Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002462.1 Hibiscus syriacus cultivar Beakdansim tig00005038_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: 90752
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2382 original size:21 final size:21
Alignment explanation
Indices: 2342--2382 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2332 TTGAGCACAC
**
2342 ATATTAAACCATTTTTATCAT
1 ATATTAAACCATTTAGATCAT
*
2363 ATATTAAACCCTTTAGATCA
1 ATATTAAACCATTTAGATCA
2383 ATCCAAGCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.41
Consensus pattern (21 bp):
ATATTAAACCATTTAGATCAT
Found at i:6026 original size:11 final size:11
Alignment explanation
Indices: 6010--6056 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
6000 AAATTTTAGT
6010 TATTAATAAAA
1 TATTAATAAAA
6021 TATTAATAAATA
1 TATTAATAAA-A
*
6033 AATTTAAT-AAA
1 TA-TTAATAAAA
6044 TATTAATAAAA
1 TATTAATAAAA
6055 TA
1 TA
6057 AATTCGAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 5 0.16
11 17 0.55
12 4 0.13
13 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TATTAATAAAA
Found at i:6043 original size:9 final size:10
Alignment explanation
Indices: 6010--6053 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 10
6000 AAATTTTAGT
6010 TATTAATAAAA
1 TATTAAT-AAA
6021 TATTAATAAA
1 TATTAATAAA
6031 TAAATTTAATAAA
1 T--A-TTAATAAA
6044 TATTAATAAA
1 TATTAATAAA
6054 ATAAATTCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 12 0.40
11 8 0.27
12 1 0.03
13 9 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TATTAATAAA
Found at i:6048 original size:23 final size:25
Alignment explanation
Indices: 6012--6060 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
6002 ATTTTAGTTA
6012 TTAATAAAATATTAAT-AAATAAAT
1 TTAATAAAATATTAATAAAATAAAT
6036 TTAAT-AAATATTAATAAAATAAAT
1 TTAATAAAATATTAATAAAATAAAT
6060 T
1 T
6061 CGAGTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
TTAATAAAATATTAATAAAATAAAT
Found at i:7235 original size:19 final size:19
Alignment explanation
Indices: 7185--7241 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
7175 TCTTAAAATG
7185 ATATGAAATAAAATATAAAAC
1 ATATGAAA-AAAATAT-AAAC
* *
7206 ATAAT-ATAAAATTATAAAC
1 AT-ATGAAAAAAATATAAAC
7225 ATATGAAAAAAATATAA
1 ATATGAAAAAAATATAA
7242 CTTATATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
18 2 0.07
19 16 0.53
20 6 0.20
21 4 0.13
22 2 0.07
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.26
Consensus pattern (19 bp):
ATATGAAAAAAATATAAAC
Found at i:21283 original size:51 final size:51
Alignment explanation
Indices: 21203--21301 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
21193 CTAAGATTAA
* *
21203 TAAAATGTATAGGAATCAATCAATGGAAGAAAAATGCTTAAAGTGCACTGG
1 TAAAATGTATAGGAACCAATCAATAGAAGAAAAATGCTTAAAGTGCACTGG
* *
21254 TAAAATGTGTAGGAACCAATCAATAGAAGAGAAATGCTTAAAGTGCAC
1 TAAAATGTATAGGAACCAATCAATAGAAGAAAAATGCTTAAAGTGCAC
21302 AAGTATGAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.22
Consensus pattern (51 bp):
TAAAATGTATAGGAACCAATCAATAGAAGAAAAATGCTTAAAGTGCACTGG
Found at i:24092 original size:64 final size:64
Alignment explanation
Indices: 23985--24114 Score: 224
Period size: 64 Copynumber: 2.0 Consensus size: 64
23975 ATTACTCAGC
*
23985 ATGGAACCAAGTCTGGAACCTTTTATATTACTCTCCTTAGCCTGGTTTTCATTTATTTATATAT
1 ATGGAACCAAGTCTGGAACCTTTTATATTACTCTCCATAGCCTGGTTTTCATTTATTTATATAT
* * *
24049 ATGGAACCAAGTCTGGAACCTTTTATATTACTCTTCATCGCCTGGTTTTCATTTTTTTATATAT
