Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007894.1 Hibiscus syriacus cultivar Beakdansim tig00110279_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: 1425917
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 7
Found at i:3240 original size:14 final size:14
Alignment explanation
Indices: 3223--3282 Score: 75
Period size: 14 Copynumber: 3.9 Consensus size: 14
3213 GCTTGGCTTA
3223 GCTCAAACGGCTCG
1 GCTCAAACGGCTCG
3237 GCTCAAACGGCTCG
1 GCTCAAACGGCTCG
3251 GCTCAGCTCAAGCGGCTCG
1 GCTCA----AA-CGGCTCG
3270 GCTCAAACGGCTC
1 GCTCAAACGGCTC
3283 CTCAGGCTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
14 25 0.61
15 2 0.05
18 2 0.05
19 12 0.29
ACGTcount: A:0.20, C:0.37, G:0.28, T:0.15
Consensus pattern (14 bp):
GCTCAAACGGCTCG
Found at i:3252 original size:19 final size:19
Alignment explanation
Indices: 3230--3274 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3220 TTAGCTCAAA
*
3230 CGGCTCGGCTCAAACGGCT
1 CGGCTCAGCTCAAACGGCT
*
3249 CGGCTCAGCTCAAGCGGCT
1 CGGCTCAGCTCAAACGGCT
3268 CGGCTCA
1 CGGCTCA
3275 AACGGCTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.16, C:0.38, G:0.31, T:0.16
Consensus pattern (19 bp):
CGGCTCAGCTCAAACGGCT
Found at i:3259 original size:33 final size:33
Alignment explanation
Indices: 3211--3282 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
3201 CTAGGCGGCT
* *
3211 CGGCTTGGCTTAGCTCAAACGGCTCGGCTCAAA
1 CGGCTCGGCTCAGCTCAAACGGCTCGGCTCAAA
*
3244 CGGCTCGGCTCAGCTCAAGCGGCTCGGCTCAAA
1 CGGCTCGGCTCAGCTCAAACGGCTCGGCTCAAA
3277 CGGCTC
1 CGGCTC
3283 CTCAGGCTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.18, C:0.35, G:0.29, T:0.18
Consensus pattern (33 bp):
CGGCTCGGCTCAGCTCAAACGGCTCGGCTCAAA
Found at i:7023 original size:18 final size:18
Alignment explanation
Indices: 7000--7034 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6990 TTCCATCCGG
*
7000 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
7018 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
7035 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:8208 original size:19 final size:19
Alignment explanation
Indices: 8186--8235 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
8176 CTAGGCGGCT
*
8186 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
*
8205 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
*
8224 CGGCTCTGCTCA
1 CGGCTCGGCTCA
8236 AACGGCTCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.16, C:0.36, G:0.28, T:0.20
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:8227 original size:14 final size:14
Alignment explanation
Indices: 8210--8243 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
8200 TCAAACGGCT
*
8210 CGGCTCAGCTCAAG
1 CGGCTCAGCTCAAA
*
8224 CGGCTCTGCTCAAA
1 CGGCTCAGCTCAAA
8238 CGGCTC
1 CGGCTC
8244 CTCAGGCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.38, G:0.26, T:0.18
Consensus pattern (14 bp):
CGGCTCAGCTCAAA
Found at i:23829 original size:95 final size:95
Alignment explanation
Indices: 23713--23915 Score: 370
Period size: 95 Copynumber: 2.1 Consensus size: 95
23703 TTAATAATAA
*
23713 TAAATCACTTTGGCCTAATTAGGATAAGATCAAAACAAAAATAAAGGTATTTGGATTAAGCAGAT
1 TAAACCACTTTGGCCTAATTAGGATAAGATCAAAACAAAAATAAAGGTATTTGGATTAAGCAGAT
23778 GCATTTAGCATATCAGAACTAATAATTTTT
66 GCATTTAGCATATCAGAACTAATAATTTTT
*
23808 TAAACCACTTTGGCCTAATTAGGATAAGATCAAAACAAAAATAAAGGTATTTGGGTTAAGCAGAT
1 TAAACCACTTTGGCCTAATTAGGATAAGATCAAAACAAAAATAAAGGTATTTGGATTAAGCAGAT
23873 GCATTTAGCATATCAGAACTAATAATTTTT
66 GCATTTAGCATATCAGAACTAATAATTTTT
23903 TAACACCAACTTT
1 TAA-ACC-ACTTT
23916 TCATACATGA
Statistics
Matches: 104, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
95 96 0.92
96 3 0.03
97 5 0.05
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (95 bp):
TAAACCACTTTGGCCTAATTAGGATAAGATCAAAACAAAAATAAAGGTATTTGGATTAAGCAGAT
GCATTTAGCATATCAGAACTAATAATTTTT
Found at i:26217 original size:30 final size:29
Alignment explanation
Indices: 26183--26240 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
26173 TTGGTTTTTC
26183 GGAATTTGAATTACTGAAAAATGAATTACT
1 GGAATTTGAATT-CTGAAAAATGAATTACT
* *
26213 GGAATTTGAATTTTGGAAAATGAATTAC
1 GGAATTTGAATTCTGAAAAATGAATTAC
26241 ATTTCTGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.34
Consensus pattern (29 bp):
GGAATTTGAATTCTGAAAAATGAATTACT
Found at i:26236 original size:14 final size:15
Alignment explanation
Indices: 26189--26240 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
26179 TTTCGGAATT
*
26189 TGAATTACTGAAAAA
1 TGAATTACTGGAAAA
**
26204 TGAATTACTGGAATT
1 TGAATTACTGGAAAA
*
26219 TGAATT-TTGGAAAA
1 TGAATTACTGGAAAA
26233 TGAATTAC
1 TGAATTAC
26241 ATTTCTGGAA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAAAA
Found at i:26427 original size:19 final size:19
Alignment explanation
Indices: 26405--26478 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
26395 ATTAAATACA
*
26405 ATAAATAATATTATTTATC
1 ATAAATAATATTATTTATT
* *
26424 ATAAA-AAAATTTTATTATT
1 ATAAATAATATTAT-TTATT
*
26443 AAAAATAAT-TTATTTATT
1 ATAAATAATATTATTTATT
*
26461 ATTAAATAGTATT-TTTAT
1 A-TAAATAATATTATTTAT
26479 AATTTTATTA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
18 12 0.28
19 27 0.63
20 4 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (19 bp):
ATAAATAATATTATTTATT
Found at i:26454 original size:17 final size:18
Alignment explanation
Indices: 26415--26461 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
26405 ATAAATAATA
26415 TTATTTATCATAAAAAAATT
1 TTATTTAT--TAAAAAAATT
26435 TTA-TTATTAAAAATAA-T
1 TTATTTATTAAAAA-AATT
26452 TTATTTATTA
1 TTATTTATTA
26462 TTAAATAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 10 0.40
18 8 0.32
19 4 0.16
20 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTTATTAAAAAAATT
Found at i:26459 original size:18 final size:18
Alignment explanation
Indices: 26407--26461 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 18
26397 TAAATACAAT
26407 AAATAATATTATTTATCATAA
1 AAATAAT-TTATTTAT--TAA
26428 AAA-AATTT-TATTATTAA
1 AAATAATTTAT-TTATTAA
26445 AAATAATTTATTTATTA
1 AAATAATTTATTTATTA
26462 TTAAATAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
17 6 0.19
18 12 0.39
19 7 0.23
20 3 0.10
21 3 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATAATTTATTTATTAA
Found at i:26474 original size:21 final size:21
Alignment explanation
Indices: 26407--26466 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
26397 TAAATACAAT
*
26407 AAATAATATTATTTATCA-TAA
1 AAATAAT-TTATTTATTATTAA
26428 AAA-AA--T-TTTATTATTAA
1 AAATAATTTATTTATTATTAA
26445 AAATAATTTATTTATTATTAA
1 AAATAATTTATTTATTATTAA
26466 A
1 A
26467 TAGTATTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
16 6 0.18
17 7 0.21
18 2 0.06
20 3 0.09
21 15 0.45
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATAATTTATTTATTATTAA
Found at i:26515 original size:31 final size:31
Alignment explanation
Indices: 26471--26533 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 31
26461 ATTAAATAGT
26471 ATTTTTATAATTTTATT-AATAAAAATATTA
1 ATTTTTATAATTTTATTAAATAAAAATATTA
*
26501 ATTTTTGTATATTTTATTGAAATAAAAATATTA
1 ATTTTTATA-ATTTTATT-AAATAAAAATATTA
26534 TAAATATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 8 0.28
31 8 0.28
33 13 0.45
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (31 bp):
ATTTTTATAATTTTATTAAATAAAAATATTA
Found at i:26686 original size:30 final size:29
Alignment explanation
Indices: 26621--26722 Score: 106
Period size: 28 Copynumber: 3.5 Consensus size: 29
26611 CTTTATTAAA
*
26621 ATATTATTTAAATATAT-AAATAATAGTAT
1 ATATTA-TTAAATATATAAAATAATATTAT
*
26650 -TCATTATTAAATATATAAAAAAATTATTAT
1 AT-ATTATTAAATATATAAAATAA-TATTAT
26680 ATATTATTAAA-ATA-AAAATAATATCT-T
1 ATATTATTAAATATATAAAATAATAT-TAT
26707 ATATTATTATAATATA
1 ATATTATTA-AATATA
26723 ATTGATTATT
Statistics
Matches: 63, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
27 13 0.21
28 20 0.32
29 15 0.24
30 14 0.22
31 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (29 bp):
ATATTATTAAATATATAAAATAATATTAT
Found at i:26694 original size:27 final size:27
Alignment explanation
Indices: 26621--26720 Score: 78
Period size: 27 Copynumber: 3.5 Consensus size: 27
26611 CTTTATTAAA
* *
26621 ATATTATTTAAATATATAAATAATAGTATT
1 ATATTA-TTAAA-ATAAAAATAATA-TCTT
* *
26651 -CATTATTAAATATATAAAAAAATTAT-TAT
1 ATATTATTAAA-ATA-AAAATAA-TATCT-T
26680 ATATTATTAAAATAAAAATAATATCTT
1 ATATTATTAAAATAAAAATAATATCTT
*
26707 ATATTATTATAATA
1 ATATTATTAAAATA
26721 TAATTGATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
27 17 0.29
28 17 0.29
29 14 0.24
30 11 0.19
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (27 bp):
ATATTATTAAAATAAAAATAATATCTT
Found at i:26765 original size:27 final size:27
Alignment explanation
Indices: 26674--26774 Score: 87
Period size: 27 Copynumber: 3.6 Consensus size: 27
26664 ATAAAAAAAT
* * * *
26674 TATTATATATTATTAAAATAAAAATAA
1 TATTATATAATATTAAAATATATATTA
* *
26701 TATCT-TATATTATTATAATATAATTGATTA
