Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007052.1 Hibiscus syriacus cultivar Beakdansim tig00018288_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: 86064
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:5830 original size:20 final size:21
Alignment explanation
Indices: 5730--5849 Score: 52
Period size: 20 Copynumber: 5.9 Consensus size: 21
5720 AATAATCAAT
* *
5730 AAATTCGCAACGCGAA-CTTC
1 AAATTCGCAACGCTAATTTTC
* * *
5750 AATTTCGCAAC-AT-AGTTTC
1 AAATTCGCAACGCTAATTTTC
* * *
5769 TAAATTCGTAACACGAATTTTTC
1 -AAATTCGCAACGCTAA-TTTTC
* * * * *
5792 AGATTCGTAAC-TTAGTTTTG
1 AAATTCGCAACGCTAATTTTC
5812 AAATTCGCAACGC-AATTTTC
1 AAATTCGCAACGCTAATTTTC
* *
5832 TAATTCGCGACGCTAATT
1 AAATTCGCAACGCTAATT
5850 CCGAATTCGC
Statistics
Matches: 72, Mismatches: 21, Indels: 13
0.68 0.20 0.12
Matches are distributed among these distances:
18 1 0.01
19 3 0.04
20 48 0.67
21 5 0.07
22 11 0.15
23 4 0.06
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (21 bp):
AAATTCGCAACGCTAATTTTC
Found at i:5896 original size:20 final size:20
Alignment explanation
Indices: 5833--5888 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
5823 GCAATTTTCT
*
5833 AATTCGCGACGCTAATTCCG
1 AATTCGCGACCCTAATTCCG
5853 AATTCGCGACCCTAATTCCG
1 AATTCGCGACCCTAATTCCG
*
5873 AATTCACGACCCTAAT
1 AATTCGCGACCCTAAT
5889 ATCGAATTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.29, C:0.32, G:0.14, T:0.25
Consensus pattern (20 bp):
AATTCGCGACCCTAATTCCG
Found at i:5922 original size:27 final size:27
Alignment explanation
Indices: 5892--5978 Score: 88
Period size: 27 Copynumber: 3.2 Consensus size: 27
5882 CCCTAATATC
* *
5892 GAATTACAAAATCGCGTTGCGAATTGT
1 GAATTACGAAATCGCGTCGCGAATTGT
* * **
5919 GAATTAGGAATTAACGTCGCGAATTGT
1 GAATTACGAAATCGCGTCGCGAATTGT
5946 GAATT-CGAAATCAGCGTCGCGAATT-T
1 GAATTACGAAATC-GCGTCGCGAATTGT
5972 GGAATTA
1 -GAATTA
5979 GCGTTGCGAA
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
26 5 0.11
27 42 0.89
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (27 bp):
GAATTACGAAATCGCGTCGCGAATTGT
Found at i:5969 original size:20 final size:20
Alignment explanation
Indices: 5946--5989 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
5936 CGCGAATTGT
5946 GAATTCGAAATCAGCGTCGC
1 GAATTCGAAATCAGCGTCGC
* * * *
5966 GAATTTGGAATTAGCGTTGC
1 GAATTCGAAATCAGCGTCGC
5986 GAAT
1 GAAT
5990 CGTGAATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (20 bp):
GAATTCGAAATCAGCGTCGC
Found at i:6015 original size:47 final size:47
Alignment explanation
Indices: 5919--6035 Score: 110
Period size: 47 Copynumber: 2.5 Consensus size: 47
5909 TGCGAATTGT
* * * * * *
5919 GAATTAGGAATTAACGTCGCGAATTGTGAATTCGAAATCAGCGTCGC
1 GAATTTGGAATTAGCGTTGCGAATCGTGAATTCGAAAACAGAGTCGC
** * *
5966 GAATTTGGAATTAGCGTTGCGAATCGTGAATTTTAAAACTGAGTTGC
1 GAATTTGGAATTAGCGTTGCGAATCGTGAATTCGAAAACAGAGTCGC
* * *
6013 GAAATT-GAGTTCGCGTTGCGAAT
1 GAATTTGGAATTAGCGTTGCGAAT
6036 TTGTTGATTA
Statistics
Matches: 57, Mismatches: 13, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
46 15 0.26
47 42 0.74
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (47 bp):
GAATTTGGAATTAGCGTTGCGAATCGTGAATTCGAAAACAGAGTCGC
Found at i:20046 original size:20 final size:20
Alignment explanation
Indices: 20021--20066 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
20011 TTTTAATAAA
*
20021 TTTTAACATAAAAT-ATATAT
1 TTTTAACA-AAAATAAAATAT
*
20041 TTTTAATAAAAATAAAATAT
1 TTTTAACAAAAATAAAATAT
20061 TTTTAA
1 TTTTAA
20067 ATTAAGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTAACAAAAATAAAATAT
Found at i:20084 original size:27 final size:27
Alignment explanation
