Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000078.1 Hibiscus syriacus cultivar Beakdansim tig00000142_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: 66794
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:50 original size:18 final size:17
Alignment explanation
Indices: 27--89 Score: 63
Period size: 18 Copynumber: 3.6 Consensus size: 17
17 GATACACATA
*
27 TTTTAAGTTGGAACTTG
1 TTTTAAGTTGAAACTTG
* * *
44 TTTTTAAGTTGCAACCATA
1 -TTTTAAGTTG-AAACTTG
*
63 TTTTAGGTTGAAACTTG
1 TTTTAAGTTGAAACTTG
80 TTTTAAGTTG
1 TTTTAAGTTG
90 TAATCATATT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
17 13 0.37
18 19 0.54
19 3 0.09
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.48
Consensus pattern (17 bp):
TTTTAAGTTGAAACTTG
Found at i:98 original size:35 final size:36
Alignment explanation
Indices: 23--110 Score: 124
Period size: 35 Copynumber: 2.5 Consensus size: 36
13 TCAAGATACA
* *
23 CATATTTTAAGTTGGAACTTGTTTTTAAGTTGCAAC
1 CATATTTTAGGTTGAAACTTGTTTTTAAGTTGCAAC
* *
59 CATATTTTAGGTTGAAACTTG-TTTTAAGTTGTAAT
1 CATATTTTAGGTTGAAACTTGTTTTTAAGTTGCAAC
*
94 CATATTTTAGATTGAAA
1 CATATTTTAGGTTGAAA
111 AATCAAACTT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 28 0.60
36 19 0.40
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (36 bp):
CATATTTTAGGTTGAAACTTGTTTTTAAGTTGCAAC
Found at i:234 original size:22 final size:23
Alignment explanation
Indices: 182--236 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
172 TCACTTGGTA
182 AAATATATTAAATTATTTGTGTAT
1 AAATATATTAAA-TATTTGTGTAT
*
206 --ATGTATTAAA-ATTTGTGTAT
1 AAATATATTAAATATTTGTGTAT
*
226 AAATTTATTAA
1 AAATATATTAA
237 GATTATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 10 0.37
22 17 0.63
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (23 bp):
AAATATATTAAATATTTGTGTAT
Found at i:3897 original size:29 final size:29
Alignment explanation
Indices: 3843--3900 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3833 ATGTTGGCCG
*
3843 TAGGTCGCTATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCGGGCGACCTAC
* *
3872 TAGGTCGCCATGTCTTTCC-GGTGACCTAC
1 TAGGTCGCCATG-CCTTCCGGGCGACCTAC
3901 AACAACGCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.14, C:0.33, G:0.26, T:0.28
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCGGGCGACCTAC
Found at i:3937 original size:20 final size:20
Alignment explanation
Indices: 3912--3969 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
3902 ACAACGCTGG
3912 GCATCCGAGGCCATCCGAAA
1 GCATCCGAGGCCATCCGAAA
*
3932 GCATCCGAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGAAA
3952 GCATCCGAGGCCATCCGA
1 GCATCCGAGGCCATCCGA
3970 CCGAGCTATG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.26, C:0.36, G:0.28, T:0.10
Consensus pattern (20 bp):
GCATCCGAGGCCATCCGAAA
Found at i:3995 original size:10 final size:10
Alignment explanation
Indices: 3910--4029 Score: 87
Period size: 10 Copynumber: 11.4 Consensus size: 10
3900 CAACAACGCT
3910 GGGCATCCGA
1 GGGCATCCGA
*
3920 GGCCATCCGA
1 GGGCATCCGA
**
3930 AAGCATCCGA
1 GGGCATCCGA
*
3940 GGCCATCCGA
1 GGGCATCCGA
*
3950 GAGCATCCGA
1 GGGCATCCGA
*
3960 GGCCATCCGA
1 GGGCATCCGA
* *
3970 CCGAGCTATGCGA
1 --GGGC-ATCCGA
3983 GGGCATCCGA
1 GGGCATCCGA
*
