Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 18 of 190
Found at i:2586345 original size:35 final size:33
Alignment explanation
Indices: 2586301--2586365 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 33
2586291 GAATATAATA
2586301 TAAATAATATAATATAATATAATATATAATTTTTAT
1 TAAATAATATAATATAA-AT-ATATA-AATTTTTAT
2586337 TAAA-AATATAATATAAATATATAAATTTT
1 TAAATAATATAATATAAATATATAAATTTT
2586366 AATATTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 6 0.21
33 5 0.17
34 2 0.07
35 12 0.41
36 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
TAAATAATATAATATAAATATATAAATTTTTAT
Found at i:2586388 original size:38 final size:41
Alignment explanation
Indices: 2586297--2586390 Score: 99
Period size: 38 Copynumber: 2.3 Consensus size: 41
2586287 ATATGAATAT
2586297 AATATAAATAATATAATATAATATAATATATAATTTTTATTA
1 AATATAAAT-ATATAATATAATATAATATATAATTTTTATTA
* *
2586339 AAAATATAATATA-AATAT-ATA-AAT-TTTAATATTTTA-TA
1 AATATA-AATATATAATATAATATAATATATAAT-TTTTATTA
2586377 CAATATAAATATAT
1 -AATATAAATATAT
2586391 TAATCGCTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
38 13 0.29
39 13 0.29
40 3 0.07
41 5 0.11
42 8 0.18
43 3 0.07
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (41 bp):
AATATAAATATATAATATAATATAATATATAATTTTTATTA
Found at i:2588025 original size:2 final size:2
Alignment explanation
Indices: 2588018--2588065 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2588008 ATTAAAATTT
2588018 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2588060 TA TA TA
1 TA TA TA
2588066 CACACACACG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2588963 original size:11 final size:11
Alignment explanation
Indices: 2588923--2588978 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 11
2588913 ATTTGATTAG
*
2588923 AATTAAGTTTGA
1 AATTAAATTT-A
2588935 ATATTAAATATATA
1 A-ATTAAAT-T-TA
2588949 AATTAAATTTA
1 AATTAAATTTA
2588960 AATTAAATTTTA
1 AATTAAA-TTTA
2588972 AATTAAA
1 AATTAAA
2588979 AAATAAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 9 0.23
12 13 0.33
13 13 0.33
14 3 0.08
15 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:2589047 original size:10 final size:10
Alignment explanation
Indices: 2589002--2589045 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
2588992 TCGAATCAAA
2589002 TTATATATTT
1 TTATATATTT
*
2589012 TTATTTATTT
1 TTATATATTT
2589022 TTATATATTT
1 TTATATATTT
*
2589032 TT-TAAATTT
1 TTATATATTT
2589041 TTATA
1 TTATA
2589046 AAATAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTATATATTT
Found at i:2589221 original size:31 final size:32
Alignment explanation
Indices: 2589154--2589226 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 32
2589144 GAACAAATCA
*
2589154 ATAAAA-TTTAATTTAAATTGAATCAAATAAT
1 ATAAAATTTTAATTTAAATTAAATCAAATAAT
*
2589185 ATAAAATTTTCATTTAAATCTAAATC-AA-AAT
1 ATAAAATTTTAATTTAAAT-TAAATCAAATAAT
*
2589216 TTAAAATTTTA
1 ATAAAATTTTA
2589227 TAATTTTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 18 0.50
32 13 0.36
33 5 0.14
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.41
Consensus pattern (32 bp):
ATAAAATTTTAATTTAAATTAAATCAAATAAT
Found at i:2591145 original size:6 final size:6
Alignment explanation
Indices: 2591136--2591164 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2591126 TGAGAATGAG
2591136 AATCAC AATCAC AATCAC AATCAC AATCA
1 AATCAC AATCAC AATCAC AATCAC AATCA
2591165 AAACCCAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.31, G:0.00, T:0.17
Consensus pattern (6 bp):
AATCAC
Found at i:2598317 original size:52 final size:51
Alignment explanation
Indices: 2598225--2598380 Score: 177
Period size: 52 Copynumber: 3.0 Consensus size: 51
2598215 GGATAAAAAA
* * * * * *
2598225 ACTTGCAAAAGAAGAATTTTAAGAGAAAGATGATTCTTAATAGGTAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAAAGAAA-AGGATTTTTAATAGGCAAGTTTG
*
2598277 ACTTGTAAGAGAAGAATTCTAAAAGGAAAAGGATTTTTAATAGGCAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAAA-GAAAAGGATTTTTAATAGGCAAGTTTG
* * * * *
2598329 ACTTACAGGAGAAGAATTCTAAGAAGAGAGGGATTTTTAATGGGCAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAA-AAGAAAAGGATTTTTAATAGGCAAGTTTG
2598381 TATGATTATA
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
52 83 0.93
53 6 0.07
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.29
Consensus pattern (51 bp):
ACTTGCAAGAGAAGAATTCTAAAAGAAAAGGATTTTTAATAGGCAAGTTTG
Found at i:2606287 original size:2 final size:2
Alignment explanation
Indices: 2606280--2606308 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2606270 TTGCATTATC
2606280 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2606309 TTTGTTCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2608051 original size:19 final size:19
Alignment explanation
Indices: 2608027--2608066 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2608017 CGCTGCTTGT
2608027 TTTCTAAAAGTAATTTGAC
1 TTTCTAAAAGTAATTTGAC
2608046 TTTCTAAAAGTAATTTGAC
1 TTTCTAAAAGTAATTTGAC
2608065 TT
1 TT
2608067 ATGTTTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (19 bp):
TTTCTAAAAGTAATTTGAC
Found at i:2608225 original size:12 final size:12
Alignment explanation
Indices: 2608218--2608247 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2608208 AATTTATTTT
2608218 TTATTTTATATA
1 TTATTTTATATA
2608230 TTATTTTATATA
1 TTATTTTATATA
*
2608242 ATATTT
1 TTATTT
2608248 AAAATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATTTTATATA
Found at i:2608405 original size:13 final size:13
Alignment explanation
Indices: 2608363--2608408 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
2608353 TTTCATTTCA
2608363 AAATTTAAT-TC-
1 AAATTTAATATCT
* *
2608374 AAATTCAATATAT
1 AAATTTAATATCT
*
2608387 ACATTTAATATCT
1 AAATTTAATATCT
2608400 AAATTTAAT
1 AAATTTAAT
2608409 CTAAATAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
11 8 0.30
12 1 0.04
13 18 0.67
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATTTAATATCT
Found at i:2613065 original size:27 final size:25
Alignment explanation
Indices: 2613026--2613097 Score: 71
Period size: 27 Copynumber: 2.9 Consensus size: 25
2613016 ACAATTCAGT
2613026 TTTAATT-GAATTAATTGATCGACTCAA
1 TTTAATTAG-ATTAATTGATCGA-TC-A
*
2613053 TTTAATTAGATTAATCGATCGATCA
1 TTTAATTAGATTAATTGATCGATCA
*
2613078 TTGAATTA-ATT--TTGATCGAT
1 TTTAATTAGATTAATTGATCGAT
2613098 TATTGAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 8 0.20
24 3 0.07
25 8 0.20
26 2 0.05
27 19 0.46
28 1 0.02
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (25 bp):
TTTAATTAGATTAATTGATCGATCA
Found at i:2613096 original size:22 final size:22
Alignment explanation
Indices: 2613030--2613104 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
2613020 TTCAGTTTTA
2613030 ATTGAATTAA--TTGATCGACTC
1 ATTGAATTAATTTTGATCGA-TC
* *
2613051 AATTTAATTAGATTAATCGATCGATC
1 -ATTGAATTA-ATT--TTGATCGATC
*
2613077 ATTGAATTAATTTTGATCGATT
1 ATTGAATTAATTTTGATCGATC
2613099 ATTGAA
1 ATTGAA
2613105 AATGATTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
22 22 0.51
23 1 0.02
24 3 0.07
25 8 0.19
26 2 0.05
27 7 0.16
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.41
Consensus pattern (22 bp):
ATTGAATTAATTTTGATCGATC
Found at i:2614143 original size:14 final size:14
Alignment explanation
Indices: 2614124--2614150 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2614114 TCAATTAATT
2614124 TTAAATTAAATTAA
1 TTAAATTAAATTAA
2614138 TTAAATTAAATTA
1 TTAAATTAAATTA
2614151 TTTTATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAAATTAAATTAA
Found at i:2614186 original size:28 final size:28
Alignment explanation
Indices: 2614133--2614187 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
2614123 TTTAAATTAA
* * *
2614133 ATTAATTAAATTAAATTATTTTATTTTT
1 ATTAATCAAATCAAATTATTTAATTTTT
2614161 ATTAATCAAATCAAATT-TATTAATTTT
1 ATTAATCAAATCAAATTAT-TTAATTTT
2614188 AAAAATAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (28 bp):
