Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007745.1 Hibiscus syriacus cultivar Beakdansim tig00110008_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: 368767
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6938 original size:23 final size:24
Alignment explanation
Indices: 6903--6956 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
6893 AAAATTAGCA
6903 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
6926 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
6950 AAGAAAA
1 AAGAAAA
6957 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:6961 original size:24 final size:23
Alignment explanation
Indices: 6903--6962 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
6893 AAAATTAGCA
6903 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
**
6926 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
6950 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
6963 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.63, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:11192 original size:23 final size:24
Alignment explanation
Indices: 11157--11210 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
11147 AAAATCAGAA
11157 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
11180 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
11204 AAGAAAA
1 AAGAAAA
11211 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:11215 original size:24 final size:23
Alignment explanation
Indices: 11157--11216 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
11147 AAAATCAGAA
11157 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
**
11180 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
11204 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
11217 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.63, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:16602 original size:15 final size:15
Alignment explanation
Indices: 16582--16621 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
16572 AAGAAATTAT
*
16582 GAAAGAAATG-AATT
1 GAAAGAAATGAAATG
16596 GATAAGAAATGAAATG
1 GA-AAGAAATGAAATG
16612 GAAAGAAATG
1 GAAAGAAATG
16622 TTATCAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 2 0.09
15 16 0.70
16 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.17
Consensus pattern (15 bp):
GAAAGAAATGAAATG
Found at i:39078 original size:19 final size:20
Alignment explanation
Indices: 39054--39096 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
39044 AGCATTTATC
*
39054 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
39073 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
39093 TTCA
1 TTCA
39097 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:39736 original size:30 final size:33
Alignment explanation
Indices: 39677--39737 Score: 85
Period size: 30 Copynumber: 1.9 Consensus size: 33
39667 TTGATAACAT
39677 TTCTATCCATTTCCTTTCTTATCATTTCCATTC
1 TTCTATCCATTTCCTTTCTTATCATTTCCATTC
39710 TTCT-TCCATTT-CTTAT-TTAT-ATTTCCAT
1 TTCTATCCATTTCCTT-TCTTATCATTTCCAT
39738 CTTAATCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 8 0.30
31 7 0.26
32 8 0.30
33 4 0.15
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.57
Consensus pattern (33 bp):
TTCTATCCATTTCCTTTCTTATCATTTCCATTC
Found at i:47058 original size:19 final size:20
Alignment explanation
Indices: 47034--47084 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
47024 CGGCCAAGAG
* *
47034 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
47053 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
47073 CATGTATTTTCA
1 CATGTATTTTCA
47085 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:51238 original size:19 final size:20
Alignment explanation
Indices: 51214--51264 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
51204 CGGCCAAGAG
* *
51214 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
51233 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
51253 CATGTATTTTCA
1 CATGTATTTTCA
51265 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:57131 original size:13 final size:13
Alignment explanation
Indices: 57115--57146 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
57105 GTGCTACAAC
57115 AAAAGAGAAAAAG
1 AAAAGAGAAAAAG
*
57128 AAAAAAGAAAAAG
1 AAAAGAGAAAAAG
57141 AAAAGA
1 AAAAGA
57147 CTCCTACATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAGAGAAAAAG
Found at i:62637 original size:19 final size:21
Alignment explanation
Indices: 62594--62645 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
62584 GAAACCCCTT
62594 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
62615 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
62634 TGAAGATACATG
1 TGAAAATACATG
62646 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:66024 original size:8 final size:8
Alignment explanation
Indices: 65996--66047 Score: 72
Period size: 8 Copynumber: 6.5 Consensus size: 8
65986 TTGGAGTGCA
65996 AAAAGAAAG
1 AAAAG-AAG
66005 AAAAGACA-
1 AAAAGA-AG
66013 AAAAGAAG
1 AAAAGAAG
66021 AAAAGAAG
1 AAAAGAAG
66029 AAAAGAAG
1 AAAAGAAG
66037 AAAA-AAG
