Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001326.1 Hibiscus syriacus cultivar Beakdansim tig00002585_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: 66269
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:4216 original size:23 final size:22
Alignment explanation
Indices: 4146--4226 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 22
4136 ACACTTAACA
4146 GTGCATCGATGCATCCCATTGAAT
1 GTGCATCGATGCA-CCC-TTGAAT
* *
4170 GTGCATCGAT--ACCCATGAAG
1 GTGCATCGATGCACCCTTGAAT
*
4190 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
4213 GTGCATCGATGCAC
1 GTGCATCGATGCAC
4227 AAGGCCATGC
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
20 13 0.27
21 3 0.06
22 3 0.06
23 19 0.40
24 10 0.21
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:4243 original size:43 final size:44
Alignment explanation
Indices: 4142--4248 Score: 110
Period size: 43 Copynumber: 2.4 Consensus size: 44
4132 TCATACACTT
* *
4142 AACAGTGCATCGATGCATCCCATTGAATGTGCATCGATACCCATG
1 AACA-TGCATCGATGCATCCCATTGAATGTGCATCGATACACAAG
** * *
4187 AAGGTGCACCGATGCA-CGCC-TTGAATGTGCATCGATGCACAAG
1 AACATGCATCGATGCATC-CCATTGAATGTGCATCGATACACAAG
**
4230 GCCATGCATCGATGCATCC
1 AACATGCATCGATGCATCC
4249 GTCGGGTTAA
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
43 33 0.67
44 14 0.29
45 2 0.04
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.21
Consensus pattern (44 bp):
AACATGCATCGATGCATCCCATTGAATGTGCATCGATACACAAG
Found at i:6360 original size:13 final size:13
Alignment explanation
Indices: 6342--6366 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6332 GCCATTTCAC
6342 ATTGATTATGAAT
1 ATTGATTATGAAT
6355 ATTGATTATGAA
1 ATTGATTATGAA
6367 ACTTATGGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGATTATGAAT
Found at i:7068 original size:64 final size:66
Alignment explanation
Indices: 6910--7069 Score: 206
Period size: 65 Copynumber: 2.5 Consensus size: 66
6900 AAATAAATTG
* *
6910 AACATCGAATGCATTTCATGCA-CTGATGCA-CATACTATGCATCGATGCACTCAGAGTTTTATG
1 AACATCGAATGCATTTCATGCATC-GATGCACCATACCATGCATCGATGCACTCAGAGTGTTATG
6973 AA
65 AA
* *
6975 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACTCAG-GCTAGTT-T
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGAG-T-GTTAT
7037 G-A
64 GAA
*
7039 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
7070 TCTTAGTGCA
Statistics
Matches: 86, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
64 32 0.37
65 49 0.57
66 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (66 bp):
AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGAGTGTTATGA
A
Found at i:7085 original size:64 final size:64
Alignment explanation
Indices: 6910--7089 Score: 194
Period size: 65 Copynumber: 2.8 Consensus size: 64
6900 AAATAAATTG
*
6910 AACATCGAATGCATTTCATGCA-CTGATGCACATACTA-TGCATCGATGCACTCAGAGTTTTATG
1 AACATCGAATGCATTTCATGCATC-GATGCAC-T-CTAGTGCATCGATGCACTCAGAGTGTTATG
6973 AA
63 AA
*
6975 AACATCGAATGCATTTGATGCATCGATGCAC-C-AGCCATGCATCGATGCACTCAG-GCTAGTT-
1 AACATCGAATGCATTTCATGCATCGATGCACTCTAG---TGCATCGATGCACTCAGAG-T-GTTA
7036 TG-A
61 TGAA
* *
7039 AACATCGAATGCATTTTATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACTC-TAGTGCATCGATGCACT
7090 AAGGGTGCAA
Statistics
Matches: 101, Mismatches: 4, Indels: 21
0.80 0.03 0.17
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
64 45 0.45
65 49 0.49
66 3 0.03
67 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTAGTGCATCGATGCACTCAGAGTGTTATGAA
Found at i:11117 original size:13 final size:13
Alignment explanation
Indices: 11061--11125 Score: 62
Period size: 13 Copynumber: 5.0 Consensus size: 13
11051 TTTTAAATTG
* *
11061 CATTTTTATACAT
1 CATTTTTAAAAAT
*
11074 CACTTTTAAAAATT
1 CATTTTTAAAAA-T
*
11088 CATTTTT-ACAA-
1 CATTTTTAAAAAT
11099 CATTTTTAAAAAT
1 CATTTTTAAAAAT
11112 CATTTTTGAAAAAT
1 CATTTTT-AAAAAT
11126 TATACTCGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
11 7 0.17
12 3 0.07
13 19 0.45
14 13 0.31
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.46
Consensus pattern (13 bp):
CATTTTTAAAAAT
