Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006878.1 Hibiscus syriacus cultivar Beakdansim tig00017523_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: 56051
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:10191 original size:15 final size:15
Alignment explanation
Indices: 10166--10237 Score: 101
Period size: 15 Copynumber: 4.9 Consensus size: 15
10156 TGGTTTTCCA
10166 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
10181 GAATTTGAATTACTG
1 GAAAATGAATTACTG
10196 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
10211 GAATTTGAATT-CTG
1 GAAAATGAATTACTG
10225 GAAAATGAATTAC
1 GAAAATGAATTAC
10238 ATTTCTGTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.25
15 36 0.75
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:10235 original size:29 final size:30
Alignment explanation
Indices: 10166--10237 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
10156 TGGTTTTCCA
10166 GAAAATGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
10196 GAAAATGAATTACTGGAATTTGAATT-CTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
10225 GAAAATGAATTAC
1 GAAAATGAATTAC
10238 ATTTCTGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (30 bp):
GAAAATGAATTACTGGAATTTGAATTACTG
Found at i:10243 original size:20 final size:20
Alignment explanation
Indices: 10220--10289 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
10210 GGAATTTGAA
10220 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
10240 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
10260 TTCTGAAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
10280 TTCTGGAAAA
1 TTCTGGAAAA
10290 CATCTGGAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:10512 original size:30 final size:29
Alignment explanation
Indices: 10455--10558 Score: 101
Period size: 29 Copynumber: 3.5 Consensus size: 29
10445 CTTTACTAAA
*
10455 ATATTATTGAAATATAT-AAATAATATTAT
1 ATATTATT-AAATATATAAAAAAATATTAT
10484 -TCATTATTAAATATATAAAAAAATTATTAT
1 AT-ATTATTAAATATATAAAAAAA-TATTAT
10514 ATATTATTAAA-ATA-AAAATATAATATCT-T
1 ATATTATTAAATATATAAAA-A-AATAT-TAT
10543 ATATTATTATAATATA
1 ATATTATTA-AATATA
10559 ATTGATTATT
Statistics
Matches: 65, Mismatches: 1, Indels: 16
0.79 0.01 0.20
Matches are distributed among these distances:
28 13 0.20
29 28 0.43
30 20 0.31
31 4 0.06
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (29 bp):
ATATTATTAAATATATAAAAAAATATTAT
Found at i:10537 original size:59 final size:59
Alignment explanation
Indices: 10455--10610 Score: 143
Period size: 54 Copynumber: 2.7 Consensus size: 59
10445 CTTTACTAAA
* *
10455 ATATTATTGAAATATATAA-ATAATATTATTCATTATTAAATATATAAAAAAATT-ATTAT
1 ATATTATTAAAATA-AAAATATAATATTATT-ATTATTAAATATATAAAAAAATTGATTAT
* * *
10514 ATATTATTAAAATAAAAATATAATA-TCTTA-TATT--AT-TATAATATAATTGATTAT
1 ATATTATTAAAATAAAAATATAATATTATTATTATTAAATATATAAAAAAATTGATTAT
* *
10568 -T-TTATATAATATTAAAAATATAATATTA-TATTATTAAAAATAT
1 ATATTAT-TAA-AATAAAAATATAATATTATTATTATTAAATATAT
10611 TAATAAATAT
Statistics
Matches: 80, Mismatches: 8, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
52 4 0.05
53 14 0.17
54 23 0.29
55 5 0.06
56 4 0.05
57 2 0.03
58 9 0.11
59 19 0.24
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (59 bp):
ATATTATTAAAATAAAAATATAATATTATTATTATTAAATATATAAAAAAATTGATTAT
Found at i:10581 original size:15 final size:16
Alignment explanation
Indices: 10543--10596 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 16
10533 ATAATATCTT
10543 ATATTATTATAATATA
1 ATATTATTATAATATA
*
10559 ATTGATTATT-TTATATA
1 A-T-ATTATTATAATATA
*
10576 ATATTA--AAAATATA
1 ATATTATTATAATATA
10590 ATATTAT
1 ATATTAT
10597 ATTATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
14 11 0.35
15 4 0.13
16 2 0.06
17 8 0.26
18 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
ATATTATTATAATATA
Found at i:10597 original size:22 final size:23
Alignment explanation
Indices: 10572--10615 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
10562 GATTATTTTA
10572 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
*
10594 TATATTATTAAAAATATTAATA
1 TATAATATTAAAAATATTAATA
10616 AATATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:10614 original size:23 final size:24
Alignment explanation
