Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005771.1 Hibiscus syriacus cultivar Beakdansim tig00013505_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: 110007
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:7178 original size:23 final size:23
Alignment explanation
Indices: 7147--7201 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
7137 AGCCTGGCCT
*
7147 GGCCTGGCCTATTTAACTAAACA
1 GGCCAGGCCTATTTAACTAAACA
7170 GGCCAGGCCTATTTAACTAAACA
1 GGCCAGGCCTATTTAACTAAACA
7193 GGCCAGGCC
1 GGCCAGGCC
7202 CAAGCCTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (23 bp):
GGCCAGGCCTATTTAACTAAACA
Found at i:7258 original size:41 final size:41
Alignment explanation
Indices: 7176--7261 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
7166 AACAGGCCAG
* *
7176 GCCTATTTAACTAAACAGGCCAGGCCCAAGCCTTTTTAAAA
1 GCCTATTTAACTAAACAGGCCAGGCCCAAGCCTATTAAAAA
** *
7217 GCCTATTTAACTAAACAGGCCAGGCTTAGGCCTATTAAAAA
1 GCCTATTTAACTAAACAGGCCAGGCCCAAGCCTATTAAAAA
7258 GCCT
1 GCCT
7262 TATAAGCCTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (41 bp):
GCCTATTTAACTAAACAGGCCAGGCCCAAGCCTATTAAAAA
Found at i:23629 original size:31 final size:31
Alignment explanation
Indices: 23582--23659 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
23572 ATTTAATGTC
* *
23582 TAAGTGACC-AAACTTAATAAAATAATAGCG
1 TAAGTGACCAAAACTTAATAAAACAATAACG
*
23612 TAAGTGACCAAAACTTAATAAAACAATAATG
1 TAAGTGACCAAAACTTAATAAAACAATAACG
23643 TAAGTGACCAAAACTTA
1 TAAGTGACCAAAACTTA
23660 TGTTTTTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 9 0.20
31 35 0.80
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (31 bp):
TAAGTGACCAAAACTTAATAAAACAATAACG
Found at i:23909 original size:27 final size:28
Alignment explanation
Indices: 23879--23936 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
23869 ATCAAAATTG
* *
23879 AATTTAAATTATAAT-AAATTTGTA-TAA
1 AATTGAAA-TATAATAAAATTTGAATTAA
*
23906 AATTGACATATAATAAAATTTGAATTAA
1 AATTGAAATATAATAAAATTTGAATTAA
23934 AAT
1 AAT
23937 AAGGTTGAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 6 0.23
27 14 0.54
28 6 0.23
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (28 bp):
AATTGAAATATAATAAAATTTGAATTAA
Found at i:24153 original size:32 final size:31
Alignment explanation
Indices: 24109--24168 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
24099 TTAACGTGAT
*
24109 CCTTGAATTTTACACT-CAATACTAATTTGAC
1 CCTTGAAATTTACA-TACAATACTAATTTGAC
*
24140 CCTTGGAAATTTACATAGAATACTAATTT
1 CCTT-GAAATTTACATACAATACTAATTT
24169 AAACCCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 5 0.20
32 20 0.80
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (31 bp):
CCTTGAAATTTACATACAATACTAATTTGAC
Found at i:30139 original size:23 final size:23
Alignment explanation
Indices: 30113--30190 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
30103 CACCACAGCT
30113 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
30136 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * * *
30159 CGTAGAATTACACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
30182 TATAATAAT
1 CAT-ATAAT
30191 GTCCATAAGG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 40 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:31440 original size:149 final size:149
Alignment explanation
Indices: 31190--31504 Score: 551
Period size: 149 Copynumber: 2.1 Consensus size: 149
31180 TATAATTACA
*
31190 CCGAAGTG-CCGCGTAGAATTGCACTGTAATGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAATGCCATATAATAATGTCCATAAGGACCACATATTA
*
31254 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
* *
31319 CCACAGAATATATATATATC
130 CCAAAGAATATACATATATC
*
31339 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAATGCCATATAATAATGTCCATAAGGACCACATATTAT
