Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005600.1 Hibiscus syriacus cultivar Beakdansim tig00013026_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: 74067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:14194 original size:38 final size:38
Alignment explanation
Indices: 14152--14244 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 38
14142 TATATGTTTA
14152 AATATTTAC-AAGATTGCTTAGCTAATACTTATAATATT
1 AATATTTACTAAGATTGCTTAGCTAATACTTAT-ATATT
*
14190 AATATTTAACTACTAAGATTGCTTAGCTCATACTTATATATT
1 AATA-TT---TACTAAGATTGCTTAGCTAATACTTATATATT
14232 AATATTTAACTAA
1 AATATTT-ACTAA
14245 TCAAATATGA
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
38 5 0.10
39 7 0.15
41 2 0.04
42 12 0.25
43 22 0.46
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (38 bp):
AATATTTACTAAGATTGCTTAGCTAATACTTATATATT
Found at i:14210 original size:43 final size:42
Alignment explanation
Indices: 14161--14243 Score: 148
Period size: 43 Copynumber: 2.0 Consensus size: 42
14151 AAATATTTAC
14161 AAGATTGCTTAGCTAATACTTATAATATTAATATTTAACTACT
1 AAGATTGCTTAGCTAATACTTAT-ATATTAATATTTAACTACT
*
14204 AAGATTGCTTAGCTCATACTTATATATTAATATTTAACTA
1 AAGATTGCTTAGCTAATACTTATATATTAATATTTAACTA
14244 ATCAAATATG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 17 0.44
43 22 0.56
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (42 bp):
AAGATTGCTTAGCTAATACTTATATATTAATATTTAACTACT
Found at i:16775 original size:19 final size:18
Alignment explanation
Indices: 16748--16785 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
16738 ATTTAAATTG
16748 ATTTTATTT-ATTTTTACC
1 ATTTTATTTCA-TTTTACC
16766 ATTTTAATTTCATTTTACC
1 ATTTT-ATTTCATTTTACC
16785 A
1 A
16786 AACCCCCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 12 0.67
20 1 0.06
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTATTTCATTTTACC
Found at i:19676 original size:17 final size:17
Alignment explanation
Indices: 19656--19712 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
19646 TCTGTTATAT
19656 TTTTATTTATTTATTTA
1 TTTTATTTATTTATTTA
* *
19673 TTTTGTTTGTTTATTTA
1 TTTTATTTATTTATTTA
19690 TTTTATTTTATTTCATTTTA
1 TTTTA-TTTATTT-A-TTTA
19710 TTT
1 TTT
19713 CAATGAAGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 19 0.58
18 6 0.18
19 1 0.03
20 7 0.21
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.77
Consensus pattern (17 bp):
TTTTATTTATTTATTTA
Found at i:19709 original size:15 final size:14
Alignment explanation
Indices: 19656--19712 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 14
19646 TCTGTTATAT
19656 TTTTATTTA-TTTA
1 TTTTATTTATTTTA
19669 -TTTATTT-TGTTT-
1 TTTTATTTAT-TTTA
*
19681 GTTTATTTATTTTA
1 TTTTATTTATTTTA
19695 TTTTATTTCATTTTA
1 TTTTATTT-ATTTTA
19710 TTT
1 TTT
19713 CAATGAAGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
12 7 0.19
13 13 0.35
14 8 0.22
15 9 0.24
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.77
Consensus pattern (14 bp):
TTTTATTTATTTTA
Found at i:23718 original size:25 final size:29
Alignment explanation
Indices: 23689--23750 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
23679 TGTTAGAAGG
*
23689 ATAAATTTAT-AAA-TTT-AAAGA-AAAA
1 ATAAATTTATAAAATTTTAAAAAATAAAA
23714 ATAAATTTATAAAATTTTAAAAAATAAAA
1 ATAAATTTATAAAATTTTAAAAAATAAAA
23743 ATAAATTT
1 ATAAATTT
23751 TTAACAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 10 0.31
26 3 0.09
27 3 0.09
28 4 0.12
29 12 0.38
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (29 bp):
ATAAATTTATAAAATTTTAAAAAATAAAA
Found at i:23746 original size:21 final size:21
Alignment explanation
