Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 31
Found at i:5170306 original size:27 final size:26
Alignment explanation
Indices: 5170251--5170314 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
5170241 TTAGTGGACG
*
5170251 AATTTAT-AAATTTGAAGAGAAAGTA
1 AATTTATAAAATTTGAAGAGAAAATA
* *
5170276 AATTTATAAAATTTTAGGACGAAAATA
1 AATTTATAAAATTTGAAGA-GAAAATA
5170303 AATTTTATAAAA
1 AA-TTTATAAAA
5170315 ATATAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.21
26 9 0.27
27 8 0.24
28 9 0.27
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.34
Consensus pattern (26 bp):
AATTTATAAAATTTGAAGAGAAAATA
Found at i:5173302 original size:16 final size:17
Alignment explanation
Indices: 5173273--5173305 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5173263 ATAATATTTT
5173273 AATATTATAATATTTGAA
1 AATATTAT-ATATTTGAA
5173291 AATATTAT-TATTTGA
1 AATATTATATATTTGA
5173306 GTTGGATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
AATATTATATATTTGAA
Found at i:5173534 original size:14 final size:14
Alignment explanation
Indices: 5173515--5173566 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
5173505 ACATAGGTCT
5173515 CGTTCGTTCGTTTA
1 CGTTCGTTCGTTTA
*
5173529 CGTTCGTGTTCATTTA
1 CGTTC--GTTCGTTTA
* *
5173545 TGTTCGTTCGGTTA
1 CGTTCGTTCGTTTA
*
5173559 TGTTCGTT
1 CGTTCGTT
5173567 TATGTTCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 20 0.62
16 12 0.38
ACGTcount: A:0.08, C:0.17, G:0.23, T:0.52
Consensus pattern (14 bp):
CGTTCGTTCGTTTA
Found at i:5173583 original size:24 final size:24
Alignment explanation
Indices: 5173535--5173586 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5173525 TTTACGTTCG
* *
5173535 TGTTCATTTATGTTCGTTCGGTTA
1 TGTTCATTTATGTTCATTCAGTTA
* *
5173559 TGTTCGTTTATGTTCATTCATTTA
1 TGTTCATTTATGTTCATTCAGTTA
5173583 TGTT
1 TGTT
5173587 TAACCCAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.13, C:0.12, G:0.17, T:0.58
Consensus pattern (24 bp):
TGTTCATTTATGTTCATTCAGTTA
Found at i:5174518 original size:16 final size:16
Alignment explanation
Indices: 5174483--5174545 Score: 85
Period size: 16 Copynumber: 4.1 Consensus size: 16
5174473 CCAACGTTTA
*
5174483 TGTTCGTTTA-GTTTG
1 TGTTCGTTTATGTTCG
*
5174498 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
5174514 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
5174530 TATTCG-TTATGTTCG
1 TGTTCGTTTATGTTCG
5174545 T
1 T
5174546 TATTTATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
15 19 0.44
16 24 0.56
ACGTcount: A:0.10, C:0.11, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:5174521 original size:31 final size:31
Alignment explanation
Indices: 5174483--5174545 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
5174473 CCAACGTTTA
* * *
5174483 TGTTCGTTTA-GTTTGTGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCGTATTC-GTTATGTTCG
5174514 TGTTCGTTTATGTTCGTATTCGTTATGTTCG
1 TGTTCGTTTATGTTCGTATTCGTTATGTTCG
5174545 T
1 T
5174546 TATTTATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.10, C:0.11, G:0.22, T:0.57
Consensus pattern (31 bp):
TGTTCGTTTATGTTCGTATTCGTTATGTTCG
Found at i:5177503 original size:14 final size:14
Alignment explanation
Indices: 5177484--5177510 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5177474 AAAAAGTAAA
5177484 AAATATTAAATAAT
1 AAATATTAAATAAT
5177498 AAATATTAAATAA
1 AAATATTAAATAA
5177511 ATCAAGGGAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATTAAATAAT
Found at i:5177526 original size:18 final size:19
Alignment explanation
Indices: 5177505--5177542 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5177495 AATAAATATT
5177505 AAATAAATC-AAGGGAAAA
1 AAATAAATCAAAGGGAAAA
5177523 AAATAAATCAAAGGGAAAA
1 AAATAAATCAAAGGGAAAA
5177542 A
1 A
5177543 TAAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.68, C:0.05, G:0.16, T:0.11
Consensus pattern (19 bp):
AAATAAATCAAAGGGAAAA
Found at i:5177548 original size:18 final size:17
Alignment explanation
Indices: 5177505--5177548 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
5177495 AATAAATATT
5177505 AAAT-AAATCAAGGGAA
1 AAATAAAATCAAGGGAA
*
5177521 AAAAATAAATCAAAGGGAA
1 AAATA-AAATC-AAGGGAA
5177540 AAATAAAAT
1 AAATAAAAT
5177549 AAAAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 3 0.13
18 9 0.39
19 11 0.48
ACGTcount: A:0.68, C:0.05, G:0.14, T:0.14
Consensus pattern (17 bp):
AAATAAAATCAAGGGAA
Found at i:5177552 original size:29 final size:30
Alignment explanation
Indices: 5177520--5177581 Score: 117
Period size: 29 Copynumber: 2.1 Consensus size: 30
5177510 AATCAAGGGA
5177520 AAAAAATAAATCAAAGGG-AAAAATAAAAT
1 AAAAAATAAATCAAAGGGAAAAAATAAAAT
5177549 AAAAAATAAATCAAAGGGAAAAAATAAAAT
1 AAAAAATAAATCAAAGGGAAAAAATAAAAT
5177579 AAA
1 AAA
5177582 TAAAAATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 18 0.56
30 14 0.44
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.13
Consensus pattern (30 bp):
AAAAAATAAATCAAAGGGAAAAAATAAAAT
Found at i:5177572 original size:18 final size:18
Alignment explanation
Indices: 5177505--5177576 Score: 70
Period size: 18 Copynumber: 4.4 Consensus size: 18
5177495 AATAAATATT
5177505 AAATAAATC-AAGGGAAAA
1 AAATAAATCAAAGGG-AAA
5177523 AAATAAATCAAAGGG-AA
1 AAATAAATCAAAGGGAAA
*
5177540 AAAT--A--AAA--TAAA
1 AAATAAATCAAAGGGAAA
5177552 AAATAAATCAAAGGGAAA
1 AAATAAATCAAAGGGAAA
5177570 AAATAAA
1 AAATAAA
5177577 ATAAATAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 16
0.71 0.03 0.26
Matches are distributed among these distances:
12 6 0.14
13 3 0.07
14 1 0.02
15 1 0.02
16 3 0.07
17 6 0.14
18 19 0.43
19 5 0.11
ACGTcount: A:0.71, C:0.04, G:0.12, T:0.12
Consensus pattern (18 bp):
AAATAAATCAAAGGGAAA
Found at i:5177670 original size:20 final size:20
Alignment explanation
Indices: 5177612--5177671 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
5177602 TTTTAAAAGT
* *
5177612 AATAAAATAAAAATAATAAGA
1 AATAAAA-AAACATAATAAAA
*
5177633 AGTAAAAAAACA-AATAAAA
1 AATAAAAAAACATAATAAAA
*
5177652 AATAAAAAAACATACTAAAA
1 AATAAAAAAACATAATAAAA
5177672 TTAAAAGGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
19 17 0.52
20 10 0.30
21 6 0.18
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (20 bp):
AATAAAAAAACATAATAAAA
Found at i:5178811 original size:9 final size:9
Alignment explanation
Indices: 5178797--5178856 Score: 72
Period size: 9 Copynumber: 6.9 Consensus size: 9
5178787 ATAAATAAGC
5178797 AATAATATA
1 AATAATATA
5178806 AATAATAATA
1 AATAAT-ATA
5178816 AATAATATA
1 AATAATATA
5178825 AAT-A-AT-
1 AATAATATA
*
5178831 AATAATAAA
1 AATAATATA
*
5178840 AATAATAAA
1 AATAATATA
5178849 AATAATAT
1 AATAATAT
5178857 TATTTAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
6 3 0.07
7 3 0.07
8 2 0.04
9 28 0.62
10 9 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
AATAATATA
Found at i:5178812 original size:3 final size:3
Alignment explanation
Indices: 5178797--5178855 Score: 59
Period size: 3 Copynumber: 19.3 Consensus size: 3
5178787 ATAAATAAGC
*
5178797 AAT AAT -AT AAAT AAT AAT AAAT AAT -AT AAAT AAT AAT AAT AAA AAT
1 AAT AAT AAT -AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT AAT AAT
*
5178843 AAT AAA AAT AAT A
1 AAT AAT AAT AAT A
5178856 TTATTTAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
2 4 0.09
3 36 0.77
4 7 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:5178819 original size:19 final size:19
Alignment explanation
Indices: 5178783--5178856 Score: 86
Period size: 19 Copynumber: 4.1 Consensus size: 19
5178773 AAAAAATTAA
**
5178783 ATAAATAAATAAGCAATAAT
1 ATAAAT-AATAATAAATAAT
5178803 ATAAATAATAATAAATAAT
1 ATAAATAATAATAAATAAT
5178822 ATAAATAATAAT-AAT-A-
1 ATAAATAATAATAAATAAT
5178838 A-AAATAATAA-AAATAAT
1 ATAAATAATAATAAATAAT
5178855 AT
1 AT
5178857 TATTTAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
15 12 0.25
16 2 0.04
17 2 0.04
18 3 0.06
19 23 0.48
20 6 0.12
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (19 bp):
ATAAATAATAATAAATAAT
Found at i:5178852 original size:15 final size:15
Alignment explanation
Indices: 5178803--5178853 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
5178793 AAGCAATAAT
5178803 ATAAATAATAATAAATA
1 ATAAA-AATAATAAA-A
* *
5178820 ATATAAATAATAATA
1 ATAAAAATAATAAAA
5178835 ATAAAAATAATAAAA
1 ATAAAAATAATAAAA
5178850 ATAA
1 ATAA
5178854 TATTATTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 18 0.60
16 8 0.27
17 4 0.13
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAAAAATAATAAAA
Found at i:5178916 original size:37 final size:38
Alignment explanation
Indices: 5178869--5179140 Score: 277
Period size: 37 Copynumber: 7.3 Consensus size: 38
5178859 TTTAAATATA
* * *
5178869 TATATATTATATTTATTTTCCAAAATGTTTT-TAAAAC
1 TATATATTATATATATTTTTCAAAATGTTTTCAAAAAC
* * *
5178906 CATACATTATATATA-TTTTCAAAATATTTTCAAAAAC
1 TATATATTATATATATTTTTCAAAATGTTTTCAAAAAC
5178943 TATATATTATATATATTTTTTCAAAATGTTTTCAAAAAC
1 TATATATTATATATA-TTTTTCAAAATGTTTTCAAAAAC
5178982 TATATA-T-TATATA----T----ATGTTTTCAAAAAC
1 TATATATTATATATATTTTTCAAAATGTTTTCAAAAAC
*
5179010 TATATATTATATAGA-TTTTCAAAATGTTTTCAAAAAC
1 TATATATTATATATATTTTTCAAAATGTTTTCAAAAAC
5179047 TATATATTATATATATGTTTTCAAAATGTTTTC-AAAAC
1 TATATATTATATATAT-TTTTCAAAATGTTTTCAAAAAC
*
5179085 TATAATATATATATATATATATATTCAAAAATCATTTTC-AAAAC
1 TAT-ATAT-TATATATAT-T-T-TTC-AAAAT-GTTTTCAAAAAC
*
5179129 TATATAATATAT
1 TATATATTATAT
5179141 TTTCAAAAAA
