Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold173
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: 2040036
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 15 of 16
Found at i:1922691 original size:59 final size:58
Alignment explanation
Indices: 1922578--1922725 Score: 151
Period size: 59 Copynumber: 2.5 Consensus size: 58
1922568 ATGCTAACGG
* *
1922578 TTTATTTAATATAAATTAAAAGTTAAAATTTATATGAATATAAATAAAAAATAAAAAA
1 TTTATTTAATATAAATTAAAAATTAAAATTTATATGAACATAAATAAAAAATAAAAAA
* * * *
1922636 TTTAGTTTGATATAAATTAAAAATTAAAATTTAT-TTAAGCA-CAAT-AAAAATATAAAA
1 TTTA-TTTAATATAAATTAAAAATTAAAATTTATATGAA-CATAAATAAAAAATAAAAAA
*
1922693 TTTATCTTACT-TAAATGATAAAAATTAATAATT
1 TTTAT-TTAATATAAAT--TAAAAATTAA-AATT
1922726 ATTTTTTATT
Statistics
Matches: 76, Mismatches: 8, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
56 6 0.08
57 18 0.24
58 20 0.26
59 32 0.42
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.39
Consensus pattern (58 bp):
TTTATTTAATATAAATTAAAAATTAAAATTTATATGAACATAAATAAAAAATAAAAAA
Found at i:1923413 original size:22 final size:21
Alignment explanation
Indices: 1923385--1923467 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 21
1923375 TCAAACTATC
1923385 TATTTAAATTTAAATTATTATT
1 TATTTAAATTTAAATTATT-TT
*
1923407 TATTT-AATTAAAAATTATTTT
1 TATTTAAATT-TAAATTATTTT
*
1923428 TATATTAATATTTATA-TATTTT
1 TAT-TTAA-ATTTAAATTATTTT
*
1923450 ATAATTAAATTTAAATTA
1 -TATTTAAATTTAAATTA
1923468 AAAATATATC
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
21 15 0.30
22 27 0.54
23 5 0.10
24 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTAAATTTAAATTATTTT
Found at i:1923468 original size:33 final size:33
Alignment explanation
Indices: 1923388--1923468 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 33
1923378 AACTATCTAT
* *
1923388 TTAAATTTAAATTATTATTTATTTAATTAAAAA
1 TTAAATTTAAATTAATATTTATATAATTAAAAA
** * * * *
1923421 TTATTTTTATATTAATATTTATATATTTTATAA
1 TTAAATTTAAATTAATATTTATATAATTAAAAA
1923454 TTAAATTTAAATTAA
1 TTAAATTTAAATTAA
1923469 AAATATATCA
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TTAAATTTAAATTAATATTTATATAATTAAAAA
Found at i:1923500 original size:32 final size:32
Alignment explanation
Indices: 1923440--1923500 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
1923430 TATTAATATT
* *
1923440 TATATATTTTATAATTAAATTTAAATTAAAAA
1 TATATATTTTATAATAAAATATAAATTAAAAA
*
1923472 TATATCATTTTA-AATAAAATATATATTAA
1 TATAT-ATTTTATAATAAAATATAAATTAA
1923501 TGTGTTAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 19 0.76
33 6 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (32 bp):
TATATATTTTATAATAAAATATAAATTAAAAA
Found at i:1928073 original size:17 final size:16
Alignment explanation
Indices: 1928047--1928086 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1928037 AAAATTAAAA
1928047 TTAAATATATTCATAT
1 TTAAATATATTCATAT
*
1928063 TTAATATATATTCGTATT
1 TTAA-ATATATTCATA-T
1928081 TTAAAT
1 TTAAAT
1928087 TTAAATAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 4 0.19
17 12 0.57
18 5 0.24
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (16 bp):
TTAAATATATTCATAT
Found at i:1928532 original size:14 final size:14
Alignment explanation
Indices: 1928503--1928531 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1928493 CAACTCGACA
1928503 TTATAATTATTATT
1 TTATAATTATTATT
1928517 TTATAATT-TTATT
1 TTATAATTATTATT
1928530 TT
1 TT
1928532 TTTCCATCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATAATTATTATT
Found at i:1928735 original size:20 final size:20
Alignment explanation
Indices: 1928712--1928751 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1928702 TATAATATTC
*
1928712 AATACTTATTTAATATTAGA
1 AATACTTATTAAATATTAGA
1928732 AATACTTATTAAATATTAGA
1 AATACTTATTAAATATTAGA
1928752 TTTTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (20 bp):
AATACTTATTAAATATTAGA
Found at i:1931889 original size:20 final size:21
Alignment explanation
Indices: 1931864--1931906 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1931854 AGTTAACAAA
1931864 AATTT-ATTTTTTATTGATTT
1 AATTTAATTTTTTATTGATTT
*
1931884 AATTTAATTTTTTGTTGATTT
1 AATTTAATTTTTTATTGATTT
1931905 AA
1 AA
1931907 AAAATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (21 bp):
AATTTAATTTTTTATTGATTT
Found at i:1931958 original size:16 final size:15
Alignment explanation
Indices: 1931939--1931968 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1931929 TATCTTATAA
1931939 AAAAATAATAAAAATT
1 AAAAATAA-AAAAATT
1931955 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
1931969 CAATTTTTAT
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAAATAAAAAAATT
Found at i:1932376 original size:30 final size:31
Alignment explanation
Indices: 1932342--1932399 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1932332 AAATTGTTAT
1932342 TTTAATAATAAAAA-A-TTATTTTTATTTAAA
1 TTTAATAATAAAAATATTTA-TTTTATTTAAA
*
1932372 TTTAATTATAAAAATATTTATTTTATTT
1 TTTAATAATAAAAATATTTATTTTATTT
1932400 TTTTATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 13 0.52
31 9 0.36
32 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
TTTAATAATAAAAATATTTATTTTATTTAAA
Found at i:1933183 original size:16 final size:16
Alignment explanation
Indices: 1933098--1933195 Score: 65
Period size: 16 Copynumber: 5.9 Consensus size: 16
1933088 ATTTAAATTA
*
1933098 TAATTATAAATATATTTT
1 TAATTAT-AATATA-TAT
*
1933116 TAATTATATCATATTTATT
1 TAATTATA--ATATATA-T
1933135 GTAATTATAA-ATATAT
1 -TAATTATAATATATAT
* * *
1933151 TAATTATTATTTTTAT
1 TAATTATAATATATAT
*
1933167 TAATTATAATAAATAT
1 TAATTATAATATATAT
*
1933183 TAATCATAA-ATAT
1 TAATTATAATATAT
1933196 TCATTACGTA
Statistics
Matches: 63, Mismatches: 12, Indels: 13
0.72 0.14 0.15
Matches are distributed among these distances:
15 11 0.17
16 25 0.40
17 5 0.08
18 9 0.14
19 5 0.08
20 8 0.13
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (16 bp):
TAATTATAATATATAT
Found at i:1935191 original size:21 final size:20
Alignment explanation
Indices: 1935147--1935192 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1935137 ACTTGAAAGT
* *
1935147 TTAAATTATAATTTAAATAC
1 TTAAATTATAATTTAAAAAA
*
1935167 TTAAATTACTATTTTAAAAAA
1 TTAAATTA-TAATTTAAAAAA
1935188 TTAAA
1 TTAAA
1935193 AAAATTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAAATTATAATTTAAAAAA
Found at i:1935459 original size:32 final size:31
Alignment explanation
Indices: 1935387--1935482 Score: 92
Period size: 31 Copynumber: 3.1 Consensus size: 31
1935377 AATTTTTATA
* *
1935387 TTTTTATTAATATTTAAATAGT-A-TTAAAT
1 TTTTTATTAATATATAAATAATAATTTAAAT
*
1935416 TTAATTA-TAATAATATAAA-AATAATTTAAAAT
1 TT-TTTATTAAT-ATATAAATAATAATTT-AAAT
* *
1935448 TTTTTATTAATATTTAAATAATACTTTAAAT
1 TTTTTATTAATATATAAATAATAATTTAAAT
1935479 TTTT
1 TTTT
1935483 AAATCAAATC
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
29 8 0.15
30 10 0.19
31 19 0.35
32 17 0.31
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (31 bp):
TTTTTATTAATATATAAATAATAATTTAAAT
Found at i:1936265 original size:14 final size:14
Alignment explanation
Indices: 1936214--1936336 Score: 78
Period size: 14 Copynumber: 8.8 Consensus size: 14
1936204 TTCGTATATT
1936214 TATATTATATTTATA
1 TATATTATATTTA-A
* *
1936229 TATTTTATTATATAA
1 TATATTA-TATTTAA
1936244 TA-ATTATATTTAA
1 TATATTATATTTAA
*
1936257 TATATTATACTTAA
1 TATATTATATTTAA
* * *
1936271 TTTTATATAAATTT-T
1 -TATAT-TATATTTAA
*
1936286 TATATTATATTT-T
1 TATATTATATTTAA
*
1936299 TA-ATTAT-TTTATT
1 TATATTATATTTA-A
1936312 TATATTATATTT-A
1 TATATTATATTTAA
1936325 TATAATTATATT
1 TAT-ATTATATT
1936337 AGTTAAGTTA
Statistics
Matches: 87, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
