Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 164 of 168
Found at i:49386705 original size:102 final size:102
Alignment explanation
Indices: 49386529--49387017 Score: 648
Period size: 102 Copynumber: 4.8 Consensus size: 102
49386519 AGTGAAAGTG
49386529 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
49386594 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
49386631 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
* *
49386696 AGCACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
* *
49386733 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
* * *
49386798 AGTACTAAGTGAAGGCTACTATGTGTACCGAAAAACT
66 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
* * * * * * * *
49386835 TTAGCCACGTATGTAGTACTATGTGAAGGCTACTACGTGAATCG-TAAA-ACTTGATCACGTGTA
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTG
* ** * **
49386898 TAGTACTATGTGAAGGCTATTATGTGAACCGTA-AA-AA
65 TAGTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCT
* * * * * * *
49386935 TTGATCACGTGTGTAGTACTATGTGAAGGCTATTATGTGAACCG-TAAA-AATTGATCACGTGTG
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAA-TGGTCACATGTG
*
49386998 TAGTACTATGTGAAGGCTAC
65 TAGTACTAAGTGAAGGCTAC
49387018 TACGTGTATC
Statistics
Matches: 350, Mismatches: 34, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
100 72 0.21
101 43 0.12
102 235 0.67
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (102 bp):
TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
Found at i:49393176 original size:13 final size:13
Alignment explanation
Indices: 49393158--49393188 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
49393148 AAATACTGTG
49393158 GAAAAGTGCTTTT
1 GAAAAGTGCTTTT
*
49393171 GAAAAGTGTTTTT
1 GAAAAGTGCTTTT
49393184 GAAAA
1 GAAAA
49393189 TTTTGAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (13 bp):
GAAAAGTGCTTTT
Found at i:49399055 original size:15 final size:15
Alignment explanation
Indices: 49399035--49399107 Score: 53
Period size: 15 Copynumber: 4.9 Consensus size: 15
49399025 TATTTGATAA
49399035 ATTAAAAAATTAAGT
1 ATTAAAAAATTAAGT
*
49399050 ATTAAAAATTTAAG-
1 ATTAAAAAATTAAGT
* *
49399064 -TTATGAAAATTAATT
1 ATTA-AAAAATTAAGT
*
49399079 ATT-AAAATTTAAGTT
1 ATTAAAAAATTAAG-T
*
49399094 ATAAAAAAAATTAA
1 AT-TAAAAAATTAA
49399108 AATAAAATAG
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
13 3 0.07
14 14 0.33
15 16 0.37
16 2 0.05
17 8 0.19
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (15 bp):
ATTAAAAAATTAAGT
Found at i:49399058 original size:14 final size:14
Alignment explanation
Indices: 49399039--49399092 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
49399029 TGATAAATTA
49399039 AAAAATTAAGTATT
1 AAAAATTAAGTATT
49399053 AAAAATTTAAGT-TAT
1 AAAAA-TTAAGTAT-T
* *
49399068 GAAAATTAATTATT
1 AAAAATTAAGTATT
*
49399082 AAAATTTAAGT
1 AAAAATTAAGT
49399093 TATAAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (14 bp):
AAAAATTAAGTATT
Found at i:49399085 original size:13 final size:13
Alignment explanation
Indices: 49399040--49399087 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
49399030 GATAAATTAA
*
49399040 AAAATTAAGTATT
1 AAAATTAATTATT
*
49399053 AAAAATTTAAGTTATG
1 -AAAA-TTAA-TTATT
49399069 AAAATTAATTATT
1 AAAATTAATTATT
49399082 AAAATT
1 AAAATT
49399088 TAAGTTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 10 0.34
14 8 0.28
15 8 0.28
16 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (13 bp):
AAAATTAATTATT
Found at i:49399094 original size:28 final size:29
Alignment explanation
Indices: 49399039--49399100 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 29
49399029 TGATAAATTA
49399039 AAAAATTAAGTATTAAAAATTTAAGTTAT
1 AAAAATTAAGTATTAAAAATTTAAGTTAT
* *
49399068 GAAAATTAATTATT-AAAATTTAAGTTAT
1 AAAAATTAAGTATTAAAAATTTAAGTTAT
49399096 AAAAA
1 AAAAA
49399101 AAATTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.37
Consensus pattern (29 bp):
AAAAATTAAGTATTAAAAATTTAAGTTAT
Found at i:49399098 original size:14 final size:14
Alignment explanation
Indices: 49399054--49399099 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
49399044 TTAAGTATTA
49399054 AAAATTTAAGTTAT
1 AAAATTTAAGTTAT
49399068 GAAAA-TTAA-TTATT
1 -AAAATTTAAGTTA-T
49399082 AAAATTTAAGTTAT
1 AAAATTTAAGTTAT
49399096 AAAA
1 AAAA
49399100 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 7 0.25
14 14 0.50
15 7 0.25
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (14 bp):
AAAATTTAAGTTAT
Found at i:49399101 original size:29 final size:30
Alignment explanation
Indices: 49399037--49399101 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
49399027 TTTGATAAAT
49399037 TAAAAAATTAAGTATTAAAAATTTAAGTTA
1 TAAAAAATTAAGTATTAAAAATTTAAGTTA
* *
49399067 T-GAAAATTAATTATT-AAAATTTAAGTTA
1 TAAAAAATTAAGTATTAAAAATTTAAGTTA
49399095 TAAAAAA
1 TAAAAAA
49399102 AATTAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 14 0.45
29 16 0.52
30 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (30 bp):
TAAAAAATTAAGTATTAAAAATTTAAGTTA
Found at i:49400735 original size:30 final size:30
Alignment explanation
Indices: 49400699--49400780 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
49400689 AATATCTCGG
49400699 TACCCATATATTTGACTTTCCAATATTTGA
1 TACCCATATATTTGACTTTCCAATATTTGA
* * *
49400729 TACCCATATCTTTGACTTTCTATTATTTGA
1 TACCCATATATTTGACTTTCCAATATTTGA
*
49400759 TACCCATATATTTGATTTTCCA
1 TACCCATATATTTGACTTTCCA
49400781 TAAATATGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (30 bp):
TACCCATATATTTGACTTTCCAATATTTGA
Found at i:49400742 original size:15 final size:15
Alignment explanation
Indices: 49400699--49400774 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 15
49400689 AATATCTCGG
49400699 TACCCATATATTTGA
1 TACCCATATATTTGA
**
49400714 CTTTCCA-ATATTTGA
1 -TACCCATATATTTGA
*
49400729 TACCCATATCTTTGA
1 TACCCATATATTTGA
** *
49400744 CTTTCTAT-TATTTGA
1 -TACCCATATATTTGA
49400759 TACCCATATATTTGA
1 TACCCATATATTTGA
49400774 T
1 T
49400775 TTTCCATAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.46
Consensus pattern (15 bp):
TACCCATATATTTGA
Found at i:49405403 original size:30 final size:30
Alignment explanation
Indices: 49405367--49405448 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
49405357 AATATCTCGG
49405367 TACCCATATCTTTGACTTTCCAATATTTCA
1 TACCCATATCTTTGACTTTCCAATATTTCA
* * *
49405397 TACCCATATCTTTGACTTTCTATTATTTGA
1 TACCCATATCTTTGACTTTCCAATATTTCA
*
49405427 TACCCATATCTTTGATTTTCCA
1 TACCCATATCTTTGACTTTCCA
49405449 TAAATATGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.46
Consensus pattern (30 bp):
TACCCATATCTTTGACTTTCCAATATTTCA
Found at i:49412043 original size:25 final size:26
Alignment explanation
Indices: 49411993--49412043 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
49411983 TAATACAAGC
* *
49411993 AAAATGGATGGGACTTTTTAATAGAA
1 AAAATGGATGGGAATTTTTAACAGAA
*
49412019 AAAATGGAT-GGAATTTTTTACAGAA
1 AAAATGGATGGGAATTTTTAACAGAA
49412044 CGACTAGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.31
Consensus pattern (26 bp):
AAAATGGATGGGAATTTTTAACAGAA
Found at i:49420780 original size:24 final size:23
Alignment explanation
Indices: 49420753--49420797 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
49420743 TATTTTGATT
49420753 ATTTTTAGTGTTT-ATATTTTTAAA
1 ATTTTTAGT-TTTGA-ATTTTTAAA
49420777 ATTTTTAGTTTTGAATTTTTA
1 ATTTTTAGTTTTGAATTTTTA
49420798 GTCATGACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (23 bp):
ATTTTTAGTTTTGAATTTTTAAA
Found at i:49422342 original size:3 final size:3
Alignment explanation
Indices: 49422336--49422365 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
49422326 ATCATTGTCG
49422336 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
49422366 AGTAATCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:49422633 original size:117 final size:118
Alignment explanation
Indices: 49422360--49423156 Score: 1008
Period size: 117 Copynumber: 6.7 Consensus size: 118
49422350 TTCTTCTTCT
* * * * *
49422360 TCTTCTAGTAATCTTGCTGGTGGATTGTTTCCTTCGTCGTCACTAGGTGGTTTCTCTCCGGCGAA
1 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCC-T--TCGTCACTAGGTGGTTTCTCGCCGGCGAA
* * *
49422425 TGGACTCTCTTCCTCGACGTCTGCTTGTAGTAATCGTTTCTCGCCGATGACCCCAATG
63 TGGACTCTCTTCCTCAACG--TGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATG
* ** * *
49422483 CCTGCTAGTAATCTTTCTGGAGGACTATCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
1 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
* * *
49422548 ACTCTCTTCCTCAACGT-CTTGTAGTAATCGTTCCTCACGGATGAGCTCAATG
66 ACTCTCTTCCTCAACGTGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATG
* * *
49422600 TCTTTTAGTAATCTTTCTGGGGGATTATCTCCTTCATCACTAGGTGGTTTCTCGCCGGCGAATGG
1 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
* * * * *
49422665 ACTTTCTTCCTCGACGTCTGCTTGTAGTAACCGTTTTTCACCGATCACCTCAATG
66 ACTCTCTTCCTCAACG--TGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATG
* *
49422720 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTTGCCGGCAAATGG
1 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
* ** *
49422785 ACTCTTTTCCTCAACGT-CTTGTAGTTTTCGTTTCTCACCGATGACCTTAATG
66 ACTCTCTTCCTCAACGTGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATG
49422837 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
1 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
* * **
49422902 ACTTTCTTCCTCAACAT-CTTGTAGTTTTCGTTTCTCACCGATGACCTCAATG
66 ACTCTCTTCCTCAACGTGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATG
*
49422954 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGCGGTTTCTCGCCGGCGAATGG
1 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
** *
49423019 ACTCTCTTCCTCGACATC-TGCTTGTAGTTTTCGTTTTCGTTTCTCACCGATGACCTCAATT
66 ACTCTCTTCCTC-A-A-CGTGCTTGTA------GTAATCGTTTCTCACCGATGACCTCAATG
* * * * * * *
49423080 TCTTTTAGTAATCTTTCTGGGGGCTTATCTCCTTCGTCACTAGGTGGTTTCTCACCAGCAAACGG
1 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
*
49423145 ACTTTCTTCCTC
66 ACTCTCTTCCTC
49423157 GACATTCTCT
Statistics
Matches: 601, Mismatches: 60, Indels: 23
0.88 0.09 0.03
Matches are distributed among these distances:
117 318 0.53
118 3 0.00
119 3 0.00
120 155 0.26
122 1 0.00
123 25 0.04
126 96 0.16
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (118 bp):
TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
ACTCTCTTCCTCAACGTGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATG
Found at i:49422692 original size:237 final size:237
Alignment explanation
Indices: 49422360--49423159 Score: 1095
Period size: 237 Copynumber: 3.3 Consensus size: 237
49422350 TTCTTCTTCT
* * * * * *
49422360 TCTTCTAGTAATCTTGCTGGTGGATTGTTTCCTTCGTCGTCACTAGGTGGTTTCTCTCCGGCGAA
1 TCTTTTAGTAATCTTTCTGGGGGATTATCTCC-T--TCGTCACTAGGTGGTTTCTCGCCGGCGAA
* * * * **
49422425 TGGACTCTCTTCCTCGACGTCTGCTTGTAGTAATCGTTTCTCGCCGATGACCCCAATGCCTGCTA
63 TGGACTTTCTTCCTCGACGTCTGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATGTCTTTTA
* *
49422490 GTAATCTTTCTGGAGGACTATCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCT
128 GTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCT
** * *
49422555 TCCTCAACGTCTTGTAGTAATCGTTCCTCACGGATGAGCTCAATG
193 TCCTCAACGTCTTGTAGTTTTCGTTCCTCACCGATGACCTCAATG
