Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004450.1 Hibiscus syriacus cultivar Beakdansim tig00009785_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 113089
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:69 original size:3 final size:3
Alignment explanation
Indices: 61--114 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
51 GATCTGTTTG
61 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA -AA TAA TAA T-A TAA TACA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
107 -AA TAA TAA
1 TAA TAA TAA
115 AAAAATAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 7 0.15
3 38 0.83
4 1 0.02
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:81 original size:17 final size:17
Alignment explanation
Indices: 61--124 Score: 80
Period size: 17 Copynumber: 3.8 Consensus size: 17
51 GATCTGTTTG
61 TAATAATAA-AATAATAA
1 TAATAATAATAA-AATAA
78 TAATAATAATAAAATAA
1 TAATAATAATAAAATAA
95 TAAT-ATAATACAAATAA
1 TAATAATAATA-AAATAA
*
112 TAA-AAAAATAAAA
1 TAATAATAATAAAA
125 AAAAAAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
16 9 0.21
17 32 0.74
18 2 0.05
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
TAATAATAATAAAATAA
Found at i:86 original size:20 final size:19
Alignment explanation
Indices: 61--104 Score: 79
Period size: 20 Copynumber: 2.3 Consensus size: 19
51 GATCTGTTTG
61 TAATAATAAAATAATAATAA
1 TAATAATAAAATAATAAT-A
81 TAATAATAAAATAATAATA
1 TAATAATAAAATAATAATA
100 TAATA
1 TAATA
105 CAAATAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAATAATAAAATAATAATA
Found at i:102 original size:25 final size:26
Alignment explanation
Indices: 73--124 Score: 56
Period size: 25 Copynumber: 2.1 Consensus size: 26
63 ATAATAAAAT
73 AATAATAATAATAATA-AAATAATAA
1 AATAATAATAATAATACAAATAATAA
* *
98 TATAATACA-AATAATA-AAAAAATAA
1 AATAATA-ATAATAATACAAATAATAA
123 AA
1 AA
125 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (26 bp):
AATAATAATAATAATACAAATAATAA
Found at i:102 original size:28 final size:28
Alignment explanation
Indices: 62--127 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
52 ATCTGTTTGT
*
62 AATAATAAAATAATA-ATAATAATAATAA
1 AATAATAAAATAATACA-AATAATAAAAA
*
90 AATAATAATATAATACAAATAATAAAAA
1 AATAATAAAATAATACAAATAATAAAAA
*
118 AATAAAAAAA
1 AATAATAAAA
128 AAAAAAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 32 0.97
29 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (28 bp):
AATAATAAAATAATACAAATAATAAAAA
Found at i:127 original size:11 final size:11
Alignment explanation
Indices: 106--148 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
96 AATATAATAC
*
106 AAATAATAAAA
1 AAATAAAAAAA
117 AAATAAAAAAA
1 AAATAAAAAAA
*
128 AAA-AAAAAAG
1 AAATAAAAAAA
138 AAATGAAAAAA
1 AAAT-AAAAAA
149 CTAGGTGTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 9 0.32
11 13 0.46
12 6 0.21
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.09
Consensus pattern (11 bp):
AAATAAAAAAA
Found at i:736 original size:123 final size:123
Alignment explanation
Indices: 489--1057 Score: 855
Period size: 123 Copynumber: 4.7 Consensus size: 123
479 GAATTAAGGC
*
489 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTAT
*
554 GAAC-TCCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
66 GAACTTCC-TCTGGAAACGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
* *
612 AATGTTGAACAA-TTCTTCTCAATATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTAT
*
676 GAACTTCCTCTGGAAACGTTTGATGTTGATCTATCTCCTTCTGTGATAAAGTCGAGCAA
66 GAACTTCCTCTGGAAACG-TTGATGTTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
* * * *
735 AAGGTTGAAC-AGTTCTTCTCATTATGAACTTCTTTTTCCTCTTCAGATGAGTTCTTTTAATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTAT
* *
799 GAACTTCCTCTGGAAACGTTGATGTTGATGTATCTCCTTCTATGATAGAGTC-ACGCAA
66 GAACTTCCTCTGGAAACGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCGA-GCAA
* *
857 AAGGTTGAACAAGTTCTTCTCATTA--AACTTGTTCTTTCTCTTC--ATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTAT
918 GAACTT-C-CTGGAAACGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCGAGC-A
66 GAACTTCCTCTGGAAACGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
973 AAGGTTGAACAAGTTC-TCTCCATTATGAACTTCTTCTTCCTCTTC-AATGAG-T-TTCTCATTA
1 AAGGTTGAACAAGTTCTTCT-CATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTA
*
1034 TGAACTCTAC-CTGGAAACGTTGAT
65 TGAACT-TCCTCTGGAAACGTTGAT
1058 CCATCGAGTG
Statistics
Matches: 411, Mismatches: 23, Indels: 28
0.89 0.05 0.06
Matches are distributed among these distances:
115 3 0.01
116 22 0.05
117 58 0.14
118 20 0.05
119 42 0.10
121 16 0.04
122 109 0.27
123 141 0.34
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTAT
GAACTTCCTCTGGAAACGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
Found at i:822 original size:245 final size:239
Alignment explanation
Indices: 489--1057 Score: 859
Period size: 245 Copynumber: 2.4 Consensus size: 239
479 GAATTAAGGC
489 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * *
554 GAAC-TCCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCGA-GCAAAATGT
66 GAACTTCC-TCTGGAAACGTTGATGTTGATCTATCTCCTTCTATGATAGAGTC-ACGCAAAAGGT
*
617 TGAACAA-TTCTTCTCAATATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTATGAACT
129 TGAACAAGTTCTTCTC-AT-TAAACTTCTTCTTCCTCTTC--ATGAGTTCTTCTCATTATGAACT
681 TCCTCTGGAAACGTTTGATGTTGATCTATCTCCTTCTGTGATAAAGTCGAGCAA
190 T-C-CTGGAAACG-TTGATGTTGATCTATCTCCTTCTGTGATAAAGTCGAGC-A
* * *
735 AAGGTTGAAC-AGTTCTTCTCATTATGAACTTCTTTTTCCTCTTCAGATGAGTTCTTTTAATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
*
799 GAACTTCCTCTGGAAACGTTGATGTTGATGTATCTCCTTCTATGATAGAGTCACGCAAAAGGTTG
66 GAACTTCCTCTGGAAACGTTGATGTTGATCTATCTCCTTCTATGATAGAGTCACGCAAAAGGTTG