11 3 0.03
12 5 0.06
13 23 0.26
14 30 0.34
15 16 0.18
16 10 0.11
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (14 bp):
TATATTATATTTAA
Found at i:1936275 original size:20 final size:19
Alignment explanation
Indices: 1936229--1936279 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
1936219 TATATTTATA
*
1936229 TATTTTATTATATAATAAT
1 TATTTTAATATATAATAAT
* *
1936248 TATATTTAATATATTATACT
1 TAT-TTTAATATATAATAAT
1936268 TAATTTT-ATATA
1 T-ATTTTAATATA
1936280 AATTTTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 8 0.30
20 17 0.63
21 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTTAATATATAATAAT
Found at i:1936325 original size:49 final size:50
Alignment explanation
Indices: 1936208--1936337 Score: 135
Period size: 49 Copynumber: 2.6 Consensus size: 50
1936198 TATTTATTCG
* *
1936208 TATATTTATATTATATTTATAT-ATTTTATTATATAATAATTATATTTAA
1 TATATTTATATTATATTTATATAAATTTATTATATAATAATTATAATTAA
* * * *
1936257 TATA-TTATACTTA-ATTTTATATAAATTT-TTATATTATATTTTTAATTAT
1 TATATTTATA-TTATA-TTTATATAAATTTATTATATAATAATTATAATTAA
*
1936306 TTTATTTATATTATATTTATAT-AATTATATTA
1 TATATTTATATTATATTTATATAAATT-TATTA
1936338 GTTAAGTTAA
Statistics
Matches: 67, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
48 10 0.15
49 44 0.66
50 13 0.19
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (50 bp):
TATATTTATATTATATTTATATAAATTTATTATATAATAATTATAATTAA
Found at i:1938382 original size:11 final size:11
Alignment explanation
Indices: 1938341--1938382 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
1938331 ATTTAAAAAT
1938341 ATATATTAATA
1 ATATATTAATA
1938352 AT-TATTATATA
1 ATATATTA-ATA
1938363 ATTATATTAATA
1 A-TATATTAATA
*
1938375 ATACATTA
1 ATATATTA
1938383 TCAATAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 5 0.19
11 12 0.44
12 5 0.19
13 5 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
ATATATTAATA
Found at i:1939390 original size:5 final size:5
Alignment explanation
Indices: 1939380--1939411 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
1939370 TTACTATCAC
1939380 TATTT TATTT TATTTT TATTT TATTT TATTT T
1 TATTT TATTT TA-TTT TATTT TATTT TATTT T
1939412 TACAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:1939401 original size:16 final size:16
Alignment explanation
Indices: 1939380--1939413 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1939370 TTACTATCAC
1939380 TATTTTATTTTATTTT
1 TATTTTATTTTATTTT
1939396 TATTTTATTTTATTTT
1 TATTTTATTTTATTTT
1939412 TA
1 TA
1939414 CAAAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TATTTTATTTTATTTT
Found at i:1941191 original size:12 final size:11
Alignment explanation
Indices: 1941147--1941187 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1941137 TTAGCATTTA
1941147 TTGAATTTAGT
1 TTGAATTTAGT
*
1941158 TTGAAATTAGT
1 TTGAATTTAGT
* *
1941169 TTGATTTTATT
1 TTGAATTTAGT
1941180 TTGAATTT
1 TTGAATTT
1941188 TATTGAATTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.59
Consensus pattern (11 bp):
TTGAATTTAGT
Found at i:1941193 original size:21 final size:20
Alignment explanation
Indices: 1941142--1941196 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
1941132 CTTATTTAGC
1941142 ATTTATTGAATTTAGTTTGA
1 ATTTATTGAATTTAGTTTGA
* * *
1941162 AATTAGTTTGATTTTATTTTGA
1 ATTTA--TTGAATTTAGTTTGA
1941184 ATTTTATTGAATT
1 A-TTTATTGAATT
1941197 CGACTTGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
20 4 0.15
21 6 0.22
22 14 0.52
23 3 0.11
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (20 bp):
ATTTATTGAATTTAGTTTGA
Found at i:1943537 original size:16 final size:17
Alignment explanation
Indices: 1943496--1943529 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
1943486 AATATTTTTT
1943496 ATATATATTTAAATTTAA
1 ATATA-ATTTAAATTTAA
1943514 ATATAATTT-AATTTAA
1 ATATAATTTAAATTTAA
1943530 TAATAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATAATTTAAATTTAA
Found at i:1943758 original size:2 final size:2
Alignment explanation
Indices: 1943751--1943776 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1943741 AATCTTTGCA
1943751 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1943777 CTAAAACTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1944233 original size:21 final size:19
Alignment explanation
Indices: 1944209--1944252 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
1944199 TATCTCTATT
*
1944209 TAAATCTTTTTAATTATTAAA
1 TAAAT-TTTTTAAAT-TTAAA
1944230 TAAA-TTTTTAAATTTAAA
1 TAAATTTTTTAAATTTAAA
1944248 TAAAT
1 TAAAT
1944253 AATTCGATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 9 0.43
19 8 0.38
21 4 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAATTTTTTAAATTTAAA
Found at i:1944239 original size:19 final size:18
Alignment explanation
Indices: 1944215--1944252 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1944205 TATTTAAATC
*
1944215 TTTTTAATTATTAAATAAA
1 TTTTTAAAT-TTAAATAAA
1944234 TTTTTAAATTTAAATAAA
1 TTTTTAAATTTAAATAAA
1944252 T
1 T
1944253 AATTCGATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTTAAATTTAAATAAA
Found at i:1944746 original size:2 final size:2
Alignment explanation
Indices: 1944739--1944818 Score: 54
Period size: 2 Copynumber: 39.5 Consensus size: 2
1944729 CAAGCACACT
* * * * *
1944739 TA TA TA TA TA TA TA TA TA TG TA TG TA TA AA TG TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1944781 CA TA TA TA CTCC TA TA -A AA TA CA TA TA TA TA TA TA TA T
1 TA TA TA TA -T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1944819 CCGAGTAATA
Statistics
Matches: 58, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
1 1 0.02
2 55 0.95
3 2 0.03
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1946317 original size:30 final size:30
Alignment explanation
Indices: 1946259--1946317 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1946249 AAAATAAAAT
*
1946259 TTAAATAAAATAATTATAATAATAATTTAG
1 TTAAATAAAATAAATATAATAATAATTTAG
* *
1946289 TTAAGTAAAATAAAATATTATAAT-ATTTA
1 TTAAATAAAAT-AAATATAATAATAATTTA
1946318 AACTTTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (30 bp):
TTAAATAAAATAAATATAATAATAATTTAG
Found at i:1946455 original size:28 final size:28
Alignment explanation
Indices: 1946418--1946474 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
1946408 TTATTTTAAA
* *
1946418 ATTTTATAAAAT-AATATTATAATAAATT
1 ATTTCATAAAATAAATATT-TAACAAATT
1946446 ATTTCATAAAATAAATATTTAACAAATT
1 ATTTCATAAAATAAATATTTAACAAATT
1946474 A
1 A
1946475 AATAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (28 bp):
ATTTCATAAAATAAATATTTAACAAATT
Found at i:1946734 original size:16 final size:16
Alignment explanation
Indices: 1946710--1946740 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1946700 TCAATTCTAT
1946710 TTTGATTTGATTTCGA
1 TTTGATTTGATTTCGA
*
1946726 TTTGCTTTGATTTCG
1 TTTGATTTGATTTCG
1946741 GTTTATAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.58
Consensus pattern (16 bp):
TTTGATTTGATTTCGA
Found at i:1947542 original size:32 final size:32
Alignment explanation
Indices: 1947500--1947588 Score: 142
Period size: 32 Copynumber: 2.8 Consensus size: 32
1947490 ATAGAGCAAT
*
1947500 ATTAATCATAAATTTGATAAATATTAAACATA
1 ATTACTCATAAATTTGATAAATATTAAACATA
*
1947532 ATTACTCATAAATTTGATAAATATTAAATATA
1 ATTACTCATAAATTTGATAAATATTAAACATA
* *
1947564 ATTACTCGTAAATTTGATGAATATT
1 ATTACTCATAAATTTGATAAATATT
1947589 TGATACAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.40
Consensus pattern (32 bp):
ATTACTCATAAATTTGATAAATATTAAACATA
Found at i:1949861 original size:15 final size:16
Alignment explanation
Indices: 1949834--1949866 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1949824 CTCATAAACC
