Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006477.1 Hibiscus syriacus cultivar Beakdansim tig00015699_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: 91097
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4426 original size:15 final size:16
Alignment explanation
Indices: 4400--4429 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4390 TTAATAAAAT
4400 AGTGTCCTATAGTCAG
1 AGTGTCCTATAGTCAG
4416 AGTGT-CTATAGTCA
1 AGTGTCCTATAGTCA
4430 AAGACCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (16 bp):
AGTGTCCTATAGTCAG
Found at i:8596 original size:21 final size:21
Alignment explanation
Indices: 8570--8642 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
8560 TTCCAGATTT
8570 ACAACGCGAACTTGGACTATC
1 ACAACGCGAACTTGGACTATC
8591 ACAACGCGAACTTGGACTATC
1 ACAACGCGAACTTGGACTATC
* * *
8612 GCAATGCGAACTTCGACTATC
1 ACAACGCGAACTTGGACTATC
* *
8633 GCAATGCGAA
1 ACAACGCGAA
8643 TATGTAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (21 bp):
ACAACGCGAACTTGGACTATC
Found at i:18926 original size:3 final size:3
Alignment explanation
Indices: 18918--18944 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
18908 TGTTCTGTCC
18918 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
18945 GGGTAAAGTA
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):
TAA
Found at i:19352 original size:16 final size:16
Alignment explanation
Indices: 19333--19366 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19323 CAATATACGA
19333 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
19349 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
19365 AT
1 AT
19367 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:19440 original size:16 final size:18
Alignment explanation
Indices: 19408--19441 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
19398 TATTAATGTA
19408 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
19426 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
19442 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:20147 original size:128 final size:129
Alignment explanation
Indices: 19910--20155 Score: 386
Period size: 128 Copynumber: 1.9 Consensus size: 129
19900 AATTTTCTTC
* *
19910 TAATTAGGTGGTGACATATGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATATGTCACCAATAACACATATCATGATCATGTGCTAACACA-GTCAGAT
* ** *
19975 TCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
65 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
20040 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACAC-GTCAGATC
1 TAATTAGGTGGTGACATATGTCACCAATAACACATATCATGATCATGTGCTAACACAGTCAGATC
20104 CTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
20156 TATATAAATA
Statistics
Matches: 106, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
128 56 0.53
130 50 0.47
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (129 bp):
TAATTAGGTGGTGACATATGTCACCAATAACACATATCATGATCATGTGCTAACACAGTCAGATC
CTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:20602 original size:35 final size:35
Alignment explanation
Indices: 20552--20627 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
20542 AATTGAATTG
* *
20552 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
20587 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
20622 AATTGA
1 AATTGA
