Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006448.1 Hibiscus syriacus cultivar Beakdansim tig00015613_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: 90643
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:9976 original size:2 final size:2
Alignment explanation
Indices: 9969--10009 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
9959 TTAGATCAGA
9969 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10010 CACACACACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11866 original size:30 final size:30
Alignment explanation
Indices: 11832--11891 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
11822 TGGCTCCCTG
* * *
11832 AACTTTTCAAAGT-TTATACTTTGGTCACTA
1 AACTTTCCAAA-TCTTATAATTTGATCACTA
11862 AACTTTCCAAATCTTATAATTTGATCACTA
1 AACTTTCCAAATCTTATAATTTGATCACTA
11892 GACTAAATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (30 bp):
AACTTTCCAAATCTTATAATTTGATCACTA
Found at i:14893 original size:24 final size:24
Alignment explanation
Indices: 14769--14883 Score: 133
Period size: 24 Copynumber: 4.8 Consensus size: 24
14759 CATAATTCAT
* * *
14769 GTCAAGTACCATATCAAAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
14793 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
* *
14817 ATCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
* * *
14841 GTC-AGATATCAGATCATAATGCAT
1 GTCAAG-TATCAGATCAGAATCCAA
14865 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
14884 ATCAAATCAA
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.03
24 76 0.95
25 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:22528 original size:9 final size:9
Alignment explanation
Indices: 22514--22557 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
22504 ACACTTATTC
22514 AATTCCAGA
1 AATTCCAGA
* *
22523 AATTCCGGT
1 AATTCCAGA
*
22532 AATTCCATA
1 AATTCCAGA
*
22541 AATTCAAGA
1 AATTCCAGA
22550 AATTCCAG
1 AATTCCAG
22558 TACTAGAATT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.27
Consensus pattern (9 bp):
AATTCCAGA
Found at i:26199 original size:10 final size:10
Alignment explanation
Indices: 26181--26220 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
26171 TTTTTTTTAA
26181 TTTAG-AAAT
1 TTTAGAAAAT
26190 TTTAGAAAAT
1 TTTAGAAAAT
26200 TTTAGAAAAT
1 TTTAGAAAAT
*
26210 TTTGGAAAAT
1 TTTAGAAAAT
26220 T
1 T
26221 CTTGTGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
9 5 0.17
10 24 0.83
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (10 bp):
TTTAGAAAAT
Found at i:26651 original size:20 final size:21
Alignment explanation
Indices: 26605--26665 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
26595 TCCCCTGTGT
26605 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
26628 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
26648 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
26666 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:30499 original size:21 final size:20
Alignment explanation
Indices: 30465--30517 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
30455 GAGTTTGTTT
*
30465 TCATTTTTCA-ATTTTGAAACA
1 TCATTTTT-ATATTTT-AAAAA
30486 TCATTTTTATATTTTAAAAA
1 TCATTTTTATATTTTAAAAA
*
30506 TAATTTCTTATA
1 TCATTT-TTATA
30518 ATCCAAAGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (20 bp):
TCATTTTTATATTTTAAAAA
Found at i:33735 original size:21 final size:21
Alignment explanation
Indices: 33711--33761 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
33701 AAAAAATTAC
33711 CTAAAACATTATTATTTCTAA
1 CTAAAACATTATTATTTCTAA
*
33732 CTAAAACATTATTATTTCTAC
1 CTAAAACATTATTATTTCTAA
33753 CTAAAACAT
1 CTAAAACAT
33762 CAATGTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (21 bp):
CTAAAACATTATTATTTCTAA
Found at i:34346 original size:22 final size:22
