Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008615.1 Hibiscus syriacus cultivar Beakdansim tig00111572_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: 61357
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:992 original size:24 final size:24
Alignment explanation
Indices: 958--1011 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
948 CTGAAACATC
958 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
982 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1006 ATCAAA
1 ATCAAA
1012 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1025 original size:24 final size:24
Alignment explanation
Indices: 958--1025 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
948 CTGAAACATC
* * *
958 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
982 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1006 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1026 TAGTACTCGC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1960 original size:20 final size:19
Alignment explanation
Indices: 1931--1979 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1921 ACTAAAACCT
*
1931 GTTGCGAATTCAAAAATCTA
1 GTTGCAAATTCAAAAATC-A
** *
1951 GTTGCAAATTTGAAATTCA
1 GTTGCAAATTCAAAAATCA
1970 GTTGCAAATT
1 GTTGCAAATT
1980 TGAAATTCCG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (19 bp):
GTTGCAAATTCAAAAATCA
Found at i:1972 original size:19 final size:19
Alignment explanation
Indices: 1950--1987 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1940 TCAAAAATCT
1950 AGTTGCAAATTTGAAATTC
1 AGTTGCAAATTTGAAATTC
1969 AGTTGCAAATTTGAAATTC
1 AGTTGCAAATTTGAAATTC
1988 CGCGTTGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (19 bp):
AGTTGCAAATTTGAAATTC
Found at i:2026 original size:40 final size:40
Alignment explanation
Indices: 1982--2058 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
1972 TGCAAATTTG
* *
1982 AAATTCCGCGTTGCGAA-TTGACT-TCTGTGTTGCGATTTAC
1 AAATT-CGCGTTACGAATTTGACTATC-GCGTTGCGATTTAC
*
2022 AAATTCGTGTTACGAATTTGACTATCGCGTTGCGATT
1 AAATTCGCGTTACGAATTTGACTATCGCGTTGCGATT
2059 GACTTTTGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 9 0.28
40 21 0.66
41 2 0.06
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (40 bp):
AAATTCGCGTTACGAATTTGACTATCGCGTTGCGATTTAC
Found at i:2026 original size:59 final size:58
Alignment explanation
Indices: 1963--2074 Score: 138
Period size: 58 Copynumber: 1.9 Consensus size: 58
1953 TGCAAATTTG
*
1963 AAATTC-AGTTGCAAATTTGAA-ATTCCGCGTTGCGAATTGACTTCTGTGTTGCGATTTAC
1 AAATTCGAGTTACAAATTTGAATA-T-CGCGTTGCG-ATTGACTTCTGTGTTGCGATTTAC
* * * *
2022 AAATTCGTGTTACGAATTTGACTATCGCGTTGCGATTGACTTTTGTGTTGCGA
1 AAATTCGAGTTACAAATTTGAATATCGCGTTGCGATTGACTTCTGTGTTGCGA
2075 ATTTGACTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
58 18 0.39
59 15 0.33
60 12 0.26
61 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.38
Consensus pattern (58 bp):
AAATTCGAGTTACAAATTTGAATATCGCGTTGCGATTGACTTCTGTGTTGCGATTTAC
Found at i:2082 original size:20 final size:20
Alignment explanation
Indices: 1991--2191 Score: 231
Period size: 20 Copynumber: 10.3 Consensus size: 20
1981 GAAATTCCGC
*
1991 GTTGCGAA-TTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
* *
2010 GTTGCG-ATTT-ACAAATTCGT
1 GTTGCGAATTTGAC--TTTTGT
* * * *
2030 GTTACGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
2050 GTTGCG-A-TTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
2068 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
2088 GTTGCGAA-TTGACTTTTTGT
1 GTTGCGAATTTGAC-TTTTGT
