Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002164.1 Hibiscus syriacus cultivar Beakdansim tig00004417_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: 72938
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:5647 original size:20 final size:20
Alignment explanation
Indices: 5590--5647 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
5580 TCACGAAATA
*
5590 TAAGATTATCAGTAAGA-ATG
1 TAAGATTATCAGGAA-ATATG
5610 TAAGATTATCA-GAGAATATG
1 TAAGATTATCAGGA-AATATG
5630 TAAGATTATCAGGAAATA
1 TAAGATTATCAGGAAATA
5648 GAATTATTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 2 0.06
20 30 0.88
21 2 0.06
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.29
Consensus pattern (20 bp):
TAAGATTATCAGGAAATATG
Found at i:5868 original size:37 final size:37
Alignment explanation
Indices: 5795--5869 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
5785 GTTGAAAAAT
* *
5795 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
5832 ATTTATATACCTTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATA--TTTTCTTTAAAAAATTGAAAATCATAAA
5869 A
1 A
5870 AGGCTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 15 0.45
38 14 0.42
39 4 0.12
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:14197 original size:13 final size:13
Alignment explanation
Indices: 14179--14203 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14169 TATAACTAAC
14179 TTTTGGGTCATTG
1 TTTTGGGTCATTG
14192 TTTTGGGTCATT
1 TTTTGGGTCATT
14204 ATTTGAATAA
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:0.08, C:0.08, G:0.28, T:0.56
Consensus pattern (13 bp):
TTTTGGGTCATTG
Found at i:21234 original size:33 final size:33
Alignment explanation
Indices: 21189--21258 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
21179 AACCTTGCAA
*
21189 ACACTTCAAGGTTTATACTCAAAAAACTTGAAT
1 ACACTTCAAGGTTTATACCCAAAAAACTTGAAT
* *
21222 ACACTTCGAGGTTTATACCCAAAAATCTTGAAT
1 ACACTTCAAGGTTTATACCCAAAAAACTTGAAT
21255 ACAC
1 ACAC
21259 ACCCTCTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (33 bp):
ACACTTCAAGGTTTATACCCAAAAAACTTGAAT
Found at i:21866 original size:22 final size:21
Alignment explanation
Indices: 21841--21886 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
21831 GAATCGATCC
21841 TTTTCATCGAGGGATCAATCAT
1 TTTTC-TCGAGGGATCAATCAT
* *
21863 TTTTCTTGAGGGATCAATCCT
1 TTTTCTCGAGGGATCAATCAT
21884 TTT
1 TTT
21887 GTGAATGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (21 bp):
TTTTCTCGAGGGATCAATCAT
Found at i:22302 original size:16 final size:16
Alignment explanation
Indices: 22290--22320 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
22280 ATGAACTAAG
22290 ATATAAATAAACTGAA
1 ATATAAATAAACTGAA
22306 ATATAAATAAACTGA
1 ATATAAATAAACTGA
22321 TTTTTTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (16 bp):
ATATAAATAAACTGAA
Found at i:22374 original size:31 final size:31
Alignment explanation
Indices: 22338--22396 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
22328 AACTTAAAAG
* *
22338 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
22369 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
22397 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:22447 original size:22 final size:22
Alignment explanation
Indices: 22421--22463 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
22411 TAATAAATTA
22421 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
22443 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
22464 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:22472 original size:22 final size:22
Alignment explanation
Indices: 22423--22471 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
22413 ATAAATTATT
**
22423 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
22445 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
22468 TAAA
1 TAAA
22472 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:22481 original size:32 final size:32
Alignment explanation
Indices: 22443--22962 Score: 372
Period size: 32 Copynumber: 18.4 Consensus size: 32
22433 CAATCCATAT
22443 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
22475 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
22505 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
22523 TTTAAAATAAATCAATACATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
22555 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
22585 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
