Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000698.1 Hibiscus syriacus cultivar Beakdansim tig00001358_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: 56371
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2316 original size:30 final size:30
Alignment explanation
Indices: 2282--2338 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2272 GCATTTTACA
2282 CCGGTTTTGCCAGTT-TTCAGCCGGTTCACC
1 CCGGTTTTGCCAGTTCTT-AGCCGGTTCACC
*
2312 CCGGTTTTGCCGGTTCTTAGCCGGTTC
1 CCGGTTTTGCCAGTTCTTAGCCGGTTC
2339 TACCGTTCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.07, C:0.32, G:0.26, T:0.35
Consensus pattern (30 bp):
CCGGTTTTGCCAGTTCTTAGCCGGTTCACC
Found at i:3620 original size:27 final size:26
Alignment explanation
Indices: 3565--3635 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 26
3555 TACAAAATAT
3565 AAATAAACAAAAATAAATAGAAGGAAA
1 AAATAAA-AAAAATAAATAGAAGGAAA
3592 AAATCAAAAAAAATAAATCA-AATGGAAA
1 AAAT-AAAAAAAATAAAT-AGAA-GGAAA
*
3620 AAGA-AAAAAATATAAA
1 AA-ATAAAAAAAATAAA
3636 AATATAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
27 27 0.69
28 11 0.28
29 1 0.03
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.13
Consensus pattern (26 bp):
AAATAAAAAAAATAAATAGAAGGAAA
Found at i:3691 original size:31 final size:33
Alignment explanation
Indices: 3573--3699 Score: 113
Period size: 31 Copynumber: 3.8 Consensus size: 33
3563 ATAAATAAAC
3573 AAAAATAAATAGAAGG-AAAAAATCAAAAAA-A-
1 AAAAATAAATAGAAGGAAAAAAAT-AAAAAATAT
* * *
3604 ATAAATCAAATGGAAAAAGAAAAAAATATAAAAATAT
1 AAAAAT-AAAT--AGAAGGAAAAAAATA-AAAAATAT
*
3641 AAAAATAAATAGAAGGAAAAGAATAAAAAATAT
1 AAAAATAAATAGAAGGAAAAAAATAAAAAATAT
*
3674 -TAAAT-AATCA-AAGGAAAAAAATAAAA
1 AAAAATAAAT-AGAAGGAAAAAAATAAAA
3700 TAAAAAACAA
Statistics
Matches: 79, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
31 23 0.29
32 9 0.11
33 8 0.10
34 17 0.22
35 12 0.15
36 5 0.06
37 5 0.06
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.15
Consensus pattern (33 bp):
AAAAATAAATAGAAGGAAAAAAATAAAAAATAT
Found at i:3718 original size:68 final size:68
Alignment explanation
Indices: 3558--3708 Score: 177
Period size: 68 Copynumber: 2.2 Consensus size: 68
3548 TGTTATATAC
* *
3558 AAAATATAAATAA-ACAAAAATAAATAGAAGGAAAAAATCAAAAAAAATAAATCAAATGGAAAAA
1 AAAATATAAA-AACATAAAAATAAATAGAAGGAAAAAATAAAAAAAAATAAATCAAATGGAAAAA
3622 GAAA
65 GAAA
*
3626 AAAATATAAAAATATAAAAATAAATAGAAGGAAAAGAATAAAAAATATTAA-ATAATCAAA-GGA
1 AAAATATAAAAACATAAAAATAAATAGAAGGAAAA-AATAAAAAA-A--AATA-AATCAAATGGA
*
3689 AAAA-AAT
61 AAAAGAAA
3696 AAAATA-AAAAACA
1 AAAATATAAAAACA
3709 AATGTTAAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
67 2 0.03
68 31 0.42
69 14 0.19
70 9 0.12
71 8 0.11
72 9 0.12
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (68 bp):
AAAATATAAAAACATAAAAATAAATAGAAGGAAAAAATAAAAAAAAATAAATCAAATGGAAAAAG
AAA
Found at i:4147 original size:16 final size:17
Alignment explanation
Indices: 4126--4159 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4116 TTCCCCGACG
*
4126 TGCTT-GCTTTTTGTTT
1 TGCTTGGCTTTTGGTTT
4142 TGCTTGGCTTTTGGTTT
1 TGCTTGGCTTTTGGTTT
4159 T
1 T
4160 TTTTTTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.00, C:0.12, G:0.24, T:0.65
Consensus pattern (17 bp):
TGCTTGGCTTTTGGTTT
Found at i:4704 original size:19 final size:19
