Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004503.1 Hibiscus syriacus cultivar Beakdansim tig00009931_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: 68523
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1116 original size:3 final size:3
Alignment explanation
Indices: 1108--1169 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
1098 GGCCCGTTTG
** *
1108 TAA TAA TAA TTT TAA TAA AAA TAA -AA TAA TAA TAA TAA TAA TAA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
*
1156 TAA AAA TAA TAA TA
1 TAA TAA TAA TAA TA
1170 GAAAATGGAG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1137 original size:20 final size:20
Alignment explanation
Indices: 1120--1167 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
1110 ATAATAATTT
1120 TAATAAAAATAAAATAATAA
1 TAATAAAAATAAAATAATAA
* *
1140 TAATAATAATAATATATAAAAA
1 TAATAAAAATAA-A-ATAATAA
1162 TAATAA
1 TAATAA
1168 TAGAAAATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 11 0.46
21 1 0.04
22 12 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TAATAAAAATAAAATAATAA
Found at i:3409 original size:29 final size:30
Alignment explanation
Indices: 3353--3411 Score: 111
Period size: 29 Copynumber: 2.0 Consensus size: 30
3343 CAATACTTAT
3353 TTTAATCTCAATATTAGGTTCAATCTAAAA
1 TTTAATCTCAATATTAGGTTCAATCTAAAA
3383 TTTAATCTCAATA-TAGGTTCAATCTAAAA
1 TTTAATCTCAATATTAGGTTCAATCTAAAA
3412 CACCTAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTAATCTCAATATTAGGTTCAATCTAAAA
Found at i:8805 original size:18 final size:18
Alignment explanation
Indices: 8782--8818 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
8772 TTCTTTTAAC
8782 ACTGAAATCATTCAATAA
1 ACTGAAATCATTCAATAA
8800 ACTGAAATCATTCAATAA
1 ACTGAAATCATTCAATAA
8818 A
1 A
8819 TTCCCGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.16, G:0.05, T:0.27
Consensus pattern (18 bp):
ACTGAAATCATTCAATAA
Found at i:9754 original size:14 final size:14
Alignment explanation
Indices: 9735--9768 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
9725 TGAAGTTGGA
9735 TGGTGCGCTCGTGG
1 TGGTGCGCTCGTGG
9749 TGGTGCGCTCGTGG
1 TGGTGCGCTCGTGG
9763 TGGTGC
1 TGGTGC
9769 TTTGTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.00, C:0.21, G:0.50, T:0.29
Consensus pattern (14 bp):
TGGTGCGCTCGTGG
Found at i:15039 original size:2 final size:2
Alignment explanation
Indices: 15032--15064 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
15022 CCTACAAACT
15032 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
15065 AATAGGTACC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:21334 original size:2 final size:2
Alignment explanation
Indices: 21327--21362 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
21317 TGTGTATTAC
21327 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
21363 GAAAAAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21961 original size:74 final size:74
Alignment explanation
Indices: 21841--21982 Score: 259
Period size: 74 Copynumber: 1.9 Consensus size: 74
21831 AATTGTAGCC
21841 TTTAGGGTAGTTTTTCTTTTGACCAAATACAAATATATATTGATCATTGTTCAATGTGTCAACTT
1 TTTAGGGTAGTTTTTCTTTTGACCAAATACAAATATATATTGATCATTGTTCAATGTGTCAACTT
21906 TTATCCCTT
66 TTATCCCTT
*
21915 TTTAGGGTAGTTTTTCTTTTGACCAAATACAAATATAT-TTGTATCATTGTTCAATGTGTCAAGT
1 TTTAGGGTAGTTTTTCTTTTGACCAAATACAAATATATATTG-ATCATTGTTCAATGTGTCAACT
21979 TTTA
65 TTTA
21983 GCCTTATAGA
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
73 3 0.05
74 63 0.95
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46
Consensus pattern (74 bp):
TTTAGGGTAGTTTTTCTTTTGACCAAATACAAATATATATTGATCATTGTTCAATGTGTCAACTT
TTATCCCTT
Found at i:23589 original size:26 final size:25
Alignment explanation
Indices: 23558--23691 Score: 77
Period size: 23 Copynumber: 5.4 Consensus size: 25
23548 ATTATGAATT
23558 TAATGATTTGATATT-TAATGATTTAG
1 TAATGATTTGAT-TTATAATGA-TTAG
*
23584 TAATGATATGATTTAGTAATGATTAG
1 TAATGATTTGATTTA-TAATGATTAG
* * * *
23610 TAATAATTT-ACTAATAATGA-TAC
1 TAATGATTTGATTTATAATGATTAG
* *
23633 TAATAATTT-TTATTATTAAT-ATT--
