Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 24 of 325
Found at i:5556013 original size:41 final size:42
Alignment explanation
Indices: 5555956--5556044 Score: 144
Period size: 41 Copynumber: 2.1 Consensus size: 42
5555946 CGGCGTTCCA
* * *
5555956 CTAAAAACCAGAGCAATAGCGGCGTTTTTGGT-AAAACGTCG
1 CTAAAAAACAGAGCAATAGCGGCGTTTGTGGTCAAAACGCCG
5555997 CTAAAAAACAGAGCAATAGCGGCGTTTGTGGTCAAAACGCCG
1 CTAAAAAACAGAGCAATAGCGGCGTTTGTGGTCAAAACGCCG
5556039 CTAAAA
1 CTAAAA
5556045 GTCATATAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 30 0.68
42 14 0.32
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (42 bp):
CTAAAAAACAGAGCAATAGCGGCGTTTGTGGTCAAAACGCCG
Found at i:5556102 original size:46 final size:45
Alignment explanation
Indices: 5556049--5556162 Score: 125
Period size: 38 Copynumber: 2.7 Consensus size: 45
5556039 CTAAAAGTCA
* *
5556049 TATAACCCCTAAAACCCTAAATCCCCAAAAATCATAAACACTAATC
1 TATAACCCCTAAAACCCTAAA-CCCCAAAAACCATAAACACTAAAC
*
5556095 TATAA-CCCTTAAACCCT--A----AAAAACCATAAACACTAAAC
1 TATAACCCCTAAAACCCTAAACCCCAAAAACCATAAACACTAAAC
* *
5556133 TATAACCCTTAAAACCTTAAACCCCAAAAA
1 TATAACCCCTAAAACCCTAAACCCCAAAAA
5556163 ACATCATATG
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
38 23 0.42
39 9 0.16
41 1 0.02
43 1 0.02
45 16 0.29
46 5 0.09
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (45 bp):
TATAACCCCTAAAACCCTAAACCCCAAAAACCATAAACACTAAAC
Found at i:5556320 original size:15 final size:16
Alignment explanation
Indices: 5556300--5556335 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5556290 GTTTAAGGTC
5556300 TATGGTTT-AGGGTTT
1 TATGGTTTAAGGGTTT
5556315 TATGGTTTAAGGGTTT
1 TATGGTTTAAGGGTTT
*
5556331 AATGG
1 TATGG
5556336 CCATGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.47
Consensus pattern (16 bp):
TATGGTTTAAGGGTTT
Found at i:5560189 original size:2 final size:2
Alignment explanation
Indices: 5560182--5560224 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5560172 TTGGTATTTC
5560182 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5560224 T
1 T
5560225 TTTCTTATGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:5563261 original size:31 final size:31
Alignment explanation
Indices: 5563223--5563300 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
5563213 TTGTTGTATT
5563223 TTATTTATATTTATATTT-AATCTA-ATTTTTA
1 TTATTTAT-TTTAT-TTTGAATCTATATTTTTA
*
5563254 TTATTTATTTTAGTTTTGATTCTATATTTTTA
1 TTATTTATTTTA-TTTTGAATCTATATTTTTA
5563286 TT-TTTATTTTTATTT
1 TTATTTA-TTTTATTT
5563301 GATAATGAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
30 7 0.17
31 21 0.50
32 14 0.33
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (31 bp):
TTATTTATTTTATTTTGAATCTATATTTTTA
Found at i:5563287 original size:6 final size:6
Alignment explanation
Indices: 5563247--5563300 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
5563237 ATTTAATCTA
* *
5563247 ATTTTT ATTATTT A-TTTT AGTTTTG ATTCTAT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATT-TTT ATTTTT A-TTTTT ATT-TTT ATTTTT ATTTTT ATTTTT
5563297 ATTT
1 ATTT
5563301 GATAATGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 4 0.10
6 24 0.60
7 12 0.30
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (6 bp):
ATTTTT
Found at i:5563323 original size:11 final size:11
Alignment explanation
Indices: 5563303--5563331 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5563293 TTTTATTTGA
5563303 TAAT-GAATTT
1 TAATAGAATTT
5563313 TAATAGAATTT
1 TAATAGAATTT
5563324 TAATAGAA
1 TAATAGAA
5563332 AATTTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (11 bp):
TAATAGAATTT
Found at i:5563427 original size:10 final size:10
Alignment explanation
Indices: 5563414--5563438 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5563404 TTTCATGACC
5563414 TTTATAATAT
1 TTTATAATAT
5563424 TTTATAATAT
1 TTTATAATAT
5563434 TTTAT
1 TTTAT
5563439 TTTTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTATAATAT
Found at i:5563654 original size:31 final size:31
Alignment explanation
Indices: 5563619--5563692 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
5563609 GTAGCGCTTG
*
5563619 TAAAAACGGCACAAATAGTTTTAGCAACGCT
1 TAAAAACGCCACAAATAGTTTTAGCAACGCT
**
5563650 TAAAAACGCCACAAATAGTTTTAGCGGCGCT
1 TAAAAACGCCACAAATAGTTTTAGCAACGCT
*
5563681 TAAAAGCGCCAC
1 TAAAAACGCCAC
5563693 TAAAGGCCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
TAAAAACGCCACAAATAGTTTTAGCAACGCT
Found at i:5565697 original size:17 final size:16
Alignment explanation
Indices: 5565654--5565703 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
5565644 TTCCTTTTTC
*
5565654 TATTCTTTTTGTTTCTT
1 TATT-TTTTTATTTCTT
*
5565671 TATTCTTTTATTTACTT
1 TATTTTTTTATTT-CTT
5565688 TATTTTTTTA-TTCTT
1 TATTTTTTTATTTCTT
5565703 T
1 T
5565704 TATTATAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 4 0.14
16 9 0.31
17 16 0.55
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (16 bp):
TATTTTTTTATTTCTT
Found at i:5565727 original size:13 final size:13
Alignment explanation
Indices: 5565708--5565751 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
5565698 TTCTTTTATT
5565708 ATAATATAATATA
1 ATAATATAATATA
*
5565721 TTAATATAATATA
1 ATAATATAATATA
5565734 AT-ATAATAATATA
1 ATAAT-ATAATATA
5565747 A-AATA
1 ATAATA
5565752 ACATTTACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 3 0.11
13 24 0.89
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATAATATAATATA
Found at i:5565730 original size:18 final size:18
Alignment explanation
Indices: 5565707--5565752 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
5565697 ATTCTTTTAT
*
5565707 TATAATATAATATATTAA
1 TATAATATAATATAATAA
5565725 TATAATATAATATAATAA
1 TATAATATAATATAATAA
*
5565743 TATAAAATAA
1 TATAATATAA
5565753 CATTTACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TATAATATAATATAATAA
Found at i:5565747 original size:5 final size:5
Alignment explanation
Indices: 5565707--5565741 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
5565697 ATTCTTTTAT
5565707 TATAA TATAA TAT-A T-TAA TATAA TATAA TATAA TA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TA
5565742 ATATAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 1 0.04
4 4 0.14
5 23 0.82
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:5568074 original size:24 final size:24
Alignment explanation
Indices: 5568032--5568077 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5568022 TTTATGGTCT
* *
5568032 AAAATTTCATGGGATAATTTTGTG
1 AAAATTTCATGCGAAAATTTTGTG
*
5568056 AAAATTTCATTCGAAAATTTTG
1 AAAATTTCATGCGAAAATTTTG
5568078 ACATTTGAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (24 bp):
AAAATTTCATGCGAAAATTTTGTG
Found at i:5569278 original size:50 final size:50
Alignment explanation
Indices: 5569209--5569407 Score: 238
Period size: 50 Copynumber: 4.0 Consensus size: 50
5569199 TAAGATGATT
** * ** *
5569209 TTAGGTCATGTGTGTAGTACTAAATATAGGCTACTAGGTGTACCAGATAG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* * *
5569259 TTAGGTCCCATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* * * * *
5569309 TTAGGTCACGTGTGTAGTTCTAAGTGCAGGCTACTACATGTACCGGATTG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* * *
5569359 TT-GGTCACATGTGTAGTACTAAGTGCAAGCTACTATGCGTACCAGATAG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
5569408 CTTCAGTTAC
Statistics
Matches: 125, Mismatches: 24, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
49 39 0.31
50 86 0.69
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (50 bp):
TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
Found at i:5569344 original size:100 final size:99
Alignment explanation
Indices: 5569209--5569393 Score: 262
Period size: 100 Copynumber: 1.9 Consensus size: 99
5569199 TAAGATGATT
* * ** *
5569209 TTAGGTCATGTGTGTAGTACTAAATATAGGCTACTAGGTGTACCAGATAGTTAGGTCCCATGTGT
1 TTAGGTCACGTGTGTAGTACTAAATACAGGCTACTACATGTACCAGATAGTT-GGTCACATGTGT
*
5569274 AGTACTAAGTGCAGGCTACTACGTGTATCAGATGG
65 AGTACTAAGTGCAAGCTACTACGTGTATCAGATGG
* * * * *
5569309 TTAGGTCACGTGTGTAGTTCTAAGTGCAGGCTACTACATGTACCGGATTGTTGGTCACATGTGTA
1 TTAGGTCACGTGTGTAGTACTAAATACAGGCTACTACATGTACCAGATAGTTGGTCACATGTGTA
5569374 GTACTAAGTGCAAGCTACTA
66 GTACTAAGTGCAAGCTACTA
5569394 TGCGTACCAG
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
99 31 0.42
100 43 0.58
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (99 bp):
TTAGGTCACGTGTGTAGTACTAAATACAGGCTACTACATGTACCAGATAGTTGGTCACATGTGTA
GTACTAAGTGCAAGCTACTACGTGTATCAGATGG
Found at i:5573053 original size:21 final size:20
Alignment explanation
Indices: 5573036--5573075 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5573026 TGCGTAAATG
5573036 AATAT-ATAATATATGTAAA
1 AATATGATAATATATGTAAA
*
5573055 AATATGATAATATATATAAA
1 AATATGATAATATATGTAAA
5573075 A
1 A
5573076 TAATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (20 bp):
AATATGATAATATATGTAAA
Found at i:5573080 original size:22 final size:20
Alignment explanation
Indices: 5573030--5573080 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
5573020 ATAATATGCG
*
5573030 TAAATGAATATATAATATATG
1 TAAAT-AATATATAATATATA
5573051 TAAA-AATATGATAATATATA
1 TAAATAATAT-ATAATATATA