Alignment explanation
Indices: 34321--34375 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
34311 GATCCTACCA
34321 AGATCTGATCCGAGTTGGATCC
1 AGATCTGATCCGAGTTGGATCC
*
34343 AGATCTGATCCGAGTTGGATCT
1 AGATCTGATCCGAGTTGGATCC
*
34365 AAATCTGATCC
1 AGATCTGATCC
34376 ATATTCGAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (22 bp):
AGATCTGATCCGAGTTGGATCC
Found at i:38631 original size:12 final size:12
Alignment explanation
Indices: 38614--38657 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
38604 TGTTATATTC
38614 TTTTTGGTCTAT
1 TTTTTGGTCTAT
* *
38626 TTTTTGTTTTAT
1 TTTTTGGTCTAT
38638 TCCTTTTGGTCTAT
1 T--TTTTGGTCTAT
38652 TTTTTG
1 TTTTTG
38658 TTTGGATGCG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 16 0.62
14 10 0.38
ACGTcount: A:0.07, C:0.09, G:0.14, T:0.70
Consensus pattern (12 bp):
TTTTTGGTCTAT
Found at i:38638 original size:26 final size:26
Alignment explanation
Indices: 38600--38660 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
38590 CCAATGCATG
* *
38600 TTTTTGTTATATTCTTTTTGGTCTAT
1 TTTTTGTTTTATTCCTTTTGGTCTAT
38626 TTTTTGTTTTATTCCTTTTGGTCTAT
1 TTTTTGTTTTATTCCTTTTGGTCTAT
38652 TTTTTGTTT
1 TTTTTGTTT
38661 GGATGCGGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.08, C:0.08, G:0.11, T:0.72
Consensus pattern (26 bp):
TTTTTGTTTTATTCCTTTTGGTCTAT
Found at i:38994 original size:3 final size:3
Alignment explanation
Indices: 38909--38981 Score: 102
Period size: 3 Copynumber: 25.7 Consensus size: 3
38899 TTCATTTGAA
38909 TAT TAT T-T ATAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38953 TAT TAT TAT TAT TA- TAT T-T T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
38982 ATAAATATTA
Statistics
Matches: 65, Mismatches: 0, Indels: 10
0.87 0.00 0.13
Matches are distributed among these distances:
2 9 0.14
3 55 0.85
4 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:40411 original size:16 final size:17
Alignment explanation
Indices: 40390--40424 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
40380 TAACAATTTG
*
40390 ATATTTTTCA-TTTAAT
1 ATATTTTGCATTTTAAT
40406 ATATTTTGCATTTTAAT
1 ATATTTTGCATTTTAAT
40423 AT
1 AT
40425 TATCGCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (17 bp):
ATATTTTGCATTTTAAT
Found at i:40523 original size:25 final size:26
Alignment explanation
Indices: 40451--40533 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 26
40441 TTTTATCTTG
* *
40451 ATTATTATTATTTTGT-TTTGTTT-T-
1 ATTATTATT-TTTTATATATGTTTATA
40475 ATTATTATTTTTTATATATGTTTA-A
1 ATTATTATTTTTTATATATGTTTATA
*
40500 ATTATTATTTTCATTAT-TAT-TTTATT
1 ATTATTATTTT--TTATATATGTTTATA
40526 ATTATTAT
1 ATTATTAT
40534 CTTAAGTCGT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
23 5 0.10
24 15 0.30
25 15 0.30
26 11 0.22
27 4 0.08
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.69
Consensus pattern (26 bp):
ATTATTATTTTTTATATATGTTTATA
Found at i:40528 original size:11 final size:11
Alignment explanation
Indices: 40452--40531 Score: 83
Period size: 11 Copynumber: 7.0 Consensus size: 11
40442 TTTATCTTGA
40452 TTATTATTATT
1 TTATTATTATT
* *
40463 TTGTT-TTGTT
1 TTATTATTATT
40473 TTATTATTATT
1 TTATTATTATT
40484 TT-TTATATATGT
1 TTATTAT-TAT-T
40496 TTAAATTATTATT
1 TT--ATTATTATT
40509 TTCATTATTATT
1 TT-ATTATTATT
40521 TTATTATTATT
1 TTATTATTATT
40532 ATCTTAAGTC
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
10 12 0.21
11 22 0.38
12 14 0.24
13 3 0.05
14 3 0.05
15 4 0.07
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.70
Consensus pattern (11 bp):
TTATTATTATT
Found at i:42844 original size:37 final size:38
Alignment explanation
Indices: 42794--42871 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 38
42784 CTTTAGAGAA
