Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397261.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_50.0, 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: 9139585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 37885 characters in sequence are not A, C, G, or T
File 10 of 19
Found at i:3705332 original size:16 final size:16
Alignment explanation
Indices: 3705290--3705332 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3705280 ATGTTATTAT
3705290 AATTATT-TATTTTTA
1 AATTATTATATTTTTA
*
3705305 AATTATTTTATTTTTA
1 AATTATTATATTTTTA
3705321 AA-TATTAATATT
1 AATTATT-ATATT
3705333 GTATAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
AATTATTATATTTTTA
Found at i:3705666 original size:23 final size:23
Alignment explanation
Indices: 3705636--3705797 Score: 92
Period size: 23 Copynumber: 7.1 Consensus size: 23
3705626 TTTATTTTAT
3705636 TTTA-ATTTTTAAATATTAATAA
1 TTTATATTTTTAAATATTAATAA
* *
3705658 TTTATATTTTATCAAAAATTAATTA
1 TTTATATTTT-T-AAATATTAATAA
*
3705683 -TTAT-TTTTTCAAATGTTAAT-A
1 TTTATATTTTT-AAATATTAATAA
* *
3705704 TTT-TATTTAT-AAT-TTAA-AT
1 TTTATATTTTTAAATATTAATAA
* * *
3705723 TTTATTATGATTATT-TATTTTATTTAA
1 TTTA-TAT--TT-TTAAATATTA-ATAA
3705750 TTT-TATATTTTAAATATTAATAA
1 TTTATAT-TTTTAAATATTAATAA
*
3705773 TTAATATTTTTAAATATTAATAA
1 TTTATATTTTTAAATATTAATAA
3705796 TT
1 TT
3705798 GATTATTAAT
Statistics
Matches: 110, Mismatches: 14, Indels: 31
0.71 0.09 0.20
Matches are distributed among these distances:
19 7 0.06
20 3 0.03
21 5 0.05
22 20 0.18
23 36 0.33
24 19 0.17
25 16 0.15
27 4 0.04
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (23 bp):
TTTATATTTTTAAATATTAATAA
Found at i:3705730 original size:47 final size:46
Alignment explanation
Indices: 3705629--3705730 Score: 102
Period size: 47 Copynumber: 2.2 Consensus size: 46
3705619 ACTTATTTTT
3705629 ATTTTATT-TTAATTTTTAAATATTAATAATTTATATTTTATCAAA
1 ATTTTATTATTAATTTTTAAATATTAATAATTTATATTTTATCAAA
* * * * **
3705674 AATTAATTATTATTTTTTCAAATGTTAAT-ATTT-TATTTATAATTTAA
1 ATTTTATTATTAATTTTT-AAATATTAATAATTTATATTT-T-ATCAAA
3705721 ATTTTATTAT
1 ATTTTATTAT
3705731 GATTATTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
45 11 0.24
46 13 0.29
47 21 0.47
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (46 bp):
ATTTTATTATTAATTTTTAAATATTAATAATTTATATTTTATCAAA
Found at i:3705797 original size:116 final size:117
Alignment explanation
Indices: 3705592--3705804 Score: 310
Period size: 115 Copynumber: 1.8 Consensus size: 117
3705582 NNNNNNNNNN
*
3705592 ATTTATAATTTAAATTTTATTAGGATTACTTATTTTTATTTTATTTTAATTTTTAAATATTAATA
1 ATTTATAATTTAAATTTTATTAGGATTACTTATTTTTATTTAATTTTAATTTTTAAATATTAATA
* *
3705657 ATTTATATTTTATCAAAAATTAATT-ATTATTTTTTCAAATGTTAATATTTT
66 ATTAATATTTTATCAAAAAATAATTGATTATTTTTTCAAATGTTAATATTTT
* *
3705708 ATTTATAATTTAAATTTTATTATGATTATTTA-TTTTATTTAATTTT-ATATTTTAAATATTAAT
1 ATTTATAATTTAAATTTTATTAGGATTACTTATTTTTATTTAATTTTAAT-TTTTAAATATTAAT
3705771 AATTAATATTTT-T-AAATATTAATAATTGATTATT
65 AATTAATATTTTATCAAA-A--AATAATTGATTATT
3705805 AATTATTAAT
Statistics
Matches: 87, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
113 3 0.03
114 4 0.05
115 38 0.44
116 36 0.41
117 6 0.07
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (117 bp):
ATTTATAATTTAAATTTTATTAGGATTACTTATTTTTATTTAATTTTAATTTTTAAATATTAATA
ATTAATATTTTATCAAAAAATAATTGATTATTTTTTCAAATGTTAATATTTT
Found at i:3706172 original size:14 final size:14
Alignment explanation
Indices: 3706155--3706210 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
3706145 AAAATATTAA
*
3706155 TAATTTTTTAATTT
1 TAATTTTGTAATTT
** *
3706169 TAA-TTTAAAATAT
1 TAATTTTGTAATTT
*
3706182 TAATTTTGTAAATT
1 TAATTTTGTAATTT
*
3706196 TAAGTTTGTAATTT
1 TAATTTTGTAATTT
3706210 T
1 T
3706211 TTTTTTTAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 10 0.31
14 22 0.69
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (14 bp):
TAATTTTGTAATTT
Found at i:3713985 original size:15 final size:16
Alignment explanation
Indices: 3713954--3713986 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3713944 TAAATTATTA
3713954 AAAATTATAAAAAAAT
1 AAAATTATAAAAAAAT
*
3713970 AAAATTA-AAAACAAT
1 AAAATTATAAAAAAAT
3713985 AA
1 AA
3713987 TTTTATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATTATAAAAAAAT
Found at i:3714202 original size:15 final size:15
Alignment explanation
Indices: 3714182--3714240 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 15
3714172 TTGCATCATG
3714182 TATATATATAATTTT
1 TATATATATAATTTT
*
3714197 TATATATAAAAATATTAT
1 TATATAT-ATAAT-TT-T
3714215 TAATTTATATATAATTTT
1 T-A--TATATATAATTTT
3714233 TATATATA
1 TATATATA
3714241 AAAATATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
15 13 0.36
16 4 0.11
17 3 0.08
18 4 0.11
19 3 0.08
20 4 0.11
21 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATATATAATTTT
Found at i:3714211 original size:21 final size:22
Alignment explanation
Indices: 3714187--3714228 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3714177 TCATGTATAT
3714187 ATATAATT-TTTATATATAAAA
1 ATATAATTATTTATATATAAAA
*
3714208 ATATTATTAATTTATATATAA
1 ATATAATT-ATTTATATATAA
3714229 TTTTTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATAATTATTTATATATAAAA
Found at i:3714224 original size:36 final size:36
Alignment explanation
Indices: 3714184--3714264 Score: 162
Period size: 36 Copynumber: 2.2 Consensus size: 36
3714174 GCATCATGTA
3714184 TATATATAATTTTTATATATAAAAATATTATTAATT
1 TATATATAATTTTTATATATAAAAATATTATTAATT
3714220 TATATATAATTTTTATATATAAAAATATTATTAATT
1 TATATATAATTTTTATATATAAAAATATTATTAATT
3714256 TATATATAA
1 TATATATAA
3714265 AGTAAGATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
TATATATAATTTTTATATATAAAAATATTATTAATT
Found at i:3714247 original size:21 final size:22
Alignment explanation
Indices: 3714223--3714265 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
3714213 ATTAATTTAT
3714223 ATATAATT-TTTATATATAAAA
1 ATATAATTATTTATATATAAAA
*
3714244 ATATTATTAATTTATATATAAA
1 ATATAATT-ATTTATATATAAA
3714266 GTAAGATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATAATTATTTATATATAAAA
Found at i:3724896 original size:30 final size:29
Alignment explanation
Indices: 3724849--3724966 Score: 105
Period size: 30 Copynumber: 4.1 Consensus size: 29
3724839 ATTTAAAAAA
* *
3724849 ATTTAA-TAAATTGTTATATTTTTATTTT
1 ATTTAATTAAATTTTTATATTATTATTTT
*
3724877 ATTTAATTAAAATTTTTATATTTTTATTTT
1 ATTTAATT-AAATTTTTATATTATTATTTT
* * * * * *
3724907 AAATTAAATAAATTTTTGTATTAATAATTA
1 -ATTTAATTAAATTTTTATATTATTATTTT
* *
3724937 ATTTAATTAAAATATTAT-TTATTATTTT
1 ATTTAATTAAATTTTTATATTATTATTTT
3724965 AT
1 AT
3724967 ATCATATACG
Statistics
Matches: 71, Mismatches: 16, Indels: 6
0.76 0.17 0.06
Matches are distributed among these distances:
28 15 0.21
29 14 0.20
30 36 0.51
31 6 0.08
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
ATTTAATTAAATTTTTATATTATTATTTT
Found at i:3724908 original size:22 final size:22
Alignment explanation
Indices: 3724866--3724911 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3724856 AAATTGTTAT
*
3724866 ATTTTTATTTTATTTAATTAAA
1 ATTTTTATATTATTTAATTAAA
* *
3724888 ATTTTTATATT-TTTATTTTAA
1 ATTTTTATATTATTTAATTAAA
3724909 ATT
1 ATT
3724912 AAATAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTTTATATTATTTAATTAAA
Found at i:3724917 original size:60 final size:58
Alignment explanation
Indices: 3724847--3724965 Score: 139
Period size: 60 Copynumber: 2.0 Consensus size: 58
3724837 TTATTTAAAA
* ** * * * *
3724847 AAATTTAATAAATTGTTATATTTTTATTTTATTTAATTAAAATTTTTATATTTTTATTTT
1 AAATTAAATAAATTGTTATATTAATAATTAATTTAATTAAAA-TATTAT-TTATTATTTT
* *
3724907 AAATTAAATAAATTTTTGTATTAATAATTAATTTAATTAAAATATTATTTATTATTTT
1 AAATTAAATAAATTGTTATATTAATAATTAATTTAATTAAAATATTATTTATTATTTT
3724965 A
1 A
3724966 TATCATATAC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
58 10 0.20
59 5 0.10
60 35 0.70
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (58 bp):
AAATTAAATAAATTGTTATATTAATAATTAATTTAATTAAAATATTATTTATTATTTT
Found at i:3729098 original size:94 final size:95
Alignment explanation
Indices: 3728932--3729117 Score: 320
Period size: 94 Copynumber: 2.0 Consensus size: 95
3728922 TTAAGAAGCC
3728932 ATTTCATGAAACAAGAAAAACTTTGCTTTTCCATTATTTATGTGGTCTCTGACATTCTAACAGGA
1 ATTTCATGAAACAAGAAAAACTTTGCTTTTCCATTATTTATGTGGTCTCTGACATTCTAACAGGA
*
3728997 CCTGCAGTTGTCACTGTATATATGGATCCA
66 CCTGCAGTTGTCACTGCATATATGGATCCA
* * *
3729027 ATTT-ATGAAGCAAGAAAAACTTTGCTTTTCCGTTATTTATGTGGTCTCTGACATTCTAACAGGC
1 ATTTCATGAAACAAGAAAAACTTTGCTTTTCCATTATTTATGTGGTCTCTGACATTCTAACAGGA
