Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001363.1 Hibiscus syriacus cultivar Beakdansim tig00002656_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: 70063
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:3471 original size:12 final size:12
Alignment explanation
Indices: 3454--3487 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
3444 CACCCCCACA
3454 CCAGATTGGCTT
1 CCAGATTGGCTT
*
3466 CCAGATTGGTTT
1 CCAGATTGGCTT
3478 CCAGATTGGC
1 CCAGATTGGC
3488 CTTCAGTCGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (12 bp):
CCAGATTGGCTT
Found at i:4762 original size:33 final size:32
Alignment explanation
Indices: 4719--4781 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
4709 AGGTATAAAC
4719 TTTTTTCACAAATAGCAGAGCATAAGTATCAA
1 TTTTTTCACAAATAGCAGAGCATAAGTATCAA
* *
4751 TTTTTTCCACAAATATCATAGCATAAGTATC
1 TTTTTT-CACAAATAGCAGAGCATAAGTATC
4782 GATATAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 6 0.21
33 22 0.79
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (32 bp):
TTTTTTCACAAATAGCAGAGCATAAGTATCAA
Found at i:5839 original size:183 final size:180
Alignment explanation
Indices: 5483--5885 Score: 452
Period size: 186 Copynumber: 2.2 Consensus size: 180
5473 CTAAAGCTCT
* * ** *
5483 ATCAGCTTAAATTCTGGTAACATTTTAGGCTCAACCCACTTTATTTGTAAAATATTAATGTTCTA
1 ATCAGCTTAAATTCTGGTAATATTTTAGGCGCAACCCACTTTATTAATAAAATATTAATGTTCCA
* * * * * * **
5548 GATCACAACTTACTTTTTTAGTGAATCATGATATTCTTGGGCGCAATTTTATTTATTATAGATAT
66 GATAACAACCTAATTTCTTAGTGAAACATGATATTCTTGGACGCAATCGTATTTATTATAGATAT
* * **
5613 TCATAATATTTTTAACTTTTATCTTATTTTGTTATCTTGAGAAAATTTAAGGTTCC
131 TC---A-ATTTTTAACTTTTAGCTTATTTTGTTATCGTGAGAAAA--TAAGGCACC
* * *
5669 ATCAGCTTAAATTCTGGTAATA-TTTAGGCGCAACTCATTTTATTAATAAAAATTTTAACT-TTC
1 ATCAGCTTAAATTCTGGTAATATTTTAGGCGCAACCCACTTTATTAAT-AAAATATTAA-TGTTC
* *
5732 CATATAACAACCTAATTTCTTAGTGAACCACATGATATTCTTGGACGCAATCGTATTTATTATAT
64 CAGATAACAACCTAATTTCTTAGTGAA--ACATGATATTCTTGGACGCAATCGTATTTATTATAG
* *
5797 ATATTC-ATTTTTAACTTTTAGCTTATTTTGTTATCGTGAGAAAATCAGGCAGC
127 ATATTCAATTTTTAACTTTTAGCTTATTTTGTTATCGTGAGAAAATAAGGCACC
* **
5850 ATCAGCTTAAAATCTAATAATATTTTAGGCGCAACC
1 ATCAGCTTAAATTCTGGTAATATTTTAGGCGCAACC
5886 TAAAATTTTA
Statistics
Matches: 184, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
181 24 0.13
182 12 0.07
183 36 0.20
185 20 0.11
186 54 0.29
187 1 0.01
188 37 0.20
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (180 bp):
ATCAGCTTAAATTCTGGTAATATTTTAGGCGCAACCCACTTTATTAATAAAATATTAATGTTCCA
GATAACAACCTAATTTCTTAGTGAAACATGATATTCTTGGACGCAATCGTATTTATTATAGATAT
TCAATTTTTAACTTTTAGCTTATTTTGTTATCGTGAGAAAATAAGGCACC
Found at i:6300 original size:10 final size:10
Alignment explanation
Indices: 6285--6315 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
6275 ATGTTAAGCT
*
6285 AGTCTGTTGG
