Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold273
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: 639416
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 15802 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:121 original size:14 final size:14
Alignment explanation
Indices: 83--121 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
73 ACACTATCCC
83 TAAACCCTAAATCA
1 TAAACCCTAAATCA
** *
97 TAAACTATAAATCG
1 TAAACCCTAAATCA
111 TAAACCCTAAA
1 TAAACCCTAAA
122 CTATAAACAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.51, C:0.23, G:0.03, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:135 original size:21 final size:22
Alignment explanation
Indices: 97--144 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
87 CCCTAAATCA
97 TAAACTATAAATCGTAAACCC-
1 TAAACTATAAATCGTAAACCCG
*
118 TAAACTATAAA-CATTAAACCCG
1 TAAACTATAAATC-GTAAACCCG
140 TAAAC
1 TAAAC
145 CACAAACACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 18 0.75
22 5 0.21
ACGTcount: A:0.50, C:0.23, G:0.04, T:0.23
Consensus pattern (22 bp):
TAAACTATAAATCGTAAACCCG
Found at i:151 original size:22 final size:21
Alignment explanation
Indices: 111--152 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
101 CTATAAATCG
* *
111 TAAACCCTAAACTATAAACAT
1 TAAACCCTAAACCACAAACAT
132 TAAACCCGTAAACCACAAACA
1 TAAACCC-TAAACCACAAACA
153 CCAACCACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.52, C:0.29, G:0.02, T:0.17
Consensus pattern (21 bp):
TAAACCCTAAACCACAAACAT
Found at i:158 original size:21 final size:20
Alignment explanation
Indices: 141--183 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
131 TTAAACCCGT
141 AAACCACAAACACCAACCACC
1 AAACCACAAACACCAACC-CC
*
162 AAACCTCAAACACCAACCCC
1 AAACCACAAACACCAACCCC
182 AA
1 AA
184 TATACCATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.51, C:0.47, G:0.00, T:0.02
Consensus pattern (20 bp):
AAACCACAAACACCAACCCC
Found at i:2289 original size:2 final size:2
Alignment explanation
Indices: 2282--2307 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2272 GATCAGAGAC
2282 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
2308 CACTGCTATA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4859 original size:11 final size:11
Alignment explanation
Indices: 4795--4906 Score: 69
Period size: 11 Copynumber: 10.5 Consensus size: 11
4785 AAATTAATCC
4795 TCTCTCAAATT
1 TCTCTCAAATT
4806 TCCTCTC-AATT
1 T-CTCTCAAATT
4817 TGCTCTC-AATT
1 T-CTCTCAAATT
4828 TGCTCTCAAATT
1 T-CTCTCAAATT
*
4840 CCT-TCCAAATT
1 TCTCT-CAAATT
4851 TCTCTCAAA--
1 TCTCTCAAATT
*
4860 --TC-CATATT
1 TCTCTCAAATT
* *
4868 TAATCTCAATTT
1 T-CTCTCAAATT
*
4880 TCTCTCAAGTT
1 TCTCTCAAATT
*
4891 TCTCTTAAATT
1 TCTCTCAAATT
4902 TCTCT
1 TCTCT
4907 TAACTCCCTT
Statistics
Matches: 81, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
6 3 0.04
7 2 0.02
10 1 0.01
11 60 0.74
12 15 0.19
ACGTcount: A:0.24, C:0.28, G:0.03, T:0.46
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:5889 original size:7 final size:7
Alignment explanation
Indices: 5877--5902 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5867 TAGTCGATTG
5877 GTATTTA
1 GTATTTA
5884 GTATTTA
1 GTATTTA
5891 GTATTTA
1 GTATTTA
5898 GTATT
1 GTATT
5903 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:6580 original size:18 final size:18
Alignment explanation
Indices: 6553--6592 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
6543 CAGGTGCGTT
*
6553 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
6571 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
6589 TCCT
1 TCCT
6593 TTTCCGAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:7014 original size:11 final size:9
Alignment explanation
Indices: 6978--7009 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
6968 TATTTGTACA
6978 AATATTTTG
1 AATATTTTG
6987 AATATTTTG
1 AATATTTTG
6996 AATATTTTG
1 AATATTTTG
7005 -ATATT
1 AATATT
7010 ATTTTATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.22
9 18 0.78
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (9 bp):
AATATTTTG
Found at i:10542 original size:125 final size:124
Alignment explanation
Indices: 10296--10641 Score: 464
Period size: 125 Copynumber: 2.8 Consensus size: 124
10286 CAAACATGCT
* * *
10296 ACTGTAGCAAAAGCGCATCCACGTGGGCGCGATTTCAGAAATTCTTCTCATAAAGTATCCTGGTA
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAGAAATTCTTCTCATAAAGCATCCTGGTA
* *
10361 GAAGCAATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGACCA
66 GAAGC-ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTCTTCCAGGACCA
*
10421 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAGAAATTCTTCTCA-AATAGCATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAGAAATTCTTCTCATAA-AGCATCCTGGT
* * * *
10485 TGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTT-TTTCAGGATCT
65 AGAAGCA--TTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTCTTCCAGGACCA
* * * * * *
10546 ACTGTAGCAAAAGCACGTCCAC-ATGGGTGCGATTTAACAAATTATTCTCATAAAACATCCTGGT
1 ACTGTAGCAAAAGCGCGTCCACGA-GGGCGCGATTTCAGAAATTCTTCTCATAAAGCATCCTGGT
*
10610 AAAAGCGATTTTATACTATTTGCTCAGAAACG
65 AGAAGC-ATTTTATACTATTTGCTCAGAAACG
10642 ATTTCAGAAA
Statistics
Matches: 196, Mismatches: 19, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
124 28 0.14
125 126 0.64
126 42 0.21
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Consensus pattern (124 bp):
ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAGAAATTCTTCTCATAAAGCATCCTGGTA
GAAGCATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATAATTTCTTCCAGGACCA
Found at i:10686 original size:65 final size:65
Alignment explanation
Indices: 10575--10705 Score: 199
Period size: 65 Copynumber: 2.0 Consensus size: 65
10565 CACATGGGTG
*
10575 CGATTTAACAAATTATTCTCATAAAACATCCTGGTAAAAGCGATTTTATACTATTTGCTCAGAAA
1 CGATTTAACAAATTATTCTCATAAAACATCCTGGTAAAAGCAATTTTATACTATTTGCTCAGAAA
* * * ** *
10640 CGATTTCAGAAATTCTTCTCATAAAGTATCCTGGTAGAAGCAATTTTATACTATTTGCTCAGAAA
1 CGATTTAACAAATTATTCTCATAAAACATCCTGGTAAAAGCAATTTTATACTATTTGCTCAGAAA
10705 C
1 C
10706 ATCAACTCGA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (65 bp):
CGATTTAACAAATTATTCTCATAAAACATCCTGGTAAAAGCAATTTTATACTATTTGCTCAGAAA
Found at i:10797 original size:190 final size:190
Alignment explanation
Indices: 10450--10832 Score: 515
Period size: 190 Copynumber: 2.0 Consensus size: 190
10440 CACGAGGGCG
* *
10450 CGATTTCAGAAATTCTTCTCAAATAGCATCCTGCTTGAAGCATTTTTTATACTATTTGCTCAGAA
1 CGATTTCAGAAATTCTTCTCAAATAGCATCCTGCTAGAAGCATATTTTATACTATTTGCTCAGAA
* * * * *
10515 ACGTCAACTCGAAATAATTTTTTCAGGATCTACTGTAGCAAAAGCACGTCCACATGGGTGCGATT
66 ACATCAACTCGAAATAATTTTTCCAGGACCAACTGTAGCAAAAGCACGTCCACATGGGCGCGATT
*
10580 TAACAAATTATTCTCATAAAACATCCTGGTAAAAGCGA-TTTTATACTATTTGCTCAGAAA
131 TAACAAATTATTCTCATAAAACATCCTGCTAAAAGC-ATTTTTATACTATTTGCTCAGAAA
* *
10640 CGATTTCAGAAATTCTTCTCATAA-AGTATCCTGGTAGAAGCA-ATTTTATACTATTTGCTCAGA
1 CGATTTCAGAAATTCTTCTCA-AATAGCATCCTGCTAGAAGCATATTTTATACTATTTGCTCAGA
* *
10703 AACATCAACTCGAAATTATTTCTTCCAGGACCAACTGTAGCAAAAGCGCGTCCACGA-GGGCGCG
65 AACATCAACTCGAAATAATTT-TTCCAGGACCAACTGTAGCAAAAGCACGTCCAC-ATGGGCGCG
* * * * **
10767 ATTTCAGAAATTCTTCTCA-AATAGCATCCTGCTTGAAGCATTTTTTATACTATTTGCTCAGAAA
128 ATTTAACAAATTATTCTCATAA-AACATCCTGCTAAAAGCA-TTTTTATACTATTTGCTCAGAAA
10831 CG
1 CG
10833 TCAACTCGAA
Statistics
Matches: 169, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
189 42 0.25
190 100 0.59
191 27 0.16
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (190 bp):
CGATTTCAGAAATTCTTCTCAAATAGCATCCTGCTAGAAGCATATTTTATACTATTTGCTCAGAA
ACATCAACTCGAAATAATTTTTCCAGGACCAACTGTAGCAAAAGCACGTCCACATGGGCGCGATT
TAACAAATTATTCTCATAAAACATCCTGCTAAAAGCATTTTTATACTATTTGCTCAGAAA
Found at i:10897 original size:315 final size:315
Alignment explanation
Indices: 10325--10956 Score: 1248
Period size: 315 Copynumber: 2.0 Consensus size: 315
10315 CACGTGGGCG
10325 CGATTTCAGAAATTCTTCTCATAAAGTATCCTGGTAGAAGCAATTTTATACTATTTGCTCAGAAA
1 CGATTTCAGAAATTCTTCTCATAAAGTATCCTGGTAGAAGCAATTTTATACTATTTGCTCAGAAA
10390 CATCAACTCGAAATTATTTCTTCCAGGACCAACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATT
66 CATCAACTCGAAATTATTTCTTCCAGGACCAACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATT
10455 TCAGAAATTCTTCTCAAATAGCATCCTGCTTGAAGCATTTTTTATACTATTTGCTCAGAAACGTC
131 TCAGAAATTCTTCTCAAATAGCATCCTGCTTGAAGCATTTTTTATACTATTTGCTCAGAAACGTC
10520 AACTCGAAATAATTTTTTCAGGATCTACTGTAGCAAAAGCACGTCCACATGGGTGCGATTTAACA
196 AACTCGAAATAATTTTTTCAGGATCTACTGTAGCAAAAGCACGTCCACATGGGTGCGATTTAACA
10585 AATTATTCTCATAAAACATCCTGGTAAAAGCGATTTTATACTATTTGCTCAGAAA
261 AATTATTCTCATAAAACATCCTGGTAAAAGCGATTTTATACTATTTGCTCAGAAA
10640 CGATTTCAGAAATTCTTCTCATAAAGTATCCTGGTAGAAGCAATTTTATACTATTTGCTCAGAAA
1 CGATTTCAGAAATTCTTCTCATAAAGTATCCTGGTAGAAGCAATTTTATACTATTTGCTCAGAAA
10705 CATCAACTCGAAATTATTTCTTCCAGGACCAACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATT
66 CATCAACTCGAAATTATTTCTTCCAGGACCAACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATT
10770 TCAGAAATTCTTCTCAAATAGCATCCTGCTTGAAGCATTTTTTATACTATTTGCTCAGAAACGTC
131 TCAGAAATTCTTCTCAAATAGCATCCTGCTTGAAGCATTTTTTATACTATTTGCTCAGAAACGTC
10835 AACTCGAAATAATTTTTTCAGGATCTACTGTAGCAAAAGGCACGTCCAC-TGGGTGCGATTTAAC
196 AACTCGAAATAATTTTTTCAGGATCTACTGTAGCAAAA-GCACGTCCACATGGGTGCGATTTAAC
10899 AAATTATTCTCATAAAACATCCTGGTAAAAGCGATTTTATACTATTTGCTCAGAAA
260 AAATTATTCTCATAAAACATCCTGGTAAAAGCGATTTTATACTATTTGCTCAGAAA
10955 CG
1 CG
10957 TCAACTCAAA
Statistics
Matches: 316, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
315 306 0.97
316 10 0.03
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (315 bp):
CGATTTCAGAAATTCTTCTCATAAAGTATCCTGGTAGAAGCAATTTTATACTATTTGCTCAGAAA
CATCAACTCGAAATTATTTCTTCCAGGACCAACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATT
TCAGAAATTCTTCTCAAATAGCATCCTGCTTGAAGCATTTTTTATACTATTTGCTCAGAAACGTC
AACTCGAAATAATTTTTTCAGGATCTACTGTAGCAAAAGCACGTCCACATGGGTGCGATTTAACA
