Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 15 of 135
Found at i:3986814 original size:18 final size:17
Alignment explanation
Indices: 3986786--3986827 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
3986776 CCATGTCAGC
3986786 AAAAA-AAATTAAACTTA
1 AAAAATAAATTAAA-TTA
*
3986803 AAATATAAATTAAATTA
1 AAAAATAAATTAAATTA
3986820 AAAAATAA
1 AAAAATAA
3986828 TATAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAATAAATTAAATTA
Found at i:3988009 original size:87 final size:85
Alignment explanation
Indices: 3987866--3988024 Score: 248
Period size: 87 Copynumber: 1.8 Consensus size: 85
3987856 AGACTTACTA
* ** *
3987866 TTGCCTTTAGGCTTAGGAGTTATGTTTGTTTTATGTTTGATTGGTATGCTGTATAAGTCGGTAGT
1 TTGCCTCTAGGCTTAGGAGTTATGTTTGTTTTATGTTTGATTGGTATGCTACATAAGTCGGCAGT
3987931 GTTTGTCTTGTCAGGGACTT
66 GTTTGTCTTGTCAGGGACTT
3987951 TTGCCTCTAGGCTTAGGAGTTATGTTT-TTGTCTAATGTTTGATTGGTATGCTACATAAGTCGGC
1 TTGCCTCTAGGCTTAGGAGTTATGTTTGTT-T-T-ATGTTTGATTGGTATGCTACATAAGTCGGC
3988015 AGTGTTTGTC
63 AGTGTTTGTC
3988025 AGGGATTGAT
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
84 2 0.03
85 27 0.40
86 1 0.01
87 37 0.55
ACGTcount: A:0.16, C:0.11, G:0.27, T:0.45
Consensus pattern (85 bp):
TTGCCTCTAGGCTTAGGAGTTATGTTTGTTTTATGTTTGATTGGTATGCTACATAAGTCGGCAGT
GTTTGTCTTGTCAGGGACTT
Found at i:3990197 original size:29 final size:29
Alignment explanation
Indices: 3990165--3990223 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3990155 TTTTTAGAAC
3990165 AAAAAGCATGCACATCAGCAGATTATAAA
1 AAAAAGCATGCACATCAGCAGATTATAAA
3990194 AAAAAGCATGCACATCAGCAGATTATAAA
1 AAAAAGCATGCACATCAGCAGATTATAAA
3990223 A
1 A
3990224 CTGTATAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.53, C:0.17, G:0.14, T:0.17
Consensus pattern (29 bp):
AAAAAGCATGCACATCAGCAGATTATAAA
Found at i:3991592 original size:18 final size:18
Alignment explanation
Indices: 3991571--3991606 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3991561 ACTTCTCTCA
*
3991571 CCCTCACCCTCACCACCT
1 CCCTCACCCTCAACACCT
3991589 CCCTCACCCTCAACACCT
1 CCCTCACCCTCAACACCT
3991607 TCACTAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.64, G:0.00, T:0.17
Consensus pattern (18 bp):
CCCTCACCCTCAACACCT
Found at i:3991634 original size:60 final size:60
Alignment explanation
Indices: 3991482--3991833 Score: 201
Period size: 60 Copynumber: 5.6 Consensus size: 60
3991472 TCATCATCAT
* * ** *
3991482 CTTCACTAACAACACCTTTACTCGAACCCTCACCAC-CTCCTTCACCCTCAACACCTTCAACAC
1 CTTCACTAACAACACCCTTACTCGAACCCTCACC-CTCACCACCTCCCTC-AC-CC-TCAACAC
* * **
3991545 CTTTACTAACAGCACCACTT-CTCTCACCCTCACCCTCACCACCTCCCTCACCCTCAACAC
1 CTTCACTAACAACACC-CTTACTCGAACCCTCACCCTCACCACCTCCCTCACCCTCAACAC
* * *
3991605 CTTCACTAACACCACCCTTACTCGAACCCTCACCACCTCTCAAACCTTCACCACCCTTACTGCCA
1 CTTCACTAACAACACCCTTACTCGAACCCT---CACC-CTC--A-C--CACCTCCCTCAC--CC-
*
3991670 TCATCCAAAC
54 TCA---ACAC
* *** * * ** * * * *
3991680 CCTCACCCTCAACACCTTTACCCTCA-CTTGAACCCTCACCACCACCATCACCCTCAACAC
1 CTTCACTAACAACACCCTTACTCGAACCCT-CACCCTCACCACCTCCCTCACCCTCAACAC
* * *
3991740 CTTCACTAACAGCACCCCTTCCCTC--ACCCTCACCCTCATCACCTCCCTCACCCTCAACAC
1 CTTCACTAACAACA-CCCTT-ACTCGAACCCTCACCCTCACCACCTCCCTCACCCTCAACAC
*
3991800 CTTCACTAATAACACCCTTACTCGAACCCTCACC
1 CTTCACTAACAACACCCTTACTCGAACCCTCACC
3991834 ACCTCTCAAA
Statistics
Matches: 219, Mismatches: 47, Indels: 49
0.70 0.15 0.16
Matches are distributed among these distances:
58 3 0.01
59 8 0.04
60 89 0.41
61 8 0.04
62 5 0.02
63 42 0.19
64 7 0.03
66 11 0.05
67 1 0.00
68 1 0.00
69 11 0.05
71 5 0.02
72 6 0.03
74 2 0.01
75 20 0.09
ACGTcount: A:0.26, C:0.51, G:0.02, T:0.21
Consensus pattern (60 bp):
CTTCACTAACAACACCCTTACTCGAACCCTCACCCTCACCACCTCCCTCACCCTCAACAC
Found at i:3991640 original size:21 final size:21
Alignment explanation
Indices: 3991614--3991665 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 21
3991604 CCTTCACTAA
*
3991614 CACCACCCTTACTCGAACCCT
1 CACCACCCTTACTCAAACCCT
*
3991635 CACCA-CC-T-CTCAAACCTT
1 CACCACCCTTACTCAAACCCT
3991653 CACCACCCTTACT
1 CACCACCCTTACT
3991666 GCCATCATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 13 0.50
19 3 0.12
20 3 0.12
21 7 0.27
ACGTcount: A:0.25, C:0.52, G:0.02, T:0.21
Consensus pattern (21 bp):
CACCACCCTTACTCAAACCCT
Found at i:3991787 original size:18 final size:18
Alignment explanation
Indices: 3991766--3991801 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3991756 CCTTCCCTCA
*
3991766 CCCTCACCCTCATCACCT
1 CCCTCACCCTCAACACCT
3991784 CCCTCACCCTCAACACCT
1 CCCTCACCCTCAACACCT
3991802 TCACTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.61, G:0.00, T:0.19
Consensus pattern (18 bp):
CCCTCACCCTCAACACCT
Found at i:3991805 original size:195 final size:195
Alignment explanation
Indices: 3991533--3991937 Score: 657
Period size: 195 Copynumber: 2.1 Consensus size: 195
3991523 TCACCCTCAA
* * *
3991533 CACCTTCAACACCTTTACTAACAGCACCACTTCTCTCACCCTCACCCTCACCACCTCCCTCACCC
1 CACCCTCAACACCTTCACTAACAGCACCACTTCCCTCACCCTCACCCTCACCACCTCCCTCACCC
* *
3991598 TCAACACCTTCACTAACACCACCCTTACTCGAACCCTCACCACCTCTCAAACCTTCACCACCCTT
66 TCAACACCTTCACTAACAACACCCTTACTCGAACCCTCACCACCTCTCAAACCCTCACCACCCTT
* ** *
3991663 ACTGCCATCATCCAAACCCTCACCCTCAACACCTTTACCCTCACTTGAACCCTCACCACCACCAT
131 ACTGCCATCATCCAAACCCTCACCCTCAACACCCTTACCCTCACCCGAACCCTCACCACCACCAC
* *
3991728 CACCCTCAACACCTTCACTAACAGCACCCCTTCCCTCACCCTCACCCTCATCACCTCCCTCACCC
1 CACCCTCAACACCTTCACTAACAGCACCACTTCCCTCACCCTCACCCTCACCACCTCCCTCACCC
*
3991793 TCAACACCTTCACTAATAACACCCTTACTCGAACCCTCACCACCTCTCAAACCCTCACCACCCTT
66 TCAACACCTTCACTAACAACACCCTTACTCGAACCCTCACCACCTCTCAAACCCTCACCACCCTT
* * * *
3991858 ATTGCCATCATCTAAACCCTCACCCTCAACACCCTTACCCTCACCCGAACCCTCACCACTACTAC
131 ACTGCCATCATCCAAACCCTCACCCTCAACACCCTTACCCTCACCCGAACCCTCACCACCACCAC
*
3991923 CACCCTCACCACCTT
1 CACCCTCAACACCTT
3991938 TATTACCATC
Statistics
Matches: 193, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
195 193 1.00
ACGTcount: A:0.26, C:0.52, G:0.02, T:0.20
Consensus pattern (195 bp):
CACCCTCAACACCTTCACTAACAGCACCACTTCCCTCACCCTCACCCTCACCACCTCCCTCACCC
TCAACACCTTCACTAACAACACCCTTACTCGAACCCTCACCACCTCTCAAACCCTCACCACCCTT
ACTGCCATCATCCAAACCCTCACCCTCAACACCCTTACCCTCACCCGAACCCTCACCACCACCAC
Found at i:3991848 original size:60 final size:60
Alignment explanation
Indices: 3991711--3991851 Score: 146
Period size: 60 Copynumber: 2.4 Consensus size: 60
3991701 CCTCACTTGA
* * * * *
3991711 ACCCTCACCACCACCATCACCCTCAACACCTTCACTAACAGCACCCCTTCCCTCACCCTC
1 ACCCTCATCACAACCCTCACCCTCAACACCTTCACTAACAACACCCCTTCACTCACCCTC
** *
3991771 ACCCTCATCACCTCCCTCACCCTCAACACCTTCACTAATAACA-CCCTT-ACTCGAACCCTC
1 ACCCTCATCACAACCCTCACCCTCAACACCTTCACTAACAACACCCCTTCACTC--ACCCTC
3991831 ACCACCTC-TCA-AACCCTCACC
1 A-C-CCTCATCACAACCCTCACC
3991852 ACCCTTATTG
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
58 3 0.04
59 5 0.07
60 53 0.77
61 4 0.06
62 4 0.06
ACGTcount: A:0.26, C:0.54, G:0.01, T:0.18
Consensus pattern (60 bp):
ACCCTCATCACAACCCTCACCCTCAACACCTTCACTAACAACACCCCTTCACTCACCCTC
Found at i:3992458 original size:64 final size:64
Alignment explanation
Indices: 3992390--3992518 Score: 206
Period size: 64 Copynumber: 2.0 Consensus size: 64
3992380 TGTGCAGACA
*
3992390 AAAAAGCAAACA-AAAAAAGCACAGCAATAAAACATGAATGAACCACTTCCAAAATAATTACTAC
1 AAAAAGCAAACAGAAAAAA-CACAGCAATAAAACATGAAGGAACCACTTCCAAAATAATTACTAC
* * *
3992454 AAAAAGCAAACAGAAACAACACAGCAATAAAACATGAAGGGATCACTTCCAAAATAATTACTAC
1 AAAAAGCAAACAGAAAAAACACAGCAATAAAACATGAAGGAACCACTTCCAAAATAATTACTAC
3992518 A
1 A
3992519 GAACAAATTA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
64 55 0.92
65 5 0.08
ACGTcount: A:0.57, C:0.20, G:0.09, T:0.14
Consensus pattern (64 bp):
AAAAAGCAAACAGAAAAAACACAGCAATAAAACATGAAGGAACCACTTCCAAAATAATTACTAC
Found at i:3993691 original size:44 final size:43
Alignment explanation
Indices: 3993622--3993705 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 43
3993612 TAAGTCCCGA
* *
3993622 AAATCTCCAAATTTTTAAACTTAAACCAAAATCTCCAAACTCG
1 AAATCTCCAAATTTTTAAACCTAAACCAAAATCCCCAAACTCG
*
3993665 AAATCTCCAAATTTCTTAAACCTAAACCAAATTCCCCAAAC
1 AAATCTCCAAATTT-TTAAACCTAAACCAAAATCCCCAAAC
3993706 CCAACAACCC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 14 0.38
44 23 0.62
ACGTcount: A:0.44, C:0.29, G:0.01, T:0.26
Consensus pattern (43 bp):
AAATCTCCAAATTTTTAAACCTAAACCAAAATCCCCAAACTCG
Found at i:3994007 original size:13 final size:13
Alignment explanation
Indices: 3993989--3994019 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
3993979 ACGGTTTAAA
3993989 TTTTTTTATTTACT
1 TTTTTTTATTT-CT
3994003 TTTTTTTATTTCT
1 TTTTTTTATTTCT
3994016 TTTT
1 TTTT
3994020 AGTTTAGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTATTTCT
Found at i:3994064 original size:18 final size:17
Alignment explanation
Indices: 3994038--3994080 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
3994028 TAAAAATTAT
3994038 TTTATTTTTTAA-TTTAA
1 TTTA-TTTTTAAGTTTAA
3994055 TTTATATTTTAAGTTTAA
1 TTTAT-TTTTAAGTTTAA
3994073 TTT-TTTTT
1 TTTATTTTT
3994081 GCTGACATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.21
17 11 0.46
18 8 0.33
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTATTTTTAAGTTTAA
