Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011117.1 Kokia drynarioides strain JFW-HI SEQ_126090, 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: 482593
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 526 characters in sequence are not A, C, G, or T
Found at i:2290 original size:30 final size:31
Alignment explanation
Indices: 2224--2333 Score: 127
Period size: 30 Copynumber: 3.6 Consensus size: 31
2214 TTTCGTTGAG
**
2224 AAATTATATTTTGACCCCTAAACTTCCCAAAA
1 AAATTATATTTTGACCCCTAAACTTTTC-AAA
*
2256 AAATTATATTTTTACCCCTAAACTTTTC-AA
1 AAATTATATTTTGACCCCTAAACTTTTCAAA
* * *
2286 AAATTATATTTTGACACTTAAAC-TTTCTAA
1 AAATTATATTTTGACCCCTAAACTTTTCAAA
2316 AAATTCAT-TTTTGACCCC
1 AAATT-ATATTTTGACCCC
2334 CTTGCCTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.06
30 37 0.54
31 2 0.03
32 25 0.37
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.39
Consensus pattern (31 bp):
AAATTATATTTTGACCCCTAAACTTTTCAAA
Found at i:9791 original size:79 final size:79
Alignment explanation
Indices: 9692--9903 Score: 291
Period size: 80 Copynumber: 2.7 Consensus size: 79
9682 AATACACTTC
* * * *
9692 AATACAGCTCCCACCAAACTTACTCATTGTATGCTTTCCATTCTTTTAAATTATTGGGATTCTAA
1 AATACAACTTCCACCAAACTTATTCATTGTATGCTTTCCATTCTTTTAAATTATTGGGATCCTAA
*
9757 GATCAACATACTAA
66 CATCAACATACTAA
*
9771 AATACAACTTCCACCAAACTTATTGA-TGCTTATGCTTTCCATTCTTTTAAATTATTGGGATCCT
1 AATACAACTTCCACCAAACTTATTCATTG--TATGCTTTCCATTCTTTTAAATTATTGGGATCCT
9835 AACATCAACATACTAA
64 AACATCAACATACTAA
* * * * * *
9851 AATACAATTTCCATCAAACTTATTCATTGTGTCCTTTTCTTTCTTTTAAATTA
1 AATACAACTTCCACCAAACTTATTCATTGTATGCTTTCCATTCTTTTAAATTA
9904 GGATAAAATA
Statistics
Matches: 117, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
78 2 0.02
79 42 0.36
80 71 0.61
81 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (79 bp):
AATACAACTTCCACCAAACTTATTCATTGTATGCTTTCCATTCTTTTAAATTATTGGGATCCTAA
CATCAACATACTAA
Found at i:10786 original size:41 final size:40
Alignment explanation
Indices: 10671--10789 Score: 150
Period size: 41 Copynumber: 2.9 Consensus size: 40
10661 AAACGCCGTA
* * **
10671 AAAGGTAGAGCAATAACGGCGCTTATGGGA-AAGCATCGCT
1 AAAGGTAGAGCAATAGCGACGCTTAT-GGACAAGCGCCGCT
* *
10711 AAAGGTAAGAGCAATAGCGACACTTATGGGCAAGCGCCGCT
1 AAAGGT-AGAGCAATAGCGACGCTTATGGACAAGCGCCGCT
10752 AAAGGTCAGAGCAATAGCGACGCTTATGGACAAGCGCC
1 AAAGGT-AGAGCAATAGCGACGCTTATGGACAAGCGCC
10790 TTTAAAAGTC
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
40 8 0.12
41 60 0.88
ACGTcount: A:0.34, C:0.21, G:0.29, T:0.15
Consensus pattern (40 bp):
AAAGGTAGAGCAATAGCGACGCTTATGGACAAGCGCCGCT
Found at i:10811 original size:41 final size:41
Alignment explanation
Indices: 10664--10819 Score: 120
Period size: 41 Copynumber: 3.8 Consensus size: 41
10654 TTTACATAAA
* * *
10664 CGCCG-TAAAAGGT-AGAGCAATAACGGCGCTTATGGGA-AAG
1 CGCCGCTAAAA-GTCAGAACAATAGCGACGCTTAT-GGACAAG
** * * * * *
10704 CATCGCTAAAGGTAAGAGCAATAGCGACACTTATGGGCAAG
1 CGCCGCTAAAAGTCAGAACAATAGCGACGCTTATGGACAAG
* *
10745 CGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGGACAAG
1 CGCCGCTAAAAGTCAGAACAATAGCGACGCTTATGGACAAG
** * * *
10786 CGCCTTTAAAAGTCATAACATTAGCGGCGCTTAT
1 CGCCGCTAAAAGTCAGAACAATAGCGACGCTTAT
10820 ATGAAAAACA
Statistics
Matches: 94, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
40 7 0.07
41 87 0.93
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (41 bp):
CGCCGCTAAAAGTCAGAACAATAGCGACGCTTATGGACAAG
Found at i:15275 original size:30 final size:29
Alignment explanation
Indices: 15219--15275 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
15209 TTGATTTAAT
* *
15219 GTGTAATTGTAAACATAAACTTTAATTTG
1 GTGTAATTATAAACATAAACTCTAATTTG
*
15248 GTGTAATTATACACATGAAACTCTAATT
1 GTGTAATTATAAACAT-AAACTCTAATT
15276 GTGATTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
GTGTAATTATAAACATAAACTCTAATTTG
Found at i:15378 original size:29 final size:29
Alignment explanation
Indices: 15346--15401 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
15336 AAATATATCA
* * *
15346 ATTTATTTTTATATTAGATAAATATAATT
1 ATTTATTTATATAATAGATAAACATAATT
*
15375 ATTTATTTATATAATATATAAACATAA
1 ATTTATTTATATAATAGATAAACATAA
15402 AATGATGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
ATTTATTTATATAATAGATAAACATAATT
Found at i:15492 original size:29 final size:30
Alignment explanation
Indices: 15450--15506 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
15440 GAATTGGATT
15450 AAATCAAAATTTCATATATAAAATTACATA
1 AAATCAAAATTTCATATATAAAATTACATA
* * *
15480 AAATTAAAA-TTCATGTATATAATTACA
1 AAATCAAAATTTCATATATAAAATTACA
15507 CATTAAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.35
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATTACATA
Found at i:15522 original size:31 final size:29
Alignment explanation
Indices: 15447--15527 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 29
15437 CAAGAATTGG
*
15447 ATTAAATCAAAATTTCATATATAAAATTAC
1 ATTAAATCAAAA-TTCATGTATAAAATTAC
* * *
15477 ATAAAATTAAAATTCATGTATATAATTACAC
1 ATTAAATCAAAATTCATGTATAAAATT--AC
*
15508 ATTAAATCATAATTCATGTA
1 ATTAAATCAAAATTCATGTA
15528 AAATTTTAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 13 0.31
30 10 0.24
31 19 0.45
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (29 bp):
ATTAAATCAAAATTCATGTATAAAATTAC
Found at i:27141 original size:23 final size:24
Alignment explanation
Indices: 27095--27147 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 24
27085 GGGATAAATT
27095 GTGAATAATGAGCCCAAAATTCAA
1 GTGAATAATGAGCCCAAAATTCAA
*
27119 GTGAATAATGAG-CCTAAATTCAA
1 GTGAATAATGAGCCCAAAATTCAA
27142 GTGAAT
1 GTGAAT
27148 TTGGGTATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (24 bp):
GTGAATAATGAGCCCAAAATTCAA
Found at i:28601 original size:23 final size:24
Alignment explanation
Indices: 28557--28601 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
28547 TGTTATGTAT
**
28557 AAAATAAAAAGATATTTTTTTACA
1 AAAATAAAAAGATATTAATTTACA
*
28581 AAAATAATAA-ATATTAATTTA
1 AAAATAAAAAGATATTAATTTA
28602 AAGATGTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAATAAAAAGATATTAATTTACA
Found at i:30539 original size:31 final size:31
Alignment explanation
Indices: 30498--30565 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
30488 GGCCTGAGTT
* * *
30498 TCAAACTGAACATTGAAGCCAAACTCAAATA
1 TCAAATTGAACATTAAAGACAAACTCAAATA
*
30529 TCAAATTGAACATTAAAGACAAACTCAATTA
1 TCAAATTGAACATTAAAGACAAACTCAAATA
*
30560 CCAAAT
1 TCAAAT
30566 AATATATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.22
Consensus pattern (31 bp):
TCAAATTGAACATTAAAGACAAACTCAAATA
Found at i:35880 original size:15 final size:16
Alignment explanation
Indices: 35850--35888 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
35840 TTGAAAAAAT
35850 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
35867 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
35882 ATAATTT
1 ATAATTT
35889 TAAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:35903 original size:24 final size:23
Alignment explanation
Indices: 35837--35903 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
35827 GGAATTAAAA
*
35837 AATTTGAAAAAATATAA-TTTTAT
1 AATTTTAAAAAAT-TAATTTTTAT
* * *
35860 TATTTTAATAATTTATATTTTTAT
1 AATTTTAAAAAATTA-ATTTTTAT
35884 AATTTTAAAAAAATTAATTT
1 AATTTT-AAAAAATTAATTT
35904 AAAATTTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
22 2 0.06
23 10 0.29
24 15 0.44
25 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
AATTTTAAAAAATTAATTTTTAT
Found at i:35904 original size:30 final size:30
Alignment explanation
Indices: 35868--35924 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
35858 ATTATTTTAA
* *
35868 TAATTTATATTTTTATAATTTTAAAAAAAT
1 TAATTTAAAATTTTATAATTTTAAAAAAAT
* *
35898 TAATTTAAAATTTTATTATTTTTAAAA
1 TAATTTAAAATTTTATAATTTTAAAAA
35925 GGTTAAAGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
TAATTTAAAATTTTATAATTTTAAAAAAAT
Found at i:35931 original size:39 final size:38
Alignment explanation
Indices: 35858--35931 Score: 87
Period size: 39 Copynumber: 1.9 Consensus size: 38
35848 ATATAATTTT
* * **
35858 ATTATTTTAATAATTTATATTTTTATAATTTTAAAAAA
1 ATTAATTTAATAATTTATATTTTTAAAAGGTTAAAAAA
35896 ATTAATTTAA-AATTTTATTATTTTTAAAAGGTTAAA
1 ATTAATTTAATAA-TTTA-TATTTTTAAAAGGTTAAA
35932 GTGTTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
37 2 0.07
38 13 0.43
39 15 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (38 bp):
ATTAATTTAATAATTTATATTTTTAAAAGGTTAAAAAA
Found at i:40297 original size:34 final size:35
Alignment explanation
Indices: 40231--40298 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
40221 ACTTAATATA
*
40231 ATATAAATTATAGTATATAGCATATTTTAACAATT
1 ATATAAATTATAGTATATAGCATATTTCAACAATT
*
40266 ATATAAGTTAT-GTATAT-GCATATTTGCAACAAT
1 ATATAAATTATAGTATATAGCATATTT-CAACAAT
40299 CTCATAATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 8 0.27
34 12 0.40
35 10 0.33
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (35 bp):
ATATAAATTATAGTATATAGCATATTTCAACAATT
Found at i:42118 original size:6 final size:6
Alignment explanation
Indices: 42109--42164 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
42099 TTAATTTTAT
* * * *
42109 TTTAAA TTTAGA TTT-AT TTTAAA TTTGAA TTTAAA -TTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
42155 TTTAAA TTTA
1 TTTAAA TTTA
