Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_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: 6483253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 29
Found at i:3773706 original size:18 final size:19
Alignment explanation
Indices: 3773677--3773719 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
3773667 TTAACTTTTT
3773677 GGTCAAAGTCAACGA-TC-
1 GGTCAAAGTCAACGAGTCG
3773694 GGTCAACAGTCAACGAGTCG
1 GGTCAA-AGTCAACGAGTCG
3773714 GGTCAA
1 GGTCAA
3773720 TAGGTTAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.26
18 9 0.39
19 2 0.09
20 6 0.26
ACGTcount: A:0.33, C:0.23, G:0.28, T:0.16
Consensus pattern (19 bp):
GGTCAAAGTCAACGAGTCG
Found at i:3773751 original size:18 final size:19
Alignment explanation
Indices: 3773730--3773765 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3773720 TAGGTTAGGT
3773730 CGGGTC-AACAGGTCGGGC
1 CGGGTCAAACAGGTCGGGC
*
3773748 CGGGTCAAACGGGTCGGG
1 CGGGTCAAACAGGTCGGG
3773766 TCAAAACTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.17, C:0.25, G:0.47, T:0.11
Consensus pattern (19 bp):
CGGGTCAAACAGGTCGGGC
Found at i:3778643 original size:65 final size:64
Alignment explanation
Indices: 3778556--3778715 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 64
3778546 GAATAAATTG
* * * ** * *
3778556 AACATCAAATGCATTTTATGCATCGATGCACATACCATGCATTGATGCACTCAGGGT-TTTATGA
1 AACATCGAATGCATTTTATGCATCGATGCACAAAACATAAATCGATGCACTCAGGCTATTT-TG-
3778620 A
64 A
* *
3778621 AACATCGAATGTATTTGATGCATCGATGCACAAAACATAAATCGATGCACTCAGGCTATTTTGA
1 AACATCGAATGCATTTTATGCATCGATGCACAAAACATAAATCGATGCACTCAGGCTATTTTGA
*
3778685 AACTTCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
3778716 TAAGTGTTCC
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 29 0.35
65 50 0.61
66 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACAAAACATAAATCGATGCACTCAGGCTATTTTGA
Found at i:3784535 original size:23 final size:23
Alignment explanation
Indices: 3784493--3784573 Score: 119
Period size: 23 Copynumber: 3.6 Consensus size: 23
3784483 TTGGTGCAGA
* * *
3784493 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAT
3784515 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCTTTGAAT
3784538 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCTTTGAAT
*
3784561 GGGAACCAATTCC
1 GGGAACCGATTCC
3784574 ATCCTTTATG
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
22 14 0.26
23 40 0.74
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAT
Found at i:3784999 original size:18 final size:17
Alignment explanation
Indices: 3784976--3785009 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3784966 TCAAAAATTG
*
3784976 TTGATTTAATTGATGTTT
1 TTGATTCAATT-ATGTTT
3784994 TTGATTCAATTATGTT
1 TTGATTCAATTATGTT
3785010 GTTTTCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (17 bp):
TTGATTCAATTATGTTT
Found at i:3786281 original size:13 final size:13
Alignment explanation
Indices: 3786263--3786287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3786253 ACCATGTCAC
3786263 ATTGATTATGAAT
1 ATTGATTATGAAT
3786276 ATTGATTATGAA
1 ATTGATTATGAA
3786288 ACTAATGACT
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:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGATTATGAAT
Found at i:3786824 original size:20 final size:20
Alignment explanation
Indices: 3786795--3786832 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3786785 TTTCAAAGGA
3786795 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
3786815 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
3786833 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:3786909 original size:28 final size:28
Alignment explanation
Indices: 3786851--3786912 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
3786841 TGAACATCGA
* *
3786851 ATGCATTTTATGCATCGATGCACATACC
1 ATGCATTTGATGCATCGATGCACATAAC
3786879 ATGCATTTGATGCATCGATGCAC-TAGAC
1 ATGCATTTGATGCATCGATGCACATA-AC
3786907 ATGCAT
1 ATGCAT
3786913 CGATGCACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 2 0.06
28 29 0.94
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (28 bp):
ATGCATTTGATGCATCGATGCACATAAC
Found at i:3793061 original size:23 final size:23
Alignment explanation
Indices: 3793029--3793088 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
3793019 GCCAACGGTT
* **
3793029 AACGGGTTTGGTTGGGTCGGGCC
1 AACGGATTTGGTCAGGTCGGGCC
3793052 AACGGATTTGGTCAGGTCGGGCC
1 AACGGATTTGGTCAGGTCGGGCC
* *
3793075 AACGGGTTGGGTCA
1 AACGGATTTGGTCA
3793089 AAACTGGTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.15, C:0.18, G:0.43, T:0.23
Consensus pattern (23 bp):
AACGGATTTGGTCAGGTCGGGCC
Found at i:3793858 original size:19 final size:20
Alignment explanation
Indices: 3793834--3793871 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3793824 TTTATATTTT
3793834 TTATTTTCT-TTATCTTTAC
1 TTATTTTCTATTATCTTTAC
*
3793853 TTATTTTCTATTTTCTTTA
1 TTATTTTCTATTATCTTTA
3793872 TATTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATTTTCTATTATCTTTAC
Found at i:3793886 original size:26 final size:25
Alignment explanation
Indices: 3793818--3793887 Score: 88
Period size: 26 Copynumber: 2.8 Consensus size: 25
3793808 TTTCTGTAGT
*
3793818 TTTATATTTATATTTTT-TATTTTC
1 TTTATATTTATTTTTTTCTATTTTC
* *
3793842 TTTATCTTTACTTATTTTCTATTTTC
1 TTTATATTTA-TTTTTTTCTATTTTC
3793868 TTTATATTTATTTTGTTTCT
1 TTTATATTTATTTT-TTTCT
3793888 TTATTTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
24 9 0.24
25 8 0.21
26 21 0.55
ACGTcount: A:0.17, C:0.09, G:0.01, T:0.73
Consensus pattern (25 bp):
TTTATATTTATTTTTTTCTATTTTC
Found at i:3793957 original size:5 final size:5
Alignment explanation
Indices: 3793949--3794062 Score: 60
Period size: 5 Copynumber: 22.4 Consensus size: 5
3793939 TATTATGTTC
* *
3793949 TTTAT TTTAT TTTAT TGTTTT TTTATT TTTACT TTTATT TCTTTT TTTAT
1 TTTAT TTTAT TTTAT T-TTAT TTTA-T TTTA-T TTTA-T T-TTAT TTTAT
* * * *
3793999 CGTTAT TTTA- TTTAT TTTAT TACTT-T TTTAT CTCA- TTTA- GTTA-
1 -TTTAT TTTAT TTTAT TTTAT T--TTAT TTTAT TTTAT TTTAT TTTAT
3794042 TTTAT TTT-T TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TT
3794063 ACTTTCATTA
Statistics
Matches: 85, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
4 18 0.21
5 39 0.46
6 24 0.28
7 4 0.05
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:3793967 original size:40 final size:39
Alignment explanation
Indices: 3793865--3794020 Score: 101
Period size: 40 Copynumber: 3.9 Consensus size: 39
3793855 ATTTTCTATT
* * * *
3793865 TTCTTTATATTTATTTTGTTTCTTTATTTATTTTTATTTTG
1 TTCTTTAT-TTTATTTT-ATTGTTTATTTATTATTATTATG
* *
3793906 TTATTGT-TTTTA-GTTATTTGTTTATTATATTATTATTATG
1 TTCTT-TATTTTATTTTA-TTGTTTATT-TATTATTATTATG
* *
3793946 TTCTTTATTTTATTTTATTGTTTTTTTATTTTTACTTTTAT-
1 TTCTTTATTTTATTTTATTGTTTATTTATTATTA---TTATG
*
3793987 TTCTTT-TTTTATCGTTA-T-TTTATTTATT-TTATTA
1 TTCTTTATTTTAT-TTTATTGTTTATTTATTATTATTA
3794021 CTTTTTTATC
Statistics
Matches: 94, Mismatches: 12, Indels: 24
0.72 0.09 0.18
Matches are distributed among these distances:
35 3 0.03
38 3 0.03
39 27 0.29
40 39 0.41
41 17 0.18
42 5 0.05
ACGTcount: A:0.17, C:0.04, G:0.05, T:0.74
Consensus pattern (39 bp):
TTCTTTATTTTATTTTATTGTTTATTTATTATTATTATG
Found at i:3793993 original size:23 final size:21
Alignment explanation
Indices: 3793949--3794026 Score: 68
Period size: 24 Copynumber: 3.4 Consensus size: 21
3793939 TATTATGTTC
3793949 TTTA-TTTTATTTTATTGTTTT
1 TTTATTTTTATTTTATT-TTTT
3793970 TTTATTTTTACTTTTATTTCTTTT
1 TTTATTTTTA-TTTTA-TT-TTTT
**
3793994 TTTATCGTTATTTTATTTATTT
1 TTTATTTTTATTTTATTT-TTT
3794016 TATTACTTTTT
1 T-TTA-TTTTT
3794027 TATCTCATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
21 5 0.11
22 11 0.24
23 13 0.28
24 17 0.37
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (21 bp):
TTTATTTTTATTTTATTTTTT
Found at i:3793996 original size:12 final size:11
Alignment explanation
Indices: 3793863--3794027 Score: 53
Period size: 12 Copynumber: 14.4 Consensus size: 11
3793853 TTATTTTCTA
* *
3793863 TTTTCTTTATA
1 TTTTTTTTATT
* *
3793874 TTTATTTTGTT
1 TTTTTTTTATT
*
3793885 TCTTTATTTATT
1 T-TTTTTTTATT
* *
3793897 TTTATTTTGTT
1 TTTTTTTTATT
*
3793908 ATTGTTTTTAGTT
1 -TTTTTTTTA-TT
* *
3793921 ATTTGTTTATT
1 TTTTTTTTATT
* * *
3793932 ATATTATTATT
1 TTTTTTTTATT
* *
3793943 ATGTTCTTTA-T
1 -TTTTTTTTATT
*
3793954 TTTATTTTATT
1 TTTTTTTTATT
*
3793965 GTTTTTTTATT
1 TTTTTTTTATT
*
3793976 TTTACTTTTATT
1 TTT-TTTTTATT
*
3793988 TCTTTTTTTATC
1 T-TTTTTTTATT
* *
3794000 GTTATTTTATT
1 TTTTTTTTATT
*
3794011 TATTTTATTACTT
1 T-TTTTTTTA-TT
3794024 TTTT
1 TTTT
3794028 ATCTCATTTA
Statistics
Matches: 106, Mismatches: 39, Indels: 17
0.65 0.24 0.10
Matches are distributed among these distances:
10 6 0.06
11 46 0.43
12 47 0.44
13 7 0.07
ACGTcount: A:0.16, C:0.04, G:0.05, T:0.75
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:3794008 original size:35 final size:32
Alignment explanation
Indices: 3793958--3794027 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
3793948 CTTTATTTTA
* * *
3793958 TTTTATTGTTTTTTTATTTTTACTTTTATTTCTTT
1 TTTTATCGTTATTTTA--TTTA-TTTTATTACTTT
3793993 TTTTATCGTTATTTTATTTATTTTATTACTTT
1 TTTTATCGTTATTTTATTTATTTTATTACTTT
3794025 TTT
1 TTT
3794028 ATCTCATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 14 0.44
33 4 0.12
35 14 0.44
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (32 bp):
TTTTATCGTTATTTTATTTATTTTATTACTTT
Found at i:3794015 original size:9 final size:9
Alignment explanation
Indices: 3793822--3794063 Score: 89
Period size: 9 Copynumber: 26.7 Consensus size: 9
3793812 TGTAGTTTTA
3793822 TATTTATATT
1 TATTTAT-TT
3793832 T-TTTATTT
1 TATTTATTT
