Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 35 of 320
Found at i:10013359 original size:53 final size:52
Alignment explanation
Indices: 10013279--10013385 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 52
10013269 TCAATATATA
* *
10013279 AGGCCTATGTGTTAGTATCTTACCTAAGGTATCAGTACATAGAATATATGTAT
1 AGGCCTATGTGTCAGTACCTTACCTAAGGTATCAGTACATAG-ATATATGTAT
*
10013332 AGGCCTATGTGTCAGTACCTTATCTAAGGTATCAGTACATAGATATATGTAT
1 AGGCCTATGTGTCAGTACCTTACCTAAGGTATCAGTACATAGATATATGTAT
10013384 AG
1 AG
10013386 ACACATAGCC
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
52 12 0.24
53 39 0.76
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.35
Consensus pattern (52 bp):
AGGCCTATGTGTCAGTACCTTACCTAAGGTATCAGTACATAGATATATGTAT
Found at i:10013898 original size:73 final size:73
Alignment explanation
Indices: 10013799--10013984 Score: 228
Period size: 73 Copynumber: 2.5 Consensus size: 73
10013789 TCACTTGGGT
* ** * *
10013799 CACACGACCAAGCCACACGCCCGTGTGCTAGGCCGTGTGAGCAATTTGGGTTGCATTATTTAGGT
1 CACACGGCCAAGCCACACGCCCGTGTGCTAGGCCGTGTGAGCAATTTGACTTACATTATTGAGGT
10013864 GCAAGGGA
66 GCAAGGGA
* * * * * *
10013872 TACATGGCCAAGCCACATGCCCGTGTGTTAGGCCGTGTTAGCAATTTGACTTATATTATTGAGGT
1 CACACGGCCAAGCCACACGCCCGTGTGCTAGGCCGTGTGAGCAATTTGACTTACATTATTGAGGT
*
10013937 GCAGGGGA
66 GCAAGGGA
* * * *
10013945 CGCACGGCCAAGTCACACGCTCGTGTGCTAGGCCATGTGA
1 CACACGGCCAAGCCACACGCCCGTGTGCTAGGCCGTGTGA
10013985 AAATACCTGA
Statistics
Matches: 92, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
73 92 1.00
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.24
Consensus pattern (73 bp):
CACACGGCCAAGCCACACGCCCGTGTGCTAGGCCGTGTGAGCAATTTGACTTACATTATTGAGGT
GCAAGGGA
Found at i:10014811 original size:24 final size:24
Alignment explanation
Indices: 10014784--10014863 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
10014774 CAATATTAGG
10014784 AAGCTCCGGAGAGCCACAATCGGA
1 AAGCTCCGGAGAGCCACAATCGGA
** * ***
10014808 AAGCTCACAAAGTGCCTTTTATCGGA
1 AAGCTC-CGGAGAGCC-ACAATCGGA
*
10014834 AAGCTTCGGAGAGCCACAATCGGA
1 AAGCTCCGGAGAGCCACAATCGGA
10014858 AAGCTC
1 AAGCTC
10014864 ACAAAGAGCT
Statistics
Matches: 40, Mismatches: 14, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
24 17 0.43
25 12 0.30
26 11 0.28
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (24 bp):
AAGCTCCGGAGAGCCACAATCGGA
Found at i:10014844 original size:50 final size:51
Alignment explanation
Indices: 10014784--10014899 Score: 173
Period size: 50 Copynumber: 2.3 Consensus size: 51
10014774 CAATATTAGG
*
10014784 AAGCTCCGGAGAGCCACAATCGGAAAGCTCACAAAGTGCCTTTTATC-GGA
1 AAGCTCCGGAGAGCCACAATCGGAAAGCTCACAAAGAGCCTTTTATCTGGA
* *
10014834 AAGCTTCGGAGAGCCACAATCGGAAAGCTCACAAAGAGCTTTTTATCTGG-
1 AAGCTCCGGAGAGCCACAATCGGAAAGCTCACAAAGAGCCTTTTATCTGGA
**
10014884 AAGCTCCAAAGAGCCA
1 AAGCTCCGGAGAGCCA
10014900 TAGATCGGGA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 57 0.97
51 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (51 bp):
AAGCTCCGGAGAGCCACAATCGGAAAGCTCACAAAGAGCCTTTTATCTGGA
Found at i:10016179 original size:30 final size:30
Alignment explanation
Indices: 10016091--10016181 Score: 119
Period size: 30 Copynumber: 3.0 Consensus size: 30
10016081 GAAAAGAGGA
* * ** *
10016091 ACCAGTAGCTCCTTTAATGCCGTTCCATAC
1 ACCAGCAGCACCTTTAATGTTGTTCCATGC
*
10016121 ACCAGCAGCACCTTTAATATTGTTCCATGC
1 ACCAGCAGCACCTTTAATGTTGTTCCATGC
*
10016151 ACCAGCAGCACCTTTAATGTTGTCCCATGC
1 ACCAGCAGCACCTTTAATGTTGTTCCATGC
10016181 A
1 A
10016182 TGCTTTCTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.29
Consensus pattern (30 bp):
ACCAGCAGCACCTTTAATGTTGTTCCATGC
Found at i:10016269 original size:38 final size:38
Alignment explanation
Indices: 10016175--10016285 Score: 107
Period size: 38 Copynumber: 2.9 Consensus size: 38
10016165 TAATGTTGTC
*
10016175 CCATGCATGCTTTCTTTAATACCTGCACATTAAATTCAG
1 CCATGCATGCTTT-TTTAACACCTGCACATTAAATTCAG
* * * *
10016214 CCATACATGTTTTTTTTAACACTTGCACATT-AATTCGG
1 CCATGCATG-CTTTTTTAACACCTGCACATTAAATTCAG
* ** *
10016252 TCATGCATGCTTGTTTTAATGCCTACACATTAAA
1 CCATGCATGCTT-TTTTAACACCTGCACATTAAA
10016286 AATCAACAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
37 2 0.04
38 27 0.47
39 25 0.44
40 3 0.05
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.39
Consensus pattern (38 bp):
CCATGCATGCTTTTTTAACACCTGCACATTAAATTCAG
Found at i:10018498 original size:19 final size:20
Alignment explanation
Indices: 10018457--10018498 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
10018447 TTTCTTCGTA
*
10018457 CTCACTCTCTTTTTTCTCACT
1 CTCAATCTCTTTTTTCT-ACT
10018478 CTCAATCTCTTTTTTCT-CT
1 CTCAATCTCTTTTTTCTACT
10018497 CT
1 CT
10018499 TTCATTTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
21 16 0.80
ACGTcount: A:0.10, C:0.36, G:0.00, T:0.55
Consensus pattern (20 bp):
CTCAATCTCTTTTTTCTACT
Found at i:10020557 original size:30 final size:30
Alignment explanation
Indices: 10020521--10020600 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 30
10020511 GAAAAGAGGA
* *
10020521 ACCAGCAGCTCCTTTAATGCCATTCCATGT
1 ACCAGCAGCTCCTTTAATGCCATTCCAAGC
* ****
10020551 ACCAGCAACTCCTTTAATATTGTTCCAAGC
1 ACCAGCAGCTCCTTTAATGCCATTCCAAGC
10020581 ACCAGCAGCTCCTTTAATGC
1 ACCAGCAGCTCCTTTAATGC
10020601 TGTCCCATGC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.26, C:0.33, G:0.12, T:0.29
Consensus pattern (30 bp):
ACCAGCAGCTCCTTTAATGCCATTCCAAGC
Found at i:10020689 original size:36 final size:38
Alignment explanation
Indices: 10020606--10020713 Score: 139
Period size: 36 Copynumber: 2.8 Consensus size: 38
10020596 AATGCTGTCC
*
10020606 CATGCATGCTTTCTTTAATACCTGCACATTAAATTTGGT
1 CATGCATGC-TTCTTTAATACCTGCACATTAAATTCGGT
* *
10020645 CATGCATGCTT-TTTAGTACTTGCACATT-AATTCGGT
1 CATGCATGCTTCTTTAATACCTGCACATTAAATTCGGT
* *
10020681 CATGCATGCTTGCTTTAATGCCTACACATTAAA
1 CATGCATGCTT-CTTTAATACCTGCACATTAAA
10020714 AATCAACAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
36 18 0.31
37 15 0.25
38 15 0.25
39 11 0.19
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (38 bp):
CATGCATGCTTCTTTAATACCTGCACATTAAATTCGGT
Found at i:10027442 original size:17 final size:18
Alignment explanation
Indices: 10027409--10027444 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10027399 CATGTGTGTA
10027409 AATAATAAACATATATTT
1 AATAATAAACATATATTT
*
10027427 AATAATAAA-TTATATTT
1 AATAATAAACATATATTT
10027444 A
1 A
10027445 CTTATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AATAATAAACATATATTT
Found at i:10027477 original size:8 final size:8
Alignment explanation
Indices: 10027464--10027499 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
10027454 TAAGTAAATG
10027464 TTATTATA
1 TTATTATA
10027472 TTATTATA
1 TTATTATA
*
10027480 TTACTATA
1 TTATTATA
10027488 TTATTATA
1 TTATTATA
10027496 TTAT
1 TTAT
10027500 ATAAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (8 bp):
TTATTATA
Found at i:10034899 original size:44 final size:45
Alignment explanation
Indices: 10034846--10034948 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 45
10034836 TGTCTTTGAC
* * *
10034846 ATGGACTTACATGAATTATTCCTATCTCCAATGCCATA-TATAAT
1 ATGGACTTACATGAATCAATCCTATCTCCAAAGCCATATTATAAT
** * *
10034890 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGAATCAATCCTATCTCCAAAGCCATA-TTATAAT
*
10034936 AAGGACTTACATG
1 ATGGACTTACATG
10034949 GCTCATTTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 32 0.65
46 17 0.35
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (45 bp):
ATGGACTTACATGAATCAATCCTATCTCCAAAGCCATATTATAAT
Found at i:10034946 original size:46 final size:44
Alignment explanation
Indices: 10034865--10034953 Score: 124
Period size: 46 Copynumber: 2.0 Consensus size: 44
10034855 CATGAATTAT
* *
10034865 TCCTATCTCCAATGCCATATATAATATGGACTTACATGGCTCAA
1 TCCTATCTCCAAAGCCATATATAATAAGGACTTACATGGCTCAA
* *
10034909 TCCTGTCTCCAAAGCCATATTTCTAATAAGGACTTACATGGCTCA
1 TCCTATCTCCAAAGCCATA--TATAATAAGGACTTACATGGCTCA
10034954 TTTCTGTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 17 0.44
46 22 0.56
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.31
Consensus pattern (44 bp):
TCCTATCTCCAAAGCCATATATAATAAGGACTTACATGGCTCAA
Found at i:10037552 original size:6 final size:6
Alignment explanation
Indices: 10037541--10037567 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
10037531 ATGTGTCGAC
10037541 TACTGT TACTGT TACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TAC
10037568 CGATTCGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:10037672 original size:59 final size:58
Alignment explanation
Indices: 10037598--10037735 Score: 196
Period size: 53 Copynumber: 2.4 Consensus size: 58
10037588 CGGATATTGT
* * *
10037598 TACTGTTACCGTTACTGTTACTGTTTTGGATTTGTTCCGATGAGGTACTCTGTGTACTA
1 TACTGTTACTGTTACTGTTACTG-TTCGGATTTGTTCCGATGAGGTACTCTGTGTACCA
10037657 TACTGTTACTGTTACTGTT-C----CGGATTTGTTCCGATGAGGTACTCTGTGTACCA
1 TACTGTTACTGTTACTGTTACTGTTCGGATTTGTTCCGATGAGGTACTCTGTGTACCA
*
10037710 TACTGCTACTGTTACTGTTACTGTTC
1 TACTGTTACTGTTACTGTTACTGTTC
10037736 CGGCTTCGGC
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
53 49 0.70
54 1 0.01
58 2 0.03
59 18 0.26
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.43
Consensus pattern (58 bp):
TACTGTTACTGTTACTGTTACTGTTCGGATTTGTTCCGATGAGGTACTCTGTGTACCA
Found at i:10037675 original size:53 final size:53
Alignment explanation
Indices: 10037608--10037728 Score: 206
Period size: 53 Copynumber: 2.3 Consensus size: 53
10037598 TACTGTTACC
** *
10037608 GTTACTGTTACTGTTTTGGATTTGTTCCGATGAGGTACTCTGTGTACTATACT
