Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003488.1 Hibiscus syriacus cultivar Beakdansim tig00007372_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: 43207
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:14891 original size:24 final size:24
Alignment explanation
Indices: 14832--14893 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
14822 CGTTCGTGAA
* *
14832 CGTTCGGTTATATTCGTTTATATG
1 CGTTCAGTTATGTTCGTTTATATG
* *
14856 CGTTTAGTTATGTTCGTTTATGTG
1 CGTTCAGTTATGTTCGTTTATATG
*
14880 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
14894 TAACCTAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.15, C:0.11, G:0.21, T:0.53
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATATG
Found at i:16420 original size:10 final size:10
Alignment explanation
Indices: 16405--16479 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
16395 GGGTCTCCAA
16405 CGTTTATGTT
1 CGTTTATGTT
16415 CGTTTATGTT
1 CGTTTATGTT
16425 CG----TGTT
1 CGTTTATGTT
*
16431 CATTTATGTT
1 CGTTTATGTT
*
16441 CGTGTT-CGTTT
1 CGT-TTATG-TT
* *
16452 ATGTTTGTGTT
1 -CGTTTATGTT
16463 CGTTTATGTT
1 CGTTTATGTT
16473 CGTTTAT
1 CGTTTAT
16480 TTATTAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.10
10 34 0.68
11 8 0.16
12 3 0.06
ACGTcount: A:0.09, C:0.11, G:0.21, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:16436 original size:16 final size:16
Alignment explanation
Indices: 16411--16475 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
16401 CCAACGTTTA
16411 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
16427 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
16443 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
16459 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
16475 T
1 T
16476 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:20527 original size:34 final size:34
Alignment explanation
Indices: 20489--20556 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
20479 ATCCGAAAAC
*
20489 CATAGTTTCATGGTAGTGAAGGTGGTCTTAATGG
1 CATAGTTTCATGGTAGTGAAGATGGTCTTAATGG
20523 CATAGTTTCATGGTAGTGAAGATGGTCTTAATGG
1 CATAGTTTCATGGTAGTGAAGATGGTCTTAATGG
20557 TTAAAGCTGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.25, C:0.09, G:0.31, T:0.35
Consensus pattern (34 bp):
CATAGTTTCATGGTAGTGAAGATGGTCTTAATGG
Found at i:21218 original size:16 final size:16
Alignment explanation
Indices: 21177--21262 Score: 66
Period size: 16 Copynumber: 5.4 Consensus size: 16
21167 GCCAAAAGAG
21177 CTGAATCGAAAGCAAC
1 CTGAATCGAAAGCAAC
* * **
21193 CTAAACCGAAATTAAC
1 CTGAATCGAAAGCAAC
21209 CTGAATCGAAAGCAA-
1 CTGAATCGAAAGCAAC
* * **
21224 TTCGAACCGAAATTAAC
1 CT-GAATCGAAAGCAAC
*
21241 CCGAATCGAAAGCAAC
1 CTGAATCGAAAGCAAC
*
21257 CCGAAT
1 CTGAAT
21263 TGATCTTAAC
Statistics
Matches: 51, Mismatches: 17, Indels: 4
0.71 0.24 0.06
Matches are distributed among these distances:
15 1 0.02
16 50 0.98
ACGTcount: A:0.44, C:0.26, G:0.15, T:0.15
Consensus pattern (16 bp):
CTGAATCGAAAGCAAC
Found at i:21272 original size:32 final size:32
Alignment explanation
Indices: 21179--21261 Score: 121
Period size: 32 Copynumber: 2.6 Consensus size: 32
21169 CAAAAGAGCT
** *
21179 GAATCGAAAGCAACCTAAACCGAAATTAACCT
1 GAATCGAAAGCAACCCGAACCGAAATTAACCC
**
21211 GAATCGAAAGCAATTCGAACCGAAATTAACCC
1 GAATCGAAAGCAACCCGAACCGAAATTAACCC
21243 GAATCGAAAGCAACCCGAA
1 GAATCGAAAGCAACCCGAA
21262 TTGATCTTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.46, C:0.25, G:0.16, T:0.13
