Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006459.1 Hibiscus syriacus cultivar Beakdansim tig00015654_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: 125079
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1425 original size:40 final size:41
Alignment explanation
Indices: 1358--1445 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 41
1348 TTCACCCTAA
*
1358 ACCCGACCCGACCCGAACAGTACA-TTTTAAAAAAAACCCG
1 ACCCGACCCGACCCGAACAGTAAATTTTTAAAAAAAACCCG
* * *
1398 ACCCGACCCGACCCGAACCCG-AAATTTTTTTAAAAAAATCCG
1 ACCCGACCCGACCCGAA-CAGTAAA-TTTTTAAAAAAAACCCG
1440 ACCCGA
1 ACCCGA
1446 TCGGGTCGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 19 0.46
41 2 0.05
42 20 0.49
ACGTcount: A:0.38, C:0.35, G:0.12, T:0.15
Consensus pattern (41 bp):
ACCCGACCCGACCCGAACAGTAAATTTTTAAAAAAAACCCG
Found at i:7155 original size:83 final size:83
Alignment explanation
Indices: 7016--7177 Score: 225
Period size: 83 Copynumber: 2.0 Consensus size: 83
7006 ATAAAACCCT
* *
7016 AAATCCCCTAAACAACATAAATTTAAGGTGAAAGGTTCAATTTTTACCCATTGACCTTCAATATT
1 AAATCCCATAAACAACATAAATCTAAGGTGAAAGGTTCAATTTTTACCCATTGACCTTCAATATT
*
7081 TCGGCGTTCTCGTTCCCC
66 CCGGCGTTCTCGTTCCCC
** * * * **
7099 AAATCCCATAAATGACATAAATCTAAGGTGAAATGTTCGATTTTTACCTATTGACCTTCCGTATT
1 AAATCCCATAAACAACATAAATCTAAGGTGAAAGGTTCAATTTTTACCCATTGACCTTCAATATT
*
7164 CCGGGGTTCTCGTT
66 CCGGCGTTCTCGTT
7178 TCTTGCAGTG
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
83 68 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (83 bp):
AAATCCCATAAACAACATAAATCTAAGGTGAAAGGTTCAATTTTTACCCATTGACCTTCAATATT
CCGGCGTTCTCGTTCCCC
Found at i:7660 original size:15 final size:15
Alignment explanation
Indices: 7637--7666 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7627 TAATGTAAAC
*
7637 AAAATAAATAAATAA
1 AAAAGAAATAAATAA
7652 AAAAGAAATAAATAA
1 AAAAGAAATAAATAA
7667 TAATGTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (15 bp):
AAAAGAAATAAATAA
Found at i:7750 original size:28 final size:26
Alignment explanation
Indices: 7714--7765 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
7704 CAAAAATATT
*
7714 TTTTTAAAAAAACTAATATTATATATGC
1 TTTTCAAAAAAA-T-ATATTATATATGC
*
7742 TTTTCAAAACAATATATTATATAT
1 TTTTCAAAAAAATATATTATATAT
7766 ATATTCGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 11 0.50
27 1 0.05
28 10 0.45
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (26 bp):
TTTTCAAAAAAATATATTATATATGC
Found at i:7794 original size:36 final size:35
Alignment explanation
Indices: 7754--8021 Score: 240
Period size: 36 Copynumber: 7.4 Consensus size: 35
7744 TTCAAAACAA
7754 TATATTATATATATATTCGAAAAATGTTTTTAAAAC
1 TATA-TATATATATATTCGAAAAATGTTTTTAAAAC
** *
7790 TATATATTATATATATTTTTAAAAATGTTTTCAAAAC
1 TATATA-TATATATA-TTCGAAAAATGTTTTTAAAAC
* *
7827 TATATATTATATATATTCTCGAAAAATATTTTCAAAAC
1 TATATA-TATATATA-T-TCGAAAAATGTTTTTAAAAC
* * *
7865 TATATATATATATATT-GAAAATTGTTTTCAAAAT
1 TATATATATATATATTCGAAAAATGTTTTTAAAAC
* *
7899 TATATATTATATATATTTTCTAAAAATATTTTTAAAAC
1 TATATA-TATATATA--TTCGAAAAATGTTTTTAAAAC
** *
7937 TATATAT-TATATATTTAAAAAATATTTTTTCAAAAC
1 TATATATATATATATTCGAAAAAT-GTTTTT-AAAAC
* *
7973 TATATAT-TATATACTT-AAAAAATATTTTTTCAAAAC
1 TATATATATATATA-TTCGAAAAAT-GTTTTT-AAAAC
8009 TATATAT-TATATA
1 TATATATATATATA
8022 CGTTATATGT
Statistics
Matches: 205, Mismatches: 17, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
34 29 0.14
35 16 0.08
36 70 0.34
37 48 0.23
38 42 0.20
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (35 bp):
TATATATATATATATTCGAAAAATGTTTTTAAAAC
Found at i:7914 original size:72 final size:72
Alignment explanation
Indices: 7742--8021 Score: 322
Period size: 72 Copynumber: 3.8 Consensus size: 72
7732 TTATATATGC
* * *
7742 TTTTCAAAACAATATATTATATATATAT-TCGAAAAATGTTTTTAAAACTATATATTATATATAT
1 TTTTCAAAACTATATATTATATATAT-TCTCGAAAAATATTTTCAAAACTATATA-T-TATATA-
7806 TTTTAAAAA-TG
62 -TTTAAAAATTG
7817 TTTTCAAAACTATATATTATATATATTCTCGAAAAATATTTTCAAAACTATATA-TATATATATT
1 TTTTCAAAACTATATATTATATATATTCTCGAAAAATATTTTCAAAACTATATATTATATAT-TT
*
7881 GAAAATTG
65 AAAAATTG
* * * *
7889 TTTTCAAAATTATATATTATATATATTTTCTAAAAATATTTTTAAAACTATATATTATATATTTA
1 TTTTCAAAACTATATATTATATATATTCTCGAAAAATATTTTCAAAACTATATATTATATATTT-
*
7954 AAAAATATT
65 AAAAAT-TG
**
7963 TTTTCAAAACTATATA-T-TATATA--CTTAAAAAATATTTTTTCAAAACTATATATTATATA
1 TTTTCAAAACTATATATTATATATATTCTCGAAAAATA--TTTTCAAAACTATATATTATATA
8022 CGTTATATGT
Statistics
Matches: 182, Mismatches: 15, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
70 9 0.05
71 6 0.03
72 88 0.48
73 13 0.07
74 17 0.09
75 49 0.27
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (72 bp):
TTTTCAAAACTATATATTATATATATTCTCGAAAAATATTTTCAAAACTATATATTATATATTTA
AAAATTG
Found at i:14289 original size:31 final size:31
Alignment explanation
Indices: 14254--14318 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
14244 ACAGCCGATG
* *
14254 GACTAAAATCGAATGAATCGATAACATTAGA
1 GACTAAAATCGAAAGAATCGATAACATTAAA
* *
14285 GACTAAAATTGAAAGAATCGATAACGTTAAA
1 GACTAAAATCGAAAGAATCGATAACATTAAA
14316 GAC
1 GAC
14319 CATTTCCCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.49, C:0.12, G:0.17, T:0.22
Consensus pattern (31 bp):
GACTAAAATCGAAAGAATCGATAACATTAAA
Found at i:15164 original size:7 final size:7
Alignment explanation
Indices: 15152--15178 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
15142 ATTGATATAT
15152 AATTAAA
1 AATTAAA
15159 AATTAAA
1 AATTAAA
15166 AATTAAA
