Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008061.1 Hibiscus syriacus cultivar Beakdansim tig00110556_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: 5800122
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 26
Found at i:3971762 original size:25 final size:26
Alignment explanation
Indices: 3971711--3971763 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
3971701 TTATATAAAA
* ** *
3971711 TTTAAAAAATAATAAAATTATATATT
1 TTTAAAAAAGAATAAAAGCATAAATT
3971737 TTTAAAAAAGAA-AAAAGCATAAATT
1 TTTAAAAAAGAATAAAAGCATAAATT
3971762 TT
1 TT
3971764 GAAATAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (26 bp):
TTTAAAAAAGAATAAAAGCATAAATT
Found at i:3976240 original size:2 final size:2
Alignment explanation
Indices: 3976233--3976267 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3976223 ATGGTTTTGA
3976233 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3976268 ATGTGTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3982148 original size:15 final size:15
Alignment explanation
Indices: 3982130--3982159 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3982120 AAAAGGTCAA
3982130 TTGCTGAAAGACCAG
1 TTGCTGAAAGACCAG
3982145 TTGCTGAAAGACCAG
1 TTGCTGAAAGACCAG
3982160 GTAAAGGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (15 bp):
TTGCTGAAAGACCAG
Found at i:3992981 original size:19 final size:19
Alignment explanation
Indices: 3992944--3992988 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3992934 TAATAATGAG
*
3992944 AATATTAATTTATATATTT
1 AATATTAATTAATATATTT
3992963 AATATTAATATAATA-ATTT
1 AATATTAAT-TAATATATTT
*
3992982 AGTATTA
1 AATATTA
3992989 TGTAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
AATATTAATTAATATATTT
Found at i:3993334 original size:30 final size:30
Alignment explanation
Indices: 3993256--3993357 Score: 118
Period size: 30 Copynumber: 3.4 Consensus size: 30
3993246 CCCGTAAAAT
* *
3993256 GTAATTCATTTTACGTAAAGCAGTTTT-AG
1 GTAATTCATTTTAAGTAAAACAGTTTTCAG
* * * *
3993285 GTAATTTATTTCATA-TAAAACAATTTTCAC
1 GTAATTCATTTTA-AGTAAAACAGTTTTCAG
3993315 GTAATTCATTTTAAGTAAAACAGTTTTCAG
1 GTAATTCATTTTAAGTAAAACAGTTTTCAG
*
3993345 GTAATCCATTTTA
1 GTAATTCATTTTA
3993358 CATAAATTAT
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
29 22 0.37
30 37 0.63
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (30 bp):
GTAATTCATTTTAAGTAAAACAGTTTTCAG
Found at i:3998292 original size:18 final size:16
Alignment explanation
Indices: 3998269--3998302 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
3998259 CTTTTTATTA
3998269 ATTAAATAATAGATATAT
1 ATTAAA-AATA-ATATAT
3998287 ATTAAAAATAATATAT
1 ATTAAAAATAATATAT
3998303 GATGTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
ATTAAAAATAATATAT
Found at i:3999987 original size:23 final size:25
Alignment explanation
Indices: 3999943--3999992 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
3999933 TATCTTCGTT
* *
3999943 TTATCATTATATGGTGTGTTTTGTA
1 TTATCATTATATGGTGTATTTTATA
*
3999968 TTATCATTATGT-GT-TATTTTATA
1 TTATCATTATATGGTGTATTTTATA
3999991 TT
1 TT
3999993 TTATATAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 9 0.41
24 2 0.09
25 11 0.50
ACGTcount: A:0.22, C:0.04, G:0.14, T:0.60
Consensus pattern (25 bp):
TTATCATTATATGGTGTATTTTATA
Found at i:4003276 original size:2 final size:2
Alignment explanation
Indices: 4003269--4003316 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
4003259 CATTTCCTTA
4003269 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
4003311 AT AT AT
1 AT AT AT
4003317 GCATAGTCTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4004284 original size:38 final size:38
Alignment explanation
Indices: 4004242--4004315 Score: 132
Period size: 38 Copynumber: 1.9 Consensus size: 38
4004232 AAAACACTAT
4004242 AGTTTAGGCACTTATTTTATATTTAAG-TCATTTTTAGC
1 AGTTTAGGCACTTATTTTATATTTAAGCT-ATTTTTAGC
4004280 AGTTTAGGCACTTATTTTATATTTAAGCTATTTTTA
1 AGTTTAGGCACTTATTTTATATTTAAGCTATTTTTA
4004316 AGCATTCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 34 0.97
39 1 0.03
ACGTcount: A:0.27, C:0.09, G:0.12, T:0.51
Consensus pattern (38 bp):
AGTTTAGGCACTTATTTTATATTTAAGCTATTTTTAGC
Found at i:4004304 original size:19 final size:20
Alignment explanation
Indices: 4004239--4004304 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 20
4004229 AAAAAAACAC
4004239 TATAGTTTAGGCACTTATTT
1 TATAGTTTAGGCACTTATTT
*
4004259 TATA-TTTAAGTCA--T-TTT
1 TATAGTTT-AGGCACTTATTT
*
4004276 TAGCAGTTTAGGCACTTATTT
1 TA-TAGTTTAGGCACTTATTT
4004297 TATA-TTTA
1 TATAGTTTA
4004305 AGCTATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 13
0.68 0.08 0.25
Matches are distributed among these distances:
17 5 0.14
18 6 0.17
19 10 0.28
20 10 0.28
21 5 0.14
ACGTcount: A:0.27, C:0.09, G:0.12, T:0.52
Consensus pattern (20 bp):
TATAGTTTAGGCACTTATTT
Found at i:4013346 original size:21 final size:21
Alignment explanation
Indices: 4013273--4013347 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
4013263 CAGTTTCCAG
* * * *
4013273 ATTCGCAACGCGATTATGACT
1 ATTCGCAATGCGATTTTCACA
4013294 A-TCGCAATGCGATTTTC-CA
1 ATTCGCAATGCGATTTTCACA
**
4013313 ATTTCGCGTTGCGATTTTCACA
1 A-TTCGCAATGCGATTTTCACA
4013335 ATTCGCAATGCGA
1 ATTCGCAATGCGA
4013348 ATAAGTAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 25 0.58
22 3 0.07
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTCGCAATGCGATTTTCACA
Found at i:4013362 original size:20 final size:21
Alignment explanation
Indices: 4013337--4013388 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
4013327 TTTTCACAAT
*
4013337 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
4013357 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
4013378 TCGCAATGCGA
1 TCGCAATGCGA
4013389 TACTGACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:4013403 original size:20 final size:20
Alignment explanation
Indices: 4013377--4013430 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
4013367 AATTTGGAAA
*
4013377 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
4013397 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
4013417 ATCGCAACGAGATA
1 ATCGCAACGCGATA
4013431 ATACAGAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:4013603 original size:12 final size:12
Alignment explanation
Indices: 4013584--4013617 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4013574 CTCTCCGGCG
4013584 ACATCCGTTCCT
1 ACATCCGTTCCT
*
4013596 ATATCCGTTCCT
1 ACATCCGTTCCT
4013608 ACATCC-TTCC
1 ACATCCGTTCC
4013618 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:4014225 original size:24 final size:24
Alignment explanation
Indices: 4014174--4014227 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
4014164 GTATTCGAAA
*
4014174 TTTGATCTTAGTCAATACCCGGAC
1 TTTGATCTTAGTCAATACCCAGAC
* * * *
4014198 TTTGATTTTGGTCAATACTCAGAT
1 TTTGATCTTAGTCAATACCCAGAC
4014222 TTTGAT
1 TTTGAT
4014228 GATGTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.43
Consensus pattern (24 bp):
TTTGATCTTAGTCAATACCCAGAC
Found at i:4014419 original size:12 final size:12
Alignment explanation
Indices: 4014402--4014426 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4014392 ATATAATCCT
4014402 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4014414 GAAGAAGAAAAA
1 GAAGAAGAAAAA
4014426 G
1 G
4014427 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:4016724 original size:20 final size:20
Alignment explanation
Indices: 4016699--4016807 Score: 166
Period size: 20 Copynumber: 5.5 Consensus size: 20
4016689 CAACGGGGAA
4016699 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
4016719 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
** *
4016739 ATCGCAACATGGAAATGATT
1 ATCGCAACGCGGAAATGACT
4016759 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
4016779 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
4016799 ATCGCAACG
1 ATCGCAACG
4016808 AGAGAATCGT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
20 79 0.96
21 3 0.04
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:4016840 original size:19 final size:20
Alignment explanation
Indices: 4016812--4016858 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
4016802 GCAACGAGAG
* *
4016812 AATCGTAATGCGAA-TTGAA
1 AATCGCAATGCGAAGATGAA
4016831 AATCGCAATGCGAAGATGAA
1 AATCGCAATGCGAAGATGAA
4016851 AATCGCAA
1 AATCGCAA
4016859 CGTGAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (20 bp):
AATCGCAATGCGAAGATGAA
Found at i:4017062 original size:14 final size:14
Alignment explanation
Indices: 4017043--4017079 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4017033 CATCAATTAA
4017043 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
4017057 ACAAATCATCTTTT
1 ACAAATCAACATTT
4017071 ACAAATCAA
1 ACAAATCAA
4017080 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:4018527 original size:42 final size:42
Alignment explanation
Indices: 4018481--4018573 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 42
4018471 CCTCTTCAAC
* *
4018481 GATGACAGTGGCCTCTTGAACGGTTGGAG-GAGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATTGGAGAG-GACTCTTGAGG
*
4018523 GATGATAGGGGCCTCTTGAACGATTGGAGAGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATTGGAGAGGACTCTTGAGG
4018565 GATGACAGG
1 GATGACAGG