1 AAAAGAAG
66044 AAAA
1 AAAA
66048 AGATTTCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
7 8 0.20
8 27 0.66
9 6 0.15
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:71601 original size:28 final size:28
Alignment explanation
Indices: 71561--71622 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
71551 AAAGAAAGAA
*
71561 AAGACAAAAAGAAGAAA-A-TTCAGAAAAG
1 AAGAAAAAAAGAA-AAAGATTTCA-AAAAG
71589 AAGAAAAAAAGAAAAAGATTTCAAAAAG
1 AAGAAAAAAAGAAAAAGATTTCAAAAAG
71617 -AGAAAA
1 AAGAAAA
71623 GCAAGCCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 9 0.29
28 18 0.58
29 4 0.13
ACGTcount: A:0.71, C:0.05, G:0.16, T:0.08
Consensus pattern (28 bp):
AAGAAAAAAAGAAAAAGATTTCAAAAAG
Found at i:75570 original size:22 final size:22
Alignment explanation
Indices: 75545--75589 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
75535 CTGCAAAACA
* *
75545 AAAGGAATGATAGGATCACTCC
1 AAAGAAATGATAAGATCACTCC
75567 AAAGAAATGATAAGATCACTCC
1 AAAGAAATGATAAGATCACTCC
75589 A
1 A
75590 CTCAACACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (22 bp):
AAAGAAATGATAAGATCACTCC
Found at i:76778 original size:19 final size:21
Alignment explanation
Indices: 76735--76786 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
76725 GAAAACCCTT
76735 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
76756 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
76775 TGAATATACATG
1 TGAAAATACATG
76787 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:79291 original size:24 final size:24
Alignment explanation
Indices: 79263--79314 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
79253 CTTGATACTT
79263 GTGGTTCCTATCTCTTTATAGATA
1 GTGGTTCCTATCTCTTTATAGATA
79287 GTGGTTCCTATCTCTTTATAGATA
1 GTGGTTCCTATCTCTTTATAGATA
79311 GTGG
1 GTGG
79315 GTCCAAGTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.44
Consensus pattern (24 bp):
GTGGTTCCTATCTCTTTATAGATA
Found at i:93922 original size:19 final size:21
Alignment explanation
Indices: 93879--93930 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
93869 GAAACCCCTT
93879 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
93900 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
93919 TGAAGATACATG
1 TGAAAATACATG
93931 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:97030 original size:22 final size:21
Alignment explanation
Indices: 96989--97033 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
96979 TTCTCTTTTT
96989 TTCTTTTCTTTTCTTCTCTTC
1 TTCTTTTCTTTTCTTCTCTTC
97010 TTCTTTTCTGATTT-TTCTCTTC
1 TTCTTTTCT--TTTCTTCTCTTC
97032 TT
1 TT
97034 TTTGTACTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.41
22 10 0.45
23 3 0.14
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCTTTTCTTTTCTTCTCTTC
Found at i:97790 original size:19 final size:21
Alignment explanation
Indices: 97747--97798 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
97737 GAAACCCCTT
97747 TGAAAATACATGATTTGTAAA
1 TGAAAATACATGATTTGTAAA
97768 TGAAAATACATGATTT-T-AA
1 TGAAAATACATGATTTGTAAA
*
97787 TGAAGATACATG
1 TGAAAATACATG
97799 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 1 0.03
21 16 0.53
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGATTTGTAAA
Found at i:100930 original size:11 final size:13
Alignment explanation
Indices: 100898--100927 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
100888 TGGCCAAAGA
100898 TGAAAAGGTATGT
1 TGAAAAGGTATGT
100911 TGAAAAGGTATG-
1 TGAAAAGGTATGT
100923 TGAAA
1 TGAAA
100928 GGTTTTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:102807 original size:19 final size:20
Alignment explanation
Indices: 102779--102818 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
102769 GAATAATAAT
102779 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
102799 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
102818 A
1 A
102819 AGAAAAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:113861 original size:22 final size:21
Alignment explanation
Indices: 113809--113861 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 21
113799 AATTTTTTTC
113809 TTTTCTTTTCTTCTTTTCTGAT
1 TTTTC-TTTCTTCTTTTCTGAT
* *
113831 TTTTC--TCTTCTTTTTTGCCT
1 TTTTCTTTCTTCTTTTCTG-AT
113851 TTTTCTTTCTT
1 TTTTCTTTCTT
113862 TTTGCACTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 11 0.42
20 6 0.23
22 9 0.35
ACGTcount: A:0.02, C:0.21, G:0.04, T:0.74
Consensus pattern (21 bp):
TTTTCTTTCTTCTTTTCTGAT
Found at i:113866 original size:18 final size:20
Alignment explanation
Indices: 113817--113864 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
113807 TCTTTTCTTT
* *
113817 TCTTCTTTTCTG-ATTTTTC
1 TCTTCTTTTTTGCCTTTTTC
113836 TCTTCTTTTTTGCCTTTTTC
1 TCTTCTTTTTTGCCTTTTTC
113856 T-TTCTTTTT
1 TCTTCTTTTT
113865 GCACTCCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.02, C:0.21, G:0.04, T:0.73
Consensus pattern (20 bp):
TCTTCTTTTTTGCCTTTTTC
Found at i:114157 original size:19 final size:20
Alignment explanation
Indices: 114129--114168 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
114119 GAATAATAAT
114129 ATAAGTAATGAAATGAAATA
