Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007449.1 Hibiscus syriacus cultivar Beakdansim tig00020386_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: 96627
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:3606 original size:19 final size:19
Alignment explanation
Indices: 3577--3683 Score: 138
Period size: 19 Copynumber: 5.9 Consensus size: 19
3567 AGATGTACCG
3577 ATGCA-CGATGCACTCTCT
1 ATGCATCGATGCACTCTCT
3595 ATGCATCGATGCACTCTCT
1 ATGCATCGATGCACTCTCT
3614 A-GCATCGATGCACTCTCT
1 ATGCATCGATGCACTCTCT
3632 ATGCATCGATGCACTCTC-
1 ATGCATCGATGCACTCTCT
*
3650 -T-C-TCGATGCA-TGCATCG
1 ATGCATCGATGCACT-C-TCT
3667 ATGCATCGATGCACTCT
1 ATGCATCGATGCACTCT
3684 TGAACAAATA
Statistics
Matches: 80, Mismatches: 0, Indels: 17
0.82 0.00 0.18
Matches are distributed among these distances:
14 1 0.01
15 9 0.11
16 3 0.04
17 1 0.01
18 24 0.30
19 32 0.40
20 9 0.11
21 1 0.01
ACGTcount: A:0.21, C:0.32, G:0.18, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCACTCTCT
Found at i:3632 original size:37 final size:34
Alignment explanation
Indices: 3582--3683 Score: 143
Period size: 37 Copynumber: 2.9 Consensus size: 34
3572 TACCGATGCA
3582 CGATGCACTCTCTATGCATCGATGCACTCTCTAGCAT
1 CGATGCACTCTCTATGCATCGATGCACTCTCT--C-T
3619 CGATGCACTCTCTATGCATCGATGCACTCTCTCT
1 CGATGCACTCTCTATGCATCGATGCACTCTCTCT
*
3653 CGATGCA-TGCATCGATGCATCGATGCACTCT
1 CGATGCACT-C-TCTATGCATCGATGCACTCT
3684 TGAACAAATA
Statistics
Matches: 62, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
33 1 0.02
34 9 0.15
35 20 0.32
37 32 0.52
ACGTcount: A:0.21, C:0.32, G:0.18, T:0.29
Consensus pattern (34 bp):
CGATGCACTCTCTATGCATCGATGCACTCTCTCT
Found at i:9582 original size:20 final size:20
Alignment explanation
Indices: 9557--9625 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 20
9547 TTGTGCATAA
9557 TGCATCGATACACTATGAAG
1 TGCATCGATACACTATGAAG
* *
9577 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGAT--A-CACTATGAA-G
9601 TGCATCGATACA-TCATGAAG
1 TGCATCGATACACT-ATGAAG
9621 ATGCA
1 -TGCA
9626 CCAATTCACT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
20 11 0.28
21 9 0.23
22 2 0.05
23 7 0.18
24 10 0.26
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (20 bp):
TGCATCGATACACTATGAAG
Found at i:9620 original size:44 final size:44
Alignment explanation
Indices: 9557--9653 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
9547 TTGTGCATAA
* *
9557 TGCATCGATACACTATGAAG-TGCATCGATGCA-TCCCTTTGAATG
1 TGCATCGATACACTATGAAGATGCACCAATGCACT-CC-TTGAATG
*
9601 TGCATCGATACA-TCATGAAGATGCACCAATTCACTCCTTGAATG
1 TGCATCGATACACT-ATGAAGATGCACCAATGCACTCCTTGAATG
9645 TGCATCGAT
1 TGCATCGAT
9654 CCAAAATGCC
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
43 1 0.02
44 34 0.72
45 11 0.23
46 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (44 bp):
TGCATCGATACACTATGAAGATGCACCAATGCACTCCTTGAATG
Found at i:11925 original size:16 final size:16
Alignment explanation
Indices: 11904--11937 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
11894 ATTTAACAAA
11904 AAGGGGAAGAAGTGTT
1 AAGGGGAAGAAGTGTT
*
11920 AAGGGGGAGAAGTGTT
1 AAGGGGAAGAAGTGTT
11936 AA
1 AA
