Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004661.1 Hibiscus syriacus cultivar Beakdansim tig00010453_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: 67352
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:8793 original size:20 final size:20
Alignment explanation
Indices: 8768--8819 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
8758 TCAATGGAAA
8768 TGGTATCGATACCATACTCT
1 TGGTATCGATACCATACTCT
*
8788 TGGTATCGGTACCATACTCT
1 TGGTATCGATACCATACTCT
*
8808 TTGTATCGATAC
1 TGGTATCGATAC
8820 TACCAATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (20 bp):
TGGTATCGATACCATACTCT
Found at i:12324 original size:22 final size:22
Alignment explanation
Indices: 12298--12343 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
12288 CTGTTTCTTT
*
12298 TAATAAACTAATTTTTGAAA-AA
1 TAATAAA-TAATTTTTCAAACAA
*
12320 TAATAAATCATTTTTCAAACAA
1 TAATAAATAATTTTTCAAACAA
12342 TA
1 TA
12344 CAATAGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37
Consensus pattern (22 bp):
TAATAAATAATTTTTCAAACAA
Found at i:13231 original size:12 final size:13
Alignment explanation
Indices: 13209--13241 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
13199 GACAATGATG
13209 GGGGAAGGAGG-AA
1 GGGG-AGGAGGAAA
13222 GGGGAGGAGGAAA
1 GGGGAGGAGGAAA
13235 GGGGAGG
1 GGGGAGG
13242 CAGAACCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (13 bp):
GGGGAGGAGGAAA
Found at i:15727 original size:21 final size:19
Alignment explanation
Indices: 15697--15736 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
15687 TTCACCACAC
*
15697 TCTTCTTATCTTCTTCTTCCT
1 TCTTCATATC-TCTT-TTCCT
15718 TCTTCATATCTCTTTTCCT
1 TCTTCATATCTCTTTTCCT
15737 CTCCAAGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.60
Consensus pattern (19 bp):
TCTTCATATCTCTTTTCCT
Found at i:17742 original size:16 final size:17
Alignment explanation
Indices: 17717--17752 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
17707 CCGATGTGTC
17717 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
17733 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
17750 ACA
1 ACA
17753 ATTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.36
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:23424 original size:21 final size:21
Alignment explanation
Indices: 23381--23465 Score: 91
Period size: 21 Copynumber: 4.1 Consensus size: 21
23371 GGCACATAGA
** *
23381 ATTTGTCTTGAATGACC-TAT
1 ATTTGTCCCGAATGACCACAT
* *
23401 ATTTGTCCCGGATGACCATAT
1 ATTTGTCCCGAATGACCACAT
* * *
23422 ATTTATCCCAAAGGACCACAT
1 ATTTGTCCCGAATGACCACAT
23443 ATTTGTCCCGAATGACCACAT
1 ATTTGTCCCGAATGACCACAT
23464 AT
1 AT
23466 AACCCTCAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
20 14 0.26
21 39 0.74
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (21 bp):
ATTTGTCCCGAATGACCACAT
Found at i:25947 original size:17 final size:17
Alignment explanation
Indices: 25927--25964 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
25917 GGAAGTCAAC
*
25927 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
25944 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
25961 GGTC
1 GGTC
25965 GGGTCAGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:25977 original size:19 final size:19
Alignment explanation
Indices: 25934--25990 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 19
25924 AACGGTCAAC
*
25934 GGTCGGGTCGGGTCAACAGTCG
