Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold456
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: 970336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:18 original size:13 final size:13
Alignment explanation
Indices: 1--69 Score: 59
Period size: 13 Copynumber: 5.2 Consensus size: 13
1 CCCCAACCCCTAA
1 CCCCAACCCCTAA
* *
14 CCCCACCCCCAAA
1 CCCCAACCCCTAA
*
27 CCCCAACCCCAAA
1 CCCCAACCCCTAA
*
40 CCCTGAA-CCCTAA
1 CCC-CAACCCCTAA
* *
53 CCCTGAACCCTTAA
1 CCC-CAACCCCTAA
67 CCC
1 CCC
70 TTGAACCCTG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
13 38 0.79
14 10 0.21
ACGTcount: A:0.30, C:0.58, G:0.03, T:0.09
Consensus pattern (13 bp):
CCCCAACCCCTAA
Found at i:25 original size:19 final size:19
Alignment explanation
Indices: 1--37 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1 CCCC-AACCCCTAACCCCAC
1 CCCCAAACCCC-AACCCCAC
20 CCCCAAACCCCAACCCCA
1 CCCCAAACCCCAACCCCA
38 AACCCTGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.30, C:0.68, G:0.00, T:0.03
Consensus pattern (19 bp):
CCCCAAACCCCAACCCCAC
Found at i:76 original size:15 final size:14
Alignment explanation
Indices: 38--92 Score: 76
Period size: 15 Copynumber: 3.9 Consensus size: 14
28 CCCAACCCCA
38 AACCCTGAACCC-T
1 AACCCTGAACCCTT
51 AACCCTGAACCCTT
1 AACCCTGAACCCTT
*
65 AACCCTTGAACCCTGC
1 AACCC-TGAACCCT-T
81 AACCCTGAACCC
1 AACCCTGAACCC
93 CTAAACTCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
13 12 0.32
14 6 0.16
15 15 0.39
16 5 0.13
ACGTcount: A:0.29, C:0.45, G:0.09, T:0.16
Consensus pattern (14 bp):
AACCCTGAACCCTT
Found at i:108 original size:30 final size:30
Alignment explanation
Indices: 31--108 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
21 CCCAAACCCC
*
31 AACCCCAAACCCT-GAACCCT--AACCCTG
1 AACCCTAAACCCTAGAACCCTGCAACCCTG
* *
58 AACCCTTAACCCTTGAACCCTGCAACCCTG
1 AACCCTAAACCCTAGAACCCTGCAACCCTG
*
88 AACCCCTAAACTCTAG-ACCCT
1 AA-CCCTAAACCCTAGAACCCT
109 AAACCCCTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
27 11 0.26
28 7 0.17
30 14 0.33
31 10 0.24
ACGTcount: A:0.31, C:0.45, G:0.08, T:0.17
Consensus pattern (30 bp):
AACCCTAAACCCTAGAACCCTGCAACCCTG
Found at i:113 original size:22 final size:22
Alignment explanation
Indices: 82--136 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
72 GAACCCTGCA
* *
82 ACCCTGAACCCCTAAACTCTAG
1 ACCCTAAACCCCTAAACACTAG
104 ACCCTAAACCCCTAAACACTAG
1 ACCCTAAACCCCTAAACACTAG
*
126 ACCCTAGACCC
1 ACCCTAAACCC
137 TAGACCTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.44, G:0.07, T:0.15
Consensus pattern (22 bp):
ACCCTAAACCCCTAAACACTAG
Found at i:285 original size:16 final size:16
Alignment explanation
Indices: 264--319 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
254 AAACCCTAAA
264 CCCAAACCCCCAAAAC
1 CCCAAACCCCCAAAAC
*
280 CCCAAACCCCTAAAAC
1 CCCAAACCCCCAAAAC
* * *
296 CCTAAA-ACTCAAAAC
1 CCCAAACCCCCAAAAC
*
311 CCTAAACCC
1 CCCAAACCC
320 TAAACTCGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 12 0.36
16 21 0.64
ACGTcount: A:0.45, C:0.48, G:0.00, T:0.07
Consensus pattern (16 bp):
CCCAAACCCCCAAAAC
Found at i:317 original size:7 final size:7
Alignment explanation
Indices: 31--324 Score: 172
Period size: 7 Copynumber: 41.4 Consensus size: 7
21 CCCAAACCCC
*
31 AACCCCA
1 AACCCTA
*
38 AACCCTG
1 AACCCTA
45 AACCCT-
1 AACCCTA
*
51 AACCCTG
1 AACCCTA
*
58 AACCCTT
1 AACCCTA
*
65 AACCCTTG
1 AACCC-TA
*
73 AACCCTGC
1 AACCCT-A
81 AACCCTGA
1 AACCCT-A
*
89 ACCCCTA
1 AACCCTA
*
96 AACTCTA
1 AACCCTA
*
103 GACCCTA
1 AACCCTA
110 AACCCCTA
1 AA-CCCTA
*
118 AACACTA
1 AACCCTA
*
125 GACCCTA
1 AACCCTA
*
132 GACCCTA
1 AACCCTA
*
139 GA-CCTCA
1 AACCCT-A
*
146 AACCCCA
1 AACCCTA
*
153 AACCCCA
1 AACCCTA
* *
160 GACCCCA
1 AACCCTA
167 AACCC-A
1 AACCCTA
*
173 AACCC-C
1 AACCCTA
*
179 AACCCCA
1 AACCCTA
186 AACCC-A
1 AACCCTA
192 AACCC-A
1 AACCCTA
198 AACTCC-A
1 AAC-CCTA
205 AACCCTA
1 AACCCTA
212 AACCCTA
1 AACCCTA
*
219 AACCCCA
1 AACCCTA
226 AACCCTA
1 AACCCTA
*
233 AAACCTAA
1 AACCCT-A
*
241 AACCTTA
1 AACCCTA
**
248 AACTTTA
1 AACCCTA
255 AACCCTA
1 AACCCTA
262 AACCC-A
1 AACCCTA
*
268 AACCCCCAA
1 AA--CCCTA
*
277 AACCCCA
1 AACCCTA
284 AACCCCTAA
1 AA-CCCT-A
293 AACCCTAA
1 AACCCT-A
* *
301 AACTCAA
1 AACCCTA
308 AACCCTA
1 AACCCTA
315 AACCCTA
1 AACCCTA
322 AAC
1 AAC
325 TCGAAACCTA
Statistics
Matches: 237, Mismatches: 35, Indels: 30
0.78 0.12 0.10
Matches are distributed among these distances:
6 35 0.15
7 148 0.62
8 48 0.20
9 6 0.03
ACGTcount: A:0.40, C:0.45, G:0.03, T:0.12
Consensus pattern (7 bp):
AACCCTA
Found at i:338 original size:21 final size:23
Alignment explanation
Indices: 282--338 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 23
272 CCCAAAACCC
*
282 CAAACCCCTAAAACCCTAAAACT
1 CAAAACCCTAAAACCCTAAAACT
305 CAAAACCCT-AAACCCT-AAACT
1 CAAAACCCTAAAACCCTAAAACT
*
326 CGAAA-CCTAAAAC
1 CAAAACCCTAAAAC
339 TTGAAGCTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 3 0.10
21 13 0.42
22 7 0.23
23 8 0.26
ACGTcount: A:0.49, C:0.37, G:0.02, T:0.12
Consensus pattern (23 bp):
CAAAACCCTAAAACCCTAAAACT
Found at i:1009 original size:21 final size:22
Alignment explanation
Indices: 976--1023 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
966 ATAAATGTAC
* *
976 TATATTATTTTTATTTA-AAAA
1 TATATTATATTTATCTAGAAAA
*
997 TATATTCTATTTATCTAGAAAA
1 TATATTATATTTATCTAGAAAA
1019 -ATATT
1 TATATT
1024 TTGTTTTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (22 bp):
TATATTATATTTATCTAGAAAA
Found at i:4963 original size:35 final size:35
Alignment explanation
Indices: 4898--4965 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
4888 TCACAAAGCA
* *
4898 TAGAAAAAGATTTCTAGATATATGTAGGAATATAT
1 TAGAAAAAGAATTCTAGATATATATAGGAATATAT
* *
4933 TAGAAAAAGAATTCTAGATATTTATGGGAATAT
1 TAGAAAAAGAATTCTAGATATATATAGGAATAT
4966 TTGAGGCCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.34
Consensus pattern (35 bp):
TAGAAAAAGAATTCTAGATATATATAGGAATATAT
Found at i:6226 original size:21 final size:21
Alignment explanation
Indices: 6186--6226 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6176 AGCACAGCGA
**
6186 GCTTGACCTTCTTCTTCTTGT
1 GCTTGACCTTCTTCGGCTTGT
*
6207 GCTTGATCTTCTTCGGCTTG
1 GCTTGACCTTCTTCGGCTTG
6227 GTGTAGGTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.05, C:0.27, G:0.20, T:0.49
Consensus pattern (21 bp):
GCTTGACCTTCTTCGGCTTGT
Found at i:7951 original size:52 final size:52
Alignment explanation
Indices: 7873--7978 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
7863 CGACGGTGGG
7873 TACTTCAGCAATCACTGATAGTGAATCCCTAGATCAAAGTAAAGCAGAGTTA
1 TACTTCAGCAATCACTGATAGTGAATCCCTAGATCAAAGTAAAGCAGAGTTA
* *
7925 TACTTCAGCAATCACTGATAGTGAATCCCTATATCAACGTAAAGCAGAGTTA
1 TACTTCAGCAATCACTGATAGTGAATCCCTAGATCAAAGTAAAGCAGAGTTA
7977 TA
1 TA
