Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005543.1 Hibiscus syriacus cultivar Beakdansim tig00012837_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: 44573
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:7851 original size:22 final size:24
Alignment explanation
Indices: 7826--7876 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
7816 TATAATCTCA
7826 AATTTTAATT-AAA-TATATCATT
1 AATTTTAATTAAAACTATATCATT
*
7848 AATTTTGATTCAAAACTATATCATT
1 AATTTTAATT-AAAACTATATCATT
7873 AATT
1 AATT
7877 GAAAAAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 9 0.36
24 3 0.12
25 13 0.52
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (24 bp):
AATTTTAATTAAAACTATATCATT
Found at i:12921 original size:29 final size:28
Alignment explanation
Indices: 12889--12955 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
12879 AATATTTTTC
12889 ATTATTAAAATTTTAAAAG-TTATAAAATA
1 ATTATTAAAATTTTAAAAGATTAT-AAA-A
***
12918 ATTATTACTTTTTTAAAAGATTATAAAA
1 ATTATTAAAATTTTAAAAGATTATAAAA
12946 ATTATTAAAA
1 ATTATTAAAA
12956 CATCAAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 8 0.26
29 19 0.61
30 4 0.13
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (28 bp):
ATTATTAAAATTTTAAAAGATTATAAAA
Found at i:15490 original size:20 final size:20
Alignment explanation
Indices: 15465--15643 Score: 125
Period size: 20 Copynumber: 8.8 Consensus size: 20
15455 ATGCGAAACA
*
15465 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* * *
15485 AAAATCGCAATGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
15505 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
15525 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
15546 AAGAATCGCAATGCGATTCAA-
1 AA-AATCGCAACGCGATT-AAG
* *
15567 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTAAG
*
15587 AAAATCGCAACGCGATTCCAG
1 AAAATCGCAACGCGATT-AAG
* * *
15608 -GAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTAAG
15627 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
15644 CCAAGAATCG
Statistics
Matches: 125, Mismatches: 23, Indels: 22
0.74 0.14 0.13
Matches are distributed among these distances:
18 1 0.01
19 3 0.02
20 98 0.78
21 9 0.07
22 14 0.11
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:15603 original size:40 final size:40
Alignment explanation
Indices: 15549--15656 Score: 180
Period size: 40 Copynumber: 2.7 Consensus size: 40
15539 ATCTTCCAAG
* *
15549 AATCGCAATGCGATTCAAAGAATCGCAACGCGATTGAGAA
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
* *
15589 AATCGCAACGCGATTCCAGGAATCGCAATGCGATTGAGAA
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
15629 AATCGCAACGCGATTCCAAGAATCGCAA
1 AATCGCAACGCGATTCCAAGAATCGCAA
15657 AACGGCAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (40 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
Found at i:15635 original size:60 final size:61
Alignment explanation
Indices: 15523--15643 Score: 192
Period size: 60 Copynumber: 2.0 Consensus size: 61
15513 AACGGTCAAA
15523 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
1 AGAAAATCGCAACGCGA-CTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
* *
15585 AGAAAATCGCAACGCGA-TTCCAGGAATCGCAATGCGATTGAGAA-AATCGCAACGCGATT
