Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004082.1 Hibiscus syriacus cultivar Beakdansim tig00008933_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: 88983
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:6825 original size:3 final size:3
Alignment explanation
Indices: 6813--6861 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
6803 CTTAGTGAGG
6813 TAA T-A TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6859 TAA
1 TAA
6862 CAATGAAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:7107 original size:23 final size:23
Alignment explanation
Indices: 7081--7128 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
7071 CTCGCATAAA
7081 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
* * *
7104 TGCACTGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACATAGAAT
7127 TG
1 TG
7129 AATTGTAGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:7138 original size:23 final size:23
Alignment explanation
Indices: 7087--7141 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
7077 TAAATGCACC
*
7087 GAAGTGCCACATAGAATTGCACT
1 GAAGTGCCACATAGAATTGAACT
* * *
7110 GAAGTGCCGCGTAGAATTGAATT
1 GAAGTGCCACATAGAATTGAACT
*
7133 GTAGTGCCA
1 GAAGTGCCA
7142 TATAAGATGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (23 bp):
GAAGTGCCACATAGAATTGAACT
Found at i:15681 original size:18 final size:18
Alignment explanation
Indices: 15658--15712 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
15648 CATCGGGACC
15658 ATATTGCAAACGGACTAA
1 ATATTGCAAACGGACTAA
* *
15676 ATATTG---AGGGAC--C
1 ATATTGCAAACGGACTAA
15689 ATATTGCAAACGGACTAA
1 ATATTGCAAACGGACTAA
15707 ATATTG
1 ATATTG
15713 GGAGATTGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
13 6 0.21
15 5 0.18
16 5 0.18
18 12 0.43
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (18 bp):
ATATTGCAAACGGACTAA
Found at i:15725 original size:31 final size:31
Alignment explanation
Indices: 15652--15712 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
15642 CAGTTACATC
15652 GGGACCATATTGCAAACGGACTAAATATTGA
1 GGGACCATATTGCAAACGGACTAAATATTGA
15683 GGGACCATATTGCAAACGGACTAAATATTG
1 GGGACCATATTGCAAACGGACTAAATATTG
15713 GGAGATTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
GGGACCATATTGCAAACGGACTAAATATTGA
Found at i:17168 original size:29 final size:30
Alignment explanation
Indices: 17134--17191 Score: 100
Period size: 29 Copynumber: 1.9 Consensus size: 30
17124 GTTACATCAT
17134 GGACCATATTGCAAA-GACTAAATGTTGAG
1 GGACCATATTGCAAACGACTAAATGTTGAG
17163 GGACCATATTGCAAACGGACTAAATGTTG
1 GGACCATATTGCAAAC-GACTAAATGTTG
17192 GAGGATTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 15 0.56
31 12 0.44
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (30 bp):
GGACCATATTGCAAACGACTAAATGTTGAG
Found at i:22808 original size:14 final size:16
Alignment explanation
Indices: 22774--22810 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
22764 TTTCGGTTCA
22774 GTTCGGGTTTTTTAACG
1 GTTCGGGTTTTTT-ACG
22791 GTTCGGG-TTTTT-CG
1 GTTCGGGTTTTTTACG
22805 GTTCGG
1 GTTCGG
22811 TTCGGTTCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
16 5 0.25
17 7 0.35
ACGTcount: A:0.05, C:0.14, G:0.35, T:0.46
Consensus pattern (16 bp):
GTTCGGGTTTTTTACG
Found at i:22813 original size:19 final size:19
Alignment explanation
Indices: 22762--22815 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
22752 CGAAACCGAT
*
22762 TTTTTCGGTTCAGTTCGGG
1 TTTTTCGGTTCGGTTCGGG
*
22781 TTTTT---TAACGGTTCGGG
1 TTTTTCGGT-TCGGTTCGGG
22798 TTTTTCGGTTCGGTTCGG
1 TTTTTCGGTTCGGTTCGG
22816 TTCGGTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 13 0.46
19 13 0.46
20 1 0.04
ACGTcount: A:0.06, C:0.15, G:0.31, T:0.48
