Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014395.1 Kokia drynarioides strain JFW-HI SEQ_129433, 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: 266598
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 106 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1249 original size:45 final size:45
Alignment explanation
Indices: 1133--1269 Score: 186
Period size: 45 Copynumber: 3.0 Consensus size: 45
1123 CCATAGCTCA
* *
1133 TCAAGGCAAGGATATCAGCCTCAGCTTGATGAGCCACTACAATAC
1 TCAAGGCAAGGATATCAGCCTCAGTTTGATGAGCCACCACAATAC
* *
1178 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATAC
1 TCAAGGCAAGGATATCAGCCTCAGTTTGATGAGCCACCACAATAC
* * * *
1223 TCAAGGGAAGGATATCAAG-CTGAGTTTGATAAGCCACCGCAATAC
1 TCAAGGCAAGGATATC-AGCCTCAGTTTGATGAGCCACCACAATAC
1268 TC
1 TC
1270 TACTCCTCCC
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
45 79 0.98
46 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (45 bp):
TCAAGGCAAGGATATCAGCCTCAGTTTGATGAGCCACCACAATAC
Found at i:1558 original size:14 final size:14
Alignment explanation
Indices: 1529--1605 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
1519 CATAACATTA
*
1529 AAACCTAAAACC-T
1 AAACCTTAAACCAT
*
1542 AAACCTTAAACCTT
1 AAACCTTAAACCAT
* *
1556 AAA-CTTGGAATCAT
1 AAACCTT-AAACCAT
*
1570 AAACCGTAAACCAT
1 AAACCTTAAACCAT
*
1584 AAA-CTTGAAACCCT
1 AAACCTT-AAACCAT
1598 AAACCTTA
1 AAACCTTA
1606 TACATGAAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
13 16 0.32
14 29 0.58
15 5 0.10
ACGTcount: A:0.47, C:0.26, G:0.05, T:0.22
Consensus pattern (14 bp):
AAACCTTAAACCAT
Found at i:1572 original size:28 final size:28
Alignment explanation
Indices: 1536--1605 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
1526 TTAAAACCTA
*
1536 AAACC-TAAACCTTAAACCTTAAACTTG
1 AAACCATAAACCTTAAACCATAAACTTG
* * *
1563 GAATCATAAACCGTAAACCATAAACTTG
1 AAACCATAAACCTTAAACCATAAACTTG
*
1591 AAACCCTAAACCTTA
1 AAACCATAAACCTTA
1606 TACATGAAAC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
27 3 0.09
28 31 0.91
ACGTcount: A:0.46, C:0.26, G:0.06, T:0.23
Consensus pattern (28 bp):
AAACCATAAACCTTAAACCATAAACTTG
Found at i:1613 original size:21 final size:21
Alignment explanation
Indices: 1570--1615 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1560 TTGGAATCAT
* *
1570 AAACCGTAAACCATAAACTTG
1 AAACCCTAAACCATAAACATG
* *
1591 AAACCCTAAACCTTATACATG
1 AAACCCTAAACCATAAACATG
1612 AAAC
1 AAAC
1616 ATTTTAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.26, G:0.07, T:0.20
Consensus pattern (21 bp):
AAACCCTAAACCATAAACATG
Found at i:1615 original size:28 final size:27
Alignment explanation
Indices: 1539--1615 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
1529 AAACCTAAAA
* * *
1539 CCTAAACCTTAAACCTTAAACTTGGAAT
1 CCTAAACCTTAAA-CATAAACTTGAAAC
* *
1567 CATAAACCGTAAACCATAAACTTGAAAC
1 CCTAAACCTTAAA-CATAAACTTGAAAC
*
1595 CCTAAACCTTATACATGAAAC
1 CCTAAACCTTAAACAT-AAAC
1616 ATTTTAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 3 0.08
28 37 0.93
ACGTcount: A:0.44, C:0.26, G:0.06, T:0.23
Consensus pattern (27 bp):
CCTAAACCTTAAACATAAACTTGAAAC
Found at i:4378 original size:4 final size:4
Alignment explanation
Indices: 4358--4406 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
4348 AACACATTAC
* * *
4358 CTTT CTTT CATT C-TT CTTT CTTT CCTCT CCTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
4406 C
1 C
4407 CCGTTTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
3 3 0.08
4 32 0.84
5 3 0.08
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (4 bp):
CTTT
Found at i:4392 original size:17 final size:15
Alignment explanation
Indices: 4358--4404 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
4348 AACACATTAC
4358 CTTTCTTTCATTCTT
1 CTTTCTTTCATTCTT
*
4373 CTTTCTTTCCTCTCCTT
1 CTTTCTTTCAT-T-CTT
*
4390 CTTTCTTTCTTTCTT
1 CTTTCTTTCATTCTT
4405 TCCCGTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 13 0.46
16 2 0.07
17 13 0.46
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (15 bp):
CTTTCTTTCATTCTT
Found at i:7881 original size:18 final size:18
Alignment explanation
Indices: 7858--7907 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
7848 ACACGCCTCA
7858 TCTCAAGC-AGCTCATGCT
1 TCTCAAGCTA-CTCATGCT
*
7876 TCTCAATCTACTCATGCT
1 TCTCAAGCTACTCATGCT
*
7894 TCTCAATCTACTCA
1 TCTCAAGCTACTCA
7908 ATCAACTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 29 0.97
19 1 0.03
ACGTcount: A:0.24, C:0.34, G:0.08, T:0.34
Consensus pattern (18 bp):
TCTCAAGCTACTCATGCT
Found at i:13349 original size:31 final size:30
Alignment explanation
Indices: 13286--13370 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 30
13276 ATTTCTTTAA
*
13286 ATGTATACAATTGAATTAAATCAAGGTTTC
1 ATGTATACAATTGAATCAAATCAAGGTTTC
13316 ATGTATAC-ATATGAATCACAATTCAA-GTTTC
1 ATGTATACAAT-TGAATCA-AA-TCAAGGTTTC
* * * *
13347 ATGTGTATAATTGCACCAAATCAA
1 ATGTATACAATTGAATCAAATCAA
13371 AATTAATGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
29 6 0.13
30 16 0.35
31 18 0.39
32 6 0.13
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (30 bp):
ATGTATACAATTGAATCAAATCAAGGTTTC
Found at i:19826 original size:26 final size:26
Alignment explanation
Indices: 19797--19847 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
19787 ATATGAAAGT
*
19797 ATTTTTATTTTTAA-ATAAAATTTTAA
1 ATTTTT-TTTTGAATATAAAATTTTAA
19823 ATTTTTTTTTGAATATAAAATTTTA
1 ATTTTTTTTTGAATATAAAATTTTA
19848 CACTTGAGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (26 bp):
ATTTTTTTTTGAATATAAAATTTTAA
Found at i:28613 original size:29 final size:30
Alignment explanation
Indices: 28575--28868 Score: 321
Period size: 29 Copynumber: 10.0 Consensus size: 30
28565 GTCCCCAAAC
28575 CTTCCAAAAATTACCATTTT-ACCCTCGAA
1 CTTCCAAAAATTACCATTTTGACCCTCGAA
* *
28604 CTTTCAAAAATCT-CAATTTTGACCC-CGAA
1 CTTCCAAAAAT-TACCATTTTGACCCTCGAA
28633 CCTTCCAAAAATTACCATTTT-ACCCTCGAA
1 -CTTCCAAAAATTACCATTTTGACCCTCGAA
* *
28663 CTT-CAAAAAATCCCATTTTGACCC-CGAA
1 CTTCCAAAAATTACCATTTTGACCCTCGAA
*
28691 CCTTCTAAAAATTACCATTTTG-CCCTCGAA
1 -CTTCCAAAAATTACCATTTTGACCCTCGAA
*
28721 CTTCCAAAAA-TCCCATTTTTGACCCT-GAA
1 CTTCCAAAAATTACCA-TTTTGACCCTCGAA
*
28750 CCTTCCAAAAACTACCATTTTG-CCCTCGAA
1 -CTTCCAAAAATTACCATTTTGACCCTCGAA
*
28780 CTTCCAAAAA-TCCCATTTTTGA-CCTCGAA
1 CTTCCAAAAATTACCA-TTTTGACCCTCGAA
*
28809 CCTTCCAAAAATTACCATTTTGTCCC-CGAA
1 -CTTCCAAAAATTACCATTTTGACCCTCGAA
*
28839 CTTCCAAAAA-TCCCATTTTTGACCC-CGAA
1 CTTCCAAAAATTACCA-TTTTGACCCTCGAA
28868 C
1 C
28869 ATCTAAAATT
Statistics
Matches: 228, Mismatches: 17, Indels: 40
0.80 0.06 0.14
Matches are distributed among these distances:
28 30 0.13
29 104 0.46
30 84 0.37
31 10 0.04
ACGTcount: A:0.32, C:0.32, G:0.06, T:0.30
Consensus pattern (30 bp):
CTTCCAAAAATTACCATTTTGACCCTCGAA
Found at i:28644 original size:59 final size:59
Alignment explanation
Indices: 28567--28868 Score: 473
Period size: 59 Copynumber: 5.1 Consensus size: 59
28557 CCCTGATGGT
* * * *
28567 CCCCAAACCTTCCAAAAATTACCATTTTACCCTCGAACTTTCAAAAATCTCAATTTTGA
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
*
28626 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCAAAAAATCCCA-TTTTGA
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* *
28684 CCCCGAACCTTCTAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * *
28743 CCCTGAACCTTCCAAAAACTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* *
28802 CCTCGAACCTTCCAAAAATTACCATTTTGTCCC-CGAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATTACCATTTT-ACCCTCGAACTTCCAAAAATCCCATTTTTGA
28861 CCCCGAAC
1 CCCCGAAC
28869 ATCTAAAATT
Statistics
Matches: 226, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
58 55 0.24
59 168 0.74
60 3 0.01
ACGTcount: A:0.32, C:0.33, G:0.06, T:0.29
Consensus pattern (59 bp):
CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
Found at i:28720 original size:117 final size:118
Alignment explanation
Indices: 28567--28868 Score: 482
Period size: 117 Copynumber: 2.6 Consensus size: 118
28557 CCCTGATGGT
* * * * *
28567 CCCCAAACCTTCCAAAAATTACCATTTTACCCTCGAACTTTCAAAAATCTCAATTTTGACCCCGA
1 CCCCGAACCTTCCAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGA
*
28632 ACCTTCCAAAAATTACCATTTTACCCTCGAACTTCAAAAAATCCCA-TTTTGA
66 ACCTTCCAAAAACTACCATTTTACCCTCGAACTTCAAAAAATCCCATTTTTGA
* *
28684 CCCCGAACCTTCTAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGACCCTGA
1 CCCCGAACCTTCCAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGA
* *
28749 ACCTTCCAAAAACTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGA
66 ACCTTCCAAAAACTACCATTTTACCCTCGAACTTCAAAAAATCCCATTTTTGA
*
28802 CCTCGAACCTTCCAAAAATTACCATTTTGTCCC-CGAACTTCCAAAAATCCCATTTTTGACCCCG
1 CCCCGAACCTTCCAAAAATTACCATTTTG-CCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
28866 AAC
65 AAC
28869 ATCTAAAATT
Statistics
Matches: 170, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
117 101 0.59
118 66 0.39
119 3 0.02
ACGTcount: A:0.32, C:0.33, G:0.06, T:0.29
Consensus pattern (118 bp):
CCCCGAACCTTCCAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGA
ACCTTCCAAAAACTACCATTTTACCCTCGAACTTCAAAAAATCCCATTTTTGA
Found at i:29142 original size:17 final size:17
Alignment explanation
Indices: 29120--29155 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
29110 TTCTCGTGGA
29120 TAATTTATCTTCTTGTT
1 TAATTTATCTTCTTGTT
29137 TAATTTATCTTCTTGTT
1 TAATTTATCTTCTTGTT
29154 TA
1 TA
29156 TCTTACTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.11, G:0.06, T:0.64
Consensus pattern (17 bp):
TAATTTATCTTCTTGTT
Found at i:41173 original size:211 final size:209
Alignment explanation
Indices: 40874--41558 Score: 969
Period size: 211 Copynumber: 3.3 Consensus size: 209
40864 TGATGCAAGC
*
40874 AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGC
1 AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGC
*
40939 TTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCTCATGAGATACGGAGAAGCGAATT
66 TTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCTGATGAGATACGGAGAAGCGAATT
* *
41004 AAAACAAACAATGCGGTCATCTTCCTGACGAGATACTAAGAAGAAGACCAAATCAAACCCAAATA
131 AAAACAAACAATGCGGTCATCTTCCTGACGAGATACTGAGAAGAAGACCAAATCAAACCC-AA-G
41069 AGGCTCGAAACGAGCA
194 AGGCTCGAAACGAGCA
* * * * *
41085 AAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCCATAAAAGGTTATC
1 AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGC
* * *
41150 TTCCTAATGAGATACTGAGAAGTGTATCAAATTCGTCTTCCTGATGAGATACGAAGAAGCGAATT
66 TTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCTGATGAGATACGGAGAAGCGAATT
41215 AAAACAAACAATGCGGTCATCTT-CTGGACGAGATACTGAGAAGAAGACCAAATCAAACCCAAGC
131 AAAACAAACAATGCGGTCATCTTCCT-GACGAGATACTGAGAAGAAGACCAAATCAAACCCAA--
*
41279 GAGGCTCGAAACAAGCA
193 GAGGCTCGAAACGAGCA
* *
41296 AAATCTTCGAACCCCAACTTCCTGATGAGACATTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGC
1 AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGC
* * * **
41361 TTCCTGATGAGATACTGAGAAGTGAACCAAATTTGTCTTCCTGATGAGGTATAGAGAAGCGAATT
66 TTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCTGATGAGATACGGAGAAGCGAATT
* * * * *
41426 GAAACGAGC-ATCGACGTGATCATCTTCCTGATGAGACACTGAGAAGAAGACC----CAAA--C-
131 AAAACAAACAAT-G-CG-G-TCATCTTCCTGACGAGATACTGAGAAGAAGACCAAATCAAACCCA
41483 -GAGGCTCGAAACGAGCA
192 AGAGGCTCGAAACGAGCA
*
41500 AAATCTTCGAACCCCAGCTTCCTGATGAGACA-TGGGGAAGCAGGTCGAAGCAATAAAAG
1 AAATCTTCGAACCCCAGCTTCCTGATGAGACACT-GAGAAGCAGGTCGAAGCAATAAAAG
41559 TCATCTTCCC
Statistics
Matches: 431, Mismatches: 35, Indels: 23
0.88 0.07 0.05
Matches are distributed among these distances:
203 1 0.00
204 71 0.16
208 1 0.00
210 10 0.02
211 315 0.73
212 2 0.00
213 1 0.00
214 28 0.06
215 2 0.00
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (209 bp):
AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGC
TTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCTGATGAGATACGGAGAAGCGAATT
AAAACAAACAATGCGGTCATCTTCCTGACGAGATACTGAGAAGAAGACCAAATCAAACCCAAGAG
GCTCGAAACGAGCA
Found at i:42160 original size:17 final size:17
Alignment explanation
Indices: 42074--42150 Score: 84
Period size: 17 Copynumber: 4.5 Consensus size: 17
42064 CCCAATCAAC
* *
42074 TTAAATTTATTTTAAAA
1 TTAAATTTATTATAAAT
* *
42091 TTAAGTTTATTCTAAAT
