Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007397.1 Hibiscus syriacus cultivar Beakdansim tig00019949_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: 106357
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1572 original size:14 final size:15
Alignment explanation
Indices: 1553--1582 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1543 AGGGATCTGA
1553 TAAAAAAT-TATTTT
1 TAAAAAATATATTTT
1567 TAAAAAATATATTTT
1 TAAAAAATATATTTT
1582 T
1 T
1583 TATTCAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAAAAATATATTTT
Found at i:7283 original size:2 final size:2
Alignment explanation
Indices: 7276--7310 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
7266 CAACTTGATG
7276 AT AT AT AT AT AT AT -T 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
7311 TCACACATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:7414 original size:7 final size:7
Alignment explanation
Indices: 7402--7426 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
7392 ATACTATCAA
7402 ATTTAAT
1 ATTTAAT
7409 ATTTAAT
1 ATTTAAT
7416 ATTTAAT
1 ATTTAAT
7423 ATTT
1 ATTT
7427 GATTAGGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTAAT
Found at i:10358 original size:26 final size:26
Alignment explanation
Indices: 10322--10460 Score: 167
Period size: 26 Copynumber: 5.5 Consensus size: 26
10312 GAGTGGTTGG
* *
10322 AAGCAGTGGTGGCTGTTGAGTGGTCC
1 AAGCGGTGGTGGTTGTTGAGTGGTCC
* *
10348 AAGCGATGGTGGTTGTCGAGTGGTCC
1 AAGCGGTGGTGGTTGTTGAGTGGTCC
10374 AAGCGGTGGTGGTTGTTGAGTGGTCC
1 AAGCGGTGGTGGTTGTTGAGTGGTCC
*
10400 AAGTGGTGGTGG-TGTTGAGTGGTCC
1 AAGCGGTGGTGGTTGTTGAGTGGTCC
** **
10425 AAGCGGAAGTGG--CATGAGTGGTCC
1 AAGCGGTGGTGGTTGTTGAGTGGTCC
*
10449 AAGTGGTGGTGG
1 AAGCGGTGGTGG
10461 CCTATTCTGG
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
24 19 0.19
25 22 0.22
26 57 0.58
ACGTcount: A:0.16, C:0.12, G:0.45, T:0.27
Consensus pattern (26 bp):
AAGCGGTGGTGGTTGTTGAGTGGTCC
Found at i:10445 original size:49 final size:51
Alignment explanation
Indices: 10338--10460 Score: 160
Period size: 49 Copynumber: 2.4 Consensus size: 51
10328 TGGTGGCTGT
* * ** **
10338 TGAGTGGTCCAAGCGATGGTGGTTGTCGAGTGGTCCAAGCGGTGGTGGTTGT
1 TGAGTGGTCCAAGTGGTGGTGGTTGTCGAGTGGTCCAAGCGGAAGTGG-TCA
*
10390 TGAGTGGTCCAAGTGGTGGTGG-TGTTGAGTGGTCCAAGCGGAAGTGG-CA
1 TGAGTGGTCCAAGTGGTGGTGGTTGTCGAGTGGTCCAAGCGGAAGTGGTCA
10439 TGAGTGGTCCAAGTGGTGGTGG
1 TGAGTGGTCCAAGTGGTGGTGG
10461 CCTATTCTGG
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
49 22 0.34
51 22 0.34
52 20 0.31
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (51 bp):
TGAGTGGTCCAAGTGGTGGTGGTTGTCGAGTGGTCCAAGCGGAAGTGGTCA
Found at i:10724 original size:14 final size:14
Alignment explanation
Indices: 10685--10724 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
10675 TATTTTTAAT
10685 ATTATAATAATAT-
1 ATTATAATAATATA
10698 A-T-TAATAATATA
1 ATTATAATAATATA
10710 ATTATAATAATATA
1 ATTATAATAATATA
10724 A
1 A
10725 ATAATGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 9 0.38
12 2 0.08
13 2 0.08
14 11 0.46
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATTATAATAATATA
Found at i:11546 original size:113 final size:115
Alignment explanation
Indices: 10989--11795 Score: 1087
Period size: 113 Copynumber: 7.2 Consensus size: 115
10979 ATTGAATTGA