*
3793840 TCTTTATCTT
1 TATTTAT-TT
*
3793850 TACTTATTTT
1 TATTTA-TTT
*
3793860 CTATTTTCTTT
1 -TA-TTTATTT
3793871 ATATTTATTT
1 -TATTTATTT
* *
3793881 TGTTT-CTT
1 TATTTATTT
3793889 TATTTATTTT
1 TATTTA-TTT
*
3793899 TATTT-TGT
1 TATTTATTT
3793907 TATTGT-TTT
1 TATT-TATTT
*
3793916 TAGTTA-TT
1 TATTTATTT
* *
3793924 TGTTTATTA
1 TATTTATTT
3793933 TA-TTATTAT
1 TATTTATT-T
*
3793942 TATGTT-CTT
1 TAT-TTATTT
3793951 TATTTTATTT
1 TA-TTTATTT
*
3793961 TA-TTGTTT
1 TATTTATTT
3793969 T-TTTATTTT
1 TATTTA-TTT
3793978 TACTTT-TATT
1 TA-TTTAT-TT
*
3793988 TCTTT-TTT
1 TATTTATTT
3793996 TATCGTTATTT
1 TAT--TTATTT
3794007 TATTTATTT
1 TATTTATTT
*
3794016 TA-TTACTT
1 TATTTATTT
*
3794024 T-TTTATCT
1 TATTTATTT
* *
3794032 CATTTA-GT
1 TATTTATTT
3794040 TATTTATTT
1 TATTTATTT
*
3794049 TTTTTATTT
1 TATTTATTT
3794058 TATTTA
1 TATTTA
3794064 CTTTCATTAC
Statistics
Matches: 173, Mismatches: 33, Indels: 53
0.67 0.13 0.20
Matches are distributed among these distances:
8 55 0.32
9 64 0.37
10 33 0.19
11 19 0.11
12 2 0.01
ACGTcount: A:0.18, C:0.05, G:0.04, T:0.73
Consensus pattern (9 bp):
TATTTATTT
Found at i:3794022 original size:41 final size:39
Alignment explanation
Indices: 3793912--3794067 Score: 115
Period size: 41 Copynumber: 3.8 Consensus size: 39
3793902 TTTGTTATTG
* *
3793912 TTTTTA-GTTATTTGTTTATTATATTA-TTATTATGTTCTT
1 TTTTTATGTTATTTTTTTATTTTATTACTT-TTAT-TTCTT
* *
3793951 TATTTTATTTTATTGTTTTT-TTATTTTTACTTTTATTTCTT
1 T-TTTTATGTTATT-TTTTTATT-TTATTACTTTTATTTCTT
3793992 TTTTTATCGTTATTTTATTTATTTTATTACTTTT-TTATCTCAT
1 TTTTTAT-GTTATTTT-TTTATTTTATTACTTTTATT-TCT--T
*
3794035 TTAGTTAT-TTATTTTTTTTATTTTATTTACTTT
1 TT-TTTATGTTA-TTTTTTTATTTTA-TTACTTT
3794068 CATTACATTT
Statistics
Matches: 96, Mismatches: 7, Indels: 24
0.76 0.06 0.19
Matches are distributed among these distances:
39 1 0.01
40 15 0.16
41 34 0.35
42 26 0.27
43 16 0.17
44 4 0.04
ACGTcount: A:0.18, C:0.05, G:0.04, T:0.73
Consensus pattern (39 bp):
TTTTTATGTTATTTTTTTATTTTATTACTTTTATTTCTT
Found at i:3799696 original size:15 final size:15
Alignment explanation
Indices: 3799676--3799723 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
3799666 TTAGCTGGGT
*
3799676 GGGCGGATGTGGGGC
1 GGGCGGATGAGGGGC
*
3799691 GGGCGGATGCGGGGC
1 GGGCGGATGAGGGGC
* *
3799706 GAGTGGATGAGGGGC
1 GGGCGGATGAGGGGC
3799721 GGG
1 GGG
3799724 TAATGTCTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.10, C:0.12, G:0.67, T:0.10
Consensus pattern (15 bp):
GGGCGGATGAGGGGC
Found at i:3806135 original size:249 final size:252
Alignment explanation
Indices: 3805694--3806193 Score: 695
Period size: 249 Copynumber: 2.0 Consensus size: 252
3805684 CACCAACACG
* * *
3805694 ATTTGTAATAACAAATTCTATCGAAATAAAAAAAAAATATCATGATCTTACCATGATGAGTTTCG
1 ATTTGTAATAACAAATTCTATCGAAATAAAAAAAAAATATCATGACCGTACCATGATGAGTCTCG
* * *
3805759 AATTATAACTCTATTTCAAACCATAGCTCTTAATACCGGTTAAGAACTTGAGGGAGAAGAAAAAT
66 AATTATAACTCTATATCAAACCATAGCTCTTAATACCAGTTAAGAACTTGAGGGACAAGAAAAAT
* * *
3805824 TAACATGAAATAAAAATAAAATAATAATTTAACCATCCTCAAATAAGATAATATTTAATGTAATT
131 TAACATGAAATAAAAATAAAATAATAAATTAACCATCCTCAAATAAAATAATATTTAATGTAACT
* *
3805889 TAACTTCTCTCACCCATGTTCACGATTTCAAATGAAAAATATATTAGTACATAACAA
196 TAACTTCTCTCACCCATATTCACGATTTCAAATGAAAAAGATATTAGTACATAACAA
* * * *
3805946 ATTTGTAATAACAAATTCTATCGGAAT-TAAATAAAA-AT-ATGGCCGTACCATGATGAGTCTCG
1 ATTTGTAATAACAAATTCTATCGAAATAAAAAAAAAATATCATGACCGTACCATGATGAGTCTCG
* * * * *
3806008 AATTATAACTCTATATCAAACTATAGCTCTTGATATCAGTTGAGAACTTGAGGGCCAA-AATAAA
66 AATTATAACTCTATATCAAACCATAGCTCTTAATACCAGTTAAGAACTTGAGGGACAAGAA-AAA
**
3806072 TTAACATGAAATAAAAATAAAAT-ATAAAATTAATTATCCTCAAATAAAATAATATTTAATGTAA
130 TTAACATGAAATAAAAATAAAATAAT-AAATTAACCATCCTCAAATAAAATAATATTTAATGTAA
* * * ** *
3806136 CTTGACTTCTCTCCCCCATATTCATGATTTCAAATGGTAAAGATATTAGTCCATAACA
194 CTTAACTTCTCTCACCCATATTCACGATTTCAAATGAAAAAGATATTAGTACATAACA
3806194 TTTGTACAAA
Statistics
Matches: 218, Mismatches: 28, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
248 4 0.02
249 179 0.82
250 2 0.01
251 7 0.03
252 26 0.12
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (252 bp):
ATTTGTAATAACAAATTCTATCGAAATAAAAAAAAAATATCATGACCGTACCATGATGAGTCTCG
AATTATAACTCTATATCAAACCATAGCTCTTAATACCAGTTAAGAACTTGAGGGACAAGAAAAAT
TAACATGAAATAAAAATAAAATAATAAATTAACCATCCTCAAATAAAATAATATTTAATGTAACT
TAACTTCTCTCACCCATATTCACGATTTCAAATGAAAAAGATATTAGTACATAACAA
Found at i:3806760 original size:11 final size:11
Alignment explanation
Indices: 3806746--3806773 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3806736 TTGAAATATG
3806746 AAATATTAAAC
1 AAATATTAAAC
3806757 AAATATTAAAC
1 AAATATTAAAC
3806768 AAATAT
1 AAATAT
3806774 ACACTCCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATATTAAAC
Found at i:3811595 original size:23 final size:23
Alignment explanation
Indices: 3811569--3811627 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
3811559 GTCACGAAAA
**
3811569 ACCACATAGAATTATCCTGAACG
1 ACCACATAGAATTATCCCAAACG
* *
3811592 ACCACATAGAATTGTCCCAAATG
1 ACCACATAGAATTATCCCAAACG
*
3811615 ACCACATAAAATT
1 ACCACATAGAATT
3811628 GCCCCGAAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.22
Consensus pattern (23 bp):
ACCACATAGAATTATCCCAAACG
Found at i:3811793 original size:15 final size:15
Alignment explanation
Indices: 3811781--3811823 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
3811771 CTCATAGGGT
3811781 ATTTTCACGTAGGAC
1 ATTTTCACGTAGGAC
* *
3811796 ATTTTCACTTAGAAC
1 ATTTTCACGTAGGAC
*
3811811 AAATTTCACGTAG
1 -ATTTTCACGTAG
3811824 CATTATCCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (15 bp):
ATTTTCACGTAGGAC
Found at i:3812537 original size:20 final size:19
Alignment explanation
Indices: 3812493--3812564 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 19
3812483 TTTCAATTAT
3812493 AGTATCGATACCTTAC-TC
1 AGTATCGATACCTTACATC
*
3812511 TTGGTATCGATACCTTCACATC
1 --AGTATCGATACCTT-ACATC
*
3812533 AGTATCGATACTACTTAAATC
1 AGTATCGATAC--CTTACATC
3812554 AGTATCGATAC
1 AGTATCGATAC
3812565 TTTTCATCGG
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
20 23 0.51
21 17 0.38
22 5 0.11
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (19 bp):
AGTATCGATACCTTACATC
Found at i:3812556 original size:21 final size:21
Alignment explanation
Indices: 3812514--3812570 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
3812504 CTTACTCTTG
*
3812514 GTATCGATAC-CTTCACATCA
1 GTATCGATACTCTTCAAATCA
3812534 GTATCGATACTACTT-AAATCA
1 GTATCGATACT-CTTCAAATCA
*
3812555 GTATCGATACTTTTCA
1 GTATCGATACTCTTCA
3812571 TCGGATTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 12 0.38
21 17 0.53
22 3 0.09
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.35
Consensus pattern (21 bp):
GTATCGATACTCTTCAAATCA
Found at i:3815462 original size:23 final size:23
Alignment explanation
Indices: 3815384--3815454 Score: 106
Period size: 23 Copynumber: 3.1 Consensus size: 23
3815374 CACCGAAGCG
* *
3815384 CCACGTAGAATTATCCCAAAGGA
1 CCACATAGAATTGTCCCAAAGGA
* *
3815407 CCACATAGAATTGTCCCGAATGA
1 CCACATAGAATTGTCCCAAAGGA
3815430 CCACATAGAATTGTCCCAAAGGA
1 CCACATAGAATTGTCCCAAAGGA
3815453 CC
1 CC
3815455 GCGTAGAACC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.18
Consensus pattern (23 bp):
CCACATAGAATTGTCCCAAAGGA
Found at i:3815613 original size:15 final size:16
Alignment explanation
Indices: 3815595--3815637 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
3815585 CTCATAGGGT
*
3815595 ATTTTCACGTAGGAC-
1 ATTTTCACGTAGAACA
*
3815610 ATTTTCACTTAGAACA
1 ATTTTCACGTAGAACA
*
3815626 AATTTCACGTAG
1 ATTTTCACGTAG
3815638 CATTATCCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (16 bp):
ATTTTCACGTAGAACA
Found at i:3818603 original size:2 final size:2
Alignment explanation
Indices: 3818596--3818624 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3818586 ATTTAAGCTT
3818596 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
3818625 GAGGTTGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3822474 original size:12 final size:13
Alignment explanation
Indices: 3822452--3822492 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
3822442 TAGTAAGAAG
3822452 TTTCTTCTTTTCT
1 TTTCTTCTTTTCT
3822465 TTTC-TCTTTTCTT
1 TTTCTTCTTTTC-T
*
3822478 TTTATTCTTTTCT
1 TTTCTTCTTTTCT
3822491 TT
1 TT
3822493 ATTTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 7 0.28
13 11 0.44
14 7 0.28
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTCTTCTTTTCT
Found at i:3822506 original size:21 final size:21
Alignment explanation
Indices: 3822459--3822506 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3822449 AAGTTTCTTC
3822459 TTTTCTTTTCTCTTTTCTTTT
1 TTTTCTTTTCTCTTTTCTTTT
*
3822480 TATTCTTTTCT-TTATT-TTTAT
1 TTTTCTTTTCTCTT-TTCTTT-T
3822501 TTTTCT
1 TTTTCT
3822507 ATTATCATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTCTTTTCTCTTTTCTTTT
Found at i:3832421 original size:4 final size:4
Alignment explanation
Indices: 3832406--3832476 Score: 73
Period size: 4 Copynumber: 18.8 Consensus size: 4
3832396 AAAATAAAAT
*
3832406 TAAA TGAA TAAA TAAA TAAA T-AA TAATA TAAA TAAA T--A TAAA T-AA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA
3832451 TAAA T-AA TAAA T-AA TAATA TAAA TAA
1 TAAA TAAA TAAA TAAA TAA-A TAAA TAA
3832477 TATATAATTA
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
2 2 0.04
3 12 0.21
4 35 0.61
5 8 0.14
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (4 bp):
TAAA
Found at i:3832426 original size:26 final size:25
Alignment explanation
Indices: 3832397--3832488 Score: 89
Period size: 26 Copynumber: 3.5 Consensus size: 25
3832387 GGACCTGAAA
