Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 14 of 240
Found at i:5168902 original size:21 final size:21
Alignment explanation
Indices: 5168876--5168916 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5168866 AGACGAGCAA
*
5168876 TACTCCACAACAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
5168897 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
5168917 TTGAGCAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:5170854 original size:16 final size:16
Alignment explanation
Indices: 5170821--5170854 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5170811 GGAGATTGTT
* *
5170821 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
5170837 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
5170853 AA
1 AA
5170855 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:5179911 original size:9 final size:9
Alignment explanation
Indices: 5179897--5179921 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5179887 GATAATATTG
5179897 AAATAAAAT
1 AAATAAAAT
5179906 AAATAAAAT
1 AAATAAAAT
5179915 AAATAAA
1 AAATAAA
5179922 TATTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:5186294 original size:22 final size:23
Alignment explanation
Indices: 5186263--5186305 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5186253 TATTATTAGA
*
5186263 TATTTATAAATTATT-ATATATT
1 TATTTATAAAATATTAATATATT
*
5186285 TATTTTTAAAATATTAATATA
1 TATTTATAAAATATTAATATA
5186306 AACATTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTTATAAAATATTAATATATT
Found at i:5187097 original size:20 final size:20
Alignment explanation
Indices: 5187069--5187110 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5187059 ATTTTGCCCC
*
5187069 ATATCTTATAATAAATATAA
1 ATATATTATAATAAATATAA
* *
5187089 ATATATTATTATATATATAA
1 ATATATTATAATAAATATAA
5187109 AT
1 AT
5187111 TTCCCAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATATTATAATAAATATAA
Found at i:5199027 original size:12 final size:12
Alignment explanation
Indices: 5199012--5199048 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
5199002 GATTAATTCT
5199012 AAAATTATATAA
1 AAAATTATATAA
*
5199024 AAAATAATAT-A
1 AAAATTATATAA
5199035 AAAATTAT-TAA
1 AAAATTATATAA
5199046 AAA
1 AAA
5199049 TTAATTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
10 1 0.05
11 12 0.55
12 9 0.41
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAATTATATAA
Found at i:5199031 original size:23 final size:21
Alignment explanation
Indices: 5199012--5199054 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5199002 GATTAATTCT
5199012 AAAATTATATAAAAAATAATATA
1 AAAATTAT-TAAAAAATAAT-TA
*
5199035 AAAATTATTAAAAATTAATT
1 AAAATTATTAAAAAATAATT
5199055 TGTTTATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 10 0.53
23 8 0.42
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATTATTAAAAAATAATTA
Found at i:5199046 original size:10 final size:11
Alignment explanation
Indices: 5199012--5199051 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
5199002 GATTAATTCT
5199012 AAAATTATATAA
1 AAAATTATAT-A
*
5199024 AAAATAATATA
1 AAAATTATATA
5199035 AAAATTAT-TA
1 AAAATTATATA
5199045 AAAATTA
1 AAAATTA
5199052 ATTTGTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 8 0.31
12 9 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAATTATATA
Found at i:5204422 original size:24 final size:24
Alignment explanation
Indices: 5204394--5204445 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
5204384 TTAGTAAGTC
** *
5204394 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTACACTAACAAATGCT
* *
5204418 AAATATATTACACTAACAAATGCT
1 AAATAAACTACACTAACAAATGCT
5204442 AAAT
1 AAAT
5204446 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAAACTACACTAACAAATGCT
Found at i:5204559 original size:54 final size:54
Alignment explanation
Indices: 5204489--5204594 Score: 212
Period size: 54 Copynumber: 2.0 Consensus size: 54
5204479 ACTTGCAAAA
5204489 AATCTCTTAGAATTTGGGTCACACAACTCTAACAATCTCCACCTTGACACGAGC
1 AATCTCTTAGAATTTGGGTCACACAACTCTAACAATCTCCACCTTGACACGAGC
5204543 AATCTCTTAGAATTTGGGTCACACAACTCTAACAATCTCCACCTTGACACGA
1 AATCTCTTAGAATTTGGGTCACACAACTCTAACAATCTCCACCTTGACACGA
5204595 ATTCTTACAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.26
Consensus pattern (54 bp):
AATCTCTTAGAATTTGGGTCACACAACTCTAACAATCTCCACCTTGACACGAGC
Found at i:5206690 original size:50 final size:51
Alignment explanation
Indices: 5206615--5206728 Score: 185
Period size: 50 Copynumber: 2.3 Consensus size: 51
5206605 CTTACGTATG
* *
5206615 ATCACTTATCACTTGTCTCTGATCAGATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* *
5206665 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
5206716 ATCACTTGTCACT
1 ATCACTTGTCACT
5206729 GATCAGAAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
50 35 0.60
51 23 0.40
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
Found at i:5222211 original size:26 final size:27
Alignment explanation
Indices: 5222182--5222245 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 27
5222172 AATTGATGTA
5222182 TAATTTAATATTAA-TTAAATAATAAT
1 TAATTTAATATTAAGTTAAATAATAAT
*
5222208 TAATTTAA-A-TAATGTTTAATAATAAT
1 TAATTTAATATTAA-GTTAAATAATAAT
5222234 TAA-TTAATATTA
1 TAATTTAATATTA
5222246 CTTATTCTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
24 3 0.09
25 5 0.15
26 23 0.70
27 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
TAATTTAATATTAAGTTAAATAATAAT
Found at i:5222227 original size:16 final size:16
Alignment explanation
Indices: 5222187--5222220 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5222177 ATGTATAATT
5222187 TAAT-ATTAA-TTAAA
1 TAATAATTAATTTAAA
5222201 TAATAATTAATTTAAA
1 TAATAATTAATTTAAA
5222217 TAAT
1 TAAT
5222221 GTTTAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 5 0.28
16 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATAATTAATTTAAA
Found at i:5222245 original size:10 final size:10
Alignment explanation
Indices: 5222186--5222245 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
5222176 GATGTATAAT
5222186 TTAATATTAA
1 TTAATATTAA
*
5222196 TTAAATAATAA
1 TT-AATATTAA
5222207 TTAAT-TTAA
1 TTAATATTAA
* *
5222216 ATAATGTTTAA
1 TTAAT-ATTAA
5222227 -TAATAATTAA
1 TTAAT-ATTAA
5222237 TTAATATTA
1 TTAATATTA
5222246 CTTATTCTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 7 0.17
10 17 0.41
11 17 0.41
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (10 bp):
TTAATATTAA
Found at i:5231077 original size:8 final size:8
Alignment explanation
Indices: 5231064--5231101 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
5231054 AATTAAAGTG
5231064 AATTATTA
1 AATTATTA
5231072 AATTATTA
1 AATTATTA
*
5231080 AATTAATAA
1 AATT-ATTA
5231089 AATTATTA
1 AATTATTA
5231097 AATTA
1 AATTA
5231102 AGGATTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
AATTATTA
Found at i:5234317 original size:28 final size:28
Alignment explanation
Indices: 5234273--5234332 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
5234263 TATATTATAC
* *
5234273 TATATTATTTTAATATTTAATAGTTTTA
1 TATATTATTTTAATATTGAAAAGTTTTA
* *
5234301 TATATT-TTTTATTTATTGAAAATTTTTA
1 TATATTATTTTA-ATATTGAAAAGTTTTA
5234329 TATA
1 TATA
5234333 GTCATCGTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (28 bp):
TATATTATTTTAATATTGAAAAGTTTTA
Found at i:5237504 original size:4 final size:4
Alignment explanation
Indices: 5237495--5237519 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5237485 CACCATTTAA
5237495 AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT A
5237520 TTACATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:5239270 original size:3 final size:3
Alignment explanation
Indices: 5239262--5239294 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5239252 CTCAGCACCC
5239262 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5239295 ATTTCTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5249158 original size:21 final size:21
Alignment explanation
Indices: 5249132--5249172 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5249122 ATCTGCTCAA
* *
5249132 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
5249153 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
5249173 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:5253674 original size:52 final size:51
Alignment explanation
Indices: 5253603--5253811 Score: 286
Period size: 52 Copynumber: 4.1 Consensus size: 51
5253593 ATCAAGTGAC
*
5253603 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGT-G
* *
5253655 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