1 AATTAAA
15173 AATTAA
1 AATTAA
15179 TTTGAAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AATTAAA
Found at i:17915 original size:17 final size:17
Alignment explanation
Indices: 17893--17928 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
17883 ATGTCTCCTC
17893 CTCCATCCCTTCAACGT
1 CTCCATCCCTTCAACGT
17910 CTCCATCCCTTCAACGT
1 CTCCATCCCTTCAACGT
17927 CT
1 CT
17929 TTGCCTGCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.47, G:0.06, T:0.31
Consensus pattern (17 bp):
CTCCATCCCTTCAACGT
Found at i:19062 original size:30 final size:31
Alignment explanation
Indices: 19028--19098 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 31
19018 AATTTATTTG
19028 TTATTATGAGTAT-AATTTTTTCAATA-CTTT
1 TTATTATGAGT-TCAATTTTTTCAATATCTTT
* *
19058 TTATTA-GAGGTTCATTTTTTTCAATATTTTT
1 TTATTATGA-GTTCAATTTTTTCAATATCTTT
19089 TTATTATGAG
1 TTATTATGAG
19099 CATATTCTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
29 3 0.09
30 20 0.57
31 10 0.29
32 2 0.06
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.58
Consensus pattern (31 bp):
TTATTATGAGTTCAATTTTTTCAATATCTTT
Found at i:22599 original size:28 final size:27
Alignment explanation
Indices: 22555--22614 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 27
22545 CAACATTTCA
*
22555 AAAGGAGATTTAGAATGTTAGATAGTGG
1 AAAGGAGATTTAAAATGTTAGA-AGTGG
*
22583 AAAGGAGATTTAAAATGTTAGAATTGG
1 AAAGGAGATTTAAAATGTTAGAAGTGG
22610 AAAGG
1 AAAGG
22615 GCACTGTACC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (27 bp):
AAAGGAGATTTAAAATGTTAGAAGTGG
Found at i:28516 original size:21 final size:22
Alignment explanation
Indices: 28481--28561 Score: 87
Period size: 21 Copynumber: 3.8 Consensus size: 22
28471 TTGGTGCAGA
*
28481 GGGAATCGA-TCCCCCCATGA-
1 GGGAACCGATTCCCCCCATGAG
**
28501 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCATG-AG
28524 GGGAACCGATTCCCCCCAT-AG
1 GGGAACCGATTCCCCCCATGAG
* *
28545 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
28562 TGGGGTTCTG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
20 8 0.16
21 25 0.49
22 1 0.02
23 17 0.33
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.16
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCATGAG
Found at i:32116 original size:36 final size:36
Alignment explanation
Indices: 32003--32121 Score: 188
Period size: 35 Copynumber: 3.3 Consensus size: 36
31993 TGGTAACCAA
32003 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
32039 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
32074 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
32111 -GTTGAAAAATG
1 CTTTGAAAAATG
32122 ATAATGGGAT
Statistics
Matches: 78, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
35 36 0.46
36 19 0.24
37 23 0.29
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:36657 original size:21 final size:21
Alignment explanation
Indices: 36633--36693 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
36623 AACTTTGAAA
36633 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
36654 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
36668 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
36689 AAATG
1 AAATG
36694 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:36724 original size:37 final size:37
Alignment explanation
Indices: 36625--36743 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
36615 TGGTAACCAA
36625 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
36662 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
36697 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
36734 -GTTGAAAAAT
1 CTTTGAAAAAT
36744 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:45998 original size:11 final size:12
Alignment explanation
Indices: 45980--46053 Score: 62
Period size: 11 Copynumber: 5.8 Consensus size: 12
45970 AATTAATTCC
45980 TAAATAAAATAA
1 TAAATAAAATAA
45992 T-AATAAAATAA
1 TAAATAAAATAA
*
46003 TCAAACTAAAAATAC
1 T-AAA-T-AAAATAA
46018 TAAATAAAAAGTAA
1 TAAAT-AAAA-TAA
46032 T-AATAAAATAA
1 TAAATAAAATAA
46043 TCAAACTAAAA
1 T-AAA-TAAAA
46054 ATCCTAAATC
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
11 15 0.29
12 5 0.10
13 13 0.25
14 12 0.23
15 7 0.13
ACGTcount: A:0.69, C:0.07, G:0.01, T:0.23
Consensus pattern (12 bp):
TAAATAAAATAA
Found at i:46038 original size:40 final size:38
Alignment explanation
Indices: 45979--46062 Score: 141
Period size: 40 Copynumber: 2.2 Consensus size: 38
45969 TAATTAATTC
45979 CTAAATAAAATAATAATAAAATAATCAAACTAAAAATA
1 CTAAATAAAATAATAATAAAATAATCAAACTAAAAATA
*
46017 CTAAATAAAAAGTAATAATAAAATAATCAAACTAAAAATC
1 CTAAAT-AAAA-TAATAATAAAATAATCAAACTAAAAATA
46057 CTAAAT
1 CTAAAT
46063 CTAAAAGGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
38 6 0.14
39 4 0.09
40 33 0.77
ACGTcount: A:0.65, C:0.10, G:0.01, T:0.24
Consensus pattern (38 bp):
CTAAATAAAATAATAATAAAATAATCAAACTAAAAATA
Found at i:47669 original size:18 final size:18
Alignment explanation
Indices: 47646--47691 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
47636 ATAAATTGAA
* *
47646 CATCGAATGTATTTCATG
1 CATCGAATGCATGTCATG
47664 CATCGAATGCATGTCATG
1 CATCGAATGCATGTCATG
47682 CATCG-ATGCA
1 CATCGAATGCA
47692 CTTGGGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 5 0.19
18 21 0.81
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (18 bp):
CATCGAATGCATGTCATG
Found at i:55826 original size:64 final size:64
Alignment explanation
Indices: 55750--55936 Score: 164
