Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008523.1 Hibiscus syriacus cultivar Beakdansim tig00111392_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: 4657139
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 18
Found at i:1415055 original size:52 final size:52
Alignment explanation
Indices: 1414968--1415246 Score: 388
Period size: 52 Copynumber: 5.2 Consensus size: 52
1414958 AAATCCCAAC
1414968 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1415021 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1415073 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
1415125 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
1415182 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
1415234 ATGAAAATCGCAA
1 ATGAAAATCGCAA
1415247 CGAGATAATC
Statistics
Matches: 216, Mismatches: 5, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
52 164 0.76
53 16 0.07
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.12
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1415091 original size:71 final size:71
Alignment explanation
Indices: 1415007--1415246 Score: 373
Period size: 71 Copynumber: 3.4 Consensus size: 71
1414997 GCAACGAGAG
*
1415007 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1415072 AATGAA
66 AATGAA
* *
1415078 AATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
1415138 TGCGAAATGAA
61 TGCGAAATGAA
1415149 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1415214 AATGAA
66 AATGAA
1415220 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
1415247 CGAGATAATC
Statistics
Matches: 154, Mismatches: 5, Indels: 20
0.86 0.03 0.11
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 5 0.03
71 121 0.79
73 6 0.04
74 3 0.02
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:1415192 original size:142 final size:138
Alignment explanation
Indices: 1414940--1415284 Score: 518
Period size: 142 Copynumber: 2.5 Consensus size: 138
1414930 CGGAAAATAC
* * *
1414940 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAA--CG
1 AATCGCAATGCGAAATGAAAATCGCAAC--GAAAATCGCAATGC-GAAATTAAAATCGCAATGCG
* *
1415003 -AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAA
63 AAGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA
1415067 TGCGAAATGAA
128 TGCGAAATGAA
1415078 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-A-AATCGCAATGCGAAATTAAAATCGCAATGCG-
1415143 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
63 AA-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
1415208 ATGCGAAATGAA
127 ATGCGAAATGAA
*
1415220 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTATAAA-CGCATTGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGA-A-AATCGCAATGCGAAATTA-AAATCGCAATGCG
1415284 A
63 A
1415285 TTTTCATTTC
Statistics
Matches: 191, Mismatches: 8, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
136 2 0.01
137 16 0.08
138 37 0.19
139 2 0.01
141 2 0.01
142 129 0.68
143 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (138 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAATCGCAATGCGAAATTAAAATCGCAATGCGAAG
AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGC
GAAATGAA
Found at i:1415247 original size:52 final size:55
Alignment explanation
Indices: 1414940--1415268 Score: 332
Period size: 52 Copynumber: 6.3 Consensus size: 55
1414930 CGGAAAATAC
* *
1414940 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAATG-A
*
1414993 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
*
1415045 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
* *
1415097 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
1415149 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
*
1415201 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAT--
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
1415253 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
1415269 TATAAACGCA
Statistics
Matches: 257, Mismatches: 6, Indels: 27
0.89 0.02 0.09
Matches are distributed among these distances:
48 9 0.04
49 1 0.00
50 1 0.00
51 2 0.01
52 181 0.70
53 24 0.09
54 7 0.03
55 6 0.02
57 26 0.10
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (55 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
Found at i:1415384 original size:19 final size:19
Alignment explanation
Indices: 1415275--1415376 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1415265 AAATTATAAA
1415275 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1415294 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1415314 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1415330 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1415347 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1415366 CGCATTGCGAT
1 CGCATTGCGAT
1415377 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:1415502 original size:14 final size:14
Alignment explanation
Indices: 1415483--1415519 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1415473 CATCAATTAC
1415483 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1415497 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1415511 ACAAATCAA
1 ACAAATCAA
1415520 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:1417470 original size:20 final size:20
Alignment explanation
Indices: 1417445--1417513 Score: 88
Period size: 19 Copynumber: 3.5 Consensus size: 20
1417435 TAGTTTACTT
* *
1417445 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTCAAAA
1417465 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
*
1417484 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACTCAAAA
*
1417503 TCGCAATGCGA
1 TCGCAACGCGA
1417514 TTTTGGTTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
19 31 0.70
20 13 0.30
ACGTcount: A:0.45, C:0.26, G:0.17, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:1417531 original size:19 final size:19
Alignment explanation
Indices: 1417509--1417637 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1417499 AAAATCGCAA
1417509 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1417528 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1417542 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1417561 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1417575 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1417594 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1417613 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1417633 TGCGA
1 TGCGA
1417638 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:1417551 original size:33 final size:33
Alignment explanation
Indices: 1417509--1417600 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1417499 AAAATCGCAA
1417509 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1417542 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1417575 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1417601 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:1417840 original size:93 final size:93
Alignment explanation
Indices: 1417681--1418153 Score: 939
Period size: 93 Copynumber: 5.1 Consensus size: 93
1417671 TTGAATGGAT
1417681 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1417746 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1417774 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1417839 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1417867 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1417932 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1417960 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1418024 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1418052 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1418117 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1418145 AAATTTACT
1 AAATTTACT
1418154 AAGCAATCTA
Statistics
Matches: 379, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.24
93 287 0.76
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1418126 original size:185 final size:186
Alignment explanation
Indices: 1417681--1418153 Score: 939
Period size: 185 Copynumber: 2.5 Consensus size: 186
1417671 TTGAATGGAT
1417681 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1417746 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1417811 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1417867 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1417932 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1417997 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1418052 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1418117 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1418154 AAGCAATCTA
Statistics
Matches: 287, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
185 155 0.54
186 132 0.46
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1419879 original size:14 final size:14
Alignment explanation
Indices: 1419860--1419949 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1419850 TTGAAATGAA
1419860 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1419874 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1419891 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1419907 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1419926 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1419940 AATCGCAACG
1 AATCGCAACG
1419950 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:1419897 original size:33 final size:33
Alignment explanation
Indices: 1419852--1419966 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1419842 TCTTTTGGTT
1419852 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1419885 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1419918 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1419951 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1419967 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:1419898 original size:19 final size:18
Alignment explanation
Indices: 1419859--1419971 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1419849 GTTGAAATGA
1419859 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1419874 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1419891 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1419907 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1419924 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1419940 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1419957 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1419972 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:1420002 original size:14 final size:14
