Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005391.1 Hibiscus syriacus cultivar Beakdansim tig00012357_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: 61407
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:4190 original size:21 final size:22
Alignment explanation
Indices: 4165--4225 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
4155 TTTTTTTGTA
* *
4165 AAAAGATATTTAAA-TAATAAT
1 AAAAGAGATTTAAAGTAAAAAT
*
4186 AAAAGCGATTTAAAGTAAAAAT
1 AAAAGAGATTTAAAGTAAAAAT
*
4208 AAAAAAAGATTTTAAAGT
1 -AAAAGAGA-TTTAAAGT
4226 TGAAAATGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 12 0.38
22 6 0.19
23 6 0.19
24 8 0.25
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.28
Consensus pattern (22 bp):
AAAAGAGATTTAAAGTAAAAAT
Found at i:4644 original size:18 final size:18
Alignment explanation
Indices: 4621--4688 Score: 127
Period size: 18 Copynumber: 3.8 Consensus size: 18
4611 AAAGTCAATC
4621 TTTGATTTTGAAAACTGT
1 TTTGATTTTGAAAACTGT
*
4639 TTTGATTTTGAAAATTGT
1 TTTGATTTTGAAAACTGT
4657 TTTGATTTTGAAAACTGT
1 TTTGATTTTGAAAACTGT
4675 TTTGATTTTGAAAA
1 TTTGATTTTGAAAA
4689 ATAAGCACAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.51
Consensus pattern (18 bp):
TTTGATTTTGAAAACTGT
Found at i:7642 original size:21 final size:24
Alignment explanation
Indices: 7607--7665 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
7597 CTATCAAAGG
7607 AGTATCAATACTACTCTATATAGT
1 AGTATCAATACTACTCTATATAGT
7631 AGTATCAATACTACTCTATATAGT
1 AGTATCAATACTACTCTATATAGT
7655 AGTATCAATAC
1 AGTATCAATAC
7666 CATTTAATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (24 bp):
AGTATCAATACTACTCTATATAGT
Found at i:11445 original size:13 final size:13
Alignment explanation
Indices: 11427--11451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11417 CTTAGTATAT
11427 TTAAAAATAAAGC
1 TTAAAAATAAAGC
11440 TTAAAAATAAAG
1 TTAAAAATAAAG
11452 GAAAAGCTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.08, T:0.24
Consensus pattern (13 bp):
TTAAAAATAAAGC
Found at i:14686 original size:20 final size:22
Alignment explanation
Indices: 14661--14705 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
14651 TCATAAAATG
*
14661 ATTTATGAATA-CA-AAATAAA
1 ATTTATCAATATCAGAAATAAA
14681 ATTTATCAATATTCAGAAATAAA
1 ATTTATCAATA-TCAGAAATAAA
14704 AT
1 AT
14706 AGATTTCGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
22 2 0.10
23 9 0.43
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (22 bp):
ATTTATCAATATCAGAAATAAA
Found at i:15792 original size:20 final size:20
Alignment explanation
Indices: 15763--15815 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
15753 ATAATTTAGA
15763 ATTA-CTAACGGAAGAATTC
1 ATTAGCTAACGGAAGAATTC
15782 ATTAGCTAACGGAAGAATTC
1 ATTAGCTAACGGAAGAATTC
15802 ATTAGCTAACGGAA
1 ATTAGCTAACGGAA
15816 TCCTCAGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25
Consensus pattern (20 bp):
ATTAGCTAACGGAAGAATTC
Found at i:16194 original size:15 final size:15
Alignment explanation
Indices: 16170--16206 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
16160 AGACTAACAG
*
16170 TTATTCCAATAATCT
1 TTATTTCAATAATCT
16185 TTATTTCAATAATCT
1 TTATTTCAATAATCT
16200 TTATTTC
1 TTATTTC
16207 TTTTTACTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.54
Consensus pattern (15 bp):
TTATTTCAATAATCT
Found at i:16344 original size:12 final size:12
Alignment explanation
Indices: 16327--16355 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
16317 GCGTTCTGAG
16327 ATTGATTTATTC
1 ATTGATTTATTC
16339 ATTGATTTATTC
1 ATTGATTTATTC
16351 ATTGA
1 ATTGA
16356 GTTGCGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (12 bp):