Indices: 20051--20125 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
20041 TTTTAATAAA
20051 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATTTTTAAATTAAGTTAAT
*
20078 AATAAAATATATTT-AA-TAAGTTAAT
1 AATAAAATATTTTTAAATTAAGTTAAT
* *
20103 ATAAAAAATACTTTTTAAGTTAA
1 A-ATAAAATA-TTTTTAAATTAA
20126 TATATATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 10 0.25
26 9 0.22
27 17 0.43
28 1 0.03
29 3 0.08
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.41
Consensus pattern (27 bp):
AATAAAATATTTTTAAATTAAGTTAAT
Found at i:20121 original size:24 final size:24
Alignment explanation
Indices: 20067--20129 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
20057 ATATTTTTAA
*
20067 ATTAAGTTAATAATAAAATATATTT
1 ATTAAGTTAAT-ATAAAAAATATTT
*
20092 AATAAGTTAATATAAAAAATACTTT
1 ATTAAGTTAATATAAAAAATA-TTT
20117 -TTAAGTTAATATA
1 ATTAAGTTAATATA
20130 TATATAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 21 0.62
25 13 0.38
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (24 bp):
ATTAAGTTAATATAAAAAATATTT
Found at i:20178 original size:2 final size:2
Alignment explanation
Indices: 20171--20224 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
20161 ACTAAGATAA
20171 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
20213 AT AT AT AT AT AT
1 AT AT AT AT AT AT
20225 CATGTTGTCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21768 original size:17 final size:18
Alignment explanation
Indices: 21746--21783 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
21736 GACAAACCAA
*
21746 AAAATACATAT-TAATTT
1 AAAATACATATCAAATTT
*
21763 AAAATATATATCAAATTT
1 AAAATACATATCAAATTT
21781 AAA
1 AAA
21784 TTTTTAGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATACATATCAAATTT
Found at i:26953 original size:20 final size:20
Alignment explanation
Indices: 26928--26965 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
26918 AAAAAAGAAC
26928 TAGTATCGATACTATACCAA
1 TAGTATCGATACTATACCAA
*
26948 TAGTATCGATACTTTACC
1 TAGTATCGATACTATACC
26966 CGCAGAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
TAGTATCGATACTATACCAA
Found at i:28007 original size:2 final size:2
Alignment explanation
Indices: 28000--28039 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
27990 ACATACATAC
* * *
28000 AT AT AT AT AT AT AT AA AT AT AA AT AT AA 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
28040 GTAATTAGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:28025 original size:12 final size:12
Alignment explanation
Indices: 28004--28038 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
27994 ACATACATAT
28004 ATATATATATAA
1 ATATATATATAA
*
28016 ATATAAATATAA
1 ATATATATATAA
28028 ATATATATATA
1 ATATATATATA
28039 TGTAATTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATATATAA
Found at i:37850 original size:16 final size:16
Alignment explanation
Indices: 37818--37852 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
37808 GAATATTTTT
37818 AAATAATTATAATAAA
1 AAATAATTATAATAAA
*
37834 AAATATTTA-AATAAA
1 AAATAATTATAATAAA
37849 AAAT
1 AAAT
37853 TTATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATAATTATAATAAA
Found at i:49174 original size:20 final size:21
Alignment explanation
Indices: 49146--49184 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
49136 TAGATAAAAC
49146 AAATAATT-ATATAAAAATTT
1 AAATAATTAATATAAAAATTT
* *
49166 AAATTATTAATTTAAAAAT
1 AAATAATTAATATAAAAAT
49185 AAGATAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATAATTAATATAAAAATTT
Found at i:51947 original size:30 final size:30
Alignment explanation
Indices: 51911--51985 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
51901 TAAGTGATAT