ATTAATCAAATCAAATTATTTAATTTTT
Found at i:2614410 original size:16 final size:16
Alignment explanation
Indices: 2614391--2614425 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2614381 CATGTATTTT
*
2614391 TTATTTTATATTTAAA
1 TTATATTATATTTAAA
*
2614407 TTATATTATATTTCAA
1 TTATATTATATTTAAA
2614423 TTA
1 TTA
2614426 ATTCAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATATTATATTTAAA
Found at i:2620257 original size:26 final size:26
Alignment explanation
Indices: 2620228--2620286 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
2620218 GCCAGTAGAG
2620228 TTAACCACTAATTTATTATAATCGAT
1 TTAACCACTAATTTATTATAATCGAT
* * * *
2620254 TTAATCATTAATTTATTCTAATTGAT
1 TTAACCACTAATTTATTATAATCGAT
2620280 TTAACCA
1 TTAACCA
2620287 ATCAAAACCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (26 bp):
TTAACCACTAATTTATTATAATCGAT
Found at i:2638943 original size:4 final size:4
Alignment explanation
Indices: 2638934--2638960 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2638924 TCCATGGTAT
2638934 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
2638961 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:2639083 original size:27 final size:27
Alignment explanation
Indices: 2639053--2639107 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2639043 CAGGATTTAA
2639053 CACTGTGTTGCAGATCTTGGAAAAGTT
1 CACTGTGTTGCAGATCTTGGAAAAGTT
2639080 CACTGTGTTGCAGATCTTGGAAAAGTT
1 CACTGTGTTGCAGATCTTGGAAAAGTT
2639107 C
1 C
2639108 TTTTTCATCC
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:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (27 bp):
CACTGTGTTGCAGATCTTGGAAAAGTT
Found at i:2640180 original size:2 final size:2
Alignment explanation
Indices: 2640173--2640204 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2640163 TAGGATTAAT
2640173 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2640205 ATTGCAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2640382 original size:8 final size:7
Alignment explanation
Indices: 2640354--2640379 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2640344 CTTTATCTTG
2640354 AAATTAA
1 AAATTAA
2640361 AAATTAA
1 AAATTAA
2640368 AAATTAA
1 AAATTAA
2640375 AAATT
1 AAATT
2640380 TAATTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
AAATTAA
Found at i:2641255 original size:9 final size:9
Alignment explanation
Indices: 2641239--2641275 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
2641229 TTAAAATAAT
2641239 TTAA-AAAA
1 TTAATAAAA
2641247 TTAATAAAA
1 TTAATAAAA
2641256 TTAATAAAA
1 TTAATAAAA
2641265 TTAATAAAA
1 TTAATAAAA
2641274 TT
1 TT
2641276 TAATTCGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 4 0.14
9 24 0.86
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TTAATAAAA
Found at i:2641257 original size:18 final size:19
Alignment explanation
Indices: 2641236--2641279 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
2641226 ATATTAAAAT
2641236 AATTTAA-AAAATTAATAA
1 AATTTAATAAAATTAATAA
2641254 AA-TTAATAAAATTAATAA
1 AATTTAATAAAATTAATAA
2641272 AATTTAAT
1 AATTTAAT
2641280 TCGAATCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.17
18 15 0.62
19 5 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTTAATAAAATTAATAA
Found at i:2641915 original size:7 final size:7
Alignment explanation
Indices: 2641903--2641946 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
2641893 AAAATTAAAA
2641903 TTTATAT
1 TTTATAT
2641910 TTTATATT
1 TTTATA-T
2641918 TTTATAT
1 TTTATAT
* *
2641925 TATAAAT
1 TTTATAT
2641932 TTTAATAT
1 TTT-ATAT
2641940 TTTATAT
1 TTTATAT
2641947 AATAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
7 18 0.58
8 13 0.42
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (7 bp):
TTTATAT
Found at i:2641923 original size:15 final size:15
Alignment explanation
Indices: 2641903--2641946 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2641893 AAAATTAAAA
2641903 TTTATATTTTATATT
1 TTTATATTTTATATT
* *
2641918 TTTATATTATAAATT
1 TTTATATTTTATATT
*
2641933 TTAATATTTTATAT
1 TTTATATTTTATAT
2641947 AATAAAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATATTTTATATT
Found at i:2641934 original size:22 final size:22
Alignment explanation
Indices: 2641908--2641952 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
2641898 TAAAATTTAT
*
2641908 ATTTT-ATATTTTTATATTATAA
1 ATTTTAATA-TTTTATATAATAA
2641930 ATTTTAATATTTTATATAATAA
1 ATTTTAATATTTTATATAATAA
2641952 A
1 A
2641953 AATACACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTTAATATTTTATATAATAA
Found at i:2650338 original size:12 final size:12
Alignment explanation
Indices: 2650323--2650347 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2650313 AAATTTGTTA
2650323 TTAAAAAAAATT
1 TTAAAAAAAATT
2650335 TTAAAAAAAATT
1 TTAAAAAAAATT
2650347 T
1 T
2650348 AGTTTTTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTAAAAAAAATT
Found at i:2650415 original size:12 final size:14
Alignment explanation
Indices: 2650400--2650431 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2650390 TTTAAATGAA
2650400 ATATAA-TAAAA-T
1 ATATAATTAAAAGT
2650412 ATATAATTAAAAGT
1 ATATAATTAAAAGT
2650426 ATATAA
1 ATATAA
2650432 AATTATTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 5 0.28
14 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (14 bp):
ATATAATTAAAAGT
Found at i:2656114 original size:15 final size:14
Alignment explanation
Indices: 2656087--2656138 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
2656077 TAATATTTAA
*
2656087 TAAATTTA-AATTT
1 TAAATTTATTATTT
2656100 TAAATTCTATTATTT
1 TAAATT-TATTATTT
*
2656115 GTAAATTTTTTATTT
1 -TAAATTTATTATTT
*
2656130 TAAAATTAT
1 TAAATTTAT
2656139 GAATTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 6 0.19
14 9 0.28
15 11 0.34
16 6 0.19
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (14 bp):
TAAATTTATTATTT
Found at i:2656718 original size:32 final size:32
Alignment explanation
Indices: 2656676--2656749 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 32
2656666 TATCATATAA
* * * *
2656676 AATATTAAAATTTATGTATTTATATTTTAT-TT
1 AATATAAAAATTTATATA-TTATAATTCATATT
*
2656708 TATATAAAAA-TTATATATTATAATTCATATT
1 AATATAAAAATTTATATATTATAATTCATATT
2656739 AATATAAAAAT
1 AATATAAAAAT
2656750 ATAATTTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
30 9 0.26
31 17 0.50
32 8 0.24
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (32 bp):
AATATAAAAATTTATATATTATAATTCATATT
Found at i:2656760 original size:22 final size:26
Alignment explanation
Indices: 2656720--2656786 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 26
2656710 TATAAAAATT
2656720 ATATATTATAATTCA-TATTAAT-ATAA
1 ATATA-TATAATT-ATTATTAATGATAA
*
2656746 A-A-ATATAATT-TTATT-TTGATAA
1 ATATATATAATTATTATTAATGATAA
2656768 ATATATATAATTATTATTA
1 ATATATATAATTATTATTA
2656787 TAATTTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
21 1 0.03
22 9 0.26
23 8 0.24
24 9 0.26
25 6 0.18
26 1 0.03
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (26 bp):
ATATATATAATTATTATTAATGATAA
Found at i:2656820 original size:13 final size:13
Alignment explanation
Indices: 2656802--2656832 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2656792 TTAAATCATA
2656802 TTATTTTTATATT
1 TTATTTTTATATT
2656815 TTATTTTTATATT
1 TTATTTTTATATT
*
2656828 ATATT
1 TTATT
2656833 CGTATCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTTTTATATT
Found at i:2666661 original size:6 final size:6
Alignment explanation
Indices: 2666650--2666674 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2666640 TCCAATCCAA
2666650 TTATAT TTATAT TTATAT TTATAT T
1 TTATAT TTATAT TTATAT TTATAT T
2666675 ATTTATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTATAT
Found at i:2673487 original size:5 final size:5
Alignment explanation
Indices: 2673477--2673504 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2673467 GTACGGAAAC
