Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000492.1 Hibiscus syriacus cultivar Beakdansim tig00000937_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: 72587
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:2708 original size:16 final size:16
Alignment explanation
Indices: 2687--2717 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2677 TCTAACTTTT
*
2687 ATATTTTTAATTTTCA
1 ATATTTTCAATTTTCA
2703 ATATTTTCAATTTTC
1 ATATTTTCAATTTTC
2718 TTAAGAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTTTCAATTTTCA
Found at i:9032 original size:29 final size:29
Alignment explanation
Indices: 9000--9064 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
8990 AGAATGAAAG
* *
9000 AAAATAAAAGTCAGTGGTTAATCTGCAAT
1 AAAATAAAAGTCAGTAGTTAATATGCAAT
*
9029 AAAATAAAAGTTAGTAGTTAATATGCAAT
1 AAAATAAAAGTCAGTAGTTAATATGCAAT
*
9058 TAAATAA
1 AAAATAA
9065 CATAGCAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (29 bp):
AAAATAAAAGTCAGTAGTTAATATGCAAT
Found at i:10387 original size:16 final size:16
Alignment explanation
Indices: 10368--10398 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10358 TTCTAACTTT
*
10368 ATATTTTTAATTTTCA
1 ATATTTTCAATTTTCA
10384 ATATTTTCAATTTTC
1 ATATTTTCAATTTTC
10399 TTAAGAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTTTCAATTTTCA
Found at i:12413 original size:21 final size:21
Alignment explanation
Indices: 12363--12420 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
12353 AAAATTAACA
*
12363 CGAGTGTATCGGTACATTCGG
1 CGAGTGTATCGGTACATTAGG
*
12384 CTA-TGTATCGGTACATTAGAG
1 CGAGTGTATCGGTACATTAG-G
12405 -GAGTGTATCGGTACAT
1 CGAGTGTATCGGTACAT
12421 CCCTTTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (21 bp):
CGAGTGTATCGGTACATTAGG
Found at i:12731 original size:13 final size:13
Alignment explanation
Indices: 12713--12744 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
12703 GATTTTCTTC
12713 TTGAAAATCATTT
1 TTGAAAATCATTT
12726 TTG-AAATCATTT
1 TTGAAAATCATTT
12738 TTGAAAA
1 TTGAAAA
12745 ATTACTCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTGAAAATCATTT
Found at i:14470 original size:13 final size:12
Alignment explanation
Indices: 14441--14474 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
14431 AATGGGCAAT
*
14441 TTTTGAAAACTA
1 TTTTGAAAACGA
14453 TTTTGAAAACGA
1 TTTTGAAAACGA
14465 TGTTTGAAAA
1 T-TTTGAAAA
14475 AAATCATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (12 bp):
TTTTGAAAACGA
Found at i:14982 original size:23 final size:21
Alignment explanation
Indices: 14955--15011 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 21
14945 CACTTGAGGT
14955 GTGTATCGATACACATTCAAG
1 GTGTATCGATACACATTCAAG
* *
14976 GAATGTATCGGTATACATTCAAG
1 G--TGTATCGATACACATTCAAG
*
14999 GTGTGTCGATACA
1 GTGTATCGATACA
15012 TAACAAGGGG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 10 0.34
23 19 0.66
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.30
Consensus pattern (21 bp):
GTGTATCGATACACATTCAAG
Found at i:31405 original size:18 final size:18
Alignment explanation
Indices: 31364--31406 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