Consensus pattern (32 bp):
GAATCGAAAGCAACCCGAACCGAAATTAACCC
Found at i:21664 original size:19 final size:17
Alignment explanation
Indices: 21642--21684 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
21632 TATTAAATTT
*
21642 ATAATAAAAATAATAGAAA
1 ATAATAAAAA-AAAAG-AA
21661 ATAACTAAAAAAAAAGAA
1 ATAA-TAAAAAAAAAGAA
21679 ATAATA
1 ATAATA
21685 TTAGATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 6 0.27
19 8 0.36
20 6 0.27
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (17 bp):
ATAATAAAAAAAAAGAA
Found at i:22151 original size:31 final size:32
Alignment explanation
Indices: 22110--22199 Score: 78
Period size: 32 Copynumber: 2.8 Consensus size: 32
22100 GGTTGATCCA
*
22110 AACCGAAAAATTAACTGATTCGATATTGAA-CC
1 AACCCAAAAATTAACTGATTCGATATT-AACCC
* * *
22142 AACCC-AAAATCTAAC-CAATCTGGTATTAACCC
1 AACCCAAAAAT-TAACTGATTC-GATATTAACCC
* *
22174 GACCCAAAAATCAACTGATTCGATAT
1 AACCCAAAAATTAACTGATTCGATAT
22200 GGACCCTATC
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
31 10 0.23
32 26 0.59
33 8 0.18
ACGTcount: A:0.42, C:0.24, G:0.10, T:0.23
Consensus pattern (32 bp):
AACCCAAAAATTAACTGATTCGATATTAACCC
Found at i:23081 original size:64 final size:64
Alignment explanation
Indices: 23001--23153 Score: 225
Period size: 64 Copynumber: 2.4 Consensus size: 64
22991 CTTACCAACT
* * * * *
23001 TGGATTTCTCGGCGTCTTCCATGCACGCTCGGGGGAATGTTTGGCGTCTTCAAGCATGGGAAAA
1 TGGATCTCTCGGCGTCTTCCATGCACGCTCGAGGGAATGCTTGACGTCTTCAAGCACGGGAAAA
*
23065 TGGATCTCTCGGCGTCTTCCATGCACGCTCGAGGGAATGCTTGACGTCTTCAAGCACGGTAAAA
1 TGGATCTCTCGGCGTCTTCCATGCACGCTCGAGGGAATGCTTGACGTCTTCAAGCACGGGAAAA
* * *
23129 TGTATCTCTCAGTGTCTTCCATGCA
1 TGGATCTCTCGGCGTCTTCCATGCA
23154 AAGGGAACAA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 80 1.00
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.29
Consensus pattern (64 bp):
TGGATCTCTCGGCGTCTTCCATGCACGCTCGAGGGAATGCTTGACGTCTTCAAGCACGGGAAAA
Found at i:23822 original size:13 final size:12
Alignment explanation
Indices: 23805--23835 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
23795 TTTTCATGTA
23805 ATTTTTAGTTGT
1 ATTTTTAGTTGT
23817 ATTTTTAGTTGT
1 ATTTTTAGTTGT
23829 ATTTTTA
1 ATTTTTA
23836 TATAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.13, T:0.68
Consensus pattern (12 bp):
ATTTTTAGTTGT
Found at i:26874 original size:14 final size:14
Alignment explanation
Indices: 26855--26894 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
26845 TGATATGATT
*
26855 TAATGATTTACTAC
1 TAATGATTTAATAC
26869 TAATGATTTAATAC
1 TAATGATTTAATAC
26883 TAATGATTTAAT
1 TAATGATTTAAT
26895 TATTTGATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TAATGATTTAATAC
Found at i:26890 original size:36 final size:35
Alignment explanation
Indices: 26849--27134 Score: 195
Period size: 36 Copynumber: 8.2 Consensus size: 35
26839 GTGTAATGAT
*
26849 ATGATTTAATGATTTACTACTAATGATTTAATACTA
1 ATGATTTAATGATTTA-TACTAATGATTTAATAATA
*
26885 ATGATTTAATTATTTGATACTAATGA-TT--TAATA
1 ATGATTTAATGATTT-ATACTAATGATTTAATAATA
* * ** * *
26918 ATGATTTGATTGCTTGCTAATAATGATTTGAACT-TTA
1 ATGATTT-AATGATTTATACTAATGATTT-AA-TAATA
* *
26955 ATGATTTAAT-AATGATTACTAAT--TTT-ATAAATA
1 ATGATTTAATGATTTA-TACTAATGATTTAAT-AATA
* *
26988 ATGATTTAA-G---TATAATGATATGATTTATTAATA
1 ATGATTTAATGATTTATACT-A-ATGATTTAATAATA
*
27021 ATGATTTAATGATTTAATATTAATGATTTAATAATA
1 ATGATTTAATGATTT-ATACTAATGATTTAATAATA
27057 ATGATTTAATGATTTGATACTAATGATTTAATAATA
1 ATGATTTAATGATTT-ATACTAATGATTTAATAATA
