Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004326.1 Hibiscus syriacus cultivar Beakdansim tig00009484_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: 97770
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4064 original size:15 final size:15
Alignment explanation
Indices: 4046--4087 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
4036 TAGTTAAAAT
4046 TTTATATATTTTATA
1 TTTATATATTTTATA
* *
4061 TTTAAATA-TTAATA
1 TTTATATATTTTATA
4075 TTTATA-ATTTTAT
1 TTTATATATTTTAT
4088 GAGATAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
13 1 0.05
14 14 0.64
15 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATATATTTTATA
Found at i:4095 original size:29 final size:27
Alignment explanation
Indices: 4046--4103 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 27
4036 TAGTTAAAAT
**
4046 TTTATATATTTTATATTTAAATATTAATA
1 TTTATATATTTTATAGATAAA-A-TAATA
4075 TTTATA-ATTTTATGAGATAAAATAATA
1 TTTATATATTTTAT-AGATAAAATAATA
4102 TT
1 TT
4104 AATAGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 7 0.27
28 8 0.31
29 11 0.42
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (27 bp):
TTTATATATTTTATAGATAAAATAATA
Found at i:6118 original size:30 final size:30
Alignment explanation
Indices: 6084--6170 Score: 124
Period size: 30 Copynumber: 3.0 Consensus size: 30
6074 TTATATGAGT
6084 TATGTGATAAAGGTATGGAAATGATATGTC
1 TATGTGATAAAGGTATGGAAATGATATGTC
*
6114 TATGTGATAAAGGTATGGAAATGATATGCC
1 TATGTGATAAAGGTATGGAAATGATATGTC
* * *
6144 AATGTGA-CAAGGTAT-GAAATAATATGT
1 TATGTGATAAAGGTATGGAAATGATATGT
6171 TTACGTAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
28 10 0.19
29 7 0.13
30 35 0.67
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (30 bp):
TATGTGATAAAGGTATGGAAATGATATGTC
Found at i:6423 original size:23 final size:23
Alignment explanation
Indices: 6389--6456 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
6379 ATTATTATAT
6389 GGCACTAC-GGTGCAATTCTACGC
1 GGCACT-CTGGTGCAATTCTACGC
* **
6412 GGCACTCTGGTGTAATTCTACAT
1 GGCACTCTGGTGCAATTCTACGC
*
6435 GGCACT-TCGGTGCAATTATACG
1 GGCACTCT-GGTGCAATTCTACG
6457 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
22 2 0.05
23 35 0.95
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (23 bp):
GGCACTCTGGTGCAATTCTACGC
Found at i:12938 original size:30 final size:30
Alignment explanation
Indices: 12904--12972 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
12894 TTATATGAGT
* * *
12904 TATGTGATAAATGTATGGAAATGATATGTC
1 TATGTGATAAAGGTATGAAAATAATATGTC
*
12934 TATGTGATAAAGGTATGAAAATAATATGTT
1 TATGTGATAAAGGTATGAAAATAATATGTC
*
12964 TACGTGATA
1 TATGTGATA
12973 CAAATTATGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (30 bp):
TATGTGATAAAGGTATGAAAATAATATGTC
Found at i:13209 original size:23 final size:23
Alignment explanation
Indices: 13179--13246 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
13169 ATTATTTTAT
13179 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
13202 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
13225 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
13247 AGCTGTGTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:13952 original size:40 final size:40
Alignment explanation
Indices: 13897--13977 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
13887 CAAAATTCTT
13897 AGAGTAATATTACAATAAAATAATCTTATTCCCAAATATA
1 AGAGTAATATTACAATAAAATAATCTTATTCCCAAATATA
* * *
13937 AGAGTAATATTACAATACAGTAATCTTATTCTCAAATATA
1 AGAGTAATATTACAATAAAATAATCTTATTCCCAAATATA
13977 A
1 A
13978 TCTTACATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (40 bp):
AGAGTAATATTACAATAAAATAATCTTATTCCCAAATATA
Found at i:15006 original size:19 final size:19
Alignment explanation
Indices: 14982--15032 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
14972 TAATTAGTGT
*
14982 ATCGATGCACTCCTCATGC
1 ATCGATGCACCCCTCATGC
15001 ATCGATGCACCCCTCATGC
