Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004595.1 Hibiscus syriacus cultivar Beakdansim tig00010267_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: 114620
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:112 original size:14 final size:14
Alignment explanation
Indices: 93--127 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
83 ATTGTTTAAT
93 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
107 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
121 TGATTTG
1 TGATTTG
128 GTTAATTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:252 original size:14 final size:17
Alignment explanation
Indices: 233--310 Score: 69
Period size: 19 Copynumber: 4.6 Consensus size: 17
223 CGAAATGGCT
233 ATCGCAA-CG-AT-AAA
1 ATCGCAAGCGAATGAAA
247 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG-AATGAAA
266 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG-AATGAAA
285 ATCGCAA-CG-A-GAAA
1 ATCGCAAGCGAATGAAA
299 ATCGCAATGCGA
1 ATCGCAA-GCGA
311 TTTTCATTCG
Statistics
Matches: 56, Mismatches: 0, Indels: 13
0.81 0.00 0.19
Matches are distributed among these distances:
14 18 0.32
15 1 0.02
16 4 0.07
17 2 0.04
18 2 0.04
19 29 0.52
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (17 bp):
ATCGCAAGCGAATGAAA
Found at i:268 original size:19 final size:19
Alignment explanation
Indices: 244--310 Score: 99
Period size: 19 Copynumber: 3.8 Consensus size: 19
234 TCGCAACGAT
244 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
263 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
282 AAAATCGCAA--CG--A-G
1 AAAATCGCAATGCGAAATG
296 AAAATCGCAATGCGA
1 AAAATCGCAATGCGA
311 TTTTCATTCG
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 29 0.64
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.13
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:353 original size:20 final size:20
Alignment explanation
Indices: 328--405 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
318 TCGCATTGCG
*
328 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
348 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
368 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
388 ATTTTTGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
406 TCAAATGAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1467 original size:24 final size:24
Alignment explanation
Indices: 1440--1493 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1430 GTATTCGAAA
* *
1440 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1464 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1488 TTTGAT
1 TTTGAT
1494 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1682 original size:12 final size:12
Alignment explanation
Indices: 1665--1689 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1655 ATATAATCCT
1665 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1677 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1689 G
1 G
1690 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3947 original size:19 final size:19
Alignment explanation
Indices: 3925--4055 Score: 67
Period size: 19 Copynumber: 7.7 Consensus size: 19
3915 GGAAATTACT
*
3925 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
3944 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3958 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
3977 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
* *
3991 TTCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* **
4010 ATCACAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
4024 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4043 ATCGCAACGCGAA
1 ATCGCAATGCGAA
4056 TTTAATTTCG
Statistics
Matches: 79, Mismatches: 18, Indels: 30
0.62 0.14 0.24
Matches are distributed among these distances:
14 24 0.30
15 3 0.04
16 6 0.08
17 6 0.08
18 3 0.04
19 37 0.47
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3967 original size:33 final size:33
Alignment explanation
Indices: 3925--4051 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
3915 GGAAATTACT
*
3925 ATCGCAATGCGAAATAAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
3958 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * * *
3990 TTTCGTAATGCGAAATGAAAATCACAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
4024 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
4052 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
32 1 0.01
33 78 0.98
34 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:4036 original size:66 final size:66
Alignment explanation
Indices: 3930--4058 Score: 222
Period size: 66 Copynumber: 2.0 Consensus size: 66
3920 TTACTATCGC
* *
3930 AATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTCG
1 AATGCGAAATAAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
3995 T
66 T
* *
3996 AATGCGAAATGAAAATCACAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 AATGCGAAATAAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
4059 AATTTCGCGT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17
Consensus pattern (66 bp):
AATGCGAAATAAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
T
Found at i:4102 original size:33 final size:33
Alignment explanation
Indices: 4051--4140 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
4041 AAATCGCAAC
* * *
4051 GCGAATTTAATTTCGCGTTGCGTTTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
4084 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
4117 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
4141 AGTACTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:4104 original size:19 final size:19
Alignment explanation
Indices: 4080--4140 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
4070 GCGTTTCTCT
4080 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
4099 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
4113 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
4132 CATTGCGAT
1 CGTTGCGAT
4141 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:4120 original size:14 final size:14
Alignment explanation
Indices: 4066--4122 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
4056 TTTAATTTCG
*
4066 CGTTGCGTTTCTCT
1 CGTTGCGATTCTCT
*
4080 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
4099 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
4113 CGTTGCGATT
1 CGTTGCGATT
4123 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.07, C:0.25, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:4262 original size:13 final size:14
Alignment explanation
Indices: 4246--4281 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4236 CATCAATTAA
4246 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
4259 ACAAATCACCTTTT
1 ACAAATCAACTTTT
4273 ACAAATCAA
1 ACAAATCAA
4282 TTAAACATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5698 original size:21 final size:21
Alignment explanation
Indices: 5632--5698 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
5622 GTGAATCGGG
*
5632 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGAC
* * **
5653 CTCTTCAACGATGACAGTGG-C
1 CTCTTGAACGGTGGGAG-GGAC
*
5674 CTCTTGAACGGTGGGAGGGAA
1 CTCTTGAACGGTGGGAGGGAC
5695 CTCT
1 CTCT
5699 CGAGGAATGA
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
20 2 0.06
21 30 0.88
22 2 0.06
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGAC
Found at i:6139 original size:91 final size:88
Alignment explanation
Indices: 5969--6153 Score: 273
Period size: 91 Copynumber: 2.0 Consensus size: 88
5959 ATATTTCAAA
*
5969 ACTTCACCAAAAGACAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 ACTTCACCAAAAGACAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
*
6034 AGAATTGGCAGCAACCGAATAAATTT
63 AGAATTGGAAGCAACCGAATAAATTT
6060 ACTTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAG
1 ACTTC-ACCAAAAGAC-AAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAG
*
6124 CAGTATTGGAAGCAACCGAATAAATTT
62 CAGAATTGGAAGCAACCGAATAAATTT
6151 ACT
1 ACT
6154 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
91 46 0.53
92 10 0.11
93 4 0.05
95 27 0.31
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (88 bp):
ACTTCACCAAAAGACAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGAAGCAACCGAATAAATTT
Found at i:6392 original size:63 final size:63
Alignment explanation
Indices: 6320--6513 Score: 370
Period size: 63 Copynumber: 3.1 Consensus size: 63
6310 TAAAGTAGAC
6320 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
*
6383 ACCTCCACACGCCATGCACCATCGTTATCACGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
*
6446 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATATCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
6509 ACCTC
1 ACCTC
6514 ATCACGTAAC
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 128 1.00
ACGTcount: A:0.25, C:0.37, G:0.18, T:0.21
Consensus pattern (63 bp):
ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:8017 original size:19 final size:19
Alignment explanation
Indices: 7966--8110 Score: 139
Period size: 19 Copynumber: 8.1 Consensus size: 19
7956 TCTTTTGGTT
*
7966 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
7985 GATAATGAGAATCGCAACGG
1 GA-AATGAAAATCGCAACGC
**
8005 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
8022 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
8038 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
8057 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
8074 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
8090 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
8109 GA
1 GA
8111 TTTTGGTTTC
Statistics
Matches: 104, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
14 19 0.18
15 2 0.02
16 4 0.04
17 3 0.03
18 2 0.02
19 57 0.55
20 17 0.16
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:8033 original size:33 final size:33
Alignment explanation
Indices: 7991--8055 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
7981 ACGAGATAAT
* **
7991 GAGAATCGCAACGGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
8024 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGAAAATCGCAACG
8056 CGAAATGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.22, G:0.26, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:8050 original size:52 final size:52
Alignment explanation
Indices: 7974--8110 Score: 211
Period size: 52 Copynumber: 2.6 Consensus size: 52
7964 TTGAAATGAA
* * * **
7974 AATCGCAACGAGATAATGAGAATCGCAACGGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
8027 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
8079 AATCGCAACGCGAAATGAAAATCGCAATGCGA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGA
8111 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
52 66 0.85
53 12 0.15
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:8719 original size:20 final size:20
Alignment explanation
Indices: 8694--8746 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
8684 GCGCTATGTA
8694 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
8714 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
8734 TATCTCGTTGCGA
1 AATCGCGTTGCGA
8747 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:8780 original size:20 final size:20
Alignment explanation
Indices: 8755--8808 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
8745 GATTTTGTAT
8755 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
8775 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
8795 TATCGCATTGCGAT
1 TATCGCATTGCGAT
8809 TTTTCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:8793 original size:61 final size:61
Alignment explanation
Indices: 8695--8811 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
8685 CGCTATGTAA
* * * * *
8695 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
8756 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
8812 TCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:8827 original size:61 final size:61
Alignment explanation
Indices: 8690--8829 Score: 160
Period size: 61 Copynumber: 2.3 Consensus size: 61
8680 AATGGCGCTA
* * * * *
8690 TGTAA-ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
* * * *
8750 TGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
8811 T-TCCAAT-TCGCGTTGCGAT
1 TGT--AATATCGCGTTGCGAT
8830 TTACTTATTC
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
60 5 0.08
61 59 0.89
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
Found at i:10073 original size:16 final size:16
Alignment explanation
Indices: 10052--10082 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10042 TTATCATTCA
*
10052 TTAATTTGAGTTAAAT
1 TTAATTCGAGTTAAAT
10068 TTAATTCGAGTTAAA
1 TTAATTCGAGTTAAA
10083 ATCTAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (16 bp):
TTAATTCGAGTTAAAT
Found at i:12162 original size:5 final size:5
Alignment explanation
Indices: 12147--12267 Score: 71
Period size: 5 Copynumber: 24.6 Consensus size: 5
12137 GATATAGGAA
* *
12147 AAAAT ATAAT AAAAT AAAGAT AACAAGT -AAAT AAAAT -AAAG AAAAT
1 AAAAT AAAAT AAAAT AAA-AT AA-AA-T AAAAT AAAAT AAAAT AAAAT
* *
12193 GAAAAT AAAGA- AACAT -AAAT AAAAT AACTAA- AAAAT -AAAG AAAAT
1 -AAAAT AAA-AT AAAAT AAAAT AAAAT AA--AAT AAAAT AAAAT AAAAT
*
12238 -AAAT -AAAT AAAAT -AAAC AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
12268 CAAGATGAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
4 24 0.26
5 49 0.54
6 14 0.15
7 4 0.04
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:12214 original size:29 final size:28
Alignment explanation
Indices: 12175--12291 Score: 94
Period size: 29 Copynumber: 3.9 Consensus size: 28
12165 GATAACAAGT
*
12175 AAATAAAATAAAGAAAAT-GAAAATAAAGA
1 AAAT-AAATAAA-AAAATAAAAAATAAAGA
*
12204 AACATAAATAAAATAACTAAAAAATAAAGA
1 AA-ATAAATAAAA-AAATAAAAAATAAAGA
12234 AAATAAATAAATAAAATAAACAAAATAAA-A
1 AAATAAATAAA-AAAAT-AA-AAAATAAAGA
* * *
12264 TAAACAAGATGAAAAGATAAAAAATAAA
1 -AAATAA-ATAAAAAAATAAAAAATAAA
12292 AACAAGAAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
28 1 0.01
29 32 0.43
30 20 0.27
31 17 0.23
32 4 0.05
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.15
Consensus pattern (28 bp):
AAATAAATAAAAAAATAAAAAATAAAGA
Found at i:12250 original size:9 final size:9
Alignment explanation
Indices: 12147--12527 Score: 93
Period size: 9 Copynumber: 41.3 Consensus size: 9
12137 GATATAGGAA
12147 AAAATATAAT
1 AAAATA-AAT
12157 AAAATAAAGAT
1 AAAAT-AA-AT
12168 AACAAGTAAAT
1 AA-AA-TAAAT
*
12179 AAAATAAAG
1 AAAATAAAT
*
12188 AAAAT---G
1 AAAATAAAT
*
12194 AAAATAAAG
1 AAAATAAAT
12203 AAACATAAAT
1 AAA-ATAAAT
*
12213 AAAATAACT
1 AAAATAAAT
12222 -AAA-AAAT
1 AAAATAAAT
12229 AAAGA-AAAT
1 AAA-ATAAAT
12238 -AAATAAAT
1 AAAATAAAT
*
12246 AAAATAAAC
1 AAAATAAAT
12255 AAAATAAAAT
1 AAAAT-AAAT
