Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007712.1 Hibiscus syriacus cultivar Beakdansim tig00109936_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: 920388
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:788184 original size:23 final size:24
Alignment explanation
Indices: 788088--788188 Score: 73
Period size: 26 Copynumber: 4.0 Consensus size: 24
788078 AATTCATAAC
* *
788088 ATTTTTTTATATATTAACTTAAACAAT
1 ATTTTATTAT-TATTAA-TTTAA-AAT
788115 ATTTT-TTA-TATTAACTTATCAAATAT
1 ATTTTATTATTATTAA-TT-T-AAA-AT
788141 ATTTTATTATTAACTTAATTTAAAAT
1 ATTTTATTATT-A-TTAATTTAAAAT
*
788167 ATTTTATTATT-TTCATTTAAAA
1 ATTTTATTATTATTAATTTAAAA
788189 AATATATTTT
Statistics
Matches: 65, Mismatches: 2, Indels: 18
0.76 0.02 0.21
Matches are distributed among these distances:
23 10 0.15
24 9 0.14
25 1 0.02
26 25 0.38
27 11 0.17
28 2 0.03
29 3 0.05
30 4 0.06
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTTTATTATTATTAATTTAAAAT
Found at i:795470 original size:32 final size:32
Alignment explanation
Indices: 795429--795491 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
795419 ATAGACACAT
*
795429 GGTAGAATTCTAATTATTTAGCTCAATACAAA
1 GGTAGAATTCTAATTAGTTAGCTCAATACAAA
795461 GGTAGAATTCTAATTAGTTAGCTCAATACAA
1 GGTAGAATTCTAATTAGTTAGCTCAATACAA
795492 CACCAACAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (32 bp):
GGTAGAATTCTAATTAGTTAGCTCAATACAAA
Found at i:797858 original size:14 final size:14
Alignment explanation
Indices: 797836--797868 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
797826 GACAAAATAA
797836 CATGATACAAAAAT
1 CATGATACAAAAAT
*
797850 CATGTTACAAAAAT
1 CATGATACAAAAAT
797864 CATGA
1 CATGA
797869 CATAATTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.24
Consensus pattern (14 bp):
CATGATACAAAAAT
Found at i:799726 original size:49 final size:49
Alignment explanation
Indices: 799641--799747 Score: 153
Period size: 49 Copynumber: 2.2 Consensus size: 49
799631 CTGCTGAATA
* *
799641 AAATAATAATAAACTAAATATAATATTTTGATTCTATCCTAATTTCTAAT
1 AAATAAT-ATAAACTAAATATAATATTTTGACTCTATCCTAATTCCTAAT
* *
799691 AAATAATATAAACTAAA-ATAATATTTTTTACTCTATCTTAATTCCTAAT
1 AAATAATATAAACTAAATATAATA-TTTTGACTCTATCCTAATTCCTAAT
799740 AAATAATA
1 AAATAATA
799748 AATCAAATCC
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
48 6 0.12
49 39 0.75
50 7 0.13
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.41
Consensus pattern (49 bp):
AAATAATATAAACTAAATATAATATTTTGACTCTATCCTAATTCCTAAT
Found at i:808133 original size:20 final size:20
Alignment explanation
Indices: 808060--808126 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
808050 TATTCCCTGG
* *
808060 TAATCTTTTATTTCCACTGG
1 TAATCTTTTATTCCCACTGA
808080 TAATCTTTTATTCCCACTGA
1 TAATCTTTTATTCCCACTGA
808100 TAATCTTTTATTCCCACTGA
1 TAATCTTTTATTCCCACTGA
808120 TAATCTT
1 TAATCTT
808127 ACATTCCGTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (20 bp):
TAATCTTTTATTCCCACTGA
Found at i:813305 original size:43 final size:44
Alignment explanation
Indices: 813203--813296 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 44
813193 ACTTTAATAG
* * * *
813203 TGACAAAAATAA-TTATCGTCACAAAATCACCAATTAAGACTAA
1 TGACAAAAACAATTTTTTGTCACAAAATCACCAACTAAGACTAA
* *
813246 TGACAAAAACAATTTTTTGTCAC-AAATCACCAACTACGACTAG
1 TGACAAAAACAATTTTTTGTCACAAAATCACCAACTAAGACTAA
813289 TGACAAAA
1 TGACAAAA
813297 TATTTTTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
43 36 0.82
44 8 0.18
ACGTcount: A:0.48, C:0.20, G:0.09, T:0.23
Consensus pattern (44 bp):
TGACAAAAACAATTTTTTGTCACAAAATCACCAACTAAGACTAA
Found at i:814990 original size:3 final size:3
Alignment explanation
Indices: 814982--815085 Score: 181
Period size: 3 Copynumber: 34.7 Consensus size: 3
814972 TTTTTATCCA
*
814982 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
815030 TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
815078 TAT TAT TA
1 TAT TAT TA
815086 AGTATATATT
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 95 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:815582 original size:20 final size:20
Alignment explanation
Indices: 815559--815597 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
815549 AGAACGGGAC
815559 AGAGAGACAGAAAAAAAAAG
1 AGAGAGACAGAAAAAAAAAG
815579 AGAGAGACAGAAAAAAAAA
1 AGAGAGACAGAAAAAAAAA
