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 26 of 26
Found at i:5497202 original size:15 final size:15
Alignment explanation
Indices: 5497182--5497230 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
5497172 GTCAAAGTTT
5497182 GGTCAACGGGTCAAC-
1 GGTCAAC-GGTCAACG
5497197 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
5497212 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
5497227 GGTC
1 GGTC
5497231 GGGTCGGGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.21
15 26 0.79
ACGTcount: A:0.24, C:0.27, G:0.35, T:0.14
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:5497209 original size:22 final size:22
Alignment explanation
Indices: 5497182--5497227 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
5497172 GTCAAAGTTT
5497182 GGTCAACGGGTCAACGGTCAAC
1 GGTCAACGGGTCAACGGTCAAC
5497204 GGTCAACGGGTCAACGGTCAAC
1 GGTCAACGGGTCAACGGTCAAC
5497226 GG
1 GG
5497228 GTCGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.35, T:0.13
Consensus pattern (22 bp):
GGTCAACGGGTCAACGGTCAAC
Found at i:5502311 original size:37 final size:37
Alignment explanation
Indices: 5502238--5502312 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
5502228 GTTAGAAAAT
** *
5502238 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATCAAAAATCATAAA
* *
5502275 ATTTATATAATTTTTTTTACAAAATCAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATCAAAAATCATAAA
5502312 A
1 A
5502313 ATGTTTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 14 0.44
38 18 0.56
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATCAAAAATCATAAA
Found at i:5503045 original size:14 final size:15
Alignment explanation
Indices: 5503013--5503046 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5503003 TATCACTTTA
5503013 ATTAAAATATTAATT
1 ATTAAAATATTAATT
*
5503028 ATTAAAATA-TATTT
1 ATTAAAATATTAATT
5503042 ATTAA
1 ATTAA
5503047 TATTTATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTAAAATATTAATT
Found at i:5503249 original size:14 final size:15
Alignment explanation
Indices: 5503232--5503268 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
5503222 TTTATGTATT
5503232 TAAT-TTTAATAAAA
1 TAATATTTAATAAAA
5503246 TAATATTTAAT-AAA
1 TAATATTTAATAAAA
5503260 T-ATATTTAA
1 TAATATTTAA
5503269 AATATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.36
14 8 0.36
15 6 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TAATATTTAATAAAA
Found at i:5503266 original size:13 final size:13
Alignment explanation
Indices: 5503236--5503276 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 13
5503226 TGTATTTAAT
5503236 TTTAATAAAATAATA
1 TTTAAT-AAAT-ATA
5503251 TTTAATAAATATA
1 TTTAATAAATATA
5503264 TTT-A-AAATATA
1 TTTAATAAATATA
5503275 TT
1 TT
5503277 AATTAATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.35
12 1 0.04
13 6 0.23
14 4 0.15
15 6 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTAATAAATATA
Found at i:5503318 original size:26 final size:24
Alignment explanation
Indices: 5503241--5503298 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
5503231 TTAATTTTAA
* *
5503241 TAAAATAATATTTAATAAATA-TATT
1 TAAAAT-ATA-TTAATTAATACTCTT
5503266 TAAAATATATTAATTAATACTCTT
1 TAAAATATATTAATTAATACTCTT
5503290 TAAAATATA
1 TAAAATATA
5503299 ATATAATACT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 9 0.30
24 15 0.50
25 6 0.20
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAAATATATTAATTAATACTCTT
Found at i:5506445 original size:23 final size:23
Alignment explanation
Indices: 5506411--5506463 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
5506401 CTCGGCTGCC
5506411 CTCGGATTCCCTCGCATAGCTCG
1 CTCGGATTCCCTCGCATAGCTCG
* *
5506434 CTCGG-TTGCCCTTGGATAGCTCG
1 CTCGGATT-CCCTCGCATAGCTCG
*
5506457 TTCGGAT
1 CTCGGAT
5506464 GGTCTCGGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 2 0.08
23 22 0.88
24 1 0.04
ACGTcount: A:0.11, C:0.32, G:0.26, T:0.30
Consensus pattern (23 bp):
CTCGGATTCCCTCGCATAGCTCG
Found at i:5510293 original size:10 final size:10
Alignment explanation
Indices: 5510280--5510316 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
5510270 CGACCGAGAC
5510280 CATCCGAAAG
1 CATCCGAAAG
5510290 CATCCGAAAG
1 CATCCGAAAG
*
5510300 GATCCGAAAG
1 CATCCGAAAG
5510310 CATCCGA
1 CATCCGA
5510317 GGCCCGATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.38, C:0.30, G:0.22, T:0.11
Consensus pattern (10 bp):
CATCCGAAAG
Found at i:5510390 original size:31 final size:32
Alignment explanation
Indices: 5510325--5510397 Score: 103
Period size: 33 Copynumber: 2.3 Consensus size: 32
5510315 GAGGCCCGAT
* *
5510325 CCGAACGAGCTATGCGAGGGCATCTGAGGGCAA
1 CCGAGCGAGCTATGCGAGGGAATC-GAGGGCAA
*
5510358 CCGAGCGAGCTATGCGAGGGAATC-CGGGCAA
1 CCGAGCGAGCTATGCGAGGGAATCGAGGGCAA
5510389 CCGAGCGAG
1 CCGAGCGAG
5510398 GGTAGGTCGC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 15 0.41
33 22 0.59
ACGTcount: A:0.26, C:0.26, G:0.38, T:0.10
Consensus pattern (32 bp):
CCGAGCGAGCTATGCGAGGGAATCGAGGGCAA
Found at i:5510478 original size:20 final size:20
Alignment explanation
Indices: 5510450--5510504 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
5510440 ACCTCGGTCG
5510450 GATGGCCTCGGATGCTCTCA
1 GATGGCCTCGGATGCTCTCA
* * *
5510470 GATGACCTCGGATGCTTTCG
1 GATGGCCTCGGATGCTCTCA
*
5510490 GATGGCCTCGAATGC
1 GATGGCCTCGGATGC
5510505 CCAGCGTGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.16, C:0.27, G:0.31, T:0.25
Consensus pattern (20 bp):
GATGGCCTCGGATGCTCTCA
Found at i:5514353 original size:14 final size:15
Alignment explanation
Indices: 5514312--5514363 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
5514302 TTTCAGAAAA
*
5514312 TGAATTACTGAAATT
1 TGAATTACTGGAATT
5514327 TGAATTACTGGAATT
1 TGAATTACTGGAATT
* **
5514342 TGAGTT-CTGGAAAA
1 TGAATTACTGGAATT
5514356 TGAATTAC
1 TGAATTAC
5514364 ATTTTTGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 11 0.35
15 20 0.65
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.37
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:5514414 original size:20 final size:20
Alignment explanation
Indices: 5514346--5514415 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
5514336 GGAATTTGAG
5514346 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
* *
5514366 TTTTGAAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
* *
5514386 TTTTGGAAAATAAATTACAT
1 TTCTGGAAAATGAATTACAT
*
5514406 TTCTAGAAAA
1 TTCTGGAAAA
5514416 CATCTGAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:5514788 original size:29 final size:28
Alignment explanation
Indices: 5514733--5514897 Score: 105
Period size: 29 Copynumber: 5.9 Consensus size: 28
5514723 CTTTACTAAA
*
5514733 ATATTATTTAAATATATAAATAATATTAT
1 ATATTA-TTAAATATATAAAAAATATTAT
5514762 -TCATTATTAAATATATAAAAAATTATTAT
1 AT-ATTATTAAATATATAAAAAA-TATTAT
*
5514791 ATATTATTAAA-ATAAAAATATAATATCT-T
1 ATATTATTAAATATATAAA-A-AATAT-TAT
** ** *
5514820 ATATTATTATAATATAATTGATTATTTTAT
1 ATATTATTA-AATAT-ATAAAAAATATTAT
* *
5514850 ATAATATTAAA-A-AT--ATAATATTAT
1 ATATTATTAAATATATAAAAAATATTAT
5514874 ATTATTA-TAAATAT-TAAAAAATAT
1 A-TATTATTAAATATATAAAAAATAT
5514898 ATTTTAAATA
Statistics
Matches: 108, Mismatches: 13, Indels: 32
0.71 0.08 0.21
Matches are distributed among these distances:
24 13 0.12
25 6 0.06
26 2 0.02
27 6 0.06
28 23 0.21
29 36 0.33
30 18 0.17
31 2 0.02
32 2 0.02
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
ATATTATTAAATATATAAAAAATATTAT
Found at i:5514899 original size:29 final size:28
Alignment explanation
Indices: 5514733--5514900 Score: 97
Period size: 28 Copynumber: 6.0 Consensus size: 28
5514723 CTTTACTAAA
5514733 ATATTATT-TAAATATATAAATAATATTATT
1 ATATTATTATAAATATA-AAA-AATA-TATT
*
5514763 -CATTATTA-AATATATAAAAAAT-TATT
1 ATATTATTATAA-ATATAAAAAATATATT
*
5514789 ATA-TATTATTAAA-AT-AAAAATATAAT
1 ATATTATTA-TAAATATAAAAAATATATT
* * * *
5514815 ATCTTA-TATTATTATAATATAAT-TGATT
1 ATATTATTATAAATATAA-AAAATAT-ATT
*
5514843 ATTTTA-TAT-AATATTAAAAATATAATATT
1 ATATTATTATAAATA-TAAAAA-AT-ATATT
5514872 ATATTATTATAAATATTAAAAAATATATT
1 ATATTATTATAAATA-TAAAAAATATATT
5514901 TTAAATATTT
Statistics
Matches: 109, Mismatches: 12, Indels: 35
0.70 0.08 0.22
Matches are distributed among these distances:
25 8 0.07
26 20 0.18
27 11 0.10
28 24 0.22
29 24 0.22
30 11 0.10
31 11 0.10
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
ATATTATTATAAATATAAAAAATATATT
Found at i:5514908 original size:52 final size:51
Alignment explanation
Indices: 5514789--5514909 Score: 124
Period size: 54 Copynumber: 2.3 Consensus size: 51