1 TAT-TATATAATATTAAAATAT-A-T-ATTA
*
26731 TTTTATATAATATTAAAATATATATTA
1 TATTATATAATATTAAAATATATATTA
26758 TATTATATAAATATTAA
1 TATTATAT-AATATTAA
26775 TAAATTAATA
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
27 28 0.47
28 11 0.18
29 2 0.03
30 19 0.32
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (27 bp):
TATTATATAATATTAAAATATATATTA
Found at i:27029 original size:42 final size:42
Alignment explanation
Indices: 26970--27080 Score: 168
Period size: 42 Copynumber: 2.6 Consensus size: 42
26960 TTACGTTCAG
* *
26970 GAAAATCAATTACGTGAAACAAACACTGGAAAACATTTTCCA
1 GAAAATGAATTACGTGAAACAAACACGGGAAAACATTTTCCA
*
27012 GAAAATGAATTACGTGAAACAAACACGGGAAAACATTTTCCG
1 GAAAATGAATTACGTGAAACAAACACGGGAAAACATTTTCCA
* * *
27054 GAAAACGAATCATGTGAAACAAACACG
1 GAAAATGAATTACGTGAAACAAACACG
27081 AGAATTCAGG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.48, C:0.18, G:0.16, T:0.18
Consensus pattern (42 bp):
GAAAATGAATTACGTGAAACAAACACGGGAAAACATTTTCCA
Found at i:27967 original size:32 final size:32
Alignment explanation
Indices: 27927--28008 Score: 112
Period size: 32 Copynumber: 2.6 Consensus size: 32
27917 CTTTATTTTG
*
27927 TTCGGGTCGGGTTGGGTTTTTAAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTTAAAGTGTGATA
* *
27959 TTTGGGTC-GGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGG-TTTTTAAAGTGTGATA
*
27991 TTCGGGTCGAGTCGGGTT
1 TTCGGGTCGGGTCGGGTT
28009 CGGGTTTAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
31 6 0.14
32 31 0.72
33 6 0.14
ACGTcount: A:0.12, C:0.09, G:0.38, T:0.41
Consensus pattern (32 bp):
TTCGGGTCGGGTCGGGTTTTTAAAGTGTGATA
Found at i:28618 original size:18 final size:18
Alignment explanation
Indices: 28581--28627 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
28571 TATGGAATTT
* *
28581 GATTTAAATT-CTTGACA
1 GATTTCAATTCCTTCACA
28598 GATTTCAATTCCTTCACA
1 GATTTCAATTCCTTCACA
*
28616 GATTCCAATTCC
1 GATTTCAATTCC
28628 CTCAAAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (18 bp):
GATTTCAATTCCTTCACA
Found at i:30610 original size:19 final size:20
Alignment explanation
Indices: 30583--30633 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
30573 AATTTTCAAT
*
30583 TTATTAATTTGACTTA-AAA
1 TTATTAATTTGACATATAAA
*
30602 TTATGAATTT-ACATATAAA
1 TTATTAATTTGACATATAAA
30621 TTAATTAATTTGA
1 TT-ATTAATTTGA
30634 TTGTATAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 4 0.15
19 14 0.54
20 7 0.27
21 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (20 bp):
TTATTAATTTGACATATAAA
Found at i:36917 original size:31 final size:31
Alignment explanation
Indices: 36856--36917 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
36846 GAGGACATTA
*
36856 TTTGTTGAGTCCGTCGACTATAAAGTGTTAC
1 TTTGTTGAGTCCGTCGACTATAAAGAGTTAC
36887 TTTGTTGAGTCCGTCGACTACTAAA-AGTTAC
1 TTTGTTGAGTCCGTCGACTA-TAAAGAGTTAC
36918 AAAATGGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (31 bp):
TTTGTTGAGTCCGTCGACTATAAAGAGTTAC
Found at i:37712 original size:43 final size:43
Alignment explanation
Indices: 37627--37721 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
37617 TATAGCGGCA
* *
37627 TTGTATAAACGCCGCTAAAGGTTATGATATTCAACTGTGTTTT
1 TTGTATAAACGCCGCTAAAGGTTATGATATTCAACGGCGTTTT
* * * *
37670 TTGTATAAACGCTGC-AATAGGTTATTATATTTAGCGGCGTTTT
1 TTGTATAAACGCCGCTAA-AGGTTATGATATTCAACGGCGTTTT
*
37713 TTCTATAAA
1 TTGTATAAA
37722 GGTTATGATA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 2 0.05
43 42 0.95
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (43 bp):
TTGTATAAACGCCGCTAAAGGTTATGATATTCAACGGCGTTTT
Found at i:37733 original size:33 final size:33
Alignment explanation
Indices: 37688--37754 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
37678 ACGCTGCAAT
* * * * *
37688 AGGTTATTATATTTAGCGGCGTTTTTTCTATAA
1 AGGTTATGATATTTAACGACATTTTTTATATAA
37721 AGGTTATGATATTTAACGACATTTTTTATATAA
1 AGGTTATGATATTTAACGACATTTTTTATATAA
37754 A
1 A
37755 CGCCGCAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.46
Consensus pattern (33 bp):
AGGTTATGATATTTAACGACATTTTTTATATAA
Found at i:38013 original size:26 final size:27
Alignment explanation
Indices: 37947--38015 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
37937 AACCATTCAA
*
37947 GTAATGTAGTTCAACATTAAGTCAAAT
1 GTAATATAGTTCAACATTAAGTCAAAT
*
37974 GTAATATAGTTCAACATTAAGTGAAAT
1 GTAATATAGTTCAACATTAAGTCAAAT
*
38001 GT-ATATCGTTCAACA
1 GTAATATAGTTCAACA
38016 ACTATAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 12 0.31
27 27 0.69
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (27 bp):
GTAATATAGTTCAACATTAAGTCAAAT
Found at i:42067 original size:15 final size:13
Alignment explanation
Indices: 42046--42082 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
42036 TGCCCTTTCT
42046 GGAGAGAGAAAGA
1 GGAGAGAGAAAGA
42059 GGAGAGAGAAAGA
1 GGAGAGAGAAAGA
42072 GGAGAGAGAAA
1 GGAGAGAGAAA
42083 ACTCAGAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (13 bp):
GGAGAGAGAAAGA
Found at i:42329 original size:29 final size:30
Alignment explanation
Indices: 42264--42344 Score: 96
Period size: 29 Copynumber: 2.7 Consensus size: 30
42254 TATTTCTCAT
*
42264 TGAACTTTAATTTATTTCTTAATTTATTCA
1 TGAACTTTAAATTATTTCTTAATTTATTCA
*
42294 TCAAACTTTAAATT-TTT-TTAATTTATTCA
1 T-GAACTTTAAATTATTTCTTAATTTATTCA
42323 CTGAACTTTAAAATTA-TTCTTA
1 -TGAACTTT-AAATTATTTCTTA
42345 TTTTGGTCAC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
29 18 0.42
30 12 0.28
31 13 0.30
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.53
Consensus pattern (30 bp):
TGAACTTTAAATTATTTCTTAATTTATTCA
Found at i:44668 original size:14 final size:14
Alignment explanation
Indices: 44651--44689 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
44641 CGTTCATTTA
44651 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
44665 CG-T---TTATGTT
1 CGTTCGGTTATGTT
44675 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
44689 C
1 C
44690 ATTTATGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 8
0.72 0.00 0.28
Matches are distributed among these distances:
10 9 0.43
11 1 0.05
13 1 0.05
14 10 0.48
ACGTcount: A:0.08, C:0.15, G:0.26, T:0.51
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:44678 original size:24 final size:24
Alignment explanation
Indices: 44638--44699 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
44628 CATAAGTCTC
*
44638 GTTCGTTCAT-TTACGTTCGGTTAT
1 GTTCGTTTATGTT-CGTTCGGTTAT
44662 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
*
44686 GTTCATTTATGTTC
1 GTTCGTTTATGTTC
44700 ATTCATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 33 0.94
25 2 0.06
ACGTcount: A:0.11, C:0.15, G:0.21, T:0.53
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGGTTAT
Found at i:44709 original size:24 final size:24
Alignment explanation
Indices: 44657--44712 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
44647 TTTACGTTCG
* * *
44657 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCATTTATGTTCATTCA
44681 GTTATGTTCATTTATGTTCATTCA
1 GTTATGTTCATTTATGTTCATTCA
*
44705 TTTATGTT
1 GTTATGTT
44713 TAACCCAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.14, C:0.11, G:0.18, T:0.57
Consensus pattern (24 bp):
GTTATGTTCATTTATGTTCATTCA
Found at i:45799 original size:10 final size:10
Alignment explanation
Indices: 45784--45858 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
45774 GGGTCTCCAA
45784 CGTTTATGTT
1 CGTTTATGTT
45794 CGTTTATGTT
1 CGTTTATGTT
45804 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
45815 ATGTTCGTGTT
1 -CGTTTATGTT
45826 CGTTTATGTT
1 CGTTTATGTT
*
45836 CG----TGGT
1 CGTTTATGTT
45842 CGTTTATGTT
1 CGTTTATGTT
45852 CGTTTAT
1 CGTTTAT
45859 TTATTAAATG
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
10 33 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.23, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:45815 original size:16 final size:16
Alignment explanation
Indices: 45790--45854 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
45780 CCAACGTTTA
45790 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
45806 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
45822 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
45838 TGGTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
45854 T
1 T
45855 TTATTTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.08, C:0.12, G:0.25, T:0.55
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:45945 original size:16 final size:16
Alignment explanation
Indices: 45924--45956 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
45914 AAAAAAAATT
45924 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
45940 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
45956 T
1 T
45957 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:47484 original size:29 final size:29
Alignment explanation
Indices: 47394--47484 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
47384 TTCTACCTAA
* *
47394 ATTTATTATGATAATTTATTTAACTTTAT