1 GTTACTGTTACTGTTCCGGATTTGTTCCGATGAGGTACTCTGTGTACCATACT
10037661 GTTACTGTTACTGTTCCGGATTTGTTCCGATGAGGTACTCTGTGTACCATACT
1 GTTACTGTTACTGTTCCGGATTTGTTCCGATGAGGTACTCTGTGTACCATACT
*
10037714 GCTACTGTTACTGTT
1 GTTACTGTTACTGTT
10037729 ACTGTTCCGG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 64 1.00
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (53 bp):
GTTACTGTTACTGTTCCGGATTTGTTCCGATGAGGTACTCTGTGTACCATACT
Found at i:10037958 original size:18 final size:18
Alignment explanation
Indices: 10037934--10037997 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 18
10037924 AATTGATTGA
10037934 TACTGAATAACTGATTAT
1 TACTGAATAACTGATTAT
* *
10037952 TATTGAATAATTGATTAT
1 TACTGAATAACTGATTAT
*
10037970 TACTGAATAACTGACTAT
1 TACTGAATAACTGATTAT
*
10037988 TACTAAATAA
1 TACTGAATAA
10037998 ATAATTGTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (18 bp):
TACTGAATAACTGATTAT
Found at i:10037997 original size:36 final size:36
Alignment explanation
Indices: 10037924--10037997 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
10037914 ATAACCGATC
* * *
10037924 AATTGATTGATACTGAATAACTGATTATTATTGAAT
1 AATTGATTGATACTGAATAACTGACTATTACTAAAT
10037960 AATTGATT-ATTACTGAATAACTGACTATTACTAAAT
1 AATTGATTGA-TACTGAATAACTGACTATTACTAAAT
10037996 AA
1 AA
10037998 ATAATTGTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 1 0.03
36 33 0.97
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (36 bp):
AATTGATTGATACTGAATAACTGACTATTACTAAAT
Found at i:10043686 original size:15 final size:17
Alignment explanation
Indices: 10043665--10043705 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
10043655 TAATCTTTTA
10043665 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
10043681 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
10043697 AAAATTATA
1 AAAATTATA
10043706 TTTTTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:10043727 original size:22 final size:22
Alignment explanation
Indices: 10043665--10043728 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
10043655 TAATCTTTTA
10043665 AAAATTATAAAAATATAAATTATT
1 AAAATTATAAAAATAT--ATTATT
* * *
10043689 AAAATAATAAAATTATATTTTT
1 AAAATTATAAAAATATATTATT
**
10043711 ACTATTATAAAAATATAT
1 AAAATTATAAAAATATAT
10043729 AATTTAATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
22 19 0.58
24 14 0.42
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATTATAAAAATATATTATT
Found at i:10044261 original size:24 final size:24
Alignment explanation
Indices: 10044234--10044289 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
10044224 TAAATTTAAA
*
10044234 ATATTTATAAAAAATTCAAAATTT
1 ATATTTATAAAAAATTCAAAATAT
* *
10044258 ATA-TTGTAAAAAATTCTAAATAT
1 ATATTTATAAAAAATTCAAAATAT
*
10044281 ATATATATA
1 ATATTTATA
10044290 TAAGTTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (24 bp):
ATATTTATAAAAAATTCAAAATAT
Found at i:10044286 original size:25 final size:23
Alignment explanation
Indices: 10044241--10044284 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
10044231 AAAATATTTA
*
10044241 TAAAAAATTCAAAATTTATATTG
1 TAAAAAATTCAAAATATATATTG
*
10044264 TAAAAAATTCTAAATATATAT
1 TAAAAAATTCAAAATATATAT
10044285 ATATATAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (23 bp):
TAAAAAATTCAAAATATATATTG
Found at i:10046460 original size:13 final size:13
Alignment explanation
Indices: 10046442--10046470 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
10046432 AAATTATTTA
10046442 AAAGTCCCTTTTC
1 AAAGTCCCTTTTC
10046455 AAAGTCCCTTTTC
1 AAAGTCCCTTTTC
10046468 AAA
1 AAA
10046471 AAAGGATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (13 bp):
AAAGTCCCTTTTC
Found at i:10047183 original size:11 final size:11
Alignment explanation
Indices: 10047167--10047191 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10047157 TCCCAAGGGG
10047167 TTTTGTAACGT
1 TTTTGTAACGT
10047178 TTTTGTAACGT
1 TTTTGTAACGT
10047189 TTT
1 TTT
10047192 ATCTTGACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (11 bp):
TTTTGTAACGT
Found at i:10048543 original size:46 final size:46
Alignment explanation
Indices: 10048476--10048569 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
10048466 AAAAAAAGTA
10048476 TGTACCACTAGAAGGGATCACTATGCAAAATAGAAGCAATAGGTAT
1 TGTACCACTAGAAGGGATCACTATGCAAAATAGAAGCAATAGGTAT
*
10048522 TGTACCACTAGAAGGGATCACTATGCAAAATAGGAGCAATAGGTAT
1 TGTACCACTAGAAGGGATCACTATGCAAAATAGAAGCAATAGGTAT
10048568 TG
1 TG
10048570 ATATTATCTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.22
Consensus pattern (46 bp):
TGTACCACTAGAAGGGATCACTATGCAAAATAGAAGCAATAGGTAT
Found at i:10052894 original size:4 final size:4
Alignment explanation
Indices: 10052885--10052910 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
10052875 CTGAAAGTAA
10052885 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
10052911 GAGGGGATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:10059460 original size:3 final size:3
Alignment explanation
Indices: 10059452--10059481 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
10059442 TTGCACAACC
10059452 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
10059482 GCCTGAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:10061703 original size:19 final size:22
Alignment explanation
Indices: 10061663--10061704 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
10061653 ATGTCCATTT
10061663 TAAATATGTTATTATCAAATAA
1 TAAATATGTTATTATCAAATAA
10061685 TAAATATG-TATT-T-AAATAA
1 TAAATATGTTATTATCAAATAA
10061704 T
1 T
10061705 GTTCAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 4 0.20
22 8 0.40
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (22 bp):
TAAATATGTTATTATCAAATAA
Found at i:10061823 original size:24 final size:24
Alignment explanation
Indices: 10061789--10061834 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
10061779 TATATGAAAT
* *
10061789 ATAAATTTTAAATATTTTTAAACA
1 ATAAATATTAAATATTTATAAACA
*
10061813 ATAAATATTAATTATTTATAAA
1 ATAAATATTAAATATTTATAAA
10061835 ATTTAATCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAACA
Found at i:10061872 original size:33 final size:32
Alignment explanation
Indices: 10061777--10061874 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 32
10061767 TTAATATTTT
*
10061777 AATATATGAAATATAAATTTTAAATATTTTTAAACA
1 AATATAT-AAAT-TATATTTTAAATA--TTTAAACA
* * * *
10061813 ATAAATATTAATTAT-TTATAAA-ATTTAATCA
1 A-ATATATAAATTATATTTTAAATATTTAAACA
10061844 GAATATATAAATTATATTTTAAATATTTAAA
1 -AATATATAAATTATATTTTAAATATTTAAA
10061875 TATAACCATT
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
31 18 0.37
32 7 0.14
33 7 0.14
34 6 0.12
35 2 0.04
36 4 0.08
37 5 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (32 bp):
AATATATAAATTATATTTTAAATATTTAAACA
Found at i:10062099 original size:13 final size:13
Alignment explanation
Indices: 10062083--10062112 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
10062073 TAGCTTTTTC
10062083 TTTTCAAAAATGT
1 TTTTCAAAAATGT
*
10062096 TTTTCAAAAGTGT
1 TTTTCAAAAATGT
10062109 TTTT
1 TTTT
10062113 GGAAAGCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (13 bp):
TTTTCAAAAATGT
Found at i:10062604 original size:19 final size:19
Alignment explanation
Indices: 10062580--10062617 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
10062570 GCCACTACTA
10062580 CCTACCATAATCAAATTTG
1 CCTACCATAATCAAATTTG
* *
10062599 CCTACCGTAATCTAATTTG
1 CCTACCATAATCAAATTTG
10062618 TTATTAACTT
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:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (19 bp):
CCTACCATAATCAAATTTG
Found at i:10063080 original size:19 final size:18
Alignment explanation
Indices: 10063054--10063097 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
10063044 AGTTTTGGGA
*
10063054 TTTGGGGGAAGTAAAATT
1 TTTGGGGGAAGTAAAAGT
10063072 TTTGAGGGGAAGTAAAAGT
1 TTTG-GGGGAAGTAAAAGT
10063091 TTTGGGG
1 TTTGGGG
10063098 AAAAAGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.30, C:0.00, G:0.39, T:0.32
Consensus pattern (18 bp):
TTTGGGGGAAGTAAAAGT
Found at i:10065840 original size:27 final size:27
Alignment explanation
Indices: 10065795--10065861 Score: 111
Period size: 27 Copynumber: 2.5 Consensus size: 27
10065785 TGAAATAATT
10065795 TGGAAAT--AAATGTAGGTTTACAAAAA
1 TGGAAATGAAAAT-TAGGTTTACAAAAA
10065821 TGGAAATGAAAATTAGGTTTACAAAAA
1 TGGAAATGAAAATTAGGTTTACAAAAA
10065848 TGGAAATGAAAATT
1 TGGAAATGAAAATT
10065862 TGCAACCTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
26 7 0.18
27 28 0.72
28 4 0.10
ACGTcount: A:0.51, C:0.03, G:0.19, T:0.27
Consensus pattern (27 bp):
TGGAAATGAAAATTAGGTTTACAAAAA
Found at i:10067190 original size:10 final size:10
Alignment explanation
Indices: 10067175--10067203 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
10067165 CCTTTTCCCA
10067175 TTTCTTTCTT
1 TTTCTTTCTT
10067185 TTTCTTTCTT
1 TTTCTTTCTT
10067195 TTT-TTTCTT
1 TTTCTTTCTT
10067204 AGTTTGGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:10067258 original size:15 final size:15
Alignment explanation
Indices: 10067238--10067266 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10067228 TTATCACCTA
10067238 TTTATTTTATTATAC
1 TTTATTTTATTATAC
10067253 TTTATTTTATTATA
1 TTTATTTTATTATA
10067267 ATAATAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATTTTATTATAC
Found at i:10067337 original size:13 final size:13
Alignment explanation
Indices: 10067319--10067356 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
10067309 TAATTTAATG
*
10067319 AATACATATTTAT
1 AATACATATATAT
10067332 AATACATATATAT
1 AATACATATATAT