Found at i:3998477 original size:25 final size:24
Alignment explanation
Indices: 3998416--3998477 Score: 61
Period size: 26 Copynumber: 2.5 Consensus size: 24
3998406 ATTAAGTAAG
**
3998416 AAACTTGAGCTTGAGCTCAACTCA
1 AAACTTGAGCTTGAGCTCAAAGCA
* *
3998440 AAATTTGAGGCTTGAGACTCAAAGCT
1 AAACTTGA-GCTTGAG-CTCAAAGCA
*
3998466 AGACTTGAGCTT
1 AAACTTGAGCTT
3998478 AATGGAGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 7 0.23
25 11 0.37
26 12 0.40
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (24 bp):
AAACTTGAGCTTGAGCTCAAAGCA
Found at i:4008244 original size:16 final size:17
Alignment explanation
Indices: 4008213--4008246 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4008203 GATGTGTCAC
4008213 TTTTTTAAAATATTTAT
1 TTTTTTAAAATATTTAT
*
4008230 TTTTTTAATAT-TTTAT
1 TTTTTTAAAATATTTAT
4008246 T
1 T
4008247 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTAAAATATTTAT
Found at i:4011887 original size:23 final size:22
Alignment explanation
Indices: 4011852--4011906 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
4011842 CAGACATTAT
4011852 AAAATAATAAGAAA-AAAATAGAA
1 AAAATAA-AAGAAATAAAATA-AA
**
4011875 AAAATAAAGAGAAATAATGTAAA
1 AAAATAAA-AGAAATAAAATAAA
4011898 AAAATAAAA
1 AAAATAAAA
4011907 TAATTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 2 0.07
23 22 0.79
24 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (22 bp):
AAAATAAAAGAAATAAAATAAA
Found at i:4018265 original size:16 final size:17
Alignment explanation
Indices: 4018244--4018281 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
4018234 ATGGTTTTTG
*
4018244 AAAAATGAAAACATAA-
1 AAAAATGAAAAAATAAT
*
4018260 AAAAATTAAAAAATAAT
1 AAAAATGAAAAAATAAT
4018277 AAAAA
1 AAAAA
4018282 GCTATTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (17 bp):
AAAAATGAAAAAATAAT
Found at i:4024367 original size:21 final size:22
Alignment explanation
Indices: 4024341--4024381 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
4024331 AAGTTTTTAC
*
4024341 TTTGAATTTTTTTA-AATTTCT
1 TTTGAATATTTTTATAATTTCT
4024362 TTTGAATATTTTTATAATTT
1 TTTGAATATTTTTATAATTT
4024382 TTAAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTGAATATTTTTATAATTTCT
Found at i:4026956 original size:40 final size:39
Alignment explanation
Indices: 4026877--4026958 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 39
4026867 CAAAACCTAT
* * *
4026877 TCACCTTGTTTTCCCTAGGAAGATGATGGTCGAAAGTAA
1 TCACCTTCTTTTCCCTAGGAAAATGATGGCCGAAAGTAA
* * *
4026916 TCACCTTCTTTTCTCTTAGGAAAATGATGGCCGGATGTAA
1 TCACCTTCTTTTC-CCTAGGAAAATGATGGCCGAAAGTAA
4026956 TCA
1 TCA
4026959 TCGGATCCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 12 0.33
40 24 0.67
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (39 bp):
TCACCTTCTTTTCCCTAGGAAAATGATGGCCGAAAGTAA
Found at i:4029936 original size:30 final size:30
Alignment explanation
Indices: 4029865--4029942 Score: 113
Period size: 30 Copynumber: 2.6 Consensus size: 30
4029855 GTGGAGCTGG
*
4029865 AGGTGGGCATGACAGTGGTTGTGGAAAGGA
1 AGGTGGGCATGGCAGTGGTTGTGGAAAGGA
4029895 AGGTGGGCATGGCAGTGG-TGATGGAAAGGA
1 AGGTGGGCATGGCAGTGGTTG-TGGAAAGGA
* *
4029925 AGGTAGGCATGGTAGTGG
1 AGGTGGGCATGGCAGTGG
4029943 GAAGGGCAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 2 0.05
30 42 0.95
ACGTcount: A:0.26, C:0.06, G:0.49, T:0.19
Consensus pattern (30 bp):
AGGTGGGCATGGCAGTGGTTGTGGAAAGGA
Found at i:4030079 original size:30 final size:30
Alignment explanation
Indices: 4030014--4030081 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
4030004 AAGGGTGATA
* * *
4030014 GTTTTGGTGGCAGCGGTGGTTTTGACGGAT
1 GTTTTGGTGGCAGCGGTGGCTTTCACAGAT
* *
4030044 TTTTTGGTGGCCGCGGTGGCTTTCACAG-T
1 GTTTTGGTGGCAGCGGTGGCTTTCACAGAT
4030073 GGTTTTGGT
1 -GTTTTGGT
4030082 AAGGGCGACA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.07, C:0.13, G:0.40, T:0.40
Consensus pattern (30 bp):
GTTTTGGTGGCAGCGGTGGCTTTCACAGAT
Found at i:4033627 original size:51 final size:51
Alignment explanation
Indices: 4033541--4033713 Score: 310
Period size: 51 Copynumber: 3.4 Consensus size: 51
4033531 GTTTCTGTGG
* *
4033541 TGGGCATGGCAAGGGTGATGGTGAATATGGTAGTAGGAATGGCAAGGGTGA
1 TGGGCATGGAAAGGGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGA
*
4033592 TGGGTATGGAAAGGGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGA
1 TGGGCATGGAAAGGGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGA
*
4033643 TGGGCATGGAAAGGGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGG
1 TGGGCATGGAAAGGGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGA
4033694 TGGGCATGGAAAGGGTGATG
1 TGGGCATGGAAAGGGTGATG
4033714 GGGATGGAAA
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 117 1.00
ACGTcount: A:0.29, C:0.04, G:0.45, T:0.22
Consensus pattern (51 bp):
TGGGCATGGAAAGGGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGA
Found at i:4033708 original size:69 final size:69
Alignment explanation
Indices: 4033630--4033783 Score: 263
Period size: 69 Copynumber: 2.2 Consensus size: 69
4033620 GGTAGTAGGA
* * *
4033630 ATGGCAAGGGTGATGGGCATGGAAAGGGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGGT
1 ATGGAAAGGGTGATGGGCATGGAAAGAGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGAT
4033695 GGGC
66 GGGC
* *
4033699 ATGGAAAGGGTGATGGGGATGGAAAGAGTGATGGTGAATATGGTAGTAGGAATGGCAAGGGTGAT
1 ATGGAAAGGGTGATGGGCATGGAAAGAGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGAT
4033764 GGGC
66 GGGC
4033768 ATGGAAAGGGTGATGG
1 ATGGAAAGGGTGATGG
4033784 TGAATATGGT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 80 1.00
ACGTcount: A:0.29, C:0.04, G:0.47, T:0.20
Consensus pattern (69 bp):
ATGGAAAGGGTGATGGGCATGGAAAGAGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGAT
GGGC
Found at i:4033756 original size:171 final size:171
Alignment explanation
Indices: 4033541--4033885 Score: 609
Period size: 171 Copynumber: 2.0 Consensus size: 171
4033531 GTTTCTGTGG
* * *
4033541 TGGGCATGGCAAGGGTGATGGTGAATATGGTAGTAGGAATGGCAAGGGTGATGGGTATGGAAAGG
1 TGGGCATGGAAAGAGTGATGGTGAATATGGTAGTAGGAATGGCAAGGGTGATGGGCATGGAAAGG
4033606 GTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGATGGGCATGGAAAGGGTGATGATGAATAT
66 GTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGATGGGCATGGAAAGGGTGATGATGAATAT
*
4033671 GGTAGTAGGAATGGCAAGGGTGGTGGGCATGGAAAGGGTGA
131 GGTAGTAGGAATGGCAAGGGTGATGGGCATGGAAAGGGTGA
*
4033712 TGGGGATGGAAAGAGTGATGGTGAATATGGTAGTAGGAATGGCAAGGGTGATGGGCATGGAAAGG
1 TGGGCATGGAAAGAGTGATGGTGAATATGGTAGTAGGAATGGCAAGGGTGATGGGCATGGAAAGG
* * *
4033777 GTGATGGTGAATATGGTAGTGGGAATGGCAAGGGTGATGGGCATGGAAAGGGTGATGGTGAATAT
66 GTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGATGGGCATGGAAAGGGTGATGATGAATAT
*
4033842 GGTAGTGGGAATGGCAAGGGTGATGGGCATGGAAAGGGTGA
131 GGTAGTAGGAATGGCAAGGGTGATGGGCATGGAAAGGGTGA
4033883 TGG
1 TGG
4033886 TGAATATGGT
Statistics
Matches: 165, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
171 165 1.00
ACGTcount: A:0.29, C:0.04, G:0.46, T:0.21
Consensus pattern (171 bp):
TGGGCATGGAAAGAGTGATGGTGAATATGGTAGTAGGAATGGCAAGGGTGATGGGCATGGAAAGG
GTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGATGGGCATGGAAAGGGTGATGATGAATAT
GGTAGTAGGAATGGCAAGGGTGATGGGCATGGAAAGGGTGA
Found at i:4033759 original size:51 final size:51
Alignment explanation
Indices: 4033699--4033924 Score: 398
Period size: 51 Copynumber: 4.4 Consensus size: 51
4033689 GGTGGTGGGC
* * *
4033699 ATGGAAAGGGTGATGGGGATGGAAAGAGTGATGGTGAATATGGTAGTAGGA
1 ATGGCAAGGGTGATGGGCATGGAAAGGGTGATGGTGAATATGGTAGTAGGA
*
4033750 ATGGCAAGGGTGATGGGCATGGAAAGGGTGATGGTGAATATGGTAGTGGGA
1 ATGGCAAGGGTGATGGGCATGGAAAGGGTGATGGTGAATATGGTAGTAGGA
*
4033801 ATGGCAAGGGTGATGGGCATGGAAAGGGTGATGGTGAATATGGTAGTGGGA
1 ATGGCAAGGGTGATGGGCATGGAAAGGGTGATGGTGAATATGGTAGTAGGA
4033852 ATGGCAAGGGTGATGGGCATGGAAAGGGTGATGGTGAATATGGTAGTAGGA
1 ATGGCAAGGGTGATGGGCATGGAAAGGGTGATGGTGAATATGGTAGTAGGA
*
4033903 ATGGCAAGGGTGGTGGGCATGG
1 ATGGCAAGGGTGATGGGCATGG
4033925 GGATGAATTT
Statistics
Matches: 169, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 169 1.00
ACGTcount: A:0.28, C:0.04, G:0.47, T:0.21
Consensus pattern (51 bp):
ATGGCAAGGGTGATGGGCATGGAAAGGGTGATGGTGAATATGGTAGTAGGA
Found at i:4033759 original size:102 final size:102
Alignment explanation
Indices: 4033540--4033866 Score: 282
Period size: 102 Copynumber: 3.2 Consensus size: 102
4033530 AGTTTCTGTG
* * * *
4033540 GTGGGCATGGCAAGGGTGATGGTGAATATGGTAGTAGGAATGGCAAGGGTGATGGGTATGGAAAG
1 GTGGGAATGGCAAGGGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGGTGGGAATGGAAAG
** * * *
4033605 GGTGATGATGAATATGG-TAGTAG-GAAT-G-GCA-AGGGT-
66 GGTGATG--G-GCATGGAAAG-AGTG-ATGGTGAATATGGTA
* * *
4033641 GATGGGCATGGAAAGGGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGGTGGGCATGGAAA
1 G-TGGGAATGGCAAGGGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGGTGGGAATGGAAA
*
4033706 GGGTGATGGGGATGGAAAGAGTGATGGTGAATATGGTA
65 GGGTGATGGGCATGGAAAGAGTGATGGTGAATATGGTA
* * * * *
4033744 GTAGGAATGGCAAGGGTGATGGGCATGGAA-AGGGT-G-ATGG--T-GAATATGGTAGTGGGAAT
1 GTGGGAATGGCAAGGGTGAT--G-AT-GAATATGGTAGTA-GGAATGGCA-AGGGTGGTGGGAAT
* *
4033803 GGCAAGGGTGATGGGCATGGAAAGGGTGATGGTGAATATGGTA
60 GGAAAGGGTGATGGGCATGGAAAGAGTGATGGTGAATATGGTA
