Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008375.1 Hibiscus syriacus cultivar Beakdansim tig00111132_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: 1210889
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 7
Found at i:704 original size:12 final size:12
Alignment explanation
Indices: 687--711 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
677 CATATATCCT
687 GAAGAAGAAAAA
1 GAAGAAGAAAAA
699 GAAGAAGAAAAA
1 GAAGAAGAAAAA
711 G
1 G
712 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:3007 original size:19 final size:19
Alignment explanation
Indices: 2985--3258 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
2975 CGGAAAATAC
*
2985 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3004 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
3018 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
3038 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3052 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3071 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3090 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
3104 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
3123 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3142 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3161 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3180 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3199 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
3213 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3232 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3251 AATCGCAA
1 AATCGCAA
3259 CGAGATAATC
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 38 0.17
15 1 0.00
16 14 0.06
17 12 0.05
18 2 0.01
19 146 0.65
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3136 original size:71 final size:74
Alignment explanation
Indices: 2985--3280 Score: 314
Period size: 71 Copynumber: 4.2 Consensus size: 74
2975 CGGAAAATAC
* *
2985 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAATG-AAATCGCA
*
3045 A--CG--A-GAG
63 ATGCGAAATGAA
*
3052 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACA-G-AATCGCAATG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATG
*
3114 CGAAATTAA
66 CGAAATGAA
3123 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAA
3188 TGCGAAATGAA
64 TGCGAAATGAA
3199 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAA
*
3259 --CG--A-GAT
64 TGCGAAATGAA
3265 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
3281 TATAAACGCA
Statistics
Matches: 203, Mismatches: 8, Indels: 34
0.83 0.03 0.14
Matches are distributed among these distances:
66 18 0.09
67 26 0.13
68 8 0.04
69 6 0.03
70 2 0.01
71 93 0.46
72 13 0.06
73 5 0.02
74 6 0.03
76 26 0.13
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (74 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATG
CGAAATGAA
Found at i:3184 original size:109 final size:104
Alignment explanation
Indices: 3013--3280 Score: 446
Period size: 109 Copynumber: 2.5 Consensus size: 104
3003 AAATCCCAAC
*
3013 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
3078 ATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
65 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
3118 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAAAT
3183 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
61 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
3227 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAAT
3281 TATAAACGCA
Statistics
Matches: 153, Mismatches: 5, Indels: 11
0.91 0.03 0.07
Matches are distributed among these distances:
104 34 0.22
105 16 0.10
106 2 0.01
107 2 0.01
108 1 0.01
109 98 0.64
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (104 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:3246 original size:161 final size:157
Alignment explanation
Indices: 2985--3296 Score: 502
Period size: 161 Copynumber: 2.0 Consensus size: 157
2975 CGGAAAATAC
*
2985 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAG
1 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
3050 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
3115 GAAATTA-AAATCGCAATGCGAAATGAA
131 GAAATTATAAA-CGCAATGCGAAATGAA
* *
3142 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
* *
3206 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGC
61 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGC
*
3271 AATGCGAAATTATAAACGCATTGCGA
126 AATGCGAAATTATAAACGCAATGCGA
3297 TTTTCATTTC
Statistics
Matches: 143, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
157 25 0.17
159 1 0.01
161 98 0.69
162 19 0.13
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (157 bp):
AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
GAAATTATAAACGCAATGCGAAATGAA
Found at i:3296 original size:52 final size:52
Alignment explanation
Indices: 3013--3280 Score: 437
Period size: 52 Copynumber: 5.0 Consensus size: 52
3003 AAATCCCAAC
3013 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
3066 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
3118 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
3175 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
3227 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
3279 AT
1 AT
3281 TATAAACGCA
Statistics
Matches: 201, Mismatches: 9, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
52 133 0.66
53 17 0.08
54 2 0.01
55 2 0.01
56 1 0.00
57 46 0.23
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:3396 original size:19 final size:19
Alignment explanation
Indices: 3287--3388 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
3277 AAATTATAAA
3287 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3306 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
3326 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
3342 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3359 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3378 CGCATTGCGAT
1 CGCATTGCGAT
3389 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:3512 original size:14 final size:14
Alignment explanation
Indices: 3493--3529 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3483 CATCAATTAC
3493 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3507 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3521 ACAAATCAA
1 ACAAATCAA
3530 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:5498 original size:14 final size:14
Alignment explanation
Indices: 5479--5535 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5469 GCGAAATGAA
*
5479 AATCGCAACGACAG
1 AATCGCAACGAAAG
5493 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
5510 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
5526 AATCGCAACG
1 AATCGCAACG
5536 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:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:5506 original size:33 final size:33
Alignment explanation
Indices: 5460--5552 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
5450 GCGAAACCAA
*
5460 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
5493 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
5526 AATCGCAACGCGAAATGAAAATTGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
5553 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:5517 original size:19 final size:19
Alignment explanation
Indices: 5423--5557 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
5413 TAGTTTACTT
* *
5423 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
5443 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
5462 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5481 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
5495 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
5514 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
5528 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
5547 TTGCAATGCGA
1 TCGCAACGCGA
5558 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.11
17 11 0.11
19 46 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:5575 original size:19 final size:19
Alignment explanation
Indices: 5553--5681 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
5543 AAAATTGCAA
5553 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5572 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
5586 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5605 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
5619 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
5638 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