10067345 -ATACATATATAT
1 AATACATATATAT
10067357 TAGATTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (13 bp):
AATACATATATAT
Found at i:10076714 original size:21 final size:21
Alignment explanation
Indices: 10076684--10076729 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
10076674 CCGTGTGGAT
10076684 CACACAGCCTGGCCCACTTAC
1 CACACAGCCTGGCCCACTTAC
* *
10076705 CACACGGCCTGGCCCAGTTAC
1 CACACAGCCTGGCCCACTTAC
10076726 CACA
1 CACA
10076730 TGCCCGTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.46, G:0.17, T:0.13
Consensus pattern (21 bp):
CACACAGCCTGGCCCACTTAC
Found at i:10080288 original size:25 final size:23
Alignment explanation
Indices: 10080222--10080289 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 23
10080212 TCAGTAATAC
*
10080222 ATATGAATTAAGTGTTAAATGAG
1 ATATGAATTAAGTGTTTAATGAG
*
10080245 ATTTATGAATTAATTGTTTAATGAAGG
1 A--TATGAATTAAGTGTTTAATG-A-G
10080272 ATATGAATTAAGTGTTTA
1 ATATGAATTAAGTGTTTA
10080290 TGTTATGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
23 1 0.03
25 34 0.89
26 1 0.03
27 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.41
Consensus pattern (23 bp):
ATATGAATTAAGTGTTTAATGAG
Found at i:10082458 original size:31 final size:27
Alignment explanation
Indices: 10082385--10082460 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 27
10082375 TGAACCTCTT
* *
10082385 AAAGGACGCCTTTGTGGTGAGACTCTA
1 AAAGGACACCTTTGTGGTGAGACTATA
*
10082412 AAAGGAAAACCTTTGTGGTGAGTACTTGATGA
1 AAAGG-ACACCTTTGTGGTGAG-AC-T-AT-A
10082444 AAAGGACACCTTTGTGG
1 AAAGGACACCTTTGTGG
10082461 CAATTTATGG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 5 0.12
28 14 0.35
29 2 0.05
30 1 0.03
31 12 0.30
32 6 0.15
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.26
Consensus pattern (27 bp):
AAAGGACACCTTTGTGGTGAGACTATA
Found at i:10082526 original size:28 final size:29
Alignment explanation
Indices: 10082479--10082533 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 29
10082469 GGATATGGAA
10082479 GCCTTTGTGGCTATCCCTAAA-AATGAAT
1 GCCTTTGTGGCTATCCCTAAAGAATGAAT
10082507 GCCTTTGTGGC-A-CCATCTAAAGAATGA
1 GCCTTTGTGGCTATCC--CTAAAGAATGA
10082534 GCTTTGCGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 2 0.08
27 1 0.04
28 16 0.67
29 5 0.21
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (29 bp):
GCCTTTGTGGCTATCCCTAAAGAATGAAT
Found at i:10084931 original size:26 final size:26
Alignment explanation
Indices: 10084902--10084954 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
10084892 GTAAATTACC
10084902 AAACCTTTACTACAACCATTAACCAT
1 AAACCTTTACTACAACCATTAACCAT
10084928 AAACCTTTACTACAACCATTAACCAT
1 AAACCTTTACTACAACCATTAACCAT
10084954 A
1 A
10084955 CTTTTGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.26
Consensus pattern (26 bp):
AAACCTTTACTACAACCATTAACCAT
Found at i:10085112 original size:17 final size:17
Alignment explanation
Indices: 10085090--10085123 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
10085080 GTTCCCTCAT
*
10085090 CTTTTAGAACATTTAAA
1 CTTTTAAAACATTTAAA
10085107 CTTTTAAAACATTTAAA
1 CTTTTAAAACATTTAAA
10085124 TATTACTCAA
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:0.12, G:0.03, T:0.41
Consensus pattern (17 bp):
CTTTTAAAACATTTAAA
Found at i:10092845 original size:16 final size:16
Alignment explanation
Indices: 10092824--10092854 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10092814 CTATGCATAC
*
10092824 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
10092840 AAAATACAAAAGACA
1 AAAATACAAAAGACA
10092855 TAATAGTGAA
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:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:10097932 original size:25 final size:25
Alignment explanation
Indices: 10097904--10097953 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
10097894 AAGGAGTCAC
10097904 AATTTATTATAAAAATAATAT-TTTA
1 AATTT-TTATAAAAATAATATGTTTA
* *
10097929 AATTTTTTTAGAAATAATATGTTTA
1 AATTTTTATAAAAATAATATGTTTA
10097954 TAATCGACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (25 bp):
AATTTTTATAAAAATAATATGTTTA
Found at i:10099106 original size:12 final size:11
Alignment explanation
Indices: 10099088--10099115 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
10099078 AAGGATTTGG
10099088 TAAAAAAAAAA
1 TAAAAAAAAAA
10099099 TAAAAAAAAAA
1 TAAAAAAAAAA
10099110 TAAAAA
1 TAAAAA
10099116 GGGATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (11 bp):
TAAAAAAAAAA
Found at i:10099355 original size:17 final size:18
Alignment explanation
Indices: 10099318--10099358 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
10099308 CCCTTATAAT
*
10099318 TATTATGAAAGGTTTTTA
1 TATTATGAAAGGTTATTA
*
10099336 TATTATGAATGG-TATTA
1 TATTATGAAAGGTTATTA
10099353 TATTAT
1 TATTAT
10099359 ATTTTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (18 bp):
TATTATGAAAGGTTATTA
Found at i:10101533 original size:15 final size:15
Alignment explanation
Indices: 10101513--10101551 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
10101503 TGCTTTGGAG
10101513 GATATTCTTGTTCAT
1 GATATTCTTGTTCAT
*
10101528 GATATTC-TGTTGAT
1 GATATTCTTGTTCAT
*
10101542 TATATTCTTG
1 GATATTCTTG
10101552 AAACTTGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (15 bp):
GATATTCTTGTTCAT
Found at i:10112104 original size:10 final size:9
Alignment explanation
Indices: 10112091--10112152 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 9
10112081 CTCTCTCCCT
10112091 TTCTCTTCTC
1 TTCT-TTCTC
10112101 TTCTTT-TC
1 TTCTTTCTC
10112109 TT-TTTCT-
1 TTCTTTCTC
10112116 TTCTTTATCTC
1 TTC-TT-TCTC
10112127 TTCTTTCTC
1 TTCTTTCTC
10112136 -TCTTTCCTC
1 TTCTTT-CTC
10112145 ATTCTTTC
1 -TTCTTTC
10112153 CATTTCTTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
7 5 0.11
8 10 0.23
9 11 0.25
10 10 0.23
11 8 0.18
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (9 bp):
TTCTTTCTC
Found at i:10113977 original size:5 final size:5
Alignment explanation
Indices: 10113967--10114014 Score: 53
Period size: 5 Copynumber: 9.2 Consensus size: 5
10113957 TGAGTCCATC
*
10113967 TATTT TATTT TATTTT TATTTT TATTT TATCTT TCTTT TA-TT TATTT
1 TATTT TATTT TA-TTT TA-TTT TATTT TAT-TT TATTT TATTT TATTT
10114014 T
1 T
10114015 TGAAGACTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 4 0.11
5 19 0.50
6 15 0.39
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:10113985 original size:11 final size:11
Alignment explanation
Indices: 10113967--10114009 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
10113957 TGAGTCCATC
10113967 TATTTTA-TTT
1 TATTTTATTTT
10113977 TATTTTTATTTT
1 TA-TTTTATTTT
*
10113989 TATTTTATCTT
1 TATTTTATTTT
*
10114000 TCTTTTATTT
1 TATTTTATTT
10114010 ATTTTTGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 2 0.07
11 21 0.75
12 5 0.18
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:10113995 original size:22 final size:22
Alignment explanation
Indices: 10113967--10114009 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
10113957 TGAGTCCATC
*
10113967 TATTTTAT-TTTATTTTTATTTT
1 TATTTTATCTTT-CTTTTATTTT
10113989 TATTTTATCTTTCTTTTATTT
1 TATTTTATCTTTCTTTTATTT
10114010 ATTTTTGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (22 bp):
TATTTTATCTTTCTTTTATTTT
Found at i:10122510 original size:25 final size:25
Alignment explanation
Indices: 10122451--10122501 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
10122441 TATAATCAAG
10122451 TATGCATTTTAAAGTTGAATAGGAA
1 TATGCATTTTAAAGTTGAATAGGAA
10122476 TATGCATTTTAAAGTTGAATAGGAA
1 TATGCATTTTAAAGTTGAATAGGAA
10122501 T
1 T
10122502 GCACGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (25 bp):
TATGCATTTTAAAGTTGAATAGGAA
Found at i:10124380 original size:4 final size:4
Alignment explanation
Indices: 10124371--10124421 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
10124361 TAAGAACAGA
* * *
10124371 GTAT GTAT GTAT GCT-T GTAT GTAT GCAT GTAG GTAT GCAT GTAT GTAT
1 GTAT GTAT GTAT G-TAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
10124419 GTA
1 GTA
10124422 CATGATTCCT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 1 0.03
4 37 0.95
5 1 0.03
ACGTcount: A:0.24, C:0.06, G:0.27, T:0.43
Consensus pattern (4 bp):
GTAT
Found at i:10124391 original size:12 final size:12
Alignment explanation
Indices: 10124373--10124419 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
10124363 AGAACAGAGT
10124373 ATGTATGTATGC
1 ATGTATGTATGC
*
10124385 TTGTATGTATGC
1 ATGTATGTATGC
*
10124397 ATGTAGGTATGC
1 ATGTATGTATGC
10124409 ATGTATGTATG
1 ATGTATGTATG
10124420 TACATGATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.23, C:0.06, G:0.28, T:0.43
Consensus pattern (12 bp):
ATGTATGTATGC
Found at i:10126950 original size:7 final size:7
Alignment explanation
Indices: 10126938--10126962 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
10126928 CACAAACCCA
10126938 AAAAAAT
1 AAAAAAT
10126945 AAAAAAT
1 AAAAAAT
10126952 AAAAAAT
1 AAAAAAT
10126959 AAAA
1 AAAA
10126963 TCTAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:10127014 original size:7 final size:7
Alignment explanation
Indices: 10127002--10127068 Score: 134
Period size: 7 Copynumber: 9.6 Consensus size: 7
10126992 AGAAAAAAAA
10127002 ATCAAGC
1 ATCAAGC
10127009 ATCAAGC
1 ATCAAGC
10127016 ATCAAGC
1 ATCAAGC
10127023 ATCAAGC
1 ATCAAGC
10127030 ATCAAGC
1 ATCAAGC
10127037 ATCAAGC
1 ATCAAGC
10127044 ATCAAGC
1 ATCAAGC
10127051 ATCAAGC
1 ATCAAGC
10127058 ATCAAGC
1 ATCAAGC
10127065 ATCA
1 ATCA
10127069 GGCCATCAGC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 60 1.00