2673477 CAATT CAATT CAATT CAATT CAATT CAA
1 CAATT CAATT CAATT CAATT CAATT CAA
2673505 AGGGGTTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (5 bp):
CAATT
Found at i:2684193 original size:45 final size:44
Alignment explanation
Indices: 2684138--2684230 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 44
2684128 CCAGAAGAGT
2684138 TTCCAGGTTGGATTAAGACAGGGGAGGTAGTAATAA-TACTGGAA
1 TTCCAGGTTGGATTAAGACAGGGGAGGTAGTAA-AACTACTGGAA
*
2684182 TTCCTAGGTTGGATTAAGGCAGGGGAGGTAGTAAAACTACTGGAA
1 TTCC-AGGTTGGATTAAGACAGGGGAGGTAGTAAAACTACTGGAA
2684227 TTCC
1 TTCC
2684231 CAGGGAAGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
44 6 0.13
45 40 0.87
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.26
Consensus pattern (44 bp):
TTCCAGGTTGGATTAAGACAGGGGAGGTAGTAAAACTACTGGAA
Found at i:2684415 original size:16 final size:16
Alignment explanation
Indices: 2684394--2684440 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
2684384 TCATTGCGAT
*
2684394 TTCACTTAAAACCCAC
1 TTCACTCAAAACCCAC
*
2684410 TTCACTCAAAATCCAC
1 TTCACTCAAAACCCAC
*
2684426 TTTA-TCCAAAACCCA
1 TTCACT-CAAAACCCA
2684441 TACCAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 1 0.04
16 25 0.96
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (16 bp):
TTCACTCAAAACCCAC
Found at i:2684678 original size:40 final size:40
Alignment explanation
Indices: 2684621--2684696 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
2684611 CGAATTCCAG
*
2684621 AAACAAAAAATCCCATCAAGCTGACTTGAATAAAAACTAA
1 AAACAAAAAATCCCATCAAACTGACTTGAATAAAAACTAA
* *
2684661 AAACAAAAAATCTCATCAAATTGACTTGAATAAAAA
1 AAACAAAAAATCCCATCAAACTGACTTGAATAAAAA
2684697 AGAATCTGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.57, C:0.17, G:0.07, T:0.20
Consensus pattern (40 bp):
AAACAAAAAATCCCATCAAACTGACTTGAATAAAAACTAA
Found at i:2685603 original size:25 final size:27
Alignment explanation
Indices: 2685572--2685645 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 27
2685562 AATAAATTAT
*
2685572 TATTTTAAATT-AATTATA-AGTAATA
1 TATTTTAAATTAAAATATATAGTAATA
* *
2685597 TATTTTAATTTAAAATATATATTAATA
1 TATTTTAAATTAAAATATATAGTAATA
**
2685624 TATTTATAAAAAAAAATATATA
1 TATTT-TAAATTAAAATATATA
2685646 AAATTAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
25 10 0.25
26 6 0.15
27 11 0.28
28 13 0.32
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (27 bp):
TATTTTAAATTAAAATATATAGTAATA
Found at i:2686389 original size:16 final size:16
Alignment explanation
Indices: 2686370--2686404 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2686360 AATAAATTAT
2686370 TTATTAATAATATAAA
1 TTATTAATAATATAAA
* *
2686386 TTATTATTATTATAAA
1 TTATTAATAATATAAA
2686402 TTA
1 TTA
2686405 ATTATAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATTAATAATATAAA
Found at i:2686407 original size:20 final size:20
Alignment explanation
Indices: 2686354--2686409 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
2686344 GTATATATAT
2686354 TTAATAAATAAATTA-TTTA
1 TTAATAAATAAATTATTTTA
2686373 TTAATAATATAAATTATTATTA
1 TTAATAA-ATAAATTATT-TTA
*
2686395 TT-ATAAATTAATTAT
1 TTAATAAATAAATTAT
2686410 AAGTAGTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 7 0.21
20 16 0.48
21 5 0.15
22 5 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAATAAATAAATTATTTTA
Found at i:2687390 original size:14 final size:14
Alignment explanation
Indices: 2687368--2687401 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2687358 AATTTAATAA
2687368 AAATT-AAATCAAT
1 AAATTAAAATCAAT
*
2687381 AAATTAAAATTAAT
1 AAATTAAAATCAAT
2687395 AAATTAA
1 AAATTAA
2687402 TAAAATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATTAAAATCAAT
Found at i:2687415 original size:18 final size:17
Alignment explanation
Indices: 2687355--2687415 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
2687345 TTTGTATAAA
*
2687355 AATAATTTAATAAAAATT
1 AATAAATTAAT-AAAATT
* *
2687373 AAATCAATAAATTAAAATT
1 -AATAAATTAA-TAAAATT
2687392 AATAAATTAATAAAATT
1 AATAAATTAATAAAATT
2687409 CAATAAA
1 -AATAAA
2687416 AAATTTAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
17 7 0.20
18 14 0.40
19 13 0.37
20 1 0.03
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAAATTAATAAAATT
Found at i:2687579 original size:12 final size:14
Alignment explanation
Indices: 2687551--2687583 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
2687541 AAGAAAAATA
2687551 TTTAATTTATCAAT
1 TTTAATTTATCAAT
2687565 TTTAATTT-T-AAT
1 TTTAATTTATCAAT
2687577 TTTAATT
1 TTTAATT
2687584 CTTATCGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 1 0.05
14 8 0.42
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTAATTTATCAAT
Found at i:2688204 original size:15 final size:15
Alignment explanation
Indices: 2688184--2688217 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2688174 ATAATATAAT
2688184 ATAAAAATTATAAAA
1 ATAAAAATTATAAAA
*
2688199 ATAAAAATTATAAAT
1 ATAAAAATTATAAAA
2688214 ATAA
1 ATAA
2688218 TATTATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAAAAATTATAAAA
Found at i:2690457 original size:16 final size:15
Alignment explanation
Indices: 2690433--2690479 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
2690423 GAATTTAATT
2690433 ATTTAATTAAATTATA
1 ATTTAATT-AATTATA
* *
2690449 ATTTTATTAATTGATT
1 ATTTAATTAATT-ATA
2690465 ATTTAATTAATTATA
1 ATTTAATTAATTATA
2690480 TGATAACAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 6 0.23
16 20 0.77
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
ATTTAATTAATTATA
Found at i:2690472 original size:12 final size:12
Alignment explanation
Indices: 2690427--2690478 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
2690417 ATGTGTGAAT
2690427 TTAATTATTTAA
1 TTAATTATTTAA
2690439 TTAA--ATTATAA
1 TTAATTATT-TAA
2690450 TT--TTA-TTAA
1 TTAATTATTTAA
*
2690459 TTGATTATTTAA
1 TTAATTATTTAA
2690471 TTAATTAT
1 TTAATTAT
2690479 ATGATAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
9 5 0.15
10 4 0.12
11 9 0.27
12 15 0.45
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
TTAATTATTTAA
Found at i:2691700 original size:18 final size:18
Alignment explanation
Indices: 2691656--2691701 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
2691646 AAATATAATA
* *
2691656 TATATTTTTTAATTTTAT
1 TATATTTTTAAATTATAT
* *
2691674 TAAAATTTTAAATTATAT
1 TATATTTTTAAATTATAT
2691692 TATATTTTTA
1 TATATTTTTA
2691702 TTTTTTATTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATATTTTTAAATTATAT
Found at i:2691702 original size:13 final size:13
Alignment explanation
Indices: 2691686--2691746 Score: 51
Period size: 13 Copynumber: 5.1 Consensus size: 13
2691676 AAATTTTAAA
2691686 TTATATTATATTT
1 TTATATTATATTT
*
2691699 TTAT-TT-T-TTA
1 TTATATTATATTT
2691709 TT-TA-TATATTT
1 TTATATTATATTT
* *
2691720 TTATTTTATATTA
1 TTATATTATATTT
*
2691733 TTATATCATATTT
1 TTATATTATATTT
2691746 T
1 T
2691747 AAATTATAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
9 2 0.06
10 5 0.14
11 5 0.14
12 3 0.08
13 21 0.58
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATATTATATTT
Found at i:2691718 original size:15 final size:14
Alignment explanation
Indices: 2691694--2691731 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2691684 AATTATATTA
2691694 TATTTT-TATTTTT
1 TATTTTATATTTTT
2691707 TA-TTTATATATTTT
1 TATTTTATAT-TTTT
2691721 TATTTTATATT
1 TATTTTATATT
2691732 ATTATATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 5 0.23
14 7 0.32
15 7 0.32
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTTTATATTTTT
Found at i:2691718 original size:21 final size:21
Alignment explanation
Indices: 2691678--2691731 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
2691668 TTTTATTAAA
*
2691678 ATTTTAAATTATATTATATTTTT
1 ATTTTATATT-TA-TATATTTTT
*
2691701 ATTTTTTATTTATATATTTTT
1 ATTTTATATTTATATATTTTT
2691722 ATTTTATATT
1 ATTTTATATT
2691732 ATTATATCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 18 0.64
22 2 0.07
