Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015328.1 Kokia drynarioides strain JFW-HI SEQ_130374, 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: 430948
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 584 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:20912 original size:5 final size:5
Alignment explanation
Indices: 20902--20929 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
20892 AACAGATATA
20902 TAATT TAATT TAATT TAATT TAATT TAA
1 TAATT TAATT TAATT TAATT TAATT TAA
20930 AGTAACATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TAATT
Found at i:24864 original size:8 final size:9
Alignment explanation
Indices: 24835--24929 Score: 63
Period size: 9 Copynumber: 10.3 Consensus size: 9
24825 AATTCACATA
24835 TTTTATAAT
1 TTTTATAAT
24844 TTTTATAACT
1 TTTTATAA-T
24854 TTTTA-AAT
1 TTTTATAAT
24862 TTTTAATAA-
1 TTTT-ATAAT
*
24871 TTTTATAGT
1 TTTTATAAT
*
24880 TTTTAATTAT
1 TTTT-ATAAT
*
24890 TTCTATATACCT
1 TT-T-TATA-AT
*
24902 TTTTTTAAT
1 TTTTATAAT
24911 TTTTAT-AT
1 TTTTATAAT
*
24919 TTATA-AAT
1 TTTTATAAT
24927 TTT
1 TTT
24930 AAATCACTCT
Statistics
Matches: 67, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
8 18 0.27
9 25 0.37
10 16 0.24
11 4 0.06
12 4 0.06
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:25607 original size:23 final size:23
Alignment explanation
Indices: 25581--25668 Score: 115
Period size: 23 Copynumber: 3.8 Consensus size: 23
25571 TTAATGTTCA
*
25581 CGAACATGTTCATTTAA-ATTAAT
1 CGAACATGTTCA-TGAACATTAAT
*
25604 CGAACATGTTCATGAACATTAAA
1 CGAACATGTTCATGAACATTAAT
25627 CGAACATGTTCATGAACATATAAT
1 CGAACATGTTCATGAACAT-TAAT
* *
25651 TGAACATGTTCACGAACA
1 CGAACATGTTCATGAACA
25669 ATTTCATGAA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
22 3 0.05
23 36 0.62
24 19 0.33
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (23 bp):
CGAACATGTTCATGAACATTAAT
Found at i:25668 original size:47 final size:46
Alignment explanation
Indices: 25580--25668 Score: 126
Period size: 47 Copynumber: 1.9 Consensus size: 46
25570 TTTAATGTTC
* *
25580 ACGAACATGTTCATTTAAATTAATCGAACATGTTCATGAACATTAA
1 ACGAACATGTTCATTGAAATTAATCGAACATGTTCACGAACATTAA
*
25626 ACGAACATGTTCA-TGAACATATAATTGAACATGTTCACGAACA
1 ACGAACATGTTCATTGAA-AT-TAATCGAACATGTTCACGAACA
25669 ATTTCATGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
45 3 0.08
46 15 0.39
47 20 0.53
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (46 bp):
ACGAACATGTTCATTGAAATTAATCGAACATGTTCACGAACATTAA
Found at i:25678 original size:24 final size:23
Alignment explanation
Indices: 25582--25678 Score: 90
Period size: 23 Copynumber: 4.1 Consensus size: 23
25572 TAATGTTCAC
*
25582 GAACATGTTCATTTAA-A-TTAAT
1 GAACATGTTCA-TGAACATTTAAT
* *
25604 CGAACATGTTCATGAACATTAAAC
1 -GAACATGTTCATGAACATTTAAT
*
25628 GAACATGTTCATGAACATATAATT
1 GAACATGTTCATGAACATTTAA-T
* *
25652 GAACATGTTCACGAACAATTTCAT
1 GAACATGTTCATGAAC-ATTTAAT
25676 GAA
1 GAA
25679 TAAAAAAATA
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
22 3 0.05
23 32 0.52
24 22 0.36
25 4 0.07
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.31
Consensus pattern (23 bp):
GAACATGTTCATGAACATTTAAT
Found at i:26287 original size:30 final size:31
Alignment explanation
Indices: 26252--26309 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
26242 TGATGGAATA
* *
26252 AAATCACAAGTACTAAATTGA-GAATGAAAT
1 AAATCACAAATACCAAATTGAGGAATGAAAT
*
26282 AAATCACAAATACCATATTGAGGAATGA
1 AAATCACAAATACCAAATTGAGGAATGA
26310 GGTATAGATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.22
Consensus pattern (31 bp):
AAATCACAAATACCAAATTGAGGAATGAAAT
Found at i:26978 original size:25 final size:27
Alignment explanation
Indices: 26922--26981 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 27
26912 ACTATTTGTG
26922 ACAAAAAAATTTAAGTAGCAACTTGAA
1 ACAAAAAAATTTAAGTAGCAACTTGAA
*
26949 A-AAAAAAA-TTACGTAGC-ACTT-ATA
1 ACAAAAAAATTTAAGTAGCAACTTGA-A
26973 ACAAAAAAA
1 ACAAAAAAA
26982 AAAGTACCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 1 0.03
24 6 0.20
25 15 0.50
26 7 0.23
27 1 0.03
ACGTcount: A:0.60, C:0.12, G:0.08, T:0.20
Consensus pattern (27 bp):
ACAAAAAAATTTAAGTAGCAACTTGAA
Found at i:37589 original size:28 final size:27
Alignment explanation
Indices: 37549--37606 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
37539 AAATGTGATT
* *
37549 TTTGGATTCTCGGGGGTAAAACGGTAA
1 TTTGGATGCTCGGGAGTAAAACGGTAA
*
37576 TTTGGATGCTTCGGGAGTAAAATGGTAA
1 TTTGGATGC-TCGGGAGTAAAACGGTAA
37604 TTT
1 TTT
37607 TTGAAAGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.26, C:0.09, G:0.31, T:0.34
Consensus pattern (27 bp):
TTTGGATGCTCGGGAGTAAAACGGTAA
Found at i:37636 original size:30 final size:28
Alignment explanation
Indices: 37585--37922 Score: 209
Period size: 29 Copynumber: 11.5 Consensus size: 28
37575 ATTTGGATGC
37585 TTCGGGAGT-AAAATGGTAATTTTTGAAAGG
1 TTCGGG-GTAAAAATGG-AATTTTTGAAA-G
* * *
37615 TTCGGGGTTCAAAATGGAATTTTTAGATAT
1 TTCGGGG-TAAAAATGGAATTTTT-GAAAG
* * *
37645 TTAGGGGT-AAAACGGTAATTTTTGGAAGG
1 TTCGGGGTAAAAATGG-AATTTTT-GAAAG
*
37674 TTCGGGGTCAAAAATGGAATTTTTAGACA-
1 TTCGGGGT-AAAAATGGAATTTTT-GAAAG
*
37703 TTCGAGGGT-AAAATGGTAATTTTGGAAAG
1 TTCG-GGGTAAAAATGG-AATTTTTGAAAG
* *
37732 TTCGAGGTTAAAAATGGAATTTTGGAAAG
1 TTCG-GGGTAAAAATGGAATTTTTGAAAG
* *
37761 TTTGAGGGTAAAAATGTAATTTTTGGAAAG
1 TTCG-GGGTAAAAATGGAATTTTT-GAAAG
* * *
37791 TTTGAGGTCAAAAAATGGAATTTTAGAAAG
1 TTCGGGGT--AAAAATGGAATTTTTGAAAG
* *
37821 TTTGGGGGGTAAAAATGTAATTTTTAGAAAG
1 -TT-CGGGGTAAAAATGGAATTTTT-GAAAG
** * * *
37852 TTTAGGTTCAAAAATAGAATTTTGGAAAG
1 TTCGGGGT-AAAAATGGAATTTTTGAAAG
* *
37881 TTTAGGGGTAAAAATGTAATTTTTGGAAA-
1 -TTCGGGGTAAAAATGGAATTTTT-GAAAG
**
37910 TTTAGGGTAAAAA
1 TTCGGGGTAAAAA
37923 ATATAGTTCT
Statistics
Matches: 248, Mismatches: 41, Indels: 40
0.75 0.12 0.12
Matches are distributed among these distances:
28 27 0.11
29 91 0.37
30 90 0.36
31 36 0.15
32 4 0.02
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (28 bp):
TTCGGGGTAAAAATGGAATTTTTGAAAG
Found at i:37663 original size:59 final size:59
Alignment explanation
Indices: 37592--38020 Score: 319
Period size: 58 Copynumber: 7.3 Consensus size: 59
37582 TGCTTCGGGA
* * *
37592 GTAAAATGGTAATTTTTGAAAGGTTCGGGGTTC-AAAATGGAATTTTTAGATA-TTTAGGG
1 GTAAAAAGGTAATTTTTGAAA-GTTCGAGGTTCAAAAATGGAA-TTTTAGAAAGTTTAGGG
* * * * *
37651 GTAAAACGGTAATTTTTGGAAGGTTCG-GGGTCAAAAATGGAATTTTTAGACA--TTCGAGG
1 GTAAAAAGGTAATTTTT-GAAAGTTCGAGGTTCAAAAATGGAA-TTTTAGAAAGTTTAG-GG
* * *
37710 GTAAAATGGTAATTTTGGAAAGTTCGAGGTT-AAAAATGGAATTTTGGAAAGTTT-GAGG
1 GTAAAAAGGTAATTTTTGAAAGTTCGAGGTTCAAAAATGGAATTTTAGAAAGTTTAG-GG
* * *
37768 GTAAAAATGTAATTTTTGGAAAGTTTGAGG-TCAAAAAATGGAATTTTAGAAAGTTTGGGGG
1 GTAAAAAGGTAATTTTT-GAAAGTTCGAGGTTC-AAAAATGGAATTTTAGAAAGTTT-AGGG
* * * *
37829 GTAAAAATGTAATTTTTAGAAAGTT-TAGGTTCAAAAATAGAATTTTGGAAAGTTTAGGG
1 GTAAAAAGGTAATTTTT-GAAAGTTCGAGGTTCAAAAATGGAATTTTAGAAAGTTTAGGG
* * * * ** * * * * *
37888 GTAAAAATGTAATTTTTGGAAA-TT-TAGGGTAAAAAATATAGTTCTAGGAATTTTGGGG
1 GTAAAAAGGTAATTTTT-GAAAGTTCGAGGTTCAAAAATGGAATTTTAGAAAGTTTAGGG
* * * * * * *
37946 GCAAAAATGTAATTTTTGGAAAGTT-TAGGTT-AAAAATGTAATTTTAGGAAGTTCAGTG
1 GTAAAAAGGTAATTTTT-GAAAGTTCGAGGTTCAAAAATGGAATTTTAGAAAGTTTAGGG
*
38004 GT-AAAATGTAATTTTTG
1 GTAAAAAGGTAATTTTTG
38021 TGAAGTTTAG
Statistics
Matches: 316, Mismatches: 41, Indels: 29
0.82 0.11 0.08
Matches are distributed among these distances:
56 1 0.00
57 21 0.07
58 113 0.36
59 103 0.33
60 49 0.16
61 28 0.09
62 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (59 bp):
GTAAAAAGGTAATTTTTGAAAGTTCGAGGTTCAAAAATGGAATTTTAGAAAGTTTAGGG
Found at i:37680 original size:29 final size:29
Alignment explanation
Indices: 37561--37788 Score: 154
Period size: 29 Copynumber: 7.8 Consensus size: 29
37551 TGGATTCTCG
* * *
37561 GGGGTAAAACGGTAA--TTTGGATGCTTC
1 GGGGTAAAATGGTAATTTTTGGAAGGTTC
*
37588 GGGAGTAAAATGGTAATTTTTGAAAGGTTC
1 GGG-GTAAAATGGTAATTTTTGGAAGGTTC
* * *
37618 GGGGTTCAAAATGG-AATTTTTAGATA-TTTA
1 GGGG-T-AAAATGGTAATTTTTGGA-AGGTTC
*
37648 GGGGTAAAACGGTAATTTTTGGAAGGTTC
1 GGGGTAAAATGGTAATTTTTGGAAGGTTC
*
37677 GGGGTCAAAAATGG-AATTTTTAGACA--TTC
1 GGGGT--AAAATGGTAATTTTTGGA-AGGTTC
*
37706 GAGGGTAAAATGGTAA-TTTTGGAAAGTTC
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTC
* * *
37735 GAGGTTAAAAATGG-AA-TTTTGGAAAGTTT
1 G-GGGT-AAAATGGTAATTTTTGGAAGGTTC
37764 GAGGGTAAAAAT-GTAATTTTTGGAA
1 G-GGGT-AAAATGGTAATTTTTGGAA
37789 AGTTTGAGGT
Statistics
Matches: 165, Mismatches: 18, Indels: 33
0.76 0.08 0.15
Matches are distributed among these distances:
27 4 0.02
28 32 0.19
29 59 0.36
30 55 0.33
31 15 0.09
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGGAAGGTTC
Found at i:37803 original size:29 final size:29
Alignment explanation
Indices: 37650--38050 Score: 265
Period size: 29 Copynumber: 13.7 Consensus size: 29
37640 GATATTTAGG
** * * *
37650 GGTAAAACGGTAATTTTTGGAAGGTTCGG
1 GGTAAAAATGTAATTTTTGGAAAGTTTGA
* * * *
37679 GGTCAAAAATGGAATTTTTAGACA-TTCGA
1 GGT-AAAAATGTAATTTTTGGAAAGTTTGA
*
37708 GGGT-AAAATGGTAA-TTTTGGAAAGTTCGA
1 -GGTAAAAAT-GTAATTTTTGGAAAGTTTGA
*
37737 GGTTAAAAATGGAA-TTTTGGAAAGTTTGA
1 GG-TAAAAATGTAATTTTTGGAAAGTTTGA
37766 GGGTAAAAATGTAATTTTTGGAAAGTTTGA
1 -GGTAAAAATGTAATTTTTGGAAAGTTTGA
* * *
37796 GGTCAAAAAATGGAA-TTTTAGAAAGTTTGGGG
1 GGT--AAAAATGTAATTTTTGGAAAGTTT--GA
*
37828 GGTAAAAATGTAATTTTTAGAAAGTTT-A
1 GGTAAAAATGTAATTTTTGGAAAGTTTGA
*
37856 GGTTCAAAAATAG-AA-TTTTGGAAAGTTTAGG
1 GG-T-AAAAAT-GTAATTTTTGGAAAGTTT-GA
37887 GGTAAAAATGTAATTTTTGGAAA-TTT-A
1 GGTAAAAATGTAATTTTTGGAAAGTTTGA
* * * * * *
37914 GGGTAAAAAATATAGTTCTAGG-AATTTTGGG
1 -GGT-AAAAATGTAATTTTTGGAAAGTTT-GA
*
37945 GGCAAAAATGTAATTTTTGGAAAGTTT-A
1 GGTAAAAATGTAATTTTTGGAAAGTTTGA
* * *
