Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold76
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: 1973630
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 106294 characters in sequence are not A, C, G, or T
File 1 of 5
Found at i:90 original size:18 final size:20
Alignment explanation
Indices: 67--110 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
57 TTTCTTCTTC
67 TTCTTCTCCTTCCTT-TT-T
1 TTCTTCTCCTTCCTTCTTAT
*
85 TTCTTCTGCTTCCTTCTTAT
1 TTCTTCTCCTTCCTTCTTAT
105 TTCTTC
1 TTCTTC
111 CGTTTCTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.61
19 2 0.09
20 7 0.30
ACGTcount: A:0.02, C:0.32, G:0.02, T:0.64
Consensus pattern (20 bp):
TTCTTCTCCTTCCTTCTTAT
Found at i:228 original size:27 final size:27
Alignment explanation
Indices: 166--243 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
156 GAAAAATCAG
166 ACCATTGGCGCCTCTCA-ATATGGCACC
1 ACCATTGGCGCCTCTCAGATA-GGCACC
** * *
193 AATAATGGCGCCTCCCAGATAGGCACC
1 ACCATTGGCGCCTCTCAGATAGGCACC
* *
220 ACCATTGGCTCCTCTGAGATAGGC
1 ACCATTGGCGCCTCTCAGATAGGC
244 GCCAATACTA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
27 37 0.93
28 3 0.08
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.21
Consensus pattern (27 bp):
ACCATTGGCGCCTCTCAGATAGGCACC
Found at i:320 original size:24 final size:25
Alignment explanation
Indices: 283--332 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
273 ACTGACCCGG
283 AAAAATAAAAAATAATATTTTATTC
1 AAAAATAAAAAATAATATTTTATTC
* * *
308 AAAAA-AAATAATATTTTTTTATTC
1 AAAAATAAAAAATAATATTTTATTC
332 A
1 A
333 TTGGCGCCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAAATAAAAAATAATATTTTATTC
Found at i:1884 original size:24 final size:25
Alignment explanation
Indices: 1847--1896 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1837 AAAAATCAAT
1847 AAAAATAAAAAATAATATTTTATTC
1 AAAAATAAAAAATAATATTTTATTC
* * *
1872 AAAAA-AAATAATATTTTTTTATTC
1 AAAAATAAAAAATAATATTTTATTC
1896 A
1 A
1897 TTGGCGCCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAAATAAAAAATAATATTTTATTC
Found at i:5278 original size:24 final size:25
Alignment explanation
Indices: 5230--5278 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
5220 TACACTAACA
*
5230 CTAAATAAAAAATTTAATCTATATT
1 CTAAATAAAAAATTTAATATATATT
* *
5255 CTAAA-AAAAACTTTAATATCTATT
1 CTAAATAAAAAATTTAATATATATT
5279 TCATATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (25 bp):
CTAAATAAAAAATTTAATATATATT
Found at i:6336 original size:40 final size:41
Alignment explanation
Indices: 6269--6352 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 41
6259 GAAATACTCC
6269 TAAATTAATCTTATTAATATAATATAATGTTTTATTTTGTA
1 TAAATTAATCTTATTAATATAATATAATGTTTTATTTTGTA
6310 TAAATTAATCTTA-TAATATAATATAATGTTTTATTTTGTA
1 TAAATTAATCTTATTAATATAATATAATGTTTTATTTTGTA
6350 TAA
1 TAA
6353 TTTTGGATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 30 0.70
41 13 0.30
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (41 bp):
TAAATTAATCTTATTAATATAATATAATGTTTTATTTTGTA
Found at i:9014 original size:14 final size:14
Alignment explanation
Indices: 9004--9042 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
8994 TACTATATTT
9004 TATTTATTATATCA
1 TATTTATTATATCA
*
9018 TATTTATCATATCA
1 TATTTATTATATCA
9032 TATTTATTATA
1 TATTTATTATA
9043 ATTGGAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTTATTATATCA
Found at i:12898 original size:42 final size:43
Alignment explanation
Indices: 12746--12888 Score: 234
Period size: 43 Copynumber: 3.3 Consensus size: 43
12736 GCGCCGAAAA
* *
12746 AAACACCGCTAAAGACCAAGACCTCTAGCGGCGCTTTTCCTAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCTAC
*
12789 AAACGCCGCTAAAGACCAAGACCTTTAGCGGTGCTTTTCCTAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCTAC
* *
12832 AAAAGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCTAC
12874 AAACGCCGCTAAAGA
1 AAACGCCGCTAAAGA
12889 TCACAACCTT
Statistics
Matches: 93, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
42 21 0.23
43 72 0.77
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.18
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCTAC
Found at i:13102 original size:147 final size:147
Alignment explanation
Indices: 12899--13180 Score: 530
Period size: 147 Copynumber: 1.9 Consensus size: 147
12889 TCACAACCTT
12899 GCGCTTCTCGCAAAAACGCCACTAAAAACATAACCTTTAACAAAATTTATTTTAATCAAATACTA
1 GCGCTTCTCGCAAAAACGCCACTAAAAACATAACCTTTAACAAAATTTATTTTAATCAAATACTA
* *
12964 TCTTTAGCGGCGCTTCTCGCAAAAACGCCACTAAAAACATAACCTTTAACAAAATTTATTTTAAT
66 TCTTTAGCGGCGCTTCTCGCAAAAACGCCACTAAAAACATAACCCTTAA-AAAAATTATTTTAAT
13029 CAAATACTATCTTTAGCG
130 CAAATACTATCTTTAGCG
13047 GCGCTTCTCGCAAAAACGCCACTAAAAA-ATAACCTTTAACAAAATTTATTTTAATCAAATACTA
1 GCGCTTCTCGCAAAAACGCCACTAAAAACATAACCTTTAACAAAATTTATTTTAATCAAATACTA
13111 TCTTTAGCGGCGCTTCTCGCAAAAACGCCACTAAAAACATAACCCTTAAAAAAATTATTTTAATC
66 TCTTTAGCGGCGCTTCTCGCAAAAACGCCACTAAAAACATAACCCTTAAAAAAATTATTTTAATC
13176 AAATA
131 AAATA
13181 ATATTTATTT
Statistics
Matches: 132, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
146 20 0.15
147 84 0.64
148 28 0.21
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.29
Consensus pattern (147 bp):
GCGCTTCTCGCAAAAACGCCACTAAAAACATAACCTTTAACAAAATTTATTTTAATCAAATACTA
TCTTTAGCGGCGCTTCTCGCAAAAACGCCACTAAAAACATAACCCTTAAAAAAATTATTTTAATC
AAATACTATCTTTAGCG
Found at i:13121 original size:73 final size:74
Alignment explanation
Indices: 12899--13180 Score: 532
Period size: 74 Copynumber: 3.8 Consensus size: 74
12889 TCACAACCTT
12899 GCGCTTCTCGCAAAAACGCCACTAAAAACATAACCTTTAACAAAATTTATTTTAATCAAATACTA
1 GCGCTTCTCGCAAAAACGCCACTAAAAACATAACCTTTAACAAAATTTATTTTAATCAAATACTA
12964 TCTTTAGCG
66 TCTTTAGCG
12973 GCGCTTCTCGCAAAAACGCCACTAAAAACATAACCTTTAACAAAATTTATTTTAATCAAATACTA
1 GCGCTTCTCGCAAAAACGCCACTAAAAACATAACCTTTAACAAAATTTATTTTAATCAAATACTA
13038 TCTTTAGCG
66 TCTTTAGCG
13047 GCGCTTCTCGCAAAAACGCCACTAAAAA-ATAACCTTTAACAAAATTTATTTTAATCAAATACTA
1 GCGCTTCTCGCAAAAACGCCACTAAAAACATAACCTTTAACAAAATTTATTTTAATCAAATACTA
13111 TCTTTAGCG
66 TCTTTAGCG
* *
13120 GCGCTTCTCGCAAAAACGCCACTAAAAACATAACCCTTAA-AAAAATTATTTTAATCAAATA
1 GCGCTTCTCGCAAAAACGCCACTAAAAACATAACCTTTAACAAAATTTATTTTAATCAAATA
13181 ATATTTATTT
Statistics
Matches: 205, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
73 93 0.45
74 112 0.55
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.29
Consensus pattern (74 bp):
GCGCTTCTCGCAAAAACGCCACTAAAAACATAACCTTTAACAAAATTTATTTTAATCAAATACTA
TCTTTAGCG
Found at i:21423 original size:41 final size:41
Alignment explanation
Indices: 21363--21600 Score: 379
Period size: 41 Copynumber: 5.8 Consensus size: 41
21353 AGATTTTATT
* * *
21363 ATTAGTGGCGTTTTTTCAAAAACGCCGCTAAAGGCACGAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCACGAGC
* * *
21404 ATTAGCGGCACTTTATCAAAAACGCCGCTAAAGGCATGAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCACGAGC
* *
21445 ATTAGGGGCGCTTTCTCAAAAACACCGCTAAAGGCACGAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCACGAGC
21486 ATTAGCGGCGC-TTCTTCAAAAACGCCGCTAAAGGCACGAGC
1 ATTAGCGGCGCTTTC-TCAAAAACGCCGCTAAAGGCACGAGC
*
21527 ATTAGCGACGCTTTCTCAAAAACGCCGCTAAAGGCACGAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCACGAGC
21568 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAG
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAG
21601 CCCCGAAAAC
Statistics
Matches: 181, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
40 3 0.02
41 175 0.97
42 3 0.02
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.19
Consensus pattern (41 bp):
ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCACGAGC
Found at i:21706 original size:39 final size:40
Alignment explanation
Indices: 21639--21774 Score: 143
Period size: 40 Copynumber: 3.4 Consensus size: 40
21629 CAGCTTTCTT
* * * * *
21639 TTTTTTGCGGCGCTTCTTGGAAAA-CGCCGCTAATACT-TA
1 TTTTTAGCGGCG-TTTTTCGAAAAGCGCCGCTAATGCTCGA
21678 TTTTTAGCGGCGTTTTTC-AAAATGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCGAAAA-GCGCCGCTAATGCTCGA
* * *
21718 TCTTTAGCGGCGTTTTACGTAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCGAAAAGCGCCGCTAATGCTCGA
* *
21758 TTTCTAGTGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
21775 TGTCTAAACG
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
37 4 0.05
38 4 0.05
39 23 0.28
40 47 0.58
41 3 0.04
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTCGAAAAGCGCCGCTAATGCTCGA
Found at i:21797 original size:12 final size:12
Alignment explanation
Indices: 21780--21805 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21770 TTTTTTGTCT
21780 AAACGCCGCTAA
1 AAACGCCGCTAA
21792 AAACGCCGCTAA
1 AAACGCCGCTAA
21804 AA
1 AA
21806 CCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:21918 original size:19 final size:18
Alignment explanation
Indices: 21884--21971 Score: 61
Period size: 18 Copynumber: 4.8 Consensus size: 18
21874 TAAGCTTAGA
21884 AATTATAAAAAATTATAG
1 AATTATAAAAAATTATAG
*
21902 AATTATAAAAATTTTATA-
1 AATTATAAAAA-ATTATAG
* * *
21920 AGTTATATAGAAATTATTG
1 AATTATA-AAAAATTATAG
* * * *
21939 AAATGATAAAAAGTAATAA
1 -AATTATAAAAAATTATAG
*
21958 AATTATTAAAAATT
1 AATTATAAAAAATT
21972 TATTAAAAGC
Statistics
Matches: 50, Mismatches: 16, Indels: 8
0.68 0.22 0.11
Matches are distributed among these distances:
18 31 0.62
19 14 0.28
20 5 0.10
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (18 bp):
AATTATAAAAAATTATAG
Found at i:21976 original size:11 final size:10
Alignment explanation
Indices: 21883--21990 Score: 50
Period size: 9 Copynumber: 11.3 Consensus size: 10
21873 TTAAGCTTAG
*
21883 AAATTATAAA
1 AAATTATTAA
21893 AAATTA-T-A
1 AAATTATTAA
*
21901 GAATTA-TAA
1 AAATTATTAA
*
21910 AAATT-TTAT
1 AAATTATTAA
* *
21919 AAGTTATATAG
1 AAATTAT-TAA
*
21930 AAATTATT-G
1 AAATTATTAA
*
21939 AAATGA-TAA
1 AAATTATTAA
* *
21948 AAAGTAAT-A
