Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008603.1 Hibiscus syriacus cultivar Beakdansim tig00111558_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: 555603
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:483560 original size:71 final size:73
Alignment explanation
Indices: 483216--483560 Score: 315
Period size: 71 Copynumber: 4.9 Consensus size: 73
483206 CGGAAAATAC
* * *
483216 AATCGCAACGCGAAATGAAAATCCCAA-C--ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGC-GAAATTAAAA-CGCAAT
*
483277 -CG--A-GAG
64 GCGAAATGAA
* * *
483283 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--GAATCGCAAT
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAAATTAAAACGCAAT
483344 GCGAAATGAA
64 GCGAAATGAA
*
483354 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAAATTAAAA-CGCAA
*
483414 TACGAAATGAA
63 TGCGAAATGAA
* *
483425 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA--GAATCGCAAT
1 AATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAAATTAAAACGCAAT
483486 GCGAAATGAA
64 GCGAAATGAA
* *
483496 AATCGCAATGCGAAATGAAAATCGCAA-CG-A-GATAATCGCAATGCGAAATTATAAACGCATTG
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAAATTA-AAACGCAATG
483558 CGA
65 CGA
483561 TTTTCATTTC
Statistics
Matches: 234, Mismatches: 19, Indels: 46
0.78 0.06 0.15
Matches are distributed among these distances:
66 44 0.19
67 29 0.12
68 11 0.05
69 8 0.03
70 4 0.02
71 86 0.37
72 15 0.06
73 2 0.01
74 5 0.02
75 1 0.00
76 29 0.12
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (73 bp):
AATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAAATTAAAACGCAATGC
GAAATGAA
Found at i:483660 original size:19 final size:19
Alignment explanation
Indices: 483551--483652 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
483541 AAATTATAAA
483551 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
483570 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
483590 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
483606 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
483623 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
483642 CGCATTGCGAT
1 CGCATTGCGAT
483653 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:483778 original size:14 final size:14
Alignment explanation
Indices: 483759--483795 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
483749 CATCAATTAC
483759 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
483773 ACAAATCATCTTTT
1 ACAAATCAACTTTT
483787 ACAAATCAA
1 ACAAATCAA
483796 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:483807 original size:12 final size:12
Alignment explanation
Indices: 483790--483862 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
483780 ATCTTTTACA
483790 AATCAATTAAAC
1 AATCAATTAAAC
*
483802 AATCAA--AAATTG
1 AATCAATTAAA--C
**
483814 AATCAACTTTTAC
1 AATCAA-TTAAAC
483827 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
483840 AATCAA-AAAAC
1 AATCAATTAAAC
483851 AATCAATTAAAC
1 AATCAATTAAAC
483863 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:483824 original size:38 final size:38
Alignment explanation
Indices: 483776--483848 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
483766 AACTTTTACA
*
483776 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
483814 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
483849 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:485704 original size:19 final size:19
Alignment explanation
Indices: 485664--485798 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
485654 TAGTTTACTT
* *
485664 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
485684 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
485703 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
485722 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
485736 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
485755 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
485769 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
485788 TCGCAATGCGA
1 TCGCAACGCGA
485799 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:485739 original size:14 final size:14
Alignment explanation
Indices: 485720--485776 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
485710 GCGAAATGAA
*
485720 AATCGCAACGACAG
1 AATCGCAACGAAAG
485734 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
485751 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
485767 AATCGCAACG
1 AATCGCAACG
485777 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:485743 original size:33 final size:33
Alignment explanation
Indices: 485701--485793 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
485691 GCGAAACCAA
*
485701 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
485734 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
485767 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
485794 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:485790 original size:52 final size:54
Alignment explanation
Indices: 485664--485798 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
485654 TAGTTTACTT