* *
864 AACAAGTTCTTCTCATTAAACTTGTTCTTTCTCTTCATGAGTTCTTCTCATTATGAACTTCCTGG
131 AACAAGTTCTTCTCATTAAACTTCTTCTTCCTCTTCATGAGTTCTTCTCATTATGAACTTCCTGG
*
929 AAACGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCGAGCA
196 AAACGTTGATGTTGATCTATCTCCTTCTGTGATAAAGTCGAGCA
973 AAGGTTGAACAAGTTC-TCTCCATTATGAACTTCTTCTTCCTCTTCA-ATGAG-T-TTCTCATTA
1 AAGGTTGAACAAGTTCTTCT-CATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
*
1034 TGAACTCTAC-CTGGAAACGTTGAT
65 TGAACT-TCCTCTGGAAACGTTGAT
1058 CCATCGAGTG
Statistics
Matches: 302, Mismatches: 15, Indels: 22
0.89 0.04 0.06
Matches are distributed among these distances:
236 27 0.09
237 3 0.01
238 19 0.06
239 67 0.22
240 9 0.03
241 1 0.00
242 24 0.08
244 18 0.06
245 113 0.37
246 21 0.07
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (239 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTTCCTCTGGAAACGTTGATGTTGATCTATCTCCTTCTATGATAGAGTCACGCAAAAGGTTG
AACAAGTTCTTCTCATTAAACTTCTTCTTCCTCTTCATGAGTTCTTCTCATTATGAACTTCCTGG
AAACGTTGATGTTGATCTATCTCCTTCTGTGATAAAGTCGAGCA
Found at i:1208 original size:74 final size:73
Alignment explanation
Indices: 1076--1293 Score: 300
Period size: 74 Copynumber: 3.0 Consensus size: 73
1066 TGATGGAAAC
* *
1076 TTGTTTCTAGTGAAATTGTCTCAAGCGAG-AC-AATCTGTTTTAAGAAAAACAATCTCAAGTGAG
1 TTGTTTCGAGTGAAATTGTCTCAAGCGAGAACAAATTTGTTTTAAGAAAAACAATCTCAAGTGAG
1139 ATAAATTA
66 ATAAATTA
* * *
1147 TTGTTTCGAGTGAAATTGTATCAAACGAGAACAAATTTTGTTTAAAGAAAAACAATCTCAAGTGA
1 TTGTTTCGAGTGAAATTGTCTCAAGCGAGAACAAA-TTTGTTTTAAGAAAAACAATCTCAAGTGA
1212 GATAAATTGA
65 GATAAATT-A
* * * *
1222 -TGTTTCGAGTGAAACTGTCTCAAGCGAGACGCAGA-TTGTTTTAAGAAAAACAATCTCAAGTAA
1 TTGTTTCGAGTGAAATTGTCTCAAGCGAGA-ACAAATTTGTTTTAAGAAAAACAATCTCAAGTGA
1285 GATAAATTA
65 GATAAATTA
1294 CTATTTGAAA
Statistics
Matches: 130, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
71 26 0.20
72 3 0.02
73 36 0.28
74 61 0.47
75 4 0.03
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (73 bp):
TTGTTTCGAGTGAAATTGTCTCAAGCGAGAACAAATTTGTTTTAAGAAAAACAATCTCAAGTGAG
ATAAATTA
Found at i:1243 original size:37 final size:36
Alignment explanation
Indices: 1128--1250 Score: 102
Period size: 37 Copynumber: 3.3 Consensus size: 36
1118 AGAAAAACAA
* *
1128 TCTCAAGTGAGATAAATTATTGTTTCGAGTGAAATTG
1 TCTCAAGCGAGATAAATTA-TGTTTCGAGTGAAACTG
* * * * ** ** **
1165 TATCAAACGAGAACAAATTTTGTTTAAAGAAAAACAA
1 TCTCAAGCGAG-ATAAATTATGTTTCGAGTGAAACTG
*
1202 TCTCAAGTGAGATAAATTGATGTTTCGAGTGAAACTG
1 TCTCAAGCGAGATAAATT-ATGTTTCGAGTGAAACTG
1239 TCTCAAGCGAGA
1 TCTCAAGCGAGA
1251 CGCAGATTGT
Statistics
Matches: 60, Mismatches: 24, Indels: 4
0.68 0.27 0.05
Matches are distributed among these distances:
36 6 0.10
37 48 0.80
38 6 0.10
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (36 bp):
TCTCAAGCGAGATAAATTATGTTTCGAGTGAAACTG
Found at i:2045 original size:22 final size:22
Alignment explanation
Indices: 2017--2067 Score: 88
Period size: 20 Copynumber: 2.4 Consensus size: 22
2007 TAAAGTTTTG
2017 ATCTTTGAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
2039 ATCTTTG--AAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
2059 ATCTTTGAA
1 ATCTTTGAA
2068 GAATGTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 20 0.74
22 7 0.26
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (22 bp):
ATCTTTGAAAAGAGAATCTATC
Found at i:3645 original size:35 final size:35
Alignment explanation
Indices: 3583--3649 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
3573 TCTTGTTGAG
3583 ATGAGCTTCCAAGAATGCCCAAATATTCATATTGCT
1 ATGAGCTTCCAAGAATGCCCAAATATTC-TATTGCT
* *
3619 ATGAGCCTT-CAA-AATGCCCCATTATTCTATT
1 ATGAG-CTTCCAAGAATGCCCAAATATTCTATT
3650 TCTGGTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 4 0.14
35 13 0.46
36 8 0.29
37 3 0.11
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (35 bp):
ATGAGCTTCCAAGAATGCCCAAATATTCTATTGCT
Found at i:8049 original size:43 final size:44
Alignment explanation
Indices: 7978--8061 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 44
7968 TGCATCAAAC
* * *
7978 AAAACTTTTACATGTAGGGGACAGCTTTCAGTCCTAACTTCAAT
1 AAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTCAAT
* * *
8022 AAAAC-TTTACATATAGGGTATAACTTTCCCTCCTAACTTC
1 AAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
8062 TCTAAAGCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 29 0.85
44 5 0.15
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (44 bp):
AAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTCAAT
Found at i:10494 original size:23 final size:24
Alignment explanation
Indices: 10467--10531 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 24
10457 AGAATAAAAT
*
10467 TAAATTAAAA-TATAACTA-AGTAA
1 TAAA-TAAAATTAAAACTATAGTAA
10490 TAAATAAAATTAAAACTATAGT-A
1 TAAATAAAATTAAAACTATAGTAA
10513 T---TAAAATATAAAACTATAG
1 TAAATAAAAT-TAAAACTATAG
10532 AACTTGTAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
20 6 0.16
21 11 0.29
22 5 0.13
23 13 0.34
24 3 0.08
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (24 bp):
TAAATAAAATTAAAACTATAGTAA
Found at i:11887 original size:3 final size:3
Alignment explanation
Indices: 11879--11977 Score: 89
Period size: 3 Copynumber: 33.0 Consensus size: 3
11869 GACATGTTTG
* *
11879 TAA TAA TAA TAA TAT TAA TAA TAA AAA TAAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* *
11924 TAA TAAA TAA TTAA TAA TAA TAG TAA TAA -ACA -AA TAA -AA TAA AAA
1 TAA T-AA TAA -TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
*
11969 TAA AAA TAA
1 TAA TAA TAA
11978 AAAAACAAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 14
0.77 0.10 0.14
Matches are distributed among these distances:
2 6 0.08
3 64 0.81
4 9 0.11