5657 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
5677 TGCGA
1 TGCGA
5682 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:5595 original size:33 final size:33
Alignment explanation
Indices: 5553--5644 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
5543 AAAATTGCAA
5553 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
5586 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
5619 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
5645 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:5974 original size:91 final size:93
Alignment explanation
Indices: 5725--6193 Score: 876
Period size: 91 Copynumber: 5.1 Consensus size: 93
5715 TTGAATGGAT
5725 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5790 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5818 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5882 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
5910 -AATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5973 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
6001 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
6064 AGTTTAGCGGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
6092 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
6157 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
6185 AAATTTACT
1 AAATTTACT
6194 AAGCAATCTA
Statistics
Matches: 366, Mismatches: 5, Indels: 10
0.96 0.01 0.03
Matches are distributed among these distances:
90 22 0.06
91 155 0.42
92 72 0.20
93 117 0.32
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:6035 original size:183 final size:184
Alignment explanation
Indices: 5725--6193 Score: 888
Period size: 183 Copynumber: 2.6 Consensus size: 184
5715 TTGAATGGAT
5725 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5790 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
5855 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATA-TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
5910 -AATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5973 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
* *
6038 TATATTCACAGTGTTAAAGAATATACAGTTTAGCGGAATTGGCAGCAACCGAAC
131 TATATTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
6092 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
6157 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
6194 AAGCAATCTA
Statistics
Matches: 279, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
182 48 0.17
183 132 0.47
184 99 0.35
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (184 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:7916 original size:14 final size:14
Alignment explanation
Indices: 7894--7983 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
7884 TTGAAATGAA
7894 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
7908 AATCACAACGCGAGATG
1 AATCGCAA--CGAGA-G
7925 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
7941 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
7960 AATCGCAACGAGAG
1 AATCGCAACGAGAG
7974 AATCGCAACG
1 AATCGCAACG
7984 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 27 0.44
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 17 0.27
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:7931 original size:33 final size:33
Alignment explanation
Indices: 7886--8000 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
7876 TCTTTTGGTT
*
7886 GAAATGAAAATCGCAACGAGAGAATCACAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
7919 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
7952 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
7985 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
8001 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:7935 original size:19 final size:18
Alignment explanation
Indices: 7893--8005 Score: 79
Period size: 19 Copynumber: 6.8 Consensus size: 18
7883 GTTGAAATGA
7893 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
*
7908 -AATCACAACGCGAGATG
1 AAATCGCAACGCGAGATG
7925 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
7941 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
7958 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
7974 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
7991 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
8006 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 6, Indels: 26
0.71 0.06 0.24
Matches are distributed among these distances:
14 23 0.30
16 15 0.19
17 12 0.16
19 27 0.35
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:8036 original size:14 final size:14
Alignment explanation
Indices: 8017--8071 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
8007 TTTGGTTTCG
8017 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
8031 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
8050 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
8064 CGTTGCGA
1 CGTTGCGA
8072 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:8049 original size:33 final size:33
Alignment explanation
Indices: 8001--8071 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
7991 AAAATCGCAA
**
8001 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
8034 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
8067 TGCGA
1 TGCGA
8072 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:8079 original size:33 final size:33
Alignment explanation
Indices: 8012--8093 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
8002 GCGATTTTGG
***
8012 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
8045 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
8078 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
8094 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:8098 original size:20 final size:20
Alignment explanation
Indices: 8024--8112 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
8014 TCGCGTTGCG
8024 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
8044 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
8057 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
8077 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
8097 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
8113 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:8234 original size:33 final size:33
Alignment explanation
Indices: 8192--8262 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
8182 AATACTAACT
*
8192 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
8225 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
8258 TGAAA
1 TGAAA
8263 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:8495 original size:22 final size:22
Alignment explanation
Indices: 8443--8497 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
8433 TGGTTGTGAG
**
8443 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
8465 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
8487 GGATTTCTTCG
1 GGATTTCTTCG
8498 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:8808 original size:60 final size:60
Alignment explanation
Indices: 8645--8813 Score: 239
Period size: 60 Copynumber: 2.8 Consensus size: 60
8635 TTAAATATCG
** *
8645 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACA
* * *** *
8706 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
*
8766 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGA
8814 ATTTGTACTA
Statistics
Matches: 92, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 66 0.72
61 26 0.28
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
Found at i:8813 original size:20 final size:20
Alignment explanation
Indices: 8643--8797 Score: 213
Period size: 20 Copynumber: 7.7 Consensus size: 20
8633 CTTTAAATAT
8643 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
8663 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
8685 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
8704 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
8724 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
8744 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
8764 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
8784 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
8798 TGTGTTCGCG
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
19 2 0.02
20 98 0.84
21 14 0.12
22 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:8875 original size:20 final size:20
Alignment explanation
Indices: 8850--8901 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
8840 AAGAATCGCG
*
8850 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
8870 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