* * * *
27093 ATTTGATAATAATGATTTA-A-AAATGATTGAATAACA
1 A--TGAT-TTAATGATTTATACTAATGATTTAATAATA
27129 ATGATT
1 ATGATT
27135 ACTAATAATG
Statistics
Matches: 199, Mismatches: 27, Indels: 51
0.72 0.10 0.18
Matches are distributed among these distances:
29 3 0.02
30 2 0.01
31 3 0.02
32 1 0.01
33 46 0.23
34 15 0.08
35 4 0.02
36 93 0.47
37 13 0.07
38 10 0.05
39 9 0.05
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.45
Consensus pattern (35 bp):
ATGATTTAATGATTTATACTAATGATTTAATAATA
Found at i:26894 original size:22 final size:22
Alignment explanation
Indices: 26869--26916 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
26859 GATTTACTAC
26869 TAATGATTTAATACTAATGATT
1 TAATGATTTAATACTAATGATT
* *
26891 TAATTATTTGATACTAATGATT
1 TAATGATTTAATACTAATGATT
26913 TAAT
1 TAAT
26917 AATGATTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (22 bp):
TAATGATTTAATACTAATGATT
Found at i:27024 original size:14 final size:14
Alignment explanation
Indices: 26978--27064 Score: 51
Period size: 14 Copynumber: 6.3 Consensus size: 14
26968 GATTACTAAT
*
26978 TTTATAAATAATGA
1 TTTATTAATAATGA
26992 TTTAAGTATAATGATATGA
1 TTT-A-T-TAAT-A-ATGA
27011 TTTATTAATAATG-
1 TTTATTAATAATGA
27024 ---ATT--TAATGA
1 TTTATTAATAATGA
* *
27033 TTTAATATTAATGA
1 TTTATTAATAATGA
*
27047 TTTAATAATAATGA
1 TTTATTAATAATGA
27061 TTTA
1 TTTA
27065 ATGATTTGAT
Statistics
Matches: 59, Mismatches: 3, Indels: 22
0.70 0.04 0.26
Matches are distributed among these distances:
8 5 0.08
10 3 0.05
12 2 0.03
14 29 0.49
15 2 0.03
16 5 0.08
17 4 0.07
18 2 0.03
19 7 0.12
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (14 bp):
TTTATTAATAATGA
Found at i:27032 original size:22 final size:22
Alignment explanation
Indices: 26986--27052 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
26976 ATTTTATAAA
26986 TAATGATTTAAGT-ATAATGA--
1 TAATGATTTAA-TAATAATGATT
*
27006 T-ATGATTTATTAATAATGATT
1 TAATGATTTAATAATAATGATT
*
27027 TAATGATTTAATATTAATGATT
1 TAATGATTTAATAATAATGATT
27049 TAAT
1 TAAT
27053 AATAATGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 1 0.03
19 15 0.38
20 1 0.03
21 1 0.03
22 22 0.55
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (22 bp):
TAATGATTTAATAATAATGATT
Found at i:27065 original size:14 final size:14
Alignment explanation
Indices: 27027--27148 Score: 90
Period size: 14 Copynumber: 9.6 Consensus size: 14
27017 AATAATGATT
*
27027 TAATGATTTAATAT
1 TAATGATTTAATAA
27041 TAATGATTTAATAA
1 TAATGATTTAATAA
27055 TAATGA--T--T--
1 TAATGATTTAATAA
* *
27063 TAATGATTTGATAC
1 TAATGATTTAATAA
27077 TAATGATTTAATAA
1 TAATGATTTAATAA
*
27091 T-A--ATTTGATAA
1 TAATGATTTAATAA
27102 TAATGATTT-A-AA
1 TAATGATTTAATAA
*
27114 -AATGATTGAATAA
1 TAATGATTTAATAA
* *
27127 CAATGA-TTACTAA
1 TAATGATTTAATAA
27140 TAATGATTT
1 TAATGATTT
27149 GAACTTTAAT
Statistics
Matches: 87, Mismatches: 8, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
8 6 0.07
10 2 0.02
11 16 0.18
12 6 0.07
13 14 0.16
14 43 0.49
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:27065 original size:22 final size:22
Alignment explanation
Indices: 27040--27112 Score: 92
Period size: 22 Copynumber: 3.2 Consensus size: 22
27030 TGATTTAATA
*
27040 TTAATGATTTAATAATAATGAT
1 TTAATGATTTGATAATAATGAT
*
27062 TTAATGATTTGATACTAATGATT
1 TTAATGATTTGATAATAATGA-T
*
27085 TAATAATAATTTGATAATAATGAT
1 T--TAATGATTTGATAATAATGAT
27109 TTAA
1 TTAA
27113 AAATGATTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
22 22 0.50