Alignment explanation
Indices: 1419983--1420037 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1419973 TTTGGTTTCG
1419983 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1419997 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1420016 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1420030 CGTTGCGA
1 CGTTGCGA
1420038 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:1420015 original size:33 final size:33
Alignment explanation
Indices: 1419967--1420037 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1419957 AAAATCGCAA
**
1419967 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1420000 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1420033 TGCGA
1 TGCGA
1420038 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:1420045 original size:33 final size:33
Alignment explanation
Indices: 1419978--1420059 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1419968 GCGATTTTGG
***
1419978 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1420011 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
1420044 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1420060 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:1420064 original size:20 final size:20
Alignment explanation
Indices: 1419990--1420078 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1419980 TCGCGTTGCG
1419990 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1420010 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
1420023 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1420043 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1420063 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1420079 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:1420200 original size:33 final size:33
Alignment explanation
Indices: 1420158--1420228 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1420148 AATACTAACT
*
1420158 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1420191 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1420224 TGAAA
1 TGAAA
1420229 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:1420461 original size:22 final size:22
Alignment explanation
Indices: 1420409--1420463 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1420399 TGGTTGTGAG
**
1420409 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1420431 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1420453 GGATTTCTTCG
1 GGATTTCTTCG
1420464 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:1420634 original size:20 final size:20
Alignment explanation
Indices: 1420609--1420801 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1420599 CTTTAAATAT
1420609 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1420629 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1420651 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1420670 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1420690 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1420710 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1420730 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1420750 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1420770 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1420790 CGCGTTGCGATT
1 CGCGTTGCGATT
1420802 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1420796 original size:60 final size:60
Alignment explanation
Indices: 1420609--1420801 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1420599 CTTTAAATAT
**
1420609 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1420670 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1420730 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1420790 CGCGTTGCGATT
1 CGCGTTGCGATT
1420802 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1420882 original size:20 final size:20
Alignment explanation
Indices: 1420857--1420908 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1420847 AAGAATCGCG
*
1420857 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1420877 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1420897 TTGCGATTCTGG
1 TTGCGATTCTGG
1420909 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:1425267 original size:42 final size:42
Alignment explanation
Indices: 1425208--1425287 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
1425198 AAAGAACTCC
1425208 ATAAGCTTCAAAACTTAATAAACGAAAGAATATCACTAAAAT
1 ATAAGCTTCAAAACTTAATAAACGAAAGAATATCACTAAAAT
**
1425250 ATAAGCTTCAACGCTTAATAAACGAAAGAATATCACTA
1 ATAAGCTTCAAAACTTAATAAACGAAAGAATATCACTA
1425288 TTCTAAGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.51, C:0.16, G:0.09, T:0.24
Consensus pattern (42 bp):
ATAAGCTTCAAAACTTAATAAACGAAAGAATATCACTAAAAT
Found at i:1426129 original size:23 final size:23
Alignment explanation
Indices: 1426103--1426156 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
1426093 ATAATAGAGA
1426103 TTAGATGAATCTCTAATTACATT
1 TTAGATGAATCTCTAATTACATT
1426126 TTAGATGAATCTCTAATTACATT
1 TTAGATGAATCTCTAATTACATT
1426149 TTAGATGA
1 TTAGATGA
1426157 GAGCTTCTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (23 bp):
TTAGATGAATCTCTAATTACATT
Found at i:1437702 original size:42 final size:42
Alignment explanation
Indices: 1437643--1437722 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
1437633 AAAGAACTCC
1437643 ATAAGCTTCAACGCTTAATAAACGAAAGAATATAACTAAAAT
1 ATAAGCTTCAACGCTTAATAAACGAAAGAATATAACTAAAAT
* *
1437685 ATAAGCTTCAACGCTTAATATACGAAAGAATATCACTA
1 ATAAGCTTCAACGCTTAATAAACGAAAGAATATAACTA
1437723 TTATAAGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.25
Consensus pattern (42 bp):
ATAAGCTTCAACGCTTAATAAACGAAAGAATATAACTAAAAT
Found at i:1445946 original size:29 final size:29
Alignment explanation
Indices: 1445904--1445959 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
1445894 TTCACCTAAT
1445904 TAAATTGATGTAAGCAATGACATCAAAAC
1 TAAATTGATGTAAGCAATGACATCAAAAC
1445933 TAAATTGATGTAAGCAATGACATCAAA
1 TAAATTGATGTAAGCAATGACATCAAA
1445960 TTAATTTAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.25
Consensus pattern (29 bp):
TAAATTGATGTAAGCAATGACATCAAAAC
Found at i:1450619 original size:29 final size:29
Alignment explanation
Indices: 1450586--1450641 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1450576 TTCACCTAAT
*
1450586 TAAATTGATGTAAGCAATTACATCAAAAC
1 TAAATTGATGTAAGCAATGACATCAAAAC
1450615 TAAATTGATGTAAGCAATGACATCAAA
1 TAAATTGATGTAAGCAATGACATCAAA
1450642 TTAATTTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (29 bp):
TAAATTGATGTAAGCAATGACATCAAAAC
Found at i:1458718 original size:31 final size:31
Alignment explanation
Indices: 1458656--1458726 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1458646 CTACGCATTC
* * *
1458656 AATACTTAAACTATAAGTTTTTATCTATTTT
1 AATACCTAAACTATAAGTTTTTACCCATTTT
*
1458687 AATACCTAAACTATTAA-TTTTTACCCGTTTT
1 AATACCTAAACTA-TAAGTTTTTACCCATTTT
*
1458718 AATATCTAA
1 AATACCTAA
1458727 CCGAGGGAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 31 0.91
32 3 0.09
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (31 bp):
AATACCTAAACTATAAGTTTTTACCCATTTT
Found at i:1459591 original size:19 final size:18
Alignment explanation
Indices: 1459569--1459607 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
1459559 TTTTCATCAA
1459569 TTTTAT-ATTTGTAAATAAT
1 TTTTATGATTT-T-AATAAT
1459588 TTTTATGATTTTAATAAT
1 TTTTATGATTTTAATAAT
1459606 TT
1 TT
1459608 AAATATAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTTATGATTTTAATAAT
Found at i:1471165 original size:31 final size:31
Alignment explanation
Indices: 1471127--1471209 Score: 121
Period size: 31 Copynumber: 2.7 Consensus size: 31
1471117 GTCTCCTAAT
* *
1471127 ATTTAGTCTATTTGCAATATGTTCCCCAAAC
1 ATTTAGTCCATTTGCAATATGATCCCCAAAC
* *
1471158 ATTTAGTCCATTTTCAATATAATCCCCAAAC
1 ATTTAGTCCATTTGCAATATGATCCCCAAAC
*
1471189 ATTTAGTCCGTTTGCAATATG
1 ATTTAGTCCATTTGCAATATG
1471210 GTCTCCGATG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.39
Consensus pattern (31 bp):
ATTTAGTCCATTTGCAATATGATCCCCAAAC
Found at i:1473197 original size:31 final size:30
Alignment explanation
Indices: 1473155--1473280 Score: 112
Period size: 31 Copynumber: 4.1 Consensus size: 30
1473145 CAGAAAGTCT
1473155 TAAA-TATTACAAAATGATCATTAAATTTCA
1 TAAATTATTACAAAATGATCATTAAATTT-A
* *
1473185 TAAATTATTACAAAAT-AGTAATAAAATTTA
1 TAAATTATTACAAAATGA-TCATTAAATTTA
* * * * *
1473215 GAGAATTGTTATAAAGTGATCATTAAACTTA
1 TA-AATTATTACAAAATGATCATTAAATTTA
* * *
1473246 TGAAATTATTAGAAAATGATCCTTAAAGTTA
1 T-AAATTATTACAAAATGATCATTAAATTTA
1473277 TAAA
1 TAAA
1473281 AAACTATTAT
Statistics
Matches: 76, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
30 10 0.13
31 64 0.84
32 2 0.03
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (30 bp):
TAAATTATTACAAAATGATCATTAAATTTA
Found at i:1473483 original size:20 final size:20
Alignment explanation
Indices: 1473455--1473507 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1473445 TTGGTTAACG
1473455 GAATGTAAGATTACCAGTGC
1 GAATGTAAGATTACCAGTGC
* *
1473475 GAATATAAGATTACCAGTGG
1 GAATGTAAGATTACCAGTGC
*
1473495 GAGTGTAAGATTA
1 GAATGTAAGATTA
1473508 TCAGGGAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.26
Consensus pattern (20 bp):
GAATGTAAGATTACCAGTGC
Found at i:1473702 original size:15 final size:15
Alignment explanation
Indices: 1473682--1473714 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1473672 ATATATTTTC
1473682 TTTAAAAAATTTAAA
1 TTTAAAAAATTTAAA
*
1473697 TTTAAAAAATTTATA
1 TTTAAAAAATTTAAA
1473712 TTT
1 TTT
1473715 TTTTTACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTAAAAAATTTAAA
Found at i:1473740 original size:35 final size:37
Alignment explanation
Indices: 1473663--1473740 Score: 97
Period size: 36 Copynumber: 2.1 Consensus size: 37
1473653 AACAAGTTGG
* * *
1473663 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTT
1 AAAAAATTTATATATTTTCTTTAAAAAATTAAAATGT
*
1473700 AAAAAATTTATAT-TTTT-TTTACAAAATTAAAAATGT
1 AAAAAATTTATATATTTTCTTTAAAAAATT-AAAATGT
1473736 AAAAA
1 AAAAA
1473741 GGTTTAATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 10 0.28
36 14 0.39
37 12 0.33
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (37 bp):
AAAAAATTTATATATTTTCTTTAAAAAATTAAAATGT
Found at i:1480520 original size:2 final size:2
Alignment explanation
Indices: 1480515--1480552 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1480505 AAAAAAAAAC
