Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 54 of 125
Found at i:16654373 original size:14 final size:14
Alignment explanation
Indices: 16654354--16654385 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
16654344 CATTAAGGCA
16654354 TCCTTAACCTCTAT
1 TCCTTAACCTCTAT
16654368 TCCTTAACCTCTAT
1 TCCTTAACCTCTAT
16654382 TCCT
1 TCCT
16654386 ATTACTCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.19, C:0.38, G:0.00, T:0.44
Consensus pattern (14 bp):
TCCTTAACCTCTAT
Found at i:16658466 original size:20 final size:21
Alignment explanation
Indices: 16658438--16658476 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
16658428 GAGCATTTGA
*
16658438 GAGATTTTTGAGAG-TTGAAT
1 GAGAATTTTGAGAGATTGAAT
16658458 GAGAATTTTGAGAGATTGA
1 GAGAATTTTGAGAGATTGA
16658477 GGAGAGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (21 bp):
GAGAATTTTGAGAGATTGAAT
Found at i:16658483 original size:22 final size:20
Alignment explanation
Indices: 16658436--16658491 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
16658426 GAGAGCATTT
*
16658436 GAGAGATTTTTGAGAGTTGA
1 GAGAGAATTTTGAGAGTTGA
16658456 -ATGAGAATTTTGAGAGATTGA
1 GA-GAGAATTTTGAGAG-TTGA
*
16658477 GGAGAGAATTATGAG
1 -GAGAGAATTTTGAG
16658492 TGAGAAATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 1 0.03
20 13 0.43
21 4 0.13
22 11 0.37
23 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.34, T:0.30
Consensus pattern (20 bp):
GAGAGAATTTTGAGAGTTGA
Found at i:16660605 original size:21 final size:21
Alignment explanation
Indices: 16660579--16660621 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
16660569 TATTATGTTA
16660579 TTTTTATATATTAATGCAATT
1 TTTTTATATATTAATGCAATT
*
16660600 TTTTTATATATTAATGTAATT
1 TTTTTATATATTAATGCAATT
16660621 T
1 T
16660622 AAAACACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTTTATATATTAATGCAATT
Found at i:16660746 original size:23 final size:24
Alignment explanation
Indices: 16660719--16660764 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
16660709 AATTTTCAAT
16660719 AAATAAAA-AATTATAAA-ATATTA
1 AAATAAAACAA-TATAAATATATTA
16660742 AAATAAAACAATATAAATATATT
1 AAATAAAACAATATAAATATATT
16660765 TTTTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATAAAACAATATAAATATATTA
Found at i:16664030 original size:21 final size:21
Alignment explanation
Indices: 16663981--16664060 Score: 97
Period size: 21 Copynumber: 3.7 Consensus size: 21
16663971 GATTTATCGT
* *
16663981 TTTTAAATTAGGGTTTAAGTC
1 TTTTAAATTAGGGTTTAGGTA
* *
16664002 TTTAAAATTAGGGTTTTGGTA
1 TTTTAAATTAGGGTTTAGGTA
*
16664023 TTTTAAATAAGGGTTTAGGATA
1 TTTTAAATTAGGGTTTAGG-TA
16664045 TTTTAAATTAAGGGTT
1 TTTTAAATT-AGGGTT
16664061 ATGGAAAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
21 33 0.67
22 10 0.20
23 6 0.12
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.46
Consensus pattern (21 bp):
TTTTAAATTAGGGTTTAGGTA
Found at i:16671019 original size:4 final size:4
Alignment explanation
Indices: 16671010--16671049 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
16671000 GATAAATGAT
16671010 CATA CATA CA-A CATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
16671050 GTATACATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.09
4 32 0.91
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:16673023 original size:20 final size:20
Alignment explanation
Indices: 16672995--16673113 Score: 83
Period size: 20 Copynumber: 5.9 Consensus size: 20
16672985 CCACGTCAGC
*
16672995 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
16673015 AAATTATTTTTTTAAAA-TA-TA
1 AAATTA---TTTTAAAATTATTA
16673036 AAATTA--TTAAAATTATTTTA
1 AAATTATTTTAAAATTA--TTA
*
16673056 AAATTAATTTAAAATTAGTTTTTA
1 AAATTATTTTAAAATTA----TTA
16673080 AAA-TA---TAAAATTATTA
1 AAATTATTTTAAAATTATTA
16673096 AAATTATTTTAAAATTAT
1 AAATTATTTTAAAATTAT
16673114 AATCATCATC
Statistics
Matches: 83, Mismatches: 1, Indels: 30
0.73 0.01 0.26
Matches are distributed among these distances:
16 12 0.14
17 4 0.05
20 30 0.36
21 8 0.10
22 11 0.13
23 10 0.12
24 8 0.10
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:16673040 original size:30 final size:29
Alignment explanation
Indices: 16673004--16673105 Score: 137
Period size: 30 Copynumber: 3.7 Consensus size: 29
16672994 CAAATGATTT
16673004 TAAAATTATTAAAATTATTTTTTTAAAATA
1 TAAAATTATTAAAATTA-TTTTTTAAAATA
16673034 TAAAATTATTAAAATTA--TTTTAAAAT-
1 TAAAATTATTAAAATTATTTTTTAAAATA
*
16673060 T--AA-T-TTAAAATTAGTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
16673085 TAAAATTATTAAAATTATTTT
1 TAAAATTATTAAAATTATTTT
16673106 AAAATTATAA
Statistics
Matches: 64, Mismatches: 1, Indels: 15
0.80 0.01 0.19
Matches are distributed among these distances:
22 9 0.14
23 1 0.02
24 11 0.17
25 1 0.02
26 1 0.02
27 11 0.17
28 1 0.02
29 12 0.19
30 17 0.27
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTAAAATA
Found at i:16673058 original size:11 final size:11
Alignment explanation
Indices: 16673034--16673113 Score: 77
Period size: 11 Copynumber: 7.8 Consensus size: 11
16673024 TTTTAAAATA
16673034 TAAAATTA--T
1 TAAAATTATTT
16673043 TAAAATTATTT
1 TAAAATTATTT
*
16673054 TAAAATTAATT
1 TAAAATTATTT
16673065 TAAAATTAGTTTT
1 TAAAATTA--TTT
16673078 TAAAA-TA---
1 TAAAATTATTT
16673085 TAAAATTA--T
1 TAAAATTATTT
16673094 TAAAATTATTT
1 TAAAATTATTT
16673105 TAAAATTAT
1 TAAAATTAT
16673114 AATCATCATC
Statistics
Matches: 61, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
7 5 0.08
8 2 0.03
9 16 0.26
11 29 0.48
12 2 0.03
13 7 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:16673087 original size:51 final size:51
Alignment explanation
Indices: 16672995--16673112 Score: 195
Period size: 51 Copynumber: 2.3 Consensus size: 51
16672985 CCACGTCAGC
* *
16672995 AAATGATTTTAAAATT-ATTAAAATTATTTTTTTAAAATATAAAATTATTA
1 AAATTATTTTAAAATTAATTAAAATTATGTTTTTAAAATATAAAATTATTA
16673045 AAATTATTTTAAAATTAATTTAAAATTA-GTTTTTAAAATATAAAATTATTA
1 AAATTATTTTAAAATTAA-TTAAAATTATGTTTTTAAAATATAAAATTATTA
16673096 AAATTATTTTAAAATTA
1 AAATTATTTTAAAATTA
16673113 TAATCATCAT
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
50 15 0.23
51 40 0.62
52 9 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (51 bp):
AAATTATTTTAAAATTAATTAAAATTATGTTTTTAAAATATAAAATTATTA
Found at i:16673625 original size:69 final size:70
Alignment explanation
Indices: 16673543--16673760 Score: 253
Period size: 80 Copynumber: 3.0 Consensus size: 70
16673533 ATCATATGAG
*
16673543 GATCCCAGGAAAGTTATGTTTGAGATAAAAATGGGGTTGGCTTTGTCTCTTACGTCTTTGCTCAT
1 GATCCCAGGAAAGTTATGTTTGCGATAAAAATGGGGTTGGCTTTGTCTCTTACGTCTTTGCTCAT
16673608 ATTTA
66 ATTTA
* * *
16673613 -ATCCCAGGAAAGTTATATTTGCGATAAAAATGGGGCTGGCTTTGTCTCTT-TGCTCATATTTTG
1 GATCCCAGGAAAGTTATGTTTGCGATAAAAATGGGGTTGGCTTTGTCTCTTACG-TC----TTT-
* *
16673676 GAAAGGATCATA-TGA
60 -----GCTCATATTTA
16673691 GGATCCCAGGAAAGTTATGTTTGCGATAAAAATGGGGTTGGCTTTGTCTCTTACGTCTTTGCTCA
1 -GATCCCAGGAAAGTTATGTTTGCGATAAAAATGGGGTTGGCTTTGTCTCTTACGTCTTTGCTCA
16673756 TATTT
65 TATTT
16673761 TGGAAAGGAT
Statistics
Matches: 122, Mismatches: 11, Indels: 29
0.75 0.07 0.18
Matches are distributed among these distances:
68 1 0.01
69 49 0.40
70 6 0.05
71 1 0.01
73 3 0.02
76 3 0.02
78 2 0.02
79 6 0.05
80 50 0.41
81 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (70 bp):
GATCCCAGGAAAGTTATGTTTGCGATAAAAATGGGGTTGGCTTTGTCTCTTACGTCTTTGCTCAT
ATTTA
Found at i:16673732 original size:149 final size:152
Alignment explanation
Indices: 16673455--16673760 Score: 546
Period size: 149 Copynumber: 2.0 Consensus size: 152
16673445 CGGGATGTTC
16673455 TAATCCCAGGAAAGTTATATTTGCGATAAAAATGGGGCTGGCTTTGTCTCTTACGTCTTTGCTCA
1 TAATCCCAGGAAAGTTATATTTGCGATAAAAATGGGGCTGGCTTTG----TTACGTCTTTGCTCA
16673520 TATTTTGGAAAGGATCATATGAGGATCCCAGGAAAGTTATGTTTGAGATAAAAATGGGGTTGGCT
62 TATTTTGGAAAGGATCATATGAGGATCCCAGGAAAGTTATGTTTGAGATAAAAATGGGGTTGGCT
16673585 TTGTCTCTTACGTCTTTGCTCATATT
127 TTGTCTCTTACGTCTTTGCTCATATT
16673611 TAATCCCAGGAAAGTTATATTTGCGATAAAAATGGGGCTGGCTTTG-T-C-TCTTTGCTCATATT
1 TAATCCCAGGAAAGTTATATTTGCGATAAAAATGGGGCTGGCTTTGTTACGTCTTTGCTCATATT
*
16673673 TTGGAAAGGATCATATGAGGATCCCAGGAAAGTTATGTTTGCGATAAAAATGGGGTTGGCTTTGT
66 TTGGAAAGGATCATATGAGGATCCCAGGAAAGTTATGTTTGAGATAAAAATGGGGTTGGCTTTGT
16673738 CTCTTACGTCTTTGCTCATATT
131 CTCTTACGTCTTTGCTCATATT
16673760 T
1 T
16673761 TGGAAAGGAT
Statistics
Matches: 149, Mismatches: 1, Indels: 7
0.95 0.01 0.04
Matches are distributed among these distances:
149 101 0.68
150 1 0.01
151 1 0.01
156 46 0.31
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (152 bp):
TAATCCCAGGAAAGTTATATTTGCGATAAAAATGGGGCTGGCTTTGTTACGTCTTTGCTCATATT
TTGGAAAGGATCATATGAGGATCCCAGGAAAGTTATGTTTGAGATAAAAATGGGGTTGGCTTTGT
CTCTTACGTCTTTGCTCATATT
Found at i:16673806 original size:87 final size:87
Alignment explanation
Indices: 16673659--16673851 Score: 377
Period size: 87 Copynumber: 2.2 Consensus size: 87
16673649 TGGCTTTGTC
*
16673659 TCTTTGCTCATATTTTGGAAAGGATCATATGAGGATCCCAGGAAAGTTATGTTTGCGATAAAAAT
1 TCTTTGCTCATATTTTGGAAAGGATCATATGAGGATCCCAGGAAAGTTATGTTTGAGATAAAAAT
16673724 GGGGTTGGCTTTGTCTCTTACG
66 GGGGTTGGCTTTGTCTCTTACG
16673746 TCTTTGCTCATATTTTGGAAAGGATCATATGAGGATCCCAGGAAAGTTATGTTTGAGATAAAAAT
1 TCTTTGCTCATATTTTGGAAAGGATCATATGAGGATCCCAGGAAAGTTATGTTTGAGATAAAAAT
16673811 GGGGTTGGCTTTGTCTCTTACG
66 GGGGTTGGCTTTGTCTCTTACG
16673833 TCTTTGCTCATATTTTGGA
1 TCTTTGCTCATATTTTGGA
16673852 TGTAAAACTC
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 105 1.00
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.37
Consensus pattern (87 bp):
TCTTTGCTCATATTTTGGAAAGGATCATATGAGGATCCCAGGAAAGTTATGTTTGAGATAAAAAT
GGGGTTGGCTTTGTCTCTTACG
Found at i:16674774 original size:15 final size:16
Alignment explanation
Indices: 16674740--16674776 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
16674730 TAAAATAACA
*
16674740 AACCAAACCCAAATTT
1 AACCAAACCCAAATTG
16674756 AACCAAACCC-AATTG
1 AACCAAACCCAAATTG
16674771 AACCAA
1 AACCAA
16674777 GTCCAAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.51, C:0.32, G:0.03, T:0.14
Consensus pattern (16 bp):
AACCAAACCCAAATTG
Found at i:16682067 original size:15 final size:16