11938 AGTAAGGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.44, T:0.18
Consensus pattern (16 bp):
AAGGGGAAGAAGTGTT
Found at i:12407 original size:65 final size:64
Alignment explanation
Indices: 12288--12432 Score: 166
Period size: 65 Copynumber: 2.2 Consensus size: 64
12278 GTACTAGTCC
* * * *** * ***
12288 ATGCATCGATGCACTCTCAATTAAATTGAATTTCGAATGCATTTGGTGTACCGATGCACTCTCT
1 ATGCATCGATGCACTCTCAATCAAATAGAATATCGAATGCATTCAATGCACCGATGCACAAGCT
*
12352 ATGCATCGATGCACTCTTGAA-CAAATAGAAATATCGAATGCATTCAATGCACCGATGCACAAGC
1 ATGCATCGATGCACTC-TCAATCAAATAG-AATATCGAATGCATTCAATGCACCGATGCACAAGC
12416 T
64 T
12417 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
12433 AAGCTATTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
64 21 0.31
65 47 0.69
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (64 bp):
ATGCATCGATGCACTCTCAATCAAATAGAATATCGAATGCATTCAATGCACCGATGCACAAGCT
Found at i:14298 original size:17 final size:16
Alignment explanation
Indices: 14259--14326 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 16
14249 TGCAAAAAAA
*
14259 ATTAATTAAA-TACAAT
1 ATTAAATAAATTA-AAT
*
14275 ATTAAATAATTTAAAT
1 ATTAAATAAATTAAAT
14291 ACTTAAATAAATTAAAT
1 A-TTAAATAAATTAAAT
*
14308 ATTAAATATAATAAAAT
1 ATTAAATA-AATTAAAT
14325 AT
1 AT
14327 ACCTTAAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
16 19 0.42
17 26 0.58
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:15417 original size:47 final size:47
Alignment explanation
Indices: 15365--15457 Score: 159
Period size: 47 Copynumber: 2.0 Consensus size: 47
15355 TTTTTTGTCT
*
15365 TAATTTAATTAAAATAATATTAAATCTAAAATTGAAAAACTGTATTA
1 TAATTTAATTAAAATAATATTAAATCTAAAAATGAAAAACTGTATTA
**
15412 TAATTTAATTACGATAATATTAAATCTAAAAATGAAAAACTGTATT
1 TAATTTAATTAAAATAATATTAAATCTAAAAATGAAAAACTGTATT
15458 GTATTAATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (47 bp):
TAATTTAATTAAAATAATATTAAATCTAAAAATGAAAAACTGTATTA
Found at i:15909 original size:4 final size:4
Alignment explanation
Indices: 15900--15933 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
15890 AGTTTATCCT
15900 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
15934 ATTATTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:16252 original size:5 final size:5
Alignment explanation
Indices: 16242--16268 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
16232 TGAGATCAGG
16242 TTTCT TTTCT TTTCT TTTCT TTTCT TT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TT
16269 CGGTTTTGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:20209 original size:21 final size:21
Alignment explanation
Indices: 20184--20223 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
20174 TAACCGTTCT
*
20184 CCGACCGAATTAATTCGGTGA
1 CCGACCGAACTAATTCGGTGA
20205 CCGACCGAACTAATTCGGT
1 CCGACCGAACTAATTCGGT
20224 TCGGTCGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.23
Consensus pattern (21 bp):
CCGACCGAACTAATTCGGTGA
Found at i:30912 original size:86 final size:85
Alignment explanation
Indices: 30768--30940 Score: 301
Period size: 86 Copynumber: 2.0 Consensus size: 85
30758 AAGTAATAAT
* *
30768 TACTAACTATGAAAAATGCACAAAATAATAGGAAAAAATTCTAGAAATATATGAATGCATTAATG
