Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003438.1 Hibiscus syriacus cultivar Beakdansim tig00007245_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: 68310
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3754 original size:18 final size:19
Alignment explanation
Indices: 3733--3774 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
3723 TTTCCCTTCA
*
3733 TCTTCTTTTTTCTTC-ATT
1 TCTTCTTATTTCTTCTATT
3751 TCTTC-TATTTCTTCTATT
1 TCTTCTTATTTCTTCTATT
*
3769 CCTTCT
1 TCTTCT
3775 CATATTCCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (19 bp):
TCTTCTTATTTCTTCTATT
Found at i:3762 original size:9 final size:9
Alignment explanation
Indices: 3741--3774 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3731 CATCTTCTTT
3741 TTTCTTC-A
1 TTTCTTCTA
3749 TTTCTTCTA
1 TTTCTTCTA
3758 TTTCTTCTA
1 TTTCTTCTA
*
3767 TTCCTTCT
1 TTTCTTCT
3775 CATATTCCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTCTTCTA
Found at i:17860 original size:19 final size:18
Alignment explanation
Indices: 17824--17858 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
17814 GAAGGCTTTA
17824 TATTTCTCTTCATCTTCT
1 TATTTCTCTTCATCTTCT
17842 TATTT-TCTTCAT-TTCT
1 TATTTCTCTTCATCTTCT
17858 T
1 T
17859 CTATTCCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 7 0.41
18 5 0.29
ACGTcount: A:0.11, C:0.23, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTCTCTTCATCTTCT
Found at i:19379 original size:18 final size:19
Alignment explanation
Indices: 19356--19397 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
19346 GTAAGAGAAT
* *
19356 ATTAAAATAA-TAAATGCG
1 ATTAAAATAATTAAAAGCA
19374 ATT-AAATAATTAAAAGCA
1 ATTAAAATAATTAAAAGCA
19392 ATTAAA
1 ATTAAA
19398 GTAAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 6 0.30
18 12 0.60
19 2 0.10
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.29
Consensus pattern (19 bp):
ATTAAAATAATTAAAAGCA
Found at i:26266 original size:91 final size:91
Alignment explanation
Indices: 26098--26266 Score: 205
Period size: 91 Copynumber: 1.9 Consensus size: 91
26088 TCGTGTGTCG
* * * * **
26098 CATAGTAGTACAGGTAGGCTACAGGGTGTGTGAGCACTTAGATGTATCCCATCAGCCTCATCATG
1 CATAGTAGTACAGGTAGGCTACAGGGTGTGTAAGCACTAAGATGTAGCCCATAAGCAGCATCATG
*
26163 ATACCTATCTCAGTTTGTGTGCATTA
66 ATACCTACCTCAGTTTGTGTGCATTA
* * * *
26189 CATAGTAGTATAGGTAGGCTAGAGGGTGTGTAAGCTCTAAGATGTAGCCCCTAAGCAGCA-CAAT
1 CATAGTAGTACAGGTAGGCTACAGGGTGTGTAAGCACTAAGATGTAGCCCATAAGCAGCATC-AT
**
26253 GATGTCTACCTCAG
65 GATACCTACCTCAG
26267 CATGTATCTT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
90 1 0.02
91 63 0.98
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (91 bp):
CATAGTAGTACAGGTAGGCTACAGGGTGTGTAAGCACTAAGATGTAGCCCATAAGCAGCATCATG
ATACCTACCTCAGTTTGTGTGCATTA
Found at i:35626 original size:15 final size:15
Alignment explanation
Indices: 35606--35636 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35596 AAAAATGAAT
35606 GCTAGAGCTTAATTA
1 GCTAGAGCTTAATTA
35621 GCTAGAGCTTAATTA
1 GCTAGAGCTTAATTA
35636 G
1 G
35637 TTAAAGGAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (15 bp):
GCTAGAGCTTAATTA
Found at i:41537 original size:20 final size:20
Alignment explanation
Indices: 41514--41552 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41504 AATAGGGTTA