Period size: 64 Copynumber: 2.9 Consensus size: 64
55740 GCATCAATCC
* *
55750 ATGCATCGATGCACCATT-GAATAAATT-GAACATCGAATGCATTTCATGCATCGATGCACTCTC
1 ATGCATCGATGCA-C-TTGGAATAAATTAAAACATCGAATGCATTTCATACATCGATGCACTCTC
55813 T
64 T
** ** *** *
55814 ATGCATCGATGCACTTGGGTTTTATTAAAACATCGAATGCATTTCATACATCGATGCACAAGCA
1 ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATACATCGATGCACTCTCT
* * * ** * * *
55878 ATGCACCGATGCACTCAGG-CTATTTTCAAACATCGAATGCATTTTATGCATCGATGCAC
1 ATGCATCGATGCACT-TGGAATAAATTAAAACATCGAATGCATTTCATACATCGATGCAC
55937 ACTTGGTGCA
Statistics
Matches: 102, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
62 2 0.02
63 6 0.06
64 92 0.90
65 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (64 bp):
ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATACATCGATGCACTCTCT
Found at i:55937 original size:64 final size:64
Alignment explanation
Indices: 55778--55937 Score: 205
Period size: 64 Copynumber: 2.5 Consensus size: 64
55768 GAATAAATTG
*** * * * * *
55778 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTAGGCTATTATTAA
* *
55842 AACATCGAATGCATTTCATACATCGATGCACAAGCAATGCACCGATGCACTCAGGCTATT-TTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACT-AGGCTATTATTAA
*
55906 AACATCGAATGCATTTTATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
55938 CTTGGTGCAC
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
64 78 0.94
65 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCAATGCACCGATGCACTAGGCTATTATTAA
Found at i:55947 original size:64 final size:63
Alignment explanation
Indices: 55778--55957 Score: 202
Period size: 64 Copynumber: 2.8 Consensus size: 63
55768 GAATAAATTG
* * * * *
55778 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCACCGATGCACTAGGCTATTATTAA
* * *
55842 AACATCGAATGCATTTCATACATCGATGCACAAGC-AATGCACCGATGCACTCAGGCTATT-TTC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCACCGATGCACT-AGGCTATTATTA
55905 A
63 A
* * *
55906 AACATCGAATGCATTTTATGCATCGATGCACACTTGGTGCACCGATTCACTA
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCACCGATGCACTA
55958 AGTGTTCCAA
Statistics
Matches: 98, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 89 0.91
65 5 0.05
66 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCACCGATGCACTAGGCTATTATTAA
Found at i:61491 original size:31 final size:31
Alignment explanation
Indices: 61445--61569 Score: 216
Period size: 31 Copynumber: 4.0 Consensus size: 31
61435 CCCGAAGGAC
*
61445 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
61476 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
61507 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
61538 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
61569 C
1 C
61570 CCTCAACCCT
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 89 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:65853 original size:31 final size:31
Alignment explanation
Indices: 65815--65939 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
65805 CCCGAAAGAC
* *
65815 CAGTCCATA-GATCCCGAAAAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
65846 CAGTCCATATGTCCCGAAGAACATAGGTAAG
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
65877 TAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
65908 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
65939 C
1 C
65940 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:69494 original size:21 final size:20
Alignment explanation
Indices: 69454--69500 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
69444 GATGAAAACA
*
69454 AAAGAAAATAAATATGTAAT
1 AAAGAAAATAAATAAGTAAT
69474 ATAAGAAAATAAA-AAGATAAT
1 A-AAGAAAATAAATAAG-TAAT
69495 AAAGAA
1 AAAGAA
69501 TATCGATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (20 bp):
AAAGAAAATAAATAAGTAAT
Found at i:77807 original size:16 final size:17
Alignment explanation
Indices: 77774--77807 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
77764 AATATGTTTT
*
77774 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
77791 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
77807 T
1 T
77808 AATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:77904 original size:20 final size:21
Alignment explanation
Indices: 77865--77905 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
77855 TAGAGTGAGC
*
77865 AATTCAAAAATTTAATAAGTA
1 AATTCAAAAAATTAATAAGTA
*
77886 AATTGAAAAAATTAA-AAGTA
1 AATTCAAAAAATTAATAAGTA
77906 TAATGAGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (21 bp):
AATTCAAAAAATTAATAAGTA
Found at i:79480 original size:3 final size:3
Alignment explanation
Indices: 79472--79544 Score: 55
Period size: 3 Copynumber: 25.0 Consensus size: 3
79462 GTAATAGTAT
* * * * *
79472 TAA TAA TAA TAA TAA TTAA TAT TAT TAA -AA TAA TAA TAT TAT TAT
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
79517 TAAA TAA TAA -AA TAA T-A TAA -AA TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
79545 ATAAATAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 8 0.13
3 47 0.78
4 5 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:79545 original size:18 final size:19
Alignment explanation
Indices: 79474--79555 Score: 73
Period size: 18 Copynumber: 4.4 Consensus size: 19
79464 AATAGTATTA
*
79474 ATAATAATAATAATTAATATT
1 ATAA-AATAATAA-TAATAAT
* *
79495 ATTAAAATAATAATATTATT
1 A-TAAAATAATAATAATAAT
*
79515 ATTAAATAATAA-AATAAT
1 ATAAAATAATAATAATAAT
79533 ATAAAATAAT-A-AATAA-
1 ATAAAATAATAATAATAAT
79549 ATAAAAT
1 ATAAAAT
