Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 18 of 356
Found at i:6331618 original size:17 final size:18
Alignment explanation
Indices: 6331596--6331634 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
6331586 CATTTTAAAA
6331596 TATTTT-AATAAAAAT-AT
1 TATTTTCAA-AAAAATCAT
6331613 TATTTTCAAAAAAATCAT
1 TATTTTCAAAAAAATCAT
6331631 TATT
1 TATT
6331635 ATTTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTTTCAAAAAAATCAT
Found at i:6332153 original size:21 final size:21
Alignment explanation
Indices: 6332127--6332166 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
6332117 GTGTATTTTT
6332127 ATATAATTTATATTTTTTAAA
1 ATATAATTTATATTTTTTAAA
6332148 ATATAATTTATATTTTTTA
1 ATATAATTTATATTTTTTA
6332167 TTTTCTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATAATTTATATTTTTTAAA
Found at i:6332167 original size:30 final size:31
Alignment explanation
Indices: 6332124--6332184 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 31
6332114 CAAGTGTATT
6332124 TTTATATAATTTATATTT-T-TTAAAATATAA
1 TTTATATAATTTAT-TTTCTATTAAAATATAA
** *
6332154 TTTATATTTTTTATTTTCTATTAAATTATAA
1 TTTATATAATTTATTTTCTATTAAAATATAA
6332185 ATTTTATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 3 0.12
30 13 0.50
31 10 0.38
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTATATAATTTATTTTCTATTAAAATATAA
Found at i:6332763 original size:19 final size:18
Alignment explanation
Indices: 6332741--6332810 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 18
6332731 TTTTTTTAAG
6332741 TTTTTATTTATTTACTTTT
1 TTTTTATTTATTTA-TTTT
* *
6332760 TTTTAAATTATTTATTTT
1 TTTTTATTTATTTATTTT
*
6332778 ATTTTATTTTATTTATTTGT
1 TTTTTA-TTTATTTATTT-T
* *
6332798 TTATTATTGATTT
1 TTTTTATTTATTT
6332811 TTTAAAAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 8 0.20
19 28 0.68
20 5 0.12
ACGTcount: A:0.21, C:0.01, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTTATTTATTTATTTT
Found at i:6332793 original size:23 final size:23
Alignment explanation
Indices: 6332729--6332800 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 23
6332719 TTACTTTTTT
6332729 CTTTTTTTTAAGTTTTTATTTATTTA
1 CTTTTTTTTAA---TTTATTTATTTA
*
6332755 CTTTTTTTTAAATTATTTATTTTA
1 CTTTTTTTTAATTTATTTA-TTTA
*
6332779 -TTTTATTTT-ATTTATTTGTTTA
1 CTTTT-TTTTAATTTATTTATTTA
6332801 TTATTGATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
22 4 0.10
23 18 0.44
24 8 0.20
26 11 0.27
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (23 bp):
CTTTTTTTTAATTTATTTATTTA
Found at i:6332892 original size:34 final size:35
Alignment explanation
Indices: 6332844--6332925 Score: 114
Period size: 35 Copynumber: 2.3 Consensus size: 35
6332834 ATTTGAAATG
6332844 TTTAATAATATATTTTTTAAAA-ATTTAAATA-TATAT
1 TTTAA-AAT-TATTTTTTAAAATATTTAAATATTAT-T
6332880 TTTAAAATTATTTTTTAAAATATTTAAATATTATT
1 TTTAAAATTATTTTTTAAAATATTTAAATATTATT
*
6332915 TTTTAAATTAT
1 TTTAAAATTAT
6332926 ATATATTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
34 12 0.28
35 23 0.53
36 8 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (35 bp):
TTTAAAATTATTTTTTAAAATATTTAAATATTATT
Found at i:6332932 original size:21 final size:23
Alignment explanation
Indices: 6332882--6332928 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
6332872 ATATATATTT
*
6332882 TAAA-ATTATTTTTTAAAATATT
1 TAAATATTATTTTTTAAAATATA
*
6332904 TAAATATTATTTTTTAAATTATA
1 TAAATATTATTTTTTAAAATATA
6332927 TA
1 TA
6332929 TATTTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TAAATATTATTTTTTAAAATATA
Found at i:6332934 original size:17 final size:14
Alignment explanation
Indices: 6332867--6332937 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 14
6332857 TTTTTAAAAA
*
6332867 TTTAAATA-TATAT
1 TTTAAATATTATTT
6332880 TTTAAA-ATTATTT
1 TTTAAATATTATTT
6332893 TTTAAA-A-TA---
1 TTTAAATATTATTT
6332902 TTTAAATATTATTT
1 TTTAAATATTATTT
6332916 TTTAAATTATATATATT
1 TTTAAA-TAT-TAT-TT
6332933 TTTAA
1 TTTAA
6332938 TAATATAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
9 6 0.12
10 1 0.02
11 2 0.04
12 3 0.06
13 17 0.35
14 6 0.12
15 3 0.06
16 3 0.06
17 7 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTAAATATTATTT
Found at i:6333149 original size:21 final size:20
Alignment explanation
Indices: 6333110--6333149 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6333100 TCTATTTAAA
* *
6333110 ATTTTAAAAAATGATATTTT
1 ATTTAAAAAAATGAAATTTT
6333130 ATTTAAAAAAAGTGAAATTT
1 ATTTAAAAAAA-TGAAATTT
6333150 GAATAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (20 bp):
ATTTAAAAAAATGAAATTTT
Found at i:6333245 original size:21 final size:21
Alignment explanation
Indices: 6333200--6333276 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
6333190 TGACTTTATT
* **
6333200 TAAAAATATATATTAAAGAGG
1 TAAAAATATATATTAAAAAAA
6333221 TAAAAATATATATTAAAAAAA
1 TAAAAATATATATTAAAAAAA
* * *
6333242 TAAAAATTTAAATTAAAAAAT
1 TAAAAATATATATTAAAAAAA
6333263 TAAAAA-ATATATTA
1 TAAAAATATATATTA
6333277 TAATTGGTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 6 0.12
21 42 0.88
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (21 bp):
TAAAAATATATATTAAAAAAA
Found at i:6334228 original size:16 final size:15
Alignment explanation
Indices: 6334190--6334228 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
6334180 CAATTTTTTT
6334190 AAAAAATTATTTATA
1 AAAAAATTATTTATA
6334205 AAATAAATTATTTTATA
1 AAA-AAATTA-TTTATA
*
6334222 TAAAAAT
1 AAAAAAT
6334229 AAATAAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 10 0.48
17 8 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAAAATTATTTATA
Found at i:6334319 original size:16 final size:18
Alignment explanation
Indices: 6334300--6334335 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6334290 CACTCATCAC
6334300 TTTTT-TTCTC-A-AATT
1 TTTTTATTCTCTAGAATT
6334315 TTTTTATTCTCTAGAATT
1 TTTTTATTCTCTAGAATT
6334333 TTT
1 TTT
6334336 ACAAGACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.28
16 5 0.28
17 1 0.06
18 7 0.39
ACGTcount: A:0.19, C:0.11, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTTATTCTCTAGAATT
Found at i:6336844 original size:15 final size:16
Alignment explanation
Indices: 6336824--6336853 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6336814 GAGGATCGTA
6336824 AATATT-TTTTTAAAT
1 AATATTATTTTTAAAT
6336839 AATATTATTTTTAAA
1 AATATTATTTTTAAA
6336854 ATTTAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATATTATTTTTAAAT
Found at i:6339653 original size:20 final size:20
Alignment explanation
Indices: 6339616--6339654 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6339606 TAATAATTCA
*
6339616 TTAATGAATTAATATAATTT
1 TTAATGAAATAATATAATTT
6339636 TTAATGATAATAAT-TAATT
1 TTAATGA-AATAATATAATT
6339655 CAGATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTAATGAAATAATATAATTT
Found at i:6340177 original size:9 final size:9
Alignment explanation
Indices: 6340142--6340187 Score: 60
Period size: 9 Copynumber: 5.2 Consensus size: 9
6340132 ACTTTTTAAA
6340142 TTATATTATT
1 TTATA-TATT
6340152 TTA-ATATT
1 TTATATATT
*
6340160 TAATA-ATT
1 TTATATATT
6340168 TTATATATT
1 TTATATATT
6340177 TTATATATT
1 TTATATATT
6340186 TT
1 TT
6340188 TTATTTATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 13 0.41
9 16 0.50
10 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTATATATT
Found at i:6340177 original size:17 final size:17
Alignment explanation
Indices: 6340148--6340187 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
6340138 TAAATTATAT
6340148 TATTTTAATATTTAATA
1 TATTTTAATATTTAATA
*
6340165 -ATTTTATATATTTTATA
1 TATTTTA-ATATTTAATA
6340182 TATTTT
1 TATTTT
6340188 TTATTTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 6 0.30