1 GGTCGGGTCGGGT---CAGTAG
25956 GGTCGGGTCGGGTCAGTAG
1 GGTCGGGTCGGGTCAGTAG
25975 GGTCGGGTCGGGTCAG
1 GGTCGGGTCGGGTCAG
25991 ACCGGTCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 21 0.62
22 13 0.38
ACGTcount: A:0.11, C:0.19, G:0.51, T:0.19
Consensus pattern (19 bp):
GGTCGGGTCGGGTCAGTAG
Found at i:25997 original size:19 final size:19
Alignment explanation
Indices: 25933--25997 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
25923 CAACGGTCAA
25933 CGGTCGGGTCGGGTCA-AC
1 CGGTCGGGTCGGGTCAGAC
25951 AGTCGGGTCGGGTCGGGTCAGTA-
1 ---C-GGTCGGGTCGGGTCAG-AC
*
25974 GGGTCGGGTCGGGTCAGAC
1 CGGTCGGGTCGGGTCAGAC
25993 CGGTC
1 CGGTC
25998 AAACCGGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 1 0.03
19 20 0.53
21 1 0.03
22 15 0.39
24 1 0.03
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (19 bp):
CGGTCGGGTCGGGTCAGAC
Found at i:33100 original size:17 final size:17
Alignment explanation
Indices: 33078--33111 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
33068 GTCAACGGTT
33078 AACGGTCGGGTCAGGTC
1 AACGGTCGGGTCAGGTC
*
33095 AACGGTCGGGTCTGGTC
1 AACGGTCGGGTCAGGTC
33112 GGGTCGGGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.24, G:0.41, T:0.21
Consensus pattern (17 bp):
AACGGTCGGGTCAGGTC
Found at i:33141 original size:9 final size:9
Alignment explanation
Indices: 33123--33200 Score: 75
Period size: 9 Copynumber: 8.3 Consensus size: 9
33113 GGTCGGGTCG
*
33123 GGTCAGACC
1 GGTCAAACC
33132 GGTCAAACC
1 GGTCAAACC
*
33141 GGTTCAGACC
1 GG-TCAAACC
*
33151 GGTCAAACG
1 GGTCAAACC
*
33160 GGTTCGAACC
1 GG-TCAAACC
*
33170 GGTCGGAACC
1 GGTC-AAACC
33180 GGTCAAACC
1 GGTCAAACC
*
33189 GATCAAACC
1 GGTCAAACC
33198 GGT
1 GGT
33201 TTTCCAGCAG
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
9 33 0.58
10 24 0.42
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:33147 original size:19 final size:19
Alignment explanation
Indices: 33125--33201 Score: 86
Period size: 19 Copynumber: 4.1 Consensus size: 19
33115 TCGGGTCGGG
33125 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
33144 TCAGACCGGTCAAACGGGT
1 TCAGACCGGTCAAACCGGT
*
33163 TC-GAACCGGTCGGAACCGG-
1 TCAG-ACCGGTC-AAACCGGT
* *
33182 TCAAACCGATCAAACCGGT
1 TCAGACCGGTCAAACCGGT
33201 T
1 T
33202 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
18 7 0.15
19 36 0.75
20 5 0.10
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:39032 original size:73 final size:74
Alignment explanation
Indices: 38935--39111 Score: 225
Period size: 73 Copynumber: 2.4 Consensus size: 74
38925 AATCTTCTTC
*** *
38935 ATCAAATTTTTCAATATATAAAAGTATCGATCATCATTGCATAAGTATCAATATTTTAAATTTTG
1 ATCAAATTTTTCAATATATAAAAGTATCGATCATCACCACATAAGTATCAATATTCTAAATTTTG
39000 ATATTT-T-T
66 AT-TTTATCT
* * * *
39008 ATCAATTTTTTCAATATTTAAAAGTATCGATCATTACCACATAAGTATCGATATTCTAAATTTTG
1 ATCAAATTTTTCAATATATAAAAGTATCGATCATCACCACATAAGTATCAATATTCTAAATTTTG
39073 ATTTTATCT
66 ATTTTATCT
* * *
39082 -TCAACTTTTTCAATATCTAAAAGTGTCGAT
1 ATCAAATTTTTCAATATATAAAAGTATCGAT
39112 ATTTAAAATT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
72 3 0.03
73 87 0.96
74 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.44
Consensus pattern (74 bp):
ATCAAATTTTTCAATATATAAAAGTATCGATCATCACCACATAAGTATCAATATTCTAAATTTTG
ATTTTATCT
Found at i:39968 original size:185 final size:184
Alignment explanation
Indices: 39295--40022 Score: 807