*
49422600 TCTTTTAGTAATCTTTCTGGGGGATTATCTCCTTCATCACTAGGTGGTTTCTCGCCGGCGAATGG
1 TCTTTTAGTAATCTTTCTGGGGGATTATCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
* * *
49422665 ACTTTCTTCCTCGACGTCTGCTTGTAGTAACCGTTTTTCACCGATCACCTCAATGTCTTTTAGTA
66 ACTTTCTTCCTCGACGTCTGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATGTCTTTTAGTA
* * *
49422730 ATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTTGCCGGCAAATGGACTCTTTTCC
131 ATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCTTCC
* *
49422795 TCAACGTCTTGTAGTTTTCGTTTCTCACCGATGACCTTAATG
196 TCAACGTCTTGTAGTTTTCGTTCCTCACCGATGACCTCAATG
* *
49422837 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
1 TCTTTTAGTAATCTTTCTGGGGGATTATCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
* * **
49422902 ACTTTCTTCCTCAAC--AT-CTTGTAGTTTTCGTTTCTCACCGATGACCTCAATGTCTTTTAGTA
66 ACTTTCTTCCTCGACGTCTGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATGTCTTTTAGTA
*
49422964 ATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGCGGTTTCTCGCCGGCGAATGGACTCTCTTCC
131 ATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCTTCC
*
49423029 TCGACATC-TGCTTGTAGTTTTCGTTTTCGTTTCTCACCGATGACCTCAATT
196 TC-A-A-CGT-CTTGTAGTTTTCG--TTC----CTCACCGATGACCTCAATG
* * * * *
49423080 TCTTTTAGTAATCTTTCTGGGGGCTTATCTCCTTCGTCACTAGGTGGTTTCTCACCAGCAAACGG
1 TCTTTTAGTAATCTTTCTGGGGGATTATCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
49423145 ACTTTCTTCCTCGAC
66 ACTTTCTTCCTCGAC
49423160 ATTCTCTTCC
Statistics
Matches: 498, Mismatches: 52, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
234 103 0.21
235 2 0.00
236 2 0.00
237 272 0.55
239 3 0.01
240 27 0.05
243 89 0.18
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (237 bp):
TCTTTTAGTAATCTTTCTGGGGGATTATCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGG
ACTTTCTTCCTCGACGTCTGCTTGTAGTAATCGTTTCTCACCGATGACCTCAATGTCTTTTAGTA
ATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCTTCC
TCAACGTCTTGTAGTTTTCGTTCCTCACCGATGACCTCAATG
Found at i:49422870 original size:354 final size:358
Alignment explanation
Indices: 49422360--49423156 Score: 1100
Period size: 354 Copynumber: 2.2 Consensus size: 358
49422350 TTCTTCTTCT
* * * * *
49422360 TCTTCTAGTAATCTTGCTGGTGGATTGTTTCCTTCGTCGTCACTAGGTGGTTTCTCTCCGGCGAA
1 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCC-T--TCGTCACTAGGTGGTTTCTCTCCGGCAAA
* *
49422425 TGGACTCTCTTCCTCGACGTCTGCTTGTAGTAATCGTTTCTCGCCGATGACCCCAATGCCTGCTA
63 TGGACTCTCTTCCTCAACG-CTGCTTGTAGTAATCGTTTCTCACCGATGACCCCAATGCCTGCTA
49422490 GTAATCTTTCTGGAGGACTATCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCT
127 GTAATCTTTCTGGAGGACTATCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCT
* * *
49422555 TCCTCAACGTCTTGTAGTAATCGTTCCTCACGGATGAGCTCAATGTCTTTTAGTAATCTTTCTGG
192 TCCTCAACATCTTGTAGTAATCGTTCCTCACCGATGACCTCAATGTCTTTTAGTAATCTTTCTGG
* * * *
49422620 GGGATTATCTCCTTCATCACTAGGTGGTTTCTCGCCGGCGAATGGACTTTCTTCCTCGACGTCTG
257 AGGATTATCTCCTTCATCACTAGGCGGTTTCTCGCCGGCGAATGGACTCTCTTCCTCGACATCTG
*
49422685 CTTGTAG-TAAC-CGTTTTTCACCGATCACCTCAATG
322 CTTGTAGTTAACTCGTTTCTCACCGATCACCTCAATG
49422720 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCT-TGCCGGCAAATG
1 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCT-CCGGCAAATG
* ** ** * **
49422784 GACTCTTTTCCTCAACG-T-CTTGTAGTTTTCGTTTCTCACCGATGACCTTAATGTCTTTTAGTA
65 GACTCTCTTCCTCAACGCTGCTTGTAGTAATCGTTTCTCACCGATGACCCCAATGCCTGCTAGTA
* * *
49422847 ATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTTTCTTCC
130 ATCTTTCTGGAGGACTATCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCTTCC
** *
49422912 TCAACATCTTGTAGTTTTCGTTTCTCACCGATGACCTCAATGTCTTTTAGTAATCTTTCTGGAGG
195 TCAACATCTTGTAGTAATCGTTCCTCACCGATGACCTCAATGTCTTTTAGTAATCTTTCTGGAGG
* *
49422977 ATTGTCTCCTTCGTCACTAGGCGGTTTCTCGCCGGCGAATGGACTCTCTTCCTCGACATCTGCTT
260 ATTATCTCCTTCATCACTAGGCGGTTTCTCGCCGGCGAATGGACTCTCTTCCTCGACATCTGCTT
** * *
49423042 GTAGTTTTCGTTTTCGTTTCTCACCGATGACCTCAATT
325 GTAGTTAAC----TCGTTTCTCACCGATCACCTCAATG
* * * * * *
49423080 TCTTTTAGTAATCTTTCTGGGGGCTTATCTCCTTCGTCACTAGGTGGTTTCTCACCAGCAAACGG
1 TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCTCCGGCAAATGG
*
49423145 ACTTTCTTCCTC
66 ACTCTCTTCCTC
49423157 GACATTCTCT
Statistics
Matches: 386, Mismatches: 43, Indels: 16
0.87 0.10 0.04
Matches are distributed among these distances:
354 221 0.57
355 3 0.01
356 1 0.00
357 43 0.11
359 1 0.00
360 117 0.30
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (358 bp):
TCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCGTCACTAGGTGGTTTCTCTCCGGCAAATGG
ACTCTCTTCCTCAACGCTGCTTGTAGTAATCGTTTCTCACCGATGACCCCAATGCCTGCTAGTAA
TCTTTCTGGAGGACTATCTCCTTCGTCACTAGGTGGTTTCTCGCCGGCGAATGGACTCTCTTCCT
CAACATCTTGTAGTAATCGTTCCTCACCGATGACCTCAATGTCTTTTAGTAATCTTTCTGGAGGA
TTATCTCCTTCATCACTAGGCGGTTTCTCGCCGGCGAATGGACTCTCTTCCTCGACATCTGCTTG
TAGTTAACTCGTTTCTCACCGATCACCTCAATG
Found at i:49423153 original size:126 final size:126
Alignment explanation
Indices: 49422925--49423161 Score: 384
Period size: 126 Copynumber: 1.9 Consensus size: 126
49422915 ACATCTTGTA
*
49422925 GTTTTCGTTTCTCACCGATGACCTCAATGTCTTTTAGTAATCTTTCTGGAGGATTGTCTCCTTCG
1 GTTTTCGTTTCTCACCGATGACCTCAATGTCTTTTAGTAATCTTTCTGGAGGATTATCTCCTTCG
* * * *
49422990 TCACTAGGCGGTTTCTCGCCGGCGAATGGACTCTCTTCCTCGACATCTGCTTGTAGTTTTC
66 TCACTAGGCGGTTTCTCACCAGCAAACGGACTCTCTTCCTCGACATCTGCTTGTAGTTTTC
* * *
49423051 GTTTTCGTTTCTCACCGATGACCTCAATTTCTTTTAGTAATCTTTCTGGGGGCTTATCTCCTTCG
1 GTTTTCGTTTCTCACCGATGACCTCAATGTCTTTTAGTAATCTTTCTGGAGGATTATCTCCTTCG
* *
49423116 TCACTAGGTGGTTTCTCACCAGCAAACGGACTTTCTTCCTCGACAT
66 TCACTAGGCGGTTTCTCACCAGCAAACGGACTCTCTTCCTCGACAT
49423162 TCTCTTCCAA
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 101 1.00
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.39
Consensus pattern (126 bp):
GTTTTCGTTTCTCACCGATGACCTCAATGTCTTTTAGTAATCTTTCTGGAGGATTATCTCCTTCG
TCACTAGGCGGTTTCTCACCAGCAAACGGACTCTCTTCCTCGACATCTGCTTGTAGTTTTC
Found at i:49423861 original size:20 final size:22
Alignment explanation
Indices: 49423821--49423861 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
49423811 CATTTTAATT
*
49423821 TTTTTTATATTTTAATTAGATA
1 TTTTTTATATTTTAATAAGATA
49423843 TTTTTTAT-TTTT-ATAAGAT
1 TTTTTTATATTTTAATAAGAT
49423862 TTTATAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTTTTATATTTTAATAAGATA
Found at i:49425414 original size:31 final size:31
Alignment explanation
Indices: 49425360--49425419 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
49425350 GTCACTAAAT
* *
49425360 TATTCGAAAGTTTTCATTTAAGTCATTGAAG
1 TATTCAAAAGTTTTCATTGAAGTCATTGAAG
* *
49425391 TATTCAAAATTTTTTATTGAAGTCATTGA
1 TATTCAAAAGTTTTCATTGAAGTCATTGA
49425420 GCTATAAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.45
Consensus pattern (31 bp):
TATTCAAAAGTTTTCATTGAAGTCATTGAAG
Found at i:49427883 original size:2 final size:2
Alignment explanation
Indices: 49427876--49427914 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
49427866 GTTAAAAAGT
49427876 TA TA TA TA 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 TA TA TA TA T
49427915 TTAAATACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49428237 original size:16 final size:16
Alignment explanation
Indices: 49428216--49428255 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
49428206 TAAATTGATG
*
49428216 ATTTTACTAACAATTA
1 ATTTTAATAACAATTA
*
49428232 ATTTTAATAATAATTA
1 ATTTTAATAACAATTA
*
49428248 GTTTTAAT
1 ATTTTAAT
49428256 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTTTAATAACAATTA
Found at i:49428254 original size:22 final size:23
Alignment explanation
Indices: 49428229--49428290 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
49428219 TTACTAACAA
* *
49428229 TTAATTTTAATAATAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
*
49428251 TTAATTTTATTAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
49428274 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
49428291 CAGGCCGGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 15 0.44
23 13 0.38
24 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:49428864 original size:27 final size:27
Alignment explanation
Indices: 49428823--49428885 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
49428813 GAGAGTCTAC
* * *
49428823 CACAGGCAGCACCAAAGGTGCCAATGG
1 CACAGGCGGTACCAAAAGTGCCAATGG
* **
49428850 CAGAGGCGGTACCAAAAGTGCCGTTGG
1 CACAGGCGGTACCAAAAGTGCCAATGG
49428877 CACAGGCGG
1 CACAGGCGG
49428886 CACCCCAACC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.27, G:0.35, T:0.10
Consensus pattern (27 bp):
CACAGGCGGTACCAAAAGTGCCAATGG
Found at i:49434262 original size:51 final size:51
Alignment explanation
Indices: 49434185--49434484 Score: 474
Period size: 51 Copynumber: 5.9 Consensus size: 51
49434175 ACTCCCTTAC
* * * * *
49434185 TTCCCTTGCTGCTGCTGATGGCTCCCCTGTTTCAGCCATTGAAGATGATTCT
1 TTCCCTT-TTGCTGATGATGACTCCCCTGTTTCAGCCATAGAAGATGGTTCT
*
49434237 TTCCCTTTTGTTGATGATGACTCCCCTGTTTCAGCCATAGAAGATGGTTCT
1 TTCCCTTTTGCTGATGATGACTCCCCTGTTTCAGCCATAGAAGATGGTTCT
49434288 TTCCCTTTTGCTGATGATGACTCCCCTGTTTCAGCCATAGAAGATGGTTCT
1 TTCCCTTTTGCTGATGATGACTCCCCTGTTTCAGCCATAGAAGATGGTTCT
49434339 TTCCCTTTTGCTGATGATGACTCCCCTGTTTCAGCCATAGAAGATGGTTCT
1 TTCCCTTTTGCTGATGATGACTCCCCTGTTTCAGCCATAGAAGATGGTTCT
* * *
49434390 TTCCCTTTTGCTGATGATGACTCCCCTGTTTCAGCCATTGAAGATAGTTTT
1 TTCCCTTTTGCTGATGATGACTCCCCTGTTTCAGCCATAGAAGATGGTTCT
* * * *
49434441 TTCCCTTTTGCTGAAGATGACTCCCCTTTTTTAGCCATTGAAGA
1 TTCCCTTTTGCTGATGATGACTCCCCTGTTTCAGCCATAGAAGA
49434485 AAGAAAAAGA
Statistics
Matches: 235, Mismatches: 13, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
51 228 0.97
52 7 0.03
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.38
Consensus pattern (51 bp):
TTCCCTTTTGCTGATGATGACTCCCCTGTTTCAGCCATAGAAGATGGTTCT
Found at i:49434282 original size:27 final size:27
Alignment explanation
Indices: 49434252--49434384 Score: 74
Period size: 27 Copynumber: 5.1 Consensus size: 27
49434242 TTTTGTTGAT
49434252 GATGACTCCCCTGTTTCAGCCATAGAA
1 GATGACTCCCCTGTTTCAGCCATAGAA
* * *
49434279 GATGGTTCTTTCCCT-TTT--G-C-T-GAT
1 GAT-G-AC-TCCCCTGTTTCAGCCATAGAA
49434303 GATGACTCCCCTGTTTCAGCCATAGAA
1 GATGACTCCCCTGTTTCAGCCATAGAA
* * *
49434330 GATGGTTCTTTCCCT-TTT--G-C-T-GAT
1 GAT-G-AC-TCCCCTGTTTCAGCCATAGAA
49434354 GATGACTCCCCTGTTTCAGCCATAGAA
1 GATGACTCCCCTGTTTCAGCCATAGAA
49434381 GATG
1 GATG
49434385 GTTCTTTCCC
Statistics
Matches: 76, Mismatches: 12, Indels: 36
0.61 0.10 0.29
Matches are distributed among these distances:
21 10 0.13
22 8 0.11
23 2 0.03
24 12 0.16
25 4 0.05
26 4 0.05
27 16 0.21
28 2 0.03
29 8 0.11
30 10 0.13
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.35
Consensus pattern (27 bp):
GATGACTCCCCTGTTTCAGCCATAGAA
Found at i:49434408 original size:24 final size:24
Alignment explanation
Indices: 49434279--49434408 Score: 56
Period size: 24 Copynumber: 5.2 Consensus size: 24
49434269 AGCCATAGAA
49434279 GATGGTTCTTTCCCTTTTGCTGAT
1 GATGGTTCTTTCCCTTTTGCTGAT
* * *
49434303 GAT-G-AC-TCCCCTGTTTCAGCCATAGAA
1 GATGGTTCTTTCCCT-TTT--G-C-T-GAT
49434330 GATGGTTCTTTCCCTTTTGCTGAT
1 GATGGTTCTTTCCCTTTTGCTGAT
* * *
49434354 GAT-G-AC-TCCCCTGTTTCAGCCATAGAA