37973 GGTTAAAAATGTAATTTTAGG-AAGTTCAGT
1 GG-TAAAAATGTAATTTTTGGAAAGTT-TGA
38003 GGT-AAAATGTAATTTTTGTG-AAGTTTAGA
1 GGTAAAAATGTAATTTTTG-GAAAGTTT-GA
* *
38032 GGTCAAAATGCAATTTTTG
1 GGTAAAAATGTAATTTTTG
38051 AAAACTATAA
Statistics
Matches: 299, Mismatches: 41, Indels: 63
0.74 0.10 0.16
Matches are distributed among these distances:
28 43 0.14
29 126 0.42
30 101 0.34
31 25 0.08
32 4 0.01
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (29 bp):
GGTAAAAATGTAATTTTTGGAAAGTTTGA
Found at i:39098 original size:6 final size:6
Alignment explanation
Indices: 39087--39173 Score: 54
Period size: 6 Copynumber: 14.0 Consensus size: 6
39077 TCTTTTTTTC
* *
39087 ATTAAT ATTAATT ATTATT ATTAATAT ATTTAT CATT-AT ATTTAA- ATTAAT
1 ATTAAT ATTAA-T ATTAAT ATT-A-AT ATTAAT -ATTAAT A-TTAAT ATTAAT
* * *
39138 ATTATT AATATT A-TAAT AATTAAT ATTAAT ATTAAT
1 ATTAAT ATTAAT ATTAAT -ATTAAT ATTAAT ATTAAT
39174 GATATTTACA
Statistics
Matches: 66, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
5 8 0.12
6 40 0.61
7 14 0.21
8 4 0.06
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (6 bp):
ATTAAT
Found at i:39158 original size:24 final size:24
Alignment explanation
Indices: 39087--39165 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 24
39077 TCTTTTTTTC
*
39087 ATTAATATTAATTATTATTATTAATA
1 ATTAATATT-ATTAATATTA-TAATA
*
39113 TATT--TATCATT-ATATT-T-A-A
1 -ATTAATATTATTAATATTATAATA
39132 ATTAATATTATTAATATTATAATA
1 ATTAATATTATTAATATTATAATA
39156 ATTAATATTA
1 ATTAATATTA
39166 ATATTAATGA
Statistics
Matches: 43, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
18 3 0.07
19 1 0.02
20 7 0.16
21 6 0.14
22 1 0.02
23 5 0.12
24 14 0.33
25 3 0.07
27 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTAATATTATTAATATTATAATA
Found at i:39179 original size:15 final size:14
Alignment explanation
Indices: 39087--39169 Score: 77
Period size: 15 Copynumber: 6.0 Consensus size: 14
39077 TCTTTTTTTC
39087 ATTAATATTAAT-T
1 ATTAATATTAATAT
*
39100 ATTATTATTAATAT
1 ATTAATATTAATAT
*
39114 ATTTATCATT-ATAT
1 ATTAAT-ATTAATAT
39128 -TTAA-ATTAATATT
1 ATTAATATTAATA-T
39141 ATTAATATT-ATAAT
1 ATTAATATTAAT-AT
39155 AATTAATATTAATAT
1 -ATTAATATTAATAT
39170 TAATGATATT
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
11 3 0.05
12 3 0.05
13 15 0.26
14 16 0.28
15 18 0.32
16 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTAATATTAATAT
Found at i:39850 original size:17 final size:17
Alignment explanation
Indices: 39824--39892 Score: 95
Period size: 17 Copynumber: 4.1 Consensus size: 17
39814 TTGGATATTA
39824 TTTAAATAAATTTAAAT
1 TTTAAATAAATTTAAAT
*
39841 TTTTAATAAATTTAAAT
1 TTTAAATAAATTTAAAT
* *
39858 TTAAAATAAACTT-AAT
1 TTTAAATAAATTTAAAT
39874 TTTAAAATAAATTTAAAT
1 TTT-AAATAAATTTAAAT
39892 T
1 T
39893 CTATTGGGCC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
16 5 0.11
17 35 0.80
18 4 0.09
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAATAAATTTAAAT
Found at i:47856 original size:11 final size:11
Alignment explanation
Indices: 47840--47872 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
47830 GGTAAAATCA
47840 TTAATATTAAG
1 TTAATATTAAG
47851 TTAATATT--G
1 TTAATATTAAG
47860 TTAATATTAAG
1 TTAATATTAAG
47871 TT
1 TT
47873 GAATCGACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.45
11 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (11 bp):
TTAATATTAAG
Found at i:58706 original size:29 final size:28
Alignment explanation
Indices: 58674--58733 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
58664 AAAGTAGAAT
* *
58674 CAAATGAAATTTTAATGTATAAAGTTGCA
1 CAAAT-AAATGTTAATGTATAAAATTGCA
*
58703 CAAAATAAATGTTGATGTATAAAATTGCA
1 C-AAATAAATGTTAATGTATAAAATTGCA
58732 CA
1 CA
58734 TTAAATCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.04
29 22 0.81
30 4 0.15
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (28 bp):
CAAATAAATGTTAATGTATAAAATTGCA
Found at i:60925 original size:59 final size:58
Alignment explanation
Indices: 60832--61087 Score: 191
Period size: 58 Copynumber: 4.3 Consensus size: 58
60822 ATCCGGGGGC
* * *
60832 AAAATGGTAATTTTGGGAAAGT--TCGGGGTTAAAAATAGAATTTTAGGTATCCGAGGGT
1 AAAATGGTAATTTTTGGAAA-TAATTGGGGTCAAAAATAGAATTTTAGGTAT-CGAGGGT
* * * * *
60890 AAAATGGTAATTTTTGGAAATAATTGGGATCAAAAATGAAAATTTTTGAAGT-TTGGGGGT
1 AAAATGGTAATTTTTGGAAATAATTGGGGTCAAAAAT-AGAA-TTTT-AGGTATCGAGGGT
* * * * * ***
60950 -AAATGGTAA-TTTTGGGAAGAATTGGGGTCAAAAATGGAATTTTGGGAAGTTTTGGGT
1 AAAATGGTAATTTTTGGAAATAATTGGGGTCAAAAATAGAATTTTAGGTA-TCGAGGGT
* * * * *
61007 AAAATGGTAATTTTTGGAAAAAAATTGGGGTC-AAATTTGAAATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGG-AAATAATTGGGGTCAAAAATAG-AATTTTAGGTA--TCGAGGGT
61068 AAAATGGTAATTTTTGGAAA
1 AAAATGGTAATTTTTGGAAA
61088 AATCGAGGTT
Statistics
Matches: 159, Mismatches: 27, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
55 1 0.01
56 4 0.03
57 9 0.06
58 51 0.32
59 31 0.19
60 33 0.21
61 27 0.17
62 3 0.02
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.34
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAATAATTGGGGTCAAAAATAGAATTTTAGGTATCGAGGGT
Found at i:60966 original size:117 final size:119
Alignment explanation
Indices: 60832--61146 Score: 338
Period size: 117 Copynumber: 2.7 Consensus size: 119
60822 ATCCGGGGGC
* *
60832 AAAATGGTAATTTTGGGAAAGTTCGGGGTTAAAAATAGAATTTTAGGTA-TCCGAGGGTAAAATG
1 AAAATGGTAATTTTGGGAAAATTCGGGGTTAAAAATAGAATTTTAGGAAGT-CGAGGGTAAAATG
* * *
60896 GTAATTTTTGG-AAATAATTGGGATCAAAAATGAAAATTTTT-GAAGTTTGGGGGT
65 GTAATTTTTGGAAAAAAATTGGGATCAAAAATG-AAATTTTTGGAAGTTCGAGGGT
* * * ***
60950 -AAATGGTAATTTTGGGAAGAATT-GGGGTCAAAAATGGAATTTTGGGAAGTTTTGGGTAAAATG
1 AAAATGGTAATTTTGGGAA-AATTCGGGGTTAAAAATAGAATTTTAGGAAGTCGAGGGTAAAATG
* **
61013 GTAATTTTTGGAAAAAAATTGGGGTCAAATTTGAAATTTTTGGAAGTTCGAGGGT
65 GTAATTTTTGGAAAAAAATTGGGATCAAAAATGAAATTTTTGGAAGTTCGAGGGT
* * * * * **
61068 AAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAGTGGAAATTTTA-GAAGTTTAGGGGTAAAAT
1 AAAATGGTAATTTTGGGAAAATTCGGGGTTAAAAATAG-AATTTTAGGAAGTCGA-GGGTAAAAT
*
61132 AGTAATTTTT-GAAAA
64 GGTAATTTTTGGAAAA
61147 GTTCGAGGGT
Statistics
Matches: 167, Mismatches: 22, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
117 68 0.41
118 35 0.21
119 40 0.24
120 24 0.14
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (119 bp):
AAAATGGTAATTTTGGGAAAATTCGGGGTTAAAAATAGAATTTTAGGAAGTCGAGGGTAAAATGG
TAATTTTTGGAAAAAAATTGGGATCAAAAATGAAATTTTTGGAAGTTCGAGGGT
Found at i:60982 original size:58 final size:58
Alignment explanation
Indices: 60886--61146 Score: 258
Period size: 59 Copynumber: 4.4 Consensus size: 58
60876 AGGTATCCGA
* *
60886 GGGTAAAATGGTAATTTTTGGAAATAATTGGGATCAAAAATGAAAATTTTTGAAGTTTGG
1 GGGTAAAATGGTAA-TTTTGGAAAAAATTGGGGTCAAAAATG-AAATTTTTGAAGTTTGG
* * * * *
60946 GGGT-AAATGGTAATTTTGGGAAGAATTGGGGTCAAAAATGGAATTTTGGGAAGTTT-T
1 GGGTAAAATGGTAATTTTGGAAAAAATTGGGGTCAAAAATGAAATTTT-TGAAGTTTGG
** * *
61003 GGGTAAAATGGTAATTTTTGGAAAAAAATTGGGGTCAAATTTGAAATTTTTGGAAGTTCGA
1 GGGTAAAATGGTAA-TTTTGG-AAAAAATTGGGGTCAAAAATGAAATTTTT-GAAGTTTGG
* * * * * *
61064 GGGTAAAATGGTAATTTTTGG-AAAAATCGAGGTTAAAAGTGGAAATTTTAGAAGTTTAG
1 GGGTAAAATGGTAA-TTTTGGAAAAAATTGGGGTCAAAAAT-GAAATTTTTGAAGTTTGG
* *
61123 GGGTAAAATAGTAATTTTTGAAAA
1 GGGTAAAATGGTAATTTTGGAAAA
61147 GTTCGAGGGT
Statistics
Matches: 168, Mismatches: 25, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
57 10 0.06
58 45 0.27
59 51 0.30
60 41 0.24
61 21 0.12
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTGGAAAAAATTGGGGTCAAAAATGAAATTTTTGAAGTTTGG
Found at i:60993 original size:30 final size:31
Alignment explanation
Indices: 60890--61041 Score: 106
Period size: 30 Copynumber: 5.1 Consensus size: 31
60880 ATCCGAGGGT
* * *
60890 AAAATGGTAATTTTTGGAAATAATTGGGATCA
1 AAAATGGTAA-TTTTGGGAAGAATTGGGGTCA
** * *
60922 AAAATGAAAATTTT-TGAAG-TTTGGGGGT--
1 AAAATGGTAATTTTGGGAAGAATT-GGGGTCA
60950 -AAATGGTAATTTTGGGAAGAATTGGGGTCA
1 AAAATGGTAATTTTGGGAAGAATTGGGGTCA
* *
60980 AAAATGG-AATTTTGGGAAG-TTTTGGGT--
1 AAAATGGTAATTTTGGGAAGAATTGGGGTCA
* *
61007 AAAATGGTAATTTTTGGAAAAAAATTGGGGTCA
1 AAAATGGTAA-TTTTGG-GAAGAATTGGGGTCA
61040 AA
1 AA
61042 TTTGAAATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 23
0.69 0.13 0.18
Matches are distributed among these distances:
27 18 0.20
28 11 0.12
29 16 0.18
30 20 0.22
31 16 0.18
32 8 0.09
33 2 0.02
ACGTcount: A:0.38, C:0.02, G:0.28, T:0.33
Consensus pattern (31 bp):
AAAATGGTAATTTTGGGAAGAATTGGGGTCA
Found at i:61094 original size:30 final size:30
Alignment explanation
Indices: 61003--61112 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 30
60993 GGGAAGTTTT
* *
61003 GGGTAAAATGGTAATTTTTGGAAAAAAATTG-
1 GGGTAAAATGGAAATTTTTGG--AAAAATCGA
* * **
61034 GGGTCAAATTTGAAATTTTTGG-AAGTTCGA
1 GGGT-AAAATGGAAATTTTTGGAAAAATCGA
*
61064 GGGTAAAATGGTAATTTTTGGAAAAATCGA
1 GGGTAAAATGGAAATTTTTGGAAAAATCGA
*
61094 GGTTAAAAGTGGAAATTTT
1 GGGTAAAA-TGGAAATTTT
61113 AGAAGTTTAG
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
29 18 0.29
30 17 0.27
31 13 0.21
32 14 0.23
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (30 bp):
GGGTAAAATGGAAATTTTTGGAAAAATCGA
Found at i:61129 original size:59 final size:58
Alignment explanation
Indices: 60827--61204 Score: 251
Period size: 59 Copynumber: 6.4 Consensus size: 58
60817 TGAATATCCG
* * * * **
60827 GGGGCAAAATGGTAA-TTTTGGGAAAGTTCGGGGTTAAAAATAG-AATTTTAG--GTATCC
1 GGGGTAAAATGGTAATTTTTGGAAAAATT--GGGTTAAAAATGGAAATTTTAGAAGT-TTA
* * * *
60884 GAGGGTAAAATGGTAATTTTTGGAAATAATTGGGATCAAAAATGAAAATTTTTGAAGTTTG
1 G-GGGTAAAATGGTAATTTTTGGAAA-AATTGGG-TTAAAAATGGAAATTTTAGAAGTTTA
* * * *
60945 GGGGT-AAATGGTAATTTTGGGAAGAATTGGGGTCAAAAATGG-AATTTTGGGAAGTTT-
1 GGGGTAAAATGGTAATTTTTGGAAAAATT-GGGTTAAAAATGGAAATTTT-AGAAGTTTA