ATTGATTTATTC
Found at i:21950 original size:20 final size:21
Alignment explanation
Indices: 21910--21951 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
21900 TCTTTTAAAT
* *
21910 TTTTTATTTTTCTTTCTTCTA
1 TTTTTATTTCTCTTTCATCTA
21931 TTTTTATTTCTC-TTCATCTA
1 TTTTTATTTCTCTTTCATCTA
21951 T
1 T
21952 AAATCCCCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTATTTCTCTTTCATCTA
Found at i:22913 original size:2 final size:2
Alignment explanation
Indices: 22906--22932 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22896 TTTTTAAAAC
22906 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
22933 CCCCCATCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23088 original size:24 final size:25
Alignment explanation
Indices: 23035--23088 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
23025 AACATAATCC
* *
23035 AAATCAGAACAGAATTCAGGTTATG
1 AAATCAGAACAGAATTCAAGTTAGG
*
23060 -TATCAGAACAGAATTCAAGTT-GG
1 AAATCAGAACAGAATTCAAGTTAGG
23083 AAATCA
1 AAATCA
23089 AATAAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (25 bp):
AAATCAGAACAGAATTCAAGTTAGG
Found at i:24266 original size:17 final size:18
Alignment explanation
Indices: 24233--24266 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24223 TCCATTCTGT
*
24233 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
24251 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
24267 GAACTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:28975 original size:17 final size:18
Alignment explanation
Indices: 28942--28975 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28932 TCCATTATGT
*
28942 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
28960 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
28976 GACCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:30354 original size:21 final size:22
Alignment explanation
Indices: 30325--30370 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
30315 CACATTCTGT
*
30325 AAATATTTACTA-AACTAACACC
1 AAATATTTAC-ACAAATAACACC
30347 AAAT-TTTACACAAATAACACC
1 AAATATTTACACAAATAACACC
30368 AAA
1 AAA
30371 ATAGAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 17 0.77
22 4 0.18
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATATTTACACAAATAACACC
Found at i:39653 original size:13 final size:13
Alignment explanation
Indices: 39635--39682 Score: 87
Period size: 13 Copynumber: 3.7 Consensus size: 13
39625 CGGACTACAG
39635 TAAGGCATAATAT
1 TAAGGCATAATAT
39648 TAAGGCATAATAT
1 TAAGGCATAATAT
39661 TAAGGCATAATAT
1 TAAGGCATAATAT
*
39674 TAAAGCATA
1 TAAGGCATA
39683 CCTGGTGAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29
Consensus pattern (13 bp):
TAAGGCATAATAT
Found at i:40143 original size:23 final size:21
Alignment explanation
Indices: 40089--40171 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
40079 GCATTTTCGT
*
40089 AAGAGCACTTTGTGTACTTGG
1 AAGAGTACTTTGTGTACTTGG
*
40110 -AGTAGTACTTTGTGTATTATGG
1 AAG-AGTACTTTGTGTACT-TGG
* *
40132 CAAGAGTACTTTGTGTACTCGT
1 -AAGAGTACTTTGTGTACTTGG
* *
40154 AATAGCACTTTGTGTACT
1 AAGAGTACTTTGTGTACT
40172 ATGGCACTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 2 0.04
21 29 0.57
22 4 0.08
23 14 0.27
24 2 0.04
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (21 bp):
AAGAGTACTTTGTGTACTTGG
Found at i:40164 original size:44 final size:44
Alignment explanation
Indices: 40089--40177 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
40079 GCATTTTCGT
* * * *
40089 AAGAGCACTTTGTGTACTTGGAGTAGTACTTTGTGTATTATGGC
1 AAGAGCACTTTGTGTACTCGGAATAGCACTTTGTGTACTATGGC
* *