1 ATGGAACCAAGTCTGGAACCTTTTATATTACTCTCCATAGCCTGGTTTTCATTTATTTATATAT
24113 AT
1 AT
24115 CAAAACTTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (64 bp):
ATGGAACCAAGTCTGGAACCTTTTATATTACTCTCCATAGCCTGGTTTTCATTTATTTATATAT
Found at i:37710 original size:35 final size:37
Alignment explanation
Indices: 37652--37723 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 37
37642 CTTAATATCG
*
37652 AAAATAAATAAATATTAATAATATGATATTTTTTTATAA
1 AAAATAAATAAATATTAATAATAT-ATA-ATTTTTATAA
37691 AAAAT-AATAAA-ATT-A-AATATATAATTTTTATAA
1 AAAATAAATAAATATTAATAATATATAATTTTTATAA
37724 TATTTATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
33 9 0.28
34 3 0.09
35 5 0.16
36 1 0.03
37 3 0.09
38 6 0.19
39 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (37 bp):
AAAATAAATAAATATTAATAATATATAATTTTTATAA
Found at i:37804 original size:140 final size:142
Alignment explanation
Indices: 37424--37808 Score: 446
Period size: 146 Copynumber: 2.7 Consensus size: 142
37414 TTTTTTTATT
*
37424 TTTATAAATAAGATATTTATTTACTTAGAAATATCAGAAAAAGACTTCTAGGTGCTTTAAGA-TA
1 TTTATAAATAAGATATTTATTTATTTA-AAATATCAGAAAAAGACTTCTAGGTGCTTTAAGACT-
37488 GCCCATTTCTTAATATTAAAAAATAAATAAATATTAATAAAACATTTCTCTAAAAATAATTAAAA
64 G-CCATTTCTTAATATTAAAAAATAAATAAATATTAATAAAACATTTCTCTAAAAATAATTAAAA
37553 TAAATTAATATATAA
128 TAAATTAATATATAA
*
37568 TTTATAAAAATAAGATATTTATTTATTTAAGAATATCAGAAAAAGACTTCTAGGTACTTTAAGAC
1 TTTAT--AAATAAGATATTTATTTATTTAA-AATATCAGAAAAAGACTTCTAGGTGCTTTAAGAC
** ** * * *
37633 AACCCATTTCTTAATA-TCGAAAATAAATAAATATTAATAATATGATATTTTTTTATAAAA-AA-
63 -TGCCATTTCTTAATATTAAAAAATAAATAAATATTAATAA-A--ACATTTCTCTA-AAAATAAT
*
37695 TAATA-AAATTAAATATATAA
123 TAAAATAAATT-AATATATAA
* * * * * * *
37715 TTT-T-TAT-A-ATATTTATTTATTTAAAATACCAGAATAGGACATCTAGTTGCTTTAAGACTGT
1 TTTATAAATAAGATATTTATTTATTTAAAATATCAGAAAAAGACTTCTAGGTGCTTTAAGACTGC
37776 CATTTCTTAATATTAAAAAATAAATAAATATTA
66 CATTTCTTAATATTAAAAAATAAATAAATATTA
37809 TTATTTAAAT
Statistics
Matches: 208, Mismatches: 22, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
139 12 0.06
140 46 0.22
141 16 0.08
142 1 0.00
143 2 0.01
144 5 0.02
145 23 0.11
146 73 0.35
147 16 0.08
148 10 0.05
149 4 0.02
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (142 bp):
TTTATAAATAAGATATTTATTTATTTAAAATATCAGAAAAAGACTTCTAGGTGCTTTAAGACTGC
CATTTCTTAATATTAAAAAATAAATAAATATTAATAAAACATTTCTCTAAAAATAATTAAAATAA
ATTAATATATAA
Found at i:39197 original size:3 final size:3
Alignment explanation
Indices: 39191--39267 Score: 92
Period size: 3 Copynumber: 26.7 Consensus size: 3
39181 TTTTTATTAT
*
39191 TAA TAA TAA TATA TAA T-A TAA TAA TAA -AA TAA TAA TAA TAG T-A
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39234 TAAA TAA -AA TAA -AA TAA TAA TAA TAA TAA TAA TA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
39268 GCAAATGGAT
Statistics
Matches: 65, Mismatches: 2, Indels: 14
0.80 0.02 0.17
Matches are distributed among these distances:
2 9 0.14
3 51 0.78
4 5 0.08
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:39261 original size:34 final size:29
Alignment explanation
Indices: 39191--39267 Score: 104
Period size: 31 Copynumber: 2.6 Consensus size: 29
39181 TTTTTATTAT
*
39191 TAATAATAATATATAATATAATAATAAAA
1 TAATAATAATATATAATAAAATAATAAAA
39220 TAATAATAATAGTATAAATAAAATAA-AATAA
1 TAATAATAATA-TAT-AATAAAATAATAA-AA
39251 TAATAATAATA-ATAATA
1 TAATAATAATATATAATA
39268 GCAAATGGAT
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
28 4 0.09
29 13 0.30