** *
42794 GTTAGGAGGGAAAGTTATCCCATACATGT-AAAGTTTT
1 GTTAGGACCGAAAGCTATCCCATACATGTAAAAGTTTT
* *
42831 GTTAGGACCGAAAGCTGTCCCCTACATGTAAAAGTTTT
1 GTTAGGACCGAAAGCTATCCCATACATGTAAAAGTTTT
42869 GTT
1 GTT
42872 TGATGCACGG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
37 24 0.69
38 11 0.31
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.32
Consensus pattern (38 bp):
GTTAGGACCGAAAGCTATCCCATACATGTAAAAGTTTT
Found at i:48831 original size:75 final size:75
Alignment explanation
Indices: 48721--48860 Score: 235
Period size: 75 Copynumber: 1.9 Consensus size: 75
48711 TAACCAATGT
* * *
48721 TGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATGTTAGCGCATTTTGAACGTTTGTAT
1 TGGGACATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTAGCGCATTTTGAACGTCTGTAT
48786 CAGCAAATAC
66 CAGCAAATAC
* *
48796 TGGGACATGCTGCAAGCCCATTTCAATCAGAATCAAGAATATTGGCGCATTTTGAACGTCTGTAT
1 TGGGACATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTAGCGCATTTTGAACGTCTGTAT
48861 TAACAAATGC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 60 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (75 bp):
TGGGACATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTAGCGCATTTTGAACGTCTGTAT
CAGCAAATAC
Found at i:50236 original size:22 final size:22
Alignment explanation
Indices: 50159--50237 Score: 104
Period size: 22 Copynumber: 3.6 Consensus size: 22
50149 ACATCTACAT
* * *
50159 TCTTCAATGATAATAGATTCTC
1 TCTTCAAAGATGATAAATTCTC
*
50181 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAAATTCTC
*
50203 TCTTCAAAGATGATAAATTTTC
1 TCTTCAAAGATGATAAATTCTC
*
50225 TTTTCAAAGATGA
1 TCTTCAAAGATGA
50238 AAGCTTTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.39
Consensus pattern (22 bp):
TCTTCAAAGATGATAAATTCTC
Found at i:50804 original size:113 final size:114
Alignment explanation
Indices: 50605--50882 Score: 400
Period size: 113 Copynumber: 2.4 Consensus size: 114
50595 GATTCGGATC
* * **
50605 CATCACTTAAATGGATCAATATTTTCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCACTT-GATGGATCAACATTGCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
*
50669 AAGAAGAAGTTCATAATAAGAAGAACTTGTTC-AACCTTTTGCTCGAATT
65 AAGAAGAAATTCATAATAAGAAGAACTTGTTCAAACCTTTTGCTCGAATT
50718 CATCACTTGATGGATCAACATTGCCA-AGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCACTTGATGGATCAACATTGCCAGAG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * * *
50782 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGTTTGAATT
65 AAGAAGAAATTCATAATAAGAAGAACTTGTTCAAACCTTTTGCTCGAATT
* * * *
50832 CATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAAAAGAACT
1 CATCACTTGATGGATCAACATTGCCAGAGAGAGTTCATAATGAGAAGAACT
50883 TGTTCAACCT
Statistics
Matches: 148, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
111 1 0.01
112 14 0.09
113 72 0.49
114 59 0.40
115 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (114 bp):
CATCACTTGATGGATCAACATTGCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAATTCATAATAAGAAGAACTTGTTCAAACCTTTTGCTCGAATT
Found at i:51084 original size:122 final size:123
Alignment explanation
Indices: 50862--51108 Score: 320
Period size: 122 Copynumber: 2.0 Consensus size: 123
50852 TTTCCAGAGA
* *
50862 AAGTTCATAATGAAAAGAACTTGTTCAACCTTTTGCATGACTCTATCACATAAGGAGATATATCA
1 AAGTTCATAATGAAAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCA
* * * *
50927 GAATCAACTTTTCCAGAGAAAGTTCGTAATAAGAAGAACTTATCTGAAG-AGGAAGAAG
66 GAATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATATGAAGAAGG-AGAAG
* ** * *
50985 AAGTTCATAATGAGAAGAACTTGTTCAACC-TTTGTTTGATTCTATCATAGAAGGAGATAGATCA
1 AAGTTCATAATGAAAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCA
* * * *
51049 GTATCAGCATTTCCAGA-AGGAGTTCATAATGAGAAGAACTCATATGAAGAAGGAGAAG
66 GAATCAACATTTCCAGAGA-AAGTTCATAATAAGAAGAACTCATATGAAGAAGGAGAAG