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:11913 original size:25 final size:25
Alignment explanation
Indices: 11883--11970 Score: 97
Period size: 25 Copynumber: 3.4 Consensus size: 25
11873 TGTTTGTAAT
11883 AATAATAATATTAATAATAAAAATA
1 AATAATAATATTAATAATAAAAATA
*
11908 AATAATAATAATATAATAATAAATAATT
1 AATAATAAT-AT-TAATAATAAA-AATA
* *
11936 AATAATAATAGTAATAA-ACAAATAA
1 AATAATAATATTAATAATAAAAAT-A
*
11961 AATAAAAATA
1 AATAATAATA
11971 AAAATAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
24 3 0.06
25 20 0.37
26 8 0.15
27 11 0.20
28 12 0.22
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (25 bp):
AATAATAATATTAATAATAAAAATA
Found at i:11920 original size:28 final size:26
Alignment explanation
Indices: 11880--11971 Score: 107
Period size: 28 Copynumber: 3.4 Consensus size: 26
11870 ACATGTTTGT
11880 AATAATAATAATATTAATAATAAAAATA
1 AATAATAATAATA-TAATAAT-AAAATA
11908 AATAATAATAATATAATAAT-AAATA
1 AATAATAATAATATAATAATAAAATA
*
11933 ATTAATAATAATAGTAATAA-ACAAATAA
1 AATAATAATAATA-TAATAATA-AAAT-A
*
11961 AATAAAAATAA
1 AATAATAATAA
11972 AAATAAAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
25 17 0.30
26 6 0.11
27 11 0.19
28 23 0.40
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (26 bp):
AATAATAATAATATAATAATAAAATA
Found at i:11971 original size:31 final size:30
Alignment explanation
Indices: 11879--11977 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 30
11869 GACATGTTTG
*
11879 TAATAATAATAATAT--TAAT-AATAAAAA
1 TAATAATAATAATATAAAAATAAATAAAAA
* *
11906 TAAATAATAATAATATAATAATAAATAATTAA
1 T-AATAATAATAATATAAAAATAAATAA-AAA
*
11938 TAATAATAGTAATA-AACAAATAAAATAAAAA
1 TAATAATAATAATATAA-AAAT-AAATAAAAA
*
11969 TAAAAATAA
1 TAATAATAA
11978 AAAAACAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
27 1 0.02
28 14 0.24
30 6 0.10
31 29 0.49
32 9 0.15
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (30 bp):
TAATAATAATAATATAAAAATAAATAAAAA
Found at i:11978 original size:6 final size:6
Alignment explanation
Indices: 11898--11999 Score: 57
Period size: 6 Copynumber: 16.3 Consensus size: 6
11888 TAATATTAAT
* * * * **
11898 AATAAA AATAAA TAATAAT AAT-AT AATAATA AATAATT AATAAT AATAGT
1 AATAAA AATAAA -AATAAA AATAAA AATAA-A AATAA-A AATAAA AATAAA
*
11948 AATAAA CAA-ATAA AATAAA AATAAA AATAAA AAAACAA AATGAAA AA-AAA
1 AATAAA -AATA-AA AATAAA AATAAA AATAAA AATA-AA AAT-AAA AATAAA
11998 AA
1 AA
12000 ACTAGTGTCT
Statistics
Matches: 80, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
5 10 0.12
6 40 0.50
7 29 0.36
8 1 0.01
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (6 bp):
AATAAA
Found at i:14014 original size:20 final size:19
Alignment explanation
Indices: 13986--14025 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
13976 GTAAAATATA
13986 TTTTTTTAATAT-TTTTATG
1 TTTTTTTAAT-TGTTTTATG
14005 TTTTTCTTAATTGTTTTATG
1 TTTTT-TTAATTGTTTTATG
14025 T
1 T
14026 AATAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.72
Consensus pattern (19 bp):
TTTTTTTAATTGTTTTATG
Found at i:15147 original size:253 final size:249
Alignment explanation
Indices: 14579--15186 Score: 859
Period size: 253 Copynumber: 2.4 Consensus size: 249
14569 CTTATTTATA
*
14579 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATATTTTATTATTATTTCGGGTC-GGTCGGGTTTCTAATTCATATATTCGGGT
* * * *
14644 GGGGTCGAGTGAAACTTTATTTTGGTCGGGTCAGGTCGGTTTTTTTAAGTGTGGTATTCGGGTCG
65 CGGGTCG-GTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAATGTGATATTCGGGTCG
* *
14709 GATCGAGTTCGGATTTAGGGTGAAAACTACCCGACCCGAAAATATATAATTTTACGTTATATATT
129 GAT---GTTCGGATTTAGGGTGAAAACTACCCGACCCAAAAATATATAATTTTACCTTATATATT
* * *
14774 TAGGAATAATTACTATAATACCCTCTATATATAATTTTTTTCAATTAAGTCACTATTTT
191 TAGGAATAATTACAATAATACCCTCTACATATAATTTTTTTAAATTAAGTCACTATTTT
*** *
14833 TATTGAATAAAAATATTTTATT-TTGGGTCGGGTCGGTTCGGATTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATATTTTATTATTATTTCGGGTCGG-TCGGGTTTCTAATTCATATATTCGGGT
14897 CGGGTCGGTGAAACTTTATTTTGGTC-GGTCGGGTCGGGTTTTTTTTAAATGTGATATTCGGGTC
65 CGGGTCGGTGAAACTTTATTTTGGTCGGGTCGGGTC-GG-TTTTTTTAAATGTGATATTCGGGTC
*
14961 GGAT-TTTGG-TTTAGGGTGAAAAATACCTGACCCGACCCAAAAAATATATAATTTTACCTTATA
128 GGATGTTCGGATTTAGGGTG--AAA-A-CT-ACCCGACCC-AAAAATATATAATTTTACCTTATA
* * *
15024 TATTTAGGAATAATTACAATAATACCC-CTCCATAT-ATTTTTTTAAATTAAGTCATTTTTTT
187 TATTTAGGAATAATTACAATAATACCCTCTACATATAATTTTTTTAAATTAAGTCACTATTTT
*
15085 TATTGAATAAAAATATTTTATTATTATTTAGGGTCAGGTCGGGTTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATATTTTATTATTATTTCGGGTC-GGTCGGGTTTCTAATTCATATATTCGGGT
15150 CGGGTCAGGTGAAACTTTATTTTGGTCGGGTCGGGTC
65 CGGGTC-GGTGAAACTTTATTTTGGTCGGGTCGGGTC
15187 TCGGATGGAT
Statistics
Matches: 318, Mismatches: 23, Indels: 25
0.87 0.06 0.07
Matches are distributed among these distances:
248 9 0.03
249 4 0.01
250 3 0.01
251 9 0.03
252 70 0.22
253 123 0.39
254 91 0.29
255 9 0.03
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (249 bp):
TATTGAATAAAAATATTTTATTATTATTTCGGGTCGGTCGGGTTTCTAATTCATATATTCGGGTC
GGGTCGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAATGTGATATTCGGGTCGGA
TGTTCGGATTTAGGGTGAAAACTACCCGACCCAAAAATATATAATTTTACCTTATATATTTAGGA
ATAATTACAATAATACCCTCTACATATAATTTTTTTAAATTAAGTCACTATTTT
Found at i:15549 original size:18 final size:17
Alignment explanation
Indices: 15505--15551 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
15495 TATGGAATTG
*
15505 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
*
15522 GATTCTAATTCCTTCACA
1 GATTCCAATTCC-TCACA
*
15540 TATTCCAATTCC
1 GATTCCAATTCC
15552 CTCATAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.28, C:0.30, G:0.06, T:0.36
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:23070 original size:16 final size:16