ACGTcount: A:0.43, C:0.28, G:0.13, T:0.15
Consensus pattern (7 bp):
ATCAAGC
Found at i:10129248 original size:67 final size:67
Alignment explanation
Indices: 10129140--10129274 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
10129130 TATTGGATCG
*
10129140 TGCGTGAGAATAATTATATCATATCTACAACACTTAGAACTTATACCATATTGATCAAGCATTGA
1 TGCGTGAGAATAATTATATCATATCTACAACACTTAAAACTTATACCATATTGATCAAGCATTGA
10129205 AA
66 AA
10129207 TGCGTGAGAATAATTATATCATATCTACAACACTTAAAACTTATACCATATTGATCAAGCATTGA
1 TGCGTGAGAATAATTATATCATATCTACAACACTTAAAACTTATACCATATTGATCAAGCATTGA
10129272 AA
66 AA
10129274 T
1 T
10129275 TTGATAGCTA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (67 bp):
TGCGTGAGAATAATTATATCATATCTACAACACTTAAAACTTATACCATATTGATCAAGCATTGA
AA
Found at i:10129738 original size:4 final size:4
Alignment explanation
Indices: 10129723--10129766 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
10129713 TATATAAAAA
* *
10129723 ATAC ATAC --AC ATAC ATAC TTAC ATAC ATAC ATGC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
10129767 GTATAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
4 32 0.94
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:10131435 original size:39 final size:36
Alignment explanation
Indices: 10131376--10131711 Score: 172
Period size: 34 Copynumber: 9.2 Consensus size: 36
10131366 TCAACTAGCT
* * *
10131376 TTAAAAATGACAGTCGTGATTGTAAATCAGCGAATTG
1 TTAAAAAT-AAAGTTGTGATTGTAAATCAACGAATTG
*
10131413 TTAGAAAATCGAAAGTTGTGATTGTAAATCAAC--ATATC
1 TTA-AAAAT--AAAGTTGTGATTGTAAATCAACGAAT-TG
* * ** ** * **
10131451 ATAAGAAT-AAGCCGTGATAATAAATCAAGGAGCT-
1 TTAAAAATAAAGTTGTGATTGTAAATCAACGAATTG
* * **
10131485 TTAAAAATGACA-TTCGTGATCGTAAATCAGTGAATTG
1 TTAAAAAT-AAAGTT-GTGATTGTAAATCAACGAATTG
* * *
10131522 TTAGAAAAGCGAAAGTTGTGGTTGTAAATAAACGAATTG
1 TTA-AAAA--TAAAGTTGTGATTGTAAATCAACGAATTG
* *
10131561 -TAAGAATAAA-TTGTGATCGTAAATCAACGAATTG
1 TTAAAAATAAAGTTGTGATTGTAAATCAACGAATTG
*
10131595 TTAGAAAATCAAAGGTTGTGATTGTAAATCAACGAATCG
1 TTA-AAAAT-AAA-GTTGTGATTGTAAATCAACGAATTG
* * * * **
10131634 -TAAGAATAAA-TCGTGATCGTAAATTAACGAGCT-
1 TTAAAAATAAAGTTGTGATTGTAAATCAACGAATTG
* *
10131667 TTAAAAATGATAA-TTGTGATAGTAAATCAACGAACTG
1 TTAAAAAT-A-AAGTTGTGATTGTAAATCAACGAATTG
10131704 TTATAAAA
1 TTA-AAAA
10131712 CCGAAGGTCA
Statistics
Matches: 225, Mismatches: 51, Indels: 45
0.70 0.16 0.14
Matches are distributed among these distances:
34 66 0.29
35 7 0.03
36 44 0.20
37 25 0.11
38 20 0.09
39 61 0.27
40 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (36 bp):
TTAAAAATAAAGTTGTGATTGTAAATCAACGAATTG
Found at i:10131577 original size:109 final size:109
Alignment explanation
Indices: 10131363--10131590 Score: 305
Period size: 109 Copynumber: 2.1 Consensus size: 109
10131353 CTTGTCGAAG
* * *
10131363 AAATCAACTAGCTTTAAAAATGACAGTCGTGATTGTAAATCAGCGAATTGTTAGAAAATCGAAAG
1 AAATCAACGAGCTTTAAAAATGACAGTCGTGATCGTAAATCAGCGAATTGTTAGAAAAGCGAAAG
* *
10131428 TTGTGATTGTAAATCAACATATCATAAGAATAAGCCGTGATAAT
66 TTGTGATTGTAAATAAACATATCATAAGAATAAACCGTGATAAT
* * *
10131472 AAATCAAGGAGCTTTAAAAATGACATTCGTGATCGTAAATCAGTGAATTGTTAGAAAAGCGAAAG
1 AAATCAACGAGCTTTAAAAATGACAGTCGTGATCGTAAATCAGCGAATTGTTAGAAAAGCGAAAG
* ** ** **
10131537 TTGTGGTTGTAAATAAACGA-ATTGTAAGAATAAATTGTGATCGT
66 TTGTGATTGTAAATAAAC-ATATCATAAGAATAAACCGTGATAAT
10131581 AAATCAACGA
1 AAATCAACGA
10131591 ATTGTTAGAA
Statistics
Matches: 102, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
109 101 0.99
110 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (109 bp):
AAATCAACGAGCTTTAAAAATGACAGTCGTGATCGTAAATCAGCGAATTGTTAGAAAAGCGAAAG
TTGTGATTGTAAATAAACATATCATAAGAATAAACCGTGATAAT
Found at i:10131620 original size:73 final size:73
Alignment explanation
Indices: 10131498--10131663 Score: 244
Period size: 73 Copynumber: 2.3 Consensus size: 73
10131488 AAAATGACAT
** * *
10131498 TCGTGATCGTAAATCAGTGAATTGTTAGAAAAGCGAAAGTTGTGGTTGTAAATAAACGAATTGTA
1 TCGTGATCGTAAATCAACGAATTGTTAGAAAAGCGAAAGTTGTGATTGTAAATAAACGAATCGTA
10131563 AGAATAAA
66 AGAATAAA
* * *
10131571 TTGTGATCGTAAATCAACGAATTGTTAGAAAATC-AAAGGTTGTGATTGTAAATCAACGAATCGT
1 TCGTGATCGTAAATCAACGAATTGTTAGAAAAGCGAAA-GTTGTGATTGTAAATAAACGAATCGT
10131635 AAGAATAAA
65 AAGAATAAA
*
10131644 TCGTGATCGTAAATTAACGA
1 TCGTGATCGTAAATCAACGA
10131664 GCTTTAAAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
72 3 0.04
73 80 0.96
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (73 bp):
TCGTGATCGTAAATCAACGAATTGTTAGAAAAGCGAAAGTTGTGATTGTAAATAAACGAATCGTA
AGAATAAA
Found at i:10131748 original size:182 final size:182
Alignment explanation
Indices: 10131389--10131769 Score: 437
Period size: 182 Copynumber: 2.1 Consensus size: 182
10131379 AAAATGACAG
*
10131389 TCGTGATTGTAAATCAGCGAATTGTTAGAAAATCGAAAGTTGTGATTGTAAATCAACATATCATA
1 TCGTGATTGTAAATCAACGAATTGTTAGAAAATCGAAAGTTGTGATTGTAAATCAACATATCATA
* * * * **
10131454 AGAATAAGCCGTGATAATAAATCAAGGAGCTTTAAAAATGACATTCGTGATCGTAAATCAGTGAA
66 AGAATAAACCGTGATAATAAATCAACGAGCTTTAAAAATGAAATTCGTGATAGTAAATCAACGAA
* * ** **** **
10131519 TTGTTAGAAAAGCGAAAGTTGTGGTTGTAAATAAACGAATTGTAAGAATAAA
131 CTGTTAGAAAACCGAAAGTCATGACCATAAATAAACGAACCGTAAGAATAAA
* * *
10131571 TTGTGATCGTAAATCAACGAATTGTTAGAAAATC-AAAGGTTGTGATTGTAAATCAACGA-ATCG
1 TCGTGATTGTAAATCAACGAATTGTTAGAAAATCGAAA-GTTGTGATTGTAAATCAAC-ATATCA
* ** *
10131634 TAAGAATAAATCGTGATCGTAAATTAACGAGCTTTAAAAATGATAATT-GTGATAGTAAATCAAC
64 TAAGAATAAACCGTGATAATAAATCAACGAGCTTTAAAAATGA-AATTCGTGATAGTAAATCAAC
* * * * *
10131698 GAACTGTTATAAAACCGAAGGTCATGACCATAAATCAGC-AGACCGTAAGAATAAG
128 GAACTGTTAGAAAACCGAAAGTCATGACCATAAATAAACGA-ACCGTAAGAATAAA
10131753 TCGTGATTGTAAATCAA
1 TCGTGATTGTAAATCAA
10131770 TGAGCTTTAA
Statistics
Matches: 164, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
181 4 0.02
182 156 0.95
183 4 0.02
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (182 bp):
TCGTGATTGTAAATCAACGAATTGTTAGAAAATCGAAAGTTGTGATTGTAAATCAACATATCATA
AGAATAAACCGTGATAATAAATCAACGAGCTTTAAAAATGAAATTCGTGATAGTAAATCAACGAA
CTGTTAGAAAACCGAAAGTCATGACCATAAATAAACGAACCGTAAGAATAAA
Found at i:10131971 original size:109 final size:109
Alignment explanation
Indices: 10131571--10131983 Score: 479
Period size: 109 Copynumber: 3.8 Consensus size: 109
10131561 TAAGAATAAA
* * * * * *
10131571 TTGTGATCGTAAATCAACGAATTGTTAGAAAATCAAAGGTTGTGATTGTAAATCAACGAATCGTA
1 TTGTGATCGTAAATCAACGAACTGTTAGAAAACCGAAGGTTGTGATCGTAAATCAGCGAACCGTA
** * * * *
10131636 AGAATAAATCGTGATCGTAAATTAACGAGCTTTAAAAATGATAA
66 AGAATAAGCCATGATCGTAAATCAACGAGCTTTAAAAATGACAG
* * ** * *
10131680 TTGTGATAGTAAATCAACGAACTGTTATAAAACCGAAGGTCATGACCATAAATCAGC-AGACCGT
1 TTGTGATCGTAAATCAACGAACTGTTAGAAAACCGAAGGTTGTGATCGTAAATCAGCGA-ACCGT
* * * *
10131744 AAGAATAAGTCGTGATTGTAAATCAATGAGCTTTAAAAATGACAG
65 AAGAATAAGCCATGATCGTAAATCAACGAGCTTTAAAAATGACAG
* * * * * *
10131789 TTGTGATCATAAATCAGCGAACTATTAGAAAACCGAA-GTTCGTGATTGTAAATTAGCGAACTGT
1 TTGTGATCGTAAATCAACGAACTGTTAGAAAACCGAAGGTT-GTGATCGTAAATCAGCGAACCGT
*
10131853 AAGAATAAGCCATGATTGTAAATCAACGAGCTTTAAAAATGACAG
65 AAGAATAAGCCATGATCGTAAATCAACGAGCTTTAAAAATGACAG
* * * * * *
10131898 TTGTGATCGTAAATTAATGAACTGTTAGAAAACTGAAGGTTGTGATCGTAAATTAGTGGACCGTA
1 TTGTGATCGTAAATCAACGAACTGTTAGAAAACCGAAGGTTGTGATCGTAAATCAGCGAACCGTA
10131963 AGAATAAGCCATGATCGTAAA
66 AGAATAAGCCATGATCGTAAA
10131984 AATGACAATT
Statistics
Matches: 256, Mismatches: 44, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
108 3 0.01
109 249 0.97
110 4 0.02
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.27
Consensus pattern (109 bp):
TTGTGATCGTAAATCAACGAACTGTTAGAAAACCGAAGGTTGTGATCGTAAATCAGCGAACCGTA
AGAATAAGCCATGATCGTAAATCAACGAGCTTTAAAAATGACAG
Found at i:10132129 original size:164 final size:164
Alignment explanation
Indices: 10131830--10132147 Score: 429
Period size: 164 Copynumber: 1.9 Consensus size: 164
10131820 ACCGAAGTTC
* * *
10131830 GTGATTGTAAATTAGCGAACTGTAAGAATAAGCCATGATTGTAAATCAACGAGCTTTAAAAATGA
1 GTGATCGTAAATCAGCGAACTGTAAGAATAAGCCATGATCGTAAATCAACGAGCTTTAAAAATGA
* * * * ** ** * *
10131895 CAGTTGTGATCGTAAATTAATGAACTGTTAGAAAACTGAAGGTTGTGATCGTAAATTAGTGGACC
66 CAATCGTGATCGTAAATTAACGAACTATTAGAAAACCAAAGGTCATGATCATAAATCAGTGGACC
10131960 GTAAGAATAAGCCATGATCGTAAAAATGACAATT
131 GTAAGAATAAGCCATGATCGTAAAAATGACAATT
* * * *
10131994 GTGATCGTAAATCAGTGGACTGTAAGAATAAGCCGTGGTCGTAAATCAACGAGCTTTAAAAATGA
1 GTGATCGTAAATCAGCGAACTGTAAGAATAAGCCATGATCGTAAATCAACGAGCTTTAAAAATGA
* * * *
10132059 CAATCGTGATCGTAAATTAGCGGACTATTAGAAAACCAAAGGTCATGATCATAAATCATTGGATC
66 CAATCGTGATCGTAAATTAACGAACTATTAGAAAACCAAAGGTCATGATCATAAATCAGTGGACC
* *
10132124 GTAAGAATAAGTCGTGATCGTAAA
131 GTAAGAATAAGCCATGATCGTAAA
10132148 TCAGCAAGCC
Statistics
Matches: 131, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
164 131 1.00
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.27
Consensus pattern (164 bp):
GTGATCGTAAATCAGCGAACTGTAAGAATAAGCCATGATCGTAAATCAACGAGCTTTAAAAATGA
CAATCGTGATCGTAAATTAACGAACTATTAGAAAACCAAAGGTCATGATCATAAATCAGTGGACC
GTAAGAATAAGCCATGATCGTAAAAATGACAATT
Found at i:10138915 original size:16 final size:16
Alignment explanation
Indices: 10138881--10138933 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
10138871 ATGGCATCAG
10138881 TCATGCAATACTCAAT
1 TCATGCAATACTCAAT
*
10138897 TCATG-AATACATCATT
1 TCATGCAATAC-TCAAT
* * *
10138913 TCATACCACACTCAAT
1 TCATGCAATACTCAAT
10138929 TCATG
1 TCATG
10138934 AGTATATAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 5 0.17
16 21 0.72
17 3 0.10
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.32
Consensus pattern (16 bp):
TCATGCAATACTCAAT
Found at i:10140699 original size:44 final size:44