5514779 AAAAATTATT
***
5514789 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATA-CTTATATTATTATAATATAAAAA
5514840 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAAAAA
1 ATATA-TTT-TA-AATATTAAAAATATAATACTTATATTATTAT-AATA-TAAAAA
5514894 ATATATTTTAAATATT
1 ATATATTTTAAATATT
5514910 TTAATAAATA
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 20 0.34
53 7 0.12
54 21 0.36
55 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATAATACTTATATTATTATAATATAAAAA
Found at i:5515150 original size:42 final size:41
Alignment explanation
Indices: 5515057--5515212 Score: 258
Period size: 41 Copynumber: 3.8 Consensus size: 41
5515047 ATGAATTACA
*
5515057 TTCCGAAAAACGAATTACGTGAAACAAATACGGAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGAAAACATT
*
5515098 TTCCGAAAAACGAATTACGTAAAACAAACACAGGAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACAC-GGAAAACATT
*
5515140 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGAAAACATT
* *
5515181 TTCCGAAAAACGAATTACATGAAATAAACACG
1 TTCCGAAAAACGAATTACGTGAAACAAACACG
5515213 AGATTTCGTG
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
41 68 0.64
42 39 0.36
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.18
Consensus pattern (41 bp):
TTCCGAAAAACGAATTACGTGAAACAAACACGGAAAACATT
Found at i:5515210 original size:83 final size:83
Alignment explanation
Indices: 5515057--5515211 Score: 265
Period size: 83 Copynumber: 1.9 Consensus size: 83
5515047 ATGAATTACA
* *
5515057 TTCCGAAAAACGAATTACGTGAAACAAATACGGAAAACATTTTCCGAAAAACGAATTACGTAAAA
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGAAAACATTTTCCGAAAAACGAATTACATAAAA
5515122 CAAACACAGGAAAACATT
66 CAAACACAGGAAAACATT
* *
5515140 TTCCGGAAAACGAATTACGTGAAACAAACACGGAAAACATTTTCCGAAAAACGAATTACATGAAA
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGAAAACATTTTCCGAAAAACGAATTACATAAAA
*
5515205 TAAACAC
66 CAAACAC
5515212 GAGATTTCGT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 67 1.00
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.18
Consensus pattern (83 bp):
TTCCGAAAAACGAATTACGTGAAACAAACACGGAAAACATTTTCCGAAAAACGAATTACATAAAA
CAAACACAGGAAAACATT
Found at i:5515572 original size:31 final size:31
Alignment explanation
Indices: 5515534--5515597 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
5515524 TAGGTTGTTC
5515534 AATGTTTCATGCTCATACAGTCACATGATCT
1 AATGTTTCATGCTCATACAGTCACATGATCT
5515565 AATGTTTCATGCTCATACAGTCACATGATCT
1 AATGTTTCATGCTCATACAGTCACATGATCT
5515596 AA
1 AA
5515598 GGTAATAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (31 bp):
AATGTTTCATGCTCATACAGTCACATGATCT
Found at i:5518640 original size:21 final size:20
Alignment explanation
Indices: 5518589--5518641 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
5518579 GGAATTTAAA
5518589 TTCTGAAAAATGAATTACAT
1 TTCTGAAAAATGAATTACAT
*
5518609 TTCTGGTAAAATGAATTACATTT
1 TTCT-GAAAAATGAATTACA--T
5518632 TTCTGAAAAA
1 TTCTGAAAAA
5518642 CATCTGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 4 0.14
21 14 0.50
22 5 0.18
23 5 0.18
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (20 bp):
TTCTGAAAAATGAATTACAT
Found at i:5518832 original size:48 final size:50
Alignment explanation
Indices: 5518736--5518833 Score: 114
Period size: 48 Copynumber: 2.0 Consensus size: 50
5518726 TACAAATATT
*
5518736 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * *
5518786 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TT-ATTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
5518834 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 21 0.50
49 13 0.31
50 8 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:5518971 original size:23 final size:23
Alignment explanation
Indices: 5518922--5518984 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
5518912 GTGTTATATT
* **
5518922 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
5518945 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
5518968 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
5518985 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:5519033 original size:27 final size:26
Alignment explanation
Indices: 5518968--5519054 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 26
5518958 CTTTATTAAA
5518968 ATATTATTTAAATATATAAATAATATTAT
1 ATATTA-TTAAATATA-AAA-AATATTAT
*
5518997 -TCATTGTTAAATATAAAAAATTATTAT
1 AT-ATTATTAAATATAAAAAA-TATTAT
*
5519024 ATATTATTAAA-AT-AAAAATATAAT
1 ATATTATTAAATATAAAAAATATTAT
*
5519048 ATCTTAT
1 ATATTAT
5519055 ATTATTATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
24 11 0.22
25 5 0.10
26 4 0.08
27 17 0.33
28 11 0.22
29 3 0.06
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (26 bp):
ATATTATTAAATATAAAAAATATTAT
Found at i:5519038 original size:26 final size:27
Alignment explanation
Indices: 5518968--5519041 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 27
5518958 CTTTATTAAA
5518968 ATATTATTTAAATATATAAATAA-TATTAT
1 ATATTA-TTAAATATA-AAA-AATTATTAT
*
5518997 -TCATTGTTAAATATAAAAAATTATTAT
1 AT-ATTATTAAATATAAAAAATTATTAT
5519024 ATATTATTAAA-ATAAAAA
1 ATATTATTAAATATAAAAA
5519042 TATAATATCT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
26 9 0.22
27 17 0.43
28 11 0.28
29 3 0.08
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (27 bp):
ATATTATTAAATATAAAAAATTATTAT
Found at i:5519095 original size:29 final size:29
Alignment explanation
Indices: 5519053--5519129 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
5519043 ATAATATCTT
* *
5519053 ATATTATTATAATAATTGATTATT-TTATATA
1 ATATTAATA-AATAAAT-ATTATTATTATA-A
5519084 ATATTAA-AAATATAATATTATTATTATAA
1 ATATTAATAAATA-AATATTATTATTATAA
5519113 ATATTAATAAATAAATA
1 ATATTAATAAATAAATA
5519130 AATAATATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 22 0.54
30 13 0.32
31 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (29 bp):
ATATTAATAAATAAATATTATTATTATAA
Found at i:5519102 original size:26 final size:26
Alignment explanation
Indices: 5519006--5519129 Score: 80
Period size: 26 Copynumber: 4.7 Consensus size: 26
5518996 TTCATTGTTA
* * *
5519006 AATATAAAAAATTATTATATATTAT-T
1 AATATTAAAAA-TATAATATTTTATAT
* *
5519032 AA-AATAAAAATATAATATCTTATAT
1 AATATTAAAAATATAATATTTTATAT
*
5519057 --TATTATAATAAT-TGATTATTTTATAT
1 AATATTA-AA-AATAT-AATATTTTATAT
5519083 AATATTAAAAATATAATATTATTATTAT
1 AATATTAAAAATATAATATT-TTA-TAT
5519111 AAATATTAATAAATA-AATA
1 -AATATTAA-AAATATAATA
5519130 AATAATATTT
Statistics
Matches: 78, Mismatches: 8, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
24 14 0.18
25 10 0.13
26 23 0.29
27 6 0.08
28 8 0.10
29 12 0.15
30 5 0.06
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (26 bp):
AATATTAAAAATATAATATTTTATAT
Found at i:5519126 original size:14 final size:14
Alignment explanation
Indices: 5519083--5519129 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
5519073 TATTTTATAT
5519083 AATATTAA-AAATA
1 AATATTAATAAATA
* *
5519096 TAATATTATTATTATA
1 -AATATTAATA-AATA
5519112 AATATTAATAAATA
1 AATATTAATAAATA
5519126 AATA
1 AATA
5519130 AATAATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 14 0.52
15 10 0.37
16 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATTAATAAATA
Found at i:5520093 original size:26 final size:26
Alignment explanation
Indices: 5520054--5520112 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
5520044 TTTTATAATA
** *
5520054 ATAAATTTTTTATAATTTT-AAAAATT
1 ATAAATTTCATAT-ATTTTGAAAAAAT
5520080 ATAAATTTCATATATTTTGAAAAAAT
1 ATAAATTTCATATATTTTGAAAAAAT
5520106 ATTAAAT
1 A-TAAAT
5520113 AATAATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 5 0.18
26 18 0.64
27 5 0.18
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
ATAAATTTCATATATTTTGAAAAAAT
Found at i:5520814 original size:333 final size:336
Alignment explanation
Indices: 5520110--5520914 Score: 1240
Period size: 333 Copynumber: 2.4 Consensus size: 336
5520100 AAAAATATTA
* * * * *
5520110 AATAATAATTAATTTGATCCCTCAATTTTAATTAAAAATTTATTTTAATATTTTTTATATTTTTA
1 AATAATAATTCATTTAAT-TCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTA
* *
5520175 AATAATTAATTTTAAAAGGCAATAATTTTTT-AAAAATATATGAAATTTATAATTTTT-AAATTA
65 AACAATTAATTTTAAAAGGAAATAATTTTTTCAAAAATATATGAAATTTATAATTTTTAAAATTA
*
5520238 TAAAATATTTATCATCATCATCATCATTTTGTAAAAGAAATATTAGTTATAAAACTTTTATAAAA
130 TAAAATATTTATCATCATCATCATCATTTTGTAAAAGAAATATTAGTAATAAAACTTTTATAAAA
* * *
5520303 TTATTCATATTTTAAAATATTTACCCTCAAAATTTTTATATACTATATTATATATATTGTGTAAT
195 TTATTCATATTTTAAAATACTTACCCTCAAAAGTTTTATATACTATATGATATATATTGTGTAAT