1 TACTAACTATGAAAAACGCACAAAATAATAGGAAAAAATTCTAGAAAGATATGAATGCATTAATG
30833 CTAACCATTCAAAATGTTCC
66 CTAACCATTCAAAATGTTCC
* *
30853 TACTAACTATGAGAAACGCATAAAATAATAGGGAAAAAATTCTAGAAAGATATGAATGCATTAAT
1 TACTAACTATGAAAAACGCACAAAATAATA-GGAAAAAATTCTAGAAAGATATGAATGCATTAAT
30918 GCTAACCATTCAAAATGTTCC
65 GCTAACCATTCAAAATGTTCC
30939 TA
1 TA
30941 ATAGTCCCAT
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
85 27 0.33
86 56 0.67
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (85 bp):
TACTAACTATGAAAAACGCACAAAATAATAGGAAAAAATTCTAGAAAGATATGAATGCATTAATG
CTAACCATTCAAAATGTTCC
Found at i:37737 original size:8 final size:8
Alignment explanation
Indices: 37724--37766 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
37714 ATTAAAAGGA
37724 TATAAAAT
1 TATAAAAT
37732 TATAAAAT
1 TATAAAAT
* *
37740 TTTAAAAGA
1 TATAAAA-T
37749 TATAAAAT
1 TATAAAAT
*
37757 TATATAAT
1 TATAAAAT
37765 TA
1 TA
37767 ATAACGATGG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
8 23 0.79
9 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (8 bp):
TATAAAAT
Found at i:37750 original size:25 final size:26
Alignment explanation
Indices: 37715--37765 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
37705 ATATTAAAAA
37715 TTAAAAGGATATAAAATTATAAAATT
1 TTAAAAGGATATAAAATTATAAAATT
*
37741 TTAAAA-GATATAAAATTATATAATT
1 TTAAAAGGATATAAAATTATAAAATT
37766 AATAACGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (26 bp):
TTAAAAGGATATAAAATTATAAAATT
Found at i:39906 original size:19 final size:20
Alignment explanation
Indices: 39882--39944 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
39872 TAACAATTAT
39882 GAATTAT-TTATTAAAATAA
1 GAATTATATTATTAAAATAA
*
39901 GAATTATATTA-TAATATTAA
1 GAATTATATTATTAA-AATAA
* * *
39921 AAATTATAATATTAACATAA
1 GAATTATATTATTAAAATAA
39941 GAAT
1 GAAT
39945 ATTATATTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
19 10 0.29
20 22 0.63
21 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.40
Consensus pattern (20 bp):
GAATTATATTATTAAAATAA
Found at i:40023 original size:24 final size:24
Alignment explanation
Indices: 39978--40058 Score: 69
Period size: 24 Copynumber: 3.2 Consensus size: 24
39968 ATTATTAATA
39978 AATATATTATTAAATATTAATTAATTT
1 AATATATTATT---TATTAATTAATTT
* *
40005 AATATATTATTTATGAATTTAA-TA
1 AATATATTATTTATTAA-TTAATTT
40029 AATATAATTAATTTATTAA-TAATTT
1 AATAT-ATT-ATTTATTAATTAATTT
40054 -ATATA
1 AATATA
40059 CTTTTAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
23 1 0.02
24 18 0.39
25 8 0.17
26 8 0.17
27 11 0.24
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (24 bp):
AATATATTATTTATTAATTAATTT
Found at i:40026 original size:29 final size:27
Alignment explanation
Indices: 39974--40036 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
39964 TGAAATTATT
*
39974 AATA-AATATATTATTAAATATTAATT
1 AATATAATATATTATTAAATATTAATA
*
40000 AATTTAATATATTATTTATGAAT-TTAATA
1 AATATAATATATTA-TTA--AATATTAATA
40029 AATATAAT
1 AATATAAT
40037 TAATTTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 3 0.10
27 9 0.30
28 3 0.10
29 12 0.40
30 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
AATATAATATATTATTAAATATTAATA