* *
51911 TTTATAT-AAGTTTAGGAGTTAAATTAACAC
1 TTTATATAAAATTTAGGA-TCAAATTAACAC
* *
51941 TTTATATAAAATTTAGGATCAAATTAATAT
1 TTTATATAAAATTTAGGATCAAATTAACAC
*
51971 TTTATCTAAAATTTA
1 TTTATATAAAATTTA
51986 ATCATTTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 30 0.77
31 9 0.23
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (30 bp):
TTTATATAAAATTTAGGATCAAATTAACAC
Found at i:52191 original size:17 final size:16
Alignment explanation
Indices: 52150--52191 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
52140 TTTTGTCTAC
52150 TAAAAATAAT-TATTT
1 TAAAAATAATATATTT
*
52165 TAATAA-AATATATTTT
1 TAAAAATAATATA-TTT
52181 TAAAAATAATA
1 TAAAAATAATA
52192 AGGTAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 3 0.14
15 7 0.32
16 8 0.36
17 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAAAATAATATATTT
Found at i:57724 original size:2 final size:2
Alignment explanation
Indices: 57717--57748 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
57707 ATATTCAAGC
57717 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
57749 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:57753 original size:2 final size:2
Alignment explanation
Indices: 57748--57822 Score: 109
Period size: 2 Copynumber: 38.5 Consensus size: 2
57738 TCTCTCTCTC
57748 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
57790 TA TA T- TA CA -A TT TC TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57823 TACAATTTCA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
1 2 0.03
2 65 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57847 original size:28 final size:28
Alignment explanation
Indices: 57777--57834 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
57767 ATATATATAT
* *
57777 ATATATATATATATATATTACAATTTCT
1 ATATATATAAATATATATTACAATTTCA
*
57805 ATATATATATATATATATTACAATTTCA
1 ATATATATAAATATATATTACAATTTCA
57833 AT
1 AT
57835 TCATTACAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (28 bp):
ATATATATAAATATATATTACAATTTCA
Found at i:61079 original size:50 final size:50
Alignment explanation
Indices: 61004--61109 Score: 212
Period size: 50 Copynumber: 2.1 Consensus size: 50
60994 GAAGCTGAGA
61004 AAACTGATGTTGCAGGATGAAGTAAACACAACTGAATTGATTTTGTTCCT
1 AAACTGATGTTGCAGGATGAAGTAAACACAACTGAATTGATTTTGTTCCT
61054 AAACTGATGTTGCAGGATGAAGTAAACACAACTGAATTGATTTTGTTCCT
1 AAACTGATGTTGCAGGATGAAGTAAACACAACTGAATTGATTTTGTTCCT
61104 AAACTG
1 AAACTG
61110 TCTTTCTGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (50 bp):
AAACTGATGTTGCAGGATGAAGTAAACACAACTGAATTGATTTTGTTCCT
Found at i:69017 original size:12 final size:12
Alignment explanation
Indices: 68984--69025 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
68974 CAACATATAG
68984 TTGATAGTTAATT
1 TTGATAGTTAA-T
*
68997 TTAATAGTTAAT
1 TTGATAGTTAAT
69009 TTGATAGTTAAT
1 TTGATAGTTAAT
69021 TTGAT
1 TTGAT
69026 TAATTGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (12 bp):
TTGATAGTTAAT
Found at i:69225 original size:20 final size:20
Alignment explanation
Indices: 69202--69240 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
69192 ATTTCTTAAG
69202 AAAATTAGTGAATA-ATTTTA
1 AAAATT-GTGAATATATTTTA
*
69222 AAAATTTTGAATATATTTT
1 AAAATTGTGAATATATTTT
69241 TTAAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (20 bp):
AAAATTGTGAATATATTTTA
Found at i:72669 original size:19 final size:18
Alignment explanation
Indices: 72645--72697 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
72635 TTATTTAATA
72645 TTAATTTTACAAATATTAT
1 TTAATTTTACAAA-ATTAT
**
72664 TTAATTATTTTAAAATTAT
1 TTAATT-TTACAAAATTAT
* *
72683 TTTATTTTAAAAAAT
1 TTAATTTTACAAAAT