30 5 0.11
31 22 0.50
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (29 bp):
TAATAATAATATATAATAAAATAATAAAA
Found at i:40106 original size:113 final size:112
Alignment explanation
Indices: 39873--40314 Score: 688
Period size: 113 Copynumber: 3.9 Consensus size: 112
39863 TGGGATAGAA
* * *
39873 TCGAGCAAAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CATCTTCAGATGAGTTCT
1 TCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* *
39937 TCTCATTATGAACACTTCTGGAAATGTTGATCCATCGAGTGATGAAT
66 TCTCATTATGAACTCTCCTGGAAATGTTGATCCATCGAGTGATGAAT
39984 TCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
*
40049 TCTCATTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGAAT
66 TCTCATTATGAACTCT-CCTGGAAATGTTGATCCATCGAGTGATGAAT
* *
40097 TCGAGCAAAAGGTTGAATAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCT
1 TCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * *
40162 TCTCATTATGAACTCTACCTGGCAATGCTGATCCATTGAGTGATGAAT
66 TCTCATTATGAACTCT-CCTGGAAATGTTGATCCATCGAGTGATGAAT
* * * * *
40210 TCGAGCAAAAGGTTGAACAAGTTCTTTTCATAATGAACTTCTTATTGCTTCTTCAGATGAGTTCT
1 TCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * *
40275 TCTCATTATGAACTCTTCTGGAAATGTTAATCCATTGAGT
66 TCTCATTATGAACTCTCCTGGAAATGTTGATCCATCGAGT
40315 AATGGATTTA
Statistics
Matches: 308, Mismatches: 21, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
111 44 0.14
112 52 0.17
113 212 0.69
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (112 bp):
TCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTCTCCTGGAAATGTTGATCCATCGAGTGATGAAT
Found at i:40707 original size:22 final size:22
Alignment explanation
Indices: 40668--40723 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
40658 AATAAAGCTT
*
40668 TCATCTTT-AACAGAGAATATA
1 TCATCTTTGAAGAGAGAATATA
*
40689 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATATA
40711 TCATCTTTGAAGA
1 TCATCTTTGAAGA
40724 ATGTAGATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATATA
Found at i:45742 original size:25 final size:25
Alignment explanation
Indices: 45707--45771 Score: 105
Period size: 25 Copynumber: 2.6 Consensus size: 25
45697 TGATTCAATT
*
45707 TTTTTTCCTTTTTTTCCTTTTTTTC
1 TTTTTTTCTTTTTTTCCTTTTTTTC
45732 TTTTTTTCTTTTTTTCCTTTTTTTC
1 TTTTTTTCTTTTTTTCCTTTTTTTC
*
45757 -TTTTTTCTTTCTTTC
1 TTTTTTTCTTTTTTTC
45772 TGATGAATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 14 0.37
25 24 0.63
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (25 bp):
TTTTTTTCTTTTTTTCCTTTTTTTC
Found at i:45771 original size:8 final size:8
Alignment explanation
Indices: 45706--45772 Score: 91
Period size: 8 Copynumber: 8.1 Consensus size: 8
45696 TTGATTCAAT
45706 TTTTTTTCC
1 TTTTTTT-C
45715 TTTTTTTCC
1 TTTTTTT-C
45724 TTTTTTTC
1 TTTTTTTC
45732 TTTTTTTC
1 TTTTTTTC
45740 TTTTTTTCC
1 TTTTTTT-C
45749 TTTTTTTC
1 TTTTTTTC
45757 -TTTTTTC
1 TTTTTTTC
*
45764 TTTCTTTC
1 TTTTTTTC
45772 T
1 T
45773 GATGAATGAG
Statistics
Matches: 55, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
7 7 0.13
8 24 0.44
9 24 0.44
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTC
Found at i:48795 original size:13 final size:14
Alignment explanation
Indices: 48779--48832 Score: 76
Period size: 13 Copynumber: 3.9 Consensus size: 14
48769 AGCAAACAAC
48779 AAATGCAAAATG-A
1 AAATGCAAAATGCA
48792 AAATGCAAAGATGCA
1 AAATGCAAA-ATGCA
48807 AAATG-AAAATGCA
1 AAATGCAAAATGCA
48820 AAGATGCAAAATG
1 AA-ATGCAAAATG