*
5253706 AAAAGTGATAAGTGATAGCTTC-GTCTATACTTATCTGATCAAGAGAC-----
1 -AAAGTGATAAGTGATAGCTTCAG-CTACACTTATCTGATCAAGAGACAAGTG
*
5253753 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC-AAGTG
5253805 ATAAGTG
1 A-AAGTG
5253812 GCTACACTTA
Statistics
Matches: 142, Mismatches: 5, Indels: 19
0.86 0.03 0.11
Matches are distributed among these distances:
46 42 0.30
47 1 0.01
51 2 0.01
52 92 0.65
53 5 0.04
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
Found at i:5253780 original size:98 final size:99
Alignment explanation
Indices: 5253595--5253811 Score: 294
Period size: 98 Copynumber: 2.1 Consensus size: 99
5253585 TACTTCTAAT
*
5253595 CAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGT
1 CAAGTGA-AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC-----GAAAGT
* *
5253660 GATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
60 GATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGA
*
5253700 CAAGTGAAAAGTGATAAGTGATAGCTTC-GTCTATACTTATCTGATCAAGAGAC-AAAGTGATAA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCAG-CTACACTTATCTGATCAAGAGACGAAAGTGATAA
*
5253763 GTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
65 GTGATAGCTTCAGCTACACTTATCTGATCAAGAGA
*
5253798 CAAAGTGATAAGTG
1 C-AAGTGAAAAGTG
5253812 GCTACACTTA
Statistics
Matches: 104, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
98 43 0.41
99 11 0.11
103 1 0.01
104 42 0.40
105 7 0.07
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (99 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACGAAAGTGATAAG
TGATAGCTTCAGCTACACTTATCTGATCAAGAGA
Found at i:5253784 original size:46 final size:46
Alignment explanation
Indices: 5253707--5253811 Score: 176
Period size: 46 Copynumber: 2.3 Consensus size: 46
5253697 TGACAAGTGA
* *
5253707 AAAGTGATAAGTGATAGCTTCGTCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTTAGTCTACACTTATCTGATCAAGAGAC
5253753 AAAGTGATAAGTGATAGCTTTAG-CTACACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGC-TTAGTCTACACTTATCTGATCAAGAGAC
5253799 AAAGTGATAAGTG
1 AAAGTGATAAGTG
5253812 GCTACACTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
46 53 0.95
47 3 0.05
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTAGTCTACACTTATCTGATCAAGAGAC
Found at i:5253819 original size:37 final size:37
Alignment explanation
Indices: 5253775--5253883 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
5253765 GATAGCTTTA
5253775 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
5253812 GCTACACTTATCTGATCAAGAAACAAAGTGAT-AGTTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAG-TG
*
5253849 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
5253884 ATCATACGTA
Statistics
Matches: 67, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
35 9 0.13
36 8 0.12
37 50 0.75
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.26
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:5255205 original size:49 final size:50
Alignment explanation
Indices: 5255135--5255230 Score: 176
Period size: 49 Copynumber: 1.9 Consensus size: 50
5255125 ACATGTGAAC
*
5255135 ATGTGATTATGTGATTTCGTGTAAGACCATAGTTGGACTATGGCATCTGT
1 ATGTGATTATGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCTGT
5255185 ATGTGATT-TGTGATTACGTGTAAGACCATAGTTGGACTATGGCATC
1 ATGTGATTATGTGATTACGTGTAAGACCATAGTTGGACTATGGCATC
5255231 GAGAAAACGA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 37 0.82
50 8 0.18
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.36
Consensus pattern (50 bp):
ATGTGATTATGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCTGT
Found at i:5258445 original size:52 final size:51
Alignment explanation
Indices: 5258374--5258582 Score: 286
Period size: 52 Copynumber: 4.1 Consensus size: 51
5258364 ATCAAGTGAC
*
5258374 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGT-G
* *
5258426 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
*
5258477 AAAAGTGATAAGTGATAGCTTC-GTCTATACTTATCTGATCAAGAGAC-----
1 -AAAGTGATAAGTGATAGCTTCAG-CTACACTTATCTGATCAAGAGACAAGTG
*
5258524 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC-AAGTG
5258576 ATAAGTG
1 A-AAGTG
5258583 GCTACACTTA
Statistics
Matches: 142, Mismatches: 5, Indels: 19
0.86 0.03 0.11
Matches are distributed among these distances:
46 42 0.30
47 1 0.01
51 2 0.01
52 92 0.65
53 5 0.04
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
Found at i:5258551 original size:98 final size:99
Alignment explanation
Indices: 5258366--5258582 Score: 294
Period size: 98 Copynumber: 2.1 Consensus size: 99
5258356 TACTTCTAAT
*
5258366 CAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGT
1 CAAGTGA-AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC-----GAAAGT
* *
5258431 GATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
60 GATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGA
*
5258471 CAAGTGAAAAGTGATAAGTGATAGCTTC-GTCTATACTTATCTGATCAAGAGAC-AAAGTGATAA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCAG-CTACACTTATCTGATCAAGAGACGAAAGTGATAA
*
5258534 GTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
65 GTGATAGCTTCAGCTACACTTATCTGATCAAGAGA
*
5258569 CAAAGTGATAAGTG
1 C-AAGTGAAAAGTG
5258583 GCTACACTTA
Statistics
Matches: 104, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
98 43 0.41
99 11 0.11
103 1 0.01
104 42 0.40
105 7 0.07
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (99 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACGAAAGTGATAAG
TGATAGCTTCAGCTACACTTATCTGATCAAGAGA
Found at i:5258555 original size:46 final size:44
Alignment explanation
Indices: 5258478--5258693 Score: 199
Period size: 37 Copynumber: 5.3 Consensus size: 44
5258468 TGACAAGTGA
*
5258478 AAAGTGATAAGTGATAGCTTCGTCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTT-G-CTACACTTATCTGATCAAGAGAC
5258524 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGC-TT-GCTACACTTATCTGATCAAGAGAC
*
5258570 AAAGTGATAA--G-T-G---GCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
*
5258607 AAAGTGATAA--G-T-G---GCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
*
5258644 AAAGTGAT-AGT--T-G---GCTACACTTATCTGATC-AGGGAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
5258680 -AAGTGATAAGTGAT
1 AAAGTGATAAGTGAT
5258694 CATACGTAAG
Statistics
Matches: 159, Mismatches: 5, Indels: 20
0.86 0.03 0.11
Matches are distributed among these distances:
35 7 0.04
36 8 0.05
37 87 0.55
38 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 50 0.31
47 3 0.02
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (44 bp):
AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
Found at i:5258590 original size:37 final size:37
Alignment explanation
Indices: 5258546--5258691 Score: 235
Period size: 37 Copynumber: 4.0 Consensus size: 37
5258536 GATAGCTTTA
*
5258546 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
5258583 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
5258620 GCTACACTTATCTGATCAAGAAACAAAGTGAT-AGTTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAG-TG
**
5258657 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
5258692 ATCATACGTA
Statistics
Matches: 104, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
35 9 0.09
36 8 0.08
37 87 0.84
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:5262364 original size:20 final size:21
Alignment explanation
Indices: 5262341--5262386 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
5262331 AAAAAAATTT
* *
5262341 AAAATAAAT-ATAATTTATTA
1 AAAATAAATAAAAATATATTA
*
5262361 AAAA-GAATAAAAATATATTA
1 AAAATAAATAAAAATATATTA
5262381 AAAATA
1 AAAATA
5262387 TTATTTAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAATAAATAAAAATATATTA
Found at i:5262628 original size:38 final size:38
Alignment explanation
Indices: 5262584--5262659 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
5262574 TAAAATAAGA
5262584 AAAAAAATACACTGCTTTAAGCCACTTGCAAAAGAACT
1 AAAAAAATACACTGCTTTAAGCCACTTGCAAAAGAACT
5262622 AAAAAAATACACTGCTTTAAGCCACTTGCAAAAGAACT
1 AAAAAAATACACTGCTTTAAGCCACTTGCAAAAGAACT
5262660 TTCAAAAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (38 bp):
AAAAAAATACACTGCTTTAAGCCACTTGCAAAAGAACT
Found at i:5267371 original size:17 final size:18
Alignment explanation
Indices: 5267351--5267394 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
5267341 TATAATCTTA
5267351 TTTTA-ATATTAATAATTT
1 TTTTATATATTAA-AATTT
*
5267369 TTTTATTTATTAAAA-TT
1 TTTTATATATTAAAATTT
5267386 TTTTATATA
1 TTTTATATA
5267395 ATCATCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 10 0.43
18 7 0.30