1480515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1480553 TCTACACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1482619 original size:12 final size:12
Alignment explanation
Indices: 1482599--1482632 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1482589 GGCGATCAAG
1482599 AAAAATATCCCT
1 AAAAATATCCCT
*
1482611 AAAATTATCCCT
1 AAAAATATCCCT
1482623 AAAAATATCC
1 AAAAATATCC
1482633 TTAAGGGCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAATATCCCT
Found at i:1484924 original size:24 final size:22
Alignment explanation
Indices: 1484871--1484925 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
1484861 TGTTCGCGAA
*
1484871 AATATGTCTACAAACACTAAACG
1 AATATGT-TACAAACAATAAACG
* *
1484894 AACATGTTGACAAACATATAAATG
1 AATATGTT-ACAAACA-ATAAACG
1484918 AATATGTT
1 AATATGTT
1484926 TGTGAACATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.04
23 13 0.50
24 12 0.46
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (22 bp):
AATATGTTACAAACAATAAACG
Found at i:1488742 original size:103 final size:105
Alignment explanation
Indices: 1488599--1488797 Score: 285
Period size: 105 Copynumber: 1.9 Consensus size: 105
1488589 TACTGCTACC
** * * * *
1488599 TGCTAAGCTGTCCATGCTGTTTAAACTTGTTAAGAGTTTTC-CAA-ATGACTTGGGTTGGGGAAT
1 TGCTAAGCTGTCCAAACTGTTTAAACTTGTTAAGAATTTTCGAAATATGACTCGGGTGGGGGAAT
* *
1488662 TATGTTTTCACCGATTATATCAAGATTATCAACTGCTCAA
66 TATGTTTTCACCAACTATATCAAGATTATCAACTGCTCAA
* *
1488702 TGCTAAGCTTTCCAAACTGTTTAAACTTGTTAAGAATTTTCGAAATATGACTCGGGTGGGGGTAT
1 TGCTAAGCTGTCCAAACTGTTTAAACTTGTTAAGAATTTTCGAAATATGACTCGGGTGGGGGAAT
*
1488767 TATGTTTTCACCAACTATATCAAGGTTATCA
66 TATGTTTTCACCAACTATATCAAGATTATCA
1488798 GCTGTTGCAT
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
103 37 0.45
104 2 0.02
105 44 0.53
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (105 bp):
TGCTAAGCTGTCCAAACTGTTTAAACTTGTTAAGAATTTTCGAAATATGACTCGGGTGGGGGAAT
TATGTTTTCACCAACTATATCAAGATTATCAACTGCTCAA
Found at i:1503564 original size:18 final size:20
Alignment explanation
Indices: 1503526--1503565 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1503516 TAATTTTTTC
1503526 ATTCATAATATTATGATTTAA
1 ATTCATAATATTA-GATTTAA
1503547 ATTCATAAT-TTA-ATTTAA
1 ATTCATAATATTAGATTTAA
1503565 A
1 A
1503566 AGTTATAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
20 3 0.16
21 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (20 bp):
ATTCATAATATTAGATTTAA
Found at i:1503975 original size:17 final size:17
Alignment explanation
Indices: 1503955--1504005 Score: 52
Period size: 20 Copynumber: 2.9 Consensus size: 17
1503945 TTATTAAATT
1503955 TTATTAATTTTTAATAA
1 TTATTAATTTTTAATAA
*
1503972 TTATTATAATATTATAATAA
1 TTA-T-TAAT-TTTTAATAA
1503992 TTATT--TTTTTAATA
1 TTATTAATTTTTAATA
1504006 CCATTCTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 7 0.24
16 1 0.03
17 3 0.10
18 2 0.07
19 5 0.17
20 11 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTAATTTTTAATAA
Found at i:1504752 original size:58 final size:59
Alignment explanation
Indices: 1504670--1504799 Score: 138
Period size: 58 Copynumber: 2.2 Consensus size: 59
1504660 ATTTTAAATT
** * * * *
1504670 AAACTTTTGAGCATTATAATTTCATCCTCAGATTATGA-C-ACATTCTAAATTGATCCC
1 AAACTTTTGAATATTATAAATTCATCCTCAAAGTATAACCTACATTCTAAATTGATCCC
* * *
1504727 AAAACTTTTGAATATTCTAAATTCATTCTCAAAGTATAACCTTCATTCTAAATTGATCCC
1 -AAACTTTTGAATATTATAAATTCATCCTCAAAGTATAACCTACATTCTAAATTGATCCC
*
1504787 TAACATTTTGAAT
1 AAAC-TTTTGAAT
1504800 GTTCCAATGA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
58 30 0.51
59 4 0.07
60 25 0.42
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.38
Consensus pattern (59 bp):
AAACTTTTGAATATTATAAATTCATCCTCAAAGTATAACCTACATTCTAAATTGATCCC
Found at i:1521493 original size:34 final size:34
Alignment explanation
Indices: 1521454--1521532 Score: 149
Period size: 34 Copynumber: 2.3 Consensus size: 34
1521444 TTCTTGAGAG
*
1521454 TTGTTTTCTCCATTTTATCAAGAGAGAATTATCT
1 TTGTTTTCTCCATTTTATCAAGAGAGAATTATCA
1521488 TTGTTTTCTCCATTTTATCAAGAGAGAATTATCA
1 TTGTTTTCTCCATTTTATCAAGAGAGAATTATCA
1521522 TTGTTTTCTCC
1 TTGTTTTCTCC
1521533 TTGGTAGATC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.48
Consensus pattern (34 bp):
TTGTTTTCTCCATTTTATCAAGAGAGAATTATCA
Found at i:1534015 original size:37 final size:37
Alignment explanation
Indices: 1533945--1534016 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 37
1533935 GAAAAATATT
* *
1533945 TATATATTTTCTTTAAAAAATTTAAATTCATAAAATG
1 TATATATTTTCTTTAAAAAATTGAAAATCATAAAATG
* *
1533982 TATATAATTTTTTTTACAAAATTGAAAAT-ATAAAA
1 TATAT-ATTTTCTTTAAAAAATTGAAAATCATAAAA
1534017 AGGTTTAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 11 0.37
38 19 0.63
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (37 bp):
TATATATTTTCTTTAAAAAATTGAAAATCATAAAATG
Found at i:1535933 original size:29 final size:29
Alignment explanation
Indices: 1535898--1535979 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
1535888 AAACTAAATT
* *
1535898 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
1535927 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
1535956 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1535980 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:1540439 original size:29 final size:29
Alignment explanation
Indices: 1540397--1540475 Score: 122
Period size: 29 Copynumber: 2.7 Consensus size: 29
1540387 ACTAAATTGA
* *
1540397 GTCATTACTTACATCATTTAATTAAAGAT
1 GTCATTGCTTACATCATTTAAGTAAAGAT
*
1540426 GTCATTGCTTACATCATTTAAGTAATGAT
1 GTCATTGCTTACATCATTTAAGTAAAGAT
1540455 GTCATTGCTTACATCAATTTA
1 GTCATTGCTTACATC-ATTTA
1540476 GTTAGGTGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 41 0.89
30 5 0.11
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (29 bp):
GTCATTGCTTACATCATTTAAGTAAAGAT
Found at i:1555381 original size:23 final size:23
Alignment explanation
Indices: 1555355--1555402 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1555345 ATAAAGTACA
*
1555355 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1555378 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1555401 AT
1 AT
1555403 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1555806 original size:21 final size:22
Alignment explanation
Indices: 1555781--1555832 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1555771 ACACTTTACA
*
1555781 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1555804 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
1555827 ATATAA
1 ATATAA
1555833 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1555817 original size:23 final size:23
Alignment explanation
Indices: 1555791--1555853 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1555781 ATATAACCAC
1555791 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1555814 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1555837 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1555854 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1556310 original size:39 final size:39
Alignment explanation
Indices: 1556256--1556342 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
1556246 TCAAGTTGTA
*
1556256 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
1556295 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1556334 GATTTTGAT
1 GATTTTGAT
1556343 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:1557118 original size:21 final size:22
Alignment explanation
Indices: 1557093--1557144 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1557083 ACACTTTACA
*
1557093 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1557116 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
1557139 ATATAA
1 ATATAA
1557145 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1557129 original size:23 final size:23
Alignment explanation
Indices: 1557103--1557165 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1557093 ATATAACCAC
1557103 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1557126 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1557149 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1557166 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1557549 original size:21 final size:22
Alignment explanation
Indices: 1557524--1557575 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1557514 ACACTTTACA
*
1557524 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1557547 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
1557570 ATATAA
1 ATATAA
1557576 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1557560 original size:23 final size:23
Alignment explanation
Indices: 1557534--1557596 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1557524 ATATAACCAC
1557534 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1557557 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1557580 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1557597 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1557685 original size:430 final size:429
Alignment explanation
Indices: 1556880--1557841 Score: 1854
Period size: 431 Copynumber: 2.2 Consensus size: 429
1556870 GAAATTAATC
* *
1556880 CAAATAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATA
1 CAAAAAATTATTTGATTGTTTTTATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATA
1556945 ATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
66 ATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
1557010 CTCACTCAAAGAGAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAA
131 CTCACTCAAAGAGAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAA
1557075 AAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
196 AAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
1557140 TATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAA
261 TATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAA
*
1557205 AAATGATCGATACTTTTTTTAAAAGTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCAT
326 AAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATGTTTCAA-TTTTTTAACAGTGTTTCAT
1557270 GTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCA
390 GTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCA
*
1557310 CAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATA
1 CAAAAAATTATTTGATTGTTTTTATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATA
1557375 ATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
66 ATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
*
1557440 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAA
