Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 66 of 121
Found at i:11352295 original size:23 final size:23
Alignment explanation
Indices: 11352255--11352299 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
11352245 TTTTTGCTTT
11352255 AAAAAAAAAAAGAAAAGAAAAGA
1 AAAAAAAAAAAGAAAAGAAAAGA
*
11352278 AAAAAATAAAAAG-GAAGAAAAG
1 AAAAAA-AAAAAGAAAAGAAAAG
11352300 GAATTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (23 bp):
AAAAAAAAAAAGAAAAGAAAAGA
Found at i:11352955 original size:25 final size:25
Alignment explanation
Indices: 11352876--11353032 Score: 163
Period size: 25 Copynumber: 6.2 Consensus size: 25
11352866 GTGTGTTTTA
* *
11352876 CATTTCATACATATTCCTAATTATGT
1 CATTTCATGCATATT-TTAATTATGT
* * *
11352902 TATTTCATGCATATTTTTAATCATAT
1 CATTTCATGCATA-TTTTAATTATGT
*
11352928 CATTTCATGCATACTTTAATTATGT
1 CATTTCATGCATATTTTAATTATGT
* *
11352953 CATTTCATGAAAATTTTAATTATGT
1 CATTTCATGCATATTTTAATTATGT
* *
11352978 CATCTT-AAGAATATTTTAATTATGT
1 CAT-TTCATGCATATTTTAATTATGT
* **
11353003 CATCTCATGCATATTTTAATTGCGT
1 CATTTCATGCATATTTTAATTATGT
11353028 CATTT
1 CATTT
11353033 GTTATATATT
Statistics
Matches: 108, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
24 1 0.01
25 73 0.68
26 32 0.30
27 2 0.02
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (25 bp):
CATTTCATGCATATTTTAATTATGT
Found at i:11358750 original size:95 final size:95
Alignment explanation
Indices: 11358650--11358833 Score: 278
Period size: 95 Copynumber: 1.9 Consensus size: 95
11358640 TAATTTTTTT
* *
11358650 CTACTATTATTGATTATTATTTACAAATTACTTCAGTAGACTTTAGTTTAATTAATTAATGATTA
1 CTACTATTATTGATTATTATTTACAAATTACTTCAGTACACTTTAATTTAATTAATTAATGATTA
*
11358715 AAAAATAAAATAAAGAGATTTTTATAGCTA
66 AAAAAGAAAATAAAGAGATTTTTATAGCTA
* * * *
11358745 CTACTATTATTGATTATTGTTTACAAATTATTTGAGTACACTTTAATTTAATTAATTAATGGTTA
1 CTACTATTATTGATTATTATTTACAAATTACTTCAGTACACTTTAATTTAATTAATTAATGATTA
* * *
11358810 AAGAGGAAAATAAAGATATTTTTA
66 AAAAAGAAAATAAAGAGATTTTTA
11358834 GCATATGAGA
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
95 79 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.43
Consensus pattern (95 bp):
CTACTATTATTGATTATTATTTACAAATTACTTCAGTACACTTTAATTTAATTAATTAATGATTA
AAAAAGAAAATAAAGAGATTTTTATAGCTA
Found at i:11360786 original size:34 final size:34
Alignment explanation
Indices: 11360743--11360812 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
11360733 AAGCTTCATT
*
11360743 TCTTTTATGCGTTAGATAACGAGGGTTCTATATC
1 TCTTTTATGCATTAGATAACGAGGGTTCTATATC
11360777 TCTTTTATGCATTAGATAACGAGGGTTCTATATC
1 TCTTTTATGCATTAGATAACGAGGGTTCTATATC
11360811 TC
1 TC
11360813 ACGTTTGGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (34 bp):
TCTTTTATGCATTAGATAACGAGGGTTCTATATC
Found at i:11363422 original size:44 final size:45
Alignment explanation
Indices: 11363372--11363465 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 45
11363362 AACTTTATCT
*
11363372 TTAATTTAATTCAATTATCTTCAATGCTATCATTT-ATTTCAAC-A
1 TTAATTTAATTCAATTATCTTCAATACTATC-TTTCATTTCAACAA
* *
11363416 TTAATTTAATTCAATTATCTTCACTACTATCTTTCGTTTCAACAA
1 TTAATTTAATTCAATTATCTTCAATACTATCTTTCATTTCAACAA
11363461 TTAAT
1 TTAAT
11363466 ATGAGAATGT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 3 0.07
44 36 0.80
45 6 0.13
ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48
Consensus pattern (45 bp):
TTAATTTAATTCAATTATCTTCAATACTATCTTTCATTTCAACAA
Found at i:11365375 original size:4 final size:4
Alignment explanation
Indices: 11365366--11365427 Score: 74
Period size: 4 Copynumber: 16.0 Consensus size: 4
11365356 TATAATTATA
* * * *
11365366 AAAT AAAT AAAT AAAT AAAT AAAT AACT AGA- AATT AAAT AAAT ACAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
11365413 AAAT AAAT -AAT AAAT
1 AAAT AAAT AAAT AAAT
11365428 TTTATAATGA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 4 0.08
4 44 0.92
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:11366636 original size:20 final size:20
Alignment explanation
Indices: 11366613--11366653 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
11366603 AACTCCCTAG
*
11366613 ATAATATAGAAAACAAGCTC
1 ATAATATAGAAAACAAACTC
11366633 ATAATATAGAAAACAAACTC
1 ATAATATAGAAAACAAACTC
11366653 A
1 A
11366654 CAAATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.07, T:0.20
Consensus pattern (20 bp):
ATAATATAGAAAACAAACTC
Found at i:11368094 original size:74 final size:72
Alignment explanation
Indices: 11367997--11368137 Score: 264
Period size: 74 Copynumber: 1.9 Consensus size: 72
11367987 GTTATTAAGT
11367997 AAATAACTTAACTTATTTACTTGAGTTATTAAACCATAAAGAAAAAGATATTTTAAGTTAAATAA
1 AAATAACTTAACTTATTTACTTGAGTTATTAAACCATAAAGAAAAAGATATTTTAAGTTAAA-AA
11368062 TAAATAAC
65 TAAATAAC
11368070 AAATAACTTTAACTTATTTACTTGAGTTATTAAACCATAAAGAAAAAGATATTTTAAGTTAAAAA
1 AAATAAC-TTAACTTATTTACTTGAGTTATTAAACCATAAAGAAAAAGATATTTTAAGTTAAAAA
11368135 TAA
65 TAA
11368138 TAGGTATGTA
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
73 12 0.18
74 55 0.82
ACGTcount: A:0.50, C:0.08, G:0.07, T:0.35
Consensus pattern (72 bp):
AAATAACTTAACTTATTTACTTGAGTTATTAAACCATAAAGAAAAAGATATTTTAAGTTAAAAAT
AAATAAC
Found at i:11369296 original size:13 final size:14
Alignment explanation
Indices: 11369289--11369353 Score: 66
Period size: 13 Copynumber: 4.9 Consensus size: 14
11369279 TTAGGGTTTT
*
11369289 GGTTTAGG-GTTAG
1 GGTTTAGGATTTAG
11369302 GGTTTA-GATTTAG
1 GGTTTAGGATTTAG
* *
11369315 GGTTTGGGATTTAA
1 GGTTTAGGATTTAG
11369329 GGTTT-GGATTTAG
1 GGTTTAGGATTTAG
11369342 AGGTTT-GGATTT
1 -GGTTTAGGATTT
11369354 GGGATTTGGG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
12 1 0.02
13 22 0.49
14 22 0.49
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (14 bp):
GGTTTAGGATTTAG
Found at i:11369303 original size:19 final size:19
Alignment explanation
Indices: 11369279--11369318 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
11369269 GGCTTAGGAT
* *
11369279 TTAGGGTTTTGGTTTAGGG
1 TTAGGGTTTAGATTTAGGG
11369298 TTAGGGTTTAGATTTAGGG
1 TTAGGGTTTAGATTTAGGG
11369317 TT
1 TT
11369319 TGGGATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.47
Consensus pattern (19 bp):
TTAGGGTTTAGATTTAGGG
Found at i:11369327 original size:14 final size:13
Alignment explanation
Indices: 11369298--11369373 Score: 82
Period size: 13 Copynumber: 5.7 Consensus size: 13
11369288 TGGTTTAGGG
*
11369298 TTAGGGTTTAGAT
1 TTAGGGTTTGGAT
11369311 TTAGGGTTTGGGAT
1 TTAGGGTTT-GGAT
*
11369325 TTAAGGTTTGGAT
1 TTAGGGTTTGGAT
11369338 TTAGAGGTTTGGAT
1 TTAG-GGTTTGGAT
*
11369352 TT-GGGATTTGGGT
1 TTAGGG-TTTGGAT
*
11369365 TTGGGGTTT
1 TTAGGGTTT
11369374 CATGAGAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
12 2 0.04
13 28 0.51
14 25 0.45
ACGTcount: A:0.16, C:0.00, G:0.38, T:0.46
Consensus pattern (13 bp):
TTAGGGTTTGGAT
Found at i:11369362 original size:27 final size:27
Alignment explanation
Indices: 11369302--11369353 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
11369292 TTAGGGTTAG
*
11369302 GGTTTAGATTTAGGGTTTGGGATTTAA
1 GGTTTGGATTTAGGGTTTGGGATTTAA
11369329 GGTTTGGATTTAGAGGTTT-GGATTT
1 GGTTTGGATTTAG-GGTTTGGGATTT
11369354 GGGATTTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (27 bp):
GGTTTGGATTTAGGGTTTGGGATTTAA
Found at i:11369367 original size:6 final size:6
Alignment explanation
Indices: 11369282--11369369 Score: 50
Period size: 6 Copynumber: 13.5 Consensus size: 6
11369272 TTAGGATTTA
* * * * *
11369282 GGGTTT TGGTTT AGGGTTA GGGTTT AGATTT AGGGTTT GGGATTT AAGGTTT
1 GGGTTT GGGTTT -GGGTTT GGGTTT GGGTTT -GGGTTT GGG-TTT -GGGTTT
* *
11369334 GGATTT AGAGGTTT GGATTT GGGATTT GGGTTT GGG
1 GGGTTT -G-GGTTT GGGTTT GGG-TTT GGGTTT GGG
11369370 GTTTCATGAG
Statistics
Matches: 61, Mismatches: 14, Indels: 14
0.69 0.16 0.16
Matches are distributed among these distances:
6 33 0.54
7 22 0.36
8 6 0.10
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (6 bp):
GGGTTT
Found at i:11369471 original size:43 final size:43
Alignment explanation
Indices: 11369392--11369479 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
11369382 ATTTATGTGA
**
11369392 CAAAATTACAAAAATGCCATTGATGGAAATACAAACTTTGATG
1 CAAAATTACAAAAATGCCATTGATAAAAATACAAACTTTGATG
** *
11369435 CAAAATTACAAAAATGCCATTGATAAAAATGTAAACTTTTATG
1 CAAAATTACAAAAATGCCATTGATAAAAATACAAACTTTGATG
11369478 CA
1 CA
11369480 TAAGAATAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (43 bp):
CAAAATTACAAAAATGCCATTGATAAAAATACAAACTTTGATG
Found at i:11371694 original size:14 final size:14
Alignment explanation
Indices: 11371675--11371701 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11371665 TTGAATATGA
11371675 CCTGATCGATCCCT
1 CCTGATCGATCCCT
11371689 CCTGATCGATCCC
1 CCTGATCGATCCC
11371702 CCCTTAAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.44, G:0.15, T:0.26
Consensus pattern (14 bp):
CCTGATCGATCCCT
Found at i:11373956 original size:25 final size:25
Alignment explanation
Indices: 11373910--11373957 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
11373900 ATGACATATA
* *
11373910 AGAAAATGATCTCTAAGTTAAAGTT
1 AGAAAATGAACTCTAAGCTAAAGTT
11373935 AGAAAATGAACTCTTAA-CTAAAG
1 AGAAAATGAACTC-TAAGCTAAAG
11373958 CAAATGATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (25 bp):
AGAAAATGAACTCTAAGCTAAAGTT
Found at i:11377469 original size:3 final size:3
Alignment explanation
Indices: 11377456--11377489 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
11377446 TGGGTTTATC
11377456 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11377490 TTTAATTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:11377935 original size:31 final size:31
Alignment explanation
Indices: 11377900--11377962 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
11377890 GGGAAATTAA
*
11377900 AATTCCGGCG-ACTTTTGAATTTTCCGACGAC
1 AATTCCGGCGAAC-TTTGAAGTTTCCGACGAC
*
11377931 AATTCCGGCGAACTTTGAAGTTTCCGGCGAC
1 AATTCCGGCGAACTTTGAAGTTTCCGACGAC
11377962 A
1 A
11377963 GACCCAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (31 bp):
AATTCCGGCGAACTTTGAAGTTTCCGACGAC
Found at i:11378048 original size:19 final size:19
Alignment explanation
Indices: 11378024--11378068 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