23 2 0.05
24 2 0.05
25 18 0.41
ACGTcount: A:0.44, C:0.01, G:0.10, T:0.45
Consensus pattern (22 bp):
TTAATGATTTGATAATAATGAT
Found at i:27286 original size:21 final size:21
Alignment explanation
Indices: 27262--27334 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
27252 TATTCAATTC
27262 ATTTAAACAAATAATCTATTA
1 ATTTAAACAAATAATCTATTA
* *
27283 ATTTAAACAAGAATAATATATGA
1 ATTTAAAC-A-AATAATCTATTA
*
27306 A-TT-AACAATTAATCTATTA
1 ATTTAAACAAATAATCTATTA
27325 ATTTAAACAA
1 ATTTAAACAA
27335 GAATAACATA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
19 10 0.23
20 3 0.07
21 16 0.37
22 3 0.07
23 11 0.26
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (21 bp):
ATTTAAACAAATAATCTATTA
Found at i:27308 original size:23 final size:21
Alignment explanation
Indices: 27262--27349 Score: 72
Period size: 23 Copynumber: 4.1 Consensus size: 21
27252 TATTCAATTC
* *
27262 ATTTAAACAAATAATCTATTA
1 ATTTAAACAAATAATATATGA
27283 ATTTAAACAAGAATAATATATGA
1 ATTTAAAC-A-AATAATATATGA
* * *
27306 A-TT-AACAATTAATCTATTA
1 ATTTAAACAAATAATATATGA
*
27325 ATTTAAACAAGAATAACATATGA
1 ATTTAAAC-A-AATAATATATGA
27348 AT
1 AT
27350 AATATATTAA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
19 10 0.19
20 3 0.06
21 14 0.27
22 4 0.08
23 21 0.40
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (21 bp):
ATTTAAACAAATAATATATGA
Found at i:27359 original size:42 final size:42
Alignment explanation
Indices: 27267--27349 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
27257 AATTCATTTA
* *
27267 AACAAATAATCTATTAATTTAAACAAGAATAATATATGAATT
1 AACAATTAATCTATTAATTTAAACAAGAATAACATATGAATT
27309 AACAATTAATCTATTAATTTAAACAAGAATAACATATGAAT
1 AACAATTAATCTATTAATTTAAACAAGAATAACATATGAAT
27350 AATATATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (42 bp):
AACAATTAATCTATTAATTTAAACAAGAATAACATATGAATT
Found at i:27772 original size:59 final size:58
Alignment explanation
Indices: 27668--27779 Score: 163
Period size: 59 Copynumber: 1.9 Consensus size: 58
27658 TTAATTATTA
** *
27668 ATTATTAATTTAATGATTTGATATTTAATGATTTAGTAATGATTACCAATAATATTTT
1 ATTATTAATTTAATGATTTGATATCAAATGATTTAGTAATAATTACCAATAATATTTT
*
27726 ATTATTAATATTTAATGATTTGATA-CAAATGATTTAGTAATAATTACTAATAAT
1 ATTATT-A-ATTTAATGATTTGATATCAAATGATTTAGTAATAATTACCAATAAT
27780 GAAATTATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
58 6 0.12
59 26 0.54
60 16 0.33
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (58 bp):
ATTATTAATTTAATGATTTGATATCAAATGATTTAGTAATAATTACCAATAATATTTT
Found at i:27781 original size:24 final size:23
Alignment explanation
Indices: 27753--27838 Score: 118
Period size: 24 Copynumber: 3.6 Consensus size: 23
27743 ATTTGATACA
27753 AATGATTTAGTAATAATTACTAAT
1 AATGATTTA-TAATAATTACTAAT
*
27777 AATGAAATTATAATAATTACTAAT
1 AATG-ATTTATAATAATTACTAAT
*
27801 AATGATTTTATAATTATTACTAAT
1 AATGA-TTTATAATAATTACTAAT
27825 AATGATTTAATAAT
1 AATGATTT-ATAAT
27839 GATTTAATAA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
23 4 0.07
24 48 0.86
25 4 0.07
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (23 bp):
AATGATTTATAATAATTACTAAT
Found at i:27837 original size:11 final size:11
Alignment explanation
Indices: 27797--27858 Score: 72
Period size: 11 Copynumber: 5.5 Consensus size: 11
27787 TAATAATTAC
27797 TAATAATGATT
1 TAATAATGATT
* *
27808 TTATAATTATT
1 TAATAATGATT
27819 ACTAATAATGATT
1 --TAATAATGATT
27832 TAATAATGATT
1 TAATAATGATT
27843 TAATAAT-ATT
1 TAATAATGATT
*
27853 AAATAA
1 TAATAA