815598 CAACAGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.72, C:0.05, G:0.23, T:0.00
Consensus pattern (20 bp):
AGAGAGACAGAAAAAAAAAG
Found at i:817221 original size:20 final size:21
Alignment explanation
Indices: 817198--817249 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
817188 AGAAATTAAA
817198 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
817218 AATTCTTTTCTTTAAAATTTTT
1 AATTCATTTATTT-AAATTTTT
817240 -ATT-ATTTATT
1 AATTCATTTATT
817250 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:824421 original size:114 final size:114
Alignment explanation
Indices: 824213--824438 Score: 371
Period size: 114 Copynumber: 2.0 Consensus size: 114
824203 AAGTGCCATG
*
824213 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * *
824278 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
66 TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
*
824327 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
824392 TGATTCGGTAGGAACCCCAGAACCGATCATTGGAATTGAAAGATGAA
66 TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAA
824439 CTGCATGATC
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGATTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
Found at i:826505 original size:50 final size:50
Alignment explanation
Indices: 826443--826572 Score: 190
Period size: 50 Copynumber: 2.6 Consensus size: 50
826433 AATCCAAGAA
*
826443 AAATGATGAATATGTTGTCAACTGTTTTACATCCAAGCAGAAGCCACAGG
1 AAATGATGAATATGTTGTCAACTGTTTTACATCCAAACAGAAGCCACAGG
* * *
826493 GAATGATGAATATGTTGTCAAATGTTTTACATCCAAACAGAAGCCACATG
1 AAATGATGAATATGTTGTCAACTGTTTTACATCCAAACAGAAGCCACAGG
* *
826543 AAATGATGAATGTGTTATCAAAC-GTTTTAC
1 AAATGATGAATATGTTGTC-AACTGTTTTAC
826573 GAACCAGTGA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
50 69 0.97
51 2 0.03
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (50 bp):
AAATGATGAATATGTTGTCAACTGTTTTACATCCAAACAGAAGCCACAGG
Found at i:827811 original size:113 final size:113
Alignment explanation
Indices: 827399--828526 Score: 1587
Period size: 113 Copynumber: 10.0 Consensus size: 113
827389 CAAAGATTCA
** * * *
827399 AATCCATCATTCAATAGATCAACATTTCC-G-GAAGAGTTCATAATGAGAATAACTCATCTGAAG
1 AATCCATCATTTGATGGATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAG
* * *
827462 AATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GCTCG
* * * * *
827511 AATTCATTATTCGATGGATCAACATTACCAG-GAAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAG
* **
827575 AAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTTGCTTA
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGCTCG
* ** * * * *
827625 AATTCATCATTCAATGGATCATCATTGCCAG-GTCAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAG
** *
827689 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCTCG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCG
* *
827738 AATTCATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
827803 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCAT-G
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TCG
*
827851 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
827916 AGGAAGAAGAAGTTTATAATGAGAAGAATTTGTTCAACCTTTTAC-CTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC-G
*
827964 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
828029 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC-CTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC-G
*
828077 AATCCATCATTTGA-GAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATG-GATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
828141 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC-CTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC-G
* * *
828190 AATCCATCATTTGAGGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTTAAGA
1 AATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
828255 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC-CTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC-G
* *
828303 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATTTGAAGA
1 AATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
828368 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCG
* * * *
828416 AATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTG
1 AATCCATCATTTGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTG
* * * *
828480 AAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAAACTTTT
62 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
828527 TGCATAATTC
Statistics
Matches: 948, Mismatches: 53, Indels: 26
0.92 0.05 0.03
Matches are distributed among these distances:
112 26 0.03
113 766 0.81
114 101 0.11
115 6 0.01
116 49 0.05
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (113 bp):
AATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCG
Found at i:828852 original size:3 final size:3
Alignment explanation
Indices: 828844--828944 Score: 184
Period size: 3 Copynumber: 33.7 Consensus size: 3
828834 TTTTTATCCA
* *
828844 TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
828892 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
828940 TAT TA
1 TAT TA
828945 AATATATATT
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:828956 original size:11 final size:11
Alignment explanation
Indices: 828940--828969 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
828930 TTATTATTAT
828940 TATTAAATATA
1 TATTAAATATA
828951 TATTAAATATA
1 TATTAAATATA
828962 TA-TAAATA
1 TATTAAATA
828970 ATAATTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAAATATA
Found at i:829425 original size:19 final size:19
Alignment explanation
Indices: 829403--829439 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
829393 GAGAACGGAC
829403 AGAGAGACAGAAAAAAAAG
1 AGAGAGACAGAAAAAAAAG
829422 AGAGAGACAGAAAAAAAA
1 AGAGAGACAGAAAAAAAA
829440 CAACAGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.70, C:0.05, G:0.24, T:0.00
Consensus pattern (19 bp):
AGAGAGACAGAAAAAAAAG
Found at i:840902 original size:13 final size:13
Alignment explanation
Indices: 840884--840910 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
840874 AAACAGCAAC
840884 TATGTCTTAGCAG
1 TATGTCTTAGCAG
840897 TATGTCTTAGCAG
1 TATGTCTTAGCAG
840910 T
1 T
840911 CGTCAATCTT
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:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (13 bp):
TATGTCTTAGCAG
Found at i:847959 original size:21 final size:21
Alignment explanation
Indices: 847935--848007 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 21
847925 ATATACTAAT
847935 TAAAAAATAATATTAAAATGA
1 TAAAAAATAATATTAAAATGA
*
847956 T-AAAAAT-ATATTAAATTGCCA
1 TAAAAAATAATATTAAAATG--A
*
847977 TAAATAAATAATA--AAAATTA
1 TAAA-AAATAATATTAAAATGA
*
847997 TAAAATATAAT
1 TAAAAAATAAT
848008 TTCATTATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
19 16 0.37
20 11 0.26
21 3 0.07
22 6 0.14
23 4 0.09
24 3 0.07
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (21 bp):
TAAAAAATAATATTAAAATGA
Found at i:850837 original size:11 final size:10
Alignment explanation
Indices: 850792--850849 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
850782 AGCTTTAAAT
850792 TTTTTATTGA
1 TTTTTATTGA
* *
850802 ATTTTATTCA
1 TTTTTATTGA
*
850812 CTTTTAATT-A
1 -TTTTTATTGA
850822 TTTTTTATTGTA
1 -TTTTTATTG-A
850834 TTTTTATTGA
1 TTTTTATTGA
850844 TTTTTA
1 TTTTTA
850850 AAAAAGTGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
10 23 0.59
11 15 0.38
12 1 0.03
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.69
Consensus pattern (10 bp):
TTTTTATTGA
Found at i:850849 original size:21 final size:21
Alignment explanation
Indices: 850792--850849 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
850782 AGCTTTAAAT
*
850792 TTTTTATTGAATTTTATTCAC
1 TTTTTATTGATTTTTATTCAC
* *
850813 TTTTAATT-ATTTTTTATTGTA-
1 TTTTTATTGA-TTTTTATT-CAC
850834 TTTTTATTGATTTTTA
1 TTTTTATTGATTTTTA
850850 AAAAAGTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
20 1 0.03
21 27 0.90
22 2 0.07
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTATTGATTTTTATTCAC
Found at i:859083 original size:31 final size:31
Alignment explanation
Indices: 859013--859071 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
859003 AAATTACACG
*
859013 TTTAGTACTTAAACTATCAGTTTTGGTTTGT
1 TTTAGTACCTAAACTATCAGTTTTGGTTTGT
* *
859044 TTTAGTACCTAAACT-TTAGTTTTTGTTT
1 TTTAGTACCTAAACTATCAGTTTTGGTTT
859072 TAATTTAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.22, C:0.10, G:0.14, T:0.54
Consensus pattern (31 bp):
TTTAGTACCTAAACTATCAGTTTTGGTTTGT
Found at i:860353 original size:13 final size:14
Alignment explanation