23 8 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTTATATTTATATATTTTT
Found at i:2691737 original size:21 final size:21
Alignment explanation
Indices: 2691689--2691738 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
2691679 TTTTAAATTA
*
2691689 TATTATATTTTTATTTTTTAT
1 TATTATATTTTTATTTTATAT
2691710 T-TATATATTTTTATTTTATAT
1 TAT-TATATTTTTATTTTATAT
2691731 TATTATAT
1 TATTATAT
2691739 CATATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (21 bp):
TATTATATTTTTATTTTATAT
Found at i:2695708 original size:2 final size:2
Alignment explanation
Indices: 2695701--2695741 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2695691 TCCAAATCTA
2695701 AT AT AT AT 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 AT AT AT AT A
2695742 AATTAACCCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2696810 original size:12 final size:11
Alignment explanation
Indices: 2696781--2696810 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
2696771 TAAATATATA
2696781 AATTAAATTTT
1 AATTAAATTTT
2696792 AATTAAATTTT
1 AATTAAATTTT
2696803 ATATTAAA
1 A-ATTAAA
2696811 AAATAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AATTAAATTTT
Found at i:2700276 original size:5 final size:5
Alignment explanation
Indices: 2700266--2700295 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
2700256 GAAATATGCT
2700266 TTTTA TTTTA TTTTA TTTTA TTTT- TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
2700296 CTATGTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:2705377 original size:51 final size:51
Alignment explanation
Indices: 2705318--2705421 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 51
2705308 TTTTGCTAGG
*
2705318 TTGCTGTTTTAGCAAGGTGTTGAACAATTTACAGTGTATCATTTCAATATC
1 TTGCTGTTTTAGCAAGGTGTTGAACAATTTACAATGTATCATTTCAATATC
* *
2705369 TTGCTGTTTTAGCAAGGTGTTGAACAGTTTACAATGTATCATTTCTATATC
1 TTGCTGTTTTAGCAAGGTGTTGAACAATTTACAATGTATCATTTCAATATC
2705420 TT
1 TT
2705422 CAGGCTTCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (51 bp):
TTGCTGTTTTAGCAAGGTGTTGAACAATTTACAATGTATCATTTCAATATC
Found at i:2705583 original size:88 final size:88
Alignment explanation
Indices: 2705434--2705614 Score: 281
Period size: 88 Copynumber: 2.1 Consensus size: 88
2705424 GGCTTCAAAA
* *
2705434 ATATTTTGGAAAATGCAATCAATTTTTGTGACAAATCTGTAGAGTGGAATTACATGAAACATGAA
1 ATATTTTGGAAAATGCAATCAATTTTTGTAACAAATCCGTAGAGTGGAATTACATGAAACATGAA
*
2705499 GCAGGTTGTATTAGCCTCTCCAT
66 GCAGGTCGTATTAGCCTCTCCAT
* * * *
2705522 ATATTTTGGAAAATGCAATCAGTTTTTGTAACAATTCCGTAGATTGGAATTATATGAAACATGAA
1 ATATTTTGGAAAATGCAATCAATTTTTGTAACAAATCCGTAGAGTGGAATTACATGAAACATGAA
* *
2705587 GCAGGTCGTATTATCCTCTGCAT
66 GCAGGTCGTATTAGCCTCTCCAT
2705610 ATATT
1 ATATT
2705615 GCTAGTATTT
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (88 bp):
ATATTTTGGAAAATGCAATCAATTTTTGTAACAAATCCGTAGAGTGGAATTACATGAAACATGAA
GCAGGTCGTATTAGCCTCTCCAT
Found at i:2709490 original size:71 final size:71
Alignment explanation
Indices: 2709402--2709535 Score: 232
Period size: 71 Copynumber: 1.9 Consensus size: 71
2709392 TGTACAATTT
*
2709402 CAAACCAGCTGCTATACTTACAAATGACTTTTCTATCATTGACTTACAAGTAGCTTTGCCCATGT
1 CAAACCAGCTGCTATACTTACAAATGACTTTGCTATCATTGACTTACAAGTAGCTTTGCCCATGT
2709467 GGTGGA
66 GGTGGA
* * *
2709473 CAAACCAGCTGCTATACTTACGAATGACTTTGCTATCATTGACTTATAATTAGCTTTGCCCAT
1 CAAACCAGCTGCTATACTTACAAATGACTTTGCTATCATTGACTTACAAGTAGCTTTGCCCAT
2709536 AAAAATTAGG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 59 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (71 bp):
CAAACCAGCTGCTATACTTACAAATGACTTTGCTATCATTGACTTACAAGTAGCTTTGCCCATGT
GGTGGA
Found at i:2714783 original size:9 final size:9
Alignment explanation
Indices: 2714769--2714797 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
2714759 ACCAGTCCAG
2714769 CCGCCACCA
1 CCGCCACCA
2714778 CCGCCACCA
1 CCGCCACCA
2714787 CCGCCACCA
1 CCGCCACCA
2714796 CC
1 CC
2714798 ACCATCCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.69, G:0.10, T:0.00
Consensus pattern (9 bp):
CCGCCACCA
Found at i:2719562 original size:26 final size:26
Alignment explanation
Indices: 2719528--2719582 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
2719518 TCTCTTCTTT
* *
2719528 TCTCTTCAAATTCTCGTGAATATCTC
1 TCTCGTCAAAGTCTCGTGAATATCTC
* * *
2719554 TCTCGTCAAAGTCTGGTGAGTCTCTC
1 TCTCGTCAAAGTCTCGTGAATATCTC
2719580 TCT
1 TCT
2719583 AGTTTTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.40
Consensus pattern (26 bp):
TCTCGTCAAAGTCTCGTGAATATCTC
Found at i:2726342 original size:21 final size:21
Alignment explanation
Indices: 2726313--2726417 Score: 72
Period size: 21 Copynumber: 5.0 Consensus size: 21
2726303 CAATGATGGA
*
2726313 TAAAGTTATTAAAATTATATT
1 TAAAATTATTAAAATTATATT
*
2726334 TAAAATTATTAAAATTTTA-T
1 TAAAATTATTAAAATTATATT
* ** *
2726354 CAGTTATTATCAAAATTAT-TT
1 TA-AAATTATTAAAATTATATT
*
2726375 TAAATATTACTAAAATTATA-T
1 TAAA-ATTATTAAAATTATATT
* * *
2726396 CATATATTATTAAAATTGTATT
1 TA-AAATTATTAAAATTATATT
2726418 AGAGGGTTAC
Statistics
Matches: 62, Mismatches: 16, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
20 2 0.03
21 58 0.94
22 2 0.03
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.48
Consensus pattern (21 bp):
TAAAATTATTAAAATTATATT
Found at i:2726369 original size:42 final size:43
Alignment explanation
Indices: 2726318--2726417 Score: 134
Period size: 42 Copynumber: 2.4 Consensus size: 43
2726308 ATGGATAAAG
* *
2726318 TTATTAAAATTATATTTAAA-ATTATTAAAATTTTATCAGT-TA
1 TTATTAAAATTATATTTAAATATTACTAAAATTATATCA-TATA
*
2726360 TTATCAAAATTAT-TTTAAATATTACTAAAATTATATCATATA
1 TTATTAAAATTATATTTAAATATTACTAAAATTATATCATATA
*
2726402 TTATTAAAATTGTATT
1 TTATTAAAATTATATT
2726418 AGAGGGTTAC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
41 7 0.14
42 41 0.82
43 2 0.04
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (43 bp):
TTATTAAAATTATATTTAAATATTACTAAAATTATATCATATA
Found at i:2726477 original size:21 final size:20
Alignment explanation
Indices: 2726451--2726559 Score: 101
Period size: 21 Copynumber: 5.2 Consensus size: 20
2726441 ATATGTTAAC
*
2726451 AAAATTTTATAAAAAATAATT
1 AAAATTTTATAAAAAATTA-T
*
2726472 AAAATTGTATAAAAAATTACT
1 AAAATTTTATAAAAAATTA-T
* *
2726493 AAAATTTTATCAAAATTTAT
1 AAAATTTTATAAAAAATTAT
*
2726513 AAAATTTATATAAAATATTAT
1 AAAATTT-TATAAAAAATTAT
* * * *
2726534 CAAATTATATTAAAAGTTATT
1 AAAATTTTATAAAAAATTA-T
2726555 AAAAT
1 AAAAT
2726560 CAAAATTATA
Statistics
Matches: 71, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.24
21 54 0.76
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (20 bp):
AAAATTTTATAAAAAATTAT
Found at i:2726484 original size:10 final size:9
Alignment explanation
Indices: 2726471--2726559 Score: 52
Period size: 10 Copynumber: 8.7 Consensus size: 9
2726461 AAAAAATAAT
2726471 TAAAATTGTA
1 TAAAATT-TA
*
2726481 TAAAAAATTA
1 T-AAAATTTA
2726491 CTAAAATTTTA
1 -TAAAA-TTTA
2726502 TCAAAATTTA
1 T-AAAATTTA
2726512 TAAAATTTATA
1 TAAAA-TT-TA
2726523 TAAAATATTA
1 TAAAAT-TTA
*
2726533 TCAAATTATA
1 TAAAATT-TA
*
2726543 TTAAAAGTTA
1 -TAAAATTTA
2726553 TTAAAAT
1 -TAAAAT
2726560 CAAAATTATA
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
9 5 0.08
10 33 0.52
11 26 0.41
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.40
Consensus pattern (9 bp):
TAAAATTTA
Found at i:2726486 original size:11 final size:10
Alignment explanation
Indices: 2726451--2726533 Score: 60
Period size: 10 Copynumber: 8.0 Consensus size: 10
2726441 ATATGTTAAC
*
2726451 AAAATTTTAT
1 AAAAATTTAT
* *
2726461 AAAAAATAAT
1 AAAAATTTAT
*
2726471 TAAAATTGTAT
1 AAAAATT-TAT
*
2726482 AAAAAATTACT
1 AAAAATTTA-T
*
2726493 AAAATTTTAT
1 AAAAATTTAT
*
2726503 CAAAATTTAT
1 AAAAATTTAT
2726513 -AAAATTTAT
1 AAAAATTTAT
2726522 ATAAAATATTAT
1 A-AAAAT-TTAT
2726534 CAAATTATAT
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
9 9 0.16
10 23 0.41
11 20 0.36
12 4 0.07