20628 GGAATGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:21158 original size:54 final size:54
Alignment explanation
Indices: 21095--21198 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 54
21085 TGAAATTTAT
* * *
21095 AATACAGTTATCGAACTTTTATTTCATTTTCAGTAAAGTCCTTGACGTTACCTC
1 AATACAGTTATCAAACATTTAGTTCATTTTCAGTAAAGTCCTTGACGTTACCTC
*
21149 AATACAGTTATCAAACATTTAGTTCATTTTCAGTAAGGTCCTTGACGTTA
1 AATACAGTTATCAAACATTTAGTTCATTTTCAGTAAAGTCCTTGACGTTA
21199 TCTCCCGTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (54 bp):
AATACAGTTATCAAACATTTAGTTCATTTTCAGTAAAGTCCTTGACGTTACCTC
Found at i:23936 original size:30 final size:29
Alignment explanation
Indices: 23902--23963 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
23892 TAAATTTGGT
23902 AAAGTTT-GGTGACCAAAGTATAAACTTTAA
1 AAAGTTTAGG-GACCAAAGTAT-AACTTTAA
* * *
23932 AAAGTTTAGGGATCAAAGTGTAATTTTAA
1 AAAGTTTAGGGACCAAAGTATAACTTTAA
23961 AAA
1 AAA
23964 ATTACAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 10 0.36
30 16 0.57
31 2 0.07
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31
Consensus pattern (29 bp):
AAAGTTTAGGGACCAAAGTATAACTTTAA
Found at i:25185 original size:24 final size:24
Alignment explanation
Indices: 25158--25206 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
25148 TGCATGACAT
25158 TGTACATAAATGTTTTATACATCA
1 TGTACATAAATGTTTTATACATCA
*
25182 TGTACATAGATGTTTTATACATCA
1 TGTACATAAATGTTTTATACATCA
25206 T
1 T
25207 CGAAAAGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (24 bp):
TGTACATAAATGTTTTATACATCA
Found at i:27242 original size:21 final size:20
Alignment explanation
Indices: 27188--27259 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
27178 GACCCAACCT
*
27188 AAAATAATATATTTATTAAAA
1 AAAATAATAT-TTAATTAAAA
* * * *
27209 AATATTAT-TTTTATTCAATA
1 AAAATAATATTTAATT-AAAA
27229 AAAATAGATATTTAATTAAAA
1 AAAATA-ATATTTAATTAAAA
27250 AAAATAATAT
1 AAAATAATAT
27260 ATAGAGGGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
19 6 0.15
20 12 0.29
21 17 0.41
22 6 0.15
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (20 bp):
AAAATAATATTTAATTAAAA
Found at i:27261 original size:22 final size:21
Alignment explanation
Indices: 27188--27261 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 21
27178 GACCCAACCT
27188 AAAATAATATATTTATT--AA
1 AAAATAATATATTTATTAAAA
* * *
27207 AAAATATTATTTTTATTCAATA
1 AAAATAATATATTTATT-AAAA
*
27229 AAAATAGATAT-TTAATTAAAA
1 AAAATA-ATATATTTATTAAAA
27250 AAAATAATATAT
1 AAAATAATATAT
27262 AGAGGGATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 15 0.34
20 4 0.09
21 10 0.23
22 12 0.27
23 3 0.07
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (21 bp):
AAAATAATATATTTATTAAAA
Found at i:34250 original size:15 final size:15
Alignment explanation
Indices: 34230--34258 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
34220 TATTTCATAA
34230 CATAATTTAAAATTG
1 CATAATTTAAAATTG
34245 CATAATTTAAAATT
1 CATAATTTAAAATT
34259 TAACTGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (15 bp):
CATAATTTAAAATTG
Found at i:34442 original size:15 final size:15
Alignment explanation
Indices: 34408--34442 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
34398 TTTTCTAACA
34408 CTATATATAAAAAAT
1 CTATATATAAAAAAT
* *
34423 TTATATATAAAATAT
1 CTATATATAAAAAAT
34438 CTATA
1 CTATA
34443 ACCAGACTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (15 bp):