4033846 GTGGGAATGGCAAGGGTGATG
1 GTGGGAATGGCAAGGGTGATG
4033867 GGCATGGAAA
Statistics
Matches: 192, Mismatches: 21, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
99 8 0.04
100 6 0.03
101 5 0.03
102 158 0.82
103 2 0.01
104 4 0.02
105 6 0.03
106 3 0.02
ACGTcount: A:0.29, C:0.04, G:0.46, T:0.22
Consensus pattern (102 bp):
GTGGGAATGGCAAGGGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGGTGGGAATGGAAAG
GGTGATGGGCATGGAAAGAGTGATGGTGAATATGGTA
Found at i:4033802 original size:120 final size:120
Alignment explanation
Indices: 4033579--4033834 Score: 449
Period size: 120 Copynumber: 2.1 Consensus size: 120
4033569 GGTAGTAGGA
* * *
4033579 ATGGCAAGGGTGATGGGTATGGAAAGGGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGAT
1 ATGGAAAGGGTGATGGGGATGGAAAGAGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGAT
*
4033644 GGGCATGGAAAGGGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGGTGGGC
66 GGGCATGGAAAGGGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGATGGGC
*
4033699 ATGGAAAGGGTGATGGGGATGGAAAGAGTGATGGTGAATATGGTAGTAGGAATGGCAAGGGTGAT
1 ATGGAAAGGGTGATGGGGATGGAAAGAGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGAT
* *
4033764 GGGCATGGAAAGGGTGATGGTGAATATGGTAGTGGGAATGGCAAGGGTGATGGGC
66 GGGCATGGAAAGGGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGATGGGC
4033819 ATGGAAAGGGTGATGG
1 ATGGAAAGGGTGATGG
4033835 TGAATATGGT
Statistics
Matches: 129, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 129 1.00
ACGTcount: A:0.29, C:0.04, G:0.46, T:0.21
Consensus pattern (120 bp):
ATGGAAAGGGTGATGGGGATGGAAAGAGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGAT
GGGCATGGAAAGGGTGATGATGAATATGGTAGTAGGAATGGCAAGGGTGATGGGC
Found at i:4036698 original size:26 final size:26
Alignment explanation
Indices: 4036669--4036721 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
4036659 TATCAATAAA
*
4036669 AATGTGCTCTCTTTTATTCT-TTTATT
1 AATGT-CTCTCTTTAATTCTCTTTATT
* *
4036695 AATGTTTTTCTTTAATTCTCTTTATT
1 AATGTCTCTCTTTAATTCTCTTTATT
4036721 A
1 A
4036722 CTTATTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.62
Consensus pattern (26 bp):
AATGTCTCTCTTTAATTCTCTTTATT
Found at i:4036828 original size:35 final size:36
Alignment explanation
Indices: 4036756--4036849 Score: 95
Period size: 35 Copynumber: 2.6 Consensus size: 36
4036746 ATGATACTCG
*
4036756 TTTTTCAT-AATTCCCTTCTAAAATTTTTCCAG-CTT
1 TTTTTC-TCAATTCCCTTTTAAAATTTTTCCAGTCTT
* * *
4036791 TTTTTCTCATTTCCCTTTTAAAATTTATT-TAGTTTT
1 TTTTTCTCAATTCCCTTTTAAAATTT-TTCCAGTCTT
**
4036827 TTTTTCTCAACCCCCTTTTAAAA
1 TTTTTCTCAATTCCCTTTTAAAA
4036850 ACACTTTTCT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
34 1 0.02
35 24 0.49
36 24 0.49
ACGTcount: A:0.22, C:0.21, G:0.02, T:0.54
Consensus pattern (36 bp):
TTTTTCTCAATTCCCTTTTAAAATTTTTCCAGTCTT
Found at i:4040939 original size:30 final size:30
Alignment explanation
Indices: 4040903--4041077 Score: 156
Period size: 30 Copynumber: 5.6 Consensus size: 30
4040893 TAGTTTCTGT
4040903 GGTGGGCATGGAAAGGGTGGAGAAGATGAA
1 GGTGGGCATGGAAAGGGTGGAGAAGATGAA
4040933 GGTGGGCATGGAAAGGGTGGAGAAGATGAA
1 GGTGGGCATGGAAAGGGTGGAGAAGATGAA
* * *
4040963 GGTGGTCATGGAAAGGGT-GATGATCTATATGGTA
1 GGTGGGCATGGAAAGGGTGGA-GA---AGAT-GAA
* * * * * * *
4040997 -GTAGGAATGGCAAGGGTGGTGGTGGAGCTAAA
1 GGTGGGCATGG-AA-AG-GGTGGAGAAGATGAA
*
4041029 GGTGGGCATGGAAAGGGTGGTGAAGATGAA
1 GGTGGGCATGGAAAGGGTGGAGAAGATGAA
*
4041059 GGTGGGCATGGCAAGGGTG
1 GGTGGGCATGGAAAGGGTG
4041078 ATGATGAATA
Statistics
Matches: 115, Mismatches: 20, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
29 2 0.02
30 79 0.69
31 1 0.01
32 3 0.03
33 20 0.17
34 4 0.03
35 1 0.01
36 4 0.03
37 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.48, T:0.18
Consensus pattern (30 bp):
GGTGGGCATGGAAAGGGTGGAGAAGATGAA
Found at i:4041033 original size:96 final size:96
Alignment explanation
Indices: 4040931--4041114 Score: 314
Period size: 96 Copynumber: 1.9 Consensus size: 96
4040921 GGAGAAGATG
* *
4040931 AAGGTGGGCATGGAAAGGGTGGAGAAGATGAAGGTGGTCATGGAAAGGGTGATGATCTATATGGT
1 AAGGTGGGCATGGAAAGGGTGGAGAAGATGAAGGTGGGCATGGAAAGGGTGATGATCAATATGGT
4040996 AGTAGGAATGGCAAGGGTGGTGGTGGAGCTA
66 AGTAGGAATGGCAAGGGTGGTGGTGGAGCTA
* * *
4041027 AAGGTGGGCATGGAAAGGGTGGTGAAGATGAAGGTGGGCATGGCAAGGGTGATGATGAATATGGT
1 AAGGTGGGCATGGAAAGGGTGGAGAAGATGAAGGTGGGCATGGAAAGGGTGATGATCAATATGGT
*
4041092 AGTAGGAATTGCAAGGGTGGTGG
66 AGTAGGAATGGCAAGGGTGGTGG
4041115 GCATGGAGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 82 1.00
ACGTcount: A:0.29, C:0.05, G:0.46, T:0.21
Consensus pattern (96 bp):
AAGGTGGGCATGGAAAGGGTGGAGAAGATGAAGGTGGGCATGGAAAGGGTGATGATCAATATGGT
AGTAGGAATGGCAAGGGTGGTGGTGGAGCTA
Found at i:4041928 original size:27 final size:27
Alignment explanation
Indices: 4041889--4041943 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
4041879 TTAACTGAAA
*
4041889 ACTACGGTAGTTTATC-CACTATTTTT
1 ACTACGGCAGTTTATCTCACTATTTTT
*
4041915 ACTACTGGCAGTTTATCTCTCTATTTTT
1 ACTAC-GGCAGTTTATCTCACTATTTTT
4041943 A
1 A
4041944 TTTTCAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.20
27 10 0.40
28 10 0.40
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (27 bp):
ACTACGGCAGTTTATCTCACTATTTTT
Found at i:4044687 original size:28 final size:27
Alignment explanation
Indices: 4044656--4044717 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
4044646 AAAACGGGAC
*
4044656 TTTTGGA-TACCCGGGGGCAAAATGGTAA
1 TTTTGGACT-CCCGAGGGCAAAATGG-AA
*
4044684 TTTTGGACTCTCGAGGGCAAAATGGAA
1 TTTTGGACTCCCGAGGGCAAAATGGAA
4044711 TTTTGGA
1 TTTTGGA
4044718 AAGTTCGGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 9 0.29
28 21 0.68
29 1 0.03
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (27 bp):
TTTTGGACTCCCGAGGGCAAAATGGAA
Found at i:4044758 original size:29 final size:29
Alignment explanation
Indices: 4044726--4044976 Score: 136
Period size: 28 Copynumber: 8.7 Consensus size: 29
4044716 GAAAGTTCGG
*
4044726 GGGTAAAGTGGTAATTTTTGGTGAAATTA
1 GGGTAAAATGGTAATTTTTGGTGAAATTA
4044755 GGGTTAAAATGG-AA-TTTT-G-GAAAGTTCGA
1 GGG-TAAAATGGTAATTTTTGGTGAAA-TT--A
*
4044784 GGGTAAAATGGTAATTTTTGGTGAAATCA
1 GGGTAAAATGGTAATTTTTGGTGAAATTA
* *
4044813 GGGTTAAAAATTG-AA-TTTT-G-AAAAGTTTA
1 GGG-T-AAAATGGTAATTTTTGGTGAAA--TTA
* * *
4044842 GGGGTAAAATAGTAA-TTTTGATGAAATCGA
1 -GGGTAAAATGGTAATTTTTGGTGAAAT-TA
* * ** *
4044872 GGTTAAAATGG-AA-TTTTGGAGAGTTTGG
1 GGGTAAAATGGTAATTTTTGGTGAAATT-A
4044900 GGGTAAAATGGTAATTTTTGGTGAAATTA
1 GGGTAAAATGGTAATTTTTGGTGAAATTA
* *
4044929 GAGTTAAAATGG-AA-TTTT-G-GAAAGTTTGG
1 G-GGTAAAATGGTAATTTTTGGTGAAA--TT-A
4044958 GGGTAAAATGGTAATTTTT
1 GGGTAAAATGGTAATTTTT
4044977 AGAAGTTTCG
Statistics
Matches: 171, Mismatches: 25, Indels: 51
0.69 0.10 0.21
Matches are distributed among these distances:
26 8 0.05
27 7 0.04
28 54 0.32
29 46 0.27
30 41 0.24
31 11 0.06
32 4 0.02
ACGTcount: A:0.35, C:0.01, G:0.29, T:0.35
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTTGGTGAAATTA
Found at i:4044775 original size:58 final size:58
Alignment explanation
Indices: 4044702--4044976 Score: 401
Period size: 58 Copynumber: 4.7 Consensus size: 58
4044692 TCTCGAGGGC
* *
4044702 AAAATGGAATTTTGGAAAGTTCGGGGGTAAAGTGGTAATTTTTGGTGAAATTAGGGTT
1 AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTT
* * *
4044760 AAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTT
1 AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTT
* * * * * *
4044818 AAAAATTGAATTTTGAAAAGTTTAGGGGTAAAATAGTAA-TTTTGATGAAA-TCGAGGTT
1 -AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATTAG-GGTT
* *
4044876 AAAATGGAATTTTGGAGAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATTAGAGTT
1 AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTT
4044934 AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTT
1 AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTT
4044977 AGAAGTTTCG
Statistics
Matches: 192, Mismatches: 21, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
57 34 0.18
58 124 0.65
59 34 0.18
ACGTcount: A:0.35, C:0.01, G:0.29, T:0.35
Consensus pattern (58 bp):
AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTT
Found at i:4045003 original size:58 final size:57
Alignment explanation
Indices: 4044668--4045035 Score: 347
Period size: 58 Copynumber: 6.4 Consensus size: 57
4044658 TTGGATACCC
* * ** *
4044668 GGGGGCAAAATGGTAA-TTTTG-GACTCTCGAGGGCAAAATGGAATTTTGGAAAGTTC
1 GGGGGTAAAATGGTAATTTTTGTGAAT-TCGAGGTTAAAATGGAATTTTGGAAAGTTT
* * *
4044724 GGGGGTAAAGTGGTAATTTTTGGTGAAATTAG-GGTTAAAATGGAATTTTGGAAAGTTC
1 GGGGGTAAAATGGTAATTTTT-GTG-AATTCGAGGTTAAAATGGAATTTTGGAAAGTTT
* * * *
4044782 GAGGGTAAAATGGTAATTTTTGGTGAAATC-AGGGTTAAAAATTGAATTTTGAAAAGTTT
1 GGGGGTAAAATGGTAATTTTT-GTGAATTCGA-GGTT-AAAATGGAATTTTGGAAAGTTT
* * * *
4044841 AGGGGTAAAATAGTAA-TTTTGATGAAATCGAGGTTAAAATGGAATTTTGGAGAGTTT
1 GGGGGTAAAATGGTAATTTTTG-TGAATTCGAGGTTAAAATGGAATTTTGGAAAGTTT
*
4044898 GGGGGTAAAATGGTAATTTTTGGTGAAATTAGA-GTTAAAATGGAATTTTGGAAAGTTT
1 GGGGGTAAAATGGTAATTTTT-GTG-AATTCGAGGTTAAAATGGAATTTTGGAAAGTTT
* * * ***
4044956 GGGGGTAAAATGGTAATTTTT-AGAAGTTTCGAGGTTAGAATGTAATTTCCTAAAGTTT
1 GGGGGTAAAATGGTAATTTTTGTGAA--TTCGAGGTTAAAATGGAATTTTGGAAAGTTT