19 6 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTATATATTAAAATTT
Found at i:5280475 original size:14 final size:14
Alignment explanation
Indices: 5280450--5280482 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5280440 ACACTTATCT
5280450 AAATATTCAAATAA
1 AAATATTCAAATAA
5280464 GAAATA-TCAAATAA
1 -AAATATTCAAATAA
5280478 AAATA
1 AAATA
5280483 ATTAGGGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 8 0.44
15 5 0.28
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATATTCAAATAA
Found at i:5289926 original size:24 final size:24
Alignment explanation
Indices: 5289899--5289944 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
5289889 AAGCTCATGC
*
5289899 GAGCCAATATC-GGATAGCTCCGAA
1 GAGCCAATAACGGGA-AGCTCCGAA
5289923 GAGCCAATAACGGGAAGCTCCG
1 GAGCCAATAACGGGAAGCTCCG
5289945 GATAGCTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.33, C:0.26, G:0.28, T:0.13
Consensus pattern (24 bp):
GAGCCAATAACGGGAAGCTCCGAA
Found at i:5292560 original size:15 final size:17
Alignment explanation
Indices: 5292531--5292562 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
5292521 TAGTTGAGAA
5292531 TTTTATGTAACAATTTT
1 TTTTATGTAACAATTTT
5292548 TTTTAT-TAA-AATTTT
1 TTTTATGTAACAATTTT
5292563 ACATAGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTATGTAACAATTTT
Found at i:5300077 original size:31 final size:30
Alignment explanation
Indices: 5300018--5300077 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
5300008 TAATTGAGTT
* *
5300018 TAAATTTTAAAATATGAAAAGTGGAATGAC
1 TAAATTTTAAAATATGAAAAATGAAATGAC
* *
5300048 TAAATTCTTAAAATTTGAAAAATTAAATGA
1 TAAATT-TTAAAATATGAAAAATGAAATGA
5300078 GTATAGAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (30 bp):
TAAATTTTAAAATATGAAAAATGAAATGAC
Found at i:5305120 original size:42 final size:42
Alignment explanation
Indices: 5305061--5305147 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
5305051 TAGCAGATAA
5305061 TGTAAGACCAGGATAAAGCCCATTGTAACTTTTCAGCAAAAC
1 TGTAAGACCAGGATAAAGCCCATTGTAACTTTTCAGCAAAAC
5305103 TGTAAGACCAGGATAAAGCCCATTGTAACTTTTCAGCAAAAC
1 TGTAAGACCAGGATAAAGCCCATTGTAACTTTTCAGCAAAAC
5305145 TGT
1 TGT
5305148 TTGGTATTCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (42 bp):
TGTAAGACCAGGATAAAGCCCATTGTAACTTTTCAGCAAAAC
Found at i:5330863 original size:3 final size:3
Alignment explanation
Indices: 5330855--5330909 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
5330845 ATTGGAGGAA
* * * * *
5330855 CTG CTG CTG CTG CTG CTG CTG TTG CTG TTG TTG TTG CTG TTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
5330903 CTG CTG C
1 CTG CTG C
5330910 AAAAGCATTG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.00, C:0.25, G:0.33, T:0.42
Consensus pattern (3 bp):
CTG
Found at i:5333585 original size:13 final size:13
Alignment explanation
Indices: 5333567--5333593 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5333557 GAGCCATGCA
5333567 GAACAAACGAAAT
1 GAACAAACGAAAT
5333580 GAACAAACGAAAT
1 GAACAAACGAAAT
5333593 G
1 G
5333594 GACTCAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.15, G:0.19, T:0.07
Consensus pattern (13 bp):
GAACAAACGAAAT
Found at i:5337761 original size:17 final size:17
Alignment explanation
Indices: 5337739--5337772 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5337729 ATCCACTAAT
*
5337739 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
5337756 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
5337773 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:5342400 original size:17 final size:17
Alignment explanation
Indices: 5342378--5342411 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5342368 ATCCACTAAT
*
5342378 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
5342395 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
5342412 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:5344982 original size:30 final size:30
Alignment explanation
Indices: 5344948--5345009 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
5344938 CTTAACAAGT
5344948 AAATGCCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
* *
5344978 AAATGTCTTTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
5345008 AA
1 AA
5345010 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAC
Found at i:5345720 original size:17 final size:17
Alignment explanation
Indices: 5345688--5345734 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
5345678 AAACTAATGG
*
5345688 TAATTTTTTTAA-GAGA
1 TAATTTTTTAAATGAGA
5345704 GT-ATTTTTTAAATGAGA
1 -TAATTTTTTAAATGAGA
5345721 TAATTTTTTTAAAT
1 TAA-TTTTTTAAAT
5345735 ATTAGTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 10 0.38
17 6 0.23
18 10 0.38
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (17 bp):
TAATTTTTTAAATGAGA
Found at i:5346906 original size:18 final size:19
Alignment explanation
Indices: 5346876--5346912 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
5346866 TTTGCAAATC
5346876 AAATATTTATTATAAATTT
1 AAATATTTATTATAAATTT
*
5346895 AAATATTT-TTATTAATTT
1 AAATATTTATTATAAATTT
5346913 TAAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AAATATTTATTATAAATTT
Found at i:5346914 original size:19 final size:18
Alignment explanation
Indices: 5346876--5346948 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 18
5346866 TTTGCAAATC
*
5346876 AAATATTTATTATAAATTT
1 AAATATTT-TTATAATTTT
5346895 AAATATTTTTATTAATTTT
1 AAATATTTTTA-TAATTTT
*
5346914 AAAATAATTTTAATAATTTT
1 -AAAT-ATTTTTATAATTTT
* *
5346934 ATA-ATTATTATAATT
1 AAATATTTTTATAATT
5346949 ATTTGAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
17 10 0.22
18 3 0.07
19 16 0.35
20 11 0.24
21 6 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AAATATTTTTATAATTTT
Found at i:5346924 original size:20 final size:20
Alignment explanation
Indices: 5346895--5346957 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
5346885 TTATAAATTT
* *
5346895 AAATATTTTTATTAATTTTA
1 AAATAATTTTAATAATTTTA
5346915 AAATAATTTTAATAATTTTA
1 AAATAATTTTAATAATTTTA
* * * * *
5346935 TAATTATTATAATTATTTGA
1 AAATAATTTTAATAATTTTA
5346955 AAA
1 AAA
5346958 ACTACATTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
AAATAATTTTAATAATTTTA
Found at i:5346928 original size:9 final size:9
Alignment explanation
Indices: 5346890--5346948 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
5346880 ATTTATTATA
*
5346890 AATTTAAAT
1 AATTTTAAT
* *
5346899 ATTTTTATT
1 AATTTTAAT
5346908 AATTTTAAAAT
1 AATTTT--AAT
5346919 AATTTTAAT
1 AATTTTAAT
5346928 AATTTT-AT
1 AATTTTAAT
5346936 AATTATT-AT
1 AATT-TTAAT
5346945 AATT
1 AATT
5346949 ATTTGAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
8 6 0.14
9 28 0.67
11 8 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTTTAAT
Found at i:5346952 original size:29 final size:29
Alignment explanation
Indices: 5346882--5346952 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
5346872 AATCAAATAT
*
5346882 TTATTATAA-ATTTAAATATTTTTATTAA
1 TTATTATAATATTTAAATAATTTTATTAA
* *
5346910 TT-TTAAAATAATTTTAATAATTTTA-TAA
1 TTATTATAAT-ATTTAAATAATTTTATTAA
5346938 TTATTATAATTATTT
1 TTATTATAA-TATTT
5346953 GAAAAACTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
27 5 0.14
28 7 0.20
29 22 0.63
30 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TTATTATAATATTTAAATAATTTTATTAA
Found at i:5348367 original size:50 final size:49
Alignment explanation
Indices: 5348261--5348365 Score: 113
Period size: 50 Copynumber: 2.1 Consensus size: 49
5348251 TTTTTGAATT
* * * * *
5348261 TTTTAAGAATTAAGACTAAATTGATAGAATGTGTAAAGTTAAGGGTTAAA
1 TTTTAA-AATTAAGACCAAATTGATAGAATGTATAAAATTAAGAGCTAAA
5348311 TTTTTAAAATTAAGACCAAATTGATAGAAT-TAATAAACATTAGAGAGCTAAA
1 -TTTTAAAATTAAGACCAAATTGATAGAATGT-ATAAA-ATTA-AGAGCTAAA
5348363 TTT
1 TTT
5348366 AATATTATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
49 1 0.02
50 26 0.57
51 12 0.26
52 7 0.15
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (49 bp):
TTTTAAAATTAAGACCAAATTGATAGAATGTATAAAATTAAGAGCTAAA
Found at i:5349007 original size:21 final size:22
Alignment explanation
Indices: 5348983--5349033 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
5348973 ATCTTTCCAT
*
5348983 TTTTGTTTTC-AGGTATATTTC
1 TTTTGTTTTCGAGGTAGATTTC
* *
5349004 TTTTGTTTCCGAGTTAGATTTC
1 TTTTGTTTTCGAGGTAGATTTC
5349026 -TTTGTTTT
1 TTTTGTTTT
5349034 GTTGTTGATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.16, T:0.63
Consensus pattern (22 bp):
TTTTGTTTTCGAGGTAGATTTC
Found at i:5350398 original size:159 final size:159
Alignment explanation
