Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_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: 10425128
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 51
Found at i:3542738 original size:33 final size:33
Alignment explanation
Indices: 3542692--3542783 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
3542682 GCGAAACCAA
*
3542692 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
3542725 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3542758 AATCGCAACGCGAAATG-AAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3542784 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 9 0.16
33 47 0.84
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:3542749 original size:19 final size:19
Alignment explanation
Indices: 3542655--3542788 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
3542645 TAGTTTACTT
* *
3542655 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
3542675 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
3542694 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3542713 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
3542727 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
3542746 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
3542760 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
3542778 TCGCAATGCGA
1 TCGCAACGCGA
3542789 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
18 12 0.12
19 35 0.36
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3542806 original size:19 final size:19
Alignment explanation
Indices: 3542784--3542912 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3542774 GAAATCGCAA
3542784 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3542803 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
3542817 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3542836 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
3542850 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
3542869 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3542888 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
3542908 TGCGA
1 TGCGA
3542913 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:3542826 original size:33 final size:33
Alignment explanation
Indices: 3542784--3542875 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
3542774 GAAATCGCAA
3542784 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
3542817 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
3542850 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
3542876 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:3543113 original size:91 final size:93
Alignment explanation
Indices: 3542956--3543416 Score: 813
Period size: 91 Copynumber: 5.1 Consensus size: 93
3542946 TTGAATGGAT
3542956 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3543021 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3543049 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3543112 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3543140 AAATTTACTTT----C--AA-ACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3543198 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
3543226 -AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3543288 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3543316 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
3543380 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3543408 AAATTTACT
1 AAATTTACT
3543417 AAGCAACTAA
Statistics
Matches: 353, Mismatches: 3, Indels: 25
0.93 0.01 0.07
Matches are distributed among these distances:
84 2 0.01
85 27 0.08
86 53 0.15
87 1 0.00
89 1 0.00
90 53 0.15
91 103 0.29
92 90 0.25
93 23 0.07
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:3543395 original size:92 final size:92
Alignment explanation
Indices: 3543154--3543416 Score: 469
Period size: 92 Copynumber: 2.9 Consensus size: 92
3543144 TTACTTTCAA
3543154 ACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCA
1 ACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCA
3543219 ACCGAAC-AATTTACTTTCAACCAAAAG
65 ACCGAACAAATTTACTTTCAACCAAAAG
*
3543246 ACAAAACAAAGACAA-A-TATATTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCA
1 ACAAAACAAAGACAATACTAT-TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCA
3543309 ACCGAACAAATTTACTTTCAACCAAAAG
65 ACCGAACAAATTTACTTTCAACCAAAAG
3543337 ACAAAACAAAGACAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAA
1 ACAAAACAAAGACAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAA
*
3543402 CCGAATAAATTTACT
66 CCGAACAAATTTACT
3543417 AAGCAACTAA
Statistics
Matches: 164, Mismatches: 3, Indels: 8
0.94 0.02 0.05
Matches are distributed among these distances:
89 3 0.02
90 50 0.30
91 37 0.23
92 71 0.43
93 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (92 bp):
ACAAAACAAAGACAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAA
CCGAACAAATTTACTTTCAACCAAAAG
Found at i:3545133 original size:33 final size:32
Alignment explanation
Indices: 3545090--3545198 Score: 170
Period size: 33 Copynumber: 3.4 Consensus size: 32
3545080 TTTTGGTTGA
3545090 AATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AATGAAAATCGCAACGAGAGAATCGCAACGCG
*
3545122 AGATGACAATCGCAACGAGAGAATCGCAACGCG
1 A-ATGAAAATCGCAACGAGAGAATCGCAACGCG
3545155 AATGAAAATCGCAACGAGAG---CGCAACGCG
1 AATGAAAATCGCAACGAGAGAATCGCAACGCG
3545184 AAATGAAAATCGCAA
1 -AATGAAAATCGCAA
3545199 TGCGATTTTG
Statistics
Matches: 73, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
29 9 0.12
30 14 0.19
32 19 0.26
33 31 0.42
ACGTcount: A:0.44, C:0.22, G:0.25, T:0.09
Consensus pattern (32 bp):
AATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:3545134 original size:19 final size:18
Alignment explanation
Indices: 3545095--3545170 Score: 71
Period size: 14 Copynumber: 4.6 Consensus size: 18
3545085 GTTGAAATGA
3545095 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
3545110 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
3545127 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
3545143 -AATCGCAACGCGA-ATG
1 AAATCGCAACGCGAGATG
3545159 AAAATCGCAACG
1 -AAATCGCAACG
3545171 AGAGCGCAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 17
0.75 0.00 0.25
Matches are distributed among these distances:
14 16 0.31
15 1 0.02
16 10 0.20
17 6 0.12
18 10 0.20
19 8 0.16
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:3545234 original size:14 final size:14
Alignment explanation
Indices: 3545215--3545269 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3545205 TTTGGTTTCG
3545215 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3545229 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3545248 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3545262 CGTTGCGA
1 CGTTGCGA
3545270 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:3545247 original size:33 final size:33
Alignment explanation
Indices: 3545199--3545269 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3545189 AAAATCGCAA
**
3545199 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3545232 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3545265 TGCGA
1 TGCGA
3545270 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:3545277 original size:33 final size:33
Alignment explanation
Indices: 3545210--3545291 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
3545200 GCGATTTTGG
***
3545210 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
3545243 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
3545276 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
3545292 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:3545296 original size:20 final size:20
Alignment explanation
Indices: 3545222--3545310 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
3545212 TCGCGTTGCG
3545222 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
3545242 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
3545255 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
3545275 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
3545295 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
3545311 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:3545452 original size:32 final size:33
Alignment explanation
Indices: 3545391--3545457 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
3545381 TACTAACTTG
*
3545391 AAATCGCAACGAGAGAATAGCAACGCGAAATGA
1 AAATCGCAACGACAGAATAGCAACGCGAAATGA
* *
3545424 AAATCGCAACGACAGAATCGTAAC-CGAAATGA
1 AAATCGCAACGACAGAATAGCAACGCGAAATGA
3545456 AA
1 AA
3545458 TCTAAGTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 10 0.32
33 21 0.68
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.10
Consensus pattern (33 bp):
AAATCGCAACGACAGAATAGCAACGCGAAATGA
Found at i:3545860 original size:20 final size:20
Alignment explanation
Indices: 3545835--3546027 Score: 210
Period size: 20 Copynumber: 9.6 Consensus size: 20
3545825 CTTTAAATAT
3545835 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3545855 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
3545877 -TCGTTGCAATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3545896 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
3545916 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3545936 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3545956 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3545976 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3545996 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3546016 CGCGTTGCGATT
1 CGCGTTGCGATT
3546028 ATGGAAAATC
Statistics
Matches: 144, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.88
21 14 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3546022 original size:60 final size:60
Alignment explanation
Indices: 3545835--3546027 Score: 242
Period size: 60 Copynumber: 3.2 Consensus size: 60
3545825 CTTTAAATAT
** *
3545835 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCAATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