1 TTAAATTTATTATAAAT
* *
42108 TTAAATTTGGTT-GAAAT
1 TTAAATTT-ATTATAAAT
42125 TTAAATTTATTATAAAT
1 TTAAATTTATTATAAAT
42142 TTAAATTTA
1 TTAAATTTA
42151 AAATTTATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
16 2 0.04
17 46 0.92
18 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTATAAAT
Found at i:42841 original size:12 final size:12
Alignment explanation
Indices: 42824--42854 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
42814 GAGATTTATT
42824 ATTATTAAAAAA
1 ATTATTAAAAAA
42836 ATTATTAAAAAA
1 ATTATTAAAAAA
42848 ATTATTA
1 ATTATTA
42855 TTAATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATTATTAAAAAA
Found at i:42841 original size:15 final size:15
Alignment explanation
Indices: 42821--42858 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
42811 AATGAGATTT
42821 ATTATTATT-AAAAA
1 ATTATTATTAAAAAA
42835 A--ATTATTAAAAAA
1 ATTATTATTAAAAAA
42848 ATTATTATTAA
1 ATTATTATTAA
42859 TTAATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 6 0.29
14 1 0.05
15 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTATTATTAAAAAA
Found at i:44101 original size:59 final size:59
Alignment explanation
Indices: 43961--44317 Score: 533
Period size: 59 Copynumber: 6.1 Consensus size: 59
43951 CCCCGATGGT
43961 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTGA
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * * * * * *
44019 CCTCGAACTTTCCAAAAATTACCATATTACCC-CTAATCTTGCAAAAATTCCATTTTTTA
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAA-CTTCCAAAAATCCCATTTTTGA
* *
44078 CCCCGAACCTTCCAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGC
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
44137 CCCCGAACCTTCCAAAAATTACCATTTTGACCC-CGAACTTCCAAAAATCCCA-TTTTGA
1 CCCCGAACCTTCCAAAAATTACCATTTT-ACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * *
44195 CCCCAAACCTTCCAAAAATTACCATTTTGCCCTCGAATTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
** *
44254 CCCTAAACCTTCCAAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
44313 CCCCG
1 CCCCG
44318 GACATCTACA
Statistics
Matches: 266, Mismatches: 27, Indels: 11
0.88 0.09 0.04
Matches are distributed among these distances:
57 6 0.02
58 92 0.35
59 162 0.61
60 6 0.02
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.30
Consensus pattern (59 bp):
CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
Found at i:44198 original size:117 final size:117
Alignment explanation
Indices: 43961--44317 Score: 547
Period size: 117 Copynumber: 3.0 Consensus size: 117
43951 CCCCGATGGT
* *
43961 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTGACCTCGA
1 CCCCGAACCTTCCAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGA
* * * * * *
44025 ACTTTCCAAAAATTACCATATTACCCCTAATCTTGCAAAAATTCCATTTTTTA
66 ACCTTCCAAAAATTACCATTTTACCCCGAA-CTTCCAAAAATCCCATTTTTGA
*
44078 CCCCGAACCTTCCAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGCCCCCGA
1 CCCCGAACCTTCCAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGA
44143 ACCTTCCAAAAATTACCATTTTGACCCCGAACTTCCAAAAATCCCA-TTTTGA
66 ACCTTCCAAAAATTACCATTTT-ACCCCGAACTTCCAAAAATCCCATTTTTGA
* * **
44195 CCCCAAACCTTCCAAAAATTACCATTTTGCCCTCGAATTTCCAAAAATCCCATTTTTGACCCTAA
1 CCCCGAACCTTCCAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGA
*
44260 ACCTTCCAAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGA
66 ACCTTCCAAAAATTACCATTTTACCC-CGAACTTCCAAAAATCCCATTTTTGA
44313 CCCCG
1 CCCCG
44318 GACATCTACA
Statistics
Matches: 220, Mismatches: 16, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
116 4 0.02
117 156 0.71
118 53 0.24
119 7 0.03
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.30
Consensus pattern (117 bp):
CCCCGAACCTTCCAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGA
ACCTTCCAAAAATTACCATTTTACCCCGAACTTCCAAAAATCCCATTTTTGA
Found at i:44265 original size:176 final size:176
Alignment explanation
Indices: 43961--44317 Score: 556
Period size: 176 Copynumber: 2.0 Consensus size: 176
43951 CCCCGATGGT
* *
43961 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTGACCTCGAA
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTGACCCCAAA
* * * * * *
44026 CTTTCCAAAAATTACCATATTACCCCTAATCTTGCAAAAATTCCATTTTTTACCCCGAACCTTCC
66 CCTTCCAAAAATTACCATATTACCCCGAATCTTCCAAAAATCCCATTTTTGACCCCAAACCTTCC
* *
44091 AAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGC
131 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
44137 CCCCGAACCTTCCAAAAATTACCATTTTGACCC-CGAACTTCCAAAAATCCCATTTTGACCCCAA
1 CCCCGAACCTTCCAAAAATTACCATTTT-ACCCTCGAACTTCCAAAAATCCCATTTTGACCCCAA
* * *
44201 ACCTTCCAAAAATTACCATTTTGCCCTCGAAT-TTCCAAAAATCCCATTTTTGACCCTAAACCTT
65 ACCTTCCAAAAATTACCATATTACCC-CGAATCTTCCAAAAATCCCATTTTTGACCCCAAACCTT
*
44265 CCAAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGA
129 CCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
44313 CCCCG
1 CCCCG
44318 GACATCTACA
Statistics
Matches: 165, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
176 157 0.95
177 8 0.05
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.30
Consensus pattern (176 bp):
CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTGACCCCAAA
CCTTCCAAAAATTACCATATTACCCCGAATCTTCCAAAAATCCCATTTTTGACCCCAAACCTTCC
AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
Found at i:49739 original size:17 final size:17
Alignment explanation
Indices: 49653--49729 Score: 84
Period size: 17 Copynumber: 4.5 Consensus size: 17
49643 CCCAATCAAC
* *
49653 TTAAATTTATTTTAAAA
1 TTAAATTTATTATAAAT
* *
49670 TTAAGTTTATTCTAAAT
1 TTAAATTTATTATAAAT
* *
49687 TTAAATTTGGTT-GAAAT
1 TTAAATTT-ATTATAAAT
49704 TTAAATTTATTATAAAT
1 TTAAATTTATTATAAAT
49721 TTAAATTTA
1 TTAAATTTA
49730 AAATTTATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
16 2 0.04
17 46 0.92
18 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTATAAAT
Found at i:50420 original size:12 final size:12
Alignment explanation
Indices: 50403--50433 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
50393 GAGATTTATT
50403 ATTATTAAAAAA
1 ATTATTAAAAAA
50415 ATTATTAAAAAA
1 ATTATTAAAAAA
50427 ATTATTA
1 ATTATTA
50434 TTAATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATTATTAAAAAA
Found at i:50420 original size:15 final size:15
Alignment explanation
Indices: 50400--50437 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
50390 AATGAGATTT
50400 ATTATTATT-AAAAA
1 ATTATTATTAAAAAA
50414 A--ATTATTAAAAAA
1 ATTATTATTAAAAAA
50427 ATTATTATTAA
1 ATTATTATTAA
50438 TTAATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 6 0.29
14 1 0.05
15 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTATTATTAAAAAA
Found at i:51680 original size:59 final size:59
Alignment explanation
Indices: 51540--51896 Score: 533
Period size: 59 Copynumber: 6.1 Consensus size: 59
51530 CCCCGATGGT
51540 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTGA
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * * * * * *
51598 CCTCGAACTTTCCAAAAATTACCATATTACCC-CTAATCTTGCAAAAATTCCATTTTTTA
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAA-CTTCCAAAAATCCCATTTTTGA
* *
51657 CCCCGAACCTTCCAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGC
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
51716 CCCCGAACCTTCCAAAAATTACCATTTTGACCC-CGAACTTCCAAAAATCCCA-TTTTGA
1 CCCCGAACCTTCCAAAAATTACCATTTT-ACCCTCGAACTTCCAAAAATCCCATTTTTGA
* * *
51774 CCCCAAACCTTCCAAAAATTACCATTTTGCCCTCGAATTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
** *
51833 CCCTAAACCTTCCAAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
51892 CCCCG
1 CCCCG
51897 GACATCTACA
Statistics
Matches: 266, Mismatches: 27, Indels: 11
0.88 0.09 0.04
Matches are distributed among these distances:
57 6 0.02
58 92 0.35
59 162 0.61
60 6 0.02
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.30
Consensus pattern (59 bp):
CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
Found at i:51777 original size:117 final size:117
Alignment explanation
Indices: 51540--51896 Score: 547
Period size: 117 Copynumber: 3.0 Consensus size: 117
51530 CCCCGATGGT
* *
51540 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTGACCTCGA
1 CCCCGAACCTTCCAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGA
* * * * * *
51604 ACTTTCCAAAAATTACCATATTACCCCTAATCTTGCAAAAATTCCATTTTTTA
66 ACCTTCCAAAAATTACCATTTTACCCCGAA-CTTCCAAAAATCCCATTTTTGA
*
51657 CCCCGAACCTTCCAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGCCCCCGA
1 CCCCGAACCTTCCAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGA
51722 ACCTTCCAAAAATTACCATTTTGACCCCGAACTTCCAAAAATCCCA-TTTTGA
66 ACCTTCCAAAAATTACCATTTT-ACCCCGAACTTCCAAAAATCCCATTTTTGA
* * **
51774 CCCCAAACCTTCCAAAAATTACCATTTTGCCCTCGAATTTCCAAAAATCCCATTTTTGACCCTAA
1 CCCCGAACCTTCCAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGA
*
51839 ACCTTCCAAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGA
66 ACCTTCCAAAAATTACCATTTTACCC-CGAACTTCCAAAAATCCCATTTTTGA
51892 CCCCG
1 CCCCG
51897 GACATCTACA
Statistics
Matches: 220, Mismatches: 16, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
116 4 0.02
117 156 0.71
118 53 0.24
119 7 0.03
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.30
Consensus pattern (117 bp):
CCCCGAACCTTCCAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGA
ACCTTCCAAAAATTACCATTTTACCCCGAACTTCCAAAAATCCCATTTTTGA
Found at i:51844 original size:176 final size:176
Alignment explanation
Indices: 51540--51896 Score: 556
Period size: 176 Copynumber: 2.0 Consensus size: 176
51530 CCCCGATGGT
* *
51540 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTGACCTCGAA
1 CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTGACCCCAAA
* * * * * *
51605 CTTTCCAAAAATTACCATATTACCCCTAATCTTGCAAAAATTCCATTTTTTACCCCGAACCTTCC
66 CCTTCCAAAAATTACCATATTACCCCGAATCTTCCAAAAATCCCATTTTTGACCCCAAACCTTCC
* *
51670 AAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGC
131 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
51716 CCCCGAACCTTCCAAAAATTACCATTTTGACCC-CGAACTTCCAAAAATCCCATTTTGACCCCAA
1 CCCCGAACCTTCCAAAAATTACCATTTT-ACCCTCGAACTTCCAAAAATCCCATTTTGACCCCAA
* * *
51780 ACCTTCCAAAAATTACCATTTTGCCCTCGAAT-TTCCAAAAATCCCATTTTTGACCCTAAACCTT
65 ACCTTCCAAAAATTACCATATTACCC-CGAATCTTCCAAAAATCCCATTTTTGACCCCAAACCTT
*
51844 CCAAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGA
129 CCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
51892 CCCCG
1 CCCCG
51897 GACATCTACA
Statistics
Matches: 165, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
176 157 0.95
177 8 0.05
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.30
Consensus pattern (176 bp):
CCCCGAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTGACCCCAAA
CCTTCCAAAAATTACCATATTACCCCGAATCTTCCAAAAATCCCATTTTTGACCCCAAACCTTCC
AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
Found at i:60573 original size:21 final size:21
Alignment explanation
Indices: 60539--60602 Score: 119
Period size: 21 Copynumber: 3.0 Consensus size: 21
60529 GCTCTATTAT
60539 GAACTTCTGTACTAACTTGAGA
1 GAACTTC-GTACTAACTTGAGA
60561 GAACTTCGTACTAACTTGAGA
1 GAACTTCGTACTAACTTGAGA
60582 GAACTTCGTACTAACTTGAGA
1 GAACTTCGTACTAACTTGAGA
60603 AGTTGACTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 35 0.83
22 7 0.17
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (21 bp):
GAACTTCGTACTAACTTGAGA
Found at i:70895 original size:22 final size:22
Alignment explanation
Indices: 70870--70913 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
70860 GACATGAGTA
70870 TGTGAGACAATTGATTAGGGAC
1 TGTGAGACAATTGATTAGGGAC
70892 TGTGAGACAATTGATTAGGGAC
1 TGTGAGACAATTGATTAGGGAC
70914 GGTGTGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.27
Consensus pattern (22 bp):
TGTGAGACAATTGATTAGGGAC
Found at i:76913 original size:56 final size:57
Alignment explanation
Indices: 76851--76975 Score: 173
Period size: 56 Copynumber: 2.2 Consensus size: 57
76841 GTGAAACAAT
** * *
76851 AGTAAAAATAACA-TCCAAACAACAAAAATAGTAACCAAAACAGCAACAAAAATAAC
1 AGTAAAAATAACATTAAAAACAACAAAAATAGCAACAAAAACAGCAACAAAAATAAC
* *
76907 AGT-AAAACAACATTAAAAACAACAAAAATAGCAATAAAAACAGCAACAAAAATAAC
1 AGTAAAAATAACATTAAAAACAACAAAAATAGCAACAAAAACAGCAACAAAAATAAC
