Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006075.1 Hibiscus syriacus cultivar Beakdansim tig00014384_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: 74035
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:1929 original size:13 final size:13
Alignment explanation
Indices: 1911--1935 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1901 ACCATGTCAC
1911 ATTGATTATGAAT
1 ATTGATTATGAAT
1924 ATTGATTATGAA
1 ATTGATTATGAA
1936 ACCAATGGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGATTATGAAT
Found at i:2117 original size:28 final size:28
Alignment explanation
Indices: 2086--2149 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
2076 GAAGTGTGTT
*
2086 AAGTGTTAAAATGTTTTTAAAAGGGGAG
1 AAGTGTTAAAATGTTTTTAAAAGAGGAG
2114 AAGTGTTAAAATGTTTTTAAAAGAGGAG
1 AAGTGTTAAAATGTTTTTAAAAGAGGAG
2142 AAGTGTTA
1 AAGTGTTA
2150 TAGTAAGGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.33
Consensus pattern (28 bp):
AAGTGTTAAAATGTTTTTAAAAGAGGAG
Found at i:2586 original size:18 final size:19
Alignment explanation
Indices: 2540--2591 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
2530 GAATGTTTTT
2540 CATGCATCGATGCACATAC
1 CATGCATCGATGCACATAC
*
2559 CATGCATCGATGCACATGC
1 CATGCATCGATGCACATAC
*
2578 C-TTCATCGATGCAC
1 CATGCATCGATGCAC
2592 TGAGGATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 12 0.39
19 19 0.61
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (19 bp):
CATGCATCGATGCACATAC
Found at i:2722 original size:17 final size:19
Alignment explanation
Indices: 2694--2742 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2684 TATTTTGAAA
2694 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
2712 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
2731 CACCGATGCACT
1 CATCGATGCACT
2743 AAGGGTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:3811 original size:41 final size:42
Alignment explanation
Indices: 3749--3834 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 42
3739 TTCCCCGAAA
*
3749 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTT
*
3791 TCCCGTG-TTGTTTCATGTAATTCGTTTTCCGAAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTT
3832 TCC
1 TCC
3835 AGGTTTGGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
41 35 0.83
42 7 0.17
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.45
Consensus pattern (42 bp):
TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTT
Found at i:4085 original size:18 final size:18
Alignment explanation
Indices: 4059--4101 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4049 ATATTTAAAT
4059 ATATT-TATTAATTTATA
1 ATATTATATTAATTTATA
* *
4076 ATATTATATTATTTTTTA
1 ATATTATATTAATTTATA
4094 ATATTATA
1 ATATTATA
4102 ATAAAATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATTATATTAATTTATA
Found at i:4286 original size:36 final size:38
Alignment explanation
Indices: 4246--4331 Score: 99
Period size: 36 Copynumber: 2.3 Consensus size: 38
4236 TATATATTTA
* *
4246 ATATTAATATAATAATCTAATAATA-T-TTTAATAAAG
1 ATATTAATATAATAATATAACAATATTATTTAATAAAG
* *
4282 ATATTTAAAAT-ATAATATAACAATATTATTTAATAAAT
1 ATA-TTAATATAATAATATAACAATATTATTTAATAAAG
4320 A-ATTAATATAAT
1 ATATTAATATAAT
4332 TTATAATGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
36 21 0.51
37 10 0.24
38 10 0.24
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (38 bp):
ATATTAATATAATAATATAACAATATTATTTAATAAAG
Found at i:4422 original size:26 final size:27
Alignment explanation
Indices: 4393--4443 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
4383 ATTATAAAAA
*
4393 TAATA-TTTAATAATAAATAA-ATTATT
1 TAATATTTTAAAAAT-AATAATATTATT
4419 TAATATTTTAAAAATAATAATATTA
1 TAATATTTTAAAAATAATAATATTA
4444 AGTTTTATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TAATATTTTAAAAATAATAATATTATT
Found at i:4913 original size:81 final size:81
Alignment explanation
Indices: 4773--5284 Score: 626
Period size: 81 Copynumber: 6.4 Consensus size: 81
4763 ATGATTATGC
* * * * *
4773 CAAAGGCACAATTAGACCATTAATCTTTCACTCAAAGGTATTTAACCTTTCATCTAACTGTCATA
1 CAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATA
* * *
4838 ATTGACATATTTATAT
66 ATTGACACATTTCTGT
*
4854 CAAATGCACAACTAGGCGATTAATCTTTTACTCAAAGGTA-TTAACCTTTTCATCTAACTGGCAT
1 CAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACC-TTTCATCTAACTGGCAT
* *
4918 AATTGACACCTTTCTTT
65 AATTGACACATTTCTGT
** * *
4935 CAAATGCACAGGTAGACCATTAATCTTTTACTCAAAGGTATTTAACCTTCCATCTAACTGGCATA
1 CAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATA
5000 ATTGACACATTTCTGT
66 ATTGACACATTTCTGT
** * ** * **
5016 CAAATGCACAGTTA-GTCATTAATCTTTTACTCAAAGAAATTTAACATTTCATCTAACTACCATA
1 CAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATA
*
5080 ATTGGCACATTTCTGT
66 ATTGACACATTTCTGT
* * **
5096 C-AATGCACAACTAGGCCATTAATC-ATTA---AAAGGTATTTAACCTTTCATTTAACTAACATA
1 CAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATA
* * * *
5156 ATTTACACCTTTATAT
66 ATTGACACATTTCTGT
*
5172 CAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACC-TTCAATCTAAATGGCAT
1 CAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTC-ATCTAACTGGCAT
*
5236 AATTGACTCATTTCTGT
65 AATTGACACATTTCTGT
* *
5253 CAAATGCACATCTAGGTCATTAATCTTTTACT
1 CAAATGCACAACTAGGCCATTAATCTTTTACT
5285 TTAAATCATA
Statistics
Matches: 369, Mismatches: 53, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
76 39 0.11
77 23 0.06
78 3 0.01
79 13 0.04
80 76 0.21
81 209 0.57
82 6 0.02
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.35
Consensus pattern (81 bp):
CAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATA
ATTGACACATTTCTGT
Found at i:5198 original size:237 final size:241
Alignment explanation