79556 GGGCAAAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
16 7 0.13
17 6 0.11
18 13 0.24
19 10 0.18
20 7 0.13
21 9 0.16
22 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAAAATAATAATAATAAT
Found at i:80662 original size:2 final size:2
Alignment explanation
Indices: 80655--80719 Score: 78
Period size: 2 Copynumber: 31.5 Consensus size: 2
80645 ATGAAATGCG
*
80655 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
80697 AC A- AT AT GAT AT GAT AT GAT AT A
1 AT AT AT AT -AT AT -AT AT -AT AT A
80720 CTACATGTAC
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
1 1 0.02
2 49 0.88
3 6 0.11
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (2 bp):
AT
Found at i:86617 original size:12 final size:12
Alignment explanation
Indices: 86600--86626 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
86590 AAACTAAAAC
86600 AAAATGAAAAGA
1 AAAATGAAAAGA
86612 AAAATGAAAAGA
1 AAAATGAAAAGA
86624 AAA
1 AAA
86627 TAGATGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (12 bp):
AAAATGAAAAGA
Found at i:87148 original size:20 final size:20
Alignment explanation
Indices: 87087--87315 Score: 221
Period size: 20 Copynumber: 11.4 Consensus size: 20
87077 GATTTTCAAG
* ** *
87087 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
87107 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
*
87127 AATTGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
87147 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
87167 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
87187 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
87207 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
87227 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
87247 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
87267 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
87287 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
87307 AATCACAAC
1 AATCGCAAC
87316 ACTGAAATTT
Statistics
Matches: 173, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 169 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:88047 original size:24 final size:24
Alignment explanation
Indices: 88008--88054 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
87998 AAATTTGGTC
88008 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
88032 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
88055 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:88246 original size:12 final size:12
Alignment explanation
Indices: 88229--88253 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
88219 ATATAATCCT
88229 GAAGAAGAAAAA
1 GAAGAAGAAAAA
88241 GAAGAAGAAAAA
1 GAAGAAGAAAAA
88253 G
1 G
88254 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:90639 original size:72 final size:72
Alignment explanation
Indices: 90549--90758 Score: 291
Period size: 72 Copynumber: 2.9 Consensus size: 72
90539 GTAACGAGAG
*
90549 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
90614 AAATGAA
66 AAATGAA
* *
90621 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
90686 AAATGAA
66 AAATGAA
* * * * * *
90693 AATCGCAACGAGAGAATCG-CAATGCGGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCATT
1 AATCGCAATGCGA-AAT-GAAAAT-CGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAAT
90755 GCGA
63 GCGA
90759 TTCTCTCGTT
Statistics
Matches: 124, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
72 100 0.81
73 19 0.15
74 5 0.04
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:90670 original size:53 final size:52
Alignment explanation
Indices: 90535--90752 Score: 302
Period size: 53 Copynumber: 4.1 Consensus size: 52
90525 CGGAAATTAC
* *
90535 AATCGTAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C--AA-GAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
90582 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
90640 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
90693 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
90746 AATCGCA
1 AATCGCA
90753 TTGCGATTCT
Statistics
Matches: 155, Mismatches: 4, Indels: 18
0.88 0.02 0.10
Matches are distributed among these distances:
47 7 0.05
49 1 0.01
50 1 0.01
52 14 0.09
53 116 0.75
55 2 0.01
56 1 0.01
57 2 0.01
58 11 0.07
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:90807 original size:19 final size:19
Alignment explanation
Indices: 90767--90854 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
90757 GATTCTCTCG
90767 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
90787 TTACGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
90806 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
90820 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
90839 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
90855 AACATAATGC
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.12
17 7 0.12
19 25 0.42
20 14 0.24
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:90828 original size:53 final size:52
Alignment explanation
Indices: 90748--90854 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 52
90738 GAAATGAAAA
90748 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTACGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTACGATTTTCATT
*
90801 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTACGATTTTCATT
90853 TC
1 TC
90855 AACATAATGC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 19 0.36
53 34 0.64
ACGTcount: A:0.14, C:0.24, G:0.16, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTACGATTTTCATT
Found at i:90964 original size:14 final size:14
Alignment explanation
Indices: 90945--90981 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
90935 CATCAATTAC
90945 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
90959 ACAAATCATCTTTT
1 ACAAATCAACTTTT
90973 ACAAATCAA
1 ACAAATCAA
90982 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:92811 original size:20 final size:20
Alignment explanation
Indices: 92780--92876 Score: 91
Period size: 20 Copynumber: 5.2 Consensus size: 20
92770 TTTTGGTTGA
92780 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*** *
92800 AATGACTGTCGCAACAAGAG
1 AATGAAAATCGCAACGAGAG
92820 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
92839 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
92854 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
92874 AAT
1 AAT
92877 CGTAACGCGA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.07
17 2 0.03
19 15 0.25
20 19 0.31
21 12 0.20
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:92832 original size:21 final size:21
Alignment explanation
Indices: 92778--92842 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
92768 TCTTTTGGTT
92778 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
*** *
92799 G-AATGACTGTCGCAACAAGA
1 GAAATGAAAATCGCAACGAGA
92819 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
92840 GAA
1 GAA
92843 TCGCAACGCG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.49, C:0.15, G:0.25, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:92846 original size:14 final size:14
Alignment explanation
Indices: 92827--92883 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
92817 GAGAAATGAA
92827 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
92841 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
92860 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
92874 AATCGTAACG
1 AATCGCAACG
92884 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:92858 original size:33 final size:33
Alignment explanation
Indices: 92778--92900 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
92768 TCTTTTGGTT
*
92778 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACAAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
92819 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
92852 GAAATGAAAATCGCAACGAGAGAATCGTAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
92885 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
92901 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
33 49 0.61
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.28
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:92936 original size:14 final size:14
Alignment explanation
Indices: 92917--92973 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
92907 TTTGGTTTCG
92917 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
92931 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
92950 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
92964 CGTTGCGATT
1 CGTTGCGATT
92974 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:92949 original size:33 final size:33
Alignment explanation
Indices: 92901--92980 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
92891 AAAATCGCAA
**
92901 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
92934 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
92967 TGCGATTTTCATTT
1 TGCGATTTTCATTT
92981 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:92986 original size:21 final size:20
Alignment explanation
Indices: 92961--93013 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
92951 GTTGCGATTC
**
92961 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATAGTCA-TTT
92982 TCTCGTTGCAGATAGTCATTT
1 TCTCGTTGC-GATAGTCATTT
*
93003 TCACGTTGCGA
1 TCTCGTTGCGA
93014 CTCTTCTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 20 0.71
22 6 0.21
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (20 bp):
TCTCGTTGCGATAGTCATTT
Found at i:93139 original size:33 final size:33
Alignment explanation
Indices: 93093--93163 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
93083 AATACTAACT
93093 TGAAAATCACAACGAGAGAATAAG-AACGCGAAA
1 TGAAAATCACAACGAGAGAAT-AGTAACGCGAAA
* *
93126 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCACAACGAGAGAATAGTAACGCGAAA
93159 TGAAA
1 TGAAA
93164 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 1 0.03
33 34 0.97
ACGTcount: A:0.51, C:0.15, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCACAACGAGAGAATAGTAACGCGAAA
Found at i:93569 original size:20 final size:20
Alignment explanation
Indices: 93544--93716 Score: 240
Period size: 20 Copynumber: 8.6 Consensus size: 20
93534 CTTTAAAAAT
93544 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
93564 CGCGTTGCGATTCTACGTAT-
1 CGCGTTGCGATT-TACGGATA
*
93584 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
93605 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
93625 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
93645 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
93665 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* ** *
93685 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
93705 CGCGTTGCGATT
1 CGCGTTGCGATT
93717 CTGGAAAATC
Statistics
Matches: 136, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
20 119 0.88
21 17 0.12
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:95707 original size:17 final size:16