27859 AAATTTTATC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
10 8 0.18
11 27 0.61
13 9 0.20
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (11 bp):
TAATAATGATT
Found at i:27864 original size:21 final size:22
Alignment explanation
Indices: 27821--27864 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
27811 TAATTATTAC
* **
27821 TAATAATGATTTAATAATGATT
1 TAATAATGATTAAATAAAAATT
27843 TAATAAT-ATTAAATAAAAATT
1 TAATAATGATTAAATAAAAATT
27864 T
1 T
27865 TATCTTTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (22 bp):
TAATAATGATTAAATAAAAATT
Found at i:28021 original size:38 final size:37
Alignment explanation
Indices: 27924--28035 Score: 113
Period size: 38 Copynumber: 3.0 Consensus size: 37
27914 AATTACTTCA
* *
27924 ATTTGATACTAATAATTTAATAATGATTACTAATGAATA
1 ATTTGATAC-AATGATTTAATAATGATTACTAAT-AATG
* * * *
27963 ATATGAT---ATGGTTTAGTAATGATTAATAATAATG
1 ATTTGATACAATGATTTAATAATGATTACTAATAATG
*
27997 ATTTGATACAAATGATTTATTAATGATTACTAATAATG
1 ATTTGATAC-AATGATTTAATAATGATTACTAATAATG
28035 A
1 A
28036 AATTATAATA
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
34 9 0.15
35 19 0.32
38 25 0.42
39 6 0.10
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.41
Consensus pattern (37 bp):
ATTTGATACAATGATTTAATAATGATTACTAATAATG
Found at i:28068 original size:24 final size:24
Alignment explanation
Indices: 27933--28068 Score: 84
Period size: 27 Copynumber: 5.5 Consensus size: 24
27923 AATTTGATAC
*
27933 TAATAATTTAATAATGATTACTAA
1 TAATGATTTAATAATGATTACTAA
* * * * *
27957 TGAATAATATGAT-ATGGTT--TAG
1 T-AATGATTTAATAATGATTACTAA
27979 TAATGATTAATAATAATGATTTGA-TACA
1 TAATGATT--TAATAATGA-TT-ACTA-A
*
28007 -AATGATTTATTAATGATTACTAA
1 TAATGATTTAATAATGATTACTAA
*
28030 TAATGAAATTATAATAATTATTACTAA
1 TAATG--ATT-TAATAATGATTACTAA
28057 TAATGATTTAAT
1 TAATGATTTAAT
28069 GGTAAAAAAC
Statistics
Matches: 87, Mismatches: 12, Indels: 26
0.70 0.10 0.21
Matches are distributed among these distances:
21 5 0.06
22 3 0.03
23 5 0.06
24 21 0.24
25 22 0.25
26 3 0.03
27 28 0.32
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.42
Consensus pattern (24 bp):
TAATGATTTAATAATGATTACTAA
Found at i:30591 original size:33 final size:32
Alignment explanation
Indices: 30531--30594 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
30521 ATAAATTTGG
*
30531 CCCCCCATGTGAAGAAGACACCGAGAAATCCA
1 CCCCCCATGTGAAGAAGACACCAAGAAATCCA
* **
30563 CCCCTCATGCTGAAGAAGATGCCAAGAAATCC
1 CCCCCCATG-TGAAGAAGACACCAAGAAATCC
30595 CAGCAGCATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 8 0.30
33 19 0.70
ACGTcount: A:0.36, C:0.33, G:0.19, T:0.12
Consensus pattern (32 bp):
CCCCCCATGTGAAGAAGACACCAAGAAATCCA
Found at i:36618 original size:21 final size:22
Alignment explanation
Indices: 36575--36618 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
36565 TTGTTTAAAT
* *
36575 AATTAAATGGTCTAATTGATAA
1 AATTAAAAGGTCTAATGGATAA
*
36597 AATTAAAAGGT-TAATGGTTAA
1 AATTAAAAGGTCTAATGGATAA
36618 A
1 A
36619 CTGGAATTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (22 bp):
AATTAAAAGGTCTAATGGATAA
Found at i:38001 original size:22 final size:23
Alignment explanation
Indices: 37975--38020 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
37965 TTTAAAGATT
*
37975 AAATTTTATAAGTTCATC-TTTA
1 AAATTTTATAAATTCATCATTTA
37997 AAATTTTATAAATTCATCATTTA
1 AAATTTTATAAATTCATCATTTA
38020 A
1 A
38021 CATAAAATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (23 bp):
AAATTTTATAAATTCATCATTTA
Done.