Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003349.1 Hibiscus syriacus cultivar Beakdansim tig00007052_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: 98060
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:13939 original size:13 final size:14
Alignment explanation
Indices: 13910--13942 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
13900 ATTAACTTCA
13910 TAAAATTAAAATAT
1 TAAAATTAAAATAT
*
13924 TAAAATT-AAATTT
1 TAAAATTAAAATAT
13937 TAAAAT
1 TAAAAT
13943 AATATGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAAATTAAAATAT
Found at i:14117 original size:2 final size:2
Alignment explanation
Indices: 14110--14139 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14100 ACCCAATACA
14110 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
14140 TAAATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17675 original size:58 final size:59
Alignment explanation
Indices: 17604--17742 Score: 181
Period size: 58 Copynumber: 2.4 Consensus size: 59
17594 GTCAGATGAT
* * ***
17604 CATTTTGTAACTTTTACTAGTTGAAGGACTCAATAAAGCATTGCCAATAGTTGA-AGAC
1 CATTTTATAACTTTTAATAGTTGAAGGACTCAATAAAGCACCACCAATAGTTGAGAGAC
* * *
17662 CATTTTATAACTTTTAATAGTTGAGGGACTCAATAAAGTACCACCTATAGTTGAGAGAC
1 CATTTTATAACTTTTAATAGTTGAAGGACTCAATAAAGCACCACCAATAGTTGAGAGAC
* *
17721 TATTTTATAATTTTTAATAGTT
1 CATTTTATAACTTTTAATAGTT
17743 AAGATACTCA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
58 46 0.66
59 24 0.34
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (59 bp):
CATTTTATAACTTTTAATAGTTGAAGGACTCAATAAAGCACCACCAATAGTTGAGAGAC
Found at i:18260 original size:15 final size:15
Alignment explanation
Indices: 18240--18269 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18230 TTTCACTTTA
18240 TTTCTTTCCCCTTCC
1 TTTCTTTCCCCTTCC
*
18255 TTTCTTTCCCTTTCC
1 TTTCTTTCCCCTTCC
18270 ACCCGTGCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTCTTTCCCCTTCC
Found at i:21159 original size:44 final size:39
Alignment explanation
Indices: 21111--21204 Score: 188
Period size: 39 Copynumber: 2.4 Consensus size: 39
21101 ATTCATATAT
21111 TCGGGTCGGGTCGGGTCTCGGATGGAGGTTCCTTTGTTC
1 TCGGGTCGGGTCGGGTCTCGGATGGAGGTTCCTTTGTTC
21150 TCGGGTCGGGTCGGGTCTCGGATGGAGGTTCCTTTGTTC
1 TCGGGTCGGGTCGGGTCTCGGATGGAGGTTCCTTTGTTC
21189 TCGGGTCGGGTCGGGT
1 TCGGGTCGGGTCGGGT
21205 GGACCAAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.04, C:0.20, G:0.44, T:0.32
Consensus pattern (39 bp):
TCGGGTCGGGTCGGGTCTCGGATGGAGGTTCCTTTGTTC
Found at i:21846 original size:75 final size:74
Alignment explanation
Indices: 21724--21915 Score: 285
Period size: 75 Copynumber: 2.5 Consensus size: 74
21714 TTTATTTAGT
* * *
21724 ATGGTATCAATACCCCCATATAAGGTACCGATACCCCTATGAACATTTTTGTTCCGAGAAATAAC
1 ATGGTACCAATACCCCC-TAT-AGGTATCGATACCCCTATGAACATTTTGGTTCCGAGAAATAAC
21789 AGAATACTCGG
64 AGAATACTCGG
*
21800 ATGGTACCTATACCCCCTATAGGGTATCGATACCCCTATGAACATTTTGGTTCCGAGAAATAACA
1 ATGGTACCAATACCCCCTATA-GGTATCGATACCCCTATGAACATTTTGGTTCCGAGAAATAACA
*
21865 GAATGCTCGG
65 GAATACTCGG
* *
21875 ATGGTACCGATACCCCCTAGTAGGTATCGATACCCCCATGA
1 ATGGTACCAATACCCCCTA-TAGGTATCGATACCCCTATGA
21916 TATGGTATCG
Statistics
Matches: 107, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
74 1 0.01
75 89 0.83
76 17 0.16
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (74 bp):
ATGGTACCAATACCCCCTATAGGTATCGATACCCCTATGAACATTTTGGTTCCGAGAAATAACAG
AATACTCGG
Found at i:21925 original size:22 final size:21
Alignment explanation
Indices: 21875--21952 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 21
21865 GAATGCTCGG
*
21875 ATGGTACCGATACCCCCTAGT