51107 AA
1 AA
51109 TTTGTTCAAC
Statistics
Matches: 107, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
121 1 0.01
122 74 0.69
123 32 0.30
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (123 bp):
AAGTTCATAATGAAAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCA
GAATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATATGAAGAAGGAGAAG
Found at i:51432 original size:3 final size:3
Alignment explanation
Indices: 51344--51419 Score: 90
Period size: 3 Copynumber: 26.7 Consensus size: 3
51334 TTCATTTGAA
* *
51344 TAT TAT T-T ATAT T-T TAT TAT TAT TAT TAT AAT TAT AAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
51388 TAT TAT TAT TAT TAT TA- TAT T-T T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
51420 ATAAATATTA
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
2 9 0.14
3 54 0.84
4 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:52954 original size:25 final size:24
Alignment explanation
Indices: 52895--52959 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
52885 TTGTTTTGTT
52895 TTTTTTATTATTATTTTTGATATA
1 TTTTTTATTATTATTTTTGATATA
** *
52919 TGTTTAAATTATTA-TTTTCATTATTA
1 T-TTTTTATTATTATTTTTGA-TA-TA
52945 TTTTTTATTATTATT
1 TTTTTTATTATTATT
52960 ATCTTAAGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
24 6 0.19
25 22 0.69
26 4 0.12
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (24 bp):
TTTTTTATTATTATTTTTGATATA
Found at i:52978 original size:2 final size:2
Alignment explanation
Indices: 52971--53011 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
52961 TCTTAAGTCG
52971 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53012 TTATTCTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54050 original size:18 final size:19
Alignment explanation
Indices: 54017--54057 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
54007 ATATATATAT
*
54017 TTTAATGTTAAGATGTTAA
1 TTTAATGTTAAGATGTGAA
*
54036 TTTAAT-TTAATATGTGAA
1 TTTAATGTTAAGATGTGAA
54054 TTTA
1 TTTA
54058 GATTAACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (19 bp):
TTTAATGTTAAGATGTGAA
Found at i:58047 original size:3 final size:3
Alignment explanation
Indices: 58041--58132 Score: 123
Period size: 3 Copynumber: 29.7 Consensus size: 3
58031 CTCCATTTTC
58041 TAT TAT TAT TAT TAT TA- TAT ATAT ATAT ATAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT -TAT -TAT TAT TAT TAT TAT TAT
* *
58088 TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT TAA AAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TA
58133 CAAACAGGCC
Statistics
Matches: 82, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.02
3 66 0.80
4 14 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:59465 original size:3 final size:3
Alignment explanation
Indices: 59457--59485 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
59447 ATATGTTTAC
59457 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
59486 TAACCATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:59690 original size:20 final size:19
Alignment explanation
Indices: 59665--59706 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
59655 TTATTTTATA
59665 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
59685 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
59704 AAT
1 AAT
59707 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:59697 original size:119 final size:118
Alignment explanation
Indices: 59563--59798 Score: 280
Period size: 121 Copynumber: 2.0 Consensus size: 118
59553 TTTAATCCTA
* * * * *
59563 TTTTAATATTTATTTATTTTCTAATAT-TAAG-AAAGGGCAGTCTTAAAATAACTGGATGTCTAT
1 TTTTAATATTTATTTATTTTCTAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC-AT
* *