** *
5520368 TTTAATGCAAAAATTTAAATAATTTTATTAAAAATGAATAAATATTATTAACTGTTGTTAAAAAT
260 TTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAATATAATTAACTGTTGTTAAAAAT
*
5520433 TTAAAATTAATG
325 TAAAAATTAATG
*
5520445 AATAATAATTCATTTGATTCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAA
1 AATAATAATTCATTTAATTCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAA
*
5520510 ACAATTAATTTTAAAAGGTAATAATTTTTTCAAAAATATATGAAATTTATAATTTTTAAAATTAT
66 ACAATTAATTTTAAAAGGAAATAATTTTTTCAAAAATATATGAAATTTATAATTTTTAAAATTAT
* * **
5520575 AAAATATTTGTCATCATCGTCATCATTTTGTAAAAGAAAT-TCTAGTAATAAATTTTTTATAAAA
131 AAAATATTTATCATCATCATCATCATTTTGTAAAAGAAATAT-TAGTAATAAAACTTTTATAAAA
*
5520639 TTATTCATATTTTAAAATACTTACCCT-TAAAGTTTTACTATA-T-TA-GAT-TATACTTGTGTA
195 TTATTCATATTTTAAAATACTTACCCTCAAAAGTTTTA-TATACTATATGATATATA-TTGTGTA
5520699 ATTTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAATATAATTAACTGTTGTTAAAA
258 ATTTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAATATAATTAACTGTTGTTAAAA
5520764 A-TAAAAATTAATG
323 ATTAAAAATTAATG
* **
5520777 AATAATAATTCATTTAATTCCTTAATTGTGCTTAAAAGTTTATTTTAATATTTTTTATATTTTTA
1 AATAATAATTCATTTAATT-CTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTA
*
5520842 AACAATTAATTTTAAAAGAAAATAATTTTTTC-AAAATATAT-AAATTT-TAATTTTTAAAATTA
65 AACAATTAATTTTAAAAGGAAATAATTTTTTCAAAAATATATGAAATTTATAATTTTTAAAATTA
5520904 TAAAA-ATTTAT
130 TAAAATATTTAT
5520915 TATTATAAAA
Statistics
Matches: 438, Mismatches: 26, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
329 5 0.01
330 20 0.05
331 6 0.01
332 42 0.10
333 144 0.33
334 74 0.17
335 53 0.12
336 94 0.21
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.46
Consensus pattern (336 bp):
AATAATAATTCATTTAATTCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAA
ACAATTAATTTTAAAAGGAAATAATTTTTTCAAAAATATATGAAATTTATAATTTTTAAAATTAT
AAAATATTTATCATCATCATCATCATTTTGTAAAAGAAATATTAGTAATAAAACTTTTATAAAAT
TATTCATATTTTAAAATACTTACCCTCAAAAGTTTTATATACTATATGATATATATTGTGTAATT
TTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAATATAATTAACTGTTGTTAAAAATT
AAAAATTAATG
Found at i:5520913 original size:23 final size:24
Alignment explanation
Indices: 5520868--5520913 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
5520858 AGAAAATAAT
*
5520868 TTTTTCAAAATATATAAATTTTAA
1 TTTTTCAAAATATATAAAATTTAA
5520892 TTTTT-AAAAT-TATAAAAATTTA
1 TTTTTCAAAATATAT-AAAATTTA
5520914 TTATTATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 12 0.60
24 5 0.25
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTTTCAAAATATATAAAATTTAA
Found at i:5532395 original size:39 final size:38
Alignment explanation
Indices: 5532352--5532430 Score: 131
Period size: 39 Copynumber: 2.1 Consensus size: 38
5532342 GTTTTGAAAT
* *
5532352 AAATATATATATAATATATAGTTTTTGAAAACTTTTTGA
1 AAATATATATATAATAAATAG-TTTTGAAAACATTTTGA
5532391 AAATATATATATAATAAATAGTTTTGAAAACATTTTGA
1 AAATATATATATAATAAATAGTTTTGAAAACATTTTGA
5532429 AA
1 AA
5532431 TAATAGGGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 18 0.47
39 20 0.53
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.42
Consensus pattern (38 bp):
AAATATATATATAATAAATAGTTTTGAAAACATTTTGA
Found at i:5532600 original size:83 final size:84
Alignment explanation
Indices: 5532454--5532702 Score: 281
Period size: 83 Copynumber: 3.0 Consensus size: 84
5532444 TCACAGCCTA
* * * * * * *
5532454 TTACAGTATAGCTCAAGGCGAGAAGGGCTATCTATCAACCAAAACCTTCGAGTTCGATTACATTC
1 TTACAGCATAACTTAAGTCGAGAAGGGCTATCTGTCAA-CAAAAACTTCGAGTTCAATTACATTC
5532519 AGCTCAATGACATATCAAAT
65 AGCTCAATGACATATCAAAT
* * *
5532539 TTATAGCATAAC-TAATGT-GAGAAGGGTTATCTGTCAATAAAAACTTCGAGTTCAATTACATTC
1 TTACAGCATAACTTAA-GTCGAGAAGGGCTATCTGTCAACAAAAACTTCGAGTTCAATTACATTC
* *
5532602 AGCTCAAGGGCATATCAAAT
65 AGCTCAATGACATATCAAAT
* ** * *
5532622 TTACAGCATAGCTTAAGTCGAGAA-AACTATATGTCAACAAAAACTATCGA-TTCAATTCCATTC
1 TTACAGCATAACTTAAGTCGAGAAGGGCTATCTGTCAACAAAAACT-TCGAGTTCAATTACATTC
*
5532685 AGCTCGATGACATATCAA
65 AGCTCAATGACATATCAA
5532703 CCGCATGGTA
Statistics
Matches: 137, Mismatches: 23, Indels: 10
0.81 0.14 0.06
Matches are distributed among these distances:
83 96 0.70
84 31 0.23
85 10 0.07
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (84 bp):
TTACAGCATAACTTAAGTCGAGAAGGGCTATCTGTCAACAAAAACTTCGAGTTCAATTACATTCA
GCTCAATGACATATCAAAT
Found at i:5539908 original size:32 final size:31
Alignment explanation
Indices: 5539871--5539946 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 31
5539861 AAAAACATAG
*
5539871 GTTTTGATCACTTACATTATTGTTT-TATTTAA
1 GTTTTGGTCACTTACATTATT-TTTATA-TTAA
* *
5539903 GTTTTGGTCATTTACGTTATTTTTATATTAA
1 GTTTTGGTCACTTACATTATTTTTATATTAA
5539934 GTTTTGGTCACTT
1 GTTTTGGTCACTT
5539947 GGACATTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
31 19 0.49
32 20 0.51
ACGTcount: A:0.21, C:0.09, G:0.13, T:0.57
Consensus pattern (31 bp):
GTTTTGGTCACTTACATTATTTTTATATTAA
Found at i:5549681 original size:30 final size:30
Alignment explanation
Indices: 5549640--5549700 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
5549630 TAAAGGGTCA
* * *
5549640 AATTGATATTTTATCTAAAGTTTAGAGATC
1 AATTAATATTTTATCTAAAATTTAAAGATC
*
5549670 AATTAATATTTTATTTAAAATTTAAAGATC
1 AATTAATATTTTATCTAAAATTTAAAGATC
5549700 A
1 A
5549701 TTAGAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (30 bp):
AATTAATATTTTATCTAAAATTTAAAGATC
Found at i:5568313 original size:34 final size:34
Alignment explanation
Indices: 5568275--5568354 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 34
5568265 TGATTAATTA
* *
5568275 AAATAATTAATACATTAATTTTACAGATGTATAT
1 AAATAATTAATACATTAATTTTACAGATATATAG
* * * * *
5568309 AAATAATTCATTCATTCATTTTATAGATATGTAG
1 AAATAATTAATACATTAATTTTACAGATATATAG
*
5568343 AAATGATTAATA
1 AAATAATTAATA
5568355 TTTCAAATTA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.41
Consensus pattern (34 bp):
AAATAATTAATACATTAATTTTACAGATATATAG
Found at i:5569227 original size:55 final size:55
Alignment explanation
Indices: 5569168--5569299 Score: 228
Period size: 55 Copynumber: 2.4 Consensus size: 55
5569158 AGGCACTGAA
* *
5569168 TGATTATCAATGTTAAAGGTTTTCAGGGCATAAGCCCAATTTTGCATCTTATGTC
1 TGATTATCTATGTTAAAGGTTTTCAAGGCATAAGCCCAATTTTGCATCTTATGTC
5569223 TGATTATCTATGTTAAAGGTTTTCAAGGCATAAGCCCAATTTTGCATCTTATGTC
1 TGATTATCTATGTTAAAGGTTTTCAAGGCATAAGCCCAATTTTGCATCTTATGTC
**
5569278 CAATTATCTATGTTAAAGGTTT
1 TGATTATCTATGTTAAAGGTTT
5569300 CGACACCGAG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 73 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (55 bp):
TGATTATCTATGTTAAAGGTTTTCAAGGCATAAGCCCAATTTTGCATCTTATGTC
Found at i:5572168 original size:46 final size:46
Alignment explanation
Indices: 5572101--5572190 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
5572091 CATAAAGTTA
*
5572101 AGAAAAACACCACAGCGCTACCAAACCAAATTCCTCTTGGATCTGC
1 AGAAAAACACCACAGCACTACCAAACCAAATTCCTCTTGGATCTGC
5572147 AGAAAAACACCACAGCACTACCAAACCAAATTCCTCTTGGATCT
1 AGAAAAACACCACAGCACTACCAAACCAAATTCCTCTTGGATCT
5572191 AAATATTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.39, C:0.32, G:0.11, T:0.18
Consensus pattern (46 bp):
AGAAAAACACCACAGCACTACCAAACCAAATTCCTCTTGGATCTGC
Found at i:5580946 original size:27 final size:27
Alignment explanation
Indices: 5580916--5580978 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
5580906 AATTATCGAG
5580916 AGGACCCGACATGAACCCTCTCTC-AA
1 AGGACCCGACATGAACCCTCTCTCTAA
* *
5580942 TAGGACCCGACATGAATCCTCTTTCTAA
1 -AGGACCCGACATGAACCCTCTCTCTAA
5580970 AGGACCCGA
1 AGGACCCGA
5580979 ACCGGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 31 0.94
28 2 0.06
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.19
Consensus pattern (27 bp):
AGGACCCGACATGAACCCTCTCTCTAA
Found at i:5592050 original size:16 final size:16
Alignment explanation
Indices: 5592029--5592060 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5592019 ATAATGATTT
5592029 AATGTTGAATGATTCA
1 AATGTTGAATGATTCA
5592045 AATGTTGAATGATTCA
1 AATGTTGAATGATTCA
5592061 GAGGCTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (16 bp):
AATGTTGAATGATTCA
Found at i:5598964 original size:27 final size:23
Alignment explanation
Indices: 5598905--5598967 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
5598895 CTGAATAATT
5598905 CAGTGCTGATTGATTCAGCAAAA
1 CAGTGCTGATTGATTCAGCAAAA
5598928 CAGTGCTGATTGATTCAGCAAAA
1 CAGTGCTGATTGATTCAGCAAAA
*
5598951 CAGTGCTGAATGATTCA
1 CAGTGCTGATTGATTCA
5598968 ACACAGAAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.27
Consensus pattern (23 bp):