1 AAATTATTAA
21957 AAATTATTAA
1 AAATTATTAA
21967 AAATTTATTAA
1 AAA-TTATTAA
**
21978 AAGCTATTAA
1 AAATTATTAA
21988 AAA
1 AAA
21991 AGTTATGAAA
Statistics
Matches: 74, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
8 8 0.11
9 28 0.38
10 21 0.28
11 17 0.23
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.35
Consensus pattern (10 bp):
AAATTATTAA
Found at i:21996 original size:22 final size:21
Alignment explanation
Indices: 21945--22001 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 21
21935 ATTGAAATGA
* *
21945 TAAAAAGTAAT-AAAA-TTAT
1 TAAAAAGTTATGAAAAGCTAT
* *
21964 TAAAAATTTATTAAAAGCTAT
1 TAAAAAGTTATGAAAAGCTAT
21985 TAAAAAAGTTATGAAAA
1 T-AAAAAGTTATGAAAA
22002 AATTATAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 9 0.30
20 4 0.13
21 4 0.13
22 13 0.43
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.32
Consensus pattern (21 bp):
TAAAAAGTTATGAAAAGCTAT
Found at i:22377 original size:19 final size:18
Alignment explanation
Indices: 22348--22402 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
22338 ATTTAAAAAT
22348 TACTACTTTTATAAATTTTA
1 TACT-CTTTTAT-AATTTTA
* *
22368 TACTCTTTTATCAGTTTAA
1 TACTCTTTTAT-AATTTTA
22387 TACT-TTTTATAATTTT
1 TACTCTTTTATAATTTT
22403 TTCTTATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 4 0.13
18 6 0.20
19 16 0.53
20 4 0.13
ACGTcount: A:0.29, C:0.11, G:0.02, T:0.58
Consensus pattern (18 bp):
TACTCTTTTATAATTTTA
Found at i:24174 original size:9 final size:9
Alignment explanation
Indices: 24160--24190 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
24150 GTTAAACGAA
24160 TCGAGTTAT
1 TCGAGTTAT
*
24169 TCGAGTTAA
1 TCGAGTTAT
24178 TCGAGTTAT
1 TCGAGTTAT
24187 TCGA
1 TCGA
24191 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:24260 original size:9 final size:9
Alignment explanation
Indices: 24243--24279 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
24233 TGAGTTTTCG
24243 AATTCGAAT
1 AATTCGAAT
*
24252 AACTCGAAT
1 AATTCGAAT
24261 AATTCGAAT
1 AATTCGAAT
24270 AATTCGAAT
1 AATTCGAAT
24279 A
1 A
24280 TGAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:24993 original size:5 final size:5
Alignment explanation
Indices: 24983--25008 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
24973 CTCGAAAATT
24983 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
25009 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:25646 original size:48 final size:49
Alignment explanation
Indices: 25593--25776 Score: 180
Period size: 48 Copynumber: 3.6 Consensus size: 49
25583 TTTTTAAAAT
25593 TTAAAA-AATTCAAAAAATATAAAAATTATTTTTAAAAATTAAAAATCA
1 TTAAAATAATTCAAAAAATATAAAAATTATTTTTAAAAATTAAAAATCA
* * *
25641 TTAAAATTATTCAAAAGTATAAAAATTATAAAAAATATTTTTTAAAACATTTTTAAAAT--
1 TTAAAATAATTC------A-AAAAA-TATAAAAATTA-TTTTTAAAA-A--TTAAAAATCA
25700 TTAAAA-AATTCAAAAAATATAAAAATTATTTTTAAAAATTAAAAATCA
1 TTAAAATAATTCAAAAAATATAAAAATTATTTTTAAAAATTAAAAATCA
* *
25748 TTAAAATTATTC-AAAAGTATAAAAATTAT
1 TTAAAATAATTCAAAAAATATAAAAATTAT
25777 AAAAAATATT
Statistics
Matches: 112, Mismatches: 8, Indels: 32
0.74 0.05 0.21
Matches are distributed among these distances:
46 7 0.06
48 29 0.26
49 17 0.15
50 10 0.09
51 5 0.04
52 1 0.01
55 1 0.01
56 5 0.04
57 10 0.09
58 13 0.12
59 7 0.06
61 7 0.06
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (49 bp):
TTAAAATAATTCAAAAAATATAAAAATTATTTTTAAAAATTAAAAATCA
Found at i:25674 original size:28 final size:27
Alignment explanation
Indices: 25596--25679 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 27
25586 TTAAAATTTA
* *
25596 AAAAATTCAAAAAATATAAAAATTATTTTT
1 AAAAATT-AAAAATTATAAAAATTA--TTC
* *
25626 AAAAATTAAAAATCATTAAAATTATTC
1 AAAAATTAAAAATTATAAAAATTATTC
* *
25653 AAAAGTATAAAAATTATAAAAAATATT
1 AAAAAT-TAAAAATTATAAAAATTATT
25680 TTTTAAAACA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
27 7 0.16
28 17 0.38
29 14 0.31
30 7 0.16
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (27 bp):
AAAAATTAAAAATTATAAAAATTATTC
Found at i:25685 original size:107 final size:107
Alignment explanation
Indices: 25582--25816 Score: 470
Period size: 107 Copynumber: 2.2 Consensus size: 107
25572 TATTTAATTA
25582 ATTTTTAAAATTTAAAAAATTCAAAAAATATAAAAATTATTTTTAAAAATTAAAAATCATTAAAA
1 ATTTTTAAAATTTAAAAAATTCAAAAAATATAAAAATTATTTTTAAAAATTAAAAATCATTAAAA
25647 TTATTCAAAAGTATAAAAATTATAAAAAATATTTTTTAAAAC
66 TTATTCAAAAGTATAAAAATTATAAAAAATATTTTTTAAAAC
25689 ATTTTTAAAATTTAAAAAATTCAAAAAATATAAAAATTATTTTTAAAAATTAAAAATCATTAAAA
1 ATTTTTAAAATTTAAAAAATTCAAAAAATATAAAAATTATTTTTAAAAATTAAAAATCATTAAAA
25754 TTATTCAAAAGTATAAAAATTATAAAAAATATTTTTTAAAAC
66 TTATTCAAAAGTATAAAAATTATAAAAAATATTTTTTAAAAC
25796 ATTTTTAAAATTTAAAAAATT
1 ATTTTTAAAATTTAAAAAATT
25817 AACTAAATGC
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 128 1.00
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (107 bp):
ATTTTTAAAATTTAAAAAATTCAAAAAATATAAAAATTATTTTTAAAAATTAAAAATCATTAAAA
TTATTCAAAAGTATAAAAATTATAAAAAATATTTTTTAAAAC
Found at i:25781 original size:28 final size:27
Alignment explanation
Indices: 25703--25786 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 27
25693 TTAAAATTTA
* *
25703 AAAAATTCAAAAAATATAAAAATTATTTTT
1 AAAAATT-AAAAATTATAAAAATTA--TTC
* *
25733 AAAAATTAAAAATCATTAAAATTATTC
1 AAAAATTAAAAATTATAAAAATTATTC
* *
25760 AAAAGTATAAAAATTATAAAAAATATT
1 AAAAAT-TAAAAATTATAAAAATTATT
25787 TTTTAAAACA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
27 7 0.16
28 17 0.38
29 14 0.31
30 7 0.16
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (27 bp):
AAAAATTAAAAATTATAAAAATTATTC
Found at i:47476 original size:21 final size:21
Alignment explanation
Indices: 47437--47476 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
47427 AGAATACAAT
*
47437 TTTGTGCTATTTTACATTAAA
1 TTTGTGCTAATTTACATTAAA
47458 TTTGTGCATAATTTA-ATTA
1 TTTGTGC-TAATTTACATTA
47477 TTTTATGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (21 bp):
TTTGTGCTAATTTACATTAAA
Found at i:54715 original size:71 final size:71
Alignment explanation
Indices: 54633--54870 Score: 413
Period size: 71 Copynumber: 3.4 Consensus size: 71
54623 ATGAATTTCC
*
54633 ATCCAATTAATACGTGAACCTAATTCCTTAGGCATTCACAAGTATTAATAATCGCTTCACGTTTG
1 ATCCAATTAATACGTGAACCTAATTCCTTAGGCATTCACAAGTACTAATAATCGCTTCACGTTTG
54698 GTCATA
66 GTCATA
* * * *
54704 ATCCAATTAATACGTGAACCTAATTCCTTAAGCATTCACATGTGCTAATAATAGCTTCACGTTTG
1 ATCCAATTAATACGTGAACCTAATTCCTTAGGCATTCACAAGTACTAATAATCGCTTCACGTTTG
54769 GTCATA
66 GTCATA
* *
54775 ATCCAATTAATACGTGAACCTTATTCCTTAGGCATTCACACGTACTAATAATCGCTTCACGTTTG
1 ATCCAATTAATACGTGAACCTAATTCCTTAGGCATTCACAAGTACTAATAATCGCTTCACGTTTG
54840 GTCATA
66 GTCATA
54846 ATCCAATTAATACGTGAACCTAATT
1 ATCCAATTAATACGTGAACCTAATT
54871 TATGCTTGAT
Statistics
Matches: 156, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 156 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (71 bp):
ATCCAATTAATACGTGAACCTAATTCCTTAGGCATTCACAAGTACTAATAATCGCTTCACGTTTG
GTCATA
Found at i:56026 original size:16 final size:16
Alignment explanation
Indices: 56005--56035 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55995 AATTGATTTA
*
56005 AATTAATTAATTTTCC
1 AATTAAATAATTTTCC
56021 AATTAAATAATTTTC
1 AATTAAATAATTTTC
56036 TCAACCCAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTAAATAATTTTCC
Found at i:66597 original size:18 final size:18
Alignment explanation
Indices: 66574--66633 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
66564 ATAGAGATTA
*
66574 GATATGAAGTTTTGTTAT
1 GATATGAAGTTTTGATAT
* * * *
66592 GATATGAAGATCTAATCT
1 GATATGAAGTTTTGATAT
66610 GATATTG-AGTTTTGATAT
1 GATA-TGAAGTTTTGATAT
66628 GATATG
1 GATATG
66634 GAATTTTGTT
Statistics
Matches: 32, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
17 2 0.06
18 28 0.88
19 2 0.06
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.43
Consensus pattern (18 bp):
GATATGAAGTTTTGATAT
Found at i:66771 original size:34 final size:34
Alignment explanation
Indices: 66722--66786 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
66712 GATACCTTAG
* *
66722 CACTTACGTGTTCTCTGGTGTTTTGGA-GGATTAA
1 CACTTACGTGCTCTCTAGTG-TTTGGATGGATTAA
*
66756 CACTTATGTGCTCTCTAGTGTTTGGATGGAT
1 CACTTACGTGCTCTCTAGTGTTTGGATGGAT
66787 CCTGTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 6 0.22
34 21 0.78
ACGTcount: A:0.17, C:0.15, G:0.26, T:0.42
Consensus pattern (34 bp):
CACTTACGTGCTCTCTAGTGTTTGGATGGATTAA
Found at i:78846 original size:87 final size:88
Alignment explanation
Indices: 78739--78916 Score: 331
Period size: 87 Copynumber: 2.0 Consensus size: 88
78729 TTAGCAATGT
*
78739 ATTTTTTTATATGTTTTATACTTATTTTAACCAAAAGACAAAAACATATAAATTTTGGTTAACTG
1 ATTTTTTTATATGATTTATACTTATTTTAACCAAAAGACAAAAACATATAAATTTTGGTTAACTG
78804 GTCAAATTAACAGAAATATTTTG
66 GTCAAATTAACAGAAATATTTTG
*
78827 ATTTTTTTTTAT-ATTTATACTTATTTTAACCAAAAGACAAAAACATATAAATTTTGGTTAACTG
1 ATTTTTTTATATGATTTATACTTATTTTAACCAAAAGACAAAAACATATAAATTTTGGTTAACTG
78891 GTCAAATTAACAGAAATATTTTG
66 GTCAAATTAACAGAAATATTTTG
78914 ATT
1 ATT
78917 CGGTTAATGT
Statistics
Matches: 88, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
87 77 0.88
88 11 0.12
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (88 bp):
ATTTTTTTATATGATTTATACTTATTTTAACCAAAAGACAAAAACATATAAATTTTGGTTAACTG
GTCAAATTAACAGAAATATTTTG
Found at i:85251 original size:13 final size:14
Alignment explanation
Indices: 85233--85261 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
85223 TAACGGGGTT
85233 GGGGAAATGGG-GA
1 GGGGAAATGGGAGA
85246 GGGGAAATGGGAGA
1 GGGGAAATGGGAGA
85260 GG
1 GG
85262 TCAAATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.31, C:0.00, G:0.62, T:0.07
Consensus pattern (14 bp):
GGGGAAATGGGAGA
Found at i:87372 original size:19 final size:18
Alignment explanation
Indices: 87343--87381 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
87333 TCGGTAGAGG