1 ATTTATTATGATAGTTTATTTAAATTTAT
** * * *
47423 A-TTACAATGATTGAG-CTATTTAAATCTAA
1 ATTTATTATGA-T-AGTTTATTTAAATTTAT
*
47452 ATTTATTATGATAGTTTATTTAATTTTAT
1 ATTTATTATGATAGTTTATTTAAATTTAT
47481 ATTT
1 ATTT
47485 TTTTATAATT
Statistics
Matches: 45, Mismatches: 13, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
28 9 0.20
29 28 0.62
30 8 0.18
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (29 bp):
ATTTATTATGATAGTTTATTTAAATTTAT
Found at i:57594 original size:34 final size:33
Alignment explanation
Indices: 57526--57610 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 33
57516 TGTATTTCAG
57526 TTAATTTTGTTTATTACCATTTAATATCAGTTAT
1 TTAATTTTGTTTATTACCATTTAATATCA-TTAT
57560 TTAATTTTGTTATCATTTACCATTTAAT-TC-TTAT
1 TTAATTTTGTT-T-A-TTACCATTTAATATCATTAT
*
57594 TGTAAGTTTGTTGTATT
1 T-TAATTTTGTT-TATT
57611 TAAATACCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
33 2 0.04
34 17 0.38
35 11 0.24
36 3 0.07
37 12 0.27
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.58
Consensus pattern (33 bp):
TTAATTTTGTTTATTACCATTTAATATCATTAT
Found at i:60701 original size:51 final size:51
Alignment explanation
Indices: 60598--60712 Score: 151
Period size: 51 Copynumber: 2.3 Consensus size: 51
60588 CCCCTACGTG
* **
60598 GCGTATAGCGCGGAACAGGGGGCGCGCTATACCCACGTGTAAGCCATGTCA
1 GCGTATAGCGCGGAACAGGGGACGCGCTATACCCACGTGTAAGCCAAATCA
* **
60649 GCGTATAGCGCGGTACAGGGGACGCGCTATACCCCACGTG-GCGCCAAATCA
1 GCGTATAGCGCGGAACAGGGGACGCGCTATA-CCCACGTGTAAGCCAAATCA
*
60700 GCATATAGCGCGG
1 GCGTATAGCGCGG
60713 GGCAGGGAGC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 48 0.86
52 8 0.14
ACGTcount: A:0.23, C:0.29, G:0.33, T:0.15
Consensus pattern (51 bp):
GCGTATAGCGCGGAACAGGGGACGCGCTATACCCACGTGTAAGCCAAATCA
Found at i:60726 original size:51 final size:50
Alignment explanation
Indices: 60601--60727 Score: 139
Period size: 51 Copynumber: 2.5 Consensus size: 50
60591 CTACGTGGCG
** *
60601 TATAGCGCGGAACAGGGGGCGCGCTATACCCACGTGTAAGCCATGTCAGCG
1 TATAGCGCGGAACA-GGGGCGCGCTATACCCACGTGTAAGCCAAATCAGCA
* **
60652 TATAGCGCGGTACAGGGGACGCGCTATACCCCACGTG-GCGCCAAATCAGCA
1 TATAGCGCGGAACAGGGG-CGCGCTATA-CCCACGTGTAAGCCAAATCAGCA
**
60703 TATAGCGCGGGGCAGGGAGCGCGCT
1 TATAGCGCGGAACAGGG-GCGCGCT
60728 TTACTGCTAC
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
50 4 0.06
51 52 0.80
52 9 0.14
ACGTcount: A:0.23, C:0.28, G:0.35, T:0.14
Consensus pattern (50 bp):
TATAGCGCGGAACAGGGGCGCGCTATACCCACGTGTAAGCCAAATCAGCA
Found at i:67016 original size:36 final size:36
Alignment explanation
Indices: 66950--67019 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
66940 AACATCGATG
*
66950 CCTCGGACTGGAACAAACTGTCCGAAGCTTTCAGCA
1 CCTCGGACTGGAACAAACTGTCAGAAGCTTTCAGCA
* *
66986 CCTCGGATTGGAACAAACTGTTCAG-TGCTTTCAG
1 CCTCGGACTGGAACAAACTG-TCAGAAGCTTTCAG
67020 AGCATAACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 27 0.90
37 3 0.10
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (36 bp):
CCTCGGACTGGAACAAACTGTCAGAAGCTTTCAGCA
Found at i:68453 original size:35 final size:35
Alignment explanation
Indices: 68407--68477 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
68397 ATCACACTTG
68407 TATTATAGATGAGATTGTGTTTTATAAGATTAAAC
1 TATTATAGATGAGATTGTGTTTTATAAGATTAAAC
68442 TATTATAGATGAGATTGTGTTTTATAAGATTAAAC
1 TATTATAGATGAGATTGTGTTTTATAAGATTAAAC
68477 T
1 T
68478 GTATATTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.37, C:0.03, G:0.17, T:0.44
Consensus pattern (35 bp):
TATTATAGATGAGATTGTGTTTTATAAGATTAAAC
Found at i:70787 original size:84 final size:83
Alignment explanation
Indices: 70693--70981 Score: 429
Period size: 84 Copynumber: 3.4 Consensus size: 83
70683 ACCGTTGTCC
70693 AAGTAAAGGGGAGAGAAGTTGAGGCTATTGATGGCTCAAATGGGATCAATGGTGATCAAGATGCT
1 AAGTAAAGGGGAGAGAAGTTGAGGCTATTGATGGCTCAAATGGGATCAATGG-GATCAAGATGCT
*
70758 GAATCTGAGAATCAATGTG
65 GAATCTGAGAATCGATGTG
* *
70777 AAGTAAAGGGG-GAAGAAGTTGAGGCTATTGATGGTTCAAATGGGATCAATGGCGATCAAGATAC
1 AAGTAAAGGGGAG-AGAAGTTGAGGCTATTGATGGCTCAAATGGGATCAATGG-GATCAAGATGC
70841 TGAATCTGAGAATCGATGTG
64 TGAATCTGAGAATCGATGTG
* * * *
70861 AAGTAAAGGGGGGAGAAGTTGAGGCTATTGATGGCTCAAATGGGGTAAACTGCGG-TCAAGCTGC
1 AAGTAAAGGGGAGAGAAGTTGAGGCTATTGATGGCTCAAATGGGATCAA-TG-GGATCAAGATGC
*
70925 GGAATCTGAGAATCGATGTG
64 TGAATCTGAGAATCGATGTG
* *
70945 AAGTAAAGGGGAGGGAAGTTGAGGGTATTGATGGCTC
1 AAGTAAAGGGGAGAGAAGTTGAGGCTATTGATGGCTC
70982 GGATGGGGTA
Statistics
Matches: 188, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
83 1 0.01
84 182 0.97
85 4 0.02
86 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.35, T:0.23
Consensus pattern (83 bp):
AAGTAAAGGGGAGAGAAGTTGAGGCTATTGATGGCTCAAATGGGATCAATGGGATCAAGATGCTG
AATCTGAGAATCGATGTG
Found at i:70988 original size:84 final size:82
Alignment explanation
Indices: 70693--71032 Score: 403
Period size: 84 Copynumber: 4.0 Consensus size: 82
70683 ACCGTTGTCC
*
70693 AAGTAAAGGGGAGAGAAGTTGAGGCTATTGATGGCTCAAATGGGATCAATG-GTGATCAAGATGC
1 AAGTAAAGGGG-GAGAAGTTGAGGCTATTGATGGCTCAAATGGGATAAATGCG-G-TCAAGATGC
* *
70757 TGAATCTGAGAATCAATGTG
63 GGAATCTGAGAATCGATGTG
* * * * *
70777 AAGTAAAGGGGGAAGAAGTTGAGGCTATTGATGGTTCAAATGGGATCAATGGCGATCAAGATACT
1 AAGTAAAGGGGG-AGAAGTTGAGGCTATTGATGGCTCAAATGGGATAAAT-GCGGTCAAGATGCG
70842 GAATCTGAGAATCGATGTG
64 GAATCTGAGAATCGATGTG
* *
70861 AAGTAAAGGGGGGAGAAGTTGAGGCTATTGATGGCTCAAATGGGGTAAACTGCGGTCAAGCTGCG
1 AAGTAAA-GGGGGAGAAGTTGAGGCTATTGATGGCTCAAATGGGATAAA-TGCGGTCAAGATGCG
70926 GAATCTGAGAATCGATGTG
64 GAATCTGAGAATCGATGTG
* * ** * ** **
70945 AAGTAAAGGGGAGGGAAGTTGAGGGTATTGATGGCTCGGATGGGGTAAACTGCGGTCAATCTTTG
1 AAGTAAAGGGG-GAGAAGTTGAGGCTATTGATGGCTCAAATGGGATAAA-TGCGGTCAAGATGCG
* *
71010 GAATCTGAGGATCGATGCG
64 GAATCTGAGAATCGATGTG
71029 AAGT
1 AAGT
71033 TGAAAGATTT
Statistics
Matches: 230, Mismatches: 20, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
83 5 0.02
84 217 0.94
85 7 0.03
86 1 0.00
ACGTcount: A:0.31, C:0.10, G:0.35, T:0.23
Consensus pattern (82 bp):
AAGTAAAGGGGGAGAAGTTGAGGCTATTGATGGCTCAAATGGGATAAATGCGGTCAAGATGCGGA
ATCTGAGAATCGATGTG
Found at i:75590 original size:29 final size:29
Alignment explanation
Indices: 75533--75591 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
75523 GTGGTGACTG
*
75533 AATTTAAATAATTTTTAACATATGGTGAT
1 AATTTAAATAATTTTTAACATATGATGAT
* *
75562 AATTTAAATAATTTTTAGCATGTGATGAT
1 AATTTAAATAATTTTTAACATATGATGAT
75591 A
1 A
75592 TGGATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (29 bp):
AATTTAAATAATTTTTAACATATGATGAT
Found at i:77995 original size:31 final size:31
Alignment explanation
Indices: 77949--78024 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
77939 CCACAATCTT
*
77949 TAAACTATCAGTTTTGGCCCGTTTTAGTACC
1 TAAACTATCAATTTTGGCCCGTTTTAGTACC
*
77980 TAAAATATCAATTTTGGCCCGTTTTAGTACC
1 TAAACTATCAATTTTGGCCCGTTTTAGTACC
*
78011 TAAACTTTCAATTT
1 TAAACTATCAATTT
78025 CTTTAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.41
Consensus pattern (31 bp):
TAAACTATCAATTTTGGCCCGTTTTAGTACC
Found at i:81083 original size:2 final size:2
Alignment explanation
Indices: 81076--81113 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
81066 GAAATACACA
81076 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
81114 TCAACATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86116 original size:29 final size:32
Alignment explanation
Indices: 86074--86152 Score: 128
Period size: 29 Copynumber: 2.6 Consensus size: 32
86064 GCTTCCGGCA
86074 TAGGTCGCCATGCACTCCGGGCGACC-T-T-G
1 TAGGTCGCCATGCACTCCGGGCGACCTTGTAG
*
86103 TAGGTCGCCATGCACTCCTGGCGACCTTGTAG
1 TAGGTCGCCATGCACTCCGGGCGACCTTGTAG
86135 TAGGTCGCCATGCACTCC
1 TAGGTCGCCATGCACTCC
86153 TCCTGCTCCT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
29 25 0.54
30 1 0.02
31 1 0.02
32 19 0.41
ACGTcount: A:0.15, C:0.34, G:0.28, T:0.23
Consensus pattern (32 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTGTAG
Found at i:86260 original size:14 final size:14
Alignment explanation
Indices: 86213--86253 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
86203 GCTCGAATGG
86213 CCTCGGTCGGATGC
1 CCTCGGTCGGATGC
86227 CCTCGGTCGGATGC
1 CCTCGGTCGGATGC
86241 CCTCGGTCGGATG
1 CCTCGGTCGGATG
86254 GCTTCGGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.07, C:0.34, G:0.37, T:0.22
Consensus pattern (14 bp):
CCTCGGTCGGATGC
Found at i:96841 original size:53 final size:53
Alignment explanation
Indices: 96756--96955 Score: 305
Period size: 53 Copynumber: 3.8 Consensus size: 53
96746 TGATGGGTCT
* * *
96756 GCTCCCTCTTG-TTCAGGGAGTAGAATTTGAATAATCTTCTGCTTACGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTTACGGGTTC
* * *
96808 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCAGCCTACGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTTACGGGTTC
* *
96861 GCTCCCTCTTGCTTCAGGGAGTAAAACTCGAACAATCTTTTG-TCTACGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCT-TACGGGTTC
96914 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
96956 GTGTGATTCT