CAGTGCTGATTGATTCAGCAAAA
Found at i:5602048 original size:23 final size:23
Alignment explanation
Indices: 5601950--5602040 Score: 112
Period size: 23 Copynumber: 4.0 Consensus size: 23
5601940 ATTTTACATG
*
5601950 TGTTGCACGTTTATGTCTGTCTA
1 TGTTGCACGTTTATCTCTGTCTA
* *
5601973 TGTTGCACGTTTATGTCTGTATA
1 TGTTGCACGTTTATCTCTGTCTA
* * *
5601996 TGTTGCACGCTTATCTTTGTCTT
1 TGTTGCACGTTTATCTCTGTCTA
5602019 TG-TGACACGTTTATCTCTGTCT
1 TGTTG-CACGTTTATCTCTGTCT
5602041 TTATGACATA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
22 2 0.03
23 57 0.97
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.48
Consensus pattern (23 bp):
TGTTGCACGTTTATCTCTGTCTA
Found at i:5607893 original size:61 final size:60
Alignment explanation
Indices: 5607786--5607946 Score: 146
Period size: 61 Copynumber: 2.7 Consensus size: 60
5607776 ACTATAACAA
* * * ** * **
5607786 TCATTTTAAATCAGTCCTTCAACTTTAAAATATTCCAATTTGATCCCCAAACTATTGA-CTC
1 TCATTCTAAATTAGTCCTTAAACTTTTGAACATTCCAATTCCATCCCCAAACTA-TGATC-C
* *
5607847 TCATTCTAAATTAGTCCTTAAACTTTTGAACATTCTAATTCCATCCCTAAACTATGATCC
1 TCATTCTAAATTAGTCCTTAAACTTTTGAACATTCCAATTCCATCCCCAAACTATGATCC
* * * * *
5607907 TCTTTCTAAATTGGTGCC-CAAACTTTTGAATAATCCAATT
1 TCATTCTAAATTAGT-CCTTAAACTTTTGAACATTCCAATT
5607947 TTATCCTCAA
Statistics
Matches: 82, Mismatches: 16, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
60 35 0.43
61 47 0.57
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.39
Consensus pattern (60 bp):
TCATTCTAAATTAGTCCTTAAACTTTTGAACATTCCAATTCCATCCCCAAACTATGATCC
Found at i:5609448 original size:18 final size:16
Alignment explanation
Indices: 5609410--5609471 Score: 67
Period size: 16 Copynumber: 4.1 Consensus size: 16
5609400 TAATATGATA
*
5609410 TTTATTTTTAAAATAT
1 TTTATATTTAAAATAT
5609426 TTTATATTTAAAATA-
1 TTTATATTTAAAATAT
* *
5609441 TTTAT-TATAATA-AT
1 TTTATATTTAAAATAT
*
5609455 TTTATGTTTAAAATAT
1 TTTATATTTAAAATAT
5609471 T
1 T
5609472 AATGTGATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 1 0.03
14 10 0.26
15 10 0.26
16 17 0.45
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TTTATATTTAAAATAT
Found at i:5609464 original size:29 final size:27
Alignment explanation
Indices: 5609412--5609471 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 27
5609402 ATATGATATT
5609412 TATTTTTAAAATATTTTATATTTAAAA
1 TATTTTTAAAATATTTTATATTTAAAA
* *
5609439 TATTTATTATAATAATTTTATGTTTAAAA
1 TATTT-TTAAAAT-ATTTTATATTTAAAA
5609468 TATT
1 TATT
5609472 AATGTGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 5 0.17
28 6 0.21
29 18 0.62
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
TATTTTTAAAATATTTTATATTTAAAA
Found at i:5611612 original size:78 final size:78
Alignment explanation
Indices: 5611510--5611857 Score: 583
Period size: 78 Copynumber: 4.5 Consensus size: 78
5611500 AAGGTACAAG
* * *
5611510 AAATGTTTCCA-AATGACAAAAAGAAGACAATGCTGAGGGTCAAGGGAAAAGAAACGAGGTAAAA
1 AAATGTTT-CAGAACGACAAAAAGAAGACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAA
5611574 CAAAAGGAGACTG-
65 CAAAAGGAGACTGC
*
5611587 AAACTGTTTCAGAACGACAAAAAGAAGACAATGATGAGGATCAAGGGAAAAGAAACGAGGCAAAA
1 AAA-TGTTTCAGAACGACAAAAAGAAGACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAA
5611652 CAAAAGGAGACTGC
65 CAAAAGGAGACTGC
5611666 AAATGTTTCAGAACGACAAAAAGAAGACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAAC
1 AAATGTTTCAGAACGACAAAAAGAAGACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAAC
5611731 AAAAGGAGACTGC
66 AAAAGGAGACTGC
*
5611744 AAATGTTTCAGAACGACAAAAAGAAGACAATGCTGAGGATCAAGGGAAAAGAAGCGAGGCAAAAC
1 AAATGTTTCAGAACGACAAAAAGAAGACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAAC
* *
5611809 AAAAGGAGACAGT
66 AAAAGGAGACTGC
* *
5611822 AAATGTTTCGGAACGACAAAAGGAAGACAATGCTGA
1 AAATGTTTCAGAACGACAAAAAGAAGACAATGCTGA
5611858 AGTACAACCT
Statistics
Matches: 258, Mismatches: 10, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
77 5 0.02
78 250 0.97
79 3 0.01
ACGTcount: A:0.49, C:0.13, G:0.26, T:0.11
Consensus pattern (78 bp):
AAATGTTTCAGAACGACAAAAAGAAGACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAAC
AAAAGGAGACTGC
Found at i:5613443 original size:18 final size:18
Alignment explanation
Indices: 5613409--5613443 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5613399 ATTGACAAAA
*
5613409 ATAATTTAATTAAAATTT
1 ATAATTTAATGAAAATTT
*
5613427 ATAATTTAATGATAATT
1 ATAATTTAATGAAAATT
5613444 ATTATTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
ATAATTTAATGAAAATTT
Found at i:5620153 original size:29 final size:29
Alignment explanation
Indices: 5620121--5620213 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 29
5620111 TATTGGTTTA
5620121 TAAATTTTAAAATATTTTATATTAATTCT
1 TAAATTTTAAAATATTTTATATTAATTCT
* * ** * *
5620150 TAAATTATGATCTCATTTTAAATTGATTCT
1 TAAATTTTAAAAT-ATTTTATATTAATTCT
* *
5620180 TAAATTTTAGAATATTTTATATTAATCCT
1 TAAATTTTAAAATATTTTATATTAATTCT
5620209 TAAAT
1 TAAAT
5620214 CAGTATCATT
Statistics
Matches: 49, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 27 0.55
30 22 0.45
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (29 bp):
TAAATTTTAAAATATTTTATATTAATTCT
Found at i:5626446 original size:28 final size:28
Alignment explanation
Indices: 5626392--5626449 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
5626382 CTTTTTCATT
* **
5626392 TAAGTTTTTAAAGTATATTTTGTCAAAA
1 TAAGTATTTAAAGTATATTTTAACAAAA
5626420 TAAGTATTTAAAGTAT-TTTATAACAAAA
1 TAAGTATTTAAAGTATATTT-TAACAAAA
5626448 TA
1 TA
5626450 GGTACCTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (28 bp):
TAAGTATTTAAAGTATATTTTAACAAAA
Found at i:5626478 original size:31 final size:29
Alignment explanation
Indices: 5626443--5626513 Score: 97
Period size: 31 Copynumber: 2.4 Consensus size: 29
5626433 TATTTTATAA
5626443 CAAAATAGGTACCTAAAATTAATTTTTTGAT
1 CAAAATAGGTACCTAAAATT-A-TTTTTGAT
** *
5626474 CAAAATAAATACCTAAAATTATTTTTGGT
1 CAAAATAGGTACCTAAAATTATTTTTGAT
5626503 CAAAATAGGTA
1 CAAAATAGGTA
5626514 TCTTAGTAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 16 0.46
30 1 0.03
31 18 0.51
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (29 bp):
CAAAATAGGTACCTAAAATTATTTTTGAT
Found at i:5627568 original size:28 final size:28
Alignment explanation
Indices: 5627537--5627592 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
5627527 TAGATAGAAT
*
5627537 GAACATATAAAGTTTTAAAAAGAA-AAAA
1 GAACATATAAA-ATTTAAAAAGAATAAAA
* *
5627565 GAACTTTTAAAATTTAAAAAGAATAAAA
1 GAACATATAAAATTTAAAAAGAATAAAA
5627593 ACAAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.62, C:0.04, G:0.09, T:0.25
Consensus pattern (28 bp):
GAACATATAAAATTTAAAAAGAATAAAA
Found at i:5628088 original size:15 final size:15
Alignment explanation
Indices: 5628068--5628097 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5628058 AGTGTTTGCC
5628068 AAAAGGTCTCCATTT
1 AAAAGGTCTCCATTT
5628083 AAAAGGTCTCCATTT
1 AAAAGGTCTCCATTT
5628098 CAGGCAATTC
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:0.13, T:0.33
Consensus pattern (15 bp):
AAAAGGTCTCCATTT
Found at i:5633802 original size:19 final size:19
Alignment explanation
Indices: 5633778--5633814 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5633768 GAGGCCCATC
5633778 TTTCAAAGAAAATAAAGAA
1 TTTCAAAGAAAATAAAGAA
*
5633797 TTTCAATGAAAATAAAGA
1 TTTCAAAGAAAATAAAGA
5633815 CTTATTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.05, G:0.11, T:0.24
Consensus pattern (19 bp):
TTTCAAAGAAAATAAAGAA
Found at i:5639825 original size:22 final size:21
Alignment explanation
Indices: 5639785--5639825 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
5639775 CTAAAGAAGT
5639785 AAAATGTTGAAAAACATAACC
1 AAAATGTTGAAAAACATAACC
5639806 AAAATGCTTGAACAAA-ATAA
1 AAAATG-TTGAA-AAACATAA
5639826 AGATATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 9 0.50
23 3 0.17
ACGTcount: A:0.59, C:0.12, G:0.10, T:0.20
Consensus pattern (21 bp):
AAAATGTTGAAAAACATAACC
Found at i:5642067 original size:13 final size:14
Alignment explanation
Indices: 5642024--5642068 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
5642014 TAATAGTTTT
5642024 AAATATAATTTTAA
1 AAATATAATTTTAA
*
5642038 AAATATAATTTCAA
1 AAATATAATTTTAA
*
5642052 AAATA-AATTTTGA
1 AAATATAATTTTAA
5642065 AAAT
1 AAAT
5642069 CCATATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (14 bp):
AAATATAATTTTAA
Found at i:5642397 original size:2 final size:2
Alignment explanation
Indices: 5642382--5642417 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5642372 GACTCATCCT