3545896 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
3545956 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
3546016 CGCGTTGCGATT
1 CGCGTTGCGATT
3546028 ATGGAAAATC
Statistics
Matches: 110, Mismatches: 22, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
60 82 0.75
61 28 0.25
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:3546108 original size:20 final size:20
Alignment explanation
Indices: 3546083--3546134 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3546073 AAGAATCGCG
*
3546083 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
3546103 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
3546123 TTGCGATTCTGG
1 TTGCGATTCTGG
3546135 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:3549251 original size:115 final size:117
Alignment explanation
Indices: 3549039--3549383 Score: 356
Period size: 115 Copynumber: 2.9 Consensus size: 117
3549029 GTCGATCTTT
* * * *
3549039 TGGGTACGATATCATTCGTTGTGAAGTTGAAATCATAGGATGACTCATTCGTTGTGAAGTTGAGC
1 TGGGCACGATATCATTCGTCGTGAAGTTGAAATCAT-GGATGACCCCTTCGTTGTGAAGTTGAGC
* * * * * *
3549104 CTCT-AATTAGATATCCTTTGTCGTGAAATTGAAACCCAATATAGATGAA-TG-
65 CT-TGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATAAAGATAAATTGC
* * * *
3549155 TGGGCACGATATCATTCGTCGTGAAGTTGAAATTATGGATGTCCCCTTCATCGTGAAGTTGAGCC
1 TGGGCACGATATCATTCGTCGTGAAGTTGAAATCATGGATGACCCCTTCGTTGTGAAGTTGAGCC
3549220 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATAAATGTTGC
66 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA--TAAAGATAAA--TTGC
* * * * *
3549276 TGATGAGCACGAT-TCCCTTCGTCTTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGTGAAGTTT
1 TG--G-GCACGATAT-CATTCGTCGTGAAGTTGAAATCATGGATGACCCCTTCGTTGTGAAG-TT
* * * *
3549340 GGGCCTTGAATTGAATATCCTTCATCGTGAAGCTGAAATCCAAT
61 GAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAT
3549384 GTAAGTTGCT
Statistics
Matches: 191, Mismatches: 26, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
114 1 0.01
115 56 0.29
116 33 0.17
117 8 0.04
120 2 0.01
121 2 0.01
123 3 0.02
124 45 0.24
125 41 0.21
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (117 bp):
TGGGCACGATATCATTCGTCGTGAAGTTGAAATCATGGATGACCCCTTCGTTGTGAAGTTGAGCC
TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATAAAGATAAATTGC
Found at i:3551279 original size:26 final size:25
Alignment explanation
Indices: 3551243--3551310 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
3551233 CTTCTTGTCC
*
3551243 CTTTTTCTTTGCTTTTTATTTTTCTT
1 CTTTTTCTTTGCTTTTT-TGTTTCTT
3551269 CTTTTTCTTTGCTTTTTTGTTTCTT
1 CTTTTTCTTTGCTTTTTTGTTTCTT
* *
3551294 -TTTATTTTTTCCTTTTT
1 CTTT-TTCTTTGCTTTTT
3551311 GCTCTTTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.08
25 18 0.47
26 17 0.45
ACGTcount: A:0.03, C:0.15, G:0.04, T:0.78
Consensus pattern (25 bp):
CTTTTTCTTTGCTTTTTTGTTTCTT
Found at i:3557049 original size:31 final size:30
Alignment explanation
Indices: 3557010--3557100 Score: 85
Period size: 31 Copynumber: 3.0 Consensus size: 30
3557000 TACGATTTAG
3557010 AGGT-AAATTGATATTTTATCTAAATTTCA
1 AGGTCAAATTGATATTTTATCTAAATTTCA
* * **
3557039 AGGGTCAAATTGTTACTTTATCTACAATTTTG
1 A-GGTCAAATTGATATTTTATCTA-AATTTCA
* * * *
3557071 AGGTTAAATTAATATTTTATGTAAAATTCA
1 AGGTCAAATTGATATTTTATCTAAATTTCA
3557101 TAAGTAAAAT
Statistics
Matches: 47, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
29 1 0.02
30 7 0.15
31 33 0.70
32 6 0.13
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (30 bp):
AGGTCAAATTGATATTTTATCTAAATTTCA
Found at i:3560852 original size:56 final size:55
Alignment explanation
Indices: 3560701--3560900 Score: 294
Period size: 56 Copynumber: 3.6 Consensus size: 55
3560691 CGCAGGGCCC
* * *
3560701 TAAAAATTAGGGACTCCGAAATCGAGTATATCTATAAGTTGTTGCCATTAATAAGCA
1 TAAAAA-TAGGG-CCCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCA
* *
3560758 TAAAAA-AGGGCTCCGAAATCGAGTATATCTATCAGTTGTTGTCATTAAGAAGCA
1 TAAAAATAGGGCCCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCA
*
3560812 TAAAAATAGAGGCCCCAAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCA
1 TAAAAATAG-GGCCCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCA
*
3560868 TAAAAATAGGGGCCCCGAAATCGAATATATCTA
1 TAAAAATA-GGGCCCCGAAATCGAGTATATCTA
3560901 AAAAATAGAG
Statistics
Matches: 132, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
54 47 0.36
55 6 0.05
56 72 0.55
57 7 0.05
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (55 bp):
TAAAAATAGGGCCCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGCA
Found at i:3562263 original size:3 final size:3
Alignment explanation
Indices: 3562257--3562281 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3562247 ATAATATATT
3562257 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
3562282 TTTAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3562546 original size:76 final size:76
Alignment explanation
Indices: 3562415--3562674 Score: 466
Period size: 76 Copynumber: 3.4 Consensus size: 76
3562405 ATGAAATATT
* *
3562415 GAAATCATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCC
1 GAAA-CATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCC
3562480 GAAGGCTTTTTG
65 GAAGGCTTTTTG
3562492 GAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
*
3562557 AAGGCTATTTG
66 AAGGCTTTTTG
* *
3562568 GAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAGACATCAAAAAACTCCCG
1 GAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
3562633 AAGGCTTTTTG
66 AAGGCTTTTTG
3562644 GAAACATCATGCACTGTAGGACTTACAGATG
1 GAAACATCATGCACTGTAGGACTTACAGATG
3562675 TGGGAAATAG
Statistics
Matches: 177, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
76 173 0.98
77 4 0.02
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
GAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
AAGGCTTTTTG
Found at i:3563000 original size:260 final size:260
Alignment explanation
Indices: 3562539--3563119 Score: 1045
Period size: 260 Copynumber: 2.2 Consensus size: 260
3562529 AGGCTTTGAA
*
3562539 AACATCAAAAAGCTCCCGAAGGCTATTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
* *
3562604 AAGGCTTTGAAGACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTA
66 AAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTA
* *
3562669 CAGATGTGGGAAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTTAACAAT
131 CAGATGTAGGAAATAGTTTAATAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTTAACAAT
*
3562734 TTCATTTTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
196 TTCATTTTAAAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
* *
3562799 AACATCAAAAAGCTCCCAAAGGTTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
* *
3562864 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAATATCATGCACTGCAGGACTTA
66 AAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTA
3562929 CAGATGTAGGAAATAGTTTAATAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTTAACAAT
131 CAGATGTAGGAAATAGTTTAATAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTTAACAAT
3562994 TTCATTTTAAAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
196 TTCATTTTAAAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
* * *
3563059 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTATATGACTTACAAATGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGA
3563120 GGGAAATAGT
Statistics
Matches: 306, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
260 306 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (260 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
AAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTA
CAGATGTAGGAAATAGTTTAATAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTTAACAAT
TTCATTTTAAAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAAC
Found at i:3563820 original size:22 final size:22
Alignment explanation
Indices: 3563795--3563871 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
3563785 CATAAAGCTT
3563795 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
3563817 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
3563839 TCATCTTTGAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATCTA
*
3563861 TCGTCTTTGAA
1 TCATCTTTGAA
3563872 GAGTGTAGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:3568516 original size:24 final size:25
Alignment explanation
Indices: 3568489--3568550 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
3568479 CCAATTTTTT
* *
3568489 TTTTCTTTTTTTCTC-CTTTTCTCC
1 TTTTATTTTTTTCTCAATTTTCTCC
*
3568513 TTTTATTTTTTT-TCAATTTTTTCC
1 TTTTATTTTTTTCTCAATTTTCTCC
3568537 TTTTGATTTTTTTC
1 TTTT-ATTTTTTTC
3568551 AAGTATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 2 0.06
24 22 0.69
25 8 0.25
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.74
Consensus pattern (25 bp):
TTTTATTTTTTTCTCAATTTTCTCC
Found at i:3573943 original size:15 final size:15
Alignment explanation
Indices: 3573921--3573958 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3573911 CTTTTCTTCG
3573921 ATATTAAAA-AATAA
1 ATATTAAAACAATAA
*
3573935 ATAATTAAAACAATTA
1 AT-ATTAAAACAATAA
3573951 ATATTAAA
1 ATATTAAA
3573959 TTTATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 13 0.62
16 6 0.29
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
ATATTAAAACAATAA
Found at i:3576135 original size:6 final size:6
Alignment explanation
Indices: 3576124--3576196 Score: 128
Period size: 6 Copynumber: 12.2 Consensus size: 6
3576114 GACACGTATT
* *
3576124 ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3576172 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
3576197 GCCGAGCCGA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.32, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:3576204 original size:5 final size:5
Alignment explanation
Indices: 3576194--3576232 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
3576184 ACCACGACCA
* * *
3576194 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