1 ATGGTATCGATACCCCCTAGT
21896 A-GGTATCGATACCCCC-ATGAT
1 ATGGTATCGATACCCCCTA-G-T
*
21917 ATGGTATCGATACCCCCTACT
1 ATGGTATCGATACCCCCTAGT
*
21938 -TAGGTACCGATACCC
1 AT-GGTATCGATACCC
21953 TCAGGCATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
19 1 0.02
20 16 0.33
21 16 0.33
22 15 0.31
23 1 0.02
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (21 bp):
ATGGTATCGATACCCCCTAGT
Found at i:21943 original size:21 final size:20
Alignment explanation
Indices: 21877--21952 Score: 82
Period size: 22 Copynumber: 3.6 Consensus size: 20
21867 ATGCTCGGAT
*
21877 GGTACCGATACCCCCTAGTA
1 GGTACCGATACCCCCTATTA
*
21897 GGTATCGATACCCCC-ATGATA
1 GGTACCGATACCCCCTAT--TA
*
21918 TGGTATCGATACCCCCTACTTA
1 -GGTACCGATACCCCCTA-TTA
21940 GGTACCGATACCC
1 GGTACCGATACCC
21953 TCAGGCATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
19 1 0.02
20 14 0.29
21 14 0.29
22 17 0.35
23 1 0.02
24 1 0.02
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (20 bp):
GGTACCGATACCCCCTATTA
Found at i:22192 original size:11 final size:11
Alignment explanation
Indices: 22176--22201 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
22166 TCAAGCAACT
22176 AGAATCAAGAG
1 AGAATCAAGAG
22187 AGAATCAAGAG
1 AGAATCAAGAG
22198 AGAA
1 AGAA
22202 AGCATCAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.08, G:0.27, T:0.08
Consensus pattern (11 bp):
AGAATCAAGAG
Found at i:27758 original size:21 final size:20
Alignment explanation
Indices: 27727--27808 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 20
27717 ATTTATGTGC
27727 ATAGAGTATCGATACCCATGA
1 ATAG-GTATCGATACCCATGA
* *
27748 TACAGGTATCGATACCCCCTTTGA
1 -ATAGGTATCGATA--CCC-ATGA
27772 ATAGGTATCGATACCCATTGA
1 ATAGGTATCGATACCCA-TGA
27793 ATAGGTATCGATACCC
1 ATAGGTATCGATACCC
27809 TCTTTGAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
21 31 0.60
22 3 0.06
23 15 0.29
24 3 0.06
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (20 bp):
ATAGGTATCGATACCCATGA
Found at i:27781 original size:23 final size:23
Alignment explanation
Indices: 27751--27854 Score: 139
Period size: 23 Copynumber: 4.7 Consensus size: 23
27741 CCCATGATAC
27751 AGGTATCGATACCCCCTTTGAAT
1 AGGTATCGATACCCCCTTTGAAT
*
27774 AGGTATCGATA--CCCATTGAAT
1 AGGTATCGATACCCCCTTTGAAT
*
27795 AGGTATCGATACCCTCTTTGAAT
1 AGGTATCGATACCCCCTTTGAAT
27818 -GAGTATCGATACCCCC-TTG-AT
1 AG-GTATCGATACCCCCTTTGAAT
27839 -GGTATCGATACCCCCT
1 AGGTATCGATACCCCCT
27855 GTCGGGTTTA
Statistics
Matches: 73, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.19
21 23 0.32
22 4 0.05
23 32 0.44
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (23 bp):
AGGTATCGATACCCCCTTTGAAT
Found at i:27799 original size:44 final size:45
Alignment explanation
Indices: 27727--27854 Score: 176
Period size: 44 Copynumber: 2.9 Consensus size: 45
27717 ATTTATGTGC
*
27727 ATAGAGTATCGATACCCA-TGATACAGGTATCGATACCCCCTTTGA
1 ATAGAGTATCGATACCCATTGA-ATAGGTATCGATACCCCCTTTGA
*
27772 ATAG-GTATCGATACCCATTGAATAGGTATCGATACCCTCTTTGA
1 ATAGAGTATCGATACCCATTGAATAGGTATCGATACCCCCTTTGA
*
27816 AT-GAGTATCGATACCCCCTTG-AT-GGTATCGATACCCCCT
1 ATAGAGTATCGATA-CCCATTGAATAGGTATCGATACCCCCT
27855 GTCGGGTTTA
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
43 16 0.21
44 47 0.62
45 13 0.17
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (45 bp):
ATAGAGTATCGATACCCATTGAATAGGTATCGATACCCCCTTTGA
Found at i:30549 original size:75 final size:75
Alignment explanation
Indices: 30444--30617 Score: 303
Period size: 75 Copynumber: 2.3 Consensus size: 75
30434 TTTATTTAGT
* * *
30444 ATGGTATCGATACCCCATATAGGGTACCGATACCCCTATGAACATTTTGGTTCCGAGAAATAACA
