
21 7 0.13
22 14 0.26
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTATTTATCTGTTATATTT
Found at i:5743958 original size:9 final size:10
Alignment explanation
Indices: 5743854--5743959 Score: 56
Period size: 11 Copynumber: 9.8 Consensus size: 10
5743844 TTTATATATA
*
5743854 TTATAATTTAT
1 TTATTATTT-T
5743865 TTATTATTATT
1 TTATTATT-TT
5743876 ATTATTTATTTAT
1 -TTA-TTATTT-T
5743889 CTGTA-TATTTT
1 -T-TATTATTTT
*
5743900 TTATTTATCTTA
1 TTA-TTAT-TTT
5743912 TTATTATTTT
1 TTATTATTTT
*
5743922 TTAATTATCTGT
1 TT-ATTAT-TTT
*
5743934 TAATT-TTTT
1 TTATTATTTT
5743943 TTATTATTTT
1 TTATTATTTT
5743953 TT-TTATT
1 TTATTATT
5743960 CGTTTATCTA
Statistics
Matches: 76, Mismatches: 8, Indels: 24
0.70 0.07 0.22
Matches are distributed among these distances:
9 13 0.17
10 12 0.16
11 24 0.32
12 18 0.24
13 7 0.09
14 2 0.03
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.71
Consensus pattern (10 bp):
TTATTATTTT
Found at i:5743979 original size:18 final size:18
Alignment explanation
Indices: 5743952--5743995 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5743942 TTTATTATTT
5743952 TTTTTATTCGTTTATCTAA
1 TTTTT-TTCGTTTATCTAA
* *
5743971 TTTTTTTCGTTTATTTGA
1 TTTTTTTCGTTTATCTAA
5743989 TTTTTTT
1 TTTTTTT
5743996 TTCTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.73
Consensus pattern (18 bp):
TTTTTTTCGTTTATCTAA
Found at i:5743993 original size:19 final size:18
Alignment explanation
Indices: 5743951--5743996 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
5743941 TTTTATTATT
5743951 TTTTTTATTCGTTTATCTA
1 TTTTTT-TTCGTTTATCTA
* *
5743970 ATTTTTTTCGTTTATTTGA
1 TTTTTTTTCGTTTATCT-A
5743989 TTTTTTTT
1 TTTTTTTT
5743997 TCTTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.74
Consensus pattern (18 bp):
TTTTTTTTCGTTTATCTA
Found at i:5744858 original size:4 final size:4
Alignment explanation
Indices: 5744851--5744898 Score: 78
Period size: 4 Copynumber: 12.0 Consensus size: 4
5744841 TTTTTTTTTA
* *
5744851 TATT TATT TATT TATT TGTT TATT TATT TATT TGTT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
5744899 AAATTAGGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:5744874 original size:16 final size:16
Alignment explanation
Indices: 5744853--5744898 Score: 92
Period size: 16 Copynumber: 2.9 Consensus size: 16
5744843 TTTTTTTATA
5744853 TTTATTTATTTATTTG
1 TTTATTTATTTATTTG
5744869 TTTATTTATTTATTTG
1 TTTATTTATTTATTTG
5744885 TTTATTTATTTATT
1 TTTATTTATTTATT
5744899 AAATTAGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (16 bp):
TTTATTTATTTATTTG
Found at i:5744967 original size:16 final size:15
Alignment explanation
Indices: 5744938--5744980 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
5744928 TTTATTTTTA
5744938 TTTTTGTTTTACTTT
1 TTTTTGTTTTACTTT
*
5744953 TTTTTATTTTCACTTT
1 TTTTTGTTTT-ACTTT
5744969 TATTTTGTTTTA
1 T-TTTTGTTTTA
5744981 TTATTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 9 0.38
16 7 0.29
17 8 0.33
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.77
Consensus pattern (15 bp):
TTTTTGTTTTACTTT
Found at i:5744969 original size:22 final size:21
Alignment explanation
Indices: 5744920--5744982 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
5744910 ATTTAATGTT
*
5744920 CTTTTATCTTTATTTTTATTTTT
1 CTTTTA-CTTT-TTTTTATTTTA
*
5744943 GTTTTACTTTTTTTTATTTTCA
1 CTTTTACTTTTTTTTATTTT-A
5744965 CTTTTA-TTTTGTTTTATT
1 CTTTTACTTTT-TTTTATT
5744983 ATTTTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 14 0.40
22 16 0.46
23 5 0.14
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.76
Consensus pattern (21 bp):
CTTTTACTTTTTTTTATTTTA
Found at i:5744980 original size:32 final size:31
Alignment explanation
Indices: 5744933--5744993 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 31
5744923 TTATCTTTAT
*
5744933 TTTTATTTTTGTTTTACTTTTTTTTATTTTCAC
1 TTTTATTTTTGTTTTA--TTATTTTATTTTCAC
5744966 TTTTA-TTTTGTTTTATTATTTTATTTTC
1 TTTTATTTTTGTTTTATTATTTTATTTTC
5744994 TTTAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 12 0.44
32 10 0.37
33 5 0.19
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (31 bp):
TTTTATTTTTGTTTTATTATTTTATTTTCAC
Found at i:5745053 original size:58 final size:58
Alignment explanation
Indices: 5744989--5745304 Score: 288
Period size: 58 Copynumber: 5.3 Consensus size: 58
5744979 TATTATTTTA
* ***
5744989 TTTTCTTTAAATAAAACCTAAAAAAAATTATTTTTGGGAAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAATAAATTTTAAAAAAAATTATTTTTGGGAAAAAGTTGAAAGTATCAAT
* *
5745047 TTTTCTTAAAAATAAATTTTCAAAAAAAA--GTTTTTGAGAAAAAGTTGAAAGTATCAAT
1 TTTTCTT-AAAATAAATTTT-AAAAAAAATTATTTTTGGGAAAAAGTTGAAAGTATCAAT
* * *** *
5745105 TTTCCTCGAAAATCAAGGAATCAAAAAAAAAAATT-TTTTTGAGAAAAA-TTGAAAGTATCAA-
1 TTTTCT-TAAAAT--A--AAT-TTTAAAAAAAATTATTTTTGGGAAAAAGTTGAAAGTATCAAT
* *
5745166 TTTTCTTTAAAAATAAATTTTCAAAAAAAGTTTTTTTTGAGG-AAAAGTTGAAAGTATCAAT
1 TTTTC-TT-AAAATAAATTTT-AAAAAAAATTATTTTTG-GGAAAAAGTTGAAAGTATCAAT
**
5745227 TTTTCTTAAAAATAAATTTTCTAAAAAA-TATTTTT-GGAGAAAAGTTGAAAGTATCAAT
1 TTTTCTT-AAAATAAATTTTAAAAAAAATTATTTTTGGGA-AAAAGTTGAAAGTATCAAT
*
5745285 TTTCCTTAAAAATAAATTTT
1 TTTTCTT-AAAATAAATTTT
5745305 TGAGGAAAAG
Statistics
Matches: 216, Mismatches: 23, Indels: 38
0.78 0.08 0.14
Matches are distributed among these distances:
56 2 0.01
58 100 0.46
59 23 0.11
60 39 0.18
61 9 0.04
62 30 0.14
63 13 0.06
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (58 bp):
TTTTCTTAAAATAAATTTTAAAAAAAATTATTTTTGGGAAAAAGTTGAAAGTATCAAT
Found at i:5745261 original size:15 final size:16
Alignment explanation
Indices: 5745224--5745261 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5745214 TGAAAGTATC
*
5745224 AATTTTTCTTAAAAAT
1 AATTTTTCTAAAAAAT
*
5745240 AAATTTTCTAAAAAAT
1 AATTTTTCTAAAAAAT
5745256 -ATTTTT
1 AATTTTT
5745262 GGAGAAAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTTTCTAAAAAAT
Found at i:5745305 original size:102 final size:102
Alignment explanation
Indices: 5745199--5745407 Score: 314
Period size: 102 Copynumber: 2.0 Consensus size: 102
5745189 AAAAAAGTTT
* * * *
5745199 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCTAAAA-AATATTTTTG
1 TTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTCAAAAATAAAGTTTC-AAAAGAATATTTTT-
*
5745263 GAGAAAA-GTTGAAAGTATCAATTTTCCTTAAAAATAAA
64 GAGAAAATGTTGAAAATATCAATTTTCCTTAAAAATAAA
* *
5745301 TTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTCGAAATTAAAGTTTCAAAAGAATATTTTTGA
1 TTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTCAAAAATAAAGTTTCAAAAGAATATTTTTGA
*
5745366 GAAAATGTTGAAAATATCAATTTTCTTTAAAAATAAA
66 GAAAATGTTGAAAATATCAATTTTCCTTAAAAATAAA
5745403 TTTTT
1 TTTTT
5745408 TCAAAAAAAT
Statistics
Matches: 97, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
101 11 0.11
102 86 0.89
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.39
Consensus pattern (102 bp):
TTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTCAAAAATAAAGTTTCAAAAGAATATTTTTGA
GAAAATGTTGAAAATATCAATTTTCCTTAAAAATAAA
Found at i:5745306 original size:44 final size:43
Alignment explanation
Indices: 5745241--5745334 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 43
5745231 CTTAAAAATA
* *
5745241 AATTTT-C-TAAAAAATATTTTTG-GAGAAAAGTTGAAAGTATC
1 AATTTTCCTTAAAAAAAATTTTTGAG-GAAAAGTTGAAAATATC
5745282 AATTTTCCTTAAAAATAAATTTTTGAGGAAAAGTTGAAAATATC
1 AATTTTCCTTAAAAA-AAATTTTTGAGGAAAAGTTGAAAATATC
5745326 AATTTTCCT
1 AATTTTCCT
5745335 CGAAATTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
41 6 0.13
42 1 0.02
43 6 0.13
44 33 0.70
45 1 0.02
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (43 bp):
AATTTTCCTTAAAAAAAATTTTTGAGGAAAAGTTGAAAATATC
Found at i:5745436 original size:60 final size:58
Alignment explanation
Indices: 5745292--5745682 Score: 404
Period size: 60 Copynumber: 6.7 Consensus size: 58
5745282 AATTTTCCTT
* ** * *
5745292 AAAAATAA-ATTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTCGAAATTAAAGTTTC
1 AAAAA-AATATTTTTGAGGAAAAGTTGAAAATATCAATTTTCTTTAAAAATAAATTTTC
*
5745350 AAAAGAATATTTTTGA-GAAAATGTTGAAAATATCAATTTTCTTTAAAAATAAATTTTTTC
