Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 31 of 190
Found at i:5384220 original size:16 final size:15
Alignment explanation
Indices: 5384176--5384235 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 15
5384166 TTTCCACCCA
*
5384176 TTCATTTCTTTCTTCT
1 TTCATTT-TTTTTTCT
*
5384192 TTTATTCTTTTTTTCCT
1 TTCATT-TTTTTTT-CT
*
5384209 TTCATTTTTTTTTTT
1 TTCATTTTTTTTTCT
5384224 TTGCATTTTTTT
1 TT-CATTTTTTT
5384236 ACTGAGTGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
15 3 0.08
16 26 0.70
17 8 0.22
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.77
Consensus pattern (15 bp):
TTCATTTTTTTTTCT
Found at i:5391313 original size:13 final size:13
Alignment explanation
Indices: 5391295--5391320 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5391285 TCACACGTGT
5391295 CCTTAGGATTTTA
1 CCTTAGGATTTTA
5391308 CCTTAGGATTTTA
1 CCTTAGGATTTTA
5391321 AGGATGTTTT
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:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
CCTTAGGATTTTA
Found at i:5391460 original size:14 final size:14
Alignment explanation
Indices: 5391437--5391539 Score: 73
Period size: 14 Copynumber: 7.1 Consensus size: 14
5391427 GTATAAAAGG
5391437 TTTAGGGTTTTGAT
1 TTTAGGGTTTTGAT
* *
5391451 TTTAGAGTTTGAAGAT
1 TTTAGGGTTT--TGAT
*
5391467 TTTAGGGTTTCGAT
1 TTTAGGGTTTTGAT
** *
5391481 TTTA-AATTTTGAGG
1 TTTAGGGTTTTGA-T
*
5391495 TTTGGGGTTTTGAT
1 TTTAGGGTTTTGAT
* *
5391509 TTAAGGGTTTGGAT
1 TTTAGGGTTTTGAT
*
5391523 TTTAGGGGTTTGGAT
1 TTTA-GGGTTTTGAT
5391538 TT
1 TT
5391540 AAGAGTTTAA
Statistics
Matches: 68, Mismatches: 16, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
13 5 0.07
14 33 0.49
15 18 0.26
16 12 0.18
ACGTcount: A:0.18, C:0.01, G:0.30, T:0.50
Consensus pattern (14 bp):
TTTAGGGTTTTGAT
Found at i:5391586 original size:17 final size:17
Alignment explanation
Indices: 5391573--5391677 Score: 105
Period size: 17 Copynumber: 6.5 Consensus size: 17
5391563 CGGATTTTGG
5391573 GGGGTTTTGGATTTT-A
1 GGGGTTTTGGATTTTAA
*
5391589 GGGGGTTTGGA-TTTAA
1 GGGGTTTTGGATTTTAA
* *
5391605 GGGATTTTGGATTTTTA
1 GGGGTTTTGGATTTTAA
**
5391622 GGGGTTTCAGATTTT-A
1 GGGGTTTTGGATTTTAA
*
5391638 -GGATTTTGGATTTT-A
1 GGGGTTTTGGATTTTAA
5391653 GGGGATTTTGGATTTT-A
1 GGGG-TTTTGGATTTTAA
5391670 GGGGTTTT
1 GGGGTTTT
5391678 AGAAACCTAG
Statistics
Matches: 74, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
15 15 0.20
16 27 0.36
17 32 0.43
ACGTcount: A:0.16, C:0.01, G:0.35, T:0.48
Consensus pattern (17 bp):
GGGGTTTTGGATTTTAA
Found at i:5391614 original size:32 final size:32
Alignment explanation
Indices: 5391577--5391677 Score: 125
Period size: 32 Copynumber: 3.1 Consensus size: 32
5391567 TTTTGGGGGG
*
5391577 TTTTGGATTTTAGGGGGTTTGGATTTAAGGGA
1 TTTTGGATTTTAGGGGGTTTGGATTTTAGGGA
*
5391609 TTTTGGATTTTTA-GGGGTTTCAGATTTTA-GGA
1 TTTTGGA-TTTTAGGGGGTTT-GGATTTTAGGGA
* *
5391641 TTTTGGATTTTAGGGGATTTTGGATTTTAGGGG
1 TTTTGGATTTTAGGGG-GTTTGGATTTTAGGGA
5391674 TTTT
1 TTTT
5391678 AGAAACCTAG
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
31 5 0.08
32 34 0.58
33 20 0.34
ACGTcount: A:0.17, C:0.01, G:0.33, T:0.50
Consensus pattern (32 bp):
TTTTGGATTTTAGGGGGTTTGGATTTTAGGGA
Found at i:5391617 original size:49 final size:48
Alignment explanation
Indices: 5391558--5391680 Score: 149
Period size: 49 Copynumber: 2.5 Consensus size: 48
5391548 AAAGGTTTGA
* * * *
5391558 GATTTCGGATTTTGGGGGGTTTTGGATTTTAGGGGGTTTGGA-TTTAAGG
1 GATTTTGGATTTT-AGGGGTTTTAGATTTTA-GGAGTTTGGATTTTAAGG
* * *
5391607 GATTTTGGATTTTTAGGGGTTTCAGATTTTAGGATTTTGGATTTTAGGG
1 GATTTTGGA-TTTTAGGGGTTTTAGATTTTAGGAGTTTGGATTTTAAGG
5391656 GATTTTGGATTTTAGGGGTTTTAGA
1 GATTTTGGATTTTAGGGGTTTTAGA
5391681 AACCTAGGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
48 23 0.36
49 37 0.58
50 4 0.06
ACGTcount: A:0.17, C:0.02, G:0.35, T:0.46
Consensus pattern (48 bp):
GATTTTGGATTTTAGGGGTTTTAGATTTTAGGAGTTTGGATTTTAAGG
Found at i:5391650 original size:7 final size:8
Alignment explanation
Indices: 5391631--5391671 Score: 50
Period size: 7 Copynumber: 5.1 Consensus size: 8
5391621 AGGGGTTTCA
5391631 GATTTTAG
1 GATTTTAG
5391639 GATTTT-G
1 GATTTTAG
5391646 GATTTTAGGG
1 GATTTTA--G
5391656 GATTTT-G
1 GATTTTAG
5391663 GATTTTAG
1 GATTTTAG
5391671 G
1 G
5391672 GGTTTTAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
7 14 0.48
8 8 0.28
10 7 0.24
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.49
Consensus pattern (8 bp):
GATTTTAG
Found at i:5393215 original size:17 final size:17
Alignment explanation
Indices: 5393193--5393227 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5393183 TATTATTGTT
*
5393193 ATTATTATTTTTAAAAA
1 ATTATTATTATTAAAAA
5393210 ATTATTATTATTAAAAA
1 ATTATTATTATTAAAAA
5393227 A
1 A
5393228 ATATAGACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTATTATTATTAAAAA
Found at i:5395044 original size:18 final size:18
Alignment explanation
Indices: 5395018--5395054 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5395008 TAAAAGGAGG
*
5395018 TGATATACAGGAAAAACT
1 TGATATACAAGAAAAACT
*
5395036 TGATGTACAAGAAAAACT
1 TGATATACAAGAAAAACT
5395054 T
1 T
5395055 TTCCTAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (18 bp):
TGATATACAAGAAAAACT
Found at i:5395592 original size:13 final size:13
Alignment explanation
Indices: 5395570--5395603 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
5395560 TAGATAATTT
5395570 AATAATTTTTA-A
1 AATAATTTTTATA
5395582 AATATATTTTTATA
1 AATA-ATTTTTATA
5395596 AATAATTT
1 AATAATTT
5395604 AAAATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 11 0.55
14 5 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATAATTTTTATA
Found at i:5400944 original size:16 final size:16
Alignment explanation
Indices: 5400923--5400957 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5400913 ATAATATCCC
5400923 TAACATCTTTTATACT
1 TAACATCTTTTATACT
*
5400939 TAACATCTTTTGTACT
1 TAACATCTTTTATACT
5400955 TAA
1 TAA
5400958 TAGAAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.03, T:0.49
Consensus pattern (16 bp):
TAACATCTTTTATACT
Found at i:5404673 original size:3 final size:3
Alignment explanation
Indices: 5404665--5404691 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5404655 TAATCAATAT
5404665 AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC
5404692 TAAACCTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:5409137 original size:24 final size:24
Alignment explanation
Indices: 5409105--5409152 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5409095 AATATATATT
*
5409105 TTATTATTATAATATTTAATTTTA
1 TTATAATTATAATATTTAATTTTA
* *
5409129 TTATAATTATTATTTTTAATTTTA
1 TTATAATTATAATATTTAATTTTA
5409153 CATAAATCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTATAATTATAATATTTAATTTTA
Found at i:5409729 original size:24 final size:20
Alignment explanation
Indices: 5409668--5409717 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
5409658 CATGATATAA
* *
5409668 ATATTAATTTTATTAATATG
1 ATATTGATTTTACTAATATG
5409688 ATATTGATTTTACTAATATG
1 ATATTGATTTTACTAATATG
5409708 ATATTGATTT
1 ATATTGATTT
5409718 GTTAACATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (20 bp):
ATATTGATTTTACTAATATG
Found at i:5409873 original size:27 final size:28
Alignment explanation
Indices: 5409822--5409876 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
5409812 TACGAAATTT
* *
5409822 AAAATTTAGTTATTTTAATATAAAAATA
1 AAAATTTAATTATTTCAATATAAAAATA
*
5409850 AAAATTTAATTCTTTCAATA-AAAAATA
1 AAAATTTAATTATTTCAATATAAAAATA
5409877 CAGTTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (28 bp):
AAAATTTAATTATTTCAATATAAAAATA
Found at i:5410026 original size:28 final size:27
Alignment explanation
Indices: 5409995--5410047 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
5409985 GTATTTAGAA
5409995 ATTTAGAAAATTTTTAGAAAATTTTAAT
1 ATTTAGAAAATTTTTAG-AAATTTTAAT
* **
5410023 ATTTTGAATTTTTTTAGAAATTTTA
1 ATTTAGAAAATTTTTAGAAATTTTA
5410048 TAATTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.53
Consensus pattern (27 bp):
ATTTAGAAAATTTTTAGAAATTTTAAT
Found at i:5410061 original size:18 final size:18
Alignment explanation
Indices: 5410032--5410070 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5410022 TATTTTGAAT
*
5410032 TTTTTTAGAAATTTTATAA
1 TTTTTTAGAAATATTA-AA
5410051 TTTTTTA-AAATATTAAA
1 TTTTTTAGAAATATTAAA
5410068 TTT
1 TTT
5410071 AATATTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 7 0.37