* *
4045014 TGGGGTCAAAAT-GCAATTTTTG
1 GGGGGT-AAAATGGTAATTTTTG
4045036 AACCATTTGG
Statistics
Matches: 262, Mismatches: 33, Indels: 31
0.80 0.10 0.10
Matches are distributed among these distances:
55 2 0.01
56 15 0.06
57 45 0.17
58 151 0.58
59 47 0.18
60 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (57 bp):
GGGGGTAAAATGGTAATTTTTGTGAATTCGAGGTTAAAATGGAATTTTGGAAAGTTT
Found at i:4045013 original size:116 final size:115
Alignment explanation
Indices: 4044702--4045035 Score: 386
Period size: 116 Copynumber: 2.9 Consensus size: 115
4044692 TCTCGAGGGC
* * * *
4044702 AAAATGGAATTTTGGAAAGTTCGGGGGTAAAGTGGTAATTTTTGGTGAAATTAG-GGTTAAAATG
1 AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTT--AG-AATTCGAGGTTAAAATG
* * *
4044766 GAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTA
63 GAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATCAGAGTTA
* * * * * *
4044819 AAAATTGAATTTTGAAAAGTTTAGGGGTAAAATAGTAATTTTGATGAAATCGAGGTTAAAATGGA
1 AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTA-GAATTCGAGGTTAAAATGGA
* *
4044884 ATTTTGGAGAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATTAGAGTT-
65 ATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATCAGAGTTA
* *
4044934 AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGTTTCGAGGTTAGAATGT
1 AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTAGAA--TTCGAGGTTAAAATGG
*** * *
4044999 AATTTCCTAAAGTTTTGGGGTCAAAAT-GCAATTTTTG
64 AATTTTGGAAAGTTTGGGGGT-AAAATGGTAATTTTTG
4045036 AACCATTTGG
Statistics
Matches: 183, Mismatches: 29, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
114 3 0.02
115 43 0.23
116 96 0.52
117 41 0.22
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (115 bp):
AAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTAGAATTCGAGGTTAAAATGGAA
TTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATCAGAGTTA
Found at i:4045026 original size:29 final size:27
Alignment explanation
Indices: 4044949--4045032 Score: 69
Period size: 29 Copynumber: 2.9 Consensus size: 27
4044939 GGAATTTTGG
* *
4044949 AAAGTTTGGGGGTAAAATGGTAATTTTT
1 AAAGTTTCGGGGTAAAAT-GTAATTTCT
* *
4044977 AGAAGTTTCGAGGTTAGAATGTAATTTCCT
1 A-AAGTTTCG-GGGTAAAATGTAATTT-CT
* *
4045007 AAAGTTTTGGGGTCAAAATGCAATTT
1 AAAGTTTCGGGGT-AAAATGTAATTT
4045033 TTGAACCATT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
28 4 0.09
29 31 0.70
30 9 0.20
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (27 bp):
AAAGTTTCGGGGTAAAATGTAATTTCT
Found at i:4046110 original size:25 final size:25
Alignment explanation
Indices: 4046060--4046110 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
4046050 ATAATTATTA
*
4046060 ATTAATAATTTCATTAATCACCATT
1 ATTAATAATTTCATTAATCACAATT
4046085 ATTAATAATTTCATTAAT-ACTAATT
1 ATTAATAATTTCATTAATCAC-AATT
4046110 A
1 A
4046111 AAATCATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTAATAATTTCATTAATCACAATT
Found at i:4046940 original size:6 final size:6
Alignment explanation
Indices: 4046931--4047024 Score: 63
Period size: 6 Copynumber: 15.8 Consensus size: 6
4046921 TTGAATTTGA
* * *
4046931 TTAAAT TTAAAT CTAAA- ATAAAT TTAAAT AAGTAAAT TTAAAT TTAAGA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAA-AT
** *
4046980 -TAAAT TTAAAT TTAAA- ACAAAT TTAAAA TT-AAT TTAAACT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAA
4047025 AGCCCAAACC
Statistics
Matches: 68, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
4 1 0.01
5 14 0.21
6 41 0.60
7 7 0.10
8 5 0.07
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:4046952 original size:17 final size:17
Alignment explanation
Indices: 4046932--4047011 Score: 94
Period size: 17 Copynumber: 4.9 Consensus size: 17
4046922 TGAATTTGAT
*
4046932 TAAATTTAAATCTAAAA
1 TAAATTTAAATTTAAAA
*
4046949 TAAATTTAAA--T-AAG
1 TAAATTTAAATTTAAAA
*
4046963 TAAATTTAAATTTAAGA
1 TAAATTTAAATTTAAAA
4046980 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
4046997 CAAATTTAAAATTAA
1 TAAATTTAAATTTAA
4047012 TTTAAACTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
14 12 0.22
15 1 0.02
16 1 0.02
17 40 0.74
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:4046958 original size:11 final size:11
Alignment explanation
Indices: 4046938--4047017 Score: 52
Period size: 11 Copynumber: 6.9 Consensus size: 11
4046928 TGATTAAATT
*
4046938 TAAATCTAAAA
1 TAAATTTAAAA
4046949 TAAATTTAAATAA
1 TAAATTT-AA-AA
*
4046962 GTAAATTTAAAT
1 -TAAATTTAAAA
* ** *
4046974 TTAAGATAAATT
1 TAAATTTAAA-A
4046986 TAAATTTAAAA
1 TAAATTTAAAA
*
4046997 CAAATTTAAAA
1 TAAATTTAAAA
*
4047008 TTAATTTAAA
1 TAAATTTAAA
4047018 CTTTAAAAGC
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
11 31 0.58
12 11 0.21
13 4 0.08
14 7 0.13
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:4046967 original size:31 final size:31
Alignment explanation
Indices: 4046932--4046990 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
4046922 TGAATTTGAT
4046932 TAAATTTAAATCTAAAATAAATTTAAATAAG
1 TAAATTTAAATCTAAAATAAATTTAAATAAG
* *
4046963 TAAATTTAAATTTAAGATAAATTTAAAT
1 TAAATTTAAATCTAAAATAAATTTAAAT
4046991 TTAAAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (31 bp):
TAAATTTAAATCTAAAATAAATTTAAATAAG
Found at i:4047013 original size:28 final size:29
Alignment explanation
Indices: 4046970--4047025 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
4046960 AAGTAAATTT
*
4046970 AAATTTAAGATAAATTTAAA-TTTAAAAC
1 AAATTTAAAATAAATTTAAACTTTAAAAC
*
4046998 AAATTTAAAATTAATTTAAACTTTAAAA
1 AAATTTAAAATAAATTTAAACTTTAAAA
4047026 GCCCAAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (29 bp):
AAATTTAAAATAAATTTAAACTTTAAAAC
Found at i:4047724 original size:6 final size:6
Alignment explanation
Indices: 4047713--4047743 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
4047703 AAGTATTCGG
4047713 CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA C
1 CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA C
4047744 TTGAATCCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCAAA
Found at i:4047834 original size:21 final size:21
Alignment explanation
Indices: 4047808--4047853 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
4047798 AAAAAGCCAA
* *
4047808 GTTTAAGGTTTAATATTTAAG
1 GTTTAAGATTCAATATTTAAG
*
4047829 GTTTAAGATTCAATTTTTAAG
1 GTTTAAGATTCAATATTTAAG
4047850 GTTT
1 GTTT
4047854 GGAGTTTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.50
Consensus pattern (21 bp):
GTTTAAGATTCAATATTTAAG
Found at i:4049171 original size:30 final size:30
Alignment explanation
Indices: 4049137--4049196 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
4049127 GTGGTGGTGC
* *
4049137 TGGTGGAGGGTTTGGTAAAGGTGGTGGATA
1 TGGTGGAGGGATTGGCAAAGGTGGTGGATA
* *
4049167 TGGTGGTGGGATTGGCAAGGGTGGTGGATA
1 TGGTGGAGGGATTGGCAAAGGTGGTGGATA
4049197 CGGAGGTGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.18, C:0.02, G:0.52, T:0.28
Consensus pattern (30 bp):
TGGTGGAGGGATTGGCAAAGGTGGTGGATA
Found at i:4049205 original size:30 final size:30
Alignment explanation
Indices: 4049156--4049253 Score: 124
Period size: 30 Copynumber: 3.3 Consensus size: 30
4049146 GTTTGGTAAA
* * * * *
4049156 GGTGGTGGATATGGTGGTGGGATTGGCAAG
1 GGTGGTGGATACGGAGGTGGAATAGGAAAG
4049186 GGTGGTGGATACGGAGGTGGAATAGGAAAG
1 GGTGGTGGATACGGAGGTGGAATAGGAAAG
* * *
4049216 GGTGGAGGATACGGAGGTGGCATAGGAAAA
1 GGTGGTGGATACGGAGGTGGAATAGGAAAG
4049246 GGTGGTGG
1 GGTGGTGG
4049254 GATTGGCAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.24, C:0.04, G:0.52, T:0.19
Consensus pattern (30 bp):
GGTGGTGGATACGGAGGTGGAATAGGAAAG
Found at i:4049250 original size:78 final size:78
Alignment explanation
Indices: 4049168--4049379 Score: 309
Period size: 78 Copynumber: 2.7 Consensus size: 78
4049158 TGGTGGATAT
* * *
4049168 GGTGGTGGGATTGGCAAGGGTGGTGGATACGGAGGTGGAATAGGAAAGGGTGGAGGATACGGAGG
1 GGTGGTGGGATTGGCAAAGGAGGAGGATACGGAGGTGGAATAGGAAAGGGTGGAGGATACGGAGG
4049233 TGGCATAGGAAAA
66 TGGCATAGGAAAA
* * *
4049246 GGTGGTGGGATTGGCAAAGGAGGAGG-TGCTGGTGGTGGAATCGGAAAGGGTGGAGGATACGGAG
1 GGTGGTGGGATTGGCAAAGGAGGAGGATAC-GGAGGTGGAATAGGAAAGGGTGGAGGATACGGAG
* *
4049310 GTGGCATCGGAAAG
65 GTGGCATAGGAAAA
* * *
4049324 GGTGGTGGGATTGGCAAAGGAGGAGGATACGGAGGTGGAATTGGTAAGGGAGGAGG
1 GGTGGTGGGATTGGCAAAGGAGGAGGATACGGAGGTGGAATAGGAAAGGGTGGAGG
4049380 CCATGGAATT
Statistics
Matches: 119, Mismatches: 13, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
77 2 0.02
78 115 0.97
79 2 0.02
ACGTcount: A:0.26, C:0.06, G:0.51, T:0.17
Consensus pattern (78 bp):
GGTGGTGGGATTGGCAAAGGAGGAGGATACGGAGGTGGAATAGGAAAGGGTGGAGGATACGGAGG
TGGCATAGGAAAA
Found at i:4049477 original size:24 final size:24
Alignment explanation
Indices: 4049447--4049517 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
4049437 TGGATATGGC
4049447 AAGGGTGGTGGTTTTGGAGGTGGAG
1 AAGGGTGGTGGTTTTGGAGGTGG-G
* ***
4049472 TA-GGTGGTGGAGCTGGAGGTGGG
1 AAGGGTGGTGGTTTTGGAGGTGGG
* *
4049495 AAGGGCGGAGGTTTTGGAGGTGG
1 AAGGGTGGTGGTTTTGGAGGTGG
4049518 TGGGGGTGGC
Statistics
Matches: 35, Mismatches: 10, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
23 2 0.06
24 32 0.91
25 1 0.03
ACGTcount: A:0.15, C:0.03, G:0.58, T:0.24
Consensus pattern (24 bp):
AAGGGTGGTGGTTTTGGAGGTGGG