Indices: 5350102--5350660 Score: 926
Period size: 159 Copynumber: 3.5 Consensus size: 159
5350092 CAGGACTTAC
* * * * * *
5350102 GGGGATAAGGTTGATAAAAATGATGACAA--GGTGTCGGATAAACGCTCAGCT-GATCAGGTGAA
1 GGGGATAAGGTTGACAAAAATAATGACAATGGGT-TC-GATAAAAGCTCTGATAG-TCAAGTG--
* *
5350164 AAAGAAGAGTTCAAATGAAGATTCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGTTGATC
61 AAA-AAGAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATC
* *
5350229 AGGTGGAAAAGAGCTCAAATGAAGTTTTCCCTAAA
125 AGGTGAAAAAGAGATCAAATGAAGTTTTCCCTAAA
5350264 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
1 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
5350329 GAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
66 GAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
5350394 AAAAGAGATCAAATGAAGTTTTCCCTAAA
131 AAAAGAGATCAAATGAAGTTTTCCCTAAA
5350423 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
1 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
*
5350488 GAGTTCAAATGAAGATGCCCCAAAAGAAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
66 GAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
5350553 AAAAGAGATCAAATGAAGTTTTCCCTAAA
131 AAAAGAGATCAAATGAAGTTTTCCCTAAA
*
5350582 GGGGATAAGGTTGACAAAAATAATGACAATGTGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
1 GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
*
5350647 GAGCTCAAATGAAG
66 GAGTTCAAATGAAG
5350661 TTTTCCCATC
Statistics
Matches: 381, Mismatches: 13, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
159 327 0.86
160 3 0.01
162 45 0.12
163 3 0.01
164 3 0.01
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.23
Consensus pattern (159 bp):
GGGGATAAGGTTGACAAAAATAATGACAATGGGTTCGATAAAAGCTCTGATAGTCAAGTGAAAAA
GAGTTCAAATGAAGATGCCCCAAAAGGAGATAAGGTGTTTGATAAAAGCTTTGATGATCAGGTGA
AAAAGAGATCAAATGAAGTTTTCCCTAAA
Found at i:5355786 original size:16 final size:15
Alignment explanation
Indices: 5355754--5355829 Score: 50
Period size: 15 Copynumber: 5.0 Consensus size: 15
5355744 CTTTTATTGT
5355754 TTTTTTTATAATAAA
1 TTTTTTTATAATAAA
**
5355769 TTTTTTTATTGTATAA
1 TTTTTTTATAATA-AA
* *
5355785 TTGTTTT-TCATAAA
1 TTTTTTTATAATAAA
5355799 TTTGTTTGT-TAATATAA
1 TTT-TTT-TATAATA-AA
*
5355816 -ATTTTTATAATAAA
1 TTTTTTTATAATAAA
5355830 AATATTACCA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
14 7 0.15
15 25 0.52
16 14 0.29
17 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.59
Consensus pattern (15 bp):
TTTTTTTATAATAAA
Found at i:5360930 original size:51 final size:51
Alignment explanation
Indices: 5360874--5361297 Score: 279
Period size: 51 Copynumber: 8.4 Consensus size: 51
5360864 TGTGGCATGG
* * * *
5360874 ACTGTGTGTAGGCCACTATATGAA-AGTGAAAG-TGTTGGTCACGTGTGTAGT
1 ACTGTGTGAAGGCTACTATATGAACCGAG-AAGCT-TTGGTCACGTGTGTAGT
* * *
5360925 ACTGTGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGT
1 ACTGTGTGAAGGCTACTATATGAACCGAGAAGCTTTGGTCACGTGTGTAGT
** * * * * * *
5360976 ACTGTGTGAAGGCTACTACGTGAATCGATAA-ATAATGGTCACATGTGTAAT
1 ACTGTGTGAAGGCTACTATATGAACCGAGAAGCT-TTGGTCACGTGTGTAGT
** * *
5361027 ACTAAGTGAAGGCTACAATATGTACCGAGAAGCTTTGGTCACGTGTGTAGT
1 ACTGTGTGAAGGCTACTATATGAACCGAGAAGCTTTGGTCACGTGTGTAGT
* * * ** * * * *
5361078 ACTTTCTGAAGGCTACTATGTGAATTGATAA-ATGATGGTCACATGTGTAGT
1 ACTGTGTGAAGGCTACTATATGAACCGAGAAGCT-TTGGTCACGTGTGTAGT
** * * * * * *
5361129 ACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTAGTCACATATGTAGT
1 ACTGTGTGAAGGCTACTATATGAACCGAGAAGCTTTGGTCACGTGTGTAGT
* ** * * * *
5361180 ACTATGTGAAGGCTACTACGTGAATCGTA-AAAC-TTGATCACGTGTATAGT
1 ACTGTGTGAAGGCTACTATATGAACCG-AGAAGCTTTGGTCACGTGTGTAGT
* * ** ** *
5361230 ACTATGTGAAGGCTATTACGTGAACCGTA-AA-AATTGATCACGTGTGTAGT
1 ACTGTGTGAAGGCTACTATATGAACCG-AGAAGCTTTGGTCACGTGTGTAGT
*
5361280 ACTATGTGAAGGCTACTA
1 ACTGTGTGAAGGCTACTA
5361298 CGTGTATCGA
Statistics
Matches: 299, Mismatches: 66, Indels: 17
0.78 0.17 0.04
Matches are distributed among these distances:
50 76 0.25
51 217 0.73
52 6 0.02
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (51 bp):
ACTGTGTGAAGGCTACTATATGAACCGAGAAGCTTTGGTCACGTGTGTAGT
Found at i:5361051 original size:102 final size:102
Alignment explanation
Indices: 5360909--5361340 Score: 496
Period size: 102 Copynumber: 4.3 Consensus size: 102
5360899 GTGAAAGTGT
* **
5360909 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTA
1 TGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTA
*
5360974 GTACTGTGTGAAGGCTACTACGTGAATCGATAAATAA
66 GTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
* *
5361011 TGGTCACATGTGTAATACTAAGTGAAGGCTACAATATGTACCGAGAAGCTTTGGTCACGTGTGTA
1 TGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTA
* * * * *
5361076 GTACTTTCTGAAGGCTACTATGTGAATTGATAAATGA
66 GTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
* * * * *
5361113 TGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTAGTCACATATGTA
1 TGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTA
*
5361178 GTACTATGTGAAGGCTACTACGTGAATCG-TAAA-ACT
66 GTACTATGTGAAGGCTACTACGTGAATCGATAAATA-A
* * * * ** * * ** *
5361214 TGATCACGTGTATAGTACTATGTGAAGGCTATTACGTGAACCGTA-AA-AATTGATCACGTGTGT
1 TGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGTCACGTGTGT
* *
5361277 AGTACTATGTGAAGGCTACTACGTGTATCGA-ATGATAA
65 AGTACTATGTGAAGGCTACTACGTGAATCGATA-AATAA
* * * *
5361315 TGGTAACATGGGTGGTACTATGTGAA
1 TGGTCACATGTGTAGTACTAAGTGAA
5361341 AACCCCAAAT
Statistics
Matches: 280, Mismatches: 45, Indels: 11
0.83 0.13 0.03
Matches are distributed among these distances:
100 40 0.14
101 63 0.22
102 177 0.63
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (102 bp):
TGGTCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTA
GTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
Found at i:5361170 original size:153 final size:150
Alignment explanation
Indices: 5360908--5361308 Score: 412
Period size: 153 Copynumber: 2.6 Consensus size: 150
5360898 AGTGAAAGTG
* * * * * *
5360908 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGT
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGATAA-ATATGGTCACGTGTGT
* * * *
5360973 AGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAATACTAAGTGAAG
65 AGTACTATGTGAAGGCTACTACGTGTATCGA-AAATAATAGTCACATATGTAATACTAAGTGAAG
* * *
5361038 GCTACAATATGTACCG-AGAAGC
129 GCTACAACATGAACCGTA-AAAC
* * ** *
5361060 TTTGGTCACGTGTGTAGTACTTTCTGAAGGCTACTATGTGAATTGATAAATGATGGTCACATGTG
1 -TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGATAAAT-ATGGTCACGTGTG
* * * * * *
5361125 TAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCT-TTAGTCACATATGTAGTACTATGTGA
64 TAGTACTATGTGAAGGCTACTACGTGTATCGAAAA--TAATAGTCACATATGTAATACTAAGTGA
* * *
5361189 AGGCTACTACGTGAATCGTAAAAC
127 AGGCTACAACATGAACCGTAAAAC
* * * * * *
5361213 TTGATCACGTGTATAGTACTATGTGAAGGCTATTACGTGAACCG-TAAAAATTGATCACGTGTGT
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGATAAATA-TGGTCACGTGTGT
5361277 AGTACTATGTGAAGGCTACTACGTGTATCGAA
65 AGTACTATGTGAAGGCTACTACGTGTATCGAA
5361309 TGATAATGGT
Statistics
Matches: 203, Mismatches: 40, Indels: 12
0.80 0.16 0.05
Matches are distributed among these distances:
150 1 0.00
151 44 0.22
152 40 0.20
153 116 0.57
154 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (150 bp):
TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGATAAATATGGTCACGTGTGTA
GTACTATGTGAAGGCTACTACGTGTATCGAAAATAATAGTCACATATGTAATACTAAGTGAAGGC
TACAACATGAACCGTAAAAC
Found at i:5363344 original size:19 final size:18
Alignment explanation
Indices: 5363303--5363347 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
5363293 TTGAAATTTT
* *
5363303 TAAAAATATAAAAATATA
1 TAAAAATTTAAAAAAATA
5363321 T-AAAATTTAAAAAAATAA
1 TAAAAATTTAAAAAAAT-A
5363339 TAAAAATTT
1 TAAAAATTT
5363348 TTTTTATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 13 0.57
18 3 0.13
19 7 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAAATTTAAAAAAATA
Found at i:5366380 original size:35 final size:35
Alignment explanation
Indices: 5366334--5366405 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
5366324 GTTATCTATA
5366334 TGGCACAGTCTTTTTTGAAATCAGGTATAAATTAT
1 TGGCACAGTCTTTTTTGAAATCAGGTATAAATTAT
5366369 TGGCACAGTCTTTTTTGAAATCAGGTATAAATTAT
1 TGGCACAGTCTTTTTTGAAATCAGGTATAAATTAT
5366404 TG
1 TG
5366406 ACATAATATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (35 bp):
TGGCACAGTCTTTTTTGAAATCAGGTATAAATTAT
Found at i:5374404 original size:43 final size:43
Alignment explanation
Indices: 5374368--5374514 Score: 240
Period size: 43 Copynumber: 3.4 Consensus size: 43
5374358 TCCCGGACAG