Alignment explanation
Indices: 16682033--16682069 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
16682023 TAAAATAACA
*
16682033 AACCAAACCCAAATTT
1 AACCAAACCCAAATTG
16682049 AACCAAACCC-AATTG
1 AACCAAACCCAAATTG
16682064 AACCAA
1 AACCAA
16682070 GTCCAAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.51, C:0.32, G:0.03, T:0.14
Consensus pattern (16 bp):
AACCAAACCCAAATTG
Found at i:16683196 original size:15 final size:16
Alignment explanation
Indices: 16683176--16683208 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
16683166 TATTAGAGAC
*
16683176 TTACTACAT-ATTATT
1 TTACTAAATAATTATT
16683191 TTACTAAATAATTATT
1 TTACTAAATAATTATT
16683207 TT
1 TT
16683209 GATTTTGGGT
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:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (16 bp):
TTACTAAATAATTATT
Found at i:16685764 original size:26 final size:26
Alignment explanation
Indices: 16685734--16685788 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
16685724 ATAGGACTGC
16685734 TTTGTAAAAGAGTCAAAATTAAGTGT
1 TTTGTAAAAGAGTCAAAATTAAGTGT
16685760 TTTGTAAAAGAGTCAAAATTAAGTGT
1 TTTGTAAAAGAGTCAAAATTAAGTGT
16685786 TTT
1 TTT
16685789 TATGAAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (26 bp):
TTTGTAAAAGAGTCAAAATTAAGTGT
Found at i:16686916 original size:36 final size:36
Alignment explanation
Indices: 16686867--16686943 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
16686857 TGATGACTAT
* *
16686867 TGTGAAAGTAAATATGTGGGTATGTTATTCATGCCA
1 TGTGAAAGAAAATATGTGGGTATATTATTCATGCCA
* * *
16686903 TGTGATAGAAAATATGTGGGTATATTCTTTATGCCA
1 TGTGAAAGAAAATATGTGGGTATATTATTCATGCCA
16686939 TGTGA
1 TGTGA
16686944 CTGATTATGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.30, C:0.08, G:0.25, T:0.38
Consensus pattern (36 bp):
TGTGAAAGAAAATATGTGGGTATATTATTCATGCCA
Found at i:16689239 original size:31 final size:31
Alignment explanation
Indices: 16689201--16689271 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
16689191 TGATAGATGA
16689201 TAAATCGATGTAAGATGGAATGATTTAACAT
1 TAAATCGATGTAAGATGGAATGATTTAACAT
16689232 TAAATCGATGTAAGATGGAATGATTTAACAT
1 TAAATCGATGTAAGATGGAATGATTTAACAT
16689263 TAAATCGAT
1 TAAATCGAT
16689272 TGTTTGATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.32
Consensus pattern (31 bp):
TAAATCGATGTAAGATGGAATGATTTAACAT
Found at i:16692632 original size:22 final size:20
Alignment explanation
Indices: 16692596--16692699 Score: 97
Period size: 22 Copynumber: 5.2 Consensus size: 20
16692586 ATTATATTGT
16692596 TGTTTTGGTGCTATTTTTTAC
1 TGTTTTGGTGCT-TTTTTTAC
*
16692617 TGTTTTGGTTGCTATTTTTTGC
1 TGTTTTGG-TGCT-TTTTTTAC
* *
16692639 TATTTTGATGCTTTTTTTA-
1 TGTTTTGGTGCTTTTTTTAC
16692658 TGTTTTGGTGC--TTTTTAC
1 TGTTTTGGTGCTTTTTTTAC
* * * *
16692676 TATTTTGGTACTGTTTTTGC
1 TGTTTTGGTGCTTTTTTTAC
16692696 TGTT
1 TGTT
16692700 ATTTTTGTTG
Statistics
Matches: 69, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
17 6 0.09
18 9 0.13
19 9 0.13
20 15 0.22
21 12 0.17
22 18 0.26
ACGTcount: A:0.09, C:0.09, G:0.19, T:0.63
Consensus pattern (20 bp):
TGTTTTGGTGCTTTTTTTAC
Found at i:16692704 original size:12 final size:12
Alignment explanation
Indices: 16692689--16692804 Score: 81
Period size: 12 Copynumber: 10.3 Consensus size: 12
16692679 TTTGGTACTG
16692689 TTTTTGCTGTTA
1 TTTTTGCTGTTA
*
16692701 -TTTT--TGTTG
1 TTTTTGCTGTTA
16692710 TTTTTGCTAG-TA
1 TTTTTGCT-GTTA
16692722 TTTTTGCTGTTA
1 TTTTTGCTGTTA
*
16692734 TTTTTGTTGTTA
1 TTTTTGCTGTTA
16692746 TTTTTG-TAG-T-
1 TTTTTGCT-GTTA
16692756 TTTTT--TGTT-
1 TTTTTGCTGTTA
* *
16692765 GTTTTACTGTTA
1 TTTTTGCTGTTA
*
16692777 TTTTTGCTATTA
1 TTTTTGCTGTTA
* *
16692789 TTTTAGTTGTTA
1 TTTTTGCTGTTA
16692801 TTTT
1 TTTT
16692805 GGTTGTTTGA
Statistics
Matches: 84, Mismatches: 10, Indels: 20
0.74 0.09 0.18
Matches are distributed among these distances:
8 1 0.01
9 10 0.12
10 9 0.11
11 11 0.13
12 52 0.62
13 1 0.01
ACGTcount: A:0.10, C:0.04, G:0.16, T:0.70
Consensus pattern (12 bp):
TTTTTGCTGTTA
Found at i:16692711 original size:21 final size:21
Alignment explanation
Indices: 16692687--16692799 Score: 86
Period size: 21 Copynumber: 5.2 Consensus size: 21
16692677 ATTTTGGTAC
16692687 TGTTTTTGCTGTTATTTTTGT
1 TGTTTTTGCTGTTATTTTTGT
16692708 TGTTTTTGCTAG-TATTTTTGCTGT
1 TGTTTTTGCT-GTTA-TTTT--TGT
* *
16692732 TATTTTTGTTGTTATTTTTGT
1 TGTTTTTGCTGTTATTTTTGT
* * *
16692753 AGTTTTT-TTGTTGTTTTACTGT
1 TGTTTTTGCTGTTATTTT--TGT
* * *
16692775 TATTTTTGCTATTATTTTAGT
1 TGTTTTTGCTGTTATTTTTGT
16692796 TGTT
1 TGTT
16692800 ATTTTGGTTG
Statistics
Matches: 72, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
20 9 0.12
21 25 0.35
22 13 0.18
23 12 0.17
24 13 0.18
ACGTcount: A:0.10, C:0.04, G:0.17, T:0.69
Consensus pattern (21 bp):
TGTTTTTGCTGTTATTTTTGT
Found at i:16693737 original size:3 final size:3
Alignment explanation
Indices: 16693729--16693756 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
16693719 TCTCTCTCAC
16693729 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
16693757 AAAATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:16694667 original size:11 final size:11
Alignment explanation
Indices: 16694651--16694675 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16694641 TATATTGAAT
16694651 TGGGTTTATAC
1 TGGGTTTATAC
16694662 TGGGTTTATAC
1 TGGGTTTATAC
16694673 TGG
1 TGG
16694676 ATTGAGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.32, T:0.44
Consensus pattern (11 bp):
TGGGTTTATAC
Found at i:16712910 original size:18 final size:18
Alignment explanation
Indices: 16712889--16712949 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
16712879 AGTTTGGCAA
16712889 ATTAATACAGTTCACCAT
1 ATTAATACAGTTCACCAT
* * *
16712907 ATTAATATAGATCACCAA
1 ATTAATACAGTTCACCAT
* * *
16712925 ATTAACACAATTCGCCAT
1 ATTAATACAGTTCACCAT
*
16712943 AATAATA
1 ATTAATA
16712950 TAATTCTCCA
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.46, C:0.20, G:0.05, T:0.30
Consensus pattern (18 bp):
ATTAATACAGTTCACCAT
Found at i:16713611 original size:20 final size:20
Alignment explanation
Indices: 16713586--16713627 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
16713576 CACACCATTA
16713586 TTTTAGACTTTAATTTTCAG
1 TTTTAGACTTTAATTTTCAG
** *
16713606 TTTTAGTTTTTAATTTTTAG
1 TTTTAGACTTTAATTTTCAG
16713626 TT
1 TT
16713628 GTGAAACGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.10, T:0.64
Consensus pattern (20 bp):
TTTTAGACTTTAATTTTCAG
Found at i:16722033 original size:15 final size:15
Alignment explanation
Indices: 16722013--16722041 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16722003 TTCCTCACAT
16722013 CAAGGGAGTTACAAA
1 CAAGGGAGTTACAAA
16722028 CAAGGGAGTTACAA
1 CAAGGGAGTTACAA
16722042 TAACAATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.14, G:0.28, T:0.14
Consensus pattern (15 bp):
CAAGGGAGTTACAAA
Found at i:16723663 original size:17 final size:17
Alignment explanation
Indices: 16723631--16723689 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
16723621 ATAATTATCC
* *
16723631 TTGCATTATTAATGTCA
1 TTGCATTTTTATTGTCA
*
16723648 TTGCATTTTTATTGTCG
1 TTGCATTTTTATTGTCA
* * **
16723665 CTGCATCTACATTGTCA
1 TTGCATTTTTATTGTCA
16723682 TTGCATTT
1 TTGCATTT
16723690 CCATATGCAT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (17 bp):
TTGCATTTTTATTGTCA
Found at i:16729581 original size:135 final size:136
Alignment explanation
Indices: 16729408--16729678 Score: 499
Period size: 135 Copynumber: 2.0 Consensus size: 136
16729398 TTATTATGAA
16729408 CATGATTTCTTAGATCAAATCAATTTAGAATCCTTTAGTGATATAAAAATGACTAAAGTAATTAC
1 CATGATTTCTTAGATCAAATCAATTTAGAATCCTTTAGTGATATAAAAATGACTAAAGTAATTAC
*
16729473 ATATCTGACTGAGGGAA-GGGGGAATGGAAATTTAGGCTAGGCACTGGTATCCCTACTTTATTTA
66 ATATCTGACTGAGGGAAGGGGGGAATGGAAATTTAGGCTAGGCACTGGTATCCCTACTTCATTTA
16729537 ACCAAG
131 ACCAAG
* *
16729543 CATGATTTCTTTGATCAAATCAATTTAGAATCCTTTAGTGATATAAATATGACTAAAGTAATTAC
1 CATGATTTCTTAGATCAAATCAATTTAGAATCCTTTAGTGATATAAAAATGACTAAAGTAATTAC
*
16729608 ATATCTGACTGAGGGAAGGGGGGAATGGAAATTTCGGCTAGGCACTGGTATCCCTACTTCATTTA
66 ATATCTGACTGAGGGAAGGGGGGAATGGAAATTTAGGCTAGGCACTGGTATCCCTACTTCATTTA
16729673 ACCAAG
131 ACCAAG
16729679 TCATTATGTT
Statistics
Matches: 131, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
135 80 0.61
136 51 0.39
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (136 bp):
CATGATTTCTTAGATCAAATCAATTTAGAATCCTTTAGTGATATAAAAATGACTAAAGTAATTAC
ATATCTGACTGAGGGAAGGGGGGAATGGAAATTTAGGCTAGGCACTGGTATCCCTACTTCATTTA
ACCAAG
Found at i:16739116 original size:24 final size:26
Alignment explanation
Indices: 16739078--16739125 Score: 82
Period size: 24 Copynumber: 1.9 Consensus size: 26
16739068 ACCATGGCTA
16739078 AAACCCGTGCTTCCAAAAACACTCAT
1 AAACCCGTGCTTCCAAAAACACTCAT
16739104 AAACCC-T-CTTCCAAAAACACTC
1 AAACCCGTGCTTCCAAAAACACTC
16739126 CGACCGCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 15 0.68
25 1 0.05
26 6 0.27
ACGTcount: A:0.40, C:0.38, G:0.04, T:0.19
Consensus pattern (26 bp):
AAACCCGTGCTTCCAAAAACACTCAT
Found at i:16739983 original size:7 final size:7
Alignment explanation
Indices: 16739971--16740000 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
16739961 AAAGAAAGAC
16739971 AAGGGAA
1 AAGGGAA
16739978 AAGGGAA
1 AAGGGAA
16739985 AAGGGAA
1 AAGGGAA
16739992 AAGGGAA
1 AAGGGAA
16739999 AA
1 AA
16740001 AGAAAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (7 bp):
AAGGGAA
Found at i:16744462 original size:18 final size:18
Alignment explanation
Indices: 16744397--16744513 Score: 65
Period size: 18 Copynumber: 6.0 Consensus size: 18
16744387 ACTATATTTT
*
16744397 TATAAAAATATT-TAGAAA
1 TATAAAAAAATTATA-AAA
*
16744415 TTTAAAAGAACATATATAAAA
1 TATAAAA-AA-AT-TATAAAA
* * * *
16744436 TACACAAAATTTTTAAAA
1 TATAAAAAAATTATAAAA
*
16744454 TATAAAAAAATTATAAAT
1 TATAAAAAAATTATAAAA
16744472 TATAAAAATATATCTATCTAAAA
1 TATAAAAA-A-AT-TA--TAAAA
*
16744495 TATTAAAAATATTATAAAA
1 TA-TAAAAAAATTATAAAA
16744514 AAATCTAAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
18 33 0.44
19 8 0.11
20 6 0.08
21 12 0.16
22 4 0.05
23 6 0.08
24 6 0.08
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (18 bp):