87343 AAGGGAAAAAGAAGAAGA
1 AAGGGAAAAAGAAGAAGA
87361 AAGGGAAAAAAGAAGAAGA
1 AAGGG-AAAAAGAAGAAGA
87380 AA
1 AA
87382 ATGTCAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (18 bp):
AAGGGAAAAAGAAGAAGA
Found at i:89316 original size:30 final size:30
Alignment explanation
Indices: 89280--89337 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
89270 TCCGAGCTAT
89280 GGGGCAAAAGTGTAATTATGCAAAAGTTTA
1 GGGGCAAAAGTGTAATTATGCAAAAGTTTA
* *
89310 GGGGCAAAATTGTAATTTTGCAAAAGTT
1 GGGGCAAAAGTGTAATTATGCAAAAGTT
89338 CGAGTCAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.29
Consensus pattern (30 bp):
GGGGCAAAAGTGTAATTATGCAAAAGTTTA
Found at i:90116 original size:20 final size:21
Alignment explanation
Indices: 90066--90116 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
90056 TGAGTTATTT
*
90066 AAGTAAGCA-AGTAAGTGAAC
1 AAGTAAGCAGAGTAAGTAAAC
*
90086 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCAGAGTAAGTAAAC
90106 AAG-AAGCAGAG
1 AAGTAAGCAGAG
90117 ACCATGATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.53, C:0.06, G:0.29, T:0.12
Consensus pattern (21 bp):
AAGTAAGCAGAGTAAGTAAAC
Found at i:97453 original size:50 final size:50
Alignment explanation
Indices: 97395--97534 Score: 154
Period size: 50 Copynumber: 2.8 Consensus size: 50
97385 TATTGAGGTT
* * * *
97395 ATGAGAGGTCCCATGTAATACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAG
** * * *
97445 ATGAGAGGTCCCCCGTAAGACCATGTCTTGGACACGGCATGGGCACCAAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAG
** * * *
97495 ATGAGAACTCCCATGTAAGGCCATATCTGGGATATGGCAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCAT
97535 TAGTAGTACA
Statistics
Matches: 72, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 72 1.00
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAG
Found at i:97816 original size:20 final size:20
Alignment explanation
Indices: 97791--97839 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
97781 TGAGTTATTT
*
97791 AAGTAAGCAAGTAAGTGAAC
1 AAGTAAGCAAGTAAGTAAAC
*
97811 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
97831 AAG-AAGCAA
1 AAGTAAGCAA
97840 AGACCATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.55, C:0.06, G:0.27, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:103045 original size:43 final size:44
Alignment explanation
Indices: 102941--103045 Score: 108
Period size: 43 Copynumber: 2.4 Consensus size: 44
102931 AACAAATATG
* * * *
102941 TGGACAAAGCCACCAAATTTGTAGACAAGCTATCATGTAGGTTA
1 TGGACAAAGCCAACAAATTCGCAGACAAGCTACCATGTAGGTTA
* * *
102985 TGGATAAA--CTACAAAATTCGCAGACAAGCTGCCATGTAGGTT-
1 TGGACAAAGCCAAC-AAATTCGCAGACAAGCTACCATGTAGGTTA
*
103027 TGGACGAAGCCAACAAATT
1 TGGACAAAGCCAACAAATT
103046 TGTAGAGAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
42 8 0.17
43 30 0.62
44 10 0.21
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (44 bp):
TGGACAAAGCCAACAAATTCGCAGACAAGCTACCATGTAGGTTA
Found at i:106070 original size:44 final size:44
Alignment explanation
Indices: 106022--106327 Score: 384
Period size: 44 Copynumber: 6.9 Consensus size: 44
106012 CAGGATCTAC
106022 AATCTTTC-ACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGT
1 AATC-TTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGT
* *
106066 AATCTTCAACCTATTCCACTGTTGTTCAGGGAGATAGAACTTGT
1 AATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGT
* ** *
106110 AATCTTCAACCTATTCCATTATTGTTCAGGGAGATAGGAATTGT
1 AATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGT
* *
106154 AATCTTCAACCTATTCCAACTGCTGTTCAGGGAGATAGGACATGC
1 AATCTTCAACCTATTCC-ACTGCTGTTCAGGGAGATAGGACTTGT
* **
106199 AATCTTCCACCTATTCCACTGCTGTTCAGGGAGATAGGA-TATAC
1 AATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACT-TGT
* *
106243 AATCTTCAACCTATTCCACTGCTATTCAGGGAGATAGGAATTGCT
1 AATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTG-T
* * * * * *
106288 -ATCTTCCACATATTCCATTCCCGATCAGGGAGATAGGACT
1 AATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACT
106328 GGCGGCTTAA
Statistics
Matches: 230, Mismatches: 27, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
43 3 0.01
44 189 0.82
45 38 0.17
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (44 bp):
AATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGT
Found at i:106192 original size:133 final size:132
Alignment explanation
Indices: 106022--106327 Score: 402
Period size: 133 Copynumber: 2.3 Consensus size: 132
106012 CAGGATCTAC
*
106022 AATCTTTCACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGTAATCTTCAACCTATTCCACTG
1 AATC-TTCACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTG
* ** * * *
106087 TTGTTCAGGGAGATAGAACT-TGTAATCTTCAACCTATTCCATTATTGTTCAGGGAGATAGGAAT
65 CTGTTCAGGGAGATAGAA-TATACAATCTTCAACCTATTCCACTACTATTCAGGGAGATAGGAAT
106151 TG-T
129 TGCT
* *
106154 AATCTTCAACCTATTCCAACTGCTGTTCAGGGAGATAGGACATGCAATCTTCCACCTATTCCACT
1 AATCTTC-ACCTATTCC-ACTGCTGTTCAGGGAGATAGGACTTGCAATCTTCAACCTATTCCACT
* *
106219 GCTGTTCAGGGAGATAGGATATACAATCTTCAACCTATTCCACTGCTATTCAGGGAGATAGGAAT
64 GCTGTTCAGGGAGATAGAATATACAATCTTCAACCTATTCCACTACTATTCAGGGAGATAGGAAT
106284 TGCT
129 TGCT
* * * * *
106288 -ATCTTCCACATATTCCATTCCCGATCAGGGAGATAGGACT
1 AATCTT-CACCTATTCCACTGCTGTTCAGGGAGATAGGACT
106328 GGCGGCTTAA
Statistics
Matches: 152, Mismatches: 17, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
131 3 0.02
132 33 0.22
133 114 0.75
134 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (132 bp):
AATCTTCACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGC
TGTTCAGGGAGATAGAATATACAATCTTCAACCTATTCCACTACTATTCAGGGAGATAGGAATTG
CT
Found at i:117262 original size:22 final size:23
Alignment explanation
Indices: 117199--117259 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
117189 ATAGTACGTG
117199 ATAAAAAGAATTAAAATAATAGTAC
1 ATAAAAA-AA-TAAAATAATAGTAC
* *
117224 GTAATAAAATAAAATAAT-GTAC
1 ATAAAAAAATAAAATAATAGTAC
117246 ATAAAAAAGATAAA
1 ATAAAAAA-ATAAA
117260 TAAATATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 10 0.32
23 14 0.45
24 2 0.06
25 5 0.16
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.23
Consensus pattern (23 bp):
ATAAAAAAATAAAATAATAGTAC
Found at i:118984 original size:133 final size:132
Alignment explanation
Indices: 118803--119107 Score: 391
Period size: 133 Copynumber: 2.3 Consensus size: 132
118793 CAGGATCTAC
* *
118803 AATCTTTCACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGTAATCTTCAACCTATTCCACTG
1 AATC-TTCACCTATTCCACTGCTGTTCAGGGAGATAGGACATGCAATCTTCAACCTATTCCACTG
* ** * * *
118868 TTGTTCAGGGAGATAGAACT-TGTAATCTTCAACCTATTCCATTATTGTTCAGGGAGATAGGAAT
65 CTGTTCAGGGAGATAGAA-TATACAATCTTCAACCTATTCCACTACTATTCAGGGAGATAGGAAT
118932 TG-T
129 TGCT
*
118935 AATCTTCAACCTATTCCAACTGCTGTTCAGGGAGATAGGACATGCAATCTTCCACCTATTCCACT
1 AATCTTC-ACCTATTCC-ACTGCTGTTCAGGGAGATAGGACATGCAATCTTCAACCTATTCCACT
* * *
119000 GCTGTTCAGGGAGATAGGATATACAATCTTCAACCTATTCCACTGCTATTCAGGGAGATAGGACT
64 GCTGTTCAGGGAGATAGAATATACAATCTTCAACCTATTCCACTACTATTCAGGGAGATAGGAAT
119065 TGCT
129 TGCT
* * * * *
119069 -ATCTTCCACATATTCCATTCCCGATCAGGGAGATAGGAC
1 AATCTT-CACCTATTCCACTGCTGTTCAGGGAGATAGGAC
119108 TGGCGGCTTA
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
131 3 0.02
132 33 0.22
133 113 0.75
134 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (132 bp):
AATCTTCACCTATTCCACTGCTGTTCAGGGAGATAGGACATGCAATCTTCAACCTATTCCACTGC
TGTTCAGGGAGATAGAATATACAATCTTCAACCTATTCCACTACTATTCAGGGAGATAGGAATTG
CT
Found at i:119107 original size:44 final size:44
Alignment explanation
Indices: 118803--119108 Score: 393
Period size: 44 Copynumber: 6.9 Consensus size: 44
118793 CAGGATCTAC
118803 AATCTTTC-ACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGT
1 AATC-TTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGT
* *
118847 AATCTTCAACCTATTCCACTGTTGTTCAGGGAGATAGAACTTGT
1 AATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGT
* ** *
118891 AATCTTCAACCTATTCCATTATTGTTCAGGGAGATAGGAATTGT
1 AATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGT
* *
118935 AATCTTCAACCTATTCCAACTGCTGTTCAGGGAGATAGGACATGC
1 AATCTTCAACCTATTCC-ACTGCTGTTCAGGGAGATAGGACTTGT
* **
118980 AATCTTCCACCTATTCCACTGCTGTTCAGGGAGATAGGA-TATAC
1 AATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACT-TGT
*
119024 AATCTTCAACCTATTCCACTGCTATTCAGGGAGATAGGACTTGCT
1 AATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTG-T
* * * * * *
119069 -ATCTTCCACATATTCCATTCCCGATCAGGGAGATAGGACT
1 AATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACT
119109 GGCGGCTTAA
Statistics
Matches: 231, Mismatches: 26, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
43 3 0.01
44 190 0.82
45 38 0.16
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (44 bp):
AATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGT
Found at i:123958 original size:109 final size:109
Alignment explanation
Indices: 123820--124043 Score: 439
Period size: 109 Copynumber: 2.1 Consensus size: 109
123810 TGTCTTCAAG
*
123820 CTATCTAAATCCTCCTCAGCCTTATTTTTCCCTTTTCTTAAAGTTTCGGCTTCGAGTTTTTGAAC
1 CTATCTAAATCCTCCTCAGCCTTATTTTTCCCTTTTCCTAAAGTTTCGGCTTCGAGTTTTTGAAC
123885 ATCTATGTCTAACCTCAAGTTCATCTTCTCTTCTTCCATTTGTT
66 ATCTATGTCTAACCTCAAGTTCATCTTCTCTTCTTCCATTTGTT
123929 CTATCTAAATCCTCCTCAGCCTTATTTTTCCCTTTTCCTAAAGTTTCGGCTTCGAGTTTTTGAAC
1 CTATCTAAATCCTCCTCAGCCTTATTTTTCCCTTTTCCTAAAGTTTCGGCTTCGAGTTTTTGAAC
123994 ATCTATGTCTAACCTCAAGTTCATCTTCTCTTCTTCCATTTGTT
66 ATCTATGTCTAACCTCAAGTTCATCTTCTCTTCTTCCATTTGTT
124038 CTATCT
1 CTATCT
124044 TCTTTTCTAA
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 114 1.00
ACGTcount: A:0.18, C:0.27, G:0.09, T:0.46
Consensus pattern (109 bp):
CTATCTAAATCCTCCTCAGCCTTATTTTTCCCTTTTCCTAAAGTTTCGGCTTCGAGTTTTTGAAC
ATCTATGTCTAACCTCAAGTTCATCTTCTCTTCTTCCATTTGTT
Found at i:127297 original size:19 final size:20
Alignment explanation