Indices: 10572--10647 Score: 86
Period size: 23 Copynumber: 3.2 Consensus size: 24
10562 GATTATTTTA
*
10572 TATAATATTAAAAATA-TAAT-AT
1 TATATTATTAAAAATATTAATAAT
*
10594 TATATTATTAAAAATATTAATAAA
1 TATATTATTAAAAATATTAATAAT
* *
10618 TATATT-TTAAATATTTTAATAAT
1 TATATTATTAAAAATATTAATAAT
10641 TAATATT
1 T-ATATT
10648 TTGATGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 15 0.33
23 19 0.41
24 12 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TATATTATTAAAAATATTAATAAT
Found at i:10623 original size:21 final size:22
Alignment explanation
Indices: 10576--10632 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
10566 ATTTTATATA
*
10576 ATATTAAAAATA-TAATATTAT
1 ATATTAAAAATATTAATATAAT
10597 ATTATTAAAAATATTAATA-AAT
1 A-TATTAAAAATATTAATATAAT
**
10619 ATATTTTAAATATT
1 ATATTAAAAATATT
10633 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 12 0.39
22 14 0.45
23 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATTAAAAATATTAATATAAT
Found at i:10880 original size:42 final size:42
Alignment explanation
Indices: 10821--10940 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
10811 ATGAATTATA
* *
10821 TTCCGGAAAACGAATTACGTGAAATAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
10863 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
10905 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
10941 TTCGGGGAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:15828 original size:20 final size:19
Alignment explanation
Indices: 15803--15856 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
15793 GCGAAATAAA
15803 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
15823 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
15843 AATCGCAACGCGAT
1 AATCGCAACGCGAT
15857 TATGAAGAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:15918 original size:21 final size:21
Alignment explanation
Indices: 15803--15918 Score: 67
Period size: 21 Copynumber: 5.6 Consensus size: 21
15793 GCGAAATAAA
*
15803 AATCGCAACGCGA-TCTCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
15823 AATCGCAAATC-AGTTCCCAG
1 AATCGCAACGCGATTTTCCAG
* **
15843 AATCGCAACGCGATTATGAAG
1 AATCGCAACGCGATTTTCCAG
* * ** *
15864 AAACGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
15884 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
15906 AATCGCAACGCGA
1 AATCGCAACGCGA
15919 ATATGAAAAT
Statistics
Matches: 68, Mismatches: 24, Indels: 7
0.69 0.24 0.07
Matches are distributed among these distances:
19 1 0.01
20 25 0.37
21 40 0.59
22 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:15931 original size:20 final size:20
Alignment explanation
Indices: 15906--16181 Score: 193
Period size: 20 Copynumber: 13.7 Consensus size: 20
15896 GATTTTCCAG
* *
15906 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
15926 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
* * **
15946 AATCGCGACGCGATTTTG-A
1 AATCGCAACGCGAATACGTA
* * *
15965 TTATCGCAACGAGTAT-CTGTAA
1 -AATCGCAACGCGAATAC-GT-A
* *
15987 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
16007 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* * *
16028 AATTGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
16048 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* ** *
16068 AATTGCAACATGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
*
16088 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
16108 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
16128 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
16149 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
16169 AATCGCAACGCGA
1 AATCGCAACGCGA
16182 TTTTTAAAGC
Statistics
Matches: 200, Mismatches: 43, Indels: 26
0.74 0.16 0.10
Matches are distributed among these distances:
19 2 0.01
20 147 0.74
21 49 0.25
22 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:16012 original size:41 final size:41
Alignment explanation
Indices: 15967--16178 Score: 313
Period size: 41 Copynumber: 5.2 Consensus size: 41
15957 GATTTTGATT
*
15967 ATCGCAACGAGTAT-CTGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATAC-GTAAAATCGCAACGCGTATCCGTAA
* *
16008 ATCGCAACGACAATACGTAAAATTGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* ** *