Statistics
Matches: 201, Mismatches: 14, Indels: 35
0.80 0.06 0.14
Matches are distributed among these distances:
28 20 0.10
29 1 0.00
30 5 0.02
32 1 0.00
33 1 0.00
36 13 0.06
37 64 0.32
38 9 0.04
39 47 0.23
40 10 0.05
41 1 0.00
42 8 0.04
43 8 0.04
44 13 0.06
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (38 bp):
TATATATTATATATATTTTTCAAAATGTTTTCAAAAAC
Found at i:5178922 original size:65 final size:65
Alignment explanation
Indices: 5178853--5179067 Score: 204
Period size: 65 Copynumber: 3.1 Consensus size: 65
5178843 AATAAAAATA
* * * *
5178853 ATATTATTTAAATATA-TATATATTATATTTATTTTCCAAAATGTTTT-TAAAACCATACATTAT
1 ATATT-TTTAAATATACTATATATTATATATATTTT-CAAAATGTTTTCAAAAACTATATATTAT
5178916 AT
64 AT
*
5178918 ATATTTTCAAAATATTTTCAAAAACTATATATTATATATATTTTTTCAAAATGTTTTCAAAAACT
1 ATATTTT-TAAATA---T-----ACTATATATTATATATA--TTTTCAAAATGTTTTCAAAAACT
5178983 ATATATTATAT
55 ATATATTATAT
*
5178994 ATATGTTTTCAAA-A-ACTATATATTATATAGATTTTCAAAATGTTTTCAAAAACTATATATTAT
1 ATAT-TTTT-AAATATACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTAT
5179057 AT
64 AT
5179059 ATATGTTTT
1 ATAT-TTTT
5179068 CAAAATGTTT
Statistics
Matches: 128, Mismatches: 7, Indels: 30
0.78 0.04 0.18
Matches are distributed among these distances:
64 2 0.02
65 53 0.41
67 16 0.12
68 1 0.01
73 1 0.01
74 14 0.11
75 11 0.09
76 24 0.19
77 6 0.05
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (65 bp):
ATATTTTTAAATATACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATAT
Found at i:5179020 original size:26 final size:28
Alignment explanation
Indices: 5178968--5179022 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
5178958 TTTTTTCAAA
5178968 ATGTTTTCAAAAACTATATATTATATAT
1 ATGTTTTCAAAAACTATATATTATATAT
5178996 ATGTTTTCAAAAACTATATATTATATA
1 ATGTTTTCAAAAACTATATATTATATA
5179023 GATTTTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (28 bp):
ATGTTTTCAAAAACTATATATTATATAT
Found at i:5179021 original size:104 final size:104
Alignment explanation
Indices: 5178893--5179102 Score: 334
Period size: 104 Copynumber: 2.0 Consensus size: 104
5178883 ATTTTCCAAA
* *
5178893 ATGTTTTTAAAACCATACATTATATATATTTTCAAAATATTTTCAAAAACTATATATTATATATA
1 ATGTTTTAAAAACCATACATTATATAGATTTTCAAAATATTTTCAAAAACTATATATTATATATA
*
5178958 TTTTTTCAAAATGTTTTCAAAAACTAT-ATAT-TATATAT
66 TGTTTTCAAAATGTTTTC-AAAACTATAATATATATATAT
* * *
5178996 ATGTTTTCAAAAACTATATATTATATAGATTTTCAAAATGTTTTCAAAAACTATATATTATATAT
1 ATGTTTT-AAAAACCATACATTATATAGATTTTCAAAATATTTTCAAAAACTATATATTATATAT
5179061 ATGTTTTCAAAATGTTTTCAAAACTATAATATATATATAT
65 ATGTTTTCAAAATGTTTTCAAAACTATAATATATATATAT
5179101 AT
1 AT
5179103 ATATATTCAA
Statistics
Matches: 98, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
103 15 0.15
104 74 0.76
105 9 0.09
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (104 bp):
ATGTTTTAAAAACCATACATTATATAGATTTTCAAAATATTTTCAAAAACTATATATTATATATA
TGTTTTCAAAATGTTTTCAAAACTATAATATATATATAT
Found at i:5179028 original size:26 final size:27
Alignment explanation
Indices: 5178970--5179033 Score: 103
Period size: 28 Copynumber: 2.4 Consensus size: 27
5178960 TTTTCAAAAT
*
5178970 GTTTTCAAAAACTATATATTATATATA
1 GTTTTCAAAAACTATATATTATATAGA
5178997 TGTTTTCAAAAACTATATATTATATAGA
1 -GTTTTCAAAAACTATATATTATATAGA
5179025 -TTTTCAAAA
1 GTTTTCAAAA
5179034 TGTTTTCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 9 0.26
28 26 0.74
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (27 bp):
GTTTTCAAAAACTATATATTATATAGA
Found at i:5179068 original size:65 final size:66
Alignment explanation
Indices: 5178932--5179072 Score: 257
Period size: 65 Copynumber: 2.1 Consensus size: 66
5178922 TTTCAAAATA
*
5178932 TTTTCAAAAACTATATATTATATATATTTTTTCAAAATGTTTTCAAAAACTATATATTATATATA
1 TTTTCAAAAACTATATATTATATAGA-TTTTTCAAAATGTTTTCAAAAACTATATATTATATATA
5178997 TG
65 TG
5178999 TTTTCAAAAACTATATATTATATAGA-TTTTCAAAATGTTTTCAAAAACTATATATTATATATAT
1 TTTTCAAAAACTATATATTATATAGATTTTTCAAAATGTTTTCAAAAACTATATATTATATATAT
5179063 G
66 G
5179064 TTTTCAAAA
1 TTTTCAAAA
5179073 TGTTTTCAAA
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
65 48 0.66
67 25 0.34
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.46
Consensus pattern (66 bp):
TTTTCAAAAACTATATATTATATAGATTTTTCAAAATGTTTTCAAAAACTATATATTATATATAT
G
Found at i:5179102 original size:44 final size:43
Alignment explanation
Indices: 5179010--5179140 Score: 145
Period size: 39 Copynumber: 3.2 Consensus size: 43
5179000 TTTCAAAAAC
5179010 TATATAT-TATATAGATTTTCAAAATGTTTTCAAAA--ACT-ATA
1 TATATATATATATAG-TTTTCAAAATGTTTTCAAAACTA-TAATA
5179051 TAT-TATATATAT-GTTTTCAAAATGTTTTCAAAACTATAATA
1 TATATATATATATAGTTTTCAAAATGTTTTCAAAACTATAATA
* *
5179092 TATATATATATATA-TATTCAAAAATCATTTTCAAAACTAT-ATA
1 TATATATATATATAGTTTTC-AAAAT-GTTTTCAAAACTATAATA
5179135 -ATATAT
1 TATATAT
5179141 TTTCAAAAAA
Statistics
Matches: 80, Mismatches: 2, Indels: 15
0.82 0.02 0.15
Matches are distributed among these distances:
39 20 0.25
40 5 0.06
41 15 0.19
42 19 0.24
43 8 0.10
44 13 0.16
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (43 bp):
TATATATATATATAGTTTTCAAAATGTTTTCAAAACTATAATA
Found at i:5180092 original size:85 final size:85
Alignment explanation
Indices: 5179962--5180167 Score: 274
Period size: 85 Copynumber: 2.4 Consensus size: 85
5179952 AACTGAATAC
* * * * * *
5179962 TTTTTGTTGACAGATA-CATTTTATCGACTTAAGCTATGCTGTAAATTTGATATGTCCTTAAGCT
1 TTTTTGTTGACAGATAGC-TCTTCTCGCCTTGAGCTACGCTATAAATTTGATATGTCCTTAAGCT
5180026 GAATGTAATCGAACTCGAAGG-
65 GAATGT-ATCGAACTCGAAGGT
*
5180047 TTTTTGTTGACAGATAGCTCTTCTCGCCTTGAGCTACGCTATAAATTTGATATGTCCTTGAGCTG
1 TTTTTGTTGACAGATAGCTCTTCTCGCCTTGAGCTACGCTATAAATTTGATATGTCCTTAAGCTG
*
5180112 AATGTATCGAACTTGAAGGT
66 AATGTATCGAACTCGAAGGT
* *
5180132 TTTTTGCTGGA-AGATAGCCCTTCTCGCCTTGAGCTA
1 TTTTTG-TTGACAGATAGCTCTTCTCGCCTTGAGCTA
5180168 TGCTGTGAAT
Statistics
Matches: 108, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
84 13 0.12
85 91 0.84
86 4 0.04
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (85 bp):
TTTTTGTTGACAGATAGCTCTTCTCGCCTTGAGCTACGCTATAAATTTGATATGTCCTTAAGCTG
AATGTATCGAACTCGAAGGT
Found at i:5183913 original size:17 final size:16
Alignment explanation
Indices: 5183882--5183915 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5183872 CACGTGAGGA
5183882 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
5183898 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
5183915 T
1 T
5183916 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:5190302 original size:19 final size:21
Alignment explanation
Indices: 5190265--5190307 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
5190255 TAACTTTTTC
5190265 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
5190285 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
5190305 TTT
1 TTT
5190308 ACATTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:5194167 original size:17 final size:16
Alignment explanation
Indices: 5194136--5194169 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5194126 CACGTGAGGA
5194136 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
5194152 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
5194169 T
1 T
5194170 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:5197690 original size:22 final size:22
Alignment explanation
Indices: 5197664--5197706 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5197654 AATATTAAAT
5197664 AAATC-AAGGGAAAAAATAAAAA
1 AAATCAAAGGG-AAAAATAAAAA
5197686 AAATCAAAGGGAAAAATAAAA
1 AAATCAAAGGGAAAAATAAAA
5197707 TTAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.72, C:0.05, G:0.14, T:0.09
Consensus pattern (22 bp):
AAATCAAAGGGAAAAATAAAAA
Found at i:5197777 original size:44 final size:43
Alignment explanation
Indices: 5197686--5197771 Score: 102
Period size: 44 Copynumber: 1.9 Consensus size: 43
5197676 AAAATAAAAA
* * *
5197686 AAATCAAAGGGAAAAATAAAATTAAAAAATATTAAATATTAAAT
1 AAATCAAAGGAAAAAATAAAAATAAAAAATATTAAAAATT-AAT
5197730 AAATCAAAGGAAAAAAATAAATAATATAAAAATA-TAAAAATT
1 AAATCAAAGG-AAAAAATAAA-AATA-AAAAATATTAAAAATT
5197772 TTAAATTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 10 0.28
45 9 0.25
46 10 0.28
47 7 0.19
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (43 bp):
AAATCAAAGGAAAAAATAAAAATAAAAAATATTAAAAATTAAT
Found at i:5198996 original size:33 final size:33
Alignment explanation
Indices: 5198954--5199018 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
5198944 ACCTGAAAGA
*
5198954 AAAAATTAAAATTAA-ATAAATAAGCAATAATAT
1 AAAAATTAAAAATAATATAAATAA-CAATAATAT
*
5198987 AAAAATTAAAAATAATATAAATAATAATAATA
1 AAAAATTAAAAATAATATAAATAACAATAATA
5199019 AATAATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 21 0.72
34 8 0.28
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (33 bp):
AAAAATTAAAAATAATATAAATAACAATAATAT
Found at i:5199000 original size:18 final size:21
Alignment explanation
Indices: 5198966--5199026 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 21
5198956 AAATTAAAAT
**
5198966 TAAATAA-ATAAGCAATAATA
1 TAAATAATATAATAAATAATA
5198986 TAAA-AAT-TAA-AAATAATA
1 TAAATAATATAATAAATAATA
5199004 TAAATAATAATAATAAATAATA
1 TAAATAAT-ATAATAAATAATA
5199026 T
1 T
5199027 TATATATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 11 0.31
19 8 0.23
20 4 0.11
21 3 0.09
22 9 0.26
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
TAAATAATATAATAAATAATA