Alignment explanation
Indices: 23049--23087 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
23039 CAAATCCGGG
*
23049 TACCCGGATTTTTGGA
1 TACCCGGATTTTCGGA
*
23065 TACCC-GATTTTCGGG
1 TACCCGGATTTTCGGA
23080 TACCCGGA
1 TACCCGGA
23088 ACTTCCGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.31
Consensus pattern (16 bp):
TACCCGGATTTTCGGA
Found at i:23155 original size:15 final size:15
Alignment explanation
Indices: 23135--23191 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
23125 CTGGATGTTA
23135 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
* * **
23150 CGGGTATCCAGATTTT
1 CGGGTA-CCCGGTAAT
*
23166 GCTGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
23182 CGGGTACCCG
1 CGGGTACCCG
23192 ATACCCGGTT
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
15 15 0.50
16 10 0.33
17 5 0.17
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.25
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:24844 original size:21 final size:21
Alignment explanation
Indices: 24796--24851 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
24786 AAACAACTCC
24796 TCTAAAGGAACGAACTAAAAT
1 TCTAAAGGAACGAACTAAAAT
24817 TCTAAAGGAACGAACT-AAAT
1 TCTAAAGGAACGAACTAAAAT
*
24837 TCTAAAAGAGACGAA
1 TCTAAAGGA-ACGAA
24852 ACATATTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 12 0.36
21 21 0.64
ACGTcount: A:0.52, C:0.14, G:0.16, T:0.18
Consensus pattern (21 bp):
TCTAAAGGAACGAACTAAAAT
Found at i:27594 original size:16 final size:17
Alignment explanation
Indices: 27561--27594 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
27551 CCTTATATTT
*
27561 TTATTTTATATTTTAAA
1 TTATTTTATATTTCAAA
27578 TTATTTT-TATTTCAAA
1 TTATTTTATATTTCAAA
27594 T
1 T
27595 AATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATTTCAAA
Found at i:33047 original size:42 final size:43
Alignment explanation
Indices: 32998--33079 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 43
32988 ACAAAAGCCA
* * *
32998 CAATAGGTCAGTGCATTATTGGC-TTTTTAAATAAAAACGTCG
1 CAATAGGTCAATACATTAGTGGCTTTTTTAAATAAAAACGTCG
*
33040 CAATAGGTCAATACATTAGTGGCTTTTTTAAATATAAACG
1 CAATAGGTCAATACATTAGTGGCTTTTTTAAATAAAAACG
33080 ATGCAAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
42 20 0.57
43 15 0.43
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (43 bp):
CAATAGGTCAATACATTAGTGGCTTTTTTAAATAAAAACGTCG
Found at i:33067 original size:121 final size:123
Alignment explanation
Indices: 32807--33035 Score: 284
Period size: 121 Copynumber: 1.9 Consensus size: 123
32797 AAAATGGTAG
* ** * * *
32807 CATTAGCGGTGTTTTTTCTAGAAATGCCGCTATAGCATCGTCTTTTGTGGCATTTTTTAAATAAA
1 CATTAGCGGCG-TTTTTCTAGAAACACCGCTATAGCATCATCTTTTGTGGCAATTTTTAAACAAA
* ** * * *
32872 CGCCGTAATAGATCAGTGCATAAGTGGCATTTTAAAATACAAACACCACAACATGCTAA
65 AGCCACAATAGATCAGTGCATAAGTGGCATTTTAAAATAAAAACACCACAACAGGCAAA
32931 CATTAGCGGCGTTTTTCTAGAAACACCGCTATAGCA-CATCTTTTGTGG-AATTTTTAAACAAAA
1 CATTAGCGGCGTTTTTCTAGAAACACCGCTATAGCATCATCTTTTGTGGCAATTTTTAAACAAAA
* * * *
32994 GCCACAATAGGTCAGTGCATTATTGGC-TTTTTAAATAAAAAC
66 GCCACAATAGATCAGTGCATAAGTGGCATTTTAAAATAAAAAC
33036 GTCGCAATAG
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
120 13 0.14
121 34 0.37
122 11 0.12
123 23 0.25
124 10 0.11
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (123 bp):
CATTAGCGGCGTTTTTCTAGAAACACCGCTATAGCATCATCTTTTGTGGCAATTTTTAAACAAAA
GCCACAATAGATCAGTGCATAAGTGGCATTTTAAAATAAAAACACCACAACAGGCAAA
Found at i:41224 original size:43 final size:44
Alignment explanation
Indices: 41177--41269 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
41167 AGGTTAACAT
*
41177 ATTTAGCGGC-GTTTTTGAAATAAACGCCACAAAAAGTTAGGCC
1 ATTTAGCGGCAGTTTTTAAAATAAACGCCACAAAAAGTTAGGCC
** * * *
41220 ATTTAATGGCATTTTTTAAAATAAACGCCGCAAAAAGTTAGGTC
1 ATTTAGCGGCAGTTTTTAAAATAAACGCCACAAAAAGTTAGGCC
41264 ATTTAG
1 ATTTAG
41270 AAACATTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 8 0.19
44 34 0.81
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (44 bp):
ATTTAGCGGCAGTTTTTAAAATAAACGCCACAAAAAGTTAGGCC
Found at i:41277 original size:44 final size:44
Alignment explanation
Indices: 41188--41297 Score: 125
Period size: 44 Copynumber: 2.5 Consensus size: 44
41178 TTTAGCGGCG
* **
41188 TTTTTGAAATAAACGCCACAAAAAGTTAGGCCATTTAATGGCAT
1 TTTTTAAAATAAACGCCACAAAAAGTTAGGCCATTTAATAACAT
* *
41232 TTTTTAAAATAAACGCCGCAAAAAGTTAGGTCATTTAGA-AACAT
1 TTTTTAAAATAAACGCCACAAAAAGTTAGGCCATTTA-ATAACAT
* *
41276 TTTTGGAACA-AAACGCCACAAA
1 TTTT-TAAAATAAACGCCACAAA
41298 TTTTAAGTCA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
44 52 0.93
45 4 0.07
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (44 bp):
TTTTTAAAATAAACGCCACAAAAAGTTAGGCCATTTAATAACAT
Found at i:45003 original size:22 final size:25
Alignment explanation
Indices: 44971--45030 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 25
44961 GTCTTTCTAT
*
44971 TATATTTTAAAAATATTTT-A-GTA
1 TATATATTAAAAATATTTTAATGTA
*
44994 TA-ATATTAAAAATATTTTAATTTA
1 TATATATTAAAAATATTTTAATGTA
45018 TATATATTAAAAA
1 TATATATTAAAAA
45031 ATAAATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 15 0.47
23 3 0.09
24 4 0.12
25 10 0.31
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
TATATATTAAAAATATTTTAATGTA
Found at i:46513 original size:87 final size:88
Alignment explanation
Indices: 46288--46585 Score: 490
Period size: 87 Copynumber: 3.4 Consensus size: 88
46278 AATTCAAATT
* * *
46288 TATTCGAACATCAGCGATTATAGCAGGGTGATTGCACGTGTACTCCTTTGTCAGTCAATAAATAG
1 TATTCGAGCATCAGCGACTATAGCAGGGTGATTGCACGTGTACTCCTTTGTTAGTCAATAAATAG
46353 CCGGTTTCATTTTAAAAAAAAAA
66 CCGGTTTCATTTTAAAAAAAAAA