*
3729091 CCTGCAGTTGTCATTGCATATATGGAT
66 CCTGCAGTTGTCACTGCATATATGGAT
3729118 GTATATGATG
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
94 82 0.95
95 4 0.05
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (95 bp):
ATTTCATGAAACAAGAAAAACTTTGCTTTTCCATTATTTATGTGGTCTCTGACATTCTAACAGGA
CCTGCAGTTGTCACTGCATATATGGATCCA
Found at i:3748885 original size:27 final size:28
Alignment explanation
Indices: 3748827--3748887 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
3748817 CATATTAAAA
* *
3748827 AAAAAAATTATTGTTACATGTCATATTG
1 AAAAAAATTATTGTTACATGCCACATTG
*
3748855 AAAAAATTTATTGTTACATGCCACATT-
1 AAAAAAATTATTGTTACATGCCACATTG
3748882 AAAAAA
1 AAAAAA
3748888 CATTTTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 6 0.20
28 24 0.80
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (28 bp):
AAAAAAATTATTGTTACATGCCACATTG
Found at i:3762675 original size:134 final size:134
Alignment explanation
Indices: 3762431--3762702 Score: 406
Period size: 134 Copynumber: 2.0 Consensus size: 134
3762421 AATTAAAGTT
*** *
3762431 ACAACATATCACTAAAACTTGTTAGATTGGTTTCAATTAATTTAAAAATGTGCAGAACAGGCTGA
1 ACAACATATCACTAAAACTTGTTAGATTGGTTTCAATTAATTTAAAAACACGCAGAACAGGCTAA
* * *
3762496 AAGCAAGTTTTCACACAGCTATTCCTTAATTCTCATTAATTATTTCTTTGAGAA-AGGCTGCTGA
66 AAGCAAGTTTT-ACACAGCTATTCCTTAATTCTCATAAATGATTTCATTGAGAACAGGCTGCTGA
3762560 GGACC
130 GGACC
3762565 ACAACATATCACTAAAACTTGTTAGATTGGTTTCAATTAATTTAAAAACACGCAGAACAGGCTTT
1 ACAACATATCACTAAAACTTGTTAGATTGGTTTCAATTAATTTAAAAACACGCAGAACAGGC--T
* *
3762630 AAAAGCAA-TTTT-CACAGCTATTCTTTGATTCTCATCAAATGATTTCATTGAGAACAGGCTGCT
64 AAAAGCAAGTTTTACACAGCTATTCCTTAATTCTCAT-AAATGATTTCATTGAGAACAGGCTGCT
3762693 GAGGACC
128 GAGGACC
3762700 ACA
1 ACA
3762703 CAGACATTTG
Statistics
Matches: 125, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
133 21 0.17
134 74 0.59
135 22 0.18
136 8 0.06
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (134 bp):
ACAACATATCACTAAAACTTGTTAGATTGGTTTCAATTAATTTAAAAACACGCAGAACAGGCTAA
AAGCAAGTTTTACACAGCTATTCCTTAATTCTCATAAATGATTTCATTGAGAACAGGCTGCTGAG
GACC
Found at i:3763144 original size:17 final size:17
Alignment explanation
Indices: 3763109--3763142 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3763099 ATAATTAAAA
*
3763109 TATTTATTTTATTATTT
1 TATTTATTCTATTATTT
3763126 TATTTATTCT-TTATTT
1 TATTTATTCTATTATTT
3763142 T
1 T
3763143 TAAAATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TATTTATTCTATTATTT
Found at i:3763287 original size:28 final size:28
Alignment explanation
Indices: 3763240--3763294 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
3763230 AAACTTAAAC
* *
3763240 CTTTTAATTTCATATTCATTCTAATTTT
1 CTTTTAATTTCAAATCCATTCTAATTTT
* *
3763268 CTTTTAATTTTAAATCCATTTTAATTT
1 CTTTTAATTTCAAATCCATTCTAATTT
3763295 AGTGAGACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (28 bp):
CTTTTAATTTCAAATCCATTCTAATTTT
Found at i:3764115 original size:17 final size:16
Alignment explanation
Indices: 3764077--3764125 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
3764067 ATTTCTTTTT
*
3764077 ATTTTCTTTATT-TTC
1 ATTTTCTTTTTTCTTC
3764092 ATGTTTCCTTTTTTCTTC
1 AT-TTT-CTTTTTTCTTC
3764110 ATTTTCTTCTTTTCTT
1 ATTTTCTT-TTTTCTT
3764126 TCCTTTTCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 2 0.07
16 6 0.21
17 16 0.55
18 5 0.17
ACGTcount: A:0.08, C:0.18, G:0.02, T:0.71
Consensus pattern (16 bp):
ATTTTCTTTTTTCTTC
Found at i:3764126 original size:24 final size:24
Alignment explanation
Indices: 3764069--3764126 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
3764059 TTATTTCAAT
* *
3764069 TTCTTTT-TATTTTCTTTATTTTC
1 TTCTTTTCTTTTTTCTTCATTTTC
* * *
3764092 ATGTTTCCTTTTTTCTTCATTTTC
1 TTCTTTTCTTTTTTCTTCATTTTC
3764116 TTCTTTTCTTT
1 TTCTTTTCTTT
3764127 CCTTTTCTCA
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.74
Consensus pattern (24 bp):
TTCTTTTCTTTTTTCTTCATTTTC
Found at i:3764973 original size:39 final size:39
Alignment explanation
Indices: 3764929--3765008 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
3764919 TCACAAAAGT
3764929 AAAAATCCAAATAATAACATTAAACAATAAAACTTCTGA
1 AAAAATCCAAATAATAACATTAAACAATAAAACTTCTGA
3764968 AAAAATCCAAATAATAACATTAAACAATAAAACTTCTGA
1 AAAAATCCAAATAATAACATTAAACAATAAAACTTCTGA
3765007 AA
1 AA
3765009 TGTCAATAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.60, C:0.15, G:0.03, T:0.23
Consensus pattern (39 bp):
AAAAATCCAAATAATAACATTAAACAATAAAACTTCTGA
Found at i:3769603 original size:17 final size:19
Alignment explanation
Indices: 3769569--3769606 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
3769559 AAGTTTCTTT
3769569 TTTTTTTTAATTTCCTTGTC
1 TTTTTTTT-ATTTCCTTGTC
3769589 TTTTTTTT-TTT-CTTGTC
1 TTTTTTTTATTTCCTTGTC
3769606 T
1 T
3769607 CTGTCCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
20 8 0.44
ACGTcount: A:0.05, C:0.13, G:0.05, T:0.76
Consensus pattern (19 bp):
TTTTTTTTATTTCCTTGTC
Found at i:3776780 original size:21 final size:23
Alignment explanation
Indices: 3776756--3776798 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3776746 AAATTAATTA
3776756 ATAAAAA-GA-TAAAAAAACACC
1 ATAAAAATGACTAAAAAAACACC
3776777 ATAAAAATGACTAAAAAAACAC
1 ATAAAAATGACTAAAAAAACAC
3776799 AAAAGAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 2 0.10
23 11 0.55
ACGTcount: A:0.70, C:0.14, G:0.05, T:0.12
Consensus pattern (23 bp):
ATAAAAATGACTAAAAAAACACC
Found at i:3794643 original size:2 final size:2
Alignment explanation
Indices: 3794636--3794665 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3794626 TTCAAACGTG
3794636 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
3794666 CACAGCTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3794766 original size:68 final size:69
Alignment explanation
Indices: 3794647--3794783 Score: 235
Period size: 68 Copynumber: 2.0 Consensus size: 69
3794637 ATATATATAT
3794647 ATATATATATATATATATACACAGCTTTGTGGCATGCCAAAAATTATACAAACAACATCATGTGC
1 ATATATATATATATATATACACAGCTTTGTGGCATGCCAAAAATTATACAAACAACATCATGTGC
3794712 GGCA
66 GGCA
3794716 ATATATATATATATATATACACA-CTTTGT-GCAATGCCAAAAA-TATGACAAACAACATCATGT
1 ATATATATATATATATATACACAGCTTTGTGGC-ATGCCAAAAATTAT-ACAAACAACATCATGT
3794778 GCGGCA
64 GCGGCA
3794784 GAGGTCCAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
67 5 0.08
68 38 0.58
69 23 0.35
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (69 bp):
ATATATATATATATATATACACAGCTTTGTGGCATGCCAAAAATTATACAAACAACATCATGTGC
GGCA
Found at i:3796080 original size:2 final size:2
Alignment explanation
Indices: 3796026--3796060 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3796016 GTGGGAGGGA
3796026 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3796061 NNNNNNNNNN
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3796081 original size:2 final size:2
Alignment explanation
Indices: 3796071--3796100 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3796061 NNNNNNNNNN
3796071 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
3796101 GATGTTAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3800368 original size:16 final size:16
Alignment explanation
Indices: 3800347--3800379 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3800337 GAATCATCTG
3800347 TATTTTTCTTCTTCTT
1 TATTTTTCTTCTTCTT
*
3800363 TATTTTTTTTCTTCTT
1 TATTTTTCTTCTTCTT
3800379 T
1 T
3800380 TTGGTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (16 bp):
TATTTTTCTTCTTCTT
Found at i:3804736 original size:4 final size:4
Alignment explanation
Indices: 3804727--3804751 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3804717 TCTTAGGCAA
3804727 AATC AATC AATC AATC AATC AATC A
1 AATC AATC AATC AATC AATC AATC A
3804752 GATTAGCTCA
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:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
AATC
Found at i:3807096 original size:37 final size:37
Alignment explanation
Indices: 3807027--3807097 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
3807017 GCTATACAAT
*** *
3807027 CCCACATCAAAGAAAAACTTTGAATGGAGAGTAAGGG
1 CCCACATCAAAGAAAAACTCCCAACGGAGAGTAAGGG
3807064 CCCACATCAAAGAAAAACTCCCAAC-GAGGAGTAA
1 CCCACATCAAAGAAAAACTCCCAACGGA-GAGTAA
3807098 TAGTGGATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 2 0.07
37 27 0.93
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.13
Consensus pattern (37 bp):
CCCACATCAAAGAAAAACTCCCAACGGAGAGTAAGGG
Found at i:3807789 original size:62 final size:62
Alignment explanation
Indices: 3807675--3807791 Score: 180
Period size: 62 Copynumber: 1.9 Consensus size: 62