2108 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
2128 GTTGCGAA-TTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
2147 G-TGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* *
2166 G-TGCGAATTTGACGTATGT
1 GTTGCGAATTTGACTTTTGT
2185 GTTGCGA
1 GTTGCGA
2192 TTTACAAATT
Statistics
Matches: 158, Mismatches: 13, Indels: 21
0.82 0.07 0.11
Matches are distributed among these distances:
18 23 0.15
19 56 0.35
20 68 0.43
21 9 0.06
22 2 0.01
ACGTcount: A:0.17, C:0.12, G:0.26, T:0.44
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:2092 original size:78 final size:78
Alignment explanation
Indices: 1991--2171 Score: 235
Period size: 78 Copynumber: 2.3 Consensus size: 78
1981 GAAATTCCGC
* *
1991 GTTGCGAA-TTGACTTCTGTGTTGCGATTTACAAATTCGTGTTACGAATTTGACTATCGCGTTGC
1 GTTGCGAATTTGACTTTTGTGTTGCGATTGAC-AATTCGTGTTACGAATTTGACTATCGCGTTGC
2055 G-ATTGACTTTTGT
65 GAATTGACTTTTGT
** * * * * *
2068 GTTGCGAATTTGACTTTTGTGTTGCGAATTGACTTTTTGTGTTGCGAATTTGACTTTTGTGTTGC
1 GTTGCGAATTTGACTTTTGTGTTGCG-ATTGACAATTCGTGTTACGAATTTGACTATCGCGTTGC
2133 GAATTGACTTTTGT
65 GAATTGACTTTTGT
2147 G-TGCGAATTTGACTTTTGTG-TGCGA
1 GTTGCGAATTTGACTTTTGTGTTGCGA
2172 ATTTGACGTA
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
76 1 0.01
77 12 0.13
78 61 0.66
79 18 0.20
ACGTcount: A:0.17, C:0.13, G:0.25, T:0.45
Consensus pattern (78 bp):
GTTGCGAATTTGACTTTTGTGTTGCGATTGACAATTCGTGTTACGAATTTGACTATCGCGTTGCG
AATTGACTTTTGT
Found at i:2253 original size:21 final size:21
Alignment explanation
Indices: 2227--2293 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
2217 GATTCGTGTT
2227 GCGAATTTGGAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
* *
2248 GTGAATTTGCAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
*
2269 GCGAATTTGGAAAATCGCAAT
1 GCGAATTTGGAAAATCGCAAC
2290 GCGA
1 GCGA
2294 TTTACATATT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (21 bp):
GCGAATTTGGAAAATCGCAAC
Found at i:3801 original size:41 final size:41
Alignment explanation
Indices: 3730--3851 Score: 210
Period size: 41 Copynumber: 3.0 Consensus size: 41
3720 TTCATTCTAC
*
3730 GTGAACTTTTGGAG-TTCATATTCCATTGAATTAATAACTA
1 GTGAACTTTTGGAGTTTCATCTTCCATTGAATTAATAACTA
3770 GTGAACTTTTGGAGTTTCATCTTCCATTGAATTAATAACTA
1 GTGAACTTTTGGAGTTTCATCTTCCATTGAATTAATAACTA
* *
3811 GTGAACTTTTGGAGTTTCATCTTCCCTTGAATTAACAACTA
1 GTGAACTTTTGGAGTTTCATCTTCCATTGAATTAATAACTA
3852 ATTTATTAGG
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
40 14 0.18
41 64 0.82
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.40
Consensus pattern (41 bp):
GTGAACTTTTGGAGTTTCATCTTCCATTGAATTAATAACTA
Found at i:7225 original size:33 final size:33
Alignment explanation
Indices: 7151--7216 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
7141 ACCATGAACA
* *
7151 GTGAACAGTGTACCGATGCATTGTTACAGTAAC
1 GTGAACAGTGTACCGATGCACTGCTACAGTAAC
7184 GTGAACAGTGTACCGATGCACTGCTACAGTAAC
1 GTGAACAGTGTACCGATGCACTGCTACAGTAAC
7217 TACTACAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (33 bp):
GTGAACAGTGTACCGATGCACTGCTACAGTAAC
Found at i:7685 original size:46 final size:45
Alignment explanation
Indices: 7613--7783 Score: 256
Period size: 46 Copynumber: 3.8 Consensus size: 45
7603 GATAAAATCT
* *
7613 CTTACCATTTAT-CCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATCCCATAAGCTAGTAAGCTTATTTTACCAATATA
7657 CTTACCATTTAATCCCATAAGCTAGTAAGCTTATTTTACCAATATA
1 CTTACCATTT-ATCCCATAAGCTAGTAAGCTTATTTTACCAATATA
*
7703 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTT-ATCCCATAAGCTAGTAAGCTTATTTTACCAATATA