Alignment explanation
Indices: 4680--4746 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
4670 GACCAAATTG
4680 AAATAAATAATAAATAATA
1 AAATAAATAATAAATAATA
4699 AAATAAA-AATAAATTAA-A
1 AAATAAATAATAAA-TAATA
*
4717 TGAATAAATAAGTAAAT-ATA
1 -AAATAAATAA-TAAATAATA
*
4737 ATATAAATAA
1 AAATAAATAA
4747 AAACTTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
18 7 0.17
19 25 0.62
20 4 0.10
21 4 0.10
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (19 bp):
AAATAAATAATAAATAATA
Found at i:4743 original size:27 final size:24
Alignment explanation
Indices: 4680--4746 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 24
4670 GACCAAATTG
4680 AAATAAATAATAAATAATAAAATAA
1 AAATAAAT-ATAAATAATAAAATAA
4705 AAATAAAT-TAAATGAAT-AAATAA
1 AAATAAATATAAAT-AATAAAATAA
4728 GTAAATATAATATAAATAA
1 --AAATA-AATATAAATAA
4747 AAACTTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
23 11 0.30
24 3 0.08
25 13 0.35
26 5 0.14
27 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (24 bp):
AAATAAATATAAATAATAAAATAA
Found at i:4861 original size:33 final size:34
Alignment explanation
Indices: 4800--4866 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
4790 ATTATATATA
* *
4800 TATATATATAATTATATCGAAAATGTTTTCTAAAT
1 TATATATATAATTATATCCAAAACGTTTTC-AAAT
*
4835 TATATATAT-ATT-TTTCCAAAACGTTTTCAAAT
1 TATATATATAATTATATCCAAAACGTTTTCAAAT
4867 GTTTTCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 4 0.14
33 13 0.45
34 3 0.10
35 9 0.31
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.46
Consensus pattern (34 bp):
TATATATATAATTATATCCAAAACGTTTTCAAAT
Found at i:5039 original size:28 final size:29
Alignment explanation
Indices: 5015--5074 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
5005 TATTATATAG
5015 TTTTTTCAAAA-GTTTTCAAACTATAATA
1 TTTTTTCAAAATGTTTTCAAACTATAATA
5043 TTTTTTCAAAATGTTTTCAAAACTA-AATA
1 TTTTTTCAAAATGTTTTC-AAACTATAATA
5072 TTT
1 TTT
5075 ATATATGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 11 0.37
29 13 0.43
30 6 0.20
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTTTTCAAAATGTTTTCAAACTATAATA
Found at i:6353 original size:85 final size:85
Alignment explanation
Indices: 6089--6532 Score: 563
Period size: 85 Copynumber: 5.2 Consensus size: 85
6079 CAGATAGTTT
* * * *
6089 TTCTCGACTTAAGCTATGTTGTAAATTTGATATGTTCTTGAGCTGAATGTAATCGAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG
*
6154 -TTT-GTTGACAGATAGCCC
66 TTTTGGTTGACAGATAACCC
*
6172 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTG-GCTGAATGTAATCGAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG
** * * *
6236 TTTTTATTGGCATATAATCC
66 TTTTGGTTGACAGATAACCC
* *
6256 TTCTCGCTTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG
*
6321 TTTTGGTTAACAGATAACCC
66 TTTTGGTTGACAGATAACCC
* * *
6341 TTCTTGCCTTGAGCTATGATGTAAATTTGATATGTCCTTGAGCT-AAGTGTACTCGAACTCGAAG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGCTGAA-TGTAATCGAACTCGAAG
* *
6405 GTTTTGGTTGACGGATAGCCC
65 GTTTTGGTTGACAGATAACCC
* * * * * *
6426 TTCTCACCTTGAGCTATGCTGTAAATTTGATATCTTCTTGAGTTGAGTGTAATCAAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG
* * * *
6491 TTTTTTTGCTGGCAGATAGCCC
66 --TTTTGGTTGACAGATAACCC
*
6513 TTATCGCCTTGAGCTATGCT
1 TTCTCGCCTTGAGCTATGCT
6533 ACAAATAGTT
Statistics
Matches: 312, Mismatches: 42, Indels: 10
0.86 0.12 0.03