22603 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
22635 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
22667 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* ** *
22689 TTTAAAATAAATCAATTCATA-TTTTAAAA--
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
22718 -------TAAATCAATCCATACTAACAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
22743 TTTAAAATAAATCAATCCATATTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
22775 TTTAAAATAAATCAATCTATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
22805 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
22823 TTTAAAATAAATCAATCTATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
22855 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
22887 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
22919 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
22951 TTTAAAATAAAT
1 TTTAAAATAAAT
22963 TATTTTAAAA
Statistics
Matches: 396, Mismatches: 25, Indels: 134
0.71 0.05 0.24
Matches are distributed among these distances:
20 3 0.01
22 69 0.17
23 9 0.02
24 7 0.02
25 1 0.00
26 46 0.12
27 1 0.00
28 4 0.01
29 1 0.00
30 3 0.01
31 6 0.02
32 246 0.62
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:22516 original size:80 final size:80
Alignment explanation
Indices: 22426--22709 Score: 453
Period size: 80 Copynumber: 3.5 Consensus size: 80
22416 AATTATTTAA
22426 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
22491 CCATACAACTACAAT
66 CCATACAACTACAAT
*
22506 AATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
22571 CCATACAACTACAAT
66 CCATACAACTACAAT
*
22586 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *
22651 CTATACTAA-TAAATTATTT
66 CCATAC-AACTACA--A--T
*
22670 AAAATAAATCAATCCATATTTTAAAATAAATCAATTCATA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATA
22710 TTTTAAAATA
Statistics
Matches: 191, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
80 150 0.79
81 2 0.01
82 1 0.01
84 1 0.01
86 37 0.19
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:22552 original size:22 final size:22
Alignment explanation
Indices: 22480--22552 Score: 53
Period size: 22 Copynumber: 3.3 Consensus size: 22
22470 AATTATTTAA
* *
22480 AATAAATCAATCCATACA-ACT
1 AATAAATAAATCAATACATACT
*
22501 ACA-ATAATAAATCAATCCATA-T
1 A-ATA-AATAAATCAATACATACT
**
22523 TTTAAAATAAATCAATACATACT
1 AAT-AAATAAATCAATACATACT
22546 AATAAAT
1 AATAAAT
22553 TATTTAAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 11
0.67 0.14 0.19
Matches are distributed among these distances:
21 2 0.05
22 32 0.84
23 4 0.11
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
AATAAATAAATCAATACATACT
Found at i:22567 original size:112 final size:111
Alignment explanation
Indices: 22443--22908 Score: 481
Period size: 112 Copynumber: 4.2 Consensus size: 111
22433 CAATCCATAT
*
22443 TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATACAACTACAAT-
1 TTTAAAATAAATCAATCCATAC-AACTAAA--A--T--AATAAATCAATCCATA-AACTAAAATA
*
22506 AATAAATCAAT-C-CAT-A-T-TTTAAAATAAATCAATAC-ATACTAATAAATTA
58 AATAAATCAATACAAATAATTATTTAAAATAAATCAAT-CTATACTAATAAATTA
* *** *
22555 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCCATACAACTAAAATAATAAATCAATCCATAAACTAAAATAAATAAATC
*
22620 CATACAAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTA
66 AATACAAAT-AATTATTTAAAATAAATCAATCTATACTAATAAATTA
* ** * *** *
22667 TTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATTCATATTTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCCATACAACTAAAATAATAAATCAATCCATAAACTAAAATAAATAAATC
* * *
22728 CATACTAACA-AATTATTTAAAATAAATCAATCCATATTAATAAATTA
66 AATAC-AA-ATAATTATTTAAAATAAATCAATCTATACTAATAAATTA
* * *** *
22775 TTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCCATACAACTAAAATAATAAATCAATCCATAAACTAAAATAAATAAATC
* *
22840 TATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTA
66 AATACAAAT-AATTATTTAAAATAAATCAATCTATACTAATAAATTA
22887 TTTAAAATAAATCAATCCATAC
1 TTTAAAATAAATCAATCCATAC
22909 TAATAAATTA
Statistics
Matches: 315, Mismatches: 22, Indels: 34
0.85 0.06 0.09
Matches are distributed among these distances:
105 5 0.02
106 25 0.08
107 1 0.00
108 95 0.30
109 6 0.02
110 4 0.01
111 10 0.03
112 169 0.54
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (111 bp):
TTTAAAATAAATCAATCCATACAACTAAAATAATAAATCAATCCATAAACTAAAATAAATAAATC
AATACAAATAATTATTTAAAATAAATCAATCTATACTAATAAATTA
Found at i:22632 original size:22 final size:22
Alignment explanation