Indices: 23722--23801 Score: 63
Period size: 24 Copynumber: 3.5 Consensus size: 21
23712 AAATAAATTT
23722 ATAAAATTTTAAAAAATAAAA
1 ATAAAATTTTAAAAAATAAAA
*
23743 ATAAATTTTTAACAAAAAATAAAA
1 ATAAAATTTT---AAAAAATAAAA
*
23767 A-AATAAATTTAAAATATATAAAA
1 ATAA-AATTTTAAAA-A-ATAAAA
23790 ATTTAAAATTTT
1 A--TAAAATTTT
23802 TAGAAGGAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 13 0.28
22 1 0.02
23 9 0.20
24 16 0.35
25 5 0.11
26 2 0.04
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAAAATTTTAAAAAATAAAA
Found at i:29952 original size:20 final size:20
Alignment explanation
Indices: 29927--29993 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
29917 TTTTCCAAAT
*
29927 TCGCAACGTGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
*
29947 TCGCAACACGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
*
29967 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATCTGTAAA
29987 TCGCAAC
1 TCGCAAC
29994 ACAGAAGTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:30010 original size:20 final size:20
Alignment explanation
Indices: 29987--30033 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
29977 AATTTGTAAA
29987 TCGCAACACAGA-AGTCAAAT
1 TCGCAACAC-GATAGTCAAAT
*
30007 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGATAGTCAAAT
30027 TCGCAAC
1 TCGCAAC
30034 GCGAAACACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (20 bp):
TCGCAACACGATAGTCAAAT
Found at i:30011 original size:40 final size:38
Alignment explanation
Indices: 29922--30017 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 38
29912 TGCGATTTTC
*
29922 CAAATTCGCAACGTGAATCTGTAAATCGCAACACGAAT
1 CAAATTCGCAACGCGAATCTGTAAATCGCAACACGAAT
*
29960 CTGTAAA-TCGCAACGCGAATTTGTAAATCGCAACACAGAAGT
1 C---AAATTCGCAACGCGAATCTGTAAATCGCAACAC-GAA-T
30002 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
30018 TAGTCAAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
38 1 0.02
39 3 0.06
40 38 0.76
41 6 0.12
42 2 0.04
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (38 bp):
CAAATTCGCAACGCGAATCTGTAAATCGCAACACGAAT
Found at i:30034 original size:20 final size:20
Alignment explanation
Indices: 29999--30037 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
29989 GCAACACAGA
29999 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
30019 AGTCAAATTCGCAACGCGA
1 AGTCAAATTCGCAACGCGA
30038 AACACAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:30167 original size:22 final size:22
Alignment explanation
Indices: 30142--30221 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
30132 TCACTCTCTA
*
30142 CGGCGACATCCATCCCCATCTC
1 CGGCGAAATCCATCCCCATCTC
30164 CGGCGAAATCCATCCCCATCTC
1 CGGCGAAATCCATCCCCATCTC
* *
30186 CGGCAAAATCCGTCCCCATCTC
1 CGGCGAAATCCATCCCCATCTC
30208 CGGCGAAATCCATC
1 CGGCGAAATCCATC
30222 TATCTCCATC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.23, C:0.45, G:0.15, T:0.17
Consensus pattern (22 bp):
CGGCGAAATCCATCCCCATCTC
Found at i:30643 original size:20 final size:19
Alignment explanation
Indices: 30607--30661 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
30597 AAAATCACAA
*
30607 TGCGATTTTAGTTTCGCGT
1 TGCGATTTTAGTTTCGCAT
*
30626 TGCGATTTTCATTTTCGCAT
1 TGCGATTTT-AGTTTCGCAT
*
30646 TGCGAATTTAAGTTTC
1 TGCG-ATTTTAGTTTC
30662 AGAAACTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 9 0.30
20 17 0.57
21 4 0.13
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.47
Consensus pattern (19 bp):
TGCGATTTTAGTTTCGCAT
Found at i:32804 original size:21 final size:21
Alignment explanation
Indices: 32780--32833 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