*
12265 AAACA-AGAT
1 AAA-ATAAAT
* *
12274 GAAA-AGAT
1 AAAATAAAT
12282 -AAA-AAAT
1 AAAATAAAT
*
12289 AAAA-ACAAG
1 AAAATA-AAT
12298 AAAA-AAAT
1 AAAATAAAT
*
12306 GAAATAAAT
1 AAAATAAAT
**
12315 AAAATATAGG
1 AAAATA-AAT
*
12325 AAAATCATAGT
1 AAAAT-A-AAT
12336 AAAA-AGAAT
1 AAAATA-AAT
**
12345 -ATGTAAAT
1 AAAATAAAT
12353 -AAATAAAT
1 AAAATAAAT
**
12361 AAAAGCAAT
1 AAAATAAAT
*
12370 AAGA-AAAT
1 AAAATAAAT
*
12378 AAAAATAGAT
1 -AAAATAAAT
12388 -AAATAAAT
1 AAAATAAAT
*
12396 AGAATATATAT
1 A-AA-ATAAAT
* *
12407 GAAGA-AAAC
1 -AAAATAAAT
*
12416 AAAATAATAA
1 AAAATAA-AT
12426 AAATATATATAT
1 AAA-ATA-A-AT
12438 AAAATAATGAT
1 AAAATAA--AT
12449 ATAAA-AATAT
1 A-AAATAA-AT
*
12459 ATAATAGAAT
1 AAAATA-AAT
12469 AAAATAAA-
1 AAAATAAAT
*
12477 AAAATTAAT
1 AAAATAAAT
*
12486 AATATAAAT
1 AAAATAAAT
*
12495 AAACATAAAGAA
1 AAA-AT-AA-AT
*
12507 AAAATATAT
1 AAAATAAAT
12516 AAAATAAAT
1 AAAATAAAT
12525 AAA
1 AAA
12528 TGAAAAAATA
Statistics
Matches: 284, Mismatches: 48, Indels: 79
0.69 0.12 0.19
Matches are distributed among these distances:
6 6 0.02
7 10 0.04
8 55 0.19
9 101 0.36
10 53 0.19
11 40 0.14
12 18 0.06
13 1 0.00
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.20
Consensus pattern (9 bp):
AAAATAAAT
Found at i:12261 original size:14 final size:13
Alignment explanation
Indices: 12147--12320 Score: 88
Period size: 14 Copynumber: 12.5 Consensus size: 13
12137 GATATAGGAA
12147 AAAATATAATAAAAT
1 AAAATA-AA-AAAAT
12162 AAAGATAACAAGTAAAT
1 AAA-ATAA-AA--AAAT
12179 AAAATAAAGAAAAT
1 AAAATAAA-AAAAT
12193 GAAAATAAAGAAACAT
1 -AAAATAAA-AAA-AT
*
12209 -AAATAAAATAACT
1 AAAATAAAA-AAAT
* *
12222 -AAA-AAATAAAG
1 AAAATAAAAAAAT
*
12233 AAAATAAATAAAT
1 AAAATAAAAAAAT
12246 AAAATAAACAAAAT
1 AAAATAAA-AAAAT
*
12260 AAAATAAACAAGAT
1 AAAATAAA-AAAAT
*
12274 GAAAAGATAAAAAAT
1 -AAAATA-AAAAAAT
*
12289 AAAA-ACAAGAAA-
1 AAAATA-AAAAAAT
*
12301 AAAATGAAATAAAT
1 AAAAT-AAAAAAAT
12315 AAAATA
1 AAAATA
12321 TAGGAAAATC
Statistics
Matches: 131, Mismatches: 12, Indels: 34
0.74 0.07 0.19
Matches are distributed among these distances:
11 2 0.02
12 10 0.08
13 32 0.24
14 40 0.31
15 27 0.21
16 13 0.10
17 7 0.05
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.16
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:12304 original size:26 final size:26
Alignment explanation
Indices: 12265--12318 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
12255 AAAATAAAAT
**
12265 AAACAAGATGAAAA-GATAAAAAATAA
1 AAACAAGAAAAAAATGA-AAAAAATAA
*
12291 AAACAAGAAAAAAATGAAATAAATAA
1 AAACAAGAAAAAAATGAAAAAAATAA
12317 AA
1 AA
12319 TATAGGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (26 bp):
AAACAAGAAAAAAATGAAAAAAATAA
Found at i:12441 original size:13 final size:13
Alignment explanation
Indices: 12425--12461 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
12415 CAAAATAATA
12425 AAAATATATATAT
1 AAAATATATATAT
12438 AAAATA-ATGATAT
1 AAAATATAT-ATAT
12451 AAAA-ATATATA
1 AAAATATATATA
12462 ATAGAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (13 bp):
AAAATATATATAT
Found at i:12441 original size:27 final size:26
Alignment explanation
Indices: 12411--12544 Score: 86
Period size: 27 Copynumber: 5.1 Consensus size: 26
12401 ATATATGAAG
12411 AAAACAAAATAATAAAAATATATATAT
1 AAAA-AAAATAATAAAAATATATATAT
*
12438 -AAAATAATGATATAAAAATATATA-AT
1 AAAAAAAAT-A-ATAAAAATATATATAT
*
12464 AGAATAAAATAA-AAAAAT-TAATAATAT
1 A-AAAAAAATAATAAAAATAT-AT-ATAT
*
12491 AAATAAACATAA-AGAAAA-A-ATATAT
1 AAA-AAAAATAATA-AAAATATATATAT
*
12516 AAAATAAATAAATGAAAAA-ATATATAT
1 AAAAAAAAT-AAT-AAAAATATATATAT
12543 AA
1 AA
12545 TTATTTATAT
Statistics
Matches: 86, Mismatches: 7, Indels: 28
0.71 0.06 0.23
Matches are distributed among these distances:
24 5 0.06
25 21 0.24
26 17 0.20
27 33 0.38
28 10 0.12
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (26 bp):
AAAAAAAATAATAAAAATATATATAT
Found at i:12479 original size:25 final size:25
Alignment explanation
Indices: 12401--12527 Score: 107
Period size: 27 Copynumber: 4.9 Consensus size: 25
12391 TAAATAGAAT
* *
12401 ATATATGAAGAAAACAAAATAATAAAA
1 ATATAT-AATAAAATAAAATAA-AAAA
* *
12428 ATATATATATAAAATAATGATATAAAA
1 ATATATA-ATAAAATAA-AATAAAAAA
*
12455 ATATATAATAGAATAAAATAAAAAA
1 ATATATAATAAAATAAAATAAAAAA
12480 AT-TAATAATATAAATAAACATAAAGAAA
1 ATAT-ATAATA-AAATAAA-ATAAA-AAA
*
12508 AAATAT-ATAAAAT-AAATAAA
1 ATATATAATAAAATAAAATAAA
12528 TGAAAAAATA
Statistics
Matches: 84, Mismatches: 9, Indels: 17
0.76 0.08 0.15
Matches are distributed among these distances:
24 6 0.07
25 17 0.20
26 19 0.23
27 32 0.38
28 9 0.11
29 1 0.01
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (25 bp):
ATATATAATAAAATAAAATAAAAAA
Found at i:12532 original size:25 final size:25
Alignment explanation
Indices: 12424--12541 Score: 82
Period size: 25 Copynumber: 4.4 Consensus size: 25
12414 ACAAAATAAT
*
12424 AAAAATATAT-ATATAAA-ATAATGA
1 AAAAATATATAAAATAAATA-AATGA
* *
12448 TATAAAA-ATATATAATAGAATAAAATAA
1 -A-AAAATATATAAAATA-AAT-AAATGA
12476 AAAAATTAATAATATAAATAAACATAAA-GA
1 AAAAA-T-AT-ATA-AAAT-AA-ATAAATGA
12506 AAAAATATATAAAATAAATAAATGA
1 AAAAATATATAAAATAAATAAATGA
12531 AAAAATATATA
1 AAAAATATATA
12542 TAATTATTTA
Statistics
Matches: 75, Mismatches: 5, Indels: 26
0.71 0.05 0.25
Matches are distributed among these distances:
24 5 0.07
25 20 0.27
26 15 0.20
27 6 0.08
28 6 0.08
29 4 0.05
30 9 0.12
31 7 0.09
32 3 0.04
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.26
Consensus pattern (25 bp):
AAAAATATATAAAATAAATAAATGA
Found at i:13350 original size:21 final size:21
Alignment explanation
Indices: 13315--13410 Score: 147
Period size: 21 Copynumber: 4.5 Consensus size: 21
13305 TTTCCAGAAC
*
13315 GCTACAAGGGTATCGATACCCT
1 GCTAC-AGTGTATCGATACCCT
13337 GCTACAGTGTATCGATACCCT
1 GCTACAGTGTATCGATACCCT
*
13358 ACTACAGTGTATCGATACCCT
1 GCTACAGTGTATCGATACCCT
*
13379 GCTACAGTGTACCGATACCCTT
1 GCTACAGTGTATCGATACCC-T
13401 GCTACAGTGT
1 GCTACAGTGT
13411 TTTCGGTCCA
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
21 53 0.77
22 16 0.23
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (21 bp):
GCTACAGTGTATCGATACCCT
Found at i:13964 original size:22 final size:22
Alignment explanation
Indices: 13936--13996 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
13926 GGCATGTGAA
* *
13936 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCTGAAGGACCTATGT
*
13958 ATTTGTCCTGAAGGACCTCTGT
1 ATTTGTCCTGAAGGACCTATGT
*
13980 ATATGTCCTGAAGGACC
1 ATTTGTCCTGAAGGACC
13997 GCGTAGACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (22 bp):
ATTTGTCCTGAAGGACCTATGT
Found at i:14972 original size:24 final size:26
Alignment explanation
Indices: 14931--14978 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
14921 TTCCATAAAT
*
14931 TCATTTATAAACTCCTTCA-CTTTAA
1 TCATTCATAAACTCCTTCATCTTTAA
*
14956 TCATTCAT-AACTTCTTCATCTTT
1 TCATTCATAAACTCCTTCATCTTT
14979 TGATTATAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.27, C:0.25, G:0.00, T:0.48
Consensus pattern (26 bp):
TCATTCATAAACTCCTTCATCTTTAA
Found at i:16644 original size:110 final size:115
Alignment explanation
Indices: 16509--17047 Score: 424
Period size: 124 Copynumber: 4.5 Consensus size: 115
16499 CTGGAAAGCT
* *
16509 CATTCGCTGTGAAGTTGAGCTTTGAATTGGATATCCTTTGTTGTGAAGTTGAAATCCAATCTA-G
1 CATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTTGTTGTGAAGTTGAAATCCAATCTAGG
* *