* * * *
10989 GGCAGACTTGTTCCACTTACTCAGAAGGGAATATCAAATCTT-GAAAAAAAAGACCTGTTCC-CT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
*
11052 TACTCTGAAGGAAATATCAGATCTT-AGAGGAGTTTGATCCACTGAATGGG
66 TACTCTGAAGGGAATATCAGATCTTGA-AGGAGTTTGATCCACTGAATGGG
* * * * **
11102 GGAAGACTTGTTCCACTTA--CTGAAGGG-A-ATCAAATATTGGG-AA-AGAGATCTATTTTGCT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
* * * * **
11161 TACTCTGAAAGGAATATC--ATCTTTAAGGAGTTCGATTCC-TTGAATCAG
66 TACTCTGAAGGGAATATCAGATCTTGAAGGAGTTTGA-TCCACTGAATGGG
11209 GGC--ACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
* *
11272 TACTCTGAAAGGAATATCAGATCTTAAAGGAGTTTGATCCACTGAATGGG
66 TACTCTGAAGGGAATATCAGATCTTGAAGGAGTTTGATCCACTGAATGGG
**
11322 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGATATGTTCCGCT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
*
11387 TACTCTGAAGGGAATATCAGATCTTGGAGGAGTTTGATCCACTGAATGGG
66 TACTCTGAAGGGAATATCAGATCTTGAAGGAGTTTGATCCACTGAATGGG
* * * *
11437 GGCAAACTTGTTCCACTTACTCTTAAGGG-A-ATCAAATCTTGGGAAAGAGATACATGTTCCGCT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
* * * **
11500 TACTCTGAAGGGAATATCAGATCTTGAAGTAGTTCGATTCC-TTGAATCAG
66 TACTCTGAAGGGAATATCAGATCTTGAAGGAGTTTGA-TCCACTGAATGGG
11550 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATC-AATCTTGGGAAA-AGAGACCTGTTCCGCT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
11613 TACTCTGAAGGGAATATCAGATCTT-ACAGGAGTTTGATCCACTGAATGGG
66 TACTCTGAAGGGAATATCAGATCTTGA-AGGAGTTTGATCCACTGAATGGG
* *
11663 GGCAGACTTGTTCCACTTACTTTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTACGCT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
* * * * *
11728 TACTATGAAGGGAATATCAAATATTGGAGGAGCTTGATCCACTGAATGGG
66 TACTCTGAAGGGAATATCAGATCTTGAAGGAGTTTGATCCACTGAATGGG
*
11778 GGCAGAGTTGTTCCACTT
1 GGCAGACTTGTTCCACTT
11796 GTCTTTAAAA
Statistics
Matches: 613, Mismatches: 58, Indels: 44
0.86 0.08 0.06
Matches are distributed among these distances:
105 14 0.02
107 30 0.05
108 13 0.02
109 41 0.07
110 4 0.01
111 37 0.06
112 7 0.01
113 227 0.37
114 29 0.05
115 211 0.34
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (115 bp):
GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
TACTCTGAAGGGAATATCAGATCTTGAAGGAGTTTGATCCACTGAATGGG
Found at i:11646 original size:341 final size:335
Alignment explanation
Indices: 10989--11795 Score: 1266
Period size: 341 Copynumber: 2.4 Consensus size: 335
10979 ATTGAATTGA
* * * *
10989 GGCAGACTTGTTCCACTTACTCAGAAGGGAATATCAAATCTT-GAAAAAAAAGACCTGTTCC-CT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
* *
11052 TACTCTGAAGGAAATATCAGATCTTAGAGGAGTTTGATCCACTGAATGGGGG-AAGACTTGTTCC
66 TACTCTGAAGGGAATATCAGATCTTGGAGGAGTTTGATCCACTGAATGGGGGCAA-ACTTGTTCC
*
11116 ACTTACTGAAGGGAATCAAATATTGGGAAAGAGATCTATTTTGCTTACTCTGAAAGGAATATCAT
130 ACTTACTGAAGGGAATCAAATATTGGGAAAGAGATCTATTTCGCTTACTCTGAAAGGAATATCAT
*
11181 CTTTAAGGAGTTCGATTCCTTGAATCAGGGCACTTGTTCCACTTACTCTGAAGGGAATATCAAAT
195 CTTGAAGGAGTTCGATTCCTTGAATCAGGGCACTTGTTCCACTTACTCTGAAGGGAATATCAAAT
11246 CTTGGGAAAGAGAGACCTGTTCCGCTTACTCTGAAAGGAATATCAGATCTTAAAGGAGTTTGATC
260 CTTGGGAAAGAGAGACCTGTTCCGCTTACTCTGAAAGGAATATCAGATCTTAAAGGAGTTTGATC
11311 CACTGAATGGG
325 CACTGAATGGG
**
11322 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGATATGTTCCGCT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