1 ATAAGTAATGAAATGAAATA
114149 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAATGAAATA
114168 A
1 A
114169 AGAACGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAATGAAATA
Found at i:121625 original size:23 final size:25
Alignment explanation
Indices: 121599--121653 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 25
121589 AACTTTACAC
*
121599 ATATATAT-ATATATTTA-TTTCAA
1 ATATATATAATATAGTTATTTTCAA
*
121622 ATAT-TATAATATAGTTATTTTCAT
1 ATATATATAATATAGTTATTTTCAA
121646 ATATATAT
1 ATATATAT
121654 TATCTATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.11
23 12 0.44
24 9 0.33
25 3 0.11
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (25 bp):
ATATATATAATATAGTTATTTTCAA
Found at i:128312 original size:23 final size:23
Alignment explanation
Indices: 128267--128312 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
128257 TTATACCTAT
*
128267 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
128290 AGATATTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
128313 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:129956 original size:30 final size:31
Alignment explanation
Indices: 129922--129992 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 31
129912 GTGCAAAAAG
* *
129922 AAAGAAAAGACAAAAAGAAGAAA-A-TTCAGA
1 AAAGAAAAGAAAAAAAGAA-AAAGATTTCAAA
129952 AAAGAAGAA-AAAAAAAGAAAAAGATTTCAAA
1 AAAGAA-AAGAAAAAAAGAAAAAGATTTCAAA
129983 AAGAGAAAAG
1 AA-AGAAAAG
129993 CAAGCCAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
29 3 0.09
30 16 0.47
31 11 0.32
32 4 0.12
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.07
Consensus pattern (31 bp):
AAAGAAAAGAAAAAAAGAAAAAGATTTCAAA
Found at i:132905 original size:23 final size:23
Alignment explanation
Indices: 132860--132905 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
132850 TTATACCTAT
*
132860 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATATTATA
*
132883 AGATAGTT-TTTCATATATATATA
1 AGATACTTATTTCATATAT-TATA
132906 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATATTATA
Found at i:138628 original size:101 final size:101
Alignment explanation
Indices: 138453--138653 Score: 393
Period size: 101 Copynumber: 2.0 Consensus size: 101
138443 ATGATGTTTC
138453 CATGTTCTAACTTATTTCTAATTTGCAGCACATTGAATCATTTACATGGAAGTGTTCTTTCTTTT
1 CATGTTCTAACTTATTTCTAATTTGCAGCACATTGAATCATTTACATGGAAGTGTTCTTTCTTTT
138518 GATCATCAATTCAAGGGAAAGAAACGAACATTATCA
66 GATCATCAATTCAAGGGAAAGAAACGAACATTATCA
*
138554 CATGTTCTAACTTATTTCTATTTTGCAGCACATTGAATCATTTACATGGAAGTGTTCTTTCTTTT
1 CATGTTCTAACTTATTTCTAATTTGCAGCACATTGAATCATTTACATGGAAGTGTTCTTTCTTTT
138619 GATCATCAATTCAAGGGAAAGAAACGAACATTATC
66 GATCATCAATTCAAGGGAAAGAAACGAACATTATC
138654 CAACTATTCA
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (101 bp):
CATGTTCTAACTTATTTCTAATTTGCAGCACATTGAATCATTTACATGGAAGTGTTCTTTCTTTT
GATCATCAATTCAAGGGAAAGAAACGAACATTATCA
Found at i:144090 original size:19 final size:19
Alignment explanation
Indices: 144048--144087 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
144038 TATCCGTTCT
*
144048 TTATTTCATTTCATTCTTA
1 TTATTTCATTTCATTCCTA
144067 TTATTTCATTTCATTACCTA
1 TTATTTCATTTCATT-CCTA
144087 T
1 T
144088 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATTTCATTTCATTCCTA
Found at i:144374 original size:9 final size:10
Alignment explanation
Indices: 144352--144416 Score: 50
Period size: 10 Copynumber: 6.8 Consensus size: 10
144342 ATTGGAGTGC
144352 AAAAAGAAAG
1 AAAAAGAAAG
*
144362 AAAAAGACA-
1 AAAAAGAAAG
144371 AAAAAGAAGAG
1 AAAAAGAA-AG
**
144382 AAAAA-TCAG
1 AAAAAGAAAG
144391 -AAAAG-AAG
1 AAAAAGAAAG
144399 -AAAAGAAAAG
1 AAAAAG-AAAG
144409 AAAAAGAA
1 AAAAAGAA
144417 TTCAAAAGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
8 11 0.25
9 9 0.20
10 14 0.32
11 10 0.23
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:144383 original size:20 final size:19
Alignment explanation
Indices: 144352--144416 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
144342 ATTGGAGTGC
144352 AAAAAGAA-AGAAAAAGACA
1 AAAAAGAAGAGAAAAA-ACA
*
144371 AAAAAGAAGAGAAAAATCA
1 AAAAAGAAGAGAAAAAACA
*
144390 GAAAAGAAGA-AAAGAAA-A
1 AAAAAGAAGAGAAA-AAACA
144408 GAAAAAGAA
1 -AAAAAGAA
144417 TTCAAAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 4 0.10
19 28 0.72
20 7 0.18
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (19 bp):
AAAAAGAAGAGAAAAAACA
Found at i:151587 original size:19 final size:21
Alignment explanation
Indices: 151557--151608 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
151547 CGGCCAAGAG
*
151557 CATGTATCTTCA-TTAAA-AT
1 CATGTATTTTCATTTAAACAT
* *
151576 CATGTCTTTTCATTTAAACGT
1 CATGTATTTTCATTTAAACAT
151597 CATGTATTTTCA
1 CATGTATTTTCA
151609 AAGGGGTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 10 0.37
20 5 0.19
21 12 0.44
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAACAT
Found at i:152348 original size:18 final size:17
Alignment explanation
Indices: 152300--152348 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
152290 ATTGGAGTGC
* *
152300 AAAAAGAAAGAAAAGAA
1 AAAAAAAAAGAATAGAA