3576233 ACGGACGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:3582108 original size:6 final size:6
Alignment explanation
Indices: 3582097--3582175 Score: 140
Period size: 6 Copynumber: 13.2 Consensus size: 6
3582087 GACACGTATT
* *
3582097 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3582145 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
3582176 GCCGAGCCGA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.32, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:3582183 original size:5 final size:5
Alignment explanation
Indices: 3582173--3582211 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
3582163 ACCACGACCA
* * *
3582173 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
3582212 ACGGACGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:3588087 original size:6 final size:6
Alignment explanation
Indices: 3588076--3588148 Score: 128
Period size: 6 Copynumber: 12.2 Consensus size: 6
3588066 GACACGTATT
* *
3588076 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3588124 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
3588149 GCCGAGCCGA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.32, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:3588156 original size:5 final size:5
Alignment explanation
Indices: 3588146--3588184 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
3588136 ACCACGACCA
* * *
3588146 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
3588185 ACGGACGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:3594060 original size:6 final size:6
Alignment explanation
Indices: 3594049--3594087 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
3594039 GACACGTATT
3594049 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
3594088 CGAGCCGAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3594097 original size:5 final size:5
Alignment explanation
Indices: 3594087--3594151 Score: 130
Period size: 5 Copynumber: 13.0 Consensus size: 5
3594077 CGACCACGAC
3594087 CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG
1 CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG
3594137 CCGAG CCGAG CCGAG
1 CCGAG CCGAG CCGAG
3594152 AGACGAGACG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 60 1.00
ACGTcount: A:0.20, C:0.40, G:0.40, T:0.00
Consensus pattern (5 bp):
CCGAG
Found at i:3594159 original size:5 final size:5
Alignment explanation
Indices: 3594151--3594184 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
3594141 GCCGAGCCGA
3594151 GAGAC GAGAC GAGAC GAGAC GAGAC G-GAC G-GAC G
1 GAGAC GAGAC GAGAC GAGAC GAGAC GAGAC GAGAC G
3594185 GCGGCGGCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.35, C:0.21, G:0.44, T:0.00
Consensus pattern (5 bp):
GAGAC
Found at i:3596008 original size:32 final size:33
Alignment explanation
Indices: 3595967--3596040 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 33
3595957 GGTAAGAAAT
* * *
3595967 TTATTTTTATGTTAGTAT-TT-TTTAAATAGTTA
1 TTATTTTTATATTAATATATTATGTAAATA-TTA
3595999 TTATTTTTATATTAATATATTATGTAAATATTA
1 TTATTTTTATATTAATATATTATGTAAATATTA
3596032 TT-TTTTTAT
1 TTATTTTTAT
3596041 TAAAATAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 23 0.62
33 7 0.19
34 7 0.19
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (33 bp):
TTATTTTTATATTAATATATTATGTAAATATTA
Found at i:3596068 original size:34 final size:31
Alignment explanation
Indices: 3595967--3596068 Score: 89
Period size: 30 Copynumber: 3.2 Consensus size: 31
3595957 GGTAAGAAAT
* * * * *
3595967 TTATTTTTATGTTAGTATTTTTTAAATAGTTA
1 TTATTTTTATATTAATA-TATTTATATAATTA
* *
3595999 TTATTTTTATATTAATATA-TTATGTAAATA
1 TTATTTTTATATTAATATATTTATATAATTA
*
3596029 TTATTTTTTTATTAAAATAATATTTATATAATTA
1 TTATTTTTATATT--AAT-ATATTTATATAATTA
3596063 TTATTT
1 TTATTT
3596069 ATTAGAATTA
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
30 19 0.34
31 1 0.02
32 18 0.32
33 3 0.05
34 15 0.27
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (31 bp):
TTATTTTTATATTAATATATTTATATAATTA
Found at i:3596079 original size:16 final size:15
Alignment explanation
Indices: 3595996--3596081 Score: 50
Period size: 15 Copynumber: 5.4 Consensus size: 15
3595986 TTTTAAATAG
*
3595996 TTATTATTT-TTATA
1 TTATTATTTATTAAA
*
3596010 TTAATATATTATGTAAATA
1 TTATTAT-TTAT-T-AA-A
*
3596029 TTATTTTTTTATTAAA
1 TTA-TTATTTATTAAA
* *
3596045 ATAATATTTA-TATAA
1 TTATTATTTATTA-AA
3596060 TTATTATTTATTAGAA
1 TTATTATTTATTA-AA
3596076 TTATTA
1 TTATTA
3596082 ATTTTTTTGC
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
14 8 0.15
15 17 0.31
16 14 0.26
17 3 0.06
18 2 0.04
19 8 0.15
20 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
TTATTATTTATTAAA
Found at i:3597825 original size:21 final size:21
Alignment explanation
Indices: 3597795--3597842 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3597785 GCAGGGGTAC
* *
3597795 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
3597816 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
3597837 ATGCCA
1 ATGCCA
3597843 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:3597872 original size:21 final size:21
Alignment explanation
Indices: 3597846--3597939 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
3597836 TATGCCATCT
* *
3597846 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
3597867 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
3597888 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
3597909 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
3597930 CCGCAGGGTT
1 CCGCAGGGTT
3597940 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:3598520 original size:33 final size:34
Alignment explanation
Indices: 3598461--3598557 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
3598451 AAATGTTTTT
*
3598461 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
3598495 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
3598528 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
3598558 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:3598564 original size:34 final size:33
Alignment explanation
Indices: 3598459--3598564 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
3598449 ATAAATGTTT
*
3598459 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
3598493 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
3598525 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
3598560 TTAAA
1 TTAAA
3598565 TTTTAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:3599341 original size:125 final size:126
Alignment explanation
Indices: 3598945--3599673 Score: 1390
Period size: 126 Copynumber: 5.8 Consensus size: 126
3598935 TTTAAGTTAT
*
3598945 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
3599010 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
3599071 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
* *
3599136 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTTGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
3599197 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
3599262 GCG-CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
3599322 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
3599387 GCG-CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
3599447 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
3599512 CCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
3599573 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
* *
3599638 GCGTCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
3599674 CCGATTATAG
Statistics
Matches: 593, Mismatches: 9, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
125 247 0.42
126 346 0.58
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (126 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:3599389 original size:251 final size:251
Alignment explanation
Indices: 3598945--3599673 Score: 1397
Period size: 251 Copynumber: 2.9 Consensus size: 251
3598935 TTTAAGTTAT
*
3598945 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
3599010 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
3599075 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
131 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCG-
*
3599140 CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTTGTG
195 CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
3599197 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
3599262 GCG-CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
3599326 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
131 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
*
3599391 CCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
196 CCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
3599447 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
3599512 CCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
3599577 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGT
131 CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCG-
3599642 CCCCGGGAACGCGCCTTCATGTGAATAGTGAA
195 CCCCGGGAACGCGCCTTCATGTGAATAGTGAA
3599674 CCGATTATAG
Statistics
Matches: 470, Mismatches: 5, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
250 122 0.26
251 250 0.53
252 98 0.21
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (251 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
CGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGCGCGC
CCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:3599754 original size:8 final size:8
Alignment explanation
Indices: 3599741--3599781 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
3599731 TCACAATCTT
3599741 TCAAATTC
1 TCAAATTC
3599749 TCAAATTC
1 TCAAATTC
* *
3599757 CCAAACTC
1 TCAAATTC
3599765 T-AAATTC
1 TCAAATTC
3599772 TCAAATTC
1 TCAAATTC
3599780 TC
1 TC
3599782 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:3602796 original size:13 final size:13
Alignment explanation
Indices: 3602778--3602817 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
3602768 TACATAAATA