*
76963 AGCAAAAATAACA
1 AGTAAAAATAACA
76976 CGAAAATAGC
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
55 8 0.14
56 43 0.73
57 8 0.14
ACGTcount: A:0.66, C:0.18, G:0.06, T:0.10
Consensus pattern (57 bp):
AGTAAAAATAACATTAAAAACAACAAAAATAGCAACAAAAACAGCAACAAAAATAAC
Found at i:76957 original size:24 final size:24
Alignment explanation
Indices: 76924--77007 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
76914 CAACATTAAA
76924 AACAACAAAAATAGCAATAAAAAC
1 AACAACAAAAATAGCAATAAAAAC
* * ** *
76948 AGCAACAAAAATAACAGCAAAAAT
1 AACAACAAAAATAGCAATAAAAAC
* *
76972 AAC-ACGAAAATAGCAATCAAAAC
1 AACAACAAAAATAGCAATAAAAAC
* *
76995 AATAAAAAAAATA
1 AACAACAAAAATA
77008 ACTCAAAAAC
Statistics
Matches: 44, Mismatches: 15, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
23 16 0.36
24 28 0.64
ACGTcount: A:0.69, C:0.15, G:0.06, T:0.10
Consensus pattern (24 bp):
AACAACAAAAATAGCAATAAAAAC
Found at i:77049 original size:21 final size:21
Alignment explanation
Indices: 76989--77062 Score: 76
Period size: 23 Copynumber: 3.3 Consensus size: 21
76979 AAATAGCAAT
* *
76989 CAAAACAATAAAAAAAATAAC
1 CAAAACAGTAAAAAAAACAAC
*
77010 TCAAAAACAGCAAAAAAAAATCAAC
1 -C-AAAACAG-TAAAAAAAA-CAAC
*
77035 CAAAACAGTAAAAAAAACCAC
1 CAAAACAGTAAAAAAAACAAC
77056 CAAAACA
1 CAAAACA
77063 ACAATATGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 10 0.23
22 9 0.20
23 13 0.30
24 9 0.20
25 3 0.07
ACGTcount: A:0.70, C:0.20, G:0.03, T:0.07
Consensus pattern (21 bp):
CAAAACAGTAAAAAAAACAAC
Found at i:85964 original size:24 final size:24
Alignment explanation
Indices: 85931--85977 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
85921 TGTGTGGGGG
85931 GGGGGTTTGGAGGCAAATTAATGTT
1 GGGGGTTTGGAGGCAAA-TAATGTT
* *
85956 GGGGG-TTGGGGGGAAATAATGT
1 GGGGGTTTGGAGGCAAATAATGT
85978 AGGTAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 9 0.45
25 5 0.25
ACGTcount: A:0.23, C:0.02, G:0.47, T:0.28
Consensus pattern (24 bp):
GGGGGTTTGGAGGCAAATAATGTT
Found at i:86034 original size:4 final size:4
Alignment explanation
Indices: 86025--86056 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
86015 ACCAAACGGG
86025 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
86057 GAAGAAGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:89330 original size:36 final size:36
Alignment explanation
Indices: 89247--89390 Score: 220
Period size: 36 Copynumber: 4.0 Consensus size: 36
89237 AACAGGCATT
* *
89247 ACCTTTGGGTCAACAGGGAGTAAAATGAG-ATCTTG
1 ACCTTTGAGTCAACAGGGAGTAAAATGAGCATCATG
*
89282 ACCTTT-AGGTCAATAGGGAGTAAAATGAGCATCATG
1 ACCTTTGA-GTCAACAGGGAGTAAAATGAGCATCATG
89318 ACCTTTGAGTCAACAGGGAGTAAAATGAGCATCATG
1 ACCTTTGAGTCAACAGGGAGTAAAATGAGCATCATG
* *
89354 ACCTTTGTGTCAACAGGGAATAAAATGAGCATCATG
1 ACCTTTGAGTCAACAGGGAGTAAAATGAGCATCATG
89390 A
1 A
89391 ACAGATATAC
Statistics
Matches: 100, Mismatches: 6, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
35 26 0.26
36 73 0.73
37 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.24
Consensus pattern (36 bp):
ACCTTTGAGTCAACAGGGAGTAAAATGAGCATCATG
Found at i:89484 original size:36 final size:36
Alignment explanation
Indices: 89442--89577 Score: 227
Period size: 36 Copynumber: 3.8 Consensus size: 36
89432 TGGTAACAAG
*
89442 CATGACCTTTGGGTCAGCAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
89478 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
* * *
89514 CATAACCTTTGTGTCAATAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
*
89550 CATGACCTTTGTGTCAACAGGGAGTAAA
1 CATGACCTTTGGGTCAACAGGGAGTAAA
89578 TCGAATATTG
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 94 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.24
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
Found at i:90341 original size:21 final size:21
Alignment explanation
Indices: 90294--90344 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
90284 GAGTGTTTAA
*
90294 TATCGGTAGAAGTGTGACATG
1 TATCGGTAGAAGTATGACATG
* *
90315 TTTCGGTAGAAGTCAT-ACTTG
1 TATCGGTAGAAGT-ATGACATG
90336 TATCGGTAG
1 TATCGGTAG
90345 TATTGTCTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.33
Consensus pattern (21 bp):
TATCGGTAGAAGTATGACATG
Found at i:91208 original size:41 final size:40
Alignment explanation
Indices: 91163--91494 Score: 351
Period size: 41 Copynumber: 8.2 Consensus size: 40
91153 GAAAAAACAA
* * *
91163 CGCTAAAGGTCAGAGAATTAGCGGCGCTTATGAGAAAGCGC
1 CGCTAAAGGTCAGAGCATTAGCGGCGTTTTTG-GAAAGCGC
* * ** *
91204 CGCTAAAGGTCAGAGCATTAGCAGCGATTTTAAAGAAGCAC
1 CGCTAAAGGTCAGAGCATTAGCGGCGTTTTTGGA-AAGCGC
*
91245 CGCTAAAGGTCAGAGCATTAACGGCGTTTTTGGAGAAGCGC
1 CGCTAAAGGTCAGAGCATTAGCGGCGTTTTTGGA-AAGCGC
*
91286 CGCTAAAGGTCAGAGCATTAGCGGCGTTTTTGTAGAAGC-C
1 CGCTAAAGGTCAGAGCATTAGCGGCGTTTTTGGA-AAGCGC
* * * * *
91326 CGCTAAAGGTCAAAGCATTAGCAGCTTTTTTGGGAAGCGT
1 CGCTAAAGGTCAGAGCATTAGCGGCGTTTTTGGAAAGCGC
* * * *
91366 CGCTAAAGGTCAGAGCATTAACGGCATTTTTGGGAAGGTGC
1 CGCTAAAGGTCAGAGCATTAGCGGCGTTTTT-GGAAAGCGC
* *
91407 CGCTACAGGTCAGAGCATTAGCGGCATTTTTGGAGAAGCGC
1 CGCTAAAGGTCAGAGCATTAGCGGCGTTTTTGGA-AAGCGC
* * * * * *
91448 CGTTAAAGGTCAGGGCATTAGTGACATTTTTGGGAAAGCGT
1 CGCTAAAGGTCAGAGCATTAGCGGCGTTTTT-GGAAAGCGC
91489 CGCTAA
1 CGCTAA
91495 TTTATTTACA
Statistics
Matches: 246, Mismatches: 40, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
39 4 0.02
40 61 0.25
41 178 0.72
42 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (40 bp):
CGCTAAAGGTCAGAGCATTAGCGGCGTTTTTGGAAAGCGC
Found at i:91884 original size:24 final size:23
Alignment explanation
Indices: 91852--91902 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
91842 TTTATAATTC
*
91852 GATTGGTATAAGTATA-TTGTTAAT
1 GATTAGTATAAG-ATACTT-TTAAT
91876 GATTAGTATAAGATACTTTTAAT
1 GATTAGTATAAGATACTTTTAAT
91899 -ATTA
1 GATTA
91903 CCTAGAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 4 0.16
23 8 0.32
24 13 0.52
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.45
Consensus pattern (23 bp):
GATTAGTATAAGATACTTTTAAT
Found at i:96812 original size:108 final size:107
Alignment explanation
Indices: 96642--96874 Score: 378
Period size: 108 Copynumber: 2.2 Consensus size: 107
96632 AATATTTAAT
* * *
96642 TCAAAATATTAAATTATTTAATTATATTAAATAAATATTCAATTATTAAAAATAGAATAAATATT
1 TCAAAATATTAAATTATTTAATTATATTAAATAAATATTAAATTATTAAAAACAGAAAAAATATT
96707 AAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAA
66 AAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAA
*
96749 TCAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAACATAAAAAATAT
1 TCAAAATATTAAATTATTTAATTATA-TTAAATAAATATTAAATTATTAAAAACAGAAAAAATAT
*
96814 TGAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAA
65 TAAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAA
* *
96857 -CTAAACTATTTAATTATT
1 TC-AAAATATTAAATTATT
96875 AAAAAAACCA
Statistics
Matches: 117, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
107 27 0.23
108 90 0.77
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (107 bp):
TCAAAATATTAAATTATTTAATTATATTAAATAAATATTAAATTATTAAAAACAGAAAAAATATT
AAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAA
Found at i:96889 original size:69 final size:70
Alignment explanation
Indices: 96816--97010 Score: 322
Period size: 69 Copynumber: 2.8 Consensus size: 70
96806 AAAAATATTG
* * *
96816 AAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACTAAACTATTTAATTATTAAAAA-
1 AAATATTTAATTATTTAATAAGTTATTTATTAAACCCTAAACCAAACTATTTAATTATTAAAAAC
96880 AACCA
66 AACCA
**
96885 AAATATTTAATTATTTAATAAGTTATTTATTAAACTTTAAACCAAACTATTTAATTATTAAAAAC
1 AAATATTTAATTATTTAATAAGTTATTTATTAAACCCTAAACCAAACTATTTAATTATTAAAAAC
96950 AACCA
66 AACCA
96955 AAATATTTAATTATTTAATAAGTTATTTATTAAACCCTAAACCCAAA-TATTTAATT
1 AAATATTTAATTATTTAATAAGTTATTTATTAAACCCTAAA-CCAAACTATTTAATT
97011 CAAAATATTT
Statistics
Matches: 117, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
69 59 0.50
70 53 0.45
71 5 0.04
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.41
Consensus pattern (70 bp):
AAATATTTAATTATTTAATAAGTTATTTATTAAACCCTAAACCAAACTATTTAATTATTAAAAAC
AACCA
Found at i:97555 original size:18 final size:18
Alignment explanation
Indices: 97532--97573 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
97522 ATATTCGTGA
*
97532 AGTTGTCTATGAACATCT
1 AGTTGTCTACGAACATCT
97550 AGTTGTCTACGAACATCT
1 AGTTGTCTACGAACATCT
97568 AGTTGT
1 AGTTGT
97574 TGATGGCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (18 bp):
AGTTGTCTACGAACATCT
Found at i:103176 original size:43 final size:44
Alignment explanation
Indices: 103128--103316 Score: 179
Period size: 43 Copynumber: 4.4 Consensus size: 44
103118 AGTTGTTAAT
* * * *
103128 TTTAGCAGCGTTTGTGAGGGAAGCAG-CGTTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGAGGGAAACTGCCGCTAAAGACCATGTTC
* * ** * *
103171 TTTAGCGACGTTTGGGA-GGTCAGTGTCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGAGGGAAACTGCCGCTAAAGACCATGTTC
* * * *
103214 TTTAGCGGCATTTGTGTGGAAAAC-GCCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGAGGGAAACTGCCGCTAAAGACCATGTTC
* * * * *
103257 TTTTGCGGTGTTTTTG-GGGAAACTGCCGTTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGAGGGAAACTGCCGCTAAAGACCATGTTC
103300 TTTAGCGGCGTTTGTGA
1 TTTAGCGGCGTTTGTGA
103317 TCTTTAGTAA
Statistics
Matches: 114, Mismatches: 28, Indels: 7
0.77 0.19 0.05
Matches are distributed among these distances:
42 9 0.08
43 103 0.90
44 2 0.02
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (44 bp):
TTTAGCGGCGTTTGTGAGGGAAACTGCCGCTAAAGACCATGTTC
Found at i:103496 original size:43 final size:43
Alignment explanation
Indices: 103327--103498 Score: 211
Period size: 43 Copynumber: 4.0 Consensus size: 43
103317 TCTTTAGTAA
* *
103327 CGTTTGTGGGATAAGCGCCGCTAAAGACCATGTTCTTTAGCAG
1 CGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGG
* * ** * * *
103370 CGTTTGTGGGAAAAGTGTCGCTAAAGGTCATGGTCTTTAGTGA
1 CGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGG
* * *
103413 CATTTAT-GGTAAAGCGCCGCTAAAGACCATGTTCTTTAGCGG
1 CGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGG
* *
103455 CGTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGG
1 CGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGG
103498 C
1 C
103499 ATTTTTTCTC
Statistics
Matches: 104, Mismatches: 24, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
42 32 0.31
43 72 0.69
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (43 bp):
CGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGG
Found at i:103502 original size:85 final size:85
Alignment explanation
Indices: 103339--103502 Score: 238
Period size: 85 Copynumber: 1.9 Consensus size: 85
103329 TTTGTGGGAT
* * * **
103339 AAGCGCCGCTAAAGACCATGTTCTTTAGCAGCGTTTGTGGGAAAAGTGTCGCTAAAGGTCATGGT
1 AAGCGCCGCTAAAGACCATGTTCTTTAGCAGCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGGT
* *
103404 CTTTAGTGACATTTATGGTA
66 CTATAGCGACATTTATGGTA
* *
103424 AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGTT
1 AAGCGCCGCTAAAGACCATGTTCTTTAGCAGCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGGT
*
103489 CTATAGCGGCATTT
66 CTATAGCGACATTT
103503 TTTCTCAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 69 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (85 bp):
AAGCGCCGCTAAAGACCATGTTCTTTAGCAGCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGGT
CTATAGCGACATTTATGGTA
Found at i:104095 original size:43 final size:43
Alignment explanation
Indices: 104043--104147 Score: 126
Period size: 43 Copynumber: 2.5 Consensus size: 43
104033 ATGTTATTCA
* *
104043 TTGACATGTTATTAAATTATAGTACTTGACT-TGTGTTAATATGG
1 TTGACATGTTATTAAATTATAGTACTTGACTCT-TATTAATAT-C
* * *
104087 TTG-CATGTTACTAAATTAAATTACTTGACTCTTATTAATATC
1 TTGACATGTTATTAAATTATAGTACTTGACTCTTATTAATATC
104129 TTGACATGTTATT-AATTAT
1 TTGACATGTTATTAAATTAT
104148 GCAGTTCATA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
42 8 0.15
43 40 0.77
44 4 0.08
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (43 bp):
TTGACATGTTATTAAATTATAGTACTTGACTCTTATTAATATC
Found at i:107009 original size:24 final size:24
Alignment explanation
Indices: 106982--107031 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
106972 CATCATACAC