3807665 CCGTGACAAG
* * * * *
3807675 TCTTTTAACCTTATTTGGCTTAGTCTTAATAATGTTACTTGTTATTTGACTTAGTGTTTATT
1 TCTTTTAACCTTATTTGACTTAGTCTTAATAATGTTACCTGCTATCTAACTTAGTGTTTATT
*
3807737 TCTTTTAACCTTATTTGACTTAGTCTTAATAATGTTGCCTGCTATCTAACTTAGT
1 TCTTTTAACCTTATTTGACTTAGTCTTAATAATGTTACCTGCTATCTAACTTAGT
3807792 ACATGTTTGG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 49 1.00
ACGTcount: A:0.22, C:0.15, G:0.12, T:0.51
Consensus pattern (62 bp):
TCTTTTAACCTTATTTGACTTAGTCTTAATAATGTTACCTGCTATCTAACTTAGTGTTTATT
Found at i:3808896 original size:50 final size:50
Alignment explanation
Indices: 3808834--3808930 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 50
3808824 GATCTTTATA
**
3808834 ACGTTCCTTATTATCTAACTTAGTCTTAAACGTATAGAATATTTCTTGAG
1 ACGTTCCTTATTATCTAACTTAACCTTAAACGTATAGAATATTTCTTGAG
** * *
3808884 ACGTTGCC-TATTATCTTGCTTAACCTTAAATGTCTAGAATATTTCTT
1 ACGTT-CCTTATTATCTAACTTAACCTTAAACGTATAGAATATTTCTT
3808931 AAATGTTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
50 38 0.95
51 2 0.05
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.43
Consensus pattern (50 bp):
ACGTTCCTTATTATCTAACTTAACCTTAAACGTATAGAATATTTCTTGAG
Found at i:3810384 original size:2 final size:2
Alignment explanation
Indices: 3810377--3810403 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3810367 CCAAGCTGAG
3810377 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
3810404 CTTGGTGCTG
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:3821171 original size:13 final size:13
Alignment explanation
Indices: 3821153--3821177 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3821143 AAATTTGTTC
3821153 GTCTAAGGGAAAA
1 GTCTAAGGGAAAA
3821166 GTCTAAGGGAAA
1 GTCTAAGGGAAA
3821178 GTTAATTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.32, T:0.16
Consensus pattern (13 bp):
GTCTAAGGGAAAA
Found at i:3826306 original size:22 final size:21
Alignment explanation
Indices: 3826276--3826321 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
3826266 TGGGTTACTT
*
3826276 ATAATATTTTAAAATATTATAA
1 ATAAGATTTTAAAATATT-TAA
*
3826298 ATAAGATTTTATAATATTTAA
1 ATAAGATTTTAAAATATTTAA
3826319 ATA
1 ATA
3826322 TTTTGAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATAAGATTTTAAAATATTTAA
Found at i:3835657 original size:15 final size:15
Alignment explanation
Indices: 3835639--3835669 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3835629 GCAAATCTGA
3835639 AAGAGACATATCTTT
1 AAGAGACATATCTTT
3835654 AAGAGACATATCTTT
1 AAGAGACATATCTTT
3835669 A
1 A
3835670 TACTGCCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (15 bp):
AAGAGACATATCTTT
Found at i:3851378 original size:24 final size:24
Alignment explanation
Indices: 3851351--3851396 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
3851341 TTTTAAGATG
*
3851351 ATTCTAACAGTTAATATATTAAAC
1 ATTCGAACAGTTAATATATTAAAC
* * *
3851375 ATTCGAATATTTAATTTATTAA
1 ATTCGAACAGTTAATATATTAA
3851397 TTAATATATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (24 bp):
ATTCGAACAGTTAATATATTAAAC
Found at i:3851938 original size:2 final size:2
Alignment explanation
Indices: 3851933--3851963 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3851923 TGTGTGTGTC
3851933 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
3851964 CAATTATTGA
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:3867891 original size:22 final size:20
Alignment explanation
Indices: 3867865--3867909 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
3867855 ATCCATAATC
*
3867865 ATAAAATATTCAAATAATATAA
1 ATAAAAT-TTCAAAAAATA-AA
*
3867887 ATAAAATTTTAAAAAATAAA
1 ATAAAATTTCAAAAAATAAA
3867907 ATA
1 ATA
3867910 CTCTATTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAAAATTTCAAAAAATAAA
Found at i:3869428 original size:30 final size:30
Alignment explanation
Indices: 3869394--3869450 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
3869384 CCAAATAAAT
**
3869394 AGAATTTCATTGAAATCCAAATTGATTTCG
1 AGAATTTCATCAAAATCCAAATTGATTTCG
* *
3869424 AGAATTTCGTCAAAATCTAAATTGATT
1 AGAATTTCATCAAAATCCAAATTGATT
3869451 CTTAATTATA
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:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (30 bp):
AGAATTTCATCAAAATCCAAATTGATTTCG
Found at i:3874627 original size:29 final size:28
Alignment explanation
Indices: 3874572--3874629 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
3874562 AACTCAATAG
* ***
3874572 ATAAGAATAAAGTAATTTTTTTAAAAAA
1 ATAAGAATAAAGTAAATTTGAGAAAAAA
*
3874600 ATAAGAATAAAGTAAATTTGAGATAAAA
1 ATAAGAATAAAGTAAATTTGAGAAAAAA
3874628 AT
1 AT
3874630 TTCAAATTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (28 bp):
ATAAGAATAAAGTAAATTTGAGAAAAAA
Found at i:3875641 original size:30 final size:30
Alignment explanation
Indices: 3875597--3875658 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
3875587 ACCAAACATG
* * * *
3875597 TTCACTACTTGCTTATGAATTGCTAAAATT
1 TTCACCACTCGCTTATAAATTACTAAAATT
*
3875627 TTCACCACTCGCTTATAAATTATTAAAATT
1 TTCACCACTCGCTTATAAATTACTAAAATT
3875657 TT
1 TT
3875659 TGCATGGTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (30 bp):
TTCACCACTCGCTTATAAATTACTAAAATT
Found at i:3876074 original size:57 final size:57
Alignment explanation
Indices: 3876001--3876113 Score: 147
Period size: 57 Copynumber: 2.0 Consensus size: 57
3875991 AATAATGTTG
* *
3876001 CATTCACTTCAAGGAATGAACAAATTTATAATT-GTTTTATTAGTAGTTCACTTGTCA
1 CATTCACTTCAAGGAATGAACAAATTTATAATTAG-TGTATTAGTAGCTCACTTGTCA
* * * **
3876058 CATTCCCTTCAGGGAATGGACGGATTTATAATTAGTGTATTAGTAGCTCACTTGTC
1 CATTCACTTCAAGGAATGAACAAATTTATAATTAGTGTATTAGTAGCTCACTTGTC
3876114 GCAATAACTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
57 47 0.98
58 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (57 bp):
CATTCACTTCAAGGAATGAACAAATTTATAATTAGTGTATTAGTAGCTCACTTGTCA
Found at i:3876125 original size:57 final size:57
Alignment explanation
Indices: 3876006--3876126 Score: 136
Period size: 57 Copynumber: 2.1 Consensus size: 57
3875996 TGTTGCATTC
* * * *
3876006 ACTTCAAGGAATGAACAAATTTATAATTGTTTTATTAGTAGTTCACTTGTCACATTC
1 ACTTCAAGGAATGAACAAATTTATAATTGTTGTATTAGTAGCTCACTTGTCACAATA
* * * ** *
3876063 CCTTCAGGGAATGGACGGATTTATAATTAG-TGTATTAGTAGCTCACTTGTCGCAATA
1 ACTTCAAGGAATGAACAAATTTATAATT-GTTGTATTAGTAGCTCACTTGTCACAATA
3876120 ACTTCAA
1 ACTTCAA
3876127 TGAACAAACA
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
57 50 0.98
58 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (57 bp):
ACTTCAAGGAATGAACAAATTTATAATTGTTGTATTAGTAGCTCACTTGTCACAATA
Found at i:3891665 original size:16 final size:17
Alignment explanation
Indices: 3891636--3891668 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3891626 AAATAGAATG
3891636 ATTTTTTATTAATATTTT
1 ATTTTTTA-TAATATTTT
3891654 ATTTTTTA-AATATTT
1 ATTTTTTATAATATTT
3891669 CAGGAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTTTATAATATTTT
Found at i:3892271 original size:34 final size:32
Alignment explanation
Indices: 3892199--3892285 Score: 102
Period size: 34 Copynumber: 2.6 Consensus size: 32
3892189 TTTTAATGTC
*
3892199 ATATATTTTATTTTTATTTATTATTATAATTTT
1 ATATATTTTA-TTTTATTTATTAATATAATTTT
*
3892232 ATATATTTTATTTTCATTTCTTTAATATAATTTT
1 ATATATTTTATTTT-ATTT-ATTAATATAATTTT
*
3892266 TTATATTATATATTTTATTT
1 ATATATT-T-TATTTTATTT
3892286 TAATTTATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
32 4 0.09
33 14 0.30
34 18 0.38
35 5 0.11
36 6 0.13
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (32 bp):
ATATATTTTATTTTATTTATTAATATAATTTT
Found at i:3892394 original size:32 final size:34
Alignment explanation
Indices: 3892320--3892400 Score: 86
Period size: 33 Copynumber: 2.5 Consensus size: 34
3892310 AAATTTTAAT
3892320 TTCTTATATT-T--TATTTTATTTTAATTTTTGA
1 TTCTTATATTATAATATTTTATTTTAATTTTTGA
*
3892351 TTCTTATATTAT-ATATTTT-TTTTAATACTTTTTA
1 TTCTTATATTATAATATTTTATTTTAAT--TTTTGA
3892385 TT-TTA-ATTATAATATT
1 TTCTTATATTATAATATT
3892401 ATAAAATATT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
31 10 0.23
32 13 0.30
33 14 0.32
34 7 0.16
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (34 bp):
TTCTTATATTATAATATTTTATTTTAATTTTTGA
Found at i:3901114 original size:25 final size:25
Alignment explanation
Indices: 3901080--3901130 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
3901070 GATACCATGT
3901080 TGATATGTT-ATACTGA-ATGATGATA
1 TGATATGTTAATA-TGATAT-ATGATA
3901105 TGATATGTTAATATGATATATGATA
1 TGATATGTTAATATGATATATGATA
3901130 T
1 T
3901131 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (25 bp):
