Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000898.1 Hibiscus syriacus cultivar Beakdansim tig00001764_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: 78464
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:2530 original size:17 final size:19
Alignment explanation
Indices: 2510--2554 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
2500 GAGGGTTTTG
2510 ATAAAAATGA-TTAAA-TA
1 ATAAAAATGATTTAAAGTA
2527 ATAAAAAATGATTTAAAGTA
1 AT-AAAAATGATTTAAAGTA
2547 A-AAAAATG
1 ATAAAAATG
2555 TAAAAGTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 2 0.08
18 15 0.60
19 5 0.20
20 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (19 bp):
ATAAAAATGATTTAAAGTA
Found at i:2533 original size:18 final size:19
Alignment explanation
Indices: 2512--2552 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2502 GGGTTTTGAT
2512 AAAAATGA-TTAAA-TAATA
1 AAAAATGATTTAAAGTAA-A
2530 AAAAATGATTTAAAGTAAA
1 AAAAATGATTTAAAGTAAA
2549 AAAA
1 AAAA
2553 TGTAAAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 10 0.48
20 3 0.14
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.24
Consensus pattern (19 bp):
AAAAATGATTTAAAGTAAA
Found at i:20547 original size:24 final size:24
Alignment explanation
Indices: 20477--20547 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
20467 CAATATTATA
*
20477 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* *
20500 CGGCACTTCGGTGCAAATTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
*
20524 TGGCACTTCGGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
20548 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
23 12 0.29
24 29 0.71
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:22588 original size:22 final size:22
Alignment explanation
Indices: 22538--22588 Score: 88
Period size: 20 Copynumber: 2.4 Consensus size: 22
22528 TTTAAATGTA
22538 ATACCTTATAATCAACCCATGC
1 ATACCTTATAATCAACCCATGC
22560 --ACCTTATAATCAACCCATGC
1 ATACCTTATAATCAACCCATGC
22580 ATACCTTAT
1 ATACCTTAT
22589 TTATGATGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 20 0.74
22 7 0.26
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.29
Consensus pattern (22 bp):
ATACCTTATAATCAACCCATGC
Found at i:25322 original size:28 final size:28
Alignment explanation
Indices: 25288--25347 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
25278 CAAAAACTTT
25288 GAATTTTAGATTGTGTGTAATCCTTTCC
1 GAATTTTAGATTGTGTGTAATCCTTTCC
25316 GAATTTTAGATTGTGTGTAATCCTTTCC
1 GAATTTTAGATTGTGTGTAATCCTTTCC
25344 -AATT
1 GAATT
25348 GCATTATTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 4 0.12
28 28 0.88
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (28 bp):
GAATTTTAGATTGTGTGTAATCCTTTCC
Found at i:27578 original size:17 final size:18
Alignment explanation
Indices: 27545--27579 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
27535 ATTAAATTAT
27545 CTATAAAAAATATTTAAA
1 CTATAAAAAATATTTAAA
*
27563 CTATATAAAA-ATTTAAA
1 CTATAAAAAATATTTAAA
27580 ATTTTAAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
CTATAAAAAATATTTAAA
Found at i:28846 original size:13 final size:13
Alignment explanation
Indices: 28828--28874 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
28818 GTATTTGTGT
28828 TGTTCGTTTATTG
1 TGTTCGTTTATTG
28841 TGTTCGTTTA-TG
1 TGTTCGTTTATTG
* *
28853 T-TT-ATTTATTA
1 TGTTCGTTTATTG
28864 TGTTCGTTTAT
1 TGTTCGTTTAT
28875 GTTAGTTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
10 4 0.14
11 4 0.14
12 5 0.18
13 15 0.54
ACGTcount: A:0.13, C:0.06, G:0.17, T:0.64
Consensus pattern (13 bp):
TGTTCGTTTATTG
Found at i:28854 original size:23 final size:22
Alignment explanation
