Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold36
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: 4808052
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18886 characters in sequence are not A, C, G, or T
File 23 of 28
Found at i:3486165 original size:19 final size:18
Alignment explanation
Indices: 3486143--3486235 Score: 52
Period size: 19 Copynumber: 5.1 Consensus size: 18
3486133 ATTTTATTAT
3486143 TTTAAATAATATTATAAAA
1 TTTAAATAATA-TATAAAA
* *
3486162 TTTAAAAAATATATTAATA
1 TTTAAATAATATA-TAAAA
3486181 TTTAATATTAA-AT-TAAAA
1 TTTAA-A-TAATATATAAAA
**
3486199 --TAAA-AATATTATACCA
1 TTTAAATAATA-TATAAAA
*
3486215 CTTAAATAATAATATAAAA
1 TTTAAATAAT-ATATAAAA
3486234 TT
1 TT
3486236 AACCGATTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 20
0.65 0.11 0.24
Matches are distributed among these distances:
13 2 0.04
14 1 0.02
15 2 0.04
16 6 0.11
18 10 0.18
19 28 0.51
20 4 0.07
21 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTAAATAATATATAAAA
Found at i:3493044 original size:24 final size:23
Alignment explanation
Indices: 3493017--3493066 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
3493007 AAAATTTTAA
3493017 ATTT-AAATATGAATATATGAATGC
1 ATTTAAAATATG-A-ATATGAATGC
*
3493041 ATTTTAAAATTTGAATATGAATGC
1 A-TTTAAAATATGAATATGAATGC
3493065 AT
1 AT
3493067 GTTATCTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
23 1 0.04
24 12 0.52
25 4 0.17
26 6 0.26
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (23 bp):
ATTTAAAATATGAATATGAATGC
Found at i:3502244 original size:3 final size:3
Alignment explanation
Indices: 3502236--3502266 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3502226 TTGTTTATTT
*
3502236 ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3502267 AGTCCACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3502478 original size:31 final size:31
Alignment explanation
Indices: 3502421--3502512 Score: 78
Period size: 33 Copynumber: 2.8 Consensus size: 31
3502411 ATTTGATAAA
*
3502421 TTTAATTTAATTAAATTTTAAATATAAATTT
1 TTTAATTTAATTAAATTATAAATATAAATTT
* * * *
3502452 TTTAATTTAAATTATATTATATTATAAACAATAT
1 TTTAATTT-AATTAAATTATA-AATATA-AATTT
*
3502486 TTT-ATTTAAATTTAATTATCAAATATA
1 TTTAATTT-AATTAAATTAT-AAATATA
3502513 TAATATTAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
31 8 0.17
32 10 0.21
33 22 0.46
34 8 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTAATTTAATTAAATTATAAATATAAATTT
Found at i:3502558 original size:20 final size:20
Alignment explanation
Indices: 3502506--3502558 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3502496 TTTAATTATC
3502506 AAATATATAATATTAATATAA
1 AAATA-ATAATATTAATATAA
* * **
3502527 AAATATTTATATTAATATTT
1 AAATAATAATATTAATATAA
3502547 AAATAATAATAT
1 AAATAATAATAT
3502559 AAACTTTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATAATAATATTAATATAA
Found at i:3503550 original size:27 final size:26
Alignment explanation
Indices: 3503519--3503572 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
3503509 ATTTATATTT
*
3503519 AATATA-TT-TTTAAGTATAAATAAAA
1 AATATATTTATTTAAATATAAA-AAAA
*
3503544 AATATATTTATTTAAATATATAAAAA
1 AATATATTTATTTAAATATAAAAAAA
3503570 AAT
1 AAT
3503573 TTAAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.24
26 9 0.36
27 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
AATATATTTATTTAAATATAAAAAAA
Found at i:3505839 original size:15 final size:16
Alignment explanation
Indices: 3505819--3505859 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
3505809 AATAAAAATA
3505819 ATTTTTAA-ATTTTTT
1 ATTTTTAACATTTTTT
3505834 ATTTTTAACGATTTTTT
1 ATTTTTAAC-ATTTTTT
3505851 ATTTATTAA
1 ATTT-TTAA
3505860 TTTAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.35
17 11 0.48
18 4 0.17
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (16 bp):
ATTTTTAACATTTTTT
Found at i:3506719 original size:15 final size:15
Alignment explanation
Indices: 3506699--3506756 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
3506689 AAAAAATTAA
3506699 TAAATTAAATTTATT
1 TAAATTAAATTTATT
* *
3506714 TAAATTATA-TTAAT
1 TAAATTAAATTTATT
* *
3506728 AAAATTTAATTTAATT
1 TAAATTAAATTT-ATT
3506744 T-AATTAAATTTAT
1 TAAATTAAATTTAT
3506757 AAAATATTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
14 12 0.36
15 19 0.58
16 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAAATTAAATTTATT
Found at i:3506732 original size:24 final size:24
Alignment explanation
Indices: 3506692--3506750 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
3506682 AAATTATAAA
* *
3506692 AAATTAATAAATTAAATTT-ATTT
1 AAATTAATTAATAAAATTTAATTT
3506715 AAATTATATTAATAAAATTTAATTT
1 AAATTA-ATTAATAAAATTTAATTT
*
3506740 AATTTAATTAA
1 AAATTAATTAA
3506751 ATTTATAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.19
24 16 0.52
25 9 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATTAATTAATAAAATTTAATTT
Found at i:3506734 original size:20 final size:20
Alignment explanation
Indices: 3506711--3506755 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3506701 AATTAAATTT
3506711 ATTTAAATT-ATATTAATAAA
1 ATTTAAATTAAT-TTAATAAA
* *
3506731 ATTTAATTTAATTTAATTAA
1 ATTTAAATTAATTTAATAAA
3506751 ATTTA
1 ATTTA
3506756 TAAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTAAATTAATTTAATAAA
Found at i:3506738 original size:29 final size:29
Alignment explanation
Indices: 3506692--3506761 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
3506682 AAATTATAAA
3506692 AAATTAAT-AAATTAAATTT-ATTTAAATT
1 AAATTAATAAAATTAAATTTAATTT-AATT
* *
3506720 ATATTAATAAAATTTAATTTAATTTAATT
1 AAATTAATAAAATTAAATTTAATTTAATT
*
3506749 AAATTTATAAAAT
1 AAATTAATAAAAT
3506762 ATTTAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 7 0.19
29 25 0.69
30 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
AAATTAATAAAATTAAATTTAATTTAATT
Found at i:3507937 original size:12 final size:12
Alignment explanation
Indices: 3507922--3507955 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
3507912 AGAAACCCGG
3507922 AGAGAAAAAAGA
1 AGAGAAAAAAGA
*
3507934 AGAGAAGAAAGA
1 AGAGAAAAAAGA
3507946 AGAGAAAAAA
1 AGAGAAAAAA
3507956 CCACCTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAGAAAAAAGA
Found at i:3510727 original size:13 final size:13
Alignment explanation
Indices: 3510688--3510734 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
3510678 TCTTACTCTT
3510688 TATTT-TTTTTAAA
1 TATTTATTTTT-AA
* *
3510701 TATTTATATATAA
1 TATTTATTTTTAA
3510714 TATTTATTTTTAA
1 TATTTATTTTTAA
*
3510727 TATATATT
1 TATTTATT
3510735 AAAATATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 25 0.89
14 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTATTTTTAA
Found at i:3510734 original size:30 final size:30
Alignment explanation
Indices: 3510686--3510743 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
3510676 ACTCTTACTC
** * *
3510686 TTTATTTTTTTTAAATATTTATATATAATA
1 TTTATTTTTAATAAATATTAAAATATAATA
*
3510716 TTTATTTTTAATATATATTAAAATATAA
1 TTTATTTTTAATAAATATTAAAATATAA
3510744 ATACGAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTATTTTTAATAAATATTAAAATATAATA
Found at i:3510818 original size:15 final size:16
Alignment explanation
Indices: 3510798--3510832 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
3510788 TTAAAAAAAA
3510798 ATTAAATA-TATTTAT
1 ATTAAATATTATTTAT
3510813 ATTAAATATTTATTTAT
1 ATTAAATA-TTATTTAT
3510830 ATT
1 ATT
3510833 CGACAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
17 10 0.56
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTAAATATTATTTAT
Found at i:3515785 original size:2 final size:2
Alignment explanation
Indices: 3515778--3515805 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3515768 CGTGAATGTG
3515778 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
3515806 GCTTTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3516067 original size:18 final size:18
Alignment explanation
Indices: 3516035--3516102 Score: 54
Period size: 20 Copynumber: 3.8 Consensus size: 18
3516025 ATTTATAATT
3516035 TATA-TTATATAAATTTAA
1 TATATTTATAT-AATTTAA
*
3516053 TATATTTATATAATTATAT
1 TATATTTATATAATT-TAA
*
3516072 TAATTTTTATATAATATT-A
1 T-ATATTTATATAAT-TTAA
3516091 TAT-TTTAT-TAAT
1 TATATTTATATAAT
3516103 AAAATTATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
16 4 0.09
17 5 0.12
18 10 0.23
19 10 0.23
20 13 0.30
21 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATTTATATAATTTAA
Found at i:3516099 original size:27 final size:26
Alignment explanation
Indices: 3516028--3516102 Score: 73
Period size: 28 Copynumber: 2.8 Consensus size: 26
3516018 TAATTAAATT
* *
3516028 TATAATTTATATTATA-TAAATTTAA
1 TATAATTTATATTTTATTAATTTTAA
*
3516053 TAT-ATTTATATAATTATATTAATTTTTA
1 TATAATTTATAT--TT-TATTAATTTTAA
3516081 TATAATATTATATTTTATTAAT
1 TATAAT-TTATATTTTATTAAT
3516103 AAAATTATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
24 8 0.20
25 3 0.07
26 1 0.02
27 9 0.22
28 12 0.29
29 2 0.05
30 6 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TATAATTTATATTTTATTAATTTTAA
Found at i:3523197 original size:17 final size:17
Alignment explanation
Indices: 3523170--3523220 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
3523160 TATTTTTAAA
3523170 AAATAATATATTTATATT
1 AAAT-ATATATTTATATT
* *
3523188 AAATATATATTTGTATA
1 AAATATATATTTATATT
3523205 AAATATAT-TTTATATT
1 AAATATATATTTATATT
3523221 TGATTTTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 6 0.21
17 19 0.66
18 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
AAATATATATTTATATT
Found at i:3528300 original size:227 final size:226
Alignment explanation
Indices: 3527865--3528312 Score: 806
Period size: 227 Copynumber: 2.0 Consensus size: 226
3527855 TCTCTTTCTC
* *
3527865 CATTTCTTCAGTAGCTTGTTTTTGTTTTTATTCATCATTTTCATTTATTTAGATATTGCCCTTGG
1 CATTTCTTCAGTAGCTTGTTTATGTTTTTATTCATCATTTTCATTTATTTAGACATTGCCCTTGG
* *
3527930 TGGTCGCCGTGACATCCATAAAAACCCATGGGTAATGAGGAAAAAACAAATATTGAGAAATTCTA
66 TGGTCGCCGTGACATCCAGAAAAACCCATGGGTAATAAGGAAAAAACAAATATTGAGAAATTCTA
*
3527995 GTAGCAGATTGGTGATAATTCCCTCAATGCGTATAAAAATCGTTATTTCATACTCCTCTCTGCTT
131 GTAGCAGATTGGTGATAATTCCCTCAATGCATATAAAAATCGTTATTTCATACTCCTCTCTGCTT
3528060 GCTGGTAACACTTATTTGTTTACATCATTTT
196 GCTGGTAACACTTATTTGTTTACATCATTTT
*
3528091 CATTTCTTCAGTAGCTTGTTTATGTTTTTATTCATCATTTTCATTTATTTAGACATTGCCTTTGG
1 CATTTCTTCAGTAGCTTGTTTATGTTTTTATTCATCATTTTCATTTATTTAGACATTGCCCTTGG
*
3528156 TGGTCGCCGTGACATCCAGAAAAACCCATGGGTAATAAGGAAAAAAACAAATATTGAGAATTTCT
66 TGGTCGCCGTGACATCCAGAAAAACCCATGGGTAATAAGG-AAAAAACAAATATTGAGAAATTCT
* *
3528221 AGTAGCAGATTGGTGATATTTCCCTCAATGCATATAAAAATTGTTATTTCATACTCCTCTCTGCT
130 AGTAGCAGATTGGTGATAATTCCCTCAATGCATATAAAAATCGTTATTTCATACTCCTCTCTGCT
3528286 TGCTGGTAACACTTATTTGTTTACATC
195 TGCTGGTAACACTTATTTGTTTACATC
3528313 TTGGTATTTT
Statistics
Matches: 212, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
226 100 0.47
227 112 0.53
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (226 bp):
CATTTCTTCAGTAGCTTGTTTATGTTTTTATTCATCATTTTCATTTATTTAGACATTGCCCTTGG
TGGTCGCCGTGACATCCAGAAAAACCCATGGGTAATAAGGAAAAAACAAATATTGAGAAATTCTA
GTAGCAGATTGGTGATAATTCCCTCAATGCATATAAAAATCGTTATTTCATACTCCTCTCTGCTT
GCTGGTAACACTTATTTGTTTACATCATTTT
Found at i:3532153 original size:17 final size:18
Alignment explanation
Indices: 3532119--3532154 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3532109 ATTAGTTTAA
*
3532119 TTTTAAAAAATCATTATT
1 TTTTAAAAAATCAATATT
3532137 TTTTAAAAAAT-AATATT
1 TTTTAAAAAATCAATATT
3532154 T
1 T
3532155 AATAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTAAAAAATCAATATT
Found at i:3539151 original size:14 final size:15
Alignment explanation
Indices: 3539132--3539160 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3539122 TATTTTATAC
3539132 ATTAATA-AAAAATA
1 ATTAATATAAAAATA
3539146 ATTAATATAAAAATA
1 ATTAATATAAAAATA
3539161 TAGTTCGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTAATATAAAAATA
Found at i:3545433 original size:3 final size:3
Alignment explanation
Indices: 3545425--3545463 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3545415 TAATGGTAGG
3545425 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3545464 GGAGCTCAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3545703 original size:22 final size:22
Alignment explanation
Indices: 3545643--3545704 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 22
3545633 TAATTTATTT
* *
3545643 TAAATTATTATTTAAATAA-TA
1 TAAAATATTATTAAAATAATTA
*
3545664 -AAAATA-T-TTAAATTTAATTA
1 TAAAATATTATTAAA-ATAATTA
3545684 TAAAATATTATTAAAATAATT
1 TAAAATATTATTAAAATAATT
3545705 TTTTAATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
18 4 0.12
19 4 0.12
20 7 0.22
21 6 0.19
22 6 0.19
23 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAAATATTATTAAAATAATTA
Found at i:3545872 original size:15 final size:16
Alignment explanation
Indices: 3545852--3545883 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3545842 GGCGACAAAA
3545852 AAATTTA-TAAATATT
1 AAATTTATTAAATATT
3545867 AAATTTATTAAATATT
1 AAATTTATTAAATATT
3545883 A
1 A
3545884 TTTTTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTTATTAAATATT
Found at i:3546181 original size:16 final size:17
Alignment explanation
Indices: 3546148--3546186 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3546138 TAAATTTAAA
3546148 TAAAATTAAAATTAATT
1 TAAAATTAAAATTAATT
**
3546165 TAAAATTATTATT-ATT
1 TAAAATTAAAATTAATT
3546181 TAAAAT
1 TAAAAT
3546187 AATAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAATTAAAATTAATT
Found at i:3546832 original size:2 final size:2
Alignment explanation
Indices: 3546827--3546853 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3546817 ATGATGCATG
3546827 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3546854 GTTGCACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3556505 original size:3 final size:3
Alignment explanation
Indices: 3556499--3556531 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3556489 TTTGTTGTTG
3556499 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3556532 GCATAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:3557760 original size:14 final size:15
Alignment explanation
Indices: 3557741--3557784 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
3557731 ACGATATAAA
3557741 TATATATTTAAAAATT
1 TATATA-TTAAAAATT
* *
3557757 TATATAATATAAATT
1 TATATATTAAAAATT
3557772 TAATATATTAAAA
1 T-ATATATTAAAA
3557785 TTGATATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATATTAAAAATT
Found at i:3557768 original size:5 final size:5
Alignment explanation
Indices: 3557758--3557850 Score: 50
Period size: 5 Copynumber: 18.4 Consensus size: 5
3557748 TTAAAAATTT
* * * * *
3557758 ATATA ATATAA ATTTA ATATA TTAAA AT-TG ATATAA ATATA AAATA A-ATTA
1 ATATA ATAT-A ATATA ATATA ATATA ATATA ATAT-A ATATA ATATA ATA-TA
* *
3557809 ACTATA ATTATA ATATA ATAAA ATAT- ATA-A ATGTA ATATA AT
1 A-TATA A-TATA ATATA ATATA ATATA ATATA ATATA ATATA AT
3557851 TATATGAATT
Statistics
Matches: 66, Mismatches: 14, Indels: 16