19 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTTTAGAAATATTAAA
Found at i:5410094 original size:16 final size:17
Alignment explanation
Indices: 5410015--5410099 Score: 52
Period size: 19 Copynumber: 5.1 Consensus size: 17
5410005 TTTTTAGAAA
*
5410015 ATTTTAATATTTTGAATT
1 ATTTTAATATTTT-AAAT
* *
5410033 TTTTTAGAAATTTTATAAT
1 ATTTTA-ATATTTTA-AAT
* * *
5410052 TTTTTAAAATATT-AA-
1 ATTTTAATATTTTAAAT
*
5410067 A-TTTAATATTTTCAAT
1 ATTTTAATATTTTAAAT
5410083 ATTTTAAT-TTTTAAAT
1 ATTTTAATATTTTAAAT
5410099 A
1 A
5410100 AAAATTATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
14 9 0.17
15 2 0.04
16 11 0.20
17 6 0.11
18 12 0.22
19 14 0.26
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (17 bp):
ATTTTAATATTTTAAAT
Found at i:5410177 original size:18 final size:20
Alignment explanation
Indices: 5410140--5410180 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
5410130 AAAATTTAAC
5410140 AATTTATTTAATGAAAAATTT
1 AATTTATTTAAT-AAAAATTT
*
5410161 AATTT-TTTAATAAAATTTT
1 AATTTATTTAATAAAAATTT
5410180 A
1 A
5410181 TATATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 6 0.32
21 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AATTTATTTAATAAAAATTT
Found at i:5410188 original size:20 final size:20
Alignment explanation
Indices: 5410146--5410188 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
5410136 TAACAATTTA
*
5410146 TTTAATGAAAAATTTAATTT
1 TTTAATGAAAAATTTAATAT
*
5410166 TTTAAT-AAAATTTTATATAT
1 TTTAATGAAAAATTTA-ATAT
5410186 TTT
1 TTT
5410189 TTAATTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTAATGAAAAATTTAATAT
Found at i:5410195 original size:35 final size:35
Alignment explanation
Indices: 5410165--5410234 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
5410155 AAATTTAATT
5410165 TTTTAATAAAATTT-TATATAT-TTTTTAATTTTTCA
1 TTTTAA-AAAATTTGTATATATATTTTTAATTTTT-A
* *
5410200 TTTTAAAAAATTTGTCTATATATTTTTAATATTTA
1 TTTTAAAAAATTTGTATATATATTTTTAATTTTTA
5410235 AATAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 7 0.23
35 13 0.42
36 11 0.35
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (35 bp):
TTTTAAAAAATTTGTATATATATTTTTAATTTTTA
Found at i:5410576 original size:18 final size:18
Alignment explanation
Indices: 5410553--5410595 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5410543 TTGTTTAAAT
* * *
5410553 AAAAATATTAAATTTTGA
1 AAAAATATAAAACTTTCA
5410571 AAAAATATAAAACTTTCA
1 AAAAATATAAAACTTTCA
5410589 AAAAATA
1 AAAAATA
5410596 ATATTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAAATATAAAACTTTCA
Found at i:5413082 original size:2 final size:2
Alignment explanation
Indices: 5413075--5413114 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5413065 CAAAGTTATT
5413075 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5413115 GTTGCATTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5413183 original size:2 final size:2
Alignment explanation
Indices: 5413176--5413215 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5413166 ATATTGACTT
5413176 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5413216 GTTGCATTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5413248 original size:101 final size:101
Alignment explanation
Indices: 5413073--5413277 Score: 410
Period size: 101 Copynumber: 2.0 Consensus size: 101
5413063 TACAAAGTTA
5413073 TTTATATATATATATATATATATATATATATATATATATATAGTTGCATTTCATGGTCTAAGAGA
1 TTTATATATATATATATATATATATATATATATATATATATAGTTGCATTTCATGGTCTAAGAGA
5413138 AGTCAAAACTGGCAAGGTATCCTCATCTATATTGAC
66 AGTCAAAACTGGCAAGGTATCCTCATCTATATTGAC
5413174 TTTATATATATATATATATATATATATATATATATATATATAGTTGCATTTCATGGTCTAAGAGA
1 TTTATATATATATATATATATATATATATATATATATATATAGTTGCATTTCATGGTCTAAGAGA
5413239 AGTCAAAACTGGCAAGGTATCCTCATCTATATTGAC
66 AGTCAAAACTGGCAAGGTATCCTCATCTATATTGAC
5413275 TTT
1 TTT
5413278 CTTCTGGTTT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 104 1.00
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (101 bp):
TTTATATATATATATATATATATATATATATATATATATATAGTTGCATTTCATGGTCTAAGAGA
AGTCAAAACTGGCAAGGTATCCTCATCTATATTGAC
Found at i:5413889 original size:14 final size:14
Alignment explanation
Indices: 5413870--5413898 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5413860 GTGCTGCTAG
5413870 AAATCTATTTTGTT
1 AAATCTATTTTGTT
5413884 AAATCTATTTTGTT
1 AAATCTATTTTGTT
5413898 A
1 A
5413899 TACTTGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (14 bp):
AAATCTATTTTGTT
Found at i:5421212 original size:5 final size:5
Alignment explanation
Indices: 5421202--5421232 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
5421192 TCTAGGCTGG
*
5421202 GGGCA GGGCA GGGCA GGGCA AGGCA GGGCA G
1 GGGCA GGGCA GGGCA GGGCA GGGCA GGGCA G
5421233 ATCGTAACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.19, G:0.58, T:0.00
Consensus pattern (5 bp):
GGGCA
Found at i:5425936 original size:17 final size:17
Alignment explanation
Indices: 5425912--5425951 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
5425902 GTTAGTAATA
5425912 CAAAAAAACT-ATAATCTC
1 CAAAAAAA-TGATAAT-TC
5425930 CAAAAAAATGATAATTC
1 CAAAAAAATGATAATTC
5425947 CAAAA
1 CAAAA
5425952 TTCATATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.60, C:0.17, G:0.03, T:0.20
Consensus pattern (17 bp):
CAAAAAAATGATAATTC
Found at i:5427358 original size:17 final size:17
Alignment explanation
Indices: 5427334--5427378 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
5427324 ATTTTAATTT
5427334 AACA-TAATATTTATAA
1 AACATTAATATTTATAA
* *
5427350 AACATTAATTTTTATAT
1 AACATTAATATTTATAA
5427367 AA-ATT-ATATTTA
1 AACATTAATATTTA
5427379 ATTATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 6 0.24
16 7 0.28
17 12 0.48
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (17 bp):
AACATTAATATTTATAA
Found at i:5427452 original size:6 final size:6
Alignment explanation
Indices: 5427433--5427479 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
5427423 TAAATTTATT
*
5427433 AATATA ATATATA AATATA AATAT- AA-ATA AATAATA AATATA TATAT
1 AATATA A-ATATA AATATA AATATA AATATA AAT-ATA AATATA AATAT
5427480 CTTGAGATAG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
4 2 0.06
5 4 0.11
6 18 0.50
7 12 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
AATATA
Found at i:5427469 original size:23 final size:25
Alignment explanation
Indices: 5427433--5427479 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
5427423 TAAATTTATT
5427433 AATATAATATATAAATATAAATATA
1 AATATAATATATAAATATAAATATA
*
5427458 AATA-AATA-ATAAATATATATAT
1 AATATAATATATAAATATAAATAT
5427480 CTTGAGATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.62
24 4 0.19
25 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
AATATAATATATAAATATAAATATA
Found at i:5432793 original size:13 final size:13
Alignment explanation
Indices: 5432775--5432801 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5432765 ATTGTGATTG
5432775 AAAAAAAAATTAT
1 AAAAAAAAATTAT
5432788 AAAAAAAAATTAT
1 AAAAAAAAATTAT
5432801 A
1 A
5432802 CTGAATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAAAAAAATTAT
Found at i:5433064 original size:23 final size:23
Alignment explanation
Indices: 5433021--5433080 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
5433011 TTTAATTATT
* *
5433021 TAAAA-TTAAATATAAATATAAA
1 TAAAATTTAAATAAAAAGATAAA
*
5433043 TAAAATTTAATTAAAAAGATAAA
1 TAAAATTTAAATAAAAAGATAAA
*
5433066 -AATAATTTGAATAAA
1 TAA-AATTTAAATAAA
5433081 TTTCAACCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 7 0.23
23 24 0.77
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (23 bp):
TAAAATTTAAATAAAAAGATAAA
Found at i:5433640 original size:23 final size:21
Alignment explanation
Indices: 5433614--5433689 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 21
5433604 AAACTATATA
5433614 TATTTTCTATTAAATTAAATTTT
1 TATTTT-TA-TAAATTAAATTTT
**
5433637 TATTTTTATATAATTTTATTTT
1 TATTTTTATA-AATTAAATTTT
*
5433659 TAATTTTTATATA-TATAATTTT
1 T-ATTTTTATAAATTA-AATTTT
5433681 TATTTTTAT
1 TATTTTTAT
5433690 TATATATATA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
21 11 0.24
22 19 0.42
23 15 0.33
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTTTATAAATTAAATTTT
Found at i:5433657 original size:22 final size:21
Alignment explanation
Indices: 5433631--5433697 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 21
5433621 TATTAAATTA
*
5433631 AATTTTTATTTTTATATAATTT
1 AATTTTTATTTTTATAT-ATAT