Found at i:40101 original size:23 final size:23
Alignment explanation
Indices: 40083--40150 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
40073 ATATAATACC
40083 ACATATTATTATAATATAATTAA
1 ACATATTATTATAATATAATTAA
* *
40106 ATATATTATTATAACACTAA--AA
1 ACATATTATTATAATA-TAATTAA
* *
40128 ACATAGTATTATATATATTATTA
1 ACATATTATTATA-ATATAATTA
40151 TATTATTACT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
22 15 0.43
23 16 0.46
24 4 0.11
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (23 bp):
ACATATTATTATAATATAATTAA
Found at i:41506 original size:23 final size:22
Alignment explanation
Indices: 41461--41506 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
41451 TTATCATTAA
*
41461 TTTCATATTATTTTATATTATT
1 TTTCATATTATTTTATATAATT
41483 TTTCATCATTAATTTTA-ATAATT
1 TTTCAT-ATT-ATTTTATATAATT
41506 T
1 T
41507 GATACTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 9 0.43
24 6 0.29
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTCATATTATTTTATATAATT
Found at i:41776 original size:19 final size:18
Alignment explanation
Indices: 41752--41813 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
41742 GAATAGCTAG
41752 TTAAAATTAAGCATCAAAA
1 TTAAAATTAAG-ATCAAAA
*
41771 TTAAAATTAATGATCAATA
1 TTAAAATTAA-GATCAAAA
* *
41790 CTAAAATTTACGTATCAAAA
1 TTAAAA-TTAAG-ATCAAAA
41810 TTAA
1 TTAA
41814 TTTTATCATG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 22 0.63
20 13 0.37
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (18 bp):
TTAAAATTAAGATCAAAA
Found at i:42558 original size:18 final size:16
Alignment explanation
Indices: 42534--42578 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
42524 TAAATTTTAA
42534 TTTTAAATAAATTAATT
1 TTTTAAATAAATT-ATT
*
42551 TATTTAAATTAATTATT
1 T-TTTAAATAAATTATT
*
42568 TTTTAATTAAA
1 TTTTAAATAAA
42579 AAATTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 8 0.33
17 5 0.21
18 11 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTAAATAAATTATT
Found at i:43327 original size:54 final size:54
Alignment explanation
Indices: 43245--43361 Score: 227
Period size: 54 Copynumber: 2.2 Consensus size: 54
43235 TCACGAGTTA
43245 GGTCATTTAATATCTTGTTTTTAAATGATAAATTCTTTTTGTATCAATAATTTT
1 GGTCATTTAATATCTTGTTTTTAAATGATAAATTCTTTTTGTATCAATAATTTT
43299 GGTCATTTAATATCTTGTTTTTAAATGATAAATTCTTTTTGTATCAATAATTTT
1 GGTCATTTAATATCTTGTTTTTAAATGATAAATTCTTTTTGTATCAATAATTTT
43353 -GTCATTTAA
1 GGTCATTTAA
43362 GGGTGTCAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 9 0.14
54 54 0.86
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (54 bp):
GGTCATTTAATATCTTGTTTTTAAATGATAAATTCTTTTTGTATCAATAATTTT
Found at i:43854 original size:9 final size:9
Alignment explanation
Indices: 43832--43872 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
43822 TAACTTTTTT
43832 TAAAAACTA
1 TAAAAACTA
43841 -AAAAATCTA
1 TAAAAA-CTA
43850 TAAAAAC-A
1 TAAAAACTA
*
43858 TAAAAAATA
1 TAAAAACTA
43867 TAAAAA
1 TAAAAA
43873 TTAAAATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
8 12 0.43
9 11 0.39
10 5 0.18
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (9 bp):
TAAAAACTA
Found at i:46100 original size:122 final size:122