Alignment explanation
Indices: 95665--95735 Score: 106
Period size: 16 Copynumber: 4.4 Consensus size: 16
95655 GGTATTACCC
* *
95665 GACCTGTTTTCAACTT
1 GACCTGTTTTTAACCT
95681 GACCTGTTTTTAACCT
1 GACCTGTTTTTAACCT
*
95697 GACTTGTTTTTAACCT
1 GACCTGTTTTTAACCT
*
95713 GACCTGTTTTTAACTT
1 GACCTGTTTTTAACCT
95729 GACCTGT
1 GACCTGT
95736 AAATGACCCG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.18, C:0.23, G:0.14, T:0.45
Consensus pattern (16 bp):
GACCTGTTTTTAACCT
Found at i:96024 original size:23 final size:24
Alignment explanation
Indices: 95990--96039 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
95980 ATGCAAAGGA
*
95990 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTCATAT
96014 AAATT-ATATAGTTTAATTCATAT
1 AAATTAATATAGTTTAATTCATAT
96037 AAA
1 AAA
96040 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTCATAT
Found at i:96618 original size:2 final size:2
Alignment explanation
Indices: 96611--96635 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
96601 ACTTTGAATA
96611 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
96636 ATTAAACATA
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:97084 original size:2 final size:2
Alignment explanation
Indices: 97077--97129 Score: 72
Period size: 2 Copynumber: 26.5 Consensus size: 2
97067 TATGTTTAAT
*
97077 TA TA TA TA TA TA TA TA TA TA CT- TA TA TA TA TA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
*
97119 TA AA TA TA TA T
1 TA TA TA TA TA T
97130 TATTCAAAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 43 0.96
3 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:97496 original size:21 final size:21
Alignment explanation
Indices: 97472--97517 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
97462 ATATAAACTT
*
97472 TAAACCCTAAACCCTAAACCA
1 TAAACACTAAACCCTAAACCA
* *
97493 TAAATACTAACCCCTAAACCA
1 TAAACACTAAACCCTAAACCA
97514 TAAA
1 TAAA
97518 TAGCAATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (21 bp):
TAAACACTAAACCCTAAACCA
Found at i:97518 original size:21 final size:21
Alignment explanation
Indices: 97478--97519 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
97468 ACTTTAAACC
97478 CTAAACCCTAAACCATAAATA
1 CTAAACCCTAAACCATAAATA
*
97499 CTAACCCCTAAACCATAAATA
1 CTAAACCCTAAACCATAAATA
97520 GCAATGTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (21 bp):
CTAAACCCTAAACCATAAATA
Found at i:97552 original size:2 final size:2
Alignment explanation
Indices: 97541--97618 Score: 104
Period size: 2 Copynumber: 39.0 Consensus size: 2
97531 ATAAACCATG
*
97541 TA TA -A TA TA TA TA AA CTA 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
** *
97583 TA TA TA TA TA TA TA TA CC TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
97619 AAGTAATAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.02
2 64 0.97
3 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:97744 original size:15 final size:15
Alignment explanation
Indices: 97724--97757 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
97714 TTATATATTT
97724 TATATAGTTTATACA
1 TATATAGTTTATACA
*
97739 TATATAGTTTATATA
1 TATATAGTTTATACA
97754 TATA
1 TATA
97758 CTATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATACA
Found at i:97753 original size:17 final size:17
Alignment explanation
Indices: 97724--97793 Score: 51
Period size: 17 Copynumber: 4.4 Consensus size: 17
97714 TTATATATTT
97724 TATATAG-TT-TATACA
1 TATATAGTTTATATACA
*
97739 TATATAGTTTATATATA
1 TATATAGTTTATATACA
* *
97756 TACTATA-TTAATATAAA
1 TA-TATAGTTTATATACA
* *
97773 TA-ATATTTTATAAAC-
1 TATATAGTTTATATACA
97788 TATATA
1 TATATA
97794 CTTTTTATAG
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
15 12 0.27
16 11 0.25
17 17 0.39
18 4 0.09
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (17 bp):
TATATAGTTTATATACA
Found at i:97843 original size:73 final size:73
Alignment explanation
Indices: 97676--97825 Score: 230
Period size: 73 Copynumber: 2.1 Consensus size: 73
97666 TAATGCATAC
* *** *
97676 ATATATATACTATATTAATATAAATTATAACATATAAATTATATATTTTATATAGTTTATACATA
1 ATATATATACTATATTAATATAAATAATATTTTATAAACTATATATTTTATATAGTTTATACATA
*
97741 TATAGTTT
66 TATAATTT
97749 ATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTT-TATAGTTTATACAT
1 ATATATATACTATATTAATATAAATAATATTTTATAAACTATATA-TTTTATATAGTTTATACAT
97813 ATATAATTT
65 ATATAATTT
97822 ATAT
1 ATAT
97826 GCATTGCTTA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
73 66 0.94
74 4 0.06
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.49
Consensus pattern (73 bp):
ATATATATACTATATTAATATAAATAATATTTTATAAACTATATATTTTATATAGTTTATACATA
TATAATTT
Found at i:97906 original size:18 final size:18
Alignment explanation
Indices: 97885--98017 Score: 74
Period size: 18 Copynumber: 7.0 Consensus size: 18
97875 TATAATAATT
97885 ATATAGTTTATAATATAA
1 ATATAGTTTATAATATAA
*
97903 ATATAGTTTATAATTTTATAT
1 ATATAGTTTATAA---TATAA
* *
97924 ACATAGTTTATATATATAGTTC
1 ATATAGTTTATA-ATATA---A
* ** *
97946 ACATA-AATATAATTTATAT
1 ATATAGTTTATAA--TATAA
* *
97965 ATATATTTTATAATA-ATT
1 ATATAGTTTATAATATA-A
97983 ATATAGTTTATAATATAA
1 ATATAGTTTATAATATAA
98001 ATATAGTTTAT-ATATAA
1 ATATAGTTTATAATATAA
98018 TTTTATATTA
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
17 7 0.08
18 41 0.45
19 9 0.10
20 6 0.07
21 19 0.21
22 10 0.11
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (18 bp):
ATATAGTTTATAATATAA
Found at i:97941 original size:98 final size:97