* * * * * * *
61002 TGGGTAAAATGGTAATTTTTGGAAAAAAATTGGGGTCAAATTTGAAATTTTTGGAAG-TTC
1 GGGGTAAAATGGTAATTTTTGG--AAAAATTGGGTTAAAAATGGAAA-TTTTAGAAGTTTA
* *
61062 GAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAGTGGAAATTTTAGAAGTTTA
1 G-GGGTAAAATGGTAATTTTTGGAAAAATTG-GGTTAAAAATGGAAATTTTAGAAGTTTA
* *
61122 GGGGTAAAATAGTAATTTTT-GAAAAGTTCGAGGGTT-AAAAT--ATAATTTTGGAGAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGAAAAATT---GGGTTAAAAATGGA-AATTTT--AGAAGTTTA
*
61182 GGGGTTAAAAT-ATAATTTTTGGA
1 GGGG-TAAAATGGTAATTTTTGGA
61205 TAGTTTAGGG
Statistics
Matches: 261, Mismatches: 34, Indels: 48
0.76 0.10 0.14
Matches are distributed among these distances:
57 12 0.05
58 63 0.24
59 82 0.31
60 66 0.25
61 36 0.14
62 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.34
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGAAAAATTGGGTTAAAAATGGAAATTTTAGAAGTTTA
Found at i:61168 original size:30 final size:29
Alignment explanation
Indices: 61047--61261 Score: 150
Period size: 30 Copynumber: 7.3 Consensus size: 29
61037 TCAAATTTGA
* *
61047 AATTTTTG-GAAGTTCGAGGG-TAAAATGGT
1 AATTTTTGAAAAGTT-GAGGGTTAAAAT-AT
* * **
61076 AATTTTTGGAAAAATCGA-GGTTAAAAGTGG
1 AATTTTT-GAAAAGTTGAGGGTTAAAA-TAT
* * * *
61106 AAATTTT-AGAAGTTTAGGGGTAAAATAGT
1 AATTTTTGAAAAGTTGAGGGTTAAAATA-T
61135 AATTTTTGAAAAGTTCGAGGGTTAAAATAT
1 AATTTTTGAAAAGTT-GAGGGTTAAAATAT
* * *
61165 AATTTTGGAGAAGTTTAGGGGTTAAAATAT
1 AATTTTTGAAAAGTTGA-GGGTTAAAATAT
* * *
61195 AATTTTTGGATAGTTTAGGGTTAAAATAT
1 AATTTTTGAAAAGTTGAGGGTTAAAATAT
* * * *
61224 AATTTCTAAACAATTTAAGGGTTAAAATAT
1 AATTTTTGAA-AAGTTGAGGGTTAAAATAT
61254 AATTTTTG
1 AATTTTTG
61262 GATAATTTAG
Statistics
Matches: 145, Mismatches: 31, Indels: 19
0.74 0.16 0.10
Matches are distributed among these distances:
28 6 0.04
29 42 0.29
30 82 0.57
31 15 0.10
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.37
Consensus pattern (29 bp):
AATTTTTGAAAAGTTGAGGGTTAAAATAT
Found at i:61246 original size:59 final size:59
Alignment explanation
Indices: 61115--61273 Score: 196
Period size: 59 Copynumber: 2.7 Consensus size: 59
61105 GAAATTTTAG
* * * * ** *
61115 AAGTTT-AGGGGTAAAATAGTAATTTTTGAAAAGTTCGAGGGTTAAAATATAATTTTGGAG
1 AAGTTTAAGGGTTAAAATA-TAATTTTTGGATAGTT-TAGGGTTAAAATATAATTTTAAAC
*
61175 AAGTTTAGGGGTTAAAATATAATTTTTGGATAGTTTAGGGTTAAAATATAATTTCTAAAC
1 AAGTTTAAGGGTTAAAATATAATTTTTGGATAGTTTAGGGTTAAAATATAATTT-TAAAC
*
61235 AA-TTTAAGGGTTAAAATATAATTTTTGGATAATTTAGGG
1 AAGTTTAAGGGTTAAAATATAATTTTTGGATAGTTTAGGG
61274 ACCTCTAGGC
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
59 53 0.61
60 24 0.28
61 10 0.11
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.38
Consensus pattern (59 bp):
AAGTTTAAGGGTTAAAATATAATTTTTGGATAGTTTAGGGTTAAAATATAATTTTAAAC
Found at i:61269 original size:30 final size:30
Alignment explanation
Indices: 61121--61270 Score: 153
Period size: 30 Copynumber: 5.0 Consensus size: 30
61111 TTAGAAGTTT
* * **
61121 AGGGGTAAAATAGTAATTTTT-GAAAAGTTCG
1 AGGGTTAAAATA-TAATTTTTGGATAA-TTTA
*
61152 AGGGTTAAAATATAA-TTTTGGAGAAGTTTA
1 AGGGTTAAAATATAATTTTTGGATAA-TTTA
* *
61182 GGGGTTAAAATATAATTTTTGGATAGTTT-
1 AGGGTTAAAATATAATTTTTGGATAATTTA
* ** *
61211 AGGGTTAAAATATAATTTCTAAACAATTTA
1 AGGGTTAAAATATAATTTTTGGATAATTTA
61241 AGGGTTAAAATATAATTTTTGGATAATTTA
1 AGGGTTAAAATATAATTTTTGGATAATTTA
61271 GGGACCTCTA
Statistics
Matches: 99, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
29 27 0.27
30 53 0.54
31 19 0.19
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (30 bp):
AGGGTTAAAATATAATTTTTGGATAATTTA
Found at i:67942 original size:59 final size:59
Alignment explanation
Indices: 67845--68166 Score: 228
Period size: 59 Copynumber: 5.4 Consensus size: 59
67835 GGATAACCGG
* * * ** * * *
67845 GGGTAAAATAGTAA-TTTTGGGAA-AATTCAAGGTTAAAAATAAAATTTTAGGTATTCAA
1 GGGTAAAATGGTAATTTTTGGAAAGAATT-AGGGACAAAAATGAAATTTTAGGAATTTAA
* * ** *
67903 GGGTAAAATGGTAATTTTTGGAAAGCA-TCGGGATCAAAAATGAAATTTTTTGAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGAAAGAATTAGGGA-CAAAAATGAAATTTTAGGAA-TTTAA
* * * **
67963 GGGTAAAATGGTAA-TTTTGGAAAGAATTAGGGACAAATATGGAATTTTGGGAATTTTT
1 GGGTAAAATGGTAATTTTTGGAAAGAATTAGGGACAAAAATGAAATTTTAGGAATTTAA
* * * **
68021 GGGTAAAATGGTAATTTTTGGAAAAAAAATTAGAGTCAAAAATGAAATTTTTA-GAAGTTCGA
1 GGGTAAAATGGTAATTTTTGG--AAAGAATTAGGGACAAAAATGAAA-TTTTAGGAA-TTTAA
* * * * * *
68083 GGGTAAAATGATAATTTTTGG-AA-AATTAGAGGTCAAAAGTGGAATTTTTGAAAGTTT-A
1 GGGTAAAATGGTAATTTTTGGAAAGAATTAG-GGACAAAAATGAAATTTTAGGAA-TTTAA
*
68141 GAGGTAAAATGGTAATTTTTAGAAAG
1 G-GGTAAAATGGTAATTTTTGGAAAG
68167 TTCGAGGGTC
Statistics
Matches: 210, Mismatches: 39, Indels: 27
0.76 0.14 0.10
Matches are distributed among these distances:
58 44 0.21
59 93 0.44
60 25 0.12
61 22 0.10
62 26 0.12
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.33
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGAAAGAATTAGGGACAAAAATGAAATTTTAGGAATTTAA
Found at i:68100 original size:120 final size:120
Alignment explanation
Indices: 67902--68165 Score: 308
Period size: 120 Copynumber: 2.2 Consensus size: 120
67892 TAGGTATTCA
** * * * *
67902 AGGGTAAAATGGTAATTTTTGG--AAAGCATCGGGATCAAAAATGAAATTTTTTGAAGTTTAGGG
1 AGGGTAAAATGGTAATTTTTGGAAAAAAAATAGAGATCAAAAATGAAATTTTTAGAAGTTGAGGG
* * *
67965 GTAAAATGGTAA-TTTTGGAAAGAATTAG-GGACAAATA-TGGAATTTTGGGAATTTT
66 GTAAAATGATAATTTTTGG-AA-AATTAGAGGACAAA-AGTGGAATTTTGGAAAGTTT
*
68020 TGGGTAAAATGGTAATTTTTGGAAAAAAAATTAGAG-TCAAAAATGAAATTTTTAGAAGTTCGA-
1 AGGGTAAAATGGTAATTTTTGGAAAAAAAA-TAGAGATCAAAAATGAAATTTTTAGAAGTT-GAG
* *
68083 GGGTAAAATGATAATTTTTGGAAAATTAGAGGTCAAAAGTGGAATTTTTGAAAGTTT
64 GGGTAAAATGATAATTTTTGGAAAATTAGAGGACAAAAGTGGAATTTTGGAAAGTTT
*
68140 AGAGGTAAAATGGTAATTTTTAGAAA
1 AG-GGTAAAATGGTAATTTTTGGAAA
68166 GTTCGAGGGT
Statistics
Matches: 124, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
118 21 0.17
119 7 0.06
120 64 0.52
121 32 0.26
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (120 bp):
AGGGTAAAATGGTAATTTTTGGAAAAAAAATAGAGATCAAAAATGAAATTTTTAGAAGTTGAGGG
GTAAAATGATAATTTTTGGAAAATTAGAGGACAAAAGTGGAATTTTGGAAAGTTT
Found at i:68131 original size:30 final size:29
Alignment explanation
Indices: 68046--68189 Score: 95
Period size: 30 Copynumber: 4.9 Consensus size: 29
68036 TTTTGGAAAA
*
68046 AAAATTAGA-GTCAAAAAT-GAAATTTTT-
1 AAAATTAGAGGTC-AAAATGGTAATTTTTG
* * *
68073 AGAAGTTCGAGGGT-AAAATGATAATTTTTGG
1 A-AAATTAGA-GGTCAAAATGGTAATTTTT-G
68104 AAAATTAGAGGTCAAAAGTGG-AATTTTTG
1 AAAATTAGAGGTCAAAA-TGGTAATTTTTG
*
68133 AAAGTTTAGAGGT-AAAATGGTAATTTTTAG
1 AAA-ATTAGAGGTCAAAATGGTAATTTTT-G
* * *
68163 AAAGTTCGAGGGTCAAAAT-ATAATTTT
1 AAAATTAGA-GGTCAAAATGGTAATTTT
68190 GGATAAGTTT
Statistics
Matches: 93, Mismatches: 11, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
27 1 0.01
28 14 0.15
29 29 0.31
30 41 0.44
31 8 0.09
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (29 bp):
AAAATTAGAGGTCAAAATGGTAATTTTTG
Found at i:68217 original size:60 final size:60
Alignment explanation
Indices: 68082--68320 Score: 235
Period size: 60 Copynumber: 4.0 Consensus size: 60
68072 TAGAAGTTCG
* * * ** *
68082 AGGGTAAAATGATAATTTTTG-GAAAATT-AGAGGTCAAAAGTGGAATTTTTGA-AAGTTT-
1 AGGGTAAAATGATAATTTTAGAG-AAGTTGAGGGGTCAAAA-TATAATTTTGGATAAGTTTA
*
68140 AGAGGTAAAATGGTAATTTTTAGA-AAGTTCGA-GGGTCAAAATATAATTTTGGATAAGTTTA
1 AG-GGTAAAATGATAA-TTTTAGAGAAGTT-GAGGGGTCAAAATATAATTTTGGATAAGTTTA
* * * *
68201 AGGGTTAAAAT-ATAATTTTAGAGAAGTTTAGGGGTCAAAATATAATTTTAGAGAAGTTTG
1 AGGG-TAAAATGATAATTTTAGAGAAGTTGAGGGGTCAAAATATAATTTTGGATAAGTTTA
*
68261 AGGGTTAAAAT-ATAATTTTAGAGAAGTTTAGGGGTCAAAATATAATTTTTGGAT-AGTTTA
1 AGGG-TAAAATGATAATTTTAGAGAAGTTGAGGGGTCAAAATATAA-TTTTGGATAAGTTTA
68321 GGGACCTTCA
Statistics
Matches: 155, Mismatches: 15, Indels: 20
0.82 0.08 0.11
Matches are distributed among these distances:
58 2 0.01
59 33 0.21
60 105 0.68
61 15 0.10
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (60 bp):
AGGGTAAAATGATAATTTTAGAGAAGTTGAGGGGTCAAAATATAATTTTGGATAAGTTTA
Found at i:68264 original size:90 final size:90
Alignment explanation
Indices: 68059--68323 Score: 287
Period size: 90 Copynumber: 3.0 Consensus size: 90
68049 ATTAGAGTCA
* **
68059 AAAATGA-AATTTTTAG-AAGTTCGAGGGT-AAAATGATAATTTTTG-GAAAATT-AGAGGTCAA
1 AAAATGATAATTTTTAGAAAGTTCGAGGGTCAAAAT-ATAATTTTAGAGAAGTTTAAG-GGTCAA
** *
68119 AAGTGGAATTTTTGA-AAGTTTAGAGGT
64 AA-TATAATTTTTGAGAAGTTTAGGGGT
* * * *
68146 AAAATGGTAATTTTTAGAAAGTTCGAGGGTCAAAATATAATTTTGGATAAGTTTAAGGGTTAAAA
1 AAAATGATAATTTTTAGAAAGTTCGAGGGTCAAAATATAATTTTAGAGAAGTTTAAGGGTCAAAA
*
68211 TATAATTTTAGAGAAGTTTAGGGGT
66 TATAATTTTTGAGAAGTTTAGGGGT
* * *
68236 CAAAAT-ATAA-TTTTAGAGAAGTTTGAGGGTTAAAATATAATTTTAGAGAAGTTTAGGGGTCAA
1 -AAAATGATAATTTTTAGA-AAGTTCGAGGGTCAAAATATAATTTTAGAGAAGTTTAAGGGTCAA
68299 AATATAATTTTTG-GATAGTTTAGGG
64 AATATAATTTTTGAGA-AGTTTAGGG
68324 ACCTTCAAGG
Statistics
Matches: 151, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
87 6 0.04
88 9 0.06
89 39 0.26
90 90 0.60
91 7 0.05
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.35
Consensus pattern (90 bp):
AAAATGATAATTTTTAGAAAGTTCGAGGGTCAAAATATAATTTTAGAGAAGTTTAAGGGTCAAAA
TATAATTTTTGAGAAGTTTAGGGGT
Found at i:68319 original size:30 final size:29
Alignment explanation
Indices: 68066--68323 Score: 195
Period size: 30 Copynumber: 8.7 Consensus size: 29
68056 TCAAAAATGA
* *
68066 AATTTTTAGAAG-TTCGAGGGT-AAAATGAT
1 AATTTTTGGAAGTTTAG-GGGTCAAAAT-AT
** * **
68095 AATTTTTGGAAAATTAGAGGTCAAAAGTGG
1 AATTTTTGGAAGTTTAGGGGTCAAAA-TAT
* * *
68125 AATTTTTGAAAGTTTAGAGGT-AAAATGGT
1 AATTTTTGGAAGTTTAGGGGTCAAAAT-AT
* *
68154 AATTTTTAGAAAG-TTCGAGGGTCAAAATAT
1 AATTTTT-GGAAGTTTAG-GGGTCAAAATAT
* *
68184 AA-TTTTGGATAAGTTTAAGGGTTAAAATAT
1 AATTTTTGG--AAGTTTAGGGGTCAAAATAT
*
68214 AATTTTAGAGAAGTTTAGGGGTCAAAATAT