42165 TTTTCAAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
5 7 0.17
6 33 0.82
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:42139 original size:23 final size:23
Alignment explanation
Indices: 42099--42164 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
42089 CGGGTCTCTT
* *
42099 TTAATTTT-ATTTTAAATTTAGA
1 TTAATTTTAAATTTAAATTTAAA
* *
42121 TTTATTTTAAATTTGAATTTAAA
1 TTAATTTTAAATTTAAATTTAAA
42144 TTAATTTTAAATTTAAATTTA
1 TTAATTTTAAATTTAAATTTA
42165 TTTTCAAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 7 0.19
23 30 0.81
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (23 bp):
TTAATTTTAAATTTAAATTTAAA
Found at i:42168 original size:17 final size:17
Alignment explanation
Indices: 42098--42158 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
42088 CCGGGTCTCT
*
42098 TTTAATTTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
42115 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* ** *
42132 TTTGAATTTAAATTAAT
1 TTTAAATTTATTTTAAA
42149 TTTAAATTTA
1 TTTAAATTTA
42159 AATTTATTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:44076 original size:29 final size:29
Alignment explanation
Indices: 44033--44231 Score: 122
Period size: 29 Copynumber: 6.8 Consensus size: 29
44023 AAAGGGCCCT
* * * *
44033 AAACTGTCCGAAAATTACAATTTTATCGCA
1 AAACT-TCCAAAAATTACATTTTTAACCCA
* *
44063 AAACTTCCAAAAATTCCATTTTTAACCCC
1 AAACTTCCAAAAATTACATTTTTAACCCA
*
44092 AAACTTCCAAAAAATACATTTTTAACCTC-
1 AAACTTCCAAAAATTACATTTTTAACC-CA
* * * * *
44121 CAACCTCCAAAAATTCCA-TTTTAACTTCG
1 AAACTTCCAAAAATTACATTTTTAAC-CCA
* *
44150 AAACTTTCAAAAATTACCA-TTTT-ACCCTC
1 AAACTTCCAAAAATTA-CATTTTTAACCC-A
* * * *
44179 TAA-TGTCCAAAAACTCCATTTTTGACCCCA
1 AAACT-TCCAAAAATTACATTTTT-AACCCA
*
44209 AAACTTTC-AAAATTACATTTTTA
1 AAACTTCCAAAAATTACATTTTTA
44232 CCTCTGAATG
Statistics
Matches: 130, Mismatches: 29, Indels: 22
0.72 0.16 0.12
Matches are distributed among these distances:
28 13 0.10
29 97 0.75
30 16 0.12
31 4 0.03
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTAACCCA
Found at i:44130 original size:58 final size:58
Alignment explanation
Indices: 44068--44287 Score: 191
Period size: 58 Copynumber: 3.8 Consensus size: 58
44058 TCGCAAAACT
* *
44068 TCCAAAAATTCCATTTTTAACCCCAAACTTCCAAAAAATACATTTTTAACCTCCAACC
1 TCCAAAAATTCCATTTTTAACCCCAAACTTTCAAAAATTACATTTTTAACCTCCAACC
* * * * **
44126 TCCAAAAATTCCA-TTTTAACTTCGAAACTTTCAAAAATTACCA-TTTTACCCTCTAATG
1 TCCAAAAATTCCATTTTTAAC-CCCAAACTTTCAAAAATTA-CATTTTTAACCTCCAACC
* * * **
44184 TCCAAAAACTCCATTTTTGACCCCAAAACTTTC-AAAATTACATTTTT-ACCTCTGAATG
1 TCCAAAAATTCCATTTTTAACCCC-AAACTTTCAAAAATTACATTTTTAACCTC-CAACC
* * * *
44242 TCTAAAAATTCCA--TTTAACCACGAACTTTCCCAAAATTACCATTTT
1 TCCAAAAATTCCATTTTTAACCCCAAACTTT-CAAAAATTA-CATTTT
44288 GCCCCCGAGA
Statistics
Matches: 134, Mismatches: 19, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
55 6 0.04
56 8 0.06
57 20 0.15
58 84 0.63
59 16 0.12
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.34
Consensus pattern (58 bp):
TCCAAAAATTCCATTTTTAACCCCAAACTTTCAAAAATTACATTTTTAACCTCCAACC
Found at i:56356 original size:206 final size:207
Alignment explanation
Indices: 56002--56430 Score: 707
Period size: 206 Copynumber: 2.1 Consensus size: 207
55992 CGATTCCCAA
* * * *
56002 CTTCCTGATGAGATATTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGAAT
1 CTTCCTGATGAGATACTGAGAAGTAGACCAAATTCATCTTCCTAACGAGATACAGAGAAGCGAAT
56067 TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGC
66 TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGC
** *
56132 TCGATGTAAGCAAATCTTCGAACCTTAGCTTCCTGATGAGATACTGAGAAGCAGG-TTGAAGTAA
131 TCGATGTAAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGATTGAAGTAA
*
56196 TAAAATGGTCTG
196 TAAAATGGTCTC
*
56208 CTTCCTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTAACGAGATACAGAGAAGCGAAT
1 CTTCCTGATGAGATACTGAGAAGTAGACCAAATTCATCTTCCTAACGAGATACAGAGAAGCGAAT
* * *
56273 TGAAACAAACGATGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
66 TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGC
* * *
56338 TCTATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATATTGAGAAGCAGGATTGAAGTAA
131 TCGATGTAAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGATTGAAGTAA
*
56403 TAAAATGGTTTC
196 TAAAATGGTCTC
56415 CTTCCTGATGAGATAC
1 CTTCCTGATGAGATAC
56431 AAAGAAGCGG
Statistics
Matches: 206, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
206 171 0.83
207 35 0.17
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (207 bp):
CTTCCTGATGAGATACTGAGAAGTAGACCAAATTCATCTTCCTAACGAGATACAGAGAAGCGAAT
TGAAACAAACGACGCGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGC
TCGATGTAAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGATTGAAGTAA
TAAAATGGTCTC
Found at i:56540 original size:168 final size:168
Alignment explanation
Indices: 56245--56604 Score: 524
Period size: 168 Copynumber: 2.1 Consensus size: 168
56235 CCAAATTCGT
* * * * * *
56245 CTTCCTAACGAGATACAGAGAAGCGAATTGAAACAAACGATGCGGTCATCTTCTTGATGAGATAC
1 CTTCCTGATGAGATACAAAGAAGCGAATTGAAACAAACGATGCGGTCATCTTCCTGATAAGACAC
* *
56310 TGAGAAGAAGACCAAATCAAACCCACGCTCTATGTGAGCAAATCTTCGAACCCCAACTTCCTGAT
66 -GAAAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGAT
* * * *
56375 GAGATATTGAGAAGCAGGATTGAAGTAATAAAATGGTTTC
130 GAGATACTGAGAAGCAAG-TCGAAGTAATAAAATGGTTAC
*
56415 CTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAACGATGCGGTCATCTTCCTGATAAGACAC
1 CTTCCTGATGAGATACAAAGAAGCGAATTGAAACAAACGATGCGGTCATCTTCCTGATAAGACAC
* * *
56480 -AAAAGAAGGCCAAATCAAACCCACGCTCGATGTGAGCAAATCTTTGAACCCCAGCTTCCTGATG
66 GAAAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATG
*
56544 AGATACTGAGAAGCAAGTCGAAGTAATAAAATGGTTAG
131 AGATACTGAGAAGCAAGTCGAAGTAATAAAATGGTTAC
* *
56582 CTTCTTGATGAGATACGAAGAAG
1 CTTCCTGATGAGATACAAAGAAG
56605 TGAACCAAAT
Statistics
Matches: 171, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
167 39 0.23
168 74 0.43
170 58 0.34
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (168 bp):
CTTCCTGATGAGATACAAAGAAGCGAATTGAAACAAACGATGCGGTCATCTTCCTGATAAGACAC
GAAAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATG
AGATACTGAGAAGCAAGTCGAAGTAATAAAATGGTTAC
Found at i:57022 original size:6 final size:6
Alignment explanation
Indices: 57013--57085 Score: 80
Period size: 6 Copynumber: 12.7 Consensus size: 6
57003 TTAATTTTAT
* * * *
57013 TTTAAA TTTAGA TTT-AT TTTAAA TTTGAA TTTAAA -TTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
57059 TTTAAA TTT-AA TCTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
57086 TTTTCAAATT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
5 11 0.20
6 43 0.80
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:57028 original size:17 final size:17
Alignment explanation
Indices: 57002--57096 Score: 82
Period size: 17 Copynumber: 5.2 Consensus size: 17
56992 TCGGGCCCCT
*
57002 TTTAATTTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
57019 TTTAGATTTATTTTAAATTTGAA
1 TTTAAATTTATTTT--A----AA
*
57042 TTTAAATTAATTTTAAA
1 TTTAAATTTATTTTAAA
* *
57059 TTTAAATTTAATCTAAA
1 TTTAAATTTATTTTAAA
57076 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
57094 TTT
1 TTT
57097 TAAAAGATTA
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
17 40 0.65
18 6 0.10
19 1 0.02
21 1 0.02
23 14 0.23
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:57043 original size:23 final size:23
Alignment explanation
Indices: 57003--57085 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
56993 CGGGCCCCTT
* *
57003 TTAATTTT-ATTTTAAATTTAGA
1 TTAATTTTAAATTTAAATTTAAA
* *
57025 TTTATTTTAAATTTGAATTTAAA
1 TTAATTTTAAATTTAAATTTAAA
57048 TTAATTTTAAATTTAAATTT-AA
1 TTAATTTTAAATTTAAATTTAAA
*
57070 TCTAAATTTAAATTTA
1 T-TAATTTTAAATTTA
57086 TTTTCAAATT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 10 0.19
23 42 0.81
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (23 bp):
TTAATTTTAAATTTAAATTTAAA
Found at i:57832 original size:15 final size:15
Alignment explanation
Indices: 57814--57901 Score: 72
Period size: 15 Copynumber: 5.7 Consensus size: 15
57804 TATTAATGGC
57814 AATAATAACTATT-TT
1 AATAATAA-TATTATT
57829 AATAATAATATTATT
1 AATAATAATATTATT
* *
57844 ATTAATAATAATGA-T
1 AATAATAAT-ATTATT
* *
57859 AATAACTATTAGTAATT
1 AATAA-TAATA-TTATT
*
57876 AATAATAATATTAAT
1 AATAATAATATTATT
57891 AATTAATAATA
1 AA-TAATAATA
57902 AGAAAAAAAC
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
14 4 0.07
15 29 0.49
16 20 0.34
17 6 0.10
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
AATAATAATATTATT
Found at i:57834 original size:3 final size:3
Alignment explanation
Indices: 57828--57902 Score: 60
Period size: 3 Copynumber: 24.0 Consensus size: 3
57818 ATAACTATTT
* * * * * *
57828 TAA TAA TAA TAT TAT TAT TAA TAA TAA TGA TAA TAA CTAT TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
*
57874 TTAA TAA TAA TAT TAA TAA TTAA TAA TAA
1 -TAA TAA TAA TAA TAA TAA -TAA TAA TAA
57903 GAAAAAAACT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
3 52 0.87
4 8 0.13
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:57837 original size:18 final size:18
Alignment explanation
Indices: 57814--57855 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
57804 TATTAATGGC
57814 AATAATAACTATT-TTAAT
1 AATAAT-ACTATTATTAAT
*
57832 AATAATATTATTATTAAT
1 AATAATACTATTATTAAT
57850 AATAAT
1 AATAAT