** *
7749 CTTGTCA-TTATTCCATAAGCTAGTAAGCTTATTTT
1 CTTACCATTTATCCCATAAGCTAGTAAGCTTATTTT
7784 CCAGTTTATC
Statistics
Matches: 118, Mismatches: 7, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
44 34 0.29
45 4 0.03
46 80 0.68
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTAGTAAGCTTATTTTACCAATATA
Found at i:7943 original size:40 final size:40
Alignment explanation
Indices: 7864--7944 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
7854 ATAGGAGTTA
* * *
7864 AATATTGCACCGAAGTGCTGAGGTCGAACTTTGCTCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAACTTTACCCACCT
*
7904 AATAATGCACCGTAGTGCTGAGGTCGGAA-TTTACCCACCT
1 AATAATGCACCGAAGTGCTGAGGTC-GAACTTTACCCACCT
7944 A
1 A
7945 GTACACCGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 33 0.92
41 3 0.08
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTGAGGTCGAACTTTACCCACCT
Found at i:19091 original size:30 final size:31
Alignment explanation
Indices: 19024--19149 Score: 100
Period size: 31 Copynumber: 4.2 Consensus size: 31
19014 GAAGGACCTA
* * *
19024 TCCAGAGGTCACAAAGACCCT--GT-AACTA
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* * *
19052 TCCAGAGGTCATAAAGAACCTCGG-AAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
*
19082 TCCATAGGTCCCAAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* ** * *
19113 TCCATATGTTC-CTTAGAACATAGGTATACTG
1 TCCATA-GGTCACAAAGAACCTAGGTAAACTG
19144 TCCATA
1 TCCATA
19150 TATCTCGAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
28 19 0.23
30 25 0.31
31 34 0.42
32 3 0.04
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGTAAACTG
Found at i:19114 original size:31 final size:31
Alignment explanation
Indices: 19064--19149 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
19054 CAGAGGTCAT
*
19064 AAAGAACCTCGG-AAACTGTCCATAGGTCCC
1 AAAGAACCTAGGTAAACTGTCCATAGGTCCC
* *
19094 AAAGAACCTAGGTAAACTGTCCATATGTTCC
1 AAAGAACCTAGGTAAACTGTCCATAGGTCCC
** * *
19125 TTAGAACATAGGTATACTGTCCATA
1 AAAGAACCTAGGTAAACTGTCCATA
19150 TATCTCGAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 11 0.23
31 37 0.77
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (31 bp):
AAAGAACCTAGGTAAACTGTCCATAGGTCCC
Found at i:19150 original size:31 final size:31
Alignment explanation
Indices: 19076--19171 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
19066 AGAACCTCGG
* *
19076 AAACTGTCCATAGGTCCCAAAGAACCTAGGT
1 AAACTGTCCATATGTCCCAAAGAACATAGGT
* **
19107 AAACTGTCCATATGTTCCTTAGAACATAGGT
1 AAACTGTCCATATGTCCCAAAGAACATAGGT
* * *
19138 ATACTGTCCATATATCTCGAAAG-ACATAGGT
1 AAACTGTCCATATGTC-CCAAAGAACATAGGT
19169 AAA
1 AAA
19172 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (31 bp):
AAACTGTCCATATGTCCCAAAGAACATAGGT
Found at i:20485 original size:64 final size:62
Alignment explanation
Indices: 20352--20512 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 62
20342 TAATGAAGGT
* * *
20352 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* *
20417 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
20481 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
20513 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.68
65 23 0.27
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:21948 original size:20 final size:21
Alignment explanation
Indices: 21906--21949 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
21896 AGAGCCCCTT
*
21906 AAAAAATAAAGTTGTTGAGAG
1 AAAAAATAAAGTTGTAGAGAG
21927 AAAAAATAAAAGTT-TAGA-AG
1 AAAAAAT-AAAGTTGTAGAGAG
21947 AAA
1 AAA
21950 TAGCTAGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 10 0.48