* *
41514 ATATACTAAAATAGAATAAT
1 ATATAATAAAATAAAATAAT
41534 ATATAATAAAATAAAATAA
1 ATATAATAAAATAAAATAA
41553 AGACTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (20 bp):
ATATAATAAAATAAAATAAT
Found at i:42877 original size:3 final size:3
Alignment explanation
Indices: 42863--42904 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
42853 TTAATAAAAC
* *
42863 ATA ATA AAA ATA ATA ATA TGTA ATA ATA A-A ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
42905 TGTATAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.88
4 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:42879 original size:22 final size:20
Alignment explanation
Indices: 42854--42902 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
42844 GATAAAAAGT
42854 TAATAAAACATAATAAAAATAA
1 TAATAAAA-ATAAT-AAAATAA
**
42876 TAATATGTAATAATAAAATAA
1 TAATA-AAAATAATAAAATAA
42897 TAATAA
1 TAATAA
42903 TATGTATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 12 0.52
22 10 0.43
23 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
TAATAAAAATAATAAAATAA
Found at i:42903 original size:24 final size:22
Alignment explanation
Indices: 42863--42913 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 22
42853 TTAATAAAAC
42863 ATAAT-AAAAATAATAATATGT
1 ATAATAAAAAATAATAATATGT
42884 AATAATAAAATAATAATAATATGT
1 -ATAATAAAA-AATAATAATATGT
42908 ATAATA
1 ATAATA
42914 TATATTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 5 0.19
23 9 0.33
24 13 0.48
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
ATAATAAAAAATAATAATATGT
Found at i:42939 original size:25 final size:27
Alignment explanation
Indices: 42905--42955 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
42895 AATAATAATA
42905 TGTATAATATATATT-T-TTTAAAAAT
1 TGTATAATATATATTATATTTAAAAAT
*
42930 TGTATGATATATATTATATTTAAAAA
1 TGTATAATATATATTATATTTAAAAA
42956 ATAATATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.61
26 1 0.04
27 8 0.35
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (27 bp):
TGTATAATATATATTATATTTAAAAAT
Found at i:42951 original size:27 final size:25
Alignment explanation
Indices: 42905--43012 Score: 77
Period size: 23 Copynumber: 4.4 Consensus size: 25
42895 AATAATAATA
42905 TGTATAATATATATTTTTTAAAAAT
1 TGTATAATATATATTTTTTAAAAAT
*
42930 TGTATGATATATATTATATTTAAAAA-
1 TGTATAATATATATT-T-TTTAAAAAT
42956 ---ATAATATA-ATTTGTTTTCAAAAAT
1 TGTATAATATATA-TT-TTTT-AAAAAT
* * *
42980 TATAT-AT-TATATATTTTCAAAAT
1 TGTATAATATATATTTTTTAAAAAT
*
43003 TATATAATAT
1 TGTATAATAT
43013 GTTTTTAAGA
Statistics
Matches: 67, Mismatches: 5, Indels: 22
0.71 0.05 0.23
Matches are distributed among these distances:
22 4 0.06
23 25 0.37
24 6 0.09
25 18 0.27
26 4 0.06
27 10 0.15
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (25 bp):
TGTATAATATATATTTTTTAAAAAT
Found at i:42984 original size:22 final size:22
Alignment explanation
Indices: 42937--43052 Score: 101
Period size: 22 Copynumber: 5.3 Consensus size: 22
42927 AATTGTATGA
* *
42937 TATATATTATA-TTTAAAAAAT
1 TATATAATATATTTTCAAAAAT
* * *
42958 AATATAATTTGTTTTCAAAAAT
1 TATATAATATATTTTCAAAAAT
42980 TATATATTATATATTTTC-AAAAT
1 TATATA--ATATATTTTCAAAAAT
* * * *
43003 TATATAATATGTTTTTAAGAAC
1 TATATAATATATTTTCAAAAAT
* *
43025 TATATTATATATTTTCAAAAAC
1 TATATAATATATTTTCAAAAAT