7979 GTTGTAAGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (52 bp):
TACTTCAGCAATCACTGATAGTGAATCCCTAGATCAAAGTAAAGCAGAGTTA
Found at i:11342 original size:3 final size:3
Alignment explanation
Indices: 11334--11365 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
11324 CCGTAGTTTT
11334 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11366 TGGCAATCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:11741 original size:48 final size:48
Alignment explanation
Indices: 11686--11783 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
11676 TATTCCTGTG
11686 CCCTTCGCTAAATGGTCTGATGATTGTTGCAACTTTCATTCTAGTGTT
1 CCCTTCGCTAAATGGTCTGATGATTGTTGCAACTTTCATTCTAGTGTT
* * *
11734 CCCTTCGCTGAATGGTCTGGTGATTGTTGCAACTTTCATTCTGGTGTT
1 CCCTTCGCTAAATGGTCTGATGATTGTTGCAACTTTCATTCTAGTGTT
11782 CC
1 CC
11784 TTTATATTCT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.41
Consensus pattern (48 bp):
CCCTTCGCTAAATGGTCTGATGATTGTTGCAACTTTCATTCTAGTGTT
Found at i:24201 original size:39 final size:39
Alignment explanation
Indices: 24147--24226 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
24137 GTTTCATGTT
24147 AAGAAAATTGGAGTCTCTAAGCATGCTCAATGAATCTAA
1 AAGAAAATTGGAGTCTCTAAGCATGCTCAATGAATCTAA
24186 AAGAAAATTGGAGTCTCTAAGCATGCTCAATGAATCTAA
1 AAGAAAATTGGAGTCTCTAAGCATGCTCAATGAATCTAA
24225 AA
1 AA
24227 ATCGAGAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (39 bp):
AAGAAAATTGGAGTCTCTAAGCATGCTCAATGAATCTAA
Found at i:24380 original size:47 final size:47
Alignment explanation
Indices: 24326--24418 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
24316 AAAACAAAAT
*
24326 TTTATATTATAATTTTACATTTTTACTTTAGATTTGTATTAAGATTG
1 TTTATATTATAATTTTACATTTCTACTTTAGATTTGTATTAAGATTG
24373 TTTATATTATAATTTTACATTTCTACTTTAGATTTGTATTAAGATT
1 TTTATATTATAATTTTACATTTCTACTTTAGATTTGTATTAAGATT
24419 TATCAAAATC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (47 bp):
TTTATATTATAATTTTACATTTCTACTTTAGATTTGTATTAAGATTG
Found at i:30531 original size:65 final size:65
Alignment explanation
Indices: 30427--30556 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
30417 GAGGAAGAAG
30427 GAGGTAGGAGACAAAAAGAAAAGAAAGTAAGTAGCAGGTGTTAGAGAATTTAAATTTTGAAGTAA
1 GAGGTAGGAGACAAAAAGAAAAGAAAGTAAGTAGCAGGTGTTAGAGAATTTAAATTTTGAAGTAA
30492 GAGGTAGGAGACAAAAAGAAAAGAAAGTAAGTAGCAGGTGTTAGAGAATTTAAATTTTGAAGTAA
1 GAGGTAGGAGACAAAAAGAAAAGAAAGTAAGTAGCAGGTGTTAGAGAATTTAAATTTTGAAGTAA
30557 TATTCTAGAC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.48, C:0.03, G:0.28, T:0.22
Consensus pattern (65 bp):
GAGGTAGGAGACAAAAAGAAAAGAAAGTAAGTAGCAGGTGTTAGAGAATTTAAATTTTGAAGTAA
Found at i:36125 original size:17 final size:17
Alignment explanation
Indices: 36094--36126 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
36084 CCAAACAATA
36094 TAATTGTATTCAATATT
1 TAATTGTATTCAATATT
36111 TAATT-TATTCTAATAT
1 TAATTGTATTC-AATAT
36127 ACCAAACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (17 bp):
TAATTGTATTCAATATT
Found at i:38014 original size:11 final size:11
Alignment explanation
Indices: 37989--38040 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
37979 ATAAATAAAT
37989 AAATAAA-TTA
1 AAATAAATTTA
37999 TAAATAAATTTA
1 -AAATAAATTTA
*
38011 AAAT-ATTTTA
1 AAATAAATTTA
38021 AAATAAAAATTTA
1 AAAT--AAATTTA
38034 AAATAAA
1 AAATAAA
38041 AATAATTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 9 0.26
11 14 0.40
12 3 0.09
13 9 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATAAATTTA
Found at i:38035 original size:13 final size:13
Alignment explanation
Indices: 38017--38043 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38007 TTTAAAATAT
38017 TTTAAAATAAAAA
1 TTTAAAATAAAAA
38030 TTTAAAATAAAAA
1 TTTAAAATAAAAA
38043 T
1 T
38044 AATTAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TTTAAAATAAAAA
Found at i:38074 original size:40 final size:40
Alignment explanation
Indices: 38034--38121 Score: 117
Period size: 39 Copynumber: 2.2 Consensus size: 40
38024 TAAAAATTTA
*
38034 AAATAAAAA-TAATTAATTAATAAAAATAAATTTATTTTT
1 AAATAAAAATTAATTAATAAATAAAAATAAATTTATTTTT
* * *
38073 AATTAAAAATTATTTTATAAATAAAAATAAATTTA-TTTT
1 AAATAAAAATTAATTAATAAATAAAAATAAATTTATTTTT
*
38112 AATTAAAAAT
1 AAATAAAAAT
38122 CACATAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 22 0.50
40 22 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (40 bp):
AAATAAAAATTAATTAATAAATAAAAATAAATTTATTTTT
Found at i:38087 original size:17 final size:18
Alignment explanation
Indices: 38010--38100 Score: 59
Period size: 17 Copynumber: 5.3 Consensus size: 18
38000 AAATAAATTT
38010 AAAA-TATTTTA-AAATA
1 AAAATTATTTTATAAATA
***
38026 AAAATT-TAAAATAAA-A
1 AAAATTATTTTATAAATA
* * *
38042 ATAATTAATTAATAAA-A
1 AAAATTATTTTATAAATA
*
38059 ATAAATTTATTTT-TAATTA
1 A-AAA-TTATTTTATAAATA
38078 AAAATTATTTTATAAATA
1 AAAATTATTTTATAAATA
38096 AAAAT
1 AAAAT
38101 AAATTTATTT
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
16 12 0.21
17 19 0.34
18 18 0.32
19 7 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATTATTTTATAAATA
Found at i:38107 original size:18 final size:18
Alignment explanation
Indices: 38027--38108 Score: 69
Period size: 18 Copynumber: 4.4 Consensus size: 18
38017 TTTAAAATAA
38027 AAATTTA-AAATAAAAAT
1 AAATTTATAAATAAAAAT
* *
38044 -AATTAATTAATAAAAAT
1 AAATTTATAAATAAAAAT
*
38061 AAATTTATTTTTAATTAAAAAT
1 AAATTTA----TAAATAAAAAT
* *
38083 TATTTTATAAATAAAAAT
1 AAATTTATAAATAAAAAT
38101 AAATTTAT
1 AAATTTAT
38109 TTTAATTAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
16 5 0.10
17 9 0.18
18 21 0.43
22 14 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTTATAAATAAAAAT
Found at i:38134 original size:39 final size:40
Alignment explanation
Indices: 38052--38136 Score: 111
Period size: 39 Copynumber: 2.1 Consensus size: 40
38042 ATAATTAATT
* ** *
38052 AATAAAAATAAATTTATTTTTAATTAAAAATTATTTTATA
1 AATAAAAATAAATTTATTTTTAATTAAAAATCATCATAAA
38092 AATAAAAATAAATTTA-TTTTAATTAAAAATCA-CATAGAA
1 AATAAAAATAAATTTATTTTTAATTAAAAATCATCATA-AA
38131 AATAAA
1 AATAAA
38137 TTTTAAGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.05
39 22 0.55
40 16 0.40
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (40 bp):
AATAAAAATAAATTTATTTTTAATTAAAAATCATCATAAA
Found at i:42915 original size:13 final size:13
Alignment explanation
Indices: 42892--42918 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42882 AATTTTTTAG
42892 TATTTATTTTATT
1 TATTTATTTTATT
42905 TATTTATTTTATT
1 TATTTATTTTATT
42918 T
1 T
42919 TAAATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TATTTATTTTATT
Found at i:43149 original size:24 final size:24
Alignment explanation
Indices: 43132--43183 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
43122 TAATTTTATT
43132 TATA-TTTT-ATTATTTAATATAA
1 TATATTTTTAATTATTTAATATAA