3832397 AAATAAAATTAAATGAATAAATAAAT
1 AAATAAAATTAAAT-AATAAATAAAT
*
3832423 AAATAATAATATAAATAA-ATATAAAT
1 AAATAA-AAT-TAAATAATAAATAAAT
*
3832449 -AATAAATAATAAATAATAATATAAAT
1 AAATAAA-ATTAAATAATAA-ATAAAT
*
3832475 AATATATAATTAAA
1 AA-ATAAAATTAAA
3832489 AACTTTATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
24 8 0.15
25 7 0.13
26 19 0.35
27 11 0.20
28 9 0.17
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.30
Consensus pattern (25 bp):
AAATAAAATTAAATAATAAATAAAT
Found at i:3832430 original size:29 final size:29
Alignment explanation
Indices: 3832413--3832489 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 29
3832403 AATTAAATGA
*
3832413 ATAAATAAATAAATAATAATATAAATAAAT
1 ATAAAT-AATAAATAATAAAATAAATAAAT
3832443 ATAAATAATAAATAAT-AAAT-AAT-AAT
1 ATAAATAATAAATAATAAAATAAATAAAT
*
3832469 ATAAATAATATATAATTAAAA
1 ATAAATAATAAATAA-TAAAA
3832490 ACTTTATAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
26 17 0.40
27 4 0.09
28 6 0.14
29 10 0.23
30 6 0.14
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (29 bp):
ATAAATAATAAATAATAAAATAAATAAAT
Found at i:3832464 original size:33 final size:33
Alignment explanation
Indices: 3832416--3832484 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
3832406 TAAATGAATA
3832416 AATAAATAAATAATAATATAAATAAAT-ATAAAT
1 AATAAATAAATAATAATA-AAATAAATAATAAAT
* *
3832449 AATAAAT-AATAAATAATAATATAAATAATATAT
1 AATAAATAAAT-AATAATAAAATAAATAATAAAT
3832482 AAT
1 AAT
3832485 TAAAAACTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (33 bp):
AATAAATAAATAATAATAAAATAAATAATAAAT
Found at i:3832524 original size:20 final size:21
Alignment explanation
Indices: 3832501--3832552 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
3832491 CTTTATAAGA
3832501 TATATTATATTTTT-AAAAAT
1 TATATTATATTTTTCAAAAAT
*
3832521 TATATAATATGTTTTCAAAAAT
1 TATATTATAT-TTTTCAAAAAT
3832543 TATA-TATATT
1 TATATTATATT
3832553 ATATATGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 10 0.36
21 8 0.29
22 10 0.36
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TATATTATATTTTTCAAAAAT
Found at i:3832525 original size:22 final size:22
Alignment explanation
Indices: 3832500--3832549 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
3832490 ACTTTATAAG
*
3832500 ATATATTATATTTTTAAAAATT
1 ATATATTATATTTTCAAAAATT
* *
3832522 ATATAATATGTTTTCAAAAATT
1 ATATATTATATTTTCAAAAATT
3832544 ATATAT
1 ATATAT
3832550 ATTATATATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
ATATATTATATTTTCAAAAATT
Found at i:3832588 original size:2 final size:2
Alignment explanation
Indices: 3832583--3832682 Score: 193
Period size: 2 Copynumber: 50.5 Consensus size: 2
3832573 TTTAAAAAAT
3832583 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3832625 T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3832666 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
3832683 GTTTTCAAAA
Statistics
Matches: 97, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 96 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3832697 original size:13 final size:13
Alignment explanation
Indices: 3832679--3832705 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3832669 ATATATATAT
3832679 ATATGTTTTCAAA
1 ATATGTTTTCAAA
3832692 ATATGTTTTCAAA
1 ATATGTTTTCAAA
3832705 A
1 A
3832706 CTATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
ATATGTTTTCAAA
Found at i:3832810 original size:37 final size:37
Alignment explanation
Indices: 3832670--3832933 Score: 206
Period size: 37 Copynumber: 7.1 Consensus size: 37
3832660 TATATATATA
*
3832670 TATATATATATATGTTTTC-AAAATATGTTTTCAAAAC
1 TATATAT-TATATGTTTTCAAAAACATGTTTTCAAAAC
** * *
3832707 TATAT-TATATACATTTTCAAAAACCAT-TTTT-TAAAT
1 TATATAT-TATATGTTTTCAAAAA-CATGTTTTCAAAAC
* **
3832743 TATATATTATACGTTTT-AAAAATGTGTTTTCAAAAC
1 TATATATTATATGTTTTCAAAAACATGTTTTCAAAAC
**
3832779 TATATATTATACATTTTCAAAAACATGTTTTCAAAAC
1 TATATATTATATGTTTTCAAAAACATGTTTTCAAAAC
* * * *
3832816 CATAT-TATATATATTTTCAAAAACCAATTTTTTTAAAAAAC
1 TATATAT-TATATGTTTTCAAAAA-C-A-TGTTTT-CAAAAC
*
3832857 TATATATTATATGTTTTC-AAAACTAT-TTTCTAAAAAC
1 TATATATTATATGTTTTCAAAAAC-ATGTTT-TCAAAAC
* *
3832894 TATTTATTATATGTTTTC-AAAA-ATATTTTCAAAAAC
1 TATATATTATATGTTTTCAAAAACATGTTTTC-AAAAC
3832930 TATA
1 TATA
3832934 CTATATTATC
Statistics
Matches: 189, Mismatches: 23, Indels: 31
0.78 0.09 0.13
Matches are distributed among these distances:
34 1 0.01
35 12 0.06
36 59 0.31
37 80 0.42
38 5 0.03
39 3 0.02
40 9 0.05
41 19 0.10
42 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (37 bp):
TATATATTATATGTTTTCAAAAACATGTTTTCAAAAC
Found at i:3836356 original size:24 final size:24
Alignment explanation
Indices: 3836329--3836402 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
3836319 TCAAGGAGAC
*
3836329 TCATCTGCTATAAAAGCACAAGCT
1 TCATCTGCTACAAAAGCACAAGCT
3836353 TCATCTGCTACAAAAGCACAAGCT
1 TCATCTGCTACAAAAGCACAAGCT
*
3836377 TCAT-TGGCTGCAAAAGCACAAGCT
1 TCATCT-GCTACAAAAGCACAAGCT
3836401 TC
1 TC
3836403 TGTAACTAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (24 bp):
TCATCTGCTACAAAAGCACAAGCT
Found at i:3841626 original size:14 final size:13
Alignment explanation
Indices: 3841605--3841631 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3841595 ATAATATAAT
3841605 ATAGTTTTTGAAA
1 ATAGTTTTTGAAA
3841618 ATAGTTTTTGAAA
1 ATAGTTTTTGAAA
3841631 A
1 A
3841632 CAAATAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (13 bp):
ATAGTTTTTGAAA
Found at i:3841648 original size:37 final size:38
Alignment explanation
Indices: 3841603--3841699 Score: 110
Period size: 37 Copynumber: 2.6 Consensus size: 38
3841593 ATATAATATA
*
3841603 ATATAGTTTTTGAAAATAGTTTTTGAAAAC-AAATAAT
1 ATATAGTTTTTGAAAACAGTTTTTGAAAACGAAATAAT
** * *
3841640 ATATAGTTTTAAAAAACGGTTTTTGAAAACGTATATAAT
1 ATATAGTTTTTGAAAACAGTTTTTGAAAACG-AAATAAT
3841679 ATA-A-TTTTTGAAAACATGTTT
1 ATATAGTTTTTGAAAACA-GTTT
3841700 CAAATATATA
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
37 35 0.71
38 5 0.10
39 9 0.18
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.41
Consensus pattern (38 bp):
ATATAGTTTTTGAAAACAGTTTTTGAAAACGAAATAAT
Found at i:3841710 original size:2 final size:2
Alignment explanation
Indices: 3841703--3841746 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3841693 CATGTTTCAA
3841703 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3841745 AT
1 AT
3841747 TTTCTAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3841840 original size:9 final size:9
Alignment explanation
Indices: 3841822--3841881 Score: 70
Period size: 9 Copynumber: 6.7 Consensus size: 9
3841812 TTTATAGTTT
3841822 TTATTATATA
1 TTATT-TATA
3841832 TTATTTATA
1 TTATTTATA
3841841 TTA-TTAT-
1 TTATTTATA
3841848 TTATATTATA
1 TTAT-TTATA
*
3841858 TTATTTATT
1 TTATTTATA
*
3841867 TTATTTATT
1 TTATTTATA
3841876 TTATTT
1 TTATTT
3841882 TTTCAGGTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
7 3 0.07
8 4 0.09
9 30 0.65
10 9 0.20
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTATTTATA
Found at i:3841845 original size:12 final size:12
Alignment explanation
Indices: 3841801--3841880 Score: 69
Period size: 12 Copynumber: 6.8 Consensus size: 12
3841791 TAAAAACATA
* *
3841801 TTATATAATTTT
1 TTATATTATTAT
*
3841813 TTATAGTTTTTA-
1 TTATA-TTATTAT
3841825 TTATA-TATTAT
1 TTATATTATTAT
3841836 TTATATTATTAT
1 TTATATTATTAT
3841848 TTATATTA-TAT
1 TTATATTATTAT
*
3841859 TATTTATT-TTAT
1 T-TATATTATTAT
*
3841871 TTATTTTATT
1 TTATATTATT
3841881 TTTTCAGGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
10 4 0.07
11 13 0.24
12 35 0.64
13 3 0.05
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (12 bp):
TTATATTATTAT
Found at i:3841850 original size:26 final size:27
Alignment explanation
Indices: 3841828--3841880 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
3841818 GTTTTTATTA
3841828 TATATTATTTATATTA-TTATTTATAT
1 TATATTATTTATATTATTTATTTATAT
*
3841854 TATATTATTTATTTTATTTATTT-TAT
1 TATATTATTTATATTATTTATTTATAT
3841880 T
1 T
3841881 TTTTCAGGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (27 bp):
TATATTATTTATATTATTTATTTATAT
Found at i:3841870 original size:14 final size:14
Alignment explanation
Indices: 3841811--3841882 Score: 71
Period size: 14 Copynumber: 5.3 Consensus size: 14
3841801 TTATATAATT
3841811 TTTTATAGTT-TTTA
1 TTTTATA-TTATTTA
*
3841825 TTATATATTATTTA
1 TTTTATATTATTTA
*
3841839 -TAT-TATTATTTA
1 TTTTATATTATTTA
*
3841851 TATTATATTATTTA
1 TTTTATATTATTTA
3841865 TTTTAT-TTATTTTA
1 TTTTATATTA-TTTA
3841879 TTTT
1 TTTT
3841883 TTCAGGTCCA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
12 9 0.18
13 9 0.18
14 32 0.64
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (14 bp):
TTTTATATTATTTA
Found at i:3843001 original size:15 final size:15
Alignment explanation
Indices: 3842981--3843013 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3842971 TATTTTTTCT
3842981 TTTAATTTTTCTATA
1 TTTAATTTTTCTATA
3842996 TTTAATTTTTCTATA
1 TTTAATTTTTCTATA
3843011 TTT
1 TTT
3843014 TTTCTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTAATTTTTCTATA
Found at i:3843896 original size:24 final size:23
Alignment explanation
Indices: 3843858--3843946 Score: 65
Period size: 24 Copynumber: 3.7 Consensus size: 23
3843848 CATTTTCATT
3843858 TTATTTTTTAT-TTTTCCATTTTC
1 TTATTTTTT-TCTTTTCCATTTTC
* *
3843881 TTCATTTTTTTCTTTTTCTTTTTC
1 TT-ATTTTTTTCTTTTCCATTTTC
* * *
3843905 TTTTTCTTTTTCTTTTTCTTTTTC
1 TTATT-TTTTTCTTTTCCATTTTC
3843929 GTT-TTCTTTTTCGTTTTC
1 -TTATT-TTTTTC-TTTTC
3843947 GTTTTCGTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
23 5 0.09
24 46 0.81
25 6 0.11
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (23 bp):