17 9 0.45
18 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTAATA
Found at i:6341930 original size:22 final size:22
Alignment explanation
Indices: 6341905--6341952 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
6341895 CTTTCAACTC
6341905 TATTAAAATTT-TTGTTGTCTTT
1 TATTAAAATTTCTTGTT-TCTTT
* **
6341927 TATTTATTTTTCTTGTTTCTTT
1 TATTAAAATTTCTTGTTTCTTT
6341949 TATT
1 TATT
6341953 TTTTTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (22 bp):
TATTAAAATTTCTTGTTTCTTT
Found at i:6341953 original size:22 final size:22
Alignment explanation
Indices: 6341916--6341957 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
6341906 ATTAAAATTT
6341916 TTGTTGTCTTTTATTTATTTTTC
1 TTGTTGTCTTTTATTT-TTTTTC
6341939 TTGTT-TCTTTTATTTTTTT
1 TTGTTGTCTTTTATTTTTTT
6341958 AAATTGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (22 bp):
TTGTTGTCTTTTATTTTTTTTC
Found at i:6341964 original size:22 final size:22
Alignment explanation
Indices: 6341916--6341973 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 22
6341906 ATTAAAATTT
**
6341916 TTGTTGTCTTTTATTTATTTTTC
1 TTGTT-TCTTTTATTTATTTTAA
6341939 TTGTTTCTTTTATTT-TTTTAAA
1 TTGTTTCTTTTATTTATTTT-AA
6341961 TTGTATTACTTTT
1 TTGT-TT-CTTTT
6341974 TAAATTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 4 0.13
22 14 0.47
23 7 0.23
24 5 0.17
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (22 bp):
TTGTTTCTTTTATTTATTTTAA
Found at i:6342447 original size:15 final size:15
Alignment explanation
Indices: 6342427--6342456 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6342417 CACTATTTAC
6342427 AATTTAGTTTTTATT
1 AATTTAGTTTTTATT
6342442 AATTTAGTTTTTATT
1 AATTTAGTTTTTATT
6342457 TTCATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
AATTTAGTTTTTATT
Found at i:6346807 original size:18 final size:18
Alignment explanation
Indices: 6346773--6346810 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
6346763 ACAAAGTATA
*
6346773 AAAAACAATATTTTTAAT
1 AAAAACAATATTATTAAT
6346791 AAAAACAA-ATTAATTAAT
1 AAAAACAATATT-ATTAAT
6346809 AA
1 AA
6346811 TAAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAACAATATTATTAAT
Found at i:6351915 original size:17 final size:17
Alignment explanation
Indices: 6351893--6351925 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6351883 AAAAATTATA
*
6351893 AAAAATTATTTTTAAAT
1 AAAAATTAATTTTAAAT
6351910 AAAAATTAATTTTAAA
1 AAAAATTAATTTTAAA
6351926 AAAGTCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAAATTAATTTTAAAT
Found at i:6352618 original size:18 final size:18
Alignment explanation
Indices: 6352592--6352627 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6352582 TATGAACAGA
*
6352592 GACAGAAGAAAAGTCTTT
1 GACACAAGAAAAGTCTTT
6352610 GACACAAGAAAAGTCTTT
1 GACACAAGAAAAGTCTTT
6352628 TTGTTGACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.22
Consensus pattern (18 bp):
GACACAAGAAAAGTCTTT
Found at i:6356791 original size:20 final size:20
Alignment explanation
Indices: 6356742--6356791 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
6356732 TAATATTATA
*
6356742 AAATTTT-ATTATTTTTAAT
1 AAATTTTAATAATTTTTAAT
* *
6356761 TAATTTCTAATAATTTTTCAT
1 AAATTT-TAATAATTTTTAAT
6356782 AAATTTTAAT
1 AAATTTTAAT
6356792 GAGCTTTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 5 0.20
20 5 0.20
21 15 0.60
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
AAATTTTAATAATTTTTAAT
Found at i:6382708 original size:30 final size:30
Alignment explanation
Indices: 6382674--6382736 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
6382664 ACTTATTTTA
6382674 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
6382704 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
6382734 TTG
1 TTG
6382737 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:6384257 original size:20 final size:22
Alignment explanation
Indices: 6384220--6384270 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
6384210 AAAGTAATAA
6384220 AAAGCTTTTTAACATATGGA-G
1 AAAGCTTTTTAACATATGGATG
* *
6384241 AAAGCTTTTTTA-GTATGGATG
1 AAAGCTTTTTAACATATGGATG
6384262 AACAGCTTT
1 AA-AGCTTT
6384271 ACTAAAGACG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 14 0.54
22 6 0.23
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (22 bp):
AAAGCTTTTTAACATATGGATG
Found at i:6386290 original size:30 final size:30
Alignment explanation
Indices: 6386254--6386316 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
6386244 TTGTATAAAA
6386254 AAATATAATTTCAATTAGAGCACTGAATTG
1 AAATATAATTTCAATTAGAGCACTGAATTG
6386284 AAATATAATTTCAATTAGAGCACTGAATTG
1 AAATATAATTTCAATTAGAGCACTGAATTG
6386314 AAA
1 AAA
6386317 AGCAACTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.32
Consensus pattern (30 bp):
AAATATAATTTCAATTAGAGCACTGAATTG
Found at i:6389264 original size:81 final size:81
Alignment explanation
Indices: 6389153--6389316 Score: 328
Period size: 81 Copynumber: 2.0 Consensus size: 81
6389143 ATTTTAAATG
6389153 TTAGCACGTCAATTTTTAGGATTTCTATAATCTATATCGAGGAACTTGTTGATGCAATTTATTTG
1 TTAGCACGTCAATTTTTAGGATTTCTATAATCTATATCGAGGAACTTGTTGATGCAATTTATTTG
6389218 CTATTCATTACTAAAC
66 CTATTCATTACTAAAC
6389234 TTAGCACGTCAATTTTTAGGATTTCTATAATCTATATCGAGGAACTTGTTGATGCAATTTATTTG
1 TTAGCACGTCAATTTTTAGGATTTCTATAATCTATATCGAGGAACTTGTTGATGCAATTTATTTG
6389299 CTATTCATTACTAAAC
66 CTATTCATTACTAAAC
6389315 TT
1 TT
6389317 TAAGTATATG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (81 bp):
TTAGCACGTCAATTTTTAGGATTTCTATAATCTATATCGAGGAACTTGTTGATGCAATTTATTTG
CTATTCATTACTAAAC
Found at i:6390073 original size:3 final size:3
Alignment explanation
Indices: 6390065--6390090 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6390055 TTTAAATTTA
6390065 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
6390091 ACTTGGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:6393652 original size:3 final size:3
Alignment explanation
Indices: 6393646--6393671 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6393636 TTTTTTTTAA
6393646 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
6393672 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:6395718 original size:46 final size:47
Alignment explanation
Indices: 6395670--6395761 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 47
6395660 ATTTCTTTTA
*
6395670 TTTATTATTAT-TAACTTTAAAAATTTTGAAATATATA-TTTGAAATAT
1 TTTATTAATATGT-ACTTTAAAAATTTT-AAATATATATTTTGAAATAT
* **
6395717 TTTATTAATATGTATTTTTTAAATTTTAAATATATATTTTGAAAT
1 TTTATTAATATGTACTTTAAAAATTTTAAATATATATTTTGAAAT
6395762 TACTTTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
46 9 0.23
47 29 0.74
48 1 0.03
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (47 bp):
TTTATTAATATGTACTTTAAAAATTTTAAATATATATTTTGAAATAT
Found at i:6395790 original size:22 final size:21
Alignment explanation
Indices: 6395752--6395806 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
6395742 TTAAATATAT
*
6395752 ATTTTGAA-ATTACTTTTTTAA
1 ATTTTAAATATTA-TTTTTTAA
6395773 ATTTTAAATATTATTTTTTAA
1 ATTTTAAATATTATTTTTTAA
6395794 ATATTTAAATATT
1 AT-TTTAAATATT
6395807 TTAAACTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTTTAAATATTATTTTTTAA
Found at i:6396207 original size:10 final size:9
Alignment explanation
Indices: 6396179--6396244 Score: 53
Period size: 9 Copynumber: 7.1 Consensus size: 9
6396169 AATATTTTTC
*
6396179 TTTTTTTAA
1 TTTTTTTAT
* *
6396188 GTTTTATAT
1 TTTTTTTAT
6396197 TTTTTCTTAT
1 TTTTT-TTAT
6396207 TTTATTTTAT
1 TTT-TTTTAT
*
6396217 TTTATTTA-
1 TTTTTTTAT
*
6396225 TTTATTTAT
1 TTTTTTTAT
6396234 TTTTTGTTAT
1 TTTTT-TTAT
6396244 T
1 T
6396245 AATTTTAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
