Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000049.1 Hibiscus syriacus cultivar Beakdansim tig00000075_pilon, 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: 62030
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3259 original size:10 final size:10
Alignment explanation
Indices: 3244--3270 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3234 GGGGCTGCTC
3244 GCTGGAAGCT
1 GCTGGAAGCT
3254 GCTGGAAGCT
1 GCTGGAAGCT
3264 GCTGGAA
1 GCTGGAA
3271 ATGATGCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.41, T:0.19
Consensus pattern (10 bp):
GCTGGAAGCT
Found at i:3842 original size:73 final size:76
Alignment explanation
Indices: 3692--3864 Score: 244
Period size: 73 Copynumber: 2.3 Consensus size: 76
3682 TCTTCAGATG
* * **
3692 AGTTCTTCTTATTATGAACTTTCTCTGGCAAAGTTAATGTTGATCTACCTTATGATGAATTCAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGG-AAA--TAATGTTGATCCACCGAATGATGAATTCAAG
3757 CAAAAAGTTGAACA
63 CAAAAAGTTGAACA
* *
3771 AGTTCTTCTCATTATGAACTTTCTCTGG-AA-AA-GTTGATCCATCGAATGATGAATTCAAGCGA
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAATAATGTTGATCCACCGAATGATGAATTCAAGCAA
3833 AAAGTTGAACA
66 AAAGTTGAACA
3844 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
3865 CTTCTTCCTT
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
73 57 0.65
74 2 0.02
77 2 0.02
79 27 0.31
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (76 bp):
AGTTCTTCTCATTATGAACTTTCTCTGGAAATAATGTTGATCCACCGAATGATGAATTCAAGCAA
AAAGTTGAACA
Found at i:3902 original size:113 final size:117
Alignment explanation
Indices: 3771--4027 Score: 301
Period size: 123 Copynumber: 2.2 Consensus size: 117
3761 AAGTTGAACA
* * *
3771 AGTTCTTCTCATTATGAACTTTCTCTGGAAA-AG-T-TGATCCATC-GA-ATGAT-GAATTCAAG
1 AGTTCTTCTCATTATGAACTTTCTATGGAAACAGATATGATCCATCTCATATGATAGAA-TCAAA
*
3830 CGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
65 C-AAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * * * *
3884 AGTTCTTCTTATTATGAACTTTTTATGGAAATGCTGATACTGATCTATCTCATTCTGTGATAGAA
1 AGTTCTTCTCATTATGAACTTTCTATGGAAA--CAGATA-TGATCCATCTCA---TATGATAGAA
* *
3949 TCAAACAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATG
60 TCAAACAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
4007 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
4028 CTTCTTCCTT
Statistics
Matches: 120, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
113 28 0.23
116 1 0.01
117 1 0.01
119 8 0.07
120 1 0.01
123 69 0.57
124 9 0.08
125 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (117 bp):
AGTTCTTCTCATTATGAACTTTCTATGGAAACAGATATGATCCATCTCATATGATAGAATCAAAC
AAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:4016 original size:40 final size:40
Alignment explanation
Indices: 3970--4067 Score: 187
Period size: 40 Copynumber: 2.5 Consensus size: 40
3960 TTGAACAAGC
*
3970 TCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
4010 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
4050 TCTTCTCATTATGAACTT
1 TCTTCTCATTATGAACTT
4068 TCTCTGGAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.18, C:0.23, G:0.09, T:0.49
Consensus pattern (40 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGT
Found at i:4207 original size:113 final size:113
Alignment explanation
Indices: 4007--4210 Score: 338
Period size: 113 Copynumber: 1.8 Consensus size: 113
3997 TCTTCAGATG
**
4007 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTGACTC
*
4072 TGGAAAAGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACA
66 TGGAAAAGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACA
4120 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC-
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-GACT
* * *
4184 CTGGCAATGCTGATCCATTGAATGATG
65 CTGGAAAAGCTGATCCATCGAATGATG
4211 GATTTAAATC
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
113 83 0.99
114 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTGACTC
TGGAAAAGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAACA
Found at i:4634 original size:23 final size:22
Alignment explanation
Indices: 4612--4653 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4602 AAATCTGATA
* *
4612 AAGCTTTCATCTTTGAAAAGAT