Period size: 185 Copynumber: 3.9 Consensus size: 184
39285 CACAATATAT
* * * *
39295 TAATAAAAATATTAATGTTTCA-ATTCGTAACCTACTTTCTTAGTGAACCATGACAATCTTAGGC
1 TAATAAAAATATTAATATTACATA-TCGCAACCTACTTTCTTAGTGAACCATGACATTCTTAGGC
* * * *
39359 CCAATCGTATTTATTGTAGATATTCATAACATTTTTAAGCTTTTAACTTATTTTGTTATCGTGGG
65 GCAACCGTATTTATTATAGATATTCATAACATTTTCAA-CTTTTAACTTATTTTGTTATCGTGGG
* * * * * *
39424 AAAATCTAAGGCTCCATCAGCTTAAATTATGGTAACAGTTTAGGCACAACTCATTTTA
129 AAAATCTAAGCCT-CATCAGCTTAAACTCTAGTAACATTTTAGGCGCAACT-ATTTTA
* * * * * *
39482 TCAATAAAAATATTAATATTTCATATCGTAACCTACATTCTTAGTTAACCATGACATTATTAGAC
1 T-AATAAAAATATTAATATTACATATCGCAACCTACTTTCTTAGTGAACCATGACATTCTTAGGC
*
39547 GCAACCGTATTTATTATAGATATTCATAACATTTTCAGCTTTTAACTT-TTTTGTTATCGTGGGA
65 GCAACCGTATTTATTATAGATATTCATAACATTTTCAACTTTTAACTTATTTTGTTATCGTGGGA
* * * * * *
39611 AAATTTAAGTCTCTATTAGCTTAGACTCTAGTAACATTTTAGGTG-AACCCATTTTA
130 AAATCTAAGCCTC-ATCAGCTTAAACTCTAGTAACATTTTAGGCGCAA-CTATTTTA
** * * * *
39667 TAATAAAAATATTCGTATTCCATATCGCAACCTACTTTCTTAGTGAATCATGATATTCTTGGGCG
1 TAATAAAAATATTAATATTACATATCGCAACCTACTTTCTTAGTGAACCATGACATTCTTAGGCG
* * * * * * *
39732 CAACCGTATTTATTATAGATATACATATCATTTTTAACTATTAACTTATTTTCTTATCATGGGAT
66 CAACCGTATTTATTATAGATATTCATAACATTTTCAACTTTTAACTTATTTTGTTATCGTGGGAA
** * *
39797 TGTCTAAGCCTCATCAACTTAAACTCTGGTAACATTTTAGGCGCAATCTATTTTA
131 AATCTAAGCCTCATCAGCTTAAACTCTAGTAACATTTTAGGCGCAA-CTATTTTA
* * * *
39852 CTAATAAATATATTAACATTACATATCGCAACCTA-TTTCTCAGTGAACCATGACATTCTTGGGC
1 -TAATAAAAATATTAATATTACATATCGCAACCTACTTTCTTAGTGAACCATGACATTCTTAGGC
** * * * * *
39916 GCAACCACATTTCTTATATATATTCATAACATTTTCAACTTTTAAATTATTTTTTTATCGTAGGA
65 GCAACCGTATTTATTATAGATATTCATAACATTTTCAACTTTTAACTTATTTTGTTATCGTGGGA
** * *
39981 ATGTCTAAGGCCCCATTAGCTTAAACTCTAGTAACATTTTAG
130 AAATCTAA-GCCTCATCAGCTTAAACTCTAGTAACATTTTAG
40023 ACACAACCTA
Statistics
Matches: 456, Mismatches: 77, Indels: 17
0.83 0.14 0.03
Matches are distributed among these distances:
184 121 0.27
185 127 0.28
186 108 0.24
187 11 0.02
188 88 0.19
189 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.39
Consensus pattern (184 bp):
TAATAAAAATATTAATATTACATATCGCAACCTACTTTCTTAGTGAACCATGACATTCTTAGGCG
CAACCGTATTTATTATAGATATTCATAACATTTTCAACTTTTAACTTATTTTGTTATCGTGGGAA
AATCTAAGCCTCATCAGCTTAAACTCTAGTAACATTTTAGGCGCAACTATTTTA
Found at i:40009 original size:186 final size:185
Alignment explanation
Indices: 39295--40022 Score: 809
Period size: 184 Copynumber: 3.9 Consensus size: 185
39285 CACAATATAT
* * * *
39295 TAATAAAAATATTAATGTTTCA-ATTCGTAACCTACTTTCTTAGTGAACCATGACAATCTTAGGC
1 TAATAAAAATATTAATATTACATA-TCGCAACCTACTTTCTTAGTGAACCATGACATTCTTAGGC
* * * *
39359 CCAATCGTATTTATTGTAGATATTCATAACATTTTTAAGCTTTTAACTTATTTTGTTATCGTGGG
65 GCAACCGTATTTATTATAGATATTCATAACATTTTCAA-CTTTTAACTTATTTTGTTATCGTGGG
* * * * * *
39424 AAAATCTAAGGCTCCATCAGCTTAAATTATGGTAACAGTTTAGGCACAACTCATTTTA
129 AAAATCTAAGGCCCCATCAGCTTAAACTCTAGTAACATTTTAGGCGCAACT-ATTTTA
* * * * * *
39482 TCAATAAAAATATTAATATTTCATATCGTAACCTACATTCTTAGTTAACCATGACATTATTAGAC
1 T-AATAAAAATATTAATATTACATATCGCAACCTACTTTCTTAGTGAACCATGACATTCTTAGGC
*
39547 GCAACCGTATTTATTATAGATATTCATAACATTTTCAGCTTTTAACTT-TTTTGTTATCGTGGGA
65 GCAACCGTATTTATTATAGATATTCATAACATTTTCAACTTTTAACTTATTTTGTTATCGTGGGA
* * * * * * * *
39611 AAATTTAAGTCTCTATTAGCTTAGACTCTAGTAACATTTTAGGTG-AACCCATTTTA
130 AAATCTAAGGCCCCATCAGCTTAAACTCTAGTAACATTTTAGGCGCAA-CTATTTTA