8 8 0.17
9 18 0.39
10 18 0.39
11 2 0.04
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:6396212 original size:15 final size:14
Alignment explanation
Indices: 6396203--6396251 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
6396193 ATATTTTTTC
6396203 TTATTTTATTTTAT
1 TTATTTTATTTTAT
6396217 TT-TATTTA-TTTAT
1 TTAT-TTTATTTTAT
6396230 TTATTTT-TTGTTAT
1 TTATTTTATT-TTAT
*
6396244 TAATTTTA
1 TTATTTTA
6396252 AAAAATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
13 12 0.41
14 17 0.59
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (14 bp):
TTATTTTATTTTAT
Found at i:6396232 original size:22 final size:22
Alignment explanation
Indices: 6396207--6396249 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6396197 TTTTTCTTAT
*
6396207 TTTATTTTATT-TTATTTATTTA
1 TTTATTTT-TTGTTATTAATTTA
6396229 TTTATTTTTTGTTATTAATTT
1 TTTATTTTTTGTTATTAATTT
6396250 TAAAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTATTTTTTGTTATTAATTTA
Found at i:6396609 original size:10 final size:10
Alignment explanation
Indices: 6396544--6396616 Score: 51
Period size: 11 Copynumber: 6.8 Consensus size: 10
6396534 GCCGAATACC
6396544 TTTAAAAATAA
1 TTTAAAAAT-A
6396555 TTTAAAAATCA
1 TTTAAAAAT-A
*
6396566 TAATTTAAAATA
1 T--TTAAAAATA
6396578 TTATAAAACA-A
1 TT-TAAAA-ATA
*
6396589 ATTAAATAATA
1 TTTAAA-AATA
6396600 TTTAAAAATA
1 TTTAAAAATA
6396610 -TTAAAAA
1 TTTAAAAA
6396617 ACTAATAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
9 7 0.14
10 10 0.20
11 24 0.47
12 3 0.06
13 7 0.14
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (10 bp):
TTTAAAAATA
Found at i:6396696 original size:21 final size:20
Alignment explanation
Indices: 6396672--6396733 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 20
6396662 TTTTGTATTA
**
6396672 TTAAAAATATATATTTAATGT
1 TTAAAAA-ATATATTTAAAAT
*
6396693 TTAAAAAAATAATATTCAAAAT
1 TT-AAAAAAT-ATATTTAAAAT
6396715 TTAAAAAATA-ATTTAAAAT
1 TTAAAAAATATATTTAAAAT
6396734 ATATTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 8 0.23
20 1 0.03
21 11 0.31
22 15 0.43
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
TTAAAAAATATATTTAAAAT
Found at i:6396707 original size:22 final size:21
Alignment explanation
Indices: 6396696--6396733 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6396686 TTAATGTTTA
6396696 AAAAAATAATATTCAAAATTT
1 AAAAAATAATATTCAAAATTT
6396717 AAAAAATAAT-TT-AAAAT
1 AAAAAATAATATTCAAAAT
6396734 ATATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAAAATAATATTCAAAATTT
Found at i:6396739 original size:11 final size:12
Alignment explanation
Indices: 6396712--6396744 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6396702 TAATATTCAA
*
6396712 AATTTAAAAAAT
1 AATTTAAAATAT
6396724 AATTTAAAATAT
1 AATTTAAAATAT
6396736 -ATTTAAAAT
1 AATTTAAAAT
6396745 TTAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATTTAAAATAT
Found at i:6396743 original size:21 final size:22
Alignment explanation
Indices: 6396719--6396778 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 22
6396709 CAAAATTTAA
6396719 AAAATAATTTAAAATATAT-TT
1 AAAATAATTTAAAATATATATT
*
6396740 AAAAT--TTAAAAATATATATT
1 AAAATAATTTAAAATATATATT
*
6396760 ATAAA-ACATTTCAAATATA
1 A-AAATA-ATTTAAAATATA
6396779 CATTTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 11 0.35
20 3 0.10
21 8 0.26
23 9 0.29
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAATAATTTAAAATATATATT
Found at i:6396744 original size:30 final size:34
Alignment explanation
Indices: 6396698--6396765 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 34
6396688 AATGTTTAAA
6396698 AAAATAATATTCAAAATTTAAAAA-ATA-ATT-T
1 AAAATAATATTCAAAATTTAAAAATATATATTAT
*
6396729 AAAAT-ATATTTAAAATTTAAAAATATATATTAT
1 AAAATAATATTCAAAATTTAAAAATATATATTAT
6396762 AAAA
1 AAAA
6396766 CATTTCAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 17 0.52
31 8 0.24
32 3 0.09
33 5 0.15
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (34 bp):
AAAATAATATTCAAAATTTAAAAATATATATTAT
Found at i:6396814 original size:10 final size:9
Alignment explanation
Indices: 6396801--6396925 Score: 58
Period size: 9 Copynumber: 13.2 Consensus size: 9
6396791 TTTTAAAATT
6396801 AATAACAAAA
1 AATAA-AAAA
*
6396811 AAT-AAATA
1 AATAAAAAA
6396819 AATAAAATAA
1 AATAAAA-AA
6396829 AATAAGAAAA
1 AATAA-AAAA
*
6396839 AATATAAAA
1 AATAAAAAA
**
6396848 CTTAAAAAA
1 AATAAAAAA
6396857 AGA-AAAAAA
1 A-ATAAAAAA
**
6396866 TTTAAAGAAA
1 AATAAA-AAA
* *
6396876 AAGACAAAA
1 AATAAAAAA
*
6396885 GATAATAAAA
1 AATAA-AAAA
6396895 AACT-AAAAA
1 AA-TAAAAAA
6396904 AATAATAAATA
1 AATAA-AAA-A
*
6396915 AGTAAAAAA
1 AATAAAAAA
6396924 AA
1 AA
6396926 AAGTGAGAGA
Statistics
Matches: 84, Mismatches: 20, Indels: 23
0.66 0.16 0.18
Matches are distributed among these distances:
8 7 0.08
9 37 0.44
10 32 0.38
11 8 0.10
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (9 bp):
AATAAAAAA
Found at i:6396818 original size:14 final size:13
Alignment explanation
Indices: 6396795--6396842 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
6396785 AAATTTTTTT
*
6396795 AAAATTAATAACAA
1 AAAATAAATAA-AA
*
6396809 AAAATAAATAAAT
1 AAAATAAATAAAA
6396822 AAAATAAAATAAGAA
1 AAAAT-AAATAA-AA
6396837 AAAATA
1 AAAATA
6396843 TAAAACTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 6 0.21
14 17 0.59
15 6 0.21
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (13 bp):
AAAATAAATAAAA
Found at i:6396822 original size:18 final size:18
Alignment explanation
Indices: 6396796--6396833 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
6396786 AATTTTTTTA
*
6396796 AAATTAATAACAA-AAAAT
1 AAATAAATAA-AATAAAAT
6396814 AAATAAATAAAATAAAAT
1 AAATAAATAAAATAAAAT
6396832 AA
1 AA
6396834 GAAAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (18 bp):
AAATAAATAAAATAAAAT
Found at i:6396903 original size:19 final size:19
Alignment explanation
Indices: 6396881--6396924 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
6396871 AGAAAAAGAC
*
6396881 AAAAGATAATAAAAAACTA
1 AAAAAATAATAAAAAACTA
* *
6396900 AAAAAATAATAAATAAGTA
1 AAAAAATAATAAAAAACTA
6396919 AAAAAA
1 AAAAAA
6396925 AAAGTGAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (19 bp):
AAAAAATAATAAAAAACTA
Found at i:6397243 original size:21 final size:22
Alignment explanation
Indices: 6397206--6397260 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
6397196 GAAAGTTTAA
*
6397206 AATACTTAAATATTT-AAAAAAT
1 AATATTTAAA-ATTTAAAAAAAT
6397228 AATATTTAAAATTTAAAAAAAT
1 AATATTTAAAATTTAAAAAAAT
*
6397250 AAT-TTCAAAAT
1 AATATTTAAAAT
6397261 ATATATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (22 bp):
AATATTTAAAATTTAAAAAAAT
Found at i:6397289 original size:24 final size:26
Alignment explanation
Indices: 6397240--6397291 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
6397230 TATTTAAAAT
6397240 TTAAAAAAATAATTTCAAAATATATA
1 TTAAAAAAATAATTTCAAAATATATA
*
6397266 TTAATAAAAT-ATTTC-AAATATATA
1 TTAAAAAAATAATTTCAAAATATATA
6397290 TT
1 TT
6397292 TCAAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 11 0.44
25 5 0.20
26 9 0.36
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (26 bp):
TTAAAAAAATAATTTCAAAATATATA
Found at i:6397328 original size:5 final size:5
Alignment explanation
Indices: 6397309--6397361 Score: 60
Period size: 5 Copynumber: 11.2 Consensus size: 5
6397299 TTTTAAAGTT
*
6397309 AATAA TAAT-A AATAA AATAA AATAA AATAA AAT-A AAT-A AAGAA AAT-A
1 AATAA -AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
6397356 AATAA A
1 AATAA A
6397362 GAAAAAAGAC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
4 14 0.33
5 25 0.60
6 3 0.07