1 ATCGATGCACCCCTCATGC
15020 ATCGATGCACCCC
1 ATCGATGCACCCC
15033 CTTAAGATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.22, C:0.41, G:0.16, T:0.22
Consensus pattern (19 bp):
ATCGATGCACCCCTCATGC
Found at i:15697 original size:18 final size:18
Alignment explanation
Indices: 15674--15708 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
15664 AGGGATTATC
*
15674 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
15692 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
15709 ATATTCAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:16119 original size:20 final size:20
Alignment explanation
Indices: 16094--16144 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
16084 TAACTAATAA
16094 AGTATGTATGTTGATTTTGT
1 AGTATGTATGTTGATTTTGT
16114 AGTATGTATGTTGATTTTGT
1 AGTATGTATGTTGATTTTGT
16134 A-TA-GTATGTTG
1 AGTATGTATGTTG
16145 GCATATAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.26
19 2 0.06
20 21 0.68
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (20 bp):
AGTATGTATGTTGATTTTGT
Found at i:17960 original size:16 final size:16
Alignment explanation
Indices: 17936--17973 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
17926 TAAAAATTTT
17936 AATTAATGTTTT-ATTA
1 AATT-ATGTTTTAATTA
17952 ATATTATGTTTTAATTA
1 A-ATTATGTTTTAATTA
17969 AATTA
1 AATTA
17974 CATTTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (16 bp):
AATTATGTTTTAATTA
Found at i:30387 original size:21 final size:21
Alignment explanation
Indices: 30361--30401 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
30351 GGAAGTCAAG
30361 AGTTTAGCAGTGATATCAGTT
1 AGTTTAGCAGTGATATCAGTT
30382 AGTTTAGCAGTGATATCAGT
1 AGTTTAGCAGTGATATCAGT
30402 GATATAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (21 bp):
AGTTTAGCAGTGATATCAGTT
Found at i:51639 original size:18 final size:19
Alignment explanation
Indices: 51616--51652 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
51606 GTCGTTGTAG
51616 GTTATAAAAATAAA-AAAA
1 GTTATAAAAATAAAGAAAA
*
51634 GTTATAAAATTAAAGAAAA
1 GTTATAAAAATAAAGAAAA
51653 AAGAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (19 bp):
GTTATAAAAATAAAGAAAA
Found at i:52480 original size:10 final size:10
Alignment explanation
Indices: 52465--52545 Score: 56
Period size: 10 Copynumber: 7.5 Consensus size: 10
52455 CATTTAAATG
52465 ATAAACGAAC
1 ATAAACGAAC
52475 ATAAACGAACAC
1 ATAAACG-A-AC
*
52487 AAACGAACGAAC
1 ATA--AACGAAC
52499 ATAAACGAAC
1 ATAAACGAAC
*
52509 TTAATAAATGAAC
1 ---ATAAACGAAC
52522 ATAAACGAAC
1 ATAAACGAAC
* *
52532 A-ACACAAAC
1 ATAAACGAAC
52541 ATAAA
1 ATAAA
52546 AAACAAACTT
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
9 7 0.12
10 26 0.46
11 1 0.02
12 8 0.14
13 10 0.18
14 4 0.07
ACGTcount: A:0.60, C:0.20, G:0.09, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:52497 original size:14 final size:14
Alignment explanation
Indices: 52478--52508 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
52468 AACGAACATA
52478 AACGAACACAAACG
1 AACGAACACAAACG
*
52492 AACGAACATAAACG
1 AACGAACACAAACG
52506 AAC
1 AAC
52509 TTAATAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.26, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:52690 original size:9 final size:10
Alignment explanation
Indices: 52662--52703 Score: 52
Period size: 9 Copynumber: 4.3 Consensus size: 10
52652 GAATATGACA
52662 AAACATATAT
1 AAACATATAT
52672 AAATCATATAT
1 AAA-CATATAT
52683 AAAC-TATAT
1 AAACATATAT
*
52692 GAACATA-AT
1 AAACATATAT
52701 AAA
1 AAA
52704 GTTTTAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 12 0.43
10 6 0.21
11 10 0.36
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (10 bp):
AAACATATAT
Found at i:52814 original size:14 final size:14
Alignment explanation
Indices: 52794--52853 Score: 74
Period size: 14 Copynumber: 4.6 Consensus size: 14
52784 GCACTCTTTT
*
52794 CGAACATAAATAAA
1 CGAACATAAATGAA