CTATATATAAAAAAT
Found at i:34803 original size:17 final size:17
Alignment explanation
Indices: 34767--34842 Score: 59
Period size: 17 Copynumber: 4.6 Consensus size: 17
34757 TTTTGTGATG
* *
34767 ATTTC-TTTACTGTATA
1 ATTTCTTTTACTATATT
*
34783 ATTTCTTTTATTATATT
1 ATTTCTTTTACTATATT
* *
34800 ATTTCTCTTACTATACT
1 ATTTCTTTTACTATATT
*
34817 A-TACTTTTACTAT-TCT
1 ATTTCTTTTACTATAT-T
*
34833 ATATCTTTTA
1 ATTTCTTTTA
34843 TTTTTGTTTT
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
16 17 0.37
17 29 0.63
ACGTcount: A:0.25, C:0.14, G:0.01, T:0.59
Consensus pattern (17 bp):
ATTTCTTTTACTATATT
Found at i:34828 original size:16 final size:17
Alignment explanation
Indices: 34786--34842 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
34776 CTGTATAATT
* * *
34786 TCTTTTATTATATTATT
1 TCTTTTACTATACTATA
*
34803 TCTCTTACTATACTATA
1 TCTTTTACTATACTATA
*
34820 -CTTTTACTATTCTATA
1 TCTTTTACTATACTATA
34836 TCTTTTA
1 TCTTTTA
34843 TTTTTGTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 14 0.42
17 19 0.58
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.60
Consensus pattern (17 bp):
TCTTTTACTATACTATA
Found at i:36600 original size:21 final size:21
Alignment explanation
Indices: 36575--36622 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
36565 ACTTCAATTC
36575 AAGCTTTAATTAACATAACCA
1 AAGCTTTAATTAACATAACCA
36596 AAGCTTTAATTAACATAACCA
1 AAGCTTTAATTAACATAACCA
36617 AAGCTT
1 AAGCTT
36623 CAATCATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.29
Consensus pattern (21 bp):
AAGCTTTAATTAACATAACCA
Found at i:39366 original size:20 final size:20
Alignment explanation
Indices: 39341--39397 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
39331 CATTTAGGAT
39341 TTATGATTTAGAGG-TTAAGG
1 TTATGATTTAG-GGTTTAAGG
39361 TTATGATTTAGGGTTTAAGG
1 TTATGATTTAGGGTTTAAGG
* *
39381 ATGAGGATTTAGGGTTT
1 -TTATGATTTAGGGTTT
39398 TAAGTTAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 2 0.06
20 17 0.52
21 14 0.42
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (20 bp):
TTATGATTTAGGGTTTAAGG
Found at i:40882 original size:15 final size:16
Alignment explanation
Indices: 40848--40882 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
40838 GTTTAGGGTT
40848 CAATTAAAGCATTAAA
1 CAATTAAAGCATTAAA
*
40864 CAATTAAATCATT-AA
1 CAATTAAAGCATTAAA
40879 CAAT
1 CAAT
40883 CAAACGATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.54, C:0.14, G:0.03, T:0.29
Consensus pattern (16 bp):
CAATTAAAGCATTAAA
Found at i:41898 original size:60 final size:61
Alignment explanation
Indices: 41832--42034 Score: 227
Period size: 60 Copynumber: 3.3 Consensus size: 61
41822 CAAAACTGAG
41832 AATTAATCCCATGCAGATGTCAAAATGGGGGAA-TAATCCCTTGCAGATGTCAGAAGGGGA
1 AATTAATCCCATGCAGATGTCAAAATGGGGGAATTAATCCCTTGCAGATGTCAGAAGGGGA
* * * *
41892 AATTAATCCCATGTAGATGT-AAGATCAGAACGGGGAATTAAT-CTTATACAGATGTCAGAATGG
1 AATTAATCCCATGCAGATGTCAAAAT--G---GGGGAATTAATCCCT-TGCAGATGTCAGAA-GG
41955 GG-
59 GGA
* * * *
41957 AATTAATCCCATGCAGATGTCAGAA-CGAGGAATTAATCCCTTGCAGATGTCAGAACGGGA
1 AATTAATCCCATGCAGATGTCAAAATGGGGGAATTAATCCCTTGCAGATGTCAGAAGGGGA
*
42017 AATTAATCCCATACAGAT
1 AATTAATCCCATGCAGAT
42035 ATCATAACGG
Statistics
Matches: 119, Mismatches: 13, Indels: 22
0.77 0.08 0.14
Matches are distributed among these distances:
59 7 0.06
60 59 0.50
61 3 0.03
64 8 0.07