Indices: 127263--127302 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
127253 AGTACAATAA
*
127263 TAATACTTATAATAATAAAT
1 TAATACTTAAAATAATAAAT
*
127283 TAATA-TTAAAATAATTAAT
1 TAATACTTAAAATAATAAAT
127302 T
1 T
127303 TGATAACAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TAATACTTAAAATAATAAAT
Found at i:131815 original size:39 final size:38
Alignment explanation
Indices: 131749--131826 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 38
131739 ATTTACACAT
* * *
131749 ATAATCACCTAACATACAAGTAGATATCACAATGCTCAA
1 ATAATCACATAACATACAAGCAGATATC-CAATACTCAA
** *
131788 ATAATCACATAACATTTAAGCATATATCCAATACTCAA
1 ATAATCACATAACATACAAGCAGATATCCAATACTCAA
131826 A
1 A
131827 AACATCTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
38 10 0.30
39 23 0.70
ACGTcount: A:0.47, C:0.22, G:0.05, T:0.26
Consensus pattern (38 bp):
ATAATCACATAACATACAAGCAGATATCCAATACTCAA
Found at i:136618 original size:21 final size:20
Alignment explanation
Indices: 136590--136632 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
136580 AAATTATCGA
*
136590 TACAGT-CCTAAATATGAGTT
1 TACAGTCCCTAAAAATGA-TT
136610 TACAGGTCCCTAAAAATGATT
1 TACA-GTCCCTAAAAATGATT
136631 TA
1 TA
136633 AGAACTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 6 0.30
22 10 0.50
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (20 bp):
TACAGTCCCTAAAAATGATT
Found at i:138005 original size:48 final size:47
Alignment explanation
Indices: 137930--138058 Score: 181
Period size: 47 Copynumber: 2.7 Consensus size: 47
137920 TGATTTGTAC
137930 AAAAATGGACAGCATTTAAGCACCAATTTGGACAGCATTAATATACTC-
1 AAAAATGGACAGCATTTAAGCA-CAATTTGGACAGCATTAATATAC-CA
* * *
137978 AACAATGGACAGCAATTAAGCATCAATTT-GACAGCATTAATATGCCA
1 AAAAATGGACAGCATTTAAGCA-CAATTTGGACAGCATTAATATACCA
138025 AAAAATGGACAGCATTTAAGCACTAATTTGGACA
1 AAAAATGGACAGCATTTAAGCAC-AATTTGGACA
138059 ACATCTTATC
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
46 2 0.03
47 40 0.56
48 30 0.42
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.24
Consensus pattern (47 bp):
AAAAATGGACAGCATTTAAGCACAATTTGGACAGCATTAATATACCA
Found at i:141116 original size:39 final size:39
Alignment explanation
Indices: 141062--141139 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
141052 CCTGATGCTC
141062 AGCTTTAAATTGCTGACAGATCAAACATTTAGAAATGAA
1 AGCTTTAAATTGCTGACAGATCAAACATTTAGAAATGAA
*
141101 AGCTTTAAATTGCTGACAGGTCAAACATTTAGAAATGAA
1 AGCTTTAAATTGCTGACAGATCAAACATTTAGAAATGAA
141140 CTCTATGATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (39 bp):
AGCTTTAAATTGCTGACAGATCAAACATTTAGAAATGAA
Found at i:143491 original size:20 final size:20
Alignment explanation
Indices: 143466--143504 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
143456 TTCTAGGTGT
143466 TCTACCTCTAACTGCAGTGG
1 TCTACCTCTAACTGCAGTGG
*
143486 TCTACCTCTAATTGCAGTG
1 TCTACCTCTAACTGCAGTG
143505 TTACTCGGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (20 bp):
TCTACCTCTAACTGCAGTGG
Found at i:144810 original size:23 final size:23
Alignment explanation
Indices: 144784--144883 Score: 87
Period size: 23 Copynumber: 4.3 Consensus size: 23
144774 TGTACAAAAA
*
144784 TGGACAACATTTAAGCACCAATT
1 TGGACAGCATTTAAGCACCAATT
* *
144807 TGGACAGCATTAATATACTCAACAA--
1 TGGACAGCATT--TA-A-GCACCAATT
* *
144832 TGGACAGCAATTAAGCATCAATT
1 TGGACAGCATTTAAGCACCAATT
* *
144855 TGGACAGCATTTAAGTACTAATT
1 TGGACAGCATTTAAGCACCAATT
144878 TGGACA
1 TGGACA
144884 ACATCTTATC
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
21 5 0.08
22 1 0.02
23 37 0.61
25 12 0.20
26 1 0.02
27 5 0.08
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (23 bp):
TGGACAGCATTTAAGCACCAATT
Found at i:146896 original size:175 final size:176
Alignment explanation
Indices: 146594--146944 Score: 695
Period size: 175 Copynumber: 2.0 Consensus size: 176
146584 TATGCGATTT
146594 AGTCCTTTTTACTGAATTAAGCATTCAAACAGTAAAATTTCTTTACGAAACTTTCACACATATAT
1 AGTCCTTTTTACTGAATTAAGCATTCAAACAGTAAAATTTCTTTACGAAACTTTCACACATATAT
146659 ATTCACATGTTATATATACCAAAAATAATATTAAAATAATTTTTTGACCTCAGATTTGTGGTTCC
66 ATTCACATGTTATATATACCAAAAATAATATTAAAATAATTTTTTGACCTCAGATTTGTGGTTCC
146724 AAAACCACTGTTCTGATTTAACTAAAATCAGGTTGTTACATTAGAG
131 AAAACCACTGTTCTGATTTAACTAAAATCAGGTTGTTACATTAGAG
146770 AGTCCTTTTT-CTGAATTAAGCATTCAAACAGTAAAATTTCTTTACGAAACTTTCACACATATAT
1 AGTCCTTTTTACTGAATTAAGCATTCAAACAGTAAAATTTCTTTACGAAACTTTCACACATATAT
146834 ATTCACATGTTATATATACCAAAAATAATATTAAAATAATTTTTTGACCTCAGATTTGTGGTTCC
66 ATTCACATGTTATATATACCAAAAATAATATTAAAATAATTTTTTGACCTCAGATTTGTGGTTCC
146899 AAAACCACTGTTCTGATTTAACTAAAATCAGGTTGTTACATTAGAG
131 AAAACCACTGTTCTGATTTAACTAAAATCAGGTTGTTACATTAGAG
146945 GTCGAATAGG
Statistics
Matches: 175, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
175 165 0.94
176 10 0.06
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (176 bp):
AGTCCTTTTTACTGAATTAAGCATTCAAACAGTAAAATTTCTTTACGAAACTTTCACACATATAT
ATTCACATGTTATATATACCAAAAATAATATTAAAATAATTTTTTGACCTCAGATTTGTGGTTCC
AAAACCACTGTTCTGATTTAACTAAAATCAGGTTGTTACATTAGAG
Found at i:147235 original size:9 final size:9
Alignment explanation
Indices: 147221--147251 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
147211 GTTAAGGAAA
147221 TCGAGTTAT
1 TCGAGTTAT
*
147230 TCGAGTTAA
1 TCGAGTTAT
147239 TCGAGTTAT
1 TCGAGTTAT
147248 TCGA
1 TCGA
147252 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:147321 original size:9 final size:9
Alignment explanation
Indices: 147304--147340 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
147294 TGAGTTTTCG
147304 AATTCGAAT
1 AATTCGAAT
*
147313 AACTCGAAT
1 AATTCGAAT
*
147322 AATTCGAGT
1 AATTCGAAT
147331 AATTCGAAT
1 AATTCGAAT
147340 A
1 A
147341 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:147590 original size:30 final size:31
Alignment explanation
Indices: 147554--147613 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
147544 AAACCTTTTA
*
147554 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
147584 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
147614 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:161505 original size:20 final size:20
Alignment explanation
Indices: 161480--161520 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
161470 GTAAATGCAA
161480 AAATAT-TTTTAAGATTTTTT
1 AAATATATTTT-AGATTTTTT
*
161500 AAATATATTTTATATTTTTT
1 AAATATATTTTAGATTTTTT
161520 A
1 A
161521 GAATTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
AAATATATTTTAGATTTTTT
Found at i:167610 original size:20 final size:22
Alignment explanation
Indices: 167587--167631 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
167577 TAAAAAGTAA
*
167587 AAATTAGAAA-ATAAA-AAAAT
1 AAATTAGAAAGAAAAATAAAAT
*
167607 AAATTTGAAAGAAAAATAAAAT
1 AAATTAGAAAGAAAAATAAAAT
167629 AAA
1 AAA
167632 AAGTTCGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (22 bp):
AAATTAGAAAGAAAAATAAAAT
Found at i:180443 original size:36 final size:36
Alignment explanation
Indices: 180396--180476 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 36
180386 TCTATAGTCC
* *
180396 CTTGTTCCTCACCTGCATCTTCTTCATC-GATCACAT
1 CTTGTTCCTCACCTACATCTTCTTCATCAG-CCACAT
* *
180432 CTTGTTCCTCACCTATATCTTTTTCATCAGCCACAT
1 CTTGTTCCTCACCTACATCTTCTTCATCAGCCACAT
*
180468 CTTCTTCCT
1 CTTGTTCCT
180477 TATCTGCGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 38 0.97
37 1 0.03
ACGTcount: A:0.16, C:0.36, G:0.06, T:0.42
Consensus pattern (36 bp):
CTTGTTCCTCACCTACATCTTCTTCATCAGCCACAT
Found at i:183216 original size:24 final size:24
Alignment explanation
Indices: 183170--183217 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
183160 AATTTTAAAA
* *
183170 AAAAAAAAGGCTTATATGCCTAAT
1 AAAAAAAAGGCATATATACCTAAT
* *
183194 AAAAAATAGGCATATATATCTAAT
1 AAAAAAAAGGCATATATACCTAAT
183218 TTAGCCAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.27
Consensus pattern (24 bp):
AAAAAAAAGGCATATATACCTAAT
Found at i:191871 original size:53 final size:53
Alignment explanation
Indices: 191814--191916 Score: 138
Period size: 53 Copynumber: 1.9 Consensus size: 53
191804 GATTTTCTTC
*
191814 TCTATTGATTCATTATGGTATTC-TCCCATGATTCTTTGT-GTTTTTCTTTCTCT
1 TCTATTGATTCATTATGGT-TTCTTCCC-TGATTCTCTGTGGTTTTTCTTTCTCT
* * *
191867 TCTATTGGTTCCTTCTGGTTTCTTCCCTGATTCTCTGTGGTTTTTCTTTC
1 TCTATTGATTCATTATGGTTTCTTCCCTGATTCTCTGTGGTTTTTCTTTC
191917 CTATGTCCGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
52 13 0.30
53 31 0.70
ACGTcount: A:0.09, C:0.21, G:0.14, T:0.56
Consensus pattern (53 bp):
TCTATTGATTCATTATGGTTTCTTCCCTGATTCTCTGTGGTTTTTCTTTCTCT
Found at i:192066 original size:1 final size:1
Alignment explanation
Indices: 192060--192100 Score: 73
Period size: 1 Copynumber: 41.0 Consensus size: 1
192050 TGCAATTAGC
*
192060 AAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
192101 GAAGAAGAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.98, C:0.00, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:192078 original size:9 final size:9
Alignment explanation
Indices: 192060--192150 Score: 57
Period size: 9 Copynumber: 10.3 Consensus size: 9
192050 TGCAATTAGC
192060 AAAA-AAAA
1 AAAAGAAAA
192068 AAAAGAAAA
1 AAAAGAAAA
192077 AAAA-AAAA
1 AAAAGAAAA
192085 AAAA-AAAA
1 AAAAGAAAA
192093 AAAA-AAAA
1 AAAAGAAAA
*
192101 GAAGAAGAAGA
1 -AA-AAGAAAA
* *
192112 AGAAGAAGA
1 AAAAGAAAA
* *
192121 AGAAGAAGA
1 AAAAGAAAA
*
192130 AGAAG-AAA
1 AAAAGAAAA
*
192138 GAAAGAAAGA
1 AAAAGAAA-A
192148 AAA
1 AAA
192151 TTGCAATGCA
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
8 29 0.41
9 33 0.46
10 6 0.08
11 3 0.04
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:192078 original size:12 final size:12
Alignment explanation
Indices: 192061--192150 Score: 67
Period size: 12 Copynumber: 7.3 Consensus size: 12
192051 GCAATTAGCA
192061 AAAAAAAAAAAG
1 AAAAAAAAAAAG
192073 AAAAAAAAAAA-
1 AAAAAAAAAAAG