AATTATTCTCATAAAACATCCTGGTAAAAGCGATTTTATACTATTTGCTCAGAAA
Found at i:10936 original size:126 final size:123
Alignment explanation
Indices: 10640--10984 Score: 442
Period size: 125 Copynumber: 2.8 Consensus size: 123
10630 TGCTCAGAAA
*
10640 CGATTTCAGAAATTCTTCTCATAAAGTATCCTGGTAGAAGCAATTTTATACTATTTGCTCAGAAA
1 CGATTTCAGAAATTCTTCTCATAAAGCATCCTGGTAGAAGC-ATTTTATACTATTTGCTCAGAAA
* * *
10705 CATCAACTCGAAATTATTTCTTCCAGGACCAACTGTAGCAAAAGCGCGTCCACGAGGGCG
65 CGTCAACTCGAAATAATTT-TTCCAGGACCAACTGTAGCAAAAGCACGTCCACGAGGGCG
* *
10765 CGATTTCAGAAATTCTTCTCA-AATAGCATCCTGCTTGAAGCATTTTTTATACTATTTGCTCAGA
1 CGATTTCAGAAATTCTTCTCATAA-AGCATCCTGGTAGAAGCA--TTTTATACTATTTGCTCAGA
* * * * *
10829 AACGTCAACTCGAAATAATTTTTTCAGGATCTACTGTAGCAAAAGGCACGTCCAC-TGGGTG
63 AACGTCAACTCGAAATAATTTTTCCAGGACCAACTGTAGCAAAA-GCACGTCCACGAGGGCG
* * * * *
10890 CGATTTAACAAATTATTCTCATAAAACATCCTGGTAAAAGCGATTTTATACTATTTGCTCAGAAA
1 CGATTTCAGAAATTCTTCTCATAAAGCATCCTGGTAGAAGC-ATTTTATACTATTTGCTCAGAAA
* *
10955 CGTCAACTCAAAATTAATTCTTCCAGGACC
65 CGTCAACTCGAAA-TAATTTTTCCAGGACC
10985 TAAAAACCCT
Statistics
Matches: 191, Mismatches: 22, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
124 37 0.19
125 103 0.54
126 51 0.27
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Consensus pattern (123 bp):
CGATTTCAGAAATTCTTCTCATAAAGCATCCTGGTAGAAGCATTTTATACTATTTGCTCAGAAAC
GTCAACTCGAAATAATTTTTCCAGGACCAACTGTAGCAAAAGCACGTCCACGAGGGCG
Found at i:34247 original size:28 final size:28
Alignment explanation
Indices: 34215--34271 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
34205 TCTTAATTAG
34215 ATGTATTTACCTATTTAGATTTCTTTTT
1 ATGTATTTACCTATTTAGATTTCTTTTT
34243 ATGTATTTACCTATTTAGATTTCTTTTT
1 ATGTATTTACCTATTTAGATTTCTTTTT
34271 A
1 A
34272 CTTTTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.60
Consensus pattern (28 bp):
ATGTATTTACCTATTTAGATTTCTTTTT
Found at i:34709 original size:84 final size:86
Alignment explanation
Indices: 34560--34740 Score: 253
Period size: 85 Copynumber: 2.1 Consensus size: 86
34550 AACAATTACA
* *
34560 ACTAAAAACTAAAATAATCCTAGCTAAAATGTACCCTTGATAATAGCATTTTATGGGACT-AAAA
1 ACTAAAAACTAAAATAATCCTAACTAAAATGTACCCATGATAATAGCATTTTATGGGACTAAAAA
34624 AATATAACTACAA-CAAATAG
66 AATATAACTACAACCAAATAG
* *
34644 ATTAAAAACTAAAATAATCCTAACTAAAAACT-TACCCATGATAATAGCATATTT-TGGGATTAA
1 ACTAAAAACTAAAATAATCCTAACT-AAAA-TGTACCCATGATAATAGCAT-TTTATGGGACTAA
*
34707 AAAAATATAATTACAACCCAAATAG
63 AAAAATATAACTACAA-CCAAATAG
34732 ACTAAAAAC
1 ACTAAAAAC
34741 CTTACACGTA
Statistics
Matches: 85, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
84 23 0.27
85 27 0.32
86 20 0.24
88 15 0.18
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (86 bp):
ACTAAAAACTAAAATAATCCTAACTAAAATGTACCCATGATAATAGCATTTTATGGGACTAAAAA
AATATAACTACAACCAAATAG
Found at i:40220 original size:14 final size:14
Alignment explanation
Indices: 40203--40235 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
40193 ATAATAACAA
*
40203 AATAGTAGCAATAT
1 AATAATAGCAATAT
40217 AATAATAGCAATAT
1 AATAATAGCAATAT
40231 AATAA
1 AATAA
40236 CGAAATGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (14 bp):
AATAATAGCAATAT
Found at i:54102 original size:13 final size:13
Alignment explanation
Indices: 54084--54110 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54074 AAACAAAAGA
54084 TAGTTTTCTAAAT
1 TAGTTTTCTAAAT
54097 TAGTTTTCTAAAT
1 TAGTTTTCTAAAT
54110 T
1 T
54111 GAAAGATATG
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:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (13 bp):
TAGTTTTCTAAAT
Found at i:55119 original size:24 final size:22
Alignment explanation
Indices: 55074--55152 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
55064 AATGTACAAT
*
55074 GGTTTGCATATATCATATATAG
1 GGTTTGCATATAACATATATAG
55096 GGTTTGCATATAACACATATATAG
1 GGTTTGCATAT-A-ACATATATAG
** ** *
55120 AATTCACATGTAACATATATAG
1 GGTTTGCATATAACATATATAG
*
55142 GGTTCGCATAT
1 GGTTTGCATAT
55153 TTGAATCTAG
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
22 28 0.62
23 2 0.04
24 15 0.33
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (22 bp):
GGTTTGCATATAACATATATAG
Found at i:55184 original size:20 final size:21
Alignment explanation
Indices: 55139--55186 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
55129 GTAACATATA
*
55139 TAGGGTTCGCATATTTGAATC
1 TAGGGTTCGCATATTTGAACC
*
55160 TAGGGTTCGCATGTTT-AACC
1 TAGGGTTCGCATATTTGAACC
55180 TAGGGTT
1 TAGGGTT
55187 TGAATGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.38
Consensus pattern (21 bp):
TAGGGTTCGCATATTTGAACC
Found at i:63824 original size:145 final size:146
Alignment explanation
Indices: 63659--63950 Score: 577
Period size: 145 Copynumber: 2.0 Consensus size: 146
63649 TCTAAATGTA
63659 AAAAAAAAAATTATATTCAATTATTTCCTTTCCTTTTTACTATTTAACCAAATAAAAATGGTTAA
1 AAAAAAAAAATTATATTCAATTATTTCCTTTCCTTTTTACTATTTAACCAAATAAAAATGGTTAA
63724 AGTTACTTTACTTGTCTTTTTTTCTATTCATTTTAACTATCCAAAAAAAGTAATGTGGTAGCATT
66 AGTTACTTTACTTGTCTTTTTTTCTATTCATTTTAACTATCCAAAAAAAGTAATGTGGTAGCATT
63789 TGTTATGATGAAAGTG
131 TGTTATGATGAAAGTG
63805 AAAAAAAAAA-TATATTCAATTATTTCCTTTCCTTTTTACTATTTAACCAAATAAAAATGGTTAA
1 AAAAAAAAAATTATATTCAATTATTTCCTTTCCTTTTTACTATTTAACCAAATAAAAATGGTTAA
63869 AGTTACTTTACTTGTCTTTTTTTCTATTCATTTTAACTATCCAAAAAAAGTAATGTGGTAGCATT
66 AGTTACTTTACTTGTCTTTTTTTCTATTCATTTTAACTATCCAAAAAAAGTAATGTGGTAGCATT
63934 TGTTATGATGAAAGTG
131 TGTTATGATGAAAGTG
63950 A
1 A
63951 TCGTTCTTCT
Statistics
Matches: 146, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
145 136 0.93
146 10 0.07
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (146 bp):
AAAAAAAAAATTATATTCAATTATTTCCTTTCCTTTTTACTATTTAACCAAATAAAAATGGTTAA
AGTTACTTTACTTGTCTTTTTTTCTATTCATTTTAACTATCCAAAAAAAGTAATGTGGTAGCATT
TGTTATGATGAAAGTG
Found at i:64858 original size:12 final size:12
Alignment explanation
Indices: 64841--64871 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
64831 TTTTAATAAG
64841 CTTTAAACTTTT
1 CTTTAAACTTTT
64853 CTTTAAACTTTT
1 CTTTAAACTTTT
64865 CTTTAAA
1 CTTTAAA
64872 GACTGAAATT
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:0.29, C:0.16, G:0.00, T:0.55
Consensus pattern (12 bp):
CTTTAAACTTTT
Found at i:70637 original size:15 final size:15
Alignment explanation
Indices: 70600--70628 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
70590 TGTTTGAAAC
70600 AAAAATATTATGTAG
1 AAAAATATTATGTAG
70615 AAAAATATTATGTA
1 AAAAATATTATGTA
70629 ATTAAATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.34
Consensus pattern (15 bp):
AAAAATATTATGTAG
Found at i:71153 original size:15 final size:16
Alignment explanation
Indices: 71120--71153 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
71110 TATCTCATTC
71120 AAAAATAATGCACTATA
1 AAAAATAATGCAC-ATA
71137 AAAAATAATGCAC-TA
1 AAAAATAATGCACATA
71152 AA
1 AA
71154 CCTATTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
17 13 0.76
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAAATAATGCACATA
Found at i:73875 original size:31 final size:28
Alignment explanation
Indices: 73812--73871 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
73802 TCCCCCTCCC
73812 TTTTCTTCTTCTTCTTATTATCTAATTG
1 TTTTCTTCTTCTTCTTATTATCTAATTG
73840 TTTTCTTCTTCTTCTTATTATCTAATTG
1 TTTTCTTCTTCTTCTTATTATCTAATTG
73868 TTTT
1 TTTT
73872 TTTCATTCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.13, C:0.17, G:0.03, T:0.67
Consensus pattern (28 bp):
TTTTCTTCTTCTTCTTATTATCTAATTG
Found at i:74486 original size:6 final size:6
Alignment explanation
Indices: 74475--74505 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
74465 NNNNNNNNNN
74475 AATATA AATATA AATATA AATATA AATATA A
1 AATATA AATATA AATATA AATATA AATATA A
74506 TATTTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:85723 original size:21 final size:22
Alignment explanation
Indices: 85699--85752 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
85689 GAGGCGGTAA
85699 CGAGGGAAGCAGCA-GCTGCAG
1 CGAGGGAAGCAGCAGGCTGCAG
*
85720 CGAGGGAAGC-GGAGGCTGCAG
1 CGAGGGAAGCAGCAGGCTGCAG
*
85741 CGAGAGAAGCAG
1 CGAGGGAAGCAG
85753 AGCATAGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.46, T:0.04
Consensus pattern (22 bp):
CGAGGGAAGCAGCAGGCTGCAG
Found at i:86182 original size:42 final size:42
Alignment explanation
Indices: 86117--86215 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
86107 GTTTACAAAC
* *
86117 AAAAACGCCGCTGAAGACTATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACTATGTTCTTTAGAGGCGCTTAGAA
86159 AAAAACGCCGCTAAAGAAC-ATGTTCTTTAGAGGCGCTTAGAA
1 AAAAACGCCGCTAAAG-ACTATGTTCTTTAGAGGCGCTTAGAA
86201 AAAAACGCCGCTAAA
1 AAAAACGCCGCTAAA
86216 ACGCTGCAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
42 52 0.96
43 2 0.04
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.20
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACTATGTTCTTTAGAGGCGCTTAGAA
Found at i:91904 original size:16 final size:16
Alignment explanation
Indices: 91883--91916 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
91873 AATAAAGAGA
* *
91883 AATAAAAAGAGTAAAG
1 AATAAAAAAAATAAAG
91899 AATAAAAAAAATAAAG
1 AATAAAAAAAATAAAG
91915 AA
1 AA
91917 AAATATGAGA
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:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
AATAAAAAAAATAAAG
Found at i:92427 original size:21 final size:22
Alignment explanation
Indices: 92403--92454 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
92393 GAATGTGAAA
92403 TTATGCTTAA-TTACATTATTT
1 TTATGCTTAATTTACATTATTT
* * *
92424 TTATACATAATTTATATTATTT
1 TTATGCTTAATTTACATTATTT
*
92446 TCATG-TTAA
1 TTATGCTTAA
92455 ATATTAATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.56
Consensus pattern (22 bp):
TTATGCTTAATTTACATTATTT
Found at i:94387 original size:19 final size:18
Alignment explanation
Indices: 94365--94403 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
94355 ATTTTTCACT