65 36 0.30
66 6 0.05
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (61 bp):
AATTAATCCCATGCAGATGTCAAAATGGGGGAATTAATCCCTTGCAGATGTCAGAAGGGGA
Found at i:41954 original size:95 final size:95
Alignment explanation
Indices: 41831--42034 Score: 260
Period size: 95 Copynumber: 2.2 Consensus size: 95
41821 TCAAAACTGA
* * *
41831 GAATTAATCCCATGCAGATGTCAAAATGGGGGAA-TAATCCCTTGCAGATGTCAGAA-GGGGAAA
1 GAATTAATCCCATACAGATGTCAAAAT-GGGGAATTAATCCCATGCAGATGTCAGAACGAGG-AA
*
41894 TTAATCCCATGTAGATGTAAGATCAGAACGGG
64 TTAATCCCATGCAGATGTAAGATCAGAACGGG
** *
41926 GAATTAATCTTATACAGATGTCAGAATGGGGAATTAATCCCATGCAGATGTCAGAACGAGGAATT
1 GAATTAATCCCATACAGATGTCAAAATGGGGAATTAATCCCATGCAGATGTCAGAACGAGGAATT
*
41991 AATCCCTTGCAGA--T--G-TCAGAACGGG
66 AATCCCATGCAGATGTAAGATCAGAACGGG
*
42016 AAATTAATCCCATACAGAT
1 GAATTAATCCCATACAGAT
42035 ATCATAACGG
Statistics
Matches: 96, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
90 26 0.27
91 1 0.01
93 1 0.01
94 6 0.06
95 59 0.61
96 3 0.03
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.24
Consensus pattern (95 bp):
GAATTAATCCCATACAGATGTCAAAATGGGGAATTAATCCCATGCAGATGTCAGAACGAGGAATT
AATCCCATGCAGATGTAAGATCAGAACGGG
Found at i:42044 original size:30 final size:30
Alignment explanation
Indices: 41831--42047 Score: 204
Period size: 30 Copynumber: 7.1 Consensus size: 30
41821 TCAAAACTGA
* * *
41831 GAATTAATCCCATGCAGATGTCAAAATGGGG
1 GAATTAATCCCATACAGATGTCAGAA-CGGG
* *
41862 GAA-TAATCCCTTGCAGATGTCAGAA-GGG
1 GAATTAATCCCATACAGATGTCAGAACGGG
* *
41890 GAAATTAATCCCATGTAGATGTAAGATCAGAACGGG
1 G-AATTAATCCCA--TACA-G-ATG-TCAGAACGGG
** *
41926 GAATTAATCTTATACAGATGTCAGAATGGG
1 GAATTAATCCCATACAGATGTCAGAACGGG
* *
41956 GAATTAATCCCATGCAGATGTCAGAACGAG
1 GAATTAATCCCATACAGATGTCAGAACGGG
* *
41986 GAATTAATCCCTTGCAGATGTCAGAACGGG
1 GAATTAATCCCATACAGATGTCAGAACGGG
* * *
42016 AAATTAATCCCATACAGATATCATAACGGG
1 GAATTAATCCCATACAGATGTCAGAACGGG
42046 GA
1 GA
42048 CTAAGCCCAT
Statistics
Matches: 154, Mismatches: 24, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
28 4 0.03
29 2 0.01
30 115 0.75
31 5 0.03
32 3 0.02
33 4 0.03
34 2 0.01
35 15 0.10
36 4 0.03
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (30 bp):
GAATTAATCCCATACAGATGTCAGAACGGG
Found at i:42636 original size:23 final size:23
Alignment explanation
Indices: 42610--42662 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
42600 GGATCGTGTA
* *
42610 GATCAAAGTCAACGGGTCGGGTC
1 GATCAAAGTCAAAGGGTCAGGTC
*
42633 GATCAAAGTCAAAGGGTCAGGTT
1 GATCAAAGTCAAAGGGTCAGGTC
42656 GATCAAA
1 GATCAAA
42663 ATTAACAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (23 bp):
GATCAAAGTCAAAGGGTCAGGTC
Found at i:45585 original size:60 final size:59
Alignment explanation
Indices: 45507--45717 Score: 176
Period size: 60 Copynumber: 3.5 Consensus size: 59
45497 CCAACAGAAA
*
45507 CAGAACGGAG-ATATAATCTCATACGGATGTCAAAACAGGGAATTAATCCCATGCAGATGT
1 CAGAACGGAGAAT-TAATCTCATACAGATGTCAAAAC-GGGAATTAATCCCATGCAGATGT
* * * * * *
45567 CAGAACGGGGAATTAATCTCATGCATATGTCATAACGGGAATTCATCCCTTGCAGATGT
1 CAGAACGGAGAATTAATCTCATACAGATGTCAAAACGGGAATTAATCCCATGCAGATGT
* * * * * * * * *
45626 CAAAATGGAGAATTAATCCCATGCAAATGTCAGAACGAGGAGTTAAT-CCATTGTATATGT
1 CAGAACGGAGAATTAATCTCATACAGATGTCAAAACG-GGAATTAATCCCA-TGCAGATGT
* * * *
45686 TAGAATGGGGAATTAAT-TCCATACATATGTCA
1 CAGAACGGAGAATTAATCT-CATACAGATGTCA
45718 GAATGAGGAC
