Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004120.1 Hibiscus syriacus cultivar Beakdansim tig00009016_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: 44924
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:489 original size:20 final size:19
Alignment explanation
Indices: 444--489 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
434 CATCTAAAAA
444 TATA-AAAAAAATATTTTT
1 TATACAAAAAAATATTTTT
*
462 TTTGACAAAAAAATATATTTT
1 TAT-ACAAAAAAATAT-TTTT
483 TATACAA
1 TATACAA
490 GAATATGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 1 0.04
20 14 0.61
21 6 0.26
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (19 bp):
TATACAAAAAAATATTTTT
Found at i:3182 original size:18 final size:19
Alignment explanation
Indices: 3147--3183 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3137 CACGGAATGT
3147 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
3167 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
3184 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:3621 original size:27 final size:27
Alignment explanation
Indices: 3563--3628 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
3553 CTAAAATATA
3563 ATATTTATTATATTTTCTATATATAATT
1 ATATTTATT-TATTTTCTATATATAATT
* *
3591 -TATTTATTTATTTATCT-TTTATATTT
1 ATATTTATTTATTT-TCTATATATAATT
*
3617 ATATTTAATTAT
1 ATATTTATTTAT
3629 GCAAACTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 12 0.36
27 21 0.64
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (27 bp):
ATATTTATTTATTTTCTATATATAATT
Found at i:9139 original size:7 final size:7
Alignment explanation
Indices: 9129--9154 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
9119 TATTTTGAAC
9129 TTTTAAA
1 TTTTAAA
9136 TTTTAAA
1 TTTTAAA
9143 TTTTAAA
1 TTTTAAA
9150 TTTTA
1 TTTTA
9155 TGTTCGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTTAAA
Found at i:9279 original size:15 final size:15
Alignment explanation
Indices: 9258--9314 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
9248 AACCGGGTAT
9258 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
* **
9273 TGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
9290 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
9305 CGGGTACCCG
1 CGGGTACCCG
9315 TAACATCCAG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.21, C:0.33, G:0.28, T:0.18
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:18419 original size:30 final size:30
Alignment explanation
Indices: 18383--18442 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
18373 ATGCCTTGAC
18383 TTATCATGTTGATTTCTGGGTTGGTTAGAA
1 TTATCATGTTGATTTCTGGGTTGGTTAGAA
18413 TTATCATGTTGATTTCTGGGTTGGTTAGAA
1 TTATCATGTTGATTTCTGGGTTGGTTAGAA
18443 CCGTTTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.07, G:0.27, T:0.47
Consensus pattern (30 bp):
TTATCATGTTGATTTCTGGGTTGGTTAGAA
Found at i:19955 original size:31 final size:30
Alignment explanation
Indices: 19920--20086 Score: 105
Period size: 31 Copynumber: 5.4 Consensus size: 30
19910 AAATAATATA
19920 TATATAATATAATATAAGTTTATATATAAAC
1 TATATAATATAATATAA-TTTATATATAAAC
19951 TATAT-ATATAA-ATTATATTTATATTATAAAC
1 TATATAATATAATA-TA-ATTTATA-TATAAAC
* *
19982 TATATAAT-TATTATAAATTATATATATAAAT
1 TATATAATATAATAT-AATT-TATATATAAAC
* * * *
20013 TATGTTTATATGAA-AT-ATATATATATATA-
1 TAT-ATAATAT-AATATAATTTATATATAAAC
* *
20042 TATATATATATATATATATATATATATATATA-
1 TATATA-ATATA-ATATA-ATTTATATATAAAC
20074 TATATATATATAA
1 TATATA-ATATAA
20087 AAGCTATATA
Statistics
Matches: 112, Mismatches: 9, Indels: 30
0.74 0.06 0.20
Matches are distributed among these distances:
28 2 0.02
29 9 0.08
30 25 0.22
31 36 0.32
32 36 0.32
33 3 0.03