Found at i:4049481 original size:42 final size:42
Alignment explanation
Indices: 4049390--4049482 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 42
4049380 CCATGGAATT
* * *
4049390 GGTGGTGGAATTGGAAAGGGTGGTGGATTTGGCGGCGGTGCC
1 GGTGGTGGAATTGGAAAGGGTGGTGGATTTGGAGGCGGAGCA
* * * * *
4049432 GGAGGTGG-ATATGGCAAGGGTGGTGGTTTTGGAGGTGGAGTA
1 GGTGGTGGAAT-TGGAAAGGGTGGTGGATTTGGAGGCGGAGCA
4049474 GGTGGTGGA
1 GGTGGTGGA
4049483 GCTGGAGGTG
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.05
42 38 0.95
ACGTcount: A:0.16, C:0.05, G:0.54, T:0.25
Consensus pattern (42 bp):
GGTGGTGGAATTGGAAAGGGTGGTGGATTTGGAGGCGGAGCA
Found at i:4051107 original size:25 final size:24
Alignment explanation
Indices: 4051065--4051122 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
4051055 TCTTTTTAAA
*
4051065 AATAAAAATTTTACATTTAAAATT
1 AATAAAAATTTTAAATTTAAAATT
** *
4051089 TTTAAAAATTTTAAAATTTTAAATT
1 AATAAAAATTTT-AAATTTAAAATT
4051114 AATAAAAAT
1 AATAAAAAT
4051123 AAATTTATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
AATAAAAATTTTAAATTTAAAATT
Found at i:4053042 original size:1 final size:1
Alignment explanation
Indices: 4053036--4053060 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
4053026 TATTGAACAT
4053036 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
4053061 GGGCTATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4053756 original size:32 final size:34
Alignment explanation
Indices: 4053699--4053763 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
4053689 GACAAAAAAA
4053699 ATACTAAATTAAGAAAAAAGGGTCAAATTTATAG
1 ATACTAAATTAAGAAAAAAGGGTCAAATTTATAG
*
4053733 ATACTAAATTAA-AAAAAA-TGTCAAATTTATA
1 ATACTAAATTAAGAAAAAAGGGTCAAATTTATA
4053764 TATCAAAGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 12 0.40
33 6 0.20
34 12 0.40
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.29
Consensus pattern (34 bp):
ATACTAAATTAAGAAAAAAGGGTCAAATTTATAG
Found at i:4053780 original size:32 final size:33
Alignment explanation
Indices: 4053699--4053781 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 33
4053689 GACAAAAAAA
* *
4053699 ATACTAAATTAAGAAAAAAGGGTCAAATTTATAG
1 ATACTAAA-TGAGAAAAAAAGGTCAAATTTATAG
* * *
4053733 ATACTAAATTA-AAAAAAATGTCAAATTTATAT
1 ATACTAAATGAGAAAAAAAGGTCAAATTTATAG
4053765 AT-C-AAAGTGAGAAAAAA
1 ATACTAAA-TGAGAAAAAA
4053782 TTTAAATACT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
30 3 0.07
31 3 0.07
32 26 0.62
33 2 0.05
34 8 0.19
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.27
Consensus pattern (33 bp):
ATACTAAATGAGAAAAAAAGGTCAAATTTATAG
Found at i:4068116 original size:30 final size:29
Alignment explanation
Indices: 4068080--4068139 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
4068070 CTTTTTTACC
4068080 TGGTATAA-AAATAATAATTAATTATGAAAA
1 TGGTATAAGAAA-AA-AATTAATTATGAAAA
* *
4068110 TGGTATAAGAAACAGATTAATTATGAAAA
1 TGGTATAAGAAAAAAATTAATTATGAAAA
4068139 T
1 T
4068140 AAGTATTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 15 0.56
30 9 0.33
31 3 0.11
ACGTcount: A:0.53, C:0.02, G:0.13, T:0.32
Consensus pattern (29 bp):
TGGTATAAGAAAAAAATTAATTATGAAAA
Found at i:4077086 original size:11 final size:11
Alignment explanation
Indices: 4077070--4077100 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
4077060 CACGAATAAG
4077070 CTCGTTTATGA
1 CTCGTTTATGA
4077081 CTCGTTTATGA
1 CTCGTTTATGA
4077092 CTCGTTTAT
1 CTCGTTTAT
4077101 TTATTAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (11 bp):
CTCGTTTATGA
Found at i:4087660 original size:3 final size:3
Alignment explanation
Indices: 4087652--4087681 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4087642 AGCTTAGTTG
4087652 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4087682 TTTATAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4094371 original size:79 final size:78
Alignment explanation
Indices: 4094271--4094428 Score: 271
Period size: 79 Copynumber: 2.0 Consensus size: 78
4094261 GTTTGAGCTA
4094271 GAAGAGAATGAATGTGATAATGAAAATGACCGGAGAGAAGAGGATCCTCGTGCCCTCATGCACCC
1 GAAGAGAATGAATGTGATAATGAAAATGACCGGAGAGAAGAGGATCCTCGTGCCCTCATGCACCC
*
4094336 AAGCTTATATGGTG
66 -AGCTTATATAGTG
* * *
4094350 GAAGGGAATGAATGTGATAATGGAAATGACTGGAGAGAAGAGGATCCTCGTGCCCTCATGCACCC
1 GAAGAGAATGAATGTGATAATGAAAATGACCGGAGAGAAGAGGATCCTCGTGCCCTCATGCACCC
4094415 AGCTTATATAGTG
66 AGCTTATATAGTG
4094428 G
1 G
4094429 GTCGCTCATT
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
78 13 0.17
79 62 0.83
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (78 bp):
GAAGAGAATGAATGTGATAATGAAAATGACCGGAGAGAAGAGGATCCTCGTGCCCTCATGCACCC
AGCTTATATAGTG
Found at i:4106354 original size:43 final size:43
Alignment explanation
Indices: 4106271--4106355 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
4106261 ATTAACATGT
* * *
4106271 TAAATTATATTACTTGACTCGTGTTAATATGGTTGTATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
*
4106314 TAAATTATATTACTTGACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
4106356 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:4107016 original size:6 final size:6
Alignment explanation
Indices: 4107007--4107111 Score: 69
Period size: 6 Copynumber: 18.0 Consensus size: 6
4106997 TAATATTATT
* * *
4107007 TTTAAA TTT-AA -TCAAA TTTAAA TTTAAA -GTAAA TTTAAA TAAATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
* * * *
4107054 TTTAAA TTTAAGA --TAAA TTTAAA TCTAAA -TAAAA TTTAAA ATTAAT
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
4107100 TTTAAA CTTAAA
1 TTTAAA TTTAAA
4107112 AATCAAAGTC
Statistics
Matches: 75, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
4 2 0.03
5 14 0.19
6 53 0.71
7 1 0.01
8 5 0.07
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:4107042 original size:17 final size:16
Alignment explanation
Indices: 4107007--4107098 Score: 109
Period size: 17 Copynumber: 5.7 Consensus size: 16
4106997 TAATATTATT
4107007 TTTAAATTT-AATCAAA
1 TTTAAATTTAAAT-AAA
4107023 TTTAAATTTAAAGTAAA
1 TTTAAATTTAAA-TAAA
4107040 TTTAAA--TAAATAAA
1 TTTAAATTTAAATAAA
4107054 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-ATAAA
*
4107071 TTTAAATCTAAATAAAA
1 TTTAAATTTAAAT-AAA
*
4107088 TTTAAAATTAA
1 TTTAAATTTAA
4107099 TTTTAAACTT
Statistics
Matches: 67, Mismatches: 3, Indels: 11
0.83 0.04 0.14
Matches are distributed among these distances:
14 10 0.15
15 4 0.06
16 14 0.21
17 38 0.57
18 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:4107242 original size:18 final size:20
Alignment explanation
Indices: 4107200--4107245 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
4107190 GTTCAAACGA
*
4107200 TTTTATATCGATTTAACTGT
1 TTTTTTATCGATTTAACTGT
4107220 TTTTTTATCGATTTAA-T-T
1 TTTTTTATCGATTTAACTGT
4107238 TTTTTTAT
1 TTTTTTAT
4107246 TTTTATCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 9 0.36
19 1 0.04
20 15 0.60
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTTTATCGATTTAACTGT
Found at i:4108378 original size:19 final size:20
Alignment explanation
Indices: 4108348--4108387 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
4108338 TTTGTTGTAT
4108348 TTAAATTTTGTTTAA-ATTAA
1 TTAAATTTTG-TTAATATTAA
4108368 TTAAA-TTTGTTAATATTAA
1 TTAAATTTTGTTAATATTAA
4108387 T
1 T
4108388 ATAATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 10 0.53
20 5 0.26
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TTAAATTTTGTTAATATTAA
Found at i:4108676 original size:19 final size:17
Alignment explanation
Indices: 4108637--4108678 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
4108627 AAGACAACGG
4108637 TATATAAAATATTATAT
1 TATATAAAATATTATAT
4108654 TATATACAAAGTA-TATA-
1 TATATA-AAA-TATTATAT
4108671 TATATAAA
1 TATATAAA
4108679 TCTTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.09
17 12 0.52
18 7 0.30
19 2 0.09
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TATATAAAATATTATAT
Found at i:4117889 original size:25 final size:24
Alignment explanation
Indices: 4117832--4117890 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
4117822 AAAAATAGGT
* *
4117832 TATA-TATTATTTTTCTAATATTA
1 TATATTATAATTTTTCTAATATCA
4117855 TATATTATAATTTTTACTAAT-TCA
1 TATATTATAATTTTT-CTAATATCA
*
4117879 TATTTTAATAAT
1 TATATT-ATAAT
4117891 AATTATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.13
24 16 0.53
25 10 0.33
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (24 bp):
TATATTATAATTTTTCTAATATCA
Found at i:4117994 original size:58 final size:59
Alignment explanation
Indices: 4117873--4118010 Score: 183
Period size: 58 Copynumber: 2.3 Consensus size: 59
4117863 AATTTTTACT
* *
4117873 AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATTATATATTATTTTATGTA
1 AATT-ATA-TTTAATAATAATTATATTAAAAATATAATTAAATTATATAATATTTTATGTA
* *
4117934 AATTGTATTTAATAATAATTATGTT-AAAATATAATTAAATTAGT-TAATATTTTTAT-TA
1 AATTATATTTAATAATAATTATATTAAAAATATAATTAAATTA-TATAATA-TTTTATGTA
4117992 AATTATATTTAATAATAAT
1 AATTATATTTAATAATAAT
4118011 CATTAAAATT
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
58 40 0.57
59 24 0.34
60 2 0.03
61 4 0.06
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (59 bp):
AATTATATTTAATAATAATTATATTAAAAATATAATTAAATTATATAATATTTTATGTA