1 AAGCTGTCATCTTTAAAAAGAT
*
4634 AATCTGTCATCTTTAAAAAG
1 AAGCTGTCATCTTTAAAAAG
4654 GGAATCTATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (22 bp):
AAGCTGTCATCTTTAAAAAGAT
Found at i:4696 original size:22 final size:22
Alignment explanation
Indices: 4618--4694 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
4608 GATAAAGCTT
* *
4618 TCATCTTTGAAAAGATAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
4640 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
4662 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
4684 TCATCTTTGAA
1 TCATCTTTGAA
4695 GAATGTAGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:5140 original size:54 final size:54
Alignment explanation
Indices: 5054--5219 Score: 251
Period size: 54 Copynumber: 3.1 Consensus size: 54
5044 AGAATAGCAG
** * *
5054 GTTCGTAAAACATTTGATGGCGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGATAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
* * *
5108 GTTTGTAAAACATTTGATAACACATTCATCCTTTACTGTAGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGATAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
* *
5162 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGATAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
5216 GTTC
1 GTTC
5220 TCAATCATTG
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 100 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (54 bp):
GTTCGTAAAACATTTGATAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
Found at i:9064 original size:32 final size:32
Alignment explanation
Indices: 9023--9084 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
9013 GAAGAAATGA
*
9023 TTGTTATGCTCATCTTGTAGAGATACTTCTCG
1 TTGTTATGCTCATCTGGTAGAGATACTTCTCG
9055 TTGTTATGCTCATCTGGTAGAGATACTTCT
1 TTGTTATGCTCATCTGGTAGAGATACTTCT
9085 TGTGTCTGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (32 bp):
TTGTTATGCTCATCTGGTAGAGATACTTCTCG
Found at i:9674 original size:9 final size:8
Alignment explanation
Indices: 9656--9745 Score: 51
Period size: 8 Copynumber: 11.2 Consensus size: 8
9646 CTTAATTTAA
9656 TTTTTTCT
1 TTTTTTCT
9664 TTTTTTC-
1 TTTTTTCT
* *
9671 CTTTTTAT
1 TTTTTTCT
* *
9679 TATTAT-T
1 TTTTTTCT
*
9686 TTTTTTAT
1 TTTTTTCT
*
9694 TTCTTTCCT
1 TT-TTTTCT
9703 TTTTTAT-T
1 TTTTT-TCT
*
9711 TTTTTTAT
1 TTTTTTCT
*
9719 TTTTTCCT
1 TTTTTTCT
9727 CTTTTTTCT
1 -TTTTTTCT
*
9736 TTTTTCCT
1 TTTTTTCT
9744 TT
1 TT
9746 CTTTGCTGGA
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
7 11 0.18
8 38 0.61
9 13 0.21
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTCT
Found at i:9699 original size:25 final size:25
Alignment explanation
Indices: 9657--9720 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
9647 TTAATTTAAT
*
9657 TTTTTCTTTTTTTCCTT-TTTATTATTA
1 TTTTT-TTTATTTCCTTCTTT-TT-TTA
* *
9684 TTTTTTTTATTTCTTTCCTTTTTTA
1 TTTTTTTTATTTCCTTCTTTTTTTA
9709 TTTTTTTTATTT
1 TTTTTTTTATTT
9721 TTTCCTCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 15 0.45
26 11 0.33
27 7 0.21
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (25 bp):
TTTTTTTTATTTCCTTCTTTTTTTA
Found at i:9731 original size:17 final size:17
Alignment explanation
Indices: 9711--9743 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9701 CTTTTTTATT
9711 TTTTTTATTTTTTCCTC
1 TTTTTTATTTTTTCCTC
*
9728 TTTTTTCTTTTTTCCT
1 TTTTTTATTTTTTCCT
9744 TTCTTTGCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTATTTTTTCCTC
Found at i:9731 original size:25 final size:25
Alignment explanation
Indices: 9681--9749 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
9671 CTTTTTATTA
9681 TTATTTTTTTTATTTCTTTCCTTTT
1 TTATTTTTTTTATTTCTTTCCTTTT
9706 TTATTTTTTTTATTT-TTTCCTCTTT
1 TTATTTTTTTTATTTCTTTCCT-TTT
**
9731 TT-TCTTTTTTCCTTTCTTT
1 TTAT-TTTTTTTATTTCTTT
9750 GCTGGATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.18
25 29 0.74
26 3 0.08
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (25 bp):
TTATTTTTTTTATTTCTTTCCTTTT
Found at i:9759 original size:27 final size:26
Alignment explanation
Indices: 9729--9782 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
9719 TTTTTCCTCT
9729 TTTTTCTTTTTTCCTTTCTTTGCTGGA
1 TTTTTCTTTTTT-CTTTCTTTGCTGGA
*
9756 TTTTTCTTTTTTCTTTCTTTGTTGGA