Alignment explanation
Indices: 10140649--10140798 Score: 177
Period size: 42 Copynumber: 3.5 Consensus size: 44
10140639 TATGTGTTTT
* *
10140649 CGTGTAAGACCACT-TCTGGGACGTTGGCATAGATATTGTGATTA
1 CGTGTAAGACCACTGTCTGGGACATTGGCATCGATATT-TGATTA
* *
10140693 CGTGTAAGACCA-TGTTTGGGACATTGGCATCG-TATTTGATTT
1 CGTGTAAGACCACTGTCTGGGACATTGGCATCGATATTTGATTA
* *
10140735 TGTGTAAGACC-CTGTCT-GGACAATGGCATCGATATTTGATTA
1 CGTGTAAGACCACTGTCTGGGACATTGGCATCGATATTTGATTA
* *
10140777 CATGTAAGACCAC-GTTTGGGAC
1 CGTGTAAGACCACTGTCTGGGAC
10140799 GTTGACATTG
Statistics
Matches: 90, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
41 13 0.14
42 40 0.44
43 10 0.11
44 27 0.30
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.33
Consensus pattern (44 bp):
CGTGTAAGACCACTGTCTGGGACATTGGCATCGATATTTGATTA
Found at i:10144097 original size:5 final size:5
Alignment explanation
Indices: 10144087--10144111 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
10144077 TAAATTGTTT
10144087 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
10144112 CCTAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:10147755 original size:12 final size:12
Alignment explanation
Indices: 10147722--10147755 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
10147712 AAAAAATATA
10147722 TTAAAACAATTC
1 TTAAAACAATTC
10147734 TTAAAACAATTC
1 TTAAAACAATTC
10147746 TTAAAACAAT
1 TTAAAACAAT
10147756 ACACAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (12 bp):
TTAAAACAATTC
Found at i:10148347 original size:31 final size:31
Alignment explanation
Indices: 10148306--10148393 Score: 126
Period size: 31 Copynumber: 2.8 Consensus size: 31
10148296 AACACAAGGG
10148306 GTCACGCCTAGGGAAGAGGCGGCATCC-CCTA
1 GTCACGCCTAGGGAAGAGGCGGCA-CCTCCTA
* *
10148337 GTCACACCTAGGGAAGAGGCGGCACCTCCTG
1 GTCACGCCTAGGGAAGAGGCGGCACCTCCTA
10148368 GTCACGCCTAGGGCAA-AGGCGGCACC
1 GTCACGCCTAGGG-AAGAGGCGGCACC
10148394 ACTGGTGACG
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
30 2 0.04
31 48 0.92
32 2 0.04
ACGTcount: A:0.23, C:0.33, G:0.33, T:0.11
Consensus pattern (31 bp):
GTCACGCCTAGGGAAGAGGCGGCACCTCCTA
Found at i:10151855 original size:8 final size:8
Alignment explanation
Indices: 10151842--10151873 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
10151832 AGATTAATTG
10151842 CAACATTA
1 CAACATTA
10151850 CAACATTA
1 CAACATTA
10151858 CAACATTA
1 CAACATTA
*
10151866 TAACATTA
1 CAACATTA
10151874 AAACTTGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (8 bp):
CAACATTA
Found at i:10151927 original size:62 final size:62
Alignment explanation
Indices: 10151860--10152151 Score: 478
Period size: 62 Copynumber: 4.7 Consensus size: 62
10151850 CAACATTACA
* *
10151860 ACATTATAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTT-TTAATATAAATTAAAT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTT-ATATAAATTAAAT
* * *
10151922 ACATTACAATATTAAAAATTAGAACAAACTTTCTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
*
10151984 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATAGAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
** *
10152046 ACATTACGGCATTAAAAATTGGAACAAACTTTGTAATAGAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
*
10152108 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATT
10152152 AGGTACATTG
Statistics
Matches: 214, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
62 212 0.99
63 2 0.01
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (62 bp):
ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
Found at i:10154271 original size:46 final size:45
Alignment explanation
Indices: 10154128--10154271 Score: 112
Period size: 46 Copynumber: 3.1 Consensus size: 45
10154118 CCCACCCATA
* * *
10154128 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCT
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCA--AATATCT
* * * * * *** *
10154175 CA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGCTCG--GATGCCCAAATATCT
10154221 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAAATATTCT
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAAATA-TCT
10154267 AGTGA
1 AGTGA
10154272 CATGTCACTT
Statistics
Matches: 74, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
44 6 0.08
45 2 0.03
46 31 0.42
47 30 0.41
48 1 0.01
49 4 0.05
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAAATATCT
Found at i:10157922 original size:47 final size:47
Alignment explanation
Indices: 10157844--10158428 Score: 927
Period size: 47 Copynumber: 12.3 Consensus size: 47
10157834 CCCTTCGAGA
* * * * * *
10157844 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
10157891 CCTGTCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10157938 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10157985 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10158032 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10158081 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10158128 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10158175 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10158224 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10158271 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10158320 CTTATCAAATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10158367 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10158414 CTTATCAAATATATA
1 CTTATCACATATATA
10158429 TCGTTTTACA
Statistics
Matches: 504, Mismatches: 28, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
47 371 0.74
49 133 0.26
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:10158090 original size:22 final size:22
Alignment explanation
Indices: 10158062--10158137 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
10158052 TTTCACATTC
10158062 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
10158084 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
10158108 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
10158131 ATCACAT
1 ATCACAT
10158138 ATATACACTT
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 18 0.46
23 5 0.13
24 5 0.13
25 11 0.28
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:10158429 original size:96 final size:94
Alignment explanation
Indices: 10157844--10158428 Score: 927
Period size: 96 Copynumber: 6.2 Consensus size: 94
10157834 CCCTTCGAGA
* * * * * * * *
10157844 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
10157909 TTTCACATTCATCACATCGGCGATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
*
10157938 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
10158003 TTTCACATTCATCACATCGGCTATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* *
10158032 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
* *
10158097 ACTTTCACATTCATCACATTGGCCATTCGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
10158128 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
* *
10158193 ACTTTCACATTCATCACATTGGCCATTCGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
10158224 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
* *
10158289 ACTTTCACATTCATCACATTGGCCATTCGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
*
10158320 CTTATCAAATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
10158385 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
*
10158414 CTTATCAAATATATA
1 CTTATCACATATATA
10158429 TCGTTTTACA
Statistics
Matches: 466, Mismatches: 21, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
94 189 0.41
96 277 0.59
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:10158429 original size:143 final size:143
Alignment explanation
Indices: 10157844--10158428 Score: 944
Period size: 143 Copynumber: 4.1 Consensus size: 143
10157834 CCCTTCGAGA
* * * * * * * *
10157844 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
10157907 ACTTTCACATTCATCACATCGGCGATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
*
10157972 TCGGCTATTAGGC
131 TCGGCCATTAGGC
*
10157985 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
* *
10158050 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
* *
10158115 TTGGCCATTCGGC
131 TCGGCCATTAGGC
10158128 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
* *
10158193 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
10158258 TCGGCCATTAGGC
131 TCGGCCATTAGGC
* *
10158271 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCA-A-ATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
10158334 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
64 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
10158399 CATCGGCCATTAGGC
129 CATCGGCCATTAGGC
*
10158414 CTTATCAAATATATA
1 CTTATCACATATATA
10158429 TCGTTTTACA
Statistics
Matches: 417, Mismatches: 23, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
141 53 0.13
143 319 0.76
144 1 0.00
145 44 0.11
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (143 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:10160230 original size:13 final size:13
Alignment explanation
Indices: 10160212--10160236 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10160202 TACTAAATTT
10160212 TCATGGATTCAAA
1 TCATGGATTCAAA
10160225 TCATGGATTCAA
1 TCATGGATTCAA
10160237 TATACCATTA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAA
Found at i:10163278 original size:30 final size:30
Alignment explanation
Indices: 10163244--10163301 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
10163234 CACGGACTGG
*
10163244 CACATGGGCGTGTGGCCAACCTGTGTGGCT
1 CACATGGGCGTGTGGCCAACCCGTGTGGCT
*
10163274 CACATGGGCGTGTGGCCATCCCGTGTGG