32770 ACTTCATAAA
* *
32780 AAGAAGCCCCTCTCATCATCG
1 AAGAGGCCCCTCTCATAATCG
*
32801 AAGAGGCCCATCTCATAATCG
1 AAGAGGCCCCTCTCATAATCG
32822 AAGAGGCCCCTC
1 AAGAGGCCCCTC
32834 CCACCGTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.35, G:0.19, T:0.17
Consensus pattern (21 bp):
AAGAGGCCCCTCTCATAATCG
Found at i:32846 original size:21 final size:21
Alignment explanation
Indices: 32822--32889 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
32812 CTCATAATCG
32822 AAGAGGCCCCTCCCACCGTTC
1 AAGAGGCCCCTCCCACCGTTC
** *
32843 AAGAGGCCCCTGTCATCGTTC
1 AAGAGGCCCCTCCCACCGTTC
* * *
32864 AAGAGGTCCCGCCCGCCGTTC
1 AAGAGGCCCCTCCCACCGTTC
32885 AAGAG
1 AAGAG
32890 CCCGATTCAC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.16
Consensus pattern (21 bp):
AAGAGGCCCCTCCCACCGTTC
Found at i:34229 original size:64 final size:66
Alignment explanation
Indices: 34150--34295 Score: 242
Period size: 68 Copynumber: 2.2 Consensus size: 66
34140 TTTTACATTG
34150 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA-TTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
34213 A
66 A
* *
34214 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTTTGCTTGTTTAATTGATTT
1 AAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAATTA--TTTTTTTGCTTGTTTAATTGATTT
34279 GTA
64 GTA
34282 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
34296 GTTTTAAATT
Statistics
Matches: 76, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
64 17 0.22
65 19 0.25
68 40 0.53
ACGTcount: A:0.29, C:0.01, G:0.18, T:0.51
Consensus pattern (66 bp):
AAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
A
Found at i:34409 original size:13 final size:14
Alignment explanation
Indices: 34373--34411 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
34363 GAAAGTCAAA
34373 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
34387 TTCG-GTTTGCGA-T
1 TTCGCG-TTGCGATT
34400 TTCGCGTTGCGA
1 TTCGCGTTGCGA
34412 ATTTGACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.08, C:0.21, G:0.31, T:0.41
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:34415 original size:14 final size:14
Alignment explanation
Indices: 34373--34415 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
34363 GAAAGTCAAA
*
34373 TTCGCGTTGCGATT
1 TTCGCGTTGCGAAT
34387 TTCG-GTTTGCG-AT
1 TTCGCG-TTGCGAAT
34400 TTCGCGTTGCGAAT
1 TTCGCGTTGCGAAT
34414 TT
1 TT
34416 GACTTTCGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (14 bp):
TTCGCGTTGCGAAT
Found at i:34432 original size:20 final size:20
Alignment explanation
Indices: 34399--34464 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
34389 CGGTTTGCGA
* *
34399 TTTCGCGTTGCGAATTTGAC
1 TTTCGTGTTACGAATTTGAC
34419 TTTCGTGTTACGAATTTGAC
1 TTTCGTGTTACGAATTTGAC
34439 TTTCGTGTTACGAATTTGAC
1 TTTCGTGTTACGAATTTGAC
*
34459 TATCGT
1 TTTCGT
34465 AACGCTTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.44
Consensus pattern (20 bp):
TTTCGTGTTACGAATTTGAC
Found at i:37913 original size:16 final size:16
Alignment explanation
Indices: 37891--37930 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
37881 GAAATCATTG
*
37891 AAAAATTATATAGAAA
1 AAAAATTATATAAAAA
* *
37907 TAAAATTATGTAAAAA
1 AAAAATTATATAAAAA
37923 AAAAATTA
1 AAAAATTA
37931 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
AAAAATTATATAAAAA
Found at i:38134 original size:20 final size:19
Alignment explanation
Indices: 38106--38159 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
38096 TTAAATTCGT
*
38106 GTTGTGAATTCGAAAATCTA
1 GTTGTGAATTTGAAAATC-A
* *
38126 GTTGCGAATTTGAAATTCA