1 GATGGTTCTTTCCCT-TTT--G-C-T-GAT
49434381 GATGGTTCTTTCCCTTTTGCTGAT
1 GATGGTTCTTTCCCTTTTGCTGAT
49434405 GATG
1 GATG
49434409 ACTCCCCTGT
Statistics
Matches: 76, Mismatches: 12, Indels: 36
0.61 0.10 0.29
Matches are distributed among these distances:
21 10 0.13
22 8 0.11
23 2 0.03
24 16 0.21
25 4 0.05
26 4 0.05
27 12 0.16
28 2 0.03
29 8 0.11
30 10 0.13
ACGTcount: A:0.16, C:0.24, G:0.21, T:0.39
Consensus pattern (24 bp):
GATGGTTCTTTCCCTTTTGCTGAT
Found at i:49436680 original size:24 final size:24
Alignment explanation
Indices: 49436652--49436703 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
49436642 TTAGTAAGTC
* *
49436652 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
49436676 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
49436700 AAAT
1 AAAT
49436704 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:49446325 original size:51 final size:51
Alignment explanation
Indices: 49446260--49447063 Score: 871
Period size: 51 Copynumber: 15.8 Consensus size: 51
49446250 GTTAATGATG
* *
49446260 ATGATGAATCCCCTGTTTCAGCCATTGAAGATGGATCTTTCCCTTTTGCTA
1 ATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTA
* *
49446311 ATGATGACTTCCCTGTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
1 ATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTA
* * *** *
49446362 ATGATGACTCCCCTGTTTCAGTCATTGAAGATGGTTCTTCCCCTGCCGCTG
1 ATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTA
** * *
49446413 CCGGTGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
1 ATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTA
* * * * *** *
49446464 ATGATGACTCCCCTATTTCATCTATTGAAGATGGTTCTTCCCCTGAAGCTG
1 ATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTA
** * * * *
49446515 CCGGTGATTCCCCTGTTTCAGCCATTGAAGAGGGTTCTTTCTCTTTTGCTA
1 ATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTA
* * * *** *
49446566 ATGATGACTCCCCTGTTTCATCTATTGAAGATGGTTCTTCCCCTGACGCTGC
1 ATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCT-A
* * *
49446618 CTG-TGGCTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
1 ATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTA
* * * *** *
49446668 ATGATGACTCCCCTGTTTCATCTATTGAAGATGGTTCTTCCCCTGAAGCTG
1 ATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTA
** * * *
49446719 CCGGTGA---CCCTGTTTCAGCCATTGAAGAGGGTTCTTTCTCTTTTGCTA
1 ATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTA
* * * * *** *
49446767 ATGATGACTCCCCTGTTTCATCTATTGAGGATGGTTCTTCCCCTGACGCTGC
1 ATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCT-A
* *
49446819 CTG-TGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
1 ATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTA
* * *** *
49446869 ATGATGGCTCCCCTGTTTCAGCCATTGAAGATGGTTCTTCCCCTGACGCTG
1 ATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTA
* * *
49446920 CTGGTGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
1 ATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTA
* * *** *
49446971 ATGATGACTCCCCTGTTTCAACCATTGAAGATGGTTCTTCCCCTGACGCTG
1 ATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTA
*
49447022 CTGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCC
1 ATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCC
49447064 TTTCTGCCGA
Statistics
Matches: 601, Mismatches: 145, Indels: 14
0.79 0.19 0.02
Matches are distributed among these distances:
48 36 0.06
50 4 0.01
51 557 0.93
52 4 0.01
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (51 bp):
ATGATGACTCCCCTGTTTCAGCCATTGAAGATGGTTCTTTCCCTTTTGCTA
Found at i:49446436 original size:102 final size:102
Alignment explanation
Indices: 49446260--49447066 Score: 1282
Period size: 102 Copynumber: 8.0 Consensus size: 102
49446250 GTTAATGATG
* * * * * *** *** * *
49446260 ATGATGAATCCCCTGTTTCAGCCATTGAAGATGGATCTTTCCCTTTTGCTAATGATGACTTCCCT
1 ATGATGACTCCCCTGTTTCATCTATTGAAGATGGTTCTTCCCCTGACGCTGCCGGTGACTCCCCT
49446325 GTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
66 GTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
*
49446362 ATGATGACTCCCCTGTTTCAGTC-ATTGAAGATGGTTCTTCCCCTGCCGCTGCCGGTGACTCCCC
1 ATGATGACTCCCCTGTTTCA-TCTATTGAAGATGGTTCTTCCCCTGACGCTGCCGGTGACTCCCC
49446426 TGTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
65 TGTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
* * *
49446464 ATGATGACTCCCCTATTTCATCTATTGAAGATGGTTCTTCCCCTGAAGCTGCCGGTGATTCCCCT
1 ATGATGACTCCCCTGTTTCATCTATTGAAGATGGTTCTTCCCCTGACGCTGCCGGTGACTCCCCT
*
49446529 GTTTCAGCCATTGAAGAGGGTTCTTTCTCTTTTGCTA
66 GTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
* *
49446566 ATGATGACTCCCCTGTTTCATCTATTGAAGATGGTTCTTCCCCTGACGCTGCCTGTGGCTCCCCT
1 ATGATGACTCCCCTGTTTCATCTATTGAAGATGGTTCTTCCCCTGACGCTGCCGGTGACTCCCCT
49446631 GTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
66 GTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
*
49446668 ATGATGACTCCCCTGTTTCATCTATTGAAGATGGTTCTTCCCCTGAAGCTGCCGGTGA---CCCT
1 ATGATGACTCCCCTGTTTCATCTATTGAAGATGGTTCTTCCCCTGACGCTGCCGGTGACTCCCCT
*
49446730 GTTTCAGCCATTGAAGAGGGTTCTTTCTCTTTTGCTA
66 GTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
* *
49446767 ATGATGACTCCCCTGTTTCATCTATTGAGGATGGTTCTTCCCCTGACGCTGCCTGTGACTCCCCT
1 ATGATGACTCCCCTGTTTCATCTATTGAAGATGGTTCTTCCCCTGACGCTGCCGGTGACTCCCCT
49446832 GTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
66 GTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
* * * *
49446869 ATGATGGCTCCCCTGTTTCAGCCATTGAAGATGGTTCTTCCCCTGACGCTGCTGGTGACTCCCCT
1 ATGATGACTCCCCTGTTTCATCTATTGAAGATGGTTCTTCCCCTGACGCTGCCGGTGACTCCCCT
49446934 GTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
66 GTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
* * * *
49446971 ATGATGACTCCCCTGTTTCAACCATTGAAGATGGTTCTTCCCCTGACGCTGCTGATGACTCCCCT
1 ATGATGACTCCCCTGTTTCATCTATTGAAGATGGTTCTTCCCCTGACGCTGCCGGTGACTCCCCT
49447036 GTTTCAGCCATTGAAGATGGTTCTTTC-CTTT
66 GTTTCAGCCATTGAAGATGGTTCTTTCTCTTT
49447067 CTGCCGATAC
Statistics
Matches: 660, Mismatches: 40, Indels: 11
0.93 0.06 0.02
Matches are distributed among these distances:
99 95 0.14
101 6 0.01
102 558 0.85
103 1 0.00
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (102 bp):
ATGATGACTCCCCTGTTTCATCTATTGAAGATGGTTCTTCCCCTGACGCTGCCGGTGACTCCCCT
GTTTCAGCCATTGAAGATGGTTCTTTCTCTTTTGCTA
Found at i:49446911 original size:30 final size:30
Alignment explanation
Indices: 49446826--49446913 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
49446816 TGCCTGTGAC
49446826 TCCCCTGTTTCAGCCATTGAAGATGGTTCT
1 TCCCCTGTTTCAGCCATTGAAGATGGTTCT
* *
49446856 TTCTCT-TTT--G-C--T-AATGATGG--C-
1 TCCCCTGTTTCAGCCATTGAA-GATGGTTCT
49446877 TCCCCTGTTTCAGCCATTGAAGATGGTTCT
1 TCCCCTGTTTCAGCCATTGAAGATGGTTCT
49446907 TCCCCTG
1 TCCCCTG
49446914 ACGCTGCTGG
Statistics
Matches: 43, Mismatches: 4, Indels: 22
0.62 0.06 0.32
Matches are distributed among these distances:
21 4 0.09
22 4 0.09
23 2 0.05
24 7 0.16
25 1 0.02
26 1 0.02
27 7 0.16
28 2 0.05
29 4 0.09
30 11 0.26
ACGTcount: A:0.15, C:0.27, G:0.19, T:0.39
Consensus pattern (30 bp):
TCCCCTGTTTCAGCCATTGAAGATGGTTCT
Found at i:49449922 original size:56 final size:55
Alignment explanation
Indices: 49449857--49450048 Score: 199
Period size: 56 Copynumber: 3.3 Consensus size: 55
49449847 TTATTATTAA
49449857 ATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTT
1 ATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTT
* * * * *
49449912 ATATGAATTTAATAAATTCATAATATATAATACTATATAATATAAT-TTAA-AATAATTATTATT
1 ATAT-AATTTAAT-AA---A-AATATATAAT-TTA-ATAA-A-ATTCTTAATATTAAATATTCTT
*
49449975 AAATATAATTTAATAAAAATATATAATTTAATAAATTTCTTAATATTAAATATTCTT
1 --ATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTT
49450032 ATATGAATTTAATAAAA
1 ATAT-AATTTAATAAAA
49450049 TCATAATATA
Statistics
Matches: 111, Mismatches: 11, Indels: 29
0.74 0.07 0.19
Matches are distributed among these distances:
55 9 0.08
56 25 0.23
57 16 0.14
58 2 0.02
59 10 0.09
60 2 0.02
61 10 0.09
62 2 0.02
63 16 0.14
64 13 0.12
65 6 0.05
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (55 bp):
ATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTT
Found at i:49449929 original size:37 final size:36
Alignment explanation
Indices: 49449874--49450057 Score: 127
Period size: 37 Copynumber: 4.7 Consensus size: 36
49449864 TTAATAAAAA
*
49449874 TATATAATTTAATAAAATTCTTAATATTAAATATTCT
1 TATATAATTTAAT-AAATTCTTAATATTAAATATTAT
*
49449911 TATATGAATTTAATAAATTCATAATA-TATAATACTATAT
1 TATAT-AATTTAATAAATTCTTAATATTA-AATA-T-TAT
* * * ** *
49449950 AATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAA
1 TATATAATTT--AATAA--ATTCTT--A-AT-ATTAAATATTAT
*
49449994 TATATAATTTAATAAATTTCTTAATATTAAATATTCT
1 TATATAATTTAATAAA-TTCTTAATATTAAATATTAT
* *
49450031 TATATGAATTTAATAAAATCATAATAT
1 TATAT-AATTTAATAAATTCTTAATAT
49450058 ATAATACTAT
Statistics
Matches: 114, Mismatches: 18, Indels: 30
0.70 0.11 0.19
Matches are distributed among these distances:
36 2 0.02
37 40 0.35
38 27 0.24
39 7 0.06
40 6 0.05
41 4 0.04
42 9 0.08
44 11 0.10
45 2 0.02
46 5 0.04
47 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (36 bp):
TATATAATTTAATAAATTCTTAATATTAAATATTAT
Found at i:49449973 original size:120 final size:120
Alignment explanation
Indices: 49449828--49450075 Score: 451
Period size: 120 Copynumber: 2.1 Consensus size: 120
49449818 ATAAATAATT
* *
49449828 TAATCATATTTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATT
1 TAAT-ATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATT
*
49449893 CTTAATATTAAATATTCTTATATGAATTTAATAAATTCATAATATATAATACTATA
65 CTTAATATTAAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATA
*
49449949 TAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAATTTC
1 TAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC
49450014 TTAATATTAAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATA
66 TTAATATTAAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATA
49450069 TAATATA
1 TAATATA
49450076 GATTAATAAT
Statistics
Matches: 123, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
120 119 0.97
121 4 0.03
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (120 bp):
TAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC
TTAATATTAAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATA
Found at i:49450010 original size:16 final size:17
Alignment explanation
Indices: 49449857--49450009 Score: 63
Period size: 18 Copynumber: 8.9 Consensus size: 17
49449847 TTATTATTAA
49449857 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
49449875 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
* ***
49449892 -TCTTAATATTAAATATTCTT
1 AT-ATAAT-TT-AATA-AAAT
49449912 ATATGAATTTAAT-AAAT
1 ATAT-AATTTAATAAAAT
* *
49449929 -TCATAATAT-ATAATACT
1 AT-ATAATTTAATAA-AAT
*
49449946 ATATAATATAATTTAAAAT
1 ATATAATTTAA--TAAAAT
* *
49449965 A-ATTA-TT-AT-TAA-
1 ATATAATTTAATAAAAT
49449977 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
49449995 ATATAATTTAATAAA
1 ATATAATTTAATAAA
49450010 TTTCTTAATA
Statistics
Matches: 100, Mismatches: 16, Indels: 39
0.65 0.10 0.25
Matches are distributed among these distances:
12 1 0.01
13 5 0.05
14 3 0.03
15 4 0.04
16 8 0.08
17 27 0.27
18 31 0.31
19 10 0.10
20 7 0.07
21 4 0.04
