Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 17 of 345
Found at i:5788615 original size:55 final size:55
Alignment explanation
Indices: 5788519--5788634 Score: 148
Period size: 55 Copynumber: 2.1 Consensus size: 55
5788509 ATTTGTAATG
* * *
5788519 TATA-TTTTTAAAATTTTAATTATTATTTTTAAAAATATTTTTTTAATTTTATA-A
1 TATATTTTTTAAAATTTTAAATATTATTTTTAAAAAT-TTTTTTTAACTTTAGATA
* *
5788573 TATATTTTTTACAATTTTAAATATTATTTTT-AAATTCTTTTTTTAACTTTAGATA
1 TATATTTTTTAAAATTTTAAATATTATTTTTAAAAAT-TTTTTTTAACTTTAGATA
5788628 TATATTT
1 TATATTT
5788635 AAATTTTAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
54 22 0.41
55 32 0.59
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (55 bp):
TATATTTTTTAAAATTTTAAATATTATTTTTAAAAATTTTTTTTAACTTTAGATA
Found at i:5789842 original size:23 final size:23
Alignment explanation
Indices: 5789815--5789860 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5789805 AAATTAATAA
*
5789815 ATTATTAAAC-ATACATTTCAAAT
1 ATTATAAAACAATA-ATTTCAAAT
5789838 ATTATAAAACTAATAATTTCAAA
1 ATTATAAAAC-AATAATTTCAAA
5789861 ACTAATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 8 0.40
25 3 0.15
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (23 bp):
ATTATAAAACAATAATTTCAAAT
Found at i:5790041 original size:36 final size:36
Alignment explanation
Indices: 5790000--5790099 Score: 109
Period size: 34 Copynumber: 2.8 Consensus size: 36
5789990 TTTTAAAATT
*
5790000 AATAATAT-AAATTAAATAAACAAAATAAAATAAGGA
1 AATAATATAAAATTAAATAAA-AAAAAAAAATAAGGA
* *
5790036 AATAATATAAAACTTAAA-AAAGAAAAAAATTAA-GA
1 AATAATATAAAA-TTAAATAAAAAAAAAAAATAAGGA
* *
5790071 AA-AAGATAAAATTTAATAAAAAAAAAAAA
1 AATAATATAAAATTAAATAAAAAAAAAAAA
5790100 AAAAGGGTGG
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
33 4 0.07
34 18 0.33
35 4 0.07
36 17 0.31
37 6 0.11
38 5 0.09
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (36 bp):
AATAATATAAAATTAAATAAAAAAAAAAAATAAGGA
Found at i:5790045 original size:18 final size:18
Alignment explanation
Indices: 5790000--5790047 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
5789990 TTTTAAAATT
* *
5790000 AATAATATAAATTAAATA
1 AATAATATAAAATAAAGA
* * *
5790018 AACAAAATAAAATAAGGA
1 AATAATATAAAATAAAGA
5790036 AATAATATAAAA
1 AATAATATAAAA
5790048 CTTAAAAAAG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (18 bp):
AATAATATAAAATAAAGA
Found at i:5790075 original size:18 final size:18
Alignment explanation
Indices: 5790052--5790099 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
5790042 ATAAAACTTA
5790052 AAAAAGAAAAAAATTAAG
1 AAAAAGAAAAAAATTAAG
* * *
5790070 AAAAAGATAAAATTTAAT
1 AAAAAGAAAAAAATTAAG
5790088 AAAAA-AAAAAAA
1 AAAAAGAAAAAAA
5790100 AAAAGGGTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (18 bp):
AAAAAGAAAAAAATTAAG
Found at i:5790100 original size:36 final size:37
Alignment explanation
Indices: 5790000--5790105 Score: 103
Period size: 36 Copynumber: 3.0 Consensus size: 37
5789990 TTTTAAAATT
* * * *
5790000 AATAATAT-AAATTAAATAAACAAAATAAAATAAGGA
1 AATAAGATAAAATTTAATAAAAAAAAAAAAATAAGGA
* * * *
5790036 AATAATATAAAACTTAA-AAAAGAAAAAAATTAA-GA
1 AATAAGATAAAATTTAATAAAAAAAAAAAAATAAGGA
*
5790071 AA-AAGATAAAATTTAATAAAAAAAAAAAAAAAAGG
1 AATAAGATAAAATTTAATAAAAAAAAAAAAATAAGG
5790106 GTGGCAGAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
34 12 0.21
35 17 0.30
36 21 0.38
37 6 0.11
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.19
Consensus pattern (37 bp):
AATAAGATAAAATTTAATAAAAAAAAAAAAATAAGGA
Found at i:5790215 original size:20 final size:19
Alignment explanation
Indices: 5790186--5790232 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
5790176 CATATTTTTT
5790186 AAAAATTAAAAA-AAAGTTA
1 AAAAATTAAAAAGAAA-TTA
5790205 AAAAATGTAAAAAGAAATTA
1 AAAAAT-TAAAAAGAAATTA
5790225 AAGAAATT
1 AA-AAATT
5790233 GTATTTACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.24
20 12 0.48
21 7 0.28
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (19 bp):
AAAAATTAAAAAGAAATTA
Found at i:5790304 original size:23 final size:23
Alignment explanation
Indices: 5790277--5790325 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
5790267 TATTATTAAA
5790277 AATATGGTT-AATATTT-AAAAATT
1 AATAT-GTTAAAT-TTTAAAAAATT
*
5790300 AATATTTTAAATTTTAAAAAATT
1 AATATGTTAAATTTTAAAAAATT
5790323 AAT
1 AAT
5790326 TTGAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
AATATGTTAAATTTTAAAAAATT
Found at i:5790325 original size:37 final size:35
Alignment explanation
Indices: 5790284--5790425 Score: 119
Period size: 37 Copynumber: 4.0 Consensus size: 35
5790274 AAAAATATGG
5790284 TTAATATTTAAAAATTAATATTTTAAATTTTAAAAAA
1 TTAAT-TTTAAAAA-TAATATTTTAAATTTTAAAAAA
* *
5790321 TTAATTTGAAAAATACAT-TTTTAAAATATATAAAAAA
1 TTAATTTTAAAAATA-ATATTTT-AAAT-TTTAAAAAA
* * * *
5790358 TTAATTTCACAAAT-ATATATCTAAA-ATTAAAAAA
1 TTAATTTTAAAAATAATAT-TTTAAATTTTAAAAAA
* * * *
5790392 ATATTTTTAAAAATAATAATTAAAATTTTAAAAA
1 TTAATTTTAAAAATAATATTTTAAATTTTAAAAA
5790426 TATACATTAC
Statistics
Matches: 83, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
34 21 0.25
35 18 0.22
36 17 0.20
37 27 0.33
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (35 bp):
TTAATTTTAAAAATAATATTTTAAATTTTAAAAAA
Found at i:5790425 original size:22 final size:22
Alignment explanation
Indices: 5790396--5790442 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
5790386 AAAAAAATAT
5790396 TTTTAAAAATAATA-ATTA-AAA
1 TTTTAAAAAT-ATACATTACAAA
5790417 TTTTAAAAATATACATTACAAA
1 TTTTAAAAATATACATTACAAA
5790439 TTTT
1 TTTT
5790443 TTAAAGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 3 0.12
21 14 0.58
22 7 0.29
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAAATATACATTACAAA
Found at i:5790554 original size:29 final size:29
Alignment explanation
Indices: 5790522--5790581 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
5790512 ACAATTTATT
*
5790522 AAGAAATA-AAATAAAAAAGTAAAAAAAAA
1 AAGAAATAGAAA-AAAAAAGGAAAAAAAAA
*
5790551 AAGAAATATGAAAATAAAAGGAAAAAAAAA
1 AAGAAATA-GAAAAAAAAAGGAAAAAAAAA
5790581 A
1 A
5790582 GTCAGGTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 8 0.30
30 16 0.59
31 3 0.11
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (29 bp):
AAGAAATAGAAAAAAAAAGGAAAAAAAAA
Found at i:5798306 original size:6 final size:6
Alignment explanation
Indices: 5798295--5798321 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5798285 ATTAAAAAAA
5798295 TAAATT TAAATT TAAATT TAAATT TAA
1 TAAATT TAAATT TAAATT TAAATT TAA
5798322 GTATTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TAAATT
Found at i:5803049 original size:2 final size:2
Alignment explanation
Indices: 5803044--5803068 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5803034 AATTTTTTAA
5803044 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5803069 AAAGTGTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5807211 original size:11 final size:11
Alignment explanation
Indices: 5807195--5807220 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5807185 ATTTTTTATA
5807195 TTTAATAATAT
1 TTTAATAATAT
5807206 TTTAATAATAT
1 TTTAATAATAT
5807217 TTTA
1 TTTA
5807221 TGTTATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTAATAATAT
Found at i:5807861 original size:14 final size:15
Alignment explanation
Indices: 5807836--5807864 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5807826 TTAAAAAAAA
5807836 TATAGCTTTATTTAT
1 TATAGCTTTATTTAT
5807851 TATAG-TTTATTTAT
1 TATAGCTTTATTTAT
5807865 AAAAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (15 bp):
TATAGCTTTATTTAT
Found at i:5811988 original size:107 final size:108
Alignment explanation
Indices: 5811866--5812079 Score: 394
Period size: 107 Copynumber: 2.0 Consensus size: 108
5811856 AAACAAAAAA
5811866 TTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAAA
1 TTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAAA
*
5811931 ATTGTATTAAATTTTTTGTTAATTACTCT-ATAAAATTTTTGC
66 ATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTGC
* *
5811973 TTAGTTTAACAAAACAATGATATGTTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAAA
1 TTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAAA
5812038 ATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