11378014 TCCGGCCAAT
11378024 TTCCGGCGAAATTCCCAGA
1 TTCCGGCGAAATTCCCAGA
* * *
11378043 TTCCGGTGAATTTTCCAGA
1 TTCCGGCGAAATTCCCAGA
*
11378062 ATCCGGC
1 TTCCGGC
11378069 ACCGGCGTTC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (19 bp):
TTCCGGCGAAATTCCCAGA
Found at i:11378297 original size:5 final size:5
Alignment explanation
Indices: 11378287--11378324 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
11378277 TTTCAGCCCT
*
11378287 CCGAG CCGAG CCGAG CCGAG CCGCA- CCAAG CCGAG CCG
1 CCGAG CCGAG CCGAG CCGAG CCG-AG CCGAG CCGAG CCG
11378325 CGATCCGAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 1 0.03
5 27 0.93
6 1 0.03
ACGTcount: A:0.21, C:0.45, G:0.34, T:0.00
Consensus pattern (5 bp):
CCGAG
Found at i:11378373 original size:16 final size:16
Alignment explanation
Indices: 11378354--11378384 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11378344 TTTTTTTTTT
*
11378354 TTTTTTTTTTTTTGAA
1 TTTTTTTTTATTTGAA
11378370 TTTTTTTTTATTTGA
1 TTTTTTTTTATTTGA
11378385 CTTTGATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.06, T:0.81
Consensus pattern (16 bp):
TTTTTTTTTATTTGAA
Found at i:11378698 original size:156 final size:157
Alignment explanation
Indices: 11378413--11378698 Score: 529
Period size: 156 Copynumber: 1.8 Consensus size: 157
11378403 TTTTTTTTCT
*
11378413 TTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
1 TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
11378478 CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
66 CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
11378543 GATAATTAATTAATTGGTTGATCTTGA
131 GATAATTAATTAATTGGTTGATCTTGA
* *
11378570 TTTTTCTTTAAATAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTTTTCTTGCATACT
1 TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
*
11378634 CTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
66 CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
11378699 AACAACTAAC
Statistics
Matches: 125, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
156 88 0.70
157 37 0.30
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.38
Consensus pattern (157 bp):
TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
GATAATTAATTAATTGGTTGATCTTGA
Found at i:11381931 original size:1 final size:1
Alignment explanation
Indices: 11381927--11381952 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
11381917 GTAATTTTTG
11381927 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
11381953 CCACAAAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11382387 original size:17 final size:16
Alignment explanation
Indices: 11382367--11382407 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
11382357 AAAAAAAGAA
11382367 AGAAAGAAGAAAAAATG
1 AGAAA-AAGAAAAAATG
*
11382384 AGAAAATGAAAAAATG
1 AGAAAAAGAAAAAATG
11382400 A-AAAAAGA
1 AGAAAAAGA
11382408 GATCCGAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 6 0.27
16 11 0.50
17 5 0.23
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (16 bp):
AGAAAAAGAAAAAATG
Found at i:11383653 original size:42 final size:42
Alignment explanation
Indices: 11383584--11384284 Score: 1010
Period size: 42 Copynumber: 17.0 Consensus size: 42
11383574 GTCTAGGAGT
11383584 ATTTATTTTT-CAAAGTTCCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTATTTTTCCAAAG-T-CGTGGTGCCTCTGTTTAGAGGAGCA
* *
11383625 ATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
11383667 ATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
11383709 ATTTATTTTT-CAAAGTTCCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTATTTTTCCAAAG-T-CGTGGTGCCTCTGTTTAGAGGAGCA
*
11383750 ATTTACTTTT-CAAAGTTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTATTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
11383792 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
11383834 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
11383875 ATTTATTTTTCC-AAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTATTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
*
11383915 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGTA
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
11383957 ATTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTATTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
11383997 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
11384039 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
11384080 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
11384122 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* *
11384163 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
11384205 ATTTA-CTTTCCAAAGTCCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTATTTTTCCAAAGT-CGTGGTGCCTCTGTTTAGAGGAGCA
* * * * *
11384245 ATTTA-CTTTCAAAAGTCGTTGAGTCTCTGTTTAGAGGAGC
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
11384285 TTCGACAAAA
Statistics
Matches: 615, Mismatches: 23, Indels: 44
0.90 0.03 0.06
Matches are distributed among these distances:
39 3 0.00
40 107 0.17
41 212 0.34
42 285 0.46
43 8 0.01
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (42 bp):
ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
Found at i:11383745 original size:83 final size:82
Alignment explanation
Indices: 11383584--11384284 Score: 1008
Period size: 83 Copynumber: 8.5 Consensus size: 82
11383574 GTCTAGGAGT
*
11383584 ATTTATTTTT-CAAAGTTCCGT--TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTG
1 ATTTATTTTTCCAAAG-T-CGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCGT-
* *
11383646 GTACCTCTGTTGAGAGGAGCA
62 GTGCCTCTGTTTAGAGGAGCA
* * *
11383667 ATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTATTTTTCAAAGTTCCGT-T
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-T-CGTGT
11383731 GCCTCTGTTTAGAGGAGCA
64 GCCTCTGTTTAGAGGAGCA
* *
11383750 ATTTACTTTT-CAAAGTTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGG
1 ATTTATTTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCGT-G
11383814 TGCCTCTGTTTAGAGGAGCA
63 TGCCTCTGTTTAGAGGAGCA
* * * *
11383834 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTATTTTTCCAAGTTCGT-TG
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TCGTGTG
11383897 CCTCTGTTTAGAGGAGCA
65 CCTCTGTTTAGAGGAGCA
*
11383915 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGTAATTTACTTTTCAAAGTTCGT-TG
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TCGTGTG
11383979 CCTCTGTTTAGAGGAGCA
65 CCTCTGTTTAGAGGAGCA
11383997 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTG
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT-GTG
11384062 CCTCTGTTTAGAGGAGCA
65 CCTCTGTTTAGAGGAGCA
11384080 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTG
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT-GTG
*
11384145 CCTCTGTTGAGAGGAGCA
65 CCTCTGTTTAGAGGAGCA
* * *
11384163 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGTCCGT-TG
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT-CGTGTG
11384227 CCTCTGTTTAGAGGAGCA
65 CCTCTGTTTAGAGGAGCA
* * * * *
11384245 ATTTA-CTTTCAAAAGTCGTTGAGTCTCTGTTTAGAGGAGC
1 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
11384285 TTCGACAAAA
Statistics
Matches: 578, Mismatches: 26, Indels: 30
0.91 0.04 0.05
Matches are distributed among these distances:
81 62 0.11
82 162 0.28
83 274 0.47
84 77 0.13
85 3 0.01
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (82 bp):
ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGTGC
CTCTGTTTAGAGGAGCA
Found at i:11383806 original size:125 final size:122
Alignment explanation
Indices: 11383584--11384284 Score: 1041
Period size: 125 Copynumber: 5.6 Consensus size: 122
11383574 GTCTAGGAGT
* * *
11383584 ATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTA
1 ATTTACTTTTCAAAG-T-CGTTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCGTGGTG
* * *
11383649 CCTCTGTTGAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
63 CCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
11383709 ATTTATTTTTCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTGGTG
1 ATTTACTTTTCAAAG-T-CGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TCGTGGTG
11383774 CCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
63 CCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* * *
11383834 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTATTTTTCCAAGTTCGT--TG
1 ATTTACTTTTCAAAGTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TCGTGGTG
*
11383897 CCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGTA
63 CCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
11383957 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTGC
1 ATTTACTTTTCAAAG-TCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCGTGGTGC
*
11384022 CTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
64 CTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
11384080 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTG
1 ATTTACTTTT-CAAAGTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTG
* * *
11384145 CCTCTGTTGAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
63 CCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
* * * *
11384205 ATTTACTTTCCAAAGTCCGTTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCAAAAGTCGTTGAGT
1 ATTTACTTTTCAAAGT-CGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTC-AAAGTCGTGGTGC
11384269 CTCTGTTTAGAGGAGC
64 CTCTGTTTAGAGGAGC
11384285 TTCGACAAAA
Statistics
Matches: 539, Mismatches: 24, Indels: 28
0.91 0.04 0.05
Matches are distributed among these distances:
122 37 0.07
123 177 0.33
124 90 0.17
125 235 0.44
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (122 bp):
ATTTACTTTTCAAAGTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCT
CTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
Found at i:11384297 original size:1 final size:1
Alignment explanation
Indices: 11384291--11384412 Score: 109
Period size: 1 Copynumber: 122.0 Consensus size: 1
11384281 GAGCTTCGAC
* * * * * *
11384291 AAAAAAAAAAAAAAAAAAAAAAAACAAAACAAAAAAAACAAAAAAACAAAAAAACAAAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *** ** *