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:6397331 original size:10 final size:9
Alignment explanation
Indices: 6397309--6397361 Score: 63
Period size: 9 Copynumber: 5.7 Consensus size: 9
6397299 TTTTAAAGTT
6397309 AATAATAATA
1 AATAA-AATA
6397319 AATAAAATAA
1 AATAAAAT-A
6397329 AATAAAATA
1 AATAAAATA
6397338 AA-ATAAATA
1 AATA-AAATA
*
6397347 AAGAAAATA
1 AATAAAATA
6397356 AATAAA
1 AATAAA
6397362 GAAAAAAGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
8 1 0.03
9 23 0.59
10 15 0.38
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (9 bp):
AATAAAATA
Found at i:6401022 original size:53 final size:53
Alignment explanation
Indices: 6400942--6401048 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
6400932 TAATGTGAGA
*
6400942 TTGGCTCTTTGAGATGTGTAAGGGCTTGTAATTGTGGCATGATAACACACACT
1 TTGGCTCTTTGAGATGCGTAAGGGCTTGTAATTGTGGCATGATAACACACACT
*
6400995 TTGGCTCTTTGAGATGCGTATGGGCTTGTAATTGTGGCATGATAACACACACT
1 TTGGCTCTTTGAGATGCGTAAGGGCTTGTAATTGTGGCATGATAACACACACT
6401048 T
1 T
6401049 GAATTTAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (53 bp):
TTGGCTCTTTGAGATGCGTAAGGGCTTGTAATTGTGGCATGATAACACACACT
Found at i:6403547 original size:15 final size:15
Alignment explanation
Indices: 6403519--6403551 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
6403509 TTACCATCAA
6403519 AAAAGAGAAGAGAAG
1 AAAAGAGAAGAGAAG
6403534 AAAA-AGAAGAAGAAG
1 AAAAGAGAAG-AGAAG
6403549 AAA
1 AAA
6403552 TGGGCGCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAAAGAGAAGAGAAG
Found at i:6404168 original size:5 final size:5
Alignment explanation
Indices: 6404158--6404188 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
6404148 AATAATTAAG
6404158 TATAT TATAT TATAT TATAT TATTAT TATAT
1 TATAT TATAT TATAT TATAT TA-TAT TATAT
6404189 ATAAAAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:6406874 original size:16 final size:16
Alignment explanation
Indices: 6406853--6406897 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
6406843 TTAATTAATT
6406853 TTAAAAATTCAATTAA
1 TTAAAAATTCAATTAA
*
6406869 TT-AAAATT-ATTTAA
1 TTAAAAATTCAATTAA
*
6406883 TTAAAAAATCAATTA
1 TTAAAAATTCAATTA
6406898 TTTTACTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 7 0.29
15 11 0.46
16 6 0.25
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAAAATTCAATTAA
Found at i:6407537 original size:28 final size:28
Alignment explanation
Indices: 6407509--6407563 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
6407499 AAAATGATAT
*
6407509 TTTAAATATTATT-ATATTTATTTTTTA
1 TTTAAATATTATTAATATTTATATTTTA
* *
6407536 TTTATATATTTTTAATATTTATATTTTA
1 TTTAAATATTATTAATATTTATATTTTA
6407564 AAAAAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTAAATATTATTAATATTTATATTTTA
Found at i:6407540 original size:17 final size:18
Alignment explanation
Indices: 6407520--6407561 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
6407510 TTAAATATTA
6407520 TTATATTTATTTTT-TAT
1 TTATATTTATTTTTATAT
6407537 TTATA--TATTTTTAATAT
1 TTATATTTATTTTT-ATAT
6407554 TTATATTT
1 TTATATTT
6407562 TAAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
15 7 0.33
17 13 0.62
19 1 0.05
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATATTTATTTTTATAT
Found at i:6407560 original size:15 final size:14
Alignment explanation
Indices: 6407514--6407562 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
6407504 GATATTTTAA
*
6407514 ATATTATTATATTT
1 ATATTTTTATATTT
6407528 AT-TTTTTAT-TTAT
1 ATATTTTTATATT-T
6407541 ATATTTTTAATATTT
1 ATATTTTT-ATATTT
6407556 ATATTTT
1 ATATTTT
6407563 AAAAAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 2 0.07
13 9 0.30
14 7 0.23
15 10 0.33
16 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
ATATTTTTATATTT
Found at i:6408949 original size:22 final size:22
Alignment explanation
Indices: 6408921--6408962 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
6408911 CATGTTAAGC
6408921 TTTATTAGATTATGACACATGA
1 TTTATTAGATTATGACACATGA
6408943 TTTATTAGATTATGACACAT
1 TTTATTAGATTATGACACAT
6408963 TAATAATGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.43
Consensus pattern (22 bp):
TTTATTAGATTATGACACATGA
Found at i:6420903 original size:21 final size:21
Alignment explanation
Indices: 6420877--6420917 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6420867 ATCTGCTCAA
* *
6420877 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
6420898 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
6420918 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:6424436 original size:17 final size:17
Alignment explanation
Indices: 6424414--6424448 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6424404 TTTAAAAGCA
6424414 TTTAAGAATACATATTT
1 TTTAAGAATACATATTT
* *
6424431 TTTAAGTATATATATTT
1 TTTAAGAATACATATTT
6424448 T
1 T
6424449 AATTTGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTAAGAATACATATTT
Found at i:6424466 original size:20 final size:20
Alignment explanation
Indices: 6424437--6424493 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
6424427 ATTTTTTAAG
*
6424437 TATATATATTTTAAT-TTGTT
1 TATATTTATTTTAATATT-TT
6424457 TATATTTATTTTAATATTTT
1 TATATTTATTTTAATATTTT
*
6424477 TAGTATTT-TTTAAATAT
1 TA-TATTTATTTTAATAT
6424494 ATATAATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 26 0.79
21 7 0.21
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (20 bp):
TATATTTATTTTAATATTTT
Found at i:6426167 original size:27 final size:27
Alignment explanation
Indices: 6426110--6426167 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
6426100 CAATAAATTT
* * **
6426110 TAAATATTTTTTAAATTTTTTCATGTT
1 TAAATATTTTTTAAATATTTTCACGAA
6426137 TAAATATTTTTTAAGATATTTTC-CGAA
1 TAAATATTTTTTAA-ATATTTTCACGAA
6426164 TAAA
1 TAAA
6426168 AATGTCATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (27 bp):
TAAATATTTTTTAAATATTTTCACGAA
Found at i:6432479 original size:24 final size:24
Alignment explanation
Indices: 6432450--6432497 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
6432440 GATGGTTGAA
*
6432450 TGATGATTTTGTGAAATAAAATAG
1 TGATGATATTGTGAAATAAAATAG
6432474 TGATGATATTGTGAAATAAAATAG
1 TGATGATATTGTGAAATAAAATAG
6432498 CGTTTGGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (24 bp):
TGATGATATTGTGAAATAAAATAG
Found at i:6441609 original size:18 final size:19
Alignment explanation
Indices: 6441565--6441609 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
6441555 CTGATTTTTC
*
6441565 TTCCTTTTGTTTTTGGGGT
1 TTCCTTTTGTTTTTGGGGA
**
6441584 TTAATTTTGTTTTT-GGGA
1 TTCCTTTTGTTTTTGGGGA
6441602 TTCCTTTT
1 TTCCTTTT
6441610 TCTTTCCATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.07, C:0.09, G:0.20, T:0.64
Consensus pattern (19 bp):
TTCCTTTTGTTTTTGGGGA
Found at i:6446780 original size:21 final size:21
Alignment explanation
Indices: 6446746--6446785 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6446736 TATTAAAGCT
*
6446746 AGTTACAATCAAACTAAACTA
1 AGTTACAATCAAACAAAACTA
6446767 AGTTAC-ATCAAAACAAAAC
1 AGTTACAATC-AAACAAAAC
6446786 AGCAATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (21 bp):
AGTTACAATCAAACAAAACTA
Found at i:6451332 original size:21 final size:21
Alignment explanation
Indices: 6451298--6451337 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6451288 TATTAAAGCT
*
6451298 AGTTACAATCAAACTAAACTA
1 AGTTACAATCAAACAAAACTA
6451319 AGTTAC-ATCAAAACAAAAC
1 AGTTACAATC-AAACAAAAC
6451338 AGCAATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (21 bp):
AGTTACAATCAAACAAAACTA
Found at i:6459890 original size:28 final size:25
Alignment explanation
Indices: 6459823--6459890 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 25
