Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005216.1 Hibiscus syriacus cultivar Beakdansim tig00011808_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: 116338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:14804 original size:2 final size:2
Alignment explanation
Indices: 14797--14843 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
14787 CTAACTACAA
14797 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
14839 AT AT A
1 AT AT A
14844 AATAATTCCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17900 original size:20 final size:21
Alignment explanation
Indices: 17848--17903 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
17838 CTATATCGAT
*
17848 AATT-GAGTTGCGAAATTGAC
1 AATTCGAGTTGCGAAAATGAC
*
17868 GAATTCGATTTGCGAAAATGA-
1 -AATTCGAGTTGCGAAAATGAC
*
17889 AATTCGCGTTGCGAA
1 AATTCGAGTTGCGAA
17904 TAGTTGTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 13 0.43
21 4 0.13
22 13 0.43
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (21 bp):
AATTCGAGTTGCGAAAATGAC
Found at i:17963 original size:20 final size:20
Alignment explanation
Indices: 17938--17975 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17928 ATTAGTATTG
*
17938 CGAAATTTGCGTTGCGAAAA
1 CGAAATTCGCGTTGCGAAAA
17958 CGAAATTCGCGTTGCGAA
1 CGAAATTCGCGTTGCGAA
17976 TTTGGAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (20 bp):
CGAAATTCGCGTTGCGAAAA
Found at i:23094 original size:53 final size:53
Alignment explanation
Indices: 23014--23116 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
23004 CTTGCATGAT
* **
23014 TCAATGTTACGGAGTAAACTTGAACTTATAGAATGCATGATTCAATGTTATGG
1 TCAATGTTACGGAATAAACTTGAACTTATAGAACACATGATTCAATGTTATGG
* *
23067 TCAATGTTATGGAATAAACTTGAACTTATAGAACACATGATTCTATGTTA
1 TCAATGTTACGGAATAAACTTGAACTTATAGAACACATGATTCAATGTTA
23117 GAATCATTAG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (53 bp):
TCAATGTTACGGAATAAACTTGAACTTATAGAACACATGATTCAATGTTATGG
Found at i:36626 original size:31 final size:31
Alignment explanation
Indices: 36591--36650 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
36581 TACACCACAA
* * *
36591 GTCATCCAATTATTAGTAAGATTGCAAATGG
1 GTCATCAAATTATTAGTAAAATTACAAATGG
36622 GTCATCAAATTATTAGTAAAATTACAAAT
1 GTCATCAAATTATTAGTAAAATTACAAAT
36651 AAGTCGTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (31 bp):
GTCATCAAATTATTAGTAAAATTACAAATGG
Found at i:40010 original size:23 final size:25
Alignment explanation
Indices: 39952--40011 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 25
39942 TCGATTTATT
*
39952 TAATCATTTAAAATATAAATAAAAAA
1 TAATCAATTAAAATAT-AATAAAAAA
** *
39978 TAATGTATTAAAAT-T-ATAAGAAA
1 TAATCAATTAAAATATAATAAAAAA
40001 TAATCAATTAA
1 TAATCAATTAA
40012 CTAAAGCTAC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 16 0.57
25 1 0.04
26 11 0.39
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (25 bp):
TAATCAATTAAAATATAATAAAAAA
Found at i:49191 original size:31 final size:31
Alignment explanation
Indices: 49147--49221 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
49137 ATTACACCAC
*
49147 AAGTCATCCAATTATTAGTAAGATTACAAAT
1 AAGTCATCCAATTATTAGTAAAATTACAAAT
* *
49178 GAGTCATCGAATTATTAGTAAAATTACAAAT
1 AAGTCATCCAATTATTAGTAAAATTACAAAT
49209 AAGTCATCCAATT
1 AAGTCATCCAATT
49222 TTAAAAGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (31 bp):
AAGTCATCCAATTATTAGTAAAATTACAAAT
Found at i:50115 original size:21 final size:22
Alignment explanation
Indices: 50086--50138 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
50076 ATTCTGACTA
50086 TCGCATTGCGATTTTCC-AAAT
1 TCGCATTGCGATTTTCCTAAAT
*
50107 TCGCGTTGCGATTTTCCTAAA-
1 TCGCATTGCGATTTTCCTAAAT
*
50128 TCGCAATGCGA
1 TCGCATTGCGA