11387 TACTCTGAAGGGAATATCAGATCTTGGAGGAGTTTGATCCACTGAATGGGGGCAAACTTGTTCCA
66 TACTCTGAAGGGAATATCAGATCTTGGAGGAGTTTGATCCACTGAATGGGGGCAAACTTGTTCCA
* * *
11452 CTTACTCTTAAGGGAATCAAATCTTGGGAAAGAGATAC-ATGTTCCGCTTACTCTGAAGGGAATA
131 CTTA--CTGAAGGGAATCAAATATTGGGAAAGAGAT-CTAT-TT-CGCTTACTCTGAAAGGAATA
*
11516 TCAGATCTTGAAGTAGTTCGATTCCTTGAATCAGGGCAGACTTGTTCCACTTACTCTGAAGGGAA
191 TC--ATCTTGAAGGAGTTCGATTCCTTGAATCAGGGC--ACTTGTTCCACTTACTCTGAAGGGAA
* *
11581 TATC-AATCTTGGGAAA-AGAGACCTGTTCCGCTTACTCTGAAGGGAATATCAGATCTTACAGGA
252 TATCAAATCTTGGGAAAGAGAGACCTGTTCCGCTTACTCTGAAAGGAATATCAGATCTTAAAGGA
11644 GTTTGATCCACTGAATGGG
317 GTTTGATCCACTGAATGGG
* *
11663 GGCAGACTTGTTCCACTTACTTTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTACGCT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
* * * * * *
11728 TACTATGAAGGGAATATCAAATATTGGAGGAGCTTGATCCACTGAATGGGGGCAGAGTTGTTCCA
66 TACTCTGAAGGGAATATCAGATCTTGGAGGAGTTTGATCCACTGAATGGGGGCAAACTTGTTCCA
11793 CTT
131 CTT
11796 GTCTTTAAAA
Statistics
Matches: 436, Mismatches: 26, Indels: 16
0.91 0.05 0.03
Matches are distributed among these distances:
333 41 0.09
334 14 0.03
335 66 0.15
336 2 0.00
337 30 0.07
338 3 0.01
339 20 0.05
341 218 0.50
342 12 0.03
343 30 0.07
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (335 bp):
GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
TACTCTGAAGGGAATATCAGATCTTGGAGGAGTTTGATCCACTGAATGGGGGCAAACTTGTTCCA
CTTACTGAAGGGAATCAAATATTGGGAAAGAGATCTATTTCGCTTACTCTGAAAGGAATATCATC
TTGAAGGAGTTCGATTCCTTGAATCAGGGCACTTGTTCCACTTACTCTGAAGGGAATATCAAATC
TTGGGAAAGAGAGACCTGTTCCGCTTACTCTGAAAGGAATATCAGATCTTAAAGGAGTTTGATCC
ACTGAATGGG
Found at i:20190 original size:14 final size:16
Alignment explanation
Indices: 20161--20193 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
20151 GAAGTGTGCC
20161 ATAAATCAGATATCAA
1 ATAAATCAGATATCAA
20177 ATAAA-CAG-TATCAA
1 ATAAATCAGATATCAA
20191 ATA
1 ATA
20194 GATATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 3 0.18
16 5 0.29
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.24
Consensus pattern (16 bp):
ATAAATCAGATATCAA
Found at i:37277 original size:14 final size:14
Alignment explanation
Indices: 37258--37285 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
37248 ATAGAACTAC
37258 TAGATGAATGCAAT
1 TAGATGAATGCAAT
37272 TAGATGAATGCAAT
1 TAGATGAATGCAAT
37286 ATGCCATCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (14 bp):
TAGATGAATGCAAT
Found at i:37876 original size:35 final size:35
Alignment explanation
Indices: 37825--37948 Score: 142
Period size: 35 Copynumber: 3.5 Consensus size: 35
37815 CCTTAGGTCC
* * *
37825 ATAAGGAATTATCAGCTGATCATTGTTGAACCTAT
1 ATAAGGAATTACCAGCTGATCAGTGCTGAACCTAT
*
37860 ATAAGGAATTACCAGCTTGATCAGAGCTGAACCTGCA-
1 ATAAGGAATTACCAGC-TGATCAGTGCTGAACCT--AT
** * *
37897 ATAAGGAATTATTAGTTGATCGGTGCTGAACCTAT
1 ATAAGGAATTACCAGCTGATCAGTGCTGAACCTAT
37932 ATAAGGAATTACCAGCT
1 ATAAGGAATTACCAGCT
37949 TGATTAGAAC
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
34 1 0.01
35 29 0.40
36 29 0.40
37 13 0.18
38 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (35 bp):
ATAAGGAATTACCAGCTGATCAGTGCTGAACCTAT
Found at i:37891 original size:36 final size:36
Alignment explanation
Indices: 37825--37965 Score: 153