1 AGTCTGTTAG
6295 AGTCTGTTAG
1 AGTCTGTTAG
6305 AGTCTGTTAG
1 AGTCTGTTAG
6315 A
1 A
6316 TTGCAGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.19, C:0.10, G:0.32, T:0.39
Consensus pattern (10 bp):
AGTCTGTTAG
Found at i:12163 original size:34 final size:34
Alignment explanation
Indices: 12102--12167 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
12092 TCAGTTCCAT
**
12102 CGAGCAAACGTTCCAGTCGTCGTCGAGCCACCGA
1 CGAGCAAACGTTCCAGTCGTCACCGAGCCACCGA
* * *
12136 CGAGCCAACGTTCCAGTCTTTACCGAGCCACC
1 CGAGCAAACGTTCCAGTCGTCACCGAGCCACC
12168 ATCGTCATCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.17
Consensus pattern (34 bp):
CGAGCAAACGTTCCAGTCGTCACCGAGCCACCGA
Found at i:12311 original size:14 final size:14
Alignment explanation
Indices: 12275--12326 Score: 63
Period size: 13 Copynumber: 3.8 Consensus size: 14
12265 CCATTAAAAA
*
12275 ACTAAACCCAAAT-C
1 ACTAAA-CCTAATCC
12289 ACTAAACCTAATCC
1 ACTAAACCTAATCC
*
12303 ACTAAACCT-ACCC
1 ACTAAACCTAATCC
12316 ACTAAACCTAA
1 ACTAAACCTAA
12327 AAAACATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 17 0.50
14 17 0.50
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACTAAACCTAATCC
Found at i:13208 original size:30 final size:30
Alignment explanation
Indices: 13174--13287 Score: 104
Period size: 30 Copynumber: 3.8 Consensus size: 30
13164 TAAAACTTAA
*
13174 AAATTTATGTTTTTGCCATTTTAGTCTTTT
1 AAATTTATGTTTGTGCCATTTTAGTCTTTT
** * *
13204 AAATTTCAT-TTTGTGATATTTTGGTCTTTA
1 AAATTT-ATGTTTGTGCCATTTTAGTCTTTT
* * * ** *
13234 AAATTTATATTTTTACTGTTTTAGACTTTT
1 AAATTTATGTTTGTGCCATTTTAGTCTTTT
*
13264 AAATTTCTGTTTGTGCCATTTTAG
1 AAATTTATGTTTGTGCCATTTTAG
13288 CCCTTTTGTT
Statistics
Matches: 64, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
29 2 0.03
30 60 0.94
31 2 0.03
ACGTcount: A:0.23, C:0.09, G:0.11, T:0.57
Consensus pattern (30 bp):
AAATTTATGTTTGTGCCATTTTAGTCTTTT
Found at i:13285 original size:60 final size:60
Alignment explanation
Indices: 13173--13285 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
13163 TTAAAACTTA
* * * *
13173 AAAATTTATGTTTTTGCCATTTTAGTCTTTTAAATTTCATTTTGTGATATTTTGGTCTTT
1 AAAATTTATATTTTTACCATTTTAGACTTTTAAATTTCATTTTGTGACATTTTGGTCTTT
** *
13233 AAAATTTATATTTTTACTGTTTTAGACTTTTAAATTTC-TGTTTGTGCCATTTT
1 AAAATTTATATTTTTACCATTTTAGACTTTTAAATTTCAT-TTTGTGACATTTT
13286 AGCCCTTTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
59 1 0.02
60 44 0.98
ACGTcount: A:0.23, C:0.09, G:0.11, T:0.58
Consensus pattern (60 bp):
AAAATTTATATTTTTACCATTTTAGACTTTTAAATTTCATTTTGTGACATTTTGGTCTTT
Found at i:19232 original size:32 final size:33
Alignment explanation
Indices: 19196--19258 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
19186 ATTCTGAAAT
* * *
19196 TGTTTCACTTGAAATAA-AATCATCTTTGAGTC
1 TGTTTCACTGGAAACAACAACCATCTTTGAGTC
19228 TGTTTCACTGGAAACAACAACCATCTTTGAG