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.43
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:49450057 original size:61 final size:61
Alignment explanation
Indices: 49449872--49450062 Score: 209
Period size: 61 Copynumber: 3.2 Consensus size: 61
49449862 ATTTAATAAA
* *
49449872 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTAATAAATTCAT
1 AATATATAATTTAATAAATTTCTTAATATTAAATATTCTTATATGAATTTAATAAAATCAT
* * * * *
49449933 AATATATAATACTATATAATATAAT-TTAA-AATAATTATTATTAAATAT-AATTTAAT--AA--
1 AATATATAAT-TTA-ATAA-AT-TTCTTAATATTAAATATTCTT--ATATGAATTTAATAAAATC
49449991 A-
60 AT
49449992 AATATATAATTTAATAAATTTCTTAATATTAAATATTCTTATATGAATTTAATAAAATCAT
1 AATATATAATTTAATAAATTTCTTAATATTAAATATTCTTATATGAATTTAATAAAATCAT
49450053 AATATATAAT
1 AATATATAAT
49450063 ACTATATAAT
Statistics
Matches: 104, Mismatches: 12, Indels: 28
0.72 0.08 0.19
Matches are distributed among these distances:
55 5 0.05
56 14 0.13
57 14 0.13
58 4 0.04
59 10 0.10
60 2 0.02
61 20 0.19
62 3 0.03
63 14 0.13
64 13 0.12
65 5 0.05
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.45
Consensus pattern (61 bp):
AATATATAATTTAATAAATTTCTTAATATTAAATATTCTTATATGAATTTAATAAAATCAT
Found at i:49453086 original size:14 final size:14
Alignment explanation
Indices: 49453067--49453094 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
49453057 AGCAGAAATC
49453067 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
49453081 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
49453095 CAAATGTGAG
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:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:49453780 original size:34 final size:34
Alignment explanation
Indices: 49453741--49453808 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
49453731 TCAAAAAGAA
49453741 AAAAGGTTTTCCTAATTTTATTTGAAAATTCCAG
1 AAAAGGTTTTCCTAATTTTATTTGAAAATTCCAG
49453775 AAAAGGTTTTCCTAATTTTATTTGAAAATTCCAG
1 AAAAGGTTTTCCTAATTTTATTTGAAAATTCCAG
49453809 TCCCTGACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (34 bp):
AAAAGGTTTTCCTAATTTTATTTGAAAATTCCAG
Found at i:49454585 original size:70 final size:70
Alignment explanation
Indices: 49454459--49454590 Score: 178
Period size: 70 Copynumber: 1.9 Consensus size: 70
49454449 CTGTACGAAC
* * * * *
49454459 TAATTAGACCACGATCCGGGATATGGGACGGGGTTATGGATGTTAGGATCTGAGCTTAAACTGCA
1 TAATTAGACCAAGATCCAGGATATGGGAAGGGGTTACGGATGTTAGGATCTAAGCTTAAACTGCA
49454524 GGAAT
66 GGAAT
*
49454529 TAATTAGACCATAG-TCCAGGATATGGGAAGGGGTTACGGATGTTAGGGT-TCAAGCTTAAACT
1 TAATTAGACCA-AGATCCAGGATATGGGAAGGGGTTACGGATGTTAGGATCT-AAGCTTAAACT
49454591 TGTCAGATGC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
69 1 0.02
70 52 0.96
71 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.27
Consensus pattern (70 bp):
TAATTAGACCAAGATCCAGGATATGGGAAGGGGTTACGGATGTTAGGATCTAAGCTTAAACTGCA
GGAAT
Found at i:49468802 original size:21 final size:21
Alignment explanation
Indices: 49468777--49468821 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
49468767 TAATAATAAA
49468777 TTTAGTTATT-TGTTTTGTAAT
1 TTTAGTT-TTATGTTTTGTAAT
* *
49468798 TTTAGTTTTATTTTTTGTTAT
1 TTTAGTTTTATGTTTTGTAAT
49468819 TTT
1 TTT
49468822 TTATTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.16, C:0.00, G:0.11, T:0.73
Consensus pattern (21 bp):
TTTAGTTTTATGTTTTGTAAT
Found at i:49470825 original size:29 final size:28
Alignment explanation
Indices: 49470793--49470857 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
49470783 TAAAAATATA
*
49470793 TAATTTTATATT-AATATATTTTTATAATT
1 TAATTTAATATTAAATATATTTTT-T-ATT
*
49470822 TAATTTAATTTTAAATATATTTTTTATT
1 TAATTTAATATTAAATATATTTTTTATT
*
49470850 TAAATTAA
1 TAATTTAA
49470858 ACTTGAGTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 10 0.31
29 11 0.34
30 11 0.34
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TAATTTAATATTAAATATATTTTTTATT
Found at i:49470833 original size:18 final size:16
Alignment explanation
Indices: 49470790--49470834 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
49470780 TATTAAAAAT
49470790 ATATAATTTTATATTA
1 ATATAATTTTATATTA
*
49470806 ATATATTTTTATAATTTA
1 ATATAATTTTAT-A-TTA
*
49470824 ATTTAATTTTA
1 ATATAATTTTA
49470835 AATATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.46
17 1 0.04
18 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATAATTTTATATTA
Found at i:49472586 original size:23 final size:23
Alignment explanation
Indices: 49472543--49472586 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
49472533 TTAACATTTT
*
49472543 ATAATTTTAATTATTTTTTAAAA
1 ATAATTTTAATTATTTCTTAAAA
*
49472566 ATAATTTTTATT-TTTGCTTAA
1 ATAATTTTAATTATTT-CTTAA
49472587 GCGGTAAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
ATAATTTTAATTATTTCTTAAAA
Found at i:49474084 original size:57 final size:54
Alignment explanation
Indices: 49473982--49474147 Score: 174
Period size: 57 Copynumber: 3.0 Consensus size: 54
49473972 TGACCATTGA
* *
49473982 TGCCATTTTTTCCGGTATCCTCAAATCC--AACAATCGAACTTGATTTTCCCTTTTT
1 TGCCA-TTTTCCCGG-ATCCTCAAATCCTTAACAACCGAACTTGA-TTTCCCTTTTT
* *
49474037 TGCCATTTTCCCCGGATCCTCAAATCCATTAACAACCGAGCTTGATTTCCCCTTTT
1 TGCCATTTT-CCCGGATCCTCAAATCC-TTAACAACCGAACTTGATTTCCCTTTTT
** * *
49474093 TGACCCATTTTCTTGGATCCTCCAACCCGTTAACAACCGAACTTGATTTCCCTTT
1 TG--CCATTTTCCCGGATCCTCAAATCC-TTAACAACCGAACTTGATTTCCCTTT
49474148 GTTAGTATTA
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
54 16 0.17
55 9 0.10
56 12 0.13
57 50 0.53
58 7 0.07
ACGTcount: A:0.22, C:0.31, G:0.10, T:0.37
Consensus pattern (54 bp):
TGCCATTTTCCCGGATCCTCAAATCCTTAACAACCGAACTTGATTTCCCTTTTT
Found at i:49476460 original size:32 final size:30
Alignment explanation
Indices: 49476390--49476465 Score: 73
Period size: 32 Copynumber: 2.4 Consensus size: 30
49476380 GAGAGTTAGA
* * *
49476390 TTTGTATTTTTTTGTAATTTTTTTATAAAT
1 TTTGAATTTTTTTGTAATCTATTTATAAAT
*
49476420 TTAT-AATTTTTTATGATAATCTATTTATATAT
1 TT-TGAATTTTTT-TG-TAATCTATTTATAAAT
49476452 TTTGAATTTCTTTT
1 TTTGAATTT-TTTT
49476466 AGATTTGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
30 9 0.24
31 4 0.11
32 21 0.57
33 3 0.08
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (30 bp):
TTTGAATTTTTTTGTAATCTATTTATAAAT
Found at i:49478428 original size:22 final size:22
Alignment explanation
Indices: 49478400--49478463 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
49478390 TTTATTGTTC
49478400 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
49478422 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
49478444 AGCCATGAGAGCTTAGTACG
1 AAACATGAGAGCTTAGTACG
49478464 ATCAGGGCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:49483122 original size:10 final size:9
Alignment explanation
Indices: 49483104--49483146 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
49483094 CTTTTATACA
49483104 TTTTAATTT
1 TTTTAATTT
49483113 TTTATAATTT
1 TTT-TAATTT
*
49483123 TTTTGATTT
1 TTTTAATTT
*
49483132 TTTGAATTT
1 TTTTAATTT
49483141 TTTTAA
1 TTTTAA
49483147 AAATAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 20 0.69
10 9 0.31
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (9 bp):
TTTTAATTT
Found at i:49487735 original size:24 final size:24
Alignment explanation
Indices: 49487703--49487749 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
49487693 TTGGGGATAA
49487703 AGCCACATGAACTCAGAACTCGGT
1 AGCCACATGAACTCAGAACTCGGT
*
49487727 AGCCACATGAACTCGGAACTCGG
1 AGCCACATGAACTCAGAACTCGG
49487750 CAACTTCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.15
Consensus pattern (24 bp):
AGCCACATGAACTCAGAACTCGGT
Found at i:49495572 original size:11 final size:11
Alignment explanation
Indices: 49495540--49495577 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
49495530 TTTTTTACAT
49495540 AAATAATA-TA
1 AAATAATATTA
49495550 AAA-AAT-TTA
1 AAATAATATTA
49495559 AAATAATATTA
1 AAATAATATTA
49495570 AAATAATA
1 AAATAATA
49495578 CAACTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.32
10 6 0.24
11 11 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATAATATTA
Found at i:49495722 original size:27 final size:27
Alignment explanation
Indices: 49495662--49495728 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
49495652 GAGGGTCTGT
* *
49495662 CACAGGCGACACCAAAGGTGTCAATGG
1 CACAGGCGACACCAAAGGTGCCAATGC
* * *
49495689 CAGAGGCGGCACCAAAGGTGCCACTGC
1 CACAGGCGACACCAAAGGTGCCAATGC
49495716 CACAGGCGACACC
1 CACAGGCGACACC
49495729 TGTGCCATGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.30, C:0.33, G:0.30, T:0.07
Consensus pattern (27 bp):
CACAGGCGACACCAAAGGTGCCAATGC
Found at i:49495916 original size:24 final size:23
Alignment explanation
Indices: 49495853--49495917 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
49495843 GTGCCGGAAA
*
49495853 AAGAAAAGAAAAAGAGAGAAAGAG
1 AAGAAAA-AAAAAGAAAGAAAGAG
* * **
49495877 AATAGAGAAAGGAGAAAGAAAGAG
1 AAGA-AAAAAAAAGAAAGAAAGAG
49495901 AAGAAAAAAAATAGAAA
1 AAGAAAAAAAA-AGAAA
49495918 AATAAGGTAT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
23 4 0.13
24 24 0.80
25 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (23 bp):
AAGAAAAAAAAAGAAAGAAAGAG
Found at i:49496119 original size:40 final size:39
Alignment explanation
Indices: 49496070--49496278 Score: 160
Period size: 40 Copynumber: 5.3 Consensus size: 39
49496060 GTTTAGTTAT
* *
49496070 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAAAC
1 TAAT-ATTATTGTTAGTTAGTATTATTGTTAGT-AAAACAC
* * *
49496111 TAATATTATTATTATGGTTAGTTATTA-GGATTAGTAAAACCCC
1 TAATATTATTGTTA--GTTAG-TATTATTG-TTAGTAAAA-CAC
* ***
49496154 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTACAC
1 TAA-TATTATTGTTAGTTAGTATTATTGTTAG-TAAAACAC
* *
49496194 T-ATATTATTGTTAG-T--TATTATTTTTAGTAAAACCC
1 TAATATTATTGTTAGTTAGTATTATTGTTAGTAAAACAC
* *
49496229 TAATTATTATTGTTAGTTAGTATTATTTTTAGTAAAAAAC
1 TAA-TATTATTGTTAGTTAGTATTATTGTTAGTAAAACAC
*
49496269 TATTATTATT
1 TAATATTATT
49496279 ATTATTATGT
Statistics
Matches: 134, Mismatches: 20, Indels: 30
0.73 0.11 0.16
Matches are distributed among these distances:
35 5 0.04
36 11 0.08
37 12 0.09
38 9 0.07
39 12 0.09
40 40 0.30
41 12 0.09
42 9 0.07
43 17 0.13
44 7 0.05
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (39 bp):
TAATATTATTGTTAGTTAGTATTATTGTTAGTAAAACAC
Found at i:49496213 original size:76 final size:76
Alignment explanation
Indices: 49496120--49496261 Score: 214
Period size: 76 Copynumber: 1.9 Consensus size: 76
49496110 CTAATATTAT
49496120 TATTATGGTTAGTTATTAGGATTAGTAAAACCCCTAATTATTATT-TTAGTTAGTATGATTGTTA
1 TATTATGGTTAGTTATTAGGATTAGTAAAA-CCCTAATTATTATTGTTAGTTAGTATGATTGTTA
49496184 GTTTTTACACTA
65 GTTTTTACACTA
* *** * *
49496196 TATTATTGTTAGTTATTATTTTTAGTAAAACCCTAATTATTATTGTTAGTTAGTATTATTTTTAG
1 TATTATGGTTAGTTATTAGGATTAGTAAAACCCTAATTATTATTGTTAGTTAGTATGATTGTTAG
49496261 T
66 T
49496262 AAAAAACTAT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
75 14 0.24
76 45 0.76
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (76 bp):
TATTATGGTTAGTTATTAGGATTAGTAAAACCCTAATTATTATTGTTAGTTAGTATGATTGTTAG
TTTTTACACTA
Found at i:49496276 original size:76 final size:77
Alignment explanation
Indices: 49496070--49496286 Score: 208
Period size: 76 Copynumber: 2.8 Consensus size: 77