Alignment explanation
Indices: 45934--46176 Score: 450
Period size: 122 Copynumber: 2.0 Consensus size: 122
45924 TAGGTAAGTA
*
45934 GACTTTTAAAATTTTAGGAACGAACCTTATAAAATTCTAAGATGATGAAAAATTATTTTTAATAT
1 GACTTTTAAAATTTTAGAAACGAACCTTATAAAATTCTAAGATGATGAAAAATTATTTTTAATAT
45999 GACAATTTTAAATTTTCAGAGGATGACGGTCTCCACTCGTCTCCCCACCCAGTCCAG
66 GACAATTTTAAATTTTCAGAGGATGACGGTCTCCACTCGTCTCCCCACCCAGTCCAG
* *
46056 GACTTTTAAAATTTTAGAAATGAACCTTATAAAATTCTAGGATGATGAAAAATTATTTTTAATAT
1 GACTTTTAAAATTTTAGAAACGAACCTTATAAAATTCTAAGATGATGAAAAATTATTTTTAATAT
*
46121 GACAATTTTAAATTTTCAGAGGATGACGGTCTCCACTCGTCTCCCCATCCAGTCCA
66 GACAATTTTAAATTTTCAGAGGATGACGGTCTCCACTCGTCTCCCCACCCAGTCCA
46177 TCTTCGGATG
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
122 117 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (122 bp):
GACTTTTAAAATTTTAGAAACGAACCTTATAAAATTCTAAGATGATGAAAAATTATTTTTAATAT
GACAATTTTAAATTTTCAGAGGATGACGGTCTCCACTCGTCTCCCCACCCAGTCCAG
Found at i:48931 original size:31 final size:31
Alignment explanation
Indices: 48877--48943 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
48867 ATGGTTGAAA
** * *
48877 GACTAAAATCGAATGGATTGATAATATTAGG
1 GACTAAAATCGAACAGATCGATAACATTAGG
* *
48908 GACTAAAATCGAACATATCGATAACGTTAGG
1 GACTAAAATCGAACAGATCGATAACATTAGG
48939 GACTA
1 GACTA
48944 TTCCCCCTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (31 bp):
GACTAAAATCGAACAGATCGATAACATTAGG
Found at i:49307 original size:23 final size:23
Alignment explanation
Indices: 49259--49308 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
49249 ATCATGACTA
*
49259 TTCATGAAAAATAATTAAGTCTT
1 TTCATGAAAAATAATTAAGTCAT
* **
49282 TTCATGAAAAATAGTTATTTCAT
1 TTCATGAAAAATAATTAAGTCAT
49305 TTCA
1 TTCA
49309 CCCCAAAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (23 bp):
TTCATGAAAAATAATTAAGTCAT
Found at i:51600 original size:18 final size:18
Alignment explanation
Indices: 51577--51622 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
51567 ACCGGTCACA
51577 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
51595 ACCCGACCCGACCCTTTG
1 ACCCGACCCGACCCGTTG
*
51613 ACCTGACCCG
1 ACCCGACCCG
51623 TTGACCGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.17, C:0.50, G:0.20, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:51620 original size:13 final size:13
Alignment explanation
Indices: 51599--51643 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
51589 CCGTTGACCC
* *
51599 GACCCGACCCTTT
1 GACCTGACCCGTT
51612 GACCTGACCCGTT
1 GACCTGACCCGTT
51625 GACCGTTGACCCGTT
1 GACC--TGACCCGTT
51640 GACC
1 GACC
51644 GTCGTTGACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 15 0.54
15 13 0.46
ACGTcount: A:0.16, C:0.40, G:0.22, T:0.22
Consensus pattern (13 bp):
GACCTGACCCGTT
Found at i:51636 original size:15 final size:15
Alignment explanation
Indices: 51604--51645 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
51594 GACCCGACCC
*
51604 GACCCTTTGACC--T
1 GACCCGTTGACCGTT
51617 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
51632 GACCCGTTGACCGT
1 GACCCGTTGACCGT
51646 CGTTGACCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 11 0.42
15 15 0.58