*
5433653 TATTTTTAATTTTTATATATAT
1 AATTTTT-ATTTTTATATATAT
5433675 AATTTTTATTTTTATTATATAT
1 AATTTTTATTTTTA-TATATAT
5433697 A
1 A
5433698 TATGTGAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
21 7 0.17
22 23 0.57
23 10 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
AATTTTTATTTTTATATATAT
Found at i:5433677 original size:15 final size:14
Alignment explanation
Indices: 5433642--5433684 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
5433632 ATTTTTATTT
5433642 TTATATAA-TTTTA
1 TTATATAATTTTTA
*
5433655 TT-TTTAATTTTTA
1 TTATATAATTTTTA
5433668 TATATATAATTTTTA
1 T-TATATAATTTTTA
5433683 TT
1 TT
5433685 TTTATTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 4 0.16
13 8 0.32
14 2 0.08
15 11 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATATAATTTTTA
Found at i:5433932 original size:54 final size:53
Alignment explanation
Indices: 5433864--5433967 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 53
5433854 AACCTAAACT
*
5433864 AGTATATAAGCTATTAATATAAAATATGAGCCTAATTCAAACTTAGACTTGATA
1 AGTATATAAACTATTAATATAAAATATGAGCCTAATTCAAACTT-GACTTGATA
* *
5433918 AGTATATAAACTATTAATATAAAGTATGAGCTTAATTCAAACTTGACTTG
1 AGTATATAAACTATTAATATAAAATATGAGCCTAATTCAAACTTGACTTG
5433968 GCTCGACCCG
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 6 0.13
54 41 0.87
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35
Consensus pattern (53 bp):
AGTATATAAACTATTAATATAAAATATGAGCCTAATTCAAACTTGACTTGATA
Found at i:5434188 original size:22 final size:22
Alignment explanation
Indices: 5434163--5434211 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
5434153 TGTAATTTTT
*
5434163 TTTTATTAAT-GATTAAACATAA
1 TTTT-TTAATGGAGTAAACATAA
* *
5434185 TTTTTTCATGGAGTAAATATAA
1 TTTTTTAATGGAGTAAACATAA
5434207 TTTTT
1 TTTTT
5434212 CACTTGAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (22 bp):
TTTTTTAATGGAGTAAACATAA
Found at i:5438190 original size:19 final size:20
Alignment explanation
Indices: 5438149--5438188 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5438139 TTGATTTTTT
*
5438149 ATTTTATAATTTTTTTTAAA
1 ATTTTATAATTTTTCTTAAA
5438169 ATTTT-TAATTTTTCCTTAAA
1 ATTTTATAATTTTT-CTTAAA
5438189 TTCGCTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTATAATTTTTCTTAAA
Found at i:5438809 original size:9 final size:8
Alignment explanation
Indices: 5438790--5438832 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
5438780 AATTATCTAA
5438790 TTTTTTAT
1 TTTTTTAT
5438798 TTTTTTAT
1 TTTTTTAT
*
5438806 TTTTTTCT
1 TTTTTTAT
* *
5438814 TTTTATGT
1 TTTTTTAT
*
5438822 TTTATTAT
1 TTTTTTAT
5438830 TTT
1 TTT
5438833 ATGATTTTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.84
Consensus pattern (8 bp):
TTTTTTAT
Found at i:5438954 original size:23 final size:23
Alignment explanation
Indices: 5438893--5438982 Score: 80
Period size: 23 Copynumber: 3.9 Consensus size: 23
5438883 TTATCTTGGT
*
5438893 TATTTATTTTTAATATTTTT-TT-
1 TATTTATCTTTAA-ATTTTTATTA
*
5438915 TATCTGAT-TTTAAATTTTTATTA
1 TAT-TTATCTTTAAATTTTTATTA
* *
5438938 TGGTTTATCTTT-AATTTTAATTA
1 T-ATTTATCTTTAAATTTTTATTA
5438961 TATTTATCTTTAAATATTTTAT
1 TATTTATCTTTAAAT-TTTTAT
5438983 CTTATTAGTT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
21 6 0.11
22 19 0.35
23 21 0.38
24 9 0.16
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (23 bp):
TATTTATCTTTAAATTTTTATTA
Found at i:5438966 original size:22 final size:23
Alignment explanation
Indices: 5438927--5438973 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
5438917 TCTGATTTTA
* *
5438927 AATTTTTATTATGGTTTATCTTT
1 AATTTTAATTATGATTTATCTTT
5438950 AATTTTAATTAT-ATTTATCTTT
1 AATTTTAATTATGATTTATCTTT
5438972 AA
1 AA
5438974 ATATTTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (23 bp):
AATTTTAATTATGATTTATCTTT
Found at i:5438983 original size:15 final size:16
Alignment explanation
Indices: 5438953--5438985 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5438943 TATCTTTAAT
*
5438953 TTTAATTATATTTATC
1 TTTAAATATATTTATC
5438969 TTTAAATAT-TTTATC
1 TTTAAATATATTTATC
5438984 TT
1 TT
5438986 ATTAGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTAAATATATTTATC
Found at i:5441302 original size:22 final size:24
Alignment explanation
Indices: 5441277--5441323 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
5441267 TTGATATTAT
5441277 TTAAAT-AATA-TAGTTTTATTTA
1 TTAAATAAATATTAGTTTTATTTA
*
5441299 TTAAATGAAATATTATTTTTATTTA
1 TTAAAT-AAATATTAGTTTTATTTA
5441324 AAATTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
24 4 0.19
25 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
TTAAATAAATATTAGTTTTATTTA
Found at i:5441324 original size:22 final size:23
Alignment explanation
Indices: 5441273--5441325 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
5441263 TCAATTGATA
5441273 TTATTTAAATAATATAGTTTTAT
1 TTATTTAAATAATATAGTTTTAT
5441296 TTA-TTAAATGAA-ATA-TTATT-T
1 TTATTTAAAT-AATATAGTT-TTAT
5441317 TTATTTAAA
1 TTATTTAAA
5441326 ATTTTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 6 0.22
22 16 0.59
23 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (23 bp):
TTATTTAAATAATATAGTTTTAT
Found at i:5449644 original size:2 final size:2
Alignment explanation
Indices: 5449637--5449665 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5449627 TTTATTAGAC
5449637 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5449666 GCAAACAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5455813 original size:12 final size:12
Alignment explanation
Indices: 5455755--5455789 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5455745 TTTGTTTTGC
5455755 TATTTTTTTATA
1 TATTTTTTTATA
*
5455767 TATTTTTTTCTA
1 TATTTTTTTATA
*
5455779 TATTTATTTAT
1 TATTTTTTTAT
5455790 TTTGATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (12 bp):
TATTTTTTTATA
Found at i:5459674 original size:106 final size:106
Alignment explanation
Indices: 5459489--5459698 Score: 402
Period size: 106 Copynumber: 2.0 Consensus size: 106
5459479 TCTTTAAAAA
* *
5459489 TCTGCTAATAATTTTAAAGGGAACTATTTAAGATGTTTTTGTCTAAAAATATCTTAAATAAGCTA
1 TCTGCTAATAATTTTAAAAGGAACTATTTAAAATGTTTTTGTCTAAAAATATCTTAAATAAGCTA
5459554 AATAAAAAAAATTGAAGAGTATTATTTAAGGCATTTTTATT
66 AATAAAAAAAATTGAAGAGTATTATTTAAGGCATTTTTATT
5459595 TCTGCTAATAATTTTAAAAGGAACTATTTAAAATGTTTTTGTCTAAAAATATCTTAAATAAGCTA
1 TCTGCTAATAATTTTAAAAGGAACTATTTAAAATGTTTTTGTCTAAAAATATCTTAAATAAGCTA
5459660 AATAAAAAAAATTGAAGAGTATTATTTAAGGCATTTTTA
66 AATAAAAAAAATTGAAGAGTATTATTTAAGGCATTTTTA
5459699 GAATAAAAAT
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 102 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (106 bp):
TCTGCTAATAATTTTAAAAGGAACTATTTAAAATGTTTTTGTCTAAAAATATCTTAAATAAGCTA
AATAAAAAAAATTGAAGAGTATTATTTAAGGCATTTTTATT
Found at i:5459863 original size:43 final size:43
Alignment explanation
Indices: 5459816--5459898 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
5459806 ATAAAAATGT
* *
5459816 ATTATTTAAGGTATTTTTGGTCCAAAAATGCCTTAAATAAAAG
1 ATTATTTAAGATATTTTTAGTCCAAAAATGCCTTAAATAAAAG
* *
5459859 ATTATTTAAGATATTTTTAGTCTAAAAATTCCTTAAATAA
1 ATTATTTAAGATATTTTTAGTCCAAAAATGCCTTAAATAA
5459899 TCCCCTTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (43 bp):
ATTATTTAAGATATTTTTAGTCCAAAAATGCCTTAAATAAAAG
Found at i:5462963 original size:18 final size:20
Alignment explanation
Indices: 5462926--5462964 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
5462916 TTAAATTAAA
*
5462926 TAAAAATAACTAAAATTAAT
1 TAAAAATAACTAAAAATAAT
5462946 TAAAAA-AA-TAAAAATAAT
1 TAAAAATAACTAAAAATAAT
5462964 T
1 T
5462965 TAACTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 2 0.11
20 6 0.33
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAAAATAACTAAAAATAAT
Found at i:5463449 original size:33 final size:31
Alignment explanation
Indices: 5463369--5463449 Score: 76
Period size: 33 Copynumber: 2.5 Consensus size: 31
5463359 AATAAATTAA
*
5463369 ATTATAAAAA-TAATAA-TTTTAATATAATAAT
1 ATTA-AAAAATTAA-AATTTTTAATACAATAAT
*
5463400 ATTAAAAAATTAAAATTTTTATATACAATCAT
1 ATTAAAAAATTAAAATTTTTA-ATACAATAAT
* *
5463432 AGTTAAAAATTTTAAATT
1 A-TTAAAAAATTAAAATT
5463450 ATTCTAGATG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 7 0.17
31 12 0.29
32 9 0.21
33 14 0.33
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (31 bp):
ATTAAAAAATTAAAATTTTTAATACAATAAT
Found at i:5469026 original size:33 final size:33
Alignment explanation
Indices: 5468898--5469037 Score: 129