8890 TTGCGATTCTGG
1 TTGCGATTCTGG
8902 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:15610 original size:27 final size:27
Alignment explanation
Indices: 15578--15668 Score: 74
Period size: 27 Copynumber: 3.7 Consensus size: 27
15568 TTTAAAAAAA
15578 TAAATTTATTATTTTTATATTTTAAAT
1 TAAATTTATTATTTTTATATTTTAAAT
* *
15605 TAAA--T-TCA-----ATATTTTATAT
1 TAAATTTATTATTTTTATATTTTAAAT
* *
15624 TAAATTTACTATTTTTATAATTTAAAT
1 TAAATTTATTATTTTTATATTTTAAAT
15651 TAAATTTGA-TATTTTTAT
1 TAAATTT-ATTATTTTTAT
15669 TAAATTTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
19 14 0.29
21 1 0.02
22 1 0.02
24 2 0.04
25 1 0.02
27 29 0.59
28 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (27 bp):
TAAATTTATTATTTTTATATTTTAAAT
Found at i:15636 original size:19 final size:18
Alignment explanation
Indices: 15591--15638 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
15581 ATTTATTATT
15591 TTTATATTTTAAATTAAA
1 TTTATATTTTAAATTAAA
* *
15609 TTCAATATTTTATATTAAA
1 TT-TATATTTTAAATTAAA
15628 TTTACTATTTT
1 TTTA-TATTTT
15639 TATAATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTATATTTTAAATTAAA
Found at i:15637 original size:46 final size:45
Alignment explanation
Indices: 15578--15675 Score: 151
Period size: 46 Copynumber: 2.2 Consensus size: 45
15568 TTTAAAAAAA
* *
15578 TAAATTTATTATTTTTATATTTTAAATTAAATTCAATATTTTATAT
1 TAAATTTACTATTTTTATAATTTAAATTAAATTCAATATTTT-TAT
**
15624 TAAATTTACTATTTTTATAATTTAAATTAAATTTGATATTTTTAT
1 TAAATTTACTATTTTTATAATTTAAATTAAATTCAATATTTTTAT
15669 TAAATTT
1 TAAATTT
15676 TTTATAATTC
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
45 10 0.21
46 38 0.79
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (45 bp):
TAAATTTACTATTTTTATAATTTAAATTAAATTCAATATTTTTAT
Found at i:15663 original size:39 final size:38
Alignment explanation
Indices: 15597--15703 Score: 101
Period size: 40 Copynumber: 2.7 Consensus size: 38
15587 TATTTTTATA
* * *
15597 TTTTA-AA-TTAAATTCAATATTTTATATTAAATTTACTAT
1 TTTTATAATTTAAATT-AA-ATTTGATATTAAATTAAAT-T
**
15636 TTTTATAATTTAAATTAAATTTGATATTTTTATTAAATT
1 TTTTATAATTTAAATTAAATTTGATA-TTAAATTAAATT
*
15675 TTTTATAATTCTAAATTAAATTTGGTATT
1 TTTTATAATT-TAAATTAAATTTGATATT
15704 TTTCATATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
39 25 0.43
40 26 0.45
41 7 0.12
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (38 bp):
TTTTATAATTTAAATTAAATTTGATATTAAATTAAATT
Found at i:15694 original size:45 final size:46
Alignment explanation
Indices: 15599--15696 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 46
15589 TTTTTATATT
** *
15599 TTAAATTAAATTCAATATTTTATATTAAATTTACTATTTTTATAAT
1 TTAAATTAAATTCAATATTTTATATTAAATTTACTATAATTATAAA
** ** *
15645 TTAAATTAAATTTGATATTTT-TATTAAATTTTTTATAATTCTAAA
1 TTAAATTAAATTCAATATTTTATATTAAATTTACTATAATTATAAA
15690 TTAAATT
1 TTAAATT
15697 TGGTATTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
45 25 0.57
46 19 0.43
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (46 bp):
TTAAATTAAATTCAATATTTTATATTAAATTTACTATAATTATAAA
Found at i:15787 original size:28 final size:29
Alignment explanation
Indices: 15726--15789 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
15716 ATTTCTAAAA
*
15726 ATAAATATGAAAAATATTAAATTTAATTT
1 ATAAATATGAAAAATAATAAATTTAATTT
*
15755 ATAAATAT-AGAAAATAATAATTTTAATTT
1 ATAAATATGA-AAAATAATAAATTTAATTT
15784 -TAAATA
1 ATAAATA
15790 GCTTTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 7 0.22
29 25 0.78
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (29 bp):
ATAAATATGAAAAATAATAAATTTAATTT
Found at i:15847 original size:17 final size:16
Alignment explanation
Indices: 15814--15846 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
15804 TTATAATATA
15814 TAAAATATATTTATTT
1 TAAAATATATTTATTT
15830 TAAAA-ATATTATATTT
1 TAAAATATATT-TATTT
15846 T
1 T
15847 TTATTAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAAAATATATTTATTT
Found at i:15980 original size:33 final size:33
Alignment explanation
Indices: 15918--15980 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
15908 ATTTTATTTT
* *
15918 TTTATTTTTCTATAATTGACAATAGTATAAAAC
1 TTTATTTTTCTATAATTAACAATAATATAAAAC
* *
15951 TTTATTTTTCTATCATTAATAATAATATAA
1 TTTATTTTTCTATAATTAACAATAATATAA
15981 GATAAATAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (33 bp):
TTTATTTTTCTATAATTAACAATAATATAAAAC
Found at i:16220 original size:6 final size:6
Alignment explanation
Indices: 16211--16243 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
16201 ATTAAAATAA
16211 AATTAG AATTAG AATTAG AATTAG AATTA- AATT
1 AATTAG AATTAG AATTAG AATTAG AATTAG AATT
16244 GATTGAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (6 bp):
AATTAG
Found at i:17175 original size:31 final size:31
Alignment explanation
Indices: 17137--17211 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
17127 AAACTTTCTA
* *
17137 AAAAAATCAATTACACTATCAAACTTAGCCC
1 AAAAAATCAATTACACCATCAAACTTAACCC
17168 AAAAAATCAATTACACCATCAAACTTAACCC
1 AAAAAATCAATTACACCATCAAACTTAACCC
17199 AAAAAATCAATTA
1 AAAAAATCAATTA
17212 AGTTCATCTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.53, C:0.24, G:0.01, T:0.21
Consensus pattern (31 bp):
AAAAAATCAATTACACCATCAAACTTAACCC
Found at i:17690 original size:26 final size:26
Alignment explanation
Indices: 17639--17706 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
17629 TAAAGTAATG
*
17639 ATTTTTTAATAATTATAATTTAATTT
1 ATTTTTTAATAACTATAATTTAATTT
* *
17665 ATTTTTTAATAACTAT-TTATTCATTT
1 ATTTTTTAATAACTATAAT-TTAATTT
*
17691 ATATTTTTAAAAACTA
1 AT-TTTTTAATAACTA
17707 GATGCCAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 1 0.03
26 23 0.64
27 12 0.33
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTTTTAATAACTATAATTTAATTT
Found at i:17812 original size:24 final size:24
Alignment explanation
Indices: 17779--17830 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
17769 CCTATTTTAG
* *
17779 TTTTCAAAAATTAAAAATTAAAACTA
1 TTTT-AAAAA-TAAAAATAAAAAATA
17805 TTTTAAAAATAAAAATAAAAAATA
1 TTTTAAAAATAAAAATAAAAAATA
17829 TT
1 TT
17831 CATAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 15 0.62
25 5 0.21
26 4 0.17
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (24 bp):
TTTTAAAAATAAAAATAAAAAATA
Found at i:17836 original size:25 final size:24
Alignment explanation
Indices: 17784--17842 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
17774 TTTAGTTTTC
* * *
17784 AAAAATTAAAAATTAAAACTATTTT
1 AAAAA-TAAAAATAAAAAATATTAT
17809 AAAAATAAAAATAAAAAATATTCAT
1 AAAAATAAAAATAAAAAATATT-AT
*
17834 AAATATAAA
1 AAAAATAAA
17843 TTAACACTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 15 0.52
25 14 0.48
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAAATAAAAATAAAAAATATTAT
Found at i:34548 original size:20 final size:20
Alignment explanation
Indices: 34519--34556 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
34509 TTTCAAAGGA
34519 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
34539 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
34557 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:34918 original size:11 final size:11
Alignment explanation
Indices: 34902--34927 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
34892 ATAATCAACT
34902 AGAATCAAGAG
1 AGAATCAAGAG
34913 AGAATCAAGAG
1 AGAATCAAGAG
34924 AGAA
1 AGAA
34928 AGCATCAAAC
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:0.58, C:0.08, G:0.27, T:0.08
Consensus pattern (11 bp):
AGAATCAAGAG
Found at i:45054 original size:23 final size:23
Alignment explanation
Indices: 45006--45055 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
44996 ATCATGACTA
*
45006 TTCATGAAAAATAATTAAGTCTT
1 TTCATGAAAAATAATTAAGTCAT
**
45029 TTCATGAAAAATAATTATTTCAT
1 TTCATGAAAAATAATTAAGTCAT
45052 TTCA
1 TTCA
45056 CCCCAAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (23 bp):
TTCATGAAAAATAATTAAGTCAT
Found at i:46919 original size:43 final size:43
Alignment explanation
Indices: 46872--46967 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 43
46862 ACAAAAAATC
* * * * * *
46872 AGGTTATTTATCGGCGTTTTAGATACAAATGCTGTAAAATGTT
1 AGGTTATTTAGCAGCGTTTTAGATACAAACGCCGGAAAAAGTT
*
46915 AGGTTATTTAGCAGTGTTTTAGATACAAACGCCGGAAAAAGTT
1 AGGTTATTTAGCAGCGTTTTAGATACAAACGCCGGAAAAAGTT
*
46958 AGTTTATTTA
1 AGGTTATTTA
46968 ACGGTAAGTC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (43 bp):
AGGTTATTTAGCAGCGTTTTAGATACAAACGCCGGAAAAAGTT
Found at i:47362 original size:12 final size:11
Alignment explanation
Indices: 47337--47374 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