3602778 TATTTAATATAAT
1 TATTTAATATAAT
3602791 TATTTAATATAA-
1 TATTTAATATAAT
*
3602803 TATTTAATATTAT
1 TATTTAATATAAT
3602816 TA
1 TA
3602818 GTTATAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTTAATATAAT
Found at i:3604322 original size:10 final size:10
Alignment explanation
Indices: 3604309--3604343 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
3604299 CCCCCAACCC
*
3604309 GGGGGGGGGG
1 GGGGGGGGGA
3604319 GGGGGGGGGA
1 GGGGGGGGGA
*
3604329 GGGGAGGGGA
1 GGGGGGGGGA
3604339 GGGGG
1 GGGGG
3604344 TTGTGGAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.09, C:0.00, G:0.91, T:0.00
Consensus pattern (10 bp):
GGGGGGGGGA
Found at i:3605442 original size:3 final size:3
Alignment explanation
Indices: 3605434--3605474 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
3605424 CTAAGAAGGT
* *
3605434 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATC ATA TTA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3605475 TCTTAATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:3607246 original size:41 final size:40
Alignment explanation
Indices: 3607201--3607318 Score: 155
Period size: 41 Copynumber: 2.9 Consensus size: 40
3607191 ATTCACGTTG
* * *
3607201 CATTTTGCATTGCGATAGTTGAAAAACGCAACGCGATTTTC
1 CATTTCGCGTTGCGATAGTTG-AAATCGCAACGCGATTTTC
* ***
3607242 CATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTT-GAAATCGCAACGCGATTTTC
3607283 CATTTCGCGTTGCGATAGTTGAAATCGCAACGCGAT
1 CATTTCGCGTTGCGATAGTTGAAATCGCAACGCGAT
3607319 CTCCATCATC
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
40 12 0.18
41 52 0.80
42 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (40 bp):
CATTTCGCGTTGCGATAGTTGAAATCGCAACGCGATTTTC
Found at i:3607292 original size:20 final size:20
Alignment explanation
Indices: 3607233--3607298 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
3607223 AAAACGCAAC
3607233 GCGATTTTCCATTTCGCGTT
1 GCGATTTTCCATTTCGCGTT
* ** **
3607253 GCGATAGTTGGAGATCGCGTT
1 GCGAT-TTTCCATTTCGCGTT
3607274 GCGATTTTCCATTTCGCGTT
1 GCGATTTTCCATTTCGCGTT
3607294 GCGAT
1 GCGAT
3607299 AGTTGAAATC
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.14, C:0.21, G:0.27, T:0.38
Consensus pattern (20 bp):
GCGATTTTCCATTTCGCGTT
Found at i:3607310 original size:20 final size:21
Alignment explanation
Indices: 3607246--3607310 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 21
3607236 ATTTTCCATT
* *
3607246 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCGATAGTTCGAAA
* * **
3607267 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTCGAAA
3607287 TCGCGTTGCGATAGTT-GAAA
1 TCGCGTTGCGATAGTTCGAAA
3607307 TCGC
1 TCGC
3607311 AACGCGATCT
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
20 20 0.59
21 14 0.41
ACGTcount: A:0.17, C:0.20, G:0.29, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTCGAAA
Found at i:3607362 original size:142 final size:143
Alignment explanation
Indices: 3607172--3607453 Score: 417
Period size: 142 Copynumber: 2.0 Consensus size: 143
3607162 AATTCGCATT
* *
3607172 GCGATCTCCACTATCGCAAATTCACGTTGCATTTTGCATTGCGATAGTTGAAAAACGCAACGCGA
1 GCGATCTCCACTATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAAACGCAACGCAA
**
3607237 TTTTCCATTTCGCGTTGCGATAGT-TGGAGATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAG
66 TTTTCCATTTCGCGTTGCGATAGTCTACAG-TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAG
3607301 TTG-AAATCGCAAC
130 TTGAAAATCGCAAC
** * * * ***
3607314 GCGATCTCCA-TCATCGCAAATTCGTGTTGTATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCA
1 GCGATCTCCACT-ATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAAACGCAACGCA
3607378 ATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAG
65 ATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAG
3607443 TTGAAAATCGC
130 TTGAAAATCGC
3607454 GTTGCGATTT
Statistics
Matches: 125, Mismatches: 12, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
141 1 0.01
142 114 0.91
143 10 0.08
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (143 bp):
GCGATCTCCACTATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAAACGCAACGCAA
TTTTCCATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
TGAAAATCGCAAC
Found at i:3607363 original size:21 final size:21
Alignment explanation
Indices: 3607347--3607523 Score: 155
Period size: 21 Copynumber: 8.6 Consensus size: 21
3607337 GTGTTGTATT
3607347 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
3607368 TCGCGTTGCAAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
* *
3607388 TCGCGTTGCGATAGTCT-ACAG
1 TCGCGTTGCGATAGT-TGAAAA
* ** **
3607409 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
3607429 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
3607450 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
3607470 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
3607491 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
3607512 TCGCGTTGCGAT
1 TCGCGTTGCGAT
3607524 TTTCCAAATT
Statistics
Matches: 119, Mismatches: 32, Indels: 10
0.74 0.20 0.06
Matches are distributed among these distances:
19 1 0.01
20 42 0.35
21 75 0.63
22 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:3607389 original size:41 final size:41
Alignment explanation
Indices: 3607344--3607502 Score: 275
Period size: 41 Copynumber: 3.9 Consensus size: 41
3607334 TTCGTGTTGT
*
3607344 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCC
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
* *
3607385 ATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTCC
3607426 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
3607467 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
3607503 AGTTGAAAAT
Statistics
Matches: 111, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
40 1 0.01
41 109 0.98
42 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (41 bp):
ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCC
Found at i:3607393 original size:20 final size:20
Alignment explanation
Indices: 3607368--3607481 Score: 113
Period size: 20 Copynumber: 5.6 Consensus size: 20
3607358 TAGTTGAAAA
*
3607368 TCGCGTTGCAATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
3607388 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
3607409 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
3607429 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
3607450 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
3607470 TCGCGTTGCGAT
1 TCGCGTTGCGAT
3607482 AGTTGAAAAT
Statistics
Matches: 73, Mismatches: 17, Indels: 8
0.74 0.17 0.08
Matches are distributed among these distances:
19 4 0.05
20 38 0.52
21 27 0.37
22 4 0.05
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:3607454 original size:62 final size:62
Alignment explanation
Indices: 3607347--3607524 Score: 182
Period size: 62 Copynumber: 2.9 Consensus size: 62
3607337 GTGTTGTATT
* * * ** **
3607347 TCGCGTTGCGATAGTTGAAAATCGCGTTGCAAT-TTTCCATTTCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGATAGTTCAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT--TCTACATG
* * ** * * *
3607409 TCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTCAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTCTACATG
*
3607470 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATT
1 TCGCGTTGCGATAGTTCAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATT
3607525 TTCCAAATTC
Statistics
Matches: 94, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
60 4 0.04
61 26 0.28
62 64 0.68
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (62 bp):
TCGCGTTGCGATAGTTCAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTCTACATG
Found at i:3607539 original size:19 final size:19
Alignment explanation
Indices: 3607515--3607557 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
3607505 TTGAAAATCG
3607515 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
3607534 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
3607553 CGTTG
1 CGTTG
3607558 TGATAGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:3607652 original size:6 final size:6
Alignment explanation
Indices: 3607641--3607673 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
3607631 GAAACGTATT
3607641 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
3607674 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3607684 original size:5 final size:5
Alignment explanation
Indices: 3607674--3607714 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
3607664 GACCACGACC
3607674 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
3607715 GCGGCGGCGG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.11
5 32 0.89
ACGTcount: A:0.37, C:0.22, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:3608098 original size:39 final size:39
Alignment explanation
Indices: 3608026--3608104 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 39
3608016 ACTATTTAAG
* * *
3608026 GCTCAATCCCACATAGTATTGGGAACAAGTATTGGTAAT
1 GCTCAATCCCACATAGTATTGGAAACAACTATTGGGAAT
3608065 GCTCAAATCCCACATAGTATTGGAAAC-ACTATTGGGAAT
1 GCTC-AATCCCACATAGTATTGGAAACAACTATTGGGAAT
3608104 G
1 G
3608105 GTATTTAAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 15 0.42
40 21 0.58
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (39 bp):
GCTCAATCCCACATAGTATTGGAAACAACTATTGGGAAT
Found at i:3608217 original size:6 final size:6
Alignment explanation
Indices: 3608201--3608313 Score: 219
Period size: 6 Copynumber: 19.0 Consensus size: 6
3608191 TCTCGTCTCG
3608201 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
3608248 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
3608296 GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT
3608314 AGTAATACGT
Statistics
Matches: 107, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.05
6 102 0.95
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:3608438 original size:41 final size:40
Alignment explanation
Indices: 3608392--3608659 Score: 249
Period size: 41 Copynumber: 6.5 Consensus size: 40