TGATATGTTAATATGATATATGATA
Found at i:3901794 original size:3 final size:3
Alignment explanation
Indices: 3901780--3901809 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3901770 ACAAAGGGGG
*
3901780 AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
3901810 GCGAATTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3920088 original size:16 final size:16
Alignment explanation
Indices: 3920055--3920086 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3920045 ATGTTATTTC
3920055 TTCTTTGCTTTTTCTT
1 TTCTTTGCTTTTTCTT
3920071 TTCTTTG-TTTTT-TT
1 TTCTTTGCTTTTTCTT
3920085 TT
1 TT
3920087 TTTCGTTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 5 0.31
16 7 0.44
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (16 bp):
TTCTTTGCTTTTTCTT
Found at i:3932263 original size:2 final size:2
Alignment explanation
Indices: 3932256--3932288 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3932246 TAATGGTTGC
3932256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3932289 TTATTAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3934743 original size:2 final size:2
Alignment explanation
Indices: 3934733--3934769 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3934723 AAAAAATTGT
*
3934733 TA TA AA 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
3934770 GAATACATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3942078 original size:89 final size:90
Alignment explanation
Indices: 3941924--3942103 Score: 317
Period size: 89 Copynumber: 2.0 Consensus size: 90
3941914 TAAATACATT
*
3941924 ATTATTAACTAATCCACAAACATCTTCAGTTAAGGTGGCAATTGAAAATTACACCCAATTTTC-A
1 ATTATTAACTAATCCACAAACATCTTCAGTTAAGGTGGCAATTGAAAATTACACCCAATTGTCAA
**
3941988 AATCAGTGGAGTCAAAATTATAACC
66 AATCAGTGGAGTCAAAACCATAACC
*
3942013 ATTATTAACTAATCCACATACATCTTCAGTTAAGGTGGCAATTGAAAATTACACCCAATTGTCAA
1 ATTATTAACTAATCCACAAACATCTTCAGTTAAGGTGGCAATTGAAAATTACACCCAATTGTCAA
3942078 AATCAGTGGAGTCAAAACCATAACC
66 AATCAGTGGAGTCAAAACCATAACC
3942103 A
1 A
3942104 CTTGCCTAAA
Statistics
Matches: 86, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 61 0.71
90 25 0.29
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.28
Consensus pattern (90 bp):
ATTATTAACTAATCCACAAACATCTTCAGTTAAGGTGGCAATTGAAAATTACACCCAATTGTCAA
AATCAGTGGAGTCAAAACCATAACC
Found at i:3952014 original size:4 final size:4
Alignment explanation
Indices: 3952007--3952033 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3951997 ACACACACAA
3952007 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
3952034 ACCTTTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:3953166 original size:18 final size:19
Alignment explanation
Indices: 3953130--3953175 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
3953120 TTTTTATATA
3953130 AATATGTAATATATTATTT
1 AATATGTAATATATTATTT
3953149 AATAT-TAATA-ATTCATTT
1 AATATGTAATATATT-ATTT
*
3953167 ATTATGTAA
1 AATATGTAA
3953176 AAGGTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 3 0.12
18 13 0.54
19 8 0.33
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (19 bp):
AATATGTAATATATTATTT
Found at i:3953808 original size:21 final size:19
Alignment explanation
Indices: 3953784--3953823 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
3953774 ATTCACATGA
*
3953784 TATTTAAATAAATTTTTAAAT
1 TATTT-AATAAA-ATTTAAAT
3953805 TATTTAATAAAATTTAAAT
1 TATTTAATAAAATTTAAAT
3953824 ACATTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 6 0.33
21 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTTAATAAAATTTAAAT
Found at i:3953913 original size:24 final size:26
Alignment explanation
Indices: 3953881--3953940 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
3953871 GTATCAAATA
* * *
3953881 AATTTTTATGA-TT-AATAATTAATT
1 AATTATTATGATTTAAAAAATTAACT
*
3953905 AATTATTATTATTTAAAAAAATTAACT
1 AATTATTATGATTT-AAAAAATTAACT
3953932 AATTATTAT
1 AATTATTAT
3953941 TAATCAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 9 0.31
25 2 0.07
27 18 0.62
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (26 bp):
AATTATTATGATTTAAAAAATTAACT
Found at i:3953949 original size:27 final size:27
Alignment explanation
Indices: 3953897--3953949 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
3953887 TATGATTAAT
* * *
3953897 AATTAATTAATTATTATTATTTAAAAA
1 AATTAACTAATTATTATTAATCAAAAA
3953924 AATTAACTAATTATTATTAATCAAAA
1 AATTAACTAATTATTATTAATCAAAA
3953950 TATCATTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (27 bp):
AATTAACTAATTATTATTAATCAAAAA
Found at i:3954071 original size:30 final size:32
Alignment explanation
Indices: 3954037--3954106 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 32
3954027 ATTATATCAA
*
3954037 ATTAATACATCAC-T-TCATCAATTATAATAT
1 ATTAACACATCACATATCATCAATTATAATAT
* * *
3954067 ATTAACATATCACATCATTATTAATTATAATAT
1 ATTAACACATCACAT-ATCATCAATTATAATAT
3954100 ATTAACA
1 ATTAACA
3954107 TATTACTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 11 0.33
31 1 0.03
33 21 0.64
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (32 bp):
ATTAACACATCACATATCATCAATTATAATAT
Found at i:3960129 original size:17 final size:17
Alignment explanation
Indices: 3960107--3960147 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
3960097 CATATATATA
3960107 TAGATTTGAATGTAA-AT
1 TAGATTTGAATG-AAGAT
3960124 TAGA-TTGAATGAAGAT
1 TAGATTTGAATGAAGAT
3960140 TAAGATTT
1 T-AGATTT
3960148 AATCCATCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.10
16 10 0.48
17 7 0.33
18 2 0.10
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (17 bp):
TAGATTTGAATGAAGAT
Found at i:3960880 original size:28 final size:27
Alignment explanation
Indices: 3960809--3960880 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
3960799 CTTTACCCAT
* *
3960809 TAGGGGTGGATGAATGCTTTTAACTCA
1 TAGGAGTGGATGAATACTTTTAACTCA
* *
3960836 TCAGGAATGGATAAATACTTTTAACTCA
1 T-AGGAGTGGATGAATACTTTTAACTCA
*
3960864 CTAGGAGTGGGTGAATA
1 -TAGGAGTGGATGAATA
3960881 GTAAAGAGGT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 1 0.03
28 34 0.94
29 1 0.03
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (27 bp):
TAGGAGTGGATGAATACTTTTAACTCA
Found at i:3976866 original size:6 final size:6
Alignment explanation
Indices: 3976855--3976884 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3976845 CTTCCTTCAC
*
3976855 ATCAAA ATCAAA ATCAAA GTCAAA ATCAAA
1 ATCAAA ATCAAA ATCAAA ATCAAA ATCAAA
3976885 TTGAATGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.63, C:0.17, G:0.03, T:0.17
Consensus pattern (6 bp):
ATCAAA
Found at i:3984041 original size:34 final size:34
Alignment explanation
Indices: 3984003--3984071 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
3983993 CCCCACACTT
3984003 AAAAAAAATTAAAAGAAACCATTACATACGGTAC
1 AAAAAAAATTAAAAGAAACCATTACATACGGTAC
*
3984037 AAAAAAAATTAAAAGAAACCATTACATATGGTAC
1 AAAAAAAATTAAAAGAAACCATTACATACGGTAC
3984071 A
1 A
3984072 GACTTCCTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.59, C:0.13, G:0.09, T:0.19
Consensus pattern (34 bp):
AAAAAAAATTAAAAGAAACCATTACATACGGTAC
Found at i:3986701 original size:2 final size:2
Alignment explanation
Indices: 3986696--3986728 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3986686 GCAAGAGTAT
3986696 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 T
3986729 GTAAAAGAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4012056 original size:22 final size:20
Alignment explanation
Indices: 4012014--4012060 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
4012004 ATATAAATAA
*
4012014 TGTTTTTTAATATTAGTTTT
1 TGTTTTCTAATATTAGTTTT
4012034 TAGTTTTCTATATATTA-TATTT
1 T-GTTTTCTA-ATATTAGT-TTT
4012056 TGTTT
1 TGTTT
4012061 ATAGTTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 12 0.52
22 10 0.43
ACGTcount: A:0.21, C:0.02, G:0.09, T:0.68
Consensus pattern (20 bp):
TGTTTTCTAATATTAGTTTT
Found at i:4018756 original size:15 final size:15
Alignment explanation
Indices: 4018747--4018803 Score: 105
Period size: 15 Copynumber: 3.8 Consensus size: 15
4018737 GTAATAAAAT
4018747 ATAATATAATTACAA
1 ATAATATAATTACAA
4018762 ATAATATAATTACAA
1 ATAATATAATTACAA
*
4018777 GTAATATAATTACAA
1 ATAATATAATTACAA
4018792 ATAATATAATTA
1 ATAATATAATTA
4018804 TAAAAAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (15 bp):
ATAATATAATTACAA
Found at i:4018852 original size:23 final size:23
Alignment explanation
Indices: 4018826--4018870 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
4018816 ATTACAGTGT
* *
4018826 TTAATATATAAATAAAATAATAA
1 TTAAAATATAAAAAAAATAATAA