1 AGAAAATCGCAACGCGACTTCCAAGAATCGCAATGCGATTCA-AAGAATCGCAACGCGATT
15644 CCAAGAATCG
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
60 37 0.66
61 2 0.04
62 17 0.30
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.17
Consensus pattern (61 bp):
AGAAAATCGCAACGCGACTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
Found at i:15652 original size:20 final size:20
Alignment explanation
Indices: 15527--15656 Score: 138
Period size: 20 Copynumber: 6.4 Consensus size: 20
15517 GTCAAAAGAA
15527 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAG
* *
15549 AATCGCAATGCGATTCAAAG
1 AATCGCAACGCGATTCCAAG
* *
15569 AATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
*
15589 AATCGCAACGCGATTCCAGG
1 AATCGCAACGCGATTCCAAG
* * *
15609 AATCGCAATGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
15629 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
15649 AATCGCAA
1 AATCGCAA
15657 AACGGCAAAA
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
19 2 0.02
20 73 0.82
21 2 0.02
22 12 0.13
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGATTCCAAG
Found at i:15778 original size:6 final size:6
Alignment explanation
Indices: 15767--15793 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
15757 GACACGTATT
15767 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
15794 CGAGACAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:16559 original size:6 final size:6
Alignment explanation
Indices: 16548--16586 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
16538 TCTCGTCTCG
16548 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
16587 AATACGTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:16757 original size:20 final size:19
Alignment explanation
Indices: 16732--17043 Score: 225
Period size: 20 Copynumber: 15.6 Consensus size: 19
16722 ATTTTCTCAA
16732 TTGCGATTCTTGGAATCGCG
1 TTGCGATT-TTGGAATCGCG
**
16752 TTGCGATTTTCTCAATCGCG
1 TTGCGATTTT-GGAATCGCG
16772 TTGCGATTATTGGAATCGCG
1 TTGCGATT-TTGGAATCGCG
**
16792 TTGCGATTTTCTCAATCGCG
1 TTGCGATTTT-GGAATCGCG
16812 TTGCGATTATTGGAATCGCG
1 TTGCGATT-TTGGAATCGCG
**
16832 TTGCGATTTTCTCAATCGCG
1 TTGCGATTTT-GGAATCGCG
16852 TTGCGATTATTGGAATCGCG
1 TTGCGATT-TTGGAATCGCG
**
16872 TTGCGATTTTCTCAATCGCG
1 TTGCGATTTT-GGAATCGCG
* *
16892 TTGCGATTCTTCGAAGATCGCA
1 TTGCGATT-TT-GGA-ATCGCG
*
16914 TTGCGATTCTTGGAATCGCA
1 TTGCGATT-TTGGAATCGCG
*
16934 TTGCGATTCTTTGG-CTCGCG
1 TTGCGA-T-TTTGGAATCGCG
*** *
16954 TTGCGATTTT-CTTTTGACCG
1 TTGCGATTTTGGAATCG--CG
**** *
16974 TTGCGATTTTCTTTTCAACG
1 TTGCGATTTTGGAATC-GCG
**
16994 TTGCGATTTTCTAAATCGCG
1 TTGCGATTTT-GGAATCGCG
17014 TTGCGATTTT-GATATCGCG
1 TTGCGATTTTGGA-ATCGCG
17033 TTGCGATTTTG
1 TTGCGATTTTG
17044 TTGGTCATTT
Statistics
Matches: 241, Mismatches: 32, Indels: 38
0.77 0.10 0.12
Matches are distributed among these distances:
18 6 0.02
19 25 0.10
20 171 0.71
21 22 0.09
22 17 0.07
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (19 bp):
TTGCGATTTTGGAATCGCG
Found at i:16787 original size:40 final size:40
Alignment explanation
Indices: 16697--17042 Score: 365
Period size: 40 Copynumber: 8.8 Consensus size: 40
16687 TTTTGCCGTT