ACGTcount: A:0.14, C:0.36, G:0.24, T:0.26
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:51651 original size:10 final size:8
Alignment explanation
Indices: 51616--51663 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 8
51606 CCCTTTGACC
51616 TGACCCGT
1 TGACCCGT
51624 TGA-CCGT
1 TGACCCGT
51631 TGACCCGT
1 TGACCCGT
51639 TGACCGTCGT
1 TGACC--CGT
51649 TGACCACTGT
1 TGACC-C-GT
51659 TGACC
1 TGACC
51664 AAAACTTTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
7 7 0.20
8 12 0.34
9 1 0.03
10 15 0.43
ACGTcount: A:0.15, C:0.33, G:0.25, T:0.27
Consensus pattern (8 bp):
TGACCCGT
Found at i:52956 original size:18 final size:18
Alignment explanation
Indices: 52930--52964 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52920 TCGAAAGGAC
*
52930 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
52948 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
52965 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:55262 original size:182 final size:181
Alignment explanation
Indices: 54955--55317 Score: 701
Period size: 182 Copynumber: 2.0 Consensus size: 181
54945 AAGGAAATTA
54955 TATGGATTTCCATTTATCTACATGTCATGTAGCATCATCTGGTAGTTAGTATTACTGAGCTTTCC
1 TATGGATTTCCATTTATCTACATGTCATGTAGCATCATCTGGTAGTTAGTATTACTGAGCTTTCC
55020 AAAGCTCACTCTATACTCACCTTTTCAGGTTAAAACAATTGTACCAGTGCATCTATCGACTTCAG
66 AAAGCTCACTCTATACTCACCTTTTCAGGTTAAAACAATTGTACCAGTGCATCTATCGACTTCAG
55085 TAAAGGAGTTCTTCCGGCGTGGTTGCAGAGTATGGTAC-TGTGATTAGGGG
131 TAAAGGAGTTCTTCCGGCGTGGTTGCAGAGTATGGTACTTGTGATTAGGGG
55135 TATGGATTTCCATTTATCTACATGTCATGTAGCATCATCTGGTAGTTATGTATTACTGAGCTTTC
1 TATGGATTTCCATTTATCTACATGTCATGTAGCATCATCTGGTAGTTA-GTATTACTGAGCTTTC
55200 CAAAGCTCACTCTATTACTCACCTTTTCAGGTTAAAACAATTGTACCAGTGCATCTATCGACTTC
65 CAAAGCTCACTCTA-TACTCACCTTTTCAGGTTAAAACAATTGTACCAGTGCATCTATCGACTTC
55265 AGTAAAGGAGTTCTTCCGGCGTGGTTGCAGAGTATGGTACTTGTGATTAGGGG
129 AGTAAAGGAGTTCTTCCGGCGTGGTTGCAGAGTATGGTACTTGTGATTAGGGG
55318 GCATGTAATT
Statistics
Matches: 180, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
180 48 0.27
181 30 0.17
182 90 0.50
183 12 0.07
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (181 bp):
TATGGATTTCCATTTATCTACATGTCATGTAGCATCATCTGGTAGTTAGTATTACTGAGCTTTCC
AAAGCTCACTCTATACTCACCTTTTCAGGTTAAAACAATTGTACCAGTGCATCTATCGACTTCAG
TAAAGGAGTTCTTCCGGCGTGGTTGCAGAGTATGGTACTTGTGATTAGGGG
Found at i:60534 original size:23 final size:26
Alignment explanation
Indices: 60471--60532 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
60461 TAATATGTTT
* *
60471 TCACCTCCCTATAATTTTATAAATTCA
1 TCACCT-CTTATAATTTTAAAAATTCA
*
60498 TCATCTCTTATAATTTTAAAAATTCA
1 TCACCTCTTATAATTTTAAAAATTCA
60524 TC-CCTCTTA
1 TCACCTCTTA
60533 ATATAAGTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 6 0.19
26 20 0.65
27 5 0.16
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (26 bp):
TCACCTCTTATAATTTTAAAAATTCA
Found at i:67123 original size:92 final size:92
Alignment explanation
Indices: 66965--67147 Score: 330
Period size: 92 Copynumber: 2.0 Consensus size: 92
66955 AGTAACAAAG
* *
66965 AAAAACGATGATGTTATTGATGCACACCTAAAGCAATAATCGTATCTAGAAGCATTATCAATCTT
1 AAAAACAATGATGTTATTGATGCACACCTAAAGCAATAATCGTATCTAGAAGCATTATCAACCTT