47327 AGAATAAACA
47337 AAGCATAACCT
1 AAGCATAACCT
*
47348 AAGCATCACCCT
1 AAGCAT-AACCT
47360 AAGCATAACCT
1 AAGCATAACCT
47371 AAGC
1 AAGC
47375 TTCCGAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.42, C:0.32, G:0.11, T:0.16
Consensus pattern (11 bp):
AAGCATAACCT
Found at i:64550 original size:2 final size:2
Alignment explanation
Indices: 64543--64571 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
64533 TTCATTCTTT
64543 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
64572 TTGATTTATT
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:67608 original size:10 final size:11
Alignment explanation
Indices: 67588--67644 Score: 53
Period size: 13 Copynumber: 4.8 Consensus size: 11
67578 AGATTCAATC
*
67588 AGAACAAAAAG
1 AGAAAAAAAAG
67599 -GAAAAAAAAG
1 AGAAAAAAAAG
67609 AGAAAAAAGCAAAG
1 AG-AAAAA--AAAG
67623 AGAAAATGAAAAG
1 AGAAAA--AAAAG
67636 AGAAAAAAA
1 AGAAAAAAA
67645 CAAAAGAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
10 9 0.23
11 4 0.10
12 5 0.13
13 14 0.36
14 6 0.15
15 1 0.03
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.02
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:67624 original size:14 final size:14
Alignment explanation
Indices: 67605--67654 Score: 59
Period size: 13 Copynumber: 3.7 Consensus size: 14
67595 AAAGGAAAAA
67605 AAAGAGAAAAAAGC
1 AAAGAGAAAAAAGC
* *
67619 AAAGAG-AAAATGA
1 AAAGAGAAAAAAGC
*
67632 AAAGAGAAAAAAAC
1 AAAGAGAAAAAAGC
67646 AAA-AGAAAA
1 AAAGAGAAAA
67655 TTGAAGAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 17 0.57
14 13 0.43
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAGAAAAAAGC
Found at i:67659 original size:27 final size:27
Alignment explanation
Indices: 67604--67655 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
67594 AAAAGGAAAA
*
67604 AAAAGAGAAAAAAGCAAAGAGAAAATG
1 AAAAGAGAAAAAAACAAAGAGAAAATG
67631 AAAAGAGAAAAAAACAAA-AGAAAAT
1 AAAAGAGAAAAAAACAAAGAGAAAAT
67656 TGAAGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (27 bp):
AAAAGAGAAAAAAACAAAGAGAAAATG
Found at i:68740 original size:32 final size:31
Alignment explanation
Indices: 68704--68810 Score: 124
Period size: 32 Copynumber: 3.4 Consensus size: 31
68694 GAAACAATGA
*
68704 GGGCATCTTTGAAGATTAAACATCAGATGTTG
1 GGGCATCTTTG-AGATTAAACATCAAATGTTG
* *
68736 GGGCATTTTTTGAGATTTAACATCAAATGTTG
1 GGGCA-TCTTTGAGATTAAACATCAAATGTTG
* * * *
68768 GGGCTTTTTTTTAGATTCAACATCAAATGTTG
1 GGGC-ATCTTTGAGATTAAACATCAAATGTTG
68800 GGGCATCTTTG
1 GGGCATCTTTG
68811 GGAATTCAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
31 4 0.06
32 55 0.86
33 5 0.08
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.38
Consensus pattern (31 bp):
GGGCATCTTTGAGATTAAACATCAAATGTTG
Found at i:69651 original size:106 final size:106
Alignment explanation
Indices: 69465--69726 Score: 429
Period size: 106 Copynumber: 2.5 Consensus size: 106
69455 ACAAATGGGC
*
69465 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
69530 CAACTTCGTAACGAAGGGACTG-TTGGTTGTCAACAAACAAT
66 CAACTTCGTAACGAAGGGA-TGATTGGTTGTCAACAAACAAT
69571 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
*
69636 CAACTTC-TCAGCGAAGGGATGATTGGTTGTCAACAAACAAT
66 CAACTTCGT-AACGAAGGGATGATTGGTTGTCAACAAACAAT
* * * * *
69677 TTCCCAGTTCCAGAGCCAACTTCAACTTCACGGCGGAGGATATTAGACTC
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
69727 AGAACAATAC
Statistics
Matches: 147, Mismatches: 7, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
105 3 0.02
106 144 0.98
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (106 bp):
TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
CAACTTCGTAACGAAGGGATGATTGGTTGTCAACAAACAAT
Found at i:70115 original size:38 final size:38
Alignment explanation
Indices: 70042--70115 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
70032 CCTTGAAATG
* *
70042 AATTTTGTCTCTCTTGAGATAGGTTCCCTTAAAACAAA
1 AATTTTGTCTCCCTTGAGACAGGTTCCCTTAAAACAAA
* * *
70080 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGGTTCCCTTAAAACA
70116 TAAACATTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (38 bp):
AATTTTGTCTCCCTTGAGACAGGTTCCCTTAAAACAAA
Found at i:70178 original size:36 final size:36
Alignment explanation
Indices: 70131--70216 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
70121 ATTGAAAACA
** * * *
70131 TTTCCCTTGAAATGAATTTTGTCTCTCTTAAGATAG
1 TTTCCCTTGAAACAAATTTTATCTCCCTTAAGACAG
*
70167 TTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTATCTCCCTTAAGACAG
*
70203 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
70217 TAAACATTGA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTATCTCCCTTAAGACAG
Found at i:70226 original size:101 final size:102
Alignment explanation
Indices: 69877--70270 Score: 504
Period size: 103 Copynumber: 3.9 Consensus size: 102
69867 AGTTTCCAAG
* * * * * * *
69877 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAATCTTTGAATATATTTTCCTTGAAACAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAACATTTCCCTTGAAATAA
* * * * * ** * * *
69941 ATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAG
65 ATTTTGTCTCTCTTAAGATAGTTTCCCTTGAAACAAAA
* * * * * *
69979 TTTTGTCTCTCTTGAGATAATTTCTCTTGAAACATAAGCATTAAAAACATTTCCCTTGAAATGAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAA
* * *
70044 TTTTGTCTCTCTTGAGATAGGTTCCCTTAAAACAAAAA
66 TTTTGTCTCTCTTAAGATAGTTTCCCTTGAAAC-AAAA
*
70082 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAA
70147 TTTTGTCTCTCTTAAGATAGTTTCCCTTGAAAC-AAA
66 TTTTGTCTCTCTTAAGATAGTTTCCCTTGAAACAAAA
*
70183 TTTTATCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAA
70248 TTTTGTCTCTCTTAAGATAGTTT
66 TTTTGTCTCTCTTAAGATAGTTT
70271 TTTTTAAAAA
Statistics
Matches: 258, Mismatches: 32, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
101 89 0.34
102 75 0.29
103 94 0.36
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (102 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAA
TTTTGTCTCTCTTAAGATAGTTTCCCTTGAAACAAAA
Found at i:70369 original size:21 final size:20
Alignment explanation
Indices: 70348--70406 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 20
70338 TTTTGGAAGT
70348 TTTTGTCTCTCTTGAGACAG
1 TTTTGTCTCTCTTGAGACAG
*
70368 ---T-T-TCTCTTGAAACAAG
1 TTTTGTCTCTCTTGAGAC-AG
70384 TTTTGTCTCTCTTGAGACAG
1 TTTTGTCTCTCTTGAGACAG
70404 TTT
1 TTT
70407 CCCTTGAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
15 10 0.32
16 3 0.10
17 1 0.03
19 1 0.03
20 6 0.19
21 10 0.32
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.46
Consensus pattern (20 bp):
TTTTGTCTCTCTTGAGACAG
Found at i:70395 original size:36 final size:36
Alignment explanation
Indices: 70297--70416 Score: 129
Period size: 36 Copynumber: 3.4 Consensus size: 36
70287 CTTTGAATCT
* * * *
70297 GTTTCCCTTGAAACAAATTTCGTCTCCCTCGAGACA
1 GTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACA
* ** *
70333 ATTTCTTTTG---GAAGTTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAG-TTTTGTCTCTCTTGAGACA
*
70367 GTTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACA
70403 GTTTCCCTTGAAAC
1 GTTTCCCTTGAAAC
70417 TTCAACCTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
33 2 0.03
34 24 0.35
36 39 0.57
37 3 0.04
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.40
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACA
Found at i:70635 original size:84 final size:84
Alignment explanation
Indices: 70490--70731 Score: 279
Period size: 84 Copynumber: 2.9 Consensus size: 84
70480 CACCAAACCC
* * * * * * * * *
70490 TCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACGTAACTCAAGGCTAGAAGGGT
1 TCGAGTTTGACTACGCTCAGCTCCAAGGG-ACATCATTTACAGCGTAGCTCAAGGCAAGAAGGGC
70555 TATCTGTCA-CCAAAAGACCT
65 TATCTGTCATCC-AAAGACCT
* * * * * *
70575 TCGAGTTTGACTATGCTCAGCTCTAAGGGACATCATTTGCAGCGTAGCTTAAGTCGAGAAGGGCT
1 TCGAGTTTGACTACGCTCAGCTCCAAGGGACATCATTTACAGCGTAGCTCAAGGCAAGAAGGGCT
70640 ATCTGTCATCCAAAGACCT
66 ATCTGTCATCCAAAGACCT
** * * *
70659 TCGAGTTTGACTACGCTCAGCTCCAAGACACACCATTTACAGCATAGCTCAAGGAAAGAAGGGCT
1 TCGAGTTTGACTACGCTCAGCTCCAAGGGACATCATTTACAGCGTAGCTCAAGGCAAGAAGGGCT
70724 ATCTGTCA
66 ATCTGTCA
70732 ATAAAATTAT
Statistics
Matches: 131, Mismatches: 25, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
84 107 0.82
85 24 0.18
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25
Consensus pattern (84 bp):
TCGAGTTTGACTACGCTCAGCTCCAAGGGACATCATTTACAGCGTAGCTCAAGGCAAGAAGGGCT
ATCTGTCATCCAAAGACCT
Found at i:72516 original size:2 final size:2
Alignment explanation
Indices: 72511--72539 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
72501 TTTTTTTAAT