Alignment explanation
Indices: 97814--98012 Score: 335
Period size: 98 Copynumber: 2.0 Consensus size: 97
97804 TTTATACATA
* *
97814 TATAATTTATATGCATTGCTTATATATATAGTTCACATAAACATAATTTATATATATAACTTATA
1 TATAATTTATATACATAGCTTATATATATAGTTCACATAAACATAATTTATATATATAACTTATA
97879 ATAATTATATAGTTTATAATATAAATATAGTT
66 ATAATTATATAGTTTATAATATAAATATAGTT
* * **
97911 TATAATTTTATATACATAGTTTATATATATAGTTCACATAAATATAATTTATATATATATTTTAT
1 TATAA-TTTATATACATAGCTTATATATATAGTTCACATAAACATAATTTATATATATAACTTAT
97976 AATAATTATATAGTTTATAATATAAATATAGTT
65 AATAATTATATAGTTTATAATATAAATATAGTT
98009 TATA
1 TATA
98013 TATAATTTTA
Statistics
Matches: 95, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
97 5 0.05
98 90 0.95
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (97 bp):
TATAATTTATATACATAGCTTATATATATAGTTCACATAAACATAATTTATATATATAACTTATA
ATAATTATATAGTTTATAATATAAATATAGTT
Found at i:97974 original size:13 final size:13
Alignment explanation
Indices: 97911--98044 Score: 70
Period size: 13 Copynumber: 10.8 Consensus size: 13
97901 AAATATAGTT
97911 TATA-ATTTTATA
1 TATATATTTTATA
* *
97923 TACATAGTTTATA
1 TATATATTTTATA
**
97936 TATATAGTTCACATA
1 TATATA-TT-TTATA
* *
97951 AATATAATTTATA
1 TATATATTTTATA
97964 TATATATTTTATA
1 TATATATTTTATA
97977 -ATA-A--TTATA
1 TATATATTTTATA
* **
97986 TAGTTTATAATATA
1 TA-TATATTTTATA
* *
98000 AATATAGTTTATA
1 TATATATTTTATA
98013 TATA-ATTTTATA
1 TATATATTTTATA
*
98025 T-TATA-TATATA
1 TATATATTTTATA
98036 T-TATATTTT
1 TATATATTTT
98045 TTTTCAAATT
Statistics
Matches: 89, Mismatches: 23, Indels: 20
0.67 0.17 0.15
Matches are distributed among these distances:
9 5 0.06
10 1 0.01
11 14 0.16
12 18 0.20
13 36 0.40
14 7 0.08
15 8 0.09
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (13 bp):
TATATATTTTATA
Found at i:99259 original size:2 final size:2
Alignment explanation
Indices: 99252--99281 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
99242 TAATATTTTA
*
99252 AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
99282 GTATGTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101198 original size:4 final size:4
Alignment explanation
Indices: 101189--101280 Score: 56
Period size: 4 Copynumber: 25.0 Consensus size: 4
101179 TCGGGCCGGG
* * * *
101189 TATA TATA TATT TAAA T-TA AATA TATA AATA T-TA TATA TATA T-TA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
101234 -ATT TAAA T-TA AATT TAT- TA-A TAT- TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
101277 TATA
1 TATA
101281 ATAATAATAA
Statistics
Matches: 65, Mismatches: 15, Indels: 16
0.68 0.16 0.17
Matches are distributed among these distances:
3 15 0.23
4 50 0.77
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TATA
Found at i:101230 original size:6 final size:6
Alignment explanation
Indices: 101189--101280 Score: 56
Period size: 6 Copynumber: 16.7 Consensus size: 6
101179 TCGGGCCGGG
* * * *
101189 TATATA TATATT TAAAT- TAAATA TATAAA TAT-TA TATATA TAT-TA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
101234 -ATTTA AAT-TA AATTTA T-TA-A TAT-TA TATATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
101277 TATA
1 TATA
101281 ATAATAATAA
Statistics
Matches: 71, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
4 4 0.06
5 24 0.34
6 43 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATA
Found at i:101238 original size:36 final size:35
Alignment explanation
Indices: 101189--101267 Score: 124
Period size: 36 Copynumber: 2.3 Consensus size: 35
101179 TCGGGCCGGG
101189 TATATATA-TATTTAAATTAAATATATAAATATTA
1 TATATATATTATTTAAATTAAATATATAAATATTA
* *
101223 TATATATATTAATTTAAATTAAATTTATTAATATTA
1 TATATATATT-ATTTAAATTAAATATATAAATATTA
101259 TATATATAT
1 TATATATAT
101268 ATATATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
34 8 0.20
35 1 0.02
36 32 0.78
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
TATATATATTATTTAAATTAAATATATAAATATTA
Found at i:101336 original size:13 final size:12
Alignment explanation
Indices: 101305--101341 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
101295 TTTTAATATT
*
101305 TATCGGGTCGGG
1 TATCGGGGCGGG
101317 TATCGGGGCGGG
1 TATCGGGGCGGG
101329 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
101342 GATTATCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:101407 original size:36 final size:36
Alignment explanation
Indices: 101360--101428 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
101350 AACCTGTCAT
* *
101360 CGTTTAGCATAAACGGTTTTTCCCTGTCCCCGTCCC
1 CGTTTAGCATAAACGATTTTTCCATGTCCCCGTCCC
*
101396 CGTTTAGCATAAACGATTTTTTCATGTCCCCGT
1 CGTTTAGCATAAACGATTTTTCCATGTCCCCGT
101429 TTAATTCGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.17, C:0.30, G:0.16, T:0.36
Consensus pattern (36 bp):
CGTTTAGCATAAACGATTTTTCCATGTCCCCGTCCC
Found at i:103323 original size:2 final size:2
Alignment explanation
Indices: 103316--103341 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
103306 AAGAACCATC
103316 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
103342 TTCATGTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:110290 original size:17 final size:16
Alignment explanation
Indices: 110265--110317 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
110255 AAATTACATT
*
110265 AATATATAAATTATTA
1 AATATATAAAATATTA
110281 AATATGATAAAATATTA
1 AATAT-ATAAAATATTA
110298 AAT-TCAATAAAATATTA
1 AATAT--ATAAAATATTA
110315 AAT
1 AAT
110318 TATTGTGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