*
67030 GGTAGCAAACATTTCCTCAAATCCACA
66 GGTAGCAAAAATTTCCTCAAATCCACA
*
67057 AAAAACAATGATGTTATTGATGCATACCTAAAGCAATAATCGTATCTAGAAGCATTATCAACCTT
1 AAAAACAATGATGTTATTGATGCACACCTAAAGCAATAATCGTATCTAGAAGCATTATCAACCTT
67122 GGTAGCAAAAATTTCCTCAAATCCAC
66 GGTAGCAAAAATTTCCTCAAATCCAC
67148 CATCTCTGGA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 87 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (92 bp):
AAAAACAATGATGTTATTGATGCACACCTAAAGCAATAATCGTATCTAGAAGCATTATCAACCTT
GGTAGCAAAAATTTCCTCAAATCCACA
Found at i:70151 original size:22 final size:22
Alignment explanation
Indices: 70124--70174 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
70114 GACGCGACAT
70124 TTGACATAATTAAACTTGATAG
1 TTGACATAATTAAACTTGATAG
70146 TTGACATAATTAAACTTGATAG
1 TTGACATAATTAAACTTGATAG
70168 TTGACAT
1 TTGACAT
70175 CCATATTAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
TTGACATAATTAAACTTGATAG
Found at i:70625 original size:43 final size:44
Alignment explanation
Indices: 70545--70647 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 44
70535 ACCCTCATTC
* *
70545 TTTCATCTTTATAATT-AGGTCCTTAAATTTTTAAATCTTA-TT
1 TTTCATCTTTATAATTGAGGTCCTTAAATTATTAAATCTAACTT
* * *
70587 TTTCACCTTTATAATTGTGGTCC-TAATATTATTCAATCTAACTT
1 TTTCATCTTTATAATTGAGGTCCTTAA-ATTATTAAATCTAACTT
70631 TTT-ATCTTTATAATTGA
1 TTTCATCTTTATAATTGA
70648 AATCTCTAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
42 18 0.35
43 28 0.55
44 5 0.10
ACGTcount: A:0.28, C:0.14, G:0.06, T:0.52
Consensus pattern (44 bp):
TTTCATCTTTATAATTGAGGTCCTTAAATTATTAAATCTAACTT
Found at i:70701 original size:44 final size:45
Alignment explanation
Indices: 70653--71015 Score: 243
Period size: 44 Copynumber: 8.2 Consensus size: 45
70643 ATTGAAATCT
* *
70653 CTAATTTTTTTTCAATC-CCTTTTTTACCTTTATAATTGAGGCCC
1 CTAATTTTTTTTCAATCTCCATTTCTACCTTTATAATTGAGGCCC
* * **
70697 CTAA--TTTTGT-AATCT-CACTTT-TAACTTTATAATTGAGGCTT
1 CTAATTTTTTTTCAATCTCCA-TTTCTACCTTTATAATTGAGGCCC
* * *
70738 TTAAGTTTTTTTTCAATCT-CACTTTCTACCTTT-TCAATTAAGGCCT
1 CTAA-TTTTTTTTCAATCTCCA-TTTCTACCTTTAT-AATTGAGGCCC
* * *
70784 CTATTTTTTTTTTCAATCTCAATTTCTACCTTTATAATTGAAGCCC
1 CTA-ATTTTTTTTCAATCTCCATTTCTACCTTTATAATTGAGGCCC
* * *
70830 CTAA--TTTTTT-AATCTCACTTTTTTTAACTTTATAATTGAGGCCC
1 CTAATTTTTTTTCAATCTC-C-ATTTCTACCTTTATAATTGAGGCCC
* ** ** * * *
70874 TTAAGCTTTTTT-AATCTCGTTTTCTAACTTTCTAATTGAGGTCC
1 CTAATTTTTTTTCAATCTCCATTTCTACCTTTATAATTGAGGCCC
*** * * *
70918 CTAA-GAATTTTCGATCT-CAATTATACCTTTATAATTGAGGCCC
1 CTAATTTTTTTTCAATCTCCATTTCTACCTTTATAATTGAGGCCC
* * * * *
70961 ATATTTTTTTTTCAATCT-CAGTTTCTACCTTTATAATTAAGGTCT
1 CTAATTTTTTTTCAATCTCCA-TTTCTACCTTTATAATTGAGGCCC
71006 CTAATTTTTT
1 CTAATTTTTT
71016 ACAATTTCAT
Statistics
Matches: 249, Mismatches: 52, Indels: 35
0.74 0.15 0.10
Matches are distributed among these distances:
41 25 0.10
42 14 0.06
43 31 0.12
44 73 0.29
45 39 0.16
46 65 0.26
47 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (45 bp):
CTAATTTTTTTTCAATCTCCATTTCTACCTTTATAATTGAGGCCC
Found at i:85121 original size:95 final size:94
Alignment explanation
Indices: 84953--85132 Score: 238
Period size: 95 Copynumber: 1.9 Consensus size: 94