*
485664 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
485722 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
485769 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
485799 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:485816 original size:19 final size:19
Alignment explanation
Indices: 485794--485922 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
485784 AAAATCGCAA
485794 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
485813 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
485827 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
485846 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
485860 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
485879 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
485898 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
485918 TGCGA
1 TGCGA
485923 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:485836 original size:33 final size:33
Alignment explanation
Indices: 485794--485885 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
485784 AAAATCGCAA
485794 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
485827 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
485860 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
485886 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:486124 original size:92 final size:93
Alignment explanation
Indices: 485966--486344 Score: 735
Period size: 92 Copynumber: 4.1 Consensus size: 93
485956 TTGAATGGAT
485966 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
486031 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
486059 AAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
486123 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
486151 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
486215 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
486243 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
486308 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
486336 AAATTTACT
1 AAATTTACT
486345 AAGCAATCTA
Statistics
Matches: 283, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
92 184 0.65
93 99 0.35
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:486278 original size:185 final size:185
Alignment explanation
Indices: 485966--486344 Score: 733
Period size: 185 Copynumber: 2.0 Consensus size: 185
485956 TTGAATGGAT
485966 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
486031 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAGACAAAACAAAGACAAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAGACAAAACAAAGACAAAT
486096 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
486151 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
486215 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACC-AAAGACAAAACAAAGACAAA
*
486280 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
130 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
486336 AAATTTACT
1 AAATTTACT
486345 AAGCAATCTA
Statistics
Matches: 192, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 69 0.36
185 123 0.64
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAGACAAAACAAAGACAAAT
ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:488064 original size:14 final size:14
Alignment explanation
Indices: 488045--488134 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
488035 TTGAAATGAA
488045 AATCGCAACGAGAG
1 AATCGCAACGAGAG
488059 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
488076 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
488092 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
488111 AATCGCAACGAGAG
1 AATCGCAACGAGAG
488125 AATCGCAACG
1 AATCGCAACG
488135 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:488082 original size:33 final size:33
Alignment explanation
Indices: 488037--488151 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
488027 TCTTTTGGTT
488037 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
488070 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
488103 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
488136 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
488152 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:488083 original size:19 final size:18
Alignment explanation
Indices: 488044--488156 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
488034 GTTGAAATGA
488044 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
488059 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
488076 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
488092 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
488109 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
488125 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
488142 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
488157 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:488187 original size:14 final size:14
Alignment explanation
Indices: 488168--488222 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
488158 TTTGGTTTCG