Period size: 36 Copynumber: 3.9 Consensus size: 36
37815 CCTTAGGTCC
* ** *
37825 ATAAGGAATTATCAGC-TGATCATTGTTGAACCTAT
1 ATAAGGAATTACCAGCTTGATCAGAGCTGAACCTAT
37860 ATAAGGAATTACCAGCTTGATCAGAGCTGAACCTGCA-
1 ATAAGGAATTACCAGCTTGATCAGAGCTGAACCT--AT
** * *
37897 ATAAGGAATTATTAG-TTGATCGGTGCTGAACCTAT
1 ATAAGGAATTACCAGCTTGATCAGAGCTGAACCTAT
* *
37932 ATAAGGAATTACCAGCTTGATTAGAACTGAACCT
1 ATAAGGAATTACCAGCTTGATCAGAGCTGAACCT
37966 GCAGAGACTT
Statistics
Matches: 87, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
34 1 0.01
35 28 0.32
36 44 0.51
37 13 0.15
38 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (36 bp):
ATAAGGAATTACCAGCTTGATCAGAGCTGAACCTAT
Found at i:37942 original size:72 final size:72
Alignment explanation
Indices: 37825--37968 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 72
37815 CCTTAGGTCC
* * *
37825 ATAAGGAATTATCAGCTGATCATTGTTGAACCTATATAAGGAATTACCAGCTTGATCAGAGCTGA
1 ATAAGGAATTATCAGCTGATCAGTGCTGAACCTATATAAGGAATTACCAGCTTGATCAGAACTGA
37890 ACCTGCA
66 ACCTGCA
* * * *
37897 ATAAGGAATTATTAGTTGATCGGTGCTGAACCTATATAAGGAATTACCAGCTTGATTAGAACTGA
1 ATAAGGAATTATCAGCTGATCAGTGCTGAACCTATATAAGGAATTACCAGCTTGATCAGAACTGA
37962 ACCTGCA
66 ACCTGCA
37969 GAGACTTCAT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (72 bp):
ATAAGGAATTATCAGCTGATCAGTGCTGAACCTATATAAGGAATTACCAGCTTGATCAGAACTGA
ACCTGCA
Found at i:43248 original size:19 final size:20
Alignment explanation
Indices: 43226--43265 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43216 TATTTCCTTA
43226 AATTAAACA-TATTTTACAT
1 AATTAAACAGTATTTTACAT
* *
43245 AATTAATCAGTATTTTTCAT
1 AATTAAACAGTATTTTACAT
43265 A
1 A
43266 TACGCAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (20 bp):
AATTAAACAGTATTTTACAT
Found at i:44672 original size:44 final size:44
Alignment explanation
Indices: 44605--44818 Score: 398
Period size: 44 Copynumber: 4.9 Consensus size: 44
44595 ACGAACGAAT
*
44605 AACGTGTGGTCGAGAAAAAAGAGTAAGTCTAATTTGAGATGAAG
1 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAG
44649 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAG
1 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAG
44693 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAG
1 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAG
44737 AAC--GT-GTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAG
1 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAG
44778 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATG
1 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATG
44819 GGACAAACTC
Statistics
Matches: 166, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
41 39 0.23
42 2 0.01
43 2 0.01
44 123 0.74
ACGTcount: A:0.39, C:0.07, G:0.29, T:0.25
Consensus pattern (44 bp):
AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAG
Found at i:44791 original size:85 final size:87
Alignment explanation
Indices: 44605--44818 Score: 396
Period size: 85 Copynumber: 2.5 Consensus size: 87
44595 ACGAACGAAT
*
44605 AACGTGTGGTCGAGAAAAAAGAGTAAGTCTAATTTGAGATGAAGAACGTGTGGTCGAGAAAATAG
1 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAGAACG-GTGGTCGAGAAAATAG
44670 AGTAAGTCTAATTTGAGATGAAG
65 AGTAAGTCTAATTTGAGATGAAG
44693 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAGAAC-GT-GTCGAGAAAATAGA