131 CTCACTC-AAAGAGAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAA
1557505 AAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATT
195 AAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATT
1557570 ATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATA
260 ATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATA
1557635 AAAAGGATCGATAC-TTTTTTAAAAGTTATGTAATTTATGTTTCAATTTTTTAACAGTGTTTCAT
325 AAAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATGTTTCAATTTTTTAACAGTGTTTCAT
1557699 GTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCA
390 GTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCA
1557739 CAAAAAATTATTTGATTGTTTTTATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATA
1 CAAAAAATTATTTGATTGTTTTTATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATA
1557804 ATATATACCGTAACGTAAAAAATAAATCATTAGACGCC
66 ATATATACCGTAACGTAAAAAATAAATCATTAGACGCC
1557842 AATTATGCCT
Statistics
Matches: 525, Mismatches: 6, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
429 161 0.31
430 165 0.31
431 199 0.38
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (429 bp):
CAAAAAATTATTTGATTGTTTTTATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATA
ATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
CTCACTCAAAGAGAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAA
AAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
TATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAA
AAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATGTTTCAATTTTTTAACAGTGTTTCATG
TTTTCCACCTACAATATTGATTTAATAATTTCATTTGCA
Found at i:1560682 original size:185 final size:184
Alignment explanation
Indices: 1560371--1560715 Score: 548
Period size: 185 Copynumber: 1.9 Consensus size: 184
1560361 TTCAAATTAC
* ** *
1560371 CGACACTTTTTTAAATTGTATCGACACATTTTTATTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTATAACAATATGGACATAAAGTACCGACACAAT
* *
1560436 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
1560501 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
131 ATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
*
1560555 CGACACTTTTTTAAATCGTATCGACACATTTTGTGA-AACACTATGGACATAAAGTACCGACACA
1 CGACACTTTTTTAAATCGTATCGACACATTTT-T-ATAACAATATGGACATAAAGTACCGACACA
*
1560619 ATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGG
64 ATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGG
* * **
1560684 TTATATTGCAAATTTACCTATTTTATTATAAT
129 TTATATTACAAAATTACCTATTACATTATAAT
1560716 ATGTTGAAAG
Statistics
Matches: 146, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
184 31 0.21
185 114 0.78
186 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (184 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTATAACAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
Found at i:1561126 original size:23 final size:23
Alignment explanation
Indices: 1561063--1561135 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
1561053 ACACTTTACA
* *
1561063 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
1561086 ATATAAACGATACTTATTACATT
1 ATATAAACGCTACCTATTACATT
** *
1561109 ATATAAGGGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
1561132 ATAT
1 ATAT
1561136 GTTTACCTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:1561399 original size:431 final size:431
Alignment explanation
Indices: 1560719--1561498 Score: 1465
Period size: 431 Copynumber: 1.8 Consensus size: 431
1560709 TTATAATATG
1560719 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGTT
*
1560784 TCAATATTTTTTAAGTATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATATTTTTTAAGCATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
1560849 CAAAAAATTAGTTGATTGTTTTGATATTTTATAAAATAATATTAAGAATTTTTAATTTAACAATA
131 CAAAAAATTAGTTGATTGTTTTGATATTTTATAAAATAATATTAAGAATTTTTAATTTAACAATA
*
1560914 ATATATACCGTAACGTAAAAAATTAATCATTAGACGCCTATAATTACTAAATTAATATTTTAAAA
196 ATATATACCGTAACGTAAAAAATTAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
*
1560979 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAA
261 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAA
1561044 AAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACTTATTACATT
326 AAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACTTATTACATT
1561109 ATATAAGGGCTACCTATTACATCATATGTTTACCTATTATA
391 ATATAAGGGCTACCTATTACATCATATGTTTACCTATTATA
*
1561150 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTT-AAAGATATGTAATTTATGT
*
1561215 TTCAAT-TTTTTTAA-CAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTG
65 TTCAATATTTTTTAAGCA-TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTG
*
1561278 CACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTAAGAATTTTTAATTTAACAA
129 CACAAAAAATTAGTTGATTGTTTTGATATTTTATAAAATAATATTAAGAATTTTTAATTTAACAA
1561343 TAATATATACCGTAACGTAAAAAATTAATCATTAGACGCCTATAATTACTAAATTAATATCTTAA
194 TAATATATACCGTAACGTAAAAAATTAATCATTAGACGCCTATAATTACTAAATTAATATCTTAA
1561408 AACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTAT
259 AACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTAT
*
1561473 AAAAAGGATAGATACTTTACAATATA
324 AAAAAGGATAGACACTTTACAATATA
1561499 TTAAAAAAGT
Statistics
Matches: 340, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
430 1 0.00
431 315 0.93
432 24 0.07
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (431 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGATATGTAATTTATGTT
TCAATATTTTTTAAGCATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
CAAAAAATTAGTTGATTGTTTTGATATTTTATAAAATAATATTAAGAATTTTTAATTTAACAATA
ATATATACCGTAACGTAAAAAATTAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAA
AAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACTTATTACATT
ATATAAGGGCTACCTATTACATCATATGTTTACCTATTATA
Found at i:1562625 original size:3 final size:3
Alignment explanation
Indices: 1562617--1562703 Score: 75
Period size: 3 Copynumber: 29.0 Consensus size: 3
1562607 ACTTGTTTGG
* * * **
1562617 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * * *
1562665 AGC TTC ATC GTC GTC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1562704 GTCAACTTCA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:1564907 original size:199 final size:198
Alignment explanation
Indices: 1564175--1565739 Score: 2859
Period size: 199 Copynumber: 7.9 Consensus size: 198
1564165 TTTAAATTAG
*
1564175 TATCGACACAAACTATATTAGTGTCGACATATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1564240 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
**
1564305 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTG-TTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTTAATTCATTCTGGAAAA
1564369 AAA
196 AAA
*
1564372 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1564437 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
**
1564502 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTTAATTCATTCTGGAAAA
1564567 AAA
196 AAA
*
1564570 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1564635 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1564700 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTTAATTCATTCTGGAAAA
1564765 CAAA
196 -AAA
*
1564769 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1564834 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
**
1564899 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTTAATTCATTCTGGAAAA
1564964 AAA
196 AAA
1564967 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATA-TCATCTCATAAAACCGGTAT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTC-TCTCATAAAACCGGTAT
1565031 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
65 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
*
1565096 TCGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTTAATTCATTCTGG-AA
1565159 AAAAA
194 AAAAA
**
1565164 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATAATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1565229 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1565294 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTTAATTCATTCTGG-AAA
1565359 AAAA
195 AAAA
1565363 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1565428 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1565493 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTTAATTCATTCTGG-AAA
1565558 AAAA
195 AAAA
*
1565562 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
1565627 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
1565692 TTGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
130 TCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
1565740 GGCCATATTG
Statistics
Matches: 1336, Mismatches: 23, Indels: 14
0.97 0.02 0.01
Matches are distributed among these distances:
196 46 0.03
197 318 0.24
198 354 0.26
199 558 0.42
200 21 0.02
201 39 0.03
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTTAATTCATTCTGGAAAA
AAA
Found at i:1565115 original size:395 final size:397
Alignment explanation
Indices: 1564175--1565739 Score: 2915
Period size: 395 Copynumber: 3.9 Consensus size: 397
1564165 TTTAAATTAG
*
1564175 TATCGACACAAACTATATTAGTGTCGACATATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1564240 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* **
1564305 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTG-TTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
1564368 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGG
1564433 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
1564498 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG
326 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG
1564563 AAAAAAA
391 AAAAAAA
*
1564570 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1564635 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1564700 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
* * *
1564765 CAAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGG
1564830 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
1564895 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG
326 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG
1564960 AAAAAAA
391 AAAAAAA
1564967 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATA-TCATCTCATAAAACCGGTAT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTC-TCTCATAAAACCGGTAT
1565031 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
65 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
1565096 TCGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
