Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168037.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_29, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14313602
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 50000 characters in sequence are not A, C, G, or T
File 11 of 74
Found at i:3132831 original size:105 final size:104
Alignment explanation
Indices: 3132650--3132845 Score: 295
Period size: 105 Copynumber: 1.9 Consensus size: 104
3132640 TAGATATTTG
* * * *
3132650 TGGCCTTTTCTCTTTCTCTCTCTAATTTAGAGTCATCTTTATGTTATTTCCTGAAAAAGCTTCTA
1 TGGCCTTTTCTCTTTCGCTCTCTAAATTAGAGTCATCTTTATGTTATTTACTAAAAAAGCTTCTA
3132715 TCATTCTAAA-TTTAGAGCCTCTTTTTTTTTATACATAGA
66 TCATTCTAAATTTTA-AGCCTCTTTTTTTTTATACATAGA
* * *
3132754 TGGCCTTTTACTCTTTCGCTCTCTAAATTAGAGTCATCTTTCTTTTCTTTACTAAAAAAGCTTCT
1 TGGCCTTTT-CTCTTTCGCTCTCTAAATTAGAGTCATCTTTATGTTATTTACTAAAAAAGCTTCT
*
3132819 ATCTTTCTAAATTTTAAGCCTCTTTTT
65 ATCATTCTAAATTTTAAGCCTCTTTTT
3132846 CTTGCACAGT
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
104 9 0.11
105 69 0.84
106 4 0.05
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.48
Consensus pattern (104 bp):
TGGCCTTTTCTCTTTCGCTCTCTAAATTAGAGTCATCTTTATGTTATTTACTAAAAAAGCTTCTA
TCATTCTAAATTTTAAGCCTCTTTTTTTTTATACATAGA
Found at i:3133054 original size:106 final size:106
Alignment explanation
Indices: 3132869--3133081 Score: 426
Period size: 106 Copynumber: 2.0 Consensus size: 106
3132859 ACAAATAGAA
3132869 TAACACATACTGTGAGACTGACAGTTTTGAAGTTCTTTTTTGTGGTTAACAGGTTAAGTGCAATA
1 TAACACATACTGTGAGACTGACAGTTTTGAAGTTCTTTTTTGTGGTTAACAGGTTAAGTGCAATA
3132934 ATCACTAGAGCATGAAAATCTCCAAAGGGCTTGACTTTGAG
66 ATCACTAGAGCATGAAAATCTCCAAAGGGCTTGACTTTGAG
3132975 TAACACATACTGTGAGACTGACAGTTTTGAAGTTCTTTTTTGTGGTTAACAGGTTAAGTGCAATA
1 TAACACATACTGTGAGACTGACAGTTTTGAAGTTCTTTTTTGTGGTTAACAGGTTAAGTGCAATA
3133040 ATCACTAGAGCATGAAAATCTCCAAAGGGCTTGACTTTGAG
66 ATCACTAGAGCATGAAAATCTCCAAAGGGCTTGACTTTGAG
3133081 T
1 T
3133082 CCTCAATCCC
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 107 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (106 bp):
TAACACATACTGTGAGACTGACAGTTTTGAAGTTCTTTTTTGTGGTTAACAGGTTAAGTGCAATA
ATCACTAGAGCATGAAAATCTCCAAAGGGCTTGACTTTGAG
Found at i:3139630 original size:2 final size:2
Alignment explanation
Indices: 3139623--3139659 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3139613 AGCAACACGA
3139623 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3139660 AAACCAGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3143432 original size:2 final size:2
Alignment explanation
Indices: 3143425--3143455 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3143415 ACCATTCTTT
3143425 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3143456 GGTGTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3149304 original size:24 final size:25
Alignment explanation
Indices: 3149272--3149320 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
3149262 AACCTAATGG
3149272 TTGAATCCAAAAA-GACACCAGTTC
1 TTGAATCCAAAAAGGACACCAGTTC
3149296 TTGAATCCAAAAAGGACACCAGTTC
1 TTGAATCCAAAAAGGACACCAGTTC
3149321 ATATTTATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.20
Consensus pattern (25 bp):
TTGAATCCAAAAAGGACACCAGTTC
Found at i:3168494 original size:22 final size:23
Alignment explanation
Indices: 3168448--3168499 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
3168438 ATTTCAAGAG
*
3168448 TAAAATATATAATATTTTTTTAT
1 TAAAATATATAATATTTATTTAT
3168471 TAAAATATTATAA-A-TTATTTAT
1 TAAAATA-TATAATATTTATTTAT
3168493 TAAAATA
1 TAAAATA
3168500 AATTATTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 14 0.52
23 8 0.30
24 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TAAAATATATAATATTTATTTAT
Found at i:3177578 original size:22 final size:21
Alignment explanation
Indices: 3177545--3177588 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
3177535 TAAAAGTTTT
* *
3177545 AAAAATTTTATTATAAATTTA
1 AAAAATTATATTACAAATTTA
*
3177566 AAAAATATATATTACATATTTA
1 AAAAAT-TATATTACAAATTTA
3177588 A
1 A
3177589 TATTTAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAAATTATATTACAAATTTA
Found at i:3179976 original size:16 final size:16
Alignment explanation
Indices: 3179952--3179992 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
3179942 AATTGAATTG
*
3179952 AATTATATATTTTTAA
1 AATTTTATATTTTTAA
3179968 AATTTTATATTTTTAA
1 AATTTTATATTTTTAA
3179984 AATTTTATA
1 AATTTTATA
3179993 AAATAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATTTTATATTTTTAA
Found at i:3181327 original size:5 final size:5
Alignment explanation
Indices: 3181296--3181338 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
3181286 ACTTTAATGC
3181296 TAAAA TGAAAA GTCAAAA TAAAA -AAAA TAAAA TAAAA TAAAA T
1 TAAAA T-AAAA -T-AAAA TAAAA TAAAA TAAAA TAAAA TAAAA T
3181339 GATTAAATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
4 4 0.12
5 20 0.59
6 5 0.15
7 5 0.15
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:3182750 original size:13 final size:13
Alignment explanation
Indices: 3182732--3182757 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3182722 CAAACAGATG
3182732 ATTAATGACAGCA
1 ATTAATGACAGCA
3182745 ATTAATGACAGCA
1 ATTAATGACAGCA
3182758 TTACCAGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
ATTAATGACAGCA
Found at i:3189225 original size:24 final size:24
Alignment explanation
Indices: 3189177--3189227 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
3189167 GAAAATATCA
*
3189177 TTTTATTTAACAAATATTTTTTAT
1 TTTTATTTAACAAATATTTTATAT
3189201 TTTTATATTAA-AAA-ATCTTTATAT
1 TTTTAT-TTAACAAATAT-TTTATAT
3189225 TTT
1 TTT
3189228 CACAAATCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 2 0.08
24 18 0.75
25 4 0.17
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTTATTTAACAAATATTTTATAT
Found at i:3197851 original size:27 final size:27
Alignment explanation
Indices: 3197821--3197873 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
3197811 ATCATCTTGC
* *
3197821 TTTA-ATTAATTTTTTTAAATAGTTATT
1 TTTATATTAATATTTTAAAATA-TTATT
3197848 TTTATATTAATATTTTAAAATATTAT
1 TTTATATTAATATTTTAAAATATTAT
3197874 ATTCCCATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTATATTAATATTTTAAAATATTATT
Found at i:3198849 original size:4 final size:4
Alignment explanation
Indices: 3198840--3198870 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
3198830 AAGGATTCAT
*
3198840 ATTC ATTC ATTC ATTC ATTC AGTC ATTC ATT
1 ATTC ATTC ATTC ATTC ATTC ATTC ATTC ATT
3198871 GTTTTTATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.23, G:0.03, T:0.48
Consensus pattern (4 bp):
ATTC
Found at i:3199809 original size:2 final size:2
Alignment explanation
Indices: 3199802--3199837 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3199792 TGGTAGGGTG
*
3199802 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3199838 GGGGCTAGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3202949 original size:22 final size:20
Alignment explanation
Indices: 3202908--3202960 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
3202898 TTTAAAAAAT
* *
3202908 AATTTAAATATATTTAATAATA
1 AATTTAAATTTTTTTAAT-A-A
*
3202930 AATTTAAATTTTTTTTATAA
1 AATTTAAATTTTTTTAATAA
3202950 AA-TTAAATTTT
1 AATTTAAATTTT
3202961 CATAATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.32
20 3 0.11
21 1 0.04
22 15 0.54
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTTAAATTTTTTTAATAA
Found at i:3203003 original size:32 final size:33
Alignment explanation
Indices: 3202962--3203025 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
3202952 TTAAATTTTC
* *
3202962 ATAATTTTTAATATA-AAAATAAATAAATAAATA
1 ATAATTTTTAACATATAAAA-AAATAAAAAAATA
3202995 ATAA-TTTTAACATATAAAAAAATAAAAAAAT
1 ATAATTTTTAACATATAAAAAAATAAAAAAAT
3203026 TTAACTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 20 0.71
33 8 0.29
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (33 bp):
ATAATTTTTAACATATAAAAAAATAAAAAAATA
Found at i:3203017 original size:24 final size:24
Alignment explanation
Indices: 3202984--3203063 Score: 67
Period size: 24 Copynumber: 3.4 Consensus size: 24
3202974 ATAAAAATAA
*
3202984 ATAAATAAATAATAATTTTAACAT
1 ATAAAAAAATAATAATTTTAACAT
* *
3203008 ATAAAAAAATAAAAAAATTTAAC-T
1 ATAAAAAAAT-AATAATTTTAACAT
* *
3203032 -TAAAAAAA-ACGTAATTTTAAAAT
1 ATAAAAAAATA-ATAATTTTAACAT
*
3203055 AAAAAAAAA
1 ATAAAAAAA
3203064 AAGACTAGAC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
21 1 0.02
22 7 0.16
23 9 0.20
24 17 0.39
25 10 0.23