16049 ATCGCAACGAGAATACGT-AAATTGCAACATGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
16089 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
16129 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
16170 ATCGCAACG
1 ATCGCAACG
16179 CGATTTTTAA
Statistics
Matches: 155, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
40 71 0.46
41 83 0.54
42 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:16766 original size:20 final size:19
Alignment explanation
Indices: 16738--16809 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
16728 TTCTAAACTT
*
16738 AAAACCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
16758 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
** *
16778 ACTATCACAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
16799 AAAATCGCAAC
1 AAAATCGCAAC
16810 GAGAGAATCG
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 28 0.67
21 14 0.33
ACGTcount: A:0.53, C:0.21, G:0.15, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:16798 original size:21 final size:21
Alignment explanation
Indices: 16753--16816 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
16743 CGCAACATGA
*
16753 AAATGAAAATCGCAAC-ACGA-
1 AAATGAAAATCACAACGA-GAG
**
16773 AAATGACTATCACAACGAGAG
1 AAATGAAAATCACAACGAGAG
*
16794 AAATGAAAATCGCAACGAGAG
1 AAATGAAAATCACAACGAGAG
16815 AA
1 AA
16817 TCGCAACGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.53, C:0.17, G:0.19, T:0.11
Consensus pattern (21 bp):
AAATGAAAATCACAACGAGAG
Found at i:16820 original size:14 final size:14
Alignment explanation
Indices: 16798--16862 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
16788 CGAGAGAAAT
16798 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
16812 GAGAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
16830 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
16845 GATAATCGCAACGC
1 GAAAATCGCAACGA
16859 GAAA
1 GAAA
16863 CCAAAATTGC
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 25 0.61
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.24
ACGTcount: A:0.46, C:0.22, G:0.23, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:16830 original size:33 final size:33
Alignment explanation
Indices: 16793--16862 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
16783 CACAACGAGA
16793 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
16826 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
16859 GAAA
1 GAAA
16863 CCAAAATTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:18799 original size:94 final size:94
Alignment explanation
Indices: 18638--19013 Score: 611
Period size: 94 Copynumber: 4.1 Consensus size: 94
18628 TAGATTGCTT
* * * *
18638 AGTAAATTTATTCGGTTGCTGCCAATACTACTAAACTGTTTATTCTTTAACACTGTGAAATTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
18703 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
18732 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
18797 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
18826 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG-
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
18890 ---TGTCTTTGTTTTGTCTATTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
18916 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
18981 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
19009 AGTAA
1 AGTAA
19014 TGCAATCCAT
Statistics
Matches: 267, Mismatches: 10, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
90 86 0.32
93 26 0.10
94 155 0.58
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:18977 original size:184 final size:184
Alignment explanation
Indices: 18638--19013 Score: 603
Period size: 184 Copynumber: 2.0 Consensus size: 184
18628 TAGATTGCTT
*
18638 AGTAAATTTATTCGGTTGCTGCCAATACTACTAAACTGTTTATTCTTTAACACTGTGAAATTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTACTAAACTGTGTATTCTTTAACACTGTGAAATTAG-
*
18703 ATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC
65 --TTGTCTTTTGTTTTGTCTATTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC
*
18768 TGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
128 TGTGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
18826 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG-