4018849 TTAAAATATAAAAAAAATAATA
1 TTAAAATATAAAAAAAATAATA
4018871 TTACTGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
TTAAAATATAAAAAAAATAATAA
Found at i:4018853 original size:12 final size:12
Alignment explanation
Indices: 4018828--4018870 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
4018818 TACAGTGTTT
4018828 AATATATAAATAA
1 AATA-ATAAATAA
*
4018841 AATAATAATTAA
1 AATAATAAATAA
*
4018853 AAT-ATAAAAAA
1 AATAATAAATAA
4018864 AATAATA
1 AATAATA
4018871 TTACTGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 9 0.35
12 13 0.50
13 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AATAATAAATAA
Found at i:4019150 original size:55 final size:53
Alignment explanation
Indices: 4019083--4019197 Score: 142
Period size: 55 Copynumber: 2.1 Consensus size: 53
4019073 TTATATTATA
* *
4019083 TATTTTATTTTAATTTTT-CTTACCTATATTATATAAATTTTAATTTATTATATGT
1 TATTTTATTTTAATTTTTGATT-CCTATATTATAT--ATTTTAATTTAATATATGT
* * * *
4019138 TATTTTATTTTAATTTTTGATTCTTATATTATATATTTTATTTTAATATTTTT
1 TATTTTATTTTAATTTTTGATTCCTATATTATATATTTTAATTTAATATATGT
4019191 TATTTTA
1 TATTTTA
4019198 ATTGTAACAT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
53 22 0.42
55 29 0.55
56 2 0.04
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (53 bp):
TATTTTATTTTAATTTTTGATTCCTATATTATATATTTTAATTTAATATATGT
Found at i:4019191 original size:15 final size:15
Alignment explanation
Indices: 4019168--4019199 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4019158 TTCTTATATT
4019168 ATATATTTTATTTTA
1 ATATATTTTATTTTA
*
4019183 ATATTTTTTATTTTA
1 ATATATTTTATTTTA
4019198 AT
1 AT
4019200 TGTAACATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATATATTTTATTTTA
Found at i:4026599 original size:3 final size:3
Alignment explanation
Indices: 4026591--4026632 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
4026581 ATCCTTGCTT
4026591 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
4026633 GCAGTGGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:4038902 original size:74 final size:74
Alignment explanation
Indices: 4038747--4038888 Score: 212
Period size: 74 Copynumber: 1.9 Consensus size: 74
4038737 AAACTTATAC
* *
4038747 TTATAAATGTGTATTCATTAAATGACGATAATTAAAATAGTTTTTATTATAATTATCAGTAAGAT
1 TTATAAATGTATATTCATTAAATGACGATAATTAAAATAGTTTTTATTAAAATTATCAGTAAGAT
4038812 TTAAACCTA
66 TTAAACCTA
* * * * * *
4038821 TTATAAATTTATATTCATTAAATGATGATCATTGAAATATTTTTTATTAAAATTATTAGTAAGAT
1 TTATAAATGTATATTCATTAAATGACGATAATTAAAATAGTTTTTATTAAAATTATCAGTAAGAT
4038886 TTA
66 TTA
4038889 TTCCATTTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (74 bp):
TTATAAATGTATATTCATTAAATGACGATAATTAAAATAGTTTTTATTAAAATTATCAGTAAGAT
TTAAACCTA
Found at i:4040092 original size:13 final size:14
Alignment explanation
Indices: 4040074--4040102 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4040064 TAGACATAAG
4040074 TTTT-AAAAATATT
1 TTTTAAAAAATATT
4040087 TTTTAAAAAATATT
1 TTTTAAAAAATATT
4040101 TT
1 TT
4040103 ACTACAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTAAAAAATATT
Found at i:4045186 original size:20 final size:20
Alignment explanation
Indices: 4045161--4045198 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4045151 ATGTGCGAGA
4045161 CAAAATGCGTATTTCATGTT
1 CAAAATGCGTATTTCATGTT
4045181 CAAAATGCGTATTTCATG
1 CAAAATGCGTATTTCATG
4045199 AATTTTATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (20 bp):
CAAAATGCGTATTTCATGTT
Found at i:4050143 original size:28 final size:29
Alignment explanation
Indices: 4050112--4050407 Score: 111
Period size: 28 Copynumber: 10.0 Consensus size: 29
4050102 TTAAATTACC
* *
4050112 AATTATTAATAATTCAAACA-AAAATAAA
1 AATTATTAATAATTAAAAAATAAAATAAA
*
4050140 AATTATTAATATTTAAAAAATAAAAT-AA
1 AATTATTAATAATTAAAAAATAAAATAAA
** * * * **
4050168 AA-TAAAAATAAATAATCATAATAACATTTA
1 AATTATTAATAATTAA--AAAATAAAATAAA
* * * * * **
4050198 AATTATAAATAAAATATTAATAGTTAAATGATC
1 AATTATTAAT--AAT-TAAAAAATAAAAT-AAA
*
4050231 AATTATTAATAATTAAAACA-AAAATAAA
1 AATTATTAATAATTAAAAAATAAAATAAA
*
4050259 AATTATTAATATTTAAAAAATAAAAT-AA
1 AATTATTAATAATTAAAAAATAAAATAAA
** * * * **
4050287 AA-TAAAAATAAATAATCATAATAACATTTA
1 AATTATTAATAATTAA--AAAATAAAATAAA
* ** * * * **
4050317 AATTATAAATAAAATATTGATAGTTAAATGATC
1 AATTATTAAT--AAT-TAAAAAATAAAAT-AAA
*
4050350 AATTATTAATAATTAAAACA-AAAATAAA
1 AATTATTAATAATTAAAAAATAAAATAAA
*
4050378 AATTATTAATATTTAAAAAATAAAATAAA
1 AATTATTAATAATTAAAAAATAAAATAAA
4050407 A
1 A
4050408 TAAAAATAAA
Statistics
Matches: 194, Mismatches: 55, Indels: 37
0.68 0.19 0.13
Matches are distributed among these distances:
27 18 0.09
28 63 0.32
29 43 0.22
30 11 0.06
31 18 0.09
32 14 0.07
33 24 0.12
34 3 0.02
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.32
Consensus pattern (29 bp):
AATTATTAATAATTAAAAAATAAAATAAA
Found at i:4050593 original size:22 final size:22
Alignment explanation
Indices: 4050562--4050603 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4050552 TAAATTATAA
*
4050562 ATCAAATATTAATAGTTAAATG
1 ATCAAATATTAATAATTAAATG
*
4050584 ATCAATTATTAATAATTAAA
1 ATCAAATATTAATAATTAAA
4050604 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (22 bp):
ATCAAATATTAATAATTAAATG
Found at i:4050600 original size:118 final size:119
Alignment explanation
Indices: 4050061--4050692 Score: 1072
Period size: 119 Copynumber: 5.3 Consensus size: 119
4050051 ATTAATATTT
* * ** * *
4050061 TAATCATAATTATATTTAAATTATAAATAAAATATTAATTTTTAAATTACCAATTATTAATAATT
1 TAATCATAATAACATTTAAATTATAAATAAAATATTAATAGTTAAATGATCAATTATTAATAATT
*
4050126 CAAACAAAAATAAAAATTATTAATATTTAAAAAATAAAATAAAATAAAAATAAA
66 AAAACAAAAATAAAAATTATTAATATTTAAAAAATAAAATAAAATAAAAATAAA
4050180 TAATCATAATAACATTTAAATTATAAATAAAATATTAATAGTTAAATGATCAATTATTAATAATT
1 TAATCATAATAACATTTAAATTATAAATAAAATATTAATAGTTAAATGATCAATTATTAATAATT
4050245 AAAACAAAAATAAAAATTATTAATATTTAAAAAATAAAATAAAATAAAAATAAA
66 AAAACAAAAATAAAAATTATTAATATTTAAAAAATAAAATAAAATAAAAATAAA
*
4050299 TAATCATAATAACATTTAAATTATAAATAAAATATTGATAGTTAAATGATCAATTATTAATAATT
1 TAATCATAATAACATTTAAATTATAAATAAAATATTAATAGTTAAATGATCAATTATTAATAATT
4050364 AAAACAAAAATAAAAATTATTAATATTTAAAAAATAAAATAAAATAAAAATAAA
66 AAAACAAAAATAAAAATTATTAATATTTAAAAAATAAAATAAAATAAAAATAAA
4050418 TAATCATAATAACATTTAAATTATAAATAAAATATTAATAGTTAAATGATCAATTATTAATAATT
1 TAATCATAATAACATTTAAATTATAAATAAAATATTAATAGTTAAATGATCAATTATTAATAATT
* * *
4050483 AAAACAAAAATAAAAATTATTAATATTTTAAAGATAAAATTAAAT-AAAATAAA
66 AAAACAAAAATAAAAATTATTAATATTTAAAAAATAAAATAAAATAAAAATAAA
* *
4050536 TAATCAAAATAACATTTAAATTATAAATCAAATATTAATAGTTAAATGATCAATTATTAATAATT
1 TAATCATAATAACATTTAAATTATAAATAAAATATTAATAGTTAAATGATCAATTATTAATAATT
* * * *
4050601 AAAA-TAAAATAAAAATTATTAATATTTTAAAGATAAAATTAAATAAAAATAAA
66 AAAACAAAAATAAAAATTATTAATATTTAAAAAATAAAATAAAATAAAAATAAA
*
4050654 TAATC-TAAATAACATTTAAATTATAAATCAAATATTAAT
1 TAATCAT-AATAACATTTAAATTATAAATAAAATATTAAT
4050693 GTTTTAAAAA
Statistics
Matches: 495, Mismatches: 16, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
117 39 0.08
118 120 0.24
119 336 0.68
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (119 bp):
TAATCATAATAACATTTAAATTATAAATAAAATATTAATAGTTAAATGATCAATTATTAATAATT
AAAACAAAAATAAAAATTATTAATATTTAAAAAATAAAATAAAATAAAAATAAA
Found at i:4050717 original size:39 final size:40
Alignment explanation
Indices: 4050669--4050769 Score: 125
Period size: 39 Copynumber: 2.5 Consensus size: 40
4050659 TAAATAACAT
* * * *
4050669 TTAAATTATAAATCAAATATTAATGTTTTAA-A-AAATTAA
1 TTAATTTATAAATAAAATATTAATATTTAAATATAAATT-A
4050708 TTAATTTATAAATAAAATATTAATATTTAAATTATAAATTA
1 TTAATTTATAAATAAAATATTAATATTTAAA-TATAAATTA
4050749 TTAATATTATAAATAAAATAT
1 TTAAT-TTATAAATAAAATAT
4050770 AAATTATTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
39 27 0.50
41 7 0.13
42 20 0.37
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (40 bp):
TTAATTTATAAATAAAATATTAATATTTAAATATAAATTA
Found at i:4050800 original size:27 final size:27
Alignment explanation
Indices: 4050735--4050800 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 27
4050725 TATTAATATT
*
4050735 TAAATTATAAATTATTAATATTATAAA
1 TAAAATATAAATTATTAATATTATAAA
4050762 TAAAATATAAATTATTAATATT-TAAGCA
1 TAAAATATAAATTATTAATATTATAA--A
4050790 TAAAATA-AAAT
1 TAAAATATAAAT
4050801 AAAAATAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 3 0.08
27 25 0.69
28 8 0.22
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
TAAAATATAAATTATTAATATTATAAA
Found at i:4050883 original size:156 final size:156
Alignment explanation
Indices: 4050551--4050890 Score: 442
Period size: 157 Copynumber: 2.2 Consensus size: 156