4018574 TGAGTCGGGC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.39, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATTGGAGAGGACTCTTGAGG
Found at i:4018968 original size:20 final size:20
Alignment explanation
Indices: 4018945--4019009 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
4018935 GAAACTTAAA
*
4018945 ATCGCAGCGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
4018965 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
**
4018985 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
4019005 ATCGC
1 ATCGC
4019010 GACGAGAGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.31, C:0.26, G:0.25, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:4019040 original size:19 final size:18
Alignment explanation
Indices: 4019018--4019084 Score: 52
Period size: 19 Copynumber: 3.8 Consensus size: 18
4019008 GCGACGAGAG
*
4019018 AATCGCAATGCGAAATGAA
1 AATCACAATGCGAAA-GAA
4019037 AATCACAA--CG--AGAA
1 AATCACAATGCGAAAGAA
* * *
4019051 AATCGCAACGCGAAACACA
1 AATCACAATGCGAAAGA-A
4019070 AATCACAATGCGAAA
1 AATCACAATGCGAAA
4019085 CTAAATTCAC
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 2 0.05
19 21 0.55
ACGTcount: A:0.51, C:0.22, G:0.16, T:0.10
Consensus pattern (18 bp):
AATCACAATGCGAAAGAA
Found at i:4019073 original size:33 final size:33
Alignment explanation
Indices: 4019011--4019077 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
4019001 GACTATCGCG
* * *
4019011 ACGAGAGAATCGCAATGCGAAATGAAAATCACA
1 ACGAGAAAATCGCAACGCGAAATCAAAATCACA
4019044 ACGAGAAAATCGCAACGCGAAA-CACAAATCACA
1 ACGAGAAAATCGCAACGCGAAATCA-AAATCACA
4019077 A
1 A
4019078 TGCGAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.51, C:0.22, G:0.18, T:0.09
Consensus pattern (33 bp):
ACGAGAAAATCGCAACGCGAAATCAAAATCACA
Found at i:4019119 original size:20 final size:19
Alignment explanation
Indices: 4019094--4019214 Score: 81
Period size: 20 Copynumber: 6.4 Consensus size: 19
4019084 ACTAAATTCA
*
4019094 CGTTGCGATTTTCATTTCCG
1 CGTTGCGATATTCATTT-CG
*
4019114 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
* *
4019133 CATTGC-A-ATTC---TCT
1 CGTTGCGATATTCATTTCG
**
4019147 CGTTGCGATAGCCATTTCCG
1 CGTTGCGATATTCATTT-CG
*
4019167 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATATTCA-TTTCG
* *
4019187 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATATTCA-TTTCG
*
4019207 TGTTGCGA
1 CGTTGCGA
4019215 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
14 7 0.09
15 1 0.01
16 2 0.02
17 3 0.04
18 1 0.01
19 8 0.10
20 56 0.69
21 3 0.04
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41
Consensus pattern (19 bp):
CGTTGCGATATTCATTTCG
Found at i:4021147 original size:20 final size:20
Alignment explanation
Indices: 4021124--4021175 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
4021114 GAAACTTAAA
4021124 ATCGCAACGAGAAAATGACT
1 ATCGCAACGAGAAAATGACT
*
4021144 ATCGCAACGCGAAAATGACT
1 ATCGCAACGAGAAAATGACT
4021164 ATCGCAACGAGA
1 ATCGCAACGAGA
4021176 TAATCGCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.13
Consensus pattern (20 bp):
ATCGCAACGAGAAAATGACT
Found at i:4021205 original size:32 final size:34
Alignment explanation
Indices: 4021144--4021238 Score: 122
Period size: 32 Copynumber: 2.9 Consensus size: 34
4021134 GAAAATGACT
* * ** *
4021144 ATCGCAACGCGAAAATGACTATCGCAACGAGATA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAAA
*
4021178 ATCGCAATGC-GAATTG-AAATCGCAACGAGAAA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAAA
4021210 ATCGCAATGCGGAAATGAAAATCGCAACG
1 ATCGCAATGCGGAAATGAAAATCGCAACG
4021239 CGAATTTGGT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 23 0.44
33 9 0.17
34 20 0.38
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.15
Consensus pattern (34 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAAA
Found at i:4021310 original size:20 final size:19
Alignment explanation
Indices: 4021285--4021372 Score: 95
Period size: 20 Copynumber: 4.5 Consensus size: 19
4021275 GCGATTCTCT
4021285 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
4021305 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
* * *
4021325 TGTTGCGATAATCATTTTG
1 CGTTGCGATAGTCATTTCG
**
4021344 TCGTTGCGATTCTCATTTCG
1 -CGTTGCGATAGTCATTTCG
*
4021364 TGTTGCGAT
1 CGTTGCGAT
4021373 TCTCGGTTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
19 12 0.21
20 43 0.74
21 3 0.05
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:4021341 original size:40 final size:39
Alignment explanation
Indices: 4021286--4021372 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 39
4021276 CGATTCTCTC
* *
4021286 GTTGCGATAGTCATTTCCG-CGTTGCGATAGTCATTTTCGT
1 GTTGCGATAATCATTT-CGTCGTTGCGATACTCA-TTTCGT
* *
4021326 GTTGCGATAATCATTTTGTCGTTGCGATTCTCATTTCGT
1 GTTGCGATAATCATTTCGTCGTTGCGATACTCATTTCGT
4021365 GTTGCGAT
1 GTTGCGAT
4021373 TCTCGGTTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
39 15 0.36
40 27 0.64
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.43
Consensus pattern (39 bp):
GTTGCGATAATCATTTCGTCGTTGCGATACTCATTTCGT
Found at i:4021741 original size:22 final size:22
Alignment explanation
Indices: 4021713--4021758 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
4021703 GATGGAGATA
*
4021713 GACGGATTTCGTCGGTGATGGG
1 GACGGATTTCGTCGGAGATGGG
4021735 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
4021757 GA
1 GA
4021759 TGAATGTCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.46, T:0.24
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:4021986 original size:20 final size:20
Alignment explanation
Indices: 4021961--4022027 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
4021951 TGTATTATTT
4021961 CGTTGCGATAGTCAGAATCG
1 CGTTGCGATAGTCAGAATCG
4021981 CGTTGCGATATGT-AGAATCG
1 CGTTGCGATA-GTCAGAATCG
*
4022001 CGTTGCGATAGTCAGTATCG
1 CGTTGCGATAGTCAGAATCG
*
4022021 CATTGCG
1 CGTTGCG
4022028 GTTTTCCAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.05
20 39 0.91
21 2 0.05
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.28
Consensus pattern (20 bp):
CGTTGCGATAGTCAGAATCG
Found at i:4022111 original size:21 final size:22
Alignment explanation
Indices: 4022059--4022111 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
4022049 ATTTACTTAT
4022059 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
4022080 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
*
4022101 TTGCATTGCGA
1 TCGCATTGCGA
4022112 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:4022456 original size:30 final size:35
Alignment explanation
Indices: 4022411--4022472 Score: 89
Period size: 32 Copynumber: 1.9 Consensus size: 35
4022401 TTAAAATATT
4022411 CTATATATAATTTTA-T-AAATAAAA-TATTAATA
1 CTATATATAATTTTATTGAAATAAAATTATTAATA
4022443 CTAT-TAT-ATTTTATTGAAATAAAATTATTA
1 CTATATATAATTTTATTGAAATAAAATTATTA
4022473 TAAATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 6 0.22
31 4 0.15
32 12 0.44
33 5 0.19
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (35 bp):
CTATATATAATTTTATTGAAATAAAATTATTAATA
Found at i:4022598 original size:20 final size:20
Alignment explanation
Indices: 4022573--4022611 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4022563 TAACAAATAA
4022573 TATT-AATAGTATTAATAAAT
1 TATTAAATA-TATTAATAAAT
*
4022593 TATTAAATATATTATTAAA
1 TATTAAATATATTAATAAA
4022612 ATAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TATTAAATATATTAATAAAT
Found at i:4022855 original size:13 final size:13
Alignment explanation
Indices: 4022837--4022866 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
4022827 AGATCGTATC
4022837 ATTATATATAAAT
1 ATTATATATAAAT
4022850 ATTATATATAAAT
1 ATTATATATAAAT
4022863 ATTA
1 ATTA
4022867 GGAGTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTATATATAAAT
Found at i:4024776 original size:28 final size:30
Alignment explanation
Indices: 4024732--4024789 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
4024722 TTAAATATAA
*
4024732 AAAATATATATTTTA-TTTTATCTTTACTT
1 AAAATATATATTTTATTTTTATCTTAACTT
4024761 AAAA-ATATATTTTATTTTTATCTTAACTT
1 AAAATATATATTTTATTTTTATCTTAACTT
4024790 TTTATAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (30 bp):
AAAATATATATTTTATTTTTATCTTAACTT
Found at i:4034175 original size:14 final size:14
Alignment explanation
Indices: 4034156--4034207 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
4034146 TTGGTATAAA
4034156 AATAATATTTTAAT
1 AATAATATTTTAAT
*
4034170 AATAATAAATATTTTAT
1 AATAAT--AT-TTTAAT
* *
4034187 TATAATATTTTAAA
1 AATAATATTTTAAT
4034201 AATAATA
1 AATAATA
4034208 ATAATAAGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 16 0.53
15 2 0.07
16 2 0.07
17 10 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AATAATATTTTAAT
Found at i:4034176 original size:17 final size:17
Alignment explanation
Indices: 4034151--4034210 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
4034141 AATTGTTGGT
*
4034151 ATAAAAATAATATTTTA
1 ATAATAATAATATTTTA
4034168 ATAATAATAAATATTTT-
1 ATAATAAT-AATATTTTA
4034185 AT--T-ATAATATTTTA
1 ATAATAATAATATTTTA
*
4034199 AAAATAATAATA
1 ATAATAATAATA
4034211 ATAAGTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
13 8 0.22
14 3 0.08
15 1 0.03
16 1 0.03
17 15 0.42
18 8 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATAATAATATTTTA
Found at i:4034661 original size:21 final size:21
Alignment explanation
Indices: 4034640--4034678 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4034630 AAACATCGTA
*
4034640 AAAT-ATTTTTCAGAAAATGT
1 AAATCATTTTACAGAAAATGT
*
4034660 AATTCATTTTACAGAAAAT
1 AAATCATTTTACAGAAAAT
4034679 ACTTTTAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 3 0.19
21 13 0.81
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (21 bp):
AAATCATTTTACAGAAAATGT
Found at i:4041571 original size:13 final size:12
Alignment explanation
Indices: 4041555--4041616 Score: 63
Period size: 13 Copynumber: 5.0 Consensus size: 12
4041545 CCTAAATTAT
4041555 AAAATATATAAAA
1 AAAATATA-AAAA
*
4041568 AAAATATAAAGGA
1 AAAATATAAA-AA
*
4041581 AAAATGATAATAA
1 AAAAT-ATAAAAA
4041594 AAAATATAAAAA
1 AAAATATAAAAA
*
4041606 ATAATA-AAAAA
1 AAAATATAAAAA
4041617 TTGATGACTA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
11 5 0.12
12 13 0.31
13 20 0.48
14 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (12 bp):
AAAATATAAAAA
Found at i:4041609 original size:19 final size:19
Alignment explanation
Indices: 4041548--4041617 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
4041538 AAATAATCCT
* *
4041548 AAATTATAAAATATATAAA
1 AAATAATAAAAAATATAAA
* **
4041567 AAA-AATATAAAGGA-AAA
1 AAATAATAAAAAATATAAA
*
4041584 ATGATAATAAAAAATATAAA
1 A-AATAATAAAAAATATAAA
4041604 AAATAATAAAAAAT
1 AAATAATAAAAAAT
4041618 TGATGACTAG
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
17 4 0.11
18 7 0.18
19 23 0.61
20 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (19 bp):
AAATAATAAAAAATATAAA
Found at i:4041612 original size:10 final size:10
Alignment explanation
Indices: 4041587--4041617 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
4041577 AGGAAAAATG
4041587 ATAATAAAAA
1 ATAATAAAAA
4041597 AT-ATAAAAA
1 ATAATAAAAA
4041606 ATAATAAAAA
1 ATAATAAAAA
4041616 AT
1 AT
4041618 TGATGACTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
ATAATAAAAA
Found at i:4047596 original size:60 final size:60
Alignment explanation
Indices: 4047539--4047654 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 60
4047529 TGCCGGAGGC
* * * *
4047539 GGAGATGGCCGAGAAGGAACTGGCGGAGGCGATGATGAAGGTGGTGGTGGTGGCGGAGAG
1 GGAGACGGACGAGAAGGAACTGGCGGAGGCGATGATGAAGGAGGAGGTGGTGGCGGAGAG
* * * * * * *
4047599 GGCGACGGAGGAGGAGGAACTGGCGGTGGCGGTGGTGTAGGAGGAGGTGGTGGCGG
1 GGAGACGGACGAGAAGGAACTGGCGGAGGCGATGATGAAGGAGGAGGTGGTGGCGG
4047655 CGGACTTATG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.20, C:0.10, G:0.57, T:0.13
Consensus pattern (60 bp):
GGAGACGGACGAGAAGGAACTGGCGGAGGCGATGATGAAGGAGGAGGTGGTGGCGGAGAG
Found at i:4055270 original size:21 final size:20
Alignment explanation
Indices: 4055246--4055287 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
4055236 GTCATACAAC
*
4055246 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
4055267 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
4055287 T
1 T
4055288 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:4059979 original size:21 final size:20
Alignment explanation
Indices: 4059955--4059996 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
4059945 GTCATACAAC
*
4059955 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
4059976 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
4059996 T
1 T
4059997 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:4063660 original size:14 final size:14
Alignment explanation
Indices: 4063641--4063668 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4063631 GAAGGGAAAT
4063641 CAATTGTTTGATCA
1 CAATTGTTTGATCA
4063655 CAATTGTTTGATCA
1 CAATTGTTTGATCA
4063669 AAACTTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
CAATTGTTTGATCA
Found at i:4063813 original size:164 final size:165
Alignment explanation
Indices: 4063603--4064088 Score: 642
Period size: 154 Copynumber: 3.0 Consensus size: 165
4063593 ATCTTTGCAC
*
4063603 GAGACTAGCGGGGGCGTGAGATTGGCGGGAAGGGAAATCAATTGTTTGATCACAATTGTTTGATC
1 GAGACT-G-GGGGGCGTGAGATTGGCGGGCAGGGAAATCAATTGTTTGATCACAATTGTTTGATC
* * *
4063668 AAAACTTTTGGTCGCTAATTCGATTCCCCGATCAAGAAATCAATTGATATTAATCCATTGACATT
64 AAAACTTTTGTTCGCTAATTCGATTACCCGATCAAGAAATCAATTGATATTAAACCATTGACATT
* *
4063733 ACCTCGTTGAACATCACCATTAACTATATCAATATCA
129 ACCTCGTTGAACATCACCATCAACTATATCGATATCA
* *
4063770 GAGACT-GGGGGCGTGAGATTGGTGGGCAGGGAAATCAATTGTTTGATCATAATTGTTTGATCAA
1 GAGACTGGGGGGCGTGAGATTGGCGGGCAGGGAAATCAATTGTTTGATCACAATTGTTTGATCAA
* *
4063834 AACTTTTGTTCGCTAATTCGATTACCCGATCAGAGAAAACAATTGATATTAAACTATTGACATTA
66 AACTTTTGTTCGCTAATTCGATTACCCGATCA-AGAAATCAATTGATATTAAACCATTGACATTA
* *
4063899 CCTCGTTGAACATCATCATCAATTATATCGATATCA
130 CCTCGTTGAACATCACCATCAACTATATCGATATCA
*
4063935 GAGACTGGCGGGGGCGCGAGATTGGCGGGCAGGG-----AA-------AT--CAATTGTTTGATC
1 GAGACT-G-GGGGGCGTGAGATTGGCGGGCAGGGAAATCAATTGTTTGATCACAATTGTTTGATC
* * * * *
4063986 AAAACTTTTGTTCGCTAATTCGATTACCTGATCGGAGAAATCAACTGGTATTAAGCCATTGACAT
64 AAAACTTTTGTTCGCTAATTCGATTACCCGATC-AAGAAATCAATTGATATTAAACCATTGACAT
*
4064051 TACCCCGTTGAACATCACCATCAACTATATCGATATCA
128 TACCTCGTTGAACATCACCATCAACTATATCGATATCA
4064089 TCGTCTTCGA
Statistics
Matches: 289, Mismatches: 25, Indels: 23
0.86 0.07 0.07
Matches are distributed among these distances:
154 104 0.36
156 2 0.01
163 2 0.01
164 85 0.29
165 67 0.23
167 6 0.02
168 23 0.08
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (165 bp):
GAGACTGGGGGGCGTGAGATTGGCGGGCAGGGAAATCAATTGTTTGATCACAATTGTTTGATCAA
AACTTTTGTTCGCTAATTCGATTACCCGATCAAGAAATCAATTGATATTAAACCATTGACATTAC
CTCGTTGAACATCACCATCAACTATATCGATATCA
Found at i:4063825 original size:14 final size:14
Alignment explanation
Indices: 4063806--4063832 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4063796 CAGGGAAATC
4063806 AATTGTTTGATCAT
1 AATTGTTTGATCAT
4063820 AATTGTTTGATCA
1 AATTGTTTGATCA
4063833 AAACTTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (14 bp):
AATTGTTTGATCAT
Found at i:4064841 original size:30 final size:30
Alignment explanation
Indices: 4064800--4064865 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
4064790 AGAACTAGAA
* *
4064800 GAACAGGCTGAAAACCGGTAAAACCGGGGT
1 GAACCGGCTGAAAACCGGCAAAACCGGGGT
**
4064830 GAACCGGCTGAAAACCGGCAAAACCGGTTT
1 GAACCGGCTGAAAACCGGCAAAACCGGGGT
4064860 GAACCG
1 GAACCG
4064866 CCAGTTCACT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.24, G:0.30, T:0.11
Consensus pattern (30 bp):
GAACCGGCTGAAAACCGGCAAAACCGGGGT
Found at i:4065661 original size:8 final size:8
Alignment explanation
Indices: 4065648--4065672 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4065638 TGAACCCGGT
4065648 TGAACCAG
1 TGAACCAG
4065656 TGAACCAG
1 TGAACCAG
4065664 TGAACCAG
1 TGAACCAG
4065672 T
1 T
4065673 ACCTTCACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (8 bp):
TGAACCAG
Found at i:4069728 original size:15 final size:16
Alignment explanation
Indices: 4069708--4069746 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
4069698 AAGTTCCGGG
4069708 TACCCGGAAATCA-GA
1 TACCCGGAAATCAGGA
* *
4069723 TACCCGAAAATCAGGG
1 TACCCGGAAATCAGGA
4069739 TACCCGGA
1 TACCCGGA
4069747 TTTGCACACC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.36, C:0.28, G:0.23, T:0.13
Consensus pattern (16 bp):
TACCCGGAAATCAGGA
Found at i:4071242 original size:18 final size:18
Alignment explanation
Indices: 4071221--4071267 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
4071211 AATATTTTTA
4071221 ATAATTTTATTTCTGTCG
1 ATAATTTTATTTCTGTCG
*
4071239 ATAATATTATTTCTGTCG
1 ATAATTTTATTTCTGTCG
*
4071257 GTAATTTTATT
1 ATAATTTTATT
4071268 CTTCTAAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.55
Consensus pattern (18 bp):
ATAATTTTATTTCTGTCG
Found at i:4078287 original size:6 final size:6
Alignment explanation
Indices: 4078276--4078302 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4078266 CAACTCTCAA
4078276 CTCCAG CTCCAG CTCCAG CTCCAG CTC
1 CTCCAG CTCCAG CTCCAG CTCCAG CTC
4078303 ATGACACCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.52, G:0.15, T:0.19
Consensus pattern (6 bp):
CTCCAG
Found at i:4087287 original size:20 final size:20
Alignment explanation
Indices: 4087262--4087299 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4087252 TTTGGTTCAC
4087262 GGAATGGAAGATTATCAGTG
1 GGAATGGAAGATTATCAGTG
*
4087282 GGAATGTAAGATTATCAG
1 GGAATGGAAGATTATCAG
4087300 GGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.26
Consensus pattern (20 bp):
GGAATGGAAGATTATCAGTG
Found at i:4087636 original size:81 final size:82
Alignment explanation
Indices: 4087543--4087728 Score: 286
Period size: 81 Copynumber: 2.3 Consensus size: 82
4087533 ATGTTTAATG
4087543 AAAGGGTAAAATTTTATTTTAACCCCTAAACTTCATATAAAATTTTAATTATAGA-TTTTTTGTT
1 AAAGGGTAAAATTTTATTTTAACCCCTAAACTTCATATAAAATTTTAATTATAGATTTTTTTGTT
4087607 GTAAATCTAAAATAGTT
66 GTAAATCTAAAATAGTT
* * * * *
4087624 TAAGGGTAAAATTTTATTTTAACCCCTGAACTTTATATAAAATTTTAATTTTAGATTTTTTTTTT
1 AAAGGGTAAAATTTTATTTTAACCCCTAAACTTCATATAAAATTTTAATTATAGATTTTTTTGTT
4087689 GTAAATCTAAAATAGTT
66 GTAAATCTAAAATAGTT
* *
4087706 AAAGGAT-AAATTTGTAATTTAAC
1 AAAGGGTAAAATTT-TATTTTAAC
4087729 ATTCGTAGAA
Statistics
Matches: 95, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
81 57 0.60
82 38 0.40