5642382 TA TA -A TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5642418 GTTGAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5643653 original size:17 final size:14
Alignment explanation
Indices: 5643633--5643676 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
5643623 TTATATTTTT
5643633 TATTTTTTTAAATAAAA
1 TATTTTTTTAAAT---A
*
5643650 TATTTTCTTAAATA
1 TATTTTTTTAAATA
5643664 TATTTTTTTAAAT
1 TATTTTTTTAAAT
5643677 CTGAACATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 13 0.52
17 12 0.48
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTTTTTAAATA
Found at i:5647697 original size:2 final size:2
Alignment explanation
Indices: 5647690--5647720 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5647680 CTCGCCTATG
5647690 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5647721 TGTAATTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5648574 original size:15 final size:15
Alignment explanation
Indices: 5648554--5648610 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
5648544 AATCGGGTAT
5648554 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
**
5648569 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
5648586 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
5648601 CGGGTACCCG
1 CGGGTACCCG
5648611 TAACATCCGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 21 0.58
16 4 0.11
17 11 0.31
ACGTcount: A:0.21, C:0.35, G:0.28, T:0.16
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:5648590 original size:17 final size:16
Alignment explanation
Indices: 5648554--5648622 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 16
5648544 AATCGGGTAT
**
5648554 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
5648569 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AAAATC
**
5648586 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
*
5648601 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
5648618 CGGGT
1 CGGGT
5648623 CGAGACACGG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
15 21 0.48
16 6 0.14
17 17 0.39
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:5648595 original size:32 final size:32
Alignment explanation
Indices: 5648554--5648622 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
5648544 AATCGGGTAT
5648554 CGGGTACCCGATTACCGGGTACCCGCAAAATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
* *
5648586 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
5648618 CGGGT
1 CGGGT
5648623 CGAGACACGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGCAAAATC
Found at i:5650441 original size:21 final size:22
Alignment explanation
Indices: 5650417--5650465 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 22
5650407 AATTGGGCAT
5650417 GCTTTTAAACGGCGTCGTTC-A
1 GCTTTTAAACGGCGTCGTTCTA
5650438 GCTTTTAAACGGCGTCGTTCTA
1 GCTTTTAAACGGCGTCGTTCTA
5650460 GCTTTT
1 GCTTTT
5650466 TTTTTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.39
Consensus pattern (22 bp):
GCTTTTAAACGGCGTCGTTCTA
Found at i:5651430 original size:22 final size:23
Alignment explanation
Indices: 5651405--5651453 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
5651395 CTAAAATGTA
*
5651405 TCATTATAACAGAAAAA-AAGTG
1 TCATTAAAACAGAAAAATAAGTG
* *
5651427 TCATTAAAATAGAAAAATACGTG
1 TCATTAAAACAGAAAAATAAGTG
5651450 TCAT
1 TCAT
5651454 AAATATACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (23 bp):
TCATTAAAACAGAAAAATAAGTG
Found at i:5662132 original size:2 final size:2
Alignment explanation
Indices: 5662125--5662149 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5662115 TATATCATTA
5662125 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5662150 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5662394 original size:21 final size:21
Alignment explanation
Indices: 5662370--5662493 Score: 67
Period size: 21 Copynumber: 6.0 Consensus size: 21
5662360 GCAAATTCGC
*
5662370 GTTACATTTCGCGGTGCGATA
1 GTTACATTTCGCGTTGCGATA
* ** *
5662391 GTTAAAAATAGCGTTGCGAT-
1 GTTACATTTCGCGTTGCGATA
* *
5662411 TTTCCATTTCGCGTTGCGATA
1 GTTACATTTCGCGTTGCGATA
** *
5662432 GTTGA-AAATAGCGTTGCGAT-
1 GTT-ACATTTCGCGTTGCGATA
* * *
5662452 TTTTCATTTCGCGTTGCGAGA
1 GTTACATTTCGCGTTGCGATA
*
5662473 GTCTACAGTT-GTCGTTGCGAT
1 GT-TACATTTCG-CGTTGCGAT
5662494 TTTCCAAATT
Statistics
Matches: 71, Mismatches: 26, Indels: 11
0.66 0.24 0.10
Matches are distributed among these distances:
20 27 0.38
21 31 0.44
22 13 0.18
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (21 bp):
GTTACATTTCGCGTTGCGATA
Found at i:5662420 original size:41 final size:41
Alignment explanation
Indices: 5662374--5662470 Score: 167
Period size: 41 Copynumber: 2.4 Consensus size: 41
5662364 ATTCGCGTTA
*
5662374 CATTTCGCGGTGCGATAGTTAAAAATAGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTAAAAATAGCGTTGCGATTTTC
* *
5662415 CATTTCGCGTTGCGATAGTTGAAAATAGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTAAAAATAGCGTTGCGATTTTC
5662456 CATTTCGCGTTGCGA
1 CATTTCGCGTTGCGA
5662471 GAGTCTACAG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTAAAAATAGCGTTGCGATTTTC
Found at i:5662426 original size:20 final size:20
Alignment explanation
Indices: 5662401--5662470 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
5662391 GTTAAAAATA
5662401 GCGTTGCGATTTTCCATTTC
1 GCGTTGCGATTTTCCATTTC
* ** ** *
5662421 GCGTTGCGATAGTTGAAAATA
1 GCGTTGCGAT-TTTCCATTTC
*
5662442 GCGTTGCGATTTTTCATTTC
1 GCGTTGCGATTTTCCATTTC
5662462 GCGTTGCGA
1 GCGTTGCGA
5662471 GAGTCTACAG
Statistics
Matches: 37, Mismatches: 12, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
20 23 0.62
21 14 0.38
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.39
Consensus pattern (20 bp):
GCGTTGCGATTTTCCATTTC
Found at i:5662843 original size:21 final size:21
Alignment explanation
Indices: 5662816--5662867 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
5662806 AATGGAAAAG
5662816 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
*
5662837 TGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
5662858 CGCAACGCGA
1 CGCAACGCGA
5662868 AATGCAACGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (21 bp):
CGCAACGCGATTTTCAACTAT
Found at i:5662875 original size:21 final size:21
Alignment explanation
Indices: 5662791--5662875 Score: 73
Period size: 21 Copynumber: 4.1 Consensus size: 21
5662781 ACAACTGTAG
*
5662791 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
5662812 A-AAGCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
* ** *
5662832 ACTATTGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
5662853 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
5662874 AC
1 AC
5662876 GCGAATTTGT
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 14 0.28
21 36 0.72
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:5663283 original size:17 final size:18
Alignment explanation
Indices: 5663251--5663284 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5663241 AAATATTTTT
5663251 TATATTTAATTTATTAAA
1 TATATTTAATTTATTAAA
5663269 TATATTTAA-TTATTAA
1 TATATTTAATTTATTAA
5663285 CTTAATCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATTTAATTTATTAAA
Found at i:5665669 original size:27 final size:27
Alignment explanation
Indices: 5665639--5665700 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
5665629 ACAATTTATT
5665639 AGATCCTATCATCAAATATAACAAGTC
1 AGATCCTATCATCAAATATAACAAGTC
5665666 AGATCCTATCATCAAATATAACAAGTC
1 AGATCCTATCATCAAATATAACAAGTC
5665693 AGATCCTA
1 AGATCCTA
5665701 CCAAATTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.26
Consensus pattern (27 bp):
AGATCCTATCATCAAATATAACAAGTC
Found at i:5665711 original size:24 final size:26
Alignment explanation
Indices: 5665639--5665712 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 26
5665629 ACAATTTATT
5665639 AGATCCTATCATCAAATATAACAAGTC
1 AGATCCTATCA-CAAATATAACAAGTC
5665666 AGATCCTATCATCAAATATAACAAGTC
1 AGATCCTATCA-CAAATATAACAAGTC
*
5665693 AGATCCTA-C-CAAATTTAACA
1 AGATCCTATCACAAATATAACA
5665713 TTCCAAACAG
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
24 10 0.22
26 1 0.02
27 35 0.76
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.26
Consensus pattern (26 bp):
AGATCCTATCACAAATATAACAAGTC
Found at i:5682213 original size:190 final size:190
Alignment explanation
Indices: 5681741--5682499 Score: 1493
Period size: 190 Copynumber: 4.0 Consensus size: 190
5681731 ACATGTATTA
5681741 ATGGAAGCCGAGTCGTGGCTTCGATTAACAATGTCACGTTTTTTATGCCGGAAACGGATCTACTT
1 ATGGAAGCCGAGTCGTGGCTTCGATTAACAATGTCACGTTTTTTATGCCGGAAACGGATCTACTT