49496060 GTTTAGTTAT
* * * *
49496070 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAAACTAATATTATTATTATGGTTAGTTA
1 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTAAAAAAC---TATTATTA-T-T-GTTAGTTA
49496135 TTAGGATTAGTAAAACCCC
59 TTAGGATTAGTAAAACCCC
*** * ***
49496154 TAATTATTATTTTAGTTAGTATGATTGTTAGTTTTTACACTA-TATTATTGTTAGTTATTATTTT
1 TAATTATTATTTTAGTTAGTATGATTGTTAGTTAAAAAACTATTATTATTGTTAGTTATTAGGAT
49496218 TAGTAAAA-CCC
66 TAGTAAAACCCC
* * *
49496229 TAATTATTATTGTTAGTTAGTATTATTTTTAG-TAAAAAACTATTATTATTATTA-TTAT
1 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTAAAAAACTATTATTATTGTTAGTTAT
49496287 GTTAGTTATT
Statistics
Matches: 113, Mismatches: 18, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
75 24 0.21
76 48 0.42
77 1 0.01
78 1 0.01
79 5 0.04
80 2 0.02
83 22 0.19
84 10 0.09
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.50
Consensus pattern (77 bp):
TAATTATTATTTTAGTTAGTATGATTGTTAGTTAAAAAACTATTATTATTGTTAGTTATTAGGAT
TAGTAAAACCCC
Found at i:49499804 original size:159 final size:157
Alignment explanation
Indices: 49499476--49500081 Score: 896
Period size: 158 Copynumber: 3.9 Consensus size: 157
49499466 NNNNNNNNNN
*
49499476 CTTTCAAAAAAATATATTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGA
1 CTTTC-AAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGA
* * * * *
49499541 AATGTATTATTTTAGTTTGTTTTTTATAT-AAATCTAGCAAAAAAATCCTTATTTTGGCCCTTTA
65 AATGTATTATTTTAGTGTATTTTTTATATAAAAT-TAG-TAAAAAACCCTTATTTTGGCCATTTA
49499605 TTCGTATTTTTCTTATTTTCGAATTTTATTA
128 TTCGTATTTTTCTTATTTTCG-ATTTTATTA
*
49499636 CTTTCAAAAAATATACTATTTTTGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAA
1 CTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAA
*
49499701 ATGTATTATTTTAGTGTGTTTTTTATATAAAATTAGTAAAAAACCCTTATTTTGGCCATTTATTC
66 ATGTATTATTTTAGTGTATTTTTTATATAAAATTAGTAAAAAACCCTTATTTTGGCCATTTATTC
49499766 GTATTTTTCTTATTTTCAGATTTTATTA
131 GTATTTTTCTTATTTTC-GATTTTATTA
*
49499794 CTTTCAAAAAATATACTATTTTTGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAA
1 CTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAA
* * *
49499859 ATGTATTATTTTAGTATATTTTTTATATAAATTTAGTAAAAAACCCTTATTTTGGCCATTTGTTC
66 ATGTATTATTTTAGTGTATTTTTTATATAAAATTAGTAAAAAACCCTTATTTTGGCCATTTATTC
49499924 AG-ATTTTTCTTATTTTCGGATTTTATTA
131 -GTATTTTTCTTATTTTC-GATTTTATTA
49499952 CTTTCAAAAAATATACTATTTTCG--------TA--TT-TATTATTTTAGTACATAATGTTTGAA
1 CTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAA
** * * * *
49500006 ATGTATTATTTTAGTGTATTTTTTATATAATTTTAATAAAAAACACTTATTTTGGCCCTTTGTTC
66 ATGTATTATTTTAGTGTATTTTTTATATAAAATTAGTAAAAAACCCTTATTTTGGCCATTTATTC
49500071 GTATTTTTCTT
131 GTATTTTTCTT
49500082 TTTCTTTTTT
Statistics
Matches: 425, Mismatches: 17, Indels: 21
0.92 0.04 0.05
Matches are distributed among these distances:
146 1 0.00
147 95 0.22
148 2 0.00
150 2 0.00
158 226 0.53
159 90 0.21
160 9 0.02
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.53
Consensus pattern (157 bp):
CTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAA
ATGTATTATTTTAGTGTATTTTTTATATAAAATTAGTAAAAAACCCTTATTTTGGCCATTTATTC
GTATTTTTCTTATTTTCGATTTTATTA
Found at i:49500317 original size:22 final size:23
Alignment explanation
Indices: 49500283--49500326 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
49500273 CAACCAATAA
49500283 ATTTCAACATATTC-TCAAGATAG
1 ATTTCAACATATTCAT-AAGATAG
*
49500306 ATTT-AACGTATTCATAAGATA
1 ATTTCAACATATTCATAAGATA
49500327 ACCTCATCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTTCAACATATTCATAAGATAG
Found at i:49503320 original size:30 final size:30
Alignment explanation
Indices: 49503286--49503406 Score: 129
Period size: 30 Copynumber: 4.4 Consensus size: 30
49503276 AAATAAAATA
*
49503286 AAATAATAAAACATAGAATGTGCATAACAT
1 AAATAATAAAACATAGAATGTACATAACAT
49503316 AAATAAT--AACATA-AA--TA-AT---A-
1 AAATAATAAAACATAGAATGTACATAACAT
* *
49503336 AAATAATAAGACATAGTATGTACATAACAT
1 AAATAATAAAACATAGAATGTACATAACAT
49503366 AAATAATAAAACATAGAATGTACATAACAT
1 AAATAATAAAACATAGAATGTACATAACAT
49503396 AAA-AATTAAAA
1 AAATAA-TAAAA
49503407 TTAAATTATG
Statistics
Matches: 75, Mismatches: 5, Indels: 22
0.74 0.05 0.22
Matches are distributed among these distances:
20 7 0.09
21 1 0.01
22 5 0.07
23 1 0.01
24 2 0.03
25 3 0.04
26 2 0.03
27 2 0.03
28 6 0.08
29 3 0.04
30 43 0.57
ACGTcount: A:0.61, C:0.08, G:0.07, T:0.24
Consensus pattern (30 bp):
AAATAATAAAACATAGAATGTACATAACAT
Found at i:49503326 original size:12 final size:12
Alignment explanation
Indices: 49503309--49503341 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
49503299 TAGAATGTGC
49503309 ATAACATAAATA
1 ATAACATAAATA
49503321 ATAACATAAATA
1 ATAACATAAATA
*
49503333 ATAAAATAA
1 ATAACATAA
49503342 TAAGACATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAACATAAATA
Found at i:49503396 original size:16 final size:16
Alignment explanation
Indices: 49503346--49503396 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
49503336 AAATAATAAG
*
49503346 ACATAGTATGTACATA
1 ACATAGAATGTACATA
*
49503362 ACATA-AATAATA-A-A
1 ACATAGAAT-GTACATA
49503376 ACATAGAATGTACATA
1 ACATAGAATGTACATA
49503392 ACATA
1 ACATA
49503397 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
14 8 0.29
15 7 0.25
16 13 0.46
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.25
Consensus pattern (16 bp):
ACATAGAATGTACATA
Found at i:49514724 original size:19 final size:18
Alignment explanation
Indices: 49514702--49514738 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
49514692 TTATTATCAA
49514702 AAATAATTATAATTATAAT
1 AAATAATTA-AATTATAAT
*
49514721 AAATAATTAAATTTTAAT
1 AAATAATTAAATTATAAT
49514739 GTCAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATAATTAAATTATAAT
Found at i:49519076 original size:4 final size:4
Alignment explanation
Indices: 49519067--49519176 Score: 220
Period size: 4 Copynumber: 27.5 Consensus size: 4
49519057 TACAAATGAA
49519067 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
49519115 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
49519163 ATAC ATAC ATAC AT
1 ATAC ATAC ATAC AT
49519177 GTAAGTATTT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 106 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:49519503 original size:189 final size:185
Alignment explanation
Indices: 49519181--49519554 Score: 563
Period size: 189 Copynumber: 2.0 Consensus size: 185
49519171 ATACATGTAA
*
49519181 GTATTTAGTTATAATAAGCACTGAAATTTCATGGAATTGTTATTGCAGTGAATAGATAGCCATGT
1 GTATATAGTTATAATAAGCACTGAAATTTCATGGAATTGTTATTGCAGTGAATAGATAGCCATGT
* * * * *
49519246 TTATCTCTTACATGCCTTCAATTGAATACATTCAAGCAAAGACTTGTTAAATGGTCTAATTACAC
66 TTAGCTATTACATGCCTTCAATTCAATACATTCAAGCAAAGACTAGTTAAATGGTCCAATTACAC
49519311 TTTTAG-CATCTCCTAAACCTTAATAATTCAATTTAATCCATTTTAGCTCCTTTAT
131 TTTTAGCCA-CTCCTAAACCTTAATAATTCAATTTAATCCATTTTAGCTCCTTTAT
* * *
49519366 GTATATAGTTATAATAAGCCCTGAAATTTCTTGGAAAGTAT-TACTATTGCAGTGAATGGATAGC
1 GTATATAGTTATAATAAGCACTGAAATTTCATGG-AA-T-TGT--TATTGCAGTGAATAGATAGC
*
49519430 CATGTTTAGCTATTACATGCCTTCAATTCAATACATTCAAGCAAAGACTAGTTAGATGGTCCAAT
61 CATGTTTAGCTATTACATGCCTTCAATTCAATACATTCAAGCAAAGACTAGTTAAATGGTCCAAT
* * *
49519495 TGCACTTTTAGCCACTCCTAAACCTTAATAATTCAATTTGATCCCTTTTAGCTCCTTTAT
126 TACACTTTTAGCCACTCCTAAACCTTAATAATTCAATTTAATCCATTTTAGCTCCTTTAT
49519555 TAAATGGAAA
Statistics
Matches: 170, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
185 31 0.18
186 2 0.01
187 2 0.01
188 1 0.01
189 132 0.78
190 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (185 bp):
GTATATAGTTATAATAAGCACTGAAATTTCATGGAATTGTTATTGCAGTGAATAGATAGCCATGT
TTAGCTATTACATGCCTTCAATTCAATACATTCAAGCAAAGACTAGTTAAATGGTCCAATTACAC
TTTTAGCCACTCCTAAACCTTAATAATTCAATTTAATCCATTTTAGCTCCTTTAT
Found at i:49533161 original size:16 final size:15
Alignment explanation
Indices: 49533131--49533172 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
49533121 AAAAATATAA
49533131 ATATTAAAATTAAAAT
1 ATATT-AAATTAAAAT
49533147 -TAGTTAAATTAAAAAT
1 ATA-TTAAATT-AAAAT
49533163 ATATTAAATT
1 ATATTAAATT
49533173 TAGAATTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.30
16 14 0.61
17 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
ATATTAAATTAAAAT
Found at i:49544977 original size:6 final size:6
Alignment explanation
Indices: 49544966--49545034 Score: 66
Period size: 6 Copynumber: 11.5 Consensus size: 6
49544956 CACCGCCAAA
* ** * **
49544966 TCCACC TCCACC TCCAGC TCCACC TCCACC TCCAAA TCCACC ACCGGC
1 TCCACC TCCACC TCCACC TCCACC TCCACC TCCACC TCCACC TCCACC
* *
49545014 TCCACC TCCAGC ACCACC TCC
1 TCCACC TCCACC TCCACC TCC
49545035 GAATCCTCCA
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.20, C:0.59, G:0.06, T:0.14
Consensus pattern (6 bp):
TCCACC
Found at i:49545005 original size:18 final size:18
Alignment explanation
Indices: 49544955--49545007 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
49544945 ACCTCCTGCA
*
49544955 CCACCGCCAAATCCACCT
1 CCACCTCCAAATCCACCT
**
49544973 CCACCTCCAGCTCCACCT
1 CCACCTCCAAATCCACCT
49544991 CCACCTCCAAATCCACC
1 CCACCTCCAAATCCACC
49545008 ACCGGCTCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.25, C:0.58, G:0.04, T:0.13
Consensus pattern (18 bp):
CCACCTCCAAATCCACCT
Found at i:49545052 original size:24 final size:26
Alignment explanation
Indices: 49545025--49545088 Score: 69
Period size: 30 Copynumber: 2.4 Consensus size: 26
49545015 CCACCTCCAG
*
49545025 CACCACCTCCGAATCCTCCACCGCCACCA
1 CACCACCTCCGAATCCTCCA---CCAGCA
49545054 GCACCACCTCCGAATCCTCCACCAG--
1 -CACCACCTCCGAATCCTCCACCAGCA
49545079 CACCACCTCC
1 CACCACCTCC
49545089 AACACCGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 10 0.30
27 3 0.09
30 20 0.61
ACGTcount: A:0.23, C:0.58, G:0.08, T:0.11
Consensus pattern (26 bp):
CACCACCTCCGAATCCTCCACCAGCA
Found at i:49545099 original size:24 final size:25
Alignment explanation
Indices: 49545043--49545100 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 25
49545033 CCGAATCCTC
49545043 CACCGCCACCAGCACCACCTCCGAA
1 CACCGCCACCAGCACCACCTCCGAA
* *
49545068 -TCCTCCACCAGCACCACCTCC-AA
1 CACCGCCACCAGCACCACCTCCGAA
49545091 CACCGCCACC
1 CACCGCCACC
49545101 GAAACCACCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.26, C:0.59, G:0.09, T:0.07
Consensus pattern (25 bp):
CACCGCCACCAGCACCACCTCCGAA
Found at i:49545205 original size:42 final size:41
Alignment explanation
Indices: 49545158--49545292 Score: 137
Period size: 42 Copynumber: 3.2 Consensus size: 41
49545148 CCTTTCCAGT
*
49545158 TCCACCTCCAAGGCCTCCTCCTTTGCCAATACCGCCTCCAAG
1 TCCACCACCAAGGCCTCCTCCTTTGCCAATACC-CCTCCAAG
* * ** ** * *
49545200 TCCACCACCATGTCCTCCTCC-AAGTCCACCACCCTTTCCAAT
1 TCCACCACCAAGGCCTCCTCCTTTG-CCAATACCC-CTCCAAG
*
49545242 TCCACCACCAGGGCCTCCTCCTTTGCCAATACCACCTCCAAG
1 TCCACCACCAAGGCCTCCTCCTTTGCCAATACC-CCTCCAAG
49545284 TCCACCACC
1 TCCACCACC
49545293 CTTTCCAATT
Statistics
Matches: 72, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
41 2 0.03
42 68 0.94
43 2 0.03
ACGTcount: A:0.21, C:0.50, G:0.09, T:0.21
Consensus pattern (41 bp):
TCCACCACCAAGGCCTCCTCCTTTGCCAATACCCCTCCAAG
Found at i:49545299 original size:18 final size:18
Alignment explanation