50139 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCTAAAT
Found at i:50149 original size:20 final size:20
Alignment explanation
Indices: 50124--50240 Score: 198
Period size: 20 Copynumber: 5.8 Consensus size: 20
50114 GCGATTTTCC
*
50124 TAAATCGCAATGCGAATACG
1 TAAATCGCAACGCGAATACG
50144 TAAATCGCAACGCGAATACG
1 TAAATCGCAACGCGAATACG
* * *
50164 TAACTTGCAATGCGAATACG
1 TAAATCGCAACGCGAATACG
50184 TAAATCGCAACGCGAATACG
1 TAAATCGCAACGCGAATACG
50204 TAAATCGCAACGCGAATACG
1 TAAATCGCAACGCGAATACG
50224 TAAATCGCAACGCGAAT
1 TAAATCGCAACGCGAAT
50241 CTGACTATCG
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 90 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (20 bp):
TAAATCGCAACGCGAATACG
Found at i:50251 original size:40 final size:40
Alignment explanation
Indices: 50127--50338 Score: 168
Period size: 40 Copynumber: 5.3 Consensus size: 40
50117 ATTTTCCTAA
* *
50127 ATCGCAATGCGAATACGTAAATCGCAACGCGAATACGTAACT
1 ATCGCAACGCGAATACGTAAATCGCAACGCGAAT-C-TGACT
* *
50169 -T-GCAATGCGAATACGTAAATCGCAACGCGAATAC-GTA-A
1 ATCGCAACGCGAATACGTAAATCGCAACGCGAAT-CTG-ACT
50207 ATCGCAACGCGAATACGTAAATCGCAACGCGAATCTGACT
1 ATCGCAACGCGAATACGTAAATCGCAACGCGAATCTGACT
* * * * *
50247 ATCGCAACGCGATTATG-ACTATCGCAACGAGATTCTGACT
1 ATCGCAACGCGAATACGTA-AATCGCAACGCGAATCTGACT
* * * * * *
50287 ATTGCAACGAG-ATTC-TGACTATCGTAACGCGATTCTGACT
1 ATCGCAACGCGAATACGT-A-AATCGCAACGCGAATCTGACT
*
50327 ATCGCAATGCGA
1 ATCGCAACGCGA
50339 TTCTGACTAT
Statistics
Matches: 142, Mismatches: 19, Indels: 19
0.79 0.11 0.11
Matches are distributed among these distances:
39 6 0.04
40 135 0.95
41 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (40 bp):
ATCGCAACGCGAATACGTAAATCGCAACGCGAATCTGACT
Found at i:50271 original size:60 final size:60
Alignment explanation
Indices: 50147--50338 Score: 169
Period size: 60 Copynumber: 3.2 Consensus size: 60
50137 GAATACGTAA
* * * * * *
50147 ATCGCAACGCGAATACGTAACTTGCAATGCGAATAC-GTA-AATCGCAACGCGAATACGTA-A
1 ATCGCAACGCGAATACGTAAATTGCAACGCGAAT-CTG-ACTATCGCAACGCGATTATG-ACT
*
50207 ATCGCAACGCGAATACGTAAATCGCAACGCGAATCTGACTATCGCAACGCGATTATGACT
1 ATCGCAACGCGAATACGTAAATTGCAACGCGAATCTGACTATCGCAACGCGATTATGACT
* * * * * * *
50267 ATCGCAACGAG-ATTC-TGACTATTGCAACGAGATTCTGACTATCGTAACGCGATTCTGACT
1 ATCGCAACGCGAATACGT-A-AATTGCAACGCGAATCTGACTATCGCAACGCGATTATGACT
*
50327 ATCGCAATGCGA
1 ATCGCAACGCGA
50339 TTCTGACTAT
Statistics
Matches: 109, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
58 1 0.01
59 7 0.06
60 101 0.93
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (60 bp):
ATCGCAACGCGAATACGTAAATTGCAACGCGAATCTGACTATCGCAACGCGATTATGACT
Found at i:50354 original size:20 final size:20
Alignment explanation
Indices: 50227--50353 Score: 191
Period size: 20 Copynumber: 6.3 Consensus size: 20
50217 GAATACGTAA
*
50227 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
*
50247 ATCGCAACGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
*
50267 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
50287 ATTGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
50307 ATCGTAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
50327 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
50347 ATCGCAA
1 ATCGCAA
50354 TACTGAATTT
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 97 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:51222 original size:24 final size:24
Alignment explanation
Indices: 51195--51248 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
51185 GTATTTGAAA
*
51195 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTAGTCAATACCCGGAC
* * *
51219 TTTGATCTTAGTCAATACTCGGAT
1 TTTGATATTAGTCAATACCCGGAC
51243 TTTGAT
1 TTTGAT
51249 GATTTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTAGTCAATACCCGGAC