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (10 bp):
AAAAATTTAT
Found at i:2726498 original size:42 final size:42
Alignment explanation
Indices: 2726451--2726559 Score: 116
Period size: 41 Copynumber: 2.6 Consensus size: 42
2726441 ATATGTTAAC
*
2726451 AAAATTTTATAAAAAATAATTAAAATTGTATA-AAAA-ATTACT
1 AAAATTTTATAAAAAATTATTAAAATT-TATATAAAATATTA-T
* *
2726493 AAAATTTTATCAAAATTTA-TAAAATTTATATAAAATATTAT
1 AAAATTTTATAAAAAATTATTAAAATTTATATAAAATATTAT
* * * *
2726534 CAAATTATATTAAAAGTTATTAAAAT
1 AAAATTTTATAAAAAATTATTAAAAT
2726560 CAAAATTATA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
40 4 0.07
41 27 0.47
42 26 0.46
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (42 bp):
AAAATTTTATAAAAAATTATTAAAATTTATATAAAATATTAT
Found at i:2726527 original size:31 final size:31
Alignment explanation
Indices: 2726473--2726559 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
2726463 AAAATAATTA
* * * * *
2726473 AAATTGTATAAAAAATTACTAAAATTTTATC
1 AAATTATATTAAAAGTTATTAAAATATTATC
*
2726504 AAAATT-TA-TAAAATTTATATAAAATATTATC
1 -AAATTATATTAAAAGTTAT-TAAAATATTATC
2726535 AAATTATATTAAAAGTTATTAAAAT
1 AAATTATATTAAAAGTTATTAAAAT
2726560 CAAAATTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
30 12 0.26
31 21 0.45
32 14 0.30
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.40
Consensus pattern (31 bp):
AAATTATATTAAAAGTTATTAAAATATTATC
Found at i:2726574 original size:11 final size:11
Alignment explanation
Indices: 2726493--2726591 Score: 59
Period size: 11 Copynumber: 8.9 Consensus size: 11
2726483 AAAAATTACT
*
2726493 AAAATTTTATC
1 AAAATTATATC
2726504 AAAATT-TAT-
1 AAAATTATATC
2726513 AAAATTTATAT-
1 AAAA-TTATATC
2726524 AAAA-TATTATC
1 AAAATTA-TATC
*
2726535 -AAATTATATT
1 AAAATTATATC
2726545 AAAAGTTATTAAAATC
1 AAAA-TTA-T---ATC
2726561 AAAATTATATC
1 AAAATTATATC
2726572 AAAGA-TA-ATC
1 AAA-ATTATATC
2726582 AAAATTATAT
1 AAAATTATAT
2726592 TGAAGTTAAT
Statistics
Matches: 72, Mismatches: 2, Indels: 28
0.71 0.02 0.27
Matches are distributed among these distances:
9 7 0.10
10 22 0.31
11 28 0.39
12 4 0.06
13 1 0.01
14 1 0.01
15 3 0.04
16 6 0.08
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (11 bp):
AAAATTATATC
Found at i:2727630 original size:30 final size:30
Alignment explanation
Indices: 2727594--2727704 Score: 125
Period size: 30 Copynumber: 4.0 Consensus size: 30
2727584 ATATAAAAGT
*
2727594 AGCCTAAGACATAAGTATATTCTATTTGAG
1 AGCCTAAGACATAAGTAAATTCTATTTGAG
2727624 AGCCTAAGACATAAGTAAA--C--------
1 AGCCTAAGACATAAGTAAATTCTATTTGAG
*
2727644 AGCCTAATACATAAGTAAATTCTATTTGAG
1 AGCCTAAGACATAAGTAAATTCTATTTGAG
*
2727674 AGCCTAAGACATAAGTAAATTCTGTTTGAG
1 AGCCTAAGACATAAGTAAATTCTATTTGAG
2727704 A
1 A
2727705 TCATAGAGGA
Statistics
Matches: 67, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
20 18 0.27
22 1 0.01
28 1 0.01
30 47 0.70
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (30 bp):
AGCCTAAGACATAAGTAAATTCTATTTGAG
Found at i:2727649 original size:20 final size:20
Alignment explanation
Indices: 2727624--2727662 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2727614 TCTATTTGAG
2727624 AGCCTAAGACATAAGTAAAC
1 AGCCTAAGACATAAGTAAAC
*
2727644 AGCCTAATACATAAGTAAA
1 AGCCTAAGACATAAGTAAA
2727663 TTCTATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (20 bp):
AGCCTAAGACATAAGTAAAC
Found at i:2727656 original size:50 final size:50
Alignment explanation
Indices: 2727594--2727692 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
2727584 ATATAAAAGT
*
2727594 AGCCTAAGACATAAGTATATTCTATTTGAGAGCCTAAGACATAAGTAAAC
1 AGCCTAAGACATAAGTAAATTCTATTTGAGAGCCTAAGACATAAGTAAAC
*
2727644 AGCCTAATACATAAGTAAATTCTATTTGAGAGCCTAAGACATAAGTAAA
1 AGCCTAAGACATAAGTAAATTCTATTTGAGAGCCTAAGACATAAGTAAA
2727693 TTCTGTTTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (50 bp):
AGCCTAAGACATAAGTAAATTCTATTTGAGAGCCTAAGACATAAGTAAAC
Found at i:2731763 original size:26 final size:26
Alignment explanation
Indices: 2731733--2731782 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
2731723 AGATTTTGAT
2731733 TTCAATTTAAATAA-TTATCTAAAATA
1 TTCAATTTAAATAATTTAT-TAAAATA
2731759 TTCAATTTAAATAATTTATTAAAA
1 TTCAATTTAAATAATTTATTAAAA
2731783 AATTTATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (26 bp):
TTCAATTTAAATAATTTATTAAAATA
Found at i:2731902 original size:2 final size:2
Alignment explanation
Indices: 2731891--2731924 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2731881 CCTTATATGT
2731891 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2731925 TAGATTTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2732095 original size:44 final size:43
Alignment explanation
Indices: 2732032--2732143 Score: 129
Period size: 44 Copynumber: 2.6 Consensus size: 43
2732022 TAAATGGTAT
*
2732032 TAAAAGTTATCAAAATTATATTTAAAATTACTAAAAATGTTTA
1 TAAAAGTTATCAAAATTATATTAAAAATTACTAAAAATGTTTA
* * *
2732075 TAAAAGGTTTTCAAAATTATATTAAAAATTATTAAAATTGTTTCA
1 TAAAA-GTTATCAAAATTATATTAAAAATTACTAAAAATGTTT-A
** *
2732120 -ATTA-TTATCAAAATTGTATTAAAA
1 TAAAAGTTATCAAAATTATATTAAAA
2732144 GGTTATCAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
42 18 0.31
43 5 0.08
44 35 0.59
45 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.41
Consensus pattern (43 bp):
TAAAAGTTATCAAAATTATATTAAAAATTACTAAAAATGTTTA
Found at i:2732100 original size:22 final size:21
Alignment explanation
Indices: 2732029--2732199 Score: 98
Period size: 22 Copynumber: 8.0 Consensus size: 21
2732019 TATTAAATGG
2732029 TATTAAAAGTTATCAAAATTA
1 TATTAAAAGTTATCAAAATTA
* *
2732050 TATTTAAAA-TTACTAAAAATGTT
1 TA-TTAAAAGTTA-TCAAAAT-TA
*
2732073 TA-TAAAAGGTTTTCAAAATTA
1 TATTAAAA-GTTATCAAAATTA
* * *
2732094 TATTAAAAATTATTAAAATTG
1 TATTAAAAGTTATCAAAATTA
* *
2732115 T-TTCAATTA-TTATCAAAATTG
1 TATT-AA-AAGTTATCAAAATTA
*
2732136 TATTAAAAGGTTATCAAAGTTA
1 TATTAAAA-GTTATCAAAATTA
* * * *
2732158 TATCAATATGTTAACAAAATTT
1 TATTAA-AAGTTATCAAAATTA
* * *
2732180 TATAAAAAATAATCAAAATT
1 TATTAAAAGTTATCAAAATT
2732200 GTACCAAAAT
Statistics
Matches: 114, Mismatches: 24, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
20 3 0.03
21 49 0.43
22 56 0.49
23 6 0.05
ACGTcount: A:0.49, C:0.05, G:0.06, T:0.40
Consensus pattern (21 bp):
TATTAAAAGTTATCAAAATTA
Found at i:2732111 original size:32 final size:33
Alignment explanation
Indices: 2732064--2732163 Score: 91
Period size: 32 Copynumber: 3.1 Consensus size: 33
2732054 TAAAATTACT
* *
2732064 AAAAATGTTTATAAAAGGTTTTCAAAATTATATT
1 AAAAATGTAT-TAAAAGGTTTTCAAAATTATATC
*
2732098 AAAAAT-TATTAAAA-TTGTTTC--AATTATTATC
1 AAAAATGTATTAAAAGGT-TTTCAAAATTA-TATC
* * *
2732129 AAAATTGTATTAAAAGGTTATCAAAGTTATATC
1 AAAAATGTATTAAAAGGTTTTCAAAATTATATC
2732162 AA
1 AA
2732164 TATGTTAACA
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
30 5 0.09
31 9 0.17
32 20 0.38
33 9 0.17
34 10 0.19
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (33 bp):
AAAAATGTATTAAAAGGTTTTCAAAATTATATC
Found at i:2732219 original size:22 final size:22
Alignment explanation
Indices: 2732194--2732265 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
2732184 AAAAATAATC
2732194 AAAATTGTACCAAAATAATATAA
1 AAAATT-TACCAAAATAATATAA
* **
2732217 AAAATTTATCAAAATTGTATAA
1 AAAATTTACCAAAATAATATAA
* *
2732239 AAAA-TTACTAAAA-ATTTATAA
1 AAAATTTACCAAAATA-ATATAA
2732260 AAAATT
1 AAAATT
2732266 ATACAATTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
21 16 0.40
22 18 0.45
23 6 0.15
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.32
Consensus pattern (22 bp):
AAAATTTACCAAAATAATATAA
Found at i:2732230 original size:10 final size:10
Alignment explanation
Indices: 2732124--2732316 Score: 59
Period size: 11 Copynumber: 18.2 Consensus size: 10
2732114 GTTTCAATTA
2732124 TTATCAAAAT
1 TTATCAAAAT
* *
2732134 TGTATTAAAAGG
1 T-TATCAAAA-T
*
2732146 TTATCAAAGT
1 TTATCAAAAT
*
2732156 TATATCAATAT
1 T-TATCAAAAT
*
2732167 GTTAACAAAATT
1 -TTATCAAAA-T
* *
2732179 TTATAAAAAA
1 TTATCAAAAT
*
2732189 TAATCAAAAT