TTATTTTTTTCTTTTCCATTTTC
Found at i:3843969 original size:18 final size:18
Alignment explanation
Indices: 3843850--3843988 Score: 117
Period size: 18 Copynumber: 7.8 Consensus size: 18
3843840 TTTTTCATCA
* *
3843850 TTTTCATTTTATTTTTTAT
1 TTTTCATTTT-CTTTTTCT
*
3843869 TTTTCCATTTTCTTCATT-T
1 TTTT-CATTTTCTT-TTTCT
*
3843888 TTTTCTTTTTCTTTTTCT
1 TTTTCATTTTCTTTTTCT
*
3843906 TTTTCTTTTTCTTTTTCT
1 TTTTCATTTTCTTTTTCT
* *
3843924 TTTTCGTTTTCTTTTTCG
1 TTTTCATTTTCTTTTTCT
* *
3843942 TTTTCGTTTTCGTTTTC-
1 TTTTCATTTTCTTTTTCT
* *
3843959 TTTTCA-TTT-TTTCTAT
1 TTTTCATTTTCTTTTTCT
3843975 TTTTCATTTT-TTTT
1 TTTTCATTTTCTTTT
3843989 CATTTCTTCT
Statistics
Matches: 103, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
15 3 0.03
16 9 0.09
17 13 0.13
18 59 0.57
19 11 0.11
20 8 0.08
ACGTcount: A:0.06, C:0.14, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTCATTTTCTTTTTCT
Found at i:3843984 original size:6 final size:6
Alignment explanation
Indices: 3843887--3843962 Score: 116
Period size: 6 Copynumber: 12.7 Consensus size: 6
3843877 TTTCTTCATT
*
3843887 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC GTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* * *
3843935 TTTTTC GTTTTC GTTTTC GTTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTT
3843963 CATTTTTTCT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:3843988 original size:26 final size:27
Alignment explanation
Indices: 3843833--3844003 Score: 85
Period size: 26 Copynumber: 6.4 Consensus size: 27
3843823 CCCCCTTTTA
*
3843833 TTCTTCTTTTTTCATCATTTTCATTTT-AT
1 TTCTTCTATTTT--TCATTTTC-TTTTCAT
3843862 TT-TT-TATTTTTCCATTTTC--TTCAT
1 TTCTTCTATTTTT-CATTTTCTTTTCAT
* * *
3843886 TT-TTTTCTTTTTCTTTTTCTTTTTC-T
1 TTCTTCTATTTTTCATTTTC-TTTTCAT
* *
3843912 TT-TTC--TTTTTCTTTTTCGTTTTCTTT
1 TTCTTCTATTTTTCATTTTC-TTTTC-AT
* ** *
3843938 TTCGTTTTCGTTTTCGTTTTCTTTTCAT
1 TTC-TTCTATTTTTCATTTTCTTTTCAT
*
3843966 TTTTTCTATTTTTCATTTT-TTTTCAT
1 TTCTTCTATTTTTCATTTTCTTTTCAT
*
3843992 TTCTTCTCTTTT
1 TTCTTCTATTTT
3844004 CTTCATGTGT
Statistics
Matches: 114, Mismatches: 16, Indels: 27
0.73 0.10 0.17
Matches are distributed among these distances:
23 2 0.02
24 29 0.25
25 7 0.06
26 32 0.28
27 20 0.18
28 7 0.06
29 7 0.06
30 10 0.09
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.75
Consensus pattern (27 bp):
TTCTTCTATTTTTCATTTTCTTTTCAT
Found at i:3844003 original size:18 final size:18
Alignment explanation
Indices: 3843955--3844009 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
3843945 TCGTTTTCGT
* *
3843955 TTTCTTTTCATTTTTTCTA
1 TTTCTTCTCTTTTTTTC-A
3843974 TTT-TTCAT-TTTTTTTCA
1 TTTCTTC-TCTTTTTTTCA
*
3843991 TTTCTTCTCTTTTCTTCA
1 TTTCTTCTCTTTTTTTCA
3844009 T
1 T
3844010 GTGTAATATC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
17 5 0.17
18 21 0.70
19 4 0.13
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTCTTCTCTTTTTTTCA
Found at i:3849180 original size:21 final size:20
Alignment explanation
Indices: 3849150--3849188 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3849140 ACAACAGAAC
3849150 TGGTCTATAG-AGGCGTTTTT
1 TGGTCTATAGCA-GCGTTTTT
3849170 TGGTCATATAGCAGCGTTT
1 TGGTC-TATAGCAGCGTTT
3849189 AAAAAGCACG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 11 0.65
22 1 0.06
ACGTcount: A:0.18, C:0.13, G:0.28, T:0.41
Consensus pattern (20 bp):
TGGTCTATAGCAGCGTTTTT
Found at i:3849976 original size:19 final size:19
Alignment explanation
Indices: 3849948--3850008 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
3849938 ATTGTTGCTT
*
3849948 TCTCTACTTCTATCGCTGC
1 TCTCTACTTCTCTCGCTGC
* *
3849967 TCTCTGCTTCTCTCCCTGC
1 TCTCTACTTCTCTCGCTGC
*
3849986 TCTCTACTTCTCTCGCTTC
1 TCTCTACTTCTCTCGCTGC
3850005 TCTC
1 TCTC
3850009 GCTTCAGCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.05, C:0.43, G:0.08, T:0.44
Consensus pattern (19 bp):
TCTCTACTTCTCTCGCTGC
Found at i:3850004 original size:9 final size:9
Alignment explanation
Indices: 3849954--3850013 Score: 57
Period size: 9 Copynumber: 6.4 Consensus size: 9
3849944 GCTTTCTCTA
*
3849954 CTTCTATCG
1 CTTCTCTCG
*
3849963 CTGCTCTCTG
1 CTTCTCTC-G
*
3849973 CTTCTCTCC
1 CTTCTCTCG
* *
3849982 CTGCTCTCTA
1 CTTCTCTC-G
3849992 CTTCTCTCG
1 CTTCTCTCG
3850001 CTTCTCTCG
1 CTTCTCTCG
3850010 CTTC
1 CTTC
3850014 AGCTTCGACT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
9 26 0.63
10 15 0.37
ACGTcount: A:0.03, C:0.43, G:0.10, T:0.43
Consensus pattern (9 bp):
CTTCTCTCG
Found at i:3851922 original size:2 final size:2
Alignment explanation
Indices: 3851915--3851939 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3851905 CAATCTAAGA
3851915 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3851940 ATAAAAAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3861837 original size:3 final size:3
Alignment explanation
Indices: 3861826--3861866 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
3861816 TTTTTTATCG
3861826 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
3861867 ATTACATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.11
3 28 0.80
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3861854 original size:19 final size:18
Alignment explanation
Indices: 3861830--3861866 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
3861820 TTATCGTTAT
3861830 TTTATTATTATTATTATTA
1 TTTATTATTATTA-TATTA
3861849 TTTATTATTATTATATTA
1 TTTATTATTATTATATTA
3861867 ATTACATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATTATTATTATATTA
Found at i:3861919 original size:10 final size:10
Alignment explanation
Indices: 3861904--3861963 Score: 75
Period size: 11 Copynumber: 5.6 Consensus size: 10
3861894 AAGCCCAATA
3861904 CAACAAGGCC
1 CAACAAGGCC
3861914 CAACAAGGCC
1 CAACAAGGCC
3861924 CAACCAAGGCC
1 CAA-CAAGGCC
3861935 CAACCAAGGCC
1 CAA-CAAGGCC
*
3861946 CAAACACGAGCC
1 C-AACAAG-GCC
3861958 CAACAA
1 CAACAA
3861964 AAATTAGGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
10 13 0.29
11 26 0.58
12 6 0.13
ACGTcount: A:0.42, C:0.42, G:0.17, T:0.00
Consensus pattern (10 bp):
CAACAAGGCC
Found at i:3861933 original size:11 final size:11
Alignment explanation
Indices: 3861907--3861948 Score: 77
Period size: 11 Copynumber: 3.9 Consensus size: 11
3861897 CCCAATACAA
3861907 CAAGGCCCAA-
1 CAAGGCCCAAC
3861917 CAAGGCCCAAC
1 CAAGGCCCAAC
3861928 CAAGGCCCAAC
1 CAAGGCCCAAC
3861939 CAAGGCCCAA
1 CAAGGCCCAA
3861949 ACACGAGCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 10 0.32
11 21 0.68
ACGTcount: A:0.38, C:0.43, G:0.19, T:0.00
Consensus pattern (11 bp):
CAAGGCCCAAC
Found at i:3866962 original size:26 final size:25
Alignment explanation
Indices: 3866931--3867010 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 25
3866921 CCAATTTTTG
3866931 ACATTCTATCTCTTTGAGACCTTG-A
1 ACATTCT-TCTCTTTGAGACCTTGAA
* *
3866956 A-A-TATTCT-TTTCA-ACCTTGAA
1 ACATTCTTCTCTTTGAGACCTTGAA
*
3866977 ACATTCCCTCTCTTTGAGACCTTGAA
1 ACATT-CTTCTCTTTGAGACCTTGAA
3867003 ACATTCTT
1 ACATTCTT
3867011 TCCACCTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
20 6 0.14
21 6 0.14
22 4 0.09
23 3 0.07
24 4 0.09
25 7 0.16
26 13 0.30
ACGTcount: A:0.26, C:0.25, G:0.09, T:0.40
Consensus pattern (25 bp):
ACATTCTTCTCTTTGAGACCTTGAA
Found at i:3868863 original size:4 final size:4
Alignment explanation
Indices: 3868854--3868934 Score: 94
Period size: 4 Copynumber: 20.8 Consensus size: 4
3868844 AAGAGTATAC
* * * *
3868854 ACAT ACAT ACAT ACGT ATAC ACAT ACAT ACAT ATAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
3868902 ACAT ACAT ATAT ACAT ACAC ACAT --AT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
3868935 CGATACATAA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.03
4 61 0.97
ACGTcount: A:0.49, C:0.23, G:0.01, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:3869632 original size:105 final size:102
Alignment explanation
Indices: 3869491--3869724 Score: 276
Period size: 105 Copynumber: 2.3 Consensus size: 102
3869481 TGAGAATTTT
* * * *
3869491 AAAACAAATTGTGTTTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
*
3869555 TAAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 T-AAAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCA
* * * *
3869596 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGGATTTGTTTCACA
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* * *
3869661 TTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
66 TAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
*
3869698 AAAACAAACTTTGTCTCGCTTGAGACA
1 AAAACAAATTTTGTCTCGCTTGAGACA
3869725 ACTTCTCTAA
Statistics
Matches: 112, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
101 2 0.02
102 25 0.22
103 4 0.04
104 4 0.04
105 76 0.68
106 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (102 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
TAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:3869720 original size:36 final size:36
Alignment explanation
Indices: 3869692--3869759 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
3869682 TGAGATCGTT
*
3869692 TTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAAC
1 TTCTCTAAAAACAAACTTTGTCTCACTTGAGACAAC
* *
3869727 TTCTCTAAAAACAAATTTTGTCTCATTTGAGAC
1 TTCTCTAAAAACAAACTTTGTCTCACTTGAGAC
3869760 TATATCTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 5 0.17
36 24 0.83
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (36 bp):
TTCTCTAAAAACAAACTTTGTCTCACTTGAGACAAC
Found at i:3870084 original size:29 final size:29
Alignment explanation
Indices: 3870042--3870138 Score: 121
Period size: 29 Copynumber: 3.5 Consensus size: 29
3870032 TTTCTCTTGA
*