*
1949834 ATAATTGAATTTTTGT
1 ATAATTGAATTTTAGT
1949850 ATAATT-AATTTTAGT
1 ATAATTGAATTTTAGT
1949865 AT
1 AT
1949867 TATTTTAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (16 bp):
ATAATTGAATTTTAGT
Found at i:1950421 original size:33 final size:35
Alignment explanation
Indices: 1950366--1950436 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 35
1950356 GTTATAAATT
*
1950366 AAATTAATAAGAATATTAATTTAATAAAAATTTAA
1 AAATGAATAAGAATATTAATTTAATAAAAATTTAA
* * *
1950401 AAATGAATAAGCATA-T-ATTTAATATAATTTTAA
1 AAATGAATAAGAATATTAATTTAATAAAAATTTAA
1950434 AAA
1 AAA
1950437 AGTTCATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 18 0.56
34 1 0.03
35 13 0.41
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (35 bp):
AAATGAATAAGAATATTAATTTAATAAAAATTTAA
Found at i:1950797 original size:13 final size:14
Alignment explanation
Indices: 1950773--1950807 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1950763 TTCATATCAA
1950773 AATAATAATATTTT
1 AATAATAATATTTT
1950787 AATAA-AATATTTT
1 AATAATAATATTTT
1950800 AA-AATAAT
1 AATAATAAT
1950808 GTTATTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 2 0.10
13 13 0.65
14 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATAATAATATTTT
Found at i:1951076 original size:15 final size:15
Alignment explanation
Indices: 1951028--1951076 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
1951018 TTCATTTATT
*
1951028 TATAAATATTTAAAA
1 TATAATTATTTAAAA
*
1951043 TAGACATATATTT-AAA
1 TATA-AT-TATTTAAAA
1951059 TATAATTATTTAAAA
1 TATAATTATTTAAAA
1951074 TAT
1 TAT
1951077 TTTTAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 5 0.18
15 11 0.39
16 7 0.25
17 5 0.18
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
TATAATTATTTAAAA
Found at i:1952850 original size:14 final size:14
Alignment explanation
Indices: 1952831--1952914 Score: 62
Period size: 14 Copynumber: 5.4 Consensus size: 14
1952821 TTTAATTAAA
1952831 TAAATATTTTTTAT
1 TAAATATTTTTTAT
1952845 TAAATATTTATTATAT
1 TAAATATTT-TT-TAT
*
1952861 TTAATAATTATTCGTTAT
1 TAAAT-ATT-TT--TTAT
*
1952879 TAAAATTATTTTATAT
1 T-AAA-TATTTTTTAT
1952895 TAAAT-TTTTTTAAT
1 TAAATATTTTTT-AT
1952909 TAAATA
1 TAAATA
1952915 ATTTAATTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
13 5 0.09
14 17 0.30
15 5 0.09
16 11 0.20
17 4 0.07
18 7 0.12
19 6 0.11
20 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (14 bp):
TAAATATTTTTTAT
Found at i:1952866 original size:16 final size:15
Alignment explanation
Indices: 1952812--1952924 Score: 54
Period size: 16 Copynumber: 7.1 Consensus size: 15
1952802 TACAATACAA
*
1952812 ATTATAATATTTAATTA
1 ATTA-AATATTT-ATTT
*
1952829 AATAAATATTT-TTT
1 ATTAAATATTTATTT
1952843 ATTAAATATTTATTAT
1 ATTAAATATTTATT-T
* *
1952859 ATTTAATAATTATTCGTT
1 ATTAAATATTTA-T--TT
*
1952877 ATTAAAATTATTT-TAT
1 ATT-AAA-TATTTATTT
1952893 ATTAAAT-TTT-TTT
1 ATTAAATATTTATTT
1952906 AATTAAATAATTTAATTT
1 -ATTAAAT-ATTT-ATTT
1952924 A
1 A
1952925 AATACTCTAA
Statistics
Matches: 75, Mismatches: 9, Indels: 24
0.69 0.08 0.22
Matches are distributed among these distances:
13 5 0.07
14 20 0.27
15 5 0.07
16 25 0.33
17 5 0.07
18 8 0.11
19 3 0.04
20 4 0.05
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (15 bp):
ATTAAATATTTATTT
Found at i:1952905 original size:15 final size:15
Alignment explanation
Indices: 1952876--1952927 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
1952866 AATTATTCGT
1952876 TATTAAAATTATTTTA
1 TATT-AAATTATTTTA
*
1952892 TATTAAATTTTTTTA
1 TATTAAATTATTTTA
* *
1952907 -ATTAAATAATTTAA
1 TATTAAATTATTTTA
1952921 T-TTAAAT
1 TATTAAAT
1952928 ACTCTAATCG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 17 0.55
15 10 0.32
16 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTAAATTATTTTA
Found at i:1953702 original size:24 final size:24
Alignment explanation
Indices: 1953675--1953743 Score: 56
Period size: 24 Copynumber: 3.0 Consensus size: 24
1953665 ATTTAAATTC
1953675 ATTTAAATTATTATTTAATAATAA
1 ATTTAAATTATTATTTAATAATAA
** *
1953699 ATTTTTATT-TTACTTTAATTATAA
1 ATTTAAATTATTA-TTTAATAATAA
**
1953723 AAATAAATTA--ATTTAA-AATAA
1 ATTTAAATTATTATTTAATAATAA
1953744 TATTATTATA
Statistics
Matches: 35, Mismatches: 8, Indels: 7
0.70 0.16 0.14
Matches are distributed among these distances:
21 4 0.11
22 5 0.14
23 4 0.11
24 22 0.63
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTAAATTATTATTTAATAATAA
Found at i:1954562 original size:28 final size:29
Alignment explanation
Indices: 1954499--1954565 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
1954489 CGAATAATTA
*
1954499 TTAATATAA-TAAAATAATAAATTTTTAT
1 TTAATTTAATTAAAATAATAAATTTTTAT
*
1954527 TTAAATTTAATTAAAA-AATAATTTTTTAAT
1 TT-AATTTAATTAAAATAATAAATTTTT-AT
1954557 TT-ATTTAAT
1 TTAATTTAAT
1954566 AATAATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 9 0.26
29 16 0.47
30 9 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TTAATTTAATTAAAATAATAAATTTTTAT
Found at i:1954708 original size:16 final size:16
Alignment explanation
Indices: 1954662--1954701 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 16
1954652 TTTTATTAAA
1954662 TAAAAATAAAATTATAATT
1 TAAAAATAAAA--A-AATT
1954681 TAAAAATAAAAAAATT
1 TAAAAATAAAAAAATT
1954697 TAAAA
1 TAAAA
1954702 TTTAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 1 0.05
19 11 0.52
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAAATAAAAAAATT
Found at i:1954960 original size:5 final size:5
Alignment explanation
Indices: 1954952--1955011 Score: 52
Period size: 5 Copynumber: 12.0 Consensus size: 5
1954942 TTTTGTTTTT
* * * *
1954952 ATTTA ATTTG ATTTGA TTTTA ATTTTT ATTTA ATTTA GTTTA ATTTA ATTT-
1 ATTTA ATTTA ATTT-A ATTTA A-TTTA ATTTA ATTTA ATTTA ATTTA ATTTA
1955003 -TTTA ATTTA
1 ATTTA ATTTA
1955012 TTAGATAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
3 3 0.07
5 33 0.77
6 7 0.16
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (5 bp):
ATTTA
Found at i:1955006 original size:27 final size:27
Alignment explanation
Indices: 1954947--1955004 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
1954937 AACGTTTTTG
*
1954947 TTTTTATTTAATTTGATTTGATTTTAA
1 TTTTTATTTAATTTGATTTGAATTTAA
1954974 TTTTTATTTAATTT-AGTTT-AATTTAA
1 TTTTTATTTAATTTGA-TTTGAATTTAA
1955000 TTTTT
1 TTTTT
1955005 TAATTTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (27 bp):
TTTTTATTTAATTTGATTTGAATTTAA
Found at i:1955992 original size:24 final size:23
Alignment explanation
Indices: 1955950--1955996 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1955940 TTCAATTTAT
*
1955950 AAATTTAAAAAATCGAAATTATTA
1 AAATTGAAAAAATCGAAA-TATTA
1955974 AAATTGAATAAAATC-AAATATTA
1 AAATTGAA-AAAATCGAAATATTA
1955997 TTTTTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 10 0.48
25 6 0.29
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (23 bp):
AAATTGAAAAAATCGAAATATTA
Found at i:1957290 original size:13 final size:13
Alignment explanation
Indices: 1957272--1957296 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1957262 ACTTGGACTC
1957272 AGATATAAATATT
1 AGATATAAATATT
1957285 AGATATAAATAT
1 AGATATAAATAT
1957297 ATATCTAATA
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:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
AGATATAAATATT
Found at i:1960230 original size:13 final size:14
Alignment explanation
Indices: 1960186--1960246 Score: 67
Period size: 13 Copynumber: 4.6 Consensus size: 14
1960176 CTCATAAAAG
1960186 AATTTAAAATATTTA
1 AATTTAAAATA-TTA
*
1960201 AA-TAAAAATATTA
1 AATTTAAAATATTA
1960214 AATTTAAAATA-TA
1 AATTTAAAATATTA
*
1960227 AATTT-AAATA-AA
1 AATTTAAAATATTA
1960239 AATTTAAA