Found at i:4121325 original size:3 final size:3
Alignment explanation
Indices: 4121314--4121348 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
4121304 ACTGTTTTTT
4121314 TTC TCTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
4121349 GAACCAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:4132732 original size:2 final size:2
Alignment explanation
Indices: 4132725--4132750 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4132715 TTAGAAAAAT
4132725 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
4132751 AAGCAGAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4148927 original size:27 final size:27
Alignment explanation
Indices: 4148889--4148950 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
4148879 GCCTCTGGCG
4148889 CCGCCGCCGATATGGCGTTAACTTCCA
1 CCGCCGCCGATATGGCGTTAACTTCCA
4148916 CCGCCGCCGATATGGCGTTAACTTCCA
1 CCGCCGCCGATATGGCGTTAACTTCCA
4148943 CCGCCGCC
1 CCGCCGCC
4148951 TCGCTTGCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.16, C:0.42, G:0.23, T:0.19
Consensus pattern (27 bp):
CCGCCGCCGATATGGCGTTAACTTCCA
Found at i:4149874 original size:23 final size:21
Alignment explanation
Indices: 4149832--4149875 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
4149822 TGTATATACA
* *
4149832 TTTAATAAAAAATATTAACTT
1 TTTAATAAAAAACATCAACTT
4149853 TTTACATAAAAACACATCAACTT
1 TTTA-ATAAAAA-ACATCAACTT
4149876 AAGATTCGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 7 0.37
23 8 0.42
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (21 bp):
TTTAATAAAAAACATCAACTT
Found at i:4154062 original size:16 final size:18
Alignment explanation
Indices: 4154036--4154068 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4154026 TTCAAACTTC
4154036 TTTTTTATCTT-TTATAA
1 TTTTTTATCTTATTATAA
4154053 TTTTTT-TCTTATTATA
1 TTTTTTATCTTATTATA
4154069 TTATTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTTATCTTATTATAA
Found at i:4160958 original size:79 final size:79
Alignment explanation
Indices: 4160873--4161135 Score: 229
Period size: 79 Copynumber: 3.2 Consensus size: 79
4160863 ATCTACATAC
4160873 ATGCAAAGAAAGGTATATATGTATATCCATGTACATACCTACCTACACATATATCACTATGCATC
1 ATGCAAAGAAAGGTATATATGTATATCCATGTACATACCTACCTACACATATATCACTATGCATC
4160938 AGACACTCAAAAAG
66 AGACACTCAAAAAG
* * * * * ** * * * *
4160952 ATGCAAAGAAAGATATATGTGCATATACATATACATATATTACATAAAAACATACATTCCCAGTA
1 ATGCAAAGAAAGGTATATATGTATATCCATGTACATA-CCTACCT--ACACATATA-T--CACT-
* * * * * *
4161017 AAGTAAGCATGTATATACATCTACAGAC
59 -A-T--GCAT-CAGACAC-TC-AAAAAG
* *
4161045 ATGCAAAGAAAGGTATATATGTATACCCATGTGCATACCTACCTACACATATATCACTATGCATC
1 ATGCAAAGAAAGGTATATATGTATATCCATGTACATACCTACCTACACATATATCACTATGCATC
4161110 AGACACTCAAAAAG
66 AGACACTCAAAAAG
4161124 ATGCAAAGAAAG
1 ATGCAAAGAAAG
4161136 ATATGTGTGC
Statistics
Matches: 134, Mismatches: 36, Indels: 28
0.68 0.18 0.14
Matches are distributed among these distances:
79 47 0.35
80 6 0.04
81 4 0.03
82 11 0.08
83 1 0.01
84 1 0.01
85 4 0.03
87 4 0.03
88 1 0.01
89 1 0.01
90 11 0.08
91 4 0.03
92 6 0.04
93 33 0.25
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (79 bp):
ATGCAAAGAAAGGTATATATGTATATCCATGTACATACCTACCTACACATATATCACTATGCATC
AGACACTCAAAAAG
Found at i:4161050 original size:172 final size:172
Alignment explanation
Indices: 4160764--4161235 Score: 881
Period size: 172 Copynumber: 2.7 Consensus size: 172
4160754 TCGAACTAAT
4160764 TCAGACACTCAAAAAGATGCAAAGAAAGATATATGTGCATATACATATACATATATTACATAAAA
1 TCAGACACTCAAAAAGATGCAAAGAAAGATATATGTGCATATACATATACATATATTACATAAAA
*
4160829 ACATGCATTCCCAGTAAAGTAAGCATGTATATACATCTACATACATGCAAAGAAAGGTATATATG
66 ACATACATTCCCAGTAAAGTAAGCATGTATATACATCTACATACATGCAAAGAAAGGTATATATG
*
4160894 TATATCCATGTACATACCTACCTACACATATATCACTATGCA
131 TATACCCATGTACATACCTACCTACACATATATCACTATGCA
4160936 TCAGACACTCAAAAAGATGCAAAGAAAGATATATGTGCATATACATATACATATATTACATAAAA
1 TCAGACACTCAAAAAGATGCAAAGAAAGATATATGTGCATATACATATACATATATTACATAAAA
*
4161001 ACATACATTCCCAGTAAAGTAAGCATGTATATACATCTACAGACATGCAAAGAAAGGTATATATG
66 ACATACATTCCCAGTAAAGTAAGCATGTATATACATCTACATACATGCAAAGAAAGGTATATATG
*
4161066 TATACCCATGTGCATACCTACCTACACATATATCACTATGCA
131 TATACCCATGTACATACCTACCTACACATATATCACTATGCA
*
4161108 TCAGACACTCAAAAAGATGCAAAGAAAGATATGTGTGCATATACATATACATATATTACATAAAA
1 TCAGACACTCAAAAAGATGCAAAGAAAGATATATGTGCATATACATATACATATATTACATAAAA
* *
4161173 ACATACATTCCCAGTATAGTAAGCATGTATATACATCTACATACAAGCAAAGAAAGGTATATA
66 ACATACATTCCCAGTAAAGTAAGCATGTATATACATCTACATACATGCAAAGAAAGGTATATA
4161236 AGAGAAACCC
Statistics
Matches: 292, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
172 292 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (172 bp):
TCAGACACTCAAAAAGATGCAAAGAAAGATATATGTGCATATACATATACATATATTACATAAAA
ACATACATTCCCAGTAAAGTAAGCATGTATATACATCTACATACATGCAAAGAAAGGTATATATG
TATACCCATGTACATACCTACCTACACATATATCACTATGCA
Found at i:4162001 original size:2 final size:2
Alignment explanation
Indices: 4161994--4162024 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4161984 GCTTTGTATA
4161994 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
4162025 ATGTATATAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4162886 original size:2 final size:2
Alignment explanation
Indices: 4162879--4162908 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4162869 GCCAAAATAT
4162879 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4162909 GGGATGGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4166796 original size:22 final size:21
Alignment explanation
Indices: 4166771--4166813 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4166761 TATTTCTTTC
4166771 AATTCTGTTTTCTTTTATTTTT
1 AATTCTG-TTTCTTTTATTTTT
*
4166793 AATTTTGTTTCTTTTATTTTT
1 AATTCTGTTTCTTTTATTTTT
4166814 CTTCAGATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.74
Consensus pattern (21 bp):
AATTCTGTTTCTTTTATTTTT
Found at i:4172359 original size:12 final size:12
Alignment explanation
Indices: 4172342--4172397 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 12
4172332 GGCAACCCAA
4172342 TTATTTTTATTT
1 TTATTTTTATTT
4172354 TTATTTTTATTT
1 TTATTTTTATTT
*
4172366 TT-TTCTCTA-TT
1 TTATT-TTTATTT
4172377 TTATTTATTTATTT
1 TTA-TT-TTTATTT
4172391 ATTATTT
1 -TTATTT
4172398 ATCCAGGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
11 6 0.17
12 17 0.47
13 6 0.17
14 4 0.11
15 3 0.08
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.79
Consensus pattern (12 bp):
TTATTTTTATTT
Found at i:4173954 original size:19 final size:19
Alignment explanation
Indices: 4173932--4173977 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
4173922 TAGGATTTAA
4173932 TATTTAATATTTAAGATAT-
1 TATTTAATATTTAA-ATATG
* *
4173951 TATTTATTATTTAAATTTG
1 TATTTAATATTTAAATATG
4173970 TATTTAAT
1 TATTTAAT
4173978 TTATGTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (19 bp):
TATTTAATATTTAAATATG
Found at i:4174821 original size:22 final size:21
Alignment explanation
Indices: 4174796--4174838 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4174786 TATTTCTTTC
4174796 AATTCTGTTTTCTTTTATTTTT
1 AATTCTG-TTTCTTTTATTTTT
*
4174818 AATTTTGTTTCTTTTATTTTT
1 AATTCTGTTTCTTTTATTTTT
4174839 TCTCAGATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.74
Consensus pattern (21 bp):
AATTCTGTTTCTTTTATTTTT
Found at i:4174839 original size:22 final size:24
Alignment explanation
Indices: 4174786--4174840 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
4174776 CCCTATTTTC
4174786 TATTTCTTTCAATTCTGTTTTCTTT
1 TATTT-TTTCAATTCTGTTTTCTTT
*
4174811 TA-TTTTT-AATTTTG-TTTCTTT
1 TATTTTTTCAATTCTGTTTTCTTT
4174832 TATTTTTTC
1 TATTTTTTC
4174841 TCAGATCGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 9 0.33
22 11 0.41
23 3 0.11
24 2 0.07
25 2 0.07
ACGTcount: A:0.13, C:0.11, G:0.04, T:0.73
Consensus pattern (24 bp):
TATTTTTTCAATTCTGTTTTCTTT
Found at i:4183040 original size:24 final size:24
Alignment explanation
Indices: 4183013--4183065 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
4183003 TTCGTTGGTG
* *
4183013 GTGGGGGTGGTGTTGTCGGTGTCA
1 GTGGGGGTGGTGGTGTCGGTGGCA
* *
4183037 GTGGCGGTGGTGGTGTTGGTGGCA
1 GTGGGGGTGGTGGTGTCGGTGGCA
4183061 GTGGG
1 GTGGG
4183066 AGTCCCTGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.04, C:0.08, G:0.58, T:0.30
Consensus pattern (24 bp):
GTGGGGGTGGTGGTGTCGGTGGCA
Found at i:4187018 original size:30 final size:30
Alignment explanation
Indices: 4186982--4187045 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
4186972 TAATGATAGG
* *
4186982 ATAATTT-GAATAATAAAGTATAATTTAAAT
1 ATAATTTAGAATAAAAAAGTA-AATATAAAT
* *
4187012 ATAATTTATAATAAAAAATTAAATATAAAT
1 ATAATTTAGAATAAAAAAGTAAATATAAAT
4187042 ATAA
1 ATAA
4187046 ATAAAAATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (30 bp):
ATAATTTAGAATAAAAAAGTAAATATAAAT
Found at i:4187037 original size:24 final size:24
Alignment explanation
Indices: 4187006--4187052 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
4186996 AAAGTATAAT
*
4187006 TTAAATAT-AATTTATAATAAAAAA
1 TTAAATATAAATATA-AATAAAAAA
4187030 TTAAATATAAATATAAATAAAAA
1 TTAAATATAAATATAAATAAAAA
4187053 TGCTCGGTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