48833 TGTTACTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
13 16 0.43
14 9 0.24
15 12 0.32
ACGTcount: A:0.57, C:0.09, G:0.19, T:0.15
Consensus pattern (14 bp):
AAATGCAAAATGCA
Found at i:48807 original size:8 final size:7
Alignment explanation
Indices: 48779--48832 Score: 76
Period size: 7 Copynumber: 7.7 Consensus size: 7
48769 AGCAAACAAC
48779 AAATGCA
1 AAATGCA
48786 AAATG-A
1 AAATGCA
48792 AAATGCA
1 AAATGCA
48799 AAGATGCA
1 AA-ATGCA
48807 AAATG-A
1 AAATGCA
48813 AAATGCA
1 AAATGCA
48820 AAGATGCA
1 AA-ATGCA
48828 AAATG
1 AAATG
48833 TGTTACTCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
6 12 0.28
7 17 0.40
8 14 0.33
ACGTcount: A:0.57, C:0.09, G:0.19, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:48807 original size:21 final size:21
Alignment explanation
Indices: 48781--48832 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
48771 CAAACAACAA
48781 ATGCAAAATGAAAATGCAAAG
1 ATGCAAAATGAAAATGCAAAG
48802 ATGCAAAATGAAAATGCAAAG
1 ATGCAAAATGAAAATGCAAAG
48823 ATGCAAAATG
1 ATGCAAAATG
48833 TGTTACTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.56, C:0.10, G:0.19, T:0.15
Consensus pattern (21 bp):
ATGCAAAATGAAAATGCAAAG
Found at i:50848 original size:21 final size:22
Alignment explanation
Indices: 50824--50864 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
50814 ATATATTAAT
* *
50824 ATATTT-TTTTTTATAAATAAG
1 ATATTTATTATTTAGAAATAAG
50845 ATATTTATTATTTAGAAATA
1 ATATTTATTATTTAGAAATA
50865 TCAGAAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (22 bp):
ATATTTATTATTTAGAAATAAG
Found at i:50962 original size:34 final size:32
Alignment explanation
Indices: 50906--50988 Score: 80
Period size: 34 Copynumber: 2.5 Consensus size: 32
50896 GCACATTTCT
50906 TAATATTA-AAAAATAAATAAAT-ATTAATAAAA
1 TAAT-TTATAAAAATAAATAAATAATTAAT-AAA
* * *
50938 TATTTCTATAAAAATAATTAAAATAAATTAATATA
1 TAATT-TATAAAAATAAAT-AAAT-AATTAATAAA
50973 TAATTTATAAAAATAA
1 TAATTTATAAAAATAA
50989 GATATTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
31 1 0.02
32 5 0.12
33 9 0.21
34 15 0.36
35 6 0.14
36 6 0.14
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (32 bp):
TAATTTATAAAAATAAATAAATAATTAATAAA
Found at i:51012 original size:146 final size:144
Alignment explanation
Indices: 50837--51210 Score: 414
Period size: 146 Copynumber: 2.6 Consensus size: 144
50827 TTTTTTTTTA
50837 TAAATAAGATATTTA-TTATTTAGAAATATCAGAAAATGACTTCTAGGTGCTTTAAGACAGCACA
1 TAAATAAGATATTTATTTATTTAG-AATATCAGAAAATGACTTCTAGGTGCTTTAAGACAGCACA
50901 TTTCTTAATATTAAAAAATAAATAAATATTAAT-A-AA-AT-A-TTTCTAT-AAAAATAATTAAA
65 TTTCTTAATATTAAAAAATAAATAAATATTAATAATAAGATAATTTTCTATAAAAAATAA-TAAA
*
50960 ATAAATTAATATATAATTT
129 AT---TAAATATATAATTT
* * * *
50979 ATAAAAATAAGATATTTATTTATTGAAGAATATCATAAAATGACTTATAGGTGCTTTAAGACATC
1 -T--AAATAAGATATTTATTTATT-TAGAATATCAGAAAATGACTTCTAGGTGCTTTAAGACAGC
* ** *
51044 CCATTTCTTAATATCGAAAAATAAATAAATATTAATAATAAGATAATTTTTTATAAAAAATAATA
62 ACATTTCTTAATATTAAAAAATAAATAAATATTAATAATAAGATAATTTTCTATAAAAAATAATA
51109 AAATTAAATATATAATTT
127 AAATTAAATATATAATTT
* * * * * * *
51127 T-TAT-A-ATATTTATTTATTTTA-AATACCAG-AATTGGACATCTAGTTGCTTTAAGACTG-TC
1 TAAATAAGATATTTATTTA-TTTAGAATATCAGAAAAT-GACTTCTAGGTGCTTTAAGACAGCAC
51186 ATTTCTTAATATTAAAAAATAAATA
64 ATTTCTTAATATTAAAAAATAAATA
51211 TATTATTTAA
Statistics
Matches: 197, Mismatches: 22, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
140 27 0.14
141 24 0.12
142 12 0.06
143 4 0.02
144 2 0.01
145 14 0.07
146 72 0.37
