Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001086.1 Hibiscus syriacus cultivar Beakdansim tig00002147_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: 84202
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:136 original size:59 final size:59
Alignment explanation
Indices: 1--140 Score: 194
Period size: 58 Copynumber: 2.4 Consensus size: 59
* * *
1 CGATTCACACACTTCG-ATCAGCAATGCCCCAATAGAGGGGTTAACATTTCCTATTGCT
1 CGATTCACACACTTCGAATCAGCAACGCCCCAACAGAGGGGTTAACATTTCCTACTGCT
* * *
59 CGATTCACACACTACGAATCAGCAACGCCCCACCATA-GGGTTAACATTTCCTACTGCT
1 CGATTCACACACTTCGAATCAGCAACGCCCCAACAGAGGGGTTAACATTTCCTACTGCT
*
117 CGATTCACAATACTTCGAATCAGC
1 CGATTCAC-ACACTTCGAATCAGC
141 TGAAGTCCTT
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
58 43 0.60
59 29 0.40
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (59 bp):
CGATTCACACACTTCGAATCAGCAACGCCCCAACAGAGGGGTTAACATTTCCTACTGCT
Found at i:198 original size:40 final size:41
Alignment explanation
Indices: 143--241 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 41
133 GAATCAGCTG
* * *
143 AAGTCCTTCGGGCCATCAGTAAGTC-TCGATCTTGATGTGT
1 AAGTCCTTTGGGCCATCAGTAAGTCTTCGAGCATGATGTGT
183 AAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGTGT
1 AAGTCCTTTGGGCCATCAGTAAGTC-TTCGAGCATGATGTGT
225 AAGT-CTTTCGGGCCATC
1 AAGTCCTTT-GGGCCATC
242 CATAAGACCT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
40 24 0.45
41 4 0.08
42 25 0.47
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.32
Consensus pattern (41 bp):
AAGTCCTTTGGGCCATCAGTAAGTCTTCGAGCATGATGTGT
Found at i:268 original size:19 final size:20
Alignment explanation
Indices: 231--275 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
221 GTGTAAGTCT
*
231 TTCGGGCCATCCATAAGACC
1 TTCGGGACATCCATAAGACC
251 TTCGGGACATCC-TAAGACC
1 TTCGGGACATCCATAAGACC
270 TTCGGG
1 TTCGGG
276 CAAGGTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.22
Consensus pattern (20 bp):
TTCGGGACATCCATAAGACC
Found at i:2049 original size:26 final size:24
Alignment explanation
Indices: 2014--2074 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
2004 ATGTTTTATG
*
2014 TATTACGTATTTATTTTTAAGTATAT
1 TATTATGTATTTA--TTTAAGTATAT
* *
2040 TATTATGTATCTATTTACGTATAT
1 TATTATGTATTTATTTAAGTATAT
*
2064 TATTATATATT
1 TATTATGTATT
2075 ACTTTGTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 19 0.63
26 11 0.37
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (24 bp):
TATTATGTATTTATTTAAGTATAT
Found at i:5178 original size:24 final size:26
Alignment explanation
Indices: 5117--5206 Score: 157
Period size: 26 Copynumber: 3.5 Consensus size: 26
5107 TAAAGAACGT
5117 AATATGTCATAATTTCAAAGCTAAAC
1 AATATGTCATAATTTCAAAGCTAAAC
5143 AATATGTCATAATTTCAAAGCTAAAC
1 AATATGTCATAATTTCAAAGCTAAAC
*
5169 -A-ATGTCATAATTTTAAAGCTAAAC
1 AATATGTCATAATTTCAAAGCTAAAC
5193 AATATGTCATAATT
1 AATATGTCATAATT
5207 CTTCAATTTA
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
24 22 0.36
25 2 0.03
26 37 0.61
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (26 bp):
AATATGTCATAATTTCAAAGCTAAAC
Found at i:11067 original size:16 final size:16
Alignment explanation
Indices: 11035--11083 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
11025 ATAAATTGAG
*
11035 AAAATAACAAT-AAAA
1 AAAATAAAAATGAAAA
**
11050 AAGTTAAAAA-GAAAA
1 AAAATAAAAATGAAAA
11065 AAAATAAAAATGAAAA
1 AAAATAAAAATGAAAA
11081 AAA
1 AAA
11084 TGTTCATTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 19 0.70
16 8 0.30