Indices: 4790--5284 Score: 696
Period size: 237 Copynumber: 2.1 Consensus size: 241
4780 ACAATTAGAC
* ** * ** *
4790 CATTAATCTTTCACTCAAAGGTATTTAACCTTTCATCTAACTGTCATAATTGACATATTTATATC
1 CATTAATCTTTTACTCAAAGAAATTTAACATTTCATCTAACTACCATAATTGACACATTTATATC
* * **
4855 AAATGCACAACTAGGCGATTAATCTTTTACTCAAAGGTATTAACCTTTTCATCTAACTGGCATAA
66 AAATGCACAACTAGGCCATTAATCTATTA--CAAAGGTATTAACCTTTTCATCTAACTAACATAA
* * **
4920 TTGACACCTTTCTTTCAAATGCACAGGTAGACCATTAATCTTTTACTCAAAGGTATTTAACCTTC
129 TTGACACCTTTATATCAAATGCACAACTAGACCATTAATCTTTTACTCAAAGGTATTTAACCTTC
* *
4985 CATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGT-TA-GT
194 AATCTAAATGGCATAATTGACACATTTCTGTCAAATGCACA-TCTAGGT
* * *
5032 CATTAATCTTTTACTCAAAGAAATTTAACATTTCATCTAACTACCATAATTGGCACATTTCTGTC
1 CATTAATCTTTTACTCAAAGAAATTTAACATTTCATCTAACTACCATAATTGACACATTTATATC
*
5097 -AATGCACAACTAGGCCATTAATC-ATTA-AAAGGTATTTAACC-TTTCATTTAACTAACATAAT
66 AAATGCACAACTAGGCCATTAATCTATTACAAAGGTA-TTAACCTTTTCATCTAACTAACATAAT
* *
5158 TTACACCTTTATATCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTCA
130 TGACACCTTTATATCAAATGCACAACTAGACCATTAATCTTTTACTCAAAGGTATTTAACCTTCA
*
5223 ATCTAAATGGCATAATTGACTCATTTCTGTCAAATGCACATCTAGGT
195 ATCTAAATGGCATAATTGACACATTTCTGTCAAATGCACATCTAGGT
5270 CATTAATCTTTTACT
1 CATTAATCTTTTACT
5285 TTAAATCATA
Statistics
Matches: 226, Mismatches: 24, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
236 1 0.00
237 122 0.54
238 23 0.10
240 3 0.01
241 22 0.10
242 55 0.24
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (241 bp):
CATTAATCTTTTACTCAAAGAAATTTAACATTTCATCTAACTACCATAATTGACACATTTATATC
AAATGCACAACTAGGCCATTAATCTATTACAAAGGTATTAACCTTTTCATCTAACTAACATAATT
GACACCTTTATATCAAATGCACAACTAGACCATTAATCTTTTACTCAAAGGTATTTAACCTTCAA
TCTAAATGGCATAATTGACACATTTCTGTCAAATGCACATCTAGGT
Found at i:5830 original size:34 final size:32
Alignment explanation
Indices: 5777--5846 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
5767 ACCTTACAAC
*
5777 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
5809 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
5843 TCCC
1 TCCC
5847 CTTTATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:6156 original size:21 final size:21
Alignment explanation
Indices: 6130--6171 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
6120 CCCAGAATGG
*
6130 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
6151 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
6172 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:6402 original size:29 final size:31
Alignment explanation
Indices: 6370--6429 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
6360 AAATTTTGAA
*
6370 TAAATTCAA-TTAAGTCCAAATA-CATTTTG
1 TAAATTCAATTTAAGTCCAAAAACCATTTTG
6399 TAAATTCAATTTAAGTCCAAAAACCATTTTG
1 TAAATTCAATTTAAGTCCAAAAACCATTTTG
6430 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 9 0.32
30 12 0.43
31 7 0.25
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.37
Consensus pattern (31 bp):
TAAATTCAATTTAAGTCCAAAAACCATTTTG
Found at i:12827 original size:33 final size:31
Alignment explanation
Indices: 12766--12874 Score: 103
Period size: 33 Copynumber: 3.4 Consensus size: 31
12756 GCATAATATC
*
12766 TATCTATAATATATACATGTACACATGCAAAA
1 TATCTAT-CTATATACATGTACACATGCAAAA
*
12798 TATCTATCTATATACA-GATACACATATGCAGAA
1 TATCTATCTATATACATG-TACAC--ATGCAAAA
* * * *
12831 TATCTATCTATTTATCTATATACACATGTAGAA
1 TATCTATCTATATA-C-ATGTACACATGCAAAA
12864 TATCTATCTAT
1 TATCTATCTAT
12875 CAATATACAT
Statistics
Matches: 66, Mismatches: 5, Indels: 11
0.80 0.06 0.13
Matches are distributed among these distances:
30 1 0.02
31 13 0.20
32 7 0.11
33 38 0.58
34 1 0.02
35 6 0.09
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (31 bp):
TATCTATCTATATACATGTACACATGCAAAA
Found at i:15118 original size:47 final size:47
Alignment explanation
Indices: 15045--15135 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 47
15035 ACAATAGAAG
* * *
15045 AACCCAGAAAAACTGAAATTATATTCTCTTAATCTAACCCTCTTTAA
1 AACCCAGAAAAACTGAAATAACATTCTCTTAATCTAACACTCTTTAA
15092 AACCCAG-AAAACTGAAATCAACATTCTCTTAATCTAACACTCTT
1 AACCCAGAAAAACTGAAAT-AACATTCTCTTAATCTAACACTCTT
15136 CTGGGATACT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 11 0.28
47 29 0.73
ACGTcount: A:0.41, C:0.25, G:0.04, T:0.30
Consensus pattern (47 bp):
AACCCAGAAAAACTGAAATAACATTCTCTTAATCTAACACTCTTTAA
Found at i:17890 original size:29 final size:29
Alignment explanation
Indices: 17833--17897 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
17823 AATTGAACCA
* * *
17833 AAATTTATCTGAAAATTATTAACCGAACT
1 AAATTAATCTGAAAATTATTAAACAAACT
* *
17862 AAATTAATTTGAAAATTATTAAATAAACT
1 AAATTAATCTGAAAATTATTAAACAAACT
*
17891 GAATTAA
1 AAATTAA
17898 CCGATTTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (29 bp):
AAATTAATCTGAAAATTATTAAACAAACT
Found at i:18111 original size:29 final size:29
Alignment explanation
Indices: 18069--18133 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
18059 ATCGAACCAA
* *
18069 AATTTATTTGAAAATTATTAACCGTACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
*
18098 AATTAATTTGAAAATTATTAACCGAATCG
1 AATTAATTTGAAAATTATTAACCGAACCG
18127 AATTAAT
1 AATTAAT
18134 CAGTTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCGAACCG
Found at i:18202 original size:127 final size:125
Alignment explanation
Indices: 17969--18384 Score: 568
Period size: 127 Copynumber: 3.4 Consensus size: 125
17959 ATCGAACCAA
* * *
17969 AATTTATTTGAAAATTATTAACCGAACCGAATTAATCAAAATTTTTTAATTATTAATCAAAGCAA
1 AATTAATTTGAAAATTATTAACCGAA-CGAATTAATC--AGTTTTTTAATTATTAATCGAAGCAA
*
18034 AAATTTGGTTAATTGGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGTACCG
63 AAATTTGGTTAATT-GGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCG
18098 AATTAATTTGAAAATTATTAACCGAATCGAATTAATCAGTTTTTTAATTATTAATCGAAGCAAAA
1 AATTAATTTGAAAATTATTAACCGAA-CGAATTAATCAGTTTTTTAATTATTAATCGAAGCAAAA
*
18163 ATTTGGTTAATTCGGCTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCG
65 ATTTGGTTAATT-GGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCG
*
18225 AATTAATTTGAAAATTATTAA-C---CG----AAT---TTTTTTAATTTTTAATCGGAA-CAAAA
1 AATTAATTTGAAAATTATTAACCGAACGAATTAATCAGTTTTTTAATTATTAATC-GAAGCAAAA
* * *
18278 ATTCGGTTAATTGATTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACTGAACCG
65 ATTTGGTTAATTG-GTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCG
* *
18340 AATTAATTTGAAAATTATTAACCGAACTGAATTAAACGGTTTTTT
1 AATTAATTTGAAAATTATTAACCGAAC-GAATTAATCAGTTTTTT
18385 CTTAAACCAT
Statistics
Matches: 260, Mismatches: 13, Indels: 30
0.86 0.04 0.10
Matches are distributed among these distances:
114 1 0.00
115 98 0.38
116 4 0.02
118 3 0.01
119 1 0.00
120 1 0.00
122 2 0.01
124 2 0.01
126 1 0.00
127 112 0.43
129 35 0.13
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (125 bp):
AATTAATTTGAAAATTATTAACCGAACGAATTAATCAGTTTTTTAATTATTAATCGAAGCAAAAA
TTTGGTTAATTGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCG
Found at i:18229 original size:115 final size:113
Alignment explanation
Indices: 18127--18362 Score: 325
Period size: 115 Copynumber: 2.1 Consensus size: 113
18117 AACCGAATCG
* *
18127 AATTAATC-AGTTTTTTAATTATTAATC-GAAGCAAAAATTTGGTTAATTCG-GCTCGGTTAATC
1 AATTAACCAAGTTTTTTAATTATTAATCGGAA-CAAAAATTCGGTTAATT-GAGCTCGGTTAATC
18189 GAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATTTGAAAAT
64 GAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATT-ATTTGAAAAT
* * * **
18240 TATTAACCGAATTTTTTTAATTTTTAATCGGAACAAAAATTCGGTTAATTGATTTCGGTTAATCG
1 AATTAACC-AAGTTTTTTAATTATTAATCGGAACAAAAATTCGGTTAATTGAGCTCGGTTAATCG
*
18305 AACCAAAATTTATTTGAAAATTATTAACTGAACCGAATTAATTTGAAAAT
65 AACCAAAATTTATTTGAAAATTATTAACCGAACCGAATT-ATTTGAAAAT
*
18355 TATTAACC
1 AATTAACC
18363 GAACTGAATT
Statistics
Matches: 111, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
113 6 0.05
114 1 0.01
115 101 0.91
116 3 0.03
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.38
Consensus pattern (113 bp):
AATTAACCAAGTTTTTTAATTATTAATCGGAACAAAAATTCGGTTAATTGAGCTCGGTTAATCGA
ACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTATTTGAAAAT
Found at i:18348 original size:29 final size:29
Alignment explanation
Indices: 18311--18374 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
18301 ATCGAACCAA
* *
18311 AATTTATTTGAAAATTATTAACTGAACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
*
18340 AATTAATTTGAAAATTATTAACCGAACTG
1 AATTAATTTGAAAATTATTAACCGAACCG
18369 AATTAA
1 AATTAA
18375 ACGGTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCGAACCG
Found at i:18954 original size:30 final size:30
Alignment explanation
Indices: 18920--18982 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
18910 AGAATATGTA
*
18920 AATATTAAGGACCAAATGTATAATAATGCC
1 AATATTAAGGACCAAATATATAATAATGCC
* *
18950 AATATTAAGGATCAAATATATAATTATGCC
1 AATATTAAGGACCAAATATATAATAATGCC
18980 AAT
1 AAT
18983 TTATTAACGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (30 bp):
AATATTAAGGACCAAATATATAATAATGCC
Found at i:19546 original size:3 final size:3
Alignment explanation
Indices: 19534--19562 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
19524 GTCACTAAAA
19534 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19563 CTATGATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:20166 original size:16 final size:17
Alignment explanation
Indices: 20133--20166 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
20123 CCATATGCTT
*
20133 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
20150 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
20166 T
1 T
20167 AATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:34298 original size:20 final size:20
Alignment explanation
Indices: 34270--34308 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34260 CAAATAACCT
*
34270 CATAGATGTTCCAAAGGATA
1 CATAGATGTCCCAAAGGATA
* *
34290 CATATATGTCCCGAAGGAT
1 CATAGATGTCCCAAAGGAT
34309 CGCGTAAACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
CATAGATGTCCCAAAGGATA
Found at i:43121 original size:215 final size:216
Alignment explanation
Indices: 42865--43564 Score: 1086
Period size: 216 Copynumber: 3.2 Consensus size: 216
42855 ATTTAAGAAT
** * *
42865 TAAATTGAACAAATAAAAAAGTACAAATAAAAAATTAAATAAATTAAACAACATACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACATACATTGATGAG
*
42930 GAATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAA-TACTAAATTATA-
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
42993 TCCATTTAAAAAGTTCTGGGCCAATTAAAAAATAGAAATAAATAATAAGTATG-GATCAATTTCA
131 T-CATTTAAAAAGTTCTGGGCCAATTAAAAAATAGAAATAAATAATAAGTATGTG-TCAATTTCA
* *
43057 GTTGCAAATAAAATTTGGAGGAT
194 GATGCAAATAAAATTTGGAGGAC
* *
43080 TAAATTGAATATATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACATACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACATACATTGATGAG
* *
43145 GGATCAAATTGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTATTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* *
43210 TCATTTAAAAAGTTAC-GGGCCAATTAAAAAATAGAAATAAGTAATAAGCATGTGTCAATTTCAG
131 TCATTTAAAAAGTT-CTGGGCCAATTAAAAAATAGAAATAAATAATAAGTATGTGTCAATTTCAG
43274 ATGCAAATAAAATTTGGAGGAC
195 ATGCAAATAAAATTTGGAGGAC
** * *
43296 TAAATTGAATGAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAATACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACATACATTGATGAG
** * * * *
43361 GGATTGAATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAAAGTACTAAGTTAAAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
*
43426 TCATTTAAAAAGTTATGGGCC-ATTAAAAAAATAGAAATAAATAATAAGTATGTGTCAATTTCAG
131 TCATTTAAAAAGTTCTGGGCCAATT-AAAAAATAGAAATAAATAATAAGTATGTGTCAATTTCAG
* *
43490 ATGCTAAGAAAATTTGGAGGAC
195 ATGCAAATAAAATTTGGAGGAC
*
43512 TAAATTGAACAAATATGAAATTAAAAATAAAAATTTAAATAAATTAAACAACA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACA
43565 CAAAGGGATC
Statistics
Matches: 445, Mismatches: 34, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
215 111 0.25
216 331 0.74
217 3 0.01
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.29
Consensus pattern (216 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACATACATTGATGAG
GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
TCATTTAAAAAGTTCTGGGCCAATTAAAAAATAGAAATAAATAATAAGTATGTGTCAATTTCAGA
TGCAAATAAAATTTGGAGGAC
Found at i:43653 original size:2 final size:2
Alignment explanation
Indices: 43648--43757 Score: 98
Period size: 2 Copynumber: 53.5 Consensus size: 2
43638 AAAACAACTA
* *
43648 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT TT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * *
43691 AGT AT AT GT AT -T AT AT AT AT AA ACT AT AT AGT TT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT
* *
43733 AT AT AT -T AT GT AT AA ACT AT AT AT A
1 AT AT AT AT AT AT AT AT A-T AT AT AT A
43758 CCATGTATAA
Statistics
Matches: 87, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
1 2 0.02
2 80 0.92
3 5 0.06
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:43732 original size:35 final size:34
Alignment explanation
Indices: 43643--43757 Score: 126
Period size: 35 Copynumber: 3.3 Consensus size: 34
43633 AAATTAAAAC
43643 AACTA-ATATATATATATATATATATATATATATA
1 AACTATATATATATATATATATAT-TATATATATA
* * * *
43677 TACTTTATATATAAAGTATATGTATTATATATATA
1 AACTATATATATATA-TATATATATTATATATATA
* *
43712 AACTATATAGTTTATATATATATA-TATTATGTATA
1 AACTATATA-TATATATATATATATTA-TATATATA
43747 AACTATATATA
1 AACTATATATA
43758 CCATGTATAA
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
34 6 0.09
35 48 0.73
36 12 0.18
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (34 bp):
AACTATATATATATATATATATATTATATATATA
Found at i:43854 original size:24 final size:26
Alignment explanation
Indices: 43826--43899 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 26
43816 CTACATAGTT
43826 TATATATAAATTATATAGTTTAT-TA
1 TATATATAAATTATATAGTTTATATA
* *
43851 -ATATATAAACTATATAATTTATATA
1 TATATATAAATTATATAGTTTATATA
*
43876 TATATATATAGTGTATATAGTTTA
1 TATATATA-AAT-TATATAGTTTA
43900 AGGTTTAGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 20 0.50
25 2 0.05
26 7 0.17
27 1 0.03
28 10 0.25
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (26 bp):
TATATATAAATTATATAGTTTATATA
Found at i:43876 original size:20 final size:20
Alignment explanation
Indices: 43653--43877 Score: 106
Period size: 20 Copynumber: 10.8 Consensus size: 20
43643 AACTAATATA
* *
43653 TATATATATATATATATATA-
1 TATATA-ATTTATATATAAAC
* *
43673 TATATACTTTATATATAAAG
1 TATATAATTTATATATAAAC
*
43693 TATATGTATTATATATATAAAC
1 TATAT-AATT-TATATATAAAC
*
43715 TATATAGTTTATATAT--A-
1 TATATAATTTATATATAAAC
*
43732 TATAT-A-TTATGTATAAAC
1 TATATAATTTATATATAAAC
* *
43750 TATATATACCATGTATAAACTAAAATAC
1 --TATATA--AT-T-TATA-TATAA-AC
*
43778 TATATAATTTATATATGAAC
1 TATATAATTTATATATAAAC
* *
43798 TAT-TGAA-CTATATAGAAAC
1 TATAT-AATTTATATATAAAC
* * *
43817 TACATAGTTTATATATAAAT
1 TATATAATTTATATATAAAC
*
43837 TATATAGTTTATTAATATATAAAC
1 TATATA----ATTTATATATAAAC
43861 TATATAATTTATATATA
1 TATATAATTTATATATA
43878 TATATATAGT
Statistics
Matches: 153, Mismatches: 29, Indels: 46
0.67 0.13 0.20
Matches are distributed among these distances:
15 7 0.05
17 6 0.04
18 1 0.01
19 23 0.15
20 55 0.36
21 7 0.05
22 18 0.12
23 2 0.01
24 19 0.12
25 1 0.01
26 8 0.05
27 4 0.03
28 2 0.01
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (20 bp):
TATATAATTTATATATAAAC
Found at i:44098 original size:22 final size:22
Alignment explanation
Indices: 44009--44098 Score: 87
Period size: 22 Copynumber: 4.2 Consensus size: 22
43999 TAACTTATTC
* *
44009 TATATGTAAACTATATATACTA
1 TATATATAAACTATATAAACTA
* *
44031 TATAGT-T-TAC-ATATGAACTA
1 TATA-TATAAACTATATAAACTA
*
44051 TATGTATAAACTATATAAACTA
1 TATATATAAACTATATAAACTA
* *
44073 TATATATAAATTATGTAAACTA
1 TATATATAAACTATATAAACTA
44095 TATA
1 TATA
44099 GTTTACATAT
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
19 1 0.02
20 12 0.22
21 4 0.07
22 37 0.67
23 1 0.02
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (22 bp):
TATATATAAACTATATAAACTA
Found at i:44307 original size:18 final size:18
Alignment explanation
Indices: 44286--44320 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
44276 ATAGTTGATA
*
44286 TTTATATATGAACTATAG
1 TTTACATATGAACTATAG
44304 TTTACATATGAACTATA
1 TTTACATATGAACTATA
44321 TATATAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (18 bp):
TTTACATATGAACTATAG
Found at i:44323 original size:31 final size:32
Alignment explanation
Indices: 44288--44359 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 32
44278 AGTTGATATT
*
44288 TATATATGAAC-TATAGTTTACATATGAACTA
1 TATATATAAACATATAGTTTACATATGAACTA
*
44319 TATATATAAACTATATAGTTTACATATGACCTA
1 TATATATAAAC-ATATAGTTTACATATGAACTA
44352 TATATATA
1 TATATATA
44360 GTTTATTAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 10 0.27
33 27 0.73
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (32 bp):
TATATATAAACATATAGTTTACATATGAACTA
Found at i:44346 original size:51 final size:51
Alignment explanation