** * * * *
39667 TAATAAAAATATTCGTATTCCATATCGCAACCTACTTTCTTAGTGAATCATGATATTCTTGGGCG
1 TAATAAAAATATTAATATTACATATCGCAACCTACTTTCTTAGTGAACCATGACATTCTTAGGCG
* * * * * * *
39732 CAACCGTATTTATTATAGATATACATATCATTTTTAACTATTAACTTATTTTCTTATCATGGGAT
66 CAACCGTATTTATTATAGATATTCATAACATTTTCAACTTTTAACTTATTTTGTTATCGTGGGAA
** * * *
39797 TGTCTAA-GCCTCATCAACTTAAACTCTGGTAACATTTTAGGCGCAATCTATTTTA
131 AATCTAAGGCCCCATCAGCTTAAACTCTAGTAACATTTTAGGCGCAA-CTATTTTA
* * * *
39852 CTAATAAATATATTAACATTACATATCGCAACCTA-TTTCTCAGTGAACCATGACATTCTTGGGC
1 -TAATAAAAATATTAATATTACATATCGCAACCTACTTTCTTAGTGAACCATGACATTCTTAGGC
** * * * * *
39916 GCAACCACATTTCTTATATATATTCATAACATTTTCAACTTTTAAATTATTTTTTTATCGTAGGA
65 GCAACCGTATTTATTATAGATATTCATAACATTTTCAACTTTTAACTTATTTTGTTATCGTGGGA
** *
39981 ATGTCTAAGGCCCCATTAGCTTAAACTCTAGTAACATTTTAG
130 AAATCTAAGGCCCCATCAGCTTAAACTCTAGTAACATTTTAG
40023 ACACAACCTA
Statistics
Matches: 453, Mismatches: 81, Indels: 15
0.83 0.15 0.03
Matches are distributed among these distances:
184 122 0.27
185 122 0.27
186 109 0.24
187 11 0.02
188 88 0.19
189 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.39
Consensus pattern (185 bp):
TAATAAAAATATTAATATTACATATCGCAACCTACTTTCTTAGTGAACCATGACATTCTTAGGCG
CAACCGTATTTATTATAGATATTCATAACATTTTCAACTTTTAACTTATTTTGTTATCGTGGGAA
AATCTAAGGCCCCATCAGCTTAAACTCTAGTAACATTTTAGGCGCAACTATTTTA
Found at i:46113 original size:21 final size:20
Alignment explanation
Indices: 46089--46129 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
46079 ATTTTACTAT
46089 ATATACATATTTATTTATTTA
1 ATATACATA-TTATTTATTTA
*
46110 ATATATATATTATTTATTTA
1 ATATACATATTATTTATTTA
46130 TTTTTCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATACATATTATTTATTTA
Found at i:46123 original size:24 final size:25
Alignment explanation
Indices: 46081--46132 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
46071 TATATTATAT
*
46081 TTTACTATATATACATATTTATTTA
1 TTTAATATATATACATATTTATTTA
*
46106 TTTAATATATATA-TTATTTATTTA
1 TTTAATATATATACATATTTATTTA
46130 TTT
1 TTT
46133 TTCCTTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTAATATATATACATATTTATTTA
Found at i:46156 original size:12 final size:12
Alignment explanation
Indices: 46126--46157 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
46116 ATATTATTTA
46126 TTTATTTTTCCT
1 TTTATTTTTCCT
46138 TTCTATTTTTCCT
1 TT-TATTTTTCCT
46151 TTTATTT
1 TTTATTT
46158 ATTTATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTATTTTTCCT
Found at i:46231 original size:2 final size:2
Alignment explanation
Indices: 46226--46263 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
46216 TTATCGTTAT
46226 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
46264 CATTATACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46329 original size:19 final size:19
Alignment explanation
Indices: 46288--46330 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
46278 TTGCATTATC
*
46288 TTTATGTATATTATATTTA
1 TTTATGTATATTACATTTA
46307 TTTATGTATATTACCATTT-
1 TTTATGTATATTA-CATTTA
46326 TTTAT
1 TTTAT
46331 ATCATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTATGTATATTACATTTA
Found at i:54014 original size:27 final size:27
Alignment explanation
Indices: 53976--54030 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
53966 CTACGACATG
53976 CTGCAATATATCAAGCATCGAAGTTAT
1 CTGCAATATATCAAGCATCGAAGTTAT