34 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (30 bp):
TATATAATATAATATAATTTATATATAAAC
Found at i:20097 original size:2 final size:2
Alignment explanation
Indices: 19915--20085 Score: 146
Period size: 2 Copynumber: 88.5 Consensus size: 2
19905 TGAAAAAATA
* *
19915 AT AT AT AT AT A- AT AT A- AT AT A- AGT TT AT AT AT AA ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT
* * *
19956 AT AT AA AT -T AT AT TT AT AT -T AT AA ACT AT AT A- AT -T AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * * * *
19994 AT AA AT -T AT AT AT AT AA AT -T AT GT TT AT AT GAA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
20035 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20077 AT AT AT AT A
1 AT AT AT AT A
20086 AAAGCTATAT
Statistics
Matches: 136, Mismatches: 19, Indels: 28
0.74 0.10 0.15
Matches are distributed among these distances:
1 10 0.07
2 123 0.90
3 3 0.02
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20305 original size:20 final size:20
Alignment explanation
Indices: 20267--20336 Score: 83
Period size: 19 Copynumber: 3.6 Consensus size: 20
20257 GAGAATATAT
20267 GGAAATTGAGAAA-TTAGAG
1 GGAAATTGAGAAATTTAGAG
20286 GGAAATTGAGAAATTTAGAG
1 GGAAATTGAGAAATTTAGAG
* * *
20306 GG-AA-TAAAAAATTTTGAAG
1 GGAAATTGAGAAATTTAG-AG
20325 GGAAATTGAGAA
1 GGAAATTGAGAA
20337 TTGAGATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
18 9 0.21
19 19 0.45
20 10 0.24
21 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.23
Consensus pattern (20 bp):
GGAAATTGAGAAATTTAGAG
Found at i:20786 original size:7 final size:7
Alignment explanation
Indices: 20755--20779 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20745 GTGAACCCTA
20755 AACCTTC
1 AACCTTC
20762 AACCTTC
1 AACCTTC
20769 AACCTTC
1 AACCTTC
20776 AACC
1 AACC
20780 CTAAACCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (7 bp):
AACCTTC
Found at i:20786 original size:14 final size:14
Alignment explanation
Indices: 20748--20786 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
20738 CTAGATCGTG
20748 AACCCTAAACCTTC
1 AACCCTAAACCTTC
* *
20762 AACCTTCAACCTTC
1 AACCCTAAACCTTC
20776 AACCCTAAACC
1 AACCCTAAACC
20787 ATGAACTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.44, G:0.00, T:0.21
Consensus pattern (14 bp):
AACCCTAAACCTTC
Found at i:20863 original size:21 final size:22
Alignment explanation
Indices: 20832--20874 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
20822 ATAAACCATG
20832 TATAGTATATATAAACTATATA
1 TATAGTATATATAAACTATATA
*
20854 TATA-TATATATAAACTTTATA
1 TATAGTATATATAAACTATATA
20875 AAGTAAATTA
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:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (22 bp):
TATAGTATATATAAACTATATA
Found at i:20966 original size:49 final size:49
Alignment explanation
Indices: 20863--20966 Score: 120
Period size: 48 Copynumber: 2.1 Consensus size: 49
20853 ATATATATAT
* * ** **
20863 ATAAACTTTATAAAGTAAATTACTTATATAGTTTATAGAAACACTATGC
1 ATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAACACTAACC
*
20912 ATAAACTATATAAAGT-AATAAAATATATAGTTTATAGAAACCCTAAACC
1 ATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAACACT-AACC
*
20961 CTAAAC
1 ATAAAC
20967 CATAAATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 24 0.52
49 22 0.48
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (49 bp):
ATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAACACTAACC
Found at i:21393 original size:2 final size:2
Alignment explanation
Indices: 21381--21422 Score: 57
Period size: 2 Copynumber: 20.0 Consensus size: 2
21371 ATAAACCAAG
*
21381 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