Matches are distributed among these distances:
82 24 0.08
83 38 0.12
84 49 0.16
85 166 0.53
86 1 0.00
87 34 0.11
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.37
Consensus pattern (85 bp):
TTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG
TTTTGGTTGACAGATAACCC
Found at i:11757 original size:11 final size:11
Alignment explanation
Indices: 11741--11766 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11731 ATTAGATACG
11741 AAATATTAAAT
1 AAATATTAAAT
11752 AAATATTAAAT
1 AAATATTAAAT
11763 AAAT
1 AAAT
11767 CAAAAGGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATATTAAAT
Found at i:11780 original size:25 final size:25
Alignment explanation
Indices: 11759--11809 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
11749 AATAAATATT
11759 AAATAAATCAAAAGGAAAAAATAAA
1 AAATAAATCAAAAGGAAAAAATAAA
*
11784 AAATAAATCAAAGGGAAAAAA-AAA
1 AAATAAATCAAAAGGAAAAAATAAA
11808 AA
1 AA
11810 TCGAAGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.76, C:0.04, G:0.10, T:0.10
Consensus pattern (25 bp):
AAATAAATCAAAAGGAAAAAATAAA
Found at i:11802 original size:18 final size:19
Alignment explanation
Indices: 11781--11827 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 19
11771 AGGAAAAAAT
11781 AAAAAATAAATCAAAGGGAA
1 AAAAAATAAATCAAA-GGAA
*
11801 AAAAAA-AAATCGAAGG-A
1 AAAAAATAAATCAAAGGAA
11818 AAAAAATAAA
1 AAAAAATAAA
11828 AAAAATAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 7 0.28
18 5 0.20
19 7 0.28
20 6 0.24
ACGTcount: A:0.74, C:0.04, G:0.13, T:0.09
Consensus pattern (19 bp):
AAAAAATAAATCAAAGGAA
Found at i:11805 original size:19 final size:18
Alignment explanation
Indices: 11781--11827 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
11771 AGGAAAAAAT
11781 AAAAAATAAATCAAAGGGA
1 AAAAAATAAATCAAA-GGA
* *
11800 AAAAAAAAAATCGAAGGA
1 AAAAAATAAATCAAAGGA
11818 AAAAAATAAA
1 AAAAAATAAA
11828 AAAAATAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.74, C:0.04, G:0.13, T:0.09
Consensus pattern (18 bp):
AAAAAATAAATCAAAGGA
Found at i:11849 original size:26 final size:27
Alignment explanation
Indices: 11799--11864 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 27
11789 AATCAAAGGG
*
11799 AAAAAAAAAAATCGAAG-GAAAAAAAT
1 AAAAAAAAAAATCGAAGAAAAAAAAAT
*
11825 AAAAAAAATAATC-AATGAAAAAAAAAT
1 AAAAAAAAAAATCGAA-GAAAAAAAAAT
*
11852 AAAATAACAAAAT
1 AAAA-AAAAAAAT
11865 TTTAAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 2 0.06
26 13 0.39
27 12 0.36
28 6 0.18
ACGTcount: A:0.77, C:0.05, G:0.06, T:0.12
Consensus pattern (27 bp):
AAAAAAAAAAATCGAAGAAAAAAAAAT
Found at i:11855 original size:25 final size:26
Alignment explanation
Indices: 11799--11848 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
11789 AATCAAAGGG
11799 AAAAAAAAAAATCGAAGGAAAAAAAT
1 AAAAAAAAAAATCGAAGGAAAAAAAT
* *
11825 AAAAAAAATAATC-AATGAAAAAAA
1 AAAAAAAAAAATCGAAGGAAAAAAA
11849 AATAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.78, C:0.04, G:0.08, T:0.10
Consensus pattern (26 bp):
AAAAAAAAAAATCGAAGGAAAAAAAT
Found at i:12432 original size:16 final size:18
Alignment explanation
Indices: 12411--12445 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
12401 TTCCCCGGCG
12411 TGCTT-GCTTTTT-GTTT
1 TGCTTGGCTTTTTGGTTT
12427 TGCTTGGCTTTTTGGTTT
1 TGCTTGGCTTTTTGGTTT
12445 T
1 T