1 AAAAAAATATTTTTGAGGAAAA-GTTGAAAATATCAATTTTCTTTAAAAATAAA--TTTTC
* *
5745410 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTC-TTAAAAATAAATTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTCTTTAAAAATAAATTTTC
* * *
5745467 -AAAAATTTTTTTTGAGGAAAAGTT-AAAAGTATCAATTTT-TTTCGAAAATCAAAGTTTTC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAA-TATCAATTTTCTTT-AAAAAT-AAA-TTTTC
* *
5745526 -AAAAAATATTTTTTGA-GAAAAGTTGAAAGTATCAATTTT-TCTTAAAAATAAATTTTT
1 AAAAAAATA-TTTTTGAGGAAAAGTTGAAAATATCAATTTTCT-TTAAAAATAAATTTTC
* * ** * *
5745583 AAAAAAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTC
1 AAAAAAAT--ATTTTTGAGGAAAAGTTGAAAATATCAATTTTCTTTAAAAATAAATTTTC
* * * *
5745643 AAAAGAATATTTTTGAGAAAAAATTAAAAATATCAATTTT
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTT
5745683 TTCTGCACAA
Statistics
Matches: 285, Mismatches: 30, Indels: 36
0.81 0.09 0.10
Matches are distributed among these distances:
55 3 0.01
56 33 0.12
57 21 0.07
58 80 0.28
59 53 0.19
60 90 0.32
61 5 0.02
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.38
Consensus pattern (58 bp):
AAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTCTTTAAAAATAAATTTTC
Found at i:5745509 original size:59 final size:58
Alignment explanation
Indices: 5745300--5745683 Score: 383
Period size: 58 Copynumber: 6.6 Consensus size: 58
5745290 TTAAAAATAA
* ** * *
5745300 ATTTTTGAGGAAAAGTTGAAAA-TATCAATTTTCCTCGAAATTAAA-GTTTCAAAAGAAT
1 ATTTTTGAGGAAAAGTT-AAAAGTATCAATTTTTCTTAAAAATAAATTTTTCAAAA-AAT
5745358 ATTTTTGA-GAAAATGTTGAAAA-TATCAA-TTTTCTTTAAAAATAAATTTTTTCAAAAAAAT
1 ATTTTTGAGGAAAA-GTT-AAAAGTATCAATTTTTC-TTAAAAATAAA-TTTTTC-AAAAAAT
* * *
5745418 ATTTTTGGGGAAAAGTTGAAAGTATCAA-TTTTCTTAAAAATAAA-TTTTCAAAAATT
1 ATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAATTTTTCAAAAAAT
* * *
5745474 TTTTTTGAGGAAAAGTTAAAAGTATCAATTTTT-TTCGAAAATCAAAGTTTTCAAAAAAT
1 ATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTT-AAAAAT-AAATTTTTCAAAAAAT
* *
5745533 ATTTTTTGA-GAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTAAAAAAAT
1 A-TTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAATTTTTCAAAAAAT
* * ** * *
5745591 AAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAA-GTTTCAAAAGAAT
1 --ATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAATTTTTCAAAA-AAT
* * *
5745651 ATTTTTGAGAAAAAATTAAAAATATCAATTTTT
1 ATTTTTGAGGAAAAGTTAAAAGTATCAATTTTT
5745684 TCTGCACAAA
Statistics
Matches: 280, Mismatches: 29, Indels: 34
0.82 0.08 0.10
Matches are distributed among these distances:
56 33 0.12
57 23 0.08
58 75 0.27
59 67 0.24
60 73 0.26
61 9 0.03
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.39
Consensus pattern (58 bp):
ATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAATTTTTCAAAAAAT
Found at i:5745561 original size:175 final size:174
Alignment explanation
Indices: 5745300--5745684 Score: 521
Period size: 175 Copynumber: 2.2 Consensus size: 174
5745290 TTAAAAATAA
** *
5745300 ATTTTTGAGGAAAAGTTGAAAATATCAATTTTCCTCGAAATTAAAGTTTCAAAAGAATATTTTTG
1 ATTTTTGAGGAAAAGTT-AAAATATCAATTTTTTTCGAAATCAAAGTTTCAAAAGAATATTTTTG
*
5745365 AGAAAATGTTGAAAATATCAA-TTTTCTTTAAAAATAAATTTTTTCAAAAAAAT-ATTTTTGGGG
65 AGAAAATGTTGAAAATATCAATTTTTC-TTAAAAATAAA-TTTTT-AAAAAAATAATTTTTGAGG
* * *
5745428 AAAAGTTGAAAGTATCAATTTT-CTTAAAAATAAATTTTCAAAA-ATT
127 AAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAAGTTTCAAAAGAAT
*
5745474 TTTTTTGAGGAAAAGTTAAAAGTATCAATTTTTTTCGAAAATCAAAGTTTTCAAAA-AATATTTT
1 ATTTTTGAGGAAAAGTTAAAA-TATCAATTTTTTTCG-AAATCAAAG-TTTCAAAAGAATA-TTT
*
5745538 TTGAGAAAA-GTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTAAAAAAATAAATTTTTGAG
62 TTGAGAAAATGTTGAAAATATCAATTTTTCTTAAAAATAAATTTTTAAAAAAAT-AATTTTTGAG
* *
5745602 GAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTCAAAAGAAT
126 GAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAAGTTTCAAAAGAAT
* *
5745651 ATTTTTGAGAAAAAATTAAAAATATCAATTTTTT
1 ATTTTTGAGGAAAAGTT-AAAATATCAATTTTTT
5745685 CTGCACAAAA
Statistics
Matches: 187, Mismatches: 14, Indels: 17
0.86 0.06 0.08
Matches are distributed among these distances:
173 12 0.06
174 34 0.18
175 67 0.36
176 42 0.22
177 28 0.15
178 4 0.02
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (174 bp):
ATTTTTGAGGAAAAGTTAAAATATCAATTTTTTTCGAAATCAAAGTTTCAAAAGAATATTTTTGA
GAAAATGTTGAAAATATCAATTTTTCTTAAAAATAAATTTTTAAAAAAATAATTTTTGAGGAAAA
GTTGAAAGTATCAATTTTCCTCAAAAATAAAGTTTCAAAAGAAT
Found at i:5748476 original size:23 final size:24
Alignment explanation
Indices: 5748450--5748499 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
5748440 TGTTTAATTA
* *
5748450 ATTAAGTT-ATAATTTATTAGTTG
1 ATTAAGTTAATAATGTAATAGTTG
*
5748473 ATT-ATTTAATAATGTAATAGTTG
1 ATTAAGTTAATAATGTAATAGTTG
5748496 ATTA
1 ATTA
5748500 TATAAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (24 bp):
ATTAAGTTAATAATGTAATAGTTG
Found at i:5748500 original size:23 final size:22
Alignment explanation
Indices: 5748457--5748521 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 22
5748447 TTAATTAAGT
* * *
5748457 TATAATTTATTAGTTGATTATT
1 TATAATATAATAGTTGATTATA
*
5748479 TAATAATGTAATAGTTGATTATA
1 T-ATAATATAATAGTTGATTATA
*
5748502 TA-AATATAATACTTGATTAT
1 TATAATATAATAGTTGATTAT
5748522 GAGTTTAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 16 0.43
22 2 0.05
23 19 0.51
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (22 bp):
TATAATATAATAGTTGATTATA
Found at i:5749431 original size:13 final size:13
Alignment explanation
Indices: 5749413--5749437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5749403 TTCTCCTATC
5749413 AAATCCATCTTAG
1 AAATCCATCTTAG
5749426 AAATCCATCTTA
1 AAATCCATCTTA
5749438 AAAAGGGCTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATCCATCTTAG
Found at i:5753980 original size:23 final size:25
Alignment explanation
Indices: 5753936--5753983 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5753926 AAAATTATGC
*
5753936 TTTATTTTTTAAAATATCTAAAATT
1 TTTATTTTTTAAAACATCTAAAATT
*
5753961 TTTATTTTTT-ACACAT-TAAAATT
1 TTTATTTTTTAAAACATCTAAAATT
5753984 ATTTTTACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 4 0.19
25 10 0.48
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTATTTTTTAAAACATCTAAAATT
Found at i:5753988 original size:25 final size:27
Alignment explanation
Indices: 5753926--5753988 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 27
5753916 GGATATTTTC
*
5753926 AAAATTATGCTTTATTTTTTAAAATATCT
1 AAAATTAT--TTTATTTTTTAAAACATCT
*
5753955 AAAA-T-TTTTATTTTTT-ACACAT-T
1 AAAATTATTTTATTTTTTAAAACATCT
5753978 AAAATTATTTT
1 AAAATTATTTT
5753989 TACTTTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
23 5 0.17
24 5 0.17
25 14 0.47
27 1 0.03
28 1 0.03
29 4 0.13
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (27 bp):
AAAATTATTTTATTTTTTAAAACATCT
Found at i:5765538 original size:35 final size:35
Alignment explanation
Indices: 5765485--5765558 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
5765475 TCGAATTAAG
* * *
5765485 TTAATCATGGACTTTTAATTTTAATTATCAATAAA
1 TTAATCATGAACTCTTAATTTTAATAATCAATAAA
*
5765520 TTAATCATGAACTCTTAATTTTAATAATCAATAAG
1 TTAATCATGAACTCTTAATTTTAATAATCAATAAA
5765555 TTAA
1 TTAA
5765559 GTTCTGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.43
Consensus pattern (35 bp):
TTAATCATGAACTCTTAATTTTAATAATCAATAAA
Found at i:5773612 original size:25 final size:24
Alignment explanation
Indices: 5773537--5773612 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 24
5773527 AAATATTTAA
*
5773537 ATTTTAA-TTTT-AATTTAATTTA
1 ATTTTAATTTTTAAATTTAATTTG
* * *
5773559 AATTTATTTTTTAAAATTTGA-TTG
1 ATTTTAATTTTT-AAATTTAATTTG
5773583 AATTTTAATTTTTAAATTTAAATTTG
1 -ATTTTAATTTTTAAATTT-AATTTG
5773609 ATTT
1 ATTT
5773613 ACAATAAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
22 5 0.12
23 4 0.10
24 8 0.20
25 21 0.51
26 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
ATTTTAATTTTTAAATTTAATTTG
Found at i:5773795 original size:19 final size:20
Alignment explanation
Indices: 5773749--5773796 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