Indices: 49545278--49545328 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
49545268 CAATACCACC
*
49545278 TCCAAGTCCACCACCCTT
1 TCCAATTCCACCACCCTT
* *
49545296 TCCAATTCCACCTCCTTT
1 TCCAATTCCACCACCCTT
*
49545314 TCCTATTCCACCACC
1 TCCAATTCCACCACC
49545329 ATGTCCTCCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.20, C:0.49, G:0.02, T:0.29
Consensus pattern (18 bp):
TCCAATTCCACCACCCTT
Found at i:49545301 original size:30 final size:30
Alignment explanation
Indices: 49545141--49545472 Score: 229
Period size: 30 Copynumber: 11.3 Consensus size: 30
49545131 ACCGCCAATG
* *
49545141 CCACCACCCTTTCCAGTTCCACCTCCAAGG
1 CCACCACCCTTTCCAATTCCACCTCCAAGT
* * * *
49545171 CCTCC-TCCTTTGCCAATACCGCCTCCAAGT
1 CCACCACCCTTT-CCAATTCCACCTCCAAGT
* *
49545201 CCACCACCATGTCC---T---CCTCCAAGT
1 CCACCACCCTTTCCAATTCCACCTCCAAGT
* * *
49545225 CCACCACCCTTTCCAATTCCACCACCAGGG
1 CCACCACCCTTTCCAATTCCACCTCCAAGT
* * *
49545255 CCTCC-TCCTTTGCCAATACCACCTCCAAGT
1 CCACCACCCTTT-CCAATTCCACCTCCAAGT
***
49545285 CCACCACCCTTTCCAATTCCACCTCCTTTT
1 CCACCACCCTTTCCAATTCCACCTCCAAGT
* *
49545315 CCTATTCCA-CC--ACC-ATGTCCTCCTCCAAGT
1 CC-A--CCACCCTTTCCAAT-TCCACCTCCAAGT
* * * * *
49545345 CCACCTCCCTTGCCAATCCCACCGCCAAGG
1 CCACCACCCTTTCCAATTCCACCTCCAAGT
* * * *
49545375 CCTCCACCTTTTCCAATCCCACCACCAAGT
1 CCACCACCCTTTCCAATTCCACCTCCAAGT
* * *
49545405 CCACCACCCTTGCCAATGCCACCACCAAGT
1 CCACCACCCTTTCCAATTCCACCTCCAAGT
* *
49545435 CCACCACCCTTTCCAATGCCACCACCAAGT
1 CCACCACCCTTTCCAATTCCACCTCCAAGT
49545465 CCACCACC
1 CCACCACC
49545473 TGCTCCACCT
Statistics
Matches: 234, Mismatches: 50, Indels: 36
0.73 0.16 0.11
Matches are distributed among these distances:
24 21 0.09
27 3 0.01
28 2 0.01
29 13 0.06
30 179 0.76
31 11 0.05
32 2 0.01
33 3 0.01
ACGTcount: A:0.21, C:0.50, G:0.08, T:0.21
Consensus pattern (30 bp):
CCACCACCCTTTCCAATTCCACCTCCAAGT
Found at i:49545323 original size:84 final size:84
Alignment explanation
Indices: 49545141--49545310 Score: 241
Period size: 84 Copynumber: 2.0 Consensus size: 84
49545131 ACCGCCAATG
* * *
49545141 CCACCACCCTTTCCAGTTCCACCTCCAAGGCCTCCTCCTTTGCCAATACCGCCTCCAAGTCCACC
1 CCACCACCCTTTCCAATTCCACCACCAAGGCCTCCTCCTTTGCCAATACCACCTCCAAGTCCACC
** *
49545206 ACCATGTCCTCCTCCAAGT
66 ACCATGTCCAACTCCAACT
*
49545225 CCACCACCCTTTCCAATTCCACCACCAGGGCCTCCTCCTTTGCCAATACCACCTCCAAGTCCACC
1 CCACCACCCTTTCCAATTCCACCACCAAGGCCTCCTCCTTTGCCAATACCACCTCCAAGTCCACC
* * * *
49545290 ACCCTTTCCAATTCCACCT
66 ACCATGTCCAACTCCAACT
49545309 CC
1 CC
49545311 TTTTCCTATT
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.20, C:0.50, G:0.08, T:0.22
Consensus pattern (84 bp):
CCACCACCCTTTCCAATTCCACCACCAAGGCCTCCTCCTTTGCCAATACCACCTCCAAGTCCACC
ACCATGTCCAACTCCAACT
Found at i:49545335 original size:18 final size:18
Alignment explanation
Indices: 49545284--49545335 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
49545274 CACCTCCAAG
* *
49545284 TCCACCACCCTTTCCAAT
1 TCCACCACCATTTCCTAT
* *
49545302 TCCACCTCCTTTTCCTAT
1 TCCACCACCATTTCCTAT
*
49545320 TCCACCACCATGTCCT
1 TCCACCACCATTTCCT
49545336 CCTCCAAGTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.48, G:0.02, T:0.33
Consensus pattern (18 bp):
TCCACCACCATTTCCTAT
Found at i:49545337 original size:120 final size:120
Alignment explanation
Indices: 49545200--49545427 Score: 357
Period size: 120 Copynumber: 1.9 Consensus size: 120
49545190 CGCCTCCAAG
* * * *
49545200 TCCACCACCATGTCCTCCTCCAAGTCCACCACCCTTTCCAATTCCACCACCAGGGCCTCCTCCTT
1 TCCACCACCATGTCCTCCTCCAAGTCCACCACCCTTGCCAATCCCACCACCAAGGCCTCCACCTT
* * *
49545265 TGCCAATACCACCTCCAAGTCCACCACCCTTTCCAATTCCACCTCCTTTTCCTAT
66 TGCCAATACCACCACCAAGTCCACCACCCTTGCCAATGCCACCTCCTTTTCCTAT
* *
49545320 TCCACCACCATGTCCTCCTCCAAGTCCACCTCCCTTGCCAATCCCACCGCCAAGGCCTCCACCTT
1 TCCACCACCATGTCCTCCTCCAAGTCCACCACCCTTGCCAATCCCACCACCAAGGCCTCCACCTT
* *
49545385 TTCCAATCCCACCACCAAGTCCACCACCCTTGCCAATGCCACC
66 TGCCAATACCACCACCAAGTCCACCACCCTTGCCAATGCCACC
49545428 ACCAAGTCCA
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
120 97 1.00
ACGTcount: A:0.21, C:0.50, G:0.07, T:0.22
Consensus pattern (120 bp):
TCCACCACCATGTCCTCCTCCAAGTCCACCACCCTTGCCAATCCCACCACCAAGGCCTCCACCTT
TGCCAATACCACCACCAAGTCCACCACCCTTGCCAATGCCACCTCCTTTTCCTAT
Found at i:49545379 original size:42 final size:42
Alignment explanation
Indices: 49545296--49545379 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
49545286 CACCACCCTT
* * * * * * *
49545296 TCCAATTCCACCTCCTTTTCCTATTCCACCACCATGTCCTCC
1 TCCAAGTCCACCTCCCTTGCCAATCCCACCACCAAGGCCTCC
*
49545338 TCCAAGTCCACCTCCCTTGCCAATCCCACCGCCAAGGCCTCC
1 TCCAAGTCCACCTCCCTTGCCAATCCCACCACCAAGGCCTCC
49545380 ACCTTTTCCA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.18, C:0.50, G:0.07, T:0.25
Consensus pattern (42 bp):
TCCAAGTCCACCTCCCTTGCCAATCCCACCACCAAGGCCTCC
Found at i:49545485 original size:18 final size:18
Alignment explanation
Indices: 49545464--49545587 Score: 81
Period size: 18 Copynumber: 6.6 Consensus size: 18
49545454 CACCACCAAG
*
49545464 TCCACCACCTGCTCCACC
1 TCCACCACCAGCTCCACC
49545482 TCCACCACCAAGCCCTCCACCTGC
1 TCCACCACC-AG--CTCCA-C--C
* * * *
49545506 TCCACCTCCACCACCAAGC
1 TCCACCACCAGCTCC-ACC
*
49545525 -CCTCCACCAGCTCCACC
1 TCCACCACCAGCTCCACC
*
49545542 TCCACCTCCAAG-TCCACC
1 TCCACCACC-AGCTCCACC
*
49545560 ACCACCACCAGCTCCACC
1 TCCACCACCAGCTCCACC
*
49545578 TCCAACACCA
1 TCCACCACCA
49545588 CCACCAAAAC
Statistics
Matches: 80, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
17 4 0.05
18 52 0.65
19 4 0.05
21 8 0.10
22 2 0.03
23 1 0.01
24 9 0.11
ACGTcount: A:0.23, C:0.59, G:0.06, T:0.12
Consensus pattern (18 bp):
TCCACCACCAGCTCCACC
Found at i:49545486 original size:15 final size:15
Alignment explanation
Indices: 49545468--49545548 Score: 53
Period size: 15 Copynumber: 5.4 Consensus size: 15
49545458 ACCAAGTCCA
49545468 CCACCTGCTCCACCT
1 CCACCTGCTCCACCT
* *
49545483 CCACC-AC-CAAGCCCT
1 CCACCTGCTCCA--CCT
49545498 CCACCTGCTCCACCT
1 CCACCTGCTCCACCT
* *
49545513 CCACC-AC-CAAGCCCT
1 CCACCTGCTCCA--CCT
*
49545528 CCACCAGCTCCACCT
1 CCACCTGCTCCACCT
49545543 CCACCT
1 CCACCT
49545549 CCAAGTCCAC
Statistics
Matches: 49, Mismatches: 9, Indels: 16
0.66 0.12 0.22
Matches are distributed among these distances:
13 4 0.08
14 2 0.04
15 37 0.76
16 2 0.04
17 4 0.08
ACGTcount: A:0.20, C:0.60, G:0.06, T:0.14
Consensus pattern (15 bp):
CCACCTGCTCCACCT
Found at i:49545487 original size:30 final size:30
Alignment explanation
Indices: 49545393--49545562 Score: 179
Period size: 30 Copynumber: 5.7 Consensus size: 30
49545383 TTTTCCAATC
*
49545393 CCACCACCAAGTCCACCACC--CTTGCCA-AT
1 CCACCACCAAGTCCACCACCTGC-T-CCACCT
* *
49545422 GCCACCACCAAGTCCACCACCCT-TTCCA-AT
1 -CCACCACCAAGTCCACCA-CCTGCTCCACCT
49545452 GCCACCACCAAGTCCACCACCTGCTCCACCT
1 -CCACCACCAAGTCCACCACCTGCTCCACCT
* *
49545483 CCACCACCAAGCCCTCCACCTGCTCCACCT
1 CCACCACCAAGTCCACCACCTGCTCCACCT
* * *
49545513 CCACCACCAAGCCCTCCACCAGCTCCACCT
1 CCACCACCAAGTCCACCACCTGCTCCACCT
*
49545543 CCACCTCCAAGTCCACCACC
1 CCACCACCAAGTCCACCACC
49545563 ACCACCAGCT
Statistics
Matches: 127, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
29 3 0.02
30 120 0.94
31 4 0.03
ACGTcount: A:0.24, C:0.56, G:0.07, T:0.13
Consensus pattern (30 bp):
CCACCACCAAGTCCACCACCTGCTCCACCT
Found at i:49545487 original size:60 final size:58
Alignment explanation
Indices: 49545363--49545562 Score: 190
Period size: 60 Copynumber: 3.3 Consensus size: 58
49545353 CTTGCCAATC
* * * * *
49545363 CCACCGCCAAGGCCTCCACCTTTTCCAATCCCACCACCAAGTCCACCACC-CTTGCCA-AT
1 CCACCACCAAGTCCACCACCCTTTCCAAT-CCACCACCAAGTCCACCACCGC-T-CCACCT
49545422 GCCACCACCAAGTCCACCACCCTTTCCAATGCCACCACCAAGTCCACCACCTGCTCCACCT
1 -CCACCACCAAGTCCACCACCCTTTCCAAT-CCACCACCAAGTCCACCACC-GCTCCACCT
* * * * * *
49545483 CCACCACCAAGCCCTCCA-CCTGCTCCACCTCCACCACCAAGCCCTCCACCAGCTCCACCT
1 CCACCACCAAGTCCACCACCCT-TTCCA-ATCCACCACCAAGTCCACCACC-GCTCCACCT
*
49545543 CCACCTCCAAGTCCACCACC
1 CCACCACCAAGTCCACCACC
49545563 ACCACCAGCT
Statistics
Matches: 118, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
59 3 0.03
60 110 0.93
61 4 0.03
62 1 0.01
ACGTcount: A:0.23, C:0.55, G:0.07, T:0.14
Consensus pattern (58 bp):
CCACCACCAAGTCCACCACCCTTTCCAATCCACCACCAAGTCCACCACCGCTCCACCT
Found at i:49545546 original size:6 final size:6
Alignment explanation
Indices: 49545535--49545622 Score: 50
Period size: 6 Copynumber: 14.2 Consensus size: 6
49545525 CCTCCACCAG
* * * * * *
49545535 CTCCAC CTCCAC CTCCAA GTCCAC CACCAC CACCAG CTCCAC CTCCAA
1 CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC
* * * **
49545583 CACCAC CACCAA AACCAC CTCCAAGAC CTCCAC CTCCAC C
1 CTCCAC CTCCAC CTCCAC CTCC---AC CTCCAC CTCCAC C
49545623 AAAACCACCC
Statistics
Matches: 63, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
6 57 0.90
9 6 0.10
ACGTcount: A:0.28, C:0.58, G:0.03, T:0.10
Consensus pattern (6 bp):
CTCCAC
Found at i:49545563 original size:30 final size:30
Alignment explanation
Indices: 49545453--49545593 Score: 167
Period size: 30 Copynumber: 4.7 Consensus size: 30
49545443 CTTTCCAATG
* *
49545453 CCACCACCAAGTCCACCACCTGCTCCACCT
1 CCACCACCAAGCCCACCACCAGCTCCACCT
* *
49545483 CCACCACCAAGCCCTCCACCTGCTCCACCT
1 CCACCACCAAGCCCACCACCAGCTCCACCT
*
49545513 CCACCACCAAGCCCTCCACCAGCTCCACCT
1 CCACCACCAAGCCCACCACCAGCTCCACCT
* * * * *
49545543 CCACCTCCAAGTCCACCACCACCACCAGCT
1 CCACCACCAAGCCCACCACCAGCTCCACCT
*
49545573 CCACCTCCAA-CACCACCACCA
1 CCACCACCAAGC-CCACCACCA
49545594 AAACCACCTC
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
30 100 1.00
ACGTcount: A:0.25, C:0.59, G:0.06, T:0.11
Consensus pattern (30 bp):
CCACCACCAAGCCCACCACCAGCTCCACCT
Found at i:49545601 original size:15 final size:15
Alignment explanation
Indices: 49545583--49545652 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
49545573 CCACCTCCAA
*
49545583 CACCACCACCAAAAC
1 CACCTCCACCAAAAC
** ***
49545598 CACCTCCAAGACCTC
1 CACCTCCACCAAAAC
49545613 CACCTCCACCAAAAC
1 CACCTCCACCAAAAC
*
49545628 CACCCCCACCACCAAACC
1 CACCTCCACCA--AAA-C
49545646 CACCTCC
1 CACCTCC
49545653 CTTAGTCAAA
Statistics
Matches: 39, Mismatches: 13, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
15 29 0.74
17 3 0.08
18 7 0.18
ACGTcount: A:0.34, C:0.59, G:0.01, T:0.06
Consensus pattern (15 bp):
CACCTCCACCAAAAC
Found at i:49545605 original size:30 final size:30
Alignment explanation
Indices: 49545507--49545642 Score: 103
Period size: 30 Copynumber: 4.5 Consensus size: 30
49545497 TCCACCTGCT
* ***
49545507 CCACCTCCACCACCAAGC-CCTCCACCAGCT
1 CCACCTCCACCACCAA-CACCACCACCAAAA
* ** **
49545537 CCACCTCCACCTCCAAGTCCACCACCACCA
1 CCACCTCCACCACCAACACCACCACCAAAA
* *
49545567 CCAGCTCCACCTCCAACACCACCACCAAAA
1 CCACCTCCACCACCAACACCACCACCAAAA
** ** *
49545597 CCACCTCCAAGACCTCCACCTCCACCAAAA
1 CCACCTCCACCACCAACACCACCACCAAAA
*
49545627 CCACCCCCACCACCAA
1 CCACCTCCACCACCAA
49545643 ACCCACCTCC
Statistics
Matches: 83, Mismatches: 22, Indels: 2
0.78 0.21 0.02
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.30, C:0.58, G:0.04, T:0.08
Consensus pattern (30 bp):
CCACCTCCACCACCAACACCACCACCAAAA
Found at i:49545623 original size:24 final size:24
Alignment explanation
Indices: 49545554--49545616 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
49545544 CACCTCCAAG
* ***