Statistics
Matches: 123, Mismatches: 24, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
59 54 0.44
60 67 0.54
61 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (59 bp):
CAGAACGGAGAATTAATCTCATACAGATGTCAAAACGGGAATTAATCCCATGCAGATGT
Found at i:45721 original size:30 final size:30
Alignment explanation
Indices: 45544--45722 Score: 173
Period size: 30 Copynumber: 6.0 Consensus size: 30
45534 TGTCAAAACA
* *
45544 GGGAATTAATCCCATGCAGATGTCAGAACG
1 GGGAATTAATCCCATGCATATGTCAGAATG
* * *
45574 GGGAATTAATCTCATGCATATGTCATAA-C
1 GGGAATTAATCCCATGCATATGTCAGAATG
* * * *
45603 GGGAATTCATCCCTTGCAGATGTCAAAATG
1 GGGAATTAATCCCATGCATATGTCAGAATG
* * *
45633 GAGAATTAATCCCATGCAAATGTCAGAACG
1 GGGAATTAATCCCATGCATATGTCAGAATG
* * * *
45663 AGGAGTTAAT-CCATTGTATATGTTAGAATG
1 GGGAATTAATCCCA-TGCATATGTCAGAATG
* *
45693 GGGAATTAATTCCATACATATGTCAGAATG
1 GGGAATTAATCCCATGCATATGTCAGAATG
45723 AGGACTAAGC
Statistics
Matches: 118, Mismatches: 28, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
29 26 0.22
30 89 0.75
31 3 0.03
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (30 bp):
GGGAATTAATCCCATGCATATGTCAGAATG
Found at i:45726 original size:60 final size:60
Alignment explanation
Indices: 45545--45726 Score: 199
Period size: 60 Copynumber: 3.0 Consensus size: 60
45535 GTCAAAACAG
* *
45545 GGAATTAATCCCA-TGCAGATGTCAGAACGGGGAATTAA-TCTCATGCATATGTCATAACG-
1 GGAATTAAT-CCATTGCAGATGTCAGAATGGGGAATTAATTC-CATGCATATGTCAGAACGA
* * * * * *
45604 GGAATTCATCCCTTGCAGATGTCAAAATGGAGAATTAATCCCATGCAAATGTCAGAACGA
1 GGAATTAATCCATTGCAGATGTCAGAATGGGGAATTAATTCCATGCATATGTCAGAACGA
* * * * * *
45664 GGAGTTAATCCATTGTATATGTTAGAATGGGGAATTAATTCCATACATATGTCAGAATGA
1 GGAATTAATCCATTGCAGATGTCAGAATGGGGAATTAATTCCATGCATATGTCAGAACGA
45724 GGA
1 GGA
45727 CTAAGCCTAT
Statistics
Matches: 100, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
58 2 0.02
59 46 0.46
60 52 0.52
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (60 bp):
GGAATTAATCCATTGCAGATGTCAGAATGGGGAATTAATTCCATGCATATGTCAGAACGA
Found at i:54968 original size:21 final size:21
Alignment explanation
Indices: 54944--55051 Score: 57
Period size: 21 Copynumber: 5.2 Consensus size: 21
54934 GATTCGCAAC
54944 GCGATAGTCGAAGTTCGCGTT
1 GCGATAGTCGAAGTTCGCGTT
* *
54965 GCGATTCATTCCAA-TT--CGTT
1 GCGA-T-AGTCGAAGTTCGCGTT
** *
54985 GCGACGGGCGAAGTTCGCGTT
1 GCGATAGTCGAAGTTCGCGTT
* *
55006 GCGATTCATTCCAA-TT--CGTT
1 GCGA-T-AGTCGAAGTTCGCGTT
* *
55026 GCGACAGGCGAAGTTCGCGTT
1 GCGATAGTCGAAGTTCGCGTT
55047 GCGAT
1 GCGAT
55052 TCATTCCAAT
Statistics
Matches: 60, Mismatches: 17, Indels: 20
0.62 0.18 0.21
Matches are distributed among these distances:
18 7 0.12
19 4 0.07
20 16 0.27
21 20 0.33
22 5 0.08
23 8 0.13
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.29
Consensus pattern (21 bp):
GCGATAGTCGAAGTTCGCGTT
Found at i:54997 original size:41 final size:41
Alignment explanation
Indices: 54952--55194 Score: 414
Period size: 41 Copynumber: 5.9 Consensus size: 41
54942 ACGCGATAGT
*
54952 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACGGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
54993 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
55034 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
* *
55075 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAAG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