Indices: 44248--44353 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 51
44238 TTATAAACTA
* * *
44248 TATAGTTTACATATAAACAATATATACTATAGTTGATATTTATATATGAAC
1 TATAGTTTACATATAAACAATATATACTAAACTTGATATTTACATATGAAC
* * *
44299 TATAGTTTACATATGAACTATATATA-TAAACTAT-ATAGTTTACATATGACC
1 TATAGTTTACATATAAACAATATATACTAAACT-TGATA-TTTACATATGAAC
44350 TATA
1 TATA
44354 TATATAGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
50 7 0.15
51 40 0.85
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (51 bp):
TATAGTTTACATATAAACAATATATACTAAACTTGATATTTACATATGAAC
Found at i:44376 original size:24 final size:24
Alignment explanation
Indices: 44330--44379 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
44320 ATATATAAAC
*
44330 TATATAGTTTACATATGACCTATA
1 TATATAGTTTACATATGAACTATA
*
44354 TATATAGTTTA-TTAGTGAACTATA
1 TATATAGTTTACATA-TGAACTATA
44378 TA
1 TA
44380 AACTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (24 bp):
TATATAGTTTACATATGAACTATA
Found at i:44392 original size:2 final size:2
Alignment explanation
Indices: 44387--44623 Score: 62
Period size: 2 Copynumber: 113.5 Consensus size: 2
44377 ATAAACTATT
* * *
44387 TA TA TA -A TA TA TA CTA TA TA TA TA AA CTA TA GTT TA TA TT TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA -TA TA TA TA TA
* * *
44429 TA TA CTA CA TA CTA TA GTT TA TA TT TA TA T- TA TA TA T- TA TA
1 TA TA -TA TA TA -TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
44470 TA TA TA TA AA T- TA TG TA TA CTA TA TA GTA TA -A TT TA CA TA TGA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA T-A
* * *
44513 -A CTA TA TA TA AA AA TCA TA TA AA CTA TA TA CTA TA GT- TGA TA
1 TA -TA TA TA TA TA TA T-A TA TA TA -TA TA TA -TA TA -TA T-A TA
* * *
44555 TT TA TA TA CTA TA TA -A AA TA -A TT TA TA CTA TA GTA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA
* *
44596 AA CTA TA TA -A TA TA TA TA AA CTA TA TA T
1 TA -TA TA TA TA TA TA TA TA TA -TA TA TA T
44624 TATGTAGTTC
Statistics
Matches: 172, Mismatches: 33, Indels: 60
0.65 0.12 0.23
Matches are distributed among these distances:
1 10 0.06
2 132 0.77
3 30 0.17
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:44417 original size:18 final size:18
Alignment explanation
Indices: 44375--44623 Score: 80
Period size: 18 Copynumber: 13.8 Consensus size: 18
44365 TTAGTGAACT
* *
44375 ATATAAACTATTTATATA
1 ATATATACTATATATATA
44393 ATATATACTATATATATA
1 ATATATACTATATATATA
*
44411 A-ACTATAGT-T-TATAT-
1 ATA-TATACTATATATATA
* *
44426 TTATATACTACATACTATA
1 ATATATACTATATA-TATA
* * *
44445 GTTTATATTTATATTATATA
1 ATATATA-CTATA-TATATA
* * *
44465 TTATATA-TATATAAATT
1 ATATATACTATATATATA
*
44482 ATGTATACTATATAGTATA
1 ATATATACTATATA-TATA
44501 AT-T-TAC-ATATGA-ACT-
1 ATATATACTATAT-ATA-TA
* *
44516 ATATATA-AAAATCATATAA
1 ATATATACTATAT-ATAT-A
44535 ACTATATACTATAGT-TGATA
1 A-TATATACTATA-TAT-ATA
* *
44555 TTTATATACTATATAAAATA
1 -ATATATACTATAT-ATATA
*
44575 ATTTATACTATAGTATAT-
1 ATATATACTATA-TATATA
44593 ATA-A-ACTATATA-ATA
1 ATATATACTATATATATA
*
44608 TATATAAACTATATAT
1 -ATATATACTATATAT
44624 TATGTAGTTC
Statistics
Matches: 172, Mismatches: 28, Indels: 61
0.66 0.11 0.23
Matches are distributed among these distances:
14 2 0.01
15 10 0.06
16 21 0.12
17 26 0.15
18 47 0.27
19 24 0.14
20 35 0.20
21 6 0.03
22 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (18 bp):
ATATATACTATATATATA
Found at i:44417 original size:20 final size:20
Alignment explanation
Indices: 44315--44622 Score: 68
Period size: 20 Copynumber: 15.1 Consensus size: 20
44305 TTACATATGA
44315 ACTATATATATAAACTATAT
1 ACTATATATATAAACTATAT
* * * * *
44335 AGTTTACATATGACCTATAT
1 ACTATATATATAAACTATAT
*
44355 A-TATAGTTTATTAGTGAACTATAT
1 ACTATA---TA-TA-TAAACTATAT
*
44379 AAACTATTTATAT-AA-TATAT
1 --ACTATATATATAAACTATAT
44399 ACTATATATATAAACTATAGT
1 ACTATATATATAAACTATA-T
* * * *
44420 -TTATATTTATATACTACAT
1 ACTATATATATAAACTATAT
* **
44439 ACTATAGTTTAT-ATTTATATT
1 ACTATA-TATATAAACTATA-T
* *
44460 A-TATATTATATATA-TATAA
1 ACTATA-TATATAAACTATAT
* * *
44479 ATTATGTATACTATA-TAGTAT
1 ACTATATATA-TAAACTA-TAT
* * * *
44500 AATTTACATATGAACTATAT
1 ACTATATATATAAACTATAT
*
44520 A-TAAAAATCATATAAACTATAT
1 ACT--ATAT-ATATAAACTATAT
**
44542 ACTATAGT-TGAT-ATTTATAT
1 ACTATA-TAT-ATAAACTATAT
* **
44562 ACTATATAAAATAATTTATACT
1 ACTATAT-ATATAAACTATA-T
44584 A-TAGTATATATAAACTATAT
1 ACTA-TATATATAAACTATAT
44604 A--ATATATATAAACTATAT
1 ACTATATATATAAACTATAT
44622 A
1 A
44623 TTATGTAGTT
Statistics
Matches: 215, Mismatches: 43, Indels: 62
0.67 0.13 0.19
Matches are distributed among these distances:
18 27 0.13
19 14 0.07
20 90 0.42
21 43 0.20
22 21 0.10
23 5 0.02
24 11 0.05
26 1 0.00
27 3 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (20 bp):
ACTATATATATAAACTATAT
Found at i:44424 original size:27 final size:27
Alignment explanation
Indices: 44394--44458 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
44384 ATTTATATAA
*
44394 TATATACTATATA-TATAAACTATAGTT
1 TATAT-CTATATACTACAAACTATAGTT
* *
44421 TATATTTATATACTACATACTATAGTT
1 TATATCTATATACTACAAACTATAGTT
*
44448 TATATTTATAT
1 TATATCTATAT
44459 TATATATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 6 0.18
27 28 0.82
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (27 bp):
TATATCTATATACTACAAACTATAGTT
Found at i:44469 original size:25 final size:26
Alignment explanation
Indices: 44401--44458 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 26
44391 TAATATATAC
* *
44401 TATATATATAAACTATAGTTTATATT
1 TATATATACATACTATAGTTTATATT
44427 TATATACTACATACTATAGTTTATATT
1 TATATA-TACATACTATAGTTTATATT
44454 TATAT
1 TATAT
44459 TATATATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 6 0.21