1 TAATGATTTGAT-TTA-TAATGATTAG
**
23656 TAATGATTTGATACA-AATGATTTAG
1 TAATGATTTGATTTATAATGA-TTAG
23681 TAATGATTTGA
1 TAATGATTTGA
23692 AATAATGAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
21 3 0.04
22 1 0.01
23 22 0.26
24 10 0.12
25 21 0.25
26 22 0.26
27 6 0.07
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (25 bp):
TAATGATTTGATTTATAATGATTAG
Found at i:23596 original size:16 final size:16
Alignment explanation
Indices: 23575--23606 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
23565 TTGATATTTA
23575 ATGATTTAGTAATGAT
1 ATGATTTAGTAATGAT
23591 ATGATTTAGTAATGAT
1 ATGATTTAGTAATGAT
23607 TAGTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (16 bp):
ATGATTTAGTAATGAT
Found at i:23719 original size:24 final size:24
Alignment explanation
Indices: 23692--23745 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
23682 AATGATTTGA
23692 AATAATGAAATT-ATAATAATTACT
1 AATAATG-AATTAATAATAATTACT
* *
23716 AATAATGATTTAATAATTATTACT
1 AATAATGAATTAATAATAATTACT
23740 AATAAT
1 AATAAT
23746 TATTTAGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (24 bp):
AATAATGAATTAATAATAATTACT
Found at i:23744 original size:13 final size:13
Alignment explanation
Indices: 23704--23749 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
23694 TAATGAAATT
*
23704 ATAATAATTACTA
1 ATAATTATTACTA
*
23717 ATAATGATT--TA
1 ATAATTATTACTA
23728 ATAATTATTACTA
1 ATAATTATTACTA
23741 ATAATTATT
1 ATAATTATT
23750 TAGTAGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 10 0.34
13 19 0.66
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (13 bp):
ATAATTATTACTA
Found at i:23750 original size:24 final size:24
Alignment explanation
Indices: 23704--23751 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
23694 TAATGAAATT
23704 ATAATAATTACTAATAATGATTTA
1 ATAATAATTACTAATAATGATTTA
* *
23728 ATAATTATTACTAATAATTATTTA
1 ATAATAATTACTAATAATGATTTA
23752 GTAGTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (24 bp):
ATAATAATTACTAATAATGATTTA
Found at i:24302 original size:7 final size:7
Alignment explanation
Indices: 24290--24362 Score: 67
Period size: 7 Copynumber: 10.6 Consensus size: 7
24280 AGTTTGGATT
24290 ACCCTAA
1 ACCCTAA
24297 ACCCTAA
1 ACCCTAA
24304 A-CCTAA
1 ACCCTAA
*
24310 ACTCTAA
1 ACCCTAA
*
24317 ACCTTAA
1 ACCCTAA
*
24324 ACTCTAA
1 ACCCTAA
* *
24331 ACTCTGA
1 ACCCTAA
*
24338 ACCCTGA
1 ACCCTAA
*
24345 ACCCTGA
1 ACCCTAA
*
24352 ACCATAA
1 ACCCTAA
24359 ACCC
1 ACCC
24363 GAGAAACCAA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
6 6 0.11
7 49 0.89
ACGTcount: A:0.40, C:0.37, G:0.04, T:0.19
Consensus pattern (7 bp):
ACCCTAA
Found at i:24326 original size:14 final size:13
Alignment explanation
Indices: 24292--24332 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
24282 TTTGGATTAC
*
24292 CCTAAACCCTAAA
1 CCTAAACTCTAAA
24305 CCTAAACTCTAAA
1 CCTAAACTCTAAA
24318 CCTTAAACTCTAAA
1 CC-TAAACTCTAAA
24332 C
1 C
24333 TCTGAACCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (13 bp):
CCTAAACTCTAAA
Found at i:27677 original size:22 final size:22
Alignment explanation
Indices: 27651--27704 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
27641 GCCGAGCTGT
27651 GCCGACCGAGACGCCTGACCGA
1 GCCGACCGAGACGCCTGACCGA
* * *
27673 GCCGACCAAGCCGTCTGACCGA
1 GCCGACCGAGACGCCTGACCGA
* *
27695 ACCGATCGAG
1 GCCGACCGAG
27705 TCGACCGAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.07
Consensus pattern (22 bp):
GCCGACCGAGACGCCTGACCGA
Found at i:27720 original size:31 final size:31
Alignment explanation
Indices: 27667--27744 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 31
27657 CGAGACGCCT
* * ** *
27667 GACCGAGCCGACCAAGCCGTCTGACCGAACC
1 GACCGAGCAGACCGAGTTGTCTGACAGAACC
* *
27698 GATCGAGTC-GACCGAGTTGTCTGACAGAGCC
1 GACCGAG-CAGACCGAGTTGTCTGACAGAACC
27729 GACCGAGCAGACCGAG
1 GACCGAGCAGACCGAG
27745 CCGAGTTGAC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
30 1 0.03
31 36 0.95
32 1 0.03
ACGTcount: A:0.26, C:0.33, G:0.31, T:0.10
Consensus pattern (31 bp):
GACCGAGCAGACCGAGTTGTCTGACAGAACC
Found at i:29357 original size:31 final size:33