5773739 ATAATAGTTT
5773749 TTTTAATTAAAATAATAAAA
1 TTTTAATTAAAATAATAAAA
* * *
5773769 ATAT-ATTAAAAT-TTAAAA
1 TTTTAATTAAAATAATAAAA
5773787 TTTTAATTAA
1 TTTTAATTAA
5773797 GCTTGTAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
18 7 0.32
19 13 0.59
20 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTTAATTAAAATAATAAAA
Found at i:5774602 original size:14 final size:14
Alignment explanation
Indices: 5774585--5774627 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
5774575 AATAAAAATA
5774585 AATTAATTTAATTT
1 AATTAATTTAATTT
5774599 AATTAATTTAATTTT
1 AATTAATTTAA-TTT
* *
5774614 AAATAATTTGATTT
1 AATTAATTTAATTT
5774628 TCAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
AATTAATTTAATTT
Found at i:5774635 original size:16 final size:15
Alignment explanation
Indices: 5774583--5774635 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
5774573 TTAATAAAAA
5774583 TAAATTAATTTAA-TT
1 TAAA-TAATTTAATTT
*
5774598 TAATTAATTTAATTT
1 TAAATAATTTAATTT
*
5774613 TAAATAATTTGATTT
1 TAAATAATTTAATTT
5774628 TCAAATAA
1 T-AAATAA
5774636 AATTATTGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
14 8 0.24
15 19 0.58
16 6 0.18
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
TAAATAATTTAATTT
Found at i:5787678 original size:10 final size:11
Alignment explanation
Indices: 5787639--5787684 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
5787629 GCTGGAACAG
5787639 CTTTTATCTTTGT
1 CTTTT-TCTTT-T
5787652 -TTTTTCTCTTT
1 CTTTTTCT-TTT
5787663 CTTTTTCTTTT
1 CTTTTTCTTTT
5787674 C-TTTTCTTTT
1 CTTTTTCTTTT
5787684 C
1 C
5787685 CTTCTTTGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.32
11 8 0.26
12 13 0.42
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (11 bp):
CTTTTTCTTTT
Found at i:5790432 original size:14 final size:14
Alignment explanation
Indices: 5790413--5790439 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5790403 CAAATCGATC
5790413 AAATTAATTTTAAT
1 AAATTAATTTTAAT
5790427 AAATTAATTTTAA
1 AAATTAATTTTAA
5790440 AATTAAATTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTAATTTTAAT
Found at i:5790485 original size:15 final size:15
Alignment explanation
Indices: 5790464--5790498 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
5790454 TTAATAAATA
5790464 AAAATAATTTAATTT
1 AAAATAATTTAATTT
*
5790479 TAAATAATTTAATTT
1 AAAATAATTTAATTT
5790494 AAAAT
1 AAAAT
5790499 TAATCGAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AAAATAATTTAATTT
Found at i:5791076 original size:16 final size:16
Alignment explanation
Indices: 5791031--5791077 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
5791021 TATATTTTAT
*
5791031 ATTTTTATATCAATATA
1 ATTTTTATAT-AAAATA
*
5791048 AATTTTA-AT-AAATA
1 ATTTTTATATAAAATA
5791062 ATTTTTATATAAAATA
1 ATTTTTATATAAAATA
5791078 TAAAAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 10 0.40
15 2 0.08
16 7 0.28
17 6 0.24
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTTTATATAAAATA
Found at i:5795847 original size:23 final size:23
Alignment explanation
Indices: 5795821--5795865 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5795811 TTTCATATTT
5795821 ATTGAAT-ATTATTTTTTAAAATA
1 ATTGAATGATT-TTTTTTAAAATA
*
5795844 ATTGTATGATTTTTTTTAAAAT
1 ATTGAATGATTTTTTTTAAAAT
5795866 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (23 bp):
ATTGAATGATTTTTTTTAAAATA
Found at i:5801206 original size:49 final size:49
Alignment explanation
Indices: 5801150--5801246 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
5801140 GGGAATTGAG
* *
5801150 AGTAAAGACTTAAACAAGTTAATTACATGTGTCACACATGTGAATAGTT
1 AGTAAAGACTTAAAAAAGTTAATTACATGTGCCACACATGTGAATAGTT
5801199 AGTAAAGACTTAAAAAAGTTAATTACATGTGCCACACATGTGAATAGT
1 AGTAAAGACTTAAAAAAGTTAATTACATGTGCCACACATGTGAATAGT
5801247 CAATTATAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.29
Consensus pattern (49 bp):
AGTAAAGACTTAAAAAAGTTAATTACATGTGCCACACATGTGAATAGTT
Found at i:5810756 original size:2 final size:2
Alignment explanation
Indices: 5810716--5810744 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5810706 CTCTCTCTCT
5810716 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
5810745 TGCATGCACA
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:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:5811052 original size:24 final size:24
Alignment explanation
Indices: 5811020--5811069 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
5811010 AGCTGGATCA
5811020 CCCACCATTTCTGTTAAACTAGAG
1 CCCACCATTTCTGTTAAACTAGAG
5811044 CCCACCATTTCTGTTAAACTAGAG
1 CCCACCATTTCTGTTAAACTAGAG
5811068 CC
1 CC
5811070 AGTTTCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.32, G:0.12, T:0.28
Consensus pattern (24 bp):
CCCACCATTTCTGTTAAACTAGAG
Found at i:5820729 original size:20 final size:22
Alignment explanation
Indices: 5820685--5820734 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
5820675 TAATTTTAGG
* *
5820685 GATACAAATACTTAATTATAGA
1 GATACAAATACTTAAATATACA
5820707 GATACAAAT-C-TAAATATACA
1 GATACAAATACTTAAATATACA
5820727 GATTACAA
1 GA-TACAA
5820735 GATTACAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.40
21 6 0.24
22 9 0.36
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.28
Consensus pattern (22 bp):
GATACAAATACTTAAATATACA
Found at i:5825550 original size:25 final size:22
Alignment explanation
Indices: 5825504--5825548 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5825494 ACCTTTCATG
5825504 TCTCCTCCAATAAACAACTTTT
1 TCTCCTCCAATAAACAACTTTT
5825526 TCTCCTCCAATAAACAACTTTT
1 TCTCCTCCAATAAACAACTTTT
5825548 T
1 T
5825549 TTCATTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (22 bp):
TCTCCTCCAATAAACAACTTTT
Found at i:5834286 original size:90 final size:90
Alignment explanation
Indices: 5834133--5834303 Score: 297
Period size: 90 Copynumber: 1.9 Consensus size: 90
5834123 TGGACAATCA
* ****
5834133 CTACCTTCATTGTATCTACTGCAAGAAGAACAACTCCTTGATCTGTCCCTATTTTTTTTGCTTCC
1 CTACCTTCATTATATCTACTGCAAGAAGAACAACTCCTTGATCTGTCCCTACGCCTTTTGCTTCC
5834198 TCTTTTAACCTTCTCCGGCATTTCG
66 TCTTTTAACCTTCTCCGGCATTTCG
5834223 CTACCTTCATTATATCTACTGCAAGAAGAACAACTCCTTGATCTGTCCCTACGCCTTTTGCTTCC
1 CTACCTTCATTATATCTACTGCAAGAAGAACAACTCCTTGATCTGTCCCTACGCCTTTTGCTTCC
5834288 TCTTTTAACCTTCTCC
66 TCTTTTAACCTTCTCC
5834304 AGAATTCTTC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 76 1.00
ACGTcount: A:0.20, C:0.31, G:0.10, T:0.39
Consensus pattern (90 bp):
CTACCTTCATTATATCTACTGCAAGAAGAACAACTCCTTGATCTGTCCCTACGCCTTTTGCTTCC
TCTTTTAACCTTCTCCGGCATTTCG
Found at i:5839905 original size:2 final size:2
Alignment explanation
Indices: 5839900--5839928 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5839890 TTTTTTTTTA
5839900 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5839929 AGGAAGTGAT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5840286 original size:30 final size:30
Alignment explanation
Indices: 5840250--5840308 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
5840240 TTGATAATTC
*
5840250 ATATATT-TATATTATATTTTATATGAAAAT
1 ATATATTGT-TATTATATTTTATATAAAAAT
*
5840280 ATATATTGTTATTTTATTTTATATAAAAA
1 ATATATTGTTATTATATTTTATATAAAAA
5840309 ATAGGAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
ATATATTGTTATTATATTTTATATAAAAAT
Found at i:5841302 original size:21 final size:21
Alignment explanation
Indices: 5841278--5841318 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5841268 ATTGATGACA
5841278 TTATTT-TTTATATTTTTAAAT
1 TTATTTATTTA-ATTTTTAAAT
5841299 TTATTTATTTAATTTTTAAA
1 TTATTTATTTAATTTTTAAA
5841319 AATATTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTTATTTAATTTTTAAAT
Found at i:5841324 original size:21 final size:21
Alignment explanation
Indices: 5841279--5841324 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5841269 TTGATGACAT
**
5841279 TATTTTTTATATTTTTAAATT
1 TATTTTTTATATTTTTAAAAA
5841300 TATTTATTTA-ATTTTTAAAAA
1 TATTT-TTTATATTTTTAAAAA
5841321 TATT
1 TATT
5841325 ACATATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTTTTTATATTTTTAAAAA
Found at i:5841343 original size:22 final size:21
Alignment explanation
Indices: 5841312--5841389 Score: 61
Period size: 23 Copynumber: 3.6 Consensus size: 21
5841302 TTTATTTAAT
*
5841312 TTTTAAAAATATTACATATTTA
1 TTTTATAAATATTA-ATATTTA
5841334 TTTTATAAATTATTAATAGTATTA
1 TTTTATAAA-TATTAATA-T-TTA
* *
5841358 TTATATATAA-ATTAATATATA
1 TTTTATA-AATATTAATATTTA
*
5841379 -TTAATAAATAT
1 TTTTATAAATAT
5841390 ATTTATATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
19 2 0.04
20 6 0.13
21 2 0.04
22 12 0.26
23 13 0.28
24 9 0.20
25 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (21 bp):
TTTTATAAATATTAATATTTA
Found at i:5841347 original size:23 final size:22
Alignment explanation
Indices: 5841288--5841380 Score: 59
Period size: 23 Copynumber: 4.0 Consensus size: 22
5841278 TTATTTTTTA
5841288 TATTTT-TAAATTTATT--TATT
1 TATTTTATAAA-TTATTAATATT
*
5841308 TAATTTT-TAAAAATATTACATATT
1 T-ATTTTAT-AAATTATTA-ATATT
5841332 TATTTTATAAATTATTAATAGTAT
1 TATTTTATAAATTATTAATA-T-T
*
5841356 TATTATATATAAATTAATATATATT
1 TATT-T-TATAAATTATTA-ATATT
5841381 AATAAATATA
Statistics
Matches: 59, Mismatches: 3, Indels: 17
0.75 0.04 0.22
Matches are distributed among these distances:
20 1 0.02
21 10 0.17
22 6 0.10
23 14 0.24
24 11 0.19
25 2 0.03
26 12 0.20
27 3 0.05
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (22 bp):
TATTTTATAAATTATTAATATT
Found at i:5841399 original size:14 final size:14
Alignment explanation
Indices: 5841359--5841400 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
5841349 ATAGTATTAT
* *
5841359 TATATATAAATTAA
1 TATATATTAATAAA
5841373 TATATATTAATAAA
1 TATATATTAATAAA
5841387 TATAT-TTATATAAA
1 TATATATTA-ATAAA
5841401 ATCAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 3 0.12
14 22 0.88
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATATTAATAAA
Found at i:5848517 original size:3 final size:3
Alignment explanation
Indices: 5848504--5848538 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
5848494 TTGGAATTTT
* *
5848504 TTA TGA TTA TTA TTA TTA TTA TTA TTA TTT TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5848539 CATAATCTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5856950 original size:16 final size:16
Alignment explanation
Indices: 5856929--5856962 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5856919 AGAACAAAAT
*
5856929 AATCATACCGGTGATG
1 AATCATACCAGTGATG
5856945 AATCATACCAGTGATG
1 AATCATACCAGTGATG
5856961 AA
1 AA
5856963 CATCGTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.24
Consensus pattern (16 bp):
AATCATACCAGTGATG
Found at i:5862963 original size:4 final size:4
Alignment explanation
Indices: 5862954--5863020 Score: 64
Period size: 4 Copynumber: 16.5 Consensus size: 4
5862944 AAATATTTAC
** * * *
5862954 AAAT AAAT AAAT GCAT AAAT -AGT AAAAT AAAT GAAAT AAAC AAAT AACT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT -AAAT AAAT AAAT AAAT
5863003 AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AA
5863021 TTATGATAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
3 2 0.04
4 42 0.84
5 6 0.12
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:5864029 original size:20 final size:20
Alignment explanation
Indices: 5863957--5864124 Score: 66
Period size: 20 Copynumber: 8.4 Consensus size: 20
5863947 AAGATTCGAA
* *
5863957 ATTCGCAATTGAAATTCAAGG
1 ATTCTCAATT-AAATTCAAAG
* *
5863978 ATTCCCAACTTGAATATCAAAG
1 ATTCTCAA-TTAAAT-TCAAAG
*
5864000 GTTCGT-AATTAAATTCAAAG
1 ATTC-TCAATTAAATTCAAAG
* *
5864020 ATTCTCAATTTGAATTTAAAG
1 ATTCTCAA-TTAAATTCAAAG
*
5864041 ACTT-GCAA--AACATTC-AAG
1 A-TTCTCAATTAA-ATTCAAAG
* * *
5864059 GTTCTCTA-CAAATTCAAAG
1 ATTCTCAATTAAATTCAAAG
5864078 ATT-TGCAATTAAATTCAAA-
1 ATTCT-CAATTAAATTCAAAG
* **
5864097 ATTTCACAAACAAA-TCAAAG
1 A-TTCTCAATTAAATTCAAAG
5864117 ATTCTCAA
1 ATTCTCAA
5864125 GATTCAAGAT
Statistics
Matches: 110, Mismatches: 22, Indels: 32
0.67 0.13 0.20
Matches are distributed among these distances:
17 2 0.02
18 11 0.10
19 25 0.23
20 29 0.26
21 29 0.26
22 14 0.13
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (20 bp):
ATTCTCAATTAAATTCAAAG
Found at i:5864146 original size:18 final size:18
Alignment explanation
Indices: 5864123--5864212 Score: 83
Period size: 19 Copynumber: 4.8 Consensus size: 18
5864113 AAAGATTCTC
*
5864123 AAGATTCAAGATTTGTAA
1 AAGATTCAAGATTTGCAA
* *
5864141 AAGATTCAAAAGTTTACAA
1 AAGATTCAAGA-TTTGCAA
* *
5864160 AAAATTTCAAGATTTACAA
1 AAGA-TTCAAGATTTGCAA
5864179 AAGATTTCAAGATTTGC-A
1 AAGA-TTCAAGATTTGCAA
*
5864197 AAGGTTCCAAGATTTG
1 AAGATT-CAAGATTTG
5864213 TAAAGAATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
17 2 0.03
18 23 0.38
19 30 0.49
20 6 0.10
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.31
Consensus pattern (18 bp):
AAGATTCAAGATTTGCAA
Found at i:5864393 original size:16 final size:16
Alignment explanation
Indices: 5864358--5864463 Score: 83
Period size: 16 Copynumber: 6.6 Consensus size: 16
5864348 AAAAGATTAA
5864358 AAATTCATAAGAATTTT
1 AAATTCATAAGAA-TTT
*
5864375 AAATTTATAAGAATTT
1 AAATTCATAAGAATTT
*
5864391 AAATTCACAAG-ATTT
1 AAATTCATAAGAATTT
**
5864406 AAATTTTTCAAGAATTT
1 AAATTCAT-AAGAATTT
*
5864423 -AATTCTTAA-AATTTT
1 AAATTCATAAGAA-TTT
* * * *
5864438 AGATTCGTAAGAACTC
1 AAATTCATAAGAATTT
5864454 AAATTCATAA
1 AAATTCATAA
5864464 TTGAGAGATT
Statistics
Matches: 71, Mismatches: 13, Indels: 11
0.75 0.14 0.12
Matches are distributed among these distances:
14 2 0.03
15 14 0.20
16 37 0.52
17 18 0.25
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (16 bp):
AAATTCATAAGAATTT
Found at i:5864423 original size:32 final size:33
Alignment explanation
Indices: 5864358--5864424 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
5864348 AAAAGATTAA
*
5864358 AAATTCATAAGAATTTTAAATTTATAAGAATTT
1 AAATTCACAAGAATTTTAAATTTATAAGAATTT
*
5864391 AAATTCACAAG-A-TTTAAATTTTTCAAGAATTT
1 AAATTCACAAGAATTTTAAATTTAT-AAGAATTT
5864423 AA
1 AA
5864425 TTCTTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 10 0.32
32 11 0.35
33 10 0.32
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (33 bp):
AAATTCACAAGAATTTTAAATTTATAAGAATTT
Found at i:5864997 original size:109 final size:109
Alignment explanation
Indices: 5864706--5865126 Score: 551
Period size: 109 Copynumber: 3.9 Consensus size: 109
5864696 TTCAAGATTT
* * * * *
5864706 CATCAAAAATTTCAAAGCTTCTCATTCGAGATCAAAGATTCTCACTT-GATAATTTTTAAAGTTT
1 CATCTAAAATTTCAAAGCTTCTCATTCGAGTTCAAAGATTCACA-TTCGATAAATTTTAGAGTTT
* * *
5864770 CACATATAAATTCAAAGGTTATCATTCAAAATATTTAAGGGTTCA
65 CACATATAAATTCAAAGGTTCTTATTCAAAAAATTTAAGGGTTCA
* * * *
5864815 CATC-AAAATTTCAAAGCTTCTCATTCTAATTTAAAGATTTTACATTCGAT-AATTTTAGAGTTT
1 CATCTAAAATTTCAAAGCTTCTCATTCGAGTTCAAAGA-TTCACATTCGATAAATTTTAGAGTTT
* * *
5864878 CACATCTAAATTCAAAGGTTTTTATTCAAAAAATTTAAGGGTTTA
65 CACATATAAATTCAAAGGTTCTTATTCAAAAAATTTAAGGGTTCA
*
5864923 CATCTAAAATTTCAAAGCTTATCATTCGAGTTCAAAGATTCACATTCGATAAATTTTAGAGTTTC
1 CATCTAAAATTTCAAAGCTTCTCATTCGAGTTCAAAGATTCACATTCGATAAATTTTAGAGTTTC
* * *
5864988 ACATATAAATTTAAAGGTTCTTATTTAAAAAATTTAGGGGTTCA
66 ACATATAAATTCAAAGGTTCTTATTCAAAAAATTTAAGGGTTCA
* * * * * **
5865032 AATCTAAAATTTCAAAGGTTTTCATTCGAGTTCAAATATTCACATTTGATAAATTTTAGAGCCTC
1 CATCTAAAATTTCAAAGCTTCTCATTCGAGTTCAAAGATTCACATTCGATAAATTTTAGAGTTTC
* *
5865097 ACATCTAAATTCAAAGGTTCTTATTTAAAA
66 ACATATAAATTCAAAGGTTCTTATTCAAAA
5865127 CTCAAAGATT
Statistics
Matches: 275, Mismatches: 33, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
108 97 0.35
109 178 0.65
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (109 bp):
CATCTAAAATTTCAAAGCTTCTCATTCGAGTTCAAAGATTCACATTCGATAAATTTTAGAGTTTC
ACATATAAATTCAAAGGTTCTTATTCAAAAAATTTAAGGGTTCA
Found at i:5865006 original size:217 final size:218
Alignment explanation
Indices: 5864706--5865126 Score: 578
Period size: 217 Copynumber: 1.9 Consensus size: 218
5864696 TTCAAGATTT
* * *
5864706 CATCAAAAATTTCAAAGCTTCTCATTCGAGATCAAAGATTCTCACTTGATAATTTTTAAAGTTTC
1 CATCAAAAATTTCAAAGCTTATCATTCGAGATCAAAGATTCACACTTGATAAATTTTAAAGTTTC
* *
5864771 ACATATAAATTCAAAGGTTATCATTCAAAATATTTAAGGGTTCACATC-AAAATTTCAAAGCTTC