1 AATTTAAA
1960247 TTTTTAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
12 11 0.27
13 14 0.34
14 14 0.34
15 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATTTAAAATATTA
Found at i:1960241 original size:12 final size:12
Alignment explanation
Indices: 1960213--1960247 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1960203 TAAAAATATT
*
1960213 AAATTTAAAATAT
1 AAATTT-AAATAA
1960226 AAATTTAAATAA
1 AAATTTAAATAA
1960238 AAATTTAAAT
1 AAATTTAAAT
1960248 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATTTAAATAA
Found at i:1960266 original size:19 final size:20
Alignment explanation
Indices: 1960229--1960269 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1960219 AAAATATAAA
**
1960229 TTTAAATAAAAATTTAAATT
1 TTTAAATAAAAATCAAAATT
1960249 TTTAAA-AAAAATCAAAATT
1 TTTAAATAAAAATCAAAATT
1960268 TT
1 TT
1960270 ATTTTAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTAAATAAAAATCAAAATT
Found at i:1960269 original size:18 final size:20
Alignment explanation
Indices: 1960229--1960270 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
1960219 AAAATATAAA
* *
1960229 TTTAAATAAAAATTTAAATT
1 TTTAAATAAAAATTCAAAAT
1960249 TTTAAA-AAAAA-TCAAAAT
1 TTTAAATAAAAATTCAAAAT
1960267 TTTA
1 TTTA
1960271 TTTTAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 5 0.25
20 6 0.30
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTAAATAAAAATTCAAAAT
Found at i:1960392 original size:21 final size:21
Alignment explanation
Indices: 1960366--1960405 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1960356 TAATTTTTTT
* *
1960366 ATATAAAATATATATATATTG
1 ATATAAAAGATAAATATATTG
1960387 ATATAAAAGATAAATATAT
1 ATATAAAAGATAAATATAT
1960406 ATAATATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
ATATAAAAGATAAATATATTG
Found at i:1962587 original size:17 final size:16
Alignment explanation
Indices: 1962539--1962588 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
1962529 ACGAATATAT
*
1962539 TAAAATTTATATAACA
1 TAAAATTTATATAATA
*
1962555 T-AAA-TTATTATCATA
1 TAAAATTTA-TATAATA
1962570 TCAAAATTTATATAATA
1 T-AAAATTTATATAATA
1962587 TA
1 TA
1962589 TAATATCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
14 3 0.11
15 9 0.33
16 2 0.07
17 10 0.37
18 3 0.11
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAATTTATATAATA
Found at i:1962999 original size:265 final size:266
Alignment explanation
Indices: 1962510--1963038 Score: 835
Period size: 266 Copynumber: 2.0 Consensus size: 266
1962500 ATATAAATAA
* * * * *
1962510 TTAAATATGATAAGAATATACGAATATATTAAAATTTATATAACATAAATTATTATCATATCAAA
1 TTAAATATGATAAAAATATACGAATATATCAAAATTTATATAACACAAACTATTATCATATAAAA
* * * *
1962575 ATTTATATAATATATAATATCTTAAATATAATTATGTTATGAAACATAAAAATTCACAAATAAAA
66 AATTATATAATATATAATATCTTAAATATAATTATGATATAAAACATAAAAATTCACAAACAAAA
* *
1962640 TATGAATATATAAATTTATCAAATCTACCTAAAATCAATTTTCAATTGCAACAAAAATCTACATT
131 TACGAATACATAAATTTATCAAATCTACCTAAAATCAATTTTCAATTGCAACAAAAATCTACATT
* *
1962705 TTTATTTTTCTTGGTCCAATCTAGATTTTGATTAAAAAAGTGATAAATAGTAAATGGCCTCAATC
196 TTTATTTTTCTTGGTCCAATCTAGATTTTGATTAAAAAAGTGATAAATAGTAAATGACCCCAATC
1962770 TTTAAG
261 TTTAAG
*
1962776 TTAAATATGATAAAAATATATGAATATATCAAAATTTATATAACACAAACTATTATCATATAAAA
1 TTAAATATGATAAAAATATACGAATATATCAAAATTTATATAACACAAACTATTATCATATAAAA
* * **
1962841 AATTATATAATATATAATATCTTAAATATAATTATGATATAAAACGTAAAAATTTATGAACAAAA
66 AATTATATAATATATAATATCTTAAATATAATTATGATATAAAACATAAAAATTCACAAACAAAA
* * * *
1962906 TACGAATACAT-AATTTATCAAATCTACTTAAAATCAATTTTCAATTGCAATACAAATTTACATT
131 TACGAATACATAAATTTATCAAATCTACCTAAAATCAATTTTCAATTGCAACAAAAATCTACATT
**
1962970 TTTATTTTTCTTGGTCCAATCTAGATTTTGATTAAAAAAGTGATAAATCTTAAATGACCCCAATC
196 TTTATTTTTCTTGGTCCAATCTAGATTTTGATTAAAAAAGTGATAAATAGTAAATGACCCCAATC
1963035 TTTA
261 TTTA
1963039 TGTCCTAAGT
Statistics
Matches: 239, Mismatches: 24, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
265 114 0.48
266 125 0.52
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (266 bp):
TTAAATATGATAAAAATATACGAATATATCAAAATTTATATAACACAAACTATTATCATATAAAA
AATTATATAATATATAATATCTTAAATATAATTATGATATAAAACATAAAAATTCACAAACAAAA
TACGAATACATAAATTTATCAAATCTACCTAAAATCAATTTTCAATTGCAACAAAAATCTACATT
TTTATTTTTCTTGGTCCAATCTAGATTTTGATTAAAAAAGTGATAAATAGTAAATGACCCCAATC
TTTAAG
Found at i:1963438 original size:20 final size:19
Alignment explanation
Indices: 1963415--1963461 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
1963405 ATTACATATA
*
1963415 ATTTTTAAATATATAAAAAT
1 ATTTTTAAAAAT-TAAAAAT
*
1963435 ATTTTTTAAAAATTAAATAT
1 A-TTTTTAAAAATTAAAAAT
1963455 ATTTTTA
1 ATTTTTA
1963462 TTTTTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.25
20 8 0.33
21 10 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTTTAAAAATTAAAAAT
Found at i:1963673 original size:8 final size:8
Alignment explanation
Indices: 1963662--1963708 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
1963652 TTTTAAAATT
1963662 TATATAAA
1 TATATAAA
1963670 TATA-AAA
1 TATATAAA
*
1963677 TATTTTAAA
1 TA-TATAAA
1963686 TATAATAAAA
1 TAT-AT-AAA
1963696 TATATAAA
1 TATATAAA
1963704 TATAT
1 TATAT
1963709 TATAAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
7 5 0.15
8 14 0.42
9 8 0.24
10 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TATATAAA
Found at i:1963693 original size:19 final size:19
Alignment explanation
Indices: 1963608--1963717 Score: 63
Period size: 18 Copynumber: 5.9 Consensus size: 19
1963598 TTGATAATAT
*
1963608 TAAATATAAT--ATTATTA
1 TAAATATAATAAAATATTA
*
1963625 TATAATATGAA-AAAATAATA
1 TA-AATAT-AATAAAATATTA
* **
1963645 TTAATTATTTTAAAAT-TTA
1 -TAAATATAATAAAATATTA
*
1963664 TATAA-AT-ATAAAATATTT
1 TA-AATATAATAAAATATTA
1963682 TAAATATAATAAAATA-TA
1 TAAATATAATAAAATATTA
*
1963700 TAAATATATTATAAATAT
1 TAAATATAATA-AAATAT
1963718 ATGAATAATT
Statistics
Matches: 70, Mismatches: 11, Indels: 21
0.69 0.11 0.21
Matches are distributed among these distances:
17 10 0.14
18 26 0.37
19 18 0.26
20 14 0.20
21 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (19 bp):
TAAATATAATAAAATATTA
Found at i:1963704 original size:27 final size:28
Alignment explanation
Indices: 1963641--1963718 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 28
1963631 ATGAAAAAAT
* *
1963641 AATAT-TAATTATTTTAAA-ATTTATATA
1 AATATATAAATATTTTAAATA-TAATATA
1963668 AATATA-AAATATTTTAAATATAATA-A
1 AATATATAAATATTTTAAATATAATATA
1963694 AATATATAAATATATTATAAATATA
1 AATATATAAATAT-TT-TAAATATA
1963719 TGAATAATTG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
26 7 0.16
27 26 0.59
28 3 0.07
29 8 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AATATATAAATATTTTAAATATAATATA
Found at i:1963718 original size:19 final size:18
Alignment explanation
Indices: 1963662--1963724 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 18
1963652 TTTTAAAATT
*
1963662 TATATAAATATAA-AATA
1 TATATAAATATAATAAAA
*
1963679 T-TTTAAATATAATAAAA
1 TATATAAATATAATAAAA
*
1963696 TATATAAATATATTATAAA
1 TATATAAATATAATA-AAA
*
1963715 TATATGAATA
1 TATATAAATA
1963725 ATTGTATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
16 10 0.26
17 5 0.13
18 11 0.29
19 12 0.32
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
TATATAAATATAATAAAA
Found at i:1963962 original size:16 final size:16
Alignment explanation
Indices: 1963936--1963977 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1963926 ATAAAATATT
1963936 TAATA-AATATAAAAA
1 TAATATAATATAAAAA
*
1963951 TAATATAATATAAATA
1 TAATATAATATAAAAA
*
1963967 TAAAATAATAT
1 TAATATAATAT
1963978 TTAAATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAATATAATATAAAAA
Found at i:1963976 original size:24 final size:24