6459813 TATGTTTTTT
*
6459823 TATTATATAATATTT-AACAATTATA
1 TATTTTATAAT-TTTAAACAATTATA
*
6459848 TATTTTAAAATTTTAAACAATTATAA
1 TATTTTATAATTTTAAACAATTAT-A
*
6459874 TATATTTTTAATGTTTA
1 TAT-TTTATAAT-TTTA
6459891 TATTATATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 3 0.09
25 18 0.51
26 4 0.11
27 6 0.17
28 4 0.11
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (25 bp):
TATTTTATAATTTTAAACAATTATA
Found at i:6466380 original size:116 final size:116
Alignment explanation
Indices: 6466244--6466479 Score: 463
Period size: 116 Copynumber: 2.0 Consensus size: 116
6466234 TACATGATTA
6466244 TTTATTTTTATTTAAATAACTATATGTTTTATTTCATTTTATTCATAATAATAGCTATTATTTAA
1 TTTATTTTTATTTAAATAACTATATGTTTTATTTCATTTTATTCATAATAATAGCTATTATTTAA
6466309 ATATAAACTCTTAACGAATTGAAAAAACACTAAAAAATTATCTCTTTTTTC
66 ATATAAACTCTTAACGAATTGAAAAAACACTAAAAAATTATCTCTTTTTTC
6466360 TTTATTTTTATTTAAATAACTATATGTTTTATTTCATTTTATTCATAATAATAGCTATTATTTAA
1 TTTATTTTTATTTAAATAACTATATGTTTTATTTCATTTTATTCATAATAATAGCTATTATTTAA
*
6466425 ATATAAACTCTTAATGAATTGAAAAAACACTAAAAAATTATCTCTTTTTTC
66 ATATAAACTCTTAACGAATTGAAAAAACACTAAAAAATTATCTCTTTTTTC
6466476 TTTA
1 TTTA
6466480 AGCTGTTTGC
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 119 1.00
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (116 bp):
TTTATTTTTATTTAAATAACTATATGTTTTATTTCATTTTATTCATAATAATAGCTATTATTTAA
ATATAAACTCTTAACGAATTGAAAAAACACTAAAAAATTATCTCTTTTTTC
Found at i:6469277 original size:4 final size:4
Alignment explanation
Indices: 6469268--6469298 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
6469258 TCTTCGCTGC
6469268 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
6469299 AATGATGCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:6471500 original size:72 final size:73
Alignment explanation
Indices: 6471385--6471528 Score: 272
Period size: 72 Copynumber: 2.0 Consensus size: 73
6471375 TGCAAAATGA
*
6471385 AAAAAAAAAAAGAATCATAAATAGTCCCATGTTTTATCAAATTTTCATGATGGTTACTTTCAATT
1 AAAAAAAAAAAGAATCATAAATAGTCCCATGTTTTATCAAATTTTCATGATAGTTACTTTCAATT
6471450 T-TTTTTG
66 TGTTTTTG
6471457 AAAAAAAAAAAGAATCATAAATAGTCCCATGTTTTATCAAATTTTCATGATAGTTACTTTCAATT
1 AAAAAAAAAAAGAATCATAAATAGTCCCATGTTTTATCAAATTTTCATGATAGTTACTTTCAATT
6471522 TGTTTTT
66 TGTTTTT
6471529 TTCAGTTTCA
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
72 65 0.93
73 5 0.07
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (73 bp):
AAAAAAAAAAAGAATCATAAATAGTCCCATGTTTTATCAAATTTTCATGATAGTTACTTTCAATT
TGTTTTTG
Found at i:6484075 original size:70 final size:68
Alignment explanation
Indices: 6483946--6484098 Score: 202
Period size: 70 Copynumber: 2.2 Consensus size: 68
6483936 ATAATTTTAA
* * *
6483946 ATTATCATGT-AACATATAAGACAAATAATGTCATGTCAGCATAAAGTACACGTGAACTACCACG
1 ATTACCATGTCAACATATAAGACAAATAATGTCATGTCAGCATAAAGCACACATGAACTACCACG
*
6484010 GAG
66 CAG
*
6484013 ATTACCATGTCAACATCATTAAGACAAATAATGTCATGTCAGCATGAAA-CACATATGAACTACC
1 ATTACCATGTCAACAT-A-TAAGACAAATAATGTCATGTCAGCAT-AAAGCACACATGAACTACC
6484077 ACGCAG
63 ACGCAG
* *
6484083 ATTACGATGCCAACAT
1 ATTACCATGTCAACAT
6484099 TGTTAACAAT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
67 9 0.12
68 5 0.07
69 1 0.01
70 57 0.76
71 3 0.04
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (68 bp):
ATTACCATGTCAACATATAAGACAAATAATGTCATGTCAGCATAAAGCACACATGAACTACCACG
CAG
Found at i:6484612 original size:3 final size:3
Alignment explanation
Indices: 6484604--6484633 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6484594 ACCCCCGAAA
6484604 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
6484634 GGCCTAAATT
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:6487317 original size:10 final size:10
Alignment explanation
Indices: 6487302--6487327 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6487292 AAGATAATTT
6487302 TATTTTCAAA
1 TATTTTCAAA
6487312 TATTTTCAAA
1 TATTTTCAAA
6487322 TATTTT
1 TATTTT
6487328 AACCTGATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (10 bp):
TATTTTCAAA
Found at i:6492611 original size:121 final size:121
Alignment explanation
Indices: 6492474--6492691 Score: 307
Period size: 121 Copynumber: 1.8 Consensus size: 121
6492464 ATCATGCATT
* * * * * *
6492474 TGAAATTTCAAAAGGATATTTGGCTA-TCTGGTCAAACGGTAAGTCGAAACCCAGCACGATT-GG
1 TGAAACTTCAAAAGGATATTTAGCTATTC-GGCCAAACAGAAAATCGAAACCCAGCAC-ATTAGG
*
6492537 GCACGATTTCTCGAATTT-TCAAACACAAAATATTGCCTCAAATTTAAGAAAACATGGA
64 ACACGATTTCTCGAATTTCT-AAACACAAAATATTGCCTCAAATTTAAGAAAACATGGA
*
6492595 TGAAACTTCAAAAGGATATTTAGTTATTCGGCCAAACAGAAAATCGAAACCCAGCACATTAGGAC
1 TGAAACTTCAAAAGGATATTTAGCTATTCGGCCAAACAGAAAATCGAAACCCAGCACATTAGGAC
*
6492660 ACGATTTCTCGAATTTCTAAACACGAAATATT
66 ACGATTTCTCGAATTTCTAAACACAAAATATT
6492692 TCCTTATTTT
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
120 3 0.04
121 79 0.93
122 3 0.04
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.26
Consensus pattern (121 bp):
TGAAACTTCAAAAGGATATTTAGCTATTCGGCCAAACAGAAAATCGAAACCCAGCACATTAGGAC
ACGATTTCTCGAATTTCTAAACACAAAATATTGCCTCAAATTTAAGAAAACATGGA
Found at i:6494977 original size:46 final size:47
Alignment explanation
Indices: 6494894--6495109 Score: 193
Period size: 47 Copynumber: 4.5 Consensus size: 47
6494884 TTGCACATAG
* * * **
6494894 TCACATATCACATACCGAGGCCATAGCCCAGCCATGGTCTTATAC-GAA
1 TCACATATCAC--ACTGATGCCATATCCCAGATATGGTCTTATACGGAA
* *
6494942 TCACATATCACACTGATGCCATATCCCAGATATGGTCTTATACAGTA
1 TCACATATCACACTGATGCCATATCCCAGATATGGTCTTATACGGAA
* * *
6494989 GCACATATCACACCGATGCCATATCCCGGATATGGTCTTATACGGAA
1 TCACATATCACACTGATGCCATATCCCAGATATGGTCTTATACGGAA
* * * * *
6495036 GCACAAATCACATTTCTCTGAAGCCATAACCCAGCTATGGTCTTATACGGAAA
1 TCACATATCACA-----CTGATGCCATATCCCAGATATGGTCTTATACGG-AA
* *
6495089 TCACATTTCACA-TGCTGCCAT
1 TCACATATCACACTGATGCCAT
6495110 GGTCCAACCA
Statistics
Matches: 139, Mismatches: 22, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
46 27 0.19
47 62 0.45
48 11 0.08
52 28 0.20
53 11 0.08
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.25
Consensus pattern (47 bp):
TCACATATCACACTGATGCCATATCCCAGATATGGTCTTATACGGAA
Found at i:6497622 original size:15 final size:15
Alignment explanation
Indices: 6497593--6497673 Score: 101
Period size: 15 Copynumber: 5.5 Consensus size: 15
6497583 AGCAAAGATA
*
6497593 AAAGAAAACC-GAAT
1 AAAGAAATCCAGAAT
*
6497607 AAAGAAATCCAAAAT
1 AAAGAAATCCAGAAT
* *
6497622 AGAGAAACCCAGAAT
1 AAAGAAATCCAGAAT
6497637 AAAGAAATCCAGAAT
1 AAAGAAATCCAGAAT
* *
6497652 AAAGAGATCCAGGAT
1 AAAGAAATCCAGAAT
6497667 AAAGAAA
1 AAAGAAA
6497674 CCCAAGATAC
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
14 9 0.16
15 47 0.84
ACGTcount: A:0.60, C:0.14, G:0.16, T:0.10
Consensus pattern (15 bp):
AAAGAAATCCAGAAT
Found at i:6497654 original size:45 final size:44
Alignment explanation
Indices: 6497593--6497677 Score: 116
Period size: 45 Copynumber: 1.9 Consensus size: 44
6497583 AGCAAAGATA
*
6497593 AAAGAAAACCGAATAAAGAAATCCAAAATAGAGAAACCCAGAAT
1 AAAGAAAACCGAATAAAGAAATCCAAAATAAAGAAACCCAGAAT
* * **
6497637 AAAGAAATCCAGAATAAAGAGATCCAGGATAAAGAAACCCA
1 AAAGAAAACC-GAATAAAGAAATCCAAAATAAAGAAACCCA
6497678 AGATACGATA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 9 0.26
45 26 0.74
ACGTcount: A:0.59, C:0.16, G:0.15, T:0.09
Consensus pattern (44 bp):
AAAGAAAACCGAATAAAGAAATCCAAAATAAAGAAACCCAGAAT
Found at i:6497682 original size:15 final size:15
Alignment explanation
Indices: 6497587--6497682 Score: 72
Period size: 15 Copynumber: 6.4 Consensus size: 15
6497577 TTATGGAGCA
*
6497587 AAGATAAAAGAAAACC
1 AAGAT-AAAGAAATCC
*
6497603 GA-ATAAAGAAATCC
1 AAGATAAAGAAATCC
* *
6497617 AAAATAGAGAAA-CC
1 AAGATAAAGAAATCC
*