TATAAAAAAATTATAAAA
Found at i:16747553 original size:27 final size:27
Alignment explanation
Indices: 16747497--16747615 Score: 111
Period size: 27 Copynumber: 4.5 Consensus size: 27
16747487 CAAAATATTG
* *
16747497 CTCTTTTGAGCCAG-AT-AGAATATCGT
1 CTCTTTCGAGCCAGAATCAGAATAAC-T
*
16747523 -TCTTTCGAGCCAGAATTAGAATAACT
1 CTCTTTCGAGCCAGAATCAGAATAACT
* *
16747549 CTCTTTCAAGCCAGAATCAGAATAACG
1 CTCTTTCGAGCCAGAATCAGAATAACT
* * *
16747576 CTCTTTCGAACTAGAATCAAAATAA-T
1 CTCTTTCGAGCCAGAATCAGAATAACT
*
16747602 GCTATTTCGAGCCA
1 -CTCTTTCGAGCCA
16747616 AAAGTATATT
Statistics
Matches: 76, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
25 12 0.16
26 3 0.04
27 61 0.80
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (27 bp):
CTCTTTCGAGCCAGAATCAGAATAACT
Found at i:16747615 original size:54 final size:52
Alignment explanation
Indices: 16747487--16747615 Score: 134
Period size: 54 Copynumber: 2.4 Consensus size: 52
16747477 CGAGCCTAGA
* * * * *
16747487 CAAAATATTGCTCTTTTGAGCCAGATAGAATATCGTTCTTTCGAGCCAGAAT
1 CAAAATAATGCTCTTTCGAGCCAGATAGAATAACGCTCTTTCGAACCAGAAT
* * * *
16747539 TAGAATAACT-CTCTTTCAAGCCAGAATCAGAATAACGCTCTTTCGAACTAGAAT
1 CAAAATAA-TGCTCTTTCGAGCCAG-AT-AGAATAACGCTCTTTCGAACCAGAAT
*
16747593 CAAAATAATGCTATTTCGAGCCA
1 CAAAATAATGCTCTTTCGAGCCA
16747616 AAAGTATATT
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
52 17 0.28
53 4 0.07
54 39 0.65
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (52 bp):
CAAAATAATGCTCTTTCGAGCCAGATAGAATAACGCTCTTTCGAACCAGAAT
Found at i:16747827 original size:26 final size:25
Alignment explanation
Indices: 16747772--16747891 Score: 114
Period size: 26 Copynumber: 4.6 Consensus size: 25
16747762 ATTTTGATTA
* * * *
16747772 GCTCATATGAGCCCAGACAGAGTTTA
1 GCTCTTATGAG-CCAGACAGAATATC
16747798 GCTCTTATGAGCCTAGACAGAATATC
1 GCTCTTATGAGCC-AGACAGAATATC
* *
16747824 GCTCTTACGAGCCAGATAGAATATC
1 GCTCTTATGAGCCAGACAGAATATC
* * *
16747849 GCTCTTACGAGCCAAAATTAGAATATC
1 GCTCTTATGAGCC-AGA-CAGAATATC
*
16747876 GCTCTTTTGAGCCAGA
1 GCTCTTATGAGCCAGA
16747892 ATTAGAATAA
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
25 26 0.32
26 35 0.43
27 20 0.25
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (25 bp):
GCTCTTATGAGCCAGACAGAATATC
Found at i:16747850 original size:25 final size:25
Alignment explanation
Indices: 16747798--16747945 Score: 125
Period size: 27 Copynumber: 5.6 Consensus size: 25
16747788 ACAGAGTTTA
* *
16747798 GCTCTTATGAGCCTAGACAGAATATC
1 GCTCTTACGAGCC-AGATAGAATATC
16747824 GCTCTTACGAGCCAGATAGAATATC
1 GCTCTTACGAGCCAGATAGAATATC
*
16747849 GCTCTTACGAGCCAAAATTAGAATATC
1 GCTCTTACGAGCC-AGA-TAGAATATC
** **
16747876 GCTCTTTTGAGCCAGAATTAGAATAAA
1 GCTCTTACGAGCCAG-A-TAGAATATC
* * *
16747903 GCTCTTTCAAGCCAGAATCAGAATAAC
1 GCTCTTACGAGCCAG-AT-AGAATATC
* *
16747930 GCTCTTTCGAACCAGA
1 GCTCTTACGAGCCAGA
16747946 ATCAAAATAA
Statistics
Matches: 105, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
25 24 0.23
26 17 0.16
27 64 0.61
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (25 bp):
GCTCTTACGAGCCAGATAGAATATC
Found at i:16747936 original size:27 final size:27
Alignment explanation
Indices: 16747815--16747978 Score: 163
Period size: 27 Copynumber: 6.1 Consensus size: 27
16747805 TGAGCCTAGA
* *
16747815 CAGAATATCGCTCTTACGAGCCAG-AT
1 CAGAATAACGCTCTTTCGAGCCAGAAT
* * *
16747841 -AGAATATCGCTCTTACGAGCCAAAAT
1 CAGAATAACGCTCTTTCGAGCCAGAAT
* * *
16747867 TAGAATATCGCTCTTTTGAGCCAGAAT
1 CAGAATAACGCTCTTTCGAGCCAGAAT
* * *
16747894 TAGAATAAAGCTCTTTCAAGCCAGAAT
1 CAGAATAACGCTCTTTCGAGCCAGAAT
*
16747921 CAGAATAACGCTCTTTCGAACCAGAAT
1 CAGAATAACGCTCTTTCGAGCCAGAAT
* * *
16747948 CAAAATAACGCTAC-TTCGAGCTAGAAG
1 CAGAATAACGCT-CTTTCGAGCCAGAAT
16747975 CAGA
1 CAGA
16747979 TTACTCCTCA
Statistics
Matches: 118, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
25 22 0.19
26 2 0.02
27 93 0.79
28 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.24
Consensus pattern (27 bp):
CAGAATAACGCTCTTTCGAGCCAGAAT
Found at i:16751890 original size:21 final size:21
Alignment explanation
Indices: 16751866--16751917 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
16751856 TGAGACAATA
16751866 CTACCGATACAAGT-ATGACTT
1 CTACCGATACAAGTCATG-CTT
* *
16751887 CTACCGAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
16751908 CTACCGATAC
1 CTACCGATAC
16751918 TAAAAACTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:16752782 original size:52 final size:52
Alignment explanation
Indices: 16752700--16752941 Score: 367
Period size: 52 Copynumber: 4.7 Consensus size: 52
16752690 ATTCCATTTA
* * * * * *
16752700 ATACTCATGATGGCACATAGTCATCGGACCTCTTAATCCGTGAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
*
16752752 ATACTCACGATGACACATAGTCATCAGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* *
16752804 ATACTCACGATGACACATTGTCATCGGACCTTTTAATTCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* *
16752856 ATTCTTACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* *
16752908 ATACTCACGATGACACATAATCATTGGACCTTTT
1 ATACTCACGATGACACATAGTCATCGGACCTTTT
16752942 CTTTATTTAC
Statistics
Matches: 172, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 172 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
Found at i:16755468 original size:15 final size:16
Alignment explanation
Indices: 16755448--16755477 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16755438 CTCACAGTTG
16755448 ATTATTT-TCACATAA
1 ATTATTTCTCACATAA
16755463 ATTATTTCTCACATA
1 ATTATTTCTCACATA
16755478 TAGTCTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTATTTCTCACATAA
Found at i:16756566 original size:52 final size:52
Alignment explanation
Indices: 16756502--16756795 Score: 480
Period size: 52 Copynumber: 5.7 Consensus size: 52
16756492 CATTAATTTA
* * * * *
16756502 ATACTCACGATGACTCATAGTCATCGGACCTCTTAATCCGTGAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* *
16756554 ATACTAATGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
16756606 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
* * *
16756658 ATACTCACGATAACCCATAGTCATTGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
*
16756710 ATTCTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
*
16756762 ATACTCACGATGACACATAGTCATCAGACCTTTT
1 ATACTCACGATGACACATAGTCATCGGACCTTTT
16756796 CTTTATTTAC
Statistics
Matches: 224, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 224 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTCAT
Found at i:16758585 original size:26 final size:26
Alignment explanation
Indices: 16758542--16758592 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
16758532 CTTCCAGAAA
* * *
16758542 TTTAGCTCATATGGGCCCATACAGAG
1 TTTAGCTCATACGAGCCCAGACAGAG
*
16758568 TTTAGCTCTTACGAGCCCAGACAGA
1 TTTAGCTCATACGAGCCCAGACAGA
16758593 ATATCGCCCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (26 bp):
TTTAGCTCATACGAGCCCAGACAGAG
Found at i:16758618 original size:25 final size:25
Alignment explanation
Indices: 16758572--16758688 Score: 126
Period size: 25 Copynumber: 4.6 Consensus size: 25
16758562 ACAGAGTTTA
16758572 GCTCTTACGAGCCCAGACAGAATATC
1 GCTCTTACGAG-CCAGACAGAATATC
* * *
16758598 GCCCTTATGAGCCAGACAGAATATT
1 GCTCTTACGAGCCAGACAGAATATC
* * *
16758623 GCTCTTACAAGTCAGATAGAATATC
1 GCTCTTACGAGCCAGACAGAATATC
*
16758648 GCTCTTACGAGCCAGAATAAGAATATC
1 GCTCTTACGAGCCAG-A-CAGAATATC
**
16758675 GCTCAGACGAGCCA
1 GCTCTTACGAGCCA
16758689 AAATTAGAAT
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
25 45 0.60
26 10 0.13
27 20 0.27
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (25 bp):
GCTCTTACGAGCCAGACAGAATATC
Found at i:16758678 original size:27 final size:27
Alignment explanation
Indices: 16758572--16758850 Score: 208
Period size: 27 Copynumber: 10.7 Consensus size: 27
16758562 ACAGAGTTTA
16758572 GCTCTTACGAGCCCAG-A-CAGAATATC
1 GCTCTTACGAG-CCAGAATCAGAATATC
* * *
16758598 GCCCTTATGAGCCAG-A-CAGAATATT
1 GCTCTTACGAGCCAGAATCAGAATATC
* *
16758623 GCTCTTACAAGTCAG-AT-AGAATATC
1 GCTCTTACGAGCCAGAATCAGAATATC
*
16758648 GCTCTTACGAGCCAGAATAAGAATATC
1 GCTCTTACGAGCCAGAATCAGAATATC
** * *
16758675 GCTCAGACGAGCCAAAATTAGAATATC
1 GCTCTTACGAGCCAGAATCAGAATATC
*
16758702 G--C-T-CGA--AAGAATCAGAATATC
1 GCTCTTACGAGCCAGAATCAGAATATC
* *
16758723 ACTCTTTCGAGCCAGAATCAGAATAAT-
1 GCTCTTACGAGCCAGAATCAGAAT-ATC
* *
16758750 GCTCTTTA-GAGCTAGAATCAGAATAAC
1 GCTC-TTACGAGCCAGAATCAGAATATC
* ** *
16758777 GCTTTTTTGAGCCAGAATCAGAATAAC
1 GCTCTTACGAGCCAGAATCAGAATATC
* * * *
16758804 GCTCTTTCGAGCCAAAATTAGAATAAC
1 GCTCTTACGAGCCAGAATCAGAATATC
* *
16758831 ACTCTTTCGAGCCAGAATCA
1 GCTCTTACGAGCCAGAATCA
16758851 AATTACTCCT
Statistics
Matches: 206, Mismatches: 34, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
21 12 0.06
23 4 0.02
24 1 0.00
25 49 0.24
26 14 0.07
27 122 0.59
28 4 0.02
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.24
Consensus pattern (27 bp):
GCTCTTACGAGCCAGAATCAGAATATC
Found at i:16768712 original size:13 final size:12
Alignment explanation
Indices: 16768694--16768726 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
16768684 ATCAGACTCA
16768694 TAAATATTATTAC
1 TAAATATT-TTAC
16768707 TAAATA-TTTAC
1 TAAATATTTTAC
16768718 TAAATATTT
1 TAAATATTT
16768727 ACTGAGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.53
12 3 0.16
13 6 0.32
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (12 bp):
TAAATATTTTAC
Found at i:16768719 original size:11 final size:11
Alignment explanation
Indices: 16768703--16768729 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
16768693 ATAAATATTA
16768703 TTACTAAATAT
1 TTACTAAATAT
16768714 TTACTAAATAT
1 TTACTAAATAT
16768725 TTACT
1 TTACT
16768730 GAGTTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (11 bp):
TTACTAAATAT
Found at i:16770670 original size:24 final size:24
Alignment explanation
Indices: 16770633--16770700 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
16770623 AAGGAGAAGA
*
16770633 AAGATTTAAGGAAGATGAAAGGCGG
1 AAGA-TTAAGGAAGATGAAAGACGG
* * *
16770658 AAGATTAAAGAAGATAAAAGATGG
1 AAGATTAAGGAAGATGAAAGACGG
* *
16770682 AAGGTTAAGGGAGATGAAA
1 AAGATTAAGGAAGATGAAA