* *
16697 TTGCGATTCTTGGAATCGCATTGCGATTTTCTCAA-----
1 TTGCGATTATTGGAATCGCGTTGCGATTTTCTCAATCGCG
*
16732 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTATTGGAATCGCGTTGCGATTTTCTCAATCGCG
16772 TTGCGATTATTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTATTGGAATCGCGTTGCGATTTTCTCAATCGCG
16812 TTGCGATTATTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTATTGGAATCGCGTTGCGATTTTCTCAATCGCG
16852 TTGCGATTATTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTATTGGAATCGCGTTGCGATTTTCTCAATCGCG
* * * ** *
16892 TTGCGATTCTTCGAAGATCGCATTGCGATTCTT-GGAATCGCA
1 TTGCGATTATT-GGA-ATCGCGTTGCGATT-TTCTCAATCGCG
* * * *
16934 TTGCGATTCTTTGG-CTCGCGTTGCGATTTTCT--TTTGACCG
1 TTGCGATT-ATTGGAATCGCGTTGCGATTTTCTCAATCG--CG
**** * *
16974 TTGCGATT-TTCTTTTCAACGTTGCGATTTTCTAAATCGCG
1 TTGCGATTATTGGAATC-GCGTTGCGATTTTCTCAATCGCG
17014 TTGCGATT-TT-GATATCGCGTTGCGATTTT
1 TTGCGATTATTGGA-ATCGCGTTGCGATTTT
17043 GTTGGTCATT
Statistics
Matches: 268, Mismatches: 26, Indels: 30
0.83 0.08 0.09
Matches are distributed among these distances:
35 34 0.13
38 4 0.01
39 16 0.06
40 178 0.66
41 2 0.01
42 30 0.11
43 4 0.01
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.40
Consensus pattern (40 bp):
TTGCGATTATTGGAATCGCGTTGCGATTTTCTCAATCGCG
Found at i:26178 original size:20 final size:20
Alignment explanation
Indices: 26137--26207 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
26127 AACGCGATTT
**
26137 CAAATTCGCAACAC-GAACTC
1 CAAATTCGCAACACAG-TTTC
*
26157 CAATTTCGCAACACAGTTTC
1 CAAATTCGCAACACAGTTTC
* *
26177 CAAATTCGCAACTCAGTTTT
1 CAAATTCGCAACACAGTTTC
26197 CAAATTCGCAA
1 CAAATTCGCAA
26208 GTCGAATTCG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
20 43 0.98
21 1 0.02
ACGTcount: A:0.35, C:0.30, G:0.10, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACACAGTTTC
Found at i:26594 original size:21 final size:21
Alignment explanation
Indices: 26543--26613 Score: 85
Period size: 20 Copynumber: 3.4 Consensus size: 21
26533 CGAATTCGAA
*
26543 TTGCGAATTTGGGAAATTCGTG
1 TTGCGAATTT-GGAAACTCGTG
26565 TTGCGAATTTGGAAACT-GTG
1 TTGCGAATTTGGAAACTCGTG
*
26585 TTGCGAAATTT-GAAA-TCGCG
1 TTGCG-AATTTGGAAACTCGTG
26605 TTGCGAATT
1 TTGCGAATT
26614 CGTTGGTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
19 5 0.11
20 19 0.42
21 11 0.24
22 10 0.22
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.35
Consensus pattern (21 bp):
TTGCGAATTTGGAAACTCGTG
Found at i:28547 original size:29 final size:29
Alignment explanation
Indices: 28514--28582 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
28504 TTTAAATATT
28514 AAAATTATGAATGAAATAAATCAAATTAA
1 AAAATTATGAATGAAATAAATCAAATTAA
* *
28543 AAAATTATGAATGACATAAATTAAATTAA
1 AAAATTATGAATGAAATAAATCAAATTAA
28572 AAAATTATGAA
1 AAAATTATGAA
28583 ATATTAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (29 bp):
AAAATTATGAATGAAATAAATCAAATTAA
Found at i:30060 original size:15 final size:15
Alignment explanation
Indices: 30012--30063 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
30002 ATCAATATTA
30012 ATATTATTAATAAATT
1 ATATT-TTAATAAATT
* *
30028 AT-TTTTAAAAAATA
1 ATATTTTAATAAATT
*
30042 ATATTTTAATATATT
1 ATATTTTAATAAATT
30057 ATATTTT