Indices: 860306--860364 Score: 54
Period size: 13 Copynumber: 4.4 Consensus size: 14
860296 TTTCAAAATA
860306 ATTAA-AATATAAT
1 ATTAATAATATAAT
* *
860319 ATTAATTTATTTAAT
1 ATTAA-TAATATAAT
860334 -TTAATAATATAAT
1 ATTAATAATATAAT
860347 ATT-ATAATA-AAT
1 ATTAATAATATAAT
*
860359 TTTAAT
1 ATTAAT
860365 TTAATAGCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
12 5 0.14
13 20 0.54
14 6 0.16
15 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTAATAATATAAT
Found at i:862684 original size:270 final size:270
Alignment explanation
Indices: 862203--862712 Score: 1002
Period size: 270 Copynumber: 1.9 Consensus size: 270
862193 CAAAAGGATA
*
862203 AATTGTTTATTAAGTCACCTATTATTATTTAATTTCTATTTTGGTCACTCAACTATTATTTATTT
1 AATTGTTTATTAAGTCACCTATTATTATTTAATATCTATTTTGGTCACTCAACTATTATTTATTT
*
862268 TAAATCATACTTAATGTTACATTTGGTTTATGTTTTGGTCTCTCATCTTTAAAAAATTAGCGGTG
66 TAAATCACACTTAATGTTACATTTGGTTTATGTTTTGGTCTCTCATCTTTAAAAAATTAGCGGTG
862333 ATGTTGATGTATCATCATAAGAGAATGCCACGTCATGATTGAAAAATAATTATTTTAACATCATT
131 ATGTTGATGTATCATCATAAGAGAATGCCACGTCATGATTGAAAAATAATTATTTTAACATCATT
862398 GTTATTTTTTTAACAGTAGGTGATTAAAATATATATATGATTTTTAATTTCTATTTTGGTCACTC
196 GTTATTTTTTTAACAGTAGGTGATTAAAATATATATATGATTTTTAATTTCTATTTTGGTCACTC
862463 AACTATGATG
261 AACTATGATG
862473 AATTGTTTATTAAGTCACCTATTATTATTTAATATCTATTTTGGTCACTCAACTATTATTTATTT
1 AATTGTTTATTAAGTCACCTATTATTATTTAATATCTATTTTGGTCACTCAACTATTATTTATTT
862538 TAAATCACACTTAATGTTACATTTGGTTTATGTTTTGGTCTCTCATCTTTAAAAAATTAGCGGTG
66 TAAATCACACTTAATGTTACATTTGGTTTATGTTTTGGTCTCTCATCTTTAAAAAATTAGCGGTG
862603 ATGTTGATGTATCATCATAAGAGAATGCCACGTCATGATTGAAAAATAATTATTTTAACATCATT
131 ATGTTGATGTATCATCATAAGAGAATGCCACGTCATGATTGAAAAATAATTATTTTAACATCATT
862668 GTTATTTTTTTAACAGTAGGTGATTAAAATATATATATGATTTTT
196 GTTATTTTTTTAACAGTAGGTGATTAAAATATATATATGATTTTT
862713 TTTTGATAAA
Statistics
Matches: 238, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
270 238 1.00
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (270 bp):
AATTGTTTATTAAGTCACCTATTATTATTTAATATCTATTTTGGTCACTCAACTATTATTTATTT
TAAATCACACTTAATGTTACATTTGGTTTATGTTTTGGTCTCTCATCTTTAAAAAATTAGCGGTG
ATGTTGATGTATCATCATAAGAGAATGCCACGTCATGATTGAAAAATAATTATTTTAACATCATT
GTTATTTTTTTAACAGTAGGTGATTAAAATATATATATGATTTTTAATTTCTATTTTGGTCACTC
AACTATGATG
Found at i:863662 original size:21 final size:21
Alignment explanation
Indices: 863633--863679 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
863623 ATTCTGACTA
863633 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
863654 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
863675 TCGCA
1 TCGCA
863680 ACGCGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:863704 original size:20 final size:20
Alignment explanation
Indices: 863675--863747 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
863665 TTTTCCTAAT
863675 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
863695 TCGTAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
* *
863715 TCGCAATGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
*
863735 TCGCAATGCGAAT
1 TCGCAACGCGAAT
863748 CTGACTATCG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:864361 original size:20 final size:20
Alignment explanation
Indices: 864336--864384 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
864326 CAACGAGTGA
864336 ATCGCAACGCGAAAATAACT
1 ATCGCAACGCGAAAATAACT
* ** *
864356 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATAACT
864376 ATCGCAACG
1 ATCGCAACG
864385 AGAGAATCGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATAACT
Found at i:864451 original size:20 final size:20
Alignment explanation
Indices: 864426--864475 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
864416 TGCGATTCTT
864426 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
864446 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
864466 GTGTTGCGAT
1 GCGTTGCGAT
864476 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:864481 original size:20 final size:20
Alignment explanation
Indices: 864443--864497 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
864433 GATAGTCAAA
* **
864443 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
864463 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
864483 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