147 4 0.02
148 15 0.08
149 2 0.01
150 1 0.01
151 12 0.06
152 8 0.04
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (144 bp):
TAAATAAGATATTTATTTATTTAGAATATCAGAAAATGACTTCTAGGTGCTTTAAGACAGCACAT
TTCTTAATATTAAAAAATAAATAAATATTAATAATAAGATAATTTTCTATAAAAAATAATAAAAT
TAAATATATAATTT
Found at i:51344 original size:14 final size:13
Alignment explanation
Indices: 51325--51372 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 13
51315 AAATAGTGAC
51325 TAAAATAATAATAT
1 TAAAATAA-AATAT
* *
51339 TAAAATAAAAGAA
1 TAAAATAAAATAT
51352 TAAAATGTAAAATAT
1 TAAAA--TAAAATAT
51367 TAAAAT
1 TAAAAT
51373 TTAGGGACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
13 9 0.32
14 8 0.29
15 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (13 bp):
TAAAATAAAATAT
Found at i:51353 original size:19 final size:20
Alignment explanation
Indices: 51325--51365 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
51315 AAATAGTGAC
* *
51325 TAAAATAATAATAT-TAAAA
1 TAAAAGAATAAAATGTAAAA
51344 TAAAAGAATAAAATGTAAAA
1 TAAAAGAATAAAATGTAAAA
51364 TA
1 TA
51366 TTAAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (20 bp):
TAAAAGAATAAAATGTAAAA
Found at i:51466 original size:15 final size:15
Alignment explanation
Indices: 51446--51485 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
51436 TTAATCGGTG
*
51446 ATTAAAATATAAGTT
1 ATTAAAATATAAATT
*
51461 ATTAAAATGTAAATT
1 ATTAAAATATAAATT
51476 ATTAAAATAT
1 ATTAAAATAT
51486 GAGGGACTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (15 bp):
ATTAAAATATAAATT
Found at i:52620 original size:3 final size:3
Alignment explanation
Indices: 52614--52711 Score: 89
Period size: 3 Copynumber: 33.3 Consensus size: 3
52604 TTTTTTATTG
*
52614 ATA ATA ATA ATA ATA ATAA ATA ATA CATA AT- ATA ATA A-A AAA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA -ATA ATA ATA ATA ATA ATA ATA
* * *
52659 ATA ATA ATA GT- ATAA ATA A-A ATA ATA CTA ATA AAA AT- ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
52702 AAA ATA ATA A
1 ATA ATA ATA A
52712 AAAACAAATG
Statistics
Matches: 78, Mismatches: 9, Indels: 16
0.76 0.09 0.16
Matches are distributed among these distances:
2 9 0.12
3 61 0.78
4 8 0.10
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:52643 original size:26 final size:23
Alignment explanation
Indices: 52615--52711 Score: 103
Period size: 23 Copynumber: 4.3 Consensus size: 23
52605 TTTTTATTGA
52615 TAATAATAATAAT-AATAAATAA
1 TAATAATAATAATAAATAAATAA
*
52637 TACATAAT-ATAATAAAAAAATAA
1 TA-ATAATAATAATAAATAAATAA
*
52660 TAATAATAGT-ATAAATAAAATAA
1 TAATAATAATAATAAAT-AAATAA
* *
52683 TACTAATAAAAATATAATAAA-AA
1 TAATAATAATAATA-AATAAATAA
52706 TAATAA
1 TAATAA
52712 AAAACAAATG
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
22 17 0.27
23 36 0.58
24 6 0.10
25 3 0.05
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.29
Consensus pattern (23 bp):
TAATAATAATAATAAATAAATAA
Found at i:52713 original size:20 final size:20
Alignment explanation
Indices: 52614--52714 Score: 114
Period size: 20 Copynumber: 5.0 Consensus size: 20
52604 TTTTTTATTG
52614 ATAATAATAATAATAATAAAT
1 ATAATAATAATAATAA-AAAT
*
52635 AATACATAAT-ATAATAAAAAA
1 -ATA-ATAATAATAATAAAAAT
* *
52656 ATAATAATAATAGTATAAAT
1 ATAATAATAATAATAAAAAT
* *
52676 AAAATAATACTAATAAAAAT
1 ATAATAATAATAATAAAAAT
*
52696 ATAATAAAAATAATAAAAA
1 ATAATAATAATAATAAAAA
52715 ACAAATGGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 5 0.08
20 43 0.65
21 3 0.05
22 10 0.15