57856 GATAATAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
AATAATACTATTATTAAT
Found at i:57881 original size:29 final size:26
Alignment explanation
Indices: 57830--57893 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 26
57820 AACTATTTTA
*
57830 ATAATAATATTATTATTAATAATAAT
1 ATAATAATATTATAATTAATAATAAT
57856 GATAATAACTATTAGTAATTAATAATAAT
1 -ATAATAA-TATTA-TAATTAATAATAAT
57885 ATTAATAAT
1 A-TAATAAT
57894 TAATAATAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 7 0.21
28 7 0.21
29 19 0.58
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (26 bp):
ATAATAATATTATAATTAATAATAAT
Found at i:57887 original size:19 final size:20
Alignment explanation
Indices: 57814--57902 Score: 85
Period size: 19 Copynumber: 4.4 Consensus size: 20
57804 TATTAATGGC
57814 AATAATAACTATTTTAATAA-T
1 AATAATAACTA--TTAATAATT
* *
57835 AAT-ATTATTATTAATAATAAT
1 AATAATAACTATTAATAAT--T
* *
57856 GATAATAACTATTAGTAATT
1 AATAATAACTATTAATAATT
57876 AATAATAA-TATTAATAATT
1 AATAATAACTATTAATAATT
57895 AATAATAA
1 AATAATAA
57903 GAAAAAAACT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
18 7 0.12
19 18 0.32
20 13 0.23
21 6 0.11
22 12 0.21
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
AATAATAACTATTAATAATT
Found at i:59002 original size:29 final size:29
Alignment explanation
Indices: 58970--59307 Score: 364
Period size: 29 Copynumber: 11.5 Consensus size: 29
58960 CTAAACTATT
*
58970 CAAAAATTACATTTTTACCCTCAAACTTC
1 CAAAAATTCCATTTTTACCCTCAAACTTC
* *
58999 CAAAAATTCCATTTTTGATCCTCGAACTTC
1 CAAAAATTCCATTTTT-ACCCTCAAACTTC
* *
59029 CAAAAATTACA-TTTTACCC-CTGAACTTC
1 CAAAAATTCCATTTTTACCCTC-AAACTTC
59057 CAAAAATTCCATTTTTACCCATCAAACTTC
1 CAAAAATTCCATTTTTACCC-TCAAACTTC
* *
59087 TAAAAATTCCATTTTGACCC-CAAAACTTC
1 CAAAAATTCCATTTTTACCCTC-AAACTTC
* *
59116 CAAAAATTCTATTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCCTCAAACTTC
*
59145 CAAAAATTCCTTTTTTGACCC-CAAAACTTC
1 CAAAAATTCCATTTTT-ACCCTC-AAACTTC
*
59175 CAAAAATTCCATTTTTACCATCAAACTTC
1 CAAAAATTCCATTTTTACCCTCAAACTTC
* *
59204 TAAAAATTCCATTTTTAACCC-CGTAACTTC
1 CAAAAATTCCATTTTT-ACCCTC-AAACTTC
* * * *
59234 CAAAAATTCAAATTTTACCCTCGAACCTC
1 CAAAAATTCCATTTTTACCCTCAAACTTC
** *
59263 CAAAAATTCCA-TTTTAATCTCGAAACTTT
1 CAAAAATTCCATTTTTACCCTC-AAACTTC
59292 CAAAAATTACCATTTT
1 CAAAAATT-CCATTTT
59308 GTCTCCAGAT
Statistics
Matches: 261, Mismatches: 32, Indels: 30
0.81 0.10 0.09
Matches are distributed among these distances:
27 1 0.00
28 29 0.11
29 129 0.49
30 98 0.38
31 4 0.02
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCTCAAACTTC
Found at i:59130 original size:59 final size:58
Alignment explanation
Indices: 58970--59307 Score: 392
Period size: 59 Copynumber: 5.8 Consensus size: 58
58960 CTAAACTATT
* * *
58970 CAAAAATTACATTTTTACCCTC-AAACTTCCAAAAATTCCATTTTTGATCCTCGAACTTC
1 CAAAAATTCCATTTTGACCC-CAAAACTTCCAAAAATTCCATTTTT-ACCCTCGAACTTC
* ** *
59029 CAAAAATTACATTTT-ACCCCTGAACTTCCAAAAATTCCATTTTTACCCATCAAACTTC
1 CAAAAATTCCATTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCC-TCGAACTTC
* *
59087 TAAAAATTCCATTTTGACCCCAAAACTTCCAAAAATTCTATTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTC
* * *
59145 CAAAAATTCCTTTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCATCAAACTTC
1 CAAAAATTCC-ATTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTC
* * ** * * *
59204 TAAAAATTCCATTTTTAACCCCGTAACTTCCAAAAATTCAAATTTTACCCTCGAACCTC
1 CAAAAATTCCA-TTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTC
* * * * *
59263 CAAAAATTCCATTTTAATCTCGAAACTTTCAAAAATTACCATTTT
1 CAAAAATTCCATTTTGACCCCAAAACTTCCAAAAATT-CCATTTT
59308 GTCTCCAGAT
Statistics
Matches: 242, Mismatches: 31, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
57 4 0.02
58 86 0.36
59 152 0.63
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (58 bp):
CAAAAATTCCATTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTC
Found at i:59142 original size:88 final size:84
Alignment explanation
Indices: 58970--59299 Score: 385
Period size: 88 Copynumber: 3.8 Consensus size: 84
58960 CTAAACTATT
* *
58970 CAAAAATTACATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGATCCTCGAACTTCCAAAAA
1 CAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCA-TTTTGA-CCTCAAACTTCCAAAAA
59035 TTACA-TTTTACCCCTGAACTTC
64 TT-CATTTTTACCCC-GAACTTC
* *
59057 CAAAAATTCCATTTTTACCCATCAAACTTCTAAAAATTCCATTTTGACCCCAAAACTTCCAAAAA
1 CAAAAATTCCATTTTTACCC-TCAAACTTCCAAAAATTCCATTTTGACCTC-AAACTTCCAAAAA
59122 TTCTATTTTTACCCTCGAACTTC
64 TTC-ATTTTTACCC-CGAACTTC
* * *
59145 CAAAAATTCCTTTTTTGACCC-CAAAACTTCCAAAAATTCCATTTTTACCATCAAACTTCTAAAA
1 CAAAAATTCCATTTTT-ACCCTC-AAACTTCCAAAAATTCCATTTTGACC-TCAAACTTCCAAAA
59209 ATTCCATTTTTAACCCCGTAACTTC
63 ATT-CATTTTT-ACCCCG-AACTTC
* * * * * * *
59234 CAAAAATTCAAATTTTACCCTCGAACCTCCAAAAATTCCATTTTAATCTCGAAACTTTCAAAAAT
1 CAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTGACCTC-AAACTTCCAAAAAT
59299 T
65 T
59300 ACCATTTTGT
Statistics
Matches: 212, Mismatches: 18, Indels: 25
0.83 0.07 0.10
Matches are distributed among these distances:
86 4 0.02
87 43 0.20
88 134 0.63
89 31 0.15
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (84 bp):
CAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTGACCTCAAACTTCCAAAAATT
CATTTTTACCCCGAACTTC
Found at i:59434 original size:29 final size:29
Alignment explanation
Indices: 59401--59465 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 29
59391 CCTCGAACTT
59401 TCCAAAAATTACCATTTTACACCCGAGAA
1 TCCAAAAATTACCATTTTACACCCGAGAA
* * *
59430 TCC-AAAATTATCATTTTACCCCCGAGTA
1 TCCAAAAATTACCATTTTACACCCGAGAA
59458 TCCAAAAA
1 TCCAAAAA
59466 GTCTCATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 25 0.78
29 7 0.22
ACGTcount: A:0.40, C:0.28, G:0.06, T:0.26
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACACCCGAGAA
Found at i:59475 original size:29 final size:28
Alignment explanation
Indices: 59413--59475 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
59403 CAAAAATTAC
*
59413 CATTTTACACCCGAGAATCCAAAATTAT
1 CATTTTACACCCGAGAATCCAAAAGTAT
* * *
59441 CATTTTACCCCCGAGTATCCAAAAAGTCT
1 CATTTTACACCCGAGAATCC-AAAAGTAT
59470 CATTTT
1 CATTTT
59476 CAACTCCGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.32
Consensus pattern (28 bp):
CATTTTACACCCGAGAATCCAAAAGTAT
Found at i:67947 original size:15 final size:16
Alignment explanation
Indices: 67929--67961 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
67919 AAATCAGTTC
67929 AAGTTCA-ATCATTTT
1 AAGTTCATATCATTTT
67944 AAGTTCATATCATTTT
1 AAGTTCATATCATTTT
67960 AA
1 AA
67962 TTAAAATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (16 bp):
AAGTTCATATCATTTT
Found at i:70459 original size:58 final size:58
Alignment explanation
Indices: 70389--70617 Score: 207
Period size: 70 Copynumber: 3.8 Consensus size: 58
70379 ACATACATAT
* * * *
70389 CATATCAACAATTATCCACATACAAAAAACCGATTCTATATCTGAATTCA-TAA-AACAA
1 CATATCAACAATTCTCTACATAC-AAAACCCGATTCTATATC-GAATTCAGCAACAACAA
* * *
70447 CATATCAACAATTCTCTACATATAAAACCCGATTC--TA-CAAATACAGCAACAACAA
1 CATATCAACAATTCTCTACATACAAAACCCGATTCTATATCGAATTCAGCAACAACAA
*
70502 CATATCAACAATTCTCTACATACAAAACCCGAGTCTATATCGAATTCGATGACGACAGCAGCAAC
1 CATATCAACAATTCTCTACATACAAAACCCGATTCTATATCGAA-T---T--------CAGCAAC
70567 AACAA
54 AACAA
* *
70572 CATATCAACAATTCTCTACATATAAAACCCGAGTCTATATCGAATT
1 CATATCAACAATTCTCTACATACAAAACCCGATTCTATATCGAATT
70618 AGATGACGAC
Statistics
Matches: 142, Mismatches: 12, Indels: 26
0.79 0.07 0.14
Matches are distributed among these distances:
53 5 0.04
54 3 0.02
55 40 0.28
57 13 0.09
58 23 0.16
59 1 0.01
66 1 0.01
69 1 0.01
70 55 0.39
ACGTcount: A:0.44, C:0.25, G:0.07, T:0.24
Consensus pattern (58 bp):
CATATCAACAATTCTCTACATACAAAACCCGATTCTATATCGAATTCAGCAACAACAA
Found at i:70573 original size:70 final size:70
Alignment explanation
Indices: 70490--70698 Score: 366
Period size: 70 Copynumber: 3.0 Consensus size: 70
70480 TCTACAAATA
*
70490 CAGCAACAACAACATATCAACAATTCTCTACATACAAAACCCGAGTCTATATCGAATTCGATGAC
1 CAGCAACAACAACATATCAACAATTCTCTACATATAAAACCCGAGTCTATATCGAATTCGATGAC
70555 GACAG
66 GACAG
*
70560 CAGCAACAACAACATATCAACAATTCTCTACATATAAAACCCGAGTCTATATCGAATTAGATGAC
1 CAGCAACAACAACATATCAACAATTCTCTACATATAAAACCCGAGTCTATATCGAATTCGATGAC
*
70625 GACCG
66 GACAG
*
70630 TAGCAACAACAACATATCAACAATTCTCTACATATAAAACCCGAGTCTATATCGAATTCGAATG-
1 CAGCAACAACAACATATCAACAATTCTCTACATATAAAACCCGAGTCTATATCGAATTCG-ATGA
70694 CGACA
65 CGACA
70699 ATAACATCAA
Statistics
Matches: 132, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
70 129 0.98
71 3 0.02
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.22
Consensus pattern (70 bp):
CAGCAACAACAACATATCAACAATTCTCTACATATAAAACCCGAGTCTATATCGAATTCGATGAC
GACAG
Found at i:89279 original size:30 final size:28
Alignment explanation
Indices: 89240--89312 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
89230 ATAAATATTA
* *
89240 AATTTATACATGAATTTTGGTTTATGTAT
1 AATTTATACATGAACTTTGATTT-TGTAT
* *
89269 AATTTGATACATAAACTTTGATTTTGTGT
1 AATTT-ATACATGAACTTTGATTTTGTAT
89298 AATTATATACATGAA
1 AATT-TATACATGAA
89313 ACTTAAATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 21 0.57
30 16 0.43
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (28 bp):
AATTTATACATGAACTTTGATTTTGTAT
Found at i:89300 original size:29 final size:29
Alignment explanation