22 6 0.29
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAGTTGTAGAGAG
Found at i:24828 original size:31 final size:31
Alignment explanation
Indices: 24793--24859 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
24783 AACAAATTAG
* * *
24793 TCACTAACTTTACCTATTTGTAACAAAATGA
1 TCACTAACGTTACCGATTTCTAACAAAATGA
* *
24824 TCACTGACGTTATCGATTTCTAACAAAATGA
1 TCACTAACGTTACCGATTTCTAACAAAATGA
24855 TCACT
1 TCACT
24860 CTATCGTTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (31 bp):
TCACTAACGTTACCGATTTCTAACAAAATGA
Found at i:28160 original size:20 final size:20
Alignment explanation
Indices: 28137--28176 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28127 TTTGGGAAAA
* *
28137 ATCGGTTTTTTTTTAACCGG
1 ATCGGATTTTTTTAAACCGG
28157 ATCGGATTTTTTTAAACCGG
1 ATCGGATTTTTTTAAACCGG
28177 TTATTTTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (20 bp):
ATCGGATTTTTTTAAACCGG
Found at i:28236 original size:12 final size:12
Alignment explanation
Indices: 28221--28266 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
28211 CGGTTTTTTT
*
28221 ACCGGATAAAAA
1 ACCGGTTAAAAA
28233 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
28248 ACCGGTTAAAAA
1 ACCGGTTAAAAA
28260 ACCGGTT
1 ACCGGTT
28267 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:28248 original size:15 final size:13
Alignment explanation
Indices: 28227--28267 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
28217 TTTTACCGGA
28227 TAAAAAACCGGTT
1 TAAAAAACCGGTT
28240 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
28254 TAAAAAACCGGTT
1 TAAAAAACCGGTT
28267 T
1 T
28268 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:30585 original size:21 final size:21
Alignment explanation
Indices: 30561--30600 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
30551 TTTATTTTAT
30561 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
30582 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
30601 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:30648 original size:33 final size:33
Alignment explanation
Indices: 30595--30693 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
30585 TTTGTTTCAA
30595 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
30627 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
30660 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
30693 T
1 T
30694 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:30722 original size:13 final size:13
Alignment explanation
Indices: 30679--30733 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
30669 TTGGAAGTAT
30679 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
30692 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
30706 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
30719 TTAAGTATTTGAA
1 TTAAGTATTTCAA
30732 TT
1 TT
30734 TATTGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:31152 original size:15 final size:15
Alignment explanation
Indices: 31127--31182 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
31117 ATCTGGAATA
*
31127 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
31142 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
31157 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
31174 TTAAAACCG
1 TTAAAACCG
31183 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:31191 original size:21 final size:18
Alignment explanation
Indices: 31146--31179 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
31136 GTTTTTTTAT