Alignment explanation
Indices: 29319--29403 Score: 99
Period size: 32 Copynumber: 2.7 Consensus size: 33
29309 TAAGGCGGCC
* * *
29319 CTTGGGTAGGCTCTGC-T-GCCCTGAGATTTTT
1 CTTGGGTAGGCTCTCCATGGCCCCGAGAATTTT
*
29350 CTTGGGTAAG-TCTCCATGGCCCCGAGAATTTT
1 CTTGGGTAGGCTCTCCATGGCCCCGAGAATTTT
29382 CTTGGGTAGGCTCT-CA-GGCCCC
1 CTTGGGTAGGCTCTCCATGGCCCC
29404 AAGATACTCC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
30 4 0.09
31 16 0.35
32 23 0.50
33 3 0.07
ACGTcount: A:0.13, C:0.27, G:0.28, T:0.32
Consensus pattern (33 bp):
CTTGGGTAGGCTCTCCATGGCCCCGAGAATTTT
Found at i:31245 original size:31 final size:31
Alignment explanation
Indices: 31209--31267 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
31199 AACTTAAAAG
* * *
31209 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
*
31240 AGTTTTACAATATTAAAATTTAAATAAT
1 AGTTTTACAATACTAAAATTTAAATAAT
31268 CCATACGACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:31343 original size:22 final size:22
Alignment explanation
Indices: 31294--31342 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
31284 ATAAATTATT
**
31294 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
31316 TAAAATAAATCAATCCGTACTAA
1 TAAAATAAATCAATCCATA-TAA
31339 TAAA
1 TAAA
31343 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:31346 original size:54 final size:54
Alignment explanation
Indices: 31282--32036 Score: 739
Period size: 54 Copynumber: 13.8 Consensus size: 54
31272 ACGACTACAA
*
31282 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCGTAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* ** *
31336 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATAAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * * * *
31393 TTTTAAAATAAAT-CAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATAC
*
31452 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
31506 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * * **
31560 TAATAAACTATTTAAAATAAATCAATCTATACAAATACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** ** **
31617 TTTTAAAATAAAT-AAATTCATACTAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
*
31672 TAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
31726 TAATAAATTATTTAAAATAAATCAATCCATACAACTATAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** **
31783 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
*
31838 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
31886 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
31940 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
31994 TAATAAATTATTTTAAAATAAATCAATCTATATTTTATAATAA
1 TAATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAA
32037 TTTATTTTAA
Statistics
Matches: 580, Mismatches: 83, Indels: 75
0.79 0.11 0.10
Matches are distributed among these distances:
48 30 0.05
49 4 0.01
50 6 0.01
51 1 0.00
52 1 0.00
53 1 0.00
54 323 0.56
55 51 0.09
56 27 0.05
57 42 0.07
58 74 0.13
59 11 0.02
60 9 0.02
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:31352 original size:32 final size:31
Alignment explanation
Indices: 31314--32021 Score: 419
Period size: 32 Copynumber: 25.5 Consensus size: 31
31304 CAATCCATAT
*
31314 TTTAAAATAAATCAATCCGTACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
31346 TTTAAAATAAATCAATCCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
* **
31376 --T--AATAAATAAATCCATA-TTTTAAA-A
1 TTTAAAATAAATCAATCCATACTAATAAATA
* *
31401 --T-AAATCAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
31430 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
31462 TTTAAAATAAATCAAT---T-C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
31484 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
31516 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
31538 TTTAAAATAAATCAATCAATACTAATAAACTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
* * *
31570 TTTAAAATAAATCAATCTATACAAATACA-A
1 TTTAAAATAAATCAATCCATACTAATAAATA
31600 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
* *