*
43154 TATATTTTTAATTATTTATTATATA
1 TATATTTTTAATTATTTAATATA-A
43179 TATAT
1 TATAT
43184 AATTATCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 4 0.15
23 4 0.15
24 12 0.46
25 6 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TATATTTTTAATTATTTAATATAA
Found at i:43156 original size:34 final size:35
Alignment explanation
Indices: 43103--43168 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 35
43093 ATAATTTTAA
*
43103 TTATTATTCAACATAAATATAATTTTATTTATATT
1 TTATTATTCAACATAAATATAATTTTAATTATATT
* * *
43138 TTATTATTTAATAT-AATATATTTTTAATTAT
1 TTATTATTCAACATAAATATAATTTTAATTAT
43169 TTATTATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 15 0.56
35 12 0.44
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (35 bp):
TTATTATTCAACATAAATATAATTTTAATTATATT
Found at i:43173 original size:14 final size:17
Alignment explanation
Indices: 43118--43187 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 17
43108 ATTCAACATA
43118 AATATAA-TT-TTATTT
1 AATATAATTTATTATTT
43133 -ATAT--TTTATTATTT
1 AATATAATTTATTATTT
*
43147 AATATAATATATT-TTT
1 AATATAATTTATTATTT
*
43163 AAT-T-ATTTATTATAT
1 AATATAATTTATTATTT
43178 ATATATAATT
1 A-ATATAATT
43188 ATCTAATGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
13 2 0.05
14 16 0.37
15 8 0.19
16 8 0.19
17 6 0.14
18 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AATATAATTTATTATTT
Found at i:43179 original size:21 final size:21
Alignment explanation
Indices: 43126--43189 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
43116 TAAATATAAT
43126 TTTATT-TATA-TTTT-ATTA
1 TTTATTATATATTTTTAATTA
43144 TTTAATATAATATATTTTTAATTA
1 TTT-AT-T-ATATATTTTTAATTA
* *
43168 TTTATTATATATATATAATTA
1 TTTATTATATATTTTTAATTA
43189 T
1 T
43190 CTAATGTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 3 0.08
19 2 0.05
20 1 0.03
21 14 0.37
22 5 0.13
23 6 0.16
24 7 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATTATATATTTTTAATTA
Found at i:43253 original size:37 final size:38
Alignment explanation
Indices: 43212--43304 Score: 116
Period size: 37 Copynumber: 2.5 Consensus size: 38
43202 ATAGTCATTT
*
43212 TAATTAATTTCATTATTACTATTAAAATTAAATTA-AA
1 TAATTAATTTCATTATTAATATTAAAATTAAATTATAA
* * ** **
43249 TAATTTATTTCATTATTAATTTTAATTTTTTATTATAA
1 TAATTAATTTCATTATTAATATTAAAATTAAATTATAA
43287 TAATTAATTTCATTATTA
1 TAATTAATTTCATTATTA
43305 TAATAAATAA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 28 0.60
38 19 0.40
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (38 bp):
TAATTAATTTCATTATTAATATTAAAATTAAATTATAA
Found at i:43325 original size:21 final size:21
Alignment explanation
Indices: 43280--43326 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
43270 TTAATTTTTT
* **
43280 ATTATAATAATTAATTTCATT
1 ATTATAATAAATAATTTCACA
*
43301 ATTATAATAAATAATTTTACA
1 ATTATAATAAATAATTTCACA
43322 ATTAT
1 ATTAT
43327 CCTTATGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTATAATAAATAATTTCACA
Found at i:44083 original size:74 final size:74
Alignment explanation
Indices: 44032--44165 Score: 172
Period size: 74 Copynumber: 1.9 Consensus size: 74
44022 TATATTCTTA
* *
44032 TATTTTAT-T-ATATTATAAT-TATATTTA-A-AATATTTTATATTTATATTAATTT-TAATATA
1 TATTTTATGTAATATTAAAATATATATTTATATAATATATTATATTTATATTAATTTATAATATA
44091 TTATTAATT
66 TTATTAATT
* *
44100 TATTTTATGTAAATTTTAAAATATATATTTATATAATATATTATATTTTTATTAATTTATGAATA
1 TATTTTATGT-AATATTAAAATATATATTTATATAATATATTATATTTATATTAATTTAT-AATA
44165 T
64 T
44166 TATATTTCTA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
68 8 0.15
69 1 0.02
71 8 0.15
72 8 0.15
73 1 0.02
74 22 0.41
75 1 0.02
76 5 0.09
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (74 bp):
TATTTTATGTAATATTAAAATATATATTTATATAATATATTATATTTATATTAATTTATAATATA
TTATTAATT
Found at i:44115 original size:32 final size:34
Alignment explanation
Indices: 44065--44128 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 34
44055 TTTAAAATAT
* *
44065 TTTATATTTATATTAATTTTAATATAT-TATTAA
1 TTTATATTTATATAAATTTTAAAATATATATTAA
*
44098 TTTAT-TTTATGTAAATTTTAAAATATATATT
1 TTTATATTTATATAAATTTTAAAATATATATT
44129 TATATAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 18 0.67
33 9 0.33
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (34 bp):
TTTATATTTATATAAATTTTAAAATATATATTAA
Found at i:44386 original size:3 final size:3
Alignment explanation
Indices: 44378--44412 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
44368 ATCAATCAAC
44378 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
44413 GGCGATCTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:47957 original size:116 final size:117
Alignment explanation
Indices: 47726--47963 Score: 433
Period size: 116 Copynumber: 2.0 Consensus size: 117
47716 ATTTCTCCTT
47726 TTCTTATTTTCTAAAGCTGAAATGAAGACTACAAACAAAATCTAGGTTTCCAGATTTTGTTTGTT
1 TTCTTATTTTCTAAAGCTGAAATGAAGACTACAAACAAAATCTAGGTTTCCAGA---T-TTTGTT
47791 TTTAGATTGTTTTTTGCTCATGAGCTAGATCCTAGAGTATTTTTTTGAATGCATGA
62 TTTAGATTGTTTTTTGCTCATGAGCTAGATCCTAGAGTATTTTTTTGAATGCATGA
47847 TTCTTATTTTCTAAAGCTGAAATGAAGACTACAAACAAAATCTAGGTTTCCAGA-TTTGTTTTTA
1 TTCTTATTTTCTAAAGCTGAAATGAAGACTACAAACAAAATCTAGGTTTCCAGATTTTGTTTTTA
47911 GATTGTTTTTTGCTCATGAGCTAGATCCTAGAGTATTTTTTTGAATGCATGA
66 GATTGTTTTTTGCTCATGAGCTAGATCCTAGAGTATTTTTTTGAATGCATGA
47963 T
1 T
47964 ATTATTTGCA
Statistics
Matches: 117, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
116 63 0.54
121 54 0.46
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (117 bp):
TTCTTATTTTCTAAAGCTGAAATGAAGACTACAAACAAAATCTAGGTTTCCAGATTTTGTTTTTA
GATTGTTTTTTGCTCATGAGCTAGATCCTAGAGTATTTTTTTGAATGCATGA
Found at i:53331 original size:2 final size:2
Alignment explanation
Indices: 53326--53362 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
53316 TGTGTGTATG
*
53326 TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53363 TCAGTGATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:53585 original size:7 final size:7
Alignment explanation
Indices: 53569--53611 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
53559 ATTATTAATT
53569 AAATTCAA
1 AAATT-AA
53577 AAATTAA
1 AAATTAA
53584 AAATATAA
1 AAAT-TAA
*
53592 AAAAT-A
1 AAATTAA
53598 AAATTAA
1 AAATTAA
53605 AAATTAA
1 AAATTAA
53612 TACACAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 5 0.16
7 15 0.48
8 11 0.35
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATTAA
Found at i:54132 original size:2 final size:2
Alignment explanation
Indices: 54125--54168 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
54115 GTATTGTCCT
54125 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
54167 TC
1 TC
54169 GTTTCGTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:57242 original size:15 final size:15
Alignment explanation