4050541 AAAATAACAT
* *
4050551 TTAAATTATAAATCAAATATTAATAGTTAAATGATCAATTATTAATAATTAAAATAAAATAAAAA
1 TTAAATTATAAAT-AAATATTAATATTTAAATGATAAATTATTAATAATTAAAATAAAATAAAAA
* **
4050616 TTATTAATATTTTAAAGATAAAATTAAATAAAAATAAATAATCTAAATAACATTTAAATTATAAA
65 TTATTAATATTTTAAAGATAAAATAAAATAAAAATAAATAATCTAAATAACAACTAAATTATAAA
4050681 TCAAATATTAATGTTTTAAAAAATTAA
130 TCAAATATTAATGTTTTAAAAAATTAA
* * *
4050708 TTAATTTATAAATAAAATATTAATATTTAAATTATAAATTATTAAT-ATTATAAATAAAATATAA
1 TTAAATTATAAAT-AAATATTAATATTTAAATGATAAATTATTAATAATTA-AAATAAAATAAAA
4050772 ATTATTAATA-TTT-AAGCATAAAATAAAATAAAAATAAATAAT-TATAATAACAACTAAATTAT
64 ATTATTAATATTTTAAAG-ATAAAATAAAATAAAAATAAATAATCTA-AATAACAACTAAATTAT
* * * *
4050834 AAATTAAATATGATTAT-TTTTAATATTAA-TGA
127 AAATCAAATAT--TAATGTTTTAA-A-AAATTAA
4050866 TTAAATTATAAAT-AATATTAATATT
1 TTAAATTATAAATAAATATTAATATT
4050891 AAAAATAAAA
Statistics
Matches: 162, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
155 5 0.03
156 68 0.42
157 69 0.43
158 18 0.11
159 2 0.01
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (156 bp):
TTAAATTATAAATAAATATTAATATTTAAATGATAAATTATTAATAATTAAAATAAAATAAAAAT
TATTAATATTTTAAAGATAAAATAAAATAAAAATAAATAATCTAAATAACAACTAAATTATAAAT
CAAATATTAATGTTTTAAAAAATTAA
Found at i:4050891 original size:18 final size:18
Alignment explanation
Indices: 4050860--4050898 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4050850 TTTTTAATAT
*
4050860 TAATGATTAAATTATAAA
1 TAATGATTAAATTAAAAA
4050878 TAAT-ATTAATATTAAAAA
1 TAATGATTAA-ATTAAAAA
4050896 TAA
1 TAA
4050899 AATAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TAATGATTAAATTAAAAA
Found at i:4050908 original size:16 final size:16
Alignment explanation
Indices: 4050870--4050919 Score: 57
Period size: 18 Copynumber: 3.0 Consensus size: 16
4050860 TAATGATTAA
*
4050870 ATTATAAATAATATTAAT
1 ATTAAAAATAA-A-TAAT
4050888 ATTAAAAATAAAATAAT
1 ATTAAAAAT-AAATAAT
4050905 -TTAAAAATAAATAAT
1 ATTAAAAATAAATAAT
4050920 CATAATAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 7 0.23
16 8 0.27
17 4 0.13
18 9 0.30
19 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTAAAAATAAATAAT
Found at i:4050913 original size:262 final size:270
Alignment explanation
Indices: 4050436--4051003 Score: 662
Period size: 274 Copynumber: 2.1 Consensus size: 270
4050426 ATAACATTTA
* *
4050436 AATTATAAATAAAATATTAATAGTTAAATGATCAATTATTAATAATTAAAACAAAAATAAAAATT
1 AATTATAAATAAAATATTAATATTTAAATGATAAATTATTAATAATTAAAACAAAAATAAAAATT
* **
4050501 ATTAATATTTTAAAGATAAAATTAAATAAAATAAATAATCAAAATAACATTTAAATTATAAATCA
66 ATTAATATTTTAAAGATAAAATAAAATAAAATAAATAATCAAAATAACAACTAAATTATAAATCA
*
4050566 AATATTAATAGTTAAATGATCAATTATTAATAATTAAAATAAAATAAAAATTATTAATATTTTAA
131 AATATGAATAGTT--AT-ATCAATTATTAATAATTAAAATAAAAT--AAATTATTAATA-TTTAA
* * * **
4050631 AGATAAAATTAAATAAAAATAAATAATC-TAAATAACATTTAAATTATAAATCAAATATTAATGT
190 AAATAAAATTAAATAAAAATAAATAATCAT-AATAACATTTAAATTATAAATAAAATACTAACAT
4050695 TTTAAAAAATT-A-ATT
254 TTTAAAAAATTAAGATT
* * *
4050710 AATTTATAAATAAAATATTAATATTTAAATTATAAATTATTAAT-ATTATAAA-TAAAATATAAA
1 AA-TTATAAATAAAATATTAATATTTAAATGATAAATTATTAATAATTA-AAACAAAAATAAAAA
* *
4050773 TTATTAATA-TTT-AAGCATAAAATAAAATAAAAATAAATAATTATAATAACAACTAAATTATAA
64 TTATTAATATTTTAAAG-ATAAAATAAAAT-AAAATAAATAATCAAAATAACAACTAAATTATAA
* * * * *
4050836 ATTAAATATGATTA-TT-T-TTAA-TATTAATGATTAAATTATAAAT-AA-TATTAATA-TTAAA
127 ATCAAATATGAATAGTTATATCAATTATTAATAATTAAAATA-AAATAAATTATTAATATTTAAA
* *
4050894 AATAAAA-TAATTTAAAAATAAATAATCATAATAACATTTAAATTATAAATAAAATACTAGCATT
191 AATAAAATTAA-ATAAAAATAAATAATCATAATAACATTTAAATTATAAATAAAATACTAACATT
* *
4050958 TTATAATATTAATGATT
255 TTAAAAAATTAA-GATT
*
4050975 AGATTATAAATAAAATATTAATATCTAAA
1 A-ATTATAAATAAAATATTAATATTTAAA
4051004 AATAAAATAA
Statistics
Matches: 257, Mismatches: 26, Indels: 31
0.82 0.08 0.10
Matches are distributed among these distances:
261 3 0.01
262 64 0.25
263 2 0.01
264 8 0.03
265 31 0.12
266 1 0.00
267 15 0.06
268 7 0.03
270 1 0.00
272 3 0.01
273 16 0.06
274 65 0.25
275 41 0.16
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.37
Consensus pattern (270 bp):
AATTATAAATAAAATATTAATATTTAAATGATAAATTATTAATAATTAAAACAAAAATAAAAATT
ATTAATATTTTAAAGATAAAATAAAATAAAATAAATAATCAAAATAACAACTAAATTATAAATCA
AATATGAATAGTTATATCAATTATTAATAATTAAAATAAAATAAATTATTAATATTTAAAAATAA
AATTAAATAAAAATAAATAATCATAATAACATTTAAATTATAAATAAAATACTAACATTTTAAAA
AATTAAGATT
Found at i:4050925 original size:106 final size:105
Alignment explanation
Indices: 4050749--4051036 Score: 343
Period size: 106 Copynumber: 2.7 Consensus size: 105
4050739 TTATAAATTA
* * * **
4050749 TTAATATT-ATAAATAAAATATAAAT--TATTAATATTTAAGCATAAAATAAAATAAAAATAAAT
1 TTAATATTAATGATTAAATTATAAATAATATTAATA-TTAAAAATAAAATAAAATAAAAATAAAT
* **
4050811 AATTATAATAACAACTAAATTATAAATTAAATA-TGATTATTT
65 AA-TATAATAACAACTAAATTATAAATAAAATACT-AGCATTT
**
4050853 TTAATATTAATGATTAAATTATAAATAATATTAATATTAAAAATAAAATAATTTAAAAATAAATA
1 TTAATATTAATGATTAAATTATAAATAATATTAATATTAAAAATAAAATAAAATAAAAATAAATA
**
4050918 ATCATAATAACATTTAAATTATAAATAAAATACTAGCATTT
66 AT-ATAATAACAACTAAATTATAAATAAAATACTAGCATTT
*
4050959 TATAATATTAATGATTAGATTATAAATAAAATATTAATATCTAAAAATAAAATAAAAT-AAAATA
1 T-TAATATTAATGATTAAATTATAAAT--AATATTAATAT-TAAAAATAAAATAAAATAAAAATA
4051023 AATATATATAATAA
62 AATA-ATATAATAA
4051037 AAGATATTTT
Statistics
Matches: 159, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
104 8 0.05
105 15 0.09
106 58 0.36
107 33 0.21
109 28 0.18
110 17 0.11
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (105 bp):
TTAATATTAATGATTAAATTATAAATAATATTAATATTAAAAATAAAATAAAATAAAAATAAATA
ATATAATAACAACTAAATTATAAATAAAATACTAGCATTT
Found at i:4051430 original size:2 final size:2
Alignment explanation
Indices: 4051423--4051452 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4051413 AAGAAGATAA
4051423 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
4051453 GTTGCAGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4057651 original size:3 final size:3
Alignment explanation
Indices: 4057643--4057685 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
4057633 TTGTTTAATA
* * * *
4057643 TAT TAT TAT TAT TAT CAT CAT CAT CAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4057686 CATTTTCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:4059403 original size:24 final size:24
Alignment explanation
Indices: 4059371--4059417 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
4059361 AATAAAATAT
*
4059371 ATAATATAAGAATA-AAAAATTAAA
1 ATAAAATAA-AATATAAAAATTAAA
4059395 ATAAAATAAAATATAAAAATTAA
1 ATAAAATAAAATATAAAAATTAA
4059418 CATTTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (24 bp):
ATAAAATAAAATATAAAAATTAAA
Found at i:4059543 original size:27 final size:26
Alignment explanation
Indices: 4059486--4059657 Score: 107
Period size: 27 Copynumber: 6.2 Consensus size: 26
4059476 TAAAGAAATG
* *
4059486 AAAAT-AAAATAATAAGAT-TATAATA
1 AAAATAAAAATAA-AATATATATATTA
* *
4059511 ATAAATGAAAATAAAATATATGACATTA
1 A-AAATAAAAATAAAATATAT-ATATTA
* ** *
4059539 AAAATATATTTAAGATATGATATTATATA
1 AAAATAAAAATAAAATAT-ATA-TAT-TA
*
4059568 AAAATTAATAATAATAATATAAATATATTA
1 AAAA-TAAAAATAA-AATAT--ATATATTA
*
4059598 AAAATAAAATATAAAATAT-TATAATA
1 AAAATAAAA-ATAAAATATATATATTA
*
4059624 ATAAATAAAAATAAAATATATGACATTA
1 A-AAATAAAAATAAAATATAT-ATATTA
4059652 AAAATA
1 AAAATA
4059658 TATTTAAGAA
Statistics
Matches: 114, Mismatches: 19, Indels: 26
0.72 0.12 0.16
Matches are distributed among these distances:
25 1 0.01
26 24 0.21
27 35 0.31
28 14 0.12
29 15 0.13
30 15 0.13
31 7 0.06
32 3 0.03
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (26 bp):
AAAATAAAAATAAAATATATATATTA
Found at i:4059597 original size:23 final size:22
Alignment explanation
Indices: 4059563--4059633 Score: 96
Period size: 21 Copynumber: 3.4 Consensus size: 22
4059553 ATATGATATT
4059563 ATATAAAA-ATTAATAATAATA
1 ATATAAAATATTAATAATAATA
*
4059584 ATATAAATATATTAAAAATAA-A
1 ATATAAA-ATATTAATAATAATA
4059606 ATATAAAATATT-ATAATAATA
1 ATATAAAATATTAATAATAATA
4059627 A-ATAAAA
1 ATATAAAA
4059634 ATAAAATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
20 12 0.27
21 14 0.31
22 9 0.20
23 10 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
ATATAAAATATTAATAATAATA
Found at i:4059722 original size:60 final size:58
Alignment explanation
Indices: 4059535--4059713 Score: 165
Period size: 53 Copynumber: 3.1 Consensus size: 58
4059525 AATATATGAC
* *
4059535 ATTAAAAATATATTTAAGATATGATATTATATAAAAATTAATAAT-AATAATATAAATAT
1 ATTAAAAAT-TATTTAAGAAATGATATTATAT-AAAATTAATAATAAAAAATATAAATAT