31618 TTTAAAATAAATAAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
31650 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
31682 TTTAAAATAAATC-A---AT-C-AAT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
31704 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
31736 TTTAAAATAAATCAATCCATAC-AACT--ATA
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
*
31765 ---ATAATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
31784 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
31816 TTTAAAATAAATCAATCCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
31846 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
31864 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
31896 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
31918 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
31950 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
31972 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
32004 TTTTAAAATAAATCAATC
1 -TTTAAAATAAATCAATC
32022 TATATTTTAT
Statistics
Matches: 544, Mismatches: 27, Indels: 209
0.70 0.03 0.27
Matches are distributed among these distances:
20 2 0.00
22 119 0.22
23 10 0.02
24 11 0.02
25 9 0.02
26 91 0.17
27 6 0.01
28 20 0.04
29 4 0.01
30 9 0.02
31 16 0.03
32 231 0.42
33 16 0.03
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (31 bp):
TTTAAAATAAATCAATCCATACTAATAAATA
Found at i:31488 original size:22 final size:22
Alignment explanation
Indices: 31462--31504 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
31452 TAATAAATTA
*
31462 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
31484 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
31505 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:31513 original size:22 final size:22
Alignment explanation
Indices: 31464--31512 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
31454 ATAAATTATT
* **
31464 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
31486 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
31509 TAAA
1 TAAA
31513 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:31622 original size:80 final size:80
Alignment explanation
Indices: 31484--31916 Score: 641
Period size: 80 Copynumber: 5.3 Consensus size: 80
31474 CAATTCATAT
* *
31484 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACAAATACA--A--T--AATAAATCAATCCATATTTTAAAATAAA
* *
31549 TCAATCAATACTAATAAACTA
60 TCAATCCATACTAATAAATTA
* * *
31570 TTTAAAATAAATCAATCTATACAAATACAATAATAAATCAATCCATATTTTAAAATAAATAAATT
1 TTTAAAATAAATCAATCCATACAAATACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
31635 CATACTAATAAATTA
66 CATACTAATAAATTA
* * *
31650 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACAAATACA--A--T--AATAAATCAATCCATATTTTAAAATAAA
31715 TCAATCCATACTAATAAATTA
60 TCAATCCATACTAATAAATTA
* *
31736 TTTAAAATAAATCAATCCATACAACTATAATAATAAATCAATCCATATTTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCCATACAAATACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
31801 CATACTAATAAATTA
66 CATACTAATAAATTA
*
31816 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCCATACAAATACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
31881 CATACTAATAAATTA
66 CATACTAATAAATTA
31896 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
31917 TTTTAAAATA
Statistics
Matches: 323, Mismatches: 18, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
80 219 0.68
82 3 0.01
84 3 0.01
86 98 0.30
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (80 bp):
TTTAAAATAAATCAATCCATACAAATACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
CATACTAATAAATTA
Found at i:31662 original size:112 final size:112
Alignment explanation
Indices: 31314--31698 Score: 462
Period size: 112 Copynumber: 3.4 Consensus size: 112
31304 CAATCCATAT
* * *
31314 TTTAAAATAAATCAATCCGTACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATACAAATACAATAA
* * *
31379 TAAATAAATCCATATTTTAAAATAAATCAATCAATCCATACAAATAAATTA
66 TAAATCAATCCATATTTTAAAATAAAT--A--AATTCATACTAATAAATTA
* **
31430 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA--T-T-CATATTTTAA-A
