Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000076.1 Hibiscus syriacus cultivar Beakdansim tig00000140_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: 82161
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:110 original size:13 final size:13
Alignment explanation
Indices: 92--117 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
82 GACTTTTCGA
92 TCAAAGTCAACGG
1 TCAAAGTCAACGG
105 TCAAAGTCAACGG
1 TCAAAGTCAACGG
118 GTTGACTCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (13 bp):
TCAAAGTCAACGG
Found at i:151 original size:29 final size:28
Alignment explanation
Indices: 115--183 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 28
105 TCAAAGTCAA
*
115 CGGGTTGACTCAGATGAGTTGACTCAATT
1 CGGGTTGACTCAGATGAGTTGACTC-AGT
*
144 CGGGTTGATTCAGATGAGTTGACTCAGT
1 CGGGTTGACTCAGATGAGTTGACTCAGT
172 CTGGGTTGACTC
1 C-GGGTTGACTC
184 GGTTAGGTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 3 0.08
29 33 0.92
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.32
Consensus pattern (28 bp):
CGGGTTGACTCAGATGAGTTGACTCAGT
Found at i:181 original size:15 final size:14
Alignment explanation
Indices: 116--183 Score: 66
Period size: 14 Copynumber: 4.7 Consensus size: 14
106 CAAAGTCAAC
116 GGGTTGACTCAGAT
1 GGGTTGACTCAGAT
*
130 GAGTTGACTCA-ATT
1 GGGTTGACTCAGA-T
*
144 CGGGTTGATTCAGAT
1 -GGGTTGACTCAGAT
* *
159 GAGTTGACTCAGTCT
1 GGGTTGACTCAG-AT
174 GGGTTGACTC
1 GGGTTGACTC
184 GGTTAGGTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
13 1 0.02
14 21 0.49
15 20 0.47
16 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.32
Consensus pattern (14 bp):
GGGTTGACTCAGAT
Found at i:7898 original size:21 final size:21
Alignment explanation
Indices: 7874--7926 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
7864 TCGGATTTCA
7874 ATCCGATCCGGATCGGTTTTT
1 ATCCGATCCGGATCGGTTTTT
7895 ATCCGATCCGGATCGGTTTTT
1 ATCCGATCCGGATCGGTTTTT
7916 ATCCGATCCGG
1 ATCCGATCCGG
7927 TTTTTTCCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.15, C:0.26, G:0.25, T:0.34
Consensus pattern (21 bp):
ATCCGATCCGGATCGGTTTTT
Found at i:8154 original size:32 final size:33
Alignment explanation
Indices: 8118--8226 Score: 170
Period size: 33 Copynumber: 3.4 Consensus size: 33
8108 ACAAAGTTTA
*
8118 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
*
8150 CGATAAATTAAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
*
8183 CGATAAATTCAAATACTTAAAAACTT-CAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
8215 CGAT-AATTGAAA
1 CGATAAATTGAAA
8227 CAAAGTTTAC
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
31 7 0.10
32 14 0.19
33 51 0.71
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (33 bp):
CGATAAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:8239 original size:21 final size:21
Alignment explanation
Indices: 8215--8256 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
8205 ACTTCAAGTT
*
8215 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAATTTA
*
8236 CGATAATTGAAATAAAATTTA
1 CGATAATTGAAACAAAATTTA
8257 AAAATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAATTTA
Found at i:25650 original size:19 final size:19
Alignment explanation
Indices: 25626--25662 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
25616 AATCCTAATC
*
25626 ATTAGGCTATAATTTAGGA
1 ATTAGGCTATAACTTAGGA
25645 ATTAGGCTATAACTTAGG
1 ATTAGGCTATAACTTAGG
25663 CAACTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (19 bp):
ATTAGGCTATAACTTAGGA
Found at i:25723 original size:74 final size:74
Alignment explanation
Indices: 25639--25787 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
25629 AGGCTATAAT
25639 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