27 23 0.79
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (26 bp):
TATATATACATACTATAGTTTATATT
Found at i:44482 original size:22 final size:22
Alignment explanation
Indices: 44448--44613 Score: 70
Period size: 22 Copynumber: 7.2 Consensus size: 22
44438 TACTATAGTT
* *
44448 TATATTTATATTATATATTATA
1 TATATATAAATTATATATTATA
*
44470 TATATATAAATTATGTA-TACTA
1 TATATATAAATTATATATTA-TA
* * *
44492 TATAGTATAATTTACATATGAACTA
1 TATA-TATAAATTATATAT-TA-TA
* * *
44517 TATATAAAAATCATATA-AACTA
1 TATATATAAATTATATATTA-TA
*
44539 TATACTAT-AGTTGATAT-TTATA
1 TATA-TATAAATT-ATATATTATA
* *
44561 TACTATATAAAATAATTTATACTATA
1 TA-TATAT-AAAT--TATATATTATA
* *
44587 GTATATATAAACTATATAATATA
1 -TATATATAAATTATATATTATA
44610 TATA
1 TATA
44614 AACTATATAT
Statistics
Matches: 109, Mismatches: 21, Indels: 28
0.69 0.13 0.18
Matches are distributed among these distances:
21 2 0.02
22 42 0.39
23 28 0.26
24 11 0.10
25 14 0.13
26 10 0.09
27 2 0.02
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (22 bp):
TATATATAAATTATATATTATA
Found at i:44602 original size:9 final size:9
Alignment explanation
Indices: 44590--44622 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
44580 TACTATAGTA
44590 TATATAAAC
1 TATATAAAC
44599 TATATAATA-
1 TATATAA-AC
44608 TATATAAAC
1 TATATAAAC
44617 TATATA
1 TATATA
44623 TTATGTAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.05
9 20 0.91
10 1 0.05
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (9 bp):
TATATAAAC
Found at i:44662 original size:18 final size:18
Alignment explanation
Indices: 44639--44785 Score: 99
Period size: 18 Copynumber: 8.3 Consensus size: 18
44629 AGTTCATTAG
*
44639 TATATATAAACTATATGT
1 TATATATAAACTATATAT
*
44657 TATATATAAAACTATACAT
1 TATATAT-AAACTATATAT
* *
44676 TATATAGT---TTAT-TAG
1 TATATA-TAAACTATATAT
* * *
44691 CATATATAAACTACATAA
1 TATATATAAACTATATAT
**
44709 TATATATAAACTATATGG
1 TATATATAAACTATATAT
*
44727 TATATATAAACTATACAT
1 TATATATAAACTATATAT
** *
44745 TATATAT-ATTTCAT-TAG
1 TATATATAAACT-ATATAT
*
44762 TATATATAAATTATATAT
1 TATATATAAACTATATAT
44780 TATATA
1 TATATA
44786 GTTCATTAGT
Statistics
Matches: 98, Mismatches: 22, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
14 1 0.01
15 6 0.06
16 3 0.03
17 14 0.14
18 58 0.59
19 15 0.15
20 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (18 bp):
TATATATAAACTATATAT
Found at i:44696 original size:52 final size:51
Alignment explanation
Indices: 44589--44977 Score: 239
Period size: 52 Copynumber: 7.3 Consensus size: 51
44579 ATACTATAGT
* * *
44589 ATATATAAACTATATAATATATATAAACTATATATTATGTAGTTCATTAGT
1 ATATATAAACTATATAATATATATAAACTATACATTATATAGTTCATTAGC
** *
44640 ATATATAAACTATATGTTATATATAAAACTATACATTATATAGTTTATTAGC
1 ATATATAAACTATATAATATATAT-AAACTATACATTATATAGTTCATTAGC
* *** **
44692 ATATATAAACTACATAATATATATAAACTATATGGTATATA-TAAACTATA-C
1 ATATATAAACTATATAATATATATAAACTATACATTATATAGTTCA-T-TAGC
* * * * * *
44743 ATTATATATA-TTTCATTAGTATATATAAATTATATATTATATAGTTCATTAGT
1 A-TATATAAACTAT-A-TAATATATATAAACTATACATTATATAGTTCATTAGC
* * * **
44796 ATATATAACCTATATAATATATGGTATATACAAACTATATATTATATAGATCATTAAT
1 ATATATAAACTATAT-A-ATA---TATAT--AAACTATACATTATATAGTTCATTAGC
* * *
44854 ATATATAACCTATATAGTATATGGTATATACAAACTATATA-T-TATAGTTCATTAGT
1 ATATATAAACTATATA--ATA---TATAT--AAACTATACATTATATAGTTCATTAGC
* ** * ** * *
44910 ATATATAAATTATATAGCATATATAAACTATATATTGGAAAGTTCATTAGT
1 ATATATAAACTATATAATATATATAAACTATACATTATATAGTTCATTAGC
*
44961 ATATTATAACCTATATA
1 ATA-TATAAACTATATA
44978 TTAATTTATT
Statistics
Matches: 277, Mismatches: 41, Indels: 39
0.78 0.11 0.11
Matches are distributed among these distances:
49 10 0.04
50 3 0.01
51 61 0.22
52 75 0.27
53 29 0.10
54 3 0.01
56 31 0.11
57 2 0.01
58 63 0.23
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (51 bp):
ATATATAAACTATATAATATATATAAACTATACATTATATAGTTCATTAGC
Found at i:44713 original size:33 final size:32
Alignment explanation
Indices: 44657--44817 Score: 133
Period size: 33 Copynumber: 4.7 Consensus size: 32
44647 AACTATATGT
* *
44657 TATATATAAAACTATACATTATATAGTTTATTAG
1 TATATAT-AAACTATATAATATATA-TTTATTAG
* * * *
44691 CATATATAAACTACATAATATATATAAACTATATGG
1 TATATATAAACTATATAATATATAT---TTAT-TAG
*
44727 TATATATAAACTATACATTATATATATTTCATTAG
1 TATATATAAACTAT--ATAATATATATTT-ATTAG
* * *
44762 TATATATAAATTATATATTATATAGTTCATTAG
1 TATATATAAACTATATAATATATA-TTTATTAG
*
44795 TATATATAACCTATATAATATAT
1 TATATATAAACTATATAATATAT
44818 GGTATATACA
Statistics
Matches: 101, Mismatches: 18, Indels: 17
0.74 0.13 0.12
Matches are distributed among these distances:
32 1 0.01
33 47 0.47
34 8 0.08
35 19 0.19
36 16 0.16
38 10 0.10
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (32 bp):
TATATATAAACTATATAATATATATTTATTAG
Found at i:44900 original size:56 final size:58
Alignment explanation
Indices: 44761--44977 Score: 272
Period size: 58 Copynumber: 3.9 Consensus size: 58
44751 TATTTCATTA
* * *
44761 GTATATATAAATTATATATTATATAGTTCATTAGTATATATAACCTATATAATATATG
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
* *
44819 GTATATACAAACTATATATTATATAGATCATTAATATATATAACCTATATAGTATATG
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
44877 GTATATACAAACTATATA-T-TATAGTTCATTAGTATATATAA---AT-TA-TATA--
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
* * ** *
44926 GCATATATAAACTATATATTGGAAAGTTCATTAGTATATTATAACCTATATA
1 GTATATACAAACTATATATTATATAGTTCATTAGTATA-TATAACCTATATA
44978 TTAATTTATT
Statistics
Matches: 141, Mismatches: 11, Indels: 16
0.84 0.07 0.10
Matches are distributed among these distances:
49 16 0.11
50 1 0.01
51 19 0.13
52 7 0.05
53 2 0.01
55 2 0.01
56 22 0.16
57 1 0.01
58 71 0.50