40133 AAGAGTACTTTGTGTACTCGTAATAGCACTTTGTGTACTATGGC
1 AAGAGCACTTTGTGTACTCGGAATAGCACTTTGTGTACTATGGC
40177 A
1 A
40178 CTTTGTGCGC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (44 bp):
AAGAGCACTTTGTGTACTCGGAATAGCACTTTGTGTACTATGGC
Found at i:44147 original size:26 final size:25
Alignment explanation
Indices: 44118--44189 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 25
44108 GGAAGTATGA
*
44118 TATATATATATATATACATATAAAC
1 TATATATATATATATACATACAAAC
* *
44143 TTATATTTATATTTATACTTATACAAAC
1 -TATATATATATATATAC--ATACAAAC
*
44171 -ATAAATATATATATACATA
1 TATATATATATATATACATA
44190 GGACTAATCA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
24 3 0.08
26 28 0.74
28 7 0.18
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (25 bp):
TATATATATATATATACATACAAAC
Found at i:44668 original size:38 final size:39
Alignment explanation
Indices: 44572--44715 Score: 146
Period size: 38 Copynumber: 3.7 Consensus size: 39
44562 GTACACACGA
* *
44572 AAGATGCATTGCACTACATGTGTCTCTTCCCTTTCCCCCCG
1 AAGATGCATTGCACTCCATGTGTCTC--CCCCTTCCCCCCG
* * * *
44613 AATACGCATTGCACTCCATGAGTCTCCCCCTT-CCCCTG
1 AAGATGCATTGCACTCCATGTGTCTCCCCCTTCCCCCCG
* * * *
44651 AAGATGCATTGCACTCCATGTGTCTCCTCGTTTCTCCCG
1 AAGATGCATTGCACTCCATGTGTCTCCCCCTTCCCCCCG
** *
44690 AAGACACATTGCACTCTATGTGTCTC
1 AAGATGCATTGCACTCCATGTGTCTC
44716 TCCCATACCT
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
38 32 0.37
39 32 0.37
41 22 0.26
ACGTcount: A:0.19, C:0.35, G:0.15, T:0.31
Consensus pattern (39 bp):
AAGATGCATTGCACTCCATGTGTCTCCCCCTTCCCCCCG
Found at i:44704 original size:39 final size:38
Alignment explanation
Indices: 44572--44715 Score: 146
Period size: 39 Copynumber: 3.7 Consensus size: 38
44562 GTACACACGA
* * *
44572 AAGATGCATTGCACTACATGTGTCTCTTCCCTTTCCCCCCG
1 AAGACGCATTGCACTCCATGTGTCTCCT-CCTTT--CCCCG
* * *
44613 AATACGCATTGCACTCCATGAGTCTCC-CCCTTCCCCTG
1 AAGACGCATTGCACTCCATGTGTCTCCTCCTTTCCCC-G
* *
44651 AAGATGCATTGCACTCCATGTGTCTCCTCGTTTCTCCCG
1 AAGACGCATTGCACTCCATGTGTCTCCTCCTTTC-CCCG
* *
44690 AAGACACATTGCACTCTATGTGTCTC
1 AAGACGCATTGCACTCCATGTGTCTC
44716 TCCCATACCT
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
37 4 0.05
38 25 0.29
39 32 0.37
40 3 0.03
41 22 0.26
ACGTcount: A:0.19, C:0.35, G:0.15, T:0.31
Consensus pattern (38 bp):
AAGACGCATTGCACTCCATGTGTCTCCTCCTTTCCCCG
Found at i:44719 original size:79 final size:79
Alignment explanation
Indices: 44572--44715 Score: 202
Period size: 77 Copynumber: 1.8 Consensus size: 79
44562 GTACACACGA
* * *
44572 AAGATGCATTGCACTACATGTGTCTCTTCCCTTTCCCCCCGAATACGCATTGCACTCCATGAGTC
1 AAGATGCATTGCACTACATGTGTCTCCTCCCTTTCCCCCCGAAGACACATTGCACTCCATGAGTC
44637 TCCCCCTTCCCCTG
66 TCCCCCTTCCCCTG
* * * * *
44651 AAGATGCATTGCACTCCATGTGTCTCCT-CGTTT-CTCCCGAAGACACATTGCACTCTATGTGTC
1 AAGATGCATTGCACTACATGTGTCTCCTCCCTTTCCCCCCGAAGACACATTGCACTCCATGAGTC
44714 TC
66 TC
44716 TCCCATACCT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
77 27 0.47
78 4 0.07
79 26 0.46
ACGTcount: A:0.19, C:0.35, G:0.15, T:0.31
Consensus pattern (79 bp):
AAGATGCATTGCACTACATGTGTCTCCTCCCTTTCCCCCCGAAGACACATTGCACTCCATGAGTC
TCCCCCTTCCCCTG
Found at i:44915 original size:12 final size:12
Alignment explanation
Indices: 44898--44983 Score: 56
Period size: 12 Copynumber: 7.2 Consensus size: 12
44888 AAAGAAATGA
44898 AAAAGAATAAAG
1 AAAAGAATAAAG
*
44910 AAAAGAAAAAAG
1 AAAAGAATAAAG
*
44922 AAGAA-AATAAAT
1 AA-AAGAATAAAG
*
44934 AATAG-A-AAAG
1 AAAAGAATAAAG
44944 AAGAAGGAATAAGAG
1 AA-AA-GAATAA-AG
*
44959 AAAA-AAGAAAG
1 AAAAGAATAAAG
44970 -AAAGAATAAGAG
1 AAAAGAATAA-AG
44982 AA
1 AA
44984 GAAAGTTAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 19
