Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000102.1 Hibiscus syriacus cultivar Beakdansim tig00000186_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: 70738
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2168 original size:35 final size:36
Alignment explanation
Indices: 2103--2170 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
2093 ATACAATCTG
*
2103 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTAAATCATCACCATAT
* *
2139 TCCATCACCA-TATCTCGCCTAAATTATCACCA
1 TCCATCACCATTATCACGCCTAAATCATCACCA
2171 ACTTATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 19 0.66
36 10 0.34
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTAAATCATCACCATAT
Found at i:2649 original size:14 final size:15
Alignment explanation
Indices: 2614--2642 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2604 AATTTGGAGT
2614 GAAAAAGAAAGAAAA
1 GAAAAAGAAAGAAAA
2629 GAAAAAG-AAGAAAA
1 GAAAAAGAAAGAAAA
2643 TCAAAAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
GAAAAAGAAAGAAAA
Found at i:6059 original size:13 final size:11
Alignment explanation
Indices: 6018--6102 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
6008 ACAATATGTC
6018 CATCACCATTAT
1 CATCACCA-TAT
*
6030 CA-CGCCTATAT
1 CATCACC-ATAT
6041 CATCACCATAGT
1 CATCACCATA-T
6053 CCATCACCATTAT
1 -CATCACCA-TAT
*
6066 CA-CGCCTATAT
1 CATCACC-ATAT
6077 CATCACCATATT
1 CATCACCATA-T
6089 CCATCACCATAT
1 -CATCACCATAT
6101 CA
1 CA
6103 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:6062 original size:36 final size:36
Alignment explanation
Indices: 6015--6119 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
6005 GATACAATAT
6015 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6051 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
6087 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6120 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:10061 original size:15 final size:16
Alignment explanation
Indices: 10018--10063 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
10008 TGGAAATATA
10018 GAAATGGAAGAAGAAAG
1 GAAATGG-AGAAGAAAG
*
10035 GAAAT-GATAAGAAAG
1 GAAATGGAGAAGAAAG
10050 GAAATGGA-AAGAAA
1 GAAATGGAGAAGAAA
10064 TGATATCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 19 0.70
16 3 0.11
17 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.09
Consensus pattern (16 bp):
GAAATGGAGAAGAAAG
Found at i:11649 original size:19 final size:18
Alignment explanation
Indices: 11627--11673 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
11617 AGTGAATAAT
11627 AATATAAGTAATGAAAAGA
1 AATATAAG-AATGAAAAGA
*
11646 AATAATAAGAATGAAATGA
1 AAT-ATAAGAATGAAAAGA
11665 AATA-AAGAA
1 AATATAAGAA
11674 AGGATAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 15 0.58
20 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (18 bp):
AATATAAGAATGAAAAGA
Found at i:12125 original size:19 final size:20
Alignment explanation
Indices: 12078--12128 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
12068 GAAACCGCTT
*
12078 TGAAAATACATGATTATTTA
1 TGAAAATACATGATTATTAA
12098 TGAAAATACATGATT-TTAA
1 TGAAAATACATGATTATTAA
*
12117 TGAAGATACATG
1 TGAAAATACATG
12129 CTCTTGGACG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTATTAA
Found at i:13946 original size:26 final size:25
Alignment explanation
Indices: 13911--13962 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
13901 TTCTATTTTT
*
13911 AAAAAAAAAACAAAAAAGGCAAAAA
1 AAAAAAAAAACAAAAAAGCCAAAAA
13936 AAAAACAAAAACAAAAAAGCCAAAAA
1 AAAAA-AAAAACAAAAAAGCCAAAAA
13962 A
1 A
13963 GCCAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.83, C:0.12, G:0.06, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAACAAAAAAGCCAAAAA
Found at i:17342 original size:19 final size:20
Alignment explanation
Indices: 17301--17351 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
17291 GAAACCCCTT
*
17301 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
17321 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
17340 TGAAGATACATG
1 TGAAAATACATG
17352 CTCTTGGACG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:19134 original size:15 final size:16
Alignment explanation
Indices: 19103--19139 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
19093 CTTTATTATC
19103 TTATTTCATCTTCTGT
1 TTATTTCATCTTCTGT
*
19119 TTATTT-ATCTTTTGT
1 TTATTTCATCTTCTGT
19134 TTATTT
1 TTATTT
19140 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTCTGT
Found at i:19534 original size:10 final size:11
Alignment explanation
Indices: 19491--19515 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19481 TATTTTTTTC
19491 AAAAAAACAAA
1 AAAAAAACAAA
19502 AAAAAAACAAA
1 AAAAAAACAAA
19513 AAA
1 AAA
19516 GGCAAAAAAA
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:19535 original size:19 final size:20
Alignment explanation
Indices: 19498--19541 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