Indices: 22559--22632 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
22549 AAATTATTTA
*
22559 AAATAAATCAATCCATACAACTACA
1 AAATAAATCAATCCATACAA--A-T
***
22584 ATAATAAATCAATCCATA-TTTT
1 A-AATAAATCAATCCATACAAAT
22606 AAAATAAATCAATCCATACAAAT
1 -AAATAAATCAATCCATACAAAT
22629 AAAT
1 AAAT
22633 TATTTAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
22 20 0.51
23 2 0.05
25 1 0.03
26 16 0.41
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATAAATCAATCCATACAAAT
Found at i:22642 original size:14 final size:14
Alignment explanation
Indices: 22625--22678 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
22615 CAATCCATAC
22625 AAATAAATTATTTA
1 AAATAAATTATTTA
*
22639 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
22656 CTAATAAATTATTTA
1 -AAATAAATTATTTA
22671 AAATAAAT
1 AAATAAAT
22679 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:22740 original size:22 final size:22
Alignment explanation
Indices: 22667--22731 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
22657 TAATAAATTA
22667 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
22689 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
22711 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
22732 CTAACAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:22971 original size:15 final size:15
Alignment explanation
Indices: 22910--23074 Score: 163
Period size: 15 Copynumber: 10.5 Consensus size: 15
22900 AATCCATACT
22910 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
* * *
22924 AATAAATCAATTCATACT
1 AATAAAT-TATT-TTA-A
22942 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
22956 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
22971 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
22993 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
23008 AGTAAATTATTTTAT
1 AATAAATTATTTTAA
23023 AATAAATTATTTTAA
1 AATAAATTATTTTAA
23038 AATAAATTATTTTAA
1 AATAAATTATTTTAA
23053 AATAAATTATTTTAA
1 AATAAATTATTTTAA
23068 AATAAAT
1 AATAAAT
23075 AACCTTATTA
Statistics
Matches: 125, Mismatches: 14, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
14 16 0.13
15 80 0.64
16 2 0.02
17 4 0.03
18 9 0.07
19 3 0.02
20 1 0.01
22 10 0.08
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.44
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:23547 original size:16 final size:16
Alignment explanation
Indices: 23506--23548 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
23496 CAGACTGCTA
* *
23506 AAATGAACTAAAATAT
1 AAATAAACTGAAATAT
23522 AAATAAACTGAAATAT
1 AAATAAACTGAAATAT
23538 AAATAAACTGA
1 AAATAAACTGA
23549 TTTTTTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (16 bp):
AAATAAACTGAAATAT
Found at i:23603 original size:31 final size:31
Alignment explanation
Indices: 23567--23625 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
23557 ACTTAAAAAG
* *
23567 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
23598 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
23626 CAATATAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:23676 original size:22 final size:22
Alignment explanation
Indices: 23650--23692 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
23640 TAATAAATTA
23650 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
23672 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
23693 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:23701 original size:22 final size:22
Alignment explanation
Indices: 23652--23700 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
23642 ATAAATTATT
**
23652 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
23674 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
23697 TAAA
1 TAAA
23701 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:23704 original size:54 final size:54
Alignment explanation
Indices: 23640--24466 Score: 544
Period size: 54 Copynumber: 15.4 Consensus size: 54
23630 ATAACTACAA
23640 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * **
23694 TAATAAATTATTTAAAATAAATCAATCGATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** **
23751 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAAT-CATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
*
23805 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * * ** * ** * **
23853 AAATAAACTATTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATAC
** *
23908 -AATCCA-TATTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