192084 AAAAAAAAAAA-
1 AAAAAAAAAAAG
*
192095 AAAAAAGAAGAAG
1 AAAAAA-AAAAAG
*
192108 AAGAAGAAGAAGAAG
1 AA-AA-AA-AAAAAG
* * *
192123 AAGAAGAAGAAG
1 AAAAAAAAAAAG
* *
192135 AAAGAAAGAAAG
1 AAAAAAAAAAAG
192147 AAAA
1 AAAA
192151 TTGCAATGCA
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
11 17 0.26
12 31 0.48
13 3 0.05
14 3 0.05
15 11 0.17
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:192105 original size:3 final size:3
Alignment explanation
Indices: 192099--192136 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
192089 AAAAAAAAAA
192099 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
192137 AGAAAGAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:196357 original size:30 final size:28
Alignment explanation
Indices: 196323--196378 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
196313 GTGATTAAAT
196323 AAAATCGACA-CAAGCAGAATTTAAAAGAAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAAA
*
196353 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
196379 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 2 0.08
30 10 0.42
31 4 0.17
ACGTcount: A:0.61, C:0.11, G:0.14, T:0.14
Consensus pattern (28 bp):
AAAATCGACAGCAAGAAATTAAAAGAAA
Found at i:198245 original size:18 final size:17
Alignment explanation
Indices: 198222--198260 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
198212 CTCTTTTTGC
198222 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATT-TCTTTT
*
198240 TCTTTTTTGATTTCTTTT
1 TC-TTTTTCATTTCTTTT
198258 TCT
1 TCT
198261 GTCTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTTCATTTCTTTT
Found at i:202371 original size:17 final size:17
Alignment explanation
Indices: 202349--202385 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
202339 AACTTAAGTT
*
202349 AAATAATAAGAAAAAGA
1 AAATAAAAAGAAAAAGA
*
202366 AAATAAAAATAAAAAGA
1 AAATAAAAAGAAAAAGA
202383 AAA
1 AAA
202386 GGAATTAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (17 bp):
AAATAAAAAGAAAAAGA
Found at i:213731 original size:25 final size:25
Alignment explanation
Indices: 213712--213808 Score: 88
Period size: 25 Copynumber: 3.9 Consensus size: 25
213702 GTATGTTCAT
213712 ATGAGCTATGAATCGGTATGCTCTC
1 ATGAGCTATGAATCGGTATGCTCTC
* ** * *
213737 ATGAGCTGTGAATCGAAAAGCTCAC
1 ATGAGCTATGAATCGGTATGCTCTC
* * *
213762 ACGAGCTGA-GAATTGGTAAGCTCTC
1 ATGAGCT-ATGAATCGGTATGCTCTC
* *
213787 ACGAGCTATAAATCGGTATGCT
1 ATGAGCTATGAATCGGTATGCT
213809 TATACGAGCT
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
24 1 0.02
25 55 0.98
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (25 bp):
ATGAGCTATGAATCGGTATGCTCTC
Found at i:217867 original size:31 final size:31
Alignment explanation
Indices: 217825--217917 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
217815 GGCTGTTACA
*
217825 CCTATACTTTTTAAATTGGTCAAGTTTAGTC
1 CCTATACTTTTTGAATTGGTCAAGTTTAGTC
* *
217856 CTTTTACTTTTTGAATTGGTCAAGTTTAGTC
1 CCTATACTTTTTGAATTGGTCAAGTTTAGTC
217887 CCTATACTTTTTGAATTGGTCAAGTTTAGTC
1 CCTATACTTTTTGAATTGGTCAAGTTTAGTC
217918 TTGACCCAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.47
Consensus pattern (31 bp):
CCTATACTTTTTGAATTGGTCAAGTTTAGTC
Found at i:223460 original size:17 final size:16
Alignment explanation
Indices: 223432--223484 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
223422 TTTGGTTCGC
223432 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
223448 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
223465 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
223481 TGTA
1 TGTA
223485 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:223549 original size:44 final size:45
Alignment explanation
Indices: 223465--223555 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
223455 GGATTAGAGG
* * *
223465 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
*
223510 TGTAATGGAATAGAGGCGTAATAG-TAATCTTA-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATC-CACTGTTTGGTTGAA
223554 TG
1 TG
223556 GAATAGAGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
44 19 0.46
45 22 0.54
ACGTcount: A:0.29, C:0.07, G:0.27, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:233363 original size:31 final size:31
Alignment explanation
Indices: 233328--233396 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
233318 CAACAAAACG
*
233328 GTCATTGAACTATTCAAAAGATTTCACTTAA
1 GTCATTGAACTATTCAAAACATTTCACTTAA
*
233359 GTCATTGAACTATTCAAAACATTTCATTTAA
1 GTCATTGAACTATTCAAAACATTTCACTTAA
233390 GTCATTG
1 GTCATTG
233397 GACAATTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (31 bp):
GTCATTGAACTATTCAAAACATTTCACTTAA
Found at i:235338 original size:11 final size:11
Alignment explanation
Indices: 235322--235352 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
235312 TTTTTTTGCA
235322 ATTTGATTTTT
1 ATTTGATTTTT
235333 ATTTGATTTTT
1 ATTTGATTTTT
*
235344 ATTTAATTT
1 ATTTGATTT
235353 CTAACTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (11 bp):
ATTTGATTTTT
Found at i:248309 original size:9 final size:9
Alignment explanation
Indices: 248295--248380 Score: 120
Period size: 9 Copynumber: 9.4 Consensus size: 9
248285 TTTGGTTAAA
248295 AATTACCCG
1 AATTACCCG
248304 AATTACCCG
1 AATTACCCG
248313 AATTACCCG
1 AATTACCCG
248322 AATTACCCG
1 AATTACCCG
*
248331 AATTAACCG
1 AATTACCCG
*
248340 AATTAACCG
1 AATTACCCG
248349 AATTA-CCG
1 AATTACCCG
*
248357 AAAAATACCCG
1 --AATTACCCG
248368 AATTACCCG
1 AATTACCCG
248377 AATT
1 AATT
248381 TTTTTTATTT
Statistics
Matches: 71, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
8 3 0.04
9 61 0.86
10 4 0.06
11 3 0.04
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:248477 original size:35 final size:35
Alignment explanation
Indices: 248438--248507 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
248428 AGTAAATTGG
248438 GTTTTAGACTTTAGTAAATTGGGTTGTCGTTTAGT
1 GTTTTAGACTTTAGTAAATTGGGTTGTCGTTTAGT
*
248473 GTTTTAGACTTTAGTAAATTGGGTTGTCTTTTAGT
1 GTTTTAGACTTTAGTAAATTGGGTTGTCGTTTAGT
248508 TTTAGTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.06, G:0.24, T:0.50
Consensus pattern (35 bp):
GTTTTAGACTTTAGTAAATTGGGTTGTCGTTTAGT
Found at i:252154 original size:21 final size:21
Alignment explanation
Indices: 252128--252179 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
252118 TTGAGCATGA
252128 GCTCGAAATAAGTTTGGGGGT
1 GCTCGAAATAAGTTTGGGGGT
252149 GCTCGAAATAAGTTTGGGGGT
1 GCTCGAAATAAGTTTGGGGGT
* *
252170 GTTCCAAATA
1 GCTCGAAATA
252180 CTCAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.29
Consensus pattern (21 bp):
GCTCGAAATAAGTTTGGGGGT
Found at i:252977 original size:42 final size:42
Alignment explanation
Indices: 252908--252995 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
252898 GTGTAACTTA
*
252908 CTGACTTAGATAACACGACCGTCTGTTAGGCTATGAAACTCT
1 CTGACTTAGATAACACGACCGTCTGTTAGGCCATGAAACTCT
* * * *
252950 CTGACTTAGATCACACGGCCGTGTGTTAGGCCATGTAACTCT
1 CTGACTTAGATAACACGACCGTCTGTTAGGCCATGAAACTCT
252992 CTGA
1 CTGA
252996 TTTGATACAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (42 bp):
CTGACTTAGATAACACGACCGTCTGTTAGGCCATGAAACTCT
Found at i:253015 original size:42 final size:42
Alignment explanation
Indices: 252908--253015 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 42
252898 GTGTAACTTA
* * * * *
252908 CTGACTTAGATAACACGACCGTCTGTTAGGCTATGAAACTCT
1 CTGACTTAGATCACAAGGCCGTGTGTTAGGCCATGAAACTCT
* *
252950 CTGACTTAGATCACACGGCCGTGTGTTAGGCCATGTAACTCT
1 CTGACTTAGATCACAAGGCCGTGTGTTAGGCCATGAAACTCT
* *
252992 CTGA-TTTGATACACAAGGTCGTGT
1 CTGACTTAGAT-CACAAGGCCGTGT
253016 CGCAAACCTT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 5 0.09
42 52 0.91
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (42 bp):
CTGACTTAGATCACAAGGCCGTGTGTTAGGCCATGAAACTCT
Found at i:254096 original size:37 final size:37
Alignment explanation
Indices: 254033--254120 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
254023 ACACAAGTAG
*
254033 TCCAACCAA-AACACGCCAAACGCTCATAAGAGCTAA
1 TCCAACCAATAACACGCCAAACACTCATAAGAGCTAA
* *
254069 TCCAACCAATAACATGCCAAACACTCATGAGAGCTAA
1 TCCAACCAATAACACGCCAAACACTCATAAGAGCTAA
254106 TCCAACCAATAACAC
1 TCCAACCAATAACAC
254121 ACCTTGACAC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 9 0.19
37 38 0.81
ACGTcount: A:0.44, C:0.33, G:0.09, T:0.14
Consensus pattern (37 bp):
TCCAACCAATAACACGCCAAACACTCATAAGAGCTAA
Found at i:262025 original size:25 final size:26
Alignment explanation
Indices: 261973--262056 Score: 89
Period size: 26 Copynumber: 3.3 Consensus size: 26
261963 GTACATAATA
** * *
261973 CCTGCTAAATATTCACCAGCTCAAAG
1 CCTGCTAAATAAACATCGGCTCAAAG
*
261999 CCTGCTAAATAAAC-TCGGCTCATAG
1 CCTGCTAAATAAACATCGGCTCAAAG
* * *
262024 CCTTCTAAGTAATCATCGGCTCAAAG
1 CCTGCTAAATAAACATCGGCTCAAAG
262050 CCTGCTA
1 CCTGCTA
262057 TTCAAGTACA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
25 19 0.40
26 28 0.60
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.25
Consensus pattern (26 bp):
CCTGCTAAATAAACATCGGCTCAAAG
Found at i:262051 original size:26 final size:25
Alignment explanation
Indices: 261991--262056 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
261981 ATATTCACCA
261991 GCTCAAAGCCTGCTAAATAAACTCG
1 GCTCAAAGCCTGCTAAATAAACTCG
* * * *
262016 GCTCATAGCCTTCTAAGTAATCATCG
1 GCTCAAAGCCTGCTAAATAAAC-TCG
262042 GCTCAAAGCCTGCTA
1 GCTCAAAGCCTGCTA
262057 TTCAAGTACA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
25 18 0.53
26 16 0.47
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (25 bp):
GCTCAAAGCCTGCTAAATAAACTCG
Found at i:263072 original size:13 final size:13
Alignment explanation
Indices: 263051--263080 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
263041 AACTAATAGA
*
263051 AACTGATTTTTCC
1 AACTAATTTTTCC
263064 AACTAATTTTTCC
1 AACTAATTTTTCC
263077 AACT
1 AACT
263081 TTTATGACCC