5573071 TAAAATAATA
1 T-AAATAATA
5573081 ATTATGAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 10 0.38
21 7 0.27
22 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (20 bp):
TAAATAATATATAATATATA
Found at i:5575139 original size:25 final size:27
Alignment explanation
Indices: 5575102--5575154 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
5575092 TCAAACATGC
5575102 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
5575128 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
5575154 A
1 A
5575155 AAACTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:5576676 original size:26 final size:26
Alignment explanation
Indices: 5576640--5576775 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
5576630 CATGAAATTC
5576640 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5576666 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5576692 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5576718 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5576744 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5576770 TTATCA
1 TTATCA
5576776 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5577406 original size:20 final size:20
Alignment explanation
Indices: 5577381--5577418 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5577371 TGGGTCTATT
5577381 TTGTAATGGGTCAAGGGTAA
1 TTGTAATGGGTCAAGGGTAA
5577401 TTGTAATGGGTCAAGGGT
1 TTGTAATGGGTCAAGGGT
5577419 GTAAATGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.37, T:0.32
Consensus pattern (20 bp):
TTGTAATGGGTCAAGGGTAA
Found at i:5577831 original size:83 final size:83
Alignment explanation
Indices: 5577692--5578266 Score: 1060
Period size: 83 Copynumber: 6.9 Consensus size: 83
5577682 TGATGACTGT
5577692 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
*
5577757 CAAACCATCTTGAGTCCG
66 CAAACCATCTTGAGTCTG
*
5577775 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGT
1 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
5577840 CAAACCATCTTGAGTCTG
66 CAAACCATCTTGAGTCTG
* *
5577858 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGAATAC
1 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
* *
5577923 CAAATCATCTTGAGTTTG
66 CAAACCATCTTGAGTCTG
* *
5577941 TTTGAGAACATTTGAGAGTCATATCTGTAATATCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
5578006 CAAACCATCTTGAGTCTG
66 CAAACCATCTTGAGTCTG
5578024 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
5578089 CAAACCATCTTGAGTCTG
66 CAAACCATCTTGAGTCTG
5578107 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
*
5578172 CAAACCATCTTGAGTCTA
66 CAAACCATCTTGAGTCTG
*
5578190 TTTGAGAACATTTGAGAGTCATATCTGTAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
5578255 CAAACCATCTTG
66 CAAACCATCTTG
5578267 GATCTGCTTT
Statistics
Matches: 475, Mismatches: 17, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 475 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (83 bp):
TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
CAAACCATCTTGAGTCTG
Found at i:5578400 original size:119 final size:119
Alignment explanation
Indices: 5578188--5578545 Score: 619
Period size: 119 Copynumber: 3.0 Consensus size: 119
5578178 ATCTTGAGTC
* * * * *
5578188 TATTTGAGAACATTTGAGAGTCATATCTG-TAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGA
1 TATTTGAGAACGTCTGAGAGTCAAATCTGCT-ATGTCCTCGATTTGTTCCTTGTAAACACAAGAA
* *
5578252 TGCCAAACCATCTTGGATCTGCTTTAGTATAAACATCTGAAGGTTAGATCTGCTA
65 TGCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTA
*
5578307 TATTTGAGAGCGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAAT
1 TATTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAAT
*
5578372 ACCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTA
66 GCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTA
5578426 TATTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAAT
1 TATTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAAT
5578491 GCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTA
66 GCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTA
5578545 T
1 T
5578546 CTTCGATCTG
Statistics
Matches: 227, Mismatches: 11, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
119 226 1.00
120 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (119 bp):
TATTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAAT
GCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTA
Found at i:5579550 original size:1 final size:1
Alignment explanation
Indices: 5579540--5579605 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
5579530 GGCCTCTCCA
* * * * * * * * *
5579540 TTTTTCTTTTTTTCTCTTTATTTTTTTCTCTTTTTCTTTTTTTTTTCTTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5579605 T
1 T
5579606 GAAATAGAAG
Statistics
Matches: 47, Mismatches: 18, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:5579553 original size:8 final size:8
Alignment explanation
Indices: 5579540--5579605 Score: 73
Period size: 8 Copynumber: 8.2 Consensus size: 8
5579530 GGCCTCTCCA
5579540 TTTTTCTT
1 TTTTTCTT
5579548 TTTTTCTCT
1 TTTTTCT-T
*
5579557 TTATT-TT
1 TTTTTCTT
*
5579564 TTTCTCTT
1 TTTTTCTT
*
5579572 TTTCTTTTT
1 TTT-TTCTT
5579581 TTTTTCTT
1 TTTTTCTT
5579589 TTTTTCTT
1 TTTTTCTT
5579597 TTTTT-TT
1 TTTTTCTT
5579604 TT
1 TT
5579606 GAAATAGAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
7 8 0.16
8 30 0.61
9 11 0.22
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Found at i:5579565 original size:14 final size:13
Alignment explanation
Indices: 5579546--5579604 Score: 70
Period size: 14 Copynumber: 4.5 Consensus size: 13
5579536 TCCATTTTTC
5579546 TTTTTTTCTCTTT
1 TTTTTTTCTCTTT
5579559 ATTTTTTTCTCTTT
1 -TTTTTTTCTCTTT
5579573 TTCTTTTT-T-TTT
1 TT-TTTTTCTCTTT
5579585 TCTTTTTT-TCTTT
1 T-TTTTTTCTCTTT
5579598 TTTTTTT
1 TTTTTTT
5579605 TGAAATAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
12 16 0.38
13 8 0.19
14 18 0.43
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTCTCTTT
Found at i:5579582 original size:19 final size:19
Alignment explanation
Indices: 5579549--5579604 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 19
5579539 ATTTTTCTTT
5579549 TTTTCTCTTTATTTTTTTCTC
1 TTTT-TCTTT-TTTTTTTCTC
*
5579570 TTTTTCTTTTTTTTTTCTT
1 TTTTTCTTTTTTTTTTCTC
5579589 TTTTTCTTTTTTTTTT
1 TTTTTCTTTTTTTTTT
5579605 TGAAATAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 25 0.74
20 5 0.15
21 4 0.12
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTTTCTTTTTTTTTTCTC
Found at i:5585975 original size:17 final size:18
Alignment explanation
Indices: 5585922--5586019 Score: 146
Period size: 18 Copynumber: 5.5 Consensus size: 18
5585912 AATCATATCT
*
5585922 TCTAAGATTGTATATCATA
1 TCTAAGATTG-CTATCATA
*
5585941 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
5585959 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
*
5585976 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
5585994 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
5586011 TCTAAGATT
1 TCTAAGATT
5586020 ACATATCATT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
17 31 0.42
18 32 0.44
19 10 0.14
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:5585980 original size:35 final size:35
Alignment explanation
Indices: 5585922--5586028 Score: 178
Period size: 35 Copynumber: 3.0 Consensus size: 35
5585912 AATCATATCT
5585922 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
5585959 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
*
5585994 TCTAAGATTGTATCATATCTAAGATTACATATCAT
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCAT
5586029 TGAAGATTAT
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
35 53 0.78
36 5 0.07
37 10 0.15
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:5586994 original size:21 final size:21
Alignment explanation
Indices: 5586970--5587009 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5586960 ACATAATTTA
5586970 TTAAA-TAATTTAATTTTAATC
1 TTAAACTAATTT-ATTTTAATC
*
5586991 TTAAACTGATTTATTTTAA
1 TTAAACTAATTTATTTTAA
5587010 GAATTTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (21 bp):
TTAAACTAATTTATTTTAATC
Found at i:5589297 original size:23 final size:23
Alignment explanation
Indices: 5589252--5589297 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5589242 TTACTATGCA
* *
5589252 TTTTTATTTTTATCCTTGTTATT
1 TTTTTATTTTTATCATTGGTATT
5589275 TTTTTATTATTTAT-ATTGGTATT
1 TTTTTATT-TTTATCATTGGTATT
5589298 ATGGTAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.17, C:0.04, G:0.07, T:0.72
Consensus pattern (23 bp):
TTTTTATTTTTATCATTGGTATT
Found at i:5602806 original size:30 final size:30
Alignment explanation
Indices: 5602772--5602832 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
5602762 TTTACAGTTA
5602772 TATTTAATATAATATAAATAATTATTTATT
1 TATTTAATATAATATAAATAATTATTTATT
* * *
5602802 TATTTAATATTATATAATTTATTATTTATT
1 TATTTAATATAATATAAATAATTATTTATT
5602832 T
1 T
5602833 CATCATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TATTTAATATAATATAAATAATTATTTATT
Found at i:5602841 original size:26 final size:26
Alignment explanation
Indices: 5602772--5602832 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