1 GTTGTGAATTTGAAAATCA
38145 GTTGTGAATTTGAAA
1 GTTGTGAATTTGAAA
38160 TTCCGCGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.37
Consensus pattern (19 bp):
GTTGTGAATTTGAAAATCA
Found at i:38147 original size:19 final size:20
Alignment explanation
Indices: 38087--38297 Score: 108
Period size: 20 Copynumber: 10.6 Consensus size: 20
38077 ACTAAAACCT
* *
38087 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTCGA
* * * *
38106 GTTGTGAATTCGAAAATCTA
1 GTTGCGAATTTGAAATTCGA
38126 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
* *
38145 GTTGTGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-CGA
** * *
38166 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGAAATTCGA
* *
38186 GTTGCGAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGA
** * *
38206 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGAAATTCGA
* *
38226 GTTGCG-ATTTACAAATTCGC
1 GTTGCGAATTT-GAAATTCGA
* * *
38246 GTTGCGAAATTGAAA-ACTGG
1 GTTGCGAATTTGAAATTC-GA
* * * *
38266 GTTGCGAAATTGGAGTTCGT
1 GTTGCGAATTTGAAATTCGA
38286 GTTGCGAATTTG
1 GTTGCGAATTTG
38298 TTGGTCATTT
Statistics
Matches: 145, Mismatches: 38, Indels: 17
0.73 0.19 0.09
Matches are distributed among these distances:
19 31 0.21
20 95 0.66
21 19 0.13
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:38170 original size:40 final size:40
Alignment explanation
Indices: 38087--38178 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 40
38077 ACTAAAACCT
* * *
38087 GTTGCGAAATT-AAATTCGTGTTGTGAATTCGAAAATCTA
1 GTTGCGAATTTGAAATTCGAGTTGTGAATTCGAAAATCGA
* * *
38126 GTTGCGAATTTGAAATTC-AGTTGTGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATTCGAGTTGTGAATTCGAAAAT-CGA
38166 GTTGCGAATTTGA
1 GTTGCGAATTTGA
38179 CTTTTGTGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 25 0.56
40 20 0.44
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (40 bp):
GTTGCGAATTTGAAATTCGAGTTGTGAATTCGAAAATCGA
Found at i:38207 original size:40 final size:40
Alignment explanation
Indices: 38157--38258 Score: 145
Period size: 40 Copynumber: 2.5 Consensus size: 40
38147 TGTGAATTTG
38157 AAATTCCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGAC
1 AAATT-CGCGTTGCGAATTTGACTTTTGTGTTGCG-ATTT-AC
*
38200 -TA-TCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTAC
1 AAATTCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTAC
*
38238 AAATTCGCGTTGCGAAATTGA
1 AAATTCGCGTTGCGAATTTGA
38259 AAACTGGGTT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
38 2 0.04
39 5 0.09
40 45 0.83
41 1 0.02
42 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.39
Consensus pattern (40 bp):
AAATTCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTAC
Found at i:45792 original size:20 final size:20
Alignment explanation
Indices: 45767--45860 Score: 118
Period size: 20 Copynumber: 4.6 Consensus size: 20
45757 TAGTTGAAAA
45767 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
45787 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
45807 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCATT
45829 T-GTCGTTGCGATTTTCCATT
1 TCG-CGTTGCGATTTTCCATT
*
45849 TCGCTTTGCGAT
1 TCGCGTTGCGAT
45861 AGTCTACAGT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
20 46 0.73
21 2 0.03
22 15 0.24
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:45838 original size:22 final size:22
Alignment explanation
Indices: 45810--45969 Score: 147
Period size: 22 Copynumber: 7.5 Consensus size: 22
45800 TTCCATTTCG
45810 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* *
45832 CGTTGCGAT--TTTCCA-TT-T
1 CGTTGCGATAGTCTACAGTTGT