Consensus pattern (19 bp):
TTTTTCGGTTCGGTTCGGG
Found at i:28462 original size:45 final size:45
Alignment explanation
Indices: 28413--28498 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
28403 AAAATAGCCA
*
28413 GAGTGCATCGATGCATGGCT-TGTGCATCGATGCATCAAATGTACT
1 GAGTGCATCGATGCATGG-TATGTGCATCGATGCATAAAATGTACT
28458 GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATG
1 GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATG
28499 CATTTGATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 1 0.03
45 38 0.97
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (45 bp):
GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGTACT
Found at i:28484 original size:19 final size:19
Alignment explanation
Indices: 28415--28492 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
28405 AATAGCCAGA
28415 GTGCATCGATGCATGGCT-T
1 GTGCATCGATGCATGG-TAT
*
28434 GTGCATCGATGCATCAAATGTACT
1 GTGCATCGATGCAT----GGTA-T
28458 GAGTGCATCGATGCATGGTAT
1 --GTGCATCGATGCATGGTAT
28479 GTGCATCGATGCAT
1 GTGCATCGATGCAT
28493 AAAATGCATT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
19 28 0.57
21 1 0.02
22 4 0.08
23 1 0.02
24 1 0.02
26 14 0.29
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.29
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:29300 original size:3 final size:3
Alignment explanation
Indices: 29292--29339 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
29282 AAATGACTAC
29292 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29340 CTCACATCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:29529 original size:3 final size:3
Alignment explanation
Indices: 29521--30516 Score: 1208
Period size: 3 Copynumber: 338.0 Consensus size: 3
29511 CAAACTCTGT
29521 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
29569 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
29617 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -AA GAA GAA GAA G-A GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
29663 G-A GAGA GAA GAA GGA GAA GAA GGA GAA GAA GAA GAA GAA GAA GAA
1 GAA GA-A GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
29708 GGA GAA GAA GGA GAA GAA G-A GAA G-A GAA GAA G-A GAA GAA G-A GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
29752 GAA GAA GAAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-A GAA GAA
1 GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * *
29797 GGA GAA GAA GAA GAA GGA GAA GAA GAA GAA GAA GAA GAA GGA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * *
29845 GAA GGA GAA GAA GAA GGA GAA GAA GAA GGAA -AA GAA GAA GGA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA GAA
* * * *
29890 GAA GGA GAA GAA GGA GAA GAA GGA GAA GAA GGA GAA GAA G-A GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
29937 G-A GAA GAA GGA GAA GAA G-A GAA GAA GAA GAA -AA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
29982 GAA GAA GAA GAA GAA GAA G-A GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
30029 -AA GAA GAA GAA GAA GGA GAA G-A GAA GAA GGA GAGA GAA G-A GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA
* * *
30072 GAA GGA GAA G-A GAA GAA G-A GAA GAA GGA GAA GAA GGA GAAA GAGA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA GA-A
* * *
30117 GAA GGA GAA GAA GGA GAA GAA GAA AAA G-A GAGA GAA GAA G-A GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA
* *
30161 GAA GAA GGA GAA GAA GAA GAAA GAA GAA GGA GAA GAAA GAAA GAA GAA
1 GAA GAA GAA GAA GAA GAA G-AA GAA GAA GAA GAA G-AA G-AA GAA GAA
* * * * * * * *
30209 GGA GAA GAA GGA GAA G-A GGA GAA GGA GGA GAA GGA G-A GAA GGA GGA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * * * * *
30255 GAA GGA GGA GAA GGA GGA GAA GGA GGA GAA -AGA GAA GAA G-A GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA
* * *
30299 GAA TG-A GAA GAAA GAA GGA GAA GAA GGA GAA GAA GGA GAA GAA GAA
1 GAA -GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
30345 GGA GAA GAA GAA GAA GAA GAA GAA GAA GAA -AA G-A GAA GAA GAA G-A
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * *
30390 GAA GGA GAA GGA GAA GAA GAA GGA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * * *
30438 GGA GAA GGA GAA GGA GAA GGA GAA G-A GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
30485 GAA GAA GAA GAA GAA GAA GAA GAA -AA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
30517 TTATTGGGTT
Statistics
Matches: 862, Mismatches: 88, Indels: 86
0.83 0.08 0.08
Matches are distributed among these distances:
2 60 0.07
3 767 0.89
4 35 0.04
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:30827 original size:20 final size:20
Alignment explanation
Indices: 30789--30827 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
30779 CCCAAAATCC
*
30789 CTATAATTTAAAATTTTCAA
1 CTATAATTTAAAATATTCAA
30809 CTATAATTCTAAAA-ATTCA
1 CTATAATT-TAAAATATTCA
30828 TATTATAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (20 bp):
CTATAATTTAAAATATTCAA
Found at i:36154 original size:13 final size:15
Alignment explanation
Indices: 36138--36169 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
36128 GCTCTCTCAA
36138 TTCTCTC-TAT-TTT
1 TTCTCTCATATATTT
36151 TTCTCTCATATATTT
1 TTCTCTCATATATTT
36166 TTCT
1 TTCT
36170 TTTGCTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 3 0.18
15 7 0.41
ACGTcount: A:0.12, C:0.22, G:0.00, T:0.66
Consensus pattern (15 bp):
TTCTCTCATATATTT
Found at i:50120 original size:13 final size:15
Alignment explanation
Indices: 50104--50135 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
50094 GCTCTCTCAA
50104 TTCTCTC-TAT-TTT
1 TTCTCTCATATATTT
50117 TTCTCTCATATATTT
1 TTCTCTCATATATTT
50132 TTCT
1 TTCT
50136 TTTGCTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 3 0.18
15 7 0.41
ACGTcount: A:0.12, C:0.22, G:0.00, T:0.66
Consensus pattern (15 bp):
TTCTCTCATATATTT
Found at i:51855 original size:20 final size:21
Alignment explanation
Indices: 51827--51876 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
51817 AATAGTATAG
*
51827 TATCAATACCAAAGG-AAGGA
1 TATCGATACCAAAGGTAAGGA
* * *
51847 TATCGATACTAAGGGTAAGGG
1 TATCGATACCAAAGGTAAGGA
51868 TATCGATAC
1 TATCGATAC
51877 TACTGTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (21 bp):
TATCGATACCAAAGGTAAGGA
Found at i:52521 original size:44 final size:44
Alignment explanation
Indices: 52462--52576 Score: 185
Period size: 44 Copynumber: 2.6 Consensus size: 44
52452 CGTGAACATA
*
52462 TGAAAATGTGATATAAGCTATATGATATGATCTAAGTGATTATG
1 TGAACATGTGATATAAGCTATATGATATGATCTAAGTGATTATG
* *
52506 TGAACATGTGATATAAGCTATATGATATGATCTATGTTATTATG
1 TGAACATGTGATATAAGCTATATGATATGATCTAAGTGATTATG
* *
52550 TGAACATATGATATAAGCTATGTGATA
1 TGAACATGTGATATAAGCTATATGATA
52577 CTAAACTATG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 66 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.37
Consensus pattern (44 bp):
TGAACATGTGATATAAGCTATATGATATGATCTAAGTGATTATG
Found at i:52790 original size:23 final size:23
Alignment explanation
Indices: 52723--52791 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
52713 AGAGTCGAGG
* *
52723 ATTT-TACGCGGTCCTTCGGGAC
1 ATTTCTACGCAGTCCTTCGGGAT
*
52745 AATTCTACGCAGTCCTTCGGGAT
1 ATTTCTACGCAGTCCTTCGGGAT
52768 ATTTCTACGCAGTCCTTCGGGAT
1 ATTTCTACGCAGTCCTTCGGGAT
52791 A
1 A
52792 ATACTATATG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 3 0.07
23 39 0.93