Indices: 89240--89316 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
89230 ATAAATATTA
* * *
89240 AATTTATACATGAATTTTGGTTTATGTAT
1 AATTTATACATAAACTTTGATTTATGTAT
*
89269 AATTTGATACATAAACTTTGATTT-TGTGT
1 AATTT-ATACATAAACTTTGATTTATGTAT
89298 AATTATATACATGAAACTT
1 AATT-TATACAT-AAACTT
89317 AAATTATGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 19 0.46
30 22 0.54
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (29 bp):
AATTTATACATAAACTTTGATTTATGTAT
Found at i:89643 original size:2 final size:2
Alignment explanation
Indices: 89604--89631 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
89594 TAATAAAAGT
89604 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
89632 GTATTGTATA
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):
TA
Found at i:109307 original size:23 final size:23
Alignment explanation
Indices: 109277--109330 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
109267 CGTGGCATCT
109277 AGTCAGCAGCTTCGAAAAGATCC
1 AGTCAGCAGCTTCGAAAAGATCC
* * * *
109300 AGTCAGCAGCTTCTAGAAGGTCT
1 AGTCAGCAGCTTCGAAAAGATCC
109323 AGTCAGCA
1 AGTCAGCA
109331 AGGACGGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.20
Consensus pattern (23 bp):
AGTCAGCAGCTTCGAAAAGATCC
Found at i:114370 original size:23 final size:23
Alignment explanation
Indices: 114314--114371 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
114304 CTGACGTGGC
* *
114314 ATCCAGTCAGCAGCTTCTAGAAG
1 ATCCAGTCAGTAGCTTCCAGAAG
114337 ATCCAGTCAGTAGCTTCCAGAAG
1 ATCCAGTCAGTAGCTTCCAGAAG
* *
114360 GTCTAGTCAGTA
1 ATCCAGTCAGTA
114372 AGGATGGACG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
ATCCAGTCAGTAGCTTCCAGAAG
Found at i:119600 original size:6 final size:6
Alignment explanation
Indices: 119589--119622 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
119579 AGCTGCACTA
119589 ATGCAC ATGCAC ATGCAC ATGCAC ATGCAC ATGC
1 ATGCAC ATGCAC ATGCAC ATGCAC ATGCAC ATGC
119623 TTTTTGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (6 bp):
ATGCAC
Found at i:121185 original size:2 final size:2
Alignment explanation
Indices: 121178--121214 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
121168 CTAGTTCACC
* *
121178 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
121215 AAAAGTAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:130168 original size:3 final size:3
Alignment explanation
Indices: 130160--130195 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
130150 TAAAAATATA
130160 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
130196 ATTTTGATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:131886 original size:59 final size:59
Alignment explanation
Indices: 131566--131886 Score: 332
Period size: 59 Copynumber: 5.5 Consensus size: 59
131556 AGAGTTTCGA
* * * * * * *
131566 GGTCGAAAATGGAGTTTTTGGACA-TTCGGGGGCAAAAATGGAATTTTTGG-AGGTTCGAA
1 GGTCAAAAATGGAATTTTTGGA-AGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTAG-G
* * * * * * *
131625 GGT-AAAATTGGGATTTTTCGGAAGTTCGAGGGTAAAAATGGAATTTTTGGGAGTTTCGA
1 GGTCAAAAATGGAATTTTT-GGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTAGG
*
131684 GGTCAAAAATGGAATTTTTGGAAGTTTTGGGGTAAAAATGGAA-TTTTGGAAGTTTTA-G
1 GGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAG-TTTAGG
* * * *
131742 GGTCAAAAATTGG-ATTTTAGAAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTTGG
1 GGTCAAAAA-TGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTAGG
* * *
131801 GGTCTAAAATGGAATTTTTGAAAGTTTGGGGGTAAAAATAGAATTTTTGGAAGTTTAGG
1 GGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTAGG
*
131860 GGT-AAAAATGAAATTTTTGGATAGTTT
1 GGTCAAAAATGGAATTTTTGGA-AGTTT
131887 AGGGACCTCC
Statistics
Matches: 225, Mismatches: 27, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
58 77 0.34
59 129 0.57
60 19 0.08
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (59 bp):
GGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTAGG
Found at i:131888 original size:30 final size:29
Alignment explanation
Indices: 131571--131890 Score: 310
Period size: 29 Copynumber: 10.9 Consensus size: 29
131561 TTCGAGGTCG
* ** *
131571 AAAATGGAGTTTTTGGACA-TTCGGGGGCA
1 AAAATGGAATTTTTGGA-AGTTTAGGGGTA
* * *
131600 AAAATGGAATTTTTGG-AGGTTCGAAGGTA
1 AAAATGGAATTTTTGGAAGTTTAG-GGGTA
* * *
131629 AAATTGGGATTTTTCGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTT-GGAAGTTTAG-GGGTA
* * *
131659 AAAATGGAATTTTTGGGAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTAGGGGT-A
*
131689 AAAATGGAATTTTTGGAAGTTTTGGGGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTA
131718 AAAATGGAA-TTTTGGAAGTTTTA-GGGTCA
1 AAAATGGAATTTTTGGAAG-TTTAGGGGT-A
* *
131747 AAAATTGG-ATTTTAGAAAGTTTAGGGGTA
1 AAAA-TGGAATTTTTGGAAGTTTAGGGGTA
* *
131776 AAAATGGAATTTTTGGAAGTTTTGGGGTCT
1 AAAATGGAATTTTTGGAAGTTTAGGGGT-A
* *
131806 AAAATGGAATTTTTGAAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTA
*
131835 AAAATAGAATTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTA
*
131864 AAAATGAAATTTTTGGATAGTTTAGGG
1 AAAATGGAATTTTTGGA-AGTTTAGGG
131891 ACCTCCAAGG
Statistics
Matches: 246, Mismatches: 31, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
27 1 0.00
28 18 0.07
29 123 0.50
30 102 0.41
31 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTAGGGGTA
Found at i:133005 original size:3 final size:3
Alignment explanation
Indices: 132988--133123 Score: 67
Period size: 3 Copynumber: 42.7 Consensus size: 3
132978 TTTCCCTTTT
* * * * * *
132988 TTA TTCA TT- TTA TTA TTA ATA TTT TTA TTA ATA TTTA TTA ATG CTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* * * *
133034 TTTA TTA CTA CTA TTTA TTA TTA ATA TTA TTA TTA TTTA TTAA ATA GTTA
1 -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA -TTA TT-A TTA -TTA
* * *
133084 TTA TTA TTA TTAA CTA TTA TTA CTA TTA ATA TTA CTTA TT
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA -TTA TT
133124 GCTGTAATTA
Statistics
Matches: 100, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
2 2 0.02
3 77 0.77
4 21 0.21
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:133061 original size:13 final size:13
Alignment explanation
Indices: 132996--133068 Score: 87
Period size: 13 Copynumber: 5.8 Consensus size: 13
132986 TTTTATTCAT
132996 TTTATTATTAATA
1 TTTATTATTAATA
133009 TTT-TTATTAATA
1 TTTATTATTAATA
* **
133021 TTTATTAATGCTA
1 TTTATTATTAATA
* *
133034 TTTATTACTACTA
1 TTTATTATTAATA
133047 TTTATTATTAATA
1 TTTATTATTAATA
133060 -TTATTATTA
1 TTTATTATTA
133069 TTTATTAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
12 21 0.40
13 31 0.60
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (13 bp):
TTTATTATTAATA
Found at i:133074 original size:13 final size:13
Alignment explanation
Indices: 132996--133123 Score: 74
Period size: 13 Copynumber: 10.5 Consensus size: 13
132986 TTTTATTCAT
*
132996 TTTATTATTAATA
1 TTTATTATTATTA
*
133009 TTT-TTATTAATA
1 TTTATTATTATTA
* **
133021 TTTATTAATGCTA
1 TTTATTATTATTA
* *
133034 TTTATTACTACTA
1 TTTATTATTATTA
133047 TTTATTATTA--A
1 TTTATTATTATTA
133058 --TATTATTATTA
1 TTTATTATTATTA
*
133069 TTTATTA--AATA
1 TTTATTATTATTA
*
133080 GTTATTATTATTA
1 TTTATTATTATTA
* *
133093 TTAACTATTATTA
1 TTTATTATTATTA
* *
133106 -CTATTAATATTA
1 TTTATTATTATTA
*
133118 CTTATT
1 TTTATT
133124 GCTGTAATTA
Statistics
Matches: 90, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
9 8 0.09
11 11 0.12
12 20 0.22
13 51 0.57
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.59
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:133103 original size:16 final size:15
Alignment explanation
Indices: 132997--133123 Score: 68
Period size: 16 Copynumber: 8.3 Consensus size: 15
132987 TTTATTCATT
*
132997 TTATTATTAATATTT
1 TTATTATTAATATTA
* *
133012 TTATTAATATTTATTAA
1 TTATTATTA-ATATT-A
* *
133029 TGCTATTTATTACTACTA
1 T--TA-TTATTAATATTA
133047 TTTATTATTAATATTA
1 -TTATTATTAATATTA
133063 TTATTATT--TATTA
1 TTATTATTAATATTA
* *
133076 --AATAGT--TATTA
1 TTATTATTAATATTA
133087 TTATTATTAACTATTA
1 TTATTATTAA-TATTA
*
133103 TTACTATTAATATTA
1 TTATTATTAATATTA
133118 CTTATT
1 -TTATT
133124 GCTGTAATTA
Statistics
Matches: 86, Mismatches: 14, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
11 9 0.10
13 9 0.10
15 21 0.24
16 32 0.37
17 3 0.03
18 1 0.01
19 6 0.07
20 5 0.06
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (15 bp):
TTATTATTAATATTA
Found at i:133878 original size:17 final size:17
Alignment explanation
Indices: 133853--133906 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
133843 ACTCTTTTAA
* **
133853 TTAAGTTTTAAATCCAT
1 TTAAATTTTAAATAAAT
*
133870 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
*
133887 TTAAATTTAAAAATAAAT
1 TTAAATTT-TAAATAAAT
133905 TT
1 TT
133907 GAATCAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 21 0.70
18 9 0.30
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:135422 original size:21 final size:22
Alignment explanation
Indices: 135396--135437 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
135386 TTTTAAAATA
*
135396 TATAAAATTGA-AAAAATATAT
1 TATAAAAATGAGAAAAATATAT
*
135417 TATAAAAATGAGAATAATATA
1 TATAAAAATGAGAAAAATATA
135438 CATACACCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (22 bp):
TATAAAAATGAGAAAAATATAT
Found at i:145653 original size:30 final size:31
Alignment explanation
Indices: 145617--145674 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