5602762 TTTACAGTTA
* *
5602772 TATTTAATATAATA-TAAATAATTATT
1 TATTT-ATTTAATATTATATAATTATT
5602798 TATTTATTTAATATTATATAATT-TAT
1 TATTTATTTAATATTATATAATTAT-T
5602824 TATTTATTT
1 TATTTATTT
5602833 CATCATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 8 0.26
26 23 0.74
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TATTTATTTAATATTATATAATTATT
Found at i:5604851 original size:16 final size:16
Alignment explanation
Indices: 5604830--5604860 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5604820 AACATTATGA
*
5604830 TTAATGGCAGACAATT
1 TTAATGGCAAACAATT
5604846 TTAATGGCAAACAAT
1 TTAATGGCAAACAAT
5604861 CCAAGTGGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (16 bp):
TTAATGGCAAACAATT
Found at i:5607674 original size:21 final size:21
Alignment explanation
Indices: 5607648--5607688 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5607638 AGACGAGCGA
* *
5607648 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
5607669 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
5607689 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:5609624 original size:16 final size:16
Alignment explanation
Indices: 5609603--5609633 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5609593 AACATTATGA
*
5609603 TTAATGGCAGACAATT
1 TTAATGGCAAACAATT
5609619 TTAATGGCAAACAAT
1 TTAATGGCAAACAAT
5609634 CCAAGTGGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (16 bp):
TTAATGGCAAACAATT
Found at i:5614024 original size:20 final size:20
Alignment explanation
Indices: 5613982--5614025 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5613972 GTATGTTTTT
*
5613982 AAAA-TTAAATTTTGACATG
1 AAAATTTAAATTTTGACATA
* *
5614001 AAAATTTAATTTTTGATATA
1 AAAATTTAAATTTTGACATA
5614021 AAAAT
1 AAAAT
5614026 ATTTTTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (20 bp):
AAAATTTAAATTTTGACATA
Found at i:5614561 original size:20 final size:20
Alignment explanation
Indices: 5614510--5614576 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
5614500 CCTGATTTTG
5614510 AAATTATGAGGGAA-CATCAAA
1 AAATTATGA-GGAAGCAT-AAA
* *
5614531 AAA-AATAAGGAAGCATAAA
1 AAATTATGAGGAAGCATAAA
*
5614550 AAATTATGAGGATGCATAAA
1 AAATTATGAGGAAGCATAAA
*
5614570 AATTTAT
1 AAATTAT
5614577 AAGGGAATAC
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
19 10 0.26
20 25 0.66
21 3 0.08
ACGTcount: A:0.55, C:0.06, G:0.16, T:0.22
Consensus pattern (20 bp):
AAATTATGAGGAAGCATAAA
Found at i:5617653 original size:18 final size:17
Alignment explanation
Indices: 5617617--5617749 Score: 194
Period size: 18 Copynumber: 7.5 Consensus size: 17
5617607 AATCATATCT
5617617 TCTAAGATTGTATATCATA
1 TCTAAGATTG-A-ATCATA
5617636 TCTAAGATTGCAATCATA
1 TCTAAGATTG-AATCATA
*
5617654 TCTAAGATTGTATCATA
1 TCTAAGATTGAATCATA
5617671 TCTAAGATTGCAATCATA
1 TCTAAGATTG-AATCATA
*
5617689 TCTAAGATTGTATCATA
1 TCTAAGATTGAATCATA
5617706 TCTAAGATTGCAATCATA
1 TCTAAGATTG-AATCATA
*
5617724 TCTAAGATTGTATCATA
1 TCTAAGATTGAATCATA
5617741 TCTAAGATT
1 TCTAAGATT
5617750 ACATATCATT
Statistics
Matches: 106, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
17 47 0.44
18 48 0.45
19 11 0.10
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (17 bp):
TCTAAGATTGAATCATA
Found at i:5617675 original size:35 final size:35
Alignment explanation
Indices: 5617617--5617758 Score: 248
Period size: 35 Copynumber: 4.0 Consensus size: 35
5617607 AATCATATCT
5617617 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
5617654 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
5617689 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
*
5617724 TCTAAGATTGTATCATATCTAAGATTACATATCAT
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCAT
5617759 TGAAGATTAT
Statistics
Matches: 103, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
35 88 0.85
36 5 0.05
37 10 0.10
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:5618301 original size:83 final size:83
Alignment explanation
Indices: 5618112--5618463 Score: 582
Period size: 83 Copynumber: 4.2 Consensus size: 83
5618102 CTTCATTTGT
* *
5618112 AAGGATGTCAAATCATCTTGAGTCTG-TTGAGAACATTTGAGAA-TCATATCTGCAAGGTCCTCG
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGA-AAGTCATATCTGCAAGGTCCTCG
*
5618175 ACTTGTTCCTTGTAAGCAC
65 ATTTGTTCCTTGTAAGCAC
* * *
5618194 AAGGATGCCTAAACCATCTTGAGTCTGTTTGAGAACATTTGAAAGTAATGTCTGCAAGGTCCTCA
1 AAGGATGCC-AAACCATCTTGAGTCTGTTTGAGAACATTTGAAAGTCATATCTGCAAGGTCCTCG
5618259 ATTTGTTCCTTGTAAGCAC
65 ATTTGTTCCTTGTAAGCAC
* *
5618278 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAAAGTCATATCTGCAAGGTCCTCGA
5618343 TTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
* *
5618361 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGA
1 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAAAGTCATATCTGCAAGGTCCTCGA
5618426 TTTGTTCCTTGTAAGCAC
66 TTTGTTCCTTGTAAGCAC
5618444 AAGGATGCCAAACCATCTTG
1 AAGGATGCCAAACCATCTTG
5618464 GATCTGCTTC
Statistics
Matches: 256, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
82 8 0.03
83 190 0.74
84 58 0.23
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (83 bp):
AAGGATGCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAAAGTCATATCTGCAAGGTCCTCGA
TTTGTTCCTTGTAAGCAC
Found at i:5618782 original size:119 final size:119
Alignment explanation
Indices: 5618387--5618976 Score: 1017
Period size: 119 Copynumber: 5.0 Consensus size: 119
5618377 CTTGAGTCTG
* * * * * *
5618387 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
*
5618452 CAAACCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
* *
5618506 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
*
5618571 CAAATCATCTTGGAT-TGCTTCAGTATAAACATCTGAAGGTTAGAT-TGTTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
* *
5618623 TTT-AGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTATAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
5618687 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
5618741 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
*
5618806 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATC
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
*
5618860 TTTGAGAACGTCTGAGAGTCAAATCTACTATGTCCTCGATTT-TTCCTTGTAAACACAAGAATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
*
5618924 CAAATCATCTTGGATCTACTTCAGTATAAACATCTGAAGGTTAGATCTGCTAT
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTAT
5618977 CTTCGATCTG
Statistics
Matches: 450, Mismatches: 18, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
116 74 0.16
117 39 0.09
118 113 0.25
119 224 0.50
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (119 bp):
TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
Found at i:5618811 original size:235 final size:238
Alignment explanation
Indices: 5618387--5618976 Score: 1017
Period size: 235 Copynumber: 2.5 Consensus size: 238
5618377 CTTGAGTCTG
* * * * * *
5618387 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
*
5618452 CAAACCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAACGT
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAACGT
*
5618517 CTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATACCAAATCATCTT
131 CTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACCAAATCATCTT
*
5618582 GGAT-TGCTTCAGTATAAACATCTGAAGGTTAGAT-TGTTATA
196 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
* *
5618623 TTT-AGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTATAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
5618687 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAACGT
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAACGT
*
5618752 CTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTT
131 CTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACCAAATCATCTT
*
5618817 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATC
196 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
*
5618860 TTTGAGAACGTCTGAGAGTCAAATCTACTATGTCCTCGATTT-TTCCTTGTAAACACAAGAATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
*
5618924 CAAATCATCTTGGATCTACTTCAGTATAAACATCTGAAGGTTAGATCTGCTAT
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTAT
5618977 CTTCGATCTG
Statistics
Matches: 334, Mismatches: 17, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
235 184 0.55
236 33 0.10
237 80 0.24
238 37 0.11
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (238 bp):
TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAACGT
CTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACCAAATCATCTT
GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
Found at i:5619016 original size:44 final size:44
Alignment explanation
Indices: 5618968--5619146 Score: 186
Period size: 44 Copynumber: 4.1 Consensus size: 44
5618958 TGAAGGTTAG
5618968 ATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAA
1 ATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAA
*
5619012 ATCTGCTATCTTC-AACTTGTTCCCTATAAACACAGGGATGCC--
1 ATCTGCTATCTTCGATC-TGTTCCCTATAAACACAGGGATGCCAA
** * * * * * * *
5619054 ATGCTGAAATCTTCAATCTGCTTCGCTGTAAGCACAGGAATGTCAG
1 AT-CTGCTATCTTCGATCTG-TTCCCTATAAACACAGGGATGCCAA
* * *