ACGTcount: A:0.80, C:0.02, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAATAAAAATGAAAA
Found at i:14660 original size:99 final size:99
Alignment explanation
Indices: 14466--14662 Score: 254
Period size: 99 Copynumber: 2.0 Consensus size: 99
14456 GGACAACTCA
* * *
14466 ATATTATAATCACCTTTATTAGGCTAGTTGAATCTTATCCATAAAGCCAAGGCATTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTAAATCTTATCCATAAAGCCAAGGCATTTAACCAATT
* *
14531 GCTCTAGAGGGATAGCTCAAGTTTTATTGTATAG
66 GCTCTAGAGGGACAACTCAAGTTTTATTGTATAG
* * ** *
14565 ATATTATAATCACCTTTATCATGCTAGCTAAATTTTATCCATAAAG-CTGGGACGTTTAACCAAT
1 ATATTATAATCACCTTTATCAGGCTAGCTAAATCTTATCCATAAAGCCAAGG-CATTTAACCAAT
* *
14629 TGTTCTAGAGGGACAACTTAAGCTTTT-TTGTATA
65 TGCTCTAGAGGGACAACTCAAG-TTTTATTGTATA
14663 TATAATATTA
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
98 3 0.04
99 77 0.92
100 4 0.05
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (99 bp):
ATATTATAATCACCTTTATCAGGCTAGCTAAATCTTATCCATAAAGCCAAGGCATTTAACCAATT
GCTCTAGAGGGACAACTCAAGTTTTATTGTATAG
Found at i:20118 original size:19 final size:19
Alignment explanation
Indices: 20094--20131 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20084 TGGGTCGCTA
20094 CTGTTGTGGACCATTGCTG
1 CTGTTGTGGACCATTGCTG
20113 CTGTTGTGGACCATTGCTG
1 CTGTTGTGGACCATTGCTG
20132 GGCTTCTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.32, T:0.37
Consensus pattern (19 bp):
CTGTTGTGGACCATTGCTG
Found at i:25675 original size:4 final size:4
Alignment explanation
Indices: 25668--25693 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
25658 GGAAGGAAGG
25668 AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
25694 ATTTACATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:40824 original size:2 final size:2
Alignment explanation
Indices: 40819--40863 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
40809 TAAAAAAAAT
40819 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40861 TA T
1 TA T
40864 TCTTGCAAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41552 original size:22 final size:21
Alignment explanation
Indices: 41519--41559 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
41509 TGTGGGACCC
41519 ATTTTTTAAA-GGGTGTCAAA
1 ATTTTTTAAAGGGGTGTCAAA
41539 ATTTTCTTGAAAGGGGTGTCA
1 ATTTT-TT-AAAGGGGTGTCA
41560 TTTTTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 3 0.17
23 8 0.44
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.39
Consensus pattern (21 bp):
ATTTTTTAAAGGGGTGTCAAA
Found at i:43379 original size:24 final size:23
Alignment explanation
Indices: 43295--43381 Score: 63
Period size: 23 Copynumber: 3.6 Consensus size: 23
43285 TAATATTATT
*
43295 ATAATTACAAATTATGTAAA-A-TA
1 ATAATTA-AAA-TATATAAACATTA
43318 ATAATATAAAA-ATATAAACATTA
1 ATAAT-TAAAATATATAAACATTA
**
43341 ATTAATTATATAATATACTAATTATTA
1 A-TAATTA-A-AATATA-TAAACATTA
43368 ATAATTAAAATATA
1 ATAATTAAAATATA
43382 AAGTAATAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
21 6 0.11
22 1 0.02
23 13 0.25
24 13 0.25
25 3 0.06
26 9 0.17
27 8 0.15
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (23 bp):
ATAATTAAAATATATAAACATTA
Found at i:43391 original size:56 final size:55
Alignment explanation
Indices: 43289--43396 Score: 125
Period size: 56 Copynumber: 1.9 Consensus size: 55
43279 CTATTATAAT
43289 ATTATTATAATTACAAATTATGTAAAATAATAATATAAAAATATAAACATTAATTA
1 ATTATTATAATTACAAATTATGTAAAATAATAATATAAAAATATAAA-ATTAATTA
* *
43345 ATTA-TATAATATACTAATTAT-TAATAATTAA-AATAT-AAAGTAATAAAATTAA