31404 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
31469 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
*
31488 CCGAAAGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
31505 CCCTCGACTC
Statistics
Matches: 158, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 157 0.99
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAATGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:33178 original size:21 final size:21
Alignment explanation
Indices: 33148--33192 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
33138 TTTTGTTTGT
33148 TTGAAGGGGTATCAG-TTCCCC
1 TTGAAGGGGTA-CAGATTCCCC
* *
33169 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACAGATTCCCC
33190 TTG
1 TTG
33193 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACAGATTCCCC
Found at i:36067 original size:28 final size:28
Alignment explanation
Indices: 36027--36083 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
36017 GGAAAACTGA
36027 CATGTCTTGCTCCGCATTACTCTTTACT
1 CATGTCTTGCTCCGCATTACTCTTTACT
36055 CATGTCTTGCTCCGCATTACTCTTTACT
1 CATGTCTTGCTCCGCATTACTCTTTACT
36083 C
1 C
36084 TTCTCGAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.14, C:0.33, G:0.11, T:0.42
Consensus pattern (28 bp):
CATGTCTTGCTCCGCATTACTCTTTACT
Found at i:36753 original size:149 final size:149
Alignment explanation
Indices: 36503--36817 Score: 585
Period size: 149 Copynumber: 2.1 Consensus size: 149
36493 TATAATTGCA
*
36503 CCGAAGTACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
36568 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
* *
36633 CACAGAATATATATATATC
131 CAAAGAATATACATATATC
36652 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
36717 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
36782 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
*
36801 CCGAAAGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
36818 CCCTCGACTC
Statistics
Matches: 161, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 161 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:38484 original size:21 final size:21
Alignment explanation
Indices: 38460--38504 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
38450 TTTTGTTCGT
*
38460 TTGAAGGGGTA-TCGGTTCCCC
1 TTGAAGGGGTACT-GATTCCCC
*
38481 TTGAATGGGTACTGATTCCCC
1 TTGAAGGGGTACTGATTCCCC
38502 TTG
1 TTG
38505 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACTGATTCCCC
Found at i:39643 original size:15 final size:15
Alignment explanation
Indices: 39623--39655 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
39613 CGTAGGACCC
39623 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
39638 CTACATCCTGAAGGA
1 CTACATCCCGAAGGA
39653 CTA
1 CTA
39656 TTATACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.18
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:39804 original size:23 final size:26
Alignment explanation
Indices: 39767--39835 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
39757 TTCTCTTGTG
39767 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
39791 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
39816 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
39836 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:39817 original size:12 final size:12
Alignment explanation
Indices: 39800--39835 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
39790 TATCATGTTC
39800 TCATATCACATG
1 TCATATCACATG
*
39812 TCATATCACATA
1 TCATATCACATG
39824 TCATATCACATG
1 TCATATCACATG
39836 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:40277 original size:64 final size:64
Alignment explanation
Indices: 40209--40351 Score: 182
Period size: 64 Copynumber: 2.2 Consensus size: 64
40199 TATTGCTGGG
* * *