72511 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
72540 GTTTGGTTTT
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:72598 original size:2 final size:2
Alignment explanation
Indices: 72587--72635 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
72577 CTTTTCATCT
72587 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
72627 TA TA TA TA T
1 TA TA TA TA T
72636 TTGATTTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:78268 original size:112 final size:112
Alignment explanation
Indices: 78071--78295 Score: 393
Period size: 112 Copynumber: 2.0 Consensus size: 112
78061 ATAGCATAAG
78071 CAAGTTCTTCTGTTTTGTCTTCATTCCCCTTTCTAACCAACGAAAATTTTCAATTATGTGTTTTA
1 CAAGTTCTTCTGTTTTGTCTTCATTCCCCTTTCTAACCAACGAAAATTTTCAATTA-GTGTTTTA
78136 TCTATTTTTTATTTAAAAAAAACATTTAATGTCGTCAC-TTTAACAAC
65 TCTATTTTTTATTTAAAAAAAACATTTAATGTCGTCACTTTTAACAAC
78183 CAAGTTCTTCTG-TTTGTCTTTCATTCCCCTTTCTAACCAACGAAAATTTTCAATTA-TGTTTTA
1 CAAGTTCTTCTGTTTTGTC-TTCATTCCCCTTTCTAACCAACGAAAATTTTCAATTAGTGTTTTA
78246 TCTAATTTTTTTATTTAAAAAAAACATTTAATGTCGTCACTTTTAACAAC
65 TCT-A-TTTTTTATTTAAAAAAAACATTTAATGTCGTCACTTTTAACAAC
78296 ACCACATGAT
Statistics
Matches: 109, Mismatches: 0, Indels: 7
0.94 0.00 0.06
Matches are distributed among these distances:
110 10 0.09
111 7 0.06
112 83 0.76
113 9 0.08
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.45
Consensus pattern (112 bp):
CAAGTTCTTCTGTTTTGTCTTCATTCCCCTTTCTAACCAACGAAAATTTTCAATTAGTGTTTTAT
CTATTTTTTATTTAAAAAAAACATTTAATGTCGTCACTTTTAACAAC
Found at i:78525 original size:17 final size:17
Alignment explanation
Indices: 78503--78538 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
78493 ATTTATTTTA
*
78503 TTACTCCTTCATTTAAT
1 TTACTCATTCATTTAAT
*
78520 TTACTCATTTATTTAAT
1 TTACTCATTCATTTAAT
78537 TT
1 TT
78539 GATAGAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.58
Consensus pattern (17 bp):
TTACTCATTCATTTAAT
Found at i:80109 original size:42 final size:42
Alignment explanation
Indices: 80062--80142 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
80052 GCCTTTGAGA
* *
80062 TATAAACGCCGCTAATTTATCACTCTATTACGGCATTTGTGG
1 TATAAACGCCGCTAAATTATCACTATATTACGGCATTTGTGG
* *
80104 TATAAACGCCGCTAAATTATCACTATATTGCGGCGTTTG
1 TATAAACGCCGCTAAATTATCACTATATTACGGCATTTG
80143 GCCTAAAACG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (42 bp):
TATAAACGCCGCTAAATTATCACTATATTACGGCATTTGTGG
Found at i:80997 original size:2 final size:2
Alignment explanation
Indices: 80990--81032 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
80980 AGGATTTTAT
*
80990 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
81032 T
1 T
81033 TGTACTTAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:81580 original size:33 final size:33
Alignment explanation
Indices: 81509--81606 Score: 139
Period size: 33 Copynumber: 3.1 Consensus size: 33
81499 AAGATGAAAA
* *
81509 AATAAGTTGGCCACCTACCAA-A-GATTTTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
81540 AAT-AGTTGGCCACCAACCAAGATGAATTTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
* *
81572 AATAAGTTGGCCACCAACCAAGATAAAATTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
81605 AA
1 AA
81607 CTTGCCAAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
30 16 0.27
31 4 0.07
32 11 0.18
33 29 0.48
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.24
Consensus pattern (33 bp):
AATAAGTTGGCCACCAACCAAGATGAATTTTCC
Found at i:86231 original size:31 final size:33
Alignment explanation
Indices: 86194--86292 Score: 121
Period size: 33 Copynumber: 3.1 Consensus size: 33
86184 AAAGATGAAA
* *
86194 AATAAGTTGGCCACCTACCAA-A-GATTTTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
*
86225 AATAAGTTAGCCACCAACCAAGATGAATTTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
* * * *
86258 AATAAGTTGACCATCAACCAAGATAAAATTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTCC
86291 AA
1 AA
86293 CTTACCAAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 19 0.33
32 1 0.02
33 38 0.66
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.25
Consensus pattern (33 bp):
AATAAGTTGGCCACCAACCAAGATGAATTTTCC
Found at i:89455 original size:21 final size:21
Alignment explanation
Indices: 89434--89475 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
89424 AGCATTGCTA
*
89434 CTCAAGAGAGTATCCATACTAC
1 CTCAA-AGAGTATCAATACTAC
*
89456 CTGAAAGAGTATCAATACTA
1 CTCAAAGAGTATCAATACTA
89476 AATGTATGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.24
Consensus pattern (21 bp):
CTCAAAGAGTATCAATACTAC
Found at i:89502 original size:20 final size:20
Alignment explanation
Indices: 89464--89502 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
89454 ACCTGAAAGA
*
89464 GTATCAATACTAAATGTATG
1 GTATCAATACTAAAGGTATG
*
89484 GTATCAATACTAAGGGTAT
1 GTATCAATACTAAAGGTAT
89503 TTTGGGATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (20 bp):
GTATCAATACTAAAGGTATG
Found at i:90517 original size:20 final size:21
Alignment explanation
Indices: 90492--90551 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
90482 ATATCAGTAC
90492 CAAGGGTAAGTATCGATACT-
1 CAAGGGTAAGTATCGATACTA
*
90512 CAAGGGTCAA-TATCAATACTA
1 CAAGGGT-AAGTATCGATACTA
* *
90533 CAAGGCTTAGTATCGATAC
1 CAAGGGTAAGTATCGATAC
90552 CATCGAAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (21 bp):
CAAGGGTAAGTATCGATACTA
Found at i:90546 original size:21 final size:20
Alignment explanation
Indices: 90500--90551 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
90490 ACCAAGGGTA
*
90500 AGTATCGATACTCAAGGGTC
1 AGTATCGATACTCAAGGCTC
* * *
90520 AATATCAATACTACAAGGCTT
1 AGTATCGATACT-CAAGGCTC
90541 AGTATCGATAC
1 AGTATCGATAC
90552 CATCGAAATG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (20 bp):
AGTATCGATACTCAAGGCTC
Found at i:92643 original size:20 final size:22
Alignment explanation
Indices: 92608--92653 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
92598 TTGAAGTACT
*
92608 ATGTTGGAATTTAGATGTTAGA
1 ATGTTGGAATTTAGATGTTAAA
92630 ATGTT-GAA-TTAGATGTTAAA
1 ATGTTGGAATTTAGATGTTAAA
92650 ATGT
1 ATGT
92654 GAAATTGGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.65
21 3 0.13
22 5 0.22
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (22 bp):
ATGTTGGAATTTAGATGTTAAA
Found at i:93202 original size:19 final size:19
Alignment explanation
Indices: 93178--93215 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
93168 ATTGGAATCA
93178 AATATTAAAATATTGATTT
1 AATATTAAAATATTGATTT
* *
93197 AATATTGAAATGTTGATTT
1 AATATTAAAATATTGATTT
93216 TGGGTTAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (19 bp):
AATATTAAAATATTGATTT
Found at i:93975 original size:47 final size:47
Alignment explanation
Indices: 93818--93965 Score: 188
Period size: 47 Copynumber: 3.1 Consensus size: 47
93808 ATGTACGATA
* * * *
93818 TGTTACTGGCAGTTTATACTGCATACTGGGCACTAAATGTGCCATAC
1 TGTTACTGACAGTTTATACTGCATACTGGGCATTGAATGTGTCATAC
* * *
93865 TGTAACTGACAGTTTATACTGCATATTGGGAATTGAATGTGTCATAC
1 TGTTACTGACAGTTTATACTGCATACTGGGCATTGAATGTGTCATAC
* * * * *
93912 TGTTAATGATAGTTTATACTGAATACTAGGCATTGAATGTGTCATAT
1 TGTTACTGACAGTTTATACTGCATACTGGGCATTGAATGTGTCATAC
93959 TGTTACT
1 TGTTACT
93966 AGTAGTTTAT
Statistics
Matches: 85, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 85 1.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.37
Consensus pattern (47 bp):
TGTTACTGACAGTTTATACTGCATACTGGGCATTGAATGTGTCATAC
Found at i:94841 original size:16 final size:15
Alignment explanation
Indices: 94816--94845 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
94806 TACATATATC
94816 TATTTTATCTTTATA
1 TATTTTATCTTTATA
94831 TATTCTTATCTTTAT
1 TATT-TTATCTTTAT
94846 TTTATTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTATCTTTATA
Found at i:95225 original size:3 final size:3
Alignment explanation
Indices: 95217--95241 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
95207 TCATGATTAT
95217 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
95242 AACCCAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:95856 original size:34 final size:35
Alignment explanation
Indices: 95791--95857 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 35
95781 ACATTGAGCT
*
95791 ATATATTGAAACTAAAAGAAATAATATAGTAAAAG
1 ATATATTGAAACTAAAAGAAATAATACAGTAAAAG
* *
95826 ATATATT-ACAAC-AAAAGATATAGTACAGTAAA
1 ATATATTGA-AACTAAAAGAAATAATACAGTAAA
95858 GGACATAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 18 0.64
35 10 0.36
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.25
Consensus pattern (35 bp):
ATATATTGAAACTAAAAGAAATAATACAGTAAAAG
Found at i:97837 original size:16 final size:16