1 TGTTTCACTGGAAACAACAACCATCTTTGAG
19259 ATTGTTCCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (33 bp):
TGTTTCACTGGAAACAACAACCATCTTTGAGTC
Found at i:19275 original size:33 final size:32
Alignment explanation
Indices: 19194--19278 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 32
19184 AAATTCTGAA
* *
19194 ATTGTTTCACTTGAAATAAAATCATCTTTGAG
1 ATTGTTTCACTTGAAACAAAACCATCTTTGAG
*
19226 -TCTGTTTCACTGGAAACAACAACCATCTTTGAG
1 AT-TGTTTCACTTGAAACAA-AACCATCTTTGAG
* *
19259 ATTGTTCCTCTTGAAACAAA
1 ATTGTTTCACTTGAAACAAA
19279 TCTTATTTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
31 1 0.02
32 16 0.36
33 26 0.59
34 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (32 bp):
ATTGTTTCACTTGAAACAAAACCATCTTTGAG
Found at i:19467 original size:33 final size:34
Alignment explanation
Indices: 19386--19494 Score: 118
Period size: 33 Copynumber: 3.3 Consensus size: 34
19376 GAAATACCCT
*
19386 TCTTTGAGTCTGTTTCCCTTGAAACAAAACAAACA
1 TCTTTGAGTTTGTTTCCCTTGAAAC-AAACAAACA
**
19421 TCTTTGA-TATTGTTTCCCTTGAAACAAATTAA-A
1 TCTTTGAGT-TTGTTTCCCTTGAAACAAACAAACA
* * *
19454 TCTTTAAGTTTGTTTCTCTTGAAAC-AA-AACCA
1 TCTTTGAGTTTGTTTCCCTTGAAACAAACAAACA
19486 TCTTTGAGT
1 TCTTTGAGT
19495 CATTCCCTTG
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
31 1 0.02
32 11 0.17
33 22 0.35
34 7 0.11
35 22 0.35
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.39
Consensus pattern (34 bp):
TCTTTGAGTTTGTTTCCCTTGAAACAAACAAACA
Found at i:19697 original size:43 final size:43
Alignment explanation
Indices: 19639--19833 Score: 184
Period size: 43 Copynumber: 4.5 Consensus size: 43
19629 TGACTTGAGC
* * *
19639 TCCTCATCACGTAGGAGCCGTGTCAACCCTAGATAACCGGTTG
1 TCCTCATCACGTAGGAACCGTGTCAACCCTAGATAACCGATCG
* * * *
19682 TCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGACCTATCG
1 TCCTCATCACGTAGGAACCGTGTCA--ACCC-TAGATAACCGATCG
* * * * *
19728 TCCTCATTACGTAGGAACCGTGTCATCACT---TGACCTGAT-T
1 TCCTCATCACGTAGGAACCGTGTCAACCCTAGATAACC-GATCG
* *
19768 TCCTCATCACGTAGGAACCGTGTCAACCCCAGATAACC-AGCCG
1 TCCTCATCACGTAGGAACCGTGTCAACCCTAGATAACCGA-TCG
19811 TCCTCATCACGTAGGAACCGTGT
1 TCCTCATCACGTAGGAACCGTGT
19834 TATCACTCTT
Statistics
Matches: 122, Mismatches: 21, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
40 31 0.25
41 3 0.02
43 50 0.41
44 2 0.02
45 4 0.03
46 32 0.26
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (43 bp):
TCCTCATCACGTAGGAACCGTGTCAACCCTAGATAACCGATCG
Found at i:19831 original size:83 final size:85
Alignment explanation
Indices: 19682--19840 Score: 216
Period size: 83 Copynumber: 1.9 Consensus size: 85
19672 TAACCGGTTG
* * * * *
19682 TCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGACCTATCGTCCTCATTACGTAGGAACC
1 TCCTCATCACATAGGAACCGTGTCA-CACCCTCAGATAACCTACCGTCCTCATCACGTAGGAACC
19747 GTGTCATCACTTGACCTGATT