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.45
Consensus pattern (82 bp):
AAAGGGTAAAATTTTATTTTAACCCCTAAACTTCATATAAAATTTTAATTATAGATTTTTTTGTT
GTAAATCTAAAATAGTT
Found at i:4088410 original size:18 final size:19
Alignment explanation
Indices: 4088387--4088429 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
4088377 CAGTAATCAT
4088387 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
*
4088405 ATTCCCACTGGTAATCTTTC
1 ATT-CCACTGGTAATCTTAC
4088425 ATTCC
1 ATTCC
4088430 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.21, C:0.30, G:0.09, T:0.40
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:4088417 original size:20 final size:20
Alignment explanation
Indices: 4088392--4088429 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4088382 ATCATATTCC
4088392 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
4088412 CTGGTAATCTTTCATTCC
1 CTGGTAATCTTACATTCC
4088430 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.29, G:0.11, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:4091217 original size:79 final size:78
Alignment explanation
Indices: 4091059--4091222 Score: 176
Period size: 79 Copynumber: 2.1 Consensus size: 78
4091049 TAGAAAAAAT
* * * * * *
4091059 AACATTTTAGATAGCGTCCAATATTAATATTTTTAGTAAAAAAATAATATTTTAAGTAGTATTTT
1 AACATTTTAAATAACGTCCAATATTAAAATTTTGAGTAAAAAAATAATATTTTAAGTAATACTTT
* *
4091124 ATCGAAAATGTTA
66 ATCAAAAATATTA
4091137 AACATTTTAAATAACG-CGCAATATTAAAATTTATGA-TAGAAAAAATAATATTTTATA-TAATA
1 AACATTTTAAATAACGTC-CAATATTAAAATTT-TGAGTA-AAAAAATAATATTTTA-AGTAATA
4091199 CTTTA-CTAAAAATATTA
62 CTTTATC-AAAAATATTA
4091216 AA-ATTTT
1 AACATTTT
4091223 TGATAATATA
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
77 1 0.01
78 35 0.48
79 36 0.49
80 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (78 bp):
AACATTTTAAATAACGTCCAATATTAAAATTTTGAGTAAAAAAATAATATTTTAAGTAATACTTT
ATCAAAAATATTA
Found at i:4091544 original size:33 final size:32
Alignment explanation
Indices: 4091507--4091581 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 32
4091497 CCCCTCCAAA
* *
4091507 TTTAAAATATTATAATTTAGACCCTTC-AATTTT
1 TTTAAAATATT-TAATTT-GACCCTACTAAATTT
* *
4091540 TTTAAAAAATTTAATTTGACTCTACTAAATTT
1 TTTAAAATATTTAATTTGACCCTACTAAATTT
4091572 TTT-AAATATT
1 TTTAAAATATT
4091582 CATATTAAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 12 0.33
32 14 0.39
33 10 0.28
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (32 bp):
TTTAAAATATTTAATTTGACCCTACTAAATTT
Found at i:4092234 original size:2 final size:2
Alignment explanation
Indices: 4092227--4092251 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4092217 TTATTATTAT
4092227 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4092252 CTTTAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4092712 original size:9 final size:9
Alignment explanation
Indices: 4092691--4092724 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
4092681 ATTTTTTTCC
4092691 TTTATCTTA-
1 TTTAT-TTAT
4092700 TTTATTTAT
1 TTTATTTAT
4092709 TTTATTTAT
1 TTTATTTAT
4092718 TTTATTT
1 TTTATTT
4092725 TTCACTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:4092713 original size:13 final size:14
Alignment explanation
Indices: 4092691--4092725 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
4092681 ATTTTTTTCC
*
4092691 TTTATCTTATTTA-
1 TTTATTTTATTTAT
4092704 TTTATTTTATTTAT
1 TTTATTTTATTTAT
4092718 TTTATTTT
1 TTTATTTT
4092726 TCACTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:4092733 original size:22 final size:22
Alignment explanation
Indices: 4092691--4092734 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4092681 ATTTTTTTCC
*
4092691 TTTATCTTATTTATTTATTTTA
1 TTTATCTTATTTATTCATTTTA
*
4092713 TTTATTTTATTT-TTCACTTTTA
1 TTTATCTTATTTATTCA-TTTTA
4092735 CCTTGTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTATCTTATTTATTCATTTTA
Found at i:4094518 original size:8 final size:8
Alignment explanation
Indices: 4094505--4094540 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
4094495 AAACATTTCA
*
4094505 TGCATTCT
1 TGCATTTT
4094513 TGCA-TTT
1 TGCATTTT
4094520 TGCATTTT
1 TGCATTTT
4094528 TGCATTTT
1 TGCATTTT
4094536 TGCAT
1 TGCAT
4094541 CTTCATCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.56
Consensus pattern (8 bp):
TGCATTTT
Found at i:4094525 original size:15 final size:16
Alignment explanation
Indices: 4094505--4094540 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
4094495 AAACATTTCA
4094505 TGCATTCTTGCA-TTT
1 TGCATTCTTGCATTTT
*
4094520 TGCATTTTTGCATTTT
1 TGCATTCTTGCATTTT
4094536 TGCAT
1 TGCAT
4094541 CTTCATCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.56
Consensus pattern (16 bp):
TGCATTCTTGCATTTT
Found at i:4094574 original size:22 final size:21
Alignment explanation
Indices: 4094532--4094574 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
4094522 CATTTTTGCA
**
4094532 TTTTTGCATCTTCATCTACAT
1 TTTTTGCATCTTCATAAACAT
*
4094553 TTTTTAGCATTTTCATAAACAT
1 TTTTT-GCATCTTCATAAACAT
4094575 GAAATTTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.51
Consensus pattern (21 bp):
TTTTTGCATCTTCATAAACAT
Found at i:4095713 original size:22 final size:22
Alignment explanation
Indices: 4095690--4095751 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
4095680 AAAAAAGGGC
4095690 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAA-AAAAGAAGCA
* *
4095713 AAAAAGGAAAAAACAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
4095734 AAAAAGAAAGAACAAAAA
1 AAAAAGAAA-AA-AAAAA
4095752 TAAAAAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 8 0.24
23 15 0.45
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:4095742 original size:20 final size:20
Alignment explanation
Indices: 4095690--4095758 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
4095680 AAAAAAGGGC
*
4095690 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAG-AAAAA-ACAAGAA-CA
4095713 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAGAACA
* * *
4095734 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
4095754 AAAAA
1 AAAAA
4095759 AGGGAACAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 17 0.41
21 7 0.17
22 6 0.15
23 10 0.24
24 1 0.02
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:4097297 original size:36 final size:36
Alignment explanation
Indices: 4097250--4097353 Score: 172
Period size: 36 Copynumber: 2.9 Consensus size: 36
4097240 GTGCTCACCA
*
4097250 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
4097286 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
* * *
4097322 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
4097354 TAAACATTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
Found at i:4097457 original size:100 final size:101
Alignment explanation
Indices: 4097268--4097722 Score: 614
Period size: 101 Copynumber: 4.5 Consensus size: 101
4097258 CTTGAGACAG
** * *
4097268 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTT-TCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCCT
4097332 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
4097369 TTTCCCTTGAAA-GAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA-TTTTGTCTCCCT
*
4097433 TGAGACAGTTTCTCTTGAAA-ATAAACATTGGAAACA
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
4097469 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCCT
*
4097534 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACA
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
4097571 TTTCCCTAGAAATGAATTTCGTCTCT-TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTT
* * * * ***
4097635 GAGACAGCTTCTCTTGAAACACAAAACCTTTGAGATTG
66 GAGACAGTTTCTCTTGAAACA-TAAA-CATTGAAAACA
* ** * *
4097673 TTTCCCTCGAAACAAATTTTGTCTC-CTATGAGACAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATGAATTTTGTCTCTCT-TGAGATAGTTTCCCTTGAAACA
4097723 CAAAATCTTT
Statistics
Matches: 318, Mismatches: 27, Indels: 16
0.88 0.07 0.04
Matches are distributed among these distances:
99 3 0.01
100 98 0.31
101 128 0.40
102 70 0.22
103 19 0.06
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.36
Consensus pattern (101 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTT
GAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:4097536 original size:37 final size:37
Alignment explanation
Indices: 4097469--4097555 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
4097459 ATTGGAAACA
** * *
4097469 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
4097505 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
4097542 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
4097556 TAAACATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 12 0.27
37 31 0.69
38 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:4097633 original size:201 final size:201
Alignment explanation
Indices: 4097268--4097722 Score: 655
Period size: 201 Copynumber: 2.2 Consensus size: 201
4097258 CTTGAGACAG
4097268 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTCTCCCTT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTCTCCCTT
* * * *
4097333 GAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAAGAGTTTTGTCTCTCTTG
66 GAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAAGAATTTCGTCTCTCTTG
* * *
4097398 AGATAGTTTCCCTTGAAACAAATTTTTTTCTCCCTTGAGACAGTTTCTCTTGAAAATAAACATTG