1 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
25704 ATTTTGTAA
66 ATTTTGTAA
25713 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
1 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
25778 ATTTTGTAA
66 ATTTTGTAA
25787 T
1 T
25788 CTATCACTCT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (74 bp):
TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
ATTTTGTAA
Found at i:29898 original size:30 final size:30
Alignment explanation
Indices: 29841--30023 Score: 314
Period size: 30 Copynumber: 6.1 Consensus size: 30
29831 GAAGGACCTA
* * *
29841 TCCAGAGGTCACAAAGACCCT-GGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
29870 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
29900 TCCAGAGGTCATAAAGATCCTTGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
29930 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
29960 TCCAGATGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
29990 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
30020 TCCA
1 TCCA
30024 TATGTTCCTT
Statistics
Matches: 146, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
29 19 0.13
30 127 0.87
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:30054 original size:31 final size:30
Alignment explanation
Indices: 30012--30109 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 30
30002 AAAGATCCTC
*
30012 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* *
30042 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
*
30073 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
30105 GGTAA
1 GGTAA
30110 ACCCTCGACT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
30 6 0.11
31 25 0.44
32 25 0.44
33 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:34172 original size:30 final size:30
Alignment explanation
Indices: 34109--34291 Score: 314
Period size: 30 Copynumber: 6.1 Consensus size: 30
34099 GAAGGACCTA
* * * *
34109 TCCAGAGGTCACAAAGA-CCCCGATAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
34138 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
34168 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
34198 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
34228 TCCAGATGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
34258 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
34288 TCCA
1 TCCA
34292 TATGTTCCTT
Statistics
Matches: 147, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 16 0.11
30 131 0.89
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:34322 original size:31 final size:30
Alignment explanation
Indices: 34280--34377 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 30
34270 AAAGATCCTC
*
34280 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* *
34310 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
*
34341 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
34373 GGTAA
1 GGTAA
34378 ACCCTCGACT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
30 6 0.11
31 25 0.44
32 25 0.44
33 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:35299 original size:21 final size:21
Alignment explanation
Indices: 35275--35319 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35265 CTATGTTCGT
* * *
35275 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
35296 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
35317 TTG
1 TTG
35320 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:37074 original size:19 final size:19
Alignment explanation
Indices: 37050--37086 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
37040 AATCCTAATC
*
37050 ATTAGGCTATAATTTAGGA
1 ATTAGGCTATAACTTAGGA
37069 ATTAGGCTATAACTTAGG