Indices: 57222--57251 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
57212 CGTTCAGCTC
57222 CTCTCCTTGTTATCT
1 CTCTCCTTGTTATCT
57237 CTCTCCTTGTTATCT
1 CTCTCCTTGTTATCT
57252 TAACATAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.33, G:0.07, T:0.53
Consensus pattern (15 bp):
CTCTCCTTGTTATCT
Found at i:57369 original size:19 final size:19
Alignment explanation
Indices: 57345--57382 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
57335 TAACTGCTAT
*
57345 GAGTTCAGTTGAAATTTAA
1 GAGTTCAATTGAAATTTAA
*
57364 GAGTTCAATTTAAATTTAA
1 GAGTTCAATTGAAATTTAA
57383 ACATTTTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.39
Consensus pattern (19 bp):
GAGTTCAATTGAAATTTAA
Found at i:58413 original size:54 final size:54
Alignment explanation
Indices: 58331--58437 Score: 214
Period size: 54 Copynumber: 2.0 Consensus size: 54
58321 CCTTTCTTGC
58331 CAATCAATGCTTTTCTTTCTACCAGCTTTAGCTACCACCTTCTCTATCCGTACA
1 CAATCAATGCTTTTCTTTCTACCAGCTTTAGCTACCACCTTCTCTATCCGTACA
58385 CAATCAATGCTTTTCTTTCTACCAGCTTTAGCTACCACCTTCTCTATCCGTAC
1 CAATCAATGCTTTTCTTTCTACCAGCTTTAGCTACCACCTTCTCTATCCGTAC
58438 TCTAATAGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.21, C:0.34, G:0.07, T:0.37
Consensus pattern (54 bp):
CAATCAATGCTTTTCTTTCTACCAGCTTTAGCTACCACCTTCTCTATCCGTACA
Found at i:59804 original size:23 final size:23
Alignment explanation
Indices: 59769--59829 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 23
59759 AAAATTAAAA
* *
59769 ATATTTAAATTTTATAAAAATTG
1 ATATTTTATTTTTATAAAAATTG
* * *
59792 ATATTTTATTTTT-TTATAATTT
1 ATATTTTATTTTTATAAAAATTG
59814 A-ATTTTAATTTTTATA
1 ATATTTT-ATTTTTATA
59830 TTATTTTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
21 5 0.17
22 13 0.43
23 12 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
ATATTTTATTTTTATAAAAATTG
Found at i:59835 original size:22 final size:21
Alignment explanation
Indices: 59794--59835 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
59784 AAAAATTGAT
*
59794 ATTTTATTTTTTTATAATTTA
1 ATTTTATTTTTATATAATTTA
*
59815 ATTTTAATTTTTATATTATTT
1 ATTTT-ATTTTTATATAATTT
59836 TATTAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
ATTTTATTTTTATATAATTTA
Found at i:60731 original size:26 final size:27
Alignment explanation
Indices: 60685--60742 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
60675 TTGAGTCAAT
*
60685 ATTTGAAACATTTAAACTTAAGA-TAA
1 ATTTGAAACATTTAAACTTAAGACAAA
*
60711 ATTTGAAACATTT-GACTTTAAGACAAA
1 ATTTGAAACATTTAAAC-TTAAGACAAA
60738 ATTTG
1 ATTTG
60743 TCTGTCTCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 19 0.68
27 7 0.25
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (27 bp):
ATTTGAAACATTTAAACTTAAGACAAA
Found at i:65607 original size:21 final size:19
Alignment explanation
Indices: 65558--65613 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
65548 GTATCGATAT
**
65558 ATTGTATCGATACATGTTC
1 ATTGTATCGATACATGGAC
*
65577 ATTATATCGATACATGGAC
1 ATTGTATCGATACATGGAC
65596 AAATTGTATCGATACATG
1 --ATTGTATCGATACATG
65614 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (19 bp):
ATTGTATCGATACATGGAC
Found at i:65702 original size:33 final size:33
Alignment explanation
Indices: 65642--65708 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
65632 CTATCACTAT
*** *
65642 TTGTATCGATACATGGTACAATCTATCGATACA
1 TTGTATCGATACATAAAAAAATCTATCGATACA
*
65675 TTGTATCGATACATAAAAAAATGTATCGATACA
1 TTGTATCGATACATAAAAAAATCTATCGATACA
65708 T
1 T
65709 AGCTTGTAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (33 bp):
TTGTATCGATACATAAAAAAATCTATCGATACA
Found at i:71820 original size:13 final size:13
Alignment explanation
Indices: 71802--71829 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
71792 ACAACATTCC
71802 TTGTATCGATACA
1 TTGTATCGATACA
71815 TTGTATCGATACA
1 TTGTATCGATACA
71828 TT
1 TT
71830 AGGTACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:73678 original size:18 final size:19
Alignment explanation
Indices: 73633--73683 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
73623 GGAGAAAATA
*
73633 AATTGTTTAAGGGGGAGAT
1 AATTGTTTAAGGGGGAGAG
*
73652 AATCGTTTAAGGGGG-GAG
1 AATTGTTTAAGGGGGAGAG
*
73670 AATTTTTTAAGGGG
1 AATTGTTTAAGGGG
73684 AGAAAAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.31
Consensus pattern (19 bp):
AATTGTTTAAGGGGGAGAG
Found at i:74265 original size:32 final size:33
Alignment explanation
Indices: 74205--74269 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
74195 CACACCCAGA
* *
74205 TGTATCGATACATGCTGCTTTGTATCGATATAT
1 TGTATCAATACATGCTGCATTGTATCGATATAT
*
74238 TGTATCAATACATG-TTCATTGTATCGATATAT
1 TGTATCAATACATGCTGCATTGTATCGATATAT
74270 GGACAAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.55
33 13 0.45
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTATCAATACATGCTGCATTGTATCGATATAT
Found at i:76017 original size:2 final size:2
Alignment explanation
Indices: 75975--75999 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
75965 TGTCGAGCAA
75975 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
76000 ATAAACTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:76974 original size:3 final size:3
Alignment explanation
Indices: 76966--76994 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
76956 TATTTTTAAT
76966 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
76995 TTGTCAGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:77178 original size:2 final size:2
Alignment explanation
Indices: 77171--77198 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
77161 GTCAGTGTAT
77171 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
77199 AATAGATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:77946 original size:2 final size:2
Alignment explanation
Indices: 77939--77963 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
77929 TTACCAGATG
77939 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
77964 GGAGCAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:78549 original size:2 final size:2
Alignment explanation
Indices: 78542--78579 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
78532 TATCTCCAAA
78542 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
78580 GCATCTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:79631 original size:2 final size:2
Alignment explanation
Indices: 79624--79668 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
79614 GTGCATGCGC
79624 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
79666 AT A
1 AT A
79669 ACTAAGCTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:80687 original size:2 final size:2
Alignment explanation
Indices: 80680--80709 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
80670 ATCCAATCGA