Statistics
Matches: 135, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
52 11 0.08
53 124 0.92
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (53 bp):
GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTTACGGGTTC
Found at i:97382 original size:41 final size:41
Alignment explanation
Indices: 97321--97413 Score: 111
Period size: 40 Copynumber: 2.3 Consensus size: 41
97311 CACTATTCCG
* *
97321 AAAAGGCTTA-AAATGGCCCGAAGGACTTATCATC-TCA-CTC
1 AAAAGACTTACAAATGACCCGAAGGA-TT-TCATCATCAGCTC
97361 AAAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTC
1 AAAAGACTTACAAATGACCCGAAGGATTTCATCATCA-GCTC
*
97403 GAAAGACTTAC
1 AAAAGACTTAC
97414 TGATGAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
39 5 0.11
40 14 0.30
41 14 0.30
42 13 0.28
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.23
Consensus pattern (41 bp):
AAAAGACTTACAAATGACCCGAAGGATTTCATCATCAGCTC
Found at i:97408 original size:42 final size:42
Alignment explanation
Indices: 97322--97532 Score: 128
Period size: 42 Copynumber: 5.2 Consensus size: 42
97312 ACTATTCCGA
* * *
97322 AAAGGCTTA-AAATGGCCCGAAGGACTTATCATC-TCA--CTCA
1 AAAGACTTACAAATGACCCGAAGGA-TT-TCATCATCATGCTCG
97362 AAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTCG
1 AAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTCG
* ** * * *
97404 AAAGACTTAC---TGA--TGAATTTACTTCA-CTACTCTTCGGT-G
1 AAAGACTTACAAATGACCCGAA-GGATTTCATC-A-TCAT-GCTCG
* * *
97443 -AAGGCTTACAAATTATCCGAAGGATTT-A--ATCATGCTCG
1 AAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTCG
** *
97481 AAAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCTCG
1 AAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTCG
97523 AAAGACTTAC
1 AAAGACTTAC
97533 TGATGGACCG
Statistics
Matches: 130, Mismatches: 23, Indels: 34
0.70 0.12 0.18
Matches are distributed among these distances:
37 6 0.05
38 18 0.14
39 34 0.26
40 16 0.12
41 17 0.13
42 36 0.28
43 3 0.02
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (42 bp):
AAAGACTTACAAATGACCCGAAGGATTTCATCATCATGCTCG
Found at i:97502 original size:39 final size:41
Alignment explanation
Indices: 97459--97547 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 41
97449 TACAAATTAT
*
97459 CCGAAGGATTT-A-ATCATGCTCGAAAGACTTACTGATGGC
1 CCGAAGGATTTCACATCATGCTCGAAAGACTTACTGATGGA
97498 CCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGA
1 CCGAAGGATTTCA-CATCATGCTCGAAAGACTTACTGATGGA
97540 CCGAAGGA
1 CCGAAGGA
97548 CTTATAAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
39 11 0.24
40 1 0.02
42 34 0.74
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (41 bp):
CCGAAGGATTTCACATCATGCTCGAAAGACTTACTGATGGA
Found at i:97687 original size:41 final size:40
Alignment explanation
Indices: 97641--97764 Score: 113
Period size: 42 Copynumber: 3.0 Consensus size: 40
97631 TCTTTTGAAA
* * *
97641 CATCTTACCCGAAGGTTTTACGGATGGCCCGAAGGACTTAT
1 CATCTTGCCCGAAGG-CTTACAGATGGCCCGAAGGACTTAT
** * *
97682 CATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAT
1 CATCTTGC-CCGAAGGCTTACAGATGGCCCGAAGGACTT-AT
* * * *
97724 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAT
1 CATCTTGCCCG-AAGGCTTACAGATGGCCCGAAGGACTTAT
97765 AAATTGTGAA
Statistics
Matches: 65, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
41 28 0.43
42 37 0.57
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (40 bp):
CATCTTGCCCGAAGGCTTACAGATGGCCCGAAGGACTTAT
Found at i:97733 original size:42 final size:41
Alignment explanation
Indices: 97658--97764 Score: 142
Period size: 42 Copynumber: 2.6 Consensus size: 41
97648 CCCGAAGGTT
* * * *
97658 TTACGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGC
1 TTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAC
* *
97699 TTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGAC
1 TTACAGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGAC
*
97741 TTACTGATGGCCCGAAGGACTTAT
1 TTACAGATGGCCCGAAGGACTTAT
97765 AAATTGTGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 21 0.38
42 35 0.62
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (41 bp):
TTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAC
Found at i:97927 original size:41 final size:41
Alignment explanation
Indices: 97877--97978 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
97867 AGGTTTTACG
* * *
97877 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTCACA
1 GATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTCACA
* * * * *
97918 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGACTCACA
97960 GATGGCCCGAAGGACTTAT
1 GATGGCCCGAAGGACTTAT
97979 AAATTGTGAA
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 16 0.33
42 33 0.67
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTCACA
Found at i:97950 original size:214 final size:213
Alignment explanation
Indices: 97492--98090 Score: 1019
Period size: 214 Copynumber: 2.8 Consensus size: 213
97482 AAGACTTACT
* * *
97492 GATGGCCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGACCGAAGGACTTATAAAT
1 GATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAAT
* * * * ** *
97557 TGTGAAATTTTGAAAATCGCATTATTTGTTTTCAAAAATTTCATCTTCTCAAAACATCGTTTTCA
66 TGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATATTTTTTA
97622 TTTTCAAATTCTTTTG-AAACATCTTACCCGAAGGTTTTACGGATGGCCCGAAGGACTTATCATC
131 TTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGGCCCGAAGGACTTATCATC
*
97686 TTGCTCTAAAGGCTTACA
196 TTGCTCTAAAGGCTCACA
97704 GATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAAT
1 GATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAAT
97769 TGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATTATTTTTT
66 TGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACA-TATTTTTT
97834 ATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGGCCCGAAGGACTTATCAT
130 ATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGGCCCGAAGGACTTATCAT
97899 CTTGCTCTAAAGGCTCACA
195 CTTGCTCTAAAGGCTCACA
*
97918 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAAT
1 GATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAAT
*
97983 TGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCTATCTTCTTAAAAC--ATTTTTTA
66 TGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATATTTTTTA
* *
98046 TTTTCAAATTC-TTTGAAAACATCTTA-CCGAAGGTCTTATGGATGG
131 TTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGG
98091 TTTGCTTCAC
Statistics
Matches: 370, Mismatches: 15, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
209 17 0.05
210 15 0.04
211 19 0.05
212 114 0.31
213 22 0.06
214 183 0.49
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (213 bp):
GATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAAT
TGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATATTTTTTA
TTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGGCCCGAAGGACTTATCATC
TTGCTCTAAAGGCTCACA
Found at i:112361 original size:4 final size:4
Alignment explanation
Indices: 112354--112380 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
112344 AAAAACTATC
112354 TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA
112381 TATGATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:114289 original size:28 final size:28
Alignment explanation
Indices: 114245--114305 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
114235 GCCAAGAGTA
*
114245 TGAACGTTCAATATTGAGCGTTCAGCTT
1 TGAACGTTCAATATTGAGCATTCAGCTT
*
114273 TGAACGTTCAATGTTGAGCATTCAGCTT
1 TGAACGTTCAATATTGAGCATTCAGCTT
114301 TGAAC
1 TGAAC
114306 TGACTCTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (28 bp):
TGAACGTTCAATATTGAGCATTCAGCTT
Found at i:115072 original size:42 final size:42
Alignment explanation
Indices: 115013--115095 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
115003 AAAATATGCG
115013 ACATTGTGACCAATCACACTA-GAGTAATTTTCATATTGGGCA
1 ACATTGTGACCAATCACAC-ACGAGTAATTTTCATATTGGGCA
*
115055 ACATTGTGACCAATCACACACGAGTGATTTTCATATTGGGC
1 ACATTGTGACCAATCACACACGAGTAATTTTCATATTGGGC
115096 GACAAATGTG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 1 0.03
42 38 0.97
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (42 bp):
ACATTGTGACCAATCACACACGAGTAATTTTCATATTGGGCA
Found at i:118758 original size:32 final size:33
Alignment explanation
Indices: 118683--118758 Score: 95
Period size: 32 Copynumber: 2.3 Consensus size: 33
118673 TTTATAATTT
*
118683 TATCTTATATATTTAGAGATAATTATTAATTTAA
1 TATCTT-TATATTTAGAGATAATTATTAATATAA
*
118717 TAT-TGTATATTTAGAGATAATTA-TAATA-ATA
1 TATCTTTATATTTAGAGATAATTATTAATATA-A
118748 TATCTTTATAT
1 TATCTTTATAT
118759 ATTATTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 1 0.03
31 8 0.22
32 24 0.65
33 1 0.03
34 3 0.08
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.50
Consensus pattern (33 bp):
TATCTTTATATTTAGAGATAATTATTAATATAA
Found at i:128466 original size:3 final size:3
Alignment explanation
Indices: 128460--128517 Score: 82
Period size: 3 Copynumber: 19.3 Consensus size: 3
128450 TTTTACTATA
* *