5374368 GGTCTTACACGAAAACACAAGTCGATGCCAACGTCCCAGACGT
1 GGTCTTACACGAAAACACAAGTCGATGCCAACGTCCCAGACGT
* * *
5374411 GATCTTACACGAAAACACAGGTTGATGCCAACGTCCCAGACGT
1 GGTCTTACACGAAAACACAAGTCGATGCCAACGTCCCAGACGT
* * *
5374454 GGTCTTACACGAAAACCCAAGTCGATGCCAACATCCTAGACGT
1 GGTCTTACACGAAAACACAAGTCGATGCCAACGTCCCAGACGT
5374497 GGTCTTACACGAAAACAC
1 GGTCTTACACGAAAACAC
5374515 TTATCAGAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 94 1.00
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (43 bp):
GGTCTTACACGAAAACACAAGTCGATGCCAACGTCCCAGACGT
Found at i:5381035 original size:2 final size:2
Alignment explanation
Indices: 5381030--5381090 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
5381020 TATATAATAA
5381030 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5381072 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
5381091 AACCCTAAGG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5401728 original size:27 final size:27
Alignment explanation
Indices: 5401698--5401752 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
5401688 ATGATGAAAT
5401698 TGATACATGGAACAAAACATTACTTGA
1 TGATACATGGAACAAAACATTACTTGA
* *
5401725 TGATACATGGAACACAACATTAGTTGA
1 TGATACATGGAACAAAACATTACTTGA
5401752 T
1 T
5401753 CCATGATGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (27 bp):
TGATACATGGAACAAAACATTACTTGA
Found at i:5403066 original size:35 final size:35
Alignment explanation
Indices: 5403020--5403095 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
5403010 TATTTTATAC
* * *
5403020 TTAATTTTTATGGTT-CTTTATGATTATCCTGCCCA
1 TTAATTCTTAT-GTTGCATTATGATTACCCTGCCCA
5403055 TTAATTCTTATGTTGCATTATGATTACCCTGCCCA
1 TTAATTCTTATGTTGCATTATGATTACCCTGCCCA
*
5403090 TCAATT
1 TTAATT
5403096 TTTTTCATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
34 3 0.08
35 33 0.92
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (35 bp):
TTAATTCTTATGTTGCATTATGATTACCCTGCCCA
Found at i:5413555 original size:10 final size:10
Alignment explanation
Indices: 5413540--5413572 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
5413530 TGAGCACTAA
5413540 ACATACACAC
1 ACATACACAC
5413550 ACATACACAC
1 ACATACACAC
5413560 ACATACACAC
1 ACATACACAC
5413570 ACA
1 ACA
5413573 CACATATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.52, C:0.39, G:0.00, T:0.09
Consensus pattern (10 bp):
ACATACACAC
Found at i:5419611 original size:27 final size:23
Alignment explanation
Indices: 5419558--5419605 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
5419548 AACATAGCAC
5419558 TAAATAAAAGCAAGAAGGCATCT
1 TAAATAAAAGCAAGAAGGCATCT
5419581 TAAATAAAAGCAAGAAGGCATCT
1 TAAATAAAAGCAAGAAGGCATCT
5419604 TA
1 TA
5419606 GGTAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.12, G:0.17, T:0.19
Consensus pattern (23 bp):
TAAATAAAAGCAAGAAGGCATCT
Found at i:5422242 original size:23 final size:23
Alignment explanation
Indices: 5422216--5422266 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
5422206 TTAACTAATT
*
5422216 TTATAAATATATATTAAAATATA
1 TTATAAATATATATTAAAAAATA
** * *
5422239 TTATACTTATTTCTTAAAAAATA
1 TTATAAATATATATTAAAAAATA
5422262 TTATA
1 TTATA
5422267 GAATTCGTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
TTATAAATATATATTAAAAAATA
Found at i:5425953 original size:19 final size:20
Alignment explanation
Indices: 5425917--5425954 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5425907 TTTAAAACTT
* *
5425917 AAAATAAAAAACAGTTTAAG
1 AAAAGAAAAAACACTTTAAG
5425937 AAAAGAAAAAA-ACTTTAA
1 AAAAGAAAAAACACTTTAA
5425955 AATATGAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.68, C:0.05, G:0.08, T:0.18
Consensus pattern (20 bp):
AAAAGAAAAAACACTTTAAG
Found at i:5431490 original size:9 final size:9
Alignment explanation
Indices: 5431476--5431567 Score: 157
Period size: 9 Copynumber: 10.2 Consensus size: 9
5431466 TCGGGTATTT
*
5431476 TTCGGTTAA
1 TTCGGGTAA
*
5431485 TTCGGTTAA
1 TTCGGGTAA
*
5431494 TTCGGTTAA
1 TTCGGGTAA
5431503 TTCGGGTAA
1 TTCGGGTAA
5431512 TTCGGGTAA
1 TTCGGGTAA
5431521 TTCGGGTAA
1 TTCGGGTAA
5431530 TTCGGGTAA
1 TTCGGGTAA
5431539 TTCGGGTAA
1 TTCGGGTAA
5431548 TTCGGGTAA
1 TTCGGGTAA
5431557 TTCGGGTAA
1 TTCGGGTAA
5431566 TT
1 TT
5431568 TTTAACCAAA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
9 82 1.00
ACGTcount: A:0.22, C:0.11, G:0.29, T:0.38
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:5431745 original size:12 final size:12
Alignment explanation
Indices: 5431728--5431752 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5431718 AGTAATTTCG
5431728 GGTCGGTTAACC
1 GGTCGGTTAACC
5431740 GGTCGGTTAACC
1 GGTCGGTTAACC
5431752 G
1 G
5431753 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:5434323 original size:63 final size:65
Alignment explanation
Indices: 5434250--5434383 Score: 227
Period size: 63 Copynumber: 2.1 Consensus size: 65
5434240 AATTAAGAGT
* *
5434250 TAATTTTTCTTAGATAATTACGTTTATTTTCTTTAAATTAAGAG-T-TTTTTTTAATTTAATGTA
1 TAATTTTTCTTAGATAAGTACATTTATTTTCTTTAAATTAAGAGTTGTTTTTTTAATTTAATGTA
5434313 TAATTTTTCTTAGATAAGTACATTTATTTTCTTTAAATTAAGAGTTGTTTTTTTAATTTAATGTA
1 TAATTTTTCTTAGATAAGTACATTTATTTTCTTTAAATTAAGAGTTGTTTTTTTAATTTAATGTA
*
5434378 TTATTT
1 TAATTT
5434384 ATTTTATTAT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
63 42 0.64
64 1 0.02
65 23 0.35
ACGTcount: A:0.30, C:0.04, G:0.08, T:0.57
Consensus pattern (65 bp):
TAATTTTTCTTAGATAAGTACATTTATTTTCTTTAAATTAAGAGTTGTTTTTTTAATTTAATGTA
Found at i:5437092 original size:30 final size:30
Alignment explanation
Indices: 5437021--5437092 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
5437011 CCACCCCAAG
* * *
5437021 TTTTTGAAAATTTTAGTTATACCCTTAAAA
1 TTTTTGAAAATTTTAATTAGACCCCTAAAA
* *
5437051 TTTTCTG-AAATTTTAATTAGGCCCCTCAAA
1 TTTT-TGAAAATTTTAATTAGACCCCTAAAA
5437081 TTTTTGAAAATT
1 TTTTTGAAAATT
5437093 ATTATTAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 2 0.06
30 31 0.89
31 2 0.06
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.46
Consensus pattern (30 bp):
TTTTTGAAAATTTTAATTAGACCCCTAAAA
Found at i:5444923 original size:185 final size:185
Alignment explanation
Indices: 5444611--5444971 Score: 551
Period size: 185 Copynumber: 2.0 Consensus size: 185
5444601 ACTAATGATC
* *
5444611 ATAACATTCTAATGATTCAAGGCCACTGCATGCATATATGTGATAAGCTCTCGTTGTTGCCTTTG
1 ATAACATTCTAATGATTCAAGGCCACTGCATGCATATATGTGATAAGCTCTCGTTGTTACCTCTG
* * *
5444676 TTGTTCCAACAATATTCACCAATATAGACACTTACTGGCTCTTCTTCATAGCTGTAAATGCATGC
66 TCGTTCCAACAATATTCACCAAAATAGACACTTACTGGCTCATCTTCATAGCTGTAAATGCATGC
* * *
5444741 AAACATGATCATTCATTCATTATTATTATCATCATTAATTTTTTTAATGGCATTT
131 AAACATGATCATTCATTCATTAGTATCATCATCATCAATTTTTTTAATGGCATTT
* *
5444796 ATAACATTCTAATGATTCAAGGCCATTGCATGCATATATTTGATAAGCTCTCGTTGTTACCTCTG
1 ATAACATTCTAATGATTCAAGGCCACTGCATGCATATATGTGATAAGCTCTCGTTGTTACCTCTG
* * * * ** *
5444861 TCGTTTCAACGATATTCACCAAAATAGACACTTGCTGTCTCATCTTTGTTGCTGTAAATGCATGC
66 TCGTTCCAACAATATTCACCAAAATAGACACTTACTGGCTCATCTTCATAGCTGTAAATGCATGC
* *
5444926 AAACATGATCATTTATTCTTTAGTATCATCATCATCAATTTTTTTA
131 AAACATGATCATTCATTCATTAGTATCATCATCATCAATTTTTTTA
5444972 CTGATGTATG
Statistics
Matches: 157, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
185 157 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (185 bp):
ATAACATTCTAATGATTCAAGGCCACTGCATGCATATATGTGATAAGCTCTCGTTGTTACCTCTG
TCGTTCCAACAATATTCACCAAAATAGACACTTACTGGCTCATCTTCATAGCTGTAAATGCATGC
AAACATGATCATTCATTCATTAGTATCATCATCATCAATTTTTTTAATGGCATTT
Found at i:5448270 original size:43 final size:43
Alignment explanation
Indices: 5448222--5448307 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
5448212 GACACACAGA
5448222 GGTAACTCATTCAGTCTCATTATGATCCCAACATGTTACACTG
1 GGTAACTCATTCAGTCTCATTATGATCCCAACATGTTACACTG
5448265 GGTAACTCATTCAGTCTCATTATGATCCCAACATGTTACACTG
1 GGTAACTCATTCAGTCTCATTATGATCCCAACATGTTACACTG
5448308 CAACCAACCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (43 bp):
GGTAACTCATTCAGTCTCATTATGATCCCAACATGTTACACTG
Found at i:5470469 original size:19 final size:20
Alignment explanation
Indices: 5470446--5470497 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
5470436 TTTATAACGT
5470446 CGTAAAAAAATTATAAAAAG
1 CGTAAAAAAATTATAAAAAG
* *
5470466 -GTAAAGAAA-TATAAAATG
1 CGTAAAAAAATTATAAAAAG
5470484 CGTAAAAAAATTAT
1 CGTAAAAAAATTAT
5470498 CGTACTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 8 0.30
19 16 0.59
20 3 0.11
ACGTcount: A:0.62, C:0.04, G:0.12, T:0.23
Consensus pattern (20 bp):
CGTAAAAAAATTATAAAAAG
Found at i:5470732 original size:20 final size:21
Alignment explanation