16770701 AGTGAAATGT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
24 31 0.89
25 4 0.11
ACGTcount: A:0.50, C:0.01, G:0.32, T:0.16
Consensus pattern (24 bp):
AAGATTAAGGAAGATGAAAGACGG
Found at i:16780285 original size:32 final size:32
Alignment explanation
Indices: 16780244--16780305 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
16780234 CATCTATTTT
*
16780244 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTAACAACACGAAAAATC
*
16780276 CATTGTTCAACTCTTTAACAACATGAAAAA
1 CATTGTTCAACTCTTTAACAACACGAAAAA
16780306 ACCAAAAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTAACAACACGAAAAATC
Found at i:16781541 original size:54 final size:54
Alignment explanation
Indices: 16781482--16781588 Score: 160
Period size: 54 Copynumber: 2.0 Consensus size: 54
16781472 GGCTAACTAT
* *
16781482 TTATTGTATCTATTCAATTTATAACTATCCTAAGTTTGACAAAGAAATCCTAAC
1 TTATTGAATCTATTCAATTTATAACTATCCTAAGTTTGACAAAGAAACCCTAAC
* * **
16781536 TTATTGAATCTATTCAATTTATAATTATCCTAGGTTTGATTAAGAAACCCTAA
1 TTATTGAATCTATTCAATTTATAACTATCCTAAGTTTGACAAAGAAACCCTAA
16781589 ACATAACATT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.40
Consensus pattern (54 bp):
TTATTGAATCTATTCAATTTATAACTATCCTAAGTTTGACAAAGAAACCCTAAC
Found at i:16783790 original size:22 final size:21
Alignment explanation
Indices: 16783765--16783810 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
16783755 TTGCATAGTT
*
16783765 TTTTTAAATAAAATTAAAAATA
1 TTTTTAAACAAAATTAAAAA-A
**
16783787 TTTTTTTACAAAATTAAAAAA
1 TTTTTAAACAAAATTAAAAAA
16783808 TTT
1 TTT
16783811 AAAACTGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTTTAAACAAAATTAAAAAA
Found at i:16793293 original size:28 final size:27
Alignment explanation
Indices: 16793262--16793350 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 27
16793252 ACAGCTCGGG
16793262 TAGAGCTTCGACATGCTTACGTCTTGGC
1 TAGAGCTTC-ACATGCTTACGTCTTGGC
* * * *
16793290 TAGAGCAT-A-ATGCCTTTATAG-CTCGGG
1 TAGAGCTTCACATG-C-TTA-CGTCTTGGC
16793317 TAGAGCTTCAACATGCTTACGTCTTGGC
1 TAGAGCTTC-ACATGCTTACGTCTTGGC
16793345 TAGAGC
1 TAGAGC
16793351 ATAATGCCTT
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 2 0.04
27 15 0.33
28 21 0.46
29 2 0.04
30 3 0.07
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.30
Consensus pattern (27 bp):
TAGAGCTTCACATGCTTACGTCTTGGC
Found at i:16793319 original size:55 final size:55
Alignment explanation
Indices: 16793254--16793761 Score: 597
Period size: 55 Copynumber: 9.2 Consensus size: 55
16793244 ACTCACGTAC
* * *
16793254 AGCTCGGGTAGAGCTTCGACATGCTTACGTCTTGGCTAGAGCATAATGCCTTTAT
1 AGCTCGGGTAGAGCTTCGACATGCTTACGTCTTGGTTAGAGCGTAATGCCATTAT
* * * *
16793309 AGCTCGGGTAGAGCTTCAACATGCTTACGTCTTGGCTAGAGCATAATGCCTTTAT
1 AGCTCGGGTAGAGCTTCGACATGCTTACGTCTTGGTTAGAGCGTAATGCCATTAT
* * * *
16793364 AGCTCGAGTAGAGCTTCAACATGCTTACGTCTTGATTAGAGCGTAATGCCATTAC
1 AGCTCGGGTAGAGCTTCGACATGCTTACGTCTTGGTTAGAGCGTAATGCCATTAT
* * * * *
16793419 AACTCGGGTAGAGCTTCAACATGCTTATGCCTTGGTTAGAGCGTAATACCATTAT
1 AGCTCGGGTAGAGCTTCGACATGCTTACGTCTTGGTTAGAGCGTAATGCCATTAT
* * * * * * * *
16793474 AGCTC-GTTATAACTTCGACATGCTTACGTATCGATTAGAGCATAATGTCATTAT
1 AGCTCGGGTAGAGCTTCGACATGCTTACGTCTTGGTTAGAGCGTAATGCCATTAT
* * * * *
16793528 TGCTCGGGTATAGCTTCGGCATGCTTACGTCTTAGTTAAAGCGTAATGCCATTAT
1 AGCTCGGGTAGAGCTTCGACATGCTTACGTCTTGGTTAGAGCGTAATGCCATTAT
* * * *
16793583 AACTCTGGTAGAGCTTCGACATGCTTATGTCTTAGTTAGAGCGTAATGCCATTAT
1 AGCTCGGGTAGAGCTTCGACATGCTTACGTCTTGGTTAGAGCGTAATGCCATTAT
* * * *
16793638 AGCTCGGGTAGAACTTCAACATGCTTACATCTCT-GTTAGAGCGTAATGCTATTAT
1 AGCTCGGGTAGAGCTTCGACATGCTTACGTCT-TGGTTAGAGCGTAATGCCATTAT
* * ** * *
16793693 AGCTCGGGTAGAGCTTTGGACGTGCTTACGTCTCAGTTAGAGCATAATGCAATTAT
1 AGCTCGGGTAGAGC-TTCGACATGCTTACGTCTTGGTTAGAGCGTAATGCCATTAT
16793749 AGCTCGGGTAGAG
1 AGCTCGGGTAGAG
16793762 ATCTAGCTTG
Statistics
Matches: 389, Mismatches: 60, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
54 41 0.11
55 301 0.77
56 47 0.12
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (55 bp):
AGCTCGGGTAGAGCTTCGACATGCTTACGTCTTGGTTAGAGCGTAATGCCATTAT
Found at i:16793322 original size:27 final size:27
Alignment explanation
Indices: 16793290--16793377 Score: 74
Period size: 27 Copynumber: 3.2 Consensus size: 27
16793280 ACGTCTTGGC
16793290 TAGAGCATAATGCCTTTATAGCTCGGG
1 TAGAGCATAATGCCTTTATAGCTCGGG
* * * *
16793317 TAGAGCTTCAACATG-C-TTA-CGTCTTGGC
1 TAGAGCAT--A-ATGCCTTTATAG-CTCGGG
*
16793345 TAGAGCATAATGCCTTTATAGCTCGAG
1 TAGAGCATAATGCCTTTATAGCTCGGG
16793372 TAGAGC
1 TAGAGC
16793378 TTCAACATGC
Statistics
Matches: 45, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
25 3 0.07
26 2 0.04
27 20 0.44
28 15 0.33
29 2 0.04
30 3 0.07
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (27 bp):
TAGAGCATAATGCCTTTATAGCTCGGG
Found at i:16793646 original size:219 final size:219
Alignment explanation
Indices: 16793254--16793761 Score: 630
Period size: 219 Copynumber: 2.3 Consensus size: 219
16793244 ACTCACGTAC
* * ** *
16793254 AGCTCGGGTAGAGCTTCGACATGCTTACGTCTTGGCTAGAGCATAATGCCTTTATAGCTCGGGTA
1 AGCTCGGGTAGAACTTCGACATGCTTACGTCTCGATTAGAGCATAATG-CATTATAGCTCGGGTA
* * * *
16793319 GAGCTTCAACATGCTTACGTCTTGGCTAGAGCATAATGCCTTTATAGCTCGAGTAGAGCTTCAAC
65 GAGCTTCAACATGCTTACGTCTTAGCTAAAGCATAATGCCATTATAACTCGAGTAGAGCTTCAAC
* **
16793384 ATGCTTACGTCTTGATTAGAGCGTAATGCCATTACAACTCGGGTAGAGCTTCAACATGCTTATGC
130 ATGCTTACGTCTTGATTAGAGCGTAATGCCATTACAACTCGGGTAGAACTTCAACATGCTTACAC
16793449 CT-TGGTTAGAGCGTAATACCATTAT
195 CTCT-GTTAGAGCGTAATACCATTAT
* * * *
16793474 AGCTC-GTTATAACTTCGACATGCTTACGTATCGATTAGAGCATAATGTCATTATTGCTCGGGTA
1 AGCTCGGGTAGAACTTCGACATGCTTACGTCTCGATTAGAGCATAATG-CATTATAGCTCGGGTA
* ** * * *
16793538 TAGCTTCGGCATGCTTACGTCTTAGTTAAAGCGTAATGCCATTATAACTCTG-GTAGAGCTTCGA
65 GAGCTTCAACATGCTTACGTCTTAGCTAAAGCATAATGCCATTATAACTC-GAGTAGAGCTTCAA
* * *
16793602 CATGCTTATGTCTT-AGTTAGAGCGTAATGCCATTATAGCTCGGGTAGAACTTCAACATGCTTAC
129 CATGCTTACGTCTTGA-TTAGAGCGTAATGCCATTACAACTCGGGTAGAACTTCAACATGCTTAC
* * *
16793666 ATCTCTGTTAGAGCGTAATGCTATTAT
193 ACCTCTGTTAGAGCGTAATACCATTAT
* * *
16793693 AGCTCGGGTAGAGCTTTGGACGTGCTTACGTCTC-AGTTAGAGCATAATGCAATTATAGCTCGGG
1 AGCTCGGGTAGAAC-TTCGACATGCTTACGTCTCGA-TTAGAGCATAATGC-ATTATAGCTCGGG
16793757 TAGAG
63 TAGAG
16793762 ATCTAGCTTG
Statistics
Matches: 244, Mismatches: 37, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
218 1 0.00
219 184 0.75
220 14 0.06
221 45 0.18
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (219 bp):
AGCTCGGGTAGAACTTCGACATGCTTACGTCTCGATTAGAGCATAATGCATTATAGCTCGGGTAG
AGCTTCAACATGCTTACGTCTTAGCTAAAGCATAATGCCATTATAACTCGAGTAGAGCTTCAACA
TGCTTACGTCTTGATTAGAGCGTAATGCCATTACAACTCGGGTAGAACTTCAACATGCTTACACC
TCTGTTAGAGCGTAATACCATTAT
Found at i:16793649 original size:27 final size:27
Alignment explanation
Indices: 16793619--16793706 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
16793609 ATGTCTTAGT
16793619 TAGAGCGTAATGCCATTATAGCTCGGG
1 TAGAGCGTAATGCCATTATAGCTCGGG
* * * * * *
16793646 TAGAACTTCAACATG-C-TTACATCTCTGT
1 TAGAGCGT--A-ATGCCATTATAGCTCGGG
*
16793674 TAGAGCGTAATGCTATTATAGCTCGGG
1 TAGAGCGTAATGCCATTATAGCTCGGG
16793701 TAGAGC
1 TAGAGC
16793707 TTTGGACGTG
Statistics
Matches: 43, Mismatches: 13, Indels: 10
0.65 0.20 0.15
Matches are distributed among these distances:
25 3 0.07
26 1 0.02
27 20 0.47
28 14 0.33
29 2 0.05
30 3 0.07
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (27 bp):
TAGAGCGTAATGCCATTATAGCTCGGG
Found at i:16793811 original size:55 final size:56
Alignment explanation
Indices: 16793553--16793794 Score: 215
Period size: 55 Copynumber: 4.4 Consensus size: 56
16793543 TCGGCATGCT
* * * * * * * * *
16793553 TACGTCTTAGTTAAAGCGTAATGCCATTATAACTCTGGTAGAGCT-TCGACATGCT
1 TACGTCTCAGTTAGAGCGTAATGCTATTATAGCTCGGGTAGAGATCTAGACGTGCC
* * * * *
16793608 TATGTCTTAGTTAGAGCGTAATGCCATTATAGCTCGGGTAGA-A-CTTCA-ACATGCT
1 TACGTCTCAGTTAGAGCGTAATGCTATTATAGCTCGGGTAGAGATC-T-AGACGTGCC
* * * * * *
16793663 TACATCTCTGTTAGAGCGTAATGCTATTATAGCTCGGGTAGAGCTTTGGACGTGCT
1 TACGTCTCAGTTAGAGCGTAATGCTATTATAGCTCGGGTAGAGATCTAGACGTGCC
* * *
16793719 TACGTCTCAGTTAGAGCATAATGCAATTATAGCTCGGGTAGAGATCTAG-CTTGCC
1 TACGTCTCAGTTAGAGCGTAATGCTATTATAGCTCGGGTAGAGATCTAGACGTGCC
*
16793774 TACGTGTCAGTTAGAGCGTAA
1 TACGTCTCAGTTAGAGCGTAA
16793795 GGTTATTTTG
Statistics
Matches: 155, Mismatches: 26, Indels: 12
0.80 0.13 0.06
Matches are distributed among these distances:
55 106 0.68
56 49 0.32
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (56 bp):
TACGTCTCAGTTAGAGCGTAATGCTATTATAGCTCGGGTAGAGATCTAGACGTGCC
Found at i:16797060 original size:33 final size:34
Alignment explanation
Indices: 16797002--16797068 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
16796992 ATATATATGC
* *
16797002 ATGGGTCTTGATTATATATAGTATATATGCATAT
1 ATGGGTATTGATTATATATAATATATATGCATAT
* *
16797036 ATGGGTATT-ATTTTATATAATATATATGTATAT
1 ATGGGTATTGATTATATATAATATATATGCATAT
16797069 GAGTTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 21 0.72
34 8 0.28
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.48
Consensus pattern (34 bp):
ATGGGTATTGATTATATATAATATATATGCATAT
Found at i:16801896 original size:31 final size:31
Alignment explanation
Indices: 16801838--16801905 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
16801828 CTATTTACAA
*
16801838 GAGTGACCAAAATAAAAATTAACTAAAACGT
1 GAGTGACCAAAATAAAAATGAACTAAAACGT
**
16801869 GAGTGACCAAAATAGGAATGATA-TAAAACGT
1 GAGTGACCAAAATAAAAATGA-ACTAAAACGT
*
16801900 TAGTGA
1 GAGTGA
16801906 TTAAAAACGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.50, C:0.10, G:0.19, T:0.21
Consensus pattern (31 bp):
GAGTGACCAAAATAAAAATGAACTAAAACGT
Found at i:16801906 original size:16 final size:15
Alignment explanation
Indices: 16801887--16801926 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 15
16801877 AAAATAGGAA
16801887 TGATATAAAACGTTAG
1 TGAT-TAAAACGTTAG
16801903 TGATTAAAAACGTTAG
1 TGATT-AAAACGTTAG
16801919 TGATTAAA
1 TGATTAAA
16801927 TTAAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (15 bp):
TGATTAAAACGTTAG
Found at i:16805169 original size:37 final size:38
Alignment explanation
Indices: 16805091--16805170 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 38