145607 TCTTTTTAAG
*
145617 TTAAATTTGATCC-TT-ACCTTTTAAAAAGAA
1 TTAAATTTGA-CCATTAACCTTTCAAAAAGAA
145647 TTAAATTTGACCATTAACCTTTCAAAAA
1 TTAAATTTGACCATTAACCTTTCAAAAA
145675 AATCGAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 2 0.08
30 12 0.48
31 11 0.44
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (31 bp):
TTAAATTTGACCATTAACCTTTCAAAAAGAA
Found at i:165688 original size:4 final size:4
Alignment explanation
Indices: 165679--165719 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
165669 ATCCACTTTC
*
165679 GTAT GTAT GTAT GTAT GCAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
165720 AATTATTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.46
Consensus pattern (4 bp):
GTAT
Found at i:167171 original size:73 final size:73
Alignment explanation
Indices: 167050--167198 Score: 262
Period size: 73 Copynumber: 2.0 Consensus size: 73
167040 AAAAAAAAAA
* * *
167050 AACCTAAACCCTTATCCTTGAAGTTTATTGAATAGAAAAACCATATTGGCAACCATTAAAGGAAG
1 AACCTAAACCCTTATCCTTGAAGTTCATTGAATAGAAAAACCACATTGGCAACCATTAAAGAAAG
167115 ATGATGCT
66 ATGATGCT
*
167123 AACCTAAACCCTTATCCTTGAAGTTCATTGAATAGAAAAATCACATTGGCAACCATTAAAGAAAG
1 AACCTAAACCCTTATCCTTGAAGTTCATTGAATAGAAAAACCACATTGGCAACCATTAAAGAAAG
167188 ATGATGCT
66 ATGATGCT
167196 AAC
1 AAC
167199 ATTCAATGAT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (73 bp):
AACCTAAACCCTTATCCTTGAAGTTCATTGAATAGAAAAACCACATTGGCAACCATTAAAGAAAG
ATGATGCT
Found at i:168713 original size:32 final size:31
Alignment explanation
Indices: 168650--168713 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
168640 TTTAATAAAA
* * *
168650 TAAAAATATATAAAATTATTAAATATTAATT
1 TAAAAATATATAAAAGTACTAAATATGAATT
168681 TAAAAATGATATAAACAGTACTAAA-ATGAATT
1 TAAAAAT-ATATAAA-AGTACTAAATATGAATT
168713 T
1 T
168714 GAATTAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 7 0.25
32 14 0.50
33 7 0.25
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (31 bp):
TAAAAATATATAAAAGTACTAAATATGAATT
Found at i:172541 original size:16 final size:16
Alignment explanation
Indices: 172503--172556 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
172493 TTGAATTCAG
172503 GTCATTTCAAG-TTAGA
1 GTCATTT-AAGTTTAGA
172519 G-CAATTTAAGTTTAGA
1 GTC-ATTTAAGTTTAGA
* *
172535 GTCATTTTAGTTT-GG
1 GTCATTTAAGTTTAGA
172550 GTCATTT
1 GTCATTT
172557 GAATTATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
15 12 0.36
16 20 0.61
17 1 0.03
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.44
Consensus pattern (16 bp):
GTCATTTAAGTTTAGA
Found at i:178078 original size:52 final size:50
Alignment explanation
Indices: 177985--178087 Score: 125
Period size: 52 Copynumber: 2.0 Consensus size: 50
177975 AAAACATTAG
* * *
177985 AGGATTGAATTAAAAACAAAATAAAACTTAAAACTAGAAATAAATAAATAAA
1 AGGATTAAATTAAAAACAAAATAAAACTTAAAACAAAAAAT-AAT-AATAAA
* * * *
178037 AGGATTAAATTAAAATCAAAATAAAATTTGAGACAAAAAATAATAATAAA
1 AGGATTAAATTAAAAACAAAATAAAACTTAAAACAAAAAATAATAATAAA
178087 A
1 A
178088 AACAAAGAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 7 0.16
51 3 0.07
52 34 0.77
ACGTcount: A:0.65, C:0.05, G:0.08, T:0.22
Consensus pattern (50 bp):
AGGATTAAATTAAAAACAAAATAAAACTTAAAACAAAAAATAATAATAAA
Found at i:180170 original size:48 final size:50
Alignment explanation
Indices: 180089--180189 Score: 118
Period size: 48 Copynumber: 2.1 Consensus size: 50
180079 CGGTTTTAAT
* * *
180089 CTTTCCCTTCAAATCTTCATGGTACCGAGTTCGCCGTTACGGCCTCAA-C
1 CTTTCCCATCAAATCTTCATGGTACAGAGTTCGCCGTTACGACCTCAATC
* * *
180138 CTTTCCCATCATAT-TTCATGGTATCAGA-TTCGCTGTTGCGACCTCAATC
1 CTTTCCCATCAAATCTTCATGGTA-CAGAGTTCGCCGTTACGACCTCAATC
180187 CTT
1 CTT
180190 CACAGCATGT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
48 25 0.57
49 19 0.43
ACGTcount: A:0.19, C:0.32, G:0.15, T:0.35
Consensus pattern (50 bp):
CTTTCCCATCAAATCTTCATGGTACAGAGTTCGCCGTTACGACCTCAATC
Found at i:180305 original size:98 final size:98
Alignment explanation
Indices: 180195--180643 Score: 539
Period size: 98 Copynumber: 4.6 Consensus size: 98
180185 TCCTTCACAG
* * *
180195 CATGTTTCTGAGGTACAAGGTTCGCCGTCGCGACTTAAACCTTTTCCTTTATATCTTCGTAGTAC
1 CATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTTCCTTCATATCTTCGTGGTAC
* * * * *
180260 CAGATTCGTCGTTACGGTTTCAAGCTTTCCCTT
66 TAGATTCGTCGTTGCGGCTTAAATCTTTCCCTT
* * *
180293 CATGTTTTTGAGGTACAAGGTTCACCGTTGCGACTTAAACCTTTCCCTTCATATCTTCGTGGTAC
1 CATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTTCCTTCATATCTTCGTGGTAC
*
180358 TAGATTCGCCGTTGCGGCTTAAATCTTTCCCTT
66 TAGATTCGTCGTTGCGGCTTAAATCTTTCCCTT
* * *
180391 CATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTAT
1 CATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTTCCTTCATATCTTCGTGGTAC
* ** *
180456 TAGATTCG-CAATTGCAACTTAAATCTTT-GCTT
66 TAGATTCGTC-GTTGCGGCTTAAATCTTTCCCTT
* * * *
180488 CATGTTTCTAATGTACAAGGTTAGCTGTTGCGACTTAAACC-TTT-CTCTCTATATCTTCGTGGT
1 CATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTTCCT-TC-ATATCTTCGTGGT
* * *
180551 ACTGGATTCGTTGTTGCGGCTTAAATCTTTTCCTT
64 ACTAGATTCGTCGTTGCGGCTTAAATCTTTCCCTT
* * ** * *
180586 CATGTTTTTGAAGTACAATATTCGTCGTTGTGACTTAAACC-TTTCCTTCCATATCTTC
1 CATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTTCCTT-CATATCTTC
180644 ATAACAAATT
Statistics
Matches: 302, Mismatches: 42, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
95 2 0.01
96 3 0.01
97 77 0.25
98 217 0.72
99 3 0.01
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (98 bp):
CATGTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTTCCTTCATATCTTCGTGGTAC
TAGATTCGTCGTTGCGGCTTAAATCTTTCCCTT
Found at i:180357 original size:49 final size:49
Alignment explanation
Indices: 180089--180643 Score: 306
Period size: 49 Copynumber: 11.4 Consensus size: 49
180079 CGGTTTTAAT
* * * * * * *
180089 CTTTCCCTTCAAATCTTCATGGTAC-CGAGTTCGCCGTTACGGCCTCAAC
1 CTTTCCCTTCATATCTTCGTGGTACAAG-GTTCGCCGTTGCGACTTAAAC
* * * * * *
180138 CTTTCCCATCATAT-TTCATGGTATC-AGATTCGCTGTTGCGACCTCAATC
1 CTTTCCCTTCATATCTTCGTGGTA-CAAGGTTCGCCGTTGCGA-CTTAAAC
* ** * * *
180187 C-TTCACAGCATGT-TTCTGAGGTACAAGGTTCGCCGTCGCGACTTAAAC
1 CTTTCCCTTCATATCTTC-GTGGTACAAGGTTCGCCGTTGCGACTTAAAC
* * * * * * * ** * *
180235 CTTTTCCTTTATATCTTCGTAGTACCAGATTCGTCGTTACGGTTTCAAG
1 CTTTCCCTTCATATCTTCGTGGTACAAGGTTCGCCGTTGCGACTTAAAC
* * * * *
180284 CTTTCCCTTCATGTTTTTGAGGTACAAGGTTCACCGTTGCGACTTAAAC
1 CTTTCCCTTCATATCTTCGTGGTACAAGGTTCGCCGTTGCGACTTAAAC
* * * *
180333 CTTTCCCTTCATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAAT
1 CTTTCCCTTCATATCTTCGTGGTACAAGGTTCGCCGTTGCGACTTAAAC
* *
180382 CTTTCCCTTCATGT-TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAAC
1 CTTTCCCTTCATATCTTC-GTGGTACAAGGTTCGCCGTTGCGACTTAAAC
* ** * ** * *
180431 CTTTCCCTCCATATCTTCGTGGTATTAGATTCGCAATTGCAACTTAAAT
1 CTTTCCCTTCATATCTTCGTGGTACAAGGTTCGCCGTTGCGACTTAAAC
* * * * *
180480 CTTT-GCTTCATGT-TTC-TAATGTACAAGGTTAGCTGTTGCGACTTAAAC
1 CTTTCCCTTCATATCTTCGT--GGTACAAGGTTCGCCGTTGCGACTTAAAC
* * ** * *
180528 CTTTCTC-TCTATATCTTCGTGGTAC-TGGATTCGTTGTTGCGGCTTAAAT
1 CTTTCCCTTC-ATATCTTCGTGGTACAAGG-TTCGCCGTTGCGACTTAAAC
* * * * ** ** * *
180577 CTTTTCCTTCATGTTTTTGAAGTACAATATTCGTCGTTGTGACTTAAAC
1 CTTTCCCTTCATATCTTCGTGGTACAAGGTTCGCCGTTGCGACTTAAAC
180626 CTTT-CCTTCCATATCTTC
1 CTTTCCCTT-CATATCTTC
180644 ATAACAAATT
Statistics
Matches: 372, Mismatches: 116, Indels: 36
0.71 0.22 0.07
Matches are distributed among these distances:
46 1 0.00
47 3 0.01
48 79 0.21
49 277 0.74
50 11 0.03
51 1 0.00
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (49 bp):
CTTTCCCTTCATATCTTCGTGGTACAAGGTTCGCCGTTGCGACTTAAAC
Found at i:180569 original size:195 final size:196
Alignment explanation
Indices: 180135--180643 Score: 571
Period size: 195 Copynumber: 2.6 Consensus size: 196
180125 TTACGGCCTC
* * * * * * * * **
180135 AACCTTTCCCATCATAT-TTCATGGTA-TCAGATTCGCTGTTGCGACCTCAATCCTTCACAGCAT
1 AACCTTTCCCTTCATATCTTCGTGGTACT-AGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT
* * **
180198 GTTTCTGAGGTACAAGGTTCGCCGTCGCGACTTAAACCTTTTCCTTTATATCTTCGTAGTACCAG
65 GTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTAGTACCAG
* *** * * *
180263 ATTCGTCGTTACGGTTTCAAGCTTTCCCTTCATGTTTTTGAGGTACAAGGTTCACCGTTGCGACT
130 ATTCGTCATTACAACTTAAAGCTTTCCCTTCATGTTTCTAAGGTACAAGGTTCACCGTTGCGACT
180328 TA
195 TA
180330 AACCTTTCCCTTCATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
1 AACCTTTCCCTTCATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
* **
180395 TTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTATTAGA
66 TTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTAGTACCAGA
* * * * *
180460 TTCG-CAATTGCAACTTAAATCTTT-GCTTCATGTTTCTAATGTACAAGGTT-AGCTGTTGCGAC
131 TTCGTC-ATTACAACTTAAAGCTTTCCCTTCATGTTTCTAAGGTACAAGGTTCA-CCGTTGCGAC
180522 TTA
194 TTA
* * ** *
180525 AACCTTTCTC-TCTATATCTTCGTGGTACTGGATTCGTTGTTGCGGCTTAAATCTTTTCCTTCAT
1 AACCTTTCCCTTC-ATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT
* * ** * * *
180589 GTTTTTGAAGTACAATATTCGTCGTTGTGACTTAAACCTTTCCTTCCATATCTTC
65 GTTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTC
180644 ATAACAAATT
Statistics
Matches: 268, Mismatches: 41, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
194 3 0.01
195 155 0.58
196 109 0.41
197 1 0.00
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (196 bp):
AACCTTTCCCTTCATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
TTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTAGTACCAGA
TTCGTCATTACAACTTAAAGCTTTCCCTTCATGTTTCTAAGGTACAAGGTTCACCGTTGCGACTT
A
Found at i:183574 original size:17 final size:18
Alignment explanation
Indices: 183547--183582 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
183537 ATTACCAATA
*
183547 AAAATGAATGATTTTTTT
1 AAAATGAATGATTATTTT
183565 AAAA-GAATGATTATTTT
1 AAAATGAATGATTATTTT
183582 A
1 A
183583 CTCTTTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (18 bp):
AAAATGAATGATTATTTT
Found at i:188769 original size:29 final size:27
Alignment explanation
Indices: 188703--188762 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 27
188693 ATTCAAAATT
*
188703 AATTTAAA-TAATTAAAAATGTTTTTA
1 AATTTAAATTAATTAAAAATGTTGTTA
188729 AATTTAAATTAATTATAAAATGTGTGTTA
1 AATTTAAATTAATTA-AAAATGT-TGTTA
188758 AATTT
1 AATTT
188763 TTATTAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 8 0.27
27 6 0.20
28 7 0.23
29 9 0.30
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (27 bp):
AATTTAAATTAATTAAAAATGTTGTTA
Found at i:190386 original size:56 final size:56
Alignment explanation
Indices: 190300--190411 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
190290 GATTTTTTAC
190300 ACATATTTTAATATACGGGTTAACAATAAACTAACTCAATCGGTAATAGTGAACCA
1 ACATATTTTAATATACGGGTTAACAATAAACTAACTCAATCGGTAATAGTGAACCA
* *
190356 ACATATTTTAATGTACGGGTTAACAATAAACTAACTCAATTGGTAATAGTGAACCA
1 ACATATTTTAATATACGGGTTAACAATAAACTAACTCAATCGGTAATAGTGAACCA
190412 CTCCTATAAC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (56 bp):
ACATATTTTAATATACGGGTTAACAATAAACTAACTCAATCGGTAATAGTGAACCA
Found at i:192803 original size:75 final size:75
Alignment explanation
Indices: 192718--192868 Score: 225
Period size: 75 Copynumber: 2.0 Consensus size: 75
192708 CATGAATTTG
* *
192718 GCAACTAGATTGTTCTGTAGTTC-GATAATGCTTAAACTTGA-AGCATGCAAAGGTAACAATTTT
1 GCAACTAGATTGTTCAGTAGTTCAG-TAATGCTTAAA-TTGAGAGCATGCAAAGGTAACAATCTT
192781 GAACACTCGATC
64 GAACACTCGATC
* *
192793 GCAACTAGATTGTTCAGTAGTTCAGTAATGCTTAAATTTAGAGCATGCAAAGGTAACAGTCTTGA
1 GCAACTAGATTGTTCAGTAGTTCAGTAATGCTTAAATTGAGAGCATGCAAAGGTAACAATCTTGA
*
192858 ATACTCGATC
66 ACACTCGATC
192868 G
1 G
192869 AATACTTTGG
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
74 3 0.04
75 65 0.94
76 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (75 bp):
GCAACTAGATTGTTCAGTAGTTCAGTAATGCTTAAATTGAGAGCATGCAAAGGTAACAATCTTGA
ACACTCGATC
Found at i:192983 original size:48 final size:48
Alignment explanation
Indices: 192911--193010 Score: 155
Period size: 48 Copynumber: 2.1 Consensus size: 48
192901 TTTGTAGGAT
* * * * *
192911 GGGTTGCTGCCATTTTCATTGAAAAGAGGAAAAACCGAAAGAAATTCC
1 GGGTTGCCGCAATTTTCATCGAAAAGAGGAAAAACCAAAAGAAACTCC
192959 GGGTTGCCGCAATTTTCATCGAAAAGAGGAAAAACCAAAAGAAACTCC
1 GGGTTGCCGCAATTTTCATCGAAAAGAGGAAAAACCAAAAGAAACTCC
193007 GGGT
1 GGGT
193011 AAGCACGGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (48 bp):
GGGTTGCCGCAATTTTCATCGAAAAGAGGAAAAACCAAAAGAAACTCC
Found at i:201160 original size:2 final size:2
Alignment explanation
Indices: 201147--201176 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
201137 TATGCTTGTA
*
201147 AT AT AA 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
201177 GTGTGTGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:204277 original size:38 final size:38
Alignment explanation
Indices: 204226--204309 Score: 141
Period size: 38 Copynumber: 2.2 Consensus size: 38
204216 GTTCTTCTAC
*
204226 TCGTTGATGGATACTAATTCGTCGTACCAATCGTCGAA
1 TCGTTGCTGGATACTAATTCGTCGTACCAATCGTCGAA
*
204264 TCGTTGCTGGATACTAATTCGTTGTACCAATCGTCGAA
1 TCGTTGCTGGATACTAATTCGTCGTACCAATCGTCGAA
*
204302 TCGCTGCT
1 TCGTTGCT
204310 TGGAGCTTGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (38 bp):
TCGTTGCTGGATACTAATTCGTCGTACCAATCGTCGAA
Found at i:212000 original size:25 final size:25
Alignment explanation
Indices: 211972--212025 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
211962 AAAACTGTTT
211972 TATTCTAC-CAAAAAAAAAGAATATA
1 TATTCTACTCAAAAAAAAA-AATATA
* * *
211997 TATTTTTCTCAAAAAAATAAATATA
1 TATTCTACTCAAAAAAAAAAATATA
212022 TATT
1 TATT
212026 AACATTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.35
Consensus pattern (25 bp):
TATTCTACTCAAAAAAAAAAATATA
Found at i:213743 original size:455 final size:455
Alignment explanation
Indices: 212892--213801 Score: 1705
Period size: 455 Copynumber: 2.0 Consensus size: 455
212882 GTTTTAAACA
*
212892 AGTTTAACTTTTTTTAATGTTTATATGGTATCTTTTATTTTATATTTTATCTTATGTGATATAAA
1 AGTTTAACATTTTTTAATGTTTATATGGTATCTTTTATTTTATATTTTATCTTATGTGATATAAA
* *
212957 TATATTATATATATAAAAAAGAAAATATATTAAAAAAGTATAAAAACAAGTTGGATTGGGCTTCA
66 TATATAATATATATAAAAAAGAAAATATATTAAAAAAGTATAAAAACAAGTCGGATTGGGCTTCA
*
213022 ACCTTTAATGTTGAAGTCTAAACTTGGCTTATATTTTAAGCGGATCTATTTTTTTGCTCAAGCCC
131 ACCTTTAATGTTGAAGTCTAAACTTGGCTTATATTTTAAGCGGATCTATTTTTTTGCTCAAACCC
213087 ATTTTTCGTACCTCATACTTTTGTCTAAATCTTCTCATATTTCAAACGAAGCCTTTAAACTTTGA
196 ATTTTTCGTACCTCATACTTTTGTCTAAATCTTCTCATATTTCAAACGAAGCCTTTAAACTTTGA
213152 CAGATAACCCAACCTATAAATAATTCTAATTTTAAGCTATAGGATTTGCATATACCTTAGGAAAG
261 CAGATAACCCAACCTATAAATAATTCTAATTTTAAGCTATAGGATTTGCATATACCTTAGGAAAG
213217 ACTGGATTCTCTTGTAGGGTTTATATGAATTTTGTATTTTCAAGTTCAATAGGTAGTTTTTCGGG
326 ACTGGATTCTCTTGTAGGGTTTATATGAATTTTGTATTTTCAAGTTCAATAGGTAGTTTTTCGGG
*
213282 TGTTGTTTTTCAAATATCCATATTAGCTACACAAGCTAGTAGACCCTTAAACTTTAAAACTTGAT
391 TGTTGTTTTTCAAATATCCATATTAGCTACACAAGCTAGTAGACCCTTAAACTTGAAAACTTGAT
213347 AGTTTAACATTTTTTAATGTTTATATGGTATCTTTTATTTTATATTTTATCTTATGTGATATAAA
1 AGTTTAACATTTTTTAATGTTTATATGGTATCTTTTATTTTATATTTTATCTTATGTGATATAAA
213412 TATATAATATATATAAAAATA-AAAATATATTAAAAAAGTATAAAAACAAGTCGGATTGGGCTTC
66 TATATAATATATATAAAAA-AGAAAATATATTAAAAAAGTATAAAAACAAGTCGGATTGGGCTTC
*
213476 AGCCTTTAATGTTGAAGTCTAAACTTGGCTTATATTTTAAGCGGATCTATTTTTTTGCTCAAACC
130 AACCTTTAATGTTGAAGTCTAAACTTGGCTTATATTTTAAGCGGATCTATTTTTTTGCTCAAACC
*
213541 CATTTTTCGTACCTCATACTTTTGTCTAAATCTTCTTATATTTCAAACGAAGCCTTTAAACTTTG
195 CATTTTTCGTACCTCATACTTTTGTCTAAATCTTCTCATATTTCAAACGAAGCCTTTAAACTTTG
*
213606 ACAGATAACCCAACCTATAAATAATTCTAATTTTAAGGTATAGGATTTGCATATACCTTAGGAAA
260 ACAGATAACCCAACCTATAAATAATTCTAATTTTAAGCTATAGGATTTGCATATACCTTAGGAAA
* * *
213671 GACTGGATTCTCTTGTAGGGTTTCTATGGATTTTGTATTTTCAAGTTCAATTGGTAGTTTTTCGG
325 GACTGGATTCTCTTGTAGGGTTTATATGAATTTTGTATTTTCAAGTTCAATAGGTAGTTTTTCGG
213736 GTGTTGTTTTTCAAATATCCATATTAGCTACACAAGCTAGTAGACCCTTAAACTTGAAAACTTGA
390 GTGTTGTTTTTCAAATATCCATATTAGCTACACAAGCTAGTAGACCCTTAAACTTGAAAACTTGA
213801 T
455 T
213802 TCGATTAATT
Statistics
Matches: 443, Mismatches: 11, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
455 442 1.00
456 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (455 bp):
AGTTTAACATTTTTTAATGTTTATATGGTATCTTTTATTTTATATTTTATCTTATGTGATATAAA
TATATAATATATATAAAAAAGAAAATATATTAAAAAAGTATAAAAACAAGTCGGATTGGGCTTCA
ACCTTTAATGTTGAAGTCTAAACTTGGCTTATATTTTAAGCGGATCTATTTTTTTGCTCAAACCC
ATTTTTCGTACCTCATACTTTTGTCTAAATCTTCTCATATTTCAAACGAAGCCTTTAAACTTTGA
CAGATAACCCAACCTATAAATAATTCTAATTTTAAGCTATAGGATTTGCATATACCTTAGGAAAG
ACTGGATTCTCTTGTAGGGTTTATATGAATTTTGTATTTTCAAGTTCAATAGGTAGTTTTTCGGG
TGTTGTTTTTCAAATATCCATATTAGCTACACAAGCTAGTAGACCCTTAAACTTGAAAACTTGAT
Found at i:220810 original size:3 final size:3
Alignment explanation
Indices: 220802--220826 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
220792 TAAGTTTTAA
220802 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
220827 TGGTGGTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:222150 original size:3 final size:3
Alignment explanation
Indices: 222144--222190 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
222134 CCTACCATCC
* *
222144 TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
222191 AGCATCAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:230021 original size:67 final size:64
Alignment explanation
Indices: 229907--230052 Score: 213
Period size: 67 Copynumber: 2.2 Consensus size: 64
229897 TCAAATTTTC
* * *
229907 TTATTATTTTTATTTATTTATTTATTATTTTTATGAATATAAATAAATATAAAATAATCTTAATT
1 TTATT-TTATTATTTATTTATTTATTATTTGTATGAATATAAATAAATATAAAATAATATTAATT
229972 TTATTTTATTATTTATTTATTTATTA-TTGTATGAATATAAATAAATAAATGTAAAATAATATTA
1 TTATTTTATTATTTATTTATTTATTATTTGTATGAATATAAATAAAT--A--TAAAATAATATTA
230036 ATT
62 ATT
230039 TTATTTTATTATTT
1 TTATTTTATTATTT
230053 TATGAATATA
Statistics
Matches: 74, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
63 19 0.26
64 20 0.27
65 6 0.08
67 29 0.39
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.57
Consensus pattern (64 bp):
TTATTTTATTATTTATTTATTTATTATTTGTATGAATATAAATAAATATAAAATAATATTAATT
Found at i:230051 original size:63 final size:62
Alignment explanation
Indices: 229910--230052 Score: 193
Period size: 63 Copynumber: 2.3 Consensus size: 62
229900 AATTTTCTTA
* *
229910 TTATTTTTATTTATTTATTTATTATTTTTATGAATATAAATAAATATAAAATAATCTTAATT
1 TTATTTTTATTTATTTATTTATTATTTGTATGAATATAAATAAATATAAAATAATATTAATT
229972 TTATTTTATTATTTATTTATTTATTA-TTGTATGAATATAAATAAATAAATGTAAAATAATATTA
1 TTA-TTT-TTATTTATTTATTTATTATTTGTATGAATATAAATAAAT--A--TAAAATAATATTA
230036 ATT
60 ATT
230039 TTA-TTTTA-TTATTT
1 TTATTTTTATTTATTT
230053 TATGAATATA
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
62 3 0.04
63 28 0.38
64 21 0.29
65 3 0.04
67 18 0.25