1 ATATTTT
30064 CGAGCTGGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 10 0.33
15 18 0.60
16 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATATTTTAATAAATT
Found at i:31192 original size:10 final size:10
Alignment explanation
Indices: 31179--31205 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
31169 AAACTATTAA
31179 TTTTAATTTG
1 TTTTAATTTG
31189 TTTTAATTTG
1 TTTTAATTTG
31199 TTTTAAT
1 TTTTAAT
31206 ATTTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (10 bp):
TTTTAATTTG
Found at i:31227 original size:18 final size:18
Alignment explanation
Indices: 31204--31247 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
31194 ATTTGTTTTA
31204 ATATTTAATTTTTTAATT
1 ATATTTAATTTTTTAATT
31222 ATATTTAATTTTTTAATT
1 ATATTTAATTTTTTAATT
31240 ATATTTAA
1 ATATTTAA
31248 AGTTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTTAATTTTTTAATT
Found at i:32180 original size:17 final size:17
Alignment explanation
Indices: 32158--32214 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
32148 TAGAGAAAAT
32158 AAAATAAATGAAATAAA
1 AAAATAAATGAAATAAA
32175 AAAATAATATGAAGATAAA
1 AAAATAA-ATGAA-ATAAA
* *
32194 AATAT-AATAAAAATAAA
1 AAAATAAAT-GAAATAAA
32211 AAAA
1 AAAA
32215 GATAAAGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 17 0.50
18 8 0.24
19 9 0.26
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.19
Consensus pattern (17 bp):
AAAATAAATGAAATAAA
Found at i:32202 original size:22 final size:18
Alignment explanation
Indices: 32153--32237 Score: 56
Period size: 17 Copynumber: 4.7 Consensus size: 18
32143 TAAGTTAGAG
32153 AAAATAAAATAAATGAAAT
1 AAAAT-AAATAAATGAAAT
32172 AAAA-AAATAATATGAAGAT
1 AAAATAAATAA-ATGAA-AT
32191 AAAAATATAAT-AA--AAAT
1 -AAAATA-AATAAATGAAAT
*
32208 AAAAAAAGATAAA-G-AAT
1 AAAATAA-ATAAATGAAAT
32225 AAAAATAAATAAA
1 -AAAATAAATAAA
32238 AATAAAGATA
Statistics
Matches: 55, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
15 1 0.02
16 7 0.13
17 18 0.33
18 13 0.24
19 6 0.11
20 5 0.09
21 2 0.04
22 3 0.05
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (18 bp):
AAAATAAATAAATGAAAT
Found at i:32225 original size:23 final size:23
Alignment explanation
Indices: 32199--32245 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
32189 ATAAAAATAT
32199 AATAAAAATAAA-AAAAGATAAAG
1 AATAAAAATAAATAAAA-ATAAAG
32222 AATAAAAATAAATAAAAATAAAG
1 AATAAAAATAAATAAAAATAAAG
32245 A
1 A
32246 TAAGCTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (23 bp):
AATAAAAATAAATAAAAATAAAG
Found at i:32240 original size:10 final size:10
Alignment explanation
Indices: 32189--32243 Score: 58
Period size: 10 Copynumber: 5.1 Consensus size: 10
32179 TAATATGAAG
32189 ATAAAAATATA
1 ATAAAAATA-A
32200 ATAAAAATAA
1 ATAAAAATAA
32210 A-AAAAGATAAAGA
1 ATAAAA-AT--A-A
32223 ATAAAAATAA
1 ATAAAAATAA
32233 ATAAAAATAA
1 ATAAAAATAA
32243 A
1 A
32244 GATAAGCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
9 4 0.10
10 16 0.41
11 10 0.26
12 1 0.03
13 4 0.10
14 4 0.10
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (10 bp):
ATAAAAATAA
Found at i:32255 original size:34 final size:33
Alignment explanation
Indices: 32158--32266 Score: 107