1 CACATGGGCGTGTGGCCAACCCGTGTGG
10163302 AAATGCCCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.12, C:0.28, G:0.38, T:0.22
Consensus pattern (30 bp):
CACATGGGCGTGTGGCCAACCCGTGTGGCT
Found at i:10172689 original size:62 final size:62
Alignment explanation
Indices: 10172600--10172717 Score: 218
Period size: 62 Copynumber: 1.9 Consensus size: 62
10172590 AGAATCCCAG
* *
10172600 GAAACATAGAATCACTAAACCTGGCTTTGATACCACTCTTTGTCAAGCCTCATTAATCCTAA
1 GAAACATAGAATCACAAAACCTGGCTTTGATACCACTCTTTGTCAAGCCTAATTAATCCTAA
10172662 GAAACATAGAATCACAAAACCTGGCTTTGATACCACTCTTTGTCAAGCCTAATTAA
1 GAAACATAGAATCACAAAACCTGGCTTTGATACCACTCTTTGTCAAGCCTAATTAA
10172718 ACGAGGTGAC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.28
Consensus pattern (62 bp):
GAAACATAGAATCACAAAACCTGGCTTTGATACCACTCTTTGTCAAGCCTAATTAATCCTAA
Found at i:10182194 original size:5 final size:5
Alignment explanation
Indices: 10182184--10182215 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
10182174 TTGTGTGTTC
10182184 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
10182216 TTCACACTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:10182198 original size:9 final size:9
Alignment explanation
Indices: 10182184--10182214 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
10182174 TTGTGTGTTC
10182184 TTTATTTTA
1 TTTATTTTA
10182193 TTTATTTTA
1 TTTATTTTA
10182202 TTTTATTTTA
1 -TTTATTTTA
10182212 TTT
1 TTT
10182215 TTTCACACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:10183081 original size:68 final size:71
Alignment explanation
Indices: 10182987--10183122 Score: 183
Period size: 72 Copynumber: 1.9 Consensus size: 71
10182977 TAATAGATTT
*
10182987 AATATTAAATTTAATTTAATACTTATC-T-T-A-ATAGGATTTTATTAATTTAATATTAAAGTGA
1 AATATTAAATTTAATTTAATACTTATCTTGTAAGATA-GATTTTATTAATTTAATATTAAAATGA
10183048 TTATCTG
65 TTATCTG
* *
10183055 AATATTGAATTTAATTTAAT-CTTTATCTTGTAGAGATATATTTTATTAATTTAATATTAAAATG
1 AATATTAAATTTAATTTAATAC-TTATCTTGTA-AGATAGATTTTATTAATTTAATATTAAAATG
10183119 ATTA
64 ATTA
10183123 AGTTTAATTA
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
67 1 0.02
68 24 0.41
69 1 0.02
70 1 0.02
72 29 0.49
73 3 0.05
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (71 bp):
AATATTAAATTTAATTTAATACTTATCTTGTAAGATAGATTTTATTAATTTAATATTAAAATGAT
TATCTG
Found at i:10183587 original size:18 final size:18
Alignment explanation
Indices: 10183561--10183598 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
10183551 AATTTACCCA
*
10183561 TATTTTTAAAGTTAAT-TT
1 TATTGTTAAA-TTAATATT
10183579 TATTGTTAAATTAATATT
1 TATTGTTAAATTAATATT
10183597 TA
1 TA
10183599 GTTTTTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (18 bp):
TATTGTTAAATTAATATT
Found at i:10188498 original size:25 final size:25
Alignment explanation
Indices: 10188461--10188509 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
10188451 GTGTTATACA
10188461 GAGAGCATAAATGTGCTAATAATCG
1 GAGAGCATAAATGTGCTAATAATCG
10188486 GAGAGCAGT-AATGTGCTAATAATC
1 GAGAGCA-TAAATGTGCTAATAATC
10188510 AAAGAGTGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (25 bp):
GAGAGCATAAATGTGCTAATAATCG
Found at i:10188515 original size:25 final size:25
Alignment explanation
Indices: 10188462--10188515 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
10188452 TGTTATACAG
**
10188462 AGAGCATAAATGTGCTAATAATCGG
1 AGAGCATAAATGTGCTAATAATCAA
10188487 AGAGCAGT-AATGTGCTAATAATCAA
1 AGAGCA-TAAATGTGCTAATAATCAA
10188512 AGAG
1 AGAG
10188516 TGCGCTAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (25 bp):
AGAGCATAAATGTGCTAATAATCAA
Found at i:10188896 original size:25 final size:25
Alignment explanation
Indices: 10188868--10188925 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
10188858 ACCCTAGCGC
** *
10188868 GCTCTCTGATTATTAGCATGTTAGT
1 GCTCTCTGATTATTAGCACATTAAT
10188893 GCTCT-TCGATTATTAGCACATTAAT
1 GCTCTCT-GATTATTAGCACATTAAT
10188918 GCTCTCTG
1 GCTCTCTG
10188926 TATAACACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.04
25 26 0.93
26 1 0.04
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACATTAAT
Found at i:10193279 original size:15 final size:15
Alignment explanation
Indices: 10193259--10193287 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10193249 TTGATTAAAA
10193259 TGTAAGTATTTATGC
1 TGTAAGTATTTATGC
10193274 TGTAAGTATTTATG
1 TGTAAGTATTTATG
10193288 TTGTCTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.48
Consensus pattern (15 bp):
TGTAAGTATTTATGC
Found at i:10195107 original size:83 final size:83
Alignment explanation
Indices: 10194968--10195136 Score: 338
Period size: 83 Copynumber: 2.0 Consensus size: 83
10194958 ATAAAAGATA
10194968 AAAGAAATTTAGTAAAGGAAGAAAAAGAGTGCAAGGAAAAAATAAATGGATAATGGAACATTTAG
1 AAAGAAATTTAGTAAAGGAAGAAAAAGAGTGCAAGGAAAAAATAAATGGATAATGGAACATTTAG
10195033 CACATTAAATATGTGTTT
66 CACATTAAATATGTGTTT
10195051 AAAGAAATTTAGTAAAGGAAGAAAAAGAGTGCAAGGAAAAAATAAATGGATAATGGAACATTTAG
1 AAAGAAATTTAGTAAAGGAAGAAAAAGAGTGCAAGGAAAAAATAAATGGATAATGGAACATTTAG
10195116 CACATTAAATATGTGTTT
66 CACATTAAATATGTGTTT
10195134 AAA
1 AAA
10195137 AATAATAAAG
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 86 1.00
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.24
Consensus pattern (83 bp):
AAAGAAATTTAGTAAAGGAAGAAAAAGAGTGCAAGGAAAAAATAAATGGATAATGGAACATTTAG
CACATTAAATATGTGTTT
Found at i:10195558 original size:16 final size:16
Alignment explanation
Indices: 10195503--10195558 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
10195493 ACAACTGAAT
10195503 TATT-CATTACAAG-TC
1 TATTCCATTAC-AGCTC
* *
10195518 TATTCTATTACAACTC
1 TATTCCATTACAGCTC
*
10195534 TATTACATTACAGCTC
1 TATTCCATTACAGCTC
10195550 TATTCCATT
1 TATTCCATT
10195559 CCTCCCAACC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 5 0.15
16 28 0.85
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.43
Consensus pattern (16 bp):
TATTCCATTACAGCTC
Found at i:10203885 original size:37 final size:37
Alignment explanation
Indices: 10203835--10203909 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
10203825 GCCGCTCCCG
10203835 TGTACCTGCACTTAAACAAACTGAAGGTTCTGTGGTC
1 TGTACCTGCACTTAAACAAACTGAAGGTTCTGTGGTC
*
10203872 TGTACCTGCACTTAAACAAACTGAAGGTTCTGTTGTC
1 TGTACCTGCACTTAAACAAACTGAAGGTTCTGTGGTC
10203909 T
1 T
10203910 CCTTAAATCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (37 bp):
TGTACCTGCACTTAAACAAACTGAAGGTTCTGTGGTC
Found at i:10208274 original size:21 final size:21
Alignment explanation
Indices: 10208236--10208275 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
10208226 TTTTTCTGTT
*
10208236 TTGAAAATTAAAATTTTAATA
1 TTGAAAATAAAAATTTTAATA
10208257 TTGAAAA-AAAAATATTTAA
1 TTGAAAATAAAAAT-TTTAA
10208276 AATTTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
TTGAAAATAAAAATTTTAATA
Found at i:10211289 original size:41 final size:40
Alignment explanation
Indices: 10211225--10211418 Score: 192
Period size: 41 Copynumber: 4.8 Consensus size: 40
10211215 TTTTAAACCT
* *
10211225 TTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCATATCA
1 TTAGCGGCGTTTTTATCTAAGCGCCACTAATGCTC-TATCA
* * * * *
10211266 TTAGTGGCGTTTTTATCTGAGCGCCACTAATTCTCTGTTCT
1 TTAGCGGCGTTTTTATCTAAGCGCCACTAATGCTCT-ATCA
* *
10211307 TTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGTATCA
1 TTAGCGGCGTTTTTATCTAAGCGCCACTAATGCTC-TATCA
* * * * *
10211348 TTAGTGGCGTTTTTATCTGAGCGCCACTAATTCTCTGTTCT
1 TTAGCGGCGTTTTTATCTAAGCGCCACTAATGCTCT-ATCA
* *
10211389 TTAGCGGCATTTTT-TGCTAAGCGCCGCTAA
1 TTAGCGGCGTTTTTAT-CTAAGCGCCACTAA
10211419 AGTTCGTGTT
Statistics
Matches: 124, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
40 3 0.02
41 120 0.97
42 1 0.01
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (40 bp):
TTAGCGGCGTTTTTATCTAAGCGCCACTAATGCTCTATCA
Found at i:10211360 original size:82 final size:82
Alignment explanation
Indices: 10211223--10211418 Score: 358
Period size: 82 Copynumber: 2.4 Consensus size: 82
10211213 TTTTTTAAAC
10211223 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCATATCATTAGTGGCGTTTTTATCTGAGC
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCATATCATTAGTGGCGTTTTTATCTGAGC
10211288 GCCACTAATTCTCTGTT
66 GCCACTAATTCTCTGTT
*
10211305 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGTATCATTAGTGGCGTTTTTATCTGAGC
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCATATCATTAGTGGCGTTTTTATCTGAGC
10211370 GCCACTAATTCTCTGTT
66 GCCACTAATTCTCTGTT
*
10211387 CTTTAGCGGCATTTTT-TGCTAAGCGCCGCTAA
1 CTTTAGCGGCGTTTTTGT-CTAAGCGCCGCTAA
10211419 AGTTCGTGTT
Statistics
Matches: 111, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
81 1 0.01
82 110 0.99
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.38
Consensus pattern (82 bp):
CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCATATCATTAGTGGCGTTTTTATCTGAGC
GCCACTAATTCTCTGTT
Found at i:10211654 original size:82 final size:82
Alignment explanation
Indices: 10211558--10211734 Score: 336
Period size: 82 Copynumber: 2.2 Consensus size: 82
10211548 GTGTACTCTA
10211558 TTAGTGGCGTTTTAAGGGAAAACGCCGCAAATATGTCTACAATTTTGTGAAAACGTCACCGTTTC
1 TTAGTGGCGTTTTAAGGGAAAACGCCGCAAATATGTCTACAATTTTGTGAAAACGTCACCGTTTC
*
10211623 TTTCTGTAATTGAAAAT
66 TTTCTGTAATTGAAAAG
*
10211640 TTAGTGGCGTTTTAAGGTAAAACGCCGCAAATATGTCTACAATTTTGTGAAAACGTCACCGTTTC
1 TTAGTGGCGTTTTAAGGGAAAACGCCGCAAATATGTCTACAATTTTGTGAAAACGTCACCGTTTC
10211705 TTTCTGTAATTGAAAAG
66 TTTCTGTAATTGAAAAG
10211722 TTAGTGGCGTTTT
1 TTAGTGGCGTTTT
10211735 TTCCGGTAGC
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 93 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (82 bp):