864498 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:864505 original size:20 final size:20
Alignment explanation
Indices: 864462--864505 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
864452 CGATAGTCAT
** *
864462 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
864482 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
864502 TTTC
1 TTTC
864506 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:866384 original size:20 final size:20
Alignment explanation
Indices: 866359--866462 Score: 121
Period size: 20 Copynumber: 5.5 Consensus size: 20
866349 AGAATAGTTT
866359 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
866379 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
866399 ACTATCACAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
866415 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
866433 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
866453 ACTATCGCAA
1 ACTATCGCAA
866463 CGAAAGAATC
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
14 6 0.08
16 4 0.06
17 4 0.06
18 4 0.06
20 53 0.75
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:866448 original size:54 final size:54
Alignment explanation
Indices: 866362--866500 Score: 199
Period size: 54 Copynumber: 2.6 Consensus size: 54
866352 ATAGTTTACT
* *
866362 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCACAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCACAACGAAAGA
** *
866416 ATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAAAGA
1 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCACAACGAAAGA
** *
866470 ATCGCAATGCG-AAATGAAAATCGCATTGCGA
1 ATCGCAATGCGAAAATGACTATCGCAATGCGA
866501 TTCTCTCGTT
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
53 17 0.22
54 60 0.78
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (54 bp):
ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCACAACGAAAGA
Found at i:866572 original size:73 final size:73
Alignment explanation
Indices: 866490--866628 Score: 233
Period size: 73 Copynumber: 1.9 Consensus size: 73
866480 GAAATGAAAA
* ** * *
866490 TCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGTATTGCGATAGTCATTTTTGCGTTGCGA
1 TCGCATTGCGATTCTCTCGTTACGATAGTCAAATTCACATTGCGATAGTCATTTTCGCATTGCGA
866555 TTTTTATT
66 TTTTTATT
866563 TCGCATTGCGATTCTCTCGTTACGATAGTCAAATTCACATTGCGATAGTCATTTTCGCATTGCGA
1 TCGCATTGCGATTCTCTCGTTACGATAGTCAAATTCACATTGCGATAGTCATTTTCGCATTGCGA
866628 T
66 T
866629 AGTCATTTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 61 1.00
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (73 bp):
TCGCATTGCGATTCTCTCGTTACGATAGTCAAATTCACATTGCGATAGTCATTTTCGCATTGCGA
TTTTTATT
Found at i:866634 original size:20 final size:20
Alignment explanation
Indices: 866509--866645 Score: 108
Period size: 20 Copynumber: 7.2 Consensus size: 20
866499 GATTCTCTCG
** *
866509 TTGCGATAGTCAAATTCGTA
1 TTGCGATAGTCATTTTCGCA
* *
866529 TTGCGATAGTCATTTTTGCG
1 TTGCGATAGTCATTTTCGCA
** *
866549 TTGCGATTTTTA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
866568 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
* ** *
866582 TTACGATAGTCAAATTCACA
1 TTGCGATAGTCATTTTCGCA
866602 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
866622 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
866642 TTGC
1 TTGC
866646 TTGCGATTTT
Statistics
Matches: 91, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
14 6 0.07
16 6 0.07
17 1 0.01
18 2 0.02
19 12 0.13
20 64 0.70
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:867227 original size:21 final size:19
Alignment explanation
Indices: 867136--867239 Score: 64
Period size: 21 Copynumber: 5.0 Consensus size: 19
867126 GACTCGCCTA
*
867136 TCATCGTTCAAGAGGCCTCC
1 TCATCGTTCAAGAGGCC-CT
*
867156 CCTATCGTTCAAGAGGCCCCT
1 TC-ATCGTTCAAGAGG-CCCT
** *
867177 ATCATCCCTCAAGAGTCCCT
1 -TCATCGTTCAAGAGGCCCT
*
867197 TCCCACCGTTCAAGAGGCCACT
1 T--CATCGTTCAAGAGGCC-CT
*
867219 GTCATCGTTGAAGAGGTCCCT
1 -TCATCGTTCAAGAGG-CCCT
867240 CCCAACATTC
Statistics
Matches: 64, Mismatches: 12, Indels: 15
0.70 0.13 0.16
Matches are distributed among these distances:
19 1 0.02
20 5 0.08
21 50 0.78
22 7 0.11
23 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
TCATCGTTCAAGAGGCCCT
Found at i:867243 original size:42 final size:42
Alignment explanation