31354 TGCTCCAACA
*
31364 TTCTTCTTTTTCTCTGTC
1 TTCTTCTTTGTCTCTGTC
*
31382 TCCTTCTTTGTCTC-GTCC
1 TTCTTCTTTGTCTCTGT-C
31400 TTCTTCT
1 TTCTTCT
31407 CGAGGTCTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.00, C:0.33, G:0.07, T:0.60
Consensus pattern (18 bp):
TTCTTCTTTGTCTCTGTC
Found at i:35465 original size:26 final size:25
Alignment explanation
Indices: 35409--35465 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
35399 CACCGATAAT
35409 ATTTTTCCCTTTTCATTTTGACCAC
1 ATTTTTCCCTTTTCATTTTGACCAC
* *
35434 -TATTTTCCGTTTTTATTTTGACCATC
1 AT-TTTTCCCTTTTCATTTTGACCA-C
35460 ATTTTT
1 ATTTTT
35466 GAAATTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 1 0.04
25 20 0.74
26 5 0.19
27 1 0.04
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.58
Consensus pattern (25 bp):
ATTTTTCCCTTTTCATTTTGACCAC
Found at i:37192 original size:13 final size:13
Alignment explanation
Indices: 37163--37206 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
37153 CAAAAGGGTG
37163 AAAATAAAATAA-A
1 AAAATAAAA-AATA
*
37176 AAAAGATAAAAATA
1 AAAATA-AAAAATA
37190 AAAATAAAAAATA
1 AAAATAAAAAATA
37203 AAAA
1 AAAA
37207 AATGTTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 18 0.67
14 9 0.33
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.14
Consensus pattern (13 bp):
AAAATAAAAAATA
Found at i:37207 original size:7 final size:7
Alignment explanation
Indices: 37163--37207 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
37153 CAAAAGGGTG
37163 AAAATAA
1 AAAATAA
37170 AATAA-AA
1 AA-AATAA
37177 AAAGAT-A
1 AAA-ATAA
37184 AAAAT-A
1 AAAATAA
37190 AAAATAA
1 AAAATAA
37197 AAAATAA
1 AAAATAA
37204 AAAA
1 AAAA
37208 ATGTTAAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
6 9 0.26
7 23 0.68
8 2 0.06
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:38477 original size:39 final size:39
Alignment explanation
Indices: 38391--38651 Score: 212
Period size: 39 Copynumber: 6.8 Consensus size: 39
38381 AATAAAATGA
* * ** *
38391 AAATTACATATTACATATAT-TTTAAAAAAATGTTTTCA
1 AAATTATATATTATATATATATTTTCAAAAATGTTTTCT
*
38429 AAATCATATATTATATATATATTTTCAAAAATGTTTTCT
1 AAATTATATATTATATATATATTTTCAAAAATGTTTTCT
* *
38468 AAATTATATA-T-TATATATATTTTCCAAAATGTTTTTTCA
1 AAATTATATATTATATATATATTTTCAAAAATG--TTTTCT
*
38507 AAACTATATAGTATATATATATATATGTTTTCAAAATTG-TTT-T
1 AAA-T-TATA-TAT-TATATATATA--TTTTCAAAAATGTTTTCT
*
38550 AAA--ACTATA-TA-ATATGTATTTTCAAAAATGTTTT-T
1 AAATTA-TATATTATATATATATTTTCAAAAATGTTTTCT
38585 AAAAATTATATATTATATATATATTTTC-AAAATGTTTTC-
1 --AAATTATATATTATATATATATTTTCAAAAATGTTTTCT
38624 AAA--ACTATA-TA-ATATATATTTTCAAAAA
1 AAATTA-TATATTATATATATATTTTCAAAAA
38652 CTATATATTA
Statistics
Matches: 186, Mismatches: 15, Indels: 47
0.75 0.06 0.19
Matches are distributed among these distances:
34 23 0.12
35 11 0.06
36 10 0.05
37 27 0.15
38 22 0.12
39 48 0.26
40 14 0.08
41 4 0.02
42 2 0.01
43 3 0.02
44 4 0.02
45 8 0.04
47 10 0.05
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (39 bp):
AAATTATATATTATATATATATTTTCAAAAATGTTTTCT
Found at i:38522 original size:46 final size:45
Alignment explanation