128460 ATT ATT ATT ATT ATA ATT ATT ATT ATA ATT ATT A-T ATAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
128505 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
128518 AATAATTACA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:134000 original size:15 final size:15
Alignment explanation
Indices: 133980--134011 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
133970 ATCAATACCT
133980 TTTTGCATACATACA
1 TTTTGCATACATACA
*
133995 TTTTGCATACATTCA
1 TTTTGCATACATACA
134010 TT
1 TT
134012 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:141352 original size:15 final size:14
Alignment explanation
Indices: 141332--141384 Score: 72
Period size: 15 Copynumber: 3.7 Consensus size: 14
141322 ATGCTTGAAG
141332 AGAAAAAGAAAAGAA
1 AGAAAAA-AAAAGAA
*
141347 AGAAAAAAAAA-AG
1 AGAAAAAAAAAGAA
141360 AGAAAAAAAAAGAA
1 AGAAAAAAAAAGAA
141374 GAGAAAAAAAA
1 -AGAAAAAAAA
141385 GGGTCAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.35
14 5 0.15
15 17 0.50
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAAAGAA
Found at i:141356 original size:13 final size:14
Alignment explanation
Indices: 141328--141385 Score: 75
Period size: 14 Copynumber: 4.1 Consensus size: 14
141318 TATTATGCTT
141328 GAAGAGAAAAAGAAAA
1 GAAGAG-AAAA-AAAA
141344 GAA-AGAAAAAAAA
1 GAAGAGAAAAAAAA
141357 -AAGAGAAAAAAAAA
1 GAAGAG-AAAAAAAA
141371 GAAGAGAAAAAAAA
1 GAAGAGAAAAAAAA
141385 G
1 G
141386 GGTCAAGGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.05
13 6 0.15
14 21 0.54
15 7 0.18
16 3 0.08
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
GAAGAGAAAAAAAA
Found at i:141362 original size:28 final size:28
Alignment explanation
Indices: 141329--141384 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
141319 ATTATGCTTG
141329 AAGAGAAAAAGAAAAGAA-AGAAAAAAAA
1 AAGAGAAAAA-AAAAGAAGAGAAAAAAAA
141357 AAGAGAAAAAAAAAGAAGAGAAAAAAAA
1 AAGAGAAAAAAAAAGAAGAGAAAAAAAA
141385 GGGTCAAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (28 bp):
AAGAGAAAAAAAAAGAAGAGAAAAAAAA
Found at i:141382 original size:17 final size:17
Alignment explanation
Indices: 141334--141384 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
141324 GCTTGAAGAG
*
141334 AAAAAGAAAAGAAAGAAA
1 AAAAAGAAGAGAAA-AAA
141352 AAAAA-AAGAG--AAAA
1 AAAAAGAAGAGAAAAAA
141366 AAAAAGAAGAGAAAAAA
1 AAAAAGAAGAGAAAAAA
141383 AA
1 AA
141385 GGGTCAAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 8 0.28
15 6 0.21
17 10 0.34
18 5 0.17
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAAGAGAAAAAA
Found at i:143297 original size:92 final size:92
Alignment explanation
Indices: 142744--143286 Score: 1014
Period size: 92 Copynumber: 5.9 Consensus size: 92
142734 AACAAGTGCC
* *
142744 ATGTGCTCATAACATCTTCTGGAATTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
142809 GAACCAATCATTGAATTTGGAAGATGA
66 GAACCAATCATTGAATTTGGAAGATGA
142836 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
142901 GAACCAATCATTGAATTTGGAAGATGA
66 GAACCAATCATTGAATTTGGAAGATGA
*
142928 ATGTGCTCATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
142993 GAACCAATCATTGAATTTGGAAGATGA
66 GAACCAATCATTGAATTTGGAAGATGA
143020 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
143085 GAACCAATCATTGAATTTGGAAGATGA
66 GAACCAATCATTGAATTTGGAAGATGA
143112 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
*
143177 GAACCAATTATTGAATTTGGAAGATGA
66 GAACCAATCATTGAATTTGGAAGATGA
* * *
143204 ATGTGCTCATAGCATCTTCTGGAATTGTTATTTGAGTTATCTGATCTGGTTTGGTATGAACCCCA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
143269 GAACCAATCATTGGAATT
66 GAACCAATCATT-GAATT
143287 AAAAGATGAA
Statistics
Matches: 441, Mismatches: 9, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
92 436 0.99
93 5 0.01
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (92 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
GAACCAATCATTGAATTTGGAAGATGA
Found at i:144215 original size:113 final size:113
Alignment explanation
Indices: 143984--144657 Score: 753
Period size: 113 Copynumber: 5.8 Consensus size: 113
143974 GCAAAGATTC
* * * * * *
143984 AAATCCATCAATTGATGGATCAGCATTACCAGATAGAGTTCATAATGAGAAGAACTCATCATCTG
1 AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTG
*
144049 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTT
63 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* *
144100 GAATTCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
144165 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTT
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * * * *
144213 GAATTCATCATTTGATGGATTAAAATTTCCAG-GTAGAGTTCACAATGAGAAGAACTCATCATTT
1 AAATTCATCACTTGATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATC---T
*
144277 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTCTG-TT
62 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * **** *
144328 CAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAA
1 -AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* * *
144393 GAAGGAAGCAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTC
65 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
*
144442 AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG
1 AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * ** *
144507 -AGGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGCAT
66 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * *
144554 -AATTCTATCACAGAAGCAGATAGATTAGCATAAACCTTTCCAGAGAAAGTTCATAATGAGAAGA
1 AAATTC-AT--C---A-C---TTGA-T-GGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGA
* * *
144618 ACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGA
54 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGA
144658 GCTTATTTAA
Statistics
Matches: 478, Mismatches: 60, Indels: 32
0.84 0.11 0.06
Matches are distributed among these distances:
111 5 0.01
112 42 0.09
113 209 0.44
114 3 0.01
115 2 0.00
116 141 0.29
117 1 0.00
118 1 0.00
121 3 0.01
122 1 0.00
123 45 0.09
124 25 0.05
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (113 bp):
AAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
Found at i:144396 original size:229 final size:229
Alignment explanation
Indices: 143982--144674 Score: 831
Period size: 229 Copynumber: 3.0 Consensus size: 229
143972 TAGCAAAGAT
* * * *
143982 TCAAATCCATCAATTGATGGATCAGCATTACCAGATAGAGTTCATAATGAGAAGAACTCATCATC
1 TCAAATTCATCAATTGATGGATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCATC
* * * *
144047 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATTCATCACT
66 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTCTGCTTAAATCCATCACT
144112 TGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
131 TGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
* *
144177 GTTCATAATGAGAAGAATTTGTTTAACCTTTTGT
196 ATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
** * * * * *
144211 TTGAATTCATCATTTGATGGATTAAAATTTCCAGGTAGAGTTCACAATGAGAAGAACTCATCATT
1 TCAAATTCATCAATTGATGGATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCATC
144276 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTCTG-TTCAAATCCATCAC
66 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTCTGCTT-AAATCCATCAC
* **** * *
144340 TTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGCAGA
130 TTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
144405 AATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
195 AATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
* *
144440 TCAAATTCATCACTTGATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACT--T-AT
1 TCAAATTCATCAATTGATGGATCAACATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCAT
* * ** * *
144501 CTGAAG-AGGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGCATAATTCTATCAC
65 CTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTCTGCTTAA----ATC-C
* * * * * *
144565 AGAAGCAGATAGATTAGCATAAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
125 ---ATCA-CTTGA-T-GGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * ** *
144630 GAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTTAACCTTTTG
184 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTG
144675 AATGACTCTA
Statistics
Matches: 393, Mismatches: 57, Indels: 21
0.83 0.12 0.04
Matches are distributed among these distances:
225 41 0.10
226 8 0.02
227 1 0.00
228 2 0.01
229 254 0.65
230 2 0.01
233 3 0.01
234 3 0.01
235 1 0.00
236 78 0.20
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (229 bp):
TCAAATTCATCAATTGATGGATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCATC
TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTCTGCTTAAATCCATCACT
TGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
ATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
Found at i:144686 original size:124 final size:123
Alignment explanation
Indices: 144467--144757 Score: 394
Period size: 124 Copynumber: 2.4 Consensus size: 123
144457 TGGATCAACA
*