46376 TATTCGAGCATCAGCGACTATAGCAGGGTGATTGCACGTGTACTCCTTTGTTAGTCAATAAATAG
1 TATTCGAGCATCAGCGACTATAGCAGGGTGATTGCACGTGTACTCCTTTGTTAGTCAATAAATAG
*
46441 CCAGTTTCATTTT-AAAAAAAAA
66 CCGGTTTCATTTTAAAAAAAAAA
* *
46463 TATTCGAGCATCAGCGACTATAGCCGGGTGATTGCACGTGTACTCCTTTGTTAGCCAATAAATAG
1 TATTCGAGCATCAGCGACTATAGCAGGGTGATTGCACGTGTACTCCTTTGTTAGTCAATAAATAG
46528 CCGGTTTCATTTTCAAAAAAAAAA
66 CCGGTTTCATTTT-AAAAAAAAAA
* * * *
46552 TATTCGAGCATTAGCGACTACAACAAGGTGATTG
1 TATTCGAGCATCAGCGACTATAGCAGGGTGATTG
46586 AGCGGTCATT
Statistics
Matches: 196, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
87 84 0.43
88 74 0.38
89 38 0.19
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (88 bp):
TATTCGAGCATCAGCGACTATAGCAGGGTGATTGCACGTGTACTCCTTTGTTAGTCAATAAATAG
CCGGTTTCATTTTAAAAAAAAAA
Found at i:46981 original size:29 final size:31
Alignment explanation
Indices: 46949--47010 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
46939 ATTTCATCAC
**
46949 TGAATTTTAA-ATTGATTT-AATTTTAGCAT
1 TGAATTTTAATATTGATTTCAATTAAAGCAT
*
46978 TGAATTTTAATTTTGATTTCAATTAAAGCAT
1 TGAATTTTAATATTGATTTCAATTAAAGCAT
47009 TG
1 TG
47011 GGTCGTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 10 0.36
30 7 0.25
31 11 0.39
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (31 bp):
TGAATTTTAATATTGATTTCAATTAAAGCAT
Found at i:48409 original size:14 final size:14
Alignment explanation
Indices: 48385--48445 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 14
48375 AATGTAAATG
*
48385 AACACAAACGAACA
1 AACATAAACGAACA
*
48399 AACCTAAACGAACA
1 AACATAAACGAACA
**
48413 AACAT-AA--AATG
1 AACATAAACGAACA
*
48424 AATATAAACGAACA
1 AACATAAACGAACA
48438 AACATAAA
1 AACATAAA
48446 ATTAATTGGG
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
11 6 0.17
12 2 0.06
13 2 0.06
14 25 0.71
ACGTcount: A:0.64, C:0.20, G:0.07, T:0.10
Consensus pattern (14 bp):
AACATAAACGAACA
Found at i:50341 original size:31 final size:31
Alignment explanation
Indices: 50257--50342 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
50247 TCAGATCGAT
* * *
50257 TTTTTTATTCAGATCAATATCAAACTGTTAA
1 TTTTTTAATCTGATCAATATCAGACTGTTAA
50288 TTTTTTAATCTCG-TCAATATCAGACTGTTAA
1 TTTTTTAATCT-GATCAATATCAGACTGTTAA
50319 TTTTTTAATCTGATCAATATCAGA
1 TTTTTTAATCTGATCAATATCAGA
50343 TCGATTGATT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
30 1 0.02
31 48 0.96
32 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (31 bp):
TTTTTTAATCTGATCAATATCAGACTGTTAA
Found at i:50368 original size:32 final size:31
Alignment explanation
Indices: 50332--50398 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
50322 TTTAATCTGA
50332 TCAATATCAGAT-CGATTGATTTTCGAATCGAG
1 TCAATATCAGATACG-TTGATTTT-GAATCGAG
* * *
50364 TCAATATCATATATGTTGATTTTGAATCGGG
1 TCAATATCAGATACGTTGATTTTGAATCGAG
50395 TCAA
1 TCAA
50399 CCTTTGGATC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 11 0.35
32 19 0.61
33 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.37
Consensus pattern (31 bp):
TCAATATCAGATACGTTGATTTTGAATCGAG
Found at i:57530 original size:21 final size:21
Alignment explanation
Indices: 57493--57532 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
57483 CCCCCTTTGA
*
57493 AGGGGAACTGATTCCCCCCAC
1 AGGGGAACTGATACCCCCCAC
57514 AGGGGAA-TCGATACCCCCC
1 AGGGGAACT-GATACCCCCC
57533 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (21 bp):
AGGGGAACTGATACCCCCCAC
Found at i:62982 original size:39 final size:38
Alignment explanation
Indices: 62898--63004 Score: 126
Period size: 39 Copynumber: 2.8 Consensus size: 38
62888 CTTAATTTAC
* *
62898 AAAAATAAATCCAATGAATTATTTCCTTTTACAGAAAAG
1 AAAAATAAATTCAATGATTTATTTCC-TTTACAGAAAAG
** *
62937 GTAAATAAATTCAATGATTTATTTCCTTT-CATAAACCAG
1 AAAAATAAATTCAATGATTTATTTCCTTTACAGAAA--AG
*
62976 AAAAATAAATTCAATGATTTATTTTCTTT
1 AAAAATAAATTCAATGATTTATTTCCTTT
63005 TAAAAAATAT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
37 5 0.09
38 3 0.05
39 50 0.86
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (38 bp):
AAAAATAAATTCAATGATTTATTTCCTTTACAGAAAAG
Found at i:63077 original size:58 final size:58
Alignment explanation
Indices: 62977--63116 Score: 149
Period size: 58 Copynumber: 2.4 Consensus size: 58
62967 ATAAACCAGA
* * * * *
62977 AAAATAAATTCAA-TGATTTATTTTCTTTTAAAAAATATAATCA-TATAATATACTTAGG
1 AAAATAAATTCAACT-ATTTATTTTATTTTAAAAAATAGAATCATTA-AAGATACATAAG
* * ** *
63035 AAAATAAATCCAACTATTTATTTTATTTTACATGATAGAATCATTAAAGATTCATAAG
1 AAAATAAATTCAACTATTTATTTTATTTTAAAAAATAGAATCATTAAAGATACATAAG
*
63093 AAAATAAATTCAACAATTTATTTT
1 AAAATAAATTCAACTATTTATTTT
63117 TTTATTCACG
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
58 65 0.96
59 3 0.04
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (58 bp):
AAAATAAATTCAACTATTTATTTTATTTTAAAAAATAGAATCATTAAAGATACATAAG
Found at i:63159 original size:101 final size:101
Alignment explanation
Indices: 63034--63222 Score: 254
Period size: 101 Copynumber: 1.9 Consensus size: 101
63024 ATATACTTAG
* * **
63034 GAAAATAAATCCAACTATTTATTTTATTTTACATGATAGAATCATTAAAGATTCAT-AAGAAAAT
1 GAAAATAAATCCAACAATTTATTTTATTTAACAAAATAGAATCATTAAAGATTC-TCAAGAAAAT
* *
63098 AAATTCAACAATTTATTTTTTTATTCACGATTCCTGA
65 AAATTCAACAACTTATTTCTTTATTCACGATTCCTGA
** * * *
63135 GAAAATAAATTTAACAATTTATTTTCTTTAACAAAATAGAATCATTTAAGATTCTCAATAAAATA
1 GAAAATAAATCCAACAATTTATTTTATTTAACAAAATAGAATCATTAAAGATTCTCAAGAAAATA
*
63200 AATTTAACAACTTATTTCTTTAT
66 AATTCAACAACTTATTTCTTTAT
63223 AAAAGATAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
100 1 0.01
101 74 0.99
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.40
Consensus pattern (101 bp):
GAAAATAAATCCAACAATTTATTTTATTTAACAAAATAGAATCATTAAAGATTCTCAAGAAAATA
AATTCAACAACTTATTTCTTTATTCACGATTCCTGA