49545554 TCCACCACCACCACCAGCTCCACC
1 TCCAACACCACCACCAAAACCACC
49545578 TCCAACACCACCACCAAAACCACC
1 TCCAACACCACCACCAAAACCACC
* *
49545602 TCCAAGACCTCCACC
1 TCCAACACCACCACC
49545617 TCCACCAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.32, C:0.57, G:0.03, T:0.08
Consensus pattern (24 bp):
TCCAACACCACCACCAAAACCACC
Found at i:49553529 original size:18 final size:18
Alignment explanation
Indices: 49553484--49553529 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
49553474 TGCACGTTTA
49553484 TAAAA-AATAAATTTATT
1 TAAAATAATAAATTTATT
* *
49553501 AAAAAT-TTAAATTTATT
1 TAAAATAATAAATTTATT
49553518 TAAAATAATAAA
1 TAAAATAATAAA
49553530 GTTAAAGCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATAATAAATTTATT
Found at i:49556456 original size:13 final size:13
Alignment explanation
Indices: 49556440--49556464 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49556430 ATCACCCCCC
49556440 AAAAAAATCAAAT
1 AAAAAAATCAAAT
49556453 AAAAAAATCAAA
1 AAAAAAATCAAA
49556465 CAAACACCCA
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:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAATCAAAT
Found at i:49558849 original size:14 final size:14
Alignment explanation
Indices: 49558830--49558857 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
49558820 AAACAAAAAT
49558830 AACCAAATAAATAA
1 AACCAAATAAATAA
49558844 AACCAAATAAATAA
1 AACCAAATAAATAA
49558858 GAGTCCAAAG
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:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (14 bp):
AACCAAATAAATAA
Found at i:49566776 original size:22 final size:20
Alignment explanation
Indices: 49566733--49566777 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
49566723 TAATTTCACT
* *
49566733 ATTTTAATATAAAATTTTAA
1 ATTTTAATATAAAAATTAAA
49566753 ATTTTAAATCATAAAAATTAAA
1 ATTTT-AAT-ATAAAAATTAAA
49566775 ATT
1 ATT
49566778 AATTATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 3 0.14
22 13 0.62
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTTAATATAAAAATTAAA
Found at i:49572159 original size:17 final size:17
Alignment explanation
Indices: 49572121--49572163 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
49572111 AAAAGTCAGA
*
49572121 AATATAATT-TTATTTT
1 AATATATTTATTATTTT
49572137 ATATATATTTATTATTTT
1 A-ATATATTTATTATTTT
49572155 AATAT-TTTA
1 AATATATTTA
49572164 AAAAGATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 5 0.21
17 11 0.46
18 8 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
AATATATTTATTATTTT
Found at i:49573307 original size:28 final size:29
Alignment explanation
Indices: 49573271--49573329 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
49573261 AATTAATAGT
* *
49573271 TTTAGGTGTCAAAATGAGA-AAAAGAAAG
1 TTTAGGTGTCAAAATGAAACAAAAAAAAG
*
49573299 TTTAGGTGTCAAATTGAAACAAAAAAAAG
1 TTTAGGTGTCAAAATGAAACAAAAAAAAG
49573328 TT
1 TT
49573330 CAAGGGCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 17 0.63
29 10 0.37
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.25
Consensus pattern (29 bp):
TTTAGGTGTCAAAATGAAACAAAAAAAAG
Found at i:49580973 original size:21 final size:21
Alignment explanation
Indices: 49580940--49580987 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
49580930 TGGGTGGATC
*
49580940 AGCTCTTACGAGCTTCTGTTA
1 AGCTTTTACGAGCTTCTGTTA
* * *
49580961 AGCTTTTATGAGCTTCTTTTC
1 AGCTTTTACGAGCTTCTGTTA
49580982 AGCTTT
1 AGCTTT
49580988 CAATCTTCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.46
Consensus pattern (21 bp):
AGCTTTTACGAGCTTCTGTTA
Found at i:49581999 original size:30 final size:31
Alignment explanation
Indices: 49581965--49582033 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
49581955 ACTTAACAAC
*
49581965 TCAATGACTT-AATAAAAACTTTTGAATAGT
1 TCAATGACTTAAATAAAAACTTTTGAATAAT
*
49581995 TCAATGACTTAAATGAAAACTTTTGAATAAT
1 TCAATGACTTAAATAAAAACTTTTGAATAAT
*
49582026 TTAATGAC
1 TCAATGAC
49582034 CAAATTGTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 10 0.29
31 25 0.71
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (31 bp):
TCAATGACTTAAATAAAAACTTTTGAATAAT
Found at i:49583743 original size:10 final size:11
Alignment explanation
Indices: 49583728--49583756 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
49583718 GGAAATTTAT
49583728 AAAAAAT-ATA
1 AAAAAATCATA
49583738 AAAAAATCATA
1 AAAAAATCATA
49583749 AAAAAATC
1 AAAAAATC
49583757 TATTAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAAATCATA
Found at i:49584005 original size:10 final size:9
Alignment explanation
Indices: 49583977--49584020 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
49583967 TTTATTTTTA
49583977 TTTTATATT
1 TTTTATATT
49583986 TTTTATATT
1 TTTTATATT
* *
49583995 TTTTGTAAT
1 TTTTATATT
49584004 TTTT-TATT
1 TTTTATATT
*
49584012 TTATATATT
1 TTTTATATT
49584021 CTTGAATTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 6 0.20
9 24 0.80
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (9 bp):
TTTTATATT
Found at i:49584005 original size:19 final size:20
Alignment explanation
Indices: 49583965--49584013 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
49583955 TCCACGTGAA
*
49583965 TTTTTATTTTTATTTTATAT
1 TTTTTATTTTTATTGTATAT
49583985 TTTTTATATTTT-TTGTA-AT
1 TTTTTAT-TTTTATTGTATAT
49584004 TTTTTATTTT
1 TTTTTATTTT
49584014 ATATATTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 9 0.33
20 11 0.41
21 4 0.15
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTTTATTTTTATTGTATAT
Found at i:49584832 original size:34 final size:34
Alignment explanation
Indices: 49584794--49584893 Score: 119
Period size: 34 Copynumber: 2.9 Consensus size: 34
49584784 TTAGGGCTTA
* *
49584794 GGGTTTTAAAAAAAGTAATTAAATTAGGTTTTTG
1 GGGTTTTAAAAAAATTAATTAAATTAGGTTTTAG
* **
49584828 GGGTTTTAAATAAATTAATTAAATTAGGGCTTAG
1 GGGTTTTAAAAAAATTAATTAAATTAGGTTTTAG
* * *
49584862 TGTTTTTAAGAAAATTAATTAAATTATGGTTT
1 GGGTTTTAAAAAAATTAATTAAATTA-GGTTT
49584894 AGTTTTCTAA
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
34 51 0.94
35 3 0.06
ACGTcount: A:0.38, C:0.01, G:0.18, T:0.43
Consensus pattern (34 bp):
GGGTTTTAAAAAAATTAATTAAATTAGGTTTTAG
Found at i:49584896 original size:34 final size:32
Alignment explanation
Indices: 49584791--49584912 Score: 113
Period size: 34 Copynumber: 3.7 Consensus size: 32
49584781 GGTTTAGGGC
* * *
49584791 TTAGGGTTTTAAAAAAAGTAATTAAATTAGGTT
1 TTAGTGTTTTTAAAAAATTAATTAAATTAGG-T
* * * *
49584824 TTTGGGGTTTTAAATAAATTAATTAAATTAGGGC
1 TTAGTGTTTTTAAA-AAATTAATTAAATTA-GGT
49584858 TTAGTGTTTTTAAGAAAATTAATTAAATTATGGT
1 TTAGTGTTTTTAA-AAAATTAATTAAATTA-GGT
*
49584892 TTAGT-TTTCTAAAAAA-TAATT
1 TTAGTGTTTTTAAAAAATTAATT
49584913 TTGTGTTTAG
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
31 5 0.07
32 4 0.05
33 17 0.23
34 46 0.61
35 3 0.04
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.43
Consensus pattern (32 bp):
TTAGTGTTTTTAAAAAATTAATTAAATTAGGT
Found at i:49585184 original size:125 final size:123
Alignment explanation
Indices: 49584962--49585357 Score: 569
Period size: 125 Copynumber: 3.2 Consensus size: 123
49584952 CTTTTGTTTT
* * ** *
49584962 TTTTTCTATATTAGTTTTTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAGATAATGTAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAA-ATAGTGT-AAAA
* * * *
49585027 ACGCTTCAAGCAGGATACACTGTCAGCAAAATTACTGAAAAAACTCTCATGTGGACGCCC
64 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAACTCCCACGTGGACGCTC
*
49585087 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGGGAAGACGGTTCTGAACAAATAGTGTAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAA-AAATAGTGTAAAAA
* *
49585152 TTGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAACAAACTCCCACGTTGACGCTC
65 -CGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAA-AAACTCCCACGTGGACGCTC
* *
49585213 TTTTTCTACAGTAGTCCCTG-AAAAATAATTTTGAGAAGACAGTTCTGAATAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAA-AAATAGTGT-AAAA
*
49585277 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGTTC
64 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAA-CTCCCACGTGGACGCTC
*
49585338 TTTTTTTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
49585358 TTTAGCCTTA
Statistics
Matches: 245, Mismatches: 21, Indels: 10
0.89 0.08 0.04
Matches are distributed among these distances:
124 8 0.03
125 195 0.80
126 42 0.17
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (123 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAATAGTGTAAAAAC
GCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAACTCCCACGTGGACGCTC
Found at i:49588439 original size:24 final size:24
Alignment explanation
Indices: 49588383--49588439 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
49588373 CATTATTTCT
49588383 ATTTTATTAAAAATATAAAAATAA
1 ATTTTATTAAAAATATAAAAATAA
*
49588407 ATTACTATT-AAAATATTAAAAATAA
1 ATT-TTATTAAAAATA-TAAAAATAA
*
49588432 CTTTTATT
1 ATTTTATT
49588440 TTTTAAATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
ATTTTATTAAAAATATAAAAATAA
Found at i:49588496 original size:90 final size:91
Alignment explanation
Indices: 49588387--49588576 Score: 337
Period size: 90 Copynumber: 2.1 Consensus size: 91
49588377 ATTTCTATTT
49588387 TATTAAAAATATAAAAATAAATTACTATTAAAATATTAAAAATAACTTTTATTTT-TTAAATGAA
1 TATT-AAAATATAAAAATAAATTACTATTAAAATATTAAAAATAACTTTTATTTTATTAAATGAA
*
49588451 ATAATATAAAAATAGTTTGTACAAATA
65 ACAATATAAAAATAGTTTGTACAAATA
* *
49588478 TATTAAAATATAAAAATAAATTACTATTAAATTATTTAAAATAACTTTTATTTTATTAAATGAAA
1 TATTAAAATATAAAAATAAATTACTATTAAAATATTAAAAATAACTTTTATTTTATTAAATGAAA
49588543 CAATATAAAAATAGTTTGTACAAATA
66 CAATATAAAAATAGTTTGTACAAATA
49588569 TATTAAAA
1 TATTAAAA
49588577 AATCAATGTT
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
90 48 0.51
91 47 0.49
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (91 bp):
TATTAAAATATAAAAATAAATTACTATTAAAATATTAAAAATAACTTTTATTTTATTAAATGAAA
CAATATAAAAATAGTTTGTACAAATA
Found at i:49588944 original size:18 final size:18
Alignment explanation
Indices: 49588918--49588960 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
49588908 GACTGGGAAA
* *
49588918 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
49588936 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
49588954 AGGATAC
1 AGGATAC
49588961 GCATCTGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:49590504 original size:14 final size:15
Alignment explanation
Indices: 49590485--49590513 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
49590475 GACTATTATA
49590485 AAAAATT-ATTAAAT
1 AAAAATTAATTAAAT
49590499 AAAAATTAATTAAAT
1 AAAAATTAATTAAAT
49590514 TTACATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAATTAATTAAAT
Found at i:49598960 original size:7 final size:7
Alignment explanation
Indices: 49598948--49598976 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
49598938 TCTCCTCCTG
49598948 TTTTAAT
1 TTTTAAT
49598955 TTTTAAT
1 TTTTAAT
49598962 TTTTAAT
1 TTTTAAT
49598969 TTTTAAT
1 TTTTAAT
49598976 T
1 T
49598977 AGAGAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTAAT
Found at i:49600340 original size:4 final size:4
Alignment explanation
Indices: 49600331--49600382 Score: 104
Period size: 4 Copynumber: 13.0 Consensus size: 4
49600321 ACTTAAAACC