19488 TTCAAAAAAA
*
19498 CAAAAAAAAAACAAAAAAGG
1 CAAAAAAAAAACAAAAAAGC
*
19518 CAAAAAAACAA-AAAAAAGC
1 CAAAAAAAAAACAAAAAAGC
19537 CAAAA
1 CAAAA
19542 TTTCAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.80, C:0.14, G:0.07, T:0.00
Consensus pattern (20 bp):
CAAAAAAAAAACAAAAAAGC
Found at i:23836 original size:15 final size:16
Alignment explanation
Indices: 23805--23841 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
23795 CTTTATTATC
23805 TTATTTCATCTTCTGT
1 TTATTTCATCTTCTGT
*
23821 TTATTT-ATCTTTTGT
1 TTATTTCATCTTCTGT
23836 TTATTT
1 TTATTT
23842 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTCTGT
Found at i:26303 original size:33 final size:33
Alignment explanation
Indices: 26259--26327 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
26249 CATCACTATA
*
26259 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
26292 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
26325 TTC
1 TTC
26328 ATTCATCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:31299 original size:24 final size:22
Alignment explanation
Indices: 31240--31299 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 22
31230 AAATTCAGCA
*
31240 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAA-AAAAGCACTCAAAAG
* *
31263 AATAAATTAAAAGCACTCGAAAAG
1 AAGAAA-AAAAAGCACTC-AAAAG
31287 AAGAAAAAGAAAG
1 AAGAAAAA-AAAG
31300 AAAGAAAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.63, C:0.12, G:0.15, T:0.10
Consensus pattern (22 bp):
AAGAAAAAAAAGCACTCAAAAG
Found at i:37153 original size:13 final size:12
Alignment explanation
Indices: 37134--37219 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
37124 ATATAGGCGT
37134 GATATGGTGATG
1 GATATGGTGATG
37146 GAATATGGTGAT-
1 G-ATATGGTGATG
*
37158 GATATAGGCG-T-
1 GATAT-GGTGATG
37169 GATAATGGTGATG
1 GAT-ATGGTGATG
37182 GACTATGGTGAT-
1 GA-TATGGTGATG
*
37194 GATATAGGCG-T-
1 GATAT-GGTGATG
37205 GATAATGGTGATG
1 GAT-ATGGTGATG
37218 GA
1 GA
37220 CAAATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:37189 original size:36 final size:36
Alignment explanation
Indices: 37116--37220 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
37106 ATTTATAAGT
* *
37116 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
37151 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
37187 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
37221 AAATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:37586 original size:18 final size:18
Alignment explanation
Indices: 37563--37608 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
37553 ACCCCTTTGA
**
37563 AAATACATGATTTTGATG
1 AAATACATGATTTAAATG
*
37581 AAATACATAATTTAAATG
1 AAATACATGATTTAAATG
37599 AAGATACATG
1 AA-ATACATG
37609 CTCTTGGCCG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.33
Consensus pattern (18 bp):
AAATACATGATTTAAATG
Found at i:45372 original size:17 final size:18
Alignment explanation
Indices: 45350--45388 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
45340 GTAGGAGTCT
45350 TTTTCTT-TTCTCTT-TTG
1 TTTTCTTCTT-TCTTGTTG
45367 TTTTCTTCTTTCTTGTTG
1 TTTTCTTCTTTCTTGTTG
45385 TTTT
1 TTTT
45389 TTTGTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (18 bp):
TTTTCTTCTTTCTTGTTG
Found at i:45818 original size:35 final size:37
Alignment explanation
Indices: 45772--45851 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
45762 TTTGAGAATT
*
45772 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
45807 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
45844 TGGTGATG
1 TGGTGATG
45852 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:50588 original size:13 final size:11
Alignment explanation
Indices: 50545--50599 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
50535 ATTGGAGTGC
50545 AAAAAG-AAAG
1 AAAAAGAAAAG
50555 AAAAAGAGAAA-
1 AAAAAGA-AAAG
**
50566 AATCAGAAAAG
1 AAAAAGAAAAG
50577 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
50590 AAAAAGAAAA
1 AAAAAGAAAA
50600 ATTCAAAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
10 9 0.25
11 14 0.39
12 5 0.14
13 8 0.22
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:50609 original size:33 final size:34
Alignment explanation
Indices: 50546--50611 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
50536 TTGGAGTGCA
50546 AAAAGAAAGAAAAAGAGAAAAATCAGAAAAGAAG
1 AAAAGAAAGAAAAAGAGAAAAATCAGAAAAGAAG
*
50580 AAAAGAAAAGAAAAAGA-AAAATTCA-AAAAGAA
1 AAAAG-AAAGAAAAAGAGAAAAATCAGAAAAGAA
50612 AGCAAGCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 7 0.23
34 12 0.40
35 11 0.37
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.05
Consensus pattern (34 bp):
AAAAGAAAGAAAAAGAGAAAAATCAGAAAAGAAG
Found at i:50830 original size:17 final size:18
Alignment explanation
Indices: 50804--50838 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
50794 ACCTTTGAAT
50804 CATTTCTTCTACT-TTTC
1 CATTTCTTCTACTCTTTC