1 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAGAACGGTGGTCGAGAAAATAGA
44756 GTAAGTCTAATTTGAGATGAAG
66 GTAAGTCTAATTTGAGATGAAG
44778 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATG
1 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATG
44819 GGACAAACTC
Statistics
Matches: 125, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
85 77 0.62
86 2 0.02
88 46 0.37
ACGTcount: A:0.39, C:0.07, G:0.29, T:0.25
Consensus pattern (87 bp):
AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAGAACGGTGGTCGAGAAAATAGA
GTAAGTCTAATTTGAGATGAAG
Found at i:45146 original size:2 final size:2
Alignment explanation
Indices: 45139--45171 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
45129 ATTAATGAGT
*
45139 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45172 GAAGGATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 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):
TA
Found at i:52379 original size:9 final size:9
Alignment explanation
Indices: 52365--52392 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
52355 AATTTTACAT
52365 ATATAAAAA
1 ATATAAAAA
52374 ATATAAAAA
1 ATATAAAAA
52383 ATATAAAAA
1 ATATAAAAA
52392 A
1 A
52393 ATCCGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
ATATAAAAA
Found at i:52469 original size:17 final size:17
Alignment explanation
Indices: 52439--52472 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
52429 TCTAATTTTA
* *
52439 ATATATTTTTATATATT
1 ATATAATTTAATATATT
52456 ATATAATTTAATATATT
1 ATATAATTTAATATATT
52473 TTAACAAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATAATTTAATATATT
Found at i:55333 original size:27 final size:27
Alignment explanation
Indices: 55275--55335 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
55265 TGTCTACCTT
*
55275 AAAATTCTATTTGTATCTACTTTATATG
1 AAAATT-TATTTGTATCTACTTTATACG
* * *
55303 -AAATTTATTTGTGTCTATTTTCTACG
1 AAAATTTATTTGTATCTACTTTATACG
55329 AAAATTT
1 AAAATTT
55336 TCTATTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (27 bp):
AAAATTTATTTGTATCTACTTTATACG
Found at i:55519 original size:24 final size:24
Alignment explanation
Indices: 55485--55532 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
55475 AACAATCTTC
55485 CCTAAAAAGGAACGTAACGGTGGA
1 CCTAAAAAGGAACGTAACGGTGGA
*
55509 CCTAAATAGGAACGTAACGGTGGA
1 CCTAAAAAGGAACGTAACGGTGGA
55533 TTTTCCTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.29, T:0.15
Consensus pattern (24 bp):
CCTAAAAAGGAACGTAACGGTGGA
Found at i:56773 original size:2 final size:2
Alignment explanation
Indices: 56766--56808 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
56756 TTAACAAAGG
56766 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
56808 A
1 A
56809 CAATTTCCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57851 original size:2 final size:2
Alignment explanation
Indices: 57844--57880 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
57834 CAACTTAATG
57844 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
57881 ATTCACACAC
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:58215 original size:23 final size:23
Alignment explanation
Indices: 58180--58226 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
58170 AGTTTGCATA
**
58180 TATGACACGTTTTCATATGTCTT
1 TATGACAAATTTTCATATGTCTT
* *