3993 GGGCAACCGA
1 GGGCATCCGA
*
4003 GCGAGCTATGCGA
1 G-G-GC-ATCCGA
*
4016 GGGAATCCGA
1 GGGCATCCGA
4026 GGGC
1 GGGC
4030 GACCGAGCGA
Statistics
Matches: 82, Mismatches: 22, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
10 62 0.76
11 5 0.06
12 5 0.06
13 10 0.12
ACGTcount: A:0.24, C:0.31, G:0.35, T:0.10
Consensus pattern (10 bp):
GGGCATCCGA
Found at i:4028 original size:33 final size:33
Alignment explanation
Indices: 3954--4040 Score: 129
Period size: 33 Copynumber: 2.6 Consensus size: 33
3944 ATCCGAGAGC
* * * *
3954 ATCCGAGGCCATCCGACCGAGCTATGCGAGGGC
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
3987 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
*
4020 ATCCGAGGGCGACCGAGCGAG
1 ATCCGAGGGCAACCGAGCGAG
4041 GGTAGGTCGC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.24, C:0.29, G:0.38, T:0.09
Consensus pattern (33 bp):
ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
Found at i:4120 original size:23 final size:23
Alignment explanation
Indices: 4094--4145 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
4084 GCCCTCGATT
*
4094 CCCTCGCATAGCTCGCTCGGTTG
1 CCCTCGCATAGCTCGCTCGGATG
*
4117 CCCTCGCATAGCTCGTTCGGATG
1 CCCTCGCATAGCTCGCTCGGATG
*
4140 GCCTCG
1 CCCTCG
4146 GTCGGATGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.10, C:0.38, G:0.27, T:0.25
Consensus pattern (23 bp):
CCCTCGCATAGCTCGCTCGGATG
Found at i:4150 original size:14 final size:14
Alignment explanation
Indices: 4128--4160 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
4118 CCTCGCATAG
*
4128 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
4142 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
4156 CTCGG
1 CTCGG
4161 ATGCTCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:4160 original size:10 final size:11
Alignment explanation
Indices: 4133--4193 Score: 58
Period size: 10 Copynumber: 5.6 Consensus size: 11
4123 CATAGCTCGT
4133 TCGGATGGCCTC
1 TCGGATGG-CTC
4145 GGTCGGATGGC-C
1 --TCGGATGGCTC
4157 TCGGAT-GCTC
1 TCGGATGGCTC
*
4167 TCGGAT-GCTT
1 TCGGATGGCTC
4177 TCGGATGGC-C
1 TCGGATGGCTC
4187 TCGGATG
1 TCGGATG
4194 CCCAGTGTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 2 0.05
10 29 0.67
11 2 0.05
12 1 0.02
13 1 0.02
14 8 0.19
ACGTcount: A:0.10, C:0.26, G:0.38, T:0.26
Consensus pattern (11 bp):
TCGGATGGCTC
Found at i:10662 original size:21 final size:21
Alignment explanation
Indices: 10621--10663 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
10611 CTATCCAAAG
* *
10621 TCCACATCCAAATAACTATCA
1 TCCAAATCCAAATAACAATCA
10642 TCCAAATCCAAA-ATACAATCA
1 TCCAAATCCAAATA-ACAATCA
10663 T
1 T
10664 ACCTCCAGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (21 bp):
TCCAAATCCAAATAACAATCA
Found at i:21382 original size:33 final size:33
Alignment explanation
Indices: 21340--21423 Score: 159
Period size: 33 Copynumber: 2.5 Consensus size: 33
21330 ATTTCCAACC
*
21340 TCTCTCTTTTATTCAAGACTCCCTGGCCACCAT
1 TCTCTCTTTTATTCAAGACTCCCTAGCCACCAT
21373 TCTCTCTTTTATTCAAGACTCCCTAGCCACCAT
1 TCTCTCTTTTATTCAAGACTCCCTAGCCACCAT
21406 TCTCTCTTTTATTCAAGA
1 TCTCTCTTTTATTCAAGA
21424 TTTCTATATA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.39
Consensus pattern (33 bp):
TCTCTCTTTTATTCAAGACTCCCTAGCCACCAT