21423 AAGTAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 33 0.92
3 3 0.08
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:21516 original size:7 final size:7
Alignment explanation
Indices: 21506--21570 Score: 58
Period size: 7 Copynumber: 9.3 Consensus size: 7
21496 TAGTTTATAG
21506 AAACCCT
1 AAACCCT
21513 AAACCCT
1 AAACCCT
21520 AAACCCT
1 AAACCCT
**
21527 AAACTTT
1 AAACCCT
*
21534 AAACCTT
1 AAACCCT
**
21541 AAATACT
1 AAACCCT
*
21548 AACCCCT
1 AAACCCT
*
21555 AAACCAT
1 AAACCCT
*
21562 AAACTCT
1 AAACCCT
21569 AA
1 AA
21571 TATAAATGGA
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (7 bp):
AAACCCT
Found at i:21557 original size:557 final size:549
Alignment explanation
Indices: 20814--22056 Score: 1903
Period size: 558 Copynumber: 2.3 Consensus size: 549
20804 CTTATAGTAC
*
20814 ATGTATGTATAAACCATGTATAGTATATATAAACTATATATATATATATATAAACTTTATAAAGT
1 ATGTATGTATAAACCAAGTATAGTATATATAAACTATATATATATATATATAAACTTTATAAAGT
20879 AAATTACTTATATAGTTTATAGAAACACTATGCATAAACTATATAAAGTAATAAAATATATAGTT
66 AAATTACTTATATAGTTTATAGAAACACTATGCATAAACTATATAAAGTAATAAAATATATAGTT
* * *
20944 TATAGAAACCCTAAACCCTAAACCATAAATTTTAAAACATAAACATTAAACCCTAAACCATGAAC
131 TATAGAAACCCTAAACCCTAAACCATAAACTTTAAAACATAAACACTAAACCCTAAACCATAAAC
*
21009 -CCAATTTAAATGGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTGGGCTTATGTATTG
196 TCCAATATAAATGGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTGGGCTTATGTATTG
21073 GGACTATGTAAACTAATGTAAATGGACTAACACTAATGTAAATTGACTTATTTTTTGGTTTTATT
261 GGACTATGTAAACTAATGTAAATGGACTAACACTAATGTAAATTGACTTATTTTTTGGTTTTATT
*
21138 ATTACTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAA
326 ATTACTTATTCATAACAACAAAATAAATGAGCTATTAATGTGAATTAACCTAACATGCAACTAAA
* *
21203 ATACTAATTATGCAAATGAAATTAATATGACATGTACTACTATTTATGAATCATATAATATGCAA
391 ATACTAATCATGCAAATGAAATT-A-ATGACATGTACTACTATTTATGAACCATATAATATGCAA
* *
21268 TGTGACATAGTAATTATTTAACACCTAATTAATCATGGTTTATATAATTTACATTTAAATAATTT
454 TGTGACATACTAATTATTTAACACCTAATTAATAATGGTTTATATAATTTACATTTAAATAATTT
21333 T-ATTAATTTTAATAAATAAATTTATATAAT
519 TAATTAATTTTAATAAATAAATTTATATAAT
21363 ATGTATGTATAAACCAAGTATAGTATATATAAACTATATATATATATATATATATA-TATAAAGT
1 ATGTATGTATAAACCAAGTATAGTATATATAAACTATATATATATATATATA-A-ACT-T----T
21427 AAATAAAGTAAATTACTTATATAGTTTATAGAAACACTATGCATAAACTATATAAAGTAATAAAA
59 --ATAAAGTAAATTACTTATATAGTTTATAGAAACACTATGCATAAACTATATAAAGTAATAAAA
* * * * *
21492 TATATAGTTTATAGAAACCCTAAACCCTAAACCCTAAACTTTAAACCTTAAATACTAACCCCTAA
122 TATATAGTTTATAGAAACCCTAAACCCTAAACCATAAACTTTAAAACATAAACACTAAACCCTAA
*
21557 ACCATAAACTCTAATATAAATGGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTGGGCT
187 ACCATAAACTCCAATATAAATGGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTGGGCT
*
21622 TATGTATTGGGCCTATGTAAACTAATGTAAATGGACTAACACTAATGTAAATTGACTTATTTTTT
252 TATGTATTGGGACTATGTAAACTAATGTAAATGGACTAACACTAATGTAAATTGACTTATTTTTT
21687 GGTTTTATTATTACTTATTCATAACAACAAAATAAATGAGCTATTAATGTGAATTAACCTAACAT
317 GGTTTTATTATTACTTATTCATAACAACAAAATAAATGAGCTATTAATGTGAATTAACCTAACAT
21752 GCAACTAAAATACTAATCATGCAAATGAAATTAATGACATGTACTACTATTTATGAACCATATAA
382 GCAACTAAAATACTAATCATGCAAATGAAATTAATGACATGTACTACTATTTATGAACCATATAA
*
21817 TATGCAATGTGACATACTAATTATTTAACACCTAATTAATAATGTTTTATATAATTTACATTTAA
447 TATGCAATGTGACATACTAATTATTTAACACCTAATTAATAATGGTTTATATAATTTACATTTAA
* ** ** *
21882 ATAATTTTAATTAATATGT-ATGTATAAA-CCATGT-AT
512 ATAATTTTAATTAAT-TTTAATAAATAAATTTATATAAT
* * * *
21918 A-GTATATATAAA-CTA-TATA-TATATATAAACTATATA-A-AGTA-A-AT-TAC-TTATATAG
1 ATGTATGTATAAACCAAGTATAGTATATATAAACTATATATATA-TATATATAAACTTTATAAAG
** *** * * * *
21973 TTTA-TAGAAACAT-GTTTATAGAAATACTATGCATAAACTATATAAAGTAATACAGTATATAG-