65 GTGTCATCACTTGACCTGATT
*
19768 TCCTCATCACGTAGGAACCGTGTCA-ACCC-CAGATAACC-AGCCGTCCTCATCACGTAGGAACC
1 TCCTCATCACATAGGAACCGTGTCACACCCTCAGATAACCTA-CCGTCCTCATCACGTAGGAACC
*
19830 GTGTTATCACT
65 GTGTCATCACT
19841 CTTAGATGGC
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
82 1 0.02
83 37 0.57
84 4 0.06
86 23 0.35
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.26
Consensus pattern (85 bp):
TCCTCATCACATAGGAACCGTGTCACACCCTCAGATAACCTACCGTCCTCATCACGTAGGAACCG
TGTCATCACTTGACCTGATT
Found at i:19925 original size:127 final size:128
Alignment explanation
Indices: 19618--20351 Score: 673
Period size: 127 Copynumber: 5.8 Consensus size: 128
19608 CGTAGGAATC
* * * ** * * **
19618 GTGTCATCACCTGA-CTTGAGCTCCTCATCACGTAGGAGCCGTGTCAACCCTAGATAACCGGTTG
1 GTGTCATCACCTGACCTAGATCTCCTCATTACGTAGGAATCGTGTCAACCCCAGATAACCAGCCG
* * * * * ** * *
19682 TCCTCATCACATAGGAACCGTGTTATCACCCTTAGATGACCTATCGTCCTCAT-TACGTAGGAAC
66 TCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCC-A-AG-ACTCATGAACAAATGAGC
*
19746 C
128 A
* * * *
19747 GTGTCATCACTTGACCT-GATTTCCTCATCACGTAGGAACCGTGTCAACCCCAGATAACCAGCCG
1 GTGTCATCACCTGACCTAGATCTCCTCATTACGTAGGAATCGTGTCAACCCCAGATAACCAGCCG
* *
19811 TCCTCATCACGTAGGAACCGTGTTATCACTCTTAGATGGCCAAGACTCATGAACAAATTAGCA
66 TCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAACAAATGAGCA
* * * * *
19874 GTGTCATCACCCGACCT-GATTTCCTCATTACGTAGAAAACGTGTCAACCCCAGATAACCAGCAG
1 GTGTCATCACCTGACCTAGATCTCCTCATTACGTAGGAATCGTGTCAACCCCAGATAACCAGCCG
* * * *
19938 TCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCACGACTCATGAAAAAATGAGCA
66 TCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAACAAATGAGCA
* * * * * * *
20001 GTGTCATCACATGA-TTAGATCTCCTCATTATGTAAGGAGTTGTGTCAA-CTCAGATAATCAGCC
1 GTGTCATCACCTGACCTAGATCTCCTCATTACGT-AGGAATCGTGTCAACCCCAGATAACCAGCC
* * * *
20064 GTCCTCATCATGTAGGAACCATGTTATCACCCTTAGATGGCCAAGACTCATGAACAGATAAGCA
65 GTCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAACAAATGAGCA
* * * * * * *
20128 GTGTCATCACCTGA-TTAGATCTCTTCATTATGTAGGAGTTGTGTCAA-CCCAGATAGCCAGTCG
1 GTGTCATCACCTGACCTAGATCTCCTCATTACGTAGGAATCGTGTCAACCCCAGATAACCAGCCG
** * * *
20191 TCCTCATCACGTAGGAA-CGTGTTATCACATTTAGATGGCC-AGAACTCTTCATCACATATGAGC
66 TCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCAAG-ACTCATGA--ACAAATGAGC
*
20254 C
128 A
* * * * * ** *
20255 GTGTCATCACC-CAACTAGATTTCCTCATTATGTAGGAATCGTGTCAATCCTTGATAACCAGAAC
1 GTGTCATCACCTGACCTAGATCTCCTCATTACGTAGGAATCGTGTCAACCCCAGATAACCAG-CC
* * ** *
20319 -TCTTCATCACGTATGAGTCATGTTATCACCCTT
65 GTCCTCATCACGTAGGAACCGTGTTATCACCCTT
20352 CCTAAAGATG
Statistics
Matches: 513, Mismatches: 81, Indels: 22
0.83 0.13 0.04
Matches are distributed among these distances:
124 2 0.00
125 26 0.05
126 49 0.10
127 295 0.58
128 35 0.07
129 104 0.20
130 2 0.00
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (128 bp):