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (58 bp):
GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
Found at i:45125 original size:60 final size:60
Alignment explanation
Indices: 45053--45165 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
45043 AACAAATTTT
45053 AAATATGAAGCTTAAATTAATAAACTAT-AAT-ATTAAATTTGGACTAAATTGAAAAAGTTG
1 AAATATGAAGCTTAAATTAATAAA-T-TGAATCATTAAATTTGGACTAAATTGAAAAAGTTG
* * *
45113 AAATATGAAGCTTAAATTAGTATATTGCATCATTAAATTTGGACTAAATTGAA
1 AAATATGAAGCTTAAATTAATAAATTGAATCATTAAATTTGGACTAAATTGAA
45166 CAAATTTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
58 1 0.02
59 3 0.06
60 44 0.92
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (60 bp):
AAATATGAAGCTTAAATTAATAAATTGAATCATTAAATTTGGACTAAATTGAAAAAGTTG
Found at i:45621 original size:113 final size:119
Alignment explanation
Indices: 45393--45725 Score: 434
Period size: 113 Copynumber: 2.8 Consensus size: 119
45383 TTTTCATTTA
* * * *
45393 TTCATCCAAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAATACCAAAAC-CAAAACATTTT
1 TTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAACACAAACCA-TTT
*
45457 CGTGTTTTTTCGATCAAACACCCAAATATTCATCCGTG-T-TC--TTCAT--TTG
65 CATGTTTTTTCGATCAAACACCCAAATATTCATCCGTGTTATCTATTCATCATTG
45506 TTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAACACAAACCATTTC
1 TTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAACACAAACCATTTC
* * *
45571 ATGTTTTTTTCGATCAAACACCCAAATTTTCATCGGTGTTCATCTATGTTCTTCATTTG
66 ATG-TTTTTTCGATCAAACACCCAAATATTCATCCGTGTT-ATCTA--TTCATCA-TTG
* *
45630 TTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTT-AAAAACA-CTGAACACAATCCATTTC
1 TTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAACACAAACCATTTC
*
45693 TTGTTTTTTCGATCAAACACCCACAA-ATTCATC
66 ATGTTTTTTCGATCAAACACCCA-AATATTCATC
45726 TATTGTTCAT
Statistics
Matches: 195, Mismatches: 12, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
113 56 0.29
114 38 0.19
115 1 0.01
117 2 0.01
121 30 0.15
122 20 0.10
123 7 0.04
124 41 0.21
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.35
Consensus pattern (119 bp):
TTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAACACAAACCATTTC
ATGTTTTTTCGATCAAACACCCAAATATTCATCCGTGTTATCTATTCATCATTG
Found at i:45904 original size:6 final size:6
Alignment explanation
Indices: 45889--45966 Score: 54
Period size: 6 Copynumber: 13.5 Consensus size: 6
45879 CCTTGACCTT
* * * *
45889 AACCCT AACCTA AACCCA AA--CA AACTCA AACCCG AACCCA AACCC-
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* ** * *
45934 AATCTG AACCCA AACCCA AACTCG AACCCA AAC
1 AACCCA AACCCA AACCCA AACCCA AACCCA AAC
45967 TATTCGAAAC
Statistics
Matches: 54, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
4 4 0.07
5 3 0.06
6 47 0.87
ACGTcount: A:0.46, C:0.42, G:0.04, T:0.08
Consensus pattern (6 bp):
AACCCA
Found at i:45944 original size:17 final size:18
Alignment explanation
Indices: 45909--45966 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
45899 TAAACCCAAA
* *
45909 CAAACTCAAACCCGAACC
1 CAAACCCAAACTCGAACC
*
45927 CAAACCCAATCT-GAACC
1 CAAACCCAAACTCGAACC
45944 CAAACCCAAACTCGAACC
1 CAAACCCAAACTCGAACC
45962 CAAAC
1 CAAAC
45967 TATTCGAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 16 0.46
18 19 0.54
ACGTcount: A:0.45, C:0.43, G:0.05, T:0.07
Consensus pattern (18 bp):
CAAACCCAAACTCGAACC
Found at i:46240 original size:31 final size:31
Alignment explanation
Indices: 46202--46609 Score: 591
Period size: 31 Copynumber: 13.5 Consensus size: 31
46192 ATAGATATAG
*
46202 ACTGGTTTATTGTTGTTGATGTAAATGATAT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
* *
46233 ATTGGTTTATTGTTGTTGATGTAAATGATAT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
46264 ACTGGTTTATTGTTGTTGATGTAAATGATGT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
*
46295 ACTGGTTTATTGATGTTGATGTAAATGATGT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
* *
46326 ATTGGTTTATTGTTGTTGATGTAGATGATGT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
* *
46357 ACTGGTTTATTGATGTTGATGTAGATGATGT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
*
46388 ATTGGTTTATTGTTGTTGATGTAAATGATGT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
* *
46419 ACTGGTTTATTGATGTTGATGTAAATGATAT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
* * *
46450 ACTGGTTTATTGCTGTAGATGTAAATGATAT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
*
46481 ACTGGTTTATTGCTGTTGATGTAAATGATGT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
*
46512 ACTGGTTTA------TTGCTGT---TGATGT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
46534 ACTGGTTTATTGTTGTTGATGTAAATGATGT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
* *
46565 ACTGGTTTATTGATGTTGATGTAAATGATAT
1 ACTGGTTTATTGTTGTTGATGTAAATGATGT
46596 ACTGGTTTATTGTT
1 ACTGGTTTATTGTT
46610 ATAATGTAAA
Statistics
Matches: 344, Mismatches: 24, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
22 15 0.04
25 6 0.02
28 6 0.02
31 317 0.92
ACGTcount: A:0.24, C:0.03, G:0.25, T:0.48
Consensus pattern (31 bp):
ACTGGTTTATTGTTGTTGATGTAAATGATGT
Found at i:46534 original size:22 final size:22
Alignment explanation
Indices: 46506--46556 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
46496 TTGATGTAAA
46506 TGATGTACTGGTTTATTGCTGT
1 TGATGTACTGGTTTATTGCTGT
*
46528 TGATGTACTGGTTTATTGTTGT
1 TGATGTACTGGTTTATTGCTGT
46550 TGATGTA
1 TGATGTA
46557 AATGATGTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.16, C:0.06, G:0.27, T:0.51
Consensus pattern (22 bp):
TGATGTACTGGTTTATTGCTGT
Found at i:46590 original size:84 final size:84
Alignment explanation
Indices: 46444--46607 Score: 274