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.57
Consensus pattern (62 bp):
TTATTTTTATTTATTTATTTATTATTTGTATGAATATAAATAAATATAAAATAATATTAATT
Found at i:235020 original size:19 final size:18
Alignment explanation
Indices: 234998--235052 Score: 92
Period size: 18 Copynumber: 3.0 Consensus size: 18
234988 AGACCTGCTC
234998 AACCCGTAAAGGAAAAGAA
1 AACCCGTAAAGGAAAA-AA
*
235017 AACCCGTAAAGGAATAAA
1 AACCCGTAAAGGAAAAAA
235035 AACCCGTAAAGGAAAAAA
1 AACCCGTAAAGGAAAAAA
235053 GAGAAAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
18 19 0.56
19 15 0.44
ACGTcount: A:0.58, C:0.16, G:0.18, T:0.07
Consensus pattern (18 bp):
AACCCGTAAAGGAAAAAA
Found at i:235053 original size:8 final size:7
Alignment explanation
Indices: 235046--235102 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 7
235036 ACCCGTAAAG
235046 GAAAAAA
1 GAAAAAA
235053 GAGAAAAA
1 GA-AAAAA
235061 GAGAAAAA
1 GA-AAAAA
*
235069 G-AAAAG
1 GAAAAAA
235075 GAAAAAAA
1 G-AAAAAA
235083 GAAGAAAA
1 GAA-AAAA
235091 G-AAAAA
1 GAAAAAA
235097 GAAAAA
1 GAAAAA
235103 GGAGAGGTCG
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
6 10 0.23
7 9 0.21
8 24 0.56
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:235073 original size:6 final size:6
Alignment explanation
Indices: 235057--235103 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
235047 AAAAAAGAGA
* *
235057 AAAAGAG AAAAAG AAAAGG AAAAA- AAGAAG -AAAAG AAAAAG AAAAAG
1 AAAA-AG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
235104 GAGAGGTCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
5 8 0.24
6 22 0.65
7 4 0.12
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:235081 original size:22 final size:22
Alignment explanation
Indices: 235048--235102 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
235038 CCGTAAAGGA
*
235048 AAAAAGAGAAAAAG-AGAAAAAG
1 AAAAAGAAAAAAAGAAG-AAAAG
*
235070 AAAAGGAAAAAAAGAAGAAAAG
1 AAAAAGAAAAAAAGAAGAAAAG
235092 AAAAAGAAAAA
1 AAAAAGAAAAA
235103 GGAGAGGTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 27 0.93
23 2 0.07
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAGAAGAAAAG
Found at i:235105 original size:29 final size:29
Alignment explanation
Indices: 235042--235101 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
235032 AAAAACCCGT
235042 AAAGGAAAAAAGAGAAAAAGAGAAAAAGA
1 AAAGGAAAAAAGAGAAAAAGAGAAAAAGA
235071 AAAGGAAAAAA-AGAAGAAA-AGAAAAAGA
1 AAAGGAAAAAAGAGAA-AAAGAGAAAAAGA
235099 AAA
1 AAA
235102 AGGAGAGGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (29 bp):
AAAGGAAAAAAGAGAAAAAGAGAAAAAGA
Found at i:236155 original size:49 final size:50
Alignment explanation
Indices: 235949--236158 Score: 162
Period size: 49 Copynumber: 4.3 Consensus size: 50
235939 TTTACAGGTT
** * *
235949 TGAAGGGAAAGATTGAAGCCGCAACGGC-AAATTTAATACCCTAGAG-ATA
1 TGAAGGGAAAGATTGAAGCCGCAACGGCGAACCTT-GTACCCTAGAGTATG
* * * * * * * *
235998 TAAAGAGAAAGGTTGAAACCGCAATGGCGAACCTTGTACCGTAG-GAACG
1 TGAAGGGAAAGATTGAAGCCGCAACGGCGAACCTTGTACCCTAGAGTATG
* * * * * *
236047 TGATGGGAAAGATTGAAGCCGCGATGGTGAATCTTGTACCCAAGAGTTAT-
1 TGAAGGGAAAGATTGAAGCCGCAACGGCGAACCTTGTACCCTAGAG-TATG
* * * *
236097 TG-AGCGAAAGGTTGAAGCAGCAACGACGAACCTTGTACCCTAGAG-ATG
1 TGAAGGGAAAGATTGAAGCCGCAACGGCGAACCTTGTACCCTAGAGTATG
236145 TGAAGGGAAAGATT
1 TGAAGGGAAAGATT
236159 AGGGCTATAA
Statistics
Matches: 120, Mismatches: 35, Indels: 12
0.72 0.21 0.07
Matches are distributed among these distances:
47 2 0.02
48 3 0.03
49 107 0.89
50 7 0.06
51 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.20
Consensus pattern (50 bp):
TGAAGGGAAAGATTGAAGCCGCAACGGCGAACCTTGTACCCTAGAGTATG
Found at i:236513 original size:20 final size:20
Alignment explanation
Indices: 236484--236524 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
236474 AGTGGGCAGA
236484 TTGAAGACCAT-CAGATCTTT
1 TTGAAGACCATCCA-ATCTTT
*
236504 TTGAATACCATCCAATCTTT
1 TTGAAGACCATCCAATCTTT
236524 T
1 T
236525 ACCCTAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (20 bp):
TTGAAGACCATCCAATCTTT
Found at i:236559 original size:40 final size:40
Alignment explanation
Indices: 236504--236628 Score: 128
Period size: 40 Copynumber: 3.1 Consensus size: 40
236494 TCAGATCTTT
236504 TTGAATACCATCCAATCTTTTACCCTAATCAAAGGGCAGA
1 TTGAATACCATCCAATCTTTTACCCTAATCAAAGGGCAGA
* ** * **
236544 TTGAATACCATCCAATCTCTTACCCCGACCATGGAGGCAGA
1 TTGAATACCATCCAATCTTTTACCCTAATCAAAG-GGCAGA
* * * *
236585 TTG-A-AGCAGTCTAATCTTTTACCCTAATTAGAGGGCAGA
1 TTGAATACCA-TCCAATCTTTTACCCTAATCAAAGGGCAGA
236624 TTGAA
1 TTGAA
236629 GTCATCCAAT
Statistics
Matches: 67, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
39 12 0.18
40 46 0.69
41 9 0.13
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (40 bp):
TTGAATACCATCCAATCTTTTACCCTAATCAAAGGGCAGA
Found at i:236675 original size:23 final size:24
Alignment explanation
Indices: 236648--236694 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
236638 TCGTTAGGTG
236648 TGCCTACT-GATTACACTGTGTGT
1 TGCCTACTGGATTACACTGTGTGT
*
236671 TGCCTACTGGATTGCACTGTGTGT
1 TGCCTACTGGATTACACTGTGTGT
236695 GCTTATTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (24 bp):
TGCCTACTGGATTACACTGTGTGT
Found at i:243810 original size:35 final size:35
Alignment explanation
Indices: 243771--243843 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
243761 TCTCTTGCAT
243771 AGACATCTTAAATCTTACCTGTTAACAAAGGAAAA
1 AGACATCTTAAATCTTACCTGTTAACAAAGGAAAA
243806 AGACATCTTAAATCTTACCTGTTAACAAAGGAAAA
1 AGACATCTTAAATCTTACCTGTTAACAAAGGAAAA
243841 AGA
1 AGA
243844 AATAACCCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (35 bp):
AGACATCTTAAATCTTACCTGTTAACAAAGGAAAA
Found at i:243946 original size:11 final size:12
Alignment explanation
Indices: 243929--243957 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
243919 ATTTGATCAA
243929 CATATTTTACAT
1 CATATTTTACAT
243941 -ATATTTTACAT
1 CATATTTTACAT
243952 CATATT
1 CATATT
243958 CAAATTGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (12 bp):
CATATTTTACAT
Found at i:256707 original size:3 final size:3
Alignment explanation
Indices: 256699--256728 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
256689 CCACCTCTAG
256699 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
256729 TTTTATTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CCT
Found at i:282698 original size:55 final size:55
Alignment explanation
Indices: 282612--282720 Score: 164
Period size: 55 Copynumber: 2.0 Consensus size: 55
282602 AAAAAAAAAT
* * *
282612 GTGTGTCGAACATTGTAGATAACATTGTTGAGAGGAATAGTCACAAACTCCAAAC
1 GTGTGTCGAACATTGTAAATAACATTATTGAGAGGAATAATCACAAACTCCAAAC
* * *
282667 GTGTGTCGAACCTTGTAAATAACATTATTGAGAGGGATAATCATAAACTCCAAA
1 GTGTGTCGAACATTGTAAATAACATTATTGAGAGGAATAATCACAAACTCCAAA
282721 TTTAAACTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (55 bp):
GTGTGTCGAACATTGTAAATAACATTATTGAGAGGAATAATCACAAACTCCAAAC
Found at i:282812 original size:16 final size:15
Alignment explanation
Indices: 282791--282820 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
282781 AACAAATTTC
282791 TTGAAATAACTCAAAT
1 TTGAAATAA-TCAAAT
282807 TTGAAATAATCAAA
1 TTGAAATAATCAAA
282821 AACTATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (15 bp):
TTGAAATAATCAAAT
Found at i:287158 original size:10 final size:11
Alignment explanation
Indices: 287124--287155 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
287114 AAAAGTGTGG
287124 AGAAAACGAAA
1 AGAAAACGAAA
287135 AGAAAA-GAAA
1 AGAAAACGAAA
287145 AGAAAACGAAA
1 AGAAAACGAAA
287156 GAAGTCACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.75, C:0.06, G:0.19, T:0.00
Consensus pattern (11 bp):
AGAAAACGAAA
Found at i:294660 original size:244 final size:242
Alignment explanation
Indices: 294214--294675 Score: 581
Period size: 244 Copynumber: 1.9 Consensus size: 242
294204 AAAATGAATT
* * * *
294214 ATATAGCACTTGTTTAAGGGACAGAAAAGATAAAAATTCTTAAAATACGTTCATCTTTCCTTCTT
1 ATATAGCACTAGTTTAAGGGACAGAAAAGATAAAAATTCCTAAAATACATTCATCTTTCCTTCCT
*
294279 GAACAATCATAATTCATAACAACCCTAACAGCAACTCAATGTGCATTAGCTCTACAAAATCCAAT
66 AAACAATCATAATTCATAACAACCCTAACAGCAACTCAATGTGCATTAGCTCTACAAAATCCAAT
* * ** * ***
294344 TACACGATAAGATAGGTGTTTCAAAATAATACCTATTACAAAAGTAAAGCAATGATAGTGGTAAT
131 TACACGATAAGATA-GAGTTTCAAAATAATACCTATTACAAAAATAAAGCAACAACAGTCACAAT
294409 GAATATCAACTTAAACAAAATGACTATGAGCATACAAATCCAAGAGTG
195 GAATATCAACTTAAACAAAATGACTATGAGCATACAAATCCAAGAGTG
* * *
294457 ATATAGTACTAGTTTAAGGGATAGAAACA-ATAATAATTCCTAAAATACATTCATCTTTCCTTCC
1 ATATAGCACTAGTTTAAGGGACAGAAA-AGATAAAAATTCCTAAAATACATTCATCTTTCCTTCC
* * **
294521 TAAACAAATCTTAATTCTTAAGTACCCTAACAGCAACTCAATTTGTGCATTAGCTCTACAAAATC
65 TAAAC-AATCATAATTCATAACAACCCTAACAGCAACTCAA--TGTGCATTAGCTCTACAAAATC
* * * * * *
294586 CAATTACATGATAAGAT-GAGTTTCAAAGTTATA-CTATTTGCAACAAAT-AATCAACAACGGTC
127 CAATTACACGATAAGATAGAGTTTCAAAATAATACCTA-TTACAA-AAATAAAGCAACAACAGTC
* *
294648 ACAATGAATATCATCTTAAACGAAATGA
190 ACAATGAATATCAACTTAAACAAAATGA
294676 AATATAGCAC
Statistics
Matches: 185, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
243 62 0.34
244 82 0.44
245 3 0.02
246 38 0.21
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (242 bp):
ATATAGCACTAGTTTAAGGGACAGAAAAGATAAAAATTCCTAAAATACATTCATCTTTCCTTCCT
AAACAATCATAATTCATAACAACCCTAACAGCAACTCAATGTGCATTAGCTCTACAAAATCCAAT