11384356 AAAAAAACAAAAACAAAAAAAACAAAATTTAAAAAAAAAAAAATCAAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11384413 TGTTGAGTTG
Statistics
Matches: 96, Mismatches: 25, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 96 1.00
ACGTcount: A:0.88, C:0.08, G:0.00, T:0.04
Consensus pattern (1 bp):
A
Found at i:11384324 original size:25 final size:24
Alignment explanation
Indices: 11384296--11384396 Score: 121
Period size: 25 Copynumber: 4.0 Consensus size: 24
11384286 TCGACAAAAA
11384296 AAAAAAAAAAAAAAAAAAACAAAAC
1 AAAAAAAAAAAAAAAAAAA-AAAAC
*
11384321 AAAAAAAACAAAAAAACAAAAAAAC
1 AAAAAAAA-AAAAAAAAAAAAAAAC
* *
11384346 AAAAAAACAAAAAAAAACAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAC
11384370 AAAAAAAACAAAATTTAAAAAAAAAAA
1 AAAAAAAA-AAAA---AAAAAAAAAAA
11384397 AATCAAAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
24 21 0.32
25 24 0.37
26 10 0.15
28 10 0.15
ACGTcount: A:0.88, C:0.09, G:0.00, T:0.03
Consensus pattern (24 bp):
AAAAAAAAAAAAAAAAAAAAAAAC
Found at i:11384630 original size:15 final size:13
Alignment explanation
Indices: 11384604--11384650 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 13
11384594 TTTTATGTAT
11384604 TTTATTATTATTA
1 TTTATTATTATTA
11384617 TTTATGTATATATTA
1 TTTAT-TAT-TATTA
*
11384632 TTTATT-TTTTTA
1 TTTATTATTATTA
*
11384644 TTAATTA
1 TTTATTA
11384651 GATTTATATG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 9 0.31
13 6 0.21
14 4 0.14
15 10 0.34
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:11384636 original size:22 final size:22
Alignment explanation
Indices: 11384595--11384707 Score: 65
Period size: 20 Copynumber: 5.6 Consensus size: 22
11384585 TCTTTTGTAT
*
11384595 TTTATGTATTTTATTATTATTA
1 TTTATGTATTATATTATTATTA
11384617 TTTATGTA-TATATTATTTATT-
1 TTTATGTATTATATTA-TTATTA
*
11384638 TTT-T-TATTA-ATTA-GATT-
1 TTTATGTATTATATTATTATTA
*
11384655 TATATGTA-TATAGTTA-TA-TA
1 TTTATGTATTATA-TTATTATTA
11384675 TTTAT-TATATATATTATT-TT-
1 TTTATGTAT-TATATTATTATTA
*
11384695 TTT-TGTAATATAT
1 TTTATGTATTATAT
11384708 ACTTGGGTTA
Statistics
Matches: 73, Mismatches: 6, Indels: 27
0.69 0.06 0.25
Matches are distributed among these distances:
17 5 0.07
18 3 0.04
19 18 0.25
20 19 0.26
21 15 0.21
22 13 0.18
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTATGTATTATATTATTATTA
Found at i:11384735 original size:3 final size:3
Alignment explanation
Indices: 11384722--11384752 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
11384712 GGGTTATATC
11384722 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11384753 TTTTAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:11385200 original size:31 final size:31
Alignment explanation
Indices: 11385165--11385227 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
11385155 GGGAAATTAA
*
11385165 AATTCCGGCG-ACTTTTGAATTTTCCGACGAC
1 AATTCCGGCGAAC-TTTGAAGTTTCCGACGAC
*
11385196 AATTCCGGCGAACTTTGAAGTTTCCGGCGAC
1 AATTCCGGCGAACTTTGAAGTTTCCGACGAC
11385227 A
1 A
11385228 GACCCAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (31 bp):
AATTCCGGCGAACTTTGAAGTTTCCGACGAC
Found at i:11385562 original size:5 final size:5
Alignment explanation
Indices: 11385552--11385589 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
11385542 TTTCAGCCCT
*
11385552 CCGAG CCGAG CCGAG CCGAG CCGCA- CCAAG CCGAG CCG
1 CCGAG CCGAG CCGAG CCGAG CCG-AG CCGAG CCGAG CCG
11385590 CGATCCGAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 1 0.03
5 27 0.93
6 1 0.03
ACGTcount: A:0.21, C:0.45, G:0.34, T:0.00
Consensus pattern (5 bp):
CCGAG
Found at i:11385958 original size:156 final size:157
Alignment explanation
Indices: 11385673--11385958 Score: 529
Period size: 156 Copynumber: 1.8 Consensus size: 157
11385663 ATTTTTTTTC
*
11385673 TTTTTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
1 TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
11385738 CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
66 CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
11385803 GATAATTAATTAATTGGTTGATCTTGA
131 GATAATTAATTAATTGGTTGATCTTGA
* *
11385830 TTTTTCTTTAAATAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTTTTCTTGCATACT
1 TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
*
11385894 CTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
66 CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
11385959 AACAACTAAC
Statistics
Matches: 125, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
156 88 0.70
157 37 0.30
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.38
Consensus pattern (157 bp):
TTTTTCTTTAAATAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACT
CCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTC
GATAATTAATTAATTGGTTGATCTTGA
Found at i:11388896 original size:38 final size:41
Alignment explanation
Indices: 11388824--11388905 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 41
11388814 AGAGGAAATT
11388824 GTATAAAAAATTCTTATTTGATTGATGATCTTGATAT-TAATG
1 GTATAAAAAATTCTTATTTGATTGATGA-CTTGAT-TCTAATG
*
11388866 GTATGAAAAATTCTTATTTGA-TGAT-A-TTGATTCTAATG
1 GTATAAAAAATTCTTATTTGATTGATGACTTGATTCTAATG
11388904 GT
1 GT
11388906 TATATCCTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
37 1 0.03
38 12 0.32
40 1 0.03
41 4 0.11
42 20 0.53
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (41 bp):
GTATAAAAAATTCTTATTTGATTGATGACTTGATTCTAATG
Found at i:11390703 original size:47 final size:49
Alignment explanation
Indices: 11390632--11390799 Score: 163
Period size: 47 Copynumber: 3.5 Consensus size: 49
11390622 CTAAGAAATA
* *
11390632 TTAAAAATCTCATTTTAAAAAGGCTTCTATAAACATAGGCTATGGAAC-T
1 TTAAAAATCAC-TTTGAAAAAGGCTTCTATAAACATAGGCTATGGAACTT
* *
11390681 TTAAAAA-CACTTTGAAAAAGGC-TCTTAAAAACA-AGG-TA-GGGACTT
1 TTAAAAATCACTTTGAAAAAGGCTTC-TATAAACATAGGCTATGGAACTT
* * * *
11390726 TTAAAATATCA-TTTTAAAAAGGCTCCTATAAATATTGGC-ATGGAACTT
1 TTAAAA-ATCACTTTGAAAAAGGCTTCTATAAACATAGGCTATGGAACTT
*
11390774 TTAAAAATCACTTTGGAAAAAAGCTT
1 TTAAAAATCACTTT-GAAAAAGGCTT
11390800 GTGTTGTATC
Statistics
Matches: 96, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
44 4 0.04
45 9 0.09
46 23 0.24
47 28 0.29
48 17 0.18
49 15 0.16
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (49 bp):
TTAAAAATCACTTTGAAAAAGGCTTCTATAAACATAGGCTATGGAACTT
Found at i:11394883 original size:20 final size:19
Alignment explanation
Indices: 11394855--11395021 Score: 81
Period size: 20 Copynumber: 8.5 Consensus size: 19
11394845 TAAAGTTTAG
*
11394855 GGGTATAGGGTTTAACATTA
1 GGGTTTAGGGTTTAAC-TTA
*
11394875 GGGTTTAGGGTTTCACTTCA
1 GGGTTTAGGGTTTAACTT-A
*
11394895 AGGTTTAGGG-TTAGACTTCA
1 GGGTTTAGGGTTTA-ACTT-A
* *
11394915 GGGTTTAGAGTTTGACATT-
1 GGGTTTAGGGTTTAAC-TTA
* * *
11394934 GGTGTTTTAGGATTTGACTTT
1 GG-G-TTTAGGGTTTAACTTA
*
11394955 GGGTTTAGGGTTTGACTCTA
1 GGGTTTAGGGTTTAACT-TA
* * *
11394975 --GCTTAAGGTTTGACTGTA
1 GGGTTTAGGGTTTAACT-TA
* **
11394993 GGTTTTAGGGTTTGATTTTA
1 GGGTTTAGGGTTT-AACTTA
11395013 GGGTTTAGG
1 GGGTTTAGG
11395022 ATTTGGTTTT
Statistics
Matches: 115, Mismatches: 21, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
18 15 0.13
19 19 0.17
20 63 0.55
21 18 0.16
ACGTcount: A:0.19, C:0.07, G:0.32, T:0.42
Consensus pattern (19 bp):
GGGTTTAGGGTTTAACTTA
Found at i:11394942 original size:21 final size:18
Alignment explanation
Indices: 11394915--11394970 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 18
11394905 TTAGACTTCA
11394915 GGGTTTAGAGTTTGACATT
1 GGGTTTAG-GTTTGACATT
*
11394934 GGTGTTTTAGGATTTGACTTT
1 GG-G-TTTAGG-TTTGACATT
11394955 GGGTTTAGGGTTTGAC
1 GGGTTTA-GGTTTGAC
11394971 TCTAGCTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 12 0.38
20 5 0.16
21 15 0.47
ACGTcount: A:0.16, C:0.05, G:0.34, T:0.45
Consensus pattern (18 bp):
GGGTTTAGGTTTGACATT
Found at i:11395054 original size:25 final size:25
Alignment explanation
Indices: 11395026--11395088 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
11395016 TTTAGGATTT
11395026 GGTTTTGGGTTTAGGGTTAAAGTAA
1 GGTTTTGGGTTTAGGGTTAAAGTAA
* * ** *
11395051 GGTTTTAGGTTTTGGGTTAGTGTTA
1 GGTTTTGGGTTTAGGGTTAAAGTAA
*
11395076 GGTTTAGGGTTTA
1 GGTTTTGGGTTTA
11395089 ATGAGAAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.46
Consensus pattern (25 bp):
GGTTTTGGGTTTAGGGTTAAAGTAA
Found at i:11398655 original size:24 final size:26
Alignment explanation
Indices: 11398604--11398655 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
11398594 CCTAAAATTG
*
11398604 AAACCCCAAATCTCCCATCAAACCCT
1 AAACCCCAAATCTCCCATAAAACCCT
*
11398630 AAACCCCAAAT-T-TCATAAAACCCT
1 AAACCCCAAATCTCCCATAAAACCCT
11398654 AA
1 AA
11398656 TGACCAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 12 0.50
25 1 0.04
26 11 0.46
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.17
Consensus pattern (26 bp):
AAACCCCAAATCTCCCATAAAACCCT
Found at i:11398687 original size:38 final size:37
Alignment explanation
Indices: 11398621--11398714 Score: 93
Period size: 38 Copynumber: 2.5 Consensus size: 37
11398611 AAATCTCCCA
* * **
11398621 TCAAACCCTAAACCCCAAATTTCATAAAACCCTAATGAC
1 TCAAACCTTAAACCCTAAATCCCATAAAACCCTAA--AC
* *
11398660 -CAAACCTTAAACCCTAAATCCCTTAAAACCTTAAAC
1 TCAAACCTTAAACCCTAAATCCCATAAAACCCTAAAC
11398696 TCAAA-CTCTAAACCCTAAA
1 TCAAACCT-TAAACCCTAAA
11398715 CCTCAAATCC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
36 4 0.09
37 15 0.32
38 28 0.60
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.21
Consensus pattern (37 bp):
TCAAACCTTAAACCCTAAATCCCATAAAACCCTAAAC
Found at i:11398813 original size:13 final size:12
Alignment explanation
Indices: 11398795--11398828 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
11398785 TTAATTCGCT
11398795 AACCCTAAATCAA
1 AACCCTAAAT-AA
11398808 AACCCTAAAATAA
1 AACCCT-AAATAA
11398821 AACCCTAA
1 AACCCTAA
11398829 CCCTAACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 2 0.10
13 14 0.70
14 4 0.20
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
AACCCTAAATAA
Found at i:11398853 original size:13 final size:13
Alignment explanation
Indices: 11398821--11398964 Score: 101
Period size: 13 Copynumber: 11.6 Consensus size: 13
11398811 CCTAAAATAA
11398821 AACCCT-AACCCT
1 AACCCTAAACCCT
*
11398833 AA--CTAAACTCT