GTGTCATCACCTGACCTAGATCTCCTCATTACGTAGGAATCGTGTCAACCCCAGATAACCAGCCG
TCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGGCCAAGACTCATGAACAAATGAGCA
Found at i:20261 original size:254 final size:254
Alignment explanation
Indices: 19618--20351 Score: 793
Period size: 254 Copynumber: 2.9 Consensus size: 254
19608 CGTAGGAATC
* * * * *
19618 GTGTCATCACCTGACTTGAGCTCCTCATCACGTAGGAGCCGTGTCAACCCTAGATAACCGGTTGT
1 GTGTCATCACCTGACTTGATCTCCTCATTACGTAGGAGACGTGTCAACCC-AGATAACCAGTCGT
* * * * * * * * *
19683 CCTCATCACATAGGAACCGTGTTATCACCCTTAGATGACC-TATCGTCCTCATTACGTAGGAACC
65 CCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC-TCATCA-TACATATGAGCC
* * * *
19747 GTGTCATCACTTGACCT-GATTTCCTCATCACGTAGGAACCGTGTCAACCCCAGATAACCAGCCG
128 GTGTCATCACATGA-CTAGATTTCCTCATTATGTAGGAATCGTGTCAACCCCAGATAACCAGCCG
* * *
19811 TCCTCATCACGTAGGAACCGTGTTATCACTCTTAGATGGCCAAGACTCATGAACAAATTAGCA
192 TCCTCATCACGTAGGAACCATGTTATCACCCTTAGATGGCCAAGACTCATGAACAAATAAGCA
* * * * *
19874 GTGTCATCACCCGACCTGATTTCCTCATTACGTAGAAAACGTGTCAACCCCAGATAACCAG-CAG
1 GTGTCATCACCTGACTTGATCTCCTCATTACGTAGGAGACGTGTCAA-CCCAGATAACCAGTC-G
* * * * *
19938 TCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCACG-ACTCATGA-AAAAATGAGCA
64 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCA-GAACTCATCATACATATGAGCC
* * * * * *
20001 GTGTCATCACATGATTAGATCTCCTCATTATGTAAGGAGTTGTGTCAA-CTCAGATAATCAGCCG
128 GTGTCATCACATGACTAGATTTCCTCATTATGT-AGGAATCGTGTCAACCCCAGATAACCAGCCG
* *
20065 TCCTCATCATGTAGGAACCATGTTATCACCCTTAGATGGCCAAGACTCATGAACAGATAAGCA
192 TCCTCATCACGTAGGAACCATGTTATCACCCTTAGATGGCCAAGACTCATGAACAAATAAGCA
* * ** *
20128 GTGTCATCACCTGA-TTAGATCTCTTCATTATGTAGGAGTTGTGTCAACCCAGATAGCCAGTCGT
1 GTGTCATCACCTGACTT-GATCTCCTCATTACGTAGGAGACGTGTCAACCCAGATAACCAGTCGT
* *
20192 CCTCATCACGTAGGAA-CGTGTTATCACATTTAGATGGCCAGAACTCTTCATCACATATGAGCCG
65 CCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCATCAT-ACATATGAGCCG
*** * ** *
20256 TGTCATCACCCAACTAGATTTCCTCATTATGTAGGAATCGTGTCAATCCTTGATAACCAGAAC-T
129 TGTCATCACATGACTAGATTTCCTCATTATGTAGGAATCGTGTCAACCCCAGATAACCAG-CCGT
* * **
20320 CTTCATCACGTATGAGTCATGTTATCACCCTT
193 CCTCATCACGTAGGAACCATGTTATCACCCTT
20352 CCTAAAGATG
Statistics
Matches: 392, Mismatches: 73, Indels: 28
0.80 0.15 0.06
Matches are distributed among these distances:
251 1 0.00
252 28 0.07
253 44 0.11
254 213 0.54
255 12 0.03
256 90 0.23
257 4 0.01
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (254 bp):
GTGTCATCACCTGACTTGATCTCCTCATTACGTAGGAGACGTGTCAACCCAGATAACCAGTCGTC
CTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCATCATACATATGAGCCGTG
TCATCACATGACTAGATTTCCTCATTATGTAGGAATCGTGTCAACCCCAGATAACCAGCCGTCCT
CATCACGTAGGAACCATGTTATCACCCTTAGATGGCCAAGACTCATGAACAAATAAGCA
Found at i:20864 original size:34 final size:34
Alignment explanation