Found at i:5199010 original size:22 final size:23
Alignment explanation
Indices: 5198980--5199032 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
5198970 TAAATAAGCA
5198980 ATAATATAAAAATTAA-AAATAAT
1 ATAATATAAAAA-TAATAAATAAT
*
5199003 ATAA-ATAATAATAATAAATAAT
1 ATAATATAAAAATAATAAATAAT
*
5199025 ATTATATA
1 ATAATATA
5199033 TATATATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 3 0.12
22 16 0.62
23 7 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
ATAATATAAAAATAATAAATAAT
Found at i:5199095 original size:37 final size:35
Alignment explanation
Indices: 5199029--5199255 Score: 197
Period size: 36 Copynumber: 6.5 Consensus size: 35
5199019 AATAATATTA
* * * *
5199029 TATATATATATTCCAAAATATTTTTAAAACCATACAT
1 TATATATAT-TTTCAAAATGTTTTCAAAACTATA-AT
*
5199066 TATATATATTTTCAAAATTTTTTCAAAAACTATATAT
1 TATATATATTTTCAAAATGTTTTC-AAAACTATA-AT
5199103 TATATATA---T---AA-GTTTTCAAAAACTATATAT
1 TATATATATTTTCAAAATGTTTTC-AAAACTATA-AT
*
5199133 TATATATATTTTCAAAATGTTTTCAAAATTATAAT
1 TATATATATTTTCAAAATGTTTTCAAAACTATAAT
* *
5199168 ATATATATTTTTTCAAAAATAATTTTCAAAACTATAA-
1 -TATATATATTTTC-AAAAT-GTTTTCAAAACTATAAT
*
5199205 TATATATATTTTCAAAAATAATTTTCAAAACTAT-A-
1 TATATATATTTTC-AAAAT-GTTTTCAAAACTATAAT
5199240 TA-ATATATTTTCAAAA
1 TATATATATTTTCAAAA
5199256 AACTGATTTT
Statistics
Matches: 168, Mismatches: 11, Indels: 26
0.82 0.05 0.13
Matches are distributed among these distances:
30 26 0.15
31 2 0.01
33 5 0.03
34 11 0.07
35 5 0.03
36 67 0.40
37 38 0.23
38 14 0.08
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.44
Consensus pattern (35 bp):
TATATATATTTTCAAAATGTTTTCAAAACTATAAT
Found at i:5199141 original size:30 final size:30
Alignment explanation
Indices: 5199085--5199141 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
5199075 TTTCAAAATT
5199085 TTTTCAAAAACTATATATTATATATATAAG
1 TTTTCAAAAACTATATATTATATATATAAG
5199115 TTTTCAAAAACTATATATTATATATAT
1 TTTTCAAAAACTATATATTATATATAT
5199142 TTTCAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (30 bp):
TTTTCAAAAACTATATATTATATATATAAG
Found at i:5199204 original size:15 final size:13
Alignment explanation
Indices: 5199177--5199234 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
5199167 TATATATATT
5199177 TTTTCAAAAATAA
1 TTTTCAAAAATAA
*
5199190 TTTTCAAAACT-A
1 TTTTCAAAAATAA
** * *
5199202 TAAT-ATATAT-A
1 TTTTCAAAAATAA
5199213 TTTTCAAAAATAA
1 TTTTCAAAAATAA
5199226 TTTTCAAAA
1 TTTTCAAAA
5199235 CTATATAATA
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
11 6 0.18
12 7 0.21
13 20 0.61
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (13 bp):
TTTTCAAAAATAA
Found at i:5207997 original size:16 final size:16
Alignment explanation
Indices: 5207976--5208006 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5207966 TACTAAAATG
*
5207976 TTTCGAGTTCAAGTTT
1 TTTCGAGCTCAAGTTT
5207992 TTTCGAGCTCAAGTT
1 TTTCGAGCTCAAGTT
5208007 GAACTTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.45
Consensus pattern (16 bp):
TTTCGAGCTCAAGTTT
Found at i:5216845 original size:117 final size:116
Alignment explanation
Indices: 5216638--5216938 Score: 381
Period size: 117 Copynumber: 2.6 Consensus size: 116
5216628 TAGTTGTTAG
* * *
5216638 AAAAGTTAGCGGTTAGCAGAGTCCAAACCATAATAATGTGGATCATATCCTGGATATGGTCACCA
1 AAAAGTTAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCTGGATA-GGTCACCA
* * **
5216703 CAAGGCCGAATTGAATAATTCAAACAAAT-TA-ACAAAATAAAATAAAATAAA
65 CAAAGCCAAATCAAATAATTCAAACAAATATATA-AAAATAAAATAAAATAAA
*
5216754 ATAAAGTTAGTGGTTAGCAGGGTCCGAACCATAATAATGTGGATCATACCCTGGATTAGGTCACC
1 A-AAAGTTAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCTGGA-TAGGTCACC
* *
5216819 ACAAAGTCAAATCAAATAATTCAAACAAATATATAAAAATAAAATAAAATGAA
64 ACAAAGCCAAATCAAATAATTCAAACAAATATATAAAAATAAAATAAAATAAA
* * * ***** *
5216872 AAAAGTTAGTGGTTAGCACAATCCGAACGATAATAACACATATCATACCCCGGATAGGTCACCAC
1 AAAAGTTAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCTGGATAGGTCACCAC
5216937 AA
66 AA
5216939 GGTCGAATTG
Statistics
Matches: 161, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
116 14 0.09
117 124 0.77
118 22 0.14
119 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (116 bp):
AAAAGTTAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCTGGATAGGTCACCAC
AAAGCCAAATCAAATAATTCAAACAAATATATAAAAATAAAATAAAATAAA
Found at i:5217013 original size:29 final size:29
Alignment explanation
Indices: 5216981--5217056 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
5216971 TAAATAACAA
5216981 TGGTTAA-AGTGCAATAAAATAAAAGTTAG
1 TGGTTAACA-TGCAATAAAATAAAAGTTAG
*
5217010 TGGTTAACATGCAATAAAATAAAAGTTAA
1 TGGTTAACATGCAATAAAATAAAAGTTAG
* * *
5217039 TAGTTAACTTGAAATAAA
1 TGGTTAACATGCAATAAA
5217057 TAACATAACA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 41 0.98
30 1 0.02
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (29 bp):
TGGTTAACATGCAATAAAATAAAAGTTAG
Found at i:5217409 original size:16 final size:16
Alignment explanation
Indices: 5217388--5217419 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5217378 AGAAGATTCC
5217388 TCCCATACTTTTGTTT
1 TCCCATACTTTTGTTT
5217404 TCCCATACTTTTGTTT
1 TCCCATACTTTTGTTT
5217420 AGCATGATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.25, G:0.06, T:0.56
Consensus pattern (16 bp):
TCCCATACTTTTGTTT
Found at i:5218702 original size:28 final size:28
Alignment explanation
Indices: 5218670--5218728 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
5218660 ACATATTTAA
* *
5218670 AAGTAATCAATAAAACAAATATAGTAGC
1 AAGTAAACAATAAAACAAATAAAGTAGC
* *
5218698 AAGTAAACAATAAAACAGATAAATTAGC
1 AAGTAAACAATAAAACAAATAAAGTAGC
5218726 AAG
1 AAG
5218729 GAAAGATACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.19
Consensus pattern (28 bp):
AAGTAAACAATAAAACAAATAAAGTAGC
Found at i:5219652 original size:31 final size:31
Alignment explanation
Indices: 5219606--5219669 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
5219596 TTATGATTTG
* *
5219606 TGATCTGTTCCAGTTCTAACTAAACTAGTAA
1 TGATCTATTCCAGTTCCAACTAAACTAGTAA
*
5219637 TGATCTATTCTAGTTCCAACTAAACTAGTAA
1 TGATCTATTCCAGTTCCAACTAAACTAGTAA
5219668 TG
1 TG
5219670 TTCTTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (31 bp):
TGATCTATTCCAGTTCCAACTAAACTAGTAA
Found at i:5221630 original size:2 final size:2
Alignment explanation
Indices: 5221623--5221664 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5221613 TATATTCTTG
5221623 AT AT AT AT 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 AT AT AT AT
5221665 TAAATTTAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5224367 original size:25 final size:25
Alignment explanation
Indices: 5224339--5224389 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
5224329 TATAATTTCA
5224339 CGCCCTCTAAATTTCTAATATAAAG
1 CGCCCTCTAAATTTCTAATATAAAG
5224364 CGCCCTCTAAATTTCTAATATAAAG
1 CGCCCTCTAAATTTCTAATATAAAG
5224389 C
1 C
5224390 CCCCAGCCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.31
Consensus pattern (25 bp):
CGCCCTCTAAATTTCTAATATAAAG
Found at i:5232504 original size:14 final size:14
Alignment explanation
Indices: 5232485--5232522 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
5232475 TATACCTTTA
*
5232485 ATGACACACTAATG
1 ATGACACACGAATG
5232499 ATGACACACGAATG
1 ATGACACACGAATG
5232513 ATGACACACG
1 ATGACACACG
5232523 CTAATTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (14 bp):
ATGACACACGAATG
Found at i:5237419 original size:2 final size:2
Alignment explanation
Indices: 5237412--5237440 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5237402 TCAATCTACA
5237412 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
5237441 CATACGACAT
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:5237614 original size:13 final size:13
Alignment explanation
Indices: 5237598--5237632 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
5237588 CGCAATGAGT
**
5237598 GTCATAAATGTGC
1 GTCATAAATGCAC
5237611 GTCATAAATGCAC
1 GTCATAAATGCAC
5237624 GTCATAAAT
1 GTCATAAAT
5237633 TTATGATGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (13 bp):
GTCATAAATGCAC
Found at i:5242293 original size:218 final size:219
Alignment explanation
Indices: 5241905--5242635 Score: 1209
Period size: 219 Copynumber: 3.3 Consensus size: 219
5241895 TCAGGAGCAA
* * *
5241905 GATCAAAATT-GCTCTCCACGGAAGAATAGTGGAAC-GTATTTTTCAGCACAGAATGAAGTCTCA
1 GATCAAAATTCGCTCTCCACGGAAGAGTAGTGGAACAG-ATTTTTCAGCAAAGTATGAAGTCTCA
*
5241968 TGAAAGAGTAGTGAGGTAACCCAATATTGAGTCTGATCTTCACGGAAGAGTAGTGAAATTAGATT
65 CGAAAGAGTAGTGAGGTAACCCAATATTGAGTCTGATCTTCACGGAAGAGTAGTGAAATTAGATT
*
5242033 CTTCTCAAGTCAATTATTCTTAACCTTCACGGAAGAGTAGTGAAGTAATGCAAATCAAGCCTTCA
130 CTTCTCAAGTCAATTATTCTCAACCTTCACGGAAGAGTAGTGAAGTAATGCAAATCAAGCCTTCA
*
5242098 CAAAA-AGTAGTGAAGCAAAAGTAT
195 CAAAAGAGTAGTGAAGCAAAAGTAG
5242122 GATCAAAATTCGCTCTCCACGGAAGAGTAGTGGAACAGATTTTTCAGCAAAGTATGAAGTCTCAC
1 GATCAAAATTCGCTCTCCACGGAAGAGTAGTGGAACAGATTTTTCAGCAAAGTATGAAGTCTCAC
* *
5242187 GAAAAAGTAGTGAGGTAACCCAATATTGAGTCTGATCTTCACGGAAGAGTAGTGAAATTAGAATC
66 GAAAGAGTAGTGAGGTAACCCAATATTGAGTCTGATCTTCACGGAAGAGTAGTGAAATTAGATTC
* *
5242252 TTCTCAAGTCAATTATTCTCAATCTTCACGGAAGAGTAGTGAAGTAATGCAAATCAAGCTTTCAC
131 TTCTCAAGTCAATTATTCTCAACCTTCACGGAAGAGTAGTGAAGTAATGCAAATCAAGCCTTCAC
* *
5242317 AAAAGAGTAGTGAAGAAAAAGCAG
196 AAAAGAGTAGTGAAGCAAAAGTAG
* *
5242341 GATCAAAATTCACTCTCCACGGAAGAGTAGTGGAATAGATTTTTCAGCAAAGTATGAAGTCTCAC