Found at i:21639 original size:23 final size:23
Alignment explanation
Indices: 21608--21697 Score: 135
Period size: 23 Copynumber: 3.9 Consensus size: 23
21598 GAAACGGATG
*
21608 TAAACGAACATAAACGAACACAA
1 TAAACGAACGTAAACGAACACAA
*
21631 TAAATGAACGTAAACGAACACAAA
1 TAAACGAACGTAAACGAACAC-AA
*
21655 TGAACGAACGTAAACGAACACAA
1 TAAACGAACGTAAACGAACACAA
*
21678 TAAATGAACGTAAACGAACA
1 TAAACGAACGTAAACGAACA
21698 TAAATGAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
23 39 0.65
24 21 0.35
ACGTcount: A:0.57, C:0.19, G:0.13, T:0.11
Consensus pattern (23 bp):
TAAACGAACGTAAACGAACACAA
Found at i:21668 original size:24 final size:24
Alignment explanation
Indices: 21570--21705 Score: 136
Period size: 24 Copynumber: 5.8 Consensus size: 24
21560 ATTTAAATGA
* *
21570 TAAACGAATACAAATGAACGAACA
1 TAAACGAACACAAATGAACGAACG
** *
21594 TAAA-GAA-ACGGATGTAAACGAACA
1 TAAACGAACACAAATG--AACGAACG
* *
21618 TAAACGAACAC-AATAAATGAACG
1 TAAACGAACACAAATGAACGAACG
21641 TAAACGAACACAAATGAACGAACG
1 TAAACGAACACAAATGAACGAACG
* *
21665 TAAACGAACAC-AATAAATGAACG
1 TAAACGAACACAAATGAACGAACG
*
21688 TAAACGAACATAAATGAA
1 TAAACGAACACAAATGAA
21706 AATAGATTTT
Statistics
Matches: 94, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
22 5 0.05
23 40 0.43
24 42 0.45
25 5 0.05
26 2 0.02
ACGTcount: A:0.57, C:0.16, G:0.15, T:0.12
Consensus pattern (24 bp):
TAAACGAACACAAATGAACGAACG
Found at i:21669 original size:47 final size:47
Alignment explanation
Indices: 21610--21705 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
21600 AACGGATGTA
21610 AACGAACATAAACGAACACAATAAATGAACGTAAACGAACACAAATG
1 AACGAACATAAACGAACACAATAAATGAACGTAAACGAACACAAATG
* *
21657 AACGAACGTAAACGAACACAATAAATGAACGTAAACGAACATAAATG
1 AACGAACATAAACGAACACAATAAATGAACGTAAACGAACACAAATG
21704 AA
1 AA
21706 AATAGATTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.57, C:0.18, G:0.14, T:0.11
Consensus pattern (47 bp):
AACGAACATAAACGAACACAATAAATGAACGTAAACGAACACAAATG
Found at i:21871 original size:14 final size:14
Alignment explanation
Indices: 21851--21917 Score: 98
Period size: 14 Copynumber: 4.8 Consensus size: 14
21841 GATTGAGCTA
*
21851 AACATAAATGAACG
1 AACATAAACGAACG
*
21865 CACATAAACGAACG
1 AACATAAACGAACG
*
21879 AACATAAATGAACG
1 AACATAAACGAACG
*
21893 AATATAAACGAACG
1 AACATAAACGAACG
21907 AACATAAACGA
1 AACATAAACGA
21918 GCATATTACC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 46 1.00
ACGTcount: A:0.57, C:0.18, G:0.13, T:0.12
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:21883 original size:28 final size:28
Alignment explanation
Indices: 21851--21914 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
21841 GATTGAGCTA
*
21851 AACATAAATGAACGCACATAAACGAACG
1 AACATAAATGAACGAACATAAACGAACG
*
21879 AACATAAATGAACGAATATAAACGAACG
1 AACATAAATGAACGAACATAAACGAACG
21907 AACATAAA
1 AACATAAA
21915 CGAGCATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.58, C:0.17, G:0.12, T:0.12
Consensus pattern (28 bp):
AACATAAATGAACGAACATAAACGAACG
Found at i:22328 original size:2 final size:2
Alignment explanation
Indices: 22321--22346 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22311 TTTAAAAATA
22321 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