94365 TTAATTTCCATTTTTAATG
1 TTAATTT-CATTTTTAATG
* *
94384 TTAATTTTATTTTTTATG
1 TTAATTTCATTTTTAATG
94402 TT
1 TT
94404 TAATAAGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (18 bp):
TTAATTTCATTTTTAATG
Found at i:94406 original size:19 final size:19
Alignment explanation
Indices: 94351--94407 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
94341 ATTTTAAAAT
* *
94351 TTTTATTTTTCA-CTTTAA
1 TTTTATTTTTAATGTTTAA
*
94369 TTTCCATTTTTAATG-TTAA
1 TTT-TATTTTTAATGTTTAA
*
94388 TTTTATTTTTTATGTTTAA
1 TTTTATTTTTAATGTTTAA
94407 T
1 T
94408 AAGGGGGTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 12 0.39
19 19 0.61
ACGTcount: A:0.23, C:0.07, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTTATTTTTAATGTTTAA
Found at i:96298 original size:26 final size:26
Alignment explanation
Indices: 96248--96304 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
96238 TTTATAAGTT
*
96248 TGAAAATGGGAATCGACTTTTAAAAA
1 TGAAAATGGGAATCGAATTTTAAAAA
96274 TGAAAAT-GGATATC-AATTTTGAAAAA
1 TGAAAATGGGA-ATCGAATTTT-AAAAA
*
96300 GGAAA
1 TGAAA
96305 CGAGAGTCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.26
Consensus pattern (26 bp):
TGAAAATGGGAATCGAATTTTAAAAA
Found at i:99593 original size:44 final size:44
Alignment explanation
Indices: 99413--99728 Score: 141
Period size: 44 Copynumber: 7.2 Consensus size: 44
99403 ACTCTTGGAA
* *
99413 AGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTAAGG
1 AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
99457 AGACAAGATCTG-CTATCTTCAACCTACTCCACTGCTG-TTCAGGG
1 AGATAAGATTTGTC-GTCTTCAATCTGCTCCACTACTGCTT-AGGG
* * * * * *
99501 AGACAAGGCTTGGT-GGCTTAAATCTGCTTCCTACTA-T-CTT-GGAA
1 AGATAA-GATTTGTCGTCTTCAATCTGC-TCC-ACTACTGCTTAGG-G
* *
99545 AGATAAGATTTGTCGTCTTCGATCTGCTGCACTACTGCTTAGGG
1 AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * *
99589 AGATAAGATCT-TCTATCTTCAACCTACTCCACTGCTGCTCAGGG
1 AGATAAGATTTGTC-GTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * * *
99633 AGACGAGGCTTGGT-GGCTTAAATCTGCTTCCCATTA-T-CTT-GGAA
1 AGA-TAAGATTTGTCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* ** *
99677 AGATAAGATTTGCCGTCTTTGATCTTCTCCACTACTGCTTAGGG
1 AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
*
99721 AGACAAGA
1 AGATAAGA
99729 CCTGTAATTT
Statistics
Matches: 190, Mismatches: 60, Indels: 44
0.65 0.20 0.15
Matches are distributed among these distances:
42 9 0.05
43 24 0.13
44 131 0.69
45 18 0.09
46 8 0.04
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.31
Consensus pattern (44 bp):
AGATAAGATTTGTCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:99597 original size:132 final size:132
Alignment explanation
Indices: 99341--99728 Score: 636
Period size: 132 Copynumber: 3.0 Consensus size: 132
99331 AGGATTTGTA
** *
99341 ATCTTCAACCTACTCCGTTGCTGCTCAGAGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCTAC-
1 ATCTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCTACT
*
99405 -TCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTAAGGAGACAAGATCTG
66 ATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTG
99469 CT
131 CT
*
99471 ATCTTCAACCTACTCCACTGCTGTTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCTACT
1 ATCTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCTACT
* * *
99536 ATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTGCACTACTGCTTAGGGAGATAAGATCTT
66 ATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTG
99601 CT
131 CT
* * *
99603 ATCTTCAACCTACTCCACTGCTGCTCAGGGAGACGAGGCTTGGTGGCTTAAATCTGCTTCCCATT
1 ATCTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCTACT
* * *
99668 ATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTTCTCCACTACTGCTTAGGGAGACAAGA
66 ATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGA
99729 CCTGTAATTT
Statistics
Matches: 239, Mismatches: 17, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
130 60 0.25
132 179 0.75
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (132 bp):
ATCTTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCTACT
ATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTG
CT
Found at i:105693 original size:25 final size:25
Alignment explanation
Indices: 105665--105719 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
105655 TTACTTCTAT
105665 CCCATCCCACCCCCTTCTACCCCAA
1 CCCATCCCACCCCCTTCTACCCCAA
105690 CCCATCCCACCCCCTTCTACCCCAA
1 CCCATCCCACCCCCTTCTACCCCAA
105715 CCCAT
1 CCCAT
105720 TTCCCAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.20, C:0.64, G:0.00, T:0.16
Consensus pattern (25 bp):
CCCATCCCACCCCCTTCTACCCCAA
Found at i:105718 original size:20 final size:20
Alignment explanation
Indices: 105658--105718 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 20
105648 AAAACTTTTA
* *
105658 CTTCTATCCCATCCCACCCC
1 CTTCTACCCCAACCCACCCC
105678 CTTCTACCCCAACCCATCCCACCCC
1 CTTCTACCCC-A---A-CCCACCCC
105703 CTTCTACCCCAACCCA
1 CTTCTACCCCAACCCA
105719 TTTCCCAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
20 13 0.38
21 2 0.06
24 1 0.03
25 18 0.53
ACGTcount: A:0.20, C:0.61, G:0.00, T:0.20
Consensus pattern (20 bp):
CTTCTACCCCAACCCACCCC
Found at i:109238 original size:11 final size:11
Alignment explanation
Indices: 109224--109248 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
109214 ACAATTATTT
109224 AAAAATTCTAA
1 AAAAATTCTAA
109235 AAAAATTCTAA
1 AAAAATTCTAA
109246 AAA
1 AAA
109249 TTTGAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAATTCTAA
Found at i:109246 original size:20 final size:20
Alignment explanation
Indices: 109223--109260 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
109213 AACAATTATT
109223 TAAAAATTCT-AAAAAAATTC
1 TAAAAATT-TGAAAAAAATTC
109243 TAAAAATTTGAAAAAAAT
1 TAAAAATTTGAAAAAAAT
109261 AAAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (20 bp):
TAAAAATTTGAAAAAAATTC
Found at i:111786 original size:17 final size:17
Alignment explanation
Indices: 111764--111796 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
111754 ACTACAACCT
111764 TTGAGATGACCAGATAA
1 TTGAGATGACCAGATAA
111781 TTGAGATGACCAGATA
1 TTGAGATGACCAGATA
111797 GCGATTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (17 bp):
TTGAGATGACCAGATAA
Found at i:117302 original size:20 final size:20
Alignment explanation
Indices: 117268--117309 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
117258 TACTATTTAA
** *
117268 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
117288 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
117308 AT
1 AT
117310 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:125762 original size:7 final size:7
Alignment explanation
Indices: 125752--125803 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
125742 TTTATTTTTA
125752 TTTACCT
1 TTTACCT
125759 TTTACCT
1 TTTACCT
125766 TTTACCT
1 TTTACCT
125773 TTTA-CT
1 TTTACCT
125779 TTT-CTCT
1 TTTAC-CT
**
125786 TTTTTCT
1 TTTACCT
*
125793 TTTACTT
1 TTTACCT
125800 TTTA
1 TTTA
125804 ATGAAATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
6 5 0.13
7 33 0.87
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTACCT
Found at i:125787 original size:20 final size:20
Alignment explanation
Indices: 125764--125801 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
125754 TACCTTTTAC
125764 CTTTTACCTTTTACTTTTCT
1 CTTTTACCTTTTACTTTTCT
**
125784 CTTTTTTCTTTTACTTTT
1 CTTTTACCTTTTACTTTT
125802 TAATGAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (20 bp):
CTTTTACCTTTTACTTTTCT
Found at i:126136 original size:21 final size:20
Alignment explanation
Indices: 126112--126175 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
126102 GGATACTTCT
*
126112 AATTAATTTAATTTTTTTAAA
1 AATTAATTTAA-TTTTCTAAA
*
126133 AATTAAGTTAATTTTCTAAA
1 AATTAATTTAATTTTCTAAA
*
126153 AATTAATTTTAAATTT-TAAA
1 AATTAA-TTTAATTTTCTAAA
126173 AAT
1 AAT
126176 AGAATATGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 21 0.55
21 17 0.45
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
AATTAATTTAATTTTCTAAA
Found at i:126211 original size:83 final size:84
Alignment explanation
Indices: 126116--126284 Score: 331
Period size: 83 Copynumber: 2.0 Consensus size: 84
126106 ACTTCTAATT
126116 AATTTAATTTTTTTAAAAATTAAGTTAATTTTCTAAAAATTAATTTTAAATTTTAAAAATAGAAT
1 AATTTAATTTTTTTAAAAATTAAGTTAATTTTCTAAAAATTAATTTTAAATTTTAAAAATAGAAT
126181 ATGGTTAGCAACCTCGTAC
66 ATGGTTAGCAACCTCGTAC
126200 AATTTAATTTTTTT-AAAATTAAGTTAATTTTCTAAAAATTAATTTTAAATTTTAAAAATAGAAT
1 AATTTAATTTTTTTAAAAATTAAGTTAATTTTCTAAAAATTAATTTTAAATTTTAAAAATAGAAT
126264 ATGGTTAGCAACCTCGTAC
66 ATGGTTAGCAACCTCGTAC
126283 AA
1 AA
126285 AAAATATAAT
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 71 0.84
84 14 0.16
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (84 bp):
AATTTAATTTTTTTAAAAATTAAGTTAATTTTCTAAAAATTAATTTTAAATTTTAAAAATAGAAT
ATGGTTAGCAACCTCGTAC
Found at i:126228 original size:20 final size:20
Alignment explanation
Indices: 126203--126241 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
126193 CTCGTACAAT
* *
126203 TTAATTTTTTTAAAATTAAG
1 TTAATTTTCTAAAAATTAAG
126223 TTAATTTTCTAAAAATTAA
1 TTAATTTTCTAAAAATTAA
126242 TTTTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (20 bp):
TTAATTTTCTAAAAATTAAG
Found at i:126255 original size:20 final size:19
Alignment explanation
Indices: 126209--126258 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
126199 CAATTTAATT
* *
126209 TTTTTAAAATTAAGTTAAT
1 TTTTAAAAATTAAGTTAAA
*
126228 TTTCTAAAAATTAATTTTAAA
1 TTT-TAAAAATTAA-GTTAAA
126249 TTTTAAAAAT
1 TTTTAAAAAT
126259 AGAATATGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 3 0.12
20 16 0.62
21 7 0.27
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTTAAAAATTAAGTTAAA
Found at i:129603 original size:16 final size:17
Alignment explanation
Indices: 129582--129628 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
129572 ATTGAAAAGA
129582 AGTAAAAAAAAGTTT-G
1 AGTAAAAAAAAGTTTCG