1 ATGGTACCGATACCCCCTATAGGGTACCGATACCCCTATGAACATTTTAGTTCCGAGAAATAACA
30509 GAATGCTCGG
66 GAATGCTCGG
30519 ATGGTACCGATACCCCCTATAGGGTACCGATACCCCTATGAACATTTTAGTTCCGAGAAATAACA
1 ATGGTACCGATACCCCCTATAGGGTACCGATACCCCTATGAACATTTTAGTTCCGAGAAATAACA
30584 GAATGCTCGG
66 GAATGCTCGG
*
30594 ATGATACCGATACCCCCTAATAGG
1 ATGGTACCGATACCCCCT-ATAGG
30618 TATTGATGCC
Statistics
Matches: 94, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
75 89 0.95
76 5 0.05
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (75 bp):
ATGGTACCGATACCCCCTATAGGGTACCGATACCCCTATGAACATTTTAGTTCCGAGAAATAACA
GAATGCTCGG
Found at i:30652 original size:22 final size:20
Alignment explanation
Indices: 30601--30672 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 20
30591 CGGATGATAC
30601 CGATACCCCCTAATAGGTAT
1 CGATACCCCCTAATAGGTAT
* * *
30621 TGATGCCCCCCATGATATGGTAT
1 CGAT-ACCCCC-TAATA-GGTAT
* *
30644 CGATACCCCCTACTTAGGTAC
1 CGATACCCCCTA-ATAGGTAT
30665 CGATACCC
1 CGATACCC
30673 TCAGACATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
20 3 0.08
21 18 0.45
22 11 0.28
23 8 0.20
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (20 bp):
CGATACCCCCTAATAGGTAT
Found at i:33866 original size:2 final size:2
Alignment explanation
Indices: 33859--33895 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
33849 ACTGCCCAGA
33859 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33896 CGCAGATAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36977 original size:14 final size:15
Alignment explanation
Indices: 36958--36992 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
36948 TTTTGTCCGG
36958 ATTATAAATATT-AT
1 ATTATAAATATTAAT
*
36972 ATTATAATTATTAAT
1 ATTATAAATATTAAT
36987 ATTATA
1 ATTATA
36993 TTATAACTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTATAAATATTAAT
Found at i:36987 original size:20 final size:20
Alignment explanation
Indices: 36958--37011 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
36948 TTTTGTCCGG
*
36958 ATTATAAATATTATATTATA
1 ATTATTAATATTATATTATA
36978 ATTATTAATATTATATTATA
1 ATTATTAATATTATATTATA
* *
36998 ACTATTATTATTAT
1 ATTATTAATATTAT
37012 TATAACAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTATTAATATTATATTATA
Found at i:37008 original size:3 final size:3
Alignment explanation
Indices: 36966--37052 Score: 52
Period size: 3 Copynumber: 29.7 Consensus size: 3
36956 GGATTATAAA
* * * *
36966 TAT TA- TAT TAT AAT TAT TAA TAT TA- TAT TAT AAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * *
37012 TAT AAC AAT TAA AAT TAA AAT TAT TAT TAG TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
37053 ATATCGCTTA
Statistics
Matches: 60, Mismatches: 22, Indels: 4
0.70 0.26 0.05
Matches are distributed among these distances:
2 4 0.07
3 56 0.93
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (3 bp):
TAT
Found at i:41617 original size:6 final size:6
Alignment explanation
Indices: 41606--41640 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
41596 TACTTACTCA
* *
41606 TCATGG TCATGG TCATGG TCATGC TCATGC TCATG
1 TCATGG TCATGG TCATGG TCATGG TCATGG TCATG
41641 ATATCGCTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (6 bp):
TCATGG
Found at i:42525 original size:18 final size:19
Alignment explanation
Indices: 42486--42525 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
42476 AAATAATAAT
*
42486 AAAATAATTTGAAGTGATCA
1 AAAATAATTT-AAGTGAGCA
42506 AAAATAATTT-AGTGAGCA
1 AAAATAATTTAAGTGAGCA
42524 AA
1 AA
42526 TTAGAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.28
Consensus pattern (19 bp):
AAAATAATTTAAGTGAGCA
Found at i:44930 original size:12 final size:11