152317 AAAAAAATAAGAATAGAA
1 AAAAAAA-AAGAATAGAA
152335 GAAAAAAAAAGAAT
1 -AAAAAAAAAGAAT
152349 TTCAAAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 6 0.21
18 15 0.54
19 7 0.25
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAGAATAGAA
Found at i:153457 original size:15 final size:15
Alignment explanation
Indices: 153437--153476 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
153427 AAGAAATTAT
*
153437 GAAAGAAATG-AATT
1 GAAAGAAATGAAATG
153451 GATAAGAAATGAAATG
1 GA-AAGAAATGAAATG
153467 GAAAGAAATG
1 GAAAGAAATG
153477 TTATCAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 2 0.09
15 16 0.70
16 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.17
Consensus pattern (15 bp):
GAAAGAAATGAAATG
Found at i:155274 original size:19 final size:21
Alignment explanation
Indices: 155244--155295 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
155234 CAGCCAAGAG
*
155244 CATGTATCTTCA-TTAAA-AT
1 CATGTATTTTCATTTAAACAT
* *
155263 CATGTCTTTTCATTTAAACGT
1 CATGTATTTTCATTTAAACAT
155284 CATGTATTTTCA
1 CATGTATTTTCA
155296 AAGGGGTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 10 0.37
20 5 0.19
21 12 0.44
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAACAT
Found at i:156035 original size:18 final size:17
Alignment explanation
Indices: 155987--156035 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
155977 ATTGGAGTGC
* *
155987 AAAAAGAAAGAAAAGAA
1 AAAAAAAAAGAATAGAA
156004 AAAAAAATAAGAATAGAA
1 AAAAAAA-AAGAATAGAA
156022 GAAAAAAAAAGAAT
1 -AAAAAAAAAGAAT
156036 TTCAAAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 6 0.21
18 15 0.54
19 7 0.25
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAGAATAGAA
Found at i:159200 original size:19 final size:21
Alignment explanation
Indices: 159176--159228 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
159166 CGGCCAAGAG
159176 CATGTATCTT-AATTAAAA-T
1 CATGTATCTTCAATTAAAAGT
* *
159195 CATGTATTTTCATTTAAAAGT
1 CATGTATCTTCAATTAAAAGT
*
159216 CATGTATTTTCAA
1 CATGTATCTTCAA
159229 AGGGGTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 9 0.31
20 7 0.24
21 13 0.45
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (21 bp):
CATGTATCTTCAATTAAAAGT
Found at i:159213 original size:20 final size:21
Alignment explanation
Indices: 159188--159227 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
159178 TGTATCTTAA
159188 TTAAAA-TCATGTATTTTCAT
1 TTAAAAGTCATGTATTTTCAT
159208 TTAAAAGTCATGTATTTTCA
1 TTAAAAGTCATGTATTTTCA
159228 AAGGGGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (21 bp):
TTAAAAGTCATGTATTTTCAT
Found at i:163024 original size:23 final size:24
Alignment explanation
Indices: 162996--163049 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
162986 AAAATCAGCA
162996 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
163019 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
163043 AAGAAAA
1 AAGAAAA
163050 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:163054 original size:24 final size:23
Alignment explanation
Indices: 162996--163055 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
162986 AAAATCAGCA
162996 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
**
163019 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
163043 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
163056 AAAGAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.63, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:168485 original size:15 final size:14
Alignment explanation
Indices: 168450--168488 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
168440 AAGAAATTAT
*
168450 GAAAGAAATGAATT
1 GAAAGAAATGAATG
168464 GATAAGAAATGAAATG
1 GA-AAGAAATG-AATG
168480 GAAAGAAAT
1 GAAAGAAAT
168489 ATTATAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 2 0.09
15 15 0.68
16 5 0.23
ACGTcount: A:0.59, C:0.00, G:0.23, T:0.18
Consensus pattern (14 bp):
GAAAGAAATGAATG
Found at i:173687 original size:16 final size:16
Alignment explanation
Indices: 173666--173697 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
173656 ATCAATTAAG
173666 AGAGCACAAGGAACAA
1 AGAGCACAAGGAACAA
173682 AGAGCACAAGGAACAA
1 AGAGCACAAGGAACAA
173698 TTGGTGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.19, G:0.25, T:0.00
Consensus pattern (16 bp):
AGAGCACAAGGAACAA
Found at i:174975 original size:23 final size:24
Alignment explanation
Indices: 174938--174982 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
174928 AATAATATAA
*
174938 GAAATGAAAATAAATAATAAGAAT
1 GAAATGAAAATAAATAAAAAGAAT
174962 GAAATG-AAATAAATAAAAAGA
1 GAAATGAAAATAAATAAAAAGA
174983 TAGAGATGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (24 bp):
GAAATGAAAATAAATAAAAAGAAT
Found at i:174976 original size:20 final size:21
Alignment explanation
Indices: 174928--174977 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
174918 AATAAAGGGT
174928 AATAATATAAGAAATGAAAATA
1 AATAA-ATAAGAAATGAAAATA
174950 AAT-AATAAG-AATG-AAATGA
1 AATAAATAAGAAATGAAAAT-A
174969 AATAAATAA
1 AATAAATAA
174978 AAAGATAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 4 0.15