144467 TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCACAATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGAAAGAAGAAGTTCACAATGAGAA
* * * * * *
144532 GAGCTTGTTCAACCTTTTGCATAATTCTATCACAGAAGCAGATAGATTAGCATAAACC
66 GAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATAAACC
* *
144590 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAA-GAGAAAGAAGAAGTTCACAATGAGA
* * * * * *
144655 AGAGCTTATTTAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAACATCATCC
65 AGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATAAACC
144714 ---CCAGCAGAAAGTTCATAATGAGAAGAACTTATCT-AA-AGAAAGAA
1 TTTCCAG-AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGAAAGAA
144758 AAGATTTTAT
Statistics
Matches: 150, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
119 8 0.05
121 6 0.04
122 28 0.19
123 38 0.25
124 70 0.47
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (123 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGAAAGAAGAAGTTCACAATGAGAA
GAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATAAACC
Found at i:144905 original size:3 final size:3
Alignment explanation
Indices: 144899--144953 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
144889 TTTTACTATA
* *
144899 ATT ATT ATT ATT ATA ATT ATT ATT ATA ATT ATT A-T ATAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
*
144944 AAT ATT ATT A
1 ATT ATT ATT A
144954 AAAAATAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:146085 original size:2 final size:2
Alignment explanation
Indices: 146072--146114 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
146062 TTATGTAATC
*
146072 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
146114 A
1 A
146115 ATTTATATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:153878 original size:2 final size:2
Alignment explanation
Indices: 153871--153897 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
153861 GGTTTTACTG
153871 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
153898 CAACATTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:162310 original size:23 final size:24
Alignment explanation
Indices: 162247--162331 Score: 118
Period size: 24 Copynumber: 3.6 Consensus size: 24
162237 AAACATAATT
* *
162247 CAGGTAAAGTATCATATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
162271 TAGGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
162295 CATGTCAA-TATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
162318 CAGGTCAGGTATCA
1 CAGGTCAAGTATCA
162332 TAACATAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
23 21 0.40
24 32 0.60
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:166971 original size:24 final size:24
Alignment explanation
Indices: 166944--167051 Score: 74
Period size: 24 Copynumber: 4.5 Consensus size: 24
166934 TATATCAAAA
* *
166944 ATCAAAACATAATTCAAGTCAAGT
1 ATCAAAACAGAATCCAAGTCAAGT
* * * *
166968 ATCATATCAGAATCCAGGTCATGT
1 ATCAAAACAGAATCCAAGTCAAGT
* * *
166992 ATCAGATCAGAATCCATGTCAA-T
1 ATCAAAACAGAATCCAAGTCAAGT
* * * *
167015 ATCAAAACATAATCTAGGTCAGGT
1 ATCAAAACAGAATCCAAGTCAAGT
* *
167039 ATCATAATAGAAT
1 ATCAAAACAGAAT
167052 TTAAATCAGA
Statistics
Matches: 65, Mismatches: 18, Indels: 2
0.76 0.21 0.02
Matches are distributed among these distances:
23 17 0.26
24 48 0.74
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.27
Consensus pattern (24 bp):
ATCAAAACAGAATCCAAGTCAAGT
Found at i:174369 original size:29 final size:29
Alignment explanation
Indices: 174327--174382 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
174317 ATTAAATCCA
*
174327 TCGATTATTAAAAGTTA-AAAATTGATCTT
1 TCGACTATTAAAAGTTACAAAA-TGATCTT
174356 TCGACTATTAAAAGTTACAAAATGATC
1 TCGACTATTAAAAGTTACAAAATGATC
174383 ATCCGGCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.36
Consensus pattern (29 bp):
TCGACTATTAAAAGTTACAAAATGATCTT
Found at i:174392 original size:29 final size:29
Alignment explanation
Indices: 174332--174393 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
174322 ATCCATCGAT
* *
174332 TATTAAAAGTTAAAAATTGATCTTTCGAC
1 TATTAAAAGTTAAAAATTGATCATCCGAC
*
174361 TATTAAAAGTTACAAAA-TGATCATCCGGC
1 TATTAAAAGTTA-AAAATTGATCATCCGAC
174390 TATT
1 TATT
174394 CATTATGTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.35
Consensus pattern (29 bp):
TATTAAAAGTTAAAAATTGATCATCCGAC
Found at i:178151 original size:21 final size:20
Alignment explanation
Indices: 178127--178168 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
178117 TTAAACTTCA
*
178127 AAATGTTTTAATTAAATTATC
1 AAATATTTTAATTAAA-TATC
*
178148 AAATATTTTAGTTAAATATC
1 AAATATTTTAATTAAATATC
178168 A
1 A
178169 TTTCATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
AAATATTTTAATTAAATATC
Found at i:178670 original size:18 final size:18
Alignment explanation
Indices: 178647--178686 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
178637 TTTCATTAAT
178647 ATTTATGTATGATATGGC
1 ATTTATGTATGATATGGC
*
178665 ATTTATGTATGATGTGGC
1 ATTTATGTATGATATGGC
178683 ATTT
1 ATTT
178687 TTTCTTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.47
Consensus pattern (18 bp):
ATTTATGTATGATATGGC
Found at i:186100 original size:19 final size:19
Alignment explanation
Indices: 186076--186120 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
186066 ATCGGTTTTT
*
186076 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCCG
* *
186095 AACCGGGTTGATCGGTCCG
1 AACCGGTTTGACCGGTCCG
186114 AACCGGT
1 AACCGGT
186121 CCGACCCGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.18, C:0.27, G:0.33, T:0.22
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCCG
Found at i:186153 original size:18 final size:18
Alignment explanation
Indices: 186124--186170 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
186114 AACCGGTCCG
186124 ACCCGA-CCGTTGACCCA
1 ACCCGACCCGTTGACCCA
*
186141 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCA
*
186159 ACCCGACTCGTT
1 ACCCGACCCGTT
186171 AATCGTTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.19, C:0.47, G:0.19, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCA
Found at i:186186 original size:14 final size:14
Alignment explanation
Indices: 186167--186195 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
186157 CGACCCGACT
186167 CGTTAATCGTTGAC
1 CGTTAATCGTTGAC
186181 CGTTAATCGTTGAC
1 CGTTAATCGTTGAC
186195 C
1 C
186196 ACCTTTGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (14 bp):
CGTTAATCGTTGAC
Found at i:187946 original size:24 final size:23
Alignment explanation
Indices: 187919--187969 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
187909 ACATGTTCAT
*
187919 GAACACATTTGTGAACATATAAAC
1 GAACACATTCGTGAACAT-TAAAC
*
187943 GAACACGTTCGTGAACATTAAAC
1 GAACACATTCGTGAACATTAAAC
187966 GAAC
1 GAAC
187970 GTTAAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (23 bp):
GAACACATTCGTGAACATTAAAC
Found at i:187978 original size:70 final size:70
Alignment explanation
Indices: 187902--188034 Score: 239
Period size: 70 Copynumber: 1.9 Consensus size: 70
187892 AAAACAACAC
* * *
187902 TAAACAAACATGTTCATGAACACATTTGTGAACATATAAACGAACACGTTCGTGAACATTAAACG
1 TAAACAAACATGTGCATGAACACATTCGTGAACATATAAACGAACACGTTCGCGAACATTAAACG
187967 AACGT
66 AACGT
187972 TAAACAAACATGTGCATGAACACATTCGTGAACATATAAACGAACACGTTCGCGAACATTAAA
1 TAAACAAACATGTGCATGAACACATTCGTGAACATATAAACGAACACGTTCGCGAACATTAAA
188035 TAAACGAACA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.23
Consensus pattern (70 bp):
TAAACAAACATGTGCATGAACACATTCGTGAACATATAAACGAACACGTTCGCGAACATTAAACG
AACGT
Found at i:188016 original size:24 final size:26
Alignment explanation
Indices: 187989--188044 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
187979 ACATGTGCAT
*
187989 GAACACATTCGTGAACA-T-ATAAAC
1 GAACACATTCGCGAACATTAATAAAC
*
188013 GAACACGTTCGCGAACATTAAATAAAC
1 GAACACATTCGCGAACATT-AATAAAC
188040 GAACA
1 GAACA
188045 TGAACACCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 15 0.56
25 1 0.04
27 11 0.41
ACGTcount: A:0.46, C:0.21, G:0.14, T:0.18
Consensus pattern (26 bp):
GAACACATTCGCGAACATTAATAAAC
Found at i:191836 original size:36 final size:36
Alignment explanation
Indices: 191789--191861 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
191779 AGTTCTGGAA
*
191789 TTAAGTGATAAAAGAATCAGCCATGGATATGTAGAT
1 TTAAGTGATAAAAGAATCAGCCATGAATATGTAGAT
191825 TTAAGTGATAAAAGAATCAGCCATGAATATGTAGAT
1 TTAAGTGATAAAAGAATCAGCCATGAATATGTAGAT
191861 T
1 T
191862 ATAATTTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (36 bp):
TTAAGTGATAAAAGAATCAGCCATGAATATGTAGAT
Found at i:193687 original size:24 final size:24
Alignment explanation
Indices: 193619--193727 Score: 80
Period size: 24 Copynumber: 4.5 Consensus size: 24
193609 AAATATTTTA
*
193619 TCTGATTTCTGA-CTTGAATTCTAT
1 TCTGATTTCTGATC-TGAATTCTGT
* *
193643 TATGA-TACATGA-CTTGAATTCTGT
1 TCTGATTTC-TGATC-TGAATTCTGT
*
193667 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* * * * *
193691 TCTAATATATGTTCTGAATTCTAT
1 TCTGATTTCTGATCTGAATTCTGT
*