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTTCTACGCAGTCCTTCGGGAT
Found at i:52870 original size:24 final size:24
Alignment explanation
Indices: 52824--52870 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
52814 ATTTCTATGT
*
52824 GGCACTTCGGTGCATATTCTACGC
1 GGCACTTCGGTGCATATTATACGC
52848 GGCACTTCGGTGCA-ATTTATACG
1 GGCACTTCGGTGCATA-TTATACG
52871 ACCTGTGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (24 bp):
GGCACTTCGGTGCATATTATACGC
Found at i:54892 original size:11 final size:11
Alignment explanation
Indices: 54876--54900 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54866 TAGTATGTTC
54876 AATAAATAAAA
1 AATAAATAAAA
54887 AATAAATAAAA
1 AATAAATAAAA
54898 AAT
1 AAT
54901 GATAGTACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AATAAATAAAA
Found at i:58601 original size:12 final size:12
Alignment explanation
Indices: 58579--58609 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
58569 TTTAATTATT
58579 ATTAT-TTTAAA
1 ATTATATTTAAA
58590 ATTATATTTAAA
1 ATTATATTTAAA
58602 ATTATATT
1 ATTATATT
58610 ATATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTATATTTAAA
Found at i:58981 original size:22 final size:22
Alignment explanation
Indices: 58956--59008 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
58946 TAGTTGAGCG
*
58956 TTTA-ATAAAATTTATTAATATT
1 TTTATATAAAATTTAAT-ATATT
*
58978 TTTATTTAAAATTTAATATATT
1 TTTATATAAAATTTAATATATT
59000 TATTATATA
1 T-TTATATA
59009 GTTAATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTATATAAAATTTAATATATT
Found at i:58988 original size:23 final size:23
Alignment explanation
Indices: 58961--59005 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
58951 GAGCGTTTAA
*
58961 TAAAATTTATTAATATTT-TTATT
1 TAAAATTTAAT-ATATTTATTATT
58984 TAAAATTTAATATATTTATTAT
1 TAAAATTTAATATATTTATTAT
59006 ATAGTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TAAAATTTAATATATTTATTATT
Found at i:64553 original size:23 final size:21
Alignment explanation
Indices: 64515--64557 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
64505 ATAATTATTT
64515 AAAAAATTAAATAAAAATATA
1 AAAAAATTAAATAAAAATATA
*
64536 AAAAATATTTAATAAAAA-ATA
1 AAAAA-ATTAAATAAAAATATA
64557 A
1 A
64558 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATA
Found at i:66013 original size:16 final size:15
Alignment explanation
Indices: 65982--66012 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
65972 TAATATTCAA
*
65982 TAAACTAATATTTTT
1 TAAAATAATATTTTT
65997 TAAAATAATATTTTT
1 TAAAATAATATTTTT
66012 T
1 T
66013 TTTCTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAAATAATATTTTT
Found at i:66545 original size:21 final size:21
Alignment explanation
Indices: 66507--66546 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
66497 TAACGAAGGT
*
66507 AGTACCGATACTCCCTATAAG
1 AGTACCGATACGCCCTATAAG
*
66528 AGTACCGATACGCTCTATA
1 AGTACCGATACGCCCTATA
66547 CTGGGCAATT
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:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (21 bp):
AGTACCGATACGCCCTATAAG
Found at i:67306 original size:14 final size:14
Alignment explanation
Indices: 67279--67314 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
67269 ATTCATTAAG
*
67279 AATAATATAGATTC
1 AATAATATAAATTC
*
67293 AATGATATAAATTC
1 AATAATATAAATTC
67307 AATAATAT
1 AATAATAT
67315 CGATTAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.36
Consensus pattern (14 bp):
AATAATATAAATTC
Found at i:74634 original size:22 final size:22
Alignment explanation
Indices: 74604--74678 Score: 95
Period size: 22 Copynumber: 3.6 Consensus size: 22
74594 GACCATTACA
*
74604 TCCCTAAGGACCACTGGATATG
1 TCCCGAAGGACCACTGGATATG