* *
55116 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACATG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
* *
55157 CAAAGTTCGCGTTGCAATTCATTCCAAATTCGTTGCGA
1 CGAAGTTCGCGTTGCGATTCATTCC-AATTCGTTGCGA
55195 TAGTCCAAAT
Statistics
Matches: 194, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
41 182 0.94
42 12 0.06
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.30
Consensus pattern (41 bp):
CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
Found at i:55090 original size:21 final size:20
Alignment explanation
Indices: 54979--55132 Score: 70
Period size: 21 Copynumber: 7.5 Consensus size: 20
54969 TTCATTCCAA
*
54979 TTCG-TTGCGACGGGCGAAG
1 TTCGCTTGCGACAGGCGAAG
** *
54998 TTCGCGTTGCGATTCATTCCAA-
1 TTCGC-TTGCGA--CAGGCGAAG
55020 TTCG-TTGCGACAGGCGAAG
1 TTCGCTTGCGACAGGCGAAG
** *
55039 TTCGCGTTGCGATTCATTCCAA-
1 TTCGC-TTGCGA--CAGGCGAAG
55061 TTCG-TTGCGACAGGCGAAG
1 TTCGCTTGCGACAGGCGAAG
** *
55080 TTCGCATTGCGATTCATTCCAA-
1 TTCGC-TTGCGA--CAGGCGAAG
*
55102 TTCG-TTGCGACAAGCGAAG
1 TTCGCTTGCGACAGGCGAAG
55121 TTCGCATTGCGA
1 TTCGC-TTGCGA
55133 TTCATTCCAA
Statistics
Matches: 99, Mismatches: 19, Indels: 32
0.66 0.13 0.21
Matches are distributed among these distances:
18 15 0.15
19 16 0.16
20 18 0.18
21 24 0.24
22 12 0.12
23 14 0.14
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (20 bp):
TTCGCTTGCGACAGGCGAAG
Found at i:55965 original size:5 final size:5
Alignment explanation
Indices: 55955--55979 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
55945 CGTGCCGCCG
55955 CCGTC CCGTC CCGTC CCGTC CCGTC
1 CCGTC CCGTC CCGTC CCGTC CCGTC
55980 TCGGGTCGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.20, T:0.20
Consensus pattern (5 bp):
CCGTC
Found at i:56180 original size:20 final size:20
Alignment explanation
Indices: 56155--56265 Score: 77
Period size: 20 Copynumber: 5.5 Consensus size: 20
56145 TTCTTCGCCT
56155 ATCGCAACGAATTCGAATGA
1 ATCGCAACGAATTCGAATGA
**
56175 ATCGCAACGCGAACTTCGCCT--
1 ATCGCAA--CGAA-TTCGAATGA
* *
56196 ATCGCAACGATTTGGAATGA
1 ATCGCAACGAATTCGAATGA
*
56216 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAA-TTCGAATGA
* *
56237 ATCGCAACGATTTGGAATGA
1 ATCGCAACGAATTCGAATGA
56257 ATCGCAACG
1 ATCGCAACG
56266 CGAACTTCGA
Statistics
Matches: 69, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
18 9 0.13
19 6 0.09
20 23 0.33
21 14 0.20
22 7 0.10
23 10 0.14
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAATTCGAATGA
Found at i:56204 original size:41 final size:41
Alignment explanation
Indices: 56131--56282 Score: 241
Period size: 41 Copynumber: 3.6 Consensus size: 41
56121 AACTTCGCCT
* * *
56131 ATCGCAACGCGAACTTCTTCGCCTATCGCAACGAATTCGAATGA
1 ATCGCAACGCGAA---CTTCGACTATCGCAACGATTTGGAATGA
*
56175 ATCGCAACGCGAACTTCGCCTATCGCAACGATTTGGAATGA
1 ATCGCAACGCGAACTTCGACTATCGCAACGATTTGGAATGA
56216 ATCGCAACGCGAACTTCGACTATCGCAACGATTTGGAATGA
1 ATCGCAACGCGAACTTCGACTATCGCAACGATTTGGAATGA
56257 ATCGCAACGCGAACTTCGACTATCGC
1 ATCGCAACGCGAACTTCGACTATCGC
56283 GTTGCGAATC
Statistics
Matches: 105, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
41 92 0.88
44 13 0.12
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGATTTGGAATGA
Found at i:56242 original size:21 final size:21
Alignment explanation
Indices: 56110--56282 Score: 112
Period size: 21 Copynumber: 8.2 Consensus size: 21