22347 CATGGATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23664 original size:15 final size:15
Alignment explanation
Indices: 23646--23699 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
23636 TTATTTTAAT
23646 AAAATTAAAATATTA
1 AAAATTAAAATATTA
23661 AAAATTAAAATACTTCTA
1 AAAATTAAAATA--T-TA
* *
23679 AAAAATAATA-ATTA
1 AAAATTAAAATATTA
23693 AAAATTA
1 AAAATTA
23700 TTTAAACAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 8 0.24
15 13 0.39
17 2 0.06
18 10 0.30
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATTAAAATATTA
Found at i:25367 original size:48 final size:48
Alignment explanation
Indices: 25311--25448 Score: 186
Period size: 48 Copynumber: 2.9 Consensus size: 48
25301 TCAAAGGTAA
** * *
25311 CTCATGAAAACATAACATAAATGCATTATCAAGAAATATACATTGTAG
1 CTCATGAAAACATAACATAAACACATTATCAAAAAATACACATTGTAG
*
25359 CTCATGAAAACATAACATAAACACATTATCAAAAAATACACTTTGTAG
1 CTCATGAAAACATAACATAAACACATTATCAAAAAATACACATTGTAG
* * * *
25407 CACATGAAAACATAACATAAAACACATTTTCAATAAGTACAC
1 CTCATGAAAACATAACAT-AAACACATTATCAAAAAATACAC
25449 CTTTTAACTT
Statistics
Matches: 80, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
48 60 0.75
49 20 0.25
ACGTcount: A:0.50, C:0.18, G:0.07, T:0.25
Consensus pattern (48 bp):
CTCATGAAAACATAACATAAACACATTATCAAAAAATACACATTGTAG
Found at i:26274 original size:23 final size:23
Alignment explanation
Indices: 26256--26314 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
26246 CTCGTATAAA
26256 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
26279 TGCACCGAAGTG-CCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
26301 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
26315 ATATAATGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 21 0.62
23 13 0.38
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:26974 original size:2 final size:2
Alignment explanation
Indices: 26967--27020 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
26957 TCTCTTAAAC
26967 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
27009 AT AT AT AT AT AT
1 AT AT AT AT AT AT
27021 TCACATGTTC
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:28067 original size:21 final size:21
Alignment explanation
Indices: 28043--28087 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28033 TCTTGTTCGT
* *
28043 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
28064 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
28085 TTG
1 TTG
28088 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:31317 original size:21 final size:22
Alignment explanation
Indices: 31256--31334 Score: 126
Period size: 22 Copynumber: 3.6 Consensus size: 22
31246 CTCGTATAAA
31256 TGCA-CGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
31278 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
31300 TGCACCGAAGTG-CCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
31321 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
31335 ATATAATGAT
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
21 20 0.37
22 27 0.50
23 7 0.13
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:33036 original size:21 final size:21
Alignment explanation
Indices: 33012--33056 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