31146 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
31163 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
31180 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:31299 original size:15 final size:17
Alignment explanation
Indices: 31273--31304 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31263 TTCTATGGGA
31273 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
31289 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
31305 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:31863 original size:31 final size:31
Alignment explanation
Indices: 31788--31865 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
31778 ATAATGGGAG
*
31788 AGTGACCATTTTATTATAAATCAATAACGTT
1 AGTGACCATTTTATTATAAATCAATAACATT
* * *
31819 AGTAACTATTTTATTATAAATCGATAACATT
1 AGTGACCATTTTATTATAAATCAATAACATT
*
31850 AGTGACCAATTTATTA
1 AGTGACCATTTTATTA
31866 CTTTTGAAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (31 bp):
AGTGACCATTTTATTATAAATCAATAACATT
Found at i:32388 original size:40 final size:41
Alignment explanation
Indices: 32277--32417 Score: 151
Period size: 40 Copynumber: 3.4 Consensus size: 41
32267 TAGAGGGATT
* *
32277 TTTAGCGGCATTTTT-TAAACAAACGCCGGTAAATACTCATAC
1 TTTAGTGGCATTTTTGT--ACAAACGCCGTTAAATACTCATAC
* * **
32319 TTTAGTGGCATTTTTATATAAATACCGTTAAATACT-ATAC
1 TTTAGTGGCATTTTTGTACAAACGCCGTTAAATACTCATAC
* *
32359 TTTAGTGGCATTTTTGTACAAACGTCGTTAAATACTCGTAC
1 TTTAGTGGCATTTTTGTACAAACGCCGTTAAATACTCATAC
* * *
32400 TTTCGTGACGTTTTTGTA
1 TTTAGTGGCATTTTTGTA
32418 ACATCCCAAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
40 35 0.42
41 33 0.40
42 14 0.17
43 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (41 bp):
TTTAGTGGCATTTTTGTACAAACGCCGTTAAATACTCATAC
Found at i:33231 original size:20 final size:20
Alignment explanation
Indices: 33177--33254 Score: 72
Period size: 19 Copynumber: 3.9 Consensus size: 20
33167 GTGAAATTAT
33177 TAAGGGTAGTATCGATACTTG
1 TAAGGGTAGTATCGATAC-TG
*
33198 TTGAAGAG--GTATCGATACTG
1 -T-AAGGGTAGTATCGATACTG
*
33218 TAAGGGTAGTATCGATACCG
1 TAAGGGTAGTATCGATACTG
* *
33238 -AAGGATGGTATCGATAC
1 TAAGGGTAGTATCGATAC
33255 CACGCAAACA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 4 0.08
19 16 0.33
20 13 0.27
21 10 0.21
22 1 0.02
23 4 0.08
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.28
Consensus pattern (20 bp):
TAAGGGTAGTATCGATACTG
Found at i:34113 original size:21 final size:21
Alignment explanation
Indices: 34087--34156 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
34077 GTCGAGGGTT
34087 TTATGTGGTCCTCCGGGATAA
1 TTATGTGGTCCTCCGGGATAA
34108 TTATGTGGTCCTCCGGGATAA
1 TTATGTGGTCCTCCGGGATAA
* * *
34129 TTATGTGGTACTTCGGGACAA
1 TTATGTGGTCCTCCGGGATAA
*
34150 ATATGTG
1 TTATGTG
34157 ACACTTCGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (21 bp):
TTATGTGGTCCTCCGGGATAA
Found at i:34162 original size:21 final size:21
Alignment explanation
Indices: 34138--34209 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
34128 ATTATGTGGT
34138 ACTTCGGGACAAATATGTGAC
1 ACTTCGGGACAAATATGTGAC
*
34159 ACTTCGGTG-CAAACCTATGTGGTC
1 ACTTCGG-GACAAA--TATGT-GAC
* *
34183 -CTTCGGGACAATTATGTGGC
1 ACTTCGGGACAAATATGTGAC
34203 ACTTCGG
1 ACTTCGG
34210 TGCAAATTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
20 2 0.05
21 22 0.52
22 2 0.05
23 14 0.33
24 2 0.05
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (21 bp):
ACTTCGGGACAAATATGTGAC
Found at i:34187 original size:44 final size:44
Alignment explanation
Indices: 34130--34215 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