66 ACATATAAATTCAAAGGTTATCATTCAAAAAATTTAAGGGTTCAAATCTAAAATTTCAAAGCTTC
* * * ** *
5864835 TCATTCTAATTTAAAGATTTTACATTCGAT-AATTTTAGAGTTTCACATCTAAATTCAAAGGTTT
131 TCATTCGAATTCAAAGA-TTCACATTCGATAAATTTTAGAGCCTCACATCTAAATTCAAAGGTTC
5864899 TTATTCAAAAAATTTAAGGGTTTA
195 TTATTCAAAAAATTTAAGGGTTTA
* * *
5864923 CATCTAAAATTTCAAAGCTTATCATTCGAGTTCAAAGATTCACA-TTCGATAAATTTTAGAGTTT
1 CATCAAAAATTTCAAAGCTTATCATTCGAGATCAAAGATTCACACTT-GATAAATTTTAAAGTTT
* * * * * *
5864987 CACATATAAATTTAAAGGTTCTTATTTAAAAAATTTAGGGGTTCAAATCTAAAATTTCAAAGGTT
65 CACATATAAATTCAAAGGTTATCATTCAAAAAATTTAAGGGTTCAAATCTAAAATTTCAAAGCTT
* * * *
5865052 TTCATTCGAGTTCAAATATTCACATTTGATAAATTTTAGAGCCTCACATCTAAATTCAAAGGTTC
130 CTCATTCGAATTCAAAGATTCACATTCGATAAATTTTAGAGCCTCACATCTAAATTCAAAGGTTC
*
5865117 TTATTTAAAA
195 TTATTCAAAA
5865127 CTCAAAGATT
Statistics
Matches: 176, Mismatches: 25, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
216 2 0.01
217 107 0.61
218 67 0.38
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (218 bp):
CATCAAAAATTTCAAAGCTTATCATTCGAGATCAAAGATTCACACTTGATAAATTTTAAAGTTTC
ACATATAAATTCAAAGGTTATCATTCAAAAAATTTAAGGGTTCAAATCTAAAATTTCAAAGCTTC
TCATTCGAATTCAAAGATTCACATTCGATAAATTTTAGAGCCTCACATCTAAATTCAAAGGTTCT
TATTCAAAAAATTTAAGGGTTTA
Found at i:5865131 original size:21 final size:21
Alignment explanation
Indices: 5865107--5865226 Score: 91
Period size: 21 Copynumber: 5.4 Consensus size: 21
5865097 ACATCTAAAT
*
5865107 TCAAAGGTTCTTATTTAAAAC
1 TCAAAGATTCTTATTTAAAAC
*
5865128 TCAAAGATTTTTATTTAAAAC
1 TCAAAGATTCTTATTTAAAAC
* *
5865149 TTCTTAAAAATT-TTCATTTTAAAAAA
1 -TC--AAAGATTCTT-A-TTT-AAAAC
*
5865175 T-AAAGATTCTTATTCAAAAC
1 TCAAAGATTCTTATTTAAAAC
*
5865195 TCCTTAAAGATTCTCATTTAAAAC
1 T-C--AAAGATTCTTATTTAAAAC
5865219 TCAAAGAT
1 TCAAAGAT
5865227 AAAAATTCTC
Statistics
Matches: 79, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
20 5 0.06
21 27 0.34
22 9 0.11
23 5 0.06
24 25 0.32
25 4 0.05
26 4 0.05
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.39
Consensus pattern (21 bp):
TCAAAGATTCTTATTTAAAAC
Found at i:5865180 original size:46 final size:45
Alignment explanation
Indices: 5865130--5865217 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 45
5865120 TTTAAAACTC
* * * *
5865130 AAAGATTTTTATTTAAAACTTCTTAAAAATTTTCATTTTAAAAAAT
1 AAAGATTCTTATTCAAAACTCCTTAAAAATTCTCA-TTTAAAAAAT
*
5865176 AAAGATTCTTATTCAAAACTCCTTAAAGATTCTCATTTAAAA
1 AAAGATTCTTATTCAAAACTCCTTAAAAATTCTCATTTAAAA
5865218 CTCAAAGATA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 7 0.19
46 30 0.81
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.41
Consensus pattern (45 bp):
AAAGATTCTTATTCAAAACTCCTTAAAAATTCTCATTTAAAAAAT
Found at i:5865202 original size:24 final size:24
Alignment explanation
Indices: 5865175--5865220 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5865165 TTTTAAAAAA
*
5865175 TAAAGATTCTTATTCAAAACTCCT
1 TAAAGATTCTCATTCAAAACTCCT
*
5865199 TAAAGATTCTCATTTAAAACTC
1 TAAAGATTCTCATTCAAAACTC
5865221 AAAGATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (24 bp):
TAAAGATTCTCATTCAAAACTCCT
Found at i:5865284 original size:24 final size:24
Alignment explanation
Indices: 5865249--5865301 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
5865239 TCAAAAATTT
*
5865249 TCATTTAGAACT-TCTTAAAGATTC
1 TCATTTAAAACTCT-TTAAAGATTC
*
5865273 TCATTTAAAACTCTTTAAAGATTT
1 TCATTTAAAACTCTTTAAAGATTC
5865297 TCATT
1 TCATT
5865302 ATTTTTAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.34, C:0.15, G:0.06, T:0.45
Consensus pattern (24 bp):
TCATTTAAAACTCTTTAAAGATTC
Found at i:5866489 original size:22 final size:23
Alignment explanation
Indices: 5866461--5866503 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5866451 CTTTCACATT
5866461 TTTTTTCAC-ATTTTCATTTTCA
1 TTTTTTCACTATTTTCATTTTCA
*
5866483 TTTTTTCACTTTTTTCATTTT
1 TTTTTTCACTATTTTCATTTT
5866504 TTTTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTTTCACTATTTTCATTTTCA
Found at i:5866508 original size:22 final size:21
Alignment explanation
Indices: 5866459--5866508 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
5866449 TCCTTTCACA
5866459 TTTTTTTTCACATTTTCATTT
1 TTTTTTTTCACATTTTCATTT
* *
5866480 TCATTTTTTCACTTTTTTCATTT
1 T-TTTTTTTCAC-ATTTTCATTT
5866503 TTTTTT
1 TTTTTT
5866509 ATTTTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 13 0.54
23 10 0.42
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTTTTCACATTTTCATTT
Found at i:5869351 original size:12 final size:12
Alignment explanation
Indices: 5869334--5869364 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
5869324 ATATGCATAA
5869334 ATGAATAAATAC
1 ATGAATAAATAC
5869346 ATGAATAAATAC
1 ATGAATAAATAC
5869358 ATGAATA
1 ATGAATA
5869365 CTTGACACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.26
Consensus pattern (12 bp):
ATGAATAAATAC
Found at i:5870852 original size:120 final size:121
Alignment explanation
Indices: 5870598--5870871 Score: 351
Period size: 120 Copynumber: 2.3 Consensus size: 121
5870588 TTTTTGCTAG
* * *
5870598 AAATTGTCTTCCAAAATGTTGGTAAGATTTTATGAAAATTATTTCTTTTCTAAAAATTAATTTTT
1 AAATTGCCTTCCAATATGTTGGTAAGGTTTTATGAAAATTATTTCTTTTCTAAAAATT-ATTTTT
* * *
5870663 ATATTTAAAAATCATAAGGTTTTTAAATATAGTTGGTAAAACCTTATTTTAAAAACT
65 ATATTAAAAAATAATAAGGTTTTTAAATATAGTTAGTAAAACCTTATTTTAAAAACT
* **
5870720 AAATTGCTTTCCAATATGTTGGTAAGGTTTTATTGAAAATTATTT-TTTCTCTTGAAATT-TTTT
1 AAATTGCCTTCCAATATGTTGGTAAGGTTTTA-TGAAAATTATTTCTTT-TCTAAAAATTATTTT
* *
5870783 TTTA-TAAAAAATTAATAAGGTTTTTTAATAT-GTTAGTAAAACCTTATTTTAAAAA-T
64 TATATTAAAAAA-TAATAAGGTTTTTAAATATAGTTAGTAAAACCTTATTTTAAAAACT
*
5870839 CAAATTGCCTTCCAATATATTGGTAAGGCTTTT
1 -AAATTGCCTTCCAATATGTTGGTAAGG-TTTT
5870872 TGTTTTATTA
Statistics
Matches: 134, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
119 1 0.01
120 54 0.40
121 28 0.21
122 31 0.23
123 20 0.15
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (121 bp):
AAATTGCCTTCCAATATGTTGGTAAGGTTTTATGAAAATTATTTCTTTTCTAAAAATTATTTTTA
TATTAAAAAATAATAAGGTTTTTAAATATAGTTAGTAAAACCTTATTTTAAAAACT
Found at i:5871045 original size:4 final size:4
Alignment explanation
Indices: 5871036--5871106 Score: 63
Period size: 4 Copynumber: 17.5 Consensus size: 4
5871026 AAATATTTAC
** * * *
5871036 AAAT AAAT AAAT GCAT AAAT -AGT AAAAT AAAT GAAAT AAAC AAAT AAAC
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT -AAAT AAAT AAAT AAAT
*
5871085 AAAC AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AA
5871107 TTATGATAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
3 2 0.04
4 46 0.85
5 6 0.11
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:5880603 original size:23 final size:22
Alignment explanation
Indices: 5880577--5880639 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 22
5880567 TTACATTGAG
5880577 TAATTTTATTTTAAAAATTCAAT
1 TAATTTTATTTTAAAAATT-AAT
** * *
5880600 TAATGGGTATTTTAGACATTAAT
1 TAAT-TTTATTTTAAAAATTAAT
*
5880623 TAGATTTTATATTAAAA
1 TA-ATTTTATTTTAAAA
5880640 TATATTTTTT
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (22 bp):
TAATTTTATTTTAAAAATTAAT
Found at i:5884454 original size:15 final size:16
Alignment explanation
Indices: 5884434--5884470 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5884424 AATGAAATTC
5884434 TATATTTTT-ACAAAA
1 TATATTTTTCACAAAA
*
5884449 TATATTTTTCAGAAAA
1 TATATTTTTCACAAAA
5884465 T-TATTT
1 TATATTT
5884471 AAAAGTAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (16 bp):
TATATTTTTCACAAAA
Found at i:5885067 original size:18 final size:20
Alignment explanation
Indices: 5885023--5885071 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
5885013 ATTTATATTT
5885023 TTTATAAATATAATAAAAATA
1 TTTAT-AATATAATAAAAATA
5885044 TATTATAAT-TAA-AAAAATA
1 T-TTATAATATAATAAAAATA
5885063 TTTATAATA
1 TTTATAATA
5885072 ATCGAAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.27
19 8 0.31
20 3 0.12
21 4 0.15
22 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTATAATATAATAAAAATA
Found at i:5885445 original size:17 final size:19
Alignment explanation