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.28
Consensus pattern (24 bp):
ATAAAAAAATAATAATTTTAACAT
Found at i:3203038 original size:25 final size:28
Alignment explanation
Indices: 3202986--3203040 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 28
3202976 AAAAATAAAT
*
3202986 AAATAAATAATAATTTTAACATATAAAA
1 AAATAAATAATAATTTTAACATAAAAAA
*
3203014 AAATAAA-AA-AA-TTTAACTTAAAAAA
1 AAATAAATAATAATTTTAACATAAAAAA
3203039 AA
1 AA
3203041 CGTAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 14 0.56
26 2 0.08
27 2 0.08
28 7 0.28
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (28 bp):
AAATAAATAATAATTTTAACATAAAAAA
Found at i:3203348 original size:18 final size:17
Alignment explanation
Indices: 3203324--3203369 Score: 76
Period size: 18 Copynumber: 2.7 Consensus size: 17
3203314 AATATTATTT
3203324 TTAATATAAATATAAAA
1 TTAATATAAATATAAAA
3203341 TTATATATAAATATAAAA
1 TTA-ATATAAATATAAAA
3203359 TTAA-ATAAATA
1 TTAATATAAATA
3203370 ATTTAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.25
17 4 0.14
18 17 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAATATAAATATAAAA
Found at i:3213792 original size:17 final size:16
Alignment explanation
Indices: 3213766--3213797 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3213756 AAAAGTTGAG
3213766 TTTTTTTTATTTTTTA
1 TTTTTTTTATTTTTTA
3213782 TTTTATTTTATTTTTT
1 TTTT-TTTTATTTTTT
3213798 TCAAACTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTTTATTTTTTA
Found at i:3216047 original size:17 final size:18
Alignment explanation
Indices: 3216022--3216059 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3216012 AATTACTTTG
3216022 TTATAATATTGCCTTA-A
1 TTATAATATTGCCTTATA
* *
3216039 TTATCATATTGTCTTATA
1 TTATAATATTGCCTTATA
3216057 TTA
1 TTA
3216060 CTTTCTAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.53
Consensus pattern (18 bp):
TTATAATATTGCCTTATA
Found at i:3216614 original size:14 final size:13
Alignment explanation
Indices: 3216594--3216636 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
3216584 AATCACACCA
3216594 AAAAAATATCAAC
1 AAAAAATATCAAC
*
3216607 AAATAAATTTCAAC
1 AAA-AAATATCAAC
3216621 -AAAAATATCAA-
1 AAAAAATATCAAC
3216632 AAAAA
1 AAAAA
3216637 TACTGGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 12 0.46
13 5 0.19
14 9 0.35
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAAAATATCAAC
Found at i:3216631 original size:12 final size:12
Alignment explanation
Indices: 3216595--3216638 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 12
3216585 ATCACACCAA
3216595 AAAAATATCAAC
1 AAAAATATCAAC
*
3216607 AAATAAATTTCAAC
1 -AA-AAATATCAAC
3216621 AAAAATATCAA-
1 AAAAATATCAAC
3216632 AAAAATA
1 AAAAATA
3216639 CTGGTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.25
12 8 0.29
13 4 0.14
14 9 0.32
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAAATATCAAC
Found at i:3217494 original size:6 final size:6
Alignment explanation
Indices: 3217483--3217526 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
3217473 ATCAAGTAGC
3217483 TTCCAT TTCCAT TTCCAT TTCCAT TTCCAT TTCCAT TTCCAT TT
1 TTCCAT TTCCAT TTCCAT TTCCAT TTCCAT TTCCAT TTCCAT TT
3217527 TTAGTACTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (6 bp):
TTCCAT
Found at i:3218240 original size:18 final size:19
Alignment explanation
Indices: 3218217--3218255 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3218207 TTTTTTTATA
3218217 AAATAAAATTATA-AAATT
1 AAATAAAATTATATAAATT
* *
3218235 AAATAATATTTTATAAATT
1 AAATAAAATTATATAAATT
3218254 AA
1 AA
3218256 TTTGAATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATAAAATTATATAAATT
Found at i:3218683 original size:21 final size:21
Alignment explanation
Indices: 3218659--3218701 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
3218649 TTAATTTAAA
3218659 AATT-AAAT-TAATTAAAACTTT
1 AATTGAAATATAA-TAAAA-TTT
3218680 AATTGAAATATAATAAAATTT
1 AATTGAAATATAATAAAATTT
3218701 A
1 A
3218702 TATATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 8 0.40
22 9 0.45
23 3 0.15
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
AATTGAAATATAATAAAATTT
Found at i:3218902 original size:14 final size:14
Alignment explanation
Indices: 3218869--3218919 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
3218859 ATTTTATTAT
**
3218869 TTAATTAATAAAAA
1 TTAATTAATATCAA
*
3218883 ATAATTAA-ATCAA
1 TTAATTAATATCAA
*
3218896 TTGAATTAATTTCAA
1 TT-AATTAATATCAA
3218911 TTAATTAAT
1 TTAATTAAT
3218920 TTTTAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 4 0.13
14 20 0.67
15 6 0.20
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (14 bp):
TTAATTAATATCAA
Found at i:3218920 original size:14 final size:15
Alignment explanation
Indices: 3218892--3218921 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3218882 AATAATTAAA
3218892 TCAATTGAATTAATT
1 TCAATTGAATTAATT
3218907 TCAATT-AATTAATT
1 TCAATTGAATTAATT
3218921 T
1 T
3218922 TTAAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (15 bp):
TCAATTGAATTAATT
Found at i:3219881 original size:13 final size:13
Alignment explanation
Indices: 3219855--3219884 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
3219845 CAAAAATTAT
3219855 AATACATGCAAAA
1 AATACATGCAAAA
3219868 AATACTATGCAAAA
1 AATAC-ATGCAAAA
3219882 AAT
1 AAT
3219885 TTTAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (13 bp):
AATACATGCAAAA
Found at i:3230220 original size:26 final size:26
Alignment explanation
Indices: 3230200--3230250 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
3230190 AATATGATAT
3230200 TAAAATAATATAAAAATATATAAAAA
1 TAAAATAATATAAAAATATATAAAAA
* *
3230226 TAATATAATATAAAATTA-ATAAAAA
1 TAAAATAATATAAAAATATATAAAAA
3230251 ATATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (26 bp):
TAAAATAATATAAAAATATATAAAAA
Found at i:3230246 original size:11 final size:11
Alignment explanation
Indices: 3230196--3230233 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
3230186 TTTAAATATG
*
3230196 ATATTAAAATA
1 ATATAAAAATA
3230207 ATATAAAAAT-
1 ATATAAAAATA
3230217 ATATAAAAATA
1 ATATAAAAATA
3230228 ATATAA
1 ATATAA
3230234 TATAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:3230251 original size:11 final size:12
Alignment explanation
Indices: 3230204--3230254 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
3230194 TGATATTAAA
3230204 ATAATATAAAAAT
1 ATAATA-AAAAAT
3230217 AT-ATAAAAATAAT
1 ATAAT-AAAA-AAT
*
3230230 ATAATATAAAAT
1 ATAATAAAAAAT
3230242 -TAATAAAAAAT
1 ATAATAAAAAAT
3230253 AT
1 AT
3230255 TTTTTTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
11 10 0.31
12 9 0.28
13 11 0.34
14 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
ATAATAAAAAAT
Found at i:3231079 original size:19 final size:18
Alignment explanation
Indices: 3231055--3231094 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
3231045 TATTTTTATT
*
3231055 TATAAAAATTTTAAATATA
1 TATAAAAA-GTTAAATATA
3231074 TAT-AAAAGTTAAATATA
1 TATAAAAAGTTAAATATA
3231091 TATA
1 TATA
3231095 TAATTCGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 12 0.63
18 4 0.21
19 3 0.16
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
TATAAAAAGTTAAATATA
Found at i:3231542 original size:18 final size:19
Alignment explanation
Indices: 3231498--3231544 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 19
3231488 TAAATTTTTT
* *
3231498 TTTTACAAATATTAATTAA
1 TTTTACAAATAATAATAAA
3231517 TTTT-CAAA-AATAATAAA
1 TTTTACAAATAATAATAAA
3231534 TTTTACAAATA
1 TTTTACAAATA
3231545 TATTAACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 11 0.46
18 8 0.33
19 5 0.21
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTTACAAATAATAATAAA
Found at i:3235506 original size:6 final size:7
Alignment explanation
Indices: 3235459--3235505 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
3235449 CTGGACCATT
3235459 TTTTTTA
1 TTTTTTA
* *
3235466 GTTCTTA
1 TTTTTTA
* *
3235473 TTTTATC
1 TTTTTTA
3235480 TTTTTTA
1 TTTTTTA
3235487 TTTTTTA
1 TTTTTTA
3235494 TTTTTTA
1 TTTTTTA
3235501 TTTTT
1 TTTTT
3235506 ACACTTCTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.81
Consensus pattern (7 bp):
TTTTTTA
Found at i:3236054 original size:21 final size:20
Alignment explanation
Indices: 3236016--3236054 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3236006 TGTAGGATTT
* *
3236016 TTTTTTTTTGTTTTTACAAA
1 TTTTTTTTGGTTTGTACAAA
3236036 TTTTTTTTGGATTTGTACA
1 TTTTTTTTGG-TTTGTACA
3236055 CAGTTTTTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.18, C:0.05, G:0.10, T:0.67
Consensus pattern (20 bp):