19 8 0.31
20 10 0.38
21 1 0.04
22 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (21 bp):
AATAAATAAGAAATGAAAATA
Found at i:179240 original size:19 final size:19
Alignment explanation
Indices: 179218--179261 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
179208 TTTATTTTCC
*
179218 TCTTTTCTTATTTTTCTCT
1 TCTTTTCTGATTTTTCTCT
*
179237 TCTTTTCTGATTTTTGTCT
1 TCTTTTCTGATTTTTCTCT
179256 TCTTTT
1 TCTTTT
179262 TGCACTCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.05, C:0.18, G:0.05, T:0.73
Consensus pattern (19 bp):
TCTTTTCTGATTTTTCTCT
Found at i:180895 original size:24 final size:24
Alignment explanation
Indices: 180863--180910 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
180853 ATAGGTATAA
180863 TATATACATATGAAAATAACTATCT
1 TATATACATATG-AAATAACTATCT
*
180888 TATA-ACATATGAAATAAGTATCT
1 TATATACATATGAAATAACTATCT
180911 ATAGGTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.50
24 7 0.32
25 4 0.18
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (24 bp):
TATATACATATGAAATAACTATCT
Found at i:181338 original size:8 final size:8
Alignment explanation
Indices: 181310--181354 Score: 65
Period size: 8 Copynumber: 5.5 Consensus size: 8
181300 TTGGAGTGCA
181310 AAAAGAAAG
1 AAAAG-AAG
181319 AAAAGACA-
1 AAAAGA-AG
181327 AAAAGAAG
1 AAAAGAAG
181335 AAAAGAAG
1 AAAAGAAG
181343 AAAAGAAG
1 AAAAGAAG
181351 AAAA
1 AAAA
181355 AAAAAGATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.03
8 27 0.79
9 6 0.18
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:192643 original size:19 final size:20
Alignment explanation
Indices: 192621--192660 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
192611 TATCTTTTAT
*
192621 TTATTTCTTTGCATT-CTTA
1 TTATTTATTTGCATTACTTA
*
192640 TTATTTATTTTCATTACTTA
1 TTATTTATTTGCATTACTTA
192660 T
1 T
192661 ATTATTACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.20, C:0.12, G:0.03, T:0.65
Consensus pattern (20 bp):
TTATTTATTTGCATTACTTA
Found at i:199863 original size:12 final size:11
Alignment explanation
Indices: 199846--199875 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
199836 TTCAAAAAAA
199846 CAAAAAAAAGG
1 CAAAAAAAAGG
199857 CACAAAAAAAGG
1 CA-AAAAAAAGG
199869 CAAAAAA
1 CAAAAAA
199876 CAAAAAAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.73, C:0.13, G:0.13, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAGG
Found at i:199880 original size:17 final size:17
Alignment explanation
Indices: 199858--199890 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
199848 AAAAAAAGGC
*
199858 ACAAAAAAAGGCAAAAA
1 ACAAAAAAAGCCAAAAA
199875 ACAAAAAAAGCCAAAA
1 ACAAAAAAAGCCAAAA
199891 TTTGAAAAAA
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:0.76, C:0.15, G:0.09, T:0.00
Consensus pattern (17 bp):
ACAAAAAAAGCCAAAAA
Found at i:211394 original size:138 final size:138
Alignment explanation
Indices: 211146--211423 Score: 556
Period size: 138 Copynumber: 2.0 Consensus size: 138
211136 TCAAACTGCC
211146 AAGGTCGACCGAAAAGAAGATGGCTTGAATTAATGGAGGCAACATCACAAAAGACTTCATCTTCA
1 AAGGTCGACCGAAAAGAAGATGGCTTGAATTAATGGAGGCAACATCACAAAAGACTTCATCTTCA
211211 TATCTCCCAATTGAAAAGGGCACAAGTACTTGCTCTATGACTTCAAACTCTTCATCTTCATTTAA
66 TATCTCCCAATTGAAAAGGGCACAAGTACTTGCTCTATGACTTCAAACTCTTCATCTTCATTTAA
211276 TCCTTGCA
131 TCCTTGCA
211284 AAGGTCGACCGAAAAGAAGATGGCTTGAATTAATGGAGGCAACATCACAAAAGACTTCATCTTCA
1 AAGGTCGACCGAAAAGAAGATGGCTTGAATTAATGGAGGCAACATCACAAAAGACTTCATCTTCA
211349 TATCTCCCAATTGAAAAGGGCACAAGTACTTGCTCTATGACTTCAAACTCTTCATCTTCATTTAA
66 TATCTCCCAATTGAAAAGGGCACAAGTACTTGCTCTATGACTTCAAACTCTTCATCTTCATTTAA
211414 TCCTTGCA
131 TCCTTGCA
211422 AA
1 AA
211424 ATGTATGGGC
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
138 140 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (138 bp):
AAGGTCGACCGAAAAGAAGATGGCTTGAATTAATGGAGGCAACATCACAAAAGACTTCATCTTCA
TATCTCCCAATTGAAAAGGGCACAAGTACTTGCTCTATGACTTCAAACTCTTCATCTTCATTTAA
TCCTTGCA
Found at i:220728 original size:21 final size:21
Alignment explanation
Indices: 220704--220745 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
220694 AATGTTCATG
220704 AATGTATCTTGGCTGAAATTC
1 AATGTATCTTGGCTGAAATTC
220725 AATGTATCTTGGCTGAAATTC
1 AATGTATCTTGGCTGAAATTC
220746 TTCCCCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (21 bp):
AATGTATCTTGGCTGAAATTC
Found at i:227609 original size:17 final size:18
Alignment explanation
Indices: 227577--227611 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
227567 AATTTTGATG
*
227577 AATGGATATTCATCTTTT
1 AATGGATATACATCTTTT
227595 AATGGA-ATACATCTTTT
1 AATGGATATACATCTTTT
227612 GGCCGAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (18 bp):
AATGGATATACATCTTTT
Found at i:235976 original size:9 final size:9
Alignment explanation
Indices: 235962--235988 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
235952 AAGTATGGGT
235962 AGAAATATC
1 AGAAATATC
235971 AGAAATATC
1 AGAAATATC
235980 AGAAATATC
1 AGAAATATC
235989 CGAGTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (9 bp):
AGAAATATC
Found at i:238492 original size:10 final size:9