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:0.30, C:0.23, G:0.03, T:0.43
Consensus pattern (13 bp):
AACTAATTTTTCC
Found at i:264999 original size:28 final size:28
Alignment explanation
Indices: 264959--265017 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
264949 ATACAACATG
*
264959 CAGCAACAGTGTGGGCCTTAGCCCAATA
1 CAGCAACAATGTGGGCCTTAGCCCAATA
264987 CAGCAACAATGTGGGCCTTAGCCCAATA
1 CAGCAACAATGTGGGCCTTAGCCCAATA
265015 CAG
1 CAG
265018 TATCTCAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.17
Consensus pattern (28 bp):
CAGCAACAATGTGGGCCTTAGCCCAATA
Found at i:265270 original size:32 final size:32
Alignment explanation
Indices: 265231--265421 Score: 204
Period size: 32 Copynumber: 6.0 Consensus size: 32
265221 ACAAATACAA
* * *
265231 TAATATGATTGGCACAAAGCCATCAATAGCAG
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
* * * *
265263 TGATATGATCGACACATAGCCATCAGTAACGG
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
* *
265295 TAATATGATCGGCACAAAGCCATCAGTAGCAA
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
* * * *
265327 TGATATGATCAGCACACAGCCATCAGTAACGG
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
* *
265359 TAATATAATCGGCACAAAGTCATCAGTAAC-G
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
* * *
265390 ATAATATGATCAGCACAAAACCATCAGCAACA
1 -TAATATGATCGGCACAAAGCCATCAGTAACA
265422 TCGCAGTAAA
Statistics
Matches: 128, Mismatches: 29, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
31 1 0.01
32 127 0.99
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (32 bp):
TAATATGATCGGCACAAAGCCATCAGTAACAG
Found at i:265332 original size:64 final size:64
Alignment explanation
Indices: 265231--265416 Score: 257
Period size: 64 Copynumber: 2.9 Consensus size: 64
265221 ACAAATACAA
* * * *
265231 TAATATGATTGGCACAAAGCCATCAATAGCAGTGATATGATC-GACACATAGCCATCAGTAACGG
1 TAATATGATCGGCACAAAGCCATCAGTAGCAATGATATGATCAG-CACACAGCCATCAGTAACGG
265295 TAATATGATCGGCACAAAGCCATCAGTAGCAATGATATGATCAGCACACAGCCATCAGTAACGG
1 TAATATGATCGGCACAAAGCCATCAGTAGCAATGATATGATCAGCACACAGCCATCAGTAACGG
* * * * * * *
265359 TAATATAATCGGCACAAAGTCATCAGTAACGATAATATGATCAGCACAAAACCATCAG
1 TAATATGATCGGCACAAAGCCATCAGTAGCAATGATATGATCAGCACACAGCCATCAG
265417 CAACATCGCA
Statistics
Matches: 110, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
64 109 0.99
65 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (64 bp):
TAATATGATCGGCACAAAGCCATCAGTAGCAATGATATGATCAGCACACAGCCATCAGTAACGG
Found at i:265397 original size:96 final size:96
Alignment explanation
Indices: 265228--265416 Score: 243
Period size: 96 Copynumber: 2.0 Consensus size: 96
265218 GCCACAAATA
** * * * *
265228 CAATAATATGATTGGCACAAAGCCATCAATAGCAGTGATATGATCGACACATAGCCATCAGTAAC
1 CAATAATATGATCAGCACAAAGCCATCAATAACAGTAATATAATCGACACAAAGCCATCAGTAAC
* * *
265293 GGTAATATGATCGGCACAAAGCCATCAGTAG
66 GATAATATGATCAGCACAAAACCATCAGTAG
* * * * * *
265324 CAATGATATGATCAGCACACAGCCATCAGTAACGGTAATATAATCGGCACAAAGTCATCAGTAAC
1 CAATAATATGATCAGCACAAAGCCATCAATAACAGTAATATAATCGACACAAAGCCATCAGTAAC
265389 GATAATATGATCAGCACAAAACCATCAG
66 GATAATATGATCAGCACAAAACCATCAG
265417 CAACATCGCA
Statistics
Matches: 78, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
96 78 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (96 bp):
CAATAATATGATCAGCACAAAGCCATCAATAACAGTAATATAATCGACACAAAGCCATCAGTAAC
GATAATATGATCAGCACAAAACCATCAGTAG
Found at i:265627 original size:24 final size:24
Alignment explanation
Indices: 265563--265639 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
265553 CCATGCTCAG
** *
265563 AATCAGTCATACAATTCACAGACA
1 AATCAGTCATTTAAATCACAGACA
* *
265587 AAACAGTCGTTTAAATCACAGACA
1 AATCAGTCATTTAAATCACAGACA
* **
265611 AATCAGTCATTTTAATCATGGACA
1 AATCAGTCATTTAAATCACAGACA
265635 AATCA
1 AATCA
265640 ATTGTTTAAC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (24 bp):
AATCAGTCATTTAAATCACAGACA
Found at i:265740 original size:27 final size:27
Alignment explanation
Indices: 265701--265866 Score: 121
Period size: 27 Copynumber: 6.1 Consensus size: 27
265691 GGTTATTTGA
* * *
265701 CCTTACAGTGGTATTTTGGTCATTTTAC
1 CCTTAGAG-GGTAATTTGATCATTTTAC
* *
265729 CCTAAGAGGGT-ATCTT-AGCCATTTTAC
1 CCTTAGAGGGTAAT-TTGA-TCATTTTAC
* *
265756 CCTTCG-GGGATAATTCGATCATTTTA-
1 CCTTAGAGGG-TAATTTGATCATTTTAC
**
265782 CCTTTCAGGGTAATTTGATCATTTTAC
1 CCTTAGAGGGTAATTTGATCATTTTAC
265809 CCTTCAG-GGGTAATTT-AGTCATTTTAC
1 CCTT-AGAGGGTAATTTGA-TCATTTTAC
* *
265836 CCTTCGAGGGT-ATTTCGATAATTTTAC
1 CCTTAGAGGGTAATTT-GATCATTTTAC
265863 CCTT
1 CCTT
265867 CGGGGGTATT
Statistics
Matches: 110, Mismatches: 16, Indels: 25
0.73 0.11 0.17
Matches are distributed among these distances:
26 29 0.26
27 71 0.65
28 10 0.09
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (27 bp):
CCTTAGAGGGTAATTTGATCATTTTAC
Found at i:265810 original size:80 final size:81
Alignment explanation
Indices: 265695--265863 Score: 211
Period size: 80 Copynumber: 2.1 Consensus size: 81
265685 CATTACGGTT
* * *
265695 ATTTGACCTTACAGTGGTATTTTGGTCATTTTACCC-TAAGAGGGT-ATCTTAGCCATTTTACCC
1 ATTTTACCTTACAGTGGTAATTTGATCATTTTACCCTTAAG-GGGTAAT-TTAGCCATTTTACCC
*
265758 TTCG-GGGATAATTCGATC
64 TTCGAGGG-TAATTCGATA
* * *
265776 ATTTTACCTTTCAG-GGTAATTTGATCATTTTACCCTTCAGGGGTAATTTAGTCATTTTACCCTT
1 ATTTTACCTTACAGTGGTAATTTGATCATTTTACCCTTAAGGGGTAATTTAGCCATTTTACCCTT
*
265840 CGAGGGTATTTCGATA
66 CGAGGGTAATTCGATA
265856 ATTTTACC
1 ATTTTACC
265864 CTTCGGGGGT
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
80 57 0.74
81 20 0.26
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (81 bp):
ATTTTACCTTACAGTGGTAATTTGATCATTTTACCCTTAAGGGGTAATTTAGCCATTTTACCCTT
CGAGGGTAATTCGATA
Found at i:265867 original size:27 final size:27
Alignment explanation
Indices: 265749--266102 Score: 269
Period size: 27 Copynumber: 13.1 Consensus size: 27
265739 TATCTTAGCC
* *
265749 ATTTTACCCTTCG-GGGATAATTCGATC
1 ATTTTACCCTTCGAGGG-TATTTCGATA
* *
265776 ATTTTACCTTTC-AGGGTAATTT-GATC
1 ATTTTACCCTTCGAGGGT-ATTTCGATA
* *
265802 ATTTTACCCTTC-AGGGGTAATTTAG-TC
1 ATTTTACCCTTCGA-GGGT-ATTTCGATA
265829 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
265856 ATTTTACCCTTCGGGGGTATTTCAAAA
1 ATTTTACCCTTCGAGGGTATTTCGATA
** *
265883 ATTTTA-TTTATTGAGGGTATTTC-AGTA
1 ATTTTACCCT-TCGAGGGTATTTCGA-TA
* *
265910 ACTTTACCCATCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
** **
265937 ATTTTACCAATCGAGGGTATTTTAATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
*
265964 ATTTTACCCTTCGAGGGTATTT-TAGTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
* * *
265991 GTTTTACCATTC-AGGGCTATTTCGGTA
1 ATTTTACCCTTCGAGGG-TATTTCGATA
* *
266018 ATTTTACCCTTCGAGGGTATCTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
266045 ACTTTACCCATCGATGGTATTTC-AGTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
* * * * *
266072 ATTTTATCCATCGAGGGCATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
266099 ATTT
1 ATTT
266103 GCCCACGAAT
Statistics
Matches: 268, Mismatches: 43, Indels: 32
0.78 0.13 0.09
Matches are distributed among these distances:
26 29 0.11
27 232 0.87
28 7 0.03
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATA
Found at i:268566 original size:34 final size:34
Alignment explanation
Indices: 268490--268568 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
268480 ATCACAATGT
* **
268490 CAGTAATCAGTAGGGCCTTTGCCCAATTTCAGTAA
1 CAGT-ATCAGTAGGGCCTTGGCCCAATAACAGTAA
* *
268525 TAGTATCAGTGGGGCCTTGGCCC-ATAACAGTAA
1 CAGTATCAGTAGGGCCTTGGCCCAATAACAGTAA
268558 CAGATATCAGT
1 CAG-TATCAGT
268569 CATGCAGTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
33 10 0.27
34 24 0.65
35 3 0.08
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (34 bp):
CAGTATCAGTAGGGCCTTGGCCCAATAACAGTAA
Found at i:269049 original size:27 final size:27
Alignment explanation
Indices: 269019--269104 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 27
269009 TCATCTCCTA
*
269019 GGGGTATAACAGTCATTTTACCCTATG
1 GGGGTATAACAGTCATTCTACCCTATG
**** *
269046 GGGGTATTTTGGTTATTCTACCCTATG
1 GGGGTATAACAGTCATTCTACCCTATG
**** *
269073 GGGGTATTTTGGTTATTCTACCCTATG
1 GGGGTATAACAGTCATTCTACCCTATG
269100 GGGGT
1 GGGGT
269105 GTTTCGGTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.40
Consensus pattern (27 bp):
GGGGTATAACAGTCATTCTACCCTATG
Found at i:288682 original size:9 final size:9
Alignment explanation
Indices: 288670--288727 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
288660 TTTGCTGAGA
288670 TTGTTGCTG
1 TTGTTGCTG
288679 TTGTTGCTG
1 TTGTTGCTG
*
288688 TTGTTGCCG
1 TTGTTGCTG
* *
288697 CTGCTGCTG
1 TTGTTGCTG
* *
288706 CTGTTGTTG
1 TTGTTGCTG
*
288715 TTGTTGTTG
1 TTGTTGCTG
288724 TTGT
1 TTGT
288728 CGGTGATTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.00, C:0.14, G:0.33, T:0.53
Consensus pattern (9 bp):
TTGTTGCTG
Found at i:299207 original size:26 final size:26
Alignment explanation
Indices: 299173--299275 Score: 136
Period size: 26 Copynumber: 4.0 Consensus size: 26
299163 ACACCAATAT
* *
299173 CGCAGCAAAACTGCCAGTAATAATGAA
1 CGCAGCAAAGCTGCCAGTAATAGT-AA
299200 -GCAGCAAAGCTGCCAGTAATAGTAA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
* * *
299225 TGCAACAAAGCTGCCAGTAACAGTAA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
*
299251 CGCAGCAAAGCTGCCAGTAACAGTA
1 CGCAGCAAAGCTGCCAGTAATAGTA
299276 TATGTGGCAA
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
25 2 0.03
26 67 0.97
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAATAGTAA
Found at i:299300 original size:52 final size:52
Alignment explanation
Indices: 299200--299301 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 52
299190 TAATAATGAA
* **
299200 GCAGCAAAGCTGCCAGTAATAGTAATGCAACAAAGCTGCCAGTAACAGTAAC
1 GCAGCAAAGCTGCCAGTAACAGTAATGCAACAAAGCCACCAGTAACAGTAAC
***
299252 GCAGCAAAGCTGCCAGTAACAGTATATGTGGCAAAGCCACCAGT-ACAGTA