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATACA-AATACAATA
** * ** * * **
31490 ATAAATCAATCCATACTAATAAATTATTTAAAAT-A-AATCAATCCA-TA
65 ATAAATCAATCCATA-TTTTAAAATAAATAAATTCATACT-AATAAATTA
* *
31537 TTTTAAAATAAATCAATCAATACTAATAAACTATTTAAAATAAATCAATCTATACAAATACAATA
1 -TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATACAAATACAATA
31602 ATAAATCAATCCATATTTTAAAATAAATAAATTCATACTAATAAATTA
65 ATAAATCAATCCATATTTTAAAATAAATAAATTCATACTAATAAATTA
31650 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
31699 AATATTTTAA
Statistics
Matches: 224, Mismatches: 33, Indels: 28
0.79 0.12 0.10
Matches are distributed among these distances:
107 3 0.01
108 50 0.22
109 2 0.01
110 1 0.00
111 18 0.08
112 87 0.39
113 17 0.08
116 46 0.21
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.34
Consensus pattern (112 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATACAAATACAATAA
TAAATCAATCCATATTTTAAAATAAATAAATTCATACTAATAAATTA
Found at i:31671 original size:166 final size:166
Alignment explanation
Indices: 31484--32036 Score: 747
Period size: 166 Copynumber: 3.4 Consensus size: 166
31474 CAATTCATAT
31484 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
* * * *
31549 TCAATCAATACTAATAAACTATTTAAAATAAATCAATCTATACAAATACAATAATAAATCAATCC
66 TCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAAATATAATAATAAATCAATCC
31614 ATATTTTAAAATAAATAAATTCATACTAATAAATTA
131 ATATTTTAAAATAAATAAATTCATACTAATAAATTA
*
31650 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
*
31715 TCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTATAATAATAAATCAATCC
66 TCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAAATATAATAATAAATCAATCC
* *
31780 ATATTTTAAAATAAATCAATCCATACTAATAAATTA
131 ATATTTTAAAATAAATAAATTCATACTAATAAATTA
*
31816 TTTAAAATAAATCAATCCATAC-AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAA
1 TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
* * *
31874 ATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATT
65 ATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAAATATAATAATAAATCAATC
** * ** * * **
31935 CATACTAATAAATTATTTAAAAT-A-AATCAATCCA-TA
130 CATA-TTTTAAAATAAATAAATTCATACT-AATAAATTA
* * *
31971 TTTTAAAATAAATCAATTCATACTAATAAATTATTTTAAAATAAATCAATCTATATTTTATAATA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATA
32036 A
64 A
32037 TTTATTTTAA
Statistics
Matches: 347, Mismatches: 28, Indels: 27
0.86 0.07 0.07
Matches are distributed among these distances:
155 4 0.01
156 44 0.13
157 17 0.05
158 1 0.00
160 68 0.20
161 1 0.00
162 1 0.00
163 25 0.07
164 1 0.00
165 2 0.01
166 183 0.53
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (166 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAAATATAATAATAAATCAATCC
ATATTTTAAAATAAATAAATTCATACTAATAAATTA
Found at i:31708 original size:134 final size:134
Alignment explanation
Indices: 31430--32000 Score: 420
Period size: 134 Copynumber: 4.2 Consensus size: 134
31420 AAATAAATTA
* * * *
31430 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATA-TTTTAAAATAA
1 TTTAAAATAAATCAATCAATACAAATAAA--A--T--AATAAATCAATCCATACTATTAAAATAA
* * ** * ** * *
31494 ATCAATCCATACT-AATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATCA
60 ATAAATTCA-ACTCAATAAA-TATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAA
*
31556 ATACTAATAAACTA-
123 AT-C-AATCAA-TAT
* * *
31570 TTTAAAATAAATCAATCTATACAAATACAATAATAAATCAATCCATA-TTTTAAAATAAATAAAT
1 TTTAAAATAAATCAATCAATACAAATAAAATAATAAATCAATCCATACTATTAAAATAAATAAAT
31634 TCATACT-AATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
66 TCA-ACTCAATAAA-TATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
31698 CAATAT
129 CAATAT
* * * * *
31704 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTATAAT-A
1 TTTAAAATAAATCAATCAATACAAATAAA--A--T--AATAAATCAATCCATACTATTAAAATAA
*
31768 ATAAA-TCAA-TCCAT--AT-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
60 ATAAATTCAACTCAATAAATATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
* *
31828 CAATCCATACA
125 CAATCAATA-T