129598 AGTAAAAAAAAGTTTCG
1 AGTAAAAAAAAGTTTCG
*
129615 AATATAAAAAAAGT
1 AGTA-AAAAAAAGT
129629 GTGCAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 15 0.54
17 4 0.14
18 9 0.32
ACGTcount: A:0.60, C:0.02, G:0.15, T:0.23
Consensus pattern (17 bp):
AGTAAAAAAAAGTTTCG
Found at i:130474 original size:54 final size:54
Alignment explanation
Indices: 130410--130519 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
130400 CTTCCACTTT
130410 TACCCAACGCAAATCATTTCATCCTGATTCTTTCATTTCAACTCCATCTTGTAA
1 TACCCAACGCAAATCATTTCATCCTGATTCTTTCATTTCAACTCCATCTTGTAA
130464 TACCCAACGCAAATCATTTCATCCTGATTCTTTCATTTCAACTCCATCTTGTAA
1 TACCCAACGCAAATCATTTCATCCTGATTCTTTCATTTCAACTCCATCTTGTAA
130518 TA
1 TA
130520 AAAAATGAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.28, C:0.29, G:0.05, T:0.37
Consensus pattern (54 bp):
TACCCAACGCAAATCATTTCATCCTGATTCTTTCATTTCAACTCCATCTTGTAA
Found at i:131141 original size:6 final size:6
Alignment explanation
Indices: 131107--131159 Score: 70
Period size: 6 Copynumber: 8.3 Consensus size: 6
131097 CAAGTGAGGT
*
131107 AAAAGA AAAACGA GAAGAGA AAAATGA AAAAGA AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAA-GA -AAAAGA AAAA-GA AAAAGA AAAAGA AAAAGA AAAAGA
131158 AA
1 AA
131160 TTGAAATTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
6 29 0.69
7 10 0.24
8 3 0.07
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:146801 original size:17 final size:18
Alignment explanation
Indices: 146776--146810 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
146766 TGTCGTTCGT
*
146776 TTTAGAAAT-ATTATTCA
1 TTTACAAATAATTATTCA
146793 TTTACAAATAATTATTCA
1 TTTACAAATAATTATTCA
146811 ATTTCAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.46
Consensus pattern (18 bp):
TTTACAAATAATTATTCA
Found at i:157218 original size:46 final size:45
Alignment explanation
Indices: 157151--157264 Score: 174
Period size: 46 Copynumber: 2.5 Consensus size: 45
157141 CACACTAATT
*
157151 TGTAGCCGAAACTACCACTGATACGTAGCCGTAGCTACCACTGAAA
1 TGTAG-CGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAAA
* *
157197 TGTAGTCGAAGCTACCACTGATAGGTAGCCGTAGCTATCACTGAAA
1 TGTAG-CGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAAA
157243 TGTAGCTGAAGCTACCACTGAT
1 TGTAGC-GAAGCTACCACTGAT
157265 CAATAACACT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 1 0.02
46 62 0.98
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (45 bp):
TGTAGCGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAAA
Found at i:157262 original size:23 final size:23
Alignment explanation
Indices: 157151--157263 Score: 136
Period size: 23 Copynumber: 4.9 Consensus size: 23
157141 CACACTAATT
* *
157151 TGTAGCCGAAACTACCACTGATA
1 TGTAGCCGAAGCTACCACTGAAA
* *
157174 CGTAGCCGTAGCTACCACTGAAA
1 TGTAGCCGAAGCTACCACTGAAA
* *
157197 TGTAGTCGAAGCTACCACTGATA
1 TGTAGCCGAAGCTACCACTGAAA
* * *
157220 GGTAGCCGTAGCTATCACTGAAA
1 TGTAGCCGAAGCTACCACTGAAA
*
157243 TGTAGCTGAAGCTACCACTGA
1 TGTAGCCGAAGCTACCACTGA
157264 TCAATAACAC
Statistics
Matches: 73, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 73 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (23 bp):
TGTAGCCGAAGCTACCACTGAAA
Found at i:162637 original size:30 final size:31
Alignment explanation
Indices: 162603--162666 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
162593 TAATCAAATT
*
162603 TCTATATA-CATGTAACATCCATAT-CATGTA
1 TCTATATATCATGTAAAAT-CATATCCATGTA
*
162633 TCTATATATCATGTAAAATCATTTCCATGTA
1 TCTATATATCATGTAAAATCATATCCATGTA
162664 TCT
1 TCT
162667 CAATTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 12 0.40
31 18 0.60
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (31 bp):
TCTATATATCATGTAAAATCATATCCATGTA
Found at i:162901 original size:25 final size:25
Alignment explanation
Indices: 162821--162904 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 25
162811 GTATGCTTAT
* * * *
162821 ACGAGCTATGAATCGGTATGCTCTC
1 ACGAGCTGTAAATCGATAAGCTCTC
* *
162846 TCGAGCTGTAAATCGATATGCTCTC
1 ACGAGCTGTAAATCGATAAGCTCTC
*
162871 ATGAGCTGTAAATCGATAAGCTCAT-
1 ACGAGCTGTAAATCGATAAGCTC-TC
162896 ACGAGCTGT
1 ACGAGCTGT
162905 GGAGTATCTG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
25 49 0.98
26 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (25 bp):
ACGAGCTGTAAATCGATAAGCTCTC
Found at i:167228 original size:3 final size:3
Alignment explanation
Indices: 167222--167252 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
167212 ATGCGTATGT
167222 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
167253 CTTAATAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:168124 original size:44 final size:44
Alignment explanation
Indices: 168064--168163 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 44
168054 TTCTAATCCA
* * * * *
168064 CTCCACTACAACTTTAGGGAGATATGA-TTTGTTCATTCAGTCTG
1 CTCCACTGCAATTTTAGGGAGATAAGACTTTCTT-ACTCAGTCTG
* *
168108 CTGCACTGCAATTTTAGGGGGATAAGACTTTCTTACTCAGTCTG
1 CTCCACTGCAATTTTAGGGAGATAAGACTTTCTTACTCAGTCTG
168152 CTCCACTGCAAT
1 CTCCACTGCAAT
168164 GCAAAAGAGA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 42 0.89
45 5 0.11
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (44 bp):
CTCCACTGCAATTTTAGGGAGATAAGACTTTCTTACTCAGTCTG
Found at i:168513 original size:117 final size:117
Alignment explanation
Indices: 168148--168500 Score: 616
Period size: 117 Copynumber: 3.0 Consensus size: 117
168138 TCTTACTCAG
*
168148 TCTGCTCCACTGCAATGCAAAAGAGATAGGATTCGCTGCCCTCAGCTTTAATCCGCTCCACTTCA
1 TCTGCTCCACTGCAATGCCAAAGAGATAGGATTCGCTGCCCTCAGCTTTAATCCGCTCCACTTCA
* * *
168213 GCTAATCCAAACTTTAACGCCAGGAAGATAAGATTCGCCATCGTGGCTTCAA
66 GCTAATCCAAGCCTTAACGCCAGGAAGATAAGATTCGCCGTCGTGGCTTCAA
*
168265 TCTGCACCACTGCAATGCCAAAGAGATAGGATTCGCTGCCCTCAGCTTTAATCCGCTCCACTTCA
1 TCTGCTCCACTGCAATGCCAAAGAGATAGGATTCGCTGCCCTCAGCTTTAATCCGCTCCACTTCA
* * *
168330 GCTTATCCAAGCCTTAACTCCAGAAAGATAAGATTCGCCGTCGTGGCTTCAA
66 GCTAATCCAAGCCTTAACGCCAGGAAGATAAGATTCGCCGTCGTGGCTTCAA
* *
168382 TCTGCTCCACTGCAATGCCAAAGAGATAGGATTCACTGCCCTTAGCTTTAATCCGCTCCACTTCA
1 TCTGCTCCACTGCAATGCCAAAGAGATAGGATTCGCTGCCCTCAGCTTTAATCCGCTCCACTTCA
168447 GCTAATCCAAGCCTTAACGCCAGGAAGATAAGATTCGCCGTCGTGGCTTCAA
66 GCTAATCCAAGCCTTAACGCCAGGAAGATAAGATTCGCCGTCGTGGCTTCAA
168499 TC
1 TC
168501 ATTTTCATTG
Statistics
Matches: 222, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 222 1.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (117 bp):
TCTGCTCCACTGCAATGCCAAAGAGATAGGATTCGCTGCCCTCAGCTTTAATCCGCTCCACTTCA
GCTAATCCAAGCCTTAACGCCAGGAAGATAAGATTCGCCGTCGTGGCTTCAA
Found at i:168644 original size:88 final size:88
Alignment explanation
Indices: 168526--169291 Score: 829
Period size: 88 Copynumber: 8.7 Consensus size: 88
168516 TCAAGGCAAT
* * * * * *
168526 AAGACT-GATGTCTTCGATCTGCTTCACTGCCAATATAGGAAGGCAAGATCTACTATTTTCAACC
1 AAGACTAG-TGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACC
* * ** * *
168590 TACTCCACTACTGCTTAGGGAGAC
65 TGCTCCACTGCAACCTAGGGAGGC
* * * * * * * ***
168614 AAGGCCAGAGTTTTCGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTTCTATCTTCAGTTT
1 AAGACTAGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCT
* *
168679 GTTGCACTGCAACCTAGGGAGGC
66 GCTCCACTGCAACCTAGGGAGGC
* * * * * * *
168702 AAGAATAGTGCCTTCAATCTGCTTCGCTGTCAGTACAGGAAGGAAAGATCTACTATTTTCAACAT
1 AAGACTAGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCT
* *
168767 GCTCCGCCGCAATCC-AGGGAGGC
66 GCTCCACTGCAA-CCTAGGGAGGC
* * * * **
168790 AAGGCTAGTGTCTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCTATCTTCAGTCT
1 AAGACTAGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCT
*
168855 GCTCCACTGCAACCTTGGGAGGC
66 GCTCCACTGCAACCTAGGGAGGC
* * * * *
168878 AAGACTGGTGTCTTCGATCTACTTCGCTGTCAATATAGGAAGGCAAGATCTGCTATTTTCAACCT
1 AAGACTAGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCT
* * *
168943 ACTCCGCTGCAACCCAGGGAGGC
66 GCTCCACTGCAACCTAGGGAGGC
* * * * **
168966 AAGGCTGGTGCCCTT-GATCTGCTTCGCTGTCGGTACAGGAAGGCAAGATCTGCTATCTTCAGTC
1 AAGACTAGTG-TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACC
169030 TGCTCCACTGCAACCTAGGGAGGC
65 TGCTCCACTGCAACCTAGGGAGGC
* * **
169054 AAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCT
1 AAGACTAGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCT
*
169119 GCTCCATTGCAACCTAGGGAGGC
66 GCTCCACTGCAACCTAGGGAGGC
* *
169142 AAGACTAGTGTCTTCGATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCT
1 AAGACTAGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCT
* * *
169207 GCTCCGCTGTAACTTAGGGAGGC
66 GCTCCACTGCAACCTAGGGAGGC
* * * * * * *
169230 AAGGCTGGTGTCTTTGATCTGCTTCACT-ACTGGTACAGGAAGACAAGATCTGCTATCTTCAA
1 AAGACTAGTGTCTTCGATCTGCTTCGCTGTC-AGTACAGGAAGGCAAGATCTGCTATCTTCAA
169292 TGATCTGTTC
Statistics
Matches: 565, Mismatches: 107, Indels: 12
0.83 0.16 0.02
Matches are distributed among these distances:
87 6 0.01
88 553 0.98
89 6 0.01
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (88 bp):
AAGACTAGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCT
GCTCCACTGCAACCTAGGGAGGC
Found at i:168878 original size:44 final size:44
Alignment explanation
Indices: 168830--169232 Score: 215
Period size: 44 Copynumber: 9.2 Consensus size: 44
168820 CGGTACAGGA
* *
168830 AGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTTGGG
1 AGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGCAACCTAGGG
* * * * ** *
168874 AGGCAAGA-CTGGTGTCTTC-GATCTACTTCGCTGTCAATATAGGA
1 AGGCAAGATCTGCTATCTTCAG-TCTGCTCCGCTG-CAACCTAGGG
* ** * *
168918 AGGCAAGATCTGCTATTTTCAACCTACTCCGCTGCAACCCAGGG
1 AGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGCAACCTAGGG
* * ** * * * *
168962 AGGCAAG-GCTGGTGCCCTTGA-TCTGCTTCGCTGTCGGTA-C-AGGA
1 AGGCAAGATCTGCT-ATCTTCAGTCTGCTCCGCTG-C--AACCTAGGG
*
169006 AGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTAGGG
1 AGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGCAACCTAGGG
* * * *
169050 AGGCAAGA-CTGGTGTCTTC-GATCTGCTTCGCTGTCAGTA-C-AGGA