1 GATCAAAATTCGCTCTCCACGGAAGAGTAGTGGAACAGATTTTTCAGCAAAGTATGAAGTCTCAC
*
5242406 GAAAGAGTAGTGAGGTAACCCAATATTGAGTCTGATTTTCACGGAAGAGTAGTGAAATTAGATTC
66 GAAAGAGTAGTGAGGTAACCCAATATTGAGTCTGATCTTCACGGAAGAGTAGTGAAATTAGATTC
* * *
5242471 TTCTCAAGTCAATTATTCTCAACCTTCACAGAAGAGTAGTAAAGTAATACAAATCAAGCCTTCAC
131 TTCTCAAGTCAATTATTCTCAACCTTCACGGAAGAGTAGTGAAGTAATGCAAATCAAGCCTTCAC
*
5242536 AAAAGACTAGTGAAGCAAAAGTAG
196 AAAAGAGTAGTGAAGCAAAAGTAG
* * *
5242560 GATCAAATTTCGCTCTCCACGGAAGAGTAGTGGAACAAATTTTTCAGCAAAGTATGAAGCCTTCA
1 GATCAAAATTCGCTCTCCACGGAAGAGTAGTGGAACAGATTTTTCAGCAAAGTATGAAGTC-TCA
5242625 C-AGAAGAGTAG
65 CGA-AAGAGTAG
5242636 AGAAGCAAAA
Statistics
Matches: 479, Mismatches: 30, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
217 10 0.02
218 177 0.37
219 280 0.58
220 12 0.03
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.25
Consensus pattern (219 bp):
GATCAAAATTCGCTCTCCACGGAAGAGTAGTGGAACAGATTTTTCAGCAAAGTATGAAGTCTCAC
GAAAGAGTAGTGAGGTAACCCAATATTGAGTCTGATCTTCACGGAAGAGTAGTGAAATTAGATTC
TTCTCAAGTCAATTATTCTCAACCTTCACGGAAGAGTAGTGAAGTAATGCAAATCAAGCCTTCAC
AAAAGAGTAGTGAAGCAAAAGTAG
Found at i:5244048 original size:8 final size:9
Alignment explanation
Indices: 5244030--5244070 Score: 54
Period size: 8 Copynumber: 5.0 Consensus size: 9
5244020 TTAAGGTAAC
5244030 TTTATAATA
1 TTTATAATA
5244039 TTTA-AATA
1 TTTATAATA
5244047 -TTATAATA
1 TTTATAATA
5244055 TTTA-AATA
1 TTTATAATA
5244063 -TTATAATA
1 TTTATAATA
5244071 GGAATATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 6 0.21
8 16 0.55
9 7 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TTTATAATA
Found at i:5244050 original size:16 final size:16
Alignment explanation
Indices: 5244031--5244070 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
5244021 TAAGGTAACT
5244031 TTATAATATTTAAATA
1 TTATAATATTTAAATA
5244047 TTATAATATTTAAATA
1 TTATAATATTTAAATA
5244063 TTATAATA
1 TTATAATA
5244071 GGAATATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATAATATTTAAATA
Found at i:5248222 original size:155 final size:155
Alignment explanation
Indices: 5247940--5248244 Score: 583
Period size: 155 Copynumber: 2.0 Consensus size: 155
5247930 AAACCATTAT
5247940 ACCAAATTCCACTAGTTAGGGTTTGTATGGCCAAAAAGAAATTTAGGGCTTGTATCGATAGTCAT
1 ACCAAATTCCACTAGTTAGGGTTTGTATGGCCAAAAAGAAATTTAGGGCTTGTATCGATAGTCAT
* *
5248005 TGAGATTGATTTTGAACGCATCGATAAATTATGAATCGTAATTACGAGATGGGTTATTATAATCA
66 TGAGATTGATTCTGAACGCACCGATAAATTATGAATCGTAATTACGAGATGGGTTATTATAATCA
5248070 TAAGATTAAATTGCTAACAAAAAAA
131 TAAGATTAAATTGCTAACAAAAAAA
*
5248095 ACCAAATTCCACTAGTTAGGGTTTGTATGGCCAAAAAGAAATTTAGGGTTTGTATCGATAGTCAT
1 ACCAAATTCCACTAGTTAGGGTTTGTATGGCCAAAAAGAAATTTAGGGCTTGTATCGATAGTCAT
5248160 TGAGATTGATTCTGAACGCACCGATAAATTATGAATCGTAATTACGAGATGGGTTATTATAATCA
66 TGAGATTGATTCTGAACGCACCGATAAATTATGAATCGTAATTACGAGATGGGTTATTATAATCA
5248225 TAAGATTAAATTGCTAACAA
131 TAAGATTAAATTGCTAACAA
5248245 GATATTATTG
Statistics
Matches: 147, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
155 147 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (155 bp):
ACCAAATTCCACTAGTTAGGGTTTGTATGGCCAAAAAGAAATTTAGGGCTTGTATCGATAGTCAT
TGAGATTGATTCTGAACGCACCGATAAATTATGAATCGTAATTACGAGATGGGTTATTATAATCA
TAAGATTAAATTGCTAACAAAAAAA
Found at i:5255980 original size:29 final size:27
Alignment explanation
Indices: 5255948--5256031 Score: 62
Period size: 28 Copynumber: 3.0 Consensus size: 27
5255938 ATATTTAATT
5255948 TATAATTCTTTCTTTTCAAAATTTTTATA
1 TATAATT-TTT-TTTTCAAAATTTTTATA
* * * *
5255977 TATACTTATTATTTTCATAATATTTATA
1 TATAATT-TTTTTTTCAAAATTTTTATA
* *
5256005 TGTATATTATTTTTTT-AATATTTTTAT
1 TATA-ATT-TTTTTTTCAAAATTTTTAT
5256032 TTTATTTTCA
Statistics
Matches: 43, Mismatches: 11, Indels: 3
0.75 0.19 0.05
Matches are distributed among these distances:
28 26 0.60
29 17 0.40
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (27 bp):
TATAATTTTTTTTTCAAAATTTTTATA
Found at i:5256012 original size:26 final size:27
Alignment explanation
Indices: 5255960--5256027 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
5255950 TAATTCTTTC
* *
5255960 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCATAATATTTATATATAC-TATTA
*
5255988 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCATAATATTTATATATACTATTA
**
5256014 TTTTTTTAATATTT
1 TTTTCATAATATTT
5256028 TTATTTTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 17 0.49
28 18 0.51
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (27 bp):
TTTTCATAATATTTATATATACTATTA
Found at i:5259335 original size:15 final size:15
Alignment explanation
Indices: 5259315--5259346 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5259305 GATCAATACC
5259315 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
5259330 TTTTGCATACATTCA
1 TTTTGCATACATGCA
5259345 TT
1 TT
5259347 ATTCATTGCA
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:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:5261290 original size:12 final size:13
Alignment explanation
Indices: 5261260--5261293 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
5261250 AGAGTTCTTT
5261260 GAAAAAGAACCAG
1 GAAAAAGAACCAG
5261273 GAAAAAGAACCAG
1 GAAAAAGAACCAG
5261286 GAAAAAGA
1 GAAAAAGA
5261294 GAAGATGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.65, C:0.12, G:0.24, T:0.00
Consensus pattern (13 bp):
GAAAAAGAACCAG
Found at i:5268426 original size:114 final size:113
Alignment explanation
Indices: 5268241--5268650 Score: 680
Period size: 113 Copynumber: 3.6 Consensus size: 113
5268231 CCAGAAGAAG
5268241 GAAGAA-TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATT
1 GAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATT
5268305 TGTTCAACCTTTTTCTCGAATTCATCACTCGATGGATCAACTTTTCCA
66 TGTTCAACCTTTTTCTCGAATTCATCACTCGATGGATCAACTTTTCCA
* * *
5268353 GAAGAAGTTTATAATAAGAAGAACTCATCTGAAGAAGGAAAAAAGAAATTCATAATGAGAAGAAT
1 GAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AAGAAGAAATTCATAATGAGAAGAAT
*
5268418 TTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAACTTTTCCA
65 TTGTTCAACCTTTTTCTCGAATTCATCACTCGATGGATCAACTTTTCCA
* * *
5268467 GAAGAAGTTTATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAATTCATAATAAGAAGAATT
1 GAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATT
* *
5268532 CGTTCAACCCTTTTCTCGAATTCATCACTCGATGGATCAACTTTTCCA
66 TGTTCAACCTTTTTCTCGAATTCATCACTCGATGGATCAACTTTTCCA
* * * *
5268580 GAAGAAGTTCATAATGAGAAGAACTCATCTAAAGAATG-AGAAGAAATCCATAATGAGAAGAACT
1 GAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATT
5268644 TGTTCAA
66 TGTTCAA
5268651 TCTTAACTTA
Statistics
Matches: 277, Mismatches: 19, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
112 35 0.13
113 133 0.48
114 109 0.39
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (113 bp):
GAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATT
TGTTCAACCTTTTTCTCGAATTCATCACTCGATGGATCAACTTTTCCA
Found at i:5268778 original size:20 final size:20
Alignment explanation
Indices: 5268723--5268780 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
5268713 TTCCATAAGG
*
5268723 AGTTCATAATGAGAAGAACTC
1 AGTTCATAATGAGAAGAA-TA
* **
5268744 A--TCAGAAAAAGAAGAATA
1 AGTTCATAATGAGAAGAATA
5268762 AGTTCATAATGAGAAGAAT
1 AGTTCATAATGAGAAGAAT
5268781 TTGTTCAATT
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
18 2 0.07
19 12 0.43
20 13 0.46
21 1 0.04
ACGTcount: A:0.52, C:0.09, G:0.19, T:0.21
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAATA
Found at i:5269047 original size:23 final size:23
Alignment explanation
Indices: 5269018--5269065 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5269008 TCCATTTGTT
*
5269018 TTTTATTTTTAATTT-TAATATTA
1 TTTTATTTAT-ATTTATAATATTA
*
5269041 TTTTATTTATATTTATATTATTA
1 TTTTATTTATATTTATAATATTA
5269064 TT
1 TT
5269066 AATAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTATTTATATTTATAATATTA
Found at i:5275605 original size:33 final size:33
Alignment explanation
Indices: 5275547--5275669 Score: 148
Period size: 33 Copynumber: 3.8 Consensus size: 33
5275537 AATTATAAAA
5275547 ATAATAAATTTAATG---ATTTTATAATACTTTG
1 ATAA-AAATTTAATGATTATTTTATAATACTTTG
* *
5275578 ATAAAAAATTAATGATTTTTTTATAATACTTTG
1 ATAAAAATTTAATGATTATTTTATAATACTTTG
* * *
5275611 ATAAAAATTTAATGATAATTTTATAGTAGTTTG
1 ATAAAAATTTAATGATTATTTTATAATACTTTG
*
5275644 AT--AAATTTAATTATTATTTTATAATA
1 ATAAAAATTTAATGATTATTTTATAATA
5275670 ATTTAATGAG
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
30 9 0.11
31 25 0.32
33 45 0.57
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (33 bp):
ATAAAAATTTAATGATTATTTTATAATACTTTG
Found at i:5282653 original size:34 final size:34
Alignment explanation
Indices: 5282610--5282694 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 34
5282600 TTAGTTATGC
*
5282610 AATAAAATAAAAGGTTAGTAAATTAATAAT-AACA
1 AATAAAATAAAAGGTTAGCAAATTAAT-ATGAACA
* * *
5282644 AATAAAATAAAA-ATTAGCAAGTTAGTATGAACA
1 AATAAAATAAAAGGTTAGCAAATTAATATGAACA
*
5282677 AATTAAATAAAAGGTTAG
1 AATAAAATAAAAGGTTAG
5282695 AATGTTAGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
32 2 0.05
33 25 0.58
34 16 0.37
ACGTcount: A:0.59, C:0.04, G:0.12, T:0.26
Consensus pattern (34 bp):
AATAAAATAAAAGGTTAGCAAATTAATATGAACA
Found at i:5288150 original size:18 final size:18
Alignment explanation
Indices: 5288127--5288165 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5288117 GCATTTGATA