23 5 0.08
ACGTcount: A:0.69, C:0.02, G:0.01, T:0.28
Consensus pattern (20 bp):
ATAATAATAATAATAAAAAT
Found at i:55383 original size:36 final size:36
Alignment explanation
Indices: 55305--55478 Score: 287
Period size: 36 Copynumber: 4.9 Consensus size: 36
55295 ACGATGTTGG
*
55305 ACATTGATACACGAATGTATCAAAGCTGATA-GATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
55340 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
55376 ACATTGATACATGAATGTACCAAAGTTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
55412 ATATTGATACACGTATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
55448 ACATTGATACACGAATGTATCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
55479 ATACTCAACT
Statistics
Matches: 128, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 30 0.23
36 98 0.77
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:56773 original size:14 final size:14
Alignment explanation
Indices: 56750--56787 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
56740 TCTGTCTATA
*
56750 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
56763 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
56778 TGCAGGGATT
1 TGCAGGGATT
56788 ACTGCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:63323 original size:36 final size:36
Alignment explanation
Indices: 63270--63408 Score: 215
Period size: 36 Copynumber: 3.9 Consensus size: 36
63260 ACGATGCTAG
* *
63270 ACATTGATACACAAATGTGCCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* * *
63306 ACATTGATATATGAATGTACCAAAGGTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
63342 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
63378 ACACTGATACACGAATGTATCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
63409 ATACTCAACT
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 93 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:66993 original size:64 final size:65
Alignment explanation
Indices: 66920--67081 Score: 161
Period size: 64 Copynumber: 2.5 Consensus size: 65
66910 ATTGTTTGAA
* *** *
66920 GGTGTATCGATGCACAAGTAGTGCATCGATGCACT-CTTTTAATCTAA-AAACATCGAATGCAAT
1 GGTGCATCGATGCACAAGTAGTGCATCGATGCACTCCCAGTAAT-AAATAAACATCGAATGCAAT
66983 T
65 T
* * * * *
66984 GGTGCATCGATGCATAAGGCA-AGCATCGATGCA-TCCCAGTAATAAATAAACATCGAATGTATT
1 GGTGCATCGATGCACAA-GTAGTGCATCGATGCACTCCCAGTAATAAATAAACATCGAATGCAAT
67047 T
65 T
** *
67048 TATGCACCGATGCACAAGTAGTGCATCGATGCAC
1 GGTGCATCGATGCACAAGTAGTGCATCGATGCAC
67082 CGATAGGGAA
Statistics
Matches: 77, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
63 5 0.06
64 70 0.91
65 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (65 bp):
GGTGCATCGATGCACAAGTAGTGCATCGATGCACTCCCAGTAATAAATAAACATCGAATGCAATT
Found at i:74410 original size:21 final size:21
Alignment explanation
Indices: 74384--74424 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
74374 TATGGGCAAA
74384 GTGTATCGATGCACATTCAAT
1 GTGTATCGATGCACATTCAAT
* *
74405 GTGTATCGGTGCACTTTCAA
1 GTGTATCGATGCACATTCAA
74425 ATAAATGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (21 bp):
GTGTATCGATGCACATTCAAT
Found at i:74454 original size:18 final size:18
Alignment explanation
Indices: 74431--74467 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
74421 TCAAATAAAT
74431 GAACATCGAATGCAATTA
1 GAACATCGAATGCAATTA
74449 GAACATCGAATGCAATTA
1 GAACATCGAATGCAATTA
74467 G
1 G
74468 TGCATTGATG
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:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (18 bp):