5619100 ATCTACTATCTTTGATCTGTTCCCTATAAACATA-GGATGCCAA
1 ATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAA
5619143 ATCT
1 ATCT
5619147 TGTTTCTTTG
Statistics
Matches: 108, Mismatches: 21, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
42 2 0.02
43 23 0.21
44 69 0.64
45 12 0.11
46 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (44 bp):
ATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGCCAA
Found at i:5620029 original size:21 final size:21
Alignment explanation
Indices: 5620005--5620046 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5619995 TCACCTTGGC
5620005 CTCTCCATTTTTTTCTTTTTT
1 CTCTCCATTTTTTTCTTTTTT
**
5620026 CTCTTTATTTTTTTCTTTTTT
1 CTCTCCATTTTTTTCTTTTTT
5620047 TTTCTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (21 bp):
CTCTCCATTTTTTTCTTTTTT
Found at i:5620030 original size:9 final size:8
Alignment explanation
Indices: 5620012--5620061 Score: 52
Period size: 7 Copynumber: 6.5 Consensus size: 8
5620002 GGCCTCTCCA
5620012 TTTTTTTC
1 TTTTTTTC
5620020 TTTTTTCTC
1 TTTTTT-TC
*
5620029 TTTATTT-
1 TTTTTTTC
*
5620036 TTTTCTT-
1 TTTTTTTC
5620043 TTTTTTTC
1 TTTTTTTC
5620051 TTTTTTT-
1 TTTTTTTC
5620058 TTTT
1 TTTT
5620062 GAAATAGAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
7 15 0.42
8 14 0.39
9 7 0.19
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTC
Found at i:5620037 original size:22 final size:21
Alignment explanation
Indices: 5620012--5620060 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
5620002 GGCCTCTCCA
5620012 TTTTTTTC-TTTTTTCTCTTT
1 TTTTTTTCTTTTTTTCTCTTT
*
5620032 ATTTTTTTCTTTTTTTTTCTTT
1 -TTTTTTTCTTTTTTTCTCTTT
5620054 TTTTTTT
1 TTTTTTT
5620061 TGAAATAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (21 bp):
TTTTTTTCTTTTTTTCTCTTT
Found at i:5620061 original size:22 final size:21
Alignment explanation
Indices: 5620011--5620061 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 21
5620001 TGGCCTCTCC
5620011 ATTTTTTTCTTTTTTCTCTTT
1 ATTTTTTTCTTTTTTCTCTTT
*
5620032 ATTTTTTTCTTTTTTTTTCTTT
1 ATTTTTTTC-TTTTTTCTCTTT
*
5620054 TTTTTTTT
1 ATTTTTTT
5620062 GAAATAGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.86
Consensus pattern (21 bp):
ATTTTTTTCTTTTTTCTCTTT
Found at i:5621546 original size:10 final size:10
Alignment explanation
Indices: 5621531--5621555 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5621521 TATATATATC
5621531 TTTTTTTCTT
1 TTTTTTTCTT
5621541 TTTTTTTCTT
1 TTTTTTTCTT
5621551 TTTTT
1 TTTTT
5621556 GAAATAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:5626409 original size:18 final size:18
Alignment explanation
Indices: 5626373--5626505 Score: 218
Period size: 18 Copynumber: 7.5 Consensus size: 18
5626363 AATCATATCT
5626373 TCTAAGATTGTATATCATA
1 TCTAAGATTGTA-ATCATA
5626392 TCTAAGATTGTAATCATA
1 TCTAAGATTGTAATCATA
5626410 TCTAAGATTGT-ATCATA
1 TCTAAGATTGTAATCATA
*
5626427 TCTAAGATTGCAATCATA
1 TCTAAGATTGTAATCATA
5626445 TCTAAGATTGT-ATCATA
1 TCTAAGATTGTAATCATA
*
5626462 TCTAAGATTGCAATCATA
1 TCTAAGATTGTAATCATA
5626480 TCTAAGATTGT-ATCATA
1 TCTAAGATTGTAATCATA
5626497 TCTAAGATT
1 TCTAAGATT
5626506 ACATATCATT
Statistics
Matches: 108, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
17 47 0.44
18 49 0.45
19 12 0.11
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (18 bp):
TCTAAGATTGTAATCATA
Found at i:5626431 original size:35 final size:35
Alignment explanation
Indices: 5626373--5626514 Score: 239
Period size: 35 Copynumber: 4.0 Consensus size: 35
5626363 AATCATATCT
*
5626373 TCTAAGATTGTATATCATATCTAAGATTGTAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
5626410 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
5626445 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
*
5626480 TCTAAGATTGTATCATATCTAAGATTACATATCAT
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCAT
5626515 TGAAGATTAT
Statistics
Matches: 102, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
35 87 0.85
36 5 0.05
37 10 0.10
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:5629345 original size:254 final size:254
Alignment explanation
Indices: 5629014--5629520 Score: 852
Period size: 254 Copynumber: 2.0 Consensus size: 254
5629004 CCCAAAAATA
* *
5629014 AGTCATTCTCTTTGTGTAATGCTTGTGAGTTTGGTAAAAGCCACAAACTGCCATATATGTCCATT
1 AGTCATTCTCTTTGTGTAATGCTTGTGAGCTTGGCAAAAGCCACAAACTGCCATATATGTCCATT
* * * * * *
5629079 AAATCAGTGTACTTTGCTCCTCTTGAGTTCATTTTTATTAACTTATGGGGTTTGGCCTCTTGTTA
66 AAATCAGTGTACTATGCTCCTCTTGAGTTCATTGTTACTAACTTATGGGGTCTAGCCCCTTGTTA
* *
5629144 CTTTTCAGGCTATCAATACTATATCTCCTTTGTGGATACATTTTTAATTCATACTTGGATTAATT
131 CTCTTCAAGCTATCAATACTATATCTCCTTTGTGGATACATTTTTAATTCATACTTGGATTAATT
* *
5629209 TTCTTAAGCAAAAGTTTGATGCATTGCAAGCCTTTTTGTCTTTCAAAACACATGTTGAT
196 TTCTTAAGAAAAAGTTTGATGCATTGCAAGCCTTATTGTCTTTCAAAACACATGTTGAT
*
5629268 AGTCATTCTCTTTGTGTAATGCTTGTGAGCTTGGCAAAAGCCACAAACTGCCATTTATGTCCATT
1 AGTCATTCTCTTTGTGTAATGCTTGTGAGCTTGGCAAAAGCCACAAACTGCCATATATGTCCATT
* *
5629333 AAATCAGTGTACTATGCTCCTCTTGAGTTCATTGTTACTGACTTGTGGGGTCTAGCCCCTTGTTA
66 AAATCAGTGTACTATGCTCCTCTTGAGTTCATTGTTACTAACTTATGGGGTCTAGCCCCTTGTTA
* *
5629398 CTCTTCAAGCTATTAATACTATATCTCCTTTGTGGATGCATTTTTAATTCATACTTGGATTAATT
131 CTCTTCAAGCTATCAATACTATATCTCCTTTGTGGATACATTTTTAATTCATACTTGGATTAATT
*
5629463 TTCTTAAGAAAAAGTTTGATGCATTGCAAGCCTTATTGTGTTTCAAAACACATGTTGA
196 TTCTTAAGAAAAAGTTTGATGCATTGCAAGCCTTATTGTCTTTCAAAACACATGTTGA
5629521 ACTACAGTTG
Statistics
Matches: 235, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
254 235 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (254 bp):
AGTCATTCTCTTTGTGTAATGCTTGTGAGCTTGGCAAAAGCCACAAACTGCCATATATGTCCATT
AAATCAGTGTACTATGCTCCTCTTGAGTTCATTGTTACTAACTTATGGGGTCTAGCCCCTTGTTA
CTCTTCAAGCTATCAATACTATATCTCCTTTGTGGATACATTTTTAATTCATACTTGGATTAATT
TTCTTAAGAAAAAGTTTGATGCATTGCAAGCCTTATTGTCTTTCAAAACACATGTTGAT
Found at i:5638365 original size:26 final size:25
Alignment explanation
Indices: 5638326--5638435 Score: 157
Period size: 26 Copynumber: 4.2 Consensus size: 25
5638316 TGATACAAAT
5638326 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAAT-GGTTAGGTAAATGTTCCA
*
5638352 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGG-TTAGGTAAATGTTCCA
*
5638378 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAAT-GGTTAGGTAAATGTTCCA
*
5638404 TGATAATGGTTTAGGTAAATGTTTCA
1 TGATAATGG-TTAGGTAAATGTTCCA
5638430 TGATAA
1 TGATAA
5638436 GAATTTCATG
Statistics
Matches: 78, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
25 4 0.05
26 72 0.92
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (25 bp):
TGATAATGGTTAGGTAAATGTTCCA
Found at i:5638383 original size:52 final size:52
Alignment explanation
Indices: 5638326--5638435 Score: 175
Period size: 52 Copynumber: 2.1 Consensus size: 52
5638316 TGATACAAAT
5638326 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
* * * * *
5638378 TGATAATGGGTTAGGTAAATGTTTCATGATAATGGTTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
5638430 TGATAA
1 TGATAA
5638436 GAATTTCATG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (52 bp):
TGATAATAGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
Found at i:5641652 original size:12 final size:12
Alignment explanation
Indices: 5641635--5641677 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
5641625 ACTCGGGGAA
*
5641635 GAGGCCATGGTC
1 GAGGCCGTGGTC
5641647 GAGGCCGTGGTC
1 GAGGCCGTGGTC
5641659 GAGGCCGTGGTC
1 GAGGCCGTGGTC
5641671 GAGGCCG
1 GAGGCCG
5641678 AGGTAGTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.12, C:0.26, G:0.49, T:0.14
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:5646649 original size:25 final size:26
Alignment explanation
Indices: 5646555--5646663 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
5646545 TGATACAAAT
5646555 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
5646581 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
5646607 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
5646633 TGATAAT-GGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5646658 TGATAA
1 TGATAA
5646664 GAATTTCATG
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 24 0.31
26 54 0.69
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:5656103 original size:12 final size:13
Alignment explanation
Indices: 5656068--5656108 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
5656058 ATTATGAGTA
*
5656068 GTTA-CCATTTCT
1 GTTATCCATTTTT
*
5656080 ATTATCCATTTTT
1 GTTATCCATTTTT
5656093 GTTAT-CATTTTT
1 GTTATCCATTTTT
5656105 GTTA
1 GTTA
5656109 AGCCTCTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.59
Consensus pattern (13 bp):
GTTATCCATTTTT
Found at i:5658474 original size:37 final size:37
Alignment explanation
Indices: 5658376--5658489 Score: 135
Period size: 37 Copynumber: 3.1 Consensus size: 37
5658366 ACATTCGTGT
* * *
5658376 TGTTATCGGGTGGATTAGCTCTTATAAGCGATT-GCTA
1 TGTTATCCGGTGGATTAGCTCTTATGAGCGATTGGC-G
*
5658413 TGTT-T-CGGTTGGATTAGCTCTTATGAGCGTTTGGCG
1 TGTTATCCGG-TGGATTAGCTCTTATGAGCGATTGGCG
* *
5658449 TGTTATCCGGTAGATTAGCTCTTATGAGTGATTGGCG
1 TGTTATCCGGTGGATTAGCTCTTATGAGCGATTGGCG
5658486 TGTT
1 TGTT
5658490 TCAATTGGAT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