Period size: 34 Copynumber: 3.2 Consensus size: 33
32148 TAGAGAAAAT
* *
32158 AAAATAAATGAAATAA-AAAAATAATATGAAG-ATA
1 AAAATAAAT-AAA-AATAAAAA-AAGATAAAGAATA
32192 AAAATATAATAAAAATAAAAAAAGATAAAGAATA
1 AAAATA-AATAAAAATAAAAAAAGATAAAGAATA
* *
32226 AAAATAAATAAAAATAAAGATAAGCTAAAGAA-A
1 AAAATAAATAAAAATAAA-AAAAGATAAAGAATA
*
32259 ATAATAAA
1 AAAATAAA
32267 AGGAAAAATA
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
33 29 0.44
34 34 0.52
35 3 0.05
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.18
Consensus pattern (33 bp):
AAAATAAATAAAAATAAAAAAAGATAAAGAATA
Found at i:32304 original size:4 final size:4
Alignment explanation
Indices: 32297--32415 Score: 56
Period size: 4 Copynumber: 30.5 Consensus size: 4
32287 ATATATAATC
* * *
32297 AATA AATA AACA AA-A CAATA ATATA AAAA ACATA AAGGA AAT- AA-A
1 AATA AATA AATA AATA -AATA A-ATA AATA A-ATA AA-TA AATA AATA
* *
32342 AATA AATA AA-A AATA AATA AACA AACA AAGTA AA-A AATA AAT- AA-A
1 AATA AATA AATA AATA AATA AATA AATA AA-TA AATA AATA AATA AATA
* * * *
32387 AAGA AATA TATA TATA TAT- AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
32416 ATAATAACAA
Statistics
Matches: 92, Mismatches: 10, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
3 17 0.18
4 61 0.66
5 14 0.15
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.19
Consensus pattern (4 bp):
AATA
Found at i:32355 original size:11 final size:11
Alignment explanation
Indices: 32335--32388 Score: 74
Period size: 11 Copynumber: 4.8 Consensus size: 11
32325 AACATAAAGG
32335 AAAT-AAAAAT
1 AAATAAAAAAT
32345 AAATAAAAAAT
1 AAATAAAAAAT
*
32356 AAATAAACAAAC
1 AAATAAA-AAAT
32368 AAAGTAAAAAAT
1 AAA-TAAAAAAT
32380 AAATAAAAA
1 AAATAAAAA
32389 GAAATATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
10 4 0.10
11 19 0.49
12 12 0.31
13 4 0.10
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.15
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:32543 original size:15 final size:16
Alignment explanation
Indices: 32532--32579 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 16
32522 AACAATAAGA
32532 AATAAAATAATAAAAT
1 AATAAAATAATAAAAT
*
32548 AAT-AAATAATAATAT
1 AATAAAATAATAAAAT
32563 AA-ATAAATAAATAAAAT
1 AATA-AAAT-AATAAAAT
32580 GATTATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 13 0.48
16 7 0.26
17 7 0.26
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AATAAAATAATAAAAT
Found at i:32545 original size:8 final size:8
Alignment explanation
Indices: 32532--32579 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
32522 AACAATAAGA
32532 AATAAAAT
1 AATAAAAT
32540 AATAAAAT
1 AATAAAAT
32548 AAT-AAAT
1 AATAAAAT
*
32555 AATAATAT
1 AATAAAAT
32563 AA-ATAAAT
1 AATA-AAAT
32571 AAATAAAAT
1 -AATAAAAT
32580 GATTATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
7 8 0.24
8 19 0.56
9 6 0.18
10 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
AATAAAAT
Found at i:32546 original size:23 final size:24
Alignment explanation
Indices: 32520--32577 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
32510 ATATCGTATA
32520 AAAACAATAAGA-AATAAAAT-AAT
1 AAAACAATAA-ATAATAAAATAAAT
* *
32543 AAAATAATAAATAATAATATAAAT
1 AAAACAATAAATAATAAAATAAAT
32567 AAATA-AATAAA