6497631 CAGAATAAAGAAATCC
1 AAG-ATAAAGAAATCC
*
6497647 -AGAATAAAGAGATCC
1 AAG-ATAAAGAAATCC
* *
6497662 AGGATAAAGAAACCC
1 AAGATAAAGAAATCC
6497677 AAGATA
1 AAGATA
6497683 CGATACTATG
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
14 13 0.20
15 47 0.73
16 4 0.06
ACGTcount: A:0.59, C:0.15, G:0.16, T:0.10
Consensus pattern (15 bp):
AAGATAAAGAAATCC
Found at i:6501001 original size:47 final size:47
Alignment explanation
Indices: 6500888--6501076 Score: 175
Period size: 47 Copynumber: 3.9 Consensus size: 47
6500878 TGCACATAGT
* * ** *
6500888 CACATATCACATACCGAGGCCATAGCTCAGCCATGGTCTTATAC-GAAT
1 CACATATCAC--ACCGATGCCATAGCCCAGATATGGTCTTATACAGAAG
* * *
6500936 CACATATCACACTGATGCCATATCCCAGATATGGTCTTATACAGTAG
1 CACATATCACACCGATGCCATAGCCCAGATATGGTCTTATACAGAAG
* *
6500983 CACATATCACACCGATGCCATATCCC-GTATATGGTCTTATACGGAAG
1 CACATATCACACCGATGCCATAGCCCAG-ATATGGTCTTATACAGAAG
* * *
6501030 CACAAATCACATTTCTCCGAAGCCATAGCCCAGCTATGGTCTTATAC
1 CACATATCACA-----CCGATGCCATAGCCCAGATATGGTCTTATAC
6501077 GGAAATCACA
Statistics
Matches: 118, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
46 27 0.23
47 54 0.46
48 10 0.08
52 26 0.22
53 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (47 bp):
CACATATCACACCGATGCCATAGCCCAGATATGGTCTTATACAGAAG
Found at i:6502668 original size:14 final size:14
Alignment explanation
Indices: 6502649--6502681 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6502639 AAAGCAGAAT
6502649 GAAAATATACAA-AA
1 GAAAATA-ACAACAA
6502663 GAAAATAACAACAA
1 GAAAATAACAACAA
6502677 GAAAA
1 GAAAA
6502682 AAAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.73, C:0.09, G:0.09, T:0.09
Consensus pattern (14 bp):
GAAAATAACAACAA
Found at i:6522290 original size:37 final size:37
Alignment explanation
Indices: 6522249--6522323 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
6522239 AGGAAAATTA
6522249 ACGATACAAAATAGATGGAGAAAGAAAGGAATTACAG
1 ACGATACAAAATAGATGGAGAAAGAAAGGAATTACAG
*
6522286 ACGATACAAAATAGATGGAGAAAGAAAGGACTTACAG
1 ACGATACAAAATAGATGGAGAAAGAAAGGAATTACAG
6522323 A
1 A
6522324 GGAGAATAGA
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:0.53, C:0.09, G:0.24, T:0.13
Consensus pattern (37 bp):
ACGATACAAAATAGATGGAGAAAGAAAGGAATTACAG
Found at i:6524822 original size:59 final size:59
Alignment explanation
Indices: 6524729--6524867 Score: 224
Period size: 59 Copynumber: 2.4 Consensus size: 59
6524719 TGTTGCTGTT
* ** * *
6524729 TACAAATTGCTTAACACTTGGTATACATGGCTGCTGGTTCGAAAAGATAACAATTGATA
1 TACAAATTGCTTAACAGTTGGTATACATAACTGCTAGTTAGAAAAGATAACAATTGATA
*
6524788 TACAAATTGCTTAACAGTTGGTATACATAACTGCTAGTTAGAAAAGATAACAGTTGATA
1 TACAAATTGCTTAACAGTTGGTATACATAACTGCTAGTTAGAAAAGATAACAATTGATA
6524847 TACAAATTGCTTAACAGTTGG
1 TACAAATTGCTTAACAGTTGG
6524868 ACAACAATTA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
59 74 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (59 bp):
TACAAATTGCTTAACAGTTGGTATACATAACTGCTAGTTAGAAAAGATAACAATTGATA
Found at i:6527671 original size:13 final size:13
Alignment explanation
Indices: 6527653--6527680 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6527643 ATGCATCACT
6527653 ATCACTACCAGAC
1 ATCACTACCAGAC
6527666 ATCACTACCAGAC
1 ATCACTACCAGAC
6527679 AT
1 AT
6527681 GTTTTCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.36, G:0.07, T:0.18
Consensus pattern (13 bp):
ATCACTACCAGAC
Found at i:6528062 original size:47 final size:48
Alignment explanation
Indices: 6527988--6528104 Score: 182
Period size: 48 Copynumber: 2.5 Consensus size: 48
6527978 AACATCATGA
*
6527988 CAGATATACACAATAAACATCAGTTTGATAAT-GCATTCATACAATGG
1 CAGATATACACAATAAACATCAATTTGATAATGGCATTCATACAATGG
*
6528035 CAGATATACACAATACACATCAATTTGATAATGGCATTCATACAATGG
1 CAGATATACACAATAAACATCAATTTGATAATGGCATTCATACAATGG
* * *
6528083 CAGAAACAAACAATAAACATCA
1 CAGATATACACAATAAACATCA
6528105 TGCACATTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
47 30 0.48
48 33 0.52
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.24
Consensus pattern (48 bp):
CAGATATACACAATAAACATCAATTTGATAATGGCATTCATACAATGG
Found at i:6528256 original size:12 final size:12
Alignment explanation
Indices: 6528235--6528299 Score: 76
Period size: 12 Copynumber: 5.4 Consensus size: 12
6528225 ATGAGTGTTT
6528235 AAAATTGAAATC
1 AAAATTGAAATC
*
6528247 AAAATCGAAATC
1 AAAATTGAAATC
6528259 AAAATTGAAATC
1 AAAATTGAAATC
* ** *
6528271 AGAATCAAAATT
1 AAAATTGAAATC
*
6528283 AAAATTGAAATA
1 AAAATTGAAATC
6528295 AAAAT
1 AAAAT
6528300 AACCCTAAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (12 bp):
AAAATTGAAATC
Found at i:6528263 original size:18 final size:18
Alignment explanation
Indices: 6528242--6528299 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
6528232 TTTAAAATTG
*
6528242 AAATCAAAATCGAAATCA
1 AAATTAAAATCGAAATCA
*
6528260 AAATTGAAATC-AGAATCA
1 AAATTAAAATCGA-AATCA
* *
6528278 AAATTAAAATTGAAATAA
1 AAATTAAAATCGAAATCA
6528296 AAAT
1 AAAT
6528300 AACCCTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
17 1 0.03
18 31 0.94
19 1 0.03
ACGTcount: A:0.62, C:0.09, G:0.07, T:0.22
Consensus pattern (18 bp):
AAATTAAAATCGAAATCA
Found at i:6528265 original size:24 final size:24
Alignment explanation
Indices: 6528235--6528299 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
6528225 ATGAGTGTTT
*
6528235 AAAATTGAAATCAAAATCGAAATC
1 AAAATTGAAATCAAAATCAAAATC
* *
6528259 AAAATTGAAATCAGAATCAAAATT
1 AAAATTGAAATCAAAATCAAAATC
*
6528283 AAAATTGAAATAAAAAT
1 AAAATTGAAATCAAAAT
6528300 AACCCTAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (24 bp):
AAAATTGAAATCAAAATCAAAATC
Found at i:6529238 original size:27 final size:27
Alignment explanation
Indices: 6529200--6529254 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
6529190 AAACTTTACT
6529200 AATATAATTAGCTTGAGTTCAAATTTC
1 AATATAATTAGCTTGAGTTCAAATTTC
6529227 AATATAATTAGCTTGAGTTCAAATTTC
1 AATATAATTAGCTTGAGTTCAAATTTC
6529254 A
1 A
6529255 TTACATACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (27 bp):
AATATAATTAGCTTGAGTTCAAATTTC
Found at i:6529549 original size:10 final size:9
Alignment explanation
Indices: 6529523--6529564 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
6529513 TTTTTGTATT
6529523 ATTTTAAT-
1 ATTTTAATA
6529531 ATTTTAATA
1 ATTTTAATA
6529540 ATTATTAATA
1 ATT-TTAATA
*
6529550 ACTTTTAGTA
1 A-TTTTAATA
6529560 ATTTT
1 ATTTT
6529565 TAATTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 8 0.27
9 7 0.23
10 13 0.43
11 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (9 bp):
ATTTTAATA
Found at i:6533368 original size:28 final size:28
Alignment explanation
Indices: 6533336--6533405 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
6533326 ATAGTAAGTC
6533336 CGCACACTTAGTGCT-TA-ATAGTCAAACT
1 CGCACACTTAGTGCTATACA-A-TCAAACT
*
6533364 CGCACACTTAGTGCTATACAATTAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
*
6533392 TGCACACTTAGTGC
1 CGCACACTTAGTGC
6533406 CAATCTCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 34 0.89
29 3 0.08
30 1 0.03
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATCAAACT
Found at i:6538123 original size:3 final size:3
Alignment explanation
Indices: 6538115--6538144 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6538105 GAAAAAATTC
6538115 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6538145 TTCATTTCAC
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:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:6538384 original size:26 final size:26
Alignment explanation
Indices: 6538348--6538410 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
6538338 TTGTGGTTGT
*
6538348 TGATTTGATTAATTAATTCCATTAAC
1 TGATTTAATTAATTAATTCCATTAAC