1 ATTAGGCTATAACTTAGG
37087 CAACTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (19 bp):
ATTAGGCTATAACTTAGGA
Found at i:37147 original size:74 final size:74
Alignment explanation
Indices: 37063--37211 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
37053 AGGCTATAAT
37063 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
1 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
37128 ATTTTGTAA
66 ATTTTGTAA
37137 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
1 TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
37202 ATTTTGTAA
66 ATTTTGTAA
37211 T
1 T
37212 CTATCATGTA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (74 bp):
TTAGGAATTAGGCTATAACTTAGGCAACTAAATATACAATAGTAAATACAAAATATTTGGAGAAT
ATTTTGTAA
Found at i:40596 original size:2 final size:2
Alignment explanation
Indices: 40589--40626 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
40579 ACATGCATCC
40589 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
40627 TGGATACAGT
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):
AT
Found at i:41006 original size:22 final size:22
Alignment explanation
Indices: 40978--41040 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
40968 GTTCTTAAGG
*
40978 AGTGGTCCTTCGGGATATATAC
1 AGTGGTCCTTCGGGACATATAC
*
41000 AGTGGTCCTTTGGGACATATAC
1 AGTGGTCCTTCGGGACATATAC
* *
41022 AGTGGTCATTCGAGACATA
1 AGTGGTCCTTCGGGACATA
41041 GTGGTCATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACATATAC
Found at i:44497 original size:64 final size:64
Alignment explanation
Indices: 44421--44548 Score: 172
Period size: 64 Copynumber: 2.0 Consensus size: 64
44411 TAGTGCTTCA
* * *
44421 GTACACTGAGAGTGCATCGATGCATA-AATATGC-TTCGATGTTTTTAAAA-AGCCTGGGTGCAT
1 GTACACTAAGAGTGCATCGATGCATAGAACA--CATTCGATG-TTTTAAAATAGCCGGGGTGCAT
44483 CG
63 CG
*
44485 GTACACTAAGAGTGCATCGATGCATAGAGCACATTCGATGTTTTAAAATAGCCGGGGTGCATCG
1 GTACACTAAGAGTGCATCGATGCATAGAACACATTCGATGTTTTAAAATAGCCGGGGTGCATCG
44549 ATGCATGGCT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
63 9 0.16
64 46 0.81
65 2 0.04
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (64 bp):
GTACACTAAGAGTGCATCGATGCATAGAACACATTCGATGTTTTAAAATAGCCGGGGTGCATCG
Found at i:47270 original size:23 final size:23
Alignment explanation
Indices: 47240--47321 Score: 82
Period size: 23 Copynumber: 3.6 Consensus size: 23
47230 GCATGGCCTT
47240 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
47263 GTGCATCGGTGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
*
47285 -TGTATCGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
47307 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
47322 TTGTATAGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
20 1 0.02
21 13 0.28
22 3 0.06
23 17 0.36
24 13 0.28
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:47334 original size:45 final size:42
Alignment explanation
Indices: 47218--47339 Score: 122
Period size: 45 Copynumber: 2.8 Consensus size: 42
47208 AAAACCCGAC
* * *
47218 GGATGCATCGATGCA-TGGCCTTGTGCATCGATGCACATTCAA
1 GGATGCATCGATGCACTTG-CATGTGTATCGATGCACATTCAA
*
47260 GGAGTGCATCGGTGCATCTT-CATGATGTATCGATGCACATTCAAA
1 GGA-TGCATCGATGCA-CTTGCATG-TGTATCGATGCACATTC-AA
*
47305 GGGATGCATCGATGCACTTGTATAGTGTATCGATG
1 -GGATGCATCGATGCACTTGCAT-GTGTATCGATG
47340 TATTATGCAC
Statistics
Matches: 66, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
42 3 0.05
43 14 0.21
44 19 0.29
45 26 0.39
46 4 0.06
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.29
Consensus pattern (42 bp):
GGATGCATCGATGCACTTGCATGTGTATCGATGCACATTCAA
Found at i:51194 original size:22 final size:21
Alignment explanation