1 AACCCTAAACCCT
11398844 AACCCTAAACCCT
1 AACCCTAAACCCT
*
11398857 AA----AAA-ACT
1 AACCCTAAACCCT
*
11398865 AACCTTAAACCCT
1 AACCCTAAACCCT
*
11398878 AAAACCT-AACCCT
1 -AACCCTAAACCCT
*
11398891 AACCCTAAACCCA
1 AACCCTAAACCCT
*
11398904 AAACCTAAA-CCT
1 AACCCTAAACCCT
* *
11398916 AACCCAAAACCCA
1 AACCCTAAACCCT
*
11398929 AAACCTAAACCCT
1 AACCCTAAACCCT
*
11398942 AACCATAAAACCCT
1 AACCCT-AAACCCT
11398956 AAACCCTAA
1 -AACCCTAA
11398965 CATAAAACCC
Statistics
Matches: 100, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
8 4 0.04
9 3 0.03
10 2 0.02
11 7 0.07
12 19 0.19
13 47 0.47
14 13 0.13
15 5 0.05
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.15
Consensus pattern (13 bp):
AACCCTAAACCCT
Found at i:11398854 original size:7 final size:7
Alignment explanation
Indices: 11398820--11398964 Score: 100
Period size: 6 Copynumber: 22.3 Consensus size: 7
11398810 CCCTAAAATA
11398820 AAACCCT
1 AAACCCT
11398827 -AACCCT
1 AAACCCT
11398833 -AA--CT
1 AAACCCT
*
11398837 AAACTCT
1 AAACCCT
11398844 -AACCCT
1 AAACCCT
11398850 AAACCCT
1 AAACCCT
**
11398857 AAAAAACT
1 -AAACCCT
*
11398865 -AACCTT
1 AAACCCT
11398871 AAACCCT
1 AAACCCT
*
11398878 AAAACCT
1 AAACCCT
11398885 -AACCCT
1 AAACCCT
11398891 -AACCCT
1 AAACCCT
11398897 AAACCC-
1 AAACCCT
*
11398903 AAAACCT
1 AAACCCT
11398910 AAA-CCT
1 AAACCCT
*
11398916 -AACCCA
1 AAACCCT
11398922 AAACCC-
1 AAACCCT
*
11398928 AAAACCT
1 AAACCCT
11398935 AAACCCT
1 AAACCCT
*
11398942 -AACCAT
1 AAACCCT
11398948 AAAACCCT
1 -AAACCCT
11398956 AAACCCT
1 AAACCCT
11398963 AA
1 AA
11398965 CATAAAACCC
Statistics
Matches: 110, Mismatches: 15, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
4 2 0.02
5 4 0.04
6 47 0.43
7 47 0.43
8 10 0.09
ACGTcount: A:0.48, C:0.38, G:0.00, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:11398916 original size:25 final size:25
Alignment explanation
Indices: 11398863--11398960 Score: 124
Period size: 25 Copynumber: 3.8 Consensus size: 25
11398853 CCCTAAAAAA
* *
11398863 CTAACCTTAAACCCTAAAACCTAACC
1 CTAACCCTAAACCC-AAAACCTAAAC
11398889 CTAACCCTAAACCCAAAACCTAAAC
1 CTAACCCTAAACCCAAAACCTAAAC
*
11398914 CTAACCCAAAACCCAAAACCTAAACC
1 CTAACCCTAAACCCAAAACCTAAA-C
* *
11398940 CTAACCATAAAACCCTAAACC
1 CTAACCCT-AAACCCAAAACC
11398961 CTAACATAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
25 33 0.52
26 20 0.31
27 11 0.17
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.13
Consensus pattern (25 bp):
CTAACCCTAAACCCAAAACCTAAAC
Found at i:11398984 original size:20 final size:21
Alignment explanation
Indices: 11398928--11398984 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
11398918 CCCAAAACCC
*
11398928 AAAA-CCTAAACCCTAACCAT
1 AAAACCCTAAACACTAACCAT
*
11398948 AAAACCCTAAACCCTAA-CAT
1 AAAACCCTAAACACTAACCAT
*
11398968 AAAACCCTAAGCACTAA
1 AAAACCCTAAACACTAA
11398985 TCCTAAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.51, C:0.33, G:0.02, T:0.14
Consensus pattern (21 bp):
AAAACCCTAAACACTAACCAT
Found at i:11400058 original size:19 final size:19
Alignment explanation
Indices: 11400036--11400074 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
11400026 TAGCCATGAT
*
11400036 TCTTTCTTGTGTCTGATTA
1 TCTTTCTTATGTCTGATTA
11400055 TCTTTCTTATGTCTGATTA
1 TCTTTCTTATGTCTGATTA
11400074 T
1 T
11400075 GTAGTCATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.13, C:0.15, G:0.13, T:0.59
Consensus pattern (19 bp):
TCTTTCTTATGTCTGATTA
Found at i:11401257 original size:141 final size:140
Alignment explanation
Indices: 11401055--11401363 Score: 364
Period size: 141 Copynumber: 2.2 Consensus size: 140
11401045 TTTATGGACT
* * *
11401055 AAAATTCATAAAATAATATTTAAATATGATCTGAAGCTTTTCACAAAAATCAACCTTAAAAAGGC
1 AAAATTCATGAAATAATATTTAAACATGATCTGAAGC-TTTCACAAAAATCAACCTTAAAAAAGC
* *
11401120 TAAATTATG-AAATGC-CTTTAAAATGT-ATTTTAGTAATTTCAC-TCTTTTCAAGGTACAATCA
65 TAAATTATGAAAATACTC-CTAAAA-GTCA-TTTAGTAATTTCACAT-TTTTCAA-GTACAATCA
*
11401181 AGA-TTTTAATGCATC
125 AGATTTTTAATACATC
11401196 AAAATTCATGAAATAATATTTAAACATGATCTAGAATG-TTTCACAAAAAAT-AA-CTTCAAAAA
1 AAAATTCATGAAATAATATTTAAACATGATCT-GAA-GCTTTCAC-AAAAATCAACCTT-AAAAA
* *
11401258 AGCTAAATTATGAAAATACTCCTAAAAGTCATTTAGTAATTTCACATTTTTGAAGTGCAATCAAG
62 AGCTAAATTATGAAAATACTCCTAAAAGTCATTTAGTAATTTCACATTTTTCAAGTACAATCAAG
*
11401323 ATTTTTAATATATC
127 ATTTTTAATACATC
* * *
11401337 AAAATTCATGCAACATTATTTAAACAT
1 AAAATTCATGAAATAATATTTAAACAT
11401364 AATATGAAAA
Statistics
Matches: 147, Mismatches: 12, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
140 14 0.10
141 110 0.75
142 21 0.14
143 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (140 bp):
AAAATTCATGAAATAATATTTAAACATGATCTGAAGCTTTCACAAAAATCAACCTTAAAAAAGCT
AAATTATGAAAATACTCCTAAAAGTCATTTAGTAATTTCACATTTTTCAAGTACAATCAAGATTT
TTAATACATC
Found at i:11401379 original size:141 final size:140
Alignment explanation
Indices: 11401055--11401424 Score: 342
Period size: 141 Copynumber: 2.6 Consensus size: 140
11401045 TTTATGGACT
* * * * * ** *
11401055 AAAATTCATAAAATAATATTTAAATATGATCTGAAGCTTTTCACAAAAATCAACCTTAAAAAGGC
1 AAAATTCATGAAACAATATTTAAACATAATAT-AAAATTTTCACAAAAATCAACCTTAAAAAAGC
* *
11401120 TAAATTATGAAATGCCTTTAAAATGTATTTTAGTAATTTCACTCTTTTCAAGGTACAATCAAGAT
65 TAAATTATGAAATACCTCTAAAATGTATTTTAGTAATTTCACTCTTTTCAAGGTACAATCAAGAT
*
11401185 TTTAATGCATC
130 TTTAATACATC
* * * *
11401196 AAAATTCATGAAATAATATTTAAACATGATCTAGAATGTTTCACAAAAAAT-AA-CTTCAAAAAA
1 AAAATTCATGAAACAATATTTAAACATAATATAAAAT-TTTCAC-AAAAATCAACCTT-AAAAAA
* *
11401259 GCTAAATTATGAAAATA-CTCCTAAAA-GTCA-TTTAGTAATTTCACAT-TTTTGAA-GTGCAAT
63 GCTAAATTATG-AAATACCT-CTAAAATGT-ATTTTAGTAATTTCAC-TCTTTTCAAGGTACAAT
*
11401319 CAAGATTTTTAATATATC
124 CAAGA-TTTTAATACATC
* * * * *
11401337 AAAATTCATGCAACATTATTTAAACATAATATGAAAATTTTCACGAAAAACCAACCCTAGAAAAG
1 AAAATTCATGAAACAATATTTAAACATAATAT-AAAATTTTCAC-AAAAATCAACCTTA-AAAAA
* * *
11401402 GCCAAATGATGAAATGCC-CTAAA
63 GCTAAATTATGAAATACCTCTAAA
11401425 GTGCAATTTT
Statistics
Matches: 191, Mismatches: 25, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
140 16 0.08
141 131 0.69
142 28 0.15
143 16 0.08
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (140 bp):
AAAATTCATGAAACAATATTTAAACATAATATAAAATTTTCACAAAAATCAACCTTAAAAAAGCT
AAATTATGAAATACCTCTAAAATGTATTTTAGTAATTTCACTCTTTTCAAGGTACAATCAAGATT
TTAATACATC
Found at i:11410712 original size:16 final size:17
Alignment explanation
Indices: 11410677--11410720 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
11410667 TTAATTATTC
11410677 AAAAAGGAAAAACAAGT
1 AAAAAGGAAAAACAAGT
* *
11410694 AAATAGGAAAAATAA-T
1 AAAAAGGAAAAACAAGT
11410710 AAAAAGGAAAA
1 AAAAAGGAAAA
11410721 GAAAAAGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.73, C:0.02, G:0.16, T:0.09
Consensus pattern (17 bp):
AAAAAGGAAAAACAAGT
Found at i:11414594 original size:137 final size:137
Alignment explanation
Indices: 11414348--11414621 Score: 494
Period size: 137 Copynumber: 2.0 Consensus size: 137
11414338 GAACCCCTGG
* **
11414348 AGTTCAGATGGCCGCCTTTGTCACTTACAAACTCGACTTATTACATTGCTCTGTATTTTGTGGAT
1 AGTTCAGATGGCCGCCTTTGTCACTTACAAACTCGACTTATTACATTGCTCTGCATTTTGCAGAT
*
11414413 AATAGTGATTCAATGGCCTCAAGGTTGAGGGTGCTTGACATACATATTAATGATGTAAGGTATTA
66 AATAGTGATTCAATGGCCTCAAGCTTGAGGGTGCTTGACATACATATTAATGATGTAAGGTATTA
11414478 TGGCAAT
131 TGGCAAT
* *
11414485 AGTTCAGATTGCCGCCTTTGTCACTTCCAAACTCGACTTATTACATTGCTCTGCATTTTGCAGAT
1 AGTTCAGATGGCCGCCTTTGTCACTTACAAACTCGACTTATTACATTGCTCTGCATTTTGCAGAT
11414550 AATAGTGATTCAATGGCCTCAAGCTTGAGGGTGCTTGACATACATATTAATGATGTAAGGTATTA
66 AATAGTGATTCAATGGCCTCAAGCTTGAGGGTGCTTGACATACATATTAATGATGTAAGGTATTA
11414615 TGGCAAT
131 TGGCAAT
11414622 TTGAATGTGA
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
137 131 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (137 bp):
AGTTCAGATGGCCGCCTTTGTCACTTACAAACTCGACTTATTACATTGCTCTGCATTTTGCAGAT
AATAGTGATTCAATGGCCTCAAGCTTGAGGGTGCTTGACATACATATTAATGATGTAAGGTATTA
TGGCAAT
Found at i:11421223 original size:3 final size:3
Alignment explanation
Indices: 11421215--11421252 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
11421205 ATTTGATTTT
11421215 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11421253 TTACATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11422116 original size:11 final size:11
Alignment explanation
Indices: 11422096--11422134 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
11422086 TGAAGTTGTA
*
11422096 GTTTTCTTTTT
1 GTTTTTTTTTT
11422107 GTTTTTTTTTT
1 GTTTTTTTTTT
11422118 GTTTTTTTTTT
1 GTTTTTTTTTT
11422129 -TTTTTT
1 GTTTTTT
11422135 GTCAAGGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 6 0.22
11 21 0.78
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.90
Consensus pattern (11 bp):
GTTTTTTTTTT
Found at i:11422117 original size:17 final size:16
Alignment explanation
Indices: 11422097--11422133 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
11422087 GAAGTTGTAG
11422097 TTTTCTTTTTGTTTTTT
1 TTTTCTTTTT-TTTTTT
*
11422114 TTTTGTTTTTTTTTTT
1 TTTTCTTTTTTTTTTT
11422130 TTTT
1 TTTT
11422134 TGTCAAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.00, C:0.03, G:0.05, T:0.92
Consensus pattern (16 bp):
TTTTCTTTTTTTTTTT
Found at i:11422134 original size:17 final size:17
Alignment explanation
Indices: 11422097--11422136 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
11422087 GAAGTTGTAG
*
11422097 TTTTCTTTTTGTTTTTT
1 TTTTGTTTTTGTTTTTT
*
11422114 TTTTGTTTTTTTTTTTT
1 TTTTGTTTTTGTTTTTT
11422131 TTTTGT
1 TTTTGT
11422137 CAAGGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (17 bp):
TTTTGTTTTTGTTTTTT
Found at i:11430151 original size:38 final size:38
Alignment explanation
Indices: 11430097--11430173 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
11430087 AGACATAAGA
*
11430097 TAGACACATTTAGCTACCTTGTTAAACATGTCTAGACC
1 TAGACACATTTAGCTACCTTGCTAAACATGTCTAGACC
* * *
11430135 TAGACACATTTGGCTACCTTGCTAAGCATGTCTATACC
1 TAGACACATTTAGCTACCTTGCTAAACATGTCTAGACC
11430173 T
1 T
11430174 TGCATCACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (38 bp):
TAGACACATTTAGCTACCTTGCTAAACATGTCTAGACC
Found at i:11445112 original size:27 final size:26
Alignment explanation