Indices: 20803--20870 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
20793 TCAGTTCCAT
* **
20803 CGAGCCAATGTTCCAGTCGTCGTCGAGCCACCGA
1 CGAGCCAACGTTCCAGTCGTCACCGAGCCACCGA
* *
20837 CGAGCCAACGTTCCAGTCTTTACCGAGCCACCGA
1 CGAGCCAACGTTCCAGTCGTCACCGAGCCACCGA
20871 GCCACCATCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.22, C:0.37, G:0.24, T:0.18
Consensus pattern (34 bp):
CGAGCCAACGTTCCAGTCGTCACCGAGCCACCGA
Found at i:21020 original size:14 final size:14
Alignment explanation
Indices: 20984--21035 Score: 63
Period size: 13 Copynumber: 3.8 Consensus size: 14
20974 CCATTAAAAA
*
20984 ACTAAACCCAAAT-C
1 ACTAAA-CCTAATCC
20998 ACTAAACCTAATCC
1 ACTAAACCTAATCC
*
21012 ACTAAACCT-ACCC
1 ACTAAACCTAATCC
21025 ACTAAACCTAA
1 ACTAAACCTAA
21036 AAAAACATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 17 0.50
14 17 0.50
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACTAAACCTAATCC
Found at i:21915 original size:30 final size:30
Alignment explanation
Indices: 21881--21993 Score: 86
Period size: 30 Copynumber: 3.8 Consensus size: 30
21871 TAAAACTTAA
* *
21881 AAATTTATGTTTTTTCCATTTTTGTCTTTT
1 AAATTTATATTTTTTCCATTTTAGTCTTTT
* * * **
21911 AAATTT-TATTTTGT-GATATTTGGTCTTCA
1 AAATTTATATTTTTTCCAT-TTTAGTCTTTT
* *
21940 AAATTTATATTTTTACTATTTTAGTCTTTT
1 AAATTTATATTTTTTCCATTTTAGTCTTTT
* * * *
21970 AAATTTCTGTTTGTGCCATTTTAG
1 AAATTTATATTTTTTCCATTTTAG
21994 ACCTTTTATT
Statistics
Matches: 63, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
28 2 0.03
29 20 0.32
30 39 0.62
31 2 0.03
ACGTcount: A:0.22, C:0.09, G:0.10, T:0.59
Consensus pattern (30 bp):
AAATTTATATTTTTTCCATTTTAGTCTTTT
Found at i:21936 original size:29 final size:30
Alignment explanation
Indices: 21881--21975 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
21871 TAAAACTTAA
* * * *
21881 AAATTTATGTTTTTTCCATTTTTGTCTTTT
1 AAATTTATATTTTTACTATTTTAGTCTTTT
* **
21911 AAATTT-TATTTTGTGA-TA-TTTGGTCTTCA
1 AAATTTATATTTT-T-ACTATTTTAGTCTTTT
21940 AAATTTATATTTTTACTATTTTAGTCTTTT
1 AAATTTATATTTTTACTATTTTAGTCTTTT
21970 AAATTT
1 AAATTT
21976 CTGTTTGTGC
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
28 1 0.02
29 22 0.43
30 28 0.55
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.61
Consensus pattern (30 bp):
AAATTTATATTTTTACTATTTTAGTCTTTT
Found at i:22643 original size:32 final size:32
Alignment explanation
Indices: 22607--22670 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
22597 AAAAATTAAA
* *
22607 AACCGGGTATCGGGTACCCGCAAAATCCGGGT
1 AACCGAGTACCGGGTACCCGCAAAATCCGGGT
* * *
22639 AACCGATTACCGGGTACCCGTAACATCCGGGT
1 AACCGAGTACCGGGTACCCGCAAAATCCGGGT
22671 CGGGACACGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (32 bp):
AACCGAGTACCGGGTACCCGCAAAATCCGGGT
Found at i:22729 original size:15 final size:16
Alignment explanation