*
52808 GGAACATAAAT---
1 CGAACATAAATGAA
52819 -GAACATAAATGAA
1 CGAACATAAATGAA
52832 CGAACATAAATGAA
1 CGAACATAAATGAA
52846 CGAACATA
1 CGAACATA
52854 TAATCGAACT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
10 10 0.24
14 31 0.76
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.15
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:52824 original size:24 final size:24
Alignment explanation
Indices: 52795--52846 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
52785 CACTCTTTTC
*
52795 GAACATAAATAAAGGAACATAAAT
1 GAACATAAATAAACGAACATAAAT
*
52819 GAACATAAATGAACGAACATAAAT
1 GAACATAAATAAACGAACATAAAT
52843 GAAC
1 GAAC
52847 GAACATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.60, C:0.12, G:0.13, T:0.15
Consensus pattern (24 bp):
GAACATAAATAAACGAACATAAAT
Found at i:52846 original size:10 final size:10
Alignment explanation
Indices: 52803--52832 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
52793 TCGAACATAA
*
52803 ATAAAGGAAC
1 ATAAATGAAC
52813 ATAAATGAAC
1 ATAAATGAAC
52823 ATAAATGAAC
1 ATAAATGAAC
52833 GAACATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.60, C:0.10, G:0.13, T:0.17
Consensus pattern (10 bp):
ATAAATGAAC
Found at i:53658 original size:34 final size:32
Alignment explanation
Indices: 53603--53706 Score: 100
Period size: 33 Copynumber: 3.1 Consensus size: 32
53593 GTGGTAAGAA
* * * *
53603 ATTTATTTTTATGTTAGTATTTTTTTAAATAGTT
1 ATTT-TTTTTATATTAATATTTATGTAAATA-TT
53637 ATTATTTTTTATATTAATATTTATGTAAATATT
1 ATT-TTTTTTATATTAATATTTATGTAAATATT
* * * *
53670 ATTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTT-TTATATTAATATTTATGTAAATATT
53703 ATTT
1 ATTT
53707 ATTTAGAATT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
32 4 0.07
33 30 0.50
34 25 0.42
35 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (32 bp):
ATTTTTTTTATATTAATATTTATGTAAATATT
Found at i:53692 original size:15 final size:18
Alignment explanation
Indices: 53647--53703 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
53637 ATTATTTTTT
53647 ATATTAATATTTATGTAA
1 ATATTAATATTTATGTAA
* *
53665 ATATTATTTTTTAT-TAA
1 ATATTAATATTTATGTAA
*
53682 A-A-TAATATTTATATAA
1 ATATTAATATTTATGTAA
*
53698 TTATTA
1 ATATTA
53704 TTTATTTAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 8 0.26
16 4 0.13
17 5 0.16
18 14 0.45
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATATTAATATTTATGTAA
Found at i:56610 original size:13 final size:14
Alignment explanation
Indices: 56592--56620 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
56582 TACATAAATA
56592 TATTTAATAT-ATT
1 TATTTAATATAATT
56605 TATTTAATATAATT
1 TATTTAATATAATT
56619 TA
1 TA
56621 ATATTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTAATATAATT
Found at i:60827 original size:11 final size:11
Alignment explanation
Indices: 60811--60835 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
60801 TAAGAGGCTC
60811 AATCCATTTAA
1 AATCCATTTAA
60822 AATCCATTTAA
1 AATCCATTTAA
60833 AAT
1 AAT
60836 TCAAATCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (11 bp):
AATCCATTTAA
Found at i:60920 original size:17 final size:17
Alignment explanation
Indices: 60898--60936 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
60888 TGAATCAAAT
60898 TAATTAGATATTACTTA
1 TAATTAGATATTACTTA
*
60915 TAATTAGATATTATTTA
1 TAATTAGATATTACTTA
60932 -AATTA
1 TAATTA
60937 ATTGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (17 bp):
TAATTAGATATTACTTA
Found at i:62125 original size:15 final size:15
Alignment explanation
Indices: 62092--62135 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
62082 AAAATATTTA
62092 ATATTATGAT-TACAAT
1 ATATTAT-ATATA-AAT
62108 ATATTATATATAAAT
1 ATATTATATATAAAT
*
62123 ATATTATTTATAA
1 ATATTATATATAA
62136 TTATGATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
ATATTATATATAAAT
Found at i:63242 original size:23 final size:21
Alignment explanation