1 AGGCAAGATCTGCTATCTTCAG-TCTGCTCCGCTG-CA--ACCTAGGG
* **
169094 AGGCAAGATCTACTATCTTCAGTCTGCTCCATTGCAACCTAGGG
1 AGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGCAACCTAGGG
* * * *
169138 AGGCAAGA-CTAG-TGTCTTC-GATCTACTTCGCTGTCAGTA-C-AGGA
1 AGGCAAGATCT-GCTATCTTCAG-TCTGCTCCGCTG-CA--ACCTAGGG
* ** * *
169182 AGGCAAGATCTGCTATTTTCAACCTGCTCCGCTGTAACTTAGGG
1 AGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGCAACCTAGGG
169226 AGGCAAG
1 AGGCAAG
169233 GCTGGTGTCT
Statistics
Matches: 262, Mismatches: 67, Indels: 60
0.67 0.17 0.15
Matches are distributed among these distances:
42 6 0.02
43 68 0.26
44 116 0.44
45 68 0.26
46 4 0.02
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (44 bp):
AGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGCAACCTAGGG
Found at i:169268 original size:176 final size:176
Alignment explanation
Indices: 168526--169291 Score: 944
Period size: 176 Copynumber: 4.4 Consensus size: 176
168516 TCAAGGCAAT
* * * * *
168526 AAGACTGATGTCTTCGATCTGCTTCACTGCCAATATAGGAAGGCAAGATCTACTATTTTCAACCT
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATTTTCAACCT
* ** * * * * *
168591 ACTCCACTACTGCTTAGGGAGACAAGGCCAGAGTTTTCGATCTGCTTCGCTGCCGGTACAGGAAG
66 ACTCCACTGCAACCTAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGCCGGTACAGGAAG
* * * *
168656 GCAAGATCTTCTATCTTCAGTTTGTTGCACTGCAACCTAGGGAGGC
131 GCAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTAGGGAGGC
* * * * * *
168702 AAGAATAGTGCCTTCAATCTGCTTCGCTGTCAGTACAGGAAGGAAAGATCTACTATTTTCAACAT
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATTTTCAACCT
* * * *
168767 GCTCCGCCGCAATCC-AGGGAGGCAAGGCTAGTGTCTTTGATCTGCTTCGCTGCCGGTACAGGAA
66 ACTCCACTGCAA-CCTAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGCCGGTACAGGAA
*
168831 GGCAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTTGGGAGGC
130 GGCAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTAGGGAGGC
* * * *
168878 AAGACTGGTGTCTTCGATCTACTTCGCTGTCAATATAGGAAGGCAAGATCTGCTATTTTCAACCT
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATTTTCAACCT
* * * * *
168943 ACTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGCCCTT-GATCTGCTTCGCTGTCGGTACAGGAA
66 ACTCCACTGCAACCTAGGGAGGCAAGGCTAGTG-TCTTCGATCTGCTTCGCTGCCGGTACAGGAA
169007 GGCAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTAGGGAGGC
130 GGCAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTAGGGAGGC
* **
169054 AAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATCTTCAGTCT
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATTTTCAACCT
* * * * * *
169119 GCTCCATTGCAACCTAGGGAGGCAAGACTAGTGTCTTCGATCTACTTCGCTGTCAGTACAGGAAG
66 ACTCCACTGCAACCTAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGCCGGTACAGGAAG
* ** * * *
169184 GCAAGATCTGCTATTTTCAACCTGCTCCGCTGTAACTTAGGGAGGC
131 GCAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTAGGGAGGC
* * * * * * * *
169230 AAGGCTGGTGTCTTTGATCTGCTTCACT-ACTGGTACAGGAAGACAAGATCTGCTATCTTCAA
1 AAGACTGGTGTCTTCGATCTGCTTCGCTGTC-AGTACAGGAAGGCAAGATCTACTATTTTCAA
169292 TGATCTGTTC
Statistics
Matches: 511, Mismatches: 74, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
175 6 0.01
176 501 0.98
177 4 0.01
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (176 bp):
AAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTACTATTTTCAACCT
ACTCCACTGCAACCTAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGCCGGTACAGGAAG
GCAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTAGGGAGGC
Found at i:170536 original size:12 final size:12
Alignment explanation
Indices: 170521--170550 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
170511 TTTTCTTTCC
170521 TTTTTTTGCTCT
1 TTTTTTTGCTCT
170533 TTTTTTTGCTCT
1 TTTTTTTGCTCT
170545 TTTTTT
1 TTTTTT
170551 ATTATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (12 bp):
TTTTTTTGCTCT
Found at i:175643 original size:7 final size:7
Alignment explanation
Indices: 175627--175656 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
175617 AAATAAAATT
175627 TAAT-AA
1 TAATAAA
175633 TAATAAA
1 TAATAAA
175640 TAATAAA
1 TAATAAA
175647 TAATAAA
1 TAATAAA
175654 TAA
1 TAA
175657 AAAAGACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TAATAAA
Found at i:186425 original size:12 final size:13
Alignment explanation
Indices: 186408--186436 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
186398 CTCATACATG
186408 AATAAATAAA-GC
1 AATAAATAAATGC
186420 AATAAATAAATGC
1 AATAAATAAATGC
186433 AATA
1 AATA
186437 GTTATAACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:194709 original size:91 final size:88
Alignment explanation
Indices: 194537--194732 Score: 241
Period size: 91 Copynumber: 2.2 Consensus size: 88
194527 AACTACAAAT
* * * * *
194537 ACTGGTGGTTTATCCACAATTTACTAGCAGCTTTCATCTGCAAAATCGTTGTGTATTCATAACCA
1 ACTGGTGGTTTATCCAAAATTTACTAGCAACTTTCATCTGCAAAATCATTGTGTACTCACAACCA
* *
194602 CTGGCAGCGTACTAACCTGCAAGC
66 CTGCCAGCATACTAACCTGCAA-C
* * *
194626 ACTTGTGGTTTATCCAAAACTTATATTAGCAACTATT-ATCTGCAAACTCATTGTGTACTCACAA
1 ACTGGTGGTTTATCCAAAA-TT-TACTAGCAACT-TTCATCTGCAAAATCATTGTGTACTCACAA
* *
194690 CTACTGCCAGCATATTAACCTGCAAC
63 CCACTGCCAGCATACTAACCTGCAAC
194716 ACTGGTGGTTTATCCAA
1 ACTGGTGGTTTATCCAA
194733 CAACAGGAGT
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
89 17 0.19
90 19 0.21
91 53 0.58
92 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (88 bp):
ACTGGTGGTTTATCCAAAATTTACTAGCAACTTTCATCTGCAAAATCATTGTGTACTCACAACCA
CTGCCAGCATACTAACCTGCAAC
Found at i:198638 original size:21 final size:22
Alignment explanation
Indices: 198563--198665 Score: 70
Period size: 21 Copynumber: 4.7 Consensus size: 22
198553 TGTTAGTACA
* * *
198563 GTGTGGATAAAACTCTC-ATTG
1 GTGTGGATAAACCACTCAAATG
* * *
198584 GTGTAGATAAAGCTACT-AATAAG
1 GTGTGGATAAA-CCACTCAA-ATG
198607 GTGTGGATAAACCACTC-AATG
1 GTGTGGATAAACCACTCAAATG
**
198628 GTGTAGG-TAAACTGCTCAAATG
1 GTGT-GGATAAACCACTCAAATG
*
198650 ATGTGGATAAACCACT
1 GTGTGGATAAACCACT
198666 AAACGATGCA
Statistics
Matches: 61, Mismatches: 14, Indels: 13
0.69 0.16 0.15
Matches are distributed among these distances:
21 26 0.43
22 24 0.39
23 11 0.18
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (22 bp):
GTGTGGATAAACCACTCAAATG
Found at i:198660 original size:22 final size:21
Alignment explanation
Indices: 198608--198665 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
198598 ACTAATAAGG
*
198608 TGTGGATAAACCACTCAATGG
1 TGTGGATAAACCACTCAATGA
**
198629 TGTAGG-TAAACTGCTCAAATGA
1 TGT-GGATAAACCACTC-AATGA
198651 TGTGGATAAACCACT
1 TGTGGATAAACCACT
198666 AAACGATGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.26
Consensus pattern (21 bp):
TGTGGATAAACCACTCAATGA
Found at i:198661 original size:43 final size:44
Alignment explanation
Indices: 198564--198665 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 44
198554 GTTAGTACAG
* * * *
198564 TGTGGATAAAACTCTCATTGGTGTAGATAAAGCTACTAATAAGG
1 TGTGGATAAACCACTCAATGGTGTAGATAAAGCTACTAATAAGA
* * *
198608 TGTGGATAAACCACTCAATGGTGTAGGTAAA-CTGCTCAA-ATGA
1 TGTGGATAAACCACTCAATGGTGTAGATAAAGCTACT-AATAAGA
198651 TGTGGATAAACCACT
1 TGTGGATAAACCACT
198666 AAACGATGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
43 21 0.42
44 29 0.58
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (44 bp):
TGTGGATAAACCACTCAATGGTGTAGATAAAGCTACTAATAAGA
Found at i:199152 original size:83 final size:82
Alignment explanation
Indices: 199057--199243 Score: 211
Period size: 83 Copynumber: 2.3 Consensus size: 82
199047 AATCTTAGGT
* * *
199057 CAAAACTATAAAATTTGTAAAATAGAGG-AAAA-TTGTAAAA-TCGAAAA-AATCGTAGCAAAAC
1 CAAAACTGTAAAATTT-CAAAACAGAGGTAAAATTTG-AAAATTCGAAAACAAT-G--GCAAAAC
199118 TGTAAAATCTGAAAAATTGTGG
61 TGTAAAATCTGAAAAATTGTGG
* * *
199140 CAAAACTGTAAAATTTCAAAACAGTGGTAAAATTTGAAAATTTGAAAAGCAATGGCAAAATTGTA
1 CAAAACTGTAAAATTTCAAAACAGAGGTAAAATTTGAAAATTCGAAAA-CAATGGCAAAACTGTA
*
199205 AAATCTGAAGAATTGTGG
65 AAATCTGAAAAATTGTGG
* *
199223 CAAAATTGTAAAATTTAAAAA
1 CAAAACTGTAAAATTTCAAAA
199244 ACTGTGGCAA
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
82 8 0.09
83 69 0.77
84 9 0.10
85 1 0.01
86 3 0.03
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.26
Consensus pattern (82 bp):
CAAAACTGTAAAATTTCAAAACAGAGGTAAAATTTGAAAATTCGAAAACAATGGCAAAACTGTAA
AATCTGAAAAATTGTGG
Found at i:199160 original size:28 final size:28
Alignment explanation
Indices: 199057--199272 Score: 138
Period size: 28 Copynumber: 7.8 Consensus size: 28
199047 AATCTTAGGT
* * * *
199057 CAAAACTATAAAATTTGTAAAATAGAGG
1 CAAAACTGTAAAATTTGAAAAATTGTGG
* * * *
199085 -AAAATTGTAAAA-TCGAAAAAATCGTAG
1 CAAAACTGTAAAATTTG-AAAAATTGTGG
*
199112 CAAAACTGTAAAATCTGAAAAATTGTGG
1 CAAAACTGTAAAATTTGAAAAATTGTGG
*
199140 CAAAACTGTAAAATTTCAAAACA--GTGG
1 CAAAACTGTAAAATTTGAAAA-ATTGTGG
* * ****
199167 TAAAA-TTTGAAAATTTGAAAAGCAATGG
1 CAAAACTGT-AAAATTTGAAAAATTGTGG
* * *
199195 CAAAATTGTAAAATCTGAAGAATTGTGG
1 CAAAACTGTAAAATTTGAAAAATTGTGG
* * *
199223 CAAAATTGTAAAATTTAAAAAACTGTGG
1 CAAAACTGTAAAATTTGAAAAATTGTGG
* *
199251 CAAAATTG-AAATTTTTGAAAAA
1 CAAAACTGTAAA-ATTTGAAAAA
199273 CAGTGAACAC
Statistics
Matches: 146, Mismatches: 33, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
26 4 0.03
27 39 0.27
28 99 0.68
29 4 0.03
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (28 bp):
CAAAACTGTAAAATTTGAAAAATTGTGG
Found at i:199260 original size:83 final size:84
Alignment explanation
Indices: 199111--199271 Score: 236
Period size: 83 Copynumber: 1.9 Consensus size: 84
199101 AAAAATCGTA
* *
199111 GCAAAACTGTAAAATCTGAAAAATTGTGGCAAAACTGTAAAATTTCAAAACAGTGGTAAAATTTG
1 GCAAAACTGTAAAATCTGAAAAATTGTGGCAAAACTGTAAAATTTAAAAACAGTGGCAAAATTTG
199176 AAA-ATTTGAAAAGCAATG
66 AAATATTTGAAAAGCAATG
* * * *
199194 GCAAAATTGTAAAATCTGAAGAATTGTGGCAAAATTGTAAAATTTAAAAAACTGTGGCAAAA-TT
1 GCAAAACTGTAAAATCTGAAAAATTGTGGCAAAACTGTAAAATTT-AAAAACAGTGGCAAAATTT
*
199258 GAAATTTTTGAAAA
65 GAAATATTTGAAAA
199272 ACAGTGAACA