TTTTTTTTGGTTTGTACAAA
Found at i:3241224 original size:39 final size:40
Alignment explanation
Indices: 3241175--3241377 Score: 198
Period size: 39 Copynumber: 4.9 Consensus size: 40
3241165 AGGCTTGGAT
*
3241175 GATCTAGTTGGATGTTTTGGACTTGAAAGGGAGTTAG-AG
1 GATCTGGTTGGATGTTTTGGACTTGAAAGGGAGTTAGAAG
*
3241214 GATCTGGTTGGATGTTTTGTACTTGAAAGGGAGTT-GAAG
1 GATCTGGTTGGATGTTTTGGACTTGAAAGGGAGTTAGAAG
3241253 GATCTGGTTGGATGTTTTGGA-TGTGAAAGGGAGTTTGAGAAGTGCTTGAAG
1 GATCTGGTTGGATGTTTTGGACT-TGAAAGGGAG-TT----A------GAAG
** * *
3241304 GATCTAATTGGATGTTTTGAACTTAAAAGGGAGTTA-AAG
1 GATCTGGTTGGATGTTTTGGACTTGAAAGGGAGTTAGAAG
* *
3241343 GATCTGGTTGGATGTTTTGGTCATGAAAGGGAGTT
1 GATCTGGTTGGATGTTTTGGACTTGAAAGGGAGTT
3241378 TGAGAAGTGT
Statistics
Matches: 136, Mismatches: 13, Indels: 30
0.76 0.07 0.17
Matches are distributed among these distances:
38 2 0.01
39 97 0.71
40 2 0.01
46 1 0.01
50 2 0.01
51 31 0.23
52 1 0.01
ACGTcount: A:0.26, C:0.05, G:0.35, T:0.34
Consensus pattern (40 bp):
GATCTGGTTGGATGTTTTGGACTTGAAAGGGAGTTAGAAG
Found at i:3241316 original size:90 final size:90
Alignment explanation
Indices: 3241212--3241386 Score: 280
Period size: 90 Copynumber: 1.9 Consensus size: 90
3241202 AGGGAGTTAG
** * * * *
3241212 AGGATCTGGTTGGATGTTTTGTACTTGAAAGGGAGTTGAAGGATCTGGTTGGATGTTTTGGAT-G
1 AGGATCTAATTGGATGTTTTGAACTTAAAAGGGAGTTAAAGGATCTGGTTGGATGTTTTGG-TCA
3241276 TGAAAGGGAGTTTGAGAAGTGCTTGA
65 TGAAAGGGAGTTTGAGAAGTGCTTGA
3241302 AGGATCTAATTGGATGTTTTGAACTTAAAAGGGAGTTAAAGGATCTGGTTGGATGTTTTGGTCAT
1 AGGATCTAATTGGATGTTTTGAACTTAAAAGGGAGTTAAAGGATCTGGTTGGATGTTTTGGTCAT
3241367 GAAAGGGAGTTTGAGAAGTG
66 GAAAGGGAGTTTGAGAAGTG
3241387 TTGGTGGTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 1 0.01
90 77 0.99
ACGTcount: A:0.26, C:0.05, G:0.35, T:0.34
Consensus pattern (90 bp):
AGGATCTAATTGGATGTTTTGAACTTAAAAGGGAGTTAAAGGATCTGGTTGGATGTTTTGGTCAT
GAAAGGGAGTTTGAGAAGTGCTTGA
Found at i:3255993 original size:24 final size:24
Alignment explanation
Indices: 3255966--3256029 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
3255956 ATAATTTTAA
3255966 ATATAATATAATAATATAAAAAAT
1 ATATAATATAATAATATAAAAAAT
* * *
3255990 ATATATTATATTTAATAT-ATAAAT
1 ATATAATATA-ATAATATAAAAAAT
3256014 ATA-AAT-T-ATAATATAA
1 ATATAATATAATAATATAA
3256030 TATTTTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
20 6 0.18
21 1 0.03
22 1 0.03
23 2 0.06
24 17 0.52
25 6 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATATAATATAATAATATAAAAAAT
Found at i:3256041 original size:32 final size:33
Alignment explanation
Indices: 3255969--3256034 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
3255959 ATTTTAAATA
*
3255969 TAATATA-ATAATATAAAAAATATATATTATATT
1 TAATATATA-AATATAAAAAATATATATAATATT
**
3256002 TAATATATAAATATAAATTATA-ATATAATATT
1 TAATATATAAATATAAAAAATATATATAATATT
3256034 T
1 T
3256035 TTTATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 10 0.34
33 18 0.62
34 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
TAATATATAAATATAAAAAATATATATAATATT
Found at i:3260660 original size:21 final size:21
Alignment explanation
Indices: 3260609--3260662 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
3260599 TATCAATAAA
3260609 AATTTATTGATTCAATCAATT
1 AATTTATTGATTCAATCAATT
*
3260630 AAGTTATTGATTCAATCAATT
1 AATTTATTGATTCAATCAATT
* *
3260651 TATTTGTTGATT
1 AATTTATTGATT
3260663 TTCATAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.50
Consensus pattern (21 bp):
AATTTATTGATTCAATCAATT
Found at i:3267484 original size:19 final size:19
Alignment explanation
Indices: 3267462--3267509 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
3267452 ATTGTAATTG
*
3267462 ATTTAAAATTAATTTAATA
1 ATTTAAAATTAATATAATA
* *
3267481 ATTTTAATTTAATATAATA
1 ATTTAAAATTAATATAATA
*
3267500 TTTATAAAAT
1 ATT-TAAAAT
3267510 ATTATTATTA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTAAAATTAATATAATA
Found at i:3268024 original size:15 final size:14
Alignment explanation
Indices: 3268004--3268038 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
3267994 ATTTTATACA
3268004 TTTAAATAAATTTT
1 TTTAAATAAATTTT
*
3268018 TTATAAATATATTTT
1 TT-TAAATAAATTTT
3268033 TTTAAA
1 TTTAAA
3268039 ATATAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAAATAAATTTT
Found at i:3268040 original size:15 final size:16
Alignment explanation
Indices: 3268014--3268043 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3268004 TTTAAATAAA
3268014 TTTTTTATAAATATAT
1 TTTTTTATAAATATAT
3268030 TTTTTTA-AAATATA
1 TTTTTTATAAATATA
3268044 AATATATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTTTATAAATATAT
Found at i:3268220 original size:31 final size:29
Alignment explanation
Indices: 3268168--3268227 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
3268158 TGATAAAAAA
*
3268168 TTTAAAATTATATTTATTTTTAATTTTAT
1 TTTAAAATTATATGTATTTTTAATTTTAT
*
3268197 TTTAAAATTTAATATGTATTTTTATTTTTAT
1 TTTAAAA-TT-ATATGTATTTTTAATTTTAT
3268228 AAAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 7 0.26
30 2 0.07
31 18 0.67
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (29 bp):
TTTAAAATTATATGTATTTTTAATTTTAT
Found at i:3281282 original size:28 final size:28
Alignment explanation
Indices: 3281224--3281282 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
3281214 ATATATAAAT
* *
3281224 ATATTTTTATTAATTAAAATATTAAATA
1 ATATTTTTATTAATTAAAATAATAAACA
* *
3281252 ATATTTTTATTAA-TATAATACATATACA
1 ATATTTTTATTAATTAAAATA-ATAAACA
3281280 ATA
1 ATA
3281283 ATAAACTAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
ATATTTTTATTAATTAAAATAATAAACA
Found at i:3281838 original size:24 final size:25
Alignment explanation
Indices: 3281811--3281860 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
3281801 GTGATATGTG
* *
3281811 AATTTATTAATTAATATAT-TAAAT
1 AATTTATTAATAAAAATATATAAAT
*
3281835 AATTTTTTAATAAAAATATATAAAT
1 AATTTATTAATAAAAATATATAAAT
3281860 A
1 A
3281861 TAATATTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AATTTATTAATAAAAATATATAAAT
Found at i:3281869 original size:26 final size:27
Alignment explanation
Indices: 3281812--3281891 Score: 83
Period size: 26 Copynumber: 3.0 Consensus size: 27
3281802 TGATATGTGA
* * *
3281812 ATTTATTAATTAATATATTAAATA-ATT
1 ATTTAATAAATAATATA-TAAATATAAT
*
3281839 TTTTAATAAA-AATATATAAATATAAT
1 ATTTAATAAATAATATATAAATATAAT
*
3281865 ATTTAATAAATAATATTATATATATAA
1 ATTTAATAAATAATA-TATAAATATAA
3281892 GATCGAGATG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
25 6 0.14
26 17 0.39
27 11 0.25
28 10 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATTTAATAAATAATATATAAATATAAT
Found at i:3281877 original size:14 final size:14
Alignment explanation
Indices: 3281830--3281881 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
3281820 ATTAATATAT
*
3281830 TAAATAATTTTTTAA
1 TAAATAA-TATTTAA
*
3281845 TAAA-AATATATAA
1 TAAATAATATTTAA
*
3281858 -ATATAATATTTAA
1 TAAATAATATTTAA
3281871 TAAATAATATT
1 TAAATAATATT
3281882 ATATATATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
12 2 0.07
13 13 0.43
14 11 0.37
15 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAATAATATTTAA
Found at i:3281885 original size:24 final size:25
Alignment explanation
Indices: 3281817--3281886 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 25
3281807 TGTGAATTTA
* * *
3281817 TTAATTAAT-ATATTAAATAATTTT
1 TTAATAAATAATATTATATAATTAT
3281841 TTAATAAA-AATATATAAATATAA-TAT
1 TTAATAAATAATAT-T--ATATAATTAT
3281867 TTAATAAATAATATTATATA
1 TTAATAAATAATATTATATA
3281887 TATAAGATCG
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
24 16 0.42
25 1 0.03
26 11 0.29
27 10 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAATAAATAATATTATATAATTAT
Found at i:3284221 original size:11 final size:12
Alignment explanation
Indices: 3284180--3284223 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
3284170 TATATTTAGT
*
3284180 TTATATTTTAGA
1 TTATATTTTATA
*
3284192 TAATTATTTTATA
1 TTA-TATTTTATA
3284205 TTATATTTTAT-
1 TTATATTTTATA
3284216 TTATATTT
1 TTATATTT
3284224 AAAAATTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 8 0.29
12 10 0.36
13 10 0.36
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:3287937 original size:17 final size:17
Alignment explanation
Indices: 3287915--3287947 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3287905 CTTTGCCCCC
3287915 TTTTTTTTT-TTTGGCT
1 TTTTTTTTTCTTTGGCT
3287931 TTTTTTTTTCTTTGGCT
1 TTTTTTTTTCTTTGGCT
3287948 GTAATAGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.00, C:0.09, G:0.12, T:0.79