Indices: 867133--867243 Score: 120
Period size: 42 Copynumber: 2.6 Consensus size: 42
867123 CCCGACTCGC
* *
867133 CTATCATCGTTCAAGAGG--CCTCCCCTATCGTTCAAGAGGCCC
1 CTATCATCGTTCAAGAGGTCCCT-CCC-ACCGTTCAAGAGGCCA
**
867175 CTATCATCCCTCAAGA-GTCCCTTCCCACCGTTCAAGAGGCCA
1 CTATCATCGTTCAAGAGGTCCC-TCCCACCGTTCAAGAGGCCA
* *
867217 CTGTCATCGTTGAAGAGGTCCCTCCCA
1 CTATCATCGTTCAAGAGGTCCCTCCCA
867244 ACATTCTAGA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
41 1 0.02
42 45 0.79
43 10 0.18
44 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CTATCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAGGCCA
Found at i:870298 original size:24 final size:24
Alignment explanation
Indices: 870264--870317 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
870254 CTGAAAAATC
*
870264 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGAACAAG
* *
870288 ATCAAAGTCCGGGTATTGAACAAG
1 ATCAAAATCCGAGTATTGAACAAG
870312 ATCAAA
1 ATCAAA
870318 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGAACAAG
Found at i:871205 original size:40 final size:38
Alignment explanation
Indices: 871158--871285 Score: 109
Period size: 40 Copynumber: 3.2 Consensus size: 38
871148 GAAATTCAGT
871158 ATTGCGATAGTCAGAATCTCGTTGCGATTTACAG-ATTCGC
1 ATTGCGAT--TCAGAATCTCGTTGCGATTTAC-GTATTCGC
* * *
871198 ATTGCGATTTACGTAT-TCGCATTGCGATTTACGTAATCGC
1 ATTGCGATTCA-GAATCTCG--TTGCGATTTACGTATTCGC
*
871238 ATTGCGATTTTCCA-AATTCGCGTTGCGATTTACGTATTCGC
1 ATTGCGA--TT-CAGAA-TCTCGTTGCGATTTACGTATTCGC
871279 ATTGCGA
1 ATTGCGA
871286 ATTAGGAAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
38 5 0.07
39 4 0.06
40 31 0.43
41 26 0.36
42 3 0.04
43 3 0.04
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (38 bp):
ATTGCGATTCAGAATCTCGTTGCGATTTACGTATTCGC
Found at i:871269 original size:41 final size:40
Alignment explanation
Indices: 871177--871285 Score: 148
Period size: 41 Copynumber: 2.7 Consensus size: 40
871167 GTCAGAATCT
**
871177 CGTTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTAC-GTATTCGCATTGCGATTTACAAATTCG
* * *
871217 CATTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG
1 CGTTGCGATTTACGTATTCGCATTGCGA-TTTACAAATTCG
871258 CGTTGCGATTTACGTATTCGCATTGCGA
1 CGTTGCGATTTACGTATTCGCATTGCGA
871286 ATTAGGAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
39 1 0.02
40 24 0.40
41 35 0.58
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCGCATTGCGATTTACAAATTCG
Found at i:871278 original size:20 final size:20
Alignment explanation
Indices: 871179--871285 Score: 144
Period size: 20 Copynumber: 5.3 Consensus size: 20
871169 CAGAATCTCG
871179 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
871199 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
871219 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* ** *
871239 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
871260 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
871280 TTGCGA
1 TTGCGA
871286 ATTAGGAAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
19 1 0.01
20 59 0.79
21 15 0.20
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:871306 original size:21 final size:21
Alignment explanation
Indices: 871282--871327 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
871272 TATTCGCATT
871282 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
871303 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
871324 GCGA
1 GCGA
871328 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:884100 original size:250 final size:251
Alignment explanation
Indices: 883656--884201 Score: 895
Period size: 250 Copynumber: 2.2 Consensus size: 251
883646 TAATGATGCT
*
883656 TGCTACATTTTGTAATCCTCTATAAGGAATTAAGTTTTGGG-TTGA-TATGAGTTCAATTGTTTA
1 TGCTAGATTTTGTAATCCTCTATAAGGAATTAAGTTTTGGGATTGATTATGAGTTCAATTGTTTA
* *
883719 TTGAGGTGTTCTGATGTTGTTTGATCCTCTTTTTGGATGAGATTTTGGGTTTATAAACATGATGT
66 TTGAGGCGTTCTGATGTTGTTTGATCCTCTTTTTGGATGAGATTTTAGGTTTATAAACATGATGT
* *
883784 AAAATAGTAGGCTTTGTTGTCTTTTGTGAACTAGGTTCTCGTAAACTTCAGGAAAATTACTTGTG
131 AAAAAAGCAGGCTTTGTTGTCTTTTGTGAACTAGGTTCTCGTAAACTTCAGGAAAATTACTTGTG
*
883849 CATTGTTCTTGGGTGAACCTCTGGCTTT-ATTGGTGCCTGAAGGTTCAGTAAATGA
196 CATTGTTCTTGGGTGAACCTCTGGATTTAATTGGTGCCTGAAGGTTCAGTAAATGA
*
883904 TGTTA-ATTTTGTAATCCTCTATAAGGAATTAAGTTTTGGGATTGATGTATGAGTTCAATTGTTT