131 AGATAATTTCCCTTGAAACAAATTTTTGTCTCCCTTGAGACAGCTTCTCTTGAAAATAAACATTG
4097463 GAAACA
196 GAAACA
** * *
4097469 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTT-TCTCCCT
4097534 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCGTCTCT-T
65 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAA-GAATTTCGTCTCTCT
*
4097598 TGAGATAATTTCCCTTGAAACAAA-TTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACACAAAAC
129 TGAGATAATTTCCCTTGAAACAAATTTTTGTCTCCCTTGAGACAGCTTCTCTTGAAA-A-TAAAC
* * ***
4097662 CTTTGAGATTG
192 ATTGGA-AACA
* * *
4097673 TTTCCCTCGAAACAAATTTTGTCTC-CTATGAGACAGTTTCTCTTGAAACA
1 TTTCCCTTGAAACAAACTTTGTCTCTCT-TGAGACAGTTTCCCTTGAAACA
4097723 CAAAATCTTT
Statistics
Matches: 226, Mismatches: 22, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
201 83 0.37
202 79 0.35
203 21 0.09
204 43 0.19
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.36
Consensus pattern (201 bp):
TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTCTCCCTT
GAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAAGAATTTCGTCTCTCTTG
AGATAATTTCCCTTGAAACAAATTTTTGTCTCCCTTGAGACAGCTTCTCTTGAAAATAAACATTG
GAAACA
Found at i:4097679 original size:67 final size:66
Alignment explanation
Indices: 4097595--4097755 Score: 218
Period size: 67 Copynumber: 2.4 Consensus size: 66
4097585 AATTTCGTCT
*
4097595 CTTTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCT-TGAGACAGCTTCTCTTGAAACACAA
1 CTTTGAGAT-TTTTCCCTTGAAACAAATTTTGTCT-CCTATGAGACAGCTTCTCTTGAAACACAA
4097659 AAC
64 AAC
* *
4097662 CTTTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCTATGAGACAGTTTCTCTTGAAACACAAA
1 CTTTGAGATT-TTTCCCTTGAAACAAATTTTGTCTCCTATGAGACAGCTTCTCTTGAAACACAAA
*
4097727 AT
65 AC
*
4097729 CTTTGA-ATTTATCTCCCTTAAAACAAA
1 CTTTGAGATTT-T-TCCCTTGAAACAAA
4097756 ATTTCGTTCT
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
65 1 0.01
66 7 0.08
67 76 0.90
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (66 bp):
CTTTGAGATTTTTCCCTTGAAACAAATTTTGTCTCCTATGAGACAGCTTCTCTTGAAACACAAAA
C
Found at i:4097935 original size:37 final size:37
Alignment explanation
Indices: 4097862--4097931 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
4097852 ATATGTTTCC
4097862 TTGGAACTAATTTCATCTCCCCGTGAGACAATTTCTT
1 TTGGAACTAATTTCATCTCCCCGTGAGACAATTTCTT
* *
4097899 TTGGAACTAAGTTT-ATCT-CTCTTGAGACAATTT
1 TTGGAACTAA-TTTCATCTCCCCGTGAGACAATTT
4097932 TCTTAAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 13 0.43
37 14 0.47
38 3 0.10
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (37 bp):
TTGGAACTAATTTCATCTCCCCGTGAGACAATTTCTT
Found at i:4099085 original size:105 final size:105
Alignment explanation
Indices: 4098582--4099553 Score: 1432
Period size: 105 Copynumber: 9.3 Consensus size: 105
4098572 GCCATCCGCG
* * * * * **
4098582 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCAAAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * * *
4098647 GGGACGGCTGGTTGTAAACAAACAAC-TTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAAC-AACAACTTTC-CAATCTCAGAGCCA
4098691 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
4098756 ACCGCTGGTTGTCAATAAACAATTTTCCCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAA-CAACAACTTT-CCAATCTCAGAGCCA
*
4098798 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
4098863 ACCGCTGGTTGTCAACAACAAATTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
*
4098903 ATTTCAACTTCACAACGAAGGATA-TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
4098967 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
4099007 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
4099072 ACCGCTGCTTGTCAACAA-AA-TTT-C-AT-TCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
* *
4099107 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
4099172 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
4099212 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
4099277 ACCGCTGCTTGTCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
*
4099317 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
4099382 ACCGCTGCTTGTCAACAA-AA-TTT-C-AT-TCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
* * *
4099417 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
4099482 ACGGCTGGTTGTCAACAAACAA-TTTCCCGGT-TCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTT-CCAATCT-CAGAGCCA
* *
4099523 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
4099554 TGGAACAATG
Statistics
Matches: 804, Mismatches: 44, Indels: 33
0.91 0.05 0.04
Matches are distributed among these distances:
100 171 0.21
101 8 0.01
102 10 0.01
103 6 0.01
104 107 0.13
105 288 0.36
106 93 0.12
107 98 0.12
108 1 0.00
109 22 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
Found at i:4099221 original size:205 final size:209
Alignment explanation
Indices: 4098582--4099553 Score: 1437
Period size: 205 Copynumber: 4.6 Consensus size: 209
4098572 GCCATCCGCG
* * * * * **
4098582 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCAAAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
4098647 GGGACGGCTGGTTGTAAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
63 GGGACCGCTGGTTGTCAACAAACAA-TTCTCAA-TTCAGAGCCAATTTCAACTTCACAACGAAGG
* *
4098712 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
126 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACA
* *
4098777 ATTTTCCCAATTTCAGAGCCA
190 ACTTT-CCAATCTCAGAGCCA
*
4098798 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
4098863 ACCGCTGGTTGTCAAC-AACAAATTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATA
66 ACCGCTGGTTGTCAACAAAC-AATTCTCAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATA
*
4098927 -TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT
129 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT
4098991 TCCAATCTCAGAGCCA
194 TCCAATCTCAGAGCCA
4099007 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
4099072 ACCGCTGCTTGTCAAC-AA-AATT-TC-ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
66 ACCGCTGGTTGTCAACAAACAATTCTCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
*
4099133 GGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTC
131 GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTC
4099198 CAATCTCAGAGCCA
196 CAATCTCAGAGCCA
4099212 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
4099277 ACCGCTGCTTGTCAAC-AACAACTTCCCAATCCCAGAGCCAATTTCAACTTCACAACGAAAGATA
66 ACCGCTGGTTGTCAACAAACAA-TTCTCAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATA
4099341 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT
129 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT
**
4099404 T-C-AT-TCAGATTCA
194 TCCAATCTCAGAGCCA
* * *
4099417 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * ** * *
4099482 ACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATA
66 ACCGCTGGTTGTCAACAAACAA-TTCTCAATT-CAGAGCCAATTTCAACTTCACAACGAAGGATA
4099547 TTGGACT
129 TTGGACT
4099554 TGGAACAATG
Statistics
Matches: 707, Mismatches: 39, Indels: 30
0.91 0.05 0.04
Matches are distributed among these distances:
204 32 0.05
205 248 0.35
206 52 0.07
207 7 0.01
208 4 0.01
209 99 0.14
210 96 0.14
211 54 0.08
212 42 0.06
213 49 0.07
214 3 0.00
216 21 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (209 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAAACAATTCTCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTC
CAATCTCAGAGCCA
Found at i:4099380 original size:310 final size:309
Alignment explanation
Indices: 4098582--4099553 Score: 1498
Period size: 310 Copynumber: 3.1 Consensus size: 309
4098572 GCCATCCGCG
* * * * * **
4098582 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCAAAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * * * *
4098647 GGGACGGCTGGTTGTAAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
63 GGGACCGCTGCTTGTCAAC-AACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGG
* *
4098712 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
127 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAA-A
4098777 ATTTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
190 A-TTT--C-A-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
*
4098842 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAAATTCCCAATCTCAGAGCCA
250 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAC-AATTTCCAATCTCAGAGCCA
*
4098903 ATTTCAACTTCACAACGAAGGATA-TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
4098967 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
4099032 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTCA
131 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTCA
*
4099097 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCA
196 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
4099162 CGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
261 CGACGAAGGGACCGCTGGTTGTCAACAACAA-TTTCCAATCTCAGAGCCA
4099212 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
4099277 ACCGCTGCTTGTCAACAACAACTTCCCAATCCCAGAGCCAATTTCAACTTCACAACGAAAGATAT
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
4099342 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTCA
131 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTCA
** * * *
4099407 TTCAGATTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