12446 TTTTGTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 7 0.41
18 5 0.29
ACGTcount: A:0.00, C:0.11, G:0.23, T:0.66
Consensus pattern (18 bp):
TGCTTGGCTTTTTGGTTT
Found at i:12971 original size:4 final size:4
Alignment explanation
Indices: 12957--13042 Score: 52
Period size: 4 Copynumber: 20.8 Consensus size: 4
12947 GACCAAATTG
* * *
12957 AAAT AAAAT AAAT -AA- AAAT AAAAA AAAT AAAT AAAT TAA- AAAT AATT
1 AAAT -AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* *
13004 AAATT AAAT GAAAT AAGT AAGT AAAT ATAAT AGAAT AAA
1 AAA-T AAAT -AAAT AAAT AAAT AAAT A-AAT A-AAT AAA
13043 AACTTATTCA
Statistics
Matches: 65, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
3 6 0.09
4 36 0.55
5 23 0.35
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:12997 original size:15 final size:15
Alignment explanation
Indices: 12957--13011 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
12947 GACCAAATTG
*
12957 AAATAAAATAAATAA-
1 AAATAAATTAAA-AAT
12972 AAATAAA--AAAAAT
1 AAATAAATTAAAAAT
12985 AAATAAATTAAAAAT
1 AAATAAATTAAAAAT
*
13000 AATTAAATTAAA
1 AAATAAATTAAA
13012 TGAAATAAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
12 2 0.06
13 10 0.28
15 24 0.67
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAAATTAAAAAT
Found at i:12998 original size:19 final size:19
Alignment explanation
Indices: 12951--13012 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
12941 GACCTAGACC
* *
12951 AAATTGAAATAAAATAAAT
1 AAATTAAAAAAAAATAAAT
*
12970 AAA-AATAAAAAAAATAAAT
1 AAATTA-AAAAAAAATAAAT
* *
12989 AAATTAAAAATAATTAAATT
1 AAATTAAAAAAAAATAAA-T
13009 AAAT
1 AAAT
13013 GAAATAAGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
19 28 0.82
20 6 0.18
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AAATTAAAAAAAAATAAAT
Found at i:13264 original size:36 final size:36
Alignment explanation
Indices: 13204--13459 Score: 172
Period size: 36 Copynumber: 7.0 Consensus size: 36
13194 TTCCAAAATG
* *
13204 TTTTCAAAAATGTTTTTTCAAAACTTTATAATATATA
1 TTTTCAAAAAT-TATTTTCAAAACTATATAATATATA
13241 TTTTCAAAAATTATTTTCAAAACTATAATATATATATA
1 TTTTCAAAAATTATTTTCAAAACTAT-ATA-ATATATA
** *
13279 TATATAT-ATTCAAAATCGTTTTCAAAACTATATAATATGTA
1 T-T-T-TCA---AAAATTATTTTCAAAACTATATAATATATA
* * *
13320 TTTTCAAAAGCGTT-TTTT-AAAACTATATATTATATT
1 TTTTCAAAA--ATTATTTTCAAAACTATATAATATATA
*** *
13356 TTTTTTCAAA-TATTTTCAAAACTATAT-ATAT-TT
1 TTTTCAAAAATTATTTTCAAAACTATATAATATATA
* *
13389 TTTTC--AAA-TGTTTTCAAAACTAATATATTATATA
1 TTTTCAAAAATTATTTTCAAAACT-ATATAATATATA
* * *
13423 TGTTT-AAAAAATATTTTAAAAACTATTTAATATATA
1 T-TTTCAAAAATTATTTTCAAAACTATATAATATATA
13459 T
1 T
13460 ATATATATAT
Statistics
Matches: 176, Mismatches: 23, Indels: 41
0.73 0.10 0.17
Matches are distributed among these distances:
31 15 0.09
32 4 0.02
33 10 0.06
34 9 0.05
35 13 0.07
36 51 0.29
37 29 0.16
38 10 0.06
39 3 0.02
40 3 0.02
41 8 0.05
42 3 0.02
43 18 0.10
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (36 bp):
TTTTCAAAAATTATTTTCAAAACTATATAATATATA
Found at i:13316 original size:79 final size:73
Alignment explanation
Indices: 13218--13455 Score: 210
Period size: 79 Copynumber: 3.3 Consensus size: 73
13208 CAAAAATGTT
*
13218 TTTTCAAAACTTTATAATATATATTTTCAAAAATTATTTTCAAAACTATAATATATATATATATA
1 TTTTCAAAACTATATAATAT-TATTTTCAAAAATT-TTTTCAAAACTATAATATATATATATAT-