Found at i:13544 original size:34 final size:34
Alignment explanation
Indices: 13489--13580 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 34
13479 TGAAAGTATT
13489 AAAATGGTTTTC-AAGTTTGGTAA-CCAACTTTG
1 AAAATGGTTTTCAAAGTTTGGTAATCCAACTTTG
****
13521 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 -AAAATGGTTTTCAAAGTTTGGT-AATCCAACTTTG
13557 AAAATGGTTTTCAAAGTTTGGTAA
1 AAAATGGTTTTCAAAGTTTGGTAA
13581 ATGTTTCTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
33 12 0.23
34 11 0.21
35 24 0.46
36 5 0.10
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.40
Consensus pattern (34 bp):
AAAATGGTTTTCAAAGTTTGGTAATCCAACTTTG
Found at i:13629 original size:36 final size:36
Alignment explanation
Indices: 13516--13634 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
13506 TGGTAACCAA
13516 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
13552 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* * *
13587 CTTTGAAAAATAGTTTTTCAAAATTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
13624 -GTTGAAAAATG
1 CTTTGAAAAATG
13635 ATAATGGGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 36 0.47
36 19 0.25
37 22 0.29
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:18135 original size:21 final size:21
Alignment explanation
Indices: 18111--18176 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
18101 AACTTTGAAA
18111 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
18132 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
18146 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
18167 AAATGTTTTT
1 AAATGGTTTT
18177 TTGAAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 4 0.11
19 4 0.11
20 4 0.11
21 14 0.40
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.47
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:18202 original size:37 final size:37
Alignment explanation
Indices: 18104--18221 Score: 163
Period size: 35 Copynumber: 3.3 Consensus size: 37
18094 GGTAACCAAC
*
18104 TTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTTC
1 TTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTTT
18141 TTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTT
1 TTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTTT
* *
18176 TTTGAAAAATAGTTTTTCAAAGTTTGGTAGATG-TTT
1 TTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTTT
*
18212 GTTGAAAAAT
1 TTTGAAAAAT
18222 GATAATGGGA
Statistics
Matches: 74, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
35 29 0.39
36 21 0.28
37 24 0.32
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.45
Consensus pattern (37 bp):
TTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTTT
Found at i:29396 original size:30 final size:29
Alignment explanation
Indices: 29362--29430 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
29352 AAAAAAGATT
* *
29362 AAATATTTTATGTATCTATTTTGACTAAAA
1 AAATATTTTAAGTATCTATTCTGAC-AAAA
* *
29392 AAATACTTGAAGTATCTATTCTGACAAAA
1 AAATATTTTAAGTATCTATTCTGACAAAA
*
29421 ATAATTTTTT
1 A-AATATTTT
29431 TATTTTAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (29 bp):
AAATATTTTAAGTATCTATTCTGACAAAA
Found at i:29743 original size:13 final size:14
Alignment explanation
Indices: 29729--29774 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
29719 GGTTTAATGG
29729 TTAGGTTTTAGGGT
1 TTAGGTTTTAGGGT
* *
29743 TTATGTTTTA-GGA
1 TTAGGTTTTAGGGT
*
29756 TT-GGGTTTAGGGT
1 TTAGGTTTTAGGGT
29769 TTAGGT
1 TTAGGT
29775 AGGAGTTTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
12 5 0.21
13 8 0.33
14 11 0.46
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTAGGTTTTAGGGT
Found at i:29754 original size:21 final size:21
Alignment explanation
Indices: 29700--29745 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
29690 GGATTTAATA
29700 TTTAATTGG-TAGGATTTAGGG
1 TTTAA-TGGTTAGGATTTAGGG
*
29721 TTTAATGGTTAGGTTTTAGGG
1 TTTAATGGTTAGGATTTAGGG
29742 TTTA
1 TTTA
29746 TGTTTTAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (21 bp):
TTTAATGGTTAGGATTTAGGG
Found at i:30868 original size:15 final size:15