Found at i:53690 original size:20 final size:20
Alignment explanation
Indices: 53665--53774 Score: 177
Period size: 20 Copynumber: 5.5 Consensus size: 20
53655 TTCATTTGAG
53665 TATCGCAACGC-GAATATGAC
1 TATCGCAACGCGGAA-ATGAC
*
53685 TATCGCAACACGGAAATGAC
1 TATCGCAACGCGGAAATGAC
53705 TATCGCAACGCGGAAATGAC
1 TATCGCAACGCGGAAATGAC
* *
53725 TAGCGCAACGCGTAAATGAC
1 TATCGCAACGCGGAAATGAC
53745 TATCGCAACGCGGAAATGAC
1 TATCGCAACGCGGAAATGAC
53765 TATCGCAACG
1 TATCGCAACG
53775 AGAGAATCGC
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
20 80 0.96
21 3 0.04
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.16
Consensus pattern (20 bp):
TATCGCAACGCGGAAATGAC
Found at i:53846 original size:20 final size:19
Alignment explanation
Indices: 53817--53885 Score: 76
Period size: 20 Copynumber: 3.8 Consensus size: 19
53807 CGCGAATTTA
*
53817 ATTTCACATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
53836 ATTTTCGCATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
53854 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
53870 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
53886 CTCTCGTTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 6 0.15
16 7 0.17
17 4 0.10
18 3 0.07
19 9 0.22
20 12 0.29
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.46
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:53864 original size:14 final size:14
Alignment explanation
Indices: 53845--53898 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
53835 CATTTTCGCA
53845 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
53859 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
53876 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
53892 TTGCGAT
1 TTGCGAT
53899 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:53880 original size:33 final size:33
Alignment explanation
Indices: 53825--53907 Score: 139
Period size: 33 Copynumber: 2.5 Consensus size: 33
53815 TAATTTCACA
53825 TTGCGATTTTCATTTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
53859 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
**
53892 TTGCGATAGTCATTTC
1 TTGCGATTTTCATTTC
53908 CGCGTTGTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 35 0.74
34 12 0.26
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:54043 original size:14 final size:14
Alignment explanation
Indices: 54024--54060 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
54014 CATCAATTAA
54024 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
54038 ACAAATCATCTTTT
1 ACAAATCAACATTT
54052 ACAAATCAA
1 ACAAATCAA
54061 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:56039 original size:20 final size:20
Alignment explanation
Indices: 56016--56065 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
56006 CGCGAAAATG
** *
56016 ACTATCGCAATGTGAATTTT
1 ACTATCGCAATACGAATTTA
56036 ACTATCGCAATACGAATTTA
1 ACTATCGCAATACGAATTTA
56056 ACTATCGCAA
1 ACTATCGCAA
56066 CGAGAGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (20 bp):
ACTATCGCAATACGAATTTA
Found at i:56151 original size:20 final size:20
Alignment explanation
Indices: 56126--56172 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
56116 GATTCTTTCG
56126 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
56146 TTGCGATAGTCATTTTCGCT
1 TTGCGATAGTCAAATTCGCA
56166 TTGCGAT
1 TTGCGAT
56173 TTTGTTGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:56183 original size:54 final size:53
Alignment explanation
Indices: 56105--56208 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 53
56095 GCGATTTTCA
56105 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGATTCTTTCGTTGCGATAGTC-AATTCGCATTGCGATAGTCAT
* * ** *