3870042 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTCGTTCCTTTTGAAT
* *
3870071 AAAAATCTTGGAGTTGGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTCGTTCCTTTTGAAT
* *
3870100 AAATATCTTTGAG-TCGTTTCTTTTG-A-
1 AAAAATCTTTGAGTTCGTTCCTTTTGAAT
3870126 AAAAA-CTTTGAGT
1 AAAAATCTTTGAGT
3870139 CTATTTATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.12
26 4 0.07
27 1 0.02
28 10 0.17
29 38 0.63
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.44
Consensus pattern (29 bp):
AAAAATCTTTGAGTTCGTTCCTTTTGAAT
Found at i:3870227 original size:52 final size:54
Alignment explanation
Indices: 3870149--3870253 Score: 169
Period size: 52 Copynumber: 2.0 Consensus size: 54
3870139 CTATTTATTT
* **
3870149 TGAAACAAAGTTTTGTCTCTCTTGAGACAA-TTT-CGTGAAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTATCTCTTGAGACAATTTTGCGAAAAAAATCTTTGAGTC
3870201 TGAAACAAAGTTTTGTATCTCTTGAGACAATTTTGCGAAAAAAATCTTTGAGT
1 TGAAACAAAGTTTTGTATCTCTTGAGACAATTTTGCGAAAAAAATCTTTGAGT
3870254 TTGTTTCTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 29 0.60
53 3 0.06
54 16 0.33
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (54 bp):
TGAAACAAAGTTTTGTATCTCTTGAGACAATTTTGCGAAAAAAATCTTTGAGTC
Found at i:3870397 original size:75 final size:75
Alignment explanation
Indices: 3870238--3870378 Score: 248
Period size: 75 Copynumber: 1.9 Consensus size: 75
3870228 CAATTTTGCG
*
3870238 AAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTCTTTCTCTCTTAAGATAGTTTCTTTTG
1 AAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTCTTTCTCTCTTAAGATAATTTCTTTTG
3870303 AAAAAAAAAA
66 AAAAAAAAAA
*
3870313 AAAAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAATT-TTGTCTCTCTTAAGATAATTTCTTTT
1 AAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTCTT-TCTCTCTTAAGATAATTTCTTTT
3870377 GA
65 GA
3870379 GACAAAAATC
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
74 2 0.03
75 61 0.97
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (75 bp):
AAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTCTTTCTCTCTTAAGATAATTTCTTTTG
AAAAAAAAAA
Found at i:3870439 original size:66 final size:67
Alignment explanation
Indices: 3870315--3870444 Score: 145
Period size: 66 Copynumber: 2.0 Consensus size: 67
3870305 AAAAAAAAAA
* * * * * *
3870315 AAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAG
1 AAAAATCTTTGAATCTGTTTCTCTTGAAACAAAATTTTGTATCTCTTAAGACAATTTCTCTTGAG
3870380 AC
66 AC
*** * **
3870382 AAAAATCTTTGAATCTGTTTCTCTT-AAATTGAATTTTGTATCTCTTGAGACCGTTTCTCTTGA
1 AAAAATCTTTGAATCTGTTTCTCTTGAAACAAAATTTTGTATCTCTTAAGACAATTTCTCTTGA
3870445 AGTAAATCTT
Statistics
Matches: 51, Mismatches: 12, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
66 29 0.57
67 22 0.43
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (67 bp):
AAAAATCTTTGAATCTGTTTCTCTTGAAACAAAATTTTGTATCTCTTAAGACAATTTCTCTTGAG
AC
Found at i:3870705 original size:64 final size:62
Alignment explanation
Indices: 3870626--3870750 Score: 178
Period size: 64 Copynumber: 2.0 Consensus size: 62
3870616 GATGGGATCC
* *
3870626 ATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGGAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTT-GAAAAA
* * **
3870690 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
3870751 TACCCATATT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
62 5 0.09
63 14 0.25
64 36 0.65
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (62 bp):
ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAA
Found at i:3870795 original size:40 final size:40
Alignment explanation
Indices: 3870732--3870811 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
3870722 TTGTCTCTCG
*
3870732 AGACAACTTCTTTTGAAAATACCCATATTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
* * *
3870772 AGACAATTTCTTTT-AAAATTACCCACCTTTGAGATTGTTT
1 AGACAACTTCTTTTGAAAA-TACCCACATTTGAGATCGTTT
3870812 TTATTAAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.40
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
Found at i:3871286 original size:35 final size:36
Alignment explanation
Indices: 3871220--3871294 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
3871210 TATTTCTTTG
* *
3871220 GAAACAAAATTCACCATCTTTGAATCGGTTTCCCTT
1 GAAACAAAATTAAACATCTTTGAATCGGTTTCCCTT
*
3871256 GAAACAAAA-TAAACATCTTTGAGATC-GTTTCTCTT
1 GAAACAAAATTAAACATCTTTGA-ATCGGTTTCCCTT
3871291 GAAA
1 GAAA
3871295 TGAATTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (36 bp):
GAAACAAAATTAAACATCTTTGAATCGGTTTCCCTT
Found at i:3871632 original size:28 final size:28
Alignment explanation
Indices: 3871582--3871635 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
3871572 TCAAAATCCA
* *
3871582 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTTCCTATTGAAACAC
3871610 ATCTTTGAGTTGGTCTCCT-TTGAAAC
1 ATCTTTGAGTTGGT-TCCTATTGAAAC
3871636 CATTATCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (28 bp):
ATCTTTGAGTTGGTTCCTATTGAAACAC
Found at i:3871798 original size:43 final size:43
Alignment explanation
Indices: 3871647--3871989 Score: 209
Period size: 40 Copynumber: 7.9 Consensus size: 43
3871637 ATTATCCTAG
* * * *
3871647 AGATAACCAG-CCGTCCTCATCACGTAGGAACCATGTTATCACCTTT
1 AGATAACCAGACC-TCCTCATCACGTAGGAGCCGTGTCA--ACC-AT
** * * * * **
3871693 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCC
1 AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCAT
*
3871736 AG---ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
1 AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCAT
* * * *
3871776 AGATAACCAG-CCGTCCTCATCACGTAGGAACCATGTTATCACCTTT
1 AGATAACCAGACC-TCCTCATCACGTAGGAGCCGTGTCA--ACC-AT
** * * * * **
3871822 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCC
1 AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCAT
*
3871865 AG---ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
1 AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCAT
* * *
3871905 AGATAACCAG-CCATCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 AGATAACCAGACC-TCCTCATCACGTAGGAGCCGTGTCA--ACC-AT
* * * *
3871951 AGATAGCCAAGAACTCTTCATCAAGTAGGAGCCGTGTCA
1 AGATAACC-AGACCTCCTCATCACGTAGGAGCCGTGTCA
3871990 CCTTTAGACG
Statistics
Matches: 228, Mismatches: 51, Indels: 35
0.73 0.16 0.11
Matches are distributed among these distances:
40 66 0.29
42 2 0.01
43 59 0.26
44 4 0.02
45 6 0.03
46 65 0.29
47 25 0.11
48 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (43 bp):
AGATAACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCAT
Found at i:3871877 original size:129 final size:129
Alignment explanation
Indices: 3871647--3871989 Score: 632
Period size: 129 Copynumber: 2.7 Consensus size: 129
3871637 ATTATCCTAG
3871647 AGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
3871712 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
3871776 AGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
3871841 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
* * *
3871905 AGATAACCAGCCATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATAGCCAAGAACTCTTC
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCC-AGAACTCTTC
* *
3871970 ATCAAGTAGGAGCCGTGTCA
65 ATCACGTATGAGCCGTGTCA
3871990 CCTTTAGACG
Statistics
Matches: 208, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
129 180 0.87
130 28 0.13
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (129 bp):
AGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
Found at i:3872201 original size:3 final size:3
Alignment explanation
Indices: 3872190--3872230 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
3872180 TTTTTTATCG
3872190 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
3872231 ATTACATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.11
3 28 0.80
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3872218 original size:19 final size:18
Alignment explanation
Indices: 3872194--3872230 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
3872184 TTATCGTTAT
3872194 TTTATTATTATTATTATTA
1 TTTATTATTATTA-TATTA
3872213 TTTATTATTATTATATTA
1 TTTATTATTATTATATTA
3872231 ATTACATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATTATTATTATATTA
Found at i:3872283 original size:10 final size:10
Alignment explanation
Indices: 3872268--3872327 Score: 75
Period size: 11 Copynumber: 5.6 Consensus size: 10
3872258 AAGCCCAATA
3872268 CAACAAGGCC
1 CAACAAGGCC
3872278 CAACAAGGCC
1 CAACAAGGCC
3872288 CAACCAAGGCC
1 CAA-CAAGGCC
3872299 CAACCAAGGCC
1 CAA-CAAGGCC
*
3872310 CAAACACGAGCC
1 C-AACAAG-GCC
3872322 CAACAA
1 CAACAA
3872328 AAATTAGGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
10 13 0.29
11 26 0.58
12 6 0.13
ACGTcount: A:0.42, C:0.42, G:0.17, T:0.00
Consensus pattern (10 bp):
CAACAAGGCC
Found at i:3872297 original size:11 final size:11
Alignment explanation
Indices: 3872271--3872312 Score: 77
Period size: 11 Copynumber: 3.9 Consensus size: 11
3872261 CCCAATACAA
3872271 CAAGGCCCAA-
1 CAAGGCCCAAC
3872281 CAAGGCCCAAC
1 CAAGGCCCAAC
3872292 CAAGGCCCAAC
1 CAAGGCCCAAC
3872303 CAAGGCCCAA
1 CAAGGCCCAA
3872313 ACACGAGCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 10 0.32
11 21 0.68
ACGTcount: A:0.38, C:0.43, G:0.19, T:0.00
Consensus pattern (11 bp):
CAAGGCCCAAC
Found at i:3876371 original size:14 final size:15
Alignment explanation
Indices: 3876341--3876374 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3876331 AACATTTTAT
*
3876341 TTATATCTATATAAA
1 TTATATATATATAAA
3876356 TTATATATAT-TAAA
1 TTATATATATATAAA
3876370 TTATA
1 TTATA
3876375 ATTGAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATATATATATAAA
Found at i:3876424 original size:29 final size:30