0.69 0.15 0.17
Matches are distributed among these distances:
4 8 0.12
5 41 0.62
6 16 0.24
7 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:3557793 original size:25 final size:23
Alignment explanation
Indices: 3557763--3557848 Score: 65
Period size: 25 Copynumber: 3.7 Consensus size: 23
3557753 AATTTATATA
3557763 ATATAAATTTAATATATTAAAATT
1 ATATAAATTTAATATA-TAAAATT
*
3557787 GATATAAATATAA-A-AT-AAATT
1 -ATATAAATTTAATATATAAAATT
3557808 A-ACTATAATTATAATATAATAAAA-T
1 ATA-TA-AATT-TAATAT-ATAAAATT
*
3557833 ATATAAATGTAATATA
1 ATATAAATTTAATATA
3557849 ATTATATGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 19
0.69 0.04 0.26
Matches are distributed among these distances:
19 1 0.02
20 3 0.06
21 8 0.16
22 5 0.10
23 8 0.16
24 4 0.08
25 17 0.34
26 4 0.08
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (23 bp):
ATATAAATTTAATATATAAAATT
Found at i:3565631 original size:2 final size:2
Alignment explanation
Indices: 3565624--3565656 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3565614 TTGATAGTAT
*
3565624 TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3565657 TTCCAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3571645 original size:2 final size:2
Alignment explanation
Indices: 3571638--3571668 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3571628 ATGATGGGTT
3571638 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3571669 GAATGGGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3572198 original size:19 final size:19
Alignment explanation
Indices: 3572156--3572198 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3572146 AATATATAAA
* *
3572156 TATTTTTAATTATTTTCAT
1 TATTTTAAATTATTTTAAT
3572175 TATTTTAAATT-TTTTAAT
1 TATTTTAAATTATTTTAAT
3572193 TGATTT
1 T-ATTT
3572199 GATATAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTTAAATTATTTTAAT
Found at i:3572288 original size:21 final size:22
Alignment explanation
Indices: 3572262--3572319 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 22
3572252 AATTCAGCTA
*
3572262 ATAAATAT-TTTTATTTTTTAT
1 ATAAATATATTTAATTTTTTAT
3572283 ATAAATATATTTAATTTTTTA-
1 ATAAATATATTTAATTTTTTAT
* *
3572304 AAAAAT-TAATTAATTT
1 ATAAATATATTTAATTT
3572320 GAAAATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.27
21 13 0.39
22 11 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATAAATATATTTAATTTTTTAT
Found at i:3572316 original size:20 final size:22
Alignment explanation
Indices: 3572274--3572319 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
3572264 AAATATTTTT
* *
3572274 ATTTTTTATATAAATATATTTA
1 ATTTTTTATAAAAATATAATTA
3572296 ATTTTTTA-AAAAAT-TAATTA
1 ATTTTTTATAAAAATATAATTA
3572316 ATTT
1 ATTT
3572320 GAAAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 5 0.23
22 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTTTATAAAAATATAATTA
Found at i:3572546 original size:16 final size:16
Alignment explanation
Indices: 3572527--3572557 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3572517 TTTTATGTAG
3572527 TAAAATTTTAAAAATT
1 TAAAATTTTAAAAATT
*
3572543 TAAAATTTTATAAAT
1 TAAAATTTTAAAAAT
3572558 AATATTTAAA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAATTTTAAAAATT
Found at i:3573495 original size:17 final size:19
Alignment explanation
Indices: 3573473--3573507 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
3573463 TATGTTAATC
3573473 ATATAAA-TA-TAAATATA
1 ATATAAATTATTAAATATA
3573490 ATATAAATTATTAAATAT
1 ATATAAATTATTAAATAT
3573508 TTCAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATAAATTATTAAATATA
Found at i:3574718 original size:3 final size:3
Alignment explanation
Indices: 3574710--3574739 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3574700 ACTGTGTTCT
*
3574710 ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3574740 TCATGCATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3575003 original size:11 final size:11
Alignment explanation
Indices: 3574987--3575020 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3574977 AACGTTGACC
3574987 TTTAAATTAAA
1 TTTAAATTAAA
*
3574998 TTTAAATTTAA
1 TTTAAATTAAA
*
3575009 TTTAATTTAAA
1 TTTAAATTAAA
3575020 T
1 T
3575021 AAAAAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:3575426 original size:6 final size:6
Alignment explanation
Indices: 3575415--3575480 Score: 57
Period size: 6 Copynumber: 10.8 Consensus size: 6
3575405 TTTAAAATTT
* *
3575415 ATATAA ATATAA CATATTTTAA ATATAA TTAT-A ATATAA AAAT-A ATATAA
1 ATATAA ATATAA -ATA---TAA ATATAA ATATAA ATATAA ATATAA ATATAA
3575465 ATAT-A ATATAA ATATA
1 ATATAA ATATAA ATATA
3575481 CGAATTATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
5 13 0.27
6 27 0.55
7 3 0.06
9 3 0.06
10 3 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (6 bp):
ATATAA
Found at i:3575452 original size:11 final size:11
Alignment explanation
Indices: 3575436--3575480 Score: 72
Period size: 11 Copynumber: 4.1 Consensus size: 11
3575426 ACATATTTTA
*
3575436 AATATAATTAT
1 AATATAAATAT
*
3575447 AATATAAAAAT
1 AATATAAATAT
3575458 AATATAAATAT
1 AATATAAATAT
3575469 AATATAAATAT
1 AATATAAATAT
3575480 A
1 A
3575481 CGAATTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATATAAATAT
Found at i:3575458 original size:35 final size:34
Alignment explanation
Indices: 3575384--3575458 Score: 80
Period size: 35 Copynumber: 2.1 Consensus size: 34
3575374 AAAATAAAAT
* *
3575384 AAATATAACATATATAAATATTTTAAAATTTATAT
1 AAATATAACATATATAAATATATTAAAA-TTATAA
* *
3575419 AAATATAACATATTTTAAATATAATTATAA-TATAA
1 AAATATAACATA-TATAAATAT-ATTAAAATTATAA
3575454 AAATA
1 AAATA
3575459 ATATAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
35 21 0.62
36 8 0.24
37 5 0.15
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (34 bp):
AAATATAACATATATAAATATATTAAAATTATAA
Found at i:3578027 original size:24 final size:24
Alignment explanation
Indices: 3578000--3578050 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3577990 AACCAAATAA
3578000 ATTTACATTAAATATTATTATATT
1 ATTTACATTAAATATTATTATATT
* ** *
3578024 ATTTATATTTGATATTATTATTTT
1 ATTTACATTAAATATTATTATATT
3578048 ATT
1 ATT
3578051 ATGTATTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
ATTTACATTAAATATTATTATATT
Found at i:3578076 original size:14 final size:16
Alignment explanation
Indices: 3578058--3578087 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3578048 ATTATGTATT
3578058 AAAAA-TAAATATATA
1 AAAAATTAAATATATA
3578073 AAAAATTAAATATAT
1 AAAAATTAAATATAT
3578088 TTATGTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAATTAAATATATA
Found at i:3578403 original size:20 final size:21
Alignment explanation
Indices: 3578368--3578407 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3578358 GATGACCAAA
3578368 AAAAATAAAAATAATAAAAAG
1 AAAAATAAAAATAATAAAAAG
*
3578389 AAAAATAAAGA-AATAAAAA
1 AAAAATAAAAATAATAAAAA
3578408 CGTTGAAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (21 bp):
AAAAATAAAAATAATAAAAAG
Found at i:3584796 original size:2 final size:2
Alignment explanation
Indices: 3584789--3584830 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3584779 TCCTTCACTA
3584789 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
3584831 CATTCAAGCT
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:3586414 original size:25 final size:24
Alignment explanation
Indices: 3586374--3586434 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
3586364 AATGTGATAT
3586374 TTTTTAAGT-AA--TTAAATA-AA
1 TTTTTAAGTAAATTTTAAATATAA
3586394 TTATTTAAGTTAAATTTTAAATATAA