1 TTTTTCTTTTTTCTTTCTTTGCTGGA
9782 T
1 T
9783 GAGTATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.04, C:0.15, G:0.11, T:0.70
Consensus pattern (26 bp):
TTTTTCTTTTTTCTTTCTTTGCTGGA
Found at i:12183 original size:14 final size:14
Alignment explanation
Indices: 12164--12246 Score: 50
Period size: 14 Copynumber: 6.2 Consensus size: 14
12154 AAATGTAATT
12164 ATGTAAAAATGAAA
1 ATGTAAAAATGAAA
12178 ATGT--AAAT-ACAA
1 ATGTAAAAATGA-AA
* *
12190 ACGTAAAAATGCAA
1 ATGTAAAAATGAAA
*
12204 ATGT--AAATGCAA
1 ATGTAAAAATGAAA
* **
12216 ATGTAAATATGTGA
1 ATGTAAAAATGAAA
* *
12230 ATGTAATAATAAAA
1 ATGTAAAAATGAAA
12244 ATG
1 ATG
12247 CAAATTGTAT
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
11 1 0.02
12 21 0.40
14 30 0.58
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.25
Consensus pattern (14 bp):
ATGTAAAAATGAAA
Found at i:12195 original size:12 final size:12
Alignment explanation
Indices: 12176--12224 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
12166 GTAAAAATGA
12176 AAATGTAAATAC
1 AAATGTAAATAC
* *
12188 AAACGTAAAAATGC
1 AAATGT--AAATAC
*
12202 AAATGTAAATGC
1 AAATGTAAATAC
12214 AAATGTAAATA
1 AAATGTAAATA
12225 TGTGAATGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 21 0.68
14 10 0.32
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.22
Consensus pattern (12 bp):
AAATGTAAATAC
Found at i:12235 original size:26 final size:26
Alignment explanation
Indices: 12166--12222 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
12156 ATGTAATTAT
*
12166 GTAAAAATGAAAATGTAAATACAAAC
1 GTAAAAATGCAAATGTAAATACAAAC
* *
12192 GTAAAAATGCAAATGTAAATGCAAAT
1 GTAAAAATGCAAATGTAAATACAAAC
12218 GTAAA
1 GTAAA
12223 TATGTGAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.58, C:0.07, G:0.14, T:0.21
Consensus pattern (26 bp):
GTAAAAATGCAAATGTAAATACAAAC
Found at i:13899 original size:27 final size:25
Alignment explanation
Indices: 13832--13906 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 25
13822 ATGAAATTTA
* *
13832 AATAAAATAAAAATATTAATAAAAAT
1 AATATAATAAAAATATT-ATGAAAAT
*
13858 AATATACATATAAATATTATGAAAAT
1 AATATA-ATAAAAATATTATGAAAAT
13884 AATAAGTAATAAAAAT-TT-TGAAA
1 AAT-A-TAATAAAAATATTATGAAA
13907 GAAAAAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
25 5 0.12
26 17 0.40
27 18 0.43
28 2 0.05
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (25 bp):
AATATAATAAAAATATTATGAAAAT
Found at i:14704 original size:11 final size:11
Alignment explanation
Indices: 14688--14714 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
14678 ATATGACTAA
14688 AATAAAATAAT
1 AATAAAATAAT
14699 AATAAAATAAT
1 AATAAAATAAT
14710 AATAA
1 AATAA
14715 TTAAAGTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:22054 original size:24 final size:24
Alignment explanation
Indices: 22022--22086 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 24
22012 TTATATGAAA
*
22022 GGATGAATTTATAAAA-CTTAA-G
1 GGATAAATTTATAAAATCTTAATG
* *
22044 AGGACTAAATTTGTAAAATTTTAATTG
1 -GGA-TAAATTTATAAAATCTTAA-TG
22071 GGATAAATTTATAAAA
1 GGATAAATTTATAAAA
22087 AATTTAATGG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 3 0.09
24 11 0.32
25 16 0.47
26 3 0.09
27 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.35
Consensus pattern (24 bp):
GGATAAATTTATAAAATCTTAATG
Found at i:22559 original size:31 final size:31
Alignment explanation
Indices: 22519--22595 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 31
22509 TGGAATGTAA
*
22519 TCACTAATATAAAAATATATCATCATATCAT
1 TCACAAATATAAAAATATATCATCATATCAT
22550 TCACAAATATAAAAATATATCATCATATCAT
1 TCACAAATATAAAAATATATCATCATATCAT
*
22581 TCACAAATACAAAAA
1 TCACAAATATAAAAA
22596 ATAATTATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (31 bp):
TCACAAATATAAAAATATATCATCATATCAT
Found at i:27164 original size:27 final size:28
Alignment explanation
Indices: 27103--27164 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 28
27093 ATTTGCAACA
* * *
27103 TGAATAGAACTCGGATTCTCAGTCAAAC
1 TGAATCGAACTCGGATTATCAGCCAAAC
* *
27131 T-ACTCGAACTCGGATTATCA-CCGAAC
1 TGAATCGAACTCGGATTATCAGCCAAAC
27157 TGAATCGA
1 TGAATCGA
27165 CTTTTTAATC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
26 5 0.19
27 21 0.78
28 1 0.04