Alignment explanation
Indices: 1963938--1964011 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
1963928 AAAATATTTA
*
1963938 ATAAATAT-AAA-AATAATATAAT
1 ATAAATATAAAATAATAATTTAAT
1963960 ATAAATATAAAATAAT-ATTTAAAT
1 ATAAATATAAAATAATAATTT-AAT
**
1963984 ATAAAT-TATCATAATATATTTAAT
1 ATAAATATAAAATAATA-ATTTAAT
1964008 ATAA
1 ATAA
1964012 TTATTGTATG
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
22 8 0.18
23 13 0.30
24 19 0.43
25 4 0.09
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAAATATAAAATAATAATTTAAT
Found at i:1963988 original size:6 final size:6
Alignment explanation
Indices: 1963938--1963989 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
1963928 AAAATATTTA
* *
1963938 ATAAAT ATAAAA AT-AAT AT-AAT ATAAAT ATAAA- ATAATAT TTAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAA-AT ATAAAT
1963984 ATAAAT
1 ATAAAT
1963990 TATCATAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 13 0.33
6 23 0.59
7 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATAAAT
Found at i:1965259 original size:29 final size:29
Alignment explanation
Indices: 1965186--1965259 Score: 121
Period size: 29 Copynumber: 2.6 Consensus size: 29
1965176 AGTTAGTTTT
*
1965186 TGAGCAAATCTGATTCTTTTGGGGGTACA
1 TGAGCAAATCTGATTTTTTTGGGGGTACA
*
1965215 TGAGCAAACCTGATTTTTTTGGGGGTACA
1 TGAGCAAATCTGATTTTTTTGGGGGTACA
*
1965244 TGAGCACATCTGATTT
1 TGAGCAAATCTGATTT
1965260 AAGTTGCCTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (29 bp):
TGAGCAAATCTGATTTTTTTGGGGGTACA
Found at i:1966057 original size:5 final size:5
Alignment explanation
Indices: 1966041--1966084 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
1966031 AATTATTTTA
* *
1966041 AATTT AAATTT AATTT AATTT GATTT GATTT AATTT AATTT AAT
1 AATTT -AATTT AATTT AATTT AATTT AATTT AATTT AATTT AAT
1966085 AAAAAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 31 0.86
6 5 0.14
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:1966114 original size:14 final size:15
Alignment explanation
Indices: 1966095--1966123 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1966085 AAAAAAATAT
1966095 ATTAAT-AATTTAAA
1 ATTAATAAATTTAAA
1966109 ATTAATAAATTTAAA
1 ATTAATAAATTTAAA
1966124 TCTAATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTAATAAATTTAAA
Found at i:1966134 original size:15 final size:15
Alignment explanation
Indices: 1966095--1966135 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1966085 AAAAAAATAT
1966095 ATTAA-TAATTTAAA
1 ATTAATTAATTTAAA
*
1966109 ATTAATAAATTT-AA
1 ATTAATTAATTTAAA
1966123 ATCTAATTAATTT
1 AT-TAATTAATTT
1966136 TAATATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAATTAATTTAAA
Found at i:1966153 original size:22 final size:21
Alignment explanation
Indices: 1966114--1966166 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
1966104 TTAAAATTAA
1966114 TAAATTTAAATCTAATTAATTT
1 TAAA-TTAAATCTAATTAATTT
* *
1966136 TAATATTAAATTTTATTAATTT
1 TAA-ATTAAATCTAATTAATTT
1966158 TAAATTAAA
1 TAAATTAAA
1966167 ATAATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 6 0.21
22 21 0.75
23 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAATTAAATCTAATTAATTT
Found at i:1966182 original size:15 final size:16
Alignment explanation
Indices: 1966162--1966219 Score: 59
Period size: 15 Copynumber: 3.7 Consensus size: 16
1966152 TAATTTTAAA
1966162 TTAAAATAA-TAAAAT
1 TTAAAATAATTAAAAT
1966177 TTAAAATAATTTAAAAT
1 TTAAAATAA-TTAAAAT
*
1966194 TT-AAATAAATT-TAAT
1 TTAAAAT-AATTAAAAT
*
1966209 TTAAATTAATT
1 TTAAAATAATT
1966220 CGAATTAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 18 0.49
16 9 0.24
17 10 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAAATAATTAAAAT
Found at i:1966194 original size:31 final size:32
Alignment explanation
Indices: 1966152--1966219 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
1966142 TAAATTTTAT
*
1966152 TAATTTTAAATTAAAAT-AATAAAATTTAAAA
1 TAATTTAAAATTAAAATAAATAAAATTTAAAA
* ** *
1966183 TAATTTAAAATTTAAATAAATTTAATTTAAAT
1 TAATTTAAAATTAAAATAAATAAAATTTAAAA
1966215 TAATT
1 TAATT
1966220 CGAATTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 15 0.48
32 16 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
TAATTTAAAATTAAAATAAATAAAATTTAAAA
Found at i:1966217 original size:10 final size:10
Alignment explanation
Indices: 1966174--1966233 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
1966164 AAAATAATAA
*
1966174 AATTTAAAAT
1 AATTTAAATT
1966184 AATTTAAAATTT
1 AATTT-AAA-TT
*
1966196 AA-ATAAATTT
1 AATTTAAA-TT
1966206 AATTTAAATT
1 AATTTAAATT
**
1966216 AATTCGAATT
1 AATTTAAATT
1966226 AATTTAAA
1 AATTTAAA
1966234 AGTGCAACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
10 29 0.73
11 8 0.20
12 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (10 bp):
AATTTAAATT
Found at i:1967520 original size:33 final size:32
Alignment explanation
Indices: 1967459--1967555 Score: 110
Period size: 31 Copynumber: 3.1 Consensus size: 32
1967449 TAAATGATTT
*
1967459 TAAAAA-ATAAATA-ATTAAAATATGATATAACA
1 TAAAAATATAAATATATTAAAAT-TTATATAA-A
*
1967491 TAAATATATAAATATATTAAAATTTATAT-AA
1 TAAAAATATAAATATATTAAAATTTATATAAA
***
1967522 TAAAAATATTTTTATATTAAAATTTATATAAA
1 TAAAAATATAAATATATTAAAATTTATATAAA
1967554 TA
1 TA
1967556 TATTTTAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
31 26 0.46
32 10 0.18
33 12 0.21
34 8 0.14
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (32 bp):
TAAAAATATAAATATATTAAAATTTATATAAA
Found at i:1967574 original size:31 final size:29
Alignment explanation
Indices: 1967504--1967595 Score: 78
Period size: 31 Copynumber: 3.0 Consensus size: 29
1967494 ATATATAAAT
* *
1967504 ATATTAAAATTTATATAATAAAAATATTTT-T
1 ATATTAAAA-TT-TAT-ATAAATATATTTTAA
1967535 ATATTAAAATTTATATAAATATATTTTAA
1 ATATTAAAATTTATATAAATATATTTTAA
* * *
1967564 ATAATATAAAAATAATATAAATACGATTTTAA
1 AT-AT-TAAAATTTATATAAATA-TATTTTAA
1967596 TACAATTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
28 12 0.23
29 5 0.10
30 4 0.08
31 24 0.46
32 7 0.13
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (29 bp):
ATATTAAAATTTATATAAATATATTTTAA
Found at i:1967584 original size:20 final size:20
Alignment explanation
Indices: 1967547--1967586 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1967537 ATTAAAATTT
* * *
1967547 ATATAAATATATTTTAAATA
1 ATATAAAAATAATATAAATA
1967567 ATATAAAAATAATATAAATA
1 ATATAAAAATAATATAAATA
1967587 CGATTTTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATAAAAATAATATAAATA
Found at i:1967793 original size:20 final size:22
Alignment explanation
Indices: 1967751--1967794 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1967741 AAAGGTAAAA
* *
1967751 TATTTTTTTAGTTTTTATAATT
1 TATTTTTTTAGATTTAATAATT
1967773 TATTTTTTTA-ATTTAAT-ATT
1 TATTTTTTTAGATTTAATAATT
1967793 TA
1 TA
1967795 AAAAAATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 5 0.25
22 10 0.50
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TATTTTTTTAGATTTAATAATT
Found at i:1968653 original size:2 final size:2
Alignment explanation
Indices: 1968646--1968678 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1968636 AAAATATTAA
1968646 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1968679 ATAAACCAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1969173 original size:16 final size:16
Alignment explanation
Indices: 1969154--1969220 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
1969144 ACGAATATAT
1969154 TAAAATTTATAAAATA
1 TAAAATTTATAAAATA
*
1969170 T-AAA-TTATTAATATA
1 TAAAATTTA-TAAAATA
*
1969185 TTAAATTTATATAAATA
1 TAAAATTTATA-AAATA
*
1969202 TAAAATATT-TTAAATA
1 TAAAAT-TTATAAAATA
1969218 TAA
1 TAA