1 GCAGCAAAGCTGCCAGTAACAGTA-ATGCAACAAAGCCACCAGTAACAGTA
299302 TACTTCCCCT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 29 0.67
53 14 0.33
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.16
Consensus pattern (52 bp):
GCAGCAAAGCTGCCAGTAACAGTAATGCAACAAAGCCACCAGTAACAGTAAC
Found at i:299673 original size:27 final size:27
Alignment explanation
Indices: 299451--299673 Score: 277
Period size: 27 Copynumber: 8.3 Consensus size: 27
299441 GGGTATAACA
299451 GTCATTTTACCCTATCG-GGGTATTTCG
1 GTCATTTTACCC-ATCGAGGGTATTTCG
* * ** *
299478 ATCATTTTACCCTTTAAGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
* *
299505 ATCATTTTACCCATCGAGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
* * * **
299532 ATTATTTTGCCCATCGAGGGTATTTTA
1 GTCATTTTACCCATCGAGGGTATTTCG
*
299559 GCCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
299586 GTCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* *
299613 GTCATTTTACCCATTGAGAGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
*
299640 GTCATTTTACCCATCGAGGGTATTTGG
1 GTCATTTTACCCATCGAGGGTATTTCG
*
299667 GTTATTT
1 GTCATTT
299674 GCCCACGAAT
Statistics
Matches: 171, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 1 0.01
27 170 0.99
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (27 bp):
GTCATTTTACCCATCGAGGGTATTTCG
Found at i:307440 original size:17 final size:17
Alignment explanation
Indices: 307418--307452 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
307408 CACGGGCTGT
307418 CACACGGCCAT-GTGACA
1 CACACGGCC-TGGTGACA
307435 CACACGGCCTGGTGACA
1 CACACGGCCTGGTGACA
307452 C
1 C
307453 GGTCCGGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 16 0.94
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (17 bp):
CACACGGCCTGGTGACA
Found at i:309181 original size:17 final size:17
Alignment explanation
Indices: 309159--309191 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
309149 GTGTGTCCAT
309159 TTCTTCTCTTCTTCTTC
1 TTCTTCTCTTCTTCTTC
*
309176 TTCTTCTCTTTTTCTT
1 TTCTTCTCTTCTTCTT
309192 TTTATAACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCTTCTCTTCTTCTTC
Found at i:318362 original size:36 final size:36
Alignment explanation
Indices: 318315--318391 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
318305 CTTTTGAATA
318315 AAAAAAGAGGGATAAAAGGGTTTTGATTAAGGTTTG
1 AAAAAAGAGGGATAAAAGGGTTTTGATTAAGGTTTG
* * * * *
318351 AAAAAATAGGGATTAAGGGGTTTTG-TTTAGGGTT-
1 AAAAAAGAGGGATAAAAGGGTTTTGATTAAGGTTTG
318385 AAAAAAG
1 AAAAAAG
318392 GATTAGAGGG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 6 0.17
35 7 0.20
36 22 0.63
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.29
Consensus pattern (36 bp):
AAAAAAGAGGGATAAAAGGGTTTTGATTAAGGTTTG
Found at i:318588 original size:22 final size:21
Alignment explanation
Indices: 318562--318639 Score: 70
Period size: 22 Copynumber: 3.7 Consensus size: 21
318552 TCGTTTTTGT
318562 TGTTTTTGAATTATTTGAAAAA
1 TGTTTTTGAATTATTTG-AAAA
* ***
318584 TGTTTTTGATTTA-TTG-GGT
1 TGTTTTTGAATTATTTGAAAA
*
318603 TATTTTTGAATTATTTGACAAA
1 TGTTTTTGAATTATTTGA-AAA
*
318625 TGTTTTTGATTTATT
1 TGTTTTTGAATTATT
318640 GAGGTTGTGA
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
19 11 0.26
20 3 0.07
21 3 0.07
22 25 0.60
ACGTcount: A:0.26, C:0.01, G:0.15, T:0.58
Consensus pattern (21 bp):
TGTTTTTGAATTATTTGAAAA
Found at i:318626 original size:41 final size:42
Alignment explanation
Indices: 318564--318645 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 42
318554 GTTTTTGTTG
318564 TTTTTGAATTATTTGAAAAATGTTTTTGATTTATTG-GGTTA
1 TTTTTGAATTATTTGAAAAATGTTTTTGATTTATTGAGGTTA
*
318605 TTTTTGAATTATTTGACAAATGTTTTTGATTTATTGAGGTT
1 TTTTTGAATTATTTGAAAAATGTTTTTGATTTATTGAGGTT
318646 GTGATTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 35 0.90
42 4 0.10
ACGTcount: A:0.26, C:0.01, G:0.17, T:0.56
Consensus pattern (42 bp):
TTTTTGAATTATTTGAAAAATGTTTTTGATTTATTGAGGTTA
Found at i:324080 original size:14 final size:15
Alignment explanation
Indices: 324063--324095 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
324053 CCTTAAATTA
324063 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
324077 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
324092 AATC
1 AATC
324096 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:324624 original size:40 final size:39
Alignment explanation
Indices: 324567--324655 Score: 133
Period size: 40 Copynumber: 2.3 Consensus size: 39
324557 TAGGTTTTTT
* *
324567 GCGGCATTTTTTGAAAGCGCCGCTAATGCTCGATCTTTA
1 GCGGCGTTTTATGAAAGCGCCGCTAATGCTCGATCTTTA
*
324606 GCGGCGTTTTATGTAAAGCGCCGCTAATGCTCGATTTTTA
1 GCGGCGTTTTATG-AAAGCGCCGCTAATGCTCGATCTTTA
*
324646 GCAGCGTTTT
1 GCGGCGTTTT
324656 TTGTCCAAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 11 0.24
40 34 0.76
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (39 bp):
GCGGCGTTTTATGAAAGCGCCGCTAATGCTCGATCTTTA
Found at i:327264 original size:6 final size:6
Alignment explanation
Indices: 327253--327277 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
327243 CATTTTAATT
327253 AGAACA AGAACA AGAACA AGAACA A
1 AGAACA AGAACA AGAACA AGAACA A
327278 AAAAATGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAACA
Found at i:338019 original size:25 final size:25
Alignment explanation
Indices: 337985--338039 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
337975 GAATTAGCAT
*
337985 ATTTGGGTGTAAAATAAAATGGGTA
1 ATTTGGGTGTAAAAGAAAATGGGTA
338010 ATTTGGGTGTAAAAGAAAATGGGTA
1 ATTTGGGTGTAAAAGAAAATGGGTA
338035 ATTTG
1 ATTTG
338040 CATGTTTGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.33
Consensus pattern (25 bp):
ATTTGGGTGTAAAAGAAAATGGGTA
Found at i:352998 original size:29 final size:29
Alignment explanation
Indices: 352961--353020 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
352951 ACTAATTAAA
352961 TTAATTAACCTAAAATAACCTAATGGAAT
1 TTAATTAACCTAAAATAACCTAATGGAAT
* *
352990 TTAATTAACCTAAGATATCCTAATGGAAT
1 TTAATTAACCTAAAATAACCTAATGGAAT
353019 TT
1 TT
353021 CCTATTCCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.35
Consensus pattern (29 bp):
TTAATTAACCTAAAATAACCTAATGGAAT
Found at i:355507 original size:18 final size:20
Alignment explanation
Indices: 355484--355521 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
355474 TATATCAATT
355484 TATAAAT-ATATT-ATAATA
1 TATAAATAATATTAATAATA
355502 TATAAATAATATTAATAATA
1 TATAAATAATATTAATAATA
355522 AAATAGAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 5 0.28
20 6 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TATAAATAATATTAATAATA
Found at i:360297 original size:48 final size:49
Alignment explanation
Indices: 360225--360323 Score: 191
Period size: 48 Copynumber: 2.0 Consensus size: 49
360215 ACTATTTCTG
360225 ACACCACTAATGTAACACCCCTTAACCGTATCCAACACCGGAATAGGGT
1 ACACCACTAATGTAACACCCCTTAACCGTATCCAACACCGGAATAGGGT
360274 ACACCACTAAT-TAACACCCCTTAACCGTATCCAACACCGGAATAGGGT
1 ACACCACTAATGTAACACCCCTTAACCGTATCCAACACCGGAATAGGGT
360322 AC
1 AC
360324 GAGGCATTAC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 39 0.78
49 11 0.22
ACGTcount: A:0.35, C:0.33, G:0.13, T:0.18
Consensus pattern (49 bp):
ACACCACTAATGTAACACCCCTTAACCGTATCCAACACCGGAATAGGGT
Found at i:378050 original size:129 final size:129
Alignment explanation
Indices: 377819--378070 Score: 387
Period size: 129 Copynumber: 2.0 Consensus size: 129
377809 TTACCAAAAT
* *** * *
377819 TTCAATCTGAGTAGACAGCGATGTCTCGGCAACGAGAATTCTAATCTACTATTGAACCAAGCCGC
1 TTCAATCTGAGTAGACAGCAACACCTCAGCAACGAGAATTCTAATCTACTATCGAACCAAGCCGC
* *
377884 AGCCTTTTATGATTCCGACCTCTACATAATCCACCCAGTTTGACAATGAACGGAAGAATGAAAC
66 AACCTTTTATGATTCCGACCTCTACATAATCCACCCAGTATGACAATGAACGGAAGAATGAAAC
* *
377948 TTCAATCTGAGTAGACAGCAACACCTCAGCAACGAGAATTCTGATCTACTATCGAACCAAGCCGT
1 TTCAATCTGAGTAGACAGCAACACCTCAGCAACGAGAATTCTAATCTACTATCGAACCAAGCCGC
* * *
378013 AACCTTTTATGATTCCGACCTCTACGTAATCCGCCCAGTATGACAATGAATGGAAGAA
66 AACCTTTTATGATTCCGACCTCTACATAATCCACCCAGTATGACAATGAACGGAAGAA
378071 ATCTCCAAAA
Statistics
Matches: 110, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
129 110 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (129 bp):
TTCAATCTGAGTAGACAGCAACACCTCAGCAACGAGAATTCTAATCTACTATCGAACCAAGCCGC
AACCTTTTATGATTCCGACCTCTACATAATCCACCCAGTATGACAATGAACGGAAGAATGAAAC
Found at i:383205 original size:18 final size:19
Alignment explanation
Indices: 383177--383213 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
383167 ACATTCACAT
383177 CTTTCCTCTCTTCTCTCCA
1 CTTTCCTCTCTTCTCTCCA
*
383196 CTTT-CTCTCTTCTTTCCA
1 CTTTCCTCTCTTCTCTCCA
383214 TTCCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.05, C:0.43, G:0.00, T:0.51
Consensus pattern (19 bp):
CTTTCCTCTCTTCTCTCCA
Found at i:391337 original size:24 final size:24
Alignment explanation
Indices: 391246--391342 Score: 124
Period size: 24 Copynumber: 4.0 Consensus size: 24
391236 TCCCCGAAAT
* * * *
391246 AATGAAATGTTTGAAAAGGTTACT
1 AATGAAAAGGTTGAAAAGGATACC
*
391270 AATGAAAAGGTTGAAAAGG-TCATC
1 AATGAAAAGGTTGAAAAGGAT-ACC
*
391294 AATGAAAAGGTCGAAAAGGATACC
1 AATGAAAAGGTTGAAAAGGATACC
391318 AATGAAAAGGTTGAAAAGGATACC
1 AATGAAAAGGTTGAAAAGGATACC
391342 A
1 A
391343 TTATATCAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
23 1 0.02
24 62 0.97
25 1 0.02
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.21
Consensus pattern (24 bp):
AATGAAAAGGTTGAAAAGGATACC
Found at i:395898 original size:20 final size:20
Alignment explanation
Indices: 395852--395917 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
395842 TATTTATAAT
* *
395852 GATTTA-CAAAATTTCTAAG
1 GATTTACCAAAATATCCAAG
*
395871 G-TTATACCAAAATATCCATG
1 GATT-TACCAAAATATCCAAG
* *
395891 GATTTACCAACATATCTAAG
1 GATTTACCAAAATATCCAAG
395911 GATTTAC
1 GATTTAC
395918 TAAAGTTCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 2 0.05
19 3 0.08
20 31 0.82