1 ATTATTATAAT-TACAAATTATGTAA-AA-TAATAATATAAAAAT-ATAAAATTAA
43397 ATAACCTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
55 18 0.39
56 25 0.54
57 3 0.07
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (55 bp):
ATTATTATAATTACAAATTATGTAAAATAATAATATAAAAATATAAAATTAATTA
Found at i:44153 original size:21 final size:21
Alignment explanation
Indices: 44127--44173 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
44117 GTTGTGGCTT
*
44127 TTGCTTCGTTATGTCTCTCTG
1 TTGCTTCATTATGTCTCTCTG
*
44148 TTGCTTCATTCTGTCTCTCTG
1 TTGCTTCATTATGTCTCTCTG
44169 TTGCT
1 TTGCT
44174 GTTTGTTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.04, C:0.26, G:0.17, T:0.53
Consensus pattern (21 bp):
TTGCTTCATTATGTCTCTCTG
Found at i:44439 original size:36 final size:36
Alignment explanation
Indices: 44394--44465 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
44384 TTCGGTTGGA
44394 GCATTAGAGGCGGTGGCCGAAATAGGCCCTAGGGTT
1 GCATTAGAGGCGGTGGCCGAAATAGGCCCTAGGGTT
44430 GCATTAGAGGCGGTGGCCGAAATAGGCCCTAGGGTT
1 GCATTAGAGGCGGTGGCCGAAATAGGCCCTAGGGTT
44466 TTTGGAATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.19, G:0.39, T:0.19
Consensus pattern (36 bp):
GCATTAGAGGCGGTGGCCGAAATAGGCCCTAGGGTT
Found at i:44698 original size:21 final size:22
Alignment explanation
Indices: 44672--44718 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
44662 TCGGGCTTGG
44672 TTGTAATC-GAGCCTGTGTGCC
1 TTGTAATCTGAGCCTGTGTGCC
*
44693 TTGTAATCTTGGGCCTGTGTGCC
1 TTGTAATC-TGAGCCTGTGTGCC
44716 TTG
1 TTG
44719 CTTTGTAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.35
23 15 0.65
ACGTcount: A:0.11, C:0.21, G:0.30, T:0.38
Consensus pattern (22 bp):
TTGTAATCTGAGCCTGTGTGCC
Found at i:45381 original size:46 final size:46
Alignment explanation
Indices: 45306--45417 Score: 174
Period size: 46 Copynumber: 2.5 Consensus size: 46
45296 TTGAATTTGC
* * * *
45306 TTCCACTACTC-TTCCGTGGAGTTTTATACTTTGTTGAAAAATCCG
1 TTCCACTACTCTTTTCGTGGAGTTTGATACTTTGCTGAAAAATCCA
45351 TTCCACTACTCTTTTCGTGGAGTTTGATACTTTGCTGAAAAATCCA
1 TTCCACTACTCTTTTCGTGGAGTTTGATACTTTGCTGAAAAATCCA
45397 TTCCACTACTCTTTT-GTGGAG
1 TTCCACTACTCTTTTCGTGGAG
45418 CTCAAATTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 17 0.27
46 45 0.73
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.40
Consensus pattern (46 bp):
TTCCACTACTCTTTTCGTGGAGTTTGATACTTTGCTGAAAAATCCA
Found at i:46006 original size:22 final size:22
Alignment explanation
Indices: 45978--46021 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
45968 AGCTTTGGTA
45978 TTTGAAAAGAGAATCTATCATC
1 TTTGAAAAGAGAATCTATCATC
*
46000 TTTGAAAAGAGAATCTGTCATC
1 TTTGAAAAGAGAATCTATCATC
46022 CTTGCAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (22 bp):
TTTGAAAAGAGAATCTATCATC
Found at i:51155 original size:45 final size:47
Alignment explanation
Indices: 51089--51176 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 47
51079 CAAATCACAT
* * * *
51089 CCTAACCTCATGCTTTCTAGTTC-CATGC-TTTGTTTGGAAAAATAA
1 CCTAACCACATGATTTATAGTTCGCATGCATTTATTTGGAAAAATAA
*
51134 CCTAACCACATGATTTATAGTTCGCATGCATTTATTTTGAAAA
1 CCTAACCACATGATTTATAGTTCGCATGCATTTATTTGGAAAA
51177 TAAAATAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 20 0.56
46 5 0.14
47 11 0.31
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (47 bp):
CCTAACCACATGATTTATAGTTCGCATGCATTTATTTGGAAAAATAA
Found at i:51787 original size:3 final size:3
Alignment explanation