Period size: 84 Copynumber: 2.0 Consensus size: 84
46434 TTGATGTAAA
*
46444 TGATATACTGGTTTATTGCTGTAGATGTAAATGATATACTGGTTTATTGCTGTTGATGTAAATGA
1 TGATATACTGGTTTATTGCTGTAGATGTAAATGATATACTGGTTTATTGATGTTGATGTAAATGA
*
46509 TGTACTGGTTTATTGCTGT
66 TATACTGGTTTATTGCTGT
* * * *
46528 TGATGTACTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGATGTTGATGTAAATGA
1 TGATATACTGGTTTATTGCTGTAGATGTAAATGATATACTGGTTTATTGATGTTGATGTAAATGA
46593 TATACTGGTTTATTG
66 TATACTGGTTTATTG
46608 TTATAATGTA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
84 74 1.00
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.46
Consensus pattern (84 bp):
TGATATACTGGTTTATTGCTGTAGATGTAAATGATATACTGGTTTATTGATGTTGATGTAAATGA
TATACTGGTTTATTGCTGT
Found at i:46648 original size:146 final size:146
Alignment explanation
Indices: 46382--46661 Score: 408
Period size: 146 Copynumber: 1.9 Consensus size: 146
46372 TTGATGTAGA
*
46382 TGATGTATTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGATGTTGATGTAAATGA
1 TGATGTACTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGATGTTGATGTAAATGA
* * * * *
46447 TATACTGGTTTATTGCTGTAGATGTAAATGATATACTGGTTTATTGCTGTTGATGTAAATGATGT
66 TATACTGGTTTATTGCTATAGATGTAAATCATATACTGGTTTATTGCAGTGGATGTAAATGATAT
46512 ACTGGTTTATTGCTGT
131 ACTGGTTTATTGCTGT
46528 TGATGTACTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGATGTTGATGTAAATGA
1 TGATGTACTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGATGTTGATGTAAATGA
* *
46593 TATACTGGTTTATTGTTATA-ATGTAAA-CA-A-ACCATGGTTTTTTTGCAAAG-GGATGTAAAT
66 TATACTGGTTTATTGCTATAGATGTAAATCATATA-C-TGG-TTTATTGC--AGTGGATGTAAAT
46653 GATATACTG
126 GATATACTG
46662 TCTGAAGCAA
Statistics
Matches: 121, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
142 1 0.01
143 2 0.02
144 4 0.03
145 14 0.12
146 99 0.82
147 1 0.01
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (146 bp):
TGATGTACTGGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGATGTTGATGTAAATGA
TATACTGGTTTATTGCTATAGATGTAAATCATATACTGGTTTATTGCAGTGGATGTAAATGATAT
ACTGGTTTATTGCTGT
Found at i:48975 original size:20 final size:20
Alignment explanation
Indices: 48946--48984 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
48936 TACTTTATTC
* *
48946 TGTTTTATATTGTTTGCTTA
1 TGTTTAATATTGCTTGCTTA
48966 TGTTTAATATTGCTTGCTT
1 TGTTTAATATTGCTTGCTT
48985 CTACTTGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (20 bp):
TGTTTAATATTGCTTGCTTA
Found at i:49857 original size:17 final size:17
Alignment explanation
Indices: 49830--49921 Score: 64
Period size: 17 Copynumber: 5.4 Consensus size: 17
49820 AAATTTTAAA
49830 AATTAATCATATTAATTT
1 AATT-ATCATATTAATTT
*
49848 AATTATCATAATAATTT
1 AATTATCATATTAATTT
* * * *
49865 -ATGATAAAATTTCAA--A
1 AATTATCATA-TT-AATTT
*
49881 AAGTAATCATATTAATTT
1 AA-TTATCATATTAATTT
*
49899 AATTATCATAATAATTT
1 AATTATCATATTAATTT
49916 AATTAT
1 AATTAT
49922 TATAAGTTTA
Statistics
Matches: 56, Mismatches: 12, Indels: 13
0.69 0.15 0.16
Matches are distributed among these distances:
16 8 0.14
17 35 0.62
18 13 0.23
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (17 bp):
AATTATCATATTAATTT
Found at i:49875 original size:51 final size:51
Alignment explanation
Indices: 49820--49916 Score: 176
Period size: 51 Copynumber: 1.9 Consensus size: 51
49810 ATATAAAACT
* *
49820 AAATTTTAAAAATTAATCATATTAATTTAATTATCATAATAATTTATGATA
1 AAATTTCAAAAAGTAATCATATTAATTTAATTATCATAATAATTTATGATA
49871 AAATTTCAAAAAGTAATCATATTAATTTAATTATCATAATAATTTA
1 AAATTTCAAAAAGTAATCATATTAATTTAATTATCATAATAATTTA
49917 ATTATTATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.43
Consensus pattern (51 bp):
AAATTTCAAAAAGTAATCATATTAATTTAATTATCATAATAATTTATGATA
Found at i:49926 original size:17 final size:17
Alignment explanation
Indices: 49886--49926 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
49876 TCAAAAAGTA
*
49886 ATCATATTAATTTAATT
1 ATCATAATAATTTAATT
49903 ATCATAATAATTTAATT
1 ATCATAATAATTTAATT
*
49920 ATTATAA
1 ATCATAA
49927 GTTTATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
ATCATAATAATTTAATT
Found at i:51363 original size:29 final size:29
Alignment explanation
Indices: 51323--51378 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
51313 TGATGATTAT
* *
51323 AAAATAATAATAAAAATATCAAACTGAAA
1 AAAATAACAATAAAAATACCAAACTGAAA
* *
51352 AAAATAACAATATATATACCAAACTGA
1 AAAATAACAATAAAAATACCAAACTGA
51379 GAATTCGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21
Consensus pattern (29 bp):
AAAATAACAATAAAAATACCAAACTGAAA
Found at i:58965 original size:3 final size:3
Alignment explanation
Indices: 58959--58992 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
58949 TACAACAAAT
58959 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
58993 TTAAACATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:59826 original size:2 final size:2
Alignment explanation
Indices: 59805--59874 Score: 113
Period size: 2 Copynumber: 35.0 Consensus size: 2
59795 ATCATTTACA
* * *
59805 AT AT AC AT AC AT AC 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
59847 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
59875 CCATATTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:63233 original size:17 final size:18
Alignment explanation
Indices: 63208--63256 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
63198 ATGTATAATT
*
63208 TAAAAAAAAT-AATTGAA
1 TAAACAAAATAAATTGAA
*
63225 TAAACAAAATAGAATTGTA
1 TAAACAAAATA-AATTGAA
63244 TAAAC-AAATAAAT
1 TAAACAAAATAAAT
63257 GACAATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 12 0.43
18 5 0.18
19 11 0.39
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.24
Consensus pattern (18 bp):
TAAACAAAATAAATTGAA
Done.