23961 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*** * * *
24015 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATAC
24068 T-AT--A-T-TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATAC
* *
24127 TAATAAATTATTTAAAATAAATCAACCCATATTTTAAAATAAATCAATCCATATTT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA--C
* * * * *
24183 TAAAATAAATCAATCTATACT-AATAAAT---TA-TTTAAAATAAATCAAT-C---C
1 T--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
24231 --AT--A-T-TTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
24279 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * **
24333 TAATAAATTATTTAAAATAAATCAATCCACACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAAT-C-CA-TATTTTAA-AATAAATCAATCCATAC
** * ** * * ** *
24390 TTTTAAAATAAAT-CAATCAATACTAATAAAT-TATTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
24445 TAATAAATTATTTAAAATAAAT
1 TAATAAATTATTTAAAATAAAT
24467 TATTTTAAAA
Statistics
Matches: 597, Mismatches: 106, Indels: 138
0.71 0.13 0.16
Matches are distributed among these distances:
39 5 0.01
40 6 0.01
42 1 0.00
43 2 0.00
44 18 0.03
45 1 0.00
47 21 0.04
48 27 0.05
49 9 0.02
50 5 0.01
52 11 0.02
53 18 0.03
54 289 0.48
55 34 0.06
56 28 0.05
57 31 0.05
58 62 0.10
59 8 0.01
60 3 0.01
62 1 0.00
63 2 0.00
64 15 0.03
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:23710 original size:32 final size:31
Alignment explanation
Indices: 23672--24466 Score: 299
Period size: 32 Copynumber: 29.4 Consensus size: 31
23662 CAATCCATAT
23672 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
* *
23704 TTTAAAATAAATCAATCGATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
23734 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
23752 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
23784 TTTAAAATAAATCAAT-CATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
23813 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
23831 TTTAAAATAAATCAATCCATACAAATAAACTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
23863 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
23895 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
* **
23917 TTTAAAATAAATCAATTCATA-TTTTAAA-A
1 TTTAAAATAAATCAATCCATACTAATAAATA
23946 -------TAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
23971 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
23993 TTTAAAATAAATCAATCCATATTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
24025 TTTAAAATAAATCAATCCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
* **
24055 --T--AATAAATCAATCTATA-TTTTAAA-A
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
24080 -------TAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
24105 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
24137 TTTAAAATAAATCAA-CC---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
24159 TTTAAAATAAATCAATCC--A----T--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
24181 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
24213 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
* **
24235 TTTAAAATAAATCAATTCATA-TTTTAAA-A
1 TTTAAAATAAATCAATCCATACTAATAAATA
24264 -------TAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
24289 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
24311 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
* *
24343 TTTAAAATAAATCAATCCACAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
24373 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
24391 TTTAAAATAAATCAATCAATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
24423 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
24455 TTTAAAATAAAT
1 TTTAAAATAAAT
24467 TATTTTAAAA
Statistics
Matches: 594, Mismatches: 38, Indels: 262
0.66 0.04 0.29
Matches are distributed among these distances:
20 3 0.01
22 179 0.30
23 27 0.05
24 12 0.02
25 20 0.03
26 58 0.10
27 3 0.01
28 13 0.02
29 3 0.01
30 8 0.01
31 21 0.04
32 247 0.42
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (31 bp):
TTTAAAATAAATCAATCCATACTAATAAATA
Found at i:23781 original size:22 final size:22
Alignment explanation
Indices: 23706--23780 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
23696 ATAAATTATT
* *
23706 TAAAATAAATCAATCGATACAA
1 TAAAATAAATCAATCCATATAA
**
23728 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
23754 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
23777 TAAA
1 TAAA
23781 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.55, C:0.16, G:0.01, T:0.28