Alignment explanation
Indices: 3876387--3876470 Score: 104
Period size: 29 Copynumber: 2.9 Consensus size: 30
3876377 TGAAGGAAGA
*
3876387 TTTACAATA-AAAATAATTTAAATTTAAAT
1 TTTAAAATATAAAATAATTTAAATTTAAAT
* *
3876416 TTTAAAATATAAAATTA-TTAAATTT-AGT
1 TTTAAAATATAAAATAATTTAAATTTAAAT
3876444 TTTAAAATATAAAA-AATCTTAAATTTA
1 TTTAAAATATAAAATAAT-TTAAATTTA
3876471 TTTTATTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
27 1 0.02
28 16 0.34
29 24 0.51
30 6 0.13
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (30 bp):
TTTAAAATATAAAATAATTTAAATTTAAAT
Found at i:3882044 original size:18 final size:19
Alignment explanation
Indices: 3882021--3882061 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3882011 CAGACGTGTA
3882021 ATTTTCAC-TTTCAAGGAT
1 ATTTTCACATTTCAAGGAT
*
3882039 ATTTTCCCATTTCAAGGAT
1 ATTTTCACATTTCAAGGAT
3882058 ATTT
1 ATTT
3882062 CAGTCATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (19 bp):
ATTTTCACATTTCAAGGAT
Found at i:3882954 original size:20 final size:20
Alignment explanation
Indices: 3882907--3882954 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
3882897 ACTAATGCCG
* * * *
3882907 GTTCAAGTTGACTCGGTCCG
1 GTTCGAGTTGACTCAGACCA
*
3882927 GTTTGAGTTGACTCAGACCA
1 GTTCGAGTTGACTCAGACCA
3882947 GTTCGAGT
1 GTTCGAGT
3882955 CGGTTCAGTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (20 bp):
GTTCGAGTTGACTCAGACCA
Found at i:3883946 original size:11 final size:11
Alignment explanation
Indices: 3883932--3883958 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3883922 CAATAAAAAT
3883932 AATTTAAATTA
1 AATTTAAATTA
3883943 AATTTAAATTA
1 AATTTAAATTA
3883954 AATTT
1 AATTT
3883959 GGGGTTTGAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:3886872 original size:6 final size:6
Alignment explanation
Indices: 3886855--3886884 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
3886845 AAAGTTAATG
3886855 GTCAACA GTCAAA GTCAAA GTCAAA GTCAA
1 GTCAA-A GTCAAA GTCAAA GTCAAA GTCAA
3886885 CGAATAGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.47, C:0.20, G:0.17, T:0.17
Consensus pattern (6 bp):
GTCAAA
Found at i:3889223 original size:13 final size:13
Alignment explanation
Indices: 3889205--3889240 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3889195 TTAGCATTGT
3889205 TAAAAGAAAATAA
1 TAAAAGAAAATAA
3889218 TAAAAGAAAATAA
1 TAAAAGAAAATAA
3889231 -AGAAAGAAAA
1 TA-AAAGAAAA
3889241 GTGAAGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 1 0.05
13 21 0.95
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (13 bp):
TAAAAGAAAATAA
Found at i:3889448 original size:3 final size:3
Alignment explanation
Indices: 3889440--3889466 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3889430 CTAATTCCTA
3889440 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
3889467 CAAACTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3890357 original size:33 final size:33
Alignment explanation
Indices: 3890310--3890380 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
3890300 TTTAATCTCT
3890310 TTTTTATTTA-TTTTTCTTCACATTTTTTGAACA
1 TTTTTATTTATTTTTTC-TCACATTTTTTGAACA
* * * *
3890343 TTTTTCTTTTTTTTTTCTCTCTTTTTTTGAACA
1 TTTTTATTTATTTTTTCTCACATTTTTTGAACA
3890376 TTTTT
1 TTTTT
3890381 TTCCCGAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 27 0.82
34 6 0.18
ACGTcount: A:0.14, C:0.13, G:0.03, T:0.70
Consensus pattern (33 bp):
TTTTTATTTATTTTTTCTCACATTTTTTGAACA
Found at i:3891191 original size:15 final size:14
Alignment explanation
Indices: 3891166--3891226 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 14
3891156 TAGTGTATCT
*
3891166 AAAAAATATAAATA
1 AAAAAAAATAAATA
3891180 ACAAAAAAATAACA-A
1 A-AAAAAAATAA-ATA
3891195 AAAAATAAATAAATA
1 AAAAA-AAATAAATA
*
3891210 AAAAGTAAATAAATA
1 AAAA-AAAATAAATA
3891225 AA
1 AA
3891227 TAAATAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 6 0.15
15 33 0.82
16 1 0.03
ACGTcount: A:0.79, C:0.03, G:0.02, T:0.16
Consensus pattern (14 bp):
AAAAAAAATAAATA
Found at i:3891198 original size:10 final size:11
Alignment explanation
Indices: 3891175--3891202 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3891165 TAAAAAATAT
3891175 AAATAACAAAA
1 AAATAACAAAA
3891186 AAATAACAAAA
1 AAATAACAAAA
3891197 AAATAA
1 AAATAA
3891203 ATAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (11 bp):
AAATAACAAAA
Found at i:3891206 original size:4 final size:4
Alignment explanation
Indices: 3891173--3891234 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
3891163 TCTAAAAAAT
*
3891173 ATAA ATAA CA-AA A-AA ATAA CA-AA A-AA ATAA ATAA ATAA A-AA GTAA
1 ATAA ATAA -ATAA ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA
3891218 ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA A
3891235 ATAATAAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
3 10 0.20
4 39 0.76
5 2 0.04
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.18
Consensus pattern (4 bp):
ATAA
Found at i:3895623 original size:36 final size:37
Alignment explanation
Indices: 3895583--3895656 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
3895573 ACGAAAAGGT
3895583 GGAACC-AAAAAAAAATCATCGACAACCAGAATCGAG
1 GGAACCAAAAAAAAAATCATCGACAACCAGAATCGAG
3895619 GGAACCAAAAAAAAAATCATCGACAACCAGAATCGAG
1 GGAACCAAAAAAAAAATCATCGACAACCAGAATCGAG
3895656 G
1 G
3895657 ATCAATAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 6 0.16
37 31 0.84
ACGTcount: A:0.53, C:0.22, G:0.18, T:0.08
Consensus pattern (37 bp):
GGAACCAAAAAAAAAATCATCGACAACCAGAATCGAG
Found at i:3896964 original size:2 final size:2
Alignment explanation
Indices: 3896957--3896994 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
3896947 TTTCATATTA
3896957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
3896995 GTGGTAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3903009 original size:32 final size:32
Alignment explanation
Indices: 3902973--3903034 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
3902963 GATTCAGACA
3902973 AAGAAGGCATCAAGAATGAGCCTTACAATTCC
1 AAGAAGGCATCAAGAATGAGCCTTACAATTCC
** *
3903005 AAGAAGGCATTGAGAATGAGCCTTAGAATT
1 AAGAAGGCATCAAGAATGAGCCTTACAATT
3903035 TGAGATATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (32 bp):
AAGAAGGCATCAAGAATGAGCCTTACAATTCC
Found at i:3904244 original size:30 final size:30
Alignment explanation
Indices: 3904208--3904300 Score: 98
Period size: 36 Copynumber: 2.9 Consensus size: 30
3904198 GATTGGAGAA
3904208 AAACCATCCT-AAGCCTTCACCGGAGAAAGC
1 AAACCAT-CTGAAGCCTTCACCGGAGAAAGC
3904238 AAACCATCTGAAGCCTTCACCGGAGAATAGTGAAGC
1 AAACCATCTGAAGCCTTCACCGGAG---A---AAGC
* *
3904274 AATCAATCTGAAGCCTTCACCGGAGAA
1 AAACCATCTGAAGCCTTCACCGGAGAA
3904301 TAGTGAAGCA
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
29 2 0.04
30 23 0.43
33 2 0.04
36 27 0.50
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.16
Consensus pattern (30 bp):
AAACCATCTGAAGCCTTCACCGGAGAAAGC
Found at i:3904283 original size:36 final size:36
Alignment explanation
Indices: 3904234--3904365 Score: 169
Period size: 36 Copynumber: 3.7 Consensus size: 36
3904224 TCACCGGAGA
3904234 AAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTG
1 AAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTG
* *
3904270 AAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTG
1 AAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTG
* * *
3904306 AAGCAAACCATCAT-AAGTC-TCACCAGAGAGTAGTG
1 AAGCAAACCATC-TGAAGCCTTCACCGGAGAATAGTG
* * *
3904341 AAGCAAAGCATCTTAAGTCTTCACC
1 AAGCAAACCATCTGAAGCCTTCACC
3904366 AAAAGTAGTG
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
34 1 0.01
35 30 0.35
36 53 0.62
37 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (36 bp):
AAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTG
Found at i:3904340 original size:35 final size:36
Alignment explanation
Indices: 3904234--3904397 Score: 167
Period size: 36 Copynumber: 4.6 Consensus size: 36
3904224 TCACCGGAGA
*
3904234 AAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTG
1 AAGCAAACCATCTGAAGCCTTCACCAGAGAATAGTG
* * *
3904270 AAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTG
1 AAGCAAACCATCTGAAGCCTTCACCAGAGAATAGTG
* *
3904306 AAGCAAACCATCAT-AAGTC-TCACCAGAGAGTAGTG
1 AAGCAAACCATC-TGAAGCCTTCACCAGAGAATAGTG
* * *
3904341 AAGCAAAGCATCTTAAGTCTTCACCA-A-AAGTAGTG
1 AAGCAAACCATCTGAAGCCTTCACCAGAGAA-TAGTG
* *
3904376 AAGCAGATCCAT-TTAAGCCTTC
1 AAGCA-AACCATCTGAAGCCTTC
3904398 TCAGAAGAGT
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
34 2 0.02
35 50 0.45
36 58 0.52
37 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (36 bp):
AAGCAAACCATCTGAAGCCTTCACCAGAGAATAGTG
Found at i:3904841 original size:51 final size:51
Alignment explanation
Indices: 3904776--3905571 Score: 921
Period size: 51 Copynumber: 15.5 Consensus size: 51
3904766 AAGATTATTT
* * * * *
3904776 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTTGAAGATGTCC
1 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * * * *
3904827 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATGC
1 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
*
3904878 GAGTTCTATACTCCTTAAAG--A-AAGGAGCGAACCCGTTTGAAGA-GATGTC
1 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATG-T-TC
* *
3904927 TGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCAG-TTGAAGATGTTC
1 -GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCC-GTTTGAAGATGTTC
* * * *
3904979 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TTAAGAGATGTTC
1 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGA-AGATGTTC
* * *
3905030 GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAATATGTTC
1 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* *
3905081 GAGTTCTATACTCCTTAAAGGAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
** *
3905132 GAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
** * ** * *
3905183 GAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCGTAAGAAGAAGATTTTT
1 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGT---TTGAAGATGTTC
*
3905237 GAGTTCTATACTCCCTGAAGAAA-AAGGGAGCGAACCCAG-TTGAAGATGTTC
1 GAGTTCTATACTCCCTAAAGAAAGAA-GGAGCGAACCC-GTTTGAAGATGTTC
* * *
3905288 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TGAAGAGATGTTC
1 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTTC
*
3905339 GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * *
3905390 GAGTTCTATTCTCCTTAAAGAAAGAAGGAACGAACCCGTTTGAAGATGTTC
1 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
*
3905441 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTTC
1 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTTC
* * * *
3905494 GAGTTCTATACTCCCTAGAGAAATAGGGAGCGAACCCATTTGTTAAAGATTGTTC
1 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG---AAGA-TGTTC
* *
3905549 GAG-TCTTATACTCTCTGAAGAAA
1 GAGTTC-TATACTCCCTAAAGAAA
3905572 TAGGGGGCAG
Statistics
Matches: 658, Mismatches: 61, Indels: 48
0.86 0.08 0.06
Matches are distributed among these distances:
48 22 0.03
49 4 0.01
50 25 0.04
51 458 0.70
52 9 0.01
53 70 0.11
54 45 0.07
55 25 0.04
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.24
Consensus pattern (51 bp):
GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
Found at i:3905338 original size:309 final size:305
Alignment explanation
Indices: 3904776--3905530 Score: 1143
Period size: 309 Copynumber: 2.4 Consensus size: 305
3904766 AAGATTATTT
* * * * * * *
3904776 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTTGAAGATGTCCGAGTTCCATACTCC
1 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCC
* * * * *
3904841 CTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGGAGC
66 TTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGGAGC
** *
3904906 GAACCCGTTTGAAGAGATGTCTGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCAGTTGA
131 GAACCCGTAAGAAGAGATGTCTGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCAGTTGA
*
3904971 AGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTAAGAGATGTTCGAGTTC
196 AGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAGATGTTCGAGTTC
*
3905036 TATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAATATGTTC
261 TATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAAGATGTTC
* *
3905081 GAGTTCTATACTCCTTAAAGGAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCT
1 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCC
* *
3905146 TTAAAGAGAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCTTTAAAGAGAGAAGG
66 TTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCTT-AA-AGA-AAGG
* * * *
3905211 AGCGAACCCGTAAGAAGAAGATTTTTGAGTTCTATACTCCCTGAAGAAA-AAGGGAGCGAACCCA
128 AGCGAACCCGTAAGAAG-AGATGTCTGAGTTCCATACTCCCTAAAGAAAGAA-GGAGCGAACCCA
3905275 GTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAGATGTTCG
191 GTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAGATGTTCG
*
3905340 AGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
256 AGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAAGATGTTC
* *
3905390 GAGTTCTATTCTCCTTAAAGAAAGAAGGAACGAACCCGTTTGAAGATGTTCGAGTTCTATACTCC
1 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCC
* *
3905455 TTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTTCGAGTTCTATACTCCCTAGAGAAATAG
66 TTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTTCGAGTTCTATACTCCTTAAAG-AA-A-
3905520 GGAGCGAACCC
126 GGAGCGAACCC
3905531 ATTTGTTAAA
Statistics
Matches: 406, Mismatches: 34, Indels: 14
0.89 0.07 0.03
Matches are distributed among these distances:
305 102 0.25
306 2 0.00
307 3 0.01
308 21 0.05
309 241 0.59
310 4 0.01
311 33 0.08
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (305 bp):
GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCC
TTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGGAGC
GAACCCGTAAGAAGAGATGTCTGAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCAGTTGA
AGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGAAGAGATGTTCGAGTTC
TATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAAGATGTTC
Found at i:3905612 original size:108 final size:108
Alignment explanation
Indices: 3905533--3905981 Score: 701
Period size: 108 Copynumber: 4.2 Consensus size: 108
3905523 GCGAACCCAT
* *
3905533 TTGTTAAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGA
*
3905598 TTGTGGGTCTTATACTCTCTGAAAAAATAGGGGGCAGACACGA
66 TTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGA
* * * *
3905641 TTGATGAAGATTG-T-GGGTCTTATACTCTCTGAAGATATAGGGGGCAGACACGATTGTTGAAGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGA
* *
3905704 TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
66 TTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGA
* * *
3905749 TTGATGAAGATTG-T-GGGTCTTATACTCTCTGAAAAAATAGGGGGCAGACACGATTGATGAAGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGA
*
3905812 TTGTGGGTCTTATACTCTCTGAAGATATA-GGGGCAGACACGA
66 TTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGA
*
3905854 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGA
3905919 TTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGA
66 TTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGA
* *
3905962 TTGTTAAAGATTATTCGAGT
1 TTGTTGAAGATTGTTCGAGT
3905982 TCCATACTCC
Statistics
Matches: 314, Mismatches: 22, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
105 24 0.08
106 72 0.23
107 77 0.25
108 141 0.45
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (108 bp):
TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGA
TTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGA
Found at i:3905626 original size:53 final size:53
Alignment explanation
Indices: 3905551--3905973 Score: 686
Period size: 53 Copynumber: 7.9 Consensus size: 53
3905541 GATTGTTCGA
*
3905551 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGG
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATTGTGG
*
3905604 GTCTTATACTCTCTGAAAAAATAGGGGGCAGACACGATTGATGAAGATTGTGG
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATTGTGG
* * *
3905657 GTCTTATACTCTCTGAAGATATAGGGGGCAGACACGATTGTTGAAGATTGTTCGA
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATTG-T-GG
*
3905712 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGG
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATTGTGG
*
3905765 GTCTTATACTCTCTGAAAAAATAGGGGGCAGACACGATTGATGAAGATTGTGG
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATTGTGG
* * *
3905818 GTCTTATACTCTCTGAAGATATA-GGGGCAGACACGATTGTTGAAGATTGTTCGA
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATTG-T-GG
*
3905872 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGG
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATTGTGG
* *
3905925 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTAAAGATT
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATT
3905974 ATTCGAGTTC
Statistics
Matches: 342, Mismatches: 23, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
52 25 0.07
53 219 0.64
54 26 0.08
55 72 0.21
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.28
Consensus pattern (53 bp):
GTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATTGTGG
Found at i:3905706 original size:161 final size:160
Alignment explanation
Indices: 3905533--3905973 Score: 837
Period size: 161 Copynumber: 2.8 Consensus size: 160
3905523 GCGAACCCAT
*
3905533 TTGTTAAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGA
3905598 TTGTGGGTCTTATACTCTCTGAAAAAATAGGGGGCAGACACGATTGATGAAGATTGTGGGTCTTA
66 TTGTGGGTCTTATACTCTCTGAAAAAATAGGGGGCAGACACGATTGATGAAGATTGTGGGTCTTA
3905663 TACTCTCTGAAGATATAGGGGGCAGACACGA
131 TACTCTCTGAAGATATA-GGGGCAGACACGA
3905694 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGA
3905759 TTGTGGGTCTTATACTCTCTGAAAAAATAGGGGGCAGACACGATTGATGAAGATTGTGGGTCTTA
66 TTGTGGGTCTTATACTCTCTGAAAAAATAGGGGGCAGACACGATTGATGAAGATTGTGGGTCTTA
3905824 TACTCTCTGAAGATATAGGGGCAGACACGA
131 TACTCTCTGAAGATATAGGGGCAGACACGA
3905854 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGA
* * *
3905919 TTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTAAAGATT
66 TTGTGGGTCTTATACTCTCTGAAAAAATAGGGGGCAGACACGATTGATGAAGATT
3905974 ATTCGAGTTC
Statistics
Matches: 276, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
160 130 0.47
161 146 0.53
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (160 bp):
TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGA
TTGTGGGTCTTATACTCTCTGAAAAAATAGGGGGCAGACACGATTGATGAAGATTGTGGGTCTTA
TACTCTCTGAAGATATAGGGGCAGACACGA
Found at i:3907167 original size:36 final size:36
Alignment explanation
Indices: 3907127--3907199 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
3907117 ACGAAAAGGT
3907127 GGAACCAAAAAAAAATCATCGACAACCAGAATCGAG
1 GGAACCAAAAAAAAATCATCGACAACCAGAATCGAG
3907163 GGAACCAAAAAAAAATCATCGACAACCAGAATCGAG
1 GGAACCAAAAAAAAATCATCGACAACCAGAATCGAG
3907199 G
1 G
3907200 ATCAATAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.52, C:0.22, G:0.18, T:0.08
Consensus pattern (36 bp):
GGAACCAAAAAAAAATCATCGACAACCAGAATCGAG
Found at i:3908493 original size:2 final size:2
Alignment explanation
Indices: 3908482--3908540 Score: 81
Period size: 2 Copynumber: 31.0 Consensus size: 2
3908472 TATGCATTTC
3908482 AT AT -T AT AT AT AT -T 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 AT AT AT AT
3908521 AT AT AT AT AT GAT AT A- AT AT