66 ATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
5812080 ACGTGTTTTT
Statistics
Matches: 103, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
107 91 0.88
108 12 0.12
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (108 bp):
TTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAAA
ATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTGC
Found at i:5813533 original size:26 final size:24
Alignment explanation
Indices: 5813489--5813538 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
5813479 ATTTGTTTTA
* *
5813489 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTAAAAT
5813513 ATATTTGATTTATTATATTTTAAAAT
1 ATATTTG-TTT-TTATATTTTAAAAT
5813539 TTTTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTAAAAT
Found at i:5827748 original size:30 final size:30
Alignment explanation
Indices: 5827678--5827748 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
5827668 TTTTTATTGG
* *
5827678 AACATTTTTATATTAATTAATTATGAAAAA
1 AACATTTTTATATTAAATAATAATGAAAAA
* *
5827708 AACATGTTTATATTAAATATATAATG-AGAA
1 AACATTTTTATATTAAATA-ATAATGAAAAA
*
5827738 AACCTTTTTAT
1 AACATTTTTAT
5827749 GGTGAATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 29 0.85
31 5 0.15
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (30 bp):
AACATTTTTATATTAAATAATAATGAAAAA
Found at i:5827959 original size:2 final size:2
Alignment explanation
Indices: 5827952--5827993 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
5827942 TTAACCTTTC
*
5827952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5827994 TAATTACATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5835029 original size:7 final size:7
Alignment explanation
Indices: 5835014--5835065 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
5835004 AAGCTCAGAG
*
5835014 TTTAGAA
1 TTTAAAA
5835021 TTTAAAA
1 TTTAAAA
*
5835028 TTAAAAA
1 TTTAAAA
*
5835035 TTTTAAA
1 TTTAAAA
*
5835042 TTCAAAA
1 TTTAAAA
*
5835049 TTTTATAA
1 -TTTAAAA
5835057 TTTAAAA
1 TTTAAAA
5835064 TT
1 TT
5835066 GAAGATAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
7 30 0.86
8 5 0.14
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (7 bp):
TTTAAAA
Found at i:5835042 original size:14 final size:14
Alignment explanation
Indices: 5835019--5835065 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
5835009 CAGAGTTTAG
*
5835019 AATTTAAAATTAAA
1 AATTTTAAATTAAA
*
5835033 AATTTTAAATTCAA
1 AATTTTAAATTAAA
*
5835047 AATTTTATAATTTAA
1 AATTTTA-AATTAAA
5835062 AATT
1 AATT
5835066 GAAGATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
AATTTTAAATTAAA
Found at i:5840877 original size:4 final size:4
Alignment explanation
Indices: 5840868--5840892 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5840858 GGTAGCTGCG
5840868 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
5840893 AGGGCAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:5846978 original size:23 final size:22
Alignment explanation
Indices: 5846936--5846979 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
5846926 TTAAGTTATA
5846936 TTATTTAAAAAATATTAATATTT
1 TTATTTAAAAAATA-TAATATTT
5846959 TTATTTAATAATAATA-AATAT
1 TTATTTAA-AA-AATATAATAT
5846980 ACATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 13 0.68
24 2 0.11
25 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTATTTAAAAAATATAATATTT
Found at i:5847184 original size:14 final size:14
Alignment explanation
Indices: 5847161--5847190 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5847151 ATTTAGTTTC
5847161 TTAATCTAATATAT
1 TTAATCTAATATAT
*
5847175 TTAATTTAATATAT
1 TTAATCTAATATAT
5847189 TT
1 TT
5847191 TAAAATTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAATCTAATATAT
Found at i:5850117 original size:7 final size:7
Alignment explanation
Indices: 5850105--5850137 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
5850095 TTTAATATTA
5850105 AAATTTT
1 AAATTTT
5850112 AAATTTT
1 AAATTTT
5850119 AAATTTT
1 AAATTTT
5850126 AAATTTT
1 AAATTTT
5850133 AAATT
1 AAATT
5850138 ATCATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
AAATTTT
Found at i:5850118 original size:21 final size:21
Alignment explanation
Indices: 5850093--5850137 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5850083 TCTAGTTTTT
*
5850093 TTTTTAATATTAAAATTTTAAA
1 TTTTAAAT-TTAAAATTTTAAA
*
5850115 TTTTAAATTTTAAATTTTAAA
1 TTTTAAATTTAAAATTTTAAA
5850136 TT
1 TT
5850138 ATCATAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTAAATTTAAAATTTTAAA
Found at i:5854019 original size:28 final size:28
Alignment explanation
Indices: 5853987--5854044 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
5853977 TATGGTGAAC
*
5853987 AATCATTAAAAAATTATTAAAAATCATA
1 AATCATAAAAAAATTATTAAAAATCATA
5854015 AATCATAAAAAAATTATTAAAAATCATA
1 AATCATAAAAAAATTATTAAAAATCATA
5854043 AA
1 AA
5854045 AAAATATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (28 bp):
AATCATAAAAAAATTATTAAAAATCATA
Found at i:5854028 original size:11 final size:11
Alignment explanation
Indices: 5854014--5854066 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
5854004 TAAAAATCAT
5854014 AAATCATAAAA
1 AAATCATAAAA
* *
5854025 AAATTAT-TAA
1 AAATCATAAAA
5854035 AAATCATAAAA
1 AAATCATAAAA
5854046 AAAT-ATAAAA
1 AAATCATAAAA
*
5854056 TAAATTATAAA
1 -AAATCATAAA
5854067 GTTGTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 14 0.40
11 16 0.46
12 5 0.14
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATCATAAAA
Found at i:5854560 original size:33 final size:31
Alignment explanation
Indices: 5854489--5854547 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
5854479 AATTTGTTAA
* *
5854489 TTAATGCATTGTCTATGTGTTCTTTCTATTT
1 TTAATGCATAGTCTATATGTTCTTTCTATTT
5854520 TTAATGCATAGTCTATATGTTCTTTCTA
1 TTAATGCATAGTCTATATGTTCTTTCTA
5854548 CTTTGATTAT
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:0.20, C:0.14, G:0.12, T:0.54
Consensus pattern (31 bp):
TTAATGCATAGTCTATATGTTCTTTCTATTT
Found at i:5855326 original size:13 final size:13
Alignment explanation
Indices: 5855310--5855335 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5855300 TCAATTAACG
5855310 AAAAATATTAATA
1 AAAAATATTAATA
5855323 AAAAATATTAATA
1 AAAAATATTAATA
5855336 GTTGTAATTT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATATTAATA
Found at i:5857371 original size:13 final size:13
Alignment explanation
Indices: 5857330--5857388 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 13
5857320 ATTTCTCTAG
5857330 ATTATTATTGAACT
1 ATTATTATT-AACT
*
5857344 ATAAATTA-TAA--
1 AT-TATTATTAACT
5857355 ATTATTATTAACT
1 ATTATTATTAACT
*
5857368 ATTATTATTAAAT
1 ATTATTATTAACT
*
5857381 AATATTAT
1 ATTATTAT
5857389 ATATGTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
10 4 0.11
11 5 0.14
13 21 0.57
14 3 0.08
15 4 0.11
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (13 bp):
ATTATTATTAACT
Found at i:5857436 original size:17 final size:17
Alignment explanation
Indices: 5857414--5857448 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5857404 AAATGAAGAA
*
5857414 AAAGAATAAAAAGAAAC
1 AAAGAAGAAAAAGAAAC
*
5857431 AAAGAAGAATAAGAAAC
1 AAAGAAGAAAAAGAAAC
5857448 A
1 A
5857449 GAGAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.06, G:0.14, T:0.06
Consensus pattern (17 bp):
AAAGAAGAAAAAGAAAC
Found at i:5859064 original size:39 final size:39
Alignment explanation
Indices: 5858957--5859091 Score: 114
Period size: 39 Copynumber: 3.4 Consensus size: 39
5858947 GACCTCGAGT
* * *
5858957 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** * ** *
5858998 CGATGAGGTACTGAGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
5859036 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
5859075 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
5859092 CCATATTGGT
Statistics
Matches: 74, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
38 18 0.24
39 36 0.49
40 4 0.05
41 14 0.19
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:5861519 original size:16 final size:16
Alignment explanation
Indices: 5861493--5861532 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
5861483 ATTAAAACTT
* *
5861493 AATATTCTAAAATATA
1 AATATTTTAAAATAAA
*
5861509 ATTATTTTAAAATAAA
1 AATATTTTAAAATAAA