1969221 TTATAACTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 3 0.07
15 10 0.24
16 14 0.33
17 13 0.31
18 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAAATTTATAAAATA
Found at i:1969183 original size:32 final size:32
Alignment explanation
Indices: 1969133--1969210 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
1969123 ATATAAATGT
**
1969133 AATATAAAAATACGAATATATTAAAATTTATA-A
1 AATAT-AAAATATTAATATATT-AAATTTATATA
*
1969166 AATATAAATTATTAATATATTAAATTTATATA
1 AATATAAAATATTAATATATTAAATTTATATA
1969198 AATATAAAATATT
1 AATATAAAATATT
1969211 TTAAATATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 9 0.22
32 26 0.65
33 5 0.12
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (32 bp):
AATATAAAATATTAATATATTAAATTTATATA
Found at i:1971006 original size:10 final size:9
Alignment explanation
Indices: 1970985--1971014 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1970975 AACCGTAAGT
*
1970985 AAAAAGATA
1 AAAAAAATA
1970994 AAAAAAATA
1 AAAAAAATA
1971003 AAAAAAATA
1 AAAAAAATA
1971012 AAA
1 AAA
1971015 TTTAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (9 bp):
AAAAAAATA
Found at i:1971410 original size:30 final size:31
Alignment explanation
Indices: 1971374--1971449 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
1971364 TTTACTTTTA
1971374 TTTAATTGAATTTT-GCAATT-AACTTTGATT
1 TTTAATTGAATTTTAGC-ATTCAACTTTGATT
* * *
1971404 TTTAATTAAATTTTATCATTCAATTTTGATT
1 TTTAATTGAATTTTAGCATTCAACTTTGATT
*
1971435 TTTGATTGAATTTTA
1 TTTAATTGAATTTTA
1971450 TCATCCGATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 16 0.41
31 23 0.59
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (31 bp):
TTTAATTGAATTTTAGCATTCAACTTTGATT
Found at i:1971883 original size:16 final size:16
Alignment explanation
Indices: 1971856--1971902 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1971846 CTCTAACCCT
1971856 AAATAT-ATAAAAAT-
1 AAATATAATAAAAATA
*
1971870 AAATATCAATAAAATTA
1 AAATAT-AATAAAAATA
1971887 AAATATAATAATAAAT
1 AAATATAATAA-AAAT
1971903 TTTAATATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.22
16 12 0.44
17 9 0.33
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATATAATAAAAATA
Found at i:1973155 original size:33 final size:32
Alignment explanation
Indices: 1973097--1973196 Score: 83
Period size: 36 Copynumber: 2.9 Consensus size: 32
1973087 CTATGGATAT
* *
1973097 ATATTTTAAAATTTATAAAAAATAAATTATTA
1 ATATATTAAAATTTATAAAAAATAAAATATTA
**
1973129 ATATATTAAAATTATATAAATTATAAAATATTTTAA
1 ATATATTAAAATT-TATAAAAAATAAAATA--TT-A
* * *
1973165 ATATATTATAATATAATAAAATATATAAATAT
1 ATATATTAAAAT-TTATAAAAAATA-AAATAT
1973197 GATATATAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
32 12 0.22
33 13 0.24
35 3 0.05
36 21 0.38
37 6 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
ATATATTAAAATTTATAAAAAATAAAATATTA
Found at i:1973166 original size:9 final size:9
Alignment explanation
Indices: 1973119--1973196 Score: 58
Period size: 9 Copynumber: 8.8 Consensus size: 9
1973109 TTATAAAAAA
1973119 TAAAT-TAT
1 TAAATATAT
1973127 T-AATATAT
1 TAAATATAT
1973135 TAAA-ATTAT
1 TAAATA-TAT
1973144 ATAAAT-TAT
1 -TAAATATAT
* *
1973153 AAAATATTT
1 TAAATATAT
1973162 TAAATATAT
1 TAAATATAT
*
1973171 TATAATATAA
1 TA-AATATAT
1973181 TAAA-ATAT
1 TAAATATAT
1973189 ATAAATAT
1 -TAAATAT
1973197 GATATATAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
7 3 0.05
8 13 0.24
9 25 0.45
10 14 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TAAATATAT
Found at i:1973166 original size:26 final size:27
Alignment explanation
Indices: 1973118--1973214 Score: 83
Period size: 28 Copynumber: 3.5 Consensus size: 27
1973108 TTTATAAAAA
* *
1973118 ATAAATTAT-TAATATATTAAA-ATTAT
1 ATAAATTATAAAATATTTTAAATA-TAT
1973144 ATAAATTATAAAATATTTTAAATATATT
1 ATAAATTATAAAATATTTTAAATATA-T
* *
1973172 ATAATATAATAAAATA-TATAAATATGAT
1 ATAA-ATTATAAAATATTTTAAATAT-AT
*
1973200 ATATAAATATAAAAT
1 ATA-AATTATAAAAT
1973215 TACCAAATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
26 9 0.15
27 12 0.20
28 26 0.44
29 12 0.20
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
ATAAATTATAAAATATTTTAAATATAT
Found at i:1973193 original size:28 final size:29
Alignment explanation
Indices: 1973141--1973214 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 29
1973131 ATATTAAAAT
*
1973141 TATATAAATTATAAAATATTTTAAATAT-A
1 TATATAAA-TATAAAATATTATAAATATGA
1973170 T-TATAATATAATAAAATA-TATAAATATGA
1 TATATAA-AT-ATAAAATATTATAAATATGA
1973199 TATATAAATATAAAAT
1 TATATAAATATAAAAT
1973215 TACCAAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
28 21 0.52
29 14 0.35
30 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (29 bp):
TATATAAATATAAAATATTATAAATATGA
Found at i:1973201 original size:13 final size:13
Alignment explanation
Indices: 1973185--1973209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1973175 ATATAATAAA
1973185 ATATATAAATATG
1 ATATATAAATATG
1973198 ATATATAAATAT
1 ATATATAAATAT
1973210 AAAATTACCA
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:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
ATATATAAATATG
Found at i:1973209 original size:21 final size:20
Alignment explanation
Indices: 1973045--1973214 Score: 81
Period size: 20 Copynumber: 8.4 Consensus size: 20
1973035 TTTATATATC
*
1973045 ATATAAATA-AAATATTAAAT
1 ATATAAATATATATA-TAAAT
1973065 AT-TAAATATATGATATAATAT
1 ATATAAATATAT-ATATAA-AT
** *
1973086 ACTATGGATATATATTTTAAAAT
1 A-TATAAATATATA-TAT-AAAT
* * * *
1973109 TTATAAAAAATAAATTATTAAT
1 ATAT-AAATATATA-TATAAAT
1973131 ATATTAAA-AT-TATATAAAT
1 ATA-TAAATATATATATAAAT
*
1973150 -TATAAA-ATAT-TTTAAAT
1 ATATAAATATATATATAAAT
1973167 ATATTATAATATA-ATA-AAAT
1 ATA-TA-AATATATATATAAAT
1973187 ATATAAATATGATATATAAAT
1 ATATAAATAT-ATATATAAAT
1973208 ATA-AAAT
1 ATATAAAT
1973215 TACCAAATAT
Statistics
Matches: 116, Mismatches: 16, Indels: 36
0.69 0.10 0.21
Matches are distributed among these distances:
17 12 0.10
18 10 0.09
19 17 0.15
20 23 0.20
21 19 0.16
22 13 0.11
23 20 0.17
24 2 0.02
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (20 bp):
ATATAAATATATATATAAAT
Found at i:1974606 original size:17 final size:18
Alignment explanation
Indices: 1974564--1974599 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1974554 AGTATAGAAT
*
1974564 TACAATCTTTTAAATATA
1 TACAATATTTTAAATATA
1974582 TACAATATTTTAAA-ATA
1 TACAATATTTTAAATATA
1974599 T
1 T
1974600 TAAATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (18 bp):
TACAATATTTTAAATATA
Found at i:1978873 original size:41 final size:41
Alignment explanation
Indices: 1978803--1978917 Score: 153
Period size: 41 Copynumber: 2.8 Consensus size: 41
1978793 CTATTTATTT
* *
1978803 AAAATAATATTAAAAAAATTA-ATTT-TAATTGAAAGTAAATA
1 AAAATAATATT--AAAAATTATTTTTATAATTAAAAGTAAATA
*
1978844 AAAATAATATTAAAGATTATTTTTATAATTAAAAGTAAATA
1 AAAATAATATTAAAAATTATTTTTATAATTAAAAGTAAATA
* *
1978885 AAAATAATATTAAACATTATTTTTATATTTAAA
1 AAAATAATATTAAAAATTATTTTTATAATTAAA
1978918 GAGATTTAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
39 7 0.10
40 3 0.04
41 57 0.85
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (41 bp):
AAAATAATATTAAAAATTATTTTTATAATTAAAAGTAAATA
Found at i:1979394 original size:18 final size:18
Alignment explanation
Indices: 1979373--1979422 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
1979363 GGGTCAAATC
1979373 AAATTTATTTTGATT-CAA
1 AAATTTATTTT-ATTACAA
*
1979391 AAATTTATTTTATTATAA
1 AAATTTATTTTATTACAA
1979409 AAATATTATTTTAT
1 AAAT-TTATTTTAT
1979423 ATTAATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 3 0.10
18 17 0.59
19 9 0.31
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (18 bp):