Indices: 51152--51191 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
51142 GAGAGTATTT
*
51152 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
51173 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
51192 ATAGTTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:54085 original size:173 final size:172
Alignment explanation
Indices: 53796--54135 Score: 479
Period size: 173 Copynumber: 2.0 Consensus size: 172
53786 TTTGGTTGTA
** * *
53796 GTTGCTTGTTGATTTCAGATAAATGCTTACACATTTATTTAAAATGAAATAATCCATTTGTCACA
1 GTTGCTTGTTGATTTCAGATAAATGAATACACATTTATTTAAAAAGAAATAATCAATTTGTCACA
* * *
53861 CTAAATGTATTTATTTTTATTTTTAAAATTATTTCATTCAAAATTTTCTATTAAAAAAGTTAACA
66 CTAAATATATCTATTTTTATTTTTAAAATTATCTCATTCAAAATTTTCTATTAAAAAAGTTAACA
*
53926 AACAACAACATT-T-AAATTTCATTTTTTATCCTTATATAACCTG
131 AACAAC-A-ATTCTAAAATTTCA-TTTTTACCCTTATATAACCTG
* ** * *
53969 GTTGCTTGTTGATTTCGGATAGTTGAATACACATTTATTTAAAAAGAAATACTCAATTTGTCCCA
1 GTTGCTTGTTGATTTCAGATAAATGAATACACATTTATTTAAAAAGAAATAATCAATTTGTCACA
* * *
54034 CTAAATATATCT-CTTTTATTTTTTAAAATTCTCTCATTCAAAATTTTCTATTAGAAAAGTTAAC
66 CTAAATATATCTATTTTTA-TTTTTAAAATTATCTCATTCAAAATTTTCTATTAAAAAAGTTAAC
54098 AAACAACAATTCTAAAATTTCATTTTTACCCTTATATA
130 AAACAACAATTCTAAAATTTCATTTTTACCCTTATATA
54136 TCCCACTATT
Statistics
Matches: 148, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
171 3 0.02
172 22 0.15
173 123 0.83
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (172 bp):
GTTGCTTGTTGATTTCAGATAAATGAATACACATTTATTTAAAAAGAAATAATCAATTTGTCACA
CTAAATATATCTATTTTTATTTTTAAAATTATCTCATTCAAAATTTTCTATTAAAAAAGTTAACA
AACAACAATTCTAAAATTTCATTTTTACCCTTATATAACCTG
Found at i:67465 original size:19 final size:19
Alignment explanation
Indices: 67441--67487 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
67431 CAATTGGTGT
67441 ATCGATGCATAAGG-AGTGC
1 ATCGATGCAT-AGGTAGTGC
*
67460 ATCGATGCATGGGTAGTGC
1 ATCGATGCATAGGTAGTGC
67479 ATCGATGCA
1 ATCGATGCA
67488 CATGTTAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 2 0.08
19 24 0.92
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (19 bp):
ATCGATGCATAGGTAGTGC
Found at i:67521 original size:20 final size:20
Alignment explanation
Indices: 67457--67548 Score: 107
Period size: 20 Copynumber: 4.5 Consensus size: 20
67447 GCATAAGGAG
*
67457 TGCATCGATGCATGGGTAG--
1 TGCATCGATGCAT-TGTAGAA
*
67476 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCA-TTG-T--AGAA
67500 TGCATCGATGCATTGTAGAA
1 TGCATCGATGCATTGTAGAA
67520 TGCATCGATGCATTGTAGAA
1 TGCATCGATGCATTGTAGAA
67540 TGCATCGAT
1 TGCATCGAT
67549 ACACTTCAAG
Statistics
Matches: 64, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
19 13 0.20
20 34 0.53
22 3 0.05
23 2 0.03
24 12 0.19
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCATTGTAGAA
Found at i:71614 original size:48 final size:48
Alignment explanation
Indices: 71539--71732 Score: 223
Period size: 48 Copynumber: 4.1 Consensus size: 48
71529 TGGTCCTCTA
*
71539 CCTTTTTCTGGATTTTTAACAGATTTGGTAGGAGGTTCTGCTCCTTTT
1 CCTTTGTCTGGATTTTTAACAGATTTGGTAGGAGGTTCTGCTCCTTTT
* * * * **
71587 CCTTTGTCTGGATTTTTGACAGTTTTGGTTGGAGTTTCTGCTCCTCCT
1 CCTTTGTCTGGATTTTTAACAGATTTGGTAGGAGGTTCTGCTCCTTTT
* * * *
71635 CCTTTGTCTGGATTTTTAACAGATTTGGTTGGAGGTTCCGTTCCTTTG
1 CCTTTGTCTGGATTTTTAACAGATTTGGTAGGAGGTTCTGCTCCTTTT
* * * **
71683 CTTTTTTCTGGATTTTTAACAGTTTTGG-A--AGGTTCTATTCCTTTT
1 CCTTTGTCTGGATTTTTAACAGATTTGGTAGGAGGTTCTGCTCCTTTT
71728 CCTTT
1 CCTTT
71733 ATCCGATGAG
Statistics
Matches: 123, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
45 17 0.14
48 106 0.86
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.49
Consensus pattern (48 bp):
CCTTTGTCTGGATTTTTAACAGATTTGGTAGGAGGTTCTGCTCCTTTT
Done.