5861525 AATATTTT
1 AATATTTT
5861533 TTACATTCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATTTTAAAATAAA
Found at i:5865269 original size:21 final size:21
Alignment explanation
Indices: 5865243--5865283 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5865233 ATCTGCTCAA
* *
5865243 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
5865264 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
5865284 TCGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:5867137 original size:12 final size:13
Alignment explanation
Indices: 5867119--5867154 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
5867109 TTTTGACTGT
5867119 TTTTCTTCAAAAA
1 TTTTCTTCAAAAA
5867132 -TTTCTTCAAAAAA
1 TTTTCTTC-AAAAA
5867145 TTTTCTTCAA
1 TTTTCTTCAA
5867155 GTGCCACCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 7 0.33
13 7 0.33
14 7 0.33
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (13 bp):
TTTTCTTCAAAAA
Found at i:5867149 original size:14 final size:14
Alignment explanation
Indices: 5867119--5867154 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
5867109 TTTTGACTGT
5867119 TTTTCTTC-AAAAA
1 TTTTCTTCAAAAAA
5867132 -TTTCTTCAAAAAA
1 TTTTCTTCAAAAAA
5867145 TTTTCTTCAA
1 TTTTCTTCAA
5867155 GTGCCACCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.33
13 5 0.24
14 9 0.43
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTTCTTCAAAAAA
Found at i:5870122 original size:13 final size:14
Alignment explanation
Indices: 5870098--5870131 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
5870088 TCGAATTATC
*
5870098 TATTAATTTTAAAA
1 TATTAATGTTAAAA
5870112 T-TTAATGTTAAAA
1 TATTAATGTTAAAA
5870125 TATTAAT
1 TATTAAT
5870132 TTCATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
TATTAATGTTAAAA
Found at i:5870319 original size:20 final size:20
Alignment explanation
Indices: 5870296--5870333 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5870286 ATTAGGATAA
5870296 AATTATCATAAT-ATTTATAT
1 AATTAT-ATAATAATTTATAT
5870316 AATTATATAATAATTTAT
1 AATTATATAATAATTTAT
5870334 TTTCATATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTATATAATAATTTATAT
Found at i:5874502 original size:30 final size:31
Alignment explanation
Indices: 5874445--5874512 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
5874435 TTGACGTAAT
**
5874445 TATATATATAGACTTTTAAATTATAATTTATA
1 TATATATATAGAAATTTAAATTATAATTTA-A
*
5874477 TATATATATA-AAATTT-AATTTTAATTTAA
1 TATATATATAGAAATTTAAATTATAATTTAA
5874506 T-TATATA
1 TATATATA
5874513 CAATTAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 6 0.18
29 2 0.06
30 11 0.33
31 4 0.12
32 10 0.30
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (31 bp):
TATATATATAGAAATTTAAATTATAATTTAA
Found at i:5875419 original size:39 final size:39
Alignment explanation
Indices: 5875352--5875429 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
5875342 TCTTTTTAAG
* * *
5875352 AAAAGACCTAACAAAATAAATAATTTTGATATTGTTATA
1 AAAAGACCTAACAAAAAAAACAAATTTGATATTGTTATA
* * *
5875391 AAAATACCTAATAAAAAAAACAAATTTGATATTTTTATA
1 AAAAGACCTAACAAAAAAAACAAATTTGATATTGTTATA
5875430 TATAGAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (39 bp):
AAAAGACCTAACAAAAAAAACAAATTTGATATTGTTATA
Found at i:5875711 original size:13 final size:13
Alignment explanation
Indices: 5875693--5875719 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5875683 AATACTTATT
5875693 TGAATTTATCATA
1 TGAATTTATCATA
5875706 TGAATTTATCATA
1 TGAATTTATCATA
5875719 T
1 T
5875720 TGATGAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
TGAATTTATCATA
Found at i:5879659 original size:181 final size:180
Alignment explanation
Indices: 5879343--5879877 Score: 993
Period size: 181 Copynumber: 3.0 Consensus size: 180
5879333 TCAGTATAAT
* *
5879343 GTTTTACAAATTGTAACATAACCTGCTAGTATGAAACTAGTTTCGGTGTAGAC-A-GTGGTTTTT
1 GTTTTACAAATTGTAACATAATCTGCTAGTATGAAACTAGTATCGGTGTAGACAATGTGGTTTTT
5879406 CAACTCTGATATTATAAAATTTTACCATTAACACTTGGAAAGATCAAGATAAAATTTGTGGGAGT
66 CAACTCTGATATTATAAAATTTTACCATTAACACTTGGAAAGATCAAGATAAAATTTGTGGGAGT
5879471 AAAGATGGCATGTATCCTACAACCACACTACATGTGGAATTAAGCTTGAA
131 AAAGATGGCATGTATCCTACAACCACACTACATGTGGAATTAAGCTTGAA
*
5879521 GTTTTACAAATTGTAACATAATCTGCTAGTATGAAGCTAGTATCGGTGTAGACAATGTGGTTTTT
1 GTTTTACAAATTGTAACATAATCTGCTAGTATGAAACTAGTATCGGTGTAGACAATGTGGTTTTT
5879586 CAACTCTGATATTATAAAATTTTACCATTTAACACTTGGAAAGATCAAGATAAAATTTGTGGGAG
66 CAACTCTGATATTATAAAATTTTACCA-TTAACACTTGGAAAGATCAAGATAAAATTTGTGGGAG
5879651 TAAAGATGGCATGTATCCTACAACCACACTACATGTGGAATTAAGCTTGAA
130 TAAAGATGGCATGTATCCTACAACCACACTACATGTGGAATTAAGCTTGAA
*
5879702 GTTTTACAAATTGTAACATAATCTGCTAGTATGAAACTAGTATCGGTGTAGACAGTGTGGTTTTT
1 GTTTTACAAATTGTAACATAATCTGCTAGTATGAAACTAGTATCGGTGTAGACAATGTGGTTTTT
*
5879767 CAACTCTGATATTATAAAATTTTACCATTAACACTCGGAAAGATCAAGATAAAATTTGTGGGAGT
66 CAACTCTGATATTATAAAATTTTACCATTAACACTTGGAAAGATCAAGATAAAATTTGTGGGAGT
*
5879832 AAAGATGGCATGTATCCTACAGCCACACTACATGTGGAATTAAGCT
131 AAAGATGGCATGTATCCTACAACCACACTACATGTGGAATTAAGCT
5879878 CGAAATCTCC
Statistics
Matches: 347, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
178 50 0.14
179 1 0.00
180 118 0.34
181 178 0.51
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.32
Consensus pattern (180 bp):
GTTTTACAAATTGTAACATAATCTGCTAGTATGAAACTAGTATCGGTGTAGACAATGTGGTTTTT
CAACTCTGATATTATAAAATTTTACCATTAACACTTGGAAAGATCAAGATAAAATTTGTGGGAGT
AAAGATGGCATGTATCCTACAACCACACTACATGTGGAATTAAGCTTGAA
Found at i:5884971 original size:2 final size:2
Alignment explanation
Indices: 5884964--5885001 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5884954 CTATTGAATA
5884964 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5885002 TTAACGCTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5885304 original size:19 final size:21
Alignment explanation
Indices: 5885280--5885318 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5885270 TATTGTACGC
5885280 TATAAA-AAT-TTTAAAATTA
1 TATAAATAATGTTTAAAATTA
*
5885299 TATAAATATTGTTTAAAATT
1 TATAAATAATGTTTAAAATT
5885319 TGAATAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (21 bp):
TATAAATAATGTTTAAAATTA
Found at i:5887041 original size:23 final size:21
Alignment explanation
Indices: 5887015--5887056 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
5887005 TATAAAATTT
5887015 AAATTAATTATTATACTTTTTTG
1 AAATTAATTATT-TA-TTTTTTG
*
5887038 AAATTATTTATTTATTTTT
1 AAATTAATTATTTATTTTT
5887057 ATATATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 2 0.11
23 11 0.61
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
AAATTAATTATTTATTTTTTG
Found at i:5887081 original size:56 final size:49
Alignment explanation
Indices: 5887012--5887173 Score: 162
Period size: 56 Copynumber: 3.1 Consensus size: 49
5887002 TAATATAAAA
*
5887012 TTTAAATTAATTATTATACTTTTTTGAAATTATTTATTTATTTTTATATAT
1 TTTAAATTTATTATTATA-TTTTTTGAAA-TATTTATTTATTTTTATATAT
* *
5887063 TTTAAATTTTATATATTATTATTTCTTGTCACTAATATTTTTTTATTTTTATATATT
1 TTTAAA-TTTAT-TATTA-TATTT-TT-TGA--AATATTTATTTATTTTTATATA-T
* * *
5887120 TCTTAAATTTATTATTATATTTTTTGAAAATATTTATATAATTATATATAT
1 T-TTAAATTTATTATTATATTTTTTG-AAATATTTATTTATTTTTATATAT
5887171 TTT
1 TTT
5887174 TATTTCTTTT
Statistics
Matches: 93, Mismatches: 8, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
50 2 0.02
51 8 0.09
52 22 0.24
53 9 0.10
54 7 0.08
55 7 0.08
56 24 0.26
57 9 0.10
58 5 0.05
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (49 bp):
TTTAAATTTATTATTATATTTTTTGAAATATTTATTTATTTTTATATAT
Found at i:5888873 original size:36 final size:36
Alignment explanation
Indices: 5888826--5888899 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
5888816 CATAAGCTGT
5888826 CTTTGGTTAAATGGTCAGATTGTTGTCAACCTCTCA
1 CTTTGGTTAAATGGTCAGATTGTTGTCAACCTCTCA
5888862 CTTTGGTTAAATGGTCAGATTGTTGTCAACCTCTCA
1 CTTTGGTTAAATGGTCAGATTGTTGTCAACCTCTCA
5888898 CT
1 CT
5888900 AATGGTGGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (36 bp):
CTTTGGTTAAATGGTCAGATTGTTGTCAACCTCTCA
Found at i:5908554 original size:17 final size:17
Alignment explanation
Indices: 5908532--5908565 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5908522 TAAAAGAACT
5908532 TGTTAATATTTAAATAA
1 TGTTAATATTTAAATAA
5908549 TGTTAATATTTAAATAA