Alignment explanation
Indices: 238473--238515 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
238463 TTTTTTGAAA
238473 TTTTGGTTT
1 TTTTGGTTT
238482 TTTTGGCTTT
1 TTTTGG-TTT
*
238492 TTTTGTTTTT
1 TTTTG-GTTT
*
238502 TTTTTGTTT
1 TTTTGGTTT
238511 TTTTG
1 TTTTG
238516 AAAAAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 13 0.46
10 15 0.54
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.81
Consensus pattern (9 bp):
TTTTGGTTT
Found at i:238503 original size:11 final size:11
Alignment explanation
Indices: 238489--238514 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
238479 TTTTTTTGGC
238489 TTTTTTTGTTT
1 TTTTTTTGTTT
238500 TTTTTTTGTTT
1 TTTTTTTGTTT
238511 TTTT
1 TTTT
238515 GAAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:239390 original size:25 final size:22
Alignment explanation
Indices: 239361--239406 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
239351 TTTTTAACCC
239361 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
239386 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
239407 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:251704 original size:23 final size:24
Alignment explanation
Indices: 251678--251731 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
251668 AAAATCAGCA
251678 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
251701 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
251725 AAGAAAA
1 AAGAAAA
251732 AGAAAGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:251736 original size:24 final size:23
Alignment explanation
Indices: 251678--251737 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
251668 AAAATCAGCA
251678 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
**
251701 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
251725 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
251738 AAAAAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.63, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:260403 original size:24 final size:21
Alignment explanation
Indices: 260369--260411 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
260359 TCCACAAGAT
*
260369 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
260391 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
260412 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:264897 original size:23 final size:24
Alignment explanation
Indices: 264859--264911 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
264849 TTCTTTTATT
264859 TTTCTTCTTTTTGAGTACTTTCAA
1 TTTCTTCTTTTTGAGTACTTTCAA
* * *
264883 TTTCTTC-TTTTGAGTGCTTTTAT
1 TTTCTTCTTTTTGAGTACTTTCAA
264906 TTTCTT
1 TTTCTT
264912 TGCTGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.11, C:0.15, G:0.09, T:0.64
Consensus pattern (24 bp):
TTTCTTCTTTTTGAGTACTTTCAA
Found at i:269654 original size:26 final size:26
Alignment explanation
Indices: 269632--269692 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
269622 CTCAAGATCG
269632 AATGAACCTTATAAAAGGGAAGATTC
1 AATGAACCTTATAAAAGGGAAGATTC
269658 AATGAACCTTATAAAAGGGAAGATTC
1 AATGAACCTTATAAAAGGGAAGATTC
269684 AATGAACCT
1 AATGAACCT
269693 AACCATGGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (26 bp):
AATGAACCTTATAAAAGGGAAGATTC
Found at i:280535 original size:11 final size:11
Alignment explanation
Indices: 280519--280558 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
280509 CTTTTTGAAT
280519 TTTTCTTTTTC
1 TTTTCTTTTTC
280530 TTTTC-TTTTC
1 TTTTCTTTTTC
280540 --TTCTTTTTC
1 TTTTCTTTTTC
*
280549 TCTTCTTTTT
1 TTTTCTTTTT
280559 GTCTTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.12
9 5 0.19
10 5 0.19
11 13 0.50
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:280543 original size:19 final size:18
Alignment explanation
Indices: 280518--280576 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 18
280508 TCTTTTTGAA
280518 TTTTTCTTTTTCTTTTCT
1 TTTTTCTTTTTCTTTTCT
*
280536 TTTCTTCTTTTTCTCTTCT
1 TTT-TTCTTTTTCTTTTCT
280555 TTTTGTCTTTTTC-TTTCT
1 TTTT-TCTTTTTCTTTTCT
280573 TTTT
1 TTTT
280577 GCACTCCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.32
19 25 0.68
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTTCTTTTTCTTTTCT
Found at i:280866 original size:13 final size:13
Alignment explanation
Indices: 280848--280878 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
280838 ATAGGATAGA
280848 GATGGATGTTGTT
1 GATGGATGTTGTT
280861 GATGGATGTTGTT
1 GATGGATGTTGTT
280874 GATGG
1 GATGG
280879 TGGCAATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (13 bp):
GATGGATGTTGTT
Found at i:285088 original size:8 final size:8
Alignment explanation
Indices: 285077--285144 Score: 81
Period size: 8 Copynumber: 8.9 Consensus size: 8
285067 CTTTTTGAAA
285077 TCTTTTTT
1 TCTTTTTT
285085 TCTTTTTT
1 TCTTTTTT
285093 TC--TTTT
1 TCTTTTTT
285099 TCTTTTTT
1 TCTTTTTT
285107 TCTTTTTT
1 TCTTTTTT
*
285115 TC-TTCTT
1 TCTTTTTT
*
285122 T-TTTTTG
1 TCTTTTTT
285129 TCTTTTCTT
1 TCTTTT-TT
285138 TCTTTTT
1 TCTTTTT
285145 GTACTCCAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
6 6 0.12
7 9 0.18