16573 A-G-T-T-GGCACAATATCAATT-GTCATGAAGTTGAAATTATGGATGGCC
66 ATGTTGTGGGCACAATATC-ATTCGTCATGAAGTTGAAATCATGAATGGCC
* * * *
16619 CCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTTTTGAAGTTAAAATCCAATCTAAA
1 CATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTTGTTGTGAAGTTGAAATCCAATCT---
* * * *
16684 GAGGGATGTTATTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGAATGGCC
63 -A-GGATG---TT-GTGGGCACAATATCATTCGTCATGAAGTTGAAATCATGAATGGCC
* * *
16743 CATTCGTTGTGAAGTTGAGCCTTGAATTGGATATACTTTGTCGTGAAGTTGATATCCAATCTAAA
1 CATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTTGTTGTGAAGTTGAAATCCAATCT--A
* * * * * *
16808 GATGAATGTTGTTGGTGGGCACGATATCCTTCGTCTTGAAGTTGAAATCGTGGATGACC
64 G--G-A---TGTT-GTGGGCACAATATCATTCGTCATGAAGTTGAAATCATGAATGGCC
* * * * *
16867 CATTCGTTGTGAATTTGAGCCTTTAATTAGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAA
1 CATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTTGTTGTGAAGTTGAAATCCAATCT--A
* ** *** * * *
16932 GATCAATGTTGCTGGTGGGCATGATATCCCACGTCGTGAAGTTGAAATCGTGGATGGCC
64 G---GATG-T--T-GTGGGCACAATATCATTCGTCATGAAGTTGAAATCATGAATGGCC
* * * * *
16991 CCTTTGTTGTGAAGTTGAGCCTTGTATTGGATATCCTTCGTTGTGAAGTTAAAATCC
1 CATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTTGTTGTGAAGTTGAAATCC
17048 TAGGGTTGTT
Statistics
Matches: 359, Mismatches: 45, Indels: 36
0.82 0.10 0.08
Matches are distributed among these distances:
110 56 0.16
114 1 0.00
116 2 0.01
117 1 0.00
121 4 0.01
122 3 0.01
123 4 0.01
124 286 0.80
127 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (115 bp):
CATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTTGTTGTGAAGTTGAAATCCAATCTAGG
ATGTTGTGGGCACAATATCATTCGTCATGAAGTTGAAATCATGAATGGCC
Found at i:16800 original size:124 final size:124
Alignment explanation
Indices: 16596--17047 Score: 652
Period size: 124 Copynumber: 3.6 Consensus size: 124
16586 TCAATTGTCA
** * *
16596 TGAAGTTGAAATTATGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTT
1 TGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTC
* * * * *
16661 TTGAAGTTAAAATCCAATCTAAAGAGGGATGTTATTGGTGGGCACGATATCCTTCGTCG
66 GTGAAGTTGAAATCCAATCTAAAGATGAATGTTGTTGGTGGGCACGATATCCTTCGTCG
* * *
16720 TGAAGTTGAAATCGTGAATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATACTTTGTC
1 TGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTC
* *
16785 GTGAAGTTGATATCCAATCTAAAGATGAATGTTGTTGGTGGGCACGATATCCTTCGTCT
66 GTGAAGTTGAAATCCAATCTAAAGATGAATGTTGTTGGTGGGCACGATATCCTTCGTCG
* * * *
16844 TGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAATTTGAGCCTTTAATTAGATATCCTTCGTC
1 TGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTC
* * * **
16909 GTGAAGTTGAAATCCAATCTAAAGATCAATGTTGCTGGTGGGCATGATATCCCACGTCG
66 GTGAAGTTGAAATCCAATCTAAAGATGAATGTTGTTGGTGGGCACGATATCCTTCGTCG
* * * *
16968 TGAAGTTGAAATCGTGGATGGCCCCTTTGTTGTGAAGTTGAGCCTTGTATTGGATATCCTTCGTT
1 TGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTC
*
17033 GTGAAGTTAAAATCC
66 GTGAAGTTGAAATCC
17048 TAGGGTTGTT
Statistics
Matches: 291, Mismatches: 37, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
124 291 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (124 bp):
TGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTC
GTGAAGTTGAAATCCAATCTAAAGATGAATGTTGTTGGTGGGCACGATATCCTTCGTCG
Found at i:17275 original size:64 final size:64
Alignment explanation
Indices: 17196--17492 Score: 486
Period size: 64 Copynumber: 4.6 Consensus size: 64
17186 TTGTGTCGCT
* * * *
17196 TTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGACTAAAACTAGAAAGTTGTTTG
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG
* *
17260 TTAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAATTGGAAAGTTGTTTG
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG
*
17324 TTGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG
*
17388 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAGCTGGAAAGTTGTTTG
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG
* * * *
17452 TTGATTCCAATATCATTCGCTGTAAAGTTGAAATTGACTCT
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
17493 AAAAGCTGCA
Statistics
Matches: 218, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 218 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (64 bp):
TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG
Found at i:25457 original size:55 final size:55
Alignment explanation
Indices: 24962--25456 Score: 511
Period size: 55 Copynumber: 8.9 Consensus size: 55
24952 TCTTCGAATG
* * * **
24962 ACGGGTCCGCTCCCCATTCTTTCA-AGGAGTATAAGACTCGAACAATCTTCAGTAA
1 ACGGGTCCGCTCTCTATTCCTTCAGA-GAGTATAAGACTCGAACAATCTTCAACAA
* * * * * * *
25017 ACGTGTCTGCTCCCTATTCATTCAGGGAGAATAAGACTCGAACAATCTTCAATAA
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAA
* *
25072 ACGGGTCCGCTCTCTATTCCTTTAGAGAGTAT-AGAACTTGAACAATCTTCAACAA
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAA
* * * *
25127 ACGAGTCCGCTCTCTATTCCTTGAGAGAGTATAGGACTCGAACAATTTTCAACAA
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAA
* *
25182 ATGGGCCCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAACAA
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAA
** *
25237 ACGATTCCGCTCTCTATTCCTTGAGAGAGTAT-AGAACTCGAACAATCTTCAACAA
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAA
* * * * *
25292 ACGGGTATGCTCCCTCCCTATT-CTATCAGAGAGTATAGGACTCAAAAAATCTTCAACAA
1 ACGGG--T-C-CGCTCTCTATTCCT-TCAGAGAGTATAAGACTCGAACAATCTTCAACAA
* ** *
25351 ACGGGTCCGTTCTCTATTCCTTCAGAGAGTATGGGACTTGAACAATCTTCATA-AA
1 ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCA-ACAA
* * *
25406 ACGGGTCTGCTC-CTTATTCGTTCA-AGGAGTATAATACTCGAACAATCTTCA
1 ACGGGTCCGCTCTC-TATTCCTTCAGA-GAGTATAAGACTCGAACAATCTTCA
25457 TTTTCTTCAC
Statistics
Matches: 372, Mismatches: 54, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
54 5 0.01
55 314 0.84
56 5 0.01
57 2 0.01
58 3 0.01
59 42 0.11
60 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (55 bp):
ACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAA
Found at i:25511 original size:37 final size:37
Alignment explanation
Indices: 25456--25533 Score: 120
Period size: 37 Copynumber: 2.1 Consensus size: 37
25446 AACAATCTTC
* * * *
25456 ATTTTCTTCACTACTCTTCTGTGAATGCTTCAGTTTG
1 ATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTG
25493 ATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTG
1 ATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTG
25530 ATTT
1 ATTT
25534 ATTTCGAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.46
Consensus pattern (37 bp):
ATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTG
Found at i:26820 original size:7 final size:7
Alignment explanation
Indices: 26804--26984 Score: 66
Period size: 7 Copynumber: 23.9 Consensus size: 7
26794 TCACCTTTTA
26804 TTTC-TT
1 TTTCTTT
26810 TTTCTTT
1 TTTCTTT
26817 TTTCATCATCT
1 TTTC-T--T-T
26828 TTT-TTT
1 TTTCTTT
26834 TTTC-TT
1 TTTCTTT
*
26840 TTTCGTT
1 TTTCTTT
26847 TTTCTTT
1 TTTCTTT
26854 TCATT-TTT
1 T--TTCTTT
* *
26862 CTTCATT
1 TTTCTTT
26869 TTTCATTT
1 TTTC-TTT
26877 TTT-TTT
1 TTTCTTT
*
26883 CTTCATTT
1 TTTC-TTT
26891 TTTCTTT
1 TTTCTTT
*
26898 TCATTTTTT
1 T--TTCTTT
*
26907 TATTATTTT
1 T-TT-CTTT
*
26916 TTTCATT
1 TTTCTTT
26923 TTTCATTT
1 TTTC-TTT
26931 TCTTCATTT
1 T-TTC-TTT
*
26940 TCTTCATT
1 T-TTCTTT
26948 TTTCGTTT
1 TTTC-TTT
26956 TTCTCTTT
1 TT-TCTTT
*
26964 TTCCTTT