Indices: 5885423--5885461 Score: 57
Period size: 16 Copynumber: 2.2 Consensus size: 19
5885413 TTGGTGTTGA
5885423 TTAAAAATTTT-ATAA-TT
1 TTAAAAATTTTAATAACTT
5885440 TT-AAAATTTTAATAACTT
1 TTAAAAATTTTAATAACTT
5885458 TTAA
1 TTAA
5885462 TATTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 4 0.21
19 1 0.05
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAAAATTTTAATAACTT
Found at i:5885447 original size:16 final size:18
Alignment explanation
Indices: 5885426--5885467 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5885416 GTGTTGATTA
5885426 AAAATTTT-ATAA-TTTT
1 AAAATTTTAATAACTTTT
5885442 AAAATTTTAATAACTTTT
1 AAAATTTTAATAACTTTT
*
5885460 AATATTTT
1 AAAATTTT
5885468 TTAAAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 4 0.17
18 11 0.48
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
AAAATTTTAATAACTTTT
Found at i:5885461 original size:10 final size:9
Alignment explanation
Indices: 5885423--5885467 Score: 51
Period size: 8 Copynumber: 5.2 Consensus size: 9
5885413 TTGGTGTTGA
*
5885423 TTAAAAATT
1 TTAATAATT
5885432 TT-ATAATT
1 TTAATAATT
5885440 TTAA-AATT
1 TTAATAATT
5885448 TTAATAACTT
1 TTAATAA-TT
5885458 TTAAT-ATT
1 TTAATAATT
5885466 TT
1 TT
5885468 TTAAAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 19 0.59
9 6 0.19
10 7 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (9 bp):
TTAATAATT
Found at i:5888856 original size:29 final size:29
Alignment explanation
Indices: 5888775--5888889 Score: 135
Period size: 30 Copynumber: 3.9 Consensus size: 29
5888765 CTTCTTTAAG
* *
5888775 TATAAATTAAAAATTAAAGGTTTATTTGAA
1 TATAAATTAAAAATTAAA-ATTTATTTGGA
5888805 TATAAATTAAAAATTAAGAATTTATTTGGA
1 TATAAATTAAAAATTAA-AATTTATTTGGA
5888835 TATAAATTAAAAATTAAAATTTTATTT-GA
1 TATAAATTAAAAATTAAAA-TTTATTTGGA
* *
5888864 GTAT-AATAAAAACATAAAAATTTATT
1 -TATAAATTAAAA-ATTAAAATTTATT
5888890 AAAATAAAGT
Statistics
Matches: 77, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
29 17 0.22
30 59 0.77
31 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.40
Consensus pattern (29 bp):
TATAAATTAAAAATTAAAATTTATTTGGA
Found at i:5889364 original size:2 final size:2
Alignment explanation
Indices: 5889357--5889386 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5889347 TATTTTAGAA
5889357 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5889387 CAAGTCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5890033 original size:20 final size:21
Alignment explanation
Indices: 5889989--5890033 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5889979 TATTTAAAAT
* * *
5889989 TATTAAAATTAAAATTTTGAT
1 TATTAAAATAAAAAATTTGAA
5890010 TATTAAAATAAAAAATTT-AA
1 TATTAAAATAAAAAATTTGAA
5890030 TATT
1 TATT
5890034 TTATTAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TATTAAAATAAAAAATTTGAA
Found at i:5890049 original size:32 final size:31
Alignment explanation
Indices: 5890008--5890077 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
5889998 TAAAATTTTG
*
5890008 ATTATTAAAATAAAAAATTTAATATTTTATTA
1 ATTATTAAAAT-AAAAATTTAATATTTTAATA
*
5890040 ATTATTAAAATTAAAATTTAATATTTTAATA
1 ATTATTAAAATAAAAATTTAATATTTTAATA
*
5890071 ATAATTA
1 ATTATTA
5890078 TGTGACAGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 24 0.69
32 11 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
ATTATTAAAATAAAAATTTAATATTTTAATA
Found at i:5890251 original size:87 final size:86
Alignment explanation
Indices: 5890091--5890255 Score: 215
Period size: 87 Copynumber: 1.9 Consensus size: 86
5890081 GACAGACATT
* *** *
5890091 TCCATTAGATTTTAATTGTTATATTTACCTAATCAATGTTAAAAGATTGACATGATTATAGAAGC
1 TCCATTAGATTTTAATTGCTATATTTACCTAATCAAACATAAAAGACTGACATGATTATAGAAGC
*
5890156 ATTGATTTGCATGTGCCGACA
66 ATTAATTTGCATGTGCCGACA
* * *
5890177 TCCATTAAGATTTTAATTGCTATATTTGCCTAATCAAACATAGAAGACTGACATGATTATA-TAG
1 TCCATT-AGATTTTAATTGCTATATTTACCTAATCAAACATAAAAGACTGACATGATTATAGAAG
*
5890241 ACCTTAATTTGCATG
65 -CATTAATTTGCATG
5890256 GCTGACAAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
86 8 0.12
87 59 0.88
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (86 bp):
TCCATTAGATTTTAATTGCTATATTTACCTAATCAAACATAAAAGACTGACATGATTATAGAAGC
ATTAATTTGCATGTGCCGACA
Found at i:5892670 original size:31 final size:32
Alignment explanation
Indices: 5892629--5892702 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 32
5892619 AAAGTTACTT
* * * *
5892629 AATTTTTATTTTTTATTTTTATATCTTTT-TA
1 AATTTATATTTTTCATTATTATATATTTTCTA
*
5892660 AATTTATATTTATCATTATTATATATTTTCTA
1 AATTTATATTTTTCATTATTATATATTTTCTA
*
5892692 ATTTTA-ATTTT
1 AATTTATATTTT
5892703 ATTTGATTAC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
31 28 0.80
32 7 0.20
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (32 bp):
AATTTATATTTTTCATTATTATATATTTTCTA
Found at i:5894694 original size:531 final size:532
Alignment explanation
Indices: 5893690--5894742 Score: 2029
Period size: 531 Copynumber: 2.0 Consensus size: 532
5893680 AAAAGCTTGG
5893690 TGAGAGATACGCATCACTGTTGCTTCAAATCTTTATTGTCAAAGGATTGGATACATGGCCCCTTT
1 TGAGAGATACGCATCACTGTTGCTTCAAATCTTTATTGTCAAAGGATTGGATACATGGCCCCTTT
5893755 TAAATTTATAAAAAAAGAGATTTTTTTTTATTTTTTAAAATTATGTTTTAAAGATGAGAAAAATA
66 TAAATTTATAAAAAAAGAGATTTTTTTTTATTTTTTAAAATTATGTTTTAAAGATGAGAAAAATA
* *
5893820 AAAAAATTATGTCAAGTTTTAATGAAGAACAACATGTAGACAAATATAAGTATTTTTTTTAGAAA
131 AAAAAATCATGTCAAGTTTTAATGAAGAACAACATATAGACAAATATAAGTATTTTTTTTAGAAA
5893885 TAAATAATAAAATATTTAATAGATACAAGCACAAATTAAAGGCAAATATAGGTACATATCTTTTT
196 TAAATAATAAAATATTTAATAGATACAAGCACAAATTAAAGGCAAATATAGGTACATATCTTTTT
* *
5893950 TGAACCTCAACTTCACCAGCACATTTTTCATTCCATCATAACATTGTAGACATCTAATTTAGTTT
261 TGAACCTCAACTTCACCAACACACTTTTCATTCCATCATAACATTGTAGACATCTAATTTAGTTT
5894015 AGGATTTTTTTAATTTAATTTTAGTATTTTAGAATTTTGTGTAGTTTAGGATTATTTGTTTTGTT
326 AGGATTTTTTTAATTTAATTTTAGTATTTTAGAATTTTGTGTAGTTTAGGATTATTTGTTTTGTT
5894080 AATTAATTGATTTTTTTTAAAGAGAAAAGTTTGATTCGGTTTGAAGTTTAATGTTCTAATTAAAA
391 AATTAATTGATTTTTTTTAAAGAGAAAAGTTTGATTCGGTTTGAAGTTTAATGTTCTAATTAAAA
* *
5894145 AAGGAATGTATTGATTTAAGAGGTGGACTTGGATTAAAAATTTAAAATTGATTTTGATTAAGAGA
456 AAGGAATGTATTGATTTAAAAGGTGGACTTGGATTAAAAATTTAAAATTGACTTTGATTAAGAGA
5894210 TTTAAAATTTGA
521 TTTAAAATTTGA
5894222 TGAGAGATACGCATCACTGTTGCTTCAAATCTTTATTGTCAAAGGATTGGATACATGGCCCCTTT
1 TGAGAGATACGCATCACTGTTGCTTCAAATCTTTATTGTCAAAGGATTGGATACATGGCCCCTTT
5894287 TAAATTTATAAAAAAAGAGA-TTTTTTTTATTTTTTAAAATTATGTTTTAAAGATGAGAAAAATA
66 TAAATTTATAAAAAAAGAGATTTTTTTTTATTTTTTAAAATTATGTTTTAAAGATGAGAAAAATA
5894351 AAAAAATCATGTCAAGTTTTAATGAAGAACAACATATAGACAAATATAAGTATTTTTTTTAGAAA
131 AAAAAATCATGTCAAGTTTTAATGAAGAACAACATATAGACAAATATAAGTATTTTTTTTAGAAA
5894416 TAAATAATAAAATATTTAATAGATACAAGCACAAATTAAAGGCAAATATAGGTACATATCTTTTT
196 TAAATAATAAAATATTTAATAGATACAAGCACAAATTAAAGGCAAATATAGGTACATATCTTTTT
5894481 TGAACCTCAACTTCACCAACACACTTTTCATTCCATCATAACGATTGTAGACATCTAATTTAGTT
261 TGAACCTCAACTTCACCAACACACTTTTCATTCCATCATAAC-ATTGTAGACATCTAATTTAGTT
5894546 TAGGATTTTTTTAATTTAATTTTAGTATTTTAGAATTTTGTGTAGTTTAGGATTATTTGTTTTGT
325 TAGGATTTTTTTAATTTAATTTTAGTATTTTAGAATTTTGTGTAGTTTAGGATTATTTGTTTTGT
5894611 TAATTAATTGA-TTTTTTTAAAGAGAAAAGTTTGATTCGGTTTGAAGTTTAATGTTCTAATTAAA
390 TAATTAATTGATTTTTTTTAAAGAGAAAAGTTTGATTCGGTTTGAAGTTTAATGTTCTAATTAAA
5894675 AAAGGAATGTATTGATTTAAAAGGTGGACTTGGATTAAAAATTTAAAATTGACTTTGATTAAGAG
455 AAAGGAATGTATTGATTTAAAAGGTGGACTTGGATTAAAAATTTAAAATTGACTTTGATTAAGAG
5894740 ATT
520 ATT
5894743 GAAACCAAGA
Statistics
Matches: 514, Mismatches: 6, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
531 331 0.64
532 183 0.36
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (532 bp):
TGAGAGATACGCATCACTGTTGCTTCAAATCTTTATTGTCAAAGGATTGGATACATGGCCCCTTT
TAAATTTATAAAAAAAGAGATTTTTTTTTATTTTTTAAAATTATGTTTTAAAGATGAGAAAAATA
AAAAAATCATGTCAAGTTTTAATGAAGAACAACATATAGACAAATATAAGTATTTTTTTTAGAAA
TAAATAATAAAATATTTAATAGATACAAGCACAAATTAAAGGCAAATATAGGTACATATCTTTTT
TGAACCTCAACTTCACCAACACACTTTTCATTCCATCATAACATTGTAGACATCTAATTTAGTTT
AGGATTTTTTTAATTTAATTTTAGTATTTTAGAATTTTGTGTAGTTTAGGATTATTTGTTTTGTT