* *
6538374 TGATTTAATTAATTGATTCTATTAAC
1 TGATTTAATTAATTAATTCCATTAAC
*
6538400 TG-TTTATTTAA
1 TGATTTAATTAA
6538411 AATTGTTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
25 8 0.24
26 25 0.76
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (26 bp):
TGATTTAATTAATTAATTCCATTAAC
Found at i:6538862 original size:13 final size:14
Alignment explanation
Indices: 6538810--6538864 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 14
6538800 AAGAAAATAA
*
6538810 TAATAATAATTAAAG
1 TAATTATAA-TAAAG
6538825 TATATTATAATAATA-
1 TA-ATTATAATAA-AG
6538840 TAA-TATAATAAAG
1 TAATTATAATAAAG
6538853 TAATTA-AATAAA
1 TAATTATAATAAA
6538865 ATGAAAGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 1 0.03
13 17 0.49
14 3 0.09
15 7 0.20
16 7 0.20
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (14 bp):
TAATTATAATAAAG
Found at i:6542284 original size:42 final size:42
Alignment explanation
Indices: 6542238--6542318 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
6542228 TAGAAAAGTT
*
6542238 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGATAGAAAGACTA
1 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGACTA
*
6542280 ACAGAGAGCAAACGTGAGAAAGAAAGAAGGAAAGAAAGA
1 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGA
6542319 AAGAAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.58, C:0.09, G:0.28, T:0.05
Consensus pattern (42 bp):
ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGACTA
Found at i:6543141 original size:47 final size:47
Alignment explanation
Indices: 6543077--6543187 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
6543067 GACATTGAGT
6543077 CGATG-AGACACTATGTGT-CGACTAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
6543124 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
*
6543171 CGGTGAAGCACTATGTG
1 CGATGAAGCACTATGTG
6543188 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:6551227 original size:23 final size:23
Alignment explanation
Indices: 6551201--6551275 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 23
6551191 AGACACTTTA
6551201 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
6551224 TGTGTCGTA--TCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
* **
6551245 TGTGTCGT-TTT-AGGCACTTTA
1 TGTGTCGTATTTCAGGCACCTCG
6551266 TGTGTCGTAT
1 TGTGTCGTAT
6551276 ATTGATCAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
21 35 0.76
22 2 0.04
23 9 0.20
ACGTcount: A:0.13, C:0.21, G:0.27, T:0.39
Consensus pattern (23 bp):
TGTGTCGTATTTCAGGCACCTCG
Found at i:6553526 original size:47 final size:47
Alignment explanation
Indices: 6553462--6553572 Score: 163
Period size: 47 Copynumber: 2.4 Consensus size: 47
6553452 GACATTGAGT
6553462 CGATG-AGACACTATGTGT-CGACTAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
6553509 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
6553556 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
6553573 CTTATCCCGG
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
47 53 0.93
48 4 0.07
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:6558421 original size:6 final size:6
Alignment explanation
Indices: 6558412--6558449 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
6558402 TCTGTACCTG
* *
6558412 ACTGTG ACTGTT ACTGTT ACTGTT ACTGTT ACCGTT AC
1 ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT AC
6558450 CATTACCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.42
Consensus pattern (6 bp):
ACTGTT
Found at i:6558455 original size:18 final size:18
Alignment explanation
Indices: 6558418--6558460 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
6558408 CCTGACTGTG
* **
6558418 ACTGTTACTGTTACTGTT
1 ACTGTTACCGTTACCATT
6558436 ACTGTTACCGTTACCATT
1 ACTGTTACCGTTACCATT
*
6558454 ACCGTTA
1 ACTGTTA
6558461 TGGTGTATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (18 bp):
ACTGTTACCGTTACCATT
Found at i:6559258 original size:42 final size:41
Alignment explanation
Indices: 6559199--6559281 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 41
6559189 AACCCACGAA
6559199 CCAGTCTTTTTTACTTTTTTTTATTCACATATACGTATCCTT
1 CCAGTCTTTTTTACTTTTTTTTATTCACATATACGTA-CCTT
6559241 CCAGTCTTTTTTACTTTTTTTTATTCACATATACGTACCTT
1 CCAGTCTTTTTTACTTTTTTTTATTCACATATACGTACCTT
6559282 TGTCTTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 4 0.10
42 37 0.90
ACGTcount: A:0.19, C:0.22, G:0.05, T:0.54
Consensus pattern (41 bp):
CCAGTCTTTTTTACTTTTTTTTATTCACATATACGTACCTT
Found at i:6567951 original size:23 final size:24
Alignment explanation
Indices: 6567925--6567984 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
6567915 ATAATTTTAA
*
6567925 TAAATAAAAATATATT-AAATTAT
1 TAAATAAAAATATATTCAAAATAT
*
6567948 TAAATAATAAATATTTTCAAAATAT
1 TAAATAA-AAATATATTCAAAATAT
*
6567973 TAAA-AATAATAT
1 TAAATAAAAATAT
6567985 GGGCAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 12 0.38
24 10 0.31
25 10 0.31
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAATAAAAATATATTCAAAATAT
Found at i:6567980 original size:24 final size:24
Alignment explanation
Indices: 6567925--6567981 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
6567915 ATAATTTTAA
*
6567925 TAAATAA-AAATATATTAAATTAT
1 TAAATAATAAATATATTAAAATAT
*
6567948 TAAATAATAAATATTTTCAAAATAT
1 TAAATAATAAATATATT-AAAATAT
6567973 TAAA-AATAA
1 TAAATAATAA
6567982 TATGGGCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 7 0.23
24 13 0.43
25 10 0.33
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
TAAATAATAAATATATTAAAATAT
Found at i:6569684 original size:11 final size:12
Alignment explanation
Indices: 6569657--6569689 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
6569647 AGATAATATG
6569657 ATAAAATACTAAA
1 ATAAAATA-TAAA
6569670 ATAAAATAT-AA
1 ATAAAATATAAA
6569681 ATAAAATAT
1 ATAAAATAT
6569690 TTTTTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 1 0.05
13 8 0.40
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAAAATATAAA
Found at i:6586277 original size:13 final size:13
Alignment explanation
Indices: 6586261--6586285 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6586251 TGCTATGGAA
6586261 AAGTACTTTTGAG
1 AAGTACTTTTGAG
6586274 AAGTACTTTTGA
1 AAGTACTTTTGA
6586286 AAAATTTAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
AAGTACTTTTGAG
Found at i:6586287 original size:26 final size:26
Alignment explanation
Indices: 6586225--6586288 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 26
6586215 AGTTCTTCAT
* **
6586225 TACTTTTAAAAAGTGTTTTTGAAAAG
1 TACTTTTGAAAAGTACTTTTGAAAAG
* * * *
6586251 TGCTATGGAAAAGTACTTTTGAGAAG
1 TACTTTTGAAAAGTACTTTTGAAAAG
6586277 TACTTTTGAAAA
1 TACTTTTGAAAA
6586289 ATTTAAGTGT
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (26 bp):
TACTTTTGAAAAGTACTTTTGAAAAG
Found at i:6590335 original size:23 final size:22
Alignment explanation
Indices: 6590309--6590382 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 22
6590299 TTTATTATTA
6590309 ATTTTAAAAATTTTGAAATATAT
1 ATTTTAAAAATTTT-AAATATAT
* **
6590332 ATTTGAAATGTTTTATAATATAT
1 ATTTTAAAAATTTTA-AATATAT
** *
6590355 -TTTTTTAAATATTAAATATAT
1 ATTTTAAAAATTTTAAATATAT
*
6590376 TTTTTAA
1 ATTTTAA
6590383 TAAAATAAAC
Statistics
Matches: 38, Mismatches: 11, Indels: 5
0.70 0.20 0.09
Matches are distributed among these distances:
21 7 0.18
22 13 0.34
23 18 0.47
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (22 bp):
ATTTTAAAAATTTTAAATATAT
Found at i:6594875 original size:6 final size:6
Alignment explanation
Indices: 6594866--6594899 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
6594856 TTGTGTACCA
* *
6594866 TTACCG TTACTG TGACTG TTACTG TTACTG TTAC