Alignment explanation
Indices: 44901--44940 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
44891 CAATCAATAT
*
44901 ATAAATATAAA
1 ATAAAAATAAA
*
44912 CTAAAAATAACA
1 ATAAAAATAA-A
44924 ATAAAAATAAA
1 ATAAAAATAAA
44935 ATAAAA
1 ATAAAA
44941 GAATCCCAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (11 bp):
ATAAAAATAAA
Found at i:48027 original size:20 final size:20
Alignment explanation
Indices: 47999--48036 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
47989 ATACTTGACC
* *
47999 CTAGGGTATCGATACTACAA
1 CTAGAGTATCAATACTACAA
48019 CTAGAGTATCAATACTAC
1 CTAGAGTATCAATACTAC
48037 CCACCTAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (20 bp):
CTAGAGTATCAATACTACAA
Found at i:48836 original size:53 final size:53
Alignment explanation
Indices: 48756--48879 Score: 203
Period size: 53 Copynumber: 2.3 Consensus size: 53
48746 GTAAGTTGAT
48756 GGGGTGTACGTTTCTGATGCAACTCCGAATTTCACCCCATATATTCGAGGGGA
1 GGGGTGTACGTTTCTGATGCAACTCCGAATTTCACCCCATATATTCGAGGGGA
* *
48809 GGGGTGTACGTTTTTGATGCAGCTCCGAATTTCACCCCATATATTCGAGGGGA
1 GGGGTGTACGTTTCTGATGCAACTCCGAATTTCACCCCATATATTCGAGGGGA
* * *
48862 CGGGTATACATTTCTGAT
1 GGGGTGTACGTTTCTGAT
48880 AGAGTTCCAG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 65 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.31
Consensus pattern (53 bp):
GGGGTGTACGTTTCTGATGCAACTCCGAATTTCACCCCATATATTCGAGGGGA
Found at i:52133 original size:24 final size:24
Alignment explanation
Indices: 52089--52136 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
52079 TTTGTTATTA
*
52089 TTATATATATTATCTATTTATTTT
1 TTATATATATTATATATTTATTTT
*
52113 TTATATAT-TTTTATATATTATTTT
1 TTATATATATTATATAT-TTATTTT
52137 CATTAAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (24 bp):
TTATATATATTATATATTTATTTT
Found at i:52225 original size:23 final size:21
Alignment explanation
Indices: 52185--52248 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
52175 ATTTGTATTA
*
52185 TTTATATCTTTTATTTTTTTC
1 TTTATATATTTTATTTTTTTC
* *
52206 TTTATATATTTTA-CTATTT-
1 TTTATATATTTTATTTTTTTC
*
52225 TTT-TATATTTT-TTCTTTTC
1 TTTATATATTTTATTTTTTTC
52244 TTTAT
1 TTTAT
52249 TTTTATCCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 11 0.32
19 6 0.18
20 5 0.15
21 12 0.35
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTATATATTTTATTTTTTTC
Found at i:52247 original size:18 final size:18
Alignment explanation
Indices: 52201--52252 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
52191 TCTTTTATTT
52201 TTTTCTTTATATATTTTAC
1 TTTTCTTTATAT-TTTTAC
* *
52220 TATTTTTTTATATTTTTTC
1 T-TTTCTTTATATTTTTAC
52239 TTTTCTTTAT-TTTT
1 TTTTCTTTATATTTT
52253 ATCCTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 4 0.14
18 8 0.28
19 7 0.24
20 10 0.34
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTCTTTATATTTTTAC
Found at i:52250 original size:34 final size:34
Alignment explanation
Indices: 52185--52291 Score: 91
Period size: 34 Copynumber: 3.1 Consensus size: 34
52175 ATTTGTATTA
* *
52185 TTTATAT-C-TTTTAT-TTTTTTC-TTTATATAT
1 TTTATATCCTTTTTATATTTTTTCTTTTCTTTAT
*
52215 TTTACTAT-TTTTTTATATTTTTTCTTTTCTTTAT
1 TTTA-TATCCTTTTTATATTTTTTCTTTTCTTTAT
52249 TTT-TATCCTTTTTATCATTTTTATCCTTTTACATTTAT
1 TTTATATCCTTTTTAT-ATTTTT-T-CTTTT-C-TTTAT
52287 TTTAT
1 TTTAT
52292 TACTTTATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 13
0.78 0.05 0.16
Matches are distributed among these distances:
30 4 0.06
31 3 0.05
32 9 0.15
33 14 0.23
34 16 0.26
35 1 0.02
36 5 0.08
37 1 0.02
38 8 0.13
39 1 0.02
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (34 bp):