5681806 CAAGCCCATTTCTTAAACTTCAATGGGGTTTTCAGCAGTGATTTCCCTGGAAATCTTCCTGCTCC
66 CAAGCCCATTTCTTAAACTTCAATGGGGTTTTCAGCAGTGATTTCCCTGGAAATCTTCCTGCTCC
5681871 ATGTAGCTACACAAATAAC-AACTTGGCGACCAAACGAGGGAAGAAACTGTACAGATTGG
131 ATGTAGCTACACAAATAACAAACTTGGCGACCAAACGAGGGAAGAAACTGTACAGATTGG
5681930 ATGGAAGCCGAGTCGTGGCTTCGATTAACAATGTCACGTTTTTTATGCCGGAAACGGATCTACTT
1 ATGGAAGCCGAGTCGTGGCTTCGATTAACAATGTCACGTTTTTTATGCCGGAAACGGATCTACTT
5681995 CAAGCCCATTTCTTAAACTTCAATGGGGTTTTCAGCAGTGATTTCCCTGGAAATCTTCCTGCTCC
66 CAAGCCCATTTCTTAAACTTCAATGGGGTTTTCAGCAGTGATTTCCCTGGAAATCTTCCTGCTCC
5682060 ATGTAGCTACACAAATAACAAACTTGGCGACCAAACGAGGGAAGAAACTGTACAGATTGG
131 ATGTAGCTACACAAATAACAAACTTGGCGACCAAACGAGGGAAGAAACTGTACAGATTGG
5682120 ATGGAAGCCGAGTCGTGGCTTCGATTAACAATGTCACGTTTTTTATGCCGGAAACGGATCTACTT
1 ATGGAAGCCGAGTCGTGGCTTCGATTAACAATGTCACGTTTTTTATGCCGGAAACGGATCTACTT
5682185 CAAGCCCATTTCTTAAACTTCAATGGGGTTTTCAGCAGTGATTTCCCTGGAAATCTTCCTGCTCC
66 CAAGCCCATTTCTTAAACTTCAATGGGGTTTTCAGCAGTGATTTCCCTGGAAATCTTCCTGCTCC
*
5682250 ATGTAGCTACACAAATAACAAACTTGGCGACCAAACGAGGAAAGAAACTGTACAGATTGG
131 ATGTAGCTACACAAATAACAAACTTGGCGACCAAACGAGGGAAGAAACTGTACAGATTGG
5682310 ATGGAAGCCGAGTCGTGGCTTCGATTAACAATGTCACGTTTTTTATGCCGGAAACGGATCTACTT
1 ATGGAAGCCGAGTCGTGGCTTCGATTAACAATGTCACGTTTTTTATGCCGGAAACGGATCTACTT
5682375 CAAGCCCATTTCTTAAACTTCAATGGGGTTTTCAGCAGTGATTTCCCTGGAAATCTTCCTGCTCC
66 CAAGCCCATTTCTTAAACTTCAATGGGGTTTTCAGCAGTGATTTCCCTGGAAATCTTCCTGCTCC
*
5682440 ATGTAGCTACACAAATAACAAGCTTGGCGACCAAACGAGGGAAGAAACTGTACAGATTGG
131 ATGTAGCTACACAAATAACAAACTTGGCGACCAAACGAGGGAAGAAACTGTACAGATTGG
5682500 CTTATAACGA
Statistics
Matches: 566, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
189 149 0.26
190 417 0.74
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (190 bp):
ATGGAAGCCGAGTCGTGGCTTCGATTAACAATGTCACGTTTTTTATGCCGGAAACGGATCTACTT
CAAGCCCATTTCTTAAACTTCAATGGGGTTTTCAGCAGTGATTTCCCTGGAAATCTTCCTGCTCC
ATGTAGCTACACAAATAACAAACTTGGCGACCAAACGAGGGAAGAAACTGTACAGATTGG
Found at i:5686438 original size:24 final size:23
Alignment explanation
Indices: 5686410--5686462 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
5686400 ATGCTTTATA
5686410 TATATTAACTTTAAAAAATATATT
1 TATATTAAC-TTAAAAAATATATT
**
5686434 TATATTAACTTATTAAATATATT
1 TATATTAACTTAAAAAATATATT
5686457 T-TATTA
1 TATATTA
5686463 TAAACTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 5 0.19
23 13 0.48
24 9 0.33
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
TATATTAACTTAAAAAATATATT
Found at i:5686468 original size:25 final size:26
Alignment explanation
Indices: 5686425--5686488 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
5686415 TAACTTTAAA
*
5686425 AAATATA-TTTA-TATTAACTTA-TT
1 AAATATATTTTATTATAAACTTATTT
5686448 AAATATATTTTATTATAAACTTATTTT
1 AAATATATTTTATTATAAACTTA-TTT
*
5686475 AAAAATATTTTATT
1 AAATATATTTTATT
5686489 TTTCTTTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 7 0.20
24 4 0.11
25 9 0.26
27 15 0.43
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (26 bp):
AAATATATTTTATTATAAACTTATTT
Found at i:5686512 original size:16 final size:17
Alignment explanation
Indices: 5686493--5686538 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
5686483 TTTATTTTTC
5686493 TTTTAGTTTAAAATATT
1 TTTTAGTTTAAAATATT
5686510 TTTTA-TGTTAAAATATT
1 TTTTAGT-TTAAAATATT
**
5686527 TTAAAGTTTAAA
1 TTTTAGTTTAAA
5686539 TAAGAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 1 0.04
17 23 0.92
18 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (17 bp):
TTTTAGTTTAAAATATT
Found at i:5686617 original size:25 final size:25
Alignment explanation
Indices: 5686583--5686631 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5686573 AATATTTTAA
*
5686583 AATAAGTTAATAATAAAAT-ATATTC
1 AATAAATTAAT-ATAAAATAATATTC
5686608 AATAAATTAATATAAAATAATATT
1 AATAAATTAATATAAAATAATATT
5686632 TCTTAAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
AATAAATTAATATAAAATAATATTC
Found at i:5686638 original size:25 final size:25
Alignment explanation
Indices: 5686586--5686656 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 25
5686576 ATTTTAAAAT
5686586 AAGTTAATAATAAAATATATTCAATA
1 AAGTTAAT-ATAAAATATATTCAATA
*
5686612 AA-TTAATATAAAATAATATTTC-TTA
1 AAGTTAATATAAAAT-ATA-TTCAATA
*
5686637 AAGTTAATATATATATATAT
1 AAGTTAATATA-AAATATAT
5686657 ATATATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
24 7 0.18
25 13 0.33
26 16 0.41
27 3 0.08
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (25 bp):
AAGTTAATATAAAATATATTCAATA
Found at i:5686650 original size:2 final size:2
Alignment explanation
Indices: 5686643--5686684 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5686633 CTTAAAGTTA
5686643 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
5686685 TTGAATTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5687350 original size:24 final size:24
Alignment explanation
Indices: 5687318--5687370 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
5687308 CTATTCTTTC
5687318 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
5687342 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
5687366 GCTTC
1 GCTTC
5687371 TTTCGAGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:5697804 original size:47 final size:48
Alignment explanation
Indices: 5697734--5697829 Score: 185
Period size: 47 Copynumber: 2.0 Consensus size: 48
5697724 TTCACTCAGT
5697734 CTCTCTCTCTCTTTTCTAAACACAATTCTTATTTTGAATGAATTATGG
1 CTCTCTCTCTCTTTTCTAAACACAATTCTTATTTTGAATGAATTATGG
5697782 CTCTCTCTCT-TTTTCTAAACACAATTCTTATTTTGAATGAATTATGG
1 CTCTCTCTCTCTTTTCTAAACACAATTCTTATTTTGAATGAATTATGG
5697829 C
1 C
5697830 GTTGAATGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 38 0.79
48 10 0.21
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (48 bp):
CTCTCTCTCTCTTTTCTAAACACAATTCTTATTTTGAATGAATTATGG
Found at i:5697919 original size:12 final size:12
Alignment explanation
Indices: 5697904--5697928 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5697894 ATTTCTTCCA
5697904 TGACTCTCTCTC
1 TGACTCTCTCTC
5697916 TGACTCTCTCTC
1 TGACTCTCTCTC
5697928 T
1 T
5697929 TGAAATCTGT
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:0.08, C:0.40, G:0.08, T:0.44
Consensus pattern (12 bp):
TGACTCTCTCTC
Found at i:5724235 original size:4 final size:4
Alignment explanation
Indices: 5724226--5724254 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
5724216 TAGAACAAAC
5724226 GAGG GAGG GAGG GAGG GAGG GAGG GAGG G
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG G
5724255 GAAAAGAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:5732472 original size:16 final size:16
Alignment explanation
Indices: 5732451--5732511 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
5732441 TAATAAATAA
5732451 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
5732467 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
* *
5732483 ACGGACATAAATGAAC
1 ACGAACATAAACGAAC
5732499 ACGAACATAAACG
1 ACGAACATAAACG
5732512 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:5733087 original size:19 final size:19
Alignment explanation
Indices: 5733063--5733105 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
5733053 TTAATGGGTT
5733063 CTTCCTGGAAAACCCATTA
1 CTTCCTGGAAAACCCATTA
5733082 CTTCCTGGAAAACCCATTA
1 CTTCCTGGAAAACCCATTA
5733101 CTTCC
1 CTTCC
5733106 GTTATTACAC
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:0.28, C:0.35, G:0.09, T:0.28
Consensus pattern (19 bp):
CTTCCTGGAAAACCCATTA
Found at i:5733619 original size:14 final size:14
Alignment explanation
Indices: 5733602--5733642 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
5733592 GATTGGATTA
*
5733602 AACATAAATGAACG
1 AACATAAACGAACG
*
5733616 AACATAACCGAACG
1 AACATAAACGAACG
*
5733630 AATATAAACGAAC
1 AACATAAACGAAC
5733643 ATAACCGAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.56, C:0.20, G:0.12, T:0.12
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:5735718 original size:16 final size:16
Alignment explanation
Indices: 5735697--5735729 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5735687 AATAGACATA
5735697 AGAAAGG-GAGAGATTG
1 AGAAAGGTGAG-GATTG
5735713 AGAAAGGTGAGGATTG
1 AGAAAGGTGAGGATTG
5735729 A
1 A
5735730 TTTGCTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.42, C:0.00, G:0.42, T:0.15
Consensus pattern (16 bp):
AGAAAGGTGAGGATTG
Found at i:5737373 original size:35 final size:34
Alignment explanation
Indices: 5737324--5737393 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 34
5737314 GTTAAAAACT
*