Found at i:63393 original size:115 final size:115
Alignment explanation
Indices: 63137--63582 Score: 484
Period size: 115 Copynumber: 3.8 Consensus size: 115
63127 ATTCCTGAGA
* * * * *
63137 AAATAAATTTAACAATTTATTTTCTTTAACAAA-ATAGAATCATTTAAGATTCTCAATAAAATAA
1 AAATAAATTCAACAATTTATTTTCCTT-ACAAAGTTAGAATCATTCAAGATTCTCAAGAAAATAA
* * * * * * * *
63201 ATTTAACAACTTATTTCTTTATAAAAGATAAAATCATCTACGATTCTCAAGA
65 ATTCAACAATTTATTCCTTTA-CAAAGTTAAAATCATTTAAGATTCTCAAGG
** * *
63253 AAATAAATTGGACAATTTATCTTCCTTACAAAGTTAGAATCATTCAAGATTCTCTAGAAAATAAA
1 AAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATCATTCAAGATTCTCAAGAAAATAAA
* * * *
63318 TTCATCCATTTATTCCGTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
66 TTCAACAATTTATTCCTTTACAAAGTTAAAATCATTTAAGATTCTCAAGG
* *
63368 AAATAAATTCAACTATTTATTTTCCTTACAAATTTAGAATCATTCAAGATTCTCAACG-AAATAA
1 AAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATCATTCAAGATTCTCAA-GAAAATAA
** * * *
63432 ATTCAACAATTTATTTTTTCTA-ATAATGTTATAATCATTCAAGATTCTCGAGG
65 ATTCAACAATTTATTCCTT-TACA-AA-GTTAAAATCATTTAAGATTCTCAAGG
* * * * * * *
63485 AAATAAATTCAACGATTTATTTTTCTTGCAAAGTTAAAATCATTTAAAATTCTTAAGAAAATAAA
1 AAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATCATTCAAGATTCTCAAGAAAATAAA
*
63550 TTCAACAATTTATTTCCCTTACAAAGTTAAAAT
66 TTCAACAATTTA-TTCCTTTACAAAGTTAAAAT
63583 TAAAGCAAGA
Statistics
Matches: 276, Mismatches: 46, Indels: 16
0.82 0.14 0.05
Matches are distributed among these distances:
115 100 0.36
116 78 0.28
117 94 0.34
118 4 0.01
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (115 bp):
AAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATCATTCAAGATTCTCAAGAAAATAAA
TTCAACAATTTATTCCTTTACAAAGTTAAAATCATTTAAGATTCTCAAGG
Found at i:63582 original size:58 final size:58
Alignment explanation
Indices: 63134--63578 Score: 468
Period size: 58 Copynumber: 7.7 Consensus size: 58
63124 ACGATTCCTG
* * *
63134 AGAAAATAAATTTAACAATTTATTTTCTTTAACAAA-ATAGAATCATTTAAGATTCTCA
1 AGAAAATAAATTCAACAATTTATTTTCCTT-ACAAAGTTAGAATCATTTAAGATTCTCA
* * * * * * * * *
63192 ATAAAATAAATTTAACAACTTA-TTTCTTTATAAAAGATAAAATCATCTACGATTCTCA
1 AGAAAATAAATTCAACAATTTATTTTCCTTA-CAAAGTTAGAATCATTTAAGATTCTCA
** * * *
63250 AGAAAATAAATTGGACAATTTATCTTCCTTACAAAGTTAGAATCATTCAAGATTCTCT
1 AGAAAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCA
* *
63308 AGAAAATAAATTCATCCATTTA--TTCCGTTACAAAGTTAGAATCATTTAAGATTCTCA
1 AGAAAATAAATTCAACAATTTATTTTCC-TTACAAAGTTAGAATCATTTAAGATTCTCA
* * * *
63365 AGGAAATAAATTCAACTATTTATTTTCCTTACAAATTTAGAATCATTCAAGATTCTCA
1 AGAAAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCA
* * * * * * *
63423 ACG-AAATAAATTCAACAATTTATTTTTTCTAATAATGTTATAATCATTCAAGATTCTCG
1 A-GAAAATAAATTCAACAATTTA-TTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCA
* * * * * * *
63482 AGGAAATAAATTCAACGATTTATTTTTCTTGCAAAGTTAAAATCATTTAAAATTCTTA
1 AGAAAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCA
*
63540 AGAAAATAAATTCAACAATTTATTTCCCTTACAAAGTTA
1 AGAAAATAAATTCAACAATTTATTTTCCTTACAAAGTTA
63579 AAATTAAAGC
Statistics
Matches: 325, Mismatches: 53, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
56 5 0.02
57 57 0.18
58 204 0.63
59 59 0.18
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (58 bp):
AGAAAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTCA
Found at i:63596 original size:117 final size:116
Alignment explanation
Indices: 63137--63582 Score: 463
Period size: 117 Copynumber: 3.8 Consensus size: 116
63127 ATTCCTGAGA
* * * * * *
63137 AAATAAATTTAACAATTTATTTTCTTTAACAAA-ATAGAATCATTTAAGATTCTCAATAAAATAA
1 AAATAAATTCAACAATTTATTTTCCTT-ACAAAGTTAGAATCATTCAAGATTCTTAAGAAAATAA
* * * * * * *
63201 ATTTAACAACTTATTT-CTTTATAAAAGATAAAATCA-TCTACGATTCTCAAGA
65 ATTCAACAATTTATTTCCCTTA-CAAAGTTAAAATCATTC-AAGATTCTCAAGG
** *
63253 AAATAAATTGGACAATTTATCTTCCTTACAAAGTTAGAATCATTCAAGATTCTCT-AGAAAATAA
1 AAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATCATTCAAGATTCT-TAAGAAAATAA
* * * * *
63317 ATTCATCCATTTA-TTCCGTTACAAAGTTAGAATCATTTAAGATTCTCAAGG
65 ATTCAACAATTTATTTCCCTTACAAAGTTAAAATCATTCAAGATTCTCAAGG
* * *
63368 AAATAAATTCAACTATTTATTTTCCTTACAAATTTAGAATCATTCAAGATTCTCAACG-AAATAA
1 AAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATCATTCAAGATTCTTAA-GAAAATAA
** * * * * *
63432 ATTCAACAATTTATTTTTTCTAATAATGTTATAATCATTCAAGATTCTCGAGG
65 ATTCAACAATTTA-TTTCCCTTACAAAGTTAAAATCATTCAAGATTCTCAAGG
* * * * * *
63485 AAATAAATTCAACGATTTATTTTTCTTGCAAAGTTAAAATCATTTAAAATTCTTAAGAAAATAAA
1 AAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATCATTCAAGATTCTTAAGAAAATAAA
63550 TTCAACAATTTATTTCCCTTACAAAGTTAAAAT
66 TTCAACAATTTATTTCCCTTACAAAGTTAAAAT
63583 TAAAGCAAGA
Statistics
Matches: 271, Mismatches: 50, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
115 95 0.35
116 80 0.30
117 96 0.35
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (116 bp):
AAATAAATTCAACAATTTATTTTCCTTACAAAGTTAGAATCATTCAAGATTCTTAAGAAAATAAA
TTCAACAATTTATTTCCCTTACAAAGTTAAAATCATTCAAGATTCTCAAGG
Found at i:63800 original size:45 final size:45
Alignment explanation
Indices: 63751--63858 Score: 144
Period size: 45 Copynumber: 2.4 Consensus size: 45
63741 TTAAATTTAG
*
63751 CAACCCAATAATCAAAAGGAACTAATCATTTGATTTTAATTTCCA
1 CAACCCAATAATCAAAAGGAACTAATCATATGATTTTAATTTCCA
* ** * **
63796 CAACCTAATAATCGTAAGGAACTAATCATATGATTTTACTTTTGA
1 CAACCCAATAATCAAAAGGAACTAATCATATGATTTTAATTTCCA
*
63841 CAGCCCAATAATCAAAAG
1 CAACCCAATAATCAAAAG
63859 TCTTAGGCTA
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (45 bp):
CAACCCAATAATCAAAAGGAACTAATCATATGATTTTAATTTCCA
Found at i:64085 original size:12 final size:12
Alignment explanation