1 TGTTAATATTTAAATAA
5908566 AATATATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
TGTTAATATTTAAATAA
Found at i:5915507 original size:63 final size:63
Alignment explanation
Indices: 5915429--5915554 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
5915419 TTAAGAAAGA
5915429 ACTATCAGATTTTCTAAAAGAAGCAACAGTTACTTACATAGAGAGCTATTTGCAAGCACTGTG
1 ACTATCAGATTTTCTAAAAGAAGCAACAGTTACTTACATAGAGAGCTATTTGCAAGCACTGTG
5915492 ACTATCAGATTTTCTAAAAGAAGCAACAGTTACTTACATAGAGAGCTATTTGCAAGCACTGTG
1 ACTATCAGATTTTCTAAAAGAAGCAACAGTTACTTACATAGAGAGCTATTTGCAAGCACTGTG
5915555 TGACTTCTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (63 bp):
ACTATCAGATTTTCTAAAAGAAGCAACAGTTACTTACATAGAGAGCTATTTGCAAGCACTGTG
Found at i:5931230 original size:25 final size:26
Alignment explanation
Indices: 5931158--5931232 Score: 100
Period size: 26 Copynumber: 2.9 Consensus size: 26
5931148 TCCCAGTTAT
* *
5931158 ATGGTTTTTCGTGAGCTTCCAGATTA
1 ATGGCTTTTCGTGAGCTTCCTGATTA
*
5931184 AAGGCTCTTT-GTGAGCTTCCTGATTA
1 ATGGCT-TTTCGTGAGCTTCCTGATTA
5931210 ATGGCTTTTCG-GAGCTTCCTGAT
1 ATGGCTTTTCGTGAGCTTCCTGAT
5931233 ATGGCTCGCT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
25 15 0.35
26 25 0.58
27 3 0.07
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (26 bp):
ATGGCTTTTCGTGAGCTTCCTGATTA
Found at i:5931313 original size:24 final size:26
Alignment explanation
Indices: 5931283--5931356 Score: 86
Period size: 24 Copynumber: 3.0 Consensus size: 26
5931273 TTTCCTATTA
*
5931283 ATGGCTCTTCA-GAGCTACTTGTTAT
1 ATGGCTCTTCATGAGCTTCTTGTTAT
* *
5931308 A-GGCTC-GCATGAGCTTCTTG-AAT
1 ATGGCTCTTCATGAGCTTCTTGTTAT
5931331 ATGGCTCTT-ATGAGCTTCTTGTTAT
1 ATGGCTCTTCATGAGCTTCTTGTTAT
5931356 A
1 A
5931357 CAGCCCGGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
23 5 0.12
24 31 0.77
25 4 0.10
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (26 bp):
ATGGCTCTTCATGAGCTTCTTGTTAT
Found at i:5931346 original size:73 final size:73
Alignment explanation
Indices: 5931186--5931347 Score: 159
Period size: 73 Copynumber: 2.2 Consensus size: 73
5931176 CCAGATTAAA
* * * *
5931186 GGCTCTTTGTGAGC-TTCCTGATTAATGGCTTTTCGGAGCTTCCTGATATGGCTCGCTTGAACTT
1 GGCTC-TT-TGAGCTTTCCTGATTAATGGCTCTTCAGAGCTACCTGATATGGCTCGCATGAACTT
5931250 CCTGATATAT
64 CCTGATATAT
* * * * * *
5931260 CGCTATCTGGAGCTTTCCT-ATTAATGGCTCTTCAGAGCTACTTGTTATAGGCTCGCATGAGCTT
1 GGCTCT-TTGAGCTTTCCTGATTAATGGCTCTTCAGAGCTACCTGATAT-GGCTCGCATGAACTT
*
5931324 CTTGA-ATAT
64 CCTGATATAT
5931333 GGCTCTTATGAGCTT
1 GGCTCTT-TGAGCTT
5931348 CTTGTTATAC
Statistics
Matches: 70, Mismatches: 14, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
72 1 0.01
73 43 0.61
74 26 0.37
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (73 bp):
GGCTCTTTGAGCTTTCCTGATTAATGGCTCTTCAGAGCTACCTGATATGGCTCGCATGAACTTCC
TGATATAT
Found at i:5938744 original size:46 final size:46
Alignment explanation
Indices: 5938692--5938912 Score: 173
Period size: 46 Copynumber: 4.8 Consensus size: 46
5938682 TATTTGGGTT
* * *
5938692 TCTGAACTCGTTGAGTTGATTCTGATTTCACTTATGGATGCGAACA
1 TCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACA
* **
5938738 TCTGAACACGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACA
* * * * * * *
5938784 TCCGAGCTCGTTGAGTTGGGTCCAAGTTC-GTGA--GATG-TAACTAGGTA
1 TCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC-----A
* * * *
5938831 TCCGAGCTTGTTGAG-TGAGTCCGAGTTCACTTATGGATGTGAACA
1 TCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACA
* * * *
5938876 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5938913 GAGGGTTACA
Statistics
Matches: 140, Mismatches: 25, Indels: 20
0.76 0.14 0.11
Matches are distributed among these distances:
42 2 0.01
43 4 0.03
45 16 0.11
46 95 0.68
47 16 0.11
49 4 0.03
50 3 0.02
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.32
Consensus pattern (46 bp):
TCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACA
Found at i:5941928 original size:15 final size:15
Alignment explanation
Indices: 5941908--5941972 Score: 71
Period size: 15 Copynumber: 4.4 Consensus size: 15
5941898 GTATCTTGGG
5941908 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
5941923 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
* *
5941938 TTTC-TCAATCTTGGA
1 TTTCTTTATTC-TGGA
*
5941953 TTTCTTTATTC-GGC
1 TTTCTTTATTCTGGA
5941967 TTTCTT
1 TTTCTT
5941973 GTTATCTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
14 12 0.29
15 25 0.61
16 4 0.10
ACGTcount: A:0.11, C:0.17, G:0.14, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:5941940 original size:30 final size:31
Alignment explanation
Indices: 5941904--5941972 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
5941894 TATCGTATCT
* *
5941904 TGGGTTTCTTTATTC-TGGATTTCTTTATTC
1 TGGGTTTCTTCAATCTTGGATTTCTTTATTC
5941934 TGGGTTTC-TCAATCTTGGATTTCTTTATTC
1 TGGGTTTCTTCAATCTTGGATTTCTTTATTC
*
5941964 -GGCTTTCTT
1 TGGGTTTCTT
5941973 GTTATCTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.29
30 24 0.71
ACGTcount: A:0.10, C:0.16, G:0.17, T:0.57
Consensus pattern (31 bp):
TGGGTTTCTTCAATCTTGGATTTCTTTATTC
Found at i:5945006 original size:43 final size:43
Alignment explanation
Indices: 5944945--5945107 Score: 290
Period size: 43 Copynumber: 3.8 Consensus size: 43
5944935 GCTGGTATTA
*
5944945 TATTCGGGCCTTCGTGCCTAGTAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
5944988 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
* *
5945031 TATTCAGGCCTTCGTGCCTAGCAGGCTTCGTGTCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
*
5945074 TATTCGGCCCTTCGTGCCTAGCAGGCTTCGTGCC
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCC
5945108 TAGCAGGCTT
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 114 1.00
ACGTcount: A:0.10, C:0.26, G:0.33, T:0.31
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
Found at i:5945104 original size:16 final size:16
Alignment explanation
Indices: 5945083--5945123 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
5945073 GTATTCGGCC
5945083 CTTCGTGCCTAGCAGG
1 CTTCGTGCCTAGCAGG
5945099 CTTCGTGCCTAGCAGG
1 CTTCGTGCCTAGCAGG
5945115 CTTCGTGCC
1 CTTCGTGCC
5945124 AGTGATGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.10, C:0.34, G:0.29, T:0.27
Consensus pattern (16 bp):
CTTCGTGCCTAGCAGG
Found at i:5945105 original size:59 final size:58
Alignment explanation
Indices: 5945035--5945157 Score: 210
Period size: 59 Copynumber: 2.1 Consensus size: 58
5945025 GATGTGTATT
* *
5945035 CAGGCCTTCGTGCCTAGCAGGCTTCGTGTCGGTGATGTGTATTCGGCCCTTCGTGCCTAG
1 CAGG-CTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTGTATTCGG-CCTTCGTGCCTAG
5945095 CAGGCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTGTATTCGGCCTTCGTGCCTAG
1 CAGGCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTGTATTCGGCCTTCGTGCCTAG
5945153 CAGGC
1 CAGGC
5945158 GTAATGCTGG
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
58 18 0.30
59 39 0.64
60 4 0.07
ACGTcount: A:0.11, C:0.28, G:0.32, T:0.28
Consensus pattern (58 bp):
CAGGCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTGTATTCGGCCTTCGTGCCTAG
Found at i:5950073 original size:46 final size:50
Alignment explanation
Indices: 5950001--5950105 Score: 146
Period size: 46 Copynumber: 2.2 Consensus size: 50
5949991 GACAGGACAG
* * *
5950001 GACAGAAATGAGCCATGTAAGTCCATA-T-CA-A-ATATATGGCTTTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATTACATATATATATGGCATTGGA
*
5950047 GACAGGAATGAGCCATGTAAGCCCATATTAGATATATATATGGCATTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATTACATATATATATGGCATTGGA
5950097 GACAGGAAT
1 GACAGGAAT
5950106 AATTCATGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
46 25 0.49
47 1 0.02
48 1 0.02
49 1 0.02
50 23 0.45
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (50 bp):
GACAGGAATGAGCCATGTAAGCCCATATTACATATATATATGGCATTGGA
Found at i:5951583 original size:46 final size:46
Alignment explanation
Indices: 5951531--5951754 Score: 204
Period size: 46 Copynumber: 4.8 Consensus size: 46
5951521 GATATTTGGG
* *
5951531 CATCCGAACTCGTTGAGTTGAGTCTGATTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAA
5951577 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAA
1 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAA
** * * * * * *
5951623 TGTCCGAGCTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGTAACTA
1 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAA--A
* * * * *
5951668 GGTATCCGAGCTCGTTGAGTTGAGTCAGTGTTCACTTATGGATGCGAA
1 --CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAA
* * * *
5951716 C-GCTCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CATC-CGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGG
5951755 GCGGGTTACA
Statistics
Matches: 147, Mismatches: 23, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
43 5 0.03
45 4 0.03
46 103 0.70
47 28 0.19
48 3 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.31
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAA
Found at i:5951692 original size:93 final size:93
Alignment explanation
Indices: 5951578--5951747 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
5951568 GGATGCGAAC
* *
5951578 ATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATG-TCCGAGCTCGTTGAGTT
1 ATCCGAACTCGTTGAGTTGAGTCAGAGTTCACTTATGGATGCAAACGCT-CGAGCTCGTTGAGTT
5951642 GAGTCCGAGTTCGTGAAATGTAACTAGGT
65 GAGTCCGAGTTCGTGAAATGTAACTAGGT
* * *
5951671 ATCCGAGCTCGTTGAGTTGAGTCAGTGTTCACTTATGGATGCGAACGCTCGAGCTCGTTGAGTTG
1 ATCCGAACTCGTTGAGTTGAGTCAGAGTTCACTTATGGATGCAAACGCTCGAGCTCGTTGAGTTG
5951736 AGTCCGAGTTCG
66 AGTCCGAGTTCG
5951748 CTTATGGGCG
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
93 70 0.99
94 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (93 bp):
ATCCGAACTCGTTGAGTTGAGTCAGAGTTCACTTATGGATGCAAACGCTCGAGCTCGTTGAGTTG
AGTCCGAGTTCGTGAAATGTAACTAGGT
Found at i:5956632 original size:4 final size:4
Alignment explanation
Indices: 5956623--5956655 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
5956613 GAGTAAGTTA
*
5956623 AAAG AAAG AAAG AAAG AAAG AAAG ATAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
5956656 GTTACAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:5957521 original size:47 final size:47
Alignment explanation
Indices: 5957457--5957567 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
5957447 GACATTGAGT
* *
5957457 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGAATTTGTTC
* * *
5957504 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGAATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGAATTTGTTC
5957551 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
5957568 CTTATCCCGG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 51 0.93
48 4 0.07
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGAATTTGTTC
Found at i:5964460 original size:182 final size:182
Alignment explanation
Indices: 5964109--5964481 Score: 693
Period size: 183 Copynumber: 2.1 Consensus size: 182
5964099 TAGAGCTCAA
5964109 AATT-TATG-TTTTATAATGAATTTTATGAGTTAGAAATTGTTAATGAGTTGATTAAAAGAGAAT
1 AATTGTATGATTTTATAATGAATTTTATGAGTTAGAAATTGTTAATGAGTTGATTAAAAGAGAAT
5964172 ATGAAGCTTAAGTTAAAGAAAAAAGATTAGTAATGGAAAAAGGACGAAATTGGAATTTTTGTAAA
66 ATGAAGCTTAAGTTAAAGAAAAAAGATTAGTAATGGAAAAAGGACGAAATTGGAATTTTTGTAAA
5964237 AGTTTGATAGAAAGTGAAAATGTGTTTTATGAATTAGTATATTGATGATTTTT
131 AGTTTGATAGAAAGTGAAAATGTGTTTTATGAATTAGTATATT-ATGATTTTT
5964290 AATTGTATGATTTTATAATGAATTTTATGAGTTAGAAATTGTTAA-GAGTTGATTAAAAGAGAAT
1 AATTGTATGATTTTATAATGAATTTTATGAGTTAGAAATTGTTAATGAGTTGATTAAAAGAGAAT
5964354 ATGAAGCTTAAGTTAAAGAAAAAAGAATTAGTAATGGAAAAAGGACGAAATTGGAATTTTTGTAA
66 ATGAAGCTTAAGTTAAAGAAAAAAG-ATTAGTAATGGAAAAAGGACGAAATTGGAATTTTTGTAA
5964419 AAGTTTGATAGAAAGTGAAAATGTG-TTTATGAATTAGTATATTATGATTTTT
130 AAGTTTGATAGAAAGTGAAAATGTGTTTTATGAATTAGTATATTATGATTTTT
5964471 AA-TGTATGATT
1 AATTGTATGATT
5964482 GTTAGTAGCA
Statistics
Matches: 189, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
180 9 0.05
181 15 0.08
182 66 0.35
183 99 0.52
ACGTcount: A:0.42, C:0.01, G:0.20, T:0.37
Consensus pattern (182 bp):
AATTGTATGATTTTATAATGAATTTTATGAGTTAGAAATTGTTAATGAGTTGATTAAAAGAGAAT
ATGAAGCTTAAGTTAAAGAAAAAAGATTAGTAATGGAAAAAGGACGAAATTGGAATTTTTGTAAA
AGTTTGATAGAAAGTGAAAATGTGTTTTATGAATTAGTATATTATGATTTTT
Found at i:5969390 original size:44 final size:44
Alignment explanation
Indices: 5969340--5969506 Score: 208
Period size: 47 Copynumber: 3.6 Consensus size: 44
5969330 TTTGAGTACT
5969340 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
5969384 TCTGATCAATGACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTA
1 TCTG----AT--C-AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
5969435 TCTGATCAGTGACAAGTGATAATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTG---ATAAGTGGTAGCTTTAGCTACACTTA
* *
5969482 TTTGATCAATGACAAGTGATAAGTG
1 TCTGATCAGTGACAAGTGATAAGTG
5969507 ATAAGTGGTA
Statistics
Matches: 107, Mismatches: 6, Indels: 20
0.80 0.05 0.15
Matches are distributed among these distances:
44 21 0.20
45 1 0.01
47 43 0.40
48 2 0.02
50 1 0.01
51 39 0.36
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.32
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:5969425 original size:51 final size:51
Alignment explanation
Indices: 5969347--5969555 Score: 302
Period size: 51 Copynumber: 4.2 Consensus size: 51
5969337 ACTTCTGATC
*
5969347 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACA
* *
5969398 AGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACA
*
5969449 AGTGAT-A---ATAAGTGGTAGCTTTAGCTACACTTATTTGATCAATGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACA
* * *
5969496 AGTGATAAGTGATAAGTGGTAAG-TGGTAGTTACACTTATCTGATCAGTGACA
1 AGTGATAAGTGATAAGTGGT-AGCT-TTAGCTACACTTATCTGATCAATGACA
5969548 AGTGATAA
1 AGTGATAA
5969556 ATGTGATCAG
Statistics
Matches: 142, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
47 43 0.30
48 1 0.01
50 1 0.01
51 64 0.45
52 33 0.23
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (51 bp):
AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACA
Found at i:5969478 original size:47 final size:46
Alignment explanation
Indices: 5969409--5969555 Score: 186
Period size: 47 Copynumber: 3.0 Consensus size: 46
5969399 GTGATAAGTG
5969409 ATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACAAGTGATA
1 ATAAGTGGTAG-TTTAGCTACACTTATCTGATCAGTGACAAGTGATA
* *
5969456 ATAAGTGGTAGCTTTAGCTACACTTATTTGATCAATGACAAGTGATAA
1 ATAAGTGGTAG-TTTAGCTACACTTATCTGATCAGTGACAAGTGAT-A
* *
5969504 GTGATAAGTGGTAAGTGGTAGTTACACTTATCTGATCAGTGACAAGTGATA
1 ---ATAAGTGGT-AGT-TTAGCTACACTTATCTGATCAGTGACAAGTGATA
5969555 A
1 A
5969556 ATGTGATCAG
Statistics
Matches: 87, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
47 43 0.49
48 2 0.02
51 11 0.13
52 31 0.36
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (46 bp):
ATAAGTGGTAGTTTAGCTACACTTATCTGATCAGTGACAAGTGATA
Found at i:5969506 original size:98 final size:99
Alignment explanation
Indices: 5969340--5969555 Score: 368
Period size: 98 Copynumber: 2.2 Consensus size: 99
5969330 TTTGAGTACT
5969340 TCTGATCAGTGACAAGTG---ATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAAGTG
1 TCTGATCAGTGACAAGTGATAATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAAGTG
**
5969402 ATAAGTGATAAGTGGT-AGTTTTAGCTACACTTA
66 ATAAGTGATAAGTGGTAAGTGGTAGCTACACTTA
*
5969435 TCTGATCAGTGACAAGTGATAATAAGTGGTAGCTTTAGCTACACTTATTTGATCAATGACAAGTG
1 TCTGATCAGTGACAAGTGATAATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAAGTG
*
5969500 ATAAGTGATAAGTGGTAAGTGGTAGTTACACTTA
66 ATAAGTGATAAGTGGTAAGTGGTAGCTACACTTA
5969534 TCTGATCAGTGACAAGTGATAA
1 TCTGATCAGTGACAAGTGATAA
5969556 ATGTGATCAG
Statistics
Matches: 113, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
95 18 0.16
98 59 0.52
99 36 0.32
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (99 bp):
TCTGATCAGTGACAAGTGATAATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACAAGTG
ATAAGTGATAAGTGGTAAGTGGTAGCTACACTTA
Found at i:5982640 original size:20 final size:20
Alignment explanation
Indices: 5982615--5982659 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
5982605 TGAAGTTTAG
*
5982615 TTTTAACAAT-ATATATTAAT
1 TTTTAA-AATGATAAATTAAT
5982635 TTTTAAAATGATAAATTAAT
1 TTTTAAAATGATAAATTAAT
5982655 TTTTA
1 TTTTA
5982660 TACGATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTTAAAATGATAAATTAAT
Found at i:5982751 original size:10 final size:10
Alignment explanation
Indices: 5982736--5982764 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5982726 AATATTAATT