35 2 0.03
36 26 0.39
37 35 0.53
38 3 0.05
ACGTcount: A:0.17, C:0.13, G:0.30, T:0.40
Consensus pattern (37 bp):
TGTTATCCGGTGGATTAGCTCTTATGAGCGATTGGCG
Found at i:5658565 original size:18 final size:18
Alignment explanation
Indices: 5658542--5658577 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5658532 CAGGTCATAA
5658542 ATCATTATAGTATAACCT
1 ATCATTATAGTATAACCT
*
5658560 ATCATTGTAGTATAACCT
1 ATCATTATAGTATAACCT
5658578 GTTTAATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (18 bp):
ATCATTATAGTATAACCT
Found at i:5661856 original size:11 final size:11
Alignment explanation
Indices: 5661840--5661874 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
5661830 GTGCAAAATA
5661840 TTATTATATTT
1 TTATTATATTT
5661851 TTATTATTATTT
1 TTATTA-TATTT
5661863 TATATTATATTT
1 T-TATTATATTT
5661875 CCTTATATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.27
12 11 0.50
13 5 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTATATTT
Found at i:5661907 original size:26 final size:24
Alignment explanation
Indices: 5661841--5661908 Score: 59
Period size: 26 Copynumber: 2.7 Consensus size: 24
5661831 TGCAAAATAT
*
5661841 TATTATATTTT-TATTATTATTTTA
1 TATTATATTTTATA-TATTATTTCA
*
5661865 TATTATATTTCCT-TATATTCTATTCA
1 TATTATATTT--TATATATTAT-TTCA
5661891 TATTATATTATTATATAT
1 TATTATATT-TTATATAT
5661909 AACTTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
24 10 0.27
25 6 0.16
26 20 0.54
27 1 0.03
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (24 bp):
TATTATATTTTATATATTATTTCA
Found at i:5665020 original size:17 final size:17
Alignment explanation
Indices: 5664998--5665032 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5664988 TTATATCAAT
5664998 GTAAGTTTATATAAAAG
1 GTAAGTTTATATAAAAG
5665015 GTAAGTTTATATAAAAG
1 GTAAGTTTATATAAAAG
5665032 G
1 G
5665033 AAGATTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (17 bp):
GTAAGTTTATATAAAAG
Found at i:5665796 original size:15 final size:14
Alignment explanation
Indices: 5665776--5665831 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
5665766 TTTGATAAAG
5665776 TGAAAAATTAAGTGT
1 TGAAAAATTAAGT-T
*
5665791 TG-AAAATTGAAGTA
1 TGAAAAATT-AAGTT
5665805 TGAAAAATTAAGTAT
1 TGAAAAATTAAGT-T
*
5665820 TGAAAAACTAAG
1 TGAAAAATTAAG
5665832 GGTGTGTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
14 12 0.34
15 23 0.66
ACGTcount: A:0.52, C:0.02, G:0.18, T:0.29
Consensus pattern (14 bp):
TGAAAAATTAAGTT
Found at i:5668388 original size:13 final size:13
Alignment explanation
Indices: 5668372--5668410 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
5668362 CTAAATACTA
5668372 AAAAATAATAAAT
1 AAAAATAATAAAT
*
5668385 -AAAATTA-AAAT
1 AAAAATAATAAAT
5668396 AAAAATAATAAAT
1 AAAAATAATAAAT
5668409 AA
1 AA
5668411 TAAAAAACGG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 4 0.18
12 12 0.55
13 6 0.27
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAATAATAAAT
Found at i:5669703 original size:73 final size:73
Alignment explanation
Indices: 5669620--5669852 Score: 322
Period size: 73 Copynumber: 3.2 Consensus size: 73
5669610 ATTTCATCTT
* *
5669620 TTATATTTGTTTTATCGATTTATTTATTCGTTTATTATTCTTTTACTTTTTAAACACTTAAATTT
1 TTATATTTGTTTTATCGATTTATTTATTTGTTTATTATTCTTTTACTTTTTAAATACTTAAATTT
*
5669685 AATATTAT
66 AATATTAC
* *
5669693 TTATATTTGTTTTATCGATTTATTTATTTGTTTAATATTCTTTTACTTCTTAAATACTTAAATTT
1 TTATATTTGTTTTATCGATTTATTTATTTGTTTATTATTCTTTTACTTTTTAAATACTTAAATTT
5669758 AATATTAC
66 AATATTAC
* *** * * * *
5669766 GTATATCAATTTTATCTATCTATTTATTTATTTATTATTCTTTTACTTTTTAAATATTTAAATTT
1 TTATATTTGTTTTATCGATTTATTTATTTGTTTATTATTCTTTTACTTTTTAAATACTTAAATTT
*
5669831 GATATTAC
66 AATATTAC
*
5669839 TTATACTTTCTTTT
1 TTATA-TTTGTTTT
5669853 CATTAAGCAC
Statistics
Matches: 139, Mismatches: 20, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
73 134 0.96
74 5 0.04
ACGTcount: A:0.28, C:0.09, G:0.03, T:0.60
Consensus pattern (73 bp):
TTATATTTGTTTTATCGATTTATTTATTTGTTTATTATTCTTTTACTTTTTAAATACTTAAATTT
AATATTAC
Found at i:5675000 original size:29 final size:29
Alignment explanation
Indices: 5674945--5675003 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5674935 ACTTGTCCAC
* ***
5674945 TTATCCCAGATTGGTACTTATGGTTTTTT
1 TTATCCCAGATTGGTACCTAAACTTTTTT
*
5674974 TTATCCTAGATTGGTACCTAAACTTTTTT
1 TTATCCCAGATTGGTACCTAAACTTTTTT
5675003 T
1 T
5675004 CCTCCACTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.20, C:0.15, G:0.14, T:0.51
Consensus pattern (29 bp):
TTATCCCAGATTGGTACCTAAACTTTTTT
Found at i:5676389 original size:59 final size:61
Alignment explanation
Indices: 5676314--5676428 Score: 171
Period size: 62 Copynumber: 1.9 Consensus size: 61
5676304 TATTTCACCC
* * * *
5676314 TTAAATTAATATAATATTTA-T-CAAGATAAATATTAGATTAAATTTAATCTTAAATCTTA
1 TTAAATTAATAAAATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAATCTTA
5676373 TTAAATTAATAAAATATTTATCTACAAGATAAACATTAAATTAAATTTAATATTAA
1 TTAAATTAATAAAATATTTA-CTACAAGATAAACATTAAATTAAATTTAATATTAA
5676429 GATAATCACT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 19 0.39
61 1 0.02
62 29 0.59
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (61 bp):
TTAAATTAATAAAATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAATCTTA
Found at i:5676482 original size:17 final size:17
Alignment explanation
Indices: 5676407--5676484 Score: 70
Period size: 17 Copynumber: 4.4 Consensus size: 17
5676397 CAAGATAAAC
5676407 ATTAAATTAAATTTAAT
1 ATTAAATTAAATTTAAT
5676424 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAA--A-TTTAAT
* **
5676444 ATT-AATTTAATAAAAT
1 ATTAAATTAAATTTAAT
5676460 ACTTAAATTAAATTTAAT
1 A-TTAAATTAAATTTAAT
5676478 ATTAAAT
1 ATTAAAT
5676485 CTATTAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
16 5 0.10
17 17 0.35
18 13 0.27
19 4 0.08
20 9 0.19
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (17 bp):
ATTAAATTAAATTTAAT
Found at i:5678838 original size:23 final size:23
Alignment explanation
Indices: 5678812--5678855 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5678802 TAATTAAACC
* * *
5678812 TTAATTTACTTAATTAATCATGT
1 TTAATTAAATTAAGTAATCATGT
5678835 TTAATTAAATTAAGTAATCAT
1 TTAATTAAATTAAGTAATCAT
5678856 TAATAATACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (23 bp):
TTAATTAAATTAAGTAATCATGT
Found at i:5681330 original size:27 final size:26
Alignment explanation
Indices: 5681298--5681382 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 26
5681288 TTTTCATCCC
5681298 AATTTTTTGACAATTTTACCCCAGTAA
1 AATTTTTTGACAATTTTACCCC-GTAA
5681325 AA--TTTTGACAATTTTACCCTCG-ATA
1 AATTTTTTGACAATTTTACCC-CGTA-A
** *
5681350 AATTTTTTGATGATTTTACTCTCGGTAA
1 AATTTTTTGACAATTTTAC-C-CCGTAA
5681378 AATTT
1 AATTT
5681383 CAAAAACATT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
24 1 0.02
25 21 0.44
26 1 0.02
27 15 0.31
28 8 0.17
29 2 0.04
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (26 bp):
AATTTTTTGACAATTTTACCCCGTAA
Found at i:5687552 original size:20 final size:20
Alignment explanation
Indices: 5687527--5687575 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
5687517 CGACTAATAT
5687527 GAGTGTCGATGACATCTTTG
1 GAGTGTCGATGACATCTTTG
5687547 GAGTGTCGATGACATCTTTG
1 GAGTGTCGATGACATCTTTG
5687567 GAGTGTCGA
1 GAGTGTCGA
5687576 AGAGGCCGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.14, G:0.33, T:0.33
Consensus pattern (20 bp):
GAGTGTCGATGACATCTTTG
Found at i:5689397 original size:39 final size:39
Alignment explanation
Indices: 5689354--5689531 Score: 194
Period size: 39 Copynumber: 4.5 Consensus size: 39
5689344 CTTCGGAACT
* *
5689354 TTAAGCCCGGATATATTTCCAGCACGCAACCTGCGGACC
1 TTAAGTCCGGATATATTTCCAGCACACAACCTGCGGACC
* * * * * **
5689393 TTAAGTCCGGATTATAATTCCATCATATAGCCTGCAAACC
1 TTAAGTCCGGA-TATATTTCCAGCACACAACCTGCGGACC
* *
5689433 TTAAGTCCGGATATATTTTCAGCACGCAACCTGCGGACC
1 TTAAGTCCGGATATATTTCCAGCACACAACCTGCGGACC
* * * * * *
5689472 TTAAGTCCAGATATATTTCCAGCATATAGCTTACGGACC
1 TTAAGTCCGGATATATTTCCAGCACACAACCTGCGGACC
5689511 TTAAGTCCGGATATATTTCCA
1 TTAAGTCCGGATATATTTCCA
5689532 AATATCATGC
Statistics
Matches: 111, Mismatches: 27, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
39 80 0.72
40 31 0.28
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (39 bp):
TTAAGTCCGGATATATTTCCAGCACACAACCTGCGGACC
Found at i:5697148 original size:39 final size:39
Alignment explanation
Indices: 5697105--5697321 Score: 254
Period size: 39 Copynumber: 5.5 Consensus size: 39
5697095 CTTCGGAACT
* *** *
5697105 TTAAGCCCGGATATATTTCCAGCACGCAACCTGCGGACC
1 TTAAGTCCGGATATATTTCCAGCATATAGCCTGCGGACC
* * * **
5697144 TTAAGTCCGGATTATAATTCAAGCATATAGCCTCCAAACC
1 TTAAGTCCGGA-TATATTTCCAGCATATAGCCTGCGGACC
* *** * **
5697184 TTAAGTCCGGATATATTTTCAGCACGCAACCTGTTGACC
1 TTAAGTCCGGATATATTTCCAGCATATAGCCTGCGGACC
* *
5697223 TTAAGTCCGGATATATTTCCAGCATATAGCTTACGGACC
1 TTAAGTCCGGATATATTTCCAGCATATAGCCTGCGGACC
5697262 TTAAGTCCGGATATATTTCCAGCATATAGCCTGCGGACC
1 TTAAGTCCGGATATATTTCCAGCATATAGCCTGCGGACC
5697301 TTAAGTCCGGATATATTTCCA
1 TTAAGTCCGGATATATTTCCA
5697322 AATATCATGC
Statistics
Matches: 145, Mismatches: 32, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