Alignment explanation
Indices: 30848--30953 Score: 70
Period size: 15 Copynumber: 6.3 Consensus size: 15
30838 CGGCTGTGCC
30848 TTCTTCTCCTCTTCT
1 TTCTTCTCCTCTTCT
*
30863 TTCTTCTCTTCCTCCTTCCC
1 TTC-T-TC-TCCT-CTT-CT
30883 TTCTTCTCTCCCTCTTCT
1 TTC-T-TCT-CCTCTTCT
*
30901 TTCTTCTCCTCCTCT
1 TTCTTCTCCTCTTCT
*
30916 TTCTT-TTCTCCTTCT
1 TTCTTCTCCT-CTTCT
30931 TTCTTCTCTCCCTCTTCT
1 TTC-T-TCT-CCTCTTCT
30949 TTCTT
1 TTCTT
30954 TGCTTCTTCC
Statistics
Matches: 74, Mismatches: 6, Indels: 21
0.73 0.06 0.21
Matches are distributed among these distances:
14 3 0.04
15 22 0.30
16 6 0.08
17 5 0.07
18 17 0.23
19 9 0.12
20 12 0.16
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (15 bp):
TTCTTCTCCTCTTCT
Found at i:30949 original size:48 final size:53
Alignment explanation
Indices: 30848--30953 Score: 159
Period size: 48 Copynumber: 2.1 Consensus size: 53
30838 CGGCTGTGCC
*
30848 TTCTTCTCCTCTTCTTTCTTCTCTTCCTCCTTCCCTTCTTCTCTCCCTCTTCT
1 TTCTTCTCCTCCTCTTTCTTCTCTTCCTCCTTCCCTTCTTCTCTCCCTCTTCT
*
30901 TTCTTCTCCTCCTCTTTC-T-T-TT-CTCCTT-CTTTCTTCTCTCCCTCTTCT
1 TTCTTCTCCTCCTCTTTCTTCTCTTCCTCCTTCCCTTCTTCTCTCCCTCTTCT
30949 TTCTT
1 TTCTT
30954 TGCTTCTTCC
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
48 24 0.47
49 6 0.12
50 2 0.04
51 1 0.02
52 1 0.02
53 17 0.33
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (53 bp):
TTCTTCTCCTCCTCTTTCTTCTCTTCCTCCTTCCCTTCTTCTCTCCCTCTTCT
Found at i:30954 original size:33 final size:33
Alignment explanation
Indices: 30858--30968 Score: 100
Period size: 33 Copynumber: 3.3 Consensus size: 33
30848 TTCTTCTCCT
* * *
30858 CTTCTTTCTTCTCTTCCTCCTTCCCTTCTTCTCTC
1 CTTCTTTCTTCTCTCCCT-CTT-CTTTCTTTTCTC
* *
30893 CCTC-TTCTT-TCTTCTCCTCCTCTTTCTTTTCTC
1 CTTCTTTCTTCTC-TC-CCTCTTCTTTCTTTTCTC
* *
30926 CTTCTTTCTTCTCTCCCTCTTCTTTCTTTGCTT
1 CTTCTTTCTTCTCTCCCTCTTCTTTCTTTTCTC
*
30959 CTTCCTTCTT
1 CTTCTTTCTT
30969 TGGTTCCTCT
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
33 39 0.63
34 15 0.24
35 8 0.13
ACGTcount: A:0.00, C:0.41, G:0.01, T:0.58
Consensus pattern (33 bp):
CTTCTTTCTTCTCTCCCTCTTCTTTCTTTTCTC
Found at i:30961 original size:15 final size:14
Alignment explanation
Indices: 30895--30983 Score: 52
Period size: 15 Copynumber: 5.8 Consensus size: 14
30885 CTTCTCTCCC
*
30895 TCTTCTTTCTTCTCC
1 TCTTCTTTCTT-TCT
*
30910 TCCTCTTTCTTTTCT
1 TCTTCTTTC-TTTCT
*
30925 CCTTCTTTCTTCTCT
1 TCTTCTTTCTT-TCT
30940 CCCTCTTCTTTCTTTGCT
1 ---TCTTCTTTCTTT-CT
* *
30958 TCTTCCTTCTTTGGT
1 TCTTCTTTCTTT-CT
*
30973 TCCTCTTTCTT
1 TCTTCTTTCTT
30984 CTCCGGTTCT
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
14 2 0.03
15 42 0.71
16 2 0.03
17 1 0.02
18 12 0.20
ACGTcount: A:0.00, C:0.36, G:0.03, T:0.61
Consensus pattern (14 bp):
TCTTCTTTCTTTCT
Found at i:30967 original size:30 final size:29
Alignment explanation
Indices: 30846--30968 Score: 103
Period size: 30 Copynumber: 4.2 Consensus size: 29
30836 GGCGGCTGTG
30846 CCTTCTTCTCCTCTTCTTTCT-TC-TCTT
1 CCTTCTTCTCCTCTTCTTTCTCTCTTCTT
* * *
30873 CCTCCTTC-CCTTCTTCTCTCCCTCTTCTT
1 CCTTCTTCTCC-TCTTCTTTCTCTCTTCTT
* *
30902 TCTTCTCCTCCTCTTTCTTT-TCTCCTTCTT
1 CCTTCTTCTCCTC-TTCTTTCTCT-CTTCTT
* *
30932 TCTTC-TCTCCCTCTTCTTTCTTTGCTTCTT
1 CCTTCTTCT-CCTCTTCTTTCTCT-CTTCTT
30962 CCTTCTT
1 CCTTCTT
30969 TGGTTCCTCT
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
26 2 0.03
27 15 0.20
28 2 0.03
29 21 0.28
30 34 0.45
31 1 0.01
ACGTcount: A:0.00, C:0.42, G:0.01, T:0.57
Consensus pattern (29 bp):
CCTTCTTCTCCTCTTCTTTCTCTCTTCTT
Found at i:30968 original size:48 final size:48
Alignment explanation
Indices: 30847--30986 Score: 144
Period size: 48 Copynumber: 2.9 Consensus size: 48
30837 GCGGCTGTGC
* * * *
30847 CTTC-TTCTCCTCTTCTTTCTTCTCTTCCTCCTTCCCTTCTTCTCTCCCT
1 CTTCTTTCTTCTCTTCTTCCTTCT-TTTCTCCTT-CTTTCTTCTCTCCCT
* * *
30896 CTTCTTTCTTCTCCTCCTCTTTCTTTTCTCCTTCTTTCTTCTCTCCCT
1 CTTCTTTCTTCTCTTCTTCCTTCTTTTCTCCTTCTTTCTTCTCTCCCT
30944 CTTCTTTCTT-TGCTTCTTCCTTCTTTGGT-TCC-TCTTTCTTCTC
1 CTTCTTTCTTCT-CTTCTTCCTTCTTT--TCTCCTTCTTTCTTCTC
30987 CGGTTCTTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