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (28 bp):
TGAATCGAACTCGGATTATCAGCCAAAC
Found at i:35340 original size:7 final size:7
Alignment explanation
Indices: 35330--35364 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
35320 TCATTTTTTT
35330 TTTTGCA
1 TTTTGCA
35337 TTTTGCA
1 TTTTGCA
35344 TTTTGCA
1 TTTTGCA
35351 TTTTGCA
1 TTTTGCA
35358 TTTTGCA
1 TTTTGCA
35365 AAGACTTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (7 bp):
TTTTGCA
Found at i:36004 original size:108 final size:103
Alignment explanation
Indices: 35853--36046 Score: 325
Period size: 108 Copynumber: 1.8 Consensus size: 103
35843 AAGTGAAGAG
35853 TTGTTTTTAATTATATAGACTACTATTATCTACCACGTTTACCATAGATTTTTTTTTCTTTTTAA
1 TTGTTTTTAATTATATAGACTACTATTATCTACCACGTTTACCATAGATTTTTTTTTCTTTTTAA
35918 TTCCAAAAGTTGGTTTAAAAAACCTTATCTAAGAGTTA
66 TTCCAAAAGTTGGTTTAAAAAACCTTATCTAAGAGTTA
* *
35956 TTGTTTTTAGTTATATAGACTGGACTATTATTAACTACCACGTTTACCATTGATTTTTTTTTCTT
1 TTGTTTTTAATTATATAGACT--ACTATTA-T--CTACCACGTTTACCATAGATTTTTTTTTCTT
36021 TTTAATTCCAAAAGTTGGTTTAAAAA
61 TTTAATTCCAAAAGTTGGTTTAAAAA
36047 GCCTGCTCAT
Statistics
Matches: 84, Mismatches: 2, Indels: 5
0.92 0.02 0.05
Matches are distributed among these distances:
103 20 0.24
105 7 0.08
106 1 0.01
108 56 0.67
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (103 bp):
TTGTTTTTAATTATATAGACTACTATTATCTACCACGTTTACCATAGATTTTTTTTTCTTTTTAA
TTCCAAAAGTTGGTTTAAAAAACCTTATCTAAGAGTTA
Found at i:39614 original size:28 final size:28
Alignment explanation
Indices: 39582--39666 Score: 143
Period size: 28 Copynumber: 3.0 Consensus size: 28
39572 TTGTTGTTGC
* **
39582 TTTCAAGCATTGACCCAACGACATAATG
1 TTTCAAGCGTTGATTCAACGACATAATG
39610 TTTCAAGCGTTGATTCAACGACATAATG
1 TTTCAAGCGTTGATTCAACGACATAATG
39638 TTTCAAGCGTTGATTCAACGACATAATG
1 TTTCAAGCGTTGATTCAACGACATAATG
39666 T
1 T
39667 AAATGGAGAG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (28 bp):
TTTCAAGCGTTGATTCAACGACATAATG
Found at i:40783 original size:14 final size:14
Alignment explanation
Indices: 40764--40790 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40754 GGCATCTGAA
40764 GGCATCCGACCGAG
1 GGCATCCGACCGAG
40778 GGCATCCGACCGA
1 GGCATCCGACCGA
40791 TGCCATTCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.37, G:0.33, T:0.07
Consensus pattern (14 bp):
GGCATCCGACCGAG
Found at i:42974 original size:20 final size:20
Alignment explanation
Indices: 42949--42988 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
42939 AATTATAAAG
* * *
42949 TTAATACAATTTAATGTTTT
1 TTAATAAAATATAAAGTTTT
42969 TTAATAAAATATAAAGTTTT
1 TTAATAAAATATAAAGTTTT
42989 GGAAATTACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
TTAATAAAATATAAAGTTTT
Found at i:43431 original size:2 final size:2
Alignment explanation
Indices: 43424--43452 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43414 TCATTTTGCA
43424 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
43453 GCTCGCCGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:46858 original size:12 final size:13
Alignment explanation
Indices: 46833--46868 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
46823 CTTAATTACG
*
46833 AAAATTTGAAATT
1 AAAATTTAAAATT
46846 AAAA-TTAAAATT
1 AAAATTTAAAATT
46858 AAAATTTAAAA
1 AAAATTTAAAA
46869 AACGTTCGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
AAAATTTAAAATT
Found at i:47035 original size:10 final size:10
Alignment explanation
Indices: 46982--47046 Score: 51
Period size: 10 Copynumber: 6.1 Consensus size: 10
46972 TTAATATAAT
46982 AATAATAATAA
1 AATAATAA-AA
46993 AATAGATAACAA
1 AATA-ATAA-AA
47005 AGATAAATAAAA
1 A-AT-AATAAAA
* *
47017 ATTAGTAAAA
1 AATAATAAAA
47027 AATAATAAAA
1 AATAATAAAA
*
47037 TA-AATAAAA
1 AATAATAAAA
47046 A
1 A
47047 GGACCAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
9 7 0.16
10 15 0.34
11 5 0.11
12 10 0.23
13 6 0.14
14 1 0.02
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.22
Consensus pattern (10 bp):
AATAATAAAA
Found at i:47160 original size:20 final size:19
Alignment explanation
Indices: 47131--47171 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
47121 ATTTGCACAA
47131 ACAAATTTAAAAGGAAAAC
1 ACAAATTTAAAAGGAAAAC
*
47150 ACAATATTTAAAGGGAAAAC