16805081 AGACTGTCGC
* * *
16805091 TGCATAAATATTCTTCAAATTGCATCTAGAATTATCGT
1 TGCATAAATATTCTTCAAATTGCACCTAGAAATATCAT
* * *
16805129 TGCATAAGTATTCTTC-AATTGCACCTAGAAATGTTAT
1 TGCATAAATATTCTTCAAATTGCACCTAGAAATATCAT
16805166 TGCAT
1 TGCAT
16805171 GAACATGTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 21 0.58
38 15 0.42
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (38 bp):
TGCATAAATATTCTTCAAATTGCACCTAGAAATATCAT
Found at i:16806021 original size:16 final size:16
Alignment explanation
Indices: 16806000--16806030 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16805990 CGTTGTGTCT
16806000 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
16806016 CATTTTATCTTTATT
1 CATTTTACCTTTATT
16806031 TTACATTATT
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:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:16809389 original size:37 final size:37
Alignment explanation
Indices: 16809334--16809435 Score: 159
Period size: 37 Copynumber: 2.8 Consensus size: 37
16809324 TTACTACTAA
*
16809334 TGTCGCTGTATGACCACTTCTAGATTACGCCCGAAAC
1 TGTCGCTGCATGACCACTTCTAGATTACGCCCGAAAC
*
16809371 TGTCGCTGCATGATCACTTCTAGATTACGCCCGAAAC
1 TGTCGCTGCATGACCACTTCTAGATTACGCCCGAAAC
* * *
16809408 TATTGCTGCATGAGCACTTCTAGATTAC
1 TGTCGCTGCATGACCACTTCTAGATTAC
16809436 ACCCAAAATT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (37 bp):
TGTCGCTGCATGACCACTTCTAGATTACGCCCGAAAC
Found at i:16809566 original size:37 final size:38
Alignment explanation
Indices: 16809481--16809567 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 38
16809471 GCACCTAAGT
*
16809481 CTGTCGCTGCATAAATATTCTTCAAATTGCATCCAGAA
1 CTGTCGCTGCATAAATATTCTTCAAATTGCACCCAGAA
* * *
16809519 CTATCACTGCATAACTATTCTTC-AATTGCACCCAGGAA
1 CTGTCGCTGCATAAATATTCTTCAAATTGCACCCA-GAA
16809557 -TGTCGCTGCAT
1 CTGTCGCTGCAT
16809568 GAGCATGTAC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
37 19 0.45
38 23 0.55
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (38 bp):
CTGTCGCTGCATAAATATTCTTCAAATTGCACCCAGAA
Found at i:16809590 original size:26 final size:27
Alignment explanation
Indices: 16809559--16809637 Score: 99
Period size: 26 Copynumber: 3.0 Consensus size: 27
16809549 CCCAGGAATG
* *
16809559 TCGCTGCATGAGCATGTACAGAATTAC
1 TCGCTGCATGAACATGTACAAAATTAC
*
16809586 T-GCTGCATGAACATGTACACAATTA-
1 TCGCTGCATGAACATGTACAAAATTAC
* *
16809611 TCGTTGCATGAACATGTCCAAAATTAC
1 TCGCTGCATGAACATGTACAAAATTAC
16809638 GCACAGAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
25 1 0.02
26 43 0.96
27 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (27 bp):
TCGCTGCATGAACATGTACAAAATTAC
Found at i:16814420 original size:47 final size:47
Alignment explanation
Indices: 16814351--16814441 Score: 173
Period size: 47 Copynumber: 1.9 Consensus size: 47
16814341 GTTGTGTCTA
*
16814351 TAACTTACATAGTGGGAATCAATGGTTATTGCAGTAATAGTTTTCTG
1 TAACTTACATAGTGAGAATCAATGGTTATTGCAGTAATAGTTTTCTG
16814398 TAACTTACATAGTGAGAATCAATGGTTATTGCAGTAATAGTTTT
1 TAACTTACATAGTGAGAATCAATGGTTATTGCAGTAATAGTTTT
16814442 ATACCGTCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (47 bp):
TAACTTACATAGTGAGAATCAATGGTTATTGCAGTAATAGTTTTCTG
Found at i:16821344 original size:16 final size:16
Alignment explanation
Indices: 16821316--16821357 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
16821306 TTATTTATTT
16821316 ATTAAATAAATAA-ACAA
1 ATTAAA-AAATAATA-AA
*
16821333 ATTAAAAAATAATAGA
1 ATTAAAAAATAATAAA
16821349 ATTAAAAAA
1 ATTAAAAAA
16821358 ATATACAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (16 bp):
ATTAAAAAATAATAAA
Found at i:16822632 original size:30 final size:29
Alignment explanation
Indices: 16822518--16822639 Score: 147
Period size: 30 Copynumber: 4.1 Consensus size: 29
16822508 ATTTTTTGAC
*
16822518 CCCCAAAGTTTTCAAAAATTCAAATTTGA
1 CCCCAAAGTTTTCAAAAATTCAAATTTAA
* *
16822547 CCCCCAAGTTTTCTAAAAATTCAAATTTCA
1 CCCCAAAGTTTTC-AAAAATTCAAATTTAA
* * *
16822577 CCCTTAAA-TTTCCAAAACTTCAAATTTAA
1 CCC-CAAAGTTTTCAAAAATTCAAATTTAA
*
16822606 TCCCCAAAGTTTTCAAAAATTAAAATTTAA
1 -CCCCAAAGTTTTCAAAAATTCAAATTTAA
16822636 CCCC
1 CCCC
16822640 GTTTTAATGT
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
29 33 0.42
30 43 0.55
31 2 0.03
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.32
Consensus pattern (29 bp):
CCCCAAAGTTTTCAAAAATTCAAATTTAA
Found at i:16834464 original size:50 final size:50
Alignment explanation
Indices: 16834321--16834447 Score: 184
Period size: 50 Copynumber: 2.5 Consensus size: 50
16834311 ATCTTTTACT
*
16834321 CCTAAAGCTATAG-AGGTGCAGATTGAAACCACAATGGCAAATCTCATACA
1 CCTAAAGCTGTAGAAGG-GCAGATTGAAACCACAATGGCAAATCTCATACA
* * * * *
16834371 CTTAAAGCTGTAGAGGGGCAGAATGAAACCGCAATGGCAAATCTCATTCA
1 CCTAAAGCTGTAGAAGGGCAGATTGAAACCACAATGGCAAATCTCATACA
16834421 CCTAAAGCTGTAGAAGGGCAGATTGAA
1 CCTAAAGCTGTAGAAGGGCAGATTGAA
16834448 GTCACAAGGA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
50 65 0.97
51 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (50 bp):
CCTAAAGCTGTAGAAGGGCAGATTGAAACCACAATGGCAAATCTCATACA
Found at i:16834548 original size:40 final size:40
Alignment explanation
Indices: 16834504--16834800 Score: 151
Period size: 40 Copynumber: 7.3 Consensus size: 40
16834494 TTACAACCTT
* *
16834504 CAATCTCTTAACCTAACCAGAAGGGAGATTAAAGACAATC
1 CAATCTTTTACCCTAACCAGAAGGGAGATTAAAGACAATC
** * *
16834544 CAATCTTTTACCCCGATCATG-AGGGAGATTGAAA-ACTATC
1 CAATCTTTTACCCTAACCA-GAAGGGAGATT-AAAGACAATC
* *
16834584 CAATCTTTTACCCTAACCAGAAGGCAGATTGAAG-CAATC
1 CAATCTTTTACCCTAACCAGAAGGGAGATTAAAGACAATC
* ** * * *
16834623 CAATCTATTACCCTAAAGTAATAGAGAGGCAGATTGAAGACCATC
1 CAATCTTTTACCCT--A--ACCAGA-AGGGAGATTAAAGACAATC
* * ** * * *
16834668 CGATCTCTTACCCCGATCATG--GGGCAAATTGAAA-ACTATC
1 CAATCTTTTACCCTAACCA-GAAGGG-AGATT-AAAGACAATC
* * * ** *
16834708 CAATCTATTACCCTAATCAAAAGACAGATTGAAA-ACCATC
1 CAATCTTTTACCCTAACCAGAAGGGAGATT-AAAGACAATC
* * * *
16834748 CAATCTTTTACCCTAATCAGAAAGTAAATTGAAA-ACAATC
1 CAATCTTTTACCCTAACCAGAAGGGAGATT-AAAGACAATC
16834788 CAATCTTTTACCC
1 CAATCTTTTACCC
16834801 CTAAAATTAT
Statistics
Matches: 200, Mismatches: 42, Indels: 30
0.74 0.15 0.11
Matches are distributed among these distances:
39 22 0.11
40 135 0.68
41 10 0.05
42 1 0.00
43 4 0.02
44 13 0.06
45 15 0.08
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (40 bp):
CAATCTTTTACCCTAACCAGAAGGGAGATTAAAGACAATC
Found at i:16834606 original size:80 final size:80
Alignment explanation
Indices: 16834504--16834801 Score: 253
Period size: 80 Copynumber: 3.7 Consensus size: 80
16834494 TTACAACCTT
* * * *
16834504 CAATCTCTTAACCTAACCAGAAGGGAGATT-AAAGACAATCCAATCTTTTACCCCGATCATGAGG
1 CAATCTCTTACCCTAACCAGAAGGGAAATTGAAA-ACAATCCAATCTATTACCCCAATCATGAGG
*
16834568 GAGATTGAAAACTATC
65 GAGATTGAAAACCATC
* * * * * *
16834584 CAATCTTTTACCCTAACCAGAAGGCAGATTG-AAGCAATCCAATCTATTACCCTAAAGTAATAGA
1 CAATCTCTTACCCTAACCAGAAGGGAAATTGAAAACAATCCAATCTATTACCC-CAA-TCAT-GA
*
16834648 GAGGCAGATTGAAGACCATC
63 G-GG-AGATTGAAAACCATC
* ** * * * **
16834668 CGATCTCTTACCCCGATCATG--GGGCAAATTGAAAACTATCCAATCTATTACCCTAATCAAAAG
1 CAATCTCTTACCCTAACCA-GAAGGG-AAATTGAAAACAATCCAATCTATTACCCCAATCATGAG
**
16834731 ACAGATTGAAAACCATC
64 GGAGATTGAAAACCATC
* * * * *
16834748 CAATCTTTTACCCTAATCAGAAAGTAAATTGAAAACAATCCAATCTTTTACCCC
1 CAATCTCTTACCCTAACCAGAAGGGAAATTGAAAACAATCCAATCTATTACCCC
16834802 TAAAATTATA
Statistics
Matches: 172, Mismatches: 35, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
79 18 0.10
80 85 0.49
81 4 0.02
82 5 0.03
83 6 0.03
84 34 0.20
85 20 0.12
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.24
Consensus pattern (80 bp):
CAATCTCTTACCCTAACCAGAAGGGAAATTGAAAACAATCCAATCTATTACCCCAATCATGAGGG
AGATTGAAAACCATC
Found at i:16834699 original size:124 final size:125
Alignment explanation
Indices: 16834529--16834763 Score: 339
Period size: 124 Copynumber: 1.9 Consensus size: 125
16834519 ACCAGAAGGG
* * *
16834529 AGATTAAAGACAATCCAATCTTTTACCCCGATCATGAGGGAGATTGAAAACTATCCAATCTTTTA
1 AGATTAAAGACAATCCAATCTCTTACCCCGATCATGAGGGAAATTGAAAACTATCCAATCTATTA
* * *
16834594 CCCTAACCAGAAGGCAGATTG-AAGCAATCCAATCTATTACCCTAAAGTAATAGAGAGGC
66 CCCTAACCAAAAGACAGATTGAAAACAATCCAATCTATTACCCTAAAGTAATAGAGAGGC
* * *
16834653 AGATTGAAGACCATCCGATCTCTTACCCCGATCATG-GGGCAAATTGAAAACTATCCAATCTATT
1 AGATTAAAGACAATCCAATCTCTTACCCCGATCATGAGGG-AAATTGAAAACTATCCAATCTATT
* * *
16834717 ACCCTAATCAAAAGACAGATTGAAAACCATCCAATCTTTTACCCTAA
65 ACCCTAACCAAAAGACAGATTGAAAACAATCCAATCTATTACCCTAA
16834764 TCAGAAAGTA
Statistics
Matches: 97, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
123 3 0.03
124 73 0.75
125 21 0.22
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (125 bp):
AGATTAAAGACAATCCAATCTCTTACCCCGATCATGAGGGAAATTGAAAACTATCCAATCTATTA
CCCTAACCAAAAGACAGATTGAAAACAATCCAATCTATTACCCTAAAGTAATAGAGAGGC
Found at i:16836547 original size:30 final size:29
Alignment explanation
Indices: 16836513--16836697 Score: 192
Period size: 30 Copynumber: 6.2 Consensus size: 29
16836503 AAAATCATTT
16836513 TTTAATCCCCAAAATTTTCAAAAATTCAAA
1 TTTAA-CCCCAAAATTTTCAAAAATTCAAA
*
16836543 TTTAACCCCCAAATTTTCTAAAAATTCAAA
1 TTTAACCCCAAAATTTTC-AAAAATTCAAA
* * * *
16836573 TTTTATCTCC-AAATTTCCAAAACTTCAAA
1 -TTTAACCCCAAAATTTTCAAAAATTCAAA
* * *
16836602 TTTAATCCCTAAAGTTTTCAAAAATTTAAA
1 TTTAA-CCCCAAAATTTTCAAAAATTCAAA
* * *
16836632 TTTAACCCTTAAATTTTTCAAAAATTTAAA
1 TTTAACCC-CAAAATTTTCAAAAATTCAAA
* *
16836662 TTTAACCCTTAAAATTTTCAAAAATTAAAA
1 TTTAACCC-CAAAATTTTCAAAAATTCAAA
16836692 TTTAAC
1 TTTAAC
16836698 TCCATTTTAA
Statistics
Matches: 135, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
28 4 0.03
29 27 0.20
30 97 0.72
31 7 0.05
ACGTcount: A:0.44, C:0.18, G:0.01, T:0.38
Consensus pattern (29 bp):
TTTAACCCCAAAATTTTCAAAAATTCAAA
Found at i:16836691 original size:16 final size:16
Alignment explanation
Indices: 16836640--16836694 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
16836630 AATTTAACCC
*
16836640 TTAAATTTTTCAAAAA
1 TTAAAATTTTCAAAAA
* ***
16836656 TTTAAA-TTT-AACCC
1 TTAAAATTTTCAAAAA
16836670 TTAAAATTTTCAAAAA
1 TTAAAATTTTCAAAAA
16836686 TTAAAATTT
1 TTAAAATTT
16836695 AACTCCATTT