45850 CGCTTTGCGATAGTCTACAGTTGT
1 CG--TTGCGATAGTCTACAGTTGT
* * **
45874 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
45893 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * * **
45915 TGTTGCGATAGTTTAAAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
45936 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
45958 CGTTGCGATAGT
1 CGTTGCGATAGT
45970 TAAAAAAAAA
Statistics
Matches: 106, Mismatches: 22, Indels: 20
0.72 0.15 0.14
Matches are distributed among these distances:
18 3 0.03
19 12 0.11
20 16 0.15
21 21 0.20
22 49 0.46
23 2 0.02
24 3 0.03
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:45843 original size:42 final size:40
Alignment explanation
Indices: 45790--45966 Score: 237
Period size: 42 Copynumber: 4.2 Consensus size: 40
45780 TTCCATTTCG
*
45790 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAATT--CGTTGCGATAGTCTACAGTTGT
*
45832 CGTTGCGATTTTCCATTTCGCTTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAATTCG--TTGCGATAGTCTACAGTTGT
45874 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCC-AATTCGTTGCGATAGTCTACAGTTGT
* **
45915 TGTTGCGATAGTTTAAAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGAT--TTT-CCAATTCGTTGCGATAGTCTACAGTTGT
45958 CGTTGCGAT
1 CGTTGCGAT
45967 AGTTAAAAAA
Statistics
Matches: 124, Mismatches: 5, Indels: 11
0.89 0.04 0.08
Matches are distributed among these distances:
40 2 0.02
41 28 0.23
42 52 0.42
43 42 0.34
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (40 bp):
CGTTGCGATTTTCCAATTCGTTGCGATAGTCTACAGTTGT
Found at i:45976 original size:43 final size:41
Alignment explanation
Indices: 45810--45975 Score: 217
Period size: 43 Copynumber: 4.0 Consensus size: 41
45800 TTCCATTTCG
** *
45810 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTT-CCATTT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTAAAAATT
**
45850 CGCTTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CG--TTGCGATAGTCTACAGTTGTCGTTGCGATTTTAAAAATT
*
45893 CGTTGCGATAGTCTACAGTTGTTGTTGCGATAGTTTAAAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGAT--TTTAAAAATT
*
45936 CGTTGCGATAGTCTACAGTTGTCGTTGCGATAGTTAAAAA
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGAT-TTTAAAAA
45976 AAAAGATTTT
Statistics
Matches: 113, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
40 2 0.02
41 28 0.25
42 39 0.35
43 44 0.39
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.39
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTAAAAATT
Found at i:46057 original size:6 final size:6
Alignment explanation
Indices: 46046--46089 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
46036 AGACACGTAT
46046 GACCAC GACCAC GACCAC GACCAC GACCAC GACC-C GACC-C GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
46090 CGAGACGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.26
6 28 0.74
ACGTcount: A:0.30, C:0.52, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:46992 original size:6 final size:6
Alignment explanation
Indices: 46981--47007 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
46971 TCTCGTCTCG
46981 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
47008 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:47125 original size:19 final size:19
Alignment explanation
Indices: 47101--47169 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
47091 CAATGAATTT
47101 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
47120 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
47142 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
47161 TCGCAACGA
1 TCGCAACGA