Consensus pattern (17 bp):
TTTTTTTTTCTTTGGCT
Found at i:3288885 original size:26 final size:26
Alignment explanation
Indices: 3288856--3288919 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
3288846 TTATTTTGTT
3288856 AATATAAAATATTATTTTAAAATATA
1 AATATAAAATATTATTTTAAAATATA
3288882 AATATAAAATATTATTTTAAAATATA
1 AATATAAAATATTATTTTAAAATATA
3288908 AATATAAAATAT
1 AATATAAAATAT
3288920 ATAAAATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AATATAAAATATTATTTTAAAATATA
Found at i:3288915 original size:13 final size:13
Alignment explanation
Indices: 3288856--3288938 Score: 78
Period size: 13 Copynumber: 6.3 Consensus size: 13
3288846 TTATTTTGTT
*
3288856 AATATAAAATATT
1 AATATAAAATATA
* *
3288869 ATTTTAAAATATA
1 AATATAAAATATA
*
3288882 AATATAAAATATT
1 AATATAAAATATA
* *
3288895 ATTTTAAAATATA
1 AATATAAAATATA
3288908 AATATAAAATATA
1 AATATAAAATATA
*
3288921 TAAAATTAAAA-ATA
1 -AATA-TAAAATATA
3288935 AATA
1 AATA
3288939 ATATATATAT
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
13 44 0.80
14 6 0.11
15 5 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAAAATATA
Found at i:3290044 original size:18 final size:17
Alignment explanation
Indices: 3289993--3290045 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
3289983 TTTTCATTCC
* *
3289993 TTGGTTCATTTTTTTTT
1 TTGGTTCATTTTTTGTG
**
3290010 TTGGTTTGTTTGTTTGTG
1 TTGGTTCATTT-TTTGTG
3290028 TTGGTTCATTTTCTTGTG
1 TTGGTTCATTTT-TTGTG
3290046 CAAAGACCAC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.04, C:0.06, G:0.23, T:0.68
Consensus pattern (17 bp):
TTGGTTCATTTTTTGTG
Found at i:3290678 original size:30 final size:30
Alignment explanation
Indices: 3290624--3290680 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
3290614 TTATTTATTT
* * *
3290624 ATATATATATTTATATAATGATATTTTTAA
1 ATATATATATTTAAAAAATAATATTTTTAA
*
3290654 ATATTTATATTTAAAAAATAATATTTT
1 ATATATATATTTAAAAAATAATATTTT
3290681 ATTAATTTCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
ATATATATATTTAAAAAATAATATTTTTAA
Found at i:3297596 original size:62 final size:61
Alignment explanation
Indices: 3297520--3297827 Score: 181
Period size: 62 Copynumber: 5.0 Consensus size: 61
3297510 TTAAAGGAGA
* * *
3297520 TTATTCAAGACGTTTTTAGCCAGAAAACACCTTTAATAATCCTTACAAAAAATTTAATAGGG
1 TTATTCAAGGCGTTTTTAGCCA-AAAACACCTTGAATAATCCTTACAAAAAATTGAATAGGG
* * * * *** * **
3297582 TTATTCAAGGCGTTTGTGGCCAAAAACGCCTTGACTAATCC-T-CTTTAAGTTTTATGATGGG
1 TTATTCAAGGCGTTTTTAGCCAAAAACACCTTGAATAATCCTTACAAAAAATTGAAT-A-GGG
* * * * * * * * * *
3297643 ATTATTCAATGTGGTTCTATCTAGAAAACATCTTGAAAAACCCTTACAAAAAATTGAATGGGG
1 -TTATTCAAGGCGTTTTTAGCCA-AAAACACCTTGAATAATCCTTACAAAAAATTGAATAGGG
* * * * *
3297706 TTATTGAAAGCATTTTTTACCCAAAAAC-CCATTGAATAATCCATTACAAAAAATTGAATAGGA
1 TTATTCAAGGC-GTTTTTAGCCAAAAACACC-TTGAATAATCC-TTACAAAAAATTGAATAGGG
* * * * ** ** *
3297769 TTACTCAAGGCATTTCTGGTAAAAAATGCCATGAATAATACCTTACAAAAAATTGAATA
1 TTATTCAAGGCGTTTTTAGCCAAAAACACCTTGAATAAT-CCTTACAAAAAATTGAATA
3297828 AGATTACTCA
Statistics
Matches: 181, Mismatches: 54, Indels: 22
0.70 0.21 0.09
Matches are distributed among these distances:
59 8 0.04
60 2 0.01
61 20 0.11
62 90 0.50
63 53 0.29
64 1 0.01
65 7 0.04
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (61 bp):
TTATTCAAGGCGTTTTTAGCCAAAAACACCTTGAATAATCCTTACAAAAAATTGAATAGGG
Found at i:3297782 original size:63 final size:62
Alignment explanation
Indices: 3297684--3297857 Score: 169
Period size: 62 Copynumber: 2.8 Consensus size: 62
3297674 CTTGAAAAAC
* * * * *
3297684 CCTTACAAAAAATTGAATGGGGTTATTGAAAGCATTT-T-TTACCCAAAAA-CCCATTGAATAAT
1 CCTTACAAAAAATTGAATAGGATTACTCAAAGCATTTCTGGTA---AAAAATCCCA-TGAATAAT
3297746 -
62 A
* *
3297746 CCATTACAAAAAATTGAATAGGATTACTCAAGGCATTTCTGGTAAAAAATGCCATGAATAATA
1 CC-TTACAAAAAATTGAATAGGATTACTCAAAGCATTTCTGGTAAAAAATCCCATGAATAATA
* * *
3297809 CCTTACAAAAAATTGAATAAGATTACTC-ACGACATTTCTGGCAAAAAAT
1 CCTTACAAAAAATTGAATAGGATTACTCAAAG-CATTTCTGGTAAAAAAT
3297858 GTCTTGCCTA
Statistics
Matches: 96, Mismatches: 10, Indels: 12
0.81 0.08 0.10
Matches are distributed among these distances:
61 2 0.02
62 56 0.58
63 35 0.36
64 1 0.01
65 2 0.02
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (62 bp):
CCTTACAAAAAATTGAATAGGATTACTCAAAGCATTTCTGGTAAAAAATCCCATGAATAATA
Found at i:3297833 original size:62 final size:62
Alignment explanation
Indices: 3297738--3297858 Score: 190
Period size: 62 Copynumber: 2.0 Consensus size: 62
3297728 AAAAACCCAT
* * *
3297738 TGAATAATCCATTACAAAAAATTGAATAGGATTACTCAAGGCATTTCTGGTAAAAAATGCCA
1 TGAATAATCCATTACAAAAAATTGAATAAGATTACTCAAGACATTTCTGGCAAAAAATGCCA
*
3297800 TGAATAATACC-TTACAAAAAATTGAATAAGATTACTCACGACATTTCTGGCAAAAAATG
1 TGAATAAT-CCATTACAAAAAATTGAATAAGATTACTCAAGACATTTCTGGCAAAAAATG
3297859 TCTTGCCTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 52 0.96
63 2 0.04
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (62 bp):
TGAATAATCCATTACAAAAAATTGAATAAGATTACTCAAGACATTTCTGGCAAAAAATGCCA
Found at i:3298439 original size:61 final size:61
Alignment explanation
Indices: 3298363--3298480 Score: 148
Period size: 62 Copynumber: 1.9 Consensus size: 61
3298353 ATTTTTGGGA
** *
3298363 AAAAAATGCCATGAATAAT-TTTTTATAAAAATAGAATGGGGTTGGTAAAGGCGTTTGTAAC
1 AAAAAATGCCATGAATAATCTTTGCA-AAAAATAGAATGGGGTTAGTAAAGGCGTTTGTAAC
** * *
3298424 AAAAAATGCTTTGAATAATCCTTTGCAAAAAATTGAATGGGGTTATTAAAGGCGTTT
1 AAAAAATGCCATGAATAAT-CTTTGCAAAAAATAGAATGGGGTTAGTAAAGGCGTTT
3298481 CTGACTAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
61 17 0.35
62 27 0.56
63 4 0.08
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (61 bp):
AAAAAATGCCATGAATAATCTTTGCAAAAAATAGAATGGGGTTAGTAAAGGCGTTTGTAAC
Found at i:3298465 original size:62 final size:62
Alignment explanation
Indices: 3298389--3298523 Score: 171
Period size: 62 Copynumber: 2.2 Consensus size: 62
3298379 AATTTTTTAT
* * * ** * * *
3298389 AAAAATAGAATGGGGTTGGTAAAGGCGTTTGTAACAAAAAATGCTTTGAATAATCCTTTGCA
1 AAAAATTGAATGGGGTTAGTAAAGGCGTTTCTAACAAAAAACACATTGAATAATCCATTACA
* * *
3298451 AAAAATTGAATGGGGTTATTAAAGGCGTTTCTGACTAAAAACACATTGAATAATCCATTACA
1 AAAAATTGAATGGGGTTAGTAAAGGCGTTTCTAACAAAAAACACATTGAATAATCCATTACA
3298513 AAAAATTGAAT
1 AAAAATTGAAT
3298524 AAGATTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (62 bp):
AAAAATTGAATGGGGTTAGTAAAGGCGTTTCTAACAAAAAACACATTGAATAATCCATTACA
Found at i:3302455 original size:52 final size:51
Alignment explanation
Indices: 3302391--3302529 Score: 156
Period size: 52 Copynumber: 2.7 Consensus size: 51
3302381 ATTGAGAAAT
* **
3302391 TTTTGGGATTTAATTCCAGAATCAATTGGCATTAAAAATGATATG-GAGAGA
1 TTTTGGGATTTAATTTCAGAATCAATTCACATTAAAAATGATA-GAGAGAGA
* *
3302442 TTGTTGGGATTTAATTTCATAATCAATTCACATT-AAATTGATAGAGAGAGA
1 TT-TTGGGATTTAATTTCAGAATCAATTCACATTAAAAATGATAGAGAGAGA
* * * **
3302493 TTTTAGGATTTGATTTTAGAATCAATTTTCATTAAAA
1 TTTTGGGATTTAATTTCAGAATCAATTCACATTAAAA
3302530 TGGAAATAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
50 26 0.35
51 21 0.28
52 27 0.36
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (51 bp):
TTTTGGGATTTAATTTCAGAATCAATTCACATTAAAAATGATAGAGAGAGA
Found at i:3302526 original size:50 final size:51
Alignment explanation
Indices: 3302396--3302531 Score: 150
Period size: 50 Copynumber: 2.7 Consensus size: 51
3302386 GAAATTTTTG
* ** *
3302396 GGATTTAATTCCAGAATCAATTGGCATTAAAAATGATATGGAGAGATTGTTG
1 GGATTTAATTTCAGAATCAATTCACATT-AAAATGATATGGAGAGATTGTTA
* *
3302448 GGATTTAATTTCATAATCAATTCACATTAAATTGATA-GAGAGAGATT-TTA
1 GGATTTAATTTCAGAATCAATTCACATTAAAATGATATG-GAGAGATTGTTA
* * **
3302498 GGATTTGATTTTAGAATCAATTTTCATTAAAATG
1 GGATTTAATTTCAGAATCAATTCACATTAAAATG
3302532 GAAATAAAAT
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
50 31 0.44
51 16 0.23
52 24 0.34
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (51 bp):
GGATTTAATTTCAGAATCAATTCACATTAAAATGATATGGAGAGATTGTTA
Found at i:3302831 original size:21 final size:21
Alignment explanation
Indices: 3302807--3302847 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3302797 TTTATTGGGT
*
3302807 TTTTGAAAATTCTTTGTCAAC
1 TTTTGAAAATTATTTGTCAAC
* *
3302828 TTTTGAGATTTATTTGTCAA
1 TTTTGAAAATTATTTGTCAA
3302848 TTTCTAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (21 bp):
TTTTGAAAATTATTTGTCAAC
Found at i:3303040 original size:14 final size:14
Alignment explanation
Indices: 3303021--3303057 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3303011 TTGTTTTAAC
*
3303021 TTTATTTTTGTTAT
1 TTTATTTATGTTAT
3303035 TTTATTTATGTTAT
1 TTTATTTATGTTAT
*
3303049 TTTGTTTAT
1 TTTATTTAT