196 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * **
4099472 CAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGT-TCCAGAGCCA
261 CGACGAAGGGACCGCTGGTTGTCAAC-AACAATTT-CCAATCT-CAGAGCCA
* *
4099523 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
4099554 TGGAACAATG
Statistics
Matches: 610, Mismatches: 36, Indels: 20
0.92 0.05 0.03
Matches are distributed among these distances:
308 2 0.00
309 133 0.22
310 253 0.41
311 46 0.08
313 3 0.00
314 2 0.00
315 2 0.00
316 100 0.16
317 45 0.07
318 3 0.00
321 21 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (309 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTCA
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAACAACAATTTCCAATCTCAGAGCCA
Found at i:4100592 original size:2 final size:2
Alignment explanation
Indices: 4100574--4100616 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
4100564 TTTATGTTAT
4100574 TA TA T- TA T- TA T- TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4100612 TA TA T
1 TA TA T
4100617 TTAATATTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 4 0.11
2 33 0.89
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:4100601 original size:23 final size:24
Alignment explanation
Indices: 4100574--4100624 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
4100564 TTTATGTTAT
4100574 TATATTAT-TATTATATATATATA
1 TATATTATATATTATATATATATA
*
4100597 TATA-TATATATTATATATATTTA
1 TATATTATATATTATATATATATA
4100620 -ATATT
1 TATATT
4100625 CTACTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TATATTATATATTATATATATATA
Found at i:4100722 original size:17 final size:17
Alignment explanation
Indices: 4100700--4100734 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4100690 ATGGTTGATT
*
4100700 TATATACCTATTATTAA
1 TATATACATATTATTAA
*
4100717 TATATATATATTATTAA
1 TATATACATATTATTAA
4100734 T
1 T
4100735 TATTTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATACATATTATTAA
Found at i:4101074 original size:9 final size:9
Alignment explanation
Indices: 4101053--4101086 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
4101043 ATTTTTTTCC
4101053 TTTATCTTA-
1 TTTAT-TTAT
4101062 TTTATTTAT
1 TTTATTTAT
4101071 TTTATTTAT
1 TTTATTTAT
4101080 TTTATTT
1 TTTATTT
4101087 TTCACTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:4101075 original size:13 final size:14
Alignment explanation
Indices: 4101053--4101087 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
4101043 ATTTTTTTCC
*
4101053 TTTATCTTATTTA-
1 TTTATTTTATTTAT
4101066 TTTATTTTATTTAT
1 TTTATTTTATTTAT
4101080 TTTATTTT
1 TTTATTTT
4101088 TCACTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:4101095 original size:22 final size:22
Alignment explanation
Indices: 4101053--4101096 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4101043 ATTTTTTTCC
*
4101053 TTTATCTTATTTATTTATTTTA
1 TTTATCTTATTTATTCATTTTA
*
4101075 TTTATTTTATTT-TTCACTTTTA
1 TTTATCTTATTTATTCA-TTTTA
4101097 CCTTATTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTATCTTATTTATTCATTTTA
Found at i:4101681 original size:15 final size:16
Alignment explanation
Indices: 4101649--4101683 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4101639 ATTATTAATC
4101649 AAATATTTAATGTTTA
1 AAATATTTAATGTTTA
*
4101665 AAATATTTTAT-TTTA
1 AAATATTTAATGTTTA
4101680 AAAT
1 AAAT
4101684 TTAACTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
AAATATTTAATGTTTA
Found at i:4103583 original size:18 final size:20
Alignment explanation
Indices: 4103525--4103597 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 20
4103515 ATCAAATATC
**
4103525 AAATAATAAAACAAT-AATA
1 AAATAATAAAATTATGAATA
4103544 AAATAATACAAATTATGAATA
1 AAATAATA-AAATTATGAATA
*
4103565 AAATAAT-AAATTTTG-ATA
1 AAATAATAAAATTATGAATA
* *
4103583 AATTAAAAAAATTAT
1 AAATAATAAAATTAT
4103598 AAAATACTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
18 8 0.18
19 21 0.47
20 5 0.11
21 11 0.24
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (20 bp):
AAATAATAAAATTATGAATA
Found at i:4115450 original size:180 final size:178
Alignment explanation
Indices: 4115150--4115510 Score: 679
Period size: 180 Copynumber: 2.0 Consensus size: 178
4115140 ATGTTTTCTG
4115150 CCCCGAGTTCGGCCTCCGAGCATGGATGTCGCAGTCTGGAACACGGCTGCAGCGTTGCCAAGATG
1 CCCCGAGTTCGGCCTCCGAGCATGGATGTCGCAGTCTGGAACACGGCTGCAGCGTTGCCAAGATG
4115215 AAATCAACTGTTCCTGCCACAAGGCAGTTGACGTAAAACTGCCGATTGGAGTGAGCGTAGAGAGT
66 AAATCAACTGTTCCTGCCACAAGGCAGTTGACGTAAAACTGCCGATTGGAGTGAGCGTAGAGAGT
4115280 GTCCTGGTATGCGCAGCATGT-CATTGGTAGAATGCCGAGAGATCCGAA
131 GTCCTGGTATGC-CAGCATGTACATTGGTAGAATGCCGAGAGATCCGAA
4115328 CCCCGAGTTCGGCCTCCGAGCATGGATGTCGCAGTCTTGGAACACGGCTGCAGCGTTGCCAAAGA
1 CCCCGAGTTCGGCCTCCGAGCATGGATGTCGCAGTC-TGGAACACGGCTGCAGCGTTGCC-AAGA
4115393 TGAAATCAACTGTTCCTGCCACAAGGCAGTTGACGTAAAACTGCCGATTGGAGTGAGCGTAGAGA
64 TGAAATCAACTGTTCCTGCCACAAGGCAGTTGACGTAAAACTGCCGATTGGAGTGAGCGTAGAGA
4115458 GTGTCCTGGTATGCCAGCATGTCACATTGGTAGAATGCCGAGAGATCCGAA
129 GTGTCCTGGTATGCCAGCATGT-ACATTGGTAGAATGCCGAGAGATCCGAA
4115509 CC
1 CC
4115511 GACACGGAGG
Statistics
Matches: 179, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
178 36 0.20
179 31 0.17
180 83 0.46
181 29 0.16
ACGTcount: A:0.25, C:0.25, G:0.30, T:0.21
Consensus pattern (178 bp):
CCCCGAGTTCGGCCTCCGAGCATGGATGTCGCAGTCTGGAACACGGCTGCAGCGTTGCCAAGATG
AAATCAACTGTTCCTGCCACAAGGCAGTTGACGTAAAACTGCCGATTGGAGTGAGCGTAGAGAGT
GTCCTGGTATGCCAGCATGTACATTGGTAGAATGCCGAGAGATCCGAA
Found at i:4119216 original size:16 final size:17
Alignment explanation
Indices: 4119195--4119226 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4119185 TTTTATTATT
4119195 ATTTAAAATA-AAAATA
1 ATTTAAAATACAAAATA
4119211 ATTTAAAATACAAAAT
1 ATTTAAAATACAAAAT
4119227 TAAATAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
ATTTAAAATACAAAATA
Found at i:4121367 original size:25 final size:24
Alignment explanation
Indices: 4121337--4121388 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
4121327 ATAGTCCATT
* * *
4121337 AAAAATTATATTTTTAAATTATAAA
1 AAAAATGAAATTTATAAATTA-AAA
4121362 AAAAATGAAATTTATAAATTAAAA
1 AAAAATGAAATTTATAAATTAAAA
4121386 AAA
1 AAA
4121389 GGGAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAAATGAAATTTATAAATTAAAA
Found at i:4132322 original size:16 final size:16
Alignment explanation
Indices: 4132301--4132339 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
4132291 ATCTATGGTC
4132301 CAACTCTAATACTCTA
1 CAACTCTAATACTCTA
*
4132317 CAACTCTAATATTCTA
1 CAACTCTAATACTCTA
4132333 CAACTCT
1 CAACTCT
4132340 TGTTAATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (16 bp):
CAACTCTAATACTCTA
Found at i:4134800 original size:28 final size:28
Alignment explanation
Indices: 4134769--4134825 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
4134759 TGATAAGTTA
* *
4134769 TTAATATATT-AATTTTCTAATAAATAAT
1 TTAAAATATTAAATTAT-TAATAAATAAT
*
4134797 TTAAAATATTAAATTATTAATTAATAAT
1 TTAAAATATTAAATTATTAATAAATAAT
4134825 T
1 T
4134826 ATTATTTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (28 bp):
TTAAAATATTAAATTATTAATAAATAAT
Found at i:4134803 original size:44 final size:43
Alignment explanation
Indices: 4134728--4134825 Score: 117
Period size: 44 Copynumber: 2.3 Consensus size: 43
4134718 TCATTCAGAA
* *
4134728 AATTATTAATTTACTAATAGATAATAAAAAATGA-TAAGTTATT
1 AATTATTAATTTACTAATAAATAATAAAAAAT-ATTAAATTATT
* **
4134771 AATATATTAATTTTCTAATAAATAATTTAAAATATTAAATTATT
1 AAT-TATTAATTTACTAATAAATAATAAAAAATATTAAATTATT
*
4134815 AATTAATAATT
1 AATTATTAATT
4134826 ATTATTTTAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 11 0.23
44 36 0.77
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (43 bp):
AATTATTAATTTACTAATAAATAATAAAAAATATTAAATTATT
Found at i:4138173 original size:16 final size:16
Alignment explanation
Indices: 4138140--4138173 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4138130 TTACTATTCA
**
4138140 CGTGAATAGTGATTTT
1 CGTGAATAGTGAAATT
4138156 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
4138172 CG
1 CG
4138174 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.35
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:4146215 original size:17 final size:17
Alignment explanation
Indices: 4146193--4146228 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
4146183 TTCCCTTGAT
4146193 CCTTGGTCAACCATAAC
1 CCTTGGTCAACCATAAC
4146210 CCTTGGTCAACCATAAC
1 CCTTGGTCAACCATAAC
4146227 CC
1 CC
4146229 ATAATCCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.39, G:0.11, T:0.22
Consensus pattern (17 bp):
CCTTGGTCAACCATAAC
Found at i:4158400 original size:20 final size:20
Alignment explanation
Indices: 4158375--4158429 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
4158365 GCGAAATAAA
4158375 AATCGCAACGCGATCTCC-AG
1 AATCGCAACGCGAT-TCCTAG
**
4158395 AATCGCAAATC-AGTTCCTAG
1 AATCGCAACGCGA-TTCCTAG
4158415 AATCGCAACGCGATT
1 AATCGCAACGCGATT
4158430 ATGAAGAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
19 4 0.14
20 23 0.82
21 1 0.04
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGATTCCTAG
Found at i:4158490 original size:21 final size:21
Alignment explanation
Indices: 4158373--4158512 Score: 67
Period size: 21 Copynumber: 6.8 Consensus size: 21