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (20 bp):
GATTTACCAAAATATCCAAG
Found at i:395978 original size:20 final size:20
Alignment explanation
Indices: 395939--395998 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
395929 AGGCTACTTG
*
395939 GAAATTTTTGTAAATCCTTA
1 GAAATTTTGGTAAATCCTTA
*
395959 GATATTTTGGTATAAT-CTTA
1 GAAATTTTGGTA-AATCCTTA
*
395979 GAAATTTTGGTAAATTCTTA
1 GAAATTTTGGTAAATCCTTA
395999 AGGGTTTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.09
20 29 0.83
21 3 0.09
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (20 bp):
GAAATTTTGGTAAATCCTTA
Found at i:396120 original size:20 final size:21
Alignment explanation
Indices: 396097--396194 Score: 82
Period size: 20 Copynumber: 4.9 Consensus size: 21
396087 ATTGGTAACT
396097 CCTTGGAAATTTTGGTATAA-
1 CCTTGGAAATTTTGGTATAAG
*
396117 CCTTAGG-AATTTTGGTA-AAT
1 CCTT-GGAAATTTTGGTATAAG
*
396137 CCTT-AAATATTTTGGTATAA-
1 CCTTGGAA-ATTTTGGTATAAG
***
396157 CCTACTAAATTTTGGTA-AAG
1 CCTTGGAAATTTTGGTATAAG
*
396177 CCTTAGAAATTTTGGTAT
1 CCTTGGAAATTTTGGTAT
396195 GCCAAAATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
19 5 0.08
20 53 0.83
21 6 0.09
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (21 bp):
CCTTGGAAATTTTGGTATAAG
Found at i:396132 original size:40 final size:38
Alignment explanation
Indices: 396077--396194 Score: 130
Period size: 40 Copynumber: 2.9 Consensus size: 38
396067 AGTTAAAAAC
* *
396077 CCTTAGAAATATTGGTAACTCCTTGGAAATTTTGGTATAA
1 CCTTAG-AATTTTGGTAAATCCTT-GAAATTTTGGTATAA
*
396117 CCTTAGGAATTTTGGTAAATCCTTAAATATTTTGGTATAA
1 CCTTA-GAATTTTGGTAAATCCTTGAA-ATTTTGGTATAA
*
396157 CCTACTA-AATTTTGGTAAAGCCTTAGAAATTTTGGTAT
1 CCT--TAGAATTTTGGTAAATCCTT-GAAATTTTGGTAT
396195 GCCAAAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
39 2 0.03
40 61 0.90
41 3 0.04
42 2 0.03
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (38 bp):
CCTTAGAATTTTGGTAAATCCTTGAAATTTTGGTATAA
Found at i:404683 original size:43 final size:42
Alignment explanation
Indices: 404616--404786 Score: 172
Period size: 43 Copynumber: 4.0 Consensus size: 42
404606 ACATAGTATT
*
404616 TCGATATGTGTTTTCATGTAAGACCACGTCTGGGACGTTGGCA
1 TCGAT-TGTGTTTACATGTAAGACCACGTCTGGGACGTTGGCA
* * * * *
404659 TCGACTTGTGTTTACGTGTAAGACCATGTCTGAGACATTTGCA
1 TCGA-TTGTGTTTACATGTAAGACCACGTCTGGGACGTTGGCA
*
404702 TCGTATT-TGATTT--GTGTAAGACC-CTGTCTGGGACAG-TGGCA
1 TCG-ATTGTG-TTTACATGTAAGACCAC-GTCTGGGAC-GTTGGCA
*
404743 TCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCA
1 TCGAT-TGTGTTTACATGTAAGACCACGTCTGGGACGTTGGCA
404786 T
1 T
404787 TGTACAAGTC
Statistics
Matches: 105, Mismatches: 12, Indels: 22
0.76 0.09 0.16
Matches are distributed among these distances:
40 2 0.02
41 28 0.27
42 5 0.05
43 67 0.64
44 3 0.03
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (42 bp):
TCGATTGTGTTTACATGTAAGACCACGTCTGGGACGTTGGCA
Found at i:407852 original size:300 final size:300
Alignment explanation
Indices: 407304--407912 Score: 1130
Period size: 300 Copynumber: 2.0 Consensus size: 300
407294 TACTAATCAT
*
407304 AATAT-ACTAATCCATGATCAAAGTATGCTTCAACCATAATTCAGCCCAAAACCGAACACAAACA
1 AATATAACTAATCCATGATCAAAGTATGCTTCAACCATAATTCAACCCAAAACCGAACACAAACA
407368 AGAAAATTAAGCCATTTTCGCATGGCTCAATTTTACATAATCAAAAATCAAGCATTTCAGCTACG
66 AGAAAATTAAGCCATTTTCGCATGGCTCAATTTTACATAATCAAAAATCAAGCATTTCAGCTACG
407433 CTATACATGCCATAAGTTCGAATTCAAACTTAACAAAATAACGAGATGAGTCAACAGTGTGATAA
131 CTATACATGCCATAAGTTCGAATTCAAACTTAACAAAATAACGAGATGAGTCAACAGTGTGATAA
*
407498 TCTTCTCTGACGATCCCCGAGCTCGTAACCAACTTCCAAAAATCTATGAAACGAAGAGCAACAGA
196 TCTTCTCTGACGATCCCCGAGCTCGTAACCAACTTCCAAAAATCTATAAAACGAAGAGCAACAGA
407563 CACACAGCAAGCTATTTAAGCTTAGTAAGCCATAAGCAAA
261 CACACAGCAAGCTATTTAAGCTTAGTAAGCCATAAGCAAA
407603 AATATAACTAATCCATGATCAAAGTATGCTTCAACCATAATTCAACCCAAAACCGAACACAAACA
1 AATATAACTAATCCATGATCAAAGTATGCTTCAACCATAATTCAACCCAAAACCGAACACAAACA
* *
407668 AGAAAATTAATCCATTTTCGCATGTCTCAATTTTACATAATCAAAAATCAAGCATTTCAGCTACG
66 AGAAAATTAAGCCATTTTCGCATGGCTCAATTTTACATAATCAAAAATCAAGCATTTCAGCTACG
* * *
407733 TTATACATGCCATAAGTTCGAATTCAAACTTAACAAAATATCGAGATGAGTCGACAGTGTGATAA
131 CTATACATGCCATAAGTTCGAATTCAAACTTAACAAAATAACGAGATGAGTCAACAGTGTGATAA
407798 TCTTCTCTGACGATCCCCGAGCTCGTAACCAACTTCCAAAAATCTATAAAACGAAGAGCAACAGA
196 TCTTCTCTGACGATCCCCGAGCTCGTAACCAACTTCCAAAAATCTATAAAACGAAGAGCAACAGA
* *
407863 CACACAGTAAGCTATTTAAGCTTAGTAAGTCATAAGCAAA
261 CACACAGCAAGCTATTTAAGCTTAGTAAGCCATAAGCAAA
407903 AATATAACTA
1 AATATAACTA
407913 TCAACAATTA
Statistics
Matches: 300, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
299 5 0.02
300 295 0.98
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.24
Consensus pattern (300 bp):
AATATAACTAATCCATGATCAAAGTATGCTTCAACCATAATTCAACCCAAAACCGAACACAAACA
AGAAAATTAAGCCATTTTCGCATGGCTCAATTTTACATAATCAAAAATCAAGCATTTCAGCTACG
CTATACATGCCATAAGTTCGAATTCAAACTTAACAAAATAACGAGATGAGTCAACAGTGTGATAA
TCTTCTCTGACGATCCCCGAGCTCGTAACCAACTTCCAAAAATCTATAAAACGAAGAGCAACAGA
CACACAGCAAGCTATTTAAGCTTAGTAAGCCATAAGCAAA
Found at i:410905 original size:43 final size:43
Alignment explanation
Indices: 410850--411159 Score: 333
Period size: 43 Copynumber: 7.3 Consensus size: 43
410840 TTTTAGAAAT
*
410850 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCAC
1 AAACACCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCAC
* * * *
410893 AAACACTGCTATAGATCAGGACCTTTAGCAGTGCTTTTTCCAC
1 AAACACCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCAC
* * *
410936 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGC-TTTTACAC
1 AAACACCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCAC
* * * * *
410978 AAACGCCGCTGTA-ACTCAAGATCTTTAGCGGCGCTTATTCCAC
1 AAACACCGCTATAGA-TCATGACCTTTAGCGGCGCTTTTTCCAC
* *
411021 AAACACCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
1 AAACACCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCAC
* * * * *
411064 AAAGGA-CGCTATAGGTCATGACTTTTAGCGGTGCTTTTCCCAC
1 AAA-CACCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCAC
* * **
411107 AAACGCCGCTATAGAACA-GACCTTTAGCGGC-AATTTTCACAC
1 AAACACCGCTATAGATCATGACCTTTAGCGGCGCTTTTTC-CAC
*
411149 AAACGCCGCTA
1 AAACACCGCTA
411160 AAAACATATC
Statistics
Matches: 227, Mismatches: 34, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
41 5 0.02
42 61 0.27
43 159 0.70
44 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (43 bp):
AAACACCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCAC
Found at i:411091 original size:128 final size:129
Alignment explanation
Indices: 410850--411159 Score: 385
Period size: 128 Copynumber: 2.4 Consensus size: 129
410840 TTTTAGAAAT
* * *
410850 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCACAAACACTGCTATAGATCAGGAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTATTCCACAAACACCGCTATAGATCAGGAC
* * *
410915 CTTTAGCAGTGCTTTTTCCACAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTT-ACAC
66 CTTTAGCAGCGCTTTTCCCACAAACGACGCTATAGATCAGGACCTTTAGCGGCGCTTTTCACAC
* * *
410978 AAACGCCGCTGTA-ACTCAAGATCTTTAGCGGCGCTTATTCCACAAACACCGCTATAGATCATGA
1 AAACGCCGCTATAGA-TCAAGACCTTTAGCGGCGCTTATTCCACAAACACCGCTATAGATCAGGA
* * * * * * * *
411042 CTTTTAGCGGCGCTTTTCCCACAAAGGACGCTATAGGTCATGACTTTTAGCGGTGCTTTTCCCAC
65 CCTTTAGCAGCGCTTTTCCCACAAACGACGCTATAGATCAGGACCTTTAGCGGCGCTTTTCACAC
* ** *
411107 AAACGCCGCTATAGAAC-AGACCTTTAGCGGCAATT-TTCACACAAACGCCGCTA
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTATTC-CACAAACACCGCTA
411160 AAAACATATC
Statistics
Matches: 155, Mismatches: 23, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
127 4 0.03
128 134 0.86
129 16 0.10
130 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (129 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTATTCCACAAACACCGCTATAGATCAGGAC
CTTTAGCAGCGCTTTTCCCACAAACGACGCTATAGATCAGGACCTTTAGCGGCGCTTTTCACAC
Found at i:411151 original size:171 final size:171
Alignment explanation
Indices: 410850--411158 Score: 478
Period size: 171 Copynumber: 1.8 Consensus size: 171
410840 TTTTAGAAAT
* *
410850 AAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTCCACAAACACTGCTATAGATCAGGAC
1 AAACACCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACACTGCTATAGATCAGGAC
* * **
410915 CTTTAGCAGTGCTTTTTCCACAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTACACAA
66 CTTTAGCAGTGCTTTTCCCACAAACGCCGCTATAGAACAGGACCTTTAGCGGCAATTTTACACAA
410980 ACGCCGCTGTAACTCAAGATCTTTAGCGGCGCTTATTCCAC
131 ACGCCGCTGTAACTCAAGATCTTTAGCGGCGCTTATTCCAC
* * * *
411021 AAACACCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCACAAAGGAC-GCTATAGGTCATGA
1 AAACACCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCACAAA-CACTGCTATAGATCAGGA
* *
411085 CTTTTAGCGGTGCTTTTCCCACAAACGCCGCTATAGAACA-GACCTTTAGCGGCAATTTTCACAC
65 CCTTTAGCAGTGCTTTTCCCACAAACGCCGCTATAGAACAGGACCTTTAGCGGCAATTTT-ACAC
411149 AAACGCCGCT
129 AAACGCCGCT
411159 AAAAACATAT
Statistics
Matches: 124, Mismatches: 12, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
170 17 0.14
171 105 0.85
172 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (171 bp):
AAACACCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCCACAAACACTGCTATAGATCAGGAC
CTTTAGCAGTGCTTTTCCCACAAACGCCGCTATAGAACAGGACCTTTAGCGGCAATTTTACACAA
ACGCCGCTGTAACTCAAGATCTTTAGCGGCGCTTATTCCAC
Found at i:414071 original size:44 final size:45
Alignment explanation
Indices: 413994--414083 Score: 173
Period size: 44 Copynumber: 2.0 Consensus size: 45
413984 ATATATCAAA
413994 TGGTTTAGATTAATTTTTTTTAAATATAAAAGCATTAATTAATTG
1 TGGTTTAGATTAATTTTTTTTAAATATAAAAGCATTAATTAATTG
414039 TGGTTTAGATTAA-TTTTTTTAAATATAAAAGCATTAATTAATTG
1 TGGTTTAGATTAATTTTTTTTAAATATAAAAGCATTAATTAATTG
414083 T
1 T
414084 ATAAAATTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 32 0.71
45 13 0.29
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (45 bp):
TGGTTTAGATTAATTTTTTTTAAATATAAAAGCATTAATTAATTG
Done.