TACACGATAAGATAGAGTTTCAAAATAATACCTATTACAAAAATAAAGCAACAACAGTCACAATG
AATATCAACTTAAACAAAATGACTATGAGCATACAAATCCAAGAGTG
Found at i:302659 original size:27 final size:26
Alignment explanation
Indices: 302610--302660 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
302600 GTGGGAGTTA
**
302610 AATATTTTTATTAGTTTTTTTTTTTT
1 AATATTTTTATTAGTTTACTTTTTTT
*
302636 AATATTTTTAATTTGTTTACTTTTT
1 AATATTTTT-ATTAGTTTACTTTTT
302661 AGTCTTTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 9 0.43
27 12 0.57
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.73
Consensus pattern (26 bp):
AATATTTTTATTAGTTTACTTTTTTT
Found at i:323527 original size:2 final size:2
Alignment explanation
Indices: 323520--323546 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
323510 ACCCATATTT
323520 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
323547 TCATTTGGGA
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:328781 original size:2 final size:2
Alignment explanation
Indices: 328776--328800 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
328766 AGTGTGTGTG
328776 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 T
328801 TAGGAGTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:332467 original size:6 final size:6
Alignment explanation
Indices: 332452--332480 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
332442 TACTTCCCCG
332452 AAAT-A AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA
332481 TTCTATACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:334868 original size:4 final size:4
Alignment explanation
Indices: 334859--334883 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
334849 ATGATGGTAC
334859 CCCA CCCA CCCA CCCA CCCA CCCA C
1 CCCA CCCA CCCA CCCA CCCA CCCA C
334884 GTGAGACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.76, G:0.00, T:0.00
Consensus pattern (4 bp):
CCCA
Found at i:352262 original size:2 final size:2
Alignment explanation
Indices: 352255--352286 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
352245 CTTGATTAGA
352255 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
352287 CAAATACAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:354006 original size:3 final size:3
Alignment explanation
Indices: 353998--354023 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
353988 TCATGGTTTT
353998 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
354024 TATGTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:370660 original size:2 final size:2
Alignment explanation
Indices: 370653--370695 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
370643 AACACAACAG
370653 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
370695 T
1 T
370696 TTTAATTATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:374595 original size:2 final size:2
Alignment explanation
Indices: 374588--374619 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
374578 TTAAGGACAA
374588 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
374620 TGAAATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:384165 original size:27 final size:27
Alignment explanation
Indices: 384135--384213 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
384125 GACACCTGTG
* *
384135 AAGGCGCCTTTGAAGGTCCCACCTCCA
1 AAGGCACCTTCGAAGGTCCCACCTCCA
***
384162 AAGGCACCTTCGAAGGTCCCACCTGTG
1 AAGGCACCTTCGAAGGTCCCACCTCCA
*
384189 AAGGCACCTTCGAAGGCCCCACCTC
1 AAGGCACCTTCGAAGGTCCCACCTC
384214 TTCAGCCACT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.16
Consensus pattern (27 bp):
AAGGCACCTTCGAAGGTCCCACCTCCA
Found at i:388138 original size:25 final size:25
Alignment explanation
Indices: 388110--388160 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
388100 CTAGAAATAG
388110 GACGACATAAATCTACCGGATTAGA
1 GACGACATAAATCTACCGGATTAGA
388135 GACGACATAAATCTACCGGATTAGA
1 GACGACATAAATCTACCGGATTAGA
388160 G
1 G
388161 TCAAATCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.20
Consensus pattern (25 bp):
GACGACATAAATCTACCGGATTAGA
Found at i:389639 original size:51 final size:51
Alignment explanation
Indices: 389537--389641 Score: 140
Period size: 51 Copynumber: 2.1 Consensus size: 51
389527 ATATATTTTT
** * *
389537 AAACTTTATCCTTCGTTCAAGTATGGTATTTAAAATTTCGGTTTATAAAAA
1 AAACTTTATCCTTCAATCAAGTATGGTATTTAAAATTTCGCTTCATAAAAA
* *
389588 AAACTTTATCCTTCAATCAAGTATGGTATTTAGAA-TTCGCTTGCATTAAAA
1 AAACTTTATCCTTCAATCAAGTATGGTATTTAAAATTTCGCTT-CATAAAAA
389639 AAA
1 AAA
389642 GTATGGTATA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 6 0.13
51 41 0.87
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.38
Consensus pattern (51 bp):
AAACTTTATCCTTCAATCAAGTATGGTATTTAAAATTTCGCTTCATAAAAA
Found at i:397857 original size:17 final size:17
Alignment explanation
Indices: 397826--397864 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
397816 TTTATTATAA
*
397826 TTTTTCACGTCTTTTTT
1 TTTTTCAAGTCTTTTTT
397843 CTTTTTCAAGT-TTTTTT
1 -TTTTTCAAGTCTTTTTT
397860 TTTTT
1 TTTTT
397865 GTTTATTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.08, C:0.13, G:0.05, T:0.74
Consensus pattern (17 bp):
TTTTTCAAGTCTTTTTT
Found at i:413834 original size:30 final size:32
Alignment explanation
Indices: 413778--413836 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
413768 AATAATAATT
413778 ATTATATTAATACTTATAAAATATACTATTTC
1 ATTATATTAATACTTATAAAATATACTATTTC
**
413810 ATTATA-TAATAC-TATATCATATACTAT
1 ATTATATTAATACTTATAAAATATACTAT
413837 AATAATAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 13 0.52
31 6 0.24
32 6 0.24
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (32 bp):
ATTATATTAATACTTATAAAATATACTATTTC
Found at i:413869 original size:2 final size:2
Alignment explanation
Indices: 413862--413900 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
413852 CATAATAGTT
413862 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
413901 GCAGCAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:416821 original size:21 final size:21
Alignment explanation
Indices: 416783--416841 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
416773 TTTTAAAATT
*
416783 TAAAAATTATTTAAAAAA-TCA
1 TAAAAATTA-TAAAAAAATTCA
*
416804 TAAAAATTATAAACAAAATTTA
1 TAAAAATTATAAA-AAAATTCA
416826 TGAAAAAGTTATAAAA
1 T-AAAAA-TTATAAAA
416842 TTTTTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 3 0.09
21 13 0.41
22 3 0.09
23 6 0.19
24 7 0.22
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (21 bp):
TAAAAATTATAAAAAAATTCA
Found at i:446444 original size:13 final size:13
Alignment explanation
Indices: 446426--446455 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
446416 AGTAAGACAA
446426 TGAACCAAGGAAT
1 TGAACCAAGGAAT
446439 TGAACCAAGGAAT
1 TGAACCAAGGAAT
446452 TGAA
1 TGAA
446456 GGATGCTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.13, G:0.23, T:0.17
Consensus pattern (13 bp):
TGAACCAAGGAAT
Found at i:450208 original size:23 final size:23
Alignment explanation
Indices: 450157--450208 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
450147 AAGCTAAAAA
*
450157 AATTTTTAGTGAAATTAAATTCT
1 AATTTTTAGTGAAATTAAAATCT
*
450180 ATATTTTTA-TGAGAATTAAAATGT
1 A-ATTTTTAGTGA-AATTAAAATCT
450204 AATTT
1 AATTT
450209 CATCATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (23 bp):
AATTTTTAGTGAAATTAAAATCT
Found at i:459994 original size:1 final size:1
Alignment explanation
Indices: 459990--460019 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
459980 NNNNNNNNNN
459990 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
460020 GGAATCTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:469884 original size:23 final size:24
Alignment explanation
Indices: 469857--469922 Score: 100
Period size: 23 Copynumber: 2.8 Consensus size: 24
469847 GAACACATAA
*
469857 AGTGCTAATCAGAGAGCACGAGAC
1 AGTGCTAATCAGAGAGCACGACAC
*
469881 -GTGCTAAACAGAGAGCAC-ACAC
1 AGTGCTAATCAGAGAGCACGACAC
469903 AGTGCTAATCAGAGAGCACG
1 AGTGCTAATCAGAGAGCACG
469923 CTAGTGTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 3 0.08
23 34 0.92
ACGTcount: A:0.38, C:0.23, G:0.27, T:0.12
Consensus pattern (24 bp):
AGTGCTAATCAGAGAGCACGACAC
Found at i:474849 original size:5 final size:5
Alignment explanation
Indices: 474839--474864 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
474829 AAATTCGTAA
474839 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
474865 GATGGCGAAT
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:480800 original size:24 final size:24
Alignment explanation
Indices: 480750--480801 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
480740 TGATTTCTTT
* *
480750 TCAGCATCATCATCCTCACTTTTC
1 TCAGCATCATCATCCTCACCTTCC
* * *
480774 TCAGCATCTTCATCTTCTCCTTCC
1 TCAGCATCATCATCCTCACCTTCC
480798 TCAG
1 TCAG
480802 AAGAGCTGCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.38, G:0.06, T:0.38
Consensus pattern (24 bp):
TCAGCATCATCATCCTCACCTTCC
Found at i:480898 original size:26 final size:26
Alignment explanation
Indices: 480862--480913 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
480852 CTATAATCAG
480862 TTAATCACAACATGCGTATTCTTACA
1 TTAATCACAACATGCGTATTCTTACA
*
480888 TTAATCTCAACATGCGTATTCTTACA
1 TTAATCACAACATGCGTATTCTTACA
480914 GCAATAAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.37
Consensus pattern (26 bp):
TTAATCACAACATGCGTATTCTTACA
Done.