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:23961 original size:76 final size:76
Alignment explanation
Indices: 23863--24501 Score: 648
Period size: 76 Copynumber: 8.1 Consensus size: 76
23853 AAATAAACTA
*
23863 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
23928 TCAATTCATAT
66 TCAATTCATAT
23939 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
*
24004 TCAATCCATAT
66 TCAATTCATAT
* * * * * * *
24015 TAATAAATTATTTAAAATAAATCAAT-C-CATACAACTA--CAATAATAAATCAATCTATATTTT
1 T-TTAAA--A--T-AAATCAATCCATACTAATA-AATTATTTAA-AATAAATCAATCCATATTTT
24076 AAAATAAATCAATCCATACAAATAAATT
58 AAAATAAATCAAT---T-C--AT--A-T
*
24104 ATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAACCCATATTTTAAAATAA
1 -TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
*
24169 ATCAATCCATAT
65 ATCAATTCATAT
*
24181 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
24246 TCAATTCATAT
66 TCAATTCATAT
24257 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
24322 TCAATCTATACTAATAAATT
66 TCAA--T-T-C--AT--A-T
* *
24342 ATTTAAAATAAATCAATCCACAC-AACTACA--A--T--AATAAATCAATCCATATTTTAAAATA
1 -TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATA
24400 AATCAATCAATACTAATAAATT
64 AATCAAT---T-C--AT--A-T
*
24422 ATTTAAAATAAATCAATTCATACTAATAAATTATTTAAAAT--A--AAT---TATTTTAAAATAA
1 -TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
*
24480 ATCAATCCATAT
65 ATCAATTCATAT
*
24492 TTTATAATAA
1 TTTAAAATAA
24502 TTTATTTTAA
Statistics
Matches: 491, Mismatches: 30, Indels: 91
0.80 0.05 0.15
Matches are distributed among these distances:
69 9 0.02
70 1 0.00
71 1 0.00
73 2 0.00
75 1 0.00
76 216 0.44
77 5 0.01
78 3 0.01
79 23 0.05
80 107 0.22
81 8 0.02
82 18 0.04
84 15 0.03
85 9 0.02
86 63 0.13
87 3 0.01
88 1 0.00
89 5 0.01
90 1 0.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (76 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TCAATTCATAT
Found at i:23968 original size:22 final size:22
Alignment explanation
Indices: 23895--23959 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
23885 TAATAAATTA
23895 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
23917 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
23939 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
23960 CTAATAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:23997 original size:22 final size:22
Alignment explanation
Indices: 23971--24015 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
23961 TAATAAATTA
23971 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
23993 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
24015 T
1 T
24016 AATAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:24022 original size:22 final size:22
Alignment explanation
Indices: 23969--24021 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
23959 ACTAATAAAT
23969 TATT-TAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
*
23990 TATTTTAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
24012 TATTAATAAA
1 TATT-ATAAA
24022 TTATTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 4 0.14
22 21 0.72
23 4 0.14
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (22 bp):
TATTATAAAATAAATCAATCCA
Found at i:24098 original size:18 final size:18
Alignment explanation
Indices: 24077--24134 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
24067 CTATATTTTA
24077 AAATAAATCAATCCATAC
1 AAATAAATCAATCCATAC
* *
24095 AAATAAAT-TAT--TTA-
1 AAATAAATCAATCCATAC
24109 AAATAAATCAATCCATAC
1 AAATAAATCAATCCATAC
*
24127 TAATAAAT
1 AAATAAAT
24135 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
14 8 0.26
15 4 0.13
17 4 0.13
18 15 0.48
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAAATCAATCCATAC
Found at i:24210 original size:22 final size:22
Alignment explanation
Indices: 24139--24209 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
24129 ATAAATTATT
* **
24139 TAAAATAAATCAACCCATATTT
1 TAAAATAAATCAATCCATATAA
**
24161 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
24183 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
24206 TAAA
1 TAAA
24210 TTATTTAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 39 0.89
23 5 0.11
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:24239 original size:22 final size:22
Alignment explanation
Indices: 24213--24277 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
24203 TAATAAATTA
24213 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