3303058 TTTTATTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (14 bp):
TTTATTTATGTTAT
Found at i:3303049 original size:23 final size:24
Alignment explanation
Indices: 3303016--3303087 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 24
3303006 ATTTTTTGTT
3303016 TTAACT-TTATTTTTGTTATTTTA
1 TTAACTCTTATTTTTGTTATTTTA
* *
3303039 TTTA-TGTTA-TTTTGTTTATTTTTA
1 TTAACTCTTATTTTTG-TTA-TTTTA
*
3303063 TTAACTCTTATTATTTCTTATTTTA
1 TTAACTCTTATT-TTTGTTATTTTA
3303088 AATTAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
22 6 0.15
23 9 0.23
24 8 0.21
25 9 0.23
26 4 0.10
27 3 0.08
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (24 bp):
TTAACTCTTATTTTTGTTATTTTA
Found at i:3304073 original size:37 final size:37
Alignment explanation
Indices: 3304030--3304106 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
3304020 ATTTTATTCT
* * * *
3304030 TTTTCATTGCT-TATATTTGCTTTATTATTTATTTTTC
1 TTTTCATTG-TGTATACTTGCTTAATTATTCATTTGTC
3304067 TTTTCATTGTGTATACTTGCTTAATTATTCATTTGTC
1 TTTTCATTGTGTATACTTGCTTAATTATTCATTTGTC
3304104 TTT
1 TTT
3304107 CTTTTTAGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 1 0.03
37 34 0.97
ACGTcount: A:0.17, C:0.12, G:0.08, T:0.64
Consensus pattern (37 bp):
TTTTCATTGTGTATACTTGCTTAATTATTCATTTGTC
Found at i:3304133 original size:45 final size:40
Alignment explanation
Indices: 3304030--3304148 Score: 120
Period size: 45 Copynumber: 2.9 Consensus size: 40
3304020 ATTTTATTCT
3304030 TTTTCATTGCTTATATTTGC-T--TTATTATTTATTTTTC
1 TTTTCATTGCTTATATTTGCTTAATTATTATTTATTTTTC
* * *
3304067 TTTTCATTG-TGTATACTTGCTTAATTATTCATTTGTCTTTCTT
1 TTTTCATTGCT-TATATTTGCTTAATTATT-ATTTAT-TTT-TC
3304110 TTTAGTCATTGCTTATATTTGCTTAATTATCTATTTATT
1 TTT--TCATTGCTTATATTTGCTTAATTAT-TATTTATT
3304149 ATATAAATAC
Statistics
Matches: 66, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
36 1 0.02
37 17 0.26
38 1 0.02
40 5 0.08
41 5 0.08
42 3 0.05
43 4 0.06
44 1 0.02
45 27 0.41
46 2 0.03
ACGTcount: A:0.18, C:0.12, G:0.08, T:0.62
Consensus pattern (40 bp):
TTTTCATTGCTTATATTTGCTTAATTATTATTTATTTTTC
Found at i:3307106 original size:51 final size:50
Alignment explanation
Indices: 3306999--3307130 Score: 153
Period size: 51 Copynumber: 2.6 Consensus size: 50
3306989 CATTTTGTTG
* ***
3306999 AAAAAAAAAAAAGAAAATTGATGGGGTAAAATGCCAATATACTTCACCCA
1 AAAAAAAAAAAAGAAAATTGATGGGGCAAAATGCCAATATACTTCAAAAA
*
3307049 AAAAAAAATAAAGAGAAATT-ATTGGGGCAAAATGCCAATATAC-TCAAAAA
1 AAAAAAAAAAAAGA-AAATTGA-TGGGGCAAAATGCCAATATACTTCAAAAA
* *
3307099 AATAAAAACAAAA-AAAATTGATGGGGTAAAAT
1 AA-AAAAAAAAAAGAAAATTGATGGGGCAAAAT
3307131 AGCAAATTAC
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
49 15 0.21
50 22 0.31
51 33 0.47
ACGTcount: A:0.58, C:0.10, G:0.14, T:0.18
Consensus pattern (50 bp):
AAAAAAAAAAAAGAAAATTGATGGGGCAAAATGCCAATATACTTCAAAAA
Found at i:3307475 original size:10 final size:11
Alignment explanation
Indices: 3307446--3307478 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
3307436 AAAAAAAGCC
3307446 AAGAGAAAGAAA
1 AAGAGAAA-AAA
3307458 AAGAGAAAAAA
1 AAGAGAAAAAA
3307469 AAG-GAAAAAA
1 AAGAGAAAAAA
3307479 GAAAACTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 6 0.29
12 8 0.38
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAGAGAAAAAA
Found at i:3308509 original size:17 final size:17
Alignment explanation
Indices: 3308487--3308530 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
3308477 ACTTAGAATT
3308487 TTACGAATCTTTCTATC
1 TTACGAATCTTTCTATC
* * *
3308504 TTACGAATTTTTTTTTC
1 TTACGAATCTTTCTATC
*
3308521 TTATGAATCT
1 TTACGAATCT
3308531 GAAAGTCCTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.55
Consensus pattern (17 bp):
TTACGAATCTTTCTATC
Found at i:3308689 original size:86 final size:86
Alignment explanation
Indices: 3308592--3308810 Score: 294
Period size: 86 Copynumber: 2.5 Consensus size: 86
3308582 TGTGAATTTG
* * * *
3308592 TCTTTGCGAATCTAGAACTTTTGCGAAACTTAAAATCTTGTGAATTTATCCTTCTTATGAATCTG
1 TCTTTGTGAATCTAGAACTTTTGCGAAACTTGAAATCTTGCGAATTTATCCTTCTTATGAATCTA
* *
3308657 AAAGTCCCTGCAAATCTGGAA
66 AAAGTCCCTGCAAACCTGAAA
* * * * *
3308678 TCTTTGTGAATCTAGAACCTTTGTGAAACTTGTAATCTTGCGAATTTATCTTTCTTGTGAATCTA
1 TCTTTGTGAATCTAGAACTTTTGCGAAACTTGAAATCTTGCGAATTTATCCTTCTTATGAATCTA
* *
3308743 AAAGTTCCTGCGAACCTGAAA
66 AAAGTCCCTGCAAACCTGAAA
* * *
3308764 TCTTTGTGAATCTAGAACTTTTACAAAACTTGAAGTCTTGCGAATTT
1 TCTTTGTGAATCTAGAACTTTTGCGAAACTTGAAATCTTGCGAATTT
3308811 GAAAGTCCTT
Statistics
Matches: 114, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 114 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (86 bp):
TCTTTGTGAATCTAGAACTTTTGCGAAACTTGAAATCTTGCGAATTTATCCTTCTTATGAATCTA
AAAGTCCCTGCAAACCTGAAA
Found at i:3308699 original size:17 final size:17
Alignment explanation
Indices: 3308669--3308704 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3308659 AGTCCCTGCA
* *
3308669 AATCTGGAATCTTTGTG
1 AATCTAGAACCTTTGTG
3308686 AATCTAGAACCTTTGTG
1 AATCTAGAACCTTTGTG
3308703 AA
1 AA
3308705 ACTTGTAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (17 bp):
AATCTAGAACCTTTGTG
Found at i:3310239 original size:47 final size:46
Alignment explanation
Indices: 3310161--3310250 Score: 110
Period size: 46 Copynumber: 1.9 Consensus size: 46
3310151 TTCAAATAAA
* * * * *
3310161 TTTATGAATCCTACCAAATTATTGGAGAATTTTCATAAATTTAAAAT
1 TTTATGAATCCTACCAAACTATT-AAAAAATTTCATAAAATTAAAAT
3310208 TTTATAGAATCC-ACCAAACTATTAAAAAATTTCATAAAATTAA
1 TTTAT-GAATCCTACCAAACTATTAAAAAATTTCATAAAATTAA
3310251 TTTTAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
46 16 0.43
47 15 0.41
48 6 0.16
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.37
Consensus pattern (46 bp):
TTTATGAATCCTACCAAACTATTAAAAAATTTCATAAAATTAAAAT
Found at i:3311920 original size:26 final size:26
Alignment explanation
Indices: 3311883--3311951 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
3311873 TCCAAACAAT
* *
3311883 AAATAATAAATAATTAAATTATATTC
1 AAATAATGAATAATAAAATTATATTC
*
3311909 AAATAATGAATAAAAAAATTATATTC
1 AAATAATGAATAATAAAATTATATTC
3311935 AAATAATGAAATAATAA
1 AAATAATG-AATAATAA
3311952 TAATATAGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
26 31 0.82
27 7 0.18
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (26 bp):
AAATAATGAATAATAAAATTATATTC
Found at i:3315478 original size:13 final size:13
Alignment explanation
Indices: 3315456--3315494 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
3315446 TTTAATTTAA
3315456 TTTATAATATTAT
1 TTTATAATATTAT
*
3315469 TTTATTATATT-T
1 TTTATAATATTAT
3315481 TATTATAATATTAT
1 T-TTATAATATTAT
3315495 ATATCAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 2 0.09
13 19 0.86
14 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTATAATATTAT
Found at i:3319591 original size:2 final size:2
Alignment explanation
Indices: 3319580--3319610 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3319570 ATTATGTCAA
3319580 AT AT -T 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
3319611 TAAGATTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3322019 original size:16 final size:17
Alignment explanation
Indices: 3321989--3322022 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3321979 TGTTATTTTA
3321989 TAAAAAAAAGGTTATAAT
1 TAAAAAAAA-GTTATAAT
3322007 TAAAAAAAA-TTATAAT
1 TAAAAAAAAGTTATAAT
3322023 GAATTACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAAAAAAAAGTTATAAT
Found at i:3323962 original size:19 final size:19
Alignment explanation
Indices: 3323934--3323972 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3323924 ATTTTAATAA
*
3323934 AATATGAATAAATACGAAT
1 AATATAAATAAATACGAAT
* *
3323953 AATATAAATATATATGAAT
1 AATATAAATAAATACGAAT
3323972 A
1 A
3323973 GATACAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.31
Consensus pattern (19 bp):
AATATAAATAAATACGAAT
Found at i:3323968 original size:29 final size:29
Alignment explanation
Indices: 3323935--3323996 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
3323925 TTTTAATAAA
*
3323935 ATATGAATAAATACGAA-TAATATAAATAT
1 ATATGAATAAATAC-AATTAATACAAATAT
* *
3323964 ATATGAATAGATACAATTAATACAATTAT
1 ATATGAATAAATACAATTAATACAAATAT
3323993 ATAT
1 ATAT
3323997 AAGAATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (29 bp):
ATATGAATAAATACAATTAATACAAATAT
Found at i:3324095 original size:27 final size:25
Alignment explanation
Indices: 3324062--3324112 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3324052 TAAATTTGAT
*
3324062 ATATTAATAATATAAAAAAATATTTAC
1 ATATTAA-AAGAT-AAAAAATATTTAC
*
3324089 ATATTAAAAGATTAAAAATATTTA