**
1565159 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATAATCTCATAAAACCG
195 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCG
1565224 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
260 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
* **
1565289 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG
325 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTG
1565354 GAAAAAAAA
390 G-AAAAAAA
1565363 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1565428 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1565493 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
1565558 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGG
* *
1565623 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTT
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTT
*
1565688 GGGATTGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
325 GGGATCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
1565740 GGCCATATTG
Statistics
Matches: 1139, Mismatches: 22, Indels: 13
0.97 0.02 0.01
Matches are distributed among these distances:
395 412 0.36
396 159 0.14
397 341 0.30
398 167 0.15
399 21 0.02
400 39 0.03
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (397 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGG
TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG
AAAAAAA
Found at i:1565303 original size:594 final size:595
Alignment explanation
Indices: 1564175--1565739 Score: 2938
Period size: 594 Copynumber: 2.6 Consensus size: 595
1564165 TTTAAATTAG
*
1564175 TATCGACACAAACTATATTAGTGTCGACATATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1564240 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1564305 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTG-TTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
1564369 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGT
196 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGT
1564434 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
261 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
*
1564499 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
326 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCAATTCATTCTGGA
**
1564564 AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACC
391 AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATAATCTCATAAAACC
1564629 GGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
456 GGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
1564694 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
521 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
*
1564759 GGAAAACAAA
586 GGAAAAAAAA
*
1564769 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1564834 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1564899 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
*
1564964 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCATCTCATAAAACCGGT
196 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGT
1565029 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
261 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
* *
1565094 GATCGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGA
326 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCAATTCATTCTGG-
1565157 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATAATCTCATAAAAC
390 AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATAATCTCATAAAAC
1565222 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
455 CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
1565287 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
520 TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC
1565352 TGGAAAAAAAA
585 TGGAAAAAAAA
1565363 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1565428 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* **
1565493 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
1565558 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGG
* *
1565623 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTT
260 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTT
*
1565688 GGGATTGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
324 GGGATCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
1565740 GGCCATATTG
Statistics
Matches: 946, Mismatches: 18, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
593 46 0.05
594 566 0.60
595 276 0.29
596 21 0.02
598 4 0.00
599 33 0.03
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (595 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGT
ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCAATTCATTCTGGA
AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATAATCTCATAAAACC
GGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT
GGAAAAAAAA
Found at i:1565904 original size:19 final size:19
Alignment explanation
Indices: 1565858--1565906 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1565848 TTATATTCAC
*
1565858 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
1565877 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1565896 ATACAAAATTA
1 ATACAAAATTA
1565907 ACTCGACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1567511 original size:18 final size:18
Alignment explanation
Indices: 1567457--1567511 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
1567447 ATGACATCGA
1567457 CTTCCTCCTCCCTCTTTT
1 CTTCCTCCTCCCTCTTTT
*
1567475 CTTCCAT-CT--CT-TCTT
1 CTTCC-TCCTCCCTCTTTT
1567490 CTTCCTCCTCCCTCTTTT
1 CTTCCTCCTCCCTCTTTT
1567508 CTTC
1 CTTC
1567512 TTCATATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 1 0.03
15 10 0.33
16 2 0.07
17 2 0.07
18 14 0.47
19 1 0.03
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (18 bp):
CTTCCTCCTCCCTCTTTT
Found at i:1567735 original size:33 final size:33
Alignment explanation
Indices: 1567698--1567763 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1567688 CATCTTAATA
*
1567698 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
1567731 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
1567764 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:1570091 original size:17 final size:18
Alignment explanation
Indices: 1570069--1570111 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1570059 ATATATCCGG
1570069 TATCATT-TTACCGGTTT
1 TATCATTGTTACCGGTTT
1570086 TATCATTTTGTTACCGGTTT
1 TATCA--TTGTTACCGGTTT
1570106 TATCAT
1 TATCAT
1570112 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 1 0.04
19 2 0.09
20 15 0.65
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (18 bp):
TATCATTGTTACCGGTTT
Found at i:1570101 original size:20 final size:20
Alignment explanation
Indices: 1570074--1570120 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1570064 TCCGGTATCA
1570074 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
1570093 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
1570114 TTTTACC
1 TTTTACC
1570121 TGTTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:1570271 original size:20 final size:20
Alignment explanation
Indices: 1570242--1570291 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1570232 CACTTTTAAA
*
1570242 TTTACCGGTTTTATCAT-TT
1 TTTACTGGTTTTATCATATT
1570261 TGTTACTGGTTTTATCATATT
1 T-TTACTGGTTTTATCATATT
1570282 TTTACCTGGT
1 TTTA-CTGGT
1570292 ATATCGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 1 0.04
20 18 0.67
21 8 0.30
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.56
Consensus pattern (20 bp):
TTTACTGGTTTTATCATATT
Found at i:1571770 original size:3 final size:3
Alignment explanation
Indices: 1571762--1571790 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1571752 CCTAACTACG
1571762 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1571791 AACCCAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1576999 original size:18 final size:19
Alignment explanation
Indices: 1576957--1576996 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1576947 TGCGTGACAC
1576957 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAG-G
*
1576977 GGAATGTAAGATTATCAGG
1 GGAATGTAAGATTACCAGG
1576996 G
1 G
1576997 AATAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.35, C:0.07, G:0.33, T:0.25
Consensus pattern (19 bp):
GGAATGTAAGATTACCAGG
Found at i:1593106 original size:23 final size:23
Alignment explanation
Indices: 1593043--1593107 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
1593033 TGTCAAAAGG
* **
1593043 CAGAAGAAAACATGTCATAAGTA
1 CAGATGAAAACATGTCATAAAAA
* * *
1593066 CAGATAAAAACGTATCATAAAAA
1 CAGATGAAAACATGTCATAAAAA
* *
1593089 TATATGAAAACATGTCATA
1 CAGATGAAAACATGTCATA
1593108 CATGCAGACT
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.22
Consensus pattern (23 bp):
CAGATGAAAACATGTCATAAAAA
Found at i:1598823 original size:49 final size:49
Alignment explanation
Indices: 1598751--1598848 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
1598741 ATTTTCACAA
* *
1598751 AAACTACTAATAAAATCCAAATTGATTATCTATACAACAATTTGAGCAT
1 AAACTACTAATAAAATCCAAATTGATTATCCATACAACAAGTTGAGCAT
* * * *
1598800 AAACTCCTAATAGAGTCCAAATTGATTATCCATACAAGAAGTTGAGCAT
1 AAACTACTAATAAAATCCAAATTGATTATCCATACAACAAGTTGAGCAT
1598849 GATTAATATC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (49 bp):
AAACTACTAATAAAATCCAAATTGATTATCCATACAACAAGTTGAGCAT
Found at i:1599157 original size:34 final size:34
Alignment explanation
Indices: 1599110--1599174 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
1599100 AGAGCAATCG
1599110 GATTCAGAACTCACAAACCATAAAAGCACATTGT
1 GATTCAGAACTCACAAACCATAAAAGCACATTGT
* * *
1599144 GATTCAGATCTCACAATCCATAAAATCACAT
1 GATTCAGAACTCACAAACCATAAAAGCACAT
1599175 ACAATGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.43, C:0.25, G:0.09, T:0.23
Consensus pattern (34 bp):
GATTCAGAACTCACAAACCATAAAAGCACATTGT
Found at i:1602021 original size:10 final size:9
Alignment explanation
Indices: 1602006--1602031 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1601996 CTGCGCACAC
1602006 AAAAAAATA
1 AAAAAAATA
1602015 AAAAAAATA
1 AAAAAAATA
1602024 AAAAAAAT
1 AAAAAAAT
1602032 TATATGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAATA
Found at i:1606212 original size:16 final size:16
Alignment explanation
Indices: 1606191--1606236 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1606181 TAGTTGGATC
1606191 GAAAGCAA-TCCAAATT
1 GAAAGCAACT-CAAATT
1606207 GAAAGCAACTCAAATT
1 GAAAGCAACTCAAATT
**
1606223 GAAATTAACTCAAA
1 GAAAGCAACTCAAA
1606237 CCGAAAGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 26 0.96