Period size: 33 Copynumber: 4.2 Consensus size: 33
5468888 TTTTAGAAAA
* * *
5468898 AAATGCCACTAAATTAGCAGCGTTTGAAGTCAC
1 AAATGCCACTAAATTAGCGGCGTTTGTAGACAC
* * *
5468931 AAACGCCACTAACTTAGTGGCGTTT-TAAGACAC
1 AAATGCCACTAAATTAGCGGCGTTTGT-AGACAC
* * ** *
5468964 AAACGCCATTAAATTAGCGATGTTCGTAGACAC
1 AAATGCCACTAAATTAGCGGCGTTTGTAGACAC
* * * *
5468997 AAATGCCACTAACTTAGTGGCGTTTGTAGAAAT
1 AAATGCCACTAAATTAGCGGCGTTTGTAGACAC
5469030 AAATGCCA
1 AAATGCCA
5469038 TTAGTCTACA
Statistics
Matches: 84, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
33 83 0.99
34 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (33 bp):
AAATGCCACTAAATTAGCGGCGTTTGTAGACAC
Found at i:5469038 original size:66 final size:65
Alignment explanation
Indices: 5468886--5469040 Score: 186
Period size: 66 Copynumber: 2.4 Consensus size: 65
5468876 AAAATAACAA
* * *
5468886 CGTTTTAGAAAAAAATGCCACTAAATTAGCAGCGTTTGAAGTCACAAACGCCACTAACTTAGTGG
1 CGTTTTAGAAAAAAATGCCATTAAATTAGCAGCGTTCGAAGACACAAACGCCACTAACTTAGTGG
* * * * * *
5468951 CGTTTTAAGACACAAACGCCATTAAATTAGC-GATGTTCGTAGACACAAATGCCACTAACTTAGT
1 CGTTTT-AGAAAAAAATGCCATTAAATTAGCAG-CGTTCGAAGACACAAACGCCACTAACTTAGT
5469015 GG
64 GG
*
5469017 CGTTTGTAGAAATAAATGCCATTA
1 CGTTT-TAGAAAAAAATGCCATTA
5469041 GTCTACAAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
65 7 0.09
66 67 0.89
67 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (65 bp):
CGTTTTAGAAAAAAATGCCATTAAATTAGCAGCGTTCGAAGACACAAACGCCACTAACTTAGTGG
Found at i:5469190 original size:14 final size:15
Alignment explanation
Indices: 5469173--5469204 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5469163 TCATAAGAAC
5469173 AAATTTAAAT-TTAT
1 AAATTTAAATATTAT
5469187 AAA-TTAAATATTAT
1 AAATTTAAATATTAT
5469201 AAAT
1 AAAT
5469205 ATTTAACTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATTTAAATATTAT
Found at i:5470617 original size:164 final size:165
Alignment explanation
Indices: 5470312--5470703 Score: 370
Period size: 165 Copynumber: 2.4 Consensus size: 165
5470302 AAAATCAAAT
* * * *
5470312 TCAATCATTCAGACAAGTTTACTATCATGTATTGAAGCTATCTAAATTGTTAAAACATAAATATA
1 TCAATCATTCAGACAAATTTAATATCATATATTGAAACTATCTAAATTGTTAAAACATAAATATA
*** * * * * * *
5470377 ATTGCAAATTATATTTTTGCCCTTTAACGGCATAACAAAGTCCTAAAAAGACATAAATAGTAACA
66 AACACAAATTACATTTTGGCCCTTTAACGACATAAAAAAGTACTAAAAAGACATAAAGAGTAACA
5470442 TTTTCACACATATCAGCCATGAAAACCAAGTTCAA
131 TTTTCACACATATCAGCCATGAAAACCAAGTTCAA
* * *
5470477 TCAATCATTTAGATAAATTTAATATCATATATTGAAAC-ATCTAAATTGTTAAAATA-AAATAAT
1 TCAATCATTCAGACAAATTTAATATCATATATTGAAACTATCTAAATTGTTAAAACATAAAT-AT
* * * *
5470540 AAACACAAATTTACATTTTGGCCTTTTAACGACATAAAAAAGTATTAAATAGATATAAACGA-TA
65 AAACACAAA-TTACATTTTGGCCCTTTAACGACATAAAAAAGTACTAAAAAGACATAAA-GAGTA
* * ** * *
5470604 A-TTTTTTACACATATCATTCGTGGAAACCAAGTT---
128 ACATTTTCACACATATCAGCCATGAAAACCAAGTTCAA
* * * ** * * * *
5470638 T-AATCATT-TGAAAAAGTTTAATATAACGTATTTAAGCTATCTAAACTGTTAAAACATAAAAAT
1 TCAATCATTCAGACAAA-TTTAATATCATATATTGAAACTATCTAAATTGTTAAAACATAAATAT
5470701 AAA
65 AAA
5470704 TGCAAGATAA
Statistics
Matches: 185, Mismatches: 36, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
159 5 0.03
160 23 0.12
161 22 0.12
162 3 0.02
163 4 0.02
164 52 0.28
165 75 0.41
166 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.33
Consensus pattern (165 bp):
TCAATCATTCAGACAAATTTAATATCATATATTGAAACTATCTAAATTGTTAAAACATAAATATA
AACACAAATTACATTTTGGCCCTTTAACGACATAAAAAAGTACTAAAAAGACATAAAGAGTAACA
TTTTCACACATATCAGCCATGAAAACCAAGTTCAA
Found at i:5470755 original size:126 final size:125
Alignment explanation
Indices: 5470594--5470834 Score: 304
Period size: 126 Copynumber: 1.9 Consensus size: 125
5470584 TTAAATAGAT
* *
5470594 ATAAACGATAATTTTTTACACATATCATTCGTGGAAACCAAGTTTAATCATTTGAAAAAGTTTAA
1 ATAAACGATAATTTTTTACACATATCATTCGTGGAAACCAAGTTCAATCATTCGAAAAAGTTTAA
* * * *
5470659 TATAACGTATTTAAGCTATCTAAACTGTTAAAACATAAAAATAAATGCAAGATAACAGAC
66 TATAACATATTGAAACTATCTAAACTGTTAAAACAGAAAAATAAATGCAAGATAACAGAC
* * * * * *
5470719 ATAAATGATAACTTTTTTGCACATGTCAATT-GTGGAAACCAAGTTCAATTATTCGGACAAGTTT
1 ATAAACGATAA-TTTTTTACACATATC-ATTCGTGGAAACCAAGTTCAATCATTCGAAAAAGTTT
* * * * *
5470783 AATATTATATATTGAAACTATTTAAACTGTTAAAATAGAATAATAAATGCAA
64 AATATAACATATTGAAACTATCTAAACTGTTAAAACAGAAAAATAAATGCAA
5470835 ATTTGCATTT
Statistics
Matches: 97, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
125 10 0.10
126 84 0.87
127 3 0.03
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (125 bp):
ATAAACGATAATTTTTTACACATATCATTCGTGGAAACCAAGTTCAATCATTCGAAAAAGTTTAA
TATAACATATTGAAACTATCTAAACTGTTAAAACAGAAAAATAAATGCAAGATAACAGAC
Found at i:5471183 original size:160 final size:160
Alignment explanation
Indices: 5470715--5471319 Score: 457
Period size: 160 Copynumber: 3.8 Consensus size: 160
5470705 GCAAGATAAC
* * ** * * **
5470715 AGACATAAATGATAACTTTTTTGCACATGTCAATTGTGGAAACCAAGTTCAATTATTCGGACAAG
1 AGACATAAATCATAAC-TTTTTACACACATCAATCGTGGAAACCAAGTTCAATCATTCAAACAAG
* * ** * *
5470780 TTTAATATTATATATTGAAA-CTATTTAAACTGTTAAA-ATAGAATAATAAATGCA-AATT-TGC
65 TTTAATATCATGTATT-AAAGCTATCCAAACTGTTAAACATA-AAT-AT-AATACATATTTATG-
* * **
5470841 ATTTTAGCCTTTTAATAGCAC-AAAAAAT-CTAAATA
125 ATTTTGGCCCTTTAACGGCACAAAAAAATGCTAAA-A
* * * * * **
5470876 A-ACATAAA-CGACAATCTTTTCACACATATCAACCGTGCAAAGTAAGTTCAATCATTCAAACAA
1 AGACATAAATC-ATAA-CTTTTTACACACATCAATCGTGGAAACCAAGTTCAATCATTCAAACAA
* * * *
5470939 GTTTAATATCATTTATTAAAGCTATCTAAACTATTAAA-ATAGAATAATAAAAGCA-ATTT-TGC
64 GTTTAATATCATGTATTAAAGCTATCCAAACTGTTAAACATA-AAT-ATAATA-CATATTTATG-
* * *
5471001 ATTTTGGCCTTTTAATGGCACAAAAAAAATGCTAAAC
125 ATTTTGGCCCTTTAACGGCAC-AAAAAAATGCTAAAA
* * *
5471038 AGACATAAA-CATAACTTTTT-CTCACATCAGTCGTGGAAACCAAGTTCATTCATTCAAACAAGT
1 AGACATAAATCATAACTTTTTACACACATCAATCGTGGAAACCAAGTTCAATCATTCAAACAAGT
* *
5471101 TTAATATCATGTATTTAAGCTATCCAAATTGTTAAAACATAAATATAACTACATATTTATG-TTC
66 TTAATATCATGTATTAAAGCTATCCAAACTGTT-AAACATAAATATAA-TACATATTTATGATT-
* * *
5471165 TT-GCCCTTTAACGGCACAACAAAGTTCTAAAA
128 TTGGCCCTTTAACGGCACAAAAAAATGCTAAAA
* ** * * *** *
5471197 AGATATAAATGGTAACTTTTTACACATATCAATCGTGGAAACTAAGTTCAATCATTTGGATAAGT
1 AGACATAAATCATAACTTTTTACACACATCAATCGTGGAAACCAAGTTCAATCATTCAAACAAGT
* * * * *
5471262 TTAATATAATGTATTGAAGCTATCCAAACTGTTAAACAAAAAAATAATTGCATATTTA
66 TTAATATCATGTATTAAAGCTATCCAAACTGTTAAACATAAATATAA-TACATATTTA
5471320 CATTTTTACC
Statistics
Matches: 364, Mismatches: 64, Indels: 33
0.79 0.14 0.07
Matches are distributed among these distances:
159 24 0.07
160 227 0.62
161 84 0.23
162 16 0.04
163 13 0.04
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (160 bp):
AGACATAAATCATAACTTTTTACACACATCAATCGTGGAAACCAAGTTCAATCATTCAAACAAGT
TTAATATCATGTATTAAAGCTATCCAAACTGTTAAACATAAATATAATACATATTTATGATTTTG
GCCCTTTAACGGCACAAAAAAATGCTAAAA
Found at i:5476479 original size:15 final size:15
Alignment explanation
Indices: 5476459--5476492 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5476449 CAAACAAAAG
5476459 CAAAAAAACATTCAA
1 CAAAAAAACATTCAA
*
5476474 CAAAAAAGCATTCAA
1 CAAAAAAACATTCAA
5476489 CAAA
1 CAAA
5476493 TAACTGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.65, C:0.21, G:0.03, T:0.12
Consensus pattern (15 bp):
CAAAAAAACATTCAA
Found at i:5477353 original size:22 final size:22
Alignment explanation
Indices: 5477328--5477377 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
5477318 TTTTTTTTAG
* *
5477328 ATTATTTAAGGCATTTTTGCAT
1 ATTATTCAAGGCATTTTTACAT
* *
5477350 ATTATTCAAGGTATTTTTACCT
1 ATTATTCAAGGCATTTTTACAT
5477372 ATTATT
1 ATTATT
5477378 GGAGATTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (22 bp):
ATTATTCAAGGCATTTTTACAT
Found at i:5477927 original size:62 final size:62
Alignment explanation
Indices: 5477806--5477971 Score: 156
Period size: 62 Copynumber: 2.7 Consensus size: 62
5477796 AAGGTATTTC
* ** * * * ***
5477806 ATTATTCAAGGCATTTTTAGCTAAAAACGCCTTCAGTAATCCGTTTCAATTTTTATGAGGAG
1 ATTATTCAAGGTATTTTTAGCTAAAAACGCCTTCAAAAATCCATATAAAAAATTATGAGGAG
* *
5477868 ATTATTCAAGGTATTTTTAGCTAAAAACGTCTTCAAAAATCCATAATAAAAAATT-TGAGGGG
1 ATTATTCAAGGTATTTTTAGCTAAAAACGCCTTCAAAAATCCAT-ATAAAAAATTATGAGGAG
* * * * *
5477930 ATTATTCAAAGTGTTTTT-GACTAAAAACACCTTTAATAATCC
1 ATTATTCAAGGTATTTTTAG-CTAAAAACGCCTTCAAAAATCC
5477972 CTTTCAATTT
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
61 1 0.01
62 79 0.93
63 5 0.06
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (62 bp):