56159 TTTCGCTTTGCGATT-TTGTTGTTGCGATTTTCATTTCGCATTGCGATAGT
1 TTTCGCATTGCGATTCTT-TCGTTGCGATAGTCAATTCGCATTGCGATAGT
56209 AAACTATTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
53 19 0.43
54 25 0.57
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.44
Consensus pattern (53 bp):
TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAATTCGCATTGCGATAGTCAT
Found at i:58181 original size:20 final size:20
Alignment explanation
Indices: 58155--58217 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
58145 TATAATTATT
*
58155 CGATTTACATATTCGCATTG
1 CGATTTACGTATTCGCATTG
*
58175 TGATTTACGTATTCGCATTG
1 CGATTTACGTATTCGCATTG
58195 CGATTTACGTATTCGCATTG
1 CGATTTACGTATTCGCATTG
58215 CGA
1 CGA
58218 ATTAGGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
CGATTTACGTATTCGCATTG
Found at i:58238 original size:21 final size:21
Alignment explanation
Indices: 58214--58254 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
58204 TATTCGCATT
58214 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
*
58235 GCGAATTTGGAAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
58255 TACGATAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:58717 original size:111 final size:111
Alignment explanation
Indices: 58523--58736 Score: 410
Period size: 111 Copynumber: 1.9 Consensus size: 111
58513 ATATATCTCT
*
58523 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATATTTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
*
58588 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATATCG
66 TGATTCATTTAATGCATGATTATTAGATTAAGAATTAAATATATCG
58634 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
58699 TGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
58737 TTTTTGTAAT
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 101 1.00
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.44
Consensus pattern (111 bp):
ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
TGATTCATTTAATGCATGATTATTAGATTAAGAATTAAATATATCG
Found at i:60259 original size:18 final size:18
Alignment explanation
Indices: 60236--60272 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
60226 GCAGCCACCG
60236 CAGCCATATATGATGTCA
1 CAGCCATATATGATGTCA
60254 CAGCCATATATGATGTCA
1 CAGCCATATATGATGTCA
60272 C
1 C
60273 CATCGCGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (18 bp):
CAGCCATATATGATGTCA
Found at i:60638 original size:12 final size:12
Alignment explanation
Indices: 60608--60646 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
60598 TGCTCAGGAC
*
60608 GACGACGACGAT
1 GACGACGATGAT
* *
60620 GAAGACGATGGT
1 GACGACGATGAT
60632 GACGACGATGAT
1 GACGACGATGAT
60644 GAC
1 GAC
60647 AATGAGGAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.18, G:0.36, T:0.13
Consensus pattern (12 bp):
GACGACGATGAT
Found at i:75084 original size:21 final size:24
Alignment explanation
Indices: 75060--75103 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 24
75050 ATTAGAATAG
75060 AAATATT-ATT-ATTT-TTTAAAA
1 AAATATTAATTCATTTATTTAAAA
75081 AAATATTAATTCATTTATTTAAA
1 AAATATTAATTCATTTATTTAAA
75104 TAATTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
22 3 0.15
23 4 0.20
24 6 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
AAATATTAATTCATTTATTTAAAA
Found at i:78817 original size:14 final size:15
Alignment explanation
Indices: 78781--78821 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
78771 GGTTTTCCGG
78781 AAAATGAATTACTGA
1 AAAATGAATTACTGA
**
78796 AATTTGAATT-CTGA
1 AAAATGAATTACTGA
78810 AAAATGAATTAC
1 AAAATGAATTAC
78822 ATCTCTGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (15 bp):
AAAATGAATTACTGA
Found at i:79205 original size:23 final size:23
Alignment explanation