43047 TATATA
1 TATATA
43053 TATTATATAT
Statistics
Matches: 74, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
21 15 0.20
22 40 0.54
23 11 0.15
24 8 0.11
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (22 bp):
TATATAATATATTTTCAAAAAT
Found at i:42995 original size:45 final size:43
Alignment explanation
Indices: 42936--43038 Score: 109
Period size: 45 Copynumber: 2.3 Consensus size: 43
42926 AAATTGTATG
*
42936 ATATA-TATTATATTTAAAAAATAATATAATTTGTTTTCAAAAA
1 ATATATTA-TATATTTAAAAAATAATATAATATGTTTTCAAAAA
** * * *
42979 TTATATATTATATATTTTCAAAATTATATAATATGTTTTTAAGAA
1 --ATATATTATATATTTAAAAAATAATATAATATGTTTTCAAAAA
*
43024 CTATATTATATATTT
1 ATATATTATATATTT
43039 TCAAAAACTA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 14 0.28
45 34 0.68
46 2 0.04
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (43 bp):
ATATATTATATATTTAAAAAATAATATAATATGTTTTCAAAAA
Found at i:43081 original size:26 final size:26
Alignment explanation
Indices: 42969--43065 Score: 90
Period size: 22 Copynumber: 4.2 Consensus size: 26
42959 ATATAATTTG
42969 TTTTCAAAAA-T-TATATATTATATA
1 TTTTCAAAAACTATATATATTATATA
*
42993 TTTTC-AAAA-T-TATATA--ATATG
1 TTTTCAAAAACTATATATATTATATA
* *
43014 TTTTTAAGAAC----TATATTATATA
1 TTTTCAAAAACTATATATATTATATA
43036 TTTTCAAAAACTATATATATTATATA
1 TTTTCAAAAACTATATATATTATATA
43062 TTTT
1 TTTT
43066 TGAAATTATT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
20 4 0.07
21 8 0.14
22 16 0.27
23 11 0.19
24 5 0.08
26 15 0.25
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTTCAAAAACTATATATATTATATA
Found at i:43830 original size:222 final size:223
Alignment explanation
Indices: 43437--43939 Score: 584
Period size: 223 Copynumber: 2.3 Consensus size: 223
43427 TTAGAAGATG
* * * *
43437 TGACTGGAAGATGGCTCCTCGCCACTGATTTAAGCCAAAATATAGTCGGTTTTGGATGTGTTTCT
1 TGACTGGAAGATGGCTCCTCACCACTGATTTAAGCCAAAATACAGTTGGTTCTGGATGTGTTTCT
* * **
43502 GGGTCAAGAATCCTCCATCGTGAAGTTGAGACTTGGCCTAAAAATTTGAATAGGTACTAGCTCCT
66 GGGTAAAGAATCCTCCATCGTGAAGTTGAGAATTGGCCTAAAAATTTGAATAGAAACTAGCTCCT
* * * * * * *
43567 TGCCGCTGACTTAAGCTAGATTGCAGTCGATTCTGGA-TTTTTTCG-AACCTAATATCCACCATC
131 TGCCGCTAACTTAACCTAGACTGCAATCAATTCTGGATTTTTTTAGAAATC-AATATCCACCATC
**
43630 ATGGAGTTGAAACTGACTTCGAAAATGTTT
195 ATGGAGTTGAAACTGACTTCGAAAA-CATT
* * ** *
43660 TGACTGGAAGATGGCTCCTCACCACTTAGTTAAGAAAAAATACAGTTGGTTCAGGATGTGTTTCT
1 TGACTGGAAGATGGCTCCTCACCACTGATTTAAGCCAAAATACAGTTGGTTCTGGATGTGTTTCT
* * * * *
43725 -GGTAAAGAATCCTCCGTTGTGAAGTTGAGAATTGGCCTAAAACCTTTGACT-GAAAACTAGTTC
66 GGGTAAAGAATCCTCCATCGTGAAGTTGAGAATTGGCCTAAAA-ATTTGAATAG-AAACTAGCTC
* * * * * **
43788 CTTGCTGCTAAGTTAACCTAGACTGCAATCAATT-TTGATTTTTTTAGAAATCAATATTCTCTGT
129 CTTGCCGCTAACTTAACCTAGACTGCAATCAATTCTGGATTTTTTTAGAAATCAATATCCACCAT
* *
43852 CATGGAGTTGAGATTGACTTCGAAAACATT
194 CATGGAGTTGAAACTGACTTCGAAAACATT
* * *
43882 TGACTGGATGATGGCTCCTCACAACTGATTTAAGCCAAAATGCAGTTGGTTCTGGATG
1 TGACTGGAAGATGGCTCCTCACCACTGATTTAAGCCAAAATACAGTTGGTTCTGGATG
43940 ACTCCTCTTC
Statistics
Matches: 232, Mismatches: 44, Indels: 9
0.81 0.15 0.03
Matches are distributed among these distances:
222 94 0.41
223 135 0.58
224 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Consensus pattern (223 bp):
TGACTGGAAGATGGCTCCTCACCACTGATTTAAGCCAAAATACAGTTGGTTCTGGATGTGTTTCT