ATTATTCAAGGTATTTTTAGCTAAAAACGCCTTCAAAAATCCATATAAAAAATTATGAGGAG
Found at i:5479927 original size:18 final size:19
Alignment explanation
Indices: 5479903--5479946 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
5479893 GGGAAGGAAC
*
5479903 AAATTAAAAGCTTTTAGAG
1 AAATTAAAAGCTTTAAGAG
5479922 -AATT-AAAGCTTTAAGAG
1 AAATTAAAAGCTTTAAGAG
5479939 AAATTAAA
1 AAATTAAA
5479947 TAAAGAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 12 0.55
18 8 0.36
19 2 0.09
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.30
Consensus pattern (19 bp):
AAATTAAAAGCTTTAAGAG
Found at i:5492886 original size:22 final size:21
Alignment explanation
Indices: 5492842--5492887 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
5492832 AAAACCAAGT
**
5492842 AAAAAAAAAAAGAAAAGCCAG
1 AAAAAAAAAAAGAAAAAACAG
*
5492863 AAAAAACAAAAAGAAAAAAGAG
1 AAAAAA-AAAAAGAAAAAACAG
5492885 AAA
1 AAA
5492888 GGAGAGTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAAGAAAAAACAG
Found at i:5504373 original size:20 final size:20
Alignment explanation
Indices: 5504348--5504387 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5504338 TAGATAGTAA
5504348 TATAGTATGGTCCATCCAAG
1 TATAGTATGGTCCATCCAAG
5504368 TATAGTATGGTCCATCCAAG
1 TATAGTATGGTCCATCCAAG
5504388 AATGATCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (20 bp):
TATAGTATGGTCCATCCAAG
Found at i:5505418 original size:45 final size:45
Alignment explanation
Indices: 5505354--5505448 Score: 190
Period size: 45 Copynumber: 2.1 Consensus size: 45
5505344 CAAGGAATAA
5505354 TTAAGGGTGTGATGATGGAGCTGTGACGGCTGTCTGAGCCCAAGG
1 TTAAGGGTGTGATGATGGAGCTGTGACGGCTGTCTGAGCCCAAGG
5505399 TTAAGGGTGTGATGATGGAGCTGTGACGGCTGTCTGAGCCCAAGG
1 TTAAGGGTGTGATGATGGAGCTGTGACGGCTGTCTGAGCCCAAGG
5505444 TTAAG
1 TTAAG
5505449 TTCTCTGGCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.25
Consensus pattern (45 bp):
TTAAGGGTGTGATGATGGAGCTGTGACGGCTGTCTGAGCCCAAGG
Found at i:5514434 original size:14 final size:14
Alignment explanation
Indices: 5514417--5514448 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5514407 AAATTAAATA
*
5514417 TAAATTTATTTTTT
1 TAAATTTATCTTTT
5514431 TAAATTTATCTTTT
1 TAAATTTATCTTTT
5514445 TAAA
1 TAAA
5514449 CATAGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TAAATTTATCTTTT
Found at i:5514812 original size:16 final size:16
Alignment explanation
Indices: 5514793--5514852 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
5514783 AATATTTTTA
5514793 AATAAATATATTAAAT
1 AATAAATATATTAAAT
* *
5514809 AATAATTTTATTAATAT
1 AATAAATATATTAA-AT
** *
5514826 AATATTTA-AATAAAT
1 AATAAATATATTAAAT
5514841 AATAAAATATAT
1 AAT-AAATATAT
5514853 ATATATATAT
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
15 5 0.15
16 19 0.58
17 9 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAAATATATTAAAT
Found at i:5514824 original size:28 final size:30
Alignment explanation
Indices: 5514770--5514844 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
5514760 ACATCTTAAT
5514770 TATATATAAAT-ATAATATTTTTAAATA-AA
1 TATAT-TAAATAATAATATTTTTAAATATAA
5514799 TATATTAAATAATAAT-TTTATT-AATATAA
1 TATATTAAATAATAATATTT-TTAAATATAA
5514828 TAT-TTAAATAAATAATA
1 TATATTAAAT-AATAATA
5514845 AAATATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
28 18 0.44
29 23 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TATATTAAATAATAATATTTTTAAATATAA
Found at i:5515907 original size:10 final size:11
Alignment explanation
Indices: 5515889--5515925 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
5515879 ATAATAATTT
5515889 TATTAATATAA
1 TATTAATATAA
5515900 TA-TAATAT-A
1 TATTAATATAA
5515909 TATTAATATAA
1 TATTAATATAA
*
5515920 AATTAA
1 TATTAA
5515926 ATTACTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 3 0.13
10 12 0.52
11 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAATATAA
Found at i:5518648 original size:13 final size:14
Alignment explanation
Indices: 5518593--5518651 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 14
5518583 TTAATTTTAT
5518593 TTATTAATTAAAATA
1 TTATTAATTAAAA-A
*
5518608 TT-TTAAATTTATGAAA
1 TTATT-AA-TTA-AAAA
5518624 TTATTAATTAAAAA
1 TTATTAATTAAAAA
5518638 TTATT-ATTAAAAA
1 TTATTAATTAAAAA
5518651 T
1 T
5518652 AAACTATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 9 0.24
14 10 0.26
15 7 0.18
16 8 0.21
17 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (14 bp):
TTATTAATTAAAAA
Found at i:5529057 original size:23 final size:23
Alignment explanation
Indices: 5529031--5529076 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
5529021 GGTATTAAGT
5529031 TAGTTTGATTTAAGCATATATTG
1 TAGTTTGATTTAAGCATATATTG
5529054 TAGTTTGATTTAAGCATATATTG
1 TAGTTTGATTTAAGCATATATTG
5529077 AGCTTATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.48
Consensus pattern (23 bp):
TAGTTTGATTTAAGCATATATTG
Found at i:5529282 original size:33 final size:32
Alignment explanation
Indices: 5529222--5529284 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
5529212 GGAGAATGTA
5529222 TGAAATGAAATTTGATCACATTACTTATTTGC
1 TGAAATGAAATTTGATCACATTACTTATTTGC
* *
5529254 TGAAATTGAAAATTTGATGAC-TTGCTTATTT
1 TGAAA-TG-AAATTTGATCACATTACTTATTT
5529285 TAGATTGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 5 0.19
33 11 0.41
34 11 0.41
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (32 bp):
TGAAATGAAATTTGATCACATTACTTATTTGC
Found at i:5531338 original size:21 final size:21
Alignment explanation
Indices: 5531314--5531365 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
5531304 GTTTACTCAT
5531314 TTACTGTTATAGTAACCAATC
1 TTACTGTTATAGTAACCAATC
*
5531335 TTACTGCTT-TAGTAACTAATC
1 TTACTG-TTATAGTAACCAATC
* *
5531356 TCACTTTTAT
1 TTACTGTTAT
5531366 TGTTGTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 2 0.08
21 22 0.85
22 2 0.08
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (21 bp):
TTACTGTTATAGTAACCAATC
Found at i:5535403 original size:22 final size:22
Alignment explanation
Indices: 5535378--5535422 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
5535368 CTTTATCTTG
5535378 AATAT-TTATATATATTTTTAAA
1 AATATATTA-ATATATTTTTAAA
5535400 AATATAATTAATATATTTTTAAA
1 AATAT-ATTAATATATTTTTAAA
5535423 TAAAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 13 0.62
24 3 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATATTAATATATTTTTAAA
Found at i:5537574 original size:23 final size:21
Alignment explanation
Indices: 5537524--5537578 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
5537514 ACATTAGTAG
*
5537524 TAAATTAAAT-AATATTATTT
1 TAAAATAAATAAATATTATTT
*
5537544 TATTAATAAATAAATATTAATTTT
1 TA-AAATAAATAAATATT-A-TTT
5537568 TAAAATAAATA
1 TAAAATAAATA
5537579 TATAAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 2 0.07
21 6 0.21
22 6 0.21
23 9 0.32
24 5 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAATAAATAAATATTATTT
Found at i:5542651 original size:10 final size:9
Alignment explanation
Indices: 5542637--5542706 Score: 54
Period size: 9 Copynumber: 7.6 Consensus size: 9
5542627 AAATTATTTA
5542637 TTATTAAAG
1 TTATTAAAG
*
5542646 TATATTAAAA
1 T-TATTAAAG
*
5542656 TTATT-TA-
1 TTATTAAAG
*
5542663 TTATTAAAA
1 TTATTAAAG
5542672 TTATTAAAG
1 TTATTAAAG
5542681 TATTATTAAAG
1 --TTATTAAAG
*
5542692 TTTATTAAAA
1 -TTATTAAAG
5542702 TTATT
1 TTATT
5542707 TATTATCAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
7 5 0.10
8 2 0.04
9 18 0.36
10 16 0.32
11 9 0.18
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (9 bp):
TTATTAAAG
Found at i:5542660 original size:26 final size:26
Alignment explanation
Indices: 5542613--5542712 Score: 108
Period size: 26 Copynumber: 4.1 Consensus size: 26
5542603 TTAATATAAC
5542613 TATTAAA--ATATTAAAAATTATTTAT
1 TATTAAAGTATATT-AAAATTATTTAT
5542638 TATTAAAGTATATTAAAATTATTTAT
1 TATTAAAGTATATTAAAATTATTTAT
* *
5542664 TATTAAAAT-TATT--AA--A-GTAT
1 TATTAAAGTATATTAAAATTATTTAT
*
5542684 TATTAAAGTTTATTAAAATTATTTAT
1 TATTAAAGTATATTAAAATTATTTAT
5542710 TAT
1 TAT
5542713 CAAAATTATT
Statistics
Matches: 63, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
20 11 0.17
21 5 0.08
23 4 0.06
25 12 0.19
26 26 0.41
27 5 0.08
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (26 bp):
TATTAAAGTATATTAAAATTATTTAT
Found at i:5542667 original size:16 final size:16
Alignment explanation
Indices: 5542648--5542722 Score: 59
Period size: 16 Copynumber: 4.8 Consensus size: 16
5542638 TATTAAAGTA
5542648 TATTAAAATTATTTAT
1 TATTAAAATTATTTAT
* *