Indices: 11445074--11445126 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
11445064 ATAAGCTGAC
11445074 ATTATTTAATCTAATCATATTCATAAT
1 ATTATTTAATCTAATCATA-TCATAAT
* *
11445101 ATTATCTT-ATCTTATCCTATCATAAT
1 ATTAT-TTAATCTAATCATATCATAAT
11445127 CTTGTGTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 7 0.30
27 14 0.61
28 2 0.09
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTATTTAATCTAATCATATCATAAT
Found at i:11446786 original size:14 final size:14
Alignment explanation
Indices: 11446767--11446795 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11446757 TTCTTATTTA
11446767 AGTATGAATGATGG
1 AGTATGAATGATGG
11446781 AGTATGAATGATGG
1 AGTATGAATGATGG
11446795 A
1 A
11446796 TTTTCATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (14 bp):
AGTATGAATGATGG
Found at i:11451790 original size:26 final size:27
Alignment explanation
Indices: 11451744--11451807 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
11451734 TCTTATAGTG
*
11451744 AGGGTTT-GGTTTAAGGCTTAAGGCTT
1 AGGGTTTAGGTTTAAGACTTAAGGCTT
* *
11451770 AGGGTTTAGGTTT-AGATTTAAGGTTT
1 AGGGTTTAGGTTTAAGACTTAAGGCTT
* *
11451796 AAGGTTAAGGTT
1 AGGGTTTAGGTT
11451808 CGGAGTTTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 27 0.84
27 5 0.16
ACGTcount: A:0.23, C:0.03, G:0.33, T:0.41
Consensus pattern (27 bp):
AGGGTTTAGGTTTAAGACTTAAGGCTT
Found at i:11451796 original size:7 final size:7
Alignment explanation
Indices: 11451751--11451807 Score: 57
Period size: 7 Copynumber: 8.6 Consensus size: 7
11451741 GTGAGGGTTT
11451751 GGTTTAA
1 GGTTTAA
*
11451758 GGCTTAA
1 GGTTTAA
* *
11451765 GGCTTAG
1 GGTTTAA
11451772 GGTTT-A
1 GGTTTAA
11451778 GGTTT-A
1 GGTTTAA
*
11451784 GATTTAA
1 GGTTTAA
11451791 GGTTTAA
1 GGTTTAA
11451798 GG-TTAA
1 GGTTTAA
11451804 GGTT
1 GGTT
11451808 CGGAGTTTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
6 16 0.38
7 26 0.62
ACGTcount: A:0.25, C:0.04, G:0.32, T:0.40
Consensus pattern (7 bp):
GGTTTAA
Found at i:11451803 original size:13 final size:13
Alignment explanation
Indices: 11451751--11451807 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
11451741 GTGAGGGTTT
11451751 GGTTTAAGGCTTAA
1 GGTTTAAGG-TTAA
* * *
11451765 GGCTTAGGGTTTA
1 GGTTTAAGGTTAA
*
11451778 GGTTT-AGATTTAA
1 GGTTTAAG-GTTAA
11451791 GGTTTAAGGTTAA
1 GGTTTAAGGTTAA
11451804 GGTT
1 GGTT
11451808 CGGAGTTTAG
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
12 1 0.03
13 23 0.70
14 9 0.27
ACGTcount: A:0.25, C:0.04, G:0.32, T:0.40
Consensus pattern (13 bp):
GGTTTAAGGTTAA
Found at i:11451839 original size:19 final size:19
Alignment explanation
Indices: 11451817--11451865 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
11451807 TCGGAGTTTA
*
11451817 GTTTAGGGTTTCTTGAGTG
1 GTTTAGGGTTTCATGAGTG
* *
11451836 GTTTAGGTTTTCATGGGTG
1 GTTTAGGGTTTCATGAGTG
*
11451855 GTTCAGGGTTT
1 GTTTAGGGTTT
11451866 GTAAGATAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.10, C:0.06, G:0.37, T:0.47
Consensus pattern (19 bp):
GTTTAGGGTTTCATGAGTG
Found at i:11451956 original size:19 final size:19
Alignment explanation
Indices: 11451881--11451979 Score: 65
Period size: 19 Copynumber: 5.2 Consensus size: 19
11451871 ATAGTGTAGC
**
11451881 GTTTGGAGGGTGGTTTGGG
1 GTTTGGAGGGTGGTTTAAG
* * *
11451900 GTTTGTAGGGTGATTTAGG
1 GTTTGGAGGGTGGTTTAAG
** * * * *
11451919 GTTTCTAAGATAGTGTAAG
1 GTTTGGAGGGTGGTTTAAG
11451938 GTTTGGAGGGTGGTTTAAG
1 GTTTGGAGGGTGGTTTAAG
* *
11451957 GTTT-CATGGGTGGTTTAAA
1 GTTTGGA-GGGTGGTTTAAG
11451976 GTTT
1 GTTT
11451980 CATAAGTGGT
Statistics
Matches: 61, Mismatches: 18, Indels: 2
0.75 0.22 0.02
Matches are distributed among these distances:
18 1 0.02
19 60 0.98
ACGTcount: A:0.17, C:0.02, G:0.40, T:0.40
Consensus pattern (19 bp):
GTTTGGAGGGTGGTTTAAG
Found at i:11451980 original size:19 final size:19
Alignment explanation
Indices: 11451945--11451992 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
11451935 AAGGTTTGGA
*
11451945 GGGTGGTTTAAGGTTTCAT
1 GGGTGGTTTAAAGTTTCAT
11451964 GGGTGGTTTAAAGTTTCAT
1 GGGTGGTTTAAAGTTTCAT
**
11451983 AAGTGGTTTA
1 GGGTGGTTTA
11451993 GCGTTTGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.21, C:0.04, G:0.33, T:0.42
Consensus pattern (19 bp):
GGGTGGTTTAAAGTTTCAT
Found at i:11451980 original size:57 final size:56
Alignment explanation
Indices: 11451833--11452001 Score: 182
Period size: 57 Copynumber: 3.0 Consensus size: 56
11451823 GGTTTCTTGA
* *
11451833 GTGGTTTAGGTTTTCATGGGTGGTTCAGGGTTTGTAAGATAGTGTAGCGTTTGGAGG
1 GTGGTTTAGG-TTTCATGGGTGGTTTAGGGTTTCTAAGATAGTGTAGCGTTTGGAGG
* * *
11451890 GTGGTTTGGGGTTT-GTAGGGTGATTTAGGGTTTCTAAGATAGTGTAAG-GTTTGGAGG
1 GTGGTTT-AGGTTTCAT-GGGTGGTTTAGGGTTTCTAAGATAGTGT-AGCGTTTGGAGG
** * *
11451947 GTGGTTTAAGGTTTCATGGGTGGTTTAAAGTTTCATAAG-TGGTTTAGCGTTTGGA
1 GTGGTTT-AGGTTTCATGGGTGGTTTAGGGTTTC-TAAGATAGTGTAGCGTTTGGA
11452002 ATTTAGGGTT
Statistics
Matches: 93, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
56 3 0.03
57 81 0.87
58 9 0.10
ACGTcount: A:0.18, C:0.04, G:0.38, T:0.40
Consensus pattern (56 bp):
GTGGTTTAGGTTTCATGGGTGGTTTAGGGTTTCTAAGATAGTGTAGCGTTTGGAGG
Found at i:11451998 original size:19 final size:18
Alignment explanation
Indices: 11451947--11451998 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
11451937 GGTTTGGAGG
**
11451947 GTGGTTTAAGGTTTCATGG
1 GTGGTTT-AGGTTTCATAA
*
11451966 GTGGTTTAAAGTTTCATAA
1 GTGGTTT-AGGTTTCATAA
11451985 GTGGTTTAGCGTTT
1 GTGGTTTAG-GTTT
11451999 GGAATTTAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 1 0.04
19 27 0.96
ACGTcount: A:0.19, C:0.06, G:0.31, T:0.44
Consensus pattern (18 bp):
GTGGTTTAGGTTTCATAA
Found at i:11454528 original size:57 final size:57
Alignment explanation
Indices: 11454408--11454577 Score: 162
Period size: 57 Copynumber: 3.0 Consensus size: 57
11454398 TTCAAACTTG
* * * * * *
11454408 GATATTCATATATCACCATCGAGTAAATGTAAATGGCTTTAGATTTCATCATCAAAT
1 GATACTCAGATATCACCATCGAGTAAATGCAAATGACTTTAGATATCACCATCAAAT
* * *
11454465 -AGTACTCAGATATCACCATCGAGTGAATGCAAATGACTTTGGATATCACCATCGAAT
1 GA-TACTCAGATATCACCATCGAGTAAATGCAAATGACTTTAGATATCACCATCAAAT
* * * * * * ** *
11454522 GATACTCAGATATTACTACCAAGCAAATGCAAATAACTTCGGATATCATCATCAAA
1 GATACTCAGATATCACCATCGAGTAAATGCAAATGACTTTAGATATCACCATCAAA
11454578 GAGAATGCAA
Statistics
Matches: 92, Mismatches: 19, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
56 1 0.01
57 90 0.98
58 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (57 bp):
GATACTCAGATATCACCATCGAGTAAATGCAAATGACTTTAGATATCACCATCAAAT
Found at i:11454585 original size:34 final size:34
Alignment explanation
Indices: 11454547--11454617 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
11454537 CTACCAAGCA
** * *
11454547 AATGCAAATAACTTCGGATATCATCATCAAAGAG
1 AATGCAAATAACTTCAAATATCACCACCAAAGAG
11454581 AATGCAAATAACTTCAAATATCACCACCAAAGAG
1 AATGCAAATAACTTCAAATATCACCACCAAAGAG
11454615 AAT
1 AAT
11454618 TTGGATATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.21
Consensus pattern (34 bp):
AATGCAAATAACTTCAAATATCACCACCAAAGAG
Found at i:11454849 original size:83 final size:81
Alignment explanation
Indices: 11454659--11454864 Score: 195
Period size: 83 Copynumber: 2.5 Consensus size: 81
11454649 AATTCCCAAA
* * * *
11454659 AAAATTTTAATGAAATTAAAAAATG-ATACTCAGATATCACCATCGAATGATTTTAAAAAAACTC
1 AAAATTTTAATGAAATTCAAACATGAATACTCAGATATCACCACCGAAAGATTTTAAAAAAACTC
11454723 AAATATCACCACCTAG
66 AAATATCACCACCTAG
* ** * *
11454739 AAATTTTTAA-GTTATTCAAGACATGAATACTCGGATATCACCACCAAGAAAG-TTTTAATGAAA
1 AAAATTTTAATGAAATTCAA-ACATGAATACTCAGATATCACCACC--GAAAGATTTTAA-AAAA
** * *
11454802 GGTCAGATTTCACCA-CTAAG
62 ACTCAAATATCACCACCT-AG
* * *
11454822 AAAATTTTAATGAAATTCAAACTTGAATGCTCAAATATCACCA
1 AAAATTTTAATGAAATTCAAACATGAATACTCAGATATCACCA
11454865 ATGAGCGTTG
Statistics
Matches: 99, Mismatches: 20, Indels: 11
0.76 0.15 0.08
Matches are distributed among these distances:
79 6 0.06
80 13 0.13
81 17 0.17
82 8 0.08
83 48 0.48
84 7 0.07
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.29
Consensus pattern (81 bp):
AAAATTTTAATGAAATTCAAACATGAATACTCAGATATCACCACCGAAAGATTTTAAAAAAACTC
AAATATCACCACCTAG
Found at i:11455287 original size:21 final size:22
Alignment explanation
Indices: 11455261--11455301 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
11455251 GATGCATTTT
*
11455261 TTCTTTTCTAT-TAAAACTTCC
1 TTCTTTACTATCTAAAACTTCC
*
11455282 TTCTTTACTATCTACAACTT
1 TTCTTTACTATCTAAAACTT
11455302 AAAATGTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (22 bp):
TTCTTTACTATCTAAAACTTCC
Found at i:11457225 original size:19 final size:19
Alignment explanation
Indices: 11457201--11457238 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11457191 TTTTTTTTTC
11457201 CTTTTTTCTTTTAGTTCTT
1 CTTTTTTCTTTTAGTTCTT
* *
11457220 CTTTTTTTTTTTATTTCTT
1 CTTTTTTCTTTTAGTTCTT
11457239 TCATTTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.05, C:0.13, G:0.03, T:0.79
Consensus pattern (19 bp):
CTTTTTTCTTTTAGTTCTT
Found at i:11457246 original size:28 final size:29
Alignment explanation
Indices: 11457189--11457247 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
11457179 ATTTCTTCCC
* *
11457189 TCTTTTTTTTTCCTTTTTTCTTTTAGTTCT
1 TCTTTTTTTTT-CTTATTTCTTTCAGTTCT
*
11457219 TCTTTTTTTTT-TTATTTCTTTCATTTCT
1 TCTTTTTTTTTCTTATTTCTTTCAGTTCT
11457247 T
1 T
11457248 TCCCTTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 15 0.58
30 11 0.42
ACGTcount: A:0.05, C:0.15, G:0.02, T:0.78
Consensus pattern (29 bp):
TCTTTTTTTTTCTTATTTCTTTCAGTTCT
Found at i:11457258 original size:36 final size:33
Alignment explanation
Indices: 11457218--11457301 Score: 80
Period size: 38 Copynumber: 2.4 Consensus size: 33
11457208 CTTTTAGTTC
11457218 TTCTTTTTTTTTTTATTTCTT-TCATTTCTTTCCCTT
1 TTCTTTTTTTTTTT-TTT-TTCTCATTT-TTT-CCTT
* *
11457254 TTCTTACTTTTTTATTTTTTTTCTTATTTTTTTCTT
1 TTCTT--TTTTTT-TTTTTTTTCTCATTTTTTCCTT
11457290 TTCTTTTTTTTT
1 TTCTTTTTTTTT
11457302 AAAGTGGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
33 1 0.02
34 6 0.14
36 13 0.31
37 5 0.12
38 14 0.33
39 3 0.07
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (33 bp):
TTCTTTTTTTTTTTTTTTTCTCATTTTTTCCTT