16 6 0.18
17 27 0.82
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
AATATATAAAATATTA
Found at i:114899 original size:29 final size:29
Alignment explanation
Indices: 114857--114915 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
114847 ATTTTCACCT
114857 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
114886 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
114915 A
1 A
114916 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:116668 original size:19 final size:20
Alignment explanation
Indices: 116578--116670 Score: 118
Period size: 19 Copynumber: 4.7 Consensus size: 20
116568 TGCAGCCTTC
* *
116578 ATGCATGGATG-ACAGCAGG
1 ATGCATCGATGCACAGCATG
*
116597 ATGCATCGATGCACAGCCTTG
1 ATGCATCGATGCACAG-CATG
*
116618 ATGCATCGATGCACAGCCTG
1 ATGCATCGATGCACAGCATG
*
116638 ATGCATCGATGCACAG-AAG
1 ATGCATCGATGCACAGCATG
116657 ATGCATCGATGCAC
1 ATGCATCGATGCAC
116671 TAATTGCATT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
19 25 0.38
20 23 0.35
21 18 0.27
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.19
Consensus pattern (20 bp):
ATGCATCGATGCACAGCATG
Found at i:116842 original size:28 final size:28
Alignment explanation
Indices: 116811--116865 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
116801 AAACTTTGAA
* * *
116811 TAAATTCAATTAAGTCCAAAAATATTTG
1 TAAATTAAATCAAGTCCAAAAACATTTG
116839 TAAATTAAATCAAGTCCAAAAACATTT
1 TAAATTAAATCAAGTCCAAAAACATTT
116866 TGCCTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (28 bp):
TAAATTAAATCAAGTCCAAAAACATTTG
Found at i:119251 original size:21 final size:21
Alignment explanation
Indices: 119217--119256 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
119207 GAAGTCGTAT
*
119217 AGCCGTTGGGGATG-TTTTGG
1 AGCCGTTGGAGATGATTTTGG
119237 AGCCGTTTGGAGATGATTTT
1 AGCCG-TTGGAGATGATTTT
119257 TCTACTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
AGCCGTTGGAGATGATTTTGG
Found at i:119413 original size:20 final size:20
Alignment explanation
Indices: 119378--119455 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
119368 CATGGATGCA
* *
119378 CAGGATGCA-GGATGCACCG
1 CAGGATGCATCGATGCACAG
119397 CAGGATGCATCGATGCACAG
1 CAGGATGCATCGATGCACAG
**
119417 CCTTGATGCATCGATGCACAG
1 -CAGGATGCATCGATGCACAG
*
119438 AAGGATGCATCGATGCAC
1 CAGGATGCATCGATGCAC
119456 TAATTGCATT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
19 9 0.18
20 23 0.46
21 18 0.36
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (20 bp):
CAGGATGCATCGATGCACAG
Found at i:119522 original size:42 final size:42
Alignment explanation
Indices: 119476--119616 Score: 207
Period size: 42 Copynumber: 3.4 Consensus size: 42
119466 CGGTGTTTGA
*
119476 GTGCATGGATGCACTAGTGCAGGTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTAGTGCAGGTGCATGGATGCACTGCAGG
*
119518 GTGCATCGATGCACTAGTGCAGGTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTAGTGCAGGTGCATGGATGCACTGCAGG
119560 GATGCATGGATGCAC---TGCAGGGATGCATGGATGCACTGCAGG
1 G-TGCATGGATGCACTAGTGCA-GG-TGCATGGATGCACTGCAGG
*
119602 GTGCATGAATGCACT
1 GTGCATGGATGCACT
119617 TTGACACCCT
Statistics
Matches: 91, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
40 4 0.04
41 14 0.15
42 61 0.67
43 12 0.13
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.22
Consensus pattern (42 bp):
GTGCATGGATGCACTAGTGCAGGTGCATGGATGCACTGCAGG
Found at i:119567 original size:21 final size:20
Alignment explanation
Indices: 119476--119616 Score: 169
Period size: 21 Copynumber: 6.8 Consensus size: 20
119466 CGGTGTTTGA
119476 GTGCATGGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
*
119498 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
*
119518 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
119540 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
119560 GATGCATGGATGCACTGCAGG
1 G-TGCATGGATGCACTGCAGG
119581 GATGCATGGATGCACTGCAGG
1 G-TGCATGGATGCACTGCAGG
*
119602 GTGCATGAATGCACT
1 GTGCATGGATGCACT
119617 TTGACACCCT
Statistics
Matches: 110, Mismatches: 3, Indels: 14
0.87 0.02 0.11
Matches are distributed among these distances:
19 8 0.07
20 29 0.26
21 41 0.37
22 28 0.25
23 4 0.04
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:119599 original size:13 final size:13
Alignment explanation
Indices: 119499--119586 Score: 55
Period size: 13 Copynumber: 6.9 Consensus size: 13
119489 CTAGTGCAGG
119499 TGCATGGATGCAC
1 TGCATGGATGCAC
119512 TGCATGG-TGCATC
1 TGCATGGATGCA-C
* *
119525 GATGCACTAG-TGCAGG
1 --TGCA-TGGATGCA-C
119541 TGCATGGATGCAC
1 TGCATGGATGCAC
119554 TGCA-GG--G-A-
1 TGCATGGATGCAC
119562 TGCATGGATGCAC
1 TGCATGGATGCAC
*
119575 TGCAGGGATGCA
1 TGCATGGATGCA
119587 TGGATGCACT
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
8 4 0.07
9 3 0.05
10 1 0.02
11 1 0.02
12 7 0.12
13 25 0.42
14 8 0.14
15 4 0.07
16 6 0.10
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.22
Consensus pattern (13 bp):
TGCATGGATGCAC
Found at i:123415 original size:26 final size:28
Alignment explanation
Indices: 123379--123433 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 28
123369 AATTTCACCT
123379 AACTAAATGATGTAAGC-ATGAC-TCAA
1 AACTAAATGATGTAAGCAATGACATCAA
*
123405 AACTAATTGATGTAAGCAATGACATCAA
1 AACTAAATGATGTAAGCAATGACATCAA
123433 A
1 A
123434 TTAATTTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 16 0.62
27 5 0.19
28 5 0.19
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (28 bp):
AACTAAATGATGTAAGCAATGACATCAA
Done.