TTTATATCCTTTTTATATTTTTTCTTTTCTTTAT
Found at i:52259 original size:18 final size:18
Alignment explanation
Indices: 52230--52289 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
52220 TATTTTTTTA
52230 TATTTTT-T-CTTTTCTT
1 TATTTTTATCCTTTTCTT
52246 TATTTTTATCCTTTT-TAT
1 TATTTTTATCCTTTTCT-T
*
52264 CATTTTTATCCTTTTACATT
1 TATTTTTATCCTTTT-C-TT
52284 TATTTT
1 TATTTT
52290 ATTACTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
16 7 0.19
17 2 0.06
18 20 0.56
20 6 0.17
21 1 0.03
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (18 bp):
TATTTTTATCCTTTTCTT
Found at i:52260 original size:9 final size:9
Alignment explanation
Indices: 52248--52278 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
52238 CTTTTCTTTA
52248 TTTTTATCC
1 TTTTTATCC
*
52257 TTTTTATCA
1 TTTTTATCC
52266 TTTTTATCC
1 TTTTTATCC
52275 TTTT
1 TTTT
52279 ACATTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTATCC
Found at i:58326 original size:41 final size:41
Alignment explanation
Indices: 58279--58376 Score: 178
Period size: 41 Copynumber: 2.4 Consensus size: 41
58269 ATTCGCGTTG
58279 CATTTCGCGTTGCGATAGTTGAAAATAGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATAGCGTTGCGATTTTC
*
58320 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATAGCGTTGCGATTTTC
*
58361 TATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
58377 TTTCCATTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATAGCGTTGCGATTTTC
Found at i:58371 original size:61 final size:61
Alignment explanation
Indices: 58306--58437 Score: 246
Period size: 61 Copynumber: 2.2 Consensus size: 61
58296 GTTGAAAATA
*
58306 GCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCTATTTC
1 GCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTC
*
58367 GCGTTGCGATTTTCCATTTCGCGTTGCTATAGTTGAAAATCGCGTTGCGATTTTCCATTTC
1 GCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTC
58428 GCGTTGCGAT
1 GCGTTGCGAT
58438 AGTTGAAAAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 69 1.00
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.40
Consensus pattern (61 bp):
GCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTC
Found at i:58410 original size:41 final size:41
Alignment explanation
Indices: 58365--58521 Score: 223
Period size: 41 Copynumber: 3.9 Consensus size: 41
58355 ATTTTCTATT
*
58365 TCGCGTTGCGATTTTCCATTTCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
58406 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
* *
58447 TCGCGTTGCGATTTTCCATTTCGCATTGCGATAGTCT-ACAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAA
*
58488 T-GTCGTTGCGATTTTCCAAATT--CGTTGCGATAGT
1 TCG-CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGT
58522 CTACAGTTGT
Statistics
Matches: 108, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
40 12 0.11
41 92 0.85
42 4 0.04
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:58424 original size:102 final size:102
Alignment explanation
Indices: 58279--58478 Score: 364
Period size: 102 Copynumber: 2.0 Consensus size: 102
58269 ATTCGCGTTG
58279 CATTTCGCGTTGCGATAGTTGAAAATAGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATAGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
* *
58344 ATCGCGTTGCGATTTTCTATTTCGCGTTGCGATTTTC
66 ATCGCGTTGCGATTTTCCATTTCGCATTGCGATTTTC
* *
58381 CATTTCGCGTTGCTATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATAGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
58446 ATCGCGTTGCGATTTTCCATTTCGCATTGCGAT
66 ATCGCGTTGCGATTTTCCATTTCGCATTGCGAT
58479 AGTCTACAAT
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 94 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.39