1 TT-TTTAAG-TAAATTTTAAATATAA
*
3586420 TTTTTATGTAAATTT
1 TTTTTAAGTAAATTT
3586435 AGTATTATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 2 0.06
21 6 0.18
22 1 0.03
23 2 0.06
24 7 0.21
25 12 0.35
26 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (24 bp):
TTTTTAAGTAAATTTTAAATATAA
Found at i:3591249 original size:7 final size:7
Alignment explanation
Indices: 3591237--3591279 Score: 61
Period size: 7 Copynumber: 6.1 Consensus size: 7
3591227 TTAATTTTTA
3591237 TTTAAAT
1 TTTAAAT
3591244 TTTAAAT
1 TTTAAAT
3591251 ATTT-AAT
1 -TTTAAAT
*
3591258 TTTATAT
1 TTTAAAT
3591265 TTTAAAT
1 TTTAAAT
3591272 TTTAAAT
1 TTTAAAT
3591279 T
1 T
3591280 ATATAACTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 3 0.09
7 26 0.81
8 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTAAAT
Found at i:3591276 original size:28 final size:28
Alignment explanation
Indices: 3591198--3591278 Score: 93
Period size: 28 Copynumber: 3.0 Consensus size: 28
3591188 ATTTCACCTA
3591198 ATTTATATTTTA-AGTTATTAAA-TTT-AAT
1 ATTTA-ATTTTATA-TT-TTAAATTTTAAAT
3591226 A-TTAATTTT-TA-TTTAAATTTTAAAT
1 ATTTAATTTTATATTTTAAATTTTAAAT
3591251 ATTTAATTTTATATTTTAAATTTTAAAT
1 ATTTAATTTTATATTTTAAATTTTAAAT
3591279 TATATAACTA
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
23 5 0.11
24 4 0.09
25 4 0.09
26 14 0.30
27 5 0.11
28 15 0.32
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (28 bp):
ATTTAATTTTATATTTTAAATTTTAAAT
Found at i:3591284 original size:21 final size:19
Alignment explanation
Indices: 3591196--3591283 Score: 81
Period size: 21 Copynumber: 4.5 Consensus size: 19
3591186 ATATTTCACC
*
3591196 TAATTTATATTTTAAGTTAT
1 TAATTTATATTTTAAATT-T
*
3591216 TAAATTTA-ATATT-AATTT
1 T-AATTTATATTTTAAATTT
* *
3591234 TTATTTAAATTTTAAATATT
1 TAATTTATATTTTAAAT-TT
3591254 TAATTTTATATTTTAAATTT
1 TAA-TTTATATTTTAAATTT
*
3591274 TAAATTATAT
1 TAATTTATAT
3591284 AACTAAATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
17 5 0.09
18 6 0.11
19 12 0.21
20 14 0.25
21 19 0.34
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (19 bp):
TAATTTATATTTTAAATTT
Found at i:3591296 original size:21 final size:20
Alignment explanation
Indices: 3591267--3591306 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
3591257 TTTTATATTT
3591267 TAAATTTTA-AATTATATAAC
1 TAAATTTTATAATTA-ATAAC
3591287 TAAATATTTATAATTAATAA
1 TAAAT-TTTATAATTAATAA
3591307 ATTAAATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATTTTATAATTAATAAC
Found at i:3591312 original size:22 final size:23
Alignment explanation
Indices: 3591245--3591326 Score: 61
Period size: 22 Copynumber: 3.8 Consensus size: 23
3591235 TATTTAAATT
* * *
3591245 TTAAATATTTA-ATTTTATAT-T
1 TTAAATATTTATAATTAATATAA
3591266 TTAAAT-TTTA-AATT-ATATAA
1 TTAAATATTTATAATTAATATAA
*
3591286 CTAAATATTTATAATTAATA-AA
1 TTAAATATTTATAATTAATATAA
*
3591308 TTAAATTACTTAT-ATTAAT
1 TTAAA-TATTTATAATTAAT
3591327 TTTTTAAGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
19 4 0.08
20 12 0.24
21 10 0.20
22 16 0.31
23 9 0.18
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAAATATTTATAATTAATATAA
Found at i:3591492 original size:30 final size:30
Alignment explanation
Indices: 3591458--3591516 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
3591448 TTTAATATAA
*
3591458 ATAATTTAATTT-ATTAAAAATAAAAATTTT
1 ATAATATAATTTGA-TAAAAATAAAAATTTT
* *
3591488 ATAATATAATTTGATAAAATTTAAAATTT
1 ATAATATAATTTGATAAAAATAAAAATTT
3591517 AAATAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (30 bp):
ATAATATAATTTGATAAAAATAAAAATTTT
Found at i:3591535 original size:24 final size:24
Alignment explanation
Indices: 3591508--3591557 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
3591498 TTGATAAAAT
* *
3591508 TTAAAATTTAAAT-AAAATTTAATA
1 TTAAAACTTAAATCAAAATATAA-A
3591532 TT-AAACTTAAATCAAAATATAAA
1 TTAAAACTTAAATCAAAATATAAA
3591555 TTA
1 TTA
3591558 CTTTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
TTAAAACTTAAATCAAAATATAAA
Found at i:3592023 original size:12 final size:13
Alignment explanation
Indices: 3591991--3592024 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
3591981 AGAAACATAT
3591991 TAAATATTTAATA
1 TAAATATTTAATA
3592004 TAAATATTTAATA
1 TAAATATTTAATA
3592017 T-AATATTT
1 TAAATATTT
3592025 TAAATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.33
13 14 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAAATATTTAATA
Found at i:3592123 original size:11 final size:11
Alignment explanation
Indices: 3592103--3592138 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
3592093 TTTTTTATTT
*
3592103 TTTAATTTAAA
1 TTTAAATTAAA
3592114 TTTAAATTAAA
1 TTTAAATTAAA
3592125 -TTAAATTAAA
1 TTTAAATTAAA
3592135 TTTA
1 TTTA
3592139 TAAAAAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:3593752 original size:2 final size:2
Alignment explanation
Indices: 3593745--3593781 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3593735 GATAATAGAA
3593745 AT AT AT AT 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 AT AT AT AT A
3593782 AACAACTGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3593982 original size:10 final size:10
Alignment explanation
Indices: 3593969--3593993 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3593959 TAAAATTATT
3593969 ATTATTATAA
1 ATTATTATAA
3593979 ATTATTATAA
1 ATTATTATAA
3593989 ATTAT
1 ATTAT
3593994 GAATAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTATTATAA
Found at i:3594458 original size:17 final size:17
Alignment explanation
Indices: 3594425--3594480 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
3594415 TTGATTAATG
*
3594425 TTTATTTTAAT-TGTTAA
1 TTTATTTTTATAT-TTAA
3594442 TTTATTTTTATATTTAA
1 TTTATTTTTATATTTAA
* * *
3594459 TATATTATTTTTATTAAA
1 TTTATT-TTTATATTTAA
3594477 TTTA
1 TTTA
3594481 AAAATAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
17 19 0.59
18 13 0.41
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
TTTATTTTTATATTTAA
Found at i:3595468 original size:15 final size:16
Alignment explanation
Indices: 3595450--3595487 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
3595440 TGTCAAGTAT
3595450 TATTTTT-TTAATAAA
1 TATTTTTGTTAATAAA
3595465 TATTTTTGTTAATAAA
1 TATTTTTGTTAATAAA
*
3595481 AATTTTT
1 TATTTTT
3595488 AAATAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TATTTTTGTTAATAAA
Found at i:3595507 original size:20 final size:22
Alignment explanation
Indices: 3595477--3595517 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
3595467 TTTTTGTTAA
3595477 TAAAAATTTTTAAATA-AATTT
1 TAAAAATTTTTAAATATAATTT
3595498 TAAAAA-TTTTAAATATAATT
1 TAAAAATTTTTAAATATAATT
3595518 AAAATATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAAAAATTTTTAAATATAATTT
Found at i:3595591 original size:17 final size:15
Alignment explanation
Indices: 3595543--3595593 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 15
3595533 ATAATTATTT
*
3595543 TAAATTTTATATAATA
1 TAAATTATATA-AATA
3595559 TAAATTAT-TAATATA
1 TAAATTATATAA-ATA
3595574 TCAAAATTATATAAATA
1 T--AAATTATATAAATA
3595591 TAA
1 TAA
3595594 TAATATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
14 1 0.03
15 8 0.27
16 7 0.23
17 11 0.37
18 3 0.10
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAATTATATAAATA
Found at i:3598676 original size:16 final size:15
Alignment explanation
Indices: 3598648--3598686 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3598638 AAGTGAATAG
*
3598648 ATAATAAAAAAAAAAT
1 ATAA-AAAAAAAAAAA
3598664 ATAAAAAATAAAAAAA