47 1 0.01
48 46 0.60
49 15 0.19
50 15 0.19
ACGTcount: A:0.00, C:0.41, G:0.02, T:0.57
Consensus pattern (48 bp):
CTTCTTTCTTCTCTTCTTCCTTCTTTTCTCCTTCTTTCTTCTCTCCCT
Found at i:32139 original size:29 final size:29
Alignment explanation
Indices: 32097--32173 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
32087 GAGGAGAAGG
32097 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
32126 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
* *
32155 CGGAGTACATGGCGACCTA
1 AGGAGTGCATGGCGACCTA
32174 TGCTGGGAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.25, C:0.27, G:0.34, T:0.14
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:32874 original size:16 final size:15
Alignment explanation
Indices: 32853--32886 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
32843 TTAAAAGTAA
32853 AATTTAGATTTTATAT
1 AATTTA-ATTTTATAT
*
32869 AATTTATTTTTATAT
1 AATTTAATTTTATAT
32884 AAT
1 AAT
32887 CATTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
AATTTAATTTTATAT
Found at i:32895 original size:23 final size:23
Alignment explanation
Indices: 32869--32937 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
32859 GATTTTATAT
32869 AATTTATTTTTATATAATCATTA
1 AATTTATTTTTATATAATCATTA
* * * *
32892 AATTAATTTTAATATAATTAATA
1 AATTTATTTTTATATAATCATTA
* * * *
32915 ATTTTAATTTTATTTAATGATTA
1 AATTTATTTTTATATAATCATTA
32938 TATATATATA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (23 bp):
AATTTATTTTTATATAATCATTA
Found at i:32918 original size:61 final size:61
Alignment explanation
Indices: 32818--32932 Score: 135
Period size: 61 Copynumber: 1.9 Consensus size: 61
32808 CACAATAATA
* * **
32818 TATATACTCATTAAATTGAGTTTTTTTAAAAGTAAAA-TTTAGATTTTATATAATTTATTTT
1 TATATAATCATTAAATTGAATTTTAATAAAAGTAAAATTTTA-ATTTTATATAATTTATTTT
* * *
32879 TATATAATCATTAAATT-AATTTTAATATAATTAATAATTTTAATTTTATTTAAT
1 TATATAATCATTAAATTGAATTTTAATAAAAGTAA-AATTTTAATTTTATATAAT
32933 GATTATATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
60 12 0.27
61 29 0.64
62 4 0.09
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (61 bp):
TATATAATCATTAAATTGAATTTTAATAAAAGTAAAATTTTAATTTTATATAATTTATTTT
Found at i:33073 original size:20 final size:21
Alignment explanation
Indices: 33044--33084 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
33034 AGTTTTCATG
*
33044 AAAATTTTAAATTTA-TATTA
1 AAAATATTAAATTTATTATTA
33064 AAAATATTAAATTTATTATTA
1 AAAATATTAAATTTATTATTA
33085 TTTTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATATTAAATTTATTATTA
Found at i:33937 original size:31 final size:30
Alignment explanation
Indices: 33886--33963 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
33876 TGGCCACCCC
*
33886 AAAATTTTAAAAATTATAATTTAGACCCTT
1 AAAATTTTAAAAAATATAATTTAGACCCTT
*
33916 AAAATTTTCAAAAAA-ATTAATTTAGTCCCTCCT
1 AAAATTTT-AAAAAATA-TAATTTAGACCCT--T
* *
33949 AATATTTAAAAAAAT
1 AAAATTTTAAAAAAT
33964 TCATATTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
30 9 0.23
31 17 0.44
32 6 0.15
33 7 0.18
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAATTTTAAAAAATATAATTTAGACCCTT
Found at i:39021 original size:22 final size:22
Alignment explanation
Indices: 38995--39053 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
38985 ACTTTTCTTT
38995 CTTTCATTTTCTTTTTCAAGTG
1 CTTTCATTTTCTTTTTCAAGTG
* **
39017 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCATTTTCTT-TTTCAAGTG
**
39040 CTTTTGTTTTCTTT
1 CTTTCATTTTCTTT
39054 GCTGAATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 13 0.43
23 17 0.57
ACGTcount: A:0.10, C:0.17, G:0.10, T:0.63
Consensus pattern (22 bp):
CTTTCATTTTCTTTTTCAAGTG
Found at i:39039 original size:23 final size:22
Alignment explanation
Indices: 38995--39043 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
38985 ACTTTTCTTT
*
38995 CTTTCATTTTCTTTTTCAAGTG
1 CTTTCAATTTCTTTTTCAAGTG
**
39017 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCAATTTCTT-TTTCAAGTG
39040 CTTT
1 CTTT
39044 TGTTTTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.12, C:0.18, G:0.10, T:0.59