Alignment explanation
Indices: 97816--97847 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
97806 ACTGCTTTCA
*
97816 AAGTTTTAATATATAT
1 AAGTTTAAATATATAT
97832 AAGTTTAAATATATAT
1 AAGTTTAAATATATAT
97848 TAATAATTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
AAGTTTAAATATATAT
Found at i:102629 original size:26 final size:23
Alignment explanation
Indices: 102603--102648 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
102593 ATCAAGGAGA
102603 AGAAGACAACTAAGGAGATATGT
1 AGAAGACAACTAAGGAGATATGT
102626 AGAAGACAACTAAGGAGATATGT
1 AGAAGACAACTAAGGAGATATGT
102649 GATCATCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.26, T:0.17
Consensus pattern (23 bp):
AGAAGACAACTAAGGAGATATGT
Found at i:104895 original size:19 final size:19
Alignment explanation
Indices: 104871--104934 Score: 101
Period size: 19 Copynumber: 3.4 Consensus size: 19
104861 GGGTCTTCAA
104871 AATCAAGCGAAATGGTGAC
1 AATCAAGCGAAATGGTGAC
104890 AATCAAGCGAAATGGTGAC
1 AATCAAGCGAAATGGTGAC
* *
104909 GATCAAGCGAAATGGTTAC
1 AATCAAGCGAAATGGTGAC
*
104928 GATCAAG
1 AATCAAG
104935 TGGAGAGGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.41, C:0.16, G:0.27, T:0.17
Consensus pattern (19 bp):
AATCAAGCGAAATGGTGAC
Found at i:106421 original size:19 final size:19
Alignment explanation
Indices: 106397--106434 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
106387 AATTCCAAAG
*
106397 TCCAAATTGGCTGCACATT
1 TCCAAATCGGCTGCACATT
106416 TCCAAATCGGCTGCACATT
1 TCCAAATCGGCTGCACATT
106435 CCACCGAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (19 bp):
TCCAAATCGGCTGCACATT
Found at i:107307 original size:19 final size:19
Alignment explanation
Indices: 107283--107346 Score: 101
Period size: 19 Copynumber: 3.4 Consensus size: 19
107273 GGGTCTTCAA
107283 AATCAAGCGAAATGGTGAC
1 AATCAAGCGAAATGGTGAC
107302 AATCAAGCGAAATGGTGAC
1 AATCAAGCGAAATGGTGAC
* *
107321 GATCAAGCGAAATGGTTAC
1 AATCAAGCGAAATGGTGAC
*
107340 GATCAAG
1 AATCAAG
107347 TGGAGAGGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.41, C:0.16, G:0.27, T:0.17
Consensus pattern (19 bp):
AATCAAGCGAAATGGTGAC
Found at i:108833 original size:19 final size:19
Alignment explanation
Indices: 108809--108846 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
108799 AATTCCAAAG
*
108809 TCCAAATTGGCTGCACATT
1 TCCAAATCGGCTGCACATT
108828 TCCAAATCGGCTGCACATT
1 TCCAAATCGGCTGCACATT
108847 CCACCGAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (19 bp):
TCCAAATCGGCTGCACATT
Found at i:112427 original size:3 final size:3
Alignment explanation
Indices: 112419--112498 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
112409 GGGGCTTAAA
112419 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
112467 ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
112499 CATCATCATC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:118967 original size:67 final size:67
Alignment explanation
Indices: 118841--119403 Score: 736
Period size: 67 Copynumber: 8.5 Consensus size: 67
118831 TTCTAAAAAT
* * * *
118841 AAGTTTTGTCTCTCTTGAGACAGTTCCT-TTTAAAAAAAAATCTTTGAGTTTGTTTCCCTTGAAA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAA
118905 CA
66 CA
* *
118907 AAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAA-AGAAAATATTTGAGTCTGTTTCCCTTGAA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AAAATCTTTGAGTCTGTTTCCCTTGAA
118971 ACA
65 ACA
* * * * *
118974 AAGTTTTGTCTCTTTTGAGATAGTTTCTCTTGAAATAAAAATCTTTGAGTTTGTTTCTCTTGAAA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAA
119039 CA
66 CA
* * * * * * *
119041 AAGTTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAGTTTTTGAATCCGTTTCCTTTAAAA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAA
119106 CA
66 CA
* * *
119108 AAGTTTTGTCTCTCTCGAGACAGTTTCTCTTGAAACAAAAGTCTTTGAGTCTGTTTCTCTTGAAA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAA
119173 CA
66 CA
* *
119175 AAG-TTTGTCTCTCTTGAGACAGTTTTTCTTG-AA-AAAAATCTTTGAGTCTGTTTCTCTTGAAA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAA
*
119237 -T
66 CA
* * *
119238 AAGTTTTGTCT-TCCTTGAGATAGTTTCTCTTGAAACACAAATCTTTGAGTATGTTTCCCTTGAA
1 AAGTTTTGTCTCT-CTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAA
119302 ACA
65 ACA
* * *
119305 AA-TTTTGTCTCTCTTGAGACAGTTTC-CTTAAAACATAAA-CATTGAGGT-TGTTTCCCTTGAA
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGA-GTCTGTTTCCCTTGAA
119366 AC-
65 ACA
*
119368 AAGTTTTGTCTCTCTTGAGACGGTTTCTCTTGAAAC
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
119404 CATTATCCCT
Statistics
Matches: 438, Mismatches: 47, Indels: 25
0.86 0.09 0.05
Matches are distributed among these distances:
63 6 0.01
64 95 0.22
65 24 0.05
66 100 0.23
67 212 0.48
68 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (67 bp):
AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAA
CA
Found at i:119000 original size:37 final size:37
Alignment explanation
Indices: 118959--119208 Score: 118
Period size: 30 Copynumber: 7.4 Consensus size: 37
118949 ATTTGAGTCT
*
118959 GTTTCCCTTGAAACAAAGTTTTGTCTCTTTTGAGATA
1 GTTTCTCTTGAAACAAAGTTTTGTCTCTTTTGAGATA
* ** * *
118996 GTTTCTCTTGAAATAAA------AATC-TTTGAGTTT
1 GTTTCTCTTGAAACAAAGTTTTGTCTCTTTTGAGATA
* *
119026 GTTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAAGTTTTGTCTCTTTTGAGATA
* * *
119063 ATTTCTCTTGAAACAAA----AG--T-TTTTGA-ATCC
1 GTTTCTCTTGAAACAAAGTTTTGTCTCTTTTGAGAT-A
* * * *
119093 GTTTC-CTTTAAAACAAAGTTTTGTCTCTCTCGAGACA
1 GTTTCTC-TTGAAACAAAGTTTTGTCTCTTTTGAGATA
* *
119130 GTTTCTCTTGAAACAAA----AG--TC-TTTGAG-TCT
1 GTTTCTCTTGAAACAAAGTTTTGTCTCTTTTGAGAT-A
* *
119160 GTTTCTCTTGAAACAAAG-TTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAAGTTTTGTCTCTTTTGAGATA
*
119196 GTTTTTCTTGAAA
1 GTTTCTCTTGAAA
119209 AAAATCTTTG
Statistics
Matches: 151, Mismatches: 36, Indels: 53
0.63 0.15 0.22
Matches are distributed among these distances:
29 2 0.01
30 62 0.41
31 5 0.03
33 3 0.02
34 1 0.01
35 2 0.01
36 20 0.13
37 54 0.36
38 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.42
Consensus pattern (37 bp):
GTTTCTCTTGAAACAAAGTTTTGTCTCTTTTGAGATA
Found at i:120921 original size:2 final size:2
Alignment explanation
Indices: 120910--120956 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
120900 TTGGCCTTGG
120910 AT AT -T 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
120951 AT AT AT
1 AT AT AT
120957 TAAGTGTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:128222 original size:2 final size:2
Alignment explanation
Indices: 128217--128246 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
128207 ACAAAAATAA
128217 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
128247 GGGTCAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128457 original size:2 final size:2
Alignment explanation
Indices: 128446--128485 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
128436 AATTTTGAAT
*
128446 TC TC -C TC TC TC TC TC TC TC TC TC TC TG TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
128486 TTTTGGCTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
TC
Found at i:133343 original size:55 final size:55
Alignment explanation
Indices: 133285--133607 Score: 399
Period size: 55 Copynumber: 5.9 Consensus size: 55
133275 TGACGAGCCT
* *** **
133285 GCTCCCTATTCGTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATATGTTT
1 GCTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACGGGTCC
* * *
133340 GCTCCCTATTCGTTCAGGGAGTATCAG-ACTCGAACAATCTTCA-ACAAACAGGTCC
1 GCTCCCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCATA-AAACGGGTCC
*
133395 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
* * *
133450 GCTCTCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
*
133505 GCTCCCTATTCCATCAGAGAGTATAGAACTC--A-AATCTTCATACAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCC
* * *
133558 GCTCCCTATTCATTCAGTGAGTATAGAACTCGAACAATCTTCATCAAACG
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACG
133608 TATTTGCTTC
Statistics
Matches: 240, Mismatches: 18, Indels: 20
0.86 0.06 0.07
Matches are distributed among these distances:
52 10 0.04
53 38 0.16
54 3 0.01
55 177 0.74
56 12 0.05
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
Found at i:134988 original size:12 final size:13
Alignment explanation
Indices: 134966--135016 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
134956 TTCTTTATTT
134966 TTTTCATTTTTCTC
1 TTTT-ATTTTTCTC
*
134980 TTTTGTTTTTCTC
1 TTTTATTTTTCTC
134993 TTTTA-TTTTCTC
1 TTTTATTTTTCTC
*
135005 TTTCATTTTTCT
1 TTTTATTTTTCT
135017 TCCATTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.33