AATTAATTGATTTTTTTTAAAGAGAAAAGTTTGATTCGGTTTGAAGTTTAATGTTCTAATTAAAA
AAGGAATGTATTGATTTAAAAGGTGGACTTGGATTAAAAATTTAAAATTGACTTTGATTAAGAGA
TTTAAAATTTGA
Found at i:5895264 original size:4 final size:4
Alignment explanation
Indices: 5895255--5895324 Score: 59
Period size: 4 Copynumber: 17.2 Consensus size: 4
5895245 CATAATTGTC
* * * * *
5895255 TATT TATT TATT TATT TGTT TGTT TGTT TATT TGTC TATTT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TA-TT TATT TATT
* * *
5895304 TGTC TATT TATG TATT TATT T
1 TATT TATT TATT TATT TATT T
5895325 GTAAATATTT
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
4 50 0.94
5 3 0.06
ACGTcount: A:0.17, C:0.03, G:0.09, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:5895319 original size:16 final size:16
Alignment explanation
Indices: 5895259--5895320 Score: 79
Period size: 16 Copynumber: 3.8 Consensus size: 16
5895249 ATTGTCTATT
*
5895259 TATTTATTTATTTGTT
1 TATTTATTTATTTGTC
* *
5895275 TGTTTGTTTATTTGTC
1 TATTTATTTATTTGTC
5895291 TATTTTATTTATTTGTC
1 TA-TTTATTTATTTGTC
*
5895308 TATTTATGTATTT
1 TATTTATTTATTT
5895321 ATTTGTAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
16 24 0.62
17 15 0.38
ACGTcount: A:0.16, C:0.03, G:0.10, T:0.71
Consensus pattern (16 bp):
TATTTATTTATTTGTC
Found at i:5895757 original size:19 final size:19
Alignment explanation
Indices: 5895733--5895769 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5895723 TAATTTCCAT
5895733 AAAATCCTACCAACATATA
1 AAAATCCTACCAACATATA
*
5895752 AAAATCTTACCAACATAT
1 AAAATCCTACCAACATAT
5895770 TTGAGGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATCCTACCAACATATA
Found at i:5897038 original size:20 final size:19
Alignment explanation
Indices: 5897010--5897053 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
5897000 AAATATTAAC
* *
5897010 TCATGTATTCATTTATGCA
1 TCATTTATTCATTCATGCA
5897029 GTCATTTATTCATTCATGCA
1 -TCATTTATTCATTCATGCA
5897049 TCATT
1 TCATT
5897054 ATGAGGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (19 bp):
TCATTTATTCATTCATGCA
Found at i:5897084 original size:61 final size:61
Alignment explanation
Indices: 5896977--5897096 Score: 186
Period size: 61 Copynumber: 2.0 Consensus size: 61
5896967 TATACATTCA
*** * **
5896977 TCATTCATGCATCATTATGAGGTAAATATTAACTCATGTATTCATTTATGCAGTCATTTAT
1 TCATTCATGCATCATTATGAGGTAAATATTAACTCAAACATCCATTTACACAGTCATTTAT
5897038 TCATTCATGCATCATTATGAGGTAAATATTAACTCAAACATCCATTTACACAGTCATTT
1 TCATTCATGCATCATTATGAGGTAAATATTAACTCAAACATCCATTTACACAGTCATTT
5897097 GTCAATCCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.39
Consensus pattern (61 bp):
TCATTCATGCATCATTATGAGGTAAATATTAACTCAAACATCCATTTACACAGTCATTTAT
Found at i:5897113 original size:61 final size:61
Alignment explanation
Indices: 5896977--5897115 Score: 165
Period size: 61 Copynumber: 2.3 Consensus size: 61
5896967 TATACATTCA
* *** * ** *
5896977 TCATTCATGCATCATTATGAGGTAAATATTAACTCATGTATTCATTTATGCAGTCATTTAT
1 TCATCCATGCATCATTATGAGGTAAATATTAACTCAAACATCCATTTACACAGTCATTTAG
*
5897038 TCATTCATGCATCATTATGAGGTAAATATTAACTCAAACATCCATTTACACAGTCATTT-G
1 TCATCCATGCATCATTATGAGGTAAATATTAACTCAAACATCCATTTACACAGTCATTTAG
5897098 TCAATCCATAG-ATCATTA
1 TC-ATCCAT-GCATCATTA
5897116 AATTATTATG
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
60 2 0.03
61 65 0.96
62 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (61 bp):
TCATCCATGCATCATTATGAGGTAAATATTAACTCAAACATCCATTTACACAGTCATTTAG
Found at i:5900084 original size:14 final size:14
Alignment explanation
Indices: 5900036--5900090 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 14
5900026 AAATTTGGGG
*
5900036 TTTTAGGTTTTGAA
1 TTTTAGGTTTTGGA
* * *
5900050 TTTTAAGATTTAGA
1 TTTTAGGTTTTGGA
5900064 GTTTTAGGTTTTGGA
1 -TTTTAGGTTTTGGA
5900079 TTTTAGGGTTTT
1 TTTTA-GGTTTT
5900091 AAAAATTTGG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 15 0.47
15 17 0.53
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (14 bp):
TTTTAGGTTTTGGA
Found at i:5900575 original size:3 final size:3
Alignment explanation
Indices: 5900567--5900613 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
5900557 TTTAATATAT
5900567 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5900614 GAACACTTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5903171 original size:17 final size:16
Alignment explanation
Indices: 5903149--5903202 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
5903139 TCTGAATGTG
5903149 GAAAAATAAAAAAAAAT
1 GAAAAA-AAAAAAAAAT
5903166 GAAAAAATAAAAAAAAT
1 GAAAAAA-AAAAAAAAT
5903183 -AAAAAAGAAAAAAAGAT
1 GAAAAAA-AAAAAAA-AT
5903200 GAA
1 GAA
5903203 CACGTATGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 14 0.42
17 17 0.52
18 2 0.06
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (16 bp):
GAAAAAAAAAAAAAAT
Found at i:5903177 original size:16 final size:16
Alignment explanation
Indices: 5903157--5903196 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
5903147 TGGAAAAATA
*
5903157 AAAAAAAATGAAAAAAT
1 AAAAAAAAT-AAAAAAG
5903174 AAAAAAAATAAAAAAG
1 AAAAAAAATAAAAAAG
5903190 AAAAAAA
1 AAAAAAA
5903197 GATGAACACG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.88, C:0.00, G:0.05, T:0.07
Consensus pattern (16 bp):
AAAAAAAATAAAAAAG
Found at i:5904674 original size:22 final size:22
Alignment explanation
Indices: 5904649--5904724 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
5904639 AAGATAAAAA
*
5904649 ATAATTTGTAAGACATTCGAGC
1 ATAATTTGTAAGACCTTCGAGC
* * *
5904671 ATAACTTGTAAGGCCTTCAAGC
1 ATAATTTGTAAGACCTTCGAGC
5904693 ATAATTCT-TAA-AGCCTTCGAGC
1 ATAATT-TGTAAGA-CCTTCGAGC
*
5904715 ATGATTTGTA
1 ATAATTTGTA
5904725 TGACTTCCGG
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
21 1 0.02
22 41 0.95
23 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (22 bp):
ATAATTTGTAAGACCTTCGAGC
Found at i:5906315 original size:4 final size:4
Alignment explanation
Indices: 5906293--5906371 Score: 79
Period size: 4 Copynumber: 19.5 Consensus size: 4
5906283 TTTATCATAA
* * * *
5906293 TTAT CTAT TTAT GTAT TTAT TTAT TTAT TTGT TTAT TTGT TTATT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTAT
* *
5906342 TTAT TTGA- CTAT TTAT GTAT TTAT TTAT TT
1 TTAT TT-AT TTAT TTAT TTAT TTAT TTAT TT
5906372 GTAAATATTT
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
3 1 0.02
4 54 0.90
5 5 0.08
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:5906761 original size:121 final size:120
Alignment explanation
Indices: 5906543--5906803 Score: 257
Period size: 121 Copynumber: 2.2 Consensus size: 120
5906533 AATAAAACAA
** *
5906543 AAAGCCTTACCAACATATTGTAAGGTAATTTGATTTTTAAAATAAGATTTTACCAACATATTGGA
1 AAAGCCTTACCAACATATTGTAAGACAATTTGATTTTTAAAATAAGATTTTACCAACATATTGAA
* * * *
5906608 GAACGTTATTAATTTTTTGTAAAGAAAAAATTTCAAGAGAAAAAAATAGTTTTCAAT
66 AAACGTTATTAATTTTTTGAAAAAAAAAAATTTCAAGA-AAAAAAATAATTTTC-AT
* * **
5906665 AAAGCCTTACCAATATATTG-GAGACAATTTGATTTTTAAGGTAA-AGTTTTACCAACATATTGA
1 AAAGCCTTACCAACATATTGTAAGACAATTTGATTTTTAAAATAAGA-TTTTACCAACATATTGA
** *
5906728 AAAATC-TTA-TAA-TTTTT-AAAATAAAAATTAATTTTTAGAAAAGAAATAATTTTCAT
65 AAAA-CGTTATTAATTTTTTGAAAA-AAAAA--AATTTCAAGAAAAAAAATAATTTTCAT
* *
5906784 AAAATCC-TACAAACATATTG
1 -AAAGCCTTACCAACATATTG
5906804 AAGGATAATT
Statistics
Matches: 116, Mismatches: 17, Indels: 15
0.78 0.11 0.10
Matches are distributed among these distances:
118 3 0.03
119 22 0.19
120 22 0.19
121 49 0.42
122 20 0.17
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (120 bp):
AAAGCCTTACCAACATATTGTAAGACAATTTGATTTTTAAAATAAGATTTTACCAACATATTGAA
AAACGTTATTAATTTTTTGAAAAAAAAAAATTTCAAGAAAAAAAATAATTTTCAT
Found at i:5906777 original size:18 final size:18
Alignment explanation
Indices: 5906736--5906780 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
5906726 GAAAAATCTT
5906736 ATAATTTTTAAAATAAAA
1 ATAATTTTTAAAATAAAA
*
5906754 ATTAATTTTTAGAAA-AGAA
1 A-TAATTTTTA-AAATAAAA
5906773 ATAATTTT
1 ATAATTTT
5906781 CATAAAATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 13 0.54
20 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (18 bp):
ATAATTTTTAAAATAAAA