59626 TTTCTGA-TATTTTTAAATAAATAAATATCTTATTTTATAAATTATATATTAATTG
65 TTTCTGATTATTTCTAAATAAATAAATATCTTA-TTTATAAA-TATATATAAATTG
* * * ** * *
59681 TTTTAATTATTTATTTATTTTTTAATATCAAAGAAAATAGCTGTCTTAAGGCACCTAGAAGTCCT
1 TTTTAA-TATTTATTTATTTTCTAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCAT
*
59746 TTTCTGATTATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATT
65 TTTCTGATTATTTCTAAATAAATAAATATCTTATTTATAAATATATATAAATT
59799 AATATATATT
Statistics
Matches: 99, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
118 6 0.06
119 31 0.31
120 19 0.19
121 43 0.43
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (118 bp):
TTTTAATATTTATTTATTTTCTAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATT
TTCTGATTATTTCTAAATAAATAAATATCTTATTTATAAATATATATAAATTG
Found at i:63614 original size:15 final size:15
Alignment explanation
Indices: 63594--63625 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
63584 GATCAATACC
63594 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
63609 TTTTGCATACATTCA
1 TTTTGCATACATGCA
63624 TT
1 TT
63626 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:70983 original size:3 final size:3
Alignment explanation
Indices: 70966--71028 Score: 50
Period size: 3 Copynumber: 23.3 Consensus size: 3
70956 AAAAAATGAA
* *
70966 AAG AAG AA- AAA AAG AAG AAG AAG AAA AAG AA- AA- AAG AAG AA- AA-
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
71009 AAG -AG AAG -AG AAG AAA AAG A
1 AAG AAG AAG AAG AAG AAG AAG A
71029 GAAAAAAGGG
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
2 14 0.28
3 36 0.72
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:70989 original size:33 final size:33
Alignment explanation
Indices: 70964--71034 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 33
70954 AGAAAAAATG
70964 AAAAGAAGAAAAAA-AGAAGAAGAAGAAAAAGAA
1 AAAAGAAGAAAAAAGAGAAG-AGAAGAAAAAGAA
70997 AAAAGAAGAAAAAAGAGAAGAGAAGAAAAAGAGA
1 AAAAGAAGAAAAAAGAGAAGAGAAGAAAAAGA-A
71031 AAAA
1 AAAA
71035 AGGGGGTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
33 26 0.72
34 10 0.28
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (33 bp):
AAAAGAAGAAAAAAGAGAAGAGAAGAAAAAGAA
Found at i:71027 original size:16 final size:16
Alignment explanation
Indices: 70952--71033 Score: 103
Period size: 16 Copynumber: 5.0 Consensus size: 16
70942 TATTATGCTT
70952 GAAGAAAAA-ATGAAAA
1 GAAGAAAAAGA-GAAAA
*
70968 GAAGAAAAAAAGAAGAA
1 GAAGAAAAAGAGAA-AA
*
70985 GAAGAAAAAGAAAAAA
1 GAAGAAAAAGAGAAAA
*
71001 GAAGAAAAAAGAGAAGA
1 GAAG-AAAAAGAGAAAA
71018 GAAGAAAAAGAGAAAA
1 GAAGAAAAAGAGAAAA
71034 AAGGGGGTCA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
16 29 0.50
17 29 0.50
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (16 bp):
GAAGAAAAAGAGAAAA
Found at i:73019 original size:225 final size:226
Alignment explanation
Indices: 72662--73650 Score: 1308
Period size: 225 Copynumber: 4.3 Consensus size: 226
72652 AGTATCAGTT
*
72662 AAAGTTTATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
*
72727 TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAATATTGCCAGGTAGAGTTCATAATGAGAA
66 TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
*
72792 GAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGC-TCAAA
131 GAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCAT-AAA
* * *
72856 TCCATCACTTGAT-GGATCAACTTTTCCAAAG
195 TCCATCACTAGATAGCATCAACTTTTCCAGAG
72887 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
*
72952 TCTACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
66 TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
* ** *
73017 GAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAAT
131 GAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATAAAT
* * * *
73082 TCATCATTCGAT-GGATCAACTTTTCC--AG