1 ACAA-ATTTAAAAGGAAAAC
47170 AC
1 AC
47172 GTCAATTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.17
Consensus pattern (19 bp):
ACAAATTTAAAAGGAAAAC
Found at i:48913 original size:84 final size:84
Alignment explanation
Indices: 48618--48945 Score: 383
Period size: 85 Copynumber: 3.9 Consensus size: 84
48608 TCTTCTTACA
* * * * * *
48618 TTGAGCTATGCTGC-AACTGATGTGCCTTTGAGCTAAATGGAATCGAACTCGAAGGGTCTTTGAT
1 TTGAGCTATGCTGCAAATTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAA-GGTCTTTGTT
* *
48682 GACAGATAACCCCTCTAG-C
65 GACAGATAACCCTTCTCGCC
* * * *
48701 TTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTATAATCAAACTCGAAGGTCTTGGTT
1 TTGAGCTATGCTGCAAA-TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTT
*
48766 GACATATAACCCTTCTCGCC
65 GACAGATAACCCTTCTCGCC
* * *
48786 TTGAGTTATGCTGTAAATTGGACATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGT
1 TTGAGCTATGCTGCAAATT-GATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGT
* *
48851 TGGCAGATAGCCCTTCTCGCC
64 TGACAGATAACCCTTCTCGCC
* * *
48872 TTGAGCTATCCTGCAAA-TGATGTGCCTTTGAGTTGAGTGTAATCGAACTCGAAGGTCTTTTGTT
1 TTGAGCTATGCTGCAAATTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTT
**
48936 GGTAGATAAC
65 GACAGATAAC
48946 TCGAAGGTCT
Statistics
Matches: 211, Mismatches: 29, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
83 13 0.06
84 78 0.37
85 84 0.40
86 36 0.17
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (84 bp):
TTGAGCTATGCTGCAAATTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTG
ACAGATAACCCTTCTCGCC
Found at i:48953 original size:26 final size:26
Alignment explanation
Indices: 48917--48969 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
48907 AGTGTAATCG
*
48917 AACTCGAAGGTCTTTTGTTGGTAGAT
1 AACTCGAAGGTCTTTTGTTGGCAGAT
48943 AACTCGAAGGTCTTTTGTTGGCAGAT
1 AACTCGAAGGTCTTTTGTTGGCAGAT
48969 A
1 A
48970 GCCCTTCTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (26 bp):
AACTCGAAGGTCTTTTGTTGGCAGAT
Found at i:49026 original size:110 final size:110
Alignment explanation
Indices: 48833--49055 Score: 392
Period size: 110 Copynumber: 2.0 Consensus size: 110
48823 AGTGTAATCG
*
48833 AACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATCCTGCAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATCCTGCAAATGATGTACC
* *
48898 TTTGAGTTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGTAGAT
66 TTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGAT
* *
48943 AACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTATC
1 AACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATCCTGCAAATGATGTACC
*
49008 TTTGAGCTGAGTGTAATCGAACTCGAAGTTCTTTTGTTGGCAGAT
66 TTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGAT
49053 AAC
1 AAC
49056 CCTTCTCGCA
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 107 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (110 bp):
AACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATCCTGCAAATGATGTACC
TTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGAT
Found at i:49131 original size:71 final size:71
Alignment explanation
Indices: 49015--49158 Score: 243
Period size: 71 Copynumber: 2.0 Consensus size: 71
49005 ATCTTTGAGC
* * *
49015 TGAGTGTAATCGAACTCGAAGTTCTTTTGTTGGCAGATAACCCTTCTCGCATTGAGCTATGCTGC
1 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCATTGAGCTATACTAC
49080 AAATGA
66 AAATGA
* *
49086 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATATCCCTTCTCGCCTTGAGCTATACTAC
1 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCATTGAGCTATACTAC
49151 AAATGA
66 AAATGA
49157 TG
1 TG
49159 TGCCTTTGAG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (71 bp):
TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCATTGAGCTATACTAC
AAATGA
Found at i:49231 original size:155 final size:155
Alignment explanation
Indices: 48943--49242 Score: 451
Period size: 155 Copynumber: 1.9 Consensus size: 155
48933 GTTGGTAGAT
* * *
48943 AACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTATC
1 AACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATACTACAAATGATGTACC
* * *
49008 TTTGAGCTGAGTGTAATCGAACTCGAAGTTCTTTTGTTGGCAGATAACCCTTCTCGCATTGAGCT
66 TTTGAGATGAGTGTAATCGAACTCGAAGTTCTTTTGTTGGCAAATAACCCTTCTCGCACTGAGCT