Indices: 64054--64092 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
64044 ATTATATGGT
64054 AATAATATCATAG
1 AATAATATCAT-G
64067 CAATAATATCATG
1 -AATAATATCATG
*
64080 AATAATATTATG
1 AATAATATCATG
64092 A
1 A
64093 TTAACGCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 12 0.50
13 1 0.04
14 11 0.46
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (12 bp):
AATAATATCATG
Found at i:65500 original size:2 final size:2
Alignment explanation
Indices: 65493--65523 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
65483 ATGTCACGTT
65493 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
65524 TTTAAAATAA
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:72933 original size:38 final size:38
Alignment explanation
Indices: 72877--72951 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
72867 CTAACTTTAA
72877 ATGTGTATGTTACTGCTAATTTAGTTTTACTATTCTTG
1 ATGTGTATGTTACTGCTAATTTAGTTTTACTATTCTTG
* *
72915 ATGTTTATGTTACTGCTAATTTCGTTTTACTATTCTT
1 ATGTGTATGTTACTGCTAATTTAGTTTTACTATTCTT
72952 TACTTTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.20, C:0.12, G:0.13, T:0.55
Consensus pattern (38 bp):
ATGTGTATGTTACTGCTAATTTAGTTTTACTATTCTTG
Found at i:79759 original size:84 final size:84
Alignment explanation
Indices: 79652--79816 Score: 303
Period size: 84 Copynumber: 2.0 Consensus size: 84
79642 TTTCTTGTCC
* *
79652 ACTAAATTTGAGATGACATACCTAAGAGAGGTTGATGTAATCTTAAGAGTTAATGTTACCAAAAT
1 ACTAAATTTGAGATGACAAACCTAAGAGAGGTTGATGTAATCTTAAGAGTTAACGTTACCAAAAT
79717 TGAAAAAGATTTTTTTAAA
66 TGAAAAAGATTTTTTTAAA
79736 ACTAAATTTGAGATGACAAACCTAAGAGAGGTTGATGTAATCTTAAGAGTTAACGTTACCAAAAT
1 ACTAAATTTGAGATGACAAACCTAAGAGAGGTTGATGTAATCTTAAGAGTTAACGTTACCAAAAT
*
79801 TGAAAAATATTTTTTT
66 TGAAAAAGATTTTTTT
79817 GAATCAAACA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.33
Consensus pattern (84 bp):
ACTAAATTTGAGATGACAAACCTAAGAGAGGTTGATGTAATCTTAAGAGTTAACGTTACCAAAAT
TGAAAAAGATTTTTTTAAA
Found at i:82801 original size:53 final size:52
Alignment explanation
Indices: 82709--82809 Score: 157
Period size: 53 Copynumber: 1.9 Consensus size: 52
82699 TGCGGTTAGG
* * *
82709 ACTTTGAATTTTTTTGCGTGTTTTGCGTGTTTCATTTACCGTATTTATAGAA
1 ACTTTGAATTTTTTTGCGTGTTTTGCATGGTTCACTTACCGTATTTATAGAA
*
82761 ACTTTGAATTTTTTTTGCGTGTTTTGTATGGTTCACTTACCGTATTTAT
1 ACTTTGAA-TTTTTTTGCGTGTTTTGCATGGTTCACTTACCGTATTTAT
82810 TGATTAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 8 0.18
53 36 0.82
ACGTcount: A:0.18, C:0.12, G:0.17, T:0.53
Consensus pattern (52 bp):
ACTTTGAATTTTTTTGCGTGTTTTGCATGGTTCACTTACCGTATTTATAGAA
Found at i:85867 original size:74 final size:74
Alignment explanation
Indices: 85746--85957 Score: 284
Period size: 74 Copynumber: 2.9 Consensus size: 74
85736 TACCCAAATA
* * * * *
85746 ATACGATATATTCGAATGAATTTTTAAAAAAGCTAAGTCTAATTTTCAGAGGTTTCTTGATGATT
1 ATACGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGTCTGATTTTCAGAGGTTTCTTGATGATT
85811 ACTT-AGTTG
66 ACTTGA-TTG
* *
85820 ATACGATGTTTTTAAATGAATTTTTAAAGAAGCTAAGTCTGATTTTCAGAGGCTTCTTGATGATT
1 ATACGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGTCTGATTTTCAGAGGTTTCTTGATGATT
85885 ACTTGATTG
66 ACTTGATTG
* * * * *
85894 ATATGATGTTTTCAAATGAATTTTTGAAGAAGCCAAG-CTTGATTTTCAAAGGTTTCTCGATGAT
1 ATACGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGTC-TGATTTTCAGAGGTTTCTTGATGAT
85958 AAGTCCTTCG
Statistics
Matches: 122, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
73 1 0.01
74 120 0.98
75 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.41
Consensus pattern (74 bp):
ATACGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGTCTGATTTTCAGAGGTTTCTTGATGATT
ACTTGATTG
Found at i:86008 original size:42 final size:41
Alignment explanation
Indices: 85952--86079 Score: 127
Period size: 41 Copynumber: 3.1 Consensus size: 41
85942 AAGGTTTCTC
85952 GATGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
1 GATGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * *
85993 GATGATTAAATCCTTCGGGTCC-TCTA-TAAGTCTTTTGAGTA-
1 GATGA-TAAGTCCTTCGGG-CCATC-AGTAAGTCTTTCGAGCAT
* * * * *
86034 GAGTAATAAGTCCTTCAGGCCATCTGTAAGACCTTCGAGCAT
1 GA-TGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
86076 GATG
1 GATG
86080 TTTTTATATG
Statistics
Matches: 68, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
40 2 0.03
41 32 0.47
42 31 0.46
43 3 0.04
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (41 bp):
GATGATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
Found at i:86221 original size:44 final size:44
Alignment explanation
Indices: 86158--86244 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
86148 TTTCTTAAAA
*
86158 CAACATTTTGCTAGATTCCATCACA-AAAGGAGTTGGATCAACAT
1 CAACATTTCGCTAGATTCCATCACATAAA-GAGTTGGATCAACAT
* *
86202 CAACATTTCGCTCGATTCCATCGCATAAAGAGTTGGATCAACA
1 CAACATTTCGCTAGATTCCATCACATAAAGAGTTGGATCAACA
86245 CTATCTCACT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 36 0.92
45 3 0.08
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.26
Consensus pattern (44 bp):
CAACATTTCGCTAGATTCCATCACATAAAGAGTTGGATCAACAT
Found at i:91064 original size:42 final size:42
Alignment explanation
Indices: 91018--91108 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 42
91008 GAATTGATCA
*
91018 ATCCTTTTCATCGAGGGATCGATCC-TTTTGGTGAAGGGACCG
1 ATCCTTTTCATCGAGGGATCGATCCATTTT-GTAAAGGGACCG
* * * * **
91060 ATCCTTTTCCTCTAGGTATTGATCCATTTTGTAAAGGGATTG
1 ATCCTTTTCATCGAGGGATCGATCCATTTTGTAAAGGGACCG
91102 ATCCTTT
1 ATCCTTT
91109 GGTCAAAGGG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 37 0.90
43 4 0.10
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (42 bp):
ATCCTTTTCATCGAGGGATCGATCCATTTTGTAAAGGGACCG