1 TGCTAGATTTTGTAATCCTCTATAAGGAATTAAGTTTTGGGATTGAT-TATGAGTTCAATTGTTT
* * * * *
883968 CTTGAGGCGTTTTGATGTTGTTTGATCCTCTTTTTGGCTGAGATTTTAGGTTTTTAAACCTGATG
65 ATTGAGGCGTTCTGATGTTGTTTGATCCTCTTTTTGGATGAGATTTTAGGTTTATAAACATGATG
*
884033 TAAAAAAGCAGGCTTTGTT-TCCTTTTGTGAACTAGGTTCTCGTAAACTTTAGGAAAATTACTTG
130 TAAAAAAGCAGGCTTTGTTGT-CTTTTGTGAACTAGGTTCTCGTAAACTTCAGGAAAATTACTTG
*
884097 TGCATTGTTCTTGGGTGAACCTCTGGATTTAATTGGTTCCTGAAGGTTCAGTAAATGA
194 TGCATTGTTCTTGGGTGAACCTCTGGATTTAATTGGTGCCTGAAGGTTCAGTAAATGA
* *
884155 TGCTAGATTTTGTATTCCTCTATAAAGAATTAAGTTTTGGGATTGAT
1 TGCTAGATTTTGTAATCCTCTATAAGGAATTAAGTTTTGGGATTGAT
884202 ATATATATAT
Statistics
Matches: 276, Mismatches: 16, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
247 35 0.13
248 8 0.03
249 1 0.00
250 163 0.59
251 30 0.11
252 39 0.14
ACGTcount: A:0.24, C:0.11, G:0.23, T:0.42
Consensus pattern (251 bp):
TGCTAGATTTTGTAATCCTCTATAAGGAATTAAGTTTTGGGATTGATTATGAGTTCAATTGTTTA
TTGAGGCGTTCTGATGTTGTTTGATCCTCTTTTTGGATGAGATTTTAGGTTTATAAACATGATGT
AAAAAAGCAGGCTTTGTTGTCTTTTGTGAACTAGGTTCTCGTAAACTTCAGGAAAATTACTTGTG
CATTGTTCTTGGGTGAACCTCTGGATTTAATTGGTGCCTGAAGGTTCAGTAAATGA
Found at i:884207 original size:2 final size:2
Alignment explanation
Indices: 884200--884239 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
884190 TTTGGGATTG
884200 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
884240 GAGTTAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:895105 original size:5 final size:5
Alignment explanation
Indices: 895095--895122 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
895085 GAGTGTATCT
895095 TTCTC TTCTC TTCTC TTCTC TTCTC TTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTC
895123 CTTTCTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TTCTC
Found at i:895128 original size:15 final size:14
Alignment explanation
Indices: 895092--895128 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
895082 AAAGAGTGTA
895092 TCTTTCTCTTCTCT
1 TCTTTCTCTTCTCT
895106 TCTCTTCTCTTCTCT
1 TCT-TTCTCTTCTCT
895121 TCCTTTCT
1 T-CTTTCT
895129 ATGTGAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 16 0.76
16 2 0.10
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (14 bp):
TCTTTCTCTTCTCT
Found at i:896150 original size:42 final size:42
Alignment explanation
Indices: 896104--896188 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
896094 TTCCAAATGC
* *
896104 GATAAATATTAATTTTAAAAATAATTATATGAAACGATAAGT
1 GATAAATAATAATTTTAAAAATAATTATATGAAACAATAAGT
896146 GATAAATAATAATTTTAAAAATAATTATATGAAACAATAAGT
1 GATAAATAATAATTTTAAAAATAATTATATGAAACAATAAGT
896188 G
1 G
896189 GATCCAACTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.34
Consensus pattern (42 bp):
GATAAATAATAATTTTAAAAATAATTATATGAAACAATAAGT
Found at i:898644 original size:20 final size:20
Alignment explanation
Indices: 898621--898670 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
898611 AAACACCTGG
*
898621 TAGTATTGATGCTACATAGA
1 TAGTATCGATGCTACATAGA
*
898641 TAGTATCGATGCTACCTAGA
1 TAGTATCGATGCTACATAGA
*
898661 GAGTATCGAT
1 TAGTATCGAT
898671 ACTTCTCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (20 bp):
TAGTATCGATGCTACATAGA
Found at i:900056 original size:9 final size:9
Alignment explanation
Indices: 900042--900096 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
900032 AAAGTATAGA
900042 TTTAAATAT
1 TTTAAATAT
900051 TTTAAATAT
1 TTTAAATAT
* *
900060 AATTATTATTAT
1 --TT-TAAATAT
900072 TTTAAA-A-
1 TTTAAATAT
900079 TTTAAATAT
1 TTTAAATAT
900088 TTTAAATAT
1 TTTAAATAT
900097 GATATTAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
7 6 0.16
8 2 0.05
9 20 0.54
10 2 0.05
11 2 0.05
12 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TTTAAATAT
Found at i:900088 original size:22 final size:21
Alignment explanation
Indices: 900048--900088 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
900038 TAGATTTAAA
*
900048 TATTTTAAATATAATTATTAT
1 TATTTTAAATATAAATATTAT
*
900069 TATTTTAAAATTTAAATATT
1 TATTTT-AAATATAAATATT
900089 TTAAATATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTTAAATATAAATATTAT
Found at i:900452 original size:17 final size:18
Alignment explanation
Indices: 900405--900453 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 18
900395 CTATCGGACG
900405 GTCAAAAAGATGTGACAA