106982 GGAGTTGAATCTTCATTTTCTACT
1 GGAGTTGAATCTTCATTTTCTACT
107006 GGAGTTGAATCTTCATTTTCTACT
1 GGAGTTGAATCTTCATTTTCTACT
107030 GG
1 GG
107032 TTCCACATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.44
Consensus pattern (24 bp):
GGAGTTGAATCTTCATTTTCTACT
Found at i:109301 original size:17 final size:17
Alignment explanation
Indices: 109270--109321 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
109260 TATTATTTTT
*
109270 AAATTAA-AAATATATA
1 AAATTAATAAAAATATA
*
109286 AAATT-TTAAAACATAT-
1 AAATTAATAAAA-ATATA
109302 AAATTAATAAAAATATA
1 AAATTAATAAAAATATA
109319 AAA
1 AAA
109322 AAAATTTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 17 0.59
17 12 0.41
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATTAATAAAAATATA
Found at i:109521 original size:17 final size:17
Alignment explanation
Indices: 109434--109526 Score: 57
Period size: 17 Copynumber: 5.3 Consensus size: 17
109424 ATACTTGTAA
109434 ATTTATAAATTTTTAGT-T
1 ATTT-TAAATTTTTA-TAT
* * *
109452 CTTTTATATGTTTATATAA
1 ATTTTAAAT-TTT-TATAT
109471 ATTTATAAATTTTT-TATT
1 ATTT-TAAATTTTTATA-T
* * *
109489 AATCTAAA-TATTATAT
1 ATTTTAAATTTTTATAT
109505 ATTTTAAATTTTTATAT
1 ATTTTAAATTTTTATAT
109522 ATTTT
1 ATTTT
109527 TCAAAATATT
Statistics
Matches: 56, Mismatches: 12, Indels: 15
0.67 0.14 0.18
Matches are distributed among these distances:
16 10 0.18
17 24 0.43
18 10 0.18
19 8 0.14
20 4 0.07
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTTTAAATTTTTATAT
Found at i:109547 original size:62 final size:64
Alignment explanation
Indices: 109481--109600 Score: 147
Period size: 64 Copynumber: 1.9 Consensus size: 64
109471 ATTTATAAAT
* * *
109481 TTTTTAT-TA-ATCTAAATAT-TATATATTTTAAATTTTTATATATTTTTCAAAATATTGTAGGC
1 TTTTTATATATATCTAAAT-TGTATATATTTTAAATTTTTATAAATTTATAAAAATATTGTAGGC
* * * *
109543 TTTTTATATATTTTTTAATTGTATATATTTTATATTTTTATAAATTTATAAAAATATT
1 TTTTTATATATATCTAAATTGTATATATTTTAAATTTTTATAAATTTATAAAAATATT
109601 TATATATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
62 7 0.15
63 3 0.06
64 38 0.79
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (64 bp):
TTTTTATATATATCTAAATTGTATATATTTTAAATTTTTATAAATTTATAAAAATATTGTAGGC
Found at i:109584 original size:17 final size:17
Alignment explanation
Indices: 109543--109589 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
109533 TATTGTAGGC
*
109543 TTTTTATATATTTTTTA
1 TTTTTATATATTTTATA
* *
109560 ATTGTATATATTTTATA
1 TTTTTATATATTTTATA
*
109577 TTTTTATAAATTT
1 TTTTTATATATTT
109590 ATAAAAATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTTTATATATTTTATA
Found at i:120291 original size:16 final size:16
Alignment explanation
Indices: 120270--120303 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
120260 AAGCATCAGC
120270 TTAGAA-CTGAAACAAG
1 TTAGAACCTG-AACAAG
120286 TTAGAACCTGAACAAG
1 TTAGAACCTGAACAAG
120302 TT
1 TT
120304 GGTTATGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.24
Consensus pattern (16 bp):
TTAGAACCTGAACAAG
Found at i:125608 original size:28 final size:28
Alignment explanation
Indices: 125568--125696 Score: 93
Period size: 28 Copynumber: 4.5 Consensus size: 28
125558 GATAGGGTCA
125568 AAAATA-AAGTTTTGTAGA-ATTTGGGGTT
1 AAAATATAA-TTTTG-AGAGATTTGGGGTT
* *
125596 AAAATATAATTTTGAAAGATTTAAGGGTT
1 AAAATATAATTTTGAGAGATTT-GGGGTT
* * * * *
125625 AAAATGTGATTTTAAGAAAGTTTGAGGGTA
1 AAAATATAATTTTGAGAGA-TTTG-GGGTT
*
125655 AAAATATAATTTTG-GAAGATTTGGGGTC
1 AAAATATAATTTTGAG-AGATTTGGGGTT
* *
125683 AAAATGTGATTTTG
1 AAAATATAATTTTG
125697 GGAAGTTTAA
Statistics
Matches: 79, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
27 2 0.03
28 31 0.39
29 26 0.33
30 20 0.25
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.37
Consensus pattern (28 bp):
AAAATATAATTTTGAGAGATTTGGGGTT
Found at i:125875 original size:59 final size:58
Alignment explanation
Indices: 125591--126011 Score: 286
Period size: 59 Copynumber: 7.2 Consensus size: 58
125581 GTAGAATTTG
* * * * * *
125591 GGGTTAAAATATAATTTT-GAAAGATTTAAGGGTTAAAATGTGATTTTA-AGAAAGTTTGA
1 GGGTCAAAATGTAATTTTAAAAAG-TTTAGGGGTCAAAATGTAATTTTAGA-AAAGTTT-A
* * ** * **
125650 GGGTAAAAATATAATTTT-GGAAGATTT-GGGGTCAAAATGTGATTTT-GGGAAGTTTAA
1 GGGTCAAAATGTAATTTTAAAAAG-TTTAGGGGTCAAAATGTAATTTTAGAAAAGTTT-A
* * ** * *
125707 AGATTGAAAT-TAAATTTTAGAAAAG-TTCGAGGTCAAAA-GTAATTTTAGAAAAGTTTAA
1 GGGTCAAAATGT-AATTTTA-AAAAGTTTAGGGGTCAAAATGTAATTTTAGAAAAGTTT-A
* * * * * * *
125765 GGGTTAAAATGTATTTTTTTAAAAAGTTTAAGGGTTAGAATGTGATTTTAGAAAATTTTA
1 GGGTCAAAATGTA--ATTTTAAAAAGTTTAGGGGTCAAAATGTAATTTTAGAAAAGTTTA
* * *
125825 GGGACAAAATGTAATTTTAGGAAAGTTTAGGGGTCAAAATATAATTTTAGAAAAGTTTA
1 GGGTCAAAATGTAATTTTA-AAAAGTTTAGGGGTCAAAATGTAATTTTAGAAAAGTTTA
** * *
125884 GGGGTCAAAACATAATTTGAAAAAGTTTAGAGGT-AAAATTGTAATTTT-GAAAAGTTTA
1 -GGGTCAAAATGTAATTTTAAAAAGTTTAGGGGTCAAAA-TGTAATTTTAGAAAAGTTTA
* * * * *
125942 AGGTTAAAATGTAATTTTATAAAAGTTTTGGGGGTCAAAATGTATTTTTAGAAAAATTTA
1 GGGTCAAAATGTAATTTTA-AAAAG-TTTAGGGGTCAAAATGTAATTTTAGAAAAGTTTA
*
126002 GGGTTAAAAT
1 GGGTCAAAAT
126012 ATGTTTTTTA
Statistics
Matches: 289, Mismatches: 55, Indels: 35
0.76 0.15 0.09
Matches are distributed among these distances:
56 1 0.00
57 42 0.15
58 67 0.23
59 101 0.35
60 62 0.21
61 16 0.06
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.36
Consensus pattern (58 bp):
GGGTCAAAATGTAATTTTAAAAAGTTTAGGGGTCAAAATGTAATTTTAGAAAAGTTTA
Found at i:126019 original size:29 final size:29
Alignment explanation
Indices: 125591--126013 Score: 249
Period size: 29 Copynumber: 14.4 Consensus size: 29
125581 GTAGAATTTG
125591 GGGTTAAAATATAATTTT-G-AAAGATTTAA
1 GGGTTAAAATATAATTTTAGAAAAG-TTT-A
* *
125620 GGGTTAAAATGTGATTTTA-AGAAAGTTTGA
1 GGGTTAAAATATAATTTTAGA-AAAGTTT-A
* * * *
125650 GGGTAAAAATATAATTTTGGAAGA-TTTG
1 GGGTTAAAATATAATTTTAGAAAAGTTTA
* * * **
125678 GGGTCAAAATGTGATTTT-GGGAAGTTTAA
1 GGGTTAAAATATAATTTTAGAAAAGTTT-A
* * * *
125707 AGATTGAAAT-TAAATTTTAGAAAAG-TTC
1 GGGTTAAAATAT-AATTTTAGAAAAGTTTA
* *
125735 GAGGTCAAAA-GTAATTTTAGAAAAGTTTAA
1 G-GGTTAAAATATAATTTTAGAAAAGTTT-A
**
125765 GGGTTAAAATGTATTTTTTTA-AAAAGTTTAA
1 GGGTTAAAA--TATAATTTTAGAAAAGTTT-A
* * * *
125796 GGGTTAGAATGTGATTTTAGAAAATTTTA
1 GGGTTAAAATATAATTTTAGAAAAGTTTA
** * *
125825 GGGACAAAATGTAATTTTAGGAAAGTTTA
1 GGGTTAAAATATAATTTTAGAAAAGTTTA
*
125854 GGGGTCAAAATATAATTTTAGAAAAGTTTA
1 -GGGTTAAAATATAATTTTAGAAAAGTTTA
* * *
125884 GGGGTCAAAACATAATTTGA-AAAAGTTTA
1 -GGGTTAAAATATAATTTTAGAAAAGTTTA
*
125913 GAGG-TAAAATTGTAATTTT-GAAAAGTTTA
1 G-GGTTAAAA-TATAATTTTAGAAAAGTTTA
* * * *
125942 AGGTTAAAATGTAATTTTATAAAAGTTTTGG
1 GGGTTAAAATATAATTTTAGAAAAG-TTT-A
* * * *
125973 GGGTCAAAATGTATTTTTAGAAAAATTTA
1 GGGTTAAAATATAATTTTAGAAAAGTTTA
126002 GGGTTAAAATAT
1 GGGTTAAAATAT
126014 GTTTTTTAAA
Statistics
Matches: 306, Mismatches: 64, Indels: 48
0.73 0.15 0.11
Matches are distributed among these distances:
27 2 0.01
28 48 0.16
29 124 0.41
30 83 0.27
31 43 0.14
32 6 0.02
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.36
Consensus pattern (29 bp):
GGGTTAAAATATAATTTTAGAAAAGTTTA
Found at i:128227 original size:210 final size:210
Alignment explanation
Indices: 127848--128621 Score: 1093
Period size: 210 Copynumber: 3.7 Consensus size: 210
127838 TAATTTTCTA
* *
127848 TATCTCATCAGGAAGATGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCATCAGGAAGAT
1 TATCTCATCAGAAAGACGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCATCAGGAAGAT
* *
127913 GGGGGTTCGAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCTACTTCTTTGTATCTC
66 GGGGGTTCGAAGTTTCACTCACATTGAGCTTCACTTCATCGATTTGGTCTACTTCTCTGTATCTC
* * * *
127978 ATCAGGAAGATGACAACATCACTTGCTTTAATCCGCTTCTCTATATCTCATCAGGAATACGGATT
131 ATCAGGAAGATGACAGCATTACTTGTTTTAATCCGCTTCTCTATATCTCATCAGGAAGACGGATT
*
128043 TGGTCCACTTCTCAG
196 TGGTCCACTTCTCTG
* *
128058 TATCTCTTCAGAAAGACGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCATCAAGAAGAT
1 TATCTCATCAGAAAGACGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCATCAGGAAGAT
** * *
128123 GGGGGTTCGAAGTTTCACTCACATTGAGCTTCGTTTCATCGATTTGTTCTACTTCTCTATATCTC
66 GGGGGTTCGAAGTTTCACTCACATTGAGCTTCACTTCATCGATTTGGTCTACTTCTCTGTATCTC
* * * **
128188 ATCAGGAAGATGATAGCATTACTTGTTTTAATCCGCTTCTCTGTATCTCAACAAAAAGACGGATT
131 ATCAGGAAGATGACAGCATTACTTGTTTTAATCCGCTTCTCTATATCTCATCAGGAAGACGGATT
*
128253 TGGTCCACTTCTTTG
196 TGGTCCACTTCTCTG
* *
128268 TATCTCATCAGAAAGACGATCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCATTAGGAAGAT
1 TATCTCATCAGAAAGACGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCATCAGGAAGAT
* * * * *
128333 TGGGTTTGGAAGTTTCACTCACATTGAGCTTCACTTCGTTGGA-TTGGTCTACTTCTCTGTATCT
66 GGGGGTTCGAAGTTTCACTCACATTGAGCTTCACTTC-ATCGATTTGGTCTACTTCTCTGTATCT
* * * ** * *
128397 CATCAGGAAGATAACCGC-TTCATTTGTTTTAATCCAATTCTCTATATCTCATCAGGAGGACAGA
130 CATCAGGAAGATGACAGCATT-ACTTGTTTTAATCCGCTTCTCTATATCTCATCAGGAAGACGGA
*
128461 TTTGGTCCACTTTTCTG
194 TTTGGTCCACTTCTCTG
* * * * *
128478 TATCTCATCAGGAAGATGACCGCTTTGTTGCTTTGACCCACTTCTCAGTATATCATTAGGAAGAT
1 TATCTCATCAGAAAGACGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCATCAGGAAGAT
* * * * * *
128543 GGGGTTTGGAAGCTTCACTCACATTGAGCTTCACTTCATTGAATTGGTCTGCTTCTCTGTATCTC
66 GGGGGTTCGAAGTTTCACTCACATTGAGCTTCACTTCATCGATTTGGTCTACTTCTCTGTATCTC
128608 ATCAGGAAGATGAC
131 ATCAGGAAGATGAC
128622 TGCTTCATTG
Statistics
Matches: 504, Mismatches: 57, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
209 5 0.01
210 496 0.98
211 3 0.01
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.36
Consensus pattern (210 bp):
TATCTCATCAGAAAGACGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCATCAGGAAGAT
GGGGGTTCGAAGTTTCACTCACATTGAGCTTCACTTCATCGATTTGGTCTACTTCTCTGTATCTC
ATCAGGAAGATGACAGCATTACTTGTTTTAATCCGCTTCTCTATATCTCATCAGGAAGACGGATT
TGGTCCACTTCTCTG
Found at i:128551 original size:86 final size:85
Alignment explanation
Indices: 128376--128541 Score: 201
Period size: 86 Copynumber: 1.9 Consensus size: 85
128366 CTTCGTTGGA
* * *
128376 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATAACCGCTTCATTTGTTTTAATCCAATTCTCTA
1 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATAACCGCTT-ATTTGCTTTAACCCAATTCTCTA
* *
128441 TATCTCATCAGGAGGACAGAT
65 TATATCATCAGGAAGACAGAT
* * * *
128462 TTGGTCCACTTTTCTGTATCTCATCAGGAAGATGACCGCTT-TGTTGCTTTGACCCACTTCTC-A
1 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATAACCGCTTAT-TTGCTTTAACCCAATTCTCTA
*
128525 GTATATCATTAGGAAGA
65 -TATATCATCAGGAAGA
128542 TGGGGTTTGG
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
84 2 0.03
85 28 0.41
86 38 0.56
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (85 bp):
TTGGTCCACTTCTCTGTATCTCATCAGGAAGATAACCGCTTATTTGCTTTAACCCAATTCTCTAT
ATATCATCAGGAAGACAGAT
Found at i:130900 original size:20 final size:20
Alignment explanation
Indices: 130875--131353 Score: 439
Period size: 20 Copynumber: 24.2 Consensus size: 20
130865 TCCGCAGTGA
*
130875 ATCAGGCTTCGTGCCGGTGT
1 ATCAGGCTTTGTGCCGGTGT
* *
130895 ATCAGGCTTTGTGCCTGTGA
1 ATCAGGCTTTGTGCCGGTGT
* * *
130915 ATTAGGCTTCGTGCCGATGT
1 ATCAGGCTTTGTGCCGGTGT
*
130935 ATCAGGCTTTGTGCCGGTGA
1 ATCAGGCTTTGTGCCGGTGT
* *
130955 ATCAGGCTTCGTGCCGGTGA
1 ATCAGGCTTTGTGCCGGTGT
* *
130975 ATCAGGCTTCGTGCCGGTGA
1 ATCAGGCTTTGTGCCGGTGT
* *
130995 ATCAGGCTTCGTGCCAGTGT
1 ATCAGGCTTTGTGCCGGTGT
131015 ATCAGGCTTTGTGCCGGTGT
1 ATCAGGCTTTGTGCCGGTGT
* * * *
131035 ATCATGCTTCGTACCGGTGA
1 ATCAGGCTTTGTGCCGGTGT
** *
131055 ATCAGGCTTCATGCTGGTGT
1 ATCAGGCTTTGTGCCGGTGT
** *
131075 ATCAGGCTTTGTGTTGGTGA
1 ATCAGGCTTTGTGCCGGTGT
* **
131095 ATCAGGCTTTGTGCCAGAAT
1 ATCAGGCTTTGTGCCGGTGT
* *
131115 ATCAGGCTTTGTGCCAGTGA
1 ATCAGGCTTTGTGCCGGTGT
131135 ATCAGGC--T-T--CGGTGT
1 ATCAGGCTTTGTGCCGGTGT
* *
131150 ATCAGGCTTTGTGCTGCTGT
1 ATCAGGCTTTGTGCCGGTGT
* * *
131170 ATTAGGCTTTGTGCCAGAG-
1 ATCAGGCTTTGTGCCGGTGT
* *
131189 ACTCAGGCTTAGTGCCGGAGT
1 A-TCAGGCTTTGTGCCGGTGT
131210 ATCAGGCTTTGTGCCGGTGT
1 ATCAGGCTTTGTGCCGGTGT
* *
131230 ATCAAGCTTTGTGCCGTTGT
1 ATCAGGCTTTGTGCCGGTGT
** *
131250 ATCAGGCTTTGTGTTGGTGA
1 ATCAGGCTTTGTGCCGGTGT
* * * *
131270 ATCAAGCTTTATGCTGGTGA
1 ATCAGGCTTTGTGCCGGTGT
* * * *
131290 ATCGGGCTTCGTGCCGATGA
1 ATCAGGCTTTGTGCCGGTGT
**
131310 ATCAGGCTTTGTTTCGGTGT
1 ATCAGGCTTTGTGCCGGTGT
* *