40209 ATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATT-AATGGGATGCATCGATGCACTACT
1 ATGCATCGATGCACCAATTGCATTCGATGTTTTCATT-TTAAAAGAG-TGCATCGATGCACTACC
*
40272 T
64 A
** *
40273 ATGCATCGATGCATGAATTGCATTCGATGTTTTTATTTTAAAAGAGTGCATCGATGCACTACCA
1 ATGCATCGATGCACCAATTGCATTCGATGTTTTCATTTTAAAAGAGTGCATCGATGCACTACCA
*
40337 ATGCATCGATACACC
1 ATGCATCGATGCACC
40352 TTCAAACAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
64 57 0.85
65 10 0.15
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACCAATTGCATTCGATGTTTTCATTTTAAAAGAGTGCATCGATGCACTACCA
Found at i:46569 original size:23 final size:26
Alignment explanation
Indices: 46532--46600 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
46522 TTCTCTTGTG
46532 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
46556 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
46581 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
46601 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:46582 original size:12 final size:12
Alignment explanation
Indices: 46565--46600 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
46555 TATCATGTTC
46565 TCATATCACATG
1 TCATATCACATG
*
46577 TCATATCACATA
1 TCATATCACATG
46589 TCATATCACATG
1 TCATATCACATG
46601 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:47016 original size:64 final size:63
Alignment explanation
Indices: 46908--47128 Score: 248
Period size: 64 Copynumber: 3.5 Consensus size: 63
46898 TAATGAAGGT
* * ** * **
46908 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTATTATTAATGGG
* **
46972 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTT-ATTATTAATGGG
* **
47036 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTT-TTATTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTA--TTAATGGG
**
47099 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
47129 ACACCTTCAA
Statistics
Matches: 136, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
62 3 0.02
63 4 0.03
64 129 0.95
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTATTAATGGG
Found at i:48918 original size:19 final size:19
Alignment explanation
Indices: 48894--48944 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
48884 TATTACTGGG
48894 ATGCATCGATGCATGCCTT
1 ATGCATCGATGCATGCCTT
48913 ATGCATCGATGCATGCCTT
1 ATGCATCGATGCATGCCTT
48932 ATGCATCGATGCA
1 ATGCATCGATGCA
48945 CCAATTGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCATGCCTT
Found at i:50663 original size:32 final size:32
Alignment explanation
Indices: 50625--50874 Score: 362
Period size: 32 Copynumber: 7.9 Consensus size: 32
50615 AGAGTCGAGG
* * *
50625 ATTACCTATGTCTTTCGAGACATATAGACAGG
1 ATTACCTATGTCTTTCGGGACATATGGACAGA
*
50657 ATTACCTATGTCTTTCGGGACATATGTACAGA
1 ATTACCTATGTCTTTCGGGACATATGGACAGA
* *
50689 ATTACATATGTCTTTCGGGACATATGGAAAGA
1 ATTACCTATGTCTTTCGGGACATATGGACAGA
* *
50721 ATTATCTATGTCTTTCGGGATATATGGACAGA
1 ATTACCTATGTCTTTCGGGACATATGGACAGA
50753 ATTACCTATGTCTTTCGGGACATATGGACAGA
1 ATTACCTATGTCTTTCGGGACATATGGACAGA
* *
50785 ATTACCTATGTCTTTCGGGACATATGAACATA
1 ATTACCTATGTCTTTCGGGACATATGGACAGA
50817 ATTACCTATGTCTTTCGGGACATATGGACAG-
1 ATTACCTATGTCTTTCGGGACATATGGACAGA
* *
50848 -TTGCCTATGT-TCTTCGGAACATATGGA
1 ATTACCTATGTCT-TTCGGGACATATGGA
50875 TAGGTCATTT
Statistics
Matches: 198, Mismatches: 19, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
29 1 0.01
30 23 0.12
32 174 0.88
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (32 bp):
ATTACCTATGTCTTTCGGGACATATGGACAGA
Found at i:52767 original size:20 final size:20
Alignment explanation
Indices: 52731--52768 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52721 TATATATTAA
52731 AAGAAAAAACTTTGAATTTT
1 AAGAAAAAACTTTGAATTTT
*
52751 AAGAAGAAA-TTTAGAATT
1 AAGAAAAAACTTT-GAATT