1 TTATCAAAAT
*
2732199 TGTACCAAAAT
1 T-TATCAAAAT
* *
2732210 AATATAAAAAAT
1 -TTAT-CAAAAT
2732222 TTATCAAAAT
1 TTATCAAAAT
* *
2732232 TGTATAAAAAA
1 T-TATCAAAAT
*
2732243 TTACTAAAAAT
1 TTA-TCAAAAT
* *
2732254 TTATAAAAAA
1 TTATCAAAAT
*
2732264 TTAT-ACAAT
1 TTATCAAAAT
* *
2732273 TTCTAACAAAT
1 TTATCA-AAAT
2732284 GTTATC-AAAT
1 -TTATCAAAAT
2732294 TATATCAAAGA-
1 T-TATCAAA-AT
*
2732305 TAATCAAAAT
1 TTATCAAAAT
2732315 TT
1 TT
2732317 TTTTCTCAAT
Statistics
Matches: 132, Mismatches: 34, Indels: 34
0.66 0.17 0.17
Matches are distributed among these distances:
9 8 0.06
10 44 0.33
11 68 0.52
12 12 0.09
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.35
Consensus pattern (10 bp):
TTATCAAAAT
Found at i:2732251 original size:21 final size:20
Alignment explanation
Indices: 2732212--2732268 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 20
2732202 ACCAAAATAA
*
2732212 TATAAAAAATTTATCAAAATT
1 TATAAAAAA-TTATAAAAATT
2732233 GTATAAAAAATTACTAAAAATT
1 -TATAAAAAATTA-TAAAAATT
2732255 TATAAAAAATTATA
1 TATAAAAAATTATA
2732269 CAATTTCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 2 0.06
21 15 0.45
22 16 0.48
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (20 bp):
TATAAAAAATTATAAAAATT
Found at i:2733507 original size:10 final size:10
Alignment explanation
Indices: 2733486--2733521 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
2733476 ATTATTATGT
2733486 AAAATA-TAA
1 AAAATATTAA
2733495 AAAATATTAA
1 AAAATATTAA
2733505 AAAATATATAA
1 AAAATAT-TAA
2733516 AAAATA
1 AAAATA
2733522 AATTGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 6 0.24
10 10 0.40
11 9 0.36
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (10 bp):
AAAATATTAA
Found at i:2733516 original size:11 final size:11
Alignment explanation
Indices: 2733489--2733521 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
2733479 ATTATGTAAA
2733489 ATATAAAAAAT
1 ATATAAAAAAT
2733500 AT-TAAAAAAT
1 ATATAAAAAAT
2733510 ATATAAAAAAT
1 ATATAAAAAAT
2733521 A
1 A
2733522 AATTGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATATAAAAAAT
Found at i:2733985 original size:16 final size:17
Alignment explanation
Indices: 2733959--2733990 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2733949 TTAACGTCTT
2733959 ATATAAATTTTTTAAAA
1 ATATAAATTTTTTAAAA
2733976 ATAT-AATTTTTTAAA
1 ATATAAATTTTTTAAA
2733991 TCAAGATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATAAATTTTTTAAAA
Found at i:2734125 original size:21 final size:21
Alignment explanation
Indices: 2734088--2734135 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2734078 AATTTTTAAA
*
2734088 TAAAATTATTTGATAAACAAC
1 TAAAATTATTTGATAAAAAAC
*
2734109 TAAAATTATTT-ATTAAAAAAT
1 TAAAATTATTTGA-TAAAAAAC
2734130 TAAAAT
1 TAAAAT
2734136 CTACAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAAATTATTTGATAAAAAAC
Found at i:2734410 original size:21 final size:20
Alignment explanation
Indices: 2734386--2734575 Score: 73
Period size: 22 Copynumber: 8.9 Consensus size: 20
2734376 TATTAAATGG
2734386 TATTAAATGTTATCAAAATTA
1 TATTAAA-GTTATCAAAATTA
* * *
2734407 TATTTAAAATCA-CAAAAAATGTT
1 TA-TTAAAGTTATC--AAAAT-TA
* *
2734430 TATAAAAGGTTTTCAAAA-TA
1 TATTAAA-GTTATCAAAATTA
* *
2734450 TATTAGAAGTTATTAAAATTG
1 TATTA-AAGTTATCAAAATTA
2734471 T-TTCAATTA-TTATCAAAATTA
1 TATT-AA--AGTTATCAAAATTA
*
2734492 TATTATAAATTATCAAAATTA
1 TATTA-AAGTTATCAAAATTA
* *
2734513 TATTAAAAGGCTATCAAAGTTA
1 TATT-AAA-GTTATCAAAATTA
* * * *
2734535 TATCAATATGTTAACAAACTTT
1 TATTAA-A-GTTATCAAAATTA
**
2734557 TATTAAAAATATCAAAATT
1 TATTAAAGTTATCAAAATT
2734576 GTATCAAAAT
Statistics
Matches: 124, Mismatches: 28, Indels: 35
0.66 0.15 0.19
Matches are distributed among these distances:
20 26 0.21
21 42 0.34
22 51 0.41
23 4 0.03
24 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (20 bp):
TATTAAAGTTATCAAAATTA
Found at i:2734530 original size:22 final size:21
Alignment explanation
Indices: 2734481--2734537 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
2734471 TTTCAATTAT
*
2734481 TATCAAAATTATATTATAAAT
1 TATCAAAATTATATTATAAAC
2734502 TATCAAAATTATATTA-AAAGGC
1 TATCAAAATTATATTATAAA--C
*
2734524 TATCAAAGTTATAT
1 TATCAAAATTATAT
2734538 CAATATGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 3 0.09
21 16 0.50
22 13 0.41
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (21 bp):
TATCAAAATTATATTATAAAC
Found at i:2734601 original size:21 final size:23
Alignment explanation
Indices: 2734570--2734617 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
2734560 TAAAAATATC
2734570 AAAATTGTATCAAAATAATA-AA
1 AAAATTGTATCAAAATAATATAA
*
2734592 AAAATT-TATCAAAATTATATAA
1 AAAATTGTATCAAAATAATATAA
2734614 AAAA
1 AAAA
2734618 CTACTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATTGTATCAAAATAATATAA
Found at i:2734616 original size:11 final size:11
Alignment explanation
Indices: 2734475--2734615 Score: 71
Period size: 11 Copynumber: 13.2 Consensus size: 11
2734465 AAATTGTTTC
2734475 AATTATTATCAA
1 AATTA-TATCAA
*
2734487 AATTATATTATA
1 AATTATATCA-A
2734499 AA-T-TATCAA
1 AATTATATCAA
*
2734508 AATTATATTAA
1 AATTATATCAA
***
2734519 AAGGCTATCAA
1 AATTATATCAA
*
2734530 AGTTATATCAA
1 AATTATATCAA
* *
2734541 TATGT-TAACAA
1 AAT-TATATCAA
* * *
2734552 ACTTTTATTAA
1 AATTATATCAA
2734563 AA--ATATCAA
1 AATTATATCAA
*
2734572 AATTGTATCAA
1 AATTATATCAA
* **
2734583 AATAATAAAAA
1 AATTATATCAA
2734594 AATT-TATCAA
1 AATTATATCAA
2734604 AATTATAT-AA
1 AATTATATCAA
2734614 AA
1 AA
2734616 AACTACTAAA
Statistics
Matches: 92, Mismatches: 29, Indels: 18
0.66 0.21 0.13
Matches are distributed among these distances:
9 10 0.11
10 18 0.20
11 55 0.60
12 9 0.10
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (11 bp):
AATTATATCAA
Found at i:2734627 original size:32 final size:31
Alignment explanation
Indices: 2734561--2734637 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 31
2734551 AACTTTTATT
*
2734561 AAAAA-TATCAAAATTGTATCAAAATAATAA
1 AAAAATTATCAAAATTATATCAAAATAATAA
*
2734591 AAAAATTTATCAAAATTATAT-AAAA-AACTACT
1 AAAAA-TTATCAAAATTATATCAAAATAA-TA-A
2734623 AAAAATTAT-AAAATT
1 AAAAATTATCAAAATT
2734638 TCTAACAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 13 0.32
31 10 0.24
32 18 0.44
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.30
Consensus pattern (31 bp):
AAAAATTATCAAAATTATATCAAAATAATAA
Found at i:2743187 original size:14 final size:15
Alignment explanation
Indices: 2743148--2743187 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
2743138 TAATAAATTT
2743148 ATAATAAATAA-ATA
1 ATAATAAATAATATA
*
2743162 ATAATTAATAATATA
1 ATAATAAATAATATA
2743177 A-AATAAATAAT
1 ATAATAAATAAT
2743188 TCAATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAATAAATAATATA
Found at i:2744781 original size:14 final size:14
Alignment explanation
Indices: 2744739--2744781 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2744729 TTATGATTGA
*
2744739 AAATAAATTTTAAT
1 AAATAAATTTTATT
2744753 AAA-AAATTTATATT
1 AAATAAATTT-TATT
*
2744767 AAATAAATTTCATT
1 AAATAAATTTTATT
2744781 A
1 A
2744782 TAATTAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 6 0.24
14 13 0.52
15 6 0.24
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATAAATTTTATT
Found at i:2745312 original size:31 final size:29
Alignment explanation
Indices: 2745247--2745317 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
2745237 TAGGATAATT
* * *
2745247 ATATAAAATATTATATTTATATCATATTTT
1 ATATAAAA-ATTATATTCATAACATATTTA
*
2745277 ATATAAAAATTATATATCATAACTTATATTA
1 ATATAAAAATTATAT-TCATAACATAT-TTA
2745308 ATATAAAAAT
1 ATATAAAAAT
2745318 ATAAAATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.20
30 16 0.46
31 12 0.34
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (29 bp):
ATATAAAAATTATATTCATAACATATTTA
Found at i:2749776 original size:20 final size:16
Alignment explanation
Indices: 2749731--2749767 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