58203 TATGACAAATTTTCTTCTGTCTT
1 TATGACAAATTTTCATATGTCTT
58226 T
1 T
58227 TGGCACATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.21, C:0.17, G:0.11, T:0.51
Consensus pattern (23 bp):
TATGACAAATTTTCATATGTCTT
Found at i:59037 original size:12 final size:12
Alignment explanation
Indices: 59020--59045 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
59010 CGGTGGCGCC
59020 AACAATTGTTGA
1 AACAATTGTTGA
59032 AACAATTGTTGA
1 AACAATTGTTGA
59044 AA
1 AA
59046 ATTAATGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (12 bp):
AACAATTGTTGA
Found at i:62519 original size:19 final size:18
Alignment explanation
Indices: 62495--62547 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 18
62485 AAATATATGT
*
62495 TTTTTAATTAAAAAAATTA
1 TTTTTAA-TAAAAAAAATA
62514 TTTTTAATAAAAAATAATA
1 TTTTTAATAAAAAA-AATA
62533 TTTTTAATAAAAAAA
1 TTTTTAATAAAAAAA
62548 CATAATTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 8 0.25
19 24 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTTTAATAAAAAAAATA
Found at i:62556 original size:18 final size:19
Alignment explanation
Indices: 62497--62558 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
62487 ATATATGTTT
* *
62497 TTTAATTAAAAAA-ATTATT
1 TTTAA-TAAAAAATAATATA
*
62516 TTTAATAAAAAATAATATT
1 TTTAATAAAAAATAATATA
62535 TTTAATAAAAAA-ACATA-A
1 TTTAATAAAAAATA-ATATA
62553 TTTAAT
1 TTTAAT
62559 TATATTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 14 0.36
19 25 0.64
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTAATAAAAAATAATATA
Found at i:66471 original size:18 final size:18
Alignment explanation
Indices: 66448--66484 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
66438 TACACAATAT
*
66448 ATAGCACCGAATGAAAAA
1 ATAGCACCGAACGAAAAA
66466 ATAGCACCGAACGAAAAA
1 ATAGCACCGAACGAAAAA
66484 A
1 A
66485 AATGATTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.57, C:0.19, G:0.16, T:0.08
Consensus pattern (18 bp):
ATAGCACCGAACGAAAAA
Found at i:70006 original size:26 final size:28
Alignment explanation
Indices: 69966--70032 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 28
69956 TATAAAAATG
*
69966 AAAACACTAAA-TTTATAAATT-T-AAA
1 AAAAAACTAAATTTTATAAATTCTCAAA
*
69991 AAAAAACTAAATTTTATAATTTCTCAAA
1 AAAAAACTAAATTTTATAAATTCTCAAA
70019 AAAGAAACGTAAAT
1 AAA-AAAC-TAAAT
70033 CCTTAAATCC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 10 0.29
26 9 0.26
27 1 0.03
28 6 0.17
29 4 0.11
30 5 0.14
ACGTcount: A:0.58, C:0.09, G:0.03, T:0.30
Consensus pattern (28 bp):
AAAAAACTAAATTTTATAAATTCTCAAA
Found at i:82362 original size:34 final size:34
Alignment explanation
Indices: 82319--82386 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
82309 ATACCTAACT
82319 TTCACCTAACTAAAATGATGTAAGCAATGACATC
1 TTCACCTAACTAAAATGATGTAAGCAATGACATC
*
82353 TTCACCTAACTAAATTGATGTAAGCAATGACATC
1 TTCACCTAACTAAAATGATGTAAGCAATGACATC
82387 AAATTAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (34 bp):
TTCACCTAACTAAAATGATGTAAGCAATGACATC
Found at i:85916 original size:21 final size:23
Alignment explanation
Indices: 85879--85930 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
85869 AAACTTAATT
* *
85879 TTAAATTTTTATATATTTTT-TA
1 TTAAATTTATATATATTTTTAGA
85901 TTAAATTTAT-TATATTTTTAGA
1 TTAAATTTATATATATTTTTAGA
85923 TTAAATTT
1 TTAAATTT