1 AGTAAATTTATTCGGTTGCTGCCAATACTACTAAACTGTGTATTCTTTAACACTGTGAAATTAGT
* *
18890 TGTC-TTTGTTTTGTCTATTGGTTGAAAGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTG
66 TGTCTTTTGTTTTGTCTATTGGTTG-AAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTG
*
18954 TGTATTCTTTAATACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
130 TGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
19009 AGTAA
1 AGTAA
19014 TGCAATCCAT
Statistics
Matches: 177, Mismatches: 10, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
183 25 0.14
184 93 0.53
188 59 0.33
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (184 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTACTAAACTGTGTATTCTTTAACACTGTGAAATTAGT
TGTCTTTTGTTTTGTCTATTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGT
GTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:19155 original size:19 final size:19
Alignment explanation
Indices: 19131--19193 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 19
19121 GCAACAAGAG
19131 AATCGCAACGAGAAATGAA
1 AATCGCAACGAGAAATGAA
19150 AATCGCAACGAG--A-G--
1 AATCGCAACGAGAAATGAA
* *
19164 AATCACAACGCGAAATGAA
1 AATCGCAACGAGAAATGAA
19183 AATCGCAACGA
1 AATCGCAACGA
19194 CAAAATCGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
14 10 0.29
16 2 0.06
17 2 0.06
19 21 0.60
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.10
Consensus pattern (19 bp):
AATCGCAACGAGAAATGAA
Found at i:19164 original size:33 final size:33
Alignment explanation
Indices: 19101--19225 Score: 164
Period size: 33 Copynumber: 3.8 Consensus size: 33
19091 AAAAATGACT
*
19101 ATCGCAACGCGAAATG--AATCGCAACAAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
19132 ATCGCAACGAGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
19165 ATCACAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
** *
19198 ATCGCAACGCGAAACCAAAATCACAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
19226 CGAAACTATA
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
31 15 0.18
33 67 0.82
ACGTcount: A:0.48, C:0.24, G:0.19, T:0.09
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:19238 original size:19 final size:19
Alignment explanation
Indices: 19194--19231 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19184 ATCGCAACGA
*
19194 CAAAATCGCAACGCGAAAC
1 CAAAATCACAACGCGAAAC
19213 CAAAATCACAACGCGAAAC
1 CAAAATCACAACGCGAAAC
19232 TATAATCGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.32, G:0.13, T:0.05
Consensus pattern (19 bp):
CAAAATCACAACGCGAAAC
Found at i:19300 original size:20 final size:20
Alignment explanation
Indices: 19275--19381 Score: 151
Period size: 20 Copynumber: 5.3 Consensus size: 20
19265 GATTCTCTCG
**
19275 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
19295 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* **
19315 TTACGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
19335 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
19355 TTGGGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
19375 TTGCGAT
1 TTGCGAT
19382 TTTAAGTTTC
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:19300 original size:34 final size:37
Alignment explanation
Indices: 19258--19347 Score: 105
Period size: 40 Copynumber: 2.4 Consensus size: 37
19248 TTTTCATTTT
*
19258 GCATTGCGAT-TC-TCTCG-TTGCGATAGTCAAATTC
1 GCATTGCGATATCATCTCGATTACGATAGTCAAATTC
*
19292 GCATTGCGATAGTCATTTTCGCATTACGATAGTCAAATTC
1 GCATTGCGATA-TCA-TCTCG-ATTACGATAGTCAAATTC
19332 GCATTGCGATAGTCAT
1 GCATTGCGATA-TCAT
19348 TTTCGCATTG
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
34 10 0.21
36 2 0.04
38 4 0.08
39 1 0.02
40 31 0.65
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.34
Consensus pattern (37 bp):
GCATTGCGATATCATCTCGATTACGATAGTCAAATTC
Found at i:21344 original size:14 final size:14
Alignment explanation
Indices: 21325--21360 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
21315 ATTGTTTAAT
21325 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
21339 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
21353 TGATTTGT
1 TGATTTGT
21361 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:21577 original size:24 final size:24
Alignment explanation
Indices: 21543--21596 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