5982736 GTATGAAAAA
1 GTATGAAAAA
5982746 GTATGAAAAA
1 GTATGAAAAA
5982756 GTAT-AAAAA
1 GTATGAAAAA
5982765 CACTTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.21
Consensus pattern (10 bp):
GTATGAAAAA
Found at i:5989148 original size:17 final size:17
Alignment explanation
Indices: 5989128--5989175 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
5989118 TAAACTATTT
5989128 AAATATTTAAATATAAA
1 AAATATTTAAATATAAA
*
5989145 AAATA--TAAAAATAAA
1 AAATATTTAAATATAAA
* *
5989160 AAACATTTTAATATAA
1 AAATATTTAAATATAA
5989176 TTATATTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 13 0.52
17 12 0.48
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATATTTAAATATAAA
Found at i:5989227 original size:37 final size:37
Alignment explanation
Indices: 5989166--5989238 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
5989156 TAAAAAACAT
5989166 TTTAATATAATTATATTAAGAATATTA-TTAAATTATA
1 TTTAATATAATTATATTAAGAATA-TAGTTAAATTATA
5989203 TTTAATAATAATTATATTAA-AATATAGTTAAATTAT
1 TTTAAT-ATAATTATATTAAGAATATAGTTAAATTAT
5989239 TTATTTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
36 2 0.06
37 19 0.56
38 13 0.38
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (37 bp):
TTTAATATAATTATATTAAGAATATAGTTAAATTATA
Found at i:5989433 original size:13 final size:13
Alignment explanation
Indices: 5989415--5989443 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5989405 ATTCAATTAC
5989415 ATTCAACTAAATA
1 ATTCAACTAAATA
5989428 ATTCAACTAAATA
1 ATTCAACTAAATA
5989441 ATT
1 ATT
5989444 AAATTACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (13 bp):
ATTCAACTAAATA
Found at i:6002193 original size:13 final size:13
Alignment explanation
Indices: 6002171--6002206 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
6002161 TCTCGAGGAC
6002171 AAAAAA-AAAAAA
1 AAAAAAGAAAAAA
6002183 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
*
6002196 GAAAAAGAAAA
1 AAAAAAGAAAA
6002207 GGACAATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:6011471 original size:21 final size:20
Alignment explanation
Indices: 6011433--6011470 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6011423 CGCCCCACAT
6011433 CATTTTAATTTAATTTTTGC
1 CATTTTAATTTAATTTTTGC
*
6011453 CA-TTTATATTTTATTTTT
1 CATTTTA-ATTTAATTTTT
6011471 TTCAATCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (20 bp):
CATTTTAATTTAATTTTTGC
Found at i:6017586 original size:26 final size:26
Alignment explanation
Indices: 6017537--6017586 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
6017527 CCCATTTTTT
*
6017537 AATAAATTTATTTAATTAATAATTAA
1 AATAAATTCATTTAATTAATAATTAA
*
6017563 AATAAATTACATTTACTTAA-AATT
1 AATAAATT-CATTTAATTAATAATT
6017587 TTGTGAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
AATAAATTCATTTAATTAATAATTAA
Found at i:6021329 original size:26 final size:26
Alignment explanation
Indices: 6021280--6021329 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
6021270 CCCATTTTTT
*
6021280 AATAAATTTATTTAATTAATAATTAA
1 AATAAATTCATTTAATTAATAATTAA
*
6021306 AATAAATTACATTTACTTAA-AATT
1 AATAAATT-CATTTAATTAATAATT
6021330 TTGTGAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
AATAAATTCATTTAATTAATAATTAA
Found at i:6025071 original size:26 final size:26
Alignment explanation
Indices: 6025022--6025071 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
6025012 CCCATTTTTT
*
6025022 AATAAATTTATTTAATTAATAATTAA
1 AATAAATTCATTTAATTAATAATTAA
*
6025048 AATAAATTACATTTACTTAA-AATT
1 AATAAATT-CATTTAATTAATAATT
6025072 TTGTGAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
AATAAATTCATTTAATTAATAATTAA
Found at i:6028812 original size:26 final size:26
Alignment explanation
Indices: 6028763--6028812 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
6028753 CCCATTTTTT
*
6028763 AATAAATTTATTTAATTAATAATTAA
1 AATAAATTCATTTAATTAATAATTAA
*
6028789 AATAAATTACATTTACTTAA-AATT
1 AATAAATT-CATTTAATTAATAATT
6028813 TTGTGAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
AATAAATTCATTTAATTAATAATTAA
Found at i:6032538 original size:26 final size:26
Alignment explanation
Indices: 6032489--6032538 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
6032479 CCCATTTTTT
*
6032489 AATAAATTTATTTAATTAATAATTAA
1 AATAAATTCATTTAATTAATAATTAA
*
6032515 AATAAATTACATTTACTTAA-AATT
1 AATAAATT-CATTTAATTAATAATT
6032539 TTGTGAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
AATAAATTCATTTAATTAATAATTAA
Found at i:6036021 original size:2 final size:2
Alignment explanation
Indices: 6036014--6036048 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
6036004 CTCCAATGCC
6036014 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6036049 GGGCTTACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6036336 original size:21 final size:21
Alignment explanation
Indices: 6036306--6036349 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
6036296 ACTGTAAACT
*
6036306 TACCTTGATACAAAATGTGAC
1 TACCTCGATACAAAATGTGAC
6036327 TACCTCGATACAAAATGTGAC
1 TACCTCGATACAAAATGTGAC
6036348 TA
1 TA
6036350 AACTTTACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (21 bp):
TACCTCGATACAAAATGTGAC
Found at i:6038648 original size:19 final size:20
Alignment explanation
Indices: 6038624--6038661 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
6038614 GGTACCACCA
6038624 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
6038643 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
6038662 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:6039003 original size:47 final size:43
Alignment explanation
Indices: 6038891--6039058 Score: 160
Period size: 44 Copynumber: 3.7 Consensus size: 43
6038881 GCCCCTAAGT
* * * * *
6038891 GAACTCGGACTCAACTCAACGAG-CCGGGCGTTCGCATCCATAAAT
1 GAACTCGGACTCAACTCAACGAGTTC-GG-ATGCGCATACAT-AAC
*
6038936 GAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCGC-A--TACA--TAAC
* * *
6038983 GAACTCGGACTCAACTCAACGAGTTCGGCATTCGCATCCATAAT
1 GAACTCGGACTCAACTCAACGAGTTCGG-ATGCGCATACATAAC
6039027 GAACTCGGACTCAACTCAACGAGTTCGGATGC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGC
6039059 TCAACCATCC
Statistics
Matches: 104, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
43 4 0.04
44 33 0.32
45 25 0.24
46 7 0.07
47 29 0.28
48 5 0.05
49 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (43 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCGCATACATAAC
Found at i:6039005 original size:92 final size:91
Alignment explanation
Indices: 6038891--6039058 Score: 293
Period size: 92 Copynumber: 1.8 Consensus size: 91
6038881 GCCCCTAAGT
*
6038891 GAACTCGGACTCAACTCAACGAG-CCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTCC-GGCATTCGCATCCAT-AATGAACTCGGACTCAACTCAA
6038955 CGAGTTCGGATGCCTAGTTACATCTCAC
64 CGAGTTCGGATGCCTAGTTACATCTCAC
*
6038983 GAACTCGGACTCAACTCAACGAGTTCGGCATTCGCATCCATAATGAACTCGGACTCAACTCAACG
1 GAACTCGGACTCAACTCAACGAGTCCGGCATTCGCATCCATAATGAACTCGGACTCAACTCAACG
6039048 AGTTCGGATGC
66 AGTTCGGATGC
6039059 TCAACCATCC
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
91 35 0.48
92 37 0.51
93 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (91 bp):
GAACTCGGACTCAACTCAACGAGTCCGGCATTCGCATCCATAATGAACTCGGACTCAACTCAACG
AGTTCGGATGCCTAGTTACATCTCAC
Found at i:6039513 original size:14 final size:14
Alignment explanation
Indices: 6039494--6039545 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
6039484 AAACAATTAC
6039494 ACTTTTGCCCCTAA
1 ACTTTTGCCCCTAA
*** *
6039508 ACTTTTGCATAATTAC
1 ACTTTTGC--CCCTAA
6039524 ACTTTTGCCCCTAA
1 ACTTTTGCCCCTAA
6039538 ACTTTTGC
1 ACTTTTGC
6039546 ATAATTACAC
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
14 18 0.64
16 10 0.36
ACGTcount: A:0.23, C:0.29, G:0.08, T:0.40
Consensus pattern (14 bp):
ACTTTTGCCCCTAA
Found at i:6039523 original size:30 final size:30
Alignment explanation
Indices: 6039488--6039566 Score: 158
Period size: 30 Copynumber: 2.6 Consensus size: 30
6039478 CTTTAAAAAC
6039488 AATTACACTTTTGCCCCTAAACTTTTGCAT
1 AATTACACTTTTGCCCCTAAACTTTTGCAT
6039518 AATTACACTTTTGCCCCTAAACTTTTGCAT
1 AATTACACTTTTGCCCCTAAACTTTTGCAT
6039548 AATTACACTTTTGCCCCTA
1 AATTACACTTTTGCCCCTA