Consensus pattern (22 bp):
CTTTCAATTTCTTTTTCAAGTG
Found at i:41192 original size:21 final size:21
Alignment explanation
Indices: 41151--41212 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
41141 TCGTTAGACA
* *
41151 GGGGGAATCGGTA-CCCATGG
1 GGGGGAATTGGTACCCCCTGG
41171 GGGGGAATTGGTACCCCCTGG
1 GGGGGAATTGGTACCCCCTGG
*
41192 GGGGAAATCT-GTACCCCCTGG
1 GGGGGAAT-TGGTACCCCCTGG
41213 ACATTTTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.32
21 24 0.65
22 1 0.03
ACGTcount: A:0.18, C:0.24, G:0.40, T:0.18
Consensus pattern (21 bp):
GGGGGAATTGGTACCCCCTGG
Found at i:41208 original size:20 final size:19
Alignment explanation
Indices: 41151--41208 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
41141 TCGTTAGACA
* *
41151 GGGGGAATCGGTACCCATGG
1 GGGGGAATCTGTACCCCT-G
41171 GGGGGAAT-TGGTACCCCCTG
1 GGGGGAATCT-GTA-CCCCTG
41191 GGGGGAAATCTGTACCCC
1 GGGGG-AATCTGTACCCC
41209 CTGGACATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
20 21 0.66
21 10 0.31
22 1 0.03
ACGTcount: A:0.19, C:0.24, G:0.40, T:0.17
Consensus pattern (19 bp):
GGGGGAATCTGTACCCCTG
Found at i:42729 original size:19 final size:20
Alignment explanation
Indices: 42686--42733 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
42676 TCTAAATCCT
*
42686 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATATCATTTTGG
* *
42706 CTTTCAAAATAT-ATTTTTG
1 TTTTCAAAATATCATTTTGG
42725 TTTTCAAAA
1 TTTTCAAAA
42734 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATATCATTTTGG
Found at i:43970 original size:21 final size:21
Alignment explanation
Indices: 43944--43995 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
43934 TGGAGCCTGG
43944 GGGAATCAGTACCCCCTCATA
1 GGGAATCAGTACCCCCTCATA
*
43965 GGGAATCGGTACCCCCTCATA
1 GGGAATCAGTACCCCCTCATA
43986 GGGAATCAGT
1 GGGAATCAGT
43996 TCCCTAAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (21 bp):
GGGAATCAGTACCCCCTCATA
Found at i:44055 original size:22 final size:22
Alignment explanation
Indices: 44030--44073 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
44020 CTGTTAGACA
44030 GGGGGAAATC-GATACCCCCTGG
1 GGGGGAAATCTG-TACCCCCTGG
*
44052 GGGGGGAATCTGTACCCCCTGG
1 GGGGGAAATCTGTACCCCCTGG
44074 ACATTCTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.18, C:0.27, G:0.39, T:0.16
Consensus pattern (22 bp):
GGGGGAAATCTGTACCCCCTGG
Found at i:50748 original size:641 final size:642
Alignment explanation
Indices: 46868--51371 Score: 8373
Period size: 642 Copynumber: 7.0 Consensus size: 642
46858 TTTGTACGAA
46868 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCCTTTAATCTTTTTACAACTTT
1 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCCTTTAATCTTTTTACAACTTT
46933 TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAT
66 TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAT
*
46998 ATATTTTTTTTGAATTGAATCGAGAAATGTAATTTTTTTACATATCGACTGTTTTGTCTCTCTCT
131 ATA-TTTTTTTGAATTGAATCGAGAAATGTAATTTTTTTACATATGGACTGTTTTGTCTCTCTCT
* * *
47063 TGATAACTGGCAAATTGTCTAAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGTACGTTTG
195 CGATAACTGGCAAATTGTTTTAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGTACGTTTG
47128 GGCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATT
260 GGCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATT
*
47193 GATTGGAGGAAGTTGTTTGTTTTTGTTGAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGT
325 GATTGGAGGAAGCTGTTTGTTTTTGTTGAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGT
47258 GATGGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAGAATGGAAGCAC
390 GATGGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAGAATGGAAGCAC
47323 TCGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGA
455 TCGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGA
47388 AGAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTCT
520 AGAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTCT
** *
47453 ACTATTAGGTTTTGGGTTTTAGAGAATGATCCCTGGTATATTCAACATAAACATTTAG
585 ACTATTAGGGATTGGGTTTTAGAGAATGATCCCTGGTATATTCAACATAAGCATTTAG