1 TTTCTTT
26971 TTTCATTT
1 TTTC-TTT
*
26979 CTTCTT
1 TTTCTT
26985 CAAGTGAAAT
Statistics
Matches: 138, Mismatches: 16, Indels: 41
0.71 0.08 0.21
Matches are distributed among these distances:
6 21 0.15
7 43 0.31
8 41 0.30
9 28 0.20
10 1 0.01
11 4 0.03
ACGTcount: A:0.08, C:0.17, G:0.01, T:0.75
Consensus pattern (7 bp):
TTTCTTT
Found at i:26839 original size:11 final size:11
Alignment explanation
Indices: 26825--26925 Score: 62
Period size: 11 Copynumber: 8.6 Consensus size: 11
26815 TTTTTCATCA
26825 TCTTTTTTTTT
1 TCTTTTTTTTT
26836 TCTTTTTCGTTTT
1 TCTTTTT--TTTT
*
26849 TCTTTTCATTTT
1 TCTTTT-TTTTT
**
26861 TC-TTCATTTT
1 TCTTTTTTTTT
*
26871 TCATTTTTTTT
1 TCTTTTTTTTT
**
26882 TCTTCATTTTT
1 TCTTTTTTTTT
26893 TCTTTTCATTTTT
1 TCTTTT--TTTTT
26906 T-TATTATTTTTT
1 TCT-TT-TTTTTT
26918 TCATTTTT
1 TC-TTTTT
26926 CATTTTCTTC
Statistics
Matches: 71, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
10 7 0.10
11 27 0.38
12 15 0.21
13 20 0.28
14 2 0.03
ACGTcount: A:0.08, C:0.13, G:0.01, T:0.78
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:26848 original size:13 final size:13
Alignment explanation
Indices: 26804--26984 Score: 72
Period size: 13 Copynumber: 13.0 Consensus size: 13
26794 TCACCTTTTA
26804 TTTC-TTTTTCTTT
1 TTTCATTTTTC-TT
**
26817 TTTCA-TCATCTT
1 TTTCATTTTTCTT
26829 TTT--TTTTTCTT
1 TTTCATTTTTCTT
*
26840 TTTCGTTTTTC-T
1 TTTCATTTTTCTT
26852 TTTCATTTTTCTTCATT
1 TTTCA--TTT-TTC-TT
*
26869 TTTCATTTTTTTT
1 TTTCATTTTTCTT
26882 TCTTCATTTTT-TCT
1 T-TTCATTTTTCT-T
26896 TTTCATTTTT-TT
1 TTTCATTTTTCTT
*
26908 ATTAT-TTTTTTCATT
1 -TT-TCATTTTTC-TT
26923 TTTCATTTTCTTCATTT
1 TTTCA-TTT-TTC--TT
26940 TCTTCATTTTTCGTT
1 T-TTCATTTTTC-TT
*
26955 TTTCTCTTTTTCCTTT
1 TTTC-ATTTTT-C-TT
26971 TTTCATTTCTTCTT
1 TTTCATTT-TTCTT
26985 CAAGTGAAAT
Statistics
Matches: 132, Mismatches: 13, Indels: 45
0.69 0.07 0.24
Matches are distributed among these distances:
11 8 0.06
12 11 0.08
13 35 0.27
14 24 0.18
15 23 0.17
16 15 0.11
17 12 0.09
18 4 0.03
ACGTcount: A:0.08, C:0.17, G:0.01, T:0.75
Consensus pattern (13 bp):
TTTCATTTTTCTT
Found at i:26879 original size:9 final size:9
Alignment explanation
Indices: 26851--26950 Score: 54
Period size: 9 Copynumber: 11.2 Consensus size: 9
26841 TTCGTTTTTC
26851 TTTTCATTT
1 TTTTCATTT
26860 TTCTTCA--T
1 TT-TTCATTT
26868 TTTTCATTT
1 TTTTCATTT
26877 TTTT--TTCT
1 TTTTCATT-T
26885 TCATTT--TTT
1 T--TTTCATTT
26894 CTTTTCATTTT
1 -TTTTCA-TTT
*
26905 TTTATTATTT
1 TTT-TCATTT
26915 TTTTCA--T
1 TTTTCATTT
26922 TTTTCATTT
1 TTTTCATTT
*
26931 TCTTCATTT
1 TTTTCATTT
*
26940 TCTTCATTT
1 TTTTCATTT
26949 TT
1 TT
26951 CGTTTTTCTC
Statistics
Matches: 74, Mismatches: 4, Indels: 26
0.71 0.04 0.25
Matches are distributed among these distances:
7 13 0.18
8 8 0.11
9 29 0.39
10 19 0.26
11 5 0.07
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTCATTT
Found at i:26879 original size:25 final size:24
Alignment explanation
Indices: 26851--26986 Score: 108
Period size: 23 Copynumber: 5.7 Consensus size: 24
26841 TTCGTTTTTC
26851 TTTTCATTTTTCTTCATTTTTCA-
1 TTTTCATTTTTCTTCATTTTTCAT
26874 TTTT--TTTTTCTTCATTTTT--T
1 TTTTCATTTTTCTTCATTTTTCAT
* *
26894 CTTTTCATTTTTTTATTATTTTTTTCAT
1 -TTTTCATTTTTCT-TCA--TTTTTCAT
26922 TTTTCA-TTTTCTTCATTTTCTTCAT
1 TTTTCATTTTTCTTCA-TTT-TTCAT
* *
26947 TTTTCGTTTTTC-TC-TTTTTCCTT
1 TTTTCATTTTTCTTCATTTTT-CAT
26970 TTTTCATTTCTTCTTCA
1 TTTTCATTT-TTCTTCA
26987 AGTGAAATAT
Statistics
Matches: 91, Mismatches: 7, Indels: 27
0.73 0.06 0.22
Matches are distributed among these distances:
21 19 0.21
22 2 0.02
23 23 0.25
24 9 0.10
25 16 0.18
26 15 0.16
27 6 0.07
28 1 0.01
ACGTcount: A:0.10, C:0.17, G:0.01, T:0.73
Consensus pattern (24 bp):
TTTTCATTTTTCTTCATTTTTCAT
Found at i:26881 original size:49 final size:52
Alignment explanation
Indices: 26822--26959 Score: 140
Period size: 54 Copynumber: 2.6 Consensus size: 52
26812 TCTTTTTTCA
*
26822 TCATCTTTTTTTTTTC-TTTTTCGTTTTTCTTTTCA-T-TTTTCTTCATTTT
1 TCATTTTTTTTTTTTCATTTTTCGTTTTTCTTTTCATTATTTTCTTCATTTT
* * * *
26871 TCATTTTTTTTTCTTCATTTTTTC-TTTTCATTTTTTTATTATTTTTTTCATTTT
1 TCATTTTTTTTTTTTCA-TTTTTCGTTTT--TCTTTTCATTATTTTCTTCATTTT
26925 TCATTTTCTTCATTTTCTTCATTTTTCGTTTTTCT
1 TCATTTT-TT--TTTT-TTCATTTTTCGTTTTTCT
26960 CTTTTTCCTT
Statistics
Matches: 71, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
49 14 0.20
50 4 0.06
51 6 0.08
52 6 0.08
53 1 0.01
54 19 0.27
55 2 0.03
56 2 0.03
57 9 0.13
58 8 0.11
ACGTcount: A:0.09, C:0.15, G:0.01, T:0.75
Consensus pattern (52 bp):
TCATTTTTTTTTTTTCATTTTTCGTTTTTCTTTTCATTATTTTCTTCATTTT
Found at i:41111 original size:16 final size:15
Alignment explanation
Indices: 41076--41114 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
41066 AATAAAAAAG
41076 GAAATAAAAACAAAC
1 GAAATAAAAACAAAC
* *
41091 AAAATATAAAACAAAT
1 GAAATA-AAAACAAAC
41107 GAAATAAA
1 GAAATAAA
41115 GAAGATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (15 bp):
GAAATAAAAACAAAC
Found at i:41188 original size:5 final size:5
Alignment explanation
Indices: 41178--41320 Score: 63
Period size: 5 Copynumber: 29.0 Consensus size: 5
41168 GATAACAAGT
*
41178 AAATA AAAT- AAACA AAATGA AAATA AAA-A AACA-A AAATA AAA-A AACA-A
1 AAATA AAATA AAATA AAAT-A AAATA AAATA AA-ATA AAATA AAATA AA-ATA
* * * *
41226 AGAAAA CAAAT- AAATA AAAT- AAACA AAATA AAATA AAAT- AAACA AGATA
1 A-AATA -AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
* * * *
41275 AAA-A GAATAA AAATA AAGACA AGAAAA AAATG AAAT- AAATA AAATA
1 AAATA AAAT-A AAATA AA-ATA A-AATA AAATA AAATA AAATA AAATA
41321 TAAGAAAATC
Statistics
Matches: 107, Mismatches: 15, Indels: 32
0.69 0.10 0.21
Matches are distributed among these distances:
4 27 0.25
5 59 0.55
6 19 0.18
7 2 0.02
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.13
Consensus pattern (5 bp):
AAATA
Found at i:41208 original size:14 final size:13
Alignment explanation
Indices: 41178--41291 Score: 84
Period size: 14 Copynumber: 7.9 Consensus size: 13
41168 GATAACAAGT
41178 AAATAAAATAAACA
1 AAATAAAATAAA-A
41192 AAATGAAAATAAAA
1 AAAT-AAAATAAAA
*
41206 AAACAAAAATAAAA
1 AAA-TAAAATAAAA
* *
41220 AAACAAAGAAAACAAA
1 AAA-TAA-AATA-AAA
41236 TAAATAAAATAAACA
1 -AAATAAAATAAA-A
41251 AAATAAAATAAAA
1 AAATAAAATAAAA
* *
41264 TAAACAAGATAAAA
1 -AAATAAAATAAAA
41278 AGAATAAAAATAAA
1 A-AAT-AAAATAAA
41292 GACAAGAAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
13 2 0.02
14 51 0.61
15 22 0.27
16 5 0.06
17 3 0.04
ACGTcount: A:0.79, C:0.05, G:0.04, T:0.12
Consensus pattern (13 bp):
AAATAAAATAAAA
Found at i:41234 original size:59 final size:59
Alignment explanation
Indices: 41151--41278 Score: 179
Period size: 59 Copynumber: 2.2 Consensus size: 59
41141 AGATATAGGG
* * * * *
41151 AAAAATAATAAAATAAGGATAACAAGTAAATAAAATAAACAAAATGAAAATAAAA-AAAC
1 AAAAATAAAAAAACAAAGAAAACAAATAAATAAAATAAACAAAAT-AAAATAAAATAAAC
41210 AAAAATAAAAAAACAAAGAAAACAAATAAATAAAATAAACAAAATAAAATAAAATAAAC
1 AAAAATAAAAAAACAAAGAAAACAAATAAATAAAATAAACAAAATAAAATAAAATAAAC
*
41269 -AAGATAAAAA
1 AAAAATAAAAA
41279 GAATAAAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
58 18 0.29
59 44 0.71
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.13
Consensus pattern (59 bp):
AAAAATAAAAAAACAAAGAAAACAAATAAATAAAATAAACAAAATAAAATAAAATAAAC
Found at i:41287 original size:9 final size:9
Alignment explanation
Indices: 41177--41285 Score: 63