488168 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
488182 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
488201 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
488215 CGTTGCGA
1 CGTTGCGA
488223 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:488385 original size:33 final size:33
Alignment explanation
Indices: 488343--488413 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
488333 AATACTAACT
*
488343 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
488376 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
488409 TGAAA
1 TGAAA
488414 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:488646 original size:22 final size:22
Alignment explanation
Indices: 488594--488648 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
488584 TGGTTGTGAG
**
488594 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
488616 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
488638 GGATTTCTTCG
1 GGATTTCTTCG
488649 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:488819 original size:20 final size:20
Alignment explanation
Indices: 488794--488987 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
488784 CTTTAAATAT
488794 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
488814 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
488836 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
488855 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
488875 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
488895 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
488915 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
488935 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
488955 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
488975 CGCGTTGCGATTT
1 CGCGTTGCGATTT
488988 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:488981 original size:60 final size:60
Alignment explanation
Indices: 488794--488987 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
488784 CTTTAAATAT
**
488794 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
488855 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
488915 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
488975 CGCGTTGCGATTT
1 CGCGTTGCGATTT
488988 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:489004 original size:21 final size:20
Alignment explanation
Indices: 488980--489056 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
488970 ATATTCGCGT
488980 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
489001 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
489021 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
489043 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
489057 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:489067 original size:20 final size:20
Alignment explanation
Indices: 489042--489093 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
489032 AAGAATCGCG
*
489042 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
489062 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
489082 TTGCGATTCTGG
1 TTGCGATTCTGG
489094 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:492264 original size:17 final size:17
Alignment explanation
Indices: 492242--492285 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
492232 ATGTAAAAAT
492242 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
492259 AAATATAAAAATTTATT
1 AAATATTTAAATTTAAA
492276 AAATATTTAA
1 AAATATTTAA
492286 TCAAGAAGGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:493656 original size:2 final size:2
Alignment explanation
Indices: 493649--493674 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
493639 CTCGGATGTG
493649 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
493675 GTATGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:504321 original size:35 final size:35
Alignment explanation
Indices: 504247--504329 Score: 89
Period size: 35 Copynumber: 2.4 Consensus size: 35
504237 TATTTTATAG
**
504247 TAAT-ATAATTATATAAATATTATTTTTTTTATTA
1 TAATAATAATTATATAAATATTATTTTTTAAATTA
* * *
504281 AAATAATATTTATATAATTATTATTTATTTAAATT-
1 TAATAATAATTATATAAATATTATTT-TTTAAATTA
504316 TAATAATTAATTAT
1 TAATAA-TAATTAT
504330 TTTTTGTACT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
34 3 0.08
35 24 0.62
36 12 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (35 bp):
TAATAATAATTATATAAATATTATTTTTTAAATTA
Found at i:504582 original size:26 final size:27
Alignment explanation
Indices: 504525--504576 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
504515 ATTAATATTC
*
504525 TATTTAAATGAATGTTTTTCTTTCTAA
1 TATTTAAATGAATGTGTTTCTTTCTAA
504552 TATTTAAATGTAAT-TGTTT-TTTCTA
1 TATTTAAATG-AATGTGTTTCTTTCTA
504577 TAATTTCTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 14 0.61
28 3 0.13
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.58
Consensus pattern (27 bp):
TATTTAAATGAATGTGTTTCTTTCTAA
Found at i:504682 original size:21 final size:21
Alignment explanation
Indices: 504656--504697 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
504646 AATAATTAAT