6039567 GGCTCAGGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.27, C:0.28, G:0.06, T:0.39
Consensus pattern (30 bp):
AATTACACTTTTGCCCCTAAACTTTTGCAT
Found at i:6039529 original size:16 final size:16
Alignment explanation
Indices: 6039508--6039561 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
6039498 TTGCCCCTAA
6039508 ACTTTTGCATAATTAC
1 ACTTTTGCATAATTAC
*** *
6039524 ACTTTTGC--CCCTAA
1 ACTTTTGCATAATTAC
6039538 ACTTTTGCATAATTAC
1 ACTTTTGCATAATTAC
6039554 ACTTTTGC
1 ACTTTTGC
6039562 CCCTAGGCTC
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
14 10 0.36
16 18 0.64
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (16 bp):
ACTTTTGCATAATTAC
Found at i:6042295 original size:25 final size:25
Alignment explanation
Indices: 6042271--6042318 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
6042261 ATGTGGAATA
*
6042271 ATGTATAGAATACA-ATATTAAAAT
1 ATGTACAGAATACACATATTAAAAT
* *
6042295 ATTTACATAATACACATATTAAAA
1 ATGTACAGAATACACATATTAAAA
6042319 ATAACTAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.33
Consensus pattern (25 bp):
ATGTACAGAATACACATATTAAAAT
Found at i:6042329 original size:25 final size:24
Alignment explanation
Indices: 6042279--6042331 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
6042269 TAATGTATAG
**
6042279 AATACAATATTAAAATATTTACAT
1 AATACAATATTAAAATAACTACAT
6042303 AATACACATATTAAAAATAACTA-AT
1 AATACA-ATATT-AAAATAACTACAT
6042328 AATA
1 AATA
6042332 ATATTCCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.24
25 11 0.44
26 8 0.32
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.32
Consensus pattern (24 bp):
AATACAATATTAAAATAACTACAT
Found at i:6043090 original size:21 final size:21
Alignment explanation
Indices: 6043064--6043104 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6043054 GAAAAGGTAA
*
6043064 TTTTTTTATTTTTTATTTCTC
1 TTTTTTTACTTTTTATTTCTC
*
6043085 TTTTTTTGCTTTTTATTTCT
1 TTTTTTTACTTTTTATTTCT
6043105 TTATGTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTTTTACTTTTTATTTCTC
Found at i:6061896 original size:15 final size:15
Alignment explanation
Indices: 6061876--6061931 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
6061866 AAAAATGTTT
6061876 TTTAATATTTAAATA
1 TTTAATATTTAAATA
* *
6061891 TTTAATATTATAATTT
1 TTTAATATT-TAAATA
* *
6061907 TTTATTTTTTAAA-A
1 TTTAATATTTAAATA
6061921 TTTAA-ATTTAA
1 TTTAATATTTAA
6061932 TGTTTTTATT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
13 5 0.16
14 4 0.12
15 12 0.38
16 11 0.34
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTAATATTTAAATA
Found at i:6061924 original size:30 final size:29
Alignment explanation
Indices: 6061873--6061943 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 29
6061863 GTAAAAAATG
* *
6061873 TTTTTTAATATTTAAATATTTAATATTATAA
1 TTTTTTATTTTTTAAATATTTAA-ATT-TAA
6061904 TTTTTTATTTTTTAAA-ATTTAAATTTAA
1 TTTTTTATTTTTTAAATATTTAAATTTAA
6061932 TGTTTTTATTTT
1 T-TTTTTATTTT
6061944 AATAAATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 4 0.11
29 13 0.35
30 6 0.16
31 14 0.38
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (29 bp):
TTTTTTATTTTTTAAATATTTAAATTTAA
Found at i:6061950 original size:29 final size:30
Alignment explanation
Indices: 6061885--6061955 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
6061875 TTTTAATATT
*
6061885 TAAATATTTAATATTATAATTTTTTATTTTT
1 TAAA-ATTTAATATTATAATTTTTTATTTTA
6061916 TAAAATTTAA-ATT-TAATGTTTTTATTTTA
1 TAAAATTTAATATTATAAT-TTTTTATTTTA
6061945 -ATAAATTTAAT
1 TA-AAATTTAAT
6061956 TGTTAAGTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
28 5 0.14
29 21 0.58
30 6 0.17
31 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (30 bp):
TAAAATTTAATATTATAATTTTTTATTTTA
Found at i:6067113 original size:11 final size:11
Alignment explanation
Indices: 6067097--6067125 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
6067087 GTTCATCTCT
6067097 TTTTGTGATTA
1 TTTTGTGATTA
6067108 TTTTGTGATTA
1 TTTTGTGATTA
6067119 TTTTGTG
1 TTTTGTG
6067126 TTAATCGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.14, C:0.00, G:0.21, T:0.66
Consensus pattern (11 bp):
TTTTGTGATTA
Found at i:6071104 original size:159 final size:160
Alignment explanation
Indices: 6070809--6071122 Score: 549
Period size: 159 Copynumber: 2.0 Consensus size: 160
6070799 CCTGTTTTTC
*
6070809 GTGATCCTGATCCCCTGACACCACCTGCGAACATTATCAAACTCAATCAGCAATTTTTTTTTATT
1 GTGATCCTGATCCCCTGACACCACCTGCGAACATTATCAAACTCAATCAGCAATTTTTTTTTACT
* *
6070874 TTTTTAACTATGATATAACATAAAAAATCAAAAGATCAGAGGAAGAAATCCAAACTAACCTGCGC
66 TTTTTAACTAAGATATAACATAAAAAATCAAAAGATCAGAAGAAGAAATCCAAACTAACCTGCGC
6070939 CCAACTGGATCTGGAGCGTTCATCTCGTTG
131 CCAACTGGATCTGGAGCGTTCATCTCGTTG
*
6070969 GTGATCCTGATCCCCTGACACCGCCTGCGAACATTATCAAACTCAATCAGCAATTTTTTTTT-CT
1 GTGATCCTGATCCCCTGACACCACCTGCGAACATTATCAAACTCAATCAGCAATTTTTTTTTACT
* *
6071033 TTTTTAACTAAGATATAACATAAGAAATCAAAAGATGAGAAGAAGAAATCCAAACTAACCTGCGC
66 TTTTTAACTAAGATATAACATAAAAAATCAAAAGATCAGAAGAAGAAATCCAAACTAACCTGCGC
* *
6071098 CGAACTGGATCTGGGGCGTTCATCT
131 CCAACTGGATCTGGAGCGTTCATCT
6071123 TGAGACTCAT
Statistics
Matches: 146, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
159 85 0.58
160 61 0.42
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (160 bp):
GTGATCCTGATCCCCTGACACCACCTGCGAACATTATCAAACTCAATCAGCAATTTTTTTTTACT
TTTTTAACTAAGATATAACATAAAAAATCAAAAGATCAGAAGAAGAAATCCAAACTAACCTGCGC
CCAACTGGATCTGGAGCGTTCATCTCGTTG
Found at i:6072286 original size:12 final size:12
Alignment explanation
Indices: 6072261--6072302 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
6072251 TATTTTGTCA
*
6072261 TTTTATTTTTTAT
1 TTTTA-TTTGTAT
6072274 TTTTATTTGTAT
1 TTTTATTTGTAT
*
6072286 TTGTATTTGTAT
1 TTTTATTTGTAT
6072298 TTTTA
1 TTTTA
6072303 GTTATGTGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 21 0.81
13 5 0.19
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTATTTGTAT
Found at i:6074480 original size:4 final size:4
Alignment explanation
Indices: 6074473--6074516 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
6074463 TGAACTATTC
* * * *
6074473 ATAT ATAT ATAT ATAT ATAT ATAG ATAG ATAG ATAT ATAG ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
6074517 GTTCTTGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (4 bp):
ATAT
Found at i:6074486 original size:8 final size:8
Alignment explanation
Indices: 6074473--6074516 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
6074463 TGAACTATTC
*
6074473 ATATATAT
1 ATATATAG
*
6074481 ATATATAT
1 ATATATAG
6074489 ATATATAG
1 ATATATAG
*
6074497 ATAGATAG
1 ATATATAG
6074505 ATATATAG
1 ATATATAG
6074513 ATAT
1 ATAT
6074517 GTTCTTGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (8 bp):
ATATATAG
Found at i:6078320 original size:19 final size:20
Alignment explanation
Indices: 6078298--6078336 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
6078288 AAATATTTTT
6078298 AACATAATGATAT-ATATAA
1 AACATAATGATATAATATAA
* *
6078317 AACATATTTATATAATATAA
1 AACATAATGATATAATATAA
6078337 TTACATGCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (20 bp):
AACATAATGATATAATATAA
Found at i:6082518 original size:3 final size:3
Alignment explanation
Indices: 6082510--6082549 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
6082500 TAAATTGACA
6082510 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
6082550 TGAATTTGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6083891 original size:30 final size:30
Alignment explanation
Indices: 6083855--6083912 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
6083845 GTTTTATTGC
* *
6083855 TAATTTTGTTATTATTTTAGAGGCATTTGT
1 TAATTTTGTTATTATTTTAAAGACATTTGT
6083885 TAATTTTGTTATTATTTTAAAGACATTT
1 TAATTTTGTTATTATTTTAAAGACATTT
6083913 ACTTGTTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (30 bp):
TAATTTTGTTATTATTTTAAAGACATTTGT
Found at i:6085400 original size:16 final size:17
Alignment explanation
Indices: 6085379--6085421 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
6085369 CAGCCTTCTT
6085379 TATAACAATCATCT-GA
1 TATAACAATCATCTCGA
* *
6085395 TATAACAA-CATTTCGC
1 TATAACAATCATCTCGA
6085411 TATAACAATCA
1 TATAACAATCA
6085422 AGTTTCTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.17
16 17 0.74
17 2 0.09