52769 CCAACAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.32
Consensus pattern (20 bp):
AAGAAAAAACTTTGAATTTT
Found at i:54298 original size:20 final size:20
Alignment explanation
Indices: 54262--54299 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54252 TATATATTAA
54262 AAGAAAAAACTTTGAATTTT
1 AAGAAAAAACTTTGAATTTT
*
54282 AAGAAGAAA-TTTAGAATT
1 AAGAAAAAACTTT-GAATT
54300 CCAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.32
Consensus pattern (20 bp):
AAGAAAAAACTTTGAATTTT
Found at i:56084 original size:10 final size:10
Alignment explanation
Indices: 56069--56120 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
56059 TTCAATAATC
56069 TGTTCGTTTA
1 TGTTCGTTTA
56079 TGTTCGTTCATTTA
1 TGTTCG----TTTA
* *
56093 TGTCCGTGTA
1 TGTTCGTTTA
56103 TGTTCGTTTA
1 TGTTCGTTTA
56113 TGTTCGTT
1 TGTTCGTT
56121 CGTTTATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 25 0.74
14 9 0.26
ACGTcount: A:0.10, C:0.13, G:0.21, T:0.56
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:56438 original size:24 final size:24
Alignment explanation
Indices: 56410--56459 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
56400 ATTGTGTTCA
*
56410 TTTACGTTTGCTCGTTTATATTCG
1 TTTACATTTGCTCGTTTATATTCG
* *
56434 TTTACATTTGTTTGTTTATATTCG
1 TTTACATTTGCTCGTTTATATTCG
56458 TT
1 TT
56460 CATTTGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTACATTTGCTCGTTTATATTCG
Found at i:56477 original size:22 final size:24
Alignment explanation
Indices: 56423--56468 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
56413 ACGTTTGCTC
56423 GTTTATATTCGTTTACATTTGTTT
1 GTTTATATTCGTTTACATTTGTTT
56447 GTTTATATTCG-TT-CATTTGTTT
1 GTTTATATTCGTTTACATTTGTTT
56469 TTGTTTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 9 0.41
23 2 0.09
24 11 0.50
ACGTcount: A:0.15, C:0.09, G:0.13, T:0.63
Consensus pattern (24 bp):
GTTTATATTCGTTTACATTTGTTT
Found at i:58460 original size:18 final size:19
Alignment explanation
Indices: 58439--58480 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
58429 TAATAGTGAG
*
58439 TTATTATAA-AATATGTTT
1 TTATTATAATAATATATTT
*
58457 TTATTATAATTATATATTT
1 TTATTATAATAATATATTT
58476 TTATT
1 TTATT
58481 TTTATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTATTATAATAATATATTT
Found at i:58562 original size:18 final size:16
Alignment explanation
Indices: 58531--58576 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 16
58521 ATAATAATTT
*
58531 TTTAAATTTATTATAG
1 TTTAAATTTATTATAA
58547 TTTAAATTGATATTATAA
1 TTTAAATT--TATTATAA
58565 TTTAAATGTTAT
1 TTTAAAT-TTAT
58577 ATTTTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 8 0.31
17 3 0.12
18 14 0.54
19 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (16 bp):
TTTAAATTTATTATAA
Found at i:68407 original size:22 final size:22
Alignment explanation
Indices: 68372--68424 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
68362 ATTTTTTACT
* *
68372 TAAATTAATCTAATATTTTAT-A
1 TAAATTATTCTAAT-TTTAATAA
*
68394 TAAATTATTTTAATTTTAATAA
1 TAAATTATTCTAATTTTAATAA
68416 TAATATTAT
1 TAA-ATTAT
68425 AAGATCATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 5 0.19
22 16 0.62
23 5 0.19
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TAAATTATTCTAATTTTAATAA
Found at i:74002 original size:60 final size:59
Alignment explanation
Indices: 73860--74010 Score: 169
Period size: 60 Copynumber: 2.5 Consensus size: 59
73850 TATTATTCTT
* ** * * *
73860 TAAATTTTTAAATATTCTAATTTCATCCTTAAACCATGACTCTCATTCTAAATTAGTCCT
1 TAAACTTTT-AATATTCTAATTTCATCCCCAAACCATGAATCCCATTCTAAATTAGTCCC
* * *
73920 TAAACCTTTTAACATTCTAATTTCATCCCCAAACTATGAATCCCATTCTAAATTGGTCCC
1 TAAA-CTTTTAATATTCTAATTTCATCCCCAAACCATGAATCCCATTCTAAATTAGTCCC
*
73980 TAAACTTTTATATATT-TCAATTTCAGCCCCA
1 TAAACTTTTA-ATATTCT-AATTTCATCCCCA