*
13283 TATATTCAAAATCG
63 T-TATTC-AAAT-A
*
13297 TTTTCAAAACTATATAATATGTATTTTCAAAAGCGTTTTTT-AAAACTAT-ATAT-TATAT-T-T
1 TTTTCAAAACTATATAATAT-TATTTTCAAAA--ATTTTTTCAAAACTATAATATATATATATAT
*
13357 TTTTTCAAATA
63 TTATTCAAATA
* * *
13368 TTTTCAAAACTATAT-ATATTTTTTTC--AAATGTTTTCAAAAC--TAATATATTATATATGTTT
1 TTTTCAAAACTATATAATATTATTTTCAAAAATTTTTTCAAAACTATAATATA-TATATATATTT
**
13428 A-AAAAATA
65 ATTCAAATA
* *
13436 TTTTAAAAACTATTTAATAT
1 TTTTCAAAACTATATAATAT
13456 ATATATATAT
Statistics
Matches: 137, Mismatches: 13, Indels: 28
0.77 0.07 0.16
Matches are distributed among these distances:
64 1 0.01
65 9 0.07
66 5 0.04
67 7 0.05
68 19 0.14
69 13 0.09
70 4 0.03
71 15 0.11
72 4 0.03
73 4 0.03
74 1 0.01
75 1 0.01
76 1 0.01
77 5 0.04
78 4 0.03
79 38 0.28
80 4 0.03
81 2 0.01
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (73 bp):
TTTTCAAAACTATATAATATTATTTTCAAAAATTTTTTCAAAACTATAATATATATATATATTTA
TTCAAATA
Found at i:13327 original size:35 final size:34
Alignment explanation
Indices: 13271--13459 Score: 152
Period size: 35 Copynumber: 5.4 Consensus size: 34
13261 AACTATAATA
*
13271 TATATATATATATATATTCAAAATCGTTTTCAAAAC
1 TATATA-ATATATATTTTCAAAAT-GTTTTCAAAAC
* * *
13307 TATATAATATGTATTTTCAAAAGCGTTTTTTAAAAC
1 TATATAATATATATTTTCAAAA-TG-TTTTCAAAAC
* * *
13343 TATATATTATATTTTTTTTC-AAATATTTTCAAAAC
1 TATATA--ATATATATTTTCAAAATGTTTTCAAAAC
*
13378 TATAT-ATAT-TTTTTTC-AAATGTTTTCAAAAC
1 TATATAATATATATTTTCAAAATGTTTTCAAAAC
* * * *
13409 TAATATATTATATATGTTTAAAAAATATTTTAAAAAC
1 T-ATATAATATATAT-TTT-CAAAATGTTTTCAAAAC
*
13446 TATTTAATATATAT
1 TATATAATATATAT
13460 ATATATATAT
Statistics
Matches: 126, Mismatches: 17, Indels: 20
0.77 0.10 0.12
Matches are distributed among these distances:
31 22 0.17
32 8 0.06
33 3 0.02
34 2 0.02
35 32 0.25
36 32 0.25
37 17 0.13
38 10 0.08
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (34 bp):
TATATAATATATATTTTCAAAATGTTTTCAAAAC
Found at i:13391 original size:32 final size:32
Alignment explanation
Indices: 13345--13417 Score: 114
Period size: 31 Copynumber: 2.3 Consensus size: 32
13335 TTTAAAACTA
13345 TATATTATATTTTTTTTCAAATATTTTCAAAAC
1 TATA-TATATTTTTTTTCAAATATTTTCAAAAC
*
13378 TATATATA-TTTTTTTCAAATGTTTTCAAAAC
1 TATATATATTTTTTTTCAAATATTTTCAAAAC
13409 TA-ATATATT
1 TATATATATT
13418 ATATATGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
30 5 0.13
31 25 0.66
32 4 0.11
33 4 0.11
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.53
Consensus pattern (32 bp):
TATATATATTTTTTTTCAAATATTTTCAAAAC
Found at i:15790 original size:21 final size:23
Alignment explanation
Indices: 15748--15791 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
15738 CATTTTAATC
15748 AAAATATTAATTATTAAATATTT
1 AAAATATTAATTATTAAATATTT
*
15771 AAAATA-TATTTATT-AATATTT
1 AAAATATTAATTATTAAATATTT
15792 CTAATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 7 0.35
23 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AAAATATTAATTATTAAATATTT
Found at i:15801 original size:22 final size:21
Alignment explanation
Indices: 15757--15819 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
15747 CAAAATATTA
*
15757 ATTATTAAATATTTAAAAT-AT
1 ATTATT-AATATTTATAATAAT
*
15778 ATTTATTAATATTTCTAATAAT
1 A-TTATTAATATTTATAATAAT
* *
15800 ATAATATAATATTTTTAATA
1 ATTAT-TAATATTTATAATA