196 CCATCACTAGATAGCATCAACTTTTCCAGAG
* * *
73110 AAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAAAAATTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* * * * * *
73174 TCAACTTTTTATTTGAATTCATCATTCGATGGATCAACTTTTCCA-G-AAAGTTCATAATGAGAA
66 TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
*
73237 GAACT--T-ATCTGAAGAGGAAGAAAAAATTCATAATGAGAAGAATTTGTTCAACCTTATT-CAT
131 GAACTCGTCATCTG-A-A-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTT-TTGCAT
** * *
73298 AATTTTATCACAGAAGGAGATAGATCAGCATCAGCTTTTCCAGAG
192 AA----ATC-C---ATCA-CTAGAT-AGCATCAACTTTTCCAGAG
* *
73343 AAAGTTCATAATGAGAAGAACTCATCTAAAGAATGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
73408 TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
66 TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
*
73473 GAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATAATT
131 GAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATAAAT
* *
73538 CTATCACAGAAGGAGATAGATCAGCATCAGCTTTTCCAGAG
196 CCATCAC---------TAGAT-AGCATCAACTTTTCCAGAG
* **
73579 AAAGTTCATAATGAGAAGAACTCATCTG-A-AA--AAGAAGAAGTTCACAATGAGAAGAGCTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
73640 TCAACCTTTTG
66 TCAACCTTTTG
73651 CATAATTCTA
Statistics
Matches: 677, Mismatches: 53, Indels: 61
0.86 0.07 0.08
Matches are distributed among these distances:
217 5 0.01
218 2 0.00
219 1 0.00
220 60 0.09
221 3 0.00
222 70 0.10
223 32 0.05
224 2 0.00
225 210 0.31
226 1 0.00
228 4 0.01
229 4 0.01
231 12 0.02
232 40 0.06
233 31 0.05
234 72 0.11
235 4 0.01
236 116 0.17
237 1 0.00
238 2 0.00
239 5 0.01
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (226 bp):
AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
GAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATAAAT
CCATCACTAGATAGCATCAACTTTTCCAGAG
Found at i:73404 original size:124 final size:123
Alignment explanation
Indices: 73206--73924 Score: 811
Period size: 124 Copynumber: 5.9 Consensus size: 123
73196 CATTCGATGG
* * * *
73206 ATCAACTTTTCC--AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAAAAATTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
* *
73269 ATGAGAAGAATTTGTTCAACCTTATT-CATAATTTTATCACAGAAGGAGATAGATCAGC
66 ATGAGAAGAACTTGTTCAACCTT-TTGCATAATTCTATCACAGAAGGAGATAGATCAGC
* *
73327 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAATGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCAT
* ** * * *
73392 AATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC-AT--C------A-TTTGAT--GG
65 AATGAGAAGAACTTGTTCAACCTTTTGCAT-AATTCTATCACAGAAGGAGATAGATCAGC
* * *
73440 ATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAG-A-AA-TT
1 ATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGAAGAAGAAGTT
*
73501 CATAATGAGAAGAATTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
62 CATAATGAGAAGAACTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
* *
73563 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG-A-AA-AAGAAGAAGTTCACA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
*
73625 ATGAGAAGAGCTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
66 ATGAGAAGAACTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
* *
73683 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATTTGAAGAAGAAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG-AAGAAGAAGTTCAT
* * * * * * *
73748 AATGAGAAGAACTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAAC
65 AATGAGAAGAACTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
* * * * * *
73807 ATCAATTTTTCCAGGGAAAGATCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAATTTTAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCAT
* * *
73872 AATAAGAATAACTTGTTCAACCCCTTTTCCA-AATTAC-ATCACAGAAGGAGATA