Period size: 9 Copynumber: 12.4 Consensus size: 9
41167 GGATAACAAG
*
41177 TAAATAAAA
1 TAAACAAAA
41186 TAAACAAAA
1 TAAACAAAA
41195 TGAAA-ATAAA
1 T-AAACA-AAA
*
41205 -AAA-ACAA
1 TAAACAAAA
*
41212 -AAATAAAA
1 TAAACAAAA
41220 -AAACAAAGA
1 TAAACAAA-A
41229 -AAAC-AAA
1 TAAACAAAA
*
41236 TAAATAAAA
1 TAAACAAAA
41245 TAAACAAAA
1 TAAACAAAA
*
41254 TAAAATAAAA
1 T-AAACAAAA
*
41264 TAAACAAGA
1 TAAACAAAA
41273 TAAA-AAGAA
1 TAAACAA-AA
41282 TAAA
1 TAAA
41286 AATAAAGACA
Statistics
Matches: 82, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
7 6 0.07
8 20 0.24
9 42 0.51
10 14 0.17
ACGTcount: A:0.78, C:0.06, G:0.04, T:0.13
Consensus pattern (9 bp):
TAAACAAAA
Found at i:41303 original size:26 final size:25
Alignment explanation
Indices: 41250--41318 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
41240 TAAAATAAAC
* *
41250 AAAATAAAATAAAAT-AAACAAGATA
1 AAAATGAAA-AAAATAAAACAAGAAA
41275 AAAA-GAATAAAAATAAAGACAAGAAA
1 AAAATGAA-AAAAATAAA-ACAAGAAA
*
41301 AAAATGAAATAAATAAAA
1 AAAATGAAAAAAATAAAA
41319 TATAAGAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
24 7 0.19
25 8 0.22
26 19 0.51
27 3 0.08
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (25 bp):
AAAATGAAAAAAATAAAACAAGAAA
Found at i:41362 original size:4 final size:4
Alignment explanation
Indices: 41353--41536 Score: 60
Period size: 4 Copynumber: 43.8 Consensus size: 4
41343 ATATGTACAT
*
41353 AATA AATA AATA AATA AA-A GCAATA AGA-A AATAA AATA GATA AATA
1 AATA AATA AATA AATA AATA --AATA A-ATA AAT-A AATA AATA AATA
* * * *
41399 AATA TAATA TATATA AAGA AA-A CA-A AAT- AATA AAAA TAATA CATA
1 AATA -AATA -A-ATA AATA AATA AATA AATA AATA AATA -AATA AATA
* * * *
41444 TATA TATA TATA TAATA ATGATA TAA-A AATA TATA TAATA GAATAA AATA
1 AATA AATA AATA -AATA A--ATA -AATA AATA AATA -AATA -AAT-A AATA
* *
41494 AATA AATA AATA AATA ACA-G AA-A AATA TATAA AATA AATA AAT
1 AATA AATA AATA AATA A-ATA AATA AATA AAT-A AATA AATA AAT
41537 GAAAAAAAGA
Statistics
Matches: 142, Mismatches: 17, Indels: 42
0.71 0.08 0.21
Matches are distributed among these distances:
3 14 0.10
4 85 0.60
5 34 0.24
6 8 0.06
7 1 0.01
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:41458 original size:21 final size:22
Alignment explanation
Indices: 41449--41502 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
41439 ACATATATAT
41449 ATATATATAATAATGATATAAA
1 ATATATATAATAATGATATAAA
41471 A-ATATAT-ATAATAGA-ATAAA
1 ATATATATAATAAT-GATATAAA
*
41491 ATAAATA-AATAA
1 ATATATATAATAA
41503 ATAAATAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 11 0.39
21 16 0.57
22 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (22 bp):
ATATATATAATAATGATATAAA
Found at i:42819 original size:2 final size:2
Alignment explanation
Indices: 42772--42808 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
42762 GATGTGTCAC
42772 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42809 CCTTCTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46824 original size:16 final size:17
Alignment explanation
Indices: 46803--46837 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
46793 TTTTATTTTT
46803 ATTT-AATATAAAAATA
1 ATTTAAATATAAAAATA
46819 ATTTAAAATATAAAAATA
1 ATTT-AAATATAAAAATA
46837 A
1 A
46838 AAATAGATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
18 13 0.76
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTTAAATATAAAAATA
Found at i:51959 original size:3 final size:3
Alignment explanation
Indices: 51946--52017 Score: 83
Period size: 3 Copynumber: 24.0 Consensus size: 3
51936 GTAATATTTA
* * *
51946 AAT AAT AAAT AAT ATT ACT ATT AAT AAT AAT AAT AAT -AT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
51991 AAT AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
52018 TTAAAATGAA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.03
3 54 0.92
4 3 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:52810 original size:76 final size:76
Alignment explanation
Indices: 52173--52783 Score: 1107
Period size: 76 Copynumber: 8.0 Consensus size: 76
52163 GGTCTTATGA
*
52173 ATGACCCTG-AGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCC-GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
* *
52237 TAGGGCTTACAG
65 AAGGACTTACAG
*
52249 ATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
52314 AGGGCTTACAG
66 AGGACTTACAG
*
52325 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
52390 AGGGCTTACAG
66 AGGACTTACAG
*
52401 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
52466 AGGACTTACAG
66 AGGACTTACAG
52477 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
52542 AGGGCTTACAG
66 AGGACTTACAG
52553 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
52618 AGGACTTACAG
66 AGGACTTACAG
*
52629 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
52694 AGGACTTACAG
66 AGGACTTACAG
*
52705 ATGACCCGAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
52770 AGGACTTACAG
66 AGGACTTACAG
52781 ATG
1 ATG
52784 TGGGAAATAA
Statistics
Matches: 520, Mismatches: 14, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
75 1 0.00
76 519 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGACTTACAG
Found at i:53902 original size:54 final size:54
Alignment explanation
Indices: 53820--53926 Score: 160
Period size: 54 Copynumber: 2.0 Consensus size: 54
53810 GAATAGCAGG
***
53820 TTCGTAAAACATTTAACAGTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGATA
1 TTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGATA
* **
53874 TTCGTAAAACATTTGACAACACATTCATCCTTTTTTGTGGCTTCTGCTCAGAT
1 TTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
53927 GTTCTCAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.38
Consensus pattern (54 bp):
TTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGATA
Found at i:56179 original size:115 final size:115
Alignment explanation
Indices: 55970--56188 Score: 323
Period size: 115 Copynumber: 1.9 Consensus size: 115
55960 GATCATGCAG
* * * * * *
55970 TTCATCTTTCAATTCCAATGATCGGTTATGGGGTTCCTACCGAATCAGATCAGATAACTCGAAGA
1 TTCATCTTTCAAATCCAATGATCGATTATGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
* *
56035 ACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCAAAA
66 ACACTTCCAAAAGATGCTATTAGGCCTCCTTATTTCTACTATGAGCAAAA
* * *
56085 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATATCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGATTATGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
56150 ACACTTCCAAAAGATGCTATT-GAGCCTCCTTATTTCTAC
66 ACACTTCCAAAAGATGCTATTAG-GCCTCCTTATTTCTAC
56189 CAAATTCAAT
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
114 1 0.01
115 91 0.99
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (115 bp):
TTCATCTTTCAAATCCAATGATCGATTATGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAAAAGATGCTATTAGGCCTCCTTATTTCTACTATGAGCAAAA
Found at i:56320 original size:93 final size:93
Alignment explanation
Indices: 56073--56358 Score: 353
Period size: 93 Copynumber: 3.0 Consensus size: 93
56063 CTTATTTCTA
* * * * * *
56073 CTATGAGCAAAATTCATCTTTCAAATCCAATGATTGATT-T-TGGAGTTCATATCAAATCAGATC
1 CTATGAGC-ACATTCATCTTCCAAATTCAATGATTGATTCTGTGG-TTTCATACCAAACCAGATC
56136 AGATAACTCAAAGAACACTTCCAAAAGATG
64 AGATAACTCAAAGAACACTTCCAAAAGATG
* * *
56166 CTATTGAGCCTCCTT-ATTTCTACCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGA
1 CTA-TGAG-CACATTCA--TCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGA
*
56230 TTAGATAACTCAAAGAACACTTCCAAAAGATG
62 TCAGATAACTCAAAGAACACTTCCAAAAGATG
* *
56262 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAG
* * * *
56327 ATAACTAAAAAAACACTTCCAGAAGATA
66 ATAACTCAAAGAACACTTCCAAAAGATG
56355 CTAT
1 CTAT
56359 TGGGTCTTCT
Statistics
Matches: 166, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
93 78 0.47
94 10 0.06
95 26 0.16
96 49 0.30
97 3 0.02
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (93 bp):
CTATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAG
ATAACTCAAAGAACACTTCCAAAAGATG
Found at i:58536 original size:11 final size:11
Alignment explanation
Indices: 58520--58568 Score: 64
Period size: 11 Copynumber: 4.4 Consensus size: 11
58510 TCAATTTTCC
58520 TTTTTCTTTTT
1 TTTTTCTTTTT
58531 TTTTTCTTTTCT
1 TTTTTCTTTT-T
58543 CTTTTT-TTTTT
1 -TTTTTCTTTTT
*
58554 CTTTTCTTTTT
1 TTTTTCTTTTT
58565 TTTT
1 TTTT
58569 CTTCTTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 4 0.12
11 19 0.58
12 5 0.15
13 5 0.15
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:58540 original size:16 final size:17
Alignment explanation
Indices: 58514--58579 Score: 91
Period size: 17 Copynumber: 3.9 Consensus size: 17
58504 CTTGATTCAA
*
58514 TTTTCCTTTTTCTTTTT
1 TTTTTCTTTTTCTTTTT
58531 TTTTTCTTTTCTCTTTTT
1 TTTTTCTTTT-TCTTTTT
58549 TTTTTC-TTTTC-TTTT
1 TTTTTCTTTTTCTTTTT
58564 TTTTTCTTCTTTCTTT
1 TTTTTCTT-TTTCTTT
58580 GCTGGATGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
15 10 0.23
16 3 0.07
17 16 0.36
18 15 0.34
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTTTCTTTTT
Found at i:58545 original size:18 final size:18
Alignment explanation
Indices: 58514--58575 Score: 92
Period size: 18 Copynumber: 3.5 Consensus size: 18
58504 CTTGATTCAA
*
58514 TTTTCCTTTT-TCTTTTT
1 TTTTTCTTTTCTCTTTTT
58531 TTTTTCTTTTCTCTTTTT
1 TTTTTCTTTTCTCTTTTT
58549 TTTTTCTTTTCT-TTTTT
1 TTTTTCTTTTCTCTTTTT
58566 TTTCTTCTTT
1 TTT-TTCTTT
58576 CTTTGCTGGA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
17 17 0.40
18 25 0.60
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTCTTTTCTCTTTTT
Found at i:58563 original size:29 final size:29
Alignment explanation
Indices: 58520--58575 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
58510 TCAATTTTCC
*
58520 TTTTTCTTTTTTTTTTCTTTTC-TCTTTTT
1 TTTTTCTTTTCTTTTT-TTTTCTTCTTTTT
58549 TTTTTCTTTTCTTTTTTTTTCTTCTTT
1 TTTTTCTTTTCTTTTTTTTTCTTCTTT
58576 CTTTGCTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (29 bp):
TTTTTCTTTTCTTTTTTTTTCTTCTTTTT
Found at i:65423 original size:3 final size:3
Alignment explanation
Indices: 65410--65479 Score: 86
Period size: 3 Copynumber: 23.0 Consensus size: 3
65400 GTAATATTTA
* * *
65410 AAT AAT AAAT AAT ATT ACT ATT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
65456 AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
65480 TTAAAATGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
3 55 0.95
4 3 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:65424 original size:18 final size:18
Alignment explanation
Indices: 65401--65479 Score: 81
Period size: 18 Copynumber: 4.2 Consensus size: 18
65391 TTGGGCTTTG
65401 TAATATTTA-AATAATAAA
1 TAATATTTATAATAAT-AA
65419 TAATATTACTATTAATAATAA
1 TAATATT--TA-TAATAATAA
* *
65440 TAATAATAATAATAATAA
1 TAATATTTATAATAATAA
65458 TAATAATTT-TAATAATAA
1 TAAT-ATTTATAATAATAA
65476 TAAT
1 TAAT
65480 TTAAAATGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
18 33 0.63
19 3 0.06
20 2 0.04
21 8 0.15
22 6 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (18 bp):
TAATATTTATAATAATAA
Found at i:71234 original size:93 final size:93
Alignment explanation
Indices: 71075--71248 Score: 312
Period size: 93 Copynumber: 1.9 Consensus size: 93
71065 TAAGCTACTT
* * *
71075 TAGTATAGAGAATAAATGGTCGATCCACAGGGACTTAGAAATTTTCAATGTTGGTTTGAATTGAT
1 TAGTATAGAGAATAAAGGGTCGATCCACAAGAACTTAGAAATTTTCAATGTTGGTTTGAATTGAT
71140 CTTGATCCAAGAAAATGCCAAAAGGATG
66 CTTGATCCAAGAAAATGCCAAAAGGATG
*
71168 TAGTATAGAGAATAAAGGGTCGATCCACAAGAACTTATAAATTTTCAATGTTGGTTTGAATTGAT
1 TAGTATAGAGAATAAAGGGTCGATCCACAAGAACTTAGAAATTTTCAATGTTGGTTTGAATTGAT
71233 CTTGATCCAAGAAAAT
66 CTTGATCCAAGAAAAT
71249 TGAAAAAAAG
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.30
Consensus pattern (93 bp):
TAGTATAGAGAATAAAGGGTCGATCCACAAGAACTTAGAAATTTTCAATGTTGGTTTGAATTGAT
CTTGATCCAAGAAAATGCCAAAAGGATG
Found at i:75092 original size:29 final size:30
Alignment explanation
Indices: 75017--75092 Score: 111
Period size: 30 Copynumber: 2.6 Consensus size: 30
75007 TTCACTTTTT
*
75017 TTTTTTC-TTTTCATAGCTTGTACTATTCAC
1 TTTTTTCATTTT-ATAGCTTATACTATTCAC
75047 TTTTTTCATTTTATAGCTTATACTATTCAC
1 TTTTTTCATTTTATAGCTTATACTATTCAC
*
75077 -TTTTTCATTTTGTAGC
1 TTTTTTCATTTTATAGC
75093 CCAATGTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
29 15 0.35
30 24 0.56
31 4 0.09
ACGTcount: A:0.18, C:0.17, G:0.07, T:0.58
Consensus pattern (30 bp):
TTTTTTCATTTTATAGCTTATACTATTCAC
Found at i:84041 original size:21 final size:21
Alignment explanation
Indices: 84015--84056 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
84005 TAAAACATTG
84015 AAACCACTAAAATTCTTGCAT
1 AAACCACTAAAATTCTTGCAT
84036 AAACCACTAAAATTCTTGCAT
1 AAACCACTAAAATTCTTGCAT
84057 CAGACTGCAT
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:0.43, C:0.24, G:0.05, T:0.29
Consensus pattern (21 bp):
AAACCACTAAAATTCTTGCAT
Found at i:88054 original size:11 final size:11
Alignment explanation
Indices: 88038--88063 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
88028 CCACCATTTT
88038 TTATATTATTA
1 TTATATTATTA
88049 TTATATTATTA
1 TTATATTATTA
88060 TTAT
1 TTAT
88064 TAAAAAATAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATATTATTA
Found at i:89223 original size:23 final size:23
Alignment explanation
Indices: 89152--89216 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
89142 TCAGACTCTA
*
89152 CTAACATTTCTAACA-CTAACCG
1 CTAACTTTTCTAACAGCTAACCG
**
89174 CTAA--TTTCTAAGTGCTAACCG
1 CTAACTTTTCTAACAGCTAACCG
89195 CTAACTTTTCTAACAGCTAACC
1 CTAACTTTTCTAACAGCTAACC
89217 ATTAACTACT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 7 0.19
21 11 0.31
22 4 0.11
23 14 0.39
ACGTcount: A:0.32, C:0.29, G:0.08, T:0.31
Consensus pattern (23 bp):
CTAACTTTTCTAACAGCTAACCG
Found at i:89536 original size:18 final size:16
Alignment explanation
Indices: 89513--89565 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 16
89503 TTGTACTTTA
89513 ATTTTAGTCCTTTTATAT
1 ATTTTA-TCCTTTTA-AT
*
89531 ATTTTAATTCTCTTTAAT
1 ATTTT-ATCCT-TTTAAT
89549 ATTTGTATCCTTTTAAT
1 ATTT-TATCCTTTTAAT
89566 TTAGTCCTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 6 0.20
18 18 0.60
19 6 0.20
ACGTcount: A:0.25, C:0.11, G:0.04, T:0.60
Consensus pattern (16 bp):
ATTTTATCCTTTTAAT
Found at i:92643 original size:3 final size:3
Alignment explanation
Indices: 92635--92690 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
92625 AGCCTCATCC
92635 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
92683 AAT AAT AA
1 AAT AAT AA
92691 AAAAACTATC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:92775 original size:62 final size:62
Alignment explanation
Indices: 92704--92829 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
92694 AACTATCCCC
*
92704 TATTTTATTCCAACGAAATAAATTCATACAATTGACCCCAACACTCAATGGACACTTGGACA