1 ATAAAAAA-AAAAAAA
3598680 ATAAAAA
1 ATAAAAA
3598687 TTTTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (15 bp):
ATAAAAAAAAAAAAA
Found at i:3598796 original size:34 final size:32
Alignment explanation
Indices: 3598736--3598800 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 32
3598726 GTTTACGGAA
3598736 TAAATTTTAAAAAAAATATTCATTAAATAAATAG
1 TAAATTTTAAAAAAAATATT-ATTAAA-AAATAG
*
3598770 TAAATTTATAAAAGAAATTATT-TTAAAAAAT
1 TAAATTT-TAAAA-AAAATATTATTAAAAAAT
3598801 TATTTTAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
33 4 0.14
34 12 0.43
35 5 0.18
36 7 0.25
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (32 bp):
TAAATTTTAAAAAAAATATTATTAAAAAATAG
Found at i:3599111 original size:38 final size:38
Alignment explanation
Indices: 3599060--3599168 Score: 130
Period size: 38 Copynumber: 2.9 Consensus size: 38
3599050 CGCCAGCCAC
* *
3599060 CAACCGCCAACCAATTCCAAATTGAATTCTCTAGCTGT
1 CAACCACCAACCAATTCCAAATTAAATTCTCTAGCTGT
*
3599098 CAACCACCAACCAATTCTAAATTAAATTCTCTAG-TCGT
1 CAACCACCAACCAATTCCAAATTAAATTCTCTAGCT-GT
** ** *
3599136 CAGTCACCAGTCAATTCCAAATTAAATTTTCTA
1 CAACCACCAACCAATTCCAAATTAAATTCTCTA
3599169 ACCGTAAGCC
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
37 1 0.02
38 60 0.98
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.29
Consensus pattern (38 bp):
CAACCACCAACCAATTCCAAATTAAATTCTCTAGCTGT
Found at i:3599213 original size:76 final size:76
Alignment explanation
Indices: 3599071--3599214 Score: 175
Period size: 76 Copynumber: 1.9 Consensus size: 76
3599061 AACCGCCAAC
* * * **
3599071 CAATTCCAAATTGAATTCTCTAGCTGTCAACCACCAACCAATTCTAAATTAAATTCTCTAGTCGT
1 CAATTCCAAATTAAATTCTCTAACCGTCAACCACCAACCAATTCTAAATTAAATTCTCTAACCGT
3599136 CAGTCACCAGT
66 CAGTCACCAGT
* * * *
3599147 CAATTCCAAATTAAATTTTCTAACCGT-AAGCCGCTAACCAATGTC-AAATTGAATTCTCTAACC
1 CAATTCCAAATTAAATTCTCTAACCGTCAA-CCACCAACCAAT-TCTAAATTAAATTCTCTAACC
3599210 GTCAG
64 GTCAG
3599215 CCAATTCAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
75 2 0.04
76 53 0.93
77 2 0.04
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.30
Consensus pattern (76 bp):
CAATTCCAAATTAAATTCTCTAACCGTCAACCACCAACCAATTCTAAATTAAATTCTCTAACCGT
CAGTCACCAGT
Found at i:3609052 original size:22 final size:22
Alignment explanation
Indices: 3609022--3609066 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
3609012 AATTAATAAA
*
3609022 ATATTTTTTTAT-ATTAATATTT
1 ATATATTTTTATAATTAA-ATTT
3609044 ATATATTTTTATAATTAAATTT
1 ATATATTTTTATAATTAAATTT
3609066 A
1 A
3609067 AATAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATATATTTTTATAATTAAATTT
Found at i:3610234 original size:2 final size:2
Alignment explanation
Indices: 3610188--3610219 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3610178 CTTTGTTAGA
3610188 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3610220 AATGAGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3611959 original size:8 final size:7
Alignment explanation
Indices: 3611927--3611961 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
3611917 GGTTATATTT
3611927 AATTTAA
1 AATTTAA
3611934 AATTTAA
1 AATTTAA
3611941 AATTTAA
1 AATTTAA
3611948 AATTTAAA
1 AATTT-AA
3611956 AATTTA
1 AATTTA
3611962 TTTATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AATTTAA
Found at i:3612369 original size:12 final size:12
Alignment explanation
Indices: 3612349--3612397 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
3612339 TCAAAAACGG
*
3612349 TTTTTTTTTTTC
1 TTTTCTTTTTTC
* *
3612361 TTTTCTTTTCTG
1 TTTTCTTTTTTC
3612373 TTTTC-TTTTTC
1 TTTTCTTTTTTC
*
3612384 TTTTCTGTTTTC
1 TTTTCTTTTTTC
3612396 TT
1 TT
3612398 GTCAGAAACC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:3612376 original size:7 final size:6
Alignment explanation
Indices: 3612349--3612397 Score: 50
Period size: 5 Copynumber: 8.3 Consensus size: 6
3612339 TCAAAAACGG
*
3612349 TTTTTT TTTTTC -TTTTC -TTTTC TGTTTTC TTTTTC -TTTTC TGTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC T-TTTTC
3612396 TT
1 TT
3612398 GTCAGAAACC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 15 0.39
6 11 0.29
7 12 0.32
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:3612382 original size:18 final size:18
Alignment explanation
Indices: 3612356--3612397 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
3612346 CGGTTTTTTT
3612356 TTTTC-TTTTCTTTTCTG
1 TTTTCTTTTTCTTTTCTG
3612373 TTTTCTTTTTCTTTTCTG
1 TTTTCTTTTTCTTTTCTG
3612391 TTTTCTT
1 TTTTCTT
3612398 GTCAGAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.79
Consensus pattern (18 bp):
TTTTCTTTTTCTTTTCTG
Found at i:3618234 original size:14 final size:14
Alignment explanation
Indices: 3618217--3618243 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3618207 ATTATAAAAT
3618217 TATATAAATATTTA
1 TATATAAATATTTA
3618231 TATATAAATATTT
1 TATATAAATATTT
3618244 TTAATATTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATATAAATATTTA
Found at i:3618598 original size:14 final size:15
Alignment explanation
Indices: 3618575--3618613 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3618565 TATTTAAAAT
3618575 ATATTAAATATATTA
1 ATATTAAATATATTA
*
3618590 ATATTAATATATTTTA
1 ATATTAA-ATATATTA
3618606 TATATTAA
1 -ATATTAA
3618614 TACGCCGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 7 0.33
17 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATTAAATATATTA
Found at i:3618598 original size:23 final size:23
Alignment explanation
Indices: 3618572--3618615 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3618562 TATTATTTAA
3618572 AATATATTAAATATATTAATATT
1 AATATATTAAATATATTAATATT
**
3618595 AATATATTTTATATATTAATA
1 AATATATTAAATATATTAATA
3618616 CGCCGCCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AATATATTAAATATATTAATATT
Found at i:3618815 original size:29 final size:28
Alignment explanation
Indices: 3618771--3618828 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
3618761 AACCTTATAT
* *
3618771 TTTTTATTATATTTAAATAAATTTTTAA
1 TTTTTATTATAATTAAATAAATATTTAA
3618799 TTTTTATTTATAATTAAATAAATATTTAA
1 TTTTTA-TTATAATTAAATAAATATTTAA
3618828 T
1 T
3618829 AGAATCAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTTTATTATAATTAAATAAATATTTAA
Found at i:3618940 original size:21 final size:21
Alignment explanation
Indices: 3618902--3618941 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3618892 TTACATACAA
*
3618902 TAAAAATATAAAATTTTATTT
1 TAAAAATATAAAAATTTATTT
3618923 TAAAAATA-AAATAATTTAT
1 TAAAAATATAAA-AATTTAT
3618942 AATTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAAATATAAAAATTTATTT
Found at i:3619612 original size:23 final size:22
Alignment explanation
Indices: 3619566--3619617 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
3619556 AAAAAGTATG
*
3619566 TATATTAAAGTACCATATTAAT
1 TATATTAAAATACCATATTAAT
* *
3619588 TATATTAAATATATCATATTTAT
1 TATATTAAA-ATACCATATTAAT
3619611 TATATTA
1 TATATTA
3619618 TTATTTTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (22 bp):
TATATTAAAATACCATATTAAT
Found at i:3624060 original size:19 final size:20
Alignment explanation
Indices: 3624038--3624079 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
3624028 TTTAAGATAA
*
3624038 TATAAATTTATAAAATTT-T
1 TATAAATTGATAAAATTTAT
*
3624057 TAT-AATTGATGAAATTTAT
1 TATAAATTGATAAAATTTAT
3624076 TATA
1 TATA
3624080 TTATAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
TATAAATTGATAAAATTTAT
Found at i:3624380 original size:2 final size:2
Alignment explanation