56100 TTTGGAATGA
*
56110 ATCGCAACGCGAACTTCGCCT
1 ATCGCAACGCGAACTTCGACT
*
56131 ATCGCAACGCGAACTTCTTCGCCT
1 ATCGCAACGCGAA---CTTCGACT
*
56155 ATCGCAA--CGAA-TTCGAAT
1 ATCGCAACGCGAACTTCGACT
*
56173 GAATCGCAACGCGAACTTCGCCT
1 --ATCGCAACGCGAACTTCGACT
* * *
56196 ATCGCAA--CG-ATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
56214 GAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* * *
56237 ATCGCAA--CG-ATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
56255 GAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
56278 ATCGC
1 ATCGC
56283 GTTGCGAATC
Statistics
Matches: 117, Mismatches: 17, Indels: 36
0.69 0.10 0.21
Matches are distributed among these distances:
18 16 0.14
19 4 0.03
20 21 0.18
21 32 0.27
22 12 0.10
23 17 0.15
24 15 0.13
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:56704 original size:18 final size:17
Alignment explanation
Indices: 56666--56713 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
56656 AAACATGTTT
*
56666 CAGATTCTAATT-CTTA
1 CAGATTCCAATTCCTTA
56682 CAGATTCCAATTCCTTCA
1 CAGATTCCAATTCCTT-A
56700 CAGATTCCAATTCC
1 CAGATTCCAATTCC
56714 CTCATAAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 11 0.38
17 3 0.10
18 15 0.52
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (17 bp):
CAGATTCCAATTCCTTA
Found at i:68504 original size:2 final size:2
Alignment explanation
Indices: 68497--68521 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
68487 TTGATTGTTG
68497 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
68522 GAGAGAGAGA
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:68526 original size:2 final size:2
Alignment explanation
Indices: 68521--68547 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
68511 ATATATATAT
68521 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
68548 ACAGAGTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:72825 original size:2 final size:2
Alignment explanation
Indices: 72818--72853 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
72808 TTTCTTGTTG
72818 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
72854 GTTGACATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74718 original size:19 final size:19
Alignment explanation
Indices: 74694--74730 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
74684 TTTGCTCCTT
*
74694 TTTTTTCGATTCCTTCTTG
1 TTTTTTCGAATCCTTCTTG
*
74713 TTTTTTCTAATCCTTCTT
1 TTTTTTCGAATCCTTCTT
74731 TCTCTTGCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.08, C:0.22, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTTTCGAATCCTTCTTG
Found at i:77806 original size:122 final size:118
Alignment explanation
Indices: 77540--77828 Score: 357
Period size: 118 Copynumber: 2.4 Consensus size: 118
77530 GTAAACTACG
* * * *
77540 CATTTAATACATAAACTATCAATTTTGATATGTTTTAGTACATAAACTTTTAATTTTTTCAAAAT
1 CATTTAGTACATAAACTATCAATTTTGGTACGTTTTAGTACATAAACTTTTAATTTTTTCAAAAC
* *
77605 CATACATGTTTAGTTTTTGTTTCATTTTAGTACCCACCTTTAAAAACTTATCA
66 CATACACGTTTAGTTTTTATTTCATTTTAGTACCCACCTTTAAAAACTTATCA
* * * *
77658 CGTTTAGTACATAAACTATCAATTTTGGTCCGTTTTAGTACCTAAACTTTTAATTTTTTTAAAAC
1 CATTTAGTACATAAACTATCAATTTTGGTACGTTTTAGTACATAAACTTTTAATTTTTTCAAAAC
* *
77723 CATACCTAACGTTTAGTTTTTATTTCATTTTAGTAACTCACCTTTCAAAACTTGA-CA
66 CATA-C--ACGTTTAGTTTTTATTTCATTTTAGT-ACCCACCTTTAAAAACTT-ATCA