131330 ATTAGGCTTTGTGCCGATGT
1 ATCAGGCTTTGTGCCGGTGT
131350 ATCA
1 ATCA
131354 AAGAACAAGT
Statistics
Matches: 372, Mismatches: 80, Indels: 14
0.80 0.17 0.03
Matches are distributed among these distances:
15 11 0.03
17 2 0.01
18 2 0.01
19 1 0.00
20 355 0.95
21 1 0.00
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.33
Consensus pattern (20 bp):
ATCAGGCTTTGTGCCGGTGT
Found at i:131427 original size:22 final size:21
Alignment explanation
Indices: 131387--131427 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
131377 ACAATGGTCG
*
131387 TCAATTACCTTAATTACTTTA
1 TCAATTACCTTAATGACTTTA
*
131408 TCAATTATCTTTAATGACTT
1 TCAATTA-CCTTAATGACTT
131428 ACCTCGTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.32, C:0.17, G:0.02, T:0.49
Consensus pattern (21 bp):
TCAATTACCTTAATGACTTTA
Found at i:134959 original size:31 final size:30
Alignment explanation
Indices: 134922--134983 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 30
134912 GTTATTTTAT
*
134922 ATATATATATATTTATAAGTTAGTGGGAGTG
1 ATATATATATATATATAAGTTAGT-GGAGTG
134953 ATATATATATATATATAAGTTAGTGGAGTG
1 ATATATATATATATATAAGTTAGTGGAGTG
134983 A
1 A
134984 GTTATTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.40
Consensus pattern (30 bp):
ATATATATATATATATAAGTTAGTGGAGTG
Found at i:135424 original size:20 final size:20
Alignment explanation
Indices: 135399--135940 Score: 530
Period size: 20 Copynumber: 27.1 Consensus size: 20
135389 CTATATATAT
* *
135399 TCAGGCTTTGTGCTGGTGAA
1 TCAGGCTTTGTGCCGGTGTA
* * *
135419 TCAGGCTTCGGGCCGCTGTA
1 TCAGGCTTTGTGCCGGTGTA
* * *
135439 TCAAGCTTTGTACCGGTGAA
1 TCAGGCTTTGTGCCGGTGTA
* *
135459 TTAGGCTTCGTGCCGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
* * *
135479 TCAAGCTTTGTGCTGGTGAA
1 TCAGGCTTTGTGCCGGTGTA
* * *
135499 TCAAGCTTCGTGCTGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
* * *
135519 TCAGGCTTCGTACCGATGTA
1 TCAGGCTTTGTGCCGGTGTA
*
135539 TCAGGCTTTGTGCCGGTGAA
1 TCAGGCTTTGTGCCGGTGTA
* **
135559 TCAGGCTTCGTGCCAATGTA
1 TCAGGCTTTGTGCCGGTGTA
* *
135579 TCAGGTTTTGTGTC-GTGTA
1 TCAGGCTTTGTGCCGGTGTA
* * *
135598 TCAGGCTTTATGCCGATGAA
1 TCAGGCTTTGTGCCGGTGTA
* * *
135618 TCAAGCTTCGTGCCGGAGTA
1 TCAGGCTTTGTGCCGGTGTA
*
135638 TCAGGCTTTGTGCCGGTGAA
1 TCAGGCTTTGTGCCGGTGTA
*
135658 TCAGGCTTCGTGCCGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
* * *
135678 TTAGGATTTGTGCCAGTGTA
1 TCAGGCTTTGTGCCGGTGTA
*
135698 TCAGGCTTTGTGCCGGTGAA
1 TCAGGCTTTGTGCCGGTGTA
* * *
135718 TCAGGCTTCGTGCTGGAGTA
1 TCAGGCTTTGTGCCGGTGTA
135738 TCAGGCTTTGTGCCGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
* **
135758 TCAGGCTTCGTGCTAGTGTA
1 TCAGGCTTTGTGCCGGTGTA
*
135778 TCAGGCTTTGTGCCGATGTA
1 TCAGGCTTTGTGCCGGTGTA
* *
135798 TCAAGCTTTGTGCCGTTGTA
1 TCAGGCTTTGTGCCGGTGTA
* * *
135818 TCAAGCTTTGTGCCGGAGAA
1 TCAGGCTTTGTGCCGGTGTA
* *
135838 TCAGGCTTTGTGTCGGTGAA
1 TCAGGCTTTGTGCCGGTGTA
* *
135858 TCAGGCTTCGTGCCGGTGAA
1 TCAGGCTTTGTGCCGGTGTA
**
135878 TCAAACTTTGTGCCGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
** *
135898 TCAGG-TCTTAAGCTGGTGTA
1 TCAGGCT-TTGTGCCGGTGTA
*
135918 TCAGGCTTTGTGTCGGTGTA
1 TCAGGCTTTGTGCCGGTGTA
135938 TCA
1 TCA
135941 AAGAACAAGT
Statistics
Matches: 418, Mismatches: 101, Indels: 6
0.80 0.19 0.01
Matches are distributed among these distances:
19 16 0.04
20 401 0.96
21 1 0.00
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.33
Consensus pattern (20 bp):
TCAGGCTTTGTGCCGGTGTA
Found at i:148162 original size:24 final size:24
Alignment explanation
Indices: 148133--148261 Score: 206
Period size: 24 Copynumber: 5.4 Consensus size: 24
148123 AAACTCTATT
148133 TGGGCTCGTAAGAGCTAATCATTT-
1 TGGGCTCGTAAGAGCTAATC-TTTC
* * *
148157 TAGGCTCATAAGAGCTAATCATTC
1 TGGGCTCGTAAGAGCTAATCTTTC
148181 TGGGCTCGTAAGAGCTAATCTTTC
1 TGGGCTCGTAAGAGCTAATCTTTC
*
148205 TGGGCTCGTAAAAGCTAATCTTTC
1 TGGGCTCGTAAGAGCTAATCTTTC
148229 TGGGCTCGTAAGAGCTAATCTTTC
1 TGGGCTCGTAAGAGCTAATCTTTC
148253 TGGGCTCGT
1 TGGGCTCGT
148262 GTTGCTAAAT
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
23 2 0.02
24 94 0.98
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (24 bp):
TGGGCTCGTAAGAGCTAATCTTTC
Found at i:150608 original size:58 final size:58
Alignment explanation
Indices: 150392--150744 Score: 327
Period size: 58 Copynumber: 6.0 Consensus size: 58
150382 TTTCAGAGAA
* * * *
150392 TTTAGGGTTAAAACGTAATTTTGGAAGA-TTTAGGGGTTAATATGTGATTTTAGG-AAAG
1 TTTAGGGTTAAAATGTAATTTTAGAAAAGTTTA-GGGTTAAAATGTGATTTT-GGAAAAG
* * * *
150450 TTTAGGGGTAAAATTGTAATTTTAGAAAA-TTTAGGGGTCAAAATATGATTTTGG-GAAG
1 TTTAGGGTTAAAA-TGTAATTTTAGAAAAGTTTA-GGGTTAAAATGTGATTTTGGAAAAG
* * * * ****
150508 TTCAAGGGTCAAAATGAAATTTTAGAAAAGTTCATAACTAAAATGTGATTTTGGAAAAG
1 TT-TAGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATGTGATTTTGGAAAAG
* * *
150567 TTTAAGGTTAAAATGTAATTTTGGAAAACTTTAGGGTTAAAATGTGATTTTGGAAAAG
1 TTTAGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATGTGATTTTGGAAAAG
* * * * * *
150625 TTTAGGGTTAAAACGTGATTTTAGAAATGTTTGGGGTTAAAATGTAATTTTAGAAAAG
1 TTTAGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATGTGATTTTGGAAAAG
* * * * * * *
150683 TTCAGGGGTAAAAATGCAATTTTGGAAAAGTTTGGAGGTCAAAATGTGACTTTGGAAAAG
1 TTTA-GGGTTAAAATGTAATTTTAGAAAAGTTTAG-GGTTAAAATGTGATTTTGGAAAAG
150743 TT
1 TT
150745 CGAGGTCAAA
Statistics
Matches: 238, Mismatches: 51, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
58 144 0.61
59 72 0.30
60 22 0.09
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.35
Consensus pattern (58 bp):
TTTAGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATGTGATTTTGGAAAAG
Found at i:150697 original size:30 final size:30
Alignment explanation
Indices: 150392--150764 Score: 295
Period size: 29 Copynumber: 12.8 Consensus size: 30
150382 TTTCAGAGAA
* * *
150392 TTTA-GGGTTAAAACGTAATTTTGGAAGA-
1 TTTAGGGGTTAAAATGTGATTTTGGAAAAG
*
150420 TTTAGGGGTTAATATGTGATTTTAGG-AAAG
1 TTTAGGGGTTAAAATGTGATTTT-GGAAAAG
* *
150450 TTTAGGGG-TAAAATTGTAATTTTAGAAAA-
1 TTTAGGGGTTAAAA-TGTGATTTTGGAAAAG
* * *
150479 TTTAGGGGTCAAAATATGATTTTGG-GAAG
1 TTTAGGGGTTAAAATGTGATTTTGGAAAAG
* * * ** *
150508 TTCAAGGGTCAAAATGAAATTTTAGAAAAG
1 TTTAGGGGTTAAAATGTGATTTTGGAAAAG
* ****
150538 TTCA-TAACTAAAATGTGATTTTGGAAAAG
1 TTTAGGGGTTAAAATGTGATTTTGGAAAAG
* * *
150567 TTTA-AGGTTAAAATGTAATTTTGGAAAAC
1 TTTAGGGGTTAAAATGTGATTTTGGAAAAG
150596 TTTA-GGGTTAAAATGTGATTTTGGAAAAG
1 TTTAGGGGTTAAAATGTGATTTTGGAAAAG
* * *
150625 TTTA-GGGTTAAAACGTGATTTTAGAAATG
1 TTTAGGGGTTAAAATGTGATTTTGGAAAAG
* *
150654 TTT-GGGGTTAAAATGTAATTTTAGAAAAG
1 TTTAGGGGTTAAAATGTGATTTTGGAAAAG
* * **
150683 TTCAGGGGTAAAAATGCAATTTTGGAAAAG
1 TTTAGGGGTTAAAATGTGATTTTGGAAAAG
* *
150713 TTT-GGAGGTCAAAATGTGACTTTGGAAAAG
1 TTTAGG-GGTTAAAATGTGATTTTGGAAAAG
* * *
150743 -TTCGAGGTCAAAATGTGATTTT
1 TTTAGGGGTTAAAATGTGATTTT
150765 TAAAGAAAAA
Statistics
Matches: 279, Mismatches: 54, Indels: 23
0.78 0.15 0.06
Matches are distributed among these distances:
28 6 0.02
29 195 0.70
30 78 0.28
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (30 bp):
TTTAGGGGTTAAAATGTGATTTTGGAAAAG
Found at i:152030 original size:27 final size:26
Alignment explanation
Indices: 151975--152031 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
151965 GTAGTGGCAG
* * *
151975 TGGTGGCAATTTGACTGGTGAGCAGT
1 TGGTGGCAATCTGACTGGCGAGCACT
152001 TGGTGGCAATGCTGACGTGGCG-GCACT
1 TGGTGGCAAT-CTGAC-TGGCGAGCACT
152028 TGGT
1 TGGT
152032 TGGAAGGGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 10 0.38
27 12 0.46
28 4 0.15
ACGTcount: A:0.16, C:0.16, G:0.40, T:0.28
Consensus pattern (26 bp):
TGGTGGCAATCTGACTGGCGAGCACT
Found at i:152967 original size:210 final size:210
Alignment explanation
Indices: 152553--153127 Score: 825
Period size: 210 Copynumber: 2.7 Consensus size: 210
152543 CTCTCGATCT
* * * *
152553 ACTTTTCTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTTAGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGACGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCAT
* *
152618 CAGGAAGATGGGGGTTCGAAGTTTCATTCACA-TGAGCTTCGCTTCATCAATTTGGTCTACTTCT
66 CAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATCAATTTGGTCTACTTCT
* * *
152682 CTGTATCTCATC-TGAAAGATGACCGCATCACTTGCTTTAATCCGCTTCTTTGTATCTCATCAGG
131 CTGTATCTCATCAAG-AAGATGACCGCATCACTTACTTTAATCCGCTTCTTTGTATCGCATCAGG
152746 AAGACGGATTTGGTCC
195 AAGACGGATTTGGTCC
* *
152762 ACTTCTCTGTATCTCATCAGGAAGACGACTGCTTTATTGCTTTGACCCACTTCTCAGTATCACAT
1 ACTTCTCTGTATCTCATCAGGAAGACGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCAT
* * *
152827 TAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTAGTCTACTTCT
66 CAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATCAATTTGGTCTACTTCT
* * * *
152892 CTGTATCTGATCAAGAAGATGACCGTATCACTTATTTTAATCTGCTT-TTCTGTATCGCATCAGG
131 CTGTATCTCATCAAGAAGATGACCGCATCACTTACTTTAATCCGCTTCTT-TGTATCGCATCAGG
* * *
152956 AGGATGGATTTGGTTC
195 AAGACGGATTTGGTCC
* * * *
152972 ACTTCTCTGTATCTCATTAGAAAGACTACCGCTTTATTGCTTTAACCCACTTCTCAGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGACGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCAT
* * * *
153037 CAGGAAGAT-GGGGTTTGGAAGTTTCACTCACATTGAGCTTCACTTCGTTAAATTGGTCTACTTC
66 CAGGAAGATGGGGGTTT-GAAGTTTCACTCACATTGAGCTTCGCTTCATCAATTTGGTCTACTTC
*
153101 TCTGTATCTCATCAAGAAGACGACCGC
130 TCTGTATCTCATCAAGAAGATGACCGC
153128 TTTATTGCTT
Statistics
Matches: 325, Mismatches: 37, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
209 97 0.30
210 227 0.70
211 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (210 bp):
ACTTCTCTGTATCTCATCAGGAAGACGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCAT
CAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATCAATTTGGTCTACTTCT
CTGTATCTCATCAAGAAGATGACCGCATCACTTACTTTAATCCGCTTCTTTGTATCGCATCAGGA
AGACGGATTTGGTCC
Found at i:153185 original size:124 final size:124
Alignment explanation
Indices: 152972--153437 Score: 700
Period size: 124 Copynumber: 3.8 Consensus size: 124
152962 GATTTGGTTC
* * *
152972 ACTTCTCTGTATCTCAT-TAGAAAGACTACCGCTTTATTGCTTTAACCCACTTCTCAGTATCTCA
1 ACTTCTCTGTATCTCATCAAG-AAGACGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCA
153036 TCAGGAAGATGGGGTTTGGAAGTTTCACTCACATTGAGCTTCACTTCGTTAAATTGGTCT
65 TCAGGAAGATGGGGTTTGGAAGTTTCACTCACATTGAGCTTCACTTCGTTAAATTGGTCT
153096 ACTTCTCTGTATCTCATCAAGAAGACGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCAT
1 ACTTCTCTGTATCTCATCAAGAAGACGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCAT
* *
153161 TAGGAAGATAGGGTTTGGAAGTTTCACTCACATTGAGCTTCACTTCGTTAAATTGGTCT
66 CAGGAAGATGGGGTTTGGAAGTTTCACTCACATTGAGCTTCACTTCGTTAAATTGGTCT
*
153220 ACTTCTCTGTATCTCATCAAGAAGACGACCGCTTTGTTGCTTTGACCCACTTCTCAGTATCTCAT
1 ACTTCTCTGTATCTCATCAAGAAGACGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCAT
* * *
153285 CAGGAAGATGGGGTTTGGAAGTTTTACTCACATTGAGATTCACTTCGTTGAATTGGTCT
66 CAGGAAGATGGGGTTTGGAAGTTTCACTCACATTGAGCTTCACTTCGTTAAATTGGTCT
* * * ** * * * **
153344 ACTTCTCTGTATCTTATCAGGAAGATGATTGCTTCATTGCTTTGACTCACTTTTTTGTATCTCAT
1 ACTTCTCTGTATCTCATCAAGAAGACGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCAT
* ** *
153409 CCGGAAGATGGATTTTTTGAAGTTTCACT
66 CAGGAAGATGG-GGTTTGGAAGTTTCACT
153438 TTTCCCTATG
Statistics
Matches: 313, Mismatches: 27, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
124 298 0.95
125 15 0.05
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.37
Consensus pattern (124 bp):
ACTTCTCTGTATCTCATCAAGAAGACGACCGCTTTATTGCTTTGACCCACTTCTCAGTATCTCAT
CAGGAAGATGGGGTTTGGAAGTTTCACTCACATTGAGCTTCACTTCGTTAAATTGGTCT
Found at i:161564 original size:24 final size:24
Alignment explanation
Indices: 161514--161565 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
161504 ATCATTATCG
* *
161514 TTTGTTCCTGTAACTGTTATTGCA
1 TTTGTTCCTGCAACTCTTATTGCA
* * *
161538 TTTGTTCCTGCATCTCTTTTTGGA
1 TTTGTTCCTGCAACTCTTATTGCA
161562 TTTG
1 TTTG
161566 CTCTAGCCTT
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:0.12, C:0.17, G:0.17, T:0.54
Consensus pattern (24 bp):
TTTGTTCCTGCAACTCTTATTGCA
Found at i:165412 original size:28 final size:29
Alignment explanation
Indices: 165380--165703 Score: 238
Period size: 29 Copynumber: 11.2 Consensus size: 29
165370 TTAAAACGTA