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
14 7 0.25
15 6 0.21
16 15 0.54
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATTTTCAAAAA
Found at i:16838336 original size:19 final size:19
Alignment explanation
Indices: 16838312--16838348 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16838302 TTTGTTGTTC
*
16838312 TGTTTTTTTTTCTTTTACT
1 TGTTTTGTTTTCTTTTACT
*
16838331 TGTTTTGTTTTGTTTTAC
1 TGTTTTGTTTTCTTTTAC
16838349 ATTTATTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.05, C:0.08, G:0.11, T:0.76
Consensus pattern (19 bp):
TGTTTTGTTTTCTTTTACT
Found at i:16838357 original size:24 final size:24
Alignment explanation
Indices: 16838306--16838357 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
16838296 GACTATTTTG
* *
16838306 TTGTTCTGTTTTTTTTTCTTTTAC
1 TTGTTCTGTTTTTTTTACATTTAC
*
16838330 TTGTTTTGTTTTGTTTTACATTTA-
1 TTGTTCTGTTTT-TTTTACATTTAC
16838354 TTGT
1 TTGT
16838358 AGACGGCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.08, C:0.08, G:0.12, T:0.73
Consensus pattern (24 bp):
TTGTTCTGTTTTTTTTACATTTAC
Found at i:16839548 original size:30 final size:31
Alignment explanation
Indices: 16839479--16839552 Score: 98
Period size: 30 Copynumber: 2.4 Consensus size: 31
16839469 TTAAATTTGT
* *
16839479 AATAATAAAATTATATTTTAATTTCTTCAAA
1 AATAATAAAAATATATTTAAATTTCTTCAAA
16839510 AATAATAAAAATATAATTTAAATTT-TT-AAA
1 AATAATAAAAATAT-ATTTAAATTTCTTCAAA
*
16839540 AATTATAAAAATA
1 AATAATAAAAATA
16839553 AACTATTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 15 0.38
31 15 0.38
32 9 0.23
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (31 bp):
AATAATAAAAATATATTTAAATTTCTTCAAA
Found at i:16839572 original size:30 final size:30
Alignment explanation
Indices: 16839507--16839576 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
16839497 TAATTTCTTC
* * *
16839507 AAAAATAATAAAAATATAATTTAAATTTTT
1 AAAAATTATAAAAATATAATTTAAAATTAT
16839537 AAAAATTATAAAAATA-AACTATTAAAATTAT
1 AAAAATTATAAAAATATAA-T-TTAAAATTAT
16839568 -AAAATTATA
1 AAAAATTATA
16839577 TTTTTATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.06
30 25 0.71
31 8 0.23
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (30 bp):
AAAAATTATAAAAATATAATTTAAAATTAT
Found at i:16843055 original size:31 final size:31
Alignment explanation
Indices: 16843017--16843094 Score: 156
Period size: 31 Copynumber: 2.5 Consensus size: 31
16843007 TTAGGATTTT
16843017 TGGCCCACACGACCTATATGGCCAGGGCGTG
1 TGGCCCACACGACCTATATGGCCAGGGCGTG
16843048 TGGCCCACACGACCTATATGGCCAGGGCGTG
1 TGGCCCACACGACCTATATGGCCAGGGCGTG
16843079 TGGCCCACACGACCTA
1 TGGCCCACACGACCTA
16843095 ACACACAACC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.21, C:0.35, G:0.29, T:0.15
Consensus pattern (31 bp):
TGGCCCACACGACCTATATGGCCAGGGCGTG
Found at i:16846885 original size:42 final size:42
Alignment explanation
Indices: 16846809--16846931 Score: 158
Period size: 42 Copynumber: 2.9 Consensus size: 42
16846799 TTCAAAACAG
* *
16846809 TAAGACAACTTT-AAAAATTCAGCAAGCATCAATTCATGGGCT
1 TAAGACAATTTTGAAAAA-TCAACAAGCATCAATTCATGGGCT
* * *
16846851 TAAGACAATTTTGAAAAATCAACAAACATTAATTCATGGTCT
1 TAAGACAATTTTGAAAAATCAACAAGCATCAATTCATGGGCT
* * *
16846893 CAAAACAATTTTGAAAAATCAACAAGCATCATTTCATGG
1 TAAGACAATTTTGAAAAATCAACAAGCATCAATTCATGG
16846932 CCTTGAAAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
42 65 0.93
43 5 0.07
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (42 bp):
TAAGACAATTTTGAAAAATCAACAAGCATCAATTCATGGGCT
Found at i:16851417 original size:26 final size:24
Alignment explanation
Indices: 16851388--16851442 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
16851378 TTTATTTTTG
* *
16851388 TTTTACTATTTGTATTTTTTATTTAA
1 TTTTACTATTT-TAATTTTT-TTCAA
*
16851414 TTTTTCTATTTTAATTTTTTTCAA
1 TTTTACTATTTTAATTTTTTTCAA
16851438 TTTTA
1 TTTTA
16851443 TTTGCTTCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 8 0.32
25 7 0.28
26 10 0.40
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (24 bp):
TTTTACTATTTTAATTTTTTTCAA
Found at i:16851423 original size:20 final size:20
Alignment explanation
Indices: 16851373--16851425 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
16851363 TACTTTAGCC
*
16851373 ATTTTTTTATTTTTGTTTTA
1 ATTTTTCTATTTTTGTTTTA
* * *
16851393 CTATTTGTATTTTT-TATTTA
1 ATTTTTCTATTTTTGT-TTTA
16851413 ATTTTTCTATTTT
1 ATTTTTCTATTTT
16851426 AATTTTTTTC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (20 bp):
ATTTTTCTATTTTTGTTTTA
Found at i:16851428 original size:14 final size:14
Alignment explanation
Indices: 16851373--16851432 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
16851363 TACTTTAGCC
* *
16851373 ATTTTTTTATTTTT
1 ATTTTTCTATTTTA
* *
16851387 GTTTTACTATTTGT-
1 ATTTTTCTATTT-TA
16851401 ATTTTT-TA-TTTA
1 ATTTTTCTATTTTA
16851413 ATTTTTCTATTTTA
1 ATTTTTCTATTTTA
16851427 ATTTTT
1 ATTTTT
16851433 TTCAATTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
11 1 0.03
12 8 0.22
13 4 0.11
14 23 0.62
15 1 0.03
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.75
Consensus pattern (14 bp):
ATTTTTCTATTTTA
Found at i:16856341 original size:18 final size:17
Alignment explanation
Indices: 16856300--16856335 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
16856290 AAATAGATAG
*
16856300 AAAAAATTAGTCAATAT
1 AAAAAATTACTCAATAT
16856317 AAAAAATTACTCAA-AT
1 AAAAAATTACTCAATAT
16856333 AAA
1 AAA
16856336 TAAAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.64, C:0.08, G:0.03, T:0.25
Consensus pattern (17 bp):
AAAAAATTACTCAATAT
Found at i:16856347 original size:3 final size:3
Alignment explanation
Indices: 16856334--16856408 Score: 54
Period size: 3 Copynumber: 26.7 Consensus size: 3
16856324 TACTCAAATA
** * *
16856334 AAT AA- AAT AAT AAT AAT ACG AA- AAC AAG AAT AA- AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
16856378 AATT AA- AAT AAT AAT CAT -AT AAT AAT AAT AA
1 AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16856409 GAAAATAAAG
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
2 12 0.20
3 44 0.75
4 3 0.05
ACGTcount: A:0.68, C:0.04, G:0.03, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:16856384 original size:17 final size:16
Alignment explanation
Indices: 16856333--16856436 Score: 65
Period size: 17 Copynumber: 6.6 Consensus size: 16
16856323 TTACTCAAAT
16856333 AAATAAAATAATAATA
1 AAATAAAATAATAATA
** * *
16856349 ATACGAAAACAAGAATA
1 A-AATAAAATAATAATA
16856366 AAATAAAATAATAAT-
1 AAATAAAATAATAATA
*
16856381 ---TAAAATAATAATC
1 AAATAAAATAATAATA
* *
16856394 ATATAATAATAATAAGA
1 AAATAA-AATAATAATA
*
16856411 AAATAAAGAAAATAA-A
1 AAATAAA-ATAATAATA
16856427 TAAATAAAAT
1 -AAATAAAAT
16856437 TAAAAAGAAC
Statistics
Matches: 67, Mismatches: 13, Indels: 16
0.70 0.14 0.17
Matches are distributed among these distances:
12 12 0.18
16 17 0.25
17 38 0.57
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.23
Consensus pattern (16 bp):
AAATAAAATAATAATA
Found at i:16856414 original size:45 final size:45
Alignment explanation
Indices: 16856330--16856430 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 45
16856320 AAATTACTCA
*
16856330 AATAAATAAAATAATAATAATACGAAAACAAGAATAAAATAAAAT
1 AATAAATAAAATAATAATAATACGAAAACAAGAAGAAAATAAAAT
* * * * * *
16856375 AATAATTAAAATAATAATCATA-TAATAATAATAAGAAAATAAAGAA
1 AATAAATAAAATAATAATAATACGAA-AACAAGAAGAAAATAAA-AT
16856421 AATAAATAAA
1 AATAAATAAA
16856431 TAAAATTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
44 2 0.04
45 34 0.74
46 10 0.22
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.23
Consensus pattern (45 bp):
AATAAATAAAATAATAATAATACGAAAACAAGAAGAAAATAAAAT
Found at i:16858113 original size:20 final size:19
Alignment explanation
Indices: 16858088--16858155 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 19
16858078 CTTTTATTTA
* *
16858088 TTTATTTTCTCAATATTATT
1 TTTATTTT-TTAATTTTATT
* *
16858108 TTTATTATATTATTTTTATT
1 TTTATT-TTTTAATTTTATT
16858128 TTTATTATTTTAATTTTATT
1 TTTATT-TTTTAATTTTATT
16858148 TTTATTTT
1 TTTATTTT
16858156 ATTCTTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.05
20 38 0.93
21 1 0.02
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTATTTTTTAATTTTATT
Found at i:16858115 original size:3 final size:3
Alignment explanation
Indices: 16858101--16858198 Score: 80
Period size: 3 Copynumber: 34.0 Consensus size: 3
16858091 ATTTTCTCAA
* * *
16858101 TAT TAT TTT TAT TA- TAT TAT TTT TAT TTT TAT TAT T-T TAAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
* * ** *
16858144 TAT TTT TAT T-T TAT TCT TAT T-T TCG TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16858190 TAT TAT TAT
1 TAT TAT TAT
16858199 ATTTACTTTA
Statistics
Matches: 74, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
2 10 0.14
3 62 0.84
4 2 0.03
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:16858118 original size:11 final size:10
Alignment explanation
Indices: 16858084--16858165 Score: 60
Period size: 11 Copynumber: 7.7 Consensus size: 10
16858074 TTTTCTTTTA
16858084 TTTATTTATT
1 TTTATTTATT
16858094 TTCTCAATATTATT
1 TT-T--AT-TTATT
16858108 TTTATTATATT
1 TTTATT-TATT
*
16858119 ATT-TTTATT
1 TTTATTTATT
16858128 TTTA-TTATT
1 TTTATTTATT
*
16858137 TTAATTTTATT
1 TTTA-TTTATT
16858148 TTTATTTTATT
1 TTTA-TTTATT
*
16858159 CTTATTT
1 TTTATTT
16858166 TCGTATTATT
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
9 14 0.24
10 8 0.14
11 27 0.46
13 3 0.05
14 7 0.12
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTATTTATT
Found at i:16867572 original size:118 final size:116
Alignment explanation
Indices: 16867351--16867589 Score: 363
Period size: 118 Copynumber: 2.0 Consensus size: 116
16867341 ATAATCTTTT
* * *
16867351 TTTTAATAATAAAAACATACAAATTAAGTATAAAATATTAAAAATAAAAAAAATAAATTAAAACA
1 TTTTGATAATAAAAACATAAAAATTAAGTATAAAATAATAAAAATAAAAAAAATAAATTAAAACA
*
16867416 CTCGGATTGCCTCCCTATAAGCGCTTGTTTAAAATCTAAGCTCAACTTCCC
66 CTCGGATTGCCTCCCCATAAGCGCTTGTTTAAAATCTAAGCTCAACTTCCC
16867467 TTTTGATAAT-AAAACATAAAAATTAAGTATAAAATAATAAAAATAAACATGAAAATAAATTAAA
1 TTTTGATAATAAAAACATAAAAATTAAGTATAAAATAATAAAAATAAA-A--AAAATAAATTAAA
* * * **