Found at i:11457275 original size:20 final size:21
Alignment explanation
Indices: 11457251--11457296 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
11457241 ATTTCTTTCC
11457251 CTTTTCTTACTTTTTTATTTT
1 CTTTTCTTACTTTTTTATTTT
* *
11457272 -TTTTCTTATTTTTTTCTTTT
1 CTTTTCTTACTTTTTTATTTT
11457292 CTTTT
1 CTTTT
11457297 TTTTTAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (21 bp):
CTTTTCTTACTTTTTTATTTT
Found at i:11457778 original size:23 final size:24
Alignment explanation
Indices: 11457743--11457788 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
11457733 TAATCAAAAA
*
11457743 ATTTTTCTTTTCCTCTTTCATTTC
1 ATTTTTCTCTTCCTCTTTCATTTC
*
11457767 ATTTTT-TCTTCCTTTTTCATTT
1 ATTTTTCTCTTCCTCTTTCATTT
11457789 TTTTCTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.09, C:0.22, G:0.00, T:0.70
Consensus pattern (24 bp):
ATTTTTCTCTTCCTCTTTCATTTC
Found at i:11457811 original size:8 final size:8
Alignment explanation
Indices: 11457744--11457814 Score: 52
Period size: 8 Copynumber: 8.4 Consensus size: 8
11457734 AATCAAAAAA
11457744 TTTTTCTT
1 TTTTTCTT
**
11457752 TTCCTCTT
1 TTTTTCTT
* *
11457760 TCATTTCAT
1 T-TTTTCTT
11457769 TTTTTCTT
1 TTTTTCTT
11457777 CCTTTTTCATT
1 --TTTTTC-TT
11457788 TTTTTCTT
1 TTTTTCTT
* *
11457796 CTTATCTT
1 TTTTTCTT
11457804 TTTTTCTT
1 TTTTTCTT
11457812 TTT
1 TTT
11457815 CCTTTACACA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
8 29 0.62
9 10 0.21
10 6 0.13
11 2 0.04
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTCTT
Found at i:11461074 original size:36 final size:35
Alignment explanation
Indices: 11461031--11461159 Score: 123
Period size: 36 Copynumber: 3.6 Consensus size: 35
11461021 ACTTCCATTA
*
11461031 AAATGTGCATGAGATGGAGTACATGTATATCTATT
1 AAATGTGCATGAGATGGAATACATGTATATCTATT
* *
11461066 AAGATGTGCATGAAATGGAATACATGTACCATCTATT
1 AA-ATGTGCATGAGATGGAATACATGTA-TATCTATT
* * * * * *
11461103 AAAAGTACTTGAGATGGAATTCATGTATCACCTGTT
1 AAATGTGCATGAGATGGAATACATGTAT-ATCTATT
* *
11461139 AATATTTGCATGAGAAGGAAT
1 AA-ATGTGCATGAGATGGAAT
11461160 GTATATACCA
Statistics
Matches: 74, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
35 2 0.03
36 50 0.68
37 22 0.30
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (35 bp):
AAATGTGCATGAGATGGAATACATGTATATCTATT
Found at i:11461169 original size:73 final size:72
Alignment explanation
Indices: 11461040--11461179 Score: 158
Period size: 73 Copynumber: 1.9 Consensus size: 72
11461030 AAAATGTGCA
* * *
11461040 TGAGATGGAGTACATGTATATCTATTAAGATGTGCATGAAATGGAATACATGTACCATC-TATTA
1 TGAGATGGAATACATGTATACCTATTAAGATGTGCATGAAATGGAATACATATACCA-CATATTA
11461104 AAAGTACT
65 AAAGTACT
* * * * **
11461112 TGAGATGGAATTCATGTATCACCTGTTAATATTTGCATGAGAA-GGAATGTATATACCACATATT
1 TGAGATGGAATACATGTAT-ACCTATTAAGATGTGCATGA-AATGGAATACATATACCACATATT
11461176 AAAA
64 AAAA
11461180 TATGCATGAG
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
72 18 0.32
73 36 0.64
74 2 0.04
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (72 bp):
TGAGATGGAATACATGTATACCTATTAAGATGTGCATGAAATGGAATACATATACCACATATTAA
AAGTACT
Found at i:11461468 original size:14 final size:14
Alignment explanation
Indices: 11461445--11461481 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
11461435 ATTCAAAGGT
*
11461445 TTTTTTTTTTTTCA
1 TTTTTGTTTTTTCA
11461459 TTTTTGTTTTTTCA
1 TTTTTGTTTTTTCA
11461473 -TTTTGTTTT
1 TTTTTGTTTT
11461482 CTTATTTAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.05, C:0.05, G:0.05, T:0.84
Consensus pattern (14 bp):
TTTTTGTTTTTTCA
Found at i:11462320 original size:21 final size:19
Alignment explanation
Indices: 11462291--11462330 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
11462281 AATTAAAGTC
11462291 AAAACATTTTTCTCATTTTTT
1 AAAACATTTTT-T-ATTTTTT
*
11462312 AAAATATTTTTTATTTTTT
1 AAAACATTTTTTATTTTTT
11462331 TCAAAATTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (19 bp):
AAAACATTTTTTATTTTTT
Found at i:11463570 original size:19 final size:19
Alignment explanation
Indices: 11463546--11463614 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 19
11463536 TAGGGATTAG
11463546 GGTTTAGGGTTTCATAAGT
1 GGTTTAGGGTTTCATAAGT
* *
11463565 GGTTTAGGGTTTGA-AGGGT
1 GGTTTAGGGTTTCATA-AGT
* * *
11463584 AGTTTAGTGTTTCATGAGT
1 GGTTTAGGGTTTCATAAGT
11463603 GGTTTAGGGTTT
1 GGTTTAGGGTTT
11463615 GGAATTTAAG
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 1 0.03
19 38 0.97
ACGTcount: A:0.17, C:0.03, G:0.36, T:0.43
Consensus pattern (19 bp):
GGTTTAGGGTTTCATAAGT
Found at i:11463576 original size:7 final size:7
Alignment explanation
Indices: 11463473--11463557 Score: 52
Period size: 7 Copynumber: 12.7 Consensus size: 7
11463463 TCTAGCTTAA
*
11463473 GGTTTAA
1 GGTTTAG
11463480 GGTTT--
1 GGTTTAG
*
11463485 GGTTTAT
1 GGTTTAG
* *
11463492 GGTATAA
1 GGTTTAG
11463499 GGTTTAG
1 GGTTTAG
*
11463506 AGTTTA-
1 GGTTTAG
**
11463512 GGTGCAG
1 GGTTTAG
*
11463519 GGTTTAA
1 GGTTTAG
11463526 GGTTTA-
1 GGTTTAG
*
11463532 GGATTAG
1 GGTTTAG
*
11463539 GGATTAG
1 GGTTTAG
11463546 GGTTTAG
1 GGTTTAG
11463553 GGTTT
1 GGTTT
11463558 CATAAGTGGT
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
5 5 0.08
6 8 0.13
7 48 0.79
ACGTcount: A:0.21, C:0.01, G:0.36, T:0.41
Consensus pattern (7 bp):
GGTTTAG
Found at i:11472513 original size:97 final size:97
Alignment explanation
Indices: 11472360--11472560 Score: 357
Period size: 97 Copynumber: 2.1 Consensus size: 97
11472350 GAACATATCA
11472360 ATCCCCTCAAGCAAGGGATCGATCAGGTAAGGCAAAATAGGCACAAAATCAAGCTTTCTCAAACA
1 ATCCCCTCAAGCAAGGGATCGATCAGGTAAGGCAAAATAGGCACAAAATCAAGCTTTCTCAAACA
* *
11472425 TGAACCAATCGATCCCCTAAGGGAGGAGATTG
66 TGAACCAATCGATCCCCTAAGGGAAGAGATCG
* * *
11472457 ATCCCTTCAAGCAAGGGATCGATCAGGTAAGGCAAAATAGGCATAAAATCAGGCTTTCTCAAACA
1 ATCCCCTCAAGCAAGGGATCGATCAGGTAAGGCAAAATAGGCACAAAATCAAGCTTTCTCAAACA
11472522 TGAACCAATCGATCCCCTAAGGGAAGAGATCG
66 TGAACCAATCGATCCCCTAAGGGAAGAGATCG
11472554 ATCCCCT
1 ATCCCCT
11472561 AAAGGCCTGA
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (97 bp):
ATCCCCTCAAGCAAGGGATCGATCAGGTAAGGCAAAATAGGCACAAAATCAAGCTTTCTCAAACA
TGAACCAATCGATCCCCTAAGGGAAGAGATCG
Found at i:11474441 original size:21 final size:22
Alignment explanation
Indices: 11474383--11474445 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
11474373 CTATTTTCAG
11474383 AATGGATCAATCCATTTTCATAA
1 AATGGATCAATCCATTTT-ATAA
**
11474406 AAT-G-TTGATCCATTTT-TAA
1 AATGGATCAATCCATTTTATAA
*
11474425 AATGGATCAATCAATTTTATA
1 AATGGATCAATCCATTTTATA
11474446 GGGAATTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
19 6 0.19
20 1 0.03
21 19 0.59
22 3 0.09
23 3 0.09
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.40
Consensus pattern (22 bp):
AATGGATCAATCCATTTTATAA
Found at i:11477762 original size:16 final size:13
Alignment explanation
Indices: 11477729--11477754 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11477719 ATAAAATATA
11477729 TAAATGCAATAAT
1 TAAATGCAATAAT
11477742 TAAATGCAATAAT
1 TAAATGCAATAAT
11477755 AGCTAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
TAAATGCAATAAT
Found at i:11479804 original size:135 final size:135
Alignment explanation
Indices: 11479562--11479833 Score: 438
Period size: 135 Copynumber: 2.0 Consensus size: 135
11479552 AAGATTGCTC
* * *
11479562 AAGATTGATCAATAATCACCAAAATTTACCAAGATTCAATCTTTTCTTCAAGAATTCTTTCACAA
1 AAGATTGATAAAGAATCACCAAAATTTACCAAGATTCAATCTTTTCTTCAAGAATTCTTACACAA
* * *
11479627 AGGCAAATTAAGCATATTAGGAATAAAAAGAACCTTATTTTACCAAGAACTAAGCAAAATTAACA
66 AGGCAAATTAAGCACATTAAGAATAAAAAGAACCTTAATTTACCAAGAACTAAGCAAAATTAACA
11479692 CATTT
131 CATTT
**
11479697 AAGATTGATAAAGAATCACCAAAATTTAGTAAGATTCAATCTTTTCTTCAAGAATTAC-TACACA
1 AAGATTGATAAAGAATCACCAAAATTTACCAAGATTCAATCTTTTCTTCAAGAATT-CTTACACA
* *
11479761 AAGGTAAATTAAGCACATTAAGAGTAAAAAGAACCTTAATTTACCAAGAACTAAGCAAAATTAAC
65 AAGGCAAATTAAGCACATTAAGAATAAAAAGAACCTTAATTTACCAAGAACTAAGCAAAATTAAC
11479826 ACATTT
130 ACATTT
11479832 AA
1 AA
11479834 ATATTGAAAA
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
135 125 0.99
136 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (135 bp):
AAGATTGATAAAGAATCACCAAAATTTACCAAGATTCAATCTTTTCTTCAAGAATTCTTACACAA
AGGCAAATTAAGCACATTAAGAATAAAAAGAACCTTAATTTACCAAGAACTAAGCAAAATTAACA
CATTT
Found at i:11490506 original size:176 final size:161
Alignment explanation
Indices: 11490296--11490735 Score: 625
Period size: 176 Copynumber: 2.7 Consensus size: 161
11490286 CAATCTATGA
* * *
11490296 TATATGATATTTTTACATGCTTAGTTCATTTTCAGCATGTAATATGCCCGTGGAAGTTTAAAGTT
1 TATATGATATTTTTTCATGCTTAGTTCTTTTTCAGCATGTAATATGCCTGTGGAAGTTTAAAGTT
11490361 TCTTCCTATCCATGTATACTGGCTTTACCTCTTTTGCATGAGGTTTTGTTGGTTCATAAAGCTTC
66 TCTTCCTATCCATGTATACTGGCTTTACCTCTTTTGCATGAGGTTTTGTTGGTTCATAAAGCTTC
11490426 AAAACTTCATCCTCCATTTATGTTAAATGAATCTATGTTATCT-GG
131 AAAACTTCATCCT-C--------------AATCTATGTTATCTAGG
*
11490471 TATATGATATTTTTTGCATGCTTAGTTCTTTTTCAGCATGTAATATGCCTGTAGAAGTTTAAAGT
1 TATATGATATTTTTT-CATGCTTAGTTCTTTTTCAGCATGTAATATGCCTGTGGAAGTTTAAAGT
11490536 TTCTTCCTATCCATGTATACTGGCTTTACCTCTTTTGCATGAGGTTTTGTTGGTTCATAAAGCTT
65 TTCTTCCTATCCATGTATACTGGCTTTACCTCTTTTGCATGAGGTTTTGTTGGTTCATAAAGCTT
11490601 CAAAACTTCATCCTCAATCTATGTTATCTAGG
130 CAAAACTTCATCCTCAATCTATGTTATCTAGG
* *
11490633 -ATATGAT-TTTTTTCATGCTTAGTTCTTTTTTAGCATGTAATATGCCTGTGGAAGTTTAATGTT
1 TATATGATATTTTTTCATGCTTAGTTCTTTTTCAGCATGTAATATGCCTGTGGAAGTTTAAAGTT
* * * *
11490696 TCTTCCTTTCCATGTGTATTGGCTTAACCTCTTTTGCATG
66 TCTTCCTATCCATGTATACTGGCTTTACCTCTTTTGCATG
11490736 CAAATTTGAT
Statistics
Matches: 252, Mismatches: 11, Indels: 20
0.89 0.04 0.07
Matches are distributed among these distances:
159 83 0.33
160 6 0.02
161 21 0.08
162 2 0.01
175 15 0.06
176 125 0.50
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.45
Consensus pattern (161 bp):
TATATGATATTTTTTCATGCTTAGTTCTTTTTCAGCATGTAATATGCCTGTGGAAGTTTAAAGTT
TCTTCCTATCCATGTATACTGGCTTTACCTCTTTTGCATGAGGTTTTGTTGGTTCATAAAGCTTC
AAAACTTCATCCTCAATCTATGTTATCTAGG
Found at i:11492777 original size:22 final size:20
Alignment explanation
Indices: 11492752--11492819 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 20
11492742 AAAAATAAAC
11492752 AAATAATAAAAATTAGTAAAAT