Indices: 63209--63266 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 21
63199 GAGTGACTAT
*
63209 AATATAATATAATATTTATTTA
1 AATATATTATAATATTT-TTTA
63231 GAATATATTATAGAATATTTTTTA
1 -AATATATTAT--AATATTTTTTA
63255 AAT-TATTGATAA
1 AATATATT-ATAA
63267 CGTTTATGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
21 2 0.06
22 4 0.13
23 14 0.45
24 4 0.13
25 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
AATATATTATAATATTTTTTA
Found at i:63247 original size:25 final size:23
Alignment explanation
Indices: 63210--63261 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
63200 AGTGACTATA
* *
63210 ATATAATATAATATTTATTTAGAAT
1 ATATTATAGAATATTT-TTTA-AAT
63235 ATATTATAGAATATTTTTTAAAT
1 ATATTATAGAATATTTTTTAAAT
63258 -TATT
1 ATATT
63262 GATAACGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.16
23 3 0.12
24 4 0.16
25 14 0.56
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
ATATTATAGAATATTTTTTAAAT
Found at i:63920 original size:14 final size:15
Alignment explanation
Indices: 63901--63930 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
63891 TTCAAATTCC
63901 TAAATATA-ATATTT
1 TAAATATATATATTT
63915 TAAATATATATATTT
1 TAAATATATATATTT
63930 T
1 T
63931 TTAGTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAAATATATATATTT
Found at i:76038 original size:2 final size:2
Alignment explanation
Indices: 76031--76066 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
76021 ACAGACTCAA
76031 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
76067 GGTCTTAGAA
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:82793 original size:19 final size:19
Alignment explanation
Indices: 82769--82812 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
82759 TTTTCCTATT
82769 GGAAGGGTAT-AATTTGAAG
1 GGAAGGGT-TGAATTTGAAG
82788 GGAAGGGTTGAATTTGAAG
1 GGAAGGGTTGAATTTGAAG
82807 GGAAGG
1 GGAAGG
82813 AAAAGGTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.34, C:0.00, G:0.43, T:0.23
Consensus pattern (19 bp):
GGAAGGGTTGAATTTGAAG
Found at i:93266 original size:3 final size:3
Alignment explanation
Indices: 93260--93320 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
93250 TATTTAAAAT
* * * *
93260 TTA TTA TTA TTA TTA TTA TAA TAA TAA TTA TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
93308 TTTA TTA ATA TTA
1 -TTA TTA TTA TTA
93321 CAAAACCCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:94442 original size:21 final size:21
Alignment explanation
Indices: 94396--94437 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
94386 TCTCTTAAAT
* *
94396 ATTATATTTTATAATTTGATC
1 ATTAAATTTTATAATTTAATC
94417 ATTAAATTTTATAATCTTAAT
1 ATTAAATTTTATAAT-TTAAT
94438 TTTAACCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTAAATTTTATAATTTAATC
Found at i:94631 original size:14 final size:15
Alignment explanation
Indices: 94612--94644 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
94602 ATTTATTAAG
94612 TTATATAA-ATATAT
1 TTATATAATATATAT
*
94626 TTATATAATATTTAT
1 TTATATAATATATAT
94641 TTAT
1 TTAT
94645 TTATTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATAATATATAT
Found at i:95000 original size:24 final size:24
Alignment explanation
Indices: 94953--94999 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
94943 CTTATTTATA
* *
94953 TAAATTAATAAATTTACTTAAAAT
1 TAAAGTAATAAATTTAATTAAAAT
94977 TAAAGTAATAAATTTAAATTAAA
1 TAAAGTAATAAATTT-AATTAAA
95000 TATATTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
TAAAGTAATAAATTTAATTAAAAT
Found at i:97076 original size:15 final size:15
Alignment explanation
Indices: 97040--97078 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
97030 AATTTACATT
97040 TTTACATTT-GCATA
1 TTTACATTTGGCATA
*
97054 TTTACATTTGGCATC
1 TTTACATTTGGCATA
*
97069 TTTGCATTTG
1 TTTACATTTG
97079 TATTGCACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (15 bp):
TTTACATTTGGCATA
Done.