GAACATCGAATGCAATTA
Found at i:76160 original size:23 final size:23
Alignment explanation
Indices: 76070--76152 Score: 121
Period size: 23 Copynumber: 3.6 Consensus size: 23
76060 CATTTTATAT
*
76070 GGCACTTCGGTACAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
76093 GGCACTTCGGTGCAATTCTACCC
1 GGCACTTCGGTGCAATTCTACGC
* * *
76116 GACACTTCAGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
76139 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
76153 TTTATACGAG
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:77597 original size:20 final size:17
Alignment explanation
Indices: 77563--77602 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 17
77553 TTCTTCGGTA
77563 TTACTCTTCCACTCTTC
1 TTACTCTTCCACTCTTC
77580 TTACTACTTCGCAGCTCTTC
1 TTACT-CTTC-CA-CTCTTC
77600 TTA
1 TTA
77603 TCTCATCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 4 0.20
19 2 0.10
20 9 0.45
ACGTcount: A:0.15, C:0.35, G:0.05, T:0.45
Consensus pattern (17 bp):
TTACTCTTCCACTCTTC
Found at i:82920 original size:29 final size:31
Alignment explanation
Indices: 82887--82948 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
82877 TTTCACTTTT
*
82887 ACCACTGATCT-TTCAATT-TTGTCAATCAA
1 ACCACTGAACTATTCAATTGTTGTCAATCAA
* *
82916 ACCACTTAACTATTTAATTGTTGTCAATCAA
1 ACCACTGAACTATTCAATTGTTGTCAATCAA
82947 AC
1 AC
82949 TACTAACCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 9 0.32
30 6 0.21
31 13 0.46
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.37
Consensus pattern (31 bp):
ACCACTGAACTATTCAATTGTTGTCAATCAA
Found at i:83663 original size:16 final size:16
Alignment explanation
Indices: 83633--83717 Score: 50
Period size: 16 Copynumber: 4.9 Consensus size: 16
83623 AATATTTAAT
*
83633 ATATAAATATTAAATAA
1 ATAT-AATATAAAATAA
83650 ATATAATATAAAATATTA
1 ATATAATATAAAATA--A
83668 AT-TAA-AT-AAATAA
1 ATATAATATAAAATAA
83681 TATTAATAATAGTATTAAATAA
1 -A-T-ATAATA-TA--AAATAA
*
83703 ATCTAATATAAAATA
1 ATATAATATAAAATA
83718 TTATTAATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 23
0.69 0.03 0.29
Matches are distributed among these distances:
13 1 0.02
14 1 0.02
15 6 0.11
16 17 0.31
17 10 0.18
18 6 0.11
19 6 0.11
20 1 0.02
21 1 0.02
22 6 0.11
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (16 bp):
ATATAATATAAAATAA
Found at i:83697 original size:53 final size:52
Alignment explanation
Indices: 83622--83792 Score: 152
Period size: 53 Copynumber: 3.2 Consensus size: 52
83612 ATATTATTAC
*
83622 TAATATTTAATATATAAATATTAAATAAATATAATATAAAATATTAATTAAATAAA
1 TAATA-TTAATA-AT-AGTATTAAATAAAT-TAATATAAAATATTAATTAAATAAA
* *
83678 TAATATTAATAATAGTATTAAATAAATCTAATATAAAATATT-ATTAATATTAT
1 TAATATTAATAATAGTATTAAATAAAT-TAATATAAAATATTAATTAA-ATAAA
* * * * *
83731 TAATAATAAAAATATGTGATT---TGAATTATTATAAAATATTATATTTTAATAAA
1 TAATATTAATAATA-GT-ATTAAATAAATTAATATAAAATATTA-A-TTAAATAAA
83784 TAATATTAA
1 TAATATTAA
83793 ATAAATCATA
Statistics
Matches: 97, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
51 13 0.13
52 9 0.09
53 54 0.56
54 7 0.07
55 9 0.09
56 5 0.05
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (52 bp):
TAATATTAATAATAGTATTAAATAAATTAATATAAAATATTAATTAAATAAA
Found at i:83722 original size:26 final size:25
Alignment explanation
Indices: 83611--83741 Score: 110
Period size: 26 Copynumber: 5.1 Consensus size: 25
83601 GCGATTTAAT
* *
83611 AATATTATTACTAAT-ATTTAATATAT
1 AATATTATTA--AATAAATTAATATAA