Indices: 79156--79218 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
79146 GTGTTATAAT
* **
79156 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
79179 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
79202 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
79219 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:79246 original size:19 final size:20
Alignment explanation
Indices: 79194--79246 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
79184 TTAAATATCT
79194 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
79213 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
79234 TTATTAAATATAT
1 TTATTAAATATAT
79247 AAATTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:79258 original size:28 final size:27
Alignment explanation
Indices: 79203--79358 Score: 79
Period size: 29 Copynumber: 5.5 Consensus size: 27
79193 TTTATTAAAA
79203 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAATATATAAATAATATTAT
**
79231 TCATTATTAAATATATAAATTTTTTTATTAT
1 T-ATTATTAAATATATAAA---TAATATTAT
* *
79262 ATATTATTAAAATAAAAAAATAATATCT-T
1 -TATTATT-AAATATATAAATAATAT-TAT
* * *
79291 ATATTATTATAATATAGTTAATTATTTTAT
1 -TATTATTA-AATATA-TAAATAATATTAT
* *
79321 ATAATATTTAAA-ATAT-AATATTA-TAT
1 -TATTA-TTAAATATATAAATAATATTAT
79347 TATTA-TAAATAT
1 TATTATTAAATAT
79359 TAATAAATTA
Statistics
Matches: 100, Mismatches: 16, Indels: 28
0.69 0.11 0.19
Matches are distributed among these distances:
23 4 0.04
24 2 0.02
25 4 0.04
26 3 0.03
27 4 0.04
28 16 0.16
29 26 0.26
30 15 0.15
31 16 0.16
32 10 0.10
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (27 bp):
TATTATTAAATATATAAATAATATTAT
Found at i:79297 original size:60 final size:62
Alignment explanation
Indices: 79185--79335 Score: 147
Period size: 60 Copynumber: 2.5 Consensus size: 62
79175 TAGTATATTT
* * * *
79185 TAAA-TATCTTTATTAAAATATTATTTAAATATATAAATAATATTATTCATTATTA-AATATA-
1 TAAATTAT-TTTATT-ATATATTATTAAAATAAAAAAATAATATTATTCATTATTATAATATAG
*
79246 TAAATTTTTTTATTATATATTATTAAAATAAAAAAATAATATCT-TAT-ATTATTATAATATAG
1 TAAATTATTTTATTATATATTATTAAAATAAAAAAATAATAT-TAT-TCATTATTATAATATAG
*
79308 TTAATTATTTTA-TATA-A-TATTTAAAATA
1 TAAATTATTTTATTATATATTA-TTAAAATA
79336 TAATATTATA
Statistics
Matches: 77, Mismatches: 7, Indels: 13
0.79 0.07 0.13
Matches are distributed among these distances:
59 2 0.03
60 41 0.53
61 22 0.29
62 12 0.16
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (62 bp):
TAAATTATTTTATTATATATTATTAAAATAAAAAAATAATATTATTCATTATTATAATATAG
Found at i:79331 original size:20 final size:19
Alignment explanation
Indices: 79280--79331 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
79270 AAAATAAAAA
79280 AATAATATCTTATATTATTAT
1 AATAATAT-TTA-ATTATTAT
* *
79301 AAT-ATAGTTAATTATTTT
1 AATAATATTTAATTATTAT
79319 ATATAATATTTAA
1 A-ATAATATTTAA
79332 AATATAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 8 0.31
19 5 0.19
20 10 0.38
21 3 0.12
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
AATAATATTTAATTATTAT
Found at i:79345 original size:22 final size:23
Alignment explanation
Indices: 79320--79363 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
79310 AATTATTTTA
79320 TATAATATT-TAAA-ATATAATAT
1 TATAATATTATAAATAT-TAATAT
*
79342 TATATTATTATAAATATTAATA
1 TATAATATTATAAATATTAATA
79364 AATTAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 9 0.47
24 2 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TATAATATTATAAATATTAATAT
Found at i:79353 original size:60 final size:57
Alignment explanation
Indices: 79206--79353 Score: 131
Period size: 60 Copynumber: 2.5 Consensus size: 57
79196 ATTAAAATAT
* * *
79206 TATTTAAATATATAAATAATATTATT-CATTATTAAATATATAAATTTTTTTATTATA