AAATTTATTTTATTACAA
Found at i:1979742 original size:22 final size:21
Alignment explanation
Indices: 1979712--1979752 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
1979702 TATTTTTATT
1979712 TAAATTTAATTATAA-AATATA
1 TAAATTTAA-TATAACAATATA
1979733 TAAATATTAATATAACAATA
1 TAAAT-TTAATATAACAATA
1979753 ATTTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATTTAATATAACAATATA
Found at i:1979823 original size:12 final size:13
Alignment explanation
Indices: 1979806--1979841 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1979796 ATCAATAGAA
1979806 TCAAATTTAAA-T
1 TCAAATTTAAACT
1979818 TCAAATTTAAACT
1 TCAAATTTAAACT
*
1979831 TAAAATTTAAA
1 TCAAATTTAAA
1979842 ATTTTTTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (13 bp):
TCAAATTTAAACT
Found at i:1979838 original size:13 final size:12
Alignment explanation
Indices: 1979808--1979841 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1979798 CAATAGAATC
*
1979808 AAATTTAAATTC
1 AAATTTAAATTA
1979820 AAATTTAAACTTA
1 AAATTTAAA-TTA
1979833 AAATTTAAA
1 AAATTTAAA
1979842 ATTTTTTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATTTAAATTA
Found at i:1981497 original size:17 final size:17
Alignment explanation
Indices: 1981445--1981499 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
1981435 ATATATACCT
*
1981445 TAAAATTTATA-CAATA
1 TAAAATTTATATAAATA
1981461 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
1981476 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
1981494 TAAAAT
1 TAAAAT
1981500 ATTTTTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
14 5 0.16
15 6 0.19
16 2 0.06
17 9 0.28
18 7 0.22
19 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:1981540 original size:18 final size:19
Alignment explanation
Indices: 1981517--1981556 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1981507 AAATAATTAT
1981517 AATATAATA-AAATATACA
1 AATATAATATAAATATACA
1981535 AATATAATATAAATATACA
1 AATATAATATAAATATACA
1981554 AAT
1 AAT
1981557 GACCATATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
AATATAATATAAATATACA
Found at i:1982929 original size:3 final size:3
Alignment explanation
Indices: 1982921--1982954 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1982911 CATGGCAATG
1982921 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1982955 TTAATTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1983702 original size:20 final size:21
Alignment explanation
Indices: 1983674--1983713 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1983664 TAAAAAGTGA
*
1983674 ATTTAAATATTAAATAAGTAC
1 ATTTAAATATTAAACAAGTAC
1983695 ATTT-AATATTAAACAAGTA
1 ATTTAAATATTAAACAAGTA
1983714 TTTAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
ATTTAAATATTAAACAAGTAC
Found at i:1984098 original size:22 final size:24
Alignment explanation
Indices: 1984073--1984116 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
1984063 TATTATATAT
1984073 TTATATAAA-TTGATA-ATTCAAA
1 TTATATAAATTTGATATATTCAAA
1984095 TTATATAAATTTGATATATTCA
1 TTATATAAATTTGATATATTCA
1984117 TATTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.45
23 6 0.30
24 5 0.25
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (24 bp):
TTATATAAATTTGATATATTCAAA
Found at i:1984130 original size:11 final size:11
Alignment explanation
Indices: 1984111--1984153 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
1984101 AAATTTGATA
1984111 TATTCATATTTT
1 TATT-ATATTTT
1984123 TATTATATTTT
1 TATTATATTTT
1984134 TATTAT-TTTT
1 TATTATATTTT
1984144 ATATTATATT
1 -TATTATATT
1984154 ATATTTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.14
11 19 0.66
12 6 0.21
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTATATTTT
Found at i:1984131 original size:17 final size:16
Alignment explanation
Indices: 1984109--1984166 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 16
1984099 ATAAATTTGA
1984109 TATATTCATATT-TTTAT
1 TATATT-ATATTATTT-T
*
1984126 TATATTTTTATTATTTT
1 TATA-TTATATTATTTT
1984143 TATATTATATTATATTT
1 TATATTATATTAT-TTT
1984160 TA-ATTAT
1 TATATTAT
1984167 TTTTTAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
16 13 0.36
17 18 0.50
18 5 0.14
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATTATATTATTTT
Found at i:1989434 original size:15 final size:15
Alignment explanation
Indices: 1989414--1989455 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
1989404 AAACAATGTT
1989414 AAAATAATTATTTTAA
1 AAAATAATT-TTTTAA
1989430 AAATATAATTTTTTAA
1 AAA-ATAATTTTTTAA
*
1989446 ATAATAATTT
1 AAAATAATTT
1989456 AATAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAATAATTTTTTAA
Found at i:1989439 original size:17 final size:17
Alignment explanation
Indices: 1989417--1989451 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1989407 CAATGTTAAA
1989417 ATAATTATTTTAAA-AAT
1 ATAATT-TTTTAAATAAT
1989434 ATAATTTTTTAAATAAT
1 ATAATTTTTTAAATAAT
1989451 A
1 A
1989452 ATTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAATTTTTTAAATAAT
Found at i:1989440 original size:14 final size:15
Alignment explanation
Indices: 1989414--1989455 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1989404 AAACAATGTT
*
1989414 AAAATAATTATTTTA
1 AAAATAATAATTTTA
*
1989429 AAAAT-ATAATTTTT
1 AAAATAATAATTTTA
*
1989443 TAAATAATAATTT
1 AAAATAATAATTT
1989456 AATAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAATAATAATTTTA
Found at i:1990122 original size:16 final size:16
Alignment explanation
Indices: 1990088--1990119 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1990078 TAAATCGATA
1990088 TTAAAAATCATATTAT
1 TTAAAAATCATATTAT
1990104 TTAAAAAT-ATA-TAT
1 TTAAAAATCATATTAT
1990118 TT
1 TT
1990120 TTATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 3 0.19
16 8 0.50
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAAATCATATTAT
Found at i:1990128 original size:17 final size:19
Alignment explanation
Indices: 1990086--1990130 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
1990076 TTTAAATCGA
*
1990086 TATTAAAAATCATATTATT
1 TATTAAATATCATATTATT
*
1990105 TA-AAAATAT-ATATT-TT
1 TATTAAATATCATATTATT
1990121 TATTAAATAT
1 TATTAAATAT
1990131 TTATATTACT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
16 4 0.18
17 11 0.50
18 5 0.23
19 2 0.09
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTAAATATCATATTATT
Found at i:1997320 original size:90 final size:90
Alignment explanation
Indices: 1997167--1997345 Score: 358
Period size: 90 Copynumber: 2.0 Consensus size: 90
1997157 TTCCAGACCT
1997167 TCCTAATACTATACAAACACCAATGTCAACTTCCCAACTTACACCTATTCGGGTAGCTGATCAAG
1 TCCTAATACTATACAAACACCAATGTCAACTTCCCAACTTACACCTATTCGGGTAGCTGATCAAG
1997232 GGGGAGATTCAGAACCAATAACTAG
66 GGGGAGATTCAGAACCAATAACTAG
1997257 TCCTAATACTATACAAACACCAATGTCAACTTCCCAACTTACACCTATTCGGGTAGCTGATCAAG
1 TCCTAATACTATACAAACACCAATGTCAACTTCCCAACTTACACCTATTCGGGTAGCTGATCAAG
1997322 GGGGAGATTCAGAACCAATAACTA
66 GGGGAGATTCAGAACCAATAACTA
1997346 AAGGTGAACT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (90 bp):
TCCTAATACTATACAAACACCAATGTCAACTTCCCAACTTACACCTATTCGGGTAGCTGATCAAG
GGGGAGATTCAGAACCAATAACTAG
Found at i:1999922 original size:20 final size:21
Alignment explanation
Indices: 1999899--1999947 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
1999889 CTGGACATGT
*
1999899 TAAAAATAT-ATGAAACATAA
1 TAAAAAAATCATGAAACATAA
1999919 TAAAAAAATGCATGAAACATAA
1 TAAAAAAAT-CATGAAACATAA
1999941 TAAAAAA
1 TAAAAAA
1999948 TGCGTAGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 8 0.31
22 18 0.69
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.20
Consensus pattern (21 bp):
TAAAAAAATCATGAAACATAA
Found at i:2000894 original size:20 final size:20