* * * ** *
77780 TATTTAGTACCTAAACTATCAGTTTTGGTTTGTTTTAATACAT-AACTTT
1 CATTTAGTACATAAACTATCAATTTTGGTACGTTTTAGTACATAAACTTT
77829 CAAAACAAAT
Statistics
Matches: 146, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
118 61 0.42
119 1 0.01
121 30 0.21
122 53 0.36
123 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.45
Consensus pattern (118 bp):
CATTTAGTACATAAACTATCAATTTTGGTACGTTTTAGTACATAAACTTTTAATTTTTTCAAAAC
CATACACGTTTAGTTTTTATTTCATTTTAGTACCCACCTTTAAAAACTTATCA
Found at i:81114 original size:20 final size:20
Alignment explanation
Indices: 81063--81103 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
81053 TCATCTTAAC
*
81063 ATAAAAT-ATATATTTATAA
1 ATAAAATAAAATATTTATAA
81082 ATAAAATAAAATATTTATAA
1 ATAAAATAAAATATTTATAA
81102 AT
1 AT
81104 TAAGTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAAATAAAATATTTATAA
Found at i:81145 original size:23 final size:23
Alignment explanation
Indices: 81104--81162 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 23
81094 ATTTATAAAT
*
81104 TAAGTTTAATA-AAATATATTTAA
1 TAAG-TTAATATAAAAATATTTAA
*
81127 TAAGTTAATATAAAAATATTTAC
1 TAAGTTAATATAAAAATATTTAA
81150 TAAAGTTAATATA
1 T-AAGTTAATATA
81163 TATAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 6 0.19
23 15 0.47
24 11 0.34
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (23 bp):
TAAGTTAATATAAAAATATTTAA
Found at i:81155 original size:24 final size:24
Alignment explanation
Indices: 81058--81162 Score: 83
Period size: 24 Copynumber: 4.3 Consensus size: 24
81048 TATTCTCATC
* *
81058 TTAACATAAAATATATATTTATAA-
1 TTAATATAAAATATAT-TTAATAAG
* *
81082 ATAAAATAAAATAT-TTATAAATTAAG
1 TTAATATAAAATATATT-T-AA-TAAG
*
81108 TTTA-ATAAAATATATTTAATAAG
1 TTAATATAAAATATATTTAATAAG
*
81131 TTAATATAAAA-ATATTTACTAAAG
1 TTAATATAAAATATATTTAAT-AAG
81155 TTAATATA
1 TTAATATA
81163 TATAAAATAT
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
22 1 0.01
23 17 0.25
24 32 0.48
25 13 0.19
26 4 0.06
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (24 bp):
TTAATATAAAATATATTTAATAAG
Found at i:81446 original size:15 final size:14
Alignment explanation
Indices: 81398--81450 Score: 65
Period size: 15 Copynumber: 3.9 Consensus size: 14
81388 TAGAATTTGG
*
81398 GGTTTAGAGTTTAA
1 GGTTTAGGGTTTAA
81412 --TTTAGGGTTTAA
1 GGTTTAGGGTTTAA
81424 GGTTTAGGGTTTAGA
1 GGTTTAGGGTTTA-A
*
81439 GTTTTAGGGTTT
1 GGTTTAGGGTTT
81451 GGAATTTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 11 0.32
14 11 0.32
15 12 0.35
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (14 bp):
GGTTTAGGGTTTAA
Found at i:82927 original size:3 final size:3
Alignment explanation
Indices: 82913--82954 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
82903 AACATGAATC
*
82913 AAG AAG AA- AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
82955 CATTTATCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:87196 original size:29 final size:29
Alignment explanation
Indices: 87154--87231 Score: 156
Period size: 29 Copynumber: 2.7 Consensus size: 29
87144 CGATTCTAAA
87154 AGTTGAATTCAGCTTCAAGTGCACATATT
1 AGTTGAATTCAGCTTCAAGTGCACATATT
87183 AGTTGAATTCAGCTTCAAGTGCACATATT
1 AGTTGAATTCAGCTTCAAGTGCACATATT
87212 AGTTGAATTCAGCTTCAAGT
1 AGTTGAATTCAGCTTCAAGT
87232 ATATAAACAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (29 bp):
AGTTGAATTCAGCTTCAAGTGCACATATT
Done.