16867531 ACACTTGTATTGCCTCCCCATAAGCGCTTGTTTAAAGTCTAAGCTTGACTTCCC
63 ACACTCGGATTGCCTCCCCATAAGCGCTTGTTTAAAATCTAAGCTCAACTTCCC
16867585 TTTTG
1 TTTTG
16867590 GAACTCACAA
Statistics
Matches: 111, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
115 35 0.32
116 10 0.09
118 66 0.59
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.31
Consensus pattern (116 bp):
TTTTGATAATAAAAACATAAAAATTAAGTATAAAATAATAAAAATAAAAAAAATAAATTAAAACA
CTCGGATTGCCTCCCCATAAGCGCTTGTTTAAAATCTAAGCTCAACTTCCC
Found at i:16875572 original size:26 final size:26
Alignment explanation
Indices: 16875536--16875615 Score: 88
Period size: 26 Copynumber: 3.1 Consensus size: 26
16875526 TTACTATTAA
* * *
16875536 TGTCGCTGTATTAGCATGTTCAGAAT
1 TGTCGTTGTATGAGCATGTCCAGAAT
* *
16875562 TGTCGTTGTATGAACATGTCCAAAAT
1 TGTCGTTGTATGAGCATGTCCAGAAT
* * *
16875588 TGTTGTTGCATGAGCACGTCCAGAAT
1 TGTCGTTGTATGAGCATGTCCAGAAT
16875614 TG
1 TG
16875616 CATCCAAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (26 bp):
TGTCGTTGTATGAGCATGTCCAGAAT
Found at i:16876001 original size:16 final size:16
Alignment explanation
Indices: 16875980--16876013 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
16875970 CTCTTTTACA
16875980 TTTCTTTTCTAAAACG
1 TTTCTTTTCTAAAACG
16875996 TTTCTTTTCTAAAACG
1 TTTCTTTTCTAAAACG
16876012 TT
1 TT
16876014 GGTGGTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (16 bp):
TTTCTTTTCTAAAACG
Found at i:16877383 original size:42 final size:40
Alignment explanation
Indices: 16877256--16877468 Score: 121
Period size: 42 Copynumber: 5.2 Consensus size: 40
16877246 TAGATTGAAG
* *
16877256 AGATTGGATGGTGTTTTTAATTTGTCCTTTAGTTAGGGTAAA
1 AGATTGGATGGTG-TTTCAATTTGCCCTTT-GTTAGGGTAAA
* * * *
16877298 AAATTGGAT-G-GTTTCAATCTGCCCCATTGTTAAGG-AAA
1 AGATTGGATGGTGTTTCAATTTG-CCCTTTGTTAGGGTAAA
* *
16877336 GAGATTAGATGGTGTCTTCAATTTGCCCTTTGGTTTGGGTAAA
1 -AGATTGGATGGTGT-TTCAATTTGCCCTTT-GTTAGGGTAAA
** * * * ** *
16877379 AGATTGGAT-G-ACTTCAATCTGTCCCATAGTCGGGGTAAG
1 AGATTGGATGGTGTTTCAATTTG-CCCTTTGTTAGGGTAAA
* * * * *
16877418 AGATTGGATGGTGTCTTTAATCTGTCCTTTATTTAGGATAAA
1 AGATTGGATGGTGT-TTCAATTTGCCCTTT-GTTAGGGTAAA
16877460 AGATTGGAT
1 AGATTGGAT
16877469 AACTTCACTC
Statistics
Matches: 127, Mismatches: 32, Indels: 24
0.69 0.17 0.13
Matches are distributed among these distances:
38 3 0.02
39 46 0.36
40 11 0.09
41 12 0.09
42 52 0.41
43 3 0.02
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.38
Consensus pattern (40 bp):
AGATTGGATGGTGTTTCAATTTGCCCTTTGTTAGGGTAAA
Found at i:16877388 original size:81 final size:81
Alignment explanation
Indices: 16877253--16877849 Score: 407
Period size: 81 Copynumber: 7.4 Consensus size: 81
16877243 GGGTAGATTG
* * * * **
16877253 AAGAGATTGGATGGTGTTTTTAATTTGTCCTTTAGTTAGGGTAAAAAATTGGATGGTTTCAATCT
1 AAGAGATTAGATGGTGTCTTCAATTTGTCCTTTAGTTAGGGTAAAAGATTGGATGACTTCAATCT
* * * *
16877318 GCCCCATTGTTAAGGA
66 ACCCCATGGTCAAGGT
* * *
16877334 AAGAGATTAGATGGTGTCTTCAATTTGCCCTTTGGTTTGGGTAAAAGATTGGATGACTTCAATCT
1 AAGAGATTAGATGGTGTCTTCAATTTGTCCTTTAGTTAGGGTAAAAGATTGGATGACTTCAATCT
** * **
16877399 GTCCCATAGTCGGGGT
66 ACCCCATGGTCAAGGT
* * * * * * *
16877415 AAGAGATTGGATGGTGTCTTTAATCTGTCCTTTATTTAGGATAAAAGATTGGATAACTTCACTCT
1 AAGAGATTAGATGGTGTCTTCAATTTGTCCTTTAGTTAGGGTAAAAGATTGGATGACTTCAATCT
*
16877480 ACCTCATGGTCAAGGT
66 ACCCCATGGTCAAGGT
* * * *
16877496 AAGAGATT-GAATGGTATTTTCAATTTGAT-CTCTAGTTAGGGTAAAAGATTAGATGACTTCAAT
1 AAGAGATTAG-ATGGTGTCTTCAATTTG-TCCTTTAGTTAGGGTAAAAGATTGGATGACTTCAAT
* * * *
16877559 CTACCCAATGGGCAGGGC
64 CTACCCCATGGTCAAGGT
* * * ** * * * *
16877577 AAGAGATTAGATAGTGTCTTCAATCTATCCACTGGTTAGGGTAAAAGGTTGAATGACTTCAATTT
1 AAGAGATTAGATGGTGTCTTCAATTTGTCCTTTAGTTAGGGTAAAAGATTGGATGACTTCAATCT
* *
16877642 ACCCTATGGTCAGGGT
66 ACCCCATGGTCAAGGT
* * * * * * * * * *
16877658 AAGAGGTTGGATGATGTCTTTAATCTATCCTCTAATTAGGGTAAAAAATTGGAT-AGTTTCAATC
1 AAGAGATTAGATGGTGTCTTCAATTTGTCCTTTAGTTAGGGTAAAAGATTGGATGA-CTTCAATC
*** * * **
16877722 TGTTCTATAAG-CGGGGT
65 TACCCCAT-GGTCAAGGT
* * **
16877739 AAGAGATTTA-ATGGTGTATTCAATTTG-CTCTCTAGTTAGAATAAAAGATTGGATGGA-TTCAA
1 AAGAGA-TTAGATGGTGTCTTCAATTTGTC-CTTTAGTTAGGGTAAAAGATTGGAT-GACTTCAA
* ** * **
16877801 TCTAACCTGTGGACGGGGT
63 TCTACCCCATGGTCAAGGT
* * *
16877820 AAGAGATTGGATGGTGTCTTTAATCTGTCC
1 AAGAGATTAGATGGTGTCTTCAATTTGTCC
16877850 CATGGTCACG
Statistics
Matches: 405, Mismatches: 98, Indels: 26
0.77 0.19 0.05
Matches are distributed among these distances:
80 7 0.02
81 391 0.97
82 6 0.01
83 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (81 bp):
AAGAGATTAGATGGTGTCTTCAATTTGTCCTTTAGTTAGGGTAAAAGATTGGATGACTTCAATCT
ACCCCATGGTCAAGGT
Found at i:16877657 original size:39 final size:39
Alignment explanation
Indices: 16877533--16877659 Score: 114
Period size: 39 Copynumber: 3.2 Consensus size: 39
16877523 ATCTCTAGTT
*
16877533 AGGGTAAAAGATT-AGATGACTTCAATCTACCCAATGGGC
1 AGGGTAAAAGATTGAGATGACTTCAATCTACCC-ATGGTC
* * * * * *
16877572 AGGGCAAGAGATTAGATAGTGTCTTCAATCTATCCACTGGTT
1 AGGGTAAAAGATT-GAGA-TGACTTCAATCTACCCA-TGGTC
* *
16877614 AGGGTAAAAGGTTGA-ATGACTTCAATTTACCCTATGGTC
1 AGGGTAAAAGATTGAGATGACTTCAATCTACCC-ATGGTC
16877653 AGGGTAA
1 AGGGTAA
16877660 GAGGTTGGAT
Statistics
Matches: 69, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
39 35 0.51
40 2 0.03
41 5 0.07
42 27 0.39
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (39 bp):
AGGGTAAAAGATTGAGATGACTTCAATCTACCCATGGTC
Found at i:16877681 original size:243 final size:241
Alignment explanation
Indices: 16877253--16877845 Score: 600
Period size: 243 Copynumber: 2.4 Consensus size: 241
16877243 GGGTAGATTG
* * * * *
16877253 AAGAGATTGGATGGTGTTTTTAATTTGTCCTTTAGTTAGGGTAAAAAATTGGATGGTTTCAATCT
1 AAGAGATTGAATGGTGTTTTCAATTTGT-CTCTAGTTAGGGTAAAAGATTGGAT-GATTCAATCT
* * * ** * * * ** *
16877318 GCCCCATTGTTAAGGAAAGAGATTAGATGGTGTCTTCAATTTGCCCTTTGGTTTGGGTAAAAGAT
64 ACCCAATGGACAGGGAAAGAGATTAGATGGTGTCTTCAATCTACCCACTGGTTAGGGTAAAAGAT
* * * * *
16877383 TGGATGACTTCAATCTGTCCCATAGTCGGGGTAAGAGATTGGATGGTGTCTTTAATCTGTCCTTT
129 TGAATGACTTCAATCTGTCCCATAGTCAGGGTAAGAGATTGGATGATGTCTTTAATCTATCCTCT
* * * *
16877448 ATTTAGGATAAAAGATTGGATAACTTCACTCTACCTC-AT-GGTCAAGGT
194 AATTAGGATAAAAAATTGGATAACTTCAATCT-CCTCTATAAG-CAAGGT
* *
16877496 AAGAGATTGAATGGTATTTTCAATTTGATCTCTAGTTAGGGTAAAAGATTAGATGACTTCAATCT
1 AAGAGATTGAATGGTGTTTTCAATTTG-TCTCTAGTTAGGGTAAAAGATTGGATGA-TTCAATCT
* * * * *
16877561 ACCCAATGGGCAGGGCAAGAGATTAGATAGTGTCTTCAATCTATCCACTGGTTAGGGTAAAAGGT
64 ACCCAATGGACAGGGAAAGAGATTAGATGGTGTCTTCAATCTACCCACTGGTTAGGGTAAAAGAT
* *
16877626 TGAATGACTTCAAT-T-TACCCTATGGTCAGGGTAAGAGGTTGGATGATGTCTTTAATCTATCCT
129 TGAATGACTTCAATCTGT-CCC-ATAGTCAGGGTAAGAGATTGGATGATGTCTTTAATCTATCCT
* ** ** **
16877689 CTAATTAGGGTAAAAAATTGGATAGTTTCAATCTGTTCTATAAGCGGGGT
192 CTAATTAGGATAAAAAATTGGATAACTTCAATCTCCTCTATAAGCAAGGT
* * **
16877739 AAGAGATTTAATGGTGTATTCAATTTGCTCTCTAGTTAGAATAAAAGATTGGATGGATTCAATCT
1 AAGAGATTGAATGGTGTTTTCAATTTG-TCTCTAGTTAGGGTAAAAGATTGGAT-GATTCAATCT
* ** * * * *
16877804 AACCTGTGGACGGGGTAAGAGATTGGATGGTGTCTTTAATCT
64 ACCCAATGGACAGGGAAAGAGATTAGATGGTGTCTTCAATCT
16877846 GTCCCATGGT
Statistics
Matches: 287, Mismatches: 56, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
241 1 0.00
242 7 0.02
243 275 0.96
244 4 0.01
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.35
Consensus pattern (241 bp):
AAGAGATTGAATGGTGTTTTCAATTTGTCTCTAGTTAGGGTAAAAGATTGGATGATTCAATCTAC
CCAATGGACAGGGAAAGAGATTAGATGGTGTCTTCAATCTACCCACTGGTTAGGGTAAAAGATTG
AATGACTTCAATCTGTCCCATAGTCAGGGTAAGAGATTGGATGATGTCTTTAATCTATCCTCTAA
TTAGGATAAAAAATTGGATAACTTCAATCTCCTCTATAAGCAAGGT
Found at i:16880091 original size:21 final size:19
Alignment explanation
Indices: 16880052--16880106 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
16880042 GTCGGCACAA
*
16880052 TCTTCTTCATTTTCTTTTTCC
1 TCTTCTTC-TCTTCTTTTT-C
*
16880073 TTTTCTTCTCTTCTCTTTTC
1 TCTTCTTCTCTTCT-TTTTC
16880093 TCTTCTTCCTCTTC
1 TCTTCTT-CTCTTC
16880107 AACACCCACA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (19 bp):
TCTTCTTCTCTTCTTTTTC
Found at i:16883968 original size:18 final size:18
Alignment explanation
Indices: 16883934--16883969 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16883924 GAGCTTGTGA
**
16883934 GTAAATGGGTTTGGATTT
1 GTAAATGGGTTCAGATTT
16883952 GTAAATGGGTTCAGATTT
1 GTAAATGGGTTCAGATTT
16883970 TAGTTTGGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.31, T:0.42
Consensus pattern (18 bp):
GTAAATGGGTTCAGATTT
Found at i:16888057 original size:23 final size:22
Alignment explanation
Indices: 16888031--16888074 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
16888021 AAAATATTTC
*
16888031 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
16888054 ATTAACTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
16888075 TTATTCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.43
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:16901420 original size:22 final size:23
Alignment explanation
Indices: 16901392--16901438 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
16901382 AACTTAAGAA
**
16901392 ATTATTTATTACTT-TTTTAAAT
1 ATTATTTAAGACTTATTTTAAAT
16901414 ATTATTTAAGACTTATTTTAAAT
1 ATTATTTAAGACTTATTTTAAAT
16901437 AT
1 AT
16901439 AAATTAAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (23 bp):
ATTATTTAAGACTTATTTTAAAT
Found at i:16901445 original size:23 final size:22
Alignment explanation
Indices: 16901402--16901446 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
16901392 ATTATTTATT
* *
16901402 ACTTTTTTAAATATTATTTAAG
1 ACTTTTTTAAATATAAATTAAG
16901424 ACTTATTTTAAATATAAATTAAG
1 ACTT-TTTTAAATATAAATTAAG
16901447 GATATAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (22 bp):
ACTTTTTTAAATATAAATTAAG
Found at i:16906371 original size:21 final size:21
Alignment explanation
Indices: 16906345--16906400 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
16906335 ATAATAGCAT
16906345 AATCCAAATATAAAGTTTAGA
1 AATCCAAATATAAAGTTTAGA
*
16906366 AATCCAAAGT-TAAAGTTTATA
1 AATCCAAA-TATAAAGTTTAGA
*
16906387 AATCCAAAGATAAA
1 AATCCAAATATAAA
16906401 ACTTCAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.54, C:0.11, G:0.09, T:0.27
Consensus pattern (21 bp):