3608382 TCTTTTTTTA
*
3608392 ACTATCGCAA-CGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACCGAA-ATGGAAAATCGCAACG-CAACTGTAG
** *
3608433 ACTATCGCAACGCGAAACAGAAAATCGCAACGCGACTGTAG
1 ACTATCGCAAC-CGAAATGGAAAATCGCAACGCAACTGTAG
** ** *
3608474 ACTATCGCAACGCGAAATGGAAAATCGC-GTGCGATTTTTCA-
1 ACTATCGCAAC-CGAAATGGAAAATCGCAACGC-AACTGT-AG
*
3608515 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTAG
1 ACTATCGCAAC-CGAAATGGAAAATCGCAACGCAACTGTAG
* * *
3608556 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA-
1 ACTATCGCAAC-CGAAATGGAAAATCGCAACGCAACTGT-AG
* * *
3608597 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA-
1 ACTATCGCAAC-CGAAATGGAAAATCGCAACGCAACTGT-AG
3608638 ACTATCGCAACGCGAAATGGAA
1 ACTATCGCAAC-CGAAATGGAA
3608660 CGCGAATTTG
Statistics
Matches: 200, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
40 3 0.01
41 176 0.88
42 17 0.09
43 4 0.02
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (40 bp):
ACTATCGCAACCGAAATGGAAAATCGCAACGCAACTGTAG
Found at i:3608482 original size:21 final size:21
Alignment explanation
Indices: 3608414--3608488 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
3608404 AATTTGGAAA
*
3608414 ATCGCAACGACAACTGTAGACT
1 ATCGCAACG-CGACTGTAGACT
*** **
3608436 ATCGCAACGCGA-AACAGAAA
1 ATCGCAACGCGACTGTAGACT
3608456 ATCGCAACGCGACTGTAGACT
1 ATCGCAACGCGACTGTAGACT
3608477 ATCGCAACGCGA
1 ATCGCAACGCGA
3608489 AATGGAAAAT
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 15 0.37
21 17 0.41
22 9 0.22
ACGTcount: A:0.37, C:0.28, G:0.21, T:0.13
Consensus pattern (21 bp):
ATCGCAACGCGACTGTAGACT
Found at i:3608519 original size:82 final size:82
Alignment explanation
Indices: 3608433--3608659 Score: 368
Period size: 82 Copynumber: 2.8 Consensus size: 82
3608423 ACAACTGTAG
**
3608433 ACTATCGCAACGCGAAACAGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAA
**
3608498 TCGC-GTGCGATTTTTCA
66 TCGCAACGCGA-TTTTCA
3608515 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAA
3608580 TCGCAACGCGATTTTCA
66 TCGCAACGCGATTTTCA
* *
3608597 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA-ACTATCGCAACGCGAAATGGAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGT-AGACTATCGCAACGCGAAATGGAA
3608660 CGCGAATTTG
Statistics
Matches: 137, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
82 132 0.96
83 5 0.04
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.18
Consensus pattern (82 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAA
TCGCAACGCGATTTTCA
Found at i:3608553 original size:123 final size:125
Alignment explanation
Indices: 3608385--3608659 Score: 409
Period size: 123 Copynumber: 2.2 Consensus size: 125
3608375 AACAAAATCT
* *
3608385 TTTTTTAACTATCGCAA--CGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGA
1 TTTTTCAACTATCGCAACGCGAA-ATGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGA
**
3608448 AACAGAAAATCGCAACGCGACTGT-AGACTATCGCAACGCGAAATGGAAAATCGC-GTGCGA
65 AACAGAAAATCGCAACGCGACTGTCA-ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
*
3608508 TTTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACG-CGACTGTAGACTATCGCAACGCGAA
1 TTTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAA
** * *
3608572 ATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
66 ACAGAAAATCGCAACGCGACTGTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
3608632 -TTTTCAACTATCGCAACGCGAAATGGAA
1 TTTTTCAACTATCGCAACGCGAAATGGAA
3608660 CGCGAATTTG
Statistics
Matches: 139, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
123 115 0.83
124 20 0.14
125 4 0.03
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (125 bp):
TTTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAA
ACAGAAAATCGCAACGCGACTGTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
Found at i:3608673 original size:41 final size:40
Alignment explanation
Indices: 3608433--3608659 Score: 289
Period size: 41 Copynumber: 5.5 Consensus size: 40
3608423 ACAACTGTAG
* * * *
3608433 ACTATCGCAACGCGAAACAGAAAATCGCAACGCGACTGT-A
1 ACTATCGCAACGCGAAA-TGGAAATCGCAACGCGATTTTCA
**
3608473 GACTATCGCAACGCGAAATGGAAAATCGC-GTGCGATTTTTCA
1 -ACTATCGCAACGCGAAATGG-AAATCGCAACGCGA-TTTTCA
* *
3608515 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGT-A
1 ACTATCGCAACGCGAAATGG-AAATCGCAACGCGATTTTCA
3608555 GACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATGG-AAATCGCAACGCGATTTTCA
3608597 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGG-AAATCGCAACGCGATTTTCA
3608638 ACTATCGCAACGCGAAATGGAA
1 ACTATCGCAACGCGAAATGGAA
3608660 CGCGAATTTG
Statistics
Matches: 168, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
40 8 0.05
41 154 0.92
42 6 0.04
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.18
Consensus pattern (40 bp):
ACTATCGCAACGCGAAATGGAAATCGCAACGCGATTTTCA
Found at i:3608981 original size:21 final size:21
Alignment explanation
Indices: 3608957--3609001 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
3608947 GTGAAAATAA
*
3608957 TACAAGTTAAAAAAACATAGT
1 TACAAGTAAAAAAAACATAGT
*
3608978 TAC-AGTAAAAAAAACCTAGT
1 TACAAGTAAAAAAAACATAGT
3608998 TACA
1 TACA
3609002 GTATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.56, C:0.13, G:0.09, T:0.22
Consensus pattern (21 bp):
TACAAGTAAAAAAAACATAGT
Found at i:3608990 original size:20 final size:20
Alignment explanation
Indices: 3608965--3609004 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3608955 AATACAAGTT
3608965 AAAAAAACATAGTTACAGTA
1 AAAAAAACATAGTTACAGTA
*
3608985 AAAAAAACCTAGTTACAGTA
1 AAAAAAACATAGTTACAGTA
3609005 TATAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.12, G:0.10, T:0.20
Consensus pattern (20 bp):
AAAAAAACATAGTTACAGTA
Found at i:3611782 original size:25 final size:24
Alignment explanation
Indices: 3611735--3611793 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
3611725 AAGATATTGA
* *
3611735 AGATGAAAGGAGTGTGTTGTGTAAG
1 AGATG-AAGGAGTGTGCTATGTAAG
*
3611760 AGATGAAGTGAGTGTGCTATGTACG
1 AGATGAAG-GAGTGTGCTATGTAAG
3611785 AGATTGAAG
1 AGA-TGAAG
3611794 ATGATGTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 3 0.10
25 21 0.72
26 5 0.17
ACGTcount: A:0.32, C:0.03, G:0.37, T:0.27
Consensus pattern (24 bp):
AGATGAAGGAGTGTGCTATGTAAG
Found at i:3613360 original size:28 final size:28
Alignment explanation
Indices: 3613328--3613384 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
3613318 TGTTCGTTTA
* *
3613328 TGTTCGTTTATTTATGTTCATTTATGTT
1 TGTTCGTTTATGTACGTTCATTTATGTT
* *
3613356 TGTTCGTTTATGTGCGTTTATTTATGTT
1 TGTTCGTTTATGTACGTTCATTTATGTT
3613384 T
1 T
3613385 AGCTCAATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.12, C:0.07, G:0.18, T:0.63
Consensus pattern (28 bp):
TGTTCGTTTATGTACGTTCATTTATGTT
Found at i:3613367 original size:14 final size:15
Alignment explanation
Indices: 3613325--3613368 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 15
3613315 ATATGTTCGT
3613325 TTATGTTCGTTTAT-
1 TTATGTTCGTTTATG
*
3613339 TTATGTTCATTTATG
1 TTATGTTCGTTTATG
3613354 TT-TGTTCGTTTATG
1 TTATGTTCGTTTATG
3613368 T
1 T
3613369 GCGTTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 25 0.93
15 2 0.07
ACGTcount: A:0.14, C:0.07, G:0.16, T:0.64
Consensus pattern (15 bp):
TTATGTTCGTTTATG
Found at i:3613375 original size:24 final size:24
Alignment explanation
Indices: 3613316--3613376 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
3613306 CGTTCGATAA
*
3613316 TATGTTCGTTTATGTTCGTTTATT
1 TATGTTCGTTTATGTTCGTTCATT
* * *
3613340 TATGTTCATTTATGTTTGTTCGTT
1 TATGTTCGTTTATGTTCGTTCATT
*
3613364 TATGTGCGTTTAT
1 TATGTTCGTTTAT
3613377 TTATGTTTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.13, C:0.08, G:0.18, T:0.61
Consensus pattern (24 bp):
TATGTTCGTTTATGTTCGTTCATT
Found at i:3613588 original size:23 final size:23
Alignment explanation
Indices: 3613556--3613635 Score: 99
Period size: 23 Copynumber: 3.4 Consensus size: 23
3613546 TTTTCATTTA
*
3613556 TGTTCGTTTACGTTCATTTATTG
1 TGTTCATTTACGTTCATTTATTG
**
3613579 TGTTCATTTACGTTTGTTCGT-TTG
1 TGTTCATTTACGTTCATT--TATTG
*
3613603 TGTTCGTTTACGTTCATTTATTG
1 TGTTCATTTACGTTCATTTATTG
3613626 TGTTCATTTA
1 TGTTCATTTA
3613636 TGTTTGTTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
22 1 0.02
23 27 0.57
24 18 0.38
25 1 0.02
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.57
Consensus pattern (23 bp):
TGTTCATTTACGTTCATTTATTG
Found at i:3613607 original size:24 final size:23
Alignment explanation
Indices: 3613556--3613645 Score: 92
Period size: 23 Copynumber: 3.9 Consensus size: 23
3613546 TTTTCATTTA
* **
3613556 TGTTCGTTTACGTTCATTTATTG
1 TGTTCATTTACGTTTGTTTATTG
3613579 TGTTCATTTACGTTTGTTCGT-TTG
1 TGTTCATTTACGTTTGTT--TATTG
* **
3613603 TGTTCGTTTACGTTCATTTATTG
1 TGTTCATTTACGTTTGTTTATTG
*
3613626 TGTTCATTTATGTTTGTTTA
1 TGTTCATTTACGTTTGTTTA
3613646 CATCTGTTCG
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
22 1 0.02
23 34 0.63
24 18 0.33
25 1 0.02
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.59
Consensus pattern (23 bp):
TGTTCATTTACGTTTGTTTATTG
Found at i:3613654 original size:47 final size:47
Alignment explanation
Indices: 3613556--3613664 Score: 155
Period size: 47 Copynumber: 2.3 Consensus size: 47
3613546 TTTTCATTTA
*** *
3613556 TGTTCGTTTACGTTCATTTATTGTGTTCATTTACGTTTGTTCGTTTG
1 TGTTCGTTTACGTTCATTTATTGTGTTCATTTACGTTTGTTCACATC
* *
3613603 TGTTCGTTTACGTTCATTTATTGTGTTCATTTATGTTTGTTTACATC
1 TGTTCGTTTACGTTCATTTATTGTGTTCATTTACGTTTGTTCACATC
*
3613650 TGTTCGTTTATGTTC
1 TGTTCGTTTACGTTC
3613665 GTTCATTTGT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.12, C:0.13, G:0.17, T:0.58
Consensus pattern (47 bp):
TGTTCGTTTACGTTCATTTATTGTGTTCATTTACGTTTGTTCACATC
Found at i:3613684 original size:24 final size:24
Alignment explanation
Indices: 3613548--3613683 Score: 105
Period size: 24 Copynumber: 5.8 Consensus size: 24
3613538 AATATATATT
* *
3613548 TTCATTTATGTTCGTTTACGTTCA
1 TTCATTTGTGTTCGTTTACGTTCG
* * *
3613572 TTTA-TTGTGTTCATTTACGTTTG
1 TTCATTTGTGTTCGTTTACGTTCG
* *
3613595 TTCGTTTGTGTTCGTTTACGTTCA