0.67 0.10 0.23
Matches are distributed among these distances:
10 8 0.14
11 9 0.16
12 27 0.48
13 4 0.07
14 4 0.07
15 4 0.07
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (12 bp):
AAAAGAATAAAG
Found at i:44927 original size:15 final size:15
Alignment explanation
Indices: 44907--44987 Score: 58
Period size: 15 Copynumber: 5.4 Consensus size: 15
44897 AAAAAGAATA
44907 AAGAAAAGAAAAAAG
1 AAGAAAAGAAAAAAG
* *
44922 AAGAAAATAAATAA-
1 AAGAAAAGAAAAAAG
* * *
44936 TAGAAAAGAAGAAGG
1 AAGAAAAGAAAAAAG
* *
44951 AATAAGAGAAAAAAG
1 AAGAAAAGAAAAAAG
*
44966 AA-AGAAAGAATAAGAG
1 AAGA-AAAGAA-AAAAG
44982 AAGAAA
1 AAGAAA
44988 GTTAAAGTCA
Statistics
Matches: 48, Mismatches: 14, Indels: 7
0.70 0.20 0.10
Matches are distributed among these distances:
14 10 0.21
15 29 0.60
16 8 0.17
17 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (15 bp):
AAGAAAAGAAAAAAG
Found at i:44940 original size:24 final size:25
Alignment explanation
Indices: 44903--44971 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 25
44893 AATGAAAAAG
44903 AATAAAGAAAAGAAAA-AAGAAGAA
1 AATAAAGAAAAGAAAAGAAGAAGAA
* * *
44927 AATAAATAATAGAAAAGAAGAAG-G
1 AATAAAGAAAAGAAAAGAAGAAGAA
*
44951 AATAAGAGAAAAAAGAAAGAA
1 AATAA-AGAAAAGA-AAAGAA
44972 AGAATAAGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
24 19 0.53
25 11 0.31
26 6 0.17
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (25 bp):
AATAAAGAAAAGAAAAGAAGAAGAA
Found at i:44976 original size:23 final size:22
Alignment explanation
Indices: 44897--44988 Score: 77
Period size: 23 Copynumber: 4.3 Consensus size: 22
44887 GAAAGAAATG
*
44897 AAAAAGAATAAAG-A-AA-AGA
1 AAAAAGAAGAAAGAATAAGAGA
* *
44916 AAAAAGAAGAAAATAAATAATAG-
1 AAAAAGAAG-AAA-GAATAAGAGA
*
44939 -AAAAGAAGAAGGAATAAGAGA
1 AAAAAGAAGAAAGAATAAGAGA
44960 AAAAAGAAAGAAAGAATAAGAGA
1 AAAAAG-AAGAAAGAATAAGAGA
*
44983 AGAAAG
1 AAAAAG
44989 TTAAAGTCAG
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
19 8 0.14
20 10 0.17
21 2 0.03
22 14 0.24
23 22 0.38
24 2 0.03
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.07
Consensus pattern (22 bp):
AAAAAGAAGAAAGAATAAGAGA
Found at i:47408 original size:23 final size:23
Alignment explanation
Indices: 47382--47425 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
47372 ATGGTAGCAA
* *
47382 ATGGATATGTCGTGGCAAATTGG
1 ATGGAAATGTCGTAGCAAATTGG
*
47405 ATGGAAATGTTGTAGCAAATT
1 ATGGAAATGTCGTAGCAAATT
47426 AAATGGTGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.32
Consensus pattern (23 bp):
ATGGAAATGTCGTAGCAAATTGG
Found at i:47431 original size:23 final size:23
Alignment explanation
Indices: 47380--47431 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
47370 GTATGGTAGC
* *
47380 AAATGGATATGTCGTGGCAAATT
1 AAATGGAAATGTCGTAGCAAATT
** *
47403 GGATGGAAATGTTGTAGCAAATT
1 AAATGGAAATGTCGTAGCAAATT
47426 AAATGG
1 AAATGG
47432 TGAAGATATT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (23 bp):
AAATGGAAATGTCGTAGCAAATT
Found at i:47469 original size:3 final size:3
Alignment explanation
Indices: 47463--47540 Score: 97
Period size: 3 Copynumber: 26.0 Consensus size: 3
47453 CCATTTGTTT
* *
47463 TTA TTA -TA TTA TTA TTA TT- TTA TTTA TCA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
*
47507 TTA TTA TTA TTA TTA TTA TTAA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
47541 CAAATAGATC
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
2 4 0.06
3 55 0.85
4 6 0.09
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:50271 original size:16 final size:16
Alignment explanation
Indices: 50252--50285 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