85931 TACTATCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTAAATTTATATATATTTTTAGA
Found at i:87065 original size:14 final size:14
Alignment explanation
Indices: 87048--87083 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
87038 AAGAAATAGT
*
87048 AAATTAAAGTAATG
1 AAATTAAAGCAATG
*
87062 AAATTAAAGCACTG
1 AAATTAAAGCAATG
87076 AAATTAAA
1 AAATTAAA
87084 TAGATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.58, C:0.06, G:0.11, T:0.25
Consensus pattern (14 bp):
AAATTAAAGCAATG
Found at i:92659 original size:23 final size:21
Alignment explanation
Indices: 92614--92659 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
92604 TAAGAGTATC
**
92614 AATATTTTAAAATAAAATTTA
1 AATATTTTAAAATAAAAAATA
92635 AATATTTTAAAATATAAAAAATA
1 AATATTTT-AAA-ATAAAAAATA
92658 AA
1 AA
92660 AAATTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 3 0.14
23 10 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AATATTTTAAAATAAAAAATA
Found at i:93493 original size:2 final size:2
Alignment explanation
Indices: 93486--93517 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
93476 AATAAATAAA
93486 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
93518 GTAGAATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:94038 original size:18 final size:18
Alignment explanation
Indices: 94016--94065 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
94006 AAAAAATAGT
*
94016 AATAATAGAAATAATAAG
1 AATAATAAAAATAATAAG
* * * *
94034 GATAATATAAAGAATAAT
1 AATAATAAAAATAATAAG
94052 AATAATAAAAATAA
1 AATAATAAAAATAA
94066 AAATGGTAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (18 bp):
AATAATAAAAATAATAAG
Found at i:94128 original size:34 final size:34
Alignment explanation
Indices: 94090--94156 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
94080 TATAAAAAGA
94090 AATAAAATAC-ATACAT-ATATATACATATAATAAT
1 AATAAAA-ACAATA-ATAATATATACATATAATAAT
* *
94124 AATAATAACAATAATAATATATATATATAATAA
1 AATAAAAACAATAATAATATATACATATAATAA
94157 AACGTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 4 0.14
34 25 0.86
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (34 bp):
AATAAAAACAATAATAATATATACATATAATAAT
Found at i:95851 original size:105 final size:105
Alignment explanation
Indices: 95669--96233 Score: 1049
Period size: 105 Copynumber: 5.4 Consensus size: 105
95659 TGTTGTTTTT
*
95669 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
95734 CAGCGGTTCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
95774 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
95839 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
95879 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGATAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
95944 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
95984 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
96049 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
96089 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
96154 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
96194 GAGTCCAATATCCTTCGTTGGGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
96234 GGTAAAACCT
Statistics
Matches: 449, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 449 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Done.