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
83 48 0.70
84 21 0.30
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (84 bp):
GCAAAACTGTAAAATCTGAAAAATTGTGGCAAAACTGTAAAATTTAAAAACAGTGGCAAAATTTG
AAATATTTGAAAAGCAATG
Found at i:199273 original size:28 final size:28
Alignment explanation
Indices: 199085--199273 Score: 161
Period size: 28 Copynumber: 6.8 Consensus size: 28
199075 AAAATAGAGG
* * *
199085 AAAATTGTAAAA-TCGAAAAAATCGTAGC
1 AAAATTGTAAAATTTGAAAAACT-GTGGC
* * *
199113 AAAACTGTAAAATCTGAAAAATTGTGGC
1 AAAATTGTAAAATTTGAAAAACTGTGGC
* * * *
199141 AAAACTGTAAAATTT-CAAAACAGTGGT
1 AAAATTGTAAAATTTGAAAAACTGTGGC
* **
199168 AAAATT-TGAAAATTTGAAAAGCAATGGC
1 AAAATTGT-AAAATTTGAAAAACTGTGGC
* * *
199196 AAAATTGTAAAATCTGAAGAATTGTGGC
1 AAAATTGTAAAATTTGAAAAACTGTGGC
*
199224 AAAATTGTAAAATTTAAAAAACTGTGGC
1 AAAATTGTAAAATTTGAAAAACTGTGGC
*
199252 AAAATTG-AAATTTTTGAAAAAC
1 AAAATTGTAAA-ATTTGAAAAAC
199274 AGTGAACACA
Statistics
Matches: 129, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 1 0.01
27 23 0.18
28 97 0.75
29 8 0.06
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.26
Consensus pattern (28 bp):
AAAATTGTAAAATTTGAAAAACTGTGGC
Found at i:200083 original size:13 final size:13
Alignment explanation
Indices: 200065--200137 Score: 51
Period size: 13 Copynumber: 5.8 Consensus size: 13
200055 CTTAAGCTTG
*
200065 CTTAATTTTATTT
1 CTTAATTTTATAT
*
200078 CTTAATTGTATAT
1 CTTAATTTTATAT
* *
200091 ATTTATTTTA-AT
1 CTTAATTTTATAT
* *
200103 -GTAATTTTATTT
1 CTTAATTTTATAT
*
200115 CTTAATTGTATAT
1 CTTAATTTTATAT
* *
200128 ATTTATTTTA
1 CTTAATTTTA
200138 ATGTTTGGAG
Statistics
Matches: 44, Mismatches: 14, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
11 7 0.16
12 3 0.07
13 34 0.77
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (13 bp):
CTTAATTTTATAT
Found at i:200117 original size:37 final size:37
Alignment explanation
Indices: 200067--200141 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
200057 TAAGCTTGCT
200067 TAATTTTATTTCTTAATTGTATATATTTATTTTAATG
1 TAATTTTATTTCTTAATTGTATATATTTATTTTAATG
200104 TAATTTTATTTCTTAATTGTATATATTTATTTTAATG
1 TAATTTTATTTCTTAATTGTATATATTTATTTTAATG
200141 T
1 T
200142 TTGGAGTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (37 bp):
TAATTTTATTTCTTAATTGTATATATTTATTTTAATG
Found at i:200138 original size:19 final size:19
Alignment explanation
Indices: 200079--200139 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
200069 ATTTTATTTC
200079 TTAATTGTATATATTTATT
1 TTAATTGTATATATTTATT
200098 TTAA-TGTA-AT-TTTATTT
1 TTAATTGTATATATTTA-TT
200115 CTTAATTGTATATATTTATT
1 -TTAATTGTATATATTTATT
200135 TTAAT
1 TTAAT
200140 GTTTGGAGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.11
17 4 0.11
18 8 0.22
19 13 0.35
20 4 0.11
21 4 0.11
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (19 bp):
TTAATTGTATATATTTATT
Found at i:205992 original size:25 final size:25
Alignment explanation
Indices: 205964--206012 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
205954 CTATTTTTGA
* *
205964 TAGTATATCCTGACACTGCTATAGG
1 TAGTATATACTGACACTACTATAGG
*
205989 TAGTATATACTGAGACTACTATAG
1 TAGTATATACTGACACTACTATAG
206013 TTAGATTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (25 bp):
TAGTATATACTGACACTACTATAGG
Found at i:211561 original size:26 final size:26
Alignment explanation
Indices: 211525--211581 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
211515 TCGAATCCTT
** *
211525 GTTCTTTCTCCGTTCTAACTCTTCGG
1 GTTCTTTCTCCACTCTAACTCTTCAG
211551 GTTCTTTCTCCACTCTAACTCTTCAG
1 GTTCTTTCTCCACTCTAACTCTTCAG
211577 GTTCT
1 GTTCT
211582 CTCCAAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.11, C:0.32, G:0.12, T:0.46
Consensus pattern (26 bp):
GTTCTTTCTCCACTCTAACTCTTCAG
Found at i:213923 original size:20 final size:20
Alignment explanation
Indices: 213898--213937 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
213888 CGTAAAATGA
*
213898 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
213918 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
213938 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:213927 original size:34 final size:34
Alignment explanation
Indices: 213884--213949 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
213874 AGTAAAATGT
*
213884 TTTTCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCGTAAAATGATTTACTGGAAAATATTTTAC
213917 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATGATTTACTGGAAAATATTTT
213950 TTGGTGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.40
35 13 0.43
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.47
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:214077 original size:16 final size:16
Alignment explanation
Indices: 214043--214076 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
214033 CATATATTAA
214043 TTTATATTAATAAATT
1 TTTATATTAATAAATT
*
214059 TTTATATT-TTAAATT
1 TTTATATTAATAAATT
214074 TTT
1 TTT
214077 TTTACATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATATTAATAAATT
Found at i:226462 original size:23 final size:25
Alignment explanation
Indices: 226421--226478 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
226411 AAAATAAGGC
226421 TAATGGCTCCTTTAATTCA-GACGT
1 TAATGGCTCCTTTAATTCACGACGT
226445 TAATGGCTCC-TTAATTCACGGACGT
1 TAATGGCTCCTTTAATTCAC-GACGT
*
226470 TATTGGCTC
1 TAATGGCTC
226479 TATTAGTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
23 8 0.26
24 10 0.32
25 13 0.42
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (25 bp):
TAATGGCTCCTTTAATTCACGACGT
Found at i:227143 original size:79 final size:79
Alignment explanation
Indices: 227012--227161 Score: 221
Period size: 79 Copynumber: 1.9 Consensus size: 79
227002 TTCTGTTTGT
* * * * *
227012 AAACAGAAATCAATTGAATAATTCTGTTTCAAGATCTTATTCCTGTCGTTCAACAGGATTTGTTC
1 AAACAGAAATCAATTCAACAATTCTGTTTCAAGATCTTATTCCTATCGTTCAACAAGATTTATTC
227077 GATTTCCTATTTTC
66 GATTTCCTATTTTC
* *
227091 AAACAGAAATCAATTCAACAATTCTGTTTCAGGA-CTCTGTTCCTATCGTTCAACAAGATTTATT
1 AAACAGAAATCAATTCAACAATTCTGTTTCAAGATCT-TATTCCTATCGTTCAACAAGATTTATT
227155 CGATTTC
65 CGATTTC
227162 TGTTGTTAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
78 2 0.03
79 61 0.97
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (79 bp):
AAACAGAAATCAATTCAACAATTCTGTTTCAAGATCTTATTCCTATCGTTCAACAAGATTTATTC
GATTTCCTATTTTC
Found at i:230393 original size:28 final size:27
Alignment explanation
Indices: 230362--230425 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
230352 AGATAAATAA
230362 AATAAAATTC-TAAAATTAAATAATCCTT
1 AATAAAATTCTTAAAATT-AATAATCC-T
* * *
230390 AATAATATTCTTAATATTAATTATCCT
1 AATAAAATTCTTAAAATTAATAATCCT
*
230417 AATATAATT
1 AATAAAATT
230426 AAAATAGAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 8 0.27
28 16 0.53
29 6 0.20
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (27 bp):
AATAAAATTCTTAAAATTAATAATCCT
Found at i:230997 original size:16 final size:17
Alignment explanation
Indices: 230972--231022 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 17
230962 AATTATATTC
*
230972 TTTTTC-TTTTTCTTT-
1 TTTTTCTTTTTTATTTA
230987 TTTTTCTTTTTTATTTA
1 TTTTTCTTTTTTATTTA
*
231004 TTTTT-ATTTTTATTTA
1 TTTTTCTTTTTTATTTA
231020 TTT
1 TTT
231023 ATTATTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
15 6 0.19
16 21 0.66
17 5 0.16
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTCTTTTTTATTTA
Found at i:231007 original size:20 final size:20
Alignment explanation
Indices: 230969--231040 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
230959 CCAAATTATA
* *
230969 TTCTTTTTCTTTTTCTTTTTT
1 TTCTTTTT-TATTTATTTTTT
230990 TTCTTTTTTATTTATTTTTAT
1 TTCTTTTTTATTTATTTTT-T
* *
231011 TT-TTATTTATTTATTATTT
1 TTCTTTTTTATTTATTTTTT
* *
231030 ATATTTTTTAT
1 TTCTTTTTTAT
231041 GCTTTAGGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.05
20 30 0.70
21 11 0.26
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.81
Consensus pattern (20 bp):
TTCTTTTTTATTTATTTTTT
Found at i:231027 original size:27 final size:26
Alignment explanation
Indices: 230978--231036 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
230968 ATTCTTTTTC
* * *
230978 TTTTTCTTTTTTTTCTTTTTTATTTA
1 TTTTTATTTTTTTTATTTATTATTTA
231004 TTTTTATTTTTATTTATTTATTATTTA
1 TTTTTATTTTT-TTTATTTATTATTTA
231031 TATTTT
1 T-TTTT
231037 TTATGCTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 10 0.36
27 14 0.50
28 4 0.14
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.81
Consensus pattern (26 bp):
TTTTTATTTTTTTTATTTATTATTTA
Found at i:231039 original size:16 final size:16
Alignment explanation
Indices: 230995--231040 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
230985 TTTTTTTCTT
230995 TTTTATTTATTT-TTA
1 TTTTATTTATTTATTA
231010 TTTTTATTTATTTATTA
1 -TTTTATTTATTTATTA
231027 TTTATATTT-TTTAT
1 TTT-TATTTATTTAT
231041 GCTTTAGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 20 0.71
17 8 0.29
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTATTTATTTATTA
Found at i:231642 original size:101 final size:102
Alignment explanation
Indices: 231519--231728 Score: 404
Period size: 101 Copynumber: 2.1 Consensus size: 102
231509 TAAACTTGAT
*
231519 TAATTTTATGAAAAGAAAGATAAAGTTAACTCTATGAATCACAATTATTTTTAGCCTAATAAGAA
1 TAATTTCATGAAAAGAAAGATAAAGTTAACTCTATGAATCACAATTATTTTTAGCCTAATAAGAA
231584 TACAACAGTGGAGATGGCATCAATTATGGAAAATCCG
66 TACAACAGTGGAGATGGCATCAATTATGGAAAATCCG
231621 TAATTTCATG-AAAGAAAGATAAAGTTAACTCTATGAATCACAATTATTTTTAGCCTAATAAGAA
1 TAATTTCATGAAAAGAAAGATAAAGTTAACTCTATGAATCACAATTATTTTTAGCCTAATAAGAA
231685 TACAACAGTGGAGATGGCATCAATTATGGAAAATCCG
66 TACAACAGTGGAGATGGCATCAATTATGGAAAATCCG
231722 TAATTTC
1 TAATTTC
231729 CTCAGAAAAC
Statistics
Matches: 107, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
101 98 0.92
102 9 0.08
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (102 bp):
TAATTTCATGAAAAGAAAGATAAAGTTAACTCTATGAATCACAATTATTTTTAGCCTAATAAGAA