33002 TCTTGTTCGT
* *
33012 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
33033 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
33054 TTG
1 TTG
33057 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:35387 original size:22 final size:22
Alignment explanation
Indices: 35361--35404 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
35351 ATTCCCTTTA
*
35361 AATATATTT-TAATCATTAATTT
1 AATAT-TTTGTAATAATTAATTT
35383 AATATTTTGTAATAATTAATTT
1 AATATTTTGTAATAATTAATTT
35405 TATAATATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
AATATTTTGTAATAATTAATTT
Found at i:37314 original size:69 final size:69
Alignment explanation
Indices: 37203--37345 Score: 286
Period size: 69 Copynumber: 2.1 Consensus size: 69
37193 ATGGCTCAAG
37203 CTTTCAACATATATTCTAGTATTGTTTTTGCTATTGCTTTATTCATAATGTTTGCGGCTTTGAGT
1 CTTTCAACATATATTCTAGTATTGTTTTTGCTATTGCTTTATTCATAATGTTTGCGGCTTTGAGT
37268 CTTC
66 CTTC
37272 CTTTCAACATATATTCTAGTATTGTTTTTGCTATTGCTTTATTCATAATGTTTGCGGCTTTGAGT
1 CTTTCAACATATATTCTAGTATTGTTTTTGCTATTGCTTTATTCATAATGTTTGCGGCTTTGAGT
37337 CTTC
66 CTTC
37341 CTTTC
1 CTTTC
37346 TTCATGAAGT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 74 1.00
ACGTcount: A:0.18, C:0.17, G:0.14, T:0.51
Consensus pattern (69 bp):
CTTTCAACATATATTCTAGTATTGTTTTTGCTATTGCTTTATTCATAATGTTTGCGGCTTTGAGT
CTTC
Found at i:41506 original size:41 final size:41
Alignment explanation
Indices: 41461--41540 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
41451 TGCATGGTAG
*
41461 CAATTGTTGAAATTTTGCATGGCATTATAGATGGCAGCCAT
1 CAATTATTGAAATTTTGCATGGCATTATAGATGGCAGCCAT
*
41502 CAATTATTGAAATTTTGCATGGCATTCTAGATGGCAGCC
1 CAATTATTGAAATTTTGCATGGCATTATAGATGGCAGCC
41541 GGTGGTTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (41 bp):
CAATTATTGAAATTTTGCATGGCATTATAGATGGCAGCCAT
Found at i:50656 original size:12 final size:12
Alignment explanation
Indices: 50636--50693 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
50626 AAATACGGTA
*
50636 TGAATAGTACCG
1 TGAACAGTACCG
*
50648 TGAACAGTA--A
1 TGAACAGTACCG
*
50658 TGAACAATACCG
1 TGAACAGTACCG
50670 TGAACAGTACC-
1 TGAACAGTACCG
50681 TGACTACAGTACC
1 TGA--ACAGTACC
50694 CGAATGTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 8 0.22
11 3 0.08
12 18 0.49
13 8 0.22
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (12 bp):
TGAACAGTACCG
Found at i:51642 original size:25 final size:23
Alignment explanation
Indices: 51614--51663 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
51604 AATTTTGTCT
51614 CGAAG-GATCGCGTAGAAATTTGCAC
1 CGAAGTGAT-GCGTAG-AA-TTGCAC
*
51639 CGAAGTGCTGCGTAGAATTGCAC
1 CGAAGTGATGCGTAGAATTGCAC
51662 CG
1 CG
51664 TAGTACCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.35
24 2 0.09
25 11 0.48
26 2 0.09
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (23 bp):
CGAAGTGATGCGTAGAATTGCAC
Found at i:64324 original size:13 final size:14
Alignment explanation
Indices: 64299--64327 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
64289 TGAACTAGCC
64299 ATTTGAGCTGGAAA
1 ATTTGAGCTGGAAA
64313 ATTTGA-CTGGAAA
1 ATTTGAGCTGGAAA
64326 AT
1 AT
64328 ATCAGGCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (14 bp):
ATTTGAGCTGGAAA
Done.