24235 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
24257 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
24278 CTAATAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:24286 original size:22 final size:22
Alignment explanation
Indices: 24137--24197 Score: 113
Period size: 22 Copynumber: 2.8 Consensus size: 22
24127 TAATAAATTA
*
24137 TTTAAAATAAATCAACCCATAT
1 TTTAAAATAAATCAATCCATAT
24159 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
24181 TTTAAAATAAATCAATC
1 TTTAAAATAAATCAATC
24198 TATACTAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:24339 original size:318 final size:316
Alignment explanation
Indices: 23640--24501 Score: 1417
Period size: 318 Copynumber: 2.7 Consensus size: 316
23630 ATAACTACAA
23640 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
23705 TTAAAATAAATCAATCGATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
*
23770 ATACTAATAAATTATTTAAAATAAATCAATCATAC-AACTACA--A--T--AATAAATCAATCCA
131 ATACTAATAAATTATTTAAAATAAATCAATCATACTAA-TAAATTATTTAAAATAAATCAA-CCA
23828 TATTTTAAAATAAATCAATCCATACAAATAAACTATTTAAAATAAATCAATCTATACTAATAAAT
194 TATTTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCTATACTAATAAAT
23893 TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCA
249 TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCA
23958 TAC
314 TAC
*
23961 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
24026 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCTATATTTTAAAATAAATCAATCC
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
*
24091 ATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAACCCA
131 ATACTAATAAATTATTTAAAATAAATCAAT-CATACTAATAAATTATTTAAAATAAATCAA-CCA
24156 TATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAAT
194 TATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAAT
24221 AAATCAATCCATATTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
259 AAATCAATCCATATTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
*
24279 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
* *
24344 TTAAAATAAATCAATCCACACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCA
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
24409 ATACTAATAAATTATTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAAT------T
131 ATACTAATAAATTATTTAAAATAAATCAA-TCATACTAATAAATTATTTAAAATAAATCAACCAT
*
24468 ATTTTAAAATAAATCAATCCATATTTTATAATAA
195 ATTTTAAAATAAATCAATCCATATTTTAAAATAA
24502 TTTATTTTAA
Statistics
Matches: 519, Mismatches: 13, Indels: 28
0.93 0.02 0.05
Matches are distributed among these distances:
311 34 0.07
318 278 0.54
319 2 0.00
320 1 0.00
321 156 0.30
322 10 0.02
323 2 0.00
324 2 0.00
326 1 0.00
327 1 0.00
328 32 0.06
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.35
Consensus pattern (316 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCC
ATACTAATAAATTATTTAAAATAAATCAATCATACTAATAAATTATTTAAAATAAATCAACCATA
TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAA
ATCAATCCATATTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
Found at i:24340 original size:22 final size:22
Alignment explanation
Indices: 24291--24339 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
24281 ATAAATTATT
**
24291 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
24313 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
24336 TAAA
1 TAAA
24340 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:24449 original size:18 final size:18
Alignment explanation
Indices: 24396--24452 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
24386 CATATTTTAA
24396 AATAAATCAA-TCAATACT
1 AATAAATCAATTC-ATACT
* *
24414 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
24428 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
24446 AATAAAT
1 AATAAAT
24453 TATTTAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
14 7 0.23
15 5 0.17
17 3 0.10
18 15 0.50
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:24475 original size:15 final size:15
Alignment explanation
Indices: 24414--24548 Score: 103
Period size: 15 Copynumber: 8.5 Consensus size: 15
24404 AATCAATACT
24414 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
* * *
24428 AATAAATCAATTCATACT
1 AATAAAT-TATT-TTA-A
24446 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
24460 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
24475 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
24497 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