1 AAATAATAAAAA-TA-TAAAAT
*
11492774 AAAT-A-AAAGATATTAAAA-
1 AAATAATAAAAATA-TAAAAT
11492792 AAATAAACTAAAAATATAAAAT
1 AAAT-AA-TAAAAATATAAAAT
11492814 AAATAA
1 AAATAA
11492820 AATCAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
18 4 0.11
19 7 0.18
20 5 0.13
21 8 0.21
22 14 0.37
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (20 bp):
AAATAATAAAAATATAAAAT
Found at i:11492780 original size:48 final size:49
Alignment explanation
Indices: 11492728--11492831 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 49
11492718 ATAGAATTTT
* * *
11492728 ATAAAATAT-TTAGTAAAAATAAAC-AAATAATA-AAAATTAGTAAAATAA
1 ATAAAATATATTA-AAAAAATAAACTAAA-AATATAAAATAAATAAAATAA
* *
11492776 ATAAAAGATATTAAAAAAATAAACTAAAAATATAAAATAAATAAAATCA
1 ATAAAATATATTAAAAAAATAAACTAAAAATATAAAATAAATAAAATAA
11492825 A-AAAATA
1 ATAAAATA
11492832 AAATGAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
48 27 0.57
49 20 0.43
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (49 bp):
ATAAAATATATTAAAAAAATAAACTAAAAATATAAAATAAATAAAATAA
Found at i:11492803 original size:13 final size:13
Alignment explanation
Indices: 11492768--11492842 Score: 53
Period size: 13 Copynumber: 5.5 Consensus size: 13
11492758 TAAAAATTAG
11492768 TAAAATAAATAAAA
1 TAAAATAAA-AAAA
* * *
11492782 GATATTAAAAAAA
1 TAAAATAAAAAAA
* *
11492795 TAAACTAAAAATA
1 TAAAATAAAAAAA
11492808 TAAAATAAATAAAA
1 TAAAATAAA-AAAA
*
11492822 TCAAAA-AATAAAA
1 T-AAAATAAAAAAA
11492835 TGAAAATA
1 T-AAAATA
11492843 GGAAAGAAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
13 30 0.64
14 13 0.28
15 4 0.09
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (13 bp):
TAAAATAAAAAAA
Found at i:11492820 original size:22 final size:21
Alignment explanation
Indices: 11492770--11492835 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 21
11492760 AAAATTAGTA
11492770 AAATAAATAAAAGATATTAAAA-
1 AAATAAATAAAA-ATA-TAAAAT
11492792 AAATAAACTAAAAATATAAAAT
1 AAATAAA-TAAAAATATAAAAT
11492814 AAATAAAATCAAAAA-ATAAAAT
1 AAAT-AAAT-AAAAATATAAAAT
11492836 GAAAATAGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.12
22 22 0.55
23 13 0.32
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.21
Consensus pattern (21 bp):
AAATAAATAAAAATATAAAAT
Found at i:11493690 original size:11 final size:11
Alignment explanation
Indices: 11493669--11493712 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
11493659 ACCGATTAGG
11493669 AAAGAAAATAAA
1 AAAG-AAATAAA
11493681 AAAGAAATAAA
1 AAAGAAATAAA
11493692 ATAA-AAATAAA
1 A-AAGAAATAAA
*
11493703 ATAGAAATAA
1 AAAGAAATAA
11493713 TAATAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 1 0.03
11 22 0.76
12 6 0.21
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.14
Consensus pattern (11 bp):
AAAGAAATAAA
Found at i:11493692 original size:16 final size:17
Alignment explanation
Indices: 11493668--11493735 Score: 61
Period size: 16 Copynumber: 4.0 Consensus size: 17
11493658 CACCGATTAG
*
11493668 GAAAGAAAATAAAAA-A
1 GAAATAAAATAAAAATA
11493684 GAAATAAAATAAAAATA
1 GAAATAAAATAAAAATA
*
11493701 -AAATAGAAATAATAATA
1 GAAATA-AAATAAAAATA
*
11493718 -ATAATAATAATAATAATA
1 GA-AATAA-AATAAAAATA
11493736 TAATATAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
16 19 0.41
17 13 0.28
18 14 0.30
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
GAAATAAAATAAAAATA
Found at i:11493698 original size:6 final size:6
Alignment explanation
Indices: 11493673--11493735 Score: 51
Period size: 6 Copynumber: 11.0 Consensus size: 6
11493663 ATTAGGAAAG
* * *
11493673 AAAATA AAAA-A GAAAT- AAAATA AAAAT- AAAATA GAAATA ATAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* * *
11493718 ATAATA ATAATA ATAATA
1 AAAATA AAAATA AAAATA
11493736 TAATATAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
5 13 0.27
6 36 0.73
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (6 bp):
AAAATA
Found at i:11493700 original size:22 final size:23
Alignment explanation
Indices: 11493673--11493724 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
11493663 ATTAGGAAAG
11493673 AAAATAAAAAAGAAATAA-AATA
1 AAAATAAAAAAGAAATAATAATA
*
11493695 AAAATAAAATAGAAATAATAATA
1 AAAATAAAAAAGAAATAATAATA
*
11493718 ATAATAA
1 AAAATAA
11493725 TAATAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (23 bp):
AAAATAAAAAAGAAATAATAATA
Found at i:11493716 original size:3 final size:3
Alignment explanation
Indices: 11493686--11493850 Score: 152
Period size: 3 Copynumber: 56.7 Consensus size: 3
11493676 ATAAAAAAGA
*
11493686 AAT AA- AAT AAA AAT AA- AAT AGA- AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
* * * *
11493729 AAT AAT -AT AAT -AT AAT ATGT TAT ACT -AT AGT -AT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
* *
11493770 AAT AAT AAT -AT GAT -AT AAC ATAT AAAT CAAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT -AAT -AAT AAT AAT AAT AAT AAT
11493816 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11493851 ACAAAAATAA
Statistics
Matches: 135, Mismatches: 13, Indels: 28
0.77 0.07 0.16
Matches are distributed among these distances:
2 17 0.13
3 109 0.81
4 8 0.06
5 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11502340 original size:2 final size:2
Alignment explanation
Indices: 11502333--11502360 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11502323 ATATACACAA
11502333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11502361 CTGTGTGCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11502492 original size:43 final size:40
Alignment explanation
Indices: 11502398--11502493 Score: 95
Period size: 43 Copynumber: 2.3 Consensus size: 40
11502388 TATATATTTT
* *
11502398 ATTAATTTTAT-AATTTTTAAAATTTTTATAAAATAAAAA
1 ATTAATTATATAAATTTTTAAAATTTTTAAAAAATAAAAA
** *
11502437 ATATTTTATATATAAATTTTTTAAATGTTTTAAAATAATATAAAA
1 AT-TAAT-TATATAAATTTTTAAAAT-TTTTAAAA-AATA-AAAA
11502482 ATTAATTATATA
1 ATTAATTATATA
11502494 TATTATATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
39 2 0.05
40 2 0.05
41 4 0.09
42 11 0.25
43 13 0.30
44 6 0.14
45 6 0.14
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (40 bp):
ATTAATTATATAAATTTTTAAAATTTTTAAAAAATAAAAA
Found at i:11504351 original size:2 final size:2
Alignment explanation
Indices: 11504346--11504380 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
11504336 ATAACATAAC
* *
11504346 AT AT AT AT AT TT AT GT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11504381 ATTTCCATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:11505629 original size:50 final size:50
Alignment explanation
Indices: 11505554--11505658 Score: 158
Period size: 50 Copynumber: 2.1 Consensus size: 50
11505544 TAGACTTGGA
* * * *
11505554 CATGCATGTTTATGCCTTTTCATTATATTTTGGAATTGGTTGCATT-ATGC
1 CATGCATGTTTATGCCTTTCCATTATATTTAGGAATTAGTTAC-TTCATGC
11505604 CATGCATGTTTATGCCTTTCCATTATATTTAGGAATTAGTTACTTCATGC
1 CATGCATGTTTATGCCTTTCCATTATATTTAGGAATTAGTTACTTCATGC
11505654 CATGC
1 CATGC
11505659 TACCAGATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
49 2 0.04
50 48 0.96
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (50 bp):
CATGCATGTTTATGCCTTTCCATTATATTTAGGAATTAGTTACTTCATGC
Found at i:11510322 original size:18 final size:18
Alignment explanation
Indices: 11510280--11510343 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 18
11510270 AAAATAATTT
11510280 TATTATATTATATTAAATAA
1 TATTAT-TTAT-TTAAATAA
11510300 GTATTATTTATTTAAATAA
1 -TATTATTTATTTAAATAA
11510319 TATT-TTTATTTTAAATATA
1 TATTATTTA-TTTAAATA-A
11510338 TATTAT
1 TATTAT
11510344 ATTAATATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.10
18 12 0.30
19 13 0.32
20 5 0.12
21 6 0.15
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TATTATTTATTTAAATAA
Found at i:11510346 original size:18 final size:18
Alignment explanation
Indices: 11510283--11510369 Score: 58
Period size: 18 Copynumber: 4.8 Consensus size: 18
11510273 ATAATTTTAT
11510283 TATATTATA--TTAAATA
1 TATATTATATTTTAAATA
*
11510299 -AGTATTATTTATTTAAATA
1 TA-TATTATAT-TTTAAATA
*
11510318 -ATATTTTTATTTTAAATA
1 TATA-TTATATTTTAAATA
*
11510336 TATATTATATTAATATTAATA
1 TATATTATATT--T-TAAATA
11510357 TA-ATTATATTTTA
1 TATATTATATTTTA
11510370 TTAATTATGA
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
15 1 0.02
16 6 0.11
17 1 0.02
18 17 0.30
19 15 0.27
20 9 0.16
21 7 0.12
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (18 bp):
TATATTATATTTTAAATA
Found at i:11510371 original size:19 final size:19
Alignment explanation
Indices: 11510281--11510374 Score: 63
Period size: 19 Copynumber: 4.8 Consensus size: 19
11510271 AAATAATTTT
*
11510281 ATTATATTATATTAA-ATA
1 ATTATATTTTATTAATATA
*
11510299 AGTAT-TATTTATTTAA-ATA
1 ATTATAT-TTTA-TTAATATA
11510318 A-TAT-TTTTATTTTAAATATA
1 ATTATATTTTA--TT-AATATA
*
11510338 TATTATATTAATATTAATATA
1 -ATTATATT-TTATTAATATA
11510359 ATTATATTTTATTAAT
1 ATTATATTTTATTAAT
11510375 TATGAAAATT
Statistics
Matches: 63, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
17 5 0.08
18 14 0.22
19 17 0.27
20 11 0.17
21 7 0.11
22 5 0.08
23 2 0.03
24 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (19 bp):
ATTATATTTTATTAATATA
Found at i:11510387 original size:27 final size:25
Alignment explanation
Indices: 11510336--11510390 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
11510326 ATTTTAAATA
* *
11510336 TATATTATATTAATATTAATATAAT
1 TATATTATATTAATATGAAAATAAT
*
11510361 TATATTTTATTAATTATGAAAATTAAT
1 TATATTATATTAA-TATGAAAA-TAAT
11510388 TAT
1 TAT
11510391 TACTAATTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 12 0.48
26 6 0.24
27 7 0.28
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TATATTATATTAATATGAAAATAAT
Found at i:11515020 original size:19 final size:19
Alignment explanation
Indices: 11514975--11515021 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
11514965 AAAAAAGGGA
*
11514975 GAAGAAGAAAGAAAGAACAT
1 GAAGAAG-AAGAAAGAAAAT
11514995 GAA-AAGAAGAAA-AAAAT
1 GAAGAAGAAGAAAGAAAAT
11515012 GAGAGAAGAA
1 GA-AGAAGAA
11515022 AAGTTGGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 6 0.25
18 7 0.29
19 8 0.33
20 3 0.12
ACGTcount: A:0.68, C:0.02, G:0.26, T:0.04
Consensus pattern (19 bp):
GAAGAAGAAGAAAGAAAAT