* ** * * * * *
4059594 ATTAAAAATAAAAT-ATAAA--ATATTATA-ATAATAAATAA-AAATAAA-ATATATGAC
1 ATTAAAAATTATTTAAGAAATGATATTATATAAAATTAATAATAAA-AAATATAAAT-AT
4059648 ATTAAAAATATATTTAAGAAATGATATTATATAAAACTTAATAATAAAAAATATAAATAT
1 ATTAAAAAT-TATTTAAGAAATGATATTATATAAAA-TTAATAATAAAAAATATAAATAT
4059708 ATTAAA
1 ATTAAA
4059714 CTTGTATTTT
Statistics
Matches: 91, Mismatches: 18, Indels: 21
0.70 0.14 0.16
Matches are distributed among these distances:
53 16 0.18
54 12 0.13
55 10 0.11
56 4 0.04
57 3 0.03
58 10 0.11
59 12 0.13
60 16 0.18
61 8 0.09
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (58 bp):
ATTAAAAATTATTTAAGAAATGATATTATATAAAATTAATAATAAAAAATATAAATAT
Found at i:4059748 original size:113 final size:113
Alignment explanation
Indices: 4059486--4059713 Score: 386
Period size: 113 Copynumber: 2.0 Consensus size: 113
4059476 TAAAGAAATG
* * *
4059486 AAAATAAAATA-ATAAGATTATAATAATAAATGAAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
* *
4059550 AAGATATGATATTATATAAAAATTAATAATAATAATATAAATATATTA
66 AAGAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
4059598 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
*
4059663 AAGAAATGATATTATATAAAACTTAATAATAAAAAATATAAATATATTA
66 AAGAAATGATATTATATAAAAATTAATAAT-AAAAATATAAATATATTA
4059712 AA
1 AA
4059714 CTTGTATTTT
Statistics
Matches: 108, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
112 11 0.10
113 78 0.72
114 19 0.18
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (113 bp):
AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
AAGAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
Found at i:4061161 original size:29 final size:29
Alignment explanation
Indices: 4061096--4061161 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
4061086 GCTGTGACGG
*
4061096 AATTATAATTTTAAATTTAAGAGAGTGAA
1 AATTAAAATTTTAAATTTAAGAGAGTGAA
* *
4061125 AATGAAAATTTTAATATTTGAGAGTA-TG-A
1 AATTAAAATTTTAA-ATTTAAGAG-AGTGAA
4061154 AATTAAAA
1 AATTAAAA
4061162 AAAATTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 20 0.65
30 10 0.32
31 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (29 bp):
AATTAAAATTTTAAATTTAAGAGAGTGAA
Found at i:4061931 original size:20 final size:20
Alignment explanation
Indices: 4061908--4061945 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4061898 AAAGAAAATC
4061908 ATAAAAAA-AATAAATATTTA
1 ATAAAAAATAA-AAATATTTA
4061928 ATAAAAAATAAAAATATT
1 ATAAAAAATAAAAATATT
4061946 ATATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAAAAAATAAAAATATTTA
Found at i:4091632 original size:19 final size:19
Alignment explanation
Indices: 4091588--4091643 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
4091578 TAAATTAAAT
4091588 AAATTATTATATTTTTATA
1 AAATTATTATATTTTTATA
***
4091607 TTTTTATTATATTTTTA-A
1 AAATTATTATATTTTTATA
*
4091625 CAAATTATAATATTTTTAT
1 -AAATTATTATATTTTTAT
4091644 TTTAAATCAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 1 0.04
19 27 0.96
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
AAATTATTATATTTTTATA
Found at i:4091805 original size:21 final size:21
Alignment explanation
Indices: 4091767--4091807 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4091757 TAATAATGAT
*
4091767 ATAATATAATAATTTAATATG
1 ATAATATAATAATGTAATATG
* *
4091788 ATAATATGATTATGTAATAT
1 ATAATATAATAATGTAATAT
4091808 TTTTTATTCA
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:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (21 bp):
ATAATATAATAATGTAATATG
Found at i:4091894 original size:17 final size:17
Alignment explanation
Indices: 4091874--4091907 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4091864 AATTTTAATT
4091874 AATTA-TTAATTATAAAA
1 AATTATTTAATTA-AAAA
4091891 AATTATTTAATTAAAAA
1 AATTATTTAATTAAAAA
4091908 TAAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTATTTAATTAAAAA
Found at i:4091910 original size:22 final size:23
Alignment explanation
Indices: 4091885--4091944 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
4091875 ATTATTAATT
*
4091885 ATAAAAAAT-TATTTAATTAAAA
1 ATAAAAAATAAATTTAATTAAAA
*
4091907 ATAAAAATATAAATTTAATTAAAT
1 ATAAAAA-ATAAATTTAATTAAAA
4091931 ATAATAAAAATAAA
1 AT-A-AAAAATAAA
4091945 AATTTACTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 7 0.22
23 2 0.06
24 13 0.41
25 6 0.19
26 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAAAAAATAAATTTAATTAAAA
Found at i:4091920 original size:27 final size:26
Alignment explanation
Indices: 4091888--4091948 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
4091878 ATTAATTATA
* *
4091888 AAAAATTATTTAATTAAAAATAAAAAT
1 AAAAATTAATTAAAT-AAAATAAAAAT
* *
4091915 ATAAATTTAATTAAATATAATAAAAAT
1 A-AAAATTAATTAAATAAAATAAAAAT
4091942 AAAAATT
1 AAAAATT
4091949 TACTTAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 5 0.18
27 12 0.43
28 11 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAAATTAATTAAATAAAATAAAAAT
Found at i:4091949 original size:27 final size:25
Alignment explanation
Indices: 4091895--4091957 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 25
4091885 ATAAAAAATT
*
4091895 ATTTAATT-AAAAATAAAAATATAA
1 ATTTAATTAAAAAATAAAAATAAAA
4091919 ATTTAATTAAATATAATAAAAATAAAA
1 ATTTAATTAAA-A-AATAAAAATAAAA
*
4091946 ATTTACTTAAAA
1 ATTTAATTAAAA
4091958 TTTTTTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 8 0.24
25 2 0.06
26 2 0.06
27 22 0.65
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
ATTTAATTAAAAAATAAAAATAAAA
Found at i:4095952 original size:31 final size:30
Alignment explanation
Indices: 4095917--4096022 Score: 126
Period size: 31 Copynumber: 3.4 Consensus size: 30
4095907 AACTCACATC
4095917 ATAAAAATTAAATTAAATAAAAATTTAAAAT
1 ATAAAAATTAAATTAAA-AAAAATTTAAAAT
4095948 ATAAAAATTAAATT-AAAAAAA-TTAAAAT
1 ATAAAAATTAAATTAAAAAAAATTTAAAAT
* *
4095976 ATTAAAAGATTAGATTAAAAAAAACTTCAAAAT
1 A-TAAAA-ATTAAATTAAAAAAAA-TTTAAAAT
*
4096009 ATAAATATTTAAAT
1 ATAAA-AATTAAAT
4096023 AAATCATACA
Statistics
Matches: 65, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
28 8 0.12
29 10 0.15
30 9 0.14
31 21 0.32
32 9 0.14
33 8 0.12
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (30 bp):
ATAAAAATTAAATTAAAAAAAATTTAAAAT
Found at i:4095958 original size:14 final size:14
Alignment explanation
Indices: 4095917--4095987 Score: 70
Period size: 14 Copynumber: 4.7 Consensus size: 14
4095907 AACTCACATC
*
4095917 ATAAAAATTAAATTAA
1 ATAAAAATTAAA--AT
4095933 ATAAAAATTTAAAAT
1 ATAAAAA-TTAAAAT
*
4095948 ATAAAAATTAAATT
1 ATAAAAATTAAAAT
*
4095962 AAAAAAATTAAAAT
1 ATAAAAATTAAAAT
4095976 ATTAAAAGATTA
1 A-TAAAA-ATTA
4095988 GATTAAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
14 19 0.40
15 12 0.26
16 11 0.23
17 5 0.11
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (14 bp):
ATAAAAATTAAAAT
Found at i:4102568 original size:24 final size:23
Alignment explanation
Indices: 4102541--4102634 Score: 78
Period size: 24 Copynumber: 4.3 Consensus size: 23
4102531 TTAAACATCA
*
4102541 ATAATTTATTATTAAATTATTAAT
1 ATAATTTGTTATTAAATTATT-AT
*
4102565 ATAA---GTGATT-AA-TATT-T
1 ATAATTTGTTATTAAATTATTAT
*
4102582 -TAATTTGTTATTAAATTATTAA
1 ATAATTTGTTATTAAATTATTAT
4102604 ATAATTTGTT-TTCAAATTAATTAT
1 ATAATTTGTTATT-AAATT-ATTAT
4102628 ATAATTT
1 ATAATTT
4102635 TTAATTTTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
16 3 0.05
17 1 0.02
19 9 0.16
20 4 0.07
21 8 0.14
22 2 0.04
23 14 0.25
24 15 0.27
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (23 bp):
ATAATTTGTTATTAAATTATTAT
Found at i:4102603 original size:19 final size:19
Alignment explanation
Indices: 4102542--4102603 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
4102532 TAAACATCAA
*
4102542 TAATTTATTATTAAATTAT
1 TAATTTGTTATTAAATTAT
* *
4102561 TAATATAAGTGATTAATATT-T
1 TAAT-T-TGTTATTAA-ATTAT
4102582 TAATTTGTTATTAAATTAT
1 TAATTTGTTATTAAATTAT
4102601 TAA
1 TAA
4102604 ATAATTTGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.09
19 15 0.44
20 2 0.06
21 11 0.32
22 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
TAATTTGTTATTAAATTAT
Found at i:4102608 original size:23 final size:24
Alignment explanation
Indices: 4102582--4102634 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
4102572 ATTAATATTT
4102582 TAATTTGTTATT-AAATT-ATTAAA
1 TAATTTGTT-TTCAAATTAATTAAA
*
4102605 TAATTTGTTTTCAAATTAATTATA
1 TAATTTGTTTTCAAATTAATTAAA
4102629 TAATTT
1 TAATTT
4102635 TTAATTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 2 0.07
23 14 0.52
24 11 0.41
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (24 bp):
TAATTTGTTTTCAAATTAATTAAA