24512 AGTAAATTATTTTAT
1 AATAAATTATTTTAA
24527 AATAAATTATTTTAA
1 AATAAATTATTTTAA
24542 AATAAAT
1 AATAAAT
24549 AACCTTATTA
Statistics
Matches: 95, Mismatches: 14, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
14 16 0.17
15 50 0.53
16 2 0.02
17 4 0.04
18 9 0.09
19 3 0.03
20 1 0.01
22 10 0.11
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:24481 original size:47 final size:49
Alignment explanation
Indices: 24414--24533 Score: 147
Period size: 52 Copynumber: 2.4 Consensus size: 49
24404 AATCAATACT
* *
24414 AATAAATTA-TTTAAAATAAATCAATTCATA-CTAATAAATTA-TTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATATATAATAAATTATTTTAA
*
24460 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATA---TATAATAAATTATTTTAA
* *
24512 AGTAAATTATTTTATAATAAAT
1 AATAAATTATTTTAAAATAAAT
24534 TATTTTAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
46 9 0.14
47 20 0.32
51 9 0.14
52 25 0.40
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (49 bp):
AATAAATTATTTTAAAATAAATCAATCCATATATAATAAATTATTTTAA
Found at i:26278 original size:13 final size:13
Alignment explanation
Indices: 26262--26312 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
26252 ACCTAAGTTA
26262 TATATTTAATTTT
1 TATATTTAATTTT
*
26275 TATACTTCAATTTAT
1 TATA-TTTAATTT-T
26290 TA-ATTT-ATTTT
1 TATATTTAATTTT
26301 TATAATTTAATT
1 TAT-ATTTAATT
26313 ATATTATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
11 3 0.10
12 4 0.13
13 10 0.32
14 11 0.35
15 3 0.10
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (13 bp):
TATATTTAATTTT
Found at i:26299 original size:26 final size:26
Alignment explanation
Indices: 26259--26322 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
26249 TATACCTAAG
*
26259 TTATA-TATTTAATTTTTATACTTCAA
1 TTATATTATTT-ATTTTTATAATTCAA
*
26285 TT-TATTAATTTATTTTTATAATTTAA
1 TTATATT-ATTTATTTTTATAATTCAA
26311 TTATATTATTTA
1 TTATATTATTTA
26323 CATATTTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 2 0.06
26 23 0.70
27 8 0.24
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (26 bp):
TTATATTATTTATTTTTATAATTCAA
Found at i:39157 original size:21 final size:20
Alignment explanation
Indices: 39128--39168 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
39118 TTACATTAAT
*
39128 ATTAATATTGCTTTATTTTA
1 ATTAATATTGCTATATTTTA
*
39148 ATTATATATTTCTATATTTTA
1 ATTA-ATATTGCTATATTTTA
39169 TTACTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTAATATTGCTATATTTTA
Found at i:40400 original size:21 final size:21
Alignment explanation
Indices: 40358--40400 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
40348 TTTCTGGGTG
* * *
40358 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
40379 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
40400 A
1 A
40401 CGAAATAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:40465 original size:67 final size:68
Alignment explanation
Indices: 40380--40531 Score: 229
Period size: 68 Copynumber: 2.2 Consensus size: 68
40370 ACCCATTCAA
* *
40380 GGGGAACCGATACCCCCTCAACG-A-AATAAATTTCCAGAATG-TTAGAGGGGAATCGGTACCCC
1 GGGGAACCGATACCCCCTCAACGTATAAGAAA-TTCCAGAATGCTT-GAGGGGAATCGATACCCC
40442 CAGGG
64 CAGGG
*
40447 GGGGAACCGATACCCCCTCATCGTATAAGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGTATAAGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
40512 GGG
66 GGG
*
40515 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
40532 ATGAGAAAAA
Statistics
Matches: 78, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
67 22 0.28
68 49 0.63
69 7 0.09
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGTATAAGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
GGG
Found at i:40933 original size:30 final size:30
Alignment explanation
Indices: 40899--40957 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
40889 GTTATATGAG
* *
40899 CTATGTGATAAAGGTATGTAAATGATATGT
1 CTATGTGATAAAGGTATGGAAATAATATGT
40929 CTATGTGATAAAGGTATGGAAATAATATG
1 CTATGTGATAAAGGTATGGAAATAATATG
40958 ACTACGCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGGAAATAATATGT
Found at i:41243 original size:22 final size:22
Alignment explanation
Indices: 41168--41235 Score: 136
Period size: 22 Copynumber: 3.1 Consensus size: 22
41158 TCCTTATGGA
41168 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
41190 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
41212 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
41234 CA
1 CA