80680 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80710 TTATCAGATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81286 original size:25 final size:25
Alignment explanation
Indices: 81237--81285 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
81227 GGAAAAACTG
*
81237 AAAAGAAAAGAAAAGAACAGTTTTT
1 AAAAGAAAAGAAAACAACAGTTTTT
81262 AAAAGAAAAG-AAACAACAGTTTTT
1 AAAAGAAAAGAAAACAACAGTTTTT
81286 TTTTCTCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.59, C:0.06, G:0.14, T:0.20
Consensus pattern (25 bp):
AAAAGAAAAGAAAACAACAGTTTTT
Found at i:86177 original size:25 final size:25
Alignment explanation
Indices: 86149--86199 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
86139 TTTATAATAA
*
86149 AAATTAGCCATAAAT-TTTGACAAAT
1 AAATAAGCC-TAAATATTTGACAAAT
**
86174 AAATAAGCCTCCATATTTGACAAAT
1 AAATAAGCCTAAATATTTGACAAAT
86199 A
1 A
86200 TAAAGGAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (25 bp):
AAATAAGCCTAAATATTTGACAAAT
Found at i:87772 original size:21 final size:21
Alignment explanation
Indices: 87747--87801 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
87737 TTGTAGCGAA
87747 CATCTTTTTTGCTAGAAGATC
1 CATCTTTTTTGCTAGAAGATC
*
87768 CATCTTTCTTGCTAGAAGATC
1 CATCTTTTTTGCTAGAAGATC
87789 CATCTTTCTTTGC
1 CATCTTT-TTTGC
87802 AAATACCCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.44
Consensus pattern (21 bp):
CATCTTTTTTGCTAGAAGATC
Found at i:91430 original size:3 final size:3
Alignment explanation
Indices: 91422--91475 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
91412 TCATTCTCCA
91422 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
91470 CTT CTT
1 CTT CTT
91476 GTCCACGTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:91686 original size:21 final size:21
Alignment explanation
Indices: 91653--91693 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
91643 GCTTGTGCCT
91653 GAACATGCGAGAGTGAAAGAA
1 GAACATGCGAGAGTGAAAGAA
*
91674 GAACA-GCGTAGAGTTAAAGA
1 GAACATGCG-AGAGTGAAAGA
91694 GTTGAGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.46, C:0.10, G:0.32, T:0.12
Consensus pattern (21 bp):
GAACATGCGAGAGTGAAAGAA
Found at i:99377 original size:3 final size:3
Alignment explanation
Indices: 99363--99411 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
99353 ATAAATAAAT
* *
99363 ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
99411 A
1 A
99412 AATGATAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:99673 original size:5 final size:5
Alignment explanation
Indices: 99658--99699 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
99648 ATATATGTTA
* *
99658 TTTGG -TTGG TTTGG TTTGG TTTGG TTT-A TTTCG TTTGG TTTG
1 TTTGG TTTGG TTTGG TTTGG TTTGG TTTGG TTTGG TTTGG TTTG
99700 ATGGGATCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 7 0.22
5 25 0.78
ACGTcount: A:0.02, C:0.02, G:0.33, T:0.62
Consensus pattern (5 bp):
TTTGG
Found at i:99682 original size:19 final size:19
Alignment explanation
Indices: 99658--99699 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
99648 ATATATGTTA
* *
99658 TTTGGTTGGTTTGGTTTGG
1 TTTGGTTGATTTCGTTTGG
*
99677 TTTGGTTTATTTCGTTTGG
1 TTTGGTTGATTTCGTTTGG
99696 TTTG
1 TTTG
99700 ATGGGATCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.02, C:0.02, G:0.33, T:0.62
Consensus pattern (19 bp):
TTTGGTTGATTTCGTTTGG
Found at i:100809 original size:28 final size:29
Alignment explanation
Indices: 100774--100830 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
100764 CCCTTACTCA
100774 AAATTTAATTG-TTTTTTTCCCT-AATAT
1 AAATTTAATTGCTTTTTTTCCCTCAATAT
*
100801 AAATATTAATTGCTTTTTTTTCCTCAATAT
1 AAAT-TTAATTGCTTTTTTTCCCTCAATAT
100831 TCATATTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 4 0.15
28 7 0.27
29 10 0.38
30 5 0.19
ACGTcount: A:0.30, C:0.12, G:0.04, T:0.54
Consensus pattern (29 bp):
AAATTTAATTGCTTTTTTTCCCTCAATAT
Found at i:104117 original size:2 final size:2
Alignment explanation
Indices: 104110--104134 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
104100 AACAAAGGAT
104110 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
104135 TAATAATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:104782 original size:2 final size:2
Alignment explanation
Indices: 104775--104812 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
104765 GTTAAGATTT
*
104775 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
104813 AAAGAGTATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:110807 original size:7 final size:7
Alignment explanation
Indices: 110789--110846 Score: 66
Period size: 7 Copynumber: 8.6 Consensus size: 7
110779 TGAAAAGGAA
*
110789 AGTATAT
1 AGTATGT
110796 AGTATGT
1 AGTATGT
*
110803 GGTATGT
1 AGTATGT
*
110810 GGTATGT
1 AGTATGT
110817 AGTATGT
1 AGTATGT
110824 AGTATGT
1 AGTATGT
*
110831 CGTA-GT
1 AGTATGT
110837 AGTA-GT
1 AGTATGT
110843 AGTA
1 AGTA
110847 GTGGAGTTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
6 11 0.24
7 35 0.76
ACGTcount: A:0.28, C:0.02, G:0.31, T:0.40
Consensus pattern (7 bp):
AGTATGT
Found at i:110819 original size:21 final size:21
Alignment explanation
Indices: 110790--110846 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
110780 GAAAAGGAAA
* * *
110790 GTATATAGTATGTGGTATGTG
1 GTATGTAGTATGTAGTATGTC
110811 GTATGTAGTATGTAGTATGTC
1 GTATGTAGTATGTAGTATGTC
110832 GTA-GTAGTA-GTAGTA
1 GTATGTAGTATGTAGTA
110847 GTGGAGTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 6 0.18
20 6 0.18
21 21 0.64
ACGTcount: A:0.26, C:0.02, G:0.32, T:0.40
Consensus pattern (21 bp):
GTATGTAGTATGTAGTATGTC
Found at i:111319 original size:2 final size:2
Alignment explanation
Indices: 111314--111350 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
111304 GCTTTTTTAA
*
111314 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
111351 CCAATCTGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:114825 original size:19 final size:18
Alignment explanation
Indices: 114797--114832 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
114787 GATGGATGAG
114797 AAGAGAAGAAAAAGATAA
1 AAGAGAAGAAAAAGATAA
*
114815 AAGATGAAGAAAATGATA
1 AAGA-GAAGAAAAAGATA
114833 GAAATGTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.11
Consensus pattern (18 bp):
AAGAGAAGAAAAAGATAA
Found at i:116224 original size:31 final size:31
Alignment explanation
Indices: 116178--116247 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
116168 AAAAAAGTTT
*
116178 TTTAAAAAATTAAAATATTAAAAA-TA-TATA
1 TTTAAAAAATAAAAATA-TAAAAATTATTATA
*
116208 TTTAAAATAATAAAAATATAAAAATTATTTTA
1 TTTAAAA-AATAAAAATATAAAAATTATTATA
116240 TTTAAAAA
1 TTTAAAAA
116248 TTAATTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 13 0.37
31 12 0.34
32 10 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
TTTAAAAAATAAAAATATAAAAATTATTATA