*
49073 ATGCTGCAAATGATGAGTGTAATCG
131 ATGCTACAAATGATGAGTGTAATCG
* *
49098 AACTCGAAGGTCTTTTGTTGGCAGATATCCCTTCTCGCCTTGAGCTATACTACAAATGATGTGCC
1 AACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATACTACAAATGATGTACC
* * *
49163 TTTGAGATGAGTGTAATCGAACTCGAAGGTT-TTTTGTTGGCAAATAGA-CTTTCTTGCCCTGAG
66 TTTGAGATGAGTGTAATCGAACTCGAA-GTTCTTTTGTTGGCAAATA-ACCCTTCTCGCACTGAG
*
49226 TTATGCTACAAATGATG
129 CTATGCTACAAATGATG
49243 TGCCTTTGAG
Statistics
Matches: 130, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
155 126 0.97
156 4 0.03
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (155 bp):
AACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATACTACAAATGATGTACC
TTTGAGATGAGTGTAATCGAACTCGAAGTTCTTTTGTTGGCAAATAACCCTTCTCGCACTGAGCT
ATGCTACAAATGATGAGTGTAATCG
Found at i:49235 original size:84 final size:84
Alignment explanation
Indices: 49086--49496 Score: 526
Period size: 84 Copynumber: 5.0 Consensus size: 84
49076 CTGCAAATGA
* * * *
49086 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATATCCCTTCTCGCCTTGAGCTATACTAC
1 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGTTATGCTAC
*
49151 AAATGATGTGCCTTTGAGA
66 AAATGATGTGCCTTTGAGC
* * * * *
49170 TGAGTGTAATCGAACTCGAAGGTTTTTTGTTGGCAAATAGACTTTCTTGCCCTGAGTTATGCTAC
1 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGTTATGCTAC
49235 AAATGATGTGCCTTTGAGC
66 AAATGATGTGCCTTTGAGC
* * * * * *
49254 TGAGTGTAATCGAACTTGAAGGTC---T-TTGGCATATAGCCTTTCTTTCCTTGAGCTATGCTGC
1 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGTTATGCTAC
* * *
49315 AAATAATGTGCTTTTAAGC
66 AAATGATGTGCCTTTGAGC
* * * * * * **
49334 TAACTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGATGT
1 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGTTATGCTAC
49398 AAATGATGTGCCTTTGAGC
66 AAATGATGTGCCTTTGAGC
* *
49417 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCATATAGCCCTTCTTGCCTTGAGTTATGTTAC
1 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGTTATGCTAC
49482 AAATGATGTGCCTTT
66 AAATGATGTGCCTTT
49497 CGAAGGTCTT
Statistics
Matches: 278, Mismatches: 45, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
80 67 0.24
81 1 0.00
82 1 0.00
83 65 0.23
84 144 0.52
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (84 bp):
TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGTTATGCTAC
AAATGATGTGCCTTTGAGC
Found at i:49411 original size:163 final size:166
Alignment explanation
Indices: 49086--49496 Score: 524
Period size: 163 Copynumber: 2.5 Consensus size: 166
49076 CTGCAAATGA
* * * *
49086 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATATCCCTTCTCGCCTTGAGCTATACTAC
1 TGAGTGTAATCGAACTCGAAGGTC--TTGTTGGCATATAGCCCTTCTTGCCTTGAGCTATGCTAC
* * * * * *
49151 AAATGATGTGCCTTTGAGATGAGTGTAATCGAACTCGAAGGTTTTTTGTTGGCAAATAGACTTTC
64 AAATGATGTGCCTTTAAGATAACTGTAATCGAACTCGAAGGTTCTTTGTTGACAAATAGACCTTC
* *
49216 TTGCCCTGAGTTATGCTACAAATGATGTGCCTTTGAGC
129 TAGCCCTGAGTTATGATACAAATGATGTGCCTTTGAGC
* * * *
49254 TGAGTGTAATCGAACTTGAAGGTC-T-TTGGCATATAGCCTTTCTTTCCTTGAGCTATGCTGCAA
1 TGAGTGTAATCGAACTCGAAGGTCTTGTTGGCATATAGCCCTTCTTGCCTTGAGCTATGCTACAA
* * * *
49317 ATAATGTGCTTTTAAGCTAACTGTAATCGAACTCGAAGG-TCTTTGTTGACAGATA-ACCCTTCT
66 ATGATGTGCCTTTAAGATAACTGTAATCGAACTCGAAGGTTCTTTGTTGACAAATAGA-CCTTCT
* **
49380 AGCCTTGAGTTATGATGTAAATGATGTGCCTTTGAGC
130 AGCCCTGAGTTATGATACAAATGATGTGCCTTTGAGC
* *
49417 TGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCATATAGCCCTTCTTGCCTTGAGTTATGTTAC
1 TGAGTGTAATCGAACTCGAAGGTC--TTGTTGGCATATAGCCCTTCTTGCCTTGAGCTATGCTAC
49482 AAATGATGTGCCTTT
64 AAATGATGTGCCTTT
49497 CGAAGGTCTT
Statistics
Matches: 207, Mismatches: 31, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
162 1 0.00
163 73 0.35
164 64 0.31
165 1 0.00
166 1 0.00
167 44 0.21
168 23 0.11
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (166 bp):
TGAGTGTAATCGAACTCGAAGGTCTTGTTGGCATATAGCCCTTCTTGCCTTGAGCTATGCTACAA
ATGATGTGCCTTTAAGATAACTGTAATCGAACTCGAAGGTTCTTTGTTGACAAATAGACCTTCTA
GCCCTGAGTTATGATACAAATGATGTGCCTTTGAGC
Found at i:49632 original size:80 final size:80
Alignment explanation
Indices: 49496--49983 Score: 733
Period size: 80 Copynumber: 6.1 Consensus size: 80
49486 GATGTGCCTT