Consensus pattern (102 bp):
CATTTCGCGTTGCGATAGTTGAAAATAGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
ATCGCGTTGCGATTTTCCATTTCGCATTGCGATTTTC
Found at i:58514 original size:19 final size:19
Alignment explanation
Indices: 58450--58518 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
58440 TTGAAAATCG
*
58450 CGTTGCGATTTTCC-ATTT
1 CGTTGCGATTTTCCAAATT
** *
58468 CGCATTGCGATAGTCTACAATGT
1 CG--TTGCGATTTTCCA-AAT-T
58491 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
58510 CGTTGCGAT
1 CGTTGCGAT
58519 AGTCTACAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
18 2 0.05
19 10 0.26
20 12 0.31
21 10 0.26
22 2 0.05
23 3 0.08
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:58673 original size:6 final size:6
Alignment explanation
Indices: 58662--58686 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
58652 GACACGTATT
58662 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
58687 GACGGACGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:59197 original size:5 final size:5
Alignment explanation
Indices: 59189--59244 Score: 58
Period size: 5 Copynumber: 10.6 Consensus size: 5
59179 CCGTCTCGAC
* * *
59189 TCGGG TCGGG CCGGG CCGGG CCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG
59242 TCG
1 TCG
59245 TGGTAATACG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
5 31 0.65
6 17 0.35
ACGTcount: A:0.00, C:0.25, G:0.55, T:0.20
Consensus pattern (5 bp):
TCGGG
Found at i:59233 original size:6 final size:6
Alignment explanation
Indices: 59212--59248 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
59202 GGCCGGGCCG
59212 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
59249 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:59366 original size:19 final size:19
Alignment explanation
Indices: 59342--59410 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
59332 CAACGACTTT
59342 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
59361 TCGCAACGATAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
59383 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
59402 TCGCAACGA
1 TCGCAACGA
59411 CAACTGTAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 22 0.56
20 2 0.05
21 2 0.05
22 13 0.33
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:59469 original size:20 final size:20
Alignment explanation
Indices: 59444--59537 Score: 100
Period size: 20 Copynumber: 4.6 Consensus size: 20
59434 ATTTTCAACT
* *
59444 ATCGCAACGCTAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
*
59464 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATGGAAA
* **
59484 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAAATG--GAAA
59506 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
59526 ATCGCAACGCGA
1 ATCGCAACGCGA
59538 TTTTCAACTA
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
20 43 0.72
21 2 0.03
22 15 0.25
ACGTcount: A:0.41, C:0.24, G:0.21, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:59507 original size:62 final size:62
Alignment explanation
Indices: 59356--59537 Score: 176
Period size: 62 Copynumber: 2.9 Consensus size: 62
59346 AACGAATTTG
* * *
59356 GAAAATCGCAACGATAACTGTAGACTATCGCAACG-AATTTGGAAAATCGCAACGAC-AACTGTA
1 GAAAATCGCAACGACAACTGTAGACTATCGCAACGCAA-ATGGAAAATCGCAACG-CGAAC-ATA
*** * * * * *
59419 GACTGTCACAACG-CGATTTTCA-ACTATCGCAACGCTAACTGGAAAATCGCAACGCGAA-ATA
1 GAAAATCGCAACGACAACTGT-AGACTATCGCAACGC-AAATGGAAAATCGCAACGCGAACATA
59480 GAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 GAAAATCGCAACGACAACTGTAGACTATCGCAACGC-AAATGGAAAATCGCAACGCGA
59538 TTTTCAACTA