Found at i:91101 original size:21 final size:21
Alignment explanation
Indices: 91077--91130 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
91067 TCCTCTAGGT
*
91077 ATTGATCCATTTTGT-AAAGGG
1 ATTGATCC-TTTGGTCAAAGGG
91098 ATTGATCCTTTGGTCAAAGGG
1 ATTGATCCTTTGGTCAAAGGG
*
91119 ATTTATCCTTTG
1 ATTGATCCTTTG
91131 CTAGGGGATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.41
Consensus pattern (21 bp):
ATTGATCCTTTGGTCAAAGGG
Found at i:93435 original size:29 final size:29
Alignment explanation
Indices: 93337--93433 Score: 176
Period size: 29 Copynumber: 3.3 Consensus size: 29
93327 TTTTGAAAAA
*
93337 GGGATCAATCATTTTTCAGAAATATACAG
1 GGGATCAATCATTTTTCAGAAATATGCAG
93366 GGGATCAATCATTTTTCAGAAATATGCAG
1 GGGATCAATCATTTTTCAGAAATATGCAG
*
93395 GGGATCAATCCTTTTTCAGAAATATGCAG
1 GGGATCAATCATTTTTCAGAAATATGCAG
93424 GGGATCAATC
1 GGGATCAATC
93434 CTCTTGTAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (29 bp):
GGGATCAATCATTTTTCAGAAATATGCAG
Found at i:94977 original size:23 final size:24
Alignment explanation
Indices: 94933--94980 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
94923 GATGCCAACA
*
94933 TCTTTTATCTTCTTCTCTTTCTTT
1 TCTTTTATCTTCTCCTCTTTCTTT
94957 TCTTTT-TCTTGCTCCTC-TTCTTT
1 TCTTTTATCTT-CTCCTCTTTCTTT
94980 T
1 T
94981 ACCATCAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (24 bp):
TCTTTTATCTTCTCCTCTTTCTTT
Found at i:96455 original size:20 final size:20
Alignment explanation
Indices: 96428--96484 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
96418 ACTGGAATCC
96428 AAGGGATCGATCCTTTATCA
1 AAGGGATCGATCCTTTATCA
* **
96448 AGGGGATCGATCCGTTGCTCA
1 AAGGGATCGATCC-TTTATCA
*
96469 AAGGGATTGATCCTTT
1 AAGGGATCGATCCTTT
96485 TGCTAGAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (20 bp):
AAGGGATCGATCCTTTATCA
Found at i:97684 original size:2 final size:2
Alignment explanation
Indices: 97677--97759 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
97667 GGTAACGATG
97677 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
97719 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
97760 TAAATTTAAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:98778 original size:18 final size:19
Alignment explanation
Indices: 98742--98779 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
98732 GTGGTATATG
*
98742 AAAAAATAGATGTTATTAT
1 AAAAAATAGAAGTTATTAT
*
98761 AAAAAATA-AAGTTTTTAT
1 AAAAAATAGAAGTTATTAT
98779 A
1 A
98780 TTATTCTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (19 bp):
AAAAAATAGAAGTTATTAT
Found at i:99259 original size:21 final size:21
Alignment explanation
Indices: 99233--99272 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
99223 TATATTATTA
*
99233 TTATT-ATCATTTTATTTTTCT
1 TTATTAATC-TTTTAGTTTTCT
99254 TTATTAATCTTTTAGTTTT
1 TTATTAATCTTTTAGTTTT
99273 ATAATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (21 bp):
TTATTAATCTTTTAGTTTTCT
Found at i:99375 original size:17 final size:16
Alignment explanation
Indices: 99331--99384 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
99321 AAAAAAAATC
*
99331 ATATTTTTATATTTTAA
1 ATATTTTTATA-ATTAA
*
99348 ATTTTTATTATAATTAA
1 ATATTT-TTATAATTAA
99365 TATATTTTTATAATATAA
1 -ATATTTTTATAAT-TAA
99383 AT
1 AT
99385 GAAATAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 18 0.58
18 13 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATATTTTTATAATTAA
Found at i:110414 original size:20 final size:20
Alignment explanation
Indices: 110391--110442 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
110381 ATCCAGGTTC
110391 CAAATTCGCAACAC-GAAAGT
1 CAAATTCGCAACACAG-AAGT
*
110411 CAAATTCGCAATACAGAAGT
1 CAAATTCGCAACACAGAAGT
110431 CAAATTCGCAAC
1 CAAATTCGCAAC
110443 GCGACTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.44, C:0.25, G:0.13, T:0.17
Consensus pattern (20 bp):
CAAATTCGCAACACAGAAGT
Found at i:110435 original size:40 final size:40
Alignment explanation
Indices: 110351--110442 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 40
110341 AAATATCCAA
* *
110351 CAAATTCGCAACACGATCTCAAATTTCGCAATCCAGGTTC
1 CAAATTCGCAACACGAACTCAAATTTCGCAATACAGGTTC
*
110391 CAAATTCGCAACACGAAAGTCAAA-TTCGCAATACAGAAG-T-
1 CAAATTCGCAACACG-AACTCAAATTTCGCAATACAG--GTTC
110431 CAAATTCGCAAC
1 CAAATTCGCAAC
110443 GCGACTTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
40 38 0.83
41 7 0.15
42 1 0.02
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (40 bp):
CAAATTCGCAACACGAACTCAAATTTCGCAATACAGGTTC
Found at i:110458 original size:40 final size:40
Alignment explanation
Indices: 110414--110502 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
110404 CGAAAGTCAA
*
110414 ATTCGCAATAC-AGAAGTC-AAATTCGCAACGCGACTTTAAG
1 ATTCGCAACACTA-AAGTCGAAATTCGCAACGCGA-TTTAAG
* * *
110454 ATTCGCAACGCTATAGTCGAAATTTGCAACGCGATTTAAG
1 ATTCGCAACACTAAAGTCGAAATTCGCAACGCGATTTAAG
110494 ATTCGCAAC
1 ATTCGCAAC
110503 GCGATACTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 28 0.65
41 15 0.35
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (40 bp):
ATTCGCAACACTAAAGTCGAAATTCGCAACGCGATTTAAG
Found at i:110503 original size:40 final size:40
Alignment explanation
Indices: 110428--110522 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 40
110418 GCAATACAGA
110428 AGTCAAATTCGCAACGCGACTTTAAGATTCGCAACGCTAT
1 AGTCAAATTCGCAACGCGACTTTAAGATTCGCAACGCTAT
* *
110468 AGTCGAAATTTGCAACGCGA-TTTAAGATTCGCAACGCGAT
1 AGTC-AAATTCGCAACGCGACTTTAAGATTCGCAACGCTAT
* *
110508 ACTCTAAAATCGCAA
1 AGTC-AAATTCGCAA
110523 TGCATTTGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
40 34 0.71
41 14 0.29
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (40 bp):
AGTCAAATTCGCAACGCGACTTTAAGATTCGCAACGCTAT
Done.