Indices: 38472--38569 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 45
38462 TTTTCTAAAT
* *
38472 TATATATTATATATAT-TTTCCAAAATGTTTTTTCAAAACTATATAG
1 TATATATTATATATATGTTTCCAAAAT-TGTTTT-AAAACTATATAA
*
38518 TATATA-TATATATATGTTTTCAAAATTGTTTTAAAACTATATAA
1 TATATATTATATATATGTTTCCAAAATTGTTTTAAAACTATATAA
*
38562 TATGTATT
1 TATATATT
38570 TTCAAAAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
44 16 0.35
45 15 0.33
46 15 0.33
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (45 bp):
TATATATTATATATATGTTTCCAAAATTGTTTTAAAACTATATAA
Found at i:38575 original size:34 final size:35
Alignment explanation
Indices: 38520--38737 Score: 151
Period size: 38 Copynumber: 6.3 Consensus size: 35
38510 CTATATAGTA
*
38520 TATATATATATATGTTTTCAAAATTGTTTT-AAAAC
1 TATATATATATATATTTTCAAAA-TGTTTTAAAAAC
* *
38555 TATATA-ATATGTATTTTCAAAAATGTTTTTAAAAATTA
1 TATATATATATATATTTTC-AAAATG-TTTTAAAAA--C
*
38593 TATATTATATATATATTTTCAAAATGTTTTCAAAAC
1 TATA-TATATATATATTTTCAAAATGTTTTAAAAAC
38629 TATATA-ATATATATTTTC----------AAAAAC
1 TATATATATATATATTTTCAAAATGTTTTAAAAAC
*
38653 TATATATTATATATATTTTCAAAAATCGTTTTCAAAAC
1 TATATA-TATATATATTTTC-AAAAT-GTTTTAAAAAC
* *
38691 TATATATCATAT-TTTTTTCAAAAATATTTTCAAAAAC
1 TATATAT-ATATATATTTTC-AAAATGTTTT-AAAAAC
*
38728 TCTAT-TATAT
1 TATATATATAT
38738 TAATATATAC
Statistics
Matches: 148, Mismatches: 12, Indels: 46
0.72 0.06 0.22
Matches are distributed among these distances:
24 11 0.07
26 12 0.08
34 24 0.16
35 20 0.14
36 13 0.09
37 22 0.15
38 27 0.18
39 8 0.05
40 11 0.07
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.47
Consensus pattern (35 bp):
TATATATATATATATTTTCAAAATGTTTTAAAAAC
Found at i:38578 original size:118 final size:122
Alignment explanation
Indices: 38416--38642 Score: 333
Period size: 118 Copynumber: 1.9 Consensus size: 122
38406 TATATTTTAA
38416 AAAAATGTTTTCAAAATCATATATTATATATATATTTTCAAAAATGTTTTCT-AAATTATATATT
1 AAAAATGTTTTCAAAATCATATATTATATATATATTTTCAAAAATGTTTT-TAAAATTATATATT
*
38480 ATATATAT-TTTCCAAAATGTTTTTTCAAAACTATATAGTATATATATATATATGTTTTC
65 ATATATATATTTCCAAAATG--TTTTCAAAACTATATAATATATATATATATATGTTTTC
* *
38539 AAAATTGTTTT-AAAA-C-TATA-TA-ATATGTATTTTCAAAAATGTTTTTAAAAATTATATATT
1 AAAAATGTTTTCAAAATCATATATTATATATATATTTTCAAAAATGTTTTT-AAAATTATATATT
*
38599 ATATATATATTTTCAAAATGTTTTCAAAACTATATAATATATAT
65 ATATATATATTTCCAAAATGTTTTCAAAACTATATAATATATAT
38643 TTTCAAAAAC
Statistics
Matches: 97, Mismatches: 4, Indels: 11
0.87 0.04 0.10
Matches are distributed among these distances:
117 1 0.01
118 45 0.46
119 22 0.23
120 14 0.14
121 1 0.01
122 4 0.04
123 10 0.10
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (122 bp):
AAAAATGTTTTCAAAATCATATATTATATATATATTTTCAAAAATGTTTTTAAAATTATATATTA
TATATATATTTCCAAAATGTTTTCAAAACTATATAATATATATATATATATGTTTTC
Found at i:38628 original size:74 final size:74
Alignment explanation
Indices: 38405--38651 Score: 300
Period size: 74 Copynumber: 3.2 Consensus size: 74
38395 TACATATTAC
* * * *
38405 ATATATTTTAAAAAAATG-TTTTCAAAATCATATATTATATATATATTTTCAAAAATGTTTTCTA
1 ATATATTTT-CAAAAATGTTTTTAAAAATTATATATTATATATATATTTTC-AAAATGTTTTCAA