1 TATTTAAA-ATATAAATTATATTATTATATTATTAAATATATAAATTATTTTATTATA
** * *
79263 TATTATTAAAATA-AAAAAATAATATCTTATATTATTATAATATAGTTAATTATTTTA-TATAA
1 TA-T-TTAAAATATAAATTAT-AT-TATTATATTATTA-AATATA-TAAATTATTTTATTAT-A
79325 TATTTAAAATATAATATTATATTATTATA
1 TATTTAAAATATAA-ATTATATTATTATA
79354 AATATTAATA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
57 8 0.11
58 6 0.08
59 8 0.11
60 21 0.29
61 14 0.19
62 16 0.22
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (57 bp):
TATTTAAAATATAAATTATATTATTATATTATTAAATATATAAATTATTTTATTATA
Found at i:79371 original size:31 final size:31
Alignment explanation
Indices: 79313--79371 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
79303 TATAGTTAAT
*
79313 TATTTTATATAATATTTAAAATATAATATTA
1 TATTTTATATAATATTAAAAATATAATATTA
79344 TATTATTATA-AATATTAATAAAT-TAATA
1 TATT-TTATATAATATTAA-AAATATAATA
79372 AATAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TATTTTATATAATATTAAAAATATAATATTA
Found at i:79610 original size:14 final size:14
Alignment explanation
Indices: 79593--79645 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
79583 GAAAAATATT
*
79593 TTACGGAAAACGAA
1 TTACGTAAAACGAA
79607 TTACGTAAAAC-AA
1 TTACGTAAAACGAA
* **
79620 ATACAAAAATACGAA
1 TTACGTAAA-ACGAA
79635 TTACGTAAAAC
1 TTACGTAAAAC
79646 AAACACAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
13 8 0.27
14 14 0.47
15 8 0.27
ACGTcount: A:0.55, C:0.15, G:0.11, T:0.19
Consensus pattern (14 bp):
TTACGTAAAACGAA
Found at i:79633 original size:28 final size:28
Alignment explanation
Indices: 79602--79657 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
79592 TTTACGGAAA
*
79602 ACGAATTACGTAAAACAAATACAAAAAT
1 ACGAATTACGTAAAACAAACACAAAAAT
79630 ACGAATTACGTAAAACAAACACAAAAAT
1 ACGAATTACGTAAAACAAACACAAAAAT
79658 TTGAAGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.61, C:0.16, G:0.07, T:0.16
Consensus pattern (28 bp):
ACGAATTACGTAAAACAAACACAAAAAT
Found at i:80783 original size:60 final size:60
Alignment explanation
Indices: 80656--80771 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
80646 ATAGTAGATT
* * *
80656 GATCATTTTGTAACCTTTAATAGTCGAATGACTCAACAAAGAACTTTCCTATAATCAGGA
1 GATCATTTTGTAACATTTAATAATCGAATGACTCAACAAAGAACTATCCTATAATCAGGA
* * * * *
80716 GATCATTTTGTAACATTTAATAAT-TAATAGACTCAATAAAGCAGTATCTTATAATC
1 GATCATTTTGTAACATTTAATAATCGAAT-GACTCAACAAAGAACTATCCTATAATC
80772 GAGGTATCAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 3 0.06
60 44 0.94
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (60 bp):
GATCATTTTGTAACATTTAATAATCGAATGACTCAACAAAGAACTATCCTATAATCAGGA
Found at i:83829 original size:17 final size:18
Alignment explanation
Indices: 83790--83836 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
83780 TGTTTATGTT
83790 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
83808 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
83825 GGAATTGGAATC
1 GGAATTGGAATC
83837 CAATTCTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:90201 original size:55 final size:50
Alignment explanation
Indices: 90105--90214 Score: 125
Period size: 55 Copynumber: 2.1 Consensus size: 50
90095 TTTTCAATTT
* *
90105 TATA-AAAAAAATTATATAAATTATATAAATTTAATTTTTAAAAATA-AAA
1 TATATAAAAAAATTATATAAATTATATAAATTCAATTGTTAAAAA-ACAAA
*
90154 TATATAAAATAATTATAGTAATATTATAGTATAATTCAACTTGTTAAAAAACAAA
1 TATATAAAAAAATTATA-TAA-ATTATA-TA-AATTCAA-TTGTTAAAAAACAAA
90209 TATATA
1 TATATA
90215 TAAGGACAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
49 4 0.08
50 11 0.22
51 3 0.06
52 6 0.12
53 2 0.04
54 7 0.14
55 18 0.35
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (50 bp):
TATATAAAAAAATTATATAAATTATATAAATTCAATTGTTAAAAAACAAA
Found at i:96667 original size:34 final size:34