41236 TTTATACGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.26
Consensus pattern (22 bp):
CAATTCTACGGGCACTTCGGTG
Found at i:47316 original size:21 final size:21
Alignment explanation
Indices: 47274--47316 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
47264 TTTCTGGGTG
* * *
47274 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
47295 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
47316 A
1 A
47317 CGAAATAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:47378 original size:66 final size:67
Alignment explanation
Indices: 47272--47446 Score: 214
Period size: 67 Copynumber: 2.6 Consensus size: 67
47262 GATTTCTGGG
* * *
47272 TGAGGGGAATCGGTACCCATTCA-AGGGGAACCGATACCCCCTCAACG-A-AATAAATTTCCAGA
1 TGAGGGGAATCGGTACCC--CCAGGGGGGAACCGATACCCCCTCAACGTATAAGAAA-TTCCAGA
47334 ATG-T
63 ATGCT
*
47338 TAGAGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCATCGTATAAGAAATTCCAGAAT
1 T-GAGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTATAAGAAATTCCAGAAT
47403 GCT
65 GCT
* * *
47406 TTAGGGGAATCGATACCCCCAGGGGGGGAACCGATTCCCCC
1 TGAGGGGAATCGGTACCCCCA-GGGGGGAACCGATACCCCC
47447 ATGAGAAAAA
Statistics
Matches: 96, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
65 2 0.02
66 23 0.24
67 46 0.48
68 25 0.26
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.18
Consensus pattern (67 bp):
TGAGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTATAAGAAATTCCAGAATG
CT
Found at i:47850 original size:30 final size:30
Alignment explanation
Indices: 47816--47874 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
47806 GTTATATGAG
* *
47816 CTATGTGATAAAGGTATGTAAATGATATGT
1 CTATGTGATAAAGGTATGGAAATAATATGT
47846 CTATGTGATAAAGGTATGGAAATAATATG
1 CTATGTGATAAAGGTATGGAAATAATATG
47875 ACTACGCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGGAAATAATATGT
Found at i:48114 original size:22 final size:22
Alignment explanation
Indices: 48086--48131 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
48076 TCCTTATGGA
48086 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
48108 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
48130 CA
1 CA
48132 TTTATACGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (22 bp):
CAATTCTACGGGCACTTCGGTG
Found at i:48139 original size:22 final size:22
Alignment explanation
Indices: 48086--48139 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
48076 TCCTTATGGA
*
48086 CAATTCTACGGGCACTTCGGTG
1 CAATTATACGGGCACTTCGGTG
*
48108 CAATTCTACGGGCACTTCGGTG
1 CAATTATACGGGCACTTCGGTG
*
48130 CATTTATACG
1 CAATTATACG
48140 AGCTGTGGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (22 bp):
CAATTATACGGGCACTTCGGTG
Found at i:48777 original size:17 final size:17
Alignment explanation
Indices: 48755--48792 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
48745 TTTTTTATAA
48755 AAAATTATTAAAA-AATT
1 AAAATT-TTAAAATAATT
48772 AAAATTTTAAAATAATT
1 AAAATTTTAAAATAATT
48789 AAAA
1 AAAA
48793 AGATAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTTTAAAATAATT
Found at i:52427 original size:18 final size:17
Alignment explanation
Indices: 52393--52456 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 17
52383 CCTCTTTATT
52393 TATTATTTTTTCAAATAAA
1 TATTATTTTTT--AATAAA
52412 TATCTATTTTTTAATAAA
1 TAT-TATTTTTTAATAAA
* *
52430 TTAATATTTATTTTATAAA
1 -TATTATTT-TTTAATAAA
52449 TATTATTT
1 TATTATTT
52457 CGGATCGGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 18 0.46
19 13 0.33
20 8 0.21
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTATTTTTTAATAAA
Found at i:63847 original size:36 final size:36
Alignment explanation
Indices: 63776--63848 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
63766 ACTATAAGAT
* *
63776 ATTTATATATTTCCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTCCTTTAAAAATTGAAAATCATAAA
*
63812 ATTTATATAATTT-TTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTCCTTTA-AAAATTGAAAATCATAAA
63848 A
1 A
63849 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 18 0.56
37 14 0.44
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.45
Consensus pattern (36 bp):
ATTTATATATTTCCTTTAAAAATTGAAAATCATAAA
Found at i:70880 original size:17 final size:16
Alignment explanation
Indices: 70860--70893 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
70850 TTTTTAGTTT
*
70860 TTTTTAGTTTTTCAAAA
1 TTTTT-GTTTTTAAAAA
70877 TTTTTGTTTTTAAAAA
1 TTTTTGTTTTTAAAAA
70893 T
1 T
70894 ATTATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTTTGTTTTTAAAAA
Done.