* ** * * *
49496 TCGAAGGTCTTTAGCAAATATCCCTTCTTTCCTTGAGCTATGCTGCAAATAATGTGCCTTTGAGC
1 TCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
49561 TGAGTGTAATCGAAC
66 TGAGTGTAATCGAAC
* * * * * * * *
49576 TCAAAGGTCTTTGGTAGATAACCCTTCTTGCCTTAAGTTATACTGCAAATGATGTGCTTTTGAGC
1 TCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
49641 TGAGTGTAATCGAAC
66 TGAGTGTAATCGAAC
* *
49656 TCGAAGGTCTTTGGCAGGTAACCCTTCTTACCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
1 TCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
49721 TGAGTGTAATCGAAC
66 TGAGTGTAATCGAAC
*
49736 TCGAAGGTCTTTGGCAGGTAGCCCTTGTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
1 TCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
49801 TGAGTGTAATCGAAC
66 TGAGTGTAATCGAAC
* * * * * *
49816 TCAAATGTCTTTGGCAGCTAGCCCTTCTTGCCTTGAGCTATACTACAAATGATGTGCCTTTAAGC
1 TCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
*
49881 TGAGTGTAATTGAAC
66 TGAGTGTAATCGAAC
*
49896 TCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATAATGTGCCTTTGAGC
1 TCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
*
49961 TGAGTGTAATTGAAC
66 TGAGTGTAATCGAAC
*
49976 TTGAAGGT
1 TCGAAGGT
49984 TTTTTGTTAA
Statistics
Matches: 370, Mismatches: 38, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 370 1.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (80 bp):
TCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
TGAGTGTAATCGAAC
Found at i:51006 original size:99 final size:99
Alignment explanation
Indices: 50822--51019 Score: 306
Period size: 99 Copynumber: 2.0 Consensus size: 99
50812 ACAACTCAAT
* *
50822 GATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAACTGGGGCGTTTAACCAAT
1 GATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAACCGGGACGTTTAACCAAT
* *
50887 TGCTCTACAGGGACAACTCAAGCTTTATTGTATA
66 TGCTCTACAGGAACAACTCAAGCTTTAATGTATA
* * * *
50921 GATATTATAATCACCTTTATCAGGTTAGTTGAATCTTATCCATAAAGCCGGGACGTTTAACCAAT
1 GATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAACCGGGACGTTTAACCAAT
* *
50986 TGCTCTAGAGGAACAGCTCAAGCTTTAATGTATA
66 TGCTCTACAGGAACAACTCAAGCTTTAATGTATA
51020 TATAATATTA
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 89 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (99 bp):
GATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAACCGGGACGTTTAACCAAT
TGCTCTACAGGAACAACTCAAGCTTTAATGTATA
Found at i:53631 original size:4 final size:4
Alignment explanation
Indices: 53614--53749 Score: 54
Period size: 4 Copynumber: 32.8 Consensus size: 4
53604 TTAAATTGAA
* *
53614 AAAT AAAT ATAT AAAT AAAT ATAA- AAA- AAGAG AAA- AAAT ATTAAT
1 AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AA-AT AAAT AAAT A--AAT
*
53659 ATAAT -AAT -AAT -AAT AAAAT AAAAT AGAT AACA- AAGAT AAAT AAAAGT
1 A-AAT AAAT AAAT AAAT -AAAT -AAAT AAAT AA-AT AA-AT AAAT -AAA-T
* *
53706 TAAT AAA- AAAT AATAA AAAT AAAT AAAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AA-AT AAAT AAAT -AAAT AAAT AAAT AAAT AAA
53750 AAGGACCAAA
Statistics
Matches: 108, Mismatches: 9, Indels: 30
0.73 0.06 0.20
Matches are distributed among these distances:
3 19 0.18
4 53 0.49
5 31 0.29
6 5 0.05
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:53637 original size:10 final size:10
Alignment explanation
Indices: 53622--53743 Score: 51
Period size: 10 Copynumber: 12.3 Consensus size: 10
53612 AAAAATAAAT
53622 ATATAAATAA
1 ATATAAATAA
*
53632 ATATAAAAAA
1 ATATAAATAA
* *
53642 AGAGAAA-AA
1 ATATAAATAA
*
53651 ATATTAATATA
1 ATATAAATA-A
53662 ATA-ATAAT-A
1 ATATA-AATAA
53671 ATA-AAATAAA
1 ATATAAAT-AA
* *
53681 ATAGATAACAA
1 ATATA-AATAA
*
53692 AGATAAATAA
1 ATATAAATAA
*
53702 A-AGTTAATAA
1 ATA-TAAATAA
*
53712 A-AAATAATAA
1 ATATA-AATAA
*
53722 AAATAAATAA
1 ATATAAATAA
53732 A-ATAAATAA
1 ATATAAATAA
53741 ATA
1 ATA
53744 AATAAAAAGG
Statistics
Matches: 86, Mismatches: 15, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
8 3 0.03
9 21 0.24
10 45 0.52
11 15 0.17
12 2 0.02
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (10 bp):
ATATAAATAA
Found at i:53672 original size:14 final size:14
Alignment explanation
Indices: 53646--53741 Score: 50
Period size: 13 Copynumber: 7.2 Consensus size: 14