39 115 0.79
40 30 0.21
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (39 bp):
TTAAGTCCGGATATATTTCCAGCATATAGCCTGCGGACC
Found at i:5697285 original size:78 final size:78
Alignment explanation
Indices: 5697105--5697321 Score: 299
Period size: 78 Copynumber: 2.8 Consensus size: 78
5697095 CTTCGGAACT
* * *
5697105 TTAAGCCCGGATATATTTCCAGCACGCAACCTGCGGACCTTAAGTCCGGATTATAATTCAAGCAT
1 TTAAGTCCGGATATATTTCCAGCACGCAACCTGCGGACCTTAAGTCCGGA-TATATTTCCAGCAT
*
5697170 ATAGCCTCCAAACC
65 ATAGCCTACAAACC
* **
5697184 TTAAGTCCGGATATATTTTCAGCACGCAACCTGTTGACCTTAAGTCCGGATATATTTCCAGCATA
1 TTAAGTCCGGATATATTTCCAGCACGCAACCTGCGGACCTTAAGTCCGGATATATTTCCAGCATA
* **
5697249 TAGCTTACGGACC
66 TAGCCTACAAACC
*** *
5697262 TTAAGTCCGGATATATTTCCAGCATATAGCCTGCGGACCTTAAGTCCGGATATATTTCCA
1 TTAAGTCCGGATATATTTCCAGCACGCAACCTGCGGACCTTAAGTCCGGATATATTTCCA
5697322 AATATCATGC
Statistics
Matches: 121, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
78 75 0.62
79 46 0.38
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (78 bp):
TTAAGTCCGGATATATTTCCAGCACGCAACCTGCGGACCTTAAGTCCGGATATATTTCCAGCATA
TAGCCTACAAACC
Found at i:5705055 original size:13 final size:13
Alignment explanation
Indices: 5705039--5705071 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5705029 TTTAATTAAA
*
5705039 TTAGTTAATTAGT
1 TTAGATAATTAGT
5705052 TTAGATAATTAGT
1 TTAGATAATTAGT
5705065 TTA-ATAA
1 TTAGATAA
5705072 AAAAAACCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:5710407 original size:6 final size:6
Alignment explanation
Indices: 5710396--5710448 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
5710386 TCCTCTTATC
* * *
5710396 TTTTTA TTTTTA TTTCTC TTTTTA TTTTTA TTTTTA TTTTTA TGTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
5710444 TTTTT
1 TTTTT
5710449 CGTTATAAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:5713362 original size:13 final size:13
Alignment explanation
Indices: 5713346--5713378 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5713336 TTTAATTAAA
*
5713346 TTAGTTAATTAGT
1 TTAGATAATTAGT
5713359 TTAGATAATTAGT
1 TTAGATAATTAGT
5713372 TTA-ATAA
1 TTAGATAA
5713379 ACAAACCCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:5716794 original size:73 final size:74
Alignment explanation
Indices: 5716656--5716837 Score: 289
Period size: 71 Copynumber: 2.5 Consensus size: 74
5716646 TGTTTTGAAA
* *
5716656 ATATGTGTAAAAATATTAGTAATTTTTCAAAAAA-ATTAGTTATTCTTTAAATGACGTTGTTATT
1 ATATGTGTAAAAATATTAGTAATTCTTCAAAAAATATTAGTAATTCTTTAAATGACGTTGTTATT
5716720 GA-TTTGTT
66 GATTTTGTT
*
5716728 -TATGTGTAAAAATATTAGTAATTCTTCAAAACAATATTAGTAATTCTTTAAATTACGTTGTTAT
1 ATATGTGTAAAAATATTAGTAATTCTTCAAAA-AATATTAGTAATTCTTTAAATGACGTTGTTAT
*
5716792 TGATTTTTTT
65 TGATTTTGTT
*
5716802 ATATGTATAAAAATATTAGTAATTCTTCAAAAAATA
1 ATATGTGTAAAAATATTAGTAATTCTTCAAAAAATA
5716838 ACAAAACGGT
Statistics
Matches: 101, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
71 30 0.30
72 2 0.02
73 30 0.30
74 9 0.09
75 30 0.30
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (74 bp):
ATATGTGTAAAAATATTAGTAATTCTTCAAAAAATATTAGTAATTCTTTAAATGACGTTGTTATT
GATTTTGTT
Found at i:5724698 original size:5 final size:6
Alignment explanation
Indices: 5724683--5724723 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
5724673 AGTTATATGC
*
5724683 TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
5724724 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 22 0.71
7 8 0.26
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:5724764 original size:13 final size:13
Alignment explanation
Indices: 5724748--5724772 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5724738 AATTTTTATG
5724748 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
5724761 ATTGGGTTGGGT
1 ATTGGGTTGGGT
5724773 TGGGTACTTG
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:5724772 original size:18 final size:18
Alignment explanation
Indices: 5724749--5724786 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
5724739 ATTTTTATGA
5724749 TTGGGTTGGGTAATTGGG
1 TTGGGTTGGGTAATTGGG
*
5724767 TTGGGTTGGGTACTTGGG
1 TTGGGTTGGGTAATTGGG
5724785 TT
1 TT
5724787 AATATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.03, G:0.47, T:0.42
Consensus pattern (18 bp):
TTGGGTTGGGTAATTGGG
Found at i:5726079 original size:29 final size:29
Alignment explanation
Indices: 5726047--5726104 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
5726037 GAATTTGATC
**
5726047 AAATAAAAAATCATGTATAAAATTACACA
1 AAATAAAAAATCACATATAAAATTACACA
* * *
5726076 AAATCAAAATTTACATATAAAATTACACA
1 AAATAAAAAATCACATATAAAATTACACA
5726105 TTAAACCAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (29 bp):
AAATAAAAAATCACATATAAAATTACACA
Found at i:5726118 original size:31 final size:29
Alignment explanation
Indices: 5726062--5726124 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 29
5726052 AAAAATCATG
*
5726062 TATAAAATTACACAAAATCAAAATTTACA
1 TATAAAATTACACAAAACCAAAATTTACA
*
5726091 TATAAAATTACACATTAAACCAAAATTTATA
1 TATAAAATTACACA--AAACCAAAATTTACA
5726122 TAT
1 TAT
5726125 TTTTTAAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 14 0.47
31 16 0.53
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (29 bp):
TATAAAATTACACAAAACCAAAATTTACA
Found at i:5726442 original size:27 final size:23
Alignment explanation
Indices: 5726385--5726429 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5726375 ATATATTGGT
* *
5726385 AATATTTTATAAATTTTATTAAA
1 AATATTATCTAAATTTTATTAAA
5726408 AATATTATCTAAATTTTATTAA
1 AATATTATCTAAATTTTATTAA
5726430 TTAATATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
AATATTATCTAAATTTTATTAAA
Found at i:5733030 original size:127 final size:127
Alignment explanation
Indices: 5732712--5733031 Score: 444
Period size: 128 Copynumber: 2.5 Consensus size: 127
5732702 AAAAATTCCT
*
5732712 TAAAACGAAGGCAATGTTTGATGTTTGGAAATTCGGGAAATTGTGCCCTACCGTGCTGGGTTTCG
1 TAAAAC-AAGGCAATGTTTGATGTTTGGAAATTCGGG-AATCGTGCCCTACCGTGCTGGGTTTCG
* * * * *
5732777 ATTTCCCGTTTGTTCAAAATAATCGAACCTTCCTTTAGAATTTCACTCGTGTTTTTCTAAATTC
64 ATTTCCCGTTTATTCAAAATAATCAAACATTCCTTTAGAATTTCACTCGTATTCTTCTAAATTC
* * * *
5732841 TAAAACAAGGCAATGTTTGATGCTTGGAAATTCGGGGAACCGTGCCCTATCGTGCTGTGTTTCGA
1 TAAAACAAGGCAATGTTTGATGTTTGGAAATTC-GGGAATCGTGCCCTACCGTGCTGGGTTTCGA
* * *
5732906 TTTCTCGTTTATTCAAAATAATCAAATATTCCTTTAGAATTTCATTCGTATTCTTC-AAATTC
65 TTTCCCGTTTATTCAAAATAATCAAACATTCCTTTAGAATTTCACTCGTATTCTTCTAAATTC
* ** *
5732968 TAAAACAAGGAAATGTTCAATGTTTGGAAGTTCGAGGAATCGTGCCCTACCGTGCTGGGTTTCG
1 TAAAACAAGGCAATGTTTGATGTTTGGAAATTCG-GGAATCGTGCCCTACCGTGCTGGGTTTCG
5733032 GTTTTTTGTT
Statistics
Matches: 168, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
126 1 0.01
127 60 0.36
128 98 0.58
129 9 0.05
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (127 bp):
TAAAACAAGGCAATGTTTGATGTTTGGAAATTCGGGAATCGTGCCCTACCGTGCTGGGTTTCGAT
TTCCCGTTTATTCAAAATAATCAAACATTCCTTTAGAATTTCACTCGTATTCTTCTAAATTC
Found at i:5733990 original size:19 final size:19
Alignment explanation
Indices: 5733962--5734040 Score: 56
Period size: 19 Copynumber: 4.2 Consensus size: 19
5733952 AATAAATATA
*
5733962 AAAATATTTAAAAACTATT
1 AAAATTTTTAAAAACTATT
*
5733981 AAAATTTTTAAGAA--ATT
1 AAAATTTTTAAAAACTATT
** ** *
5733998 ATGATTTTTTTAAATTATT
1 AAAATTTTTAAAAACTATT
5734017 AAAAATTATTT-AAAACTATT
1 -AAAATT-TTTAAAAACTATT
5734037 AAAA
1 AAAA
5734041 ACAATGTTAA
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
17 12 0.27
19 19 0.42
20 11 0.24
21 3 0.07
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (19 bp):
AAAATTTTTAAAAACTATT
Found at i:5734038 original size:20 final size:20
Alignment explanation
Indices: 5733960--5734041 Score: 59
Period size: 20 Copynumber: 4.3 Consensus size: 20
5733950 AAAATAAATA
5733960 TAAAAA-TATTTAAAAACTAT
1 TAAAAATTATTT-AAAACTAT
5733980 T-AAAATT-TTTAAGAA--AT
1 TAAAAATTATTTAA-AACTAT
** * * *
5733997 T-ATGATTTTTTTAAATTAT
1 TAAAAATTATTTAAAACTAT
5734016 TAAAAATTATTTAAAACTAT
1 TAAAAATTATTTAAAACTAT
5734036 TAAAAA
1 TAAAAA
5734042 CAATGTTAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
17 9 0.19
18 6 0.12
19 12 0.25
20 21 0.44
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
TAAAAATTATTTAAAACTAT
Found at i:5734337 original size:11 final size:10
Alignment explanation
Indices: 5734300--5734369 Score: 51
Period size: 10 Copynumber: 7.1 Consensus size: 10
5734290 ATCATTATTT
5734300 ATAATTCTTT-
1 ATAATT-TTTA
*
5734310 ATAATTCTTA
1 ATAATTTTTA
5734320 ATAATTTTTA
1 ATAATTTTTA
5734330 ATTAATTTCTT-
1 A-TAATTT-TTA
5734341 AT-A-TTTT-
1 ATAATTTTTA
*
5734348 ATAATTATTA
1 ATAATTTTTA
5734358 ATAATTATTTA
1 ATAATT-TTTA
5734369 A
1 A
5734370 GAAATTACTC
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
7 4 0.08
8 3 0.06
9 6 0.12
10 23 0.47
11 11 0.22
12 2 0.04
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:5734352 original size:21 final size:22
Alignment explanation
Indices: 5734314--5734354 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
5734304 TTCTTTATAA
5734314 TTCTTAATAATTTTTAATTAAT
1 TTCTTAATAATTTTTAATTAAT
5734336 TTCTT-AT-ATTTTATAATTA
1 TTCTTAATAATTTT-TAATTA