165380 ATTTTGG-AAGATTT-AGGGTCAAAATGTG
1 ATTTTGGAAAG-TTTGAGGGTCAAAATGTG
* *
165408 ATTTTGGGAAA-TTTAAGGGT-AAAATGTA
1 ATTTT-GGAAAGTTTGAGGGTCAAAATGTG
*
165436 ATTTTGG-AAGATTTGGGGGTCAAAATGTG
1 ATTTTGGAAAG-TTTGAGGGTCAAAATGTG
* **
165465 ATTTTGGAAAGTTCG-GAGGTCAAAATGAA
1 ATTTTGGAAAGTTTGAG-GGTCAAAATGTG
* *
165494 ATTTTAGAAAAGTTCGA-GGTCAAAATGTG
1 ATTTT-GGAAAGTTTGAGGGTCAAAATGTG
165523 ATTTTGGAAAAGTTT-AGGGATCAAAATGTG
1 ATTTTGG-AAAGTTTGAGGG-TCAAAATGTG
*
165553 ATTTGGGAAAGTTTGAGGGT-AAAATGTG
1 ATTTTGGAAAGTTTGAGGGTCAAAATGTG
* *
165581 ATTTTAGAAAAGTTTGAGGGTTAAAATGTG
1 ATTTT-GGAAAGTTTGAGGGTCAAAATGTG
*** * * * *
165611 ACTTTAAAAAAGTTTAAGGATTAAAATGTA
1 A-TTTTGGAAAGTTTGAGGGTCAAAATGTG
* * * * *
165641 ATTTTAGAAAAG-TTCAAGGTTAAAATGTA
1 ATTTT-GGAAAGTTTGAGGGTCAAAATGTG
* * *
165670 ATTTTGGAAAAG-TTCAGGGTTAAAATTTG
1 ATTTTGG-AAAGTTTGAGGGTCAAAATGTG
165699 ATTTT
1 ATTTT
165704 TTTTAAAAAT
Statistics
Matches: 248, Mismatches: 29, Indels: 37
0.79 0.09 0.12
Matches are distributed among these distances:
26 2 0.01
27 2 0.01
28 43 0.17
29 129 0.52
30 69 0.28
31 3 0.01
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (29 bp):
ATTTTGGAAAGTTTGAGGGTCAAAATGTG
Found at i:165564 original size:88 final size:87
Alignment explanation
Indices: 165423--165703 Score: 300
Period size: 88 Copynumber: 3.2 Consensus size: 87
165413 GGGAAATTTA
* * * * *
165423 AGGG-TAAAATGTAATTTTGGAAGA-TTTGGGGGTCAAAATGTGATTTTGGAAAGTTCGGAGGTC
1 AGGGTTAAAATGTGATTTTGGAAAAGTTTAGGGATCAAAATGTGATTTAGGAAAGTTC-GAGGT-
*
165486 AAAATGAAATTTTAGAAAAGTTCG
64 AAAATGTAATTTTAGAAAAGTTCG
* * *
165510 A-GGTCAAAATGTGATTTTGGAAAAGTTTAGGGATCAAAATGTGATTTGGGAAAGTTTGAGGGTA
1 AGGGTTAAAATGTGATTTTGGAAAAGTTTAGGGATCAAAATGTGATTTAGGAAAGTTCGA-GGTA
* *
165574 AAATGTGATTTTAGAAAAGTTTG
65 AAATGTAATTTTAGAAAAGTTCG
* ** * * * * *
165597 AGGGTTAAAATGTGACTTTAAAAAAGTTTAAGGATTAAAATGTAATTTTAGAAAAGTTCAAGGTT
1 AGGGTTAAAATGTGATTTTGGAAAAGTTTAGGGATCAAAATGTGA-TTTAGGAAAGTTCGAGG-T
*
165662 AAAATGTAATTTTGGAAAAGTTC-
64 AAAATGTAATTTTAGAAAAGTTCG
*
165685 AGGGTTAAAATTTGATTTT
1 AGGGTTAAAATGTGATTTT
165704 TTTTAAAAAT
Statistics
Matches: 162, Mismatches: 26, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
86 2 0.01
87 42 0.26
88 86 0.53
89 32 0.20
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (87 bp):
AGGGTTAAAATGTGATTTTGGAAAAGTTTAGGGATCAAAATGTGATTTAGGAAAGTTCGAGGTAA
AATGTAATTTTAGAAAAGTTCG
Found at i:166054 original size:87 final size:87
Alignment explanation
Indices: 165908--166084 Score: 291
Period size: 87 Copynumber: 2.0 Consensus size: 87
165898 AGGAAAAAAC
* * *
165908 ATGCGGATCCTAGTTGCGAAGCGGGTCGGATCCGGGTCTAAGGCTGGGTCTGAGACAAAACTACT
1 ATGCGAATCCTAGTTGCGAAGCAGGTCGAATCCGGGTCTAAGGCTGGGTCTGAGACAAAACTACT
165973 TCGTTTTGGCCTTTAAGTTTAG
66 TCGTTTTGGCCTTTAAGTTTAG
* * **
165995 ATGCGAATCCTAGTTGCGGAGCAGGTCGAATCCGGGTTTGGGGCTGGGTCTGAGACAAAACTACT
1 ATGCGAATCCTAGTTGCGAAGCAGGTCGAATCCGGGTCTAAGGCTGGGTCTGAGACAAAACTACT
166060 TCGTTTTGGCCTTTAAGTTTAG
66 TCGTTTTGGCCTTTAAGTTTAG
166082 ATG
1 ATG
166085 TCAAAACGAC
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (87 bp):
ATGCGAATCCTAGTTGCGAAGCAGGTCGAATCCGGGTCTAAGGCTGGGTCTGAGACAAAACTACT
TCGTTTTGGCCTTTAAGTTTAG
Found at i:172529 original size:29 final size:29
Alignment explanation
Indices: 172484--172560 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
172474 GCACCAGGTT
*
172484 GTGTATCAGCCCATGTGGCTCACATGGTC
1 GTGTATCAGCCCGTGTGGCTCACATGGTC
172513 GTGTATCAGCCCGTGTGGCTCACATGGTC
1 GTGTATCAGCCCGTGTGGCTCACATGGTC
* **
172542 ATGTGCCCAGCCCGTGTGG
1 GTGT-ATCAGCCCGTGTGG
172561 AATGATCTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 31 0.72
30 12 0.28
ACGTcount: A:0.14, C:0.29, G:0.31, T:0.26
Consensus pattern (29 bp):
GTGTATCAGCCCGTGTGGCTCACATGGTC
Found at i:178820 original size:13 final size:13
Alignment explanation
Indices: 178804--178829 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
178794 ACCACACACC
178804 TCTTTTTTTTTTT
1 TCTTTTTTTTTTT
178817 TCTTTTTTTTTTT
1 TCTTTTTTTTTTT
178830 GGTTTGAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TCTTTTTTTTTTT
Found at i:183068 original size:17 final size:15
Alignment explanation
Indices: 183034--183080 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 15
183024 CCACATCAGC
*
183034 AAAAAAATTTAAAGTT
1 AAAAAAA-TTAAAATT
183050 AAAATATAATTAAAATT
1 AAAA-A-AATTAAAATT
183067 AAAAAAATTAAAAT
1 AAAAAAATTAAAAT
183081 ACCCTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 9 0.32
16 5 0.18
17 12 0.43
18 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (15 bp):
AAAAAAATTAAAATT
Found at i:183620 original size:27 final size:28
Alignment explanation
Indices: 183585--183652 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
183575 GGGTGGTCGA
183585 ATTTGGAGATTTGTGGTAAGAG-TTTTG
1 ATTTGGAGATTTGTGGTAAGAGTTTTTG
* * * *
183612 ATTTGGAGATTTTTGTTTAGGGTTTTTG
1 ATTTGGAGATTTGTGGTAAGAGTTTTTG
183640 ATTTTGGAGATTT
1 A-TTTGGAGATTT
183653 TGGGTTAGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 18 0.51
28 6 0.17
29 11 0.31
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.51
Consensus pattern (28 bp):
ATTTGGAGATTTGTGGTAAGAGTTTTTG
Found at i:183660 original size:29 final size:27
Alignment explanation
Indices: 183585--183660 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 27
183575 GGGTGGTCGA
*
183585 ATTTGGAGA-TTTGTGGTAAGAGTTTTG
1 ATTTGGAGATTTTG-GGTTAGAGTTTTG
* * *
183612 ATTTGGAGATTTTTGTTTAGGGTTTTTG
1 ATTTGGAGATTTTGGGTTAGAG-TTTTG
183640 ATTTTGGAGATTTTGGGTTAG
1 A-TTTGGAGATTTTGGGTTAG
183661 TGCTCTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 14 0.35
28 9 0.22
29 17 0.43
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (27 bp):
ATTTGGAGATTTTGGGTTAGAGTTTTG
Found at i:184032 original size:14 final size:14
Alignment explanation
Indices: 184013--184039 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
184003 GTGGTGGAAA
184013 TCAAAATAAAAAAC
1 TCAAAATAAAAAAC
184027 TCAAAATAAAAAA
1 TCAAAATAAAAAA
184040 TTCATTTGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.15
Consensus pattern (14 bp):
TCAAAATAAAAAAC
Found at i:184256 original size:9 final size:9
Alignment explanation
Indices: 184232--184290 Score: 51
Period size: 9 Copynumber: 7.1 Consensus size: 9
184222 TGATAATATT
184232 ATAATTTTAAA
1 ATAATTTT--A
184243 ATAATTTTA
1 ATAATTTTA
184252 ATAATTTT-
1 ATAATTTTA
184260 AT-ATTTTA
1 ATAATTTTA
184268 A-AA----A
1 ATAATTTTA
184272 ATAATTTTA
1 ATAATTTTA
184281 ATAATTTTA
1 ATAATTTTA
184290 A
1 A
184291 AATAATTTGC
Statistics
Matches: 41, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
7 5 0.12
8 4 0.10
9 20 0.49
11 8 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATAATTTTA
Found at i:184257 original size:20 final size:20
Alignment explanation
Indices: 184232--184298 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
184222 TGATAATATT
184232 ATAATTTTAAAATAATTTT--A
1 ATAATTTT--AATAATTTTAAA
184252 ATAATTTT-AT-ATTTTAAAAA
1 ATAATTTTAATAATTTT--AAA
184272 ATAATTTTAATAATTTTAAA
1 ATAATTTTAATAATTTTAAA
184292 ATAATTT
1 ATAATTT
184299 GCTAACGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
16 5 0.12
17 2 0.05
20 27 0.66
21 2 0.05
22 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAATTTTAATAATTTTAAA
Found at i:184282 original size:29 final size:28
Alignment explanation
Indices: 184224--184289 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 28
184214 GAACGGGATG
*
184224 ATAATATTATAATTTTAAAATAATTTTA
1 ATAATTTTATAATTTTAAAATAATTTTA
184252 ATAATTTTAT-ATTTTAAAAAATAATTTTA
1 ATAATTTTATAATTTT--AAAATAATTTTA
184281 ATAATTTTA
1 ATAATTTTA
184290 AAATAATTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
27 5 0.14
28 9 0.26
29 21 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATAATTTTATAATTTTAAAATAATTTTA
Found at i:186531 original size:15 final size:15
Alignment explanation
Indices: 186511--186542 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
186501 ATGGACTTTA
186511 TTTTTATTTGTTTGT
1 TTTTTATTTGTTTGT
*
186526 TTTTTATTTTTTTGT
1 TTTTTATTTGTTTGT
186541 TT
1 TT
186543 ATGGGCTGGA
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:0.06, C:0.00, G:0.09, T:0.84
Consensus pattern (15 bp):
TTTTTATTTGTTTGT
Found at i:186947 original size:36 final size:36
Alignment explanation
Indices: 186896--186984 Score: 117
Period size: 36 Copynumber: 2.5 Consensus size: 36
186886 CGAAGGGAGG
* * *
186896 AGACGAGGCCAAAGATCAACTCC-GACGTGCTCATGA
1 AGACGAGGCCGAAGATCAAC-CCTAACGTGCGCATGA
*
186932 AGACGAGGCCGAAGATTAACCCTAACGTGCGCATGA
1 AGACGAGGCCGAAGATCAACCCTAACGTGCGCATGA
*
186968 AGACGAGGCTGAAGATC
1 AGACGAGGCCGAAGATC
186985 TAGTGGATTC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 2 0.04
36 44 0.96
ACGTcount: A:0.34, C:0.25, G:0.28, T:0.13
Consensus pattern (36 bp):
AGACGAGGCCGAAGATCAACCCTAACGTGCGCATGA
Found at i:187862 original size:23 final size:23
Alignment explanation
Indices: 187835--187884 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
187825 GATGAAACCA
187835 ATTTTTAT-AATTTTTAATAATTT
1 ATTTTTATGAA-TTTTAATAATTT
187858 ATTTTTATGAATTTTAATAATTT
1 ATTTTTATGAATTTTAATAATTT
187881 ATTT
1 ATTT
187885 AATAGAATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 24 0.92
24 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
ATTTTTATGAATTTTAATAATTT
Found at i:189444 original size:21 final size:21
Alignment explanation
Indices: 189415--189459 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
189405 TGTTTTAAAC
* * *
189415 TTTATTTTTAATATAATTATT
1 TTTAATTTTAATAAAAATATT
189436 TTTAATTTTAATAAAAATATT
1 TTTAATTTTAATAAAAATATT
189457 TTT
1 TTT
189460 TTTAGTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTAATTTTAATAAAAATATT
Found at i:192926 original size:14 final size:15
Alignment explanation
Indices: 192907--192936 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
192897 AATAGAGTTT
192907 AAAGTAAAAA-AAAA
1 AAAGTAAAAACAAAA
192921 AAAGTAAAAACAAAA
1 AAAGTAAAAACAAAA
192936 A
1 A
192937 GATTCAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.83, C:0.03, G:0.07, T:0.07
Consensus pattern (15 bp):
AAAGTAAAAACAAAA
Found at i:196698 original size:27 final size:27
Alignment explanation
Indices: 196660--196715 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
196650 ACCACTCCCT
196660 TAACACCTAAATGTCATAATATTCTAC
1 TAACACCTAAATGTCATAATATTCTAC
196687 TAACACCTAAATGTCATAATATTCTAC
1 TAACACCTAAATGTCATAATATTCTAC
196714 TA
1 TA
196716 TCTCATTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.34
Consensus pattern (27 bp):
TAACACCTAAATGTCATAATATTCTAC
Found at i:205636 original size:21 final size:22
Alignment explanation
Indices: 205610--205748 Score: 104
Period size: 23 Copynumber: 6.1 Consensus size: 22
205600 ATACAGAACA
*
205610 AACAGAGAGTAC-CAAAGTACT
1 AACAGAGAGCACACAAAGTACT
* *
205631 AACAGAGAGCACA-TAAGTGCTGGGT
1 AACAGAGAGCACACAAAGTAC----T
*
205656 AACAGAGAGCACACACAA-TGCT
1 AACAGAGAGCACACA-AAGTACT
*
205678 AAACAGAGAGTACACAAAGTACT
1 -AACAGAGAGCACACAAAGTACT
*
205701 AATCAGAGAGCACACAAAGTGCT
1 AA-CAGAGAGCACACAAAGTACT
* * *
205724 AGTCAGAGAGCACACACAGTGCT
1 A-ACAGAGAGCACACAAAGTACT
205747 AA
1 AA
205749 TAACAGAGAG
Statistics
Matches: 96, Mismatches: 11, Indels: 21
0.75 0.09 0.16
Matches are distributed among these distances:
21 16 0.17
22 5 0.05
23 56 0.58
25 14 0.15
26 3 0.03
27 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (22 bp):
AACAGAGAGCACACAAAGTACT
Found at i:205682 original size:23 final size:23
Alignment explanation
Indices: 205656--205782 Score: 116
Period size: 23 Copynumber: 5.4 Consensus size: 23
205646 AGTGCTGGGT
205656 AACAGAGAGCACACACAATGCTA
1 AACAGAGAGCACACACAATGCTA
* *
205679 AACAGAGAGTACACA-AAGTACTA
1 AACAGAGAGCACACACAA-TGCTA
*
205702 ATCAGAGAGCACACA-AAGTGCTA
1 AACAGAGAGCACACACAA-TGCTA
** *
205725 GTCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAATGCT-A
* *
205749 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAATGCTA
205773 AACAGAGAGC
1 AACAGAGAGC
205783 GCGCTGGTGT
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.02
23 66 0.74
24 3 0.03
25 15 0.17
26 3 0.03
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACACAATGCTA
Found at i:205687 original size:48 final size:44
Alignment explanation
Indices: 205631--205782 Score: 121
Period size: 48 Copynumber: 3.2 Consensus size: 44
205621 CCAAAGTACT
205631 AACAGAGAGCACATAAGTGCTGGGTAACAGAGAGCACACACAATGCTA
1 AACAGAGAGCACA-AAGTGCT---TAACAGAGAGCACACACAATGCTA
*
205679 AACAGAGAGTACACAAAGTAC-TAATCAGAGAGCACACA-AAGTGCTA
1 AACAGAGAG--CACAAAGTGCTTAA-CAGAGAGCACACACAA-TGCTA
** * *
205725 GTCAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAGAC-GTGCTA
1 AACAGAGAGCACA-A-AGTGCT--TAACAGAGAGCAC-ACACAATGCTA
205773 AACAGAGAGC
1 AACAGAGAGC
205783 GCGCTGGTGT
Statistics
Matches: 85, Mismatches: 8, Indels: 22
0.74 0.07 0.19
Matches are distributed among these distances:
44 4 0.05
45 6 0.07
46 29 0.34
48 32 0.38
49 10 0.12
50 4 0.05
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (44 bp):
AACAGAGAGCACAAAGTGCTTAACAGAGAGCACACACAATGCTA
Found at i:205708 original size:46 final size:47
Alignment explanation
Indices: 205657--205782 Score: 141
Period size: 46 Copynumber: 2.7 Consensus size: 47
205647 GTGCTGGGTA
*
205657 ACAGAGAGCACACACAATGCTAAACAGAGAGTACACAAAGTACTAAT
1 ACAGAGAGCACACACAATGCTAAACAGAGAGCACACAAAGTACTAAT
** * *
205704 -CAGAGAGCACACA-AAGTGCTAGTCAGAGAGCACACACAGTGCTAAT
1 ACAGAGAGCACACACAA-TGCTAAACAGAGAGCACACAAAGTACTAAT
* *
205750 AACAGAGAGCACGAGAC-GTGCTAAACAGAGAGC
1 -ACAGAGAGCAC-ACACAATGCTAAACAGAGAGC
205783 GCGCTGGTGT
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
45 2 0.03
46 38 0.58
48 23 0.35
49 2 0.03
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (47 bp):
ACAGAGAGCACACACAATGCTAAACAGAGAGCACACAAAGTACTAAT
Found at i:205731 original size:69 final size:69
Alignment explanation
Indices: 205609--205758 Score: 207
Period size: 69 Copynumber: 2.1 Consensus size: 69
205599 TATACAGAAC
* *
205609 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGTAACAGAGAGCACACACAA
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAGT-ACAGAGAGCACACACAA
205674 TGCT-
65 TGCTA
205678 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AGT-CAGAGAGCACACAC
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAGTACAGAGAGCACACAC
*
205741 AGTGCTA
63 AATGCTA
205748 ATAACAGAGAG
1 A-AACAGAGAG
205759 CACGAGACGT
Statistics
Matches: 73, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
69 32 0.44
70 12 0.16
71 22 0.30
72 7 0.10
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (69 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAGTACAGAGAGCACACACAAT
GCTA
Found at i:206611 original size:18 final size:18
Alignment explanation
Indices: 206588--206625 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
206578 GAAATTAAAC
206588 TATAATTCAAAACTCTTG
1 TATAATTCAAAACTCTTG
206606 TATAATTCAAAACTCTTG
1 TATAATTCAAAACTCTTG
206624 TA
1 TA
206626 GTACTTACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (18 bp):
TATAATTCAAAACTCTTG
Found at i:207712 original size:18 final size:18
Alignment explanation
Indices: 207691--207726 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
207681 TTTAAAAATT
*
207691 ATAAAAATATTCAAAAAA
1 ATAAAAAAATTCAAAAAA
*
207709 ATAAAAAAATTTAAAAAA
1 ATAAAAAAATTCAAAAAA
207727 TATATGTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (18 bp):
ATAAAAAAATTCAAAAAA
Found at i:208736 original size:35 final size:35
Alignment explanation
Indices: 208690--208762 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
208680 TTTTATGTGT
208690 TAGTCTGATGATTAGGGTGTTTATCATTTCAAATA
1 TAGTCTGATGATTAGGGTGTTTATCATTTCAAATA
* *
208725 TAGTCTGATGATTAGGGTGTTTATCGTTTTAAATA
1 TAGTCTGATGATTAGGGTGTTTATCATTTCAAATA
208760 TAG
1 TAG
208763 CTTGAGTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (35 bp):
TAGTCTGATGATTAGGGTGTTTATCATTTCAAATA
Found at i:208849 original size:21 final size:20
Alignment explanation
Indices: 208815--208853 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
208805 TGTAATTCAT
208815 TAAAAATATATATTATTTTG
1 TAAAAATATATATTATTTTG
*
208835 TAAAATATATGTATTATTT
1 TAAAA-ATATATATTATTT
208854 AATAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
TAAAAATATATATTATTTTG
Found at i:208859 original size:21 final size:21
Alignment explanation
Indices: 208815--208865 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
208805 TGTAATTCAT
**
208815 TAAAA-ATATATATTATTTTG
1 TAAAATATATATATTATTTAA
*
208835 TAAAATATATGTATTATTTAA
1 TAAAATATATATATTATTTAA
208856 T-AAATATATA
1 TAAAATATATA
208866 ATTCTTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (21 bp):
TAAAATATATATATTATTTAA
Found at i:208930 original size:23 final size:23
Alignment explanation
Indices: 208900--208955 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
208890 AAATTTTGAT
208900 ATTAAACCAAACCCAATAACACA
1 ATTAAACCAAACCCAATAACACA
208923 ATTAAACCAAACCCAATAACACA
1 ATTAAACCAAACCCAATAACACA
*
208946 ATTAACCCAA
1 ATTAAACCAA
208956 TTAAAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.55, C:0.30, G:0.00, T:0.14
Consensus pattern (23 bp):
ATTAAACCAAACCCAATAACACA
Found at i:209886 original size:14 final size:14
Alignment explanation
Indices: 209867--209898 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
209857 CATATGTATG
209867 GTGTAACCTAATCC
1 GTGTAACCTAATCC
209881 GTGTAACCTAATCC
1 GTGTAACCTAATCC
209895 GTGT
1 GTGT
209899 TTTTCAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (14 bp):
GTGTAACCTAATCC
Found at i:213210 original size:21 final size:21
Alignment explanation
Indices: 213166--213208 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
213156 ATTTTAAAAT
*
213166 ATTTTTATGAAGTATTTCTAA
1 ATTTTTATGAAGTATTGCTAA
213187 ATTTTTATGAAGTATATGCTAA
1 ATTTTTATGAAGTAT-TGCTAA
213209 TTATCACAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.49
Consensus pattern (21 bp):
ATTTTTATGAAGTATTGCTAA
Found at i:216440 original size:59 final size:57
Alignment explanation
Indices: 216322--216670 Score: 269
Period size: 59 Copynumber: 5.9 Consensus size: 57
216312 AAAATTTGCT
*
216322 TGGTCGACACCCTTTTTCAGTC-AGAT-AAAAAATATAATTTTTT-GTGTTGGCCATACAA
1 TGGTCGACACCCTTTTT-A-TCTA-ATAAAAAAATA-AATTTTTTGGTGTTGGCCATGCAA
* *
216380 TGGCCGACACCCTTATTTATCTAATAAAAAAATCAAATTTTTTGGTGTTTGCCATGCAA
1 TGGTCGACACCCTT-TTTATCTAATAAAAAAAT-AAATTTTTTGGTGTTGGCCATGCAA
* * * * **
216439 TGATCGACACCCTTTTT-TTTAGATAAAAAATTTCAAAATTTTTTTGTGTTGGTTATGCAA
1 TGGTCGACACCCTTTTTATCTA-ATAAAAAA-AT--AAATTTTTTGGTGTTGGCCATGCAA
* * * ** * *
216499 TGGTCGACACCTCCTTTTCTCGAATAAAAAAATTGCATTTTTAGGTGTTGACCATGCAA
1 TGGTCGACACC-CTTTTTATCTAATAAAAAAA-TAAATTTTTTGGTGTTGGCCATGCAA
* * * * *
216558 CGGTCGACACCCTTTTTTTGTCAGAT-AAAAAATACAATTTTTT-GTGTAGGCCATACAA
1 TGGTCGACACCCTTTTTATCT-A-ATAAAAAAATA-AATTTTTTGGTGTTGGCCATGCAA
* * * * *
216616 TGGCCGACACCACTATTTATTTGATAAAAAAATTAAATTTTTTGGTGTCGGCCAT
1 TGGTCGACACC-CTTTTTATCTAATAAAAAAA-TAAATTTTTTGGTGTTGGCCAT
216671 TTTCAGATAA
Statistics
Matches: 231, Mismatches: 42, Indels: 35
0.75 0.14 0.11
Matches are distributed among these distances:
57 9 0.04
58 83 0.36
59 90 0.39
60 33 0.14
61 14 0.06
62 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (57 bp):
TGGTCGACACCCTTTTTATCTAATAAAAAAATAAATTTTTTGGTGTTGGCCATGCAA
Found at i:216500 original size:119 final size:118
Alignment explanation
Indices: 216325--216663 Score: 402
Period size: 119 Copynumber: 2.9 Consensus size: 118
216315 ATTTGCTTGG
** *
216325 TCGACACCCTTTTTCAGTCAGATAAAAAATATAATTTTTTGTGTTGGCCATACAATGGCCGACAC
1 TCGACACCCTTTTTTTGTCAGATAAAAAATAAAATTTTTTGTGTTGGCCATACAATGGCCGACAC
* *
216390 C-CTTATTTATCTAATAAAAAAATCAAATTTTTTGGTGTTTG-CCATGCAATGA
66 CAC-TATTTATCTAATAAAAAAATTAAATTTTTTGGTGTTTGACCATGCAACGA
** * *
216442 TCGACACCCTTTTTTT-T-AGATAAAAAATTTCAAAATTTTTTTGTGTTGGTTATGCAATGGTCG
1 TCGACACCCTTTTTTTGTCAGATAAAAAA--T-AAAA-TTTTTTGTGTTGGCCATACAATGGCCG
* * * ** * *
216505 ACACCTCCT-TTTCTCGAATAAAAAAATTGCATTTTTAGGTG-TTGACCATGCAACGG
62 ACACC-ACTATTTATCTAATAAAAAAATTAAATTTTTTGGTGTTTGACCATGCAACGA
* *
216561 TCGACACCCTTTTTTTGTCAGATAAAAAATACAATTTTTTGTGTAGGCCATACAATGGCCGACAC
1 TCGACACCCTTTTTTTGTCAGATAAAAAATAAAATTTTTTGTGTTGGCCATACAATGGCCGACAC
* *
216626 CACTATTTATTTGATAAAAAAATTAAATTTTTTGGTGT
66 CACTATTTATCTAATAAAAAAATTAAATTTTTTGGTGT
216664 CGGCCATTTT
Statistics
Matches: 182, Mismatches: 29, Indels: 21
0.78 0.12 0.09
Matches are distributed among these distances:
115 10 0.05
116 3 0.02
117 67 0.37
118 9 0.05
119 80 0.44
120 2 0.01
121 11 0.06
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (118 bp):
TCGACACCCTTTTTTTGTCAGATAAAAAATAAAATTTTTTGTGTTGGCCATACAATGGCCGACAC
CACTATTTATCTAATAAAAAAATTAAATTTTTTGGTGTTTGACCATGCAACGA
Found at i:216693 original size:216 final size:216
Alignment explanation
Indices: 216454--216879 Score: 617
Period size: 216 Copynumber: 2.0 Consensus size: 216
216444 GACACCCTTT
* * * ** *
216454 TTTTTAGATAAAAAATTTCAAAATTTTTTTGTGTTGGTTATGCAATGGTCGACACCTC-CTTTTC
1 TTTTCAGATAAAAAATTTCAAAATTTTTTGGTGTTAGCCATGCAATGGTCAACACC-CACTTTTC
* *
216518 TCGAATAAAAAAATTGCA-TTTTTAGGTGTT-GACCATGCAACGGTCGACACCCTTTTTTTGTCA
65 TCGAATAAAAAAATTGCATTTTTTA-GTGTTAG-CCATGCAACGGCCGACACCCCTTTTTTGTCA
* *
216581 GATAAAAAATACAA-TTTTTTGTGTAGGCCATACAATGGCCGACACCACTATTTATTTGATAAAA
128 GAT-AAAAATACAATTTTTTTGTGTAGGCCATACAATGACCGACACCACTATTTATCTGATAAAA
* *
216645 AAATTAAATTTTTTGGTGTCGGCCA
192 AAATCAAATTTTTGGGTGTCGGCCA
216670 TTTTCAGATAAAAAATTTCAAAATTTTTTGGTGTTAGCCATGCAATGGTCAACACCCACTTTTCT
1 TTTTCAGATAAAAAATTTCAAAATTTTTTGGTGTTAGCCATGCAATGGTCAACACCCACTTTTCT
* ** * *
216735 CGGATAAAAATTTTTCATTTTTTAGTGTTAGCCATGCAATGGCCGACACCCCTTTTTTGTCAGAT
66 CGAATAAAAAAATTGCATTTTTTAGTGTTAGCCATGCAACGGCCGACACCCCTTTTTTGTCAGAT
* *
216800 AAAAATACAATTTTTTTGTGTTGGCCATACAATGACCGACACCCCTATTTATCTGATAAAAAAAT
131 AAAAATACAATTTTTTTGTGTAGGCCATACAATGACCGACACCACTATTTATCTGATAAAAAAAT
216865 CAAATTTTTGGGTGT
196 CAAATTTTTGGGTGT
216880 TAGCTATACA
Statistics
Matches: 187, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
215 11 0.06
216 169 0.90
217 7 0.04
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (216 bp):
TTTTCAGATAAAAAATTTCAAAATTTTTTGGTGTTAGCCATGCAATGGTCAACACCCACTTTTCT
CGAATAAAAAAATTGCATTTTTTAGTGTTAGCCATGCAACGGCCGACACCCCTTTTTTGTCAGAT
AAAAATACAATTTTTTTGTGTAGGCCATACAATGACCGACACCACTATTTATCTGATAAAAAAAT
CAAATTTTTGGGTGTCGGCCA
Found at i:216827 original size:58 final size:57
Alignment explanation
Indices: 216691--216918 Score: 194
Period size: 59 Copynumber: 3.9 Consensus size: 57
216681 AAAATTTCAA
* * * * *
216691 AATTTTTTGGTGTTAGCCATGCAATGGTCAACACCCAC-TTTTCTCGGATAAAAATTTTTC
1 AATTTTTTGGTGTTAGCCATACAATGGCCAACACCC-CTTTTTATCAGATAAAAA---TAC
* * * *
216751 -ATTTTTTAGTGTTAGCCATGCAATGGCCGACACCCCTTTTTTGTCAGATAAAAATAC
1 AATTTTTTGGTGTTAGCCATACAATGGCCAACACCCC-TTTTTATCAGATAAAAATAC
* * * * * * *
216808 AATTTTTTTGTGTTGGCCATACAATGACCGACACCCCTATTTATCTGATAAAAAAATC
1 AATTTTTTGGTGTTAGCCATACAATGGCCAACACCCCTTTTTATCAGATAAAAATA-C
* *
216866 AAATTTTTGGGTGTTAGCTATACAATGGCCAACACTCCC-TTTT-TCAGATAAAA
1 -AATTTTTTGGTGTTAGCCATACAATGGCCAACAC-CCCTTTTTATCAGATAAAA
216919 GAATTTTAAA
Statistics
Matches: 140, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
57 17 0.12
58 43 0.31
59 63 0.45
60 17 0.12
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (57 bp):
AATTTTTTGGTGTTAGCCATACAATGGCCAACACCCCTTTTTATCAGATAAAAATAC
Found at i:217155 original size:61 final size:61
Alignment explanation
Indices: 217083--217420 Score: 368
Period size: 61 Copynumber: 5.6 Consensus size: 61
217073 AAAAAATTGT
* *
217083 ATTTTTGGGTGTTGGCCATGCAATGTCCGACATCCCCTTTTTCAGATAAAAAAAATTCAAA
1 ATTTTTTGGTGTTGGCCATGCAATGTCCGACACCCCCTTTTTCAGATAAAAAAAATTCAAA
* *
217144 ATTTTTTGGTGTTGACCATGCAATGGT-CGACA-CCCCTTTTCTC-GAATAAAAAAATTTCAAA
1 ATTTTTTGGTGTTGGCCATGCAAT-GTCCGACACCCCCTTTT-TCAG-ATAAAAAAAATTCAAA
* * * *
217205 ATTTTTTGGTGTTGGCCATGCAAT-TATCGAAACCCCCTGTTATCAGAT-AAAAAAATTCAAT
1 ATTTTTTGGTGTTGGCCATGCAATGT-CCGACACCCCCT-TTTTCAGATAAAAAAAATTCAAA
* * * * *
217266 TTTTTTTGGTGTTGGTCATGCAATGGCCGACACCCCCTGTTATCAGATAAAAAAATTTCAAA
1 ATTTTTTGGTGTTGGCCATGCAATGTCCGACACCCCCT-TTTTCAGATAAAAAAAATTCAAA
* * ** **
217328 ATTTTTTTGTGTTGGCCATGCAATGACCGACACCCCCTTTTT-ATTTGGTAAAAAATT--AA
1 ATTTTTTGGTGTTGGCCATGCAATGTCCGACACCCCCTTTTTCAGAT-AAAAAAAATTCAAA
* *
217387 ATTTTTTGGTGTTGGCCATGTAATGGCCGACACC
1 ATTTTTTGGTGTTGGCCATGCAATGTCCGACACC