47170 CAACTGTAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 22 0.56
20 2 0.05
21 2 0.05
22 13 0.33
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:47147 original size:22 final size:22
Alignment explanation
Indices: 47118--47190 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
47108 GAATTTGGAA
47118 AATCGCAACGACAACTGTAGAC
1 AATCGCAACGACAACTGTAGAC
* * * *
47140 TATCGCAACG--AA-TTTGGAA
1 AATCGCAACGACAACTGTAGAC
47159 AATCGCAACGACAACTGTAGAC
1 AATCGCAACGACAACTGTAGAC
* *
47181 CATCACAACG
1 AATCGCAACG
47191 CGAAATGGAA
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 13 0.34
20 2 0.05
21 2 0.05
22 21 0.55
ACGTcount: A:0.40, C:0.26, G:0.18, T:0.16
Consensus pattern (22 bp):
AATCGCAACGACAACTGTAGAC
Found at i:47158 original size:41 final size:41
Alignment explanation
Indices: 47101--47249 Score: 169
Period size: 41 Copynumber: 3.6 Consensus size: 41
47091 CAATGAATTT
*
47101 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATATGGAAAATCGCAACGACAACTGTAGACTA
* *
47142 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACCA
1 TCGCAACGAATATGGAAAATCGCAACGACAACTGTAGACTA
* * * *
47183 TCACAACGCGAA-ATGGAAAATCGCAACG-CGATTTTCA-ACTA
1 TCGCAA--CGAATATGGAAAATCGCAACGACAACTGT-AGACTA
*
47224 TCGCAACGCAAAATGGAAAATCGCAA
1 TCGCAACG-AATATGGAAAATCGCAA
47250 TGCGATTTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 71 0.75
42 16 0.17
43 4 0.04
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.17
Consensus pattern (41 bp):
TCGCAACGAATATGGAAAATCGCAACGACAACTGTAGACTA
Found at i:47211 original size:20 final size:20
Alignment explanation
Indices: 47186--47254 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
47176 TAGACCATCA
47186 CAACGCGAAATGGAAAATCG
1 CAACGCGAAATGGAAAATCG
** ** *
47206 CAACGCGATTTTCAACTATCG
1 CAACGCGAAATGGAA-AATCG
*
47227 CAACGCAAAATGGAAAATCG
1 CAACGCGAAATGGAAAATCG
*
47247 CAATGCGA
1 CAACGCGA
47255 TTTTCAACTA
Statistics
Matches: 35, Mismatches: 13, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 21 0.60
21 14 0.40
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
CAACGCGAAATGGAAAATCG
Found at i:47228 original size:21 final size:21
Alignment explanation
Indices: 47202--47273 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 21
47192 GAAATGGAAA
47202 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* ** ** *
47223 ATCGCAACGCAAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
*
47243 ATCGCAATGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
47264 ATCGCAACGC
1 ATCGCAACGC
47274 TAAATGCAAC
Statistics
Matches: 36, Mismatches: 14, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 13 0.36
21 23 0.64
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:47255 original size:41 final size:41
Alignment explanation
Indices: 47138--47279 Score: 162
Period size: 41 Copynumber: 3.5 Consensus size: 41
47128 ACAACTGTAG
** * * *
47138 ACTATCGCAACG-AATTTGGAAAATCGCAACGACAACTGT-A
1 ACTATCGCAACGCAAAATGGAAAATCGCAACG-CGATTTTCA
* * *
47178 GACCATCACAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCAAAATGGAAAATCGCAACGCGATTTTCA
*
47220 ACTATCGCAACGCAAAATGGAAAATCGCAATGCGATTTTCA
1 ACTATCGCAACGCAAAATGGAAAATCGCAACGCGATTTTCA
*
47261 ACTATCGCAACGCTAAATG
1 ACTATCGCAACGCAAAATG
47280 CAACGCGAAT
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
41 69 0.80
42 17 0.20
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGCAAAATGGAAAATCGCAACGCGATTTTCA
Found at i:47283 original size:21 final size:21
Alignment explanation
Indices: 47218--47283 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
47208 ACGCGATTTT