TTAAATATAAATATAAATAAAAAA
Found at i:4196109 original size:16 final size:16
Alignment explanation
Indices: 4196073--4196109 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
4196063 ATTAACTGCG
*
4196073 AAAAAATAAAAATAAA
1 AAAAAATAAAAACAAA
4196089 AAAAAATAAAAACAAA
1 AAAAAATAAAAACAAA
4196105 GAAAA
1 -AAAA
4196110 GAGATGCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.86, C:0.03, G:0.03, T:0.08
Consensus pattern (16 bp):
AAAAAATAAAAACAAA
Found at i:4197151 original size:7 final size:7
Alignment explanation
Indices: 4197139--4197177 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
4197129 ATATTCTAAA
4197139 TAAATTT
1 TAAATTT
4197146 TAAATTT
1 TAAATTT
4197153 TAAATTT
1 TAAATTT
4197160 TAAATTT
1 TAAATTT
4197167 TAAATTT
1 TAAATTT
4197174 TAAA
1 TAAA
4197178 ACTCTTGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TAAATTT
Found at i:4202332 original size:22 final size:22
Alignment explanation
Indices: 4202290--4202333 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4202280 TAAGAGTTAT
* *
4202290 AAAATATCAAAATAATTACAAC
1 AAAATATAAAAATAATAACAAC
4202312 AAAATAGTAAAAAT-ATAACAAC
1 AAAATA-TAAAAATAATAACAAC
4202334 GCAATGGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.66, C:0.11, G:0.02, T:0.20
Consensus pattern (22 bp):
AAAATATAAAAATAATAACAAC
Found at i:4202459 original size:13 final size:13
Alignment explanation
Indices: 4202441--4202465 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4202431 TTTGTTCAAA
4202441 CTTATTTTTTTAG
1 CTTATTTTTTTAG
4202454 CTTATTTTTTTA
1 CTTATTTTTTTA
4202466 TTCAAACACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.72
Consensus pattern (13 bp):
CTTATTTTTTTAG
Found at i:4203826 original size:82 final size:82
Alignment explanation
Indices: 4203568--4203827 Score: 387
Period size: 82 Copynumber: 3.2 Consensus size: 82
4203558 TCGCGTCTGA
* *
4203568 TGCCTTCAACTTTACCTTTCTCTCTCGCTTTTCCTCTCAATTGTTCGGTCTGAGAGCTAGATTTG
1 TGCCTTCAGCTTT-TCTTTCTCTCTCGCTTTTCCTCTCAATTGTTCGGTCTGAGAGCTAGATTTG
*
4203633 CCTCAATTGTTTGATTCT
65 CCTCAATTGTTTGCTTCT
* * *
4203651 TGCCTTCAGATTTTCTTTCTTTCTCGCTTTTCCTCTCAATTGTTCGGTCTGAGAGATAGATTTGC
1 TGCCTTCAGCTTTTCTTTCTCTCTCGCTTTTCCTCTCAATTGTTCGGTCTGAGAGCTAGATTTGC
4203716 CTCAATTGTTTGCTTCT
66 CTCAATTGTTTGCTTCT
* * **
4203733 TGCCTTAAGCTTTTCTTTCTCTCTCGCTTTTCCTCTCAACTGTTTC-GTCTGAGAGCTCTATTTG
1 TGCCTTCAGCTTTTCTTTCTCTCTCGCTTTTCCTCTCAATTG-TTCGGTCTGAGAGCTAGATTTG
*
4203797 CCTCAATTGTTTGCCTCT
65 CCTCAATTGTTTGCTTCT
*
4203815 TCCCTTCAGCTTT
1 TGCCTTCAGCTTT
4203828 CCTCAAGTTA
Statistics
Matches: 160, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
82 146 0.91
83 14 0.09
ACGTcount: A:0.13, C:0.27, G:0.14, T:0.46
Consensus pattern (82 bp):
TGCCTTCAGCTTTTCTTTCTCTCTCGCTTTTCCTCTCAATTGTTCGGTCTGAGAGCTAGATTTGC
CTCAATTGTTTGCTTCT
Found at i:4210786 original size:54 final size:54
Alignment explanation
Indices: 4210679--4210789 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 54
4210669 CTAATTTAAA
* *
4210679 AATACTTATTATCAATTTCATATGAAATTTTGTTTAAGTACTCGTATTTGTTGC
1 AATACTTATTATCAATTTCATATGAAATTTTGTTTAAGTACTCATATTCGTTGC
* * * * *
4210733 AATATTTATTATCGATTTGATAT-AAAGTTTTGTTTAAGTATTTATATTCGTTGC
1 AATACTTATTATCAATTTCATATGAAA-TTTTGTTTAAGTACTCATATTCGTTGC
4210787 AAT
1 AAT
4210790 TGATCGTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
53 3 0.06
54 46 0.94
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.50
Consensus pattern (54 bp):
AATACTTATTATCAATTTCATATGAAATTTTGTTTAAGTACTCATATTCGTTGC
Found at i:4215033 original size:17 final size:17
Alignment explanation
Indices: 4215013--4215045 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4215003 ATAGTACAAT
4215013 AAAAATATAA-TTTAAAA
1 AAAAATA-AACTTTAAAA
4215030 AAAAATAAACTTTAAA
1 AAAAATAAACTTTAAA
4215046 TACAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAATAAACTTTAAAA
Found at i:4226086 original size:22 final size:22
Alignment explanation
Indices: 4226061--4226111 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 22
4226051 AGTTCAAATT
*
4226061 TTAATAGAATTA-ATGTTTATTG
1 TTAATAGAAATATAT-TTTATTG
*
4226083 TTAA-AAAAATATATTTTATTG
1 TTAATAGAAATATATTTTATTG
4226104 TTCAATAG
1 TT-AATAG
4226112 GGTTATATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
21 14 0.61
22 8 0.35
23 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (22 bp):
TTAATAGAAATATATTTTATTG
Found at i:4227979 original size:14 final size:14
Alignment explanation
Indices: 4227960--4228008 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
4227950 ACCGTTAGCT
4227960 ACCACGTCATCACG
1 ACCACGTCATCACG
**
4227974 ACCACGTCAT--TT
1 ACCACGTCATCACG
4227986 ACCACGTCATCACG
1 ACCACGTCATCACG
4228000 ACCACGTCA
1 ACCACGTCA
4228009 GCACCACGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 10 0.34
14 19 0.66
ACGTcount: A:0.29, C:0.41, G:0.12, T:0.18
Consensus pattern (14 bp):
ACCACGTCATCACG
Found at i:4227995 original size:26 final size:26
Alignment explanation
Indices: 4227959--4228008 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
4227949 AACCGTTAGC
4227959 TACCACGTCATCACGACCACGTCATT
1 TACCACGTCATCACGACCACGTCATT
4227985 TACCACGTCATCACGACCACGTCA
1 TACCACGTCATCACGACCACGTCA
4228009 GCACCACGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.40, G:0.12, T:0.20
Consensus pattern (26 bp):
TACCACGTCATCACGACCACGTCATT
Found at i:4231647 original size:9 final size:9
Alignment explanation
Indices: 4231633--4231708 Score: 53
Period size: 9 Copynumber: 9.1 Consensus size: 9
4231623 ACAAATGATT
4231633 TTAAAATTA
1 TTAAAATTA
4231642 TTAAAATTA
1 TTAAAATTA
*
4231651 TTTTTTAAA-TA
1 ---TTAAAATTA
4231662 -TAAAATTA
1 TTAAAATTA
4231670 TTAAAATTA
1 TTAAAATTA
4231679 TT----TT-
1 TTAAAATTA
4231683 TTAAAA-TA
1 TTAAAATTA
4231691 -TAAAATTA
1 TTAAAATTA
4231699 TTAAAATTA
1 TTAAAATTA
4231708 T
1 T
4231709 AATCATTATC
Statistics
Matches: 53, Mismatches: 2, Indels: 24
0.67 0.03 0.30
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
7 10 0.19
8 4 0.08
9 28 0.53
11 2 0.04
12 5 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TTAAAATTA
Found at i:4231674 original size:28 final size:29
Alignment explanation
Indices: 4231634--4231708 Score: 143
Period size: 28 Copynumber: 2.6 Consensus size: 29
4231624 CAAATGATTT
4231634 TAAAATTATTAAAATTATTTTTT-AAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
4231662 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
4231691 TAAAATTATTAAAATTAT
1 TAAAATTATTAAAATTAT
4231709 AATCATTATC
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 23 0.50
29 23 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTAAAATA
Found at i:4231688 original size:13 final size:13
Alignment explanation
Indices: 4231642--4231689 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
4231632 TTTAAAATTA
4231642 TTAAAATTATTTT
1 TTAAAATTATTTT
* * *
4231655 TTAAATATAAAATTA
1 TTAAA-AT-TATTTT
4231670 TTAAAATTATTTT
1 TTAAAATTATTTT
4231683 TTAAAAT
1 TTAAAAT
4231690 ATAAAATTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 15 0.56
14 4 0.15
15 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAAAATTATTTT
Found at i:4231704 original size:16 final size:16
Alignment explanation
Indices: 4231657--4231710 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
4231647 ATTATTTTTT
4231657 AAATATAAAATTATTA
1 AAATATAAAATTATTA
* *
4231673 AAAT-T--ATTTTTTA
1 AAATATAAAATTATTA
4231686 AAATATAAAATTATTA
1 AAATATAAAATTATTA
4231702 AAATTATAA
1 AAA-TATAA
4231711 TCATTATCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
13 10 0.33
14 1 0.03
15 1 0.03
16 13 0.43
17 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATATAAAATTATTA
Found at i:4232612 original size:20 final size:22
Alignment explanation
Indices: 4232587--4232627 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4232577 AAAGAATAAG
4232587 ATAATTTT-AT-ATTTTAAAAA
1 ATAATTTTAATAATTTTAAAAA
4232607 ATAATTTTAATAATTTTAAAA
1 ATAATTTTAATAATTTTAAAA
4232628 TCATTTGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAATTTTAATAATTTTAAAAA
Found at i:4232628 original size:20 final size:19
Alignment explanation
Indices: 4232587--4232627 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 19
4232577 AAAGAATAAG
4232587 ATAATTTTATATTTTAAAAA
1 ATAATTTTATATTTT-AAAA
4232607 ATAATTTTAATAATTTTAAAA
1 ATAATTTT-AT-ATTTTAAAA
4232628 TCATTTGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATAATTTTATATTTTAAAA
Found at i:4233525 original size:30 final size:31
Alignment explanation
Indices: 4233456--4233526 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 31
4233446 TTTACCACTT
*
4233456 TAATTATATAGCTTATTTGTCATTAAAAAAAA
1 TAATTATATAGCTTAATTGTCATT-AAAAAAA
* * *
4233488 TACTTATATAGCTTAATTGTTATT-AGAAAA
1 TAATTATATAGCTTAATTGTCATTAAAAAAA
4233518 TAATTATAT
1 TAATTATAT
4233527 GGCATACCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 13 0.38
32 21 0.62
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (31 bp):
TAATTATATAGCTTAATTGTCATTAAAAAAA
Found at i:4249159 original size:31 final size:31
Alignment explanation
Indices: 4249094--4249160 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