Indices: 5470709--5470748 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5470699 TATAAAAAAA
*
5470709 TTAC-AGTTTTTTATATTTTT
1 TTACGAGTTTTTTAAATTTTT
*
5470729 TTACGATTTTTTTAAATTTT
1 TTACGAGTTTTTTAAATTTT
5470749 AATAATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (21 bp):
TTACGAGTTTTTTAAATTTTT
Found at i:5496895 original size:13 final size:13
Alignment explanation
Indices: 5496877--5496941 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 13
5496867 AGTTTAGTAT
*
5496877 TGTTTTTGAGAAG
1 TGTTTTTGAAAAG
*
5496890 TGTTTTTAAAAAG
1 TGTTTTTGAAAAG
** *
5496903 TGTCGTGGAAAAG
1 TGTTTTTGAAAAG
* *
5496916 TGATTTTGAGAAG
1 TGTTTTTGAAAAG
*
5496929 TATTTTTGAAAAG
1 TGTTTTTGAAAAG
5496942 ATTGGTTTAA
Statistics
Matches: 38, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.32, C:0.02, G:0.26, T:0.40
Consensus pattern (13 bp):
TGTTTTTGAAAAG
Found at i:5501749 original size:12 final size:13
Alignment explanation
Indices: 5501726--5501754 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
5501716 ATAAATAAAA
5501726 ATAAATAAAACAT
1 ATAAATAAAACAT
5501739 ATAAA-AAAACAT
1 ATAAATAAAACAT
5501751 ATAA
1 ATAA
5501755 TTTTCGGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (13 bp):
ATAAATAAAACAT
Found at i:5505881 original size:25 final size:25
Alignment explanation
Indices: 5505853--5505901 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
5505843 AATATGTAAA
5505853 GTTAATTTAAAATTTTCATCGACCG
1 GTTAATTTAAAATTTTCATCGACCG
*
5505878 GTTAATTTAAAATTTTCATTGACC
1 GTTAATTTAAAATTTTCATCGACC
5505902 CAGTTGGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (25 bp):
GTTAATTTAAAATTTTCATCGACCG
Found at i:5509891 original size:21 final size:22
Alignment explanation
Indices: 5509862--5509908 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
5509852 CAGAAGGAGT
*
5509862 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
5509884 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
5509905 GAGT
1 GAGT
5509909 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:5511271 original size:24 final size:23
Alignment explanation
Indices: 5511191--5511271 Score: 58
Period size: 25 Copynumber: 3.3 Consensus size: 23
5511181 TTATCTTAAA
5511191 AATTAATATTTTAGTATTAAAAA-AT
1 AATTAA-A-TTTAGT-TTAAAAATAT
* **
5511216 AATTTAATTTTTTTTAAAAAT-T
1 AATTAAATTTAGTTTAAAAATAT
5511238 AATAGCTAAATTTAGTTTAAAAATGAT
1 AAT---TAAATTTAGTTTAAAAAT-AT
5511265 AATTAAA
1 AATTAAA
5511272 ATGACAAATG
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
22 11 0.25
23 4 0.09
24 5 0.11
25 20 0.45
27 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.44
Consensus pattern (23 bp):
AATTAAATTTAGTTTAAAAATAT
Found at i:5527234 original size:3 final size:3
Alignment explanation
Indices: 5527226--5527266 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
5527216 AATGGAAATA
*
5527226 ATC ATC ATC AGC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
5527267 ATATATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.32, G:0.02, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:5528461 original size:16 final size:17
Alignment explanation
Indices: 5528426--5528459 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5528416 AGGGTATTTT
5528426 ATAAAAATATTATAAAA
1 ATAAAAATATTATAAAA
5528443 ATAAAAAT-TTACTAAAA
1 ATAAAAATATTA-TAAAA
5528460 TATTATAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAAATATTATAAAA
Found at i:5528545 original size:27 final size:27
Alignment explanation
Indices: 5528449--5528543 Score: 140
Period size: 26 Copynumber: 3.5 Consensus size: 27
5528439 AAAAATAAAA
* *
5528449 ATTTACTAAAATATTATAACTTTTTTTT
1 ATTTACCAAAATATTACAAC-TTTTTTT
5528477 ATTTACCAAAATATTACAA-TTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTT
5528503 ATTTACCAAAATATATA-AACTTTTTTT
1 ATTTACCAAAATAT-TACAACTTTTTTT
5528530 ATTTACCAAAATAT
1 ATTTACCAAAATAT
5528544 ATCAAAAAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
26 23 0.37
27 23 0.37
28 17 0.27
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTACCAAAATATTACAACTTTTTTT
Found at i:5528641 original size:27 final size:26
Alignment explanation
Indices: 5528587--5528671 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 26
5528577 TTGACACCAA
*
5528587 CCAATTAAATTGGCGGCACCAAAT-GTG
1 CCAAATAAATTGGCGGCACC--ATGGTG
*
5528614 CCAAATAAATTGGTGGCACCATTGGTG
1 CCAAATAAATTGGCGGCACCA-TGGTG
* *
5528641 CCAAAGT-CATTAGCGGCACCATGGTG
1 CCAAA-TAAATTGGCGGCACCATGGTG
5528667 CCAAA
1 CCAAA
5528672 AGAAAAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
25 1 0.02
26 11 0.22
27 37 0.74
28 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.21
Consensus pattern (26 bp):
CCAAATAAATTGGCGGCACCATGGTG
Found at i:5528773 original size:19 final size:19
Alignment explanation
Indices: 5528746--5528815 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
5528736 TCAACTCATT
*
5528746 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
5528765 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
5528783 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
5528802 TTTTAATTTAATAA
1 TTTTAATTTAATAA
5528816 ACTATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:5528796 original size:37 final size:37
Alignment explanation
Indices: 5528751--5528821 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
5528741 TCATTTTTTT
5528751 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
5528788 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
5528822 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:5529241 original size:27 final size:28
Alignment explanation
Indices: 5529188--5529256 Score: 122
Period size: 27 Copynumber: 2.5 Consensus size: 28
5529178 TTTTTTTTAT
*
5529188 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAACTTGTA
5529216 ATATTTTGGTAAAT-AAAAAAACTTGTA
1 ATATTTTGGTAAATAAAAAAAACTTGTA
5529243 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
5529257 TTTTATTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 26 0.65
28 14 0.35
ACGTcount: A:0.46, C:0.01, G:0.13, T:0.39
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAACTTGTA
Found at i:5540053 original size:23 final size:23
Alignment explanation
Indices: 5540026--5540071 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
5540016 TTTTTGTTAA
5540026 GCCTGTATGTTCATTCATTTTGC
1 GCCTGTATGTTCATTCATTTTGC
5540049 GCCTGTATGTTCATTCATTTTGC
1 GCCTGTATGTTCATTCATTTTGC
5540072 AATTTTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.22, G:0.17, T:0.48
Consensus pattern (23 bp):
GCCTGTATGTTCATTCATTTTGC
Found at i:5544364 original size:22 final size:24
Alignment explanation
Indices: 5544339--5544383 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5544329 TCATACATTA
5544339 TAAAAG-AAAATA-CAAAAAAAAG
1 TAAAAGAAAAATATCAAAAAAAAG
*
5544361 TAAAGGAAAAATATCAAAAAAAA
1 TAAAAGAAAAATATCAAAAAAAA
5544384 AATGAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 6 0.30
24 9 0.45
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (24 bp):
TAAAAGAAAAATATCAAAAAAAAG
Found at i:5557849 original size:10 final size:10
Alignment explanation
Indices: 5557834--5557862 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
5557824 TCATCTTTCC
5557834 TATTATATCA
1 TATTATATCA
5557844 TATTATATCA
1 TATTATATCA
5557854 TATTATATC
1 TATTATATC
5557863 TATGTGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (10 bp):
TATTATATCA
Found at i:5558521 original size:11 final size:12
Alignment explanation
Indices: 5558493--5558523 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
5558483 AAATTACTTT
5558493 TAAAAAATATTG
1 TAAAAAATATTG
5558505 TAAAAAATATTG
1 TAAAAAATATTG
5558517 TAAAAAA
1 TAAAAAA
5558524 GTAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (12 bp):
TAAAAAATATTG
Found at i:5560855 original size:13 final size:13
Alignment explanation
Indices: 5560837--5560861 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5560827 TTTAATAAAA
5560837 TTTTATATTTAAT
1 TTTTATATTTAAT
5560850 TTTTATATTTAA
1 TTTTATATTTAA
5560862 AAATTCTAAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTATATTTAAT
Found at i:5576574 original size:46 final size:46
Alignment explanation
Indices: 5576502--5576657 Score: 264
Period size: 46 Copynumber: 3.5 Consensus size: 46
5576492 TAATCAGTGA
*
5576502 CAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
5576548 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
5576594 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
5576639 C-AGAGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