AATCCAAATATAAAGTTTAGA
Found at i:16913217 original size:95 final size:95
Alignment explanation
Indices: 16913097--16913300 Score: 327
Period size: 95 Copynumber: 2.1 Consensus size: 95
16913087 GTATCCTAAC
* * * * * *
16913097 TACCGATAAAAGCATATACAAAACTATCGATACCTACTATGCAACTACCGATATAACCCAAGTTA
1 TACCGATACAAGCACACACAAAACTACCGATACCTACTATGCAACTACCGATACAACCCAAGTCA
16913162 ATGAGCAACCTCTCTCATACTCTGTACTTG
66 ATGAGCAACCTCTCTCATACTCTGTACTTG
* *
16913192 TACCGATACAAGCACACACAGAACTACCGATACTTACTATGCAACTACCGATACAACCCAAGTCA
1 TACCGATACAAGCACACACAAAACTACCGATACCTACTATGCAACTACCGATACAACCCAAGTCA
*
16913257 ATGAGCAACCTCTCTCTTACTCTGTACTTG
66 ATGAGCAACCTCTCTCATACTCTGTACTTG
16913287 TACCGATACAAGCA
1 TACCGATACAAGCA
16913301 TGGGTTCTAC
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
95 100 1.00
ACGTcount: A:0.36, C:0.29, G:0.11, T:0.24
Consensus pattern (95 bp):
TACCGATACAAGCACACACAAAACTACCGATACCTACTATGCAACTACCGATACAACCCAAGTCA
ATGAGCAACCTCTCTCATACTCTGTACTTG
Found at i:16913885 original size:44 final size:44
Alignment explanation
Indices: 16913827--16913976 Score: 164
Period size: 44 Copynumber: 3.5 Consensus size: 44
16913817 TTATGCTTTA
*
16913827 TCGAGTCATAAGTCTTCCTTTTTAATAATATTCTTACGTTCATT
1 TCGAGTCATGAGTCTTCCTTTTTAATAATATTCTTACGTTCATT
* * * * * * *
16913871 TCAAGTCATGAGTCTTCC--TTT-ATCACATCCTCA-TTCTCATC
1 TCGAGTCATGAGTCTTCCTTTTTAATAATATTCTTACGT-TCATT
* * *
16913912 CCGAGACATGAGTCTTCCTTTTTAATAATATTCTTACGCTCATT
1 TCGAGTCATGAGTCTTCCTTTTTAATAATATTCTTACGTTCATT
16913956 TCGAGTCATGAGTCTTCCTTT
1 TCGAGTCATGAGTCTTCCTTT
16913977 ATCACATCCT
Statistics
Matches: 81, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
40 1 0.01
41 27 0.33
42 3 0.04
43 3 0.04
44 47 0.58
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.43
Consensus pattern (44 bp):
TCGAGTCATGAGTCTTCCTTTTTAATAATATTCTTACGTTCATT
Found at i:16913928 original size:41 final size:41
Alignment explanation
Indices: 16913877--16914017 Score: 174
Period size: 41 Copynumber: 3.4 Consensus size: 41
16913867 CATTTCAAGT
16913877 CATGAGTCTTCCTTTATCACATCCTCATTCTCATCCCGAGA
1 CATGAGTCTTCCTTTATCACATCCTCATTCTCATCCCGAGA
* * * * ** ** *
16913918 CATGAGTCTTCCTTTTTAATAATATTCTTACGCTCATTTCGAGT
1 CATGAGTCTTCC--TTT-ATCACATCCTCATTCTCATCCCGAGA
16913962 CATGAGTCTTCCTTTATCACATCCTCATTCTCATCCCGAGA
1 CATGAGTCTTCCTTTATCACATCCTCATTCTCATCCCGAGA
16914003 CATGAGTCTTCCTTT
1 CATGAGTCTTCCTTT
16914018 TAAACATCAA
Statistics
Matches: 79, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
41 44 0.56
42 3 0.04
43 3 0.04
44 29 0.37
ACGTcount: A:0.21, C:0.29, G:0.11, T:0.39
Consensus pattern (41 bp):
CATGAGTCTTCCTTTATCACATCCTCATTCTCATCCCGAGA
Found at i:16913940 original size:85 final size:85
Alignment explanation
Indices: 16913828--16914018 Score: 346
Period size: 85 Copynumber: 2.2 Consensus size: 85
16913818 TATGCTTTAT
* * *
16913828 CGAGTCATAAGTCTTCCTTTTTAATAATATTCTTACGTTCATTTCAAGTCATGAGTCTTCCTTTA
1 CGAGACATGAGTCTTCCTTTTTAATAATATTCTTACGCTCATTTCAAGTCATGAGTCTTCCTTTA
16913893 TCACATCCTCATTCTCATCC
66 TCACATCCTCATTCTCATCC
*
16913913 CGAGACATGAGTCTTCCTTTTTAATAATATTCTTACGCTCATTTCGAGTCATGAGTCTTCCTTTA
1 CGAGACATGAGTCTTCCTTTTTAATAATATTCTTACGCTCATTTCAAGTCATGAGTCTTCCTTTA
16913978 TCACATCCTCATTCTCATCC
66 TCACATCCTCATTCTCATCC
16913998 CGAGACATGAGTCTTCCTTTT
1 CGAGACATGAGTCTTCCTTTT
16914019 AAACATCAAG
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 102 1.00
ACGTcount: A:0.23, C:0.26, G:0.10, T:0.41
Consensus pattern (85 bp):
CGAGACATGAGTCTTCCTTTTTAATAATATTCTTACGCTCATTTCAAGTCATGAGTCTTCCTTTA
TCACATCCTCATTCTCATCC
Found at i:16930094 original size:27 final size:26
Alignment explanation
Indices: 16930054--16930105 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
16930044 AAGAAGAAGG
16930054 TTTTTTGAAAGGTATGTTTATGTTTTA
1 TTTTTTGAAAGGTAT-TTTATGTTTTA
** *
16930081 TTTTTTGATTGGTATTTTATTTTTT
1 TTTTTTGAAAGGTATTTTATGTTTT
16930106 GATTAATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.67
Consensus pattern (26 bp):
TTTTTTGAAAGGTATTTTATGTTTTA
Found at i:16932019 original size:24 final size:24
Alignment explanation
Indices: 16931981--16932030 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
16931971 GTTTAAGCCC
* **
16931981 GAGCCCGAGCCTGAGCTTGAGCAT
1 GAGCCCAAGCCTGAGCCCGAGCAT
*
16932005 GAGCCCAAGCTTGAGCCCGAGCAT
1 GAGCCCAAGCCTGAGCCCGAGCAT
16932029 GA
1 GA
16932031 TCTCGAGCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.30, G:0.32, T:0.14
Consensus pattern (24 bp):
GAGCCCAAGCCTGAGCCCGAGCAT
Found at i:16932026 original size:18 final size:18
Alignment explanation
Indices: 16931981--16932026 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
16931971 GTTTAAGCCC
**
16931981 GAGCCCGAGCCTGAGCTT
1 GAGCCCGAGCCCAAGCTT
**
16931999 GAGCATGAGCCCAAGCTT
1 GAGCCCGAGCCCAAGCTT
16932017 GAGCCCGAGC
1 GAGCCCGAGC
16932027 ATGATCTCGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.22, C:0.33, G:0.33, T:0.13
Consensus pattern (18 bp):
GAGCCCGAGCCCAAGCTT
Found at i:16932136 original size:27 final size:28
Alignment explanation
Indices: 16932097--16932157 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
16932087 GCTCGAGTCG
* **
16932097 TATCATCTGGGGTGG-TCAGGTGATGGA
1 TATCATCTAGGGTGGTTCAGGCAATGGA
*
16932124 TATCATCTAGGGTGGTTTAGGCAATGGA
1 TATCATCTAGGGTGGTTCAGGCAATGGA
16932152 TATCAT
1 TATCAT
16932158 ACGGTTAGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.23, C:0.11, G:0.33, T:0.33
Consensus pattern (28 bp):
TATCATCTAGGGTGGTTCAGGCAATGGA
Found at i:16932166 original size:22 final size:22
Alignment explanation
Indices: 16932140--16932183 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
16932130 CTAGGGTGGT
*
16932140 TTAGGCAATGGATATCATACGG
1 TTAGGCAATGGATATAATACGG
*
16932162 TTAGGCCATGGATATAATACGG
1 TTAGGCAATGGATATAATACGG
16932184 GTTGGTCGAG
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:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (22 bp):
TTAGGCAATGGATATAATACGG
Found at i:16932610 original size:28 final size:27
Alignment explanation
Indices: 16932546--16932617 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
16932536 TATTGGACAT
*
16932546 TTTTCATTTGGAATTAATTACGTTTATA
1 TTTTCATTT-GAATTAATTAAGTTTATA
** **
16932574 AATGAATTTGAAATTAATTAAGTTTATA
1 TTTTCATTTG-AATTAATTAAGTTTATA
16932602 TTTTCATTT-AATTAAT
1 TTTTCATTTGAATTAAT
16932618 ATTTTTTATG
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
26 7 0.21
27 1 0.03
28 26 0.76
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.51
Consensus pattern (27 bp):
TTTTCATTTGAATTAATTAAGTTTATA
Found at i:16932651 original size:26 final size:26
Alignment explanation
Indices: 16932585--16932664 Score: 101
Period size: 26 Copynumber: 3.1 Consensus size: 26
16932575 ATGAATTTGA
* *
16932585 AATTAATTAAGTTTATATTT-TCATTT
1 AATTAATTATGTTTATGTTTGT-ATTT
*
16932611 AATTAA-TATTTTTTATGTTTGTATTT
1 AATTAATTA-TGTTTATGTTTGTATTT
16932637 AATTAATTATGTTTATGTTTGTATTT
1 AATTAATTATGTTTATGTTTGTATTT
16932663 AA
1 AA
16932665 GGTTTTGGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
25 2 0.04
26 42 0.89
27 3 0.06
ACGTcount: A:0.31, C:0.01, G:0.07, T:0.60
Consensus pattern (26 bp):
AATTAATTATGTTTATGTTTGTATTT
Found at i:16945078 original size:30 final size:29
Alignment explanation
Indices: 16945024--16945101 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 29
16945014 CAAAGTCAAA
16945024 GTCAACGGGTC-AA-CGGGTTCATGGGTCG
1 GTCAACGGGTCAAAGCGGG-TCATGGGTCG
*
16945052 GTCAACGGGTCAAAGCGGGTCAATGGGTTG
1 GTCAACGGGTCAAAGCGGGTC-ATGGGTCG
16945082 GTCAACGGGTCAAAGCGGGT
1 GTCAACGGGTCAAAGCGGGT
16945102 TAGGCTCACG
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
28 11 0.24
29 4 0.09
30 31 0.67
ACGTcount: A:0.22, C:0.19, G:0.40, T:0.19
Consensus pattern (29 bp):
GTCAACGGGTCAAAGCGGGTCATGGGTCG
Found at i:16949031 original size:19 final size:18
Alignment explanation
Indices: 16949004--16949047 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
16948994 ATCGTGTTAG
*
16949004 AAATATTGTAATCGATTAA
1 AAATTTTGTAATC-ATTAA
*
16949023 AAATTTTGTTATCATTAA
1 AAATTTTGTAATCATTAA
*
16949041 CAATTTT
1 AAATTTT
16949048 TGGTATCTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (18 bp):
AAATTTTGTAATCATTAA
Found at i:16950320 original size:15 final size:13
Alignment explanation
Indices: 16950291--16950316 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16950281 ATTTTTATTG
16950291 AAATATTAATTTT
1 AAATATTAATTTT
16950304 AAATATTAATTTT
1 AAATATTAATTTT
16950317 TTAATTTTTT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAATATTAATTTT
Found at i:16951317 original size:18 final size:18
Alignment explanation
Indices: 16951247--16951317 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
16951237 ACCGGATATG
*
16951247 AAAATTTGTAACTAAATACC
1 AAAATTTCTAA-TAAA-ACC
* *
16951267 -AAATTTCTATTGAATACC
1 AAAATTTCTAAT-AAAACC
* *
16951285 GATATTTCTAATAAAACC
1 AAAATTTCTAATAAAACC
16951303 AAAATTTCTAATAAA
1 AAAATTTCTAATAAA
16951318 TAATGAAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
18 22 0.54
19 19 0.46
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.34
Consensus pattern (18 bp):
AAAATTTCTAATAAAACC
Found at i:16952269 original size:12 final size:12
Alignment explanation
Indices: 16952249--16952278 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16952239 TCCCCCCAGT
16952249 CACAACCACAGC
1 CACAACCACAGC
*
16952261 CACAGCCACAGC
1 CACAACCACAGC
16952273 CACAAC
1 CACAAC
16952279 ACCGCAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.50, G:0.10, T:0.00
Consensus pattern (12 bp):
CACAACCACAGC
Found at i:16956628 original size:18 final size:18
Alignment explanation
Indices: 16956605--16956666 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
16956595 TGCCAAGTCA
16956605 CGAGCTCACTTTAAGCTG
1 CGAGCTCACTTTAAGCTG
*
16956623 CGAGCTCA-TCTACA-CTTG
1 CGAGCTCACTTTA-AGC-TG
* *
16956641 CGAGCTCACTTGAAGTTG
1 CGAGCTCACTTTAAGCTG
*
16956659 TGAGCTCA
1 CGAGCTCA
16956667 TCCAAATTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
17 4 0.11
18 29 0.83
19 2 0.06
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (18 bp):
CGAGCTCACTTTAAGCTG
Done.