4249084 AAAAGCCGAC
* *
4249094 AATTTGACTCTTTTTGAAAAATTGATGATGA
1 AATTTGACTCTTTTTAAAAAATTGAGGATGA
* *
4249125 AATTTGACTC-TTTTAAAAAGATTGAGGGTTA
1 AATTTGACTCTTTTTAAAAA-ATTGAGGATGA
4249156 AATTT
1 AATTT
4249161 TGCTCAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (31 bp):
AATTTGACTCTTTTTAAAAAATTGAGGATGA
Found at i:4254749 original size:31 final size:31
Alignment explanation
Indices: 4254712--4254776 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
4254702 TACACTTTGA
* *
4254712 TCATTGAACTATT-TAAAAGTTTTCATTTAAG
1 TCATTGAACTATTCAAAAAATTTT-ATTTAAG
*
4254743 TCATTGAATTATTCAAAAAATTTTATTTAAG
1 TCATTGAACTATTCAAAAAATTTTATTTAAG
4254774 TCA
1 TCA
4254777 CTGGTTGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 22 0.73
32 8 0.27
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (31 bp):
TCATTGAACTATTCAAAAAATTTTATTTAAG
Found at i:4260584 original size:22 final size:22
Alignment explanation
Indices: 4260542--4260585 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4260532 CACAAATTTC
* *
4260542 TTCTCTAAGTTTCTCTCTAATT
1 TTCTATAAGTTTCTCACTAATT
4260564 TTCTATAA-TTTCTCACTTAATT
1 TTCTATAAGTTTCTCAC-TAATT
4260586 ATCAAAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.23, C:0.20, G:0.02, T:0.55
Consensus pattern (22 bp):
TTCTATAAGTTTCTCACTAATT
Found at i:4260702 original size:29 final size:29
Alignment explanation
Indices: 4260660--4260725 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
4260650 AAATCAATCT
* *
4260660 CATCAAAATTATTTTTTTAGAGCACATCA
1 CATCAAAATTATTTTTTCAGAACACATCA
* * *
4260689 CATCAAATTTATTTTTTCAGAACTCATCT
1 CATCAAAATTATTTTTTCAGAACACATCA
4260718 CATCAAAA
1 CATCAAAA
4260726 ATCGTTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.38
Consensus pattern (29 bp):
CATCAAAATTATTTTTTCAGAACACATCA
Found at i:4261206 original size:19 final size:19
Alignment explanation
Indices: 4261155--4261225 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
4261145 AAATTACAAA
* *
4261155 AAAAAATCAAATTAATTTT
1 AAAAATTCAAAATAATTTT
**
4261174 CAAAAATTTTAAATAATTTT
1 -AAAAATTCAAAATAATTTT
*
4261194 TAAAATTCAAAAT-ATTTGT
1 AAAAATTCAAAATAATTT-T
4261213 AAAAATTCAAAAT
1 AAAAATTCAAAAT
4261226 TTATATTTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
18 4 0.10
19 23 0.55
20 15 0.36
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:4261854 original size:18 final size:18
Alignment explanation
Indices: 4261829--4261871 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4261819 AAATATTTAC
4261829 TTTTTTTTC-TTTCCCTT
1 TTTTTTTTCATTTCCCTT
*
4261846 TTCTTTTTTCATTTCTCTT
1 TT-TTTTTTCATTTCCCTT
4261865 TTTTTTT
1 TTTTTTT
4261872 CCTTCTACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 2 0.09
18 12 0.52
19 9 0.39
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTTTCATTTCCCTT
Found at i:4261854 original size:19 final size:19
Alignment explanation
Indices: 4261829--4261871 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
4261819 AAATATTTAC
4261829 TTTTTTTTC-TTTCCCTTT
1 TTTTTTTTCATTTCCCTTT
* *
4261847 TCTTTTTTCATTTCTCTTT
1 TTTTTTTTCATTTCCCTTT
4261866 TTTTTT
1 TTTTTT
4261872 CCTTCTACTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTTTTCATTTCCCTTT
Found at i:4264688 original size:25 final size:24
Alignment explanation
Indices: 4264627--4264690 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 24
4264617 ATTATTTTCT
* * *
4264627 ATATAAAAATAAAT-TTAAAAAAT
1 ATATTAAAATAAATATCAAAAAAA
*
4264650 ATATT-ACATCAAATATACAAAAAAA
1 ATATTAAAAT-AAATAT-CAAAAAAA
4264675 ATATTAAAATAAATAT
1 ATATTAAAATAAATAT
4264691 TTCCCAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
22 3 0.09
23 8 0.25
24 1 0.03
25 17 0.53
26 3 0.09
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (24 bp):
ATATTAAAATAAATATCAAAAAAA
Found at i:4272985 original size:26 final size:28
Alignment explanation
Indices: 4272918--4272988 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 28
4272908 ACCGGCTTGC
* * *
4272918 ATTTGGTATCTAAACTTTTTTTTTCCTA
1 ATTTGATATATAAACTTTTTTTGTCCTA
* *
4272946 ATTTTATACATAAA-TTTTTTTGTCC-A
1 ATTTGATATATAAACTTTTTTTGTCCTA
*
4272972 ATTTGATATTTAAACTT
1 ATTTGATATATAAACTT
4272989 GTAAAACATA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
26 12 0.35
27 12 0.35
28 10 0.29
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.55
Consensus pattern (28 bp):
ATTTGATATATAAACTTTTTTTGTCCTA
Found at i:4280569 original size:23 final size:23
Alignment explanation
Indices: 4280543--4280588 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
4280533 AAGTTTTAAT
4280543 TTGATTGAAATAATTTCCCTAAC
1 TTGATTGAAATAATTTCCCTAAC
*
4280566 TTGATTGAATTAATTTCCCTAAC
1 TTGATTGAAATAATTTCCCTAAC
4280589 GTTTCTAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (23 bp):
TTGATTGAAATAATTTCCCTAAC
Found at i:4284856 original size:24 final size:24
Alignment explanation
Indices: 4284811--4284887 Score: 57
Period size: 24 Copynumber: 3.1 Consensus size: 24
4284801 ACAACAATTC
* ** *
4284811 CAACAGAAACAGCTCCTCCAACAA
1 CAACAGCAACAGCAACTGCAACAA
4284835 CAACAGCAACAGCAACTGCAACTTCAA
1 CAACAGCAACAGCAACTGCAA---CAA
* *
4284862 CAACAACAAGAGCAACATG-AACAA
1 CAACAGCAACAGCAAC-TGCAACAA
4284886 CA
1 CA
4284888 GTTACAGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
24 22 0.51
27 19 0.44
28 2 0.05
ACGTcount: A:0.49, C:0.32, G:0.10, T:0.08
Consensus pattern (24 bp):
CAACAGCAACAGCAACTGCAACAA
Found at i:4292781 original size:22 final size:22
Alignment explanation
Indices: 4292756--4292799 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4292746 ATGAACCCAT
*
4292756 TCATAAAAAGACTAACTGTTTC
1 TCATAAAAAAACTAACTGTTTC
4292778 TCATAAAAAAACTAACTGTTTC
1 TCATAAAAAAACTAACTGTTTC
4292800 AGGTTGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (22 bp):
TCATAAAAAAACTAACTGTTTC
Found at i:4300376 original size:31 final size:31
Alignment explanation
Indices: 4300318--4300376 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
4300308 TTGGCCCATT
* * * *
4300318 TTAGTCCCTAATATTATTAGATATTCCCAAA
1 TTAGTCCCAAACATTATCAGACATTCCCAAA
*
4300349 TTAGTCCCAAACATTATCAGACGTTCCC
1 TTAGTCCCAAACATTATCAGACATTCCC
4300377 GATTCAATCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.34
Consensus pattern (31 bp):
TTAGTCCCAAACATTATCAGACATTCCCAAA
Found at i:4301284 original size:30 final size:28
Alignment explanation
Indices: 4301236--4301291 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
4301226 TGATTTGTAA
*
4301236 AATTTTAAAATATTAAAATATCTAATATAT
1 AATTTTAAAATATGAAAAT-T-TAATATAT
4301266 AATTTTAAAAT-TAGAAAATTTAATAT
1 AATTTTAAAATAT-GAAAATTTAATAT
4301292 TATTTTTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 6 0.25
29 2 0.08
30 16 0.67
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
AATTTTAAAATATGAAAATTTAATATAT
Found at i:4301322 original size:15 final size:16
Alignment explanation
Indices: 4301291--4301349 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 16
4301281 AAATTTAATA
4301291 TTATTTTTGTAATTTT
1 TTATTTTTGTAATTTT
4301307 TTATTTTTAGT-ATTTT
1 TTATTTTT-GTAATTTT
*
4301323 TAATAATTTTGATAATTTT
1 T--TATTTTTG-TAATTTT
*
4301342 TCATTTTT
1 TTATTTTT
4301350 AAAAGTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
16 14 0.40
17 8 0.23
18 7 0.20
19 6 0.17
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (16 bp):
TTATTTTTGTAATTTT
Found at i:4304226 original size:4 final size:4
Alignment explanation
Indices: 4304219--4304246 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
4304209 TTACTCGATA
4304219 GGTG GGTG GGTG GGTG GGTG GGTG GGTG
1 GGTG GGTG GGTG GGTG GGTG GGTG GGTG
4304247 AGTTTCATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.75, T:0.25
Consensus pattern (4 bp):
GGTG
Found at i:4307193 original size:16 final size:16
Alignment explanation
Indices: 4307168--4307205 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
4307158 TTTTAAAATG
4307168 ATAAA-TTTTTAATTT
1 ATAAATTTTTTAATTT
4307183 ATAAATTTTTTTAATTT
1 ATAAA-TTTTTTAATTT
4307200 -TAAATT
1 ATAAATT
4307206 AGTAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 4 0.19
17 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATAAATTTTTTAATTT
Found at i:4307193 original size:17 final size:16
Alignment explanation
Indices: 4307173--4307205 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
4307163 AAATGATAAA
4307173 TTTTTAATTTATAAATT
1 TTTTTAATTT-TAAATT
4307190 TTTTTAATTTTAAATT
1 TTTTTAATTTTAAATT
4307206 AGTAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTAATTTTAAATT
Found at i:4312331 original size:53 final size:53
Alignment explanation
Indices: 4312251--4312364 Score: 156
Period size: 53 Copynumber: 2.2 Consensus size: 53
4312241 CACGGGCTAG
* * * * *
4312251 CACATGGGCGTGTGTTAGGGTGTGTGTATACTGTTTTGAGGCATATGAGCTTA
1 CACATGGGCGTGTGTCAGGGAGTGTGTATACTGTTTTGAGGAACATGAGCTGA
* * *
4312304 CACATGGGCGTGTGTCAGGGAGTGTGTATATTGTTTTGGGGAACATGGGCTGA
1 CACATGGGCGTGTGTCAGGGAGTGTGTATACTGTTTTGAGGAACATGAGCTGA
4312357 CACATGGG
1 CACATGGG
4312365 TGTGGGTACA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.19, C:0.12, G:0.37, T:0.32
Consensus pattern (53 bp):
CACATGGGCGTGTGTCAGGGAGTGTGTATACTGTTTTGAGGAACATGAGCTGA
Done.