4158363 ATGCGAAATA
*
4158373 AAAATCGCAACGCGA-TCTCC
1 AAAATCGCAACGCGATTATCC
* ** *
4158393 AGAATCGCAAATC-AGT-TCC
1 AAAATCGCAACGCGATTATCC
* *
4158412 TAGAATCGCAACGCGATTAT-G
1 -AAAATCGCAACGCGATTATCC
* * *
4158433 AAGAATCGCAATGCGATAATAC
1 AA-AATCGCAACGCGATTATCC
* ** *
4158455 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTATCC
**
4158476 AAAATCGCAACGCGAACAT--
1 AAAATCGCAACGCGATTATCC
4158495 ATAAATCGCAACGCGATT
1 A-AAATCGCAACGCGATT
4158513 CTGACTATCG
Statistics
Matches: 89, Mismatches: 24, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
19 5 0.06
20 37 0.42
21 44 0.49
22 3 0.03
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTATCC
Found at i:4158563 original size:20 final size:20
Alignment explanation
Indices: 4158519--4158688 Score: 171
Period size: 20 Copynumber: 8.4 Consensus size: 20
4158509 GATTCTGACT
* *
4158519 ATCGTAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
4158540 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
4158560 ATCGAAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
4158580 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
4158600 ATCTCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
4158620 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
4158640 ATCGTAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
4158661 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
4158681 ATCGCAAC
1 ATCGCAAC
4158689 ACGGTTTTTA
Statistics
Matches: 118, Mismatches: 28, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
20 86 0.73
21 32 0.27
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:4158585 original size:81 final size:80
Alignment explanation
Indices: 4158524--4158688 Score: 249
Period size: 81 Copynumber: 2.0 Consensus size: 80
4158514 TGACTATCGT
* * *
4158524 AACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCGAAACGAGAATACGTAAATCGCAACG
1 AACGAGAATACGT-AAATCGCAACGCGTATCCGTAAATCGAAACGACAATACGTAAATCGCAACG
4158589 CGTATCTGTAAATCTC
65 CGTATCTGTAAATCTC
* *
4158605 AACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCGTAACGACAATACGTAAAATCGCAACG
1 AACGAGAATACGTAAATCGCAACGCGTATCCGTAAATCGAAACGACAATACGT-AAATCGCAACG
* *
4158670 CGTATCCGTAAATCGC
65 CGTATCTGTAAATCTC
4158686 AAC
1 AAC
4158689 ACGGTTTTTA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
80 37 0.49
81 39 0.51
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (80 bp):
AACGAGAATACGTAAATCGCAACGCGTATCCGTAAATCGAAACGACAATACGTAAATCGCAACGC
GTATCTGTAAATCTC
Found at i:4158591 original size:40 final size:41
Alignment explanation
Indices: 4158519--4158684 Score: 248
Period size: 40 Copynumber: 4.1 Consensus size: 41
4158509 GATTCTGACT
* *
4158519 ATCGTAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGTAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
4158560 ATCGAAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGTAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
4158600 ATC-TCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGT-AACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
4158640 ATCGTAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGTAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
4158681 ATCG
1 ATCG
4158685 CAACACGGTT
Statistics
Matches: 113, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
40 72 0.64
41 41 0.36
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (41 bp):
ATCGTAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:4159310 original size:21 final size:21
Alignment explanation
Indices: 4159249--4159327 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
4159239 TTCTAAACTT
4159249 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
4159269 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
** *
4159289 ACTATCGCAATGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
4159310 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
4159328 TCGCAACGCG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 29 0.58
21 21 0.42
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:4159430 original size:52 final size:53
Alignment explanation
Indices: 4159352--4159484 Score: 187
Period size: 52 Copynumber: 2.5 Consensus size: 53
4159342 CAAAATCGCA
* * *
4159352 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTT-CTCG
1 TTGCGATTTTCATTTCTCGTTGCGATTATCTCGTTGCGATTTTCATTTCCCCG
*
4159404 TTGCGATTTTCATTTCTCGTTGCGATTATTTCGTTGCGATTTTCATTTCCCCG
1 TTGCGATTTTCATTTCTCGTTGCGATTATCTCGTTGCGATTTTCATTTCCCCG
** *
4159457 TTGCGATAGTCATTCTTTCGTTGCGATT
1 TTGCGATTTTCATT-TCTCGTTGCGATT
4159485 TTCATTTCAA
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
52 45 0.62
53 15 0.21
54 12 0.17
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.48
Consensus pattern (53 bp):
TTGCGATTTTCATTTCTCGTTGCGATTATCTCGTTGCGATTTTCATTTCCCCG
Found at i:4159460 original size:20 final size:19
Alignment explanation
Indices: 4159352--4159492 Score: 149
Period size: 19 Copynumber: 7.8 Consensus size: 19
4159342 CAAAATCGCA
*
4159352 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCTCG
4159371 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCTCG
4159385 TTGCGATTTTCATTTCTCG
1 TTGCGATTTTCATTTCTCG
4159404 TTGCGATTTTCATTTCTCG
1 TTGCGATTTTCATTTCTCG
4159423 TTGCGA--TT-A-TT-TCG
1 TTGCGATTTTCATTTCTCG
*
4159437 TTGCGATTTTCATTTCCCCG
1 TTGCGATTTTCATTT-CTCG
** *
4159457 TTGCGATAGTCATTCTTTCG
1 TTGCGATTTTCATT-TCTCG
4159477 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
4159493 AACCAAAAGA
Statistics
Matches: 101, Mismatches: 9, Indels: 24
0.75 0.07 0.18
Matches are distributed among these distances:
14 19 0.19
15 2 0.02
16 6 0.06
17 6 0.06
18 2 0.02
19 37 0.37
20 28 0.28
21 1 0.01
ACGTcount: A:0.11, C:0.22, G:0.18, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCTCG
Found at i:4161397 original size:21 final size:21
Alignment explanation
Indices: 4161373--4161439 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
4161363 TCATTCCTCG
4161373 AGAGTCCCTTCCCACCGTTCA
1 AGAGTCCCTTCCCACCGTTCA
* * *
4161394 AGAGGCCACTGT--CATCGTTGA
1 AGAGTCC-CT-TCCCACCGTTCA
*
4161415 AGAGGTCCC-TCCCACCATTCA
1 AGA-GTCCCTTCCCACCGTTCA
4161436 AGAG
1 AGAG
4161440 CCTGATTCAC
Statistics
Matches: 34, Mismatches: 7, Indels: 11
0.65 0.13 0.21
Matches are distributed among these distances:
19 1 0.03
20 1 0.03
21 26 0.76
22 5 0.15
23 1 0.03
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (21 bp):
AGAGTCCCTTCCCACCGTTCA
Found at i:4161397 original size:42 final size:42
Alignment explanation
Indices: 4161321--4161439 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
4161311 GACTCACCTG
* * * *
4161321 TCATCCCTC-AAGA-GTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCAT-CCTCGAAGAGGTCC-CTCCCACCGTTCAAGAGGCCACTA
*
4161363 TCATTCCTCG-AGA-GTCCCTTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTCGAAGAGGTCCC-TCCCACCGTTCAAGAGGCCACTA
* * *
4161405 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCGTTCAAGAG
4161440 CCTGATTCAC
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
41 5 0.08
42 53 0.83
43 6 0.09
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:4162799 original size:14 final size:14
Alignment explanation
Indices: 4162780--4162815 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4162770 ATTGTTTAAT
4162780 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
4162794 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
4162808 TGATTTGT
1 TGATTTGT
4162816 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:4162969 original size:33 final size:33
Alignment explanation
Indices: 4162922--4163015 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 33
4162912 AAAAATGACT
* * *
4162922 ATCGTAATGCGAAATGAAAATCTCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCTCAACGACAAA
*
4162955 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCTCAACGACAAA
4162988 ATCGCAATGCGAAACT-AAAATCTCAACG
1 ATCGCAATGCGAAA-TGAAAATCTCAACG
4163016 CGAAACTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 54 0.98
34 1 0.02
ACGTcount: A:0.46, C:0.20, G:0.18, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCTCAACGACAAA
Found at i:4162978 original size:19 final size:19
Alignment explanation
Indices: 4162922--4163020 Score: 58
Period size: 19 Copynumber: 5.7 Consensus size: 19
4162912 AAAAATGACT
*
4162922 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
4162941 ATCTCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
4162955 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4162974 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
4162988 ATCGCAATGCGAAACT-AAA
1 ATCGCAATGCGAAA-TGAAA
* *
4163007 ATCTCAACGCGAAA
1 ATCGCAATGCGAAA
4163021 CTAAATTCGC
Statistics
Matches: 61, Mismatches: 8, Indels: 22
0.67 0.09 0.24
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 30 0.49
ACGTcount: A:0.46, C:0.20, G:0.18, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4163021 original size:19 final size:19
Alignment explanation
Indices: 4162954--4163030 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 19
4162944 TCAACGAGAG
*
4162954 AATCGCAATGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
4162973 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
*
4162987 AATCGCAATGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