74011 GATTCATCCA
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 7 0.09
60 66 0.86
61 4 0.05
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.40
Consensus pattern (59 bp):
TAAACTTTTAATATTCTAATTTCATCCCCAAACCATGAATCCCATTCTAAATTAGTCCC
Found at i:74246 original size:60 final size:60
Alignment explanation
Indices: 74132--74307 Score: 157
Period size: 60 Copynumber: 2.9 Consensus size: 60
74122 CGAACATTTT
* * * * *
74132 AGGAT-AAAATTGAAATATTCAAAAAGTTTG-GGACCAATTTAGGATGAAAATCATAGCTTG
1 AGGATGAAAATTGAAATGTTC-AAAAGTTTGAGGACTAATTTAGAAT-AAAGTCATAGCTTA
* * **
74192 TGGATGAAAATT-AAATGTTCAAAATTTTGAGGACTAATTTAGAATAATAGTCATATTTTA
1 AGGATGAAAATTGAAATGTTCAAAAGTTTGAGGACTAATTTAGAATAA-AGTCATAGCTTA
* *
74252 AGGATG-GAATTGAAATGTAT-AAAAGTTT-AGGAACTAATTTAGAATGAGAGTCATAG
1 AGGATGAAAATTGAAATGT-TCAAAAGTTTGAGG-ACTAATTTAGAAT-AAAGTCATAG
74308 ATTGGGGACA
Statistics
Matches: 95, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
59 17 0.18
60 70 0.74
61 8 0.08
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.32
Consensus pattern (60 bp):
AGGATGAAAATTGAAATGTTCAAAAGTTTGAGGACTAATTTAGAATAAAGTCATAGCTTA
Found at i:80407 original size:19 final size:19
Alignment explanation
Indices: 80383--80419 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
80373 GTTTTTTTTT
80383 TGTATTTCTCT-TCTCTCTG
1 TGTATTT-TCTGTCTCTCTG
80402 TGTATTTTCTGTCTCTCT
1 TGTATTTTCTGTCTCTCT
80420 TTTCTCTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.05, C:0.24, G:0.11, T:0.59
Consensus pattern (19 bp):
TGTATTTTCTGTCTCTCTG
Found at i:80799 original size:3 final size:3
Alignment explanation
Indices: 80793--80856 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
80783 AATAATTATT
* **
80793 TAA TAA TAA T-A TAA TATA TAA TATT TAA TAA TAA TAA TTT TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TA-A TAA TAA TAA TAA TAA TAA TAA
80839 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
80857 ATAAATAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 45 0.87
4 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:80808 original size:22 final size:24
Alignment explanation
Indices: 80782--80828 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
80772 AATGGGCATG
80782 TAATA-AT-TATTTAATAATAATA
1 TAATATATATATTTAATAATAATA
80804 TAATATATAATATTTAATAATAATA
1 TAATATAT-ATATTTAATAATAATA
80829 ATTTTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.23
23 2 0.09
25 15 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TAATATATATATTTAATAATAATA
Found at i:81344 original size:116 final size:116
Alignment explanation
Indices: 81204--81661 Score: 850
Period size: 116 Copynumber: 4.0 Consensus size: 116
81194 AAAAGCGGAT
81204 CTGGCAATGTTAATCCATCATATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATG
1 CTGGCAATGTTAATCCATCATATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATG
81269 AACTTATTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
66 AACTTATTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
81320 CTGGCAATGTTAATCCATCATATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATG
1 CTGGCAATGTTAATCCATCATATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATG
*
81385 AACTTATTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTAC
66 AACTTATTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
*
81436 CTGGCAATGTTAATCAATCATATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATG
1 CTGGCAATGTTAATCCATCATATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATG
*
81501 AACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
66 AACTTATTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
81552 CTGGCAATGTTAATCCATCATATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATG
1 CTGGCAATGTTAATCCATCATATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATG
* *
81617 AACTTCTTCTTCCTTCTTC--AT-ATGAGTTCTTCTCATTATGAACTC
66 AACTTATTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTC
81662 GAATTGGAAA
Statistics
Matches: 336, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
113 23 0.07
114 2 0.01
116 311 0.93
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.38
Consensus pattern (116 bp):
CTGGCAATGTTAATCCATCATATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATG
AACTTATTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
Found at i:81640 original size:24 final size:23
Alignment explanation
Indices: 81605--81649 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
81595 TGAACAAATT
81605 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
81629 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
81650 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:82101 original size:23 final size:22
Alignment explanation
Indices: 82079--82120 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
82069 AAATCCGATA
* *
82079 AAGCTTTCATCTTTGAAAAGAT
1 AAGCTGTCATCTTTAAAAAGAT
*
82101 AATCTGTCATCTTTAAAAAG
1 AAGCTGTCATCTTTAAAAAG
82121 GGAATCTATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (22 bp):
AAGCTGTCATCTTTAAAAAGAT
Found at i:82111 original size:22 final size:22
Alignment explanation
Indices: 82085--82139 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
82075 GATAAAGCTT
* *
82085 TCATCTTTGAAAAGATAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
82107 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
82129 TCATCTTTGAA
1 TCATCTTTGAA
82140 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:84912 original size:115 final size:114
Alignment explanation
Indices: 84598--84938 Score: 574
Period size: 114 Copynumber: 3.0 Consensus size: 114
84588 GATCATGCAG
* * * * * * *
84598 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTAAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
84663 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
* *
84712 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCATATAACTCAAAGA
1 TTCATCTTTAAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
84777 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
84826 TTCATCTTTAAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTAAAATCCAATGATTGG-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
84891 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
65 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
84939 CATGGCACTT
Statistics
Matches: 214, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
114 128 0.60
115 86 0.40
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTAAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
Found at i:90468 original size:14 final size:14
Alignment explanation
Indices: 90448--90485 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
90438 TGCCAAATGC
90448 AAATGTAAATATGT
1 AAATGTAAATATGT
* *
90462 GAATGTAAAAATGT
1 AAATGTAAATATGT
90476 AAATGTAAAT
1 AAATGTAAAT
90486 TATTTAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.32
Consensus pattern (14 bp):
AAATGTAAATATGT
Found at i:90654 original size:29 final size:26
Alignment explanation
Indices: 90602--90654 Score: 70
Period size: 29 Copynumber: 1.9 Consensus size: 26
90592 GATGTAAATT
*
90602 TAAAAATGTAAATGTAAATACAAACA
1 TAAAAATGTAAATGAAAATACAAACA
90628 TAAAAATGTTCAAATGCAAAATACAAA
1 TAAAAATG-T-AAATG-AAAATACAAA
90655 TGCATGTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 8 0.35
27 1 0.04
28 5 0.22
29 9 0.39
ACGTcount: A:0.60, C:0.09, G:0.08, T:0.23
Consensus pattern (26 bp):
TAAAAATGTAAATGAAAATACAAACA
Found at i:92087 original size:14 final size:15
Alignment explanation