5542664 TATTAAAATTATTAAAG
1 TATTAAAATTATT-TAT
**
5542681 TATT---ATTAAAGT-T
1 TATTAAAATT-ATTTAT
5542694 TATTAAAATTATTTAT
1 TATTAAAATTATTTAT
*
5542710 TATCAAAATTATT
1 TATTAAAATTATT
5542723 AATATTCAAG
Statistics
Matches: 44, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
13 4 0.09
14 3 0.07
15 3 0.07
16 29 0.66
17 5 0.11
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (16 bp):
TATTAAAATTATTTAT
Found at i:5542698 original size:46 final size:46
Alignment explanation
Indices: 5542635--5542724 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
5542625 AAAAATTATT
*
5542635 TATTATTAAAGTATATTAAAATTATTTATTATTAAAATTATTAAAG
1 TATTATTAAAGTATATTAAAATTATTTATTATCAAAATTATTAAAG
*
5542681 TATTATTAAAGTTTATTAAAATTATTTATTATCAAAATTATTAA
1 TATTATTAAAGTATATTAAAATTATTTATTATCAAAATTATTAA
5542725 TATTCAAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (46 bp):
TATTATTAAAGTATATTAAAATTATTTATTATCAAAATTATTAAAG
Found at i:5542756 original size:20 final size:21
Alignment explanation
Indices: 5542733--5542771 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5542723 AATATTCAAG
*
5542733 AATAATTAA-ATTTAAATAAT
1 AATAATTAATATTAAAATAAT
*
5542753 AATATTTAATATTAAAATA
1 AATAATTAATATTAAAATA
5542772 TTATATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATAATTAATATTAAAATAAT
Found at i:5542917 original size:21 final size:22
Alignment explanation
Indices: 5542896--5542937 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5542886 AATGGTAATA
5542896 TTTATTATT-AAAATATTTATAT
1 TTTA-TATTGAAAATATTTATAT
5542918 TTTATATTGAAAATATTTAT
1 TTTATATTGAAAATATTTAT
5542938 TATCAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTATATTGAAAATATTTATAT
Found at i:5542930 original size:22 final size:22
Alignment explanation
Indices: 5542854--5542937 Score: 68
Period size: 21 Copynumber: 3.8 Consensus size: 22
5542844 ATAGTATCAC
*
5542854 TATTCTTAAAATA-TTAT-TTT
1 TATTATTAAAATATTTATATTT
** *
5542874 TATTAATATTAAAATGGTAATA-TT
1 TA-T--TATTAAAATATTTATATTT
5542898 TATTATTAAAATATTTATATTT
1 TATTATTAAAATATTTATATTT
5542920 TA-TATTGAAAATATTTAT
1 TATTATT-AAAATATTTAT
5542938 TATCAAATCA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
20 2 0.04
21 18 0.35
22 15 0.29
23 9 0.18
24 7 0.14
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (22 bp):
TATTATTAAAATATTTATATTT
Found at i:5543166 original size:45 final size:45
Alignment explanation
Indices: 5543053--5543166 Score: 124
Period size: 45 Copynumber: 2.5 Consensus size: 45
5543043 ATAATAAGAA
*
5543053 ATTATTTAAAATATTAATATTAAGAAAATAATATTATTATATTATTT
1 ATTA-TTAAAATATTAATA-TAATAAAATAATATTATTATATTATTT
** * * *
5543100 AACATT-AATTATTAAAATAATAAAGATATTATTA-TATATTATTT
1 ATTATTAAAATATTAATATAATAAA-ATAATATTATTATATTATTT
*
5543144 ATTATTAAAATAATAATATAATA
1 ATTATTAAAATATTAATATAATA
5543167 CTATTTATTA
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
44 20 0.37
45 30 0.56
46 2 0.04
47 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.46
Consensus pattern (45 bp):
ATTATTAAAATATTAATATAATAAAATAATATTATTATATTATTT
Found at i:5543187 original size:37 final size:36
Alignment explanation
Indices: 5543077--5543190 Score: 120
Period size: 37 Copynumber: 3.1 Consensus size: 36
5543067 TAATATTAAG
* * **
5543077 AAAATAATATTATTATATTATTTAACATTAATTATT
1 AAAATAATAATATAATATTATTTATTATTAATTATT
* * * *
5543113 AAAATAATAAAGATATTATTATATATTATTTATTATT
1 AAAATAAT-AATATAATATTATTTATTATTAATTATT
* *
5543150 AAAATAATAATATAATACTATTTATTATTGAAATATT
1 AAAATAATAATATAATATTATTTATTATT-AATTATT
5543187 AAAA
1 AAAA
5543191 ATATTTATGT
Statistics
Matches: 62, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
36 25 0.40
37 37 0.60
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (36 bp):
AAAATAATAATATAATATTATTTATTATTAATTATT
Found at i:5543213 original size:24 final size:24
Alignment explanation
Indices: 5543154--5543217 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
5543144 ATTATTAAAA
* *
5543154 TAATAATATAATACTATTTATTAT
1 TAATAATATAAAAATATTTATTAT
*
5543178 TGA-AATATTAAAAATATTTATGT-T
1 TAATAATA-TAAAAATATTTAT-TAT
5543202 TAATAATATAAAAATA
1 TAATAATATAAAAATA
5543218 AAAATATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 4 0.12
24 24 0.73
25 5 0.15
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (24 bp):
TAATAATATAAAAATATTTATTAT
Found at i:5543292 original size:22 final size:20
Alignment explanation
Indices: 5543267--5543317 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
5543257 TAATATTTTC
5543267 ATTTTTTAATTAAAATTAAATA
1 ATTTTTTAATTAAAA-T-AATA
* *
5543289 ATTTTTTTATTAATATAATA
1 ATTTTTTAATTAAAATAATA
*
5543309 ATATTTTAA
1 ATTTTTTAA
5543318 GTCGAATCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 11 0.44
21 1 0.04
22 13 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTTTTAATTAAAATAATA
Found at i:5543920 original size:54 final size:54
Alignment explanation
Indices: 5543834--5543939 Score: 194
Period size: 54 Copynumber: 2.0 Consensus size: 54
5543824 TATTTTCTAG
*
5543834 TTTTTCTTGCTTTCATCATATGATTCTGGTCAAACAAGATATCTTATAGCAACA
1 TTTTTCTTGCTTTCATCATATGATTCTGGTCAAACAAGATATCTCATAGCAACA
*
5543888 TTTTTCTTGCTTTCATCATATGATTCTTGTCAAACAAGATATCTCATAGCAA
1 TTTTTCTTGCTTTCATCATATGATTCTGGTCAAACAAGATATCTCATAGCAA
5543940 ATAACATAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (54 bp):
TTTTTCTTGCTTTCATCATATGATTCTGGTCAAACAAGATATCTCATAGCAACA
Found at i:5556652 original size:2 final size:2
Alignment explanation
Indices: 5556645--5556675 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5556635 CAAAATATTT
*
5556645 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5556676 GCACTCATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5559788 original size:100 final size:100
Alignment explanation
Indices: 5559615--5559819 Score: 374
Period size: 100 Copynumber: 2.0 Consensus size: 100
5559605 TATTTGAGTG
* * *
5559615 TTATTCCAAATGTTTAATGCATGTATGATGGTTAGTTTAGTAATTTGTGTGTAGTGTTTGGCTAA
1 TTATTCCAAATATTTAATGCATGTATGATGGTTAGTTTAGTAATTTGTATGTAGTGTTTCGCTAA
5559680 GTATGTATGTTTTCATGGTTTCTTCACTAGTTAGT
66 GTATGTATGTTTTCATGGTTTCTTCACTAGTTAGT
*
5559715 TTATTCCATATATTTAATGCATGTATGATGGTTAGTTTAGTAATTTGTATGTAGTGTTTCGCTAA
1 TTATTCCAAATATTTAATGCATGTATGATGGTTAGTTTAGTAATTTGTATGTAGTGTTTCGCTAA
5559780 GTATGTATGTTTTCATGGTTTCTTCACTAGTTAGT
66 GTATGTATGTTTTCATGGTTTCTTCACTAGTTAGT
5559815 TTATT
1 TTATT
5559820 ATATGTTTGA
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 101 1.00
ACGTcount: A:0.22, C:0.08, G:0.20, T:0.49
Consensus pattern (100 bp):
TTATTCCAAATATTTAATGCATGTATGATGGTTAGTTTAGTAATTTGTATGTAGTGTTTCGCTAA
GTATGTATGTTTTCATGGTTTCTTCACTAGTTAGT
Found at i:5560356 original size:62 final size:61
Alignment explanation
Indices: 5560259--5560376 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 61
5560249 TACATGTTCT
* * **
5560259 ATGCATTAAAGTTTACATTTTCATTAATGACATTTTGGTAATTTTTGCTACATGCATTTCCC
1 ATGCATCAAAGTTTACATTTTAACCAATGACATTTTGGTAA-TTTTGCTACATGCATTTCCC
* * *
5560321 ATGCATCAAAGTTTGCATTTTAACCAATGCCATTTTGGTAATTTTGTTACATGCAT
1 ATGCATCAAAGTTTACATTTTAACCAATGACATTTTGGTAATTTTGCTACATGCAT
5560377 CAAAGTTTGC
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
61 14 0.29
62 35 0.71
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (61 bp):
ATGCATCAAAGTTTACATTTTAACCAATGACATTTTGGTAATTTTGCTACATGCATTTCCC
Found at i:5560426 original size:50 final size:50
Alignment explanation
Indices: 5560320--5560419 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
5560310 ATGCATTTCC
*
5560320 CATGCATCAAAGTTTGCATTTTAACCAATGCCATTTTGGTAATTTTGTTA
1 CATGCATCAAAGTTTGCATTTTAACCAATGCCATTTTAGTAATTTTGTTA
* *
5560370 CATGCATCAAAGTTTGCACTTTT-ATCAATGGCATTTTAGTAATTTTGTTA
1 CATGCATCAAAGTTTGCA-TTTTAACCAATGCCATTTTAGTAATTTTGTTA
5560420 TTTGCATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 42 0.91
51 4 0.09
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (50 bp):
CATGCATCAAAGTTTGCATTTTAACCAATGCCATTTTAGTAATTTTGTTA
Found at i:5560460 original size:7 final size:7
Alignment explanation
Indices: 5560448--5560635 Score: 71
Period size: 7 Copynumber: 28.9 Consensus size: 7
5560438 ACCCCAAATG
5560448 TAAACCC
1 TAAACCC
5560455 TAAACCC
1 TAAACCC
*
5560462 TGAA-CC
1 TAAACCC
* *
5560468 TTAACCT
1 TAAACCC
**
5560475 TAAATTC
1 TAAACCC
5560482 TAAA-CC
1 TAAACCC
*
5560488 -AAATCC
1 TAAACCC
5560494 TAAACCC
1 TAAACCC
**
5560501 TAAATAC
1 TAAACCC
*
5560508 TAGA-CC
1 TAAACCC
*
5560514 TAAATCC
1 TAAACCC