65 AATGAGAAGAACTTGTTCAA--CCTTTTGCATAATT-CTATCACAGAAGGAGATA
73925 TTATCATCCC
Statistics
Matches: 510, Mismatches: 55, Indels: 62
0.81 0.09 0.10
Matches are distributed among these distances:
111 5 0.01
112 36 0.07
113 33 0.06
114 2 0.00
115 9 0.02
116 12 0.02
117 3 0.01
118 3 0.01
119 3 0.01
120 110 0.22
121 17 0.03
122 3 0.01
123 65 0.13
124 179 0.35
125 22 0.04
126 8 0.02
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (123 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
Found at i:74130 original size:3 final size:3
Alignment explanation
Indices: 74124--74188 Score: 80
Period size: 3 Copynumber: 21.7 Consensus size: 3
74114 CTCCATTTTC
74124 TAT TAT TAT TAT T-T TAT ATAT TAT TAT TAT TAT TAT T-T TATT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA-T TAT
* *
74169 TAT TAT TAA AAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
74189 CAAACAGGCC
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 4 0.07
3 44 0.81
4 6 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:74156 original size:24 final size:24
Alignment explanation
Indices: 74124--74176 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
74114 CTCCATTTTC
74124 TATTATTATTATTTTATATATTAT
1 TATTATTATTATTTTATATATTAT
*
74148 TATTATTATTATTTTATTTATTAT
1 TATTATTATTATTTTATATATTAT
74172 TATTA
1 TATTA
74177 AAATTATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
TATTATTATTATTTTATATATTAT
Found at i:75515 original size:3 final size:3
Alignment explanation
Indices: 75507--75538 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
75497 TGTTTACTTT
*
75507 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
75539 TAACCATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:76489 original size:20 final size:21
Alignment explanation
Indices: 76461--76500 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
76451 TAAAAATAAA
76461 AAATAAGAA-AAAACAAAGAT
1 AAATAAGAATAAAACAAAGAT
* *
76481 AAATTAGAATCAAACAAAGA
1 AAATAAGAATAAAACAAAGA
76501 AAAAAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.70, C:0.07, G:0.10, T:0.12
Consensus pattern (21 bp):
AAATAAGAATAAAACAAAGAT
Found at i:76892 original size:20 final size:20
Alignment explanation
Indices: 76869--76940 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
76859 AAATTCGCGT
76869 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
76889 TGCGA-TA-GTCAGAATCGCAA
1 TGCGATTACGT-A-AATCGCAA
*
76909 TGCGAATACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
76929 TGCGATTACGTA
1 TGCGATTACGTA
76941 TTCGCATTGC
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
18 2 0.04
19 3 0.06
20 37 0.79
21 3 0.06
22 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (20 bp):
TGCGATTACGTAAATCGCAA
Found at i:77526 original size:19 final size:20
Alignment explanation
Indices: 77481--77528 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
77471 TTTGAGAATG
**
77481 AAAATCGCAACGCGGAAATG
1 AAAATCGCAACGCGGAAACC
**
77501 ACTATCGCAACGC-GAAACC
1 AAAATCGCAACGCGGAAACC
77520 AAAATCGCA
1 AAAATCGCA
77529 TTGCGATTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.44, C:0.27, G:0.19, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACGCGGAAACC
Found at i:77546 original size:19 final size:19
Alignment explanation
Indices: 77524--77583 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
77514 GAAACCAAAA
*
77524 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
77543 TCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
77563 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
77582 TC
1 TC
77584 AACCAAAAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:77580 original size:20 final size:20
Alignment explanation
Indices: 77524--77582 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