1 AATTTTTG-GAAGTTTAGGGGTCAAAATAT
* *
68244 AATTTTAGAGAAGTTT-GAGGGTTAAAATAT
1 AATTTTTG-GAAGTTTAG-GGGTCAAAATAT
*
68274 AATTTTAGAGAAGTTTAGGGGTCAAAATAT
1 AATTTTTG-GAAGTTTAGGGGTCAAAATAT
68304 AATTTTTGGATAGTTTAGGG
1 AATTTTTGGA-AGTTTAGGG
68324 ACCTTCAAGG
Statistics
Matches: 191, Mismatches: 23, Indels: 29
0.79 0.09 0.12
Matches are distributed among these distances:
28 2 0.01
29 35 0.18
30 140 0.73
31 13 0.07
32 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (29 bp):
AATTTTTGGAAGTTTAGGGGTCAAAATAT
Found at i:69401 original size:9 final size:9
Alignment explanation
Indices: 69387--69424 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
69377 AAAGTGTTAT
69387 TTAATATTA
1 TTAATATTA
69396 TTAATATTA
1 TTAATATTA
*
69405 TTATTATTA
1 TTAATATTA
*
69414 TTATTATTA
1 TTAATATTA
69423 TT
1 TT
69425 CATTAATGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TTAATATTA
Found at i:69406 original size:3 final size:3
Alignment explanation
Indices: 69391--69489 Score: 81
Period size: 3 Copynumber: 32.0 Consensus size: 3
69381 TGTTATTTAA
* ** *
69391 TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TCAT TAAT GCT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT T-AT TAT TAT
* * * * * *
69438 TAT TAT TAA GATT TAT TAT TAG TGT TAT TAG TAA TAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
69484 TAT TAT
1 TAT TAT
69490 CATTGATGAT
Statistics
Matches: 75, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
3 69 0.92
4 6 0.08
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:70106 original size:6 final size:6
Alignment explanation
Indices: 70095--70187 Score: 72
Period size: 6 Copynumber: 16.0 Consensus size: 6
70085 TTACAATAAT
* * *
70095 TTTAAA TTTAAA TATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTTAGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
* *
70143 -CTAAA TTTAAA TTTACAA --TAAA TTT-AA TCTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
70188 ATGAGCTGAG
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
4 2 0.03
5 17 0.25
6 41 0.59
7 9 0.13
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:70131 original size:17 final size:17
Alignment explanation
Indices: 70095--70187 Score: 100
Period size: 17 Copynumber: 5.4 Consensus size: 17
70085 TTACAATAAT
70095 TTTAAATTTAAATATAAA
1 TTTAAATTTAAAT-TAAA
*
70113 TTTAAACTTAAATTAAA
1 TTTAAATTTAAATTAAA
* *
70130 TTTAAATTTTAGACTAAA
1 TTTAAA-TTTAAATTAAA
70148 TTTAAATTTACAA-TAAA
1 TTTAAATTTA-AATTAAA
*
70165 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAATTAAA
70182 TTTAAA
1 TTTAAA
70188 ATGAGCTGAG
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
16 5 0.08
17 31 0.48
18 29 0.45
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:75614 original size:30 final size:30
Alignment explanation
Indices: 75550--75749 Score: 273
Period size: 30 Copynumber: 6.7 Consensus size: 30
75540 TTCGAGGTCG
*
75550 AAAATGGAATTTTTGGAAGTTTGGGGGT-A
1 AAAATGGAATTTTTGGAAGTTTTGGGGTAA
* *
75579 AAAATGGAATTTTTGGAAGCTTCGGGGTAA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTAA
* *
75609 AAAATGGAATTTTTGGAAGCTTCGGGGTAA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTAA
*
75639 AAAATGGAATTTTTGGAAGTTTTGAGGTTAA
1 AAAATGGAATTTTTGGAAGTTTTG-GGGTAA
75670 AAAATGGGAA-TTTTGGAAG-TTTGGGGT-A
1 AAAAT-GGAATTTTTGGAAGTTTTGGGGTAA
* *
75698 AAAATGGGATTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTAA
*
75728 AAAATGGGATTTTTGGAAGTTT
1 AAAATGGAATTTTTGGAAGTTT
75750 AGAGGCAAAT
Statistics
Matches: 158, Mismatches: 7, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
27 3 0.02
28 15 0.09
29 37 0.23
30 80 0.51
31 19 0.12
32 4 0.03
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.35
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTAA
Found at i:75701 original size:89 final size:90
Alignment explanation
Indices: 75550--75754 Score: 283
Period size: 89 Copynumber: 2.3 Consensus size: 90
75540 TTCGAGGTCG
*
75550 AAAATGGAATTTTTGGAAG-TTTGGGGGTAAAAATGGAATTTTTGGAAGCTTCGGGGTAAAAAAT
1 AAAATGGAATTTTTGGAAGTTTTGAGGGTAAAAATGGAATTTTTGGAAGCTTCGGGGTAAAAAAT
75614 GGAATTTTTGGAAGCTTCGGGGTAA
66 GGAATTTTTGGAAGCTTCGGGGTAA
* *
75639 AAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAAATGGGAA-TTTTGGAAG-TTTGGGGT-AAAA
1 AAAATGGAATTTTTGGAAGTTTTGAGGGT-AAAAAT-GGAATTTTTGGAAGCTTCGGGGTAAAAA
* * * *
75701 ATGGGATTTTTGGAAGTTTTGGGGTTA
64 ATGGAATTTTTGGAAGCTTCGGGGTAA
* *
75728 AAAATGGGATTTTTGGAAGTTTAGAGG
1 AAAATGGAATTTTTGGAAGTTTTGAGG
75755 CAAATTTGTA
Statistics
Matches: 104, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
89 71 0.68
90 14 0.13
91 15 0.14
92 4 0.04
ACGTcount: A:0.32, C:0.02, G:0.32, T:0.34
Consensus pattern (90 bp):
AAAATGGAATTTTTGGAAGTTTTGAGGGTAAAAATGGAATTTTTGGAAGCTTCGGGGTAAAAAAT
GGAATTTTTGGAAGCTTCGGGGTAA
Found at i:75771 original size:59 final size:58
Alignment explanation
Indices: 75550--75749 Score: 285
Period size: 59 Copynumber: 3.4 Consensus size: 58
75540 TTCGAGGTCG
* * *
75550 AAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGCTTCGGGGTAA
1 AAAATGGAATTTTTGGAAGTTT-GGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTA
* *
75609 AAAATGGAATTTTTGGAAGCTTCGGGGTAAAAAATGGAATTTTTGGAAGTTTTGAGGTTAA
1 AAAATGGAATTTTTGGAAG-TTTGGGGT-AAAAATGGAATTTTTGGAAGTTTTGGGGTT-A
*
75670 AAAATGGGAA-TTTTGGAAGTTTGGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGTTA
1 AAAAT-GGAATTTTTGGAAGTTTGGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTA
*
75728 AAAATGGGATTTTTGGAAGTTT
1 AAAATGGAATTTTTGGAAGTTT
75750 AGAGGCAAAT
Statistics
Matches: 127, Mismatches: 9, Indels: 11
0.86 0.06 0.07
Matches are distributed among these distances:
57 3 0.02
58 18 0.14
59 52 0.41
60 35 0.28
61 15 0.12
62 4 0.03
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.35
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTTGGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTA
Found at i:77697 original size:17 final size:17
Alignment explanation
Indices: 77672--77742 Score: 72
Period size: 17 Copynumber: 4.1 Consensus size: 17
77662 GGACTTTTAA
* **
77672 TTAAGTTTTAAATCCAT
1 TTAAATTTTAAATAAAT
*
77689 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
77706 TTAAA-TTTAAAGTAAAT
1 TTAAATTTTAAA-TAAAT
*
77723 TTAAATTTAAAAATAAAT
1 TTAAATTT-TAAATAAAT
77741 TT
1 TT
77743 GAATCAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
16 5 0.11
17 28 0.62
18 9 0.20
19 3 0.07
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:77701 original size:6 final size:6
Alignment explanation
Indices: 77687--77733 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
77677 TTTTAAATCC
* *
77687 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-GTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
77733 A
1 A
77734 AATAAATTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 8 0.23
6 27 0.77
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (6 bp):
ATTTAA
Found at i:80290 original size:2 final size:2
Alignment explanation
Indices: 80283--80316 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
80273 TATTATTTTA
80283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80317 TTGTTGCAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82833 original size:22 final size:22
Alignment explanation
Indices: 82806--82850 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
82796 TCTGTTGTTC
82806 TATGTAGTTTTATTTATTCATT
1 TATGTAGTTTTATTTATTCATT
82828 TATGTAGTTTTATTTATTCATT
1 TATGTAGTTTTATTTATTCATT
82850 T
1 T
82851 TAGACCAAAA
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:0.22, C:0.04, G:0.09, T:0.64
Consensus pattern (22 bp):
TATGTAGTTTTATTTATTCATT
Found at i:90050 original size:3 final size:3
Alignment explanation
Indices: 90042--90072 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
90032 AAAGGCAATT
90042 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
90073 TGAATAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:91428 original size:22 final size:21
Alignment explanation
Indices: 91385--91429 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
91375 TATTTAATAT
* *
91385 ATAATATTTCAATTATTATTA
1 ATAATATTTCAAATAATATTA
*
91406 ATAATATATTCAAATAATGTTA
1 ATAATAT-TTCAAATAATATTA
91428 AT
1 AT
91430 TTTGATATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (21 bp):
ATAATATTTCAAATAATATTA
Found at i:92101 original size:2 final size:2
Alignment explanation
Indices: 92096--92122 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
92086 TCTCTTTAGT
92096 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
92123 TAAAAAGCTT
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:99614 original size:27 final size:27
Alignment explanation
Indices: 99565--99621 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
99555 ATAATGTTTT
* *
99565 TAATTTTACTTTATAATGCTATACATA
1 TAATGTTACTTTATAATGATATACATA
*
99592 TAATGTTACTTTATATAT-ATATATATA
1 TAATGTTACTTTATA-ATGATATACATA
99619 TAA
1 TAA
99622 AAGAACAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (27 bp):
TAATGTTACTTTATAATGATATACATA
Found at i:99737 original size:17 final size:18
Alignment explanation
Indices: 99704--99750 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
99694 TAAGAGTTAT
99704 AATAATTATACATTTAA-A
1 AATAATTATA-ATTTAATA
99722 AATAATTATAATTTAATA
1 AATAATTATAATTTAATA
99740 AA-AATTATAAT
1 AATAATTATAAT
99751 AATTATTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAATTATAATTTAATA
Found at i:104410 original size:16 final size:15
Alignment explanation
Indices: 104381--104409 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
104371 GGATATAATA
104381 AAATATTAAAAAAAT
1 AAATATTAAAAAAAT
104396 AAATATTAAAAAAA
1 AAATATTAAAAAAA