Indices: 92063--92128 Score: 61
Period size: 14 Copynumber: 4.6 Consensus size: 15
92053 ATTATTGAAT
92063 ATAAT-AAATAAATA
1 ATAATAAAATAAATA
92077 A-AATAAAAT-AATA
1 ATAATAAAATAAATA
*
92090 ATAATAATAATATATA
1 ATAATAA-AATAAATA
*
92106 A-AA-AATAATAAGTA
1 ATAATAA-AATAAATA
92120 ATAATAAAA
1 ATAATAAAA
92129 AATTTGAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
13 8 0.19
14 20 0.47
15 9 0.21
16 6 0.14
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (15 bp):
ATAATAAAATAAATA
Found at i:92091 original size:3 final size:3
Alignment explanation
Indices: 92063--92126 Score: 64
Period size: 3 Copynumber: 21.3 Consensus size: 3
92053 ATTATTGAAT
92063 ATA ATAA ATAA ATA A-A ATA A-A ATA ATA ATA ATA ATA ATA TATA A-A
1 ATA AT-A AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
92108 A-A ATA ATA AGTA ATA ATA A
1 ATA ATA ATA A-TA ATA ATA A
92127 AAAATTTGAA
Statistics
Matches: 55, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
2 8 0.15
3 34 0.62
4 13 0.24
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:92098 original size:17 final size:17
Alignment explanation
Indices: 92063--92128 Score: 68
Period size: 17 Copynumber: 3.9 Consensus size: 17
92053 ATTATTGAAT
92063 ATAATAAATAAATAAAATA
1 ATAAT-AAT-AATAAAATA
92082 A-AATAATAAT--AATA
1 ATAATAATAATAAAATA
92096 ATAATATATAA-AAAATA
1 ATAATA-ATAATAAAATA
92113 ATAAGTAATAATAAAA
1 ATAA-TAATAATAAAA
92129 AATTTGAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
14 5 0.12
15 4 0.10
16 7 0.17
17 15 0.37
18 9 0.22
19 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
ATAATAATAATAAAATA
Found at i:92100 original size:33 final size:33
Alignment explanation
Indices: 92063--92126 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
92053 ATTATTGAAT
92063 ATAATAAATAAATAAAATAA-AA-TAATAATAATA
1 ATAATAAAT-AA-AAAATAATAAGTAATAATAATA
*
92096 ATAATATATAAAAAATAATAAGTAATAATAA
1 ATAATAAATAAAAAATAATAAGTAATAATAA
92127 AAAATTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 7 0.25
32 4 0.14
33 17 0.61
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (33 bp):
ATAATAAATAAAAAATAATAAGTAATAATAATA
Found at i:93777 original size:19 final size:19
Alignment explanation
Indices: 93753--93789 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
93743 GTTTTTTTTT
93753 TGTATTTCTCT-TCTCTCTG
1 TGTATTT-TCTGTCTCTCTG
93772 TGTATTTTCTGTCTCTCT
1 TGTATTTTCTGTCTCTCT
93790 TTTCTCTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.05, C:0.24, G:0.11, T:0.59
Consensus pattern (19 bp):
TGTATTTTCTGTCTCTCTG
Found at i:94179 original size:3 final size:3
Alignment explanation
Indices: 94173--94239 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
94163 AATAATTATT
* **
94173 TAA TAA TAA T-A TAA TATA TAA TAA TATT TAA TAA TAA TAA TTT TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA
94219 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
94240 ATAAATAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 48 0.87
4 5 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:94254 original size:9 final size:10
Alignment explanation
Indices: 94173--94251 Score: 62
Period size: 9 Copynumber: 8.3 Consensus size: 10
94163 AATAATTATT
94173 TAATAATAATA
1 TAATAATAA-A
94184 TAAT-ATATAA
1 TAATAATA-AA
* *
94194 TAATATTTAA
1 TAATAATAAA
94204 TAATAAT-AA
1 TAATAATAAA
**
94213 TTTTAAT-AA
1 TAATAATAAA
94222 TAATAAT-AA
1 TAATAATAAA
94231 TAATAATAAA
1 TAATAATAAA
94241 T-A-AATAAA
1 TAATAATAAA
94249 TAA
1 TAA
94252 AATGGGTAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
8 7 0.12
9 25 0.44
10 19 0.33
11 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAATAATAAA
Found at i:100050 original size:10 final size:10
Alignment explanation
Indices: 100035--100063 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