Indices: 51771--51803 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
51761 TAAATAAATA
51771 AAT AAT -AT ATAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
51804 GACTAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:52691 original size:14 final size:14
Alignment explanation
Indices: 52672--52698 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52662 TGACCGAAAT
52672 ATACCCTAGGGTTG
1 ATACCCTAGGGTTG
52686 ATACCCTAGGGTT
1 ATACCCTAGGGTT
52699 TCTGAAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (14 bp):
ATACCCTAGGGTTG
Found at i:52929 original size:21 final size:22
Alignment explanation
Indices: 52903--52949 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
52893 TCAGGCTTGG
52903 TTGTAA-TTGGGCCTGTGTGCC
1 TTGTAACTTGGGCCTGTGTGCC
52924 TTGTAATCTTGGGCCTGTGTGCC
1 TTGTAA-CTTGGGCCTGTGTGCC
52947 TTG
1 TTG
52950 CTTTGTAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 6 0.25
23 18 0.75
ACGTcount: A:0.09, C:0.19, G:0.32, T:0.40
Consensus pattern (22 bp):
TTGTAACTTGGGCCTGTGTGCC
Found at i:53000 original size:14 final size:16
Alignment explanation
Indices: 52971--53002 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
52961 ACCTTCGAGC
52971 TTTACAAATAATAATA
1 TTTACAAATAATAATA
52987 TTTA-AAAT-ATAATA
1 TTTACAAATAATAATA
53001 TT
1 TT
53003 ATTATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTACAAATAATAATA
Found at i:57585 original size:23 final size:23
Alignment explanation
Indices: 57559--57634 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
57549 ATTAGACTAG
*
57559 TGAGTTATTGGAATGTATTACTT
1 TGAGTTATTGGAATGTCTTACTT
57582 TGAGTTATTGGAATGTCTTACTT
1 TGAGTTATTGGAATGTCTTACTT
57605 TGAGTTATTGGAATGTCTTACTT
1 TGAGTTATTGGAATGTCTTACTT
*
57628 TAAGTTA
1 TGAGTTA
57635 CTTCCAAGCT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.47
Consensus pattern (23 bp):
TGAGTTATTGGAATGTCTTACTT
Found at i:62180 original size:20 final size:20
Alignment explanation
Indices: 62155--62203 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
62145 TGAAAAGATT
* *
62155 TAATAAAATAAAATAGATAA
1 TAATAAAATAAAAGAGAAAA
62175 TAAT-AAATAAAAGAGAAAA
1 TAATAAAATAAAAGAGAAAA
*
62194 TAACAAAATA
1 TAATAAAATA
62204 TTAGTAGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.20
Consensus pattern (20 bp):
TAATAAAATAAAAGAGAAAA
Found at i:62271 original size:17 final size:18
Alignment explanation
Indices: 62235--62276 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
62225 AGGGTTTTTA
*
62235 AAATAAAATATTAGAATT
1 AAATAAAATATAAGAATT
*
62253 AAATAAAATA-AATAATT
1 AAATAAAATATAAGAATT
62270 AAATAAA
1 AAATAAA
62277 TAATTTAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATAAAATATAAGAATT
Found at i:62945 original size:12 final size:12
Alignment explanation
Indices: 62930--62957 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
62920 ATACCTAAAA
62930 AAATAATATTCT
1 AAATAATATTCT
62942 AAATAATATTCT
1 AAATAATATTCT
62954 AAAT
1 AAAT
62958 CCTAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATAATATTCT
Found at i:63011 original size:25 final size:24
Alignment explanation
Indices: 62964--63011 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
62954 AAATCCTAAT
* **
62964 TAAAATACTAAAACATATTTAAAC
1 TAAAATACTAAAACAAAGATAAAC
62988 TAAAATACCTAAAACAAAGATAAA
1 TAAAATA-CTAAAACAAAGATAAA
63012 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.23
Consensus pattern (24 bp):
TAAAATACTAAAACAAAGATAAAC
Found at i:63095 original size:76 final size:75
Alignment explanation