104410 AAACACATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATATTAAAAAAAT
Found at i:107561 original size:17 final size:17
Alignment explanation
Indices: 107539--107594 Score: 87
Period size: 17 Copynumber: 3.3 Consensus size: 17
107529 TATTTCAAAT
107539 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
107556 TTTAAATTTAAAAT-AA
1 TTTAAATTTAAAATAAA
*
107572 TTCTAAACTTAAAATAAA
1 TT-TAAATTTAAAATAAA
107590 TTTAA
1 TTTAA
107595 TACAAAGTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
16 4 0.11
17 28 0.78
18 4 0.11
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:113030 original size:29 final size:29
Alignment explanation
Indices: 112997--113084 Score: 79
Period size: 31 Copynumber: 3.0 Consensus size: 29
112987 AATTTACAAT
* * *
112997 AATTGGATCAAATCAAAATTTCATGTATA-
1 AATTGCATAAAATC-AAAGTTCATGTATAC
*
113026 AATTGCATAAAATCAAAGTTCATGTGTAC
1 AATTGCATAAAATCAAAGTTCATGTATAC
* * *
113055 AATTGCACATTAAACCATAGTTCATGTATA
1 AATTG--CATAAAATCAAAGTTCATGTATA
113085 GTTTTGCTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 12 0.25
29 17 0.35
31 19 0.40
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (29 bp):
AATTGCATAAAATCAAAGTTCATGTATAC
Found at i:114380 original size:31 final size:30
Alignment explanation
Indices: 114321--114388 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
114311 ATTTTAAATA
*
114321 AACAAATATGAACGAAAACTTTAAAATTTTT
1 AACAAATATGAACGAAAACTATAAAA-TTTT
* *
114352 AACAAATATGAATGAAATA-TATATAATTTT
1 AACAAATATGAACGAAA-ACTATAAAATTTT
114382 AA-AAATA
1 AACAAATA
114389 AACAAACAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 5 0.15
30 6 0.18
31 21 0.64
32 1 0.03
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (30 bp):
AACAAATATGAACGAAAACTATAAAATTTT
Found at i:128891 original size:2 final size:2
Alignment explanation
Indices: 128874--128907 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
128864 CAAACAGAAA
* *
128874 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
128908 CCTGCTTGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:130812 original size:26 final size:26
Alignment explanation
Indices: 130783--130840 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
130773 AAAAAATTTT
*
130783 AATTATAT-ATAATTTA-AAAATATAAA
1 AATTATATAAAAATTTATAAAA-A-AAA
130809 AATTAT-TAAAAATTTATAAAAAAAA
1 AATTATATAAAAATTTATAAAAAAAA
130834 AATTATA
1 AATTATA
130841 ATTAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
25 10 0.36
26 14 0.50
27 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
AATTATATAAAAATTTATAAAAAAAA
Found at i:140406 original size:28 final size:28
Alignment explanation
Indices: 140374--140430 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
140364 AAAACATAGA
140374 GGTAGAAAGGAATAGTTTCAATTGATAT
1 GGTAGAAAGGAATAGTTTCAATTGATAT
*
140402 GGTAGTAAGGAATAGTTTCAATTGATAT
1 GGTAGAAAGGAATAGTTTCAATTGATAT
140430 G
1 G
140431 AAAATTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (28 bp):
GGTAGAAAGGAATAGTTTCAATTGATAT
Found at i:144852 original size:52 final size:52
Alignment explanation
Indices: 144785--145041 Score: 320
Period size: 52 Copynumber: 4.9 Consensus size: 52
144775 TAAATGAAGA
* * * *
144785 GGTCTGCTGATTAAGTATCATCGTGAGTATATGAATCCTTTACGAATTAAAC
1 GGTCTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAAC
* *
144837 GGTCTGATGACTAAGTGTCATCATGAGTATACGAATCCTTTACGGATTAAAC
1 GGTCTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAAC
* * * * *
144889 GATCCGATGACTAAGTGTCATCGTGAGTATACGAATCATTTACGGATTAAAT
1 GGTCTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAAC
* * * *
144941 AGTCTGATGACTAAGTGTCATCGTGAGTATATGGATCATTTACGAATTAAGA-
1 GGTCTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAA-AC
* * *
144993 GGTCCGATGACTCTA-TGTCATCGTGAGTATATGAATCCCTTACGGATTA
1 GGTCTGATGACT-AAGTGTCATCGTGAGTATATGAATCCTTTACGGATTA
145042 TAAGGTCCGG
Statistics
Matches: 179, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
52 177 0.99
53 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (52 bp):
GGTCTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAAC
Found at i:145070 original size:156 final size:156
Alignment explanation
Indices: 144786--145080 Score: 373
Period size: 156 Copynumber: 1.9 Consensus size: 156
144776 AAATGAAGAG
* * * *
144786 GTCTGCTGATTAAGTATCATCGTGAGTATATGAATCCTTTACGAATTAAACGGTCTGATGACTAA
1 GTCTGATGACTAAGTATCATCGTGAGTATATGAATCATTTACGAATTAAACGGTCCGATGACTAA
* * *
144851 GTGTCATCATGAGTATACGAATCCTTTACGGATTAAACGATCCGATGACTAAGTGTCATCGTGAG
66 GTGTCATCATGAGTATACGAATCCCTTACGGATTAAACGATCCGATGACTAAGGGTCACCGTGAG
144916 TATACGAATCATTTACGGATTAAATA
131 TATACGAATCATTTACGGATTAAATA
* *
144942 GTCTGATGACTAAGTGTCATCGTGAGTATATGGATCATTTACGAATTAAGA-GGTCCGATGACTC
1 GTCTGATGACTAAGTATCATCGTGAGTATATGAATCATTTACGAATTAA-ACGGTCCGATGACT-
* * * * * **
145006 TA-TGTCATCGTGAGTATATGAATCCCTTACGGATTATAA-GGTCCGGT-AGCTGTGGGTCACCG
64 AAGTGTCATCATGAGTATACGAATCCCTTACGGATTA-AACGATCCGATGA-CTAAGGGTCACCG
*
145068 TGAGTATATGAAT
127 TGAGTATACGAAT
145081 GAAGTGAAAT
Statistics
Matches: 118, Mismatches: 17, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
155 1 0.01
156 113 0.96
157 4 0.03
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (156 bp):
GTCTGATGACTAAGTATCATCGTGAGTATATGAATCATTTACGAATTAAACGGTCCGATGACTAA
GTGTCATCATGAGTATACGAATCCCTTACGGATTAAACGATCCGATGACTAAGGGTCACCGTGAG
TATACGAATCATTTACGGATTAAATA
Found at i:146577 original size:41 final size:41
Alignment explanation
Indices: 146520--146633 Score: 210
Period size: 41 Copynumber: 2.8 Consensus size: 41
146510 GAACACTGAC
146520 TGTTAGAATTGGGTGACTAGAATTCTTGTTAAGGTGGAGAT
1 TGTTAGAATTGGGTGACTAGAATTCTTGTTAAGGTGGAGAT
*
146561 TGTTAGAATTGAGTGACTAGAATTCTTGTTAAGGTGGAGAT
1 TGTTAGAATTGGGTGACTAGAATTCTTGTTAAGGTGGAGAT
*
146602 TGTTAAAATTGGGTGACTAGAATTCTTGTTAA
1 TGTTAGAATTGGGTGACTAGAATTCTTGTTAA
146634 AATAAAATTT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.29, C:0.05, G:0.28, T:0.38
Consensus pattern (41 bp):
TGTTAGAATTGGGTGACTAGAATTCTTGTTAAGGTGGAGAT
Found at i:149773 original size:41 final size:41
Alignment explanation
Indices: 149716--149811 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
149706 CTGTTCGTAG
* * *
149716 AGAATTCTTGTCAAGGTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGAGTGACT
149757 AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGAGTGACT
1 AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGAGTGACT
149798 AGAATTCTTGTTAA
1 AGAATTCTTGTTAA
149812 AATAAAATTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.36
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGAGTGACT
Found at i:150459 original size:27 final size:26
Alignment explanation
Indices: 150424--150474 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
150414 AAGAAAATGG
150424 AGTGAACAAAATCAAAACCACGAAAAA
1 AGTGAACAAAAT-AAAACCACGAAAAA
* * *
150451 AGTGGACAAAGTAAAACCATGAAA
1 AGTGAACAAAATAAAACCACGAAA
150475 CTGTGGACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.59, C:0.16, G:0.16, T:0.10
Consensus pattern (26 bp):
AGTGAACAAAATAAAACCACGAAAAA
Found at i:151308 original size:48 final size:48
Alignment explanation
Indices: 151256--151350 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
151246 GAAATAAAAC
* * *
151256 AGTTTTGGATTTTTTATTATTATTTAATTTTAAGC-CAAAAGAGTTGTA
1 AGTTTTGGATTTATCATTATTATTTAATTTCAA-CTCAAAAGAGTTGTA
*
151304 AGTTTTGGGTTTATCATTATTATTTAATTTCAACTCAAAAGAGTTGT
1 AGTTTTGGATTTATCATTATTATTTAATTTCAACTCAAAAGAGTTGT
151351 GTTTTAGTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 1 0.02
48 41 0.98
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (48 bp):
AGTTTTGGATTTATCATTATTATTTAATTTCAACTCAAAAGAGTTGTA
Found at i:152081 original size:27 final size:27
Alignment explanation
Indices: 152050--152101 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
152040 ACAGATATAA
152050 AAATTAATT-TTTATAATGATACATTAG
1 AAATTAATTATTTAT-ATGATACATTAG
*
152077 AAATTAATTATTTATATGATTCATT
1 AAATTAATTATTTATATGATACATT
152102 TGTTAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (27 bp):
AAATTAATTATTTATATGATACATTAG
Found at i:152793 original size:32 final size:32
Alignment explanation
Indices: 152740--152809 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
152730 AATAGTAAAT
152740 TTATAA-AAGAAAAAAAAAAGTCCAAATCCTC
1 TTATAATAAGAAAAAAAAAAGTCCAAATCCTC
* *
152771 TTATAATAATAAAAAAAGAAGTCCAAATCCTC
1 TTATAATAAGAAAAAAAAAAGTCCAAATCCTC
152803 TTATAAT
1 TTATAAT
152810 TTTGTTTGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 6 0.17
32 30 0.83
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (32 bp):
TTATAATAAGAAAAAAAAAAGTCCAAATCCTC
Found at i:155880 original size:27 final size:27
Alignment explanation
Indices: 155845--155906 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
155835 CAGAAAAGAT
155845 AACTATAACTACTTTGGCAACTACAAG
1 AACTATAACTACTTTGGCAACTACAAG
155872 AACTATAACTACTTTGGCAACTACAAG
1 AACTATAACTACTTTGGCAACTACAAG
*
155899 -GCTATAAC
1 AACTATAAC
155907 AATCTGTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 7 0.21
27 27 0.79
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (27 bp):
AACTATAACTACTTTGGCAACTACAAG
Found at i:158513 original size:28 final size:28
Alignment explanation
Indices: 158464--158521 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
158454 GTAATTTCAA
*
158464 ATTAAGTATTAATTAGAAATTAATTATT
1 ATTAAGTATTAATAAGAAATTAATTATT
*
158492 ATTAAGT-TTATATAAGATATTAATTATT
1 ATTAAGTATTA-ATAAGAAATTAATTATT
158520 AT
1 AT
158522 AACATATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 3 0.11
28 24 0.89
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (28 bp):
ATTAAGTATTAATAAGAAATTAATTATT