49600331 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
49600379 ATGT
1 ATGT
49600383 GTTAGTGTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:49600987 original size:64 final size:64
Alignment explanation
Indices: 49600881--49601011 Score: 174
Period size: 64 Copynumber: 2.0 Consensus size: 64
49600871 TTTAATTCAC
* *** *
49600881 TTTTAATCGGTTTAATTTGCATCTTAGTATGATCTCAACTCAATTGGTCAGATTAATATGATCT
1 TTTTAATCGGTTTAATTTGCATCTTAGTATAATCTCAACTCAATCCATCAGATTAATATGATAT
* * *
49600945 TTTTGATCGGTTTAATTTTCATCTTAGTATAATCT-AGGCTCAATCCATCAGATTAATATGATAT
1 TTTTAATCGGTTTAATTTGCATCTTAGTATAATCTCA-ACTCAATCCATCAGATTAATATGATAT
49601009 TTT
1 TTT
49601012 ATTCCATGGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 1 0.02
64 57 0.98
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (64 bp):
TTTTAATCGGTTTAATTTGCATCTTAGTATAATCTCAACTCAATCCATCAGATTAATATGATAT
Found at i:49620274 original size:29 final size:29
Alignment explanation
Indices: 49620236--49620301 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
49620226 TTTTTTGTCA
* *
49620236 CCAATTATGAAAAGTTACAAAATGATCAC
1 CCAACTATGAAAAGTTACAAAATAATCAC
*
49620265 CCAACTATGAAAAGTTAGAAAATAATCAC
1 CCAACTATGAAAAGTTACAAAATAATCAC
*
49620294 TCAACTAT
1 CCAACTAT
49620302 TCAATTTAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.24
Consensus pattern (29 bp):
CCAACTATGAAAAGTTACAAAATAATCAC
Found at i:49633257 original size:39 final size:39
Alignment explanation
Indices: 49633189--49633372 Score: 253
Period size: 39 Copynumber: 4.6 Consensus size: 39
49633179 AATAAATATA
* * * *
49633189 TTTATTTTTTTTAATTTTAAAATATTTTTTACATACTTT
1 TTTAATTTTTTAAATTTTAAAATATTTTTAAAATACTTT
49633228 TTTAATTTTTTAAAATTTTAAAATATTTTTAAAATA-TTT
1 TTTAATTTTTT-AAATTTTAAAATATTTTTAAAATACTTT
* *
49633267 TTAAAATTTTTTAAATTTTAAAATATTTTTAAAATATTTT
1 TT-TAATTTTTTAAATTTTAAAATATTTTTAAAATACTTT
*
49633307 TTTAATTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
1 TTTAATTTTTTAAATTTTAAAATATTTTTAAAATAC-TTT
49633347 TTTAATTTTTTAAAATTTTTAAAATA
1 TTTAATTTTTT-AAA-TTTTAAAATA
49633373 AAAATGGGCC
Statistics
Matches: 130, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
39 70 0.54
40 48 0.37
41 2 0.02
42 10 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (39 bp):
TTTAATTTTTTAAATTTTAAAATATTTTTAAAATACTTT
Found at i:49633259 original size:11 final size:11
Alignment explanation
Indices: 49633203--49633372 Score: 124
Period size: 11 Copynumber: 16.9 Consensus size: 11
49633193 TTTTTTTTAA
49633203 TTTTAAAATAT
1 TTTTAAAATAT
* *
49633214 TTTTTACATACT
1 TTTTAAAATA-T
*
49633226 TTTT-TAAT-T
1 TTTTAAAATAT
49633235 TTTT-AAA-A-
1 TTTTAAAATAT
49633243 TTTTAAAATAT
1 TTTTAAAATAT
49633254 TTTTAAAATAT
1 TTTTAAAATAT
49633265 TTTTAAAAT-T
1 TTTTAAAATAT
49633275 TTTT--AA-A-
1 TTTTAAAATAT
49633282 TTTTAAAATAT
1 TTTTAAAATAT
49633293 TTTTAAAATAT
1 TTTTAAAATAT
**
49633304 TTTTTTAAT-T
1 TTTTAAAATAT
*
49633314 TTTT----TAA
1 TTTTAAAATAT
49633321 TTTTAAAATAT
1 TTTTAAAATAT
49633332 TTTTAAAATACT
1 TTTTAAAATA-T
**
49633344 TTTTTTAAT-T
1 TTTTAAAATAT
49633354 TTTT-AAA-AT
1 TTTTAAAATAT
49633363 TTTTAAAATA
1 TTTTAAAATA
49633373 AAAATGGGCC
Statistics
Matches: 128, Mismatches: 12, Indels: 38
0.72 0.07 0.21
Matches are distributed among these distances:
6 1 0.01
7 8 0.06
8 6 0.05
9 19 0.15
10 20 0.16
11 61 0.48
12 13 0.10
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:49633284 original size:79 final size:79
Alignment explanation
Indices: 49633194--49633372 Score: 261
Period size: 79 Copynumber: 2.2 Consensus size: 79
49633184 ATATATTTAT
* * *
49633194 TTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTAATTTTTTAAAATTTTAAAATATTTTTA
1 TTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTAATTTTTT-AAATTTTAAAATATTTTTA
49633259 AAATA-TTTTTAAAA
65 AAATACTTTTTAAAA
* *
49633273 TTTTTTAAATTTTAAAATATTTTTAAAATATTTTTTTAATTTTTTTAATTTTAAAATATTTTTAA
1 TTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTAATTTTTTAAATTTTAAAATATTTTTAA
**
49633338 AATACTTTTTTTAA
66 AATACTTTTTAAAA
49633352 TTTTTTAAAATTTTTAAAATA
1 TTTTTT-AAA-TTTTAAAATA
49633373 AAAATGGGCC
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
78 23 0.26
79 54 0.60
80 3 0.03
81 10 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (79 bp):
TTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTAATTTTTTAAATTTTAAAATATTTTTAA
AATACTTTTTAAAA
Found at i:49633365 original size:8 final size:9
Alignment explanation
Indices: 49633234--49633371 Score: 87
Period size: 9 Copynumber: 14.1 Consensus size: 9
49633224 CTTTTTTAAT
49633234 TTTTTAAAA
1 TTTTTAAAA
*
49633243 TTTTAAAATA
1 TTTTTAAA-A
49633253 TTTTTAAAATA
1 TTTTT-AAA-A
49633264 TTTTTAAAA
1 TTTTTAAAA
*
49633273 TTTTTTAAA
1 TTTTTAAAA
*
49633282 TTTTAAAATA
1 TTTTTAAA-A
49633292 TTTTTAAAATA
1 TTTTT-AAA-A
**
49633303 TTTTTTTAA
1 TTTTTAAAA
**
49633312 TTTTTTTAA
1 TTTTTAAAA
*
49633321 TTTTAAAATA
1 TTTTTAAA-A
49633331 TTTTTAAAATA
1 TTTTT-AAA-A
* *
49633342 CTTTTTTTAAT
1 --TTTTTAAAA
49633353 TTTTTAAAA
1 TTTTTAAAA
49633362 TTTTTAAAA
1 TTTTTAAAA
49633371 T
1 T
49633372 AAAAATGGGC
Statistics
Matches: 105, Mismatches: 16, Indels: 16
0.77 0.12 0.12
Matches are distributed among these distances:
9 54 0.51
10 19 0.18
11 25 0.24
12 2 0.02
13 5 0.05
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:49634341 original size:31 final size:31
Alignment explanation
Indices: 49634303--49634369 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
49634293 TAAACATACC
* *
49634303 ATTTGGTATTTGAATTTCGTTTTGATGTTCA
1 ATTTGGTATTTGAATTTCGCTTTAATGTTCA
*
49634334 ATTTGGTATTTGAATTTGGCTTTAATGTTCA
1 ATTTGGTATTTGAATTTCGCTTTAATGTTCA
*
49634365 CTTTG
1 ATTTG
49634370 ATATCCAACG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.07, G:0.19, T:0.54
Consensus pattern (31 bp):
ATTTGGTATTTGAATTTCGCTTTAATGTTCA
Found at i:49636982 original size:25 final size:23
Alignment explanation
Indices: 49636925--49636984 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
49636915 AAATTGTGTT
* * *
49636925 TATATTAAGAAATTGTTAAAAAT
1 TATATTAATATATTGTTAAAAAA
49636948 TATATT--TATATTGATTAATAAAA
1 TATATTAATATATTG-TTAA-AAAA
49636971 TATATTAATATATT
1 TATATTAATATATT
49636985 TAATTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 5 0.17
22 4 0.13
23 15 0.50
25 6 0.20
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (23 bp):
TATATTAATATATTGTTAAAAAA
Found at i:49637192 original size:22 final size:23
Alignment explanation
Indices: 49637167--49637213 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
49637157 TTTAAGTTGA
49637167 TAAA-TTTATCTT-TTTATCTTTT
1 TAAATTTTATCTTATTTAT-TTTT
*
49637189 TAAATTTTATTTTATTTATTTTT
1 TAAATTTTATCTTATTTATTTTT
49637212 TA
1 TA
49637214 CTTTGCACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.18
23 13 0.59
24 5 0.23
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (23 bp):
TAAATTTTATCTTATTTATTTTT
Found at i:49641910 original size:101 final size:98
Alignment explanation
Indices: 49641728--49641915 Score: 234
Period size: 101 Copynumber: 1.9 Consensus size: 98
49641718 ACAAAAGTTA
* * * * *
49641728 ATAAACATATTTAATAATATTGATTAAAAAATTGTCGAATTTTGACTTTCTTTTTAAAACAAACC
1 ATAAACATATTTAATAATAGTGATTAAAAAACTGTCAAAATTTGACTTTCTTTTCAAAACAAACC
49641793 CACTAAACATTTTTCATCTGCACAACTAAATTG
66 CACTAAACATTTTTCATCTGCACAACTAAATTG
* * *
49641826 ATAAATATATTTAATAATAGTGATTAAAAAACAACTGTTAAAATTTGACTTTCTTTTCAAAGCAA
1 ATAAACATATTTAATAATAGTGATT--AAAA-AACTGTCAAAATTTGACTTTCTTTTCAAAACAA
* * *
49641891 GCTCTC-AAATCATTTTTCATCTGCA
63 ACCCACTAAA-CATTTTTCATCTGCA
49641916 TCAAACAAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
98 23 0.31
100 7 0.09
101 45 0.60
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (98 bp):
ATAAACATATTTAATAATAGTGATTAAAAAACTGTCAAAATTTGACTTTCTTTTCAAAACAAACC
CACTAAACATTTTTCATCTGCACAACTAAATTG
Found at i:49645569 original size:2 final size:2
Alignment explanation
Indices: 49645562--49645595 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
49645552 ATACTTGAAC
*
49645562 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49645596 GGTTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:49651056 original size:57 final size:56
Alignment explanation
Indices: 49650985--49651115 Score: 154
Period size: 57 Copynumber: 2.3 Consensus size: 56
49650975 ATTAGAGCCT
** * * * *
49650985 AAATTTTTTTTCAAGTTCGATATTGAGCTTGACAATTGTTCTCATATTAAGACTTG
1 AAATTTTTTTTCAAGTTAAATACTGAACTTGACAATTGTACCCATATTAAGACTTG
* ** *
49651041 AAATTTTTTATTCAAGTTAAATCCTGAACTTGACAATTGTACCCATATTGGGGCTTG
1 AAATTTTTT-TTCAAGTTAAATACTGAACTTGACAATTGTACCCATATTAAGACTTG
*
49651098 AATTTTTTTTTCAAGTTA
1 AAATTTTTTTTCAAGTTA
49651116 GTCCTTGAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
56 18 0.29
57 45 0.71
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (56 bp):
AAATTTTTTTTCAAGTTAAATACTGAACTTGACAATTGTACCCATATTAAGACTTG
Found at i:49656708 original size:18 final size:17
Alignment explanation
Indices: 49656687--49656723 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
49656677 TTATTTAAAT
49656687 TTAATAATAAAATTTATA
1 TTAAT-ATAAAATTTATA
*
49656705 TTAATATGAAATTTATA
1 TTAATATAAAATTTATA
49656722 TT
1 TT
49656724 TTAAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TTAATATAAAATTTATA
Found at i:49657701 original size:19 final size:19
Alignment explanation
Indices: 49657674--49657720 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
49657664 AATACTTTTA
49657674 TTAAA-TTTTTT-AAAT-T
1 TTAAATTTTTTTAAAATAT
49657690 TTAAAATTTTTTTAAAATACT
1 TT-AAATTTTTTTAAAATA-T
49657711 TTAAATTTTT
1 TTAAATTTTT
49657721 AAATACTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.08
17 3 0.12
18 6 0.23
19 4 0.15
20 8 0.31
21 3 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAAATTTTTTTAAAATAT
Found at i:49657701 original size:29 final size:29
Alignment explanation
Indices: 49657651--49657761 Score: 122
Period size: 30 Copynumber: 3.9 Consensus size: 29
49657641 ATTTTTATTA
49657651 TTTTT-AATTTTAAAATACTTTTATTAAAT
1 TTTTTAAATTTTAAAATACTTTT-TTAAAT
49657680 TTTTTAAATTTTAAAAT--TTTTTTAAAAT
1 TTTTTAAATTTTAAAATACTTTTTT-AAAT
** *
49657708 ACTTTAAATTTTTAAATACTTTTTTAAAT
1 TTTTTAAATTTTAAAATACTTTTTTAAAT
* *
49657737 TTTATTTAATTTT-AAATAATTTTTT
1 TTT-TTAAATTTTAAAATACTTTTTT
49657762 TGGTATTTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
27 2 0.03
28 22 0.31
29 21 0.30
30 25 0.36
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTTAAATTTTAAAATACTTTTTTAAAT
Found at i:49672543 original size:16 final size:17
Alignment explanation
Indices: 49672513--49672545 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
49672503 TTGTTTATTA
*
49672513 TTTAATAAATGTAATAT
1 TTTAATAAATATAATAT
49672530 TTTAAT-AATATAATAT
1 TTTAATAAATATAATAT
49672546 AATAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAAATATAATAT
Found at i:49672689 original size:9 final size:9
Alignment explanation
Indices: 49672675--49672709 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
49672665 CACAATATAA
49672675 TAATAATAT
1 TAATAATAT
49672684 TAATAATAT
1 TAATAATAT
49672693 TAATAAT-T
1 TAATAATAT
49672701 TAATAATAT
1 TAATAATAT
49672710 ATTTTTACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TAATAATAT
Done.