TTAGTGGCGTTTTAAGGGAAAACGCCGCAAATATGTCTACAATTTTGTGAAAACGTCACCGTTTC
TTTCTGTAATTGAAAAG
Found at i:10212655 original size:8 final size:10
Alignment explanation
Indices: 10212633--10212669 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
10212623 TATTTTTACT
10212633 TATATATGGA
1 TATATATGGA
*
10212643 TATATATGAA
1 TATATATGGA
10212653 TATATATGGA
1 TATATATGGA
10212663 TATATAT
1 TATATAT
10212670 ATAGTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (10 bp):
TATATATGGA
Found at i:10212778 original size:27 final size:27
Alignment explanation
Indices: 10212737--10212788 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
10212727 AATAAACAAA
* *
10212737 TAAATAAGTTAGTAATTATTTATTTGT
1 TAAATAAATTAGTAATTAATTATTTGT
*
10212764 TAAATAAATTGGTAATTAATTATTT
1 TAAATAAATTAGTAATTAATTATTT
10212789 AAAAGTAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (27 bp):
TAAATAAATTAGTAATTAATTATTTGT
Found at i:10215144 original size:74 final size:74
Alignment explanation
Indices: 10215066--10215212 Score: 294
Period size: 74 Copynumber: 2.0 Consensus size: 74
10215056 AATAAAATAT
10215066 AAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTAA
1 AAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTAA
10215131 TAATTATAA
66 TAATTATAA
10215140 AAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTAA
1 AAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTAA
10215205 TAATTATA
66 TAATTATA
10215213 TTAGTAATGT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (74 bp):
AAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTATTAA
TAATTATAA
Found at i:10215277 original size:19 final size:19
Alignment explanation
Indices: 10215253--10215479 Score: 100
Period size: 19 Copynumber: 12.5 Consensus size: 19
10215243 TATTAAATAA
10215253 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
*
10215272 TACATAAT-ACATT-TAACT
1 TACATAATAAC-TTACAACT
*
10215290 TACAT--T-ACTTACATA-A
1 TACATAATAACTTACA-ACT
10215306 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
10215325 TACATAATACATTTAACTTACAACT
1 TAC---ATA-A--TAACTTACAACT
**
10215350 TACATAAT-ACATT-TGACT
1 TACATAATAAC-TTACAACT
* *
10215368 GACATAAT-ACATT-TAACT
1 TACATAATAAC-TTACAACT
* *
10215386 TACA-ACTTAC--ACAA--
1 TACATAATAACTTACAACT
10215400 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
* *
10215419 TACATAAT-ACATAATAACT
1 TACATAATAAC-TTACAACT
* *
10215438 TACA-ACTTAC--ACAA--
1 TACATAATAACTTACAACT
10215452 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
10215471 TACATAATA
1 TACATAATA
10215480 CATAATAACT
Statistics
Matches: 161, Mismatches: 19, Indels: 56
0.68 0.08 0.24
Matches are distributed among these distances:
14 8 0.05
15 10 0.06
16 14 0.09
17 11 0.07
18 43 0.27
19 52 0.32
21 1 0.01
22 6 0.04
23 1 0.01
25 15 0.09
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.33
Consensus pattern (19 bp):
TACATAATAACTTACAACT
Found at i:10215291 original size:18 final size:18
Alignment explanation
Indices: 10215268--10215389 Score: 74
Period size: 18 Copynumber: 6.4 Consensus size: 18
10215258 AATAACTTAC
10215268 AACTTACATAATACATTT
1 AACTTACATAATACATTT
*
10215286 AACTTACATTACTTACA--T
1 AACTTACA-TA-ATACATTT
*
10215304 AA--TACATAATA-ACTTAC
1 AACTTACATAATACA-TT-T
10215321 AACTTACATAATACATTTAACTT
1 AACTTACATAATACA--T---TT
10215344 ACAACTTACATAATACATTT
1 --AACTTACATAATACATTT
* *
10215364 GACTGACATAATACATTT
1 AACTTACATAATACATTT
10215382 AACTTACA
1 AACTTACA
10215390 ACTTACACAA
Statistics
Matches: 80, Mismatches: 9, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
13 1 0.01
14 2 0.03
15 2 0.03
16 4 0.05
17 2 0.03
18 33 0.41
19 11 0.14
20 7 0.09
21 1 0.01
23 1 0.01
24 1 0.01
25 15 0.19
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:10215332 original size:26 final size:26
Alignment explanation
Indices: 10215249--10215654 Score: 579
Period size: 26 Copynumber: 16.1 Consensus size: 26
10215239 ATTTTATTAA
10215249 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
10215275 ATAATACAT-TTAACTTACATTACTTAC
1 ATAATACATAATAACTTACA--ACTTAC
10215302 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
10215328 ATAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
10215353 ATAATAC---AT---TT--GACTGAC
1 ATAATACATAATAACTTACAACTTAC
*
10215371 ATAATACATT-TAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
10215396 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
10215422 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
10215448 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
10215474 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
10215500 ATAATACAT-TTAACTTGCAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
10215525 ACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
10215551 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
*
10215577 ATAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
* *
10215602 ACAATACAT-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
10215627 ATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTAC
10215653 AT
1 AT
10215655 TTAACTTACA
Statistics
Matches: 343, Mismatches: 23, Indels: 28
0.87 0.06 0.07
Matches are distributed among these distances:
18 12 0.03
20 3 0.01
23 3 0.01
25 113 0.33
26 188 0.55
27 15 0.04
28 9 0.03
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (26 bp):
ATAATACATAATAACTTACAACTTAC
Found at i:10215500 original size:19 final size:19
Alignment explanation
Indices: 10215426--10215556 Score: 65
Period size: 19 Copynumber: 7.5 Consensus size: 19
10215416 ACTTACATAA
10215426 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
* * *
10215445 TACACAAT-ACATAATAACT
1 TACATAATAAC-TTACAACT
*
10215464 TAC-----AACTTACATA-A
1 TACATAATAACTTACA-ACT
10215478 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
*
10215497 TACATAAT-ACATT-TAACT
1 TACATAATAAC-TTACAACT
* * *
10215515 TGCA-ACTTAC--ACAA--
1 TACATAATAACTTACAACT
10215529 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
10215548 TACATAATA
1 TACATAATA
10215557 CATAATAACT
Statistics
Matches: 81, Mismatches: 14, Indels: 34
0.63 0.11 0.26
Matches are distributed among these distances:
14 9 0.11
15 7 0.09
16 2 0.02
17 6 0.07
18 14 0.17
19 43 0.53
ACGTcount: A:0.48, C:0.21, G:0.01, T:0.31
Consensus pattern (19 bp):
TACATAATAACTTACAACT
Found at i:10215530 original size:77 final size:76
Alignment explanation
Indices: 10215373--10215654 Score: 492
Period size: 77 Copynumber: 3.7 Consensus size: 76
10215363 TGACTGACAT
* * *
10215373 AATACATTTAACTTACAACTTACACAATACATAATAACTTACAACTTACATAATACATAATAACT
1 AATACATATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACAT-TTAACT
10215438 TACAACTTACAC
65 TACAACTTACAC
10215450 AATACATAATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACT
1 AATACAT-ATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACT
*
10215515 TGCAACTTACAC
65 TACAACTTACAC
10215527 AATACATAATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACT
1 AATACAT-ATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACT
10215592 TACAACTTACAC
65 TACAACTTACAC
*
10215604 AATACATTTAACTTACAACTTACATAATACATAATAACTTACAACTTACAT
1 AATACATATAACTTACAACTTACATAATACATAATAACTTACAACTTACAT
10215655 TTAACTTACA
Statistics
Matches: 198, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
76 43 0.22
77 106 0.54
78 49 0.25
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (76 bp):
AATACATATAACTTACAACTTACATAATACATAATAACTTACAACTTACATAATACATTTAACTT
ACAACTTACAC
Found at i:10215662 original size:11 final size:10
Alignment explanation
Indices: 10215646--10215699 Score: 55
Period size: 9 Copynumber: 5.7 Consensus size: 10
10215636 AATAACTTAC
10215646 AACTTACATTT
1 AACTTACA-TT
10215657 AACTTACA-T
1 AACTTACATT
10215666 AA--TACATTT
1 AACTTACA-TT
10215675 AACTTACA-T
1 AACTTACATT
10215684 AACTTACA-T
1 AACTTACATT
10215693 AACTTAC
1 AACTTAC
10215700 CATTGCAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 4 0.10
9 23 0.59
11 12 0.31
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (10 bp):
AACTTACATT
Found at i:10215683 original size:18 final size:18
Alignment explanation
Indices: 10215620--10215685 Score: 89
Period size: 18 Copynumber: 3.6 Consensus size: 18
10215610 TTTAACTTAC
*
10215620 AACTTACATAATACATAAT
1 AACTTACATAATACAT-TT
*
10215639 AACTTACA-ACTTACATTT
1 AACTTACATA-ATACATTT
10215657 AACTTACATAATACATTT
1 AACTTACATAATACATTT
10215675 AACTTACATAA
1 AACTTACATAA
10215686 CTTACATAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 28 0.67
19 14 0.33
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:10215695 original size:18 final size:18
Alignment explanation
Indices: 10215535--10215699 Score: 69
Period size: 18 Copynumber: 9.5 Consensus size: 18
10215525 ACAATACATA
10215535 ATAACTTAC--AACTTAC
1 ATAACTTACATAACTTAC
*
10215551 ATAATACATA-ATAACTTAC
1 AT-A-ACTTACATAACTTAC
10215570 --AACTTACATAA--TAC
1 ATAACTTACATAACTTAC
10215584 ATTTAACTTAC--AACTTAC
1 A--TAACTTACATAACTTAC
*
10215602 ACAA--TACATTTAACTTAC
1 ATAACTTACA--TAACTTAC
*
10215620 --AACTTACATAATACATA-
1 ATAACTTACAT-A-ACTTAC
10215637 ATAACTTAC--AACTTAC
1 ATAACTTACATAACTTAC
10215653 ATTTAACTTACATAA--TAC
1 A--TAACTTACATAACTTAC
10215671 ATTTAACTTACATAACTTAC
1 A--TAACTTACATAACTTAC
10215691 ATAACTTAC
1 ATAACTTAC
10215700 CATTGCAATT
Statistics
Matches: 116, Mismatches: 5, Indels: 54
0.66 0.03 0.31
Matches are distributed among these distances:
14 6 0.05
15 8 0.07
16 16 0.14
17 2 0.02
18 64 0.55
19 14 0.12
20 6 0.05
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAACTTACATAACTTAC
Found at i:10221172 original size:21 final size:21
Alignment explanation
Indices: 10221146--10221216 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
10221136 CTACAACTTA
* *
10221146 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
10221167 AAGCAGCGACTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* * *
10221188 AAGCGGAGGCTGCAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGGG
10221209 AAGCAGAG
1 AAGCAGAG
10221217 CAGAGCAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.34, C:0.18, G:0.45, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:10221459 original size:14 final size:14
Alignment explanation
Indices: 10221440--10221473 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
10221430 ATTGCTATTG
10221440 GTTGCTTTTGAAAT
1 GTTGCTTTTGAAAT
10221454 GTTGCTTTTGAAAT
1 GTTGCTTTTGAAAT
*
10221468 TTTGCT
1 GTTGCT
10221474 ACAGGAGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.09, G:0.21, T:0.53
Consensus pattern (14 bp):
GTTGCTTTTGAAAT
Found at i:10221638 original size:43 final size:42
Alignment explanation
Indices: 10221525--10221909 Score: 377
Period size: 42 Copynumber: 9.2 Consensus size: 42
10221515 CAAAAATAGT
* * * *
10221525 GGCGTTTTGTATAAAAGCGCCACTAAAGAACATGTTCTTTTGC
1 GGCGTTTT-TTTAAAAACGCCGCTAAAGAACATGTTCTTTAGC
* * *
10221568 GGCG--TTTGTAAAAATGCCACTAAAGAACATGTTCTTTAGC
1 GGCGTTTTTTTAAAAACGCCGCTAAAGAACATGTTCTTTAGC
***** * *
10221608 GGCGATTAGAAAAAAAACGCCGCTAAAGAACATGATCTTTAGT
1 GGCG-TTTTTTTAAAAACGCCGCTAAAGAACATGTTCTTTAGC
* *
10221651 GGCGTTTTCCCTT--AAGCGCCGCTAAAGAACATGTTCTTTAGC
1 GGCGTTTT--TTTAAAAACGCCGCTAAAGAACATGTTCTTTAGC
** * * *
10221693 GGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGT
1 GGCGTTTTTTTAAAAACGCCGCTAAAGAACATGTTCTTTAGC
* *
10221735 GGCATTTTTTTACAAACGCCGCTAAAGAACATGTTCTTTAGC
1 GGCGTTTTTTTAAAAACGCCGCTAAAGAACATGTTCTTTAGC
** * *
10221777 GGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGC
1 GGCGTTTTTTTAAAAACGCCGCTAAAGAACATGTTCTTTAGC
* *
10221819 GGCGTTTTTTCT--AAGCGCCGCTAAAGAACATGATCTTTAGC
1 GGCGTTTTTT-TAAAAACGCCGCTAAAGAACATGTTCTTTAGC
** * * *
10221860 GGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAAC
1 GGCGTTTTTTTAAAAACGCCGCTAAAGAACATGTTCTTTAGC
10221902 GGCGTTTT
1 GGCGTTTT
10221910 GTTTGTAAAC
Statistics
Matches: 295, Mismatches: 37, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
40 37 0.13
41 41 0.14
42 181 0.61
43 36 0.12
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (42 bp):
GGCGTTTTTTTAAAAACGCCGCTAAAGAACATGTTCTTTAGC
Found at i:10221689 original size:42 final size:42
Alignment explanation
Indices: 10221625--10221909 Score: 432
Period size: 42 Copynumber: 6.8 Consensus size: 42
10221615 AGAAAAAAAA
* **
10221625 CGCCGCTAAAGAACATGATCTTTAGTGGCG-TTTTCCCTTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC-TAAG
*
10221667 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* * * *
10221709 CGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTAC-AAA
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-CTAAG
*
10221751 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
10221793 CGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
10221834 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* *
10221876 CGCCGCTAAAGAACATGGTCTTTAACGGCGTTTT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT
10221910 GTTTGTAAAC
Statistics
Matches: 224, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
41 42 0.19
42 176 0.79
43 6 0.03
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
Found at i:10221864 original size:83 final size:83
Alignment explanation
Indices: 10221539--10221909 Score: 449
Period size: 84 Copynumber: 4.4 Consensus size: 83
10221529 TTTTGTATAA
* * * * ** ** *
10221539 AAGCGCCACTAAAGAACATGTTCTTTTGCGGCG-TTTGTAAAAATGCCACTAAAGAACATGTTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCTAAGCGCCGCTAAAGAACATGTTCT
*******
10221603 TTAGCGGCGATTAGAAAAA
66 TTAGCGGCG-TTTTTTTCT
* * **
10221622 AAACGCCGCTAAAGAACATGATCTTTAGTGGCGTTTTCCCTTAAGCGCCGCTAAAGAACATGTTC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTC-TAAGCGCCGCTAAAGAACATGTTC
10221687 TTTAGCGGCGTTTTTTTCT
65 TTTAGCGGCGTTTTTTTCT
* * * *
10221706 AAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTT-TACAAACGCCGCTAAAGAACATGTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCT--AAGCGCCGCTAAAGAACATGTT
10221770 CTTTAGCGGCGTTTTTTTCT
64 CTTTAGCGGCGTTTTTTTCT
*
10221790 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCTAAGCGCCGCTAAAGAACATGATCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCTAAGCGCCGCTAAAGAACATGTTCT
10221855 TTAGCGGCGTTTTTTTCT
66 TTAGCGGCGTTTTTTTCT
* *
10221873 AAGCGCCGCTAAAGAACATGGTCTTTAACGGCGTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT
10221910 GTTTGTAAAC
Statistics
Matches: 251, Mismatches: 32, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
82 1 0.00
83 103 0.41
84 116 0.46
85 31 0.12
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (83 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCTAAGCGCCGCTAAAGAACATGTTCT
TTAGCGGCGTTTTTTTCT
Found at i:10222692 original size:14 final size:14
Alignment explanation
Indices: 10222673--10222700 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10222663 GAAGAAGCTT
10222673 TCGATTATTCCAAA
1 TCGATTATTCCAAA
10222687 TCGATTATTCCAAA
1 TCGATTATTCCAAA
10222701 CAAACATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
TCGATTATTCCAAA
Found at i:10225706 original size:22 final size:23
Alignment explanation
Indices: 10225672--10225715 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
10225662 AATTGTGACA
*
10225672 AAAAAAATCTTTAAGTATCAAATT
1 AAAAAAA-CTTTAAGTACCAAATT
*
10225696 AAAAAAA-TTTATGTACCAAA
1 AAAAAAACTTTAAGTACCAAA
10225716 GTGAGTGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
24 7 0.39
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.30
Consensus pattern (23 bp):
AAAAAAACTTTAAGTACCAAATT
Found at i:10229485 original size:27 final size:26
Alignment explanation
Indices: 10229440--10229501 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
10229430 TATTTTCTCG
10229440 AAATTTTACCAAGGGTAAAATCATCAA
1 AAATTTTACCAAGGGTAAAATCATC-A
* * **
10229467 AAATTTTACCGAGGTTAAAATTGTCA
1 AAATTTTACCAAGGGTAAAATCATCA
10229493 AAATTTTAC
1 AAATTTTAC
10229502 TAGGATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 10 0.32
27 21 0.68
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (26 bp):
AAATTTTACCAAGGGTAAAATCATCA
Found at i:10236427 original size:22 final size:23
Alignment explanation
Indices: 10236400--10236452 Score: 92
Period size: 22 Copynumber: 2.4 Consensus size: 23
10236390 TCTTGTAGTA
10236400 GTCTTCAACACTCCTACTCCCCT
1 GTCTTCAACACTCCTACTCCCCT
10236423 -TCTTCAACACTCCTACTCCCCT
1 GTCTTCAACACTCCTACTCCCCT
10236445 GT-TTCAAC
1 GTCTTCAAC
10236453 GTCTGCAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.19, C:0.45, G:0.04, T:0.32
Consensus pattern (23 bp):
GTCTTCAACACTCCTACTCCCCT
Found at i:10238345 original size:55 final size:55
Alignment explanation
Indices: 10238279--10238390 Score: 197
Period size: 55 Copynumber: 2.0 Consensus size: 55
10238269 ATTATATGGC
* * *
10238279 AGCCTTGTATTTGAAATTTTAAATTCAAATACAAACTACTTGTTCTTATCCTTGA
1 AGCCTTGTATTTGAAATTTGAAATTCAAACACAAACTACTTGATCTTATCCTTGA
10238334 AGCCTTGTATTTGAAATTTGAAATTCAAACACAAACTACTTGATCTTATCCTTGA
1 AGCCTTGTATTTGAAATTTGAAATTCAAACACAAACTACTTGATCTTATCCTTGA
10238389 AG
1 AG
10238391 TTGACGCTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (55 bp):
AGCCTTGTATTTGAAATTTGAAATTCAAACACAAACTACTTGATCTTATCCTTGA
Found at i:10241282 original size:44 final size:44
Alignment explanation
Indices: 10241219--10241307 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
10241209 CTCATAGATG
10241219 TAAGAAAATTGAACTATGTAGACATATCGCAATATTCTTATTTT
1 TAAGAAAATTGAACTATGTAGACATATCGCAATATTCTTATTTT
10241263 TAAGAAAATTGAACTATGTAGACATATCGCAATATTCTTATTTT
1 TAAGAAAATTGAACTATGTAGACATATCGCAATATTCTTATTTT
10241307 T
1 T
10241308 TCTTTATCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.39
Consensus pattern (44 bp):
TAAGAAAATTGAACTATGTAGACATATCGCAATATTCTTATTTT
Found at i:10242866 original size:19 final size:19
Alignment explanation
Indices: 10242826--10242871 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
10242816 CGGAAAATGA
*
10242826 TTTCTGGAAAATAATTTAAT
1 TTTCTGGAAAAT-ATTAAAT
10242846 TTTCTGGAAAAT-TTAATAT
1 TTTCTGGAAAATATTAA-AT
10242865 TTTCTGG
1 TTTCTGG
10242872 TGTTTGGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 3 0.12
19 9 0.38
20 12 0.50
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (19 bp):
TTTCTGGAAAATATTAAAT
Found at i:10243311 original size:15 final size:15
Alignment explanation
Indices: 10243291--10243342 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
10243281 ACTACAAAAC
10243291 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
10243306 ATTTATAATTGTAATAATT
1 ATTTATTA-T-TAAT-A-T
*
10243325 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
10243340 ATT
1 ATT
10243343 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 11 0.37
16 2 0.07
17 7 0.23
18 2 0.07
19 8 0.27
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:10243508 original size:7 final size:7
Alignment explanation
Indices: 10243496--10243524 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
10243486 TCATATTTTT
10243496 TTTATTC
1 TTTATTC
10243503 TTTATTC
1 TTTATTC
10243510 TTTATTC
1 TTTATTC
10243517 TTTATTC
1 TTTATTC
10243524 T
1 T
10243525 CTCCATCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATTC
Done.