47511 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCCTTTAATCTTTTTACAACTTT
1 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCCTTTAATCTTTTTACAACTTT
47576 TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAT
66 TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAT
47641 ATATTTTTTTGAATTGAATCGAGAAATGTAATTTTTTTACATATGGACTGTTTTGTCTCTCTCTC
131 ATATTTTTTTGAATTGAATCGAGAAATGTAATTTTTTTACATATGGACTGTTTTGTCTCTCTCTC
* * *
47706 GATAATTGGCAAATTGTTTTAGGGTTTTCATCCATTCGTCTAGGGTTTGTGTGTTGCACGTTTGG
196 GATAACTGGCAAATTGTTTTAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGTACGTTTGG
47771 GCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATTG
261 GCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATTG
47836 ATTGGAGGAAGCTGTTTGTTTTTGTTGAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGTG
326 ATTGGAGGAAGCTGTTTGTTTTTGTTGAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGTG
* *
47901 CTGGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCATAATGGAAGCACT
391 ATGGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAGAATGGAAGCACT
47966 CGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGAA
456 CGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGAA
48031 GAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTCTA
521 GAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTCTA
** *
48096 CTATTAGGTTTTGGGTTTTAGAGAATGATCCCTGGTATATTCAACATAAACATTTAG
586 CTATTAGGGATTGGGTTTTAGAGAATGATCCCTGGTATATTCAACATAAGCATTTAG
48153 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCCTTTAATCTTTTTACAACTTT
1 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCCTTTAATCTTTTTACAACTTT
48218 TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAT
66 TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAT
48283 ATATTTTTTTGAATTGAATCGAGAAATGTAATTTTTTTTACATATGGACTGTTTTGTCTCTCTCT
131 ATATTTTTTTGAATTGAATCGAGAAATGTAA-TTTTTTTACATATGGACTGTTTTGTCTCTCTCT
* *
48348 CGATAACTGGCAAATTGTTTTAGGGTTTTCATCCATTCGTCTAGGGTTTGTGTGTTGCACGTTTG
195 CGATAACTGGCAAATTGTTTTAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGTACGTTTG
48413 GGCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATT
260 GGCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATT
48478 GATTGGAGGAAGCTGTTTGTTTTTGTTGAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGT
325 GATTGGAGGAAGCTGTTTGTTTTTGTTGAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGT
* *
48543 GCTGGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCATAATGGAAGCAC
390 GATGGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAGAATGGAAGCAC
48608 TCGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGA
455 TCGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGA
*
48673 AGAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTACCAATTCT
520 AGAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTCT
* * *
48738 ACTATTAGGGATTGGGTTTTGGAGAATGATCCCTGGTACATTCAACATAAGCTTTTAG
585 ACTATTAGGGATTGGGTTTTAGAGAATGATCCCTGGTATATTCAACATAAGCATTTAG
*
48796 TTTTGATATAAATAAAATTTAATCATTTTAAAATTTAACCTCCCCTTTAATCTTTTTACAACTTT
1 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCCTTTAATCTTTTTACAACTTT
48861 TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAT
66 TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAT
48926 ATATTTTTTTTGAATTGAATCGAGAAATGTAATTTTTTTACATATGGACTGTTTTGTCTCTCTCT
131 ATA-TTTTTTTGAATTGAATCGAGAAATGTAATTTTTTTACATATGGACTGTTTTGTCTCTCTCT
* * *
48991 TGATAACTGGCAAATTGTCTAAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGTACGTTTG
195 CGATAACTGGCAAATTGTTTTAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGTACGTTTG
49056 GGCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATT
260 GGCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATT
*
49121 GATTGGAGGAAGTTGTTTGTTTTTGTTGAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGT
325 GATTGGAGGAAGCTGTTTGTTTTTGTTGAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGT
*
49186 GATGGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAGAATGGAAACAC
390 GATGGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAGAATGGAAGCAC
49251 TCGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGA
455 TCGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGA
49316 AGAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTCT
520 AGAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTCT
** * *
49381 ACTATTAGGTTTTGAGTTTTAGAGAATGATCCCTGGTATATTCAACATAAACATTTAG
585 ACTATTAGGGATTGGGTTTTAGAGAATGATCCCTGGTATATTCAACATAAGCATTTAG
49439 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCCTTTAATCTTTTTACAACTTT
1 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCCTTTAATCTTTTTACAACTTT
49504 TTAAACCAA-TTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAT
66 TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAT
49568 ATATTTTTTTGAATTGAATCGAGAAATGTAATTTTTTTTACATATGGACTGTTTTGTCTCTCTCT
131 ATATTTTTTTGAATTGAATCGAGAAATGTAA-TTTTTTTACATATGGACTGTTTTGTCTCTCTCT
* *
49633 CGATAACTGGCAAATTGTTTTAGGGTTTTCATCCATTCGTCTAGGGTTTGTGTGTTGCACGTTTG
195 CGATAACTGGCAAATTGTTTTAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGTACGTTTG
49698 GGCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATT
260 GGCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATT
49763 GATTGGAGGAAGCTGTTTGTTTTTGTTGAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGT
325 GATTGGAGGAAGCTGTTTGTTTTTGTTGAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGT
* *
49828 GCTGGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCATAATGGAAGCAC
390 GATGGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAGAATGGAAGCAC
49893 TCGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGA
455 TCGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGA
*
49958 AGAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTACCAATTCT
520 AGAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTCT
* * *
50023 ACTATTAGGGATTGGGTTTTGGAGAATGATCCCTGGTACATTCAACATAAGCTTTTAG
585 ACTATTAGGGATTGGGTTTTAGAGAATGATCCCTGGTATATTCAACATAAGCATTTAG
*
50081 TTTTGATATAAATAAAATTTAATCATTTTAAAATTTAACCTCCCCTTTAATCTTTTTACAACTTT
1 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCCTTTAATCTTTTTACAACTTT
*
50146 TTAAACCAATTTCCAGTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAT
66 TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAT
*
50211 ATATTTTTTTGAATTGAATCGAGAAATGTAATTTTTTTACATATGGATTGTTTTGTCTCTCTCTC
131 ATATTTTTTTGAATTGAATCGAGAAATGTAATTTTTTTACATATGGACTGTTTTGTCTCTCTCTC
*
50276 GATAACTGGCAAATTGTTTTAGGGTTTTCGTCGATTCGTCTAGGGTTTGTGTGTTGTACGTTTGG
196 GATAACTGGCAAATTGTTTTAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGTACGTTTGG
50341 GCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATTG
261 GCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATTG
*
50406 ATTGGAGGAAGTTGTTTGTTTTTGTTGAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGTG
326 ATTGGAGGAAGCTGTTTGTTTTTGTTGAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGTG
**
50471 ATGGTGTTGTGACTGTCCATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAGAATGGAAGCACT
391 ATGGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAGAATGGAAGCACT
* *
50536 CGTTGGTATGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTATGCAAAAGATTGC-GGGGAA
456 CGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGAA
50600 GAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTCTA
521 GAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTCTA
*
50665 CTATTAGGGATTGGGTTTTAGAGAATGATCCCTTGTATATTCAACATAAGCATTTAG
586 CTATTAGGGATTGGGTTTTAGAGAATGATCCCTGGTATATTCAACATAAGCATTTAG
50722 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCCTTTAATCTTTTTACAACTTT
1 TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCCTTTAATCTTTTTACAACTTT
50787 TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAT
66 TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAT
* *
50852 ATATTTTTTTGAATTGAATCGAGAAATTTTATTTTTTTTACATATGGACTGTTTTGTCTCTCTCT
131 ATATTTTTTTGAATTGAATCGAGAAA-TGTAATTTTTTTACATATGGACTGTTTTGTCTCTCTCT
50917 CGATAACTGGCAAATTGTTTTAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGTACGTTTG
195 CGATAACTGGCAAATTGTTTTAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGTACGTTTG
50982 GGCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATT
260 GGCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATT
51047 GATTGGAGGAAGCTGTTTGTTTTTGTTGAAGAACACTCTCTTTGATTTCTTTCCCCTGAGATCAG
325 GATTGGAGGAAGCTGTTTGTTTTTGTTGAAGAACACTCTC-TTGATTTCTTTCCCCTGAGATCAG
* * *
51112 TGATGGTGTTGTGATTGTTAATCCTTCCAAAGTTGTTTTGAAGAGGGGATTTCAGAATGGAAGCA
389 TGATGGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAGAATGGAAGCA
*
51177 CTCGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTATGCAAAAGATTGCGGGGG
454 CTCGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGG
* *
51242 AAGAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTGCCTTTGCTAATTC
519 AAGAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTC
* * *
51307 TACTATTAGGGATTGGGTTTTGGAGAATGATCCCTGGTACATTCAACATAAGCTTTTAG
584 TACTATTAGGGATTGGGTTTTAGAGAATGATCCCTGGTATATTCAACATAAGCATTTAG
51366 TTTTGA
1 TTTTGA
51372 GAAAATGGGA
Statistics
Matches: 3763, Mismatches: 91, Indels: 13
0.97 0.02 0.00
Matches are distributed among these distances:
641 305 0.08
642 1799 0.48
643 1503 0.40
644 156 0.04
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (642 bp):
TTTTGATATAAATAAAATTAAATCATTTTAAAATTTAACCTCCCCTTTAATCTTTTTACAACTTT
TTAAACCAATTTCCATTCTTTTATTCTTTTCTTTCGTCTATTTGTTTGATTAAATTTGATTTGAT
ATATTTTTTTGAATTGAATCGAGAAATGTAATTTTTTTACATATGGACTGTTTTGTCTCTCTCTC
GATAACTGGCAAATTGTTTTAGGGTTTTCGTCCATTCGTCTAGGGTTTGTGTGTTGTACGTTTGG
GCGTTCTTGATCCAAGCCTTTATGTAGGTTTTGGACTTGAGGGTCTTTTGGTATGGTCGTAATTG
ATTGGAGGAAGCTGTTTGTTTTTGTTGAAGAACACTCTCTTGATTTCTTTCCCCTGAGATCAGTG
ATGGTGTTGTGACTGTTAATCCTCCCAAAGATGTTTTGAAGAGGGGATTTCAGAATGGAAGCACT
CGTTGGTAGGGCAGTTCATTGGTTCAGCTCCAAATTTCAGCTCTAGGCAAAAGATTGCGGGGGAA
GAACTCGATGGTAAAGGTTAGTCTTGATGGTTCTTACTTGTATGCTTTTTCCTTTGCCAATTCTA
CTATTAGGGATTGGGTTTTAGAGAATGATCCCTGGTATATTCAACATAAGCATTTAG
Found at i:55565 original size:15 final size:15
Alignment explanation
Indices: 55545--55574 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55535 TCCCACTGTT
55545 CTTTTAAGCTATTAA
1 CTTTTAAGCTATTAA
*
55560 CTTTTAAGTTATTAA
1 CTTTTAAGCTATTAA
55575 TAAAGATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (15 bp):
CTTTTAAGCTATTAA
Found at i:55847 original size:28 final size:30
Alignment explanation
Indices: 55781--55849 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 30
55771 ATTAACGAAC
55781 AGAGATAAA--ATATATTATATATAAAAAA
1 AGAGATAAATTATATATTATATATAAAAAA
* *
55809 AGAGATTAATTATATATTCTA-ATAAAAAA
1 AGAGATAAATTATATATTATATATAAAAAA
*
55838 AG-GGTAAATTAT
1 AGAGATAAATTAT
55850 GCATTTAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 16 0.46
29 10 0.29
30 9 0.26
ACGTcount: A:0.57, C:0.01, G:0.10, T:0.32
Consensus pattern (30 bp):
AGAGATAAATTATATATTATATATAAAAAA
Found at i:58790 original size:17 final size:17
Alignment explanation
Indices: 58768--58825 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
58758 CCATCACAAG
*
58768 AAAATGGATTGCAACTT
1 AAAATGGATTGAAACTT
** *
58785 AAAATGGGGTGAAACTAG
1 AAAATGGATTGAAACT-T
* *
58803 AAAATAGATTGTAACTT
1 AAAATGGATTGAAACTT
58820 AAAATG
1 AAAATG
58826 TGCAACCTAT
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (17 bp):
AAAATGGATTGAAACTT
Found at i:63651 original size:20 final size:19
Alignment explanation
Indices: 63607--63651 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
63597 GATTTTCGTT
* * *
63607 TGAAAACTAAAATGGATTT
1 TGAAAACCAAAATGAATTA
63626 TGAAAACCAAAATGAAATTA
1 TGAAAACCAAAATG-AATTA
63646 TGAAAA
1 TGAAAA
63652 AAGATTTAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (19 bp):
TGAAAACCAAAATGAATTA
Found at i:65041 original size:20 final size:20
Alignment explanation
Indices: 65008--65057 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
64998 CTCATAAACA
65008 GTACCGATACTGTTCATAAG
1 GTACCGATACTGTTCATAAG
* * *
65028 GTATCGATATTGTTTATAAG
1 GTACCGATACTGTTCATAAG
65048 GTACCGATAC
1 GTACCGATAC
65058 CAAAGGTAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (20 bp):
GTACCGATACTGTTCATAAG
Done.