*
74626 TCCCGAAGGACCAC----TACG
1 TCCCGAAGGACCACTGGATATG
74644 TCCCGAAGGACCACTGGATATG
1 TCCCGAAGGACCACTGGATATG
*
74666 TTCCGAAGGACCA
1 TCCCGAAGGACCA
74679 TTATAACCCT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 17 0.38
22 28 0.62
ACGTcount: A:0.28, C:0.31, G:0.24, T:0.17
Consensus pattern (22 bp):
TCCCGAAGGACCACTGGATATG
Found at i:74648 original size:18 final size:18
Alignment explanation
Indices: 74585--74658 Score: 76
Period size: 18 Copynumber: 3.9 Consensus size: 18
74575 GTGAATATTT
*
74585 GTCCCGAAGGACCATTAC
1 GTCCCGAAGGACCACTAC
* * *
74603 ATCCCTAAGGACCACTGGATAT
1 GTCCCGAAGGACCAC----TAC
74625 GTCCCGAAGGACCACTAC
1 GTCCCGAAGGACCACTAC
74643 GTCCCGAAGGACCACT
1 GTCCCGAAGGACCACT
74659 GGATATGTTC
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
18 30 0.67
22 15 0.33
ACGTcount: A:0.28, C:0.34, G:0.22, T:0.16
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAC
Found at i:74653 original size:40 final size:40
Alignment explanation
Indices: 74584--74678 Score: 154
Period size: 40 Copynumber: 2.4 Consensus size: 40
74574 AGTGAATATT
* *
74584 TGTCCCGAAGGACCATTACATCCCTAAGGACCACTGGATA
1 TGTCCCGAAGGACCACTACATCCCGAAGGACCACTGGATA
*
74624 TGTCCCGAAGGACCACTACGTCCCGAAGGACCACTGGATA
1 TGTCCCGAAGGACCACTACATCCCGAAGGACCACTGGATA
*
74664 TGTTCCGAAGGACCA
1 TGTCCCGAAGGACCA
74679 TTATAACCCT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.28, C:0.31, G:0.23, T:0.18
Consensus pattern (40 bp):
TGTCCCGAAGGACCACTACATCCCGAAGGACCACTGGATA
Found at i:79822 original size:22 final size:21
Alignment explanation
Indices: 79772--79909 Score: 123
Period size: 22 Copynumber: 6.9 Consensus size: 21
79762 AGTGAATATT
79772 TGTCCCGAAGGACCA-T--TA
1 TGTCCCGAAGGACCACTGATA
* *
79790 CGTCCCTAAGGACCACTGGATA
1 TGTCCCGAAGGACCACT-GATA
*
79812 TGTCCCGAAGGACCACT-ACA
1 TGTCCCGAAGGACCACTGATA
79832 --TCCCGAAGGACCACTGAATA
1 TGTCCCGAAGGACCACTG-ATA
* * *
79852 TGTCTCGAATGACCACT-ACA
1 TGTCCCGAAGGACCACTGATA
*
79872 --TCCCGAAGAACCACTGGATA
1 TGTCCCGAAGGACCACT-GATA
79892 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
79910 TAACCCTCGA
Statistics
Matches: 94, Mismatches: 14, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
18 40 0.43
19 1 0.01
20 8 0.09
21 1 0.01
22 44 0.47
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (21 bp):
TGTCCCGAAGGACCACTGATA
Found at i:79837 original size:18 final size:18
Alignment explanation
Indices: 79774--79886 Score: 82
Period size: 18 Copynumber: 5.8 Consensus size: 18
79764 TGAATATTTG
* *
79774 TCCCGAAGGACCATTACG
1 TCCCGAAGGACCACTACA
* *
79792 TCCCTAAGGACCACTGGATA
1 TCCCGAAGGACCACT--ACA
79812 TGTCCCGAAGGACCACTACA
1 --TCCCGAAGGACCACTACA
*
79832 TCCCGAAGGACCACTGAATA
1 TCCCGAAGGACCACT--ACA
* *
79852 TGTCTCGAATGACCACTACA
1 --TCCCGAAGGACCACTACA
*
79872 TCCCGAAGAACCACT
1 TCCCGAAGGACCACT
79887 GGATATGTCC
Statistics
Matches: 74, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
18 40 0.54
20 7 0.09
22 27 0.36
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.18
Consensus pattern (18 bp):
TCCCGAAGGACCACTACA
Found at i:79841 original size:40 final size:40
Alignment explanation
Indices: 79772--79908 Score: 211
Period size: 40 Copynumber: 3.4 Consensus size: 40
79762 AGTGAATATT
* * *
79772 TGTCCCGAAGGACCATTACGTCCCTAAGGACCACTGGATA
1 TGTCCCGAAGGACCACTACATCCCGAAGGACCACTGGATA
*
79812 TGTCCCGAAGGACCACTACATCCCGAAGGACCACTGAATA
1 TGTCCCGAAGGACCACTACATCCCGAAGGACCACTGGATA
* * *
79852 TGTCTCGAATGACCACTACATCCCGAAGAACCACTGGATA
1 TGTCCCGAAGGACCACTACATCCCGAAGGACCACTGGATA
79892 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
79909 GTAACCCTCG
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.18
Consensus pattern (40 bp):