4163006 AATCTCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
4163025 ATTCGC
1 AATCGC
4163031 GTTACGATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.21
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 31 0.65
ACGTcount: A:0.45, C:0.23, G:0.16, T:0.16
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:4163103 original size:14 final size:14
Alignment explanation
Indices: 4163049--4163105 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
4163039 TTTCATTTCG
*
4163049 CGTTGCGATTCCCT
1 CGTTGCGATTCTCT
*
4163063 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
4163080 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
4163096 CGTTGCGATT
1 CGTTGCGATT
4163106 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 16 0.46
16 7 0.20
17 6 0.17
19 6 0.17
ACGTcount: A:0.11, C:0.26, G:0.21, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:4163142 original size:20 final size:19
Alignment explanation
Indices: 4163026--4163188 Score: 95
Period size: 19 Copynumber: 9.3 Consensus size: 19
4163016 CGAAACTAAA
* *
4163026 TTCGCGTTACGATTTTCAT
1 TTCGCGTTGCGATATTCAT
4163045 TTCGCGTTGCG--ATTC--
1 TTCGCGTTGCGATATTCAT
* * *
4163060 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATATTCAT
*
4163078 TTCGCATTGCG--ATTC--
1 TTCGCGTTGCGATATTCAT
* *
4163093 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATATTCAT
* *
4163111 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATATTCAT
4163130 TTCCGCGTTGCGATATTCAT
1 TT-CGCGTTGCGATATTCAT
4163150 ATTCGCGTTGC-A-A-T--T
1 -TTCGCGTTGCGATATTCAT
* *
4163165 TTCACGTTGCGATTTTCAT
1 TTCGCGTTGCGATATTCAT
4163184 TTCGC
1 TTCGC
4163189 ATTGTGATTC
Statistics
Matches: 106, Mismatches: 21, Indels: 34
0.66 0.13 0.21
Matches are distributed among these distances:
14 25 0.24
15 2 0.02
16 6 0.06
17 8 0.08
18 1 0.01
19 39 0.37
20 23 0.22
21 2 0.02
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATATTCAT
Found at i:4163179 original size:106 final size:106
Alignment explanation
Indices: 4163028--4163237 Score: 296
Period size: 106 Copynumber: 2.0 Consensus size: 106
4163018 AAACTAAATT
* * *
4163028 CGCGTTACGATTTTCATTTCGCGTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTC
1 CGCGTTACGATATTCATTTCGCGTTGCAATTCCCACGTTGCGATTTTCATTTCGCATTGCGATTC
** * *
4163093 TCTCGTTGCGATTTTCATTT-CGCATTGCGATAGTCATTTC
66 TCTCGTTGCGATAGTAATTTCCGCATTGCGATAGACATTTC
* ** *
4163133 CGCGTTGCGATATTCATATTCGCGTTGCAATTTTCACGTTGCGATTTTCATTTCGCATTGTGATT
1 CGCGTTACGATATTCAT-TTCGCGTTGCAATTCCCACGTTGCGATTTTCATTTCGCATTGCGATT
*
4163198 CTCTCGTTGCGATAGTAATTTCCGCGTTGCGATAGACATT
65 CTCTCGTTGCGATAGTAATTTCCGCATTGCGATAGACATT
4163238 AAGATGATTA
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
105 15 0.16
106 60 0.66
107 16 0.18
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (106 bp):
CGCGTTACGATATTCATTTCGCGTTGCAATTCCCACGTTGCGATTTTCATTTCGCATTGCGATTC
TCTCGTTGCGATAGTAATTTCCGCATTGCGATAGACATTTC
Found at i:4163219 original size:33 final size:33
Alignment explanation
Indices: 4163030--4163210 Score: 209
Period size: 33 Copynumber: 5.3 Consensus size: 33
4163020 ACTAAATTCG
* * *
4163030 CGTTACGATTTTCATTTCGCGTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
4163063 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
4163096 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CT
* * * * *
4163135 CGTTGCGATATTCATATTCGCGTTGCAATTTTCA
1 CGTTGCGATTTTCAT-TTCGCATTGCGATTCTCT
*
4163169 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
4163202 CGTTGCGAT
1 CGTTGCGAT
4163211 AGTAATTTCC
Statistics
Matches: 126, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
33 80 0.63
34 15 0.12
35 3 0.02
38 2 0.02
39 15 0.12
40 11 0.09
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:4170851 original size:18 final size:18
Alignment explanation
Indices: 4170828--4170862 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4170818 AGGGATATGC
*
4170828 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGAGACAT
4170846 AGTGGTCCTTCGAGACA
1 AGTGGTCCTTCGAGACA
4170863 AATATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGAGACAT
Found at i:4172958 original size:21 final size:21
Alignment explanation
Indices: 4172932--4172976 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
4172922 GATTTCTGGG
*
4172932 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
4172953 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
4172974 CAA
1 CAA
4172977 ACGAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4174350 original size:32 final size:31
Alignment explanation
Indices: 4174308--4174435 Score: 127
Period size: 31 Copynumber: 4.1 Consensus size: 31
4174298 AGAGTCGAGG
4174308 GTTTACCTATGTTCTACAGAACATATGGACA
1 GTTTACCTATGTTCTACAGAACATATGGACA
*
4174339 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACAGA-ACATATGGACA
* *
4174371 GTATACCTATGTTCTA-AGGAATATATGGACA
1 GTTTACCTATGTTCTACA-GAACATATGGACA
* * * * *
4174402 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACAGAACATATGGACA
4174433 GTT
1 GTT
4174436 ACCGAGGATC
Statistics
Matches: 79, Mismatches: 11, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
31 51 0.65
32 28 0.35
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACAGAACATATGGACA
Found at i:4174521 original size:30 final size:30
Alignment explanation
Indices: 4174421--4174523 Score: 161
Period size: 30 Copynumber: 3.4 Consensus size: 30
4174411 GGTTCTTCGG
* *
4174421 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
4174451 GACCTCTAGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
4174481 GACCTCTGGATAGTTACCAAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
4174511 AACCTCTGGATAG
1 GACCTCTGGATAG
4174524 GTCCTTCGGG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:4177500 original size:21 final size:21
Alignment explanation
Indices: 4177474--4177518 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4177464 GATTTCTGGG
* *
4177474 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
4177495 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
4177516 CAA
1 CAA
4177519 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4178892 original size:32 final size:31
Alignment explanation
Indices: 4178850--4178958 Score: 134
Period size: 31 Copynumber: 3.5 Consensus size: 31
4178840 AGAGTCGAGG
4178850 GTTTACCTATGTTCTACAGAACATATGGACA
1 GTTTACCTATGTTCTACAGAACATATGGACA
*
4178881 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACAGA-ACATATGGACA
*
4178913 GTATACCTATGTTCTA-AGGAACATATGGACA
1 GTTTACCTATGTTCTACA-GAACATATGGACA
*
4178944 GTTTACCTAGGTTCT
1 GTTTACCTATGTTCT
4178959 TCGTGACCTA
Statistics
Matches: 67, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
31 39 0.58
32 28 0.42
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTACAGAACATATGGACA
Found at i:4178923 original size:31 final size:31
Alignment explanation
Indices: 4178870--4178977 Score: 112
Period size: 31 Copynumber: 3.5 Consensus size: 31
4178860 GTTCTACAGA
4178870 ACATATGGACAGTTTTACCTATGTCTTTCGAG
1 ACATATGGACAG-TTTACCTATGTCTTTCGAG
* ***
4178902 ACATATGGACAGTATACCTATGTTCTAAGGA-
1 ACATATGGACAGTTTACCTATG-TCTTTCGAG
* *
4178933 ACATATGGACAGTTTACCTAGGT-TCTTCGTG
1 ACATATGGACAGTTTACCTATGTCT-TTCGAG
*
4178964 ACCTATGGACAGTT
1 ACATATGGACAGTT
4178978 ACCGAGGATC
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
29 1 0.02
30 2 0.03
31 42 0.68
32 17 0.27
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (31 bp):
ACATATGGACAGTTTACCTATGTCTTTCGAG
Found at i:4178996 original size:30 final size:30
Alignment explanation
Indices: 4178938--4179062 Score: 169
Period size: 30 Copynumber: 4.1 Consensus size: 30
4178928 AAGGAACATA
* * ** *
4178938 TGGACAGTTTACCTAGGTTCTTCGTGACCTA
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
4178969 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
4178999 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* *
4179029 TGGATAGTTACCGAGGATCTTTATAACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
4179059 TGGA
1 TGGA
4179063 TAGGTCCTTC
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
30 80 0.92
31 7 0.08
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:4179063 original size:30 final size:30
Alignment explanation
Indices: 4178962--4179065 Score: 181
Period size: 30 Copynumber: 3.5 Consensus size: 30
4178952 AGGTTCTTCG
* *
4178962 TGACCTATGGACAGTTACCGAGGATCTTTA
1 TGACCTCTGGATAGTTACCGAGGATCTTTA
4178992 TGACCTCTGGATAGTTACCGAGGATCTTTA
1 TGACCTCTGGATAGTTACCGAGGATCTTTA
4179022 TGACCTCTGGATAGTTACCGAGGATCTTTA
1 TGACCTCTGGATAGTTACCGAGGATCTTTA
*
4179052 TAACCTCTGGATAG
1 TGACCTCTGGATAG
4179066 GTCCTTCGGG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (30 bp):
TGACCTCTGGATAGTTACCGAGGATCTTTA
Found at i:4179942 original size:20 final size:21
Alignment explanation
Indices: 4179893--4179946 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
4179883 TCTGGAATCC
4179893 CAGTCTCGATACCAAACCCCT
1 CAGTCTCGATACCAAACCCCT
**
4179914 TGGTCTCGATACCAAA-CCCT
1 CAGTCTCGATACCAAACCCCT
*
4179934 CAGTATCGATACC
1 CAGTCTCGATACC
4179947 CCTTTAAGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.28, C:0.37, G:0.13, T:0.22
Consensus pattern (21 bp):
CAGTCTCGATACCAAACCCCT
Done.