Indices: 28828--28904 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
28818 GTATTTGTGT
28828 TGTTCGTTTATTGTGTTCGTTTA
1 TGTTCGTTTATT-TGTTCGTTTA
**
28851 TGTTTATTTATTATGTTCGTTTA
1 TGTTCGTTTATT-TGTTCGTTTA
* *
28874 TGTTAGTTTA--CGTTCGTTTA
1 TGTTCGTTTATTTGTTCGTTTA
*
28894 TATTCGTTTAT
1 TGTTCGTTTAT
28905 CATTTAAATG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 17 0.38
23 28 0.62
ACGTcount: A:0.14, C:0.08, G:0.17, T:0.61
Consensus pattern (22 bp):
TGTTCGTTTATTTGTTCGTTTA
Found at i:28874 original size:10 final size:10
Alignment explanation
Indices: 28861--28904 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
28851 TGTTTATTTA
28861 TTATGTTCGT
1 TTATGTTCGT
*
28871 TTATGTTAGT
1 TTATGTTCGT
*
28881 TTACGTTCGT
1 TTATGTTCGT
*
28891 TTATATTCGT
1 TTATGTTCGT
28901 TTAT
1 TTAT
28905 CATTTAAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.59
Consensus pattern (10 bp):
TTATGTTCGT
Found at i:36894 original size:20 final size:20
Alignment explanation
Indices: 36869--36935 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
36859 TTGTTTAATC
36869 TAAAATGTTATATAAGTTTG
1 TAAAATGTTATATAAGTTTG
* ** *
36889 TAAAATATTAT-TTTGTTTAATC
1 TAAAATGTTATATAAG-TT--TG
*
36911 TAAAAAGTTATATAAGTTTG
1 TAAAATGTTATATAAGTTTG
36931 TAAAA
1 TAAAA
36936 AGTTTCGATT
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
19 2 0.06
20 18 0.53
22 12 0.35
23 2 0.06
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.45
Consensus pattern (20 bp):
TAAAATGTTATATAAGTTTG
Found at i:36894 original size:42 final size:42
Alignment explanation
Indices: 36847--36935 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
36837 ATTTTTAATT
*
36847 TAAAATATTATTTTGTTTAATCTAAAATGTTATATAAGTTTG
1 TAAAATATTATTTTGTTTAATCTAAAAAGTTATATAAGTTTG
36889 TAAAATATTATTTTGTTTAATCTAAAAAGTTATATAAGTTTG
1 TAAAATATTATTTTGTTTAATCTAAAAAGTTATATAAGTTTG
36931 TAAAA
1 TAAAA
36936 AGTTTCGATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (42 bp):
TAAAATATTATTTTGTTTAATCTAAAAAGTTATATAAGTTTG
Found at i:36921 original size:22 final size:22
Alignment explanation
Indices: 36840--36915 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
36830 TAAGATGATT
*
36840 TTTAATTTAAAATATTATTTTG
1 TTTAATCTAAAATATTATTTTG
* **
36862 TTTAATCTAAAATGTTATATAAG
1 TTTAATCTAAAATATTAT-TTTG
*
36885 -TT--TGTAAAATATTATTTTG
1 TTTAATCTAAAATATTATTTTG
36904 TTTAATCTAAAA
1 TTTAATCTAAAA
36916 AGTTATATAA
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
19 2 0.05
20 13 0.32
22 24 0.59
23 2 0.05
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (22 bp):
TTTAATCTAAAATATTATTTTG
Found at i:38670 original size:39 final size:39
Alignment explanation
Indices: 38616--38694 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
38606 GAAACTCTAA
38616 GGTTCTAAGTTTTTTCAAATATTTGGAGGATCACCTCAT
1 GGTTCTAAGTTTTTTCAAATATTTGGAGGATCACCTCAT
38655 GGTTCTAAGTTTTTTCAAATATTTGGAGGATCACCTCAT
1 GGTTCTAAGTTTTTTCAAATATTTGGAGGATCACCTCAT
38694 G
1 G
38695 CCCGAATGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (39 bp):
GGTTCTAAGTTTTTTCAAATATTTGGAGGATCACCTCAT
Found at i:40631 original size:13 final size:13
Alignment explanation
Indices: 40613--40663 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 13
40603 TAACTGTAGA
40613 AAACAGACTGTGT
1 AAACAGACTGTGT
40626 AAACAGACTGTGT
1 AAACAGACTGTGT
*
40639 AGAAAACAGACTGTAGA
1 ---AAACAGACTGT-GT
40656 AAACAGAC
1 AAACAGAC
40664 AAGTCTGTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
13 13 0.39
14 8 0.24
16 11 0.33
17 1 0.03
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.16
Consensus pattern (13 bp):
AAACAGACTGTGT
Found at i:40639 original size:29 final size:30