1 AAA-ACAATAAA
32578 ATGATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 1 0.03
23 16 0.53
24 12 0.40
25 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAACAATAAATAATAAAATAAAT
Found at i:32554 original size:20 final size:21
Alignment explanation
Indices: 32525--32579 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
32515 GTATAAAAAC
*
32525 AATAAGAAATAAAATAATA-A
1 AATAATAAATAAAATAATATA
32545 AATAATAAAT--AATAATATA
1 AATAATAAATAAAATAATATA
32564 AATAAATAAATAAAAT
1 AAT-AATAAATAAAAT
32580 GATTATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.23
19 4 0.13
20 16 0.53
22 3 0.10
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (21 bp):
AATAATAAATAAAATAATATA
Found at i:33775 original size:31 final size:31
Alignment explanation
Indices: 33713--33778 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
33703 TAATAACGTG
* * * **
33713 ATATTTTTATACATGTTTAATTGATTTCATA
1 ATATTTTCATAAATGTTTAACTGATGACATA
*
33744 ATATTTTCATAAATGTTTTACTGATGACATA
1 ATATTTTCATAAATGTTTAACTGATGACATA
33775 ATAT
1 ATAT
33779 GTATTACATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (31 bp):
ATATTTTCATAAATGTTTAACTGATGACATA
Found at i:35750 original size:51 final size:50
Alignment explanation
Indices: 35690--35792 Score: 134
Period size: 51 Copynumber: 2.0 Consensus size: 50
35680 CGTGCTCATG
** * * *
35690 CACCGCGTTATACGATGATTTGGCGTCACGTGAGGTATAGCGCGCCCCCTA
1 CACCGCGTTATACGATGAGCTGGCGCCACGTG-GGTATAGCGCGACCCATA
* *
35741 CACCGCGTTATACGGTGAGCTGGCGCCATGTGGGTATAGCGCGACCCATA
1 CACCGCGTTATACGATGAGCTGGCGCCACGTGGGTATAGCGCGACCCATA
35791 CA
1 CA
35793 GTGCGCTATA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
50 18 0.40
51 27 0.60
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.21
Consensus pattern (50 bp):
CACCGCGTTATACGATGAGCTGGCGCCACGTGGGTATAGCGCGACCCATA
Found at i:38821 original size:3 final size:3
Alignment explanation
Indices: 38810--38852 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
38800 TCATCATCAC
* * * *
38810 CGT CAT CGT CGT CAT TGT CGT CGT CGT CGT CGT CGC CGT CGT C
1 CGT CGT CGT CGT CGT CGT CGT CGT CGT CGT CGT CGT CGT CGT C
38853 ATCTTGCACA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.05, C:0.35, G:0.28, T:0.33
Consensus pattern (3 bp):
CGT
Found at i:40989 original size:20 final size:19
Alignment explanation
Indices: 40961--40999 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
40951 TCTTAAAAAG
*
40961 AGAGTATTTGAGAGAAATTT
1 AGAGAATTTGAGA-AAATTT
40981 AGAGAATTTGAGAAAATTT
1 AGAGAATTTGAGAAAATTT
41000 GGTGTGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (19 bp):
AGAGAATTTGAGAAAATTT
Found at i:43859 original size:39 final size:40
Alignment explanation
Indices: 43792--43867 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 40
43782 TACTTGACAT
43792 ATCCATCTATTTCAACTTAGTTTCAAATCTAAACCTCTAA
1 ATCCATCTATTTCAACTTAGTTTCAAATCTAAACCTCTAA
* *
43832 ATCCCTCT-TTTCAACTTAGTTTGAAATCTAAACCTC
1 ATCCATCTATTTCAACTTAGTTTCAAATCTAAACCTC
43868 CAAGTGTCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 27 0.79
40 7 0.21
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (40 bp):
ATCCATCTATTTCAACTTAGTTTCAAATCTAAACCTCTAA
Done.