Indices: 3624373--3624403 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3624363 AGCAAAACGT
3624373 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3624404 GGAGGGAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3624697 original size:2 final size:2
Alignment explanation
Indices: 3624690--3624721 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3624680 ACACAATCTA
3624690 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3624722 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3624726 original size:2 final size:2
Alignment explanation
Indices: 3624721--3624748 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3624711 TCTCTCTCTC
3624721 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
3624749 CTTTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3625379 original size:13 final size:13
Alignment explanation
Indices: 3625363--3625388 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3625353 TAATAAATTA
3625363 TATAAATATTAAT
1 TATAAATATTAAT
3625376 TATAAATATTAAT
1 TATAAATATTAAT
3625389 AACAAAAAAA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATAAATATTAAT
Found at i:3627583 original size:17 final size:16
Alignment explanation
Indices: 3627542--3627582 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
3627532 ATTCAAATCA
*
3627542 ATTTAAAATTTAAATT
1 ATTTAAAATTTAAATG
*
3627558 ATTTTAAAATTTATATG
1 A-TTTAAAATTTAAATG
3627575 ATTTAAAA
1 ATTTAAAA
3627583 AATATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATTTAAAATTTAAATG
Found at i:3627935 original size:2 final size:2
Alignment explanation
Indices: 3627930--3627992 Score: 80
Period size: 2 Copynumber: 33.0 Consensus size: 2
3627920 CTCTCTTTAG
*
3627930 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT -T GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3627969 A- AT AT AT AT AT AT AT AT CAT AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT AT
3627993 CAAACTCAGT
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
1 4 0.07
2 49 0.89
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3628212 original size:22 final size:24
Alignment explanation
Indices: 3628167--3628209 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
3628157 TAAAATATAA
3628167 ATTTTATTATTTATAATTATTTAT
1 ATTTTATTATTTATAATTATTTAT
3628191 ATTTT-TTA-TTATAA-TATTT
1 ATTTTATTATTTATAATTATTT
3628210 TATGTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 6 0.32
23 3 0.16
24 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
ATTTTATTATTTATAATTATTTAT
Found at i:3630596 original size:13 final size:12
Alignment explanation
Indices: 3630561--3630597 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
3630551 AATTTTGATT
*
3630561 TAATTAATTTATA
1 TAATT-ATTTTTA
3630574 TAATTATTTTTA
1 TAATTATTTTTA
3630586 TAATTATTTTTA
1 TAATTATTTTTA
3630598 AAAATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TAATTATTTTTA
Found at i:3631564 original size:3 final size:3
Alignment explanation
Indices: 3631556--3631600 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3631546 AAATTGATTC
3631556 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3631601 AATTTTTGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3632920 original size:19 final size:21
Alignment explanation
Indices: 3632876--3632919 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3632866 TAAACTTATT
*
3632876 TTTTATAAAATTATAATTAAA
1 TTTTATAAAATCATAATTAAA
*
3632897 TTTTATAAAATCA-ATTTAAA
1 TTTTATAAAATCATAATTAAA
3632917 TTT
1 TTT
3632920 AAAAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTATAAAATCATAATTAAA
Found at i:3635157 original size:2 final size:2
Alignment explanation
Indices: 3635150--3635178 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3635140 GATCCTTTAA
3635150 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
3635179 AAATAAGAAG
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:3639013 original size:23 final size:23
Alignment explanation
Indices: 3638983--3639038 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
3638973 AAATTTTTAC
*
3638983 TTTTTTTAAAT-TTATGTAATTAA
1 TTTTTTTAAATATTA-ATAATTAA
*
3639006 TTTTTTTAAATATTAATAATTTA
1 TTTTTTTAAATATTAATAATTAA
3639029 TTTTTTTAAA
1 TTTTTTTAAA
3639039 GAAAACCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 27 0.90
24 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTTTTTAAATATTAATAATTAA
Found at i:3640012 original size:22 final size:22
Alignment explanation
Indices: 3639979--3640046 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 22
3639969 AAATTATTAA
*
3639979 ATATACAA-ATAATATATATTT
1 ATATAAAATATAATATATATTT
3640000 ATATAAAATAT-A-ATATATTT
1 ATATAAAATATAATATATATTT
3640020 AT-T-AAATATATATATTATATTT
1 ATATAAAATATA-ATA-TATATTT
3640042 ATATA
1 ATATA
3640047 TTTTTAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
18 6 0.15
19 1 0.03
20 11 0.28
21 9 0.23
22 11 0.28
23 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATAAAATATAATATATATTT
Found at i:3640157 original size:3 final size:3
Alignment explanation
Indices: 3640149--3640188 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
3640139 CTTAACAAGG
*
3640149 ATT ATT ATT ATT ATT ATT ATT ATT ATT AGT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
3640189 TAATTTGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 32 0.94
4 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3641009 original size:104 final size:103
Alignment explanation
Indices: 3640859--3641064 Score: 241
Period size: 104 Copynumber: 2.0 Consensus size: 103
3640849 CTGTAGTAGC
* * * * * * * * *
3640859 TTAAAGAAAATATTTTGTTTGTGTTGTTATGTTTAGACTGTGTTTATATGTATTAATTCAACTTT
1 TTAAAGAAAAGATTTTGTTGGTGTTATTATATTTAAACTGTGTTTATACGAAGTAATTAAACTTT
* * *
3640924 CGGTGGTTTTCATAGATTTAATTGAAAATTTTTCTGCCA
66 CGATGGTTTTCATAGAATTAACTG-AAATTTTTCTGCCA
* * * *
3640963 TTAAAGAAAGGATTTTGTTGGTGTTATTATATTTAAATTTTTTTTATACGAAGTAATTAAACTTT
1 TTAAAGAAAAGATTTTGTTGGTGTTATTATATTTAAACTGTGTTTATACGAAGTAATTAAACTTT
* *
3641028 CGATGGTTTTCGTAGAATTAACTGAATTTTTTCTGCC
66 CGATGGTTTTCATAGAATTAACTGAAATTTTTCTGCC
3641065 TTCTGTTCAC
Statistics
Matches: 84, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
103 12 0.14
104 72 0.86
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (103 bp):
TTAAAGAAAAGATTTTGTTGGTGTTATTATATTTAAACTGTGTTTATACGAAGTAATTAAACTTT
CGATGGTTTTCATAGAATTAACTGAAATTTTTCTGCCA
Found at i:3643658 original size:18 final size:19
Alignment explanation
Indices: 3643623--3643657 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
3643613 ATTCCTGATT
3643623 TCTTATTGTTTCTTTTTTC
1 TCTTATTGTTTCTTTTTTC
3643642 TCTT-TTGTTT-TTTTTT
1 TCTTATTGTTTCTTTTTT
3643658 TTTTTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.03, C:0.11, G:0.06, T:0.80
Consensus pattern (19 bp):
TCTTATTGTTTCTTTTTTC
Found at i:3648471 original size:2 final size:2
Alignment explanation
Indices: 3648464--3648492 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3648454 ATAATTCTTG
3648464 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
3648493 TTAGAGACTT
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:3650070 original size:228 final size:228
Alignment explanation
Indices: 3649637--3650350 Score: 786
Period size: 228 Copynumber: 3.1 Consensus size: 228
3649627 TTGCAAACGA
* * * * * * * *
3649637 TATGCAGATCTTCGTGAAAACCCTGACCGGCAAGACCATAACTCTCGAGGTCGAGAGTTCCGACA
1 TATGCAAATCTTTGTCAAAACCTTGACTGGCAAGACCATAACCCTGGAGGTCGAGAGCTCCGACA
* * * * * * * *
3649702 CGATCGAGAACGTCAAGGCTAAAATCCAGGATAAAGAAGGAATCCCTCCTGACCAGCAGCGTCTT