Found at i:116231 original size:45 final size:45
Alignment explanation
Indices: 116182--116268 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 45
116172 AAGTTTTTTA
116182 AAAAATTAAAATA-TTAAAAATATATATT-TAAAATAATAAAAATAT
1 AAAAATTAAAATATTTAAAAAT-TA-ATTATAAAATAATAAAAATAT
*** *
116227 AAAAATTATTTTATTTAAAAATTAATTATTAAATAATAAAAA
1 AAAAATTAAAATATTTAAAAATTAATTATAAAATAATAAAAA
116269 ATTTATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 3 0.08
45 25 0.69
46 8 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (45 bp):
AAAAATTAAAATATTTAAAAATTAATTATAAAATAATAAAAATAT
Found at i:118595 original size:20 final size:20
Alignment explanation
Indices: 118552--118597 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
118542 TTTTAAATTT
**
118552 TATTTATTTTTTAATTTTTG
1 TATTTATTTTTTAATTTTAA
118572 TATTTATTTTCTTAA-TTTAA
1 TATTTATTTT-TTAATTTTAA
118592 TATTTA
1 TATTTA
118598 AGTATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (20 bp):
TATTTATTTTTTAATTTTAA
Found at i:126747 original size:16 final size:17
Alignment explanation
Indices: 126720--126751 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
126710 ATAATAATAA
126720 TTAAATAATAAAAAATT
1 TTAAATAATAAAAAATT
126737 TTAAA-AATAAAAAAT
1 TTAAATAATAAAAAAT
126752 AAAAACTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAAATAATAAAAAATT
Found at i:127701 original size:2 final size:2
Alignment explanation
Indices: 127694--127721 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
127684 AAGGTGATAA
127694 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
127722 CAAGCAAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:127975 original size:5 final size:5
Alignment explanation
Indices: 127967--127991 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
127957 AAGTTCAGGT
127967 CAGCC CAGCC CAGCC CAGCC CAGCC
1 CAGCC CAGCC CAGCC CAGCC CAGCC
127992 TCTCCTCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
CAGCC
Found at i:128060 original size:6 final size:6
Alignment explanation
Indices: 128049--128081 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
128039 CTTCTCTTTC
*
128049 CTTCAA CTTCAA CTTCAA CTTCAA CTTCGA CTT
1 CTTCAA CTTCAA CTTCAA CTTCAA CTTCAA CTT
128082 TCAATCTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.27, C:0.33, G:0.03, T:0.36
Consensus pattern (6 bp):
CTTCAA
Found at i:132002 original size:2 final size:2
Alignment explanation
Indices: 131995--132020 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
131985 TTTCTAATTC
131995 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
132021 GCATGATCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:137202 original size:6 final size:6
Alignment explanation
Indices: 137191--137219 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
137181 AAGATGTGAT
137191 CTAATA CTAATA CTAATA CTAATA CTAAT
1 CTAATA CTAATA CTAATA CTAATA CTAAT
137220 GGTATAGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.34
Consensus pattern (6 bp):
CTAATA
Found at i:144107 original size:24 final size:24
Alignment explanation
Indices: 144075--144122 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
144065 AGTAATCATT
144075 AATCTTTGTTCTAAATGGTTTCTA
1 AATCTTTGTTCTAAATGGTTTCTA
144099 AATCTTTGTTCTAAATGGTTTCTA
1 AATCTTTGTTCTAAATGGTTTCTA
144123 TTGTAAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (24 bp):
AATCTTTGTTCTAAATGGTTTCTA
Found at i:153105 original size:20 final size:21
Alignment explanation
Indices: 153076--153114 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
153066 ATTATATATT
153076 ATTATCTGTTAAA-ATTTATA
1 ATTATCTGTTAAATATTTATA
*
153096 ATTATTTGTTAAATATTTA
1 ATTATCTGTTAAATATTTA
153115 ATATTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (21 bp):
ATTATCTGTTAAATATTTATA
Found at i:153693 original size:3 final size:3
Alignment explanation
Indices: 153685--153718 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
153675 TGAACAAAAT
153685 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
153719 ATAAACACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:153737 original size:2 final size:2
Alignment explanation
Indices: 153730--153771 Score: 59
Period size: 2 Copynumber: 20.5 Consensus size: 2
153720 TAAACACATT
153730 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA -A TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA T-A TA T
153772 TACTATTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 1 0.03
2 33 0.89
3 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:154837 original size:6 final size:6
Alignment explanation
Indices: 154828--154853 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
154818 AGCAGCCCCA
154828 TACTGC TACTGC TACTGC TACTGC TA
1 TACTGC TACTGC TACTGC TACTGC TA
154854 GGGCCTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.15, T:0.35
Consensus pattern (6 bp):
TACTGC
Found at i:170209 original size:30 final size:33
Alignment explanation
Indices: 170175--170236 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
170165 ATATGAATAT
*
170175 ATGTA-TAAAATTT-TA-TAATATAAATTATTA
1 ATGTATTAAAATTTATATTAATATAAAATATTA
170205 ATGTATTAAAATTTATATTAATATAAAATATT
1 ATGTATTAAAATTTATATTAATATAAAATATT
170237 TTAAATACGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 5 0.18
31 8 0.29
32 2 0.07
33 13 0.46
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (33 bp):
ATGTATTAAAATTTATATTAATATAAAATATTA
Found at i:170231 original size:17 final size:17
Alignment explanation
Indices: 170178--170233 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 17
170168 TGAATATATG
170178 TATAAAATTT-TA-TAA
1 TATAAAATTTATATTAA
*
170193 TATAAATTATTA-ATGT-A
1 TATAAAAT-TTATAT-TAA
170210 T-TAAAATTTATATTAA
1 TATAAAATTTATATTAA
170226 TATAAAAT
1 TATAAAAT
170234 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
15 11 0.34
16 12 0.38
17 8 0.25
18 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
TATAAAATTTATATTAA
Found at i:173597 original size:25 final size:25
Alignment explanation
Indices: 173501--173600 Score: 86
Period size: 26 Copynumber: 4.1 Consensus size: 25
173491 CAATTTGTTA
* *
173501 TAATAAAATAAATATTTTATAAAAAT
1 TAATAAAATAAA-ATATTATAAAATT
* *
173527 AAATAAAATAAAAATATTATGAAA--
1 TAATAAAAT-AAAATATTATAAAATT
*
173551 TAATAATAATAATA-ATT-T--AATT
1 TAATAA-AATAAAATATTATAAAATT
173573 TAATAAAATAAAATATTATAAAATT
1 TAATAAAATAAAATATTATAAAATT
173598 TAA
1 TAA
173601 ATTATTGATA
Statistics
Matches: 60, Mismatches: 6, Indels: 17
0.72 0.07 0.20
Matches are distributed among these distances:
20 2 0.03
21 6 0.10
22 10 0.17
23 4 0.07
24 8 0.13
25 10 0.17
26 17 0.28
27 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (25 bp):
TAATAAAATAAAATATTATAAAATT
Found at i:173683 original size:2 final size:2
Alignment explanation