Indices: 62901--63069 Score: 222
Period size: 76 Copynumber: 2.3 Consensus size: 75
62891 AAATTCTAAT
* * * * *
62901 TAAAAC-TATTTAAACAAAAATACCT-AAA-AAA-ATAATAT-TCTAAATAATATTCTAAATCCT
1 TAAAACATATTTAAACTAAAATACCTAAAACAAAGATAAAATAT-AAAATAATATCCTAAAACCT
62961 AATTAAAATAC
65 AATTAAAATAC
*
62972 TAAAACATATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATCCTAAAACTT
1 TAAAACATATTTAAACTAAAATACCTAAAACAAAGATAAAATAT-AAAATAATATCCTAAAACCT
63037 AATTAAAATAC
65 AATTAAAATAC
*
63048 TAAAACCTATTTAAACTAAAAT
1 TAAAACATATTTAAACTAAAAT
63070 TCAAAGATAA
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
71 6 0.07
72 18 0.21
73 3 0.04
74 3 0.04
75 6 0.07
76 49 0.58
ACGTcount: A:0.58, C:0.12, G:0.01, T:0.29
Consensus pattern (75 bp):
TAAAACATATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAATAATATCCTAAAACCTA
ATTAAAATAC
Found at i:64754 original size:5 final size:5
Alignment explanation
Indices: 64744--64791 Score: 62
Period size: 5 Copynumber: 9.6 Consensus size: 5
64734 TGTTCAGAGA
* *
64744 AAAAT AAAAT AAAAT AAATT AAAAT AAAAT -AAAT AGAAT GAAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAA
64792 GCTAGCTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 4 0.11
5 29 0.78
6 4 0.11
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:64769 original size:20 final size:20
Alignment explanation
Indices: 64744--64791 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
64734 TGTTCAGAGA
*
64744 AAAATAAAATAAAATA-AATT
1 AAAATAAAAT-AAATAGAATG
64764 AAAATAAAATAAATAGAATG
1 AAAATAAAATAAATAGAATG
64784 AAAATAAA
1 AAAATAAA
64792 GCTAGCTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (20 bp):
AAAATAAAATAAATAGAATG
Found at i:70108 original size:39 final size:39
Alignment explanation
Indices: 70054--70133 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
70044 ATTCTTCATG
70054 CTCGTGTTTCGATATCTGGATCTAGATCTACTAATTCAC
1 CTCGTGTTTCGATATCTGGATCTAGATCTACTAATTCAC
70093 CTCGTGTTTCGATATCTGGATCTAGATCTACTAATTCAC
1 CTCGTGTTTCGATATCTGGATCTAGATCTACTAATTCAC
70132 CT
1 CT
70134 GGGTTAATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.39
Consensus pattern (39 bp):
CTCGTGTTTCGATATCTGGATCTAGATCTACTAATTCAC
Found at i:70143 original size:14 final size:14
Alignment explanation
Indices: 70124--70152 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
70114 CTAGATCTAC
70124 TAATTCACCTGGGT
1 TAATTCACCTGGGT
70138 TAATTCACCTGGGT
1 TAATTCACCTGGGT
70152 T
1 T
70153 TCTTCTGGTC
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:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (14 bp):
TAATTCACCTGGGT
Found at i:71217 original size:19 final size:19
Alignment explanation
Indices: 71189--71299 Score: 54
Period size: 19 Copynumber: 5.9 Consensus size: 19
71179 AAATAATATT
*
71189 CTAAATCCTAATTAAAATA
1 CTAAAACCTAATTAAAATA
* *
71208 CTAAAACCTATTTAAACTA
1 CTAAAACCTAATTAAAATA
* *
71227 --AAATACCTAA-AACAAAGA
1 CTAAA-ACCTAATTA-AAATA
** *
71245 -TAAAATATAA-AAATAATA
1 CTAAAACCTAATTAA-AATA
*
71263 TCCTAAAACTTAATTAAAATA
1 -C-TAAAACCTAATTAAAATA
71284 CTAAAACCT-ATTAAAA
1 CTAAAACCTAATTAAAA
71300 CTAAAATAAA
Statistics
Matches: 70, Mismatches: 14, Indels: 17
0.69 0.14 0.17
Matches are distributed among these distances:
17 5 0.07
18 24 0.34
19 26 0.37
20 1 0.01
21 12 0.17
22 2 0.03
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.27
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:71224 original size:70 final size:74
Alignment explanation