Statistics
Matches: 94, Mismatches: 19, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
61 12 0.13
62 53 0.56
63 27 0.29
64 2 0.02
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.17
Consensus pattern (62 bp):
GAAAATCGCAACGACAACTGTAGACTATCGCAACGCAAATGGAAAATCGCAACGCGAACATA
Found at i:59551 original size:83 final size:83
Alignment explanation
Indices: 59397--59561 Score: 197
Period size: 83 Copynumber: 2.0 Consensus size: 83
59387 AACGAATTTG
* ** * * * *
59397 GAAAATCGCAACGACAACTGTAGACTGTCACAACGCGATTTTCAACTATCGCAACGCTAACTGGA
1 GAAAATCGCAACGACAACTGTAGACTATCACAACGCGAAATGCAACAATCGCAACGCGAACTGCA
59462 AAATCGCAACGCGAAATA
66 AAATCGCAACGCGAAATA
* * ** *
59480 GAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAA-AATCGCAACGCGATTTTCA
1 GAAAATCGCAACGACAACTGTAGACTATCACAACGCGAAATGCAACAATCGCAACGCGAACTGCA
*
59544 ACTATCGCAACGCGAAAT
66 A-AATCGCAACGCGAAAT
59562 GCAACGCGAA
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
82 14 0.21
83 54 0.79
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.18
Consensus pattern (83 bp):
GAAAATCGCAACGACAACTGTAGACTATCACAACGCGAAATGCAACAATCGCAACGCGAACTGCA
AAATCGCAACGCGAAATA
Found at i:59560 original size:41 final size:42
Alignment explanation
Indices: 59354--59562 Score: 198
Period size: 41 Copynumber: 5.0 Consensus size: 42
59344 GCAACGAATT
* *
59354 TGGAAAATCGCAACGATAACTGTAGACTATCGCAA--CGAATT
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAA-A
* * **
59395 TGGAAAATCGCAACGACAACTGTAGACTGTCACAACGCGATT
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
** * **
59437 TTCAACTATCGCAACG-CTAACTG--GAAAATCGCAACGCGAAA
1 TGGAA-AATCGCAACGAC-AACTGTAGACTATCGCAACGCGAAA
*
59478 TAGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
* * *
59520 TGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAA
59561 TG
1 TG
59563 CAACGCGAAT
Statistics
Matches: 138, Mismatches: 22, Indels: 16
0.78 0.12 0.09
Matches are distributed among these distances:
40 14 0.10
41 71 0.51
42 36 0.26
43 17 0.12
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (42 bp):
TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
Found at i:63099 original size:3 final size:3
Alignment explanation
Indices: 63091--63121 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
63081 TAACCTTACT
63091 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
63122 ATAGCAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:64702 original size:18 final size:19
Alignment explanation
Indices: 64667--64703 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
64657 CACGGAATGT
64667 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
64687 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
64704 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:65544 original size:19 final size:19
Alignment explanation
Indices: 65520--65560 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
65510 ATACATTAAC
65520 ATAAAA-AAACATAGTTCAA
1 ATAAAAGAAACAT-GTTCAA
*
65539 ATAAAAGAAAGATGTTCAA
1 ATAAAAGAAACATGTTCAA
65558 ATA
1 ATA
65561 CTTAACACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.61, C:0.07, G:0.10, T:0.22
Consensus pattern (19 bp):
ATAAAAGAAACATGTTCAA
Found at i:70524 original size:27 final size:28
Alignment explanation
Indices: 70493--70616 Score: 101
Period size: 32 Copynumber: 4.2 Consensus size: 28
70483 AATATTTTCA
*
70493 ATAAAA-TACTTAATAATAACAAAACCG
1 ATAAAATTACTGAATAATAACAAAACCG
*
70520 ATAAAATTTTACTAGACATATTAACAAAACCG
1 ATAAAA--TTACT-GA-ATAATAACAAAACCG
70552 ATAAAACTTTACTGAATATGATAACAAAACCG
1 ATAAAA--TTACTGAATA--ATAACAAAACCG
* *
70584 ACAAAA-TACCT-AATAATAACAAAATCG