17 1 0.04
ACGTcount: A:0.52, C:0.17, G:0.11, T:0.20
Consensus pattern (16 bp):
GAAAGCAACTCAAATT
Found at i:1614088 original size:11 final size:12
Alignment explanation
Indices: 1614067--1614097 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
1614057 TAAATATTAA
1614067 AAATATAATATT
1 AAATATAATATT
1614079 AAAT-TAATATT
1 AAATATAATATT
1614090 AAATATAA
1 AAATATAA
1614098 CTTTTGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATATAATATT
Found at i:1615040 original size:2 final size:2
Alignment explanation
Indices: 1615033--1615057 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1615023 TGTAATCACC
1615033 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 A
1615058 ACTAGGAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1616059 original size:41 final size:41
Alignment explanation
Indices: 1616012--1616089 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1616002 ATTCGCGTTG
1616012 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
1616053 CATTTCGCGTTGTGATAGTTGAAAATCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1616090 AGTTGAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:1616084 original size:62 final size:62
Alignment explanation
Indices: 1616016--1616147 Score: 230
Period size: 62 Copynumber: 2.1 Consensus size: 62
1616006 GCGTTGCATT
1616016 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTG-TGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCT-ATAGTTGAAAA
*
1616078 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTGCATTTCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCTATAGTTGAAAA
*
1616140 TCACGTTG
1 TCGCGTTG
1616148 AGATTTTCCA
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
62 66 0.99
63 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.36
Consensus pattern (62 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCTATAGTTGAAAA
Found at i:1616123 original size:41 final size:41
Alignment explanation
Indices: 1616078--1616192 Score: 194
Period size: 41 Copynumber: 2.8 Consensus size: 41
1616068 TAGTTGAAAA
*
1616078 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTGCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
* * *
1616119 TCGCGTTGCTATAGTTGAAAATCACGTTGAGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1616160 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1616193 AGTCTACAGT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (41 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
Found at i:1616188 original size:103 final size:103
Alignment explanation
Indices: 1616009--1616195 Score: 338
Period size: 103 Copynumber: 1.8 Consensus size: 103
1615999 GAAATTCGCG
* * *
1616009 TTGCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGTGATAGTTG
1 TTGCATTTCGCGTTGCGATAGTTGAAAATCACGTTGAGATTTTCCATTTCGCGTTGCGATAGTTG
1616074 AAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATT
66 AAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATT
*
1616112 TTGCATTTCGCGTTGCTATAGTTGAAAATCACGTTGAGATTTTCCATTTCGCGTTGCGATAGTTG
1 TTGCATTTCGCGTTGCGATAGTTGAAAATCACGTTGAGATTTTCCATTTCGCGTTGCGATAGTTG
1616177 AAAATCGCGTTGCGATAGT
66 AAAATCGCGTTGCGATAGT
1616196 CTACAGTTGT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 80 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (103 bp):
TTGCATTTCGCGTTGCGATAGTTGAAAATCACGTTGAGATTTTCCATTTCGCGTTGCGATAGTTG
AAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATT
Found at i:1616213 original size:22 final size:22
Alignment explanation
Indices: 1616184--1616236 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1616174 TTGAAAATCG
1616184 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* *
1616206 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
1616228 CGTTACGAT
1 CGTTGCGAT
1616237 TTTCCAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:1616864 original size:5 final size:5
Alignment explanation
Indices: 1616856--1616890 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
1616846 CCGTCTCGTC
1616856 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG
1616891 GTCGTGGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.20, G:0.60, T:0.20
Consensus pattern (5 bp):
TCGGG
Found at i:1617069 original size:41 final size:41
Alignment explanation
Indices: 1616992--1617097 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 41
1616982 CAACGAATTT
1616992 TCGCAACGAATTTGGAAAAT-----CGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1617028 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
*
1617069 TCGCAACGCGAA-ATGGAAAATCGCAACGA
1 TCGCAA--CGAATTTGGAAAATCGCAACGA
1617098 ATTTGGAAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 8
0.87 0.01 0.11
Matches are distributed among these distances:
36 20 0.32
41 22 0.35
42 16 0.26
43 4 0.06
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.18
Consensus pattern (41 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
Found at i:1617093 original size:20 final size:19
Alignment explanation
Indices: 1617077--1617113 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1617067 TATCGCAACG
1617077 CGAA-ATGGAAAATCGCAA
1 CGAATATGGAAAATCGCAA
*
1617095 CGAATTTGGAAAATCGCAA
1 CGAATATGGAAAATCGCAA
1617114 TGACAACTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (19 bp):
CGAATATGGAAAATCGCAA
Found at i:1617122 original size:61 final size:60
Alignment explanation
Indices: 1617027--1617157 Score: 210
Period size: 61 Copynumber: 2.2 Consensus size: 60
1617017 ACTGTAGACT
1617027 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAA-ATGGAAA
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAA--CGAATATGGAAA
* * *
1617088 ATCGCAACGAATTTGGAAAATCGCAATGACAACTGTAGACTATCGCAACTAATTTGGAAA
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATATGGAAA
1617148 ATCGCAACGA
1 ATCGCAACGA
1617158 CAACTGTAGA
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
59 3 0.05
60 16 0.24
61 47 0.71
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (60 bp):
ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATATGGAAA
Found at i:1617142 original size:41 final size:41
Alignment explanation
Indices: 1617088--1617196 Score: 166
Period size: 41 Copynumber: 2.6 Consensus size: 41
1617078 GAAATGGAAA
*
1617088 ATCGCAACGAATTTGGAAAATCGCAATGACAACTGTAGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
*
1617129 ATCGCAACTAATTTGGAAAATCGCAACGACAACTGTAGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
*
1617170 ATCGCAACGCGAA-CTGGAAAATCGCAA
1 ATCGCAA--CGAATTTGGAAAATCGCAA
1617197 AGCGATTTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
41 46 0.74
42 13 0.21
43 3 0.05
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACT
Found at i:1617163 original size:102 final size:97
Alignment explanation
Indices: 1616992--1617196 Score: 347
Period size: 102 Copynumber: 2.1 Consensus size: 97
1616982 CAACGAATTT
1616992 TCGCAACGAATTTGGAAAATCGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCAACGAC
1 TCGCAACGAATTTGGAAAATCGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCAACGAC
1617057 AACTGTAGACTATCGCAACGCGAAATGGAAAA
66 AACTGTAGACTATCGCAACGCGAAATGGAAAA
*
1617089 TCGCAACGAATTTGGAAAATCGCAATGACAACTGTAGACTATCGCAACTAATTTGGAAAATCGCA
1 TCGCAACGAATTTGGAAAAT--C---GACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCA
*
1617154 ACGACAACTGTAGACTATCGCAACGCGAACTGGAAAA
61 ACGACAACTGTAGACTATCGCAACGCGAAATGGAAAA
1617191 TCGCAA
1 TCGCAA
1617197 AGCGATTTTC
Statistics
Matches: 101, Mismatches: 2, Indels: 5
0.94 0.02 0.05
Matches are distributed among these distances:
97 20 0.20
99 1 0.01
102 80 0.79
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (97 bp):
TCGCAACGAATTTGGAAAATCGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCAACGAC
AACTGTAGACTATCGCAACGCGAAATGGAAAA
Found at i:1617235 original size:102 final size:102
Alignment explanation
Indices: 1617012--1617259 Score: 299
Period size: 102 Copynumber: 2.4 Consensus size: 102
1617002 TTTGGAAAAT
**
1617012 CGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACG
1 CGACAACTGTAGAAAATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACG
*
1617077 CGAAATGGAAAATCGCAACGAATTTGGAAAATCGCAA
66 CGAAATGGAAAATCGCAACGAATTTGCAAAATCGCAA
* ** *
1617114 TGACAACTGTAGACTATCGCAACTAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACG
1 CGACAACTGTAGAAAATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACG
* * * *
1617179 CGAACTGGAAAATCGCAAAGCG-ATTTTCAACTATCGTAA
66 CGAAATGGAAAATCGC-AA-CGAATTTGCAA-AATCGCAA
*
1617218 CG-CGAACTG-A-AAAATCGCAACACGAA-ATGGAAAATCGCAACG
1 CGAC-AACTGTAGAAAATCGC-A-ACGAATTTGGAAAATCGCAACG
1617260 CGATTTTCGC
Statistics
Matches: 128, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
102 84 0.66
103 26 0.20
104 18 0.14
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (102 bp):
CGACAACTGTAGAAAATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACG
CGAAATGGAAAATCGCAACGAATTTGCAAAATCGCAA
Found at i:1617290 original size:19 final size:19
Alignment explanation
Indices: 1617266--1617334 Score: 84
Period size: 19 Copynumber: 3.5 Consensus size: 19
1617256 AACGCGATTT
1617266 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* **
1617285 TCGCAACGACAACTTTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
1617307 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
1617326 TCGCAACGA
1 TCGCAACGA
1617335 CAACTGTAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 23 0.56
20 2 0.05
21 2 0.05
22 14 0.34
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:1617290 original size:177 final size:178
Alignment explanation
Indices: 1617089--1617440 Score: 580
Period size: 177 Copynumber: 2.0 Consensus size: 178
1617079 AAATGGAAAA
* *
1617089 TCGCAACGAATTTGGAAAATCGCAATGACAACTGTAGACTATCGCAACTAATTTGGAAAATCGCA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCA
* *
1617154 ACGACAACTGTAGACTATCGCAACGCGAACTGGAAAATCGCAAAGCGATTTTCAACTATCGTAAC
66 ACGACAACTGTAGACTATCGCAACGCGAACTGAAAAATCGCAAAGCGATTTTCAACTATCGCAAC
*
1617219 GCGA-ACTGAAAAATCGCAACACGAAATGGAAAATCGCAACGCGATTT
131 GCGATACTCAAAAATCGCAACACGAAATGGAAAATCGCAACGCGATTT
*
1617266 TCGCAACGAATTTGGAAAATCGCAACGACAACTTTAGACTATCGCAACGAATTTGGAAAATCGCA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCA
*
1617331 ACGACAACTGTAGACTATCGCAACGCGAACTGAAAAATCGCAATGCGATTTTCAACTATCGCAAC
66 ACGACAACTGTAGACTATCGCAACGCGAACTGAAAAATCGCAAAGCGATTTTCAACTATCGCAAC
** ** * *
1617396 GCGATTTTCAACTATCGCAACGCGAACTGGAAAATCGCAACGCGA
131 GCGATACTCAAAAATCGCAACACGAAATGGAAAATCGCAACGCGA