15820 TTATAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 14 0.40
22 21 0.60
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTATTAATATTTATAATAAT
Found at i:15824 original size:22 final size:22
Alignment explanation
Indices: 15784--15832 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
15774 ATATATTTAT
15784 TAATATTTCTAATAATATAATA
1 TAATATTTCTAATAATATAATA
* *
15806 TAATATTTTTAATATTATAATA
1 TAATATTTCTAATAATATAATA
*
15828 AAATA
1 TAATA
15833 ATCAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATTTCTAATAATATAATA
Found at i:15847 original size:23 final size:23
Alignment explanation
Indices: 15817--15860 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
15807 AATATTTTTA
15817 ATATTATAATAAAATAATCAATT
1 ATATTATAATAAAATAATCAATT
*
15840 ATATTATAATAATATAATCAA
1 ATATTATAATAAAATAATCAA
15861 ATATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (23 bp):
ATATTATAATAAAATAATCAATT
Found at i:15857 original size:53 final size:50
Alignment explanation
Indices: 15793--15891 Score: 137
Period size: 53 Copynumber: 1.9 Consensus size: 50
15783 TTAATATTTC
*
15793 TAATAATATAAT-ATAATATTTTTAATATTATAATAAAATAATCAATTATATTA
1 TAATAATATAATCA-AATATTTTT-AT-TT-TAATAAAATAATAAATTATATTA
*
15846 TAATAATATAATCAAATATTTTTATTTTAATAATATAATAAATTAT
1 TAATAATATAATCAAATATTTTTATTTTAATAAAATAATAAATTAT
15892 TAATAAAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
50 17 0.40
51 2 0.05
52 2 0.05
53 21 0.49
54 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (50 bp):
TAATAATATAATCAAATATTTTTATTTTAATAAAATAATAAATTATATTA
Found at i:18797 original size:22 final size:22
Alignment explanation
Indices: 18772--18818 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
18762 CATTGTGACC
18772 TTGCATTCTCATTTGACATACA
1 TTGCATTCTCATTTGACATACA
18794 TTGCATTCTCATTTGACATACA
1 TTGCATTCTCATTTGACATACA
18816 TTG
1 TTG
18819 GGAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.43
Consensus pattern (22 bp):
TTGCATTCTCATTTGACATACA
Found at i:19477 original size:16 final size:16
Alignment explanation
Indices: 19456--19487 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
19446 TAGGCTAATA
19456 AAATTAATGTGCTTTG
1 AAATTAATGTGCTTTG
19472 AAATTAATGTGCTTTG
1 AAATTAATGTGCTTTG
19488 GTTGTACCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (16 bp):
AAATTAATGTGCTTTG
Found at i:19585 original size:2 final size:2
Alignment explanation
Indices: 19574--19609 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
19564 TATTTATGAT
19574 TA TA -A TA 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 TA TA TA TA T
19610 TGGTTCTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25105 original size:14 final size:14
Alignment explanation
Indices: 25086--25124 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
25076 CTTTCATCTA
*
25086 ATCTCTCTATCTCT
1 ATCTCTATATCTCT
25100 ATCTCTATATCTCT
1 ATCTCTATATCTCT
25114 ATCTCTATATC
1 ATCTCTATATC
25125 CTCCACCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.21, C:0.31, G:0.00, T:0.49
Consensus pattern (14 bp):
ATCTCTATATCTCT
Found at i:27376 original size:25 final size:24
Alignment explanation
Indices: 27348--27418 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
27338 GAACTCAAAA
* *
27348 AAAATTAGAAGTTCGATTGAAGCCT
1 AAAATTAG-AGCTCAATTGAAGCCT
* *