21533 CTGAAAAATC
21543 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
21567 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
21591 ATCAAA
1 ATCAAA
21597 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:21610 original size:24 final size:24
Alignment explanation
Indices: 21543--21610 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
21533 CTGAAAAATC
* * *
21543 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
21567 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
21591 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
21611 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:22158 original size:20 final size:20
Alignment explanation
Indices: 22075--22160 Score: 120
Period size: 20 Copynumber: 4.3 Consensus size: 20
22065 CCATTTCTCG
*
22075 TTGCGATTTACAG-ATTCGAA
1 TTGCGATTTAC-GTATTCGCA
22095 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* *
22115 TTGCGATTTACGTAATCACA
1 TTGCGATTTACGTATTCGCA
*
22135 TTGCGATTTACGTATTCGCG
1 TTGCGATTTACGTATTCGCA
22155 TTGCGA
1 TTGCGA
22161 ATTAGGAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
19 1 0.02
20 58 0.98
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:22181 original size:21 final size:21
Alignment explanation
Indices: 22157--22202 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
22147 TATTCGCGTT
22157 GCGAATTAG-GAAAATCGCAAC
1 GCGAATTAGTG-AAATCGCAAC
* *
22178 GCGAATTTGTGAAATCGCAAT
1 GCGAATTAGTGAAATCGCAAC
22199 GCGA
1 GCGA
22203 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (21 bp):
GCGAATTAGTGAAATCGCAAC
Found at i:22300 original size:20 final size:20
Alignment explanation
Indices: 22253--22485 Score: 222
Period size: 20 Copynumber: 11.6 Consensus size: 20
22243 TACCGGAGAT
*
22253 CGCGTTGCGAATTATC-GAT-
1 CGCGTTGCGATTTA-CGGATA
*
22272 CGTGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
22292 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
22312 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
22333 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
22353 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* * *
22373 CGCGTTGCAATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
22393 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
22413 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* * *
22433 TGTCGTTACGATTTACAGATA
1 CG-CGTTGCGATTTACGGATA
22454 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
22475 CTCGTTGCGAT
1 CGCGTTGCGAT
22486 AGTCAGAATC
Statistics
Matches: 171, Mismatches: 34, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
18 1 0.01
19 15 0.09
20 104 0.61
21 51 0.30
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:22358 original size:40 final size:41
Alignment explanation
Indices: 22275--22485 Score: 327
Period size: 41 Copynumber: 5.2 Consensus size: 41
22265 TATCGATCGT
*
22275 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
*
22316 GTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
* *
22356 GTTGCGATTTACAGATACGCGTTGC-AATTTACGTATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
*
22396 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
* * * *
22437 GTTACGATTTACAGATACGCGTTGCGATTTTACGGATACTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
22478 GTTGCGAT
1 GTTGCGAT
22486 AGTCAGAATC
Statistics
Matches: 155, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 1 0.01
40 72 0.46
41 82 0.53
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (41 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
Found at i:22499 original size:41 final size:39
Alignment explanation
Indices: 22288--22546 Score: 240
Period size: 40 Copynumber: 6.4 Consensus size: 39
22278 GCGATTTACG
* *
22288 GATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACG
1 GATACGCGTTGCGATTTTACGTATTCTCGTTGCGA-TT-CA
*
22329 GATACGCATTGCGA-TTTACGTATTCTCGTTGCGATTTACA
1 GATACGCGTTGCGATTTTACGTATTCTCGTTGCGA-TT-CA
* *
22369 GATACGCGTTGC-AATTTACGTATTCTCGTTGCGATTTACG
1 GATACGCGTTGCGATTTTACGTATTCTCGTTGCGA-TT-CA
* *
22409 GATACGCGTTGCGATTTTACGTATTGTCGTTACGATTTACA
1 GATACGCGTTGCGATTTTACGTATTCTCGTTGCGA-TT-CA
* *
22450 GATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGTCA
1 GATACGCGTTGCGATTTTACGTATTCTCGTTGCGAT--TCA
* *
22491 GA-ATCGCGTTGCGATTTATA--TGTTCGCGTTGCGATTTTCA
1 GATA-CGCGTTGCGATTT-TACGTATTCTCGTTGCGA--TTCA
* *
22531 TATTCGCGTTGCGATT
1 GATACGCGTTGCGATT
22547 CTGGAAAATC
Statistics
Matches: 190, Mismatches: 19, Indels: 19
0.83 0.08 0.08
Matches are distributed among these distances:
39 1 0.01
40 100 0.53
41 85 0.45
42 4 0.02
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (39 bp):
GATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTCA
Found at i:22517 original size:20 final size:20
Alignment explanation
Indices: 22494--22546 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
22484 ATAGTCAGAA
*
22494 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
22514 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
22534 TCGCGTTGCGATT
1 TCGCGTTGCGATT
22547 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:22538 original size:40 final size:40
Alignment explanation
Indices: 22249--22546 Score: 231
Period size: 40 Copynumber: 7.4 Consensus size: 40
22239 GCGATACCGG
* * *
22249 AGAT-CGCGTTGCGAATTAT-CGATCGTGTTGCGATTTAC
1 AGATACGCGTTGCGATTTATACGTTCGCGTTGCGATTTAC
* *
22287 GGATACGCGTTGCGATTT-TACGTATTGTCGTTGCGATTTAC
1 AGATACGCGTTGCGATTTATACGT-TCG-CGTTGCGATTTAC
* * *
22328 GGATACGCATTGCGA-TT-TACGTATTCTCGTTGCGATTTAC
1 AGATACGCGTTGCGATTTATACG--TTCGCGTTGCGATTTAC
* *
22368 AGATACGCGTTGC-AATT-TACGTATTCTCGTTGCGATTTAC
1 AGATACGCGTTGCGATTTATACG--TTCGCGTTGCGATTTAC
* * *
22408 GGATACGCGTTGCGATTT-TACGTATTGTCGTTACGATTTAC
1 AGATACGCGTTGCGATTTATACGT-TCG-CGTTGCGATTTAC
* * *
22449 AGATACGCGTTGCGATTT-TACGGATACTCGTTGCGATAGT-C
1 AGATACGCGTTGCGATTTATAC-G-TTCGCGTTGCGAT-TTAC
* *
22490 AGA-ATCGCGTTGCGATTTATATGTTCGCGTTGCGATTTTC
1 AGATA-CGCGTTGCGATTTATACGTTCGCGTTGCGATTTAC
* *
22530 ATATTCGCGTTGCGATT
1 AGATACGCGTTGCGATT
22547 CTGGAAAATC
Statistics
Matches: 216, Mismatches: 27, Indels: 32
0.79 0.10 0.12
Matches are distributed among these distances:
38 4 0.02
39 17 0.08
40 97 0.45
41 92 0.43
42 5 0.02
43 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (40 bp):
AGATACGCGTTGCGATTTATACGTTCGCGTTGCGATTTAC
Found at i:25604 original size:23 final size:23
Alignment explanation
Indices: 25578--25655 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
25568 CACCACAGCT
25578 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
25601 CATATAATTACACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
25624 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
25647 TATAATAAT
1 CAT-ATAAT
25656 GTCCATAAGA
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 39 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:25833 original size:103 final size:103
Alignment explanation
Indices: 25669--25879 Score: 397
Period size: 103 Copynumber: 2.0 Consensus size: 103
25659 CATAAGAACT
*
25669 ACATATCATTCCTTAAGAATCATATACATATCCTAGGGATCAAGTATGTGTCTCACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATCCTAAGGATCAAGTATGTGTCTCACCAGACTTCA
25734 CACATGTTCCAAAGAATACATATATGTCCCGAAGGACC
66 CACATGTTCCAAAGAATACATATATGTCCCGAAGGACC
25772 ACATATCATTCCTTAAGAATCATATACATATGCC-AAGGATCAAGTATGTGTCTCACCAGACTTC
1 ACATATCATTCCTTAAGAATCATATACATAT-CCTAAGGATCAAGTATGTGTCTCACCAGACTTC
25836 ACACATGTTCCAAAGAATACATATATGTCCCGAAGGACC
65 ACACATGTTCCAAAGAATACATATATGTCCCGAAGGACC
25875 ACATA
1 ACATA
25880 GACCCTCGAC
Statistics
Matches: 106, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
103 104 0.98
104 2 0.02
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (103 bp):
ACATATCATTCCTTAAGAATCATATACATATCCTAAGGATCAAGTATGTGTCTCACCAGACTTCA
CACATGTTCCAAAGAATACATATATGTCCCGAAGGACC
Found at i:28494 original size:35 final size:34
Alignment explanation
Indices: 28409--28495 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
28399 AATAAAATTT
*
28409 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
28443 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
28481 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
28496 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:30716 original size:111 final size:111
Alignment explanation
Indices: 30583--30804 Score: 399
Period size: 111 Copynumber: 2.0 Consensus size: 111
30573 ATTACAAAAA
*