1 AT AT AT AT AT -AT AT AT AT AT
3908541 GTGGTAATAA
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
1 4 0.08
2 46 0.88
3 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3908506 original size:15 final size:15
Alignment explanation
Indices: 3908482--3908540 Score: 86
Period size: 15 Copynumber: 4.0 Consensus size: 15
3908472 TATGCATTTC
3908482 ATATTATATATAT-T
1 ATATTATATATATAT
3908496 ATATATATATATATAT
1 ATAT-TATATATATAT
3908512 ATATTATATATATAT
1 ATATTATATATATAT
*
3908527 ATATGATATA-ATAT
1 ATATTATATATATAT
3908541 GTGGTAATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
14 8 0.19
15 29 0.69
16 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
ATATTATATATATAT
Found at i:3908508 original size:17 final size:17
Alignment explanation
Indices: 3908482--3908540 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 17
3908472 TATGCATTTC
3908482 ATAT-TATATATATTAT
1 ATATATATATATATTAT
3908498 ATATATATATATATATATT
1 ATATATATATATAT-TA-T
*
3908517 ATATATATATATATGAT
1 ATATATATATATATTAT
3908534 ATA-ATAT
1 ATATATAT
3908541 GTGGTAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
16 8 0.21
17 13 0.33
18 3 0.08
19 15 0.38
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
ATATATATATATATTAT
Found at i:3912153 original size:14 final size:14
Alignment explanation
Indices: 3912134--3912186 Score: 106
Period size: 14 Copynumber: 3.8 Consensus size: 14
3912124 AAGAATACTT
3912134 AATGAATGAGTGAA
1 AATGAATGAGTGAA
3912148 AATGAATGAGTGAA
1 AATGAATGAGTGAA
3912162 AATGAATGAGTGAA
1 AATGAATGAGTGAA
3912176 AATGAATGAGT
1 AATGAATGAGT
3912187 AGTAGCCTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.28, T:0.23
Consensus pattern (14 bp):
AATGAATGAGTGAA
Found at i:3912337 original size:59 final size:56
Alignment explanation
Indices: 3912267--3912384 Score: 150
Period size: 59 Copynumber: 2.1 Consensus size: 56
3912257 AATTTCTTTG
3912267 ATTTAACCATAACCACTCATTTAAAAATTCAAAATTAAAATAATATTTTAAATAT-T-TTT
1 ATTTAACCATAACCA-TCATTT-AAAATTCAAAA-TAAAAT-A-ATTTTAAATATATATTT
* * *
3912326 ATTTAAGCATAACCATCATTTTAAATTTAAAATAAAATAATTTTAAATATATATTT
1 ATTTAACCATAACCATCATTTAAAATTCAAAATAAAATAATTTTAAATATATATTT
3912382 ATT
1 ATT
3912385 CTTTTAACCA
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
54 11 0.20
55 2 0.04
56 12 0.22
57 9 0.17
58 6 0.11
59 14 0.26
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.42
Consensus pattern (56 bp):
ATTTAACCATAACCATCATTTAAAATTCAAAATAAAATAATTTTAAATATATATTT
Found at i:3918138 original size:26 final size:26
Alignment explanation
Indices: 3918109--3918161 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
3918099 TACAAAAGTG
* *
3918109 ACCAACATTATCTTATTCATGTATTT
1 ACCAACATTATATTATTCATGCATTT
3918135 ACCAACATTATATTATTCATGCATTT
1 ACCAACATTATATTATTCATGCATTT
3918161 A
1 A
3918162 TCAATATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (26 bp):
ACCAACATTATATTATTCATGCATTT
Found at i:3920430 original size:6 final size:6
Alignment explanation
Indices: 3920419--3920479 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
3920409 GACACGTATT
* * *
3920419 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3920467 ACCACG ACCACG A
1 ACCACG ACCACG A
3920480 GCCGAGCCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.30, C:0.49, G:0.16, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:3920487 original size:5 final size:5
Alignment explanation
Indices: 3920477--3920525 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
3920467 ACCACGACCA
* * * *
3920477 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
3920526 ACGCGGACGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.16, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:3925800 original size:98 final size:96
Alignment explanation
Indices: 3925629--3925822 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 96
3925619 ATGTTTTGGA
3925629 GTGAGTTGAGAAGCTGAATATAGCTCTCTATTTAGGCTAGAATAGGGTTAAAGTCGTCCATAAAA
1 GTGAGTTGAGAAGCTGAATATAGCTCTCTATTTAGGCTAGAATAGGGTTAAAGTCGTCCATAAAA
3925694 TTTCAGGATTAAACCTC-TATTTGTAACAGC
66 TTTCAGGATTAAACCTCTTATTTGTAACAGC
3925724 GTGAGTTGAGAAGCTGAATATAGCTCTCTATTTATAGGCTAGAAATAGGGTTAAAGTCGTCCATA
1 GTGAGTTGAGAAGCTGAATATAGCTCTCTA-TT-TAGGCTAG-AATAGGGTTAAAGTCGTCCATA
3925789 AAATTTCAGGATTAAACCTCTTATTTGTAACAGC
63 AAATTTCAGGATTAAACCTCTTATTTGTAACAGC
3925823 TGAAACGACT
Statistics
Matches: 95, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
95 30 0.32
96 2 0.02
97 8 0.08
98 42 0.44
99 13 0.14
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (96 bp):
GTGAGTTGAGAAGCTGAATATAGCTCTCTATTTAGGCTAGAATAGGGTTAAAGTCGTCCATAAAA
TTTCAGGATTAAACCTCTTATTTGTAACAGC
Found at i:3926224 original size:6 final size:6
Alignment explanation
Indices: 3926213--3926279 Score: 107
Period size: 6 Copynumber: 11.2 Consensus size: 6
3926203 GACACGTATT
* * *
3926213 ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCCCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3926261 ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG A
3926280 GCCGAGCCGA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.30, C:0.51, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:3926287 original size:5 final size:5
Alignment explanation
Indices: 3926277--3926325 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
3926267 ACCACGACCA
* * * *
3926277 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
3926326 ACGGACGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.16, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:3928024 original size:51 final size:51
Alignment explanation
Indices: 3927964--3928065 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
3927954 GATAAATAGG
3927964 TATTTCTTAAATTATCACCTTGAAAAAAAAGAGTATTGCAATTCAAATGCT
1 TATTTCTTAAATTATCACCTTGAAAAAAAAGAGTATTGCAATTCAAATGCT
3928015 TATTTCTTAAATTATCACCTTGAAAAAAAAGAGTATTGCAATTCAAATGCT
1 TATTTCTTAAATTATCACCTTGAAAAAAAAGAGTATTGCAATTCAAATGCT
3928066 AAGGAAAGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (51 bp):
TATTTCTTAAATTATCACCTTGAAAAAAAAGAGTATTGCAATTCAAATGCT
Found at i:3928578 original size:21 final size:21
Alignment explanation
Indices: 3928553--3928595 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3928543 AAGTTTGTTT
3928553 TGATGATTAAAACATGTTCAA
1 TGATGATTAAAACATGTTCAA
3928574 TGATGATTAAAACATGTTCAA
1 TGATGATTAAAACATGTTCAA
3928595 T
1 T
3928596 CTTCCTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (21 bp):
TGATGATTAAAACATGTTCAA
Found at i:3930244 original size:99 final size:99
Alignment explanation
Indices: 3930127--3930324 Score: 396
Period size: 99 Copynumber: 2.0 Consensus size: 99
3930117 TGACATATTC
3930127 TAAATATGTCAAAAGTTGAATATAAAATTCATTGATCATTTTTTATTATATATGATGTTTATCAT
1 TAAATATGTCAAAAGTTGAATATAAAATTCATTGATCATTTTTTATTATATATGATGTTTATCAT
3930192 GAATTTATATGATGTTATTGCAAATGTTATTTCG
66 GAATTTATATGATGTTATTGCAAATGTTATTTCG
3930226 TAAATATGTCAAAAGTTGAATATAAAATTCATTGATCATTTTTTATTATATATGATGTTTATCAT
1 TAAATATGTCAAAAGTTGAATATAAAATTCATTGATCATTTTTTATTATATATGATGTTTATCAT
3930291 GAATTTATATGATGTTATTGCAAATGTTATTTCG
66 GAATTTATATGATGTTATTGCAAATGTTATTTCG
3930325 GGTATGAACT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.46
Consensus pattern (99 bp):
TAAATATGTCAAAAGTTGAATATAAAATTCATTGATCATTTTTTATTATATATGATGTTTATCAT
GAATTTATATGATGTTATTGCAAATGTTATTTCG
Found at i:3931813 original size:11 final size:11
Alignment explanation
Indices: 3931773--3931832 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
3931763 TTATATTTCG
3931773 TTATATTATTA
1 TTATATTATTA
3931784 TTAATATT-TT-
1 TT-ATATTATTA
*
3931794 TTTTATTATTA
1 TTATATTATTA
3931805 TTATATTA-TA
1 TTATATTATTA
3931815 TT-TATTATATA
1 TTATATTAT-TA
3931826 TATATAT
1 T-TATAT
3931833 ATTTTTGATG
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
9 9 0.22
10 8 0.20
11 14 0.35
12 6 0.15
13 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATATTATTA
Found at i:3931886 original size:23 final size:23
Alignment explanation
Indices: 3931860--3931979 Score: 120
Period size: 23 Copynumber: 5.3 Consensus size: 23
3931850 GATTTGATAA
*
3931860 GTAGTGGTTGATTATTTTAATAT
1 GTAGTGGTTGATTATTTTAATAG
* * *
3931883 GTAG-GGTT-TTTATTTTAACAT
1 GTAGTGGTTGATTATTTTAATAG
3931904 GTAGT-GTTGATTATTTTTAATAG
1 GTAGTGGTTGATTA-TTTTAATAG
* * *
3931927 ATAGTGGTTTGATTATTTTTACAG
1 GTAGTGG-TTGATTATTTTAATAG
* *
3931951 GTAGTAGTTTATTATTTTAATAG
1 GTAGTGGTTGATTATTTTAATAG
3931974 GTAGTG
1 GTAGTG
3931980 ATCTTAATAT
Statistics
Matches: 78, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
21 18 0.23
22 7 0.09
23 33 0.42
24 13 0.17
25 7 0.09
ACGTcount: A:0.26, C:0.02, G:0.22, T:0.51
Consensus pattern (23 bp):
GTAGTGGTTGATTATTTTAATAG
Found at i:3931897 original size:21 final size:22
Alignment explanation
Indices: 3931860--3932007 Score: 87
Period size: 23 Copynumber: 6.8 Consensus size: 22
3931850 GATTTGATAA
3931860 GTAGTGGTTGATTATTTTAATAT
1 GTAG-GGTTGATTATTTTAATAT
* *
3931883 GTAGGGTT-TTTATTTTAACAT
1 GTAGGGTTGATTATTTTAATAT
*
3931904 GTAGTGTTGATTATTTTTAATA-
1 GTAGGGTTGATTA-TTTTAATAT
* * *
3931926 GATAGTGGTTTGATTATTTTTACAG
1 G-TAG-GG-TTGATTATTTTAATAT
* * *
3931951 GTAGTAGTTTATTATTTTAATAG
1 GTAG-GGTTGATTATTTTAATAT
*
3931974 GTA--G-TG---ATCTTAATAT
1 GTAGGGTTGATTATTTTAATAT
*
3931990 GTAGTGTTGATTATTTTA
1 GTAGGGTTGATTATTTTA
3932008 TTAGGTAGTG
Statistics
Matches: 97, Mismatches: 16, Indels: 25
0.70 0.12 0.18
Matches are distributed among these distances:
16 11 0.11
18 1 0.01
19 3 0.03
20 1 0.01
21 18 0.19
22 13 0.13
23 30 0.31
24 12 0.12
25 8 0.08
ACGTcount: A:0.26, C:0.02, G:0.20, T:0.51
Consensus pattern (22 bp):
GTAGGGTTGATTATTTTAATAT
Done.