** * * * * ** * * **
31839 ACTACAAT-AATAAATCAATCCATATTTTAA-AATAAATCAATCCATACTAATAAATTATTTAAA
1 TTTAAAATAAATCAATCAATACA-AATAAAATAATAAATCAATCCATACTATTAAAATAAATAAA
* * ** *
31902 AT-AAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
65 TTCAACTCAATAAATA-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
31966 CCATAT
129 CAATAT
*
31972 TTTAAAATAAATCAATTC-ATACTAATAAA
1 TTTAAAATAAATCAA-TCAATACAAATAAA
32001 TTATTTTAAA
Statistics
Matches: 357, Mismatches: 52, Indels: 51
0.78 0.11 0.11
Matches are distributed among these distances:
128 22 0.06
129 6 0.02
130 5 0.01
132 2 0.01
133 11 0.03
134 220 0.62
135 20 0.06
136 9 0.03
137 1 0.00
138 5 0.01
139 3 0.01
140 48 0.13
141 5 0.01
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (134 bp):
TTTAAAATAAATCAATCAATACAAATAAAATAATAAATCAATCCATACTATTAAAATAAATAAAT
TCAACTCAATAAATATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCA
ATAT
Found at i:31733 original size:22 final size:22
Alignment explanation
Indices: 31684--31732 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
31674 ATAAATTATT
**
31684 TAAAATAAATCAATCAATATTT
1 TAAAATAAATCAATCAATATAA
*
31706 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCAATA-TAA
31729 TAAA
1 TAAA
31733 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCAATATAA
Found at i:31813 original size:22 final size:23
Alignment explanation
Indices: 31738--31812 Score: 89
Period size: 22 Copynumber: 3.2 Consensus size: 23
31728 ATAAATTATT
*
31738 TAAAATAAATCAATCCATACAACTA
1 TAAAATAAATCAATCCATACTA--A
**
31763 TAATAATAAATCAATCCATA-TTT
1 TAA-AATAAATCAATCCATACTAA
31786 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
31809 TAAA
1 TAAA
31813 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:31893 original size:22 final size:23
Alignment explanation
Indices: 31818--31892 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
31808 ATAAATTATT
31818 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
31840 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
31866 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
31889 TAAA
1 TAAA
31893 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:31922 original size:22 final size:22
Alignment explanation
Indices: 31896--31938 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
31886 TAATAAATTA
31896 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
31918 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
31939 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:31947 original size:22 final size:22
Alignment explanation
Indices: 31898--31946 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
31888 ATAAATTATT
**
31898 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
31920 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
31943 TAAA
1 TAAA
31947 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:31976 original size:22 final size:22
Alignment explanation
Indices: 31950--31992 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
31940 TAATAAATTA
31950 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
31972 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
31993 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:32001 original size:22 final size:22
Alignment explanation
Indices: 31952--32000 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
31942 ATAAATTATT
**
31952 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
31974 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
31997 TAAA
1 TAAA
32001 TTATTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:32015 original size:15 final size:15
Alignment explanation
Indices: 31995--32158 Score: 220
Period size: 15 Copynumber: 10.5 Consensus size: 15
31985 AATTCATACT
31995 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
32010 AATAAATCAATCTATATTTTAT
1 AAT--A--AAT-TAT--TTTAA
*
32032 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
32047 AATAAATTATTTTAC
1 AATAAATTATTTTAA
32062 AATAAATTATTTTAA
1 AATAAATTATTTTAA
32077 AATAAATTATTTTAA
1 AATAAATTATTTTAA
32092 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