5737324 ATATTAATATACTAAATTAAAAGCATGTCCCATAA
1 ATATTAATAAACTAAATTAAAAGCATG-CCCATAA
* *
5737359 ATATTAATAAACTAAATTAGAAGCATGCCTATAA
1 ATATTAATAAACTAAATTAAAAGCATGCCCATAA
5737393 A
1 A
5737394 CTTATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 7 0.22
35 25 0.78
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (34 bp):
ATATTAATAAACTAAATTAAAAGCATGCCCATAA
Found at i:5748416 original size:2 final size:2
Alignment explanation
Indices: 5748411--5748450 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5748401 AATGTGCGTG
5748411 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5748451 GATAGATAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5748473 original size:12 final size:12
Alignment explanation
Indices: 5748456--5748497 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
5748446 ATATAGATAG
*
5748456 ATAGATAAATCA
1 ATAGATAAATAA
*
5748468 ATAGATAGATAA
1 ATAGATAAATAA
*
5748480 ATAAATAAATAA
1 ATAGATAAATAA
5748492 ATAGAT
1 ATAGAT
5748498 GGATCAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.26
Consensus pattern (12 bp):
ATAGATAAATAA
Found at i:5748473 original size:16 final size:16
Alignment explanation
Indices: 5748452--5748486 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5748442 ATATATATAG
*
5748452 ATAGATAGATAAATCA
1 ATAGATAGATAAATAA
5748468 ATAGATAGATAAATAA
1 ATAGATAGATAAATAA
5748484 ATA
1 ATA
5748487 AATAAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.60, C:0.03, G:0.11, T:0.26
Consensus pattern (16 bp):
ATAGATAGATAAATAA
Found at i:5748473 original size:20 final size:20
Alignment explanation
Indices: 5748448--5748497 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
5748438 ATATATATAT
* *
5748448 ATAGATAGATAGATAAATCA
1 ATAGATAGATAAATAAATAA
5748468 ATAGATAGATAAATAAATAA
1 ATAGATAGATAAATAAATAA
*
5748488 ATAAATAGAT
1 ATAGATAGAT
5748498 GGATCAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.60, C:0.02, G:0.12, T:0.26
Consensus pattern (20 bp):
ATAGATAGATAAATAAATAA
Found at i:5748487 original size:24 final size:24
Alignment explanation
Indices: 5748448--5748520 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 24
5748438 ATATATATAT
* * *
5748448 ATAGATAGATAGATAAATCAATAG
1 ATAGATAAATAAATAAATAAATAG
5748472 ATAGATAAATAAATAAATAAATAG
1 ATAGATAAATAAATAAATAAATAG
* *
5748496 ATGGATCAAATTGAAATAAAAAAAT
1 ATAGAT-AAA-T-AAATAAATAAAT
5748521 CTTTATGTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
24 26 0.63
25 3 0.07
26 1 0.02
27 11 0.27
ACGTcount: A:0.60, C:0.03, G:0.12, T:0.25
Consensus pattern (24 bp):
ATAGATAAATAAATAAATAAATAG
Found at i:5754231 original size:2 final size:2
Alignment explanation
Indices: 5754224--5754265 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5754214 AACAAACTTC
5754224 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
5754266 TTCTCTTGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5755494 original size:13 final size:13
Alignment explanation
Indices: 5755478--5755502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5755468 TCATTATTAT
5755478 TTCTATCAATTCC
1 TTCTATCAATTCC
5755491 TTCTATCAATTC
1 TTCTATCAATTC
5755503 ATTATATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCTATCAATTCC
Found at i:5755578 original size:17 final size:16
Alignment explanation
Indices: 5755546--5755587 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
5755536 TTAGAATGTA
*
5755546 AAATTAATTTTTTATT
1 AAATTATTTTTTTATT
*
5755562 ATATTATTTTTTATATT
1 AAATTATTTTTT-TATT
5755579 AAATTATTT
1 AAATTATTT
5755588 GATCAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
AAATTATTTTTTTATT
Found at i:5765017 original size:18 final size:21
Alignment explanation
Indices: 5764976--5765020 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
5764966 TTCGAAGGTG
5764976 TGTTTTCTCTCTCTGTCTCTC
1 TGTTTTCTCTCTCTGTCTCTC
*
5764997 TGTTTTCTC-CTGTGT-T-TC
1 TGTTTTCTCTCTCTGTCTCTC
5765015 TGTTTT
1 TGTTTT
5765021 GTTCATGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 1 0.04
20 5 0.22
21 9 0.39
ACGTcount: A:0.00, C:0.24, G:0.13, T:0.62
Consensus pattern (21 bp):
TGTTTTCTCTCTCTGTCTCTC
Found at i:5768476 original size:19 final size:20
Alignment explanation
Indices: 5768437--5768472 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
5768427 GGGTAATAAT
5768437 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
5768457 ATAAG-AATG-AAATAAA
1 ATAAGTAATGAAAATAAA
5768473 ATAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 4 0.25
20 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:5773683 original size:5 final size:5
Alignment explanation
Indices: 5773675--5773729 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
5773665 TGCTTTCTCT
5773675 TTTTC TTTTC TTTTC TTCTT- TTCTTC TTTTC TTCTT- TTTGTC TTTTC
1 TTTTC TTTTC TTTTC TT-TTC TT-TTC TTTTC TT-TTC TTT-TC TTTTC
5773722 -TTTC TTTT
1 TTTTC TTTT
5773730 TGCACTCCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
4 5 0.11
5 30 0.68
6 9 0.20
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:5773693 original size:8 final size:8
Alignment explanation
Indices: 5773682--5773729 Score: 71
Period size: 8 Copynumber: 5.9 Consensus size: 8
5773672 TCTTTTTCTT
5773682 TTCTTTTC
1 TTCTTTTC
5773690 TTCTTTTC
1 TTCTTTTC
5773698 TTCTTTTC
1 TTCTTTTC
5773706 TTCTTTT-
1 TTCTTTTC
5773713 TGTCTTTTC
1 T-TCTTTTC
5773722 TTTCTTTT
1 -TTCTTTT
5773730 TGCACTCCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.03
8 29 0.78
9 6 0.16
10 1 0.03
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (8 bp):
TTCTTTTC
Found at i:5777856 original size:13 final size:13
Alignment explanation
Indices: 5777838--5777862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5777828 AATATTAATT
5777838 ATATATTAAATAA
1 ATATATTAAATAA
5777851 ATATATTAAATA
1 ATATATTAAATA
5777863 TATTTATGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATATTAAATAA
Found at i:5780873 original size:8 final size:8
Alignment explanation
Indices: 5780860--5780900 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
5780850 CTCATTTTCA
5780860 GAGAATTT
1 GAGAATTT
5780868 GAGAATTT
1 GAGAATTT
*
5780876 -AGAGTTT
1 GAGAATTT
*
5780883 GGGAATTT
1 GAGAATTT
5780891 GAGAATTT
1 GAGAATTT
5780899 GA
1 GA
5780901 AAGATTGTGA
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:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:5781199 original size:128 final size:128
Alignment explanation
Indices: 5780971--5781598 Score: 1123
Period size: 128 Copynumber: 4.9 Consensus size: 128
5780961 TAATCGGAGT
*
5780971 ACTATTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
* *
5781036 CATTGCCCTATTATGTCACTCATGTCCCTTGGGGACACTAGATATATTAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* * *
5781099 ACTATTCACATGAAGGCGCATTCCCAGGGGTGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
5781164 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
5781227 ACTATTCACATGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
*
5781291 CGTTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
5781354 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
* * *
5781419 CATTGCCCTATTATGTCACTCATGTCCCTTGGTGACACTAGATATATCAGTACCTATTATTGC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
5781482 ACTATTCACATGAAGGTGCGTTCCCGGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
5781547 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
5781599 AATCAGGTAA
Statistics
Matches: 480, Mismatches: 19, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
127 125 0.26
128 355 0.74
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:5781458 original size:255 final size:255
Alignment explanation
Indices: 5780971--5781598 Score: 1121
Period size: 255 Copynumber: 2.5 Consensus size: 255
5780961 TAATCGGAGT
*
5780971 ACTATTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTCATCAGAGAATATGTTAT
* *
5781036 CATTGCCCTATTATGTCACTCATGTCCCTTGGGGACACTAGATATATTAGTACCTATTATTTCAC
65 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
5781101 TATTCACATGAAGGCGCATTCCCAGGGGTGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
130 TATTCACATGAAGGCGCATTCCCAGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
*
5781166 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
195 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTGC
*
5781227 ACTATTCACATGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATC
*
5781292 GTTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACT
66 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACT
* * *