*
5288127 CTCTGGACGAGGTTGTTC
1 CTCTGGACGAGCTTGTTC
* *
5288145 CTCTGGAGGTGCTTGTTC
1 CTCTGGACGAGCTTGTTC
5288163 CTC
1 CTC
5288166 GTGCTGCTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.26, G:0.31, T:0.36
Consensus pattern (18 bp):
CTCTGGACGAGCTTGTTC
Found at i:5295776 original size:13 final size:13
Alignment explanation
Indices: 5295758--5295782 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5295748 TCGAATATAC
5295758 TTAGAAAATCTTT
1 TTAGAAAATCTTT
5295771 TTAGAAAATCTT
1 TTAGAAAATCTT
5295783 AAAATTCGTT
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:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTAGAAAATCTTT
Found at i:5296008 original size:20 final size:23
Alignment explanation
Indices: 5295980--5296037 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 23
5295970 TTCCCCTTGA
5295980 AGTGCATCGATGCAT-TC-T-AC
1 AGTGCATCGATGCATCTCTTAAC
*
5296000 AGTGTATCGATGCATCTCTTAAC
1 AGTGCATCGATGCATCTCTTAAC
5296023 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
5296038 CTACCCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.44
21 2 0.06
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (23 bp):
AGTGCATCGATGCATCTCTTAAC
Found at i:5296116 original size:19 final size:19
Alignment explanation
Indices: 5296092--5296128 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5296082 TAAGGGGGTG
5296092 CATCGATGCACTCCTTATA
1 CATCGATGCACTCCTTATA
5296111 CATCGATGCACTCCTTAT
1 CATCGATGCACTCCTTAT
5296129 GCATATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.32, G:0.11, T:0.32
Consensus pattern (19 bp):
CATCGATGCACTCCTTATA
Found at i:5297474 original size:20 final size:19
Alignment explanation
Indices: 5297445--5297523 Score: 95
Period size: 20 Copynumber: 4.1 Consensus size: 19
5297435 ATCATATTGT
5297445 CCAGGGGTACAGATTCCCC
1 CCAGGGGTACAGATTCCCC
* *
5297464 CCATAGGGTACCGATTCCCC
1 CCA-GGGGTACAGATTCCCC
* *
5297484 CCAGGGGGATAGATTCCCC
1 CCAGGGGTACAGATTCCCC
*
5297503 CCAGGGGGTACCGATTCCCC
1 CCA-GGGGTACAGATTCCCC
5297523 C
1 C
5297524 TGTCTAACGG
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
19 18 0.37
20 31 0.63
ACGTcount: A:0.19, C:0.38, G:0.27, T:0.16
Consensus pattern (19 bp):
CCAGGGGTACAGATTCCCC
Found at i:5297499 original size:39 final size:39
Alignment explanation
Indices: 5297445--5297523 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
5297435 ATCATATTGT
* *
5297445 CCAGGGGTACAGATTCCCCCCATAGGGTACCGATTCCCC
1 CCAGGGGGACAGATTCCCCCCAGAGGGTACCGATTCCCC
* *
5297484 CCAGGGGGATAGATTCCCCCCAGGGGGTACCGATTCCCC
1 CCAGGGGGACAGATTCCCCCCAGAGGGTACCGATTCCCC
5297523 C
1 C
5297524 TGTCTAACGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.19, C:0.38, G:0.27, T:0.16
Consensus pattern (39 bp):
CCAGGGGGACAGATTCCCCCCAGAGGGTACCGATTCCCC
Found at i:5297661 original size:20 final size:20
Alignment explanation
Indices: 5297621--5297675 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
5297611 TAATTGTTTT
*
5297621 CATCCCCAAACGGCTCCAAAA
1 CATCCCC-AACGACTCCAAAA
*
5297642 CATCCCCAACGACTCTAAAA
1 CATCCCCAACGACTCCAAAA
5297662 CATCCCCAACGACT
1 CATCCCCAACGACT
5297676 ATATACGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 25 0.78
21 7 0.22
ACGTcount: A:0.36, C:0.44, G:0.07, T:0.13
Consensus pattern (20 bp):
CATCCCCAACGACTCCAAAA
Found at i:5297882 original size:21 final size:21
Alignment explanation
Indices: 5297856--5297895 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5297846 CCATTAGTGA
*
5297856 ATTTTGTTTACTTATTTTATC
1 ATTTTGTTTACTTAGTTTATC
5297877 ATTTTGTTTACTTAGTTTA
1 ATTTTGTTTACTTAGTTTA
5297896 GCCCAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.65
Consensus pattern (21 bp):
ATTTTGTTTACTTAGTTTATC
Found at i:5301026 original size:24 final size:20
Alignment explanation
Indices: 5300969--5301026 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
5300959 TTCCCCTTGA
*
5300969 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
5300989 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
5301012 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
5301027 CTACCCATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
21 1 0.03
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:5302133 original size:65 final size:65
Alignment explanation
Indices: 5302025--5302218 Score: 241
Period size: 65 Copynumber: 3.0 Consensus size: 65
5302015 AGGGATAATT
* *
5302025 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAAGGTTA
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
* * * * * *
5302090 TGTTTCAAGAGGAACTGCCTGAAGATAGAAAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTT
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGGGAAACAATCTCAAAG-GTT
*
5302155 T
65 A
* *
5302156 TGTTTCAACAA-AAATTATCTCAAGAGA-AACAAAATTTGTTTCAA-GGAAACAATCTCAAAGGT
1 TGTTTCAA-AAGAAACTGTCTCAAGAGAGAA-AAAATTTGTTTCAAGGGAAACAATCTCAAAGGT
5302218 T
64 T
5302219 TTATCAATTT
Statistics
Matches: 109, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
64 2 0.02
65 72 0.66
66 34 0.31
67 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (65 bp):
TGTTTCAAAAGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTA
Found at i:5302187 original size:21 final size:20
Alignment explanation
Indices: 5302162--5302207 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
5302152 TTTTTGTTTC
5302162 AACAAAAATTATCTCAAGAGA
1 AACAAAAATTATCTCAAG-GA
* * *
5302183 AACAAAATTTGTTTCAAGGA
1 AACAAAAATTATCTCAAGGA
5302203 AACAA
1 AACAA
5302208 TCTCAAAGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.54, C:0.13, G:0.11, T:0.22
Consensus pattern (20 bp):
AACAAAAATTATCTCAAGGA
Found at i:5302587 original size:37 final size:37
Alignment explanation
Indices: 5302468--5302596 Score: 109
Period size: 37 Copynumber: 3.5 Consensus size: 37
5302458 ATCTCAAAGG
* ** *
5302468 AAAAATGTCTCAAGCGAGACAAAA-AAAATTTTGAGA
1 AAAAATATCTCAAGCGAGACAAAATTTAATTTTAAGA
* * * * * * *
5302504 GAAATTGTCTCAAGCAAGAAAAAATTT-GTTTCAAGA
1 AAAAATATCTCAAGCGAGACAAAATTTAATTTTAAGA
* *
5302540 GAAAACTATCTCAAGCGAGACAAAATTTATTTTTAAGA
1 -AAAAATATCTCAAGCGAGACAAAATTTAATTTTAAGA
*
5302578 AAAAATATCTCTAGCGAGA
1 AAAAATATCTCAAGCGAGA
5302597 TGACACTTTG
Statistics
Matches: 72, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
36 26 0.36
37 39 0.54
38 7 0.10
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (37 bp):
AAAAATATCTCAAGCGAGACAAAATTTAATTTTAAGA
Found at i:5306454 original size:15 final size:15
Alignment explanation
Indices: 5306416--5306454 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5306406 TAAAGGGCAG
*
5306416 AAAAATAAAGTACTA
1 AAAAATAAAATACTA
**
5306431 AAATTTAAAATACTA
1 AAAAATAAAATACTA
5306446 AAAAATAAA
1 AAAAATAAA
5306455 TAAAAAAAGA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (15 bp):
AAAAATAAAATACTA
Found at i:5306622 original size:33 final size:34
Alignment explanation
Indices: 5306542--5306622 Score: 107
Period size: 33 Copynumber: 2.4 Consensus size: 34
5306532 TAATAATAAT
*
5306542 AAATAAAATAAAA-ATTAGCAAGTTAGTATGAAC
1 AAATAAAATAAAATGTTAGCAAGTTAGTATGAAC
5306575 AAATAAAATAAAATGTTAG-AATGTTAGT-TCGAAC
1 AAATAAAATAAAATGTTAGCAA-GTTAGTAT-GAAC
5306609 -AATAAAATAAAATG
1 AAATAAAATAAAATG
5306623 AATGCTAGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
33 30 0.68
34 14 0.32
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.26
Consensus pattern (34 bp):
AAATAAAATAAAATGTTAGCAAGTTAGTATGAAC
Found at i:5310300 original size:37 final size:37
Alignment explanation
Indices: 5310247--5310351 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
5310237 CATTTTCGGC
*
5310247 CTACTAGGATTCAAACTCCTAAAAATAGGATATAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
5310284 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
5310321 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
5310352 CCACAAGCAT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:5310809 original size:29 final size:29
Alignment explanation
Indices: 5310776--5310900 Score: 101
Period size: 30 Copynumber: 4.1 Consensus size: 29
5310766 TATTTAATTA
5310776 TATTTTATTTATTTATTATAATTTTTTTTC
1 TATTTTATTTATTTATTAT-ATTTTTTTTC
* * *
5310806 -ATTTTTCTTTGTTATATTATATTATTTTTC
1 TA-TTTTATTTATT-TATTATATTTTTTTTC
*
5310836 TATTATTATATATATTTA-TATTATTTTTTATC
1 TATT-TTAT-T-TATTTATTA-TATTTTTTTTC
* * *
5310868 TATGTTTACTTATTTACTATATTTTTTTAC
1 TAT-TTTATTTATTTATTATATTTTTTTTC
5310898 TAT
1 TAT
5310901 ATTTTCCTAA
Statistics
Matches: 76, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
29 1 0.01
30 38 0.50
31 15 0.20
32 18 0.24
33 4 0.05
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.68
Consensus pattern (29 bp):
TATTTTATTTATTTATTATATTTTTTTTC
Found at i:5310854 original size:24 final size:23
Alignment explanation
Indices: 5310806--5310851 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
5310796 ATTTTTTTTC
*
5310806 ATTTTTCTTTGTTATATTATATT
1 ATTTTTCTTTATTATATTATATT
5310829 ATTTTTCTATTATTATA-TATATT
1 ATTTTTCT-TTATTATATTATATT
5310852 TATATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (23 bp):
ATTTTTCTTTATTATATTATATT
Found at i:5310898 original size:13 final size:13
Alignment explanation
Indices: 5310880--5310905 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5310870 TGTTTACTTA
5310880 TTTACTATATTTT
1 TTTACTATATTTT
5310893 TTTACTATATTTT
1 TTTACTATATTTT