Alignment explanation
Indices: 40607--40663 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
40597 ATGTATTAAC
*
40607 TGTAGAAAACAGACTGT-GTAAACAGACTG
1 TGTAGAAAACAGACTGTAGAAAACAGACTG
40636 TGTAGAAAACAGACTGTAGAAAACAGAC
1 TGTAGAAAACAGACTGTAGAAAACAGAC
40664 AAGTCTGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.46, C:0.14, G:0.23, T:0.18
Consensus pattern (30 bp):
TGTAGAAAACAGACTGTAGAAAACAGACTG
Found at i:40655 original size:14 final size:14
Alignment explanation
Indices: 40605--40663 Score: 84
Period size: 14 Copynumber: 4.1 Consensus size: 14
40595 TCATGTATTA
40605 ACTGTAGAAAACAG
1 ACTGTAGAAAACAG
*
40619 ACTGT-GTAAACAG
1 ACTGTAGAAAACAG
40632 ACTGTGTAGAAAACAG
1 AC--TGTAGAAAACAG
40648 ACTGTAGAAAACAG
1 ACTGTAGAAAACAG
40662 AC
1 AC
40664 AAGTCTGTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
13 9 0.22
14 19 0.47
15 3 0.08
16 9 0.22
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (14 bp):
ACTGTAGAAAACAG
Found at i:42953 original size:51 final size:51
Alignment explanation
Indices: 42877--42977 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
42867 TAAGGAAATG
*
42877 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGTTGAAATTCCTTGTAACTA
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
42928 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
42978 CCCCCTGAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (51 bp):
ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
Found at i:44746 original size:14 final size:15
Alignment explanation
Indices: 44711--44754 Score: 72
Period size: 14 Copynumber: 2.9 Consensus size: 15
44701 CCTGATACCA
44711 TGTAGAAAACAGACTG
1 TGTAGAAAACAGAC-G
44727 TGTAGAAAACAGAC-
1 TGTAGAAAACAGACG
44741 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
44755 AAGTCTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.50
16 14 0.50
ACGTcount: A:0.48, C:0.14, G:0.23, T:0.16
Consensus pattern (15 bp):
TGTAGAAAACAGACG
Found at i:50525 original size:4 final size:4
Alignment explanation
Indices: 50518--50548 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
50508 ACTGCAATGA
50518 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATG
50549 AGAGTACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.48, T:0.26
Consensus pattern (4 bp):
ATGG
Found at i:51891 original size:13 final size:13
Alignment explanation
Indices: 51873--51963 Score: 83
Period size: 13 Copynumber: 6.3 Consensus size: 13
51863 GTCACAACCC
51873 GACCCGACCCGTT
1 GACCCGACCCGTT
51886 GACCCGACCCCCGTT
1 GACCCGA--CCCGTT
*
51901 TACCCGACCCGTT
1 GACCCGACCCGTT
51914 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
51932 GACCCGACCCGTT
1 GACCCGACCCGTT
*
51945 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
51960 GACC
1 GACC
51964 GTTGACGGAG
Statistics
Matches: 66, Mismatches: 3, Indels: 16
0.78 0.04 0.19
Matches are distributed among these distances:
13 30 0.45
15 24 0.36
18 12 0.18
ACGTcount: A:0.15, C:0.46, G:0.22, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:51892 original size:18 final size:18
Alignment explanation
Indices: 51869--51942 Score: 83
Period size: 18 Copynumber: 4.6 Consensus size: 18
51859 ACCAGTCACA
51869 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
51887 ACCCGA-CC--CCCGTT-
1 ACCCGACCCGACCCGTTG
*
51901 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
51915 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
51933 ACCCGACCCG
1 ACCCGACCCG
51943 TTGACCGTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
10 1 0.02
11 2 0.04
13 6 0.13
15 6 0.13
17 2 0.04
18 29 0.63