193715 TTTGATTTCTGAT
1 TCTGATTTCTGAT
193728 ATCTCCGTTT
Statistics
Matches: 65, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
23 2 0.03
24 60 0.92
25 3 0.05
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:201393 original size:37 final size:37
Alignment explanation
Indices: 201352--201425 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
201342 TTGACATAAT
*
201352 TTAGCATATATATTATCTAATTTAATAGTTAAAAGTC
1 TTAGCATATATATTATCTAATTTAATAGCTAAAAGTC
*
201389 TTAGCATATATGTTATCTAATTTAATAGCTAAAAGTC
1 TTAGCATATATATTATCTAATTTAATAGCTAAAAGTC
201426 CAAAAAAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.42
Consensus pattern (37 bp):
TTAGCATATATATTATCTAATTTAATAGCTAAAAGTC
Found at i:206948 original size:60 final size:59
Alignment explanation
Indices: 206840--206967 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 59
206830 TCGGGTGACT
* * *
206840 ATTTTGTAACTTTTAATAGTCGAGGGACTCAATAAAGCAACGCTCTATAGTTGGAGGACC
1 ATTTTGTAACTTTAAATAGTCGAGGGACTCAATAAAACAACGCTCTATAATTGG-GGACC
* * *
206900 ATTTTGTAACTTTAAATAGTCGAGGGACTTAATAAAATAGTAC-C-CTATAATTGGGTACC
1 ATTTTGTAACTTTAAATAGTCGAGGGACTCAATAAAACA--ACGCTCTATAATTGGGGACC
206959 ATTTGTGTA
1 ATTT-TGTA
206968 TTTTACCCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
59 8 0.14
60 48 0.81
61 1 0.02
62 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.34
Consensus pattern (59 bp):
ATTTTGTAACTTTAAATAGTCGAGGGACTCAATAAAACAACGCTCTATAATTGGGGACC
Found at i:213772 original size:21 final size:21
Alignment explanation
Indices: 213748--213787 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
213738 TAGTAGTCAA
*
213748 ATCATAATTTTGAAAACTTCT
1 ATCATAATTTTCAAAACTTCT
**
213769 ATCATGTTTTTCAAAACTT
1 ATCATAATTTTCAAAACTT
213788 AATGTTAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (21 bp):
ATCATAATTTTCAAAACTTCT
Found at i:215430 original size:31 final size:31
Alignment explanation
Indices: 215386--215461 Score: 134
Period size: 31 Copynumber: 2.5 Consensus size: 31
215376 ACGTGGCAGT
* *
215386 CCATCTGCTATGTTTAAGTTACCAATTTAGC
1 CCATCTTCCATGTTTAAGTTACCAATTTAGC
215417 CCATCTTCCATGTTTAAGTTACCAATTTAGC
1 CCATCTTCCATGTTTAAGTTACCAATTTAGC
215448 CCATCTTCCATGTT
1 CCATCTTCCATGTT
215462 ATCCGTCACG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (31 bp):
CCATCTTCCATGTTTAAGTTACCAATTTAGC
Found at i:215525 original size:21 final size:21
Alignment explanation
Indices: 215501--215548 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
215491 GTCATGTCAA
*
215501 CACCGTGGACTACCACATCAG
1 CACCGTGAACTACCACATCAG
* * * *
215522 CACCATGAACTTCCACGTTAG
1 CACCGTGAACTACCACATCAG
215543 CACCGT
1 CACCGT
215549 AACGGTCAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.38, G:0.17, T:0.19
Consensus pattern (21 bp):
CACCGTGAACTACCACATCAG
Found at i:218035 original size:21 final size:21
Alignment explanation
Indices: 218011--218050 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
218001 CAATTTTTTT
218011 TACTAAAA-CTGATAGTTTATG
1 TACTAAAATC-GATAGTTTATG
218032 TACTAAAATCGATAGTTTA
1 TACTAAAATCGATAGTTTA
218051 GATACCTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (21 bp):
TACTAAAATCGATAGTTTATG
Found at i:218224 original size:21 final size:21
Alignment explanation
Indices: 218195--218248 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
218185 TTATTTTACT
* *
218195 TTTAAGATATTTAACATATAC
1 TTTATGATATTTAAAATATAC
**
218216 TTTATGATATACAAAATATAC
1 TTTATGATATTTAAAATATAC
218237 TTTAT-ATATTTA
1 TTTATGATATTTA
218249 CAGGAGCGGA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (21 bp):
TTTATGATATTTAAAATATAC
Found at i:219248 original size:21 final size:21
Alignment explanation
Indices: 219222--219261 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
219212 GACTATCGCA
219222 TTGCGATTTCCCAAATTCGTG
1 TTGCGATTTCCCAAATTCGTG
* *
219243 TTGCGATTTTCCTAATTCG
1 TTGCGATTTCCCAAATTCG
219262 CAATGCGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (21 bp):
TTGCGATTTCCCAAATTCGTG
Found at i:219268 original size:21 final size:21
Alignment explanation
Indices: 219217--219269 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
219207 ATTCTGACTA
219217 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
** * *
219238 TCGTGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
219259 TCGCAATGCGA
1 TCGCATTGCGA
219270 ATACGTAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:220172 original size:24 final size:24
Alignment explanation
Indices: 220145--220198 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
220135 GTATTTGAAA
220145 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
220169 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
220193 TTTGAT
1 TTTGAT
220199 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:221345 original size:18 final size:18
Alignment explanation
Indices: 221322--221370 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
221312 AAAGGCAATC
*
221322 AAAATCGCAATCATCTTT
1 AAAATCCCAATCATCTTT
221340 AAAATCCCAATCATCTTT
1 AAAATCCCAATCATCTTT
221358 AAAATCCCAATCA
1 AAAATCCCAATCA
221371 CAATCGGCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.29
Consensus pattern (18 bp):
AAAATCCCAATCATCTTT
Found at i:221611 original size:20 final size:19
Alignment explanation
Indices: 221583--221637 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
221573 CAATCATCTT
*
221583 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
221603 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
221622 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
221638 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:221647 original size:14 final size:14
Alignment explanation
Indices: 221628--221715 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
221618 GCGAAATGAA
221628 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
221642 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
221661 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
221675 AATTGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
221694 AATCGCAACGAGGG
1 AATCGCAACGAGAG
221708 AATCGCAA
1 AATCGCAA
221716 AGCGAAATGA
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 26 0.46
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 19 0.33
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:221652 original size:33 final size:33
Alignment explanation
Indices: 221610--221736 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
221600 GGAAATGACT
221610 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
221643 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
221676 ATTGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
221709 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
221737 CGAATTTAGT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:221666 original size:19 final size:18
Alignment explanation
Indices: 221590--221740 Score: 92
Period size: 19 Copynumber: 8.7 Consensus size: 18
221580 CTTAATGTCT
**
221590 ATCGCAACGCGGAAATGACT
1 ATCGCAA-GC-GAAATGAAA
221610 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
221629 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
221643 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
221662 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
*
221676 ATTGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
221695 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
221709 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
221728 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
221741 TTTAGTTTCG
Statistics
Matches: 102, Mismatches: 13, Indels: 33
0.69 0.09 0.22
Matches are distributed among these distances:
14 26 0.25
15 5 0.05
16 6 0.06
17 6 0.06
18 5 0.05
19 45 0.44
20 9 0.09
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.13
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:221758 original size:19 final size:18
Alignment explanation
Indices: 221736--221810 Score: 59
Period size: 19 Copynumber: 4.2 Consensus size: 18
221726 AAATCGCAAC
221736 GCGAATTTAGTTTCGCGTT
1 GCGAATTTA-TTTCGCGTT
*
221755 GCG-ATTT-TGT--CGTT
1 GCGAATTTATTTCGCGTT
*
221769 GCGATTTTTATTTCGCGTT
1 GCGA-ATTTATTTCGCGTT
* *
221788 GCGATTTTCATTTCGCATT
1 GCGAATTT-ATTTCGCGTT
221807 GCGA
1 GCGA
221811 TAGTCATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
14 7 0.15
16 5 0.11
17 2 0.04
18 8 0.17
19 24 0.52
ACGTcount: A:0.13, C:0.17, G:0.24, T:0.45
Consensus pattern (18 bp):
GCGAATTTATTTCGCGTT
Found at i:221811 original size:19 final size:19
Alignment explanation
Indices: 221767--221811 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
221757 GATTTTGTCG
* *
221767 TTGCGATTTTTATTTCGCG
1 TTGCGATTTTCATTTCGCA
221786 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
221805 TTGCGAT
1 TTGCGAT
221812 AGTCATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.13, C:0.18, G:0.20, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:221817 original size:19 final size:19