5781357 ATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCAT
131 ATTCACATGAAGGCGCATTCCCAGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCAT
* *
5781422 TGCCCTATTATGTCACTCATGTCCCTTGGTGACACTAGATATATCAGTACCTATTATTGC
196 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTGC
*
5781482 ACTATTCACATGAAGGTGCGTTCCCGGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCC-GGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
5781547 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
5781599 AATCAGGTAA
Statistics
Matches: 356, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
255 238 0.67
256 118 0.33
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (255 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATC
ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACT
ATTCACATGAAGGCGCATTCCCAGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCAT
TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTGC
Found at i:5782069 original size:26 final size:27
Alignment explanation
Indices: 5782031--5782089 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
5782021 TATATTTAAA
*
5782031 TTTAAATTTGAATAAT-T-ATTTTTAT
1 TTTAAATTTGAATAATATAATTTGTAT
5782056 TTTAAATTTCGAATAATATAATTTGTAT
1 TTTAAATTT-GAATAATATAATTTGTAT
5782084 TTTAAA
1 TTTAAA
5782090 AACATTTATC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 9 0.30
26 7 0.23
27 1 0.03
28 13 0.43
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (27 bp):
TTTAAATTTGAATAATATAATTTGTAT
Found at i:5782696 original size:21 final size:21
Alignment explanation
Indices: 5782608--5782701 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
5782598 TATGGTATAA
*
5782608 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
5782629 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
5782650 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
5782671 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
5782692 AACCCTGCGG
1 AACCCTGCGG
5782702 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:5784513 original size:31 final size:33
Alignment explanation
Indices: 5784478--5784546 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 33
5784468 CTAAATAAGT
* *
5784478 AATAATTATATAAAT-ATTATTTTAATA-AAAA
1 AATAATTATATAAATAAATATATTAATATAAAA
* *
5784509 AATAA-TATTTACATAAATATATTAATATAAAA
1 AATAATTATATAAATAAATATATTAATATAAAA
5784541 AATAAT
1 AATAAT
5784547 AATTATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
30 7 0.23
31 15 0.48
32 9 0.29
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
AATAATTATATAAATAAATATATTAATATAAAA
Found at i:5784525 original size:34 final size:32
Alignment explanation
Indices: 5784477--5784551 Score: 98
Period size: 34 Copynumber: 2.3 Consensus size: 32
5784467 TCTAAATAAG
*
5784477 TAATAATTATATAAATATTATTTTAATA-AAAAAA
1 TAATAATTACATAAATA-TA--TTAATATAAAAAA
*
5784511 TAATATTTACATAAATATATTAATATAAAAAA
1 TAATAATTACATAAATATATTAATATAAAAAA
5784543 TAATAATTA
1 TAATAATTA
5784552 TTTAAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 6 0.16
32 14 0.38
33 2 0.05
34 15 0.41
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (32 bp):
TAATAATTACATAAATATATTAATATAAAAAA
Found at i:5785587 original size:14 final size:16
Alignment explanation
Indices: 5785564--5785650 Score: 53
Period size: 14 Copynumber: 5.6 Consensus size: 16
5785554 AGTACATATT
5785564 AATT-TAATATTA-AA
1 AATTATAATATTATAA
5785578 AA-TATAATATTATTAA
1 AATTATAATATTA-TAA
*
5785594 AATTATAATAATATTAA
1 AATTATAATATTA-TAA
* *
5785611 ATATTTTAATAAT-TAA
1 A-ATTATAATATTATAA
*
5785627 TATT-T--TATTATTAA
1 AATTATAATATTA-TAA
5785641 AATTATAATA
1 AATTATAATA
5785651 AGATATTAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
12 3 0.05
13 1 0.02
14 17 0.29
15 4 0.07
16 7 0.12
17 16 0.28
18 10 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTATAATATTATAA
Found at i:5785593 original size:17 final size:17
Alignment explanation
Indices: 5785568--5785611 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
5785558 CATATTAATT
5785568 TAATATTAAAAATATAA
1 TAATATTAAAAATATAA
* *
5785585 TATTATTAAAATTATAA
1 TAATATTAAAAATATAA
5785602 TAATATTAAA
1 TAATATTAAA
5785612 TATTTTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATATTAAAAATATAA
Found at i:5785642 original size:64 final size:65
Alignment explanation
Indices: 5785483--5785650 Score: 166
Period size: 64 Copynumber: 2.6 Consensus size: 65
5785473 GATACTCTTA
* * * * *
5785483 ATTTTAGTTATTAGTATTTTATTAAT-ATAATACTAA-ATTATTAAACATTATATATTATTATAA
1 ATTTTAGTAATTAATATTTTATTATTAAAAATA-TAATATTATTAAACATTATATAATATTATAA
5785546 T
65 T
* * *
5785547 ATATTTGAGTACA-TATTAATTTAATATTAAAAATATAATATTATTAAA-ATTATAATAATATTA
1 AT-TTT-AGTA-ATTAATATTTTATTATTAAAAATATAATATTATTAAACATTAT-ATAATATTA
5785610 -AAT
62 TAAT
* *
5785613 ATTTTAATAATTAATATTTTATTATTAAAATTATAATA
1 ATTTTAGTAATTAATATTTTATTATTAAAAATATAATA
5785651 AGATATTAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 14
0.77 0.11 0.13
Matches are distributed among these distances:
63 1 0.01
64 28 0.33
65 6 0.07
66 27 0.32
67 23 0.27
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (65 bp):
ATTTTAGTAATTAATATTTTATTATTAAAAATATAATATTATTAAACATTATATAATATTATAAT
Found at i:5785817 original size:19 final size:18
Alignment explanation
Indices: 5785779--5785813 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5785769 ACAAAGAAAC
*
5785779 TAGAAAAATGAATTACAT
1 TAGAAAAATCAATTACAT
5785797 TAGAAAAATCAATTACA
1 TAGAAAAATCAATTACA
5785814 ATTATCAAAT
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:0.57, C:0.09, G:0.09, T:0.26
Consensus pattern (18 bp):
TAGAAAAATCAATTACAT
Found at i:5785884 original size:14 final size:14
Alignment explanation
Indices: 5785867--5785894 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5785857 ATATCAAACA
5785867 CCGAAAAATATTTT
1 CCGAAAAATATTTT
5785881 CCGAAAAATATTTT
1 CCGAAAAATATTTT
5785895 TTAAGTATCA
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:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
CCGAAAAATATTTT
Found at i:5786592 original size:2 final size:2
Alignment explanation
Indices: 5786581--5786652 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
5786571 AAATAACCAT
5786581 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5786622 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5786653 TATGATGTTA
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5790177 original size:21 final size:21
Alignment explanation
Indices: 5790151--5790192 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5790141 CCAGAATGGG
*
5790151 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
5790172 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
5790193 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:5790322 original size:19 final size:19
Alignment explanation
Indices: 5790298--5790345 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
5790288 AAGCCTCGGG
*
5790298 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAATAGTAAA
5790317 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAATAGTAAA
*
5790336 TTACTATTCA
1 TTACTGTTCA
5790346 TAAAAACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (19 bp):
TTACTGTTCAAATAGTAAA
Found at i:5790442 original size:29 final size:31
Alignment explanation
Indices: 5790401--5790469 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 31
5790391 TATTTTTGTA
*
5790401 AATTTTGAATAAATTCAATT-AAGTCCAAATAC
1 AATTTTG--TAAATTCAATTCAAGTCCAAAAAC
5790433 -ATTTTGTAAATTCAATTCAAGTCCAAAAAC
1 AATTTTGTAAATTCAATTCAAGTCCAAAAAC
5790463 AATTTTG
1 AATTTTG
5790470 CCTTAAATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 11 0.32
30 11 0.32
31 12 0.35
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (31 bp):
AATTTTGTAAATTCAATTCAAGTCCAAAAAC
Found at i:5790478 original size:34 final size:29
Alignment explanation
Indices: 5790410--5790469 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
5790400 AAATTTTGAA
*
5790410 TAAATTCAATTAAGTCCAAATACATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
5790439 TAAATTCAATTCAAGTCCAAAAACAATTTTG
1 TAAATTCAATT-AAGTCCAAAAAC-ATTTTG
5790470 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:5799150 original size:16 final size:16
Alignment explanation
Indices: 5799129--5799160 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5799119 TAGAGAGACA
5799129 AAAATAAATTATCAAT
1 AAAATAAATTATCAAT
*
5799145 AAAATATATTATCAAT
1 AAAATAAATTATCAAT
5799161 TCATTTACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATAAATTATCAAT
Done.