8 29 0.57
9 7 0.14
ACGTcount: A:0.00, C:0.15, G:0.01, T:0.84
Consensus pattern (8 bp):
TCTTTTTT
Found at i:285098 original size:14 final size:14
Alignment explanation
Indices: 285081--285144 Score: 76
Period size: 14 Copynumber: 4.4 Consensus size: 14
285071 TTGAAATCTT
285081 TTTTTCTTTTTTTC
1 TTTTTCTTTTTTTC
285095 TTTTTCTTTTTTTC
1 TTTTTCTTTTTTTC
285109 TTTTTTTCTTCTTTTT-
1 --TTTTTCTT-TTTTTC
*
285125 TTTGTCTTTTCTTTC
1 TTTTTCTTTT-TTTC
285140 TTTTT
1 TTTTT
285145 GTACTCCAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
13 2 0.05
14 24 0.56
15 4 0.09
16 8 0.19
17 5 0.12
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (14 bp):
TTTTTCTTTTTTTC
Found at i:285102 original size:22 final size:22
Alignment explanation
Indices: 285077--285144 Score: 102
Period size: 22 Copynumber: 3.0 Consensus size: 22
285067 CTTTTTGAAA
285077 TCTTTTTTTCTTTTTTTCTTTT
1 TCTTTTTTTCTTTTTTTCTTTT
285099 TCTTTTTTTCTTTTTTTCTTCTT
1 TCTTTTTTTCTTTTTTTCTT-TT
*
285122 T-TTTTTGTCTTTTCTTTCTTTT
1 TCTTTTTTTCTTTT-TTTCTTTT
285144 T
1 T
285145 GTACTCCAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
22 34 0.79
23 9 0.21
ACGTcount: A:0.00, C:0.15, G:0.01, T:0.84
Consensus pattern (22 bp):
TCTTTTTTTCTTTTTTTCTTTT
Found at i:285113 original size:30 final size:31
Alignment explanation
Indices: 285077--285144 Score: 104
Period size: 30 Copynumber: 2.2 Consensus size: 31
285067 CTTTTTGAAA
*
285077 TCTTTTTTTCTT-TTTTTCTTTTTCTTTT-TT
1 TCTTTTTTTCTTCTTTTT-TTTGTCTTTTCTT
285107 TCTTTTTTTCTTCTTTTTTTTGTCTTTTCTT
1 TCTTTTTTTCTTCTTTTTTTTGTCTTTTCTT
285138 TCTTTTT
1 TCTTTTT
285145 GTACTCCAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 21 0.60
31 14 0.40
ACGTcount: A:0.00, C:0.15, G:0.01, T:0.84
Consensus pattern (31 bp):
TCTTTTTTTCTTCTTTTTTTTGTCTTTTCTT
Found at i:287074 original size:21 final size:21
Alignment explanation
Indices: 287049--287092 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
287039 AAGGAAGATT
287049 AATGAAATG-ATAAAGATAAGG
1 AATGAAATGAATAAAGA-AAGG
287070 AATGAAATGAAATAAAGAAAGG
1 AATGAAATG-AATAAAGAAAGG
287092 A
1 A
287093 TATAGATGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.43
22 5 0.24
23 7 0.33
ACGTcount: A:0.61, C:0.00, G:0.23, T:0.16
Consensus pattern (21 bp):
AATGAAATGAATAAAGAAAGG
Found at i:287788 original size:15 final size:15
Alignment explanation
Indices: 287768--287809 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
287758 GGATGTAAAG
287768 GCATCTTCATGGGCA
1 GCATCTTCATGGGCA
287783 GCATCTTCATGGGCA
1 GCATCTTCATGGGCA
*
287798 ACATCATTCATG
1 GCATC-TTCATG
287810 AAAGGTCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (15 bp):
GCATCTTCATGGGCA
Found at i:289396 original size:19 final size:20
Alignment explanation
Indices: 289366--289405 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
289356 GAATAATATT
289366 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
289386 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
289405 A
1 A
289406 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:293667 original size:14 final size:13
Alignment explanation
Indices: 293637--293670 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
293627 TTTTGAATTC
*
293637 TTTTTCTTTTCTT
1 TTTTTCTTTTCTA
293650 TTTTTCTTTTCTGA
1 TTTTTCTTTTCT-A
293664 TTTTTCT
1 TTTTTCT
293671 CTTATTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTTCTA
Found at i:295464 original size:26 final size:26
Alignment explanation
Indices: 295434--295490 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
295424 TCCCATCCTT
* *
295434 ATTTCATTTCA-TTTCTTATATTTATC
1 ATTTCATTTAACTTTCTT-TATTAATC
295460 ATTTCATTTAATCTTTCTTTATTAATC
1 ATTTCATTTAA-CTTTCTTTATTAATC
295487 ATTT
1 ATTT
295491 TCCTTTCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 10 0.37
27 11 0.41
28 6 0.22
ACGTcount: A:0.25, C:0.14, G:0.00, T:0.61
Consensus pattern (26 bp):
ATTTCATTTAACTTTCTTTATTAATC
Found at i:295784 original size:11 final size:11
Alignment explanation
Indices: 295719--295785 Score: 57
Period size: 11 Copynumber: 5.7 Consensus size: 11
295709 ATTGGAGTGC
295719 AAAAAG-AAAG
1 AAAAAGAAAAG
295729 AAAAAGATAAA-
1 AAAAAGA-AAAG
*
295740 AAAAAGAAGAG
1 AAAAAGAAAAG
295751 AAAAATCAGAAAAG
1 -AAAA--AGAAAAG
295765 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
295778 AAAAAGAA
1 AAAAAGAA
295786 TTCAAAAGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
10 8 0.17
11 14 0.29
12 8 0.17
13 7 0.15
14 8 0.17
15 3 0.06
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:299509 original size:42 final size:42
Alignment explanation
Indices: 299450--299576 Score: 254
Period size: 42 Copynumber: 3.0 Consensus size: 42
299440 AATTTCTCTT
299450 CAAATTTCTTTGTGAACTTTATCAATTAAACAAGTATAGTTC
1 CAAATTTCTTTGTGAACTTTATCAATTAAACAAGTATAGTTC
299492 CAAATTTCTTTGTGAACTTTATCAATTAAACAAGTATAGTTC
1 CAAATTTCTTTGTGAACTTTATCAATTAAACAAGTATAGTTC
299534 CAAATTTCTTTGTGAACTTTATCAATTAAACAAGTATAGTTC
1 CAAATTTCTTTGTGAACTTTATCAATTAAACAAGTATAGTTC
299576 C
1 C
299577 TATACTTGTG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 85 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.40