*
50821 CATTTTTTCTACTCTTTC
1 CATTTCTTCTACTCTTTC
50839 TACCCTAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (18 bp):
CATTTCTTCTACTCTTTC
Found at i:54817 original size:19 final size:20
Alignment explanation
Indices: 54793--54832 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
54783 TATCCCATCC
54793 TTATTTCATTTAATT-CTTA
1 TTATTTCATTTAATTACTTA
* *
54812 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTAATTACTTA
54832 T
1 T
54833 ATTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTAATTACTTA
Found at i:55140 original size:13 final size:11
Alignment explanation
Indices: 55097--55151 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
55087 ATTGGAGTGC
55097 AAAAAG-AAAG
1 AAAAAGAAAAG
55107 AAAAAGAGAAA-
1 AAAAAGA-AAAG
**
55118 AATCAGAAAAG
1 AAAAAGAAAAG
55129 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
55142 AAAAAGAAAA
1 AAAAAGAAAA
55152 ATTCAAAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
10 9 0.25
11 14 0.39
12 5 0.14
13 8 0.22
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:55161 original size:33 final size:34
Alignment explanation
Indices: 55098--55163 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
55088 TTGGAGTGCA
55098 AAAAGAAAGAAAAAGAGAAAAATCAGAAAAGAAG
1 AAAAGAAAGAAAAAGAGAAAAATCAGAAAAGAAG
*
55132 AAAAGAAAAGAAAAAGA-AAAATTCA-AAAAGAA
1 AAAAG-AAAGAAAAAGAGAAAAATCAGAAAAGAA
55164 AGCAAGCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 7 0.23
34 12 0.40
35 11 0.37
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.05
Consensus pattern (34 bp):
AAAAGAAAGAAAAAGAGAAAAATCAGAAAAGAAG
Found at i:59366 original size:19 final size:20
Alignment explanation
Indices: 59342--59381 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
59332 TATCCCATCC
59342 TTATTTCATTTAATT-CTTA
1 TTATTTCATTTAATTACTTA
* *
59361 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTAATTACTTA
59381 T
1 T
59382 ATTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTAATTACTTA
Found at i:59689 original size:13 final size:11
Alignment explanation
Indices: 59646--59700 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
59636 ATTGGAGTGC
59646 AAAAAG-AAAG
1 AAAAAGAAAAG
59656 AAAAAGAGAAA-
1 AAAAAGA-AAAG
**
59667 AATCAGAAAAG
1 AAAAAGAAAAG
59678 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
59691 AAAAAGAAAA
1 AAAAAGAAAA
59701 ATTCAAAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
10 9 0.25
11 14 0.39
12 5 0.14
13 8 0.22
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:59710 original size:33 final size:34
Alignment explanation
Indices: 59647--59712 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
59637 TTGGAGTGCA
59647 AAAAGAAAGAAAAAGAGAAAAATCAGAAAAGAAG
1 AAAAGAAAGAAAAAGAGAAAAATCAGAAAAGAAG
*
59681 AAAAGAAAAGAAAAAGA-AAAATTCA-AAAAGAA
1 AAAAG-AAAGAAAAAGAGAAAAATCAGAAAAGAA
59713 AGCAAGCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 7 0.23
34 12 0.40
35 11 0.37
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.05
Consensus pattern (34 bp):
AAAAGAAAGAAAAAGAGAAAAATCAGAAAAGAAG
Found at i:63913 original size:19 final size:20
Alignment explanation
Indices: 63889--63928 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
63879 TATCCCATCC
63889 TTATTTCATTTAATT-CTTA
1 TTATTTCATTTAATTACTTA
* *
63908 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTAATTACTTA
63928 T
1 T
63929 ATTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTAATTACTTA
Found at i:67249 original size:19 final size:20
Alignment explanation
Indices: 67225--67264 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
67215 TATCATTTCC
67225 TTATTTCATATCATT-CTTA
1 TTATTTCATATCATTACTTA
* *
67244 TTATTTCTTTTCATTACTTA
1 TTATTTCATATCATTACTTA
67264 T
1 T
67265 ATTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTCATATCATTACTTA
Found at i:67553 original size:17 final size:17
Alignment explanation
Indices: 67515--67553 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
67505 ATTGGAGTGC
67515 AAAAAGAAAGAAAAAGA
1 AAAAAGAAAGAAAAAGA
*
67532 GAAAAGAAGAGAAAAA-A
1 AAAAAGAA-AGAAAAAGA
67549 AAAAA
1 AAAAA
67554 AAAAAATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAGAAAAAGA
Found at i:68789 original size:21 final size:22
Alignment explanation
Indices: 68765--68807 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
68755 TTATACCTAT
68765 AGATACTTATTTCATAT-TATA
1 AGATACTTATTTCATATATATA
*
68786 AGATAGTTATTTCATATATATA
1 AGATACTTATTTCATATATATA
68808 TATATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (22 bp):
AGATACTTATTTCATATATATA
Found at i:70446 original size:16 final size:16
Alignment explanation
Indices: 70411--70440 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
70401 TTGGAGTGAA
70411 AAAAGAAAGAAAAGAC
1 AAAAGAAAGAAAAGAC
70427 AAAAG-AAGAAAAGA
1 AAAAGAAAGAAAAGA
70441 AGAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAGAAAGAAAAGAC
Done.