65 TAAATTACTTATATAGTTTATAGAAACACTATGCATAAACTATATAAAGTAATAAAATATATAGT
22035 TTATAGAAACCCTAAACCCTAA
130 TTATAGAAACCCTAAACCCTAA
22057 TATAAATGGA
Statistics
Matches: 643, Mismatches: 37, Indels: 42
0.89 0.05 0.06
Matches are distributed among these distances:
535 22 0.03
536 46 0.07
537 5 0.01
538 7 0.01
540 1 0.00
544 1 0.00
545 1 0.00
548 2 0.00
549 53 0.08
550 5 0.01
551 19 0.03
552 4 0.01
553 2 0.00
554 10 0.02
555 4 0.01
556 104 0.16
557 143 0.22
558 214 0.33
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (549 bp):
ATGTATGTATAAACCAAGTATAGTATATATAAACTATATATATATATATATAAACTTTATAAAGT
AAATTACTTATATAGTTTATAGAAACACTATGCATAAACTATATAAAGTAATAAAATATATAGTT
TATAGAAACCCTAAACCCTAAACCATAAACTTTAAAACATAAACACTAAACCCTAAACCATAAAC
TCCAATATAAATGGACTAGCACTAATGCATATATATTTGTAATAAAAGAGTGGGCTTATGTATTG
GGACTATGTAAACTAATGTAAATGGACTAACACTAATGTAAATTGACTTATTTTTTGGTTTTATT
ATTACTTATTCATAACAACAAAATAAATGAGCTATTAATGTGAATTAACCTAACATGCAACTAAA
ATACTAATCATGCAAATGAAATTAATGACATGTACTACTATTTATGAACCATATAATATGCAATG
TGACATACTAATTATTTAACACCTAATTAATAATGGTTTATATAATTTACATTTAAATAATTTTA
ATTAATTTTAATAAATAAATTTATATAAT
Found at i:21927 original size:20 final size:19
Alignment explanation
Indices: 21895--21953 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 19
21885 ATTTTAATTA
*
21895 ATAT-GTATGTATAAACCAT
1 ATATAGTATATATAAACC-T
*
21914 GTATAGTATATATAAA-CT
1 ATATAGTATATATAAACCT
21932 ATATA-TATATATAAA-CT
1 ATATAGTATATATAAACCT
21949 ATATA
1 ATATA
21954 AAGTAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 17 0.47
18 5 0.14
19 4 0.11
20 10 0.28
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (19 bp):
ATATAGTATATATAAACCT
Found at i:21934 original size:9 final size:9
Alignment explanation
Indices: 21922--21955 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
21912 ATGTATAGTA
21922 TATATAAAC
1 TATATAAAC
*
21931 TATATATA-
1 TATATAAAC
21939 TATATAAAC
1 TATATAAAC
21948 TATATAAA
1 TATATAAA
21956 GTAAATTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (9 bp):
TATATAAAC
Found at i:21942 original size:17 final size:18
Alignment explanation
Indices: 21915--21953 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
21905 ATAAACCATG
21915 TATAGTATATATAAACTA
1 TATAGTATATATAAACTA
21933 TATA-TATATATAAACTA
1 TATAGTATATATAAACTA
21950 TATA
1 TATA
21954 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
TATAGTATATATAAACTA
Found at i:22398 original size:13 final size:13
Alignment explanation
Indices: 22366--22392 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22356 TAATTTACAT
22366 TTAAATAATTTTA
1 TTAAATAATTTTA
22379 TTAAATAATTTTA
1 TTAAATAATTTTA
22392 T
1 T
22393 ATAATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:22430 original size:20 final size:20
Alignment explanation
Indices: 22407--22445 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
22397 TATGTATCTA
* *
22407 TAAACCATGTATAGTATATG
1 TAAACCATATATAATATATG
*
22427 TAAACTATATATAATATAT
1 TAAACCATATATAATATAT
22446 ATATATATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (20 bp):
TAAACCATATATAATATATG
Found at i:22479 original size:2 final size:2
Alignment explanation
Indices: 22432--22470 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
22422 ATATGTAAAC
22432 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22471 AACTATATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:22577 original size:14 final size:14
Alignment explanation
Indices: 22554--22614 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
22544 TAGTTTATAG
* *
22554 AAACCTTAAACCTT
1 AAACCCTAAACCAT
*
22568 AAACCCTAAATCAT
1 AAACCCTAAACCAT
*
22582 AAACCCTAAATCAT
1 AAACCCTAAACCAT