77514 GAAACCAAAA
*
77524 TCGCATTGCGATTTTCA-TT
1 TCGCGTTGCGATTTTCATTT
**
77543 TCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCATTT
77563 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
77583 CAACCAAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 14 0.41
20 20 0.59
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATTT
Found at i:78579 original size:12 final size:12
Alignment explanation
Indices: 78562--78586 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
78552 TCTTCGGGGA
78562 CTTTTTCTTCTT
1 CTTTTTCTTCTT
78574 CTTTTTCTTCTT
1 CTTTTTCTTCTT
78586 C
1 C
78587 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:78788 original size:24 final size:24
Alignment explanation
Indices: 78761--78814 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
78751 CTAAAACATC
* *
78761 ATCAAAATCCGAGTATTGATCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
78785 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
78809 ATCAAA
1 ATCAAA
78815 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:79565 original size:20 final size:20
Alignment explanation
Indices: 79540--79627 Score: 131
Period size: 20 Copynumber: 4.4 Consensus size: 20
79530 TGTATTATCT
*
79540 CGTTGCGATAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
79560 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
* * *
79580 CGATGTGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
*
79600 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
79620 CGTTGCGA
1 CGTTGCGA
79628 TTTTGTATTA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:80262 original size:31 final size:29
Alignment explanation
Indices: 80198--80256 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
80188 AATATAAATA
* *
80198 TAAATATATATATTAATATTATCTTCACT
1 TAAAAATATATATTAATATTATCTTAACT
* *
80227 TAAAAATATATTTTATTATTATCTTAACT
1 TAAAAATATATATTAATATTATCTTAACT
80256 T
1 T
80257 TTAAAAGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (29 bp):
TAAAAATATATATTAATATTATCTTAACT
Found at i:83354 original size:29 final size:30
Alignment explanation
Indices: 83307--83385 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
83297 ATATAAATAT
* * *
83307 AAATATATATTAATATTATCTTC-ACTTAA
1 AAATATATTTTATTATTATCTTCAAATTAA
*
83336 AAATATATTTTATTCTTAT-TTCAAATTAA
1 AAATATATTTTATTATTATCTTCAAATTAA
83365 AAATATA-TTTATTATTATCTT
1 AAATATATTTTATTATTATCTT
83386 AATTTTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
28 13 0.30
29 30 0.70
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.51
Consensus pattern (30 bp):
AAATATATTTTATTATTATCTTCAAATTAA
Found at i:83516 original size:27 final size:28
Alignment explanation
Indices: 83428--83518 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 28
83418 AAATATATTT
* * **
83428 TAATATATTTTTAAAAGTTAAGTTAATAA
1 TAATATATTTTT-AATGTGAAAATAATAA
* * *
83457 TAAAATATTTTTAATTTGAAAAAAATAA
1 TAATATATTTTTAATGTGAAAATAATAA
* *
83485 T-ATATATTTTT-ATGTGAATATAATAG
1 TAATATATTTTTAATGTGAAAATAATAA
83511 TAATATAT
1 TAATATAT
83519 ATATATAAAT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
26 12 0.24
27 15 0.31
28 11 0.22
29 11 0.22
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (28 bp):
TAATATATTTTTAATGTGAAAATAATAA
Found at i:87905 original size:14 final size:14
Alignment explanation
Indices: 87886--87931 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 14
87876 AACAAATTCC
*
87886 AAATATTCAAATGA
1 AAATATTCATATGA
*
87900 AAATATTTATAT-A
1 AAATATTCATATGA
87913 AAA-ATTCATA-GA
1 AAATATTCATATGA
87925 AAATATT
1 AAATATT
87932 ATTGTATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
12 10 0.37
13 7 0.26
14 10 0.37
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (14 bp):
AAATATTCATATGA
Done.