47218 CAACTATCGCAACGCAAAATG
1 CAACTATCGCAACGCAAAATG
* * * * ** *
47239 GAA-AATCGCAATGCGATTTT
1 CAACTATCGCAACGCAAAATG
*
47259 CAACTATCGCAACGCTAAATG
1 CAACTATCGCAACGCAAAATG
47280 CAAC
1 CAAC
47284 GCGAATTTGC
Statistics
Matches: 30, Mismatches: 14, Indels: 2
0.65 0.30 0.04
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.39, C:0.26, G:0.15, T:0.20
Consensus pattern (21 bp):
CAACTATCGCAACGCAAAATG
Found at i:48565 original size:16 final size:16
Alignment explanation
Indices: 48544--48579 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
48534 AAAACTCTAG
48544 TAGCAGCCTTCCACTT
1 TAGCAGCCTTCCACTT
48560 TAGCAGCCTTCCACTT
1 TAGCAGCCTTCCACTT
48576 TAGC
1 TAGC
48580 CATCCCGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.19, C:0.36, G:0.14, T:0.31
Consensus pattern (16 bp):
TAGCAGCCTTCCACTT
Found at i:56540 original size:23 final size:23
Alignment explanation
Indices: 56509--56562 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
56499 TTTAGCTTGC
*
56509 AAATAAACATGTTC-ACGAA-CCTT
1 AAATGAACATGTTCGA-GAATCC-T
56532 AAATGAACATGTTCGAGAATCCT
1 AAATGAACATGTTCGAGAATCCT
56555 AAATGAAC
1 AAATGAAC
56563 GAACGAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 25 0.89
24 3 0.11
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (23 bp):
AAATGAACATGTTCGAGAATCCT
Found at i:58220 original size:209 final size:209
Alignment explanation
Indices: 57860--58281 Score: 826
Period size: 209 Copynumber: 2.0 Consensus size: 209
57850 TCTTAGGCTT
*
57860 AGAACATGAAGTGAGAGGAATTGGCTAGACCAGTTACAGAATATCGGTCTGCAGAAAGATAACCT
1 AGAACATGAAGTGAGAGGAATTGGCTAGACCAGTTACAGAATATCGGTCTGCAGAAAGACAACCT
57925 CAGTAGACCACCTCGTCGAGGGGACGCATCAATTAGCTAAAGGCCAAAGTCTTTCTATGGCTCAA
66 CAGTAGACCACCTCGTCGAGGGGACGCATCAATTAGCTAAAGGCCAAAGTCTTTCTATGGCTCAA
57990 AACTATCAACCATGAGGTCCAAGCATGAAACAAGCAGACAATAAAGTTTGTCTAGGATGAGAGAC
131 AACTATCAACCATGAGGTCCAAGCATGAAACAAGCAGACAATAAAGTTTGTCTAGGATGAGAGAC
58055 TTGATAAATTAACA
196 TTGATAAATTAACA
58069 AGAACATGAAGTGAGAGGAATTGGCTAGACCAGTTACAGAATATCGGTCTGCAGAAAGACAACCT
1 AGAACATGAAGTGAGAGGAATTGGCTAGACCAGTTACAGAATATCGGTCTGCAGAAAGACAACCT
58134 CAGTAGACCACCTCGTCGAGGGGACGCATCAATTAGCTAAAGGCCAAAGTCTTTCTATGGCTCAA
66 CAGTAGACCACCTCGTCGAGGGGACGCATCAATTAGCTAAAGGCCAAAGTCTTTCTATGGCTCAA
*
58199 AACTATCAACCATGAGGTCCAAGCATGAAACAAGCAGACAATACAGTTTGTCTAGGATGAGAGAC
131 AACTATCAACCATGAGGTCCAAGCATGAAACAAGCAGACAATAAAGTTTGTCTAGGATGAGAGAC
58264 TTGATAAATTAACA
196 TTGATAAATTAACA
58278 AGAA
1 AGAA
58282 TAAACAACAA
Statistics
Matches: 211, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
209 211 1.00
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (209 bp):
AGAACATGAAGTGAGAGGAATTGGCTAGACCAGTTACAGAATATCGGTCTGCAGAAAGACAACCT
CAGTAGACCACCTCGTCGAGGGGACGCATCAATTAGCTAAAGGCCAAAGTCTTTCTATGGCTCAA
AACTATCAACCATGAGGTCCAAGCATGAAACAAGCAGACAATAAAGTTTGTCTAGGATGAGAGAC
TTGATAAATTAACA
Found at i:59973 original size:2 final size:2
Alignment explanation
Indices: 59966--60019 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
59956 TACAGGCACA
59966 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60008 AT AT AT AT AT AT
1 AT AT AT AT AT AT
60020 CATACAAACC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60527 original size:12 final size:11
Alignment explanation
Indices: 60510--60568 Score: 55
Period size: 12 Copynumber: 5.0 Consensus size: 11
60500 GAATAAATCA
*
60510 ATAAACAAGCTT
1 ATAAACGAG-TT
60522 ATAAACGAGTT
1 ATAAACGAGTT
60533 CATAAACGAGTTT
1 -ATAAACGAG-TT
* *
60546 ATAAACGAACTC
1 ATAAACG-AGTT
60558 ATAAACGAGTT
1 ATAAACGAGTT