Found at i:158838 original size:27 final size:26
Alignment explanation
Indices: 158800--158853 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
158790 GAAAGAAAAG
*
158800 GAAAAAGAGAAGAAACAAGATTTTAA
1 GAAAAAGAGAAGAAACAAGATTATAA
*
158826 GAAAAATGAGAAGAGACAAGATTATAA
1 GAAAAA-GAGAAGAAACAAGATTATAA
158853 G
1 G
158854 TGCATAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.59, C:0.04, G:0.22, T:0.15
Consensus pattern (26 bp):
GAAAAAGAGAAGAAACAAGATTATAA
Found at i:171051 original size:23 final size:24
Alignment explanation
Indices: 171004--171056 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
170994 TAAAAGTGTT
* *
171004 AATAACTAGAATTGAATTTTAAAA
1 AATAAATAGAATTAAATTTTAAAA
*
171028 AATAAATAG-ATTAAATTTTTAAA
1 AATAAATAGAATTAAATTTTAAAA
*
171051 ATTAAA
1 AATAAA
171057 AGTACAATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.36
Consensus pattern (24 bp):
AATAAATAGAATTAAATTTTAAAA
Found at i:175554 original size:29 final size:28
Alignment explanation
Indices: 175511--175586 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
175501 TAATTGGACT
* *
175511 TAAATTTT-GAATTAAAAGTA-AAGAAAC
1 TAAATTTTAAAATTAAAAATACAA-AAAC
*
175538 TAAATTATTAAAATTAAAAATACAAATAC
1 TAAATT-TTAAAATTAAAAATACAAAAAC
*
175567 TAAATTTTAAATTTACAAAA
1 TAAATTTTAAAATTA-AAAA
175587 AATACAAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 6 0.15
28 10 0.24
29 23 0.56
30 2 0.05
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (28 bp):
TAAATTTTAAAATTAAAAATACAAAAAC
Found at i:175802 original size:13 final size:15
Alignment explanation
Indices: 175773--175816 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
175763 TTCGACTTAA
175773 TTTAGTTATTG-ATTT
1 TTTAGTT-TTGAATTT
175788 TTTA-TTTT-AA-TT
1 TTTAGTTTTGAATTT
175800 TTTAGTTTTGAATTT
1 TTTAGTTTTGAATTT
175815 TT
1 TT
175817 AAATTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 6 0.24
13 7 0.28
14 4 0.16
15 8 0.32
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.70
Consensus pattern (15 bp):
TTTAGTTTTGAATTT
Found at i:175813 original size:14 final size:14
Alignment explanation
Indices: 175773--175817 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
175763 TTCGACTTAA
*
175773 TTTAGTTATTGATTT
1 TTTAGTT-TTGAATT
175788 TTTA-TTTT-AATT
1 TTTAGTTTTGAATT
175800 TTTAGTTTTGAATT
1 TTTAGTTTTGAATT
175814 TTTA
1 TTTA
175818 AATTTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 7 0.26
13 6 0.22
14 10 0.37
15 4 0.15
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (14 bp):
TTTAGTTTTGAATT
Found at i:175826 original size:26 final size:27
Alignment explanation
Indices: 175773--175827 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
175763 TTCGACTTAA
* *
175773 TTTAGTTATTGATTTTTTATTTTAATT
1 TTTAGTTATTGATTTTTAAATTTAATT
175800 TTTAGTT-TTGAATTTTTAAATTT-ATT
1 TTTAGTTATTG-ATTTTTAAATTTAATT
175826 TT
1 TT
175828 AACAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (27 bp):
TTTAGTTATTGATTTTTAAATTTAATT
Found at i:178950 original size:19 final size:19
Alignment explanation
Indices: 178926--178989 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
178916 ATTTTATACT
178926 TTTTTAATTTTGGACATAA
1 TTTTTAATTTTGGACATAA
178945 TTTTTAACAATTTT----ATACA
1 TTTTT---AATTTTGGACATA-A
*
178964 TTTTTAAATTTGGACATAA
1 TTTTTAATTTTGGACATAA
178983 TTTTTAA
1 TTTTTAA
178990 CAATTTTGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 16
0.68 0.02 0.30
Matches are distributed among these distances:
16 5 0.14
18 3 0.08
19 19 0.53
20 3 0.08
22 6 0.17
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (19 bp):
TTTTTAATTTTGGACATAA
Found at i:178962 original size:38 final size:38
Alignment explanation
Indices: 178911--178996 Score: 154
Period size: 38 Copynumber: 2.3 Consensus size: 38
178901 CCGATCCTAA
* *
178911 TAACAATTTTATACTTTTTTAATTTTGGACATAATTTT
1 TAACAATTTTATACATTTTTAAATTTGGACATAATTTT
178949 TAACAATTTTATACATTTTTAAATTTGGACATAATTTT
1 TAACAATTTTATACATTTTTAAATTTGGACATAATTTT
178987 TAACAATTTT
1 TAACAATTTT
178997 GTCGATATGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (38 bp):
TAACAATTTTATACATTTTTAAATTTGGACATAATTTT
Found at i:179916 original size:29 final size:30
Alignment explanation
Indices: 179892--180065 Score: 153
Period size: 30 Copynumber: 5.9 Consensus size: 30
179882 TTTTAGGTTT
179892 AAAATGTGATTTTAGAGAAGTTTAGGGGTC
1 AAAATGTGATTTTAGAGAAGTTTAGGGGTC
* *
179922 AAAATGTGATTTTTGAGAAGTTT-GGAAGTC
1 AAAATGTGATTTTAGAGAAGTTTAGG-GGTC
* *
179952 AAAATGTAATTTT-GGGAAGTTTAGGGGTC
1 AAAATGTGATTTTAGAGAAGTTTAGGGGTC
* * * * *
179981 AAAATATAATTGT-GAAAAGTTTAGTGGTC
1 AAAATGTGATTTTAGAGAAGTTTAGGGGTC
* * * *
180010 AAAATATAATTTT-GAAAAAGTTTAGGGGTT
1 AAAATGTGATTTTAG-AGAAGTTTAGGGGTC
* *
180040 AAAATATGATTTTGGA-AAGTTT-GGGG
1 AAAATGTGATTTTAGAGAAGTTTAGGGG
180066 ACTGCTTGGG
Statistics
Matches: 126, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
28 4 0.03
29 56 0.44
30 65 0.52
31 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.35
Consensus pattern (30 bp):
AAAATGTGATTTTAGAGAAGTTTAGGGGTC
Found at i:179927 original size:30 final size:29
Alignment explanation
Indices: 179900--180065 Score: 167
Period size: 29 Copynumber: 5.7 Consensus size: 29
179890 TTAAAATGTG
*
179900 ATTTTAGAGAAGTTTAGGGGTCAAAATGTGA
1 ATTTT-GAGAAGTTTAGGGGTCAAAATAT-A
* * *
179931 TTTTTGAGAAGTTT-GGAAGTCAAAATGTA
1 ATTTTGAGAAGTTTAGG-GGTCAAAATATA
*
179960 ATTTTGGGAAGTTTAGGGGTCAAAATATA
1 ATTTTGAGAAGTTTAGGGGTCAAAATATA
* * *
179989 ATTGTGAAAAGTTTAGTGGTCAAAATATA
1 ATTTTGAGAAGTTTAGGGGTCAAAATATA
* * *
180018 ATTTTGAAAAAGTTTAGGGGTTAAAATATG
1 ATTTTG-AGAAGTTTAGGGGTCAAAATATA
180048 ATTTTG-GAAAGTTT-GGGG
1 ATTTTGAG-AAGTTTAGGGG
180066 ACTGCTTGGG
Statistics
Matches: 116, Mismatches: 15, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
28 4 0.03
29 61 0.53
30 47 0.41
31 4 0.03
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.36
Consensus pattern (29 bp):
ATTTTGAGAAGTTTAGGGGTCAAAATATA
Found at i:179985 original size:59 final size:58
Alignment explanation
Indices: 179892--180063 Score: 193
Period size: 59 Copynumber: 2.9 Consensus size: 58
179882 TTTTAGGTTT
* *
179892 AAAATGTGATTTTAGAGAAGTTTAGGGGTCAAAATGTGATTTTTGAGAAGTTTGGAAGTC
1 AAAATGTAATTTT-GAGAAGTTTAGGGGTCAAAATATGATTTTTGA-AAGTTTGGAAGTC
* * * * **
179952 AAAATGTAATTTTGGGAAGTTTAGGGGTCAAAATAT-AATTGTGAAAAGTTTAGTGGTC
1 AAAATGTAATTTTGAGAAGTTTAGGGGTCAAAATATGATTTTTG-AAAGTTTGGAAGTC
* * * *
180010 AAAATATAATTTTGAAAAAGTTTAGGGGTTAAAATATGATTTTGGAAAGTTTGG
1 AAAATGTAATTTTG-AGAAGTTTAGGGGTCAAAATATGATTTTTGAAAGTTTGG
180064 GGACTGCTTG
Statistics
Matches: 93, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
58 28 0.30
59 49 0.53
60 16 0.17
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (58 bp):
AAAATGTAATTTTGAGAAGTTTAGGGGTCAAAATATGATTTTTGAAAGTTTGGAAGTC
Found at i:182458 original size:31 final size:31
Alignment explanation
Indices: 182420--182481 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
182410 ATCCAAGGCA
182420 AATTTTTGCGTTATTCAAAG-AAGTAAACTTG
1 AATTTTTGCGTTA-TCAAAGAAAGTAAACTTG
* *
182451 AATTTTTGCTTTATCCAAGAAAGTAAACTTG
1 AATTTTTGCGTTATCAAAGAAAGTAAACTTG
182482 GAAGGTTGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (31 bp):
AATTTTTGCGTTATCAAAGAAAGTAAACTTG
Found at i:184958 original size:22 final size:22
Alignment explanation
Indices: 184933--184975 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
184923 CCACGATCCT
*
184933 AAACCCTAAACCTTAAACTTTA
1 AAACCCTAAACATTAAACTTTA
*
184955 AAACCTTAAACATTAAACTTT
1 AAACCCTAAACATTAAACTTT
184976 GAACCCTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (22 bp):
AAACCCTAAACATTAAACTTTA
Found at i:184960 original size:15 final size:15
Alignment explanation
Indices: 184940--184971 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
184930 CCTAAACCCT
*
184940 AAACCTTAAACTTTA
1 AAACCTTAAACATTA
184955 AAACCTTAAACATTA
1 AAACCTTAAACATTA
184970 AA
1 AA
184972 CTTTGAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (15 bp):
AAACCTTAAACATTA
Found at i:185463 original size:5 final size:5
Alignment explanation
Indices: 185453--185479 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
185443 CATCTTCCCC
185453 ACCCA ACCCA ACCCA ACCCA ACCCA AC
1 ACCCA ACCCA ACCCA ACCCA ACCCA AC
185480 AACTGCTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.59, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCCA
Found at i:194650 original size:22 final size:21
Alignment explanation
Indices: 194607--194650 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
194597 AATTGAGATT
*
194607 AATTTATGATTTTGAAATAAA
1 AATTTATGATTTTGAAAAAAA
194628 AATTTATG-TTTCGTGAAAAAAA
1 AATTTATGATTT--TGAAAAAAA
194650 A
1 A
194651 CAATAACTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 3 0.15
21 8 0.40
22 9 0.45
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (21 bp):
AATTTATGATTTTGAAAAAAA
Found at i:195009 original size:17 final size:18
Alignment explanation
Indices: 194977--195010 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
194967 GAAAATAGTA
194977 TTAAAAAAAAACATCATT
1 TTAAAAAAAAACATCATT
*
194995 TTAAAAAGAAA-ATCAT
1 TTAAAAAAAAACATCAT
195011 AAAGTTGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.62, C:0.09, G:0.03, T:0.26
Consensus pattern (18 bp):
TTAAAAAAAAACATCATT
Found at i:200870 original size:14 final size:14
Alignment explanation
Indices: 200851--200879 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
200841 TGCTTTTTTA
200851 TTTTTTTTT-TATT
1 TTTTTTTTTGTATT
200864 TTTTTTTTTGTATT
1 TTTTTTTTTGTATT
200878 TT
1 TT
200880 CAAAGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.07, C:0.00, G:0.03, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTGTATT
Found at i:200872 original size:12 final size:11