1 ATAAAATTA-CTGAATAATAACAAAACCG
*
70611 ACAAAA
1 ATAAAA
70617 ATAATAATAT
Statistics
Matches: 83, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
27 23 0.28
29 6 0.07
30 9 0.11
31 3 0.04
32 42 0.51
ACGTcount: A:0.56, C:0.16, G:0.06, T:0.23
Consensus pattern (28 bp):
ATAAAATTACTGAATAATAACAAAACCG
Found at i:70550 original size:32 final size:31
Alignment explanation
Indices: 70499--70590 Score: 116
Period size: 32 Copynumber: 2.9 Consensus size: 31
70489 TTCAATAAAA
*
70499 TACTTAATA-ATAACAAAACCGATAAAATTT
1 TACTGAATATATAACAAAACCGATAAAATTT
*
70529 TACTAGACATAT-TAACAAAACCGATAAAACTT
1 TACT-GA-ATATATAACAAAACCGATAAAATTT
*
70561 TACTGAATATGATAACAAAACCGACAAAAT
1 TACTGAATAT-ATAACAAAACCGATAAAAT
70591 ACCTAATAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
30 8 0.15
31 3 0.06
32 42 0.79
ACGTcount: A:0.52, C:0.16, G:0.07, T:0.25
Consensus pattern (31 bp):
TACTGAATATATAACAAAACCGATAAAATTT
Found at i:75588 original size:14 final size:15
Alignment explanation
Indices: 75569--75597 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
75559 CCCCCTTTTT
75569 ATTATATAA-AAATA
1 ATTATATAATAAATA
75583 ATTATATAATAAATA
1 ATTATATAATAAATA
75598 GGAAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTATATAATAAATA
Found at i:78567 original size:20 final size:21
Alignment explanation
Indices: 78544--78582 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
78534 TTGAGATAAT
78544 ATTAAAATCTTA-AAAATTAA
1 ATTAAAATCTTATAAAATTAA
*
78564 ATTAAAATGTTATAAAATT
1 ATTAAAATCTTATAAAATT
78583 CTAAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
ATTAAAATCTTATAAAATTAA
Found at i:79664 original size:13 final size:13
Alignment explanation
Indices: 79646--79670 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
79636 AAATCAACTA
79646 TTAAATATTTAAT
1 TTAAATATTTAAT
79659 TTAAATATTTAA
1 TTAAATATTTAA
79671 AAAAATTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAAATATTTAAT
Found at i:84511 original size:32 final size:31
Alignment explanation
Indices: 84462--84564 Score: 118
Period size: 33 Copynumber: 3.2 Consensus size: 31
84452 TTTTTAACCG
84462 CTAACTTTGCTAACTTTTA-TTTATTTGTTCATA
1 CTAAC-TT-CTAACTTTTATTTTA-TTGTTCATA
84495 CTAACATTCTAACTTTTATTTTATTGTTCATA
1 CTAAC-TTCTAACTTTTATTTTATTGTTCATA
* * *
84527 CTAACTCACTAACATTTTATTTTATTGCTCAAA
1 CTAACT-TCTAAC-TTTTATTTTATTGTTCATA
84560 CTAAC
1 CTAAC
84565 CCGCTAATTC
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
31 1 0.02
32 29 0.46
33 33 0.52
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (31 bp):
CTAACTTCTAACTTTTATTTTATTGTTCATA
Found at i:84545 original size:33 final size:32
Alignment explanation
Indices: 84471--84564 Score: 120
Period size: 32 Copynumber: 2.9 Consensus size: 32
84461 GCTAACTTTG
*
84471 CTAACTTTTA-TTTATTTGTTCATACTAACATT
1 CTAACTTTTATTTTA-TTGTTCATACTAACATA
84503 CTAACTTTTATTTTATTGTTCATACTAAC-TCA
1 CTAACTTTTATTTTATTGTTCATACTAACAT-A
* *
84535 CTAACATTTTATTTTATTGCTCAAACTAAC
1 CTAAC-TTTTATTTTATTGTTCATACTAAC
84565 CCGCTAATTC
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
31 1 0.02
32 29 0.52
33 26 0.46
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.49
Consensus pattern (32 bp):
CTAACTTTTATTTTATTGTTCATACTAACATA
Found at i:88572 original size:24 final size:24
Alignment explanation
Indices: 88540--88595 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
88530 CTATTCTTTC
88540 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
88564 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
88588 GCTTCAAT
1 GCTTCAAT
88596 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Done.