1 GTCAAAAAGATGTGACAA
* *
900423 TTC--AAATATGTGAC-A
1 GTCAAAAAGATGTGACAA
900438 GTCAAAAAGATGTGAC
1 GTCAAAAAGATGTGAC
900454 GATAAAAAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
15 3 0.12
16 10 0.40
17 10 0.40
18 2 0.08
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.22
Consensus pattern (18 bp):
GTCAAAAAGATGTGACAA
Found at i:900689 original size:31 final size:31
Alignment explanation
Indices: 900653--900729 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
900643 AAAATATAAA
*
900653 AGTTTAGGCACTAAAACAGACCAAAACTGAT
1 AGTTTAGGTACTAAAACAGACCAAAACTGAT
* * *
900684 AGTTTAGGTACTAAAACGGATCAAAATTGAT
1 AGTTTAGGTACTAAAACAGACCAAAACTGAT
*
900715 AATTTAGGTACTAAA
1 AGTTTAGGTACTAAA
900730 CATGTAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (31 bp):
AGTTTAGGTACTAAAACAGACCAAAACTGAT
Found at i:901010 original size:2 final size:2
Alignment explanation
Indices: 901003--901050 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
900993 ATGTGTAATA
901003 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
*
901045 TT AT AT
1 AT AT AT
901051 TTGGTTGTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:908594 original size:30 final size:30
Alignment explanation
Indices: 908560--908616 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
908550 CAATACGTGT
908560 TTATACGATCCCGTCGATTTTAGTAAGACG
1 TTATACGATCCCGTCGATTTTAGTAAGACG
**
908590 TTATACGATCTTGTCGATTTTAGTAAG
1 TTATACGATCCCGTCGATTTTAGTAAG
908617 TTGTTCTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (30 bp):
TTATACGATCCCGTCGATTTTAGTAAGACG
Found at i:908633 original size:30 final size:30
Alignment explanation
Indices: 908572--908641 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
908562 ATACGATCCC
*
908572 GTCGATTTTAGTAAGACGTTATACGATCTT
1 GTCGATTTTAGTAAGACGTTATACGACCTT
** * *
908602 GTCGATTTTAGTAAGTTGTTCTATGACCTT
1 GTCGATTTTAGTAAGACGTTATACGACCTT
908632 GTCGATTTTA
1 GTCGATTTTA
908642 ATGCGGCCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.44
Consensus pattern (30 bp):
GTCGATTTTAGTAAGACGTTATACGACCTT
Found at i:919700 original size:20 final size:20
Alignment explanation
Indices: 919675--919766 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
919665 TTTTCCCAAT
919675 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
** *
919695 TCGCAA-GCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
919714 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
919735 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
919756 TCGCAATGCGA
1 TCGCAATGCGA
919767 TACTGACTAT
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
19 10 0.17
20 23 0.40
21 25 0.43
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:919716 original size:40 final size:41
Alignment explanation
Indices: 919672--919766 Score: 174
Period size: 40 Copynumber: 2.3 Consensus size: 41
919662 CGATTTTCCC
919672 AATTCGCAATGCGAATAAGTAAATCGCAA-GCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
919712 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
919753 AAATCGCAATGCGA
1 AATTCGCAATGCGA
919767 TACTGACTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 29 0.55
41 24 0.45
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:919779 original size:41 final size:41
Alignment explanation
Indices: 919694--919827 Score: 114
Period size: 41 Copynumber: 3.3 Consensus size: 41
919684 GAATAAGTAA
* * *
919694 ATCGCAA-GCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
919734 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
919775 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
919816 TTCGCAACGCGA
1 ATCGCAACGCGA
919828 TACTGACTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
40 11 0.14
41 65 0.83
42 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:919780 original size:20 final size:20
Alignment explanation
Indices: 919755--919848 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
919745 AATTGGGAAA
*
919755 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
919775 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
919796 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
919816 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
919836 TTCGCAACGCGAT
1 ATCGCAACGCGAT
919849 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Done.