Indices: 173676--173711 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
173666 TAGATTTGAT
173676 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
173712 AACAAAAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:175437 original size:23 final size:21
Alignment explanation
Indices: 175388--175451 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 21
175378 TTTATCTGTT
* * *
175388 AAAAATAAAAAAG-AATGATA
1 AAAAATAAAAAGGAAAAGAAA
*
175408 AAAAATAAATATGGAAAGAGAAA
1 AAAAATAAA-AAGGAAA-AGAAA
175431 AAAAATAAAAAGGAAAAGAAA
1 AAAAATAAAAAGGAAAAGAAA
175452 GAAGAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 9 0.25
21 7 0.19
22 8 0.22
23 12 0.33
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (21 bp):
AAAAATAAAAAGGAAAAGAAA
Found at i:175704 original size:2 final size:2
Alignment explanation
Indices: 175699--175723 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
175689 ATATATATAT
175699 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
175724 ATAATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:178353 original size:2 final size:2
Alignment explanation
Indices: 178346--178374 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
178336 ATTGTATCAT
178346 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
178375 GCTCTAGTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:180379 original size:3 final size:3
Alignment explanation
Indices: 180373--180405 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
180363 GGAGGAGGAG
*
180373 GAA GAA GAA GAA GAA GAA GAA GGA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
180406 AACTTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:198799 original size:15 final size:15
Alignment explanation
Indices: 198779--198809 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
198769 TACAAAAACA
198779 AAAAAATAAATAAAT
1 AAAAAATAAATAAAT
*
198794 AAAAAATAAATCAAT
1 AAAAAATAAATAAAT
198809 A
1 A
198810 TTCCCAATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAAAATAAATAAAT
Found at i:199213 original size:2 final size:2
Alignment explanation
Indices: 199206--199240 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
199196 CAGTAGGAAA
* *
199206 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
199241 CAAAATACCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:199227 original size:16 final size:16
Alignment explanation
Indices: 199206--199240 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
199196 CAGTAGGAAA
199206 ATATATATATATACAT
1 ATATATATATATACAT
199222 ATATATATATATACAT
1 ATATATATATATACAT
199238 ATA
1 ATA
199241 CAAAATACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATATATATATACAT
Found at i:204189 original size:13 final size:13
Alignment explanation
Indices: 204171--204196 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
204161 TCAATTTATC
204171 TTTATTATTAAAT
1 TTTATTATTAAAT
204184 TTTATTATTAAAT
1 TTTATTATTAAAT
204197 ATTTTACGCA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTATTATTAAAT
Found at i:205802 original size:42 final size:43
Alignment explanation
Indices: 205740--205823 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
205730 TTACGTATCT
* *
205740 AAATTCTATAAAAAGTTTAAAAATTTGTTAAGAACATAATTTA
1 AAATTCTATAAAAACTTTAAAAATCTGTTAAGAACATAATTTA
* *
205783 AAATT-TATGAAAACTTTAAAAATCTGTTAGGAACATAATTT
1 AAATTCTATAAAAACTTTAAAAATCTGTTAAGAACATAATTT
205824 TAATTGCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 32 0.86
43 5 0.14
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (43 bp):
AAATTCTATAAAAACTTTAAAAATCTGTTAAGAACATAATTTA
Found at i:206489 original size:2 final size:2
Alignment explanation
Indices: 206482--206521 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
206472 ATGATAATAC
*
206482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
206522 AACCTAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:207264 original size:24 final size:25
Alignment explanation
Indices: 207237--207285 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
207227 TGTACTATTC
**
207237 ATATATAAATTTCAT-ACATTATCT
1 ATATATAAATCACATGACATTATCT
207261 ATATATAAATCACATGACATTATCT
1 ATATATAAATCACATGACATTATCT
207286 CATTAAGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (25 bp):
ATATATAAATCACATGACATTATCT
Found at i:207705 original size:6 final size:6
Alignment explanation
Indices: 207688--207724 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
207678 TTTAAAATAG
* *
207688 TGATCA TAATCA TGATCA TGATCA TGATCA TGCTCA T
1 TGATCA TGATCA TGATCA TGATCA TGATCA TGATCA T
207725 CCTACATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (6 bp):
TGATCA
Found at i:207895 original size:2 final size:2
Alignment explanation
Indices: 207888--207912 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
207878 ATTTGATACC
207888 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
207913 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:207917 original size:2 final size:2
Alignment explanation
Indices: 207912--207941 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
207902 ATATATATAT
207912 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
207942 CATAGGGCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:209230 original size:2 final size:2
Alignment explanation
Indices: 209218--209246 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
209208 ATCGTGATGG
209218 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
209247 GAGTACATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:211159 original size:2 final size:2
Alignment explanation
Indices: 211152--211182 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
211142 TACTACAGTT
211152 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
211183 GGCTGTTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:211672 original size:2 final size:2
Alignment explanation
Indices: 211665--211696 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
211655 CTACTGGGTA
211665 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
211697 TACCAACTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:222857 original size:16 final size:15
Alignment explanation
Indices: 222832--222875 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
222822 ATATTTTTAG
222832 AAATTAATAAAATAA
1 AAATTAATAAAATAA
222847 AAATATAATAATAA-AA
1 AAAT-TAATAA-AATAA
*
222863 AAATTAATGAAAT
1 AAATTAATAAAAT
222876 TGAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 2 0.08
15 9 0.36
16 12 0.48
17 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (15 bp):
AAATTAATAAAATAA
Found at i:228197 original size:12 final size:12
Alignment explanation
Indices: 228180--228212 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
228170 TCTCTTTTGT