60569 TGTTTGTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 4 0.10
12 32 0.82
13 3 0.08
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (11 bp):
ATAAACGAGTT
Found at i:60564 original size:24 final size:24
Alignment explanation
Indices: 60510--60569 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
60500 GAATAAATCA
* * **
60510 ATAAACAAGCTTATAAACGAGTTC
1 ATAAACGAGTTTATAAACGAACTC
60534 ATAAACGAGTTTATAAACGAACTC
1 ATAAACGAGTTTATAAACGAACTC
60558 ATAAACGAGTTT
1 ATAAACGAGTTT
60570 GTTTGTAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (24 bp):
ATAAACGAGTTTATAAACGAACTC
Found at i:62628 original size:60 final size:60
Alignment explanation
Indices: 62513--62646 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 60
62503 ATCGAATGAC
** * * * * * *
62513 CATTTTGTAACTTTTAATAGTCGAGTGACTGAACAAAACAACTCTTTGTAGTTGGGTGAT
1 CATTTTGTAACTTTTAATAGTCGAGAAACTCAACAAAACAAATCTCTATAATTGGGAGAT
*
62573 CATTTTGTAACTTTTAATAGTCGAGAAACTCAACAAAATAATATC-CTATAATTGGGAGAT
1 CATTTTGTAACTTTTAATAGTCGAGAAACTCAACAAAACAA-ATCTCTATAATTGGGAGAT
62633 CATTTGTGT-ACTTT
1 CATTT-TGTAACTTT
62647 ACCCAATATA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
60 58 0.92
61 5 0.08
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTCGAGAAACTCAACAAAACAAATCTCTATAATTGGGAGAT
Found at i:63047 original size:23 final size:21
Alignment explanation
Indices: 63020--63061 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
63010 CGAATAAGTT
*
63020 AAAATATTATTATAATATTAATA
1 AAAATAATATT-TAA-ATTAATA
63043 AAAATAATATTTAAATTAA
1 AAAATAATATTTAAATTAA
63062 ACTGATGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATAATATTTAAATTAATA
Found at i:65860 original size:21 final size:21
Alignment explanation
Indices: 65834--65889 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
65824 TTATGGGTTG
65834 TGTGCATCGATGCATCTTCAA
1 TGTGCATCGATGCATCTTCAA
*
65855 TGTGCATCGATGTATCTTCAA
1 TGTGCATCGATGCATCTTCAA
**
65876 TGTATATCGATGCA
1 TGTGCATCGATGCA
65890 CTCTCAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.36
Consensus pattern (21 bp):
TGTGCATCGATGCATCTTCAA
Found at i:66754 original size:18 final size:18
Alignment explanation
Indices: 66731--66783 Score: 106
Period size: 18 Copynumber: 2.9 Consensus size: 18
66721 GTTCTTAAGG
66731 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
66749 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
66767 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
66784 AATATATAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:70344 original size:13 final size:13
Alignment explanation
Indices: 70323--70352 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
70313 GATCCTTCTG
70323 TTTACACGTATTT
1 TTTACACGTATTT
*
70336 TTTATACGTATTT
1 TTTACACGTATTT
70349 TTTA
1 TTTA
70353 AAAGTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (13 bp):
TTTACACGTATTT
Found at i:71370 original size:2 final size:2
Alignment explanation
Indices: 71363--71394 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
71353 ACATACATAC
71363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71395 GTTTTTCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73477 original size:10 final size:10
Alignment explanation
Indices: 73462--73503 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
73452 AGAGGTGACG
73462 AAAAAAAA-T
1 AAAAAAAACT
73471 AAAAAAAACT
1 AAAAAAAACT
73481 AAAAAAAACT
1 AAAAAAAACT
**
73491 AAAGTAAACT
1 AAAAAAAACT
73501 AAA
1 AAA
73504 TAAGCATACT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.79, C:0.07, G:0.02, T:0.12
Consensus pattern (10 bp):
AAAAAAAACT
Done.