1 TTCATTTGTGTTCGTTTACGTTCG
* * * *
3613619 TTTA-TTGTGTTCATTTATGTTTG
1 TTCATTTGTGTTCGTTTACGTTCG
* ** * *
3613642 TTTACATCTGTTCGTTTATGTTCG
1 TTCATTTGTGTTCGTTTACGTTCG
*
3613666 TTCATTTGTGTTTGTTTA
1 TTCATTTGTGTTCGTTTA
3613684 TCATTTAAAT
Statistics
Matches: 85, Mismatches: 25, Indels: 4
0.75 0.22 0.04
Matches are distributed among these distances:
23 36 0.42
24 49 0.58
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.59
Consensus pattern (24 bp):
TTCATTTGTGTTCGTTTACGTTCG
Found at i:3614042 original size:58 final size:59
Alignment explanation
Indices: 3613951--3614100 Score: 157
Period size: 58 Copynumber: 2.5 Consensus size: 59
3613941 ATTATCATTC
* **
3613951 TTCTAAATT-GATCTCTAAACTTTTAAATGTTTCATTTTTC-CCT-AAACTATGA-CTATAA
1 TTCTAAATTAG-TCTCTAAACTTTTGAACATTTCA-TTTTCACCTCAAACTATGACCT-TAA
*
3614009 TTCTAAATTAGTC-CTTAAACTTTTGAACATTTCATTTTCATCCTCAAACTATGACCTTCA
1 TTCTAAATTAGTCTC-TAAACTTTTGAACATTTCATTTTCA-CCTCAAACTATGACCTTAA
* *
3614069 TTCTAAATTGGTCTCCAAACTTTTTGAACATT
1 TTCTAAATTAGTCTCTAAAC-TTTTGAACATT
3614101 CCAATTTAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 13
0.80 0.06 0.13
Matches are distributed among these distances:
57 6 0.08
58 27 0.35
59 4 0.05
60 27 0.35
61 14 0.18
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (59 bp):
TTCTAAATTAGTCTCTAAACTTTTGAACATTTCATTTTCACCTCAAACTATGACCTTAA
Found at i:3614117 original size:60 final size:60
Alignment explanation
Indices: 3613994--3614121 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 60
3613984 ATTTTTCCCT
* * * * *
3613994 AAACTATGACTATAATTCTAAATTAGTCCTTAAACTTTTGAACATTTCATTTTCATCCTC
1 AAACTATGACTATAATTCTAAATTAGTCCTCAAACTTTTGAACATTCCAATTTAATCCAC
* *
3614054 AAACTATGACCT-TCATTCTAAATTGGT-CTCCAAACTTTTTGAACATTCCAATTTAAT-CAC
1 AAACTATGA-CTATAATTCTAAATTAGTCCT-CAAAC-TTTTGAACATTCCAATTTAATCCAC
3614114 AAACTATG
1 AAACTATG
3614122 TGTATATACT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
59 2 0.03
60 36 0.62
61 20 0.34
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.38
Consensus pattern (60 bp):
AAACTATGACTATAATTCTAAATTAGTCCTCAAACTTTTGAACATTCCAATTTAATCCAC
Found at i:3617317 original size:2 final size:2
Alignment explanation
Indices: 3617310--3617353 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3617300 ATTAGGGGGA
3617310 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3617352 AT
1 AT
3617354 TGGGCTTGGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3624611 original size:864 final size:867
Alignment explanation
Indices: 3622929--3624663 Score: 2624
Period size: 864 Copynumber: 2.0 Consensus size: 867
3622919 CCAATTTGAC
* * *
3622929 AACTGTCATTTTCGATGTCAAATAAATTCCTTCATCTCAATTAATAAATTAGGAAATACGTAGTA
1 AACTGTCATTTTCGATGTCAAATAAATTCCTTCATCTCAATTAATAAATAAAGAAATACATAGTA
* * * *
3622994 TAGAGAAATAAGGGGCGAATCCTCAGGGACTTAGAAAATTATATTTTTATGTTTGAATGGTTCTA
66 TAGAGAAATAAGGGGCGAATCCTCAAGGACTTAGAAAATCACAATTTTATGTTTGAATGGTTCTA
* *** *
3623059 ACCATGCTCGAATAGTAAAAAAAAGGTTTATAATATGAGATTTAAATAGTAAAAATGATTAAATA
131 ACCAGGCGAAAATAGTAAAAAAAAGGTTTATAATATGAGATTTAAATAGTAAAAACGATTAAATA
*
3623124 AATAAAAGCAATTTAAGAAAAAAATAAGAGAATAAAAATTATGAATAAATAAGGTAAAAATAGCC
196 AATAAAAGCAATTAAAGAAAAAAATAAGAGAATAAAAATTATGAATAAATAAGGTAAAAATAGCC
* * * * **
3623189 TCAAGCTTCATTTTGACTCAATTTCCTTTATATCATCGAATAAGATTTTTCATTTGGGATTCACG
261 TCAAGCTTCACTTTGACTCAATTTCCTCTAGATCATCGAATAAGATTTTCCATCCGGGATTCACG
*
3623254 TCGGTTACTTTGTCTACAAGGGCTATCCCCGTGACTCTATCTTGTATACCGAATACCCAAGGCAA
326 TCGGTTACTTTGTCTACAAGGGCAATCCCCGTGACTCTATCTTGTATACCGAATACCCAAGGCAA
* * *
3623319 TCTTTGACTTCGGCTTTGGGAATTGATTCTATCAATATCAATTGTCGTAGATCAATTATCGTTTA
391 TCTTTGACTTCGGCTTCGGGAATTGATTCTATCAACATCAATTGTCGTAGATCAATTACCGTTTA
* * * *
3623384 AGTTCGTAGCGACTGACTCGGATTGTTGCTTCCATAACCGTCAATTCTGATCTCAAATCCCTCTT
456 AGTTCGTAGCGACCGACTCAGATTGTTGCTTCAATAACCGTCAATTCCGATCTCAAATCCCTCTT
* *
3623449 GGCAAAACTATCTCGCCAAGTGTGTTCTCAGGAAGTCGAATGTGCTTTCTATAAGCCGAATCTTC
521 GGCAAAACCATCTCGCCAAGTGTGTTCCCAGGAAGTCGAATGTGCTTTCTATAAGCCGAATCTTC
* *
3623514 CTCCCACACATTTAATCGCAACAACCTCTTGACCAAAGTCAATCTTTGATTTTGAAAACTGTTTT
586 CTCCCACACATTTAATCGCAACAACCTATTGACCAAAGTCAATCTTTGATTTTAAAAACTGTTTT
* * * *
3623579 GATTTTGAAAAATAAGTGCAGAGATTGGGAGAGATATTATGAATGTATTAAGGGCCTGTTTCAAT
651 GATTTTGAAAAATAAGCGCAGAGATTGAGAGAGATATTATGAAGGTATTAAGGGCCTATTTCAAT
* *
3623644 TCTCCCGTTGGAATTGAGTCATCGCGTCAGATCTCGGCTTATGAAAAATTTAGCTAAGCATGACA
716 TCTCCCGTTGGAATTGAGTCATCGCATCAGATCTCGGCTTATGAAAAAATTAGCTAAGCATGACA
*
3623709 AAAGGCATACTTAGCATATTAAAAACAAAGATTGAAAATAAAAGAAAAATGAAAACTTGGAAAGT
781 AAAGGCATACTTAGCATATTAAAAACAAAGATTGAAAATAAAAGAAAAATGAAAACTTGAAAAGT
3623774 -AAAAAGAGAAATG-ATTAATAA
846 AAAAAAGAGAAA-GCATTAATAA
* ** *
3623795 AACTGTCATTTT-GATGTCAAATAAATTCTTTTTTCTCAATTAATAAATAAAGAAATCCATAGTA
1 AACTGTCATTTTCGATGTCAAATAAATTCCTTCATCTCAATTAATAAATAAAGAAATACATAGTA
*
3623859 TAGAGAAATAAGGGTCGAATCCTCAAGGACTTAGAAAATCACAATTTTATGTTTGAATGGTTCTA
66 TAGAGAAATAAGGGGCGAATCCTCAAGGACTTAGAAAATCACAATTTTATGTTTGAATGGTTCTA
*** *
3623924 ACCAGGCGAAAATAGTAAAAAGGGGGGGTTTTGTAATATGAGATTTAAATAGTAAAAACGATTAA
131 ACCAGGCGAAAATAGTAAAAA--AAAGG-TTTATAATATGAGATTTAAATAGTAAAAACGATTAA
* * ** * * * * *
3623989 ATAAATAAAATCAATTAAAG-TAAAAATAAGAGGGTGAATATTCTGAATAAATACGGT-AATATA
193 ATAAATAAAAGCAATTAAAGAAAAAAATAAGAGAATAAAAATTATGAATAAATAAGGTAAAAATA
* *
3624052 GCCTCAAGCTTCGCTTTGACTCAATTTCCTCTAGAT-ATCGAATAAGATTTTCCCTCCGGGATTC
258 GCCTCAAGCTTCACTTTGACTCAATTTCCTCTAGATCATCGAATAAGATTTTCCATCCGGGATTC
* * *
3624116 ATGTCGGTTTCTTTGTCTACAAGTGCAATCCCCGTGACTCTATCTTGTATACCGAATACCCAAGG
323 ACGTCGGTTACTTTGTCTACAAGGGCAATCCCCGTGACTCTATCTTGTATACCGAATACCCAAGG
* *
3624181 CAATCTTTGA-TTCCGGCTTCGGGAATTGATTCTATCAACATCAATTTTTGTAGATCAATTACCG
388 CAATCTTTGACTT-CGGCTTCGGGAATTGATTCTATCAACATCAATTGTCGTAGATCAATTACCG
* * * *
3624245 TTTATGTTCGTGGC-ACCGACTCAGATTGTTGCTTCAATAATCGTCAATTCCGATCTCAATTCCC
452 TTTAAGTTCGTAGCGACCGACTCAGATTGTTGCTTCAATAACCGTCAATTCCGATCTCAAATCCC
* * * * *
3624309 TTTTGGCGAAGCCATCTCGCCAAGTGTGTTCCCAGGAAGTCGAATTTGCTTTCTATAAGCTGAAT
517 TCTTGGCAAAACCATCTCGCCAAGTGTGTTCCCAGGAAGTCGAATGTGCTTTCTATAAGCCGAAT
3624374 CTTCCTCCCACACATTTAATCGCAACAACCTATTGACCAAAGTCAATCTTTGATTTTAAAAACTG
582 CTTCCTCCCACACATTTAATCGCAACAACCTATTGACCAAAGTCAATCTTTGATTTTAAAAACTG
3624439 TTTTGATTTTGAAAAATAAGCGCAGAGATTGAGAGAGATATT-TCGAAGGTATTAAGGGCCTATT
647 TTTTGATTTTGAAAAATAAGCGCAGAGATTGAGAGAGATATTAT-GAAGGTATTAAGGGCCTATT
* *
3624503 TCAATTCTCCCGTTGGAATTGAGTCATCGCATCAGCTCTCGGCTTGTGAAAAAATTAGCTAAGCA
711 TCAATTCTCCCGTTGGAATTGAGTCATCGCATCAGATCTCGGCTTATGAAAAAATTAGCTAAGCA
* ** * * *
3624568 TGTCAAAATTCATACTTATCTTATTAAAAACAAAGATTGAAAATAAAAGAAAAATTAAAACTTGA
776 TGACAAAAGGCATACTTAGCATATTAAAAACAAAGATTGAAAATAAAAGAAAAATGAAAACTTGA
*
3624633 AAAGTAAAAAAGAGAAAGCTTTAATAA
841 AAAGTAAAAAAGAGAAAGCATTAATAA
3624660 AACT
1 AACT
3624664 AGAGAGAAAA
Statistics
Matches: 781, Mismatches: 81, Indels: 15
0.89 0.09 0.02
Matches are distributed among these distances:
863 1 0.00
864 350 0.45
865 297 0.38
866 49 0.06
867 32 0.04
868 52 0.07
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (867 bp):
AACTGTCATTTTCGATGTCAAATAAATTCCTTCATCTCAATTAATAAATAAAGAAATACATAGTA
TAGAGAAATAAGGGGCGAATCCTCAAGGACTTAGAAAATCACAATTTTATGTTTGAATGGTTCTA
ACCAGGCGAAAATAGTAAAAAAAAGGTTTATAATATGAGATTTAAATAGTAAAAACGATTAAATA
AATAAAAGCAATTAAAGAAAAAAATAAGAGAATAAAAATTATGAATAAATAAGGTAAAAATAGCC
TCAAGCTTCACTTTGACTCAATTTCCTCTAGATCATCGAATAAGATTTTCCATCCGGGATTCACG
TCGGTTACTTTGTCTACAAGGGCAATCCCCGTGACTCTATCTTGTATACCGAATACCCAAGGCAA
TCTTTGACTTCGGCTTCGGGAATTGATTCTATCAACATCAATTGTCGTAGATCAATTACCGTTTA
AGTTCGTAGCGACCGACTCAGATTGTTGCTTCAATAACCGTCAATTCCGATCTCAAATCCCTCTT
GGCAAAACCATCTCGCCAAGTGTGTTCCCAGGAAGTCGAATGTGCTTTCTATAAGCCGAATCTTC
CTCCCACACATTTAATCGCAACAACCTATTGACCAAAGTCAATCTTTGATTTTAAAAACTGTTTT
GATTTTGAAAAATAAGCGCAGAGATTGAGAGAGATATTATGAAGGTATTAAGGGCCTATTTCAAT
TCTCCCGTTGGAATTGAGTCATCGCATCAGATCTCGGCTTATGAAAAAATTAGCTAAGCATGACA
AAAGGCATACTTAGCATATTAAAAACAAAGATTGAAAATAAAAGAAAAATGAAAACTTGAAAAGT
AAAAAAGAGAAAGCATTAATAA
Found at i:3624686 original size:23 final size:23
Alignment explanation
Indices: 3624660--3624707 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
3624650 GCTTTAATAA
3624660 AACTAGAGAGAAAAGAATATTGC
1 AACTAGAGAGAAAAGAATATTGC
3624683 AACTAGAGAGAAAAGAATATTGC
1 AACTAGAGAGAAAAGAATATTGC
3624706 AA
1 AA
3624708 TTTGAGTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.21, T:0.17
Consensus pattern (23 bp):
AACTAGAGAGAAAAGAATATTGC
Found at i:3631308 original size:20 final size:20
Alignment explanation
Indices: 3631274--3631329 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
3631264 ATTTTTGTTA
* *
3631274 TTTTGTTTCTATTTTTTTTATG
1 TTTT-TTTCT-TTTTTTTTCTC
*
3631296 TCTTTTTTCTTTTCTTTTCTC
1 T-TTTTTTCTTTTTTTTTCTC
3631317 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
3631330 CGAACAACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.38
21 9 0.31
22 6 0.21
23 3 0.10
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.80
Consensus pattern (20 bp):
TTTTTTTCTTTTTTTTTCTC
Found at i:3635852 original size:172 final size:172
Alignment explanation
Indices: 3635566--3635909 Score: 688
Period size: 172 Copynumber: 2.0 Consensus size: 172
3635556 GGGACTTAGA
3635566 AAATTACAATTTTATGTTTGAATGGTTTTAACCAGACGAAAATAGTAAAAAAGGGGGGTTTTGTA
1 AAATTACAATTTTATGTTTGAATGGTTTTAACCAGACGAAAATAGTAAAAAAGGGGGGTTTTGTA
3635631 ATATGAGATTTAAATAGTAAAAAATGATTAAATAAATAAAGCAATTAAAGTAAAAATAAGAAGGT
66 ATATGAGATTTAAATAGTAAAAAATGATTAAATAAATAAAGCAATTAAAGTAAAAATAAGAAGGT
3635696 AAAGATTGTGAATAAATACGGTAAAAATAGCCTCAAGCTTCG
131 AAAGATTGTGAATAAATACGGTAAAAATAGCCTCAAGCTTCG
3635738 AAATTACAATTTTATGTTTGAATGGTTTTAACCAGACGAAAATAGTAAAAAAGGGGGGTTTTGTA
1 AAATTACAATTTTATGTTTGAATGGTTTTAACCAGACGAAAATAGTAAAAAAGGGGGGTTTTGTA
3635803 ATATGAGATTTAAATAGTAAAAAATGATTAAATAAATAAAGCAATTAAAGTAAAAATAAGAAGGT
66 ATATGAGATTTAAATAGTAAAAAATGATTAAATAAATAAAGCAATTAAAGTAAAAATAAGAAGGT
3635868 AAAGATTGTGAATAAATACGGTAAAAATAGCCTCAAGCTTCG
131 AAAGATTGTGAATAAATACGGTAAAAATAGCCTCAAGCTTCG