5310906 CCTAACGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTACTATATTTT
Found at i:5311078 original size:17 final size:16
Alignment explanation
Indices: 5311051--5311116 Score: 66
Period size: 17 Copynumber: 4.1 Consensus size: 16
5311041 TTATACATAC
5311051 ATTTTTATATTTTTATAT
1 ATTTTT-TATTTTTAT-T
5311069 ATTTTTTA-TTTTATT
1 ATTTTTTATTTTTATT
*
5311084 A--TTTTATTTATATT
1 ATTTTTTATTTTTATT
*
5311098 ATTTATTTATTTTCATT
1 ATTT-TTTATTTTTATT
5311115 AT
1 AT
5311117 GGTTTTAGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
13 5 0.12
14 7 0.17
15 2 0.05
16 7 0.17
17 14 0.34
18 6 0.15
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (16 bp):
ATTTTTTATTTTTATT
Found at i:5311090 original size:13 final size:14
Alignment explanation
Indices: 5311066--5311107 Score: 63
Period size: 13 Copynumber: 3.2 Consensus size: 14
5311056 TATATTTTTA
5311066 TATATT-TTTTATT
1 TATATTATTTTATT
5311079 T-TATTATTTTATT
1 TATATTATTTTATT
5311092 TATATTA-TTTATT
1 TATATTATTTTATT
5311105 TAT
1 TAT
5311108 TTTCATTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.15
13 18 0.67
14 5 0.19
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TATATTATTTTATT
Found at i:5311116 original size:13 final size:13
Alignment explanation
Indices: 5311054--5311107 Score: 62
Period size: 13 Copynumber: 4.4 Consensus size: 13
5311044 TACATACATT
5311054 TTTATATT-TTTA
1 TTTATATTATTTA
*
5311066 --TATATTTTTTA
1 TTTATATTATTTA
5311077 TTT-TATTATTTTA
1 TTTATATTA-TTTA
5311090 TTTATATTATTTA
1 TTTATATTATTTA
5311103 TTTAT
1 TTTAT
5311108 TTTCATTATG
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
10 6 0.17
11 4 0.11
12 4 0.11
13 17 0.47
14 5 0.14
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTATATTATTTA
Found at i:5311116 original size:26 final size:26
Alignment explanation
Indices: 5311053--5311105 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
5311043 ATACATACAT
* *
5311053 TTTTA-TATTTT-TATATATTTTTTA
1 TTTTATTATTTTATTTATATTATTTA
5311077 TTTTATTATTTTATTTATATTATTTA
1 TTTTATTATTTTATTTATATTATTTA
5311103 TTT
1 TTT
5311106 ATTTTCATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.20
25 6 0.24
26 14 0.56
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTATTATTTTATTTATATTATTTA
Found at i:5311223 original size:18 final size:19
Alignment explanation
Indices: 5311201--5311244 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5311191 TATATATATA
*
5311201 TTTTTCTTC-ATTT-ATTT
1 TTTTTATTCAATTTCATTT
5311218 TATTTTATTCAATTTCATTT
1 T-TTTTATTCAATTTCATTT
5311238 TTTTTAT
1 TTTTTAT
5311245 ATTTGTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.04
18 7 0.30
19 10 0.43
20 5 0.22
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTATTCAATTTCATTT
Found at i:5312433 original size:19 final size:19
Alignment explanation
Indices: 5312409--5312445 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
5312399 ATCTTACTAA
5312409 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
5312428 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
5312446 ATCATCTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:5318655 original size:106 final size:106
Alignment explanation
Indices: 5317485--5318654 Score: 1851
Period size: 106 Copynumber: 11.0 Consensus size: 106
5317475 ATATCGTGCC
* * * ** *
5317485 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCATA-AAACAACTTCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA-ACAAACAACTTCC
5317549 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
5317591 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
5317656 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
5317697 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTTAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
5317762 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
5317803 ACTCAAGACAACGCAAGTTCAACTACATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
5317868 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
5317909 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
5317974 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
5318015 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
5318080 AATTTCAGAGCCAATTTCAACTTCATAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
5318121 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
5318186 AATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
5318227 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
5318292 ACTTTCGGAGCCAATTTCAACTTCACA-CGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
5318332 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
5318397 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGAATATTGC
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGG-ATATTGG
* * * *
5318439 ACTCGAGACAACGTAAGTTCAACTTCAGGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
5318504 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
5318545 ACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
5318610 GATTCCAGAGCCAATTTTAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
5318651 ACTC
1 ACTC
5318655 GGAACAATGC
Statistics
Matches: 994, Mismatches: 66, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
105 102 0.10
106 794 0.80
107 98 0.10
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:5319456 original size:37 final size:37
Alignment explanation
Indices: 5319403--5319507 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
5319393 AATTTTCGTC
*
5319403 CTACTAGGATTCAAACTCCTAAAAATAGGATATAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
5319440 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
5319477 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
5319508 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:5319950 original size:23 final size:24
Alignment explanation
Indices: 5319922--5319969 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
5319912 TGTATATATA
5319922 TATTTAATTAT-ATTTTATTT-ATT
1 TATTT-ATTATAATTTTATTTCATT
*
5319945 TATTTATTATAATTTTTTTTCATT
1 TATTTATTATAATTTTATTTCATT
5319969 T
1 T
5319970 TCTTTACGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (24 bp):
TATTTATTATAATTTTATTTCATT
Found at i:5320066 original size:13 final size:13
Alignment explanation
Indices: 5320048--5320073 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5320038 TGTTTACTTA
5320048 TTTACTATATTTT
1 TTTACTATATTTT
5320061 TTTACTATATTTT
1 TTTACTATATTTT
5320074 CCTAACGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTACTATATTTT
Found at i:5320168 original size:30 final size:29
Alignment explanation
Indices: 5320134--5320217 Score: 73
Period size: 33 Copynumber: 2.7 Consensus size: 29
5320124 CTATGATTAC
5320134 TATTTTTTTAGTTAATATTATATGTA-TATT
1 TATTTTTTTA-TTAATATTATAT-TACTATT
*
5320164 TATTTTTCATTTATTTATTATTATTATTACTATT
1 TA-TTTT--TTTA-TTAATATTA-TATTACTATT
*
5320198 TATTATTTTATT-ATATTATA
1 TATTTTTTTATTAATATTATA
5320218 CATACATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
28 2 0.04
29 5 0.11
30 4 0.09
31 8 0.18
33 17 0.38
34 9 0.20
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (29 bp):
TATTTTTTTATTAATATTATATTACTATT
Found at i:5320197 original size:19 final size:17
Alignment explanation
Indices: 5320158--5320263 Score: 78
Period size: 18 Copynumber: 6.1 Consensus size: 17
5320148 ATATTATATG
*
5320158 TATATTTATT-TTTCAT
1 TATATTTATTATTTTAT
5320174 T-TATTTATTATTATTAT
1 TATATTTATTATT-TTAT
5320191 TACTATTTATTATTTTAT
1 TA-TATTTATTATTTTAT
*
5320209 TATATTATACATACATTTT-T
1 TATATT-T--AT-TATTTTAT
*
5320229 ATATTTTTATATATTTT-T
1 -TATATTTAT-TATTTTAT
5320247 TAT-TTTATTATTTTAT
1 TATATTTATTATTTTAT
5320263 T
1 T
5320264 TATACTATTT
Statistics
Matches: 76, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
15 14 0.18
16 10 0.13
17 11 0.14
18 16 0.21
19 11 0.14
20 4 0.05
21 10 0.13
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (17 bp):
TATATTTATTATTTTAT
Found at i:5320209 original size:8 final size:8
Alignment explanation
Indices: 5320177--5320263 Score: 52
Period size: 8 Copynumber: 9.8 Consensus size: 8
5320167 TTTTCATTTA
5320177 TTTATTAT
1 TTTATTAT
5320185 TATTATTACT
1 T-TTATTA-T
5320195 ATTTATTAT
1 -TTTATTAT
5320204 TTTATTAT
1 TTTATTAT
*
5320212 ATTATACATACAT
1 -TT-T--AT-TAT
5320225 TTT-TATATT
1 TTTAT-TA-T
5320234 TTTATATAT
1 TTTAT-TAT
5320243 TTT-TTAT
1 TTTATTAT
5320250 TTTATTAT
1 TTTATTAT
5320258 TTTATT
1 TTTATT
5320264 TATACTATTT
Statistics
Matches: 66, Mismatches: 2, Indels: 22
0.73 0.02 0.24
Matches are distributed among these distances:
7 6 0.09
8 23 0.35
9 17 0.26
10 12 0.18
11 2 0.03
12 4 0.06
13 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTATTAT
Found at i:5320250 original size:17 final size:16
Alignment explanation
Indices: 5320223--5320260 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 16
5320213 TTATACATAC
5320223 ATTTTTATATTTTTATAT
1 ATTTTTATA-TTTTAT-T
5320241 ATTTTT-TATTTTATT
1 ATTTTTATATTTTATT
5320256 ATTTT
1 ATTTT
5320261 ATTTATACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 6 0.30
17 2 0.10
18 6 0.30
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTTATATTTTATT
Found at i:5320262 original size:13 final size:14
Alignment explanation
Indices: 5320173--5320279 Score: 57
Period size: 13 Copynumber: 7.6 Consensus size: 14
5320163 TTATTTTTCA
5320173 TTTATTTATTATTAT
1 TTTATTTA-TATTAT
5320188 TATTACTATT-TATTAT