83637 AA-A-TATTAAATAAATATAATATAA
1 AATATTATTAAATAAAT-TAATATAA
83661 AATATTAATTAAATAAA-TAATATTAA
1 AATATT-ATTAAATAAATTAATA-TAA
*
83687 TAATAGTATTAAATAAATCTAATATAA
1 -AATATTATTAAATAAAT-TAATATAA
*
83714 AATATTATT-AATATTATTAATAATAA
1 AATATTATTAAATA-AATTAAT-ATAA
83740 AA
1 AA
83742 ATATGTGATT
Statistics
Matches: 89, Mismatches: 5, Indels: 22
0.77 0.04 0.19
Matches are distributed among these distances:
22 3 0.03
23 2 0.02
24 14 0.16
25 15 0.17
26 32 0.36
27 18 0.20
28 5 0.06
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (25 bp):
AATATTATTAAATAAATTAATATAA
Found at i:83725 original size:16 final size:16
Alignment explanation
Indices: 83653--83727 Score: 55
Period size: 16 Copynumber: 4.4 Consensus size: 16
83643 TAAATAAATA
83653 TAATATAAAATATTAAT
1 TAATATAAAATATT-AT
*
83670 TAA-ATAAATAATATTAA
1 TAATAT-AA-AATATTAT
*
83687 TAATAGTATTAAATA-AAT
1 TAATA-TA--AAATATTAT
83705 CTAATATAAAATATTAT
1 -TAATATAAAATATTAT
83722 TAATAT
1 TAATAT
83728 TATTAATAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 17
0.69 0.06 0.25
Matches are distributed among these distances:
16 13 0.28
17 11 0.24
18 11 0.24
19 10 0.22
20 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (16 bp):
TAATATAAAATATTAT
Found at i:83731 original size:12 final size:12
Alignment explanation
Indices: 83606--83738 Score: 62
Period size: 12 Copynumber: 10.8 Consensus size: 12
83596 AATATGCGAT
83606 TTAATAATATTA
1 TTAATAATATTA
*
83618 TTACTAATA-T-
1 TTAATAATATTA
*
83628 TTAATATATAAATA
1 TTAATA-AT-ATTA
*
83642 TTAAATAAATATAA
1 TT-AAT-AATATTA
83656 TATAA-AATATTAA
1 T-TAATAATATT-A
*
83669 TTAAATAAATAATA
1 TT-AAT-AATATTA
*
83683 TTAATAATAGTA
1 TTAATAATATTA
83695 TTAAATAA-ATCTA
1 TT-AATAATAT-TA
* *
83708 AT-ATAA-AATA
1 TTAATAATATTA
*
83718 TTATTAATATTA
1 TTAATAATATTA
83730 TTAATAATA
1 TTAATAATA
83739 AAAATATGTG
Statistics
Matches: 92, Mismatches: 14, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
10 8 0.09
11 11 0.12
12 35 0.38
13 16 0.17
14 10 0.11
15 11 0.12
16 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.42
Consensus pattern (12 bp):
TTAATAATATTA
Found at i:83902 original size:27 final size:25
Alignment explanation
Indices: 83855--83906 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
83845 TAGATATATC
*
83855 TAATTAATAATATTGATTTAAACTAT
1 TAATTAATAATATTCATTT-AACTAT
83881 TAATCTAATAATATTTCA-TTAACTAT
1 TAAT-TAATAATA-TTCATTTAACTAT
83907 AATATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 10 0.43
27 10 0.43
28 3 0.13
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (25 bp):
TAATTAATAATATTCATTTAACTAT
Found at i:86297 original size:26 final size:26
Alignment explanation
Indices: 86206--86290 Score: 143
Period size: 26 Copynumber: 3.3 Consensus size: 26
86196 GTACTAAATT
* *
86206 TTACATTCGAAACATTAACTTATACA
1 TTACATTAGAAACATTAACTTCTACA
86232 TTACATTAGAAACATTAACTTCTACA
1 TTACATTAGAAACATTAACTTCTACA
*
86258 TTGCATTAGAAACATTAACTTCTACA
1 TTACATTAGAAACATTAACTTCTACA
86284 TTACATT
1 TTACATT
86291 TGTAACACCC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (26 bp):
TTACATTAGAAACATTAACTTCTACA
Found at i:86496 original size:17 final size:16
Alignment explanation
Indices: 86469--86500 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
86459 ACAGTAAAAC
86469 ACAGTATGAACAGTGA
1 ACAGTATGAACAGTGA
86485 ACAGTAATGAACAGTG
1 ACAGT-ATGAACAGTG
86501 CCGAATGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (16 bp):
ACAGTATGAACAGTGA
Done.