1617441 AATGGAAAAT
Statistics
Matches: 161, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
177 128 0.80
178 33 0.20
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (178 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCA
ACGACAACTGTAGACTATCGCAACGCGAACTGAAAAATCGCAAAGCGATTTTCAACTATCGCAAC
GCGATACTCAAAAATCGCAACACGAAATGGAAAATCGCAACGCGATTT
Found at i:1617312 original size:22 final size:22
Alignment explanation
Indices: 1617284--1617355 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
1617274 AATTTGGAAA
1617284 ATCGCAACGACAACTTTAGACT
1 ATCGCAACGACAACTTTAGACT
* **
1617306 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTTTAGACT
*
1617325 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTTTAGACT
1617347 ATCGCAACG
1 ATCGCAACG
1617356 CGAACTGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
19 14 0.35
20 2 0.05
21 2 0.05
22 22 0.55
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTTTAGACT
Found at i:1617323 original size:41 final size:41
Alignment explanation
Indices: 1617266--1617355 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
1617256 AACGCGATTT
*
1617266 TCGCAACGAATTTGGAAAATCGCAACGACAACTTTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1617307 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1617348 TCGCAACG
1 TCGCAACG
1617356 CGAACTGAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (41 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
Found at i:1617366 original size:41 final size:41
Alignment explanation
Indices: 1617266--1617373 Score: 155
Period size: 41 Copynumber: 2.6 Consensus size: 41
1617256 AACGCGATTT
* *
1617266 TCGCAACGAATTTGGAAAATCGCAACGACAACTTTAGACTA
1 TCGCAACGAATCTGGAAAATCGCAACGACAACTGTAGACTA
*
1617307 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATCTGGAAAATCGCAACGACAACTGTAGACTA
*
1617348 TCGCAACGCGAA-CTGAAAAATCGCAA
1 TCGCAA--CGAATCTGGAAAATCGCAA
1617374 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
41 46 0.74
42 12 0.19
43 4 0.06
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (41 bp):
TCGCAACGAATCTGGAAAATCGCAACGACAACTGTAGACTA
Found at i:1617393 original size:21 final size:21
Alignment explanation
Indices: 1617367--1617522 Score: 122
Period size: 21 Copynumber: 7.6 Consensus size: 21
1617357 GAACTGAAAA
*
1617367 ATCGCAATGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
1617388 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
1617409 ATCGCAACGCGAACTGGAA-A
1 ATCGCAACGCGATTTTCAACT
** ** *
1617429 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
** ** *
1617449 ATCGCAACGCGAACTGGAA-A
1 ATCGCAACGCGATTTTCAACT
1617469 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
1617490 ATCGCAACGCGATTTTCAA-T
1 ATCGCAACGCGATTTTCAACT
*
1617510 AATCGAAACGCGA
1 -ATCGCAACGCGA
1617523 AATGCAACGC
Statistics
Matches: 119, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
20 54 0.45
21 65 0.55
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:1617440 original size:218 final size:218
Alignment explanation
Indices: 1617088--1617485 Score: 516
Period size: 218 Copynumber: 1.8 Consensus size: 218
1617078 GAAATGGAAA
* * * *
1617088 ATCGCAACGAATTTGGAAAATCGCAATGACAACTGTAGACTATCGCAACTAATTTGGAAAATCGC
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATCTGAAAAATCGC
* ** * * *
1617153 AACGACAACTGTAGACTATCGCAACGCGAACTGGAAAATCGCAAAGCGATTTTCAACTATCGTAA
66 AACGACAACTGTAGACTATCGCAACGCGAACTGCAAAATCGCAAAGCGAACTGCAACAATCGCAA
*
1617218 CGCGAACTGAAAAATCGCAACACGAAATGGAAAATCGCAACGCGATTTTCGCAACGAATTTGGAA
131 CGCGAAATGAAAAATCGCAACACGAAATGGAAAATCGCAACGCGATTTTCGCAACGAATTTGGAA
1617283 AATCGCAACGACAACTTTAGACT
196 AATCGCAACGACAACTTTAGACT
1617306 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAA-CTGAAAAATC
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAA--CGAATCTGAAAAATC
* * * * ** * * * *
1617370 GCAATG-CGATTTTCA-ACTATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAA-AATC
64 GCAACGACAACTGT-AGACTATCGCAACGCGAACTGCAA-AATCGCAAAGCGAACTGCAACAATC
* * *
1617432 GCAACGCGAAATGGAAAATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTC
127 GCAACGCGAAATGAAAAATCGCAACACGAAATGGAAAATCGCAACGCGATTTTC
1617486 AACTATCGCA
Statistics
Matches: 152, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
218 121 0.80
219 28 0.18
220 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (218 bp):
ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATCTGAAAAATCGC
AACGACAACTGTAGACTATCGCAACGCGAACTGCAAAATCGCAAAGCGAACTGCAACAATCGCAA
CGCGAAATGAAAAATCGCAACACGAAATGGAAAATCGCAACGCGATTTTCGCAACGAATTTGGAA
AATCGCAACGACAACTTTAGACT
Found at i:1617470 original size:102 final size:100
Alignment explanation
Indices: 1617190--1617523 Score: 332
Period size: 102 Copynumber: 3.3 Consensus size: 100
1617180 GAACTGGAAA
* * * *
1617190 ATCGCAAAGCGATTTTCAACTATCGTAACGCGAACTGAAAAATCGCAACACGAAATGGAAAATCG
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAAATCGCAACGCGAAATGGAAAATCG
** ** *
1617255 CAACGCG-A-T---TTTCGCAA-CGAATTTGGAA-A
66 CAACGCGAACTGAAAATCGCAAGCG-ATTTTCAACT
* * * *
1617284 ATCGCAACGACAACTTT-AGACTATCGCAA--CGAATTTGGAAAATCGCAACGAC-AACTGTAGA
1 ATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAA-CTGGAAAATCGCAACG-CGAAATG--GA
**
1617345 CTATCGCAACGCGAACTGAAAAATCGCAATGCGATTTTCAACT
60 AAATCGCAACGCGAACTG-AAAATCGCAA-GCGATTTTCAACT
1617388 ATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAAATCGCAACGCGAAATGGAAAATCG
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAAATCGCAACGCGAAATGGAAAATCG
1617453 CAACGCGAACTGGAAAATCGCAACGCGATTTTCAACT
66 CAACGCGAACT-GAAAATCGCAA-GCGATTTTCAACT
*
1617490 ATCGCAACGCGATTTTCAA-TAATCGAAACGCGAA
1 ATCGCAACGCGATTTTCAACT-ATCGCAACGCGAA
1617524 ATGCAACGCG
Statistics
Matches: 196, Mismatches: 23, Indels: 34
0.77 0.09 0.13
Matches are distributed among these distances:
93 4 0.02
94 26 0.13
95 15 0.08
96 13 0.07
97 1 0.01
98 1 0.01
101 1 0.01
102 77 0.39
103 23 0.12
104 31 0.16
105 4 0.02
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (100 bp):
ATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAAATCGCAACGCGAAATGGAAAATCG
CAACGCGAACTGAAAATCGCAAGCGATTTTCAACT
Found at i:1620752 original size:167 final size:167
Alignment explanation
Indices: 1620476--1620810 Score: 670
Period size: 167 Copynumber: 2.0 Consensus size: 167
1620466 ACACAATACT
1620476 TCCAAATACATAGAGGTTTGAATAATCAACTGGTTTACCAGTCCACATCTCCATTGGTGTCTTCA
1 TCCAAATACATAGAGGTTTGAATAATCAACTGGTTTACCAGTCCACATCTCCATTGGTGTCTTCA
1620541 GCTCTATTGTAGTTGATGGAGCTCGATTCACCAAATAACATGCGATATTGACTACTTCTGCTCAG
66 GCTCTATTGTAGTTGATGGAGCTCGATTCACCAAATAACATGCGATATTGACTACTTCTGCTCAG
1620606 AAAGATTTTTCTAGGCATGCATCCCTCAACATTGCTC
131 AAAGATTTTTCTAGGCATGCATCCCTCAACATTGCTC
1620643 TCCAAATACATAGAGGTTTGAATAATCAACTGGTTTACCAGTCCACATCTCCATTGGTGTCTTCA
1 TCCAAATACATAGAGGTTTGAATAATCAACTGGTTTACCAGTCCACATCTCCATTGGTGTCTTCA
1620708 GCTCTATTGTAGTTGATGGAGCTCGATTCACCAAATAACATGCGATATTGACTACTTCTGCTCAG
66 GCTCTATTGTAGTTGATGGAGCTCGATTCACCAAATAACATGCGATATTGACTACTTCTGCTCAG
1620773 AAAGATTTTTCTAGGCATGCATCCCTCAACATTGCTC
131 AAAGATTTTTCTAGGCATGCATCCCTCAACATTGCTC
1620810 T
1 T
1620811 TGTTCTTTCT
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 168 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (167 bp):
TCCAAATACATAGAGGTTTGAATAATCAACTGGTTTACCAGTCCACATCTCCATTGGTGTCTTCA
GCTCTATTGTAGTTGATGGAGCTCGATTCACCAAATAACATGCGATATTGACTACTTCTGCTCAG
AAAGATTTTTCTAGGCATGCATCCCTCAACATTGCTC
Found at i:1624200 original size:60 final size:59
Alignment explanation
Indices: 1624116--1624274 Score: 194
Period size: 60 Copynumber: 2.7 Consensus size: 59
1624106 GATGAATTTG
* * * *
1624116 GGGATGGAATTGGAATATTCAAAAGTTTAGGGGCCAATTTAGAAAGATGA-TCATAGTTT
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAAAGA-GAGTCATAGTTT
* * * * *
1624175 AGGGATGAAATTAGAATGTTTAAAAGTTTAAGTACTAATTTAGAATGAGAGTCATAGTTT
1 -GGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAGTCATAGTTT
*
1624235 GAGGATGAAATTAAAATATTCAAAAGTTTAAGGACCAATT
1 G-GGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATT
1624275 AAAATGAGGA
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
59 3 0.04
60 80 0.96
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (59 bp):
GGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAGTCATAGTTT
Found at i:1628950 original size:159 final size:155
Alignment explanation
Indices: 1628727--1629023 Score: 463
Period size: 159 Copynumber: 1.9 Consensus size: 155
1628717 TCAACATGTT
**
1628727 TTCTATCAGGTATGCACTAAACCACATATTTTCTTTCTTTCCTAGTTTTGTTTATCAAATTAGTC
1 TTCTATCAGGTATGCACTAAACCACATATTTTCTTTCTTTCCTAGTTTTGTGGATCAAATTAGTC
* * *
1628792 GAA-TTTTGGAATTTCCTTGGTGGGTTTCTTTTCCCCTGGAAAAAGAACTTAAAAGTTCTCCAAA
66 -AACTTTTGGAAATTCCTTGGTGGGTTTCTTTTCCCCTGAAAAAAGAACTCAAAAGTTCTCCAAA
1628856 ACCTGCAACTCCTTCAACCATGTGTC
130 ACCTGCAACTCCTTCAACCATGTGTC
*
1628882 TTCTATCAGGTATGCACTAAAACCACAGT-TTTTCTTTCTTTTTTCTTAGTTTTGTGGATCAAAT
1 TTCTATCAGGTATGCACT-AAACCACA-TATTTTCTTTC---TTTCCTAGTTTTGTGGATCAAAT
*
1628946 TAGTCAACTTTTGGAAATTCCTTGGTGGGTTTCTTTTCCCCTTAAAAAAGAACTCAAAAGTTCTC
61 TAGTCAACTTTTGGAAATTCCTTGGTGGGTTTCTTTTCCCCTGAAAAAAGAACTCAAAAGTTCTC
1629011 CAAAACCTGCAAC
126 CAAAACCTGCAAC
1629024 CTTTTCAACC
Statistics
Matches: 129, Mismatches: 7, Indels: 8
0.90 0.05 0.06
Matches are distributed among these distances:
155 18 0.14
156 17 0.13
157 1 0.01
158 2 0.02
159 91 0.71
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (155 bp):
TTCTATCAGGTATGCACTAAACCACATATTTTCTTTCTTTCCTAGTTTTGTGGATCAAATTAGTC
AACTTTTGGAAATTCCTTGGTGGGTTTCTTTTCCCCTGAAAAAAGAACTCAAAAGTTCTCCAAAA
CCTGCAACTCCTTCAACCATGTGTC
Found at i:1633514 original size:12 final size:12
Alignment explanation
Indices: 1633473--1633508 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
1633463 AAATTAGAGT
1633473 AAATAAGAAATA
1 AAATAAGAAATA
1633485 AAATAAGAAATA
1 AAATAAGAAATA
1633497 AAATAAGAAATA
1 AAATAAGAAATA
1633509 GGATAATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (12 bp):
AAATAAGAAATA
Found at i:1633831 original size:29 final size:29
Alignment explanation
Indices: 1633789--1633848 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1633779 CACTTAATAA
1633789 TTTCACATATCAATTTTTTAACACTAAGG
1 TTTCACATATCAATTTTTTAACACTAAGG
1633818 TTTCACATATCAATTTTTTAACACTAAGG
1 TTTCACATATCAATTTTTTAACACTAAGG
1633847 TT
1 TT
1633849 AATCAATAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (29 bp):
TTTCACATATCAATTTTTTAACACTAAGG
Found at i:1634291 original size:15 final size:15
Alignment explanation