Found at i:11516079 original size:21 final size:21
Alignment explanation
Indices: 11516050--11516147 Score: 86
Period size: 20 Copynumber: 5.0 Consensus size: 21
11516040 TTGAAACCCA
*
11516050 AAACCCTAAAACCCTAAATCAT
1 AAACCCT-AAACCCTAAACCAT
* *
11516072 AAA-CCTAAATCCTAAACCTT
1 AAACCCTAAACCCTAAACCAT
11516092 AAACCCTAAACCCTAAACC-T
1 AAACCCTAAACCCTAAACCAT
*
11516112 TAA-CCTAAACGCC-AAACC--
1 AAACCCTAAAC-CCTAAACCAT
11516130 -AACCC-AAACCCTAAACCA
1 AAACCCTAAACCCTAAACCA
11516148 ACCCCTAAGC
Statistics
Matches: 66, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
16 2 0.03
17 11 0.17
18 2 0.03
19 12 0.18
20 19 0.29
21 17 0.26
22 3 0.05
ACGTcount: A:0.47, C:0.37, G:0.01, T:0.15
Consensus pattern (21 bp):
AAACCCTAAACCCTAAACCAT
Found at i:11516138 original size:17 final size:17
Alignment explanation
Indices: 11516093--11516151 Score: 66
Period size: 17 Copynumber: 3.3 Consensus size: 17
11516083 CTAAACCTTA
11516093 AACCCTAAACCCTAAACC
1 AACCC-AAACCCTAAACC
*
11516111 TTAACCTAAACGCC-AAACC
1 --AACCCAAAC-CCTAAACC
11516130 AACCCAAACCCTAAACC
1 AACCCAAACCCTAAACC
11516147 AACCC
1 AACCC
11516152 CTAAGCCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 2 0.06
17 18 0.51
19 9 0.26
20 6 0.17
ACGTcount: A:0.44, C:0.44, G:0.02, T:0.10
Consensus pattern (17 bp):
AACCCAAACCCTAAACC
Found at i:11516145 original size:7 final size:7
Alignment explanation
Indices: 11516043--11516146 Score: 80
Period size: 7 Copynumber: 15.7 Consensus size: 7
11516033 TACATATTTG
*
11516043 AAACCCA
1 AAACCCT
11516050 AAACCCT
1 AAACCCT
11516057 AAAACCCT
1 -AAACCCT
* *
11516065 AAATCAT
1 AAACCCT
11516072 AAA-CCT
1 AAACCCT
*
11516078 AAATCCT
1 AAACCCT
*
11516085 AAACCTT
1 AAACCCT
11516092 AAACCCT
1 AAACCCT
11516099 AAACCCT
1 AAACCCT
11516106 AAA-CCT
1 AAACCCT
*
11516112 TAA-CCT
1 AAACCCT
11516118 AAACGCC-
1 AAAC-CCT
11516125 AAA-CC-
1 AAACCCT
11516130 -AACCC-
1 AAACCCT
11516135 AAACCCT
1 AAACCCT
11516142 AAACC
1 AAACC
11516147 AACCCCTAAG
Statistics
Matches: 81, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
4 2 0.02
5 4 0.05
6 20 0.25
7 46 0.57
8 9 0.11
ACGTcount: A:0.47, C:0.38, G:0.01, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:11516146 original size:13 final size:13
Alignment explanation
Indices: 11516043--11516155 Score: 58
Period size: 13 Copynumber: 8.7 Consensus size: 13
11516033 TACATATTTG
*
11516043 AAACCCAAAACCC
1 AAACCCTAAACCC
*
11516056 TAAAACCCTAAA-TC
1 --AAACCCTAAACCC
* *
11516070 ATAAACCTAAATCCT
1 A-AACCCTAAA-CCC
*
11516085 AAACCTTAAACCC
1 AAACCCTAAACCC
*
11516098 TAAACCCTAAACCT
1 -AAACCCTAAACCC
*
11516112 TAA-CCTAAACGCC
1 AAACCCTAAAC-CC
11516125 AAA-CC--AACCC
1 AAACCCTAAACCC
11516135 AAACCCTAAA-CC
1 AAACCCTAAACCC
*
11516147 AACCCCTAA
1 AAACCCTAA
11516156 GCCTAAAGAC
Statistics
Matches: 76, Mismatches: 14, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
10 5 0.07
11 5 0.07
12 18 0.24
13 19 0.25
14 19 0.25
15 10 0.13
ACGTcount: A:0.47, C:0.38, G:0.01, T:0.14
Consensus pattern (13 bp):
AAACCCTAAACCC
Found at i:11528392 original size:4 final size:4
Alignment explanation
Indices: 11528385--11528437 Score: 56
Period size: 4 Copynumber: 12.8 Consensus size: 4
11528375 AAGAGAAAAA
11528385 AATG AATG AATTG AA-- AAGTG AATG AATG AATG AAAGTG AATG AATG
1 AATG AATG AA-TG AATG AA-TG AATG AATG AATG -AA-TG AATG AATG
11528431 AATG AAT
1 AATG AAT
11528438 TTAAATGATA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
2 2 0.05
4 29 0.67
5 10 0.23
6 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AATG
Found at i:11528420 original size:18 final size:18
Alignment explanation
Indices: 11528385--11528436 Score: 86
Period size: 18 Copynumber: 2.8 Consensus size: 18
11528375 AAGAGAAAAA
11528385 AATGAATGAATTGAAAAGTG
1 AATGAATGAA-TG-AAAGTG
11528405 AATGAATGAATGAAAGTG
1 AATGAATGAATGAAAGTG
11528423 AATGAATGAATGAA
1 AATGAATGAATGAA
11528437 TTTAAATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 20 0.62
19 2 0.06
20 10 0.31
ACGTcount: A:0.52, C:0.00, G:0.25, T:0.23
Consensus pattern (18 bp):
AATGAATGAATGAAAGTG
Found at i:11529184 original size:52 final size:52
Alignment explanation
Indices: 11529071--11529225 Score: 186
Period size: 55 Copynumber: 2.9 Consensus size: 52
11529061 CACAACTCAA
*
11529071 CCTTTTCAAATTAAGATTTTTTTTTATGTTTGTTGTCTATCTTCTTCATATGAGC
1 CCTTTTCAAATTAAGATTTTTTTTTATGTTTGTTGTCTA---TCTTCATATGAAC
*
11529126 CTTTTTCAAATTAAGATTTTTTTTTATGTTTGTTGTCTATCTTCATA-GAAAC
1 CCTTTTCAAATTAAGATTTTTTTTTATGTTTGTTGTCTATCTTCATATG-AAC
* * * * * *
11529178 CCTTTTCAAATTGAGGTTTCTTTTTAAAGTTTATTGCCTATCTTCATA
1 CCTTTTCAAATTAAGATTT-TTTTTTATGTTTGTTGTCTATCTTCATA
11529226 AGAGTCTTTA
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
51 1 0.01
52 26 0.29
53 24 0.27
55 38 0.43
ACGTcount: A:0.23, C:0.14, G:0.10, T:0.53
Consensus pattern (52 bp):
CCTTTTCAAATTAAGATTTTTTTTTATGTTTGTTGTCTATCTTCATATGAAC
Found at i:11529296 original size:51 final size:51
Alignment explanation
Indices: 11529071--11529302 Score: 187
Period size: 52 Copynumber: 4.4 Consensus size: 51
11529061 CACAACTCAA
* * * * * * *
11529071 CCTTTTCAAATTAAGATTTTTTTTTATGTTTGTTGTCTATCTTCTTCATATGAG
1 CCTTTTCAAAATGAGATTTTTTTTAAAGTTTATTGCCTA---TCTTCATAAGAG
* * * * * * * *
11529125 CCTTTTTCAAATTAAGATTTTTTTTTATGTTTGTTGTCTATCTTCATAGAAAC
1 CC-TTTTCAAAATGAGATTTTTTTTAAAGTTTATTGCCTATCTTCATA-AGAG
* *
11529178 CCTTTTCAAATTGAGGTTTCTTTTTAAAGTTTATTGCCTATCTTCATAAGAG
1 CCTTTTCAAAATGAGATTT-TTTTTAAAGTTTATTGCCTATCTTCATAAGAG
* * * * *
11529230 TCTTTATCAAAATGAGATTTTTTTTAAAGTTCT-TTGCTTATCTTTATAGGTG
1 CCTTT-TCAAAATGAGATTTTTTTTAAAGTT-TATTGCCTATCTTCATAAGAG
11529282 CCTTTTCAAAATGAGATTTTT
1 CCTTTTCAAAATGAGATTTTT
11529303 AAAAAGTTCC
Statistics
Matches: 154, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
51 16 0.10
52 59 0.38
53 40 0.26
54 2 0.01
55 37 0.24
ACGTcount: A:0.24, C:0.13, G:0.12, T:0.51
Consensus pattern (51 bp):
CCTTTTCAAAATGAGATTTTTTTTAAAGTTTATTGCCTATCTTCATAAGAG
Found at i:11529327 original size:51 final size:51
Alignment explanation
Indices: 11529213--11529344 Score: 131
Period size: 51 Copynumber: 2.6 Consensus size: 51
11529203 AAAGTTTATT
* * * ** * *
11529213 GCCTATCTTCATAAGAGTCTTTATCAAAATGAGATTTTTTTTAAAGTTCTTT
1 GCCTATCTTTATAGGAGCCTTT-TCAAAATGAGATTTTTTAAAAAGTTCCTA
* *
11529265 GCTTATCTTTATAGGTGCCTTTTCAAAATGAGA-TTTTTAAAAAGTTCCCTA
1 GCCTATCTTTATAGGAGCCTTTTCAAAATGAGATTTTTTAAAAAGTT-CCTA
* * *
11529316 GCCTATGTTTATAGGAGCCCTTCCAAAAT
1 GCCTATCTTTATAGGAGCCTTTTCAAAAT
11529345 TGAAATTATC
Statistics
Matches: 65, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
50 11 0.17
51 37 0.57
52 17 0.26
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.41
Consensus pattern (51 bp):
GCCTATCTTTATAGGAGCCTTTTCAAAATGAGATTTTTTAAAAAGTTCCTA
Found at i:11530727 original size:30 final size:30
Alignment explanation
Indices: 11530691--11530761 Score: 110
Period size: 28 Copynumber: 2.4 Consensus size: 30
11530681 GAAAGGCTGG
11530691 AAACATAAAAAAAAAATAAGGGAGAAGAAA
1 AAACATAAAAAAAAAATAAGGGAGAAGAAA
*
11530721 AAACAT--AAAAAAAATAAGGGAGAGGAAA
1 AAACATAAAAAAAAAATAAGGGAGAAGAAA
*
11530749 AAACACAAAAAAA
1 AAACATAAAAAAA
11530762 TTGAAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 26 0.70
30 11 0.30
ACGTcount: A:0.73, C:0.06, G:0.15, T:0.06
Consensus pattern (30 bp):
AAACATAAAAAAAAAATAAGGGAGAAGAAA
Found at i:11536368 original size:16 final size:17
Alignment explanation
Indices: 11536330--11536388 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
11536320 TTGCATGAAC
11536330 TTGCATAATTAATATTATAT
1 TTGCATAA-T-ATATT-TAT
*
11536350 TTGCATGATA-ATTTAT
1 TTGCATAATATATTTAT
* *
11536366 TTGCCTAATATATTTGT
1 TTGCATAATATATTTAT
11536383 TTGCAT
1 TTGCAT
11536389 TATTAATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
16 11 0.33
17 13 0.39
18 1 0.03
19 1 0.03
20 7 0.21
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (17 bp):
TTGCATAATATATTTAT
Found at i:11536397 original size:21 final size:20
Alignment explanation
Indices: 11536371--11536451 Score: 65
Period size: 20 Copynumber: 3.8 Consensus size: 20
11536361 TTTATTTGCC
11536371 TAATATATTTGTTTGCATTAT
1 TAATATATTTGTTTG-ATTAT
*
11536392 TAATATATTTATTTGTGTGATTTAT
1 T-A-ATA--TATTTGTTTGA-TTAT
*
11536417 TAATATATTTGCATT-ATTAT
1 TAATATATTTG-TTTGATTAT
*
11536437 TAATATATTTATTTG
1 TAATATATTTGTTTG
11536452 TACGATTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
19 2 0.04
20 14 0.29
21 8 0.17
22 2 0.04
23 6 0.12
24 2 0.04
25 14 0.29
ACGTcount: A:0.31, C:0.02, G:0.09, T:0.58
Consensus pattern (20 bp):
TAATATATTTGTTTGATTAT
Found at i:11536485 original size:47 final size:45
Alignment explanation
Indices: 11536371--11536508 Score: 179
Period size: 47 Copynumber: 3.0 Consensus size: 45
11536361 TTTATTTGCC
** *
11536371 TAATATATTTGTTTGCATTATTAATATATTTATTTGTGTGATTTAT
1 TAATATATTTGCATG-ATTATTAATATATTTATTTGTATGATTTAT
* *
11536417 TAATATATTTGCATTATTATTAATATATTTATTTGTACGATTATATT
1 TAATATATTTGCATGATTATTAATATATTTATTTGTATGATT-TA-T
*
11536464 TAATTTGA-TTGCATGATTATTAATATATTTATTTGTATGATTTAT
1 TAATAT-ATTTGCATGATTATTAATATATTTATTTGTATGATTTAT
11536509 ACATTTAATT
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
45 26 0.32
46 16 0.20
47 38 0.47
48 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (45 bp):
TAATATATTTGCATGATTATTAATATATTTATTTGTATGATTTAT
Found at i:11536503 original size:24 final size:24
Alignment explanation
Indices: 11536376--11536505 Score: 112
Period size: 24 Copynumber: 5.5 Consensus size: 24
11536366 TTGCCTAATA
*
11536376 TATTTGTTTGCATTATTAATATATT
1 TATTTGTATG-ATTATTAATATATT
*
11536401 TATTTGTGTGATTTATT-A-ATA--
1 TATTTGTATGA-TTATTAATATATT
* *
11536422 TATTTGCATTATTATTAATATATT
1 TATTTGTATGATTATTAATATATT
* *
11536446 TATTTGTACGATTA-T-ATTTAATT
1 TATTTGTATGATTATTAATAT-ATT
*
11536469 TGA-TTGCATGATTATTAATATATT
1 T-ATTTGTATGATTATTAATATATT
11536493 TATTTGTATGATT
1 TATTTGTATGATT
11536506 TATACATTTA
Statistics
Matches: 83, Mismatches: 12, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
20 5 0.06
21 9 0.11
22 6 0.07
23 18 0.22
24 28 0.34
25 17 0.20
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (24 bp):
TATTTGTATGATTATTAATATATT
Done.