Alignment explanation
Indices: 200844--200871 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
200834 ATCATTGTGC
200844 TTTTTTATTTT
1 TTTTTTATTTT
200855 TTTTTTATTTT
1 TTTTTTATTTT
200866 TTTTTT
1 TTTTTT
200872 TGTATTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:205077 original size:36 final size:35
Alignment explanation
Indices: 205036--205116 Score: 126
Period size: 36 Copynumber: 2.3 Consensus size: 35
205026 TTGGCATGTT
*
205036 GTTGCAGGTACTAATGAATTCGTATTTGTTTTATGA
1 GTTGCAGGTACTAATGAATTCATATTTG-TTTATGA
* *
205072 GTTGCAAGTACTAATGGATTCATATTTGTTTATGA
1 GTTGCAGGTACTAATGAATTCATATTTGTTTATGA
205107 GTTGCAGGTA
1 GTTGCAGGTA
205117 TTAGTGGCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 16 0.39
36 25 0.61
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.42
Consensus pattern (35 bp):
GTTGCAGGTACTAATGAATTCATATTTGTTTATGA
Found at i:205334 original size:3 final size:3
Alignment explanation
Indices: 205328--205358 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
205318 TTCTTTATTA
*
205328 TGT TGT TGA TGT TGT TGT TGT TGT TGT TGT T
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT T
205359 TAATAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.32, T:0.65
Consensus pattern (3 bp):
TGT
Found at i:213562 original size:30 final size:31
Alignment explanation
Indices: 213520--213586 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
213510 GTTTACATTT
*
213520 CAGTCCCTCAAC-TTTGAAAATGTGACAAAA
1 CAGTCCCTCAACTTTTGAAAATATGACAAAA
* *
213550 TAGTCTCTCAACTTTTGAAAATATGACAAAA
1 CAGTCCCTCAACTTTTGAAAATATGACAAAA
213581 CAGTCC
1 CAGTCC
213587 TTTTCTGTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 10 0.32
31 21 0.68
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (31 bp):
CAGTCCCTCAACTTTTGAAAATATGACAAAA
Found at i:228591 original size:27 final size:27
Alignment explanation
Indices: 228561--228617 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
228551 AGCTAAGACA
228561 TAATCATCAAAAAAAAATTCGGCCATT
1 TAATCATCAAAAAAAAATTCGGCCATT
228588 TAATCATCAAAAAAAAATTCGGCCATT
1 TAATCATCAAAAAAAAATTCGGCCATT
228615 TAA
1 TAA
228618 AAGAAACAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.49, C:0.18, G:0.07, T:0.26
Consensus pattern (27 bp):
TAATCATCAAAAAAAAATTCGGCCATT
Found at i:230911 original size:24 final size:24
Alignment explanation
Indices: 230868--230913 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
230858 TAAAGTGATT
*
230868 ATTTCGTAACAAAATATTAACATC
1 ATTTCGTAACAAAACATTAACATC
*
230892 ATTTCGTAACAAAACGTTAACA
1 ATTTCGTAACAAAACATTAACA
230914 CAAGTGATTA
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:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (24 bp):
ATTTCGTAACAAAACATTAACATC
Found at i:232610 original size:59 final size:59
Alignment explanation
Indices: 232534--232657 Score: 151
Period size: 59 Copynumber: 2.1 Consensus size: 59
232524 CCTTGGGATG
* * **
232534 AGTGCTAGAAAAGAATGAGTGAAAAGAGTTTGAG-CCTGTGTTGCTTGGACTTGGGAACA
1 AGTGCTAGAAAAGAATGAATGAAAAGAGTTTGAGTAC-AAGTTGCTTGGACTTGGGAACA
* * * * *
232593 AGTGTTAGAATAGAATGAATGCATAGGGTTTGAGTACAAGTTGCTTGGACTTGGGAACA
1 AGTGCTAGAAAAGAATGAATGAAAAGAGTTTGAGTACAAGTTGCTTGGACTTGGGAACA
232652 AGTGCT
1 AGTGCT
232658 CTATAGGGGT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 53 0.98
60 1 0.02
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.27
Consensus pattern (59 bp):
AGTGCTAGAAAAGAATGAATGAAAAGAGTTTGAGTACAAGTTGCTTGGACTTGGGAACA
Found at i:236812 original size:7 final size:7
Alignment explanation
Indices: 236802--236871 Score: 86
Period size: 7 Copynumber: 10.0 Consensus size: 7
236792 TTTCAACTAA
*
236802 GGTTTAC
1 GGTTTAG
236809 GGTTTAG
1 GGTTTAG
*
236816 GGTTTAA
1 GGTTTAG
**
236823 GACTTAG
1 GGTTTAG
236830 GGTTTAG
1 GGTTTAG
236837 GGTTTAG
1 GGTTTAG
236844 GGTTTAG
1 GGTTTAG
236851 GGTTTAG
1 GGTTTAG
* *
236858 GGCTTAA
1 GGTTTAG
236865 GGTTTAG
1 GGTTTAG
236872 AATATCAAAG
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.19, C:0.04, G:0.37, T:0.40
Consensus pattern (7 bp):
GGTTTAG
Found at i:236823 original size:21 final size:21
Alignment explanation
Indices: 236799--236871 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
236789 AAGTTTCAAC
*
236799 TAAGGTTTACGGTTTAGGGTT
1 TAAGGTTTAGGGTTTAGGGTT
**
236820 TAAGACTTAGGGTTTAGGGTT
1 TAAGGTTTAGGGTTTAGGGTT
* *
236841 TAGGGTTTAGGGTTTAGGGCT
1 TAAGGTTTAGGGTTTAGGGTT
236862 TAAGGTTTAG
1 TAAGGTTTAG
236872 AATATCAAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.21, C:0.04, G:0.36, T:0.40
Consensus pattern (21 bp):
TAAGGTTTAGGGTTTAGGGTT
Found at i:240403 original size:105 final size:107
Alignment explanation
Indices: 240212--240415 Score: 331
Period size: 105 Copynumber: 1.9 Consensus size: 107
240202 GCATATAACA
* * * *
240212 CATCTAAGGTTTACTAAGCGGAAAAAATATTAGCAATTTCATATTTCCATTGCATGGGGCCTCAT
1 CATCTAAGGTTTACTAAGAGGAAAAAATATGAGCAATTTCATATTTCCATTACATGAGGCCTCAT
240277 AACATATGAATCCACAATTCAGAGCAAACTTTTATGCTCAAT
66 AACATATGAATCCACAATTCAGAGCAAACTTTTATGCTCAAT
*
240319 CATCTAAGGTTTACTAAGAGG-AAAAA-ATGAGCAATTTCGTATTTCCATTACATGAGGCCTCAT
1 CATCTAAGGTTTACTAAGAGGAAAAAATATGAGCAATTTCATATTTCCATTACATGAGGCCTCAT
* *
240382 AACATATGAATCCATAGTTCAGAGCAAACTTTTA
66 AACATATGAATCCACAATTCAGAGCAAACTTTTA
240416 AGTTCAATAA
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
105 65 0.72
106 5 0.06
107 20 0.22
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (107 bp):
CATCTAAGGTTTACTAAGAGGAAAAAATATGAGCAATTTCATATTTCCATTACATGAGGCCTCAT
AACATATGAATCCACAATTCAGAGCAAACTTTTATGCTCAAT
Found at i:258470 original size:49 final size:49
Alignment explanation
Indices: 258415--258512 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
258405 ACATCATAAC
258415 TTTATTTTTAGGTTGAATTGAACAAAATA-TATTTTAAAAGAAGTTTTAG
1 TTTATTTTTAGGTTGAATTGAACAAAATATTATTTTAAAA-AAGTTTTAG
* * * *
258464 TTTATTTTTAGGTTTAATTGAACACAATATTTTTTTTAAAAAGTTTTAG
1 TTTATTTTTAGGTTGAATTGAACAAAATATTATTTTAAAAAAGTTTTAG
258513 GTGATGTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 36 0.82
50 8 0.18
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.49
Consensus pattern (49 bp):
TTTATTTTTAGGTTGAATTGAACAAAATATTATTTTAAAAAAGTTTTAG
Found at i:264036 original size:228 final size:230
Alignment explanation
Indices: 263631--264096 Score: 677
Period size: 228 Copynumber: 2.0 Consensus size: 230
263621 GTACTACTTT
* *
263631 AGTGTATTAATTTTCCTCAACTGGTCGTTTTCTGCTTCTAGTTGAGGGAACCCTAGTTGTACCAT
1 AGTGTGTTAATTTTCCTCAACTGGTCGTTTTCTGCTTCTAGTTGAGGGAACCCTAGTTGCACCAT
* *
263696 CTTTTTTGTAAAATGCATTGCATTCATGCTAATTACGTATTCGATTGTCTTTTTGTTGCATGGTA
66 CTTTTTTGTAAAATGCATTGCACTCATGCTAATTACGTATTAGATTGTCTTTTTGTTGCATGGTA
* * *
263761 AAATGGCCCATCAAAATTATAACCACTGTTTTTCTATTTAGGTTGACGTGATGTCACACTTGCAT
131 AAATGGCCCATCAAAATTATAACCACTGTTTTTCTATTTAAGTTGACGTGATGTCACACTTACAG
* * * *
263826 GGCAGCCTAAATGAAACCATCTTAGTTCGTGCTGG
196 GGCAGCCTAAAAGAAACCATCTTACTACGGGCTGG
* * * * *
263861 AGTGTGTTAATTTTCCTCAACTGGTTGTTTTGTGTTTTTAGTTGAGGGAACCCTAGTTGCACCGT
1 AGTGTGTTAATTTTCCTCAACTGGTCGTTTTCTGCTTCTAGTTGAGGGAACCCTAGTTGCACCAT
* * * *
263926 C-TTTTTGTGAACTGCATTGCACTCATGTTAATTACTGT-TTAGATTGTC-TTTTGTTGCATTGT
66 CTTTTTTGTAAAATGCATTGCACTCATGCTAATTAC-GTATTAGATTGTCTTTTTGTTGCATGGT
* **
263988 AATATGGCCCATCAAAATTATAACCGTTGTTTTTCTATTTAAGTTGACGTGATGTCACACTTACA
130 AAAATGGCCCATCAAAATTATAACCACTGTTTTTCTATTTAAGTTGACGTGATGTCACACTTACA
* *
264053 GGGCAGCCTAAAAGACACCTTCTTACTACGGGCTGG
195 GGGCAGCCTAAAAGAAACCATCTTACTACGGGCTGG
264089 AGTGTGTT
1 AGTGTGTT
264097 TGTTAGTGCC
Statistics
Matches: 210, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
228 110 0.52
229 39 0.19
230 61 0.29
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (230 bp):
AGTGTGTTAATTTTCCTCAACTGGTCGTTTTCTGCTTCTAGTTGAGGGAACCCTAGTTGCACCAT
CTTTTTTGTAAAATGCATTGCACTCATGCTAATTACGTATTAGATTGTCTTTTTGTTGCATGGTA
AAATGGCCCATCAAAATTATAACCACTGTTTTTCTATTTAAGTTGACGTGATGTCACACTTACAG
GGCAGCCTAAAAGAAACCATCTTACTACGGGCTGG
Found at i:269726 original size:18 final size:18
Alignment explanation
Indices: 269700--269757 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 18
269690 TACCTTTGAG
*
269700 TATTTATCTCTAATTTCA
1 TATTCATCTCTAATTTCA
269718 TATTCATCTCTAATTTTGTCA
1 TATTCATCTCTAA--TT-TCA
269739 TGATTCATCTCTAATTTCA
1 T-ATTCATCTCTAATTTCA
269758 ACATGGCAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
18 12 0.34
19 3 0.09
20 4 0.11
21 4 0.11
22 12 0.34
ACGTcount: A:0.26, C:0.19, G:0.03, T:0.52
Consensus pattern (18 bp):
TATTCATCTCTAATTTCA
Found at i:269744 original size:22 final size:21
Alignment explanation
Indices: 269700--269755 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 21
269690 TACCTTTGAG
*
269700 TATTTATCTCTAA--TT-TCA
1 TATTCATCTCTAATTTTGTCA
269718 TATTCATCTCTAATTTTGTCA
1 TATTCATCTCTAATTTTGTCA
269739 TGATTCATCTCTAATTT
1 T-ATTCATCTCTAATTT
269756 CAACATGGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 12 0.36
20 2 0.06
21 4 0.12
22 15 0.45
ACGTcount: A:0.25, C:0.18, G:0.04, T:0.54
Consensus pattern (21 bp):
TATTCATCTCTAATTTTGTCA
Found at i:270964 original size:19 final size:19
Alignment explanation
Indices: 270940--270980 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
270930 ATTTTTAGAG
*
270940 ATTCTAAGTAAGAGATATT
1 ATTCTAAGTAAGAAATATT
*
270959 ATTCTAATTAAGAAATATT
1 ATTCTAAGTAAGAAATATT
270978 ATT
1 ATT
270981 TCCGTAGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (19 bp):
ATTCTAAGTAAGAAATATT
Found at i:275837 original size:4 final size:4
Alignment explanation
Indices: 275828--275878 Score: 84
Period size: 4 Copynumber: 12.8 Consensus size: 4
275818 CTGCTCTCTT
* *