53636 AAAAAAAGAG
*
53646 AAAA-AATATTAAT
1 AAAATAATAATAAT
*
53659 ATAATAATAATAAT
1 AAAATAATAATAAT
53673 AAAATAA-AATAGAT
1 AAAATAATAATA-AT
53687 AACAA-AGAT-A-AAT
1 AA-AATA-ATAATAAT
53700 AAAAGT--TAATAA-
1 AAAA-TAATAATAAT
*
53712 AAAATAATAAAAAT
1 AAAATAATAATAAT
53726 -AAATAA-AATAAAT
1 AAAATAATAAT-AAT
53739 AAA
1 AAA
53742 TAAATAAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 27
0.67 0.05 0.28
Matches are distributed among these distances:
11 2 0.03
12 9 0.14
13 27 0.42
14 22 0.34
15 4 0.06
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:53725 original size:9 final size:9
Alignment explanation
Indices: 53659--53751 Score: 50
Period size: 9 Copynumber: 10.1 Consensus size: 9
53649 AAATATTAAT
*
53659 ATAATAATA
1 ATAATAAAA
53668 ATAAT-AAA
1 ATAATAAAA
*
53676 ATAA-AATAG
1 ATAATAA-AA
* *
53685 ATAACAAAG
1 ATAATAAAA
53694 ATAAATAAAA
1 AT-AATAAAA
*
53704 GTTAATAAAAA
1 -ATAAT-AAAA
53715 ATAATAAAA
1 ATAATAAAA
53724 ATAA-ATAAA
1 ATAATA-AAA
*
53733 ATAA-ATAA
1 ATAATAAAA
53741 ATAAATAAAA
1 AT-AATAAAA
53751 A
1 A
53752 GGACCAAAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
8 12 0.18
9 32 0.48
10 18 0.27
11 5 0.07
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (9 bp):
ATAATAAAA
Found at i:53863 original size:20 final size:20
Alignment explanation
Indices: 53838--53876 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
53828 TTACACAAAC
53838 ATATTTAAAAGGAAAACACA
1 ATATTTAAAAGGAAAACACA
*
53858 ATATTTAAAGGGAAAACAC
1 ATATTTAAAAGGAAAACAC
53877 GTCAATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (20 bp):
ATATTTAAAAGGAAAACACA
Found at i:56028 original size:81 final size:81
Alignment explanation
Indices: 55893--56050 Score: 255
Period size: 81 Copynumber: 2.0 Consensus size: 81
55883 TTAAATAGTC
*
55893 GGAGACTCAACAAAGCAACTCCCTATAATAAGAGGATCATTTTGTAACTTTTAATAGTTGAAGAA
1 GGAGACTCAACAAAGCAACTCCCTATAATAAGAGGATCATTTTGTAACTTTTAATAGTTAAAGAA
*
55958 CTCAACAAAGCAACTT
66 CCCAACAAAGCAACTT
* * *
55974 GGAGACTCAACAAAGTAACTCCCTATAATCAA-ATGATCATTTTGTAATTTTTAATAGTTAAAGA
1 GGAGACTCAACAAAGCAACTCCCTATAAT-AAGAGGATCATTTTGTAACTTTTAATAGTTAAAGA
56038 ACCCAACAAAGCA
65 ACCCAACAAAGCA
56051 GCGTCCTATA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
81 69 0.97
82 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (81 bp):
GGAGACTCAACAAAGCAACTCCCTATAATAAGAGGATCATTTTGTAACTTTTAATAGTTAAAGAA
CCCAACAAAGCAACTT
Found at i:56175 original size:14 final size:11
Alignment explanation
Indices: 56142--56171 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
56132 AGATGTTTCC
56142 CTTTCTTCCAT
1 CTTTCTTCCAT
56153 CTTTCTTCCAT
1 CTTTCTTCCAT
56164 CTTTCTTC
1 CTTTCTTC
56172 TTCCTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.07, C:0.37, G:0.00, T:0.57
Consensus pattern (11 bp):
CTTTCTTCCAT
Found at i:56411 original size:43 final size:42
Alignment explanation
Indices: 56326--56411 Score: 111
Period size: 45 Copynumber: 2.0 Consensus size: 42
56316 GAGTTAAAAG
* *
56326 AAAAATAAAATAACTTCGTTGAATCAAAGGGAGTCCAAAGAAA
1 AAAAATAAAATAACTTAGTTGAATCAAAGAGAGTCC-AAGAAA
*
56369 AAAAATATATAATAACTTATTTGAATCAAAGAGAGTCC-AGAAA
1 AAAAATA-A-AATAACTTAGTTGAATCAAAGAGAGTCCAAGAAA
56412 TTTGAGTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 12 0.32
44 1 0.03
45 25 0.66
ACGTcount: A:0.53, C:0.10, G:0.14, T:0.22
Consensus pattern (42 bp):
AAAAATAAAATAACTTAGTTGAATCAAAGAGAGTCCAAGAAA
Found at i:56910 original size:29 final size:29
Alignment explanation
Indices: 56855--56910 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
56845 TTTTAGGAGG
* **
56855 AAATAAATTTATAAAATTTTAAGAAATGA
1 AAATAAATTAATAAAATAGTAAGAAATGA
56884 AAATAAATTAATAAAAATAGTAA-AAAT
1 AAATAAATTAAT-AAAATAGTAAGAAAT
56911 ATATGATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 15 0.65
30 8 0.35
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.30
Consensus pattern (29 bp):
AAATAAATTAATAAAATAGTAAGAAATGA
Found at i:60070 original size:2 final size:2
Alignment explanation
Indices: 60063--60091 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
60053 AAAAGTTTTC
60063 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60092 CATACAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.