ACGTcount: A:0.16, C:0.51, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:51935 original size:8 final size:8
Alignment explanation
Indices: 51924--51969 Score: 57
Period size: 7 Copynumber: 6.4 Consensus size: 8
51914 GACCCGACCC
51924 GACCCGTT
1 GACCCGTT
51932 GACCC---
1 GACCCGTT
51937 GACCCGTT
1 GACCCGTT
51945 GA-CCGTT
1 GACCCGTT
51952 GACCCGTT
1 GACCCGTT
51960 GA-CCGTT
1 GACCCGTT
51967 GAC
1 GAC
51970 GGAGTTGACC
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.42
8 14 0.42
ACGTcount: A:0.15, C:0.37, G:0.26, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:51956 original size:46 final size:45
Alignment explanation
Indices: 51869--51963 Score: 138
Period size: 46 Copynumber: 2.1 Consensus size: 45
51859 ACCAGTCACA
*
51869 ACCCGACCCGACCCGTTGACCCGACCCCCGTTTACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGA-CCCCGTTGACCCGACCCGTTG
*
51915 ACCCGACCCGACCCGTTGACCCGA-CCCGTTGACCGTTGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCCGTTGACC--CGACCCGTTG
51961 ACC
1 ACC
51964 GTTGACGGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
44 9 0.20
46 36 0.80
ACGTcount: A:0.16, C:0.47, G:0.21, T:0.16
Consensus pattern (45 bp):
ACCCGACCCGACCCGTTGACCCGACCCCGTTGACCCGACCCGTTG
Found at i:51957 original size:15 final size:15
Alignment explanation
Indices: 51924--51969 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
51914 GACCCGACCC
*
51924 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
51937 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
51952 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
51967 GAC
1 GAC
51970 GGAGTTGACC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.40
15 18 0.60
ACGTcount: A:0.15, C:0.37, G:0.26, T:0.22
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:53328 original size:18 final size:18
Alignment explanation
Indices: 53302--53337 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53292 TCGAAAGGAC
*
53302 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
53320 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
53338 CGGATGAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:54568 original size:24 final size:24
Alignment explanation
Indices: 54464--54570 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
54454 ATATTTTATC
*
54464 TGATTTCTGATTTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
** * * *
54488 TGACATCTGATCTGAAATCTGTTC
1 TGATTTCTGATCTGAATTATGTTT
* * * * * *
54512 TGATTCCTAACCTGGATTCTGTTA
1 TGATTTCTGATCTGAATTATGTTT
* *
54536 TGATATCTGATCTGAATTATATTT
1 TGATTTCTGATCTGAATTATGTTT
54560 TGATTTCTGAT
1 TGATTTCTGAT
54571 ATCTCCGTTT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTATGTTT
Found at i:58093 original size:22 final size:23
Alignment explanation
Indices: 58065--58131 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 23
58055 TTAAAAATTT
*
58065 AAAATTATTATATATATT-TTAA
1 AAAATTATTATATATTTTATTAA
*
58087 AAAATTA-GATAT-TTTTATTAA
1 AAAATTATTATATATTTTATTAA
*
58108 AACATTATT-TATATTTTATTAA
1 AAAATTATTATATATTTTATTAA
58130 AA
1 AA
58132 TTTCATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
20 3 0.08
21 17 0.45
22 18 0.47
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (23 bp):
AAAATTATTATATATTTTATTAA
Found at i:58347 original size:20 final size:20
Alignment explanation
Indices: 58310--58348 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
58300 AAAAGACATA
* * *
58310 TAATATTAATAATTTTTAAT
1 TAATATCAACAATATTTAAT
58330 TAATATCAACAATATTTAA
1 TAATATCAACAATATTTAA
58349 AATAGATAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATATCAACAATATTTAAT
Found at i:61183 original size:22 final size:22
Alignment explanation