Alignment explanation
Indices: 221778--221819 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
221768 TGCGATTTTT
* **
221778 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATAGTC
221797 ATTTCGCATTGCGATAGTC
1 ATTTCGCATTGCGATAGTC
221816 ATTT
1 ATTT
221820 TTGCCCTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (19 bp):
ATTTCGCATTGCGATAGTC
Found at i:221938 original size:14 final size:14
Alignment explanation
Indices: 221919--221955 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
221909 CATCAATTAA
221919 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
221933 ACAAATCATCTTTT
1 ACAAATCAACTTTT
221947 ACAAATCAA
1 ACAAATCAA
221956 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:224522 original size:2 final size:2
Alignment explanation
Indices: 224515--224551 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
224505 TGAATCCTAA
224515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
224552 ACTAATGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:226071 original size:26 final size:27
Alignment explanation
Indices: 226013--226065 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
226003 AGACTTTACG
226013 AGTAAAACTTAAAAGACTTCATGCACC
1 AGTAAAACTTAAAAGACTTCATGCACC
* *
226040 AGTAAAA-TTTAAAGATTTCATGCACC
1 AGTAAAACTTAAAAGACTTCATGCACC
226066 CTTAAACCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.26
Consensus pattern (27 bp):
AGTAAAACTTAAAAGACTTCATGCACC
Found at i:227036 original size:3 final size:3
Alignment explanation
Indices: 227028--227066 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
227018 TCATTTCGTC
227028 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
227067 GCATTAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:239861 original size:2 final size:2
Alignment explanation
Indices: 239854--239881 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
239844 AGAGTCAATA
239854 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
239882 TACAAATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:241427 original size:9 final size:10
Alignment explanation
Indices: 241413--241455 Score: 63
Period size: 9 Copynumber: 4.4 Consensus size: 10
241403 ATGAAAAATG
241413 TAATTAA-AA
1 TAATTAATAA
241422 TAATTAATAA
1 TAATTAATAA
241432 TAATATAATAA
1 TAAT-TAATAA
241443 TAA-TAATAA
1 TAATTAATAA
241452 TAAT
1 TAAT
241456 ATTTTTTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 16 0.52
10 6 0.19
11 9 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
TAATTAATAA
Found at i:241434 original size:3 final size:3
Alignment explanation
Indices: 241420--241456 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
241410 ATGTAATTAA
241420 AAT AATT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT A
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
241457 TTTTTTAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:241448 original size:17 final size:18
Alignment explanation
Indices: 241420--241453 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
241410 ATGTAATTAA
241420 AATAATTAATAATAATAT
1 AATAATTAATAATAATAT
241438 AATAA-TAATAATAATA
1 AATAATTAATAATAATA
241454 ATATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATAATTAATAATAATAT
Found at i:245475 original size:50 final size:50
Alignment explanation
Indices: 245421--245528 Score: 162
Period size: 50 Copynumber: 2.2 Consensus size: 50
245411 ACTCTCGATT
** * * *
245421 ATATTCGAGGTTAAGTTAGATTGATTTTCTAAATAAGATATTTATATATA
1 ATATTCGAGGTTAAGTTAGATCAAATTTCTAAATAAGAGATTTATACATA
245471 ATATTCGAGGTTAAGTTAGATCAAATTTCTAAATAAGAGATTTATACATA
1 ATATTCGAGGTTAAGTTAGATCAAATTTCTAAATAAGAGATTTATACATA
*
245521 ATACTCGA
1 ATATTCGA
245529 ATTTGAGATT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (50 bp):
ATATTCGAGGTTAAGTTAGATCAAATTTCTAAATAAGAGATTTATACATA
Found at i:251484 original size:20 final size:20
Alignment explanation
Indices: 251454--251495 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
251444 GACTGAAGAC
251454 AGATAAAAATA-TACCATAA
1 AGATAAAAATAGTACCATAA
251473 AGATAGAAAATATGTACCATAA
1 AGATA-AAAATA-GTACCATAA
251495 A
1 A
251496 AACATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 6 0.30
22 9 0.45
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.21
Consensus pattern (20 bp):
AGATAAAAATAGTACCATAA
Found at i:253379 original size:32 final size:32
Alignment explanation
Indices: 253304--253381 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 32
253294 CAACCCGAAA
* *
253304 TCGTGTTATAAACTTTTCAAATCAAACAAAAT
1 TCGTATTATAATCTTTTCAAATCAAACAAAAT
253336 TCGTATTATAATCTTTTCAAATCAAACAAAAT
1 TCGTATTATAATCTTTTCAAATCAAACAAAAT
253368 TCGTATTATAATCT
1 TCGTATTATAATCT
253382 CACCATTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.38
Consensus pattern (32 bp):
TCGTATTATAATCTTTTCAAATCAAACAAAAT
Found at i:260422 original size:16 final size:18
Alignment explanation
Indices: 260394--260429 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
260384 ATCTCAAAGA
260394 GACATCTTTTGATC-ACT
1 GACATCTTTTGATCGACT
260411 GACATC-TTTGATCGACT
1 GACATCTTTTGATCGACT
260428 GA
1 GA
260430 AAAATTACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (18 bp):
GACATCTTTTGATCGACT
Found at i:262633 original size:41 final size:41
Alignment explanation
Indices: 262580--262735 Score: 170
Period size: 41 Copynumber: 3.8 Consensus size: 41
262570 CGCAACCCAG
* *
262580 TTTCCAATTTCGTAATGCGAATATGTAAATCGCATTGCGAT
1 TTTCCAAATTCGTAACGCGAATATGTAAATCGCATTGCGAT
* ** *
262621 TTTCCAAATTCGTAACGTGAATATGTAAATCGCAACGCGAA
1 TTTCCAAATTCGTAACGCGAATATGTAAATCGCATTGCGAT
** * ** *
262662 TTTGTAAA-TCGCATTGCGAATTTGTAAATCGCATTGCGAT
1 TTTCCAAATTCGTAACGCGAATATGTAAATCGCATTGCGAT
* * *
262702 TTTTCAAATTCGTAACGTGAATCTGTAAATCGCA
1 TTTCCAAATTCGTAACGCGAATATGTAAATCGCA
262736 ACGCGAATTT
Statistics
Matches: 91, Mismatches: 23, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 30 0.33
41 61 0.67
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (41 bp):
TTTCCAAATTCGTAACGCGAATATGTAAATCGCATTGCGAT
Found at i:262662 original size:20 final size:20
Alignment explanation
Indices: 262596--262757 Score: 137
Period size: 20 Copynumber: 8.0 Consensus size: 20
262586 ATTTCGTAAT
* **
262596 GCGAATATGTAAATCGCATT
1 GCGAATTTGTAAATCGCAAC
* ** *
262616 GCGATTTTCCAAATTCGTAAC
1 GCGAATTTGTAAA-TCGCAAC
* *
262637 GTGAATATGTAAATCGCAAC
1 GCGAATTTGTAAATCGCAAC
**
262657 GCGAATTTGTAAATCGCATT
1 GCGAATTTGTAAATCGCAAC
**
262677 GCGAATTTGTAAATCGCATT
1 GCGAATTTGTAAATCGCAAC
* *
262697 GCG-ATTTTTCAAATTCGTAAC
1 GCGAATTTGT-AAA-TCGCAAC
* *
262718 GTGAATCTGTAAATCGCAAC
1 GCGAATTTGTAAATCGCAAC
262738 GCGAATTTGTAAATCGCAAC
1 GCGAATTTGTAAATCGCAAC
262758 ACAGAAGTCA
Statistics
Matches: 111, Mismatches: 27, Indels: 8
0.76 0.18 0.05
Matches are distributed among these distances:
19 5 0.05
20 81 0.73
21 21 0.19
22 4 0.04
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (20 bp):
GCGAATTTGTAAATCGCAAC
Found at i:262688 original size:81 final size:81
Alignment explanation
Indices: 262595--262755 Score: 295
Period size: 81 Copynumber: 2.0 Consensus size: 81
262585 AATTTCGTAA
262595 TGCGAATATGTAAATCGCATTGCGATTTTCCAAATTCGTAACGTGAATATGTAAATCGCAACGCG
1 TGCGAATATGTAAATCGCATTGCGATTTTCCAAATTCGTAACGTGAATATGTAAATCGCAACGCG
262660 AATTTGTAAATCGCAT
66 AATTTGTAAATCGCAT
* * *
262676 TGCGAATTTGTAAATCGCATTGCGATTTTTCAAATTCGTAACGTGAATCTGTAAATCGCAACGCG
1 TGCGAATATGTAAATCGCATTGCGATTTTCCAAATTCGTAACGTGAATATGTAAATCGCAACGCG
262741 AATTTGTAAATCGCA
66 AATTTGTAAATCGCA
262756 ACACAGAAGT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (81 bp):
TGCGAATATGTAAATCGCATTGCGATTTTCCAAATTCGTAACGTGAATATGTAAATCGCAACGCG
AATTTGTAAATCGCAT
Found at i:262795 original size:40 final size:40
Alignment explanation
Indices: 262751--262861 Score: 143
Period size: 40 Copynumber: 2.8 Consensus size: 40
262741 AATTTGTAAA
*
262751 TCGCAACACAGAAGTCAAATTCGCAACGCGGTAGTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
* * ** *
262791 TCGCAATACAAAAGTCAAATTCATAACGCGATAGTCAATT
1 TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
*
262831 TCGCAACGC-GAAAGTCAAATTCGCAACGCGA
1 TCGCAACACAG-AAGTCAAATTCGCAACGCGA
262862 AACACAATAT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (40 bp):
TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
Found at i:262863 original size:20 final size:20
Alignment explanation
Indices: 262762--262863 Score: 123
Period size: 20 Copynumber: 5.1 Consensus size: 20
262752 CGCAACACAG
*
262762 AAGTCAAATTCGCAACGCGG
1 AAGTCAAATTCGCAACGCGA
* ** *
262782 TAGTCAAATTCGCAATACAA
1 AAGTCAAATTCGCAACGCGA
**
262802 AAGTCAAATTCATAACGCGA
1 AAGTCAAATTCGCAACGCGA
* *
262822 TAGTCAATTTCGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
262842 AAGTCAAATTCGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
262862 AA
1 AA
262864 CACAATATTA
Statistics
Matches: 65, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
AAGTCAAATTCGCAACGCGA
Done.