*
38469 AATTATATATTAT
64 AACTATATA--AT
* *
38482 ATATATTTTCCAAAATGTTTTTTCAAAACTATATAGTATATATATATATATGTTTTCAAAATTGT
1 ATATATTTTCAAAAATG-TTTTT-AAAA--AT-TA-TATAT-TATATATATATTTTCAAAA-TGT
38547 TTT-AAAACTATATAAT
58 TTTCAAAACTATATAAT
*
38563 ATGTATTTTCAAAAATGTTTTTAAAAATTATATATTATATATATATTTTCAAAATGTTTTCAAAA
1 ATATATTTTCAAAAATGTTTTTAAAAATTATATATTATATATATATTTTCAAAATGTTTTCAAAA
38628 CTATATAAT
66 CTATATAAT
38637 ATATATTTTCAAAAA
1 ATATATTTTCAAAAA
38652 CTATATATTA
Statistics
Matches: 149, Mismatches: 11, Indels: 23
0.81 0.06 0.13
Matches are distributed among these distances:
73 6 0.04
74 45 0.30
75 5 0.03
76 8 0.05
77 11 0.07
78 4 0.03
79 7 0.05
80 5 0.03
81 19 0.13
82 1 0.01
83 18 0.12
84 20 0.13
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (74 bp):
ATATATTTTCAAAAATGTTTTTAAAAATTATATATTATATATATATTTTCAAAATGTTTTCAAAA
CTATATAAT
Found at i:38633 original size:38 final size:36
Alignment explanation
Indices: 38518--38650 Score: 143
Period size: 34 Copynumber: 3.7 Consensus size: 36
38508 AACTATATAG
*
38518 TATATATATATATATGTTTTCAAAATTGTTTTAAAAC
1 TATATATATATATATATTTTCAAAA-TGTTTTAAAAC
* *
38555 --TATATA-ATATGTATTTTCAAAAATGTTTTTAAAAAT
1 TATATATATATATATATTTTC-AAAATG-TTTT-AAAAC
38591 TATATATTATATATATATTTTCAAAATGTTTTCAAAAC
1 TATATA-TATATATATATTTTCAAAATGTTTT-AAAAC
38629 --TATATA-ATATATATTTTCAAAA
1 TATATATATATATATATTTTCAAAA
38651 ACTATATATT
Statistics
Matches: 83, Mismatches: 6, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
34 28 0.34
35 16 0.19
36 8 0.10
38 12 0.14
39 8 0.10
40 11 0.13
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (36 bp):
TATATATATATATATATTTTCAAAATGTTTTAAAAC
Found at i:38656 original size:24 final size:25
Alignment explanation
Indices: 38619--38677 Score: 95
Period size: 26 Copynumber: 2.4 Consensus size: 25
38609 TTTCAAAATG
38619 TTTTC-AAAACTATATA-ATATATA
1 TTTTCAAAAACTATATATATATATA
38642 TTTTCAAAAACTATATATTATATATA
1 TTTTCAAAAACTATATA-TATATATA
38668 TTTTCAAAAA
1 TTTTCAAAAA
38678 TCGTTTTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
23 5 0.15
24 11 0.33
26 17 0.52
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (25 bp):
TTTTCAAAAACTATATATATATATA
Found at i:38657 original size:62 final size:63
Alignment explanation
Indices: 38580--38714 Score: 188
Period size: 62 Copynumber: 2.2 Consensus size: 63
38570 TTCAAAAATG
* *
38580 TTTTTAAAAATTATATATTATATATATATTTTC-AAAAT-GTTTTCAAAACTATATA--ATATAT
1 TTTTCAAAAACTATATA-T-TATATATATTTTCAAAAATCGTTTTCAAAACTATATATCATAT-T
38641 A
63 A
*
38642 TTTTCAAAAACTATATATTATATATATTTTCAAAAATCGTTTTCAAAACTATATATCATATTT
1 TTTTCAAAAACTATATATTATATATATTTTCAAAAATCGTTTTCAAAACTATATATCATATTA
38705 TTTTCAAAAA
1 TTTTCAAAAA
38715 TATTTTCAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
60 13 0.20
61 6 0.09
62 32 0.48
63 11 0.17
64 4 0.06
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.47
Consensus pattern (63 bp):
TTTTCAAAAACTATATATTATATATATTTTCAAAAATCGTTTTCAAAACTATATATCATATTA
Found at i:39435 original size:16 final size:16
Alignment explanation
Indices: 39416--39462 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