32107 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
32122 AATAAATTATTTTAT
1 AATAAATTATTTTAA
32137 AATAAATTATTTTAA
1 AATAAATTATTTTAA
32152 AATAAAT
1 AATAAAT
32159 AACCTTATTA
Statistics
Matches: 134, Mismatches: 8, Indels: 14
0.86 0.05 0.09
Matches are distributed among these distances:
15 114 0.85
17 4 0.03
18 2 0.01
19 3 0.02
20 4 0.03
22 7 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:33866 original size:7 final size:7
Alignment explanation
Indices: 33814--33862 Score: 89
Period size: 7 Copynumber: 7.0 Consensus size: 7
33804 TTTATGTGTA
33814 GGAAAGG
1 GGAAAGG
33821 GGAAAGG
1 GGAAAGG
33828 GGAAAGG
1 GGAAAGG
33835 GGAAAGG
1 GGAAAGG
33842 GGAAAGG
1 GGAAAGG
33849 GGAAAGG
1 GGAAAGG
*
33856 AGAAAGG
1 GGAAAGG
33863 AGAACTCTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (7 bp):
GGAAAGG
Found at i:48055 original size:16 final size:17
Alignment explanation
Indices: 48034--48066 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
48024 TATCTTCACA
*
48034 CAAGGT-CTTTTTGATT
1 CAAGGTCCTGTTTGATT
48050 CAAGGTCCTGTTTGATT
1 CAAGGTCCTGTTTGATT
48067 ATTCCACACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.18, C:0.15, G:0.21, T:0.45
Consensus pattern (17 bp):
CAAGGTCCTGTTTGATT
Found at i:55343 original size:19 final size:19
Alignment explanation
Indices: 55316--55355 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
55306 GATAAAGATT
* *
55316 AATTTAAACATTGTATTTA
1 AATTCAAACATTGCATTTA
55335 AATTCAAACATTGCATTTA
1 AATTCAAACATTGCATTTA
55354 AA
1 AA
55356 GGTTGCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (19 bp):
AATTCAAACATTGCATTTA
Found at i:56670 original size:22 final size:21
Alignment explanation
Indices: 56645--56687 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
56635 TTGTGGGGTT
56645 TTTTTAATAAA-AAATATTTTTA
1 TTTTT-ATAAATAAAT-TTTTTA
*
56667 TTTTTTTAAATAAATTTTTTA
1 TTTTTATAAATAAATTTTTTA
56688 AAATTATCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTATAAATAAATTTTTTA
Found at i:59340 original size:60 final size:62
Alignment explanation
Indices: 59223--59345 Score: 232
Period size: 60 Copynumber: 2.0 Consensus size: 62
59213 TCCAGTCTTA
59223 AGAGGTAGGTTTGATTTTACTTTATATATATATATATGTATTGTTTAAATATGAATATTAAT
1 AGAGGTAGGTTTGATTTTACTTTATATATATATATATGTATTGTTTAAATATGAATATTAAT
59285 AGAGGTAGGTTTGATTTTAC-TT-TATATATATATATGTATTGTTTAAATATGAATATTAAT
1 AGAGGTAGGTTTGATTTTACTTTATATATATATATATGTATTGTTTAAATATGAATATTAAT
59345 A
1 A
59346 ATGAATTAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
60 39 0.64
61 2 0.03
62 20 0.33
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.48
Consensus pattern (62 bp):
AGAGGTAGGTTTGATTTTACTTTATATATATATATATGTATTGTTTAAATATGAATATTAAT
Found at i:67344 original size:35 final size:36
Alignment explanation
Indices: 67298--67368 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
67288 AAAATTTTAA
67298 AAATGATAAGCAGTT-TATAAGCACCTCTCATCTGT
1 AAATGATAAGCAGTTATATAAGCACCTCTCATCTGT
67333 AAATGATAAGCAGTTATATAAGCACCTCTCATCTGT
1 AAATGATAAGCAGTTATATAAGCACCTCTCATCTGT
67369 TGAGTTTGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 15 0.43
36 20 0.57
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (36 bp):
AAATGATAAGCAGTTATATAAGCACCTCTCATCTGT
Found at i:67433 original size:20 final size:20
Alignment explanation
Indices: 67408--67447 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
67398 TTGATACCTA
* *
67408 ATGCAGTTATTCAAAGAATT
1 ATGCAGCTATGCAAAGAATT
*
67428 ATGCAGCTATGCACAGAATT
1 ATGCAGCTATGCAAAGAATT
67448 TTTGGAAGGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (20 bp):
ATGCAGCTATGCAAAGAATT
Found at i:68458 original size:25 final size:25
Alignment explanation
Indices: 68430--68481 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
68420 TTATTTAAAA
** *
68430 TTATAAATTAAATTGAAAACTATTC
1 TTATAAATTAAATCAAAAACTAATC
68455 TTATAAATTAAATCAAAAACTAATC
1 TTATAAATTAAATCAAAAACTAATC
68480 TT
1 TT
68482 TATGACATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (25 bp):
TTATAAATTAAATCAAAAACTAATC
Done.