2749721 TTCACTCTTC
2749731 AAAT-ATATTTATTCA
1 AAATCATATTTATTCA
2749746 AAATCATATTTATTCA
1 AAATCATATTTATTCA
2749762 AAATCA
1 AAATCA
2749768 GTAATATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATCATATTTATTCA
Found at i:2752221 original size:19 final size:20
Alignment explanation
Indices: 2752197--2752238 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
2752187 TCAGACTATC
2752197 CTTAATTTTCT-TCGAATCT
1 CTTAATTTTCTATCGAATCT
* *
2752216 CTTAATTTTTTATTGAATCT
1 CTTAATTTTCTATCGAATCT
2752236 CTT
1 CTT
2752239 CTAATCTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.21, C:0.17, G:0.05, T:0.57
Consensus pattern (20 bp):
CTTAATTTTCTATCGAATCT
Found at i:2752339 original size:2 final size:2
Alignment explanation
Indices: 2752332--2752386 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
2752322 GCTGAGATTA
2752332 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2752374 CT CT CT CT CT CT C
1 CT CT CT CT CT CT C
2752387 ATGGTGTGCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2753634 original size:2 final size:2
Alignment explanation
Indices: 2753627--2753652 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2753617 CAATATTTTC
2753627 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
2753653 GTATGTATGT
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:2755624 original size:15 final size:15
Alignment explanation
Indices: 2755604--2755635 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2755594 GACCATGTTT
2755604 TTTTTAATTTTAAAA
1 TTTTTAATTTTAAAA
2755619 TTTTTAATTTTAAAA
1 TTTTTAATTTTAAAA
2755634 TT
1 TT
2755636 AATTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTAATTTTAAAA
Found at i:2756905 original size:11 final size:12
Alignment explanation
Indices: 2756881--2756909 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2756871 CAATCTATCA
2756881 TATTTAATTTTT
1 TATTTAATTTTT
2756893 TATTTAA-TTTT
1 TATTTAATTTTT
2756904 TATTTA
1 TATTTA
2756910 CTCATTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTTAATTTTT
Found at i:2757114 original size:14 final size:14
Alignment explanation
Indices: 2757095--2757128 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2757085 AATACTTGCT
2757095 AAAAAGAAAAAAAA
1 AAAAAGAAAAAAAA
**
2757109 AAAAAGAAACTAAA
1 AAAAAGAAAAAAAA
2757123 AAAAAG
1 AAAAAG
2757129 GATAGATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.85, C:0.03, G:0.09, T:0.03
Consensus pattern (14 bp):
AAAAAGAAAAAAAA
Found at i:2759552 original size:18 final size:18
Alignment explanation
Indices: 2759529--2759566 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2759519 TAGAAAGAAA
2759529 TGATATTTGATTAAAGAT
1 TGATATTTGATTAAAGAT
2759547 TGATATTTGATTAAAGAT
1 TGATATTTGATTAAAGAT
2759565 TG
1 TG
2759567 CAGATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (18 bp):
TGATATTTGATTAAAGAT
Found at i:2769057 original size:30 final size:30
Alignment explanation
Indices: 2769019--2769116 Score: 112
Period size: 29 Copynumber: 3.3 Consensus size: 30
2769009 TTGCAAAAAG
2769019 AATTTATTTAAGTACAAATTAAAAA-TAAA
1 AATTTATTTAAGTACAAATTAAAAATTAAA
*
2769048 AATTTTATTTTAA-TATAAATTAAAAATTAAA
1 AA-TTTA-TTTAAGTACAAATTAAAAATTAAA
* * * *
2769079 AACTCACTT-CGTACAAATTAAAAATTAAA
1 AATTTATTTAAGTACAAATTAAAAATTAAA
2769108 AATTTATTT
1 AATTTATTT
2769117 GAATGTAATA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
29 27 0.48
30 18 0.32
31 11 0.20
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (30 bp):
AATTTATTTAAGTACAAATTAAAAATTAAA
Found at i:2769093 original size:59 final size:58
Alignment explanation
Indices: 2769030--2769140 Score: 163
Period size: 59 Copynumber: 1.9 Consensus size: 58
2769020 ATTTATTTAA
*
2769030 GTACAAATTAAAAA-TAAAAATTTTATTTTAATATAAATTAAAAAT-TAAAAACTCACTTC
1 GTACAAATTAAAAATTAAAAA-TTTATTTGAATAT-AA-TAAAAATATAAAAACTCACTTC
*
2769089 GTACAAATTAAAAATTAAAAATTTATTTGAATGTAATAAAAATATAAAAACT
1 GTACAAATTAAAAATTAAAAATTTATTTGAATATAATAAAAATATAAAAACT
2769141 TATCTACGAC
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
57 7 0.15
58 10 0.21
59 25 0.52
60 6 0.12
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.34
Consensus pattern (58 bp):
GTACAAATTAAAAATTAAAAATTTATTTGAATATAATAAAAATATAAAAACTCACTTC
Found at i:2779948 original size:16 final size:18
Alignment explanation
Indices: 2779916--2779949 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
2779906 AAAATTTTAA
2779916 ATTTTTAGAAGAAAAGTG
1 ATTTTTAGAAGAAAAGTG
2779934 ATTTTTA-AA-AAAAGTG
1 ATTTTTAGAAGAAAAGTG
2779950 TAGATTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (18 bp):
ATTTTTAGAAGAAAAGTG
Found at i:2785177 original size:17 final size:17
Alignment explanation
Indices: 2785134--2785177 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2785124 AATTAAATAG
* *
2785134 ATAAAATTATTATTTAA
1 ATAAAATTATGAATTAA
* *
2785151 ATATATTTATGAATTAA
1 ATAAAATTATGAATTAA
2785168 ATAAAATTAT
1 ATAAAATTAT
2785178 ATAACTTGAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATAAAATTATGAATTAA
Found at i:2786461 original size:17 final size:17
Alignment explanation
Indices: 2786423--2786455 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2786413 AAAAGTTAAA
2786423 AATTTAAAATATAATTT
1 AATTTAAAATATAATTT
2786440 AATTT-AAATAT-ATTT
1 AATTTAAAATATAATTT
2786455 A
1 A
2786456 TTATTTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 6 0.38
17 5 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTTAAAATATAATTT
Found at i:2787828 original size:76 final size:77
Alignment explanation
Indices: 2787739--2787885 Score: 278
Period size: 76 Copynumber: 1.9 Consensus size: 77
2787729 CCTTTGTACA
2787739 AAGAGTTAACTCTCTGAAGTCAGCAAGTGATCATTCTATACAAAATTGGA-GGAAAACCCATTTA
1 AAGAGTTAACTCTCTGAAGTCAGCAAGTGATCATTCTATACAAAATTGGAGGGAAAACCCATTTA
2787803 CATGTATACATG
66 CATGTATACATG
*
2787815 AAGAGTTAACTCTCTGAAGTCAGCAAGTGATCATTCTCTACAAAATTGGAGGGAAAACCCATTTA
1 AAGAGTTAACTCTCTGAAGTCAGCAAGTGATCATTCTATACAAAATTGGAGGGAAAACCCATTTA
2787880 CATGTA
66 CATGTA
2787886 CCATATATTG
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
76 49 0.71
77 20 0.29
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (77 bp):
AAGAGTTAACTCTCTGAAGTCAGCAAGTGATCATTCTATACAAAATTGGAGGGAAAACCCATTTA
CATGTATACATG
Found at i:2788654 original size:13 final size:13
Alignment explanation
Indices: 2788636--2788671 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 13
2788626 ATACACAAAC
2788636 AAGTAATAATGTT
1 AAGTAATAATGTT
2788649 AAGTAAT-A--TT
1 AAGTAATAATGTT
2788659 AAGTAATAATGTT
1 AAGTAATAATGTT
2788672 TTTCCATAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
10 9 0.45
11 1 0.05
12 1 0.05
13 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (13 bp):
AAGTAATAATGTT
Found at i:2793443 original size:23 final size:23
Alignment explanation
Indices: 2793413--2793461 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
2793403 AACATACAAA
2793413 AACATACATCAGATGAAGTAGAT
1 AACATACATCAGATGAAGTAGAT
2793436 AACATACATCAGATGAAGTAGAT
1 AACATACATCAGATGAAGTAGAT
2793459 AAC
1 AAC
2793462 TTGTATATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.20
Consensus pattern (23 bp):
AACATACATCAGATGAAGTAGAT
Found at i:2796576 original size:33 final size:33
Alignment explanation
Indices: 2796529--2796600 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
2796519 ATACATTTTC
2796529 AATTG-AAAGATAACCAAAGTGAAATACAACGA
1 AATTGTAAAGATAACCAAAGTGAAATACAACGA
*
2796561 AATTGTAAAGCTAACCAAAGTGAAATACAACGA
1 AATTGTAAAGATAACCAAAGTGAAATACAACGA
2796594 AATTGTA
1 AATTGTA
2796601 GAGAATTCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 5 0.13
33 33 0.87
ACGTcount: A:0.53, C:0.12, G:0.15, T:0.19
Consensus pattern (33 bp):
AATTGTAAAGATAACCAAAGTGAAATACAACGA
Found at i:2803922 original size:23 final size:23
Alignment explanation
Indices: 2803892--2803939 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2803882 CCAAATCCAG