50242 GATCAATATC
*
50252 TTTTTGCATACATTCA
1 TTTTTGCACACATTCA
*
50268 TTTTTTCACACATTCA
1 TTTTTGCACACATTCA
50284 TT
1 TT
50286 ATTCATTGCA
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:0.24, C:0.21, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTTTGCACACATTCA
Found at i:59373 original size:110 final size:108
Alignment explanation
Indices: 59165--59377 Score: 277
Period size: 110 Copynumber: 2.0 Consensus size: 108
59155 AGCAAGATTT
* *
59165 GAATCCATCACTCAATGGATCAACATTGCCAGAGAAAGTTCATAATAAGAACTCATCTGAAGAAG
1 GAATCCATCACTCAAGGGATCAACATTGCCAGAGAAAGTTCATAATAAAAACTCATCTGAAGAAG
*
59230 GAAGAAAGTTCAAAATGAGAAGAATTTGTTCAACCTTTCGCTC
66 GAAGAAAGTTCAAAATGAGAAGAACTTGTTCAACCTTTCGCTC
* * * * *
59273 GAATTCATCACTC-AGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAAACTTATCTGAAG-
1 GAATCCATCACTCAAGGGATCAACATTGCCAGAGAAAGTTCATAAT-A-AAAACTCATCTGAAGA
* * *
59336 AGGAAGAAGAAGTTTATAATGAGAAGAGCTTGTTCAACCTTT
64 AGGAAG-A-AAGTTCAAAATGAGAAGAACTTGTTCAACCTTT
59378 TGCCTGATTC
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
107 28 0.31
108 19 0.21
109 14 0.16
110 29 0.32
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (108 bp):
GAATCCATCACTCAAGGGATCAACATTGCCAGAGAAAGTTCATAATAAAAACTCATCTGAAGAAG
GAAGAAAGTTCAAAATGAGAAGAACTTGTTCAACCTTTCGCTC
Found at i:59597 original size:191 final size:193
Alignment explanation
Indices: 59230--59639 Score: 596
Period size: 191 Copynumber: 2.1 Consensus size: 193
59220 TCTGAAGAAG
* * *
59230 GAAGAAAGTTCAAAATGAGAAGAATTTGTTCAACCTTTCGCTCGAATTCATCACTCAGGGATCAG
1 GAAG-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTCGCTCGAATTAATCACTCAGGGATCAG
* *
59295 CTTTTCCAGAGAAAGTTCATAATGAGAAAACTTATCTGAAGAGGAAGAAGAAGTTTATAATGAGA
65 CTTTTCCAGAGAAAATTCATAATGAGAAAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
* * * *
59360 AGAGCTTGTTCAACCTTTTGCCTGATTCTATCACAGAAGGAGATAGA-T-CATC-ACTTTTCCA
130 AGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATTACATCAACATTTCCA
* * ** *
59421 GAGGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTCGCTTTAATTAATCACTCGATGGATCAG
1 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCGCTCGAATTAATCACTC-AGGGATCAG
*
59486 CTTTTCCAGAGAAAATTCATAATGAGAAGAACTTATCTGAATAGGAAGAAGAAGTTCATAATGAG
65 CTTTTCCAGAGAAAATTCATAATGAGAA-AACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAG
*
59551 AAGAGCTTGTTCAACCTTTT-TATGACTCTATCACAGAAGAAGATAGATTAGCATCAACATTTCC
129 AAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATTA-CATCAACATTTCC
59615 A
193 A
*
59616 GAAG-TGTTCATAATGAGAAGAACT
1 GAAGAAGTTCATAATGAGAAGAACT
59640 CATATAAAGA
Statistics
Matches: 195, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
190 45 0.23
191 61 0.31
192 55 0.28
194 23 0.12
195 11 0.06
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.29
Consensus pattern (193 bp):
GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCGCTCGAATTAATCACTCAGGGATCAGC
TTTTCCAGAGAAAATTCATAATGAGAAAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
GAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAAGATAGATTACATCAACATTTCCA
Found at i:59952 original size:3 final size:3
Alignment explanation
Indices: 59940--60012 Score: 82
Period size: 3 Copynumber: 25.0 Consensus size: 3
59930 CCATTTGTTT
* *
59940 TTA TTA -TA TTA TTA TTA TT- TTAA TTA TCA CT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
59983 TTA TTA TTA TTA TTA TTAA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
60013 CAACAGATCC
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 7 0.12
3 48 0.80
4 5 0.08
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Done.