34120 CCGGGATAAT
34130 TATGTGGTACTTCGGGACAAATATGTGACACTTCGGTGCAAACC
1 TATGTGGTACTTCGGGACAAATATGTGACACTTCGGTGCAAACC
* * *
34174 TATGTGGTCCTTCGGGACAATTATGTGGCACTTCGGTGCAAA
1 TATGTGGTACTTCGGGACAAATATGTGACACTTCGGTGCAAA
34216 TTACGAGCTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (44 bp):
TATGTGGTACTTCGGGACAAATATGTGACACTTCGGTGCAAACC
Found at i:36367 original size:21 final size:21
Alignment explanation
Indices: 36342--36383 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
36332 CCATAATGGG
*
36342 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
36363 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
36384 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:41762 original size:20 final size:20
Alignment explanation
Indices: 41690--41770 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 20
41680 GAACCCCAGG
* **
41690 GGGGGTATCGATTCCATTGT
1 GGGGGTATCGATTCCCTCAT
* * *
41710 GGGGGGATCGGTTCCCCTTCAAA
1 GGGGGTATCGATT-CCC-TC-AT
* *
41733 GGGGGAATCGGTTCCCTCAT
1 GGGGGTATCGATTCCCTCAT
41753 GGGGGTATCGATTCCCTC
1 GGGGGTATCGATTCCCTC
41771 TGCACCAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
20 28 0.58
21 4 0.08
22 4 0.08
23 12 0.25
ACGTcount: A:0.15, C:0.23, G:0.35, T:0.27
Consensus pattern (20 bp):
GGGGGTATCGATTCCCTCAT
Found at i:45431 original size:21 final size:20
Alignment explanation
Indices: 45388--45431 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
45378 TCAAAAGAAG
*
45388 TTTTGAGATCATCAATTTTC
1 TTTTGAGATCATCAATTTCC
45408 TTTTGATGATCATC-ATTTACC
1 TTTTGA-GATCATCAATTT-CC
45429 TTT
1 TTT
45432 GAAAGTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.52
Consensus pattern (20 bp):
TTTTGAGATCATCAATTTCC
Found at i:45432 original size:20 final size:20
Alignment explanation
Indices: 45389--45433 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
45379 CAAAAGAAGT
* *
45389 TTTGAGATCATCAATTTTCT
1 TTTGAGATCATCAATTTACC
45409 TTTGATGATCATC-ATTTACC
1 TTTGA-GATCATCAATTTACC
45429 TTTGA
1 TTTGA
45434 AAGTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (20 bp):
TTTGAGATCATCAATTTACC
Found at i:45586 original size:22 final size:21
Alignment explanation
Indices: 45544--45586 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
45534 GAGTTTATTT
*
45544 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
45565 TCATTTTT-ATATTTTAATAACA
1 TCATTTTTCA-ATTTTAA-AACA
45587 ATTTCTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 14 0.74
22 4 0.21
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:52924 original size:44 final size:44
Alignment explanation
Indices: 52869--52954 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
52859 CAGTGACAAT
52869 TATGCGGTCCTTCGGGACAAATATGTGGCACTTCGGTGCAAACC
1 TATGCGGTCCTTCGGGACAAATATGTGGCACTTCGGTGCAAACC
* *
52913 TATGTGGTCCTTCGGGACAATTATGTGGCACTTCGGTGCAAA
1 TATGCGGTCCTTCGGGACAAATATGTGGCACTTCGGTGCAAA
52955 TTACGAGCTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (44 bp):
TATGCGGTCCTTCGGGACAAATATGTGGCACTTCGGTGCAAACC
Found at i:52925 original size:23 final size:21
Alignment explanation
Indices: 52863--52948 Score: 79
Period size: 21 Copynumber: 4.0 Consensus size: 21
52853 GGTTCTCAGT
* *
52863 GACAATTATGCGGTCCTTCGG
1 GACAAATATGTGGTCCTTCGG
52884 GACAAATATGTGG-CACTTCGG
1 GACAAATATGTGGTC-CTTCGG
52905 TG-CAAACCTATGTGGTCCTTCGG
1 -GACAAA--TATGTGGTCCTTCGG
*
52928 GACAATTATGTGG-CACTTCGG
1 GACAAATATGTGGTC-CTTCGG
52949 TGCAAATTAC
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
20 2 0.04
21 34 0.62
22 2 0.04
23 16 0.29