TGTCCCGAAGGACCACTACATCCCGAAGGACCACTGGATA
Found at i:84101 original size:19 final size:19
Alignment explanation
Indices: 84077--84115 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
84067 CGAGGTTTGG
*
84077 AAACATTATCAAGACCATT
1 AAACATGATCAAGACCATT
*
84096 AAACATGATCAAGATCATT
1 AAACATGATCAAGACCATT
84115 A
1 A
84116 GAACTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.26
Consensus pattern (19 bp):
AAACATGATCAAGACCATT
Found at i:84808 original size:93 final size:93
Alignment explanation
Indices: 84698--84892 Score: 320
Period size: 93 Copynumber: 2.1 Consensus size: 93
84688 CCTCCATTTA
* * *
84698 AACAAGAAACAATTCACCACATACGTATTCATGCAATCTATATGGCAATCAGA-TTAAACAATTG
1 AACAAGAAGCAATTCACCACATACGTATTCATGCAATCTATATGGAAATC-GATTTAAACAATTC
*
84762 AACGTGTATAACATTATTTCCTCTATTCG
65 AACATGTATAACATTATTTCCTCTATTCG
*
84791 AACAAGAAGCAATTCACCACATATGTATTCATGCAATCTATATGGAAATCGATTTAAACAATTCA
1 AACAAGAAGCAATTCACCACATACGTATTCATGCAATCTATATGGAAATCGATTTAAACAATTCA
*
84856 ACATGTATAACATTCTTTCCTCTATTCG
66 ACATGTATAACATTATTTCCTCTATTCG
84884 AACAAGAAG
1 AACAAGAAG
84893 TAAACACTCA
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
92 2 0.02
93 93 0.98
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (93 bp):
AACAAGAAGCAATTCACCACATACGTATTCATGCAATCTATATGGAAATCGATTTAAACAATTCA
ACATGTATAACATTATTTCCTCTATTCG
Found at i:84926 original size:93 final size:92
Alignment explanation
Indices: 84698--84917 Score: 230
Period size: 93 Copynumber: 2.4 Consensus size: 92
84688 CCTCCATTTA
* * * * ** * *
84698 AACAAGAAACAATTCACCACATACGTATTCATGCAATCTATATGGCAATCAGATTAAACAATTGA
1 AACAAGAAGCAATACACCACATATGCA-TCACACAATCTATATGGAAATCAGATTAAACAATTCA
*
84763 ACGTGTATAACATTATTTCCTCTATTCG
65 ACATGTATAACATTATTTCCTCTATTCG
* * **
84791 AACAAGAAGCAATTCACCACATATGTATTCATGCAATCTATATGGAAATC-GATTTAAACAATTC
1 AACAAGAAGCAATACACCACATATGCA-TCACACAATCTATATGGAAATCAGA-TTAAACAATTC
*
84855 AACATGTATAACATTCTTTCCTCTATTCG
64 AACATGTATAACATTATTTCCTCTATTCG
* *
84884 AACAAGAAGTAA-ACACTCATTATATGCA-CACACA
1 AACAAGAAGCAATACAC-CA-CATATGCATCACACA
84918 CACATATATA
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
92 9 0.08
93 97 0.87
94 6 0.05
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (92 bp):
AACAAGAAGCAATACACCACATATGCATCACACAATCTATATGGAAATCAGATTAAACAATTCAA
CATGTATAACATTATTTCCTCTATTCG
Found at i:87173 original size:20 final size:20
Alignment explanation
Indices: 87149--87236 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 20
87139 GCAATTTGGA
*
87149 AAATCGCAATGCGATTACGT
1 AAATCGCAATGCGAATACGT
* *
87169 CAATCGCAATACGAATACGT
1 AAATCGCAATGCGAATACGT
* *
87189 AAATCGTAATGTGAATACGT
1 AAATCGCAATGCGAATACGT
* **
87209 AAATCGCAATGCAAATATAT
1 AAATCGCAATGCGAATACGT
87229 AAATCGCA
1 AAATCGCA
87237 GCGCGAATCT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (20 bp):
AAATCGCAATGCGAATACGT
Found at i:87254 original size:20 final size:20
Alignment explanation
Indices: 87231--87277 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
87221 AAATATATAA
* *
87231 ATCGCAGCGCGAATCTGACT
1 ATCGCAACGAGAATCTGACT
*
87251 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGAATCTGACT
87271 ATCGCAA
1 ATCGCAA
87278 TACTGAATTT
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:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAGAATCTGACT
Found at i:88142 original size:24 final size:24
Alignment explanation
Indices: 88115--88161 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
88105 GTATTCAAAA
88115 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
*
88139 TTTGATCTTGGTCAATACTCGGA
1 TTTGATCTTGGTCAATACCCGGA
88162 TTGATGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Done.