Indices: 1634249--1634300 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
1634239 TGAGACATTA
1634249 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
** *
1634264 CCCATCCTGCATCCG
1 CCCGCCCCGCATCCG
*
1634279 CCCGCCCCACATCCG
1 CCCGCCCCGCATCCG
1634294 CCCGCCC
1 CCCGCCC
1634301 AGTTAAATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.10, C:0.65, G:0.15, T:0.10
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:1636275 original size:112 final size:112
Alignment explanation
Indices: 1635794--1636369 Score: 902
Period size: 113 Copynumber: 5.1 Consensus size: 112
1635784 GATACTTATA
* * * * * * *
1635794 ATAAAATATCAACACTATCAACATATTCGGTAGCGATATACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1635859 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATTGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATTGATACATTTTT
* *
1635905 ATAAAGTATCGACACTTTCAATATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
1635970 TTTGTTATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATTGATACATTTTT
* *
1636018 ATAAAGTATCGACGCTTTCAATATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1636083 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATTGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATTGATACATTTTT
* * *
1636131 ATAAAGTATGGACACTTTCAATATATCAGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* ** *
1636196 TTTGTCATTTTTTTATCTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATTGATACATTTTT
* *
1636243 ATAAAATATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATATACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
1636308 TTTGTCATTTTTTTACCTGTTATATTATTATGGATTAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATTGATACATTTTT
1636355 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
1636370 AAACCGACAA
Statistics
Matches: 428, Mismatches: 35, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
111 62 0.14
112 154 0.36
113 212 0.50
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATTGATACATTTTT
Found at i:1636324 original size:20 final size:20
Alignment explanation
Indices: 1636279--1636324 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1636269 CCGGTAGCGC
*
1636279 TTTACCTGTTTTGTCATTTA
1 TTTACCGGTTTTGTCATTTA
* *
1636299 TATACCGGTTTTGTCATTTT
1 TTTACCGGTTTTGTCATTTA
1636319 TTTACC
1 TTTACC
1636325 TGTTATATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.15, C:0.17, G:0.11, T:0.57
Consensus pattern (20 bp):
TTTACCGGTTTTGTCATTTA
Found at i:1645270 original size:60 final size:60
Alignment explanation
Indices: 1645198--1645310 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
1645188 AACATATTAA
* **
1645198 ATAGTCATATGACTATTTTGTAACTTTTAATAGTCGGGAGACTCAAAAAAACAACACCCT
1 ATAGTCATATGACCATTTTGTAACTTTTAATAGTCAAGAGACTCAAAAAAACAACACCCT
* * *
1645258 ATAGTCGA-ATGACCATTTTTTAACTTTTAATAGTCAAGTGACTCAACAAAACA
1 ATAGTC-ATATGACCATTTTGTAACTTTTAATAGTCAAGAGACTCAAAAAAACA
1645311 TCTCTATAGT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 45 0.98
61 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (60 bp):
ATAGTCATATGACCATTTTGTAACTTTTAATAGTCAAGAGACTCAAAAAAACAACACCCT
Found at i:1649606 original size:35 final size:35
Alignment explanation
Indices: 1649565--1649675 Score: 113
Period size: 35 Copynumber: 3.2 Consensus size: 35
1649555 AAAACAATCC
*
1649565 TCAATTTCATTTTAAACAACAAATTCCAAAGTAAT
1 TCAATTTCATTTTAAACAACAAATTCCAAAATAAT
*
1649600 TCAATTTCA--TTAAAC-CCTAAATTCCAAAATAAT
1 TCAATTTCATTTTAAACAAC-AAATTCCAAAATAAT
* * * * *
1649633 TCAATTACATTCTAAA-ACTCAAATTCTAAAATACT
1 TCAATTTCATTTTAAACA-ACAAATTCCAAAATAAT
1649668 TCAATTTC
1 TCAATTTC
1649676 TTTCTTTTAT
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
32 1 0.02
33 28 0.44
35 33 0.52
36 1 0.02
ACGTcount: A:0.44, C:0.20, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTTTAAACAACAAATTCCAAAATAAT
Found at i:1650314 original size:15 final size:15
Alignment explanation
Indices: 1650294--1650350 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
1650284 AACCGGATAT
1650294 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
**
1650309 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
1650326 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
1650341 CGGGTACCCG
1 CGGGTACCCG
1650351 TAACATCTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 21 0.58
16 4 0.11
17 11 0.31
ACGTcount: A:0.21, C:0.35, G:0.28, T:0.16
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:1651015 original size:35 final size:35
Alignment explanation
Indices: 1650967--1651078 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 35
1650957 ATTCCTCCTT
* *
1650967 AAATTGAAATATTTTAGAATTTGAGTTTTAGAATG
1 AAATTGAATTATTTTAGAATTTGAGGTTTAGAATG
* * *
1651002 TAATTGAATTATTTTGGAATTT-AGGGTTTAGAATA
1 AAATTGAATTATTTTAGAATTTGA-GGTTTAGAATG
* *
1651037 AAATTGAATTACTTTAGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTAGAATTTGAGGTTTAGAATG
1651072 AAATTGA
1 AAATTGA
1651079 GGAATGTTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
34 1 0.02
35 64 0.98
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTGAGGTTTAGAATG
Found at i:1651897 original size:13 final size:13
Alignment explanation
Indices: 1651879--1651908 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1651869 AGGATTTGGA
1651879 GATTTAAAATTTT
1 GATTTAAAATTTT
1651892 GATTTAAAATTTT
1 GATTTAAAATTTT
1651905 -ATTT
1 GATTT
1651909 GACATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (13 bp):
GATTTAAAATTTT
Found at i:1653695 original size:39 final size:39
Alignment explanation
Indices: 1653641--1653727 Score: 174
Period size: 39 Copynumber: 2.2 Consensus size: 39
1653631 CTCTCAGATA
1653641 ACTCTTTGCTATCATTCACCAGTGCAAGCAATGCCAATT
1 ACTCTTTGCTATCATTCACCAGTGCAAGCAATGCCAATT
1653680 ACTCTTTGCTATCATTCACCAGTGCAAGCAATGCCAATT
1 ACTCTTTGCTATCATTCACCAGTGCAAGCAATGCCAATT
1653719 ACTCTTTGC
1 ACTCTTTGC
1653728 CAAATCTTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (39 bp):
ACTCTTTGCTATCATTCACCAGTGCAAGCAATGCCAATT
Found at i:1657155 original size:12 final size:12
Alignment explanation
Indices: 1657138--1657172 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1657128 ATTTGGATAT
* *
1657138 TATCAAGATGTC
1 TATCAACATGAC
1657150 TATCAACATGAC
1 TATCAACATGAC
1657162 TATCAACATGA
1 TATCAACATGA
1657173 ATAGTACCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (12 bp):
TATCAACATGAC
Found at i:1664385 original size:60 final size:59
Alignment explanation
Indices: 1664315--1664467 Score: 166
Period size: 60 Copynumber: 2.6 Consensus size: 59
1664305 AATTGGTCCT
* * *
1664315 AAACTTTTAAATATTCCAATGTT-ATCCATAAACTATGA-CTATCATTCTAAATTAGTCGTC
1 AAACTTTTAAACATTCCAAT-TTCATCC-CAAACTATAACCT-TCATTCTAAATTAGTCGTC
* * **
1664375 AAACTTTTAAACATTTCAATTTCATCCCAAACTATAACCTTTATTCTAAATTAGTCCAC
1 AAACTTTTAAACATTCCAATTTCATCCCAAACTATAACCTTCATTCTAAATTAGTCGTC
* * *
1664434 AAACATTTTGAACATTCTAATTTCATTCCAAACT
1 AAAC-TTTTAAACATTCCAATTTCATCCCAAACT
1664468 GTATGTATAT
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
59 30 0.38
60 49 0.62
ACGTcount: A:0.37, C:0.21, G:0.04, T:0.38
Consensus pattern (59 bp):
AAACTTTTAAACATTCCAATTTCATCCCAAACTATAACCTTCATTCTAAATTAGTCGTC
Found at i:1664703 original size:60 final size:60
Alignment explanation
Indices: 1664591--1664758 Score: 155
Period size: 60 Copynumber: 2.8 Consensus size: 60
1664581 TTGGATGAAG
* ** * * * *
1664591 TTGAGGATGAATTTGGAATATTCAAAAGTTTGAGGAAC-AATATAGAAA-GAGAGTCATAGT
1 TTGAGGATAAATTTAAAATATTCAAAAATTTAAGG-ACTAAT-TAAAAATGAGAGTCATAAT
* * *
1664651 TT-AGGGATGAAA-TTAAAATGTTCAAAAATTTAATGACTAATTAAAAATGAGAGTTATAAT
1 TTGA-GGAT-AAATTTAAAATATTCAAAAATTTAAGGACTAATTAAAAATGAGAGTCATAAT
* * *
1664711 TTGAGGATAAATTTAAAATATTTAAAAATTTAAGGATTAATTTAAAAT
1 TTGAGGATAAATTTAAAATATTCAAAAATTTAAGGACTAATTAAAAAT
1664759 AAAGTTATAA
Statistics
Matches: 87, Mismatches: 15, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
59 11 0.13
60 73 0.84
61 3 0.03
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.33
Consensus pattern (60 bp):
TTGAGGATAAATTTAAAATATTCAAAAATTTAAGGACTAATTAAAAATGAGAGTCATAAT
Found at i:1665182 original size:22 final size:22
Alignment explanation
Indices: 1665149--1665199 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1665139 ATAGCATTTA
*
1665149 TTATAGTT-TAAAAAACTATAT
1 TTATAATTATAAAAAACTATAT
*
1665170 ATT-TAATTATAAAAAAGTATAT
1 -TTATAATTATAAAAAACTATAT
1665192 TTATAATT
1 TTATAATT
1665200 CCTACTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (22 bp):
TTATAATTATAAAAAACTATAT
Found at i:1667292 original size:19 final size:19
Alignment explanation
Indices: 1667270--1667306 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1667260 CAAAAAGTCA
1667270 AGATTTTACAATTTTATAT
1 AGATTTTACAATTTTATAT
1667289 AGATTTTACAATTTTATA
1 AGATTTTACAATTTTATA
1667307 CCATCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (19 bp):
AGATTTTACAATTTTATAT
Found at i:1667458 original size:17 final size:18
Alignment explanation
Indices: 1667433--1667467 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1667423 TAATATTCGA
*
1667433 TAAAGTAATACTT-TTTT
1 TAAAATAATACTTGTTTT
1667450 TAAAATAATACTTGTTTT
1 TAAAATAATACTTGTTTT
1667468 GGTCTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (18 bp):
TAAAATAATACTTGTTTT
Found at i:1669542 original size:23 final size:23
Alignment explanation
Indices: 1669511--1669554 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1669501 TTATTTAAAA
1669511 TTAAAAAATTAAAAATATATTTT
1 TTAAAAAATTAAAAATATATTTT
* *
1669534 TTAACAAATTAAAATTATATT
1 TTAAAAAATTAAAAATATATT
1669555 AAAAAAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAAAAAATTAAAAATATATTTT
Found at i:1672229 original size:13 final size:13
Alignment explanation
Indices: 1672210--1672241 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1672200 TGTTTTAATA
1672210 ATATAAAATTTTC
1 ATATAAAATTTTC
*
1672223 GTATAAAATTTTC
1 ATATAAAATTTTC
1672236 ATATAA
1 ATATAA
1672242 GATGAACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (13 bp):
ATATAAAATTTTC
Found at i:1673494 original size:28 final size:28
Alignment explanation
Indices: 1673454--1673511 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
1673444 ATGGAGTTAG
*
1673454 ATTTTTCATCTTCAACCGAATTAACTTT
1 ATTTTTCATCTTCAACCGAATCAACTTT
*
1673482 ATTTTTCTTCTTCAACCGAATCAACTTT
1 ATTTTTCATCTTCAACCGAATCAACTTT
1673510 AT
1 AT
1673512 CCTTTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.22, G:0.03, T:0.47
Consensus pattern (28 bp):
ATTTTTCATCTTCAACCGAATCAACTTT
Done.