5560521 TAAACCC
1 TAAACCC
5560528 -AAA-CC
1 TAAACCC
* *
5560533 TTAACCA
1 TAAACCC
* *
5560540 TAAAACT
1 TAAACCC
*
5560547 TAAGCCC
1 TAAACCC
5560554 T-AACCC
1 TAAACCC
5560560 T-AACCC
1 TAAACCC
5560566 TAAA-CC
1 TAAACCC
* *
5560572 -AAAACT
1 TAAACCC
5560578 TAAA-CC
1 TAAACCC
*
5560584 AAAACCC
1 TAAACCC
*
5560591 T-AACCT
1 TAAACCC
5560597 TAAACCC
1 TAAACCC
*
5560604 TAAAACC
1 TAAACCC
5560611 --AACCC
1 TAAACCC
*
5560616 TTAACCC
1 TAAACCC
* *
5560623 CAAACCT
1 TAAACCC
5560630 TAAACC
1 TAAACC
5560636 AATATCTAAA
Statistics
Matches: 132, Mismatches: 36, Indels: 26
0.68 0.19 0.13
Matches are distributed among these distances:
5 12 0.09
6 40 0.30
7 80 0.61
ACGTcount: A:0.44, C:0.35, G:0.02, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:5560505 original size:26 final size:27
Alignment explanation
Indices: 5560470--5560527 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
5560460 CCTGAACCTT
* *
5560470 AACCTTAAATTCTAAACC-AAATCCTA
1 AACCCTAAATACTAAACCTAAATCCTA
*
5560496 AACCCTAAATACTAGACCTAAATCCTA
1 AACCCTAAATACTAAACCTAAATCCTA
5560523 AACCC
1 AACCC
5560528 AAACCTTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 15 0.54
27 13 0.46
ACGTcount: A:0.45, C:0.31, G:0.02, T:0.22
Consensus pattern (27 bp):
AACCCTAAATACTAAACCTAAATCCTA
Found at i:5560579 original size:31 final size:31
Alignment explanation
Indices: 5560541--5560602 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
5560531 CCTTAACCAT
* **
5560541 AAAACTTAAGCCCTAACCCTAACCCTAAACC
1 AAAACTTAAACCAAAACCCTAACCCTAAACC
*
5560572 AAAACTTAAACCAAAACCCTAACCTTAAACC
1 AAAACTTAAACCAAAACCCTAACCCTAAACC
5560603 CTAAAACCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.47, C:0.35, G:0.02, T:0.16
Consensus pattern (31 bp):
AAAACTTAAACCAAAACCCTAACCCTAAACC
Found at i:5560614 original size:19 final size:20
Alignment explanation
Indices: 5560561--5560619 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
5560551 CCCTAACCCT
*
5560561 AACCCT-AAACCAAAACTTA
1 AACCCTAAAACCAAACCTTA
*
5560580 AA-CC-AAAACCCTAACCTTA
1 AACCCTAAAA-CCAAACCTTA
*
5560599 AACCCTAAAACCAACCCTTA
1 AACCCTAAAACCAAACCTTA
5560619 A
1 A
5560620 CCCCAAACCT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
18 5 0.16
19 12 0.38
20 11 0.34
21 4 0.12
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.15
Consensus pattern (20 bp):
AACCCTAAAACCAAACCTTA
Found at i:5560621 original size:19 final size:19
Alignment explanation
Indices: 5560555--5560622 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
5560545 CTTAAGCCCT
5560555 AACCC-TAACCCT-AAACC
1 AACCCTTAACCCTAAAACC
** *
5560572 AAAACTTAAACC-AAAACCC
1 AACCCTTAACCCTAAAA-CC
5560591 TAA-CCTTAAACCCTAAAACC
1 -AACCCTT-AACCCTAAAACC
5560611 AACCCTTAACCC
1 AACCCTTAACCC
5560623 CAAACCTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
17 3 0.08
18 8 0.21
19 12 0.31
20 12 0.31
21 4 0.10
ACGTcount: A:0.46, C:0.40, G:0.00, T:0.15
Consensus pattern (19 bp):
AACCCTTAACCCTAAAACC
Found at i:5560723 original size:18 final size:20
Alignment explanation
Indices: 5560688--5560728 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5560678 GCATTTCATT
*
5560688 TTTTTTTATTGTTACATGCA
1 TTTTTTAATTGTTACATGCA
5560708 TTTTTTAATTG-T-CATGCA
1 TTTTTTAATTGTTACATGCA
5560726 TTT
1 TTT
5560729 CATATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 1 0.05
20 10 0.50
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.61
Consensus pattern (20 bp):
TTTTTTAATTGTTACATGCA
Found at i:5561667 original size:7 final size:8
Alignment explanation
Indices: 5561656--5561686 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
5561646 AAAAATTGAA
5561656 AAAAAATG
1 AAAAAATG
5561664 AAAAAATG
1 AAAAAATG
5561672 AAAAAATTG
1 AAAAAA-TG
5561681 AAAAAA
1 AAAAAA
5561687 ACAAAAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (8 bp):
AAAAAATG
Found at i:5561667 original size:9 final size:9
Alignment explanation
Indices: 5561655--5561687 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
5561645 GAAAAATTGA
5561655 AAAAAAATG
1 AAAAAAATG
5561664 -AAAAAATG
1 AAAAAAATG
*
5561672 AAAAAATTG
1 AAAAAAATG
5561681 AAAAAAA
1 AAAAAAA
5561688 CAAAAAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (9 bp):
AAAAAAATG
Found at i:5561692 original size:17 final size:17
Alignment explanation
Indices: 5561655--5561693 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5561645 GAAAAATTGA
**
5561655 AAAAAAATGAAAAAATG
1 AAAAAAATGAAAAAAAC
*
5561672 AAAAAATTGAAAAAAAC
1 AAAAAAATGAAAAAAAC
5561689 AAAAA
1 AAAAA
5561694 GTATGTTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.10
Consensus pattern (17 bp):
AAAAAAATGAAAAAAAC
Found at i:5565321 original size:134 final size:134
Alignment explanation
Indices: 5565148--5565441 Score: 393
Period size: 134 Copynumber: 2.2 Consensus size: 134
5565138 GAAATTACTC
*
5565148 CTAAGAGATATTTTGATAATTTCACA-TTTTCAAGATACAATGAAGGTTTTCAAAATTTTAAAAT
1 CTAAGAGATATTTTGATAATTTCACACTTTTCAAGATACAATCAAGGTTTTCAAAATTTTAAAAT
* * * * *
5565212 ATTATAAAATCATGATTTGAAACTTT-TCATGAAATTTTGA-CTTCGAGAAGGTCAAATTACAAA
66 AGTATAAAATCATGATCTAAAACTTTACCA--AAATTTTGATCTT-GAAAAGGTCAAATTACAAA
*
5565275 AATATAT
128 AATACAT
*
5565282 CTAAG-GATATTTTGATAATTTCACACTTTTCAAGGTACAATCAAGGTTTTCAAAATTTTAAAAT
1 CTAAGAGATATTTTGATAATTTCACACTTTTCAAGATACAATCAAGGTTTTCAAAATTTTAAAAT
* *
5565346 AGTATAAAATCTTGATCTAAAACTTTAACCAAAATTTTGATCTTGAAAAGGTCAAATTACAAATA
66 AGTATAAAATCATGATCTAAAACTTT-ACCAAAATTTTGATCTTGAAAAGGTCAAATTACAAAAA
*
5565411 TACCT
130 TACAT
*
5565416 CT-AGCA-ATATTTTGGTAATTTCACAC
1 CTAAG-AGATATTTTGATAATTTCACAC
5565442 ATCCCAAAAT
Statistics
Matches: 142, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
133 22 0.15
134 115 0.81
135 3 0.02
136 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (134 bp):
CTAAGAGATATTTTGATAATTTCACACTTTTCAAGATACAATCAAGGTTTTCAAAATTTTAAAAT
AGTATAAAATCATGATCTAAAACTTTACCAAAATTTTGATCTTGAAAAGGTCAAATTACAAAAAT
ACAT
Found at i:5566088 original size:37 final size:37
Alignment explanation
Indices: 5566038--5566167 Score: 134
Period size: 37 Copynumber: 3.5 Consensus size: 37
5566028 GGAGTTAGAA
* * *
5566038 TAATAAGATAGTACATACATTTTATCTCATACACATTT
1 TAATAA-ATAGTACATGCATTTTATCTCATGCACATAT
* ** * *
5566076 TAATAAACAGTACATGCATTACATTTCATGCACGTAT
1 TAATAAATAGTACATGCATTTTATCTCATGCACATAT
* * * *
5566113 TAATAGATAGTACATGTATTTTATCTCATGCATATCT
1 TAATAAATAGTACATGCATTTTATCTCATGCACATAT
*
5566150 TAATAAAGAGTACATGCA
1 TAATAAATAGTACATGCA
5566168 CTAAGCACAT
Statistics
Matches: 72, Mismatches: 20, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
37 66 0.92
38 6 0.08
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (37 bp):
TAATAAATAGTACATGCATTTTATCTCATGCACATAT
Found at i:5566829 original size:22 final size:22
Alignment explanation
Indices: 5566778--5566829 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
5566768 AAAAAGAGGG
* * * *
5566778 AAAAGAGAAAAATAAGGAGAAG
1 AAAAGAAAAAAATAAAGAAAAA
*
5566800 AAAGGAAAAAAATAAAGAAAAA
1 AAAAGAAAAAAATAAAGAAAAA
5566822 AAAAGAAA
1 AAAAGAAA
5566830 GGAAGTTTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (22 bp):
AAAAGAAAAAAATAAAGAAAAA
Found at i:5566920 original size:26 final size:23
Alignment explanation
Indices: 5566880--5566937 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 23
5566870 AGGATAAAGA
5566880 AGAAGAAAAAGAAGAAAAGAAGG
1 AGAAGAAAAAGAAGAAAAGAAGG
*
5566903 AGAAGACAATAAGAAAGAAAAGAAAG
1 AGAAGA-AA-AAG-AAGAAAAGAAGG
5566929 A-AAGAAAAA
1 AGAAGAAAAA
5566938 AAAATGAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 8 0.26
24 4 0.13
25 7 0.23
26 12 0.39
ACGTcount: A:0.72, C:0.02, G:0.24, T:0.02
Consensus pattern (23 bp):
AGAAGAAAAAGAAGAAAAGAAGG
Found at i:5567477 original size:3 final size:3
Alignment explanation
Indices: 5567469--5567499 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5567459 AAAAATTTCC
5567469 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5567500 TTGAAGAATG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5578928 original size:10 final size:10
Alignment explanation
Indices: 5578915--5578950 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
5578905 ATGAAGAAAG
5578915 AAAAACAAAA
1 AAAAACAAAA
5578925 AAAAACAAAA
1 AAAAACAAAA
*
5578935 TAAAACATAAA
1 AAAAACA-AAA
5578946 AAAAA
1 AAAAA
5578951 ACCTAGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.86, C:0.08, G:0.00, T:0.06
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:5581028 original size:22 final size:22