GGGTAAAGAATCCTCCATCGTGAAGTTGAGAATTGGCCTAAAAATTTGAATAGAAACTAGCTCCT
TGCCGCTAACTTAACCTAGACTGCAATCAATTCTGGATTTTTTTAGAAATCAATATCCACCATCA
TGGAGTTGAAACTGACTTCGAAAACATT
Found at i:46869 original size:20 final size:22
Alignment explanation
Indices: 46823--46877 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
46813 AATTATACGT
46823 GGTCTTTTGAGACATATATGTA
1 GGTCTTTTGAGACATATATGTA
* *
46845 -TTCTTTTGA-ACATGTATG-A
1 GGTCTTTTGAGACATATATGTA
46864 GGTCTTTTGAGACA
1 GGTCTTTTGAGACA
46878 CCTGCTTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.04
20 16 0.57
21 11 0.39
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (22 bp):
GGTCTTTTGAGACATATATGTA
Found at i:46976 original size:23 final size:23
Alignment explanation
Indices: 46941--46987 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
46931 CTTATGGATA
*
46941 AATTTTATATGGCA-TTACGGTGC
1 AATTATATATGGCACTT-CGGTGC
*
46964 AATTATATGTGGCACTTCGGTGC
1 AATTATATATGGCACTTCGGTGC
46987 A
1 A
46988 TTTCTACGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (23 bp):
AATTATATATGGCACTTCGGTGC
Found at i:47968 original size:17 final size:18
Alignment explanation
Indices: 47936--47969 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47926 CTTTTTCTCT
*
47936 CTTTTTTCTTTTTTTATC
1 CTTTTTTCTTATTTTATC
47954 CTTTTTTC-TATTTTAT
1 CTTTTTTCTTATTTTAT
47970 ATATTGCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (18 bp):
CTTTTTTCTTATTTTATC
Found at i:53561 original size:28 final size:27
Alignment explanation
Indices: 53518--53575 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
53508 ATATGTATAC
*
53518 TATATATATTTTAAAAACT-ATATAATA
1 TATATATATTTCAAAAA-TGATATAATA
53545 TATATTATATTTCAAAAATGATATAATA
1 TATA-TATATTTCAAAAATGATATAATA
53573 TAT
1 TAT
53576 TTTCCAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (27 bp):
TATATATATTTCAAAAATGATATAATA
Found at i:53592 original size:24 final size:22
Alignment explanation
Indices: 53513--53699 Score: 103
Period size: 22 Copynumber: 7.8 Consensus size: 22
53503 TAATAATATG
53513 TATACTAT-ATATATTTTAAAAA
1 TATA-TATAATATATTTTAAAAA
53535 CTATATAATATATATTATATTTCAAAAA
1 -TATAT-ATA-ATA-TAT-TTT-AAAAA
*
53563 T-GATATAATATATTTTCCAAAATTA
1 TATATATAATATATTTT--AAAA--A
*
53588 TATATATTATATATGTTTTCAAAAA
1 TATATA-TA-ATATATTTT-AAAAA
* * *
53613 CTATATATTATATGTTTTGAAAA
1 -TATATATAATATATTTTAAAAA
*
53636 T-TATATAATGTATTTTTAAAAA
1 TATATATAATATA-TTTTAAAAA
*
53658 -ATATATTATATATTTTTAAAAA
1 TATATATAATATA-TTTTAAAAA
53680 CTATATATATTATATATTTT
1 -TATATATA--ATATATTTT
53700 TGAAATTATT
Statistics
Matches: 133, Mismatches: 12, Indels: 36
0.73 0.07 0.20
Matches are distributed among these distances:
21 8 0.06
22 32 0.24
23 18 0.14
24 18 0.14
25 14 0.11
26 19 0.14
27 11 0.08
28 13 0.10
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (22 bp):
TATATATAATATATTTTAAAAA
Found at i:53657 original size:22 final size:22
Alignment explanation
Indices: 53543--53686 Score: 105
Period size: 22 Copynumber: 6.3 Consensus size: 22
53533 AACTATATAA
* *
53543 TATATATTATA-TTTCAAAAA-
1 TATATAATATATTTTTAAAAAC
*
53563 TGATATAATATATTTTCCAAAATTA-
1 T-ATATAATATATTTT-TAAAA--AC
53588 TATATATTATATATGTTTTCAAAAAC
1 TATATA--ATATAT-TTTT-AAAAAC
* * *
53614 TATATATTATATGTTTTGAAAAT