TACAACAGTGGAGATGGCATCAATTATGGAAAATCCG
Found at i:232498 original size:4 final size:4
Alignment explanation
Indices: 232465--232522 Score: 50
Period size: 4 Copynumber: 14.5 Consensus size: 4
232455 CCAAATAAGT
* *
232465 AATA AAT- AATA AA-A CA-A AATA AAGA AATA AATA AAGTA AATAA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AA-TA AAT-A AATA
232512 AATAA AATA AA
1 AAT-A AATA AA
232523 AATAAAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
3 7 0.16
4 26 0.58
5 12 0.27
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.19
Consensus pattern (4 bp):
AATA
Found at i:232506 original size:9 final size:9
Alignment explanation
Indices: 232465--232522 Score: 66
Period size: 9 Copynumber: 6.7 Consensus size: 9
232455 CCAAATAAGT
232465 AATAAATAA
1 AATAAATAA
* *
232474 TA-AAACAA
1 AATAAATAA
*
232482 AATAAA-GA
1 AATAAATAA
232490 AATAAATAA
1 AATAAATAA
*
232499 AGTAAATAA
1 AATAAATAA
232508 AATAAATAA
1 AATAAATAA
232517 AATAAA
1 AATAAA
232523 AATAAAAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
8 13 0.32
9 27 0.68
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.19
Consensus pattern (9 bp):
AATAAATAA
Found at i:240388 original size:13 final size:13
Alignment explanation
Indices: 240353--240391 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
240343 AGGTAGGCAA
*
240353 CTTTTTTTTTACG
1 CTTTTTTTTTGCG
*
240366 -ATTTTTTTTGCG
1 CTTTTTTTTTGCG
240378 CTTTTTTTTTGCG
1 CTTTTTTTTTGCG
240391 C
1 C
240392 AAAGCTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.05, C:0.15, G:0.13, T:0.67
Consensus pattern (13 bp):
CTTTTTTTTTGCG
Found at i:241009 original size:31 final size:31
Alignment explanation
Indices: 240971--241031 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
240961 GACAAATTAT
240971 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTC
241002 AAGAGTAATTGAATCCTAATAAAACTCTTT
1 AAGAGTAATTGAATCCTAATAAAACTCTTT
241032 AAAATTTGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.33
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTC
Found at i:249930 original size:24 final size:24
Alignment explanation
Indices: 249903--249955 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
249893 TTAAATTGAG
*
249903 GTTAAGGGCTCCTTTAATTCA-GAC
1 GTTAAGGGCT-CATTAATTCAGGAC
*
249927 GTTAATGGCTCATTAATTCATGGAC
1 GTTAAGGGCTCATTAATTCA-GGAC
249952 GTTA
1 GTTA
249956 TTTGCTTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.36
24 9 0.36
25 7 0.28
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (24 bp):
GTTAAGGGCTCATTAATTCAGGAC
Found at i:254550 original size:32 final size:32
Alignment explanation
Indices: 254491--254551 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
254481 TTTTTTCAAA
* * *
254491 TTTCAAGTTAATTGAATCAAGTTATTTGATTT
1 TTTCAAGTCAATCGAATCAAGTAATTTGATTT
254523 TTTCAAGTCAAGTCGAAT-AAGTAATTTGA
1 TTTCAAGTCAA-TCGAATCAAGTAATTTGA
254552 GTTTCAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 20 0.80
33 5 0.20
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (32 bp):
TTTCAAGTCAATCGAATCAAGTAATTTGATTT
Found at i:254702 original size:18 final size:18
Alignment explanation
Indices: 254668--254705 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
254658 AACATTACAA
254668 AAAAATTCAAAGTATTTAT
1 AAAAATTCAAAG-ATTTAT
254687 AAAAATTCTAAA-ATTTAT
1 AAAAATTC-AAAGATTTAT
254705 A
1 A
254706 TTTTAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 8 0.44
20 3 0.17
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (18 bp):
AAAAATTCAAAGATTTAT
Found at i:254756 original size:43 final size:43
Alignment explanation
Indices: 254709--254852 Score: 146
Period size: 43 Copynumber: 3.3 Consensus size: 43
254699 ATTTATATTT
254709 TAATATATAAAATTTGAAATTTGAAATTTCTAAAGAATCTAAA
1 TAATATATAAAATTTGAAATTTGAAATTTCTAAAGAATCTAAA
** ** ** ** * **
254752 TAATATATAAAAAAAGTTAAAAATTAAAAAAATCTAAA-TTTATATT
1 TAATATAT---AAAA-TTTGAAATTTGAAATTTCTAAAGAATCTAAA
254798 TAATATATAAAATTTGAAATTTGAAATTTCTAAAGAATCTAAA
1 TAATATATAAAATTTGAAATTTGAAATTTCTAAAGAATCTAAA
254841 TAATATATAAAA
1 TAATATATAAAA
254853 AAAGTTAAAA
Statistics
Matches: 74, Mismatches: 22, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
42 16 0.22
43 27 0.36
46 15 0.20
47 16 0.22
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (43 bp):
TAATATATAAAATTTGAAATTTGAAATTTCTAAAGAATCTAAA
Found at i:254813 original size:89 final size:90
Alignment explanation
Indices: 254687--254878 Score: 359
Period size: 89 Copynumber: 2.1 Consensus size: 90
254677 AAGTATTTAT
*
254687 AAAAATTCTAAAATTTATATTTTAATATATAAAATTTGAAATTTGAAATTTCTAAAGAATCTAAA
1 AAAAAATCT-AAATTTATATTTTAATATATAAAATTTGAAATTTGAAATTTCTAAAGAATCTAAA
254752 TAATATATAAAAAAAGTTAAAAATTA
65 TAATATATAAAAAAAGTTAAAAATTA
254778 AAAAAATCTAAATTTATA-TTTAATATATAAAATTTGAAATTTGAAATTTCTAAAGAATCTAAAT
1 AAAAAATCTAAATTTATATTTTAATATATAAAATTTGAAATTTGAAATTTCTAAAGAATCTAAAT
254842 AATATATAAAAAAAGTTAAAAATTA
66 AATATATAAAAAAAGTTAAAAATTA
254867 AAAAAATCTAAA
1 AAAAAATCTAAA
254879 ATAATAATTT
Statistics
Matches: 100, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
89 83 0.83
90 9 0.09
91 8 0.08
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (90 bp):
AAAAAATCTAAATTTATATTTTAATATATAAAATTTGAAATTTGAAATTTCTAAAGAATCTAAAT
AATATATAAAAAAAGTTAAAAATTA
Found at i:260233 original size:6 final size:6
Alignment explanation
Indices: 260224--260251 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
260214 AGAAAGAGCC
260224 AAAGCT AAAGCT AAAGCT AAAGCT AAAG
1 AAAGCT AAAGCT AAAGCT AAAGCT AAAG
260252 ATTAAAAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.14, G:0.18, T:0.14
Consensus pattern (6 bp):
AAAGCT
Found at i:261337 original size:128 final size:129
Alignment explanation
Indices: 261193--261451 Score: 511
Period size: 128 Copynumber: 2.0 Consensus size: 129
261183 ATAAATTCAA
261193 AATATTTATAAAAATTTCAAAATTTATATTTAAAAATATATATAAAGAACATTAAAATTTTAAAA
1 AATATTTATAAAAATTTCAAAATTTATATTTAAAAATATATATAAAGAACATTAAAATTTTAAAA
261258 ATACTCTAAAATAATAATTTTGGGAATTTAAATAACTTAATTAATTATTCAAGATTATCATACT
66 ATACTCTAAAATAATAATTTTGGGAATTTAAATAACTTAATTAATTATTCAAGATTATCATACT
261322 AATATTTAT-AAAATTTCAAAATTTATATTTAAAAATATATATAAAGAACATTAAAATTTTAAAA
1 AATATTTATAAAAATTTCAAAATTTATATTTAAAAATATATATAAAGAACATTAAAATTTTAAAA
261386 ATACTCTAAAATAATAATTTTGGGAATTTAAATAACTTAATTAATTATTCAAGATTATCATACT
66 ATACTCTAAAATAATAATTTTGGGAATTTAAATAACTTAATTAATTATTCAAGATTATCATACT
261450 AA
1 AA
261452 AGTATTTTTT
Statistics
Matches: 130, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
128 121 0.93
129 9 0.07
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (129 bp):
AATATTTATAAAAATTTCAAAATTTATATTTAAAAATATATATAAAGAACATTAAAATTTTAAAA
ATACTCTAAAATAATAATTTTGGGAATTTAAATAACTTAATTAATTATTCAAGATTATCATACT
Found at i:262116 original size:13 final size:12
Alignment explanation
Indices: 262100--262137 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
262090 TTTAAATAAT
262100 TATAAAAAATTGA
1 TATAAAAAATT-A
262113 TATAAAAAATTA
1 TATAAAAAATTA
*
262125 T-TTAAAAATTA
1 TATAAAAAATTA
262136 TA
1 TA
262138 ATAACTAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 10 0.43
12 2 0.09
13 11 0.48
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (12 bp):
TATAAAAAATTA
Found at i:262417 original size:18 final size:20
Alignment explanation
Indices: 262394--262442 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
262384 GTGATGGTTA
262394 TTTTAATTTTAG-TT-ATTT
1 TTTTAATTTTAGATTAATTT
*
262412 TTTTAATTTAAGATTAATTT
1 TTTTAATTTTAGATTAATTT
*
262432 TTTTATTTTTA
1 TTTTAATTTTA
262443 ATAATTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 11 0.42
19 2 0.08
20 13 0.50
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTTAATTTTAGATTAATTT
Found at i:262434 original size:19 final size:18
Alignment explanation
Indices: 262394--262439 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
262384 GTGATGGTTA
* *
262394 TTTTAATTTTAGTTATTT
1 TTTTAATTTAAGTTAATT
262412 TTTTAATTTAAGATTAATT
1 TTTTAATTTAAG-TTAATT
*
262431 TTTTTATTT
1 TTTTAATTT
262440 TTAATAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTTAATTTAAGTTAATT
Found at i:262447 original size:18 final size:18
Alignment explanation
Indices: 262394--262448 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
262384 GTGATGGTTA
* *
262394 TTTTAATTTTAGTTATTT
1 TTTTAATTTTAATAATTT
*
262412 TTTTAATTTAAGATTAATTT
1 TTTTAATTTTA-A-TAATTT
*
262432 TTTTATTTTTAATAATT
1 TTTTAATTTTAATAATT
262449 ATTTAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 15 0.50
19 1 0.03
20 14 0.47
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (18 bp):
TTTTAATTTTAATAATTT
Found at i:271998 original size:15 final size:16
Alignment explanation
Indices: 271968--271998 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
271958 CATAATTTCA
271968 TAATATTTTCAACAAT
1 TAATATTTTCAACAAT
271984 TAATATTTT-AACAAT
1 TAATATTTTCAACAAT
271999 CCAACCGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATATTTTCAACAAT
Found at i:274838 original size:13 final size:15
Alignment explanation
Indices: 274816--274847 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
274806 ATATAGAGGT
274816 AAAATAAATTA-TTA
1 AAAATAAATTATTTA
274830 AAAAT-AATTATTTA
1 AAAATAAATTATTTA
274844 AAAA
1 AAAA
274848 AAGACATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAATAAATTATTTA
Found at i:275651 original size:55 final size:53
Alignment explanation
Indices: 275567--275675 Score: 182
Period size: 55 Copynumber: 2.0 Consensus size: 53
275557 GCTATATTGT
* *
275567 TACTCATGGGACTTTCTTATTATGGTCATCCTAAATTTTTTTTTGATTAATTTGG
1 TACTCATGGGACCTTCTTATTATGGTCATCCCAAA--TTTTTTTGATTAATTTGG
275622 TACTCATGGGACCTTCTTATTATGGTCATCCCAAATTTTTTTGATTAATTTGG
1 TACTCATGGGACCTTCTTATTATGGTCATCCCAAATTTTTTTGATTAATTTGG
275675 T
1 T
275676 CACCTCAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
53 19 0.37
55 33 0.63