217421 AACTTCCCTT
Statistics
Matches: 238, Mismatches: 28, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
59 34 0.14
60 11 0.05
61 134 0.56
62 56 0.24
63 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (61 bp):
ATTTTTTGGTGTTGGCCATGCAATGTCCGACACCCCCTTTTTCAGATAAAAAAAATTCAAA
Found at i:217242 original size:122 final size:121
Alignment explanation
Indices: 217083--217420 Score: 418
Period size: 122 Copynumber: 2.8 Consensus size: 121
217073 AAAAAATTGT
* *
217083 ATTTTTGGGTGTTGGCCATGCAATGT-CCGACATCCCCTTTTTCAGATAAAAAAAATTCAAAATT
1 ATTTTTTGGTGTTGGCCATGCAAT-TACCGACACCCCCTTTTTCAGAT-AAAAAAATTCAAAATT
* * * *
217147 TTTTGGTGTTGACCATGCAATGGTCGACACCCCTTTTCTC-GAATAAAAAAATTTCAAA
64 TTTTGGTGTTGGCCATGCAATGGCCGACACCCCTGTTATCAG-ATAAAAAAATTTCAAA
* * * **
217205 ATTTTTTGGTGTTGGCCATGCAATTATCGAAACCCCCTGTTATCAGATAAAAAAATTCAATTTTT
1 ATTTTTTGGTGTTGGCCATGCAATTACCGACACCCCCT-TTTTCAGATAAAAAAATTCAAAATTT
*
217270 TTTGGTGTTGGTCATGCAATGGCCGACACCCCCTGTTATCAGATAAAAAAATTTCAAA
65 TTTGGTGTTGGCCATGCAATGGCCGACA-CCCCTGTTATCAGATAAAAAAATTTCAAA
* * *
217328 ATTTTTTTGTGTTGGCCATGCAATGACCGACACCCCCTTTTT-ATTTGGT-AAAAAATT--AAAT
1 ATTTTTTGGTGTTGGCCATGCAATTACCGACACCCCCTTTTTCA---GATAAAAAAATTCAAAAT
*
217389 TTTTTGGTGTTGGCCATGTAATGGCCGACACC
63 TTTTTGGTGTTGGCCATGCAATGGCCGACACC
217421 AACTTCCCTT
Statistics
Matches: 187, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
120 2 0.01
121 32 0.17
122 75 0.40
123 75 0.40
124 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (121 bp):
ATTTTTTGGTGTTGGCCATGCAATTACCGACACCCCCTTTTTCAGATAAAAAAATTCAAAATTTT
TTGGTGTTGGCCATGCAATGGCCGACACCCCTGTTATCAGATAAAAAAATTTCAAA
Found at i:217331 original size:123 final size:121
Alignment explanation
Indices: 217083--217420 Score: 416
Period size: 123 Copynumber: 2.8 Consensus size: 121
217073 AAAAAATTGT
* * *
217083 ATTTTTGGGTGTTGGCCATGCAATGT-CCGACATCCCCTTTTTCAGATAAAAAAAATTCAAAATT
1 ATTTTTTGGTGTTGGCCATGCAAT-TACCGACACCCCCTTTATCAGAT-AAAAAAATTC-AAATT
* * * *
217147 TTTTGGTGTTGACCATGCAATGGTCGACA-CCCCTTTTCTCGAATAAAAAAATTTCAAA
63 TTTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTATCGAATAAAAAAATTTCAAA
* * *
217205 ATTTTTTGGTGTTGGCCATGCAATTATCGAAACCCCCTGTTATCAGATAAAAAAATTCAATTTTT
1 ATTTTTTGGTGTTGGCCATGCAATTACCGACACCCCCT-TTATCAGATAAAAAAATTCAA-ATTT
*
217270 TTTGGTGTTGGTCATGCAATGGCCGACACCCCCTGTTATC-AGATAAAAAAATTTCAAA
64 TTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTATCGA-ATAAAAAAATTTCAAA
* * ** *
217328 ATTTTTTTGTGTTGGCCATGCAATGACCGACACCCCCTTTTTATTTGGT-AAAAAATT-AAATTT
1 ATTTTTTGGTGTTGGCCATGCAATTACCGACACCCCC--TTTATCAGATAAAAAAATTCAAATTT
*
217391 TTTGGTGTTGGCCATGTAATGGCCGACACC
64 TTTGGTGTTGGCCATGCAATGGCCGACACC
217421 AACTTCCCTT
Statistics
Matches: 188, Mismatches: 21, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
121 34 0.18
122 73 0.39
123 74 0.39
124 6 0.03
125 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (121 bp):
ATTTTTTGGTGTTGGCCATGCAATTACCGACACCCCCTTTATCAGATAAAAAAATTCAAATTTTT
TGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTATCGAATAAAAAAATTTCAAA
Found at i:218260 original size:17 final size:17
Alignment explanation
Indices: 218238--218290 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
218228 AAAAAATAAT
218238 AATTAGAATATACAGGA
1 AATTAGAATATACAGGA
218255 AATTAG-A-A-A-A--A
1 AATTAGAATATACAGGA
*
218266 AATTAAAATATACAGGA
1 AATTAGAATATACAGGA
218283 AATTAGAA
1 AATTAGAA
218291 ATTAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
11 6 0.21
12 1 0.04
13 2 0.07
14 2 0.07
15 2 0.07
16 1 0.04
17 14 0.50
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.23
Consensus pattern (17 bp):
AATTAGAATATACAGGA
Found at i:218270 original size:28 final size:28
Alignment explanation
Indices: 218238--218321 Score: 105
Period size: 28 Copynumber: 2.9 Consensus size: 28
218228 AAAAAATAAT
*
218238 AATTAGAATATACAGGAAATTAGAAAAA
1 AATTAAAATATACAGGAAATTAGAAAAA
218266 AATTAAAATATACAGGAAATTAGAAATTAA
1 AATTAAAATATACAGGAAATTAGAAA--AA
* * * *
218296 ATTTAAAATAAAAACGAAATTAGAAA
1 AATTAAAATATACAGGAAATTAGAAA
218322 TTAAATTTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
28 25 0.51
30 24 0.49
ACGTcount: A:0.62, C:0.04, G:0.11, T:0.24
Consensus pattern (28 bp):
AATTAAAATATACAGGAAATTAGAAAAA
Found at i:218304 original size:30 final size:30
Alignment explanation
Indices: 218244--218333 Score: 130
Period size: 30 Copynumber: 3.1 Consensus size: 30
218234 TAATAATTAG
*
218244 AATATACAGGAAATTAGAAA--AAAATTAA
1 AATATACAGGAAATTAGAAATTAAATTTAA
218272 AATATACAGGAAATTAGAAATTAAATTTAA
1 AATATACAGGAAATTAGAAATTAAATTTAA
* * *
218302 AATAAAAACGAAATTAGAAATTAAATTTAA
1 AATATACAGGAAATTAGAAATTAAATTTAA
218332 AA
1 AA
218334 AGTAAACTGA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
28 20 0.36
30 36 0.64
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.26
Consensus pattern (30 bp):
AATATACAGGAAATTAGAAATTAAATTTAA
Found at i:218843 original size:24 final size:24
Alignment explanation
Indices: 218816--218869 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
218806 GCCTCGTAAT
* *
218816 CGGGCTGGTAATCGGCCTCGTTCG
1 CGGGCTGGTAAGCGGCCTCGTTCA
* * *
218840 CGGGCTTGTCAGCGGGCTCGTTCA
1 CGGGCTGGTAAGCGGCCTCGTTCA
218864 CGGGCT
1 CGGGCT
218870 CGTCATTGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.07, C:0.30, G:0.39, T:0.24
Consensus pattern (24 bp):
CGGGCTGGTAAGCGGCCTCGTTCA
Found at i:219560 original size:21 final size:20
Alignment explanation
Indices: 219520--219561 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
219510 TTTTTTAAAA
* *
219520 TTCGAAAATATAAAAGATAT
1 TTCGAAAATAAAAAAAATAT
219540 TTCGAAAATAGAAAAAAATAT
1 TTCGAAAATA-AAAAAAATAT
219561 T
1 T
219562 ATAAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.29
Consensus pattern (20 bp):
TTCGAAAATAAAAAAAATAT
Found at i:220632 original size:22 final size:22
Alignment explanation
Indices: 220604--220663 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
220594 TGAGGTGTTG
* *
220604 GTGAGCTGGAATTTTGGTTT-T
1 GTGAGCTGGAATATTGGTTTAA
220625 GCTGAGCTGGAATATTGGTTTAA
1 G-TGAGCTGGAATATTGGTTTAA
220648 GTGAGCTGGAA-ATTGG
1 GTGAGCTGGAATATTGG
220664 GTGGTCCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 6 0.17
22 28 0.80
23 1 0.03
ACGTcount: A:0.22, C:0.07, G:0.35, T:0.37
Consensus pattern (22 bp):
GTGAGCTGGAATATTGGTTTAA
Found at i:220859 original size:86 final size:86
Alignment explanation
Indices: 220757--221156 Score: 495
Period size: 86 Copynumber: 4.6 Consensus size: 86
220747 ATTTAAAAAA
* * *
220757 TGATAAAAATTGTAATATAGTAATAATAATTTTTATTTAAACATTTAAAATTAATAAATAATGCA
1 TGATAAAAATTATAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGCA
*
220822 TTGTCAAAGCAACACATTATT
66 TTGTCAAATCAACACATTATT
* ** * * *
220843 TGATAAAAAATATAATATAATAATAATTTTTTTTATTTAAATATATAAAATTAATGAATAATGTA
1 TGATAAAAATTATAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGCA
*
220908 TTGTCAAATCAACATATTATT
66 TTGTCAAATCAACACATTATT
220929 TGATAAAAATTATAATATAATAATAATAATTTTTATTTAAATATTT-AAATTAATTAAATAATGC
1 TGATAAAAATTATAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAA-TAAATAATGC
220993 ATTGTCAAATCAACACATTATT
65 ATTGTCAAATCAACACATTATT
* * * *
221015 TGATAAAAATTAT-A-AT-ATAATAATAATTTATACTTTAAATA-TGAAAATTTGATAAAGAATG
1 TGATAAAAATTATAATATAATAATAATAATTTTTA-TTTAAATATTTAAAA-TTAATAAATAATG
* * * * *
221076 TATTATTAAATTAACACAATATT
64 CATTGTCAAATCAACACATTATT
* * **
221099 TGATATAAATTGTAATATAATTAATAATCTTTTTTATTTAAATAATGTTAAAATTAAT
1 TGATAAAAATTATAATATAA-TAATAATAATTTTTATTTAAAT-AT-TTAAAATTAAT
221157 TTTAAATGTA
Statistics
Matches: 269, Mismatches: 34, Indels: 19
0.84 0.11 0.06
Matches are distributed among these distances:
83 16 0.06
84 50 0.19
85 12 0.04
86 161 0.60
87 8 0.03
88 13 0.05
89 4 0.01
90 5 0.02
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (86 bp):
TGATAAAAATTATAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGCA
TTGTCAAATCAACACATTATT
Found at i:221043 original size:172 final size:171
Alignment explanation
Indices: 220757--221157 Score: 549
Period size: 172 Copynumber: 2.3 Consensus size: 171
220747 ATTTAAAAAA
* *
220757 TGATAAAAATTGTAATATAGTAATAATAATTTTTATTTAAACATTTAAAATTAA-TAAATAATGC
1 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATTAAATAATGC
*
220821 ATTGTCAAAGCAACACATTATTTGATAAAAAATATAATATAATAATAATTTTTTTTA-TTTAAAT
66 ATTGTCAAAGCAACACATTATTTGATAAAAAATATAATATAATAATAA---TTTATACTTTAAAT
* * * * *
220885 AT-ATAAAATTAATGAATAATGTATTGTCAAATCAACATATTATT
128 ATGA-AAAATTAATAAAGAATGTATTATCAAATCAACACAATATT
*
220929 TGATAAAAATTATAATATAATAATAATAATTTTTATTTAAATATTT-AAATTAATTAAATAATGC
1 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATTAAATAATGC
* *
220993 ATTGTCAAATCAACACATTATTTGATAAAAATTATAATATAATAATAATTTATACTTTAAATATG
66 ATTGTCAAAGCAACACATTATTTGATAAAAAATATAATATAATAATAATTTATACTTTAAATATG
* * * *
221058 AAAATTTGATAAAGAATGTATTATTAAATTAACACAATATT
131 AAAAATTAATAAAGAATGTATTATCAAATCAACACAATATT
* **
221099 TGATATAAATTGTAATATAATTAATAATCTTTTTTATTTAAATAATGTTAAAATTAATT
1 TGATAAAAATTGTAATATAA-TAATAATAATTTTTATTTAAAT-AT-TTAAAATTAATT
221158 TTAAATGTAA
Statistics
Matches: 203, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
169 5 0.02
170 58 0.29
171 28 0.14
172 101 0.50
173 2 0.01
174 9 0.04
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (171 bp):
TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATTAAATAATGC
ATTGTCAAAGCAACACATTATTTGATAAAAAATATAATATAATAATAATTTATACTTTAAATATG
AAAAATTAATAAAGAATGTATTATCAAATCAACACAATATT
Found at i:221300 original size:16 final size:16
Alignment explanation
Indices: 221267--221300 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
221257 ATTAATTATC
*
221267 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
*
221283 AAATTAATTTTAAATT
1 AAATTAATTTCAAATT
221299 AA
1 AA
221301 TTTTTACACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:228927 original size:17 final size:17
Alignment explanation
Indices: 228905--228939 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
228895 CTTTTAAATT
* *
228905 TAAAATTAAAAATAAAG
1 TAAAATAAAAAAAAAAG
228922 TAAAATAAAAAAAAAAG
1 TAAAATAAAAAAAAAAG
228939 T
1 T
228940 GTGAAGGACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (17 bp):
TAAAATAAAAAAAAAAG
Found at i:229021 original size:14 final size:15
Alignment explanation
Indices: 228996--229033 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
228986 CGACATCTAT
228996 TTTTATAATTTTTTTA
1 TTTTA-AATTTTTTTA
229012 -TTTAAA-TTTTTTA
1 TTTTAAATTTTTTTA
229025 TTTTAAATT
1 TTTTAAATT
229034 ATGTCACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
13 7 0.35
14 8 0.40
15 5 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTAAATTTTTTTA
Found at i:229468 original size:19 final size:19
Alignment explanation
Indices: 229446--229510 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 19
229436 AAATTACAAA
229446 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTTTT
*
229465 AAAATTCAAAAT-ATTTATA
1 AAAATTCAAAATAATTT-TT
229484 AAAATTCCAAAATTTATATTTTT
1 AAAATT-CAAAA--TA-ATTTTT
229507 AAAA
1 AAAA
229511 AAAAAATCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 4 0.11
19 19 0.50
20 5 0.13
22 1 0.03
23 5 0.13
24 4 0.11
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:229551 original size:9 final size:10
Alignment explanation
Indices: 229510--229553 Score: 56
Period size: 9 Copynumber: 4.5 Consensus size: 10
229500 TATTTTTAAA
229510 AAAAAAATCT
1 AAAAAAATCT
229520 -AAAAAATCT
1 AAAAAAATCT
*
229529 AAAAAATATAT
1 AAAAAA-ATCT
229540 AAAAAAAT-T
1 AAAAAAATCT
229549 AAAAA
1 AAAAA
229554 TTTTAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
9 15 0.48
10 7 0.23
11 9 0.29
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAAAAATCT
Found at i:229834 original size:18 final size:20
Alignment explanation
Indices: 229798--229834 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
229788 AATTTAACTC
*
229798 AAAAAAATTTAAATCAAATT
1 AAAAAAATTAAAATCAAATT
229818 AAAAAAA-TAAAAT-AAAT
1 AAAAAAATTAAAATCAAAT
229835 AAGATCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 5 0.31
20 7 0.44
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAAAATTAAAATCAAATT
Done.