Found at i:5908063 original size:20 final size:21
Alignment explanation
Indices: 5908012--5908063 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
5908002 GGACGATAAT
5908012 TAATTTTTTA-ATATAAATTA
1 TAATTTTTTATATATAAATTA
* *
5908032 TAGTTTAATTATATATAAA-TA
1 TAATTT-TTTATATATAAATTA
5908053 TAATTTTTTAT
1 TAATTTTTTAT
5908064 TAAATTAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 9 0.35
21 10 0.38
22 7 0.27
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TAATTTTTTATATATAAATTA
Found at i:5910670 original size:37 final size:37
Alignment explanation
Indices: 5910628--5910705 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
5910618 GCGAATTTTA
*
5910628 TAAAT-ATCAATTTTTAAAAATTATGGATCAATCAAAT
1 TAAATAAT-AATTTTTAAAAATTATGAATCAATCAAAT
*
5910665 TAAATAATAATTTTTAAAAATTATGAATCTATCAAAT
1 TAAATAATAATTTTTAAAAATTATGAATCAATCAAAT
5910702 TAAA
1 TAAA
5910706 CTCTAAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.38
Consensus pattern (37 bp):
TAAATAATAATTTTTAAAAATTATGAATCAATCAAAT
Found at i:5912813 original size:18 final size:18
Alignment explanation
Indices: 5912790--5912826 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5912780 CATTTTAACT
5912790 TAATCAATGAATTTTCCA
1 TAATCAATGAATTTTCCA
5912808 TAATCAATGAATTTTCCA
1 TAATCAATGAATTTTCCA
5912826 T
1 T
5912827 TCTGGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (18 bp):
TAATCAATGAATTTTCCA
Found at i:5915867 original size:30 final size:31
Alignment explanation
Indices: 5915824--5915895 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 31
5915814 TTCGACGTGA
*
5915824 TAATATAATATAAAAAATT-TATTTATATATTT
1 TAATATAA-AT-AAAAATTATATTTATATATAT
* *
5915856 TAA-ATAAATAAATATTATATTTATTTATAT
1 TAATATAAATAAAAATTATATTTATATATAT
5915886 TAATATAAAT
1 TAATATAAAT
5915896 TTTAATATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 6 0.17
30 16 0.46
31 10 0.29
32 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TAATATAAATAAAAATTATATTTATATATAT
Found at i:5916293 original size:30 final size:31
Alignment explanation
Indices: 5916259--5916321 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
5916249 TAAATTTGAT
5916259 ATTAAAAATT-AATATAAT-TATATA-ATATAA
1 ATTAAAAATTAAATAT-ATGTATATATAT-TAA
*
5916289 ATTAAAATTTAAATATATGTATATATATTAA
1 ATTAAAAATTAAATATATGTATATATATTAA
5916320 AT
1 AT
5916322 ACATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 11 0.38
31 16 0.55
32 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (31 bp):
ATTAAAAATTAAATATATGTATATATATTAA
Found at i:5916312 original size:31 final size:30
Alignment explanation
Indices: 5916259--5916321 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
5916249 TAAATTTGAT
5916259 ATTAAAAATTAATATAATTATATA-ATATAA
1 ATTAAAAATTAATATAATTATATATAT-TAA
*
5916289 ATTAAAATTTAA-ATATATGTATATATATTAA
1 ATTAAAAATTAATATA-AT-TATATATATTAA
5916320 AT
1 AT
5916322 ACATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 3 0.10
30 13 0.45
31 11 0.38
32 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (30 bp):
ATTAAAAATTAATATAATTATATATATTAA
Found at i:5922775 original size:15 final size:15
Alignment explanation
Indices: 5922755--5922792 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
5922745 ATTTAATTTT
*
5922755 TATTAAAATTTTAAA
1 TATTAAAATGTTAAA
5922770 TATTAAAATGTTAAA
1 TATTAAAATGTTAAA
5922785 -ATTAAAAT
1 TATTAAAAT
5922793 ATAACAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TATTAAAATGTTAAA
Found at i:5922786 original size:107 final size:106
Alignment explanation
Indices: 5922660--5922873 Score: 243
Period size: 108 Copynumber: 2.0 Consensus size: 106
5922650 TTATATTCAA
*** * * *
5922660 TAAATATAAAATATAAAAATTATTGTATTAAGATATCTAT-TC-ACATACTAAATATAAAACGTA
1 TAAATATAAAATATAAAAATTAAAATA-TAACAAATCTATATCAACATACTAAATATAAAACATA
* * *
5922723 TTTCTTAATTTTTGTCAAATACATTTAATTTTTATTAAAATTT
65 TTTCTTAATTTTTATCAAACACATTT-ACTTTTATTAAAATTT
* * * * * *
5922766 TAAATATTAAAATGTTAAAATTAAAATATAACAAATTTGTATCAACATATTAAATATAAAATATA
1 TAAATA-TAAAATATAAAAATTAAAATATAACAAATCTATATCAACATACTAAATATAAAACATA
*
5922831 TTTTTTAATTTTTATCAAACACATTTACTTTTATTAAAATTT
65 TTTCTTAATTTTTATCAAACACATTTACTTTTATTAAAATTT
5922873 T
1 T
5922874 TTAGACGGTC
Statistics
Matches: 89, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
106 14 0.16
107 34 0.38
108 41 0.46
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (106 bp):
TAAATATAAAATATAAAAATTAAAATATAACAAATCTATATCAACATACTAAATATAAAACATAT
TTCTTAATTTTTATCAAACACATTTACTTTTATTAAAATTT
Found at i:5926166 original size:28 final size:26
Alignment explanation
Indices: 5926119--5926172 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
5926109 TTCTTATTCC
5926119 TTTAAATCAAACCTTATTTAAATGATT
1 TTTAAATCAAACCTTATTTAAA-GATT
*
5926146 TTTATAATCAAATC-TAGTTTAAAGATT
1 TTTA-AATCAAACCTTA-TTTAAAGATT
5926173 CTAAATAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (26 bp):
TTTAAATCAAACCTTATTTAAAGATT
Found at i:5926724 original size:17 final size:16
Alignment explanation
Indices: 5926704--5926738 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5926694 ATATTAGATG
5926704 AATTAAAATATTTTTAA
1 AATT-AAATATTTTTAA
*
5926721 AATTTAATATTTTTAA
1 AATTAAATATTTTTAA
5926737 AA
1 AA
5926739 AAATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTAAATATTTTTAA
Found at i:5926805 original size:31 final size:31
Alignment explanation
Indices: 5926767--5926859 Score: 123
Period size: 31 Copynumber: 3.0 Consensus size: 31
5926757 TAAAATAATA
**
5926767 AAATTTTAATTTTTATATTCATATAAAAATT
1 AAATTTTAATTTTTATATAAATATAAAAATT
*
5926798 AAATTTTAAATTTTATATAAATATAAAAATT
1 AAATTTTAATTTTTATATAAATATAAAAATT
* ** *
5926829 AAATTGTAATTTACACATAAATATAAAAATT
1 AAATTTTAATTTTTATATAAATATAAAAATT
5926860 CTTTTTATAA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (31 bp):
AAATTTTAATTTTTATATAAATATAAAAATT
Found at i:5927021 original size:14 final size:14
Alignment explanation
Indices: 5927002--5927028 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5926992 AAAATTAGTA
5927002 ATTAAATTAAAATT
1 ATTAAATTAAAATT
5927016 ATTAAATTAAAAT
1 ATTAAATTAAAAT
5927029 AATATGAAAA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTAAATTAAAATT
Found at i:5928473 original size:2 final size:2
Alignment explanation
Indices: 5928466--5928493 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5928456 CAGGTAAATA
5928466 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
5928494 CTTTTGCTGA
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:5941503 original size:33 final size:33
Alignment explanation
Indices: 5941466--5941531 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
5941456 CATCGAATAC
*
5941466 CTATCAAACATAATAATTTAAGCATAATGTATA
1 CTATCAAACATAATAATTTAAACATAATGTATA
5941499 CTATCAAACATAATAATTTAAACATAATGTATA
1 CTATCAAACATAATAATTTAAACATAATGTATA
5941532 AATCACTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (33 bp):
CTATCAAACATAATAATTTAAACATAATGTATA
Found at i:5944819 original size:24 final size:24
Alignment explanation
Indices: 5944787--5944832 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
5944777 ATTTTCAAAG
5944787 AAAACCAGTAATCACAAATCTTGC
1 AAAACCAGTAATCACAAATCTTGC
5944811 AAAACCAGTAATCACAAATCTT
1 AAAACCAGTAATCACAAATCTT
5944833 ACTCATTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.24, G:0.07, T:0.22
Consensus pattern (24 bp):
AAAACCAGTAATCACAAATCTTGC
Found at i:5945545 original size:2 final size:2
Alignment explanation
Indices: 5945538--5945562 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5945528 AACTTTCTTA
5945538 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
5945563 AGTAATAGAT
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:5950302 original size:21 final size:21
Alignment explanation
Indices: 5950263--5950302 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5950253 TTAAAATAAC
* * *
5950263 AAAATTATAAATAAGTTTAAT
1 AAAATTAAAAAAAAATTTAAT
5950284 AAAATTAAAAAAAAATTTA
1 AAAATTAAAAAAAAATTTA
5950303 TGTTTTCGTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (21 bp):
AAAATTAAAAAAAAATTTAAT
Done.