1 T-TTA-T-TTATATTAT
5320204 TTTA-TTATATTAT
1 TTTATTTATATTAT
** *
5320217 ACATACATTTTTA-TAT
1 ---TTTATTTATATTAT
*
5320233 TTT-TATATATT-T
1 TTTATTTATATTAT
5320245 TTTATTT-TATTAT
1 TTTATTTATATTAT
*
5320258 TTTATTTATACTA-
1 TTTATTTATATTAT
5320271 TTTATTTAT
1 TTTATTTAT
5320280 TTTCATTATG
Statistics
Matches: 71, Mismatches: 9, Indels: 26
0.67 0.08 0.25
Matches are distributed among these distances:
12 14 0.20
13 27 0.38
14 4 0.06
15 4 0.06
16 15 0.21
17 5 0.07
18 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTTATATTAT
Found at i:5324008 original size:21 final size:21
Alignment explanation
Indices: 5323982--5324046 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
5323972 AAGACAATCA
*
5323982 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
5324003 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
5324024 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
5324045 AG
1 AG
5324047 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:5324122 original size:33 final size:33
Alignment explanation
Indices: 5324080--5324143 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
5324070 AAATAGATGG
*
5324080 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTAA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTAA
*
5324113 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGT
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGT
5324144 GATCTTAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.45, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTAA
Found at i:5324415 original size:33 final size:33
Alignment explanation
Indices: 5324332--5324416 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 33
5324322 AAAATATGAA
5324332 GAAGAAAAGAGGGAGGA-G--GAAGAAGAGATG
1 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
5324362 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
1 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
*
5324395 GAAGAAATGA-GGAGGAAGGAAG
1 GAAGAAAAGAGGGAGG-AGGAAG
5324417 TCGATGTCAT
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
30 17 0.34
31 1 0.02
32 5 0.10
33 27 0.54
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.04
Consensus pattern (33 bp):
GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
Found at i:5325379 original size:4 final size:4
Alignment explanation
Indices: 5325370--5325398 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
5325360 TAAGAGATTG
5325370 GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
5325399 AAAGGACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:5326109 original size:184 final size:184
Alignment explanation
Indices: 5325796--5326513 Score: 1294
Period size: 184 Copynumber: 3.9 Consensus size: 184
5325786 ATATCATCAT
* *
5325796 AAAGTGTCGATACCTTTTTAAAAAGTGTCGATTGAAAAAATATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
*
5325861 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGATTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
**
5325926 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTGTAGAATGGATGAAA
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
*
5325980 AAAATGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
* *
5326045 ATAGGTAATTTTGTAATATAACTGGTATAGATATACCGGTTTTGTGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
5326110 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
5326164 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
* * *
5326229 ATAGGTAATTTTGTAATATAACCGATATAGATATACTGGTTTTATGAGAGAATAAGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
*
5326294 TATATCGACACTTTTTAATATTGTGTCACTACTTTATGTCCAGAATGGATGAAA
131 TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
*
5326348 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCAGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
*
5326413 ATAGGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
5326478 TATATCGACACTTTTTAATATTGTGTC-CATACTTTA
131 TATATCGACACTTTTTAATATTGTGTCGC-TACTTTA
5326514 AGTAACGCGG
Statistics
Matches: 513, Mismatches: 20, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
183 1 0.00
184 512 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (184 bp):
AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGGTCTACAACC
TATATCGACACTTTTTAATATTGTGTCGCTACTTTATGTCCAGAATGGATGAAA
Found at i:5330130 original size:87 final size:86
Alignment explanation
Indices: 5330026--5330192 Score: 253
Period size: 87 Copynumber: 1.9 Consensus size: 86
5330016 AAATAGGTCA
* *
5330026 ATATAAGTGCTACCTATTACATTATATAAGTGCTACCTAATATGTTATTGTACTTAATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
*
5330091 CCGGTTAAATACATATTTTATT
66 CCGATTAAATA-ATATTTTATT
* * * *
5330113 ATATAAGCGCTATCTATTACATTATATAAGCGTTATCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
*
5330178 TCGATTAAATAATAT
66 CCGATTAAATAATAT
5330193 AACATAACCG
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
86 4 0.06
87 68 0.94
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (86 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
CCGATTAAATAATATTTTATT
Found at i:5330160 original size:23 final size:23
Alignment explanation
Indices: 5330110--5330154 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5330100 TACATATTTT
*
5330110 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTATCTAATAC
*
5330133 ATTATATAAGCGTTATCTAATA
1 ATTATATAAGCGCTATCTAATA
5330155 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (23 bp):
ATTATATAAGCGCTATCTAATAC
Found at i:5333447 original size:16 final size:16
Alignment explanation
Indices: 5333423--5333459 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
5333413 AATCATAAAT
5333423 ATTAT-TAATATTCTA
1 ATTATATAATATTCTA
5333438 ATTATATAATATTCTA
1 ATTATATAATATTCTA
5333454 ATTATA
1 ATTATA
5333460 AAAATGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTATATAATATTCTA
Found at i:5333472 original size:19 final size:18
Alignment explanation
Indices: 5333432--5333487 Score: 71
Period size: 19 Copynumber: 3.2 Consensus size: 18
5333422 TATTATTAAT
*
5333432 ATTCTAATTAT-ATAAT-
1 ATTCTAATTATAAAAATA
5333448 ATTCTAATTATAAAAATGA
1 ATTCTAATTATAAAAAT-A
*
5333467 ATTCTAATAATAAAAATA
1 ATTCTAATTATAAAAATA
5333485 ATT
1 ATT
5333488 ATAAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 11 0.31
17 4 0.11
18 4 0.11
19 16 0.46
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (18 bp):
ATTCTAATTATAAAAATA
Found at i:5339605 original size:19 final size:19
Alignment explanation
Indices: 5339569--5339605 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5339559 ATGACCAACA
* *
5339569 AAATCGCAATGCGGTCTCT
1 AAATCGCAACGCGATCTCT
5339588 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
5339606 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:5339702 original size:21 final size:21
Alignment explanation
Indices: 5339679--5339787 Score: 78
Period size: 21 Copynumber: 5.3 Consensus size: 21
5339669 AATTAGCGTT
* *
5339679 GCGATTTTAGAAAATCGCAAT
1 GCGATTATAGAAAATCGCAAC
* *
5339700 GCGAATAT-GTAAATCGCAAC
1 GCGATTATAGAAAATCGCAAC
* * *
5339720 GCGATAATACATAATCGCAAC
1 GCGATTATAGAAAATCGCAAC
* **
5339741 GCGATTCT-GACTATCGCAAC
1 GCGATTATAGAAAATCGCAAC
* * * *
5339761 GCGATAATACATAATCGCAAT
1 GCGATTATAGAAAATCGCAAC
5339782 GCGATT
1 GCGATT
5339788 TTCAAAGCGA
Statistics
Matches: 65, Mismatches: 21, Indels: 4
0.72 0.23 0.04
Matches are distributed among these distances:
20 31 0.48
21 34 0.52
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (21 bp):
GCGATTATAGAAAATCGCAAC
Found at i:5339736 original size:41 final size:41
Alignment explanation
Indices: 5339691--5339785 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
5339681 GATTTTAGAA
5339691 AATCGCAATGCGAATATGTA-AATCGCAACGCGATAATACAT
1 AATCGCAATGCGAATATG-ACAATCGCAACGCGATAATACAT
* * * *
5339732 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
1 AATCGCAATGCGAATATGACAATCGCAACGCGATAATACAT
5339773 AATCGCAATGCGA
1 AATCGCAATGCGA
5339786 TTTTCAAAGC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 1 0.02
41 47 0.98
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (41 bp):
AATCGCAATGCGAATATGACAATCGCAACGCGATAATACAT
Found at i:5339969 original size:22 final size:21
Alignment explanation
Indices: 5339919--5339971 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
5339909 TCACTCTCTA
*
5339919 CGGCGACATCCTCCCCATCTC
1 CGGCGAAATCCTCCCCATCTC
**
5339940 CGATGAAATCCGTCCCCATCTC
1 CGGCGAAATCC-TCCCCATCTC
5339962 CGGCGAAATC
1 CGGCGAAATC
5339972 TGTCGATCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.21, C:0.43, G:0.17, T:0.19
Consensus pattern (21 bp):
CGGCGAAATCCTCCCCATCTC
Found at i:5340255 original size:21 final size:22
Alignment explanation
Indices: 5340205--5340257 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
5340195 TCACTCTCTA
*
5340205 CGGCGACATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
**
5340227 CGATGAAATCCGT-CCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
5340248 CGGCGAAATC
1 CGGCGAAATC
5340258 TGTCTATCCT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.21, C:0.42, G:0.19, T:0.19
Consensus pattern (22 bp):
CGGCGAAATCCGTCCCCATCTC
Found at i:5340763 original size:40 final size:39
Alignment explanation
Indices: 5340641--5340789 Score: 139
Period size: 40 Copynumber: 3.9 Consensus size: 39
5340631 AATAGTCAAA
*