1 TATTTTATTCCAACGAAATAAATTCATACAATTGACCCCAACACTCAATGCACACTTGGACA
92766 TATTTTATTCCAACGAAATAAATTCATACAATTGACCCCAACACTCAATGCACACTTGGACA
1 TATTTTATTCCAACGAAATAAATTCATACAATTGACCCCAACACTCAATGCACACTTGGACA
92828 TA
1 TA
92830 GTATTAAGCA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.28
Consensus pattern (62 bp):
TATTTTATTCCAACGAAATAAATTCATACAATTGACCCCAACACTCAATGCACACTTGGACA
Found at i:93813 original size:21 final size:18
Alignment explanation
Indices: 93769--93820 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 18
93759 TACCTTTCTC
93769 TTAGTATCGATACTCACA
1 TTAGTATCGATACTCACA
* *
93787 TCAGTATCGATACTAATTACA
1 TTAGTATCGATAC---TCACA
93808 TTAGTATCGATAC
1 TTAGTATCGATAC
93821 CGCATATCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 12 0.43
21 16 0.57
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (18 bp):
TTAGTATCGATACTCACA
Found at i:99623 original size:22 final size:22
Alignment explanation
Indices: 99588--99629 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
99578 ACACTGTTAA
*
99588 GCATTTAGTATTTCCTCTAAAG
1 GCATTTAGTATTTCATCTAAAG
99610 GCATTTAG-ACTTTCATCTAA
1 GCATTTAGTA-TTTCATCTAA
99630 CTTGCATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (22 bp):
GCATTTAGTATTTCATCTAAAG
Found at i:100061 original size:63 final size:63
Alignment explanation
Indices: 99658--100059 Score: 707
Period size: 63 Copynumber: 6.4 Consensus size: 63
99648 TTCTTCCAAA
* * *
99658 TGCATAGTTAGGCATTTAATCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCATTAT
1 TGCACAGTTAGGCATTTATTCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCATGAT
*
99721 TGCACAGTTAGGCATTTATTCTTTTACTCAAAGGTATTTAGCCTTTCATCTAACTTGCATGAT
1 TGCACAGTTAGGCATTTATTCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCATGAT
*
99784 TGCACAGTTAGGCATTTATTCTTTTACTCAAAGGCATTTATCCTTTCATCTAACTTGCATGAT
1 TGCACAGTTAGGCATTTATTCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCATGAT
* *
99847 TGCACAATTAGGTATTTATTCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCATGAT
1 TGCACAGTTAGGCATTTATTCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCATGAT
99910 TGCACAGTTAGGCATTTATTCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCATGAT
1 TGCACAGTTAGGCATTTATTCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCATGAT
* *
99973 TGCACA-TATAGACATTTATTCTTTCACTCAAAGGCATTTAGCCTTTCATCTAACTTGCATGAT
1 TGCACAGT-TAGGCATTTATTCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCATGAT
100036 TGCACAGTTAGGCATTTATTCTTT
1 TGCACAGTTAGGCATTTATTCTTT
100060 CATTTTAAAA
Statistics
Matches: 323, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
62 1 0.00
63 321 0.99
64 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (63 bp):
TGCACAGTTAGGCATTTATTCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTTGCATGAT
Found at i:100487 original size:22 final size:21
Alignment explanation
Indices: 100445--100499 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
100435 CGGCTCAATA
100445 GTATCGATAC-CCATACCATG
1 GTATCGATACTCCATACCATG
* *
100465 GTATCGATACTTCTATACTATG
1 GTATCGATAC-TCCATACCATG
100487 GTA-CTGATACTCC
1 GTATC-GATACTCC
100500 CTTTCAGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 10 0.34
21 3 0.10
22 16 0.55
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (21 bp):
GTATCGATACTCCATACCATG
Found at i:105056 original size:19 final size:19
Alignment explanation
Indices: 105032--105109 Score: 77
Period size: 19 Copynumber: 3.9 Consensus size: 19
105022 GGGCGTTTGG
105032 ATGGGAATGTGAGATTCTC
1 ATGGGAATGTGAGATTCTC
105051 ATGGGAATGTGAGATTC-C
1 ATGGGAATGTGAGATTCTC
* * *
105069 AATAGGAATGGAATCCACATTCTC
1 -ATGGGAAT-G--T-GAGATTCTC
105093 ATGGGAATGTGAGATTC
1 ATGGGAATGTGAGATTC
105110 CAATAGGAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
18 1 0.02
19 29 0.62
20 2 0.04
22 2 0.04
23 12 0.26
24 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (19 bp):
ATGGGAATGTGAGATTCTC
Found at i:105092 original size:42 final size:42
Alignment explanation
Indices: 105045--105134 Score: 180
Period size: 42 Copynumber: 2.1 Consensus size: 42
105035 GGAATGTGAG
105045 ATTCTCATGGGAATGTGAGATTCCAATAGGAATGGAATCCAC
1 ATTCTCATGGGAATGTGAGATTCCAATAGGAATGGAATCCAC
105087 ATTCTCATGGGAATGTGAGATTCCAATAGGAATGGAATCCAC
1 ATTCTCATGGGAATGTGAGATTCCAATAGGAATGGAATCCAC
105129 ATTCTC
1 ATTCTC
105135 CCATTTGGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (42 bp):
ATTCTCATGGGAATGTGAGATTCCAATAGGAATGGAATCCAC
Found at i:105118 original size:19 final size:19
Alignment explanation
Indices: 105035--105120 Score: 68
Period size: 19 Copynumber: 4.3 Consensus size: 19
105025 CGTTTGGATG
*
105035 GGAATGTGAGATTCTCATG
1 GGAATGTGAGATTCTCATA
105054 GGAATGTGAGATTC-CAATA
1 GGAATGTGAGATTCTC-ATA
* * *
105073 GGAATGGAATCCACATTCTCATG
1 GGAAT-G--T-GAGATTCTCATA
105096 GGAATGTGAGATTC-CAATA
1 GGAATGTGAGATTCTC-ATA
105115 GGAATG
1 GGAATG
105121 GAATCCACAT
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
18 2 0.04
19 34 0.64
20 2 0.04
22 2 0.04
23 12 0.23
24 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.27
Consensus pattern (19 bp):
GGAATGTGAGATTCTCATA
Found at i:106149 original size:23 final size:23
Alignment explanation
Indices: 106105--106149 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
106095 ATTGAAACGA
* *
106105 TAAACGAACATATTCATGAACAC
1 TAAACGAACACATTCATAAACAC
* *
106128 TAAATGAACACATTCGTAAACA
1 TAAACGAACACATTCATAAACA
106150 TATAAATAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.09, T:0.22
Consensus pattern (23 bp):
TAAACGAACACATTCATAAACAC
Found at i:106277 original size:30 final size:30
Alignment explanation
Indices: 106214--106277 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
106204 AATGAATACA
* * *
106214 AACACCTTCAAAAATAAATAAACAAATATG
1 AACACCTTCAAAAATAAACAAACAAACACG
* * *
106244 AACACTTTCAAATATAAACAAACGAACACG
1 AACACCTTCAAAAATAAACAAACAAACACG
106274 AACA
1 AACA
106278 TAACTTTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.58, C:0.20, G:0.05, T:0.17
Consensus pattern (30 bp):
AACACCTTCAAAAATAAACAAACAAACACG
Found at i:106776 original size:21 final size:21
Alignment explanation
Indices: 106742--106789 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
106732 AAAAGATAAA
*
106742 ATTTAATTCGCCAATCATTTTT
1 ATTT-ATTAGCCAATCATTTTT
106764 ATTTATTAGCCAATCATTTTT
1 ATTTATTAGCCAATCATTTTT
106785 ATTTA
1 ATTTA
106790 CTGCCTTCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.29, C:0.15, G:0.04, T:0.52
Consensus pattern (21 bp):
ATTTATTAGCCAATCATTTTT
Found at i:107076 original size:2 final size:2
Alignment explanation
Indices: 107071--107144 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
107061 ATACGTTGAG
107071 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
107113 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
107145 GTTGAAAACA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:107489 original size:45 final size:46
Alignment explanation
Indices: 107440--107530 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
107430 AAACATCGAA
* *
107440 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATACACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATACACTCAG
* *
107485 TGCATTTGATGCATCGATGCACAAGACTATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATACACTCAG
107531 GCTTTTTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATACACTCAG
Done.