3635910 CTCCGACTCA
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 172 1.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.28
Consensus pattern (172 bp):
AAATTACAATTTTATGTTTGAATGGTTTTAACCAGACGAAAATAGTAAAAAAGGGGGGTTTTGTA
ATATGAGATTTAAATAGTAAAAAATGATTAAATAAATAAAGCAATTAAAGTAAAAATAAGAAGGT
AAAGATTGTGAATAAATACGGTAAAAATAGCCTCAAGCTTCG
Found at i:3637524 original size:17 final size:17
Alignment explanation
Indices: 3637489--3637526 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3637479 TAGAAATTTT
*
3637489 ATTAAAAATATATATAA
1 ATTAAAAATATAGATAA
3637506 ATTAAAAATCATAGA-AA
1 ATTAAAAAT-ATAGATAA
3637523 ATTA
1 ATTA
3637527 TATATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (17 bp):
ATTAAAAATATAGATAA
Found at i:3639196 original size:20 final size:20
Alignment explanation
Indices: 3639171--3639228 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
3639161 TTTGGTTCAC
3639171 GGAATGTAAGATTACCAGTA
1 GGAATGTAAGATTACCAGTA
*
3639191 GGAATGTAAAATTACCAGTA
1 GGAATGTAAGATTACCAGTA
3639211 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
3639229 GGAATAGGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTA
Found at i:3641058 original size:18 final size:18
Alignment explanation
Indices: 3640988--3641058 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 18
3640978 TGAGATTTGC
*
3640988 TTGTAATATGGGCTTCAGG
1 TTGTAAT-TGGGCTTCGGG
*
3641007 TTGTAATCGGGCCTT-GGG
1 TTGTAATTGGG-CTTCGGG
* *
3641025 TT-AAATTTGAGCCTTCGGG
1 TTGTAA-TTG-GGCTTCGGG
3641044 TTGTAATTGGGCTTC
1 TTGTAATTGGGCTTC
3641059 ACATTTGGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
17 2 0.05
18 17 0.43
19 19 0.47
20 2 0.05
ACGTcount: A:0.17, C:0.14, G:0.31, T:0.38
Consensus pattern (18 bp):
TTGTAATTGGGCTTCGGG
Found at i:3641944 original size:15 final size:15
Alignment explanation
Indices: 3641924--3641986 Score: 81
Period size: 15 Copynumber: 4.2 Consensus size: 15
3641914 CACCTTGGCC
*
3641924 TCGAGTTCATCATCT
1 TCGAGTTCATCTTCT
*
3641939 TCGAGTTCATCTTCA
1 TCGAGTTCATCTTCT
*
3641954 TCGAGTTCGTCTTCT
1 TCGAGTTCATCTTCT
* *
3641969 TCAAGTTCGTCTTCT
1 TCGAGTTCATCTTCT
3641984 TCG
1 TCG
3641987 GATGTATCAG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.14, C:0.27, G:0.16, T:0.43
Consensus pattern (15 bp):
TCGAGTTCATCTTCT
Found at i:3645347 original size:17 final size:16
Alignment explanation
Indices: 3645325--3645357 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
3645315 TATGTCAATG
3645325 AATATTATTTTATTTAT
1 AATATTA-TTTATTTAT
3645342 AATATTATTTATTTAT
1 AATATTATTTATTTAT
3645358 TTATTCTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
AATATTATTTATTTAT
Found at i:3645889 original size:14 final size:14
Alignment explanation
Indices: 3645870--3645904 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
3645860 CATTAAAAAA
3645870 CGTTACGATGCAGG
1 CGTTACGATGCAGG
3645884 CGTTACGATGCAGG
1 CGTTACGATGCAGG
3645898 CGTTACG
1 CGTTACG
3645905 CTGCGTTGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.23
Consensus pattern (14 bp):
CGTTACGATGCAGG
Found at i:3660192 original size:172 final size:172
Alignment explanation
Indices: 3659906--3660249 Score: 638
Period size: 172 Copynumber: 2.0 Consensus size: 172
3659896 CTATTATTTA
*
3659906 TGACATCGACCTCATTGATCACTCATTTTTGGTCATTCCTTCACTTGGAGCAACAAACAACAACA
1 TGACATCGACCTCATTGATCACCCATTTTTGGTCATTCCTTCACTTGGAGCAACAAACAACAACA
3659971 TTCTTTTCTTGCAAGGAAGTTAGACAGAGTCTTAGTTAACCAAATCTGGATGAGCAGCTTTAAGA
66 TTCTTTTCTTGCAAGGAAGTTAGACAGAGTCTTAGTTAACCAAATCTGGATGAGCAGCTTTAAGA
3660036 ATTCACACGTTGAATTTCTTGCTCCTGGGAGTCT-TGATCACT
131 ATTCACACGTTGAATTTCTTGCTCCT-GGAGTCTCTGATCACT
*
3660078 TGACATCGACCTCATTGATCACCCTTTTTTTGGTCATTCCTTCACTTGGAGCAACAAACAACAAC
1 TGACATCGACCTCATTGATCACCC-ATTTTTGGTCATTCCTTCACTTGGAGCAACAAACAACAAC
3660143 ATTC-TTTCTTGCAAGGAAGTTAGACAGAGTCTTAGTTAACCAAATCTGGATGAGCAGCTTTAAG
65 ATTCTTTTCTTGCAAGGAAGTTAGACAGAGTCTTAGTTAACCAAATCTGGATGAGCAGCTTTAAG
3660207 AATTCACACGTTGAATTTCTTGCTCCTGGAGTCTCTGATCACT
130 AATTCACACGTTGAATTTCTTGCTCCTGGAGTCTCTGATCACT
3660250 GCTTATCTTT
Statistics
Matches: 168, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
171 7 0.04
172 118 0.70
173 43 0.26
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.33
Consensus pattern (172 bp):
TGACATCGACCTCATTGATCACCCATTTTTGGTCATTCCTTCACTTGGAGCAACAAACAACAACA
TTCTTTTCTTGCAAGGAAGTTAGACAGAGTCTTAGTTAACCAAATCTGGATGAGCAGCTTTAAGA
ATTCACACGTTGAATTTCTTGCTCCTGGAGTCTCTGATCACT
Found at i:3663499 original size:50 final size:50
Alignment explanation
Indices: 3663380--3663505 Score: 137
Period size: 50 Copynumber: 2.5 Consensus size: 50
3663370 TTAGCAGGAA
* * * * *
3663380 AGCGCGCCTCCTGAACCGTGCTATATGTTGATTTGGCTCCACGTGGATAT
1 AGCGCGCCTCCTGAACCGCGCTATACGGTGATCTGGCACCACGTGGATAT
* * * * *
3663430 AGCGTGCCCCCT-ACCCCGCGATATACGGTGATCTGGCACCACGTGGGTAT
1 AGCGCGCCTCCTGA-ACCGCGCTATACGGTGATCTGGCACCACGTGGATAT
*
3663480 AGCGCGCCTCCTGATCCGCGCTATAC
1 AGCGCGCCTCCTGAACCGCGCTATAC
3663506 CTGGATATCT
Statistics
Matches: 60, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
49 1 0.02
50 58 0.97
51 1 0.02
ACGTcount: A:0.17, C:0.33, G:0.26, T:0.24
Consensus pattern (50 bp):
AGCGCGCCTCCTGAACCGCGCTATACGGTGATCTGGCACCACGTGGATAT
Found at i:3668646 original size:21 final size:21
Alignment explanation
Indices: 3668621--3668660 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3668611 GGAGGTTTAG
* *
3668621 GGTTTGTATTTTAGAGATTAT
1 GGTTTATATATTAGAGATTAT
*
3668642 GGTTTATATATTAGGGATT
1 GGTTTATATATTAGAGATT
3668661 GAAATTAATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (21 bp):
GGTTTATATATTAGAGATTAT
Found at i:3668907 original size:2 final size:2
Alignment explanation
Indices: 3668900--3668926 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3668890 ATTAGAGTGA
3668900 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
3668927 CCAACCCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3681787 original size:130 final size:130
Alignment explanation
Indices: 3681646--3681893 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
3681636 TATTTATATA
* *
3681646 ATCAATTTGGTCCTAAATTAAATTAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
3681711 TTAGCACATGATCATGACACGTGTCATTGGTGACACTTGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
*
3681776 ATCAATTTGGTCCTAAATTAAATAAAATTTAATGAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
3681841 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
3681894 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:3681924 original size:130 final size:129
Alignment explanation
Indices: 3681660--3681924 Score: 291
Period size: 130 Copynumber: 2.0 Consensus size: 129
3681650 ATTTGGTCCT
* * *
3681660 AAATTAAATTAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
3681725 TGACACGTGTCATTGGTGACACTTGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
*
3681790 AAATTAAATAAAATTTAATGAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
3681855 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
3681919 -A
128 CA
3681920 AAATT
1 AAATT
3681925 TGGGTCTTGG
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
130 98 0.88
132 8 0.07
133 5 0.05
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:3682253 original size:28 final size:27
Alignment explanation
Indices: 3682222--3682284 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
3682212 AGTTGATACA
*
3682222 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
3682250 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
3682278 ATATTTT
1 ATATTTT
3682285 CATATTTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:3682381 original size:16 final size:18
Alignment explanation
Indices: 3682360--3682393 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
3682350 ATTTCTTATT
3682360 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
3682376 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
3682394 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:3682540 original size:21 final size:21
Alignment explanation
Indices: 3682516--3682558 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3682506 TATTACCTTA
3682516 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
3682537 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
3682558 A
1 A
3682559 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:3682576 original size:35 final size:35
Alignment explanation
Indices: 3682527--3682612 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
3682517 ATTGAAGTAT
** * *
3682527 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
3682562 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
3682597 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
3682613 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:3692335 original size:42 final size:42
Alignment explanation
Indices: 3692283--3692490 Score: 290
Period size: 42 Copynumber: 5.2 Consensus size: 42
3692273 TGATGTTGAT
*
3692283 TTTA-TTTAGACTTATTGAGACTTATTAGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
*
3692324 TTTATTTTAGACTTATTAAGACTT-A-A-----A-GGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
* * *
3692358 TTTATTTTAGACATATTGAGACTTAATGGTGTTATGATGTTA
1 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
* *
3692400 TTTATTTTAGACTTATTGAGACTTAATGGTGTTATGATGTTA
1 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
3692442 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
3692484 TTTATTT
1 TTTATTT
3692491 ACTTGTTTAT
Statistics
Matches: 149, Mismatches: 9, Indels: 17
0.85 0.05 0.10
Matches are distributed among these distances:
34 29 0.19
35 2 0.01
40 1 0.01
41 5 0.03
42 112 0.75
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (42 bp):
TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
Found at i:3692360 original size:34 final size:34
Alignment explanation
Indices: 3692317--3692392 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
3692307 TTAGTGTTAT
*
3692317 GGTGTTATTTATTTTAGACTTATTAAGACTTAAA