5734355 TTAATAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (22 bp):
TTCTTAATAATTTTTAATTAAT
Found at i:5738736 original size:30 final size:30
Alignment explanation
Indices: 5738696--5738781 Score: 147
Period size: 30 Copynumber: 2.9 Consensus size: 30
5738686 CACGGGCTAC
*
5738696 CACATCGGCGTGTGGCCAGCCCGTGTGGTT
1 CACATGGGCGTGTGGCCAGCCCGTGTGGTT
5738726 CACATGGGCGTGTGGCCAGCCCGTGTGGTT
1 CACATGGGCGTGTGGCCAGCCCGTGTGGTT
5738756 CACATGGGCGTGT-GCTCAGCCCGTGT
1 CACATGGGCGTGTGGC-CAGCCCGTGT
5738782 AGGATTGGCT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 2 0.04
30 52 0.96
ACGTcount: A:0.10, C:0.29, G:0.37, T:0.23
Consensus pattern (30 bp):
CACATGGGCGTGTGGCCAGCCCGTGTGGTT
Found at i:5738739 original size:17 final size:17
Alignment explanation
Indices: 5738717--5738769 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
5738707 GTGGCCAGCC
5738717 CGTGTGGTTCACATGGG
1 CGTGTGGTTCACATGGG
**
5738734 CGTGTGG--C-CA-GCC
1 CGTGTGGTTCACATGGG
5738747 CGTGTGGTTCACATGGG
1 CGTGTGGTTCACATGGG
5738764 CGTGTG
1 CGTGTG
5738770 CTCAGCCCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
13 8 0.29
14 2 0.07
15 2 0.07
16 2 0.07
17 14 0.50
ACGTcount: A:0.09, C:0.23, G:0.42, T:0.26
Consensus pattern (17 bp):
CGTGTGGTTCACATGGG
Found at i:5740630 original size:6 final size:6
Alignment explanation
Indices: 5740621--5740729 Score: 139
Period size: 6 Copynumber: 18.3 Consensus size: 6
5740611 GAAGTTTAAT
* * * * * * * *
5740621 AAAATA AAAATA AACAGA AAGATA AAGATA AAGATA AAGATA AAGATT
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
5740669 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
5740717 AAAAT- AAAATA AA
1 AAAATA AAAATA AA
5740730 TGAAATGGAC
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
5 5 0.05
6 90 0.95
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:5742438 original size:20 final size:20
Alignment explanation
Indices: 5742407--5742459 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
5742397 TAATAAACAA
5742407 TAAAT-AAATAAAATGAT-C
1 TAAATAAAATAAAATGATAC
5742425 TAAATAATAATAAAA-GATAC
1 TAAATAA-AATAAAATGATAC
5742445 TAAATAAAATAAAAT
1 TAAATAAAATAAAAT
5742460 AAATAAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 15 0.48
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (20 bp):
TAAATAAAATAAAATGATAC
Found at i:5755483 original size:206 final size:206
Alignment explanation
Indices: 5755103--5755658 Score: 790
Period size: 206 Copynumber: 2.7 Consensus size: 206
5755093 AAATTTGCTT
* *
5755103 CTTCGATTTGTTCTTTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* * * * * *
5755168 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAAGGCTACCAAACCATCTT
66 GTGAAAGCTAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * * **
5755233 GGATATGCTTCAGTCTAATCATCTAAAGGTTAGATCTACTATGTGTCTGCTCTCCGTCGAATATG
131 GGATCTGCTTCAGTATAAACATCTAAAGGCCAGATCTACTATGTGTCTGCTCTCCGTCGAATATG
*
5755298 GAGATGCCAAA
196 GAGACGCCAAA
* *
5755309 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGACTTGCCTCAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* * * * *
5755374 GTGAAAGCTAAATCAACTATGAT-TTTGATTTGTTCCTTGTAAACATAAGGATGCCAAATCATCT
66 GTGAAAGCTAAATCAGCTATG-TCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
* * * * *
5755438 TGGATCTGCTTTAGTATAAACATCTGAGGGCCAGATCTGCTATGTGTCTGCTCTTCGTCGAATAT
130 TGGATCTGCTTCAGTATAAACATCTAAAGGCCAGATCTACTATGTGTCTGCTCTCCGTCGAATAT
5755503 GGAGACGCCAAA
195 GGAGACGCCAAA
* * *
5755515 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACATAAGCAT
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* * * *
5755580 GTAAAAGCTAAATTAGCAATGTCTTCAATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCTAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
5755645 GGATCTTGCTTCAG
131 GGATC-TGCTTCAG
5755659 CCAGATCTGC
Statistics
Matches: 306, Mismatches: 41, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
205 1 0.00
206 297 0.97
207 8 0.03
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (206 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
GTGAAAGCTAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
GGATCTGCTTCAGTATAAACATCTAAAGGCCAGATCTACTATGTGTCTGCTCTCCGTCGAATATG
GAGACGCCAAA
Found at i:5756568 original size:21 final size:21
Alignment explanation
Indices: 5756543--5756583 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5756533 CTCTTCTCTC
* *
5756543 TTTTTCTTTTTTTTGTTTTTTG
1 TTTTT-TTTCTTTTGATTTTTG
5756565 TTTTTTTTCTTTTGATTTT
1 TTTTTTTTCTTTTGATTTT
5756584 CTATTTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.85
Consensus pattern (21 bp):
TTTTTTTTCTTTTGATTTTTG
Found at i:5756571 original size:25 final size:23
Alignment explanation
Indices: 5756543--5756604 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 23
5756533 CTCTTCTCTC
* *
5756543 TTTTTCTTTTTTTTGTTTTTTGTTT
1 TTTTTCTTTTTTTT-CTATTTG-TT
5756568 TTTTTCTTTTGATTTTCTATTTGTT
1 TTTTTCTTTT--TTTTCTATTTGTT
5756593 TTTTTCTTTTTT
1 TTTTTCTTTTTT
5756605 GATTTTCGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 2 0.06
25 22 0.67
26 5 0.15
27 4 0.12
ACGTcount: A:0.03, C:0.06, G:0.06, T:0.84
Consensus pattern (23 bp):
TTTTTCTTTTTTTTCTATTTGTT
Found at i:5756590 original size:26 final size:27
Alignment explanation
Indices: 5756561--5756611 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
5756551 TTTTTTGTTT
5756561 TTTGTTTTTTT-TCTTTTGATTTTCTA
1 TTTGTTTTTTTCTCTTTTGATTTTCTA
*
5756587 TTTGTTTTTTTCTTTTTTGATTTTC
1 TTTGTTTTTTTCTCTTTTGATTTTC
5756612 GAAACCTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.06, C:0.08, G:0.08, T:0.78
Consensus pattern (27 bp):
TTTGTTTTTTTCTCTTTTGATTTTCTA
Found at i:5761467 original size:19 final size:19
Alignment explanation
Indices: 5761445--5761496 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
5761435 ATGTAATATT
**
5761445 TAATAATAAATTTAAAATA
1 TAATAATAAATAAAAAATA
5761464 TAAT-ATATAATAAAAAATA
1 TAATAATA-AATAAAAAATA
5761483 TAAT-ATATAATAAA
1 TAATAATA-AATAAA
5761497 TTTCCAGAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 3 0.10
19 27 0.90
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAATAATAAATAAAAAATA
Found at i:5761467 original size:26 final size:26
Alignment explanation
Indices: 5761432--5761494 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
5761422 GCATATAAAA
* * * *
5761432 AAAATGTAATATTTAATAATAAATTT
1 AAAATATAATATATAATAAAAAATAT
5761458 AAAATATAATATATAATAAAAAATAT
1 AAAATATAATATATAATAAAAAATAT
*
5761484 AATATATAATA
1 AAAATATAATA
5761495 AATTTCCAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (26 bp):
AAAATATAATATATAATAAAAAATAT
Found at i:5761471 original size:7 final size:7
Alignment explanation
Indices: 5761438--5761494 Score: 50
Period size: 7 Copynumber: 8.7 Consensus size: 7
5761428 AAAAAAAATG
*
5761438 TAATATT
1 TAATATA
5761445 TAATA-A
1 TAATATA
*
5761451 TAA-ATT
1 TAATATA
*
5761457 TAAAATA
1 TAATATA
5761464 TAATATA
1 TAATATA
5761471 TAATA-A
1 TAATATA
*
5761477 -AAAATA
1 TAATATA
5761483 TAATATA
1 TAATATA
5761490 TAATA
1 TAATA
5761495 AATTTCCAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
5 4 0.10
6 8 0.20
7 28 0.70
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
TAATATA
Found at i:5762014 original size:8 final size:7
Alignment explanation
Indices: 5761965--5762019 Score: 51
Period size: 8 Copynumber: 7.6 Consensus size: 7
5761955 GGCCTCTCCA
5761965 TTTTTCT
1 TTTTTCT
5761972 TTTTTCT
1 TTTTTCT
5761979 CTTTTT-T
1 -TTTTTCT
*
5761986 TATTTTTT
1 T-TTTTCT
5761994 TCTTTTCT
1 T-TTTTCT
5762002 TTTTTCCT
1 TTTTT-CT
5762010 TTTTT-T
1 TTTTTCT
5762016 TTTT
1 TTTT
5762020 GAAATAGAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
6 6 0.14
7 16 0.38
8 20 0.48
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:5766389 original size:26 final size:25
Alignment explanation
Indices: 5766360--5766409 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
5766350 AATGAGCATA
* *
5766360 TAAAAAATGATATTTAATAATAAATT
1 TAAAAAATAATATATAATAA-AAATT
*
5766386 TAAAATATAATATATAATAAAAAT
1 TAAAAAATAATATATAATAAAAAT
5766410 ATATTTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (25 bp):
TAAAAAATAATATATAATAAAAATT
Found at i:5766445 original size:17 final size:17
Alignment explanation
Indices: 5766387--5766445 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
5766377 TAATAAATTT
5766387 AAAATATAA-TATATAA
1 AAAATATAATTATATAA
5766403 TAAAA-ATATATT-TAT-A
1 -AAAATATA-ATTATATAA
*
5766419 AGAATAATAATTATATAA
1 AAAAT-ATAATTATATAA
5766437 AAAATATAA
1 AAAATATAA
5766446 AATTATTGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 3 0.09
16 7 0.21
17 18 0.53
18 6 0.18
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATATAATTATATAA
Found at i:5766981 original size:17 final size:18
Alignment explanation
Indices: 5766928--5767053 Score: 175
Period size: 19 Copynumber: 6.9 Consensus size: 18
5766918 AATCATATCT
*
5766928 TCTAAGATTGTATATCATA
1 TCTAAGATTG-CTATCATA
*
5766947 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
5766965 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
*
5766982 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
5767000 TCTAAGATT-CTATCATA
1 TCTAAGATTGCTATCATA
*