Alignment explanation
Indices: 2000847--2000921 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
2000837 AAAAAGACAT
*
2000847 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
2000866 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
2000887 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
2000907 AATGTATCGATACAT
1 AATGTATCGATACAT
2000922 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:2000915 original size:40 final size:39
Alignment explanation
Indices: 2000844--2000921 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
2000834 GGTAAAAAGA
* *
2000844 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
2000883 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
2000922 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:2005027 original size:13 final size:13
Alignment explanation
Indices: 2005009--2005040 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2004999 GAATTTATTT
2005009 TATAAATAAATAC
1 TATAAATAAATAC
*
2005022 TATAAATAAATAT
1 TATAAATAAATAC
2005035 TATAAA
1 TATAAA
2005041 AATAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (13 bp):
TATAAATAAATAC
Found at i:2005062 original size:12 final size:12
Alignment explanation
Indices: 2005035--2005071 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2005025 AAATAAATAT
2005035 TATAAAA-ATAA
1 TATAAAATATAA
2005046 T-TAAAATATAA
1 TATAAAATATAA
2005057 TATAAAATATAA
1 TATAAAATATAA
2005069 TAT
1 TAT
2005072 TAACATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.21
11 6 0.25
12 13 0.54
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TATAAAATATAA
Found at i:2005176 original size:16 final size:17
Alignment explanation
Indices: 2005137--2005177 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2005127 ATTTAAATTT
2005137 AATTAT-AATATAATAA
1 AATTATAAATATAATAA
*
2005153 AATATATAAATATTA-AA
1 AAT-TATAAATATAATAA
2005170 AATTATAA
1 AATTATAA
2005178 TAATTCAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.36
17 8 0.36
18 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATTATAAATATAATAA
Found at i:2005516 original size:4 final size:5
Alignment explanation
Indices: 2005445--2005514 Score: 56
Period size: 5 Copynumber: 14.2 Consensus size: 5
2005435 TTAACTTATG
* * * * *
2005445 AATTA AATTA AATTG AA-TA TATTT AATT- GATCA AATTA AATTA AATTAA
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATT-A
2005494 AATTA AATT- AATTCA AATTA A
1 AATTA AATTA AATT-A AATTA A
2005515 TTTTTAATTT
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
4 8 0.16
5 34 0.67
6 9 0.18
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:2006148 original size:18 final size:17
Alignment explanation
Indices: 2006116--2006175 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 17
2006106 ATATTTTTTA
2006116 TTATAATAT-TTATATT
1 TTATAATATATTATATT
2006132 TTATAATATAATTATATATT
1 TTATAATAT-A-T-TATATT
2006152 TTATAATAATGATTATAATT
1 TTATAAT-AT-ATTAT-ATT
2006172 TTAT
1 TTAT
2006176 TTTACTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
16 9 0.24
19 4 0.11
20 21 0.57
21 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TTATAATATATTATATT
Found at i:2006149 original size:20 final size:20
Alignment explanation
Indices: 2006106--2006175 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 20
2006096 AACCTGAATC
* * *
2006106 ATATTTTTTATTATAATATTT
1 ATATTTTATAATATAAT-TAT
2006127 ATATTTTATAATATAATTAT
1 ATATTTTATAATATAATTAT
*
2006147 ATATTTTATAATAATGATTAT
1 ATATTTTATAAT-ATAATTAT
2006168 A-ATTTTAT
1 ATATTTTAT
2006176 TTTACTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 21 0.48
21 23 0.52
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (20 bp):
ATATTTTATAATATAATTAT
Found at i:2007088 original size:6 final size:6
Alignment explanation
Indices: 2007072--2007108 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
2007062 CAAAATTTTG
2007072 AATTCTA AATTTA AATTTA AATTTA AATTT- AATTTA A
1 AATT-TA AATTTA AATTTA AATTTA AATTTA AATTTA A
2007109 CTTGATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.17
6 20 0.69
7 4 0.14
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (6 bp):
AATTTA
Found at i:2007100 original size:18 final size:18
Alignment explanation
Indices: 2007072--2007108 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
2007062 CAAAATTTTG
2007072 AATTCTAAATTTAAATTTA
1 AATTCTAAATTT-AATTTA
2007091 AATT-TAAATTTAATTTA
1 AATTCTAAATTTAATTTA
2007108 A
1 A
2007109 CTTGATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 7 0.39
19 4 0.22
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
AATTCTAAATTTAATTTA
Found at i:2007171 original size:20 final size:21
Alignment explanation
Indices: 2007136--2007175 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2007126 AATTCGAATC
2007136 ATTATTCTTAATATTAATATA
1 ATTATTCTTAATATTAATATA
*
2007157 ATTATT-TTTATATTAATAT
1 ATTATTCTTAATATTAATAT
2007176 TTATATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTATTCTTAATATTAATATA
Found at i:2007257 original size:12 final size:12
Alignment explanation
Indices: 2007240--2007265 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2007230 CTTATATACT
2007240 TAGTTTCATTTC
1 TAGTTTCATTTC
2007252 TAGTTTCATTTC
1 TAGTTTCATTTC
2007264 TA
1 TA
2007266 TGCCTATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.15, G:0.08, T:0.58
Consensus pattern (12 bp):
TAGTTTCATTTC
Found at i:2008407 original size:16 final size:15
Alignment explanation
Indices: 2008385--2008433 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
2008375 AATATTTAAT
2008385 TTAATTTATTAATATAA
1 TTAATTT-TTAATA-AA
*
2008402 TT-ATTTTTAAGAAA
1 TTAATTTTTAATAAA
2008416 TTAATTTTTTAATAAA
1 TTAA-TTTTTAATAAA
2008432 TT
1 TT
2008434 TAAAATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 4 0.14
15 6 0.21
16 16 0.57
17 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
TTAATTTTTAATAAA
Found at i:2008469 original size:21 final size:22
Alignment explanation
Indices: 2008421--2008469 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
2008411 AGAAATTAAT
2008421 TTTTTAATAAATTTAAAATTTA
1 TTTTTAATAAATTTAAAATTTA
** * *
2008443 AATTTAA-ATATTTATAATTTA
1 TTTTTAATAAATTTAAAATTTA
2008464 TTTTTA
1 TTTTTA
2008470 TTTTTAAATT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTTAATAAATTTAAAATTTA
Found at i:2013905 original size:22 final size:23
Alignment explanation
Indices: 2013877--2013932 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
2013867 TGGACATGTT
2013877 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
2013899 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
2013922 AAAAATGCATG
1 AAAAATGCATG
2013933 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:2014890 original size:20 final size:20
Alignment explanation
Indices: 2014843--2014917 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
2014833 AAAAAGACAT
*
2014843 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
2014862 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
2014883 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
*
2014903 AATGCATCGATACAT
1 AATGTATCGATACAT
2014918 CAGGGTATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:2014912 original size:40 final size:39
Alignment explanation
Indices: 2014840--2014917 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
2014830 GGTAAAAAGA
* * *
2014840 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATACATCGATACATT
* *
2014879 CATACATGTATCGATATATTGAAAAATGCATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATACATCGATACAT
2014918 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATACATCGATACATT
Done.