24 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (21 bp):
GACAAATATGTGGTCCTTCGG
Found at i:53047 original size:17 final size:17
Alignment explanation
Indices: 53027--53059 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53017 AGTATTATAC
53027 GTCTGGACAAATTAAAA
1 GTCTGGACAAATTAAAA
*
53044 GTCTGGGCAAATTAAA
1 GTCTGGACAAATTAAA
53060 CAAATGGTTA
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:0.42, C:0.12, G:0.21, T:0.24
Consensus pattern (17 bp):
GTCTGGACAAATTAAAA
Found at i:53674 original size:40 final size:41
Alignment explanation
Indices: 53619--53712 Score: 136
Period size: 40 Copynumber: 2.3 Consensus size: 41
53609 GTGTTACAGT
*
53619 TTTTATACAAACGCCGCCAAAGACTCGTAATTTAGTGGT-A
1 TTTTATACAAACGCCGCCAAAGACTAGTAATTTAGTGGTGA
* * * *
53659 TTTTATACAAACGCCGCTAAAGACTATTATTTTAGTGGTGT
1 TTTTATACAAACGCCGCCAAAGACTAGTAATTTAGTGGTGA
53700 TTTTATACAAACG
1 TTTTATACAAACG
53713 TCACAATTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 35 0.73
41 13 0.27
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (41 bp):
TTTTATACAAACGCCGCCAAAGACTAGTAATTTAGTGGTGA
Found at i:56348 original size:21 final size:21
Alignment explanation
Indices: 56319--56377 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
56309 TGATTTATTA
*
56319 TTATAGATTTCAAGTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
*
56340 TTATGGATTTCAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
56361 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
56378 ATTGGATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.22, C:0.07, G:0.20, T:0.51
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:56766 original size:41 final size:41
Alignment explanation
Indices: 56692--56795 Score: 102
Period size: 41 Copynumber: 2.5 Consensus size: 41
56682 AAATAACGGT
* * * *
56692 GTTTGAAGAAAACACCACTAAATATCATAACCTTTAGCGTC
1 GTTTGAAAAAAACGCCGCTAAATATCATAACCTTTAGCGGC
* * * *
56733 GTTTGAAAAAAACGCCGCTACATTTCATTACCTTTTGCGGC
1 GTTTGAAAAAAACGCCGCTAAATATCATAACCTTTAGCGGC
* *
56774 GTTTTTAAAAAAA-GCCGTTAAA
1 G-TTTGAAAAAAACGCCGCTAAA
56796 AACCTATAAC
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
41 41 0.80
42 10 0.20
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (41 bp):
GTTTGAAAAAAACGCCGCTAAATATCATAACCTTTAGCGGC
Found at i:60482 original size:21 final size:21
Alignment explanation
Indices: 60456--60508 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
60446 GTTTCCAGAT
60456 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
60477 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
60498 TCGCAATGCGA
1 TCGCAACGCGA
60509 TTTTCCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:60555 original size:21 final size:20
Alignment explanation
Indices: 60530--60600 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 20
60520 CGTTGCAATA
*
60530 GTTGCGATTAATTCCATGTTC
1 GTTGCGATT-ATTCCAAGTTC
* *
60551 GTTGCGA-TAGTCGAAGTTCGC
1 GTTGCGATTATTCCAAGTT--C
60572 GTTGCGATTTATTCCAAGTTC
1 GTTGCGA-TTATTCCAAGTTC
60593 GTTGCGAT
1 GTTGCGAT
60601 AGTCCAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
19 7 0.17
20 2 0.05
21 23 0.56
23 9 0.22
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTATTCCAAGTTC
Found at i:60708 original size:6 final size:6
Alignment explanation
Indices: 60697--60728 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
60687 GACACGTATT
60697 ACCACG ACCACG ACCACG ACCACG A-CACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
60729 CGAGACGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Done.