84943 TATAATATTA
** **
84953 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGCTAAACTCCCCGTCTTTATTTA
1 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGCTAAACTCCCCGGATTTATGGA
* *
85018 TAATATTCAACTAGCCTGATAAAGGTGAT
66 TAAGATTCAACTAACCTGATAAAGGTGAT
* *
85047 TATACTATACAATAAAGCTTGAGTTGTTCCTCTA-AGGCAATTGGTTAAACGT-CCCGGATTTAT
1 TATA-TATACAATAAAGCTTGAGTTGTCCCTCTAGA-GCAATTGGCTAAAC-TCCCCGGATTTAT
*
85110 GGATAAGATTCAGCTAACCTGAT
63 GGATAAGATTCAACTAACCTGAT
85133 GATAAAGGTG
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
94 5 0.07
95 68 0.92
96 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGCTAAACTCCCCGGATTTATGGA
TAAGATTCAACTAACCTGATAAAGGTGAT
Found at i:96382 original size:240 final size:240
Alignment explanation
Indices: 95947--96460 Score: 816
Period size: 240 Copynumber: 2.1 Consensus size: 240
95937 TTTGCGGACA
* *
95947 ATATTCAAGTCAAGGCTCAACTTCAAAACGAAGGGGCCATCCACGATTTTAACTTCACGACGAAG
1 ATATTCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTTAACTTCACGAAGAAG
96012 GATATCGTGCCAACTCTAGATTGGATTTCAACTTCATGATGAAGGATATCCAATTCACAACTCAA
66 GATATCGTGCCAACTCTAGATTGGATTTCAACTTCATGATGAAGGATATCCAATTCACAACTCAA
* * ** * *
96077 CTTCATGGCGAAGGGGCTTCCCAATTTCATTTGGAGCCAATTTCAACTTGACGGCGAAGGATATT
131 CTTCACGGCGAAGAGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTTCACGACGAAGGATATT
*
96142 GGACTCGAAATAATACAAGCTTGGATTTCAACTTCACGACGAAGG
196 GGACTCGAAACAATACAAGCTTGGATTTCAACTTCACGACGAAGG
* *
96187 ATATTCAAGTCAAGGCTTAACTTCACAATGAAGGGGCCATCCACGATTTTAACTTCACGAAGAAG
1 ATATTCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTTAACTTCACGAAGAAG
* *
96252 GATATCGTGTCAAGTCTAGATTGGATTT-AACCTTCATGATGAAGGATATCCAATTCA-AAGCTC
66 GATATCGTGCCAACTCTAGATTGGATTTCAA-CTTCATGATGAAGGATATCCAATTCACAA-CTC
* * * *
96315 AACTTCACGGTGAAGAGGCTTTCCAATTTCATTCAGAGCCAATTTCAACTTCACGATGAATGATA
129 AACTTCACGGCGAAGAGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTTCACGACGAAGGATA
* *
96380 TTGGACTCGAAACAATACAAGCTTGGATTTCAACTTCACGATGAATG
194 TTGGACTCGAAACAATACAAGCTTGGATTTCAACTTCACGACGAAGG
*
96427 ATATTCAACTCAAGGCTCAACTTCACAACGAAGG
1 ATATTCAAGTCAAGGCTCAACTTCACAACGAAGG
96461 ATATTCAAGT
Statistics
Matches: 250, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
239 4 0.02
240 246 0.98
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (240 bp):
ATATTCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTTAACTTCACGAAGAAG
GATATCGTGCCAACTCTAGATTGGATTTCAACTTCATGATGAAGGATATCCAATTCACAACTCAA
CTTCACGGCGAAGAGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTTCACGACGAAGGATATT
GGACTCGAAACAATACAAGCTTGGATTTCAACTTCACGACGAAGG
Found at i:96452 original size:34 final size:34
Alignment explanation
Indices: 96409--96494 Score: 136
Period size: 34 Copynumber: 2.5 Consensus size: 34
96399 AGCTTGGATT
* * *
96409 TCAACTTCACGATGAATGATATTCAACTCAAGGC
1 TCAACTTCACAACGAAGGATATTCAACTCAAGGC
*
96443 TCAACTTCACAACGAAGGATATTCAAGTCAAGGC
1 TCAACTTCACAACGAAGGATATTCAACTCAAGGC
96477 TCAACTTCACAACGAAGG
1 TCAACTTCACAACGAAGG
96495 GGTCATCCAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.22
Consensus pattern (34 bp):
TCAACTTCACAACGAAGGATATTCAACTCAAGGC
Done.