1 TATATAATATAT-TTTTAAAAAC
* *
53637 TATATAATGTATTTTTAAAAAA
1 TATATAATATATTTTTAAAAAC
*
53659 TATATTATATATTTTTAAAAAC
1 TATATAATATATTTTTAAAAAC
53681 TATATA
1 TATATA
53687 TATTATATAT
Statistics
Matches: 101, Mismatches: 13, Indels: 18
0.77 0.10 0.14
Matches are distributed among these distances:
20 1 0.01
21 9 0.09
22 35 0.35
23 19 0.19
24 15 0.15
25 3 0.03
26 12 0.12
27 7 0.07
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.47
Consensus pattern (22 bp):
TATATAATATATTTTTAAAAAC
Found at i:53700 original size:26 final size:25
Alignment explanation
Indices: 53507--53700 Score: 133
Period size: 26 Copynumber: 7.9 Consensus size: 25
53497 TAGTACTAAT
* *
53507 AATATGTATACTATATATATTTTAAA
1 AATATATATATTATATAT-TTTTAAA
*
53533 AACTATATA-ATATATATTATATTTCAAA
1 AA-TATATATAT-TATA-TAT-TTTTAAA
**
53561 AATGATATA-A-TATAT-TTTCCAAA
1 AAT-ATATATATTATATATTTTTAAA
*
53584 ATTATATATATTATATATGTTTTCAAA
1 AATATATATATTATATAT-TTTT-AAA
* * *
53611 AA-CTATATATTATAT-GTTTTGAA
1 AATATATATATTATATATTTTTAAA
*
53634 AAT-TATATA--ATGTATTTTT-AA
1 AATATATATATTATATATTTTTAAA
53655 AA-A-ATATATTATATATTTTTAAA
1 AATATATATATTATATATTTTTAAA
53678 AACTATATATATTATATATTTTT
1 AA-TATATATATTATATATTTTT
53701 GAAATTATTT
Statistics
Matches: 136, Mismatches: 14, Indels: 36
0.73 0.08 0.19
Matches are distributed among these distances:
20 5 0.04
21 7 0.05
22 18 0.13
23 23 0.17
24 10 0.07
25 3 0.02
26 38 0.28
27 14 0.10
28 18 0.13
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (25 bp):
AATATATATATTATATATTTTTAAA
Found at i:66317 original size:20 final size:20
Alignment explanation
Indices: 66292--66329 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
66282 AAACCTTTTT
66292 AAAAAACTATA-TATATATTC
1 AAAAAA-TATATTATATATTC
66312 AAAAAATATATTATATAT
1 AAAAAATATATTATATAT
66330 GTTTCAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAAAATATATTATATATTC
Found at i:66379 original size:14 final size:14
Alignment explanation
Indices: 66360--66388 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
66350 AAACTATATT
66360 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
66374 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
66388 A
1 A
66389 CTATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
ATATGTTTTCAAAA
Found at i:66410 original size:38 final size:38
Alignment explanation
Indices: 66309--66561 Score: 281
Period size: 38 Copynumber: 6.7 Consensus size: 38
66299 TATATATATA
* *
66309 TTCAAAAAATATATTATATATG-TTTCAAAAA-ACCGTT
1 TTCAAAAACTATATTATATATGTTTTCAAAAATA-TGTT
66346 TT-AAAAACTATA-T-TATATGTTTTCAAAAATATGTT
1 TTCAAAAACTATATTATATATGTTTTCAAAAATATGTT
*
66381 TTCAAAAACTATATTATATATGTTTTCAAAAACCAT-TT
1 TTCAAAAACTATATTATATATGTTTTCAAAAA-TATGTT
* * *
66419 TTTAAAAAATATATATATTATATG-TTTCCAAAATATGTT
1 TTCAAAAACTATAT-TA-TATATGTTTTCAAAAATATGTT
**
66458 TTCAAAAACTATATTATATATGTTTTCAAAAA-ACCATT
1 TTCAAAAACTATATTATATATGTTTTCAAAAATA-TGTT
*
66496 TTAAAAAACTATA-TATTATATGTTTTCAAAAATATGTT
1 TTCAAAAACTATATTA-TATATGTTTTCAAAAATATGTT
*
66534 TTCAAAAACTATATATATTATATATTTT
1 TTCAAAAACTATAT-TA-TATATGTTTT
66562 TGAAATTATT
Statistics
Matches: 184, Mismatches: 17, Indels: 27
0.81 0.07 0.12
Matches are distributed among these distances:
34 6 0.03
35 15 0.08
36 20 0.11
37 12 0.07
38 86 0.47
39 27 0.15