13 18 0.55
14 4 0.12
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.75
Consensus pattern (13 bp):
TTTTATTTTTCTC
Found at i:135014 original size:13 final size:13
Alignment explanation
Indices: 134967--135050 Score: 72
Period size: 12 Copynumber: 6.9 Consensus size: 13
134957 TCTTTATTTT
134967 TTTCATTTTTCTC
1 TTTCATTTTTCTC
**
134980 TTTTGTTTTTCTC
1 TTTCATTTTTCTC
*
134993 TTTTA-TTTTCTC
1 TTTCATTTTTCTC
135005 TTTCA-TTTT-TC
1 TTTCATTTTTCTC
*
135016 TTCCA-TTTTCT-
1 TTTCATTTTTCTC
135027 TTTCATTTTT-TC
1 TTTCATTTTTCTC
**
135039 CATCATTTTTCT
1 TTTCATTTTTCT
135051 TTTTTCTCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
11 15 0.25
12 28 0.47
13 16 0.27
ACGTcount: A:0.08, C:0.20, G:0.01, T:0.70
Consensus pattern (13 bp):
TTTCATTTTTCTC
Found at i:135022 original size:11 final size:12
Alignment explanation
Indices: 134986--135035 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 12
134976 TCTCTTTTGT
**
134986 TTTTCTCTTTTA
1 TTTTCTCTTCCA
*
134998 TTTTCTCTTTCA
1 TTTTCTCTTCCA
135010 TTTT-TCTTCCA
1 TTTTCTCTTCCA
*
135021 TTTTCT-TTTCA
1 TTTTCTCTTCCA
135032 TTTT
1 TTTT
135036 TTCCATCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
11 18 0.53
12 16 0.47
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTCTCTTCCA
Found at i:135045 original size:23 final size:22
Alignment explanation
Indices: 134997--135053 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
134987 TTTCTCTTTT
*
134997 ATTTTCTCTTTCATTTTTCTTCC
1 ATTTTCT-TTTCATTTTTCATCC
135020 ATTTTCTTTTCATTTTTTCCAT-C
1 ATTTTCTTTTCA-TTTTT-CATCC
135043 ATTTTTCTTTT
1 A-TTTTCTTTT
135054 TTCTCATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.17
23 14 0.47
24 11 0.37
ACGTcount: A:0.11, C:0.21, G:0.00, T:0.68
Consensus pattern (22 bp):
ATTTTCTTTTCATTTTTCATCC
Found at i:135060 original size:16 final size:16
Alignment explanation
Indices: 135026--135093 Score: 70
Period size: 16 Copynumber: 4.2 Consensus size: 16
135016 TTCCATTTTC
135026 TTTTCATTTTTTCCATCAT
1 TTTTC-TTTTTT-C-TCAT
135045 TTTTCTTTTTTCTCAT
1 TTTTCTTTTTTCTCAT
*
135061 TTTTCTTTTCT-TC-T
1 TTTTCTTTTTTCTCAT
*
135075 TTTTC-TTCTTCTCAT
1 TTTTCTTTTTTCTCAT
135090 TTTT
1 TTTT
135094 ATTATTTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
13 3 0.07
14 8 0.18
15 7 0.16
16 14 0.32
17 1 0.02
18 6 0.14
19 5 0.11
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTCTTTTTTCTCAT
Found at i:135071 original size:14 final size:14
Alignment explanation
Indices: 135041--135093 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
135031 ATTTTTTCCA
135041 TCATTTTTCTTTTTTC
1 TCATTTTTC--TTTTC
135057 TCATTTTTCTTTTC
1 TCATTTTTCTTTTC
135071 TTC-TTTTTCTTCTTC
1 -TCATTTTTCTT-TTC
135086 TCATTTTT
1 TCATTTTT
135094 ATTATTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 15 0.44
15 10 0.29
16 9 0.26
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.74
Consensus pattern (14 bp):
TCATTTTTCTTTTC
Found at i:136687 original size:15 final size:15
Alignment explanation
Indices: 136667--136702 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
136657 AATCTCCATA
136667 TACTTTAAGCATTTT
1 TACTTTAAGCATTTT
136682 TACTTTAAGCATTTT
1 TACTTTAAGCATTTT
136697 TACTTT
1 TACTTT
136703 GCGTTCAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.56
Consensus pattern (15 bp):
TACTTTAAGCATTTT
Found at i:139351 original size:25 final size:25
Alignment explanation
Indices: 139323--139378 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
139313 GAGCCATATC
139323 TTGGTACAATCTGACAATCGAGGCT
1 TTGGTACAATCTGACAATCGAGGCT
139348 TTGGTACAATCTGACAATCGAGGCT
1 TTGGTACAATCTGACAATCGAGGCT
139373 TTGGTA
1 TTGGTA
139379 TCTTCCTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (25 bp):
TTGGTACAATCTGACAATCGAGGCT
Found at i:144873 original size:45 final size:46
Alignment explanation
Indices: 144806--144909 Score: 174
Period size: 45 Copynumber: 2.3 Consensus size: 46
144796 CCATGCTTTG
144806 TTATTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
1 TTATTCA-AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
*
144853 TTATTCAAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
*
144898 TTATTTAAAAAA
1 TTATTCAAAAAA
144910 CGAAAATAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
45 39 0.71
46 9 0.16
47 7 0.13
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (46 bp):
TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
Found at i:151095 original size:22 final size:22
Alignment explanation
Indices: 151065--151130 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
151055 TTAAAAATCG
151065 AATATATAAACGAACGATAAACA
1 AATA-ATAAACGAACGATAAACA
*
151088 AATAATAAAAC-AACGCTAAACA
1 AATAAT-AAACGAACGATAAACA
* * * *
151110 AACACTAAATGAACGTTAAAC
1 AATAATAAACGAACGATAAAC
151131 GAACATGTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 3 0.08
22 25 0.69
23 8 0.22
ACGTcount: A:0.59, C:0.17, G:0.08, T:0.17
Consensus pattern (22 bp):
AATAATAAACGAACGATAAACA
Found at i:151158 original size:24 final size:24
Alignment explanation
Indices: 151131--151207 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 24
151121 AACGTTAAAC
151131 GAACATGTTCAAGAATAAATTCGT
1 GAACATGTTCAAGAATAAATTCGT
* *
151155 GAACAT-ATAAACGAACGCTAAA--C--
1 GAACATGTTCAA-GAA---TAAATTCGT
151178 GAACATGTTCAAGAATAAATTCGT
1 GAACATGTTCAAGAATAAATTCGT
151202 GAACAT
1 GAACAT
151208 ATAAACGAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
20 4 0.10
22 1 0.03
23 12 0.30
24 18 0.45
25 1 0.03
27 4 0.10
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (24 bp):
GAACATGTTCAAGAATAAATTCGT
Found at i:151177 original size:47 final size:47
Alignment explanation
Indices: 151115--151234 Score: 213
Period size: 47 Copynumber: 2.6 Consensus size: 47
151105 AAACAAACAC
*
151115 TAAATGAACGTTAAACGAACATGTTCAAGAATAAATTCGTGAACATA
1 TAAACGAACGTTAAACGAACATGTTCAAGAATAAATTCGTGAACATA
*
151162 TAAACGAACGCTAAACGAACATGTTCAAGAATAAATTCGTGAACATA
1 TAAACGAACGTTAAACGAACATGTTCAAGAATAAATTCGTGAACATA
*
151209 TAAACGAACGTTAAACGGACATGTTC
1 TAAACGAACGTTAAACGAACATGTTC
151235 GTGAACATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (47 bp):
TAAACGAACGTTAAACGAACATGTTCAAGAATAAATTCGTGAACATA
Found at i:151240 original size:23 final size:23
Alignment explanation
Indices: 151214--151293 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
151204 ACATATAAAC
* *
151214 GAACGTTAAACGGACATGTTCGT
1 GAACATTAAACGAACATGTTCGT
** * *
151237 GAACATATAAACGAACACATTTGC
1 GAACAT-TAAACGAACATGTTCGT
*
151261 GAACATTAAATGAACATGTTCGT
1 GAACATTAAACGAACATGTTCGT
*
151284 GAACAATAAA
1 GAACATTAAA
151294 TAAACGAACA
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
23 26 0.59
24 18 0.41
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.24
Consensus pattern (23 bp):
GAACATTAAACGAACATGTTCGT
Found at i:151253 original size:47 final size:47
Alignment explanation
Indices: 151155--151303 Score: 127
Period size: 47 Copynumber: 3.1 Consensus size: 47
151145 ATAAATTCGT
* ** * * ****
151155 GAACATATAAACGAACGCTAAACGAACATGTTCAAGAATAAATTCGT
1 GAACATATAAACGAACGTTAAACGAACATGTTCGTGAACATATAAAC
*
151202 GAACATATAAACGAACGTTAAACGGACATGTTCGTGAACATATAAAC
1 GAACATATAAACGAACGTTAAACGAACATGTTCGTGAACATATAAAC
* *** * *
151249 GAACACATTTGCGAACATTAAATGAACATGTTCGTGAACAATAAATAAAC
1 GAACATATAAACGAACGTTAAACGAACATGTTCGTGAAC-AT--ATAAAC
151299 GAACA
1 GAACA
151304 CCAACACCTT
Statistics
Matches: 82, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
47 69 0.84
48 2 0.02
50 11 0.13
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.21
Consensus pattern (47 bp):
GAACATATAAACGAACGTTAAACGAACATGTTCGTGAACATATAAAC
Found at i:152940 original size:15 final size:17
Alignment explanation
Indices: 152920--152956 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
152910 AGTTTAACTC
152920 TTATTAT-T-TAAAATT
1 TTATTATGTATAAAATT
152935 TTATTATGTATAAAATT
1 TTATTATGTATAAAATT
*
152952 ATATT
1 TTATT
152957 TAAAAAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 1 0.05
17 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTATTATGTATAAAATT
Found at i:155482 original size:70 final size:70
Alignment explanation
Indices: 155368--155512 Score: 272
Period size: 70 Copynumber: 2.1 Consensus size: 70
155358 TTTATTTTAT
*
155368 TTGTTCAAACCAAATGTGTAAACTATTTATCTTACATAGTCATGGACCATTTCACTTTAGCCTTT
1 TTGTTCAAACCAAATGTGTAAACTATTTATCTTACATAGGCATGGACCATTTCACTTTAGCCTTT
155433 TATAA
66 TATAA
*
155438 TTGTTCAAACCAAATGTGTAAACTATTTATCTTACATAGGCATGGACCATTTCACTTTAGCTTTT
1 TTGTTCAAACCAAATGTGTAAACTATTTATCTTACATAGGCATGGACCATTTCACTTTAGCCTTT
155503 TATAA
66 TATAA
155508 TTGTT