Alignment explanation
Indices: 5580967--5581030 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
5580957 AAGAAAAAAG
5580967 AAAGAAAAAA-AAA-TGAAGGAAA
1 AAAGAAAAAAGAAAGT-AA-GAAA
**
5580989 AAAG-AAAGGGAAAG--AGAAA
1 AAAGAAAAAAGAAAGTAAGAAA
5581008 AAAGAAAAAAGAAAGTAAGAAA
1 AAAGAAAAAAGAAAGTAAGAAA
5581030 A
1 A
5581031 GGGTTCAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
19 8 0.24
20 9 0.27
21 3 0.09
22 13 0.39
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (22 bp):
AAAGAAAAAAGAAAGTAAGAAA
Found at i:5583653 original size:11 final size:11
Alignment explanation
Indices: 5583630--5583667 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5583620 CTAAATATAT
*
5583630 TTAAATTCA-A
1 TTAAAATCATA
5583640 TTAAAATCATA
1 TTAAAATCATA
*
5583651 TTAAAATGATA
1 TTAAAATCATA
5583662 TTAAAA
1 TTAAAA
5583668 AACAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (11 bp):
TTAAAATCATA
Found at i:5584694 original size:15 final size:15
Alignment explanation
Indices: 5584676--5584720 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
5584666 TTTTTGACAA
5584676 AAAAG-AAAAAAAGTT
1 AAAAGAAAAAAAAG-T
5584691 AAAAGAATAAAAAAGT
1 AAAAGAA-AAAAAAGT
5584707 AAAAGTAAAAAAAA
1 AAAAG-AAAAAAAA
5584721 TTTGATATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 5 0.19
16 13 0.48
17 9 0.33
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (15 bp):
AAAAGAAAAAAAAGT
Found at i:5584709 original size:16 final size:17
Alignment explanation
Indices: 5584681--5584720 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
5584671 GACAAAAAAG
5584681 AAAAAAAGTTAAAAG-A
1 AAAAAAAGTTAAAAGTA
5584697 ATAAAAAAG-TAAAAGTA
1 A-AAAAAAGTTAAAAGTA
5584714 AAAAAAA
1 AAAAAAA
5584721 TTTGATATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (17 bp):
AAAAAAAGTTAAAAGTA
Found at i:5585186 original size:20 final size:20
Alignment explanation
Indices: 5585150--5585192 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
5585140 AAACAAAATC
*
5585150 TTTAAAAATATT-TTTTATA
1 TTTAAAAATATTATTTAATA
5585169 TTTAAAAGATATTATTTAATA
1 TTTAAAA-ATATTATTTAATA
5585190 TTT
1 TTT
5585193 TTTACAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTAAAAATATTATTTAATA
Found at i:5585491 original size:15 final size:14
Alignment explanation
Indices: 5585452--5585504 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
5585442 TAAATCTTTT
5585452 AAAAGAAAAAGTAA
1 AAAAGAAAAAGTAA
*
5585466 AAAAAATAAAAGTAA
1 AAAAGA-AAAAGTAA
*
5585481 AAAAGCAAAAAGCAA
1 AAAAG-AAAAAGTAA
*
5585496 AAAATAAAA
1 AAAAGAAAA
5585505 TAAAATTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 9 0.27
15 23 0.70
16 1 0.03
ACGTcount: A:0.79, C:0.04, G:0.09, T:0.08
Consensus pattern (14 bp):
AAAAGAAAAAGTAA
Found at i:5587402 original size:37 final size:37
Alignment explanation
Indices: 5587360--5587430 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
5587350 GGTCTGAACC
5587360 CAATTAGGCCCATTTGTGTCCAGGCCTAATTAGGGCT
1 CAATTAGGCCCATTTGTGTCCAGGCCTAATTAGGGCT
* *
5587397 CAATTAGGCCCATTTGTGTTCGGGCCTAATTAGG
1 CAATTAGGCCCATTTGTGTCCAGGCCTAATTAGG
5587431 TCAGTCTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (37 bp):
CAATTAGGCCCATTTGTGTCCAGGCCTAATTAGGGCT
Found at i:5589222 original size:15 final size:16
Alignment explanation
Indices: 5589202--5589258 Score: 80
Period size: 15 Copynumber: 3.4 Consensus size: 16
5589192 AAGGCTAACG
5589202 TTATATTATATTA-TA
1 TTATATTATATTATTA
5589217 TTATATTATATTATTA
1 TTATATTATATTATTA
5589233 TTATTATTATTATTATTA
1 TTA-TATTA-TATTATTA
5589251 TTTATATT
1 -TTATATT
5589259 TTTTATTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
15 13 0.34
16 5 0.13
17 5 0.13
18 12 0.32
19 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATATTATATTATTA
Found at i:5589233 original size:3 final size:3
Alignment explanation
Indices: 5589205--5589252 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
5589195 GCTAACGTTA
5589205 TAT TA- TAT TA- TAT TA- TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5589249 TAT T
1 TAT T
5589253 TATATTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 8 0.20
3 33 0.80
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:5589236 original size:6 final size:5
Alignment explanation
Indices: 5589202--5589258 Score: 69
Period size: 5 Copynumber: 10.4 Consensus size: 5
5589192 AAGGCTAACG
5589202 TTATA TTATA TTATA TTATA TTATA TTATTA TTATTA TTATTA TTATTA
1 TTATA TTATA TTATA TTATA TTATA TTA-TA TTA-TA TTA-TA TTA-TA
5589251 TTTATA TT
1 -TTATA TT
5589259 TTTTATTTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
5 25 0.50
6 22 0.44
7 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TTATA
Found at i:5590341 original size:20 final size:21
Alignment explanation
Indices: 5590316--5590357 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
5590306 CTTTCAATAA
5590316 AAATAAAAAAAAAT-ATTTTT
1 AAATAAAAAAAAATAATTTTT
*
5590336 AAATAAACAAAAATAATTTTT
1 AAATAAAAAAAAATAATTTTT
5590357 A
1 A
5590358 TCCTCTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATAAAAAAAAATAATTTTT
Found at i:5598756 original size:41 final size:41
Alignment explanation
Indices: 5598666--5598756 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
5598656 AAAGATAAAT
* * * ** *
5598666 ATTCAGGCTAATGAAAGATGGTTTCTTTACCAAATATGTGT
1 ATTCAGGTTGATGAAAGATGGTTTCTTTACCAAAGACATGC
*
5598707 ATTCAGGTTGATGAAAGATGGTTTCTTTACTAAAGACATGC
1 ATTCAGGTTGATGAAAGATGGTTTCTTTACCAAAGACATGC
*
5598748 ATTTAGGTT
1 ATTCAGGTT
5598757 AATAAAATGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (41 bp):
ATTCAGGTTGATGAAAGATGGTTTCTTTACCAAAGACATGC
Found at i:5599114 original size:119 final size:120
Alignment explanation
Indices: 5598910--5599416 Score: 531
Period size: 119 Copynumber: 4.2 Consensus size: 120
5598900 CACTCATTTA
* ** * *
5598910 ATCTTGGCTCAGTCCAGATCATTTCTTATGATTCGTAATTTCATCCCGATCATTTATTTTCGACC
1 ATCTTGGCTTAGTCCAGATCATTTCTTATGATTCGTGGTTTCATCCCAATCATTTATTTTTGACC
* * *
5598975 TCGACTCGATCCTAGTCACTTTACTTTGACTCATGGTTTCATCCCGATCA-TTCG
66 TCGACTCAATCCTAGTCACTTTATTTTGACTCATGATTTCATCCCGATCACTTCG
* * * * *
5599029 ATCTTAGCTCAATCCAGATCATTTCTTATGATTTGTGGCTTT-ATCCCAATCATTTATTTTTAAC
1 ATCTTGGCTTAGTCCAGATCATTTCTTATGATTCGTGG-TTTCATCCCAATCATTTATTTTTGAC
* * *** *
5599093 CTCGACTCAATCCTGGTCACTTTATTTTGACTCATGATTTTATTGTGGTCACTT-G
65 CTCGACTCAATCCTAGTCACTTTATTTTGACTCATGATTTCATCCCGATCACTTCG
* * * *
5599148 ATCTTGGCTTAGTCTAGATCATTTCTTATGATTCGTGGTTTTATCTCGATCATTTATTTTTGACC
1 ATCTTGGCTTAGTCCAGATCATTTCTTATGATTCGTGGTTTCATCCCAATCATTTATTTTTGACC
* * * * * * * * *
5599213 TCGACTTAGTCCTGGCCGCTTTATTTTAACTCGTGGTTTCATCCCGATCACTTAG
66 TCGACTCAATCCTAGTCACTTTATTTTGACTCATGATTTCATCCCGATCACTTCG
* * *
5599268 -TCTTGGCTTAGTCCAGATCATTTCTTATGATTCGTGGTTTCATCTCAATAATTTATTTTTTACC
1 ATCTTGGCTTAGTCCAGATCATTTCTTATGATTCGTGGTTTCATCCCAATCATTTATTTTTGACC
* * * * * * *
5599332 TCAACTCGATCCTAGTCATTTTTTTTTCTGACTTATGATATCATTCCGATCA--TCTG
66 TCGACTCAATCCTAGTCA-CTTTATTT-TGACTCATGATTTCATCCCGATCACTTC-G
* * *
5599388 ATCTTAGCTTAGTCCAGGTCATTTTTTAT
1 ATCTTGGCTTAGTCCAGATCATTTCTTAT
5599417 ATTTGTAGAT
Statistics
Matches: 319, Mismatches: 61, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
118 3 0.01
119 260 0.82
120 13 0.04
121 43 0.13
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (120 bp):
ATCTTGGCTTAGTCCAGATCATTTCTTATGATTCGTGGTTTCATCCCAATCATTTATTTTTGACC
TCGACTCAATCCTAGTCACTTTATTTTGACTCATGATTTCATCCCGATCACTTCG
Found at i:5599631 original size:3 final size:3
Alignment explanation
Indices: 5599613--5599667 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
5599603 TATGGCATAC
* *
5599613 TAT TAT TAA TAC TAT TATT TAT TAT TAT TAT TA- TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
5599657 TAT TA- TAT TAT
1 TAT TAT TAT TAT
5599668 ATTTTTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
2 6 0.13
3 36 0.80
4 3 0.07
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:5599635 original size:19 final size:21
Alignment explanation
Indices: 5599613--5599670 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
5599603 TATGGCATAC
5599613 TATTATTA-A-TACTATTATT-
1 TATTATTATATTA-TATTATTA
5599632 TATTATTATTATTATATTATTA
1 TATTATTA-TATTATATTATTA
5599654 TATTATTATATTATATT
1 TATTATTATATTATATT
5599671 TTTTTTTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.23
21 17 0.49
22 10 0.29
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTATTATATTATATTATTA
Done.