2803892 TATCACTTGACTAGGATCATTCT
1 TATCACTTGACTAGGATCATTCT
2803915 TATCACTTGACTAGGATCATTCT
1 TATCACTTGACTAGGATCATTCT
2803938 TA
1 TA
2803940 CTGTCAGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (23 bp):
TATCACTTGACTAGGATCATTCT
Found at i:2808748 original size:21 final size:21
Alignment explanation
Indices: 2808722--2808764 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2808712 TATTCTCTCT
*
2808722 CAACATTAGAAATTGTAGGTG
1 CAACATTAGAAATTCTAGGTG
2808743 CAACATTAGAAATTCTAGGTG
1 CAACATTAGAAATTCTAGGTG
2808764 C
1 C
2808765 TATTTCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (21 bp):
CAACATTAGAAATTCTAGGTG
Found at i:2823472 original size:11 final size:11
Alignment explanation
Indices: 2823456--2823482 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2823446 ACTGCAGAAG
2823456 TTACACACTAA
1 TTACACACTAA
2823467 TTACACACTAA
1 TTACACACTAA
2823478 TTACA
1 TTACA
2823483 TTATGTAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (11 bp):
TTACACACTAA
Found at i:2826360 original size:18 final size:18
Alignment explanation
Indices: 2826337--2826573 Score: 103
Period size: 18 Copynumber: 13.1 Consensus size: 18
2826327 AATCTTACTT
2826337 ATAAATAATATTATATTAATAA
1 ATAAATAATATTATA-T--T-A
2826359 ATAAATAATATTATATTA
1 ATAAATAATATTATATTA
*
2826377 ATAAATAATA-TACTGTTA
1 ATAAATAATATTA-TATTA
2826395 AT--AT-A-A-TATATTA
1 ATAAATAATATTATATTA
2826408 AT--A-AATA--ATATTA
1 ATAAATAATATTATATTA
*
2826421 AGAAATAATATTATATTA
1 ATAAATAATATTATATTA
* *
2826439 ATAAATAA-A--ACAATA
1 ATAAATAATATTATATTA
*
2826454 ATAAATATTATTAATTTAATTA
1 ATAAATAATATT-A--T-ATTA
*
2826476 ATAAATATTATAATAATATATGA
1 ATAAATA--AT-AT--TATATTA
2826499 ATAAATAAT-TTATTATTA
1 ATAAATAATATTA-TATTA
2826517 ATAAATAATA-TACTATTA
1 ATAAATAATATTA-TATTA
*
2826535 ATATAAT-ATATTAATAAATA
1 ATA-AATAATATT-AT-ATTA
* *
2826555 ATAAATAATTTTATTTTA
1 ATAAATAATATTATATTA
2826573 A
1 A
2826574 GATTTTTAAT
Statistics
Matches: 171, Mismatches: 17, Indels: 58
0.70 0.07 0.24
Matches are distributed among these distances:
13 15 0.09
14 4 0.02
15 13 0.08
16 7 0.04
17 5 0.03
18 59 0.35
19 13 0.08
20 11 0.06
21 3 0.02
22 25 0.15
23 10 0.06
24 2 0.01
25 2 0.01
26 1 0.01
27 1 0.01
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (18 bp):
ATAAATAATATTATATTA
Found at i:2826506 original size:52 final size:50
Alignment explanation
Indices: 2826395--2826561 Score: 145
Period size: 49 Copynumber: 3.4 Consensus size: 50
2826385 TATACTGTTA
* * * *
2826395 ATATAATATATTAATAAATAATATTAAGAAATAATATTATA-T-TAATAA-
1 ATATAATA-AATAATAAATATTATTAATAAATAATATAATATTATAATAAT
*
2826443 ATA-AA-ACAATAATAAATATTATTAATTTAATTAATA-AATATTATAATAAT
1 ATATAATA-AATAATAAATATTATTAA--TAAATAATATAATATTATAATAAT
* *
2826493 ATATGAATAAATAAT--TTATTATTAATAAATAATATACTATTA-ATATAAT
1 ATAT-AATAAATAATAAATATTATTAATAAATAATATAATATTATA-ATAAT
2826542 ATATTAATAAATAATAAATA
1 ATA-TAATAAATAATAAATA
2826562 ATTTTATTTT
Statistics
Matches: 96, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
46 17 0.18
47 5 0.05
48 20 0.21
49 30 0.31
50 13 0.14
51 2 0.02
52 8 0.08
53 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (50 bp):
ATATAATAAATAATAAATATTATTAATAAATAATATAATATTATAATAAT
Found at i:2826561 original size:11 final size:11
Alignment explanation
Indices: 2826351--2826562 Score: 64
Period size: 11 Copynumber: 18.7 Consensus size: 11
2826341 ATAATATTAT
2826351 ATTAATAAATA
1 ATTAATAAATA
* *
2826362 AATAAT-ATTA
1 ATTAATAAATA
2826372 TATTAATAAATA
1 -ATTAATAAATA
*
2826384 A-T-AT-ACT-
1 ATTAATAAATA
*
2826391 GTTAATATAATA
1 ATTAATA-AATA
2826403 TATTAATAAATAA
1 -ATTAATAAAT-A
*
2826416 TATTAAGAAATA
1 -ATTAATAAATA
* *
2826428 A-TATTATATTA
1 ATTAATA-AATA
*
2826439 ATAAATAAA-A
1 ATTAATAAATA
*
2826449 CAATAATAAAT-
1 -ATTAATAAATA
* *
2826460 ATTATTAATTTA
1 ATTAATAA-ATA
2826472 ATTAATAAATA
1 ATTAATAAATA
*
2826483 TTATAAT-AATA
1 AT-TAATAAATA
*
2826494 TATGAATAAATA
1 -ATTAATAAATA
* * *
2826506 ATTTATTATTA
1 ATTAATAAATA
*
2826517 ATAAATAATATA
1 ATTAATAA-ATA
2826529 CTATTAATATAATA
1 --ATTAATA-AATA
2826543 TATTAATAAATA
1 -ATTAATAAATA
*
2826555 ATAAATAA
1 ATTAATAA
2826563 TTTTATTTTA
Statistics
Matches: 144, Mismatches: 35, Indels: 44
0.65 0.16 0.20
Matches are distributed among these distances:
8 3 0.02
9 4 0.03
10 14 0.10
11 56 0.39
12 32 0.22
13 25 0.17
14 9 0.06
15 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (11 bp):
ATTAATAAATA
Found at i:2826620 original size:19 final size:18
Alignment explanation
Indices: 2826577--2826644 Score: 75
Period size: 19 Copynumber: 3.7 Consensus size: 18
2826567 ATTTTAAGAT
* *
2826577 TTTTAATATTAACACAATA
1 TTTTAATATTAA-ATATTA
2826596 TTTTAATATTAAATATTA
1 TTTTAATATTAAATATTA
*
2826614 TTATTAATATATAATTATT-
1 TT-TTAATAT-TAAATATTA
2826633 TTTTAATATTAA
1 TTTTAATATTAA
2826645 GAATTTAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
17 3 0.07
18 13 0.30
19 21 0.48
20 7 0.16
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTAATATTAAATATTA
Found at i:2826675 original size:25 final size:26
Alignment explanation
Indices: 2826647--2826705 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
2826637 AATATTAAGA
2826647 ATTTAATAATAAAT-AGTTTCAATAT
1 ATTTAATAATAAATAAGTTTCAATAT
* * *
2826672 ATTTTATTAATAAATAATTTTTAATAT
1 A-TTTAATAATAAATAAGTTTCAATAT
2826699 -TTTAATA
1 ATTTAATA
2826706 GTTATATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 7 0.25
26 12 0.43
27 9 0.32
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (26 bp):
ATTTAATAATAAATAAGTTTCAATAT
Found at i:2829017 original size:2 final size:2
Alignment explanation
Indices: 2829010--2829047 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2829000 CTTTACTTAC
2829010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2829048 GCCTTTAGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2835371 original size:61 final size:62
Alignment explanation
Indices: 2835293--2835466 Score: 183
Period size: 63 Copynumber: 2.8 Consensus size: 62
2835283 ATTTAGCATG
* * *
2835293 AAAAATGGCTTAAATAATATTCTAAAAAA-TTGATCAGCATTATTTAAGACGTTTTCTAGCC
1 AAAAATGCCTTAAATAATATTCTAAAAAATTTGATCAGCATTATTTAAGACATTTTCTAGCA
* * * * * *
2835354 AGAAATGCCTTAAATAATTTTCTATAAAAATTTGAATAAG-ATTATTTAAGGCATTTTTTGGCA
1 AAAAATGCCTTAAATAATATTCTA-AAAAATTTG-ATCAGCATTATTTAAGACATTTTCTAGCA
*** *
2835417 AAAAATATATTAAATAATCTTCTAAAAAATTTGATCA-CTATTATTTAAGA
1 AAAAATGCCTTAAATAATATTCTAAAAAATTTGATCAGC-ATTATTTAAGA
2835467 TTTTTTTTAT
Statistics
Matches: 92, Mismatches: 16, Indels: 9
0.79 0.14 0.08
Matches are distributed among these distances:
61 24 0.26
62 24 0.26
63 40 0.43
64 4 0.04
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (62 bp):
AAAAATGCCTTAAATAATATTCTAAAAAATTTGATCAGCATTATTTAAGACATTTTCTAGCA
Found at i:2835992 original size:61 final size:60
Alignment explanation
Indices: 2835860--2835993 Score: 164
Period size: 62 Copynumber: 2.2 Consensus size: 60
2835850 AAAAAACGTC
* * * *
2835860 TTAAATAATCCTCTTTAAAAAATATTAAAGATTATTTAAGGTATTTTTTATCAAAAAATATT
1 TTAAATAAT-CTCTTTAAAAAAAATAAAAGATTATTTAAGGTATTTTTAAT-AAAAAATACT
2835922 TTAAATAATC-CTTTAAAAAAAATAAAATGGATTATTTAAGGTATTTCTTAAT-AAAAATACT
1 TTAAATAATCTCTTTAAAAAAAATAAAA--GATTATTTAAGGTATTT-TTAATAAAAAATACT
*
2835983 TTGAATAATCT
1 TTAAATAATCT
2835994 TCAATATTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
60 15 0.24
61 18 0.29
62 26 0.41
63 4 0.06
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (60 bp):
TTAAATAATCTCTTTAAAAAAAATAAAAGATTATTTAAGGTATTTTTAATAAAAAATACT
Found at i:2836605 original size:13 final size:13
Alignment explanation
Indices: 2836587--2836618 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2836577 TTAAATCATA
2836587 TTATTTTTATATT
1 TTATTTTTATATT
2836600 TTATTTTTATATT
1 TTATTTTTATATT
*
2836613 ATATTT
1 TTATTT
2836619 ATGTCATGTT
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:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
TTATTTTTATATT
Done.