5340641 TTCGCGTTACGATAGTCATTTTCGTGTTGCGATTTTCAT
1 TTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCAT
* * * ** *
5340680 TTCGGGTTGCGAT--T-A-TCTC--ATTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTC-AT
5340714 TTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCA-T
* ** *
5340754 TTCGTGTTGCGATTTTCATTATCGTGTTGCGATTTT
1 TTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTT
5340790 AAGTTTCAGA
Statistics
Matches: 85, Mismatches: 17, Indels: 15
0.73 0.15 0.13
Matches are distributed among these distances:
33 9 0.11
34 13 0.15
35 3 0.04
36 2 0.02
37 2 0.02
38 3 0.04
39 12 0.14
40 41 0.48
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (39 bp):
TTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCAT
Found at i:5340787 original size:20 final size:20
Alignment explanation
Indices: 5340656--5340789 Score: 120
Period size: 20 Copynumber: 7.0 Consensus size: 20
5340646 GTTACGATAG
5340656 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
*
5340676 TCA-TTTCGGGTTGCGA--T
1 TCATTTTCGTGTTGCGATTT
* * **
5340693 T-A-TCTC--ATTGCGATAG
1 TCATTTTCGTGTTGCGATTT
** * **
5340709 TCAAATTCGCGTTGCGATAG
1 TCATTTTCGTGTTGCGATTT
5340729 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
5340749 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
*
5340769 TCATTATCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
5340789 T
1 T
5340790 AAGTTTCAGA
Statistics
Matches: 95, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
14 6 0.06
16 5 0.05
17 3 0.03
18 2 0.02
19 12 0.13
20 67 0.71
ACGTcount: A:0.15, C:0.16, G:0.22, T:0.47
Consensus pattern (20 bp):
TCATTTTCGTGTTGCGATTT
Found at i:5342735 original size:20 final size:20
Alignment explanation
Indices: 5342710--5342775 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
5342700 CTTAAAAATT
5342710 GCAACGCGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
*
5342730 GCAACGCGGAAATGACTATC
1 GCAACGCGAAAATGACTATC
**
5342750 GCAACGCGAATTTGACTATC
1 GCAACGCGAAAATGACTATC
5342770 GCAACG
1 GCAACG
5342776 GGATAATCGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.17
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:5342817 original size:33 final size:34
Alignment explanation
Indices: 5342767--5342840 Score: 114
Period size: 33 Copynumber: 2.2 Consensus size: 34
5342757 GAATTTGACT
* *
5342767 ATCGCAACGGGATAATCGCAATGCG-AAATAAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
*
5342800 ATCGCAACGAGAAAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
5342834 ATCGCAA
1 ATCGCAA
5342841 TGTGAATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 23 0.62
34 14 0.38
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (34 bp):
ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
Found at i:5342833 original size:20 final size:19
Alignment explanation
Indices: 5342780--5342842 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
5342770 GCAACGGGAT
*
5342780 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAA
5342799 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
5342813 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
5342833 AATCGCAATG
1 AATCGCAATG
5342843 TGAATTTAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
14 10 0.27
15 1 0.03
16 2 0.05
17 2 0.05
19 9 0.24
20 13 0.35
ACGTcount: A:0.49, C:0.17, G:0.19, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:5342874 original size:19 final size:20
Alignment explanation
Indices: 5342847--5342884 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5342837 GCAATGTGAA
*
5342847 TTTAGTTTCGCGTTGCGATT
1 TTTAGTTTCGCATTGCGATT
5342867 TTTA-TTTCGCATTGCGAT
1 TTTAGTTTCGCATTGCGAT
5342885 AGTCAAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
TTTAGTTTCGCATTGCGATT
Found at i:5343478 original size:21 final size:22
Alignment explanation
Indices: 5343451--5343512 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
5343441 TCTCCTATCG
5343451 TTCAAGAGGCCCCTATCATCCC
1 TTCAAGAGGCCCCTATCATCCC
* ** *
5343473 TT-AAGAGTCCCCTCCCA-CCG
1 TTCAAGAGGCCCCTATCATCCC
*
5343493 TTCAAGAGGCCCCTGTCATC
1 TTCAAGAGGCCCCTATCATC
5343513 ATTGAAGAGG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 4 0.13
21 24 0.77
22 3 0.10
ACGTcount: A:0.21, C:0.40, G:0.16, T:0.23
Consensus pattern (22 bp):
TTCAAGAGGCCCCTATCATCCC
Found at i:5343495 original size:42 final size:42
Alignment explanation
Indices: 5343449--5343542 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 42
5343439 CCTCTCCTAT
*
5343449 CGTTCAAGAGGCCCCTATCATCCCTT-AAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCAT-CATTGAAGAGGT-CCCTCCCAC
* *
5343491 CGTTCAAGAGGCCCCTGTCATCATTGAAGAGGTTCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCATTGAAGAGGTCCCTCCCAC
*
5343533 CATTCAAGAG
1 CGTTCAAGAG
5343543 CCTGATTCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
41 3 0.07
42 41 0.89
43 2 0.04
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTATCATCATTGAAGAGGTCCCTCCCAC
Found at i:5344818 original size:36 final size:35
Alignment explanation
Indices: 5344771--5344896 Score: 108
Period size: 36 Copynumber: 3.4 Consensus size: 35
5344761 AAAAGTTGAT
5344771 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTGC
1 TTGTTTAATTGATGTGTAAATAATT-TTATTTGTGC
* * *** *
5344807 TTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAGTTGAT
1 TTGTTTAATTGATGTGT-AAA--TAATTT-TATTTG-TG-C
*
5344848 TTGTTTAATTGATGTGTAAATAATTTTTATTTGTTC
1 TTGTTTAATTGATGTGTAAATAA-TTTTATTTGTGC
*
5344884 TTATTTAATTGAT
1 TTGTTTAATTGAT
5344897 TGAAATGTAA
Statistics
Matches: 69, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
36 28 0.41
37 4 0.06
38 6 0.09
39 10 0.14
40 5 0.07
41 16 0.23
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.54
Consensus pattern (35 bp):
TTGTTTAATTGATGTGTAAATAATTTTATTTGTGC
Found at i:5344834 original size:14 final size:14
Alignment explanation
Indices: 5344815--5344851 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
5344805 GCTTGTTTAA
5344815 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
5344829 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
5344843 TTGATTTGT
1 TTGATTTGT
5344852 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:5344879 original size:77 final size:78
Alignment explanation
Indices: 5344752--5344918 Score: 273
Period size: 77 Copynumber: 2.1 Consensus size: 78
5344742 GCTTGTTTAA
*
5344752 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGCTTGTTTAATT
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGCTTATTTAATT
5344817 GATT-TGTAAAAG
66 GATTATGTAAAAG
* *
5344829 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTTTTATTTGTTCTTATTTAATT
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGCTTATTTAATT
5344894 GATTGAAATGTAAAAG
66 GATT---ATGTAAAAG
5344910 TTGATTTGT
1 TTGATTTGT
5344919 TGATTTCAAT
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
77 66 0.80
81 17 0.20
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.51
Consensus pattern (78 bp):
TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGCTTATTTAATT
GATTATGTAAAAG
Found at i:5344995 original size:19 final size:20
Alignment explanation
Indices: 5344971--5345047 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
5344961 AGGTACACTT
*
5344971 TCGCAACGCTAAACTC-AAA
1 TCGCAACGCGAAACTCAAAA
* *
5344990 TCGCAATGCGAAAGTCAAAA
1 TCGCAACGCGAAACTCAAAA
*
5345010 TCGCAATGCGAAAGC-CAAAA
1 TCGCAACGCGAAA-CTCAAAA
*
5345030 TCGCAACGCGAAAGTCAA
1 TCGCAACGCGAAACTCAA
5345048 TTCCCGTTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 13 0.27
20 36 0.73
ACGTcount: A:0.43, C:0.26, G:0.18, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:5345012 original size:20 final size:20
Alignment explanation
Indices: 5344987--5345047 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
5344977 CGCTAAACTC
5344987 AAATCGCAATGCGAAAGTCA
1 AAATCGCAATGCGAAAGTCA
*
5345007 AAATCGCAATGCGAAAGCCA
1 AAATCGCAATGCGAAAGTCA
*
5345027 AAATCGCAACGCGAAAGTCA
1 AAATCGCAATGCGAAAGTCA
5345047 A
1 A
5345048 TTCCCGTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (20 bp):
AAATCGCAATGCGAAAGTCA
Found at i:5345120 original size:20 final size:20
Alignment explanation
Indices: 5345086--5345330 Score: 262
Period size: 20 Copynumber: 12.8 Consensus size: 20
5345076 GCAATTTTCT
*
5345086 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCA
** *
5345106 CGTTGTAATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
5345126 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
5345146 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
**
5345166 CGTTGCGAT--T----TTGG
1 CGTTGCGATAGTCAAATTCA
* *
5345180 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCA
*
5345200 CGTTGCGATAGTCAAATTTA
1 CGTTGCGATAGTCAAATTCA
* *
5345220 CGTTGCGAT--T---TTTGA
1 CGTTGCGATAGTCAAATTCA
*
5345235 -GTTACGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
5345254 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
5345274 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
*
5345294 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
*
5345314 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
5345331 GAATGTGTAA
Statistics
Matches: 190, Mismatches: 23, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
14 18 0.09
15 3 0.02
16 2 0.01
18 2 0.01
19 3 0.02
20 162 0.85
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Done.