Consensus pattern (42 bp):
CAAATTTCTTTGTGAACTTTATCAATTAAACAAGTATAGTTC
Found at i:299865 original size:27 final size:26
Alignment explanation
Indices: 299811--299867 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
299801 TCCCATCCTT
* *
299811 ATTTCATTTCATTTCTTATATTTATC
1 ATTTCATTTAATTTCTTATATTAATC
299837 ATTTCATTTAATCTTCCTT-TATTAATC
1 ATTTCATTTAAT-TT-CTTATATTAATC
299864 ATTT
1 ATTT
299868 TCCTTTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 11 0.41
27 13 0.48
28 3 0.11
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTCATTTAATTTCTTATATTAATC
Found at i:306074 original size:19 final size:20
Alignment explanation
Indices: 306050--306092 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
306040 AGCATTTATC
*
306050 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
306069 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
306089 TTCA
1 TTCA
306093 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:306699 original size:15 final size:16
Alignment explanation
Indices: 306669--306706 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
306659 TCTTTGATAA
*
306669 CATTTTTATCCATTTC
1 CATTCTTATCCATTTC
*
306685 CTTTCTTAT-CATTTC
1 CATTCTTATCCATTTC
306700 CATTCTT
1 CATTCTT
306707 CTTCAATTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (16 bp):
CATTCTTATCCATTTC
Found at i:311593 original size:14 final size:14
Alignment explanation
Indices: 311574--311600 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
311564 TAAGATACTA
311574 TTTCCATCACCATC
1 TTTCCATCACCATC
311588 TTTCCATCACCAT
1 TTTCCATCACCAT
311601 AGTTCATCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.37
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:312026 original size:13 final size:13
Alignment explanation
Indices: 312006--312041 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
311996 TGCTGCAACA
312006 AAAG-AGAAAAAG
1 AAAGAAGAAAAAG
312018 AAAGAAGAAAAAG
1 AAAGAAGAAAAAG
*
312031 AAAAAAGAAAA
1 AAAGAAGAAAA
312042 GACTCCTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAGAAGAAAAAG
Found at i:333825 original size:2 final size:2
Alignment explanation
Indices: 333818--333854 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
333808 GATAGTTATT
*
333818 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
333855 GTTATTATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:337706 original size:17 final size:16
Alignment explanation
Indices: 337659--337712 Score: 81
Period size: 16 Copynumber: 3.3 Consensus size: 16
337649 TTCCAAAAAC
337659 AAGTGCTTATACATCT
1 AAGTGCTTATACATCT
337675 AAGTGCTTATACATCT
1 AAGTGCTTATACATCT
* *
337691 AAGTGCTTGTTACATCC
1 AAGTGCTT-ATACATCT
337708 AAGTG
1 AAGTG
337713 ACACAATCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
16 24 0.69
17 11 0.31
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (16 bp):
AAGTGCTTATACATCT
Found at i:343830 original size:19 final size:20
Alignment explanation
Indices: 343802--343841 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
343792 GAATAATAAT
343802 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
* *
343822 ATAAG-AATGTAATGAAATA
1 ATAAGTAATGAAAAGAAATA
343841 A
1 A
343842 AGAAAGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:357999 original size:21 final size:21
Alignment explanation
Indices: 357975--358019 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
357965 TTGTTTGAAA
*
357975 TTTTGGCTTTTTTGGCTTTTT
1 TTTTGGCTTTTTTGCCTTTTT
* *
357996 TTTTTGTTTTTTTGCCTTTTT
1 TTTTGGCTTTTTTGCCTTTTT
358017 TTT
1 TTT
358020 GAAAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.09, G:0.13, T:0.78
Consensus pattern (21 bp):
TTTTGGCTTTTTTGCCTTTTT
Found at i:364301 original size:25 final size:26
Alignment explanation
Indices: 364273--364327 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
364263 TTTGCTTTTC
*
364273 TTCTTTTTTGAGTGC-T-AGATTTGTT
1 TTCTTTTTGGAGTGCTTCA-ATTTGTT
364298 TTCTTTTTGGAGTGCTTCAATTTGTT
1 TTCTTTTTGGAGTGCTTCAATTTGTT
364324 TTCT
1 TTCT
364328 GATTTTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 14 0.52
26 12 0.44
27 1 0.04
ACGTcount: A:0.11, C:0.11, G:0.18, T:0.60
Consensus pattern (26 bp):
TTCTTTTTGGAGTGCTTCAATTTGTT
Found at i:366858 original size:19 final size:18
Alignment explanation
Indices: 366834--366871 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
366824 TAATAAAGGG
366834 AATAAT-ATATAGTAATGAA
1 AATAATAATA-AG-AATGAA
366853 AATAATAATAAGAATGAA
1 AATAATAATAAGAATGAA
366871 A
1 A
366872 TTAAATAAAG
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:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (18 bp):
AATAATAATAAGAATGAA
Found at i:366870 original size:18 final size:19
Alignment explanation
Indices: 366834--366871 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
366824 TAATAAAGGG
366834 AATAATATATAGTAATGAA
1 AATAATATATAGTAATGAA
366853 AATAATA-ATAAG-AATGAA
1 AATAATATAT-AGTAATGAA
366871 A
1 A
366872 TTAAATAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (19 bp):
AATAATATATAGTAATGAA
Done.