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (17 bp):
TATAACAATCATCTCGA
Found at i:6089323 original size:46 final size:46
Alignment explanation
Indices: 6089270--6089445 Score: 182
Period size: 46 Copynumber: 3.8 Consensus size: 46
6089260 TATTTGGGCA
*
6089270 TCCGAACTCGTTGAGTTGCGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
6089316 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
6089361 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
6089409 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
6089446 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 5 0.05
46 59 0.56
47 29 0.27
48 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:6089425 original size:93 final size:93
Alignment explanation
Indices: 6089266--6089438 Score: 294
Period size: 93 Copynumber: 1.9 Consensus size: 93
6089256 GGGATATTTG
* * *
6089266 GGCATCCGAACTCGTTGAGTTGCGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCGAACTCGTTGAG
6089331 TTGAGTCCGAGTTCGTGAAATGTAACTA
66 TTGAGTCCGAGTTCGTGAAATGTAACTA
*
6089359 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACG-CCTGAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCC-GAACTCGTTGA
6089423 GTTGAGTCCGAGTTCG
65 GTTGAGTCCGAGTTCG
6089439 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAAATGTAACTA
Found at i:6091330 original size:2 final size:2
Alignment explanation
Indices: 6091325--6091359 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6091315 TATATATATA
6091325 TG TG 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 TG TG T
6091360 TGAAAATGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:6092961 original size:68 final size:68
Alignment explanation
Indices: 6092852--6092989 Score: 222
Period size: 68 Copynumber: 2.0 Consensus size: 68
6092842 AATTTGACGG
* * *
6092852 TAGTTGTTCCGGCAACGATTGTAACATTTCGTAGCTCAGACCCGGTAATCAGGTCGGGCGAGGGG
1 TAGTTGTTCCGGCAACGATTGTAACATTTAGTAGCTCAGACCCGGCAATCAGGTCGGGCAAGGGG
6092917 TGT
66 TGT
* * *
6092920 TAGTTGTTCTGGCAATGATTGTAACATTTAGTAGCTTAGACCCGGCAATCAGGTCGGGCAAGGGG
1 TAGTTGTTCCGGCAACGATTGTAACATTTAGTAGCTCAGACCCGGCAATCAGGTCGGGCAAGGGG
6092985 TGT
66 TGT
6092988 TA
1 TA
6092990 TAGTCCCTGG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.28
Consensus pattern (68 bp):
TAGTTGTTCCGGCAACGATTGTAACATTTAGTAGCTCAGACCCGGCAATCAGGTCGGGCAAGGGG
TGT
Found at i:6099016 original size:16 final size:17
Alignment explanation
Indices: 6098995--6099026 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
6098985 TCTTTCTTTC
6098995 TTTCTTTT-TTTTTTTT
1 TTTCTTTTGTTTTTTTT
6099011 TTTCTTTTGTTTTTTT
1 TTTCTTTTGTTTTTTT
6099027 GGTGGGCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.91
Consensus pattern (17 bp):
TTTCTTTTGTTTTTTTT
Found at i:6102799 original size:31 final size:31
Alignment explanation
Indices: 6102735--6102800 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
6102725 TTAGTCATTT
* * * ***
6102735 TATTATTTGTAAATTGTATATTTAATTTTTA
1 TATTATATGTAAATTATAGATTTAATCACTA
6102766 TATTATATGTAAATTATAGATTTAATCACTA
1 TATTATATGTAAATTATAGATTTAATCACTA
6102797 TATT
1 TATT
6102801 TTTAAAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (31 bp):
TATTATATGTAAATTATAGATTTAATCACTA
Found at i:6104282 original size:31 final size:32
Alignment explanation
Indices: 6104247--6104321 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 32
6104237 GAACTTTTTT
6104247 TAGTTTAGT-AGCTTAAATAAAAACTTTT-AAA
1 TAGTTTAGTGA-CTTAAATAAAAACTTTTCAAA
* * * * *
6104278 TAGTTCAGTGATTTATATGAAAACTTTTCGAA
1 TAGTTTAGTGACTTAAATAAAAACTTTTCAAA
6104310 TAGTTTAGTGAC
1 TAGTTTAGTGAC
6104322 CAAATTGTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
31 22 0.63
32 13 0.37
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (32 bp):
TAGTTTAGTGACTTAAATAAAAACTTTTCAAA
Found at i:6106413 original size:18 final size:18
Alignment explanation
Indices: 6106390--6106432 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
6106380 AAATACAAAT
6106390 ACCCAAAACCCATTTACA
1 ACCCAAAACCCATTTACA
6106408 ACCCAAAACCCATTTACA
1 ACCCAAAACCCATTTACA
6106426 ACCCAAA
1 ACCCAAA
6106433 CACTTAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.14
Consensus pattern (18 bp):
ACCCAAAACCCATTTACA
Found at i:6106932 original size:7 final size:7
Alignment explanation
Indices: 6106889--6106934 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
6106879 ACAAATACCA
*
6106889 AAAAAAT
1 AAAAAAC
6106896 AAAAAAC
1 AAAAAAC
*
6106903 AAAAAGC
1 AAAAAAC
6106910 AAAAAA-
1 AAAAAAC
*
6106916 AATAAA-
1 AAAAAAC
6106922 AAAAAAC
1 AAAAAAC
6106929 AAAAAA
1 AAAAAA
6106935 ATAGAATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
6 10 0.30
7 23 0.70
ACGTcount: A:0.87, C:0.07, G:0.02, T:0.04
Consensus pattern (7 bp):
AAAAAAC
Found at i:6108360 original size:54 final size:56
Alignment explanation
Indices: 6108245--6108360 Score: 130
Period size: 56 Copynumber: 2.1 Consensus size: 56
6108235 TTATATATTG
* * * * *
6108245 TATGTATTTTCTTATTATATGTGTATGTATAGTATGTACGTATTCTTTAATATTAT
1 TATGTATTTTCTTAATATATGTATATATATAGTATGTACGTATTATTTAATATTAC
* * *
6108301 TATGTATTTT-TTAAATATATGTATATATATATTA-GTACTTA-TATTTAGTATTAC
1 TATGTATTTTCTT-AATATATGTATATATATAGTATGTACGTATTATTTAATATTAC
6108355 TATGTA
1 TATGTA
6108361 AACGTCTTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
54 16 0.31
55 8 0.16
56 27 0.53
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.54
Consensus pattern (56 bp):
TATGTATTTTCTTAATATATGTATATATATAGTATGTACGTATTATTTAATATTAC
Found at i:6110643 original size:20 final size:22
Alignment explanation
Indices: 6110599--6110654 Score: 80
Period size: 20 Copynumber: 2.6 Consensus size: 22
6110589 TACTATTAAA
6110599 ATTCTTATATTAAGAGTTATAT
1 ATTCTTATATTAAGAGTTATAT
* *
6110621 ATTTTTTTATTAAGAG-T-TAT
1 ATTCTTATATTAAGAGTTATAT
6110641 ATTCTTATATTAAG
1 ATTCTTATATTAAG
6110655 TTAGATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 15 0.50
21 1 0.03
22 14 0.47
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.54
Consensus pattern (22 bp):
ATTCTTATATTAAGAGTTATAT
Found at i:6111624 original size:2 final size:2
Alignment explanation
Indices: 6111617--6111645 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6111607 GCTTGAAAGC
6111617 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6111646 GATTTTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6114453 original size:2 final size:2
Alignment explanation
Indices: 6114448--6114480 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6114438 CACTTTTTTA
6114448 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6114481 AATAATTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6119662 original size:61 final size:61
Alignment explanation
Indices: 6119567--6119689 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
6119557 CAGCAAAAAG
6119567 ATACCCCCATTGATTTTTGCCGACTTAAAACATAGAAAGCAGGCAATGAACAACTATTTTC
1 ATACCCCCATTGATTTTTGCCGACTTAAAACATAGAAAGCAGGCAATGAACAACTATTTTC
*
6119628 ATACCCCCATTGATTTTTTCCGACTTAAAACATAGAAAGCAGGCAATGAACAACTATTTTC
1 ATACCCCCATTGATTTTTGCCGACTTAAAACATAGAAAGCAGGCAATGAACAACTATTTTC
6119689 A
1 A
6119690 GCACCCCTCT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (61 bp):
ATACCCCCATTGATTTTTGCCGACTTAAAACATAGAAAGCAGGCAATGAACAACTATTTTC
Found at i:6126930 original size:21 final size:21
Alignment explanation
Indices: 6126904--6126945 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6126894 AAAGTTCCTT
6126904 AGTTAATAACTAGATGACATA
1 AGTTAATAACTAGATGACATA
**
6126925 AGTTAATCTCTAGATGACATA
1 AGTTAATAACTAGATGACATA
6126946 CAGAACTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (21 bp):
AGTTAATAACTAGATGACATA
Found at i:6134393 original size:46 final size:46
Alignment explanation
Indices: 6134340--6134432 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
6134330 AGTAGAAAAT
6134340 TATGTACTTGAAAGCATCTTCTCATCAAACTTTATAGAAAATCCCC
1 TATGTACTTGAAAGCATCTTCTCATCAAACTTTATAGAAAATCCCC
6134386 TATGTACTTGAAAGCATCTTCTCATCAAACTTTATAGAAAATCCCC
1 TATGTACTTGAAAGCATCTTCTCATCAAACTTTATAGAAAATCCCC
6134432 T
1 T
6134433 TTTTTAGCAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.33
Consensus pattern (46 bp):
TATGTACTTGAAAGCATCTTCTCATCAAACTTTATAGAAAATCCCC
Done.