*
504656 ATTATTTATTATAAAAAATTA
1 ATTATTAATTATAAAAAATTA
* *
504677 ATTATTAATTTTAAAATATTA
1 ATTATTAATTATAAAAAATTA
504698 TAATAATTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTAATTATAAAAAATTA
Found at i:511144 original size:16 final size:17
Alignment explanation
Indices: 511115--511147 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
511105 TTTATATATT
511115 ATTTTTTTCAATTAAATC
1 ATTTTTTT-AATTAAATC
511133 ATTTTTTT-ATTAAAT
1 ATTTTTTTAATTAAAT
511148 AAAAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTTTTAATTAAATC
Found at i:515418 original size:17 final size:17
Alignment explanation
Indices: 515396--515430 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
515386 ACACAAATGC
515396 ATGCATACTGGCACGTA
1 ATGCATACTGGCACGTA
* *
515413 ATGCATATTGGCATGTA
1 ATGCATACTGGCACGTA
515430 A
1 A
515431 GAGTGAAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (17 bp):
ATGCATACTGGCACGTA
Found at i:522376 original size:2 final size:2
Alignment explanation
Indices: 522337--522363 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
522327 GAAATTACTG
522337 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
522364 CATTTTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:524854 original size:23 final size:22
Alignment explanation
Indices: 524789--524854 Score: 53
Period size: 23 Copynumber: 2.8 Consensus size: 22
524779 AGCTTATTTA
*
524789 ATTTAAAAAAAAACATATTTTAAAT
1 ATTT-AAAAAAAA-ATA-TTCAAAT
*
524814 -TTTAAATATAAAATTATTCAAAT
1 ATTTAAA-A-AAAAATATTCAAAT
524837 ATTTAAAAAATAAATATT
1 ATTTAAAAAA-AAATATT
524855 AAAAATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
22 2 0.06
23 16 0.47
24 12 0.35
25 4 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTTAAAAAAAAATATTCAAAT
Found at i:524863 original size:20 final size:21
Alignment explanation
Indices: 524842--524880 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
524832 CAAATATTTA
524842 AAAAAT-AAA-TATTAAAAAT
1 AAAAATAAAATTATTAAAAAT
524861 AAAAATAAAATTATTAAAAA
1 AAAAATAAAATTATTAAAAA
524881 AAGTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 3 0.17
21 9 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAATAAAATTATTAAAAAT
Found at i:529709 original size:52 final size:50
Alignment explanation
Indices: 529643--529771 Score: 195
Period size: 52 Copynumber: 2.5 Consensus size: 50
529633 GGAGATGCAC
*
529643 ATACTTACACCGGTGTAAGTATGTGTTTATTTTTAGGTTGGGAGATGTAAAT
1 ATACTTACACCGGTGTAAGTATGTGTTTATTTTTAGGTTGGGAAATGT--AT
* * * *
529695 GTATTTACAGCGGTGTAAGTATATGTTTATTTTTAGGTTGGGAAATGTAT
1 ATACTTACACCGGTGTAAGTATGTGTTTATTTTTAGGTTGGGAAATGTAT
529745 ATACTTACACCGGTGTAAGTATGTGTT
1 ATACTTACACCGGTGTAAGTATGTGTT
529772 AATTGATACA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 25 0.37
52 43 0.63
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (50 bp):
ATACTTACACCGGTGTAAGTATGTGTTTATTTTTAGGTTGGGAAATGTAT
Found at i:530111 original size:41 final size:41
Alignment explanation
Indices: 530023--530179 Score: 118
Period size: 42 Copynumber: 3.8 Consensus size: 41
530013 AATTGATACT
* * * *
530023 TTAGCGGCGTTTTTAGTAAAAACGCTGCAATAGAGTTGACA
1 TTAGCGGCGTTTTTAGCAAAAACGCCGCAATAGAGTGGAAA
* *
530064 TATAGCGGCGTTTTTA-CAAAAATGCCGCAATAGGGTGGCAAA
1 T-TAGCGGCGTTTTTAGCAAAAACGCCGCAATAGAGTGG-AAA
* * * * * * ***
530106 TTAGCGGCGTTTATACCACAAACGCCACAATAAAATAGTTCA
1 TTAGCGGCGTTTTTAGCAAAAACGCCGCAATAGAGT-GGAAA
* **
530148 TTTGCGGCGTTTTTATTAAAAACGCCGCAATA
1 TTAGCGGCGTTTTTAGCAAAAACGCCGCAATA
530180 TTCTGATATA
Statistics
Matches: 90, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
41 31 0.34
42 58 0.64
43 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (41 bp):
TTAGCGGCGTTTTTAGCAAAAACGCCGCAATAGAGTGGAAA
Found at i:531610 original size:11 final size:11
Alignment explanation
Indices: 531594--531622 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
531584 TTTTACTCGT
531594 ACCAAATTCTA
1 ACCAAATTCTA
531605 ACCAAATTCTA
1 ACCAAATTCTA
531616 ACCAAAT
1 ACCAAAT
531623 ATCTGAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (11 bp):
ACCAAATTCTA
Found at i:533141 original size:28 final size:28
Alignment explanation
Indices: 533110--533163 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
533100 TTATGAGTGC
533110 ATATAATAT-TTGTCATGGAAGTTTATCA
1 ATAT-ATATCTTGTCATGGAAGTTTATCA
* *
533138 ATATTTCTCTTGTCATGGAAGTTTAT
1 ATATATATCTTGTCATGGAAGTTTAT
533164 ATTTTCTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (28 bp):
ATATATATCTTGTCATGGAAGTTTATCA
Found at i:539689 original size:21 final size:21
Alignment explanation
Indices: 539619--539711 Score: 80
Period size: 21 Copynumber: 4.4 Consensus size: 21
539609 AGCGGAAAAT
*
539619 GAAGCAAGGGAAA-CAGAGAGA
1 GAAGC-AGCGAAAGCAGAGAGA
* * **
539640 GCAGCAGCGGAAGCAGCTAGA
1 GAAGCAGCGAAAGCAGAGAGA
*
539661 GCAGCAGCGAAAGCAGAGAGA
1 GAAGCAGCGAAAGCAGAGAGA
** *
539682 GAAGCAGCGGCAGCACAGAGA
1 GAAGCAGCGAAAGCAGAGAGA
*
539703 GAGGCAGCG
1 GAAGCAGCG
539712 GCAGAACATA
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 5 0.09
21 53 0.91
ACGTcount: A:0.40, C:0.19, G:0.40, T:0.01
Consensus pattern (21 bp):