1 TTACTG TTACTG TTACTG TTACTG TTACTG TTAC
6594900 CGTTGCGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.44
Consensus pattern (6 bp):
TTACTG
Found at i:6595064 original size:18 final size:17
Alignment explanation
Indices: 6595041--6595093 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
6595031 GTTTGCTACG
6595041 GAATAATTGACTGTTACT
1 GAATAATTGACTGTTA-T
6595059 GAATAAATT-ACTGTTAT
1 GAAT-AATTGACTGTTAT
* *
6595076 TATATAACTGACTGTTAT
1 GA-ATAATTGACTGTTAT
6595094 AGAGTAACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 5 0.17
18 21 0.70
19 4 0.13
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (17 bp):
GAATAATTGACTGTTAT
Found at i:6596758 original size:21 final size:19
Alignment explanation
Indices: 6596741--6596794 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
6596731 TGGTTTATAT
6596741 TATTAAAAAATATATTTAA
1 TATTAAAAAATATATTTAA
*
6596760 TATTTAAAAAATAAAATTTAA
1 TA-TTAAAAAAT-ATATTTAA
*
6596781 AATTTAAAAAATAT
1 TA-TTAAAAAATAT
6596795 TAAAAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.07
20 10 0.33
21 18 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTAAAAAATATATTTAA
Found at i:6596806 original size:21 final size:20
Alignment explanation
Indices: 6596743--6596806 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 20
6596733 GTTTATATTA
* * *
6596743 TTAAAAAATATATTTAATAT
1 TTAAAAAATAAAATAAATAT
6596763 TTAAAAAATAAAATTTAAA-AT
1 TTAAAAAATAAAA--TAAATAT
6596784 TTAAAAAATATTAAA-AAATAT
1 TTAAAAAATA--AAATAAATAT
6596805 TT
1 TT
6596807 CAAATATGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
20 14 0.39
21 16 0.44
22 3 0.08
23 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TTAAAAAATAAAATAAATAT
Found at i:6597490 original size:7 final size:7
Alignment explanation
Indices: 6597478--6597502 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6597468 TCGAGTTCAA
6597478 TCATATT
1 TCATATT
6597485 TCATATT
1 TCATATT
6597492 TCATATT
1 TCATATT
6597499 TCAT
1 TCAT
6597503 GTCCTTAATT
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:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (7 bp):
TCATATT
Found at i:6597762 original size:8 final size:8
Alignment explanation
Indices: 6597725--6597762 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
6597715 AAAAATTTAC
6597725 ATTTTT-T
1 ATTTTTCT
*
6597732 ATTATTCT
1 ATTTTTCT
*
6597740 ATTTTTAT
1 ATTTTTCT
6597748 ATTTTTCT
1 ATTTTTCT
6597756 ATTTTTC
1 ATTTTTC
6597763 AAATTTCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
7 5 0.19
8 21 0.81
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (8 bp):
ATTTTTCT
Found at i:6600542 original size:28 final size:29
Alignment explanation
Indices: 6600502--6600560 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
6600492 TTTAATAAAG
6600502 TCCCAAATCCCTG-TTTTTTTTCCTTAGT
1 TCCCAAATCCCTGTTTTTTTTTCCTTAGT
*
6600530 TCCCAAATCCCTGTTTTTTTTTTCTTAGT
1 TCCCAAATCCCTGTTTTTTTTTCCTTAGT
6600559 TC
1 TC
6600561 AAAAAAGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.14, C:0.27, G:0.07, T:0.53
Consensus pattern (29 bp):
TCCCAAATCCCTGTTTTTTTTTCCTTAGT
Found at i:6605093 original size:46 final size:47
Alignment explanation
Indices: 6604820--6605088 Score: 393
Period size: 46 Copynumber: 5.8 Consensus size: 47
6604810 TTCGACATGA
* * * * *
6604820 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCACGT
* ** * *
6604866 TGCCATGGTATCATTCAACCATGGTCTTATTCATTTCCCTGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCACGT
6604913 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCACGT
6604959 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCACGT
* * *
6605005 TGCCATGGTATCTTTCAACCATGGTCTTACAC-GTTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCACGT
6605051 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTC
6605089 TATCAAAAAG
Statistics
Matches: 205, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
46 164 0.80
47 41 0.20
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.39
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATGTCACGT
Found at i:6607251 original size:11 final size:11
Alignment explanation
Indices: 6607235--6607286 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
6607225 TATACTAAAT
6607235 AAATAATAATA
1 AAATAATAATA
*
6607246 AAATAAT-ATT
1 AAATAATAATA
* *
6607256 AAATATCTCATA
1 AAATA-ATAATA
*
6607268 AAATATTAATA
1 AAATAATAATA
6607279 AAATAATA
1 AAATAATA
6607287 TTATCTAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:6608403 original size:17 final size:17
Alignment explanation
Indices: 6608381--6608414 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
6608371 TGAGTTCTAG
6608381 TAGCTATAGGAA-TCAAA
1 TAGCTAT-GGAATTCAAA
6608398 TAGCTATGGAATTCAAA
1 TAGCTATGGAATTCAAA
6608415 ATTTGAGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (17 bp):
TAGCTATGGAATTCAAA
Found at i:6609607 original size:26 final size:24
Alignment explanation
Indices: 6609578--6609694 Score: 69
Period size: 25 Copynumber: 4.6 Consensus size: 24
6609568 CTTATGAGTG
6609578 TCCCGATATATGGCTCTTCGTGAGCT
1 TCCCGATATATGGCTC-TC-TGAGCT
* *
6609604 TCCCGAT-TAAAGGCTATTTCATGAGCT
1 TCCCGATAT-ATGGC--TCTC-TGAGCT
* *
6609631 TCCTGAT-TAATGACTCTCTGGAGCT
1 TCCCGATAT-ATGGCTCTCT-GAGCT
* *
6609656 TCCCGATAT-TGGCTCGCTTGAACT
1 TCCCGATATATGGCTCTC-TGAGCT
*
6609680 TCACGATATATGGCT
1 TCCCGATATATGGCT
6609695 ATCCGGAATT
Statistics
Matches: 72, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
24 19 0.26
25 21 0.29
26 12 0.17
27 19 0.26
28 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (24 bp):
TCCCGATATATGGCTCTCTGAGCT
Found at i:6613869 original size:31 final size:31
Alignment explanation
Indices: 6613831--6613905 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
6613821 AGTTAGCATC
**
6613831 TTAATGACTTAAATAAAAACTTTTGGATAAT
1 TTAATGACTTAAATAAAAACTTTTAAATAAT
* * *
6613862 TTAATGACTTCAATGAAAATTTTTAAATAAT
1 TTAATGACTTAAATAAAAACTTTTAAATAAT
*
6613893 TTAGTGAC-TAAAT
1 TTAATGACTTAAAT
6613906 TATAACTTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 4 0.11
31 33 0.89
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (31 bp):
TTAATGACTTAAATAAAAACTTTTAAATAAT
Found at i:6614239 original size:21 final size:21
Alignment explanation
Indices: 6614206--6614280 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
6614196 AAAAATATAT
* * *
6614206 TTTTACATCATATAATTAAAA
1 TTTTAAATAATATAATAAAAA
6614227 TTTTAAATAATATAATAAAAA
1 TTTTAAATAATATAATAAAAA
6614248 --TTAAATTAA-A-AATAAAATA
1 TTTTAAA-TAATATAATAAAA-A
6614267 TTGTTAAA-AATATA
1 TT-TTAAATAATATA
6614281 TGATGTTTCG
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
18 7 0.16
19 7 0.16
20 5 0.11
21 19 0.43
22 6 0.14
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (21 bp):
TTTTAAATAATATAATAAAAA
Found at i:6614253 original size:19 final size:21
Alignment explanation
Indices: 6614215--6614268 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 21
6614205 TTTTTACATC
*
6614215 ATATAATTAAAATTTTAAATA
1 ATATAATTAAAATATTAAATA
6614236 ATATAA-TAAAA-ATTAAATTA
1 ATATAATTAAAATATTAAA-TA
6614256 A-A-AA-TAAAATATT
1 ATATAATTAAAATATT
6614269 GTTAAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.23
19 9 0.30
20 8 0.27
21 6 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATATAATTAAAATATTAAATA
Found at i:6614711 original size:18 final size:19
Alignment explanation
Indices: 6614688--6614723 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6614678 ATTTTAATAA
6614688 TTTTT-ATTTTTTATAAAG
1 TTTTTAATTTTTTATAAAG
*
6614706 TTTTTAATTTTTTTTAAA
1 TTTTTAATTTTTTATAAA
6614724 ATAATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTTAATTTTTTATAAAG
Done.