Indices: 71146--71307 Score: 224
Period size: 76 Copynumber: 2.2 Consensus size: 74
71136 TAATTAAAGT
* * * *
71146 TATTTAAACTAAAATACCT-A-AAA-ATAACAT-TTAAAATAATATTCTAAATCCTAATTAAAAT
1 TATTTAAACTAAAATACCTAACAAAGATAAAATATAAAAATAATATCCTAAAACCTAATTAAAAT
71207 ACTAAAACC
66 ACTAAAACC
*
71216 TATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATCCTAAAACTTAATTAAA
1 TATTTAAACTAAAATACCT--AACAAAGATAAAATATAAAAATAATATCCTAAAACCTAATTAAA
71281 ATACTAAAACC
64 ATACTAAAACC
*
71292 TATTAAAACTAAAATA
1 TATTTAAACTAAAATA
71308 AAAAGATAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
70 19 0.24
73 1 0.01
74 3 0.04
75 6 0.08
76 51 0.64
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (74 bp):
TATTTAAACTAAAATACCTAACAAAGATAAAATATAAAAATAATATCCTAAAACCTAATTAAAAT
ACTAAAACC
Found at i:78754 original size:18 final size:17
Alignment explanation
Indices: 78715--78757 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
78705 ATTATATGGA
78715 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
78731 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
78749 TATTATTAT
1 TATTATTAT
78758 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:79066 original size:14 final size:13
Alignment explanation
Indices: 79002--79067 Score: 53
Period size: 14 Copynumber: 4.8 Consensus size: 13
78992 TTTGTTATTA
79002 TTATTTTGTTTTAT
1 TTATTTT-TTTTAT
79016 TTATTTTCTTTT-T
1 TTATTTT-TTTTAT
*
79029 CTTTTTCTTTTTTAT
1 -TTATT-TTTTTTAT
* *
79044 ATATATTTTATTAT
1 TTAT-TTTTTTTAT
79058 TTATTTTTTT
1 TTATTTTTTT
79068 ACTTACTATT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
13 6 0.15
14 31 0.76
15 4 0.10
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.79
Consensus pattern (13 bp):
TTATTTTTTTTAT
Found at i:80237 original size:20 final size:20
Alignment explanation
Indices: 80212--80249 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
80202 ACCTTACTAA
80212 CTCTTTTCATTTT-TTTCCCT
1 CTCTTTT-ATTTTATTTCCCT
80232 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
80250 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.66
Consensus pattern (20 bp):
CTCTTTTATTTTATTTCCCT
Found at i:84054 original size:183 final size:182
Alignment explanation
Indices: 83746--84182 Score: 795
Period size: 183 Copynumber: 2.4 Consensus size: 182
83736 ATTAAATCCG
83746 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
83811 ATAGATTATGTTCAAACTATGACATTGCTCGGACACTTGGCAATTCGATGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGATGTTTGCTCCACTGC-T
*
83876 TTGTCAGGCCAAAGACTTTGTGATAAGATGAACCCTTTAGTGATTTATCCCTC
130 TTGTCAGGCCAAAGACTTTGTGATAAGATGAACCCTTCAGTGATTTATCCCTC
*
83929 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAATCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* *
83994 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTTCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGATGTTTGCTCCACTGCTT
* *
84059 TGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TGTCAGGCCAAAGACTTTGTGATAAGATGAACCCTTCAGTGATTTATCCCTC
84111 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGA-GAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
84175 ATAGATTA
66 ATAGATTA
84183 CATTCAAATC
Statistics
Matches: 246, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
181 33 0.13
182 89 0.36
183 124 0.50
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (182 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGATGTTTGCTCCACTGCTT
TGTCAGGCCAAAGACTTTGTGATAAGATGAACCCTTCAGTGATTTATCCCTC
Done.