27373 AAAATTTGAGCTCAATTGAAGCTT
1 AAAATTAGAGCTCAATTGAAGCCT
27397 AAAATTTA-AGCTCAATTGAAGC
1 AAAA-TTAGAGCTCAATTGAAGC
27419 GAAAGAATAG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
24 31 0.77
25 9 0.22
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (24 bp):
AAAATTAGAGCTCAATTGAAGCCT
Found at i:27392 original size:24 final size:24
Alignment explanation
Indices: 27363--27418 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
27353 TAGAAGTTCG
*
27363 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTAAGCTCA
*
27387 ATTGAAGCTTAAAATTTAAGCTCA
1 ATTGAAGCCTAAAATTTAAGCTCA
27411 ATTGAAGC
1 ATTGAAGC
27419 GAAAGAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTAAGCTCA
Found at i:29179 original size:22 final size:22
Alignment explanation
Indices: 29136--29179 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29126 GAAAGTCAAT
* * *
29136 GGTCAACGGTCGGGTTGGGTCG
1 GGTCAACAGTCGGGTCGAGTCG
29158 GGTCAACAGTCGGGTCGAGTCG
1 GGTCAACAGTCGGGTCGAGTCG
29180 AGTCGGTCGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.20, G:0.45, T:0.20
Consensus pattern (22 bp):
GGTCAACAGTCGGGTCGAGTCG
Found at i:36481 original size:14 final size:14
Alignment explanation
Indices: 36462--36490 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
36452 GTCGGGACAA
36462 CGGTCGGGTCGGGT
1 CGGTCGGGTCGGGT
36476 CGGTCGGGTCGGGT
1 CGGTCGGGTCGGGT
36490 C
1 C
36491 AGACCGGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.55, T:0.21
Consensus pattern (14 bp):
CGGTCGGGTCGGGT
Found at i:45339 original size:29 final size:29
Alignment explanation
Indices: 45284--45340 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
45274 TGAAATCAGG
*
45284 TTTTATGTATTTTTAATTTGGGTTTTGCA
1 TTTTATGTATTTTTAATTTGAGTTTTGCA
* *
45313 TTTTATTTATTTTT-ATTTTAGTCTTTGC
1 TTTTATGTATTTTTAATTTGAGT-TTTGC
45341 TTGTCTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.16, C:0.05, G:0.12, T:0.67
Consensus pattern (29 bp):
TTTTATGTATTTTTAATTTGAGTTTTGCA
Found at i:53110 original size:20 final size:20
Alignment explanation
Indices: 53085--53203 Score: 175
Period size: 20 Copynumber: 6.0 Consensus size: 20
53075 TTTCTCACGA
*
53085 ATTTGTAAATCCTCCGGGTC
1 ATTTGTAAATCCTACGGGTC
**
53105 ATTTGTAAATCCTACATGTC
1 ATTTGTAAATCCTACGGGTC
53125 ATTTGTAAATCCTACGGGTC
1 ATTTGTAAATCCTACGGGTC
*
53145 ATTTGTAAATCCTCCGGGTC
1 ATTTGTAAATCCTACGGGTC
* *
53165 ATTTGTAAATCCTTCTGGTC
1 ATTTGTAAATCCTACGGGTC
*
53185 ATTTGTAAATCCTTCGGGT
1 ATTTGTAAATCCTACGGGT
53204 TATATGTTAG
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 90 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTTGTAAATCCTACGGGTC
Found at i:53186 original size:60 final size:60
Alignment explanation
Indices: 53085--53203 Score: 204
Period size: 60 Copynumber: 2.0 Consensus size: 60
53075 TTTCTCACGA
53085 ATTTGTAAATCCTCCGGGTCATTTGTAAATCCTACATGTCATTTGTAAATCCTACGGGTC
1 ATTTGTAAATCCTCCGGGTCATTTGTAAATCCTACATGTCATTTGTAAATCCTACGGGTC
* *
53145 ATTTGTAAATCCTCCGGGTCATTTGTAAATCCTTC-TGGTCATTTGTAAATCCTTCGGGT
1 ATTTGTAAATCCTCCGGGTCATTTGTAAATCCTACAT-GTCATTTGTAAATCCTACGGGT
53204 TATATGTTAG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
59 1 0.02
60 55 0.98
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.39
Consensus pattern (60 bp):
ATTTGTAAATCCTCCGGGTCATTTGTAAATCCTACATGTCATTTGTAAATCCTACGGGTC
Done.