5576658 ATCATACGTA
Statistics
Matches: 107, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
43 12 0.11
44 5 0.05
45 19 0.18
46 71 0.66
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:5577258 original size:36 final size:36
Alignment explanation
Indices: 5577211--5577283 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
5577201 TGGTAATGCC
5577211 TCGTACCCTATTCCGGTGTTGGATACGAGTAAGGGG
1 TCGTACCCTATTCCGGTGTTGGATACGAGTAAGGGG
*
5577247 TCGTACCCTATTCCGGTGTTGGATACGGGTAAGGGG
1 TCGTACCCTATTCCGGTGTTGGATACGAGTAAGGGG
5577283 T
1 T
5577284 GTTACACATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.18, C:0.19, G:0.34, T:0.29
Consensus pattern (36 bp):
TCGTACCCTATTCCGGTGTTGGATACGAGTAAGGGG
Found at i:5577391 original size:33 final size:33
Alignment explanation
Indices: 5577329--5577391 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
5577319 ATAATAATTA
* *
5577329 TATTAAAATATGATTAAATTATTTATTATTTTT
1 TATTAAAATATGATTAAAATAATTATTATTTTT
5577362 TATTAAAATAT-ATTCAACAATAATT-TTATT
1 TATTAAAATATGATT-AA-AATAATTATTATT
5577392 AAAATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
32 3 0.12
33 18 0.69
34 5 0.19
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (33 bp):
TATTAAAATATGATTAAAATAATTATTATTTTT
Found at i:5577584 original size:16 final size:16
Alignment explanation
Indices: 5577560--5577613 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
5577550 TGAATTACTG
*
5577560 ATTATAACTCTATTCC
1 ATTACAACTCTATTCC
*
5577576 ATTACAACTCTATTCA
1 ATTACAACTCTATTCC
*
5577592 ATTACAGC-CTTATTCC
1 ATTACAACTC-TATTCC
5577608 ATTACA
1 ATTACA
5577614 GTAACCAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 1 0.03
16 32 0.97
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:5577614 original size:16 final size:17
Alignment explanation
Indices: 5577566--5577614 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 17
5577556 ACTGATTATA
5577566 ACTCTATTCCATTACA-
1 ACTCTATTCCATTACAG
*
5577582 ACTCTATTCAATTACAG
1 ACTCTATTCCATTACAG
*
5577599 CCT-TATTCCATTACAG
1 ACTCTATTCCATTACAG
5577615 TAACCAAACG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 27 0.93
17 2 0.07
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.37
Consensus pattern (17 bp):
ACTCTATTCCATTACAG
Found at i:5579593 original size:4 final size:4
Alignment explanation
Indices: 5579584--5579610 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5579574 CGACCACCCT
5579584 TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA
5579611 TGCTTTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:5579913 original size:14 final size:13
Alignment explanation
Indices: 5579896--5579941 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
5579886 TTTAAAGTTA
5579896 TAAAAATAAATTTT
1 TAAAAATAAA-TTT
5579910 TAAAAAT--A-TT
1 TAAAAATAAATTT
5579920 TAAAAATAAATATT
1 TAAAAATAAAT-TT
5579934 TAAAAATA
1 TAAAAATA
5579942 TAAAAAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.32
12 2 0.07
14 17 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAAAATAAATTT
Found at i:5579923 original size:24 final size:23
Alignment explanation
Indices: 5579896--5579957 Score: 88
Period size: 24 Copynumber: 2.7 Consensus size: 23
5579886 TTTAAAGTTA
5579896 TAAAAATAAATTTTTAAAAATATT
1 TAAAAATAAATTTTTAAAAATA-T
*
5579920 TAAAAATAAATATTTAAAAATAT
1 TAAAAATAAATTTTTAAAAATAT
* *
5579943 AAAAAATAGATTTTT
1 TAAAAATAAATTTTT
5579958 TTTTAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 13 0.38
24 21 0.62
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TAAAAATAAATTTTTAAAAATAT
Found at i:5582047 original size:20 final size:21
Alignment explanation
Indices: 5582002--5582051 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
5581992 ATTTTAAATT
*
5582002 TAAAAAA-TATGTAAAAATTA
1 TAAAAAATTATGTAAAAAGTA
*
5582022 T-TAAAATTAT-TAAAAAGTA
1 TAAAAAATTATGTAAAAAGTA
5582041 TAAAAAATTAT
1 TAAAAAATTAT
5582052 ATTTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (21 bp):
TAAAAAATTATGTAAAAAGTA
Found at i:5582950 original size:18 final size:18
Alignment explanation
Indices: 5582904--5582952 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
5582894 GACTTTGTAC
5582904 TTTTTCTTTTTAATCATT
1 TTTTTCTTTTTAATCATT
*
5582922 TTTATT-ATTTTATAT-ATT
1 TTT-TTCTTTTTA-ATCATT
5582940 TTTTTCTTTTTAA
1 TTTTTCTTTTTAA
5582953 CTTTCCTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTCTTTTTAATCATT
Found at i:5585450 original size:33 final size:33
Alignment explanation
Indices: 5585408--5585472 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
5585398 CTAAAAAAAC
*
5585408 CAATTGCAAACAATCTTTCAATAATGCTTTTAA
1 CAATTGCAAACAATCTTTCAACAATGCTTTTAA
*
5585441 CAATTGCAAACAATCTTTTAACAATGCTTTTA
1 CAATTGCAAACAATCTTTCAACAATGCTTTTA
5585473 TCATTTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.37
Consensus pattern (33 bp):
CAATTGCAAACAATCTTTCAACAATGCTTTTAA
Found at i:5585950 original size:51 final size:51
Alignment explanation
Indices: 5585886--5585993 Score: 207
Period size: 51 Copynumber: 2.1 Consensus size: 51
5585876 TTTTGATACT
5585886 TTTTCAGCAATACTATTAATTGGGTCTGTTCCTTCTAGTTCAACAGAAGTTA
1 TTTT-AGCAATACTATTAATTGGGTCTGTTCCTTCTAGTTCAACAGAAGTTA
5585938 TTTTAGCAATACTATTAATTGGGTCTGTTCCTTCTAGTTCAACAGAAGTTA
1 TTTTAGCAATACTATTAATTGGGTCTGTTCCTTCTAGTTCAACAGAAGTTA
5585989 TTTTA
1 TTTTA
5585994 CTTGTATAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 52 0.93
52 4 0.07
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.43
Consensus pattern (51 bp):
TTTTAGCAATACTATTAATTGGGTCTGTTCCTTCTAGTTCAACAGAAGTTA
Found at i:5597713 original size:124 final size:124
Alignment explanation
Indices: 5597493--5597743 Score: 502
Period size: 124 Copynumber: 2.0 Consensus size: 124
5597483 TAGAATGAGA
5597493 AAGGAGATGGTAGAGAGTAACTTTGATAAAGAAACAGTCGGATGCACCGGGACAACTGATACTCA
1 AAGGAGATGGTAGAGAGTAACTTTGATAAAGAAACAGTCGGATGCACCGGGACAACTGATACTCA
5597558 TAGTAGAAATCAAGGTTCAGGTCTTCGCAGGGAGCCCTCCTTCTCTCGCTGGGTCGATG
66 TAGTAGAAATCAAGGTTCAGGTCTTCGCAGGGAGCCCTCCTTCTCTCGCTGGGTCGATG
5597617 AAGGAGATGGTAGAGAGTAACTTTGATAAAGAAACAGTCGGATGCACCGGGACAACTGATACTCA
1 AAGGAGATGGTAGAGAGTAACTTTGATAAAGAAACAGTCGGATGCACCGGGACAACTGATACTCA
5597682 TAGTAGAAATCAAGGTTCAGGTCTTCGCAGGGAGCCCTCCTTCTCTCGCTGGGTCGATG
66 TAGTAGAAATCAAGGTTCAGGTCTTCGCAGGGAGCCCTCCTTCTCTCGCTGGGTCGATG
5597741 AAG
1 AAG
5597744 ATGGGATAAT
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 127 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.22
Consensus pattern (124 bp):
AAGGAGATGGTAGAGAGTAACTTTGATAAAGAAACAGTCGGATGCACCGGGACAACTGATACTCA
TAGTAGAAATCAAGGTTCAGGTCTTCGCAGGGAGCCCTCCTTCTCTCGCTGGGTCGATG
Found at i:5603982 original size:13 final size:14
Alignment explanation
Indices: 5603956--5603995 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
5603946 CGCTTAAGGG
5603956 ATTTACATCATTATT
1 ATTTACA-CATTATT
5603971 A-TTACACATTA-T
1 ATTTACACATTATT
5603983 ATTTACAC-TTATT
1 ATTTACACATTATT
5603996 TGGAAGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 5 0.22
13 12 0.52
14 5 0.22
15 1 0.04
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTACACATTATT
Found at i:5604429 original size:21 final size:22
Alignment explanation
Indices: 5604395--5604448 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
5604385 CACACTAAAT
*
5604395 ATAAAAAAATAATAACATTTTA
1 ATAAAAAAATAATAAAATTTTA
*
5604417 ATAAAAAGA-AATAAAATTTT-
1 ATAAAAAAATAATAAAATTTTA
*
5604437 -TTAAAAAATAAT
1 ATAAAAAAATAAT
5604449 TTAATGTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 6 0.22
20 3 0.11
21 10 0.37
22 8 0.30
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
ATAAAAAAATAATAAAATTTTA
Found at i:5607843 original size:3 final size:3
Alignment explanation
Indices: 5607835--5607870 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5607825 CAAGACATTA
5607835 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
5607871 TTGCTTTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:5613679 original size:6 final size:6
Alignment explanation
Indices: 5613668--5613696 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5613658 CTCTCTCCTG
5613668 TCCAGC TCCAGC TCCAGC TCCAGC TCCAG
1 TCCAGC TCCAGC TCCAGC TCCAGC TCCAG
5613697 GAGCAGTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.48, G:0.17, T:0.17
Consensus pattern (6 bp):
TCCAGC
Found at i:5621261 original size:104 final size:104
Alignment explanation
Indices: 5621133--5621320 Score: 274
Period size: 104 Copynumber: 1.8 Consensus size: 104
5621123 GACAATTGAC
* *