** *
22596 AAACTTTAAACAAT
1 AAACCCTAAACCAT
22610 AAACC
1 AAACC
22615 ATAATGTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (14 bp):
AAACCCTAAACCAT
Found at i:22803 original size:14 final size:14
Alignment explanation
Indices: 22784--22830 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
22774 ATTTTTTCTT
22784 TATATAAATTAAAC
1 TATATAAATTAAAC
22798 TATAT-AATT----
1 TATATAAATTAAAC
22807 TATATAAATTAAAC
1 TATATAAATTAAAC
*
22821 TATATTAATT
1 TATATAAATT
22831 TTCCATTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:22809 original size:23 final size:24
Alignment explanation
Indices: 22782--22831 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
22772 TTATTTTTTC
22782 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
22805 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
22829 TTT
1 TTT
22832 TCCATTACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:28188 original size:67 final size:67
Alignment explanation
Indices: 28080--28214 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
28070 AAGATGGATC
*
28080 GTTTTACATGCTGAGAGGAAACAATCAGAGAGAACCACTTATCGGAGAAGATATTGGTGTTTACT
1 GTTTTACATGCTGAAAGGAAACAATCAGAGAGAACCACTTATCGGAGAAGATATTGGTGTTTACT
28145 AT
66 AT
*
28147 GTTTTACATGCTGAAAGGAAACAATCAGAGAGAACCACTTATCGGAGAAGATGTTGGTGTTTACT
1 GTTTTACATGCTGAAAGGAAACAATCAGAGAGAACCACTTATCGGAGAAGATATTGGTGTTTACT
28212 AT
66 AT
28214 G
1 G
28215 CAGATTATTA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (67 bp):
GTTTTACATGCTGAAAGGAAACAATCAGAGAGAACCACTTATCGGAGAAGATATTGGTGTTTACT
AT
Found at i:29322 original size:41 final size:41
Alignment explanation
Indices: 29277--29404 Score: 134
Period size: 43 Copynumber: 3.1 Consensus size: 41
29267 ACAAATGCTG
* * * *
29277 CTAAAATTCATTATATAGTGGCATTTTTTAC-TGAAACATCA
1 CTAAAAGTCATTATATAGTGGCGTTTTTCACGT-AAACACCA
* * *
29318 CTAAAGGTCATGATATATAGTGGCGTTTTACACGTAAACGCCA
1 CTAAAAGTCAT--TATATAGTGGCGTTTTTCACGTAAACACCA
**
29361 CTAAAAGTCA-TATATAGTGGCGTTTTTCACACAAACACCA
1 CTAAAAGTCATTATATAGTGGCGTTTTTCACGTAAACACCA
29401 CTAA
1 CTAA
29405 GTTTAATTGA
Statistics
Matches: 72, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
40 30 0.42
41 9 0.12
43 32 0.44
44 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (41 bp):
CTAAAAGTCATTATATAGTGGCGTTTTTCACGTAAACACCA
Found at i:37370 original size:19 final size:19
Alignment explanation
Indices: 37346--37383 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
37336 ATACTACTAT
37346 GTATAGGGGTATCGATACC
1 GTATAGGGGTATCGATACC
37365 GTATAGGGGTATCGATACC
1 GTATAGGGGTATCGATACC
37384 ACTTTGGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (19 bp):
GTATAGGGGTATCGATACC
Found at i:39500 original size:13 final size:13
Alignment explanation
Indices: 39484--39508 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39474 TGAAAACTAT
39484 TTTGAAAAATAAG
1 TTTGAAAAATAAG
39497 TTTGAAAAATAA
1 TTTGAAAAATAA
39509 TAGTTCGTAT
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:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (13 bp):
TTTGAAAAATAAG
Found at i:40058 original size:21 final size:21
Alignment explanation
Indices: 40032--40104 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 21
40022 CGATACAAGG
40032 GTATCAATACCCGTTGAAGAA
1 GTATCAATACCCGTTGAAGAA
* *
40053 GTATCAGTA-CTGTT-AAGAACA
1 GTATCAATACCCGTTGAAG-A-A
* * *
40074 ATATCAATACCCATTGAAGCA
1 GTATCAATACCCGTTGAAGAA
*
40095 GTATCGATAC
1 GTATCAATAC
40105 TATGCTAGTA
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
19 3 0.08
20 5 0.13
21 25 0.64
22 3 0.08
23 3 0.08
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.26
Consensus pattern (21 bp):
GTATCAATACCCGTTGAAGAA
Done.