100025 ATCTTAATTA
100035 ATCCGAATCG
1 ATCCGAATCG
100045 ATCCGAATCG
1 ATCCGAATCG
100055 ATCCGAATC
1 ATCCGAATC
100064 ATACATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (10 bp):
ATCCGAATCG
Found at i:103061 original size:30 final size:30
Alignment explanation
Indices: 103027--103124 Score: 87
Period size: 30 Copynumber: 3.4 Consensus size: 30
103017 TTATGAATGG
* * *
103027 AATAATTTTTAAAGGTGTAGATTAATATAT
1 AATAATATTTAAAGGTGTAGATTAATACAA
* ** *
103057 AATAATATTTATTA-GT-TTTA-TAA-ACAG
1 AATAATATTTA-AAGGTGTAGATTAATACAA
*
103084 AATAATTTTTAAAGGTGTAGATTAATACAA
1 AATAATATTTAAAGGTGTAGATTAATACAA
103114 AATAATATTTA
1 AATAATATTTA
103125 TTTGAAGGTA
Statistics
Matches: 51, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
26 1 0.02
27 14 0.27
28 5 0.10
29 5 0.10
30 25 0.49
31 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (30 bp):
AATAATATTTAAAGGTGTAGATTAATACAA
Found at i:103751 original size:61 final size:61
Alignment explanation
Indices: 103622--103751 Score: 152
Period size: 61 Copynumber: 2.1 Consensus size: 61
103612 ATGCAAGGAC
*** * * *
103622 ACTTAGTGTAGGTGGTGGGCACAACCTTATGTGACATATTTGGATCAGCACTAGAGTATAA
1 ACTTAGTGTAGGTGGTGGGCACAACCTTATGTGACATATACAGATCAACAATAGAGCATAA
* * * * *
103683 ACCTAGTGTAGGTGGTGGGCACGACTTTATGTGTCATATACAGATCAACAATAGAGCGTAA
1 ACTTAGTGTAGGTGGTGGGCACAACCTTATGTGACATATACAGATCAACAATAGAGCATAA
*
103744 GCTTAGTG
1 ACTTAGTG
103752 CAGATTTAGA
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.28
Consensus pattern (61 bp):
ACTTAGTGTAGGTGGTGGGCACAACCTTATGTGACATATACAGATCAACAATAGAGCATAA
Found at i:105396 original size:28 final size:27
Alignment explanation
Indices: 105328--105398 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 27
105318 CATATTTAAT
*
105328 AATTAAAATAAT-ATATATATTCAGTA
1 AATTAAAATAATAATATATATTCAGAA
*
105354 AATTAAGATAA-AATATATACTTCA-AA
1 AATTAAAATAATAATATATA-TTCAGAA
*
105380 AAGTTAACATAATAATATA
1 AA-TTAAAATAATAATATA
105399 ATTTATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
26 20 0.53
27 12 0.32
28 6 0.16
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.34
Consensus pattern (27 bp):
AATTAAAATAATAATATATATTCAGAA
Found at i:105414 original size:31 final size:33
Alignment explanation
Indices: 105378--105444 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 33
105368 ATATACTTCA
* *
105378 AAAAGTTAACATAATAATATAAT-T-TATTTTT
1 AAAAGTTAACATAAGAATAAAATCTATATTTTT
* *
105409 AAAAGTTTATATAAGAATAAAATCTATATTTTT
1 AAAAGTTAACATAAGAATAAAATCTATATTTTT
105442 AAA
1 AAA
105445 TTAAAATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 19 0.63
32 1 0.03
33 10 0.33
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (33 bp):
AAAAGTTAACATAAGAATAAAATCTATATTTTT
Found at i:105466 original size:27 final size:27
Alignment explanation
Indices: 105434--105518 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 27
105424 AATAAAATCT
105434 ATATTTTTAAATTAAAATTAA-AATAAA
1 ATATTTTTAAATT-AAATTAATAATAAA
*
105461 ATATTTTTAAATTAAGTTAATAATAAA
1 ATATTTTTAAATTAAATTAATAATAAA
* * *
105488 ATATATTT-AA-TAAGTTAATATACAAA
1 ATATTTTTAAATTAAATTAATA-ATAAA
105514 ATATT
1 ATATT
105519 ATACCATATT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
25 10 0.19
26 16 0.31
27 26 0.50
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (27 bp):
ATATTTTTAAATTAAATTAATAATAAA
Found at i:107737 original size:17 final size:18
Alignment explanation
Indices: 107702--107747 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
107692 GCCAAGTGAC
107702 AATTTTATAAATGTATT-
1 AATTTTATAAATGTATTA
*
107719 AATTTTAATAAAT-TTTTA
1 AATTTT-ATAAATGTATTA
*
107737 AATTTTTTAAA
1 AATTTTATAAA
107748 ACTTTCGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
AATTTTATAAATGTATTA
Done.