1 ATATTAAAAGATAAAAAATATTTA
3324113 ATAATCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.50
26 4 0.18
27 7 0.32
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
ATATTAAAAGATAAAAAATATTTAC
Found at i:3324969 original size:2 final size:2
Alignment explanation
Indices: 3324962--3324992 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3324952 TTAATATCTT
3324962 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3324993 GAAGGAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3329504 original size:2 final size:2
Alignment explanation
Indices: 3329497--3329529 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3329487 CATGCCCGCC
3329497 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
3329530 CACACGTATG
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:3330456 original size:3 final size:3
Alignment explanation
Indices: 3330450--3330495 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3330440 ACAAATTTCG
3330450 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3330496 AGAAAAGGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3338640 original size:14 final size:14
Alignment explanation
Indices: 3338623--3338655 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3338613 TAAATATTTA
3338623 AAATATA-ATTATAT
1 AAATATATA-TATAT
3338637 AAATATATATATAT
1 AAATATATATATAT
3338651 AAATA
1 AAATA
3338656 ATTAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.94
15 1 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATATATATATAT
Found at i:3342181 original size:37 final size:38
Alignment explanation
Indices: 3342115--3342186 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 38
3342105 AAAGCACCCA
3342115 ATATCAAGATCCTACGGGGGAACAACATATTAAGTTAG
1 ATATCAAGATCCTACGGGGGAACAACATATTAAGTTAG
* *
3342153 ATATCAAGATCCTA-TGGGGAACATCATATTAAGT
1 ATATCAAGATCCTACGGGGGAACAACATATTAAGT
3342187 CTTTTTTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 18 0.56
38 14 0.44
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26
Consensus pattern (38 bp):
ATATCAAGATCCTACGGGGGAACAACATATTAAGTTAG
Found at i:3342231 original size:16 final size:16
Alignment explanation
Indices: 3342210--3342241 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3342200 CTGACTAAAT
3342210 CTATCAAAAGAAAGTA
1 CTATCAAAAGAAAGTA
*
3342226 CTATCAACAGAAAGTA
1 CTATCAAAAGAAAGTA
3342242 GAATCAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.19
Consensus pattern (16 bp):
CTATCAAAAGAAAGTA
Found at i:3342247 original size:16 final size:16
Alignment explanation
Indices: 3342212--3342250 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3342202 GACTAAATCT
*
3342212 ATCAAAAGAAAGTACT
1 ATCAAAAGAAAGTACA
* *
3342228 ATCAACAGAAAGTAGA
1 ATCAAAAGAAAGTACA
3342244 ATCAAAA
1 ATCAAAA
3342251 TGTTAACAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.59, C:0.13, G:0.13, T:0.15
Consensus pattern (16 bp):
ATCAAAAGAAAGTACA
Found at i:3346096 original size:13 final size:13
Alignment explanation
Indices: 3346078--3346103 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3346068 AAAATTTCTT
3346078 TCCCTTAATACTG
1 TCCCTTAATACTG
3346091 TCCCTTAATACTG
1 TCCCTTAATACTG
3346104 GAAACCTTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (13 bp):
TCCCTTAATACTG
Found at i:3354579 original size:22 final size:22
Alignment explanation
Indices: 3354522--3354580 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
3354512 TAATACAAAT
* *
3354522 ATAAAATACAATTTTAAAATTTA
1 ATAAAATA-AATATAAAAATTTA
* *
3354545 ACAATAAT-TATATAAAAATTTA
1 ATAA-AATAAATATAAAAATTTA
3354567 ATAAAATAAATATA
1 ATAAAATAAATATA
3354581 TATTTCATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
21 3 0.11
22 19 0.68
23 3 0.11
24 3 0.11
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAAAATAAATATAAAAATTTA
Found at i:3355250 original size:19 final size:19
Alignment explanation
Indices: 3355228--3355279 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
3355218 TAATTTTAAA
3355228 TTATATAAAATATTAAAAT
1 TTATATAAAATATTAAAAT
** *
3355247 TTATATATTTATATT-ATAT
1 TTATATA-AAATATTAAAAT
3355266 TTATATAAAA-ATTA
1 TTATATAAAATATTA
3355280 TATATTATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
17 3 0.12
18 1 0.04
19 17 0.65
20 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATATAAAATATTAAAAT
Found at i:3355373 original size:23 final size:23
Alignment explanation
Indices: 3355329--3355385 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
3355319 TTTTTTAATT
*
3355329 TTATTAAA-TTTATATATAATAA
1 TTATTAAATTTTAAATATAATAA
3355351 TTATTAAATTTTAAAT-TACATAA
1 TTATTAAATTTTAAATATA-ATAA
* *
3355374 TTTTTATATTTT
1 TTATTAAATTTT
3355386 TATTTATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.33
23 20 0.67
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTATTAAATTTTAAATATAATAA
Found at i:3357142 original size:32 final size:32
Alignment explanation
Indices: 3357097--3357158 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
3357087 TAAAATAAAT
*
3357097 AAATTTAATAATTTTTATATTTATATCATATA
1 AAATTTAATAATTTATATATTTATATCATATA
3357129 AAATATTAA-AATTTATATATTTATATCATA
1 AAAT-TTAATAATTTATATATTTATATCATA
3357159 ATTTACGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
AAATTTAATAATTTATATATTTATATCATATA
Found at i:3357296 original size:11 final size:12
Alignment explanation
Indices: 3357273--3357312 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
3357263 ATCGTATTTT
3357273 TTATATTTTTATA
1 TTATA-TTTTATA
3357286 TTATA-TTTATA
1 TTATATTTTATA
*
3357297 TCATATTTTATA
1 TTATATTTTATA
3357309 TTAT
1 TTAT
3357313 TAAATCTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.42
12 9 0.38
13 5 0.21
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:3358940 original size:15 final size:16
Alignment explanation
Indices: 3358920--3358949 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3358910 TGGGTACTTC
3358920 TGTTTTTT-TTTTTTT
1 TGTTTTTTGTTTTTTT
3358935 TGTTTTTTGTTTTTT
1 TGTTTTTTGTTTTTT
3358950 AGTTGTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (16 bp):
TGTTTTTTGTTTTTTT
Found at i:3370685 original size:24 final size:24
Alignment explanation
Indices: 3370649--3370695 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
3370639 TTTCAAACTC
3370649 AGGGTGGAATATGAGTGGCTACGT
1 AGGGTGGAATATGAGTGGCTACGT
*
3370673 AGGGTGGAGTATGAGTGGCTACG
1 AGGGTGGAATATGAGTGGCTACG
3370696 AAGAGAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.45, T:0.23
Consensus pattern (24 bp):
AGGGTGGAATATGAGTGGCTACGT
Found at i:3383954 original size:2 final size:2
Alignment explanation
Indices: 3383947--3383973 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3383937 AACATAGCAA
3383947 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 A
3383974 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3385314 original size:30 final size:31
Alignment explanation
Indices: 3385278--3385339 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
3385268 TTTAGGATTT
3385278 AGTTAC-GAAAATTGCAGTAACTATCAAACC
1 AGTTACGGAAAATTGCAGTAACTATCAAACC
3385308 AGTTACGGAAAATTGCAGTAACTATCAAACC
1 AGTTACGGAAAATTGCAGTAACTATCAAACC
3385339 A
1 A
3385340 ATTTATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 6 0.19
31 25 0.81
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.23
Consensus pattern (31 bp):
AGTTACGGAAAATTGCAGTAACTATCAAACC
Found at i:3386311 original size:13 final size:12
Alignment explanation
Indices: 3386293--3386318 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3386283 TCATTAAAAT
3386293 TTAAAAAAATAA
1 TTAAAAAAATAA
3386305 TTAAAAAAATAA
1 TTAAAAAAATAA
3386317 TT
1 TT
3386319 TCGCGAGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TTAAAAAAATAA
Found at i:3387508 original size:12 final size:13
Alignment explanation
Indices: 3387491--3387520 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
3387481 AGAAACAATT
3387491 AAATTAAAAAT-A
1 AAATTAAAAATCA
3387503 AAATTAAAAATCA
1 AAATTAAAAATCA
3387516 AAATT
1 AAATT
3387521 GATAGATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATTAAAAATCA
Found at i:3387949 original size:22 final size:22
Alignment explanation
Indices: 3387921--3387965 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3387911 TTAACCCATT
* *
3387921 TTTAAGTATGTAATTTAGCCTA
1 TTTAAGTAAGCAATTTAGCCTA
3387943 TTTAAGTAAGCAATTTAGCCTA
1 TTTAAGTAAGCAATTTAGCCTA
3387965 T
1 T
3387966 GTTTGGATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.42
Consensus pattern (22 bp):
TTTAAGTAAGCAATTTAGCCTA