275828 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATAC ATGC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
275876 ATA
1 ATA
275879 TATATGTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:281120 original size:12 final size:12
Alignment explanation
Indices: 281103--281137 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
281093 GGATGAATAG
281103 CACCGGCACTGA
1 CACCGGCACTGA
281115 CACCGGCACTGA
1 CACCGGCACTGA
281127 CACCGGCACTG
1 CACCGGCACTG
281138 GTAGACTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.23, C:0.43, G:0.26, T:0.09
Consensus pattern (12 bp):
CACCGGCACTGA
Found at i:281935 original size:21 final size:22
Alignment explanation
Indices: 281906--281947 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
281896 TTGATAACAT
* *
281906 GAATTTTATTT-TATAGTTTTC
1 GAATATTATTTGTAAAGTTTTC
281927 GAATATTATTTGTAAAGTTTT
1 GAATATTATTTGTAAAGTTTT
281948 AAAGTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (22 bp):
GAATATTATTTGTAAAGTTTTC
Found at i:282003 original size:18 final size:17
Alignment explanation
Indices: 281970--282004 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
281960 TAAATATTTA
*
281970 AAAAATAATTTTTAAAT
1 AAAAATAATTTATAAAT
281987 AAAAATAATTTAATAAAT
1 AAAAATAATTT-ATAAAT
282005 TCCATATGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAAATAATTTATAAAT
Found at i:283903 original size:18 final size:20
Alignment explanation
Indices: 283866--283905 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
283856 TAGCTAATTA
283866 AAAATAAGAATAGGTAAAAT
1 AAAATAAGAATAGGTAAAAT
*
283886 AAAATAA-AATA-TTAAAAT
1 AAAATAAGAATAGGTAAAAT
283904 AA
1 AA
283906 TCAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 4 0.21
20 7 0.37
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (20 bp):
AAAATAAGAATAGGTAAAAT
Found at i:284570 original size:34 final size:34
Alignment explanation
Indices: 284532--284607 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
284522 CATAATCTAA
* * *
284532 ACCCAAATATTTTTAATTTTTTATCTTTTATCTT
1 ACCCAAATATTTCTAATATTTTATCTTTTACCTT
284566 ACCCAAATATTTCTAATATTTTATCTTTTACCTT
1 ACCCAAATATTTCTAATATTTTATCTTTTACCTT
284600 ACCCAAAT
1 ACCCAAAT
284608 GTTGTTTAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (34 bp):
ACCCAAATATTTCTAATATTTTATCTTTTACCTT
Found at i:289171 original size:20 final size:20
Alignment explanation
Indices: 289143--289181 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
289133 TTATGACTTT
*
289143 CATTATTAAGTTTAATTAAC
1 CATTATTAACTTTAATTAAC
*
289163 CATTTTTAACTTTAATTAA
1 CATTATTAACTTTAATTAA
289182 ACCTATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (20 bp):
CATTATTAACTTTAATTAAC
Found at i:289190 original size:20 final size:20
Alignment explanation
Indices: 289148--289190 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
289138 ACTTTCATTA
* *
289148 TTAAGTTTAATTAACCATTT
1 TTAACTTTAATTAACCATAT
289168 TTAACTTTAATTAAACC-TAT
1 TTAACTTTAATT-AACCATAT
289188 TTA
1 TTA
289191 TAACCAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (20 bp):
TTAACTTTAATTAACCATAT
Found at i:289194 original size:22 final size:20
Alignment explanation
Indices: 289153--289194 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
289143 CATTATTAAG
*
289153 TTTAATTAACCATTTTTAAC
1 TTTAATTAACCATTTATAAC
289173 TTTAATTAAACCTATTTATAAC
1 TTTAATT-AACC-ATTTATAAC
289195 CAATTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTAATTAACCATTTATAAC
Found at i:298241 original size:206 final size:206
Alignment explanation
Indices: 297887--298297 Score: 786
Period size: 206 Copynumber: 2.0 Consensus size: 206
297877 AAACTCAATT
297887 ATGCAAAATTGTTAGTTTAATAGGAAAAAAATATCATTATAAATTAGATTATTAGCAAATTATCT
1 ATGCAAAATTGTTAGTTTAATAGGAAAAAAATATCATTATAAATTAGATTATTAGCAAATTATCT
297952 TTGTTGAGTGGCTCTGACATTCATTGTCTGTACTTGTTCTTCAAAATGGTCACTTTGTGGAAACA
66 TTGTTGAGTGGCTCTGACATTCATTGTCTGTACTTGTTCTTCAAAATGGTCACTTTGTGGAAACA
298017 GAAATGTAGGGCTAAAGTACTGAAATGGAAAATAGTAAACAACCTCTGAAATCAAATGGCTTGCT
131 GAAATGTAGGGCTAAAGTACTGAAATGGAAAATAGTAAACAACCTCTGAAATCAAATGGCTTGCT
298082 TTTTTTTTTTA
196 TTTTTTTTTTA
* *
298093 ATGCAAAATTGTTAGTTTAATAGGAAAAAAATATCATTATGAATTAGATTATTAGCATATTATCT
1 ATGCAAAATTGTTAGTTTAATAGGAAAAAAATATCATTATAAATTAGATTATTAGCAAATTATCT
298158 TTGTTGAGTGGCTCTGACATTCATTGTCTGTACTTGTTCTTCAAAATGGTCACTTTGTGGAAACA
66 TTGTTGAGTGGCTCTGACATTCATTGTCTGTACTTGTTCTTCAAAATGGTCACTTTGTGGAAACA
* *
298223 GAAATGTAGGGCTAAAGTACTGAAATGGAAAATAGTAAACGACCTCTGAACTCAAATGGCTTGCT
131 GAAATGTAGGGCTAAAGTACTGAAATGGAAAATAGTAAACAACCTCTGAAATCAAATGGCTTGCT
298288 TTTTTTTTTT
196 TTTTTTTTTT
298298 CCTTTTATTG
Statistics
Matches: 201, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
206 201 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (206 bp):
ATGCAAAATTGTTAGTTTAATAGGAAAAAAATATCATTATAAATTAGATTATTAGCAAATTATCT
TTGTTGAGTGGCTCTGACATTCATTGTCTGTACTTGTTCTTCAAAATGGTCACTTTGTGGAAACA
GAAATGTAGGGCTAAAGTACTGAAATGGAAAATAGTAAACAACCTCTGAAATCAAATGGCTTGCT
TTTTTTTTTTA
Found at i:304797 original size:2 final size:2
Alignment explanation
Indices: 304790--304827 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
304780 CAGCGCTCCT
304790 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
304828 CACTTACTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:305908 original size:57 final size:57
Alignment explanation
Indices: 305815--305937 Score: 228
Period size: 57 Copynumber: 2.2 Consensus size: 57
305805 TATTAGATTG
* *
305815 AAGGATGACCAAGTGGCCTCTAAAGATGATAATTGTTGTTTGACAGCAAGAAGAGAC
1 AAGGCTGACCAAGTGACCTCTAAAGATGATAATTGTTGTTTGACAGCAAGAAGAGAC
305872 AAGGCTGACCAAGTGACCTCTAAAGATGATAATTGTTGTTTGACAGCAAGAAGAGAC
1 AAGGCTGACCAAGTGACCTCTAAAGATGATAATTGTTGTTTGACAGCAAGAAGAGAC
305929 AAGGCTGAC
1 AAGGCTGAC
305938 GAGTCTGAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (57 bp):
AAGGCTGACCAAGTGACCTCTAAAGATGATAATTGTTGTTTGACAGCAAGAAGAGAC
Found at i:307729 original size:20 final size:19
Alignment explanation
Indices: 307704--307744 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
307694 TTTTTAGTTA
* *
307704 TTTTATATATTTGTATATTT
1 TTTTATAAATTTAT-TATTT
307724 TTTTATAAATTTATTATTT
1 TTTTATAAATTTATTATTT
307743 TT
1 TT
307745 AGTTCTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTATAAATTTATTATTT
Found at i:314917 original size:22 final size:22
Alignment explanation
Indices: 314883--314925 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
314873 GAGATTAAAA
*
314883 AAAAAACTTAAGT-CTCAAATTG
1 AAAAAACTCAAGTGCT-AAATTG
*
314905 AAAAAAGTCAAGTGCTAAATT
1 AAAAAACTCAAGTGCTAAATT
314926 AGACATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.26
Consensus pattern (22 bp):
AAAAAACTCAAGTGCTAAATTG
Found at i:321548 original size:22 final size:22
Alignment explanation
Indices: 321520--321563 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
321510 GTGTGAATGG
321520 AATTTTTAGATTTTACAAGCAA
1 AATTTTTAGATTTTACAAGCAA
321542 AATTTTTAGATTTTACAAGCAA
1 AATTTTTAGATTTTACAAGCAA
321564 GATTAGGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (22 bp):
AATTTTTAGATTTTACAAGCAA
Found at i:336330 original size:18 final size:18
Alignment explanation
Indices: 336309--336343 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
336299 TATACTTATT
336309 TTTTTTAAATCAAATATA
1 TTTTTTAAATCAAATATA
336327 TTTTTTAAATCAAATAT
1 TTTTTTAAATCAAATAT
336344 TGGAAGGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTTTAAATCAAATATA
Found at i:340866 original size:11 final size:11
Alignment explanation
Indices: 340850--340878 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
340840 GAGTTACGAC
340850 TCAACTCGATA
1 TCAACTCGATA
340861 TCAACTCGATA
1 TCAACTCGATA
340872 TCAACTC
1 TCAACTC
340879 AATCAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.34, C:0.31, G:0.07, T:0.28
Consensus pattern (11 bp):
TCAACTCGATA
Found at i:343533 original size:29 final size:28
Alignment explanation
Indices: 343474--343537 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
343464 TACACATTTT
**
343474 AAATTTAGTTTATATATTTTTATTTGTAA
1 AAATTTAGTTTATATATTTTTATTT-CCA
343503 AAATTTAGTATTAT-TATTTTT-TATTCCA
1 AAATTTAGT-TTATATATTTTTAT-TTCCA
343531 AAATTTA
1 AAATTTA
343538 AATTAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 9 0.29
29 18 0.58
30 4 0.13
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (28 bp):
AAATTTAGTTTATATATTTTTATTTCCA
Found at i:353102 original size:24 final size:23
Alignment explanation
Indices: 353071--353116 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
353061 TTATGAAAAA
353071 GTTCCATTACTAAAAGTTTCTATC
1 GTTCCATTACTAAAAG-TTCTATC
353095 GTTCCATTACTAAAAGTTCTAT
1 GTTCCATTACTAAAAGTTCTAT
353117 AGTACGTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (23 bp):
GTTCCATTACTAAAAGTTCTATC
Found at i:358322 original size:30 final size:29
Alignment explanation
Indices: 358288--358346 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
358278 GAATTGGATC
*
358288 AAATCAAGATTTAATGTATAAAATTGCACA
1 AAATCAA-AGTTAATGTATAAAATTGCACA
* *
358318 AAATCAAAGTTCATGTATATAATTGCACA
1 AAATCAAAGTTAATGTATAAAATTGCACA
358347 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (29 bp):
AAATCAAAGTTAATGTATAAAATTGCACA
Found at i:358362 original size:31 final size:29
Alignment explanation
Indices: 358301--358365 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
358291 TCAAGATTTA
*
358301 ATGTATAAAATTGCACAAAATCAAAGTTC
1 ATGTATAAAATTGCACAAAACCAAAGTTC
*
358330 ATGTATATAATTGCACATTAAACCATAA-TTC
1 ATGTATAAAATTGCACA--AAACCA-AAGTTC
358361 ATGTA
1 ATGTA
358366 CAATTTTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 16 0.52
31 13 0.42
32 2 0.06
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (29 bp):
ATGTATAAAATTGCACAAAACCAAAGTTC
Done.