72698 GAGAAATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 7 0.25
19 16 0.57
20 5 0.18
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATTTTACAAAATTAT
Found at i:72673 original size:22 final size:24
Alignment explanation
Indices: 72634--72679 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
72624 AATGTTTAGA
72634 ATTATTTAATATTAATTTTACAAAT
1 ATTATTTAATATTAATTTTA-AAAT
72659 ATTATTT-A-ATT-ATTTTAAAAT
1 ATTATTTAATATTAATTTTAAAAT
72680 TATTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.19
22 6 0.29
23 3 0.14
24 1 0.05
25 7 0.33
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTATTTAATATTAATTTTAAAAT
Found at i:73170 original size:32 final size:33
Alignment explanation
Indices: 73134--73211 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
73124 TAAATCATGT
73134 TTTGCCCCCTTA-TTTTTTACAATTAATTATAC
1 TTTGCCCCCTTATTTTTTTACAATTAATTATAC
* ***
73166 TTTGCCCCCTCATTTTTTTATGGTTAATTATAC
1 TTTGCCCCCTTATTTTTTTACAATTAATTATAC
*
73199 TTTGTCCCTCTTA
1 TTTG-CCCCCTTA
73212 AGTTGGAATC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 11 0.29
33 21 0.55
34 6 0.16
ACGTcount: A:0.19, C:0.23, G:0.06, T:0.51
Consensus pattern (33 bp):
TTTGCCCCCTTATTTTTTTACAATTAATTATAC
Found at i:78978 original size:15 final size:15
Alignment explanation
Indices: 78958--78988 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
78948 CAAAAGATAA
78958 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
78973 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
78988 A
1 A
78989 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:79979 original size:25 final size:26
Alignment explanation
Indices: 79932--80006 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 26
79922 AAGGTGTTTT
* *
79932 AAATATATTTTTAATATTATATTATTT-
1 AAATAT-TTTTTATTTTTAT-TTATTTG
*
79959 ATAGTATTTTTTATTTTTATTTATTTG
1 A-AATATTTTTTATTTTTATTTATTTG
79986 AAAT-TTTTTTATTTTTTATTT
1 AAATATTTTTTA-TTTTTATTT
80007 TTTTTAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
25 7 0.17
26 17 0.41
27 13 0.32
28 4 0.10
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (26 bp):
AAATATTTTTTATTTTTATTTATTTG
Found at i:81996 original size:43 final size:41
Alignment explanation
Indices: 81843--82006 Score: 148
Period size: 42 Copynumber: 3.9 Consensus size: 41
81833 AATTGATGTT
** * * * *
81843 CTAATTTTTTCAATCTCAAATTTTATCTTTATAATTAAGTCT
1 CTAATTTTTT-AATCTCACTTTTTACCTTTATAATTGAGGCA
** * * * *
81885 CTAATTTTCTCGATTTCATTTTTTACCTTTATAATCGAGGCC
1 CTAATTTT-TTAATCTCACTTTTTACCTTTATAATTGAGGCA
* *
81927 CTAATTTTTTAATCTCGCTTTCTACCTTTATAATTGAGGTCA
1 CTAATTTTTTAATCTCACTTTTTACCTTTATAATTGAGG-CA
* *
81969 TTATTTTTTTTAATCTCACTTTTTACCTTTATAATTGA
1 CTA-ATTTTTTAATCTCACTTTTTACCTTTATAATTGA
82007 ACCCCTATTT
Statistics
Matches: 97, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
41 24 0.25
42 41 0.42
43 32 0.33
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.52
Consensus pattern (41 bp):
CTAATTTTTTAATCTCACTTTTTACCTTTATAATTGAGGCA
Found at i:82019 original size:43 final size:43
Alignment explanation
Indices: 81904--82020 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 43
81894 TCGATTTCAT
* * *
81904 TTTTTACCTTTATAATCGAGGCCCTA--ATTTTTTAATCTCGC
1 TTTTTACCTTTATAATTGAGGCCCTATTTTTTTTTAATCTCAC
* * *
81945 TTTCTACCTTTATAATTGAGGTCAT-TATTTTTTTTAATCTCAC
1 TTTTTACCTTTATAATTGAGGCCCTAT-TTTTTTTTAATCTCAC
**
81988 TTTTTACCTTTATAATTGAACCCCTATTTTTTT
1 TTTTTACCTTTATAATTGAGGCCCTATTTTTTT
82021 CAATTTATAA
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
41 21 0.34
43 39 0.64
44 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (43 bp):
TTTTTACCTTTATAATTGAGGCCCTATTTTTTTTTAATCTCAC
Done.