40 18 0.10
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (38 bp):
TTCAAAAACTATATTATATATGTTTTCAAAAATATGTT
Found at i:66465 original size:77 final size:76
Alignment explanation
Indices: 66309--66561 Score: 356
Period size: 77 Copynumber: 3.3 Consensus size: 76
66299 TATATATATA
* * * *
66309 TTCAAAAAATATATTATATATG-TTTCAAAAAACCGTTTTAAAAACTATAT-TA-TATGT-TTTC
1 TTCAAAAACTATATTATATATGTTTTCAAAAAACCATTTTAAAAAATATATATATTATATGTTTC
66370 AAAAATATGTT
66 AAAAATATGTT
66381 TTCAAAAACTATATTATATATGTTTTC-AAAAACCATTTTTTAAAAAATATATATATTATATGTT
1 TTCAAAAACTATATTATATATGTTTTCAAAAAACCA--TTTTAAAAAATATATATATTATATGTT
*
66445 TCCAAAATATGTT
64 TCAAAAATATGTT
*
66458 TTCAAAAACTATATTATATATGTTTTCAAAAAACCATTTTAAAAAA-CTATATATTATATGTTTT
1 TTCAAAAACTATATTATATATGTTTTCAAAAAACCATTTTAAAAAATATATATATTATATG-TTT
66522 CAAAAATATGTT
65 CAAAAATATGTT
*
66534 TTCAAAAACTATATATATTATATATTTT
1 TTCAAAAACTATAT-TA-TATATGTTTT
66562 TGAAATTATT
Statistics
Matches: 163, Mismatches: 8, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
72 28 0.17
73 4 0.02
74 14 0.09
75 15 0.09
76 42 0.26
77 43 0.26
78 17 0.10
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (76 bp):
TTCAAAAACTATATTATATATGTTTTCAAAAAACCATTTTAAAAAATATATATATTATATGTTTC
AAAAATATGTT
Found at i:66532 original size:14 final size:14
Alignment explanation
Indices: 66513--66541 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
66503 ACTATATATT
66513 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
66527 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
66541 A
1 A
66542 CTATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
ATATGTTTTCAAAA
Found at i:66585 original size:14 final size:14
Alignment explanation
Indices: 66543--66592 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
66533 TTTCAAAAAC
66543 TATATATATTATATA
1 TATATATATTAT-TA
* * *
66558 TTTTTGAAATTATTA
1 TATAT-ATATTATTA
66573 TATATATATTATTA
1 TATATATATTATTA
66587 TATATA
1 TATATA
66593 CTACATAATG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 14 0.50
15 8 0.29
16 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
TATATATATTATTA
Found at i:66592 original size:115 final size:114
Alignment explanation
Indices: 66309--66556 Score: 305
Period size: 115 Copynumber: 2.2 Consensus size: 114
66299 TATATATATA
* * *
66309 TTCAAAAAATATAT-TA-TATATGTTT-CAAAAAACCGTT-TTAAAAACTATAT-TATATGTTTT
1 TTCAAAAAATATATATATTATATGTTTCCAAAATA-TGTTATCAAAAACTATATATATATGTTTT
** *
66369 CAAAAATATGTTTTCAAAAACTATATTATATATGTTTTCAAAAACCATTT
65 CAAAAATACATTTTAAAAAACTATATTATATATGTTTTCAAAAACCATTT
* *
66419 TTTAAAAAATATATATATTATATGTTTCCAAAATATGTTTTCAAAAACTATATTATATATGTTTT
1 TTCAAAAAATATATATATTATATGTTTCCAAAATATGTTATCAAAAACTATA-TATATATGTTTT
*
66484 CAAAAA-ACCATTTTAAAAAACTATA-TATTATATGTTTTCAAAAA-TATGTT
65 CAAAAATA-CATTTTAAAAAACTATATTA-TATATGTTTTCAAAAACCAT-TT
*
66534 TTCAAAAACTATATATATTATAT
1 TTCAAAAAATATATATATTATAT
66557 ATTTTTGAAA
Statistics
Matches: 119, Mismatches: 10, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
110 13 0.11
111 2 0.02
112 12 0.10
113 17 0.14
114 6 0.05
115 69 0.58
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (114 bp):
TTCAAAAAATATATATATTATATGTTTCCAAAATATGTTATCAAAAACTATATATATATGTTTTC
AAAAATACATTTTAAAAAACTATATTATATATGTTTTCAAAAACCATTT
Done.