Indices: 61158--61207 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
61148 CTACGACGAC
* *
61158 ATCCGTCCCCATCTCCGGTGAA
1 ATCCGTCCCCATCTCCAGCGAA
61180 ATCCGTCCCCATCTCCAGCGAA
1 ATCCGTCCCCATCTCCAGCGAA
61202 ATCCGT
1 ATCCGT
61208 ATATCTCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.42, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCAGCGAA
Found at i:61307 original size:16 final size:16
Alignment explanation
Indices: 61283--61316 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61273 ATGGTTAGTT
*
61283 TTTTTAATTATTTTTA
1 TTTTGAATTATTTTTA
*
61299 TTTTGAATTTTTTTTA
1 TTTTGAATTATTTTTA
61315 TT
1 TT
61317 ATTATTAGAT
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:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTGAATTATTTTTA
Found at i:61594 original size:19 final size:19
Alignment explanation
Indices: 61543--61596 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
61533 AGTAGTTTCT
*
61543 GAAACTTAAATTCGCAACGC
1 GAAAC-TAAAATCGCAACGC
*
61563 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
61583 GAAACTAAAATCGC
1 GAAACTAAAATCGC
61597 GTTGCGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:63153 original size:21 final size:21
Alignment explanation
Indices: 63110--63159 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
63100 GTTAAGGGAG
*
63110 TTACGTGATGAGGTAAGTGCT
1 TTACGTGATGAGGTAAGTACT
* **
63131 TTGCGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTAAGTACT
63152 TTACGTGA
1 TTACGTGA
63160 CGACAATGTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.12, G:0.34, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTAAGTACT
Found at i:63597 original size:21 final size:21
Alignment explanation
Indices: 63571--63641 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
63561 TCTATCATCG
63571 TTCAAGAGGCCCCTCCCACCA
1 TTCAAGAGGCCCCTCCCACCA
** * *
63592 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCCTCCCACCA
* *
63613 TTCAAGAAGTCCCTCCCACCA
1 TTCAAGAGGCCCCTCCCACCA
63634 TTCAAGAG
1 TTCAAGAG
63642 CCCGATTCAC
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.25, C:0.38, G:0.17, T:0.20
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCCACCA
Found at i:65389 original size:6 final size:6
Alignment explanation
Indices: 65370--65408 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
65360 GTGAAGCTGG
** *
65370 TTTTGA TTGGGA TTTTGA TTTTGA TTGTGA TTTTGA TTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTT
65409 CCTTTTGCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (6 bp):
TTTTGA
Found at i:65393 original size:18 final size:18
Alignment explanation
Indices: 65370--65408 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
65360 GTGAAGCTGG
65370 TTTTGATTGGGATTTTGA
1 TTTTGATTGGGATTTTGA
*
65388 TTTTGATTGTGATTTTGA
1 TTTTGATTGGGATTTTGA
65406 TTT
1 TTT
65409 CCTTTTGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (18 bp):
TTTTGATTGGGATTTTGA
Found at i:67739 original size:24 final size:24
Alignment explanation
Indices: 67688--67739 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
67678 ATCTGAGTAT
** *
67688 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
67712 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
67736 TGAC
1 TGAC
67740 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:68746 original size:21 final size:20
Alignment explanation
Indices: 68672--68809 Score: 93
Period size: 20 Copynumber: 6.8 Consensus size: 20
68662 AAAATTAAAT
* *
68672 TTCGTGATGCGAATTCGAAA
1 TTCGTGTTGCGAATTTGAAA
* * * *
68692 ATCGAGTTTCGAATTCAGAAA
1 TTCGTGTTGCGAATT-TGAAA
* *
68713 -TCGAGTTGTGAATTTGAAA
1 TTCGTGTTGCGAATTTGAAA