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.49
Consensus pattern (53 bp):
TACTCATGGGACCTTCTTATTATGGTCATCCCAAATTTTTTTGATTAATTTGG
Found at i:279294 original size:12 final size:11
Alignment explanation
Indices: 279271--279306 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
279261 TGAAAAAGAA
279271 AATTAAAATCT
1 AATTAAAATCT
279282 AATTAAAATTCT
1 AATTAAAA-TCT
*
279294 AATTAAAAACT
1 AATTAAAATCT
279305 AA
1 AA
279307 GTCTAAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (11 bp):
AATTAAAATCT
Found at i:282684 original size:25 final size:25
Alignment explanation
Indices: 282656--282714 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
282646 GATAAACGGC
* *
282656 AAGCTCTTTCGAGCAAAATAACAGT
1 AAGCTCATACGAGCAAAATAACAGT
** *
282681 AAGCTCATACGAGCTGAGTAACAGT
1 AAGCTCATACGAGCAAAATAACAGT
282706 AAGCTCATA
1 AAGCTCATA
282715 AGAGTTGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (25 bp):
AAGCTCATACGAGCAAAATAACAGT
Found at i:287863 original size:12 final size:12
Alignment explanation
Indices: 287829--287863 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
287819 TTCACAAAGC
*
287829 ATATTCAGATAT
1 ATATTCACATAT
287841 ATATTCAACATAT
1 ATATTC-ACATAT
287854 ATATTCACAT
1 ATATTCACAT
287864 TACAAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (12 bp):
ATATTCACATAT
Found at i:289121 original size:20 final size:19
Alignment explanation
Indices: 289088--289143 Score: 103
Period size: 20 Copynumber: 2.9 Consensus size: 19
289078 AATTGTTTTA
289088 ATATTTAATTTAATTATTC
1 ATATTTAATTTAATTATTC
289107 ATATTTAATTTTAATTATTC
1 ATATTTAA-TTTAATTATTC
289127 ATATTTAATTTAATTAT
1 ATATTTAATTTAATTAT
289144 CTAACCTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 17 0.47
20 19 0.53
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATTTAATTTAATTATTC
Found at i:289695 original size:110 final size:110
Alignment explanation
Indices: 289502--289837 Score: 636
Period size: 110 Copynumber: 3.0 Consensus size: 110
289492 ACAAGTGAAG
* *
289502 TAATTTCGCAATTTCTCTAAACTTTTGGGTCAAGTTGTAAATCAAAAAAATATCTTTAAAAATTT
1 TAATTTCGCAATTTCTCTAAACTTTTGGGTCAAGTTGTAAATCAGAAAAATATCTCTAAAAATTT
289567 TCTGAAATAATCTCTTCAGTGAATTTTCTCTCTACAACTTTCTCT
66 TCTGAAATAATCTCTTCAGTGAATTTTCTCTCTACAACTTTCTCT
289612 TAATTTCGCAATTTCTCTAAACTTTTGGGTCAAGTTGTAAATCAGAAAAATATCTCTAAAAATTT
1 TAATTTCGCAATTTCTCTAAACTTTTGGGTCAAGTTGTAAATCAGAAAAATATCTCTAAAAATTT
289677 TCTGAAATAATCTCTTCAGTGAATTTTCTCTCTACAACTTTCTCT
66 TCTGAAATAATCTCTTCAGTGAATTTTCTCTCTACAACTTTCTCT
289722 TAATTTCGCAATTTCTCTAAACTTTTGGGTCAAGTTGTAAATCAGAAAAATATCTCTAAAAATTT
1 TAATTTCGCAATTTCTCTAAACTTTTGGGTCAAGTTGTAAATCAGAAAAATATCTCTAAAAATTT
*
289787 TCTGAAATAATCTCTTCAGTGAATTTTCTCTCTACAACTTTTTCT
66 TCTGAAATAATCTCTTCAGTGAATTTTCTCTCTACAACTTTCTCT
289832 TGAATT
1 T-AATT
289838 CAAGTTGTGT
Statistics
Matches: 222, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
110 218 0.98
111 4 0.02
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (110 bp):
TAATTTCGCAATTTCTCTAAACTTTTGGGTCAAGTTGTAAATCAGAAAAATATCTCTAAAAATTT
TCTGAAATAATCTCTTCAGTGAATTTTCTCTCTACAACTTTCTCT
Found at i:289948 original size:17 final size:17
Alignment explanation
Indices: 289926--289958 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
289916 TCACTTTAAT
*
289926 ATTAAATTTAATATTAG
1 ATTAAAATTAATATTAG
289943 ATTAAAATTAATATTA
1 ATTAAAATTAATATTA
289959 AATCTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
ATTAAAATTAATATTAG
Found at i:290040 original size:37 final size:35
Alignment explanation
Indices: 289999--290100 Score: 87
Period size: 37 Copynumber: 2.7 Consensus size: 35
289989 AGATAAACAC
289999 TAAATTAAATTTAATATTAAGATAATTACTTTAATAT
1 TAAATTAAATTTAATATTAAGATAATTA-TTTAAT-T
** * *
290036 TAAATTAATAAAATACTATTAAGATAAGTATTTAATT
1 TAAATT-A-AATTTAATATTAAGATAATTATTTAATT
* * *
290073 TAATTTAATATTAAACTATTAAAATAAT
1 TAAATTAA-ATTTAA-TATTAAGATAAT
290101 ATTATTTTTG
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
35 1 0.02
36 3 0.06
37 22 0.44
38 7 0.14
39 17 0.34
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (35 bp):
TAAATTAAATTTAATATTAAGATAATTATTTAATT
Found at i:302378 original size:45 final size:44
Alignment explanation
Indices: 302234--302378 Score: 136
Period size: 47 Copynumber: 3.2 Consensus size: 44
302224 TTCAGAATAT
*
302234 TATAAAAA-AATTAAGATTTATAATGTAAATAAAATATTATAAAA
1 TATAAAAATAA-TAAAATTTATAATGTAAATAAAATATTATAAAA
* * *
302278 TGAT-AAAATGATAACAATTATCGATAAT-T-AATAAAAAATTGTAACAA
1 T-ATAAAAATAATAA-AATT-T--ATAATGTAAATAAAATATTATAA-AA
*
302325 CTACAAAAATAATAAAATGTTATAATGTAAATAAAATATTATAAAA
1 -TATAAAAATAATAAAAT-TTATAATGTAAATAAAATATTATAAAA
302371 TATAAAAA
1 TATAAAAA
302379 AAAGAATTAT
Statistics
Matches: 80, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
44 8 0.10
45 18 0.22
46 17 0.21
47 21 0.26
48 16 0.20
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (44 bp):
TATAAAAATAATAAAATTTATAATGTAAATAAAATATTATAAAA
Found at i:303849 original size:23 final size:23
Alignment explanation
Indices: 303804--303849 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
303794 GATTTTCTTA
**
303804 TACTTTATTTTCTTATTTCTTTT
1 TACTTTATTTTCTTATTAATTTT
303827 TACTTTATTTTACTT-TTAATTTT
1 TACTTTATTTT-CTTATTAATTTT
303850 AGTTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (23 bp):
TACTTTATTTTCTTATTAATTTT
Found at i:316266 original size:15 final size:16
Alignment explanation
Indices: 316240--316272 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
316230 TATTTGGGCC
316240 TTTAATTTTTTTTAAT
1 TTTAATTTTTTTTAAT
316256 TTTAA-TTTTTTTAAT
1 TTTAATTTTTTTTAAT
316271 TT
1 TT
316273 ATTATTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTAATTTTTTTTAAT
Found at i:316772 original size:40 final size:41
Alignment explanation
Indices: 316670--316773 Score: 113
Period size: 41 Copynumber: 2.6 Consensus size: 41
316660 TTCGGTCTAT
* **
316670 TCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATTTAC
1 TCCACTGTAATCTCAGGGAGATAAGACCTGATGCAATCCAC
* * * * *
316711 TCTACTGTAATTTCAGAGAGATAAGATCT--TGTTAATCCAC
1 TCCACTGTAATCTCAGGGAGATAAGACCTGATG-CAATCCAC
316751 TCCACTGTAATCTCAGGGAGATA
1 TCCACTGTAATCTCAGGGAGATA
316774 GGATTACCGG
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
39 2 0.04
40 24 0.47
41 25 0.49
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (41 bp):
TCCACTGTAATCTCAGGGAGATAAGACCTGATGCAATCCAC
Found at i:316995 original size:44 final size:44
Alignment explanation
Indices: 316849--316997 Score: 158
Period size: 44 Copynumber: 3.4 Consensus size: 44
316839 GCTTGTGCTT
* * * **
316849 AGGGAGATAAGATCTGCTTCCTTAGTCTGCCCCACTGTGACTTC
1 AGGGAGATAAGACCTGCTTACTCAGTCTGCCCCACTGCAACTTC
* * *
316893 AGGGGGATAAGACTTG-TCATCTTC-GATCTGCCCCACTGCAACTTC
1 AGGGAGATAAGACCTGCTTA-C-TCAG-TCTGCCCCACTGCAACTTC
* * *
316938 AGGGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACTTC
1 AGGGAGATAAGACCTGCTTACTCAGTCTGCCCCACTGCAACTTC
316982 AGGGAGATAAGACCTG
1 AGGGAGATAAGACCTG
316998 ATGCGATCCA
Statistics
Matches: 87, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
43 1 0.01
44 49 0.56
45 35 0.40
46 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.26
Consensus pattern (44 bp):
AGGGAGATAAGACCTGCTTACTCAGTCTGCCCCACTGCAACTTC
Found at i:317157 original size:216 final size:216
Alignment explanation
Indices: 316919--317339 Score: 707
Period size: 216 Copynumber: 1.9 Consensus size: 216
316909 TCATCTTCGA
* * *
316919 TCTGCCCCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACTTCAG
1 TCTGCCCCACTGCAACTTCAGGGGCATAAGACCTGCTTACTCAGTCTGCTCCACTGCAACCTCAG
* *
316984 GGAGATAAGACCTGATGCGATCCACTCTGCTGCAACTTTAGAGAGATAAGATCTATTACTTTAAT
66 GGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAAT
* *
317049 CCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTTCCTTACACTTGAAGA
131 CCGCTCCACTACAACTTCAGGGAGATAAGATTATCGACTTCAATCTGCTTCCTTACACTTGAAGA
317114 TAAGATTCGCCGCTTCTTCAG
196 TAAGATTCGCCGCTTCTTCAG
** * * * *
317135 TCTGCCCCACTGTGACTTCAGGGGCATAAGACTTGTTTTCTCAGTTTGCTCCACTGCAACCTCAG
1 TCTGCCCCACTGCAACTTCAGGGGCATAAGACCTGCTTACTCAGTCTGCTCCACTGCAACCTCAG
317200 GGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAAT
66 GGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAAT
*
317265 CTGCTCCACTACAACTTCAGGGAGATAAGATTATCGACTTCAATCTGCTTCCTTACACTTGAAGA
131 CCGCTCCACTACAACTTCAGGGAGATAAGATTATCGACTTCAATCTGCTTCCTTACACTTGAAGA
*
317330 TAGGATTCGC
196 TAAGATTCGC
317340 TGTCTTCAAT
Statistics
Matches: 190, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
216 190 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (216 bp):
TCTGCCCCACTGCAACTTCAGGGGCATAAGACCTGCTTACTCAGTCTGCTCCACTGCAACCTCAG
GGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAAT
CCGCTCCACTACAACTTCAGGGAGATAAGATTATCGACTTCAATCTGCTTCCTTACACTTGAAGA
TAAGATTCGCCGCTTCTTCAG
Found at i:317510 original size:125 final size:126
Alignment explanation
Indices: 317362--317593 Score: 412
Period size: 125 Copynumber: 1.8 Consensus size: 126
317352 GATCCGCTAC
317362 TGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGGTCAGGGAAATAGGACTTG
1 TGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGGTCAGGGAAATAGGACTTG
*
317427 TGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCAATATTCACTGATTTGT
66 TGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCAATATTCACTGATTTGT
* * *
317488 TGCTTAGGG-GACAAGATCTGCAATTTCTAACCTATTCCACTGCTGGTTAGGGACATAGGACTTG
1 TGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGGTCAGGGAAATAGGACTTG
*
317552 TGGCTTAAATCTGCTTCCCTACTCTTGGGGAAGATAAGATTC
66 TGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTC
317594 ACCGTCTTCG
Statistics
Matches: 101, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
125 92 0.91
126 9 0.09
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (126 bp):
TGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGGTCAGGGAAATAGGACTTG
TGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCAATATTCACTGATTTGT
Done.