1 GGTGTTATTTATTTTAGACATATTAAGACTTAAA
* *
3692351 GGTGTTATTTATTTTAGACATATTGAGACTTAAT
1 GGTGTTATTTATTTTAGACATATTAAGACTTAAA
3692385 GGTGTTAT
1 GGTGTTAT
3692393 GATGTTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.47
Consensus pattern (34 bp):
GGTGTTATTTATTTTAGACATATTAAGACTTAAA
Found at i:3692411 original size:76 final size:78
Alignment explanation
Indices: 3692273--3692490 Score: 289
Period size: 76 Copynumber: 2.7 Consensus size: 78
3692263 TGAATATTAT
*
3692273 TGATGTTGATTT-TATTTAGACTTATTGAGACTTATTAGTGTTATGGTGTTATTTATTTTAGACT
1 TGATGTT-ATTTAT-TTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTATTTATTTTAGACT
3692337 TATTAAGACTTAA-A
64 TATTAAGACTTAATA
* * * *
3692351 -GGTGTTATTTATTTTAGACATATTGAGACTTAATGGTGTTATGATGTTATTTATTTTAGACTTA
1 TGATGTTATTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTATTTATTTTAGACTTA
*
3692415 TTGAGACTTAATGGTGTTA
66 TTAAGACTTAA------TA
3692434 TGATGTTATTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTATTTATTT
1 TGATGTTATTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTATTTATTT
3692491 ACTTGTTTAT
Statistics
Matches: 121, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
76 62 0.51
77 6 0.05
83 1 0.01
84 52 0.43
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (78 bp):
TGATGTTATTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTATTTATTTTAGACTTA
TTAAGACTTAATA
Found at i:3693904 original size:15 final size:15
Alignment explanation
Indices: 3693880--3693918 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
3693870 AATTCACTTA
*
3693880 AAATCGATAAAATTC
1 AAATCAATAAAATTC
3693895 AAATCAATAAAATTC
1 AAATCAATAAAATTC
3693910 AAATCAATA
1 AAATCAATA
3693919 GTTGTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.59, C:0.13, G:0.03, T:0.26
Consensus pattern (15 bp):
AAATCAATAAAATTC
Found at i:3694103 original size:20 final size:21
Alignment explanation
Indices: 3694078--3694129 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
3694068 GACCAACAAA
3694078 TTCGCAACGCGA-TCTCCAAT
1 TTCGCAACGCGAGTCTCCAAT
* *
3694098 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGAGTCTCCAAT
3694118 TTCGCAACGCGA
1 TTCGCAACGCGA
3694130 ATTTAATTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 23 0.85
21 2 0.07
ACGTcount: A:0.25, C:0.35, G:0.15, T:0.25
Consensus pattern (21 bp):
TTCGCAACGCGAGTCTCCAAT
Found at i:3695075 original size:24 final size:24
Alignment explanation
Indices: 3695048--3695101 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3695038 GTATTCGAAA
3695048 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
3695072 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
3695096 TTTGAT
1 TTTGAT
3695102 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:3697389 original size:18 final size:18
Alignment explanation
Indices: 3697366--3697401 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3697356 AAGCAAAAGG
*
3697366 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
3697384 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
3697402 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:3697748 original size:20 final size:20
Alignment explanation
Indices: 3697725--3697788 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
3697715 AATAAGAGTT
3697725 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
* *
3697745 GCGAAAGACAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
***
3697765 ATAATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
3697785 GCGA
1 GCGA
3697789 AATCGCAAAC
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCAAC
Found at i:3697956 original size:25 final size:25
Alignment explanation
Indices: 3697922--3697973 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
3697912 AACAAATCAA
*
3697922 TTAAACATTGTTGTGGGTACATTAT
1 TTAAACATTGTTATGGGTACATTAT
3697947 TTAAACATTGTTATGGGTACATTAT
1 TTAAACATTGTTATGGGTACATTAT
3697972 TT
1 TT
3697974 GGAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (25 bp):
TTAAACATTGTTATGGGTACATTAT
Found at i:3698382 original size:18 final size:18
Alignment explanation
Indices: 3698361--3698397 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3698351 GTAATTGGAG
3698361 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
3698379 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
3698397 T
1 T
3698398 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:3698404 original size:24 final size:24
Alignment explanation
Indices: 3698353--3698405 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3698343 TTTCATATGT
* * *
3698353 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
3698377 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
3698401 AATTT
1 AATTT
3698406 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:3698749 original size:39 final size:39
Alignment explanation
Indices: 3698706--3698794 Score: 160
Period size: 39 Copynumber: 2.3 Consensus size: 39
3698696 TCCGATGCTC
3698706 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
* *
3698745 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
3698784 ATCAAAATCTA
1 ATCAAAATCTA
3698795 CAACTTGAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (39 bp):
ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:3700639 original size:21 final size:21
Alignment explanation
Indices: 3700615--3700713 Score: 112
Period size: 21 Copynumber: 4.7 Consensus size: 21
3700605 GCGGGCAAGA
*
3700615 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
3700636 CCTCTTGAACGATGAGAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
3700657 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGAGAGGGG
* *
3700678 CCTCTTGAACTAT-AGGAGGCG
1 CCTCTTGAACGATGA-GAGGGG
*
3700699 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
3700714 TAGGTGCATC
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.03
21 61 0.94
22 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:3703351 original size:20 final size:20
Alignment explanation
Indices: 3703326--3703469 Score: 152
Period size: 20 Copynumber: 7.2 Consensus size: 20
3703316 GCGTAAAAAC
3703326 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
3703346 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
3703366 ATTTGACTTAT-GTGTTGCG-
1 ATTTGACTT-TCGCGTTGCGA
* ** *
3703385 ATTT-ACAAATTCGC-ACGTGA
1 ATTTGAC--TTTCGCGTTGCGA
*
3703405 ATTTGACTTTCGCGTTGCAA
1 ATTTGACTTTCGCGTTGCGA
3703425 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
3703445 AATTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
3703465 ATTTG
1 ATTTG
3703470 GAAAATCGCA
Statistics
Matches: 100, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
18 2 0.02
19 12 0.12
20 83 0.83
21 3 0.03
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:3705338 original size:22 final size:21
Alignment explanation
Indices: 3705296--3705338 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3705286 TAATTAAATA
*
3705296 TTTAATATAATATTATATTTT
1 TTTAATAGAATATTATATTTT
*
3705317 TTTAATTAGAATACT-TATTTT
1 TTTAA-TAGAATATTATATTTT
3705338 T
1 T
3705339 ACATGAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTAATAGAATATTATATTTT
Found at i:3705831 original size:15 final size:15
Alignment explanation
Indices: 3705807--3705840 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3705797 ACGTTTAACA
*
3705807 TTTT-TGTATTATAT
1 TTTTATGTATTATAC
3705821 TTTTATGTATTATAC
1 TTTTATGTATTATAC
3705836 TTTTA
1 TTTTA
3705841 GGTGCTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATGTATTATAC
Found at i:3706268 original size:21 final size:21
Alignment explanation
Indices: 3706235--3706284 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3706225 GAGAATGGTA
*
3706235 AATTCGAG-ATTAGGGTTAGG
1 AATTCAAGTATTAGGGTTAGG
*
3706255 AATTCAAGTATTAGGTTTAGG
1 AATTCAAGTATTAGGGTTAGG
* *
3706276 GATTTAAGT
1 AATTCAAGT
3706285 TTGGATTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (21 bp):
AATTCAAGTATTAGGGTTAGG
Found at i:3715060 original size:26 final size:26
Alignment explanation
Indices: 3715026--3715082 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
3715016 TTTAAACATT
3715026 TATTATAAAATAAACTTTTGAATAGA
1 TATTATAAAATAAACTTTTGAATAGA
*
3715052 TATTGTAAAATAAACTTTTGAATAGA
1 TATTATAAAATAAACTTTTGAATAGA
3715078 TATTA
1 TATTA
3715083 CTTTTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (26 bp):
TATTATAAAATAAACTTTTGAATAGA
Found at i:3715390 original size:2 final size:2
Alignment explanation
Indices: 3715383--3715483 Score: 202
Period size: 2 Copynumber: 50.5 Consensus size: 2
3715373 TTTACATAAA
3715383 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3715425 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3715467 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
3715484 TTCATACATG
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 99 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3718399 original size:15 final size:15
Alignment explanation
Indices: 3718379--3718434 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
3718369 GACACACCGT
3718379 AAAATAAAAGAAACA
1 AAAATAAAAGAAACA
3718394 AAAATAAAA-ACCAA-A
1 AAAATAAAAGA--AACA
*
3718409 ATTTAATAAAAGAAACA
1 A--AAATAAAAGAAACA
3718426 AAAATAAAA
1 AAAATAAAA
3718435 CATCAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
14 1 0.03
15 18 0.55
16 4 0.12
17 9 0.27
18 1 0.03
ACGTcount: A:0.77, C:0.07, G:0.04, T:0.12
Consensus pattern (15 bp):
AAAATAAAAGAAACA
Found at i:3718422 original size:32 final size:33
Alignment explanation
Indices: 3718381--3718446 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
3718371 CACACCGTAA
3718381 AATAAAAGAAACAAAAATAAAA-ACCAAAATTT
1 AATAAAAGAAACAAAAATAAAACACCAAAATTT
*
3718413 AATAAAAGAAACAAAAATAAAACATCAAAATTT
1 AATAAAAGAAACAAAAATAAAACACCAAAATTT
3718446 A
1 A
3718447 TGTGGAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 22 0.69
33 10 0.31
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.17
Consensus pattern (33 bp):
AATAAAAGAAACAAAAATAAAACACCAAAATTT
Done.