30583 TTAATTCTTAATCTAATCATCATACATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
30648 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
*
30694 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
30759 AATTAAAACATTAAAATGTTACCGTATCAGTAAAGTGTAGAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
30805 ATGATTTCCA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:30909 original size:17 final size:18
Alignment explanation
Indices: 30866--30906 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
30856 GAATTATATT
30866 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
30883 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
30901 ATTAAA
1 AGTAAA
30907 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:30967 original size:10 final size:10
Alignment explanation
Indices: 30948--30978 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
30938 CTTAAAAAGA
*
30948 GAGAGTATTT
1 GAGAGAATTT
30958 GAGAGAATTT
1 GAGAGAATTT
30968 GAGAGAATTT
1 GAGAGAATTT
30978 G
1 G
30979 GTGGGATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:31427 original size:2 final size:2
Alignment explanation
Indices: 31420--31466 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
31410 TAAGATAGAT
31420 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
31462 TA TA T
1 TA TA T
31467 TTAAATTATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31998 original size:16 final size:16
Alignment explanation
Indices: 31977--32037 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
31967 TAATAAATAA
**
31977 ACGAACATAAACGCGC
1 ACGAACATAAACGAAC
31993 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
32009 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
32025 ACGAACATAAACG
1 ACGAACATAAACG
32038 TTGGAGACCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.52, C:0.26, G:0.15, T:0.07
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:33134 original size:24 final size:24
Alignment explanation
Indices: 33097--33166 Score: 90
Period size: 24 Copynumber: 2.9 Consensus size: 24
33087 AGATTGAGTT
33097 AAACATAAAT-GAATGAACATAAAC
1 AAACAT-AATCGAATGAACATAAAC
33121 AAACATAATCGAATGAACATAAAC
1 AAACATAATCGAATGAACATAAAC
* *
33145 TAACATAA-CTGAACGAACATAA
1 AAACATAATC-GAATGAACATAA
33167 CCGAACGTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.10
24 38 0.90
ACGTcount: A:0.59, C:0.16, G:0.09, T:0.17
Consensus pattern (24 bp):
AAACATAATCGAATGAACATAAAC
Found at i:45174 original size:20 final size:21
Alignment explanation
Indices: 45138--45189 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
45128 TTAAATACAT
**
45138 TTATATGATATTTTTTAGTTA
1 TTATATGATATCATTTAGTTA
*
45159 -TATATGATATCATTTATTTA
1 TTATATGATATCATTTAGTTA
*
45179 TTATATTATAT
1 TTATATGATAT
45190 ATTAATATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.60
Consensus pattern (21 bp):
TTATATGATATCATTTAGTTA
Found at i:45191 original size:23 final size:22
Alignment explanation
Indices: 45138--45191 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
45128 TTAAATACAT
45138 TTATATGATATTTTTTAGTTATA
1 TTATAT-ATATTTTTTAGTTATA
45161 -TATGATATCATTTATTTA-TTATA
1 TTAT-ATAT-ATTT-TTTAGTTATA
45184 TTATATAT
1 TTATATAT
45192 TAATATGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
22 5 0.19
23 15 0.56
24 7 0.26
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (22 bp):
TTATATATATTTTTTAGTTATA
Found at i:46271 original size:24 final size:24
Alignment explanation
Indices: 46244--46293 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
46234 GTAAATTAAA
46244 TATTTTTGTTACCACCTTCCATGT
1 TATTTTTGTTACCACCTTCCATGT
46268 TATTTTTGTTACCACCTTCCATGT
1 TATTTTTGTTACCACCTTCCATGT
46292 TA
1 TA
46294 CATCAAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.18, C:0.24, G:0.08, T:0.50
Consensus pattern (24 bp):
TATTTTTGTTACCACCTTCCATGT
Found at i:46734 original size:20 final size:20
Alignment explanation
Indices: 46709--46749 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
46699 ATTCACTCAT
46709 GTGGATTTGGTTAGTGTTGG
1 GTGGATTTGGTTAGTGTTGG
46729 GTGGATTTGGTTAGTGTTGG
1 GTGGATTTGGTTAGTGTTGG
46749 G
1 G
46750 AGCTCCTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.46, T:0.44
Consensus pattern (20 bp):
GTGGATTTGGTTAGTGTTGG
Done.