Found at i:3389075 original size:16 final size:16
Alignment explanation
Indices: 3389056--3389087 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3389046 AATTTGAATA
3389056 ATCGGATTATTGAAGG
1 ATCGGATTATTGAAGG
3389072 ATCGGATTATTGAAGG
1 ATCGGATTATTGAAGG
3389088 TGATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.31
Consensus pattern (16 bp):
ATCGGATTATTGAAGG
Found at i:3392996 original size:25 final size:25
Alignment explanation
Indices: 3392959--3393006 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
3392949 GTGCTTAGAC
* *
3392959 ATACCTTTTAGCAAACCATTCAGAA
1 ATACCATTCAGCAAACCATTCAGAA
* *
3392984 ATACCATTCAGCATACGATTCAG
1 ATACCATTCAGCAAACCATTCAG
3393007 TAAACCAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.27
Consensus pattern (25 bp):
ATACCATTCAGCAAACCATTCAGAA
Found at i:3393115 original size:102 final size:102
Alignment explanation
Indices: 3392927--3393115 Score: 252
Period size: 102 Copynumber: 1.9 Consensus size: 102
3392917 AAGAAACATC
* * * * * * *
3392927 ATTCAGTAAACCAATCAATAATGTGCTTAGACATACCTTTTAGCAAACCATTCAGAAATACCATT
1 ATTCAGCAAACAAATCAATAATGTGCTTAGACACACCATTCAGCAAACCATTCAAAAATACAATT
* **
3392992 CAGCATACGATTCAGTAAACCAATATCATACAATATT
66 CAGCAAACGATTCAACAAACCAATATCATACAATATT
* *
3393029 ATTCAGCAAACAAATCAATAATGTGCTTAGACACACCATTCAGTAAACTATTCAAAAATACAATT
1 ATTCAGCAAACAAATCAATAATGTGCTTAGACACACCATTCAGCAAACCATTCAAAAATACAATT
* *
3393094 CAGCAAACTATTCAACCAACCA
66 CAGCAAACGATTCAACAAACCA
3393116 TTCAGTATAC
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
102 73 1.00
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26
Consensus pattern (102 bp):
ATTCAGCAAACAAATCAATAATGTGCTTAGACACACCATTCAGCAAACCATTCAAAAATACAATT
CAGCAAACGATTCAACAAACCAATATCATACAATATT
Found at i:3394757 original size:187 final size:185
Alignment explanation
Indices: 3393928--3394867 Score: 863
Period size: 188 Copynumber: 5.0 Consensus size: 185
3393918 TTTATACAAA
* * *
3393928 AAGACATC-TTTAATAATCTCAAATA-TTTTTAAAAGGAATTTATTGAATGTATTTGTTCTAAAA
1 AAGACA-CATTTAATAATCTCAAATATTTTTTAAAA-GAAATTATTGAAGGCATTTGTTCTAAAA
* * *
3393991 AAATACCTTCAATAATTATGTACA-AAATTTTAAA-AAAATTATTGAAAGCATTTTTCTGGAATA
64 AAATACCTTCAATAATTATGTACATAAA--TTAAATGAAATCATTG-AAGCATTTTTCTAGAATA
* *
3394054 AACGCCTTCACTAACCATCTTAAAATTTGAGTGATG-GATATT-AAAGGCGTTTTTCACTAG
126 AACTCCTTCACTAACCATCTTAAAATTTGAGT-ATGAAATATTGAAA-GCGTTTTTCACTAG
* * * * * * *
3394114 AAGACGCATTTAATAATCTTAAAAATTTTTTAAAAGAATTTATTGAAGACGTTTATTCTAAAAAA
1 AAGACACATTTAATAATCTCAAATATTTTTTAAAAGAAATTATTGAAGGCATTTGTTCTAAAAAA
* ** * *
3394179 ATACCTTCAATAATTATATATGTAAATTAAATGGAATCAGTGAATGCATTTTTCTAGAATAAA-T
66 ATACCTTCAATAATTATGTACATAAATTAAATGAAATCATTGAA-GCATTTTTCTAGAATAAACT
* * * * *
3394243 GCCTTCATTAACCATTTTAAAATTTGAGTAGTGAAATATTGAAGGTGTTTTTAACT-G
130 -CCTTCACTAACCATCTTAAAATTTGAGTA-TGAAATATTGAAAGCGTTTTTCACTAG
* * * * *
3394300 AAAAACACATTTAATAATCTCAAATATTTTTAAAAAGAAATTATTGAAAGCGTTTGTTCTCAAGA
1 -AAGACACATTTAATAATCTCAAATATTTTTTAAAAGAAATTATTGAAGGCATTTGTTCT-AAAA
* * ** * **
3394365 AAACACCTTCAATAATTATGTACA-AAGTTAAAAAAAAATTATTGAAGGTGTTTTTCTAGAATAA
64 AAATACCTTCAATAATTATGTACATAAATT-AAATGAAATCATTGAA-GCATTTTTCTAGAATAA
* ** * * *
3394429 ACGCCATT-ACTAACTTTCTTAAAATTTGAGTGCT-AGTATATTGAAGGCGTTTTTCACTAG
127 ACTCC-TTCACTAACCATCTTAAAATTTGAGT-ATGA-AATATTGAAAGCGTTTTTCACTAG
* * * * * *
3394489 AAGATACTTTTAATAATCCTAAAAAAATGTTTT-AAA-AAATTATTGAAGGTATTTGTTCTAAAA
1 AAGACACATTTAATAAT-CT-CAAATATTTTTTAAAAGAAATTATTGAAGGCATTTGTTCTAAAA
* * *
3394552 AAA-AGCCTTTACTAATTATGTACATAAATTAAATGAAATCATTGAATGCAATTTTTTTAGAATA
64 AAATA-CCTTCAATAATTATGTACATAAATTAAATGAAATCATTGAA-GC-ATTTTTCTAGAATA
* ** * ** *
3394616 AACTCATTCACTAACTGTCTTAAAATTTGAGTATTGAAATATCGAAAGTATTTTTTACT-G
126 AACTCCTTCACTAACCATCTTAAAATTTGAGTA-TGAAATATTGAAAGCGTTTTTCACTAG
** * *
3394676 AAAGATGCCTTTAATAATCTCAAATATTTTTTAAAA-AAATTATTGAAGGCATTTGTTCTCAAAA
1 -AAGACACATTTAATAATCTCAAATATTTTTTAAAAGAAATTATTGAAGGCATTTGTTCTAAAAA
* * * *
3394740 AATACCTTCAATAATTATATACATAAATTAAATGGAAA-CAGTGAAGGTATTTTTCTAGCATAAA
65 AATACCTTCAATAATTATGTACATAAATTAAAT-GAAATCATTGAA-GCATTTTTCTAGAATAAA
* * * *
3394804 -TACCTTCACTAACCATCTAAAAATTTGAGTAATGGAATATTGAAGGCGTTTTGCACTAG
128 CT-CCTTCACTAACCATCTTAAAATTTGAGT-ATGAAATATTGAAAGCGTTTTTCACTAG
3394863 AAGAC
1 AAGAC
3394868 GCTTTAAATA
Statistics
Matches: 609, Mismatches: 113, Indels: 64
0.77 0.14 0.08
Matches are distributed among these distances:
185 10 0.02
186 186 0.31
187 190 0.31
188 206 0.34
189 9 0.01
190 8 0.01
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (185 bp):
AAGACACATTTAATAATCTCAAATATTTTTTAAAAGAAATTATTGAAGGCATTTGTTCTAAAAAA
ATACCTTCAATAATTATGTACATAAATTAAATGAAATCATTGAAGCATTTTTCTAGAATAAACTC
CTTCACTAACCATCTTAAAATTTGAGTATGAAATATTGAAAGCGTTTTTCACTAG
Found at i:3394914 original size:374 final size:365
Alignment explanation
Indices: 3393926--3394940 Score: 1083
Period size: 374 Copynumber: 2.7 Consensus size: 365
3393916 GTTTTATACA
* * * * *
3393926 AAAAGACATCTTTAATAATCTCAAATA-TTTTTAAAAGGAATTTATTGAATGTATTTGTTCTAAA
1 AAAA-ACACCTTTAATAATCTCAAATATTTTTTAAAA-GAAATTATTGAAAGCATTTGTTCTCAA
* * *
3393990 AAAATACCTTCAATAATTATGTACAAAATTTTAAAAAAATTATTGAAAGCATTTTTCTGGAATAA
64 AAAATACCTTCAATAATTATGTACAAAA--TTAAAAAAATTATTGAAGGTATTTTTCTAGAATAA
*
3394055 ACGCCTTCACTAACCATCTTAAAATTTGAGTGATGGATATTAAAGGCGTTTTTCACTAGAAGACG
127 ACGCCTTCACTAACCATCTTAAAATTTGAGTGATGGATATTGAAGGCGTTTTTCACTAGAAGACG
** *
3394120 CATTTAATAATCTTAAAAATTTTTTAAAAGAATTTATTGAAGACGT-TTATTCTAAAAAAATACC
192 C-TTTAATAATCTTAAAAA---AATAAAAGAA-TTATTGAAG--GTATTTTTCTAAAAAAATACC
** * *
3394184 TTCAATAATTATATATGTAAATTAAATGGAATCAGTGAATGCATTTTTCTAGAATAAATGCCTTC
250 TTCAATAATTATATACATAAATTAAATGAAATCAGTGAATGCATTTTTCTAGAATAAATGCATTC
* * * * *
3394249 ATTAACCATTTTAAAATTTGAGTAGTGAAATATTGAAGGTGTTTTTAACTG
315 ACTAACCATCTTAAAATTTGAGTAGTGAAATATCGAAAGTATTTTTAACTG
* * *
3394300 AAAAACACATTTAATAATCTCAAATATTTTTAAAAAGAAATTATTGAAAGCGTTTGTTCTCAAGA
1 AAAAACACCTTTAATAATCTCAAATATTTTTTAAAAGAAATTATTGAAAGCATTTGTTCTCAA-A
* * *
3394365 AAACACCTTCAATAATTATGTACAAAGTTAAAAAAAAATTATTGAAGGTGTTTTTCTAGAATAAA
65 AAATACCTTCAATAATTATGTACAAAATT--AAAAAAATTATTGAAGGTATTTTTCTAGAATAAA
** * * *
3394430 CGCCATT-ACTAACTTTCTTAAAATTTGAGTGCTAGTATATTGAAGGCGTTTTTCACTAGAAGAT
128 CGCC-TTCACTAACCATCTTAAAATTTGAGTGAT-GGATATTGAAGGCGTTTTTCACTAGAAGAC
* *
3394494 ACTTTTAATAATCCTAAAAAAATGTTTTAAAA-AATTATTGAAGGTATTTGTTCTAAAAAAA-AG
191 GC-TTTAATAATCTTAAAAAAA-----TAAAAGAATTATTGAAGGTATTT-TTCTAAAAAAATA-
* * * * *
3394557 CCTTTACTAATTATGTACATAAATTAAATGAAATCATTGAATGCAATTTTTTTAGAATAAACT-C
248 CCTTCAATAATTATATACATAAATTAAATGAAATCAGTGAATGC-ATTTTTCTAGAATAAA-TGC
** * *
3394621 ATTCACTAACTGTCTTAAAATTTGAGTATTGAAATATCGAAAGTATTTTTTACTG
311 ATTCACTAACCATCTTAAAATTTGAGTAGTGAAATATCGAAAGTATTTTTAACTG
* ** *
3394676 AAAGATGCCTTTAATAATCTCAAATATTTTTTAAAA-AAATTATTGAAGGCATTTGTTCTCAAAA
1 AAAAACACCTTTAATAATCTCAAATATTTTTTAAAAGAAATTATTGAAAGCATTTGTTCTCAAAA
* * * * *
3394740 AATACCTTCAATAATTATATACATAAATTAAATGGAAA-CAGTGAAGGTATTTTTCTAGCATAAA
66 AATACCTTCAATAATTATGTACA-AAATTAAA--AAAATTATTGAAGGTATTTTTCTAGAATAAA
** * * *
3394804 TACCTTCACTAACCATCTAAAAATTTGAGTAATGGAATATTGAAGGCGTTTTGCACTAGAAGACG
128 CGCCTTCACTAACCATCTTAAAATTTGAGTGATGG-ATATTGAAGGCGTTTTTCACTAGAAGACG
* * * * * *
3394869 CTTTAAATAAATTTTATCAAAAAATAAAATGAATTAGTCAAGGTATTTTTCTTGAATAAATGCCT
192 CTTT-AAT-AATCTTA--AAAAAATAAAA-GAATTATTGAAGGTATTTTTC-TAAAAAAATACCT
3394934 TCAATAA
251 TCAATAA
3394941 CCCTTTAAAA
Statistics
Matches: 533, Mismatches: 79, Indels: 58
0.80 0.12 0.09
Matches are distributed among these distances:
372 7 0.01
373 56 0.11
374 225 0.42
375 139 0.26
376 94 0.18
377 12 0.02
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (365 bp):
AAAAACACCTTTAATAATCTCAAATATTTTTTAAAAGAAATTATTGAAAGCATTTGTTCTCAAAA
AATACCTTCAATAATTATGTACAAAATTAAAAAAATTATTGAAGGTATTTTTCTAGAATAAACGC
CTTCACTAACCATCTTAAAATTTGAGTGATGGATATTGAAGGCGTTTTTCACTAGAAGACGCTTT
AATAATCTTAAAAAAATAAAAGAATTATTGAAGGTATTTTTCTAAAAAAATACCTTCAATAATTA
TATACATAAATTAAATGAAATCAGTGAATGCATTTTTCTAGAATAAATGCATTCACTAACCATCT
TAAAATTTGAGTAGTGAAATATCGAAAGTATTTTTAACTG
Found at i:3402959 original size:2 final size:2
Alignment explanation
Indices: 3402952--3402983 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3402942 GCATGCGAGT
3402952 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3402984 GCGGCCATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3403060 original size:2 final size:2
Alignment explanation
Indices: 3403053--3403089 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3403043 ATTCATCCTC