5767017 TCTAAGATTGCATATCACA
1 TCTAAGATTGC-TATCATA
5767036 TCTAAGATTGCATATCAT
1 TCTAAGATTGC-TATCAT
5767054 TGAAGATTAT
Statistics
Matches: 97, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
17 32 0.33
18 32 0.33
19 33 0.34
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:5766986 original size:35 final size:35
Alignment explanation
Indices: 5766928--5767045 Score: 191
Period size: 35 Copynumber: 3.3 Consensus size: 35
5766918 AATCATATCT
5766928 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
5766965 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
* *
5767000 TCTAAGATTCTATCATATCTAAGATTGCATATCACA
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCATA
5767036 TCTAAGATTG
1 TCTAAGATTG
5767046 CATATCATTG
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
35 53 0.69
36 14 0.18
37 10 0.13
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:5767061 original size:17 final size:18
Alignment explanation
Indices: 5766928--5767050 Score: 96
Period size: 17 Copynumber: 6.8 Consensus size: 18
5766918 AATCATATCT
* *
5766928 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATAT-ACA
*
5766947 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATAT-ACA
*
5766965 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATAT-ACA
*
5766982 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATAT-ACA
*
5767000 TCTAAGATT-C-TATCATA
1 TCTAAGATTGCATAT-ACA
5767017 TCTAAGATTGCATATCACA
1 TCTAAGATTGCATAT-ACA
5767036 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
5767051 CATTGAAGAT
Statistics
Matches: 96, Mismatches: 2, Indels: 12
0.87 0.02 0.11
Matches are distributed among these distances:
17 32 0.33
18 32 0.33
19 32 0.33
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (18 bp):
TCTAAGATTGCATATACA
Found at i:5785402 original size:13 final size:13
Alignment explanation
Indices: 5785384--5785409 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5785374 CAACTAATCA
5785384 AAATTAATTTGGT
1 AAATTAATTTGGT
5785397 AAATTAATTTGGT
1 AAATTAATTTGGT
5785410 TGGATGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
AAATTAATTTGGT
Found at i:5786767 original size:14 final size:15
Alignment explanation
Indices: 5786729--5786757 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5786719 TTTTTCTTTT
5786729 TAAGATTATTTCTAA
1 TAAGATTATTTCTAA
5786744 TAAGATTATTTCTA
1 TAAGATTATTTCTA
5786758 TAAATTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (15 bp):
TAAGATTATTTCTAA
Found at i:5790117 original size:45 final size:45
Alignment explanation
Indices: 5790033--5790154 Score: 106
Period size: 45 Copynumber: 2.7 Consensus size: 45
5790023 GAAGTTTTTT
* * * * *
5790033 TTTTATGTATCCGCATGTTTGAAT-CTGCTATACCCATGAAGT-TTC
1 TTTTATGAATCCGCATGTATGAGTCCT-CCATATCCATGAA-TCTTC
*
5790078 TTTTATGAATCCGCATGTATGAGTCCTCCATATCTATGAATCTTC
1 TTTTATGAATCCGCATGTATGAGTCCTCCATATCCATGAATCTTC
** ** *
5790123 TTAAACAAATTCGCATGTATGAGTCCT-CATAT
1 TTTTATGAATCCGCATGTATGAGTCCTCCATAT
5790155 AATAATTCGC
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
44 6 0.09
45 56 0.88
46 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.39
Consensus pattern (45 bp):
TTTTATGAATCCGCATGTATGAGTCCTCCATATCCATGAATCTTC
Found at i:5803385 original size:29 final size:30
Alignment explanation
Indices: 5803347--5803433 Score: 103
Period size: 29 Copynumber: 3.0 Consensus size: 30
5803337 GCTTGGAATT
5803347 GATTCGGGCC-AGATGGGCCATATGAATGTA
1 GATT-GGGCCTAGATGGGCCATATGAATGTA
5803377 -ATTTGGGCCTA-ATGGGCCATATGAATG-A
1 GA-TTGGGCCTAGATGGGCCATATGAATGTA
* *
5803405 GATTGGGCCTAG-TGGGCTATATGCATGTA
1 GATTGGGCCTAGATGGGCCATATGAATGTA
5803434 TGTAGACTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
28 23 0.46
29 24 0.48
30 3 0.06
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.28
Consensus pattern (30 bp):
GATTGGGCCTAGATGGGCCATATGAATGTA
Found at i:5803420 original size:28 final size:29
Alignment explanation
Indices: 5803347--5803433 Score: 99
Period size: 28 Copynumber: 3.0 Consensus size: 29
5803337 GCTTGGAATT
5803347 GATTCGGGCC-AGATGGGCCATATGAATGTA
1 GATT-GGGCCTAG-TGGGCCATATGAATGTA
*
5803377 -ATTTGGGCCTAATGGGCCATATGAATG-A
1 GA-TTGGGCCTAGTGGGCCATATGAATGTA
* *
5803405 GATTGGGCCTAGTGGGCTATATGCATGTA
1 GATTGGGCCTAGTGGGCCATATGAATGTA
5803434 TGTAGACTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
28 23 0.47
29 23 0.47
30 3 0.06
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.28
Consensus pattern (29 bp):
GATTGGGCCTAGTGGGCCATATGAATGTA
Found at i:5805195 original size:15 final size:15
Alignment explanation
Indices: 5805172--5805211 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
5805162 TTTGTCTATT
5805172 ATTTATTATTTATTTG
1 ATTT-TTATTTATTTG
5805188 ATTTTTATTTATTTG
1 ATTTTTATTTATTTG
*
5805203 ATTATTATT
1 ATTTTTATT
5805212 CTTACTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (15 bp):
ATTTTTATTTATTTG
Found at i:5808849 original size:30 final size:30
Alignment explanation
Indices: 5808753--5808898 Score: 109
Period size: 30 Copynumber: 4.9 Consensus size: 30
5808743 CGTGTGACCG
* * *
5808753 ACACGGGCTAGCCACACACCTGTGT-AATC
1 ACACAGGCTAGCCACACACCCGTGTGAGTC
* * ** *
5808782 GACACGGGCTAGCTACATGCCCATGTGA-TC
1 -ACACAGGCTAGCCACACACCCGTGTGAGTC
* *
5808812 AATACAGGTTAGCCACACACCCGTGTGAGTC
1 -ACACAGGCTAGCCACACACCCGTGTGAGTC
* * *
5808843 ACACAGGCTAGCAACACACTCGTGTGAGTT
1 ACACAGGCTAGCCACACACCCGTGTGAGTC
* *
5808873 ACAC-GAGCTAGCCACACCCCCATGTG
1 ACACAG-GCTAGCCACACACCCGTGTG
5808899 CCAGCTCGGG
Statistics
Matches: 91, Mismatches: 22, Indels: 6
0.76 0.18 0.05
Matches are distributed among these distances:
29 1 0.01
30 87 0.96
31 3 0.03
ACGTcount: A:0.27, C:0.32, G:0.23, T:0.18
Consensus pattern (30 bp):
ACACAGGCTAGCCACACACCCGTGTGAGTC
Found at i:5811364 original size:27 final size:26
Alignment explanation
Indices: 5811329--5811440 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
5811319 AGCATGGCTG
* *
5811329 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
5811355 CCAGATACAGATAATCGTGGCAGAACCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
5811383 CCAGAACAGATATATGTGGTAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
5811410 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
5811437 CCAG
1 CCAG
5811441 GACGCTTCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 6 0.08
27 52 0.70
28 16 0.22
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:5811393 original size:54 final size:54
Alignment explanation
Indices: 5811329--5811440 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
5811319 AGCATGGCTG
*
5811329 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAACCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAACCA
** * * *
5811383 CCAGAACAGATATATGTGGTAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAACCA
5811437 CCAG
1 CCAG
5811441 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 34 0.67
55 17 0.33
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAACCA
Found at i:5812878 original size:24 final size:24
Alignment explanation
Indices: 5812851--5812921 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
5812841 CTAGATTTCC
**
5812851 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
5812875 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
5812899 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
5812922 CTCCTGACAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.25, C:0.38, G:0.01, T:0.35
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:5817053 original size:6 final size:6
Alignment explanation
Indices: 5817035--5817072 Score: 58
Period size: 6 Copynumber: 6.0 Consensus size: 6
5817025 TAGATTTATG
5817035 ATAAAA GATAAAA ATAAAA TATAAAA ATAAAA ATAAAA
1 ATAAAA -ATAAAA ATAAAA -ATAAAA ATAAAA ATAAAA
5817073 TATAGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 18 0.60
7 12 0.40
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:5817053 original size:13 final size:12
Alignment explanation
Indices: 5817035--5817072 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
5817025 TAGATTTATG
5817035 ATAAAAGATAAAA
1 ATAAAA-ATAAAA
5817048 ATAAAATATAAAA
1 ATAAAA-ATAAAA
5817061 ATAAAAATAAAA
1 ATAAAAATAAAA
5817073 TATAGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 6 0.25
13 18 0.75
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (12 bp):
ATAAAAATAAAA
Found at i:5817066 original size:19 final size:19
Alignment explanation
Indices: 5817035--5817081 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
5817025 TAGATTTATG
5817035 ATAAAAGATAAAAATAAAAT
1 ATAAAA-ATAAAAATAAAAT
5817055 ATAAAAATAAAAATAAAAT
1 ATAAAAATAAAAATAAAAT
5817074 ATAGAAAA
1 ATA-AAAA
5817082 AATGAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (19 bp):
ATAAAAATAAAAATAAAAT
Found at i:5817611 original size:7 final size:8
Alignment explanation
Indices: 5817594--5817627 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
5817584 TGGGAGTTTA
5817594 TTTTTGTT
1 TTTTTGTT
5817602 TTTTTGTT
1 TTTTTGTT
5817610 TTTTTG-T
1 TTTTTGTT
5817617 TTTTTGTT
1 TTTTTGTT
5817625 TTT
1 TTT
5817628 ACTGGTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (8 bp):
TTTTTGTT
Done.