68732 TTCAGTGTTGCGAATTTGGAAA
1 TTC-GTGTTGCGAATTT-GAAA
* *
68754 -TCGCGTTGCGAATTT-AAC
1 TTCGTGTTGCGAATTTGAAA
* * *
68772 TTCTGTGTTGCGAAATTGTAG
1 TTC-GTGTTGCGAATTTGAAA
*
68793 TTCGTGTTGTGAATTTG
1 TTCGTGTTGCGAATTTG
68810 TTGGTCATTT
Statistics
Matches: 93, Mismatches: 18, Indels: 14
0.74 0.14 0.11
Matches are distributed among these distances:
18 2 0.02
19 6 0.06
20 60 0.65
21 21 0.23
22 4 0.04
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (20 bp):
TTCGTGTTGCGAATTTGAAA
Found at i:68746 original size:41 final size:40
Alignment explanation
Indices: 68701--68785 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 40
68691 AATCGAGTTT
*
68701 CGAATTCAGAAATCGAGTTGTGAATTTGAAATTCAGTGTTG
1 CGAATTCAGAAATCGAGTTGCGAATTT-AAATTCAGTGTTG
** * * *
68742 CGAATTTGGAAATCGCGTTGCGAATTTAACTTCTGTGTTG
1 CGAATTCAGAAATCGAGTTGCGAATTTAAATTCAGTGTTG
68782 CGAA
1 CGAA
68786 ATTGTAGTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
40 15 0.39
41 23 0.61
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (40 bp):
CGAATTCAGAAATCGAGTTGCGAATTTAAATTCAGTGTTG
Found at i:68807 original size:40 final size:41
Alignment explanation
Indices: 68709--68809 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 41
68699 TTCGAATTCA
* *
68709 GAAATCGAGTTGTGAATTTGAAATTCAGTGTTGCGAATTTG
1 GAAATCGCGTTGTGAATTTGAAATTCAGTGTTGCGAAATTG
* * *
68750 GAAATCGCGTTGCGAATTT-AACTTCTGTGTTGCGAAATTG
1 GAAATCGCGTTGTGAATTTGAAATTCAGTGTTGCGAAATTG
* ** *
68790 TAGTTCGTGTTGTGAATTTG
1 GAAATCGCGTTGTGAATTTG
68810 TTGGTCATTT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
40 32 0.65
41 17 0.35
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.39
Consensus pattern (41 bp):
GAAATCGCGTTGTGAATTTGAAATTCAGTGTTGCGAAATTG
Found at i:71654 original size:72 final size:73
Alignment explanation
Indices: 71537--71687 Score: 189
Period size: 72 Copynumber: 2.1 Consensus size: 73
71527 TAGATATTCA
* * * **
71537 ATGTTTTCAACATTAGTTTTTAAAATATTTGTATTATAATAATTATTTAAAAA-ATTATTATTTG
1 ATGTTTTCAACATTAGTTTTTAAAATATCTATATTATAAAAATTA-TTAAAAATATTATTATAGG
*
71601 ATATGAGTT
65 ACATGAGTT
* * * *
71610 ATGTTTTCAATATTA-TTTTTTAAGTATCTATTTTATAAAAATTATTAAAAATATTATTATAGGA
1 ATGTTTTCAACATTAGTTTTTAAAATATCTATATTATAAAAATTATTAAAAATATTATTATAGGA
71674 CATGAGTT
66 CATGAGTT
71682 ATGTTT
1 ATGTTT
71688 ATATATTTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
71 7 0.10
72 46 0.69
73 14 0.21
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (73 bp):
ATGTTTTCAACATTAGTTTTTAAAATATCTATATTATAAAAATTATTAAAAATATTATTATAGGA
CATGAGTT
Found at i:76265 original size:61 final size:59
Alignment explanation
Indices: 76155--76302 Score: 183
Period size: 61 Copynumber: 2.4 Consensus size: 59
76145 ATTAAAACAT
* * *
76155 TCAAAAGTTTGGGAACTAATATAGAATGAGAGTCATAGTTTGGAGATGAAATT-GTAATGC
1 TCAAAAGTTTGGGATC-AATTTAGAATGAGAGTCATAGTTTGGAGATGAAATTAG-AATAC
* *
76215 TCAAAAGTTTAGGGATCAATTTAAGAATGAGAGTCATAGTTTATGA-ATGAAATTAGAATAT
1 TCAAAAGTTT-GGGATCAATTT-AGAATGAGAGTCATAGTTT-GGAGATGAAATTAGAATAC
76276 TCAAAAGTTTGAGGATCAATTTAGAAT
1 TCAAAAGTTTG-GGATCAATTTAGAAT
76303 AAAAGCTATA
Statistics
Matches: 78, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
60 20 0.26
61 55 0.71
62 3 0.04
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.32
Consensus pattern (59 bp):
TCAAAAGTTTGGGATCAATTTAGAATGAGAGTCATAGTTTGGAGATGAAATTAGAATAC
Found at i:77212 original size:3 final size:3
Alignment explanation
Indices: 77204--77254 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
77194 TATAGACATC
77204 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
77252 TAT
1 TAT
77255 ATGTAAATCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Done.