66 CGATCGAGAACGTCAAGGCCAAAATCCAAGACAAAGAAGGAATCCCACCAGACCAACAACGTCTC
* * * * *
3649767 ATCTTCGCCGGCAAACAGCTCGAAGATGGTCGTACTTTGGCGGATTATAACATCCAGAAGGAGTC
131 ATCTTCGCCGGGAAACAGCTCGAAGACGGCCGTACTTTGGCTGATTATAACATCCAAAAGGAGTC
* * *
3649832 GACCCTCCACCTTGTTCTCCGCCTTCGTGGGGG
196 GACCCTCCACCTTGTTCTCAGGCTTCGTGGAGG
* * *
3649865 TATGCAAATCTTTGTCAAAACCTTGACTGGCAAGACCATCACCCTGGAAGTGGAGAGCTCCGACA
1 TATGCAAATCTTTGTCAAAACCTTGACTGGCAAGACCATAACCCTGGAGGTCGAGAGCTCCGACA
* * * *
3649930 CCATCGAGAACGTCAAGGCCAAAATCCAAGACAAAGAAGGCATCCCACCCGACCAACAACGACTC
66 CGATCGAGAACGTCAAGGCCAAAATCCAAGACAAAGAAGGAATCCCACCAGACCAACAACGTCTC
* *
3649995 ATCTTCGCCGGGAAACAACTTGAAGACGGCCGTACTTTGGCTGATTATAACATCCAAAAGGAGTC
131 ATCTTCGCCGGGAAACAGCTCGAAGACGGCCGTACTTTGGCTGATTATAACATCCAAAAGGAGTC
* * * *
3650060 AACTCTCCACCTTGTACTCAGGCTCCGTGGAGG
196 GACCCTCCACCTTGTTCTCAGGCTTCGTGGAGG
* * * * *
3650093 TATGCAAATCTTTGTCAAAACCTTGACAGGGAAGACTATAACCCTGGAGGTCGAGAGTTCGGACA
1 TATGCAAATCTTTGTCAAAACCTTGACTGGCAAGACCATAACCCTGGAGGTCGAGAGCTCCGACA
* * * * * * *
3650158 CGATTGATAACGTTAAGG-CAAAGATTCAAGATAAGGAAGGAATCCCACCAGACCAACAACGTTT
66 CGATCGAGAACGTCAAGGCCAAA-ATCCAAGACAAAGAAGGAATCCCACCAGACCAACAACGTCT
* * * * ** * * * * * *
3650222 GATCTTCGCTGGGAAGCAGCTCGAGGACGGGAGGACCTTGGCTGACTACAATATCCAGAAA-GAA
130 CATCTTCGCCGGGAAACAGCTCGAAGACGGCCGTACTTTGGCTGATTATAACATCCA-AAAGGAG
* *
3650286 TCGACCCTTCACCTTG-TCTTGAGGCTTCGTGGAGG
194 TCGACCCTCCACCTTGTTC-TCAGGCTTCGTGGAGG
* * *
3650321 AATGCAGATCTTTGTCAAGACCTTGACTGG
1 TATGCAAATCTTTGTCAAAACCTTGACTGG
3650351 TAAAACAATC
Statistics
Matches: 404, Mismatches: 79, Indels: 6
0.83 0.16 0.01
Matches are distributed among these distances:
227 5 0.01
228 396 0.98
229 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.21
Consensus pattern (228 bp):
TATGCAAATCTTTGTCAAAACCTTGACTGGCAAGACCATAACCCTGGAGGTCGAGAGCTCCGACA
CGATCGAGAACGTCAAGGCCAAAATCCAAGACAAAGAAGGAATCCCACCAGACCAACAACGTCTC
ATCTTCGCCGGGAAACAGCTCGAAGACGGCCGTACTTTGGCTGATTATAACATCCAAAAGGAGTC
GACCCTCCACCTTGTTCTCAGGCTTCGTGGAGG
Found at i:3650371 original size:228 final size:226
Alignment explanation
Indices: 3649637--3650535 Score: 744
Period size: 228 Copynumber: 3.9 Consensus size: 226
3649627 TTGCAAACGA
* * * * * * * * * *
3649637 TATGCAGATCTTCGTGAAAACCCTGACCGGCAAGACCATAACTCTCGAGGTCGAGAGTTCCGACA
1 TATGCAAATCTTTGTCAAAACCTTGACTGGCAAGACAATCACCCTGGAGGTCGAGAGCTCCGACA
* * * * * *
3649702 CGATCGAGAACGTCAAGGCTAAAATCCAGGATAAAGAAGGAATCCCTCCTGACCAGCAGCGTCTT
66 CGATCGAGAACGTCAAGGC-AAAATCCAAGACAAAGAAGGAATCCCACCAGACCAACAACGT-TT
* * ** * * *
3649767 ATCTTCGCCGGCAAACAGCTCGAAGATGGTCGTACTTTGGCGGATTATAACATCCAGAAGGAGTC
129 ATCTTCGCCGGCAAACAACTCGAAGACGGGAGGACTTTGGCTGATTATAACATCCAGAAAGAGTC
* * *
3649832 GACCCTCCACCTTGT-TCTCCGCCTTCGTGGGGG
194 GACCCTCCACCTTGTCT-TCAGGCTTCGTGGAGG
* * *
3649865 TATGCAAATCTTTGTCAAAACCTTGACTGGCAAGACCATCACCCTGGAAGTGGAGAGCTCCGACA
1 TATGCAAATCTTTGTCAAAACCTTGACTGGCAAGACAATCACCCTGGAGGTCGAGAGCTCCGACA
* * * * *
3649930 CCATCGAGAACGTCAAGGCCAAAATCCAAGACAAAGAAGGCATCCCACCCGACCAACAACGACTC
66 CGATCGAGAACGTCAAGG-CAAAATCCAAGACAAAGAAGGAATCCCACCAGACCAACAACG-TTT
* * ** *
3649995 ATCTTCGCCGGGAAACAACTTGAAGACGGCCGTACTTTGGCTGATTATAACATCCA-AAAGGAGT
129 ATCTTCGCCGGCAAACAACTCGAAGACGGGAGGACTTTGGCTGATTATAACATCCAGAAA-GAGT
* * *
3650059 CAACTCTCCACCTTGTAC-TCAGGCTCCGTGGAGG
193 CGACCCTCCACCTTGT-CTTCAGGCTTCGTGGAGG
* * * * * *
3650093 TATGCAAATCTTTGTCAAAACCTTGACAGGGAAGACTATAACCCTGGAGGTCGAGAGTTCGGACA
1 TATGCAAATCTTTGTCAAAACCTTGACTGGCAAGACAATCACCCTGGAGGTCGAGAGCTCCGACA
* * * * * *
3650158 CGATTGATAACGTTAAGGCAAAGATTCAAGATAAGGAAGGAATCCCACCAGACCAACAACGTTTG
66 CGATCGAGAACGTCAAGGCAAA-ATCCAAGACAAAGAAGGAATCCCACCAGACCAACAACGTTT-
* * * * * * * * * *
3650223 ATCTTCGCTGGGAAGCAGCTCGAGGACGGGAGGACCTTGGCTGACTACAATATCCAGAAAGAATC
129 ATCTTCGCCGGCAAACAACTCGAAGACGGGAGGACTTTGGCTGATTATAACATCCAGAAAGAGTC
* *
3650288 GACCCTTCACCTTGTCTTGAGGCTTCGTGGAGG
194 GACCCTCCACCTTGTCTTCAGGCTTCGTGGAGG
* * * * * * * * * *
3650321 AATGCAGATCTTTGTCAAGACCTTGACTGGTAAAACAATCACCATGGAGGTGGAAAGCTCGGATA
1 TATGCAAATCTTTGTCAAAACCTTGACTGGCAAGACAATCACCCTGGAGGTCGAGAGCTCCGACA
* * * * * * * * * * * * *
3650386 CAATTGAAAATGTCAAGGCCAAGATTCAGGACAAGGAAGGGATACCC-CCAGATCAGCAAAGGCT
66 CGATCGAGAACGTCAAGG-CAAAATCCAAGACAAAGAAGGAAT-CCCACCAGACCAAC-AACGTT
* * * * * * * * * *
3650450 TATCTTTGCTGGCAAGCAATTAGAGGATGGGAGGACATTAGCTGATTATAACATTCAGAAAGAGT
128 TATCTTCGCCGGCAAACAACTCGAAGACGGGAGGACTTTGGCTGATTATAACATCCAGAAAGAGT
* *
3650515 CTACCCTTCACCTTGTTCTTC
193 CGACCCTCCACCTTG-TCTTC
3650536 GTCTCCGTGG
Statistics
Matches: 547, Mismatches: 111, Indels: 25
0.80 0.16 0.04
Matches are distributed among these distances:
227 8 0.01
228 520 0.95
229 19 0.03
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.21
Consensus pattern (226 bp):
TATGCAAATCTTTGTCAAAACCTTGACTGGCAAGACAATCACCCTGGAGGTCGAGAGCTCCGACA
CGATCGAGAACGTCAAGGCAAAATCCAAGACAAAGAAGGAATCCCACCAGACCAACAACGTTTAT
CTTCGCCGGCAAACAACTCGAAGACGGGAGGACTTTGGCTGATTATAACATCCAGAAAGAGTCGA
CCCTCCACCTTGTCTTCAGGCTTCGTGGAGG
Found at i:3651411 original size:11 final size:12
Alignment explanation
Indices: 3651397--3651467 Score: 51
Period size: 12 Copynumber: 5.9 Consensus size: 12
3651387 ATTTTATTTA
3651397 ATTT-TTTAAAT
1 ATTTATTTAAAT
3651408 ATTTATGTT-AAT
1 ATTTAT-TTAAAT
3651420 ATTTATTTGAATAT
1 ATTTATTT-AA-AT
**
3651434 ACTTTAAATAAAT
1 A-TTTATTTAAAT
*
3651447 ATATATTTAAA-
1 ATTTATTTAAAT
3651458 ATTT-TTTAAA
1 ATTTATTTAAA
3651468 AAATAATATA
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
10 6 0.12
11 9 0.19
12 17 0.35
13 6 0.12
14 5 0.10
15 5 0.10
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (12 bp):
ATTTATTTAAAT
Found at i:3651495 original size:17 final size:16
Alignment explanation
Indices: 3651468--3651522 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
3651458 ATTTTTTAAA
3651468 AAATAATATATTTATATT
1 AAAT-ATATATTTAT-TT
*
3651486 AAATATATATATATTT
1 AAATATATATTTATTT
*
3651502 AAATTTAATATTTATTT
1 AAATAT-ATATTTATTT
3651519 AAAT
1 AAAT
3651523 TTAATTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 7 0.21
17 22 0.67
18 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AAATATATATTTATTT
Found at i:3651511 original size:21 final size:21
Alignment explanation
Indices: 3651473--3651527 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
3651463 TTAAAAAATA
* *
3651473 ATATATTTATATTAAATATAT
1 ATATATTTAAATTTAATATAT
3651494 ATATATTTAAATTT-A-ATAT
1 ATATATTTAAATTTAATATAT
3651513 -T-TATTTAAATTTAAT
1 ATATATTTAAATTTAAT
3651528 TAATTTATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 11 0.37
18 2 0.07
19 4 0.13
20 1 0.03
21 12 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATATTTAAATTTAATATAT
Found at i:3651523 original size:17 final size:17
Alignment explanation
Indices: 3651475--3651527 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
3651465 AAAAAATAAT
*
3651475 ATATTTATATTAAATAT-
1 ATATTTAT-TTAAATTTA
*
3651492 ATATATATTTAAATTTA
1 ATATTTATTTAAATTTA
3651509 ATATTTATTTAAATTTA
1 ATATTTATTTAAATTTA
3651526 AT
1 AT
3651528 TAATTTATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 7 0.22
17 25 0.78
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTTATTTAAATTTA
Found at i:3652601 original size:3 final size:3
Alignment explanation
Indices: 3652593--3652631 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
3652583 ATCTAATAAA
*
3652593 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT AAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