228180 GTGTGTGTGCAC
1 GTGTGTGTGCAC
228192 GTGTGTGTGCAC
1 GTGTGTGTGCAC
*
228204 GCGTGTGTG
1 GTGTGTGTG
228213 TGTTTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.15, G:0.45, T:0.33
Consensus pattern (12 bp):
GTGTGTGTGCAC
Found at i:228469 original size:2 final size:2
Alignment explanation
Indices: 228462--228510 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
228452 TAAAATGGGC
228462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
228504 TA TA TA T
1 TA TA TA T
228511 GAATGAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:232792 original size:47 final size:47
Alignment explanation
Indices: 232718--232814 Score: 176
Period size: 47 Copynumber: 2.1 Consensus size: 47
232708 ATGCTCTCCA
* *
232718 GCATTGGCAGAATTATTTTGCATGTTATTCCTTTCATCCCATGTTTT
1 GCATCGGCAGAATTATGTTGCATGTTATTCCTTTCATCCCATGTTTT
232765 GCATCGGCAGAATTATGTTGCATGTTATTCCTTTCATCCCATGTTTT
1 GCATCGGCAGAATTATGTTGCATGTTATTCCTTTCATCCCATGTTTT
232812 GCA
1 GCA
232815 ACGTAATTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.20, C:0.21, G:0.16, T:0.43
Consensus pattern (47 bp):
GCATCGGCAGAATTATGTTGCATGTTATTCCTTTCATCCCATGTTTT
Found at i:234070 original size:42 final size:43
Alignment explanation
Indices: 234011--234096 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
234001 TAAAGTTATA
234011 TGTGTATTTGTCTGCTAA-TTATTAGCATTTTTTATCTCGACT
1 TGTGTATTTGTCTGCTAATTTATTAGCATTTTTTATCTCGACT
234053 TGTGTATTTGTCTGCTAATTTATTAGCATTTTTTATCTCGACT
1 TGTGTATTTGTCTGCTAATTTATTAGCATTTTTTATCTCGACT
234096 T
1 T
234097 ACTGTTGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 18 0.42
43 25 0.58
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.53
Consensus pattern (43 bp):
TGTGTATTTGTCTGCTAATTTATTAGCATTTTTTATCTCGACT
Found at i:236880 original size:42 final size:42
Alignment explanation
Indices: 236814--236895 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
236804 ATTGACAAGA
*
236814 GCAATAGAGAAGTCATTTACATGAATTGGGGGCTTACTGATG
1 GCAATAGAGAAGTCATGTACATGAATTGGGGGCTTACTGATG
*
236856 GCAATAGAGAAGTCATGTAGATGAATTGGGGGCTTACTGA
1 GCAATAGAGAAGTCATGTACATGAATTGGGGGCTTACTGA
236896 AATATGTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (42 bp):
GCAATAGAGAAGTCATGTACATGAATTGGGGGCTTACTGATG
Found at i:237627 original size:91 final size:92
Alignment explanation
Indices: 237470--237651 Score: 321
Period size: 91 Copynumber: 2.0 Consensus size: 92
237460 AGGAGCTTAG
* *
237470 TGCTCTGGGAAAAGGAAAGAGAAGCCGTAAGCAGGTATTCTATTATCACCATAACTTCAAAATTT
1 TGCTCTGGAAAAAGGAAAGAGAAGCAGTAAGCAGGTATTCTATTATCACCATAACTTCAAAATTT
237535 GATTAGTCAGATAGTGATTTGTTTAAA
66 GATTAGTCAGATAGTGATTTGTTTAAA
* *
237562 TGCTCTGGAAAAAGGAAAGAGAAGCAGTAAGCA-GTATTCTTTTATCACCATAACTTCAAACTTT
1 TGCTCTGGAAAAAGGAAAGAGAAGCAGTAAGCAGGTATTCTATTATCACCATAACTTCAAAATTT
237626 GATTAGTCAGATAGTGATTTGTTTAA
66 GATTAGTCAGATAGTGATTTGTTTAA
237652 GGCACCTTAA
Statistics
Matches: 86, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
91 55 0.64
92 31 0.36
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (92 bp):
TGCTCTGGAAAAAGGAAAGAGAAGCAGTAAGCAGGTATTCTATTATCACCATAACTTCAAAATTT
GATTAGTCAGATAGTGATTTGTTTAAA
Found at i:239349 original size:145 final size:143
Alignment explanation
Indices: 239086--239373 Score: 468
Period size: 145 Copynumber: 2.0 Consensus size: 143
239076 CTTGGAGAAA
* ** * *
239086 TGTTGATTTTTCATGTATGATATAAAATTTTGGATGTTTTTATGCGTTTTGAAGGATACTTTGCA
1 TGTTGATTTTTCATGCATGATATAAAAAATTGGATGTTTTAATGCATTTTGAAGGATACTTTGCA
* *
239151 GTAAGTGTTTTAGGCTACTAAAAAGTTAAGGGAAATATAAAAGTAATTTTAGTTTAAATTATGAT
66 GTAAGTGTTTTAGGCAACTAAAAAGTTAAGGAAAATATAAAAGTAATTTTAGTTT-AATT-TGAT
239216 TGGAAAGTTACAGTG
129 TGGAAAGTTACAGTG
* * *
239231 TGTTGATTTTTCTTGCGTGATATAAAAAATTGGATGTTTTAATGCATTTTGAAGGATGCTTTGCA
1 TGTTGATTTTTCATGCATGATATAAAAAATTGGATGTTTTAATGCATTTTGAAGGATACTTTGCA
239296 GTAAGTGTTTTAGGCAACTAAAAAGTTAAGGAAAATATAAAAGTAATTTTAGTTTAATTTGATTG
66 GTAAGTGTTTTAGGCAACTAAAAAGTTAAGGAAAATATAAAAGTAATTTTAGTTTAATTTGATTG
239361 GAAAGTTACAGTG
131 GAAAGTTACAGTG
239374 CGATTGAAAT
Statistics
Matches: 133, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
143 19 0.14
144 4 0.03
145 110 0.83
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (143 bp):
TGTTGATTTTTCATGCATGATATAAAAAATTGGATGTTTTAATGCATTTTGAAGGATACTTTGCA
GTAAGTGTTTTAGGCAACTAAAAAGTTAAGGAAAATATAAAAGTAATTTTAGTTTAATTTGATTG
GAAAGTTACAGTG
Found at i:241054 original size:63 final size:64
Alignment explanation
Indices: 240977--241104 Score: 240
Period size: 63 Copynumber: 2.0 Consensus size: 64
240967 ATATTATCTG
*
240977 TTGCTAAAGCTGGTTTTTAGCTGTTGCATGAACATTGAAATTTTAAATGAATTTTACAGATGCT
1 TTGCTAAAGCTGGTTTTTAGCTGTTGCATGAACATTGAAATTTTAAATGAATTTCACAGATGCT
241041 TTGCT-AAGCTGGTTTTTAGCTGTTGCATGAACATTGAAATTTTAAATGAATTTCACAGATGCT
1 TTGCTAAAGCTGGTTTTTAGCTGTTGCATGAACATTGAAATTTTAAATGAATTTCACAGATGCT
241104 T
1 T
241105 GCAGACTTAC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
63 58 0.92
64 5 0.08
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41
Consensus pattern (64 bp):
TTGCTAAAGCTGGTTTTTAGCTGTTGCATGAACATTGAAATTTTAAATGAATTTCACAGATGCT
Found at i:242932 original size:2 final size:2
Alignment explanation
Indices: 242925--242960 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
242915 ACTTGTTAAA
242925 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
242961 TAGCTTTCGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:243477 original size:3 final size:3
Alignment explanation
Indices: 243469--243493 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
243459 AAAAAGTCTA
243469 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
243494 TAGTAGCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:243656 original size:2 final size:2
Alignment explanation
Indices: 243649--243677 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
243639 TGAGGACCCA
243649 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
243678 GTCATGTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:246880 original size:26 final size:26
Alignment explanation
Indices: 246851--246903 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
246841 AATGTAGTGG
246851 AAAAGAAAGTAACGTAAATTTCTCAC
1 AAAAGAAAGTAACGTAAATTTCTCAC
246877 AAAAGAAAGTAACGTAAATTTCTCAC
1 AAAAGAAAGTAACGTAAATTTCTCAC
246903 A
1 A
246904 GGTTATTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.15, G:0.11, T:0.23
Consensus pattern (26 bp):
AAAAGAAAGTAACGTAAATTTCTCAC
Found at i:252909 original size:2 final size:2
Alignment explanation
Indices: 252891--252928 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
252881 AGGTAAATTT
* *
252891 AG AG GG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
252929 GGAGCAAGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
AG
Done.