Found at i:4103928 original size:12 final size:12
Alignment explanation
Indices: 4103911--4103966 Score: 53
Period size: 12 Copynumber: 4.4 Consensus size: 12
4103901 CTTGACGACC
4103911 AAGAGGGAGAAA
1 AAGAGGGAGAAA
4103923 AAGA-GGAGGAAA
1 AAGAGGGA-GAAA
4103935 AAGAGGAAGAGAAA
1 AAGAGG--GAGAAA
4103949 AA-AGAGGAGAAA
1 AAGAG-GGAGAAA
4103961 GAAGAG
1 -AAGAG
4103967 AAAGCTGAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
11 3 0.08
12 18 0.49
13 5 0.14
14 9 0.24
15 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (12 bp):
AAGAGGGAGAAA
Found at i:4103938 original size:24 final size:26
Alignment explanation
Indices: 4103911--4103966 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
4103901 CTTGACGACC
4103911 AAGAGG-GAG-AAAAAGAGGAGGAAA-
1 AAGAGGAGAGAAAAAAGAGGA-GAAAG
4103935 AAGAGGAAGAGAAAAAAGAGGAGAAAG
1 AAGAGG-AGAGAAAAAAGAGGAGAAAG
4103962 AAGAG
1 AAGAG
4103967 AAAGCTGAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.21
26 7 0.25
27 15 0.54
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (26 bp):
AAGAGGAGAGAAAAAAGAGGAGAAAG
Found at i:4121558 original size:20 final size:20
Alignment explanation
Indices: 4121510--4121560 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
4121500 TGATAGGGAA
* *
4121510 TGGATTTTTGAGTGTTAAGT
1 TGGATTTTTGGGTATTAAGT
*
4121530 TAGATTTTTGGGTATTAAGT
1 TGGATTTTTGGGTATTAAGT
*
4121550 TGGACTTTTGG
1 TGGATTTTTGG
4121561 AAGTTAGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.02, G:0.29, T:0.49
Consensus pattern (20 bp):
TGGATTTTTGGGTATTAAGT
Found at i:4154273 original size:20 final size:19
Alignment explanation
Indices: 4154227--4154274 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
4154217 AAATTAGTTT
* * *
4154227 TAGGGTTTTTAATCGATTT
1 TAGGGTTTTCAATCGAGTC
*
4154246 TAGAGTTTTCATATCGAGTC
1 TAGGGTTTTCA-ATCGAGTC
4154266 TAGGGTTTT
1 TAGGGTTTT
4154275 TTGAATTGCT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.21, C:0.08, G:0.23, T:0.48
Consensus pattern (19 bp):
TAGGGTTTTCAATCGAGTC
Found at i:4154381 original size:21 final size:22
Alignment explanation
Indices: 4154317--4154378 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
4154307 AGGATTATTG
4154317 AATTGA-TTTAGGATTTTTTAA
1 AATTGATTTTAGGATTTTTTAA
* *
4154338 AATCGATTATAGGATTTTTTAA
1 AATTGATTTTAGGATTTTTTAA
*
4154360 AATTGATTTTAGGGTTTTT
1 AATTGATTTTAGGATTTTT
4154379 AAATTAGTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
21 5 0.14
22 30 0.86
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.52
Consensus pattern (22 bp):
AATTGATTTTAGGATTTTTTAA
Found at i:4154382 original size:20 final size:20
Alignment explanation
Indices: 4154211--4154383 Score: 68
Period size: 19 Copynumber: 8.6 Consensus size: 20
4154201 GGGTATTACA
*
4154211 GTTTTCAAATT-AGTTTTAGG
1 GTTTTTAAATTGA-TTTTAGG
* *
4154231 GTTTTT-AATCGATTTTAGA
1 GTTTTTAAATTGATTTTAGG
* * * * *
4154250 GTTTTCATATCGAGTCTAGG
1 GTTTTTAAATTGATTTTAGG
* * *
4154270 GTTTTTTGAATTGCTTTTAGT
1 G-TTTTTAAATTGATTTTAGG
* *
4154291 G-TTTTAAAGT-AGTTTAAGG
1 GTTTTTAAATTGA-TTTTAGG
* * *
4154310 ATTATTGAATTGA-TTTAGG
1 GTTTTTAAATTGATTTTAGG
* * *
4154329 ATTTTTTAAAATCGATTATAGG
1 -GTTTTT-AAATTGATTTTAGG
*
4154351 ATTTTTTAAAATTGATTTTAGG
1 -GTTTTT-AAATTGATTTTAGG
4154373 GTTTTTAAATT
1 GTTTTTAAATT
4154384 AGTTCAAGAG
Statistics
Matches: 110, Mismatches: 34, Indels: 18
0.68 0.21 0.11
Matches are distributed among these distances:
19 31 0.28
20 31 0.28
21 23 0.21
22 25 0.23
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.50
Consensus pattern (20 bp):
GTTTTTAAATTGATTTTAGG
Found at i:4154475 original size:22 final size:22
Alignment explanation
Indices: 4154450--4154533 Score: 57
Period size: 22 Copynumber: 3.9 Consensus size: 22
4154440 TTTTGGGTTT
4154450 TGAATCGATTTTAGGATTTTAG
1 TGAATCGATTTTAGGATTTTAG
* *
4154472 TGAAAC-AGTTTTAGGGTTTT-G
1 TGAATCGA-TTTTAGGATTTTAG
* * * * *
4154493 -AAATCAATTTAAGGGTTTTAT
1 TGAATCGATTTTAGGATTTTAG
* *
4154514 TGAACCGATTTTAAGATTTT
1 TGAATCGATTTTAGGATTTT
4154534 GAATTGGTTT
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
20 14 0.30
21 3 0.07
22 29 0.63
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (22 bp):
TGAATCGATTTTAGGATTTTAG
Found at i:4154526 original size:42 final size:42
Alignment explanation
Indices: 4154439--4154517 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
4154429 CATTGAATTG
* *
4154439 GTTTT-GGGTTTTG-AATCGATTTTAGGATTTTAGTGAAACA
1 GTTTTAGGGTTTTGAAATCAATTTAAGGATTTTAGTGAAACA
* *
4154479 GTTTTAGGGTTTTGAAATCAATTTAAGGGTTTTATTGAA
1 GTTTTAGGGTTTTGAAATCAATTTAAGGATTTTAGTGAA
4154518 CCGATTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 5 0.15
41 8 0.24
42 20 0.61
ACGTcount: A:0.27, C:0.04, G:0.24, T:0.46
Consensus pattern (42 bp):
GTTTTAGGGTTTTGAAATCAATTTAAGGATTTTAGTGAAACA
Found at i:4155621 original size:16 final size:16
Alignment explanation
Indices: 4155583--4155621 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4155573 AAATAAGAGC
*
4155583 AACAGAGAGACAGAGA
1 AACAGAGAGACAAAGA
* *
4155599 CAGAGAGAGACAAAGA
1 AACAGAGAGACAAAGA
4155615 AACAGAG
1 AACAGAG
4155622 CAAAAAATGG
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.13, G:0.31, T:0.00
Consensus pattern (16 bp):
AACAGAGAGACAAAGA
Found at i:4169043 original size:20 final size:20
Alignment explanation
Indices: 4169020--4169060 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4169010 AGACAGGAAA
* * *
4169020 AGGAGGAGAAGAAGAAAAAG
1 AGGAAGAGAAAAACAAAAAG
4169040 AGGAAGAGAAAAACAAAAAG
1 AGGAAGAGAAAAACAAAAAG
4169060 A
1 A
4169061 AGATGGAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (20 bp):
AGGAAGAGAAAAACAAAAAG
Found at i:4171633 original size:7 final size:7
Alignment explanation
Indices: 4171621--4171673 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 7
4171611 ATACCCTTGA
4171621 TTATAAT
1 TTATAAT
4171628 TTATAAT
1 TTATAAT
4171635 TTATAAT
1 TTATAAT
4171642 TTGA-AAT
1 TT-ATAAT
*
4171649 AT-TAAT
1 TTATAAT
4171655 TT-T--T
1 TTATAAT
4171659 TTATAAT
1 TTATAAT
4171666 TTATAAT
1 TTATAAT
4171673 T
1 T
4171674 AAAACTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 3 0.08
5 1 0.03
6 5 0.13
7 29 0.74
8 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (7 bp):
TTATAAT
Found at i:4171723 original size:16 final size:17
Alignment explanation
Indices: 4171688--4171726 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
4171678 CTTTAATATG
* *
4171688 ATTAATTATTTTTAAGT
1 ATTAATTATATTTAAAT
4171705 ATTAATT-TATTTAAAT
1 ATTAATTATATTTAAAT
4171721 ATTAAT
1 ATTAAT
4171727 AATTTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTAATTATATTTAAAT
Found at i:4171845 original size:21 final size:21
Alignment explanation
Indices: 4171821--4171862 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4171811 TTAATTTTAA
* * *
4171821 TTTCTTTTTTTTTTTTCTCTT
1 TTTCTTCTTTTCTTTCCTCTT
4171842 TTTCTTCTTTTCTTTCCTCTT
1 TTTCTTCTTTTCTTTCCTCTT
4171863 GTGTTGCCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTCTTCTTTTCTTTCCTCTT
Found at i:4175376 original size:58 final size:58
Alignment explanation
Indices: 4175282--4175394 Score: 181
Period size: 58 Copynumber: 1.9 Consensus size: 58
4175272 AAAGTGGAAA
*
4175282 GGTGGAGACACAACCTCCAATAACATGAAATAGAAAACTACCACTAACAATAAAAAAG
1 GGTGGAGACACAACCTCCAACAACATGAAATAGAAAACTACCACTAACAATAAAAAAG
* * * *
4175340 GGTGGAGACACAACCTCCAACAACATGAAATGGAAAACTGCCCCTACCAATAAAA
1 GGTGGAGACACAACCTCCAACAACATGAAATAGAAAACTACCACTAACAATAAAA
4175395 TAGGAACCAC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.48, C:0.24, G:0.15, T:0.13
Consensus pattern (58 bp):
GGTGGAGACACAACCTCCAACAACATGAAATAGAAAACTACCACTAACAATAAAAAAG
Found at i:4182461 original size:5 final size:5
Alignment explanation
Indices: 4182444--4182502 Score: 91
Period size: 5 Copynumber: 11.8 Consensus size: 5
4182434 ATTGACATCC
* * *
4182444 TGGGT TGCGT TGGCT TGGGT TGGCT TGGGT TGGGT TGGGT TGGGT TGGGT
1 TGGGT TGGGT TGGGT TGGGT TGGGT TGGGT TGGGT TGGGT TGGGT TGGGT
4182494 TGGGT TGGG
1 TGGGT TGGG
4182503 AGAGCTAAGC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.00, C:0.05, G:0.56, T:0.39
Consensus pattern (5 bp):
TGGGT
Found at i:4188148 original size:16 final size:16
Alignment explanation
Indices: 4188123--4188154 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4188113 AATCGTTTCC
*
4188123 TCTCTTTCTCTCTCAA
1 TCTCTCTCTCTCTCAA
4188139 TCTCTCTCTCTCTCAA
1 TCTCTCTCTCTCTCAA
4188155 AAGAAGTGTG
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:0.12, C:0.41, G:0.00, T:0.47
Consensus pattern (16 bp):
TCTCTCTCTCTCTCAA
Done.