1 TTGTT
155513 TAAATATTGA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.41
Consensus pattern (70 bp):
TTGTTCAAACCAAATGTGTAAACTATTTATCTTACATAGGCATGGACCATTTCACTTTAGCCTTT
TATAA
Found at i:159427 original size:31 final size:31
Alignment explanation
Indices: 159352--159419 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
159342 TTGCAATACA
*
159352 GTCCCCCAATATTTAGTTCATTTGCAAAATG
1 GTCCCCCAACATTTAGTTCATTTGCAAAATG
*
159383 GTCCCCCAACATTTAG-TCTATTTGCAATATG
1 GTCCCCCAACATTTAGTTC-ATTTGCAAAATG
159414 GTCCCC
1 GTCCCC
159420 GACCATTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (31 bp):
GTCCCCCAACATTTAGTTCATTTGCAAAATG
Found at i:161414 original size:31 final size:31
Alignment explanation
Indices: 161346--161420 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
161336 TGAAACGGTC
* *
161346 GGGGACCATATTGTAAACAGACGAAATGTTA
1 GGGGACTATATTGCAAACAGACGAAATGTTA
* * *
161377 GGGGACTATATTGCAAACGGACTAAATGTTG
1 GGGGACTATATTGCAAACAGACGAAATGTTA
*
161408 GGGGACTGTATTG
1 GGGGACTATATTG
161421 GAAGTTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.32, C:0.12, G:0.31, T:0.25
Consensus pattern (31 bp):
GGGGACTATATTGCAAACAGACGAAATGTTA
Found at i:161519 original size:17 final size:17
Alignment explanation
Indices: 161497--161529 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
161487 TACCCTAATT
161497 TTTATAATATATTTATC
1 TTTATAATATATTTATC
161514 TTTATAATATATTTAT
1 TTTATAATATATTTAT
161530 TTAAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTATAATATATTTATC
Found at i:161532 original size:15 final size:16
Alignment explanation
Indices: 161497--161537 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
161487 TACCCTAATT
161497 TTTATAATATATTTATC
1 TTTATAATATATTTA-C
161514 TTTATAATATATTTA-
1 TTTATAATATATTTAC
*
161529 TTTAAAATA
1 TTTATAATA
161538 ATTGATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.35
17 15 0.65
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTATAATATATTTAC
Found at i:164423 original size:66 final size:63
Alignment explanation
Indices: 164337--164590 Score: 233
Period size: 66 Copynumber: 3.9 Consensus size: 63
164327 TGAAGTGAAT
* * * * * *
164337 ATGGAGGAGAAGGAAATGATAATTGTTGAGGTTGTGTGGACAGTAATGGAGGAACTGAATGTGGA
1 ATGGAAGAGATGGAGATGATAATTGTTGAGGATGTGTGGA-AG--ATGGATGAAGTGAATGTGGA
164402 G
63 G
* * *
164403 ATGGAAGAGATAGAGATGATAATTGTTGTGGATGTGTGGATGGGGATGGATGAAGTGAATGTGGA
1 ATGGAAGAGATGGAGATGATAATTGTTGAGGATGTGTGGA---AGATGGATGAAGTGAATGTGGA
164468 G
63 G
* * *
164469 ATGGAAGAGATGGAGATGATAACTGTTGTAGTG-TCTTGATGG-AGATGGATGAAGTGAAAGTGG
1 ATGGAAGAGATGGAGATGATAATTGTTG-AG-GAT-GTG-TGGAAGATGGATGAAGTGAATGTGG
164532 AG
62 AG
* * * * *
164534 ATGGAGGAGACGGAGATGATAATTGTTGTGGATGTGTGATGGAGATGAATGAAGTGA
1 ATGGAAGAGATGGAGATGATAATTGTTGAGGATGTGTG--GAAGATGGATGAAGTGA
164591 GTGTAAAAAA
Statistics
Matches: 156, Mismatches: 22, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
62 2 0.01
63 3 0.02
64 3 0.02
65 60 0.38
66 79 0.51
67 2 0.01
68 4 0.03
69 3 0.02
ACGTcount: A:0.32, C:0.02, G:0.40, T:0.26
Consensus pattern (63 bp):
ATGGAAGAGATGGAGATGATAATTGTTGAGGATGTGTGGAAGATGGATGAAGTGAATGTGGAG
Found at i:164610 original size:65 final size:65
Alignment explanation
Indices: 164315--164590 Score: 289
Period size: 65 Copynumber: 4.3 Consensus size: 65
164305 TGGAGATGAC
* * * * *
164315 GATGGAGATGGGTGAAGTGAATAT-G-GA-GG-AGA-A-GGAAATGATAATTGTTGAGGTTGTGT
1 GATGGAGATGGATGAAGTGAATGTGGAGATGGAAGAGACGGAGATGATAATTGTTGTGGATGTGT
* * * * **
164374 GGACAGTA-ATGGAGGAACTGAATGTGGAGATGGAAGAGATAGAGATGATAATTGTTGTGGATGT
1 -GA-TGGAGATGGATGAAGTGAATGTGGAGATGGAAGAGACGGAGATGATAATTGTTGTGGATGT
164438 GT
64 GT
* * * *
164440 GGATGGGGATGGATGAAGTGAATGTGGAGATGGAAGAGATGGAGATGATAACTGTTGTAG-TGTC
1 -GATGGAGATGGATGAAGTGAATGTGGAGATGGAAGAGACGGAGATGATAATTGTTGTGGATGT-
*
164504 TT
64 GT
* *
164506 GATGGAGATGGATGAAGTGAAAGTGGAGATGGAGGAGACGGAGATGATAATTGTTGTGGATGTGT
1 GATGGAGATGGATGAAGTGAATGTGGAGATGGAAGAGACGGAGATGATAATTGTTGTGGATGTGT
*
164571 GATGGAGATGAATGAAGTGA
1 GATGGAGATGGATGAAGTGA
164591 GTGTAAAAAA
Statistics
Matches: 179, Mismatches: 27, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
60 15 0.08
61 3 0.02
62 2 0.01
63 2 0.01
64 3 0.02
65 78 0.44
66 76 0.42
ACGTcount: A:0.32, C:0.02, G:0.41, T:0.26
Consensus pattern (65 bp):
GATGGAGATGGATGAAGTGAATGTGGAGATGGAAGAGACGGAGATGATAATTGTTGTGGATGTGT
Found at i:173481 original size:2 final size:2
Alignment explanation
Indices: 173474--173509 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
173464 ATATTTTTCA
173474 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
173510 CAATTATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:185966 original size:13 final size:13
Alignment explanation
Indices: 185948--185977 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
185938 AAATAAATAA
185948 AAAATATTTTAAC
1 AAAATATTTTAAC
*
185961 AAAATATTTTAAT
1 AAAATATTTTAAC
185974 AAAA
1 AAAA
185978 AATAAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAATATTTTAAC
Found at i:186638 original size:17 final size:18
Alignment explanation
Indices: 186616--186650 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
186606 ATAACATTGC
186616 GAAAA-TACAAATAATAA
1 GAAAATTACAAATAATAA
*
186633 GAAAATTACAATTAATAA
1 GAAAATTACAAATAATAA
186651 TAATAATGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (18 bp):
GAAAATTACAAATAATAA
Found at i:191527 original size:5 final size:5
Alignment explanation
Indices: 191517--191545 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
191507 TTTTCGTTCT
191517 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
191546 TCCTTGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:191529 original size:26 final size:25
Alignment explanation
Indices: 191487--191535 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
191477 AACCCGATTT
191487 TTCTTTTTTTTCAATTTCTATTTTCG
1 TTCTTTTTTTTCAATTT-TATTTTCG
*
191513 TTCTTTTTATTT-TATTTTATTTT
1 TTCTTTTT-TTTCAATTTTATTTT
191536 ATTTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 6 0.29
26 12 0.57
27 3 0.14
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (25 bp):
TTCTTTTTTTTCAATTTTATTTTCG
Found at i:192714 original size:5 final size:5
Alignment explanation
Indices: 192704--192762 Score: 66
Period size: 5 Copynumber: 11.8 Consensus size: 5
192694 TCATTTGGAA
* * * *
192704 AAAAC AAAAC AAAAG AAAAG AAAAA AAAAG AAAAG AAAA- AAAAA AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
192753 AAAAAG AAAA
1 -AAAAG AAAA
192763 AAATCGTGCA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.08
5 39 0.81
6 5 0.10
ACGTcount: A:0.86, C:0.03, G:0.10, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:192727 original size:15 final size:14
Alignment explanation
Indices: 192704--192757 Score: 72
Period size: 14 Copynumber: 3.7 Consensus size: 14
192694 TCATTTGGAA
*
192704 AAAACAAAACAAAAG
1 AAAAGAAAA-AAAAG
192719 AAAAGAAAAAAAAAG
1 AAAAG-AAAAAAAAG
*
192734 AAAAGAAAAAAAAA
1 AAAAGAAAAAAAAG
192748 AAAAGAAAAA
1 AAAAGAAAAA
192758 GAAAAAAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 18 0.50
15 14 0.39
16 4 0.11
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:192730 original size:1 final size:1
Alignment explanation
Indices: 192702--192765 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
192692 TTTCATTTGG
* * * * * * * *
192702 AAAAAACAAAACAAAAGAAAAGAAAAAAAAAGAAAAGAAAAAAAAAAAAAGAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
192766 TCGTGCAAAG
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:192732 original size:20 final size:19
Alignment explanation
Indices: 192702--192765 Score: 92
Period size: 20 Copynumber: 3.3 Consensus size: 19
192692 TTTCATTTGG
* *
192702 AAAAAACAAAACAAAAGAA
1 AAAAAAAAAAAGAAAAGAA
192721 AAGAAAAAAAAAGAAAAGAA
1 AA-AAAAAAAAAGAAAAGAA
192741 AAAAAAAAAAAGAAAAAGAA
1 AAAAAAAAAAAG-AAAAGAA
192761 AAAAA
1 AAAAA
192766 TCGTGCAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
19 12 0.29
20 29 0.71
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAGAAAAGAA
Found at i:192765 original size:15 final size:15
Alignment explanation
Indices: 192704--192762 Score: 84
Period size: 15 Copynumber: 3.9 Consensus size: 15
192694 TCATTTGGAA
* *
192704 AAAACAAAACAAAAG
1 AAAAGAAAAAAAAAG
192719 AAAAGAAAAAAAAAG
1 AAAAGAAAAAAAAAG
192734 AAAAGAAAAAAAAA-
1 AAAAGAAAAAAAAAG
192748 AAAAGAAAAAGAAAA
1 AAAAGAAAAA-AAAA
192763 AAATCGTGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
14 10 0.24
15 31 0.76
ACGTcount: A:0.86, C:0.03, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAAAAG
Done.