3652632 ATTGAACAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:3653814 original size:21 final size:23
Alignment explanation
Indices: 3653790--3653834 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3653780 TATAATAATT
3653790 ATAA-TTA-CATTTTTAATTATA
1 ATAATTTATCATTTTTAATTATA
* *
3653811 ATAATTTATGATTTTTATTTATA
1 ATAATTTATCATTTTTAATTATA
3653834 A
1 A
3653835 AAAAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 3 0.15
23 13 0.65
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATAATTTATCATTTTTAATTATA
Found at i:3654348 original size:19 final size:20
Alignment explanation
Indices: 3654332--3654379 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 20
3654322 TAAATTATTA
3654332 AAATAT-TAATATTTTATAT
1 AAATATATAATATTTTATAT
3654351 AAATATATAATATTTTAAATAT
1 AAATATATAATATTTT--ATAT
3654373 AAATATA
1 AAATATA
3654380 ATTACATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.23
20 9 0.35
22 11 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATATATAATATTTTATAT
Found at i:3654353 original size:20 final size:21
Alignment explanation
Indices: 3654326--3654379 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
3654316 ATAAAATAAA
3654326 TTAT-TAAAATAT-TAATATT
1 TTATATAAAATATATAATATT
3654345 TTATAT-AAATATATAATATT
1 TTATATAAAATATATAATATT
*
3654365 TTAAATATAAATATA
1 TTATATA-AAATATA
3654380 ATTACATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 10 0.33
20 13 0.43
22 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTATATAAAATATATAATATT
Found at i:3654378 original size:35 final size:33
Alignment explanation
Indices: 3654311--3654378 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 33
3654301 TATATCAAAA
*
3654311 TTTATATAAAATAAATTATTAAAATATTAATAT
1 TTTATATAAAATAAATTATTAAAATATAAATAT
*
3654344 TTTATATAAATATATAA-TATTTTAAATATAAATAT
1 TTTATATAAA-ATA-AATTA-TTAAAATATAAATAT
3654379 AATTACATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 10 0.33
34 5 0.17
35 15 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
TTTATATAAAATAAATTATTAAAATATAAATAT
Found at i:3654719 original size:26 final size:28
Alignment explanation
Indices: 3654684--3654736 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 28
3654674 TATTTAAATA
3654684 TATATTTTATTTATA-TTTA-AAAATTT
1 TATATTTTATTTATATTTTATAAAATTT
3654710 TATATTTTATTTATATTTTATAAAATT
1 TATATTTTATTTATATTTTATAAAATT
3654737 GATATAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 15 0.60
27 4 0.16
28 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
TATATTTTATTTATATTTTATAAAATTT
Found at i:3654884 original size:22 final size:22
Alignment explanation
Indices: 3654853--3654896 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3654843 TTATATGTAT
* *
3654853 AAATTTTATTTATAAATTATAA
1 AAATTATATTTATAAATAATAA
3654875 AAATTATATTTATAAATAATAA
1 AAATTATATTTATAAATAATAA
3654897 TTAAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATTATATTTATAAATAATAA
Found at i:3654916 original size:25 final size:26
Alignment explanation
Indices: 3654874--3654928 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
3654864 ATAAATTATA
* * *
3654874 AAAATTATATTTATAAATAA-TAATT
1 AAAATTAAATTAAAAAATAATTAATT
*
3654899 AAAATTAAATTAAAAAATAATTGATT
1 AAAATTAAATTAAAAAATAATTAATT
3654925 AAAA
1 AAAA
3654929 ACTAATATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (26 bp):
AAAATTAAATTAAAAAATAATTAATT
Found at i:3655155 original size:15 final size:16
Alignment explanation
Indices: 3655105--3655188 Score: 59
Period size: 18 Copynumber: 5.0 Consensus size: 16
3655095 TAAAAATTAA
3655105 AATATTCATATCATATTT
1 AATATT-ATAT-ATATTT
*
3655123 -ATATT-TATAT-TTAA
1 AATATTATATATATT-T
3655137 AATATTATATAT-TTT
1 AATATTATATATATTT
3655152 AATAAATTATAATATATTT
1 AAT--ATTAT-ATATATTT
3655171 ATATATTATACTATATTT
1 A-ATATTATA-TATATTT
3655189 TTATTTTTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
13 2 0.04
14 2 0.04
15 11 0.20
16 7 0.13
17 11 0.20
18 16 0.29
19 4 0.07
20 2 0.04
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (16 bp):
AATATTATATATATTT
Found at i:3655178 original size:18 final size:18
Alignment explanation
Indices: 3655128--3655210 Score: 66
Period size: 18 Copynumber: 4.7 Consensus size: 18
3655118 TATTTATATT
*
3655128 TATATTTAAAATATTAT-A
1 TATATTT-ATATATTATAA
*
3655146 TAT-TTTAATAAATTATAA
1 TATATTT-ATATATTATAA
*
3655164 TATATTTATATATTATAC
1 TATATTTATATATTATAA
* * *
3655182 TATATTTTTAT-TTTTAT
1 TATATTTATATATTATAA
3655199 TATATTT-TATAT
1 TATATTTATATAT
3655211 AAAATTTTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
16 3 0.05
17 23 0.42
18 26 0.47
19 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATTTATATATTATAA
Found at i:3655240 original size:23 final size:23
Alignment explanation
Indices: 3655190--3655241 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
3655180 ACTATATTTT
*
3655190 TATTTTTATTATATTTTATATAA
1 TATTTTAATTATATTTTATATAA
* *
3655213 AATTTTAATTAT-TTTTAATATTA
1 TATTTTAATTATATTTT-ATATAA
3655236 TATTTT
1 TATTTT
3655242 TGGAGCATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TATTTTAATTATATTTTATATAA
Found at i:3655744 original size:13 final size:14
Alignment explanation
Indices: 3655731--3655771 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
3655721 ATTTATGTAA
3655731 TTAATAATATTAAT
1 TTAATAATATTAAT
*
3655745 TTAAAAAT-TTATAT
1 TTAATAATATTA-AT
3655759 TTAAT-ATATTAAT
1 TTAATAATATTAAT
3655772 ATATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAATAATATTAAT
Found at i:3656379 original size:17 final size:17
Alignment explanation
Indices: 3656357--3656391 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3656347 CAATAAATAA
*
3656357 TTTATTTAAATTTAAGT
1 TTTATTAAAATTTAAGT
*
3656374 TTTATTAAAATTTTAGT
1 TTTATTAAAATTTAAGT
3656391 T
1 T
3656392 AAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (17 bp):
TTTATTAAAATTTAAGT
Found at i:3657021 original size:24 final size:24
Alignment explanation
Indices: 3656972--3657021 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
3656962 TTTTTGGTAC
*
3656972 AAAATTATAATCTAAAAATATAAA
1 AAAATTATAATATAAAAATATAAA
* *
3656996 AAAATTATATATATTAAAATTTAAA
1 AAAATTATA-ATATAAAAATATAAA
3657021 A
1 A
3657022 TTTAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (24 bp):
AAAATTATAATATAAAAATATAAA
Found at i:3658244 original size:18 final size:19
Alignment explanation
Indices: 3658204--3658244 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
3658194 TTTAATTAAG
*
3658204 AATTTAATTTTTTATATTT
1 AATTTAATTTTTTATATTA
3658223 AATTT-ATTATTTT-TATTA
1 AATTTAATT-TTTTATATTA
3658241 AATT
1 AATT
3658245 CACTTTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
AATTTAATTTTTTATATTA
Found at i:3661868 original size:24 final size:24
Alignment explanation
Indices: 3661841--3661887 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3661831 TATAAAATAA
*
3661841 ATATAATAA-AATTATTAATATATT
1 ATAT-ATAATAATTAATAATATATT
*
3661865 ATATTTAATAATTAATAATATAT
1 ATATATAATAATTAATAATATAT
3661888 ATTAAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATATATAATAATTAATAATATATT
Found at i:3662188 original size:26 final size:26
Alignment explanation
Indices: 3662159--3662210 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3662149 TAAATCAGAG
3662159 TTATTTATT-AGTTAAATTATAATTTA
1 TTATTTATTAAGTTAAATTA-AATTTA
* *
3662185 TTATTTTTTAATTTAAATTAAATTTA
1 TTATTTATTAAGTTAAATTAAATTTA
3662211 AATAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (26 bp):
TTATTTATTAAGTTAAATTAAATTTA
Done.