GAAGCAGCGAAAGCAGAGAGA
Found at i:539712 original size:21 final size:21
Alignment explanation
Indices: 539635--539727 Score: 80
Period size: 21 Copynumber: 4.4 Consensus size: 21
539625 AGGGAAACAG
* *
539635 AGAGAGCAGCAGCGGAAGCAGC
1 AGAGAGAAGCAGCGGCAGCA-C
* * ** *
539657 -TAGAGCAGCAGCGAAAGCAG
1 AGAGAGAAGCAGCGGCAGCAC
539677 AGAGAGAAGCAGCGGCAGCAC
1 AGAGAGAAGCAGCGGCAGCAC
* *
539698 AGAGAGAGGCAGCGGCAGAAC
1 AGAGAGAAGCAGCGGCAGCAC
*
539719 ATAGAGAAG
1 AGAGAGAAG
539728 TAATGTATCA
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.40, C:0.19, G:0.39, T:0.02
Consensus pattern (21 bp):
AGAGAGAAGCAGCGGCAGCAC
Found at i:540265 original size:43 final size:41
Alignment explanation
Indices: 540063--540331 Score: 155
Period size: 43 Copynumber: 6.2 Consensus size: 41
540053 CATACATTTA
* * * * *
540063 GCGGCGTTTTTGATAAAAACGCCGCAAAATCTCAATACATATTCT
1 GCGGCG-TTTT-ATGAAAACGCCGCTAAATATCAAAACCTA-T-T
* * * * ** *
540108 GCGGCGTTTTTAGGAAAACGCCGGTAAAAATAAAAATTTACT
1 GCGGCG-TTTTATGAAAACGCCGCTAAATATCAAAACCTATT
* * *
540150 GCGGCGTTTTGGAAGAAAACGCCGCTAAACATCAACGA-CTATT
1 GCGGCGTTTT--ATGAAAACGCCGCTAAATATCAA-AACCTATT
* * * *
540193 GCGGCGTTTGTCTGCCAAATGCCGTTAAATATCAAAACCTATT
1 GCGGCGTTT-TATG-AAAACGCCGCTAAATATCAAAACCTATT
* *
540236 GCGGCGTTTTAATGATAAACGCCGCTAAATATCAATACCTTTT
1 GCGGCGTTTT-ATGA-AAACGCCGCTAAATATCAAAACCTATT
* * ***
540279 GCGGCGTTTGT-TGAACAATCGCCGCTATATGTTGTAACCTATT
1 GCGGCGTTT-TATGAA-AA-CGCCGCTAAATATCAAAACCTATT
540322 GCGGCGTTTT
1 GCGGCGTTTT
540332 TTGTTGAAAA
Statistics
Matches: 175, Mismatches: 38, Indels: 25
0.74 0.16 0.11
Matches are distributed among these distances:
41 5 0.03
42 16 0.09
43 121 0.69
44 22 0.13
45 11 0.06
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTTATGAAAACGCCGCTAAATATCAAAACCTATT
Found at i:541222 original size:23 final size:23
Alignment explanation
Indices: 541192--541247 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
541182 AGATACATTT
541192 TTATAATTTTCATACAATATATA
1 TTATAATTTTCATACAATATATA
541215 TTATAATTTTCATACAATATATA
1 TTATAATTTTCATACAATATATA
541238 TTATAATTTT
1 TTATAATTTT
541248 TAATTTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATAATTTTCATACAATATATA
Found at i:541930 original size:2 final size:2
Alignment explanation
Indices: 541888--541916 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
541878 AAATATTGTA
541888 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
541917 GTTTGGTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:546505 original size:59 final size:58
Alignment explanation
Indices: 546386--546560 Score: 160
Period size: 59 Copynumber: 3.0 Consensus size: 58
546376 ATACCCCGGT
* * * * * *
546386 GACCATTTTGTAACTTTCAATAGTTAAAGAACTTAACAAAGCAACTT-CCTATAGTC-AAG
1 GACCATTTTGTAACTTTTAATAATTAAGGAACTCAACAAA-C-A-TTACCCATAATCAAAG
* * *
546445 GAGCCA-TTTGTAACTTTTAATAGTTGA-GAGACTCAACAAAACATTACCCGTAATCAAAG
1 GA-CCATTTTGTAACTTTTAATAATTAAGGA-ACTCAAC-AAACATTACCCATAATCAAAG
* * *
546504 GACTATTTTGTAACTTTTAATAATTAAGGAACTCAACAAATATTACCTATAATCAAA
1 GACCATTTTGTAACTTTTAATAATTAAGGAACTCAACAAACATTACCCATAATCAAA
546561 AGACTACTTG
Statistics
Matches: 97, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
57 2 0.02
58 28 0.29
59 59 0.61
60 8 0.08
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (58 bp):
GACCATTTTGTAACTTTTAATAATTAAGGAACTCAACAAACATTACCCATAATCAAAG
Found at i:546578 original size:58 final size:59
Alignment explanation
Indices: 546453--546578 Score: 150
Period size: 59 Copynumber: 2.2 Consensus size: 59
546443 AGGAGCCATT
* * * * *
546453 TGTAACTTTTAATAGTTGAGAGACTCAACAAAACATTACCCGTAATCAAAGGACTATTT
1 TGTAACTTTTAATAATTAAGAGACTCAACAAAACATTACCCATAATCAAAAGACTATTG
* *
546512 TGTAACTTTTAATAATTAAG-GAACTCAAC-AAATATTACCTATAATCAAAAGACTACTTG
1 TGTAACTTTTAATAATTAAGAG-ACTCAACAAAACATTACCCATAATCAAAAGACTA-TTG
546571 TGT-ACTTT
1 TGTAACTTT
546579 ATCCTTAGTA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
58 28 0.48
59 30 0.52
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (59 bp):
TGTAACTTTTAATAATTAAGAGACTCAACAAAACATTACCCATAATCAAAAGACTATTG
Found at i:546747 original size:24 final size:24
Alignment explanation
Indices: 546720--546770 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
546710 TTCGTTTATA
546720 TATAAGTTTATTTATTGACTAATT
1 TATAAGTTTATTTATTGACTAATT
* *
546744 TATAAGTTTATTTATTGATTAGTT
1 TATAAGTTTATTTATTGACTAATT
546768 TAT
1 TAT
546771 TCGGAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (24 bp):
TATAAGTTTATTTATTGACTAATT
Found at i:548839 original size:2 final size:2
Alignment explanation
Indices: 548832--548860 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
548822 TCATAAAATT
548832 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 T
548861 TTACAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:552162 original size:2 final size:2
Alignment explanation
Indices: 552157--552184 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
552147 TATATAATTA
552157 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
552185 GCTCAACTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.