5621133 CATTACTTATTGGTCGACTTTATGGCTCTTT-GCCCTCCAAGGGTGAACCGTCCTCAAGCGTA-A
1 CATTACTTATTGCTCGACTTTATGGCT-TTTCACCCTCCAAGGGTGAACCGTCCTCAAGCGTATA
*
5621196 TCCTGAACAATTGCCTACAAGTGTAATTCCAGACGATGGTT
65 TCC-GAACAATTGCCCACAAGTGTAATTCCAGACGATGGTT
* *
5621237 CATTACTTATTGCT-GAACTTTATGGCTTTTCACCCTCTAAGGGTGAACCGTCCTCAAGCGTATT
1 CATTACTTATTGCTCG-ACTTTATGGCTTTTCACCCTCCAAGGGTGAACCGTCCTCAAGCGTATA
*
5621301 TCCGAACGATTGCCCACAAG
65 TCCGAACAATTGCCCACAAG
5621321 CATAATCTCG
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
103 4 0.05
104 68 0.91
105 3 0.04
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (104 bp):
CATTACTTATTGCTCGACTTTATGGCTTTTCACCCTCCAAGGGTGAACCGTCCTCAAGCGTATAT
CCGAACAATTGCCCACAAGTGTAATTCCAGACGATGGTT
Found at i:5621344 original size:104 final size:104
Alignment explanation
Indices: 5621133--5621363 Score: 236
Period size: 104 Copynumber: 2.2 Consensus size: 104
5621123 GACAATTGAC
* *
5621133 CATTACTTATTGGTCG-ACTTTATGGCTCTTTGCCCTCCAAGGGTGAACCGTCCTCAAGCGTAAT
1 CATTACTTATTGCT-GAACTTTATGGCTCTTTACCCTCCAAGGGTGAACCGTCCTCAAGCGTAAT
* ** * ****
5621197 CCTGAACAATTGCCTACAAGTGTAATTCCAGACGATGGTT
65 CCTGAACAATTGCCCACAAGCATAATTCCAGACAACAACT
* *
5621237 CATTACTTATTGCTGAACTTTATGGCT-TTTCACCCTCTAAGGGTGAACCGTCCTCAAGCGTATT
1 CATTACTTATTGCTGAACTTTATGGCTCTTT-ACCCTCCAAGGGTGAACCGTCCTCAAGCGTA-A
* *
5621301 TCC-GAACGATTGCCCACAAGCATAATCTCGA-ACAACAACT
64 TCCTGAACAATTGCCCACAAGCATAAT-TCCAGACAACAACT
* * * *
5621341 CATTAATTGTTGCTCAATTTTAT
1 CATTACTTATTGCTGAACTTTAT
5621364 AACTCTCACA
Statistics
Matches: 105, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
103 4 0.04
104 95 0.90
105 6 0.06
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (104 bp):
CATTACTTATTGCTGAACTTTATGGCTCTTTACCCTCCAAGGGTGAACCGTCCTCAAGCGTAATC
CTGAACAATTGCCCACAAGCATAATTCCAGACAACAACT
Found at i:5629917 original size:3 final size:3
Alignment explanation
Indices: 5629911--5629949 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
5629901 ATCATCATTG
5629911 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
5629950 CTCAAAGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:5632423 original size:7 final size:7
Alignment explanation
Indices: 5632411--5632460 Score: 84
Period size: 7 Copynumber: 7.1 Consensus size: 7
5632401 TAATTTGATG
5632411 AAATTTA
1 AAATTTA
5632418 AAATTTA
1 AAATTTA
5632425 AAATTTA
1 AAATTTA
5632432 AAATTTA
1 AAATTTA
5632439 AAATTTA
1 AAATTTA
5632446 AAA-TTA
1 AAATTTA
5632452 AAATCTTA
1 AAAT-TTA
5632460 A
1 A
5632461 TATTCGTGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.15
7 31 0.76
8 4 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:5636666 original size:85 final size:85
Alignment explanation
Indices: 5636523--5636696 Score: 287
Period size: 85 Copynumber: 2.0 Consensus size: 85
5636513 GAAGAAAAAG
* *
5636523 GATAGGTATGAAAAAAATCTAGGGTCTCCTTTTAAGTGAAGGACGAGAATAATCACAATTAACAA
1 GATAGGCATGAAAAAAATCTAGGGTCTCCTTTTAAGTGAAGGACGAAAATAATCACAATTAACAA
*
5636588 GGTGC-CCTTACTGCTTTGCA
66 GGT-CACCTTACTGCATTGCA
* *
5636608 GATAGGCATGAAAAAAATCTAGGGTTTCCTTTTAAGTGAAGGATGAAAATAATCACAATTAACAA
1 GATAGGCATGAAAAAAATCTAGGGTCTCCTTTTAAGTGAAGGACGAAAATAATCACAATTAACAA
5636673 GGTCACCTTACTGCATTGCA
66 GGTCACCTTACTGCATTGCA
5636693 GATA
1 GATA
5636697 ACCTTTTTGA
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
84 1 0.01
85 82 0.99
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (85 bp):
GATAGGCATGAAAAAAATCTAGGGTCTCCTTTTAAGTGAAGGACGAAAATAATCACAATTAACAA
GGTCACCTTACTGCATTGCA
Found at i:5639338 original size:59 final size:61
Alignment explanation
Indices: 5639241--5639428 Score: 238
Period size: 67 Copynumber: 3.0 Consensus size: 61
5639231 CAGCTCCAAT
* *
5639241 ATTAC-CAAAACATTACAAAAGCTGTAATAATTTGTGTAATTGGTTAATGTTTTGT-A-TA
1 ATTACACAAAACATTACAAAAGTTGTAATAATTTGTGTAATTGGGTAATGTTTTGTGAGTA
*
5639299 ATTACACAAAACATTACGAAAGTTGTAATAATTTGTGTAATTGGGTAATGCTTTGTGTGATTGCG
1 ATTACACAAAACATTACAAAAGTTGTAATAATTTGTGTAATTGGGTAATG-TTT-TGTGA----G
5639364 TA
60 TA
* *
5639366 ATTACACAATACATTACAAAAGTTGTAATAATTTGTATAATTGGGTAATTGTTTTGTGTAGTA
1 ATTACACAAAACATTACAAAAGTTGTAATAATTTGTGTAATTGGGTAA-TGTTTTGTG-AGTA
5639429 GAAGCTTATG
Statistics
Matches: 113, Mismatches: 6, Indels: 17
0.83 0.04 0.12
Matches are distributed among these distances:
58 5 0.04
59 41 0.36
60 3 0.03
61 3 0.03
62 1 0.01
63 3 0.03
66 4 0.04
67 51 0.45
68 2 0.02
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (61 bp):
ATTACACAAAACATTACAAAAGTTGTAATAATTTGTGTAATTGGGTAATGTTTTGTGAGTA
Found at i:5639353 original size:20 final size:20
Alignment explanation
Indices: 5639330--5639367 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5639320 GTTGTAATAA
*
5639330 TTTGTGTAATTGGGTAATGC
1 TTTGTGTAATTGCGTAATGC
*
5639350 TTTGTGTGATTGCGTAAT
1 TTTGTGTAATTGCGTAAT
5639368 TACACAATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.05, G:0.29, T:0.47
Consensus pattern (20 bp):
TTTGTGTAATTGCGTAATGC
Found at i:5639580 original size:110 final size:110
Alignment explanation
Indices: 5639387--5639593 Score: 414
Period size: 110 Copynumber: 1.9 Consensus size: 110
5639377 CATTACAAAA
5639387 GTTGTAATAATTTGTATAATTGGGTAATTGTTTTGTGTAGTAGAAGCTTATGGAAAGCTTATTTT
1 GTTGTAATAATTTGTATAATTGGGTAATTGTTTTGTGTAGTAGAAGCTTATGGAAAGCTTATTTT
5639452 AGAAGCTCACCCTAAAAGTTCTCGCAACATTGCAAAAGTTGTAAT
66 AGAAGCTCACCCTAAAAGTTCTCGCAACATTGCAAAAGTTGTAAT
5639497 GTTGTAATAATTTGTATAATTGGGTAATTGTTTTGTGTAGTAGAAGCTTATGGAAAGCTTATTTT
1 GTTGTAATAATTTGTATAATTGGGTAATTGTTTTGTGTAGTAGAAGCTTATGGAAAGCTTATTTT
5639562 AGAAGCTCACCCTAAAAGTTCTCGCAACATTG
66 AGAAGCTCACCCTAAAAGTTCTCGCAACATTG
5639594 TGCAAGGGAT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 97 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (110 bp):
GTTGTAATAATTTGTATAATTGGGTAATTGTTTTGTGTAGTAGAAGCTTATGGAAAGCTTATTTT
AGAAGCTCACCCTAAAAGTTCTCGCAACATTGCAAAAGTTGTAAT
Found at i:5648199 original size:29 final size:30
Alignment explanation
Indices: 5648140--5648197 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5648130 TTCGAGCCTT
*
5648140 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
5648170 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
5648198 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:5648427 original size:13 final size:13
Alignment explanation
Indices: 5648409--5648440 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5648399 TTTCCAGCAA
5648409 TTATGAATTTATT
1 TTATGAATTTATT
5648422 TTATGAATTTATT
1 TTATGAATTTATT
*
5648435 TGATGA
1 TTATGA
5648441 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:5648648 original size:50 final size:50
Alignment explanation
Indices: 5648535--5648776 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
5648525 ATTTGGGTAA
* * *
5648535 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
5648591 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
5648641 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
5648691 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
5648741 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
5648777 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:5648724 original size:100 final size:103
Alignment explanation
Indices: 5648535--5648784 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
5648525 ATTTGGGTAA
5648535 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
5648600 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
5648641 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
5648703 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
5648741 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
5648785 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:5659641 original size:20 final size:19
Alignment explanation
Indices: 5659603--5659642 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5659593 ATATTCACCT
* *
5659603 TAAAATGTGAAATCAAATA
1 TAAAATGTCAAAACAAATA
5659622 TAAAATGTCAAACACAAATA
1 TAAAATGTCAAA-ACAAATA
5659642 T
1 T
5659643 TATAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.25
Consensus pattern (19 bp):
TAAAATGTCAAAACAAATA
Found at i:5664221 original size:12 final size:13
Alignment explanation
Indices: 5664183--5664224 Score: 56
Period size: 11 Copynumber: 3.5 Consensus size: 13
5664173 TATTCTTTTA
5664183 TTTTTAAAATAC-
1 TTTTTAAAATACT
5664195 -TTTTAAAATACT
1 TTTTTAAAATACT
5664207 TTTTTAAAAT--T
1 TTTTTAAAATACT
5664218 TTTTTAA
1 TTTTTAA
5664225 TTTTAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 19 0.68
13 9 0.32
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTAAAATACT
Done.