Alignment explanation
Indices: 96624--96694 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
96614 TTATGTTCGT
96624 TCTGGTTTGTGGTTTTGTTCTATGTTGCTCCAAC
1 TCTGGTTTGTGGTTTTGTTCTATGTTGCTCCAAC
96658 TCTGGTTTGTGGTTTTGTTCTATGTTGCTCCAAC
1 TCTGGTTTGTGGTTTTGTTCTATGTTGCTCCAAC
96692 TCT
1 TCT
96695 TCACTACACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.08, C:0.18, G:0.23, T:0.51
Consensus pattern (34 bp):
TCTGGTTTGTGGTTTTGTTCTATGTTGCTCCAAC
Found at i:105081 original size:2 final size:2
Alignment explanation
Indices: 105074--105102 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
105064 AATTCTAAAT
105074 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
105103 TAATAATACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:106334 original size:6 final size:6
Alignment explanation
Indices: 106323--106347 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
106313 TCGGCTCGGC
106323 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
106348 GTATCCAACA
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:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:109990 original size:21 final size:21
Alignment explanation
Indices: 109964--110003 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
109954 CTATCTCTAA
*
109964 CTTAAACCCTAAATTATAAGT
1 CTTAAACCCTAAATCATAAGT
*
109985 CTTAAAGCCTAAATCATAA
1 CTTAAACCCTAAATCATAA
110004 CTCCATAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (21 bp):
CTTAAACCCTAAATCATAAGT
Found at i:116058 original size:13 final size:13
Alignment explanation
Indices: 116040--116065 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
116030 GCTGGGCATC
116040 CGAGGCCATCCGA
1 CGAGGCCATCCGA
116053 CGAGGCCATCCGA
1 CGAGGCCATCCGA
116066 AAGCATCCGA
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:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (13 bp):
CGAGGCCATCCGA
Found at i:116072 original size:33 final size:34
Alignment explanation
Indices: 116035--116099 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
116025 AACACGCTGG
116035 GCATCCGAGGCCATCCGA-CGAGGCCATCCGAAA
1 GCATCCGAGGCCATCCGACCGAGGCCATCCGAAA
* *
116068 GCATCCGAGGTCATCCGACCGAGGGCATCCGA
1 GCATCCGAGGCCATCCGACCGAGGCCATCCGA
116100 GGGCAACCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.25, C:0.35, G:0.29, T:0.11
Consensus pattern (34 bp):
GCATCCGAGGCCATCCGACCGAGGCCATCCGAAA
Found at i:116099 original size:10 final size:10
Alignment explanation
Indices: 116033--116137 Score: 57
Period size: 10 Copynumber: 9.5 Consensus size: 10
116023 CCAACACGCT
116033 GGGCATCCGA
1 GGGCATCCGA
*
116043 GGCCATCCGA
1 GGGCATCCGA
116053 CGAGGCCATCCGA
1 -G-GG-CATCCGA
**
116066 AAGCATCCGA
1 GGGCATCCGA
*
116076 GGTCATCCGACCGA
1 GGGCAT----CCGA
116090 GGGCATCCGA
1 GGGCATCCGA
*
116100 GGGCAACCGA
1 GGGCATCCGA
*
116110 GTGAGCTATGCGA
1 G-G-GC-ATCCGA
*
116123 GGGAATCCGA
1 GGGCATCCGA
116133 GGGCA
1 GGGCA
116138 ACCTACAAGA
Statistics
Matches: 71, Mismatches: 14, Indels: 20
0.68 0.13 0.19
Matches are distributed among these distances:
10 42 0.59
11 4 0.06
12 4 0.06
13 12 0.17
14 9 0.13
ACGTcount: A:0.25, C:0.30, G:0.35, T:0.10
Consensus pattern (10 bp):
GGGCATCCGA
Found at i:116258 original size:11 final size:10
Alignment explanation
Indices: 116218--116266 Score: 64
Period size: 10 Copynumber: 4.8 Consensus size: 10
116208 GCTCGGTTGC
116218 CCTCGGATGG
1 CCTCGGATGG
116228 CCTCGGAT-G
1 CCTCGGATGG
116237 CTCTCGGATGG
1 C-CTCGGATGG
*
116248 CTTCGGGATGG
1 CCTC-GGATGG
116259 CCTCGGAT
1 CCTCGGAT
116267 TCCCAGCGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 21 0.62
11 11 0.32
ACGTcount: A:0.10, C:0.29, G:0.37, T:0.24
Consensus pattern (10 bp):
CCTCGGATGG
Done.