54003 CTGCAATATATCAAGCATCGAAGTTAT
1 CTGCAATATATCAAGCATCGAAGTTAT
54030 C
1 C
54031 CAGAGGAAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (27 bp):
CTGCAATATATCAAGCATCGAAGTTAT
Found at i:55335 original size:7 final size:6
Alignment explanation
Indices: 55304--55345 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
55294 GCCCTAAATT
55304 GAAAAA GAAAAA GAAAAA -AGAAAA GAGAAAA G-AAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GA-AAAA GA-AAAA GAAAAA GAAAAA
55346 TAAGGTGGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 6 0.18
6 20 0.61
7 7 0.21
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:56382 original size:42 final size:43
Alignment explanation
Indices: 56269--56392 Score: 135
Period size: 42 Copynumber: 2.9 Consensus size: 43
56259 CGAATGGGCC
* * * * *
56269 ATCCACGATTTTAACTCCATAACGAAGGATATCGTACCCACAC
1 ATCCACGATTTCAACTTCACAACGAAGGATATCGTGCCCACAA
* * * *
56312 ATCTATGATTTCAAC-TCACGACGGAGGATATCGTGCCCACAA
1 ATCCACGATTTCAACTTCACAACGAAGGATATCGTGCCCACAA
* *
56354 ATCCACG-TTTCAACTTCACAATGAAGGATATCATGCCCA
1 ATCCACGATTTCAACTTCACAACGAAGGATATCGTGCCCA
56393 TCTACACAAG
Statistics
Matches: 65, Mismatches: 15, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
41 7 0.11
42 46 0.71
43 12 0.18
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (43 bp):
ATCCACGATTTCAACTTCACAACGAAGGATATCGTGCCCACAA
Found at i:58420 original size:22 final size:21
Alignment explanation
Indices: 58366--58421 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
58356 TTCTCAGTTT
* *
58366 TATATTATATTTTACTATATA
1 TATATTATTTTTTAATATATA
* *
58387 CATATTTTTTTTTTAATATATA
1 TATA-TTATTTTTTAATATATA
58409 TATATATATTTTT
1 TATAT-TATTTTT
58422 ATTTTTTATT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATTATTTTTTAATATATA
Found at i:58697 original size:24 final size:24
Alignment explanation
Indices: 58657--58720 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
58647 CTATACTTTG
* *
58657 TTTATTTATTTCGTTTTTCTTGTA
1 TTTATTTATTTCCTTTTTATTGTA
*
58681 TTTATTT-TCTTCCTTTTTATTTTA
1 TTTATTTAT-TTCCTTTTTATTGTA
58705 TTTATTTATTTTCCTT
1 TTTATTTA-TTTCCTT
58721 ATTTTTATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 1 0.03
24 26 0.76
25 6 0.18
26 1 0.03
ACGTcount: A:0.12, C:0.11, G:0.03, T:0.73
Consensus pattern (24 bp):
TTTATTTATTTCCTTTTTATTGTA
Found at i:65120 original size:23 final size:22
Alignment explanation
Indices: 65078--65159 Score: 96
Period size: 22 Copynumber: 3.8 Consensus size: 22
65068 TTAGTGCAGA
*
65078 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
65100 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
* *
65123 GGGAACCAATA-CCCC-TGTAG
1 GGGAACCGATACCCCCTTGAAG
*
65143 GGGAATCGATACCCCCT
1 GGGAACCGATACCCCCT
65160 GGGGTTCTAG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 13 0.26
21 4 0.08
22 18 0.36
23 15 0.30
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.18
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:66699 original size:18 final size:19
Alignment explanation
Indices: 66685--66722 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
66675 GATGAACCAG
66685 AACAGCACGAGGAACAAGC
1 AACAGCACGAGGAACAAGC
*
66704 AATAGCA-GAGGAACAAGC
1 AACAGCACGAGGAACAAGC
66722 A
1 A
66723 CACCAAGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.50, C:0.21, G:0.26, T:0.03
Consensus pattern (19 bp):
AACAGCACGAGGAACAAGC
Done.