Indices: 22709--22749 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
22699 CAGAAGTTCC
22709 GGTACCCGGAAAT-CG
1 GGTACCCGGAAATCCG
*
22724 GGTACCCGAAAATCCG
1 GGTACCCGGAAATCCG
22740 GGTACCCGGA
1 GGTACCCGGA
22750 TTTGCAGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.27, C:0.29, G:0.32, T:0.12
Consensus pattern (16 bp):
GGTACCCGGAAATCCG
Found at i:30736 original size:20 final size:18
Alignment explanation
Indices: 30711--30757 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 18
30701 TTAATCTCAA
30711 TATCGATACTCTCCTAGGAG
1 TATCGATACTCT-C-AGGAG
30731 TATCGATA--CTCAGGAG
1 TATCGATACTCTCAGGAG
30747 TATCGATACTC
1 TATCGATACTC
30758 ACCCTACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 13 0.52
17 1 0.04
18 3 0.12
20 8 0.32
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (18 bp):
TATCGATACTCTCAGGAG
Found at i:30747 original size:16 final size:16
Alignment explanation
Indices: 30726--30758 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
30716 ATACTCTCCT
30726 AGGAGTATCGATACTC
1 AGGAGTATCGATACTC
30742 AGGAGTATCGATACTC
1 AGGAGTATCGATACTC
30758 A
1 A
30759 CCCTACTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (16 bp):
AGGAGTATCGATACTC
Found at i:35014 original size:2 final size:2
Alignment explanation
Indices: 35007--35101 Score: 174
Period size: 2 Copynumber: 47.5 Consensus size: 2
34997 AAGCTATGAT
35007 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
35049 TA TA TA TA TA TA TA TA TA TA TA CTA TA TA TA TA TA -A 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
35091 TA TA TA TA TA T
1 TA TA TA TA TA T
35102 GAATCTATGT
Statistics
Matches: 91, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.01
2 88 0.97
3 2 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:41149 original size:10 final size:10
Alignment explanation
Indices: 41134--41158 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41124 TATTGTCGTA
41134 AAATAATTAT
1 AAATAATTAT
41144 AAATAATTAT
1 AAATAATTAT
41154 AAATA
1 AAATA
41159 TATTTTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAATAATTAT
Found at i:44241 original size:2 final size:2
Alignment explanation
Indices: 44198--44228 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44188 GATATGTAAG
44198 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 A
44229 CGAAAGTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63099 original size:21 final size:21
Alignment explanation
Indices: 63047--63101 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
63037 GAGTTACCCT
* *
63047 CGACGGCCGTAATAGCGTCCG
1 CGACGGCCGCAATAGCGCCCG
**
63068 CGATAAG-CGCAATAGCGCCCG
1 CGA-CGGCCGCAATAGCGCCCG
63089 CGACGGCCGCAAT
1 CGACGGCCGCAAT
63102 CACGGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.24, C:0.35, G:0.31, T:0.11
Consensus pattern (21 bp):
CGACGGCCGCAATAGCGCCCG
Done.