3403053 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3403090 GCGGCCATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3403132 original size:106 final size:105
Alignment explanation
Indices: 3402952--3403159 Score: 398
Period size: 106 Copynumber: 2.0 Consensus size: 105
3402942 GCATGCGAGT
*
3402952 TATATATATATATATATATATATATATATATAGCGGCCATCCATCACTTTCTCTTAAAAATAACG
1 TATATATATATATATATATATATATATATATAGCGGCCATCCATCACTTTCTCTTAAAAATAACA
3403017 CATGCACCAAAGCTAAAAAAATATTGATTCATCCTCTATA
66 CATGCACCAAAGCTAAAAAAATATTGATTCATCCTCTATA
3403057 TATATATATATATATATATATATATATATATATGCGGCCATCCATCACTTTCTCTTAAAAATAAC
1 TATATATATATATATATATATATATATATATA-GCGGCCATCCATCACTTTCTCTTAAAAATAAC
3403122 ACATGCACCAAAGCTAAAAAAATATTGATTCATCCTCT
65 ACATGCACCAAAGCTAAAAAAATATTGATTCATCCTCT
3403160 CTCTCTATGT
Statistics
Matches: 101, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
105 32 0.32
106 69 0.68
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (105 bp):
TATATATATATATATATATATATATATATATAGCGGCCATCCATCACTTTCTCTTAAAAATAACA
CATGCACCAAAGCTAAAAAAATATTGATTCATCCTCTATA
Found at i:3406622 original size:20 final size:22
Alignment explanation
Indices: 3406592--3406634 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3406582 CTTTATCTTT
*
3406592 TTTTGTTATTTATA-TTTTTCA
1 TTTTGTTATTTAAAGTTTTTCA
3406613 TTTT-TTATTTAAAGTTTTTCA
1 TTTTGTTATTTAAAGTTTTTCA
3406634 T
1 T
3406635 ATAACATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.70
Consensus pattern (22 bp):
TTTTGTTATTTAAAGTTTTTCA
Found at i:3411602 original size:19 final size:18
Alignment explanation
Indices: 3411574--3411625 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
3411564 TGTACAAAAT
*
3411574 AAAATGCAAATAAAATAGAA
1 AAAAT-CAAATAAAAT-CAA
*
3411594 AAAATCAAATCAAATCAA
1 AAAATCAAATAAAATCAA
*
3411612 AAAATAAAATAAAA
1 AAAATCAAATAAAA
3411626 AAAGGAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 14 0.50
19 9 0.32
20 5 0.18
ACGTcount: A:0.73, C:0.08, G:0.04, T:0.15
Consensus pattern (18 bp):
AAAATCAAATAAAATCAA
Found at i:3412438 original size:3 final size:3
Alignment explanation
Indices: 3412430--3412474 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3412420 TTTAAAACAA
3412430 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3412475 CAAATAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3412989 original size:18 final size:18
Alignment explanation
Indices: 3412966--3413004 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3412956 CTTCACAAGA
*
3412966 ATTTC-AAATTTCGTAAAG
1 ATTTCAAAAGTTCGT-AAG
3412984 ATTTCAAAAGTTCGTAAG
1 ATTTCAAAAGTTCGTAAG
3413002 ATT
1 ATT
3413005 CCATATTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (18 bp):
ATTTCAAAAGTTCGTAAG
Found at i:3412989 original size:35 final size:32
Alignment explanation
Indices: 3412872--3412990 Score: 89
Period size: 35 Copynumber: 3.5 Consensus size: 32
3412862 ATTACAAAAG
3412872 TTCGT-AAGATTTCAGATTCACAAGGATTCTAAAT
1 TTCGTAAAGATTTCA-ATTCACAA-GATTC-AAAT
* * * * *
3412906 TTCGCAAAGGTTTCAAATTCGCAAGAGTCCAAAC
1 TTCGTAAAGATTTC-AATTCACAAGA-TTCAAAT
*
3412940 TT-GTAAAAGTTTTCAACTTCACAAGAATTTCAAAT
1 TTCGT-AAAGATTTCAA-TTCACAAG-A-TTCAAAT
3412975 TTCGTAAAGATTTCAA
1 TTCGTAAAGATTTCAA
3412991 AAGTTCGTAA
Statistics
Matches: 66, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
33 3 0.05
34 26 0.39
35 34 0.52
36 3 0.05
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (32 bp):
TTCGTAAAGATTTCAATTCACAAGATTCAAAT
Found at i:3413079 original size:17 final size:17
Alignment explanation
Indices: 3412950--3413080 Score: 63
Period size: 17 Copynumber: 7.5 Consensus size: 17
3412940 TTGTAAAAGT
* *
3412950 TTTCAACTTCACAAGAA
1 TTTCAAATTCACAAGGA
** *
3412967 TTTCAAATTTCGTAAAGA
1 TTTCAAA-TTCACAAGGA
**
3412985 TTTCAAAAGTTCGTAA-GA
1 TTTC-AAA-TTCACAAGGA
* *
3413003 TTCCATATTCACAAGGA
1 TTTCAAATTCACAAGGA
* *
3413020 TTGCAAATTTTAC-A-GA
1 TTTCAAA-TTCACAAGGA
3413036 TATTCCAAATTCACAAAGG-
1 T-TT-CAAATTCAC-AAGGA
*
3413055 TTTTAAATTCACAAGGA
1 TTTCAAATTCACAAGGA
3413072 TTTCAAATT
1 TTTCAAATT
3413081 TTGTAGAATA
Statistics
Matches: 87, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
16 12 0.14
17 37 0.43
18 25 0.29
19 12 0.14
20 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (17 bp):
TTTCAAATTCACAAGGA
Found at i:3413256 original size:19 final size:19
Alignment explanation
Indices: 3413232--3413369 Score: 112
Period size: 19 Copynumber: 7.6 Consensus size: 19
3413222 CAGGTTTGCT
3413232 AGAAATTCAAAGATTCGTA
1 AGAAATTCAAAGATTCGTA
*
3413251 AGAAATTC-AA-ATTTGTA
1 AGAAATTCAAAGATTCGTA
* *
3413268 AAAAATTC-AAG-TTCATA
1 AGAAATTCAAAGATTCGTA
**
3413285 AGAAATTTGAAGATTCGTA
1 AGAAATTCAAAGATTCGTA
* * *
3413304 AGAGATTC-ATG-TTTGTA
1 AGAAATTCAAAGATTCGTA
3413321 AGAAATTCAAAGATTCGTA
1 AGAAATTCAAAGATTCGTA
* *
3413340 A-AAACTTTAAAGATTTC-CA
1 AGAAA-TTCAAAGA-TTCGTA
3413359 AGAAATTCAAA
1 AGAAATTCAAA
3413370 ACCTAAAGCT
Statistics
Matches: 94, Mismatches: 17, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
17 37 0.39
18 12 0.13
19 39 0.41
20 6 0.06
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.30
Consensus pattern (19 bp):
AGAAATTCAAAGATTCGTA
Found at i:3413273 original size:17 final size:18
Alignment explanation
Indices: 3413234--3413343 Score: 82
Period size: 17 Copynumber: 6.1 Consensus size: 18
3413224 GGTTTGCTAG
*
3413234 AAATTCAAAGATTCGTAAG
1 AAATTC-AAGATTCGTAAA
*
3413253 AAATTCAA-ATTTGTAAA
1 AAATTCAAGATTCGTAAA
*
3413270 AAATTCAAG-TTCATAAGA
1 AAATTCAAGATTCGTAA-A
* * *
3413288 AATTTGAAGATTCGTAAG
1 AAATTCAAGATTCGTAAA
* * * *
3413306 AGATTCATG-TTTGTAAG
1 AAATTCAAGATTCGTAAA
3413323 AAATTCAAAGATTCGTAAA
1 AAATTC-AAGATTCGTAAA
3413342 AA
1 AA
3413344 CTTTAAAGAT
Statistics
Matches: 69, Mismatches: 17, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
17 32 0.46
18 17 0.25
19 20 0.29
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (18 bp):
AAATTCAAGATTCGTAAA
Found at i:3413274 original size:36 final size:35
Alignment explanation
Indices: 3413234--3413343 Score: 114
Period size: 36 Copynumber: 3.1 Consensus size: 35
3413224 GGTTTGCTAG
*
3413234 AAATTCAAAGATTCGTAAGAAATTCAA-ATTTGTAAA
1 AAATTC-AAG-TTCGTAAGAAATTCAAGATTCGTAAA
* * *
3413270 AAATTCAAGTTCATAAGAAATTTGAAGATTCGTAAG
1 AAATTCAAGTTCGTAAGAAA-TTCAAGATTCGTAAA
* * *
3413306 AGATTCATGTTTGTAAGAAATTCAAAGATTCGTAAA
1 AAATTCAAGTTCGTAAGAAATTC-AAGATTCGTAAA
3413342 AA
1 AA
3413344 CTTTAAAGAT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
34 10 0.17
35 9 0.15
36 41 0.68
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (35 bp):
AAATTCAAGTTCGTAAGAAATTCAAGATTCGTAAA
Found at i:3413289 original size:53 final size:55
Alignment explanation
Indices: 3413232--3413369 Score: 158
Period size: 53 Copynumber: 2.5 Consensus size: 55
3413222 CAGGTTTGCT
*
3413232 AGAAATTCAAAGATTCGTAAGAAATTCAAATTTGTAAAAAATTC-AAG-TTCATA
1 AGAAATTTAAAGATTCGTAAGAAATTCAAATTTGTAAAAAATTCAAAGATTCATA
* * ** * *
3413285 AGAAATTTGAAGATTCGTAAGAGATTCATGTTTGTAAGAAATTCAAAGATTCGTA
1 AGAAATTTAAAGATTCGTAAGAAATTCAAATTTGTAAAAAATTCAAAGATTCATA
*
3413340 A-AAACTTTAAAGATTTC-CAAGAAATTCAAA
1 AGAAA-TTTAAAGA-TTCGTAAGAAATTCAAA
3413370 ACCTAAAGCT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
53 38 0.55
54 6 0.09
55 22 0.32
56 3 0.04
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.30
Consensus pattern (55 bp):
AGAAATTTAAAGATTCGTAAGAAATTCAAATTTGTAAAAAATTCAAAGATTCATA
Found at i:3413519 original size:44 final size:45
Alignment explanation
Indices: 3413469--3413723 Score: 216
Period size: 45 Copynumber: 5.7 Consensus size: 45
3413459 CATCCAAAAG
** * *
3413469 TCAAAGATTTTCATT-GAAAAATTATAGGATTCACATATGAAATT
1 TCAAAGATTCACATTAGAAAAATTTTGGGATTCACATATGAAATT
* * * *
3413513 TCAAAGATTCACATT-CATAAATTTTGGGATTCAC-TTTCAAAATTT
1 TCAAAGATTCACATTAGAAAAATTTTGGGATTCACATAT-GAAA-TT
* * * *
3413558 TCAAAGATTCACATTCA-AAAAATTTTGAGATTTACCTTTGAAATT
1 TCAAAGATTCACATT-AGAAAAATTTTGGGATTCACATATGAAATT
** * * **
3413603 TCAAAGATTCTTATTAAAAAAAATTTTGGGATTCTCATATGAAAGC
1 TCAAAGATTCACATT-AGAAAAATTTTGGGATTCACATATGAAATT
** *
3413649 T-AAAGATTTTCATT-GAAAAATTTTGGGATTCATATATGAAATT
1 TCAAAGATTCACATTAGAAAAATTTTGGGATTCACATATGAAATT
* * *
3413692 TTAAATATTCACATTCGAAAAATTTTGGGATT
1 TCAAAGATTCACATTAGAAAAATTTTGGGATT
3413724 TTGCATCCAA
Statistics
Matches: 171, Mismatches: 32, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
43 27 0.16
44 41 0.24
45 60 0.35
46 40 0.23
47 3 0.02
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (45 bp):
TCAAAGATTCACATTAGAAAAATTTTGGGATTCACATATGAAATT
Done.