39406 AGCTATGCTA
39416 TAAATTTGATATGCCG
1 TAAATTTGATATGCCG
39432 TAAATTTGATATGCCG
1 TAAATTTGATATGCCG
39448 TAAATTTGATATGCC
1 TAAATTTGATATGCC
39463 CTTGAGCTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (16 bp):
TAAATTTGATATGCCG
Found at i:48173 original size:29 final size:29
Alignment explanation
Indices: 48141--48205 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
48131 AGAATGAAAG
* *
48141 AAAATAAAAGTCAGTGGTTAATCTGCAAT
1 AAAATAAAAGTCAGTAGTTAATATGCAAT
*
48170 AAAATAAAAGTTAGTAGTTAATATGCAAT
1 AAAATAAAAGTCAGTAGTTAATATGCAAT
*
48199 TAAATAA
1 AAAATAA
48206 CATAGCAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (29 bp):
AAAATAAAAGTCAGTAGTTAATATGCAAT
Found at i:49536 original size:16 final size:16
Alignment explanation
Indices: 49517--49547 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49507 TTCTAACTTT
*
49517 ATATTTTTAATTTTCA
1 ATATTTTCAATTTTCA
49533 ATATTTTCAATTTTC
1 ATATTTTCAATTTTC
49548 TTAAGAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTTTCAATTTTCA
Found at i:51585 original size:21 final size:21
Alignment explanation
Indices: 51535--51592 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
51525 AAAATTAACA
*
51535 CGAGTGTATCGGTACATTCGG
1 CGAGTGTATCGGTACATTAGG
*
51556 CTA-TGTATCGGTACATTAGAG
1 CGAGTGTATCGGTACATTAG-G
51577 -GAGTGTATCGGTACAT
1 CGAGTGTATCGGTACAT
51593 CCCTTTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (21 bp):
CGAGTGTATCGGTACATTAGG
Found at i:51904 original size:13 final size:13
Alignment explanation
Indices: 51886--51917 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
51876 GATTTTCTTC
51886 TTGAAAATCATTT
1 TTGAAAATCATTT
51899 TTG-AAATCATTT
1 TTGAAAATCATTT
51911 TTGAAAA
1 TTGAAAA
51918 ATTACTCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTGAAAATCATTT
Found at i:53644 original size:13 final size:12
Alignment explanation
Indices: 53615--53648 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
53605 AATGGGCAAT
*
53615 TTTTGAAAACTA
1 TTTTGAAAACGA
53627 TTTTGAAAACGA
1 TTTTGAAAACGA
53639 TGTTTGAAAA
1 T-TTTGAAAA
53649 AAATCATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (12 bp):
TTTTGAAAACGA
Found at i:54163 original size:23 final size:21
Alignment explanation
Indices: 54136--54192 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
54126 CACTTGAGGT
*
54136 GTGTATCGATACACATTCAAG
1 GTGTATCGATACACACTCAAG
* *
54157 GAATGTATCGGTATACACTCAAG
1 G--TGTATCGATACACACTCAAG
*
54180 GTGTGTCGATACA
1 GTGTATCGATACA
54193 TAGCAAGGGG
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
21 10 0.36
23 18 0.64
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (21 bp):
GTGTATCGATACACACTCAAG
Found at i:70520 original size:18 final size:18
Alignment explanation
Indices: 70479--70521 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
70469 TGCTCCAACA
*
70479 TTCTTCTTTTTCTCTGTC
1 TTCTTCTTTGTCTCTGTC
*
70497 TCCTTCTTTGTCTC-GTCC
1 TTCTTCTTTGTCTCTGT-C
70515 TTCTTCT
1 TTCTTCT
70522 CGAGGTCTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.00, C:0.33, G:0.07, T:0.60
Consensus pattern (18 bp):
TTCTTCTTTGTCTCTGTC
Done.